Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:685623 original size:113 final size:112
Alignment explanation
Indices: 685360--685688 Score: 415
Period size: 113 Copynumber: 3.0 Consensus size: 112
685350 TTAGAACGTT
* ** *
685360 TTGGATAAGTTAAACATTAGAACGTTAT-TCAAACTTGCATTTTTGAATGTAACAACTTGGATAA
1 TTGGATAAGTTAAACATTACAACACTATAT-AAACTTCCATTTTTGAATGTAACAACTTGGATAA
** *
685424 G-------TTACAACGTTATTCAAACTTCAATCTTTGAATGTAACAAC
65 GTTAAACATTACAACACTATTTAAACTTCAATCTTTGAATGTAACAAC
**
685465 TTGGATAAGTTAAACATTACAACGTTATATAAACTTCCATTTTTGAATGTAACAACTTGGATAAG
1 TTGGATAAGTTAAACATTACAACACTATATAAACTTCCATTTTTGAATGTAACAACTTGGATAAG
*
685530 TTAAGAGATTACAACACTATTTAAACTTTCAAT-TTTGAATGTAACAAC
66 TTAA-ACATTACAACACTATTTAAAC-TTCAATCTTTGAATGTAACAAC
* * *
685578 TTTGATAAGTTAAACATTACAACACTATTTAAACTTTCATTTTTGAATGTAACAACTTGGATAAG
1 TTGGATAAGTTAAACATTACAACACTATATAAACTTCCATTTTTGAATGTAACAACTTGGATAAG
* * * *
685643 TTAAACATTTCAACACTTTTTGAACTTCCATCTTTGAATGTAACAA
66 TTAAACATTACAACACTATTTAAACTTCAATCTTTGAATGTAACAA
685689 ATAAGTTAAA
Statistics
Matches: 198, Mismatches: 15, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
105 61 0.31
106 1 0.01
111 5 0.03
112 31 0.16
113 94 0.47
114 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (112 bp):
TTGGATAAGTTAAACATTACAACACTATATAAACTTCCATTTTTGAATGTAACAACTTGGATAAG
TTAAACATTACAACACTATTTAAACTTCAATCTTTGAATGTAACAAC
Found at i:685638 original size:169 final size:161
Alignment explanation
Indices: 685360--685688 Score: 401
Period size: 169 Copynumber: 2.0 Consensus size: 161
685350 TTAGAACGTT
* ** *
685360 TTGGATAAGTTAAACATTAGAACGTTATTCAAACTTGCATTTTTGAATGTAACAACTTGGATAAG
1 TTGGATAAGTTAAACATTACAACACTATTCAAACTTGCAATTTTGAATGTAACAACTTGGATAAG
** *
685425 TTACAACGTTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAAC-G
66 TTACAACACTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACAC
*
685489 TTATATAAACTTCCATTTTTGAATGTAACAAC
131 TT-TATAAACTTCCATCTTTGAATGTAACAAC
* * * *
685521 TTGGATAAGTTAAGAGATTACAACACTATTTAAACTTTCAATTTTGAATGTAACAACTTTGATAA
1 TTGGATAAGTTAA-ACATTACAACACTATTCAAACTTGCAATTTTGAATGTAACAACTTGGATAA
* *
685586 GTTAAACATTACAACACTATTTAAACTTTC-ATTTTTGAATGTAACAACTTGGATAAGTTAAACA
65 G-------TTACAACACTATTCAAAC-TTCAATCTTTGAATGTAACAACTTGGATAAGTTAAACA
* * *
685650 TTTCAACACTTTTTGAACTTCCATCTTTGAATGTAACAA
122 TTACAACACTTTATAAACTTCCATCTTTGAATGTAACAA
685689 ATAAGTTAAA
Statistics
Matches: 141, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
161 13 0.09
162 44 0.31
169 79 0.56
170 5 0.04
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (161 bp):
TTGGATAAGTTAAACATTACAACACTATTCAAACTTGCAATTTTGAATGTAACAACTTGGATAAG
TTACAACACTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACAC
TTTATAAACTTCCATCTTTGAATGTAACAAC
Found at i:685862 original size:56 final size:56
Alignment explanation
Indices: 685729--685992 Score: 253
Period size: 56 Copynumber: 4.7 Consensus size: 56
685719 AAAATGTTTT
* * * *
685729 GTTAAGACATTACAATGCTATTCAAACTTCCATCTTTCAATGTAACAACTTGGATAA
1 GTTAA-ACATTACAATGTTATTCAAACTTCCATCTTTGAATATAAAAACTTGGATAA
* *** * * * * *
685786 GTTGAATGCTATAATATTATTCAAACTTCCATTTTTAAATATAAAAACTTTGATAA
1 GTTAAACATTACAATGTTATTCAAACTTCCATCTTTGAATATAAAAACTTGGATAA
* * * * *
685842 ATTAAACATTACAATGTTATTCAAA-TTCTAATCTTTGAATATTATAACTTGGATAG
1 GTTAAACATTACAATGTTATTCAAACTTC-CATCTTTGAATATAAAAACTTGGATAA
* * * * *
685898 GTGAAACATTACAACGTTATTCAAACTTCAATATTTGAATGTAAAAACTTGGATAA
1 GTTAAACATTACAATGTTATTCAAACTTCCATCTTTGAATATAAAAACTTGGATAA
* * * *
685954 GTTCAACATTACAACGTTATTGAAAC-TCCATATTTGAAT
1 GTTAAACATTACAATGTTATTCAAACTTCCATCTTTGAAT
685993 GTAACAACCT
Statistics
Matches: 167, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
55 15 0.09
56 145 0.87
57 7 0.04
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (56 bp):
GTTAAACATTACAATGTTATTCAAACTTCCATCTTTGAATATAAAAACTTGGATAA
Found at i:685876 original size:112 final size:110
Alignment explanation
Indices: 685730--686000 Score: 283
Period size: 112 Copynumber: 2.4 Consensus size: 110
685720 AAATGTTTTG
* * * *
685730 TTAAGACATTACAATGCTATTCAAACTTCCATCTTTCAATGTAACAACTTGGATAAGTTGAATGC
1 TTAA-ACATTACAATGTTATTCAAA-TTCCATCTTTGAATGTAACAACTTGGAT-AGGTGAA-AC
* * * * *
685795 -TATAATATTATTCAAACTTCCATTTTTAAATATAAAAACTTTGATAAA
62 ATACAACATTATTCAAACTTCAATATTTAAATATAAAAACTTGGATAAA
* * * *
685843 TTAAACATTACAATGTTATTCAAATTCTAATCTTTGAATATTATAACTTGGATAGGTGAAACATT
1 TTAAACATTACAATGTTATTCAAATTC-CATCTTTGAATGTAACAACTTGGATAGGTGAAACA-T
* * * *
685908 ACAACGTTATTCAAACTTCAATATTTGAATGTAAAAACTTGGATAAG
64 ACAACATTATTCAAACTTCAATATTTAAATATAAAAACTTGGATAAA
* * * * *
685955 TTCAACATTACAACGTTATTGAAACTCCATATTTGAATGTAACAAC
1 TTAAACATTACAATGTTATTCAAATTCCATCTTTGAATGTAACAAC
686001 CTGAGTATGT
Statistics
Matches: 129, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
110 1 0.01
111 23 0.18
112 101 0.78
113 4 0.03
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (110 bp):
TTAAACATTACAATGTTATTCAAATTCCATCTTTGAATGTAACAACTTGGATAGGTGAAACATAC
AACATTATTCAAACTTCAATATTTAAATATAAAAACTTGGATAAA
Found at i:686198 original size:150 final size:147
Alignment explanation
Indices: 685903--686313 Score: 468
Period size: 150 Copynumber: 2.7 Consensus size: 147
685893 GATAGGTGAA
* * * *
685903 ACATTACAACGTTATTCAAACTTCAATATTTGAATGTAAAAACTTGGATAAGTTCAACATTACAA
1 ACATTAGAATGTTATTCAAACTTCAATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAA
** * * * *
685968 CGTTATTGAAAC-TCCATATTTGAATGTAACAACCTGAGTATGTTAAACTCTTTAATTCGTAAAC
66 CACTATTTAAACTTCCATATTTGAA-GTAACAACTTGA-TAAGTTAAACTCTTTAATTCATAAAC
686032 ATTAAACTATTGTGTTAAG
129 ATTAAACTATTGTGTTAAG
* * * * *
686051 ATATTAGAATGTTATTCAAACTTCCATATTTGAATGTATCATCTTGGACAAGTTAATACATTACA
1 ACATTAGAATGTTATTCAAACTTCAATATTTGAATGTAACAACTTGGATAAGTTAA-ACATTACA
* * * *
686116 ACACAATTTAAACTTCCATCTTTGAACGTAATAACTTAGATAAGTTAAACTCTTTAGTTCATAAA
65 ACACTATTTAAACTTCCATATTTGAA-GTAACAACTT-GATAAGTTAAACTCTTTAATTCATAAA
*
686181 CATTAAAGCT-TTTTGTTAAG
128 CATTAAA-CTATTGTGTTAAG
* ** * * * *
686201 ACATTATAATCCTATTCAAACTTAAATCTTTAAAAGTAACAACTTGGATAAGTTAAGACATTACA
1 ACATTAGAATGTTATTCAAACTTCAATATTTGAATGTAACAACTTGGATAAGTTAA-ACATTACA
686266 ACACTA-TTAGAACTTCCATATTTGAGAGTAACAACTTGGATAAGTTAA
65 ACACTATTTA-AACTTCCATATTTGA-AGTAACAACTT-GATAAGTTAA
686314 GATATTTCAG
Statistics
Matches: 219, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
148 47 0.21
149 20 0.09
150 147 0.67
151 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (147 bp):
ACATTAGAATGTTATTCAAACTTCAATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAA
CACTATTTAAACTTCCATATTTGAAGTAACAACTTGATAAGTTAAACTCTTTAATTCATAAACAT
TAAACTATTGTGTTAAG
Found at i:686571 original size:169 final size:168
Alignment explanation
Indices: 686212--686767 Score: 453
Period size: 169 Copynumber: 3.3 Consensus size: 168
686202 CATTATAATC
* * * * *
686212 CTATTCAAACTTAAATCTTTAAAAGTAACAACTTGGATAAGTTAAGACATTACAACACTATT-AG
1 CTATTCAAACTTTAATCTTTGAATGTAACAACTTCGATAAGTTAA-ACACTACAACACTATTCA-
* * * * ** * *
686276 AACTTCCATATTTGAGA-GTAACAACTTGGATAAGTTAAGATATTTCAGCGCTATTCAAACAT-C
64 AACTTCCAT-TTTGA-ATGTAACAAATTGGATAAGATAAAACATTAAAACACTATTCAAACATAC
** * ** ** * *
686339 TATAATTGAACGTAACAACTTGGATAAGTTC-AACTCTACGACT
127 -ATCTTTGAACATAACAAAATGGATAAG-TCAAACAATACAACA
* * * *
686382 CTACTCAAACCTCT-ATCTTTGAATGTAACAACTTCGATATGTTAAACCCTACAACACTATTCAA
1 CTATTCAAA-CTTTAATCTTTGAATGTAACAACTTCGATAAGTTAAACACTACAACACTATTCAA
* * *
686446 ACTTTCATCTTTGAATGTAACAAATTGGATAAGAT-AAACATTAAAACA-TCATTCAAA-TTTCA
65 ACTTCCAT-TTTGAATGTAACAAATTGGATAAGATAAAACATTAAAACACT-ATTCAAACATAC-
*** ** *
686508 ATCTTTGATTGTAACAACTTGGATAAGTTAAGACAATACAACA
127 ATCTTTGAACATAACAAAATGGATAAGTCAA-ACAATACAACA
* * * * * * **
686551 CTATTTAAACTTTAATCTTTGAATGTAACAATTTTGATAAGTTAAGGCATTACAACGCTATTTGA
1 CTATTCAAACTTTAATCTTTGAATGTAACAACTTCGATAAGTTAA-ACACTACAACACTATTCAA
* * * * * *
686616 ACTTCCATTTTGAATGTAACAACTTTGATAAGTTAAAACATTACAACACTATTTAAACATACATT
65 ACTTCCATTTTGAATGTAACAAATTGGATAAGATAAAACATTAAAACACTATTCAAACATACATC
* **
686681 TTTGAACATAACAAAATGGATAAGTCAAACATTACAATG
130 TTTGAACATAACAAAATGGATAAGTCAAACAATACAACA
* * *
686720 TTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACA
1 CTATTCAAACTTTAATCTTTGAATGTAACAACTTCGATAAGTTAAACA
686768 TCAAAATGTT
Statistics
Matches: 308, Mismatches: 66, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
167 3 0.01
168 45 0.15
169 157 0.51
170 98 0.32
171 5 0.02
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (168 bp):
CTATTCAAACTTTAATCTTTGAATGTAACAACTTCGATAAGTTAAACACTACAACACTATTCAAA
CTTCCATTTTGAATGTAACAAATTGGATAAGATAAAACATTAAAACACTATTCAAACATACATCT
TTGAACATAACAAAATGGATAAGTCAAACAATACAACA
Found at i:686590 original size:113 final size:109
Alignment explanation
Indices: 686212--686767 Score: 413
Period size: 113 Copynumber: 4.9 Consensus size: 109
686202 CATTATAATC
* * * * * *
686212 CTATTCAAACTTAAATCTTTAAAAGTAACAACTTGGATAAGTTAAGACATTACAACACTATT-AG
1 CTATTTAAACTTTAATCTTTGAATGTAACAAATTGGATAAG-TAA-ACATTACAACTC-ATTCA-
* * * * * * *
686276 AACTTCCATATTTGAGA-GTAACAACTTGGATAAGTTAAGATATTTCAGCG
62 AA-TTTCATCTTTGA-ATGTAACAACTTGGATAAGTTAA-ACAATACAACA
* * ** * * * * *
686326 CTATTCAAACATCT-ATAATTGAACGTAACAACTTGGATAAGTTCAAC-TCTACGACTCTACTCA
1 CTATTTAAAC-TTTAATCTTTGAATGTAACAAATTGGATAAG-TAAACAT-TACAACTC-ATTCA
** * * **
686389 AACCTCTATCTTTGAATGTAACAACTTCGATATGTTAAACCCTACAACA
62 AATTTC-ATCTTTGAATGTAACAACTTGGATAAGTTAAACAATACAACA
* * *
686438 CTATTCAAACTTTCATCTTTGAATGTAACAAATTGGATAAGATAAACATTAAAACATCATTCAAA
1 CTATTTAAACTTTAATCTTTGAATGTAACAAATTGGATAAG-TAAACATTACAAC-TCATTCAAA
*
686503 TTTCAATCTTTGATTGTAACAACTTGGATAAGTTAAGACAATACAACA
64 TTTC-ATCTTTGAATGTAACAACTTGGATAAGTTAA-ACAATACAACA
* * * * *
686551 CTATTTAAACTTTAATCTTTGAATGTAACAATTTTGATAAGTTAAGGCATTACAACGCTATTTGA
1 CTATTTAAACTTTAATCTTTGAATGTAACAAATTGGATAAG-TAA-ACATTACAACTC-A-TTCA
* * * *
686616 ACTTCCAT-TTTGAATGTAACAACTTTGATAAGTTAAAACATTACAACA
62 AATTTCATCTTTGAATGTAACAACTTGGATAAGTT-AAACAATACAACA
* * ** * * *
686664 CTATTTAAAC-ATACATTTTTGAACATAACAAAATGGATAAGTCAAACATTACAATGTTATTCAA
1 CTATTTAAACTTTA-ATCTTTGAATGTAACAAATTGGATAAGT-AAACATTACAA-CTCATTCAA
686728 ACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACA
63 A-TTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACA
686768 TCAAAATGTT
Statistics
Matches: 355, Mismatches: 69, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
111 6 0.02
112 107 0.30
113 184 0.52
114 50 0.14
115 8 0.02
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (109 bp):
CTATTTAAACTTTAATCTTTGAATGTAACAAATTGGATAAGTAAACATTACAACTCATTCAAATT
TCATCTTTGAATGTAACAACTTGGATAAGTTAAACAATACAACA
Found at i:686767 original size:56 final size:56
Alignment explanation
Indices: 686195--687351 Score: 621
Period size: 56 Copynumber: 20.1 Consensus size: 56
686185 AAAGCTTTTT
* ** * *
686195 GTTAAGACATTATAATC-CTATTCAAACTTAAATCTTTAAAAGTAACAACTTGGATAA
1 GTTAA-ACATTACAA-CACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* *
686252 GTTAAGACATTACAACACTATT-AGAACTTCCATATTTGAGA-GTAACAACTTGGATAA
1 GTTAA-ACATTACAACACTATTCA-AACTTTCATCTTTGA-ATGTAACAACTTGGATAA
* * * * * ** *
686309 GTTAAGATATTTCAGCGCTATTCAAAC-ATCTATAATTGAACGTAACAACTTGGATAA
1 GTTAA-ACATTACAACACTATTCAAACTTTC-ATCTTTGAATGTAACAACTTGGATAA
* * * * * * *
686366 GTTCAAC-TCTACGACTCTACTCAAAC-CTCTATCTTTGAATGTAACAACTTCGATAT
1 GTTAAACAT-TACAACACTATTCAAACTTTC-ATCTTTGAATGTAACAACTTGGATAA
** *
686422 GTTAAACCCTACAACACTATTCAAACTTTCATCTTTGAATGTAACAAATTGGATAA
1 GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * *
686478 GATAAACATTAAAACA-TCATTCAAA-TTTCAATCTTTGATTGTAACAACTTGGATAA
1 GTTAAACATTACAACACT-ATTCAAACTTTC-ATCTTTGAATGTAACAACTTGGATAA
* * * * *
686534 GTTAAGACAATACAACACTATTTAAACTTTAATCTTTGAATGTAACAATTTTGATAA
1 GTTAA-ACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * ** * *
686591 GTTAAGGCATTACAACGCTATTTGAACTTCCAT-TTTGAATGTAACAACTTTGATAA
1 GTTAA-ACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * ** **
686647 GTTAAAACATTACAACACTATTTAAACATACATTTTTGAACATAACAAAATGGATAA
1 GTT-AAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* ***
686704 GTCAAACATTACAATGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
1 GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * *** * * * * ** ** * * *
686760 GTTAAACATCAAAATGTTTTGTTAAGACATTACAATGCTATTCAAACTTCCATCTTTGA-AT
1 GTTAAACATTACAACACTAT-TCAA-AC-TTTC-AT-CT-TTGAATGTAACAACTTGGATAA
* ** * * * ** * * * **
686821 GTAACAAC-TTGGATA-A--GTT-AAGACATTATAACTCTATTTAAACT-TCCATTTTCA-AA
1 GTTA-AACATTACA-ACACTATTCAA-AC-TT-TCA-TCT-TTGAATGTAACAACTTGGATAA
* *
686877 TGTTACAAC-TTGGATAAGCTAGAC-ATT-ACAACGTTATTCAAACTTTTATTTTTGAATGTAAC
1 -GTTA-AACATT--ACAA-C---ACTATTCA-AAC--T-TTC--A--TC----TTTGAATGTAAC
686939 AACTTGGATAA
46 AACTTGGATAA
** * * ** *
686950 GTTAAACATTACAACGTTATTCAAACTTCCATATTCAAATGTAACAACTTGAATAA
1 GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* ** * *
687006 GTTAAGACATTACAACACTATTTAAAAATTCATATTTGAATGTAACAACTTGGAAAA
1 GTTAA-ACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * *
687063 GTTAAATATTACAACATTATTCAACCTTTCATCTTTGAAAGTAACAACTTGGATAA
1 GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
** *
687119 GTTAAAC-TCTACAATGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAA
1 GTTAAACAT-TACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * ** * *
687175 GTTAAAC-TCTACAACACCATACAAACTCCCATCTCTCAATGTAACAACTTGGATAA
1 GTTAAACAT-TACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * *
687231 GTTAAGACATTACAACAGTATTCAAACTTCCATCCTTAAATGCAACAACTTGGATAA
1 GTTAA-ACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * * **
687288 GTTAAACATTACATCACTATTCAAAGTTTCATATTTGAACGTAAAAAAAATGGATAA
1 GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGT-AACAACTTGGATAA
687345 GTTAAAC
1 GTTAAAC
687352 TCTTTAGTTC
Statistics
Matches: 860, Mismatches: 185, Indels: 110
0.74 0.16 0.10
Matches are distributed among these distances:
55 7 0.01
56 436 0.51
57 324 0.38
58 12 0.01
59 5 0.01
60 3 0.00
61 8 0.01
62 17 0.02
63 1 0.00
64 7 0.01
65 4 0.00
66 1 0.00
67 7 0.01
68 2 0.00
69 1 0.00
70 3 0.00
71 8 0.01
72 12 0.01
73 2 0.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (56 bp):
GTTAAACATTACAACACTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
Found at i:686860 original size:190 final size:189
Alignment explanation
Indices: 686591--686958 Score: 522
Period size: 190 Copynumber: 1.9 Consensus size: 189
686581 ATTTTGATAA
* ** *
686591 GTTAAGGCATTACAACGCTATTTGAACTTCCATTTTGAATGTAACAACTTTGATAAGTTAAAACA
1 GTTAAGACATTACAACGCTATTCAAACTTCCATTTTGAATGTAACAACTTGGATAAGTTAAAACA
** *
686656 TTACAACACTATTTAAACATACATTTTTGAACATAACAAAATGGATAAG-TCAAACATTACAATG
66 TTACAACACTATTTAAACATACATTTTCAAACATAACAAAATGGATAAGCT-AAACATTACAACG
686720 TTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACATCAAAATGTTTT
130 TTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACATCAAAATGTTTT
* *
686780 GTTAAGACATTACAATGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
1 GTTAAGACATTACAACGCTATTCAAACTTCCAT-TTTGAATGTAACAACTTGGATAAGTTAAAAC
* * * * ** * ** *
686845 ATTATAACTCTATTTAAACTTCCATTTTCAAATGTTACAACTTGGATAAGCTAGACATTACAACG
65 ATTACAACACTATTTAAACATACATTTTCAAACATAACAAAATGGATAAGCTAAACATTACAACG
* *
686910 TTATTCAAACTTTTATTTTTGAATGTAACAACTTGGATAAGTTAAACAT
130 TTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACAT
686959 TACAACGTTA
Statistics
Matches: 156, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
189 29 0.19
190 126 0.81
191 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (189 bp):
GTTAAGACATTACAACGCTATTCAAACTTCCATTTTGAATGTAACAACTTGGATAAGTTAAAACA
TTACAACACTATTTAAACATACATTTTCAAACATAACAAAATGGATAAGCTAAACATTACAACGT
TATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTTAAACATCAAAATGTTTT
Found at i:686971 original size:246 final size:247
Alignment explanation
Indices: 686534--687015 Score: 635
Period size: 246 Copynumber: 2.0 Consensus size: 247
686524 ACTTGGATAA
* * * * *
686534 GTTAAGACAATACAACACTATTTAAACTTTAATCTTTGAATGTAACAATTTTGATAAGTTAAGGC
1 GTTAAGACAATACAACACTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * *
686599 ATTACAACGCTATTTGAACTTCCATTTTGAATGTAACAACTTTGATAAGTTAAAACATTACAACA
66 ATTACAACGCTATTTAAACTTCCATTTTAAATGTAACAACTTGGATAAGCTAAAACATTACAACA
* *
686664 CTATTTAAACATACATTTTTGAACATAACAAAATGGATAAGTCAAACATTACAATGTTATTCAAA
131 CTATTCAAACATACATTTTTGAACATAACAAAATGGATAAGTCAAACATTACAACGTTATTCAAA
* * ** *
686729 CTTTCATCTTTGAATGTAACAACTTGGATAAGTTAA-ACATCAAAATGTTTT
196 CTTCCATATTCAAATGTAACAACTTGAATAAGTTAAGACATCAAAATGTTTT
* ** *
686780 GTTAAGACATTACAATGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
1 GTTAAGACAATACAACACTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * *
686845 ATTATAACTCTATTTAAACTTCCATTTTCAAATGTTACAACTTGGATAAGCT-AGACATTACAAC
66 ATTACAACGCTATTTAAACTTCCATTTT-AAATGTAACAACTTGGATAAGCTAAAACATTACAAC
** * ** ** ** *
686909 GTTATTCAAACTTTTATTTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGTTATTCAA
130 ACTATTCAAACATACATTTTTGAACATAACAAAATGGATAAGTCAAACATTACAACGTTATTCAA
686974 ACTTCCATATTCAAATGTAACAACTTGAATAAGTTAAGACAT
195 ACTTCCATATTCAAATGTAACAACTTGAATAAGTTAAGACAT
687016 TACAACACTA
Statistics
Matches: 200, Mismatches: 34, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
246 177 0.88
247 23 0.12
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (247 bp):
GTTAAGACAATACAACACTATTCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
ATTACAACGCTATTTAAACTTCCATTTTAAATGTAACAACTTGGATAAGCTAAAACATTACAACA
CTATTCAAACATACATTTTTGAACATAACAAAATGGATAAGTCAAACATTACAACGTTATTCAAA
CTTCCATATTCAAATGTAACAACTTGAATAAGTTAAGACATCAAAATGTTTT
Found at i:687014 original size:113 final size:113
Alignment explanation
Indices: 686780--687312 Score: 632
Period size: 113 Copynumber: 4.7 Consensus size: 113
686770 AAAATGTTTT
* * *
686780 GTTAAGACATTACAATGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
1 GTTAAGACATTACAACGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAA-AC
* * *
686845 ATTATAAC-TCTATTTAAACTTCCATTTTCAAATGTTACAACTTGGATAA
65 ATTACAACAT-TATTCAAACTTCCATTTTCAAATGTAACAACTTGGATAA
* * * *
686894 GCT-AGACATTACAACGTTATTCAAACTTTTATTTTTGAATGTAACAACTTGGATAAGTTAAACA
1 GTTAAGACATTACAACGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * *
686958 TTACAACGTTATTCAAACTTCCATATTCAAATGTAACAACTTGAATAA
66 TTACAACATTATTCAAACTTCCATTTTCAAATGTAACAACTTGGATAA
* * ** * *
687006 GTTAAGACATTACAACACTATTTAAAAATTCATATTTGAATGTAACAACTTGGAAAAGTTAAATA
1 GTTAAGACATTACAACGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * *
687071 TTACAACATTATTCAACCTTTCATCTTTGAAA-GTAACAACTTGGATAA
66 TTACAACATTATTCAAACTTCCAT-TTTCAAATGTAACAACTTGGATAA
*
687119 GTTAA-AC-TCTACAATGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAAC
1 GTTAAGACAT-TACAACGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAAC
** * * *
687182 -TCTACAACACCATACAAACTCCCATCTCTC-AATGTAACAACTTGGATAA
65 AT-TACAACATTATTCAAACTTCCAT-TTTCAAATGTAACAACTTGGATAA
* ** * *
687231 GTTAAGACATTACAACAG-TATTCAAACTTCCATCCTTAAATGCAACAACTTGGATAAGTTAAAC
1 GTTAAGACATTACAAC-GCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAAC
* *
687295 ATTACATCACTATTCAAA
65 ATTACAACATTATTCAAA
687313 GTTTCATATT
Statistics
Matches: 358, Mismatches: 51, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
111 4 0.01
112 136 0.38
113 208 0.58
114 10 0.03
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (113 bp):
GTTAAGACATTACAACGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAACA
TTACAACATTATTCAAACTTCCATTTTCAAATGTAACAACTTGGATAA
Found at i:687076 original size:169 final size:168
Alignment explanation
Indices: 686780--689776 Score: 1089
Period size: 169 Copynumber: 17.8 Consensus size: 168
686770 AAAATGTTTT
*
686780 GTTAAGACATTACAATGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAGAC
1 GTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * *
686845 ATTATAACTCTATTT-AAACTTCCATTTTCAAATGTTACAACTTGGATAAGCTAGACATTACAAC
65 ATTACAACACTATTTAAAACTT-CATTTT-AAATGTAACAACTTGGATAAGTTAAACATTACAAC
* *
686909 GTTATTCAAACTTTTATTTTTGAATGTAACAACTTGGATAA
128 GTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * ** *
686950 GTTAAACATTACAACGTTATTCAAACTTCCATATTCAAATGTAACAACTTGAATAAGTTAAGACA
1 GTTAAACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGACA
* * * * *
687015 TTACAACACTATTTAAAAATTCATATTTGAATGTAACAACTTGGAAAAGTTAAATATTACAACAT
66 TTACAACACTATTTAAAACTTCAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAACGT
* *
687080 TATTCAACCTTTCATCTTTGAAAGTAACAACTTGGATAA
130 TATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
*
687119 GTTAAAC-TCTACAATGCTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAA-AC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * *
687182 -TCTACAACACCA--TACAAACTCCCATCTCTCAATGTAACAACTTGGATAAGTTAAGACATTAC
65 AT-TACAACACTATTTA-AAACT-TCAT-TTTAAATGTAACAACTTGGATAAGTTAA-ACATTAC
* * * *
687244 AACAG-TATTCAAACTTCCATCCTTAAATGCAACAACTTGGATAA
125 AAC-GTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * * **
687288 GTTAAACATTAC-ATCACTATTCAAAGTTTCATATTTGAACGTAAAAAAAATGGATAAGTTAA-A
1 GTTAAACATTACAAT-GCTATTCAAACTTCCATATTTGAATGT-AACAACTTGGATAAGTTAAGA
* * * ** * *
687351 CTCTTTAGTTCGTAA-AC-A--TCAAACTGT-TTTGTTAAGACATTACAA--T-G-TTA-TTCAA
64 --CATTA---C--AACACTATTTAAAACT-TCATT-TTAA-ATGTAACAACTTGGATAAGTT-AA
* * * ** ** * * *
687406 AC-TTCCATC--T-TTGAATGTAACAAC-TTG---G--AGAA----GTTAA
118 ACATTACAACGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
** * *
687443 G----ACATTACAACACTGA-TCAAACTTCCATGTTTTAATGTAACAACTTGGATAAGTTAA-AC
1 GTTAAACATTACAATGCT-ATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
** * * * **
687502 ATTACAACGTTA-TTCAAACTTCCATCTTTGAATGTAATAACTTAAATAAGTTAAAC-TCTACAA
65 ATTACAACACTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACAT-TACAA
*** *
687565 AACTATTCAAAC-TTCATCTTTGAATGTAACAACTTAGATAA
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * *
687606 GTTAAAC-TCTAC---GCTATTCAAACTTCTATATTTGAATGTAATAGCTTGGATAAGTTAAGAC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * * * *
687667 ATTA-AA-ACGATATTCAAACTTCCATATTTGATTATAACAACTTGGATAAGTTAGACATTATAA
65 ATTACAACACTAT-TTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAA
** * * * * *
687730 CACTATTTAAACTTTCATATTTGAATTTAACGACTTGGAGAA
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * * *
687772 GTTAAGACATTACAACGCTATTTAAAGTTCAATCTTTAAATGT---AACTTGGATAAGTTAA-AC
1 GTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * * *
687833 -TCTACAACTCCA-TTCAAATTTCCATATTTGAATGTAACAACTTGGATAAGTTAAAC--TAAAA
65 AT-TACAACACTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAA
** * * * **
687894 CACTATTAAAACTTTCATATTTGAATTTATTAACTTGGATAA
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * *
687936 ATTAAGACATTACAATGCTATTCAAACTTCAATCTTTGAATGTAATAACTTGGATAAGTTAA-AA
1 GTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
** ** * * * * *
688000 ATTATGACGTTA-TTCAAACTTCCCTCTTTAAATGTATCAAATTGGATAAGTTAAAC-TCTAAAA
65 ATTACAACACTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACAT-TACAA
* * * * * *
688063 AGCTATTCAAAC-TTCAATATTTGAATGTAACAACCTAGAAAA
127 CGTTATTCAAACTTTC-ATCTTTGAATGTAACAACTTGGATAA
* * *
688105 GTTAAAC-TCTACATTGCTATTCAAACTTCCATCTTTGAGTGTAACAACGTT-GATAAGTTAAGA
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAAC-TTGGATAAGTTAAGA
* *
688168 CATTACAA-AGCTA-TTCAAACTTCCATCTTTAAATATAACAACTTGGATAAGTTAAAACATTAC
64 CATTACAACA-CTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTT-AAACATTAC
** * *
688231 AACACTATACAAACTTCCATCTTTGAATGTAACAACTTGGATAA
125 AACGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * ** * * *
688275 ATTAAAC--T-C--T-TTAGTTCGTAAAAATCAAAGTGTTTTG-TTG-AGAC-A-TT--ATTAAG
1 GTTAAACATTACAATGCTA-TTC--AAACTTC-CA-T-ATTTGAATGTA-ACAACTTGGA-TAAG
* ** * * * ** * * * ***
688328 CTATTCAAATGTCCATCTTTTAATGTAATAACTTGGATAACTTAAGCAT-T-ACAAC-CCCAT--
58 TTA-AGACAT-TACAAC-ACT-ATTTAA-AACTT-CAT--TTTAA--ATGTAACAACTTGGATAA
* * ** * ** ** * ** *
688388 -TCAAAC-TTCCATATTTTAGTGTAACAACTTGGATAAGTTAAACATTACAACTCT--ATTCAAA
113 GTTAAACATTACA-ACGTTA-T-TCA-AACTTTCAT-CTTTGAATGTAACAACT-TGGA-T--AA
* * * * * ** * * * *
688449 CTTCCATCTTTA-AATG-TA-T-GAACTTGGATAAATT-AAAGATTACAACATT--AT---TCAA
1 GTT-AAACATTACAATGCTATTCAAACTTCCAT-ATTTGAATG-TAACAAC-TTGGATAAGTTAA
* * ** * * * * * *** *
688504 -AC-TTCCATCTTTGAATGTAACAACTTGGA---TAAGT-TAA-AATTTGTATTTCTTAAACATC
62 GACATTACAACACT--ATTTAA-AACTT-CATTTTAAATGTAACAACTTGGATAAGTTAAACATT
* * * * ** * * * *
688562 A-AAGTGTTTTGTTAAGACGTTACAACGCTACTCAAATTTCTATCTTATCCACTTGGACAA
123 ACAA-CGTTAT-TCAA-AC-TT-----TC-A-TC---TTTGAAT-GTAACAACTTGGATAA
* * * * *
688622 GTTAAGACATTATAACGCTATTCAAACTTCCATATTTGAAAGCAACAACTTGAATAAGTTAA-AC
1 GTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * * *
688686 -TCTACAATACTA-TTCAAACTTCCATCTTTGAATGTAACAACTGGGATAAGTGAAATATTACAA
65 AT-TACAACACTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAA
* * *
688749 CATTATTCAAACTTTCATATTTGAATGTAACAACTTCGATAA
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * *
688791 GTTAAAC-TCTACAATTCTATTCAAACTTTCATATTTGAATGTAACAACTTGAATAAGTTAA-AC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * *
688854 -TCTACAACGCTA-TTCAAACTTCCATCTTTGAAGGTAACAAATT-GATAAGTTAAACATTACAA
65 AT-TACAACACTATTTAAAACTT-CAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAA
* * * *
688916 CGCTATTCAAACTTTCATCTCTGAATGTATCAACTTGGATAT
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * * * *
688958 GTTAAGACATTACAATGCGATTCAAACTTCCATTTTTTAAAGTAATAAATTGGTTAAGTTAA-AC
1 GTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * * *
689022 ATTAAAACATTA-TTCAAACTTTCATTTTTGAATGTAACAACTTGGATAAATTAAACACTACAAC
65 ATTACAACACTATTTAAAAC-TTCA-TTTTAAATGTAACAACTTGGATAAGTTAAACATTACAAC
* * *
689086 TTTATTCAAACTTTCATCTTTGATTGTATCAACTTGGATAA
128 GTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* *
689127 GTTAAAC-TCTACAGTGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAA-AC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * *
689190 ATTACAACACTA-TTCAAACTTCTGTATTTGAATGTATCAACTTGGATAAGTTAAGACATTATAA
65 ATTACAACACTATTTAAAACTTC-AT-TTTAAATGTAACAACTTGGATAAGTTAA-ACATTACAA
* * * * * *
689254 TGCTATTAAAACTTCCATTTTTGAATGCAACAACTTGGATAA
127 CGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * *** * * *
689296 GTTAAACACTATAACATTATTCAAACTTCTATTTTTTAATGTAACAACTTGGATAAGTTAA-ACA
1 GTTAAACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGACA
* * * * * *
689360 TCACAACATTA-TTCAAACTTCTATATTTGAATGTAATAACATGGAAAAGTTAAGACATTACGAC
66 TTACAACACTATTTAAAACTTC-AT-TTTAAATGTAACAACTTGG---A--TAAG---TTA--A-
* * *
689424 ACTATTAAAACATACAACGCTATTTAAAC-TTCTATCTTTGAATGTAACAACTTCGATAA
118 AC-A-T------TACAACGTTATTCAAACTTTC-ATCTTTGAATGTAACAACTTGGATAA
* * * * ** *
689483 GTTAAAC-TCTACAACGCTATTTAAACTTCAATCTTTGAATGTAACAACTTAAATGAGTTAA-AC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
** * * * * **
689546 ATTACAA-TGTTTTTCAAACTTCTAATTTTGAATTTAACAACTTGGATAAGTTAAACCCTACAAC
65 ATTACAACACTATTTAAAACTTC--ATTTTAAATGTAACAACTTGGATAAGTTAAACATTACAAC
* * * * *
689610 -TATATTAAAACCTGCATCTTTGATTGTAACAACGTGGATAA
128 GT-TATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
* * * * * *
689651 GTTAAAC-TCTACAACGCTATTCAAACTTTCATCTTTGAGTGTATCAACTTGGATATGTTAA-AC
1 GTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGAC
* * * * * * *
689714 ATTATAACATTA-TTCAAACTACCCTATTTGAATGTAACAACATGGATAAGTTAAACATTACAA
65 ATTACAACACTATTTAAAACT-TCAT-TTTAAATGTAACAACTTGGATAAGTTAAACATTACAA
689777 TGCTATTTGT
Statistics
Matches: 2174, Mismatches: 450, Indels: 408
0.72 0.15 0.13
Matches are distributed among these distances:
143 2 0.00
145 3 0.00
146 12 0.01
147 4 0.00
148 6 0.00
150 24 0.01
151 32 0.01
152 2 0.00
153 4 0.00
154 7 0.00
155 5 0.00
157 1 0.00
159 6 0.00
161 5 0.00
162 3 0.00
163 11 0.01
164 130 0.06
165 82 0.04
166 87 0.04
167 173 0.08
168 530 0.24
169 576 0.26
170 115 0.05
171 15 0.01
172 34 0.02
173 26 0.01
174 32 0.01
175 18 0.01
176 17 0.01
177 27 0.01
178 2 0.00
179 10 0.00
180 9 0.00
181 10 0.00
182 10 0.00
183 16 0.01
184 3 0.00
186 3 0.00
187 120 0.06
188 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (168 bp):
GTTAAACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAGACA
TTACAACACTATTTAAAACTTCATTTTAAATGTAACAACTTGGATAAGTTAAACATTACAACGTT
ATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAA
Found at i:687097 original size:359 final size:359
Alignment explanation
Indices: 686438--687312 Score: 951
Period size: 359 Copynumber: 2.5 Consensus size: 359
686428 CCCTACAACA
*
686438 CTATTCAAACTTTCATCTTTGAATGTAACAAATTGGATAAGATAAACATTAAAACATCATTCAAA
1 CTATTCAAACTTCCATCTTTGAATGTAACAAATTGGATAAGATAAACATTAAAACATCATTCAAA
* * * * *
686503 TTTCAATCTTTGATTGTAACAACTTGGATAAGTTAAGACAATACAACACTATTTAAACTTTAATC
66 CTTCAATCTTTAAATGTAACAACTTGGATAAGCTAAGACAATACAACACTATTCAAACTTTAATC
* * * ** **
686568 TTTGAATGTAACAATTTTGATAAGTTAAGGCATTACAACGCTATTTGAACTTCCATTTTGAATGT
131 TTTGAATGTAACAACTTGGATAAGTTAAGACATTACAACGCTATTCAAACTTCCATTTCAAATGT
* *
686633 AACAACTTTGATAAGTTAAAACATTACAACACTATTTAAACATACATTTTTGAACATAACAAAAT
196 AACAACTTTGATAAGTTAAAACATTACAACACTATTTAAAAATACATATTTGAACATAACAAAAT
* ** *
686698 GGATAAGTCAAACATTACAATGTTATTCAAACTTTCATCTTTGAATGTAACAACTTGGATAAGTT
261 GGAAAAGTCAAACATTACAACATTATTCAAACTTTCATCTTTGAAAGTAACAACTTGGATAAGTT
686763 AAACATCAAAATGTTTTGTTAAGACATTACAATG
326 AAACATCAAAATGTTTTGTTAAGACATTACAATG
* * * *
686797 CTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAGACATTATAAC-TCTATTTA
1 CTATTCAAACTTCCATCTTTGAATGTAACAAATTGGATAAGATAA-ACATTAAAACATC-ATTCA
* * * ** *
686861 AACTTCCAT-TTTCAAATGTTACAACTTGGATAAGCT-AGACATTACAACGTTATTCAAACTTTT
64 AACTTCAATCTTT-AAATGTAACAACTTGGATAAGCTAAGACAATACAACACTATTCAAACTTTA
* *
686924 ATTTTTGAATGTAACAACTTGGATAAGTTAA-ACATTACAACGTTATTCAAACTTCCATATTCAA
128 ATCTTTGAATGTAACAACTTGGATAAGTTAAGACATTACAACGCTATTCAAACTTCCAT-TTCAA
* * **
686988 ATGTAACAAC-TTGAATAAGTTAAGACATTACAACACTATTTAAAAATTCATATTTGAATGTAAC
192 ATGTAACAACTTTG-ATAAGTTAAAACATTACAACACTATTTAAAAATACATATTTGAACATAAC
** * * *
687052 AACTTGGAAAAGTTAAATATTACAACATTATTCAACCTTTCATCTTTGAAAGTAACAACTTGGAT
256 AAAATGGAAAAGTCAAACATTACAACATTATTCAAACTTTCATCTTTGAAAGTAACAACTTGGAT
687117 AAGTT-AA-A-C------------T----C--TACAATG
321 AAGTTAAACATCAAAATGTTTTGTTAAGACATTACAATG
* * * * * * *
687135 CTATTCAAACTTTCATATTTGAATGTAACAACTTGGATAAGTTAAAC-TCTACAACACCATACAA
1 CTATTCAAACTTCCATCTTTGAATGTAACAAATTGGATAAGATAAACAT-TAAAACATCATTCAA
* * * * * * * **
687199 ACTCCCATCTCTCAATGTAACAACTTGGATAAGTTAAGACATTACAACAGTATTCAAACTTCCAT
65 ACTTCAATCTTTAAATGTAACAACTTGGATAAGCTAAGACAATACAACACTATTCAAACTTTAAT
* * * * *
687264 CCTTAAATGCAACAACTTGGATAAGTTAA-ACATTACATCACTATTCAAA
130 CTTTGAATGTAACAACTTGGATAAGTTAAGACATTACAACGCTATTCAAA
687313 GTTTCATATT
Statistics
Matches: 445, Mismatches: 62, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
336 1 0.00
337 38 0.09
338 120 0.27
340 1 0.00
344 1 0.00
356 1 0.00
357 1 0.00
358 28 0.06
359 215 0.48
360 39 0.09
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (359 bp):
CTATTCAAACTTCCATCTTTGAATGTAACAAATTGGATAAGATAAACATTAAAACATCATTCAAA
CTTCAATCTTTAAATGTAACAACTTGGATAAGCTAAGACAATACAACACTATTCAAACTTTAATC
TTTGAATGTAACAACTTGGATAAGTTAAGACATTACAACGCTATTCAAACTTCCATTTCAAATGT
AACAACTTTGATAAGTTAAAACATTACAACACTATTTAAAAATACATATTTGAACATAACAAAAT
GGAAAAGTCAAACATTACAACATTATTCAAACTTTCATCTTTGAAAGTAACAACTTGGATAAGTT
AAACATCAAAATGTTTTGTTAAGACATTACAATG
Found at i:687492 original size:150 final size:150
Alignment explanation
Indices: 687231--687501 Score: 368
Period size: 150 Copynumber: 1.8 Consensus size: 150
687221 ACTTGGATAA
*
687231 GTTAAGACATTACAACAGTATTCAAACTTCCATCCTTAAATGCAACAACTTGGATAAGTTAAACA
1 GTTAAGACATTACAACAGTATTCAAACTTCCATCCTTAAATGCAACAACTTGGAGAAGTTAAACA
* * *
687296 TTACATCACTATTCAAAGTTTCATATTTGAACGTAAAAAAAATGGATAAGTTAAACTCTTTAGTT
66 TTACAACACTATTCAAACTTCCATATTTGAACGTAAAAAAAATGGATAAGTTAAACTCTTTAGTT
687361 CGTAAACATCAAACTGTTTT
131 CGTAAACATCAAACTGTTTT
* * * *
687381 GTTAAGACATTACAA-TGTTATTCAAACTTCCATCTTTGAATGTAACAACTTGGAGAAGTTAAGA
1 GTTAAGACATTACAACAG-TATTCAAACTTCCATCCTTAAATGCAACAACTTGGAGAAGTTAA-A
* * * * **
687445 CATTACAACACTGA-TCAAACTTCCATGTTTTAATGT-AACAACTTGGATAAGTTAAAC
64 CATTACAACACT-ATTCAAACTTCCATATTTGAACGTAAAAAAAATGGATAAGTTAAAC
687502 ATTACAACGT
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
149 1 0.01
150 73 0.70
151 29 0.28
152 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (150 bp):
GTTAAGACATTACAACAGTATTCAAACTTCCATCCTTAAATGCAACAACTTGGAGAAGTTAAACA
TTACAACACTATTCAAACTTCCATATTTGAACGTAAAAAAAATGGATAAGTTAAACTCTTTAGTT
CGTAAACATCAAACTGTTTT
Found at i:687536 original size:56 final size:56
Alignment explanation
Indices: 687381--688281 Score: 896
Period size: 56 Copynumber: 16.1 Consensus size: 56
687371 AAACTGTTTT
* * *
687381 GTTAAGACATTACAATGTTATTCAAACTTCCATCTTTGAATGTAACAACTTGGAGAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * *
687438 GTTAAGACATTACAACACTGA-TCAAACTTCCATGTTTTAATGTAACAACTTGGATAA
1 GTTAA-ACATTACAACGCT-ATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * **
687495 GTTAAACATTACAACGTTATTCAAACTTCCATCTTTGAATGTAATAACTTAAATAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
** *
687551 GTTAAAC-TCTACAAAACTATTCAAACTT-CATCTTTGAATGTAACAACTTAGATAA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * *
687606 GTTAAAC--T-CTACGCTATTCAAACTTCTATATTTGAATGTAATAGCTTGGATAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * *
687659 GTTAAGACATTAAAACGATATTCAAACTTCCATATTTGATTATAACAACTTGGATAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * * * * *
687716 GTTAGACATTATAACACTATTTAAACTTTCATATTTGAATTTAACGACTTGGAGAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * *
687772 GTTAAGACATTACAACGCTATTTAAAGTTCAATCTTTAAATGT---AACTTGGATAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * *
687826 GTTAAAC-TCTACAACTCCATTCAAATTTCCATATTTGAATGTAACAACTTGGATAA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * * **
687882 GTTAAAC--TAAAACACTATTAAAACTTTCATATTTGAATTTATTAACTTGGATAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * *
687936 ATTAAGACATTACAATGCTATTCAAACTTCAATCTTTGAATGTAATAACTTGGATAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* ** * * * * *
687993 GTTAAAAATTATGACGTTATTCAAACTTCCCTCTTTAAATGTATCAAATTGGATAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * * *
688049 GTTAAAC-TCTAAAAAGCTATTCAAACTTCAATATTTGAATGTAACAACCTAGAAAA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
** *
688105 GTTAAAC-TCTACATTGCTATTCAAACTTCCATCTTTGAGTGTAACAACGTT-GATAA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATCTTTGAATGTAACAAC-TTGGATAA
* * *
688161 GTTAAGACATTACAAAGCTATTCAAACTTCCATCTTTAAATATAACAACTTGGATAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* *
688218 GTTAAAACATTACAACACTATACAAACTTCCATCTTTGAATGTAACAACTTGGATAA
1 GTT-AAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
*
688275 ATTAAAC
1 GTTAAAC
688282 TCTTTAGTTC
Statistics
Matches: 696, Mismatches: 126, Indels: 45
0.80 0.15 0.05
Matches are distributed among these distances:
52 15 0.02
53 56 0.08
54 58 0.08
55 37 0.05
56 267 0.38
57 259 0.37
58 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (56 bp):
GTTAAACATTACAACGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
Found at i:687553 original size:113 final size:112
Alignment explanation
Indices: 687381--689783 Score: 1244
Period size: 112 Copynumber: 21.2 Consensus size: 112
687371 AAACTGTTTT
* * * *
687381 GTTAAGACATTACAATGTTATTCAAACTTCCATCTTTGAATGTAACAACTTGGAGAAGTTAAGAC
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA-AC
* *
687446 ATTACAACACTGA-TCAAACTTCCATGTTTTAATGTAACAACTTGGATAA
64 ATTACAACACT-ATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * **
687495 GTTAAACATTACAACGTTATTCAAACTTCCATCTTTGAATGTAATAACTTAAATAAGTTAAAC-T
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACAT
* *
687559 CTACAAAACTATTCAAACTT-CATCTTTGAATGTAACAACTTAGATAA
66 -TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * *
687606 GTTAAAC--T-CTACGCTATTCAAACTTCTATATTTGAATGTAATAGCTTGGATAAGTTAAGACA
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA-ACA
* * * *
687668 TTAAAACGA-TATTCAAACTTCCATATTTGATTATAACAACTTGGATAA
65 TTACAAC-ACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * * * *
687716 GTTAGACATTATAACACTATTTAAACTTTCATATTTGAATTTAACGACTTGGAGAAGTTAAGACA
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA-ACA
* * * * *
687781 TTACAACGCTATTTAAAGTTCAATCTTTAAATGT---AACTTGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * *
687826 GTTAAAC-TCTACAACTCCATTCAAATTTCCATATTTGAATGTAACAACTTGGATAAGTTAAAC-
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * * * * **
687889 -TAAAACACTATTAAAACTTTCATATTTGAATTTATTAACTTGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * *
687936 ATTAAGACATTACAATGCTATTCAAACTTCAATCTTTGAATGTAATAACTTGGATAAGTTAAAAA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
** ** * * * *
688001 TTATGACGTTATTCAAACTTCCCTCTTTAAATGTATCAAATTGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * *
688049 GTTAAAC-TCTAAAAAGCTATTCAAACTTCAATATTTGAATGTAACAACCTAGAAAAGTTAAAC-
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
*** *
688112 TCTACATTGCTATTCAAACTTCCATCTTTGAGTGTAACAACGTT-GATAA
65 T-TACAACACTATTCAAACTTCCATCTTTGAATGTAACAAC-TTGGATAA
* * * *
688161 GTTAAGACATTACAAAGCTATTCAAACTTCCATCTTTAAATATAACAACTTGGATAAGTTAAAAC
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTT-AAAC
*
688226 ATTACAACACTATACAAACTTCCATCTTTGAATGTAACAACTTGGATAA
64 ATTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * *** * * * *
688275 ATTAAACTCTTTAGTTCG-TA---AAA-ATCAAAGTGTTTTG-TTG-AGAC-A-TT--ATTAAGC
1 GTTAAA--CATTACAACGCTATTCAAACTTC-CA-T-ATTTGAATGTA-ACAACTTGGA-TAAG-
* * * ** * ** * * ***
688329 TATTCAA-ATGTCCATCTTTTAATGTAATAACTTGGATAACTTAAGCAT-T-ACAAC-CCCAT--
58 --TTAAACAT-TACAAC-ACT-AT-TCA-AACTTCCAT--CTT-TGAATGTAACAACTTGGATAA
* * *** * ** * * ** * *
688388 -TCAAAC-TTCCATATTTTAGTGTAACAACTTGGATAAGTTAAACATTACAACTCT--AT---TC
1 GTTAAACATTACA-ACGCTA-T-TCA-AACTTCCAT-ATTTGAATGTAACAACT-TGGATAAGTT
* * ** ** ** * *
688446 AAAC-TTCCATCTTTAAATGT-ATGAACTTGGATAAATT-AAAGATTACAACATT--AT--
60 AAACATTACAACACT--AT-TCA--AACTTCCAT-CTTTGAATG-TAACAAC-TTGGATAA
* * * * ** ** * * * * ***
688500 -TCAAAC-TT-CCA-TCT-TTGAATGTAACA-ACTTGGATAAGTTAA-AATTTGTATTTCTTAAA
1 GTTAAACATTACAACGCTATTCAAACTTCCATA-TTTGA-ATG-TAACAACTTGGATAAGTTAAA
* *** * * ** * * * *
688558 CATCA-AAGTGTTTTGTTAAGACGTTACAACGCTACTCAAATTTCTATCTTATCCACTTGGACAA
63 CATTACAA-CACTAT-TCAA-AC-TT----C-C-A-TC---TTTGAAT-GTAACAACTTGGATAA
* * * *
688622 GTTAAGACATTATAACGCTATTCAAACTTCCATATTTGAAAGCAACAACTTGAATAAGTTAAAC-
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* *
688686 TCTACAATACTATTCAAACTTCCATCTTTGAATGTAACAACTGGGATAA
65 T-TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * ** * *
688735 GTGAAATATTACAACATTATTCAAACTTTCATATTTGAATGTAACAACTTCGATAAGTTAAAC-T
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACAT
** * * *
688799 CTACAATTCTATTCAAACTTTCATATTTGAATGTAACAACTTGAATAA
66 -TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * *
688847 GTTAAAC-TCTACAACGCTATTCAAACTTCCATCTTTGAAGGTAACAAATT-GATAAGTTAAACA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * * * *
688910 TTACAACGCTATTCAAACTTTCATCTCTGAATGTATCAACTTGGATAT
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * * * * *
688958 GTTAAGACATTACAATGCGATTCAAACTTCCATTTTTTAAAGTAATAAATTGGTTAAGTTAAACA
1 GTTAA-ACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * * *
689023 TTAAAACATTATTCAAACTTTCATTTTTGAATGTAACAACTTGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * ** * * * *
689071 ATTAAACACTACAACTTTATTCAAACTTTCATCTTTGATTGTATCAACTTGGATAAGTTAAAC-T
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACAT
***
689135 CTACAGTGCTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
66 -TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* ** *
689183 GTTAAACATTACAACACTATTCAAACTTCTGTATTTGAATGTATCAACTTGGATAAGTTAAGACA
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA-ACA
* ** * * *
689248 TTATAATGCTATTAAAACTTCCATTTTTGAATGCAACAACTTGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * ** * * *
689296 GTTAAACACTATAACATTATTCAAACTTCTATTTTTTAATGTAACAACTTGGATAAGTTAAACAT
1 GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACAT
* * * * * * *
689361 CACAACATTATTCAAACTTCTATATTTGAATGTAATAACATGGAAAA
66 TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * *
689408 GTTAAGACATTACGACACTATTAAAACATACAACGCTATTTAAACTTCTATCTTTGAATGTAACA
1 GTTAA-ACATTACAACGCTATT----C--A-AA--C---TT---C--C-ATATTTGAATGTAACA
* * * * **
689473 ACTTCGATAAGTTAAAC-TCTACAACGCTATTTAAACTTCAATCTTTGAATGTAACAACTTAAAT
47 ACTTGGATAAGTTAAACAT-TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGAT
*
689537 GA
111 AA
* * * * * *
689539 GTTAAACATTACAATGTTTTTCAAACTTCTA-ATTTTGAATTTAACAACTTGGATAAGTTAAACC
1 GTTAAACATTACAACGCTATTCAAACTTCCATA-TTTGAATGTAACAACTTGGATAAGTTAAACA
* * * * * *
689603 CTACAACTA-TATTAAAACCTGCATCTTTGATTGTAACAACGTGGATAA
65 TTACAAC-ACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
* * * * *
689651 GTTAAAC-TCTACAACGCTATTCAAACTTTCATCTTTGAGTGTATCAACTTGGATATGTTAAACA
1 GTTAAACAT-TACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACA
* * * * * *
689715 TTATAACATTATTCAAACTACCCTATTTGAATGTAACAACATGGATAA
65 TTACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
*
689763 GTTAAACATTACAATGCTATT
1 GTTAAACATTACAACGCTATT
689784 TGTTGAGTCA
Statistics
Matches: 1759, Mismatches: 390, Indels: 282
0.72 0.16 0.12
Matches are distributed among these distances:
103 1 0.00
104 3 0.00
105 7 0.00
106 6 0.00
107 26 0.01
108 49 0.03
109 39 0.02
110 117 0.07
111 166 0.09
112 673 0.38
113 399 0.23
114 62 0.04
115 17 0.01
116 10 0.01
117 12 0.01
118 12 0.01
119 9 0.01
120 6 0.00
121 1 0.00
122 1 0.00
123 5 0.00
124 5 0.00
125 6 0.00
126 8 0.00
127 22 0.01
128 14 0.01
129 1 0.00
130 12 0.01
131 70 0.04
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (112 bp):
GTTAAACATTACAACGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACAT
TACAACACTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAA
Found at i:688392 original size:56 final size:56
Alignment explanation
Indices: 688328--688540 Score: 268
Period size: 56 Copynumber: 3.8 Consensus size: 56
688318 CATTATTAAG
* * *
688328 CTATTCAAA-TGTCCATCTTTTAATGTAATAACTTGGATAACTTAAGCATTACAACC
1 CTATTCAAACT-TCCATCTTTTAATGTAACAACTTGGATAAGTTAAGCATTACAACA
* * * * *
688384 CCATTCAAACTTCCATATTTTAGTGTAACAACTTGGATAAGTTAAACATTACAACT
1 CTATTCAAACTTCCATCTTTTAATGTAACAACTTGGATAAGTTAAGCATTACAACA
* ** *
688440 CTATTCAAACTTCCATCTTTAAATGTATGAACTTGGATAAATTAAAG-ATTACAACA
1 CTATTCAAACTTCCATCTTTTAATGTAACAACTTGGATAAGTT-AAGCATTACAACA
* *
688496 TTATTCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAA
1 CTATTCAAACTTCCATCTTTTAATGTAACAACTTGGATAAGTTAA
688541 AATTTGTATT
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
55 2 0.01
56 129 0.96
57 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (56 bp):
CTATTCAAACTTCCATCTTTTAATGTAACAACTTGGATAAGTTAAGCATTACAACA
Found at i:688706 original size:56 final size:56
Alignment explanation
Indices: 688612--689434 Score: 784
Period size: 56 Copynumber: 14.6 Consensus size: 56
688602 TATCTTATCC
* * * * *
688612 ACTTGGACAAGTTAAGACAT-TATAACGCTATTCAAACTTCCATATTTGAAAGCAACA
1 ACTTGGATAAGTTAA-AC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * *
688669 ACTTGAATAAGTTAAACTCTACAATACTATTCAAACTTCCATCTTTGAATGTAACA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * * *
688725 ACTGGGATAAGTGAAA-TATTACAACATTATTCAAACTTTCATATTTGAATGTAACA
1 ACTTGGATAAGTTAAACT-CTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* ** *
688781 ACTTCGATAAGTTAAACTCTACAATTCTATTCAAACTTTCATATTTGAATGTAACA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * *
688837 ACTTGAATAAGTTAAACTCTACAACGCTATTCAAACTTCCATCTTTGAAGGTAACA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * * * *
688893 AATT-GATAAGTTAAACAT-TACAACGCTATTCAAACTTTCATCTCTGAATGTATCA
1 ACTTGGATAAGTTAAAC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* ** * * * * *
688948 ACTTGGATATGTTAAGACAT-TACAATGCGATTCAAACTTCCATTTTTTAAAGTAATA
1 ACTTGGATAAGTTAA-AC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * * * *
689005 AATTGGTTAAGTTAAACAT-TAAAACATTATTCAAACTTTCATTTTTGAATGTAACA
1 ACTTGGATAAGTTAAAC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * ** * * * *
689061 ACTTGGATAAATTAAACACTACAACTTTATTCAAACTTTCATCTTTGATTGTATCA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
*** *
689117 ACTTGGATAAGTTAAACTCTACAGTGCTATTCAAACTTCCATCTTTGAATGTAACA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
** *
689173 ACTTGGATAAGTTAAACAT-TACAACACTATTCAAACTTCTGTATTTGAATGTATCA
1 ACTTGGATAAGTTAAAC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* ** * * *
689229 ACTTGGATAAGTTAAGACAT-TATAATGCTATTAAAACTTCCATTTTTGAATGCAACA
1 ACTTGGATAAGTTAA-AC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * * * *
689286 ACTTGGATAAGTTAAACACTATAACATTATTCAAACTTCTATTTTTTAATGTAACA
1 ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * *
689342 ACTTGGATAAGTTAAACATC-ACAACATTATTCAAACTTCTATATTTGAATGTAATA
1 ACTTGGATAAGTTAAAC-TCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
* * * *
689398 ACATGGAAAAGTTAAGACAT-TACGACACTATTAAAAC
1 ACTTGGATAAGTTAA-AC-TCTACAACACTATTCAAAC
689435 ATACAACGCT
Statistics
Matches: 642, Mismatches: 111, Indels: 26
0.82 0.14 0.03
Matches are distributed among these distances:
55 49 0.08
56 469 0.73
57 124 0.19
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (56 bp):
ACTTGGATAAGTTAAACTCTACAACACTATTCAAACTTCCATATTTGAATGTAACA
Found at i:688983 original size:168 final size:168
Alignment explanation
Indices: 688607--689776 Score: 1016
Period size: 168 Copynumber: 6.8 Consensus size: 168
688597 ATTTCTATCT
* * * * * *
688607 TATCCACTTGGACAAGTTAAGACATTATAACGCTATTCAAACTTCCATATTTGAAAGCAACAACT
1 TATCAACTTGGATAAGTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
* * * *
688672 TGAATAAGTTAAAC-TCTACAATACTATTCAAACTTCCATCTTTGAATGTAACAACTGGGATAAG
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAACT-TGATAAG
* * * *
688736 TGAAATATTACAACATTATTCAAACTTTCATATTTGAATG
129 TTAAACATTACAACACTATTCAAACTTTCATCTTTGAATG
* * * *
688776 TAACAACTTCGATAAGTTAAAC-TCTACAATTCTATTCAAACTTTCATATTTGAATGTAACAACT
1 TATCAACTTGGATAAGTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
* * * * *
688840 TGAATAAGTTAAAC-TCTACAACGCTATTCAAACTTCCATCTTTGAAGGTAACAAATTGATAAGT
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAACTTGATAAGT
* *
688904 TAAACATTACAACGCTATTCAAACTTTCATCTCTGAATG
130 TAAACATTACAACACTATTCAAACTTTCATCTTTGAATG
* * * * * * *
688943 TATCAACTTGGATATGTTAAGACATTACAATGCGATTCAAACTTCCATTTTTTAAAGTAATAAAT
1 TATCAACTTGGATAAGTTAA-ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
* * * * * *
689008 TGGTTAAGTTAAACAT-TAAAACATTATTCAAACTTTCATTTTTGAATGTAACAACTTGGATAAA
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAACTT-GATAAG
* ** *
689072 TTAAACACTACAACTTTATTCAAACTTTCATCTTTGATTG
129 TTAAACATTACAACACTATTCAAACTTTCATCTTTGAATG
* *
689112 TATCAACTTGGATAAGTTAAAC-TCTACAGTGCTATTCAAACTTCCATCTTTGAATGTAACAACT
1 TATCAACTTGGATAAGTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
** *
689176 TGGATAAGTTAAACAT-TACAACACTATTCAAACTTCTGTATTTGAATGTATCAACTTGGATAAG
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAACTT-GATAAG
* ** * * *
689240 TTAAGACATTATAATGCTATTAAAACTTCCATTTTTGAATG
129 TTAA-ACATTACAACACTATTCAAACTTTCATCTTTGAATG
* * * * *** * * *
689281 CAACAACTTGGATAAGTTAAACACTATAACATTATTCAAACTTCTATTTTTTAATGTAACAACTT
1 TATCAACTTGGATAAGTTAAACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTT
* * * * *
689346 GGATAAGTTAAACATC-ACAACATTATTCAAACTTCTATATTTGAATGTAATAACATGGAAAAGT
66 GGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAAC-TTGATAAGT
*
689410 TAAGACATTACGACACTATTAAAACATACAACGCTATTTAAACTTCTATCTTTGAATG
130 TAA-ACATTACAACACTATT----C--A-AA--C----T----TTC-ATCTTTGAATG
* * * * * *
689468 TAACAACTTCGATAAGTTAAAC-TCTACAACGCTATTTAAACTTCAATCTTTGAATGTAACAACT
1 TATCAACTTGGATAAGTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
** * *** * * *
689532 TAAATGAGTTAAACAT-TACAATGTTTTTCAAACTTCTA-ATTTTGAATTTAACAACTTGGATAA
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATA-TTTGAATGTAACAACTT-GATAA
** * * * *
689595 GTTAAACCCTACAACTA-TATTAAAACCTGCATCTTTGATTG
128 GTTAAACATTACAAC-ACTATTCAAACTTTCATCTTTGAATG
* * * * * * *
689636 TAACAACGTGGATAAGTTAAAC-TCTACAACGCTATTCAAACTTTCATCTTTGAGTGTATCAACT
1 TATCAACTTGGATAAGTTAAACAT-TACAATGCTATTCAAACTTCCATATTTGAATGTAACAACT
* * * * * *
689700 TGGATATGTTAAACAT-TATAACATTATTCAAACTACCCTATTTGAATGTAACAACATGGATAAG
65 TGGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAAC-TTGATAAG
689764 TTAAACATTACAA
129 TTAAACATTACAA
689777 TGCTATTTGT
Statistics
Matches: 820, Mismatches: 146, Indels: 71
0.79 0.14 0.07
Matches are distributed among these distances:
167 59 0.07
168 387 0.47
169 232 0.28
170 1 0.00
175 1 0.00
176 2 0.00
177 1 0.00
178 1 0.00
179 2 0.00
180 1 0.00
182 1 0.00
186 15 0.02
187 117 0.14
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (168 bp):
TATCAACTTGGATAAGTTAAACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTT
GGATAAGTTAAACATCTACAACACTATTCAAACTTCCATATTTGAATGTAACAACTTGATAAGTT
AAACATTACAACACTATTCAAACTTTCATCTTTGAATG
Found at i:689498 original size:56 final size:56
Alignment explanation
Indices: 689431--689784 Score: 335
Period size: 56 Copynumber: 6.3 Consensus size: 56
689421 GACACTATTA
*
689431 AAACA-TACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTCGATAAGTT
1 AAACATTACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTGGATAAGTT
* ** *
689486 AAAC-TCTACAACGCTATTTAAACTTCAATCTTTGAATGTAACAACTTAAATGAGTT
1 AAACAT-TACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTGGATAAGTT
* * *
689542 AAACATTACAATG-TTTTTCAAACTTCTAAT-TTTGAATTTAACAACTTGGATAAGTT
1 AAACATTACAACGCTATTT-AAACTTCT-ATCTTTGAATGTAACAACTTGGATAAGTT
** ** * * * *
689598 AAACCCTACAACTATATTAAAACCTGC-ATCTTTGATTGTAACAACGTGGATAAGTT
1 AAACATTACAACGCTATTTAAA-CTTCTATCTTTGAATGTAACAACTTGGATAAGTT
* * * *
689654 AAAC-TCTACAACGCTATTCAAACTT-TCATCTTTGAGTGTATCAACTTGGATATGTT
1 AAACAT-TACAACGCTATTTAAACTTCT-ATCTTTGAATGTAACAACTTGGATAAGTT
* ** * * ** * *
689710 AAACATTATAACATTATTCAAACTACCCTATTTGAATGTAACAACATGGATAAGTT
1 AAACATTACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTGGATAAGTT
*
689766 AAACATTACAATGCTATTT
1 AAACATTACAACGCTATTT
689785 GTTGAGTCAA
Statistics
Matches: 240, Mismatches: 46, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
55 12 0.05
56 218 0.91
57 10 0.04
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (56 bp):
AAACATTACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTGGATAAGTT
Found at i:689507 original size:75 final size:76
Alignment explanation
Indices: 689355--689508 Score: 179
Period size: 75 Copynumber: 2.1 Consensus size: 76
689345 TGGATAAGTT
* * *
689355 AAACATCACAACATTATTCAAACTTCTATATTTGAATGTAATAACATGGAAAAGTTAAGACATTA
1 AAACATCACAACACTATTCAAACTTCTATATTTGAATGTAACAACATCGAAAAGTTAAGACATTA
*
689420 CGACACTATTA
66 CAACACTATTA
* * * * *
689431 AAACAT-ACAACGCTATTTAAACTTCTATCTTTGAATGTAACAACTTCGATAAGTTAA-AC-TCT
1 AAACATCACAACACTATTCAAACTTCTATATTTGAATGTAACAACATCGAAAAGTTAAGACAT-T
* *
689493 ACAACGCTATTT
65 ACAACACTATTA
689505 AAAC
1 AAAC
689509 TTCAATCTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
73 1 0.02
74 16 0.24
75 43 0.65
76 6 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (76 bp):
AAACATCACAACACTATTCAAACTTCTATATTTGAATGTAACAACATCGAAAAGTTAAGACATTA
CAACACTATTA
Found at i:689578 original size:187 final size:187
Alignment explanation
Indices: 689255--689774 Score: 463
Period size: 187 Copynumber: 2.9 Consensus size: 187
689245 ACATTATAAT
* * * *
689255 GCTATTAAAACTTCCATTTTTGAATGCAACAACTTGGATAAGTTAAACACTATAACATTATTCAA
1 GCTATTAAAACTTCCATCTTTGAATGCAACAACTTCGATAAGTTAAACACTACAACACTATTCAA
* * * **
689320 ACTTCTATTTTTTAATGTAACAACTTGGATAAGTTAAACATCACAACATTATTCAAACTTCTATA
66 ACTTCAATCTTTGAATGTAACAACTTAAATAAGTTAAACATCACAACATTATTCAAACTTCTATA
*
689385 TTTGAATGTAATAACATGGAAAAGTTAAGACATTACGACACTATTAAAACATACAAC
131 TTTGAATGTAACAACATGGAAAAGTTAAGACATTACGACACTATTAAAACATACAAC
* * * * * *
689442 GCTATTTAAACTTCTATCTTTGAATGTAACAACTTCGATAAGTTAAACTCTACAACGCTATTTAA
1 GCTATTAAAACTTCCATCTTTGAATGCAACAACTTCGATAAGTTAAACACTACAACACTATTCAA
* * ** *
689507 ACTTCAATCTTTGAATGTAACAACTTAAATGAGTTAAACATTACAATGTTTTTCAAACTTCTA-A
66 ACTTCAATCTTTGAATGTAACAACTTAAATAAGTTAAACATCACAACATTATTCAAACTTCTATA
* * * **
689571 TTTTGAATTTAACAACTTGGATAAGTTAA-ACCCTAC-A-ACTA-T-----AT-----
131 -TTTGAATGTAACAACATGGAAAAGTTAAGACATTACGACACTATTAAAACATACAAC
* * * * * * * *
689615 --TA--AAA-CCTGCATCTTTGATTGTAACAACGTGGATAAGTTAAACTCTACAACGCTATTCAA
1 GCTATTAAAACTTCCATCTTTGAATGCAACAACTTCGATAAGTTAAACACTACAACACTATTCAA
* * ** * * * * **
689675 ACTTTC-ATCTTTGAGTGTATCAACTTGGATATGTTAAACATTATAACATTATTCAAACTACCCT
66 AC-TTCAATCTTTGAATGTAACAACTTAAATAAGTTAAACATCACAACATTATTCAAACTTCTAT
*
689739 ATTTGAATGTAACAACATGGATAAGTTAA-ACATTAC
130 ATTTGAATGTAACAACATGGAAAAGTTAAGACATTAC
689775 AATGCTATTT
Statistics
Matches: 279, Mismatches: 51, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
168 125 0.45
169 6 0.02
171 2 0.01
178 2 0.01
183 1 0.00
184 4 0.01
185 1 0.00
186 6 0.02
187 132 0.47
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (187 bp):
GCTATTAAAACTTCCATCTTTGAATGCAACAACTTCGATAAGTTAAACACTACAACACTATTCAA
ACTTCAATCTTTGAATGTAACAACTTAAATAAGTTAAACATCACAACATTATTCAAACTTCTATA
TTTGAATGTAACAACATGGAAAAGTTAAGACATTACGACACTATTAAAACATACAAC
Found at i:690736 original size:29 final size:29
Alignment explanation
Indices: 690703--690829 Score: 227
Period size: 29 Copynumber: 4.4 Consensus size: 29
690693 TTCTCCAACT
* *
690703 AGAGTATCGATACAAGTATCGATACTTAG
1 AGAGTATCGATGCCAGTATCGATACTTAG
690732 AGAGTATCGATGCCAGTATCGATACTTAG
1 AGAGTATCGATGCCAGTATCGATACTTAG
690761 AGAGTATCGATGCCAGTATCGATACTTAG
1 AGAGTATCGATGCCAGTATCGATACTTAG
*
690790 AGAGTATCGATGCCAGTATCTATACTTAG
1 AGAGTATCGATGCCAGTATCGATACTTAG
690819 AGAGTATCGAT
1 AGAGTATCGAT
690830 ACTTAGAGAG
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (29 bp):
AGAGTATCGATGCCAGTATCGATACTTAG
Found at i:690769 original size:46 final size:46
Alignment explanation
Indices: 690717--690875 Score: 201
Period size: 46 Copynumber: 3.2 Consensus size: 46
690707 TATCGATACA
690717 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATG
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATAC-T------TA--GA-G
*
690773 CCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCTATACTTAGAG
1 --AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAG
690821 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAG
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAG
690867 AGTATCGAT
1 AGTATCGAT
690876 GCCAGTATCG
Statistics
Matches: 99, Mismatches: 2, Indels: 12
0.88 0.02 0.11
Matches are distributed among these distances:
46 54 0.55
48 1 0.01
49 2 0.02
51 2 0.02
57 1 0.01
58 39 0.39
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (46 bp):
AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAG
Found at i:690828 original size:75 final size:75
Alignment explanation
Indices: 690746--690906 Score: 313
Period size: 75 Copynumber: 2.1 Consensus size: 75
690736 TATCGATGCC
*
690746 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCT
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
690811 ATACTTAGAG
66 ATACTTAGAG
690821 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
690886 ATACTTAGAG
66 ATACTTAGAG
690896 AGTATCGATAC
1 AGTATCGATAC
690907 CAAAGTAGCC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 85 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (75 bp):
AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
ATACTTAGAG
Found at i:690853 original size:29 final size:29
Alignment explanation
Indices: 690821--690904 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
690811 ATACTTAGAG
690821 AGTATCGATACTTAGAGAGTATCGATGCC
1 AGTATCGATACTTAGAGAGTATCGATGCC
690850 AGTATCGATACTTAGAGAGTATCGATGCC
1 AGTATCGATACTTAGAGAGTATCGATGCC
690879 AGTATCGATACTTAGAGAGTATCGAT
1 AGTATCGATACTTAGAGAGTATCGAT
690905 ACCAAAGTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (29 bp):
AGTATCGATACTTAGAGAGTATCGATGCC
Found at i:690854 original size:58 final size:56
Alignment explanation
Indices: 690703--690904 Score: 244
Period size: 58 Copynumber: 3.7 Consensus size: 56
690693 TTCTCCAACT
*
690703 AGAGTATCGATACAAGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAG
1 AGAGTATCGATACCAGTA-CGATAC-TAGAGAGTATCGATGCCAGTATCGATACTTAG
* *
690761 AGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCTATACTTAG
1 AGAGTATCGATACCAGTA-CGATAC-TAGAGAGTATCGATGCCAGTATCGATACTTAG
690819 AGAGTATCG-----A-TAC--T--TAGAGAGTATCGATGCCAGTATCGATACTTAG
1 AGAGTATCGATACCAGTACGATACTAGAGAGTATCGATGCCAGTATCGATACTTAG
*
690865 AGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGAT
1 AGAGTATCGATACCAGTA-CGATAC-TAGAGAGTATCGAT
690905 ACCAAAGTAG
Statistics
Matches: 128, Mismatches: 4, Indels: 24
0.82 0.03 0.15
Matches are distributed among these distances:
46 40 0.31
49 1 0.01
51 2 0.02
52 4 0.03
53 2 0.02
55 1 0.01
58 78 0.61
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (56 bp):
AGAGTATCGATACCAGTACGATACTAGAGAGTATCGATGCCAGTATCGATACTTAG
Found at i:690897 original size:104 final size:104
Alignment explanation
Indices: 690717--690904 Score: 376
Period size: 104 Copynumber: 1.8 Consensus size: 104
690707 TATCGATACA
690717 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
690782 ATACTTAGAGAGTATCGATGCCAGTATCTATACTTAGAG
66 ATACTTAGAGAGTATCGATGCCAGTATCTATACTTAGAG
690821 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
1 AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
690886 ATACTTAGAGAGTATCGAT
66 ATACTTAGAGAGTATCGAT
690905 ACCAAAGTAG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 84 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (104 bp):
AGTATCGATACTTAGAGAGTATCGATGCCAGTATCGATACTTAGAGAGTATCGATGCCAGTATCG
ATACTTAGAGAGTATCGATGCCAGTATCTATACTTAGAG
Found at i:692571 original size:23 final size:23
Alignment explanation
Indices: 692545--692608 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
692535 CAGCTCATAT
692545 AATTACACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACGTAG
* *
692568 AATTTCACC-AGAGTGCCGCGTAG
1 AATTACACCGA-AGTGCCACGTAG
* *
692591 AATTGCACCGTAGTGCCA
1 AATTACACCGAAGTGCCA
692609 TATAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACGTAG
Found at i:692787 original size:103 final size:103
Alignment explanation
Indices: 692624--692841 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
692614 TAATGTCCAT
* * * *
692624 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTTTGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
692689 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
692727 AAGGACCACATATAATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
692792 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
692830 AAGGACCACATA
1 AAGGACCACATA
692842 GACTCTCTAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:693400 original size:64 final size:67
Alignment explanation
Indices: 693290--693417 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 67
693280 ATTTTCATCT
693290 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
693355 TA
66 TA
*
693357 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTT
693418 TCTTTTTAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.56
65 15 0.25
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:693435 original size:64 final size:62
Alignment explanation
Indices: 693302--693462 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
693292 TAATGGAGGT
* * *
693302 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
693367 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* * *
693431 ATGCATCGATGCAATGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
693463 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:705158 original size:23 final size:23
Alignment explanation
Indices: 705127--705186 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
705117 CACCACAACT
* *
705127 CATATAATTACACCAAAGTACCA
1 CATAGAATTGCACCAAAGTACCA
* *
705150 CATAGAATTGCACCAGAGTACCG
1 CATAGAATTGCACCAAAGTACCA
*
705173 CGTAGAATTGCACC
1 CATAGAATTGCACC
705187 GTAGTGCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (23 bp):
CATAGAATTGCACCAAAGTACCA
Found at i:705382 original size:103 final size:103
Alignment explanation
Indices: 705211--705428 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
705201 TAATGTCCAT
* * *
705211 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTAACCA
*
705276 GACTTCACTCATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
705314 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGCTCAAGTATGTGTCTAACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTAACCA
705379 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
705417 AAGGACCACATA
1 AAGGACCACATA
705429 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTAACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:706012 original size:64 final size:66
Alignment explanation
Indices: 705874--706012 Score: 180
Period size: 64 Copynumber: 2.1 Consensus size: 66
705864 GCCATTTTCA
*
705874 TCTTTTAATGGAGGTATGCATCGATGCACTAGACCATGCATCGATGCATAAATCCTATTCGATGT
1 TCTTTTAATGGAGGTATGAATCGATGCACT--ACCATGCATCGATGCATAAATCCTATTCGATGT
705939 TTG
64 TTG
* *
705942 T-ATTTAATGG-GG-ATGAATCGATGCACT-CCTTATGCATCGATGCCTAAATCCTATTCGATGT
1 TCTTTTAATGGAGGTATGAATCGATGCACTACC--ATGCATCGATGCATAAATCCTATTCGATGT
706003 TT-
64 TTG
706005 TCTTTTAA
1 TCTTTTAA
706013 ATTAATGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
62 2 0.03
63 1 0.02
64 36 0.56
65 14 0.22
66 2 0.03
67 8 0.12
68 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (66 bp):
TCTTTTAATGGAGGTATGAATCGATGCACTACCATGCATCGATGCATAAATCCTATTCGATGTTT
G
Found at i:709600 original size:20 final size:20
Alignment explanation
Indices: 709577--709632 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
709567 ATTAAAACAG
*
709577 TGTATATATATATGTATGTA
1 TGTATATATATAAGTATGTA
*
709597 TGTATATGTATAAGTATGTAA
1 TGTATATATATAAGTATGT-A
* *
709618 AGTGTATATATAAGT
1 TGTATATATATAAGT
709633 TCAAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.45
Consensus pattern (20 bp):
TGTATATATATAAGTATGTA
Found at i:710278 original size:42 final size:42
Alignment explanation
Indices: 710231--710312 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
710221 ACGATGCTAT
* *
710231 AAGAACAATATTGGTA-TTTGATGAATAATATCAATACTAAGG
1 AAGAACAATATTGGTACTGT-AAGAATAATATCAATACTAAGG
710273 AAGAACAATATTGGTACTGTAAGAATAATATCAATACTAA
1 AAGAACAATATTGGTACTGTAAGAATAATATCAATACTAA
710313 ATGCACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.29
Consensus pattern (42 bp):
AAGAACAATATTGGTACTGTAAGAATAATATCAATACTAAGG
Found at i:710310 original size:20 final size:21
Alignment explanation
Indices: 710253--710311 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
710243 GGTATTTGAT
710253 GAATAATATCAATACTAAGGAA
1 GAATAATATCAATACT-AGGAA
* *** *
710275 GAACAATATTGGTACT-GTAA
1 GAATAATATCAATACTAGGAA
710295 GAATAATATCAATACTA
1 GAATAATATCAATACTA
710312 AATGCACAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
20 15 0.56
22 12 0.44
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (21 bp):
GAATAATATCAATACTAGGAA
Found at i:712582 original size:56 final size:56
Alignment explanation
Indices: 712478--712669 Score: 224
Period size: 56 Copynumber: 3.4 Consensus size: 56
712468 TTCATTTTTT
* * * * * * *
712478 AATGTATCAACTTGGACAAGTT-AACATTACAACGCTATACAAATTTCCATATCTG
1 AATGTAACAACTTGGATAAGTTAAACATTAAAACGTTATTCAAAATTCCATATTTG
* * * * *
712533 AATATAACAACTTGGATAAATTAAACATTAAAATGTTATTCAAACTTCCATCTTTG
1 AATGTAACAACTTGGATAAGTTAAACATTAAAACGTTATTCAAAATTCCATATTTG
* * * * *
712589 AATGTAACAAATTGGAGAAGTTAAACATTCAAACATTATTCAAAATTCAATATTTG
1 AATGTAACAACTTGGATAAGTTAAACATTAAAACGTTATTCAAAATTCCATATTTG
712645 AATGTAACAACTTGGATAAGTTAAA
1 AATGTAACAACTTGGATAAGTTAAA
712670 TTCTACAACG
Statistics
Matches: 113, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
55 18 0.16
56 95 0.84
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (56 bp):
AATGTAACAACTTGGATAAGTTAAACATTAAAACGTTATTCAAAATTCCATATTTG
Found at i:712669 original size:112 final size:111
Alignment explanation
Indices: 712457--712669 Score: 266
Period size: 112 Copynumber: 1.9 Consensus size: 111
712447 TGGTTCAATA
* * * * * * *
712457 TTATTAAAACTTTCATTTTTTAATGTATCAACTTGGACAAGTTAACATTACAACGCTATACAAAT
1 TTATTAAAACTTCCATCTTTGAATGTAACAAATTGGACAAGTTAACATTACAACACTATACAAAA
*
712522 TTCCATATCTGAATATAACAACTTGGATAAATTAAACATTAAAATG
66 TTCAATATCTGAATATAACAACTTGGATAAATTAAACATTAAAATG
* * * *
712568 TTATTCAAACTTCCATCTTTGAATGTAACAAATTGGAGAAGTTAAACATT-CAAACATTATTCAA
1 TTATTAAAACTTCCATCTTTGAATGTAACAAATTGGACAAGTT-AACATTAC-AACACTATACAA
* * *
712632 AATTCAATATTTGAATGTAACAACTTGGATAAGTTAAA
64 AATTCAATATCTGAATATAACAACTTGGATAAATTAAA
712670 TTCTACAACG
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
111 37 0.44
112 48 0.56
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (111 bp):
TTATTAAAACTTCCATCTTTGAATGTAACAAATTGGACAAGTTAACATTACAACACTATACAAAA
TTCAATATCTGAATATAACAACTTGGATAAATTAAACATTAAAATG
Found at i:715117 original size:108 final size:107
Alignment explanation
Indices: 714999--715571 Score: 308
Period size: 118 Copynumber: 5.1 Consensus size: 107
714989 CATTAGTATT
714999 ATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCTGATAGAGCCTTAGAAATCCG
1 ATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCTGAT-GAGCCTTAGAAATCCG
715064 AAGATAACATAACTAGTTAATTACTGGAAACATTATTAAGCATA
65 AAGATAACATAACTAGTTAATTACT-GAAACATTATTAAGCATA
* ** * *
715108 AT-AACATATTACATAGCGCTTATG--TAACGTAATAGGAAGCACAATA-TTAAAGCTGATGGGG
1 ATCAACATA-T---TAG-G-TAATGCCTAA---AAT-GTTA-C-CAA-AGTTTAAGCTGAT-GAG
* * ** * * *
715169 CCTTAGAAATCC-ACA-ATAACA-AAATAGGTTAATTACT-TAATTTTTTTATCAGTATT
52 CCTTAGAAATCCGA-AGATAACATAACTA-GTTAATTACTGAAACATTATTA--AGCATA
** *
715225 ATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATTGAGCCTTAGAACTCCG
1 ATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCTGA-TGAGCCTTAGAAATCCG
* *
715290 ACGATAACATAACCT-GTTAATTACTGGAAACATTATCAAGCATA
65 AAGATAACATAA-CTAGTTAATTACT-GAAACATTATTAAGCATA
** * * * * *
715334 AT-AACATATTAGGTAGCGCTTTTGTAACATATTAGGTAGCACATTATTAAAGCTGATGAGGCCT
1 ATCAACATATTAGGTAATGC----CTAA-A-A-T-GTTACCAAAGT-TT-AAGCTGATGA-GCCT
* * * * * * * * * *
715398 TATAAATCCCATGATAACA-AAATAGGTTAATTAATTAATTTC-TTA-TCAGTATT
55 TAGAAATCCGAAGATAACATAACTA-GTTAATTACTGAA--ACATTATTAAGCATA
* *
715451 ATCAACATATTAGGTTATGCCTAAAATGTTACCAAAGTTTAAGCTGATGAAGCCTTAGAAATTCG
1 ATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCTGATG-AGCCTTAGAAATCCG
* * ** * * *
715516 AAAATAAAATAACCGGTTAATTACTTGAAACATTATCAAGCTTT
65 AAGATAACATAACTAGTTAATTAC-TGAAACATTATTAAGCATA
*
715560 ATCAAAATATTA
1 ATCAACATATTA
715572 CCATGTACAT
Statistics
Matches: 341, Mismatches: 74, Indels: 98
0.66 0.14 0.19
Matches are distributed among these distances:
107 2 0.01
108 83 0.24
109 51 0.15
110 11 0.03
111 11 0.03
112 12 0.04
113 4 0.01
114 14 0.04
115 11 0.03
116 14 0.04
117 40 0.12
118 86 0.25
119 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (107 bp):
ATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTTAAGCTGATGAGCCTTAGAAATCCGA
AGATAACATAACTAGTTAATTACTGAAACATTATTAAGCATA
Found at i:715311 original size:226 final size:225
Alignment explanation
Indices: 714841--715556 Score: 1033
Period size: 226 Copynumber: 3.2 Consensus size: 225
714831 AAATATTGAC
*
714841 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGCAGCGCTTAT
1 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
* * * * * * *
714906 GTAACGTAATAGGTAGCGCCTTTTTAAAGCTGA-CGGGCCTTAGAAATTCTACGATAAAAAAATA
66 GTAACGTAATAGGTAGCACATTATTAAAGCTGATGGGGCCTTAGAAA-TCCACAATAACAAAATA
** *
714970 GGTTAATTACTTAATTTACCATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAA
130 GGTTAATTACTTAATTTATTATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAA
*
715035 GTTTAAGCTGATAGAGCCTTAGAAATCCGAA
195 GTTTAAGCTGATTGAGCCTTAGAAATCCGAA
** * **
715066 GATAACATAACTAGTTAATTACTGGAAACATTATTAAGCATAATAACATATTACATAGCGCTTAT
1 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
* *
715131 GTAACGTAATAGGAAGCACAATATTAAAGCTGATGGGGCCTTAGAAATCCACAATAACAAAATAG
66 GTAACGTAATAGGTAGCACATTATTAAAGCTGATGGGGCCTTAGAAATCCACAATAACAAAATAG
* **
715196 GTTAATTACTTAATTTTTTTATCAGTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAA
131 GTTAATTACTTAA-TTTATTATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAA
* *
715261 GTTTAAGCTGATTGAGCCTTAGAACTCCGAC
195 GTTTAAGCTGATTGAGCCTTAGAAATCCGAA
* *
715292 GATAACATAACCTGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTTT
1 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
* * * *
715357 GTAACATATTAGGTAGCACATTATTAAAGCTGATGAGGCCTTATAAATCC-CATGATAACAAAAT
66 GTAACGTAATAGGTAGCACATTATTAAAGCTGATGGGGCCTTAGAAATCCACA--ATAACAAAAT
* * *
715421 AGGTTAATTAATTAATTTCTTATCAGTATTATCAACATATTAGGTTATGCCTAAAATGTTACCAA
129 AGGTTAATTACTTAATTTATTATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAA
*
715486 AGTTTAAGCTGA-TGAAGCCTTAGAAATTCGAA
194 AGTTTAAGCTGATTG-AGCCTTAGAAATCCGAA
* * *
715518 AATAAAATAACCGGTTAATTACTTGAAACATTATCAAGC
1 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGC
715557 TTTATCAAAA
Statistics
Matches: 438, Mismatches: 48, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
225 119 0.27
226 295 0.67
227 24 0.05
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (225 bp):
GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
GTAACGTAATAGGTAGCACATTATTAAAGCTGATGGGGCCTTAGAAATCCACAATAACAAAATAG
GTTAATTACTTAATTTATTATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAG
TTTAAGCTGATTGAGCCTTAGAAATCCGAA
Found at i:715959 original size:2 final size:2
Alignment explanation
Indices: 715952--716003 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
715942 TAAGTATGGA
715952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
715994 AT AT AT AT AT
1 AT AT AT AT AT
716004 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:716008 original size:2 final size:2
Alignment explanation
Indices: 716003--716029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
715993 TATATATATA
716003 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
716030 TTCTATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:732882 original size:29 final size:29
Alignment explanation
Indices: 732839--732921 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
732829 CTCACCTAAC
732839 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
732869 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
732898 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
732922 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:737588 original size:29 final size:29
Alignment explanation
Indices: 737545--737627 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
737535 CTCACCTAAC
737545 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
737575 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
737604 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
737628 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:739193 original size:17 final size:17
Alignment explanation
Indices: 739154--739187 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
739144 AGATGAGATT
*
739154 AGAAGAAGGAAAAGAAA
1 AGAAAAAGGAAAAGAAA
739171 AGAAAAAGGAAAA-AAA
1 AGAAAAAGGAAAAGAAA
739187 A
1 A
739188 CTAAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAAAGGAAAAGAAA
Found at i:740951 original size:21 final size:20
Alignment explanation
Indices: 740923--740961 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
740913 CACTGTAGGA
*
740923 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
740943 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
740962 GACTTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:745817 original size:20 final size:20
Alignment explanation
Indices: 745792--745829 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
745782 GTACTGAGGC
745792 TGAGAAAATATTTAAGGCGT
1 TGAGAAAATATTTAAGGCGT
745812 TGAGAAAATATTTAAGGC
1 TGAGAAAATATTTAAGGC
745830 CCTGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (20 bp):
TGAGAAAATATTTAAGGCGT
Found at i:745840 original size:20 final size:20
Alignment explanation
Indices: 745791--745833 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
745781 CGTACTGAGG
*
745791 CTGAGAAAATATTTAAGGCG
1 CTGAGAAAATATTTAAGGCC
*
745811 TTGAGAAAATATTTAAGGCC
1 CTGAGAAAATATTTAAGGCC
745831 CTG
1 CTG
745834 CAAAAATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (20 bp):
CTGAGAAAATATTTAAGGCC
Found at i:746147 original size:25 final size:25
Alignment explanation
Indices: 746109--746161 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
746099 AAGTTTCAAG
* *
746109 GGAATTCTACAATTTGAAAGAGTGT
1 GGAATGCTACAATTCGAAAGAGTGT
*
746134 GGAATGCTATAATTCGAAAGAGTGT
1 GGAATGCTACAATTCGAAAGAGTGT
746159 GGA
1 GGA
746162 TTGTCGAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (25 bp):
GGAATGCTACAATTCGAAAGAGTGT
Found at i:750384 original size:23 final size:23
Alignment explanation
Indices: 750354--750450 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
750344 GAGTCGAGGG
*
750354 TCTATGTGGCACTTCGGTGCAAA
1 TCTATGTGGCACTTCGGTACAAA
*
750377 TCTATGTGGTCA-TTCAG-A-ATAA
1 TCTATGTGG-CACTTCGGTACA-AA
*
750399 T-TATGTGGCACTTCGATACAAA
1 TCTATGTGGCACTTCGGTACAAA
*
750421 -CTTATGTAGCACTTCGGTACAAA
1 TC-TATGTGGCACTTCGGTACAAA
750444 TCTATGT
1 TCTATGT
750451 TTTCATTCGG
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.03
21 11 0.18
22 6 0.10
23 38 0.63
24 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (23 bp):
TCTATGTGGCACTTCGGTACAAA
Found at i:753327 original size:160 final size:162
Alignment explanation
Indices: 753051--753373 Score: 623
Period size: 160 Copynumber: 2.0 Consensus size: 162
753041 TAAAGGATTT
753051 ATCAGACCCAGTGTGTCACCTTGGGGTGCTCCAATTTTATTTGTAAAGAAGAAAGACGGCTTGAT
1 ATCAGACCCAG-GTGTCACCTTGGGGTGCTCCAATTTTATTTGTAAAGAAGAAAGACGGCTTGAT
753116 GCGCCTTTGTATTGATTATCGACAACTTAACAACGTGACCATAAAGAACAAGTATCCTCTTCCAA
65 GCGCCTTTGTATTGATTATCGACAACTTAACAACGTGACCATAAAGAACAAGTATCCTCTTCCAA
753181 GGATTGATGACTTA-TTGATCAACTCAAAGGAG
130 GGATTGATGACTTATTTGATCAACTCAAAGGAG
753213 ATCAGACCCA-GTGTCACCTTGGGGTGCTCCAATTTTATTTGTAAAGAAGAAAGACGGCTTGATG
1 ATCAGACCCAGGTGTCACCTTGGGGTGCTCCAATTTTATTTGTAAAGAAGAAAGACGGCTTGATG
753277 CGCCTTTGTATTGATTATCGACAACTTAACAACGTGACCATAAAGAACAAGTATCCTCTTCCAAG
66 CGCCTTTGTATTGATTATCGACAACTTAACAACGTGACCATAAAGAACAAGTATCCTCTTCCAAG
753342 GATTGATGACTTATTTGATCAACTCAAAGGAG
131 GATTGATGACTTATTTGATCAACTCAAAGGAG
753374 CTGATGTGTT
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 132 0.82
161 18 0.11
162 10 0.06
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (162 bp):
ATCAGACCCAGGTGTCACCTTGGGGTGCTCCAATTTTATTTGTAAAGAAGAAAGACGGCTTGATG
CGCCTTTGTATTGATTATCGACAACTTAACAACGTGACCATAAAGAACAAGTATCCTCTTCCAAG
GATTGATGACTTATTTGATCAACTCAAAGGAG
Found at i:756653 original size:20 final size:21
Alignment explanation
Indices: 756598--756654 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
756588 TGAATTTGAA
756598 GAGT-AGTATCGATACTGGTT
1 GAGTAAGTATCGATACTGGTT
*
756618 GAGTAAGGTATTGATACTGAGTT
1 GAGTAA-GTATCGATACTG-GTT
*
756641 G-G-GAGTATCGATAC
1 GAGTAAGTATCGATAC
756655 CAAGGGTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 12 0.39
23 4 0.13
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.32
Consensus pattern (21 bp):
GAGTAAGTATCGATACTGGTT
Found at i:760180 original size:34 final size:36
Alignment explanation
Indices: 760112--760180 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
760102 AAAAATAAAT
*
760112 CAAAATAAATGGAAAATGATAAACGACGGGATGGAC
1 CAAAATAAATCGAAAATGATAAACGACGGGATGGAC
*
760148 CAAAATAAATCTAAAATG-TAAAC-ACGGGATGGA
1 CAAAATAAATCGAAAATGATAAACGACGGGATGGA
760181 ATCAAACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 10 0.32
35 5 0.16
36 16 0.52
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.16
Consensus pattern (36 bp):
CAAAATAAATCGAAAATGATAAACGACGGGATGGAC
Found at i:762782 original size:5 final size:5
Alignment explanation
Indices: 762772--762804 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
762762 CACTAACCTT
762772 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
762805 TATATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:762797 original size:9 final size:9
Alignment explanation
Indices: 762773--762803 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
762763 ACTAACCTTT
762773 TTTATTTTA
1 TTTATTTTA
762782 TTTTATTTTA
1 -TTTATTTTA
762792 TTTATTTTA
1 TTTATTTTA
762801 TTT
1 TTT
762804 TTATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:762797 original size:14 final size:15
Alignment explanation
Indices: 762772--762804 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
762762 CACTAACCTT
762772 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
762787 TTTTA-TTTATTTTA
1 TTTTATTTTATTTTA
762801 TTTT
1 TTTT
762805 TATATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:762805 original size:15 final size:15
Alignment explanation
Indices: 762771--762813 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
762761 CCACTAACCT
762771 TTTTTATTTTATTTTA
1 TTTTTA-TTTATTTTA
762787 -TTTTATTTATTTTA
1 TTTTTATTTATTTTA
*
762801 TTTTTATATATTT
1 TTTTTATTTATTT
762814 GTTTGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:762812 original size:19 final size:19
Alignment explanation
Indices: 762773--762813 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
762763 ACTAACCTTT
*
762773 TTTATTTTATTTTATTTTA
1 TTTATTTTATTTTATTATA
762792 TTTATTTTATTTT-TATATA
1 TTTATTTTATTTTAT-TATA
762811 TTT
1 TTT
762814 GTTTGAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTTATTTTATTATA
Found at i:763068 original size:75 final size:74
Alignment explanation
Indices: 762910--763074 Score: 242
Period size: 75 Copynumber: 2.2 Consensus size: 74
762900 GCTAACTTTT
* * *
762910 CTAACTTACTAGCATTTTAACTTTTTATTTTATTGTTCATATTAACATTAACTTCTTTATTTTTA
1 CTAACTTACTAACATTCTAACTTTTTATTTTATTGTTCATACTAACATTAACTTCTTTATTTTTA
*
762975 TCGTTCTTA
66 TCGTCCTTA
* *
762984 CTAACTTACTAACATTCTAAC-TTTTATTTTATTGTTCATACTAACATAATGACTTTTTTATTTT
1 CTAACTTACTAACATTCTAACTTTTTATTTTATTGTTCATACTAACAT--TAACTTCTTTATTTT
*
763048 TATTGTCCTTA
64 TATCGTCCTTA
763059 CTAACTTACTAACATT
1 CTAACTTACTAACATT
763075 TTATTTTTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
73 25 0.30
74 19 0.23
75 38 0.46
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.52
Consensus pattern (74 bp):
CTAACTTACTAACATTCTAACTTTTTATTTTATTGTTCATACTAACATTAACTTCTTTATTTTTA
TCGTCCTTA
Found at i:763077 original size:34 final size:33
Alignment explanation
Indices: 762988--763086 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 33
762978 TTCTTACTAA
*
762988 CTTACTAACATT-CTAACTTTTA-TTTTATTGTT
1 CTTACTAAC-TTACTAACTTTTATTTTTATTGTC
* * * *
763020 CATACTAACATAATGACTTTTTTATTTTTATTGTC
1 CTTACTAACTTACTAAC--TTTTATTTTTATTGTC
763055 CTTACTAACTTACTAACATTTTATTTTTATTG
1 CTTACTAACTTACTAAC-TTTTATTTTTATTG
763087 CACAAACTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 11 0.21
34 19 0.36
35 22 0.42
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (33 bp):
CTTACTAACTTACTAACTTTTATTTTTATTGTC
Found at i:763858 original size:5 final size:5
Alignment explanation
Indices: 763844--763884 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
763834 TTTCACCTCG
*
763844 TTTTA TTTTTA TTTTG TTTTA TTTTA TTTTA TTTTCA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT
763885 TATCTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:772573 original size:220 final size:220
Alignment explanation
Indices: 772072--773000 Score: 1022
Period size: 220 Copynumber: 4.2 Consensus size: 220
772062 AAATCTATTA
* * * * * *
772072 TCTCTAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTTAACTCCGGCAAAGAATTTACCT
1 TCTCCAGATTGACTCGATTTCCTCAACAAGAAGGAACAACGTCATCTCCAGCAAACAATTTACCT
* * *
772137 AAAAATGACCAGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAACATCAAATTATCACCAAT
66 AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCTCCAA-
* * * *
772202 ATTGACCCGATCTCCT-AATTGCTAAGGAGCAGTGTCATCCTCAGACAATTAGATTTCCTCAATG
130 ATTGACCCGATCTCCTCAA-CGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATTTCCTCAACG
** * * * *
772266 TTAAGGAACCATGTTATCTCTAAATTA
194 CGAAGAAACCGTGTTGTCTCTAAATTT
* * * *
772293 TCTCCTGATTGACTCGATTTCCTCAACGAGAAGTAACAACGTCATCTCCAGCAGACAATTTACCT
1 TCTCCAGATTGACTCGATTTCCTCAACAAGAAGGAACAACGTCATCTCCAGCAAACAATTTACCT
* *
772358 AAAAATGACAAGATCTCTTCAACACGGATGAGCAGTTTCATCTTCAACATCAAATTATCTCCAAA
66 AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCTCCAAA
** * * *
772423 TTGACCTTATCTCCTCAACGCAAAGGAGCAGTGTCATCCTTAGAAAATCAGATTTCCTCAACACG
131 TTGACCCGATCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATTTCCTCAACGCG
*
772488 AAGAAACCGTGTTGTCTCCAAATTT
196 AAGAAACCGTGTTGTCTCTAAATTT
* ** *
772513 TCTCCAGATTGAC-CTGATTTCATCAACAAGAAGGAACGTCGTTATCTCCAGCAAACAATTTACC
1 TCTCCAGATTGACTC-GATTTCCTCAACAAGAAGGAACAACGTCATCTCCAGCAAACAATTTACC
* *
772577 TGAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTTAACATCAAATTATCTCCAG
65 TAAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCTCCA-
* * * *
772642 AA-TGACCCGATCTCCTCAATGCAAATGAGCAGTGTCATCCTCAGACAATCAGATCTCCTTAACG
129 AATTGACCCGATCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATTTCCTCAACG
* *
772706 CGAAGAAACTGTGTTGTCTTTAAA-TT
194 CGAAGAAACCGTGTTGTCTCTAAATTT
* * * ** * *
772732 ACATCTAGATTGACTCGATTTCCTCAACGAGAAAAAACAGCATCATCTCCAGCAAACAATTTACC
1 TC-TCCAGATTGACTCGATTTCCTCAACAAGAAGGAACAACGTCATCTCCAGCAAACAATTTACC
* * * * * * * * *
772797 TGAAAACGACCAGATCTTTTCAACACGGATGAGTAGTGTCGTCTTCAACACCAAGTTTTTTTCCA
65 TAAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAA-ATTATCTCCA
* ** * * * * * **
772862 ATTTGACTGGATCTCCTTAACGCGAAGGAGCAGTGTCATCCTCAGACGATCAGACTTCTTCAATA
129 AATTGACCCGATCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATTTCCTCAACG
* * *** * * *
772927 TGAAGGAACCACATTATCTCCAAAGTAT
194 CGAAGAAACCGTGTTGTCTCTAAA-TTT
* * * * *
772955 T-TCCATATTGACCCAATTTCCTCAACAAGAATGAACAATGTCATCT
1 TCTCCAGATTGACTCGATTTCCTCAACAAGAAGGAACAACGTCATCT
773001 TCAACAAATG
Statistics
Matches: 590, Mismatches: 109, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
219 4 0.01
220 360 0.61
221 225 0.38
223 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (220 bp):
TCTCCAGATTGACTCGATTTCCTCAACAAGAAGGAACAACGTCATCTCCAGCAAACAATTTACCT
AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCTCCAAA
TTGACCCGATCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATTTCCTCAACGCG
AAGAAACCGTGTTGTCTCTAAATTT
Found at i:772950 original size:441 final size:442
Alignment explanation
Indices: 772072--772992 Score: 1174
Period size: 441 Copynumber: 2.1 Consensus size: 442
772062 AAATCTATTA
* * *
772072 TCTCTAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTTAACTCCGGCAAAGAATTTACCT
1 TCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTTAACTCCAGCAAACAATTTACCT
* *
772137 AAAAATGACCAGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAACATCAAATTATCACCAAT
66 AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCACCAAT
* * * * *
772202 ATTGACCCGATCTCCTAATTGCTAAGGAGCAGTGTCATCCTCAGACAATTAGATTTCCTCAATGT
131 ATTGACCCGATCTCCTAATTGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATCTCCTCAACGC
* * **
772267 TAAGGAACCATGTTATCTCTAAATTATCTCCTGATTGACTCGATTTCCTCAACGAGAAGTAACAA
196 GAAGAAACCATGTTATCTCTAAATTATCTCCTGATTGACTCGATTTCCTCAACGAGAAAAAACAA
* * * *
772332 CGTCATCTCCAGCAGACAATTTACCTAAAAATGACAAGATCTCTTCAACACGGATGAGCAGTTTC
261 CATCATCTCCAGCAAACAATTTACCTAAAAACGACAAGATCTCTTCAACACGGATGAGCAGTGTC
* *
772397 ATCTTCAACATCAAATTATCTCCAAATTGACCTTATCTCCTCAACGCAAAGGAGCAGTGTCATCC
326 ATCTTCAACACCAAATTATCTCCAAATTGACCTGATCTCCTCAACGCAAAGGAGCAGTGTCATCC
* * *** * *
772462 TTAGAAAATCAGATTTCCTCAACACGAAGAAACCGTGTTGTCTCCAAA-TTT
391 TCAGAAAATCAGACTTCCTCAACACGAAGAAACCACATTATCTCCAAAGTAT
* * ** *
772513 TCTCCAGATTGACCTGATTTCATCAACAAGAAGGAACGTCGTTATCTCCAGCAAACAATTTACCT
1 TCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTTAACTCCAGCAAACAATTTACCT
* * *
772578 GAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTTAACATCAAATTATCTCCAGA
66 AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCACCA-A
* *
772643 -A-TGACCCGATCTCCTCAA-TGCAAATGAGCAGTGTCATCCTCAGACAATCAGATCTCCTTAAC
130 TATTGACCCGATCTCCT-AATTGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATCTCCTCAAC
** * *
772705 GCGAAGAAACTGTGTTGTCTTTAAATTA-CAT-CTAGATTGACTCGATTTCCTCAACGAGAAAAA
194 GCGAAGAAACCATGTTATCTCTAAATTATC-TCCT-GATTGACTCGATTTCCTCAACGAGAAAAA
* * * * *
772768 ACAGCATCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCTTTTCAACACGGATGAGTAG
257 ACAACATCATCTCCAGCAAACAATTTACCTAAAAACGACAAGATCTCTTCAACACGGATGAGCAG
* * * * * * *
772833 TGTCGTCTTCAACACCAAGTTTTTTTCCAATTTGA-CTGGATCTCCTTAACGCGAAGGAGCAGTG
322 TGTCATCTTCAACACCAA-ATTATCTCCAAATTGACCT-GATCTCCTCAACGCAAAGGAGCAGTG
** * * * *
772897 TCATCCTCAGACGATCAGACTTCTTCAATATGAAGGAACCACATTATCTCCAAAGTAT
385 TCATCCTCAGAAAATCAGACTTCCTCAACACGAAGAAACCACATTATCTCCAAAGTAT
* * *
772955 T-TCCATATTGACCCAATTTCCTCAACAAGAATGAACAA
1 TCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAA
772993 TGTCATCTTC
Statistics
Matches: 407, Mismatches: 66, Indels: 14
0.84 0.14 0.03
Matches are distributed among these distances:
439 3 0.01
440 175 0.43
441 225 0.55
442 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (442 bp):
TCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTTAACTCCAGCAAACAATTTACCT
AAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACATCAAATTATCACCAAT
ATTGACCCGATCTCCTAATTGCAAAGGAGCAGTGTCATCCTCAGACAATCAGATCTCCTCAACGC
GAAGAAACCATGTTATCTCTAAATTATCTCCTGATTGACTCGATTTCCTCAACGAGAAAAAACAA
CATCATCTCCAGCAAACAATTTACCTAAAAACGACAAGATCTCTTCAACACGGATGAGCAGTGTC
ATCTTCAACACCAAATTATCTCCAAATTGACCTGATCTCCTCAACGCAAAGGAGCAGTGTCATCC
TCAGAAAATCAGACTTCCTCAACACGAAGAAACCACATTATCTCCAAAGTAT
Found at i:775421 original size:5 final size:5
Alignment explanation
Indices: 775408--775449 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
775398 TATTTTCACC
*
775408 TATTT TCATTT CATTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT T-ATTT TATTT TATTT TATTT TATTT TATTT TATTT T
775450 TGTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:780042 original size:19 final size:19
Alignment explanation
Indices: 780028--780067 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
780018 CCAAAAAACA
780028 AAGAAAAAAAGAAAAAAAG
1 AAGAAAAAAAGAAAAAAAG
* *
780047 AAGAAAGAGAGAAAAATAAG
1 AAGAAAAAAAGAAAAA-AAG
780067 A
1 A
780068 CAACAAGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAAG
Found at i:780621 original size:21 final size:20
Alignment explanation
Indices: 780535--780692 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
780525 AAATGACCAA
**
780535 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
780554 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
780574 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
780594 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
780615 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
780636 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
780656 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
780677 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
780693 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:780721 original size:20 final size:20
Alignment explanation
Indices: 780660--780888 Score: 203
Period size: 20 Copynumber: 11.4 Consensus size: 20
780650 GATTTTCAAG
* ** *
780660 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
780680 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
780700 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
780720 AACCGCAACATGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
780740 AATAGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
780760 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
780780 TATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
780800 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
780820 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
780840 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
780860 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
780880 AATCACAAC
1 AATCGCAAC
780889 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.02
20 168 0.97
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:781778 original size:12 final size:12
Alignment explanation
Indices: 781761--781785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
781751 ATATAATCCT
781761 GAAGAAGAAAAA
1 GAAGAAGAAAAA
781773 GAAGAAGAAAAA
1 GAAGAAGAAAAA
781785 G
1 G
781786 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:783157 original size:21 final size:21
Alignment explanation
Indices: 783099--783162 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 21
783089 TCTTTTGGTT
783099 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
783120 G-AATGACTGTCGC-ACGAGA
1 GAAATGAAAATCGCAACGAGA
783139 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
783160 GAA
1 GAA
783163 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 7 0.20
20 18 0.51
21 10 0.29
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:783159 original size:19 final size:19
Alignment explanation
Indices: 783099--783206 Score: 102
Period size: 19 Copynumber: 5.8 Consensus size: 19
783089 TCTTTTGGTT
783099 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
***
783118 GAGAATGACTGTCGC-ACGAGA
1 GA-AATGAAAATCGCAAC--GA
783139 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
783158 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
783172 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
783191 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
783207 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 34 0.47
20 18 0.25
21 6 0.08
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:783242 original size:14 final size:14
Alignment explanation
Indices: 783223--783279 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
783213 TTTGGTTTCG
783223 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
783237 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
783256 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
783270 CGTTGCGATT
1 CGTTGCGATT
783280 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:783255 original size:33 final size:33
Alignment explanation
Indices: 783207--783286 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
783197 AAAATCGCAA
**
783207 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
783240 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
783273 TGCGATTTTCATTT
1 TGCGATTTTCATTT
783287 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:783292 original size:21 final size:21
Alignment explanation
Indices: 783267--783340 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
783257 GTTGCGATTC
783267 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
783288 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
783309 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
783330 TCTCGTTGCGA
1 TCTCGTTGCGA
783341 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:783462 original size:33 final size:33
Alignment explanation
Indices: 783420--783490 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
783410 AATACTAACT
783420 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
783453 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
783486 TGAAA
1 TGAAA
783491 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:783895 original size:20 final size:20
Alignment explanation
Indices: 783870--784042 Score: 197
Period size: 20 Copynumber: 8.6 Consensus size: 20
783860 CTTTAAAAAT
783870 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
783890 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
783910 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
783931 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
783951 TGTATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
783971 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
783991 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
784011 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
784031 CGCGTTGCGATT
1 CGCGTTGCGATT
784043 CTGGAAAATC
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
20 112 0.86
21 18 0.14
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:787633 original size:139 final size:137
Alignment explanation
Indices: 787298--787740 Score: 502
Period size: 139 Copynumber: 3.2 Consensus size: 137
787288 TATGACTAGC
* * * * *
787298 TCTCCTCAAAGTGTAGGAGCAAC-GTCATTCTTAGGCAATCAGACTTCCTCATCATGTAGGAATC
1 TCTCCTCAACGCGTAGGAGC-ACTGTCATCCTTAGGCAATCAGACTTCCTCATCACGTAGGAACC
* * * *
787362 GTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGGCATCCTCATCACGTAAGAACAATGTCATCC
65 GTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTCATCACGTAAGAAAAATGTCGTCC
787427 AC--CAAA
130 ACGACAAA
* * * *
787433 -CTCTTCAACGTGTAGGAGCA-TCGTCATCCTCAAGCAATCAGACTTCCTCATCACGTAGGAACC
1 TCTCCTCAACGCGTAGGAGCACT-GTCATCCTTAGGCAATCAGACTTCCTCATCACGTAGGAACC
* * ** * * *
787496 GTGTTGTCTCTAAATTATCCCTAAAGACGGTTAGACTTTTTTATCACATAAGAATAATGTCGTCC
65 GTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTCATCACGTAAGAAAAATGTCGTCC
787561 ATCGACTAAA
130 A-CGAC-AAA
* * * *
787571 TCTCCTCAACACGTAGGAGCACTGTAATCCTTAGGCAATCAGACTACCTCATCACGTAGGAACCT
1 TCTCCTCAACGCGTAGGAGCACTGTCATCCTTAGGCAATCAGACTTCCTCATCACGTAGGAACCG
* * * *
787636 TGTTGTCTCCAAATTATCCCTAGAGAGGGCTAGA-TGTCCTCATCACGTAGGAAAAATGTTGTCC
66 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACT-TCCTCATCACGTAAGAAAAATGTCGTCC
*
787700 ACCGACCATA
130 A-CGA-CAAA
* *
787710 TCTCCTCAACGCGTAGGAGCAATATCATCCT
1 TCTCCTCAACGCGTAGGAGCACTGTCATCCT
787741 CAAACAACCA
Statistics
Matches: 256, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
133 1 0.00
134 109 0.43
135 1 0.00
137 1 0.00
138 4 0.02
139 138 0.54
140 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (137 bp):
TCTCCTCAACGCGTAGGAGCACTGTCATCCTTAGGCAATCAGACTTCCTCATCACGTAGGAACCG
TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTCATCACGTAAGAAAAATGTCGTCCA
CGACAAA
Found at i:787892 original size:83 final size:83
Alignment explanation
Indices: 787826--788046 Score: 300
Period size: 83 Copynumber: 2.7 Consensus size: 83
787816 TCATTCTCCA
* * * * *
787826 ACCATATCTCCTCAATGCGTAGGAGCAGCGTCATCCTTAAACAACCAGACTTTCTTC-AAACGAA
1 ACCAGATCTCCTCAATGCGAAGGAGTAGTGTCATCCTTAAACAACCAGAC-TTCCTCGAAACGAA
787890 GGAACAATGTCATCCACCG
65 GGAACAATGTCATCCACCG
* * * *
787909 ACCAGATCTCCTCAACGCGAAGGAGTAGTGTCATCCTTAGACAACCGGACTTCCTCGACACGAAG
1 ACCAGATCTCCTCAATGCGAAGGAGTAGTGTCATCCTTAAACAACCAGACTTCCTCGAAACGAAG
*
787974 GAACAATGTCGTCCACCG
66 GAACAATGTCATCCACCG
* * * *
787992 ACCAGATCTCCTCAATGGGAAGGAGTAGTGTCATCCTTAGATAATCAGACTTCCT
1 ACCAGATCTCCTCAATGCGAAGGAGTAGTGTCATCCTTAAACAACCAGACTTCCT
788047 TAATGCTAGG
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
82 5 0.04
83 117 0.96
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (83 bp):
ACCAGATCTCCTCAATGCGAAGGAGTAGTGTCATCCTTAAACAACCAGACTTCCTCGAAACGAAG
GAACAATGTCATCCACCG
Found at i:787930 original size:40 final size:40
Alignment explanation
Indices: 787886--788015 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
787876 TTTCTTCAAA
787886 CGAAGGAACAATGTCATCCACCGACCAGATCTCCTCAACG
1 CGAAGGAACAATGTCATCCACCGACCAGATCTCCTCAACG
** * * * * * *
787926 CGAAGGAGTAGTGTCATCCTTAGACAACCGGA-CTTCCTCGACA
1 CGAAGGAACAATGTCATCC--A-CCGACCAGATC-TCCTCAACG
* *
787969 CGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAATG
1 CGAAGGAACAATGTCATCCACCGACCAGATCTCCTCAACG
*
788009 GGAAGGA
1 CGAAGGA
788016 GTAGTGTCAT
Statistics
Matches: 66, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
40 34 0.52
41 2 0.03
42 2 0.03
43 28 0.42
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (40 bp):
CGAAGGAACAATGTCATCCACCGACCAGATCTCCTCAACG
Found at i:789373 original size:19 final size:18
Alignment explanation
Indices: 789346--789385 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
789336 AACTTGTTTC
789346 TTTTCTCTTTGCTCTTTGT
1 TTTTCTCTTTGCTCTTT-T
*
789365 TTTTTTCTTTGCTCTTTT
1 TTTTCTCTTTGCTCTTTT
789383 TTT
1 TTT
789386 CTTTGCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.75
Consensus pattern (18 bp):
TTTTCTCTTTGCTCTTTT
Found at i:789384 original size:15 final size:14
Alignment explanation
Indices: 789364--789409 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 14
789354 TTGCTCTTTG
789364 TTTTTTTCTTTGCT
1 TTTTTTTCTTTGCT
789378 CTTTTTTTCTTTGCT
1 -TTTTTTTCTTTGCT
789393 TTTTTTCTCTTTG-T
1 TTTTTT-TCTTTGCT
789407 TTT
1 TTT
789410 GATTGAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTTGCT
Found at i:793391 original size:12 final size:12
Alignment explanation
Indices: 793374--793419 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
793364 TAAATTTAAT
*
793374 TAATAACAATAC
1 TAATAATAATAC
*
793386 TAATAATAATAG
1 TAATAATAATAC
793398 TAATAATAATA-
1 TAATAATAATAC
793409 TAAATAATAAT
1 T-AATAATAAT
793420 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 1 0.03
12 30 0.97
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:795277 original size:3 final size:3
Alignment explanation
Indices: 795269--795307 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
795259 AGACTCGTTT
795269 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
795308 ACGTTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:799306 original size:44 final size:43
Alignment explanation
Indices: 799208--799324 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 43
799198 TGGAATATTA
*
799208 GGGTATTTTTTGAAGGCTTGTATCATCCAAAAATAATAAATGTTG
1 GGGTATTTTTTGAAGGC--ATATCATCCAAAAATAATAAATGTTG
* * *
799253 GGG-AATTTTTGAAGGCATATCA-GCAAGAAATGATAAATGTTG
1 GGGTATTTTTTGAAGGCATATCATCCAA-AAATAATAAATGTTG
799295 GGGTATTTTTTTGAAGGTTCATATCATCCA
1 GGGTA-TTTTTTGAAGG--CATATCATCCA
799325 GGAATACAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
41 3 0.05
42 22 0.37
43 1 0.02
44 22 0.37
45 3 0.05
46 7 0.12
47 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36
Consensus pattern (43 bp):
GGGTATTTTTTGAAGGCATATCATCCAAAAATAATAAATGTTG
Found at i:803019 original size:21 final size:20
Alignment explanation
Indices: 802980--803020 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
802970 TACAACGTAT
802980 AAAACATATATCATAATATA
1 AAAACATATATCATAATATA
803000 AAAACATCATAT-ATATATATA
1 AAAACAT-ATATCATA-ATATA
803021 TAACAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAACATATATCATAATATA
Found at i:812143 original size:3 final size:3
Alignment explanation
Indices: 812135--812166 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
812125 TTTGTTTTAT
812135 TTA TTA TTA TTA TT- TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
812167 ATTTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:812154 original size:11 final size:11
Alignment explanation
Indices: 812138--812174 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
812128 GTTTTATTTA
812138 TTATTATTATT
1 TTATTATTATT
812149 TTATTATTATT
1 TTATTATTATT
*
812160 ATATTA-TA-T
1 TTATTATTATT
812169 TTATTA
1 TTATTA
812175 AATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 16 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTATTATT
Found at i:812172 original size:14 final size:15
Alignment explanation
Indices: 812132--812174 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 15
812122 TCATTTGTTT
812132 TATTTATTATTATTA
1 TATTTATTATTATTA
812147 T-TTTATTATTATTA
1 TATTTATTATTATTA
812161 TATTATATTTATTA
1 TATT-TA-TTATTA
812175 AATAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 2 0.08
17 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATTATTATTA
Found at i:812252 original size:14 final size:15
Alignment explanation
Indices: 812227--812260 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
812217 GGCCCGATTA
812227 CAAACTAGACTGGCC
1 CAAACTAGACTGGCC
812242 CAAAC-AGACTGGCC
1 CAAACTAGACTGGCC
812256 CAAAC
1 CAAAC
812261 CTAATAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.38, C:0.35, G:0.18, T:0.09
Consensus pattern (15 bp):
CAAACTAGACTGGCC
Found at i:813587 original size:15 final size:15
Alignment explanation
Indices: 813567--813637 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
813557 ATCCTATAGT
813567 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
813582 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
813596 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
813612 TTTTATTTTATTATTAC
1 TTTTA--ATATTATTAC
*
813629 TTTTGATAT
1 TTTTAATAT
813638 ATGTTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:813677 original size:11 final size:11
Alignment explanation
Indices: 813602--813677 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
813592 TTTCATTTTA
813602 ATTATTATTATT
1 ATTATT-TTATT
813614 -TTATTTTATT
1 ATTATTTTATT
813624 ATTACTTTTGA-T
1 ATTA-TTTT-ATT
813636 A-TATGTTTAAATT
1 ATTAT-TTT--ATT
* *
813649 ATTATCTTCATG
1 ATTAT-TTTATT
813661 ATTATTTTATT
1 ATTATTTTATT
813672 ATTATT
1 ATTATT
813678 ATTAAGTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.12
11 23 0.45
12 14 0.27
13 3 0.06
14 5 0.10
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:813908 original size:17 final size:16
Alignment explanation
Indices: 813888--813928 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
813878 ATAAATATCC
813888 TATTTTTATATATATAT
1 TATTTTTATATATA-AT
*
813905 TA-TTTTAT-TTTAAT
1 TATTTTTATATATAAT
813919 TATTTTTATA
1 TATTTTTATA
813929 GAAATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 6 0.29
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATATATAAT
Found at i:814054 original size:2 final size:2
Alignment explanation
Indices: 814047--814078 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
814037 ATAAAAATAA
814047 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814079 TTTCTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:819577 original size:7 final size:7
Alignment explanation
Indices: 819565--819681 Score: 60
Period size: 7 Copynumber: 15.4 Consensus size: 7
819555 TCCAGCAAAG
819565 AAAGAAA
1 AAAGAAA
819572 AAAGAAA
1 AAAGAAA
819579 AATCCAGCAAA
1 AA---AG-AAA
819590 GAAAGAAAA
1 -AAAG-AAA
819599 AAAGAAAA
1 AAAG-AAA
819607 AAGAGGAAA
1 AA-A-GAAA
819616 AAAGAAA
1 AAAGAAA
*
819623 AAA-AAG
1 AAAGAAA
819629 AAA-AAA
1 AAAGAAA
*
819635 AAAGGAA
1 AAAGAAA
**
819642 AGGGATAA
1 AAAGA-AA
*
819650 AAATAAA
1 AAAGAAA
819657 AAA-ACAA
1 AAAGA-AA
819664 AAAGGAAA
1 AAA-GAAA
819672 AAAGAAA
1 AAAGAAA
819679 AAA
1 AAA
819682 TTGAATCAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
6 11 0.12
7 37 0.42
8 20 0.23
9 12 0.14
10 3 0.03
11 3 0.03
12 2 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:819584 original size:26 final size:27
Alignment explanation
Indices: 819554--819633 Score: 103
Period size: 26 Copynumber: 3.0 Consensus size: 27
819544 TATTATACTC
819554 ATCCAGCAAAGAAAG-AAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
819580 ATCCAGCAAAGAAAGAAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
** *
819607 A-AGAGGAAA-AAAGAAAAAAAAGAAAA
1 ATCCAGCAAAGAAAG-AAAAAAAGAAAA
819633 A
1 A
819634 AAAAGGAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 4 0.08
26 33 0.67
27 12 0.24
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.03
Consensus pattern (27 bp):
ATCCAGCAAAGAAAGAAAAAAAGAAAA
Found at i:819604 original size:8 final size:8
Alignment explanation
Indices: 819591--819635 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
819581 TCCAGCAAAG
819591 AAAGAAAA
1 AAAGAAAA
819599 AAAGAAAA
1 AAAGAAAA
*
819607 AAGAGGAAA
1 AA-AGAAAA
819616 AAAGAAAAA
1 AAAG-AAAA
819625 AAAGAAAA
1 AAAGAAAA
819633 AAA
1 AAA
819636 AAGGAAAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:819609 original size:19 final size:19
Alignment explanation
Indices: 819587--819642 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
819577 AAAATCCAGC
819587 AAAGAAAGAAAAAAAGAAA
1 AAAGAAAGAAAAAAAGAAA
* *
819606 AAAG-AGGAAAAAAGAAAAA
1 AAAGAAAGAAAAAA-AGAAA
*
819625 AAAGAAA-AAAAAAGGAAA
1 AAAGAAAGAAAAAAAGAAA
819643 GGGATAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 11 0.37
19 18 0.60
20 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAAAAAGAAA
Found at i:819629 original size:34 final size:34
Alignment explanation
Indices: 819591--819676 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
819581 TCCAGCAAAG
819591 AAAGAAAAAAAGAAAAAAGAGGA-AAAAAGAAAAA
1 AAAGAAAAAAAGAAAAAAGAGGATAAAAA-AAAAA
* *
819625 AAAGAAAAAAA-AAGGAAAG-GGATAAAAATAAAA
1 AAAGAAAAAAAGAA-AAAAGAGGATAAAAAAAAAA
* *
819658 AAA-CAAAAAGGAAAAAAGA
1 AAAGAAAAAAAGAAAAAAGA
819677 AAAAATTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
32 9 0.21
33 14 0.33
34 20 0.47
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.02
Consensus pattern (34 bp):
AAAGAAAAAAAGAAAAAAGAGGATAAAAAAAAAA
Found at i:822378 original size:31 final size:32
Alignment explanation
Indices: 822326--822386 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
822316 GCACATATAA
*
822326 AATCTGTCAAACTCTGTAATTGATGAATTCAG
1 AATCTGTCAAACTCTGCAATTGATGAATTCAG
822358 AATCTGTC-AACTCTGCAATTGATGAATTC
1 AATCTGTCAAACTCTGCAATTGATGAATTC
822387 GGACCACATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
AATCTGTCAAACTCTGCAATTGATGAATTCAG
Found at i:823366 original size:112 final size:113
Alignment explanation
Indices: 823213--823747 Score: 853
Period size: 112 Copynumber: 4.8 Consensus size: 113
823203 TTTTTCTTAA
* *
823213 AACATTTCAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
823278 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
* * * *
823326 AACATTTCCA-GAAGAGTTAATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATATT
1 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
823390 GAGAAGAACTTATTCAACCTTTCGCTTGAATTCATCATTCGATGAATC
66 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
* * *
823438 AGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCGTCTGAA-AAAGAAGAAGAAGTTCATAAT
1 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
823502 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
66 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
* *
823550 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCGTCTGAA-AAAGAAGAAGAAGTTCATAAT
1 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
823614 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
* *
823662 AGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAAT
1 AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
823726 AAGAAGAATTTGTTCAACTTTT
66 GAGAAGAACTTGTTCAACTTTT
823748 ATGATTCTAT
Statistics
Matches: 393, Mismatches: 27, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
112 355 0.90
113 38 0.10
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGAATC
Found at i:823516 original size:20 final size:19
Alignment explanation
Indices: 823454--823517 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
823444 ACCAGGTAGA
823454 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
823473 CGTCTGAAAAAGAAGAAGAA--
1 -GT-TCATAATG-AGAAGAACT
823493 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
823513 GTTCA
1 GTTCA
823518 ACTTTTTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 2 0.06
20 7 0.21
21 5 0.15
22 7 0.21
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:823628 original size:20 final size:19
Alignment explanation
Indices: 823566--823629 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
823556 ACCAGGTAGA
823566 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
823585 CGTCTGAAAAAGAAGAAGAA--
1 -GT-TCATAATG-AGAAGAACT
823605 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
823625 GTTCA
1 GTTCA
823630 ACTTTTTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 2 0.06
20 7 0.21
21 5 0.15
22 7 0.21
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:823857 original size:68 final size:69
Alignment explanation
Indices: 823761--823894 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 69
823751 ATTCTATCAC
* * *
823761 AGAAGGAGATAGATCAACATCAACATTTCCAGAAG-TGTTCATAATGAGAAGAACTCATCTGAAG
1 AGAAGAAGATAGATCAACATCAACATTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
823825 ATGA
66 ATGA
* * **
823829 AGAAGAAGATCGATCAATATCAGTATTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AGAAGAAGATAGATCAACATCAACATTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
823894 A
66 A
823895 AGGAGATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 30 0.52
69 28 0.48
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (69 bp):
AGAAGAAGATAGATCAACATCAACATTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
ATGA
Found at i:824125 original size:14 final size:14
Alignment explanation
Indices: 824108--824143 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
824098 ATTTGTTTTA
824108 TTTATTATTATTAT
1 TTTATTATTATTAT
*
824122 TTTAATATTATTAT
1 TTTATTATTATTAT
*
824136 TATATTAT
1 TTTATTAT
824144 ATTTATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:824132 original size:17 final size:16
Alignment explanation
Indices: 824106--824151 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
824096 TCATTTGTTT
824106 TATT-TATTATTATTA
1 TATTATATTATTATTA
*
824121 TTTTAATATTATTATTA
1 TATT-ATATTATTATTA
824138 TATTATATTTATTA
1 TATTATA-TTATTA
824152 AATAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 3 0.12
16 3 0.12
17 20 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:825603 original size:14 final size:15
Alignment explanation
Indices: 825545--825605 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
825535 ATCCTATAGT
825545 TTTTAA-TATTATTA
1 TTTTAATTATTATTA
825559 CTTTTAATT-TCT-TTCA
1 -TTTTAATTAT-TATT-A
825575 TTTTAATTATTATTA
1 TTTTAATTATTATTA
*
825590 TTTT-ATTTTTATTA
1 TTTTAATTATTATTA
825604 TT
1 TT
825606 ACTTTTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
14 11 0.28
15 23 0.57
16 6 0.15
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAATTATTATTA
Found at i:827861 original size:35 final size:35
Alignment explanation
Indices: 827815--827890 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
827805 AAAACAGTCC
* *
827815 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
827850 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
827885 TCAATT
1 TCAATT
827891 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:828433 original size:130 final size:130
Alignment explanation
Indices: 828287--828534 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
828277 TATTTATATA
* **
828287 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
828352 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCGAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCGAATTATTTATATATGCT
828417 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
828482 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCGAATTA
828535 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCGAATTATTTATATATGCT
Found at i:828565 original size:130 final size:129
Alignment explanation
Indices: 828301--828565 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
828291 ATTTGGTCCT
* ** *
828301 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
828366 TGACACGTGTCATTGGTGACACATGTCACCACCGAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCGAATTAAGAAAATAAGCTATCAAAGAAGT-CA
828431 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
828496 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCGAATT--AAGAAAA-TAAGCTATCAAAGAAGT
828560 -A
128 CA
828561 AAATT
1 AAATT
828566 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCGAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:828891 original size:28 final size:27
Alignment explanation
Indices: 828860--828922 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
828850 AGTTGATACA
*
828860 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
828888 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
828916 ATATTTT
1 ATATTTT
828923 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:829023 original size:16 final size:18
Alignment explanation
Indices: 829002--829035 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
828992 ATTTCTTATT
829002 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
829018 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
829036 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:830978 original size:17 final size:17
Alignment explanation
Indices: 830956--830996 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
830946 GGTAGCATGA
830956 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
830973 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
830990 CCGGTTC
1 CCGGTTC
830997 TGAAAACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.10, C:0.37, G:0.29, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGGT
Found at i:832153 original size:16 final size:16
Alignment explanation
Indices: 832108--832162 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
832098 TATAAATAAT
* * *
832108 CTGACTTGTTATTAAA
1 CTGACTTGATATTTAC
*
832124 CTGATTTGATATTTAC
1 CTGACTTGATATTTAC
832140 CTGACTTGATATTTAC
1 CTGACTTGATATTTAC
*
832156 ATGACTT
1 CTGACTT
832163 ATAAATTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (16 bp):
CTGACTTGATATTTAC
Found at i:833841 original size:17 final size:16
Alignment explanation
Indices: 833805--833845 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
833795 GCTCTTTAAA
* *
833805 AGAATTACATTAAGAG
1 AGAATTATATTAAAAG
833821 AGAATTATATTCAAAAG
1 AGAATTATATT-AAAAG
833838 AGAATTAT
1 AGAATTAT
833846 GATTTGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (16 bp):
AGAATTATATTAAAAG
Found at i:838390 original size:13 final size:13
Alignment explanation
Indices: 838371--838407 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
838361 AACCCGACCC
838371 GACCCGACCCGCTT
1 GACCCGACCCG-TT
838385 -ACCCGACCCGTT
1 GACCCGACCCGTT
838397 GACCCGACCCG
1 GACCCGACCCG
838408 ACCCGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:850377 original size:24 final size:24
Alignment explanation
Indices: 850350--850433 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
850340 TGAATTTTGT
*
850350 TATGATACCTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
850374 TATGATA-TTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
850397 TCTGATACATGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
850421 TATGATACTTGAC
1 TATGATACTTGAC
850434 TTGAATTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:855094 original size:24 final size:24
Alignment explanation
Indices: 855066--855156 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
855056 TCAAATTTGA
* *
855066 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
855090 GTTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
855113 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
855137 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
855157 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:855135 original size:47 final size:48
Alignment explanation
Indices: 855066--855156 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
855056 TCAAATTTGA
* * * *
855066 ATTCTGTTATGATACCTGACCTGGGTTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
855113 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
855157 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:856791 original size:30 final size:31
Alignment explanation
Indices: 856733--856793 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
856723 TAACAATTCA
**
856733 CAACTTTTCCAAAATTAATGATATGGTCCCC
1 CAACTTTTAAAAAATTAATGATATGGTCCCC
856764 CAACTTTTAAAAAATTACAT-A-ATGGTCCCC
1 CAACTTTTAAAAAATTA-ATGATATGGTCCCC
856794 AAAATTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 16 0.59
32 2 0.07
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (31 bp):
CAACTTTTAAAAAATTAATGATATGGTCCCC
Done.