Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 195 of 259
Found at i:62398655 original size:29 final size:27
Alignment explanation
Indices: 62398617--62398674 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 27
62398607 ATGTATATTT
62398617 ATAATTCAATCAATATAAATTCAATCAA
1 ATAATTCAATCAATATAAATTCAAT-AA
62398645 ATAATTTCAATCAATATAAATTCAATAA
1 ATAA-TTCAATCAATATAAATTCAATAA
62398673 AT
1 AT
62398675 TTATCGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAATTCAATCAATATAAATTCAATAA
Found at i:62408791 original size:3 final size:3
Alignment explanation
Indices: 62408783--62408812 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
62408773 GAAACAACGT
62408783 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
62408813 GGGATTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:62410174 original size:16 final size:16
Alignment explanation
Indices: 62410155--62410189 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
62410145 TAAGAAAATA
* *
62410155 ATATTTTATTATTATT
1 ATATTATATTACTATT
62410171 ATATTATATTACTATT
1 ATATTATATTACTATT
62410187 ATA
1 ATA
62410190 ATTAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATATTACTATT
Found at i:62412814 original size:13 final size:13
Alignment explanation
Indices: 62412796--62412827 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
62412786 ATGCACATTC
62412796 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
*
62412809 TCTTTTTTGTTTT
1 TCTTTTTTCTTTT
62412822 TCTTTT
1 TCTTTT
62412828 GTTTGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:62414178 original size:21 final size:21
Alignment explanation
Indices: 62414154--62414229 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
62414144 GCAGGCTACT
62414154 ACGTGTACCGGATAATTGGTC
1 ACGTGTACCGGATAATTGGTC
** *
62414175 ACGTGTATAGTACTAAGTGTAGGCTAC
1 ACGTGTACCGGA-TAA-T-T-GG-T-C
62414202 TACGTGTACCGGATAATTGGTC
1 -ACGTGTACCGGATAATTGGTC
62414224 ACGTGT
1 ACGTGT
62414230 GTAGTATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 3 0.07
25 3 0.07
26 2 0.05
27 4 0.10
28 9 0.21
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
ACGTGTACCGGATAATTGGTC
Found at i:62414189 original size:49 final size:49
Alignment explanation
Indices: 62414124--62414301 Score: 302
Period size: 49 Copynumber: 3.6 Consensus size: 49
62414114 ATGACTTCGA
62414124 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* *
62414173 TCACGTGTATAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* *
62414222 TCACGTGTGTAGTATTAAGTGCAGGCTACTACGTGTACCGAATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* *
62414271 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
62414302 TGCGTACCAG
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 120 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
Found at i:62414309 original size:49 final size:49
Alignment explanation
Indices: 62414088--62414301 Score: 295
Period size: 49 Copynumber: 4.3 Consensus size: 49
62414078 ATATGATCAA
* * * *
62414088 TAAGTGCAGGCTACTATGCGTACTC-AATGACTTCGATCACGTGTGTAGTAC
1 TAAGTGCAGGCTACTACGTGTAC-CGAAT-AATT-GGTCACGTGTGTAGTAC
* *
62414139 TAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTGTATAGTAC
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
* * *
62414188 TAAGTGTAGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTAT
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
* *
62414237 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTAC
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
62414286 TAAGTGCAGGCTACTA
1 TAAGTGCAGGCTACTA
62414302 TGCGTACCAG
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
49 121 0.82
50 4 0.03
51 23 0.16
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
Found at i:62415773 original size:25 final size:26
Alignment explanation
Indices: 62415723--62415772 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
62415713 ATTAACTTAA
*
62415723 TTAGAGTGATTAAAATAAAATAAAAT
1 TTAGAGTGATCAAAATAAAATAAAAT
*
62415749 TTAGAGTGATCAAAATAAGATAAA
1 TTAGAGTGATCAAAATAAAATAAA
62415773 TCCGATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (26 bp):
TTAGAGTGATCAAAATAAAATAAAAT
Found at i:62420449 original size:23 final size:23
Alignment explanation
Indices: 62420423--62420471 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
62420413 CTTTAAAATA
* *
62420423 AATAGTTATTTTCTTTTTTATAT
1 AATACTTATTTTATTTTTTATAT
* *
62420446 AATACTTTTTTTATTTTTTATTT
1 AATACTTATTTTATTTTTTATAT
62420469 AAT
1 AAT
62420472 TTAATATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
AATACTTATTTTATTTTTTATAT
Found at i:62420829 original size:89 final size:88
Alignment explanation
Indices: 62420608--62420835 Score: 294
Period size: 89 Copynumber: 2.6 Consensus size: 88
62420598 ATGCAATTTG
* *
62420608 GGAACATGTCAATGGTGAACATTGAAATTGAGGGAAACCATGTTTGTGGGGAAGTAATTCAGTGG
1 GGAACATGTCAATGGTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGG
*
62420673 TGGAAACCATAAAAAGGCGATTCA
65 TGGAAACCATAAAAAGGCAATTCA
* * * * ** *
62420697 GGAATATGTCAATGGTGAACATTGAAATCAAAGAAAATTATGTTTATGGGGAAGTAACTCAATGG
1 GGAACATGTCAATGGTGAACATTGAAAT-GAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGG
* * *
62420762 TGGAAACCATAGAAGGGTAATTCA
65 TGGAAACCATAAAAAGGCAATTCA
* *
62420786 GGAACATGACAATGGTGAACATTGAAACTGAGGGGAACCATGTTTGTGGG
1 GGAACATGTCAATGGTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGG
62420836 TTAACTCAGA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
88 1 0.01
89 113 0.98
90 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (88 bp):
GGAACATGTCAATGGTGAACATTGAAATGAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGGT
GGAAACCATAAAAAGGCAATTCA
Found at i:62423721 original size:45 final size:45
Alignment explanation
Indices: 62423671--62423762 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
62423661 ACTAAGATGA
62423671 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
1 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
62423716 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
1 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
62423761 TT
1 TT
62423763 TAATCTGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (45 bp):
TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
Found at i:62424890 original size:216 final size:216
Alignment explanation
Indices: 62424512--62425163 Score: 1205
Period size: 216 Copynumber: 3.0 Consensus size: 216
62424502 GCTTCAGGCG
*
62424512 TGTATTACTTTATTTTGAACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
* *
62424577 TAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATAAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
*
62424642 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTA
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
62424707 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
* *
62424728 TGTGTTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGAATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
*
62424793 CAGCTGGTATGTGAGATTTTTTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
* *
62424858 ATGTTTTGCAAATATGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGTGAGGATCTAATTG
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
62424923 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
62424944 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
*
62425009 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTTAGTAAATGAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
*
62425074 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGGTCTAATTG
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
62425139 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
62425160 TGTA
1 TGTA
62425164 ATTTCTTTGA
Statistics
Matches: 420, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 420 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (216 bp):
TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
AGATAATGATGATCCATTCCA
Found at i:62426204 original size:26 final size:26
Alignment explanation
Indices: 62426142--62426237 Score: 79
Period size: 26 Copynumber: 3.7 Consensus size: 26
62426132 TACAAAGTAT
**
62426142 ATATAGTATT-AAAAATATGTACATA
1 ATATAGTATTAAAAAATACATACATA
* **
62426167 ATATGGCGTTAAAAAATACATACATA
1 ATATAGTATTAAAAAATACATACATA
* *
62426193 ATATAGTATTAAATATATACATAAGATA
1 ATATAGTATTAAA-AAATACAT-ACATA
**
62426221 ATAT-GTAAAAAAAAATA
1 ATATAGTATTAAAAAATA
62426238 GTATTCGAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
25 7 0.13
26 27 0.49
27 13 0.24
28 8 0.15
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.31
Consensus pattern (26 bp):
ATATAGTATTAAAAAATACATACATA
Found at i:62426534 original size:2 final size:2
Alignment explanation
Indices: 62426518--62426577 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
62426508 AATATTAAAA
* *
62426518 AT AT AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
62426559 AT ACG AT AT AT AC AT AT AT
1 AT A-T AT AT AT AT AT AT AT
62426578 TAGAAATGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:62426763 original size:3 final size:3
Alignment explanation
Indices: 62426676--62426746 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
62426666 ATACTAGTAC
* *
62426676 TAA TAA TAT TAA TAA TGAA T-A TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
62426721 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
62426747 TATGCATATA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:62426868 original size:26 final size:25
Alignment explanation
Indices: 62426802--62426944 Score: 98
Period size: 25 Copynumber: 5.8 Consensus size: 25
62426792 GTATAAAATA
* ** *
62426802 ATAATAATAATATTAAAAGTATGTAT
1 ATAAT-ATAATATTAAAAATACATAC
* * *
62426828 GTAATATAGTGTTAAAAATACATAC
1 ATAATATAATATTAAAAATACATAC
*
62426853 ATAATATAATTATTAAAAATATATAC
1 ATAATATAA-TATTAAAAATACATAC
* * *
62426879 ACAATATAATA--AAATATAC-GA-
1 ATAATATAATATTAAAAATACATAC
* *
62426900 ATAATATGATATTAAAAATATATAC
1 ATAATATAATATTAAAAATACATAC
*
62426925 ATAATGTAA-AGTTAAAAATA
1 ATAATATAATA-TTAAAAATA
62426945 ATATATATAA
Statistics
Matches: 89, Mismatches: 22, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
21 9 0.10
22 1 0.01
23 12 0.13
24 2 0.02
25 39 0.44
26 26 0.29
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATAATATTAAAAATACATAC
Found at i:62426961 original size:14 final size:15
Alignment explanation
Indices: 62426937--62426965 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62426927 AATGTAAAGT
62426937 TAAAAATAATATATA
1 TAAAAATAATATATA
62426952 TAAAAA-AATATATA
1 TAAAAATAATATATA
62426966 CATAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATAATATATA
Found at i:62426964 original size:16 final size:17
Alignment explanation
Indices: 62426938--62426970 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62426928 ATGTAAAGTT
*
62426938 AAAAATAATATATATAA
1 AAAAATAATATACATAA
62426955 AAAAAT-ATATACATAA
1 AAAAATAATATACATAA
62426971 TATCTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAATATACATAA
Found at i:62426982 original size:25 final size:26
Alignment explanation
Indices: 62426942--62427004 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
62426932 AAAGTTAAAA
*
62426942 ATAATATATATAAAAA-AATATATAC
1 ATAATATATATAAAAAGAATATACAC
* *
62426967 ATAATATCTATTAAAAGAATATACAC
1 ATAATATATATAAAAAGAATATACAC
*
62426993 CTAATATATATA
1 ATAATATATATA
62427005 CATGTATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATATATATAAAAAGAATATACAC
Found at i:62427254 original size:21 final size:21
Alignment explanation
Indices: 62427230--62427274 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
62427220 ATAGTACTAA
*
62427230 TAATAATAATACTAAAATAAT
1 TAATAATAATAATAAAATAAT
** *
62427251 TAATTTTAATAATAAAGTAAT
1 TAATAATAATAATAAAATAAT
62427272 TAA
1 TAA
62427275 AAAAGGACCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATAAAATAAT
Found at i:62428381 original size:69 final size:70
Alignment explanation
Indices: 62428290--62428441 Score: 261
Period size: 70 Copynumber: 2.2 Consensus size: 70
62428280 GCTTGGGCTA
*
62428290 TATGGGTGTGGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTA-AAATTTGGGCTTTGGGTAC
1 TATGGG-GTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTAC
62428354 TTAGGG
65 TTAGGG
*
62428360 TATGGGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAATTTTGGGCTTTGGGTACT
1 TATGGGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTACT
*
62428425 TGGGG
66 TAGGG
62428430 TATGGGGTTGGT
1 TATGGGGTTGGT
62428442 AATTTGGTGG
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 37 0.47
70 41 0.53
ACGTcount: A:0.15, C:0.04, G:0.39, T:0.41
Consensus pattern (70 bp):
TATGGGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTACT
TAGGG
Found at i:62431742 original size:5 final size:5
Alignment explanation
Indices: 62431732--62431776 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
62431722 AACATATGTG
62431732 AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAA
62431777 GAACACACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 33 0.87
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:62431758 original size:22 final size:22
Alignment explanation
Indices: 62431732--62431776 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62431722 AACATATGTG
62431732 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
62431754 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
62431776 A
1 A
62431777 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAA
Found at i:62431759 original size:17 final size:17
Alignment explanation
Indices: 62431737--62431772 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
62431727 ATGTGAAAAT
62431737 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
62431754 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
62431771 AA
1 AA
62431773 TAAAGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:62437831 original size:50 final size:52
Alignment explanation
Indices: 62437777--62437885 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 52
62437767 AATAAAGTAA
62437777 TGCATTATGTAACTTTAATGTTAG-TTAAGTATGCATCA-TAAA-TAATGACT
1 TGCATTATGTAACTTTAATGTTAGTTTAAGTATGCATCATTAAATTAA-GACT
* * * *
62437827 TGCATTATGTAACTTTCATGTTAGTTTAAGTCTGCATTATTAAATTAAGTCT
1 TGCATTATGTAACTTTAATGTTAGTTTAAGTATGCATCATTAAATTAAGACT
62437879 TGCATTA
1 TGCATTA
62437886 AATAACTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 23 0.44
51 12 0.23
52 14 0.27
53 3 0.06
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (52 bp):
TGCATTATGTAACTTTAATGTTAGTTTAAGTATGCATCATTAAATTAAGACT
Found at i:62438051 original size:9 final size:9
Alignment explanation
Indices: 62438033--62438105 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
62438023 TTTATTTAAG
62438033 TTAA-GTGT
1 TTAATGTGT
62438041 TTAATGTGT
1 TTAATGTGT
62438050 TT--TGTGT
1 TTAATGTGT
62438057 TTAATAAGTGT
1 TTAAT--GTGT
*
62438068 TCAAATGTGT
1 T-TAATGTGT
*
62438078 TTAATATG-
1 TTAATGTGT
62438086 TT--TGT-T
1 TTAATGTGT
62438092 TTAATGTGT
1 TTAATGTGT
62438101 TTAAT
1 TTAAT
62438106 TGCAGGTGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.14
8 9 0.18
9 18 0.35
10 5 0.10
11 5 0.10
12 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.55
Consensus pattern (9 bp):
TTAATGTGT
Found at i:62440001 original size:26 final size:29
Alignment explanation
Indices: 62439961--62440013 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
62439951 TTAGTATTAT
62439961 TAGTATTACTATTTTTATAAC-TATGTAC
1 TAGTATTACTATTTTTATAACGTATGTAC
*
62439989 TAGTA-TA-TATTTTTATTACGTATGT
1 TAGTATTACTATTTTTATAACGTATGT
62440014 GTATACACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 7 0.30
28 5 0.22
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (29 bp):
TAGTATTACTATTTTTATAACGTATGTAC
Found at i:62440012 original size:27 final size:29
Alignment explanation
Indices: 62439948--62440013 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
62439938 TATTTTTATA
*
62439948 TTATTA-GTAT-TATTAGTATTACTATTT
1 TTATTACGTATGTACTAGTATTACTATTT
*
62439975 TTATAAC-TATGTACTAGTA-TA-TATTT
1 TTATTACGTATGTACTAGTATTACTATTT
62440001 TTATTACGTATGT
1 TTATTACGTATGT
62440014 GTATACACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 11 0.33
27 15 0.45
28 7 0.21
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (29 bp):
TTATTACGTATGTACTAGTATTACTATTT
Found at i:62440114 original size:3 final size:3
Alignment explanation
Indices: 62440106--62440135 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
62440096 TATTCCAATG
62440106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62440136 GTTTATGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62461109 original size:2 final size:2
Alignment explanation
Indices: 62461096--62461132 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
62461086 TTGAAAAGAA
* *
62461096 AT AT AT AA AT AT AT AT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62461133 AATTGATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62464375 original size:291 final size:291
Alignment explanation
Indices: 62463851--62464437 Score: 1165
Period size: 291 Copynumber: 2.0 Consensus size: 291
62463841 AGGATAATTT
62463851 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
1 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
62463916 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
66 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
62463981 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
131 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
62464046 TAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCATTA
196 TAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCATTA
62464111 TCAAATGGTGATGAAGCAGCTTTAATAATAA
261 TCAAATGGTGATGAAGCAGCTTTAATAATAA
62464142 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
1 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
62464207 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
66 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
*
62464272 TAATGGTTAACATGGTCATAACTATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
131 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
62464337 TAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCATTA
196 TAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCATTA
62464402 TCAAATGGTGATGAAGCAGCTTTAATAATAA
261 TCAAATGGTGATGAAGCAGCTTTAATAATAA
62464433 ATTGA
1 ATTGA
62464438 TGATAATAAT
Statistics
Matches: 295, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
291 295 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (291 bp):
ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
TAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCATTA
TCAAATGGTGATGAAGCAGCTTTAATAATAA
Found at i:62468270 original size:19 final size:22
Alignment explanation
Indices: 62468224--62468270 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
62468214 ATTGAGTGGT
62468224 TAATTAGACTTTAATTAAGTAA
1 TAATTAGACTTTAATTAAGTAA
*
62468246 -ATTTAG-C-TTAATTAAG-AA
1 TAATTAGACTTTAATTAAGTAA
62468264 TAATTAG
1 TAATTAG
62468271 TGGAAAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 1 0.05
21 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
TAATTAGACTTTAATTAAGTAA
Found at i:62468470 original size:21 final size:22
Alignment explanation
Indices: 62468446--62468486 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
62468436 TTATTTTATT
*
62468446 ATATTGTAAT-TTATATTAATG
1 ATATTATAATGTTATATTAATG
*
62468467 ATATTATAATGTTATTTTAA
1 ATATTATAATGTTATATTAA
62468487 CAATTGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
ATATTATAATGTTATATTAATG
Found at i:62468626 original size:5 final size:5
Alignment explanation
Indices: 62468579--62468619 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
62468569 AAGAAATTGT
62468579 TATTA TA-T- TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
62468620 ATTATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 30 0.88
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:62470063 original size:6 final size:6
Alignment explanation
Indices: 62470052--62470081 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
62470042 ATTTAATTAT
62470052 ATGAAA ATGAAA ATGAAA ATGAAA AGTGAA
1 ATGAAA ATGAAA ATGAAA ATGAAA A-TGAA
62470082 TTGAATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
ATGAAA
Found at i:62470400 original size:6 final size:6
Alignment explanation
Indices: 62470389--62470415 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62470379 ATGTGCCGAC
62470389 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
62470416 CGATTCGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:62470445 original size:45 final size:45
Alignment explanation
Indices: 62470395--62470503 Score: 182
Period size: 45 Copynumber: 2.4 Consensus size: 45
62470385 CGACTACTGT
*
62470395 TACTGTTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* * *
62470440 TACTGTTACTGTTACCGTTATCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
62470485 TACTGTTACTGTTACTGTT
1 TACTGTTACTGTTACTGTT
62470504 CCGGATTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:62470447 original size:51 final size:49
Alignment explanation
Indices: 62470372--62470504 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 49
62470362 TTACTGATCA
* * *
62470372 GGCAC-TTATGTGCCGACTACTGTTACTGTTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTT-C-GTTACCGATTC
*
62470422 GGCACTTTGTGTGTCGAATACTGTTACTGTTAC----CGTTATCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTCGTTACCGATTC
* *
62470467 AGCACTTTGTGTGTTGAATACTGTTACTGTTACTGTTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTC
62470505 CGGATTTGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
45 41 0.57
46 1 0.01
49 1 0.01
50 5 0.07
51 24 0.33
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (49 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTCGTTACCGATTC
Found at i:62470689 original size:18 final size:18
Alignment explanation
Indices: 62470666--62470833 Score: 97
Period size: 18 Copynumber: 9.3 Consensus size: 18
62470656 TAAAGGTATA
*
62470666 AAATAACTGATTATTTCT
1 AAATAACTGATTATTACT
* *
62470684 AAATAATTGACTATTACT
1 AAATAACTGATTATTACT
** * *
62470702 GGATAA-TAGACTGTTACT
1 AAATAACT-GATTATTACT
*
62470720 AAATAACTGAATATTACT
1 AAATAACTGATTATTACT
* *
62470738 GAATAAATGATTATTACT
1 AAATAACTGATTATTACT
* * *
62470756 GAATAACTGATTGTCACT
1 AAATAACTGATTATTACT
* * * *
62470774 GAATAAATGACTGTTACT
1 AAATAACTGATTATTACT
* * * *
62470792 GAATAACTTAATTGTTATT
1 AAATAAC-TGATTATTACT
* *
62470811 GAATATCTGATT-TTACT
1 AAATAACTGATTATTACT
62470828 AAATAA
1 AAATAA
62470834 TTGACTGTTA
Statistics
Matches: 119, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
17 9 0.08
18 95 0.80
19 15 0.13
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (18 bp):
AAATAACTGATTATTACT
Found at i:62470753 original size:54 final size:54
Alignment explanation
Indices: 62470666--62470797 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 54
62470656 TAAAGGTATA
* * * * * *
62470666 AAATAACTGATTATTTCTAAATAATTGACTATTACTGGATAA-TAGACTGTTACT
1 AAATAACTGAATATTACTGAATAAATGACTATTACTGAATAACT-GACTGTCACT
* *
62470720 AAATAACTGAATATTACTGAATAAATGATTATTACTGAATAACTGATTGTCACT
1 AAATAACTGAATATTACTGAATAAATGACTATTACTGAATAACTGACTGTCACT
* * * *
62470774 GAATAAATGACTGTTACTGAATAA
1 AAATAACTGAATATTACTGAATAA
62470798 CTTAATTGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 64 0.98
55 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (54 bp):
AAATAACTGAATATTACTGAATAAATGACTATTACTGAATAACTGACTGTCACT
Found at i:62470833 original size:54 final size:55
Alignment explanation
Indices: 62470695--62470852 Score: 160
Period size: 54 Copynumber: 2.9 Consensus size: 55
62470685 AATAATTGAC
* * * * * *
62470695 TATTACTGGATAA-TAGACTGTTACTAAATAACTGAATATTACTGAATAA-ATGAT
1 TATTACTGAATAACT-GATTGTTACTAAATAAATGACTGTTACTGAATAACATAAT
* * *
62470749 TATTACTGAATAACTGATTGTCACTGAATAAATGACTGTTACTGAATAACTTAAT
1 TATTACTGAATAACTGATTGTTACTAAATAAATGACTGTTACTGAATAACATAAT
* * * * *
62470804 TGTTATTGAATATCTGATT-TTACTAAATAATTGACTGTTACTGGATAAC
1 TATTACTGAATAACTGATTGTTACTAAATAAATGACTGTTACTGAATAAC
62470853 CGATCAATTG
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 66 0.77
55 20 0.23
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (55 bp):
TATTACTGAATAACTGATTGTTACTAAATAAATGACTGTTACTGAATAACATAAT
Found at i:62470851 original size:18 final size:18
Alignment explanation
Indices: 62470685--62470931 Score: 129
Period size: 18 Copynumber: 13.3 Consensus size: 18
62470675 ATTATTTCTA
*
62470685 AATAATTGACTATTACTG
1 AATAATTGACTGTTACTG
* * *
62470703 GATAATAGACTGTTACTA
1 AATAATTGACTGTTACTG
* * *
62470721 AATAACTGAATATTACTG
1 AATAATTGACTGTTACTG
* * *
62470739 AATAAATGATTATTACTG
1 AATAATTGACTGTTACTG
* * *
62470757 AATAACTGATTGTCACTG
1 AATAATTGACTGTTACTG
*
62470775 AATAAATGACTGTTACTG
1 AATAATTGACTGTTACTG
* * *
62470793 AATAACTTAATTGTTATTG
1 AATAA-TTGACTGTTACTG
* *
62470812 AAT-ATCTGA-TTTTACTA
1 AATAAT-TGACTGTTACTG
62470829 AATAATTGACTGTTACTGG
1 AATAATTGACTGTTACT-G
* *
62470848 ATAACCGATCAATTGATTGATACTG
1 ---A---AT-AATTGACTGTTACTG
* ** * *
62470873 AATAACTGGTTATTATTG
1 AATAATTGACTGTTACTG
* *
62470891 AATAATTGATTGTTACCG
1 AATAATTGACTGTTACTG
*
62470909 AATAACTGACTGTTACTG
1 AATAATTGACTGTTACTG
62470927 AATAA
1 AATAA
62470932 ACAATTGTTC
Statistics
Matches: 174, Mismatches: 43, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
17 12 0.07
18 131 0.75
19 14 0.08
22 2 0.01
25 3 0.02
26 12 0.07
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (18 bp):
AATAATTGACTGTTACTG
Found at i:62474979 original size:46 final size:46
Alignment explanation
Indices: 62474907--62474999 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
62474897 ATTTATTTGA
* * *
62474907 TTCTTCCCAATCTCTAACATTTGACTCACAAAATTGTATGCAAACT
1 TTCTCCCCAATCTCTAACATTAGACTCACAAAATTGTATACAAACT
62474953 TTCTCCCCAATCTCTAACATTAGACTCACAAAATTGTATACAAACT
1 TTCTCCCCAATCTCTAACATTAGACTCACAAAATTGTATACAAACT
62474999 T
1 T
62475000 ACAGTCTCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (46 bp):
TTCTCCCCAATCTCTAACATTAGACTCACAAAATTGTATACAAACT
Found at i:62476687 original size:19 final size:18
Alignment explanation
Indices: 62476645--62476688 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
62476635 ATGTTGACGT
*
62476645 ATAAATTATTTTTCGTTA
1 ATAAACTATTTTTCGTTA
*
62476663 ACTAAACTATTTTTTGTATA
1 A-TAAACTATTTTTCGT-TA
62476683 ATAAAC
1 ATAAAC
62476689 ACAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (18 bp):
ATAAACTATTTTTCGTTA
Found at i:62478497 original size:17 final size:16
Alignment explanation
Indices: 62478455--62478497 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
62478445 AATATATTTT
62478455 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
62478471 TAGAAAATATTTTAAAA
1 TA-AAAATATTTTAAAA
62478488 TAAAATATAT
1 TAAAA-ATAT
62478498 GATTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAATATTTTAAAA
Found at i:62482779 original size:26 final size:26
Alignment explanation
Indices: 62482719--62482781 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
62482709 TTTATTTACG
*
62482719 AAAT-TAAAAA-ACCTTATTATTAAT
1 AAATATAAAAATAACTTATTATTAAT
*
62482743 ATATATAAAAATAACTTA-TATTAAT
1 AAATATAAAAATAACTTATTATTAAT
*
62482768 AAATGATCAAAATA
1 AAAT-ATAAAAATA
62482782 TGCGGTTAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.09
25 16 0.50
26 13 0.41
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATATAAAAATAACTTATTATTAAT
Found at i:62483024 original size:14 final size:14
Alignment explanation
Indices: 62482985--62483027 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
62482975 ATTTAATTAT
62482985 TTTTAATTATTCAAAA
1 TTTTAATT-TT-AAAA
*
62483001 TTTAATATTTTAAAA
1 TTTTA-ATTTTAAAA
62483016 TTTTAATTTTAA
1 TTTTAATTTTAA
62483028 CTCAAACGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 8 0.33
16 6 0.25
17 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAATTTTAAAA
Found at i:62492883 original size:41 final size:41
Alignment explanation
Indices: 62492826--62492928 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
62492816 AGTAGTGGCT
62492826 GCAAAAGGTCTAGCATTAGCAGCATTTATGAGAAAAACGCC
1 GCAAAAGGTCTAGCATTAGCAGCATTTATGAGAAAAACGCC
* *
62492867 GCAAAAGGTCTAGCATTAGCGGCGTTTATGAGAAAAACGCC
1 GCAAAAGGTCTAGCATTAGCAGCATTTATGAGAAAAACGCC
* * *
62492908 TCAAAAAGTCAAGCATTAGCA
1 GCAAAAGGTCTAGCATTAGCA
62492929 AAAACGCCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (41 bp):
GCAAAAGGTCTAGCATTAGCAGCATTTATGAGAAAAACGCC
Found at i:62493939 original size:79 final size:77
Alignment explanation
Indices: 62493805--62493956 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 77
62493795 TGCCTTAGTA
* * *
62493805 TTTTTCCCAAAATCTATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTGAAATCTCTTCTGT-
1 TTTTTCCCAAAATCGATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTAT-TC
62493869 TTTTTTCCCCTTC
65 TTTTTTCCCCTTC
* *
62493882 TTTTTCCCAAAATCGGTTCCCCCCTCCCCCTCGAAATCCCAAAATTTCACCTAAAATCTCTTATT
1 TTTTTCCCAAAATCGATT-CCCCCT-CCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTATT
62493947 CTTTTTTCCC
64 CTTTTTTCCC
62493957 ATTTTATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 16 0.24
78 7 0.10
79 44 0.66
ACGTcount: A:0.22, C:0.37, G:0.04, T:0.37
Consensus pattern (77 bp):
TTTTTCCCAAAATCGATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTATTCT
TTTTTCCCCTTC
Found at i:62493985 original size:79 final size:77
Alignment explanation
Indices: 62493803--62493990 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 77
62493793 AATGCCTTAG
* * *
62493803 TATTTTTCCCAAAATCTATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTGAAATCTCTTCTG
1 TATTTTTCCCAAAATCCATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTATG
62493868 TTTTTTTCCCCT
66 TTTTTTTCCCCT
* ** *
62493880 TCTTTTTCCCAAAATCGGTTCCCCCCTCCCCCTCGAAATCCCAAAATTTCACCTAAAATCTCTTA
1 TATTTTTCCCAAAATCCATT-CCCCCT-CCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTA
*
62493945 T-TCTTTTTTCCCATTT
64 TGT-TTTTTTCCC--CT
62493961 TATTTTTCCC-AAA-CCATTCTCCCCTACCCC
1 TATTTTTCCCAAAATCCATTC-CCCCT-CCCC
62493991 GATTCCCTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
77 17 0.18
78 8 0.09
79 56 0.60
80 3 0.03
81 10 0.11
ACGTcount: A:0.22, C:0.37, G:0.03, T:0.37
Consensus pattern (77 bp):
TATTTTTCCCAAAATCCATTCCCCCTCCCCACGAAATCCCAAAATTTCACCTAAAATCTCTTATG
TTTTTTTCCCCT
Found at i:62494052 original size:25 final size:25
Alignment explanation
Indices: 62494024--62494098 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
62494014 ATTTCCCCAA
62494024 ATTGGCAGCCCACTGCTGCATCTCC
1 ATTGGCAGCCCACTGCTGCATCTCC
* **
62494049 ATTGGCAGGCTGCTGCTGCATCTCC
1 ATTGGCAGCCCACTGCTGCATCTCC
* * * *
62494074 ATCGGCAGCCCTCTGTTGCTTCTCC
1 ATTGGCAGCCCACTGCTGCATCTCC
62494099 TTGTAAGTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.12, C:0.37, G:0.23, T:0.28
Consensus pattern (25 bp):
ATTGGCAGCCCACTGCTGCATCTCC
Found at i:62506055 original size:24 final size:24
Alignment explanation
Indices: 62506019--62506064 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
62506009 TTTAATTTTC
62506019 AAAATTTTAAAAAAATAAAAATAA
1 AAAATTTTAAAAAAATAAAAATAA
62506043 AAAACTTTT-AAAAAATAAAAAT
1 AAAA-TTTTAAAAAAATAAAAAT
62506065 TACATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATTTTAAAAAAATAAAAATAA
Found at i:62506095 original size:30 final size:30
Alignment explanation
Indices: 62506061--62506190 Score: 142
Period size: 30 Copynumber: 4.4 Consensus size: 30
62506051 TAAAAAATAA
*
62506061 AAATTACATTTTGACCCCTAAACTTT-TCCT
1 AAATTACATTTTGACCCCTAAACTTTCT-TT
* *
62506091 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTACATTTTGACCCCTAAACTTTCTTT
* * *
62506121 AAATTTCACTTAGACCCCTAAACTTTCTTT
1 AAATTACATTTTGACCCCTAAACTTTCTTT
*
62506151 AAATTACATTTT-AACCCTAAA-TTT-TTT
1 AAATTACATTTTGACCCCTAAACTTTCTTT
62506178 AAAAATTACATTT
1 --AAATTACATTT
62506191 AGCCCCAGGA
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
27 3 0.03
28 3 0.03
29 19 0.22
30 61 0.70
31 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAACTTTCTTT
Found at i:62518732 original size:14 final size:14
Alignment explanation
Indices: 62518713--62518742 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62518703 GTTGAGGTAA
*
62518713 TTTCAATTTATGTT
1 TTTCAATTTATATT
62518727 TTTCAATTTATATT
1 TTTCAATTTATATT
62518741 TT
1 TT
62518743 GCAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:62518771 original size:87 final size:86
Alignment explanation
Indices: 62518657--62519222 Score: 586
Period size: 87 Copynumber: 6.7 Consensus size: 86
62518647 TGCTTGTCAA
* * * *
62518657 AAAAAGTCGACTCATATTGCGAAAGGTGAGTTGAGCCTTAGGACACGTTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
62518722 ATGTTTTTCAATTTATATTTTGC
65 CTGTTTTTCAATTTATATTTT-C
* * *
62518745 AAAAATCAATTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *
62518810 TGTTCTT-AA-TGACTATTTT-
66 TGTTTTTCAATTTA-TATTTTC
* *
62518829 -TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
62518892 TGTTTTTTCCAATCTATATTTTTC
66 TG-TTTTT-CAATTTATA-TTTTC
* * *
62518916 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *
62518981 CGTTTTTCAATTTATGTTTTTC
66 TGTTTTTCAATTTAT-ATTTTC
* * * * *
62519003 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACAAGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
62519068 TGTTTTT---TTT-TA----A
66 TGTTTTTCAATTTATATTTTC
** * * *
62519081 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
62519146 CTGTCTTTC-----A-A-----
65 CTGTTTTTCAATTTATATTTTC
* *
62519157 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTCAATT
62519222 T
64 T
62519223 TTTGCTTTTT
Statistics
Matches: 410, Mismatches: 53, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
75 32 0.08
76 5 0.01
77 23 0.06
78 5 0.01
79 56 0.14
82 12 0.03
83 53 0.13
84 3 0.01
85 6 0.01
86 13 0.03
87 133 0.32
88 59 0.14
89 10 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (86 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTTCAATTTATATTTTC
Found at i:62518942 original size:171 final size:168
Alignment explanation
Indices: 62518577--62519222 Score: 624
Period size: 171 Copynumber: 3.9 Consensus size: 168
62518567 GTTTTTTCTG
* * * * ***
62518577 TTTTCAAAATTCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
* * * * * *
62518642 ATTACTGCTTGTCAA-A--A-----AAAGTCGACTCATATTGCGAAAGGTGAGTTGAGCCTTAGG
66 ATTTCTG-TTCTTAATACTATTTTTAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
62518699 ACACGTTGAGGTAATTTCAATTTATG-TTTTTCAATTTATA
129 ACACGCTGAGGTAATTTCAATTTCTGTTTTTTCAA-TTATA
* * *
62518739 TTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTATTTTC
1 TTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
*
62518804 AATTTCTGTTCTTAATGACTATTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
65 AATTTCTGTTCTTAAT-ACTATTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
62518869 ACACGCTGAGGT-ATTTCAATTTCTGTTTTTTCCAATCTATA
129 ACACGCTGAGGTAATTTCAATTTCTGTTTTTT-CAAT-TATA
62518910 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
1 -TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
* * * * * *
62518975 GATTTCCGTTTTTCAATTTA-TGTTTTTCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCC
65 AATTTCTGTTCTT-AA--TACTATTTTT---AAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * *
62519039 TCGGGACAAGCTGAGGTAATTTCAATTCCTGTTTTTT---TT-TA
124 TCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTTCAATTATA
* ** *
62519080 ----AAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
*** *
62519141 AATTTCTG-TCTT--T-C-A--AAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGT
65 AATTTCTGTTCTTAATACTATTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-
*
62519199 CACACGCTGAGGTATTTTCAATTT
129 -ACACGCTGAGGTAATTTCAATTT
62519223 TTTGCTTTTT
Statistics
Matches: 411, Mismatches: 48, Indels: 56
0.80 0.09 0.11
Matches are distributed among these distances:
154 35 0.09
156 20 0.05
160 1 0.00
162 9 0.02
163 59 0.14
164 1 0.00
165 8 0.02
166 58 0.14
169 12 0.03
170 51 0.12
171 78 0.19
172 13 0.03
173 1 0.00
174 1 0.00
175 46 0.11
176 18 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (168 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
ATTTCTGTTCTTAATACTATTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
ACGCTGAGGTAATTTCAATTTCTGTTTTTTCAATTATA
Found at i:62519111 original size:79 final size:75
Alignment explanation
Indices: 62519003--62519267 Score: 273
Period size: 79 Copynumber: 3.4 Consensus size: 75
62518993 TATGTTTTTC
* * * *
62519003 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACAAGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTCC
* *
62519068 TGTTTTTTTTTAA
66 TG---TCTTTCAA
** ** * *
62519081 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTC
62519146 CTGTCTTTCAA
65 CTGTCTTTCAA
* *
62519157 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GACACGCTGAGGTATTTTCAA-T
** *
62519222 TTTTGCTTTTTC-A
63 TCCTG-TCTTTCAA
*
62519235 AAAGATCAACTCATAATT-CGAGAGGTGAGTTGA
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
62519268 ACTTCGGGTC
Statistics
Matches: 158, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
75 30 0.19
76 11 0.07
77 19 0.12
78 38 0.24
79 60 0.38
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTCC
TGTCTTTCAA
Found at i:62519263 original size:78 final size:76
Alignment explanation
Indices: 62518984--62519313 Score: 298
Period size: 78 Copynumber: 4.3 Consensus size: 76
62518974 CGATTTCCGT
* * * * *
62518984 TTTTCAA-TTTATGTTTTTC-AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTC-GGGAC
1 TTTTCAATTTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGCAC
*
62519046 AAGCTGAGGTA
66 ACGCTGAGGTA
* * * ** * *
62519057 ATTTCAATTCCTGTTTTTTTTTAAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
1 TTTTCAATT--T-TTTGTTTTTCAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAG
*
62519122 G-ACACGTTGAGGTA
62 GCACACGCTGAGGTA
* *
62519136 TTTTCAA-TTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTC
1 TTTTCAATTTTTTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG-C
62519200 ACACGCTGAGGTA
64 ACACGCTGAGGTA
* * *
62519213 TTTTCAATTTTTTGCTTTTTCAAAAGATCAACTCATAATT-CGAGAGGTGAGTTGAA-CTTCGGG
1 TTTTCAATTTTTTG-TTTTTCAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTT-AAGCCTCAGG
* * *
62519276 TCGCATC-CCGAGCTA
63 -CACA-CGCTGAGGTA
62519291 TTTTCAATTTTTTTGTTTTTCAA
1 TTTTCAA-TTTTTTGTTTTTCAA
62519314 TAAAGAATGA
Statistics
Matches: 212, Mismatches: 29, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
73 6 0.03
74 1 0.00
75 38 0.18
76 8 0.04
77 26 0.12
78 68 0.32
79 64 0.30
80 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (76 bp):
TTTTCAATTTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGCAC
ACGCTGAGGTA
Found at i:62519483 original size:24 final size:24
Alignment explanation
Indices: 62519453--62519498 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
62519443 TTTAATTTTC
62519453 AAAATTTTAAAAAAATAAAAATAA
1 AAAATTTTAAAAAAATAAAAATAA
*
62519477 AAAATTTTCAAAAAATAAAAAT
1 AAAATTTTAAAAAAATAAAAAT
62519499 TGCATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATTTTAAAAAAATAAAAATAA
Found at i:62519535 original size:30 final size:29
Alignment explanation
Indices: 62519495--62519623 Score: 109
Period size: 30 Copynumber: 4.4 Consensus size: 29
62519485 CAAAAAATAA
62519495 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTGCATTTTGACCCCTAAAC-TTTCCT
* * *
62519525 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTGCATTTTGACCCCTAAACTTTC-CT
* ** *
62519555 AAATTTCACCTAGACCCCTAAACTTTCCTT
1 AAATTGCATTTTGACCCCTAAACTTTCC-T
* * *
62519585 AAAATGCATTTT-AACCCTAAA-TTTTCT
1 AAATTGCATTTTGACCCCTAAACTTTCCT
*
62519612 AAAATTACATTT
1 -AAATTGCATTT
62519624 AGCCCCAGAA
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
27 1 0.01
28 13 0.16
29 12 0.15
30 53 0.67
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
AAATTGCATTTTGACCCCTAAACTTTCCT
Found at i:62520684 original size:17 final size:17
Alignment explanation
Indices: 62520645--62520686 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
62520635 ATTTTATAAC
*
62520645 TATATTATGTACATATA
1 TATATTTTGTACATATA
62520662 TATATTTTGTACATATCA
1 TATATTTTGTACATAT-A
62520680 T-TATTTT
1 TATATTTT
62520687 ATATTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (17 bp):
TATATTTTGTACATATA
Found at i:62520835 original size:13 final size:13
Alignment explanation
Indices: 62520817--62520841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62520807 TTTTTATGTA
62520817 TATATTATTATTT
1 TATATTATTATTT
62520830 TATATTATTATT
1 TATATTATTATT
62520842 ACCAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATTATTATTT
Found at i:62520841 original size:19 final size:20
Alignment explanation
Indices: 62520748--62520842 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 20
62520738 TAATATTTTC
*
62520748 TTTTATTGTAGATATTATTAT
1 TTTTA-TGTATATATTATTAT
* **
62520769 TATTACATATAT-TTATTAT
1 TTTTATGTATATATTATTAT
* ** *
62520788 ATGCATATATATA-TATGTAT
1 TTTTATGTATATATTAT-TAT
62520808 TTTTATGTATATATTATTAT
1 TTTTATGTATATATTATTAT
62520828 TTTATAT-TAT-TATTA
1 TTT-TATGTATATATTA
62520843 CCAAATATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 22 0.39
20 25 0.44
21 10 0.18
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTATGTATATATTATTAT
Found at i:62539727 original size:18 final size:18
Alignment explanation
Indices: 62539704--62539740 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
62539694 TTAAAAATTC
*
62539704 TTTATATATAAAGTTTAT
1 TTTATATACAAAGTTTAT
*
62539722 TTTATATACAAATTTTAT
1 TTTATATACAAAGTTTAT
62539740 T
1 T
62539741 GGAGTTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTATATACAAAGTTTAT
Found at i:62540208 original size:22 final size:23
Alignment explanation
Indices: 62540166--62540211 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
62540156 AATATTAGTT
62540166 TTTTATTTTTCTCTTGTCATGAG
1 TTTTATTTTTCTCTTGTCATGAG
*
62540189 TTTTCTTTTTCTCTTG-CATGAG
1 TTTTATTTTTCTCTTGTCATGAG
62540211 T
1 T
62540212 AAATAGTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (23 bp):
TTTTATTTTTCTCTTGTCATGAG
Found at i:62542921 original size:3 final size:3
Alignment explanation
Indices: 62542913--62542960 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
62542903 GTATATACAT
* * *
62542913 ATA ATA ATA ATG ATG ATA ATC ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
62542961 TGAAAATACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:62544182 original size:17 final size:17
Alignment explanation
Indices: 62544160--62544193 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62544150 GACGGGTTAT
62544160 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
62544177 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
62544194 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:62546453 original size:32 final size:32
Alignment explanation
Indices: 62546414--62546487 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
62546404 GTGTCCCAAG
62546414 CCACACGGGCATGTGTGATCACACAGCCCCAC
1 CCACACGGGCATGTGTGATCACACAGCCCCAC
62546446 CCACACGGGCATGTGTGATCACACAGCCCCAC
1 CCACACGGGCATGTGTGATCACACAGCCCCAC
62546478 CCACACGGGC
1 CCACACGGGC
62546488 GTGACACTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.24, C:0.42, G:0.23, T:0.11
Consensus pattern (32 bp):
CCACACGGGCATGTGTGATCACACAGCCCCAC
Found at i:62568966 original size:19 final size:18
Alignment explanation
Indices: 62568908--62568967 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
62568898 TCAAAAGATA
62568908 ATTTATCCTTATTAAATAT
1 ATTTATCCTTATT-AATAT
* *
62568927 ATTTAGT-GTTA-T-ATCT
1 ATTTA-TCCTTATTAATAT
62568943 ATTTATCCTTATTAATTAT
1 ATTTATCCTTATTAA-TAT
62568962 ATTTAT
1 ATTTAT
62568968 TCTAACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 1 0.03
16 11 0.34
17 1 0.03
18 2 0.06
19 16 0.50
20 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTATCCTTATTAATAT
Found at i:62576889 original size:76 final size:76
Alignment explanation
Indices: 62576803--62576955 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
62576793 ATTGATGTAG
62576803 TCAGTTCATAGGTAGAAGAGTGACCGAAACTGATTAATCCGGTCATCAAAGCTTACAGAAGCAGC
1 TCAGTTCATAGGTAGAAGAGTGACCGAAACTGATTAATCCGGTCATCAAAGCTTACAGAAGCAGC
62576868 AAAATTAGGAC
66 AAAATTAGGAC
62576879 TCAGTTCATAGGTAGAAGAGTGACCGAAACTGATTAATCCGGTCATCAAAGCTTACAGAAGCAGC
1 TCAGTTCATAGGTAGAAGAGTGACCGAAACTGATTAATCCGGTCATCAAAGCTTACAGAAGCAGC
62576944 AAAATTAGGAC
66 AAAATTAGGAC
62576955 T
1 T
62576956 TACTTGTTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (76 bp):
TCAGTTCATAGGTAGAAGAGTGACCGAAACTGATTAATCCGGTCATCAAAGCTTACAGAAGCAGC
AAAATTAGGAC
Found at i:62577063 original size:22 final size:22
Alignment explanation
Indices: 62577038--62577084 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
62577028 TAAGAAACAG
* *
62577038 GATTTAGTTAGATGTCAGAAGA
1 GATTTAATTAGATCTCAGAAGA
*
62577060 GATTTAATTAGTTCTCAGAAGA
1 GATTTAATTAGATCTCAGAAGA
62577082 GAT
1 GAT
62577085 GAAATAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (22 bp):
GATTTAATTAGATCTCAGAAGA
Found at i:62578200 original size:26 final size:26
Alignment explanation
Indices: 62578164--62578215 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
62578154 ATGTTGAAAT
62578164 GGGAATGAAGAAAACCGTTAAACAAG
1 GGGAATGAAGAAAACCGTTAAACAAG
62578190 GGGAATGAAGAAAACCGTTAAACAAG
1 GGGAATGAAGAAAACCGTTAAACAAG
62578216 TGCTAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.27, T:0.12
Consensus pattern (26 bp):
GGGAATGAAGAAAACCGTTAAACAAG
Found at i:62583363 original size:13 final size:14
Alignment explanation
Indices: 62583345--62583385 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
62583335 TTTACTGATA
62583345 CAGATA-ATAGAAT
1 CAGATATATAGAAT
* *
62583358 CAGATATGTTGAAT
1 CAGATATATAGAAT
62583372 -AGATATATAGAAT
1 CAGATATATAGAAT
62583385 C
1 C
62583386 CTACCCACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (14 bp):
CAGATATATAGAAT
Found at i:62590158 original size:15 final size:17
Alignment explanation
Indices: 62590134--62590168 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
62590124 GTTAAGGACT
62590134 AAATTGAAAAG-TGATA
1 AAATTGAAAAGATGATA
62590150 AAATT-AAAAGATGATA
1 AAATTGAAAAGATGATA
62590166 AAA
1 AAA
62590169 AATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (17 bp):
AAATTGAAAAGATGATA
Found at i:62593568 original size:13 final size:14
Alignment explanation
Indices: 62593531--62593571 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
62593521 TTTATAGATA
62593531 CAGATA-ACAGAAT
1 CAGATATACAGAAT
* *
62593544 CAGATGTGCAGAAT
1 CAGATATACAGAAT
62593558 -AGATATACAGAAT
1 CAGATATACAGAAT
62593571 C
1 C
62593572 CTACCCCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:62597756 original size:9 final size:9
Alignment explanation
Indices: 62597713--62597756 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
62597703 TTATATAGAA
62597713 TTTTTTTAT
1 TTTTTTTAT
* *
62597722 CTTTTCTAAT
1 -TTTTTTTAT
62597732 TTTTTTGTAT
1 TTTTTT-TAT
62597742 TTTTTTTAT
1 TTTTTTTAT
62597751 TTTTTT
1 TTTTTT
62597757 AGAATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:62598603 original size:25 final size:24
Alignment explanation
Indices: 62598556--62598604 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
62598546 CTATCGGACC
* * *
62598556 TTTTCTCTTGATTAGTAACAAAAA
1 TTTTCTCTTGATAAGAAAAAAAAA
62598580 TTTTCTCATTGATAAGAAAAAAAAA
1 TTTTCTC-TTGATAAGAAAAAAAAA
62598605 ATAGTCTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (24 bp):
TTTTCTCTTGATAAGAAAAAAAAA
Found at i:62602392 original size:27 final size:27
Alignment explanation
Indices: 62602341--62602441 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
62602331 TACTGAAATG
* *
62602341 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * * *
62602368 CCCTCGATTTATAGAATTACTATTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
* *
62602395 CCATCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
62602422 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTACAAAATTAC
62602442 TGAAATACCC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCATTTTA
Found at i:62602451 original size:27 final size:27
Alignment explanation
Indices: 62602321--62602444 Score: 108
Period size: 27 Copynumber: 4.6 Consensus size: 27
62602311 AATACTTTAG
* ** *
62602321 TTTACCAAATTACTGAAATGCCCTCGA
1 TTTACAAAATTACTGATTTACCCTCGA
* * *
62602348 TTTATAGAATTAC-CATTTTACCCTCGA
1 TTTACAAAATTACTGA-TTTACCCTCGA
* * *
62602375 TTTATAGAATTACT-ATTTCACCATCGA
1 TTTACAAAATTACTGATTT-ACCCTCGA
* *
62602402 TTTACAAAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACTGATTTACCCTCGA
62602429 TTTACAAAATTACTGA
1 TTTACAAAATTACTGA
62602445 AATACCCCTA
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.05
27 71 0.91
28 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
TTTACAAAATTACTGATTTACCCTCGA
Found at i:62602466 original size:27 final size:27
Alignment explanation
Indices: 62602436--62602845 Score: 563
Period size: 27 Copynumber: 15.3 Consensus size: 27
62602426 CGATTTACAA
* *
62602436 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
62602463 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
62602490 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
62602517 AATTACCGAAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
62602544 AATTACCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
62602571 AATTACCGAAATACCCCTACATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
62602598 AATTATCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
62602625 AATTACTGAAACACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
62602652 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
62602679 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
62602706 AATTACCGGAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
62602733 AATTATCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
62602760 AATTACCGAAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
62602787 AATTACTAAAATACCCCTGTATGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
62602814 AATTACCGAGATA-CCTTGTGGGGTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
62602839 AATTACC
1 AATTACC
62602846 ATTTTGCCCT
Statistics
Matches: 341, Mismatches: 42, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
25 7 0.02
26 8 0.02
27 326 0.96
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:62603324 original size:22 final size:22
Alignment explanation
Indices: 62603272--62603327 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
62603262 TTAAATCCTT
* *
62603272 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
62603294 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
62603316 TTGATTATGGCT
1 CTGATTATGGCT
62603328 GTATGCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:62603524 original size:27 final size:27
Alignment explanation
Indices: 62603494--62603595 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
62603484 ATTCTGTTAA
* *
62603494 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
*
62603521 GTGGCTATGCCACAAATATCT-ATTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
62603548 GTGGCTCTACCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* *
62603575 GTGACTCA-GTCACAATATCTG
1 GTGGCT-ATGCCACAATATCTG
62603596 ATAACTGAGC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.11
27 48 0.79
28 6 0.10
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:62603773 original size:25 final size:25
Alignment explanation
Indices: 62603743--62603800 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
62603733 TTCTGATTTT
* * *
62603743 TGATTCTGTTACCTGATACTGATTC
1 TGATTCTGTCACCTAATACTAATTC
* *
62603768 TGATTCTATCACCTAATTCTAATTC
1 TGATTCTGTCACCTAATACTAATTC
62603793 TGATTCTG
1 TGATTCTG
62603801 ATTCTAGTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (25 bp):
TGATTCTGTCACCTAATACTAATTC
Found at i:62606848 original size:16 final size:16
Alignment explanation
Indices: 62606827--62606857 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62606817 AGTCCTAATT
62606827 TATTTATTCGTTTATC
1 TATTTATTCGTTTATC
*
62606843 TATTTATTGGTTTAT
1 TATTTATTCGTTTAT
62606858 ACATACCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (16 bp):
TATTTATTCGTTTATC
Found at i:62606984 original size:18 final size:18
Alignment explanation
Indices: 62606961--62607000 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62606951 TTATCTTGGT
62606961 TATTATTATCTTATTATC
1 TATTATTATCTTATTATC
* * *
62606979 TATTATTGTTTTATTATT
1 TATTATTATCTTATTATC
62606997 TATT
1 TATT
62607001 CACTCATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATCTTATTATC
Found at i:62607893 original size:9 final size:9
Alignment explanation
Indices: 62607859--62607936 Score: 54
Period size: 9 Copynumber: 8.3 Consensus size: 9
62607849 AGTTTATTAT
62607859 TATTTTTT-
1 TATTTTTTA
*
62607867 TCTTTTTTA
1 TATTTTTTA
*
62607876 AATTGTTTTA
1 TATT-TTTTA
62607886 TATTTTTTA
1 TATTTTTTA
*
62607895 TATTATGTATTT
1 TATT-T-T-TTA
62607907 TATTTTATT-
1 TATTTT-TTA
62607916 TCATTTTTT-
1 T-ATTTTTTA
62607925 TATTTTTTA
1 TATTTTTTA
62607934 TAT
1 TAT
62607937 ATACATATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
8 14 0.24
9 18 0.31
10 18 0.31
11 2 0.03
12 6 0.10
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTTTTTA
Found at i:62614743 original size:16 final size:16
Alignment explanation
Indices: 62614727--62614767 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 16
62614717 TTAAAAAAAT
62614727 TAAAAAGAATGATAATTA
1 TAAAAA-AAT-ATAATTA
62614745 TAAAAAAATATAATTA
1 TAAAAAAATATAATTA
62614761 TAAAAAA
1 TAAAAAA
62614768 TCCAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TAAAAAAATATAATTA
Found at i:62617134 original size:32 final size:32
Alignment explanation
Indices: 62617098--62617162 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
62617088 TGTATGCATT
62617098 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
62617130 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
62617162 T
1 T
62617163 GGCAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:62618675 original size:26 final size:26
Alignment explanation
Indices: 62618646--62618698 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
62618636 TTTACAATTT
62618646 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
62618672 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
62618698 T
1 T
62618699 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:62620375 original size:54 final size:54
Alignment explanation
Indices: 62620310--62620420 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
62620300 AATGTTCTTG
62620310 TCATTAATGTGTTACCCTCATAGGATACTCTTAATTTCTTTGGGTTAAATCCAT
1 TCATTAATGTGTTACCCTCATAGGATACTCTTAATTTCTTTGGGTTAAATCCAT
*
62620364 TCATTAGTGTGTTACCCTCATAGGATACTCTTAATTTCTTTGGGTTAAATCCAT
1 TCATTAATGTGTTACCCTCATAGGATACTCTTAATTTCTTTGGGTTAAATCCAT
62620418 TCA
1 TCA
62620421 CCTAGTATGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (54 bp):
TCATTAATGTGTTACCCTCATAGGATACTCTTAATTTCTTTGGGTTAAATCCAT
Found at i:62624694 original size:22 final size:24
Alignment explanation
Indices: 62624660--62624709 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
62624650 AATTAACTTC
*
62624660 TTTTAATGTTA-TTA-AAATTTTA
1 TTTTAATGATATTTATAAATTTTA
* *
62624682 TTTTTATGATATTTATATATTTTA
1 TTTTAATGATATTTATAAATTTTA
62624706 TTTT
1 TTTT
62624710 CCGAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 3 0.13
24 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTAATGATATTTATAAATTTTA
Found at i:62628598 original size:12 final size:11
Alignment explanation
Indices: 62628577--62628616 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 11
62628567 TTAATACATG
62628577 ATATAAAAATA
1 ATATAAAAATA
62628588 ATATCAAAAATA
1 ATAT-AAAAATA
62628600 ATATGAAAAATA
1 ATAT-AAAAATA
62628612 ATATA
1 ATATA
62628617 TTTTAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:62628641 original size:18 final size:16
Alignment explanation
Indices: 62628609--62628654 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
62628599 AATATGAAAA
62628609 ATAATATATTTTAATT
1 ATAATATATTTTAATT
*
62628625 ATAATATA-TTTAATA
1 ATAATATATTTTAATT
*
62628640 ATAAT-TATGTTAATT
1 ATAATATATTTTAATT
62628655 TATATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 2 0.08
15 16 0.62
16 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAATATATTTTAATT
Found at i:62628758 original size:15 final size:15
Alignment explanation
Indices: 62628723--62628774 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62628713 TTAAGAATTT
*
62628723 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62628737 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62628751 TATTTAATAATAAT-
1 TATTTAATTATAATA
62628765 TATGTTAATT
1 TAT-TTAATT
62628775 TATATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62628835 original size:119 final size:119
Alignment explanation
Indices: 62628607--62629008 Score: 759
Period size: 119 Copynumber: 3.4 Consensus size: 119
62628597 ATAATATGAA
*
62628607 AAATAATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCA
1 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATA-TTTATAGTATCA
* * *
62628672 TATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATT
65 TATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
62628727 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTATAGTATCAT
1 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTATAGTATCAT
62628792 ATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
66 ATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
62628846 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTATAGTATCAT
1 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTATAGTATCAT
62628911 ATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
66 ATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
62628965 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
62629009 TAAATATGAT
Statistics
Matches: 278, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
119 227 0.82
120 51 0.18
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (119 bp):
AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTATAGTATCAT
ATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATT
Found at i:62628877 original size:15 final size:15
Alignment explanation
Indices: 62628842--62628893 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62628832 TTAAGAATTT
*
62628842 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62628856 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62628870 TATTTAATAATAAT-
1 TATTTAATTATAATA
62628884 TATGTTAATT
1 TAT-TTAATT
62628894 TATATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62628991 original size:16 final size:16
Alignment explanation
Indices: 62628970--62629011 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
62628960 TTATTAAATT
*
62628970 ATATATTTTAATTATA
1 ATATATTTTAATAATA
62628986 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
62629001 AT-TATGTTTAA
1 ATATAT-TTTAA
62629012 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:62628996 original size:15 final size:15
Alignment explanation
Indices: 62628961--62629002 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
62628951 TTAAGAATTT
*
62628961 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62628975 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62628989 TATTTAATAATAAT
1 TATTTAATTATAAT
62629003 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62629247 original size:16 final size:16
Alignment explanation
Indices: 62629225--62629294 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 16
62629215 TTGATTTGCT
*
62629225 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
* *
62629241 GTTACACTTCTATTCC
1 ATTACACCTCTATTCC
* *
62629257 ATTACGCCTTTATTCC
1 ATTACACCTCTATTCC
*
62629273 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
62629289 AATACA
1 ATTACA
62629295 GCGAACCAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:62634135 original size:18 final size:20
Alignment explanation
Indices: 62634111--62634163 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
62634101 TATATAAGTT
*
62634111 TAAAATTATAAAAAA-TTTA
1 TAAAATTATAAAAAAGTTAA
62634130 -AAAATTATATAAAAAGTTAA
1 TAAAATTATA-AAAAAGTTAA
62634150 TAAAATTA-AAAAAA
1 TAAAATTATAAAAAA
62634164 AATAACATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.30
19 10 0.33
20 4 0.13
21 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAATTATAAAAAAGTTAA
Found at i:62634142 original size:20 final size:21
Alignment explanation
Indices: 62634117--62634166 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
62634107 AGTTTAAAAT
*
62634117 TATAAAAAATTTA-AAAATTA
1 TATAAAAAATTAATAAAATTA
*
62634137 TATAAAAAGTTAATAAAATTA
1 TATAAAAAATTAATAAAATTA
*
62634158 -AAAAAAAAT
1 TATAAAAAAT
62634167 AACATGAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TATAAAAAATTAATAAAATTA
Found at i:62635289 original size:19 final size:21
Alignment explanation
Indices: 62635250--62635289 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
62635240 TGTGAAAAGT
62635250 ATATATCATTTGTTTATATTA
1 ATATATCATTTGTTTATATTA
*
62635271 ATAT-TCATTTTTTTA-ATTA
1 ATATATCATTTGTTTATATTA
62635290 TAACATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
ATATATCATTTGTTTATATTA
Found at i:62653394 original size:30 final size:30
Alignment explanation
Indices: 62653358--62653414 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
62653348 ACGGCCATGA
62653358 CACACGGGCGTGTGGCCTACCCGTGTGTAT
1 CACACGGGCGTGTGGCCTACCCGTGTGTAT
**
62653388 CACACGGGCGTGTGGTTTACCCGTGTG
1 CACACGGGCGTGTGGCCTACCCGTGTG
62653415 AAAATACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.28, G:0.35, T:0.25
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCTACCCGTGTGTAT
Found at i:62664530 original size:36 final size:36
Alignment explanation
Indices: 62664435--62664540 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 36
62664425 CAGGTAAACT
* * * *
62664435 AACGTCTTACACCCAACGCTAGTCGGATAACCCAAC
1 AACGTCTTGCGCCCAACGCTAGTCGCATAAACCAAC
* * * * * *
62664471 AATGTTTTGCGCCCAGCGATAGTCGCATAAATCGAC
1 AACGTCTTGCGCCCAACGCTAGTCGCATAAACCAAC
* *
62664507 AACGTCTTGCGCCCAAAGCTAGTCGGTATAAACC
1 AACGTCTTGCGCCCAACGCTAGTC-GCATAAACC
62664541 GATGATGTCA
Statistics
Matches: 52, Mismatches: 17, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
36 45 0.87
37 7 0.13
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (36 bp):
AACGTCTTGCGCCCAACGCTAGTCGCATAAACCAAC
Found at i:62664689 original size:76 final size:76
Alignment explanation
Indices: 62664505--62664720 Score: 218
Period size: 76 Copynumber: 2.8 Consensus size: 76
62664495 GCATAAATCG
** ** *
62664505 ACAACGTCTTGCGCCCAAAGCTAGTCGGTATAAACCGATGATGTCAAATATGTGCCCAGCACTAG
1 ACAACGTCTTGCGCCCAGTGCTAGTC-AAATAAACCGACGATGTCAAATATGTGCCCAGCACTAG
* *
62664570 TCAGATAACCCG
65 TCAGATAAACCA
* * * *
62664582 ATAATGTTTTGCGCCCAGTGCTAGTCAAATAAACCGACGATGTCAAATGTGTGCCCAGCACTAGT
1 ACAACGTCTTGCGCCCAGTGCTAGTCAAATAAACCGACGATGTCAAATATGTGCCCAGCACTAGT
62664647 C-GAATAAACCA
66 CAG-ATAAACCA
* * * ** * * * * *
62664658 ACAACGTCTTGTGCCTAGTGTTAGTTGAATAAACCAACAATGTTAAATATGAGCCCAACACTA
1 ACAACGTCTTGCGCCCAGTGCTAGTCAAATAAACCGACGATGTCAAATATGTGCCCAGCACTA
62664721 CTTGGATAAC
Statistics
Matches: 113, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
75 1 0.01
76 91 0.81
77 21 0.19
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (76 bp):
ACAACGTCTTGCGCCCAGTGCTAGTCAAATAAACCGACGATGTCAAATATGTGCCCAGCACTAGT
CAGATAAACCA
Found at i:62670122 original size:29 final size:28
Alignment explanation
Indices: 62670090--62670190 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
62670080 GTAGCCATAG
62670090 AGGCTTTCCTTTGACAGAGATTGCCACAA
1 AGGCTTTCCTTT-ACAGAGATTGCCACAA
* *
62670119 AGGCATTTCATTT-CAGAGATTTGCCACAG
1 AGGC-TTTCCTTTACAGAGA-TTGCCACAA
* * *
62670148 AGGCATT-CTTAAACAGAGGTTGCCACAA
1 AGGCTTTCCTT-TACAGAGATTGCCACAA
62670176 AGGCTTTCCTTTACA
1 AGGCTTTCCTTTACA
62670191 TTCAATACTC
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.03
28 25 0.43
29 24 0.41
30 7 0.12
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (28 bp):
AGGCTTTCCTTTACAGAGATTGCCACAA
Found at i:62670205 original size:32 final size:32
Alignment explanation
Indices: 62670169--62670276 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 32
62670159 AACAGAGGTT
62670169 GCCACAAAGGCTTTCCTTTACATTCAATACTC
1 GCCACAAAGGCTTTCCTTTACATTCAATACTC
* * ** * * *
62670201 GCCACAAAGGCTTTACTGT-C-TAGAGT-TTT
1 GCCACAAAGGCTTTCCTTTACATTCAATACTC
* * *
62670230 GCTAGAAAGGCTATCCTTTACATTCAATACTC
1 GCCACAAAGGCTTTCCTTTACATTCAATACTC
62670262 GCCACAAAGGCTTTC
1 GCCACAAAGGCTTTC
62670277 GTGTCCAGAA
Statistics
Matches: 53, Mismatches: 20, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
29 15 0.28
30 4 0.08
31 4 0.08
32 30 0.57
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (32 bp):
GCCACAAAGGCTTTCCTTTACATTCAATACTC
Found at i:62670295 original size:29 final size:28
Alignment explanation
Indices: 62670262--62670331 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
62670252 TTCAATACTC
* *
62670262 GCCACAAAGGCTTTCGTGTCCAGAATTGT
1 GCCACAAAGGCTTTC-TATCCAGAATTGA
* *
62670291 GCCACAAAGGCTTTTCTATCTAGATTTGA
1 GCCACAAAGGC-TTTCTATCCAGAATTGA
62670320 GCCACAAAGGCT
1 GCCACAAAGGCT
62670332 ATCCTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.03
29 31 0.86
30 4 0.11
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (28 bp):
GCCACAAAGGCTTTCTATCCAGAATTGA
Found at i:62670300 original size:61 final size:61
Alignment explanation
Indices: 62670168--62670302 Score: 200
Period size: 61 Copynumber: 2.2 Consensus size: 61
62670158 AAACAGAGGT
* * * *
62670168 TGCCACAAAGGCTTTCCTTTACATTCAATACTCGCCACAAAGGCTTTACTGTCTAGAGTTT
1 TGCCACAAAGGCTATCCTTTACATTCAATACTCGCCACAAAGGCTTTACTGTCCAGAATTG
* *
62670229 TGCTAGAAAGGCTATCCTTTACATTCAATACTCGCCACAAAGGCTTT-CGTGTCCAGAATTG
1 TGCCACAAAGGCTATCCTTTACATTCAATACTCGCCACAAAGGCTTTAC-TGTCCAGAATTG
62670290 TGCCACAAAGGCT
1 TGCCACAAAGGCT
62670303 TTTCTATCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
60 1 0.02
61 64 0.98
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (61 bp):
TGCCACAAAGGCTATCCTTTACATTCAATACTCGCCACAAAGGCTTTACTGTCCAGAATTG
Found at i:62671291 original size:11 final size:11
Alignment explanation
Indices: 62671275--62671305 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
62671265 TTATGATATG
62671275 ATTTCGTGAAA
1 ATTTCGTGAAA
62671286 ATTTCGTGAAA
1 ATTTCGTGAAA
62671297 ATTTCGTGA
1 ATTTCGTGA
62671306 TGAAATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (11 bp):
ATTTCGTGAAA
Found at i:62675673 original size:26 final size:27
Alignment explanation
Indices: 62675634--62675689 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
62675624 TTATAATATT
** * *
62675634 AAATAAAATTTTATTATTAT-TTTGAA
1 AAATAAAAAATTATAATTATATTTAAA
62675660 AAATAAAAAATTATAATTATATTTAAA
1 AAATAAAAAATTATAATTATATTTAAA
62675687 AAA
1 AAA
62675690 ACATGTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
AAATAAAAAATTATAATTATATTTAAA
Found at i:62675950 original size:185 final size:184
Alignment explanation
Indices: 62675634--62676058 Score: 643
Period size: 185 Copynumber: 2.3 Consensus size: 184
62675624 TTATAATATT
* * *
62675634 AAATAAAATTTTATTATTATTTTGAAAAATAAAAAATTATAATTATATTTAAAAAAACATGTCAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAAAAATTATATTTAAAAAAACATGTCAC
* **
62675699 TTAGTACATAATTTGTGGCATAAATTACGCTTTTCCATAACATTATAACTTTCAGTTATATTTAT
66 TTAGTACATAACTTGTGGCATAAATTACGCTTTTCCATAACATTATAACTTTCAACTATATTTAT
* * *
62675764 TCATTACGAATCTTTTCTAAAAGCTATGCTTATTTGATTAAATCTATTCAGATGC
131 TCATTACGAAT-TTTTCTAAAAGCTATGCTTATTTGAATAAATCTACTCAAATGC
* *
62675819 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAAAAATTATGTTTAAAAAAATATGTCAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAAAAATTATATTTAAAAAAACATGTCAC
* * *
62675884 TTAGTACATAACTTGTGGCATAAGTTACGCTTTTCCATAACATTATAGCTTTCAACTATGTTTAT
66 TTAGTACATAACTTGTGGCATAAATTACGCTTTTCCATAACATTATAACTTTCAACTATATTTAT
* * * *
62675949 TCATTACGAATTTTTTTTAAAGTTATGCTTATTTGAATAAATCTACTCAAATGG
131 TCATTACGAATTTTTCTAAAAGCTATGCTTATTTGAATAAATCTACTCAAATGC
* ** *
62676003 AAATAAAAATTTATTATTGTTTTGAAAAATAAAAAATAATTATTGTATTTAAAAAA
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAAAAATTATATTTAAAAAA
62676059 TTATTTGCAC
Statistics
Matches: 217, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
184 87 0.40
185 130 0.60
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (184 bp):
AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAAAAATTATATTTAAAAAAACATGTCAC
TTAGTACATAACTTGTGGCATAAATTACGCTTTTCCATAACATTATAACTTTCAACTATATTTAT
TCATTACGAATTTTTCTAAAAGCTATGCTTATTTGAATAAATCTACTCAAATGC
Found at i:62676036 original size:26 final size:27
Alignment explanation
Indices: 62676003--62676059 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
62675993 ACTCAAATGG
* * *
62676003 AAATAAAAATTTATTATTGT-TTTGAA
1 AAATAAAAAATAATTATTGTATTTAAA
62676029 AAATAAAAAATAATTATTGTATTTAAA
1 AAATAAAAAATAATTATTGTATTTAAA
62676056 AAAT
1 AAAT
62676060 TATTTGCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (27 bp):
AAATAAAAAATAATTATTGTATTTAAA
Found at i:62678471 original size:18 final size:18
Alignment explanation
Indices: 62678448--62678484 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
62678438 TTACCATATT
62678448 ACATGGTATTAATCTATA
1 ACATGGTATTAATCTATA
62678466 ACATGGTATTAATCTATA
1 ACATGGTATTAATCTATA
62678484 A
1 A
62678485 GCTAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
ACATGGTATTAATCTATA
Found at i:62682094 original size:32 final size:32
Alignment explanation
Indices: 62682053--62682113 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
62682043 GTTAATTTCG
62682053 TGTGTTATTATGATTAATTAGTTCCAAACTAT
1 TGTGTTATTATGATTAATTAGTTCCAAACTAT
62682085 TGTGTTATTATGATTAATTAGTTCCAAAC
1 TGTGTTATTATGATTAATTAGTTCCAAAC
62682114 CATATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (32 bp):
TGTGTTATTATGATTAATTAGTTCCAAACTAT
Found at i:62683007 original size:30 final size:30
Alignment explanation
Indices: 62682971--62683033 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
62682961 ACTTATTTTA
*
62682971 TTGTTAATTTTTTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
62683001 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
62683031 TTG
1 TTG
62683034 CTTGTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:62685921 original size:12 final size:13
Alignment explanation
Indices: 62685899--62685927 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
62685889 AAATTAAATT
62685899 TATTAAATATTAA
1 TATTAAATATTAA
62685912 TATT-AATATTAA
1 TATTAAATATTAA
62685924 TATT
1 TATT
62685928 TTTAATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTAAATATTAA
Found at i:62686252 original size:26 final size:26
Alignment explanation
Indices: 62686200--62686280 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 26
62686190 AAGAATATAT
* *
62686200 TTTTTATTTAATA-TTAAATAATTATA
1 TTTTTATTTAATATTTAAA-CATAATA
*
62686226 TTTTTATTAAATATTTAAACATAATA
1 TTTTTATTTAATATTTAAACATAATA
62686252 --TTTATTTAATATTT--ACATAATA
1 TTTTTATTTAATATTTAAACATAATA
*
62686274 ATTTTAT
1 TTTTTAT
62686281 ATTTTAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
22 8 0.17
24 18 0.38
26 17 0.35
27 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTTATTTAATATTTAAACATAATA
Found at i:62688319 original size:18 final size:18
Alignment explanation
Indices: 62688288--62688326 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
62688278 ATCAAATTTT
62688288 TTAAACTAATAATTATATA
1 TTAAACTAATAATTATA-A
62688307 TTAAACT-ATAATTATAA
1 TTAAACTAATAATTATAA
62688324 TTA
1 TTA
62688327 TCACAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAACTAATAATTATAA
Found at i:62694682 original size:10 final size:10
Alignment explanation
Indices: 62694663--62694691 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
62694653 TGAATTGTTA
62694663 AATATA-ATT
1 AATATATATT
62694672 AATATATATT
1 AATATATATT
62694682 AATATATATT
1 AATATATATT
62694692 TTTTCATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATATATATT
Done.