Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:410061 original size:193 final size:191
Alignment explanation
Indices: 409249--410131 Score: 1169
Period size: 182 Copynumber: 4.7 Consensus size: 191
409239 AGTTGAATTT
* * *
409249 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACTCTCAGACAATCAGACTTCCTAA
1 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
* *
409314 TCACGAAGGAACCGTATTGTCCCCAAATTATCTCTTGATTGACCCAATTTCCTCATCACGAAGGA
66 TCACGAAAGAACCGTATTGT-CCCAAATTATCTCTTGA-TGACCCGATTTCCTCATCACGAAGGA
* * * *
409379 ACAGA-TTCATAATCGAAAATGACCCGATCTCTTCATCGAGGATGAGCAGTGTCGTCTTCAACA
129 ACA-ACGTCATAATAGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
* * *
409442 TCAAATCGACCAGATCTCCTCATCACGAAGGAGCA-TCGTCACCCTCAGACAATCAGACTTTCTC
1 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGT-GTCACCCTCAGACAATCAGACTTCCTC
* * * * * * *
409506 ATCACGAAGGAAACGTATTATCCCCAA--A-----T--TGACCCGATTCCCTCATCAAGAAGAAA
65 ATCACGAAAGAACCGTATTGTCCCAAATTATCTCTTGATGACCCGATTTCCTCATCACGAAGGAA
* * *
409562 CAACGTCATAATTGAAAATAACCCGATCTCTTTATCGCGGATGAGCAGTATCGTCTTCAACA
130 CAACGTCATAATAGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
409624 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
1 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
* * * *
409689 TCACGAAGGAACCGTATTGTCCC-CA-GA----TTG--G-CCCGAATTCCTCATCACGAAGGAAC
66 TCACGAAAGAACCGTATTGTCCCAAATTATCTCTTGATGACCCGATTTCCTCATCACGAAGGAAC
* * *
409745 AACCTCATAATAAAAAATAACCCGATCTCTTCATCGCAGATGAGCAGTGTCGTCTTCAACA
131 AACGTCATAATAGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
* * * *
409806 TCAAACCGACCCGATCTCCTAATCACGAAGGAGCAATGTCACCCTCAAACAATCAAACTTCCTCA
1 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
409871 TCACGAAAGAACCGTATTGTCCTCAAATTATCTCTTGACTGACCCGATTTCCTCATCACGAAGGA
66 TCACGAAAGAACCGTATTGTCC-CAAATTATCTCTTGA-TGACCCGATTTCCTCATCACGAAGGA
* * *
409936 ACATCGTCATAATCGAAAATGACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
129 ACAACGTCATAATAGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
* *
409999 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGGCAATCAGACTTCCTCA
1 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
* * *
410064 TCA-TAAAGGAACCGTATTGCCCCCAAATTATCTCTTGATTGACCAGATTTCCTCATCACGAAGG
66 TCACGAAA-GAACCGTATTG-TCCCAAATTATCTCTTGA-TGACCCGATTTCCTCATCACGAAGG
410128 AACA
128 AACA
410132 TCGTGAGCAG
Statistics
Matches: 614, Mismatches: 57, Indels: 38
0.87 0.08 0.05
Matches are distributed among these distances:
181 2 0.00
182 317 0.52
183 4 0.01
184 1 0.00
185 2 0.00
189 3 0.00
190 1 0.00
192 10 0.02
193 272 0.44
194 2 0.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (191 bp):
TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
TCACGAAAGAACCGTATTGTCCCAAATTATCTCTTGATGACCCGATTTCCTCATCACGAAGGAAC
AACGTCATAATAGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
Found at i:410135 original size:193 final size:193
Alignment explanation
Indices: 409714--410131 Score: 649
Period size: 193 Copynumber: 2.2 Consensus size: 193
409704 ATTGTCCCCA
* * * *
409714 GATTGGCCCGAATTCCTCATCACGAAGGAACAACCTCATAATAAAAAATAACCCGATCTCTTCAT
1 GATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATAGAAAATAACCCGATCTCTTCAT
* * *
409779 CGCAGATGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTAATCACGAAGGAGCAATG
66 CGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTG
* * *
409844 TCACCCTCAAACAATCAAACTTCCTCATCACGAAA-GAACCGTATTGTCCTCAAATTATCTCTT
131 TCACCCTCAGACAATCAGACTTCCTCATCAC-AAAGGAACCGTATTGTCCCCAAATTATCTCTT
* * * *
409907 GACTGACCCGATTTCCTCATCACGAAGGAACATCGTCATAATCGAAAATGACCCGATCTCTTCAT
1 GATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATAGAAAATAACCCGATCTCTTCAT
*
409972 CGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTG
66 CGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTG
* * *
410037 TCACCCTCAGGCAATCAGACTTCCTCATCATAAAGGAACCGTATTGCCCCCAAATTATCTCTT
131 TCACCCTCAGACAATCAGACTTCCTCATCACAAAGGAACCGTATTGTCCCCAAATTATCTCTT
*
410100 GATTGACCAGATTTCCTCATCACGAAGGAACA
1 GATTGACCCGATTTCCTCATCACGAAGGAACA
410132 TCGTGAGCAG
Statistics
Matches: 204, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
192 3 0.01
193 201 0.99
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (193 bp):
GATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATAGAAAATAACCCGATCTCTTCAT
CGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTG
TCACCCTCAGACAATCAGACTTCCTCATCACAAAGGAACCGTATTGTCCCCAAATTATCTCTT
Found at i:421209 original size:33 final size:35
Alignment explanation
Indices: 421138--421209 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
421128 TTTTTATATT
*
421138 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TATATAAATATTATCAA
*
421174 TTTAATTTT-TAAAGAAA-ATATAAATATT-TACAA
1 TTTAATTTTGTAAAAAAATATATAAATATTAT-CAA
421207 TTT
1 TTT
421210 GTAATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 1 0.03
33 16 0.48
35 7 0.21
36 9 0.27
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAAATATATAAATATTATCAA
Found at i:421390 original size:20 final size:20
Alignment explanation
Indices: 421354--421391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
421344 ATCCTATTCC
**
421354 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
421374 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
421392 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:429135 original size:20 final size:20
Alignment explanation
Indices: 429061--429143 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
429051 AGCAGAACCC
*
429061 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
429080 CTGTGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGAATCGATT-CCC-T
** *
429103 CAAAGGGGAATCGGTTCCCT
1 CAGGGGGGAATCGATTCCCT
*
429123 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
429143 C
1 C
429144 TGCACAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.58
21 6 0.12
22 12 0.24
23 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.35, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:442579 original size:42 final size:41
Alignment explanation
Indices: 442513--442619 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 41
442503 TTCACAATTT
* * * *
442513 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * **
442554 CTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
442596 ATAAGTCCTTCGGACCATCCGTAA
1 ATAAATCCTTCGGGCCATCAGTAA
442620 AACCTTCGGG
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:442764 original size:214 final size:214
Alignment explanation
Indices: 442395--442797 Score: 707
Period size: 214 Copynumber: 1.9 Consensus size: 214
442385 AGTGAAGCAA
* *
442395 ACCATCCATAAGACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATGATGTTTTA
1 ACCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTA
* * *
442460 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
442525 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTTAGAGC
442590 AAGATGATAAGTCCTTCGG
196 AAGATGATAAGTCCTTCGG
* * *
442609 ACCATCCGTAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAACGATGTTTTG
1 ACCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTA
442674 AGAAGATGAAATTTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCG
*
442739 GTCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTT
131 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTT
442798 CACCGAAGAG
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 178 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (214 bp):
ACCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTA
AGAAGATGAAATTTTTGAAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGG
Found at i:442897 original size:42 final size:42
Alignment explanation
Indices: 442835--442916 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
442825 CAGTAAGTGA
*
442835 CATCAGTAAGTCTTTTGAGCATGATGATGAAATCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
*
442877 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
442917 ATAATTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
Found at i:443025 original size:42 final size:41
Alignment explanation
Indices: 442962--443048 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
442952 AAATTCATCA
*
442962 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGCCATTT
* *
443004 GTAAGTCTTTCGAGTGA-GATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAG-CATGATGATAAATCCTTCGGGCCATTT
443045 -TAAG
1 GTAAG
443049 CCTTCTCGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 4 0.10
41 16 0.39
42 20 0.49
43 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGCCATTT
Found at i:448827 original size:23 final size:23
Alignment explanation
Indices: 448801--448845 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
448791 TATATGTTCA
* *
448801 TAAACGTATTCATTTAGTGTTTG
1 TAAACATATACATTTAGTGTTTG
*
448824 TAAACATGTACATTTAGTGTTT
1 TAAACATATACATTTAGTGTTT
448846 ATGAACATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (23 bp):
TAAACATATACATTTAGTGTTTG
Found at i:448852 original size:23 final size:23
Alignment explanation
Indices: 448811--448855 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
448801 TAAACGTATT
*
448811 CATTTAGTGTTTGTAAACATGTA
1 CATTTAGTGTTTATAAACATGTA
*
448834 CATTTAGTGTTTATGAACATGT
1 CATTTAGTGTTTATAAACATGT
448856 TTGTTCAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (23 bp):
CATTTAGTGTTTATAAACATGTA
Found at i:449165 original size:12 final size:12
Alignment explanation
Indices: 449121--449165 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
449111 AACATAAATG
*
449121 AATGAGTTGATA
1 AATGAGTTCATA
449133 AATGAGCTT-ATA
1 AATGAG-TTCATA
*
449145 AACGAGTTCATA
1 AATGAGTTCATA
449157 AATGAGTTC
1 AATGAGTTC
449166 GTTCGTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (12 bp):
AATGAGTTCATA
Found at i:463197 original size:2 final size:2
Alignment explanation
Indices: 463190--463220 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
463180 ATATTATTAT
463190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
463221 TACAAGCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:464598 original size:11 final size:11
Alignment explanation
Indices: 464582--464651 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
464572 TTCATTTTAA
464582 TTATTATTATT
1 TTATTATTATT
464593 TTATTATTACTT
1 TTATTATTA-TT
464605 TTGA-TA-TATGT
1 TT-ATTATTAT-T
464616 TTAAATTATTATCT
1 TT--ATTATTAT-T
* *
464630 TCATGATTATT
1 TTATTATTATT
464641 TTATTATTATT
1 TTATTATTATT
464652 ATTAAGTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 1 0.02
11 24 0.51
12 14 0.30
13 3 0.06
14 5 0.11
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (11 bp):
TTATTATTATT
Found at i:465045 original size:140 final size:139
Alignment explanation
Indices: 464780--465046 Score: 319
Period size: 140 Copynumber: 1.9 Consensus size: 139
464770 TTGATATATT
* * *
464780 TTTATTTTTTAATATCTAAGAAAAGAGCTGTCTTAAAATACCTAGAAGTCCTTTTCTGATATTCT
1 TTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCTTTTCTGATATTCT
* * * * **
464845 TAAATAAATAAATGTCCTAATTTTATAAATTGTATATATATTAATCTATTTTTTAGATAAATGTT
66 TAAATAAATAAATATCCTAATTTTATAAATTATAAATATATTAA-CAATTTAGTAGATAAATGTT
464910 TTAATATTTA
130 TTAATATTTA
* *
464920 TTTATTTTTTAATATCAAAGGAAGGAACTGTCTTAAAACACCTAGAAG-CTCTTTTCTGATATT-
1 TTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTC-CTTTTCTGATATTC
* *
464983 TCTAAATAAATAAATAT-CTTATTTATATAAATTAATAAATTTACTTAA-AATTATAGTA-ATAA
65 T-TAAATAAATAAATATCCTAATTT-TATAAATT-ATAAATATA-TTAACAATT-TAGTAGATAA
465045 AT
125 AT
465047 TTGAATTAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
139 8 0.07
140 87 0.81
141 9 0.08
142 4 0.04
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (139 bp):
TTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCTTTTCTGATATTCT
TAAATAAATAAATATCCTAATTTTATAAATTATAAATATATTAACAATTTAGTAGATAAATGTTT
TAATATTTA
Found at i:469829 original size:2 final size:2
Alignment explanation
Indices: 469822--469875 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
469812 TGTTTCATTA
469822 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
469864 AT AT AT AT AT AT
1 AT AT AT AT AT AT
469876 CCTTGGTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470089 original size:18 final size:17
Alignment explanation
Indices: 470061--470094 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
470051 CTTGTCCAAC
470061 AAAGAAAGAAGAAAAAA
1 AAAGAAAGAAGAAAAAA
470078 AAAGAGAAGAAGAAAAA
1 AAAGA-AAGAAGAAAAA
470095 GGAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAGAAAAAA
Found at i:472481 original size:83 final size:83
Alignment explanation
Indices: 472336--472720 Score: 540
Period size: 83 Copynumber: 4.6 Consensus size: 83
472326 GAACAAATGC
* * *
472336 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
* *
472401 CATTGAAATTGGAAGAGG
66 CATTGAAATTGAAAGATG
* * * *
472419 AATGTGCTAACT-CCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAG
1 AATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAA
* *
472483 TTATTGAATTTGAAAGATG
65 TCATTGAAATTGAAAGATG
* *
472502 AATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
* *
472567 CATTGAATTTGGAAGATG
66 CATTGAAATTGAAAGATG
* * * * *
472585 AATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGATTTATCTGATATGGTTTGGCAGAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
* *
472650 TATT-AAATCTTAAAGATG
66 CATTGAAAT-TGAAAGATG
472668 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
472721 AGTATGAACC
Statistics
Matches: 268, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
82 4 0.01
83 263 0.98
84 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
CATTGAAATTGAAAGATG
Found at i:472616 original size:166 final size:166
Alignment explanation
Indices: 472336--472720 Score: 603
Period size: 166 Copynumber: 2.3 Consensus size: 166
472326 GAACAAATGC
* * *
472336 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
* *
472401 CATTGAAATTGGAAGAGGAATGTGCTAACTCCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 CATTGAAATTGGAAGAGGAATATGCTAACTCCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATA
* *
472466 TGGTTTGGTAAAACCAGTTATTGAAT-TTGAAAGATG
131 TGGTTTGGCAAAACCAGTTATTAAATCTT-AAAGATG
* *
472502 AATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
* * * * *
472567 CATTGAATTTGGAAGATGAATATGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGATTTATCTGAT
66 CATTGAAATTGGAAGAGGAATATGCTAACT-CCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
*
472631 ATGGTTTGGCAGAACCAGTTATTAAATCTTAAAGATG
130 ATGGTTTGGCAAAACCAGTTATTAAATCTTAAAGATG
472668 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
472721 AGTATGAACC
Statistics
Matches: 201, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 1 0.00
166 198 0.99
167 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (166 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
CATTGAAATTGGAAGAGGAATATGCTAACTCCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATA
TGGTTTGGCAAAACCAGTTATTAAATCTTAAAGATG
Found at i:474067 original size:74 final size:75
Alignment explanation
Indices: 473975--474146 Score: 222
Period size: 74 Copynumber: 2.3 Consensus size: 75
473965 ATTAACAAGA
* * *
473975 AGCAAATATTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
474040 TA-TT-TATC
66 CACTTGTATC
* * ** *
474048 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
474113 ACACTTGTATT
65 ACACTTGTATC
*
474124 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
474147 GGCCCACAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 3 0.04
74 55 0.65
75 21 0.25
76 6 0.07
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:475093 original size:54 final size:53
Alignment explanation
Indices: 475022--475176 Score: 220
Period size: 54 Copynumber: 2.9 Consensus size: 53
475012 GAAATCTTGG
*
475022 CAGAAGCCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGACCATCTGAA
1 CAGAAGCCACAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* * *
475076 CAGAAACCACATGAAAGGATGAATGTGTTATCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
***
475130 CAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCAC-AGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
475177 CTGCTATTCT
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 88 0.98
55 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (53 bp):
CAGAAGCCACAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:476314 original size:76 final size:76
Alignment explanation
Indices: 476232--476646 Score: 776
Period size: 76 Copynumber: 5.5 Consensus size: 76
476222 CTATTTCCCA
*
476232 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
476297 AGCCTTAGGGT
66 AGCCTTAGGGT
476308 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
476373 AGCCTTAGGGT
66 AGCCTTAGGGT
*
476384 TATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
476449 AGCCTTCGGGT
66 AGCCTTAGGGT
* *
476460 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
476525 AGCCTTAGGGT
66 AGCCTTAGGGT
476536 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
476601 AGCCTTAGGGT
66 AGCCTTAGGGT
*
476612 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
476647 CATTTCCATC
Statistics
Matches: 329, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 329 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:476797 original size:15 final size:15
Alignment explanation
Indices: 476777--476815 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
476767 TTAAATTTTA
*
476777 TTATTATTATTAAAT
1 TTATTATTACTAAAT
476792 TTATTATTACTAAAT
1 TTATTATTACTAAAT
*
476807 ATA-TATTAC
1 TTATTATTAC
476816 AAGCCCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTATTACTAAAT
Found at i:478983 original size:21 final size:21
Alignment explanation
Indices: 478959--479019 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
478949 AACTTTGAAA
478959 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
478980 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
478994 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
479015 AAATG
1 AAATG
479020 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:479050 original size:37 final size:37
Alignment explanation
Indices: 478951--479069 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
478941 CAGTAACCAA
478951 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
478988 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
479023 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
479060 -GTTGAAAAAT
1 CTTTGAAAAAT
479070 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:479973 original size:36 final size:36
Alignment explanation
Indices: 479926--480002 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
479916 AGTACACAAT
479926 TACTTTGGATTATATTTCACTCTAGTTAGATCTCCC
1 TACTTTGGATTATATTTCACTCTAGTTAGATCTCCC
479962 TACTTTGGATTATATTTCACTCTAGTTAGATCTCCC
1 TACTTTGGATTATATTTCACTCTAGTTAGATCTCCC
*
479998 AACTT
1 TACTT
480003 CATGGTTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.44
Consensus pattern (36 bp):
TACTTTGGATTATATTTCACTCTAGTTAGATCTCCC
Found at i:480742 original size:17 final size:17
Alignment explanation
Indices: 480720--480753 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
480710 ACCGAGTGTT
480720 GACTTGGTTAGTTTTAG
1 GACTTGGTTAGTTTTAG
480737 GACTTGGTTAGTTTTAG
1 GACTTGGTTAGTTTTAG
480754 TTGTTATTCT
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:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (17 bp):
GACTTGGTTAGTTTTAG
Found at i:490533 original size:120 final size:114
Alignment explanation
Indices: 490322--490557 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 114
490312 AAGCCTTTTT
* *
490322 TTTGGCTGACACCTGTCTATAAATGATTTTCACCGTTAAAAACACTAATGTGTCATATTTAACTA
1 TTTGGCTGACACCTATCTATAAATGATTTTCACCGATAAAAACACTAATGTGTCATATTTAACTA
* * *
490387 GTCATTTTGCTTGCAATGATATTGAATTATATTTTCTATTGGGTCCTTTG
66 ATCATTTCGCTTGCAATGATATTGAATTATA-TTTCTATTGGGGCCTTTG
* **
490437 TTTGGCTGACACCTAATATCTATAAATGTTTTTCATTGATAAAAACACTAATGCCT-TCATGATT
1 TTTGGCTGACACC---TATCTATAAATGATTTTCACCGATAAAAACACTAATG--TGTCAT-ATT
** * *
490501 TAGTTAATCATTTCGCTTGCAATGATATTGAATTATATTTCTTTTGGGGCTTTTG
60 TAACTAATCATTTCGCTTGCAATGATATTGAATTATATTTCTATTGGGGCCTTTG
490556 TT
1 TT
490558 ATAATTTGGT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
115 13 0.13
118 32 0.31
119 21 0.20
120 37 0.36
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (114 bp):
TTTGGCTGACACCTATCTATAAATGATTTTCACCGATAAAAACACTAATGTGTCATATTTAACTA
ATCATTTCGCTTGCAATGATATTGAATTATATTTCTATTGGGGCCTTTG
Found at i:499835 original size:22 final size:22
Alignment explanation
Indices: 499807--499859 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
499797 GTTACTAAAT
499807 AATATTTTATATAAAATATTAG
1 AATATTTTATATAAAATATTAG
499829 AATATTTTATATAAAATATTAG
1 AATATTTTATATAAAATATTAG
499851 AATATTTTA
1 AATATTTTA
499860 AATATGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
AATATTTTATATAAAATATTAG
Found at i:500443 original size:6 final size:6
Alignment explanation
Indices: 500432--500470 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
500422 TAATATGATT
* * *
500432 TTTTAA TTTTAA TTTTAT TTTTAT TTTTAT TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
500471 GATCGATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAA
Found at i:500453 original size:12 final size:12
Alignment explanation
Indices: 500432--500470 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
500422 TAATATGATT
*
500432 TTTTAATTTTAA
1 TTTTATTTTTAA
*
500444 TTTTATTTTTAT
1 TTTTATTTTTAA
500456 TTTTATTTTTAA
1 TTTTATTTTTAA
500468 TTT
1 TTT
500471 GATCGATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:500459 original size:7 final size:6
Alignment explanation
Indices: 500431--500466 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
500421 TTAATATGAT
* *
500431 TTTTTA ATTTTA ATTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
500467 ATTTGATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:508207 original size:19 final size:19
Alignment explanation
Indices: 508183--508220 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
508173 TAACTCCGAG
508183 GGCTTGTCTGTCGAGAAGA
1 GGCTTGTCTGTCGAGAAGA
508202 GGCTTGTCTGTCGAGAAGA
1 GGCTTGTCTGTCGAGAAGA
508221 ACTCAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (19 bp):
GGCTTGTCTGTCGAGAAGA
Found at i:508229 original size:19 final size:19
Alignment explanation
Indices: 508188--508229 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
508178 CCGAGGGCTT
* *
508188 GTCTGTCGAGAAGAGGCTT
1 GTCTGTCGAGAAGAGACTA
508207 GTCTGTCGAGAAGA-ACTCA
1 GTCTGTCGAGAAGAGACT-A
508226 GTCT
1 GTCT
508230 TCATTCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (19 bp):
GTCTGTCGAGAAGAGACTA
Found at i:513899 original size:18 final size:18
Alignment explanation
Indices: 513868--513914 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
513858 TCTTGTGCAC
513868 AAAAA-AAT-AAATATTT
1 AAAAATAATAAAATATTT
513884 AAAAATAATAAAATATTT
1 AAAAATAATAAAATATTT
* *
513902 AGAAATTATAAAA
1 AAAAATAATAAAA
513915 ATTGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 5 0.19
17 3 0.11
18 19 0.70
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATAATAAAATATTT
Found at i:516326 original size:15 final size:16
Alignment explanation
Indices: 516293--516327 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
516283 CTAGAGCTGG
*
516293 CAATGCTGACCCAAAC
1 CAATCCTGACCCAAAC
516309 CAATCCTGACCC-AAC
1 CAATCCTGACCCAAAC
516324 CAAT
1 CAAT
516328 TTGAACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.37, C:0.40, G:0.09, T:0.14
Consensus pattern (16 bp):
CAATCCTGACCCAAAC
Found at i:517382 original size:32 final size:33
Alignment explanation
Indices: 517346--517411 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 33
517336 ATAAGTATGC
517346 ACATTAACCATACTC-AAAGAAAATATCTAAAT
1 ACATTAACCATACTCAAAAGAAAATATCTAAAT
517378 ACATTAACCATACTCTAAAAGAAAATATCTAAAT
1 ACATTAACCATACTC-AAAAGAAAATATCTAAAT
517412 CTCAGTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 15 0.47
34 17 0.53
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (33 bp):
ACATTAACCATACTCAAAAGAAAATATCTAAAT
Found at i:519403 original size:29 final size:29
Alignment explanation
Indices: 519359--519416 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
519349 AAAATAAAAA
* *
519359 ACATAAATAGGGGTTCATTTCTTTTATTT
1 ACATAAATAAGAGTTCATTTCTTTTATTT
519388 ACATAAATAAGAGTTCATTTCTTTTATTT
1 ACATAAATAAGAGTTCATTTCTTTTATTT
519417 CGCCCCGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
ACATAAATAAGAGTTCATTTCTTTTATTT
Found at i:526281 original size:17 final size:16
Alignment explanation
Indices: 526242--526297 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
526232 CTATAAAAAA
*
526242 ATTAATTAAA-TATAAT
1 ATTAAATAAATTA-AAT
*
526258 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
526274 ACTTAAATAAATT-AAT
1 A-TTAAATAAATTAAAT
*
526290 ATAAAATA
1 ATTAAATA
526298 TACATTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:533558 original size:35 final size:34
Alignment explanation
Indices: 533473--533559 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
533463 ATTTGGTATT
*
533473 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
533507 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
533545 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
533560 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:534147 original size:18 final size:18
Alignment explanation
Indices: 534124--534158 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
534114 GCGATGGCGG
534124 CATCATATATGGCTGCGA
1 CATCATATATGGCTGCGA
534142 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
534159 GTGGCTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:535808 original size:111 final size:111
Alignment explanation
Indices: 535671--535892 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
535661 ATTACAAAAA
*
535671 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
535736 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
535782 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
535847 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
535893 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:537854 original size:26 final size:27
Alignment explanation
Indices: 537799--537854 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
537789 TCGTTAAAAA
*
537799 AAATTATTATTTGATTCGTTGCTTGTT
1 AAATTATTATTTGATTCGTTGCTCGTT
* *
537826 AAATTTTTATTTGATTTG-TGCTCGTT
1 AAATTATTATTTGATTCGTTGCTCGTT
537852 AAA
1 AAA
537855 AATATTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (27 bp):
AAATTATTATTTGATTCGTTGCTCGTT
Found at i:538333 original size:12 final size:12
Alignment explanation
Indices: 538311--538343 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
538301 CGTTAAGATC
538311 TCAAG-TCGAAT
1 TCAAGTTCGAAT
538322 TCAAGTTCGAAT
1 TCAAGTTCGAAT
*
538334 TCGAGTTCGA
1 TCAAGTTCGA
538344 GTTGCTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (12 bp):
TCAAGTTCGAAT
Found at i:540840 original size:45 final size:42
Alignment explanation
Indices: 540736--540828 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
540726 CTGAAGGCGT
*
540736 TGATGGTGTCGGTGTTGGGTGGTAGCCACCACCGCTTCCATG
1 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
540778 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
1 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
540820 TGATGGTGT
1 TGATGGTGT
540829 TTCATGAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.13, C:0.22, G:0.37, T:0.29
Consensus pattern (42 bp):
TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
Found at i:546513 original size:21 final size:20
Alignment explanation
Indices: 546427--546625 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
546417 AAATGACCAA
**
546427 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
546446 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
546466 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
546486 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
546507 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
546528 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
546548 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
546569 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
546589 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
546610 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
546626 ACACATAAAT
Statistics
Matches: 134, Mismatches: 39, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
19 16 0.12
20 56 0.42
21 62 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:546575 original size:20 final size:20
Alignment explanation
Indices: 546427--546644 Score: 113
Period size: 20 Copynumber: 10.8 Consensus size: 20
546417 AAATGACCAA
546427 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
546446 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
546466 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
546485 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
546507 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
546527 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
546548 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
546569 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
546589 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
546610 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
546629 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
546645 TATCCGTAAA
Statistics
Matches: 146, Mismatches: 42, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 69 0.47
21 58 0.40
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:546587 original size:41 final size:41
Alignment explanation
Indices: 546508--546619 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
546498 GCGATTCTTG
*
546508 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
546550 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
546591 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
546620 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:546654 original size:20 final size:20
Alignment explanation
Indices: 546592--546762 Score: 218
Period size: 20 Copynumber: 8.6 Consensus size: 20
546582 CGATTTTCCA
* ** *
546592 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
546612 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
546632 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
546652 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
546672 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
546692 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
546712 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
546732 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
546752 AAATCGCAACG
1 AAATCGCAACG
546763 ATAATACATA
Statistics
Matches: 132, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 129 0.98
21 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:547204 original size:33 final size:33
Alignment explanation
Indices: 547165--547235 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
547155 TTCACTTAGA
* *
547165 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
547198 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
547231 TTTCA
1 TTTCA
547236 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:547341 original size:21 final size:20
Alignment explanation
Indices: 547315--547420 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
547305 TGTAGAAGAG
547315 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
547336 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
547356 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
547377 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
547391 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
547410 TCGCAACGAGA
1 TCGCAACGAGA
547421 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:547359 original size:20 final size:21
Alignment explanation
Indices: 547313--547391 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
547303 TTTGTAGAAG
*
547313 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
547335 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
547354 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
547376 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
547392 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:547372 original size:41 final size:38
Alignment explanation
Indices: 547308--547424 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
547298 TTCAATTTGT
* *
547308 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
547346 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
547387 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
547420 AGAAT
1 AGAAT
547425 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:547397 original size:14 final size:14
Alignment explanation
Indices: 547378--547431 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
547368 AAATGAAAAG
547378 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
547392 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
547411 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
547425 CGCAACG
1 CGCAACG
547432 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:547407 original size:33 final size:33
Alignment explanation
Indices: 547367--547436 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
547357 CGCAACGAGA
547367 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
547400 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
547433 GAAA
1 GAAA
547437 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:547443 original size:33 final size:33
Alignment explanation
Indices: 547373--547447 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
547363 GAGAGAAATG
* **
547373 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
547406 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
547439 AAAATCGCA
1 AAAATCGCA
547448 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:547465 original size:19 final size:19
Alignment explanation
Indices: 547443--547540 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
547433 GAAACCAAAA
*
547443 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
547462 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
547476 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
547495 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
547509 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
547528 TCGCGTTGCGATT
1 TCGCGTTGCGATT
547541 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:547484 original size:14 final size:14
Alignment explanation
Indices: 547465--547554 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
547455 TTTCATTTCG
547465 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
547479 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
547498 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
547512 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
547529 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
547545 CGTTGCGATT
1 CGTTGCGATT
547555 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:547490 original size:33 final size:33
Alignment explanation
Indices: 547448--547562 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
547438 CAAAATCGCA
547448 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
547481 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
547514 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
547547 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
547563 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:549409 original size:92 final size:92
Alignment explanation
Indices: 549253--549447 Score: 365
Period size: 93 Copynumber: 2.1 Consensus size: 92
549243 TAGATTGCTT
549253 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTA-
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
549317 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
549344 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
549409 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
549437 AGTAAATTTAT
1 AGTAAATTTAT
549448 CCATTCAAGT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 31 0.31
92 32 0.32
93 37 0.37
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (92 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:549529 original size:19 final size:20
Alignment explanation
Indices: 549489--549532 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
549479 TAGTTTACTT
*
549489 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAACTCAAAA
*
549509 TCGCAACGCGAAAC-CAAAA
1 TCGCAACACGAAACTCAAAA
549528 TCGCA
1 TCGCA
549533 TTGCGATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.45, C:0.30, G:0.14, T:0.11
Consensus pattern (20 bp):
TCGCAACACGAAACTCAAAA
Found at i:549569 original size:19 final size:19
Alignment explanation
Indices: 549545--549643 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
549535 GCGATTCTTT
549545 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
549564 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
549578 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
549597 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
* *
549616 CGTTGTGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
549636 TGTTGCGA
1 CGTTGCGA
549644 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.17
16 1 0.02
17 1 0.02
18 1 0.02
19 39 0.60
20 12 0.18
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:549575 original size:33 final size:33
Alignment explanation
Indices: 549528--549606 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
549518 GAAACCAAAA
* * **
549528 TCGCATTGCGATTCTTTCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTCTGTCGTTGCGATTTTCATT
549561 TCGCGTTGCGATTCTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTGTCGTTGCGATTTTCATT
549594 TCGCGTTGCGATT
1 TCGCGTTGCGATT
549607 TTGGTTTCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (33 bp):
TCGCGTTGCGATTCTGTCGTTGCGATTTTCATT
Found at i:551476 original size:12 final size:12
Alignment explanation
Indices: 551459--551496 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
551449 AGTTGATTCA
551459 ATTGTTTAATTG
1 ATTGTTTAATTG
*
551471 ATTGTTT-TTTG
1 ATTGTTTAATTG
551482 ATTGTTTAATTG
1 ATTGTTTAATTG
551494 ATT
1 ATT
551497 TGTAAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (12 bp):
ATTGTTTAATTG
Found at i:551583 original size:14 final size:14
Alignment explanation
Indices: 551564--551599 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
551554 ATTGTTTAAT
551564 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
551578 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
551592 TGATTTGT
1 TGATTTGT
551600 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:551722 original size:19 final size:19
Alignment explanation
Indices: 551706--551822 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
551696 AAAAATGACT
551706 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
551725 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
551744 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
551763 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
551777 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
551796 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
551816 ATCGCAA
1 ATCGCAA
551823 CGAGAGAACC
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.64
20 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:551785 original size:33 final size:36
Alignment explanation
Indices: 551706--551822 Score: 159
Period size: 33 Copynumber: 3.2 Consensus size: 36
551696 AAAAATGACT
551706 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
551744 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
551777 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
551816 ATCGCAA
1 ATCGCAA
551823 CGAGAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.41
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.38
39 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:551788 original size:52 final size:53
Alignment explanation
Indices: 551724--551840 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
551714 GCGAAATGAA
551724 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
551776 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
*
551829 AACCGCAATGCG
1 AATCGCAATGCG
551841 TTTATAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:551884 original size:33 final size:33
Alignment explanation
Indices: 551847--552103 Score: 261
Period size: 33 Copynumber: 7.5 Consensus size: 33
551837 TGCGTTTATA
551847 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
551880 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
*
551918 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
551951 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
551991 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
552022 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
552055 ATTTCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
*
552088 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
552104 GTAATTTCCG
Statistics
Matches: 190, Mismatches: 17, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
31 9 0.05
32 5 0.03
33 105 0.55
34 1 0.01
35 12 0.06
36 11 0.06
37 2 0.01
38 33 0.17
39 3 0.02
40 9 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:551893 original size:19 final size:19
Alignment explanation
Indices: 551869--552103 Score: 285
Period size: 19 Copynumber: 13.4 Consensus size: 19
551859 GATTCTCTCG
551869 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
551888 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
551907 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
551926 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
551940 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
551959 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
551978 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
551992 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
552011 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
552030 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
552044 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
552063 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
552077 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
552096 TTGCGATT
1 TTGCGATT
552104 GTAATTTCCG
Statistics
Matches: 188, Mismatches: 8, Indels: 40
0.80 0.03 0.17
Matches are distributed among these distances:
14 29 0.15
16 23 0.12
17 23 0.12
19 113 0.60
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:551944 original size:52 final size:52
Alignment explanation
Indices: 551888--552075 Score: 367
Period size: 52 Copynumber: 3.6 Consensus size: 52
551878 TCATTTCGCA
*
551888 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
551940 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
551992 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
552044 TTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCAT
552076 GTTGGGATTT
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 135 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:552111 original size:52 final size:51
Alignment explanation
Indices: 551880--552103 Score: 326
Period size: 52 Copynumber: 4.3 Consensus size: 51
551870 TGCGATTTTC
*
551880 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
551931 A-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTC-G-CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
551983 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATT-TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* * * *
552035 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATGTTGGGATTTTC-
1 ATT-TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT-TTCGCA-TTGCG
552088 ATTTCGCGTTGCGATT
1 ATTTCGCGTTGCGATT
552104 GTAATTTCCG
Statistics
Matches: 161, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
50 3 0.02
51 2 0.01
52 143 0.89
53 8 0.05
54 5 0.03
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (51 bp):
ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
Found at i:554400 original size:12 final size:12
Alignment explanation
Indices: 554383--554407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
554373 TCTTCGGGGA
554383 CTTTTTCTTCTT
1 CTTTTTCTTCTT
554395 CTTTTTCTTCTT
1 CTTTTTCTTCTT
554407 C
1 C
554408 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:554616 original size:24 final size:24
Alignment explanation
Indices: 554582--554628 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
554572 CTGAAACATC
554582 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
554606 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
554629 GACCAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:555336 original size:20 final size:20
Alignment explanation
Indices: 555308--555557 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
555298 AAATTTCAGT
* *
555308 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
555328 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
555348 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
555368 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
555388 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
555408 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
555428 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
555448 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
555468 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
555488 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
555508 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
555528 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
555548 GTTGCGATTT
1 GTTGCGATTT
555558 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:555574 original size:21 final size:21
Alignment explanation
Indices: 555544--555626 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
555534 ATTTTCATAT
*
555544 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
555565 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
555586 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
555607 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
555627 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:555617 original size:42 final size:43
Alignment explanation
Indices: 555524--555622 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
555514 ATTTATGTGT
* *
555524 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
555565 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
555607 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
555623 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:559211 original size:36 final size:36
Alignment explanation
Indices: 559159--559271 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
559149 CTTGCACCAA
559159 TTTCATCTCAGA-CTGCAACAAGGATGTAGCCTTCAG
1 TTTCATCTCA-ATCTGCAACAAGGATGTAGCCTTCAG
***
559195 TTTCATCTCAATCTGCAATTGGGATGTAGCC-TCTAG
1 TTTCATCTCAATCTGCAACAAGGATGTAGCCTTC-AG
* * * *
559231 TTTCATCTC-ATAATGCAGCATGGATGCAGCCTTCAG
1 TTTCATCTCAAT-CTGCAACAAGGATGTAGCCTTCAG
559267 TTTCA
1 TTTCA
559272 GCTCTACCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
35 5 0.08
36 57 0.89
37 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (36 bp):
TTTCATCTCAATCTGCAACAAGGATGTAGCCTTCAG
Found at i:565266 original size:5 final size:5
Alignment explanation
Indices: 565239--565319 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
565229 TATAATCTTA
* * *
565239 ATTTT ATTGTT ATTTTT ACTTT ATTTT ATCTC ATTTTT ATTTT ATTTT
1 ATTTT ATT-TT A-TTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT
*
565287 ATTTT ATTTT ATCATTT A--TC ATTTT ATTTT ATT
1 ATTTT ATTTT AT--TTT ATTTT ATTTT ATTTT ATT
565320 AATTGTTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 2 0.03
5 44 0.72
6 9 0.15
7 6 0.10
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:565277 original size:16 final size:15
Alignment explanation
Indices: 565258--565299 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
565248 TTATTTTTAC
565258 TTTATTTTATCTCATT
1 TTTATTTTATCTCA-T
* *
565274 TTTATTTTATTTTAT
1 TTTATTTTATCTCAT
565289 TTTATTTTATC
1 TTTATTTTATC
565300 ATTTATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTATCTCAT
Found at i:565295 original size:21 final size:21
Alignment explanation
Indices: 565239--565319 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 21
565229 TATAATCTTA
*
565239 ATTTTATTGTTATTTTTACTTT
1 ATTTTATT-TTATTTTTATTTT
* *
565261 ATTTTATCTCATTTTTATTTT
1 ATTTTATTTTATTTTTATTTT
565282 ATTTTATTTTATTTTATCATTTAT
1 ATTTTATTTTATTTT-T-ATTT-T
565306 CATTTTATTTTATT
1 -ATTTTATTTTATT
565320 AATTGTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 24 0.48
22 8 0.16
23 4 0.08
24 1 0.02
25 13 0.26
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (21 bp):
ATTTTATTTTATTTTTATTTT
Found at i:572072 original size:184 final size:183
Alignment explanation
Indices: 571760--572118 Score: 641
Period size: 184 Copynumber: 2.0 Consensus size: 183
571750 ATTAAATTTT
571760 AAATATTATATATATTATATATAACATATGAGCTCAACCCAAACAATTTAAAACCCAATTAATAA
1 AAATATTATATATATTATATATAACATATGAGCTCAACCCAAACAATTTAAAACCCAATTAATAA
571825 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
571890 TTATTTTATAATTACATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAA
131 TTATTTTATAATTACATATTATTTAAATTAATTATAAACT-TTTTTTTAATTAA
*
571944 AAATATTATATATATTATATATAACATATG-GACT-AAGCCCAAACCATTTAAAACCCAATTAAT
1 AAATATTATATATATTATATATAACATATGAG-CTCAA-CCCAAACAATTTAAAACCCAATTAAT
*
572007 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATGTAAAAT
64 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
*
572072 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTT
129 TTTTATTTTATAATTACATATTATTTAAATTAATTATAAACTTTTTT
572119 AGAATAAAAA
Statistics
Matches: 169, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
183 8 0.05
184 161 0.95
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (183 bp):
AAATATTATATATATTATATATAACATATGAGCTCAACCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTACATATTATTTAAATTAATTATAAACTTTTTTTTAATTAA
Found at i:572264 original size:31 final size:30
Alignment explanation
Indices: 572206--572265 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
572196 CCGAAATTTA
**
572206 TTCGGTTCGGTTAATATTTTAGAAAAAAAG
1 TTCGGTTCGGTTAATATTAAAGAAAAAAAG
*
572236 TTCGGTTCGGTTAATGGTTAAAGAAAAAAA
1 TTCGGTTCGGTTAAT-ATTAAAGAAAAAAA
572266 AAGTTTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (30 bp):
TTCGGTTCGGTTAATATTAAAGAAAAAAAG
Found at i:573518 original size:2 final size:2
Alignment explanation
Indices: 573511--573539 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
573501 TTAGATATGT
573511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
573540 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:573544 original size:2 final size:2
Alignment explanation
Indices: 573539--573565 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
573529 TATATATATA
573539 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
573566 TCATAGTAAT
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:587038 original size:51 final size:51
Alignment explanation
Indices: 586981--587185 Score: 238
Period size: 51 Copynumber: 4.0 Consensus size: 51
586971 AACTTGAAAA
* * * *
586981 ATCTTCAAATGATAAGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTTG
1 ATCTTCAAATAATAAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* *
587032 ATCTTCAACA-AATATGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCG
1 ATCTTCAA-ATAATAAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* ** * *
587083 ATCTTCAAAAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
1 ATCTTCAAATAATAAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
*
587134 ATCTTC-AATAA-ACATGTCCGCTCCCTATTGCTTCAGAGAGTAT-GGAACTCG
1 ATCTTCAAATAATA-A-GTCCGCTCCCTATTCCTTCAGAGAGTATAGG-ACTCG
587185 A
1 A
587186 ACATCTTCTT
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
50 6 0.05
51 126 0.95
52 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (51 bp):
ATCTTCAAATAATAAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
Found at i:587108 original size:102 final size:102
Alignment explanation
Indices: 586996--587185 Score: 301
Period size: 102 Copynumber: 1.9 Consensus size: 102
586986 CAAATGATAA
* * * *
586996 GTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAATATGTCCACTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
587061 CCTTCAGAGAGTATAGG-ACTCGATCTTCAAAAAATGT
66 CCTTCAGAGAGTAT-GGAACTCGATCTTCAAAAAATGT
* *
587098 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACATGTCCGCTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
*
587163 GCTTCAGAGAGTATGGAACTCGA
66 CCTTCAGAGAGTATGGAACTCGA
587186 ACATCTTCTT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 2 0.03
102 78 0.98
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (102 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
CCTTCAGAGAGTATGGAACTCGATCTTCAAAAAATGT
Found at i:587229 original size:54 final size:54
Alignment explanation
Indices: 587171--587413 Score: 423
Period size: 54 Copynumber: 4.5 Consensus size: 54
587161 TTGCTTCAGA
*
587171 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
587225 GAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
587279 GAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
587333 GAGTATGGAACTCGAACATCTTCTTCTTATGGGTTCACTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
587387 GAGTATGGAACTTGAACATGTTCTTCT
1 GAGTATGGAACTCGAACATCTTCTTCT
587414 GCTTTACTAC
Statistics
Matches: 182, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 182 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.37
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:587841 original size:37 final size:37
Alignment explanation
Indices: 587790--587913 Score: 153
Period size: 37 Copynumber: 3.4 Consensus size: 37
587780 TTGCTCCAAC
* * *
587790 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
*
587827 ACTCTTCGGTGAAGGCTTAAGATA-G-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAA-AAAGGATTTGCTTCACT
* * *
587863 ACTCTTTGGTGAAGGCTCAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
*
587900 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
587914 ACTTGGCTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 1 0.01
36 29 0.38
37 44 0.58
38 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
Found at i:597835 original size:21 final size:21
Alignment explanation
Indices: 597809--597882 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
597799 GTTTCCAGAT
*
597809 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTGGACTA
597830 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
* *
597851 TCGCAATGCAAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
*
597872 TCGCAATGCGA
1 TCGCAACGCGA
597883 TTTACATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:597921 original size:21 final size:21
Alignment explanation
Indices: 597891--597985 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
597881 GATTTACATA
*
597891 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
597912 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
597933 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
597954 TT--CGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
597973 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
597986 TTATTCCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 14 0.23
21 48 0.77
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:597961 original size:19 final size:19
Alignment explanation
Indices: 597937--598002 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
597927 TCCAAGTTCG
597937 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* ** * *
597956 CGTTGCAATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
597975 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
597998 CGTTG
1 CGTTG
598003 TGATAGTCCA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 14 0.42
21 12 0.36
22 1 0.03
23 6 0.18
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:598009 original size:42 final size:40
Alignment explanation
Indices: 597916--598013 Score: 151
Period size: 40 Copynumber: 2.4 Consensus size: 40
597906 TCCAAGTTCG
597916 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
* *
597956 CGTTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATT
*
597998 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
598014 AATCGTAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 27 0.53
41 2 0.04
42 22 0.43
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:598013 original size:61 final size:60
Alignment explanation
Indices: 597897--598019 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
597887 CATATTCGCA
* * ** *
597897 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCAATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGATAGTCCAAAATCG
* * *
597958 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGTGATAGTCCAAAATCG
1 TTGCAATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAATTCCGTTGCGATAGTCCAAAATCG
598019 T
1 T
598020 AACGACTGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
61 43 0.83
63 9 0.17
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (60 bp):
TTGCAATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCCGTTGCGATAGTCCAAAATCG
Found at i:598587 original size:6 final size:6
Alignment explanation
Indices: 598576--598614 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
598566 TCTCGTCTCG
598576 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
598615 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:598737 original size:21 final size:21
Alignment explanation
Indices: 598711--598822 Score: 88
Period size: 21 Copynumber: 5.3 Consensus size: 21
598701 ACTTTGGACT
598711 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
598732 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
598753 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
** * *
598774 ATCGCAACGCGAACCTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
598795 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
598816 ATCGCAA
1 ATCGCAA
598823 TGCAAACTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
19 16 0.24
21 35 0.51
23 17 0.25
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:598766 original size:42 final size:42
Alignment explanation
Indices: 598707--598889 Score: 278
Period size: 42 Copynumber: 4.3 Consensus size: 42
598697 TGCGACTTTG
598707 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
598749 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
598791 GACTATCGCAACAAATTTGGAATAAATCGCAATGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
598833 GACTATCGCAACGAATTT-GAACGCGAACTCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAA---TAAATCGCAACGCGAACTTC
598877 GACTATCGCAACG
1 GACTATCGCAACG
598890 CGAACTTGGA
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 3 0.02
42 96 0.75
44 29 0.23
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:598887 original size:21 final size:21
Alignment explanation
Indices: 598732--598914 Score: 110
Period size: 21 Copynumber: 8.6 Consensus size: 21
598722 TTTGGAATAA
598732 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
598753 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
598772 AAATCGCAACGCGAACCTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * * *
598795 ATCGCAA--CAAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* *
598814 AAATCGCAATGCAAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* *
598837 ATCGCAA--CGAA-TTTGAACGCGA
1 ATCGCAACGCGAACTTCG-A--C-T
598859 ACTCGCAACGCGAACTTCGACT
1 A-TCGCAACGCGAACTTCGACT
*
598881 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
598902 ATCGCAATGCGAA
1 ATCGCAACGCGAA
598915 TATGTAAATT
Statistics
Matches: 124, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.02
19 20 0.16
21 67 0.54
22 2 0.02
23 24 0.19
25 5 0.04
26 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:599134 original size:31 final size:31
Alignment explanation
Indices: 599099--599180 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
599089 GTTATTTTCT
*
599099 CTAAATTTTAAATTAAATATTAACTTGACCA
1 CTAAATTTTAAATAAAATATTAACTTGACCA
* * * *
599130 CTAAATTTTGAATAAAATAATAATTTGATCA
1 CTAAATTTTAAATAAAATATTAACTTGACCA
*
599161 CTAAATTTTAGATAAAATAT
1 CTAAATTTTAAATAAAATAT
599181 CAATTTAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (31 bp):
CTAAATTTTAAATAAAATATTAACTTGACCA
Found at i:603646 original size:24 final size:24
Alignment explanation
Indices: 603619--603665 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
603609 AAACTTATAT
* *
603619 TAAAATTTTAGGGGTTTAAAATTG
1 TAAAATTTTAGAGGTGTAAAATTG
603643 TAAAATTTTAGAGGTGTAAAATT
1 TAAAATTTTAGAGGTGTAAAATT
603666 AAACTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (24 bp):
TAAAATTTTAGAGGTGTAAAATTG
Found at i:605339 original size:82 final size:82
Alignment explanation
Indices: 605202--605361 Score: 284
Period size: 82 Copynumber: 2.0 Consensus size: 82
605192 TATCAATGGA
* *
605202 CTGCAGATTCCATGCATTTCGATCCCAGGTTCCTCCATTGCAATAATGGATGCCATTACTGTGAA
1 CTGCAGATTCCATGCATTTCAATCCCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
605267 GTTCTTTCTGCTTCGCG
66 GTTCTTTCTGCTTCGCG
* *
605284 CTGCAGATTCCATGCATTTCAATCTCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAG
1 CTGCAGATTCCATGCATTTCAATCCCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
605349 GTTCTTTCTGCTT
66 GTTCTTTCTGCTT
605362 TGTGCTTGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (82 bp):
CTGCAGATTCCATGCATTTCAATCCCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
GTTCTTTCTGCTTCGCG
Found at i:608965 original size:17 final size:18
Alignment explanation
Indices: 608943--608980 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
608933 CCCAAACATG
608943 CCTCTCCC-AATTACCCT
1 CCTCTCCCTAATTACCCT
*
608960 CCTCTCCCTCATTACCCT
1 CCTCTCCCTAATTACCCT
608978 CCT
1 CCT
608981 GATCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.13, C:0.55, G:0.00, T:0.32
Consensus pattern (18 bp):
CCTCTCCCTAATTACCCT
Found at i:609742 original size:15 final size:15
Alignment explanation
Indices: 609718--609753 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
609708 GGAGAGAACA
*
609718 CAAAATGGATTTAAC
1 CAAAACGGATTTAAC
609733 CAAAACGGATTTAAC
1 CAAAACGGATTTAAC
609748 CAAAAC
1 CAAAAC
609754 AGCCCTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.19
Consensus pattern (15 bp):
CAAAACGGATTTAAC
Found at i:617405 original size:13 final size:13
Alignment explanation
Indices: 617338--617399 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
617328 TGCGTCATAA
*
617338 ATTTATGACGCGC
1 ATTTATGACGCAC
**
617351 ATTTATGACATAC
1 ATTTATGACGCAC
* *
617364 ATTTATGGCACAC
1 ATTTATGACGCAC
*
617377 ATTTATGACGCGC
1 ATTTATGACGCAC
617390 ATTTATGACG
1 ATTTATGACG
617400 TTCATTGAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:617482 original size:85 final size:85
Alignment explanation
Indices: 617377--617542 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 85
617367 TATGGCACAC
* * *
617377 ATTTATGACGCGCATTTATGACGTT-CATTGAGCGTCATTGAAGC-C-C-CCGTTATAAATTAAG
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCACACACCATTA-AAA--AAG
*
617438 ATGACACACATTTGTGTGTCATAA
62 ATGACACACATTCGTGTGTCATAA
* * *
617462 ATTTATGATACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACACCATTAAAAAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACACCATTAAAAAAGATGA
617527 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
617543 GTGATTGTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
84 2 0.03
85 58 0.83
86 1 0.01
87 4 0.06
88 5 0.07
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACACCATTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:618897 original size:75 final size:76
Alignment explanation
Indices: 618797--619003 Score: 249
Period size: 75 Copynumber: 2.7 Consensus size: 76
618787 CGTTGTACAA
* * *
618797 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCATATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
** *
618861 AAACTGTTTAG
66 AAACCATTCAG
* * * * *
618872 GGGGGAATCGGTTCCTCATAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCATATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
618936 AAACCATTCAG
66 AAACCATTCAG
* * *
618947 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCTTCTGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCATATGGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
619004 TTTGGCTTTG
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
75 82 0.74
76 6 0.05
77 23 0.21
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCATATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
AAACCATTCAG
Found at i:619630 original size:17 final size:17
Alignment explanation
Indices: 619608--619651 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
619598 TTCATAAATC
619608 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
619625 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
619642 -AAATATCCAA
1 CAAA-ATCCAA
619652 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:619643 original size:9 final size:8
Alignment explanation
Indices: 619603--619653 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
619593 CACCATTCAT
619603 AAATCC-A
1 AAATCCAA
619610 AAATCCAA
1 AAATCCAA
*
619618 CAATCCACA
1 AAATCCA-A
619627 AAAT-CAA
1 AAATCCAA
619634 ACAATCCAA
1 A-AATCCAA
619643 AATATCCAA
1 AA-ATCCAA
619652 AA
1 AA
619654 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:621612 original size:21 final size:21
Alignment explanation
Indices: 621588--621627 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
621578 CAGAACCCCA
*
621588 GGGGGCTATCGATTCCCCTGT
1 GGGGGCAATCGATTCCCCTGT
* *
621609 GGGGGGAATCGGTTCCCCT
1 GGGGGCAATCGATTCCCCT
621628 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGCAATCGATTCCCCTGT
Found at i:621662 original size:20 final size:21
Alignment explanation
Indices: 621608--621670 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
621598 GATTCCCCTG
621608 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
621632 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
621652 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
621671 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:625313 original size:21 final size:21
Alignment explanation
Indices: 625289--625338 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
625279 GAAGTTTTAA
625289 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTTCTTTTGAT
625310 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTTCTTTTGAT
625331 GATCATCA
1 GATCATCA
625339 TTGACCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (21 bp):
GATCATCAATTTTCTTTTGAT
Found at i:625330 original size:18 final size:20
Alignment explanation
Indices: 625283--625338 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 20
625273 TCAAAAGAAG
*
625283 TTTTAAGATCATCAATTTTC
1 TTTTATGATCATCAATTTTC
625303 TTTTGATGATCATCAATTTTC
1 TTTT-ATGATCATCAATTTTC
625324 TTTTGATGATCATCA
1 TTTT-ATGATCATCA
625339 TTGACCTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTTATGATCATCAATTTTC
Found at i:625347 original size:21 final size:21
Alignment explanation
Indices: 625289--625347 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
625279 GAAGTTTTAA
**
625289 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTACCTTTTGAT
**
625310 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTACCTTTTGAT
625331 GATCATC-ATTGACCTTT
1 GATCATCAATT-ACCTTT
625348 GAAAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (21 bp):
GATCATCAATTACCTTTTGAT
Found at i:627569 original size:74 final size:75
Alignment explanation
Indices: 627400--627604 Score: 252
Period size: 75 Copynumber: 2.7 Consensus size: 75
627390 CCGTTGTACA
* * * * *
627400 AGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
** *
627464 AAAACTGTTT
66 AAAACCATTC
*
627474 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
*
627538 CCAAACCATTC
65 CAAAACCATTC
* ** *
627549 AGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGTTTCCCTCTAAGCAATCTGGAA
1 AGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
627605 TTTTTGGCTT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
74 22 0.19
75 62 0.55
76 29 0.26
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.23
Consensus pattern (75 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
AAAACCATTC
Found at i:640685 original size:18 final size:17
Alignment explanation
Indices: 640662--640696 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
640652 CAAACCGGTT
640662 CGACCCGACCCGTTGACC
1 CGACCCGA-CCGTTGACC
640680 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
640697 GTTAACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:640778 original size:29 final size:28
Alignment explanation
Indices: 640746--640904 Score: 83
Period size: 29 Copynumber: 5.5 Consensus size: 28
640736 TTACATTCTA
640746 GTAATTATTTTGAAAATAGTGCTATTTTT
1 GTAATTATTTT-AAAATAGTGCTATTTTT
** ** * *
640775 GTAAAAAAAAAATTAAAAAAG-G-TAATTTT
1 GT---AATTATTTTAAAATAGTGCTATTTTT
* * * *
640804 GTAA-T-TTTTAAAAAAATGATATTTTA
1 GTAATTATTTTAAAATAGTGCTATTTTT
* *
640830 GTAATTATTTTAAAAATGGTGCTATTTTG
1 GTAATTATTTT-AAAATAGTGCTATTTTT
* *
640859 GTAATTCTTTTTAAAAATGGTGCTATTTTT
1 GTAATT-ATTTT-AAAATAGTGCTATTTTT
*
640889 GTAATTTTTTTTAAAA
1 GTAA-TTATTTTAAAA
640905 AAAGGTGTTA
Statistics
Matches: 101, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
24 8 0.08
25 1 0.01
26 11 0.11
27 1 0.01
28 4 0.04
29 32 0.32
30 31 0.31
31 8 0.08
32 5 0.05
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.47
Consensus pattern (28 bp):
GTAATTATTTTAAAATAGTGCTATTTTT
Found at i:640857 original size:17 final size:17
Alignment explanation
Indices: 640835--640887 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
640825 TTTTAGTAAT
640835 TATTTTAAAAATGGTGC
1 TATTTTAAAAATGGTGC
***
640852 TATTTTGGTAAT--T-C
1 TATTTTAAAAATGGTGC
640866 T-TTTTAAAAATGGTGC
1 TATTTTAAAAATGGTGC
640882 TATTTT
1 TATTTT
640888 TGTAATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 7 0.27
14 2 0.08
15 2 0.08
16 2 0.08
17 13 0.50
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (17 bp):
TATTTTAAAAATGGTGC
Found at i:640873 original size:30 final size:29
Alignment explanation
Indices: 640823--640905 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 29
640813 AAAAAAATGA
*
640823 TATTTTAGTAATTATTTTAAAAATGGTGC
1 TATTTTAGTAATTTTTTTAAAAATGGTGC
*
640852 TATTTTGGTAATTCTTTTTAAAAATGGTGC
1 TATTTTAGTAATT-TTTTTAAAAATGGTGC
*
640882 TATTTTTGTAATTTTTTTTAAAAA
1 TATTTTAGTAA-TTTTTTTAAAAA
640906 AAGGTGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 12 0.24
30 35 0.71
31 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (29 bp):
TATTTTAGTAATTTTTTTAAAAATGGTGC
Found at i:645116 original size:17 final size:18
Alignment explanation
Indices: 645094--645127 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
645084 AGTTTTTTTT
645094 GGATTTTT-GGGAATTTA
1 GGATTTTTAGGGAATTTA
645111 GGATTTTTAGGGAATTT
1 GGATTTTTAGGGAATTT
645128 TGGGTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (18 bp):
GGATTTTTAGGGAATTTA
Found at i:645135 original size:18 final size:17
Alignment explanation
Indices: 645090--645136 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
645080 TTCTAGTTTT
645090 TTTTGGATTTTTGGGAA
1 TTTTGGATTTTTGGGAA
*
645107 TTTAGGATTTTTAGGGAA
1 TTTTGGATTTTT-GGGAA
*
645125 TTTTGGGTTTTT
1 TTTTGGATTTTT
645137 CAAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (17 bp):
TTTTGGATTTTTGGGAA
Done.