Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1154836 original size:52 final size:51
Alignment explanation
Indices: 1154753--1154865 Score: 192
Period size: 52 Copynumber: 2.2 Consensus size: 51
1154743 AAATGCTATT
1154753 GCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG-ATC
1154806 GCAATGCGAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGATC
1 GCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGATC
1154857 GCAATGCGA
1 GCAATGCGA
1154866 TTTCATTTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
51 24 0.41
52 28 0.47
53 7 0.12
ACGTcount: A:0.43, C:0.18, G:0.26, T:0.13
Consensus pattern (51 bp):
GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGATC
Found at i:1154890 original size:19 final size:19
Alignment explanation
Indices: 1154855--1155061 Score: 209
Period size: 19 Copynumber: 11.7 Consensus size: 19
1154845 CAACGAGAGA
*
1154855 TCGCAATGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1154873 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1154892 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1154909 TCG--TTGCGATTTT-ATT
1 TCGCATTGCGATTTTCATT
1154925 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1154944 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1154961 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1154977 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1154996 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1155014 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1155032 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1155048 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1155062 CTCGTTGCGA
Statistics
Matches: 159, Mismatches: 9, Indels: 41
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.14
15 3 0.02
16 16 0.10
17 5 0.03
18 40 0.25
19 48 0.30
20 24 0.15
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1154939 original size:52 final size:51
Alignment explanation
Indices: 1154861--1155073 Score: 276
Period size: 52 Copynumber: 4.1 Consensus size: 51
1154851 GAGATCGCAA
*
1154861 TGCGATTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1154913 TGCGATTTTATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1154965 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCAT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG--T
*
1155021 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATT-TCTCGT
1 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1155067 TGCGATT
1 TGCGATT
1155074 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 6, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
45 2 0.01
46 6 0.04
48 2 0.01
49 2 0.01
51 12 0.08
52 108 0.72
53 2 0.01
54 3 0.02
55 1 0.01
56 6 0.04
57 5 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (51 bp):
TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1154986 original size:70 final size:71
Alignment explanation
Indices: 1154855--1155061 Score: 246
Period size: 70 Copynumber: 2.9 Consensus size: 71
1154845 CAACGAGAGA
* * * * * * *
1154855 TCGCAATGCGATTTCATTT-TGCATTGCGATTTTCAT-TTCCGCA-TTGCGATTCTCTCGTTGCG
1 TCGCATTGCGATTTCATTTCCGCATTGCGATTCTCATGTTGCG-ATTTTC-ATT-TCGCATTGCG
1154917 ATTTT-ATT
63 ATTTTCATT
1154925 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGA-TTTCATTTCGCATTGCGA
1 TCGCATTGCGA-TTTCATTTCCGCATTGCGATTCTCAT-GTTGCGATTTTCATTTCGCATTGCGA
1154988 TTTTCATT
64 TTTTCATT
* *
1154996 TCGCATTGCGATTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTCATTTCCGCATTGCGATTCTCATGTTGCGATTTTCATTTCGCATTGCGATT
1155061 T
66 T
1155062 CTCGTTGCGA
Statistics
Matches: 121, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
70 52 0.43
71 48 0.40
72 17 0.14
73 4 0.03
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTCATTTCCGCATTGCGATTCTCATGTTGCGATTTTCATTTCGCATTGCGATT
TTCATT
Found at i:1157569 original size:24 final size:24
Alignment explanation
Indices: 1157535--1157581 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1157525 CTGAAACATC
1157535 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1157559 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1157582 GACCAAATTT
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:1158294 original size:20 final size:20
Alignment explanation
Indices: 1158269--1158454 Score: 232
Period size: 20 Copynumber: 9.3 Consensus size: 20
1158259 AAATTTCAGT
* * *
1158269 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1158289 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1158309 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1158329 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
1158349 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATACGC
1158369 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1158389 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1158409 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1158429 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1158449 GTTGCG
1 GTTGCG
1158455 TACTACTTCT
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.02
20 143 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1158989 original size:20 final size:20
Alignment explanation
Indices: 1158961--1159189 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
1158951 AAATTTCAGT
* * *
1158961 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1158981 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1159001 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1159021 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1159041 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1159061 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1159081 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1159101 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1159121 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1159141 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1159161 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1159181 GTTGCGATT
1 GTTGCGATT
1159190 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1159127 original size:692 final size:695
Alignment explanation
Indices: 1157759--1159144 Score: 2640
Period size: 692 Copynumber: 2.0 Consensus size: 695
1157749 GACCCAACAA
1157759 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTGTGAAACACTAATGTAAGCAATGA
1 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTGTGAAACACTAATGTAAGCAATGA
1157824 ATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTAACATTTCTCTGATAAGATAGCCTA
66 ATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTAACATTTCTCTGATAAGATAGCCTA
1157889 AATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTAA
131 AATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTA-AGTTTCATAAGTTAA
*
1157954 CTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGCATATATTGTAAAACACCATGAA
195 CTTTGGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGCATATATTGTAAAACACCATGAA
1158019 CATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCATG
260 CATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCATG
1158084 GTTGTAAATTAATTTACTAAACAGACGCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGGATG
325 GTTGTAAATTAATTTACTAAACAGACGCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGGATG
1158149 TCATTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCGATT
390 TCATTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCGATT
1158214 TAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATACCCAAAATTTCAGTGTTGCGATTT
455 TAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATACCCAAAATTTCAGTGTTGCGATTT
1158279 ACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGA
520 ACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGA
*
1158344 TTATCGTTGCGATTTATGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGC
585 TTATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGC
1158409 GTTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCG
650 GTTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCG
1158455 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
1 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATC-TGTGAAACACTAATGTAAGCAATG
*
1158520 AATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
65 AATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTAACATTTCTCTGATAAGATAGCCT
1158585 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATT-AGTTTCATAAGTTAA
130 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAAGTTTCATAAGTTAA
1158649 CTTTGGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGCA-ATATTGTAAAACACCATGAA
195 CTTTGGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGCATATATTGTAAAACACCATGAA
1158713 CATTAT-CCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC-TTAGATGATTTCATG
260 CATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCATG
1158776 GTTGTAAATTAATTTACTAAACA-A-GCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGGATG
325 GTTGTAAATTAATTTACTAAACAGACGCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGGATG
*
1158839 TCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCGATT
390 TCATTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCGATT
*
1158904 TAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATACCCAAAATTTCAGTGTTGTGAT
455 TAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAG-T-TATACCCAAAATTTCAGTGTTGCGAT
1158969 TTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
518 TTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1159034 GATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATAC
583 GATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATAC
*
1159099 GCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGCGTTG
648 GCGTTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTG
1159145 TGATTTATGT
Statistics
Matches: 681, Mismatches: 6, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
690 139 0.20
691 2 0.00
692 237 0.35
693 42 0.06
694 26 0.04
695 58 0.09
696 40 0.06
697 137 0.20
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (695 bp):
TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTGTGAAACACTAATGTAAGCAATGA
ATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTAACATTTCTCTGATAAGATAGCCTA
AATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAAGTTTCATAAGTTAAC
TTTGGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGCATATATTGTAAAACACCATGAAC
ATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCATGG
TTGTAAATTAATTTACTAAACAGACGCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGGATGT
CATTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCGATTT
AGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATACCCAAAATTTCAGTGTTGCGATTTA
CAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGAT
TATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCG
TTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCG
Found at i:1159985 original size:4 final size:4
Alignment explanation
Indices: 1159976--1160016 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
1159966 TCTCAAGGTA
* *
1159976 TATG TATG TATG TATG TATG TATG TATA TTTG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1160017 GGCAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:1162045 original size:14 final size:11
Alignment explanation
Indices: 1161998--1162035 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
1161988 AGCAAATAAA
1161998 ACATAATAATT
1 ACATAATAATT
1162009 ACATAATAATT
1 ACATAATAATT
1162020 ACATAATAATT
1 ACATAATAATT
1162031 ACATA
1 ACATA
1162036 CCACTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
ACATAATAATT
Found at i:1169470 original size:11 final size:11
Alignment explanation
Indices: 1169454--1169480 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1169444 AGCAAATAAA
1169454 ACATAATAATT
1 ACATAATAATT
1169465 ACATAATAATT
1 ACATAATAATT
1169476 ACATA
1 ACATA
1169481 TAAGTTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (11 bp):
ACATAATAATT
Found at i:1169483 original size:21 final size:21
Alignment explanation
Indices: 1169454--1169495 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169444 AGCAAATAAA
1169454 ACATAATAA-TTACATAATAATT
1 ACATAATAAGTT-CATAA-AATT
1169476 ACAT-ATAAGTTCATAAAATT
1 ACATAATAAGTTCATAAAATT
1169496 CCATTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (21 bp):
ACATAATAAGTTCATAAAATT
Found at i:1169553 original size:11 final size:11
Alignment explanation
Indices: 1169537--1169562 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1169527 AGCAAATAAA
1169537 ACATAATAATT
1 ACATAATAATT
1169548 ACATAATAATT
1 ACATAATAATT
1169559 ACAT
1 ACAT
1169563 GCCACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ACATAATAATT
Found at i:1173696 original size:22 final size:20
Alignment explanation
Indices: 1173647--1173697 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
1173637 CATGATTCAT
*
1173647 ATGATATGTGATAGAAGAAA
1 ATGATATGTGATACAAGAAA
*
1173667 ATACATATGTGATTACAAGAGAA
1 AT-GATATGTGA-TACAAGA-AA
1173690 ATGATATG
1 ATGATATG
1173698 AGTAAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 11 0.44
23 4 0.16
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGATATGTGATACAAGAAA
Found at i:1180817 original size:22 final size:22
Alignment explanation
Indices: 1180792--1180842 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1180782 AGTCAAGGGT
* *
1180792 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCATTCGGGACAAA
1180814 TTCATAGGTCATTCGGGACAAA
1 TTCATAGGTCATTCGGGACAAA
1180836 TCTCATA
1 T-TCATA
1180843 TGCCACTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (22 bp):
TTCATAGGTCATTCGGGACAAA
Found at i:1185202 original size:34 final size:34
Alignment explanation
Indices: 1185143--1185209 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1185133 TTCTTGAGAG
1185143 TTGTTTTCTCCTTTTCATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTCATC-AGAGAGAAGTTGTTA
*
1185177 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-CATCAGAGAGAAGTTGT
1185210 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTCATCAGAGAGAAGTTGTTA
Found at i:1189803 original size:34 final size:34
Alignment explanation
Indices: 1189742--1189808 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1189732 TTCTTGAGAG
*
1189742 TTGTTTTCTCCTTTTTATCGAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
1189776 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
1189809 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:1190841 original size:35 final size:35
Alignment explanation
Indices: 1190795--1191066 Score: 328
Period size: 35 Copynumber: 7.8 Consensus size: 35
1190785 AACACTTTAC
* *
1190795 TCGAAAGTGCAATGCTTTCTTCCGTTCGACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * *
1190830 TCGAAAGTGCAATGCTTCCTTTCGTTCTACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * *
1190865 TTGAAAGTGTGATGCCTCCTTCCGTTCGACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * * *
1190900 TCAAAAGTGCGATGCCTCCTTCCATTTGACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * *
1190935 TCGAAAGTACGAAGCTTCCTTCCGTTCTACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * *
1190970 TCGAAAGTGCGATGCCTCCTTCTGTTTGACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* * * *
1191005 TCAAAAGTGTGATTCTTCCTTCCTTTCGACTTGAA
1 TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
* *
1191040 TCGAAAGTGCGACGCTTCCTTTCGTTC
1 TCGAAAGTGCGATGCTTCCTTCCGTTC
1191067 TTCTTATTAA
Statistics
Matches: 197, Mismatches: 40, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 197 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (35 bp):
TCGAAAGTGCGATGCTTCCTTCCGTTCGACTTGAA
Found at i:1190984 original size:105 final size:104
Alignment explanation
Indices: 1190798--1191067 Score: 380
Period size: 105 Copynumber: 2.6 Consensus size: 104
1190788 ACTTTACTCG
* * *
1190798 AAAGTGCAATGCTTTCTTCCGTTCGACTTGAATCGAAAGTGC-AATGCTTCCTTTCGTTCTACTT
1 AAAGTGCGATGCTTCCTTCC-TTTGACTTGAATCGAAAGTGCGAA-GCTTCCTTTCGTTCTACTT
* *
1190862 GAATTGAAAGTGTGATGCCTCCTTCCGTTCGACTTGAATCA
64 GAATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCA
* * *
1190903 AAAGTGCGATGCCTCCTTCCATTTGACTTGAATCGAAAGTACGAAGCTTCCTTCCGTTCTACTTG
1 AAAGTGCGATGCTTCCTTCC-TTTGACTTGAATCGAAAGTGCGAAGCTTCCTTTCGTTCTACTTG
* *
1190968 AATCGAAAGTGCGATGCCTCCTTCTGTTTGACTTGAATCA
65 AATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCA
* * *
1191008 AAAGTGTGATTCTTCCTTCCTTTCGACTTGAATCGAAAGTGCGACGCTTCCTTTCGTTCT
1 AAAGTGCGATGCTTCCTTCCTTT-GACTTGAATCGAAAGTGCGAAGCTTCCTTTCGTTCT
1191068 TCTTATTAAC
Statistics
Matches: 146, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
104 3 0.02
105 141 0.97
106 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (104 bp):
AAAGTGCGATGCTTCCTTCCTTTGACTTGAATCGAAAGTGCGAAGCTTCCTTTCGTTCTACTTGA
ATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCA
Found at i:1193670 original size:31 final size:31
Alignment explanation
Indices: 1193624--1193683 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1193614 AACTTTTAAA
* * *
1193624 ATTATATAATGATCATTACATTAATCAAATT
1 ATTATAAAATAATCATTAAATTAATCAAATT
*
1193655 ATTATAAAATAATCATTAAATTTATCAAA
1 ATTATAAAATAATCATTAAATTAATCAAA
1193684 AGTTTGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTATAAAATAATCATTAAATTAATCAAATT
Found at i:1193909 original size:2 final size:2
Alignment explanation
Indices: 1193874--1193899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1193864 TGAATTTTGA
1193874 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
1193900 TGTTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1194568 original size:2 final size:2
Alignment explanation
Indices: 1194561--1194585 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1194551 GAACCCATAG
1194561 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 T
1194586 TTTGTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1194616 original size:77 final size:76
Alignment explanation
Indices: 1194494--1194638 Score: 281
Period size: 77 Copynumber: 1.9 Consensus size: 76
1194484 ATTCCCATTA
1194494 ATATATATATATTATTTTGTTTATGCCTTGTTTTTGTTTGGAAGAGAATGAATACAAGAACCCAT
1 ATATATATATATTATTTTGTTTATGCCTTGTTTTTGTTTGGAAGAGAATGAATACAAGAACCCAT
1194559 AGTATATATAT
66 AGTATATATAT
1194570 ATATATATATATATATTTTGTTTATGCCTTGTTTTTGTTTGGAAGAGAATGAATACAAGAACCCA
1 ATATATATATAT-TATTTTGTTTATGCCTTGTTTTTGTTTGGAAGAGAATGAATACAAGAACCCA
1194635 TAGT
65 TAGT
1194639 TTTTTTGGGT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 12 0.18
77 56 0.82
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (76 bp):
ATATATATATATTATTTTGTTTATGCCTTGTTTTTGTTTGGAAGAGAATGAATACAAGAACCCAT
AGTATATATAT
Found at i:1194886 original size:21 final size:21
Alignment explanation
Indices: 1194860--1194913 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1194850 ATTTAACGAG
1194860 TTATAGGTAGAGGGCAGAACT
1 TTATAGGTAGAGGGCAGAACT
1194881 TTATAGGTAGAGGGCAGAACT
1 TTATAGGTAGAGGGCAGAACT
1194902 TTATAGGTAGAG
1 TTATAGGTAGAG
1194914 AGACTCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.26
Consensus pattern (21 bp):
TTATAGGTAGAGGGCAGAACT
Found at i:1195386 original size:2 final size:2
Alignment explanation
Indices: 1195381--1195427 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1195371 AAAATGGAAT
1195381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1195423 TA TA T
1 TA TA T
1195428 GGGGTATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1195834 original size:103 final size:103
Alignment explanation
Indices: 1195653--1195845 Score: 266
Period size: 103 Copynumber: 1.9 Consensus size: 103
1195643 TCATAATCAT
* * *
1195653 ATATATATATATATATATTTGGTATAATCACCTATATCTGATTGTATAGGTAAGAGCGACCCTCA
1 ATATATATATATATATAATTGGTATAATCACATATATCTGATTGTATAGGTAAGAGAGACCCTCA
*
1195718 CAACTTATATTGTTACATTCGCAAACATCAGTATTTGA
66 CAACGTATATTGTTACATTCGCAAACATCAGTATTTGA
* * *
1195756 ATATATATATATATATAATTGGTATAATCACATGTATTTGATTGTATAGGTAA-ATGAGACCTTC
1 ATATATATATATATATAATTGGTATAATCACATATATCTGATTGTATAGGTAAGA-GAGACCCTC
*
1195820 ACAATCCGT-T-TTGTTCCATTCGCAAA
65 ACAA--CGTATATTGTTACATTCGCAAA
1195846 AAACAGAAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
102 1 0.01
103 75 0.95
104 1 0.01
105 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (103 bp):
ATATATATATATATATAATTGGTATAATCACATATATCTGATTGTATAGGTAAGAGAGACCCTCA
CAACGTATATTGTTACATTCGCAAACATCAGTATTTGA
Found at i:1196372 original size:17 final size:17
Alignment explanation
Indices: 1196338--1196389 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1196328 GCCAGACAAA
* *
1196338 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
1196355 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
1196372 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
1196387 TTT
1 TTT
1196390 CTACTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:1196466 original size:16 final size:17
Alignment explanation
Indices: 1196439--1196471 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1196429 AAGTAGGACC
*
1196439 AATTTGAAATTTTAATT
1 AATTTGAAATTTGAATT
1196456 AATTT-AAATTTGAATT
1 AATTTGAAATTTGAATT
1196472 CATTATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTTGAAATTTGAATT
Found at i:1203458 original size:2 final size:2
Alignment explanation
Indices: 1203453--1203508 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1203443 CATTTTTTTA
1203453 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
1203495 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1203509 TAGTATTCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1209495 original size:29 final size:30
Alignment explanation
Indices: 1209463--1209537 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
1209453 TTATATATAG
*
1209463 GTGCTAAAATGTAAATAAAAAAAATTAAA-
1 GTGCTAAAATGTAAATAAAAAAAAGTAAAT
* * * *
1209492 GTGCTGAAACT-AAAATTACAAAAAGTAAAT
1 GTGCT-AAAATGTAAATAAAAAAAAGTAAAT
*
1209522 GTACTAAAATGTAAAT
1 GTGCTAAAATGTAAAT
1209538 GCATAATTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.25
Consensus pattern (30 bp):
GTGCTAAAATGTAAATAAAAAAAAGTAAAT
Found at i:1211563 original size:35 final size:34
Alignment explanation
Indices: 1211513--1211649 Score: 141
Period size: 35 Copynumber: 3.9 Consensus size: 34
1211503 AACAATTTCC
* * *
1211513 TTAAGTGAAGAAAAA-TTGTTTCAAGATGAACATTT
1 TTAAGTG-AGAAAAATTTGTTTTAAGA-AAACAATT
*
1211548 TTAAGTGAGATAAAATTTATTTTAAGGAAAACAATT
1 TTAAGTGAGA-AAAATTTGTTTTAA-GAAAACAATT
*
1211584 TTAAGTGAGAAAAATTTGTTTTAAGAAAAACAATC
1 TTAAGTGAGAAAAATTTGTTTTAAG-AAAACAATT
* *
1211619 TCAAGTGATATAAAATTTGTTTTTAAGAAAA
1 TTAAGTGAGA-AAAATTTG-TTTTAAGAAAA
1211650 AACACTCTCA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
34 4 0.05
35 40 0.45
36 35 0.40
37 9 0.10
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (34 bp):
TTAAGTGAGAAAAATTTGTTTTAAGAAAACAATT
Found at i:1211604 original size:71 final size:72
Alignment explanation
Indices: 1211513--1211650 Score: 172
Period size: 71 Copynumber: 1.9 Consensus size: 72
1211503 AACAATTTCC
** * * * *
1211513 TTAAGTGAAGAAAAATTGTTTCAAGATGAACATTTTTAAGTGAGATAAAATTT-ATTTTAAGGAA
1 TTAAGTGAAGAAAAATTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATTTGATTTTAAGAAA
1211577 AACAATT
66 AACAATT
* * *
1211584 TTAAGTG-AGAAAAATTTGTTTTAAGAAAAACAATCTCAAGTGATATAAAATTTGTTTTTAAGAA
1 TTAAGTGAAGAAAAA-TTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATTTGATTTTAAGAA
1211648 AAA
65 AAA
1211651 ACACTCTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
70 7 0.12
71 38 0.68
72 11 0.20
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (72 bp):
TTAAGTGAAGAAAAATTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATTTGATTTTAAGAAA
AACAATT
Found at i:1211605 original size:20 final size:19
Alignment explanation
Indices: 1211545--1211608 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
1211535 AAGATGAACA
1211545 TTTTTAAGTGAGATAAAATT
1 TTTTTAAGTGAGA-AAAATT
1211565 TATTTTAAG-GA-AAACAA--
1 T-TTTTAAGTGAGAAA-AATT
1211582 -TTTTAAGTGAGAAAAATT
1 TTTTTAAGTGAGAAAAATT
1211600 TGTTTTAAG
1 T-TTTTAAG
1211609 AAAAACAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
15 7 0.19
16 4 0.11
17 3 0.08
18 2 0.06
19 3 0.08
20 10 0.28
21 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.41
Consensus pattern (19 bp):
TTTTTAAGTGAGAAAAATT
Found at i:1211659 original size:38 final size:36
Alignment explanation
Indices: 1211550--1211672 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
1211540 GAACATTTTT
* * * *
1211550 AAGTGAGATAAAATTTATTTTAAGGAAAACAATTTT
1 AAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTC
1211586 AAGTGAGA-AAAATTTGTTTTAAGAAAAACAATCTC
1 AAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTC
* *
1211621 AAGTGATATAAAATTTGTTTTTAAGAAAAAACACTCTC
1 AAGTGAGATAAAATTTG-TTTTAAG-AAAAACAATCTC
1211659 AAGTGAGATAAAAT
1 AAGTGAGATAAAAT
1211673 CTTGAGTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
35 30 0.39
36 16 0.21
37 7 0.09
38 24 0.31
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (36 bp):
AAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTC
Found at i:1220010 original size:23 final size:23
Alignment explanation
Indices: 1219984--1220031 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1219974 ATAAAGTACA
*
1219984 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1220007 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1220030 AT
1 AT
1220032 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1220483 original size:23 final size:23
Alignment explanation
Indices: 1220457--1220519 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1220447 ATATAACCAC
*
1220457 TACCTATTACATTATATAAATGA
1 TACCTATTACATTATATAAACGA
* *
1220480 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1220503 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1220520 TTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1220893 original size:426 final size:429
Alignment explanation
Indices: 1220098--1221146 Score: 2000
Period size: 426 Copynumber: 2.5 Consensus size: 429
1220088 TATTACATTA
*
1220098 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1220163 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1220228 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1220293 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
196 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
1220358 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACTTT
261 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACTTT
*
1220423 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAATGATACCTATT
326 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
1220488 ACATTATATAAGCGCTACCTATTACATCATA-TTTTACC
391 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1220526 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1220590 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1220655 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1220720 ATAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATC
* *
1220783 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGATACTT
260 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACTT
1220848 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
325 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
*
1220913 TACATTATATAAGCGGTACCTATTACATCATATTTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1220953 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1221018 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1221083 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAA-TTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1221147 CAACATTAAC
Statistics
Matches: 611, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
426 226 0.37
427 188 0.31
428 197 0.32
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (429 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGACACTTT
TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1220898 original size:21 final size:22
Alignment explanation
Indices: 1220873--1220945 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
1220863 ACACTTTACA
*
1220873 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1220896 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
* * *
1220919 ATATAAGCGGTACCTATTACATC
1 ATATAAAC-ATACCTATTACATT
1220942 ATAT
1 ATAT
1220946 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 44 0.98
24 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1220909 original size:23 final size:23
Alignment explanation
Indices: 1220883--1220945 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1220873 ATATAACCAC
1220883 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1220906 TACCTATTACATTATATAAGCGG
1 TACCTATTACATTATATAAACGA
*
1220929 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1220946 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1221415 original size:39 final size:39
Alignment explanation
Indices: 1221361--1221446 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1221351 CAAGTTGTAG
*
1221361 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1221400 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1221439 ATTTTGAT
1 ATTTTGAT
1221447 GAGCATCAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1221726 original size:18 final size:18
Alignment explanation
Indices: 1221703--1221739 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1221693 CGAAATATAT
1221703 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1221721 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1221739 A
1 A
1221740 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1222211 original size:22 final size:23
Alignment explanation
Indices: 1222170--1222222 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
1222160 TTTACAATAT
*
1222170 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGATACCTATTAC
1222193 ATTATATAA-CGATACCTATTAC
1 ATTATATAAGCGATACCTATTAC
1222215 ATTATATA
1 ATTATATA
1222223 CTTGTAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGATACCTATTAC
Found at i:1225356 original size:181 final size:183
Alignment explanation
Indices: 1224702--1225357 Score: 1132
Period size: 181 Copynumber: 3.6 Consensus size: 183
1224692 ACACATTTTA
* *
1224702 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
1224767 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACA-TATAATTATGGGTTCCGA--
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1224829 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
*
1224882 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
*
1224947 ACCGGTATATTTATACCTGTTATATTACAAAATTATC--TTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
*
1225010 TGTAAATGTTGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
* *
1225063 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGATTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
*
1225128 ACCGG--TATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1225191 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
1225244 GACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA-A
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
* * * **
1225307 ACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATTTTATTATAAT
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
1225358 ATGTTGAAAG
Statistics
Matches: 454, Mismatches: 15, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
178 5 0.01
179 54 0.12
180 134 0.30
181 261 0.57
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
Found at i:1225687 original size:21 final size:23
Alignment explanation
Indices: 1225661--1225723 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 23
1225651 TCCACAGTGG
1225661 AAAAAGTATAGACACTTT-TA-T
1 AAAAAGTATAGACACTTTATATT
* *
1225682 AAAAAGGATAGATACTTTACAATATT
1 AAAAAGTATAGACACTTT---ATATT
1225708 AAAAAGTATAGACACT
1 AAAAAGTATAGACACT
1225724 CAAATGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 16 0.48
25 2 0.06
26 15 0.45
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (23 bp):
AAAAAGTATAGACACTTTATATT
Found at i:1226823 original size:3 final size:3
Alignment explanation
Indices: 1226815--1226889 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
1226805 ACTTGTTTGG
* * * ** * *
1226815 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
1226863 ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1226890 GTCAGCTTCA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.24, C:0.35, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1226832 original size:12 final size:12
Alignment explanation
Indices: 1226815--1226901 Score: 93
Period size: 12 Copynumber: 7.2 Consensus size: 12
1226805 ACTTGTTTGG
1226815 ATCATCATCTTC
1 ATCATCATCTTC
*
1226827 ATCATCATCATC
1 ATCATCATCTTC
*
1226839 GTCATCATCTTC
1 ATCATCATCTTC
** *
1226851 ATCGCCAGCTTC
1 ATCATCATCTTC
*
1226863 ATCATCATCATC
1 ATCATCATCTTC
*
1226875 ATCGTCATCTTC
1 ATCATCATCTTC
* *
1226887 ATCGTCAGCTTC
1 ATCATCATCTTC
1226899 ATC
1 ATC
1226902 TTCTGCGACC
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1226863 original size:36 final size:36
Alignment explanation
Indices: 1226823--1226901 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
1226813 GGATCATCAT
*
1226823 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* *
1226859 CTTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
1226895 CTTCATC
1 CTTCATC
1226902 TTCTGCGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:1226902 original size:18 final size:18
Alignment explanation
Indices: 1226843--1226904 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1226833 ATCATCGTCA
*
1226843 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
1226861 TCATCATCATCATCATCG
1 TCATCTTCATCGTCAGCT
1226879 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
1226897 TCATCTTC
1 TCATCTTC
1226905 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:1226904 original size:6 final size:6
Alignment explanation
Indices: 1226819--1226904 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
1226809 GTTTGGATCA
* * * * * * * *
1226819 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCA
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1226867 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1226905 TGCGACCGCT
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1229023 original size:197 final size:197
Alignment explanation
Indices: 1228358--1229827 Score: 2756
Period size: 197 Copynumber: 7.5 Consensus size: 197
1228348 TTTAAATTAG
1228358 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1228423 ATTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1228487 CGACAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1228551 AA
196 AA
1228553 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1228618 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
1228683 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTTTGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1228748 AAA
195 AAA
1228751 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
* *
1228816 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1228881 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1228946 AA
196 AA
*
1228948 TATCGACACAAACCATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1229013 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1229078 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACTCTGTTTTCCATTCATTCTGGAAAT-
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1229142 AA
196 AA
1229144 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1229209 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1229273 CGACAC-TTTT-TATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT-
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1229335 AA
196 AA
1229337 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1229402 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1229467 CGACACTTTTTATATATGGCTCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGG--AA
*
1229532 AAAAA
193 ATAAA
1229537 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1229602 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1229667 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1229732 AA
196 AA
*
1229734 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1229799 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
1229828 CCTTTTGGCC
Statistics
Matches: 1244, Mismatches: 21, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
193 136 0.11
194 56 0.05
195 156 0.13
196 138 0.11
197 373 0.30
198 192 0.15
199 31 0.02
200 162 0.13
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
AA
Found at i:1229175 original size:393 final size:393
Alignment explanation
Indices: 1228358--1229827 Score: 2761
Period size: 393 Copynumber: 3.7 Consensus size: 393
1228348 TTTAAATTAG
1228358 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1228423 ATTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1228487 CGACACTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
131 CGACACTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
1228552 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
196 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
1228617 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
261 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
* *
1228682 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTTTGAAAA
326 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG-GAA
1228747 AAAA
390 AAAA
1228751 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1228816 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTGGGAT
66 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1228881 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
*
1228946 AATATCGACACAAACCATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
195 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
1229011 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
260 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
1229076 ATCGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACTCTGTTTTCCATTCATTCTGGAA
325 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
*
1229140 ATAA
390 AAAA
1229144 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1229209 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1229273 CGACACTTTT-TATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT-A
131 CGACACTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
1229336 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
196 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
1229401 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
261 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
1229466 TCGACACTTTTTATATATGGCTCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
326 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG---
1229531 AAAAAA
388 AAAAAA
1229537 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1229602 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1229667 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
*
1229732 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCCATAAAACCGGTA
195 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
1229797 TAATTGTACCGGTTAGATTGAAAAATTACAT
260 TAATTGTACCGGTTAGATTGAAAAATTACAT
1229828 CCTTTTGGCC
Statistics
Matches: 1052, Mismatches: 15, Indels: 16
0.97 0.01 0.01
Matches are distributed among these distances:
389 162 0.15
390 79 0.08
391 4 0.00
392 51 0.05
393 273 0.26
394 111 0.11
395 225 0.21
396 52 0.05
397 95 0.09
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (393 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
AAA
Found at i:1229998 original size:19 final size:19
Alignment explanation
Indices: 1229952--1230000 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1229942 TTATATTCAC
*
1229952 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1229971 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1229990 ATACAAAATTA
1 ATACAAAATTA
1230001 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1231923 original size:21 final size:21
Alignment explanation
Indices: 1231883--1231947 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1231873 CCCCTTATGC
* *
1231883 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1231904 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1231925 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1231946 CT
1 CT
1231948 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1234352 original size:19 final size:20
Alignment explanation
Indices: 1234321--1234365 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1234311 CACTTTTAAA
1234321 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1234340 TGTTACC-GTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1234360 TTTACC
1 TTTACC
1234366 TGGTATATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1235821 original size:28 final size:27
Alignment explanation
Indices: 1235774--1235827 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
1235764 ATGGTTATAT
*
1235774 ATCTATTATTATTTTTATTTGATTATCG
1 ATCTATTA-TATTTTTATTTAATTATCG
1235802 ATCTATTA-ATTTTATCATTTAATTAT
1 ATCTATTATATTTT-T-ATTTAATTAT
1235828 TTAAATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 1 0.04
28 17 0.74
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (27 bp):
ATCTATTATATTTTTATTTAATTATCG
Found at i:1238565 original size:21 final size:21
Alignment explanation
Indices: 1238540--1238581 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1238530 CATATACTGA
1238540 AAGTGAAGATAGTCTTCTCTG
1 AAGTGAAGATAGTCTTCTCTG
1238561 AAGTGAAGATAGTCTTCTCTG
1 AAGTGAAGATAGTCTTCTCTG
1238582 GCCTGCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
AAGTGAAGATAGTCTTCTCTG
Found at i:1239448 original size:125 final size:126
Alignment explanation
Indices: 1239130--1239599 Score: 660
Period size: 126 Copynumber: 3.7 Consensus size: 126
1239120 CAAAGTGGTG
* * *
1239130 AAAGCGCGTTCCCGGGGGCGTGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAAGCGCGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* * * *
1239195 ATATCACTCATATCCCCTGGGGAACTAATCAT-TCAGTACCTATTATTTCTGAGGGGACTT
66 ATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
*** * * *
1239255 AAAAGCGCGTTCTAAGGGGAGCGCCTTCGATTATTCTATCAGAGAATATGTTATCATTGCCCTAT
1 -AAAGCGCGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
* * * *
1239320 TATGTCATTCATGTCCCCCGGGGAACTATTCATGTCAGTGCCTAGTATTT-TTAGGGGACTT
65 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
* *
1239381 ATAAGCGCGTTCCTGGGGG-GCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGTCCTAT
1 A-AAGCGCGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1239445 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
65 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
* * * * * *
1239507 GAAAGTGTGTTCCCGGGGGCGCGCCTTCGCTTATTTTGTCAGCGAATTTGTTATCATTGCCCTTT
1 -AAAGCGCGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1239572 TATGTCACTCATGT-CCCCGGGGAACTAT
65 TATGTCACTCATGTCCCCCGGGGAACTAT
1239600 AGATGGATGG
Statistics
Matches: 304, Mismatches: 35, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
125 90 0.30
126 145 0.48
127 69 0.23
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (126 bp):
AAAGCGCGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
ATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
Found at i:1239577 original size:252 final size:257
Alignment explanation
Indices: 1238882--1239599 Score: 871
Period size: 252 Copynumber: 2.8 Consensus size: 257
1238872 GTGAAGGTAT
1238882 GTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC
1 GTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC
* * * * * *
1238947 TCATGTCCCTCGGGGGCACTATTCATGTCAATACCCA--A------AGTGG---TGAAAGCACGT
66 TCATGTCCC-CCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGT
* * * *
1239001 TCCCGGGGGCTCGCCTAT-GATTGTTTTGTCAGAGAATATGTTATCATTGCCCTCTTATATCACT
130 TCCCGGGGGCGCGCCT-TCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACT
* * *
1239065 CATGTCCCCCGAGGAACTATTCATGTTAGTACCTATTATTTATGAGGGGACTTGGCAAAGTGGTG
194 CATGTCCCCCGGGGAACTATTCATGTCAGTACCTAGTATTTATGAGGGGACTT----AA---GT-
1239130 AAAGCGC
251 AAAGCGC
* *
1239137 GTTCCCGGGGGCGTGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATATCAC
1 GTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC
* * * *
1239202 TCATATCCCCTGGGGAACTAATCAT-TCAGTACCTATTATTTCTGAGGGGACTTAAAAGCGCGTT
66 TCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGTT
*** * * * *
1239266 CTAAGGGGAGCGCCTTCGATTATTCTATCAGAGAATATGTTATCATTGCCCTATTATGTCATTCA
131 CCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCA
* *
1239331 TGTCCCCCGGGGAACTATTCATGTCAGTGCCTAGTATTT-TTAGGGGACTT-A-T-AAGCGC
196 TGTCCCCCGGGGAACTATTCATGTCAGTACCTAGTATTTATGAGGGGACTTAAGTAAAGCGC
* * * *
1239389 GTTCCTGGGGG-GCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCAC
1 GTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC
* *
1239453 TCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGAAAGTGTGTT
66 TCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGTT
* * * *
1239518 CCCGGGGGCGCGCCTTCGCTTATTTTGTCAGCGAATTTGTTATCATTGCCCTTTTATGTCACTCA
131 CCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCA
1239583 TGT-CCCCGGGGAACTAT
196 TGTCCCCCGGGGAACTAT
1239600 AGATGGATGG
Statistics
Matches: 400, Mismatches: 50, Indels: 30
0.83 0.10 0.06
Matches are distributed among these distances:
251 84 0.21
252 109 0.27
253 8 0.02
254 14 0.04
255 72 0.18
258 1 0.00
261 4 0.01
263 11 0.03
264 97 0.24
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (257 bp):
GTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC
TCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGTT
CCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCA
TGTCCCCCGGGGAACTATTCATGTCAGTACCTAGTATTTATGAGGGGACTTAAGTAAAGCGC
Found at i:1239761 original size:23 final size:22
Alignment explanation
Indices: 1239735--1239837 Score: 72
Period size: 23 Copynumber: 4.8 Consensus size: 22
1239725 TGAAGTTTGA
1239735 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGAT-AAATGTTATGG
* * *
1239758 ATAAATTGAATAAATGTGAAGTG
1 ATAAATTGGATAAATGTTATG-G
* * *
1239781 ATCAGTTGG-T---TGTT-TGA
1 ATAAATTGGATAAATGTTATGG
1239798 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGAT-AAATGTTATGG
**
1239821 ATAAATTAAATAAATGT
1 ATAAATTGGATAAATGT
1239838 GAAGTGATAA
Statistics
Matches: 59, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
17 7 0.12
18 2 0.03
19 3 0.05
22 19 0.32
23 28 0.47
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (22 bp):
ATAAATTGGATAAATGTTATGG
Found at i:1239797 original size:63 final size:63
Alignment explanation
Indices: 1239729--1239856 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
1239719 GTTATATGAA
* *
1239729 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTAAATAAATGTGAAGTGATAAGTTGGTT
1239792 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTAAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTAAATAAATGTGAAGTGATAAGTTGGTT
1239855 GT
1 GT
1239857 GGCATTGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATGGATAAATTAAATAAATGTGAAGTGATAAGTTGGTT
Found at i:1240645 original size:21 final size:20
Alignment explanation
Indices: 1240606--1240666 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1240596 CATAAAACCC
* * *
1240606 TGCGGACTAGGCATCTAACA
1 TGCGGGCTAGGAATGTAACA
*
1240626 TGGCGGGCTAGGAATGTAACCC
1 T-GCGGGCTAGGAATGTAA-CA
*
1240648 TGAGGGCTAGGAATGTAAC
1 TGCGGGCTAGGAATGTAAC
1240667 CCTACGAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (20 bp):
TGCGGGCTAGGAATGTAACA
Found at i:1240667 original size:21 final size:21
Alignment explanation
Indices: 1240630--1240669 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1240620 CTAACATGGC
1240630 GGGCTAGGAATGTAACCCTGA
1 GGGCTAGGAATGTAACCCTGA
1240651 GGGCTAGGAATGTAACCCT
1 GGGCTAGGAATGTAACCCT
1240670 ACGAAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCCTGA
Found at i:1242343 original size:25 final size:23
Alignment explanation
Indices: 1242309--1242360 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
1242299 TTCATGATAA
1242309 ATTAAAATTAAAAATAATAATAAAT
1 ATTAAAATTAAAAATAA-AA-AAAT
* **
1242334 ATTAACATTAATTATAAAAAAAT
1 ATTAAAATTAAAAATAAAAAAAT
1242357 ATTA
1 ATTA
1242361 CCATATCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 2 0.08
25 14 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTAAAATTAAAAATAAAAAAAT
Found at i:1242461 original size:20 final size:20
Alignment explanation
Indices: 1242436--1242473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242426 ATAACTGTAA
1242436 ACAAAAAA-AATATAATTAGC
1 ACAAAAAATAAT-TAATTAGC
1242456 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
1242474 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGC
Found at i:1242534 original size:14 final size:15
Alignment explanation
Indices: 1242462--1242552 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 15
1242452 TAGCACAAAA
1242462 AATAATTAAT-TAAT
1 AATAATTAATATAAT
*
1242476 AA-ATTTAA-ATAAAT
1 AATAATTAATAT-AAT
1242490 AATAA-TAATATAAAT
1 AATAATTAATAT-AAT
* *
1242505 ATTATTTAATAAATAAT
1 AATAATTAAT--ATAAT
1242522 AATAATT-ATATAAT
1 AATAATTAATATAAT
*
1242536 TAT-ATTAATATAA-
1 AATAATTAATATAAT
1242549 AATA
1 AATA
1242553 TAACAACTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
13 11 0.18
14 23 0.38
15 10 0.17
16 6 0.10
17 8 0.13
18 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAATTAATATAAT
Found at i:1242537 original size:29 final size:29
Alignment explanation
Indices: 1242462--1242545 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
1242452 TAGCACAAAA
1242462 AATAATTAATTA-ATAA--ATTTAAATAAAT
1 AATAA-TAATTATATAATTATTT-AATAAAT
*
1242490 AATAATAA-TATAAATATTATTTAATAAAT
1 AATAATAATTATATA-ATTATTTAATAAAT
1242519 AATAATAATTATATAATTATATTAATA
1 AATAATAATTATATAATTAT-TTAATA
1242546 TAAAATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
26 2 0.04
27 5 0.10
28 6 0.12
29 20 0.42
30 15 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAATAATTATATAATTATTTAATAAAT
Found at i:1242549 original size:32 final size:33
Alignment explanation
Indices: 1242462--1242549 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 33
1242452 TAGCACAAAA
* *
1242462 AATAAT-TAATTA-ATAAATTTAAATAAATAAT
1 AATAATATAATTATATTAATATAAATAAATAAT
* *
1242493 AATAATATAAATATTATTTA-ATAAAT-AATAAT
1 AATAATATAATTA-TATTAATATAAATAAATAAT
*
1242525 AATTATATAATTATATTAATATAAA
1 AATAATATAATTATATTAATATAAA
1242550 ATATAACAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
31 11 0.24
32 27 0.59
33 5 0.11
34 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AATAATATAATTATATTAATATAAATAAATAAT
Found at i:1242554 original size:23 final size:22
Alignment explanation
Indices: 1242460--1242554 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 22
1242450 ATTAGCACAA
*
1242460 AAAATA-ATTAATTAATAAAT-T
1 AAAATATA-TAATTAATTAATAT
* *
1242481 TAAATAAATAA-TAA-TAATAT
1 AAAATATATAATTAATTAATAT
* *
1242501 -AAATAT-TATTTAATAAATAAT
1 AAAATATATAATTAATTAAT-AT
1242522 AATAATTATATAATTATATTAATAT
1 AA-AA-TATATAATTA-ATTAATAT
1242547 AAAATATA
1 AAAATATA
1242555 ACAACTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
18 2 0.04
19 11 0.19
20 7 0.12
21 10 0.18
22 2 0.04
23 6 0.11
24 5 0.09
25 9 0.16
26 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATATATAATTAATTAATAT
Found at i:1243285 original size:64 final size:64
Alignment explanation
Indices: 1243157--1243285 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
1243147 ATGTTATATC
* * *
1243157 ATTTAATCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATTTAATAAAATAGGT
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAACAGGT
**
1243221 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAACAGGT
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAACAGGT
1243285 A
1 A
1243286 GCGCTTATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (64 bp):
ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAACAGGT
Found at i:1243302 original size:87 final size:87
Alignment explanation
Indices: 1243193--1243477 Score: 525
Period size: 87 Copynumber: 3.3 Consensus size: 87
1243183 AATAACATAT
*
1243193 TAGGTAGCGCTTATTTAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
1 TAGGTAGCGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
1243258 AGGTAGCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
* *
1243280 CAGGTAGCGCTTATATAATAAAATATGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
1 TAGGTAGCGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
1243345 AGGTAGCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
* *
1243367 TAGGTAGCGCTTATATAATAAAATAGGTATTTATCCGGAAATATTATCAAGTACAATAACATATT
1 TAGGTAGCGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
1243432 AGGTAGCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
1243454 TAGGTAGCGCTTATATAATAAAAT
1 TAGGTAGCGCTTATATAATAAAAT
1243478 TTTCTAACTA
Statistics
Matches: 191, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 191 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATATT
AGGTAGCGCTTATATAATGTAA
Found at i:1243370 original size:23 final size:23
Alignment explanation
Indices: 1243344--1243395 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1243334 AATAACATAT
**
1243344 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
1243367 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1243390 TAGGTA
1 TAGGTA
1243396 TTTATCCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1243934 original size:20 final size:20
Alignment explanation
Indices: 1243909--1243955 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1243899 TTTATACCGG
*
1243909 TTACATTGTAAATTTACTTA
1 TTACATTGTAAATCTACTTA
1243929 TTACATTGTAAATCTACTTA
1 TTACATTGTAAATCTACTTA
1243949 TTACATT
1 TTACATT
1243956 ATAATTATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (20 bp):
TTACATTGTAAATCTACTTA
Found at i:1243939 original size:198 final size:200
Alignment explanation
Indices: 1243487--1243939 Score: 605
Period size: 203 Copynumber: 2.3 Consensus size: 200
1243477 TTTTCTAACT
* * * *
1243487 AAACCGGTATATTTATAGCGGTAACATTGCAAATTTACTTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACTTATTACATTGTAATTATCGGTTTCGA
*
1243552 TGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTC
66 TGTTTTTGGGATCGATAT-ATTTTAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTC
1243617 ATTATGGAAAAAAGTATAGACACAAAGTTAAAACGTGTTGTGTCGATACATTATGTAAACCTATT
130 ATTATGGAAAAAAGTATAGACAC-AAGTTAAAAC-TGTTGTGTCGATACATTATGTAAACCTATT
*
1243682 TTCTCATA
193 CTCTCATA
* * *
1243690 AAACCGGTATATTTCTACCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACTTATTACATTGTAATTATCGGTTTCGA
* * *
1243755 TGTTTTTGGGATCGATACT-TTTAATAAATGTATCGACAC-TTATGTATGCACCTGGTTTGGCAT
66 TGTTTTTGGGATCGATA-TATTT--TAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCAT
* ** * * * **
1243818 TCATTATGGATAAAACA-TATCGACAC-TTTTTAAA-T-TT-TTTCGATATATTATGTTGACCTA
128 TCATTATGGA-AAAA-AGTATAGACACAAGTTAAAACTGTTGTGTCGATACATTATGTAAACCTA
1243878 TTCTCTCATA
191 TTCTCTCATA
1243888 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACTTATTACATTGTAA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACTTATTACATTGTAA
1243940 ATCTACTTAT
Statistics
Matches: 222, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
198 77 0.35
199 2 0.01
200 1 0.00
202 8 0.04
203 105 0.47
204 28 0.13
205 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (200 bp):
AAACCGGTATATTTATACCGGTTACATTGTAAATTTACTTATTACATTGTAATTATCGGTTTCGA
TGTTTTTGGGATCGATATATTTTAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCA
TTATGGAAAAAAGTATAGACACAAGTTAAAACTGTTGTGTCGATACATTATGTAAACCTATTCTC
TCATA
Found at i:1244562 original size:21 final size:21
Alignment explanation
Indices: 1244520--1244564 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1244510 CGGTACAAAA
*
1244520 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATAATTATTT
1244541 TTACCTAAAACATCAATT-TTT
1 TTACCTAAAACAT-AATTATTT
1244562 TTA
1 TTA
1244565 ACATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (21 bp):
TTACCTAAAACATAATTATTT
Found at i:1244874 original size:42 final size:43
Alignment explanation
Indices: 1244806--1244889 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 43
1244796 CTCTCATTAT
* * *
1244806 AATATAATTAATGATATATTATTTTTATTATAATA-AATAATA
1 AATATAATTAATAATATATTATTTTTAATAAAATATAATAATA
* *
1244848 AATATAATTTATAATA-ATTTTATTTTAATAAAATATAATAAT
1 AATATAATTAATAATATATTAT-TTTTAATAAAATATAATAAT
1244890 CATAATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.11
42 25 0.71
43 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (43 bp):
AATATAATTAATAATATATTATTTTTAATAAAATATAATAATA
Found at i:1244884 original size:31 final size:30
Alignment explanation
Indices: 1244843--1244936 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
1244833 TTATAATAAA
*
1244843 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
1244873 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
1244903 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
1244931 TAATAA
1 TAATAA
1244937 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:1244936 original size:14 final size:14
Alignment explanation
Indices: 1244854--1244940 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
1244844 AATAAATATA
**
1244854 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
1244869 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
1244882 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
1244896 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
1244910 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
1244924 ATTTTAATAATAAT
1 ATTTTAATAATAAT
1244938 ATT
1 ATT
1244941 GACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:1244936 original size:28 final size:28
Alignment explanation
Indices: 1244868--1244936 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1244858 ATAATAATTT
*
1244868 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
1244895 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
1244923 TATTTTAATAATAA
1 TATTTTAATAATAA
1244937 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:1245094 original size:2 final size:2
Alignment explanation
Indices: 1245089--1245150 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1245079 TTTATTGTAT
1245089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1245130 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1245151 TTTATTTTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1245653 original size:31 final size:32
Alignment explanation
Indices: 1245617--1245709 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 32
1245607 TATACACAAC
* ** *
1245617 AATAACAAAACCAGTACTGCC-TTTTTTATAT
1 AATAACAAAACCAATACCACCTTTTTTTAGAT
*
1245648 AATAACAAAATCAATACCACCTTTTTTTTAGAT
1 AATAACAAAACCAATACCACC-TTTTTTTAGAT
* * *
1245681 AATAACAAAATCGATATCACCTTTTTTTA
1 AATAACAAAACCAATACCACCTTTTTTTA
1245710 ATCGTATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 17 0.32
32 8 0.15
33 28 0.53
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (32 bp):
AATAACAAAACCAATACCACCTTTTTTTAGAT
Found at i:1245683 original size:33 final size:33
Alignment explanation
Indices: 1245638--1245708 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1245628 CAGTACTGCC
*
1245638 TTTTTTATATAATAACAAAATCAATACCACCTT
1 TTTTTTAGATAATAACAAAATCAATACCACCTT
* *
1245671 TTTTTTAGATAATAACAAAATCGATATCACCTT
1 TTTTTTAGATAATAACAAAATCAATACCACCTT
1245704 TTTTT
1 TTTTT
1245709 AATCGTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (33 bp):
TTTTTTAGATAATAACAAAATCAATACCACCTT
Found at i:1250628 original size:116 final size:117
Alignment explanation
Indices: 1250358--1250804 Score: 770
Period size: 117 Copynumber: 3.8 Consensus size: 117
1250348 GGGGACTTGG
* *
1250358 CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
* *
1250423 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACC
66 TTGCCCTATTATATCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
* *
1250475 CAAAGTGGTGAAGGCGCGTTCCCGGGGACGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
*
1250540 TTTCCCTATTATATCACTCATGTCCCTC-GGGGCACTATTCATGTCAGTACC
66 TTGCCCTATTATATCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
* * *
1250591 CAAAGTGGTGAAGGCGCGTTCCCGGGGGTGCGCCTTCGATTATTTTGTCAAAGAATATGTTATCA
1 CAAAGTGGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
*
1250656 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
66 TTGCCCTATTATATCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
*
1250708 CAAAGTGGTGAAGGCGCGTTCCCAGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
*
1250773 TTGCCCTATTATATCACTCATGTCCCCCGGGG
66 TTGCCCTATTATATCACTCATGTCCCTCGGGG
1250805 AACTATAGAT
Statistics
Matches: 311, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
116 110 0.35
117 201 0.65
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (117 bp):
CAAAGTGGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
TTGCCCTATTATATCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACC
Found at i:1250765 original size:233 final size:233
Alignment explanation
Indices: 1250358--1250810 Score: 800
Period size: 233 Copynumber: 1.9 Consensus size: 233
1250348 GGGGACTTGG
*
1250358 CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAAAGAATATGTTATCA
1250423 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCCAAAGTGGTGAAG
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCCAAAGTGGTGAAG
* *
1250488 GCGCGTTCCCGGGGACGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTTCCCTATTATA
131 GCGCGTTCCCGGGGACGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATA
* *
1250553 TCACTCATGTCCCTCGGGGCACTATTCATGTCAGTACC
196 TCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACC
* * * *
1250591 CAAAGTGGTGAAGGCGCGTTCCCGGGGGTGCGCCTTCGATTATTTTGTCAAAGAATATGTTATCA
1 CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAAAGAATATGTTATCA
*
1250656 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAG
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCCAAAGTGGTGAAG
1250721 GCGCGTTCCCAGGGG-CGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
131 GCGCGTTCCC-GGGGACGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
1250785 ATCACTCATGTCCCCCGGGGAACTAT
195 ATCACTCATGTCCCCCGGGGAACTAT
1250811 AGATGGATGG
Statistics
Matches: 209, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
233 205 0.98
234 4 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (233 bp):
CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAAAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCCAAAGTGGTGAAG
GCGCGTTCCCGGGGACGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATA
TCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACC
Found at i:1250971 original size:23 final size:23
Alignment explanation
Indices: 1250945--1251047 Score: 87
Period size: 23 Copynumber: 4.7 Consensus size: 23
1250935 ATGTGAAGTT
1250945 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
*
1250968 TGAATAAATTGAAT-AAATGTTAA
1 TGAATAAATTGGATAAAATGTT-A
*
1250991 GTG-ATCAATTGG-T----TGTT-
1 -TGAATAAATTGGATAAAATGTTA
*
1251008 TGAATATATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
1251031 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
1251048 TGTGAAGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
16 2 0.03
17 7 0.11
18 1 0.02
19 4 0.06
22 12 0.19
23 35 0.56
24 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.18, T:0.37
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:1251010 original size:63 final size:63
Alignment explanation
Indices: 1250942--1251066 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
1250932 GTTATGTGAA
*
1250942 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTTAAGTGATCAA-TTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGAT-AAGTTGGTT
* *
1251005 GTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGT
1251067 CGTGACATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 2 0.03
63 56 0.97
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:1251041 original size:40 final size:41
Alignment explanation
Indices: 1250963--1251041 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
1250953 TTGGATAAAA
*
1250963 TGTTATGAATAAATTGAATAAATGTTAAGTGATCAATTGGT
1 TGTTATGAATAAATTGAATAAATGTTAAGTGATAAATTGGT
* * *
1251004 TGTT-TGAATATATTGGATAAAATGTTATG-GATAAATTG
1 TGTTATGAATAAATTGAAT-AAATGTTAAGTGATAAATTG
1251042 AATAAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 20 0.61
41 13 0.39
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (41 bp):
TGTTATGAATAAATTGAATAAATGTTAAGTGATAAATTGGT
Found at i:1251295 original size:34 final size:34
Alignment explanation
Indices: 1251257--1251329 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1251247 TTAAGTTGAA
1251257 TTTAATGTTAAATTTTGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTTGAATACCATAATTTGTAT
* *
1251291 TTTAATTTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTTGAATACCATAATTTGTAT
*
1251325 ATTAA
1 TTTAA
1251330 AAACATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTTGAATACCATAATTTGTAT
Found at i:1251889 original size:21 final size:21
Alignment explanation
Indices: 1251865--1251904 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1251855 ATAACCTGGC
1251865 GGGCTAGGAATGTAACCCTAA
1 GGGCTAGGAATGTAACCCTAA
1251886 GGGCTAGGAATGTAACCCT
1 GGGCTAGGAATGTAACCCT
1251905 GCGGAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCCTAA
Found at i:1251932 original size:42 final size:42
Alignment explanation
Indices: 1251886--1251968 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
1251876 GTAACCCTAA
* *
1251886 GGGCTAGGAATGTAACCCTGCGGAGATGGCATATAAACTGGT
1 GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGGT
* ** * * *
1251928 GGGCTTGGCCTATACCCCTGAGGAGATGGCATCTGAACTGG
1 GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGG
1251969 AAGGCTGGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (42 bp):
GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGGT
Found at i:1253683 original size:15 final size:15
Alignment explanation
Indices: 1253647--1253711 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
1253637 AAAAAATAAT
*
1253647 TAAATAATAAATGTAAA
1 TAAATAAT-AAT-TATA
1253664 TAAATAATAATTATA
1 TAAATAATAATTATA
* *
1253679 TAAAT-ATTATTTTAA
1 TAAATAATAATTAT-A
* *
1253694 TAAAAAATATTTATA
1 TAAATAATAATTATA
1253709 TAA
1 TAA
1253712 TTATATTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 6 0.15
15 17 0.44
16 8 0.21
17 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TAAATAATAATTATA
Found at i:1254504 original size:18 final size:18
Alignment explanation
Indices: 1254481--1254515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1254471 GGGTACGACA
1254481 TATAAAAAAATTTAAAAT
1 TATAAAAAAATTTAAAAT
* *
1254499 TATAAATAGATTTAAAA
1 TATAAAAAAATTTAAAA
1254516 AATCATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAAAAAAATTTAAAAT
Found at i:1258025 original size:18 final size:19
Alignment explanation
Indices: 1257990--1258025 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1257980 CACGGAATGT
1257990 AAGATTACCAGTGGAATAA
1 AAGATTACCAGTGGAATAA
1258009 AAGATTACCAG-GGAATA
1 AAGATTACCAGTGGAATA
1258026 GGATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGTGGAATAA
Found at i:1267244 original size:32 final size:32
Alignment explanation
Indices: 1267208--1267271 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1267198 TCTCAATTGG
* *
1267208 ATCACATCGGGATCACAAGATTGATTGTGCTT
1 ATCACATAGGGATCAAAAGATTGATTGTGCTT
1267240 ATCACATAGGGATCAAAAGATTGATTGTGCTT
1 ATCACATAGGGATCAAAAGATTGATTGTGCTT
1267272 TTATGGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (32 bp):
ATCACATAGGGATCAAAAGATTGATTGTGCTT
Found at i:1269308 original size:29 final size:29
Alignment explanation
Indices: 1269266--1269326 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1269256 GAATTGGTCG
1269266 TGTGTTTCAATCTAGACTAGTTTAATTCA
1 TGTGTTTCAATCTAGACTAGTTTAATTCA
1269295 TGTGTTTCAATCTAGACTAGTTTAATTCA
1 TGTGTTTCAATCTAGACTAGTTTAATTCA
1269324 TGT
1 TGT
1269327 ATTCCCTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (29 bp):
TGTGTTTCAATCTAGACTAGTTTAATTCA
Found at i:1270060 original size:2 final size:2
Alignment explanation
Indices: 1270053--1270090 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1270043 CATTCCCTGC
1270053 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
1270091 TTGGGTTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1278011 original size:29 final size:28
Alignment explanation
Indices: 1277979--1278041 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1277969 TTTTTACAAG
* *
1277979 TTTTATTTATT-TTAAATATATAGTTTTAA
1 TTTTATTCATTGTTAAAT-TATA-TGTTAA
*
1278008 TTTTATTCATTGTTTAATTATATGTTAA
1 TTTTATTCATTGTTAAATTATATGTTAA
1278036 TTTTAT
1 TTTTAT
1278042 ATGTTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 14 0.47
30 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTATTCATTGTTAAATTATATGTTAA
Found at i:1278295 original size:20 final size:19
Alignment explanation
Indices: 1278270--1278311 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1278260 CTATTTTATA
1278270 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
1278290 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1278309 AAT
1 AAT
1278312 ATAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1278306 original size:119 final size:117
Alignment explanation
Indices: 1278178--1278402 Score: 276
Period size: 119 Copynumber: 1.9 Consensus size: 117
1278168 CCTGTTTTAA
* * * * *
1278178 TATTTATTTTTTAATAT-TAAGAAAGGGCAT-TCTTAAAACAACTGGATGTCCATTTTCTGATAT
1 TATTTATTTTTTAATATAAAAAAAAGAG-ATGTCTTAAAACAACTAGATAT-CATTTTCTGATAT
* *
1278241 TTTTAAATAAATAAATATCCTAT-TTTATAAATTATATATTAATTATTTTAATTATT
64 TTATAAATAAATAAATAT--TATGTTTATAAA-TATATATAAATTATTTTAATTATT
* ** *
1278297 TATTTATTTTTTAATATAAAAAAAAGAGTTGTCTTAAGGCACCTAGATATCATTTTCTGATATTT
1 TATTTATTTTTTAATATAAAAAAAAGAGATGTCTTAAAACAACTAGATATCATTTTCTGATATTT
*
1278362 ATAAATAAATAAATATTTTGTTTATAAATATATATAAATTA
66 ATAAATAAATAAATATTATGTTTATAAATATATATAAATTA
1278403 ATATTTTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
117 14 0.15
118 8 0.09
119 48 0.53
120 21 0.23
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (117 bp):
TATTTATTTTTTAATATAAAAAAAAGAGATGTCTTAAAACAACTAGATATCATTTTCTGATATTT
ATAAATAAATAAATATTATGTTTATAAATATATATAAATTATTTTAATTATT
Found at i:1278398 original size:29 final size:30
Alignment explanation
Indices: 1278361--1278424 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1278351 TTCTGATATT
1278361 TATAAATAAATAAATATTTTGTTT-ATAAA
1 TATAAATAAATAAATATTTTGTTTCATAAA
* * * *
1278390 TATATATAAATTAATATTTTTTTTCATAAT
1 TATAAATAAATAAATATTTTGTTTCATAAA
1278420 TATAA
1 TATAA
1278425 TTTTGAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TATAAATAAATAAATATTTTGTTTCATAAA
Found at i:1279004 original size:42 final size:42
Alignment explanation
Indices: 1278945--1279029 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1278935 GCCAATCAAA
1278945 CACAAATGCCAAACGCCGAATTACTTTGACAGAATTTGTTAT
1 CACAAATGCCAAACGCCGAATTACTTTGACAGAATTTGTTAT
1278987 CACAAATGCCAAACGCCGAATTACTTTGACAGAATTTGTTAT
1 CACAAATGCCAAACGCCGAATTACTTTGACAGAATTTGTTAT
1279029 C
1 C
1279030 TTTCTCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (42 bp):
CACAAATGCCAAACGCCGAATTACTTTGACAGAATTTGTTAT
Found at i:1311885 original size:17 final size:17
Alignment explanation
Indices: 1311863--1311897 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1311853 AGTCAATGGT
*
1311863 CAGTCAACGGTGATCAA
1 CAGTCAACAGTGATCAA
*
1311880 CAGTCAACAGTGGTCAA
1 CAGTCAACAGTGATCAA
1311897 C
1 C
1311898 GACGGTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (17 bp):
CAGTCAACAGTGATCAA
Found at i:1321459 original size:16 final size:16
Alignment explanation
Indices: 1321438--1321468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1321428 AATAATAAAA
*
1321438 TAATAAATATTAATAG
1 TAATAAATATAAATAG
1321454 TAATAAATATAAATA
1 TAATAAATATAAATA
1321469 TAAAAGGTTT
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:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAATAAATATAAATAG
Found at i:1327112 original size:20 final size:21
Alignment explanation
Indices: 1327087--1327179 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
1327077 TTTTGCCAAT
*
1327087 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1327107 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
1327128 TCGCAATGTGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
1327148 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1327169 TCGCAATGCGA
1 TCGCAATGCGA
1327180 TACTGATTAT
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 25 0.46
21 29 0.54
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1327132 original size:41 final size:41
Alignment explanation
Indices: 1327087--1327179 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
1327077 TTTTGCCAAT
*
1327087 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
*
1327128 TCGCAATGTGAATAAGTAAATCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
1327169 TCGCAATGCGA
1 TCGCAATGCGA
1327180 TACTGATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
Found at i:1327214 original size:21 final size:20
Alignment explanation
Indices: 1327165--1327215 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1327155 GCGAATTGGG
* *
1327165 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
1327185 ATTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
1327206 AAAATCGCAA
1 AAAATCGCAA
1327216 CGAGATACTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:1327241 original size:19 final size:20
Alignment explanation
Indices: 1327213--1327252 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1327203 TAAAAAATCG
1327213 CAACGAGATACT-ACTTTCA
1 CAACGAGATACTGACTTTCA
*
1327232 CAACGCGATACTGACTTTCA
1 CAACGAGATACTGACTTTCA
1327252 C
1 C
1327253 GTAGAAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (20 bp):
CAACGAGATACTGACTTTCA
Found at i:1327993 original size:18 final size:18
Alignment explanation
Indices: 1327972--1328016 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1327962 TCCACTTCGG
*
1327972 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1327990 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1328008 GAGCCATCA
1 GAGCCATCA
1328017 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1328548 original size:19 final size:20
Alignment explanation
Indices: 1328494--1328560 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1328484 TAGTTTACTT
* *
1328494 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1328514 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1328534 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1328553 TCGCAACG
1 TCGCAACG
1328561 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1328583 original size:15 final size:14
Alignment explanation
Indices: 1328549--1328594 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
1328539 ATGCGAAATG
1328549 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1328563 AAAATCGCAACG-C
1 AAAATCGCAACGAC
*
1328576 GAAAAATCGCAATGAC
1 --AAAATCGCAACGAC
1328592 AAA
1 AAA
1328595 GCGAAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 15 0.54
15 11 0.39
16 1 0.04
ACGTcount: A:0.52, C:0.24, G:0.15, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1328608 original size:24 final size:26
Alignment explanation
Indices: 1328541--1328641 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 26
1328531 CTATCGCAAT
* *
1328541 GCGAAATGAAAATCGCAACGACAAAA
1 GCGAAATGAAAATCGCAATGACAACA
* **
1328567 TCGCAACGCGAAAAATCGCAATGACAA-A
1 GCG-AA-ATG-AAAATCGCAATGACAACA
*
1328595 GCGAAATG-AAATCGCAATGACAATCGC
1 GCGAAATGAAAATCGCAATGACAA-C-A
1328622 GCGAAATGAAAATCGCAATG
1 GCGAAATGAAAATCGCAATG
1328642 CGATTTGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
24 15 0.25
26 3 0.05
27 12 0.20
28 15 0.25
29 15 0.25
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (26 bp):
GCGAAATGAAAATCGCAATGACAACA
Found at i:1328621 original size:12 final size:12
Alignment explanation
Indices: 1328580--1328621 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1328570 CAACGCGAAA
1328580 AATCGCAATGAC
1 AATCGCAATGAC
* *
1328592 AAAGCGAAATGA-
1 -AATCGCAATGAC
1328604 AATCGCAATGAC
1 AATCGCAATGAC
1328616 AATCGC
1 AATCGC
1328622 GCGAAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.38
12 6 0.25
13 9 0.38
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (12 bp):
AATCGCAATGAC
Found at i:1328733 original size:20 final size:19
Alignment explanation
Indices: 1328699--1328753 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1328689 GTTGCATTTT
*
1328699 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1328718 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1328738 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1328754 TTAAGTTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1330640 original size:19 final size:19
Alignment explanation
Indices: 1330627--1330694 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1330617 TATGCAACGA
1330627 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1330646 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1330665 AAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1330679 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1330695 TTTTCATTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1330769 original size:20 final size:20
Alignment explanation
Indices: 1330712--1330769 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1330702 TCGCATTGCG
* *
1330712 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1330732 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1330752 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1330770 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1334372 original size:33 final size:33
Alignment explanation
Indices: 1334330--1334456 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1334320 GGAAATTACT
1334330 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1334363 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1334395 TTTCGCAATGTGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1334429 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1334457 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1334437 original size:66 final size:66
Alignment explanation
Indices: 1334331--1334463 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1334321 GAAATTACTA
*
1334331 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1334396 T
66 T
* *
1334397 TCGCAATGTGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1334462 T
66 T
1334463 T
1 T
1334464 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1334478 original size:19 final size:20
Alignment explanation
Indices: 1334456--1334498 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1334446 AAATCGCAAC
1334456 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1334475 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1334495 GCGA
1 GCGA
1334499 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1334483 original size:14 final size:14
Alignment explanation
Indices: 1334484--1334517 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1334474 TGCGATTTTC
1334484 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1334498 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1334512 ATTTTC
1 ATTTTC
1334518 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1334658 original size:14 final size:14
Alignment explanation
Indices: 1334639--1334675 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1334629 CATCAATTAA
1334639 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1334653 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1334667 ACAAATCAA
1 ACAAATCAA
1334676 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1336088 original size:21 final size:21
Alignment explanation
Indices: 1336022--1336088 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1336012 GTGAATCGGG
*
1336022 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1336042 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1336064 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1336085 CTCT
1 CTCT
1336089 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Done.