Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 39
Found at i:1411833 original size:20 final size:20
Alignment explanation
Indices: 1411808--1411848 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1411798 ATTTTCTTTG
1411808 AAAATTTTA-TTTGAAAAATT
1 AAAA-TTTACTTTGAAAAATT
1411828 AAAATTTACTTTGAAAAATT
1 AAAATTTACTTTGAAAAATT
1411848 A
1 A
1411849 CTCCCCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAATTTACTTTGAAAAATT
Found at i:1412260 original size:21 final size:21
Alignment explanation
Indices: 1412236--1412282 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1412226 CATGTCGAGC
*
1412236 CTATCATCCACTGCATTGAAT
1 CTATCATCCACTGCATCGAAT
* *
1412257 CTATCATCTATTGCATCGAAT
1 CTATCATCCACTGCATCGAAT
1412278 CTATC
1 CTATC
1412283 TCGAGTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (21 bp):
CTATCATCCACTGCATCGAAT
Found at i:1423977 original size:25 final size:22
Alignment explanation
Indices: 1423948--1423998 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1423938 AACGCTTAGC
1423948 GCCACCACCGACCGCCGCTTTG
1 GCCACCACCGACCGCCGCTTTG
**
1423970 GCCACCACCGACCTTCGCTTTG
1 GCCACCACCGACCGCCGCTTTG
1423992 GCCACCA
1 GCCACCA
1423999 TCACCGGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.49, G:0.20, T:0.16
Consensus pattern (22 bp):
GCCACCACCGACCGCCGCTTTG
Found at i:1424382 original size:18 final size:19
Alignment explanation
Indices: 1424345--1424382 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1424335 ATGCCCCTTT
1424345 TTTTCTCTTTATTTTTTCC
1 TTTTCTCTTTATTTTTTCC
1424364 TTTTCT-TTT-TTTGTTTCC
1 TTTTCTCTTTATTT-TTTCC
1424382 T
1 T
1424383 CCCCTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 9 0.50
19 6 0.33
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTATTTTTTCC
Found at i:1425294 original size:18 final size:18
Alignment explanation
Indices: 1425273--1425308 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1425263 AAGGGTTTTG
* *
1425273 GTAAAAATATATTAAATA
1 GTAAAAAGAGATTAAATA
1425291 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGATTAAATA
1425309 AAAGGCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
GTAAAAAGAGATTAAATA
Found at i:1438202 original size:21 final size:21
Alignment explanation
Indices: 1438160--1438203 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1438150 ACCTCGGGAG
*
1438160 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1438181 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1438202 CT
1 CT
1438204 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1438827 original size:31 final size:31
Alignment explanation
Indices: 1438789--1438859 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1438779 ATTTAACAAA
1438789 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
* * ***
1438820 AAGGGGGAGTAAGTTTTTTATGTGCTATAGT
1 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1438851 AAGGGGGAG
1 AAGGGGGAG
1438860 TAAGTTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.28
Consensus pattern (31 bp):
AAGGGGGAGAAAATTTAAGATGTGCTATAGT
Found at i:1438860 original size:31 final size:31
Alignment explanation
Indices: 1438808--1438868 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1438798 AAAATTTAAG
1438808 ATGTGCTATAGTAAGGGGGAGTAAGTTTTTT
1 ATGTGCTATAGTAAGGGGGAGTAAGTTTTTT
1438839 ATGTGCTATAGTAAGGGGGAGTAAGTTTTT
1 ATGTGCTATAGTAAGGGGGAGTAAGTTTTT
1438869 CAAAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.33, T:0.38
Consensus pattern (31 bp):
ATGTGCTATAGTAAGGGGGAGTAAGTTTTTT
Found at i:1446160 original size:20 final size:20
Alignment explanation
Indices: 1446148--1446185 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1446138 TCGATACTGT
*
1446148 AAGGGTAGTATCGATACCCA
1 AAGGATAGTATCGATACCCA
1446168 AAGGATAGTATCGATACC
1 AAGGATAGTATCGATACC
1446186 ATCTTTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (20 bp):
AAGGATAGTATCGATACCCA
Found at i:1446865 original size:21 final size:20
Alignment explanation
Indices: 1446841--1446911 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 20
1446831 TTATGTTGTC
1446841 CTTCAGGACAAATATGTGGCA
1 CTTC-GGACAAATATGTGGCA
*
1446862 CTTCGGTGCAAATCTATGTGGTCA
1 CTTCGG-ACAAA--TATGTGG-CA
* *
1446886 -TTCGGGATAATTATGTGGCA
1 CTTC-GGACAAATATGTGGCA
1446906 CTTCGG
1 CTTCGG
1446912 TGCAAATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
20 6 0.15
21 18 0.45
23 12 0.30
24 4 0.10
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (20 bp):
CTTCGGACAAATATGTGGCA
Found at i:1446889 original size:23 final size:22
Alignment explanation
Indices: 1446849--1446920 Score: 89
Period size: 21 Copynumber: 3.3 Consensus size: 22
1446839 TCCTTCAGGA
1446849 CAAA-TATGTGGCACTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
1446870 CAAATCTATGTGGTCA-TTCGG-G
1 CAAAT-TATGTGG-CACTTCGGTG
1446892 -ATAATTATGTGGCACTTCGGTG
1 CA-AATTATGTGGCACTTCGGTG
1446914 CAAATTA
1 CAAATTA
1446921 CAAGCTGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
20 2 0.05
21 17 0.39
22 10 0.23
23 13 0.30
24 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (22 bp):
CAAATTATGTGGCACTTCGGTG
Found at i:1449264 original size:19 final size:19
Alignment explanation
Indices: 1449240--1449278 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1449230 CTTGTTAATT
1449240 AAATTTGGGTTGAAATTAA
1 AAATTTGGGTTGAAATTAA
1449259 AAATTTGGGTTGAAATTAA
1 AAATTTGGGTTGAAATTAA
1449278 A
1 A
1449279 TTCCTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
AAATTTGGGTTGAAATTAA
Found at i:1449369 original size:44 final size:45
Alignment explanation
Indices: 1449304--1449398 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 45
1449294 AGAATATGAT
* *
1449304 TTAAATTGATTATTTATTTTAAAATG-AGTTTTAAA-TAAGTAATAA
1 TTAAATTGAATATTTAATTTAAAA-GAAGTTTTAAATTAA-TAATAA
1449349 TTAAATT-AATATTTAATTTAAAAGAAGTTTTAAATTAATAATAA
1 TTAAATTGAATATTTAATTTAAAAGAAGTTTTAAATTAATAATAA
1449393 TTAAAT
1 TTAAAT
1449399 AAGTTAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.02
44 35 0.76
45 10 0.22
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (45 bp):
TTAAATTGAATATTTAATTTAAAAGAAGTTTTAAATTAATAATAA
Found at i:1450110 original size:18 final size:18
Alignment explanation
Indices: 1450087--1450122 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1450077 CCACGCCTTC
*
1450087 ATCAATATTGTTTCTAGG
1 ATCAATATTGTGTCTAGG
1450105 ATCAATATTGTGTCTAGG
1 ATCAATATTGTGTCTAGG
1450123 TTCGAGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (18 bp):
ATCAATATTGTGTCTAGG
Found at i:1456754 original size:226 final size:226
Alignment explanation
Indices: 1456324--1456774 Score: 701
Period size: 226 Copynumber: 2.0 Consensus size: 226
1456314 TGACATGCTC
*
1456324 TTGTAGTACAGCATGTAGTGCACTATTTATGTATGTTTCGTTCCAATTTTAGACAGGTTTTCATG
1 TTGTAGTACAGCATGTAGTGCACTAGTTATGTATGTTTCGTTCCAATTTTAGACAGGTTTTCATG
* * * *
1456389 ATATGCTTGTTTTGTTGCAGGCCAAAGAGAAAGTGATTAAACAATGATCTATTTTTTTATAGCTG
66 ATATGCTCGTTTTGTTACAGGCCAAAGAGAAAGTGATAAAACAATGATCTATTTTTATATAGCTG
*
1456454 GTTAGATATTTCATGAGATGGTGCTGTAGGTTGTCATGAATTGCTTAACAACTCATTCCTCTTAA
131 GTTAGATATTTCATGAGATGGTGCTGTAGGTTGTCATGAATTGCTTAACAACTCATGCCTCTTAA
* *
1456519 CC-CCCCCCCCCCCCGGGGGGAAAACTATCTA
196 CCACCCCCCCCCCCC-GCGGGAAAACCATCTA
* * * * *
1456550 TTGTAGTGCAGCATGTAGTGTACTAGTTGTGTATGTTTTGTTCCAATTTTAGATAGGTTTTCATG
1 TTGTAGTACAGCATGTAGTGCACTAGTTATGTATGTTTCGTTCCAATTTTAGACAGGTTTTCATG
* * * *
1456615 CTATGCTCGTTTTGTTACAGGCTAAAGAGAAGGTGATAAAACAATTATCTA-TTTTATATAGCTG
66 ATATGCTCGTTTTGTTACAGGCCAAAGAGAAAGTGATAAAACAATGATCTATTTTTATATAGCTG
1456679 GTTAGATATTTCATGAGATGGTGCTGTAGGTTGTCATGAATTGCTTAAC-ACTCATGCCTCTTAA
131 GTTAGATATTTCATGAGATGGTGCTGTAGGTTGTCATGAATTGCTTAACAACTCATGCCTCTTAA
1456743 CCAAACCCCCCCCCCCCGCGGGAAAACCATCT
196 CC--ACCCCCCCCCCCCGCGGGAAAACCATCT
1456775 CACTTTGTGT
Statistics
Matches: 205, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
224 16 0.08
225 61 0.30
226 116 0.57
227 12 0.06
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (226 bp):
TTGTAGTACAGCATGTAGTGCACTAGTTATGTATGTTTCGTTCCAATTTTAGACAGGTTTTCATG
ATATGCTCGTTTTGTTACAGGCCAAAGAGAAAGTGATAAAACAATGATCTATTTTTATATAGCTG
GTTAGATATTTCATGAGATGGTGCTGTAGGTTGTCATGAATTGCTTAACAACTCATGCCTCTTAA
CCACCCCCCCCCCCCGCGGGAAAACCATCTA
Found at i:1463204 original size:11 final size:11
Alignment explanation
Indices: 1463188--1463221 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1463178 TAAAAATAAG
1463188 GGTACAAGTTA
1 GGTACAAGTTA
1463199 GGTACAAGTTA
1 GGTACAAGTTA
1463210 GGTACAAGTTA
1 GGTACAAGTTA
1463221 G
1 G
1463222 TAGCTGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.26
Consensus pattern (11 bp):
GGTACAAGTTA
Found at i:1466685 original size:23 final size:22
Alignment explanation
Indices: 1466663--1466723 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1466653 TCGTGTGAGC
*
1466663 CTTTAAATTTGAGAGATGAGAG
1 CTTTAAGTTTGAGAGATGAGAG
**
1466685 CTAGAGAGTTTGAGAGATGAGAG
1 CTTTA-AGTTTGAGAGATGAGAG
1466708 CTTATAAGTTTGAGAG
1 CTT-TAAGTTTGAGAG
1466724 TGTATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.09
23 28 0.88
24 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (22 bp):
CTTTAAGTTTGAGAGATGAGAG
Found at i:1470413 original size:39 final size:39
Alignment explanation
Indices: 1470308--1470495 Score: 222
Period size: 39 Copynumber: 4.8 Consensus size: 39
1470298 TATTTACAGA
* *
1470308 CTCCTC-GACTTTGTACTCAGGGTAAGTCCTTACCGTAGG
1 CTCCTCTG-CTTTGTGCTCAGGGTAAGTCCTTACTGTAGG
** * *
1470347 -TCCTCAACTTTCTGCTCAGGGTAAGTCCTTACTGCAGG
1 CTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGG
*
1470385 CTTCT-TAGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGG
1 CTCCTCT-GCTTTGTGCTCAGGGTAAGTCCTTACTGTAGG
** *
1470424 CTCCTCTGCTTTGTG-TACATAGTAAGTCCTTACGGTAGG
1 CTCCTCTGCTTTGTGCT-CAGGGTAAGTCCTTACTGTAGG
*
1470463 CTCCTCTGCTTTGTGCACAGGGTAAGTCCTTAC
1 CTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTAC
1470496 CGCAAGTCCT
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 33 0.26
39 92 0.73
40 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (39 bp):
CTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGG
Found at i:1470512 original size:39 final size:40
Alignment explanation
Indices: 1470316--1470516 Score: 200
Period size: 39 Copynumber: 5.2 Consensus size: 40
1470306 GACTCCTCGA
* * *
1470316 CTTTGTACTCAGGGTAAGTCCTTACCGTAGG-TCCTCA-A
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAGGCTCCTTATG
* * * *
1470354 CTTTCTGCTCAGGGTAAGTCCTTACTGCAGGCTTCTTA-G
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAGGCTCCTTATG
* *
1470393 CTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCC-TCTG
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAGGCTCCTTATG
** * *
1470432 CTTTGTG-TACATAGTAAGTCCTTACGGTAGGCTCC-TCTG
1 CTTTGTGCT-CAGGGTAAGTCCTTACCGTAGGCTCCTTATG
* * *
1470471 CTTTGTGCACAGGGTAAGTCCTTACCGCAAG-TCCTTATG
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAGGCTCCTTATG
1470510 CTTTGTG
1 CTTTGTG
1470517 TATAAGGCCC
Statistics
Matches: 137, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
38 32 0.23
39 105 0.77
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (40 bp):
CTTTGTGCTCAGGGTAAGTCCTTACCGTAGGCTCCTTATG
Found at i:1476032 original size:14 final size:14
Alignment explanation
Indices: 1476009--1476040 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1475999 TCAATCTTTT
1476009 ATTA-ATTAATATA
1 ATTATATTAATATA
1476022 ATTATATTAATATA
1 ATTATATTAATATA
1476036 ATTAT
1 ATTAT
1476041 TTTTATCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATATTAATATA
Found at i:1481374 original size:30 final size:30
Alignment explanation
Indices: 1481331--1481394 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
1481321 AAGCCTTATA
* ** *
1481331 AAAAATTAGGGACCATTTTG-TAATTTTTG
1 AAAAACTAGGGACCAAATTGATAATTTTGG
1481360 AAAAACTAGAGGACCAAATTGATAATTTTGG
1 AAAAACTAG-GGACCAAATTGATAATTTTGG
1481391 AAAA
1 AAAA
1481395 GTTTTAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.28
30 9 0.31
31 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (30 bp):
AAAAACTAGGGACCAAATTGATAATTTTGG
Found at i:1482365 original size:2 final size:2
Alignment explanation
Indices: 1482358--1482405 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1482348 CACTACAGTG
1482358 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
1482400 TA TA TA
1 TA TA TA
1482406 AATTACTCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1487050 original size:30 final size:28
Alignment explanation
Indices: 1486977--1487068 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
1486967 CCAAATTTTG
* * *
1486977 GTTAGTGACCAAAATATAAATTTTAAAA
1 GTTAGGGACTAAAATATAAATTTAAAAA
* *
1487005 GTTAAGTAGCTAAAATATAAACTTTAGAAAA
1 GTTAGGGA-CTAAAATATAAA-TTTA-AAAA
*
1487036 GTTAGGGACTAAAATGATAATTTTAAAAA
1 GTTAGGGACTAAAAT-ATAAATTTAAAAA
1487065 GTTA
1 GTTA
1487069 CAATCCAGCC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.10
29 19 0.37
30 14 0.27
31 14 0.27
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (28 bp):
GTTAGGGACTAAAATATAAATTTAAAAA
Found at i:1490627 original size:2 final size:2
Alignment explanation
Indices: 1490620--1490672 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1490610 ATCTTAAGAC
* *
1490620 AT AT AT AT AC AT AT AT AT AT AT AT AC 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
1490662 AT AT AT AT AT A
1 AT AT AT AT AT A
1490673 GACGAGTAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1491701 original size:24 final size:24
Alignment explanation
Indices: 1491661--1491706 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1491651 CATTGAATAC
* *
1491661 TTGTATATTTGATATTCTTGATGT
1 TTGTACATTTGATATTCCTGATGT
1491685 TTGTACATTTAGA-ATTCCTGAT
1 TTGTACATTT-GATATTCCTGAT
1491707 ACTCAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
TTGTACATTTGATATTCCTGATGT
Found at i:1495792 original size:24 final size:24
Alignment explanation
Indices: 1495762--1495903 Score: 189
Period size: 24 Copynumber: 5.9 Consensus size: 24
1495752 AACCATAATT
* *
1495762 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* * *
1495786 CAGGTCAAGTATTATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1495810 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1495834 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
1495858 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
1495882 CATGTCAAGTATCAGATCAGAA
1 CATGTCAAGTATCAGATCAGAA
1495904 ATCAAATCGA
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 2 0.02
24 103 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:1495853 original size:12 final size:12
Alignment explanation
Indices: 1495819--1495878 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1495809 CCAAGTCAAG
*
1495819 TATCAGATCAGA
1 TATCATATCAGA
*
1495831 -ATCCATGTCAGA
1 TAT-CATATCAGA
1495843 TATCATATCAGA
1 TATCATATCAGA
*
1495855 -ATCCATGTCAGA
1 TAT-CATATCAGA
*
1495867 TATCAGATCAGA
1 TATCATATCAGA
1495879 ATCCATGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 4 0.11
12 30 0.79
13 4 0.11
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (12 bp):
TATCATATCAGA
Found at i:1498225 original size:17 final size:17
Alignment explanation
Indices: 1498203--1498239 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1498193 ATCAACGATT
*
1498203 AACGCATGTCACCGGTC
1 AACGCATGTCAACGGTC
1498220 AACGCATGTCAACGGTC
1 AACGCATGTCAACGGTC
1498237 AAC
1 AAC
1498240 AGTCAACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (17 bp):
AACGCATGTCAACGGTC
Found at i:1500473 original size:24 final size:24
Alignment explanation
Indices: 1500417--1500531 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
1500407 CATAATTCAT
* *
1500417 GTCAAGTATCATATCAAAAT-CAA
1 GTCAAGTATCAGATCAGAATCCAA
1500440 GGT-AATGTATCAGATCAGAATCCAA
1 -GTCAA-GTATCAGATCAGAATCCAA
*
1500465 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
1500489 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
1500513 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
1500532 ATCAAATCGA
Statistics
Matches: 83, Mismatches: 3, Indels: 10
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.05
24 72 0.87
25 7 0.08
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1500548 original size:48 final size:48
Alignment explanation
Indices: 1500448--1500550 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 48
1500438 AAGGTAATGT
** *
1500448 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
*
1500496 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG-AA
1500544 ATCAGAT
1 ATCAGAT
1500551 AAAATATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.02
48 45 0.92
49 3 0.06
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:1509881 original size:20 final size:20
Alignment explanation
Indices: 1509856--1509894 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1509846 GAGACAACCC
*
1509856 ATTTTTTTTTATTTCATTTA
1 ATTTTTTTTAATTTCATTTA
*
1509876 ATTTTTTTTAATTTTATTT
1 ATTTTTTTTAATTTCATTT
1509895 TTAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTAATTTCATTTA
Found at i:1509902 original size:11 final size:11
Alignment explanation
Indices: 1509872--1509913 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1509862 TTTTATTTCA
1509872 TTTAATTT-TT
1 TTTAATTTATT
1509882 TTTAATTTTATT
1 TTTAA-TTTATT
*
1509894 TTTAATTTATA
1 TTTAATTTATT
*
1509905 TTTATTTTA
1 TTTAATTTA
1509914 CTGGGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.18
11 16 0.57
12 7 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTAATTTATT
Found at i:1509911 original size:22 final size:22
Alignment explanation
Indices: 1509872--1509913 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1509862 TTTTATTTCA
*
1509872 TTTAATTTTTTTTAATTTTATT
1 TTTAATTTTATTTAATTTTATT
1509894 TTTAATTTATATTT-ATTTTA
1 TTTAATTT-TATTTAATTTTA
1509914 CTGGGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTAATTTTATTTAATTTTATT
Found at i:1509943 original size:20 final size:22
Alignment explanation
Indices: 1509897--1509943 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1509887 TTTTATTTTT
*
1509897 AATTTATATTTATTTTACTGGG
1 AATTTATATTTATTTTACTAGG
* *
1509919 TATTTAT-TTTATTTT-CTATG
1 AATTTATATTTATTTTACTAGG
1509939 AATTT
1 AATTT
1509944 TTAGGTTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (22 bp):
AATTTATATTTATTTTACTAGG
Found at i:1511403 original size:11 final size:11
Alignment explanation
Indices: 1511387--1511429 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
1511377 GAGACATTAC
1511387 CCGCCCCGCAT
1 CCGCCCCGCAT
1511398 CCGCCCCGCAT
1 CCGCCCCGCAT
1511409 CCACCCGCCCCGCAT
1 ----CCGCCCCGCAT
1511424 CCGCCC
1 CCGCCC
1511430 GCCTCACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 17 0.61
15 11 0.39
ACGTcount: A:0.09, C:0.67, G:0.16, T:0.07
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:1511418 original size:15 final size:15
Alignment explanation
Indices: 1511398--1511444 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1511388 CGCCCCGCAT
1511398 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCAC
*
1511413 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCAC
* *
1511428 CCGCCTCACATCCAC
1 CCGCCCCGCATCCAC
1511443 CC
1 CC
1511445 ACCCAGCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.13, C:0.66, G:0.13, T:0.09
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:1513192 original size:11 final size:11
Alignment explanation
Indices: 1513176--1513228 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1513166 TTTATATAGA
1513176 ATATATTAAAT
1 ATATATTAAAT
1513187 ATATATTCAATAT
1 ATATATT-AA-AT
* *
1513200 ATTCTATTAATT
1 A-TATATTAAAT
*
1513212 ATATATTCAAT
1 ATATATTAAAT
1513223 ATATAT
1 ATATAT
1513229 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 20 0.59
12 4 0.12
13 5 0.15
14 5 0.15
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATTAAAT
Found at i:1513208 original size:25 final size:25
Alignment explanation
Indices: 1513179--1513226 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1513169 ATATAGAATA
1513179 TATTAAATATATATTCAATATATTC
1 TATTAAATATATATTCAATATATTC
*
1513204 TATTAATTATATATTCAATATAT
1 TATTAAATATATATTCAATATAT
1513227 ATATATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTAAATATATATTCAATATATTC
Found at i:1513265 original size:13 final size:13
Alignment explanation
Indices: 1513247--1513272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1513237 ATTTAAAATA
1513247 AAATAAATATAAT
1 AAATAAATATAAT
1513260 AAATAAATATAAT
1 AAATAAATATAAT
1513273 TTCTGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAAATATAAT
Found at i:1514886 original size:25 final size:22
Alignment explanation
Indices: 1514860--1514902 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1514850 AATAAAAAAC
*
1514860 AACAAATTGATCTTCATAAATG
1 AACAAATTAATCTTCATAAATG
1514882 AACAAATTAATCTTCATAAAT
1 AACAAATTAATCTTCATAAAT
1514903 TTGATTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
AACAAATTAATCTTCATAAATG
Found at i:1517241 original size:7 final size:7
Alignment explanation
Indices: 1517231--1517320 Score: 180
Period size: 7 Copynumber: 12.9 Consensus size: 7
1517221 TTCTTTTTCC
1517231 TTCTTCA
1 TTCTTCA
1517238 TTCTTCA
1 TTCTTCA
1517245 TTCTTCA
1 TTCTTCA
1517252 TTCTTCA
1 TTCTTCA
1517259 TTCTTCA
1 TTCTTCA
1517266 TTCTTCA
1 TTCTTCA
1517273 TTCTTCA
1 TTCTTCA
1517280 TTCTTCA
1 TTCTTCA
1517287 TTCTTCA
1 TTCTTCA
1517294 TTCTTCA
1 TTCTTCA
1517301 TTCTTCA
1 TTCTTCA
1517308 TTCTTCA
1 TTCTTCA
1517315 TTCTTC
1 TTCTTC
1517321 CTTCAATTCC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 83 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCTTCA
Found at i:1522911 original size:21 final size:21
Alignment explanation
Indices: 1522885--1522947 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1522875 ATATAAAATT
* *
1522885 TGTCCCAAAAGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
*
1522906 TGTCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACCTCATATA
*
1522927 TATCCCGAAGGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
1522948 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:1523016 original size:2 final size:2
Alignment explanation
Indices: 1523009--1523054 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1522999 ATGGGCTTAA
1523009 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
1523051 AT AT
1 AT AT
1523055 TATCCATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1523434 original size:17 final size:18
Alignment explanation
Indices: 1523412--1523446 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1523402 TTCTATGACT
1523412 TAACTCTT-GATCGTTTC
1 TAACTCTTCGATCGTTTC
1523429 TAACTCTTCGATCGTTTC
1 TAACTCTTCGATCGTTTC
1523447 AAAACTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (18 bp):
TAACTCTTCGATCGTTTC
Found at i:1523803 original size:20 final size:20
Alignment explanation
Indices: 1523780--1523829 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1523770 TTGGCTTATG
1523780 GTATCGATACTGTTCAACAA
1 GTATCGATACTGTTCAACAA
1523800 GTATCGATACTGTTCAACAA
1 GTATCGATACTGTTCAACAA
1523820 GTATCGATAC
1 GTATCGATAC
1523830 CCCTACTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGTTCAACAA
Found at i:1525144 original size:14 final size:15
Alignment explanation
Indices: 1525120--1525149 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1525110 AAGATGTCCC
1525120 TTTTAATAAAATATG
1 TTTTAATAAAATATG
1525135 TTTT-ATAAAATATG
1 TTTTAATAAAATATG
1525149 T
1 T
1525150 ATGAAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTTAATAAAATATG
Found at i:1525323 original size:25 final size:25
Alignment explanation
Indices: 1525274--1525323 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1525264 TTTGCTCATT
* *
1525274 TAAAAAAGAGAAAATAAATACAAAA
1 TAAAAAAAAGAAAATAAAGACAAAA
*
1525299 TAAAAAAAAGAAAATAAAGAGAAAA
1 TAAAAAAAAGAAAATAAAGACAAAA
1525324 AGGTTTACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (25 bp):
TAAAAAAAAGAAAATAAAGACAAAA
Found at i:1525708 original size:10 final size:11
Alignment explanation
Indices: 1525683--1525711 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1525673 GATAACGAGG
1525683 AACATAAATAA
1 AACATAAATAA
1525694 AACATAAAT-A
1 AACATAAATAA
1525704 AACATAAA
1 AACATAAA
1525712 CATATAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (11 bp):
AACATAAATAA
Found at i:1530382 original size:38 final size:38
Alignment explanation
Indices: 1530307--1530383 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
1530297 AGATGGAGGG
* * * * *
1530307 TCGGGTGGAGGGTGTATATTTTTCGGGTTGGATCGGGT
1 TCGGGTGGAGGATGTATAATTTTCAGGTAGGACCGGGT
1530345 TCGGGTGGAGGATGTATAATTTTCAGGTCAGG-CCGGGT
1 TCGGGTGGAGGATGTATAATTTTCAGGT-AGGACCGGGT
1530383 T
1 T
1530384 AACAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 31 0.94
39 2 0.06
ACGTcount: A:0.14, C:0.10, G:0.42, T:0.34
Consensus pattern (38 bp):
TCGGGTGGAGGATGTATAATTTTCAGGTAGGACCGGGT
Found at i:1545588 original size:24 final size:24
Alignment explanation
Indices: 1545561--1545646 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
1545551 TCAAATTTGA
*
1545561 ATTCTGTTATGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
1545585 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
1545608 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
1545632 ATTCTGATATGATAC
1 ATTCTGATATGATAC
1545647 TTGATTTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.37
24 34 0.63
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:1547817 original size:18 final size:18
Alignment explanation
Indices: 1547794--1547829 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1547784 GTCATAACCC
1547794 GACCCGACCCGTTGACCG
1 GACCCGACCCGTTGACCG
1547812 GACCCGACCCGTTGACCG
1 GACCCGACCCGTTGACCG
1547830 TTGACCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.44, G:0.28, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCG
Found at i:1550291 original size:24 final size:24
Alignment explanation
Indices: 1550264--1550349 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
1550254 TCAAATTTGA
* *
1550264 ATTCTGTTATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
1550288 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACATGG
* * *
1550311 ATTCTGATATGATACATGGCTTGG
1 ATTCTGATATGATACTTGACATGG
1550335 ATTCTGATATGATAC
1 ATTCTGATATGATAC
1550350 CTGATTTGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 22 0.39
24 34 0.61
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1550479 original size:35 final size:35
Alignment explanation
Indices: 1550431--1550503 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
1550421 TGGAGGAAGA
*
1550431 TTACTTGGAGGTTCCTCGGCTGTGTGCTCAGGGCC
1 TTACTTAGAGGTTCCTCGGCTGTGTGCTCAGGGCC
* *
1550466 TTACTTAGCGGTTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTAGAGGTTCCTCGGCTGTGTGCTCAGGGCC
1550501 TTA
1 TTA
1550504 TATGATGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.10, C:0.26, G:0.30, T:0.34
Consensus pattern (35 bp):
TTACTTAGAGGTTCCTCGGCTGTGTGCTCAGGGCC
Found at i:1550576 original size:2 final size:2
Alignment explanation
Indices: 1550569--1550597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1550559 GGGATGGGGG
1550569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1550598 GTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1551883 original size:27 final size:27
Alignment explanation
Indices: 1551851--1551913 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
1551841 TGTGAATTAT
* *
1551851 TGGGTCATCATATTGCTTGAATTGGAA
1 TGGGTCATCACATTGCTTGAATAGGAA
1551878 TGGGTCATCACATTGCTTGAATAGGAA
1 TGGGTCATCACATTGCTTGAATAGGAA
1551905 TGGGTCATC
1 TGGGTCATC
1551914 CCAATAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.33
Consensus pattern (27 bp):
TGGGTCATCACATTGCTTGAATAGGAA
Found at i:1564255 original size:21 final size:22
Alignment explanation
Indices: 1564216--1564257 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1564206 TACTTAGCAT
1564216 TTGAAAAATAAAAATAAAAAGC
1 TTGAAAAATAAAAATAAAAAGC
*
1564238 TTGAAAAATAAAGA-AAAAAG
1 TTGAAAAATAAAAATAAAAAG
1564258 AAGAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (22 bp):
TTGAAAAATAAAAATAAAAAGC
Found at i:1570761 original size:16 final size:16
Alignment explanation
Indices: 1570740--1570772 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1570730 GGAACATTAA
1570740 TGGTAATGATGTTATT
1 TGGTAATGATGTTATT
1570756 TGGTAATGATGTTATT
1 TGGTAATGATGTTATT
1570772 T
1 T
1570773 CCCTTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (16 bp):
TGGTAATGATGTTATT
Found at i:1592650 original size:18 final size:18
Alignment explanation
Indices: 1592629--1592664 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1592619 GGGGGGTTTG
*
1592629 GTAAAATGAGATTAAATA
1 GTAAAAAGAGATTAAATA
1592647 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGATTAAATA
1592665 AATAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (18 bp):
GTAAAAAGAGATTAAATA
Found at i:1592670 original size:19 final size:18
Alignment explanation
Indices: 1592630--1592670 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1592620 GGGGGTTTGG
* *
1592630 TAAAATGAGATTAAATAG
1 TAAAAAGAGATTAAATAA
1592648 TAAAAAGAGATTAAATAAA
1 TAAAAAGAGATTAAAT-AA
1592667 TAAA
1 TAAA
1592671 GTAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
TAAAAAGAGATTAAATAA
Found at i:1595695 original size:12 final size:12
Alignment explanation
Indices: 1595670--1595739 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1595660 ACGGAGATAT
* *
1595670 CAGAAATCAAAA
1 CAGAATTCAGAA
1595682 CAGAATTCAGAA
1 CAGAATTCAGAA
1595694 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * *
1595706 CAGAATCCATAT
1 CAGAATTCAGAA
*
1595718 CAGAAATCAGAA
1 CAGAATTCAGAA
1595730 CAGAATTCAG
1 CAGAATTCAG
1595740 GTCATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.89
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1595697 original size:24 final size:24
Alignment explanation
Indices: 1595670--1595739 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
1595660 ACGGAGATAT
*
1595670 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * * *
1595694 CAGATATTAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
1595718 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
1595740 GTCATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1602143 original size:16 final size:16
Alignment explanation
Indices: 1602122--1602154 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1602112 TAAGAAATAA
1602122 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602138 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602154 A
1 A
1602155 ATTTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1602242 original size:16 final size:16
Alignment explanation
Indices: 1602221--1602265 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
1602211 TAATAAATAA
1602221 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602237 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602253 ACGAACATAAACG
1 ACGAACATAAACG
1602266 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1603377 original size:14 final size:14
Alignment explanation
Indices: 1603360--1603406 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1603350 AATGAACATA
1603360 AACGAACATAACCG
1 AACGAACATAACCG
*
1603374 AACGAACATAAACG
1 AACGAACATAACCG
*
1603388 AACATAACATAACCG
1 AAC-GAACATAACCG
1603403 AACG
1 AACG
1603407 TTCACGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1604891 original size:19 final size:19
Alignment explanation
Indices: 1604867--1604912 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1604857 TATTAAATTG
1604867 CGGCCGCAATATAGTGTAA
1 CGGCCGCAATATAGTGTAA
1604886 CGGCCGCAATATAGTGTAA
1 CGGCCGCAATATAGTGTAA
1604905 CGGCCGCA
1 CGGCCGCA
1604913 TCGTAACGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (19 bp):
CGGCCGCAATATAGTGTAA
Found at i:1605707 original size:18 final size:19
Alignment explanation
Indices: 1605684--1605734 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1605674 CTCCTGACAT
*
1605684 TTGATATCATACTG-GAAA
1 TTGATACCATACTGTGAAA
* *
1605702 TTGATACCATACTGTTAAG
1 TTGATACCATACTGTGAAA
1605721 TTGATACCATACTG
1 TTGATACCATACTG
1605735 ATTTGAGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATACCATACTGTGAAA
Found at i:1607233 original size:51 final size:51
Alignment explanation
Indices: 1607130--1607236 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
1607120 CCTTTGCAAA
* ** *
1607130 AAGGCGCGGCCCATGCATCGCGCCTTACCTTGATGTGGCGCCACGTGGGGT
1 AAGGCGCGGCCCATGCACCGCGCCTTACCTTGACATGGCGCCACGTGCGGT
*
1607181 AAGGCGCGGCCCATGCACCGCGCCTTATGC-TGACATGGCGCCACGCT-CGGT
1 AAGGCGCGGCCCATGCACCGCGCCTTA-CCTTGACATGGCGCCACG-TGCGGT
1607232 AAGGC
1 AAGGC
1607237 ACGGTGCATG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.16, C:0.34, G:0.34, T:0.17
Consensus pattern (51 bp):
AAGGCGCGGCCCATGCACCGCGCCTTACCTTGACATGGCGCCACGTGCGGT
Found at i:1607507 original size:17 final size:18
Alignment explanation
Indices: 1607485--1607519 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1607475 TCTTTAAGGT
1607485 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
1607502 ATATTTTGTTAGTATTTA
1 ATATTTTATTAGTATTTA
1607520 TTTAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:1613507 original size:29 final size:29
Alignment explanation
Indices: 1613452--1613507 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1613442 GATATTTACA
* *
1613452 GGTTGAGAGGATTATTGTTTGATGTTTTC
1 GGTTGAGAGGATTATTGTGTGAAGTTTTC
*
1613481 GGTTGAGAGG-TTGTTGTGTGAAAGTTT
1 GGTTGAGAGGATTATTGTGTG-AAGTTT
1613508 ATGGGGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.45
Consensus pattern (29 bp):
GGTTGAGAGGATTATTGTGTGAAGTTTTC
Found at i:1613687 original size:40 final size:40
Alignment explanation
Indices: 1613626--1613702 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
1613616 GACTGTCAAG
* *
1613626 AAGGTACGACCCATGCACCGCGTCATACCCTACGTGGCAT
1 AAGGTACGACCCATGCACCGCGCCATACCCAACGTGGCAT
* * *
1613666 AAGGTGCGGCCCATG-AGCCGCGCCTTACCCAACGTGG
1 AAGGTACGACCCATGCA-CCGCGCCATACCCAACGTGG
1613703 TGCCATGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.03
40 30 0.97
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (40 bp):
AAGGTACGACCCATGCACCGCGCCATACCCAACGTGGCAT
Found at i:1615517 original size:2 final size:2
Alignment explanation
Indices: 1615512--1615572 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1615502 TTTTTTAGAT
1615512 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
1615554 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1615573 TTTATTATCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1615517 original size:23 final size:24
Alignment explanation
Indices: 1615473--1615520 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1615463 TTTTATGCAT
* *
1615473 TTTTTTTTTTTACTTTAGTATATA
1 TTTTATTTTTTACATTAGTATATA
*
1615497 TTTTATTTTTTAGATTA-TATATA
1 TTTTATTTTTTACATTAGTATATA
1615520 T
1 T
1615521 ATATATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTATTTTTTACATTAGTATATA
Found at i:1615628 original size:35 final size:35
Alignment explanation
Indices: 1615588--1615697 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 35
1615578 TATCAATTTT
*
1615588 ATTAATTTATCTATATATATATATTTACTATTTTT
1 ATTAATTTATCTATATATATATATTTATTATTTTT
* * * *
1615623 TTTAATTTTTTTAT-TATATATATATATTATTTTT
1 ATTAATTTATCTATATATATATATTTATTATTTTT
* * *
1615657 ACTT-TTTTAT-TAT-TAT-TTTATTTATT-TATTT
1 A-TTAATTTATCTATATATATATATTTATTATTTTT
*
1615688 ATTTATTTAT
1 ATTAATTTAT
1615698 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
30 2 0.03
31 10 0.16
32 8 0.13
33 6 0.10
34 22 0.36
35 13 0.21
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (35 bp):
ATTAATTTATCTATATATATATATTTATTATTTTT
Found at i:1615663 original size:40 final size:39
Alignment explanation
Indices: 1615593--1615720 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 39
1615583 ATTTTATTAA
* *
1615593 TTTATCTATATATATA-TATTTACTATTTTTTTTAATTTT
1 TTTATTTATATATATATTATTT-TTATTTTTTTTAATTTT
1615632 TTTATTATATATATATATTATTTTTACTTTTTTATTATTATTTT
1 TTTATT-TATATATATATTATTTTTA-TTTTTT-TTA--ATTTT
* * *
1615676 ATTTATTTATTTATTTATT-TATTTATTTTTTTTATATTTAT
1 -TTTATTTATATATATATTATTTTTATTTTTTTTA-ATTT-T
1615717 TTTA
1 TTTA
1615721 CTTACTATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
39 5 0.07
40 21 0.28
41 15 0.20
42 9 0.12
43 5 0.07
44 15 0.20
45 6 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (39 bp):
TTTATTTATATATATATTATTTTTATTTTTTTTAATTTT
Found at i:1615682 original size:4 final size:4
Alignment explanation
Indices: 1615673--1615805 Score: 71
Period size: 4 Copynumber: 32.8 Consensus size: 4
1615663 TTATTATTAT
1615673 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTT- TTATA TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA
* * * * * *
1615721 CTTA -CTA TTT- TATA TTTGC TTTC TTTA TCTTA TCT- TTTA TTTAA TTTA
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTTA T-TTA TTTA TTTA TTT-A TTTA
* * *
1615769 TTT- TTTC TTTA TTTTAA TTTAA TTAA TTAA TTTA TTT
1 TTTA TTTA TTTA -TTT-A TTT-A TTTA TTTA TTTA TTT
1615806 CTTACCTTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
3 14 0.13
4 63 0.60
5 27 0.26
6 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1615733 original size:44 final size:42
Alignment explanation
Indices: 1615599--1615736 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 42
1615589 TTAATTTATC
* *
1615599 TATATATATA-TATTTACTATTTTTTTTA-ATTT-TTTTATTA
1 TATATTTATATTATTT-TTATTTTTTTTATATTTATTTTATTA
* *
1615639 TATATATATATTATTTTTA-CTTTTTTAT-TATTATTTTATTTA
1 TATATTTATATTATTTTTATTTTTTTTATAT-TTATTTTA-TTA
*
1615681 TTTATTTAT-TTATTTATTTATTTTTTTTATATTTATTTTACTTA
1 TATATTTATATTA-TT-TTTATTTTTTTTATATTTATTTTA-TTA
1615725 CTAT-TTTATATT
1 -TATATTTATATT
1615737 TGCTTTCTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
39 8 0.10
40 14 0.17
41 13 0.16
42 12 0.15
43 4 0.05
44 24 0.30
45 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (42 bp):
TATATTTATATTATTTTTATTTTTTTTATATTTATTTTATTA
Found at i:1615768 original size:21 final size:21
Alignment explanation
Indices: 1615744--1615789 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1615734 ATTTGCTTTC
1615744 TTTATCTTATCTTT-TATTTAA
1 TTTATCTTATCTTTAT-TTTAA
* *
1615765 TTTATTTTTTCTTTATTTTAA
1 TTTATCTTATCTTTATTTTAA
1615786 TTTA
1 TTTA
1615790 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATCTTATCTTTATTTTAA
Found at i:1618834 original size:7 final size:7
Alignment explanation
Indices: 1618823--1618883 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
1618813 ACAAAAAGAA
1618823 AAAAATAG
1 AAAAA-AG
1618831 AAAAAAG
1 AAAAAAG
* *
1618838 CAAAGAG
1 AAAAAAG
*
1618845 AAAATA-
1 AAAAAAG
1618851 AAAAAAG
1 AAAAAAG
1618858 AAAAAAG
1 AAAAAAG
1618865 AAAATTGAAG
1 AAAA---AAG
1618875 AAAAAAG
1 AAAAAAG
1618882 AA
1 AA
1618884 GACAAGATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
6 5 0.11
7 27 0.61
8 5 0.11
10 7 0.16
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:1618856 original size:20 final size:21
Alignment explanation
Indices: 1618824--1618883 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
1618814 CAAAAAGAAA
* *
1618824 AAAATAGAAAAAAGCAAAGAG
1 AAAATAGAAAAAAGAAAAAAG
1618845 AAAATA-AAAAAAGAAAAAAG
1 AAAATAGAAAAAAGAAAAAAG
1618865 AAAATTGAAGAAAAAAGAA
1 AAAA-T--AGAAAAAAGAA
1618884 GACAAGATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 16 0.48
21 7 0.21
23 1 0.03
24 9 0.27
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (21 bp):
AAAATAGAAAAAAGAAAAAAG
Found at i:1618863 original size:15 final size:15
Alignment explanation
Indices: 1618815--1618883 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1618805 CCATCAGAAC
*
1618815 AAAAAGAAAAAAATA
1 AAAAAGAAAAAAAGA
* **
1618830 GAAAA-AAGCAAAGA
1 AAAAAGAAAAAAAGA
* *
1618844 GAAAATAAAAAAAGA
1 AAAAAGAAAAAAAGA
*
1618859 AAAAAGAAAATTGAAGA
1 AAAAAGAAAA--AAAGA
1618876 AAAAAGAA
1 AAAAAGAA
1618884 GACAAGATGC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
14 11 0.26
15 19 0.45
17 12 0.29
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:1618880 original size:27 final size:27
Alignment explanation
Indices: 1618818--1618885 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1618808 TCAGAACAAA
* *
1618818 AAGAAAAAAATAGAAAAAAGCAAAGAG
1 AAGAAAAAAAAAGAAAAAAGAAAAGAG
**
1618845 AA-AATAAAAAAAGAAAAAAGAAAATTG
1 AAGAA-AAAAAAAGAAAAAAGAAAAGAG
*
1618872 AAGAAAAAAGAAGA
1 AAGAAAAAAAAAGA
1618886 CAAGATGCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.06
27 30 0.88
28 2 0.06
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (27 bp):
AAGAAAAAAAAAGAAAAAAGAAAAGAG
Found at i:1619015 original size:69 final size:69
Alignment explanation
Indices: 1618925--1619059 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
1618915 TCAAACTATT
*
1618925 AGATTGATCAAGCACAATCATTTCTGAATCACTTAATCACT-TCACTCGAAGATCATAGAGCATC
1 AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCT-ACTCGAAGATCATAGAGCATC
1618989 AAATG
65 AAATG
* *
1618994 AGATTGATCAAGCACAATCATTTTTGAATCACTGAATCACTCTACTCGAAGATCATGGAGCATCA
1 AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCTACTCGAAGATCATAGAGCATCA
1619059 A
66 A
1619060 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 61 0.98
70 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (69 bp):
AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCTACTCGAAGATCATAGAGCATCA
AATG
Found at i:1620037 original size:32 final size:32
Alignment explanation
Indices: 1619989--1620101 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
1619979 TGAGGGCATC
* *
1619989 TTTGAAGATTCGACATCAAATATTGGGCCATTT
1 TTTG-AGATTCAACATCAAATATTGGGACATTT
* * * *
1620022 TTTTAGATTTAACATCAAATGTTGGGATATTT
1 TTTGAGATTCAACATCAAATATTGGGACATTT
* * *
1620054 TTTGAGATTCAACATCGAATATTGGGGCA-TC
1 TTTGAGATTCAACATCAAATATTGGGACATTT
*
1620085 TTTGGGAATTCAACATC
1 TTTGAG-ATTCAACATC
1620102 CTGATGCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
31 6 0.09
32 56 0.86
33 3 0.05
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGACATTT
Found at i:1620803 original size:106 final size:106
Alignment explanation
Indices: 1620679--1621012 Score: 416
Period size: 106 Copynumber: 3.2 Consensus size: 106
1620669 ATATCGTGCC
* * *
1620679 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGTTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
1620744 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1620785 ACTCGAGACAACAAAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
* * *
1620850 AATTTCGGAGCCAATTTCAACTTCACAGTGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * ** * * **
1620891 ACTAGAGATAGCACAAGCTCAACTTCACAGCAAAGGGGTGGTTGACTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
* * * * * *
1620956 AGTTCCAGAGCCAATTTTAACTTAACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1620997 ACTCGAAACAATACAA
1 ACTCGAGACAACACAA
1621013 CTTACTTGGA
Statistics
Matches: 193, Mismatches: 35, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
106 193 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1621343 original size:65 final size:65
Alignment explanation
Indices: 1621223--1621380 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 65
1621213 TTTGGAACTA
*
1621223 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATT
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATT
* * * * * *
1621288 AATTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACA-AAATC-TTTAAATCTGTTTCCCTTGAAA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC-ATTTCCCTTGAAA
**
1621351 CA
64 TT
* *
1621353 AATTTCGTCTCCCTTTGAGACATTTTCT
1 AATTTTGTCTCCC-TTGAGACAGTTTCT
1621381 TTTGGAACTA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 9 0.12
65 56 0.74
66 11 0.14
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (65 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATT
Found at i:1621460 original size:103 final size:102
Alignment explanation
Indices: 1621290--1621474 Score: 248
Period size: 103 Copynumber: 1.8 Consensus size: 102
1621280 TTGAAATTAA
* * * * *
1621290 TTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCGTGAAAGCTATTTCCCTTGAAACAAA
1621355 TTTCGTCTCCCTTTGAGACATTTTCTTTTGGAACTAAG
66 TTTCGTCTCCC-TTGAGACATTTTCTTTTGGAACTAAG
**
1621393 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CAGTGAAAGC-ATTTCCCTTGAAATG
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATC-GTGAAAGCTATTTCCCTTGAAACA
* *
1621456 AATTTTGTCTCTCTTGAGA
64 AATTTCGTCTCCCTTGAGA
1621475 TAGTTTCTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
102 6 0.08
103 57 0.80
104 8 0.11
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (102 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCGTGAAAGCTATTTCCCTTGAAACAAA
TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
Found at i:1621525 original size:65 final size:65
Alignment explanation
Indices: 1621393--1621539 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 65
1621383 TGGAACTAAG
**
1621393 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACAGTGAAAGCATTTCCCTTGAAATGAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACAGTGAAAGCATTTCCCTTGAAACAAA
** * *
1621458 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCTGTTTCCCTTGAAACA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CAGTGAAAGC-ATTTCCCTTGAAACA
1621521 AA
64 AA
** *
1621523 TTTCATCTCCCTTGAGA
1 TTTTGTCTCTCTTGAGA
1621540 CATTTTCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
64 6 0.08
65 65 0.92
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACAGTGAAAGCATTTCCCTTGAAACAAA
Found at i:1621636 original size:167 final size:167
Alignment explanation
Indices: 1621144--1621662 Score: 833
Period size: 167 Copynumber: 3.1 Consensus size: 167
1621134 GTGTCCAAGT
* * * * *
1621144 TTTC-CTTGAAACAAAATATTTAAATATGTTTTCATTGAAACTAATTTCGTCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
* * *
1621208 TTTCTTTTGGAACTAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
66 TTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
*
1621273 ATTTCCCTTGAAATTAATTTTGTCTCTCTTGAGATAG
131 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
*
1621310 TTTTTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTTGAGACA
1 TTTCTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAATTTCGTCTCCC-TTGAGACA
* * *
1621375 TTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACAGTGAAAG
65 TTTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1621440 CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
130 CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
* *
1621478 TTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
1621543 TTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
66 TTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
* * * *
1621608 ATTTCCATTGAGATGATTTTTTTCTCTCTTGAGATAG
131 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
* *
1621645 GTTCCCTTGAAACAAAAT
1 TTTCTCTTGAAACAAAAT
1621663 TTTGTCTCCC
Statistics
Matches: 326, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
166 3 0.01
167 166 0.51
168 157 0.48
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (167 bp):
TTTCTCTTGAAACAAAATCTTTAAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
TTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
Found at i:1621639 original size:102 final size:101
Alignment explanation
Indices: 1621442--1621824 Score: 389
Period size: 102 Copynumber: 3.8 Consensus size: 101
1621432 AGTGAAAGCA
** * * * *
1621442 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
** ** * *
1621505 TGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACAT
65 AATTTCCCTTGAAATGAATTTTATCTCTCTTGAGA-AT
** * * *
1621543 TTTCTTTTGGAACTAAGTTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * * * *
1621608 -ATTTCCATTGAGATGATTTTTTTCTCTCTTGAGATAG
65 AATTTCCCTTGAAATGAATTTTATCTCTCTTGAGA-AT
* *
1621645 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * * *
1621710 -ATTTCCCTTGAAATGAATTTTGTCACTCATGAGATT
65 AATTTCCCTTGAAATGAATTTTATCTCTCTTGAGAAT
* *
1621746 GTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAGA-ATAAACTTTGAAAA
1 -TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAA-ACATAAACATTGAAAA
*
1621810 CAATTTCCTTTGAAA
64 CAATTTCCCTTGAAA
1621825 CAAAATCTTT
Statistics
Matches: 235, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
101 55 0.23
102 174 0.74
103 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
ATTTCCCTTGAAATGAATTTTATCTCTCTTGAGAAT
Found at i:1621692 original size:204 final size:203
Alignment explanation
Indices: 1621443--1621822 Score: 455
Period size: 204 Copynumber: 1.9 Consensus size: 203
1621433 GTGAAAGCAT
** * * * * *
1621443 TTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCT
1 TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAA-CATTGAAAAC-
* * * ** * *
1621506 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACAT-TTTCTTTTGGAACTAAGTTTTGTCTCC
64 ATTTCCCTTGAAACAAATTTCATCACCCATGAGA-ATGTTTCCCTTGAAAC-AAATTTTGTCTCC
* *
1621570 CTTGAGATAGTTTCTCTTGAA-ACATAAACATTGAAAAC-ATTTCCATTGAGATGATTTTTTTCT
127 CTTAAGACAGTTTCTCTTGAAGA-ATAAACATTGAAAACAATTTCCATTGAGATGATTTTTTTCT
1621633 CTCTTGAGATAGG
191 CTCTTGAGATAGG
1621646 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACA
1 TTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACA
** ** * *
1621711 TTTCCCTTGAAATGAATTTTGTCACTCATGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTT
65 TTTCCCTTGAAACAAATTTCATCACCCATGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTT
* *
1621776 AAGACAGTTTCTCTTGAAGAATAAACTTTGAAAACAATTTCCTTTGA
130 AAGACAGTTTCTCTTGAAGAATAAACATTGAAAACAATTTCCATTGA
1621823 AACAAAATCT
Statistics
Matches: 147, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
203 57 0.39
204 84 0.57
205 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (203 bp):
TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACAT
TTCCCTTGAAACAAATTTCATCACCCATGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTA
AGACAGTTTCTCTTGAAGAATAAACATTGAAAACAATTTCCATTGAGATGATTTTTTTCTCTCTT
GAGATAGG
Found at i:1621935 original size:36 final size:36
Alignment explanation
Indices: 1621892--1621960 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1621882 TTTTGGAAGT
* *
1621892 TTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1621928 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1621961 TTCAATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1622018 original size:33 final size:34
Alignment explanation
Indices: 1621978--1622060 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 34
1621968 TTTGAATACA
*
1621978 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1622011 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1622045 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
1622061 CAAACCCTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 16 0.33
34 32 0.67
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
Found at i:1623235 original size:2 final size:2
Alignment explanation
Indices: 1623230--1623256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1623220 TTTTTTTGAT
1623230 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1623257 TATTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1623423 original size:13 final size:12
Alignment explanation
Indices: 1623303--1623425 Score: 74
Period size: 13 Copynumber: 10.2 Consensus size: 12
1623293 ATATTTACTA
1623303 TTTTT-TTTATT
1 TTTTTATTTATT
*
1623314 TTTTTATTATATA
1 TTTTTATT-TATT
* * * *
1623327 TATATATATATA
1 TTTTTATTTATT
* *
1623339 TTATT-TTTACT
1 TTTTTATTTATT
1623350 TTTTTA-TTATT
1 TTTTTATTTATT
* *
1623361 ATTTTAATTATT
1 TTTTTATTTATT
1623373 TGTTTTATTTATT
1 T-TTTTATTTATT
*
1623386 TATTTT-TTTCTT
1 T-TTTTATTTATT
*
1623398 CTTTTTCTTTATT
1 -TTTTTATTTATT
1623411 TTTTATATTTATT
1 TTTT-TATTTATT
1623424 TT
1 TT
1623426 ACTTACTATT
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
11 21 0.25
12 26 0.31
13 38 0.45
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:1640017 original size:19 final size:19
Alignment explanation
Indices: 1639993--1640029 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1639983 ACAAAACCTG
1639993 TTGCAACCTAAATTCTCAA
1 TTGCAACCTAAATTCTCAA
*
1640012 TTGCAACCTAATTTCTCA
1 TTGCAACCTAAATTCTCA
1640030 TTTCCAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (19 bp):
TTGCAACCTAAATTCTCAA
Found at i:1644520 original size:389 final size:389
Alignment explanation
Indices: 1643857--1644559 Score: 1334
Period size: 389 Copynumber: 1.8 Consensus size: 389
1643847 GGTGAAAATG
*
1643857 TGCCCAAACATGGTAATGAGTTCCTGTAAAAATAGGAACATGTGTTTAAGGAGCATTTGAAGAAT
1 TGCCCAAACATGGTAATGAGTTCCTGTAAAAATAGGAACATGTGTTTAAGGAGCATTTGAAGAAA
1643922 CCATTTTAGAAAACACTTTAAAAACTCAAACTCTCAAAGTGTTTTAATCACCCACAAATAGTAAT
66 CCATTTTAGAAAACACTTTAAAAACTCAAACTCTCAAAGTGTTTTAATCACCCACAAATAGTAAT
1643987 AGAACCTCACAACCCTCAAGAAACATATCTGATTACCACTGTTAATGTTAAACCAAGAAAACAAG
131 AGAACCTCACAACCCTCAAGAAACATATCTGATTACCACTGTTAATGTTAAACCAAGAAAACAAG
*
1644052 TTTGAGAGCAAAAAGAAGATGAGGAGCAGAAAAACAAAAGAGAAAAGAATGCAAAAAGTCCAAAC
196 TTTGAGAGCAAAAAGAAGAGGAGGAGCAGAAAAACAAAAGAGAAAAGAATGCAAAAAGTCCAAAC
* * *
1644117 AAAGATAGAGAGGTTTTCACTGCGCTCTCATTATTCTTAGCCAATTTTTTGTAACCTTGTCGATG
261 AAAGATAGAGAGGTTTTCACTACGCTCTCATTATTCTTAGACAAATTTTTGTAACCTTGTCGATG
1644182 GATCTTCATCAGTTTATACTACCCTCCGCAAGGTAAGAGATCTCAAATAGACTCTCATCTTAAC
326 GATCTTCATCAGTTTATACTACCCTCCGCAAGGTAAGAGATCTCAAATAGACTCTCATCTTAAC
1644246 TGCCCAAACATGGTAATGAGTTCCTGTAAAAATAGGAACATGTGTTTAAGGAGCATTTGAAGAAA
1 TGCCCAAACATGGTAATGAGTTCCTGTAAAAATAGGAACATGTGTTTAAGGAGCATTTGAAGAAA
1644311 CCATTTTAGAAAACACTTTAAAAACTCAAACTCTCAAAGTGTTTTAATCACCCACAAATAGTAAT
66 CCATTTTAGAAAACACTTTAAAAACTCAAACTCTCAAAGTGTTTTAATCACCCACAAATAGTAAT
* *
1644376 AGAACCTCACAACCCTCAAGAAACATCTCTTATTACCACTGTTAATGTTAAACCAAGAAAACAAG
131 AGAACCTCACAACCCTCAAGAAACATATCTGATTACCACTGTTAATGTTAAACCAAGAAAACAAG
*
1644441 TTTGAGAGCAAAAAGAAGAGGAGGAGCAGAAAAACAAAAGAGAAAAGAATGCAAAAAGTCTAAAC
196 TTTGAGAGCAAAAAGAAGAGGAGGAGCAGAAAAACAAAAGAGAAAAGAATGCAAAAAGTCCAAAC
1644506 AAAGATAGAGAGGTTTTCACTACGCTCTCATTATTCTTAGACAAATTTTTGTAA
261 AAAGATAGAGAGGTTTTCACTACGCTCTCATTATTCTTAGACAAATTTTTGTAA
1644560 GGGTGTTCCT
Statistics
Matches: 306, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
389 306 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (389 bp):
TGCCCAAACATGGTAATGAGTTCCTGTAAAAATAGGAACATGTGTTTAAGGAGCATTTGAAGAAA
CCATTTTAGAAAACACTTTAAAAACTCAAACTCTCAAAGTGTTTTAATCACCCACAAATAGTAAT
AGAACCTCACAACCCTCAAGAAACATATCTGATTACCACTGTTAATGTTAAACCAAGAAAACAAG
TTTGAGAGCAAAAAGAAGAGGAGGAGCAGAAAAACAAAAGAGAAAAGAATGCAAAAAGTCCAAAC
AAAGATAGAGAGGTTTTCACTACGCTCTCATTATTCTTAGACAAATTTTTGTAACCTTGTCGATG
GATCTTCATCAGTTTATACTACCCTCCGCAAGGTAAGAGATCTCAAATAGACTCTCATCTTAAC
Found at i:1646599 original size:2 final size:2
Alignment explanation
Indices: 1646594--1646675 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1646584 ATGATATTTG
1646594 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
1646636 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
1646676 TAAAACATGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1646883 original size:14 final size:14
Alignment explanation
Indices: 1646864--1646891 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1646854 GTAATCCCTA
1646864 AAATCCCTAACCTC
1 AAATCCCTAACCTC
1646878 AAATCCCTAACCTC
1 AAATCCCTAACCTC
1646892 CATTCGAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATCCCTAACCTC
Found at i:1648084 original size:96 final size:95
Alignment explanation
Indices: 1647920--1648143 Score: 313
Period size: 96 Copynumber: 2.3 Consensus size: 95
1647910 GGTCATCTCC
* * * * *
1647920 AATATGATCGTTCTTGATTTATGGATCATGGAATCTAGTGGTTTATGAACTATGATTACTTGAAA
1 AATATGATCGTTCATGATTTATGGATCAT-GAATCTACTAGTTTATGAACAATGATTACCTGAAA
* * *
1647985 TGTGTTATCTGGTTTCCTGTTTTCACTGGAA
65 TGTGTTATATGGTTTCCTATTTTCACTAGAA
* *
1648016 AATATGATCGTTCATGGTTTATGGATCATGAAGTCTACTAGTTTATGATCAATGATTACCTGAAA
1 AATATGATCGTTCATGATTTATGGATCATGAA-TCTACTAGTTTATGAACAATGATTACCTGAAA
*
1648081 TGTGTTATATGGTTTCTTATTTTCACTAGAA
65 TGTGTTATATGGTTTCCTATTTTCACTAGAA
* *
1648112 AATATTATCGTTCCTGATTTATGGATCATGAA
1 AATATGATCGTTCATGATTTATGGATCATGAA
1648144 ATATACTGGT
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
95 3 0.03
96 110 0.97
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (95 bp):
AATATGATCGTTCATGATTTATGGATCATGAATCTACTAGTTTATGAACAATGATTACCTGAAAT
GTGTTATATGGTTTCCTATTTTCACTAGAA
Found at i:1650960 original size:15 final size:14
Alignment explanation
Indices: 1650931--1650976 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1650921 GTATGAGTCA
1650931 ACCCGTTGACTTTG
1 ACCCGTTGACTTTG
1650945 ACCCGTTGACCTTTG
1 ACCCGTTGA-CTTTG
* *
1650960 A-CCGTTAAATTTG
1 ACCCGTTGACTTTG
1650973 ACCC
1 ACCC
1650977 AAAAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.18
14 17 0.61
15 6 0.21
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (14 bp):
ACCCGTTGACTTTG
Found at i:1651809 original size:17 final size:18
Alignment explanation
Indices: 1651787--1651822 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1651777 ATTTATCGAA
1651787 AGTATGATATTGGA-ATG
1 AGTATGATATTGGAGATG
1651804 AGTATGATATTGGAGATG
1 AGTATGATATTGGAGATG
1651822 A
1 A
1651823 CCTGAGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (18 bp):
AGTATGATATTGGAGATG
Found at i:1652986 original size:96 final size:96
Alignment explanation
Indices: 1652869--1653162 Score: 426
Period size: 96 Copynumber: 3.1 Consensus size: 96
1652859 CACTGATTTG
* * *
1652869 CTGGTTTATGAACTATGGTTACTTGAAATATGTTCTCTGGTTACATGTTTTCACTGTAAAATATG
1 CTGGTTTATGAACTATGGTTACTTGAAATATGTTATCTGGTTTCATGTTTTCACTGAAAAATATG
* * *
1652934 ATTGTTCTTGATTTATGGATCATGGAATCTA
66 ATCGTTCCTGATTTATGGATCATGAAATCTA
* * * * * * * *
1652965 GTGGTTTATAAACTATGGTTACCTGAAATATATTATTTGGTTTCTTATTTTCACTGGAAAATATG
1 CTGGTTTATGAACTATGGTTACTTGAAATATGTTATCTGGTTTCATGTTTTCACTGAAAAATATG
1653030 ATCGTTCCTGATTTATGGATCATGAAATCTA
66 ATCGTTCCTGATTTATGGATCATGAAATCTA
* *
1653061 CTGGTTTATGAACTATGGTTACTTGAAATATGTTATCTGGTTTCCTGTTTTCATTGAAAAATATG
1 CTGGTTTATGAACTATGGTTACTTGAAATATGTTATCTGGTTTCATGTTTTCACTGAAAAATATG
* *
1653126 GTCGTTCCTGATTTATAGATCATGAAATCTA
66 ATCGTTCCTGATTTATGGATCATGAAATCTA
1653157 CTGGTT
1 CTGGTT
1653163 ACTACTTGAA
Statistics
Matches: 174, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 174 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (96 bp):
CTGGTTTATGAACTATGGTTACTTGAAATATGTTATCTGGTTTCATGTTTTCACTGAAAAATATG
ATCGTTCCTGATTTATGGATCATGAAATCTA
Found at i:1656065 original size:17 final size:17
Alignment explanation
Indices: 1656043--1656076 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1656033 CTTCCATTTC
1656043 ATTGTCCCGTTAATTCA
1 ATTGTCCCGTTAATTCA
1656060 ATTGTCCCGTTAATTCA
1 ATTGTCCCGTTAATTCA
1656077 TTATTGGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
ATTGTCCCGTTAATTCA
Found at i:1663482 original size:11 final size:11
Alignment explanation
Indices: 1663468--1663503 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1663458 AGGTAATGAA
*
1663468 AAATGGTAAAT
1 AAATAGTAAAT
1663479 AAATAGTAAAT
1 AAATAGTAAAT
*
1663490 AAATAGCAAAT
1 AAATAGTAAAT
1663501 AAA
1 AAA
1663504 ATGATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.22
Consensus pattern (11 bp):
AAATAGTAAAT
Found at i:1664021 original size:23 final size:23
Alignment explanation
Indices: 1663995--1664043 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1663985 ATAAAGAACC
*
1663995 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAAAAT-CCATT
*
1664018 AAAATAAAGTTTAAAAATCCATT
1 AAAATAAAGCTTAAAAATCCATT
1664041 AAA
1 AAA
1664044 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAAAATCCATT
Found at i:1667368 original size:20 final size:20
Alignment explanation
Indices: 1667327--1667369 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1667317 AGAAAAGTAC
* *
1667327 AAGTTAAAAATGAAATATAA
1 AAGTTAAAAATGAAAGAAAA
*
1667347 AAGTTAAAGATGAAAGAAAA
1 AAGTTAAAAATGAAAGAAAA
1667367 AAG
1 AAG
1667370 AAAAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AAGTTAAAAATGAAAGAAAA
Found at i:1674888 original size:23 final size:23
Alignment explanation
Indices: 1674862--1674910 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1674852 ATAAAGAACC
*
1674862 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
1674885 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
1674908 AAA
1 AAA
1674911 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:1675843 original size:13 final size:13
Alignment explanation
Indices: 1675825--1675858 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1675815 ATCAAGACTG
1675825 TGCATTTTGCATA
1 TGCATTTTGCATA
1675838 TGCATTTTGCATA
1 TGCATTTTGCATA
*
1675851 TGTATTTT
1 TGCATTTT
1675859 TATTTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53
Consensus pattern (13 bp):
TGCATTTTGCATA
Found at i:1676378 original size:19 final size:19
Alignment explanation
Indices: 1676354--1676415 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
1676344 ACAGAGATCA
1676354 TGATGGGAAAAATGAAAGT
1 TGATGGGAAAAATGAAAGT
1676373 TGATGGGAAAAATGAAAGT
1 TGATGGGAAAAATGAAAGT
* *
1676392 TGATGGGAAAAACGAAAGC
1 TGATGGGAAAAATGAAAGT
1676411 TGATG
1 TGATG
1676416 AGGTGAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.45, C:0.03, G:0.32, T:0.19
Consensus pattern (19 bp):
TGATGGGAAAAATGAAAGT
Found at i:1679504 original size:37 final size:37
Alignment explanation
Indices: 1679463--1679542 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
1679453 TTCGACATTC
* *
1679463 GAAGCAAATCAATATTAAGCTTTCACGGAAGAGTAGT
1 GAAGCAAATCAATATTAAGCCTTCACGGAAGAATAGT
* *
1679500 GAAGCAAGTCAATATTAAGCCTTCATGGAAGAATAGT
1 GAAGCAAATCAATATTAAGCCTTCACGGAAGAATAGT
*
1679537 AAAGCA
1 GAAGCA
1679543 TACTCATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (37 bp):
GAAGCAAATCAATATTAAGCCTTCACGGAAGAATAGT
Found at i:1679737 original size:109 final size:109
Alignment explanation
Indices: 1679605--1680251 Score: 567
Period size: 109 Copynumber: 5.9 Consensus size: 109
1679595 AATAGACTAA
* * * *
1679605 TTTTATGAAGATGGTTCCAGTCTTATACTCTCTGAAAGAATAGGGAGCAGAAACATTTTCCGAAG
1 TTTT-TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAAACATTTTCTGAAG
* * * * *
1679670 ATTATTCAAG-TCCATACTCCCTGAAAGAATAGGGAGAAGATACA
65 ATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGCAGACACG
* * * *
1679714 TTTGTTGAAGATTGTTCGAGTCTTATTCTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAG
1 TTT-TTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAAACATTTTCTGAAG
** * ** * *
1679779 ATTGTTTGAG-TCTTATAATCTATAAAATAATAGGGAGCAGACACG
65 ATTGTTCAAGTTC-TATACTCCCTGAAAGAATAGGGAGCAGACACG
* * * ** * *
1679824 TTTCCTGAAGATTGTTCGAGTCCTATACTCTCTGAAAGAATATAGAGCA-AACACGTTTTCTAAA
1 TTT-TTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAA-ACATTTTCTGAA
* * *
1679888 GATTGTTCGAGTTCTATACTCCTTGAAAGAATATGGAGCAGACACG
64 GATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGCAGACACG
* * * * * *
1679934 TCTGTTGAAGATTGTTCGAGTTTTATACTCTCTAAAAGAATATGG-GC-GAACCCATTTT-TAGA
1 T-TTTTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAA-ACATTTTCT-GA
* * * *
1679996 AGATTGTTCAAGCTCTATACTTCCTGAAAGAATATGGAGCAGACCCG
63 AGATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGCAGACACG
* * * * * * * *
1680043 TTTTTCAAAGATTGTTCAAGTCCTATACTCCCTGAAAAAATAGAGAGCGGAACCATTTTCTTAAG
1 TTTTT-GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAAACATTTTCTGAAG
* * *
1680108 ATTGTTCAAGTCCT-TACTCCCT-AAACGAATAGGGAGCAGACCCA
65 ATTGTTCAAGTTCTATACTCCCTGAAA-GAATAGGGAGCAGACACG
* * * * **
1680152 TTTTCTGAAGATTATTC-AGGTCATATACTCCCTGAAAGAATAGGGAACGGATTCATTTT-TCGA
1 TTTT-TGAAGATTGTTCGA-GTCTTATACTCCCTGAAAGAATAGGGAGCAGAAACATTTTCT-GA
* * *
1680215 AGATTGTTCGAGTTCTATTCTTCCTGAAAGAATAGGG
63 AGATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGG
1680252 GGCGGACCCT
Statistics
Matches: 441, Mismatches: 80, Indels: 33
0.80 0.14 0.06
Matches are distributed among these distances:
108 9 0.02
109 234 0.53
110 188 0.43
111 10 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (109 bp):
TTTTTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAAACATTTTCTGAAGA
TTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGCAGACACG
Found at i:1679759 original size:55 final size:54
Alignment explanation
Indices: 1679547--1680251 Score: 525
Period size: 55 Copynumber: 12.9 Consensus size: 54
1679537 AAAGCATACT
* * * * **
1679547 CATTTTATGAAGATGGTTCGAGTCTGATA-TCCCCTGAAGGAATAGTGAAATAGACTA
1 CATTTT-TGAAGATTGTTCGAGTCTTATACT-CCCTGAAAGAATAG-GGAGCAGAC-A
* * * *
1679604 -ATTTTATGAAGATGGTTCCAGTCTTATACTCTCTGAAAGAATAGGGAGCAGAAA
1 CATTTT-TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* * * * * *
1679658 CATTTTCCGAAGATTATTCAAGTC-CATACTCCCTGAAAGAATAGGGAGAAGATA
1 CATTTT-TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
*
1679712 CATTTGTTGAAGATTGTTCGAGTCTTATTCTCCCTGAAAGAATAGGGAGCAGACA
1 CATTT-TTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* * * * ** * *
1679767 CGTTTGCTGAAGATTGTTTGAGTCTTATAATCTATAAAATAATAGGGAGCAGACA
1 CATTT-TTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* * * * ** *
1679822 CGTTTCCTGAAGATTGTTCGAGTCCTATACTCTCTGAAAGAATATAGAGCAAACA
1 CATTT-TTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* * * *
1679877 CGTTTTCTAAAGATTGTTCGAGT-TCTATACTCCTTGAAAGAATATGGAGCAGACA
1 CATTTT-TGAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAGGGAGCAGACA
* * * * * * *
1679932 CGTCTGTTGAAGATTGTTCGAGTTTTATACTCTCTAAAAGAATATGG-GC-GAACC
1 CAT-TTTTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAG-ACA
* * * *
1679986 CATTTTTAGAAGATTGTTCAAG-CTCTATACTTCCTGAAAGAATATGGAGCAGACC
1 CATTTTT-GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAGGGAGCAGACA
* * * * * * *
1680041 CGTTTTTCAAAGATTGTTCAAGTCCTATACTCCCTGAAAAAATAGAGAGCGGA-A
1 CATTTTT-GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* * * *
1680095 CCATTTTCTTAAGATTGTTCAAGTCCT-TACTCCCT-AAACGAATAGGGAGCAGACC
1 -CATTTT-TGAAGATTGTTCGAGTCTTATACTCCCTGAAA-GAATAGGGAGCAGACA
* * * * **
1680150 CATTTTCTGAAGATTATTC-AGGTCATATACTCCCTGAAAGAATAGGGAACGGATT
1 CATTTT-TGAAGATTGTTCGA-GTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
* *
1680205 CATTTTTCGAAGATTGTTCGAGT-TCTATTCTTCCTGAAAGAATAGGG
1 CATTTTT-GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAGGG
1680252 GGCGGACCCT
Statistics
Matches: 534, Mismatches: 90, Indels: 50
0.79 0.13 0.07
Matches are distributed among these distances:
53 9 0.02
54 125 0.23
55 351 0.66
56 48 0.09
57 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (54 bp):
CATTTTTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACA
Found at i:1679814 original size:164 final size:164
Alignment explanation
Indices: 1679610--1680251 Score: 602
Period size: 164 Copynumber: 3.9 Consensus size: 164
1679600 ACTAATTTTA
* * *
1679610 TGAAGATGGTTCCAGTCTTATACTCTCTGAAAGAATAGGGAGCAGAAACATTTTCCGAAGATTAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGAAACATTTTCCGAAGATTAT
* *
1679675 TCAAGTCCATACTCCCTGAAAGAATAGGGAGAAGATACATTTGTT-GAAGATTGTTCGAG-TCTT
66 TCAAGTCCATACTCCCTGAAAGAATAGGGAGAAGACACATTT-TTCAAAGATTGTTCGAGTTC-T
*
1679738 ATTCTCCCTGAAAGAATAGGGAGCAGACACGTTTGC
129 ATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGC
* * * * * * *
1679774 TGAAGATTGTTTGAGTCTTATAATCTATAAAATAATAGGGAGCAGACAC-GTTTCCTGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGAAACATTTTCC-GAAGATTA
* * ** *
1679838 TTCGAGTCCTATACTCTCTGAAAGAATATAGAGCAA-ACAC-GTTTTCTAAAGATTGTTCGAGTT
65 TTCAAGTCC-ATACTCCCTGAAAGAATAGGGAG-AAGACACATTTTTC-AAAGATTGTTCGAGTT
* * * *
1679901 CTATACTCCTTGAAAGAATATGGAGCAGACACGTCTGT
127 CTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGC
* * * ** *
1679939 TGAAGATTGTTCGAGTTTTATACTCTCTAAAAGAATATGG-GC-GAACCCATTTTTAGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGAA-ACATTTTCCGAAGATTA
* * * * * * * *
1680002 TTCAAGCTCTATACTTCCTGAAAGAATATGGAGCAGACCCGTTTTTCAAAGATTGTTCAAGTCCT
65 TTCAAG-TCCATACTCCCTGAAAGAATAGGGAGAAGACACATTTTTCAAAGATTGTTCGAGTTCT
* * * * *
1680067 ATACTCCCTGAAAAAATAGAGAGCGGA-ACCATTTTC
129 ATACTCCCTGAAAGAATAGGGAGCAGACA-CGTTTGC
* * * * * ** *
1680103 TTAAGATTGTTCAAGTCCT-TACTCCCTAAACGAATAGGGAGCAGACCCATTTTCTGAAGATTAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGAAACATTTTCCGAAGATTAT
* * * ** *
1680167 TCAGGTCATATACTCCCTGAAAGAATAGGGA-ACGGATTCATTTTTCGAAGATTGTTCGAGTTCT
66 TCAAGTC-CATACTCCCTGAAAGAATAGGGAGA-AGACACATTTTTCAAAGATTGTTCGAGTTCT
* *
1680231 ATTCTTCCTGAAAGAATAGGG
129 ATACTCCCTGAAAGAATAGGG
1680252 GGCGGACCCT
Statistics
Matches: 384, Mismatches: 78, Indels: 32
0.78 0.16 0.06
Matches are distributed among these distances:
163 30 0.08
164 236 0.61
165 114 0.30
166 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (164 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGAAACATTTTCCGAAGATTAT
TCAAGTCCATACTCCCTGAAAGAATAGGGAGAAGACACATTTTTCAAAGATTGTTCGAGTTCTAT
ACTCCCTGAAAGAATAGGGAGCAGACACGTTTGC
Found at i:1683621 original size:13 final size:13
Alignment explanation
Indices: 1683605--1683630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1683595 AAGACAATAT
1683605 TGCAAGACCATGC
1 TGCAAGACCATGC
1683618 TGCAAGACCATGC
1 TGCAAGACCATGC
1683631 GACCTCCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
TGCAAGACCATGC
Found at i:1689924 original size:20 final size:20
Alignment explanation
Indices: 1689899--1689956 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1689889 TTCCCATTGA
* *
1689899 AGTGCATTGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
1689919 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
1689942 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1689957 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:1694936 original size:80 final size:80
Alignment explanation
Indices: 1694803--1694962 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
1694793 TATCACCAAC
1694803 TGAGGGCATTCAAAAAAGGGGTGAGATGGGTAGTCATTGATTCTTAGATTTGTTTTTTAAGATGA
1 TGAGGGCATTCAAAAAAGGGGTGAGATGGGTAGTCATTGATTCTTAGATTTGTTTTTTAAGATGA
1694868 GGAAAAGAAAAAAGA
66 GGAAAAGAAAAAAGA
*
1694883 TGAGGGCATTCGAAAAAGGGGTGAGATGGGTAGTCATTGATTCTTAGATTTGTTTTTTAAGATGA
1 TGAGGGCATTCAAAAAAGGGGTGAGATGGGTAGTCATTGATTCTTAGATTTGTTTTTTAAGATGA
1694948 GGAAAAGAAAAAAGA
66 GGAAAAGAAAAAAGA
1694963 AGAGACATGG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (80 bp):
TGAGGGCATTCAAAAAAGGGGTGAGATGGGTAGTCATTGATTCTTAGATTTGTTTTTTAAGATGA
GGAAAAGAAAAAAGA
Found at i:1699146 original size:20 final size:20
Alignment explanation
Indices: 1699121--1699158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1699111 AAAGAGCAAC
1699121 AACGGTTAACCTGAAAATCT
1 AACGGTTAACCTGAAAATCT
**
1699141 AACGGTTGGCCTGAAAAT
1 AACGGTTAACCTGAAAAT
1699159 TTAAAGGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (20 bp):
AACGGTTAACCTGAAAATCT
Found at i:1699167 original size:20 final size:20
Alignment explanation
Indices: 1699130--1699168 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1699120 CAACGGTTAA
*
1699130 CCTGAAAATCTAACGGTTGG
1 CCTGAAAATCTAAAGGTTGG
*
1699150 CCTGAAAATTTAAAGGTTG
1 CCTGAAAATCTAAAGGTTG
1699169 ACTCTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
CCTGAAAATCTAAAGGTTGG
Found at i:1702053 original size:64 final size:66
Alignment explanation
Indices: 1701938--1702102 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 66
1701928 CATCCCCTGA
* * *
1701938 CGGGTGCATCGATGCACTA-TCTATGCATCGGTACATAAATCTCATTCGATGTTTGCA-TTTT-A
1 CGGGTGCATCGATGCACTACT-TGTGCATCGATACATAAATCACATTCGATGTTTGCATTTTTAA
1702000 AG
65 AG
* * * **
1702002 CGGGTGCATCGATGCACTACTTGTGCATCGATACACT-GATGACATTTGATGTTTTTATTTTTAA
1 CGGGTGCATCGATGCACTACTTGTGCATCGATACA-TAAATCACATTCGATGTTTGCATTTTTAA
1702066 AG
65 AG
* * * *
1702068 -GAGTGCATCGATACACTTCATGTGCATCGATACAT
1 CGGGTGCATCGATGCACTACTTGTGCATCGATACAT
1702103 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
64 46 0.54
65 36 0.42
66 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (66 bp):
CGGGTGCATCGATGCACTACTTGTGCATCGATACATAAATCACATTCGATGTTTGCATTTTTAAA
G
Found at i:1712119 original size:39 final size:39
Alignment explanation
Indices: 1712074--1712214 Score: 124
Period size: 39 Copynumber: 3.6 Consensus size: 39
1712064 CCTCGATTTT
* *
1712074 ACCACTTCCATATTCATCTTCACCTACTCAACAAGTGTC
1 ACCACTTCCATATTCATCTCCACATACTCAACAAGTGTC
* * * * *
1712113 CCCACTTTCATCTTCATCTCCACATACTCCACAAGTTTC
1 ACCACTTCCATATTCATCTCCACATACTCAACAAGTGTC
* ** **
1712152 ACAACTTCCATCCTCATCTCCACATACTTTACAAAGT-TC
1 ACCACTTCCATATTCATCTCCACATACTCAAC-AAGTGTC
* *
1712191 ACCACCTCCATCCTT-ATCTCCACA
1 ACCACTTCCAT-ATTCATCTCCACA
1712215 AGCTTCACCT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 78 0.93
40 6 0.07
ACGTcount: A:0.27, C:0.40, G:0.03, T:0.30
Consensus pattern (39 bp):
ACCACTTCCATATTCATCTCCACATACTCAACAAGTGTC
Done.