Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 7 of 316
Found at i:1985425 original size:46 final size:46
Alignment explanation
Indices: 1985373--1985506 Score: 259
Period size: 46 Copynumber: 2.9 Consensus size: 46
1985363 AGTGTGCTCT
1985373 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1985419 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1985465 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1985507 TTGAAAGATA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1985505 original size:16 final size:16
Alignment explanation
Indices: 1985484--1985522 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1985474 AATGTGTAAG
1985484 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
1985500 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
1985516 ACCATGG
1 ACCATGG
1985523 CAACATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (16 bp):
ACCATGGTTGAAAGAT
Found at i:1991177 original size:341 final size:341
Alignment explanation
Indices: 1990554--1991194 Score: 867
Period size: 341 Copynumber: 1.9 Consensus size: 341
1990544 TGGAATGCAA
* *
1990554 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTGGTGAAGTCGCTGAGCTAAAAGAAAATTCAG
1 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
* * ** * * **
1990619 ACTTGTTTTCTAAGCCCGAGATTTTGCGTCTACGTCATCTGCCCAAACTAAAGACTGTATACCAT
66 ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATACCAT
* * ** *
1990684 CATGCTCTGCCTTTCCCACAGCTGAAGAAAATATACATTACAGGATGCCCAATGTTAAAGAAGCT
131 CATGCTCTACCTTTCCCACAGCTGAAGAAAATACACATTACAAAATGCCCAATGCTAAAGAAGCT
*
1990749 CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGTGGGATGGTGGA
196 CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGAGGGATGGTGGA
*
1990814 AAGATGTCGAATGAGAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
261 AAGATGTAGAATGAGAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
1990879 TGTTGGTTATTAATTG
326 TGTTGGTTATTAATTG
* * * * * *
1990895 AGGTTTAGAAGAAATGATCAGTGAGGAAAAACTTAGTGAAGTCGCTGAGCTAAAGGGAAATTCAA
1 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
* * *
1990960 ACTTGTTTTCTAAGCTAGAGTTTTTGCATCTAAATAATCTGCCCAAAATGAAGACAATATACCCA
66 ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATA-CCA
* * * * ** *
1991025 -CATGCTCTACTTTTTCCGCAGCTGAAGAGAAT-CACAATTTTAAAATGCCCAATGCTGAAGAAG
130 TCATGCTCTACCTTTCCCACAGCTGAAGAAAATACAC-ATTACAAAATGCCCAATGCTAAAGAAG
* * * *
1991088 TTCCCACTAAACTCCAATAGTGCAAAAGGAC-GAAGGCTTGTCATTGAAGGAGATGAGGGATGGT
194 CTCCCACTAAACTCCAATAGTGCAAAAAGACAG-AGGATGGTCATTGAAGGAGATGAGGGATGGT
* *
1991152 GGAAAGATGTAGGATG-GAAGGATGAATCCACTCAAATTGCTTT
258 GGAAAGATGTAGAATGAG-AGGATGAATCCACTAAAATTGCTTT
1991195 ACTCTCTTCT
Statistics
Matches: 257, Mismatches: 39, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
340 4 0.02
341 250 0.97
342 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (341 bp):
AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATACCAT
CATGCTCTACCTTTCCCACAGCTGAAGAAAATACACATTACAAAATGCCCAATGCTAAAGAAGCT
CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGAGGGATGGTGGA
AAGATGTAGAATGAGAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
TGTTGGTTATTAATTG
Found at i:1993480 original size:30 final size:30
Alignment explanation
Indices: 1993446--1993508 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1993436 ATTTATTTTA
* *
1993446 TTGTTTATTTTTTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
1993476 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1993506 TTG
1 TTG
1993509 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:1993612 original size:18 final size:18
Alignment explanation
Indices: 1993591--1993630 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1993581 GAAATATTTA
*
1993591 TTTTGATGT-TTCTAGTAT
1 TTTTGATGTATTATA-TAT
1993609 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
1993627 TTTT
1 TTTT
1993631 AAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:2001046 original size:30 final size:30
Alignment explanation
Indices: 2001012--2001074 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2001002 ACTTATTTTA
*
2001012 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTATAAAGGCAT
*
2001042 TTGTTAATTTTGTTATTATTATAGAGGCAT
1 TTGTTAATTTTGTTATTATTATAAAGGCAT
2001072 TTG
1 TTG
2001075 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTATAAAGGCAT
Found at i:2001694 original size:9 final size:9
Alignment explanation
Indices: 2001667--2001710 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
2001657 AGTATTTTAA
2001667 TTATAATTT
1 TTATAATTT
2001676 TTAATAATTT
1 TT-ATAATTT
2001686 TTGAT-ATTT
1 TT-ATAATTT
2001695 TTATAATTT
1 TTATAATTT
2001704 TT-TAATT
1 TTATAATT
2001711 AACAAATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.22
9 14 0.44
10 11 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
TTATAATTT
Found at i:2006698 original size:21 final size:22
Alignment explanation
Indices: 2006652--2006694 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2006642 TGTAAAAGTG
*
2006652 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
2006674 ATTT-TCTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
2006694 A
1 A
2006695 ATTTACAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:2011568 original size:24 final size:24
Alignment explanation
Indices: 2011541--2011590 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2011531 AAACTATGAG
*
2011541 TAAGTTTAAAATTATAATGGTAAT
1 TAAGTTTAAAAATATAATGGTAAT
2011565 TAAGTTTAAAAATATAATGGTAAT
1 TAAGTTTAAAAATATAATGGTAAT
2011589 TA
1 TA
2011591 TGTAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (24 bp):
TAAGTTTAAAAATATAATGGTAAT
Found at i:2012072 original size:21 final size:21
Alignment explanation
Indices: 2012039--2012097 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
2012029 ATTTTAAGAA
**
2012039 TTGTTTTGGTATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
*
2012060 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
2012082 AT-TTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
2012098 GATTTATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 15 0.48
22 10 0.32
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:2012081 original size:22 final size:21
Alignment explanation
Indices: 2012053--2012128 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 21
2012043 TTTGGTATTA
2012053 TTTTTATTTGTTTTAATATTTG
1 TTTTTATTT-TTTTAATATTTG
*
2012075 TTTTTATATTTTTAAATATATTTG
1 TTTTTAT-TTTTT-TA-ATATTTG
*
2012099 ATTTATTATATTTTTAA-ATTT-
1 -TTT-TTATTTTTTTAATATTTG
2012120 TTTTTATTT
1 TTTTTATTT
2012129 AATGAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.11
20 3 0.07
22 14 0.31
23 4 0.09
24 8 0.18
25 7 0.16
26 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTATTTTTTTAATATTTG
Found at i:2012129 original size:26 final size:26
Alignment explanation
Indices: 2012068--2012117 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2012058 ATTTGTTTTA
2012068 ATATTTG-TTT-TTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
2012092 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
2012118 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:2026991 original size:20 final size:20
Alignment explanation
Indices: 2026935--2026993 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2026925 TACCCCACTC
*
2026935 TTAA-TTTTAATCCAATTAA
1 TTAAGTTTTAATACAATTAA
* * *
2026954 -AAAGTTTTCATTATAATTAA
1 TTAAGTTTT-AATACAATTAA
2026974 TTAAGTTTTAATACAATTAA
1 TTAAGTTTTAATACAATTAA
2026994 CACCTGACAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.07
19 4 0.13
20 17 0.57
21 7 0.23
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAAGTTTTAATACAATTAA
Found at i:2029798 original size:17 final size:17
Alignment explanation
Indices: 2029776--2029810 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2029766 GCCCAATTTA
*
2029776 ACTAATGTCTAATGAAT
1 ACTAATGTCTAAGGAAT
*
2029793 ACTAATGTTTAAGGAAT
1 ACTAATGTCTAAGGAAT
2029810 A
1 A
2029811 AACAACACAA
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:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (17 bp):
ACTAATGTCTAAGGAAT
Found at i:2031058 original size:19 final size:18
Alignment explanation
Indices: 2031002--2031059 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2030992 TCACATCAAC
*
2031002 AAATAATTTTAAAATTAA
1 AAATAAATTTAAAATTAA
* * *
2031020 AAA-ATATTCAAAAAATAA
1 AAATAAATT-TAAAATTAA
2031038 AAATAAATTTAAAATTCAA
1 AAATAAATTTAAAATT-AA
2031057 AAA
1 AAA
2031060 AATAGCATGA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 3 0.10
18 18 0.60
19 9 0.30
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATTTAAAATTAA
Found at i:2033252 original size:40 final size:40
Alignment explanation
Indices: 2033208--2033430 Score: 237
Period size: 40 Copynumber: 5.6 Consensus size: 40
2033198 GCTCCTCGTT
*
2033208 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
* *
2033248 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCA
* *
2033288 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCA
*
2033328 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAAT-TCGCA
* * * * *
2033367 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCA
2033408 C-AA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
2033431 ACAGCATTCA
Statistics
Matches: 161, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
38 3 0.02
39 44 0.27
40 105 0.65
41 8 0.05
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
Found at i:2033392 original size:79 final size:80
Alignment explanation
Indices: 2033208--2033431 Score: 289
Period size: 79 Copynumber: 2.8 Consensus size: 80
2033198 GCTCCTCGTT
* * *
2033208 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
2033272 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
*
2033288 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
2033352 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
* * *
2033367 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
2033428 CGGA
63 CGGA
2033432 CAGCATTCAA
Statistics
Matches: 129, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
78 12 0.09
79 60 0.47
80 55 0.43
81 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:2035103 original size:14 final size:14
Alignment explanation
Indices: 2035081--2035110 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2035071 TGAAAAATGG
*
2035081 ATTAGAAAATATTT
1 ATTAAAAAATATTT
2035095 ATTAAAAAATATTT
1 ATTAAAAAATATTT
2035109 AT
1 AT
2035111 GAAATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTAAAAAATATTT
Found at i:2036261 original size:15 final size:14
Alignment explanation
Indices: 2036241--2036282 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2036231 CGATGAATTT
2036241 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
2036256 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
2036271 ATTGAATTATAT
1 ATTGAATTATAT
2036283 AATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:2036725 original size:21 final size:21
Alignment explanation
Indices: 2036682--2036741 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2036672 TGTATTTCAA
2036682 GCACCTCGTGTGTCGTATCAG
1 GCACCTCGTGTGTCGTATCAG
* *
2036703 GCACCTCGTGTGTCGTTTTAG
1 GCACCTCGTGTGTCGTATCAG
* **
2036724 GCACTTTATGTGTCGTAT
1 GCACCTCGTGTGTCGTAT
2036742 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (21 bp):
GCACCTCGTGTGTCGTATCAG
Found at i:2040076 original size:24 final size:24
Alignment explanation
Indices: 2040049--2040096 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2040039 TATACCCACT
2040049 TGTCAAATCTAAAAATTATAATTA
1 TGTCAAATCTAAAAATTATAATTA
2040073 TGTCAAATCTAAAAATTATAATTA
1 TGTCAAATCTAAAAATTATAATTA
2040097 AAATGTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
TGTCAAATCTAAAAATTATAATTA
Found at i:2040306 original size:21 final size:21
Alignment explanation
Indices: 2040269--2040308 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2040259 AATGGGACCG
*
2040269 CTGATGTGGCAAGTTAACTAA
1 CTGATGTGCCAAGTTAACTAA
2040290 CTGATGTGACCAA-TTAACT
1 CTGATGTG-CCAAGTTAACT
2040309 TACCACGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
CTGATGTGCCAAGTTAACTAA
Found at i:2041736 original size:30 final size:30
Alignment explanation
Indices: 2041700--2041762 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2041690 ACTTATTTTA
2041700 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
2041730 TTGTTAATTTTGTTATTATTTTACAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
2041760 TTG
1 TTG
2041763 CTTGTTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:2041911 original size:12 final size:12
Alignment explanation
Indices: 2041881--2041913 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2041871 TATATTTTTT
2041881 AAAATT-ATATA
1 AAAATTAATATA
2041892 AAAA-TAATATA
1 AAAATTAATATA
2041903 AAAATTAATAT
1 AAAATTAATAT
2041914 GGGCAGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:2043523 original size:3 final size:3
Alignment explanation
Indices: 2043515--2043545 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2043505 GACAGTGAAC
2043515 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
2043546 AGTAGCGGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:2045788 original size:23 final size:23
Alignment explanation
Indices: 2045753--2045798 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2045743 TAGTTGATCC
2045753 TGTTAAAAATTATTA-ATTTAATT
1 TGTTAAAAATTATTATA-TTAATT
* *
2045776 TGTTGAAATTTATTATATTAATT
1 TGTTAAAAATTATTATATTAATT
2045799 CTTTTAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
TGTTAAAAATTATTATATTAATT
Found at i:2046440 original size:18 final size:18
Alignment explanation
Indices: 2046417--2046453 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2046407 CTACTTTCAT
2046417 TGTTCTTCACTACTGAAA
1 TGTTCTTCACTACTGAAA
2046435 TGTTCTTCACTACTGAAA
1 TGTTCTTCACTACTGAAA
2046453 T
1 T
2046454 TTTAAGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGTTCTTCACTACTGAAA
Found at i:2046574 original size:32 final size:32
Alignment explanation
Indices: 2046533--2046596 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2046523 GGAGCATGAG
2046533 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
2046565 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
2046597 CAATCCCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (32 bp):
TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
Found at i:2047398 original size:12 final size:12
Alignment explanation
Indices: 2047378--2047424 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
2047368 GATTTAATAT
*
2047378 ATGTATATGTAC
1 ATGTATATGTAA
*
2047390 ATGTCTATGTAA
1 ATGTATATGTAA
2047402 ATGTATAAATGTAA
1 ATGTAT--ATGTAA
2047416 ATGTATATG
1 ATGTATATG
2047425 AATCTTACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 18 0.60
14 12 0.40
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (12 bp):
ATGTATATGTAA
Found at i:2047415 original size:14 final size:14
Alignment explanation
Indices: 2047396--2047422 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2047386 GTACATGTCT
2047396 ATGTAAATGTATAA
1 ATGTAAATGTATAA
2047410 ATGTAAATGTATA
1 ATGTAAATGTATA
2047423 TGAATCTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
ATGTAAATGTATAA
Found at i:2053423 original size:17 final size:17
Alignment explanation
Indices: 2053384--2053427 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2053374 GGGTAGCAAA
*
2053384 AGCAAAGGCAGCAGTAGC
1 AGCAAA-GCAGCAGCAGC
*
2053402 -CCAAAGCAGCAGCAGC
1 AGCAAAGCAGCAGCAGC
2053418 AGCAAAGCAG
1 AGCAAAGCAG
2053428 GTAAGGGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.41, C:0.27, G:0.30, T:0.02
Consensus pattern (17 bp):
AGCAAAGCAGCAGCAGC
Found at i:2059997 original size:35 final size:35
Alignment explanation
Indices: 2059957--2060027 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2059947 AAGTGCATAA
2059957 TGTTCTTTAGGTAAAACTTTGAAGTCCAATTTTCC
1 TGTTCTTTAGGTAAAACTTTGAAGTCCAATTTTCC
2059992 TGTTCTTTAGGTAAAACTTTGAAGTCCAATTTTCC
1 TGTTCTTTAGGTAAAACTTTGAAGTCCAATTTTCC
2060027 T
1 T
2060028 ATACTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (35 bp):
TGTTCTTTAGGTAAAACTTTGAAGTCCAATTTTCC
Found at i:2063534 original size:70 final size:70
Alignment explanation
Indices: 2063416--2063586 Score: 204
Period size: 70 Copynumber: 2.5 Consensus size: 70
2063406 CTGGTCTTAG
* * *** * *
2063416 CTTTAAATTTAGTCGAAA-CTTAATATAATTATTGGATATCGAAGAATTTCA-AACTAATATAT-
1 CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAA-TAATATATA
*
2063478 AGCTCAA
65 ACCT-AA
* *
2063485 CTTTAAATTTAGTCAAAACCCTAATATGATTATCAAATATTAAAAAATTTCAGAATAATATATAA
1 CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAATAATATATAA
*
2063550 CCTGA
66 CCTAA
2063555 CTTTAAATTTAGTCAAAACCCTAATATAATTA
1 CTTTAAATTTAGTCAAAACCCTAATATAATTA
2063587 CTAAATAGAC
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
69 17 0.20
70 65 0.75
71 5 0.06
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (70 bp):
CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAATAATATATAA
CCTAA
Found at i:2069604 original size:14 final size:14
Alignment explanation
Indices: 2069585--2069651 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 14
2069575 GTTTGCAGGT
*
2069585 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
2069599 AAAATGATTTCTGG
1 AAAATGATTTCCGG
* * *
2069613 AAAATAATTTCTTGA
1 AAAATGATTTC-CGG
2069628 AAAATGATTTCTC-G
1 AAAATGATTTC-CGG
2069642 AAAATGATTT
1 AAAATGATTT
2069652 ACTTTTCTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 32 0.71
15 13 0.29
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:2069637 original size:15 final size:14
Alignment explanation
Indices: 2069598--2069651 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
2069588 ATGTTTTCCG
*
2069598 GAAAATGATTTCTG
1 GAAAATGATTTCTT
*
2069612 GAAAATAATTTCTT
1 GAAAATGATTTCTT
*
2069626 GAAAAATGATTTCTC
1 G-AAAATGATTTCTT
2069641 GAAAATGATTT
1 GAAAATGATTT
2069652 ACTTTTCTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
GAAAATGATTTCTT
Found at i:2070497 original size:15 final size:15
Alignment explanation
Indices: 2070477--2070584 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
2070467 TTTATGGAAA
2070477 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
2070492 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
2070506 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2070522 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2070536 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2070552 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2070566 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
2070582 ATC
1 ATC
2070585 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:2070514 original size:30 final size:30
Alignment explanation
Indices: 2070471--2070594 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
2070461 TCCATATTTA
* *
2070471 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2070501 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2070531 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2070561 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2070592 TGG
1 TGG
2070595 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2075189 original size:15 final size:15
Alignment explanation
Indices: 2075169--2075276 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
2075159 TTTATGGAAA
2075169 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
2075184 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
2075198 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2075214 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2075228 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2075244 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2075258 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
2075274 ATC
1 ATC
2075277 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:2075206 original size:30 final size:30
Alignment explanation
Indices: 2075163--2075286 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
2075153 TCCATATTTA
* *
2075163 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2075193 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2075223 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2075253 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2075284 TGG
1 TGG
2075287 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2089240 original size:16 final size:17
Alignment explanation
Indices: 2089215--2089248 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2089205 TTCAAAACTA
2089215 TACATAAACTTT-ATTT
1 TACATAAACTTTAATTT
*
2089231 TACATTAACTTTAATTT
1 TACATAAACTTTAATTT
2089248 T
1 T
2089249 TTTTCTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TACATAAACTTTAATTT
Found at i:2092343 original size:32 final size:32
Alignment explanation
Indices: 2092305--2092370 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2092295 TTACTCACTC
2092305 TATTTTATATTGATTAGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
2092337 TATTTTATATTGATTAGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
2092369 TA
1 TA
2092371 GAGAATTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (32 bp):
TATTTTATATTGATTAGATTGTAATTGTAATT
Found at i:2094415 original size:9 final size:10
Alignment explanation
Indices: 2094393--2094429 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2094383 AATGACTCCT
*
2094393 AAAATTTTTG
1 AAAATTTTTA
2094403 AAAATTTTTA
1 AAAATTTTTA
2094413 AAAA-TTTTA
1 AAAATTTTTA
2094422 AAAATTTT
1 AAAATTTT
2094430 CATTATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:2099814 original size:21 final size:20
Alignment explanation
Indices: 2099788--2099827 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2099778 CCACAACCTA
2099788 ATATTAATTTCTATATTTTTT
1 ATATTAATTT-TATATTTTTT
* *
2099809 ATATTACTTTTTTATTTTT
1 ATATTAATTTTATATTTTT
2099828 ATTATAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
ATATTAATTTTATATTTTTT
Found at i:2106070 original size:31 final size:31
Alignment explanation
Indices: 2106035--2106102 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2106025 TAAAAGCTAG
2106035 TGACTT-AATTGAAAACGTTT-GAATAATTCAA
1 TGACTTGAATT-AAAAC-TTTCGAATAATTCAA
* *
2106066 TGACTTGAATTAAAACTTTCGAATAATTTAG
1 TGACTTGAATTAAAACTTTCGAATAATTCAA
2106097 TGACTT
1 TGACTT
2106103 TTTGGTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
TGACTTGAATTAAAACTTTCGAATAATTCAA
Found at i:2120462 original size:16 final size:16
Alignment explanation
Indices: 2120441--2120479 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
2120431 TCGGAAAAAA
2120441 AATCAAATTTTGAGTT
1 AATCAAATTTTGAGTT
2120457 AATCAAA--TTGAGTT
1 AATCAAATTTTGAGTT
*
2120471 ATTCAAATT
1 AATCAAATT
2120480 ATTCAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (16 bp):
AATCAAATTTTGAGTT
Found at i:2120694 original size:19 final size:20
Alignment explanation
Indices: 2120652--2120706 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
2120642 CAAAAATTAT
*
2120652 AAAATAATTTTCACAAATTTC
1 AAAATAATTTTTA-AAATTTC
2120673 AAAATAATTTTTAAAA-TTC
1 AAAATAATTTTTAAAATTTC
*
2120692 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
2120707 ATCCTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 8 0.25
20 3 0.09
21 12 0.38
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTTC
Found at i:2120707 original size:19 final size:19
Alignment explanation
Indices: 2120652--2120708 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2120642 CAAAAATTAT
*
2120652 AAAATAATTTTCACAAATTTC
1 AAAATAATTTT-A-AAAATTC
*
2120673 AAAATAATTTTTAAAATTC
1 AAAATAATTTTAAAAATTC
2120692 AAAAT-ATTTATAAAAAT
1 AAAATAATTT-TAAAAAT
2120709 CCTAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.12
19 17 0.53
21 11 0.34
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:2129103 original size:20 final size:20
Alignment explanation
Indices: 2129078--2129127 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2129068 TGGCTTAAAA
2129078 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2129098 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2129115 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2129128 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2133742 original size:20 final size:20
Alignment explanation
Indices: 2133717--2133766 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2133707 TGGCTTAAAA
2133717 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2133737 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2133754 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2133767 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2135198 original size:19 final size:21
Alignment explanation
Indices: 2135174--2135218 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2135164 TTTCATAAAA
2135174 AAAAATTAGAT-C-AAATTAT
1 AAAAATTAGATACAAAATTAT
*
2135193 AAAAA-TATATACAAAATTAT
1 AAAAATTAGATACAAAATTAT
2135213 AAAAAT
1 AAAAAT
2135219 ATTTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATTAGATACAAAATTAT
Found at i:2135289 original size:20 final size:20
Alignment explanation
Indices: 2135264--2135307 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2135254 AAAATTATTT
*
2135264 AATAAAATAATAATTTTATA
1 AATAAAATAATAATCTTATA
2135284 AATAAAATAATAATCTTATA
1 AATAAAATAATAATCTTATA
2135304 AATA
1 AATA
2135308 TAACAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAATAATAATCTTATA
Found at i:2136507 original size:20 final size:19
Alignment explanation
Indices: 2136478--2136516 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
2136468 AAATTACAGG
2136478 AAAATGAAAGTAAAAAGAA
1 AAAATGAAAGTAAAAAGAA
2136497 AAAATTGAAAGTAAAAAGAA
1 AAAA-TGAAAGTAAAAAGAA
2136517 TTAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATGAAAGTAAAAAGAA
Found at i:2137886 original size:13 final size:13
Alignment explanation
Indices: 2137870--2137905 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2137860 TTTTAATCAA
2137870 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
*
2137883 TTTTGTTTTTGTT
1 TTTTTTTTTTGTT
2137896 TTTTTCTTTT
1 TTTTT-TTTT
2137906 AATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:2137944 original size:24 final size:24
Alignment explanation
Indices: 2137912--2137992 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
2137902 TTTTAATTAT
*
2137912 TTTCC-TTTTTTTAATTATTTGTG
1 TTTCCATTTTTTTAATTATTTTTG
** * *
2137935 TTTCCATTTTAATCATTTTTTTTG
1 TTTCCATTTTTTTAATTATTTTTG
**
2137959 TTT-TTTTTCTTTTAATTATTTTTG
1 TTTCCATTT-TTTTAATTATTTTTG
2137983 TTTCCATTTT
1 TTTCCATTTT
2137993 GATCCAACCT
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
23 8 0.19
24 31 0.74
25 3 0.07
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTCCATTTTTTTAATTATTTTTG
Found at i:2137981 original size:18 final size:19
Alignment explanation
Indices: 2137897--2137962 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
2137887 GTTTTTGTTT
2137897 TTTTCTTTTAATTATTTTC
1 TTTTCTTTTAATTATTTTC
* *
2137916 CTTT-TTTTAATTATTTGTG
1 TTTTCTTTTAATTATTT-TC
* *
2137935 TTTCCATTTTAATCATTTT-
1 TTTTC-TTTTAATTATTTTC
*
2137954 TTTTGTTTT
1 TTTTCTTTT
2137963 TTTTCTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
18 16 0.43
19 9 0.24
20 1 0.03
21 11 0.30
ACGTcount: A:0.15, C:0.09, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTCTTTTAATTATTTTC
Found at i:2138012 original size:48 final size:48
Alignment explanation
Indices: 2137920--2138012 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
2137910 ATTTTCCTTT
***
2137920 TTTTAATTATTTGTGTTTCCATTTTAATCATTTTTTTTGTTTTTTTTC
1 TTTTAATTATTTGTGTTTCCATTTTAATCAACCTTTTTGTTTTTTTTC
* *
2137968 TTTTAATTATTTTTGTTTCCATTTTGATCCAACCTTTTTGTTTTT
1 TTTTAATTATTTGTGTTTCCATTTTAAT-CAACCTTTTTGTTTTT
2138013 ATGCTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 26 0.67
49 13 0.33
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (48 bp):
TTTTAATTATTTGTGTTTCCATTTTAATCAACCTTTTTGTTTTTTTTC
Found at i:2141842 original size:3 final size:3
Alignment explanation
Indices: 2141834--2141874 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2141824 TCGTTTTTGA
2141834 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2141875 TCAGGCTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2149825 original size:67 final size:66
Alignment explanation
Indices: 2149754--2149886 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 66
2149744 TCTAACTATT
2149754 AACAATTATAAATTAGCCACCAATATTATCAAATTTGATTTTTTTTTCACTCGTAGTCCATTTTT
1 AACAATTATAAATTAGCCACCAATATTATCAAATTTGA-TTTTTTTTCACTCGTAGTCCATTTTT
2149819 GG
65 GG
2149821 AACAATTATAAATTAGCCACCAATATTATCAAATTTGATTTTTTTTCACTCGTAGTCCATTTTTG
1 AACAATTATAAATTAGCCACCAATATTATCAAATTTGATTTTTTTTCACTCGTAGTCCATTTTTG
2149886 G
66 G
2149887 TCACTAACTA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 28 0.42
67 38 0.58
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (66 bp):
AACAATTATAAATTAGCCACCAATATTATCAAATTTGATTTTTTTTCACTCGTAGTCCATTTTTG
G
Found at i:2154162 original size:15 final size:15
Alignment explanation
Indices: 2154142--2154190 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2154132 AGTTTTAAAT
2154142 ATTAAAAATAAAGAA
1 ATTAAAAATAAAGAA
* * *
2154157 ATTAAATATATA-AT
1 ATTAAAAATAAAGAA
*
2154171 TTTAAAAATAAAGAA
1 ATTAAAAATAAAGAA
2154186 ATTAA
1 ATTAA
2154191 TTAACCTAGC
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
ATTAAAAATAAAGAA
Found at i:2158258 original size:31 final size:31
Alignment explanation
Indices: 2158190--2158272 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
2158180 ATGGTCATTG
*
2158190 AACTATTCGAA-AGTTTTCATTTAAGTCACTA
1 AACTATTC-AAGAGTTTTTATTTAAGTCACTA
2158221 AACTATTCAAGAGTTTTTATTTAAGTCACTA
1 AACTATTCAAGAGTTTTTATTTAAGTCACTA
**
2158252 GGCTATT-AAG-GTTTTT-TTTAA
1 AACTATTCAAGAGTTTTTATTTAA
2158273 AAGGTCGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
30 5 0.10
31 32 0.67
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (31 bp):
AACTATTCAAGAGTTTTTATTTAAGTCACTA
Found at i:2159015 original size:32 final size:32
Alignment explanation
Indices: 2158977--2159041 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2158967 GAGAACAACT
2158977 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
2159009 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
2159041 A
1 A
2159042 ATAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (32 bp):
ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
Found at i:2162281 original size:23 final size:23
Alignment explanation
Indices: 2162251--2162298 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2162241 AATTGGGACA
* *
2162251 AAAAAAATTCAAGTATCAAATTG
1 AAAAAAATTCAAGTACCAAAGTG
*
2162274 AAAAAAATTCAGGTACCAAAGTG
1 AAAAAAATTCAAGTACCAAAGTG
2162297 AA
1 AA
2162299 TATTGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (23 bp):
AAAAAAATTCAAGTACCAAAGTG
Found at i:2168764 original size:16 final size:15
Alignment explanation
Indices: 2168741--2168784 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2168731 ACGATGCTTT
**
2168741 AAAAAAATATTTTTA
1 AAAAAAATAAATTTA
2168756 AATAAAAATAAATTTA
1 AA-AAAAATAAATTTA
2168772 AAAAAAATTAAAT
1 AAAAAAA-TAAAT
2168785 ATGGACGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAAATAAATTTA
Found at i:2173264 original size:3 final size:3
Alignment explanation
Indices: 2173256--2173281 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2173246 CAAGCTCAAC
2173256 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2173282 AAAATCGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2183001 original size:80 final size:80
Alignment explanation
Indices: 2182800--2183324 Score: 442
Period size: 79 Copynumber: 6.5 Consensus size: 80
2182790 AACATCGTTG
* * * * * * *
2182800 GTTTTTCCTCTTGAAAATTCTCAGAAAATATTCACAGATTCACTCAAAGGAAATATAG-AAATAG
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATT-ACTC-AAGGAAATACAGCAAA-AG
*
2182864 CAAAAGGGTATCAGAA-TT
63 CAAAAGGGCATCA-AACTT
* *
2182882 GGTTTCCCTTCATGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-C
1 GTTTTCCC-TCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAA-AAGC
*
2182946 AAAAAGGGCA-CAAACTA
64 -AAAAGGGCATCAAACTT
* * * * *
2182963 GTTTTCCCTCAGGCGAATTCCCATAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
*
2183028 AAGGGAATC-AACATT
66 AAGGGCATCAAAC-TT
** * ** *
2183043 GTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACATCAAAAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
* *
2183107 AAGGACATCAAATTT
66 AAGGGCATCAAACTT
* * * *
2183122 GGTCT-CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTGAAGGAAATACAGCAAAAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
* *
2183186 AAGGGTATCGAA-TT
66 AAGGGCATCAAACTT
* * * * * * * *
2183200 GATTTCTCC-CATTCAAATT-CCAGAAAAAATTTCACAAATTATTCAAGCAAATTCAACAAGAGC
1 GTTTTC-CCTCATGCAAATTCCCAG-AAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGC
* * * **
2183263 AAAAGGGTACCTAACCA
64 AAAAGGGCATCAAACTT
* * *
2183280 GTGTTCCCTCAAT-CAAATTCCCAGAAAAAATTTCACATATTACTC
1 GTTTTCCCTC-ATGCAAATTCCCAG-AAAATTTTCACAAATTACTC
2183325 CAGAAAAACT
Statistics
Matches: 361, Mismatches: 65, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
78 40 0.11
79 125 0.35
80 101 0.28
81 47 0.13
82 21 0.06
83 27 0.07
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (80 bp):
GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
AAGGGCATCAAACTT
Found at i:2188040 original size:75 final size:75
Alignment explanation
Indices: 2187913--2188065 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
2187903 CTTCGTTCTC
* *
2187913 CAAAGGATTGTCCTAATATAACATAGCCAGCGACAAAAAGAATCAAATTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
2187978 AATAATACAG
66 AATAATACAG
* *
2187988 CAAAGGATTGTCCTGATATAACATAGCCAGCAACAAAAAGAATCAGACTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
*
2188053 AATAGTACAG
66 AATAATACAG
2188063 CAA
1 CAA
2188066 CATGAGGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (75 bp):
CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
AATAATACAG
Found at i:2191676 original size:161 final size:145
Alignment explanation
Indices: 2191242--2191981 Score: 551
Period size: 147 Copynumber: 5.0 Consensus size: 145
2191232 GAGTGAATTT
* * * * *
2191242 GAGATAGGAAGTAACAAAAAACGAGGCAATTAGACTGAAAG-GTATCGAAATAAAATTGAAAAAA
1 GAGATAGGAAGT--TAAAAAACAAGGCAAATAGACT-AAAGAGTATTGAAATAAATTTGAAAAAA
** * * *
2191306 AAACCACAAAAAACCAGAGTCAAGAACACCACGAAAGATCAAATGCTCAAGCGAATAACCAATAA
63 AAA--AC-CTAACCCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAA
* *
2191371 ATCGGA-GATTTTCAGCAAAATTA
125 A-C-AATGATTTTCAGCAAAA-TC
* * *
2191394 GAGATATGAAGTTAAAAAACAAGGCAAATAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAA
1 GAGATAGGAAGTTAAAAAACAAGGCAAATAGACTAAAGAGTATTGAAATAAATTTGAAAAAAAAA
* * *
2191459 ACCTAACTCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATATAACAAT
66 ACCTAACCCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATA-AACAAT
2191524 GATTTTCAGCAAAATC
130 GATTTTCAGCAAAATC
* ** *
2191540 GAGCTAGGAAGTTTAAAAAAAAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGA
1 GAGATAGGAAG-TT------AAAAAA-CAAGGCAAATAGACTAAAGAGTATTGAAATAAATTT--
*
2191605 AAAGAAAAAAAAAACACCTAACCCAGAGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAAT
56 ---G-AAAAAAAAA-ACCTAACCCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAAT
*
2191670 AACCAATAAAACAATGATTTTCAGCGAAATC
116 AACCAAT-AAACAATGATTTTCAGCAAAATC
* * * * * *
2191701 GA-ACTA-TAA---AAAAAA-AGGGGCAATTAGAGTAAAGGGTATTGGAATAAATTTG--AAAAA
1 GAGA-TAGGAAGTTAAAAAACA-AGGCAAATAGACTAAAGAGTATTGAAATAAATTTGAAAAAAA
* *** * * * *
2191758 AAA---AACCCAGAGCCAAGAATC-TCACCCAAGCTCGAATGCTCAAACGAACAACCAATAAAGC
64 AAACCTAACCCAGAGCCAAGAA-CACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAA-C
*
2191819 AATGATTTTCAGCAAATTC
127 AATGATTTTCAGCAAAATC
* * * * * * * *
2191838 GAGCTATGAAGTTAAAAAAACAAGGCAATTATACTAAAGAGAATTGAAATAAAATCGAAAAAACA
1 GAGATAGGAAGTT-AAAAAACAAGGCAAATAGACTAAAGAGTATTGAAATAAATTTGAAAAAAAA
* * * ** * * *
2191903 CA-CTAACCCAAAGCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAA-AAACAA
65 AACCTAACCCAGAGCCAAGAA-CACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAC--
2191965 AAATGATTTTCAGCAAA
127 -AATGATTTTCAGCAAA
2191982 TTCTAGCTGG
Statistics
Matches: 488, Mismatches: 63, Indels: 79
0.77 0.10 0.13
Matches are distributed among these distances:
136 3 0.01
137 64 0.13
138 3 0.01
140 1 0.00
141 7 0.01
142 33 0.07
143 1 0.00
144 8 0.02
145 3 0.01
146 60 0.12
147 81 0.17
148 5 0.01
149 32 0.07
150 48 0.10
152 11 0.02
153 6 0.01
154 31 0.06
159 1 0.00
160 11 0.02
161 78 0.16
162 1 0.00
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (145 bp):
GAGATAGGAAGTTAAAAAACAAGGCAAATAGACTAAAGAGTATTGAAATAAATTTGAAAAAAAAA
ACCTAACCCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAACAATG
ATTTTCAGCAAAATC
Found at i:2191942 original size:146 final size:141
Alignment explanation
Indices: 2191613--2191989 Score: 417
Period size: 137 Copynumber: 2.7 Consensus size: 141
2191603 GAAAAGAAAA
* * ** * * *
2191613 AAAAAACAC-CTAACCCAGAGCCAA-AAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAA
1 AAAAAACACACTAACCCAGAGCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAA
* ** * * *
2191676 TAAAACAATGATTTTCAGCGAAA-TCGAACTATAAAAAAAAAGGGGCAATTAGAGTAAAGGGTAT
65 TAAAACAATGATTTTCAGC-AAATTCGAGCTATAAAAAAAAAAAGGCAATTAGACTAAAGAGAAT
* * *
2191740 TGGAATAAATTTG
129 TGAAATAAAATCG
* *
2191753 AAAAAA-A-A--AACCCAGAGCCAAGAATCTCACCCAAGCTCGAATGCTCAAACGAACAACCAAT
1 AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
* *
2191814 AAAGCAATGATTTTCAGCAAATTCGAGCTATGAAGTTAAAAAAACAAGGCAATTATACTAAAGAG
66 AAAACAATGATTTTCAGCAAATTCGAGCTAT-AA---AAAAAAA-AAGGCAATTAGACTAAAGAG
2191879 AATTGAAATAAAATCG
126 AATTGAAATAAAATCG
* *
2191895 AAAAAACACACTAACCCAAAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAA
1 AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
* *
2191960 AACAAAAATGATTTTCAGCAAATTCTAGCT
66 AA-AACAATGATTTTCAGCAAATTCGAGCT
2191990 GGGAATTGAA
Statistics
Matches: 197, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
136 3 0.02
137 65 0.33
138 5 0.03
139 1 0.01
140 6 0.03
141 7 0.04
142 33 0.17
143 1 0.01
144 1 0.01
146 51 0.26
147 24 0.12
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (141 bp):
AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
AAAACAATGATTTTCAGCAAATTCGAGCTATAAAAAAAAAAAGGCAATTAGACTAAAGAGAATTG
AAATAAAATCG
Found at i:2192905 original size:30 final size:30
Alignment explanation
Indices: 2192868--2192939 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
2192858 TGATACGTTG
*
2192868 AACTTTGATTTGGTGT-AATTATACACATGA
1 AACTTTGATTTGGT-TCAAATATACACATGA
* * *
2192898 AATTTTGATTGTGGTTCAAATGTATACATGA
1 AACTTTGATT-TGGTTCAAATATACACATGA
2192929 AACTTTGATTT
1 AACTTTGATTT
2192940 TGATTCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (30 bp):
AACTTTGATTTGGTTCAAATATACACATGA
Found at i:2192929 original size:31 final size:31
Alignment explanation
Indices: 2192892--2192954 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2192882 GTAATTATAC
* *
2192892 ACATGAAATTTTGATTGTGGTTCAAATGTAT
1 ACATGAAACTTTGATTGTGATTCAAATGTAT
* *
2192923 ACATGAAACTTTGATTTTGATTCAATTGTAT
1 ACATGAAACTTTGATTGTGATTCAAATGTAT
2192954 A
1 A
2192955 TATTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (31 bp):
ACATGAAACTTTGATTGTGATTCAAATGTAT
Found at i:2196625 original size:37 final size:39
Alignment explanation
Indices: 2196573--2196661 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 39
2196563 ATTTAACCTG
* * *
2196573 ATTTACTATTTTAAAAAATAATTTTATATATAAT-TAAA-T
1 ATTTA-TATATTAAAAAATAAATATAT-TATAATGTAAATT
*
2196612 ATTTA-ATATTAAAAATTAAATATATTATAATGTAAATT
1 ATTTATATATTAAAAAATAAATATATTATAATGTAAATT
2196650 ATTTATATATTA
1 ATTTATATATTA
2196662 GGATTTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
36 6 0.14
37 20 0.47
38 6 0.14
39 11 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
ATTTATATATTAAAAAATAAATATATTATAATGTAAATT
Found at i:2199024 original size:60 final size:60
Alignment explanation
Indices: 2198949--2199073 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
2198939 TAAATAGTTA
*
2198949 GGTGACCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTCATAG-CTG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTC-G
* * *
2199009 GGTGACCAAAGAAGAAATTTACTAATACTTGAGTGACTATTTTGTAACTTTTCATAGTCG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTCG
2199069 GGTGA
1 GGTGA
2199074 AAAAATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (60 bp):
GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTCG
Found at i:2201472 original size:5 final size:5
Alignment explanation
Indices: 2201459--2201494 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2201449 TTTATTAGTA
* *
2201459 AAAAT AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
2201495 GAGGATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:2203708 original size:28 final size:29
Alignment explanation
Indices: 2203677--2203734 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2203667 AAAGTGATTT
2203677 AAATG-AAATAATTA-GGGCTAAAATGATA
1 AAATGAAAAT-ATTAGGGGCTAAAATGATA
*
2203705 AAATGAAAATATTAGGGGCTAAAATTATA
1 AAATGAAAATATTAGGGGCTAAAATGATA
2203734 A
1 A
2203735 TTAAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.26
Consensus pattern (29 bp):
AAATGAAAATATTAGGGGCTAAAATGATA
Found at i:2206841 original size:2 final size:2
Alignment explanation
Indices: 2206834--2206862 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2206824 AGAGTATAGT
2206834 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2206863 AAAAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2210790 original size:32 final size:29
Alignment explanation
Indices: 2210722--2210792 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2210712 CATATCATTA
* *
2210722 TAAAATAAATATAATTCATGCAAAAAAAATT
1 TAAAA-AAATATAATTCAT-AAAAAAAAAAT
*
2210753 TAAAAATATATAATTCATAAAAAAATAAGAT
1 TAAAAAAATATAATTCATAAAAAAA-AA-AT
2210784 TAAAAAAAT
1 TAAAAAAAT
2210793 TTAAAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 6 0.18
30 14 0.41
31 14 0.41
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (29 bp):
TAAAAAAATATAATTCATAAAAAAAAAAT
Found at i:2213134 original size:235 final size:233
Alignment explanation
Indices: 2212706--2213295 Score: 756
Period size: 235 Copynumber: 2.5 Consensus size: 233
2212696 TTATCAAGAT
* * * * * *
2212706 ATTGAGACTACCCCTTCAAGATTTTGTTGTCCATAGATAACCATGTATTTAGCCTTTATTTATTC
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTA-T-
* * * * *
2212771 CCCCCTATATAATAAAATTGGTCAAATTTCATTGAAAGTACCTCTATTATTTGTTTTTTTTCACA
64 -CCCCTA-ATAATAAAATCGGTCAAATTTCATAGAAAGTCCCTCTATTA--T-TTTTTTTCCAAA
* * * *
2212836 AATTTAGCCTCTCTACTATAATTTAATAATTTCTTAGTTGATTGGAGGGTACCGAATCAAGTTAC
124 AATTTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTAC
*
2212901 AGTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGGTC
189 AGTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
2212946 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATCC
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATCC
*
2213011 CCATAAATAATAAAATCGGTCAAATTTCATAGAAACTCCCTCTATTATTTTTTTTCCAAAAATTT
66 CC-T-AATAATAAAATCGGTCAAATTTCATAGAAAGTCCCTCTATTATTTTTTTTCCAAAAATTT
* * * * *
2213076 AATCTCTCTATTATAATTTGATCATTTCTTGGGTGAGTGGAGAGTACCGAATCAAGTTACAGTTC
129 AACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACAGTTC
* *
2213141 AAGAGAGTGGGATTATATCAACAAAGTTTGACTAATGATC
194 AAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
* * * * * *
2213181 ATTGAGAGTGTCCTTTTCAAGATTTTGCTGCCCAAATATAACCATGAATTTAGCCTTTATTTTTT
1 ATTGAGAATG-CCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATC
** * *
2213246 CCC---T-ATAAAATCAATCAAATTTCATAGAAAGTCTCTTTATTATTTTTTTT
65 CCCTAATAATAAAATCGGTCAAATTTCATAGAAAGTCCCTCTATTATTTTTTTT
2213296 ACGGATTTAA
Statistics
Matches: 312, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
230 41 0.13
231 1 0.00
235 117 0.38
236 53 0.17
237 4 0.01
238 38 0.12
239 2 0.01
240 56 0.18
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (233 bp):
ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATCC
CCTAATAATAAAATCGGTCAAATTTCATAGAAAGTCCCTCTATTATTTTTTTTCCAAAAATTTAA
CCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACAGTTCAA
GAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
Found at i:2221474 original size:29 final size:27
Alignment explanation
Indices: 2221442--2221512 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 27
2221432 TTGGAATTTT
2221442 AAATATAAAAAATAGGACTAAATTCCTGA
1 AAATATAAAAAATAGGACTAAATT-CT-A
2221471 AAATA-AAAGTAAAT-GGACTAAATTCTA
1 AAATATAAA--AAATAGGACTAAATTCTA
*
2221498 AATATATAAAGAATA
1 AA-ATATAAAAAATA
2221513 CATGGACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
27 6 0.17
28 8 0.22
29 18 0.50
30 4 0.11
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (27 bp):
AAATATAAAAAATAGGACTAAATTCTA
Found at i:2221678 original size:36 final size:36
Alignment explanation
Indices: 2221631--2221699 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
2221621 TTATATCTCG
2221631 TAATCTTATATTTTGTACTAAAATTACCTTAATATA
1 TAATCTTATATTTTGTACTAAAATTACCTTAATATA
2221667 TAATCTTATATTTTGTACTAAAATTACCTTAAT
1 TAATCTTATATTTTGTACTAAAATTACCTTAAT
2221700 TGGATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.48
Consensus pattern (36 bp):
TAATCTTATATTTTGTACTAAAATTACCTTAATATA
Found at i:2221871 original size:27 final size:25
Alignment explanation
Indices: 2221833--2221885 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
2221823 TGAATCTGAA
2221833 ATTTTAAATAAATTTACTATTTTTTTT
1 ATTTTAAATAAA-TTA-TATTTTTTTT
* *
2221860 ATTTTAATTAAATTATCTTTTTTTT
1 ATTTTAAATAAATTATATTTTTTTT
2221885 A
1 A
2221886 CCAAAACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTTAAATAAATTATATTTTTTTT
Found at i:2225102 original size:21 final size:21
Alignment explanation
Indices: 2225061--2225103 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2225051 AAAACAATCG
*
2225061 TTGAATTTTGAAACGTTTTAA
1 TTGAATTTTGAAACGTATTAA
*
2225082 TTGAATTTTTTAAA-GTATTAA
1 TTGAA-TTTTGAAACGTATTAA
2225103 T
1 T
2225104 ATCGTCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGAATTTTGAAACGTATTAA
Found at i:2234434 original size:23 final size:24
Alignment explanation
Indices: 2234396--2234444 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2234386 TTTGAATCAG
2234396 TTTTCTTTAATGTTTAATAA-TTAT
1 TTTTCTTTAATGTTT-ATAATTTAT
*
2234420 TTTTCTTT-ATTTTTATAATTTAT
1 TTTTCTTTAATGTTTATAATTTAT
2234443 TT
1 TT
2234445 AATTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 11 0.48
24 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTCTTTAATGTTTATAATTTAT
Found at i:2238020 original size:30 final size:28
Alignment explanation
Indices: 2237973--2238038 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 28
2237963 TTTGGGTCAG
*
2237973 GACTAAAATTTTAAAATTAAAAAGTACAAT
1 GACTAAAATTATAAAATTAAAAA-TAC-AT
*
2238003 GACTAAAATTGAT-AAATTTAAAATACAT
1 GACTAAAATT-ATAAAATTAAAAATACAT
2238031 GAACTAAA
1 G-ACTAAA
2238039 TCCACAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.09
29 9 0.28
30 19 0.59
31 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (28 bp):
GACTAAAATTATAAAATTAAAAATACAT
Found at i:2240942 original size:13 final size:13
Alignment explanation
Indices: 2240920--2240950 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2240910 ACGATTTAAC
*
2240920 GATCAGTATGGTA
1 GATCAATATGGTA
2240933 GATCAATATGGTA
1 GATCAATATGGTA
2240946 GATCA
1 GATCA
2240951 GTACATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (13 bp):
GATCAATATGGTA
Found at i:2241669 original size:21 final size:18
Alignment explanation
Indices: 2241636--2241679 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 18
2241626 TTTCGGTTAT
2241636 CTTTTTTAATTTTTAGTG
1 CTTTTTTAATTTTTAGTG
2241654 ACTTTTTCTGAATTTTTAGTG
1 -CTTTTT-T-AATTTTTAGTG
2241675 CTTTT
1 CTTTT
2241680 AAGTGATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (18 bp):
CTTTTTTAATTTTTAGTG
Found at i:2243951 original size:30 final size:29
Alignment explanation
Indices: 2243882--2243951 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
2243872 GGGTTTGCTT
* * *
2243882 AAAATTTTCAAAAATTTTAGAGACTTAATT
1 AAAATTTT-AAAAATTATAGAGACATAATG
* *
2243912 AGAATTTTTAAAAATTATAGAAGGCATAATG
1 A-AAATTTTAAAAATTATAG-AGACATAATG
2243943 AAAATTTTA
1 AAAATTTTA
2243952 GAATCACATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAATTTTAAAAATTATAGAGACATAATG
Found at i:2260326 original size:6 final size:7
Alignment explanation
Indices: 2260305--2260329 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2260295 ATAAAAAAAT
2260305 AATTAAA
1 AATTAAA
2260312 AATTAAA
1 AATTAAA
2260319 AATTAAA
1 AATTAAA
2260326 AATT
1 AATT
2260330 TTAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:2261086 original size:62 final size:61
Alignment explanation
Indices: 2260964--2261087 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 61
2260954 TAAATTGATA
* * *
2260964 AAAAATAAATAATGTAATCATATTTTAATATAATTATTATTTAATATAATTTAATAAAAAT
1 AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
* * * *
2261025 AAAAATATATAATTTAATAATGTTTTTAATATAAATATT-TTT-ATATTAAATTATATTAAAAT
1 AAAAATAAATAATGTAATAAT-ATTTTAATATAAATATTATTTAATA-TAAATTA-ATAAAAAT
2261087 A
1 A
2261088 TTTTTTAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
60 3 0.06
61 27 0.51
62 23 0.43
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (61 bp):
AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
Found at i:2261088 original size:32 final size:31
Alignment explanation
Indices: 2261059--2261120 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2261049 TTTAATATAA
*
2261059 ATATT-TTTATATTAAATTATATTAAAATAT
1 ATATTATTTATATTAAATTATAGTAAAATAT
* *
2261089 TTTTTAGTTTATATTAAATTATAGTAAAATAT
1 ATATTA-TTTATATTAAATTATAGTAAAATAT
2261121 TTAATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
32 24 0.89
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATATTATTTATATTAAATTATAGTAAAATAT
Found at i:2261092 original size:27 final size:28
Alignment explanation
Indices: 2261057--2261132 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 28
2261047 TTTTTAATAT
*
2261057 AAATA-TT-TTTATATTAAATTATATTA
1 AAATATTTATTTATATTAAATTATAGTA
2261083 AAATATTTTTTAGTTTATATTAAATTATAGTA
1 AAATA---TTTA-TTTATATTAAATTATAGTA
*
2261115 AAATATTTAATATATATT
1 AAATATTT-ATTTATATT
2261133 TTTTTATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
26 5 0.12
29 10 0.24
30 3 0.07
32 23 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AAATATTTATTTATATTAAATTATAGTA
Found at i:2264368 original size:8 final size:9
Alignment explanation
Indices: 2264345--2264371 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2264335 TTTGGCTACC
2264345 TATTTTTAA
1 TATTTTTAA
2264354 TATTTTTAA
1 TATTTTTAA
2264363 TATTTTTAA
1 TATTTTTAA
2264372 AGTCAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:2266796 original size:20 final size:20
Alignment explanation
Indices: 2266772--2266818 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2266762 ATTTAATTTA
*
2266772 ATTGCATTGTGTG-TTGTTT
1 ATTGCATTGGGTGTTTGTTT
2266791 ACTTGC-TTGGGTGTTTGTTT
1 A-TTGCATTGGGTGTTTGTTT
2266811 -TTGCATTG
1 ATTGCATTG
2266819 CGTATGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.55
Consensus pattern (20 bp):
ATTGCATTGGGTGTTTGTTT
Found at i:2269552 original size:31 final size:31
Alignment explanation
Indices: 2269517--2269597 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
2269507 TCGAAGCCTT
2269517 TTAAAATTTTTTAAAATTTTAATTAT-CTCCC
1 TTAAAATTTTTTAAAATTTTAATTATAC-CCC
*
2269548 TT-AAAGTTTTTAAAAGTTTTAATTATACCCC
1 TTAAAATTTTTTAAAA-TTTTAATTATACCCC
* *
2269579 -AAAAATTTTTAAAAATTTT
1 TTAAAATTTTTTAAAATTTT
2269598 GATCAGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 16 0.37
31 26 0.60
32 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (31 bp):
TTAAAATTTTTTAAAATTTTAATTATACCCC
Found at i:2269588 original size:30 final size:30
Alignment explanation
Indices: 2269518--2269597 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
2269508 CGAAGCCTTT
*
2269518 TAAAATTTTTTAAAATTTTAATTATCTCCC
1 TAAAAATTTTTAAAATTTTAATTATCTCCC
* *
2269548 TTAAAGTTTTTAAAAGTTTTAATTATAC-CCC
1 TAAAAATTTTTAAAA-TTTTAATTAT-CTCCC
2269579 -AAAAATTTTTAAAAATTTT
1 TAAAAATTTTT-AAAATTTT
2269598 GATCAGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
30 25 0.58
31 17 0.40
32 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAAATTTTTAAAATTTTAATTATCTCCC
Found at i:2271890 original size:10 final size:11
Alignment explanation
Indices: 2271863--2271897 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2271853 GAAAAAATTT
2271863 TAATTTAAAAA
1 TAATTTAAAAA
2271874 TAATTTAAAAA
1 TAATTTAAAAA
*
2271885 T-TTTTAAAAA
1 TAATTTAAAAA
2271895 TAA
1 TAA
2271898 AGATAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATTTAAAAA
Found at i:2274229 original size:23 final size:23
Alignment explanation
Indices: 2274186--2274243 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
2274176 ATTATTAAAT
*
2274186 TTATTATATTATATAATCTAATA
1 TTATTATATTATATAATCTAACA
2274209 TTATTAGTA-TATATACA-CTAACA
1 TTATTA-TATTATATA-ATCTAACA
*
2274232 TATATTAAATTA
1 T-TATTATATTA
2274244 ACAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTATTATATTATATAATCTAACA
Found at i:2276273 original size:15 final size:17
Alignment explanation
Indices: 2276252--2276292 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
2276242 TAACCCTTTA
2276252 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
2276268 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
2276284 AAAATTATA
1 AAAATTATA
2276293 TTTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:2278093 original size:7 final size:7
Alignment explanation
Indices: 2278081--2278108 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2278071 AATAATCTAA
2278081 GGGCAAG
1 GGGCAAG
2278088 GGGCAAG
1 GGGCAAG
2278095 GGGCAAG
1 GGGCAAG
2278102 GGGCAAG
1 GGGCAAG
2278109 TAAGGGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.57, T:0.00
Consensus pattern (7 bp):
GGGCAAG
Found at i:2284175 original size:18 final size:18
Alignment explanation
Indices: 2284154--2284207 Score: 83
Period size: 18 Copynumber: 3.0 Consensus size: 18
2284144 AGGGATATAT
2284154 AGATATATATATATAATA
1 AGATATATATATATAATA
*
2284172 AGATATAAATATATAATA
1 AGATATATATATATAATA
2284190 AGATGATATATATA-AATA
1 AGAT-ATATATATATAATA
2284208 GTTATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 25 0.76
19 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
AGATATATATATATAATA
Found at i:2285494 original size:23 final size:23
Alignment explanation
Indices: 2285467--2285515 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2285457 TCGGGCTGGT
*
2285467 GTTGGTTTTGGGTATTGGGCTAG
1 GTTGGTTTAGGGTATTGGGCTAG
2285490 GTTGGTTTAGGGTATTGGGCTAG
1 GTTGGTTTAGGGTATTGGGCTAG
2285513 GTT
1 GTT
2285516 AGTTGGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.04, G:0.43, T:0.43
Consensus pattern (23 bp):
GTTGGTTTAGGGTATTGGGCTAG
Found at i:2286160 original size:132 final size:132
Alignment explanation
Indices: 2285922--2286456 Score: 809
Period size: 132 Copynumber: 4.0 Consensus size: 132
2285912 CGCCATCGTC
* * * * * *
2285922 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAGGATCTGCGTCGTCGATCCAC
1 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
* * * * *
2285987 TTCCAATCATTATAGGAAGATAGGACATGTTATCTTTGATCTACTTCACGTCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGAC
2286052 AA
131 AA
* * * *
2286054 GATCTGCTTTCTGCGATCTACTCCGCCATCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
1 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
*
2286119 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGAC
2286184 AA
131 AA
*
2286186 GATCTGCTTTCTGCGATCCACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
*
2286251 TTCCTATCAATATAGGAAGATAAGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGAC
2286316 AA
131 AA
*
2286318 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATATTCGATCCAC
1 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
* * * * ** *
2286383 TTCCTACCAATATAGAAAGATAGGATCTGTTATCTTCGATCTGCTTTGCTGCCAAATACAGGAAG
66 TTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCAC-GCC-AATACATGAAG
*
2286448 GCAA
129 ACAA
2286452 GATCT
1 GATCT
2286457 ACAATCTTTA
Statistics
Matches: 367, Mismatches: 34, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
132 346 0.94
133 3 0.01
134 18 0.05
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (132 bp):
GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
TTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGAC
AA
Found at i:2286379 original size:44 final size:43
Alignment explanation
Indices: 2285922--2286423 Score: 331
Period size: 44 Copynumber: 11.4 Consensus size: 43
2285912 CGCCATCGTC
* * * * *
2285922 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAG
1 GATCTGC-ATCTTCGATCCACTTC-CCACCAATATAGGAAGACAA
* * * * * * *
2285967 GATCTGCGTCGTCGATCCACTTCCAATCATTATAGGAAGATAG
1 GATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * * * ** * *
2286010 GA-CATGTTATCTTTGATCTACTTCACGTCAATACATGAAGACAA
1 GATC-TG-CATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * * * * *
2286054 GATCTGCTTTCTGCGATCTACTCCGCCATCAATATGGGAAGACAA
1 GATCTGC-ATCTTCGATCCACTTC-CCACCAATATAGGAAGACAA
* * * * * *
2286099 GATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAG
1 GATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * * * * *
2286142 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGC-ATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * *
2286186 GATCTGCTTTCTGCGATCCACTTCGCCACCAATATGGGAAGACAA
1 GATCTGC-ATCTTCGATCCACTTC-CCACCAATATAGGAAGACAA
* * *
2286231 GATCTGCATCTTCGATCCACTTCCTATCAATATAGGAAGATAA
1 GATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * * * * * *
2286274 GACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTG-CATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
* * * *
2286318 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGC-ATCTTCGATCCACTTC-CCACCAATATAGGAAGACAA
* * * * *
2286363 GATCTGCATATTCGATCCACTTCCTACCAATATAGAAAGATAG
1 GATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
*
2286406 GATCTGTTATCTTCGATC
1 GATCTG-CATCTTCGATC
2286424 TGCTTTGCTG
Statistics
Matches: 348, Mismatches: 98, Indels: 23
0.74 0.21 0.05
Matches are distributed among these distances:
42 1 0.00
43 82 0.24
44 192 0.55
45 73 0.21
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
GATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAGACAA
Found at i:2286481 original size:46 final size:46
Alignment explanation
Indices: 2286431--2286624 Score: 125
Period size: 46 Copynumber: 4.3 Consensus size: 46
2286421 ATCTGCTTTG
*
2286431 CTGCCAAATACAGGAAGGCAAGATCTACAATCTTTAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCA
* ** * *
2286477 CTGCCAAATACAGGGA-G-ATAGAGT-TATC-GGCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGCA-AGA-TCTA-CAATCTTCAATCTATTCCA
*** * * * * * ** * *
2286522 CTG--TGGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CG
1 CTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCT-ATTCCA
*
2286565 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCA
2286611 CTGCCAAATACAGG
1 CTGCCAAATACAGG
2286625 GAGATAGAAT
Statistics
Matches: 106, Mismatches: 30, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
42 8 0.08
43 15 0.14
44 3 0.03
45 24 0.23
46 56 0.53
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCA
Found at i:2286725 original size:134 final size:134
Alignment explanation
Indices: 2286414--2286735 Score: 547
Period size: 134 Copynumber: 2.4 Consensus size: 134
2286404 AGGATCTGTT
* * *
2286414 ATCTTCGATCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTACAATCTTTAATCTATTCCACT
1 ATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
* *
2286479 GCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATC
66 GCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTGGTCAAGGAGGTAAAATC
2286544 TGCC
131 TGCC
*
2286548 ATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
1 ATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
*
2286613 GCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTTGTCAAGGAGGTAAAATC
66 GCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTGGTCAAGGAGGTAAAATC
2286678 TGCC
131 TGCC
* *
2286682 ATCTTCGATCTGCTTCGCTGCCAAATACAGAAAAGCAAGATCTG-ATATCTTCAA
1 ATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
2286736 CCAGCTCTGC
Statistics
Matches: 177, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
133 1 0.01
134 176 0.99
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (134 bp):
ATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT
GCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTGGTCAAGGAGGTAAAATC
TGCC
Found at i:2286823 original size:86 final size:87
Alignment explanation
Indices: 2286682--2286860 Score: 252
Period size: 86 Copynumber: 2.1 Consensus size: 87
2286672 AAAATCTGCC
* *
2286682 ATCTTCGATCTGCTTCGCTGCCAAATACAGAAAAGCAAGATCTGATATCTTCAACCAGCTCTGCT
1 ATCTTCGATCTACTTCGCTGCCAAATACAGAAAAGCAAGATCTGATAACTTCAACCAGCTCTGCT
2286747 ACAAACGAGAGAGGCAAGGTTT
66 ACAAACGAGAGAGGCAAGGTTT
* * * * * * *
2286769 GTCTTCGATCTACTTCGCTGTC-AGTGCAGGAAGGCAAGATCTGGTAACTTCAACCAGCTCTGCT
1 ATCTTCGATCTACTTCGCTGCCAAATACAGAAAAGCAAGATCTGATAACTTCAACCAGCTCTGCT
* *
2286833 ACGACCGAGAGAGGCAAGGTTT
66 ACAAACGAGAGAGGCAAGGTTT
2286855 ATCTTC
1 ATCTTC
2286861 AATTTTTACT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 61 0.76
87 19 0.24
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (87 bp):
ATCTTCGATCTACTTCGCTGCCAAATACAGAAAAGCAAGATCTGATAACTTCAACCAGCTCTGCT
ACAAACGAGAGAGGCAAGGTTT
Found at i:2291001 original size:19 final size:20
Alignment explanation
Indices: 2290977--2291020 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2290967 CGTGAAAGTC
* *
2290977 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
2290996 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
2291016 -AATGC
1 TAATGC
2291021 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:2293373 original size:18 final size:18
Alignment explanation
Indices: 2293352--2293405 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
2293342 AGGGATATAT
2293352 AGATATATATATATAATA
1 AGATATATATATATAATA
* *
2293370 AGATATAAATATATGATA
1 AGATATATATATATAATA
2293388 AGATGATATATATA-AATA
1 AGAT-ATATATATATAATA
2293406 GTTATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
AGATATATATATATAATA
Found at i:2293412 original size:35 final size:34
Alignment explanation
Indices: 2293352--2293421 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 34
2293342 AGGGATATAT
2293352 AGATATATATATATAATAAGATATAAATATATGATA
1 AGATATATATATATAATAAGATAT-AATA-ATGATA
*
2293388 AGATGATATATATA-AAT-AGTTATAATAATGATA
1 AGAT-ATATATATATAATAAGATATAATAATGATA
2293421 A
1 A
2293422 TAGGACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 7 0.22
34 4 0.12
35 5 0.16
36 7 0.22
37 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (34 bp):
AGATATATATATATAATAAGATATAATAATGATA
Found at i:2294693 original size:23 final size:23
Alignment explanation
Indices: 2294666--2294714 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2294656 TCGGGCTGGT
*
2294666 GTTGGTTTTGGGTATTGGGCTAG
1 GTTGGTTTAGGGTATTGGGCTAG
2294689 GTTGGTTTAGGGTATTGGGCTAG
1 GTTGGTTTAGGGTATTGGGCTAG
2294712 GTT
1 GTT
2294715 AGTTGGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.04, G:0.43, T:0.43
Consensus pattern (23 bp):
GTTGGTTTAGGGTATTGGGCTAG
Found at i:2299186 original size:25 final size:25
Alignment explanation
Indices: 2299159--2299207 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
2299149 AAAAAGTTAC
2299159 AAATTATAAAAAAATGA-AAAAAATCA
1 AAATT-TAAAAAAAT-ATAAAAAATCA
2299185 AAATTTAAAAAAATATAAAAAAT
1 AAATTTAAAAAAATATAAAAAAT
2299208 GTTCATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
AAATTTAAAAAAATATAAAAAATCA
Found at i:2301597 original size:21 final size:20
Alignment explanation
Indices: 2301549--2301593 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2301539 AAAAGTATAG
2301549 AAAAT-TATTAAATATTAAA
1 AAAATATATTAAATATTAAA
* * *
2301568 ATAATATATTTAATTTTAAA
1 AAAATATATTAAATATTAAA
2301588 AAAATA
1 AAAATA
2301594 ATATGGGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATATTAAATATTAAA
Found at i:2302965 original size:31 final size:31
Alignment explanation
Indices: 2302927--2302997 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2302917 TTAATATATT
* *
2302927 ATTTGGTATTTGATTTTGGCTTAAACATTCA
1 ATTTGGTATTTGAGTTTGACTTAAACATTCA
* * *
2302958 ATTTGGTACTTGAGTTTGACTTTAATATTCA
1 ATTTGGTATTTGAGTTTGACTTAAACATTCA
*
2302989 ATTTAGTAT
1 ATTTGGTAT
2302998 CTAAACCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTTGGTATTTGAGTTTGACTTAAACATTCA
Found at i:2311331 original size:41 final size:41
Alignment explanation
Indices: 2311286--2311368 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2311276 ATTTAATACT
2311286 CGGATTATCATTTTCGCTCCATTTTGTCTTTAGAATTACCG
1 CGGATTATCATTTTCGCTCCATTTTGTCTTTAGAATTACCG
*
2311327 CGGATTATCATTTTCGCTCCATTTTGTCTTTAGGATTACCG
1 CGGATTATCATTTTCGCTCCATTTTGTCTTTAGAATTACCG
2311368 C
1 C
2311369 TGTCCAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (41 bp):
CGGATTATCATTTTCGCTCCATTTTGTCTTTAGAATTACCG
Found at i:2312231 original size:23 final size:26
Alignment explanation
Indices: 2312191--2312237 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
2312181 TTTCTTTTTT
2312191 TGATATATTTTCGATT-AAATTTTCA
1 TGATATATTTTCGATTAAAATTTTCA
*
2312216 TGATATA-TTTC-TTTAAAATTTT
1 TGATATATTTTCGATTAAAATTTT
2312238 TAGATGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 11 0.55
25 7 0.35
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (26 bp):
TGATATATTTTCGATTAAAATTTTCA
Found at i:2315090 original size:5 final size:5
Alignment explanation
Indices: 2315080--2315107 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2315070 ACTATTCACC
2315080 CTACA CTACA CTACA CTACA CTACA CTA
1 CTACA CTACA CTACA CTACA CTACA CTA
2315108 AACTCATCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (5 bp):
CTACA
Found at i:2315608 original size:4 final size:4
Alignment explanation
Indices: 2315599--2315654 Score: 67
Period size: 4 Copynumber: 13.2 Consensus size: 4
2315589 GTAAGTACCT
* *
2315599 TACA TACA TACA TACA TACA TACA TACA TATA TACA CACGCA TAACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA--CA T-ACA TACA
2315650 TACA T
1 TACA T
2315655 TCTAATCACC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 39 0.87
5 3 0.07
6 2 0.04
7 1 0.02
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:2316792 original size:3 final size:3
Alignment explanation
Indices: 2316784--2316813 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2316774 ATTTTGTCAC
2316784 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2316814 CATTTGCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2323414 original size:20 final size:20
Alignment explanation
Indices: 2323377--2323415 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2323367 GAATCATATA
*
2323377 TTTATATAATATACAAAAAC
1 TTTATATAATATAAAAAAAC
2323397 TTTATATAAGT-TAAAAAAA
1 TTTATATAA-TATAAAAAAA
2323416 AAATTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
TTTATATAATATAAAAAAAC
Found at i:2335443 original size:29 final size:30
Alignment explanation
Indices: 2335389--2335464 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
2335379 CCTTATACTA
* * *
2335389 TTAATAATATAGGGAGTAAATCGATCCA-T
1 TTAATAATAGAGGGATTAAATCGATCAAGT
* *
2335418 TTAATAATAGAGGGATTAATTTGATCAAGT
1 TTAATAATAGAGGGATTAAATCGATCAAGT
*
2335448 TCTTATAATAGAGGGAT
1 T-TAATAATAGAGGGAT
2335465 CTCACTTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.59
30 2 0.05
31 14 0.36
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
TTAATAATAGAGGGATTAAATCGATCAAGT
Found at i:2337830 original size:313 final size:307
Alignment explanation
Indices: 2337046--2337988 Score: 881
Period size: 313 Copynumber: 3.0 Consensus size: 307
2337036 CAAATTTCTT
* * * * *
2337046 AATTCATAAAATAAGAATCAAGATACATGAATCCATACAAGTATTAGTCATACCGATATCAATTA
1 AATTCATGAAATAAGAA-CAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCA
* * * *
2337111 GGTTCAGTTATTAACACCATTAAAACGTACAAAGAGCACAGGGATTTGGGTATATTTTAATCTTT
65 -GTTCAATTATTAACACCATTAAAACATACAAAGAGCACAGAGATTTGGGTATATTTTAACCTTT
* * * *
2337176 AAACAGGTTTTGTTTTTCTTCCCCAACTTCATTTCTCAAACCTAATACTTTCATCCAAACCATTC
129 AAACA-G-TTT-ATTTTCTTCCTCAACTTAATTTCTCAAATCTAATACTTTCATCC-AA--A-TC
** * * * ** *
2337241 ATTCCAAAAAACGAACAA-AACTTCGAGCTTGAACAAGTGGGTT-GACCCTCGGAAAAGCCTTAA
187 AACCCAAAAAACAAACAATAGCTTCGAGCTTGAACAAGT-CGTTCGA-CC-CAAAAAAGCCCT-A
* * * *
2337304 AGGGGGCAACTTGGATCACCAAGATTGGGTGGTCTAAAAATCTGGTTAAACACTACCACAA
248 A-GGGGCAGCTTGGATCACCATGATTGGGTGGTCTAAAAATATGGTTAAACCCTACCACAA
* *
2337365 ATTTTATGAAATAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCAA
1 AATTCATGAAATAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATC-A
* ** * * * * * *
2337430 GTCCAATCGTTAACATCGTTAAAA-AGTACAAAGAGCACAGCGACTT-CGAACTATTTTAACCTT
65 GTTCAATTATTAACACCATTAAAACA-TACAAAGAGCACAGAGATTTGGGTA-TATTTTAACCTT
** * * * *
2337493 TAAATGGATTGTTGTTGCTTCCTCAACTTTATTTCTCAAATCTAATACTTTCATCCAAATCACCC
128 TAAACAGTTTATT-TT-CTTCCTCAACTTAATTTCTCAAATCTAATACTTTCATCCAAATCAACC
*
2337558 CAAAAGATC-AA-AATGAGTCTTCGAGCTTGAACAAGTCGTTCGACCCAAAACAAGCCCTAAGGG
191 CAAAA-AACAAACAAT-AG-CTTCGAGCTTGAACAAGTCGTTCGACCCAAAA-AAGCCCTAAGGG
* * * *
2337621 AGCAGCTTGGATCACCATGATTGAGTTGTCTAAAAATATTGTTAAACCCTACCCCAA
252 -GCAGCTTGGATCACCATGATTGGGTGGTCTAAAAATATGGTTAAACCCTACCACAA
* * *
2337678 AATTCATGAACA-AA-AACAAGATACAAGAACCCATACAAGTATTAATCACACCAATAACAATCA
1 AATTCATGAA-ATAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCA
*
2337741 GTTCTAATTATTAACACCATTAAAACATACACAAATAGCACAGAGATTTGGGTATATTTTAA-CT
65 GTTC-AATTATTAACACCATTAAAACAT--ACAAAGAGCACAGAGATTTGGGTATATTTTAACCT
* * ** *
2337805 TCTAAACCAGTTTATTTTCTTCCTCATCTCAATTTCT-TGATCCT-ATCACTTTCATCTAAA-CT
127 T-TAAA-CAGTTTATTTTCTTCCTCAACTTAATTTCTCAAAT-CTAAT-ACTTTCATCCAAATC-
* ** * * * *
2337867 AACCCAAAAACCAAACAATAAG--TCGAGCTTGAACAAGTC-ACCCAGCTATGAAAAAACCCTAA
187 AACCCAAAAAACAAACAAT-AGCTTCGAGCTTGAACAAGTCGTTCGACCCA--AAAAAGCCCTAA
*
2337929 GGGGCAGCTTGGATCACCATGATTGGGTGGTCTAAAAACATGGTTAAACCCTACCACAA
249 GGGGCAGCTTGGATCACCATGATTGGGTGGTCTAAAAATATGGTTAAACCCTACCACAA
2337988 A
1 A
2337989 TGCCAATAAT
Statistics
Matches: 516, Mismatches: 81, Indels: 63
0.78 0.12 0.10
Matches are distributed among these distances:
310 56 0.11
311 32 0.06
312 77 0.15
313 118 0.23
314 51 0.10
315 29 0.06
316 6 0.01
317 39 0.08
318 93 0.18
319 15 0.03
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (307 bp):
AATTCATGAAATAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCAG
TTCAATTATTAACACCATTAAAACATACAAAGAGCACAGAGATTTGGGTATATTTTAACCTTTAA
ACAGTTTATTTTCTTCCTCAACTTAATTTCTCAAATCTAATACTTTCATCCAAATCAACCCAAAA
AACAAACAATAGCTTCGAGCTTGAACAAGTCGTTCGACCCAAAAAAGCCCTAAGGGGCAGCTTGG
ATCACCATGATTGGGTGGTCTAAAAATATGGTTAAACCCTACCACAA
Done.