Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 35 of 168
Found at i:9358691 original size:23 final size:23
Alignment explanation
Indices: 9358665--9358709 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9358655 AAGAGATTTG
* *
9358665 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
9358688 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
9358710 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:9358942 original size:19 final size:19
Alignment explanation
Indices: 9358889--9358999 Score: 159
Period size: 19 Copynumber: 5.6 Consensus size: 19
9358879 TACAAATTAA
*
9358889 ATATCTAAGATTACAAAATC
1 ATATCTAAGATTAC-ATATC
*
9358909 ATATCTTCCAAGATTGCATATC
1 ATATC-T--AAGATTACATATC
9358931 ATATCTAAGATTACATATC
1 ATATCTAAGATTACATATC
*
9358950 ATATCTAAGATTGCATATC
1 ATATCTAAGATTACATATC
9358969 ATATCTAAGATTACATATC
1 ATATCTAAGATTACATATC
9358988 ATATCTAAGATT
1 ATATCTAAGATT
9359000 GCATTTCCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
19 60 0.72
20 5 0.06
21 2 0.02
22 9 0.11
23 7 0.08
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATCTAAGATTACATATC
Found at i:9358969 original size:38 final size:38
Alignment explanation
Indices: 9358889--9359003 Score: 185
Period size: 38 Copynumber: 2.9 Consensus size: 38
9358879 TACAAATTAA
*
9358889 ATATCTAAGATTACAAAATCATATCTTCCAAGATTGCATATC
1 ATATCTAAGATTAC-ATATCATATC-T--AAGATTGCATATC
9358931 ATATCTAAGATTACATATCATATCTAAGATTGCATATC
1 ATATCTAAGATTACATATCATATCTAAGATTGCATATC
9358969 ATATCTAAGATTACATATCATATCTAAGATTGCAT
1 ATATCTAAGATTACATATCATATCTAAGATTGCAT
9359004 TTCCTTAAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 48 0.67
40 1 0.01
41 9 0.12
42 14 0.19
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (38 bp):
ATATCTAAGATTACATATCATATCTAAGATTGCATATC
Found at i:9361851 original size:18 final size:20
Alignment explanation
Indices: 9361828--9361868 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
9361818 AGTAAAAAAT
*
9361828 CATGTTTAG-GT-TCATTTG
1 CATGTTTAGTGTCACATTTG
9361846 CATGTTTAGTGTCACATTTG
1 CATGTTTAGTGTCACATTTG
9361866 CAT
1 CAT
9361869 ATATTAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (20 bp):
CATGTTTAGTGTCACATTTG
Found at i:9365257 original size:25 final size:26
Alignment explanation
Indices: 9365210--9365258 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
9365200 GATAGGTTGA
**
9365210 ATATTTTATTATTATTTTATTATAAG
1 ATATTTTATTATTAAATTATTATAAG
*
9365236 ATATTTTA-TATTAAATTGTTATA
1 ATATTTTATTATTAAATTATTATA
9365259 TTTTATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATATTTTATTATTAAATTATTATAAG
Found at i:9366466 original size:16 final size:14
Alignment explanation
Indices: 9366435--9366474 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
9366425 ATTACTATAT
9366435 AATAAAATTATTTA
1 AATAAAATTATTTA
9366449 AATAAAATATATTTTA
1 AATAAAAT-TA-TTTA
*
9366465 AATTAAATTA
1 AATAAAATTA
9366475 AGTAATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAAAATTATTTA
Found at i:9369576 original size:69 final size:67
Alignment explanation
Indices: 9369481--9369614 Score: 182
Period size: 69 Copynumber: 2.0 Consensus size: 67
9369471 TGATTAAACT
*
9369481 TAATCACTTTAATATTAAATTGATAAAATACTTACCAAGATAAA-TATTAGAA-TAAATTTAATA
1 TAATCACTTTAATATTAAATTAATAAAATAC-TACCAAGA-AAATTATTA-AATTAAA-TTAATA
9369544 TTAAGA
62 TTAAGA
* **
9369550 TAATCACTTTAATGTTAAATTAATAAAATACTATTAAGAAAATTATTAAATTAAATTAATATTAA
1 TAATCACTTTAATATTAAATTAATAAAATACTACCAAGAAAATTATTAAATTAAATTAATATTAA
9369615 ATCTATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
67 15 0.25
68 15 0.25
69 29 0.49
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (67 bp):
TAATCACTTTAATATTAAATTAATAAAATACTACCAAGAAAATTATTAAATTAAATTAATATTAA
GA
Found at i:9373705 original size:24 final size:24
Alignment explanation
Indices: 9373673--9373719 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9373663 ACACACATCT
*
9373673 TTCCCATGACCCGAGTTCGCATTG
1 TTCCCATGACCCCAGTTCGCATTG
*
9373697 TTCCCATGACCCCAGTTTGCATT
1 TTCCCATGACCCCAGTTCGCATT
9373720 CTAGTTTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.32
Consensus pattern (24 bp):
TTCCCATGACCCCAGTTCGCATTG
Found at i:9374944 original size:175 final size:175
Alignment explanation
Indices: 9374653--9375004 Score: 659
Period size: 175 Copynumber: 2.0 Consensus size: 175
9374643 AGAGTAAAGA
* *
9374653 ATAGATAATACAAACAACAATAATACACGATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
1 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
9374718 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
66 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
9374783 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
131 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
*
9374828 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCGCGTC
1 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
*
9374893 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGTAAGAG
66 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
*
9374958 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATTTTTTTCC
131 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
9375003 AT
1 AT
9375005 GTTGCATCAA
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 172 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (175 bp):
ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
Found at i:9381809 original size:50 final size:51
Alignment explanation
Indices: 9381734--9381869 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 51
9381724 GTGAAGTTGC
9381734 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAAT-G-A
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-CAGAATAGCA
* * * * * * *
9381784 TAGGTCGCATGTGTAGTACTATGTGCAAGCTACTATGTGTACCGGATAGCT
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACAGAATAGCA
* *
9381835 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
9381870 TGTGAACCGG
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.06
50 38 0.53
51 30 0.42
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (51 bp):
TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACAGAATAGCA
Found at i:9381860 original size:51 final size:50
Alignment explanation
Indices: 9381738--9381879 Score: 169
Period size: 51 Copynumber: 2.8 Consensus size: 50
9381728 AGTTGCTAGG
* * * *
9381738 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
* * * * *
9381788 TCGCATGTGTAGTACTATGTGCAAGCTACTATGTGTACCGG-ATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-ATAGA
*
9381839 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
9381880 GTATCATTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 2 0.03
50 36 0.47
51 39 0.51
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
Found at i:9391160 original size:20 final size:20
Alignment explanation
Indices: 9391131--9391170 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9391121 AAGTGTGACT
*
9391131 GAGTTTGTGTCGAGAGTCAA
1 GAGTTGGTGTCGAGAGTCAA
*
9391151 GAGTTGGTGTTGAGAGTCAA
1 GAGTTGGTGTCGAGAGTCAA
9391171 CTTGACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (20 bp):
GAGTTGGTGTCGAGAGTCAA
Found at i:9399219 original size:15 final size:16
Alignment explanation
Indices: 9399181--9399222 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
9399171 TTTAAAAATA
*
9399181 AAATTAAAATATTAAT
1 AAATTAATATATTAAT
*
9399197 AAACTAATAT-TTAAT
1 AAATTAATATATTAAT
*
9399212 TAATTAATATA
1 AAATTAATATA
9399223 AAATATCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTAATATATTAAT
Found at i:9401206 original size:12 final size:12
Alignment explanation
Indices: 9401188--9401255 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
9401178 GCTCACACGC
9401188 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
9401200 TCGTGTGCTAGG
1 CCGTGTGCTAGG
* *
9401212 CCGTGTGCCAAG
1 CCGTGTGCTAGG
* *
9401224 CCATGTGCCAGG
1 CCGTGTGCTAGG
*
9401236 CTGTGTGCTAGG
1 CCGTGTGCTAGG
9401248 CCGTGTGC
1 CCGTGTGC
9401256 AACCTTTTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.25
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:9402461 original size:39 final size:39
Alignment explanation
Indices: 9402407--9402484 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
9402397 CTCACATATA
9402407 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
1 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
9402446 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
1 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
9402485 GCTCATACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (39 bp):
ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
Found at i:9402522 original size:25 final size:25
Alignment explanation
Indices: 9402481--9402568 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
9402471 TCCTGTACAT
*
9402481 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTATAAATCG
* *
9402506 GTATGCTC-TCACTAGCTATAAATTG
1 GTATGCTCAT-ACGAGCTATAAATCG
* * *
9402531 GTAAGCTCATACAAGCT-GAAATCG
1 GTATGCTCATACGAGCTATAAATCG
* *
9402555 ATAAGCTCATACGA
1 GTATGCTCATACGA
9402569 CATGAAATCA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
24 18 0.35
25 33 0.63
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCG
Found at i:9406509 original size:22 final size:22
Alignment explanation
Indices: 9406475--9406530 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
9406465 CCCCAACTAG
* *
9406475 AAGGGTGCA-GTACCTCTTGAAA
1 AAGGGTG-AGGTACCCCATGAAA
*
9406497 AAGGGTGAGGTACCCCATGAAT
1 AAGGGTGAGGTACCCCATGAAA
9406519 AA-GGTGAGGTAC
1 AAGGGTGAGGTAC
9406531 TTGGGTCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (22 bp):
AAGGGTGAGGTACCCCATGAAA
Found at i:9409163 original size:27 final size:27
Alignment explanation
Indices: 9409125--9409179 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
9409115 GGAGAGTGAA
9409125 TGGCTGAAATTTATTTACTACTTTTAG
1 TGGCTGAAATTTATTTACTACTTTTAG
9409152 TGGCTGAAATTTATTTACTACTTTTAG
1 TGGCTGAAATTTATTTACTACTTTTAG
9409179 T
1 T
9409180 AGCCATTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (27 bp):
TGGCTGAAATTTATTTACTACTTTTAG
Found at i:9409250 original size:2 final size:2
Alignment explanation
Indices: 9409238--9409269 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
9409228 CATTCATTTC
9409238 CA CA CA TCA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA -CA CA CA CA CA CA CA CA CA CA CA CA C
9409270 TCTCTCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:9412879 original size:185 final size:185
Alignment explanation
Indices: 9412567--9412938 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 185
9412557 ATCATCCTAG
9412567 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
1 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
9412632 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
66 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
9412697 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
131 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
*
9412752 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACTATGAGA
1 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
9412817 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
66 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
9412882 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
131 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
9412937 GA
1 GA
9412939 TGAGGACCCA
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 186 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (185 bp):
GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
Found at i:9416077 original size:15 final size:16
Alignment explanation
Indices: 9416057--9416086 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9416047 TAACAAATAA
9416057 TATATAAT-TATATTT
1 TATATAATATATATTT
9416072 TATATAATATATATT
1 TATATAATATATATT
9416087 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:9417866 original size:3 final size:3
Alignment explanation
Indices: 9417858--9417895 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
9417848 TGAGGATCTC
*
9417858 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
9417896 TCCCACAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9418636 original size:160 final size:161
Alignment explanation
Indices: 9418446--9418763 Score: 557
Period size: 161 Copynumber: 2.0 Consensus size: 161
9418436 AGTGTGGCAA
* *
9418446 TAGATATGTACATGCCTAGGATTGGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
1 TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
*
9418511 GACTCAC-TTTTTTTCTAGGGTCCTACCTGGTGTACAGTATCTATTAACTTCTATATTTTCATTC
66 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
*
9418575 TCTCTATTGTTTTTAATATTAGGGGCATGCC
131 TCTCTATTGTTTTTAATAGTAGGGGCATGCC
* * *
9418606 TAGATATGTACATGCCCGGGATTAGATTTGCCTTGGAAAAAGTTTATATTTAAGCTGTCAAACTT
1 TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
*
9418671 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTCACTTCTATATTTTCATTC
66 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
9418736 TCTCTATTGTTTTTAATAGTAGGGGCAT
131 TCTCTATTGTTTTTAATAGTAGGGGCAT
9418764 TGTTCATCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
160 67 0.45
161 82 0.55
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (161 bp):
TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
TCTCTATTGTTTTTAATAGTAGGGGCATGCC
Found at i:9420905 original size:56 final size:50
Alignment explanation
Indices: 9420809--9421052 Score: 167
Period size: 50 Copynumber: 4.8 Consensus size: 50
9420799 ATTTGGGTAA
* * * * *
9420809 AGAGATCCAATGTAAGACCATGTTTGGGACATGGTATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
9420865 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
9420915 AGATGTCCC-TCGTAAGACCATGTCTGGGAGATGGCATGGGCACCGATATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * * * *
9420965 AGA---ACCATGTTAGACCATATTTGGGATATGACATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
9421011 AAACATCCCATGTAAGACCATGTCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
9421053 TGTTATTATC
Statistics
Matches: 155, Mismatches: 27, Indels: 19
0.77 0.13 0.09
Matches are distributed among these distances:
45 1 0.01
46 5 0.03
47 27 0.17
48 1 0.01
49 31 0.20
50 49 0.32
53 3 0.02
55 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:9424268 original size:17 final size:18
Alignment explanation
Indices: 9424235--9424269 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9424225 GCTTGTTTGC
*
9424235 TTAAGTTGAAATGAATGA
1 TTAAGTTGAAATCAATGA
9424253 TTAAGTT-AAATCAATGA
1 TTAAGTTGAAATCAATGA
9424270 CCCTATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (18 bp):
TTAAGTTGAAATCAATGA
Found at i:9427744 original size:17 final size:18
Alignment explanation
Indices: 9427717--9427752 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9427707 AAATTTGAGA
*
9427717 ATTTATTTTGAATTTATT
1 ATTTATTTTGAAATTATT
9427735 ATTT-TTTTGAAATTATT
1 ATTTATTTTGAAATTATT
9427752 A
1 A
9427753 CAAAAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
ATTTATTTTGAAATTATT
Found at i:9430200 original size:50 final size:51
Alignment explanation
Indices: 9430115--9430213 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
9430105 AGCAGGTTGG
* * *
9430115 ACAAGTTAGAATCTATATAGAACTACTCCTCTTCTATTTGATATTGATTGC
1 ACAAGTTAGAATCTATATAGAACTAATCCTCTTCTATTTAAAATTGATTGC
* *
9430166 ACAAG-TAGAA-CTAGTATAGAACTAATCTTTTTCTATTTAAAATTGATT
1 ACAAGTTAGAATCTA-TATAGAACTAATCCTCTTCTATTTAAAATTGATT
9430214 AGAATAAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.07
50 34 0.81
51 5 0.12
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (51 bp):
ACAAGTTAGAATCTATATAGAACTAATCCTCTTCTATTTAAAATTGATTGC
Found at i:9434374 original size:20 final size:20
Alignment explanation
Indices: 9434345--9434393 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
9434335 TGTTTAGGTT
*
9434345 CATTTGCATTTTTAGTGTCA
1 CATTTTCATTTTTAGTGTCA
9434365 CATTTTCATTTTTAGTGTCA
1 CATTTTCATTTTTAGTGTCA
*
9434385 TATTTTCAT
1 CATTTTCAT
9434394 ATATTAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.55
Consensus pattern (20 bp):
CATTTTCATTTTTAGTGTCA
Found at i:9444007 original size:13 final size:13
Alignment explanation
Indices: 9443989--9444013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9443979 GGGTTTTCTA
9443989 TGTGTTCAATTTG
1 TGTGTTCAATTTG
9444002 TGTGTTCAATTT
1 TGTGTTCAATTT
9444014 CTCAATTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (13 bp):
TGTGTTCAATTTG
Found at i:9449871 original size:20 final size:21
Alignment explanation
Indices: 9449841--9449880 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9449831 TCCTCTTTGG
*
9449841 AAGGTGGATATCATGATACCT
1 AAGGTGGATATCACGATACCT
9449862 AAGG-GGATATCACGATACC
1 AAGGTGGATATCACGATACC
9449881 ACTGAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
AAGGTGGATATCACGATACCT
Found at i:9453887 original size:20 final size:18
Alignment explanation
Indices: 9453837--9453888 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
9453827 TCTACAAGTA
9453837 AATATTAAATTAA-ATGT
1 AATATTAAATTAATATGT
*
9453854 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TGT
9453874 AATATTAAATTAATA
1 AATATTAAATTAATA
9453889 AAACACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATGT
Found at i:9453912 original size:24 final size:23
Alignment explanation
Indices: 9453881--9453930 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
9453871 TTTAATATTA
*
9453881 AATTAATA-AAACACTATTAAGAT
1 AATTAATATAAA-ACTATTAAAAT
*
9453904 AATTAAATATTAAACTATTAAAAT
1 AATT-AATATAAAACTATTAAAAT
9453928 AAT
1 AAT
9453931 ATTATTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTAATATAAAACTATTAAAAT
Found at i:9455523 original size:16 final size:16
Alignment explanation
Indices: 9455502--9455532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9455492 CTATGCATGT
*
9455502 AAAATATAAAAGATAA
1 AAAATACAAAAGATAA
9455518 AAAATACAAAAGATA
1 AAAATACAAAAGATA
9455533 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATACAAAAGATAA
Found at i:9464460 original size:23 final size:23
Alignment explanation
Indices: 9464429--9464474 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9464419 GGAGGTGGGC
9464429 TTCGCGCACCCTATAACTATACA
1 TTCGCGCACCCTATAACTATACA
* *
9464452 TTCGGGCACCCTATTACTATACA
1 TTCGCGCACCCTATAACTATACA
9464475 GCAGTTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (23 bp):
TTCGCGCACCCTATAACTATACA
Found at i:9470906 original size:27 final size:26
Alignment explanation
Indices: 9470869--9470933 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
9470859 AGTAGAGTTG
*
9470869 CCAGTACAGT-ATATGTGGCA-AAGCCA
1 CCAGAACAGTAAT-TGTGGCAGAA-CCA
9470895 CCAGCAACAGTAATTGTGGCAGAACCA
1 CCAG-AACAGTAATTGTGGCAGAACCA
9470922 CCAGAAGCAGTA
1 CCAGAA-CAGTA
9470934 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 6 0.18
27 24 0.71
28 4 0.12
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (26 bp):
CCAGAACAGTAATTGTGGCAGAACCA
Found at i:9471107 original size:28 final size:27
Alignment explanation
Indices: 9471063--9471157 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
9471053 TTCCCTAATG
*
9471063 GGGTATTAT-GGTAATTTTACCCATCGG
1 GGGTATT-TCGGTAATTTTACCCATCGA
*
9471090 GGGTATTTCAGGTAATTTTACTCATCGA
1 GGGTATTTC-GGTAATTTTACCCATCGA
*
9471118 GGGTATTTCGATAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCATCGA
*
9471145 GGGTATTGCGGTA
1 GGGTATTTCGGTA
9471158 CAGCTAACGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 34 0.57
28 25 0.42
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCATCGA
Found at i:9481850 original size:26 final size:26
Alignment explanation
Indices: 9481788--9481881 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
9481778 AGTATTGGTG
* **
9481788 GCTTTGCTACATATATTGTTACTGGCA
1 GCTTTGCTGCA-ATATCATTACTGGCA
* * *
9481815 ACTTTACTGCAATACTGA-TACTGGCA
1 GCTTTGCTGCAATA-TCATTACTGGCA
* *
9481841 GCTTCGCTGCGATATCATTACTGGCA
1 GCTTTGCTGCAATATCATTACTGGCA
*
9481867 GCTTTGCTGCGATAT
1 GCTTTGCTGCAATAT
9481882 TGGTGTGTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.04
26 43 0.80
27 9 0.17
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
GCTTTGCTGCAATATCATTACTGGCA
Found at i:9482019 original size:33 final size:33
Alignment explanation
Indices: 9481976--9482040 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
9481966 TTGCATTATT
* *
9481976 GCACTATACTATTACTGTATTGGGCTAAGGCCC
1 GCACTATACTATTACTGAATAGGGCTAAGGCCC
* *
9482009 GCACTGTACTATTACTGAATAGGGCTCAGGCC
1 GCACTATACTATTACTGAATAGGGCTAAGGCC
9482041 TAGATTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (33 bp):
GCACTATACTATTACTGAATAGGGCTAAGGCCC
Found at i:9487864 original size:33 final size:33
Alignment explanation
Indices: 9487807--9487883 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
9487797 TGCATTATTG
* * * *
9487807 CACTATACTATTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
*
9487840 CACTGTACTGTTACTGAATAGGGCTTAGGCCCA
1 CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
*
9487873 GACTGTTACTG
1 CACTG-TACTG
9487884 CATGTTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (33 bp):
CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
Found at i:9488365 original size:13 final size:14
Alignment explanation
Indices: 9488341--9488369 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9488331 ATCTCCTAAA
9488341 AATCTGGAAAACAT
1 AATCTGGAAAACAT
9488355 AATCT-GAAAACAT
1 AATCTGGAAAACAT
9488368 AA
1 AA
9488370 CTTGCACGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (14 bp):
AATCTGGAAAACAT
Found at i:9512007 original size:16 final size:16
Alignment explanation
Indices: 9511988--9512031 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
9511978 ATATATCTTA
9511988 AAAATTATATAAATAT
1 AAAATTATATAAATAT
* *
9512004 AAAATAATA-AAATTT
1 AAAATTATATAAATAT
*
9512019 AAAAATATATAAA
1 AAAATTATATAAA
9512032 ATATTCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:9512014 original size:25 final size:25
Alignment explanation
Indices: 9511986--9512034 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9511976 TTATATATCT
*
9511986 TAAAAATTATATAA-ATATAAAATAA
1 TAAAAATTA-AAAATATATAAAATAA
*
9512011 TAAAATTTAAAAATATATAAAATA
1 TAAAAATTAAAAATATATAAAATA
9512035 TTCATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAATTAAAAATATATAAAATAA
Found at i:9515014 original size:163 final size:162
Alignment explanation
Indices: 9514776--9515069 Score: 421
Period size: 163 Copynumber: 1.8 Consensus size: 162
9514766 TAATCCATAG
* * *
9514776 CAAGATCAACAAAAAAAATCATTGTCGATAAGCACCTCAAGACAAAAACACTGTCGTAAAAAAAG
1 CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACACTGTAGTAAAAAAAC
* **
9514841 ACCGCAAAGAACCTAGCTCACACTCCAAATTTAATCTTCTCTCTTCAGTTTCTACTAAGTCCTTA
66 ACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACT-AGTCCTTA
9514906 TTAAAAGTCTCTTAACATCTGTGTAATCGACAA
130 TTAAAAGTCTCTTAACATCTGTGTAATCGACAA
* * * *
9514939 CAAGATCAACAAAACAAACCATTGTTGATAAGCACCTCAAGAC-AAAGCACCT-TATTAAAAAAA
1 CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACA-CTGTAGTAAAAAAA
** * *
9515002 CCATTGCAAAGAACTTAGCTAACACTCCATATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTT
65 -CACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTT
9515067 ATT
129 ATT
9515070 GTAGTAGGGC
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
162 24 0.21
163 91 0.79
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (162 bp):
CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACACTGTAGTAAAAAAAC
ACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTTAT
TAAAAGTCTCTTAACATCTGTGTAATCGACAA
Found at i:9528585 original size:51 final size:50
Alignment explanation
Indices: 9528461--9528645 Score: 167
Period size: 51 Copynumber: 3.7 Consensus size: 50
9528451 AAAGTGATGG
* * * * * * *
9528461 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAG-ATAGG
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAT-GA
* * *
9528511 TCGCATGTGTAGTACTATGTGCAGACTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * * *
9528562 TCACGTGTATAGTACTATATGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
*
9528613 TCACATGTTTAGTACTATGTGCAGGCTACTATG
1 TCACATGTATAGTACTATGTGCAGGCTACTATG
9528646 TGAACCGGTA
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 39 0.36
51 69 0.63
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:9528722 original size:46 final size:43
Alignment explanation
Indices: 9528649--9528747 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
9528639 TACTATGTGA
*
9528649 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
9528692 ACCGGATATCATTTATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
9528738 ACCGTGTATC
1 ACCG-GTATC
9528748 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 26 0.54
47 4 0.08
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:9528892 original size:16 final size:16
Alignment explanation
Indices: 9528871--9528902 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9528861 TGATTGAAAG
*
9528871 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
9528887 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
9528903 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:9530327 original size:5 final size:5
Alignment explanation
Indices: 9530319--9530351 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
9530309 TTGTTTTCTT
9530319 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
9530352 TATGCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:9531730 original size:75 final size:75
Alignment explanation
Indices: 9531637--9531787 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
9531627 CATGCAAGCC
9531637 TATGGTAATGACTTTTCATGTTTGACTATCGAGTGCTTTGAGTGATTTGAGTGAATCTTTAGTGA
1 TATGGTAATGACTTTTCATGTTTGACTATCGAGTGCTTTGAGTGATTTGAGTGAATCTTTAGTGA
9531702 GGATGTTGAT
66 GGATGTTGAT
9531712 TATGGTAATGACTTTTCATGTTTGACTATCGAGTGCTTTGAGTGATTTGAGTGAATCTTTAGTGA
1 TATGGTAATGACTTTTCATGTTTGACTATCGAGTGCTTTGAGTGATTTGAGTGAATCTTTAGTGA
9531777 GGATGTTGAT
66 GGATGTTGAT
9531787 T
1 T
9531788 CTTGTTGATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (75 bp):
TATGGTAATGACTTTTCATGTTTGACTATCGAGTGCTTTGAGTGATTTGAGTGAATCTTTAGTGA
GGATGTTGAT
Found at i:9540738 original size:33 final size:33
Alignment explanation
Indices: 9540696--9540763 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
9540686 TTCATTTTCG
9540696 ATACGCATTTATTGAAGAGAAGACATGATCGGT
1 ATACGCATTTATTGAAGAGAAGACATGATCGGT
9540729 ATACGCATTTATTGAAGAGAAGACATGATCGGT
1 ATACGCATTTATTGAAGAGAAGACATGATCGGT
9540762 AT
1 AT
9540764 GGTCTTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (33 bp):
ATACGCATTTATTGAAGAGAAGACATGATCGGT
Found at i:9542034 original size:13 final size:13
Alignment explanation
Indices: 9542016--9542042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9542006 ATATTTTTTT
9542016 TAAAAATAATATA
1 TAAAAATAATATA
9542029 TAAAAATAATATA
1 TAAAAATAATATA
9542042 T
1 T
9542043 GTATGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:9544435 original size:34 final size:34
Alignment explanation
Indices: 9544363--9544493 Score: 174
Period size: 34 Copynumber: 3.8 Consensus size: 34
9544353 AATTTTTGGT
*
9544363 TTAGGGTTTAGAGTTTTTTAAAAAAAATTAATTAAA
1 TTAGGGTTTAGAG-TTTTT-AAATAAATTAATTAAA
* * * *
9544399 TTAGGTTTTAGGGGTTTTAAATAAATAAATTAAA
1 TTAGGGTTTAGAGTTTTTAAATAAATTAATTAAA
9544433 TTAGGGTTTAGAGTTTTTAAGA-AAATTAATTAAA
1 TTAGGGTTTAGAGTTTTTAA-ATAAATTAATTAAA
*
9544467 TTAGGGTTTAGAGTTTTTAAATTAATT
1 TTAGGGTTTAGAGTTTTTAAATAAATT
9544494 TTGTTTTTAG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 1 0.01
34 66 0.80
35 5 0.06
36 11 0.13
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (34 bp):
TTAGGGTTTAGAGTTTTTAAATAAATTAATTAAA
Found at i:9544744 original size:125 final size:125
Alignment explanation
Indices: 9544608--9544942 Score: 483
Period size: 125 Copynumber: 2.7 Consensus size: 125
9544598 AAAGATAATT
* ** * *
9544608 TCAAAAACGCTTCATGCAGGATGCTTTGTCAGCAAAATTACTAAAAAAAGCTCCTAAGTGGACAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
*
9544673 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAATTGGTG
66 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
* * * * * *
9544733 TCAAAAACGCTTCAAGCAGCATGCACAGTCAACAAAAATACTGAAAAGAGCTCCCACGTGGACAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
* * *
9544798 TCTTTTTCTATAGTAGTTCCTAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATGGTG
66 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
* *
9544858 TCAAAAATGCTTCAAGCAGGATACACTGTCAGCAAAATTGA-TGAAAAAAAGCTCCCACGTGGAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACT-AAAAAAAGCTCCCACGTGGAC
*
9544922 GCTCTTTTTCTACAGTAGTTC
64 ACTCTTTTTCTACAGTAGTTC
9544943 TTATTTGGCC
Statistics
Matches: 183, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
125 144 0.79
126 39 0.21
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (125 bp):
TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
Found at i:9548436 original size:18 final size:18
Alignment explanation
Indices: 9548413--9548450 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9548403 GAAAAGGGAA
*
9548413 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
9548431 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
9548449 AC
1 AC
9548451 GCACCTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:9557732 original size:6 final size:6
Alignment explanation
Indices: 9557718--9557768 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
9557708 AAAAATTACA
9557718 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TCCTTCTA- TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T--TT-TAT TTTTAT TTTTAT
9557766 TTT
1 TTT
9557769 GCAGGTAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 12 0.29
6 24 0.59
8 3 0.07
9 2 0.05
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:9560544 original size:37 final size:37
Alignment explanation
Indices: 9560502--9560613 Score: 224
Period size: 37 Copynumber: 3.0 Consensus size: 37
9560492 ATTTTAGTGG
9560502 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
9560539 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
9560576 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
9560613 A
1 A
9560614 GCTAGCCGCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (37 bp):
ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
Found at i:9564675 original size:19 final size:21
Alignment explanation
Indices: 9564635--9564675 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9564625 AATTTATGTC
9564635 AAATATTTATATTATTGAATT
1 AAATATTTATATTATTGAATT
*
9564656 AAAT-TTTATATT-TTGTATT
1 AAATATTTATATTATTGAATT
9564675 A
1 A
9564676 GTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
AAATATTTATATTATTGAATT
Found at i:9565171 original size:43 final size:43
Alignment explanation
Indices: 9565108--9565366 Score: 249
Period size: 42 Copynumber: 6.1 Consensus size: 43
9565098 CGCCGCTAAA
* * *
9565108 TTTTCCACATAAACGCCGCTATAGAACATGACCTTTAGCCGCGC
1 TTTTCC-CACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * *
9565152 TTTTCCCACAAACGTCGCTAAAGAACATGTCATTTAGCGGCGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * * * *
9565195 TTTT-CCACAAACCCCACCATAGAGCATGACCTTTAG-GAGCGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCG-GCGC
* *** * * * *
9565237 TTTT-CCACAAGCGCTATTATAGAGCATGACCTTTAGTGGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * *
9565279 TTTTCCCACAAACGCTGCCAAAGAACATGA-CTTTAGCGGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* *
9565321 -TTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCAGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
9565363 TTTT
1 TTTT
9565367 AGTAAAAATG
Statistics
Matches: 180, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
41 28 0.16
42 88 0.49
43 58 0.32
44 6 0.03
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
Found at i:9569051 original size:40 final size:40
Alignment explanation
Indices: 9568988--9569120 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 40
9568978 ATTTGGACAA
*
9568988 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTATAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGC-TTTATAG
** * * * *
9569029 -AAACGCCGCTAAAGGTCGAGCATTAGTGGCGCTTTCTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
* * *
9569068 AAAACGCCGCTAAAAAT-AA-TATTAGCGGCG-TTTTTCG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
9569105 AAAAGCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
9569121 GCCTAAGCCC
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
37 14 0.18
38 15 0.20
39 6 0.08
40 41 0.54
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
Found at i:9569288 original size:40 final size:41
Alignment explanation
Indices: 9569148--9569308 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
9569138 TTCTAAGTTT
*
9569148 TGGGGCCTTTAGCGGCGTTTTAGAAC-AAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTG-ACGAAGCGCCGCTAATGC
* *
9569189 TGGGGCCTTTAGAGGCGTTTTTGAGGAAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
*
9569230 TGGGGCCTTTAGCGGCGTTTTTTACGAAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
* **
9569271 T-CGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAAT
9569309 AATAATAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
40 34 0.31
41 75 0.69
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (41 bp):
TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
Found at i:9569443 original size:21 final size:20
Alignment explanation
Indices: 9569419--9569470 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
9569409 ATTTCGTTGT
*
9569419 ATTTATTATATATGATAACAA
1 ATTTATT-TAAATGATAACAA
9569440 ATTTACATTTAAATGATAACAA
1 ATTT--ATTTAAATGATAACAA
9569462 ATTATATTT
1 ATT-TATTT
9569471 TTTAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTATTTAAATGATAACAA
Found at i:9569997 original size:14 final size:13
Alignment explanation
Indices: 9569946--9570010 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
9569936 TATTAAATAA
9569946 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
*
9569960 GGGTTAGAGGTTAGG
1 GGTTTAG-GGTTA-G
* *
9569975 GGCTGAGGGTTATG
1 GGTTTAGGGTTA-G
9569989 GGTTTAGGGTTCAG
1 GGTTTAGGGTT-AG
9570003 GGTTTAGG
1 GGTTTAGG
9570011 ATTTAAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 34 0.81
15 7 0.17
ACGTcount: A:0.15, C:0.03, G:0.49, T:0.32
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:9570021 original size:15 final size:14
Alignment explanation
Indices: 9569946--9570021 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
9569936 TATTAAATAA
9569946 GGTTTAGGGGTT-AG
1 GGTTTA-GGGTTAAG
* *
9569960 GGGTTAGAGGTTAGG
1 GGTTTAG-GGTTAAG
* * *
9569975 GGCTGAGGGTTATG
1 GGTTTAGGGTTAAG
*
9569989 GGTTTAGGGTTCAG
1 GGTTTAGGGTTAAG
*
9570003 GGTTTAGGATTTAAG
1 GGTTTAGG-GTTAAG
9570018 GGTT
1 GGTT
9570022 AATGGTCGGG
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 1 0.02
14 33 0.69
15 14 0.29
ACGTcount: A:0.17, C:0.03, G:0.46, T:0.34
Consensus pattern (14 bp):
GGTTTAGGGTTAAG
Found at i:9570788 original size:29 final size:30
Alignment explanation
Indices: 9570717--9570788 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
9570707 GCCAATGTCC
* *
9570717 AATTTAAGGTTTAGGGGTTAGGGGTTTAAG
1 AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
* * *
9570747 AATTAAATG-TTAGGGGTTAAGAG-TTAGG
1 AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
9570775 AATTTAAGGTTTAG
1 AATTTAAGGTTTAG
9570789 AGATTTAGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 11 0.32
29 16 0.47
30 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (30 bp):
AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
Found at i:9575324 original size:43 final size:42
Alignment explanation
Indices: 9575234--9575561 Score: 327
Period size: 43 Copynumber: 7.6 Consensus size: 42
9575224 TGTTTTTAGT
* * * * *
9575234 GGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGAA-AAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
9575276 GGCGTTTGTGGTAAAAGCACCGCTAAAGGTCTTCAGCTATAGC
1 GGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
9575319 GGCGTTTGTGGAAAAAGCGTCGCTAAAGATCTTAATCTATAGC
1 GGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
9575362 GGCATTTGTAAGAAAAGCGCCGCTAAAGATCCTGATCTATAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
9575405 GGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
1 GGCGTTTG-TGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * * *
9575448 GGCGTTTGTAGCAAAAGCGCCGTTAAAAGTCATGGTCTTTAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * *
9575491 GGCGTTTGTAGG-AAAGCGCCGCTAAAGCTCATGGTCTTTAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
*
9575533 GGCGTTTGTTGCGGAAAGCGCCGCTAAAG
1 GGCGTTTG-TG-GAAAAGCGCCGCTAAAG
9575562 TTAGCGATGC
Statistics
Matches: 247, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
42 60 0.24
43 170 0.69
44 17 0.07
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (42 bp):
GGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
Found at i:9575499 original size:129 final size:128
Alignment explanation
Indices: 9575268--9575561 Score: 367
Period size: 129 Copynumber: 2.3 Consensus size: 128
9575258 AAAGGTTTGT
* * *
9575268 TCTATAGCGGCGTTTG-TGGTAAAAGCACCGCTAAAGGTCTTCAGCTATAGCGGCGTTTGTGGAA
1 TCTATAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAA
* * *
9575332 AAAGCGTCGCTAAAGATCTTAATCTATAGCGGCATTTGTAAGAAAAGCGCCGCTAAAGATCCTGA
65 AAAGCGCCGCTAAAGATCATAATCTATAGCGGCATTTGT-AGAAAAGCGCCGCTAAAGATCATGA
* * *
9575397 TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTAGCAA
1 TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAAA
* ** * * * * *
9575462 AAGCGCCGTTAAA-AGTCATGGTCTTTAGCGGCGTTTGTAGGAAAGCGCCGCTAAAGCTCATGG
66 AAGCGCCGCTAAAGA-TCATAATCTATAGCGGCATTTGTAGAAAAGCGCCGCTAAAGATCATGA
* *
9575525 TCTTTAGCGGCGTTTGTTGCGGAAAGCGCCGCTAAAG
1 TCTATAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAG
9575562 TTAGCGATGC
Statistics
Matches: 143, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
128 40 0.28
129 100 0.70
130 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (128 bp):
TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAAA
AAGCGCCGCTAAAGATCATAATCTATAGCGGCATTTGTAGAAAAGCGCCGCTAAAGATCATGA
Found at i:9576222 original size:15 final size:16
Alignment explanation
Indices: 9576202--9576235 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9576192 GAAAGATGAG
*
9576202 AAAAAAAT-AACAATA
1 AAAAAAATGAAAAATA
9576217 AAAAAAATGAAAAATA
1 AAAAAAATGAAAAATA
9576233 AAA
1 AAA
9576236 GAAACTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAATGAAAAATA
Found at i:9576730 original size:41 final size:41
Alignment explanation
Indices: 9576650--9576739 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
9576640 TACATATTCC
*
9576650 CGGCGTTTGGACAAAAAATTGCCACTATTGCTCAACTTTTTG
1 CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAAC-TTTTG
* *
9576692 CGGCGTTTGGACCAAAAA-CGCCACTATTGCTCACCTTTTG
1 CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAACTTTTG
*
9576732 CAGCGTTT
1 CGGCGTTT
9576740 TTCTTGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 12 0.27
41 15 0.34
42 17 0.39
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (41 bp):
CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAACTTTTG
Found at i:9582020 original size:33 final size:33
Alignment explanation
Indices: 9581974--9582043 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
9581964 CACAAAGATC
*
9581974 CAAACGTTTATATGCTCATCAAATACATATAAA
1 CAAACGTTCATATGCTCATCAAATACATATAAA
* * * * *
9582007 CAAATGTTCATATGCTTATCCATTACATATAAC
1 CAAACGTTCATATGCTCATCAAATACATATAAA
9582040 CAAA
1 CAAA
9582044 ATCATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (33 bp):
CAAACGTTCATATGCTCATCAAATACATATAAA
Found at i:9582145 original size:41 final size:41
Alignment explanation
Indices: 9582087--9582277 Score: 337
Period size: 41 Copynumber: 4.6 Consensus size: 41
9582077 CTTAATTTAA
* *
9582087 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
9582129 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
9582170 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
9582211 CGGATCACCGGCACTTAGCTTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
9582252 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
9582278 ACGTATAGTC
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 139 0.97
42 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:9588376 original size:16 final size:16
Alignment explanation
Indices: 9588355--9588395 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
9588345 CATAGATAAA
*
9588355 TTTTAAGGTCCAAACT
1 TTTTAAGGACCAAACT
9588371 TTTTAAGGACCAAACT
1 TTTTAAGGACCAAACT
9588387 TTTTAAGGA
1 TTTTAAGGA
9588396 GGGAATGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (16 bp):
TTTTAAGGACCAAACT
Found at i:9590396 original size:21 final size:22
Alignment explanation
Indices: 9590356--9590397 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9590346 GAGCATTTGA
9590356 GATTTTTTTTACTTTCTTATTC
1 GATTTTTTTTACTTTCTTATTC
9590378 GATTCTTTTTTA-TTT-TTATT
1 GATT-TTTTTTACTTTCTTATT
9590398 TTATTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (22 bp):
GATTTTTTTTACTTTCTTATTC
Found at i:9593769 original size:3 final size:3
Alignment explanation
Indices: 9593761--9593794 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9593751 ATTAGTTTAC
9593761 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9593795 TCCAAACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9598749 original size:14 final size:14
Alignment explanation
Indices: 9598731--9598765 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9598721 GTGATGTGAA
*
9598731 AAAAATGAAAAGAT
1 AAAAATGAAAAAAT
*
9598745 GAAAATGAAAAAAT
1 AAAAATGAAAAAAT
9598759 AAAAATG
1 AAAAATG
9598766 GAGAGGCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAAAAT
Found at i:9601009 original size:44 final size:44
Alignment explanation
Indices: 9600075--9601075 Score: 1077
Period size: 44 Copynumber: 22.7 Consensus size: 44
9600065 AGATATTATA
* * * * *
9600075 TTCATGTATTAACATGAAGTAGATCAGAGAAAACATATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
*
9600119 TTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * *
9600163 TTCATGTATTGACATGAAGTAGATCAGAGGTAATGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600207 TTCATGTATTGACATGAAGTAGATCAGAGAAAACAGATATTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600251 TTCATGTATTGACATGAAGTAGATCAGAGAAAACATATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* *
9600295 TTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTGTA
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600339 TTCATGTATTGACATTAAGTAGATCAGAGGTAATGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * * *
9600383 TTCATGTATTGACATGAAGTAGATCAGATAAAACATATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* *
9600427 TTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* *
9600471 TTCATGTATTGACATGAAGTAGATCAAAGATAATGGATATTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600515 TTCATGTATTGACATGAAGTAGATTAGAGTTAATGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600559 TTCATGTATTGACATGAAGTGGATCAGAGAAAACAGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600603 TTCATGTATTGGCGTGAAGTAGATCAAAGA-AAGTGGATCTTATC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* * * *
9600647 TTCATGTATTGGCGTGAAGTAGATCCAAGA-AAGTGGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* * *
9600691 TTCATGTATTGACATGAAGTAGATCAGAGATAACAGATCTTATC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * * *
9600735 TTCATGTATTGGCGTGAAGTAGATCGAAGA-AATCAAATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAAT-AGATCTTGTC
* *
9600779 TTCATGTATT-AGCGTGAAGTAGATCAAAGA-AAGTATATCTTGTC
1 TTCATGTATTGA-CATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* * * * * *
9600823 TTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGGAGGTCTTATC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* * *
9600867 TTCATGTATTGGCATGAAGTAGATCGAAGA-AAGCAGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* * * **
9600911 TTCATGTGTTGGCATGAAGTAGATCGAAGATAGCAGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
* * *
9600955 TTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTC
1 TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
*** **** *
9600999 TTCCCATATTGGGGGCGAAGTAGATCGAAGA-AAGTAGATCTTGTC
1 TTCATGTATT-GACATGAAGTAGATCAAAGATAA-TAGATCTTGTC
* *
9601044 TTCCCATGTATTGGC--GAAATAGATCAAAGATA
1 TT--CATGTATTGACATGAAGTAGATCAAAGATA
9601076 CAAGTCTTAT
Statistics
Matches: 839, Mismatches: 106, Indels: 23
0.87 0.11 0.02
Matches are distributed among these distances:
43 4 0.00
44 794 0.95
45 34 0.04
46 2 0.00
47 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (44 bp):
TTCATGTATTGACATGAAGTAGATCAAAGATAATAGATCTTGTC
Found at i:9602570 original size:3 final size:3
Alignment explanation
Indices: 9602562--9602619 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
9602552 ATTAGTTTAC
9602562 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9602610 TAT TAT TAT T
1 TAT TAT TAT T
9602620 TCCATACACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9626440 original size:45 final size:45
Alignment explanation
Indices: 9626376--9626462 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
9626366 AACAAATACT
*
9626376 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
9626421 CGGTGGAATT-AGCACATAGCAACCACCTTACTAATCAATGAT
1 CGGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGAT
9626463 ATTCAGTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:9626571 original size:51 final size:49
Alignment explanation
Indices: 9626471--9626658 Score: 160
Period size: 51 Copynumber: 3.7 Consensus size: 49
9626461 ATATTCAGTT
* * * * *
9626471 CACATAGTAGCCTGCACATAGTACTACTCATGTGACCATTACCACCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CA-AAACATCCGATA
*
9626522 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CAAAAC-ATCCGATA
** * * * * ** * * *
9626573 TGCATAATAACCTGCACATGGTACTACACACGCGACCCATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACA-TCCGATA
**
9626623 CATTTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
9626659 CATCACTTTC
Statistics
Matches: 108, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.01
50 38 0.35
51 69 0.64
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACATCCGATA
Found at i:9631574 original size:14 final size:16
Alignment explanation
Indices: 9631555--9631586 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
9631545 CTAAAAAGAC
9631555 ATTTAG-AATGA-ACA
1 ATTTAGCAATGATACA
9631569 ATTTAGCAATGATACA
1 ATTTAGCAATGATACA
9631585 AT
1 AT
9631587 AAATATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (16 bp):
ATTTAGCAATGATACA
Found at i:9637816 original size:48 final size:48
Alignment explanation
Indices: 9637745--9637841 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
9637735 AAATTCGTGA
*
9637745 AGCAATAGCACTCACCTTATTAGTGTGGCTTTTGTTTATTTATTTTTC
1 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
9637793 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
1 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
9637841 A
1 A
9637842 TGACATATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (48 bp):
AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
Found at i:9644753 original size:20 final size:18
Alignment explanation
Indices: 9644706--9644813 Score: 60
Period size: 20 Copynumber: 5.8 Consensus size: 18
9644696 CAAGATAAAC
9644706 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
9644723 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
9644743 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
* *
9644762 ATTAAGATAAATATTAAAT
1 ATTAA-ATTAATATTTAAT
* *
9644781 -TTAATTTAATATTAAATCT
1 ATTAAATTAATATTTAA--T
*
9644800 ATTAAAATAATATT
1 ATTAAATTAATATT
9644814 ATTTTTGGAA
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
17 18 0.26
18 5 0.07
19 14 0.20
20 32 0.46
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:9644811 original size:68 final size:71
Alignment explanation
Indices: 9644670--9644814 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
9644660 TATTAAATCT
*
9644670 TATTAAAGTAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAAGTAATAAAATATCTATCTA-AAGATAAACATTAAATTAAATTTAATATTAAGATAATC
***
9644735 ACTTTAA
65 AAAATAA
* * * * *
9644742 TATTAAATTAATAAAATA-CTAT-T-AAGATAAATATTAAATTTAATTTAATATTAA-ATCTATT
1 TATTAAAGTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAAGAT-AATC
9644803 AAAATAA
65 AAAATAA
9644810 TATTA
1 TATTA
9644815 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
67 2 0.03
68 40 0.63
70 1 0.02
71 3 0.05
72 17 0.27
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (71 bp):
TATTAAAGTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAAGATAATCA
AAATAA
Found at i:9648797 original size:22 final size:21
Alignment explanation
Indices: 9648763--9648806 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
9648753 TTCCCATACA
9648763 TCTCTCTCTCTTTCACTTACTT
1 TCTCTCTCTCTTTCACTT-CTT
*
9648785 TCTCTCT-TCCTTTCCCTTCTT
1 TCTCTCTCT-CTTTCACTTCTT
9648806 T
1 T
9648807 GTTTTCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.57
Consensus pattern (21 bp):
TCTCTCTCTCTTTCACTTCTT
Found at i:9651496 original size:2 final size:2
Alignment explanation
Indices: 9651489--9651542 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
9651479 CAAGCTATGC
9651489 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
*
9651531 AT AT AT AC AT AT
1 AT AT AT AT AT AT
9651543 TGTTAAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9652399 original size:27 final size:29
Alignment explanation
Indices: 9652360--9652425 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
9652350 TACTCATGGA
* *
9652360 TTATATATATAATT-TTTAGAATTTA-TT
1 TTATAAATTTAATTATTTAGAATTTATTT
**
9652387 TTATAAATTTAATTATTTTTAATTTATTT
1 TTATAAATTTAATTATTTAGAATTTATTT
9652416 TTATAGAATT
1 TTATA-AATT
9652426 ATTGTTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 12 0.38
28 9 0.28
29 7 0.22
30 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
TTATAAATTTAATTATTTAGAATTTATTT
Found at i:9652785 original size:3 final size:3
Alignment explanation
Indices: 9652777--9652811 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9652767 ATAGTTTACC
9652777 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9652812 AACTACTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9652964 original size:25 final size:25
Alignment explanation
Indices: 9652930--9652982 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
9652920 GAGTGCCTTA
9652930 TCAATCAGTCTGGGAAAGGTTTGAT
1 TCAATCAGTCTGGGAAAGGTTTGAT
9652955 TCAATCAGTCTGGGAAAGGTTTGAT
1 TCAATCAGTCTGGGAAAGGTTTGAT
9652980 TCA
1 TCA
9652983 GAAGATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (25 bp):
TCAATCAGTCTGGGAAAGGTTTGAT
Found at i:9653218 original size:2 final size:2
Alignment explanation
Indices: 9653211--9653236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9653201 CCTTCTTTAT
9653211 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
9653237 AAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9655096 original size:12 final size:12
Alignment explanation
Indices: 9655079--9655103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9655069 ACTTCAGCAA
9655079 TTGGATATAAAG
1 TTGGATATAAAG
9655091 TTGGATATAAAG
1 TTGGATATAAAG
9655103 T
1 T
9655104 CACAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TTGGATATAAAG
Found at i:9675549 original size:22 final size:22
Alignment explanation
Indices: 9675521--9675673 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
9675511 TTTATTGTTC
*
9675521 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
9675543 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
9675565 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
9675587 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
9675609 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
9675631 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
9675653 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
9675674 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:9681948 original size:215 final size:217
Alignment explanation
Indices: 9681558--9681995 Score: 601
Period size: 215 Copynumber: 2.0 Consensus size: 217
9681548 ACGGTCAAAC
* * *
9681558 CTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTATCCTGGATACTCAGTTCAAACAGTCTT
1 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
* * *
9681623 CTTTCTTTTTTTCTTTTTTTTTTTGGAGGCTCGGTTAGCGGAATGTTTGTAAGTTTTCAATTTGT
66 CTTTC-----TTC--TTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGT
* * * *
9681688 CACTTGAACCTTTTTACGCGAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCA
124 CACTCGAACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCA
9681753 GTCACATTTTCGAAACTTTCACTCATAAA
189 GTCACATTTTCGAAACTTTCACTCATAAA
*
9681782 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGTTACTCAATTCAAACAGTCTT
1 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
* *
9681847 CTTTC-TC-TTTTTTTTGGAGGCCCGGTTGGCGAAATGTTTGTAAGTTCTCAATTTTTCACTCGA
66 CTTTCTTCTTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGTCACTCGA
* * * * * * **
9681910 ACCGTTTTACATAAGATGAAATGGCAACCCAAGCACTTCACTCTGGTTACTAAGTTCGGTCATGT
131 ACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCAGTCACAT
*
9681975 TTTTGAAACTTTCACTCATAA
196 TTTCGAAACTTTCACTCATAA
9681996 CTTGAGCCTT
Statistics
Matches: 192, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
215 124 0.65
218 2 0.01
224 66 0.34
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (217 bp):
CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
CTTTCTTCTTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGTCACTCGA
ACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCAGTCACAT
TTTCGAAACTTTCACTCATAAA
Found at i:9682308 original size:22 final size:22
Alignment explanation
Indices: 9682276--9682317 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9682266 GCAGCAAAAA
9682276 TCATGCATATTTACCATTTTTC
1 TCATGCATATTTACCATTTTTC
*
9682298 TCATGCTTATTTACCATTTT
1 TCATGCATATTTACCATTTT
9682318 ACTTACCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.52
Consensus pattern (22 bp):
TCATGCATATTTACCATTTTTC
Found at i:9684054 original size:41 final size:41
Alignment explanation
Indices: 9684038--9684232 Score: 363
Period size: 41 Copynumber: 4.8 Consensus size: 41
9684028 CTTATAGCTT
* *
9684038 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
9684079 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
9684120 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
9684161 GATTCAAATCACCGGCACGTAGCCTACTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
9684202 GATTCAAATCACCGGCACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
9684233 CGCTTAGCCT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 150 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:9689579 original size:12 final size:12
Alignment explanation
Indices: 9689564--9689588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9689554 AATAATTAAA
9689564 TAAATTTGAATT
1 TAAATTTGAATT
9689576 TAAATTTGAATT
1 TAAATTTGAATT
9689588 T
1 T
9689589 TGTAATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAAATTTGAATT
Found at i:9690050 original size:20 final size:20
Alignment explanation
Indices: 9689990--9690055 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
9689980 TCCAGCTCCT
* *
9689990 TTAGCTCGTTTCAGCTCCAA
1 TTAGCTCGTTTAAGCTCAAA
* * ** * *
9690010 TCAGTTCACTTGAGCTTAAA
1 TTAGCTCGTTTAAGCTCAAA
9690030 TTAGCTCGTTTAAGCTCAAA
1 TTAGCTCGTTTAAGCTCAAA
9690050 TTAGCT
1 TTAGCT
9690056 GACTTTCAGC
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
TTAGCTCGTTTAAGCTCAAA
Found at i:9690753 original size:23 final size:21
Alignment explanation
Indices: 9690727--9690778 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
9690717 TAATGATTTT
9690727 TGTGTGAACATGTTAAATAAC
1 TGTGTGAACATGTTAAATAAC
9690748 TGTGTGAACATGTTAAATAAC
1 TGTGTGAACATGTTAAATAAC
*
9690769 TATGTGAACA
1 TGTGTGAACA
9690779 AAATTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGTGAACATGTTAAATAAC
Found at i:9692505 original size:15 final size:15
Alignment explanation
Indices: 9692485--9692531 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
9692475 GTTTAATGGC
9692485 TTAATAATGGCCATG
1 TTAATAATGGCCATG
9692500 TTAATAAT-GCCAAT-
1 TTAATAATGGCC-ATG
* *
9692514 ATGATAATGGCCATG
1 TTAATAATGGCCATG
9692529 TTA
1 TTA
9692532 CGAATAGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (15 bp):
TTAATAATGGCCATG
Found at i:9698947 original size:25 final size:25
Alignment explanation
Indices: 9698898--9699211 Score: 152
Period size: 25 Copynumber: 12.6 Consensus size: 25
9698888 GAATTAATTA
* *
9698898 GAAAGCCTTTGTGTCGTAAT-ATATG
1 GAAAGCCTTTGTGGC-TAATCTTATG
*
9698923 GAAAGCCTTTGTGGTTAATCTTAT-
1 GAAAGCCTTTGTGGCTAATCTTATG
** * * *
9698947 GAAATGTTTTTGTGG-TGTAT-TGTCTA
1 GAAA-GCCTTTGTGGCT-AATCT-TATG
*
9698973 GAAAACCTTTGTGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* * * * * *
9698998 AAAAACATTTATGGCTATTATT-TG
1 GAAAGCCTTTGTGGCTAATCTTATG
*
9699022 GAAAGCCTTTATGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* * *
9699047 AAAAACCTTTGTGGCGT-AT-TATCTG
1 GAAAGCCTTTGTGGC-TAATCT-TATG
* * *
9699072 GAAATCCTTTGTGGATAATTTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* **
9699097 AAAAAACTTTGTGGCATAGTATC-TA--
1 GAAAGCCTTTGTGGC-TA--ATCTTATG
* *
9699122 GAAAGCCTTTGTGGCTAATATTA-A
1 GAAAGCCTTTGTGGCTAATCTTATG
* *
9699146 GAGAAGCTTTTGTGGCGT-AT-TGTCTG
1 GA-AAGCCTTTGTGGC-TAATCT-TATG
9699172 GAAAGCCTTTGTGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
9699197 GAAAG-CTATTGTGGC
1 GAAAGCCT-TTGTGGC
9699212 GTATTGTATG
Statistics
Matches: 220, Mismatches: 45, Indels: 48
0.70 0.14 0.15
Matches are distributed among these distances:
22 2 0.01
23 2 0.01
24 39 0.18
25 159 0.72
26 14 0.06
27 2 0.01
28 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (25 bp):
GAAAGCCTTTGTGGCTAATCTTATG
Found at i:9698982 original size:50 final size:50
Alignment explanation
Indices: 9698905--9699226 Score: 333
Period size: 50 Copynumber: 6.5 Consensus size: 50
9698895 TTAGAAAGCC
* * * * ***
9698905 TTTGTGTCGTAATATATGGAAAGCCTTTGTGGTTAATCTTATGAAATGTT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * * * *
9698955 TTTGTGGTGTATTGTCTAGAAAACCTTTGTGGCTAATCTTATGAAAAACA
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * * *
9699005 TTTATGGC-TATTATTTGGAAAGCCTTTATGGCTAATCTTATGAAAAACC
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
9699054 TTTGTGGCGTATTATCTGGAAATCCTTTGTGGATAATTTTATGAAAAAAC-
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATG-AAAAACT
* * * * * * *
9699104 TTTGTGGCATAGTATCTAGAAAGCCTTTGTGGCTAATATTAAGAGAAGCT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
9699154 TTTGTGGCGTATTGTCTGGAAAGCCTTTGTGGCTAATCTTATGGAAAGCT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
9699204 ATTGTGGCGTATTGTATGGAAAG
1 TTTGTGGCGTATTATCTGGAAAG
9699227 ATTGTTGAAG
Statistics
Matches: 224, Mismatches: 45, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
49 46 0.21
50 172 0.77
51 6 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (50 bp):
TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
Found at i:9699159 original size:100 final size:98
Alignment explanation
Indices: 9698923--9699196 Score: 334
Period size: 99 Copynumber: 2.8 Consensus size: 98
9698913 GTAATATATG
* * * *
9698923 GAAAGCCTTTGTGGTTAATCTTATGAAATGTTTTTGTGGTGTATTGTCTAGAAAACCTTTGTGGC
1 GAAAGCCTTTGTGGCTAATCTTATGAAA-GCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
* * *
9698988 TAATCTTATGAAAAACATTTATGGCTATTATTTG
65 TAATCTTATGAAAAACATTTATGGCTAGTATCTA
* * * * * *
9699022 GAAAGCCTTTATGGCTAATCTTATGAAAAACCTTTGTGGCGTATTATCTGGAAATCCTTTGTGGA
1 GAAAGCCTTTGTGGCTAATCTTATG-AAAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
* *
9699087 TAATTTTATGAAAAA-ACTTTGTGGCATAGTATCTA
65 TAATCTTATGAAAAACA-TTTATGGC-TAGTATCTA
* * *
9699122 GAAAGCCTTTGTGGCTAATATTAAGAGAAGCTTTTGTGGCGTATTGTCTGGAAAGCCTTTGTGGC
1 GAAAGCCTTTGTGGCTAATCTTATGA-AAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
9699187 TAATCTTATG
65 TAATCTTATG
9699197 GAAAGCTATT
Statistics
Matches: 147, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
98 1 0.01
99 73 0.50
100 73 0.50
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (98 bp):
GAAAGCCTTTGTGGCTAATCTTATGAAAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGCT
AATCTTATGAAAAACATTTATGGCTAGTATCTA
Found at i:9699221 original size:25 final size:24
Alignment explanation
Indices: 9699149--9699226 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 24
9699139 ATATTAAGAG
*
9699149 AAGCTTTTGTGGCGTATTGTCTGGA
1 AAGC-TTTGTGGCGTATTGTATGGA
9699174 AAGCCTTTGTGGC-TAATCT-TATGGA
1 AAG-CTTTGTGGCGT-AT-TGTATGGA
9699199 AAGCTATTGTGGCGTATTGTATGGA
1 AAGCT-TTGTGGCGTATTGTATGGA
9699224 AAG
1 AAG
9699227 ATTGTTGAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
24 4 0.09
25 39 0.85
26 3 0.07
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (24 bp):
AAGCTTTGTGGCGTATTGTATGGA
Found at i:9708344 original size:31 final size:31
Alignment explanation
Indices: 9708308--9708386 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
9708298 TGATAGTACA
*
9708308 GTATAAATATGCAAATCTGATAGATTACAAG
1 GTATAAATATGCAAATCTGATAGATCACAAG
* *
9708339 GTATAAATATGCAAATATGATAGATCACATG
1 GTATAAATATGCAAATCTGATAGATCACAAG
*
9708370 GTAT-GATATGCAAATCT
1 GTATAAATATGCAAATCT
9708387 AAATGATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (31 bp):
GTATAAATATGCAAATCTGATAGATCACAAG
Found at i:9710073 original size:20 final size:20
Alignment explanation
Indices: 9710035--9710073 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9710025 GTAAATTAGT
* *
9710035 CGATAACCTTCTCTTTTCCC
1 CGATAACCTTCACTATTCCC
*
9710055 CGATCACCTTCACTATTCC
1 CGATAACCTTCACTATTCC
9710074 TTCTTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.05, T:0.36
Consensus pattern (20 bp):
CGATAACCTTCACTATTCCC
Found at i:9720575 original size:33 final size:33
Alignment explanation
Indices: 9720532--9720597 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
9720522 GGCAACATAA
*
9720532 GATTGTGTAGATCCTATTTCTATCAATGCAGTG
1 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
9720565 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
1 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
9720598 TAAGGCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (33 bp):
GATTGCGTAGATCCTATTTCTATCAATGCAGTG
Found at i:9722036 original size:26 final size:26
Alignment explanation
Indices: 9722006--9722067 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
9721996 TACCTACAGT
9722006 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* * * * *
9722032 AGTTTTAGATTATCATAGCATGTTTC
1 AGTTTCAGAATATCATAACATATATC
9722058 AGTTTCAGAA
1 AGTTTCAGAA
9722068 CACTTACAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:9722821 original size:34 final size:33
Alignment explanation
Indices: 9722777--9722843 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
9722767 GCACAGTTGA
*
9722777 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCC-ATTCAGTAT-AGTG
*
9722812 ACAGT-TTGGGCCTTAGCCCATTCAGTATAGTG
1 ACAGTCTTGGGCCTAAGCCCATTCAGTATAGTG
9722844 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.13
33 8 0.27
34 13 0.43
35 5 0.17
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (33 bp):
ACAGTCTTGGGCCTAAGCCCATTCAGTATAGTG
Found at i:9725574 original size:17 final size:16
Alignment explanation
Indices: 9725552--9725633 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 16
9725542 AAATAAGTTT
9725552 AAGAAAATAAATAATAA
1 AAGAAAATAAA-AATAA
9725569 AAGAAAATAAAGCAACTAA
1 AAGAAAATAAA--AA-TAA
* *
9725588 AACAAAATTAAAAA-GA
1 AAGAAAA-TAAAAATAA
9725604 AAGATAAATAAAAATAA
1 AAGA-AAATAAAAATAA
*
9725621 AAGAAAACAAAAA
1 AAGAAAATAAAAA
9725634 AAATAAATTC
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
16 18 0.33
17 19 0.35
18 4 0.07
19 9 0.17
20 4 0.07
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (16 bp):
AAGAAAATAAAAATAA
Found at i:9725579 original size:10 final size:10
Alignment explanation
Indices: 9725564--9725640 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
9725554 GAAAATAAAT
9725564 AATAAAAGAA
1 AATAAAAGAA
*
9725574 AAT-AAAGCA
1 AATAAAAGAA
* *
9725583 ACTAAAACAA
1 AATAAAAGAA
9725593 AATTAAAAAGAA
1 AA-T-AAAAGAA
9725605 AGATAAATA-AA
1 A-ATAAA-AGAA
9725616 AATAAAAGAA
1 AATAAAAGAA
*
9725626 AACAAAA-AA
1 AATAAAAGAA
9725635 AATAAA
1 AATAAA
9725641 TTCAATGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 15 0.28
10 21 0.40
11 7 0.13
12 9 0.17
13 1 0.02
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.12
Consensus pattern (10 bp):
AATAAAAGAA
Found at i:9725712 original size:26 final size:26
Alignment explanation
Indices: 9725673--9725723 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
9725663 AAGGTAATTG
*
9725673 TAATAATAACAGTA-AAAAATTAAAAA
1 TAATAAAAACAGTAGAAAAA-TAAAAA
*
9725699 TAATAAAAATAGTAGAAAAATAAAA
1 TAATAAAAACAGTAGAAAAATAAAA
9725724 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.22
Consensus pattern (26 bp):
TAATAAAAACAGTAGAAAAATAAAAA
Found at i:9725812 original size:23 final size:22
Alignment explanation
Indices: 9725778--9725821 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
9725768 AAAATTAGGA
*
9725778 AAATAAAAATAAATAATATAAC
1 AAATAAAAATAAATAAAATAAC
9725800 AAATAATAAATAAATAAAATAA
1 AAATAA-AAATAAATAAAATAA
9725822 AAGGGGTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAAAATAAATAAAATAAC
Found at i:9725821 original size:16 final size:15
Alignment explanation
Indices: 9725747--9725813 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
9725737 TAAGTATAAG
9725747 AATAAAAAATAAATA
1 AATAAAAAATAAATA
*
9725762 GAATAAAAAATTAGGA-A
1 -AATAAAAAA-TA-AATA
9725779 AAT-AAAAATAAATA
1 AATAAAAAATAAATA
*
9725793 ATATAACAAAT-AATA
1 A-ATAAAAAATAAATA
9725808 AATAAA
1 AATAAA
9725814 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 1 0.02
14 8 0.19
15 12 0.29
16 17 0.40
17 3 0.07
18 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (15 bp):
AATAAAAAATAAATA
Found at i:9733174 original size:11 final size:11
Alignment explanation
Indices: 9733158--9733187 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
9733148 AATTTTACGT
9733158 ATTACCAATGC
1 ATTACCAATGC
9733169 ATTACCAATGC
1 ATTACCAATGC
9733180 ATTACCAA
1 ATTACCAA
9733188 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (11 bp):
ATTACCAATGC
Found at i:9741365 original size:30 final size:30
Alignment explanation
Indices: 9741331--9741387 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
9741321 CGAGCTTTGA
9741331 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
1 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
* * * *
9741361 GGCAAAATTGTAATTTTGCCAAAGTTT
1 GGCAAAAGTGTAAATATGCAAAAGTTT
9741388 GAGTTAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (30 bp):
GGCAAAAGTGTAAATATGCAAAAGTTTAGG
Found at i:9741760 original size:26 final size:26
Alignment explanation
Indices: 9741723--9741773 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
9741713 ATTGGATAAA
9741723 AAGGGGTCGCTAAGTGCAGATTCCCC
1 AAGGGGTCGCTAAGTGCAGATTCCCC
* *
9741749 AAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGTCGCTAAGTGCAGATTCCC
9741774 AAATTATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (26 bp):
AAGGGGTCGCTAAGTGCAGATTCCCC
Found at i:9741841 original size:43 final size:42
Alignment explanation
Indices: 9741749--9742114 Score: 331
Period size: 43 Copynumber: 8.7 Consensus size: 42
9741739 CAGATTCCCC
** *
9741749 AAGGGGTTGCTAAGTGCTGATT-C-CCAAAT-TATTGATTCTA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATAT-TTGATTGTA
9741789 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
** * * * *
9741833 AAGGGGTTGCTCTGTGCTGATTCC-CCATATCA-CTGAATATA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTA
*
9741874 AAGGTGGTTGCTAAGTGCTGATTACACCGTATATTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * *
9741918 AAGGGGTTGCTATGTGTTGATTCCACCATATATTTGATTGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * * *
9741961 AAGGGGTTGCTATGTGCTGATTCC-CCGTATCA-CTGAATATA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTA
* *
9742002 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * *
9742046 AAGGGGTTGCTATGTGCTGATTCC-CTGTATCA-CTGAATT-T-
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTG-ATTGTA
*
9742086 AAGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGG-GGTTGCTAAGTGCTGATTCCACCG
9742115 AGTAACGGAT
Statistics
Matches: 268, Mismatches: 39, Indels: 36
0.78 0.11 0.10
Matches are distributed among these distances:
40 8 0.03
41 46 0.17
42 67 0.25
43 131 0.49
44 16 0.06
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTA
Found at i:9741979 original size:128 final size:126
Alignment explanation
Indices: 9741749--9742069 Score: 486
Period size: 128 Copynumber: 2.5 Consensus size: 126
9741739 CAGATTCCCC
** * *
9741749 AAGG-GGTTGCTAAGTGCTGATTC-CCAAATTATTGATTCT-AAAGGTGGTTGCTAAGTGCTGAT
1 AAGGTGGTTGCTAAGTGCTGATTCACCGTATT-TTGATTGTGAAAGG-GGTTGCTATGTGCTGAT
* *
9741811 TCCACCGTATATTTGATTGTGAAAGGGGTTGCTCTGTGCTGATTCCCCATATCACTGAATATA
64 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
*
9741874 AAGGTGGTTGCTAAGTGCTGATTACACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGAT
1 AAGGTGGTTGCTAAGTGCTGATT-CACCGTAT-TTTGATTGTGAAAGGGGTTGCTATGTGCTGAT
*
9741939 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATA
64 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
*
9742002 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGAAAGGGGTTGCTATGTGCTGAT
1 AAGGTGGTTGCTAAGTGCTGATT-CACCGTAT-TTTGATTGTGAAAGGGGTTGCTATGTGCTGAT
9742067 TCC
64 TCC
9742070 CTGTATCACT
Statistics
Matches: 179, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
125 4 0.02
126 18 0.10
127 1 0.01
128 150 0.84
129 6 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (126 bp):
AAGGTGGTTGCTAAGTGCTGATTCACCGTATTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTC
CACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
Found at i:9742070 original size:85 final size:86
Alignment explanation
Indices: 9741749--9742113 Score: 344
Period size: 85 Copynumber: 4.3 Consensus size: 86
9741739 CAGATTCCCC
* * *
9741749 AAGGGGTTGCTAAGTGCTGATT-C-CCAAAT-TATTGATTCT-AAAGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATCT-TTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* *
9741810 TTCCACCGTATATTTGATTGTGA
65 TTCC-CCGTATATCTGAATGTGA
** * * *
9741833 AAGGGGTTGCTCTGTGCTGATTCC-CCATATCACTGAA-TAT-AAAGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATC-TTTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* * *
9741895 TTACACCGTATATTTGATTGTGA
65 TT-CCCCGTATATCTGAATGTGA
* * * * *
9741918 AAGGGGTTGCTATGTGTTGATTCCACCATATATTTGATTGTGAAAGG-GGTTGCTATGTGCTGAT
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGAT
*
9741982 TCCCCGTATCA-CTGAATAT-A
66 TCCCCGTAT-ATCTGAATGTGA
* *
9742002 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGAAAGG-GGTTGCTATGTGCTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* *
9742066 TTCCCTGTATCA-CTGAAT-T-T
65 TTCCCCGTAT-ATCTGAATGTGA
*
9742086 AAGGTGGTTGCTAAGTGCTGAATCCACC
1 AAGG-GGTTGCTAAGTGCTGATTCCACC
9742114 GAGTAACGGA
Statistics
Matches: 244, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
84 53 0.22
85 157 0.64
86 29 0.12
87 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (86 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGAT
TCCCCGTATATCTGAATGTGA
Found at i:9750264 original size:3 final size:3
Alignment explanation
Indices: 9750256--9750322 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
9750246 TACTTTACAA
* *
9750256 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9750304 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
9750323 TGGTTGTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:9765659 original size:25 final size:25
Alignment explanation
Indices: 9765622--9765708 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
9765612 AACTCACCAC
9765622 AGCTCGTATGAGCTTACCGATTTAT
1 AGCTCGTATGAGCTTACCGATTTAT
* * * *
9765647 AGCTCGTAGGAGCTTATCTATATT-C
1 AGCTCGTATGAGCTTACCGAT-TTAT
* *
9765672 AGCTCGGAAGAGCTTACCG-TTTAT
1 AGCTCGTATGAGCTTACCGATTTAT
*
9765696 CGCTCGTATGAGC
1 AGCTCGTATGAGC
9765709 CTACATGTAC
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 33 0.69
26 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTTAT
Found at i:9767017 original size:28 final size:29
Alignment explanation
Indices: 9766985--9767042 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
9766975 GTCGTGTGTC
9766985 CCCATTCCGAATG-CCACACGGCCTGAGA
1 CCCATTCCGAATGCCCACACGGCCTGAGA
*
9767013 CCCATTTCGAATGCCCACACGGCCTGAGA
1 CCCATTCCGAATGCCCACACGGCCTGAGA
9767042 C
1 C
9767043 ACGGGCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.24, C:0.40, G:0.21, T:0.16
Consensus pattern (29 bp):
CCCATTCCGAATGCCCACACGGCCTGAGA
Found at i:9767664 original size:13 final size:12
Alignment explanation
Indices: 9767646--9767676 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
9767636 AAGAGTTAAA
9767646 TAAAAATTTAATT
1 TAAAAA-TTAATT
9767659 TAAAAATTAATT
1 TAAAAATTAATT
9767671 TAAAAA
1 TAAAAA
9767677 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAAATTAATT
Done.