Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 19 of 410
Found at i:4919984 original size:60 final size:60
Alignment explanation
Indices: 4919891--4920005 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
4919881 CATTTTGATA
* * *
4919891 CTTGAATTTAGTTTCAATGTTTAAATTAGTACTTAAAGTTT-TCTTTGGTCCAATTAGATG
1 CTTGAACTTAGTTTCAAGGTTCAAATTAGTACTTAAAGTTTAT-TTTGGTCCAATTAGATG
* * *
4919951 CTTGAACTTAGTTTTAAGGTTCAATTTGGTACTTAAAGTTTATTTTGGTCCAATT
1 CTTGAACTTAGTTTCAAGGTTCAAATTAGTACTTAAAGTTTATTTTGGTCCAATT
4920006 TAAGTACCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (60 bp):
CTTGAACTTAGTTTCAAGGTTCAAATTAGTACTTAAAGTTTATTTTGGTCCAATTAGATG
Found at i:4925777 original size:54 final size:54
Alignment explanation
Indices: 4925627--4926004 Score: 230
Period size: 54 Copynumber: 7.0 Consensus size: 54
4925617 AACATCCTAC
* * * * * * *
4925627 GGTTCACTGATTTACAATCGTAACC-TCTCACTTACTACATTTTTAGAATCTTACG
1 GGTTCACTGATTTACGATTGTCACCTTCT-ACTTACAAGATTTTAAGAATCTTA-T
** * * * * * *
4925682 GGTT-GTTGATTTACGA-TGGCGACCTCCTATTTACGATATTTTAAGAATTTTAT
1 GGTTCACTGATTTACGATTGTC-ACCTTCTACTTACAAGATTTTAAGAATCTTAT
* * * * **
4925735 AGTTCACTAATTTACGATTTTCACCTTCTACTTACAAGATTTTAAGAATATTGC
1 GGTTCACTGATTTACGATTGTCACCTTCTACTTACAAGATTTTAAGAATCTTAT
* ** * * *
4925789 GATTCACCCATTTACGATTGTGACCTTTTACTTACAAGATTTCAAGAATCTTAT
1 GGTTCACTGATTTACGATTGTCACCTTCTACTTACAAGATTTTAAGAATCTTAT
* * ** * * * *
4925843 GGTTCGCTGATTTAC-AATCACAACCTTCTATTTACAAGATTTCAA-AGATTTTAC
1 GGTTCACTGATTTACGATTGTC-ACCTTCTACTTACAAGATTTTAAGA-ATCTTAT
*** * * *
4925897 GGTTGGTTGATTTACGATCGTGACCTTCTACTTATAAGATTTTAAGAATCTTAT
1 GGTTCACTGATTTACGATTGTCACCTTCTACTTACAAGATTTTAAGAATCTTAT
* * * * *
4925951 GATTCA-TCGATTTACAATCG-CAACCATCTACTTACAAGATTTTCAGAATCTTAT
1 GGTTCACT-GATTTACGATTGTC-ACCTTCTACTTACAAGATTTTAAGAATCTTAT
4926005 AATTCTTCGA
Statistics
Matches: 244, Mismatches: 69, Indels: 21
0.73 0.21 0.06
Matches are distributed among these distances:
53 8 0.03
54 226 0.93
55 10 0.04
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (54 bp):
GGTTCACTGATTTACGATTGTCACCTTCTACTTACAAGATTTTAAGAATCTTAT
Found at i:4926015 original size:54 final size:53
Alignment explanation
Indices: 4925757--4926099 Score: 198
Period size: 54 Copynumber: 6.4 Consensus size: 53
4925747 TACGATTTTC
* * ** ** * * * **
4925757 ACCTTCTACTTACAAGATTTTAAGAATATTGCGATTCACCCATTTACGATTGTG
1 ACCTTCTACTTACAAGA-TTTCAGAATCTTATGATTCTTCGATTTACAATCGCA
* * * *
4925811 ACCTTTTACTTACAAGATTTCAAGAATCTTATGGTTC-GCTGATTTACAATCACA
1 ACCTTCTACTTACAAGATTTC-AGAATCTTATGATTCTTC-GATTTACAATCGCA
* * * * * * * **
4925865 ACCTTCTATTTACAAGATTTCAAAGATTTTACGGTTGGTT-GATTTACGATCGTG
1 ACCTTCTACTTACAAGATTTCAGA-ATCTTATGATT-CTTCGATTTACAATCGCA
* * *
4925919 ACCTTCTACTTATAAGATTTTAAGAATCTTATGATTCATCGATTTACAATCGCA
1 ACCTTCTACTTACAAGA-TTTCAGAATCTTATGATTCTTCGATTTACAATCGCA
* * * *
4925973 ACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTCGATTTACGATCGCG
1 ACCTTCTACTTACAAGA-TTTCAGAATCTTATGATTCTTCGATTTACAATCGCA
* *
4926027 A-CTTCCTACTTATAAGATCTT-AGAAT-TT-CGCAGTTCATT-GATTT-CAGATCGCA
1 ACCTT-CTACTTACAAGAT-TTCAGAATCTTATG-A-TTC-TTCGATTTACA-ATCGCA
* *
4926080 ACCTTTTACTTACAATATTT
1 ACCTTCTACTTACAAGATTT
4926100 TAAAAATCTC
Statistics
Matches: 223, Mismatches: 52, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
52 6 0.03
53 39 0.17
54 173 0.78
55 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (53 bp):
ACCTTCTACTTACAAGATTTCAGAATCTTATGATTCTTCGATTTACAATCGCA
Found at i:4926017 original size:108 final size:108
Alignment explanation
Indices: 4925757--4926100 Score: 326
Period size: 108 Copynumber: 3.2 Consensus size: 108
4925747 TACGATTTTC
* * ** * * *
4925757 ACCTTCTACTTACAAGATTTTAAGAATATTGCGATTCACCCATTTACGATTGTGACCTTTTACTT
1 ACCTTCTACTTACAAGATTTTCAGAATATTACGATTCTTCGATTTACGATCGTGACCTTCTACTT
* * * * *
4925822 ACAAGATTTCAAGAATCTTATGGTTC-GCTGATTTACAATCACA
66 ATAAGATTTTAAGAATCTTATGATTCATC-GATTTACAATCGCA
* * * * *
4925865 ACCTTCTATTTACAAGA-TTTCAAAGATTTTACGGTTGGTT-GATTTACGATCGTGACCTTCTAC
1 ACCTTCTACTTACAAGATTTTCAGA-ATATTACGATT-CTTCGATTTACGATCGTGACCTTCTAC
4925928 TTATAAGATTTTAAGAATCTTATGATTCATCGATTTACAATCGCA
64 TTATAAGATTTTAAGAATCTTATGATTCATCGATTTACAATCGCA
* * ** *
4925973 ACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTCGATTTACGATCGCGA-CTTCCTACT
1 ACCTTCTACTTACAAGATTTTCAGAATATTACGATTCTTCGATTTACGATCGTGACCTT-CTACT
* * *
4926037 TATAAGATCTT-AGAAT-TT-CGCAGTTCATTGATTT-CAGATCGCA
65 TATAAGATTTTAAGAATCTTATG-A-TTCATCGATTTACA-ATCGCA
* *
4926080 ACCTTTTACTTACAATATTTT
1 ACCTTCTACTTACAAGATTTT
4926101 AAAAATCTCG
Statistics
Matches: 195, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
105 1 0.01
106 5 0.03
107 49 0.25
108 133 0.68
109 7 0.04
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (108 bp):
ACCTTCTACTTACAAGATTTTCAGAATATTACGATTCTTCGATTTACGATCGTGACCTTCTACTT
ATAAGATTTTAAGAATCTTATGATTCATCGATTTACAATCGCA
Found at i:4926481 original size:54 final size:54
Alignment explanation
Indices: 4926173--4926537 Score: 182
Period size: 55 Copynumber: 6.7 Consensus size: 54
4926163 CAATTTGATG
* * * *
4926173 ATTTCATATCGTAATTTTTTAACTTACAAGA-TTTCAAAGTCTTGCGGTTCGTCA
1 ATTTCATATCGCAA-CTTTTAACTTACAAGATTTTCAAAATCTCGCGGTTCGTCA
* * * *** ** *
4926227 ATTTCAGATCACAACTTTTTAA-TTGACAAGATCCTT-AAAATCTCATAGTTCACCG
1 ATTTCATATCGCAAC-TTTTAACTT-ACAAGAT-TTTCAAAATCTCGCGGTTCGTCA
* * * * * * *
4926282 ATTTTATATCACAACCTTTTAAATTACAATATTTTCATAATCTCACGGTTC-ACTA
1 ATTTCATATCGCAA-CTTTTAACTTACAAGATTTTCAAAATCTCGCGGTTCGTC-A
* * * * * ** ** *
4926337 ATTTTAGATCGCGACATTTTAACTTACAATATTTTCAGAATCTCGCAATTCACCG
1 ATTTCATATCGCAAC-TTTTAACTTACAAGATTTTCAAAATCTCGCGGTTCGTCA
* * * * * * *
4926392 ATTTTAAATTGTAAACTTTTAACTTACCAAG-TTTTCATAATCTTGTGGTTCGTCA
1 ATTTCATATCG-CAACTTTTAACTTA-CAAGATTTTCAAAATCTCGCGGTTCGTCA
* * * **
4926447 ATTTCATATCGCAACTTTTAACTTACAAGATTTTCAAAATTTTGGGGTTCGTTG
1 ATTTCATATCGCAACTTTTAACTTACAAGATTTTCAAAATCTCGCGGTTCGTCA
* * * * *
4926501 ATTTCAAATCTCAACTTTTTAATTTATAATATTTTCA
1 ATTTCATATCGCAAC-TTTTAACTTACAAGATTTTCA
4926538 GGGTCTTGCA
Statistics
Matches: 238, Mismatches: 59, Indels: 27
0.73 0.18 0.08
Matches are distributed among these distances:
53 6 0.03
54 72 0.30
55 149 0.63
56 11 0.05
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (54 bp):
ATTTCATATCGCAACTTTTAACTTACAAGATTTTCAAAATCTCGCGGTTCGTCA
Found at i:4928534 original size:13 final size:13
Alignment explanation
Indices: 4928516--4928542 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4928506 ACATGCCTAA
4928516 TAAGATGACGGTG
1 TAAGATGACGGTG
4928529 TAAGATGACGGTG
1 TAAGATGACGGTG
4928542 T
1 T
4928543 GCCATTAGCA
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:0.30, C:0.07, G:0.37, T:0.26
Consensus pattern (13 bp):
TAAGATGACGGTG
Found at i:4931210 original size:24 final size:26
Alignment explanation
Indices: 4931162--4931210 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4931152 GGTTTTAATT
* *
4931162 TTTTAATTTTTTATAAAATTTATTAA
1 TTTTAATTTTATATAAAATTAATTAA
4931188 TTTTAATTTTAT-TAAAA-TAATTA
1 TTTTAATTTTATATAAAATTAATTA
4931211 GTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTAATTTTATATAAAATTAATTAA
Found at i:4933133 original size:2 final size:2
Alignment explanation
Indices: 4933126--4933153 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4933116 AAGTAAACAA
4933126 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
4933154 GCACCTACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4935985 original size:19 final size:22
Alignment explanation
Indices: 4935961--4936005 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
4935951 TTTATATTTT
4935961 ATTATTTT-TAAAT-AAAA-AA
1 ATTATTTTATAAATCAAAATAA
4935980 ATTATTTTATAAATCAAAATAA
1 ATTATTTTATAAATCAAAATAA
4936002 ATTA
1 ATTA
4936006 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 4 0.17
22 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATTTTATAAATCAAAATAA
Found at i:4939100 original size:22 final size:22
Alignment explanation
Indices: 4939059--4939142 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 22
4939049 AAAAAACTGC
* *
4939059 TGCTATT-TTTTAC-TTTTTTT
1 TGCTATTATTTTTCATTATTTT
*
4939079 TGCCATTATTTTTCATTA-TTT
1 TGCTATTATTTTTCATTATTTT
*
4939100 TGCTATCA--TTTCATTATTATAT
1 TGCTATTATTTTTCATTATT-T-T
*
4939122 TGCTATTATTTTATTATTATT
1 TGCTATTATTTT-TCATTATT
4939143 ATTATTTGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 15 0.31
22 10 0.20
24 2 0.04
25 7 0.14
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (22 bp):
TGCTATTATTTTTCATTATTTT
Found at i:4941091 original size:13 final size:13
Alignment explanation
Indices: 4941073--4941097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4941063 TATGTGGAGG
4941073 ATGACATGGCAAC
1 ATGACATGGCAAC
4941086 ATGACATGGCAA
1 ATGACATGGCAA
4941098 ATTTTCAATT
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
ATGACATGGCAAC
Found at i:4942971 original size:15 final size:15
Alignment explanation
Indices: 4942949--4942990 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4942939 TACTCATCAT
4942949 CTATTATGTAATGCCA
1 CTATTATG-AATGCCA
*
4942965 C-ATTATGAATTCCA
1 CTATTATGAATGCCA
*
4942979 CTATTACGAATG
1 CTATTATGAATG
4942991 ATCCTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 14 0.64
16 1 0.05
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (15 bp):
CTATTATGAATGCCA
Found at i:4947822 original size:23 final size:22
Alignment explanation
Indices: 4947774--4947832 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
4947764 GTATTTAAAT
* * *
4947774 TAAATTATAGTTTTTAGAATAG
1 TAAATTATAATTTTTAAAAGAG
*
4947796 TAAAATTATAATTTTTAAAAGAT
1 T-AAATTATAATTTTTAAAAGAG
*
4947819 TAAATTAAAATTTT
1 TAAATTATAATTTT
4947833 ATCATTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
TAAATTATAATTTTTAAAAGAG
Found at i:4947823 original size:22 final size:24
Alignment explanation
Indices: 4947772--4947832 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
4947762 AAGTATTTAA
*
4947772 ATTAAATTATAGTTTTTAGAATAG
1 ATTAAATTATAATTTTTAGAATAG
*
4947796 -TAAAATTATAATTTTTA-AA-AG
1 ATTAAATTATAATTTTTAGAATAG
*
4947817 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
4947833 ATCATTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
ATTAAATTATAATTTTTAGAATAG
Found at i:4957629 original size:22 final size:24
Alignment explanation
Indices: 4957603--4957679 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
4957593 ACTTTACAAT
*
4957603 TATTTTTAT-TTAATTTAATTATA
1 TATTTTTATAATAATTTAATTATA
*
4957626 -ATTTTTATAATATTTTAATTATA
1 TATTTTTATAATAATTTAATTATA
* * *
4957649 TATTTTTTATAAGATTTTATAATATA
1 TA-TTTTTATAATAATTTA-ATTATA
4957675 TATTT
1 TATTT
4957680 CATTTAACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.17
23 12 0.26
24 1 0.02
25 18 0.39
26 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (24 bp):
TATTTTTATAATAATTTAATTATA
Found at i:4957642 original size:23 final size:25
Alignment explanation
Indices: 4957616--4957679 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
4957606 TTTTATTTAA
*
4957616 TTTAATTATA-A-TTTTTATAATAT
1 TTTAATTATATATTTTTTATAAGAT
4957639 TTTAATTATATATTTTTTATAAGAT
1 TTTAATTATATATTTTTTATAAGAT
*
4957664 TTTATAATATATATTT
1 TTTA-ATTATATATTT
4957680 CATTTAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 10 0.28
24 1 0.03
25 15 0.42
26 10 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTAATTATATATTTTTTATAAGAT
Found at i:4957691 original size:26 final size:25
Alignment explanation
Indices: 4957616--4957692 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
4957606 TTTTATTTAA
* *
4957616 TTTAATTATA-ATTT-TTATAATAT
1 TTTAAATATATATTTATTATAACAT
* * *
4957639 TTTAATTATATATTTTTTATAAGAT
1 TTTAAATATATATTTATTATAACAT
4957664 TTTATAATATATATTTCATT-TAACAT
1 TTTA-AATATATATTT-ATTATAACAT
4957690 TTT
1 TTT
4957693 GAAGTTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 10 0.22
24 4 0.09
25 12 0.26
26 18 0.39
27 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (25 bp):
TTTAAATATATATTTATTATAACAT
Found at i:4959351 original size:31 final size:32
Alignment explanation
Indices: 4959293--4959357 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
4959283 AATTTATATT
**
4959293 TTATGTATTATTATATTAAGTTATTT-AAATA
1 TTATGTATTATTATATTAAACTATTTAAAATA
*
4959324 TTATTTATTATTATATTTAAACT-TTTAAAATA
1 TTATGTATTATTATA-TTAAACTATTTAAAATA
4959356 TT
1 TT
4959358 TCATGTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (32 bp):
TTATGTATTATTATATTAAACTATTTAAAATA
Found at i:4959467 original size:61 final size:63
Alignment explanation
Indices: 4959287--4959467 Score: 147
Period size: 61 Copynumber: 2.9 Consensus size: 63
4959277 TAGATTAATT
* * * * * **
4959287 TATATTTTATGTATTATTATA-TTAAGTTATTTAAATATTATTTATTATTATATTTAAACTTTTA
1 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTA-AATTA-ATTTAAAC-AATA
4959351 A
63 A
* * * * * * * *
4959352 AATATTTCATGTGTAATTAAATTTATAAATAATTTATTAATT-TTAAAAGT-ATTTAAA-AAT-A
1 TATATTTTATGTGTAATTATATTTA-AATTAATTAAAT-ATTATTTAAATTAATTTAAACAATAA
4959413 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTA
1 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTA
4959468 TTTTTAATTT
Statistics
Matches: 88, Mismatches: 23, Indels: 14
0.70 0.18 0.11
Matches are distributed among these distances:
59 3 0.03
60 15 0.17
61 28 0.32
62 1 0.01
64 7 0.08
65 16 0.18
66 5 0.06
67 10 0.11
68 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (63 bp):
TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTAAACAATAA
Found at i:4979304 original size:17 final size:17
Alignment explanation
Indices: 4979282--4979315 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4979272 CACATACATC
*
4979282 ATCTTCATGTAAATTAA
1 ATCTTCATGCAAATTAA
4979299 ATCTTCATGCAAATTAA
1 ATCTTCATGCAAATTAA
4979316 CATACTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
ATCTTCATGCAAATTAA
Found at i:4982632 original size:2 final size:2
Alignment explanation
Indices: 4982625--4982653 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4982615 GCTAGGAGTA
4982625 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4982654 TATATATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4989784 original size:13 final size:14
Alignment explanation
Indices: 4989766--4989796 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4989756 ATCTTTTTTA
4989766 TTTAAATTTAT-TT
1 TTTAAATTTATATT
4989779 TTTAAATTTATATT
1 TTTAAATTTATATT
4989793 TTTA
1 TTTA
4989797 TTTAAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTAAATTTATATT
Found at i:4990817 original size:25 final size:25
Alignment explanation
Indices: 4990789--4990841 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4990779 GACATGTGAC
*
4990789 AAACAGAAATTA-ATAAAATTAATAA
1 AAACAGAAAATATAT-AAATTAATAA
**
4990814 AAACTTAAAATATATAAATTAATAA
1 AAACAGAAAATATATAAATTAATAA
4990839 AAA
1 AAA
4990842 AAGTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (25 bp):
AAACAGAAAATATATAAATTAATAA
Found at i:4992545 original size:23 final size:25
Alignment explanation
Indices: 4992519--4992565 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
4992509 TATCATTCAT
*
4992519 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
4992542 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
4992566 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:4992886 original size:46 final size:46
Alignment explanation
Indices: 4992826--4993091 Score: 316
Period size: 46 Copynumber: 6.0 Consensus size: 46
4992816 TTTGATGTGA
* * * * * *
4992826 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
4992872 TGCCATGGTATCTTTCAACCCTGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
4992918 TGCCATGGTATCTTTCAACTATGGTCTTACACATCTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4992964 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
4993010 TGTCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4993048 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
4993092 AGAGCACACT
Statistics
Matches: 190, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
38 32 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 144 0.76
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:4993056 original size:38 final size:38
Alignment explanation
Indices: 4993005--4993080 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4992995 CATTTCATAT
*
4993005 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
4993043 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
4993081 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:4995228 original size:11 final size:11
Alignment explanation
Indices: 4995212--4995259 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
4995202 CTTTATATAC
4995212 TAATAAAATAA
1 TAATAAAATAA
4995223 TAATAAAATATA
1 TAATAAAATA-A
* * *
4995235 TTATTAAAGTAT
1 -TAATAAAATAA
4995247 TAATAAAATAA
1 TAATAAAATAA
4995258 TA
1 TA
4995260 TTTATCTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
11 20 0.69
12 1 0.03
13 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:4995242 original size:24 final size:24
Alignment explanation
Indices: 4995206--4995261 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
4995196 TTCTTTCTTT
*
4995206 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* * *
4995230 ATATATTATTAAAGTATTAATAAA
1 ATATATTAATAAAATAATAATAAA
4995254 ATAATATT
1 AT-ATATT
4995262 TATCTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:4996824 original size:2 final size:2
Alignment explanation
Indices: 4996819--4996846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4996809 AGATATATGC
4996819 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
4996847 TTGTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5003816 original size:3 final size:3
Alignment explanation
Indices: 5003808--5003832 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5003798 AGTCCAAAAA
5003808 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
5003833 TTTCACACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5007257 original size:3 final size:3
Alignment explanation
Indices: 5007186--5007241 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
5007176 TCATGCCATC
*
5007186 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5007234 ATT ATT AT
1 ATT ATT AT
5007242 CCTAATGAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5007495 original size:18 final size:18
Alignment explanation
Indices: 5007448--5007498 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
5007438 TTAAAAATTA
*
5007448 TAAATATCAAAAAAT-AT
1 TAAATATAAAAAAATAAT
* *
5007465 CAAA-ACAATAAAAATAAT
1 TAAATATAA-AAAAATAAT
5007483 TAAATATAAAAAAATA
1 TAAATATAAAAAAATA
5007499 TGAATATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 12 0.46
19 3 0.12
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAATATAAAAAAATAAT
Found at i:5007579 original size:20 final size:17
Alignment explanation
Indices: 5007517--5007570 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5007507 GATTTAAAGT
5007517 TATAAATATT-ATAAAAA
1 TATAAA-ATTAATAAAAA
*
5007534 TA-AAATTCTAATAAAAA
1 TATAAAAT-TAATAAAAA
5007551 TATAAAATTAAT-AAAA
1 TATAAAATTAATAAAAA
5007567 TATA
1 TATA
5007571 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.38
17 15 0.47
18 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAATTAATAAAAA
Found at i:5007587 original size:21 final size:22
Alignment explanation
Indices: 5007548--5007609 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
5007538 ATTCTAATAA
*
5007548 AAATA-TAAAA-TTAATAAAAT
1 AAATATTAAAATTTTATAAAAT
*
5007568 ATAT-TTAAAATTTTATAAAA-
1 AAATATTAAAATTTTATAAAAT
**
5007588 AAATATTAAAATCCTATAAAAT
1 AAATATTAAAATTTTATAAAAT
5007610 CATAAAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATTAAAATTTTATAAAAT
Found at i:5008193 original size:12 final size:12
Alignment explanation
Indices: 5008176--5008208 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5008166 CTGCCTGCCG
5008176 ATATTAATTTTT
1 ATATTAATTTTT
5008188 ATATT-ATTTTT
1 ATATTAATTTTT
5008199 ATA-TAATTTT
1 ATATTAATTTT
5008209 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:5008801 original size:10 final size:9
Alignment explanation
Indices: 5008696--5008812 Score: 52
Period size: 9 Copynumber: 13.1 Consensus size: 9
5008686 TTATGTTTTT
5008696 TTTTTATAA
1 TTTTTATAA
5008705 TTTTTATAA
1 TTTTTATAA
* *
5008714 GTTATATCAA
1 TTTTTAT-AA
**
5008724 TTTAAATATA
1 TTTTTATA-A
5008734 TTTTT-T-A
1 TTTTTATAA
5008741 TTTTTA-AGA
1 TTTTTATA-A
* *
5008750 CTTCTAATACA
1 -TTTTTATA-A
5008761 TTTTT-TAA
1 TTTTTATAA
*
5008769 GTTTTACTAA
1 TTTTTA-TAA
5008779 -TTTTAT--
1 TTTTTATAA
5008785 TTTTTATAA
1 TTTTTATAA
5008794 TTTATTAT-A
1 TTT-TTATAA
5008803 TTTTTATAA
1 TTTTTATAA
5008812 T
1 T
5008813 ATTACAAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
7 12 0.15
8 10 0.12
9 33 0.40
10 25 0.30
11 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5017156 original size:69 final size:69
Alignment explanation
Indices: 5017045--5017183 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
5017035 GATAGGAAAA
*
5017045 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
5017110 GCTG
66 GCTG
5017114 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
5017179 GCTG
66 GCTG
5017183 A
1 A
5017184 TAGAGTCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:5023408 original size:3 final size:3
Alignment explanation
Indices: 5023400--5023455 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5023390 TATCAAAATG
5023400 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5023448 AAT AAT AA
1 AAT AAT AA
5023456 ATTAGCTGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5024621 original size:7 final size:7
Alignment explanation
Indices: 5024609--5024638 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5024599 CATATACCCC
5024609 ATTATCA
1 ATTATCA
5024616 ATTATCA
1 ATTATCA
5024623 ATTATCA
1 ATTATCA
5024630 ATTATCA
1 ATTATCA
5024637 AT
1 AT
5024639 ACAACTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTATCA
Found at i:5032988 original size:28 final size:26
Alignment explanation
Indices: 5032946--5033022 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 26
5032936 ATTTGTCTAA
5032946 ATTTTATTTCATTATTATTTATT-AATAT
1 ATTTTATTT--TTATTATTTATTCAAT-T
*
5032974 TTTTTATCATTTTATTATTATATTGCAATT
1 ATTTTAT--TTTTATTATT-TATT-CAATT
5033004 ATTTTATTTTTATTATTTA
1 ATTTTATTTTTATTATTTA
5033023 AATATTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.05
28 24 0.57
29 4 0.10
30 9 0.21
31 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (26 bp):
ATTTTATTTTTATTATTTATTCAATT
Found at i:5033511 original size:3 final size:3
Alignment explanation
Indices: 5033505--5033582 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
5033495 GAATAATATG
* *
5033505 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT T-T CTCT TCT TAT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT
* *
5033550 TCT TCT TCT TTT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5033583 GCTTATCTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 1 0.02
3 63 0.97
4 1 0.02
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:5033531 original size:21 final size:21
Alignment explanation
Indices: 5033505--5033580 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
5033495 GAATAATATG
5033505 TCTTCTTCTTCTTTTTCTTCT
1 TCTTCTTCTTCTTTTTCTTCT
*
5033526 TCTTCTTCTTCTTTCTCTTCT
1 TCTTCTTCTTCTTTTTCTTCT
*
5033547 TATTCTTCTTCTTTTTCTTCT
1 TCTTCTTCTTCTTTTTCTTCT
*
5033568 TTTTCTTCTTCTT
1 TCTTCTTCTTCTT
5033581 CTGCTTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTCTTCTTCTTTTTCTTCT
Found at i:5034716 original size:13 final size:12
Alignment explanation
Indices: 5034692--5034725 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5034682 TGTTTAATTA
5034692 TATTAAGATAAT
1 TATTAAGATAAT
5034704 TATTAAGGATAAT
1 TATTAA-GATAAT
*
5034717 TATTTAGAT
1 TATTAAGAT
5034726 TTAAATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (12 bp):
TATTAAGATAAT
Found at i:5034752 original size:10 final size:10
Alignment explanation
Indices: 5034737--5034788 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
5034727 TAAATTTAGG
5034737 ATTTATTTTT
1 ATTTATTTTT
*
5034747 ATTTATCTTT
1 ATTTATTTTT
* *
5034757 AATTATCTTT
1 ATTTATTTTT
*
5034767 ATTTATTTGT
1 ATTTATTTTT
5034777 ATTTATCTTTT
1 ATTTAT-TTTT
5034788 A
1 A
5034789 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:5035533 original size:13 final size:13
Alignment explanation
Indices: 5035517--5035542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5035507 TTCCATTTTA
5035517 ATTTTTGCAATTT
1 ATTTTTGCAATTT
5035530 ATTTTTGCAATTT
1 ATTTTTGCAATTT
5035543 CAATTCAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTTTTGCAATTT
Found at i:5038813 original size:39 final size:39
Alignment explanation
Indices: 5038752--5038838 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
5038742 GACTTAATGT
5038752 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
* * *
5038791 CTAGTAGGCCTCGTGCCGGTGATAAGTTCAGGTTTATAC
1 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
5038830 CTAGCAGGC
1 CTAGCAGGC
5038839 TAATTGCCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (39 bp):
CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
Found at i:5038847 original size:39 final size:39
Alignment explanation
Indices: 5038752--5038851 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 39
5038742 GACTTAATGT
* *
5038752 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
* * *
5038791 CTAGTAGGCCTCGTGCCGGTGATAAGTTCAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
*
5038830 CTAGCAGG-CTAATTGCCGGTGA
1 CTAGCAGGCCT-AGTGCCGGTGA
5038852 AATAATAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 2 0.04
39 52 0.96
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (39 bp):
CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
Found at i:5041909 original size:29 final size:29
Alignment explanation
Indices: 5041841--5041933 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
5041831 TAACCCAATT
* *
5041841 TTTATTTTATTTTTATTTATTTTGTTTATTAT
1 TTTATTTTA-TTTTA-TT-TTTTATTTATTAA
* * *
5041873 TTTCTTTTGTTTTCTTTTTTATTTATTAA
1 TTTATTTTATTTTATTTTTTATTTATTAA
* * *
5041902 TTTATTTTATTTTATTATTTATTAATTTA
1 TTTATTTTATTTTATTTTTTATTTATTAA
5041931 TTT
1 TTT
5041934 GGATATTAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 37 0.74
30 2 0.04
31 4 0.08
32 7 0.14
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (29 bp):
TTTATTTTATTTTATTTTTTATTTATTAA
Found at i:5041919 original size:25 final size:22
Alignment explanation
Indices: 5041838--5041933 Score: 81
Period size: 22 Copynumber: 4.2 Consensus size: 22
5041828 AGGTAACCCA
*
5041838 ATTTTTATT-TTATTTTTATTT
1 ATTTTTTTTATTATTTTTATTT
*
5041859 ATTTTGTTTATTATTTTCT-TTT
1 ATTTTTTTTATTATTTT-TATTT
*
5041881 GTTTTCTTTT-TTATTTATTAATTT
1 ATTTT-TTTTATTATTT-TT-ATTT
5041905 ATTTTATTTTATTATTTATTAATTT
1 ATTTT-TTTTATTATTT-TT-ATTT
5041930 ATTT
1 ATTT
5041934 GGATATTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.11
22 21 0.34
23 5 0.08
24 11 0.18
25 18 0.29
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
ATTTTTTTTATTATTTTTATTT
Found at i:5046567 original size:20 final size:19
Alignment explanation
Indices: 5046544--5046586 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5046534 AAACCCAAAG
* *
5046544 GAAACAAAACGGGAAAGAAA
1 GAAACAAAAAGAGAAAG-AA
*
5046564 GAAAGAAAAAGAGAAAGAA
1 GAAACAAAAAGAGAAAGAA
5046583 GAAA
1 GAAA
5046587 GAAAGCCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (19 bp):
GAAACAAAAAGAGAAAGAA
Found at i:5047552 original size:41 final size:39
Alignment explanation
Indices: 5047466--5047588 Score: 142
Period size: 41 Copynumber: 3.1 Consensus size: 39
5047456 CTTCGAGTCG
* * * *
5047466 ATGAGGCACTGAGTGCTAATTTACT-TTGG-TTTAATCA
1 ATGAGACACTGGGTGTTAATTTACTATTGGATTTATTCA
*
5047503 ATGAGACACTGGGTGTTAATTTACTACTTCGGATTTATTCG
1 ATGAGACACTGGGTGTTAATTTACTA-TT-GGATTTATTCA
* *
5047544 ATGAGACACTGGGTGTCAATTTACTAGTTGGAATTATTCA
1 ATGAGACACTGGGTGTTAATTTACTA-TTGGATTTATTCA
5047584 ATGAG
1 ATGAG
5047589 GTATCGGGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
37 22 0.30
39 2 0.03
40 16 0.22
41 33 0.45
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (39 bp):
ATGAGACACTGGGTGTTAATTTACTATTGGATTTATTCA
Found at i:5047810 original size:16 final size:15
Alignment explanation
Indices: 5047789--5047841 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
5047779 ATTATATACT
5047789 TATGAATTGAGTATGG
1 TATGAATTGAGTAT-G
*
5047805 TATGAAATGATGTAT-
1 TATGAATTGA-GTATG
5047820 TCATGAATTGAGTATTG
1 T-ATGAATTGAGTA-TG
5047837 TATGA
1 TATGA
5047842 CTGATGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 4 0.13
16 22 0.71
17 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.40
Consensus pattern (15 bp):
TATGAATTGAGTATG
Found at i:5052827 original size:23 final size:21
Alignment explanation
Indices: 5052797--5052840 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5052787 TATTTCAACA
*
5052797 ATTATTTATATATTTATCATTTT
1 ATTATTTA-A-ATTTATAATTTT
5052820 ATTATTTAAATTTATAATTTT
1 ATTATTTAAATTTATAATTTT
5052841 CAGTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 1 0.05
23 8 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTAAATTTATAATTTT
Found at i:5058032 original size:28 final size:28
Alignment explanation
Indices: 5057987--5058040 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5057977 CAAATGCCTA
*
5057987 TTTTTGTAATTATTTTATTTTCTATACC
1 TTTTTGTAATTATATTATTTTCTATACC
*
5058015 TTTTTCGTAATTA-ATTATTTTTTATA
1 TTTTT-GTAATTATATTATTTTCTATA
5058041 TTATTTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTTGTAATTATATTATTTTCTATACC
Found at i:5058036 original size:29 final size:27
Alignment explanation
Indices: 5057987--5058040 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
5057977 CAAATGCCTA
*
5057987 TTTTTGTAATTATTTTATTTTCTATACC
1 TTTTTGTAATTATTATATTTT-TATACC
5058015 TTTTTCGTAATTAATTAT-TTTTTATA
1 TTTTT-GTAATT-ATTATATTTTTATA
5058041 TTATTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.39
29 10 0.43
30 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTGTAATTATTATATTTTTATACC
Found at i:5062009 original size:24 final size:24
Alignment explanation
Indices: 5061914--5062013 Score: 96
Period size: 24 Copynumber: 4.1 Consensus size: 24
5061904 AAACTTTGTC
* **
5061914 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCA-ATATCGGGAAGCTCATAA
* * * *
5061939 GAGTCAATATCAGGAAGTTCA-AGC
1 GAGCCAATATCGGGAAGCTCATA-A
5061963 GAGCCAATATCGGGAAGCTCATAA
1 GAGCCAATATCGGGAAGCTCATAA
5061987 GAGCC-ATATTCGGGAAGCTCATAA
1 GAGCCAATA-TCGGGAAGCTCATAA
5062011 GAG
1 GAG
5062014 TTGCAGTGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
23 3 0.05
24 53 0.85
25 6 0.10
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCATAA
Found at i:5064578 original size:7 final size:7
Alignment explanation
Indices: 5064562--5064593 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5064552 CAAACTCATA
*
5064562 CAAAGAT
1 CAAAGCT
5064569 CAAAGCT
1 CAAAGCT
5064576 CAAAGCT
1 CAAAGCT
5064583 CAAAGCT
1 CAAAGCT
5064590 CAAA
1 CAAA
5064594 TTTTGAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (7 bp):
CAAAGCT
Found at i:5065917 original size:20 final size:19
Alignment explanation
Indices: 5065894--5065936 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
5065884 TTTCAGTGTA
5065894 ATTAA-ATTTATAAATAATAT
1 ATTAATATTTA-AAAT-ATAT
5065914 ATTAATTATTTAAAATATAT
1 ATTAA-TATTTAAAATATAT
5065934 ATT
1 ATT
5065937 TTATGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATATTTAAAATATAT
Found at i:5065940 original size:18 final size:19
Alignment explanation
Indices: 5065899--5065954 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
5065889 GTGTAATTAA
5065899 ATTTATAAATAATATATTAATT
1 ATTTA-AAAT-ATATATT-ATT
5065921 ATTTAAAATATATATT-TT
1 ATTTAAAATATATATTATT
* *
5065939 ATGTATAAT-TATATTA
1 ATTTAAAATATATATTA
5065955 AGCTATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 6 0.19
18 9 0.29
20 7 0.23
21 4 0.13
22 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTAAAATATATATTATT
Found at i:5077215 original size:18 final size:18
Alignment explanation
Indices: 5077163--5077215 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
5077153 ATCAACAAAT
* * *
5077163 AATTTTAAATATGTAGAA
1 AATTTAAAATATATATAA
5077181 ATATTTAAAA-ATA-ATAA
1 A-ATTTAAAATATATATAA
5077198 AATTTAAAATATATATAA
1 AATTTAAAATATATATAA
5077216 TGTATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.28
17 7 0.24
18 7 0.24
19 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AATTTAAAATATATATAA
Found at i:5078784 original size:46 final size:44
Alignment explanation
Indices: 5078725--5078839 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
5078715 ACAGGACAGA
* *
5078725 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
5078771 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
5078815 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
5078840 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:5078820 original size:44 final size:45
Alignment explanation
Indices: 5078725--5078858 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
5078715 ACAGGACAGA
* *
5078725 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
5078771 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
5078815 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5078859 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:5084506 original size:44 final size:45
Alignment explanation
Indices: 5084411--5084544 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 45
5084401 ACAGGACAGA
* * *
5084411 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
5084457 ACAGGATTAAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
5084501 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5084545 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 37 0.50
45 1 0.01
46 36 0.49
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:5086783 original size:21 final size:20
Alignment explanation
Indices: 5086757--5086795 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5086747 GATATTGTTA
5086757 TTTTTTAATAAATTTTTTGAT
1 TTTTTTAAT-AATTTTTTGAT
5086778 TTTTTTAATAATTTTTTG
1 TTTTTTAATAATTTTTTG
5086796 TTATGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTTAATAATTTTTTGAT
Found at i:5087677 original size:46 final size:45
Alignment explanation
Indices: 5087617--5087882 Score: 339
Period size: 46 Copynumber: 6.0 Consensus size: 45
5087607 TTTGACATGA
* * * * * *
5087617 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
5087663 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
5087709 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
5087755 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
5087801 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
5087839 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
5087883 AGAGCACACT
Statistics
Matches: 197, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 149 0.76
47 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:5087846 original size:38 final size:38
Alignment explanation
Indices: 5087795--5087870 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5087785 ACATTTTATA
5087795 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
5087833 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
5087871 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:5090033 original size:11 final size:11
Alignment explanation
Indices: 5090017--5090068 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5090007 TATACTAAAT
5090017 AAATAATAATA
1 AAATAATAATA
*
5090028 AAATAAT-ATT
1 AAATAATAATA
* *
5090038 AAATATCTCATA
1 AAATA-ATAATA
*
5090050 AAATATTAATA
1 AAATAATAATA
5090061 AAATAATA
1 AAATAATA
5090069 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:5093371 original size:15 final size:16
Alignment explanation
Indices: 5093335--5093371 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5093325 CCATGTTAAC
5093335 TTAATAAAAACAAGAT
1 TTAATAAAAACAAGAT
*
5093351 TTAATAACAACAAGA-
1 TTAATAAAAACAAGAT
5093366 TTAATA
1 TTAATA
5093372 TGATTCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (16 bp):
TTAATAAAAACAAGAT
Found at i:5094516 original size:4 final size:4
Alignment explanation
Indices: 5094507--5094532 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5094497 TTAATTTCTT
5094507 CAAA CAAA CAAA CAAA CAAA CAAA CA
1 CAAA CAAA CAAA CAAA CAAA CAAA CA
5094533 TCCAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:5095229 original size:14 final size:13
Alignment explanation
Indices: 5095210--5095246 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
5095200 GGAGAAGTAG
5095210 AAAAGAATGGAAAA
1 AAAAGAA-GGAAAA
5095224 AAAAGAA--AAAA
1 AAAAGAAGGAAAA
5095235 AAAAGAAGGAAA
1 AAAAGAAGGAAA
5095247 GTTGAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.52
13 3 0.14
14 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAAGAAGGAAAA
Found at i:5095947 original size:26 final size:24
Alignment explanation
Indices: 5095917--5095966 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5095907 AAATAAAAAA
*
5095917 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
5095943 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
5095967 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:5101960 original size:17 final size:16
Alignment explanation
Indices: 5101929--5101976 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
5101919 ATCTTTCTAG
*
5101929 ATATTTTTTAAAATATA
1 ATATTTTATAAAATA-A
*
5101946 ATATTTTATACAATAA
1 ATATTTTATAAAATAA
5101962 A-ATTTTA-AAAATAA
1 ATATTTTATAAAATAA
5101976 A
1 A
5101977 AAAATTTAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 2 0.07
17 13 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTTTATAAAATAA
Found at i:5102110 original size:37 final size:38
Alignment explanation
Indices: 5102045--5102118 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 38
5102035 TGAAGTTGTC
5102045 ATGTGTCAATTCAACCTTTTTTTTTAATATAAAGTGTT
1 ATGTGTCAATTCAACCTTTTTTTTTAATATAAAGTGTT
5102083 ATGTGTCAATTCAA-CTTTTTTTTTAATATAAAGTGT
1 ATGTGTCAATTCAACCTTTTTTTTTAATATAAAGTGT
5102119 GACACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (38 bp):
ATGTGTCAATTCAACCTTTTTTTTTAATATAAAGTGTT
Found at i:5112620 original size:66 final size:66
Alignment explanation
Indices: 5112514--5112667 Score: 202
Period size: 66 Copynumber: 2.3 Consensus size: 66
5112504 TAAGAACTTG
* * * * *
5112514 AGAAGACTCGATATCTTGTTCAGGAGCTTGGGAAGACTCAATA-TGCCGATCAAGATCTTGGGAT
1 AGAAGACTTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTG-CGATCAAGAGCTTAGGAT
5112578 TA
65 TA
* * *
5112580 AGAAGACTTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGTTTAGGAGCTTAGGATT
1 AGAAGACTTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGATCAAGAGCTTAGGATT
5112645 A
66 A
* *
5112646 AGAAGACCTGATATCTCATTCA
1 AGAAGACTTGATATCTCGTTCA
5112668 AAAGTTTGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 75 0.97
67 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (66 bp):
AGAAGACTTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGATCAAGAGCTTAGGATT
A
Found at i:5119408 original size:5 final size:5
Alignment explanation
Indices: 5119394--5119440 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
5119384 TAACACATAT
* * *
5119394 ATTCA TTTCA ATTCA ATTCA ATTCA A-TCA ACTTTA AATCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA A-TTCA ATTCA ATTCA AT
5119441 AATCAAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:5127333 original size:18 final size:18
Alignment explanation
Indices: 5127299--5127424 Score: 94
Period size: 18 Copynumber: 7.1 Consensus size: 18
5127289 TCATTAACTC
* *
5127299 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAGTTAT
*
5127316 TCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAGTTAT
* **
5127334 TCGGTAACAATCAAATAT
1 TCAGTAACAATCAGTTAT
* *
5127352 TCAGTAATAACCAGTTAT
1 TCAGTAACAATCAGTTAT
* * *
5127370 TCAATAACAGTCTA-ATAT
1 TCAGTAACAATC-AGTTAT
* * *
5127388 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
*
5127406 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAGTTAT
5127424 T
1 T
5127425 TATTATCTTT
Statistics
Matches: 82, Mismatches: 24, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
17 5 0.06
18 76 0.93
19 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (18 bp):
TCAGTAACAATCAGTTAT
Found at i:5127353 original size:36 final size:36
Alignment explanation
Indices: 5127313--5127418 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 36
5127303 AACAATTATT
*
5127313 TATTCAGTAACAGTCAGTTATTCGGTAACAATCAAA
1 TATTCAGTAACAGTCAGTTATTCAGTAACAATCAAA
* ** * * *
5127349 TATTCAGTAATAACCAGTTATTCAATAACAGTCTAA
1 TATTCAGTAACAGTCAGTTATTCAGTAACAATCAAA
* * *
5127385 TATCCAGTAACAGTCAATTATTCAGTAATAATCA
1 TATTCAGTAACAGTCAGTTATTCAGTAACAATCA
5127419 GTTATTTATT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (36 bp):
TATTCAGTAACAGTCAGTTATTCAGTAACAATCAAA
Found at i:5127624 original size:23 final size:23
Alignment explanation
Indices: 5127542--5127628 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
5127532 CCTGATCAGT
*
5127542 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
5127564 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
5127584 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
5127607 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
5127629 TCAATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:5128006 original size:15 final size:15
Alignment explanation
Indices: 5127981--5128021 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
5127971 TCATATATAT
5127981 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
5127997 TATAAATTCAATCAA
1 TATAAATTCAATCAA
*
5128012 AATAAATTCA
1 TATAAATTCA
5128022 TTATATCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:5128707 original size:5 final size:5
Alignment explanation
Indices: 5128690--5128733 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
5128680 TTACTTATTT
5128690 ATATA ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
5128734 TATTTTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:5132837 original size:30 final size:30
Alignment explanation
Indices: 5132803--5132870 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
5132793 TGGCCCAAGA
*
5132803 GTAAATACTCAAAA-TTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTT-AAGGACTAATAGT
*
5132833 GTAAATATGAAAAGTTTAAGGACTAATAGT
1 GTAAATATCAAAAGTTTAAGGACTAATAGT
*
5132863 GAAAATAT
1 GTAAATAT
5132871 TTTAAGGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATCAAAAGTTTAAGGACTAATAGT
Found at i:5135344 original size:46 final size:46
Alignment explanation
Indices: 5135292--5135564 Score: 413
Period size: 46 Copynumber: 5.9 Consensus size: 46
5135282 GTGTGCTCTT
** *
5135292 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
**
5135338 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
5135384 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
5135430 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* * *
5135476 TGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* * * * *
5135522 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
5135565 TCATGTCAAA
Statistics
Matches: 215, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 214 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:5144778 original size:15 final size:17
Alignment explanation
Indices: 5144746--5144781 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5144736 TGTTGAAATA
5144746 AAAT-TATATCTAATTT
1 AAATATATATCTAATTT
5144762 AAATATATAT-TAA-TT
1 AAATATATATCTAATTT
5144777 AAATA
1 AAATA
5144782 GTCCAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATATCTAATTT
Found at i:5149502 original size:49 final size:49
Alignment explanation
Indices: 5149428--5149528 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
5149418 AATTTTTTTT
* *
5149428 TTATGTTTGTGAGGTCTTACCCAATGAATAATTTACTATAAATCAATTC
1 TTATGTTTGTGAGGTCTTACCCAATGAATAATTTACTATAAACCAACTC
** * * *
5149477 TTATGTTTGTGAGG-CTTTATTCAATGAGTAGTTTATTATAAACCAACTC
1 TTATGTTTGTGAGGTC-TTACCCAATGAATAATTTACTATAAACCAACTC
5149526 TTA
1 TTA
5149529 CAAAATAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (49 bp):
TTATGTTTGTGAGGTCTTACCCAATGAATAATTTACTATAAACCAACTC
Found at i:5154592 original size:23 final size:23
Alignment explanation
Indices: 5154536--5154595 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
5154526 AAGTATTAGC
5154536 TTTTACAAGCTTTCTGAGAATTTTA
1 TTTT-CAAG-TTTCTGAGAATTTTA
*
5154561 TATTT-AAGTTT-TGAGAGTTCTTA
1 T-TTTCAAGTTTCTGAGAATT-TTA
5154584 TTTTCAAGTTTC
1 TTTTCAAGTTTC
5154596 GGGATTTAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
22 10 0.33
23 13 0.43
24 3 0.10
25 1 0.03
26 3 0.10
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (23 bp):
TTTTCAAGTTTCTGAGAATTTTA
Found at i:5155478 original size:74 final size:74
Alignment explanation
Indices: 5155389--5155538 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
5155379 CACATGGTAC
5155389 CATGGTCACATCTCCCCATTGCCCACCCATACATTCATGGTTCCATTTTAACTACCCTTTCCATG
1 CATGGTCACATCTCCCCATTGCCCACCCATACATTCATGGTTCCATTTTAACTACCCTTTCCATG
5155454 ACATCTATA
66 ACATCTATA
5155463 CATGGTCACATCTCCCCATTGCCCACCCATACATTCATGGTTCCATTTTAACTACCCTTTCCATG
1 CATGGTCACATCTCCCCATTGCCCACCCATACATTCATGGTTCCATTTTAACTACCCTTTCCATG
5155528 ACATCTATA
66 ACATCTATA
5155537 CA
1 CA
5155539 ACTATATAGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.25, C:0.35, G:0.08, T:0.32
Consensus pattern (74 bp):
CATGGTCACATCTCCCCATTGCCCACCCATACATTCATGGTTCCATTTTAACTACCCTTTCCATG
ACATCTATA
Found at i:5155503 original size:35 final size:35
Alignment explanation
Indices: 5155389--5155503 Score: 85
Period size: 35 Copynumber: 3.2 Consensus size: 35
5155379 CACATGGTAC
5155389 CATGGTCACATCTCCCCATTGCCCACCCATACATT
1 CATGGTCACATCTCCCCATTGCCCACCCATACATT
* * ** *
5155424 CATGGTTC-CATTTTAACTACCC-TT-TCCATGACAT-CTATA
1 CATGG-TCACA---T--CTCCCCATTGCCCA-CCCATAC-ATT
5155463 CATGGTCACATCTCCCCATTGCCCACCCATACATT
1 CATGGTCACATCTCCCCATTGCCCACCCATACATT
5155498 CATGGT
1 CATGGT
5155504 TCCATTTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
34 5 0.09
35 20 0.34
36 7 0.12
38 7 0.12
39 14 0.24
40 5 0.09
ACGTcount: A:0.23, C:0.37, G:0.10, T:0.30
Consensus pattern (35 bp):
CATGGTCACATCTCCCCATTGCCCACCCATACATT
Found at i:5156073 original size:20 final size:19
Alignment explanation
Indices: 5156050--5156094 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
5156040 ATAAATAACT
5156050 TAATTGTACCCTTTGGACAA
1 TAATT-TACCCTTTGGACAA
*
5156070 TAATTTGCCCTTTGGACAA
1 TAATTTACCCTTTGGACAA
5156089 TAATTT
1 TAATTT
5156095 GAGCATACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (19 bp):
TAATTTACCCTTTGGACAA
Found at i:5156082 original size:19 final size:19
Alignment explanation
Indices: 5156058--5156095 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5156048 CTTAATTGTA
5156058 CCCTTTGGACAATAATTTG
1 CCCTTTGGACAATAATTTG
5156077 CCCTTTGGACAATAATTTG
1 CCCTTTGGACAATAATTTG
5156096 AGCATACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (19 bp):
CCCTTTGGACAATAATTTG
Found at i:5157846 original size:15 final size:15
Alignment explanation
Indices: 5157828--5157974 Score: 87
Period size: 15 Copynumber: 9.8 Consensus size: 15
5157818 AAGCCAAAGG
*
5157828 AGCTGGTGGTGGGGT
1 AGCTGGTGGTGGAGT
* *
5157843 AGCTGGAGGAGGAGT
1 AGCTGGTGGTGGAGT
* *
5157858 TGCTGGTGGAGGAGT
1 AGCTGGTGGTGGAGT
* * * *
5157873 AGCAGGAGGGGGAGA
1 AGCTGGTGGTGGAGT
* *
5157888 AGCAGGTGGTGGGGT
1 AGCTGGTGGTGGAGT
* * *
5157903 AGCCGGCGGTGGAGA
1 AGCTGGTGGTGGAGT
* *
5157918 AGCCGGTGGGGGAGT
1 AGCTGGTGGTGGAGT
* * *
5157933 TGCGGGAGGTGGAGT
1 AGCTGGTGGTGGAGT
* * * *
5157948 AGCCGGGGGAGGAGA
1 AGCTGGTGGTGGAGT
5157963 AGCTGGTGGTGG
1 AGCTGGTGGTGG
5157975 GGAGCTAACG
Statistics
Matches: 99, Mismatches: 33, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 99 1.00
ACGTcount: A:0.18, C:0.10, G:0.58, T:0.15
Consensus pattern (15 bp):
AGCTGGTGGTGGAGT
Found at i:5157865 original size:30 final size:30
Alignment explanation
Indices: 5157828--5157926 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
5157818 AAGCCAAAGG
* *
5157828 AGCTGGTGGTGGGGTAGCTGGAGGAGGAGT
1 AGCTGGTGGTGGGGTAGCAGGAGGAGGAGA
* * * *
5157858 TGCTGGTGGAGGAGTAGCAGGAGGGGGAGA
1 AGCTGGTGGTGGGGTAGCAGGAGGAGGAGA
* * * *
5157888 AGCAGGTGGTGGGGTAGCCGGCGGTGGAGA
1 AGCTGGTGGTGGGGTAGCAGGAGGAGGAGA
*
5157918 AGCCGGTGG
1 AGCTGGTGG
5157927 GGGAGTTGCG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.18, C:0.10, G:0.57, T:0.15
Consensus pattern (30 bp):
AGCTGGTGGTGGGGTAGCAGGAGGAGGAGA
Found at i:5157926 original size:60 final size:60
Alignment explanation
Indices: 5157832--5157946 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
5157822 CAAAGGAGCT
* ** *
5157832 GGTGGTGGGGTAGCTGGAGGAGGAGTTGCTGGTGGAGGAGTAGCAGGAGGGGGAGAAGCA
1 GGTGGTGGGGTAGCCGGAGGAGGAGAAGCCGGTGGAGGAGTAGCAGGAGGGGGAGAAGCA
* * * * * *
5157892 GGTGGTGGGGTAGCCGGCGGTGGAGAAGCCGGTGGGGGAGTTGCGGGAGGTGGAG
1 GGTGGTGGGGTAGCCGGAGGAGGAGAAGCCGGTGGAGGAGTAGCAGGAGGGGGAG
5157947 TAGCCGGGGG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.17, C:0.09, G:0.59, T:0.15
Consensus pattern (60 bp):
GGTGGTGGGGTAGCCGGAGGAGGAGAAGCCGGTGGAGGAGTAGCAGGAGGGGGAGAAGCA
Found at i:5157944 original size:30 final size:30
Alignment explanation
Indices: 5157862--5157961 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
5157852 AGGAGTTGCT
* * *
5157862 GGTGGAGGAGTAGCAGGAGGGGGAGAAGCA
1 GGTGGGGGAGTAGCAGGAGGTGGAGAAGCC
* *
5157892 GGTGGTGGG-GTAGCCGGCGGTGGAGAAGCC
1 GGTGG-GGGAGTAGCAGGAGGTGGAGAAGCC
* * *
5157922 GGTGGGGGAGTTGCGGGAGGTGGAGTAGCC
1 GGTGGGGGAGTAGCAGGAGGTGGAGAAGCC
5157952 GG-GGGAGGAG
1 GGTGGG-GGAG
5157962 AAGCTGGTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
29 6 0.10
30 50 0.86
31 2 0.03
ACGTcount: A:0.19, C:0.10, G:0.60, T:0.11
Consensus pattern (30 bp):
GGTGGGGGAGTAGCAGGAGGTGGAGAAGCC
Found at i:5162169 original size:15 final size:15
Alignment explanation
Indices: 5162151--5162181 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5162141 ATTATTAATA
5162151 ATTATTTTTTTAAAT
1 ATTATTTTTTTAAAT
*
5162166 ATTATTTTTTTTAAT
1 ATTATTTTTTTAAAT
5162181 A
1 A
5162182 CATGCATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATTTTTTTAAAT
Found at i:5162359 original size:25 final size:25
Alignment explanation
Indices: 5162313--5162361 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5162303 ATATTATATA
* ** *
5162313 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTACGTACATACTTTTAAC
5162338 ACTATATTACGTACATACTTTTAA
1 ACTATATTACGTACATACTTTTAA
5162362 TATCATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (25 bp):
ACTATATTACGTACATACTTTTAAC
Found at i:5162844 original size:27 final size:26
Alignment explanation
Indices: 5162814--5162865 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5162804 ATGTATACAT
*
5162814 TTTTAAATACTATATTATATACATATA
1 TTTTAAATACCATA-TATATACATATA
* *
5162841 TTTTTAATACCATATATGTACATAT
1 TTTTAAATACCATATATATACATAT
5162866 CATTATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTAAATACCATATATATACATATA
Found at i:5162990 original size:12 final size:12
Alignment explanation
Indices: 5162957--5162999 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5162947 TTTAATATAG
* *
5162957 TATTATTTTATA
1 TATTATTATATT
*
5162969 TATCATTATATT
1 TATTATTATATT
*
5162981 TATTATTATACT
1 TATTATTATATT
5162993 TATTATT
1 TATTATT
5163000 TTCGCTATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTATATT
Found at i:5165016 original size:25 final size:26
Alignment explanation
Indices: 5164979--5165030 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5164969 TCAAACATGC
5164979 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
5165005 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
5165030 A
1 A
5165031 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:5166599 original size:26 final size:26
Alignment explanation
Indices: 5166514--5166647 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
5166504 ACATGAATTC
5166514 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5166540 TTATCATG-AACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
*
5166564 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5166590 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5166616 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5166642 TTATCA
1 TTATCA
5166648 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
24 11 0.11
25 26 0.25
26 65 0.64
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5170755 original size:25 final size:26
Alignment explanation
Indices: 5170718--5170769 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5170708 TCAAACATGC
5170718 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
5170744 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
5170769 A
1 A
5170770 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:5172331 original size:50 final size:52
Alignment explanation
Indices: 5172252--5172385 Score: 236
Period size: 50 Copynumber: 2.6 Consensus size: 52
5172242 ACATGAATTC
*
5172252 TTATCATGAAACATTTACCTAACCCATTATCATG-AACATTTACCTAAC-CA
1 TTATCATGAAACATTTACCTAACCTATTATCATGAAACATTTACCTAACTCA
5172302 TTATCATGAAACATTTACCTAACCTATTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCTATTATCATGAAACATTTACCTAACTCA
*
5172354 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGAAACATTTACCTAACCTATTATCA
5172386 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
50 33 0.41
51 14 0.17
52 33 0.41
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCTATTATCATGAAACATTTACCTAACTCA
Found at i:5172337 original size:26 final size:26
Alignment explanation
Indices: 5172252--5172385 Score: 220
Period size: 26 Copynumber: 5.2 Consensus size: 26
5172242 ACATGAATTC
*
5172252 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
5172278 TTATCATG-AACATTTACCTAACC-A
1 TTATCATGAAACATTTACCTAACCTA
5172302 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5172328 TTATCATGAAACATTTACCTAA-CTCA
1 TTATCATGAAACATTTACCTAACCT-A
*
5172354 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5172380 TTATCA
1 TTATCA
5172386 ATTTGTATCA
Statistics
Matches: 103, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
24 9 0.09
25 32 0.31
26 60 0.58
27 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5176030 original size:13 final size:13
Alignment explanation
Indices: 5176012--5176044 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5176002 AACCCCGAAT
5176012 CTTAAACCCTAAA
1 CTTAAACCCTAAA
5176025 CTTAAACCCTAAA
1 CTTAAACCCTAAA
*
5176038 CTCAAAC
1 CTTAAAC
5176045 ATTAAACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (13 bp):
CTTAAACCCTAAA
Found at i:5176064 original size:20 final size:19
Alignment explanation
Indices: 5176014--5176070 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 19
5176004 CCCCGAATCT
5176014 TAAACCCTAAACTTAAACCC
1 TAAA-CCTAAACTTAAACCC
5176034 TAAA-CTCAAACATTAAACTCC
1 TAAACCT-AAAC-TTAAAC-CC
5176055 -AAACCTAAACCTTAAA
1 TAAACCTAAA-CTTAAA
5176071 TCTTGAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 21 0.66
21 5 0.16
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAACCTAAACTTAAACCC
Found at i:5180492 original size:16 final size:16
Alignment explanation
Indices: 5180471--5180502 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5180461 TATGTTAGAG
5180471 CACATAAATTTGAAAT
1 CACATAAATTTGAAAT
*
5180487 CACATATATTTGAAAT
1 CACATAAATTTGAAAT
5180503 TTTTTTCAAA
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:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (16 bp):
CACATAAATTTGAAAT
Found at i:5180689 original size:18 final size:19
Alignment explanation
Indices: 5180652--5180688 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5180642 TTTAAAAAAA
5180652 TATAAA-ATTTTGAATTTT
1 TATAAATATTTTGAATTTT
5180670 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
5180689 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:5180694 original size:18 final size:19
Alignment explanation
Indices: 5180658--5180694 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5180648 AAAATATAAA
*
5180658 ATTTTGAATTTTTATAAAT
1 ATTTTGAATTTTTAAAAAT
5180677 ATTTTGAA-TTTTAAAAAT
1 ATTTTGAATTTTTAAAAAT
5180695 TATTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAAAT
Found at i:5180695 original size:28 final size:28
Alignment explanation
Indices: 5180664--5180717 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5180654 TAAAATTTTG
* *
5180664 AATTTTTAT-AAATATTTTGAATTTTAAA
1 AATTATTATGAAA-ATTTTGAAATTTAAA
5180692 AATTATTATGAAAATTTTGAAATTTA
1 AATTATTATGAAAATTTTGAAATTTA
5180718 TTTTGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (28 bp):
AATTATTATGAAAATTTTGAAATTTAAA
Found at i:5180698 original size:19 final size:19
Alignment explanation
Indices: 5180658--5180728 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
5180648 AAAATATAAA
*
5180658 ATTTTGAATTTTTATAAA-T
1 ATTTTGAA-TTTTAAAAATT
5180677 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* * *
5180696 ATTATGAAAATTTTGAAATTT
1 ATTTTG--AATTTTAAAAATT
*
5180717 ATTTTGTATTTT
1 ATTTTGAATTTT
5180729 TTGTTGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.19
19 19 0.44
21 16 0.37
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:5181464 original size:21 final size:21
Alignment explanation
Indices: 5181440--5181482 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5181430 TCCACAATAC
5181440 TAAAAACATTAAAATAAATGT
1 TAAAAACATTAAAATAAATGT
5181461 TAAAAACATTAAAATAAATGT
1 TAAAAACATTAAAATAAATGT
5181482 T
1 T
5181483 CCCCAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAACATTAAAATAAATGT
Found at i:5181512 original size:19 final size:20
Alignment explanation
Indices: 5181488--5181526 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5181478 ATGTTCCCCA
5181488 ACAAATTGA-AAATAAATTT
1 ACAAATTGATAAATAAATTT
*
5181507 ACAAATTGATTAATAAATTT
1 ACAAATTGATAAATAAATTT
5181527 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ACAAATTGATAAATAAATTT
Found at i:5182384 original size:3 final size:3
Alignment explanation
Indices: 5182376--5182402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5182366 AGAATTATAA
5182376 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5182403 TTAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5184218 original size:7 final size:7
Alignment explanation
Indices: 5184206--5184231 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5184196 TGCTAAATTG
5184206 TATCATA
1 TATCATA
5184213 TATCATA
1 TATCATA
5184220 TATCATA
1 TATCATA
5184227 TATCA
1 TATCA
5184232 AATTTACGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (7 bp):
TATCATA
Found at i:5184332 original size:2 final size:2
Alignment explanation
Indices: 5184314--5184348 Score: 52
Period size: 2 Copynumber: 16.5 Consensus size: 2
5184304 GGTAAAAACT
5184314 TA TA TCA TA TA TCA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA T
5184349 TAAGAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 27 0.87
3 4 0.13
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5185174 original size:3 final size:3
Alignment explanation
Indices: 5185166--5185197 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5185156 TGAAGGCAGA
5185166 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5185198 AATTTAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5194108 original size:111 final size:111
Alignment explanation
Indices: 5193908--5194119 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 111
5193898 CAGCTCCAGG
* * *
5193908 AAGCCTCTCATTTGCTCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAATCCAT
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
*
5193973 AGCTCGAACTGAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
66 AGCTCGAACTAAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
* * *
5194019 AAGCCTCTCACTTGATCTCAAACTTTGCCTTCTTGCATTGCTTACACCGA-CTGCATTTAACCCA
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACC-ATCTGCATTTAACCCA
* * **
5194083 TTGCTCGATAC-AAGCTCGCTGGTACCTTCATCAAACC
65 TAGCTCGA-ACTAAGCTCACCAGTACCTTCATCAAACC
5194120 GCACTGATGA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 85 0.97
112 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (111 bp):
AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
AGCTCGAACTAAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
Found at i:5195862 original size:89 final size:90
Alignment explanation
Indices: 5195745--5195933 Score: 226
Period size: 89 Copynumber: 2.1 Consensus size: 90
5195735 AAGTCTTTAC
* *
5195745 TTTTTT-CACTCAATTGAGTACTTCAACTTTCAAAATGCAT-AAAAAAAGACCCTCAAACTTTTT
1 TTTTTTACACTCAATTGAGCACTTCAACTTTCAAAATACATAAAAAAAAGACCCTCAAAC-TTTT
*
5195808 TCA-AAAAAA-AATTAAGCCCCTACCT
65 TCACAAAAAACAATTAAGCCCATA-CT
* * * * *
5195833 TTTTTTACACTCAATTTG-GCACTTGAACTTTCAAAATATATAAAAAAAAATACCTTCAAGCTTT
1 TTTTTTACACTCAA-TTGAGCACTTCAACTTTCAAAATACAT-AAAAAAAAGACCCTCAAACTTT
5195897 TTCACAAAAAAGCAATTAAGCCCATACT
64 TTCACAAAAAA-CAATTAAGCCCATACT
5195925 TTTTTTACA
1 TTTTTTACA
5195934 TAAAAAATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
88 6 0.07
89 26 0.30
90 10 0.12
91 21 0.24
92 11 0.13
93 12 0.14
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (90 bp):
TTTTTTACACTCAATTGAGCACTTCAACTTTCAAAATACATAAAAAAAAGACCCTCAAACTTTTT
CACAAAAAACAATTAAGCCCATACT
Found at i:5196116 original size:18 final size:18
Alignment explanation
Indices: 5196079--5196148 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
5196069 AATACAAGTT
*
5196079 ATAAAAAGTATTAAACTTTA
1 ATAAAAA-TA-TAAAATTTA
5196099 ATAAAAATATAAAATTTA
1 ATAAAAATATAAAATTTA
* * * *
5196117 TTAAAATTGTAAAATTTT
1 ATAAAAATATAAAATTTA
5196135 ATAAAAATCATAAA
1 ATAAAAAT-ATAAA
5196149 TAATTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 28 0.68
19 6 0.15
20 7 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAATATAAAATTTA
Found at i:5196149 original size:18 final size:17
Alignment explanation
Indices: 5196077--5196159 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 17
5196067 TCAATACAAG
5196077 TTATAAAAAGTATTAAACTT
1 TTATAAAAA-TA-TAAA-TT
* *
5196097 TAATAAAAATATAAAAT
1 TTATAAAAATATAAATT
* *
5196114 TTATTAAAATTGTAAAATT
1 TTA-TAAAAATAT-AAATT
*
5196133 TTATAAAAATCATAAATAA
1 TTATAAAAAT-ATAAAT-T
5196152 TTATAAAA
1 TTATAAAA
5196160 TGTATCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.06
18 21 0.42
19 18 0.36
20 8 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TTATAAAAATATAAATT
Found at i:5196418 original size:10 final size:9
Alignment explanation
Indices: 5196365--5196489 Score: 85
Period size: 9 Copynumber: 13.2 Consensus size: 9
5196355 TTTTGGTACG
5196365 ATAATTTTT
1 ATAATTTTT
5196374 AT-ATTTTT
1 ATAATTTTT
*
5196382 ATAAATTTT
1 ATAATTTTT
*
5196391 ATATTTCTTT
1 ATAATT-TTT
* *
5196401 ACATTTTTTT
1 ATA-ATTTTT
5196411 ATAATTTTCTT
1 ATAA-TTT-TT
*
5196422 ACAATTTTT
1 ATAATTTTT
5196431 ATAATTGTTT
1 ATAATT-TTT
*
5196441 ATGATTTTT
1 ATAATTTTT
5196450 ATAATTTTTTTT
1 ATAA---TTTTT
*
5196462 CTAATTTTT
1 ATAATTTTT
5196471 A-ATATTTTT
1 ATA-ATTTTT
5196480 AT-ATTTTT
1 ATAATTTTT
5196488 AT
1 AT
5196490 TAAAATTTAA
Statistics
Matches: 93, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
8 17 0.18
9 36 0.39
10 24 0.26
11 8 0.09
12 8 0.09
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
ATAATTTTT
Done.