Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 162 of 259
Found at i:52855047 original size:23 final size:23
Alignment explanation
Indices: 52854945--52855048 Score: 172
Period size: 23 Copynumber: 4.5 Consensus size: 23
52854935 TGGTTGCTGC
*
52854945 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
* *
52854968 TGTTTATATGCTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
52854991 TGTTTAAATGTTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
*
52855014 TATTTAAATGTTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
52855037 TGTTTAAATGTT
1 TGTTTAAATGTT
52855049 CTTTGTTTAG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (23 bp):
TGTTTAAATGTTGTAAATTGAAG
Found at i:52856833 original size:22 final size:22
Alignment explanation
Indices: 52856803--52856844 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52856793 AGTCGCTATA
*
52856803 AATTATAGTGACTAGTTTTTAT
1 AATTATAGTGACTAATTTTTAT
*
52856825 AATTTTAGTGACTAATTTTT
1 AATTATAGTGACTAATTTTT
52856845 TTCTCCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (22 bp):
AATTATAGTGACTAATTTTTAT
Found at i:52857751 original size:26 final size:26
Alignment explanation
Indices: 52857722--52857829 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
52857712 TGGTACAAAT
52857722 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
52857748 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
52857774 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
52857800 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
52857826 TGAT
1 TGAT
52857830 GGCATTTCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:52859342 original size:26 final size:26
Alignment explanation
Indices: 52859312--52859364 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
52859302 TTTATAGTTT
52859312 TACCCCTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* *
52859338 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
52859364 T
1 T
52859365 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:52862260 original size:21 final size:21
Alignment explanation
Indices: 52862236--52862276 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52862226 TGTCACATTT
52862236 TCAAGCT-CTTCTTCGGGTTTA
1 TCAAGCTCCTT-TTCGGGTTTA
*
52862257 TCAATCTCCTTTTCGGGTTT
1 TCAAGCTCCTTTTCGGGTTT
52862277 CAATGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.46
Consensus pattern (21 bp):
TCAAGCTCCTTTTCGGGTTTA
Found at i:52862398 original size:93 final size:92
Alignment explanation
Indices: 52862217--52862720 Score: 357
Period size: 93 Copynumber: 5.3 Consensus size: 92
52862207 ATAGAAGATA
* *
52862217 ATAGCTTTTTGTCACATTTTCAAGCTCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTCAATG
1 ATAG-TTTTTGTCACCTTTTCAAGCTCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTCAATA
* * * * *
52862282 AAGATGATGGTCATTTTCGTTTAATTTT
65 AAGACGATAGTCACTTTCATTTAAGTTT
* * ** *
52862310 ATAGTTTTCTGTCACCTTTTAAAGCTCTTCTTTGGGTTTATCGGTCTTCTTTTCGGGTTTCAATA
1 ATAGTTTT-TGTCACCTTTTCAAGCTCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTCAATA
*
52862375 AAGACGATAGTCGCTTTCATTTAAGTTT
65 AAGACGATAGTCACTTTCATTTAAGTTT
* * * ** *
52862403 ATACTATTTTGTTAACTTTTCAAGCTCTTCTTCTTCACGTTTACCAATCTCCTTTTCGGG-TTCT
1 ATAGT-TTTTGTCACCTTTTCAAG--C-TCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTC-
* * * * ** **
52862467 GATGAAGACGATAGCCATTTTTGTTTAAGAAT
61 AATAAAGACGATAGTCACTTTCATTTAAGTTT
* * * * * * * ** *
52862499 GTACCTTTCTGTCACATTTTCAGGCTCTTCTTCAGGTTTACCAATCTCCTTTTCAAG-TTCTGAT
1 ATA-GTTTTTGTCACCTTTTCAAGCTCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTC-AAT
* * * **
52862563 GAAGACAATAGTCTCTTTTGTTTAAGTTT
64 AAAGACGATAGTCACTTTCATTTAAGTTT
* * ** * * *
52862592 ATACATTTTTGTTACCTTTTCAAGCTCTTCTTCTTCGGGTTTATTGATCTCCTTCTCGGGTTCCG
1 ATA-GTTTTTGTCACCTTTTCAAG--C-TCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTCA
* **
52862657 ATAACA-ACGGTAGTCACTTTTGTTTAAGTTT
62 ATAA-AGACGATAGTCACTTTCATTTAAGTTT
* *
52862688 ATAGTTTGCTGCCACCTTTTTCAAGCTCTTCTT
1 ATAGTTT-TTGTCACC-TTTTCAAGCTCTTCTT
52862721 TGGATTTCTT
Statistics
Matches: 327, Mismatches: 70, Indels: 27
0.77 0.17 0.06
Matches are distributed among these distances:
92 4 0.01
93 168 0.51
94 11 0.03
95 9 0.03
96 122 0.37
97 13 0.04
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (92 bp):
ATAGTTTTTGTCACCTTTTCAAGCTCTTCTTCGGGTTTATCAATCTCCTTTTCGGGTTTCAATAA
AGACGATAGTCACTTTCATTTAAGTTT
Found at i:52867006 original size:115 final size:115
Alignment explanation
Indices: 52866832--52867063 Score: 437
Period size: 115 Copynumber: 2.0 Consensus size: 115
52866822 TAAATTTGCC
* * *
52866832 AATTTGGCTGCCATATGACTTGTTATGATGGAAATGAATATGCTAAGTTGGCAATTTTTTTATAG
1 AATTTGGCTGCCATATGACTTGTTAGGATGGAAATGAATATGCTAAGTTGACAAATTTTTTATAG
52866897 AAACTATTAACCGCGTAAATTATTGGACTCGGATTTTCAAATTGAAAAAG
66 AAACTATTAACCGCGTAAATTATTGGACTCGGATTTTCAAATTGAAAAAG
52866947 AATTTGGCTGCCATATGACTTGTTAGGATGGAAATGAATATGCTAAGTTGACAAATTTTTTATAG
1 AATTTGGCTGCCATATGACTTGTTAGGATGGAAATGAATATGCTAAGTTGACAAATTTTTTATAG
52867012 AAACTATTAACCGCGTAAATTATTGGACTCGGATTTTCAAATTGAAAAAG
66 AAACTATTAACCGCGTAAATTATTGGACTCGGATTTTCAAATTGAAAAAG
52867062 AA
1 AA
52867064 AGAGGATATA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (115 bp):
AATTTGGCTGCCATATGACTTGTTAGGATGGAAATGAATATGCTAAGTTGACAAATTTTTTATAG
AAACTATTAACCGCGTAAATTATTGGACTCGGATTTTCAAATTGAAAAAG
Found at i:52870584 original size:133 final size:133
Alignment explanation
Indices: 52870353--52870619 Score: 525
Period size: 133 Copynumber: 2.0 Consensus size: 133
52870343 GCTTCAATTC
52870353 TATTACAAACCCTAGATCCAGATACCGAACTCATACACCACTAGCATGACACGAGTTTGCAGATG
1 TATTACAAACCCTAGATCCAGATACCGAACTCATACACCACTAGCATGACACGAGTTTGCAGATG
*
52870418 ATTCATACAATCACCCTTTCAATCAATCGCACGGCAATCAAGCCTAGTCATCAGTTCTTCTTCAC
66 ATTCATACAATCACCCTTTCAATCAATCACACGGCAATCAAGCCTAGTCATCAGTTCTTCTTCAC
52870483 ACT
131 ACT
52870486 TATTACAAACCCTAGATCCAGATACCGAACTCATACACCACTAGCATGACACGAGTTTGCAGATG
1 TATTACAAACCCTAGATCCAGATACCGAACTCATACACCACTAGCATGACACGAGTTTGCAGATG
52870551 ATTCATACAATCACCCTTTCAATCAATCACACGGCAATCAAGCCTAGTCATCAGTTCTTCTTCAC
66 ATTCATACAATCACCCTTTCAATCAATCACACGGCAATCAAGCCTAGTCATCAGTTCTTCTTCAC
52870616 ACT
131 ACT
52870619 T
1 T
52870620 TTGTACGAAA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.26
Consensus pattern (133 bp):
TATTACAAACCCTAGATCCAGATACCGAACTCATACACCACTAGCATGACACGAGTTTGCAGATG
ATTCATACAATCACCCTTTCAATCAATCACACGGCAATCAAGCCTAGTCATCAGTTCTTCTTCAC
ACT
Found at i:52878376 original size:31 final size:31
Alignment explanation
Indices: 52878318--52878378 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
52878308 TTAACAACTC
* *
52878318 AGTGACTTAAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAAACAAAAACTTTTAAATAGTTT
*
52878349 AGTGACTTAAACGAAAA-TTTTCAAATAGTT
1 AGTGACTTAAACAAAAACTTTT-AAATAGTT
52878379 CAATGACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (31 bp):
AGTGACTTAAACAAAAACTTTTAAATAGTTT
Found at i:52878429 original size:29 final size:29
Alignment explanation
Indices: 52878374--52878429 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
52878364 AATTTTCAAA
* * *
52878374 TAGTTCAATGACCAAATTGTAACTTTTTT
1 TAGTTCAATGACCAAAATGAAAATTTTTT
52878403 TAGTT-AAGTGACCAAAATGAAAATTTT
1 TAGTTCAA-TGACCAAAATGAAAATTTT
52878430 CTCATAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TAGTTCAATGACCAAAATGAAAATTTTTT
Found at i:52881058 original size:41 final size:41
Alignment explanation
Indices: 52880993--52881185 Score: 296
Period size: 41 Copynumber: 4.7 Consensus size: 41
52880983 CCTTTCGGGG
**
52880993 CTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
52881034 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* * * * *
52881075 CTTTAGCGGCGTTTCTGGAAAGGTGCCGCTAAAGCTCAGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
52881116 CTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
52881157 CTTTAGCGGCGTTTTTTGAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
52881186 AAAAACATTT
Statistics
Matches: 135, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:52881384 original size:16 final size:16
Alignment explanation
Indices: 52881351--52881384 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52881341 AAAAATGGAA
*
52881351 AATTTAAAATACTATT
1 AATTTAAAATAATATT
*
52881367 AATTTAAAATAATTTT
1 AATTTAAAATAATATT
52881383 AA
1 AA
52881385 AGTTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAAATAATATT
Found at i:52881842 original size:16 final size:17
Alignment explanation
Indices: 52881823--52881864 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
52881813 AAATTCTTTA
52881823 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
52881839 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
52881856 TAAAATAAT
1 T-AAATAAT
52881865 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:52882081 original size:21 final size:22
Alignment explanation
Indices: 52882057--52882097 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
52882047 ATGGTTTATT
52882057 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
*
52882078 GTTTAGGGGTTAGGGATTTA
1 GTTTAAGGGTTAGGGATTTA
52882098 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:52882468 original size:22 final size:22
Alignment explanation
Indices: 52882442--52882486 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
52882432 ACTAATAATT
52882442 TTTAACAAATAAAATAAA-AAAA
1 TTTAACAAAT-AAATAAATAAAA
52882464 TTTAACAAATAAATAAATAAAA
1 TTTAACAAATAAATAAATAAAA
52882486 T
1 T
52882487 CACTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TTTAACAAATAAATAAATAAAA
Found at i:52882572 original size:38 final size:39
Alignment explanation
Indices: 52882489--52882573 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
52882479 AATAAAATCA
*
52882489 CTAAAAATAAGCATTAGCGGCGCTTTTCGGAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
* * *
52882528 CTAAAAATGAGCATTAGTGGCG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAA-CGCCG
*
52882567 CAAAAAA
1 CTAAAAA
52882574 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
Found at i:52883445 original size:38 final size:38
Alignment explanation
Indices: 52883365--52883446 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
52883355 GGTTACAAAC
* * * *
52883365 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
52883403 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
52883441 TTTATC
1 TTTATC
52883447 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:52887657 original size:43 final size:43
Alignment explanation
Indices: 52887610--52887697 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
52887600 GTTTGTTTTT
* *
52887610 AAAGCGTCGCTAAAGGTCAGGGTCTTTAGCGACGTTTGTTGGA
1 AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
* *
52887653 AAAGCGTCGCTAAAGGTCATCGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
52887696 AA
1 AA
52887698 GCGCCACTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (43 bp):
AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
Found at i:52889499 original size:12 final size:11
Alignment explanation
Indices: 52889440--52889499 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
52889430 TTTTTATAAA
*
52889440 AAATAAAATTT
1 AAATAAAATAT
* *
52889451 ATATAAAATCT
1 AAATAAAATAT
52889462 -AATAAAATAT
1 AAATAAAATAT
*
52889472 AAATTAAAAAATT
1 AAA-TAAAATA-T
52889485 AAATAAAATTAT
1 AAATAAAA-TAT
52889497 AAA
1 AAA
52889500 AAAGTAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
10 8 0.21
11 11 0.28
12 15 0.38
13 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:52889695 original size:26 final size:26
Alignment explanation
Indices: 52889666--52889736 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
52889656 GTTATACATC
52889666 ATTAATAAATAATAAAATTAT-ATCTT
1 ATTAATAAATAATAAAATTATGA-CTT
* *
52889692 ATTATTAAATAA-AAAAATATGACTT
1 ATTAATAAATAATAAAATTATGACTT
* *
52889717 ATAAATAAATACTAATAATT
1 ATTAATAAATAATAA-AATT
52889737 TTATTTAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
25 19 0.53
26 14 0.39
27 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (26 bp):
ATTAATAAATAATAAAATTATGACTT
Found at i:52890001 original size:18 final size:19
Alignment explanation
Indices: 52889968--52890003 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52889958 AAAGTTAACT
*
52889968 TTTTAGTGTGTAATTTGGG
1 TTTTAGGGTGTAATTTGGG
52889987 TTTTAGGGT-TAATTTGG
1 TTTTAGGGTGTAATTTGG
52890004 TGAAAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.53
Consensus pattern (19 bp):
TTTTAGGGTGTAATTTGGG
Found at i:52895744 original size:42 final size:42
Alignment explanation
Indices: 52895696--52895776 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
52895686 GAAGGGTAAA
52895696 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
1 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
*
52895738 TTTATGTTTGAATTTATATGAGCTTACTAAACACTAGTT
1 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTT
52895777 GCTTACATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (42 bp):
TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
Found at i:52899559 original size:24 final size:24
Alignment explanation
Indices: 52899532--52899579 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52899522 CCCTCACTAT
52899532 CAACAT-TGTCCCCACCCTCAGTCC
1 CAACATCT-TCCCCACCCTCAGTCC
* *
52899556 CAACATCTTCTCCACCTTCAGTCC
1 CAACATCTTCCCCACCCTCAGTCC
52899580 TAGAATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.21, C:0.48, G:0.06, T:0.25
Consensus pattern (24 bp):
CAACATCTTCCCCACCCTCAGTCC
Found at i:52902748 original size:20 final size:20
Alignment explanation
Indices: 52902723--52902764 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
52902713 AGAGGAGATT
52902723 AATCTGGATCTTAGGTGAAA
1 AATCTGGATCTTAGGTGAAA
52902743 AATCTGGATCTTAGGTGAAA
1 AATCTGGATCTTAGGTGAAA
52902763 AA
1 AA
52902765 GTAAGGCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
AATCTGGATCTTAGGTGAAA
Found at i:52904856 original size:48 final size:50
Alignment explanation
Indices: 52904797--52904892 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 50
52904787 TTCCAAAAAA
* *
52904797 TAATAATATTTTAATAGTTTGATATTAAATTAA-AT-TTAATATTAATCT
1 TAATAATATTTTAATAATTTAATATTAAATTAATATCTTAATATTAATCT
* *
52904845 TAATAGTATTTTATTAATTTAATATTAAATTAATTATCTTAATATTAA
1 TAATAATATTTTAATAATTTAATATTAAATTAA-TATCTTAATATTAA
52904893 GTCTAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 29 0.71
50 2 0.05
51 10 0.24
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (50 bp):
TAATAATATTTTAATAATTTAATATTAAATTAATATCTTAATATTAATCT
Found at i:52904872 original size:11 final size:11
Alignment explanation
Indices: 52904829--52904878 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
52904819 TATTAAATTA
52904829 AATTTAATATT
1 AATTTAATATT
*
52904840 AATCTTAATAGT
1 AAT-TTAATATT
52904852 -ATTT--TATT
1 AATTTAATATT
52904860 AATTTAATATT
1 AATTTAATATT
*
52904871 AAATTAAT
1 AATTTAAT
52904879 TATCTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 3 0.09
9 4 0.12
10 2 0.06
11 16 0.50
12 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTAATATT
Found at i:52909374 original size:200 final size:200
Alignment explanation
Indices: 52909031--52909431 Score: 714
Period size: 200 Copynumber: 2.0 Consensus size: 200
52909021 GATGACTTGA
* * *
52909031 TTACTATTTGATGGTAGTTGGCTTTTCATGAATGAAGATGTAATGATTACCATGAGATAAAATAG
1 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
*
52909096 AATCATATAAGGAGAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
66 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
*
52909161 TATGATAAGGTCATTGAA-AGAGCATTGATTGAGTTGATTTAGTACTGGTATGCTATTGGGGAGA
131 TATGATAAGGTCATTGAACA-AGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGA
52909225 GCTCGG
195 GCTCGG
*
52909231 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGGGATAAAATAA
1 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
*
52909296 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTGAGGATATCCTATGAGGATAACACACT
66 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
*
52909361 TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTGTTGGGGAGAG
131 TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGAG
52909426 CTCGG
196 CTCGG
52909431 T
1 T
52909432 CATGATACTA
Statistics
Matches: 192, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
200 191 0.99
201 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (200 bp):
TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGAG
CTCGG
Found at i:52913364 original size:27 final size:27
Alignment explanation
Indices: 52913312--52913373 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
52913302 GGAATACATA
* * *
52913312 ATGTATGTGTGTATATGTAATATATTT
1 ATGTATTTCTGTATATGTAATATATTC
*
52913339 ATGTATTTCTGTATATGTTAA-GTATTC
1 ATGTATTTCTGTATATG-TAATATATTC
*
52913366 ATGCATTT
1 ATGTATTT
52913374 GCCCATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (27 bp):
ATGTATTTCTGTATATGTAATATATTC
Found at i:52913514 original size:30 final size:30
Alignment explanation
Indices: 52913478--52913535 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
52913468 ATGTGTATAT
*
52913478 ATATGCATATCCGTATGTGTATATATATGC
1 ATATGCATATACGTATGTGTATATATATGC
*
52913508 ATATGCATATACGTATGTGTATGTATAT
1 ATATGCATATACGTATGTGTATATATAT
52913536 ATTAAGCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
ATATGCATATACGTATGTGTATATATATGC
Found at i:52913523 original size:24 final size:24
Alignment explanation
Indices: 52913472--52913523 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
52913462 GTAGGAATGT
* **
52913472 GTATATATATGCATATCCGTATGT
1 GTATATATATGCATATCCATATAC
*
52913496 GTATATATATGCATATGCATATAC
1 GTATATATATGCATATCCATATAC
52913520 GTAT
1 GTAT
52913524 GTGTATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (24 bp):
GTATATATATGCATATCCATATAC
Found at i:52914269 original size:12 final size:12
Alignment explanation
Indices: 52914232--52914277 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
52914222 TTTATCTGTG
52914232 TGTGTATATATA
1 TGTGTATATATA
** *
52914244 TGTGTGCATCTA
1 TGTGTATATATA
52914256 TGTGTATATATA
1 TGTGTATATATA
*
52914268 TGTATATATA
1 TGTGTATATA
52914278 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (12 bp):
TGTGTATATATA
Found at i:52916309 original size:20 final size:21
Alignment explanation
Indices: 52916286--52916330 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
52916276 TTTCTTTGTC
*
52916286 ATAATCATA-TTTAA-ATGTTT
1 ATAAT-ATATTTTAATATGTTG
52916306 ATAA-ATATTTTAATATGTTG
1 ATAATATATTTTAATATGTTG
52916326 ATAAT
1 ATAAT
52916331 TAATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 3 0.14
19 5 0.24
20 13 0.62
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
ATAATATATTTTAATATGTTG
Found at i:52917699 original size:22 final size:22
Alignment explanation
Indices: 52917673--52917720 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
52917663 GATTTGTGAG
* *
52917673 TATAAATGAATTTGGCTTTTTA
1 TATAAACGAATTTGCCTTTTTA
52917695 TATAAACGAATTTGCCTTTTTA
1 TATAAACGAATTTGCCTTTTTA
52917717 TATA
1 TATA
52917721 GACAAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (22 bp):
TATAAACGAATTTGCCTTTTTA
Found at i:52920760 original size:43 final size:43
Alignment explanation
Indices: 52920712--52920794 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
52920702 AAAAAAGCGT
52920712 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
1 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
* * * *
52920755 CGCTAAAGAACATGGCTTTTAGCGGCGCTTTTGTCACAAA
1 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAA
52920795 AGCCATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
Found at i:52921573 original size:13 final size:14
Alignment explanation
Indices: 52921546--52921575 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52921536 TACTAATGAC
52921546 TAATTAAACCATTA
1 TAATTAAACCATTA
52921560 TAATTAAA-CATTA
1 TAATTAAACCATTA
52921573 TAA
1 TAA
52921576 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAAACCATTA
Found at i:52925882 original size:40 final size:40
Alignment explanation
Indices: 52925827--52925962 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
52925817 TTTGGTCAAC
* **
52925827 CTATAGCGGCGTTTTTTAAAAAGTACCGCTAATGCTCGAT
1 CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
* * *
52925867 CTATAGTGGCATTTTTCAAAAAGCGCCGCTGATGCTCGA-
1 CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
*
52925906 CTTATAGCGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
1 C-TATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
*
52925947 CTATAGTGGCGTTTTT
1 CTATAGCGGCGTTTTT
52925963 GGTCCTAGTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 80 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (40 bp):
CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
Found at i:52931051 original size:6 final size:6
Alignment explanation
Indices: 52931040--52931069 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
52931030 CGACGAAAAA
*
52931040 GACGGG GACGGG GACGGT GACGGG GACGGG
1 GACGGG GACGGG GACGGG GACGGG GACGGG
52931070 TCGGATATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.63, T:0.03
Consensus pattern (6 bp):
GACGGG
Found at i:52936496 original size:20 final size:20
Alignment explanation
Indices: 52936467--52936506 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52936457 AGTGATATGA
52936467 TAAAAAAAAATTAA-AAATAT
1 TAAAAAAAAA-TAATAAATAT
*
52936487 TAAAATAAAATAATAAATAT
1 TAAAAAAAAATAATAAATAT
52936507 ACCATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAAAAATAATAAATAT
Found at i:52939284 original size:10 final size:10
Alignment explanation
Indices: 52939269--52939298 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
52939259 AAAGCCTAAT
52939269 CCAAAATAAA
1 CCAAAATAAA
52939279 CCAAAATAAA
1 CCAAAATAAA
52939289 CCAAAATAAA
1 CCAAAATAAA
52939299 AATAAACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (10 bp):
CCAAAATAAA
Found at i:52943197 original size:15 final size:14
Alignment explanation
Indices: 52943162--52943198 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52943152 TTTCTGTCGC
52943162 GATTTTTAGTTTTA
1 GATTTTTAGTTTTA
*
52943176 GACTTTTAGTTTTA
1 GATTTTTAGTTTTA
52943190 GGATTTTTA
1 -GATTTTTA
52943199 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.59
Consensus pattern (14 bp):
GATTTTTAGTTTTA
Found at i:52944987 original size:8 final size:8
Alignment explanation
Indices: 52944976--52945020 Score: 58
Period size: 7 Copynumber: 5.8 Consensus size: 8
52944966 TATTATTTTG
52944976 AAATTTAA
1 AAATTTAA
52944984 AAATTT-A
1 AAATTTAA
52944991 AAATTT-A
1 AAATTTAA
52944998 AAATTTAA
1 AAATTTAA
*
52945006 AATTTTATA
1 AAATTTA-A
52945015 AAATTT
1 AAATTT
52945021 TAGTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 14 0.42
8 13 0.39
9 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTAA
Found at i:52944995 original size:7 final size:7
Alignment explanation
Indices: 52944976--52945010 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
52944966 TATTATTTTG
52944976 AAATTTAA
1 AAATTT-A
52944984 AAATTTA
1 AAATTTA
52944991 AAATTTA
1 AAATTTA
52944998 AAATTTA
1 AAATTTA
52945005 AAATTT
1 AAATTT
52945011 TATAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:52945002 original size:14 final size:15
Alignment explanation
Indices: 52944976--52945020 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
52944966 TATTATTTTG
52944976 AAATTTAAAAATTTA
1 AAATTTAAAAATTTA
52944991 AAATTT-AAAATTTA
1 AAATTTAAAAATTTA
52945005 AAATTTTATAAAATTT
1 AAA-TTTA-AAAATTT
52945021 TAGTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.41
15 9 0.33
17 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTAAAAATTTA
Found at i:52947177 original size:20 final size:18
Alignment explanation
Indices: 52947140--52947178 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
52947130 TATATAACTT
*
52947140 AATTTTTATAACAATTAG
1 AATTTTTATAAAAATTAG
52947158 AATTATTTATAAGAAATTAG
1 AATT-TTTATAA-AAATTAG
52947178 A
1 A
52947179 TGAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTTTTATAAAAATTAG
Found at i:52949531 original size:6 final size:6
Alignment explanation
Indices: 52949520--52949559 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
52949510 CAACCGAACA
*
52949520 TTCACC TTCACC TTCACC CTCACC TTCACC TTCACC TTCA
1 TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTCA
52949560 AGGTAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCACC
Found at i:52954123 original size:33 final size:33
Alignment explanation
Indices: 52954081--52954180 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
52954071 CAAACCTTCC
**
52954081 ACGGAAACCGCTGATTCGGAACAGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
*
52954114 ACGGAAACCGCTGGTTCCAAACAGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
* * * *
52954147 ACGGAAACCGCCGACTCCAAGCAACCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
52954180 A
1 A
52954181 AACCTTCATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.29, C:0.34, G:0.30, T:0.07
Consensus pattern (33 bp):
ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
Found at i:52954208 original size:42 final size:42
Alignment explanation
Indices: 52954145--52954319 Score: 167
Period size: 42 Copynumber: 4.2 Consensus size: 42
52954135 CAGCCGGCGA
* * *
52954145 CGACGGAAACCGCCG-ACTCCAAGCAACCGGCGACGAAACCTT
1 CGACGGAAAAC-CCGAAATCCAAACAACCGGCGACGAAACCTT
* *
52954187 C-ATCGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
1 CGA-CGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
*
52954229 CGACGGAAACCCCGAAATCCAAACAACCGGCGACGAAACCTT
1 CGACGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
* ** * * *** *
52954271 TGAAAG-AAACCTCGGAATCTAAACAATTAGCGACGAAACCGT
1 CGACGGAAAACC-CGAAATCCAAACAACCGGCGACGAAACCTT
52954313 CGACGGA
1 CGACGGA
52954320 CACATCAGAA
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
41 8 0.07
42 99 0.92
43 1 0.01
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (42 bp):
CGACGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
Found at i:52954287 original size:84 final size:83
Alignment explanation
Indices: 52954145--52954319 Score: 203
Period size: 84 Copynumber: 2.1 Consensus size: 83
52954135 CAGCCGGCGA
* * *
52954145 CGACGGAAACCGCCGACTCCAAGCAACCGGCGACGAAACCTTCATCGGAAAACCCGGAATCCAAA
1 CGACGGAAACCGCCGAATCCAAACAACCGGCGACGAAACCTT-ATCGAAAAACCCGGAATCCAAA
* *
52954210 AAACCGGCGACGAAACCTT
65 AAACCAGCGACGAAACCGT
*
52954229 CGACGGAAACC-CCGAAATCCAAACAACCGGCGACGAAACCTT-T-GAAAGAAACCTCGGAATCT
1 CGACGGAAACCGCCG-AATCCAAACAACCGGCGACGAAACCTTATCG-AA-AAACC-CGGAATCC
* **
52954291 AAACAATTAGCGACGAAACCGT
62 AAAAAACCAGCGACGAAACCGT
52954313 CGACGGA
1 CGACGGA
52954320 CACATCAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
81 1 0.01
82 2 0.03
83 8 0.10
84 67 0.86
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (83 bp):
CGACGGAAACCGCCGAATCCAAACAACCGGCGACGAAACCTTATCGAAAAACCCGGAATCCAAAA
AACCAGCGACGAAACCGT
Found at i:52955574 original size:16 final size:16
Alignment explanation
Indices: 52955543--52955579 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
52955533 ATGTGAATAA
52955543 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
52955559 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
52955575 TATTA
1 TATTA
52955580 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:52955629 original size:22 final size:22
Alignment explanation
Indices: 52955603--52955646 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52955593 ATATTCAATA
52955603 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAATAAATTAT
* * *
52955625 ATTTATTATATTAATAATTTAT
1 ATTTATTAAAATAATAAATTAT
52955647 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAAAATAATAAATTAT
Found at i:52958551 original size:16 final size:17
Alignment explanation
Indices: 52958524--52958563 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
52958514 ATTTAATGTG
52958524 TAATTAATTTAAAATTC
1 TAATTAATTTAAAATTC
*
52958541 TAATTAA-TTAAAATTT
1 TAATTAATTTAAAATTC
52958557 TAATTAA
1 TAATTAA
52958564 AAATCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAATTTAAAATTC
Found at i:52961254 original size:14 final size:15
Alignment explanation
Indices: 52961235--52961267 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52961225 ACACTAAAAT
52961235 TTATTTTA-AAATAA
1 TTATTTTATAAATAA
*
52961249 TTATTTTATAGATAA
1 TTATTTTATAAATAA
52961264 TTAT
1 TTAT
52961268 ATGATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATTTTATAAATAA
Found at i:52969154 original size:15 final size:15
Alignment explanation
Indices: 52969134--52969188 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
52969124 ATATGATGTT
52969134 TTTTAGGGTTTAGAG
1 TTTTAGGGTTTAGAG
* *
52969149 TTTTAGGGGTTATAG
1 TTTTAGGGTTTAGAG
* *
52969164 -TTTAGTGTTTAGGAC
1 TTTTAGGGTTTA-GAG
52969179 TTTTAGGGTT
1 TTTTAGGGTT
52969189 CAAGGGTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 9 0.29
15 14 0.45
16 8 0.26
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (15 bp):
TTTTAGGGTTTAGAG
Found at i:52969250 original size:53 final size:52
Alignment explanation
Indices: 52969135--52969250 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 52
52969125 TATGATGTTT
* *
52969135 TTTAGGGTTTAGAGTTTTAGGGGTTATAGTTTAGTGTTTAGGACTTTTAGGG
1 TTTAAGGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGACTTTTAGGG
* * * * **
52969187 TTCAAGGGTTTAGTGTTTTAGGGGTTATAGATTAGTGTTTATGATTTTTTTTGG
1 TTTAA-GGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGA-CTTTTAGGG
52969241 TTTAAGGTTT
1 TTTAAGGTTT
52969251 TACAGAAAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
52 3 0.06
53 40 0.75
54 10 0.19
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (52 bp):
TTTAAGGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGACTTTTAGGG
Found at i:52969293 original size:41 final size:41
Alignment explanation
Indices: 52969247--52969400 Score: 181
Period size: 41 Copynumber: 3.8 Consensus size: 41
52969237 TTGGTTTAAG
*
52969247 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* * **
52969288 GTTTTACCGAAAGCGCCGCTAATGCTCTAGTTTTTAATGGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* *
52969329 GTTTTACCGAAAGCGCCGCTATTGCTCT-GTTTTTAGCGGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* * *
52969369 G--TTCCA-AAAACGCCGCTATTGCTCTGTGTTTT
1 GTTTTACAGAAAGCGCCGCTAATGCTCTG-GTTTT
52969401 ACAATTTTTG
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
37 18 0.18
38 3 0.03
39 5 0.05
40 11 0.11
41 63 0.63
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
Found at i:52973470 original size:26 final size:26
Alignment explanation
Indices: 52973421--52973470 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
52973411 AATTAACTTT
*
52973421 AATATTAAATTTAATCTAAAATTATA
1 AATATTAAATTAAATCTAAAATTATA
* * *
52973447 AATATTAGATTAAATTTAATATTA
1 AATATTAAATTAAATCTAAAATTA
52973471 AATCTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTAAATTAAATCTAAAATTATA
Found at i:52973750 original size:23 final size:23
Alignment explanation
Indices: 52973724--52973767 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
52973714 CTGGCCATTG
52973724 GGACACTATCTTA-CCAGCCACCA
1 GGACACTATC-TACCCAGCCACCA
52973747 GGACACTATCTACCCAGCCAC
1 GGACACTATCTACCCAGCCAC
52973768 TGGCATCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.16
Consensus pattern (23 bp):
GGACACTATCTACCCAGCCACCA
Found at i:52975271 original size:15 final size:15
Alignment explanation
Indices: 52975247--52975276 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52975237 TATAAATGCA
*
52975247 AAATATAAAAGACAT
1 AAATACAAAAGACAT
52975262 AAATACAAAAGACAT
1 AAATACAAAAGACAT
52975277 TGTACAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:52988110 original size:88 final size:86
Alignment explanation
Indices: 52987947--52988155 Score: 240
Period size: 88 Copynumber: 2.4 Consensus size: 86
52987937 CTAGAATTAG
* * * **
52987947 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGGAATAGATCGAAGGCAACGAGCTTTAACCCC
1 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAACCCC
* *
52988012 CTAAGTAGTAGGGTAACAAGC
66 CGAAGCAGTAGGGTAACAAGC
* *
52988033 TGAAGTTCATAGATCTTATCACCC-TAAGCAGTAGGGAAACAGATCCAAAATAACGAGCTTTAAC
1 TGAA-TTCACAGATCTTA-C-CCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAAC
52988097 CCCCGAAGCAGTAGGGTAACAAGC
63 CCCCGAAGCAGTAGGGTAACAAGC
** * * * *
52988121 CAAATTTACAGACCTTAACCCCAAAAGTAGTAGGG
1 TGAATTCACAGATCTT-ACCCCATAAGCAGTAGGG
52988156 TAATAGGCTG
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
86 7 0.07
87 32 0.31
88 60 0.59
89 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (86 bp):
TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAACCCC
CGAAGCAGTAGGGTAACAAGC
Found at i:52988140 original size:43 final size:43
Alignment explanation
Indices: 52988004--52988158 Score: 123
Period size: 44 Copynumber: 3.6 Consensus size: 43
52987994 GCAACGAGCT
* * * * * *
52988004 TTAACCCCCTAAGTAGTAGGGTAACAAGCTGAAGTTCATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAATTAACAGACC
* * * * * *
52988048 TTATCACCCTAAGCAGTAGGGAAACAGATCCAAAATAAC-GAGCT
1 TTAACCCCCTAAGCAGTAGGGTAACA-AGCCAAATTAACAGA-CC
* *
52988092 TTAACCCCCGAAGCAGTAGGGTAACAAGCCAAATTTACAGACC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAACAGACC
** *
52988135 TTAACCCCAAAAGTAGTAGGGTAA
1 TTAACCCCCTAAGCAGTAGGGTAA
52988159 TAGGCTGAAA
Statistics
Matches: 85, Mismatches: 23, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
43 33 0.39
44 50 0.59
45 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAACAGACC
Found at i:52988340 original size:44 final size:44
Alignment explanation
Indices: 52988275--52988426 Score: 143
Period size: 44 Copynumber: 3.5 Consensus size: 44
52988265 AGATCTCAAC
* * * *
52988275 CCCCTAAGCAGTAGGGAAACAGATTGAAGATGAT-GAG-TCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAA-AT-ATACAGACCTTAAA
* *
52988319 CCCCTAAGTAGTAGGGTAACAGGTT-AAATTTACAGACCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATATACAGACCTTAAA
* * * *
52988362 CCCCTAAGCAGTAGGGTAACAGGTTG-AAT-TCAAAGGGCTTTAAC
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATAT-ACA-GACCTTAAA
52988406 CCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGTAACA
52988427 AGCAGAATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 37 0.40
44 49 0.53
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (44 bp):
CCCCTAAGCAGTAGGGTAACAGGTTGAAATATACAGACCTTAAA
Found at i:52988375 original size:43 final size:44
Alignment explanation
Indices: 52988313--52988426 Score: 158
Period size: 43 Copynumber: 2.6 Consensus size: 44
52988303 GATGATGAGT
* * *
52988313 CTTAAACCCCTAAGTAGTAGGGTAACAGGTTAAATTTACA-GAC
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
* *
52988356 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAATTCAAAGGGC
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
* *
52988400 TTTAACCCCCTAAGCAGTAGGGTAACA
1 CTTAAACCCCTAAGCAGTAGGGTAACA
52988427 AGCAGAATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 36 0.57
44 27 0.43
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
Found at i:52988492 original size:87 final size:87
Alignment explanation
Indices: 52988259--52988511 Score: 210
Period size: 87 Copynumber: 2.9 Consensus size: 87
52988249 CAGATTAAAG
* * * * * * * *
52988259 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGA-AGATGATGAGTCTTAAACCCC
1 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACAGA-TAATAGAAGATGGGCCTTAACCCCC
* * *
52988323 TAAGTAGTAGGGTAACAGGTTAA
65 TAAGCAGTAGGGTAACAAGTCAA
* * ** *
52988346 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAATTCAA-A-GGGCTTTAACCCC
1 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACA-GAT-AATAGAAGATGGGCCTTAACCCC
52988409 CTAAGCAGTAGGGTAACAAG-CAGA
64 CTAAGCAGTAGGGTAACAAGTCA-A
** * * * **
52988433 ATTTGTAGATCTT-ATCACCCTAAGCAGTAGGGAAACAGATCATAGAAGATGGGCCTTAACCCTT
1 ATTTACAGACCTTAAAC-CCCTAAGCAGTAGGGAAACAGATAATAGAAGATGGGCCTTAACCCCC
*
52988497 TACGCAGTAGGGTAA
65 TAAGCAGTAGGGTAA
52988512 TAGGCTGAAA
Statistics
Matches: 130, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
85 4 0.03
86 6 0.05
87 116 0.89
88 3 0.02
89 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (87 bp):
ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACAGATAATAGAAGATGGGCCTTAACCCCCT
AAGCAGTAGGGTAACAAGTCAA
Found at i:52988729 original size:43 final size:44
Alignment explanation
Indices: 52988620--52988730 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 44
52988610 CCATCAAGCT
* * * *
52988620 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAAATA
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTATAAACA
*** * * *
52988664 TTATTGCCTTAAGCAATAGGGTAACAAGC-CAAATTT-TCAAACC
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTAT-AAACA
52988707 TTAAACCCCTAAGCAGTAGGGTAA
1 TTAAACCCCTAAGCAGTAGGGTAA
52988731 TAGGTTGAGT
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
42 1 0.02
43 27 0.52
44 24 0.46
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (44 bp):
TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTATAAACA
Found at i:52990286 original size:15 final size:15
Alignment explanation
Indices: 52990252--52990290 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52990242 CTTATGTTGT
* *
52990252 TTATTATTTATTATAT
1 TTATTA-TTATCATAC
52990268 TTATTATTATCATAC
1 TTATTATTATCATAC
52990283 TTATTATT
1 TTATTATT
52990291 TATGAGCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTATCATAC
Found at i:52996823 original size:41 final size:41
Alignment explanation
Indices: 52996764--52996844 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
52996754 TCTCTTGTCT
52996764 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
1 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
*
52996805 ATCCCCAAATTTGCCCACCATAAGGTTGTATCTAACCCAA
1 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAA
52996845 CCTAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.25
Consensus pattern (41 bp):
ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
Found at i:52998578 original size:19 final size:19
Alignment explanation
Indices: 52998537--52998578 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52998527 TTAATTAATT
*
52998537 ATTTAATTTTAATTTTAAT
1 ATTTAATTTTAATTTTAAG
*
52998556 ATTTAA-TTTAGTATTTAAG
1 ATTTAATTTTAAT-TTTAAG
52998575 ATTT
1 ATTT
52998579 TTTCTCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTTAATTTTAATTTTAAG
Found at i:52998658 original size:14 final size:14
Alignment explanation
Indices: 52998639--52998666 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52998629 TTCTTTATTC
52998639 CACATTATTGATTT
1 CACATTATTGATTT
52998653 CACATTATTGATTT
1 CACATTATTGATTT
52998667 GTGTACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
CACATTATTGATTT
Found at i:52999362 original size:16 final size:16
Alignment explanation
Indices: 52999341--52999373 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52999331 ATAATTGAAT
52999341 AAGTAAACCTTAATCA
1 AAGTAAACCTTAATCA
52999357 AAGTAAACCTTAATCA
1 AAGTAAACCTTAATCA
52999373 A
1 A
52999374 TGAACTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AAGTAAACCTTAATCA
Found at i:53003719 original size:43 final size:42
Alignment explanation
Indices: 53003632--53003741 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 42
53003622 CAACTTTTGC
* *
53003632 TAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATGAGACTTCATG
* * * *
53003674 TAAGACTATAGCTGGGCTATTGGCATCGATATGAGATTTTATG
1 TAAGACCATAGCTGGGATA-TGGCATCGATATGAGACTTCATG
**
53003717 TAAGACCATATTTGGGATATGGCAT
1 TAAGACCATAGCTGGGATATGGCAT
53003742 TGGTACAGCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
TAAGACCATAGCTGGGATATGGCATCGATATGAGACTTCATG
Found at i:53006497 original size:8 final size:8
Alignment explanation
Indices: 53006477--53006532 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
53006467 TTATTTGTTT
53006477 TATT-TTA
1 TATTATTA
*
53006484 TGTTATTA
1 TATTATTA
53006492 TATTATTA
1 TATTATTA
53006500 TATTATTA
1 TATTATTA
53006508 TATTA-TA
1 TATTATTA
*
53006515 TTATAATTA
1 -TATTATTA
53006524 TTATTATTA
1 -TATTATTA
53006533 CTTAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 5 0.12
8 27 0.64
9 10 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATTATTA
Found at i:53006498 original size:3 final size:3
Alignment explanation
Indices: 53006486--53006532 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
53006476 TTATTTTATG
*
53006486 TTA TTA -TA TTA TTA -TA TTA TTA -TA TTA -TA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53006530 TTA
1 TTA
53006533 CTTAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 8 0.21
3 30 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:53008771 original size:39 final size:39
Alignment explanation
Indices: 53008717--53008794 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
53008707 AGAAGTTAAT
53008717 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
1 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
53008756 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
1 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
53008795 CCCGCTTAAA
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:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (39 bp):
TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
Found at i:53012872 original size:26 final size:26
Alignment explanation
Indices: 53012843--53012896 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
53012833 TTGTGAAACA
53012843 TAGGTATGGTATCATCCATACTGAGT
1 TAGGTATGGTATCATCCATACTGAGT
*
53012869 TAGGTATGGTATTATCCATACTGAGT
1 TAGGTATGGTATCATCCATACTGAGT
53012895 TA
1 TA
53012897 AGAAACGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (26 bp):
TAGGTATGGTATCATCCATACTGAGT
Found at i:53012908 original size:35 final size:35
Alignment explanation
Indices: 53012869--53012953 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 35
53012859 CATACTGAGT
*
53012869 TAGGTATGGTATTAT-CCATACTGAGTT-AAGAAACG
1 TAGGTATGGTATT-TCCCATACCGAGTTGAA-AAACG
* * *
53012904 TAGGTATGGCATTTCCCATACCGAGTTGTAAAATG
1 TAGGTATGGTATTTCCCATACCGAGTTGAAAAACG
53012939 TAGGTATGGTATTTC
1 TAGGTATGGTATTTC
53012954 AATGAGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 41 0.95
36 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (35 bp):
TAGGTATGGTATTTCCCATACCGAGTTGAAAAACG
Found at i:53014280 original size:14 final size:14
Alignment explanation
Indices: 53014261--53014292 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53014251 ACGTATAATG
53014261 AACTCGAATCATAA
1 AACTCGAATCATAA
*
53014275 AACTCGAATCGTAA
1 AACTCGAATCATAA
53014289 AACT
1 AACT
53014293 ATTTATAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (14 bp):
AACTCGAATCATAA
Found at i:53014822 original size:17 final size:17
Alignment explanation
Indices: 53014800--53014832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53014790 AGACTATGTA
*
53014800 ATGTTAGTTTTCTTAAC
1 ATGTTAATTTTCTTAAC
53014817 ATGTTAATTTTCTTAA
1 ATGTTAATTTTCTTAA
53014833 GTACCACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (17 bp):
ATGTTAATTTTCTTAAC
Found at i:53017156 original size:16 final size:15
Alignment explanation
Indices: 53017137--53017179 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
53017127 TGCATATAAT
*
53017137 TATTTTATTGTAATTA
1 TATTTTATTGTAA-AA
53017153 TATTTATATT-TAAAA
1 TATTT-TATTGTAAAA
53017168 TATTTTATTGTA
1 TATTTTATTGTA
53017180 TTTTTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 8 0.33
16 8 0.33
17 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTTTATTGTAAAA
Found at i:53017307 original size:21 final size:22
Alignment explanation
Indices: 53017268--53017314 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
53017258 TTTTAACATT
**
53017268 TTTTTATTTGTGTGGTTTTATA
1 TTTTTATTTGTGTAATTTTATA
*
53017290 TTTTT-TTTGTGTAATTTTTTA
1 TTTTTATTTGTGTAATTTTATA
53017311 TTTT
1 TTTT
53017315 AATTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (22 bp):
TTTTTATTTGTGTAATTTTATA
Found at i:53018131 original size:128 final size:128
Alignment explanation
Indices: 53017903--53018159 Score: 451
Period size: 128 Copynumber: 2.0 Consensus size: 128
53017893 AACCAGTGGG
*
53017903 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAATTAGGTTT
1 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
* *
53017968 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTTACTTAGGTTT
66 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
* *
53018031 CCCACTACTAAATCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
1 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
**
53018096 AGGGTAAATTACACCAACAGTCACCCAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
66 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
53018159 C
1 C
53018160 ATTTCAATCA
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 122 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (128 bp):
CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
Found at i:53018741 original size:6 final size:6
Alignment explanation
Indices: 53018725--53018926 Score: 199
Period size: 6 Copynumber: 32.7 Consensus size: 6
53018715 TTCGATTTAA
* * *
53018725 ATTTAG ATTTTA ATTTTG ATTTTG ATTTCG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
** ** *
53018773 ATTTTG ATTTTG ATTTCA ATTTTG AAACACTCACTG ATTCTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ----A-T-TTTG ATTTTG ATTTTG
** **
53018821 ATTTTG ATTTCA ATTTCA ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
* * *
53018869 ATTTTG ATTTCT- ATTTCG ATTTTG ATTTTG ATTTTG ATTTCG ATTTGG
1 ATTTTG ATTT-TG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
53018917 ATTTTG ATTT
1 ATTTTG ATTT
53018927 AAGGTTATTT
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
6 159 0.96
7 2 0.01
8 1 0.01
10 1 0.01
11 1 0.01
12 2 0.01
ACGTcount: A:0.21, C:0.06, G:0.14, T:0.59
Consensus pattern (6 bp):
ATTTTG
Found at i:53021286 original size:8 final size:8
Alignment explanation
Indices: 53021273--53021320 Score: 78
Period size: 8 Copynumber: 6.0 Consensus size: 8
53021263 CTAGATCGGC
53021273 AAAAGCCG
1 AAAAGCCG
53021281 AAAAGCCG
1 AAAAGCCG
*
53021289 AAATGCCG
1 AAAAGCCG
53021297 AAAAGCCG
1 AAAAGCCG
*
53021305 AAATGCCG
1 AAAAGCCG
53021313 AAAAGCCG
1 AAAAGCCG
53021321 GTATTTTGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.46, C:0.25, G:0.25, T:0.04
Consensus pattern (8 bp):
AAAAGCCG
Found at i:53021298 original size:16 final size:16
Alignment explanation
Indices: 53021277--53021320 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
53021267 ATCGGCAAAA
53021277 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
53021293 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
53021309 GCCGAAAAGCCG
1 GCCGAAAAGCCG
53021321 GTATTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.41, C:0.27, G:0.27, T:0.05
Consensus pattern (16 bp):
GCCGAAAAGCCGAAAT
Found at i:53021596 original size:28 final size:28
Alignment explanation
Indices: 53021564--53021625 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
53021554 TAAATGTGCT
*
53021564 ATTATACCCCTATGTATACAAAATTACC
1 ATTATACCCCTATGTATACAAAATGACC
*
53021592 ATTATACCCCTATGTATGCAAAATGACC
1 ATTATACCCCTATGTATACAAAATGACC
*
53021620 TTTATA
1 ATTATA
53021626 ACGCTAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (28 bp):
ATTATACCCCTATGTATACAAAATGACC
Found at i:53021798 original size:27 final size:27
Alignment explanation
Indices: 53021737--53021826 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
53021727 AGGAAGCGTC
53021737 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
53021765 CTAGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
53021792 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
53021821 CTGGTG
1 CTGGTG
53021827 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 24 0.45
29 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:53021837 original size:29 final size:28
Alignment explanation
Indices: 53021747--53021837 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
53021737 CTGGTGGCTA
* * * *
53021747 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
53021775 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
53021802 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
53021831 TGTCACA
1 TGCCACA
53021838 TTTTCTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 15 0.28
29 15 0.28
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:53021845 original size:55 final size:56
Alignment explanation
Indices: 53021737--53021851 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
53021727 AGGAAGCGTC
* *
53021737 CTGGTGGCTATGCCACAAATTATCTGTTCTAGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
* * * *
53021792 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTAGTGACCCTGCCACATATATCTGTAT
53021848 CTGG
1 CTGG
53021852 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
Found at i:53024207 original size:66 final size:66
Alignment explanation
Indices: 53023990--53024211 Score: 336
Period size: 67 Copynumber: 3.3 Consensus size: 66
53023980 TTTTAGTCAT
* * ** * *
53023990 TTTTTTAATATGCCTATAGTGATTGTTTTTGTGTGTGACTATTTTTTAATATACATGTTGTTGAC
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACT-GTTTTTAATATACATGTTGTTGAC
53024055 TA
65 TA
*
53024057 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTTAATATACATGATGTTGAC
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTG-TTTTTAATATACATGTTGTTGAC
53024122 TA
65 TA
* *
53024124 TTTTTTAATATGTATGCAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
53024189 A
66 A
*
53024190 TTTTTTAATATGCATGCAGTGA
1 TTTTTTAATATGCATACAGTGA
53024212 GTATTTTTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
66 45 0.31
67 98 0.69
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (66 bp):
TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
A
Found at i:53024216 original size:25 final size:26
Alignment explanation
Indices: 53024165--53024239 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
53024155 TGTATGACTG
* **
53024165 TTTTTAATATACATGTTGTTGACTA-T
1 TTTTTAATATGCATGCAG-TGACTATT
*
53024191 TTTTTAATATGCATGCAGTGAGTATT
1 TTTTTAATATGCATGCAGTGACTATT
53024217 TTTTAATAATATGCATGCAGTGA
1 TTTT--TAATATGCATGCAGTGA
53024240 TTGTTGGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.12
26 20 0.48
28 17 0.40
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (26 bp):
TTTTTAATATGCATGCAGTGACTATT
Found at i:53024297 original size:95 final size:94
Alignment explanation
Indices: 53024092--53024339 Score: 353
Period size: 95 Copynumber: 2.6 Consensus size: 94
53024082 TTGGTGTGTA
* * *
53024092 TGACTGTTTTTTAATATACATG-ATGTTGACTA-TTTTT--TAATATGTATGCAGTGATTGTTGG
1 TGACTATTTTTTAATATGCATGCA-G-TGACTATTTTTTAATAATATGCATGCAGTGATTGTTGG
53024153 TGTGTATGACTGTTTTTAATATACATGTTGT
64 TGTGTATGACTGTTTTTAATATACATGTTGT
*
53024184 TGACTATTTTTTAATATGCATGCAGTGAGTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
1 TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
*
53024249 T-TATGACTGGTTTTTTAATGTACATGTTGT
66 TGTATGACT-G-TTTTTAATATACATGTTGT
* * *
53024279 TGACTATTTTTTAATATGCATGCAATGACTATTTTTTAATAATATGCATGTAGTTATTGTT
1 TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTT
53024340 TTTAGGGGGG
Statistics
Matches: 141, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
91 5 0.04
92 26 0.18
93 8 0.06
94 27 0.19
95 75 0.53
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (94 bp):
TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
TGTATGACTGTTTTTAATATACATGTTGT
Found at i:53026415 original size:17 final size:17
Alignment explanation
Indices: 53026393--53026425 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53026383 TAATTCACTT
53026393 TTCATATACAA-TCAATA
1 TTCATAT-CAATTCAATA
53026410 TTCATATCAATTCAAT
1 TTCATATCAATTCAAT
53026426 TAATCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
TTCATATCAATTCAATA
Found at i:53026456 original size:10 final size:10
Alignment explanation
Indices: 53026444--53026495 Score: 77
Period size: 10 Copynumber: 5.2 Consensus size: 10
53026434 CATAATCATA
*
53026444 ATTCAATTCA
1 ATTCAATTCT
*
53026454 ATTCTATTCT
1 ATTCAATTCT
53026464 ATTCAATTCT
1 ATTCAATTCT
53026474 ATTCAATTCT
1 ATTCAATTCT
*
53026484 ATTCTATTCT
1 ATTCAATTCT
53026494 AT
1 AT
53026496 ACCACAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTCAATTCT
Found at i:53026467 original size:15 final size:15
Alignment explanation
Indices: 53026444--53026492 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
53026434 CATAATCATA
53026444 ATTCAATTCAATTCT
1 ATTCAATTCAATTCT
*
53026459 ATTCTATTCAATTCT
1 ATTCAATTCAATTCT
*
53026474 ATTCAATTCTATTCT
1 ATTCAATTCAATTCT
53026489 ATTC
1 ATTC
53026493 TATACCACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTCAATTCAATTCT
Found at i:53026493 original size:5 final size:5
Alignment explanation
Indices: 53026444--53026495 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
53026434 CATAATCATA
* * * *
53026444 ATTCA ATTCA ATTCT ATTCT ATTCA ATTCT ATTCA ATTCT ATTCT ATTCT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT
53026494 AT
1 AT
53026496 ACCACAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (5 bp):
ATTCT
Found at i:53028019 original size:27 final size:26
Alignment explanation
Indices: 53027989--53028050 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
53027979 AGATAATTAA
53027989 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
53028016 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
53028043 AATAAAAT
1 AATAAAAT
53028051 AGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:53029627 original size:15 final size:15
Alignment explanation
Indices: 53029607--53029663 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
53029597 TTAATATCTG
*
53029607 AAAATAATAAATAAT
1 AAAATAATAAATAAA
53029622 AAAATAATAAGATAAA
1 AAAATAATAA-ATAAA
53029638 ATAAATAA-AAATAAA
1 A-AAATAATAAATAAA
53029653 AATAA-AATAAA
1 AA-AATAATAAA
53029664 AATTGGGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 3 0.08
15 21 0.57
16 7 0.19
17 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:53029661 original size:11 final size:11
Alignment explanation
Indices: 53029612--53029666 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
53029602 ATCTGAAAAT
53029612 AATAAATAATAA
1 AATAAA-AATAA
53029624 AATAATAAGATAA
1 AATAA-AA-ATAA
*
53029637 AATAAATA-AA
1 AATAAAAATAA
53029647 AATAAAAATAA
1 AATAAAAATAA
53029658 AATAAAAAT
1 AATAAAAAT
53029667 TGGGTTGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.24
11 12 0.32
12 7 0.18
13 10 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:53029663 original size:21 final size:25
Alignment explanation
Indices: 53029612--53029663 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 25
53029602 ATCTGAAAAT
53029612 AATAAATAATAAAATAATAAGATAA
1 AATAAATAATAAAATAATAAGATAA
53029637 AATAAAT-A-AAAATAA-AA-ATAA
1 AATAAATAATAAAATAATAAGATAA
53029658 AATAAA
1 AATAAA
53029664 AATTGGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.37
22 2 0.07
23 7 0.26
24 1 0.04
25 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (25 bp):
AATAAATAATAAAATAATAAGATAA
Found at i:53033701 original size:30 final size:30
Alignment explanation
Indices: 53033656--53033715 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53033646 ATTTAATACG
*
53033656 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
53033686 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
53033716 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:53036063 original size:10 final size:10
Alignment explanation
Indices: 53036048--53036079 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
53036038 TAAATACAAT
53036048 TAATTAAAGA
1 TAATTAAAGA
53036058 TAATTAAAGA
1 TAATTAAAGA
53036068 TAATTAAA-A
1 TAATTAAAGA
53036077 TAA
1 TAA
53036080 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:53036105 original size:27 final size:26
Alignment explanation
Indices: 53036075--53036136 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
53036065 AGATAATTAA
53036075 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
53036102 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
53036129 AATAAAAT
1 AATAAAAT
53036137 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:53037286 original size:21 final size:21
Alignment explanation
Indices: 53037260--53037311 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
53037250 CAAGTTGTTG
* **
53037260 CCCCAACTCAGCAATAGGCTA
1 CCCCAACTCAGCAAGAGAATA
* *
53037281 CCCCAAATTAGCAAGAGAATA
1 CCCCAACTCAGCAAGAGAATA
53037302 CCCCAACTCA
1 CCCCAACTCA
53037312 ACAGGCTGCC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAGAATA
Found at i:53038402 original size:12 final size:12
Alignment explanation
Indices: 53038366--53038408 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
53038356 ACTTCAGGCA
*
53038366 TCTTCATTTTTCC
1 TCTTC-TTTTTCT
*
53038379 TCTTCTTCTTCT
1 TCTTCTTTTTCT
*
53038391 TCTTTTTTTTCT
1 TCTTCTTTTTCT
53038403 TCTTCT
1 TCTTCT
53038409 CCTTCGTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTTTCT
Found at i:53040194 original size:15 final size:16
Alignment explanation
Indices: 53040174--53040208 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53040164 TTGGCTAGGT
53040174 TTTTG-AGGTAAGCTA
1 TTTTGAAGGTAAGCTA
53040189 TTTTGAAGGTAAGCTA
1 TTTTGAAGGTAAGCTA
53040205 TTTT
1 TTTT
53040209 CAAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGAAGGTAAGCTA
Found at i:53041524 original size:23 final size:24
Alignment explanation
Indices: 53041497--53041542 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53041487 TAAATTTTGT
53041497 TCTATTATT-TAAA-TTTTATTTTA
1 TCTA-TATTATAAATTTTTATTTTA
53041520 TCTATATTATAAATTTTTATTTT
1 TCTATATTATAAATTTTTATTTT
53041543 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTATATTATAAATTTTTATTTTA
Found at i:53041552 original size:25 final size:22
Alignment explanation
Indices: 53041501--53041553 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
53041491 TTTTGTTCTA
53041501 TTATTTAAATTTTATTTTATCT
1 TTATTTAAATTTTATTTTATCT
* *
53041523 ATATTATAAATTTTTATTTTTATTT
1 TTATT-TAAA-TTTTA-TTTTATCT
53041548 TTATTT
1 TTATTT
53041554 TGATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 6 0.24
25 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTAAATTTTATTTTATCT
Found at i:53041588 original size:25 final size:24
Alignment explanation
Indices: 53041560--53041608 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
53041550 ATTTTGATGT
53041560 ATATAAATACTTTTATTTAAAAAAA
1 ATAT-AATACTTTTATTTAAAAAAA
**
53041585 ATATTTTACTTTTATTTAAAAAAA
1 ATATAATACTTTTATTTAAAAAAA
53041609 TATTATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAATACTTTTATTTAAAAAAA
Found at i:53041609 original size:23 final size:24
Alignment explanation
Indices: 53041567--53041612 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
53041557 TGTATATAAA
53041567 TACTTTTATTTAAAAAAAATATTT
1 TACTTTTATTTAAAAAAAATATTT
53041591 TACTTTTATTT-AAAAAAATATT
1 TACTTTTATTTAAAAAAAATATT
53041613 ATTTCTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TACTTTTATTTAAAAAAAATATTT
Found at i:53041621 original size:21 final size:23
Alignment explanation
Indices: 53041567--53041612 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
53041557 TGTATATAAA
53041567 TACTTTTATTTAAAAAAAATATTT
1 TACTTTTATTTAAAAAAAATA-TT
53041591 TACTTTTATTT-AAAAAAATATT
1 TACTTTTATTTAAAAAAAATATT
53041613 ATTTCTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 9 0.41
24 11 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TACTTTTATTTAAAAAAAATATT
Found at i:53045367 original size:3 final size:3
Alignment explanation
Indices: 53045361--53045388 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53045351 TATTAAAATT
53045361 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53045389 CTACCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53046401 original size:47 final size:47
Alignment explanation
Indices: 53046332--53046428 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
53046322 CCTATTTTTA
**
53046332 GGCTCAGCCCGGACCCAATAAATGGGCATGATTTTTTAGTTGAGCTC
1 GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
* * *
53046379 GGCTCGGCCCGGGCCCAATAAATGAACATTATTTTTTAGTTGAGCTC
1 GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
53046426 GGC
1 GGC
53046429 CCAAACCCGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (47 bp):
GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
Found at i:53046441 original size:47 final size:46
Alignment explanation
Indices: 53046339--53046441 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 46
53046329 TTAGGCTCAG
** * **
53046339 CCCGGACCCAATAAATGGGCATGATTTTTTAGTTGAGCTCGGCTCGG
1 CCCGG-CCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCCAA
*
53046386 CCCGGGCCCAATAAATGAACATTATTTTTTAGTTGAGCTCGGCCCAAA
1 CCC-GGCCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCC-AA
53046434 CCCGGCCC
1 CCCGGCCC
53046442 GACCCAGCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 43 0.90
48 5 0.10
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (46 bp):
CCCGGCCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCCAA
Found at i:53052824 original size:29 final size:28
Alignment explanation
Indices: 53052748--53052824 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 28
53052738 ATTGAACCTG
* *
53052748 AATTTTAAAATTTAAAAAATAGAGAGACTA
1 AATTTT-AAATTT-AAAAGTAGAAAGACTA
** * *
53052778 AATTTCTAAAAATAAAAGTATAAAGATTA
1 AATTT-TAAATTTAAAAGTAGAAAGACTA
53052807 AATTTTAAATTTATAAAG
1 AATTTTAAATTTA-AAAG
53052825 AAATAGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.16
29 21 0.57
30 9 0.24
31 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.34
Consensus pattern (28 bp):
AATTTTAAATTTAAAAGTAGAAAGACTA
Found at i:53065538 original size:24 final size:23
Alignment explanation
Indices: 53065461--53065545 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
53065451 CTTATTGTTA
53065461 ATATTTT-AATA--TATAAAATAT
1 ATATTTTAAATATTTATAAAAT-T
* *
53065482 AAATTTTAAATATTTTTAAGCAATT
1 ATATTTTAAATATTTATAA--AATT
* *
53065507 A-ATATTAATTATTTATAAAATGT
1 ATATTTTAAATATTTATAAAAT-T
53065530 ATATTTTAAATATTTA
1 ATATTTTAAATATTTA
53065546 AATATAACCA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 6 0.12
22 7 0.14
23 2 0.04
24 30 0.60
25 2 0.04
26 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATTTATAAAATT
Found at i:53065579 original size:21 final size:21
Alignment explanation
Indices: 53065503--53065580 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
53065493 ATTTTTAAGC
*
53065503 AATTA-ATATTAATTATTTAT
1 AATTATATATTAAATATTTAT
*
53065523 AAAATGTATATTTTAAATATTTA-
1 --AAT-TATATATTAAATATTTAT
*
53065546 AA-TATAACCATTAAATATTTAT
1 AATTAT-A-TATTAAATATTTAT
53065568 AATTATATATTAA
1 AATTATATATTAA
53065581 CACATTTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 18 0.40
22 6 0.13
23 5 0.11
24 12 0.27
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (21 bp):
AATTATATATTAAATATTTAT
Found at i:53066104 original size:9 final size:9
Alignment explanation
Indices: 53066090--53066114 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53066080 TCATATGACG
53066090 TTTTTAAAT
1 TTTTTAAAT
53066099 TTTTTAAAT
1 TTTTTAAAT
53066108 TTTTTAA
1 TTTTTAA
53066115 TTCGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:53068753 original size:18 final size:17
Alignment explanation
Indices: 53068720--53068758 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53068710 TTGTATAAAT
53068720 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53068738 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53068755 TGTG
1 TGTG
53068759 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53068853 original size:75 final size:75
Alignment explanation
Indices: 53068763--53068910 Score: 296
Period size: 75 Copynumber: 2.0 Consensus size: 75
53068753 AATGTGGAAG
53068763 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
53068828 GGTTGAACAT
66 GGTTGAACAT
53068838 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
53068903 GGTTGAAC
66 GGTTGAAC
53068911 TTAGGAATAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (75 bp):
GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
GGTTGAACAT
Found at i:53069086 original size:23 final size:23
Alignment explanation
Indices: 53069059--53069134 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
53069049 AGTGTTATTG
53069059 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
53069082 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53069105 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53069128 ATCAGTG
1 ATCAGTG
53069135 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:53071812 original size:30 final size:30
Alignment explanation
Indices: 53071776--53071835 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53071766 ACTACCAAAG
53071776 ATACTCTAAATACATGAGAAAACTTGAAAA
1 ATACTCTAAATACATGAGAAAACTTGAAAA
53071806 ATACTCTAAATACATGAGAAAACTTGAAAA
1 ATACTCTAAATACATGAGAAAACTTGAAAA
53071836 GATCTTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.23
Consensus pattern (30 bp):
ATACTCTAAATACATGAGAAAACTTGAAAA
Done.