Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 87 of 163
Found at i:24617234 original size:43 final size:43
Alignment explanation
Indices: 24617173--24617257 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
24617163 CAAGAGGGAC
*
24617173 AGATTGAAACCACATTCCAATCATTTACCCCTAATCATGAGGT
1 AGATTGAAACCACATTCCAATCATTTACCCCTAATCAAGAGGT
* * *
24617216 AGATTGAAGCCACATTCCAATCATTTATCCCTAGTCAAGAGG
1 AGATTGAAACCACATTCCAATCATTTACCCCTAATCAAGAGG
24617258 GGCAGATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (43 bp):
AGATTGAAACCACATTCCAATCATTTACCCCTAATCAAGAGGT
Found at i:24617483 original size:122 final size:121
Alignment explanation
Indices: 24617307--24617691 Score: 590
Period size: 122 Copynumber: 3.2 Consensus size: 121
24617297 ATGGGTTAAG
* *
24617307 CAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGGAGCTCA
1 CAATGAAGCAGTCATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGGAGCTCA
*
24617372 TGTGAGTAAAACTTTGAAACCTCATCTTCCTGATGAGATACAAAAAAGTGGGTTAGA
66 TGTGAGTAAAACTTTGAAACC-CATCTTCCTGATGAGATACAAAAAAGTGGGTCAGA
* *
24617429 CAATGAAGCAGTTATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGCAGAGCTCA
1 CAATGAAGCAGTCATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGGAGCTCA
* * *
24617494 TATGAGTAAAACTTTGAAACCCCATCTTCTTGATGAGATACAGAAAAGTGGGTCAGA
66 TGTGAGTAAAACTTTGAAA-CCCATCTTCCTGATGAGATACAAAAAAGTGGGTCAGA
* * *
24617551 CAATGAAGCGGTCATCTTCTTGATGAGATACACAGAAGTAGACCAAATCAATGAAGCGAAGCTCA
1 CAATGAAGCAGTCATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGGAGCTCA
** * *
24617616 TGTGAGTAAAACTTCAAAACCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAGA
66 TGTGAGTAAAACTTTGAAACCC-ATCTTCCTGATGAGATACAAAAAAGTGGGTCAGA
* *
24617673 CAACGAAGCGGTCATCTTC
1 CAATGAAGCAGTCATCTTC
24617692 CTACTAAGAT
Statistics
Matches: 242, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 3 0.01
122 237 0.98
123 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (121 bp):
CAATGAAGCAGTCATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGGAGCTCA
TGTGAGTAAAACTTTGAAACCCATCTTCCTGATGAGATACAAAAAAGTGGGTCAGA
Found at i:24617702 original size:122 final size:121
Alignment explanation
Indices: 24617285--24617755 Score: 576
Period size: 122 Copynumber: 3.9 Consensus size: 121
24617275 CTTCTTAAGA
*
24617285 AGATACAGAGAAA-TGGGTTA-AGCAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTAG
1 AGATACAGA-AAAGTGGGTCAGA-CAATGAAGCAGTCATCTTCCTGATGAGATACA-AGAAGTAG
* * **
24617348 ACCAAATCAATGAAGCGGAGCTCATGTGAGTAAAACTTTGAAA-CCTCATCTTCCTGATG
63 ACCAAATCAATGAAGCGAAGCTCATATGAGTAAAACTTCAAAACCCT-ATCTTCCTGATG
* * * *
24617407 AGATACAAAAAAGTGGGTTAGACAATGAAGCAGTTATCTTCTTGATGAGATACAAAGAAGTAGAC
1 AGATACAGAAAAGTGGGTCAGACAATGAAGCAGTCATCTTCCTGATGAGATAC-AAGAAGTAGAC
** * *
24617472 CAAATCAATGAAGC-AGAGCTCATATGAGTAAAACTTTGAAACCCCATCTTCTTGATG
65 CAAATCAATGAAGCGA-AGCTCATATGAGTAAAACTTCAAAACCCTATCTTCCTGATG
* *
24617529 AGATACAGAAAAGTGGGTCAGACAATGAAGCGGTCATCTTCTTGATGAGATACACAGAAGTAGAC
1 AGATACAGAAAAGTGGGTCAGACAATGAAGCAGTCATCTTCCTGATGAGATACA-AGAAGTAGAC
*
24617594 CAAATCAATGAAGCGAAGCTCATGTGAGTAAAACTTCAAAACCCTATCTTCCTGATG
65 CAAATCAATGAAGCGAAGCTCATATGAGTAAAACTTCAAAACCCTATCTTCCTGATG
* * * * *
24617651 AGATACAGAGAAGTGGGTCAGACAACGAAGCGGTCATCTTCCT-ACTAAGATACAAGAAG-CGAA
1 AGATACAGAAAAGTGGGTCAGACAATGAAGCAGTCATCTTCCTGA-TGAGATACAAGAAGTAG-A
* * * * *
24617714 CCAAAACAATGAGGTGAAGCTCAATACGAGTGAAACTTCAAA
64 CCAAATCAATGAAGCGAAGCTC-ATATGAGTAAAACTTCAAA
24617756 TTTCATTTTC
Statistics
Matches: 312, Mismatches: 27, Indels: 20
0.87 0.08 0.06
Matches are distributed among these distances:
120 1 0.00
121 30 0.10
122 276 0.88
123 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (121 bp):
AGATACAGAAAAGTGGGTCAGACAATGAAGCAGTCATCTTCCTGATGAGATACAAGAAGTAGACC
AAATCAATGAAGCGAAGCTCATATGAGTAAAACTTCAAAACCCTATCTTCCTGATG
Found at i:24620034 original size:44 final size:44
Alignment explanation
Indices: 24619963--24620050 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
24619953 CCCCAGAACT
* * *
24619963 TTCCAAATATTCGGATTTGACCCCCAAACTTTGC-AAAAATTACA
1 TTCCAAAAATTCAGATTTGACCCCCAAAC-TTCCTAAAAATTACA
* *
24620007 TTCCAAAAATTCAGATTTTACCTCCAAACTTCCTAAAAATTACA
1 TTCCAAAAATTCAGATTTGACCCCCAAACTTCCTAAAAATTACA
24620051 CTTTGACTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (44 bp):
TTCCAAAAATTCAGATTTGACCCCCAAACTTCCTAAAAATTACA
Found at i:24638383 original size:6 final size:6
Alignment explanation
Indices: 24638372--24638426 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
24638362 TCTTCAAGCT
* * * *
24638372 CTTCTC CTTCTC CTTCTC CTTCTC CTTCCC CTTCCC CTTCCC CTTCCC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC
24638420 CTTCCC C
1 CTTCCC C
24638427 CTTCATTGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CTTCCC
Found at i:24638395 original size:18 final size:18
Alignment explanation
Indices: 24638372--24638426 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
24638362 TCTTCAAGCT
* *
24638372 CTTCTCCTTCTCCTTCTC
1 CTTCTCCTTCCCCTTCCC
24638390 CTTCTCCTTCCCCTTCCC
1 CTTCTCCTTCCCCTTCCC
*
24638408 CTTCCCCTTCCCCTTCCC
1 CTTCTCCTTCCCCTTCCC
24638426 C
1 C
24638427 CTTCATTGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (18 bp):
CTTCTCCTTCCCCTTCCC
Found at i:24638971 original size:16 final size:16
Alignment explanation
Indices: 24638950--24638980 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
24638940 TTAATGAAAG
24638950 TGCAAATCTATCCGGA
1 TGCAAATCTATCCGGA
24638966 TGCAAATCTATCCGG
1 TGCAAATCTATCCGG
24638981 TTTTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (16 bp):
TGCAAATCTATCCGGA
Found at i:24638987 original size:91 final size:91
Alignment explanation
Indices: 24638890--24639055 Score: 332
Period size: 91 Copynumber: 1.8 Consensus size: 91
24638880 AATTTTTGGA
24638890 TTTTTTTTCTATCAAGTTTTAGTAGATAAATTGTAGTTTTATATTTGATCTTAATGAAAGTGCAA
1 TTTTTTTTCTATCAAGTTTTAGTAGATAAATTGTAGTTTTATATTTGATCTTAATGAAAGTGCAA
24638955 ATCTATCCGGATGCAAATCTATCCGG
66 ATCTATCCGGATGCAAATCTATCCGG
24638981 TTTTTTTTCTATCAAGTTTTAGTAGATAAATTGTAGTTTTATATTTGATCTTAATGAAAGTGCAA
1 TTTTTTTTCTATCAAGTTTTAGTAGATAAATTGTAGTTTTATATTTGATCTTAATGAAAGTGCAA
24639046 ATCTATCCGG
66 ATCTATCCGG
24639056 TTGTCAAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (91 bp):
TTTTTTTTCTATCAAGTTTTAGTAGATAAATTGTAGTTTTATATTTGATCTTAATGAAAGTGCAA
ATCTATCCGGATGCAAATCTATCCGG
Found at i:24643902 original size:2 final size:2
Alignment explanation
Indices: 24643897--24643940 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
24643887 AAAAAAACTA
24643897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24643939 AT
1 AT
24643941 TGAGGGGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24644367 original size:2 final size:2
Alignment explanation
Indices: 24644360--24644401 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
24644350 ACCTCTACTT
24644360 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CAG AG AG CAG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG -AG AG
24644402 TAATTTGGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24651183 original size:24 final size:24
Alignment explanation
Indices: 24651132--24651186 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
24651122 TCTTCCAGTT
*
24651132 AAACTCTACTTATTTGTTTCAATT
1 AAACTCTACTTATTTGTTTCAATC
** * *
24651156 AAACTCTGTTTATTTGTTTTAGTC
1 AAACTCTACTTATTTGTTTCAATC
24651180 AAACTCT
1 AAACTCT
24651187 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTACTTATTTGTTTCAATC
Found at i:24654975 original size:78 final size:78
Alignment explanation
Indices: 24654799--24655016 Score: 197
Period size: 78 Copynumber: 2.8 Consensus size: 78
24654789 TTTTATTTGT
* * * * *
24654799 AAATAGAAATTAATAGAATAATTCTG-TTTCGAGATTTATTCCTGTCATTCAATAGAATTTATTT
1 AAATAGAAATTAATTGAACAATTCTGTTTTAG-GATTTATTCCTGTCATTCAATAGAATTTAATC
* * * *
24654863 AATTTTTTGTTTCC
65 AAGTGTCTATTTCC
** * * * *
24654877 AAGCAGAATTTAATTAAACAATTCTGTTTTAGGATTTATTCCTGTCTTTCAATAGAATTTAATCG
1 AAATAGAAATTAATTGAACAATTCTGTTTTAGGATTTATTCCTGTCATTCAATAGAATTTAATCA
*
24654942 AGTGTCTATTTTC
66 AGTGTCTATTTCC
* * * * * *
24654955 AAATAGAAATAAATTGAACAATTCTATTTCAAGATTATATTCCTG-CAGTTCAACATAATTTA
1 AAATAGAAATTAATTGAACAATTCTGTTTTAGGATT-TATTCCTGTCA-TTCAATAGAATTTA
24655017 TTTGATTTTT
Statistics
Matches: 110, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
78 86 0.78
79 24 0.22
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (78 bp):
AAATAGAAATTAATTGAACAATTCTGTTTTAGGATTTATTCCTGTCATTCAATAGAATTTAATCA
AGTGTCTATTTCC
Found at i:24660347 original size:309 final size:308
Alignment explanation
Indices: 24659749--24660359 Score: 1039
Period size: 309 Copynumber: 2.0 Consensus size: 308
24659739 ATTCATGTGG
* *
24659749 GGGATTATTGGAAAAAATGGATTTTTGGAAACTTTGAGGCATATTCTCAATTGGTAAAGGTGGTG
1 GGGATTATTAGAAAAAATGGATTTTTAGAAACTTTGAGGCATATTCTCAATTGGTAAAGGTGGTG
** *
24659814 ATTTGAATCATAAAATTATAATTTTATATTCTACTCTGTGAAACCTTTATAACGGTATATCATAT
66 ATTTGAATCATAAAATTATAATTTTATATTCTACTCCATGAAACCTTTACAACGGTATATCATAT
24659879 GCTCAAAATGATTGAATGATGAATGAAAAATGCTCAAAGTAAGCCACTTGTGAATTATGTTGAGG
131 GCTCAAAATGATTGAATGATGAATGAAAAATGCTCAAAGTAAGCCACTTGTGAATTATGTTGAGG
*
24659944 AAATGGAAAGCTTAGATCCCACATTGATTTGATATCAAGTGAAGAATATGTTTATATATATGAAC
196 AAATGGAAAGCTTAGATCCCACATTGATTAGATATCAAGTGAAGAATATGTTTATATATATGAAC
24660009 CAACTTTGTGGTTATTGAATGAGTAAGTTAAAACTCTCCCTCGTGCGCA
261 CAACTTTGTGGTTATTGAA-GAGTAAGTTAAAACTCTCCCTCGTGCGCA
* * * *
24660058 GGGATTGTTAGAAAATATGGATTTTTAGAAATTTTGAGGCATATTCTCAGTTGGTAAAGGTGGTG
1 GGGATTATTAGAAAAAATGGATTTTTAGAAACTTTGAGGCATATTCTCAATTGGTAAAGGTGGTG
* *
24660123 ATTTTAATCATAAAATTATAATTTTATATTCTACTCCATGAGACCTTTACAACGGTATATCATAT
66 ATTTGAATCATAAAATTATAATTTTATATTCTACTCCATGAAACCTTTACAACGGTATATCATAT
24660188 GCTCAAAATGATTGAATGATGAATGAGAAATTAATGCTCAAAGTAAGCCACTTGTGAATTATGTT
131 GCTCAAAATGATTGAATGATGAAT--GAAA--AATGCTCAAAGTAAGCCACTTGTGAATTATGTT
*
24660253 GAGGAAATGGAAAGCTTAGATCCCACATTGATTAGATATCAAGTTAAGAATATGTTTATATATAT
192 GAGGAAATGGAAAGCTTAGATCCCACATTGATTAGATATCAAGTGAAGAATATGTTTATATATAT
24660318 GAACCAACTTTGTGGTTATTG-A-A-TAAGTTAAAACTCTCCCTC
257 GAACCAACTTTGTGGTTATTGAAGAGTAAGTTAAAACTCTCCCTC
24660360 ACGTGCAGAG
Statistics
Matches: 285, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
309 162 0.57
310 1 0.00
311 4 0.01
312 1 0.00
313 117 0.41
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (308 bp):
GGGATTATTAGAAAAAATGGATTTTTAGAAACTTTGAGGCATATTCTCAATTGGTAAAGGTGGTG
ATTTGAATCATAAAATTATAATTTTATATTCTACTCCATGAAACCTTTACAACGGTATATCATAT
GCTCAAAATGATTGAATGATGAATGAAAAATGCTCAAAGTAAGCCACTTGTGAATTATGTTGAGG
AAATGGAAAGCTTAGATCCCACATTGATTAGATATCAAGTGAAGAATATGTTTATATATATGAAC
CAACTTTGTGGTTATTGAAGAGTAAGTTAAAACTCTCCCTCGTGCGCA
Found at i:24663330 original size:80 final size:80
Alignment explanation
Indices: 24663220--24663456 Score: 332
Period size: 80 Copynumber: 3.0 Consensus size: 80
24663210 TCCTGGCACT
* * *
24663220 TTAACCAACAACTAATCCGTCAAATATTGGCACCTAGTGCCTAGCGGATAAACCGCAAATGTGAG
1 TTAACCAACAAAT-ATCCGTCAAATCTTGGCACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAG
24663285 CCCAGCTCTAGTTGGA
65 CCCAGCTCTAGTTGGA
* * * * * *
24663301 TTAACCAATAAATATCCGTCAAATCTTGGCACCCAGTGCCTAGTGGATAAACTGTAAAAGTGATC
1 TTAACCAACAAATATCCGTCAAATCTTGGCACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAGC
* *
24663366 TCAACTCTAGTTGGA
66 CCAGCTCTAGTTGGA
* *
24663381 TTAACCAACAAATATCCATCAAATCTTGGCA-CTCAGTGCCTAGCGGATAAGCCGCAAAAGTGAG
1 TTAACCAACAAATATCCGTCAAATCTTGGCACCT-AGTGCCTAGCGGATAAACCGCAAAAGTGAG
24663445 CCCAGCTCTAGT
65 CCCAGCTCTAGT
24663457 CAGTTAAACT
Statistics
Matches: 134, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 1 0.01
80 122 0.91
81 11 0.08
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (80 bp):
TTAACCAACAAATATCCGTCAAATCTTGGCACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAGC
CCAGCTCTAGTTGGA
Found at i:24671706 original size:18 final size:18
Alignment explanation
Indices: 24671685--24671723 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
24671675 TATTTTATAT
24671685 TTTCAGTTGTTTTTCTCA
1 TTTCAGTTGTTTTTCTCA
24671703 TTTCAGTTGTTTTTCTCA
1 TTTCAGTTGTTTTTCTCA
24671721 TTT
1 TTT
24671724 GAATAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.64
Consensus pattern (18 bp):
TTTCAGTTGTTTTTCTCA
Found at i:24680056 original size:25 final size:25
Alignment explanation
Indices: 24680026--24680123 Score: 98
Period size: 25 Copynumber: 4.1 Consensus size: 25
24680016 GAACGTGTCA
24680026 ATATCATAACAAATCATACCATATC
1 ATATCATAACAAATCATACCATATC
*
24680051 ATATCATAAC-GA--AT--CATATC
1 ATATCATAACAAATCATACCATATC
** *
24680071 ATATCATAATGAATCATGCCATATC
1 ATATCATAACAAATCATACCATATC
* **
24680096 ATAACATAACAAATCATATAATATC
1 ATATCATAACAAATCATACCATATC
24680121 ATA
1 ATA
24680124 ATGAATTGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
20 15 0.25
21 1 0.02
22 2 0.03
23 2 0.03
24 1 0.02
25 38 0.64
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (25 bp):
ATATCATAACAAATCATACCATATC
Found at i:24680113 original size:20 final size:21
Alignment explanation
Indices: 24680026--24680142 Score: 80
Period size: 20 Copynumber: 5.6 Consensus size: 21
24680016 GAACGTGTCA
* * *
24680026 ATATCATAACA-AATCATACC
1 ATATCATATCATAATCAAATC
*
24680046 ATATCATATCATAA-CGAATC
1 ATATCATATCATAATCAAATC
*
24680066 ATATCATATCATAATGAATCATGCC
1 ATATCATATCATAATCAA--AT--C
*
24680091 ATATCATAACATAA-CAAATC
1 ATATCATATCATAATCAAATC
* * *
24680111 ATATAATATCATAAT-GAATT
1 ATATCATATCATAATCAAATC
*
24680131 GTATCATATCAT
1 ATATCATATCAT
24680143 GTCCTACCCA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
20 53 0.70
21 3 0.04
22 2 0.03
23 2 0.03
24 2 0.03
25 14 0.18
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (21 bp):
ATATCATATCATAATCAAATC
Found at i:24680142 original size:45 final size:45
Alignment explanation
Indices: 24680025--24680129 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
24680015 AGAACGTGTC
** * *
24680025 AATATCATAACAAATCATACCATATCATATCATAACGAATCATAT
1 AATATCATAATGAATCATACCATATCATAACATAACAAATCATAT
* *
24680070 CATATCATAATGAATCATGCCATATCATAACATAACAAATCATAT
1 AATATCATAATGAATCATACCATATCATAACATAACAAATCATAT
24680115 AATATCATAATGAAT
1 AATATCATAATGAAT
24680130 TGTATCATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.30
Consensus pattern (45 bp):
AATATCATAATGAATCATACCATATCATAACATAACAAATCATAT
Found at i:24684788 original size:10 final size:10
Alignment explanation
Indices: 24684775--24684801 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24684765 AAGTCAAACC
24684775 GTTGACCGGT
1 GTTGACCGGT
24684785 GTTGACCGGT
1 GTTGACCGGT
24684795 GTTGACC
1 GTTGACC
24684802 ACCGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.37, T:0.30
Consensus pattern (10 bp):
GTTGACCGGT
Found at i:24684831 original size:7 final size:7
Alignment explanation
Indices: 24684821--24684885 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
24684811 CGACTATTGA
24684821 TTGACCG
1 TTGACCG
*
24684828 TTGA-CT
1 TTGACCG
*
24684834 TTGACCA
1 TTGACCG
*
24684841 TTGATCG
1 TTGACCG
24684848 TTGACCG
1 TTGACCG
*
24684855 TTGA-CT
1 TTGACCG
24684861 TTGACCG
1 TTGACCG
*
24684868 TTGA-CT
1 TTGACCG
24684874 TTGACCG
1 TTGACCG
24684881 TTGAC
1 TTGAC
24684886 TTTTTTTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
6 15 0.33
7 31 0.67
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (7 bp):
TTGACCG
Found at i:24684839 original size:13 final size:13
Alignment explanation
Indices: 24684821--24684888 Score: 109
Period size: 13 Copynumber: 5.2 Consensus size: 13
24684811 CGACTATTGA
24684821 TTGACCGTTGACT
1 TTGACCGTTGACT
* *
24684834 TTGACCATTGATCG
1 TTGACCGTTGA-CT
24684848 TTGACCGTTGACT
1 TTGACCGTTGACT
24684861 TTGACCGTTGACT
1 TTGACCGTTGACT
24684874 TTGACCGTTGACT
1 TTGACCGTTGACT
24684887 TT
1 TT
24684889 TTTTAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 39 0.78
14 11 0.22
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:24684849 original size:20 final size:20
Alignment explanation
Indices: 24684820--24684885 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
24684810 CCGACTATTG
24684820 ATTGACCGTTGACTTTGACC
1 ATTGACCGTTGACTTTGACC
* *
24684840 ATTGATCGTTGACCGTTGA-C
1 ATTGACCGTTGA-CTTTGACC
*
24684860 TTTGACCGTTGACTTTGACC
1 ATTGACCGTTGACTTTGACC
*
24684880 GTTGAC
1 ATTGAC
24684886 TTTTTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTGACCGTTGACTTTGACC
Found at i:24685934 original size:3 final size:3
Alignment explanation
Indices: 24685926--24685966 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
24685916 TCTATTCTAT
24685926 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24685967 TTGGGATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24696376 original size:24 final size:24
Alignment explanation
Indices: 24696265--24696364 Score: 173
Period size: 24 Copynumber: 4.2 Consensus size: 24
24696255 ACTTTGTTTG
*
24696265 GGCTCGTAAGAGCTAATCATTCTG
1 GGCTCGTAAGAGCTAATCATTCTA
24696289 GGCTCGTAAGAGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
* *
24696313 GGCACGTAAGTGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
24696337 GGCTCGTAAGAGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
24696361 GGCT
1 GGCT
24696365 TGTGTTGGCT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATCATTCTA
Found at i:24700751 original size:24 final size:24
Alignment explanation
Indices: 24700714--24700816 Score: 152
Period size: 24 Copynumber: 4.3 Consensus size: 24
24700704 TTAAACTCTG
*
24700714 TCTGGGCTCGTAAGAGGTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
* * * *
24700738 TTTGGGCTCATAAGAGTTAATCAG
1 TCTGGGCTCGTAAGAGCTAATCAT
24700762 TCTGGGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
*
24700786 TCTGGGCTCTTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
24700810 TCTGGGC
1 TCTGGGC
24700817 CCGTGTTGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAT
Found at i:24707986 original size:16 final size:16
Alignment explanation
Indices: 24707965--24707998 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24707955 TAAGTGTTAC
24707965 ATTAATATTATTGAAT
1 ATTAATATTATTGAAT
24707981 ATTAATATTATTGAAT
1 ATTAATATTATTGAAT
24707997 AT
1 AT
24707999 AATGGTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTAATATTATTGAAT
Found at i:24712657 original size:19 final size:19
Alignment explanation
Indices: 24712636--24712700 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
24712626 TAAGTTAACA
24712636 TTTAATTAATTTTTTAAAAT
1 TTTAA-TAATTTTTTAAAAT
*
24712656 TTTAAAAAATATTTTTAATAAT
1 TTT-AATAAT-TTTTTAA-AAT
*
24712678 TTTAATGA-TTTTTAAAAT
1 TTTAATAATTTTTTAAAAT
24712696 TTTAA
1 TTTAA
24712701 AAAATTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.21
19 7 0.18
20 6 0.15
21 12 0.31
22 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAATAATTTTTTAAAAT
Found at i:24725738 original size:21 final size:23
Alignment explanation
Indices: 24725693--24725747 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 23
24725683 AACGTAGGTT
*
24725693 ATATATTAT--TTTTATAATATT
1 ATATATTATAATTTTATAATATC
24725714 ATATATTATAATTTT-TAAT-TC
1 ATATATTATAATTTTATAATATC
*
24725735 ATATTTTAATAAT
1 ATATATT-ATAAT
24725748 AATTATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 16 0.55
22 9 0.31
23 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATTATAATTTTATAATATC
Found at i:24728803 original size:22 final size:23
Alignment explanation
Indices: 24728759--24728801 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
24728749 TGCCAATTAA
*
24728759 TTTTTCCTTTCTTTATTCTTTTG
1 TTTTTCCTTCCTTTATTCTTTTG
24728782 TTTTT-CTTCCTTT-TTCTTTT
1 TTTTTCCTTCCTTTATTCTTTT
24728802 TGAAAATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTTCCTTCCTTTATTCTTTTG
Found at i:24741795 original size:47 final size:47
Alignment explanation
Indices: 24741730--24741824 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
24741720 TGTTTTGAGC
24741730 AGTTAAACATTGATTACATGTTTCCTTATGATGTAGGTATCGATTTG
1 AGTTAAACATTGATTACATGTTTCCTTATGATGTAGGTATCGATTTG
24741777 AGTTAAACATTGATTACATGTTTCCTTATGATGTAGGTATCGATTTG
1 AGTTAAACATTGATTACATGTTTCCTTATGATGTAGGTATCGATTTG
24741824 A
1 A
24741825 AGACAAATCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (47 bp):
AGTTAAACATTGATTACATGTTTCCTTATGATGTAGGTATCGATTTG
Found at i:24743597 original size:15 final size:16
Alignment explanation
Indices: 24743570--24743599 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24743560 TAAGCAAGTA
24743570 AAGAGTGGTAAAAGAC
1 AAGAGTGGTAAAAGAC
24743586 AAGAGT-GTAAAAGA
1 AAGAGTGGTAAAAGA
24743600 GCAATAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.03, G:0.30, T:0.13
Consensus pattern (16 bp):
AAGAGTGGTAAAAGAC
Found at i:24746353 original size:12 final size:12
Alignment explanation
Indices: 24746336--24746383 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
24746326 TTTAAAATTT
24746336 AAAATTTATAAA
1 AAAATTTATAAA
24746348 AAAA-TTATAAA
1 AAAATTTATAAA
24746359 CAAAATTTA-AAA
1 -AAAATTTATAAA
*
24746371 ATAATTTATAAA
1 AAAATTTATAAA
24746383 A
1 A
24746384 TTATAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 14 0.44
12 15 0.47
13 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:24746384 original size:12 final size:12
Alignment explanation
Indices: 24746338--24746384 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
24746328 TAAAATTTAA
24746338 AATTTATAAAA-
1 AATTTATAAAAT
* *
24746349 AAATTATAAACAA
1 AATTTATAAA-AT
24746362 AATTTA-AAAAT
1 AATTTATAAAAT
24746373 AATTTATAAAAT
1 AATTTATAAAAT
24746385 TATAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 16 0.53
12 9 0.30
13 5 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
AATTTATAAAAT
Found at i:24766353 original size:19 final size:19
Alignment explanation
Indices: 24766307--24766355 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
24766297 TTATATATAC
*
24766307 TTTGAATTTTAAAAATTAT
1 TTTGATTTTTAAAAATTAT
*
24766326 TTTCAATTTTTAAAAATTAT
1 TTT-GATTTTTAAAAATTAT
24766346 TTTGATTTTT
1 TTTGATTTTT
24766356 TTGTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTGATTTTTAAAAATTAT
Found at i:24771219 original size:21 final size:21
Alignment explanation
Indices: 24771195--24771248 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
24771185 GTGGTGATGG
*
24771195 TTCTATCGATACAATG-ATGAC
1 TTCTAACGATACAATGCATG-C
* *
24771216 TTCTACCGAAACAATGCATGC
1 TTCTAACGATACAATGCATGC
24771237 TTCTAACGATAC
1 TTCTAACGATAC
24771249 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTAACGATACAATGCATGC
Found at i:24772346 original size:195 final size:195
Alignment explanation
Indices: 24771996--24772441 Score: 569
Period size: 195 Copynumber: 2.3 Consensus size: 195
24771986 TACCAGTACC
* * * *
24771996 CGATGCTGCTCACACGAGCTATCAAGGACTTGTAACATATGCAGTACC-CTAGCCATCGGTACGG
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTC-AGCCATCGATACGG
* * * * **
24772060 TGTCTGTCTATATAATTGTCTTCTAACGATGCTGCTCACACGAGCTATCGGGTGTATGCACTTAT
65 TATCTGTCTATATAACTGTCTCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCACTTAT
* * * * **
24772125 GCGTACGACCTAGCCATCGCAGGGCCTGTAATCCATTCTAGGATTCATGT-CTCTTTTTTTGACT
130 GCATACAACCTAACCATCGCAGGGCCTGTAATCCATTCTAGGATTC-TGTACTCATTTCCTGACT
24772189 CA
194 CA
*
24772191 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
*
24772256 ATCTGTGC-ATATAACTGT-TCCCTAACGATGCTGCTCACACTAGCTATCGAGAATATGCACTTA
66 ATCTGT-CTATATAACTGTCT-CCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCACTTA
* * * * *
24772319 TGCATA-AATCTCAACCATCGTAGGGCCTGTAATCCATTCTTGGGTTCTTTACTCATTTCCTGAC
129 TGCATACAACCT-AACCATCGCAGGGCCTGTAATCCATTCTAGGATTCTGTACTCATTTCCTGAC
*
24772383 TGA
193 TCA
* * *
24772386 CGATACTTCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCAT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCAT
24772442 TGCGTCGGTT
Statistics
Matches: 218, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
194 6 0.03
195 210 0.96
196 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (195 bp):
CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
ATCTGTCTATATAACTGTCTCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCACTTATG
CATACAACCTAACCATCGCAGGGCCTGTAATCCATTCTAGGATTCTGTACTCATTTCCTGACTCA
Found at i:24772939 original size:16 final size:16
Alignment explanation
Indices: 24772915--24772946 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24772905 TCCTTACAAA
*
24772915 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
24772931 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
24772947 AAAAATTTCT
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:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:24781436 original size:17 final size:17
Alignment explanation
Indices: 24781394--24781437 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
24781384 TGTTAGTAAG
*
24781394 CATTGTCACTGCATTTC
1 CATTGTCATTGCATTTC
* *
24781411 CATTGTCATTTCATTTT
1 CATTGTCATTGCATTTC
24781428 CATTGTCATT
1 CATTGTCATT
24781438 ACAATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:24790856 original size:207 final size:207
Alignment explanation
Indices: 24790522--24791096 Score: 603
Period size: 207 Copynumber: 2.7 Consensus size: 207
24790512 TTTTTAGGAT
* * *
24790522 GAAGTTAAAATTTTTAA-TTTTGAAAAAAATGTTTTTGGATTAATTTTTTGTTTGAGAGAAGCAC
1 GAAGTTAAAA-TTTTAACTTTTGAAAAAAATGTTTTTGGATCAATTTTTGGTTTGAGAGAAGTAC
* * * * *
24790586 TTTTTCTCTTAAAAACTAATTTGTTTAGGAATGTTTTTATTCCAAAATTGCTTCTTCAAAATAAT
65 TTTTTCTCTCAAAAAC----TTGTTTAAGAATGTTTTTGTCCCAAAATTGCTTCTTAAAAATAAT
* * * * *
24790651 ACTAAATAAACCCTTAATCATTTTAATTAGGTCTAGTTTAGGAATGCTTCTCAAAAA-TGCTTTG
126 ACTAAATAAACCTTTAATCATTTTAATTAGGTCTAGTTTAAGAAT-ATTCTAAAAAAGTG-TTTC
* **
24790715 GGAAGAAACATTTTTGGGGA
189 GGAA-AAACATTTCTGAAGA
* *
24790735 GAAGTTAAAATTTTAACTTTTG-AAAAAATGTTTTTAGATCAATTTTTGGTTTG-GAGAA-TAGT
1 GAAGTTAAAATTTTAACTTTTGAAAAAAATGTTTTTGGATCAATTTTTGGTTTGAGAGAAGTACT
24790797 TTTTCTCTCAGAAAACTTGTTTAAGAATGTTTTTGTCCCAAAATTGCTTCTTAAAAATAATACTA
66 TTTTCTCTCA-AAAACTTGTTTAAGAATGTTTTTGTCCCAAAATTGCTTCTTAAAAATAATACTA
* * * *
24790862 AATCAACCTTTAATCATTTTAATTAGGTTTAGTTTAAGAATATTTTAAAAAAGTGTTTCTGAAAA
130 AATAAACCTTTAATCATTTTAATTAGGTCTAGTTTAAGAATATTCTAAAAAAGTGTTTCGGAAAA
* *
24790927 GCATTTCTGAATA
195 ACATTTCTGAAGA
* * * *
24790940 GAAGTTAAAATTTTCAGCTTTTGAAAAAAATGCTTTTGGGA-CTAATTTTTGGCTTGAAAGAAGT
1 GAAGTTAAAATTTT-AACTTTTGAAAAAAATG-TTTTTGGATC-AATTTTTGGTTTGAGAGAAGT
* * * * * *
24791004 ATTTTTTTCTCTCAAAAATAACTTGTTTAA-AA-ATATTTGTCTCAAAATAT--TTTTTAAAAAC
63 A-CTTTTTCTCTC--AAA-AACTTGTTTAAGAATGTTTTTGTCCCAAAAT-TGCTTCTTAAAAAT
* *
24791065 AATACTAAACAAACTTTTAATCATTTTAATTA
123 AATACTAAATAAACCTTTAATCATTTTAATTA
24791097 ATCACCTGAA
Statistics
Matches: 310, Mismatches: 38, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
205 24 0.08
206 21 0.07
207 93 0.30
208 18 0.06
209 4 0.01
210 51 0.16
211 33 0.11
212 39 0.13
213 27 0.09
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (207 bp):
GAAGTTAAAATTTTAACTTTTGAAAAAAATGTTTTTGGATCAATTTTTGGTTTGAGAGAAGTACT
TTTTCTCTCAAAAACTTGTTTAAGAATGTTTTTGTCCCAAAATTGCTTCTTAAAAATAATACTAA
ATAAACCTTTAATCATTTTAATTAGGTCTAGTTTAAGAATATTCTAAAAAAGTGTTTCGGAAAAA
CATTTCTGAAGA
Found at i:24791043 original size:14 final size:14
Alignment explanation
Indices: 24791026--24791063 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
24791016 CAAAAATAAC
24791026 TTGTTTAAAAATAT
1 TTGTTTAAAAATAT
* *
24791040 TTGTCTCAAAATAT
1 TTGTTTAAAAATAT
24791054 TT-TTTAAAAA
1 TTGTTTAAAAA
24791064 CAATACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (14 bp):
TTGTTTAAAAATAT
Found at i:24791764 original size:26 final size:27
Alignment explanation
Indices: 24791735--24791786 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
24791725 ATTTCATAAA
24791735 ATATTAAAATATTTTTA-A-AATATTAT
1 ATATTAAAAT-TTTTTATACAATATTAT
*
24791761 ATATTAATATTTTTTATACAATATTA
1 ATATTAAAATTTTTTATACAATATTA
24791787 AAACAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 10 0.43
27 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATTAAAATTTTTTATACAATATTAT
Found at i:24793915 original size:21 final size:23
Alignment explanation
Indices: 24793859--24793915 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
24793849 ATAAAATAAT
* *
24793859 TTTTTAAATTTTTTAAATCATTC
1 TTTTTAAATTTTATAAATCACTC
* *
24793882 TTTTTAAA-ATTAT-AATTACTC
1 TTTTTAAATTTTATAAATCACTC
24793903 -TTTTAAATTTTAT
1 TTTTTAAATTTTAT
24793916 GATGATGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 7 0.25
21 10 0.36
22 3 0.11
23 8 0.29
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTAAATTTTATAAATCACTC
Found at i:24797069 original size:26 final size:25
Alignment explanation
Indices: 24797023--24797072 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
24797013 AATTTAATTT
*
24797023 TTAAAAAATTGTTATTCAAAAAAAA
1 TTAAAAAATTGTTAATCAAAAAAAA
24797048 TTAAAAAAGTTGTTGAAT-AAAAAAA
1 TTAAAAAA-TTGTT-AATCAAAAAAA
24797073 TATTTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 12 0.55
27 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (25 bp):
TTAAAAAATTGTTAATCAAAAAAAA
Found at i:24798852 original size:29 final size:29
Alignment explanation
Indices: 24798810--24798865 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
24798800 ATTGAAAATC
24798810 TACTACTGGAAATAAGCACATTTACTTTG
1 TACTACTGGAAATAAGCACATTTACTTTG
*
24798839 TACTACTGGAAATAAGCACGTTTACTT
1 TACTACTGGAAATAAGCACATTTACTT
24798866 CGTGCTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (29 bp):
TACTACTGGAAATAAGCACATTTACTTTG
Found at i:24800066 original size:20 final size:20
Alignment explanation
Indices: 24800038--24800086 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
24800028 TCATATGGAC
* * *
24800038 ATTCATTAAAGAACCAGAAG
1 ATTCTTTAAAAAACCAAAAG
24800058 ATTCTTTAAAAAACCAAAAG
1 ATTCTTTAAAAAACCAAAAG
24800078 ATTCTTTAA
1 ATTCTTTAA
24800087 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (20 bp):
ATTCTTTAAAAAACCAAAAG
Found at i:24803742 original size:16 final size:16
Alignment explanation
Indices: 24803723--24803778 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
24803713 TAAAAATACA
24803723 TAAAAATATTAAATAT
1 TAAAAATATTAAATAT
24803739 T-AAAATAATTAAATA-
1 TAAAAAT-ATTAAATAT
*
24803754 TAAATAT-TTAAAATAAT
1 TAAAAATATT-AAAT-AT
24803771 TAAAAATA
1 TAAAAATA
24803779 ATATGATCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 10 0.31
16 14 0.44
17 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAATATTAAATAT
Found at i:24803752 original size:23 final size:23
Alignment explanation
Indices: 24803726--24803779 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
24803716 AAATACATAA
24803726 AAATATTAAATA-TTAAAATAATT
1 AAATA-TAAATATTTAAAATAATT
24803749 AAATATAAATATTTAAAATAATT
1 AAATATAAATATTTAAAATAATT
*
24803772 AAAAATAA
1 AAATATAA
24803780 TATGATCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATAAATATTTAAAATAATT
Found at i:24807567 original size:17 final size:17
Alignment explanation
Indices: 24807529--24807567 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
24807519 TATTGCTTCT
*
24807529 TAAAAATACTTTTGGGA
1 TAAAAATACTTTTGAGA
* *
24807546 CAAAAATATTTTTGAGA
1 TAAAAATACTTTTGAGA
24807563 TAAAA
1 TAAAA
24807568 GCATTATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (17 bp):
TAAAAATACTTTTGAGA
Found at i:24808503 original size:22 final size:22
Alignment explanation
Indices: 24808456--24808503 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
24808446 TTTACTCTAT
* *
24808456 AATTTCAAATGTACGAAGATTG
1 AATTTCAAATGTACGAAGACTA
*
24808478 AATTTCAAATGTATGAAGACTA
1 AATTTCAAATGTACGAAGACTA
24808500 AATT
1 AATT
24808504 CCTGAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCAAATGTACGAAGACTA
Found at i:24815121 original size:834 final size:834
Alignment explanation
Indices: 24813511--24816015 Score: 4374
Period size: 834 Copynumber: 3.0 Consensus size: 834
24813501 ATTAGTAACT
*
24813511 ACCCCAGTTGGATCTCTCGATCTCCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
1 ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
*
24813576 TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCATGGATGGGTAATACCAATTTTGGGTTGA
66 TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGATGGGTAATACCAATTTTGGGTTGA
*
24813641 TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGTGTTTGTTTTG-TGCTCTTCCTTTCCC
131 TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTG-TTTGATGCTCTTCCTTTCCC
*
24813705 AACTAGCTGATCCGAAAGGTAAAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCC
195 AAATAGCTGATCCGAAAGGT-AAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCC
* *
24813770 TTAATTCCCTAAAATGGAATAAGTTACTCATGGCTTCTCACTTCATCAATAACATAATATATGAA
259 TTAATTCCCTAAAATGGAATTAGTTCCTCATGGCTTCTCACTTCATCAATAACATAATATATGAA
*
24813835 AACATGTAAATTAAGAATTGAATGAAAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAA
324 AACATGTAAATCAAGAATTGAATGAAAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAA
24813900 TTCCTCGATCGTTTACGCGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAACAAATAAACTAAAA
389 TTCCTCGATCGTTTACGCGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAACAAATAAACTAAAA
* *
24813965 CTGAAAAATTAAAAGCTAACTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAACTTT
454 CTGAAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAGCTTT
* * * * *
24814030 TGCATGGCCGTTTTTCCTCAACCCTAAGTCAGCTACCTTCCTTT-GTGTTTAAGTTGCATTATGA
519 TACATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGT-CTTTCGTGTTTAAGTTGCATTGTGA
*
24814094 AGACGAAAATGGCCCTTGTAGAATGTAGAGTTGGAGTTTGAGGCTGATGTCGCGACACACCAGGA
583 AGACGAAAATGGCCCTTGTAG-ATGTAGAGTTGGAGTTTGAGGCCGATGTCGCGACACACCAGGA
*
24814159 CCTGTGTTGCGATGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAG
647 CCTGTGTTGCGACGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAG
*
24814224 AGCTGTCTATGTCGCGACAAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGTGCA
712 AGCTGTCTATGTCGCGACGAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGTGCA
*
24814289 CTCATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCATCTTAAAAGTAATAATACA
777 CTCATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCACCTTAAAAGTAATAATACA
24814347 ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
1 ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
* * * **
24814412 TGTTACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGGTGGGTAAGATTAATTTTGGGTTGA
66 TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGATGGGTAATACCAATTTTGGGTTGA
** *
24814477 TTCCTGCTTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTGTTTGATGCTCTTCCTTTCCCA
131 TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTGTTTGATGCTCTTCCTTTCCCA
* *
24814542 AATAGTTGATCCGAAAGGTAAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCCCT
196 AATAGCTGATCCGAAAGGTAAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCCTT
* * *
24814607 AATTCTCTAAAATGGAATTAGTTCCTCATGGTTTCTCACTTCATCAGTAACATAATATATGAAAA
261 AATTCCCTAAAATGGAATTAGTTCCTCATGGCTTCTCACTTCATCAATAACATAATATATGAAAA
24814672 CATGTAAATCAAGAATTGAATG-AAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAATT
326 CATGTAAATCAAGAATTGAATGAAAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAATT
* * *
24814736 TCTCGATCGTTTACGTGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAATAAATAAACTAAAACT
391 CCTCGATCGTTTACGCGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAACAAATAAACTAAAACT
24814801 GAAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAGCTTTTA
456 GAAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAGCTTTTA
24814866 CATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGTCTTTCGTGTTTAAGTTGCATTGTGAAGA
521 CATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGTCTTTCGTGTTTAAGTTGCATTGTGAAGA
* *
24814931 CGAAAATGGCCCTTGTATGATGTAGAGTTGGAGTTTGAGGCCGATGTTGCGACACACCAAGACCT
586 CGAAAATGGCCCTTGTA-GATGTAGAGTTGGAGTTTGAGGCCGATGTCGCGACACACCAGGACCT
24814996 GTGTTGCGACGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAGAGC
650 GTGTTGCGACGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAGAGC
* * *
24815061 TGTCTATGTTGCGACGAAGTGGTCAGTATCACTCTGACTTACTGTTACTAGTCTACTGTGCACTC
715 TGTCTATGTCGCGACGAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGTGCACTC
24815126 ATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCACCTTAAAAGTAATAATACA
780 ATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCACCTTAAAAGTAATAATACA
*
24815181 ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCACTAGA
1 ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
*
24815246 TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGATGGGTAATACCAATTTTGGGTTCA
66 TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGATGGGTAATACCAATTTTGGGTTGA
24815311 TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTGTTTGATGCTCTTCCTTTCCCA
131 TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTGTTTGATGCTCTTCCTTTCCCA
*
24815376 AATAGCTGATCCGAAAGGTAAAACCCTTGTAAAACAATAATAAATTATTCATACGTCTACTCCTT
196 AATAGCTGATCCGAAAGGTAAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCCTT
24815441 AATTCCCT-AAATGGAATTAGTTCCTCATGGCTTCTCACTTCATCAATAACATAATATATGAAAA
261 AATTCCCTAAAATGGAATTAGTTCCTCATGGCTTCTCACTTCATCAATAACATAATATATGAAAA
* *
24815505 CATGTAAATCAAGAATTGAATGAAAAAAAAACTAAATTGTATTTAGCGATATATCGGGAAAAATT
326 CATGTAAATCAAGAATTGAATGAAAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAATT
* * * * *
24815570 CCTCGATCATTTACACGAGTTTTTACAATCTCTTTTCAAAAGCTAAAAACAAATAAACTAAAAAT
391 CCTCGATCGTTTACGCGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAACAAATAAACTAAAACT
* *
24815635 -TAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAATGCTAAAGGT-CTATTTATAGCTTTTA
456 GAAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAGCTTTTA
* *
24815698 CATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGTCCTTCGTGTTTATGTTGCATTGTGAAGA
521 CATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGTCTTTCGTGTTTAAGTTGCATTGTGAAGA
* *
24815763 TGAAAATGGCCCTTATAGGATGTAGAGTTGGAGTTTGAGGCCGATGTCGCGACACACCAGGACCT
586 CGAAAATGGCCCTTGTA-GATGTAGAGTTGGAGTTTGAGGCCGATGTCGCGACACACCAGGACCT
* *
24815828 GTGTTGCGACGTAGGAGTCAGTCTTGGAATTCTTCACTGTTGATCCCTTTGTTGTGACATAGAGC
650 GTGTTGCGACGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAGAGC
* *
24815893 TGTCTATGTCGCGACGAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGCGGACTC
715 TGTCTATGTCGCGACGAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGTGCACTC
*
24815958 ATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTTACCTTAAAAGTAATAATACA
780 ATGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCACCTTAAAAGTAATAATACA
24816013 ACC
1 ACC
24816016 ACCTCAGCAC
Statistics
Matches: 1583, Mismatches: 82, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
832 319 0.20
833 125 0.08
834 812 0.51
835 131 0.08
836 196 0.12
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (834 bp):
ACCCCAGTTGGATCTCTCGATCTTCCACTGATATAGTGAGTCGATAGAGATTACTTATCGCTAGA
TGTCACAATCTGAACTGGTTTGGGGAAAAGGTGTTCACGGATGGGTAATACCAATTTTGGGTTGA
TTCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGCGTTTGTTTGATGCTCTTCCTTTCCCA
AATAGCTGATCCGAAAGGTAAAACCCTTGTAAAACAACAATAAATTATTCATACGTCTACTCCTT
AATTCCCTAAAATGGAATTAGTTCCTCATGGCTTCTCACTTCATCAATAACATAATATATGAAAA
CATGTAAATCAAGAATTGAATGAAAAAAAAACTAAATTGTATTAAGCGATCTATCGGGAAAAATT
CCTCGATCGTTTACGCGAGTTTCTACAATCTCGTTTCAAAAGCTAAAAACAAATAAACTAAAACT
GAAAAATTAAAAGCTAAGTAATTGTGTCTAAACCCTAGTGCTAAAGGTCCTATTTATAGCTTTTA
CATGGTCGTTTTTCCTCAACCTTAAGTCAGCTACCGTCTTTCGTGTTTAAGTTGCATTGTGAAGA
CGAAAATGGCCCTTGTAGATGTAGAGTTGGAGTTTGAGGCCGATGTCGCGACACACCAGGACCTG
TGTTGCGACGTAGGAGGCAGTCTTGGAATTCTTCACTGCTGATCCCTTTGTTGTGACATAGAGCT
GTCTATGTCGCGACGAAGTGGTCAGTATCACTATGACTTACTGCTACTAGTCTACTGTGCACTCA
TGAAGTATGTTAGCTAACCTTTAGGCCTTGTTTCACCTTAAAAGTAATAATACA
Found at i:24826581 original size:12 final size:10
Alignment explanation
Indices: 24826551--24826587 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
24826541 TTATATTTTT
24826551 AAAAAATATA
1 AAAAAATATA
24826561 AAAAAATATA
1 AAAAAATATA
24826571 AAAGAATATATA
1 AAA-AA-ATATA
24826583 AAAAA
1 AAAAA
24826588 GTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 13 0.52
11 4 0.16
12 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAAAATATA
Found at i:24826638 original size:23 final size:22
Alignment explanation
Indices: 24826611--24826658 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
24826601 AAATCTAGAA
*
24826611 AAAAAACCTAAAACAAAACCCC
1 AAAAAACCTAAAACAAAAACCC
* *
24826633 CAAAAACCTTAAACAAAAACCC
1 AAAAAACCTAAAACAAAAACCC
24826655 AAAA
1 AAAA
24826659 CTGATCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.29, G:0.00, T:0.06
Consensus pattern (22 bp):
AAAAAACCTAAAACAAAAACCC
Found at i:24826884 original size:22 final size:21
Alignment explanation
Indices: 24826859--24826914 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
24826849 CCAAAACAAT
24826859 ATAAAAATGTACATA-AAATACC
1 ATAAAAATGT-C-TACAAATACC
24826881 AT-AAAATGTCTACTAAATACC
1 ATAAAAATGTCTAC-AAATACC
24826902 AT-AAAATGTCTAC
1 ATAAAAATGTCTAC
24826915 TTATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 27 0.84
22 2 0.06
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (21 bp):
ATAAAAATGTCTACAAATACC
Found at i:24826915 original size:21 final size:21
Alignment explanation
Indices: 24826874--24826915 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24826864 AATGTACATA
24826874 AAATACCATAAAATGTCTACT
1 AAATACCATAAAATGTCTACT
24826895 AAATACCATAAAATGTCTACT
1 AAATACCATAAAATGTCTACT
24826916 TATTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (21 bp):
AAATACCATAAAATGTCTACT
Found at i:24827035 original size:16 final size:16
Alignment explanation
Indices: 24827007--24827051 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
24826997 AAATTTTATT
24827007 TTTTAA-ATT-AAATA
1 TTTTAATATTAAAATA
24827021 TTTTAATATTAAAATA
1 TTTTAATATTAAAATA
*
24827037 TTAT-ATATTCAAAAT
1 TTTTAATATT-AAAAT
24827052 CAACAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTAATATTAAAATA
Found at i:24827673 original size:22 final size:22
Alignment explanation
Indices: 24827631--24827697 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
24827621 GCTCTCCGTT
* *
24827631 ATTTAGCACGTATAGTGCTCTCC
1 ATTTAGCACAT-TTGTGCTCTCC
24827654 ATTTAGCACATTTGTGCTCTCC
1 ATTTAGCACATTTGTGCTCTCC
* * *
24827676 GTTTAACACCTTTGTGCTCTCC
1 ATTTAGCACATTTGTGCTCTCC
24827698 GTTCATGAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 29 0.74
23 10 0.26
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.39
Consensus pattern (22 bp):
ATTTAGCACATTTGTGCTCTCC
Found at i:24827698 original size:22 final size:22
Alignment explanation
Indices: 24827645--24827700 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
24827635 AGCACGTATA
* *
24827645 GTGCTCTCCATTTAGCACATTT
1 GTGCTCTCCGTTTAACACATTT
*
24827667 GTGCTCTCCGTTTAACACCTTT
1 GTGCTCTCCGTTTAACACATTT
24827689 GTGCTCTCCGTT
1 GTGCTCTCCGTT
24827701 CATGAGCGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.16, T:0.41
Consensus pattern (22 bp):
GTGCTCTCCGTTTAACACATTT
Found at i:24839615 original size:16 final size:16
Alignment explanation
Indices: 24839591--24839634 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
24839581 TGTTGATTAT
24839591 ATATATATTTTTATAA
1 ATATATATTTTTATAA
* * *
24839607 ATTTATATTTATATTA
1 ATATATATTTTTATAA
24839623 ATATAT-TTTTTA
1 ATATATATTTTTA
24839635 ATTCCAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATATTTTTATAA
Found at i:24840204 original size:2 final size:2
Alignment explanation
Indices: 24840197--24840241 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
24840187 TAAAGCGAGC
24840197 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24840239 GA G
1 GA G
24840242 GCTAAGGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24857340 original size:20 final size:22
Alignment explanation
Indices: 24857298--24857344 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
24857288 ACTACACCAA
24857298 AGGCATCGAAGATGCATAACAG
1 AGGCATCGAAGATGCATAACAG
*
24857320 AGGCATCGAAG-TGTA-AACAG
1 AGGCATCGAAGATGCATAACAG
24857340 AGGCA
1 AGGCA
24857345 CCAAAGTGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 11 0.46
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (22 bp):
AGGCATCGAAGATGCATAACAG
Found at i:24857351 original size:20 final size:20
Alignment explanation
Indices: 24857315--24857352 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24857305 GAAGATGCAT
* *
24857315 AACAGAGGCATCGAAGTGTA
1 AACAGAGGCACCAAAGTGTA
24857335 AACAGAGGCACCAAAGTG
1 AACAGAGGCACCAAAGTG
24857353 CGAACCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.11
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGTA
Found at i:24862075 original size:11 final size:11
Alignment explanation
Indices: 24862061--24862136 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
24862051 GATAATCACT
24862061 TTAATATTAAA
1 TTAATATTAAA
24862072 TTAATA--AAA
1 TTAATATTAAA
*
24862081 -TACTATTAAA
1 TTAATATTAAA
*
24862091 ATAAGTATTAAA
1 TTAA-TATTAAA
24862103 TTAA-ATTTAATA
1 TTAATA-TTAA-A
24862115 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
24862128 ATAATATTA
1 TTAATATTA
24862137 TTTTAGAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:24862076 original size:20 final size:18
Alignment explanation
Indices: 24862029--24862135 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 18
24862019 CAAGATAAAC
24862029 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
24862046 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
24862066 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
24862085 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
24862102 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
24862122 ATTAAAATAATATT
1 ATTAAATTAATATT
24862136 ATTTTAGAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
17 16 0.23
18 9 0.13
19 22 0.31
20 23 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:24862123 original size:37 final size:36
Alignment explanation
Indices: 24862061--24862136 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
24862051 GATAATCACT
24862061 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
24862098 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
24862134 TTA
1 TTA
24862137 TTTTAGAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:24874849 original size:21 final size:21
Alignment explanation
Indices: 24874825--24874882 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
24874815 TAGAGGTAAA
24874825 ACTTGTATCAGTAGAA-GAGTC
1 ACTTGTATCAGTAGAACGA-TC
* *
24874846 ACTTGTATCAATAGAACTATC
1 ACTTGTATCAGTAGAACGATC
*
24874867 ACTTGTATCGGTAGAA
1 ACTTGTATCAGTAGAA
24874883 ATTTGCACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACGATC
Found at i:24881927 original size:40 final size:41
Alignment explanation
Indices: 24881871--24881963 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
24881861 AATTTTCAAA
* **
24881871 AAATCGAAGTAAATATATTAGCACATAGTGCATCATTGGAT
1 AAATCGAAGTAAATATACTAGCACATAGTGCATCACCGGAT
* *
24881912 AAATCG-AGTAAATATACTGGCACGTAGTGCATCACCGGAT
1 AAATCGAAGTAAATATACTAGCACATAGTGCATCACCGGAT
24881952 AAATCGAAGTAA
1 AAATCGAAGTAA
24881964 TTTGCGCTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 35 0.76
41 11 0.24
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (41 bp):
AAATCGAAGTAAATATACTAGCACATAGTGCATCACCGGAT
Found at i:24882074 original size:62 final size:62
Alignment explanation
Indices: 24881925--24882143 Score: 273
Period size: 62 Copynumber: 3.6 Consensus size: 62
24881915 TCGAGTAAAT
* * * *
24881925 ATACTGGCACGTAGTGCATCACCGGATAAATCGAAGTAATTTGCGCTCA--GCTAACATGTC
1 ATACTGGCACATAGTGCATCACCGGATAAACCGAAGTAATTTGCGCTCAGGGCTATCATATC
* * *
24881985 ATATTGGGACATAGTGCATCATCGGATAAACCGAAGTAATTTGCGCTCAGGGCTATCATATC
1 ATACTGGCACATAGTGCATCACCGGATAAACCGAAGTAATTTGCGCTCAGGGCTATCATATC
* * * * * *
24882047 ATACTAGCCCATAGTGCATCACCGGATAAACCGAAGTAATCTGTGCTCAGGACTATCATTTC
1 ATACTGGCACATAGTGCATCACCGGATAAACCGAAGTAATTTGCGCTCAGGGCTATCATATC
* *
24882109 ATACTGGCACATCA-TGCATCATCGTATAAACCGAA
1 ATACTGGCACAT-AGTGCATCACCGGATAAACCGAA
24882144 ATATAAACCT
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 44 0.32
62 91 0.67
63 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (62 bp):
ATACTGGCACATAGTGCATCACCGGATAAACCGAAGTAATTTGCGCTCAGGGCTATCATATC
Found at i:24895046 original size:29 final size:28
Alignment explanation
Indices: 24895013--24895263 Score: 121
Period size: 29 Copynumber: 8.7 Consensus size: 28
24895003 AAACTGTTTA
*
24895013 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTAACCCC-AACTTTCC
*
24895042 AAAATT-CCATTTTAACCCCGA-TTTCACC
1 AAAATTACCATTTTAACCCCAACTTT--CC
* *
24895070 AAAAATTACCATTTT-ACCCTTGAACTTCCC
1 -AAAATTACCATTTTAACCC--CAACTTTCC
** *
24895100 AAAA-T-CTTGTTTTAACCCCGA-TTTCACC
1 AAAATTAC-CATTTTAACCCCAACTTT--CC
24895128 AAAAATTACCATTTT-ACCCTCGAACTTTCC
1 -AAAATTACCATTTTAACCC-C-AACTTTCC
* *
24895158 AAAA-TCCCATCTTTAACCCCGA-TTTCACC
1 AAAATTACCAT-TTTAACCCCAACTTT--CC
* *
24895187 AAAAATTACCATTTTATCCCGAACTTTCC
1 -AAAATTACCATTTTAACCCCAACTTTCC
* *
24895216 AAAA-TCCCATTTTAACCTCAA-TTTCACC
1 AAAATTACCATTTTAACCCCAACTTT--CC
*
24895244 AAAAATTA-CATTTTTACCCC
1 -AAAATTACCATTTTAACCCC
24895264 CGAAAGTAAA
Statistics
Matches: 168, Mismatches: 26, Indels: 56
0.67 0.10 0.22
Matches are distributed among these distances:
26 8 0.05
27 19 0.11
28 33 0.20
29 58 0.35
30 34 0.20
31 11 0.07
32 5 0.03
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTAACCCCAACTTTCC
Found at i:24895278 original size:58 final size:58
Alignment explanation
Indices: 24895012--24895267 Score: 372
Period size: 58 Copynumber: 4.4 Consensus size: 58
24895002 TAAACTGTTT
* *
24895012 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTAACCCCGATTTCACC
** * ***
24895070 AAAAATTACCATTTTACCCTTGAACTTCCCAAAATCTTGTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTAACCCCGATTTCACC
*
24895128 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATCCCATCTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCAT-TTTAACCCCGATTTCACC
* * *
24895187 AAAAATTACCATTTTA-TCCCGAACTTTCCAAAATCCCATTTTAACCTCAATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTAACCCCGATTTCACC
24895244 AAAAATTA-CATTTTTACCCCCGAA
1 AAAAATTACCA-TTTTACCCCCGAA
24895268 AGTAAAAAAA
Statistics
Matches: 177, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
56 2 0.01
57 29 0.16
58 112 0.63
59 34 0.19
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTAACCCCGATTTCACC
Found at i:24907780 original size:201 final size:200
Alignment explanation
Indices: 24907416--24908256 Score: 1132
Period size: 201 Copynumber: 4.2 Consensus size: 200
24907406 GGAATAGTTC
* * * * *
24907416 AACAAGTGAGGCGGTCATCTTCTTGATGAGATATAAAGAAGAATATCAACTCAACGCTCAACACG
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACG
* * *
24907481 AGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAAAGGTT
66 AGCAAATCTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGTT
* *
24907546 AGCTTTCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGGTCCAGAGAAGCGA
131 AGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
24907611 ATTAA
196 ATTAA
*
24907616 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCATCGCTCAAACAC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTC-AACAC
** *
24907681 GAGCAAATCTTCGGACTCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
65 GAGCAAATCTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
* * * *
24907746 TAACTTCCTGACGAGACACAGAGAAGTAGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
130 TAGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
24907811 AATTAA
195 AATTAA
* *
24907817 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGCGCTCAAACAC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTC-AACAC
* * * *
24907882 GAGCAAATCTTCAGACTCAGCTTTCTGATGAGACATTGAGAAGCAAGTCGAAGCAATAAAAAGGT
65 GAGCAAATCTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
*
24907947 TAGCTTCCTGATGAGACACAGAA-AAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAGC
130 TAGCTTCCTGATGAGACACA-AAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGC
24908011 GAA-T--
194 GAATTAA
* ** * *
24908015 -------GATGCGGTTGTCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCA
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACG
* * * * * * *
24908073 AGCAAGTTTTCAAACCCAGCTTCCTGATGA-AGTACTGAGAAGCAGGTCGAAGCAGTAAAAATGC
66 AGCAAATCTTCAAACCCAGCTTCCTGATGAGA-CACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
* *
24908137 TAGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTAAGGAGATCCGGAGAAGCG
130 TAGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
24908202 AATTAA
195 AATTAA
** * * * *
24908208 AACAAATGATTGCGGTCATCCT-CTCGATGAGACACAGAGAAGAAGACCA
1 AACAAGCGA-GGCGGTCATCTTCCT-GATGAGATACAGAGAAGAATACCA
24908257 GTTCAAGAAA
Statistics
Matches: 573, Mismatches: 52, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
189 3 0.01
190 116 0.20
191 48 0.08
200 58 0.10
201 347 0.61
202 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (200 bp):
AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACG
AGCAAATCTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGTT
AGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
ATTAA
Found at i:24909432 original size:3 final size:3
Alignment explanation
Indices: 24909426--24909468 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
24909416 TATGGCATTC
* * *
24909426 ATA ATA ATA ATG TTA ATA ATA ATA ATA ATA ATA TATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
24909469 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:24909444 original size:12 final size:12
Alignment explanation
Indices: 24909427--24909468 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
24909417 ATGGCATTCA
*
24909427 TAATAATAATGT
1 TAATAATAATAT
*
24909439 TAATAATAATAA
1 TAATAATAATAT
24909451 TAATAATATATAT
1 TAATAATA-ATAT
24909464 TAATA
1 TAATA
24909469 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:24910173 original size:32 final size:33
Alignment explanation
Indices: 24910131--24910199 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
24910121 TTATTTGCGT
* *
24910131 ATTTGGTCCTTCCACAT-TTTTTAATTA-TTTTA
1 ATTTAGTCCTT-CACATACTTTTAATTATTTTTA
**
24910163 ATTTAGTCCTTTTCATACTTTTAATTATTTTTA
1 ATTTAGTCCTTCACATACTTTTAATTATTTTTA
24910196 ATTT
1 ATTT
24910200 GGCCTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 3 0.10
32 19 0.61
33 9 0.29
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.59
Consensus pattern (33 bp):
ATTTAGTCCTTCACATACTTTTAATTATTTTTA
Found at i:24910542 original size:30 final size:30
Alignment explanation
Indices: 24910508--24910669 Score: 131
Period size: 30 Copynumber: 5.5 Consensus size: 30
24910498 CAAACTTTCC
24910508 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
* * ** *
24910538 AAAATTAC-TATTTTACCCCCGAACTC-CCT
1 AAAATTCCAT-TTTTAACCCCGATTTCACCA
* * *
24910567 AAAATCCCGTTTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
*
24910597 AAAATTTCCA-TTTTACCCCCGAACTTT--CC-
1 AAAA-TTCCATTTTTAACCCCG-A-TTTCACCA
* *
24910626 AAAATCCCA-TTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
*
24910655 AAAATTACATTTTTA
1 AAAATTCCATTTTTA
24910670 CCCTCAAAAG
Statistics
Matches: 101, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 15 0.15
29 32 0.32
30 43 0.43
31 4 0.04
32 3 0.03
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:24910571 original size:59 final size:59
Alignment explanation
Indices: 24910478--24910672 Score: 288
Period size: 59 Copynumber: 3.3 Consensus size: 59
24910468 TAAACTATTT
* * *
24910478 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * *
24910537 AAAAATTACTATTTTACCCCCGAAC-TCCCTAAAATCCCGTTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCC-AAAATCCCATTTTTAACCTCGATTTCACC
*
24910596 AAAAATTTCCATTTTACCCCCGAACTTTCCAAAATCCCA-TTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
24910654 AAAAATTA-CATTTTTACCC
1 AAAAATTACCA-TTTTACCC
24910673 TCAAAAGTCC
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
57 2 0.02
58 37 0.30
59 80 0.66
60 3 0.02
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
Found at i:24912879 original size:30 final size:30
Alignment explanation
Indices: 24912845--24912910 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
24912835 AAGGAAAAAT
* *
24912845 GAGGTCAAAAATGAAATTTTAGAAAGTTTG
1 GAGGTCAAAAATAAAATTTTAGAAAGTTTA
* **
24912875 GAGGTTAAATTTAAAATTTTAGAAAGTTTA
1 GAGGTCAAAAATAAAATTTTAGAAAGTTTA
24912905 GAGGTC
1 GAGGTC
24912911 GAATTCCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
GAGGTCAAAAATAAAATTTTAGAAAGTTTA
Found at i:24912983 original size:30 final size:29
Alignment explanation
Indices: 24912858--24913031 Score: 131
Period size: 30 Copynumber: 5.9 Consensus size: 29
24912848 GTCAAAAATG
* *
24912858 AAATTTTAGAAAGTTTG-GAGGTTAAATTTA
1 AAATTTTAGAAAGTTTGAG-GGTCAAA-TTC
*
24912888 AAATTTTAGAAAGTTT-AGAGGTCGAATTC
1 AAATTTTAGAAAGTTTGAG-GGTCAAATTC
* * * *
24912917 CAATTTTTGTAAAGTTT-AAGGTCAAATTG
1 AAATTTTAG-AAAGTTTGAGGGTCAAATTC
* *
24912946 GAATTTTCAAAAAGTTTGAGGGTCAAATTC
1 AAATTTT-AGAAAGTTTGAGGGTCAAATTC
* * *
24912976 AAATTTTCGGAAAGTATG-GGGTCAAACTC
1 AAATTTT-AGAAAGTTTGAGGGTCAAATTC
* *
24913005 AAATTTTTGGAAAGTTTGGGGGTCAAA
1 AAA-TTTTAGAAAGTTTGAGGGTCAAA
24913032 AAATTATTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
29 52 0.44
30 67 0.56
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (29 bp):
AAATTTTAGAAAGTTTGAGGGTCAAATTC
Found at i:24916239 original size:12 final size:13
Alignment explanation
Indices: 24916213--24916242 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
24916203 TCGGACTCAT
24916213 AAATATTTAATAA
1 AAATATTTAATAA
24916226 AAATATTT-ATAA
1 AAATATTTAATAA
24916238 AAATA
1 AAATA
24916243 AATTGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATATTTAATAA
Found at i:24919444 original size:21 final size:21
Alignment explanation
Indices: 24919420--24919473 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
24919410 AGAAGTTTAG
24919420 GTTGTATCGGTAGAAC-CCAGA
1 GTTGTATCGGTAGAACTCC-GA
*
24919441 GTTGTATCGGTAGAACTCCTA
1 GTTGTATCGGTAGAACTCCGA
*
24919462 GTTCTATCGGTA
1 GTTGTATCGGTA
24919474 AAATTCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
GTTGTATCGGTAGAACTCCGA
Found at i:24922872 original size:29 final size:30
Alignment explanation
Indices: 24922809--24922877 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
24922799 GTGAAAAAAG
* *
24922809 TGAAAAG-TGATAGGTCAAAGTATGAATAT
1 TGAAAAGTTGAGAGGTCAAAGTATAAATAT
* * *
24922838 TCAAAAGTTGAGAGGTTAAAGTGTAAAT-T
1 TGAAAAGTTGAGAGGTCAAAGTATAAATAT
24922867 TGAAAAGTTGA
1 TGAAAAGTTGA
24922878 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.29
Consensus pattern (30 bp):
TGAAAAGTTGAGAGGTCAAAGTATAAATAT
Found at i:24924259 original size:4 final size:4
Alignment explanation
Indices: 24924250--24924465 Score: 69
Period size: 4 Copynumber: 53.8 Consensus size: 4
24924240 TATGACATAC
* *
24924250 AAAT AAAT -AAT AAAT AAAT CAAT AAAATT AAAT -AAT GAAT AAAT ATAATT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT AAAT AAAT AAAT A-AA-T
* * * * *
24924300 AAAT AAAGGT AAAG ATAT AAAT AGCAT AAA- AAAT -AAC AAAT ATAT AAAAT
1 AAAT AAA--T AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT -AAAT
* * ** *
24924350 ACAT AAA- AAAT AAAT AAAT AAAGTT AAAT AAAG GCA- AAAT -TAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAA--T AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
24924397 AACAT -AA- AAAT GAAT -AAC AAAT AAAT AAAT AAAAG AAGAA AAAT AAAT
1 AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT AAAT AAAT
* *
24924445 AAA- AATT AAAT -ACT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAA
24924466 ATAATGCAAA
Statistics
Matches: 155, Mismatches: 32, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
3 26 0.17
4 95 0.61
5 23 0.15
6 11 0.07
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:24924394 original size:75 final size:77
Alignment explanation
Indices: 24924278--24924425 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 77
24924268 TCAATAAAAT
* * * *
24924278 TAAATAATGAATAAATATAATTAAATAAAGGTAAAGATATAAATAGCAT-AAAA-AATAACAAAT
1 TAAAAAATAAATAAATATAATTAAATAAAGGCAAAGATATAAATAACATAAAAAGAATAACAAAT
*
24924341 ATATAAAATACA
66 AAATAAAATACA
24924353 TAAAAAATAAATAAATA-AAGTTAAATAAAGGCAAA-ATTATAAATAACATAAAAATGAATAACA
1 TAAAAAATAAATAAATATAA-TTAAATAAAGGCAAAGA-TATAAATAACATAAAAA-GAATAACA
24924416 AATAAATAAA
63 AATAAATAAA
24924426 TAAAAGAAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
74 3 0.05
75 40 0.63
76 4 0.06
78 16 0.25
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (77 bp):
TAAAAAATAAATAAATATAATTAAATAAAGGCAAAGATATAAATAACATAAAAAGAATAACAAAT
AAATAAAATACA
Found at i:24924424 original size:26 final size:22
Alignment explanation
Indices: 24924391--24924447 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 22
24924381 AGGCAAAATT
*
24924391 ATAAATAACATAAAAATGAATAACAA
1 ATAAATAA-AT-AAAA-GAAGAA-AA
24924417 ATAAATAAATAAAAGAAGAAAA
1 ATAAATAAATAAAAGAAGAAAA
24924439 ATAAATAAA
1 ATAAATAAA
24924448 AATTAAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.37
23 5 0.17
24 4 0.13
25 2 0.07
26 8 0.27
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.18
Consensus pattern (22 bp):
ATAAATAAATAAAAGAAGAAAA
Found at i:24956885 original size:22 final size:22
Alignment explanation
Indices: 24956856--24956903 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
24956846 CGCAAGCACT
*
24956856 CTTC-AACATCTCTTGATTTTG
1 CTTCTAACATCTCTTGATTCTG
24956877 CTTCTAACATCTCTTGATTCTG
1 CTTCTAACATCTCTTGATTCTG
24956899 CTTCT
1 CTTCT
24956904 TTCTCATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48
Consensus pattern (22 bp):
CTTCTAACATCTCTTGATTCTG
Found at i:24970463 original size:6 final size:6
Alignment explanation
Indices: 24970452--24970490 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
24970442 TGATCAAAAT
* * *
24970452 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
24970491 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:24980466 original size:17 final size:17
Alignment explanation
Indices: 24980446--24980497 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
24980436 TTTAAGTTAG
24980446 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*** *
24980463 ATTTGCATAAAATTTAA
1 ATTTATTTTAAATTTAA
*
24980480 ATTTATTATAAATTTAA
1 ATTTATTTTAAATTTAA
24980497 A
1 A
24980498 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:24981241 original size:10 final size:10
Alignment explanation
Indices: 24981226--24981259 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
24981216 AACCAAACTC
*
24981226 ATTAATATTA
1 ATTAATAATA
24981236 ATTAATAATA
1 ATTAATAATA
*
24981246 ATAAATAATA
1 ATTAATAATA
24981256 ATTA
1 ATTA
24981260 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAATAATA
Found at i:24982345 original size:30 final size:29
Alignment explanation
Indices: 24982311--24982470 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
24982301 TGAACTTTCT
24982311 AAAATTCCATTTTTAACCCCAATTTCACC
1 AAAATTCCATTTTTAACCCCAATTTCACC
*
24982340 AAAAATTACCA-TTTTACCCCCAAACTTT--CC
1 -AAAATT-CCATTTTTAACCCC-AA-TTTCACC
*
24982370 AAAATTCCATTTTTAACCCCAGTTTCACC
1 AAAATTCCATTTTTAACCCCAATTTCACC
24982399 AAAAATTACCA-TTTT-ACCCTCGAAATTT--CC
1 -AAAATT-CCATTTTTAACCC-C--AATTTCACC
*
24982429 AAAA-TCTCATTTTTAACCCCGATTTCACC
1 AAAATTC-CATTTTTAACCCCAATTTCACC
24982458 AAAATTCCATTTT
1 AAAATTCCATTTT
24982471 GCCCCCGGAG
Statistics
Matches: 108, Mismatches: 5, Indels: 35
0.73 0.03 0.24
Matches are distributed among these distances:
27 8 0.07
28 7 0.06
29 42 0.39
30 36 0.33
31 8 0.07
32 7 0.06
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCAATTTCACC
Found at i:24982396 original size:59 final size:59
Alignment explanation
Indices: 24982303--24982476 Score: 250
Period size: 59 Copynumber: 3.0 Consensus size: 59
24982293 CTAGTCCCTG
* *
24982303 AACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCA
1 AACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACCATTTTACCCCCA
*
24982362 AACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACCATTTTACCCTCGA
1 AACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACCATTTTACCC-CCA
*
24982422 AA-TTTCCAAAA-TCTCATTTTTAACCCC-GATTTCACC-AAAATT-CCATTTTGCCCCC
1 AACTTTCCAAAATTC-CATTTTTAACCCCAG-TTTCACCAAAAATTACCATTTTACCCCC
24982477 GGAGGTCAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 9
0.88 0.04 0.07
Matches are distributed among these distances:
56 1 0.01
57 10 0.09
58 9 0.08
59 83 0.78
60 4 0.04
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (59 bp):
AACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACCATTTTACCCCCA
Found at i:24995117 original size:114 final size:114
Alignment explanation
Indices: 24994859--24995109 Score: 457
Period size: 114 Copynumber: 2.2 Consensus size: 114
24994849 AGGTGGTCAT
*
24994859 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCAAGCAAATCTTCGAACCAA
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCGAACCAA
24994924 GCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAG
66 GCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAG
* *
24994973 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAATGCGAGCAAATCTTCGAACCAA
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCGAACCAA
*
24995038 GCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAG
66 GCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAG
*
24995087 CTTCTTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
24995110 TGGACCAAAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 132 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (114 bp):
CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCGAACCAA
GCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAG
Found at i:24995230 original size:314 final size:314
Alignment explanation
Indices: 24994659--24995260 Score: 965
Period size: 314 Copynumber: 1.9 Consensus size: 314
24994649 AGGCGATCAT
* * ** * *
24994659 CTTCCTGATGAGATGCAGAGAAGAGCACCAACTCAATGCTCAATGCGAGCAAATTTTCGAACCCA
1 CTTCCTGATGAGATACAGAGAAGAACACCAACTCAACACTCAATGCGAGCAAATCTTCGAACCAA
* *
24994724 GCTTCTTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGATAC
66 GCTTCCTGATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGATAC
* * *
24994789 AAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGCGAGGTG
131 AAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGAGAATTAAAACAAGCGAGGCG
* *
24994854 GTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCAAGCAAATCTTCGA
196 GTCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCGA
* *
24994919 AC-CAAGCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAG
261 ACTC-AGCTTCCTGATAAGACACTAAGAAGCAAGTCAAAGCAATAAAATGGTTAG
*
24994973 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAATGCGAGCAAATCTTCGAACCAA
1 CTTCCTGATGAGATACAGAGAAGAACACCAACTCAACACTCAATGCGAGCAAATCTTCGAACCAA
* *
24995038 GCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATAC
66 GCTTCCTGATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGATAC
* * *
24995103 AGAGAAGTGGACCAAATTCGTCTTCCTTAGGAGATCCAAAGAAGAGAATTGAAACGAA-CGAGGC
131 AAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGAGAATTAAAAC-AAGCGAGGC
* *
24995167 GGTCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACACTCAACGCGAGCCAATCTTCG
195 GGTCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCG
24995232 AACTCAGCTTCCTGATAAGACACTAAGAA
260 AACTCAGCTTCCTGATAAGACACTAAGAA
24995261 ACAGGTCGAA
Statistics
Matches: 263, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
314 260 0.99
315 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (314 bp):
CTTCCTGATGAGATACAGAGAAGAACACCAACTCAACACTCAATGCGAGCAAATCTTCGAACCAA
GCTTCCTGATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGATAC
AAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGAGAATTAAAACAAGCGAGGCG
GTCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACACTCAACGCAAGCAAATCTTCGA
ACTCAGCTTCCTGATAAGACACTAAGAAGCAAGTCAAAGCAATAAAATGGTTAG
Found at i:24995651 original size:17 final size:17
Alignment explanation
Indices: 24995611--24995682 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
24995601 CAATGAGATA
*
24995611 TAAATTTAGTTTT-AAGT
1 TAAATTTA-TTTTAAATT
*
24995628 TAGATTTATTTTAAATT
1 TAAATTTATTTTAAATT
*** *
24995645 TAAATTTGCATAAAATT
1 TAAATTTATTTTAAATT
*
24995662 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
24995679 TAAA
1 TAAA
24995683 ATTAAAATTA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
16 4 0.10
17 38 0.90
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:24996426 original size:10 final size:10
Alignment explanation
Indices: 24996411--24996444 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
24996401 AACCAAACTC
*
24996411 ATTAATATTA
1 ATTAATAATA
24996421 ATTAATAATA
1 ATTAATAATA
*
24996431 ATAAATAATA
1 ATTAATAATA
24996441 ATTA
1 ATTA
24996445 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAATAATA
Found at i:24997626 original size:59 final size:59
Alignment explanation
Indices: 24997534--24997825 Score: 405
Period size: 59 Copynumber: 5.0 Consensus size: 59
24997524 CTAGTCCCCG
* *
24997534 AACTTTCCAAAATTCCATTTTTAA-CCTCGGTTTCACCATAAATTACCATTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCCT-AGTTTCACCAAAAATTACCATTTTACCCCTA
* *
24997593 AACTTTCCAAATTTCCATTTTTAACCCTAGTTTCACCAAAAATTATCATTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCCTAGTTTCACCAAAAATTACCATTTTACCCCTA
*
24997652 AACTTTCCAAAATTCCATTTTGTAA-CCTCGATTTCACCAAAAATTACCATTTTA-CCCTCA
1 AACTTTCCAAAATTCCATTTT-TAACCCTAG-TTTCACCAAAAATTACCATTTTACCCCT-A
* * *
24997712 AACTTTCCAAAATTCTATTTTTAACCCTAATTTCACCAAAAATTACCATTTTACCCCCA
1 AACTTTCCAAAATTCCATTTTTAACCCTAGTTTCACCAAAAATTACCATTTTACCCCTA
* * * *
24997771 AACTTTCCAAAATCCCATTTTTAACCCCAATTTCACC-AAAATT-CCATTTTGCCCC
1 AACTTTCCAAAATTCCATTTTTAACCCTAGTTTCACCAAAAATTACCATTTTACCCC
24997826 CGGAGATCAA
Statistics
Matches: 212, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
57 11 0.05
58 6 0.03
59 140 0.66
60 55 0.26
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (59 bp):
AACTTTCCAAAATTCCATTTTTAACCCTAGTTTCACCAAAAATTACCATTTTACCCCTA
Found at i:24997631 original size:29 final size:30
Alignment explanation
Indices: 24997540--24997820 Score: 80
Period size: 29 Copynumber: 9.5 Consensus size: 30
24997530 CCCGAACTTT
* **
24997540 CCAAAATTCCATTTTTAA-CCTCGGTTTCA
1 CCAAATTTCCATTTTTAACCCTAAGTTTCA
* * *
24997569 CCATAAATTACCA-TTTTACCCCTAAACTTT--
1 CC--AAATTTCCATTTTTAACCCT-AAGTTTCA
24997599 CCAAATTTCCATTTTTAACCCT-AGTTTCA
1 CCAAATTTCCATTTTTAACCCTAAGTTTCA
* *
24997628 CCAAAAATTAT-CA-TTTTACCCCTAAACTTT--
1 CC--AAATT-TCCATTTTTAACCCT-AAGTTTCA
* *
24997658 CCAAAATTCCATTTTGTAA-CCT-CGATTTCA
1 CCAAATTTCCATTTT-TAACCCTAAG-TTTCA
* *
24997688 CCAAAAATTACCA-TTTT-ACCCTCAAACTTT--
1 CC--AAATTTCCATTTTTAACCCT--AAGTTTCA
* *
24997718 CCAAAATTCTATTTTTAACCCTAA-TTTCA
1 CCAAATTTCCATTTTTAACCCTAAGTTTCA
* * * *
24997747 CCAAAAATTACCA-TTTTACCCCCAAACTTT--
1 CC--AAATTTCCATTTTTA-ACCCTAAGTTTCA
* * *
24997777 CCAAAATCCCATTTTTAACCCCAA-TTTCA
1 CCAAATTTCCATTTTTAACCCTAAGTTTCA
*
24997806 CCAAAATTCCATTTT
1 CCAAATTTCCATTTT
24997821 GCCCCCGGAG
Statistics
Matches: 185, Mismatches: 32, Indels: 70
0.64 0.11 0.24
Matches are distributed among these distances:
27 11 0.06
28 37 0.20
29 45 0.24
30 40 0.22
31 31 0.17
32 21 0.11
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (30 bp):
CCAAATTTCCATTTTTAACCCTAAGTTTCA
Found at i:24997651 original size:30 final size:30
Alignment explanation
Indices: 24997564--24997768 Score: 121
Period size: 29 Copynumber: 6.9 Consensus size: 30
24997554 TTAACCTCGG
*
24997564 TTTCACCATAAATTACCATTTTACCCCTAAAC
1 TTTCACCAAAAATTACCATTTTACCCCT--AC
* * *
24997596 TTT--CC--AAATTTCCATTTTTAACCCTAG
1 TTTCACCAAAAATTACCA-TTTTACCCCTAC
*
24997623 TTTCACCAAAAATTATCATTTTACCCCTAAAC
1 TTTCACCAAAAATTACCATTTTACCCCT--AC
* *
24997655 TTT--CC-AAAATT-CCATTTTGTAACCTCGA-
1 TTTCACCAAAAATTACCA-TTT-T-ACCCCTAC
*
24997683 TTTCACCAAAAATTACCATTTTACCCTCAAAC
1 TTTCACCAAAAATTACCATTTTACCC-C-TAC
* * *
24997715 TTT--CC-AAAATT-CTATTTTTAACCCTAA
1 TTTCACCAAAAATTACCA-TTTTACCCCTAC
24997742 TTTCACCAAAAATTACCATTTTACCCC
1 TTTCACCAAAAATTACCATTTTACCCC
24997769 CAAACTTTCC
Statistics
Matches: 133, Mismatches: 18, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
27 8 0.06
28 16 0.12
29 39 0.29
30 34 0.26
31 23 0.17
32 13 0.10
ACGTcount: A:0.33, C:0.28, G:0.01, T:0.37
Consensus pattern (30 bp):
TTTCACCAAAAATTACCATTTTACCCCTAC
Found at i:24997746 original size:119 final size:118
Alignment explanation
Indices: 24997529--24997825 Score: 447
Period size: 119 Copynumber: 2.5 Consensus size: 118
24997519 GCTCTCTAGT
* * *
24997529 CCCCGAACTTTCCAAAATTCCATTTTTAACCTCGGTTTCACCATAAATTACCATTTTACCCCTAA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAA
* * *
24997594 ACTTTCCAAATTTCCATTTTTAACCCTAGTTTCACCAAAAATTATCATTTTAC
66 ACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
*
24997647 CCCTAAACTTTCCAAAATTCCATTTTGTAACCTCGATTTCACCAAAAATTACCATTTTA-CCCTC
1 CCCCAAACTTTCCAAAATTCCATTTT-TAACCTCGATTTCACCAAAAATTACCATTTTACCCCT-
*
24997711 AAACTTTCCAAAATTCTATTTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
64 AAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
* * * *
24997766 CCCCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACC-AAAATT-CCATTTTGCCCC
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCC
24997826 CGGAGATCAA
Statistics
Matches: 163, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
116 7 0.04
117 9 0.06
118 42 0.26
119 105 0.64
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.35
Consensus pattern (118 bp):
CCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAA
ACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
Found at i:24997798 original size:30 final size:29
Alignment explanation
Indices: 24997577--24997800 Score: 90
Period size: 29 Copynumber: 7.6 Consensus size: 29
24997567 CACCATAAAT
* *
24997577 TACCA-TTTTACCCCTAAACTTTCCAAAT
1 TACCATTTTTACCCCCAAACTTTCCAAAA
* * * *
24997605 TTCCATTTTTA-ACCC-TAGTTTCACCAAAAA
1 TACCATTTTTACCCCCAAACTTT--CC-AAAA
* *
24997635 TTATCA-TTTTACCCCTAAACTTTCCAAAA
1 -TACCATTTTTACCCCCAAACTTTCCAAAA
* * * *
24997664 TTCCATTTTGTAACCTC-GA-TTTCACCAAAAA
1 TACCATTTT-TACCCCCAAACTTT--CC-AAAA
*
24997695 TTACCA-TTTTACCCTCAAACTTTCCAAAA
1 -TACCATTTTTACCCCCAAACTTTCCAAAA
* * * *
24997724 TTCTATTTTTA-ACCCTAA-TTTCACCAAAAA
1 TACCATTTTTACCCCCAAACTTT--CC-AAAA
24997754 TTACCA-TTTTACCCCCAAACTTTCCAAAA
1 -TACCATTTTTACCCCCAAACTTTCCAAAA
* *
24997783 TCCCATTTTTAACCCCAA
1 TACCATTTTTACCCCCAA
24997801 TTTCACCAAA
Statistics
Matches: 141, Mismatches: 32, Indels: 45
0.65 0.15 0.21
Matches are distributed among these distances:
27 7 0.05
28 23 0.16
29 41 0.29
30 35 0.25
31 21 0.15
32 14 0.10
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.36
Consensus pattern (29 bp):
TACCATTTTTACCCCCAAACTTTCCAAAA
Found at i:25002683 original size:14 final size:14
Alignment explanation
Indices: 25002654--25002682 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25002644 ATATTGCTAA
25002654 TTAATTATAAATTT
1 TTAATTATAAATTT
25002668 TTAATT-TAAATTT
1 TTAATTATAAATTT
25002681 TT
1 TT
25002683 TGCATTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTATAAATTT
Found at i:25015807 original size:18 final size:18
Alignment explanation
Indices: 25015784--25015853 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 18
25015774 ATAATTTTAG
25015784 AAAATTATTTTTATAAAA
1 AAAATTATTTTTATAAAA
*
25015802 AAAATTA-TGTTA-AAAA
1 AAAATTATTTTTATAAAA
*
25015818 ATAA-TATTTTTTATGAATAA
1 AAAATTA-TTTTTAT-AA-AA
* *
25015838 TATATTATTTTTATAA
1 AAAATTATTTTTATAA
25015854 TATATAGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.05
16 7 0.17
17 8 0.20
18 7 0.17
19 4 0.10
20 10 0.25
21 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTATTTTTATAAAA
Found at i:25019957 original size:52 final size:52
Alignment explanation
Indices: 25019667--25019945 Score: 257
Period size: 52 Copynumber: 5.4 Consensus size: 52
25019657 GATTCACTTC
* * ** * *
25019667 ATTCATATACTCACGATGACACATAGCCA-CTAAACC-TTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATC-GGACCATT-TAATCCGTAAAGG
* * * * * * *
25019719 ATTCGTATACTCAGGATGACACATAGCCA-CTAGACC-TTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATC-GGACCATT-TAATCCGTAAAGG
* * * * * *
25019771 ATTCATATACTTATGATAACA-TAGAGTCATCAGATC-TCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACT-TAGTCATCGGACCAT-TTAATCCGTAAAGG
*
25019823 A-TCTATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGG
1 ATTC-ATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCGTAAAGG
*
25019875 ATTCATATACTCACAATGACACTTAGTCATCGGACCATTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCGTAAAGG
25019927 ATTCATATACTCACGATGA
1 ATTCATATACTCACGATGA
25019946 TTCATAATCA
Statistics
Matches: 198, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
51 2 0.01
52 190 0.96
53 6 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCGTAAAGG
Found at i:25019957 original size:156 final size:156
Alignment explanation
Indices: 25019671--25019966 Score: 334
Period size: 156 Copynumber: 1.9 Consensus size: 156
25019661 CACTTCATTC
* * **
25019671 ATATACTCACGATGACACATAGCCACTAAACCTTATAATCCGCAAGGGATTCGTATACTCAGGAT
1 ATATACTCACGATGACACATAGCCACTAAACCTTATAATCCGCAAAGGATTCATATACTCACAAT
* * *
25019736 GACACATAGCCACTAGACCTTATAATCCGCAAGGGATTCATATACTTATGATAACATAGAGTCAT
66 GACACATAGCCACTAGACCTTATAATCCGCAAAGGATTCATATACTCACGATAACATAGAGTCAT
*
25019801 CAGATCTCTTAATCCGTAAAGGATCT
131 CAGACCTCTTAATCCGTAAAGGATCT
* * ** *
25019827 ATATACTCACGATGACACTTAGTCA-TCGGACCGTT-TAATCCGTAAAGGATTCATATACTCACA
1 ATATACTCACGATGACACATAGCCACT-AAACC-TTATAATCCGCAAAGGATTCATATACTCACA
* * * * *
25019890 ATGACACTTAGTCA-TCGGACCATT-TAATCCGTAAAGGATTCATATACTCACGATGATTCATA-
64 ATGACACATAGCCACT-AGACC-TTATAATCCGCAAAGGATTCATATACTCACGAT-A-ACATAG
25019952 A-TCATCAGACCTCTT
125 AGTCATCAGACCTCTT
25019967 CGTTTATGGC
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
155 2 0.02
156 104 0.90
157 6 0.05
158 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (156 bp):
ATATACTCACGATGACACATAGCCACTAAACCTTATAATCCGCAAAGGATTCATATACTCACAAT
GACACATAGCCACTAGACCTTATAATCCGCAAAGGATTCATATACTCACGATAACATAGAGTCAT
CAGACCTCTTAATCCGTAAAGGATCT
Found at i:25030113 original size:71 final size:71
Alignment explanation
Indices: 25029997--25030140 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
25029987 TCTAGTATAC
25029997 TAAGAATAGCATGCTTCAATTTCTTCTTTAATCCCTCTTGAATGTTGATGAATTCTATTGACTAT
1 TAAGAATAGCATGCTTCAATTTCTTCTTTAATCCCTCTTGAATGTTGATGAATTCTATTGACTAT
25030062 TAATTG
66 TAATTG
25030068 TAAGAATAGCATGCTTCAATTTCTTCTTTAATCCCTCTTGAATGTTGATGAATTCTATTGACTAT
1 TAAGAATAGCATGCTTCAATTTCTTCTTTAATCCCTCTTGAATGTTGATGAATTCTATTGACTAT
25030133 TAATTG
66 TAATTG
25030139 TA
1 TA
25030141 TACGGAAGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (71 bp):
TAAGAATAGCATGCTTCAATTTCTTCTTTAATCCCTCTTGAATGTTGATGAATTCTATTGACTAT
TAATTG
Found at i:25032810 original size:123 final size:123
Alignment explanation
Indices: 25032307--25032794 Score: 762
Period size: 123 Copynumber: 4.0 Consensus size: 123
25032297 TCTACTATCT
* * *
25032307 TTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGAAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
*
25032372 TATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAA
66 TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTCCATGTTTTTAATATTCAA
* * * * *
25032430 TTTCCTTTTATAAAATATCTCATATTAAAATGGATATATTCCATTAGAGAAATATATGGAAGGGT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* * *
25032495 TATTAAAACATTATATCCTCTCCAAATGGATAATAACTTCCATGTTTTTAATATTTAA
66 TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTCCATGTTTTTAATATTCAA
* *
25032553 TTTCCTTTTATATAATATCTCATATTAAATTGGAAACATTCCTTTAAAGAAATATATGGAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* *
25032618 TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTTCATGTTTCTAATATTCAA
66 TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTCCATGTTTTTAATATTCAA
* * * *
25032676 TTTCCCTTTATATAATCTCCCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGATT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* * *
25032741 TATTAAAACATTATATCATTTCCAAAAGGATATTTACTTCCATG-TTTTAATATT
66 TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTCCATGTTTTTAATATT
25032795 TAACGAAACC
Statistics
Matches: 332, Mismatches: 33, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
122 9 0.03
123 323 0.97
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (123 bp):
TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTCCATGTTTTTAATATTCAA
Found at i:25037540 original size:83 final size:80
Alignment explanation
Indices: 25037390--25037549 Score: 230
Period size: 83 Copynumber: 2.0 Consensus size: 80
25037380 TTGATTTGCA
* * *
25037390 TATTCTTGTCAACTTAGTGTGAGCAGCATCGTTAGGGAACAATTATATGTACAGATACTGTATCG
1 TATTCTCGTCAACTTAGTATGAGCAGCATCGTTAGGGAACAATTATATGTACAGATACCGTATCG
25037455 ATGGCTGAGGTATCG
66 ATGGCTGAGGTATCG
* * *
25037470 TATTCTCGTCAGCTTAGTATGAGCAGCATCGTATACTGGTAACAGTTATATGTACAGATACCGTA
1 TATTCTCGTCAACTTAGTATGAGCAGCATCGT-TA--GGGAACAATTATATGTACAGATACCGTA
*
25037535 TCGATGGTTGAGGTA
63 TCGATGGCTGAGGTA
25037550 CCGCATATGT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
80 29 0.41
81 2 0.03
83 39 0.56
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (80 bp):
TATTCTCGTCAACTTAGTATGAGCAGCATCGTTAGGGAACAATTATATGTACAGATACCGTATCG
ATGGCTGAGGTATCG
Found at i:25042737 original size:28 final size:27
Alignment explanation
Indices: 25042637--25042732 Score: 113
Period size: 28 Copynumber: 3.4 Consensus size: 27
25042627 CGAAATGTGG
25042637 AAGCCTTTGTGGCTATTC-TGATATGTGA
1 AAGCCTTTGTGGCTATTCTTGATA--TGA
*
25042665 AAGCCTTTGTGGCTATTCTCTAATATGA
1 AAGCCTTTGTGGCTATTCT-TGATATGA
* * *
25042693 AAGTCTTTGTGGTTGTTCTTTGATATGA
1 AAGCCTTTGTGGCTATTC-TTGATATGA
25042721 AAGCCTTTGTGG
1 AAGCCTTTGTGG
25042733 TTGTTTTCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 54 0.92
29 1 0.02
30 4 0.07
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.42
Consensus pattern (27 bp):
AAGCCTTTGTGGCTATTCTTGATATGA
Found at i:25044532 original size:16 final size:16
Alignment explanation
Indices: 25044511--25044545 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
25044501 ACACCATAAA
25044511 ACAAAAAAAATATTTT
1 ACAAAAAAAATATTTT
25044527 ACAAAAAAAATATTTT
1 ACAAAAAAAATATTTT
25044543 ACA
1 ACA
25044546 TGCAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
ACAAAAAAAATATTTT
Found at i:25049695 original size:29 final size:30
Alignment explanation
Indices: 25049627--25049703 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
25049617 TTTGAACCAA
* * *
25049627 CATCCATAAACTATGACACCTATTCTAAATT
1 CATCCCTAAACTATCA-AACTATTCTAAATT
* *
25049658 GATCTCTAAACT-TCAAACTATTCT-AATT
1 CATCCCTAAACTATCAAACTATTCTAAATT
25049686 ACATCCCTAAACTATCAA
1 -CATCCCTAAACTATCAA
25049704 GGATATATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.11
29 18 0.49
30 6 0.16
31 9 0.24
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (30 bp):
CATCCCTAAACTATCAAACTATTCTAAATT
Found at i:25049836 original size:17 final size:17
Alignment explanation
Indices: 25049809--25049848 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
25049799 AAAATTTAGA
25049809 AAAATAAATGAATCTTGT
1 AAAA-AAATGAATCTTGT
* *
25049827 AAAAAAATGAATGTTTT
1 AAAAAAATGAATCTTGT
25049844 AAAAA
1 AAAAA
25049849 TCTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (17 bp):
AAAAAAATGAATCTTGT
Found at i:25052885 original size:21 final size:21
Alignment explanation
Indices: 25052859--25052922 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
25052849 GATACCTAAT
25052859 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
* *
25052880 AAAAGGTATCAATACTTGTTG
1 AAAAGGTATCGATACTTTTTG
25052901 AAAAGGTATCGATACATTTTTG
1 AAAAGGTATCGATAC-TTTTTG
25052923 TCATTGTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:25054760 original size:15 final size:15
Alignment explanation
Indices: 25054740--25054793 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
25054730 ATGAATTAAA
25054740 CAATTTAATTTTTAT
1 CAATTTAATTTTTAT
25054755 CAATTTTAAATTTTTTAAT
1 CAA-TTT-AA-TTTTT-AT
*
25054774 -AATTTAATTCTTAT
1 CAATTTAATTTTTAT
25054788 CAATTT
1 CAATTT
25054794 TAAAATACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 2 0.06
15 12 0.36
16 5 0.15
17 5 0.15
18 7 0.21
19 2 0.06
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
CAATTTAATTTTTAT
Found at i:25054768 original size:16 final size:16
Alignment explanation
Indices: 25054743--25054797 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
25054733 AATTAAACAA
*
25054743 TTTAATTTTTATCAAT
1 TTTAAATTTTATCAAT
*
25054759 TTTAAATTTT-TTAAT
1 TTTAAATTTTATCAAT
25054774 AATTT-AATTCTTATCAAT
1 --TTTAAATT-TTATCAAT
25054792 TTTAAA
1 TTTAAA
25054798 ATACCAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 4 0.13
16 16 0.52
17 7 0.23
18 4 0.13
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAAATTTTATCAAT
Found at i:25054771 original size:18 final size:17
Alignment explanation
Indices: 25054746--25054797 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
25054736 TAAACAATTT
25054746 AATTTTTATCAATTTTA
1 AATTTTTATCAATTTTA
25054763 AATTTTT-T-AATAATTT-
1 AATTTTTATCAAT--TTTA
*
25054779 AATTCTTATCAATTTTA
1 AATTTTTATCAATTTTA
25054796 AA
1 AA
25054798 ATACCAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
15 3 0.10
16 10 0.34
17 13 0.45
18 3 0.10
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTTATCAATTTTA
Found at i:25055527 original size:28 final size:28
Alignment explanation
Indices: 25055479--25055545 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
25055469 TTGTCTTGCG
* * *
25055479 TTTAATATTTTGATGGTTTTTTCATGCA
1 TTTAATATTTTAATGGTTTTTCCATACA
* *
25055507 TTTAATGTTTTAAT-GTATTTTCCCTACA
1 TTTAATATTTTAATGGT-TTTTCCATACA
25055535 TTTAATATTTT
1 TTTAATATTTT
25055546 TTTCATTGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTAATATTTTAATGGTTTTTCCATACA
Found at i:25061671 original size:58 final size:59
Alignment explanation
Indices: 25061607--25061725 Score: 170
Period size: 58 Copynumber: 2.0 Consensus size: 59
25061597 TTATTTTTCA
* *
25061607 TTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTT-C-ATTTCTCCAT
1 TTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATG-TTTCCTATTTCTCCAT
* **
25061665 TTTTCATTTTCATTTTTGAGAAAACCTTAATAATTTCCAAATGTTTCCTATTTCTCCAT
1 TTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGTTTCCTATTTCTCCAT
25061724 TT
1 TT
25061726 CTCCATTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 3 0.06
58 39 0.72
59 12 0.22
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (59 bp):
TTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGTTTCCTATTTCTCCAT
Found at i:25069657 original size:12 final size:13
Alignment explanation
Indices: 25069642--25069670 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25069632 AAGGATTTAA
25069642 TTAAACTTT-GGG
1 TTAAACTTTAGGG
25069654 TTAAACTTTAGGG
1 TTAAACTTTAGGG
25069667 TTAA
1 TTAA
25069671 TTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (13 bp):
TTAAACTTTAGGG
Found at i:25074000 original size:27 final size:27
Alignment explanation
Indices: 25073961--25074017 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
25073951 ACCGGTCAAA
* *
25073961 ATTTTGTATTTGGCTCGAATGAGCGAT
1 ATTTTATAATTGGCTCGAATGAGCGAT
*
25073988 ATTTTATAATTGGCTCGGATGAGCGAT
1 ATTTTATAATTGGCTCGAATGAGCGAT
25074015 ATT
1 ATT
25074018 CTGTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (27 bp):
ATTTTATAATTGGCTCGAATGAGCGAT
Found at i:25074934 original size:19 final size:19
Alignment explanation
Indices: 25074907--25074959 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
25074897 GTGTAAGGAG
* *
25074907 AAATTTTCAATTTTGCCTA
1 AAATGTTCAGTTTTGCCTA
25074926 AAATGTTCAGTTTTGCCTA
1 AAATGTTCAGTTTTGCCTA
25074945 AAATGTTCAGTTTTG
1 AAATGTTCAGTTTTG
25074960 GTCTCTGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (19 bp):
AAATGTTCAGTTTTGCCTA
Found at i:25077799 original size:7 final size:7
Alignment explanation
Indices: 25077775--25077871 Score: 58
Period size: 7 Copynumber: 13.9 Consensus size: 7
25077765 ACCCGAACCC
*
25077775 GTTGACC
1 GTTGACA
* *
25077782 GTTAACC
1 GTTGACA
25077789 GTTGACA
1 GTTGACA
25077796 GTTGACCA
1 GTTGA-CA
*
25077804 -TTGACC
1 GTTGACA
25077810 GTTGACA
1 GTTGACA
25077817 GTTGACCA
1 GTTGA-CA
25077825 -TTGACCA
1 GTTGA-CA
25077832 -TTGACA
1 GTTGACA
*
25077838 GTTGACC
1 GTTGACA
*
25077845 GTTAATC-
1 GTTGA-CA
*
25077852 GTTGACT
1 GTTGACA
*
25077859 GTTGACC
1 GTTGACA
25077866 GTTGAC
1 GTTGAC
25077872 TTTTTTTAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
6 4 0.05
7 66 0.88
8 5 0.07
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (7 bp):
GTTGACA
Found at i:25077800 original size:21 final size:21
Alignment explanation
Indices: 25077775--25077868 Score: 125
Period size: 21 Copynumber: 4.5 Consensus size: 21
25077765 ACCCGAACCC
25077775 GTTGACCGTTAACCGTTGACA
1 GTTGACCGTTAACCGTTGACA
* *
25077796 GTTGACCATTGACCGTTGACA
1 GTTGACCGTTAACCGTTGACA
* * *
25077817 GTTGACCATTGACCATTGACA
1 GTTGACCGTTAACCGTTGACA
* *
25077838 GTTGACCGTTAATCGTTGACT
1 GTTGACCGTTAACCGTTGACA
25077859 GTTGACCGTT
1 GTTGACCGTT
25077869 GACTTTTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
GTTGACCGTTAACCGTTGACA
Done.