Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 79 of 93
Found at i:30268865 original size:2 final size:2
Alignment explanation
Indices: 30268858--30268940 Score: 125
Period size: 2 Copynumber: 42.0 Consensus size: 2
30268848 ACAAACATAC
*
30268858 AT AT AT AT AT AT AT NAT AC AT AT AT AT -T 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
*
30268900 AT AT AT AT AT AT AT AT A- AT AT AT AC 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
30268941 TCTTCTGCAA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.03
2 70 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30271060 original size:38 final size:38
Alignment explanation
Indices: 30271018--30271134 Score: 216
Period size: 38 Copynumber: 3.1 Consensus size: 38
30271008 ATATTACATT
* *
30271018 TCTAAAAAAGTACTTATAAATTAAATTTTACAACGTTA
1 TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
30271056 TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
1 TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
30271094 TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
1 TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
30271132 TCT
1 TCT
30271135 TTTCAATATT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (38 bp):
TCTAAAAAAGTACTTATAAATCAATTTTTACAACGTTA
Found at i:30277827 original size:18 final size:18
Alignment explanation
Indices: 30277774--30277838 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
30277764 ACACATTTAA
* *
30277774 TTAATCGTGTTAATCGTGT
1 TTAAACGTGTT-ATCGTAT
* * *
30277793 TTAAACGTATAAACGTAT
1 TTAAACGTGTTATCGTAT
*
30277811 TTAATCGTGTTATCGTAT
1 TTAAACGTGTTATCGTAT
30277829 TTAAACGTGT
1 TTAAACGTGT
30277839 ATACAGGACA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
18 28 0.78
19 8 0.22
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (18 bp):
TTAAACGTGTTATCGTAT
Found at i:30278520 original size:15 final size:15
Alignment explanation
Indices: 30278502--30278560 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
30278492 CAATAATTAT
30278502 AAAA-ACAATTATAAC
1 AAAACACAA-TATAAC
*
30278517 AAAATA-AA-ATAAC
1 AAAACACAATATAAC
30278530 AAAACATCAAATATAAC
1 AAAACA-C-AATATAAC
*
30278547 AAAACAAAATATAA
1 AAAACACAATATAA
30278561 AATTAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 10 0.27
15 13 0.35
16 3 0.08
17 11 0.30
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAACACAATATAAC
Found at i:30278547 original size:17 final size:15
Alignment explanation
Indices: 30278511--30278560 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
30278501 TAAAAACAAT
*
30278511 TATAACAAAA-TAAA
1 TATAACAAAACAAAA
30278525 -ATAACAAAACATCAAA
1 TATAACAAAACA--AAA
30278541 TATAACAAAACAAAA
1 TATAACAAAACAAAA
30278556 TATAA
1 TATAA
30278561 AATTAGGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.29
15 8 0.26
16 3 0.10
17 11 0.35
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (15 bp):
TATAACAAAACAAAA
Found at i:30298899 original size:18 final size:19
Alignment explanation
Indices: 30298867--30298904 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
30298857 ATAGAAATCG
*
30298867 TTAATATATGGGTTATTTA
1 TTAATATATGGGTTACTTA
*
30298886 TTAAT-TATGTGTTACTTA
1 TTAATATATGGGTTACTTA
30298904 T
1 T
30298905 GGAACTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (19 bp):
TTAATATATGGGTTACTTA
Found at i:30299395 original size:272 final size:272
Alignment explanation
Indices: 30298909--30299418 Score: 817
Period size: 272 Copynumber: 1.9 Consensus size: 272
30298899 ACTTATGGAA
* * *
30298909 CTCTTTTTTTATGATTTATTATTAATTATAAACTTATATTATATAAAAATTATTTTTATATTTTC
1 CTCTTTTTTTATAATTCATTATTAATTATAAACTTATATTATATAAAAAATATTTTTATATTTTC
*
30298974 AAAATTTTATTTTAAATAGATAAAAAAATAAAGTTAATTTTTTTATTTTGAATAAAGAAATTCGT
66 AAAATTTTATTTTAAATAGATAAAAAAATAAAATTAATTTTTTTATTTTGAATAAAGAAATTCGT
* * *
30299039 GATAAATAACAAGTTATTTATTAAATACCTTTTATGGTAATTTTAACTAAAATTAAAATTTATAT
131 GATAAATAAAAAGTTATTTATTAAATACATTTTATGATAATTTTAACTAAAATTAAAATTTATAT
*
30299104 AAGTTATTTTGCCAAACAACTTCTATATAAAAAAGAGCTTATATGAATTATGTGTTACTTATAAA
196 AAGTTATTTTGCCAAACAACTTATATATAAAAAAGAGCTTATATGAATTATGTGTTACTTATAAA
30299169 TTATTTGTAGTG
261 TTATTTGTAGTG
* *
30299181 CTCTTTTTTTATAATTCATTATTAATTATAAACTTTATGTTATATAAAAAATCTTTTTATATTTT
1 CTCTTTTTTTATAATTCATTATTAATTATAAAC-TTATATTATATAAAAAATATTTTTATA-TTT
**
30299246 TTTAAA-TTTATTTTAAATAGAT-AAAAAATAAAATTAATTTTTTTATTTTGAATAAAGAAATTC
64 TCAAAATTTTATTTTAAATAGATAAAAAAATAAAATTAATTTTTTTATTTTGAATAAAGAAATTC
* * * *
30299309 GTTATTAATAAAAAGTTATTTATTAAATACATTTTATGATAATTTTAACTAAAATTATAGTTTAT
129 GTGATAAATAAAAAGTTATTTATTAAATACATTTTATGATAATTTTAACTAAAATTAAAATTTAT
* * *
30299374 ATAAGTTGTTTTGCCAAACAACTTATCTATAAAAAATAGCTTATA
194 ATAAGTTATTTTGCCAAACAACTTATATATAAAAAAGAGCTTATA
30299419 AAAAGTAAAT
Statistics
Matches: 217, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
272 170 0.78
273 40 0.18
274 7 0.03
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (272 bp):
CTCTTTTTTTATAATTCATTATTAATTATAAACTTATATTATATAAAAAATATTTTTATATTTTC
AAAATTTTATTTTAAATAGATAAAAAAATAAAATTAATTTTTTTATTTTGAATAAAGAAATTCGT
GATAAATAAAAAGTTATTTATTAAATACATTTTATGATAATTTTAACTAAAATTAAAATTTATAT
AAGTTATTTTGCCAAACAACTTATATATAAAAAAGAGCTTATATGAATTATGTGTTACTTATAAA
TTATTTGTAGTG
Found at i:30300052 original size:20 final size:20
Alignment explanation
Indices: 30300029--30300112 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 20
30300019 AATATAGGTA
30300029 AAAAAATTAAAATAAAATAT
1 AAAAAATTAAAATAAAATAT
* **
30300049 AAAATA-TAAAA-ATTATAT
1 AAAAAATTAAAATAAAATAT
* * *
30300067 TAAAAATGAAAATAAAACAT
1 AAAAAATTAAAATAAAATAT
* * * *
30300087 ATAATATTATAATAAAAAAT
1 AAAAAATTAAAATAAAATAT
30300107 AAAAAA
1 AAAAAA
30300113 ATATATGACA
Statistics
Matches: 45, Mismatches: 17, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
18 9 0.20
19 9 0.20
20 27 0.60
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (20 bp):
AAAAAATTAAAATAAAATAT
Found at i:30300072 original size:27 final size:26
Alignment explanation
Indices: 30300029--30300118 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 26
30300019 AATATAGGTA
* *
30300029 AAAAAATTAAAAT-AAAATATAAAAT
1 AAAAAATTATATTAAAAATATAAAAT
*
30300054 ATAAAAATTATATTAAAAAT-GAAAAT
1 A-AAAAATTATATTAAAAATATAAAAT
* * *
30300080 AAAACATATAATATT-ATAATAAAAAAT
1 AAAA-A-ATTATATTAAAAATATAAAAT
*
30300107 AAAAAAATATAT
1 AAAAAATTATAT
30300119 GACATTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
25 9 0.17
26 22 0.42
27 21 0.40
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (26 bp):
AAAAAATTATATTAAAAATATAAAAT
Found at i:30300105 original size:33 final size:32
Alignment explanation
Indices: 30300037--30300110 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
30300027 TAAAAAAATT
*
30300037 AAAATAAAATATAAAATATAAAAATTATATTA
1 AAAATAAAATATAAAATATAAAAATTATATAA
*
30300069 AAAATGAAAATA-AAACATAT-AATATTATAATAA
1 AAAAT-AAAATATAAA-ATATAAAAATTAT-ATAA
30300102 AAAATAAAA
1 AAAATAAAA
30300111 AAATATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
32 19 0.51
33 18 0.49
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (32 bp):
AAAATAAAATATAAAATATAAAAATTATATAA
Found at i:30300367 original size:15 final size:15
Alignment explanation
Indices: 30300343--30300376 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30300333 CTGCAATTAC
*
30300343 ATTACTTGTAATCAT
1 ATTACCTGTAATCAT
30300358 ATTACCTGTAATCAT
1 ATTACCTGTAATCAT
30300373 ATTA
1 ATTA
30300377 TATTGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTACCTGTAATCAT
Found at i:30300856 original size:20 final size:18
Alignment explanation
Indices: 30300820--30300859 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
30300810 TATCTAACAA
*
30300820 AAATATTTTTTTGAAATT
1 AAATATTTTTTTAAAATT
30300838 AAATATTTATTTTAAAAATT
1 AAATATTT-TTTT-AAAATT
30300858 AA
1 AA
30300860 TGAATCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AAATATTTTTTTAAAATT
Found at i:30309952 original size:3 final size:3
Alignment explanation
Indices: 30309944--30309968 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30309934 CTTGGCGGAC
30309944 GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG G
30309969 TGGTAGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:30336095 original size:81 final size:81
Alignment explanation
Indices: 30335960--30336122 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
30335950 AAGATATGTC
*
30335960 AAATATAGTAGTTTTCAAAAAATTCAAGTTGGAAGACACTGACTAAATGTTAAAACTAGATAGGG
1 AAATATAGTAGTTTTCAAAAAATTCAAGTTGAAAGACACTGACTAAATGTTAAAACTAGATAGGG
30336025 GGAGTTCATTCCAGCA
66 GGAGTTCATTCCAGCA
*
30336041 AAATATAGTAGTTTTCAAAAAATTCAAGTTGAAAGACACTGATTAAATGTTAAAACTAGATAGGG
1 AAATATAGTAGTTTTCAAAAAATTCAAGTTGAAAGACACTGACTAAATGTTAAAACTAGATAGGG
30336106 GGAGTTCATTCCAGCA
66 GGAGTTCATTCCAGCA
30336122 A
1 A
30336123 TAAACTCCCT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (81 bp):
AAATATAGTAGTTTTCAAAAAATTCAAGTTGAAAGACACTGACTAAATGTTAAAACTAGATAGGG
GGAGTTCATTCCAGCA
Found at i:30337997 original size:23 final size:23
Alignment explanation
Indices: 30337971--30338023 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
30337961 TTTTTAAAAA
*
30337971 TTTAAATAAAT-ATTTCTTTTTAT
1 TTTAAATAAATGAATT-TTTTTAT
** *
30337994 TTTATTTAATTGAATTTTTTTAT
1 TTTAAATAAATGAATTTTTTTAT
30338017 TTTAAAT
1 TTTAAAT
30338024 TTAATAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTAAATAAATGAATTTTTTTAT
Found at i:30345489 original size:5 final size:5
Alignment explanation
Indices: 30345479--30345506 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30345469 GAAATGAGTT
30345479 TGGGG TGGGG TGGGG TGGGG TGGGG TGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG TGG
30345507 TAAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (5 bp):
TGGGG
Found at i:30355604 original size:61 final size:59
Alignment explanation
Indices: 30355510--30355630 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 59
30355500 ACACGTCAAT
30355510 AAATTAATTTATTTTTTATTTTTTTTTCTTCATTAAAAAAATATTTATTTAAGTGTTTG
1 AAATTAATTTATTTTTTATTTTTTTTTCTTCATTAAAAAAATATTTATTTAAGTGTTTG
30355569 NAAATTAATTTTATTTTTTA-TTTTTTTTCATTCATTAAAAAAATATTTATTTAAGTGTTTG
1 -AAATTAA-TTTATTTTTTATTTTTTTTTC-TTCATTAAAAAAATATTTATTTAAGTGTTTG
30355630 A
1 A
30355631 TTCAGTAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
60 17 0.29
61 42 0.71
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (59 bp):
AAATTAATTTATTTTTTATTTTTTTTTCTTCATTAAAAAAATATTTATTTAAGTGTTTG
Found at i:30356153 original size:18 final size:18
Alignment explanation
Indices: 30356130--30356167 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30356120 CCATTGGATT
30356130 ATATATA-TAGTTAATAGG
1 ATATATAGTAGTTAAT-GG
*
30356148 ATATATAGTATTTAATGG
1 ATATATAGTAGTTAATGG
30356166 AT
1 AT
30356168 TAAATGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (18 bp):
ATATATAGTAGTTAATGG
Found at i:30366767 original size:16 final size:16
Alignment explanation
Indices: 30366743--30366776 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30366733 TTTCTTAAGT
* *
30366743 AAAATGAAAAAGATAA
1 AAAAAGAAAAAAATAA
30366759 AAAAAGAAAAAAATAA
1 AAAAAGAAAAAAATAA
30366775 AA
1 AA
30366777 GAGAAGAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAGAAAAAAATAA
Found at i:30366995 original size:24 final size:23
Alignment explanation
Indices: 30366968--30367012 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
30366958 TTAAAAATAT
30366968 AATAAACAAAAAAATGATGAAATG
1 AATAAA-AAAAAAATGATGAAATG
**
30366992 AATAAATGAAAAATGATGAAA
1 AATAAAAAAAAAATGATGAAA
30367013 AAAGAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.18
Consensus pattern (23 bp):
AATAAAAAAAAAATGATGAAATG
Found at i:30367770 original size:129 final size:129
Alignment explanation
Indices: 30367539--30367811 Score: 422
Period size: 129 Copynumber: 2.1 Consensus size: 129
30367529 CCACCAGATC
** * *
30367539 CGCCACCGGTTGGGGGAGAGTCGACTTGTCCCACGCCGCAAGGAGAAGTTCGCCGGCGGAGAAGA
1 CGCCACCGGTTGGGGGAGAACCGACTTGACCCACGCCGCAAGGAGAAGCTCGCCGGCGGAGAAGA
* * * *
30367604 AACCAGACCATCGACGCCGCCCGATCTGTCGCTGGAAGGAAGAGCCGATCCAGGAC-AGCTGCGA
66 AACCAGACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGG-CGAGCAGCGA
* *
30367668 CGCCACCGGTTGGGGGAGAACCGACTTGACCCACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGG
1 CGCCACCGGTTGGGGGAGAACCGACTTGACCCACGCCGCAAGGAGAAGCTCGCCGGCGGAGAAGA
* *
30367733 AACCAGACCATTGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGA
66 AACCAGACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGCAGCGA
30367797 CGCCACCGGTTGGGG
1 CGCCACCGGTTGGGG
30367812 AAGCCGACCG
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
128 1 0.01
129 130 0.99
ACGTcount: A:0.23, C:0.31, G:0.36, T:0.10
Consensus pattern (129 bp):
CGCCACCGGTTGGGGGAGAACCGACTTGACCCACGCCGCAAGGAGAAGCTCGCCGGCGGAGAAGA
AACCAGACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGCAGCGA
Found at i:30368442 original size:23 final size:22
Alignment explanation
Indices: 30368411--30368454 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
30368401 AGGCTAAAAG
30368411 ATTAAATTAAGAAATTAAAAATT
1 ATTAAATTAAG-AATTAAAAATT
* *
30368434 ATTAGATTAAGCATTAAAAAT
1 ATTAAATTAAGAATTAAAAAT
30368455 AATAAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTAAATTAAGAATTAAAAATT
Found at i:30370217 original size:22 final size:22
Alignment explanation
Indices: 30370094--30370224 Score: 93
Period size: 22 Copynumber: 6.0 Consensus size: 22
30370084 AGTTTTGGTG
* *
30370094 GTTTTTAAGCATTGTGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* * *
30370116 GTTTTTAAGTATTACGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* * *
30370138 -ATTTTAGGTATTGCGTGATTA
1 GTTTTTAGGCATTGCGTGACTA
* * * *
30370159 GTTTTTAGGTATTACATGACTG
1 GTTTTTAGGCATTGCGTGACTA
** *
30370181 GTTAATATGACATTGCGTGACTA
1 GTTTTTA-GGCATTGCGTGACTA
**
30370204 GTTGATAGGCATTGCGTGACT
1 GTTTTTAGGCATTGCGTGACT
30370225 GGTTAGTAAG
Statistics
Matches: 86, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 17 0.20
22 53 0.62
23 16 0.19
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTGACTA
Found at i:30370240 original size:23 final size:23
Alignment explanation
Indices: 30370175--30370240 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
30370165 AGGTATTACA
* * *
30370175 TGACTGGTTAATATGACATTGCG
1 TGACTGGTTAGTAAGGCATTGCG
*
30370198 TGACTAGTT-G-ATAGGCATTGCG
1 TGACTGGTTAGTA-AGGCATTGCG
30370220 TGACTGGTTAGTAAGGCATTG
1 TGACTGGTTAGTAAGGCATTG
30370241 TCTAAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.46
23 17 0.49
24 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.33
Consensus pattern (23 bp):
TGACTGGTTAGTAAGGCATTGCG
Found at i:30370240 original size:45 final size:45
Alignment explanation
Indices: 30370147--30370240 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 45
30370137 AATTTTAGGT
* ** * *
30370147 ATTGCGTGATTAGTTTTTAGGTATTACATGACTGGTTAATATGAC
1 ATTGCGTGACTAGTTGATAGGCATTACATGACTGGTTAATAAGAC
* * * *
30370192 ATTGCGTGACTAGTTGATAGGCATTGCGTGACTGGTTAGTAAGGC
1 ATTGCGTGACTAGTTGATAGGCATTACATGACTGGTTAATAAGAC
30370237 ATTG
1 ATTG
30370241 TCTAAAAATC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (45 bp):
ATTGCGTGACTAGTTGATAGGCATTACATGACTGGTTAATAAGAC
Found at i:30371575 original size:16 final size:16
Alignment explanation
Indices: 30371531--30371575 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
30371521 TCTCTCATGG
*
30371531 ATTT-TTTTTTATAAA
1 ATTTATTTTTTAAAAA
*
30371546 TTTTATTGTTTTAAAAA
1 ATTTATT-TTTTAAAAA
30371563 ATTTATTTTTTAA
1 ATTTATTTTTTAA
30371576 GAGCTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
ATTTATTTTTTAAAAA
Found at i:30378017 original size:11 final size:11
Alignment explanation
Indices: 30377989--30378019 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
30377979 GCACACACTG
*
30377989 AAAAAAAAAAT
1 AAAAAATAAAT
30378000 AAAAAATAAAT
1 AAAAAATAAAT
30378011 AAAAAATAA
1 AAAAAATAA
30378020 CTTCCCCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:30387172 original size:2 final size:2
Alignment explanation
Indices: 30387165--30387210 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
30387155 TGGCTTTGCT
30387165 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30387206 TC TC T
1 TC TC T
30387211 GTCATAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30406864 original size:16 final size:16
Alignment explanation
Indices: 30406843--30406873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30406833 GAGATCTTAC
30406843 TGATTGAGGGTGAGGG
1 TGATTGAGGGTGAGGG
*
30406859 TGATTGAGTGTGAGG
1 TGATTGAGGGTGAGG
30406874 ACGTCATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (16 bp):
TGATTGAGGGTGAGGG
Found at i:30413678 original size:63 final size:63
Alignment explanation
Indices: 30413579--30413703 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
30413569 GATTCTATTG
* *
30413579 TACAAGTTTTCTCAATGTTATGTTCATAAACTTTTTACGTACATGCATTTCCAAATTCACACA
1 TACAAGTTTTCTCAATGTTATGTTCATAAACCTTTTACATACATGCATTTCCAAATTCACACA
**
30413642 TACAAGTTTTCTTGATGTTATGTTCATAAACCTTTTACATACATGCATTTCCAAATTCACAC
1 TACAAGTTTTCTCAATGTTATGTTCATAAACCTTTTACATACATGCATTTCCAAATTCACAC
30413704 GTGTGTCTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (63 bp):
TACAAGTTTTCTCAATGTTATGTTCATAAACCTTTTACATACATGCATTTCCAAATTCACACA
Found at i:30421067 original size:17 final size:17
Alignment explanation
Indices: 30421045--30421086 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
30421035 CTTCTCCTTT
30421045 CTATTTATATTATTTAA
1 CTATTTATATTATTTAA
30421062 CTATTTATA-TATTTAA
1 CTATTTATATTATTTAA
*
30421078 TTA-TTATAT
1 CTATTTATAT
30421087 AAAATCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
CTATTTATATTATTTAA
Found at i:30421126 original size:7 final size:7
Alignment explanation
Indices: 30421114--30421148 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
30421104 ATTTAATTAG
30421114 TTATATT
1 TTATATT
30421121 TTATATT
1 TTATATT
30421128 TTATATAT
1 TTATAT-T
30421136 ATTATATT
1 -TTATATT
30421144 TTATA
1 TTATA
30421149 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.69
8 2 0.08
9 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTATATT
Found at i:30421140 original size:16 final size:16
Alignment explanation
Indices: 30421115--30421148 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30421105 TTTAATTAGT
*
30421115 TATATTTTATATTTTA
1 TATATATTATATTTTA
30421131 TATATATTATATTTTA
1 TATATATTATATTTTA
30421147 TA
1 TA
30421149 AATTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATATTATATTTTA
Found at i:30426362 original size:10 final size:10
Alignment explanation
Indices: 30426343--30426413 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
30426333 TGTAGACACC
*
30426343 TAAATAAAAA
1 TAAATTAAAA
*
30426353 AAAATTAAAA
1 TAAATTAAAA
*
30426363 TTAAATTAAAT
1 -TAAATTAAAA
*
30426374 TAAATTAAAT
1 TAAATTAAAA
*
30426384 TAAATT-AAT
1 TAAATTAAAA
*
30426393 TAAATAAATAA
1 TAAATTAA-AA
*
30426404 TAATTTAAAA
1 TAAATTAAAA
30426414 AAAAAATGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
9 8 0.16
10 27 0.54
11 15 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:30426368 original size:5 final size:5
Alignment explanation
Indices: 30426354--30426401 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
30426344 AAATAAAAAA
30426354 AAATT AAAATT AAATT AAATT AAATT AAATT AAATT -AATT AAA-T AAAT
1 AAATT -AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
30426402 AATAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:30426407 original size:15 final size:15
Alignment explanation
Indices: 30426361--30426408 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30426351 AAAAAATTAA
30426361 AATTAAATTAAAT-T
1 AATTAAATTAAATAT
30426375 AAATTAAATTAAAT-T
1 -AATTAAATTAAATAT
30426390 AATTAAA-TAAATAAT
1 AATTAAATTAAAT-AT
30426405 AATT
1 AATT
30426409 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 19 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAATTAAATAT
Found at i:30455931 original size:20 final size:20
Alignment explanation
Indices: 30455906--30455943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30455896 TTAGGGTTTC
30455906 AAACACCACAAACCTCACAA
1 AAACACCACAAACCTCACAA
* *
30455926 AAACACCGCAAATCTCAC
1 AAACACCACAAACCTCAC
30455944 TCCAAACACA
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:0.50, C:0.39, G:0.03, T:0.08
Consensus pattern (20 bp):
AAACACCACAAACCTCACAA
Found at i:30465190 original size:7 final size:7
Alignment explanation
Indices: 30465173--30465222 Score: 50
Period size: 6 Copynumber: 6.9 Consensus size: 7
30465163 TTAAAATAGA
30465173 AAAAAAG
1 AAAAAAG
30465180 -AAAAAG
1 AAAAAAG
30465186 AAAAAAAG
1 -AAAAAAG
30465194 AAAAAAG
1 AAAAAAG
30465201 AAGTAAAATG
1 AA--AAAA-G
30465211 AAAAAA-
1 AAAAAAG
30465217 AAAAAA
1 AAAAAA
30465223 CTCAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 12 0.32
7 9 0.24
8 10 0.26
9 4 0.11
10 3 0.08
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:30475725 original size:45 final size:46
Alignment explanation
Indices: 30475638--30475750 Score: 185
Period size: 45 Copynumber: 2.5 Consensus size: 46
30475628 TTAAGTCTTT
30475638 ATATCATTAATTATGTATGTGAAATTTTCTTACTAATGTAACATTGA
1 ATATCATTAATTATGTATGTG-AATTTTCTTACTAATGTAACATTGA
30475685 ATATCATTAATTATGTATGTG-ATTTTCTTACTAATGTAACATTGA
1 ATATCATTAATTATGTATGTGAATTTTCTTACTAATGTAACATTGA
*
30475730 ATATGA-TAATATATGTATGTG
1 ATATCATTAAT-TATGTATGTG
30475751 GAAGCATTGG
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
44 4 0.06
45 39 0.61
47 21 0.33
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (46 bp):
ATATCATTAATTATGTATGTGAATTTTCTTACTAATGTAACATTGA
Found at i:30487731 original size:22 final size:22
Alignment explanation
Indices: 30487706--30487872 Score: 70
Period size: 21 Copynumber: 7.3 Consensus size: 22
30487696 TGAAAATTAT
30487706 GTGACTAGTTTTTAAGCATTGC
1 GTGACTAGTTTTTAAGCATTGC
** ** *
30487728 GTGACT-GACTTTGGGCATTAC
1 GTGACTAGTTTTTAAGCATTGC
*
30487749 GTGACTGGTTTCTGATAAGGCATTGC
1 GTGACTAGTTT-T--TAA-GCATTGC
** ** *
30487775 GTGACT-GACTTTCGGTATTGC
1 GTGACTAGTTTTTAAGCATTGC
*
30487796 GTGACTAGTTTTTTATAAGATATTGC
1 GTGACTAG--TTTT-TAAG-CATTGC
* **
30487822 GTGACTTGTTAGTAAGGCATTGC
1 GTGACTAGTTTTTAA-GCATTGC
* *
30487845 GTGACTAG-TTATAAGGCATTGT
1 GTGACTAGTTTTTAA-GCATTGC
30487867 GTGACT
1 GTGACT
30487873 TATGCATTGC
Statistics
Matches: 107, Mismatches: 27, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
21 28 0.26
22 27 0.25
23 16 0.15
24 6 0.06
25 5 0.05
26 25 0.23
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
GTGACTAGTTTTTAAGCATTGC
Found at i:30487774 original size:47 final size:47
Alignment explanation
Indices: 30487701--30487827 Score: 145
Period size: 47 Copynumber: 2.8 Consensus size: 47
30487691 ATTTTTGAAA
* *
30487701 ATTATGTGACTAGTTT-T--TAA-GCATTGCGTGACTGACTTTGGGC
1 ATTACGTGACTAGTTTCTGATAAGGCATTGCGTGACTGACTTTCGGC
* *
30487744 ATTACGTGACTGGTTTCTGATAAGGCATTGCGTGACTGACTTTCGGT
1 ATTACGTGACTAGTTTCTGATAAGGCATTGCGTGACTGACTTTCGGC
* * * **
30487791 ATTGCGTGACTAGTTTTTTATAAGATATTGCGTGACT
1 ATTACGTGACTAGTTTCTGATAAGGCATTGCGTGACT
30487828 TGTTAGTAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 14 0.20
44 1 0.01
46 3 0.04
47 52 0.74
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (47 bp):
ATTACGTGACTAGTTTCTGATAAGGCATTGCGTGACTGACTTTCGGC
Found at i:30487843 original size:23 final size:22
Alignment explanation
Indices: 30487808--30487873 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
30487798 GACTAGTTTT
**
30487808 TTATAAGATATTGCGTGACTTG
1 TTATAAGGCATTGCGTGACTTG
*
30487830 TTAGTAAGGCATTGCGTGACTAG
1 TTA-TAAGGCATTGCGTGACTTG
*
30487853 TTATAAGGCATTGTGTGACTT
1 TTATAAGGCATTGCGTGACTT
30487874 ATGCATTGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (22 bp):
TTATAAGGCATTGCGTGACTTG
Found at i:30487934 original size:21 final size:22
Alignment explanation
Indices: 30487906--30487961 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
30487896 ATGCAATGTA
30487906 TAAAAACTAGTCAAGTAAT-ACC
1 TAAAAACTAGTCAAGTAATGA-C
* * *
30487928 T-AAAACTAATTACGTAATGAC
1 TAAAAACTAGTCAAGTAATGAC
30487949 TAAAAACTAGTCA
1 TAAAAACTAGTCA
30487962 CATGGTGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (22 bp):
TAAAAACTAGTCAAGTAATGAC
Found at i:30489724 original size:81 final size:81
Alignment explanation
Indices: 30489617--30489844 Score: 318
Period size: 81 Copynumber: 2.8 Consensus size: 81
30489607 ATTTAAATTG
* *
30489617 GACCAATTAAAAATTAGTTATTGATCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGA
1 GACCAATCAAAATTTAGTTATTGATCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGA
30489682 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* *
30489698 GACCAATCAAAATTTAGTTATTGATCATCCAATTTATCTCTAAATAACTCAAGATAATTTAGAGA
1 GACCAATCAAAATTTAGTTATTGATCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGA
30489763 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* * * ** * * *
30489779 AACTAATCAAAATTTAATTATT-AGTCATTTAATTTATCTCT-AAT-AATTATACTAATTTAGAG
1 GACCAATCAAAATTTAGTTATTGA-TCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAG
30489841 ATAA
65 ATAA
30489845 AAATCAAATT
Statistics
Matches: 132, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
79 17 0.13
80 4 0.03
81 111 0.84
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.40
Consensus pattern (81 bp):
GACCAATCAAAATTTAGTTATTGATCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGA
TAATATTCATATTTTT
Found at i:30490066 original size:111 final size:111
Alignment explanation
Indices: 30489863--30490124 Score: 427
Period size: 111 Copynumber: 2.4 Consensus size: 111
30489853 TTTAATTATT
* * * *
30489863 TAATTTATCTCTAAATAAATTAAGATAGTTTAGAGATAATACCGAACTTCGGCCAATCAAAATTC
1 TAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAATACCGAAATTCAGCCAATCAAAATTC
*
30489928 AAGGACTCAAGGTTCGATCAATCAAAAGACTTTTAATGAGTCATCA
66 AAGGACTCAAGGTCCGATCAATCAAAAGACTTTTAATGAGTCATCA
*
30489974 TAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAATACCTAAATTCAGCCAATCAAAATTC
1 TAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAATACCGAAATTCAGCCAATCAAAATTC
* *
30490039 AAGGACTCAAGGTCC-AGCTAATGAAAAGACTTTTAATGAGTCATCA
66 AAGGACTCAAGGTCCGATC-AATCAAAAGACTTTTAATGAGTCATCA
*
30490085 TAATTTATCTTTAAATAAATTAAAATAATTTAGAGATAAT
1 TAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAAT
30490125 TCAAAGAGGC
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
110 2 0.01
111 139 0.99
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (111 bp):
TAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAATACCGAAATTCAGCCAATCAAAATTC
AAGGACTCAAGGTCCGATCAATCAAAAGACTTTTAATGAGTCATCA
Found at i:30490236 original size:18 final size:18
Alignment explanation
Indices: 30490215--30490255 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
30490205 GAGGCATGTG
*
30490215 AAGATTGGGAGGCA-TTCA
1 AAGATTGAGA-GCATTTCA
30490233 AAGATTGAGAGCATTTCA
1 AAGATTGAGAGCATTTCA
30490251 AAGAT
1 AAGAT
30490256 CAAGAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
AAGATTGAGAGCATTTCA
Found at i:30490389 original size:20 final size:20
Alignment explanation
Indices: 30490350--30490389 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30490340 ATCAAGCGAA
*
30490350 GTTCGTGATCAAGATAAAGT
1 GTTCGTGATCAAAATAAAGT
*
30490370 GTTCGTGATCAAAATTAAGT
1 GTTCGTGATCAAAATAAAGT
30490390 CGTGAAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTCGTGATCAAAATAAAGT
Found at i:30496539 original size:3 final size:3
Alignment explanation
Indices: 30496531--30496577 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
30496521 GTTTATATAT
*
30496531 TTA TTA TTA TTT TTAA TTA TTTA TTA TT- TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
30496576 TT
1 TT
30496578 TTTTACTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 29 0.76
4 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:30496556 original size:17 final size:20
Alignment explanation
Indices: 30496522--30496580 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 20
30496512 TATTACTTTG
30496522 TTTATA-TATTTATTATTATT
1 TTTATATTA-TTATTATTATT
30496542 TTTA-ATTA-T-TTATTA-T
1 TTTATATTATTATTATTATT
30496558 TTTATATTATTATTATTATT
1 TTTATATTATTATTATTATT
30496578 TTT
1 TTT
30496581 TACTATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.15
17 10 0.29
18 2 0.06
19 7 0.21
20 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTATTATT
Found at i:30513404 original size:10 final size:10
Alignment explanation
Indices: 30513391--30513423 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
30513381 CCTATATGTA
30513391 TATATATATG
1 TATATATATG
30513401 TATATATATG
1 TATATATATG
*
30513411 TATATGTATG
1 TATATATATG
30513421 TAT
1 TAT
30513424 CTATCTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:30513416 original size:6 final size:6
Alignment explanation
Indices: 30513383--30513419 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30513373 GGTAGTTTCC
*
30513383 TATATG TATATA TATATG TATA-- TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
30513420 GTATCTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.15
6 23 0.85
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:30513806 original size:13 final size:13
Alignment explanation
Indices: 30513788--30513832 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
30513778 AATATTAAGT
30513788 TTAATATAAAATA
1 TTAATATAAAATA
30513801 TTAATA-AAAATA
1 TTAATATAAAATA
30513813 TTTAAT-T-AAATA
1 -TTAATATAAAATA
30513825 TTAA-ATAA
1 TTAATATAA
30513833 TTGAATACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.18
12 12 0.43
13 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATATAAAATA
Found at i:30515297 original size:31 final size:31
Alignment explanation
Indices: 30515259--30515367 Score: 200
Period size: 31 Copynumber: 3.5 Consensus size: 31
30515249 GTGTCAGCGT
30515259 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
30515290 TGGCGTGTTACAACATGTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
30515321 TGGCGTGTTACAATATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
30515352 TGGCGTGTTACAACAT
1 TGGCGTGTTACAACAT
30515368 GTTGACAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:30522403 original size:118 final size:117
Alignment explanation
Indices: 30522075--30522411 Score: 435
Period size: 118 Copynumber: 2.9 Consensus size: 117
30522065 TATGCTAAGC
30522075 TGACACGTTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCATTATTGTGAGGTGA
1 TGACAC-TTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCATTATTGTGAGGTGA
* * * * * *
30522140 CA-TAGCATGCCCCATCTTGTGGTGACAAGATTAGTGGAAGCAGATAGTTGGCG
65 CACGA-CACGCCCCATCTTGTGGTGACACGCTGAGTGGAAACAGATAGTTGGCG
* * * *
30522193 TGACA-TGCTGAGTGCATGCAGATTTCTGTGGTAACACGCTGACTTCTTGTAGTATTGTGGGGTG
1 TGACACT--TGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCATTATTGTGAGGTG
** * * *
30522257 ACACGGTACACCCCAACTAGTGGTGACACGCTGAGTGGAAACAGATAGTTGGCG
64 ACACGACACGCCCCATCTTGTGGTGACACGCTGAGTGGAAACAGATAGTTGGCG
* * * *
30522311 TGACACTATGAGTACATGCAAATTTCTGTGGTGACATGCTAACTTCTTGCATTATTGTGAGGTGA
1 TGACACT-TGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCATTATTGTGAGGTGA
*
30522376 CACGACACGCCCCATCTTGTGGTGACACACTGAGTG
65 CACGACACGCCCCATCTTGTGGTGACACGCTGAGTG
30522412 CATGCAGATT
Statistics
Matches: 185, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
116 1 0.01
118 183 0.99
119 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (117 bp):
TGACACTTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCATTATTGTGAGGTGAC
ACGACACGCCCCATCTTGTGGTGACACGCTGAGTGGAAACAGATAGTTGGCG
Found at i:30522410 original size:87 final size:87
Alignment explanation
Indices: 30522310--30522489 Score: 256
Period size: 87 Copynumber: 2.1 Consensus size: 87
30522300 GATAGTTGGC
* * *
30522310 GTGACACTATGAGTACATGCAAATTTCTGTGGTGACATGCTAACTTCTTGCATTATTGTGAGG-T
1 GTGACACTATGAGTACATGCAAATTTCTGTGGTGACACGCTAACTTCTTACAGTATTGTG-GGAT
30522374 GACACGACACGCCCCATCTTGTG
65 GACACGACACGCCCCATCTTGTG
* * * *
30522397 GTGACAC-ACTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTATAGTATTGTGGGAT
1 GTGACACTA-TGAGTACATGCAAATTTCTGTGGTGACACGCTAACTTCTTACAGTATTGTGGGAT
*
30522461 GACACGGCACGCCCCATCTTGTG
65 GACACGACACGCCCCATCTTGTG
30522484 GTGACA
1 GTGACA
30522490 AGCTAAGTGA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
86 3 0.04
87 80 0.96
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (87 bp):
GTGACACTATGAGTACATGCAAATTTCTGTGGTGACACGCTAACTTCTTACAGTATTGTGGGATG
ACACGACACGCCCCATCTTGTG
Found at i:30522520 original size:87 final size:87
Alignment explanation
Indices: 30522336--30522526 Score: 210
Period size: 87 Copynumber: 2.2 Consensus size: 87
30522326 ATGCAAATTT
* * ** *
30522336 CTGTGGTGACATGCTAACTTCTTGCATTATTGTGAGGTGACACGACACGCCCCATCTTGTGGTGA
1 CTGTGGTGACACGCTGACTTCTTATAGTATTGTGAGGTGACACGACACGCCCCATCTTGTGGTGA
* * ** * *
30522401 CACACTGAGTGCATGCAGATTT
66 CACACTAAGTGAAACCAGAATA
*
30522423 CTGTGGTGACACGCTGACTTCTTATAGTATTGTG-GGATGACACGGCACGCCCCATCTTGTGGTG
1 CTGTGGTGACACGCTGACTTCTTATAGTATTGTGAGG-TGACACGACACGCCCCATCTTGTGGTG
30522487 ACA-AGCTAAGTGAAACCA-AATA
65 ACACA-CTAAGTGAAACCAGAATA
30522509 CT-TGGCATGACACGCTGA
1 CTGTGG--TGACACGCTGA
30522527 GCCGCTGGTG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
85 3 0.03
86 7 0.08
87 78 0.89
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (87 bp):
CTGTGGTGACACGCTGACTTCTTATAGTATTGTGAGGTGACACGACACGCCCCATCTTGTGGTGA
CACACTAAGTGAAACCAGAATA
Found at i:30527972 original size:31 final size:31
Alignment explanation
Indices: 30527753--30527976 Score: 315
Period size: 31 Copynumber: 7.2 Consensus size: 31
30527743 CCATAATATG
* *
30527753 GTAACATGCCATGCATATAACGTAAAATGTG
1 GTAACACGCCATGCATATAACGTAAAATGTT
*
30527784 GTAACACGCCATGCATATAACGTAAAATGTG
1 GTAACACGCCATGCATATAACGTAAAATGTT
30527815 GTAACACGCCATGCATATAACGTAAAATGTT
1 GTAACACGCCATGCATATAACGTAAAATGTT
* *
30527846 GTAACACGTCATGCATATAATGTAAAATGTT
1 GTAACACGCCATGCATATAACGTAAAATGTT
* *
30527877 GTAACACGTCATGCATATAACGTAAAATGTG
1 GTAACACGCCATGCATATAACGTAAAATGTT
* * *
30527908 GTAACACGTCATGCATATAATGTAAAATATT
1 GTAACACGCCATGCATATAACGTAAAATGTT
* **
30527939 GTAACACGCCATGCGTATCAA-GTCGAATGTT
1 GTAACACGCCATGCATAT-AACGTAAAATGTT
30527970 GTAACAC
1 GTAACAC
30527977 ACCAATGCTG
Statistics
Matches: 178, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
31 176 0.99
32 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (31 bp):
GTAACACGCCATGCATATAACGTAAAATGTT
Found at i:30528713 original size:47 final size:47
Alignment explanation
Indices: 30528659--30528968 Score: 329
Period size: 47 Copynumber: 6.6 Consensus size: 47
30528649 ATGGAGTCTG
* * * * *
30528659 ACAAACTCTAAACCCTACCGTGTCATAGATTCCCTCCATGACGTGTC
1 ACAAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
* * *
30528706 ACAAACTCTAAACGCTGGCGTGTCACAGATTCCCTCTATGACATGTC
1 ACAAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
* ** * *
30528753 ACGAAA-TCTGAACGTTAATGTGTCACAGATTCCCTCCATGGCGTGTC
1 AC-AAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
* * * *
30528800 ACGAACACTGAATGCT-GACGTGTCACAAATTCCCTCCATGACATGTC
1 ACAAACTCTGAACGCTAG-CGTGTCACAGATTCCCTCCATGACATGTC
* * * * *
30528847 ACGAATTCTGAACACTGGCGTGTCACAGATTCCCTCCATGACGTGTC
1 ACAAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
* * *
30528894 ACAAACTTTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCATGTC
1 ACAAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
* *
30528941 ACAAACTCTAAAC-CTTGTCGTGTCACAG
1 ACAAACTCTGAACGCTAG-CGTGTCACAG
30528969 CCGTGTCACA
Statistics
Matches: 217, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
46 5 0.02
47 208 0.96
48 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (47 bp):
ACAAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGACATGTC
Found at i:30528798 original size:94 final size:94
Alignment explanation
Indices: 30528677--30528942 Score: 370
Period size: 94 Copynumber: 2.8 Consensus size: 94
30528667 TAAACCCTAC
* * *
30528677 CGTGTCATAGATTCCCTCCATGACGTGTCACAAACTCTAAACGCTGGCGTGTCACAGATTCCCTC
1 CGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCTGGCGTGTCACAAATTCCCTC
* **
30528742 TATGACATGTCACGAAATCTGAACGTTAA
66 CATGACATGTCACGAAATCTGAACACTAA
* * * * * *
30528771 TGTGTCACAGATTCCCTCCATGGCGTGTCACGAACACTGAATGCTGACGTGTCACAAATTCCCTC
1 CGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCTGGCGTGTCACAAATTCCCTC
* **
30528836 CATGACATGTCACGAATTCTGAACACTGG
66 CATGACATGTCACGAAATCTGAACACTAA
* *
30528865 CGTGTCACAGATTCCCTCCATGACGTGTCACAAACTTTGAACGCTAGCGTGTCACAAATTCCCTC
1 CGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCTGGCGTGTCACAAATTCCCTC
*
30528930 CATGGCATGTCAC
66 CATGACATGTCAC
30528943 AAACTCTAAA
Statistics
Matches: 148, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 148 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (94 bp):
CGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCTGGCGTGTCACAAATTCCCTC
CATGACATGTCACGAAATCTGAACACTAA
Found at i:30528906 original size:141 final size:141
Alignment explanation
Indices: 30528677--30528942 Score: 381
Period size: 141 Copynumber: 1.9 Consensus size: 141
30528667 TAAACCCTAC
* * * *
30528677 CGTGTCATAGATTCCCTCCATGACGTGTCACAAACTCTAAACGCTGGCGTGTCACAGATTCCCTC
1 CGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTGGCGTGTCACAGATTCCCTC
* * * * *
30528742 TATGACATGTCACGAAATCTGAACGTTAATGTGTCACAGATTCCCTCCATGGCGTGTCACGAACA
66 CATGACATGTCACGAAATCTGAACGCTAACGTGTCACAAATTCCCTCCATGGCATGTCACGAACA
30528807 CTGAATGCTGA
131 CTGAATGCTGA
* * *
30528818 CGTGTCACAAATTCCCTCCATGACATGTCACGAATTCTGAACACTGGCGTGTCACAGATTCCCTC
1 CGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTGGCGTGTCACAGATTCCCTC
* * *
30528883 CATGACGTGTCAC-AAACTTTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCATGTCAC
66 CATGACATGTCACGAAA-TCTGAACGCTAACGTGTCACAAATTCCCTCCATGGCATGTCAC
30528943 AAACTCTAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
140 3 0.03
141 106 0.97
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (141 bp):
CGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTGGCGTGTCACAGATTCCCTC
CATGACATGTCACGAAATCTGAACGCTAACGTGTCACAAATTCCCTCCATGGCATGTCACGAACA
CTGAATGCTGA
Found at i:30528944 original size:23 final size:23
Alignment explanation
Indices: 30528772--30528945 Score: 93
Period size: 23 Copynumber: 7.4 Consensus size: 23
30528762 GAACGTTAAT
*
30528772 GTGTCACAGATTCCCTCCATGGC
1 GTGTCACAAATTCCCTCCATGGC
* * **
30528795 GTGTCACGAA--CACTGAATGCTGAC
1 GTGTCACAAATTCCCTCCATG--G-C
*
30528819 GTGTCACAAATTCCCTCCATGAC
1 GTGTCACAAATTCCCTCCATGGC
* * ****
30528842 ATGTCACGAATTCTGAACACTGGC
1 GTGTCACAAATTCCCTCCA-TGGC
* *
30528866 GTGTCACAGATTCCCTCCATGAC
1 GTGTCACAAATTCCCTCCATGGC
**** *
30528889 GTGTCACAAACTTTGAACGC-TAGC
1 GTGTCACAAA-TTCCCTC-CATGGC
30528913 GTGTCACAAATTCCCTCCATGGC
1 GTGTCACAAATTCCCTCCATGGC
*
30528936 ATGTCACAAA
1 GTGTCACAAA
30528946 CTCTAAACCT
Statistics
Matches: 104, Mismatches: 38, Indels: 18
0.65 0.24 0.11
Matches are distributed among these distances:
21 6 0.06
22 1 0.01
23 50 0.48
24 40 0.38
25 1 0.01
26 6 0.06
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (23 bp):
GTGTCACAAATTCCCTCCATGGC
Found at i:30528963 original size:94 final size:93
Alignment explanation
Indices: 30528659--30528968 Score: 365
Period size: 94 Copynumber: 3.3 Consensus size: 93
30528649 ATGGAGTCTG
* * * *
30528659 ACAAACTCTAAACCCTACCGTGTCATAGATTCCCTCCATGACGTGTCACAAACTCTAAACGCTGG
1 ACAAACTCTAAACCTTATCGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCT-G
* *
30528724 CGTGTCACAGATTCCCTCTATGACATGTC
65 CGTGTCACAAATTCCCTCCATGACATGTC
* * * * * *
30528753 ACGAAA-TCTGAACGTTAAT-GTGTCACAGATTCCCTCCATGGCGTGTCACGAACACTGAATGCT
1 AC-AAACTCTAAACCTT-ATCGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCT
30528816 GACGTGTCACAAATTCCCTCCATGACATGTC
64 G-CGTGTCACAAATTCCCTCCATGACATGTC
* * * ** *
30528847 ACGAATTCTGAACAC-TGGCGTGTCACAGATTCCCTCCATGACGTGTCACAAACTTTGAACGCTA
1 ACAAACTCTAAAC-CTTATCGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCT-
*
30528911 GCGTGTCACAAATTCCCTCCATGGCATGTC
64 GCGTGTCACAAATTCCCTCCATGACATGTC
*
30528941 ACAAACTCTAAACCTTGTCGTGTCACAG
1 ACAAACTCTAAACCTTATCGTGTCACAG
30528969 CCGTGTCACA
Statistics
Matches: 182, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
93 4 0.02
94 173 0.95
95 5 0.03
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (93 bp):
ACAAACTCTAAACCTTATCGTGTCACAGATTCCCTCCATGACGTGTCACAAACTCTGAACGCTGC
GTGTCACAAATTCCCTCCATGACATGTC
Found at i:30528963 original size:141 final size:140
Alignment explanation
Indices: 30528659--30528967 Score: 379
Period size: 141 Copynumber: 2.2 Consensus size: 140
30528649 ATGGAGTCTG
* * * *
30528659 ACAAACTCTAAACCCT-ACCGTGTCATAGATTCCCTCCATGACGTGTCACAAACTCTAAACGCTG
1 ACAAACTCTAAA-CCTGA-CGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTG
* * * *
30528723 GCGTGTCACAGATTCCCTCTATGACATGTCACGAAATCTGAACGTTAATGTGTCACAGATTCCCT
64 GCGTGTCACAGATTCCCTCCATGACATGTCACGAAATCTGAACGCTAACGTGTCACAAATTCCCT
*
30528788 CCATGGCGTGTC
129 CCATGGCATGTC
* * ** * * *
30528800 ACGAACACTGAATGCTGACGTGTCACAAATTCCCTCCATGACATGTCACGAATTCTGAACACTGG
1 ACAAACTCT-AAACCTGACGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTGG
* * *
30528865 CGTGTCACAGATTCCCTCCATGACGTGTCAC-AAACTTTGAACGCTAGCGTGTCACAAATTCCCT
65 CGTGTCACAGATTCCCTCCATGACATGTCACGAAA-TCTGAACGCTAACGTGTCACAAATTCCCT
30528929 CCATGGCATGTC
129 CCATGGCATGTC
*
30528941 ACAAACTCTAAACCTTGTCGTGTCACA
1 ACAAACTCTAAACC-TGACGTGTCACA
30528968 GCCGTGTCAC
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
140 6 0.04
141 131 0.94
142 3 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (140 bp):
ACAAACTCTAAACCTGACGTGTCACAAATTCCCTCCATGACATGTCACAAACTCTAAACACTGGC
GTGTCACAGATTCCCTCCATGACATGTCACGAAATCTGAACGCTAACGTGTCACAAATTCCCTCC
ATGGCATGTC
Found at i:30529002 original size:58 final size:57
Alignment explanation
Indices: 30528912--30529059 Score: 197
Period size: 58 Copynumber: 2.5 Consensus size: 57
30528902 TGAACGCTAG
* * * * * * *
30528912 CGTGTCACAAATTCCCTCCATGGCATGTCACAAACTCTAAACCTTGTCGTGTCACAGC
1 CGTGTCACACATT-CCACCATGTCGTGTCACAAACTCTAAACCCTGCCGTGTCACAAC
30528970 CGTGTCACACATTCCAACCATGTCGTGTCACAAACTCTAAACCCTGCCGTGTCACAAC
1 CGTGTCACACATTCC-ACCATGTCGTGTCACAAACTCTAAACCCTGCCGTGTCACAAC
*
30529028 CGTATCACACATTCTCACCATGTCGTGTCACA
1 CGTGTCACACATTC-CACCATGTCGTGTCACA
30529060 TATTCCCAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 77 0.96
59 1 0.01
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.25
Consensus pattern (57 bp):
CGTGTCACACATTCCACCATGTCGTGTCACAAACTCTAAACCCTGCCGTGTCACAAC
Found at i:30529058 original size:23 final size:23
Alignment explanation
Indices: 30529032--30529082 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
30529022 CACAACCGTA
* *
30529032 TCACACATTCTCACCATGTCGTG
1 TCACACATTCCCAACATGTCGTG
* *
30529055 TCACATATTCCCAACATGTCGTT
1 TCACACATTCCCAACATGTCGTG
30529078 TCACA
1 TCACA
30529083 AACTCTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.31
Consensus pattern (23 bp):
TCACACATTCCCAACATGTCGTG
Found at i:30544897 original size:2 final size:2
Alignment explanation
Indices: 30544890--30544924 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30544880 TGGGTGGCTT
*
30544890 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30544925 TAAGTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30544991 original size:2 final size:2
Alignment explanation
Indices: 30544986--30545020 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30544976 GAAATAGNCT
30544986 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30545021 AGTTTCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30544998 original size:93 final size:93
Alignment explanation
Indices: 30544892--30545075 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
30544882 GGTGGCTTTA
30544892 TATATAAATATATATATATATATATATATATAT-TAAGTTTACTTTAAATGAATTGAATATTTTG
1 TATATAAATATATATATATATATATATATATATATAAGTTT-CTTTAAATGAATTGAATATTTTG
30544956 TTCCTTTATCTTCTATATATGAAATAGNCT
65 TTCCTTTATCTTCTATATATGAAATAG-CT
*
30544986 TATATATA-ATATATATATATATATATATATATATAAGTTTCTTTAAATGAATTGAATATTTTGT
1 TATATAAATATATATATATATATATATATATATATAAGTTTCTTTAAATGAATTGAATATTTTGT
30545050 TCCTTTATCTTCTATATATGAAATAG
66 TCCTTTATCTTCTATATATGAAATAG
30545076 GGTCAAGCAT
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
93 74 0.84
94 14 0.16
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (93 bp):
TATATAAATATATATATATATATATATATATATATAAGTTTCTTTAAATGAATTGAATATTTTGT
TCCTTTATCTTCTATATATGAAATAGCT
Found at i:30547454 original size:34 final size:35
Alignment explanation
Indices: 30547411--30547480 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
30547401 CTGTTGAGTA
* *
30547411 GTTCATTTCCTTAAATG-TTTTTTGACTTTCACAG
1 GTTCATTTCCTGAAATGTTTTTTTGACTTCCACAG
30547445 GTTCATTTCCTGAAATGTTTTTTTGACTTCCACAG
1 GTTCATTTCCTGAAATGTTTTTTTGACTTCCACAG
30547480 G
1 G
30547481 GTGTACTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 16 0.48
35 17 0.52
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (35 bp):
GTTCATTTCCTGAAATGTTTTTTTGACTTCCACAG
Found at i:30553342 original size:2 final size:2
Alignment explanation
Indices: 30553335--30553415 Score: 91
Period size: 2 Copynumber: 42.5 Consensus size: 2
30553325 TGCCAAAACA
* * *
30553335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AGC AT -T NT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
30553376 AT A- AT AT AT AT AT AT AT -T AT AT AT AT -T 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
30553415 A
1 A
30553416 ATAGCATTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
1 5 0.07
2 62 0.91
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30553382 original size:24 final size:26
Alignment explanation
Indices: 30553344--30553423 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
30553334 AATATATATA
30553344 TATATATATATATATATATAATAGCAT
1 TATATA-ATATATATATATAATAGCAT
* **
30553371 TNTA-AATA-ATATATATATATATTAT
1 TATATAATATATATATATA-ATAGCAT
*
30553396 ATATATTATATATATATATAATAGCAT
1 -TATATAATATATATATATAATAGCAT
30553423 T
1 T
30553424 CTTAATTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 9 0.21
25 8 0.19
26 5 0.12
27 11 0.26
28 9 0.21
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (26 bp):
TATATAATATATATATATAATAGCAT
Found at i:30553919 original size:2 final size:2
Alignment explanation
Indices: 30553912--30553936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30553902 CATATAAATT
30553912 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30553937 GCAGCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30566311 original size:2 final size:2
Alignment explanation
Indices: 30566304--30566354 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
30566294 AGGCAAATTT
*
30566304 TA TA TA TA TA TA TA TA T- TA TA T- TA CTA CTA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA
30566346 TA TA TA TA T
1 TA TA TA TA T
30566355 GGGTGCATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.84
3 5 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30577649 original size:26 final size:26
Alignment explanation
Indices: 30577615--30577674 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
30577605 GTAGTCATTT
30577615 TTGGTTCTACAAGTTGTTGCAAAATA
1 TTGGTTCTACAAGTTGTTGCAAAATA
30577641 TTGGTTCTACAAGTTGTTGCAAAATA
1 TTGGTTCTACAAGTTGTTGCAAAATA
30577667 TTGGTTCT
1 TTGGTTCT
30577675 GAATATAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (26 bp):
TTGGTTCTACAAGTTGTTGCAAAATA
Found at i:30579972 original size:21 final size:21
Alignment explanation
Indices: 30579946--30580002 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
30579936 TTTTTTTCAA
30579946 CATGACGTGTAACAACCTAAC
1 CATGACGTGTAACAACCTAAC
*
30579967 CATGACATGTAACAACCTAAC
1 CATGACGTGTAACAACCTAAC
30579988 CATGACGTGTAACAA
1 CATGACGTGTAACAA
30580003 TAATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.19
Consensus pattern (21 bp):
CATGACGTGTAACAACCTAAC
Found at i:30580084 original size:45 final size:45
Alignment explanation
Indices: 30580018--30580270 Score: 328
Period size: 45 Copynumber: 5.6 Consensus size: 45
30580008 TTTTTGTTCA
* * * *
30580018 ACATGGCGTATAACAACCTAACCATGGCTTATCACATGTTATTGT
1 ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
*
30580063 ACATGACGTGTAACAATCTAACCATGGCTTGTCACATGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
* **
30580108 ACATGACGTGTAACAATCTAATTATGGCTTGTCACATGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
*
30580153 ATATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
*** * * * * *
30580198 ACATGGTATGTAACAACCTAACCATAGCTTGCCATATATTTTTAT
1 ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
*
30580243 ACATGGCGTGTAACAACCT-ACCTATGGC
1 ACATGACGTGTAACAACCTAACC-ATGGC
30580271 ATGTAACAAC
Statistics
Matches: 184, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 3 0.02
45 181 0.98
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (45 bp):
ACATGACGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGT
Found at i:30580286 original size:66 final size:66
Alignment explanation
Indices: 30580200--30580325 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
30580190 GTTTTTGTAC
* * * *
30580200 ATGGTATGTAACAACCTAACCAT-AGCTTGCCATATATTTTTATACATGGCGTGTAACAACCTAC
1 ATGGCATGTAACAACCTAACCATGA-CTTGCCACATATTTTTATACATAGCGTATAACAACCTAC
30580264 CT
65 CT
* * *
30580266 ATGGCATGTAACAACCTAACCATGATTTGTCACATATTTTTGTACATAGCGTATAACAAC
1 ATGGCATGTAACAACCTAACCATGACTTGCCACATATTTTTATACATAGCGTATAACAAC
30580326 ACAGCGTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (66 bp):
ATGGCATGTAACAACCTAACCATGACTTGCCACATATTTTTATACATAGCGTATAACAACCTACC
T
Found at i:30580823 original size:18 final size:18
Alignment explanation
Indices: 30580802--30580836 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30580792 TAATTAAATA
30580802 AAAAAATATAA-ATTTAAT
1 AAAAAATA-AATATTTAAT
30580820 AAAAAATAAATATTTAA
1 AAAAAATAAATATTTAA
30580837 ATTTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATAAATATTTAAT
Found at i:30580886 original size:233 final size:241
Alignment explanation
Indices: 30580556--30581154 Score: 677
Period size: 253 Copynumber: 2.5 Consensus size: 241
30580546 TTAATGTAAT
* * * *
30580556 AAGTTAATTAAGTAAAAATAATTTAAATTTAATAAAAAATAAATATTTAAA-TTTATATTCTTAG
1 AAGTTAATTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTTATTTTC-TCG
* *
30580620 GGTAAAAGTGTTTAACGATGTACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
65 GTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
*
30580685 TTATAATT-CAA-AAT-TG-G-TAT-A-GAAAAAC-ATTGATGTAAAAACTTGTAAATGTGAAAT
130 TTATAATTAAAATAATATGAGCTATGACGAAAAACAATTGATGTAAAAACTTGTAAATGTGAAAT
* * *
30580742 AACTAAATTTTAAATATTAATGTAAATGTGTGGGAGTTAACATAA-A
195 AACTAAAATTTAAATATTAATGTAAATGTATGAGAGTTAACATAACA
*
30580788 AAGTTAATTAAATAAAAA-AATATAAATTTAATAAAAAATAAATATTTAAATTTCTATTTTCTCG
1 AAGTTAATTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTT-TATTTTCTCG
*
30580852 AGTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAATGATAAAAATA
65 -GTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
* *
30580917 ATTATAGTTAAAAATTAATATGAAAAAGCTTTGACGAAAAACTGTAAGAATTGATGTAAAAACTT
129 ATTATAATT-AAAA-TAATATG----AGCTATGACGAAAAAC------AATTGATGTAAAAACTT
* * * * *
30580982 GTAAATGTGGAATAATTAAAATTTAAATCTTAATGTAAGTGTATGAGAGTTAACGTAACA
182 GTAAATGTGAAATAACTAAAATTTAAATATTAATGTAAATGTATGAGAGTTAACATAACA
* * * * *
30581042 AA-TCAATTAAGGAAAAACAATCTAAATTTAATGAAAAAT-AATATTTAAA-TTTATATTCTCGG
1 AAGTTAATTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTTATTTTCTCGG
* * *** * *
30581104 ATTAAATGTATTTATTAACATACAAATTTTAATTTTTAAATAAAAAATAAT
66 -TTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT
30581155 TATAGTTTAA
Statistics
Matches: 310, Mismatches: 31, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
231 31 0.10
232 21 0.07
233 75 0.24
235 2 0.01
237 3 0.01
238 2 0.01
243 1 0.00
244 2 0.01
245 1 0.00
246 7 0.02
250 1 0.00
251 52 0.17
252 2 0.01
253 88 0.28
254 22 0.07
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (241 bp):
AAGTTAATTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTTATTTTCTCGG
TTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAAT
TATAATTAAAATAATATGAGCTATGACGAAAAACAATTGATGTAAAAACTTGTAAATGTGAAATA
ACTAAAATTTAAATATTAATGTAAATGTATGAGAGTTAACATAACA
Found at i:30581320 original size:27 final size:25
Alignment explanation
Indices: 30581290--30581350 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
30581280 ATTTTATTGA
* *
30581290 ATTAAATTAATTATATATTTTTTTAAT
1 ATTAAAATAA-TA-ATATTTTTATAAT
30581317 ATTAAAATAATAATATTTTTATAAT
1 ATTAAAATAATAATATTTTTATAAT
*
30581342 -TTATAATAA
1 ATTAAAATAA
30581351 AAAACAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.26
25 12 0.39
26 2 0.06
27 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAAAATAATAATATTTTTATAAT
Found at i:30588661 original size:30 final size:30
Alignment explanation
Indices: 30588634--30588712 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
30588624 CCCGGACCAA
* *
30588634 AGCCGCCAGGTCCCCCTGGACCAGGACCCC
1 AGCCTCCAGGCCCCCCTGGACCAGGACCCC
30588664 AGCCTCCAGGCCCCCCTGGACCAGGACCCC
1 AGCCTCCAGGCCCCCCTGGACCAGGACCCC
30588694 AGCCTCCAGGCCCCCCTGG
1 AGCCTCCAGGCCCCCCTGG
30588713 TCCTCCTGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.15, C:0.52, G:0.25, T:0.08
Consensus pattern (30 bp):
AGCCTCCAGGCCCCCCTGGACCAGGACCCC
Found at i:30588708 original size:15 final size:15
Alignment explanation
Indices: 30588654--30588707 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
30588644 TCCCCCTGGA
30588654 CCAGGACCCCAGCCT
1 CCAGGACCCCAGCCT
30588669 CCAGG-CCCC--CCT
1 CCAGGACCCCAGCCT
30588681 GGACCAGGACCCCAGCCT
1 ---CCAGGACCCCAGCCT
30588699 CCAGG-CCCC
1 CCAGGACCCC
30588708 CCTGGTCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.09
14 8 0.24
15 15 0.45
16 4 0.12
18 3 0.09
ACGTcount: A:0.17, C:0.56, G:0.22, T:0.06
Consensus pattern (15 bp):
CCAGGACCCCAGCCT
Found at i:30588726 original size:9 final size:9
Alignment explanation
Indices: 30588696--30588737 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
30588686 AGGACCCCAG
*
30588696 CCTCCAGGC
1 CCTCCTGGC
* *
30588705 CCCCCTGGT
1 CCTCCTGGC
30588714 CCTCCTGGC
1 CCTCCTGGC
30588723 CCTCCTGGC
1 CCTCCTGGC
30588732 CCTCCT
1 CCTCCT
30588738 CCCGGTCCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.57, G:0.19, T:0.21
Consensus pattern (9 bp):
CCTCCTGGC
Found at i:30592652 original size:2 final size:2
Alignment explanation
Indices: 30592645--30592688 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
30592635 AATCAATGAC
30592645 GA GA GA GA GA GA GA GA GA GA GA GA GA G- 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
30592686 GA G
1 GA G
30592689 GACCCCGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30597030 original size:2 final size:2
Alignment explanation
Indices: 30597023--30597062 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30597013 CGTGTCATTC
30597023 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
30597063 GACTGAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30597270 original size:41 final size:40
Alignment explanation
Indices: 30597225--30597320 Score: 97
Period size: 41 Copynumber: 2.4 Consensus size: 40
30597215 CATATTAGGT
* *
30597225 TATTAGATTATATTATTGAGATATAATATGTTATGATAGAC
1 TATTAGATTATATTATTAAGATATAATATGTTATAATAG-C
* * * *
30597266 TATTAGGTT-TAACTGTTAAGATATAATATGTTATAATAGG
1 TATTAGATTAT-ATTATTAAGATATAATATGTTATAATAGC
30597306 T-TTAGATTTATATTA
1 TATTAGA-TTATATTA
30597321 AAACTTAATG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
39 4 0.09
40 6 0.14
41 33 0.77
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.46
Consensus pattern (40 bp):
TATTAGATTATATTATTAAGATATAATATGTTATAATAGC
Found at i:30597747 original size:19 final size:19
Alignment explanation
Indices: 30597723--30597764 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
30597713 ATTTATTTTT
30597723 AAAAATTAAAATAATAGAA
1 AAAAATTAAAATAATAGAA
* *
30597742 AAAAATTCACATAATAGAA
1 AAAAATTAAAATAATAGAA
30597761 AAAA
1 AAAA
30597765 GAAAAACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAATTAAAATAATAGAA
Found at i:30597916 original size:12 final size:12
Alignment explanation
Indices: 30597899--30597965 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
30597889 TAAATAGAAT
*
30597899 AAAAATTAATAA
1 AAAAATAAATAA
30597911 AAAAATAAATAA
1 AAAAATAAATAA
*
30597923 TAATAAT-AATAA
1 -AAAAATAAATAA
* * *
30597935 TAATATAAAT-T
1 AAAAATAAATAA
*
30597946 TAAAA-AAATAA
1 AAAAATAAATAA
30597957 AAAAATAAA
1 AAAAATAAA
30597966 ATTGAGTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
10 4 0.10
11 11 0.26
12 22 0.52
13 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:30597960 original size:7 final size:8
Alignment explanation
Indices: 30597896--30597966 Score: 52
Period size: 8 Copynumber: 7.9 Consensus size: 8
30597886 GAGTAAATAG
30597896 AATAAAAA
1 AATAAAAA
30597904 TTAATAAAAA
1 --AATAAAAA
30597914 AATAAATAA
1 AATAAA-AA
*
30597923 TAATAATAAT
1 -AATAA-AAA
30597933 AATAATATAA
1 AATAA-A-AA
*
30597943 ATTTAAAAA
1 A-ATAAAAA
30597952 AATAAAAA
1 AATAAAAA
30597960 AATAAAA
1 AATAAAA
30597967 TTGAGTGAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 19 0.37
9 12 0.23
10 17 0.33
11 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAAAAA
Found at i:30618458 original size:17 final size:18
Alignment explanation
Indices: 30618436--30618470 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
30618426 TTAGTTAAAT
30618436 GTAGAACATGAT-TGATA
1 GTAGAACATGATATGATA
*
30618453 GTAGAAGATGATATGATA
1 GTAGAACATGATATGATA
30618471 AGTGAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (18 bp):
GTAGAACATGATATGATA
Found at i:30659189 original size:30 final size:30
Alignment explanation
Indices: 30659155--30659212 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
30659145 GCACAAGGGC
30659155 AATTAAAAAGATCAGTCATCAGCAGGAAGA
1 AATTAAAAAGATCAGTCATCAGCAGGAAGA
30659185 AATTAAAAAGATCAGTCATCAGCAGGAA
1 AATTAAAAAGATCAGTCATCAGCAGGAA
30659213 ATTGCAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (30 bp):
AATTAAAAAGATCAGTCATCAGCAGGAAGA
Found at i:30662888 original size:12 final size:12
Alignment explanation
Indices: 30662871--30662896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30662861 CCTGTACTTA
30662871 AACCAAGTTCAG
1 AACCAAGTTCAG
30662883 AACCAAGTTCAG
1 AACCAAGTTCAG
30662895 AA
1 AA
30662897 AGGGACTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AACCAAGTTCAG
Found at i:30667647 original size:26 final size:26
Alignment explanation
Indices: 30667553--30667653 Score: 89
Period size: 25 Copynumber: 4.0 Consensus size: 26
30667543 TTACGGCATT
* *
30667553 CATCCACTTTTGGTGGT-AAATTATC
1 CATCCACTTCTAGTGGTAAAATTATC
* * *
30667578 TATTCACTTCTAGTGGCAAAATTATC
1 CATCCACTTCTAGTGGTAAAATTATC
* ** * *
30667604 CTTAGA-TTCTAATAGTAAAATTATC
1 CATCCACTTCTAGTGGTAAAATTATC
*
30667629 CATCCACTTCTGGTGGTAAAATTAT
1 CATCCACTTCTAGTGGTAAAATTAT
30667654 AATTAAAATT
Statistics
Matches: 56, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
25 31 0.55
26 25 0.45
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (26 bp):
CATCCACTTCTAGTGGTAAAATTATC
Found at i:30694646 original size:2 final size:2
Alignment explanation
Indices: 30694641--30694689 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
30694631 TTTTGTTTTT
*
30694641 TC TC TC TC TAC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TT TC
1 TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30694683 TC TC TC T
1 TC TC TC T
30694690 AATGCCGTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30700220 original size:23 final size:22
Alignment explanation
Indices: 30700178--30700221 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
30700168 ATCTTAATTT
*
30700178 TTATATATTTTAATATAATTAA
1 TTATATATTTTAATAAAATTAA
30700200 TTATATTATTATT-ATAAAATTA
1 TTATA-TATT-TTAATAAAATTA
30700222 GAAGGCTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATATTTTAATAAAATTAA
Found at i:30702351 original size:44 final size:44
Alignment explanation
Indices: 30702288--30702375 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
30702278 GAATACTAAG
*
30702288 AGGTATTGATAGGATTAAACTGCATTCATCTGGAAGGAAAACGC
1 AGGTATTGATAGGATTAAACTGCATTCATATGGAAGGAAAACGC
30702332 AGGTATTGATAGGATTAAACTGCATTCATATGGAAGGAAAACGC
1 AGGTATTGATAGGATTAAACTGCATTCATATGGAAGGAAAACGC
30702376 TCCTTACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (44 bp):
AGGTATTGATAGGATTAAACTGCATTCATATGGAAGGAAAACGC
Found at i:30702369 original size:24 final size:23
Alignment explanation
Indices: 30702298--30702369 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
30702288 AGGTATTGAT
30702298 AGGATTAAACTGCATTCATCTGGA
1 AGGATTAAACTGCATTCAT-TGGA
*
30702322 AGGA--AAAC-GCAGGT-ATT-GA
1 AGGATTAAACTGCA-TTCATTGGA
30702341 TAGGATTAAACTGCATTCATATGGA
1 -AGGATTAAACTGCATTCAT-TGGA
30702366 AGGA
1 AGGA
30702370 AAACGCTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
19 2 0.05
20 5 0.13
21 5 0.13
22 10 0.26
23 5 0.13
24 9 0.24
25 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (23 bp):
AGGATTAAACTGCATTCATTGGA
Found at i:30702807 original size:10 final size:8
Alignment explanation
Indices: 30702780--30702832 Score: 61
Period size: 8 Copynumber: 6.0 Consensus size: 8
30702770 AATTAAATAA
30702780 ATTTTTATT
1 ATTTTTA-T
30702789 ATTTTATTAT
1 A-TTT-TTAT
30702799 ATTTAATTAT
1 ATTT--TTAT
30702809 ATTTTTAT
1 ATTTTTAT
30702817 ATTTTTAT
1 ATTTTTAT
30702825 ATTTTTAT
1 ATTTTTAT
30702833 TTTGAGTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 20 0.49
9 4 0.10
10 14 0.34
11 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:30702816 original size:18 final size:17
Alignment explanation
Indices: 30702783--30702832 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
30702773 TAAATAAATT
30702783 TTTATTAT-TTTATTATA
1 TTTATTATATTT-TTATA
30702800 TTTAATTATATTTTTATA
1 TTT-ATTATATTTTTATA
30702818 TTT-TTATATTTTTAT
1 TTTATTATATTTTTAT
30702833 TTTGAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.39
17 3 0.10
18 13 0.42
19 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTATATTTTTATA
Found at i:30722425 original size:242 final size:244
Alignment explanation
Indices: 30721995--30722471 Score: 735
Period size: 242 Copynumber: 2.0 Consensus size: 244
30721985 TTAAAGTATC
* * **
30721995 CCCCCCTGTAGGTTTGTGTACTCTCTTGATTTGTCATTTCTTAATTGATGAGGTGTGCTTTATGC
1 CCCCCCTGTAGGTTTGTGTACTCTCATGATTTGTCATATC---ATTGATGAGGCATGCTTTATGC
* * *
30722060 ACTTTCCTGAGTGCCACATAGATCTGTTATATCTAGCCAGAACTTGAATTGAGGAATTGAAATCT
63 ACTTTCCTGAGTGCCACATAGATCTGTTATATCTAGCCAGAACTTGAATTCAAGAATTGAAATCA
* * *
30722125 AGGAACAGAAAATTGATTGTGAGAATTTTGCTTGCTATTCATTCTGGAACTTAGAACAATAATGC
128 AGGAACAGAAAATTGATTGTGAGAATTTTGCTAGCTATGCATTCTAGAACTTAGAACAATAATGC
30722190 TTTAAACTTATCACTTGTATGCTGTTGATGCAGCCTGTAAGAGAAGGTTATT
193 TTTAAACTTATCACTTGTATGCTGTTGATGCAGCCTGTAAGAGAAGGTTATT
** *
30722242 CCCCCCTGTAGGTTTGTGTGTTCTCATGATTTGTTATATC-TTGATGAGGCATGCTTTATGCAC-
1 CCCCCCTGTAGGTTTGTGTACTCTCATGATTTGTCATATCATTGATGAGGCATGCTTTATGCACT
* * *
30722305 TTCCTGAGTGCGACTTAGATCTGTTATATCTAGCCAGAACTTGCATTCAAGAATTGAAATCAAGG
66 TTCCTGAGTGCCACATAGATCTGTTATATCTAGCCAGAACTTGAATTCAAGAATTGAAATCAAGG
*
30722370 AACAGAAAATTGATTTTGAGAATTTTGCTAGCTATGCATTGC-AGAACTTAGAACAATAATGCTT
131 AACAGAAAATTGATTGTGAGAATTTTGCTAGCTATGCATT-CTAGAACTTAGAACAATAATGCTT
*
30722434 TAAGCTTATCACTTGTATGCTGTTGATGCAGCCTGTAA
195 TAAACTTATCACTTGTATGCTGTTGATGCAGCCTGTAA
30722472 AGGACACTGG
Statistics
Matches: 211, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
242 154 0.73
243 22 0.10
247 35 0.17
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (244 bp):
CCCCCCTGTAGGTTTGTGTACTCTCATGATTTGTCATATCATTGATGAGGCATGCTTTATGCACT
TTCCTGAGTGCCACATAGATCTGTTATATCTAGCCAGAACTTGAATTCAAGAATTGAAATCAAGG
AACAGAAAATTGATTGTGAGAATTTTGCTAGCTATGCATTCTAGAACTTAGAACAATAATGCTTT
AAACTTATCACTTGTATGCTGTTGATGCAGCCTGTAAGAGAAGGTTATT
Found at i:30726621 original size:24 final size:24
Alignment explanation
Indices: 30726594--30726649 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
30726584 ATACGTTATG
30726594 ATGTTATAAGTCATGTACAAAAAT
1 ATGTTATAAGTCATGTACAAAAAT
* *
30726618 ATGTTACATGTCATGTACAAAAAT
1 ATGTTATAAGTCATGTACAAAAAT
30726642 ATGTTATA
1 ATGTTATA
30726650 TATCATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (24 bp):
ATGTTATAAGTCATGTACAAAAAT
Found at i:30726655 original size:24 final size:24
Alignment explanation
Indices: 30726594--30726656 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
30726584 ATACGTTATG
30726594 ATGTTATA-AGTCATGTACAAAAAT
1 ATGTTATATA-TCATGTACAAAAAT
* *
30726618 ATGTTACATGTCATGTACAAAAAT
1 ATGTTATATATCATGTACAAAAAT
30726642 ATGTTATATATCATG
1 ATGTTATATATCATG
30726657 ATTAAGTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (24 bp):
ATGTTATATATCATGTACAAAAAT
Found at i:30726713 original size:45 final size:45
Alignment explanation
Indices: 30726619--30726740 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 45
30726609 TACAAAAATA
* * * *
30726619 TGTTACATGTCATGTACAAAAATATGTTATATATCATGATTAAGT
1 TGTTACATGTCATGTACAAAAATATGTGACACATCATGATTAAGC
* * * * * *
30726664 TGTTACACGTCATGTGCAAAAACATGTGACACGTCATGGTTAGGC
1 TGTTACATGTCATGTACAAAAATATGTGACACATCATGATTAAGC
* * *
30726709 TGTTATATATTATGTACAAAAATATGTGACAC
1 TGTTACATGTCATGTACAAAAATATGTGACAC
30726741 TCCATGTACA
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (45 bp):
TGTTACATGTCATGTACAAAAATATGTGACACATCATGATTAAGC
Found at i:30726928 original size:45 final size:42
Alignment explanation
Indices: 30726871--30726980 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 42
30726861 TTGTTACATG
*
30726871 CCATGATTAGGTTGTTACACGTCATGTGCAAAAACATGTGACACGT
1 CCATGGTTAGGTTGTTA-ACGTCATGT--AAAAACATGTGACAC-T
*
30726917 -CATGGTTAGGTTGTT-ATGT-A--TAAAAACATGTGACACT
1 CCATGGTTAGGTTGTTAACGTCATGTAAAAACATGTGACACT
30726954 CCATGGTTAGGTTGTTATACGTCATGT
1 CCATGGTTAGGTTGTTA-ACGTCATGT
30726981 TGAAAAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
37 1 0.02
38 30 0.55
40 4 0.07
41 1 0.02
42 1 0.02
43 4 0.07
45 14 0.25
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (42 bp):
CCATGGTTAGGTTGTTAACGTCATGTAAAAACATGTGACACT
Found at i:30727110 original size:29 final size:30
Alignment explanation
Indices: 30727056--30727113 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
30727046 GTTTCACGCC
* *
30727056 ATGTTGAAAAAAAATACTGTTGTTACACGGT
1 ATGTTGAAAAAAAATA-TATTATTACACGGT
30727087 ATGTTGAAAAAAAAT-TATTATTACACG
1 ATGTTGAAAAAAAATATATTATTACACG
30727114 TCATATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
31 15 0.60
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (30 bp):
ATGTTGAAAAAAAATATATTATTACACGGT
Found at i:30729484 original size:18 final size:19
Alignment explanation
Indices: 30729461--30729501 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
30729451 AATATAACTT
* *
30729461 AAAATATTAAACA-AAATA
1 AAAATATAAAAAATAAATA
30729479 AAAATATAAAAAATAAATA
1 AAAATATAAAAAATAAATA
30729498 AAAA
1 AAAA
30729502 ATTGAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAATATAAAAAATAAATA
Found at i:30730341 original size:3 final size:3
Alignment explanation
Indices: 30730333--30730357 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30730323 CACTTGACAA
30730333 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
30730358 CGAGTATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30732004 original size:21 final size:21
Alignment explanation
Indices: 30731965--30732004 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30731955 ATTATTTAAT
*
30731965 TTTTTAAATAATTTTTATACC
1 TTTTTAAATAATTTATATACC
30731986 TTTTTAAAT-ATTATATATA
1 TTTTTAAATAATT-TATATA
30732005 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAAATAATTTATATACC
Found at i:30734655 original size:14 final size:14
Alignment explanation
Indices: 30734636--30734669 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30734626 GAGGGAGTCC
30734636 CTCTCTTTCTCTCT
1 CTCTCTTTCTCTCT
*
30734650 CTCTCTTTCTCTTT
1 CTCTCTTTCTCTCT
30734664 CTCTCT
1 CTCTCT
30734670 GTGCTAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
CTCTCTTTCTCTCT
Found at i:30735858 original size:30 final size:30
Alignment explanation
Indices: 30735813--30735870 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
30735803 TTCCACAACG
*
30735813 TGTCTAGTGCTGTCATAAATGAAGCTTTCT
1 TGTCTAGTGCGGTCATAAATGAAGCTTTCT
*
30735843 TGTCTTGTGCGGTCATAAATGAAGCTTT
1 TGTCTAGTGCGGTCATAAATGAAGCTTT
30735871 TTCGTGTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (30 bp):
TGTCTAGTGCGGTCATAAATGAAGCTTTCT
Found at i:30739968 original size:21 final size:20
Alignment explanation
Indices: 30739942--30740004 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
30739932 ATCTAAGGTT
30739942 TCTGGTTCACATAAATCAAAA
1 TCTGGTTC-CATAAATCAAAA
30739963 TCTGGTTCGCATAAATCAAAA
1 TCTGGTTC-CATAAATCAAAA
*
30739984 ACTGGCTTCCATGAAA-CAAAA
1 TCTGG-TTCCAT-AAATCAAAA
30740005 GGCTCACCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (20 bp):
TCTGGTTCCATAAATCAAAA
Found at i:30750075 original size:14 final size:14
Alignment explanation
Indices: 30750058--30750087 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30750048 AAATTAAAGT
30750058 ATTATATTAGAACC
1 ATTATATTAGAACC
30750072 ATTATATTAGAACC
1 ATTATATTAGAACC
30750086 AT
1 AT
30750088 CACGGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (14 bp):
ATTATATTAGAACC
Found at i:30754141 original size:10 final size:11
Alignment explanation
Indices: 30754107--30754261 Score: 75
Period size: 11 Copynumber: 13.5 Consensus size: 11
30754097 TTATATAAAC
30754107 TATTAATAATT
1 TATTAATAATT
30754118 TATTAAATTAATT
1 TATT-AA-TAATT
30754131 T-TTAATAATT
1 TATTAATAATT
*
30754141 T-TCAATAATT
1 TATTAATAATT
*
30754151 TATTAATTATT
1 TATTAATAATT
* *
30754162 AAATAATAATT
1 TATTAATAATT
* *
30754173 TACTAGT-ATT
1 TATTAATAATT
*
30754183 AACTGTCAATAATT
1 TA-T-T-AATAATT
**
30754197 TA-TAATGAAAA
1 TATTAAT-AATT
30754208 TATTAATAATT
1 TATTAATAATT
*
30754219 TATCTTATTAATAT
1 TA--TTAATAAT-T
*
30754233 TTTTAATAATT
1 TATTAATAATT
*
30754244 TATTTTATAATT
1 TA-TTAATAATT
*
30754256 TTTTAA
1 TATTAA
30754262 ATTTATAATT
Statistics
Matches: 107, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
10 22 0.21
11 39 0.36
12 25 0.23
13 15 0.14
14 6 0.06
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TATTAATAATT
Found at i:30754169 original size:32 final size:33
Alignment explanation
Indices: 30754111--30754173 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
30754101 ATAAACTATT
**
30754111 AATAATTTATTAAATTAATTTTTAATAATTTTC
1 AATAATTTATTAAATTAATTAATAATAATTTTC
30754144 AATAATTTATT-AATT-ATTAAATAATAATTT
1 AATAATTTATTAAATTAATT-AATAATAATTT
30754174 ACTAGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 3 0.11
32 13 0.48
33 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTTATTAAATTAATTAATAATAATTTTC
Found at i:30754267 original size:21 final size:25
Alignment explanation
Indices: 30754210--30754261 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
30754200 AATGAAAATA
30754210 TTAATAATTTATCTTATTAATATTT
1 TTAATAATTTATCTTATTAATATTT
*
30754235 TTAATAATTTATTTTA-TAAT-TTT
1 TTAATAATTTATCTTATTAATATTT
30754258 TTAA
1 TTAA
30754262 ATTTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.27
24 4 0.15
25 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTAATAATTTATCTTATTAATATTT
Found at i:30755540 original size:47 final size:47
Alignment explanation
Indices: 30755478--30755641 Score: 274
Period size: 47 Copynumber: 3.5 Consensus size: 47
30755468 TGCATATAAG
* * *
30755478 TTTACTTAACAAATAAGTAAAATAATTACACTATTCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACAATGCATTTTATAAAT
*
30755525 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACAATGCATTTTATAAAT
*
30755572 TTTACCTAACAAATAAGTAAAATAATTACACAATGCATTTCATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACAATGCATTTTATAAAT
*
30755619 TTTGCCTAACAAATAAGTAAAAT
1 TTTACCTAACAAATAAGTAAAAT
30755642 CATACAAAAT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 111 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (47 bp):
TTTACCTAACAAATAAGTAAAATAATTACACAATGCATTTTATAAAT
Found at i:30756705 original size:15 final size:15
Alignment explanation
Indices: 30756685--30756751 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
30756675 GATATTATGT
30756685 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
30756700 TTAAATTT-AA-AAA
1 TTAAATTTAAATAAA
* *
30756713 -T-AA-TTAATCATTAT
1 TTAAATTTAA--ATAAA
*
30756727 TTAAATTTAAACAAA
1 TTAAATTTAAATAAA
30756742 TTAAATTTAA
1 TTAAATTTAA
30756752 GTACAATGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
10 2 0.05
11 3 0.08
12 1 0.03
13 4 0.10
14 3 0.08
15 21 0.52
16 2 0.05
17 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:30756708 original size:21 final size:21
Alignment explanation
Indices: 30756684--30756751 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
30756674 GGATATTATG
30756684 TTTAAATTTAAATAAATTAAA
1 TTTAAATTTAAATAAATTAAA
** *
30756705 TTTAAAAATAATTAATCATT--A
1 TTTAAATTTAAATAA--ATTAAA
*
30756726 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAATAAATTAAA
30756747 TTTAA
1 TTTAA
30756752 GTACAATGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
21 30 0.83
23 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAATTTAAATAAATTAAA
Found at i:30765018 original size:17 final size:17
Alignment explanation
Indices: 30764996--30765034 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
30764986 TATCTCCATT
30764996 TCTCATTCTTGTGCTTG
1 TCTCATTCTTGTGCTTG
30765013 TCTCATTCTTGTGCTTG
1 TCTCATTCTTGTGCTTG
30765030 TCTCA
1 TCTCA
30765035 AATTTATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.08, C:0.26, G:0.15, T:0.51
Consensus pattern (17 bp):
TCTCATTCTTGTGCTTG
Found at i:30777542 original size:26 final size:27
Alignment explanation
Indices: 30777513--30777569 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30777503 CTTTAAAAAA
30777513 TTATTTTAAAAAT-TTTAAATAAATTT
1 TTATTTTAAAAATATTTAAATAAATTT
* ** *
30777539 TTATTTTTATTATATTTAATTAAATTT
1 TTATTTTAAAAATATTTAAATAAATTT
30777566 TTAT
1 TTAT
30777570 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTTTAAAAATATTTAAATAAATTT
Done.