Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008796.1 Hibiscus syriacus cultivar Beakdansim tig00111941_pilon, whole genome shotgun sequence
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: 1607457
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 7
Found at i:2381 original size:23 final size:23
Alignment explanation
Indices: 2338--2391 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2328 TAAATGTTCA
*
2338 ATTCATTTAACATTCACGAACAT
1 ATTCGTTTAACATTCACGAACAT
**
2361 -TTACGTTTAACATTCGTGAACAT
1 ATT-CGTTTAACATTCACGAACAT
2384 ATTCGTTT
1 ATTCGTTT
2392 GGCATTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 22 0.85
24 2 0.08
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTCGTTTAACATTCACGAACAT
Found at i:2504 original size:21 final size:23
Alignment explanation
Indices: 2463--2504 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2453 CCACTAATCC
2463 TTAAGCTCTAAAAGTTTCACAGT
1 TTAAGCTCTAAAAGTTTCACAGT
*
2486 TTAAGCT-TCAAAG-TTCACA
1 TTAAGCTCTAAAAGTTTCACA
2505 TTGTGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (23 bp):
TTAAGCTCTAAAAGTTTCACAGT
Found at i:11176 original size:22 final size:22
Alignment explanation
Indices: 11149--11196 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11139 TTCTGTATAT
*
11149 TATAATATAT-TAGATTATTATC
1 TATAATAT-TCTAAATTATTATC
11171 TATAATATTCTAAATTATTATC
1 TATAATATTCTAAATTATTATC
11193 TATA
1 TATA
11197 TAAATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAATATTCTAAATTATTATC
Found at i:11205 original size:13 final size:13
Alignment explanation
Indices: 11187--11212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11177 ATTCTAAATT
11187 ATTATCTATATAA
1 ATTATCTATATAA
11200 ATTATCTATATAA
1 ATTATCTATATAA
11213 TTAGATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTATCTATATAA
Found at i:11544 original size:41 final size:41
Alignment explanation
Indices: 11458--11799 Score: 323
Period size: 41 Copynumber: 8.3 Consensus size: 41
11448 AGTTCATCGA
* * *
11458 TAGTGGCGTTTTT-TCAACAAAATGCCGCAAAAGAGTCGTACTT
1 TAGTGGCGTTTTTAT--AC-AAACGCCGCTAAAGACTCGTACTT
** * * *
11501 TAGTGGCGTTTTTATACAAACGCCATTAAAGATTCATATTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
11542 TAGTGGCGTTTTTATACAAACGCCGCTATAGACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * * * * *
11583 TAATGGTGTTTTTATACAAATGCTGTTATACACTTGTA-TT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
*
11623 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAACA-ACTCGTACTT
1 -TAGTGGCGTTT-T-TATACAAACGCCGCTAA-AGACTCGTACTT
11667 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
11708 TAGT-GCGTTTTTATACAAACGCCACTATACACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * * *
11748 TAGTGGGGTTTTTATTCAAACGCCGCTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
*
11789 TAGTGACGTTT
1 TAGTGGCGTTT
11800 GTAAACACAA
Statistics
Matches: 250, Mismatches: 41, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
40 39 0.16
41 161 0.64
42 4 0.02
43 42 0.17
44 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:11793 original size:165 final size:166
Alignment explanation
Indices: 11493--11801 Score: 458
Period size: 165 Copynumber: 1.9 Consensus size: 166
11483 CGCAAAAGAG
* * *
11493 TCGTACTTTAGTGGCGTTTTTATACAAACGCCATTAAAGATTCATATTTTAGTGGCGTTTTTATA
1 TCGTACTTTAGTGGCGTTTTTATACAAACGCCACTAAAGACTCATACTTTAGTGGCGTTTTTATA
* * ** * * * * *
11558 CAAACGCCGCTATAGACTTGTACTTTAATGGTGTTTTTATACAAATGCTGTTATACACTTGTATT
66 CAAACGCCACTATACACTCATACTTTAATGGGGTTTTTATACAAACGCCGCTATACACTTGTACT
*
11623 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAACAAC
131 ATAGTGACGTTTGTGTTTACAAACGCCGCTAACAAC
* *
11659 TCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT-GCGTTTTTATA
1 TCGTACTTTAGTGGCGTTTTTATACAAACGCCACTAAAGACTCATACTTTAGTGGCGTTTTTATA
* *
11723 CAAACGCCACTATACACTCATACTTTAGTGGGGTTTTTATTCAAACGCCGCTATACACTTGTACT
66 CAAACGCCACTATACACTCATACTTTAATGGGGTTTTTATACAAACGCCGCTATACACTTGTACT
11788 ATAGTGACGTTTGT
131 ATAGTGACGTTTGT
11802 AAACACAAAC
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
165 78 0.62
166 48 0.38
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (166 bp):
TCGTACTTTAGTGGCGTTTTTATACAAACGCCACTAAAGACTCATACTTTAGTGGCGTTTTTATA
CAAACGCCACTATACACTCATACTTTAATGGGGTTTTTATACAAACGCCGCTATACACTTGTACT
ATAGTGACGTTTGTGTTTACAAACGCCGCTAACAAC
Found at i:14963 original size:43 final size:43
Alignment explanation
Indices: 14882--15193 Score: 371
Period size: 43 Copynumber: 7.2 Consensus size: 43
14872 ATGGTAATTA
14882 GCGGCGTTTGTATCAAAACCAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCAAAA--AACGCCGCTATAGATATGACCTTTT
*
14927 GCGGCGTTTGTATCAAAAAACGCCGTTATAGATATGACCTTTT
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGACCTTTT
*
14970 GCGGCGTTTGTAT-ACAAAAGCGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCA-AAAAACGCCGCTATAGATATGACCTTTT
* * ** *
15013 GCGGCGTTTGTAT-ACAAAAACTCAGCTATAGATCGGACATTTT
1 GCGGCGTTTGTATCA-AAAAACGCCGCTATAGATATGACCTTTT
* * * *
15056 GCTGCGTTTGTATCCAAAAACGCCACTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGACCTTTT
* * *
15099 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATATGACATTTT
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
15142 GCGGCATTTAT-TGC-AAAAACCCCGCTATAGATCTTGACTTTTT
1 GCGGCGTTTGTAT-CAAAAAACGCCGCTATAGAT-ATGACCTTTT
15185 GCGGCGTTT
1 GCGGCGTTT
15194 TTATTTTACA
Statistics
Matches: 235, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
42 19 0.08
43 198 0.84
45 18 0.08
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGACCTTTT
Found at i:15943 original size:20 final size:19
Alignment explanation
Indices: 15895--15944 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
15885 AAATGACCAA
* *
15895 CAAATTCGCAATGCGATCT
1 CAAATTCGCAAAGCGAACT
15914 CAAATTCGCAAAGCGAACT
1 CAAATTCGCAAAGCGAACT
*
15933 CTAATTTCGCAA
1 C-AAATTCGCAA
15945 CCCAGTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAAAGCGAACT
Found at i:16002 original size:20 final size:21
Alignment explanation
Indices: 15979--16066 Score: 94
Period size: 20 Copynumber: 4.3 Consensus size: 21
15969 AATCTGTAAA
15979 TCGCAACACAGA-AGTCAAAT
1 TCGCAACACAGATAGTCAAAT
* *
15999 TCGCAACGCA-ATAGTTAAAT
1 TCGCAACACAGATAGTCAAAT
*
16019 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
* *
16039 TCGCAACACGGA-ATTTCAAAT
1 TCGCAACACAGATA-GTCAAAT
16060 TCGCAAC
1 TCGCAAC
16067 TGAATTTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.02
20 43 0.73
21 15 0.25
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (21 bp):
TCGCAACACAGATAGTCAAAT
Found at i:16002 original size:40 final size:40
Alignment explanation
Indices: 15913--16045 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 40
15903 CAATGCGATC
* * * * ***
15913 TCAAATTCGCAAAGCGAA-CTCTAATTTCGCAACCCAGTTT
1 TCAAATTCGCAACGCGAATCTGTAA-ATCGCAACACAGAAG
*
15953 TCAATTTCGCAACGCGAATCTGTAAATCGCAACACAGAAG
1 TCAAATTCGCAACGCGAATCTGTAAATCGCAACACAGAAG
* *
15993 TCAAATTCGCAACGC-AAT-AGTTAAATTCGCAACGC-GATAG
1 TCAAATTCGCAACGCGAATCTG-TAAA-TCGCAACACAGA-AG
16033 TCAAATTCGCAAC
1 TCAAATTCGCAAC
16046 ACGGAATTTC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 9 0.12
40 63 0.81
41 5 0.06
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (40 bp):
TCAAATTCGCAACGCGAATCTGTAAATCGCAACACAGAAG
Found at i:16059 original size:21 final size:21
Alignment explanation
Indices: 16033--16086 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
16023 AACGCGATAG
16033 TCAAATTCGCAACACGGAATT
1 TCAAATTCGCAACACGGAATT
*
16054 TCAAATTCGC-A-ACTGAATT
1 TCAAATTCGCAACACGGAATT
16073 TCAAATTCGCAACA
1 TCAAATTCGCAACA
16087 AGTTTTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 17 0.57
20 2 0.07
21 11 0.37
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (21 bp):
TCAAATTCGCAACACGGAATT
Found at i:16073 original size:19 final size:19
Alignment explanation
Indices: 15993--16085 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 19
15983 AACACAGAAG
*
15993 TCAAATTCGCAACGCAATAGT
1 TCAAATTCGCAACGGAAT--T
*
16014 T-AAATTCGCAACGCG-ATAG
1 TCAAATTCGCAACG-GAAT-T
16033 TCAAATTCGCAACACGGAATT
1 TCAAATTCGC-A-ACGGAATT
*
16054 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGGAATT
16073 TCAAATTCGCAAC
1 TCAAATTCGCAAC
16086 AAGTTTTAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
19 21 0.34
20 23 0.37
21 13 0.21
22 5 0.08
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (19 bp):
TCAAATTCGCAACGGAATT
Found at i:16079 original size:60 final size:59
Alignment explanation
Indices: 15951--16085 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
15941 GCAACCCAGT
* *
15951 TTTCAATTTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCAA
1 TTTCAAATTCGCAACGCGAATCAGTAAATCGCAACACAGAAGTCAAATTCGCAACGCAA
* *
16010 TAGTT-AAATTCGCAACGCG-AT-AGTCAAATTCGCAACACGGAATTTCAAATTCGCAACTG-AA
1 T--TTCAAATTCGCAACGCGAATCAGT-AAA-TCGCAACACAGAA-GTCAAATTCGCAAC-GCAA
16071 TTTCAAATTCGCAAC
1 TTTCAAATTCGCAAC
16086 AAGTTTTAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
58 2 0.03
59 8 0.12
60 36 0.55
61 18 0.28
62 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (59 bp):
TTTCAAATTCGCAACGCGAATCAGTAAATCGCAACACAGAAGTCAAATTCGCAACGCAA
Found at i:16263 original size:16 final size:16
Alignment explanation
Indices: 16242--16280 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16232 TCCCCATCTC
* *
16242 TAATTTTGTTTTTACA
1 TAATTTTATTTCTACA
*
16258 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
16274 TAATTTT
1 TAATTTT
16281 TCAATGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:17022 original size:25 final size:25
Alignment explanation
Indices: 16977--17028 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
16967 GTCAGTATTC
* *
16977 GAAATTTGATCTTGGTCAATACCCG
1 GAAATTTAATCTTGGGCAATACCCG
* *
17002 GAAATTTAATCTTGGGGAATACTCG
1 GAAATTTAATCTTGGGCAATACCCG
17027 GA
1 GA
17029 TTTTGATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (25 bp):
GAAATTTAATCTTGGGCAATACCCG
Found at i:17948 original size:21 final size:21
Alignment explanation
Indices: 17924--18022 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
17914 GCGGGCAGGA
* *
17924 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * *
17945 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
** *
17966 TTTCTTCG-ATGATGAAAGGGG
1 CCTCTT-GAATGATGAGAGGGG
*
17987 CCTCTTGAATGAT-AGGAGGCG
1 CCTCTTGAATGATGA-GAGGGG
18008 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
18023 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:18020 original size:42 final size:42
Alignment explanation
Indices: 17924--18022 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
17914 GCGGGCAGGA
* * * * *
17924 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
** *
17966 TTTCTTCG-ATGATGAAAGGGGCCTCTTGAATGATAGGAGGCG
1 CCTCTT-GAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
18008 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
18023 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (42 bp):
CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:18198 original size:4 final size:4
Alignment explanation
Indices: 18166--18215 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
18156 GGGCCGCTAA
* * * *
18166 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
18214 AA
1 AA
18216 TACCGAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:18466 original size:21 final size:21
Alignment explanation
Indices: 18438--18487 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
18428 ACCATTATCT
18438 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
*
18459 TGACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
18480 TCACGTAA
1 TCACGTAA
18488 TTCCCCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:20182 original size:19 final size:19
Alignment explanation
Indices: 20131--20184 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
20121 AGAAGTTTCT
* *
20131 GAAACTTAAATTCGCAATGC
1 GAAAC-TAAAATCGCAACGC
*
20151 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
20171 GAAACTAAAATCGC
1 GAAACTAAAATCGC
20185 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:20220 original size:14 final size:14
Alignment explanation
Indices: 20197--20228 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
20187 TGCGATTTTC
20197 ATTTTCGTGTTGTG
1 ATTTTCGTGTTGTG
*
20211 ATTTTTGTGTTGTG
1 ATTTTCGTGTTGTG
20225 ATTT
1 ATTT
20229 AGGGTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.25, T:0.62
Consensus pattern (14 bp):
ATTTTCGTGTTGTG
Found at i:20728 original size:40 final size:41
Alignment explanation
Indices: 20668--20839 Score: 223
Period size: 40 Copynumber: 4.3 Consensus size: 41
20658 ACGTTTGACT
20668 TTCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-AA
* * *
20708 TTCGAGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACAA
*
20749 -TCGCGTTGCGAATTTGACTT-TGTGTTGCGAATTTGACTA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACAA
* *
20788 -CCGCGTTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACAAA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-AA
20827 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
20840 ATTGGAAACT
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.02
39 42 0.36
40 67 0.57
41 5 0.04
42 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.40
Consensus pattern (41 bp):
TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACAA
Found at i:20815 original size:20 final size:20
Alignment explanation
Indices: 20673--20818 Score: 158
Period size: 20 Copynumber: 7.3 Consensus size: 20
20663 TGACTTTCGC
20673 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
20693 GTTGCG-ATTT-ACAAATTC-GA
1 GTTGCGAATTTGAC---TTCTGT
*
20713 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
20733 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
20753 GTTGCGAATTTGACTT-TGT
1 GTTGCGAATTTGACTTCTGT
* * *
20772 GTTGCGAATTTGACTACCGC
1 GTTGCGAATTTGACTTCTGT
*
20792 GTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
20812 GTTGCGA
1 GTTGCGA
20819 TTTACAAATT
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
18 2 0.02
19 23 0.22
20 68 0.66
21 8 0.08
22 2 0.02
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:20872 original size:119 final size:119
Alignment explanation
Indices: 20661--20883 Score: 306
Period size: 119 Copynumber: 1.9 Consensus size: 119
20651 CGTAAAAACG
** *
20661 TTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCGAATTTGA
1 TTTGACTACCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCGAATTGGA
*** * * *
20726 CTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGAA
66 CAACTGGGTTACGAATTGGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGAA
* *
20780 TTTGACTACCGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAAATTGG
1 TTTGACTACCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCG-AATTGG
*
20845 A-AACTGGGTTACGAAATTGGAGT-TCGCGTTGCGAATTTG
65 ACAACTGGGTTACG-AATTGGACTATCGCGTTGCGAATTTG
20884 TTGGTCATTT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
119 77 0.86
120 13 0.14
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (119 bp):
TTTGACTACCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCGAATTGGA
CAACTGGGTTACGAATTGGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGAA
Found at i:20879 original size:20 final size:19
Alignment explanation
Indices: 20826--20879 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
20816 CGATTTACAA
20826 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** * *
20845 AAACTGGGTTACGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
20865 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
20880 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:21707 original size:29 final size:30
Alignment explanation
Indices: 21669--21741 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 30
21659 TAAAAAATAT
21669 AAAATAAATATTAAATTA-TAATT-TTATTA
1 AAAAT-AATATTAAATTATTAATTGTTATTA
* * *
21698 AAAATGAATA-CACATTATTAATTGTTGTTA
1 AAAAT-AATATTAAATTATTAATTGTTATTA
21728 AAAATAATAATTAA
1 AAAATAAT-ATTAA
21742 TGAATAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
28 5 0.15
29 17 0.50
30 11 0.32
31 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAATAATATTAAATTATTAATTGTTATTA
Found at i:21855 original size:20 final size:19
Alignment explanation
Indices: 21819--21858 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21809 AAACAATTAA
*
21819 TTTTAAAAGTTAAGAAATT
1 TTTTAAAAATTAAGAAATT
*
21838 TTTTAAAAATATATGAAATT
1 TTTTAAAAAT-TAAGAAATT
21858 T
1 T
21859 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
TTTTAAAAATTAAGAAATT
Found at i:22035 original size:51 final size:51
Alignment explanation
Indices: 21977--22078 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
21967 TACTTACCCT
* * *
21977 CAAAGTTTTTCTAGACTATATTATA-AGTATAAGATTTTAAAAGGGTTAAAA
1 CAAAGTTTTCCTAGACTATACTATACA-TATAAGATTTTAAAAGGGTCAAAA
* *
22028 CAAAGTTTTCCTAGACTATACTATACATATAGGATTTTTAAAGGGTCAAAA
1 CAAAGTTTTCCTAGACTATACTATACATATAAGATTTTAAAAGGGTCAAAA
22079 AGTCATTAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (51 bp):
CAAAGTTTTCCTAGACTATACTATACATATAAGATTTTAAAAGGGTCAAAA
Found at i:24442 original size:16 final size:16
Alignment explanation
Indices: 24421--24452 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24411 TTAATGTTAT
24421 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
24437 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
24453 ATTTTCTTAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:25047 original size:19 final size:20
Alignment explanation
Indices: 25003--25047 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24993 ATTTATTTTT
*
25003 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
25023 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
25042 AATAAA
1 AATAAA
25048 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:27987 original size:29 final size:29
Alignment explanation
Indices: 27954--28038 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
27944 AATCAATGGA
27954 CTATTTTATAAATTTTAATAGTCGAGGGG
1 CTATTTTATAAATTTTAATAGTCGAGGGG
*
27983 CTATTTGT-TATAA--TCAAT-G--GA----
1 CTATTT-TATA-AATTTTAATAGTCGAGGGG
28004 CTATTTTATAAATTTTAATAGTCGAGGGG
1 CTATTTTATAAATTTTAATAGTCGAGGGG
28033 CTATTT
1 CTATTT
28039 GTGTACTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 24
0.62 0.03 0.35
Matches are distributed among these distances:
20 3 0.07
21 8 0.19
22 4 0.10
23 1 0.02
25 4 0.10
27 1 0.02
28 4 0.10
29 14 0.33
30 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
CTATTTTATAAATTTTAATAGTCGAGGGG
Found at i:28016 original size:50 final size:50
Alignment explanation
Indices: 27941--28040 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
27931 ACCAACACCC
27941 TATAATCAATGGACTATTTTATAAATTTTAATAGTCGAGGGGCTATTTGT
1 TATAATCAATGGACTATTTTATAAATTTTAATAGTCGAGGGGCTATTTGT
27991 TATAATCAATGGACTATTTTATAAATTTTAATAGTCGAGGGGCTATTTGT
1 TATAATCAATGGACTATTTTATAAATTTTAATAGTCGAGGGGCTATTTGT
28041 GTACTTTACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (50 bp):
TATAATCAATGGACTATTTTATAAATTTTAATAGTCGAGGGGCTATTTGT
Found at i:28242 original size:11 final size:11
Alignment explanation
Indices: 28226--28256 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
28216 TTTCCAAACG
28226 TGTTCGTTTGA
1 TGTTCGTTTGA
28237 TGTTCGTTTGA
1 TGTTCGTTTGA
28248 TGTTCGTTT
1 TGTTCGTTT
28257 ATATGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (11 bp):
TGTTCGTTTGA
Found at i:28275 original size:23 final size:23
Alignment explanation
Indices: 28259--28323 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
28249 GTTCGTTTAT
28259 ATGTTTGTTTAGCGTTCGTGAAC
1 ATGTTTGTTTAGCGTTCGTGAAC
* * ** *
28282 ATATTCGTTTATTGTTCGCGAAC
1 ATGTTTGTTTAGCGTTCGTGAAC
28305 ATGTTTGTTTAGCGTTCGT
1 ATGTTTGTTTAGCGTTCGT
28324 TTATCATTCC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (23 bp):
ATGTTTGTTTAGCGTTCGTGAAC
Found at i:29004 original size:17 final size:19
Alignment explanation
Indices: 28979--29015 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28969 ATTCGGTTAA
28979 TTTCGAA-TTA-ATAAAAT
1 TTTCGAATTTATATAAAAT
*
28996 TTTCTAATTTATATAAAAT
1 TTTCGAATTTATATAAAAT
29015 T
1 T
29016 AAATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTCGAATTTATATAAAAT
Found at i:29325 original size:183 final size:183
Alignment explanation
Indices: 29005--29389 Score: 613
Period size: 183 Copynumber: 2.1 Consensus size: 183
28995 TTTTCTAATT
*
29005 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
*
29068 TATAAAATAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
66 TATAAAATAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
* *
29133 AATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AG-CTCATATGTTA
131 AATCTTAAATTATTAATTGGATTTTAAATGATTTGGG-TTGAGTC-CATATGTTA
*
29186 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTATAATTAATTTAAATAATAAATAA
*
29250 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAAT-AAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
29314 T-AGATCTTAAATTATTAATTGGATTTTTAATGATTTGGGTTGAGTCCATATGTTA
129 TGA-ATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGTCCATATGTTA
29369 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
29390 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
181 7 0.04
182 10 0.05
183 162 0.85
184 11 0.06
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
TATAAAATAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
AATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGTCCATATGTTA
Found at i:32934 original size:24 final size:24
Alignment explanation
Indices: 32905--32951 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
32895 GACTCTCCAG
32905 CCCTTACCCAGCCGTTCTTGACTC
1 CCCTTACCCAGCCGTTCTTGACTC
32929 CCCTTACCCAGCCGTTCTTGACT
1 CCCTTACCCAGCCGTTCTTGACT
32952 GAACTCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.45, G:0.13, T:0.30
Consensus pattern (24 bp):
CCCTTACCCAGCCGTTCTTGACTC
Found at i:34051 original size:19 final size:19
Alignment explanation
Indices: 34006--34051 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
33996 ATGAACATAA
*
34006 TTCACGTTTTGATTCAACT
1 TTCACTTTTTGATTCAACT
* * *
34025 TCCTCTTTTTGCTTCAACT
1 TTCACTTTTTGATTCAACT
34044 TTCACTTT
1 TTCACTTT
34052 CTTCAATCTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (19 bp):
TTCACTTTTTGATTCAACT
Found at i:43465 original size:21 final size:21
Alignment explanation
Indices: 43441--43495 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
43431 TCATTTTGGC
43441 ATTTGATTTATTATCCGACTA
1 ATTTGATTTATTATCCGACTA
43462 ATTTGATTTATTATCCGACTA
1 ATTTGATTTATTATCCGACTA
*
43483 GTTTGATTTATTA
1 ATTTGATTTATTA
43496 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (21 bp):
ATTTGATTTATTATCCGACTA
Found at i:46658 original size:20 final size:20
Alignment explanation
Indices: 46633--46725 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
46623 TTTTCACAAT
46633 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
46653 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
46673 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
46694 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
46715 TCGCAATGCGA
1 TCGCAATGCGA
46726 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:46675 original size:41 final size:41
Alignment explanation
Indices: 46630--46725 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
46620 CGATTTTCAC
46630 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
46671 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
46712 AAATCGCAATGCGA
1 AATTCGCAATGCGA
46726 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:46679 original size:21 final size:20
Alignment explanation
Indices: 46633--46725 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
46623 TTTTCACAAT
*
46633 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
46653 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
46673 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
46694 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
46715 TCGCAATGCGA
1 TCGCAATGCGA
46726 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:46738 original size:41 final size:41
Alignment explanation
Indices: 46652--46786 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
46642 GAATAAGTAA
* * *
46652 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
46693 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
46734 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
46775 TTCGCAACGCGA
1 ATCGCAACGCGA
46787 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:46739 original size:20 final size:20
Alignment explanation
Indices: 46714--46808 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
46704 AATTGGGAAA
*
46714 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
46734 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
46755 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
46775 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
46795 TTCGCAACGCGATA
1 ATCGCAACGCGATA
46809 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:47311 original size:20 final size:20
Alignment explanation
Indices: 47288--47325 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47278 TTAGTTTCTC
47288 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
47308 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
47326 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:48662 original size:18 final size:18
Alignment explanation
Indices: 48641--48685 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
48631 TCCACTTCGG
*
48641 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
48659 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
48677 GAGCCATCA
1 GAGCCATCA
48686 TCTAATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:49212 original size:19 final size:20
Alignment explanation
Indices: 49158--49224 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
49148 TAGTTTACTT
* *
49158 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
49178 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
49198 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
49217 TCGCAACG
1 TCGCAACG
49225 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:49251 original size:19 final size:19
Alignment explanation
Indices: 49158--49260 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
49148 TAGTTTACTT
* **
49158 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
49178 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
49198 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49217 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
49231 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49250 TCGCAATGCGA
1 TCGCAACGCGA
49261 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:49301 original size:19 final size:19
Alignment explanation
Indices: 49286--49389 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
49276 GCGATTTTGT
49286 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
49304 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
49323 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* **
49343 CATTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
49362 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
49382 TGTTGCGA
1 CGTTGCGA
49390 AAGTAAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.11
19 35 0.48
20 30 0.41
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:49351 original size:39 final size:38
Alignment explanation
Indices: 49297--49370 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
49287 GTTGCGATTT
* **
49297 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGTCATTTCGCATTGCGATAGC
*
49335 CATTTCCGCATTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCATTGCGATAGTCATTTCGCATTGCGAT
49371 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 5 0.16
39 26 0.84
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (38 bp):
CATTTCGCATTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:52560 original size:24 final size:24
Alignment explanation
Indices: 52504--52562 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
52494 AGTCAGTATT
* *
52504 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
52528 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
52552 CGAATTTTGAT
1 CGAAATTTGAT
52563 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:52754 original size:12 final size:12
Alignment explanation
Indices: 52737--52761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52727 ATATAATCCC
52737 GAAGAAGAAAAA
1 GAAGAAGAAAAA
52749 GAAGAAGAAAAA
1 GAAGAAGAAAAA
52761 G
1 G
52762 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:55069 original size:19 final size:19
Alignment explanation
Indices: 55047--55111 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
55037 GGAAATTACT
55047 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
55066 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
55080 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
55099 ATCGCAACGCGAA
1 ATCGCAATGCGAA
55112 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:55070 original size:39 final size:33
Alignment explanation
Indices: 55047--55109 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
55037 GGAAATTACT
*
55047 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
55080 ATCGCAATGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCGCAACGCG
55110 AATTTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
Found at i:55129 original size:19 final size:20
Alignment explanation
Indices: 55107--55149 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55097 AAATCGCAAC
55107 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
55126 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
55146 GCGA
1 GCGA
55150 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:55134 original size:14 final size:14
Alignment explanation
Indices: 55135--55168 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55125 TGCGATTTTC
55135 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
55149 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
55163 ATTTTC
1 ATTTTC
55169 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:55309 original size:14 final size:14
Alignment explanation
Indices: 55290--55326 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
55280 CATCAATTAA
55290 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
55304 ACAAATCACCTTTT
1 ACAAATCAACTTTT
55318 ACAAATCAA
1 ACAAATCAA
55327 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:56747 original size:21 final size:21
Alignment explanation
Indices: 56681--56747 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
56671 GTGAATCGGG
*
56681 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
56701 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
56723 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
56744 CTCT
1 CTCT
56748 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:56766 original size:42 final size:41
Alignment explanation
Indices: 56681--56803 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
56671 GTGAATCGGG
* * * * *
56681 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
56723 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
56765 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
56804 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:58887 original size:33 final size:33
Alignment explanation
Indices: 58830--58928 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
58820 ACGAGATAAT
*
58830 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
58864 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
58897 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
58929 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:58922 original size:19 final size:19
Alignment explanation
Indices: 58805--59008 Score: 221
Period size: 19 Copynumber: 11.1 Consensus size: 19
58795 TCTTTTGGTT
*
58805 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
58824 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
58844 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
58862 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
58878 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
58896 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
58911 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
58931 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
58950 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
58969 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
58988 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
59007 GA
1 GA
59009 TTTTGGTTTC
Statistics
Matches: 159, Mismatches: 13, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 82 0.52
20 46 0.29
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:59037 original size:19 final size:19
Alignment explanation
Indices: 59004--59048 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
58994 AAAATCGCAA
*
59004 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
59023 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
59042 TGCGATT
1 TGCGATT
59049 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:59624 original size:18 final size:19
Alignment explanation
Indices: 59601--59638 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
59591 GAATGGCGCT
59601 AAGTAA-ATCGCGTTGCGA
1 AAGTAAGATCGCGTTGCGA
*
59619 AAGTAAGTATCTCGTTGCGA
1 AAGTAAG-ATCGCGTTGCGA
59639 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
AAGTAAGATCGCGTTGCGA
Found at i:59699 original size:41 final size:41
Alignment explanation
Indices: 59608--59742 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
59598 GCTAAGTAAA
* * * ** *
59608 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* *
59648 ATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* ** * *
59690 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCACATTGCGATTTTCCCAAT
59731 TCGCGTTGCGAT
1 TCGCGTTGCGAT
59743 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.94
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
Found at i:59700 original size:21 final size:21
Alignment explanation
Indices: 59674--59744 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
59664 CAGTATCACA
59674 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
59695 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
*
59715 TTGCGAATTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
59736 TTGCGATTT
1 TTGCGATTT
59745 ACTTATTCGC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:59713 original size:20 final size:20
Alignment explanation
Indices: 59688--59761 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
59678 GATTTTCCCA
*
59688 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
59708 ATTCGCATTGCGAATTTCCCA
1 ATTCGCATTGCG-ATTTACTT
*
59729 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
59749 ATTCGCATTGCGA
1 ATTCGCATTGCGA
59762 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:59743 original size:41 final size:41
Alignment explanation
Indices: 59672--59764 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
59662 GTCAGTATCA
*
59672 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
59713 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
59754 CATTGCGAATT
1 CATTGCGAATT
59765 GGGAAAATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:62920 original size:3 final size:3
Alignment explanation
Indices: 62914--62968 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
62904 TTTCATCATC
*
62914 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
62959 TTA TTA TTA T
1 TTA TTA TTA T
62969 ATAAATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:62939 original size:17 final size:18
Alignment explanation
Indices: 62914--62968 Score: 85
Period size: 17 Copynumber: 3.1 Consensus size: 18
62904 TTTCATCATC
62914 TTATTATTATTATTATTA
1 TTATTATTATTATTATTA
62932 TT-TTATTATTATTATTA
1 TTATTATTATTATTATTA
*
62949 TTAATATATATTATTATTA
1 TTATTAT-TATTATTATTA
62968 T
1 T
62969 ATAAATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 17 0.50
18 5 0.15
19 12 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATTATTATTATTA
Found at i:63243 original size:20 final size:20
Alignment explanation
Indices: 63218--63270 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
63208 CGAAGCTATA
*
63218 TGGTGAGTCACCACATAGTT
1 TGGTGACTCACCACATAGTT
63238 TGGTGACTCACCACATAGTT
1 TGGTGACTCACCACATAGTT
*
63258 CGGTGACTCACCA
1 TGGTGACTCACCA
63271 AACTTCACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (20 bp):
TGGTGACTCACCACATAGTT
Found at i:65097 original size:26 final size:23
Alignment explanation
Indices: 65050--65102 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
65040 TAATTCTTTC
* *
65050 TTTTCAAAATTTTTATACTTATT
1 TTTTCAAAATTTATATAATTATT
65073 ATTTTCATAATATTTATATAATTATT
1 -TTTTCA-AA-ATTTATATAATTATT
65099 TTTT
1 TTTT
65103 ATTAATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 6 0.24
26 13 0.52
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTCAAAATTTATATAATTATT
Found at i:65101 original size:24 final size:24
Alignment explanation
Indices: 65050--65100 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
65040 TAATTCTTTC
* *
65050 TTTTCAAAATTTTTATACTTATTA
1 TTTTCAAAATATTTATACTAATTA
*
65074 TTTTCATAATATTTATA-TAATTA
1 TTTTCAAAATATTTATACTAATTA
65097 TTTT
1 TTTT
65101 TTATTAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTCAAAATATTTATACTAATTA
Found at i:74514 original size:22 final size:22
Alignment explanation
Indices: 74488--74541 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
74478 ATCTACACTC
*
74488 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCCTCTT
74510 TTCAAAGATGATAGATCCTCTT
1 TTCAAAGATGATAGATCCTCTT
74532 TTCAAAGATG
1 TTCAAAGATG
74542 GACGCTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGATAGATCCTCTT
Found at i:75457 original size:76 final size:77
Alignment explanation
Indices: 75212--75543 Score: 430
Period size: 76 Copynumber: 4.4 Consensus size: 77
75202 CTATTTCCCA
*
75212 CATCCGTAAGACCTACAGTGCA-GTATGTTTTCACAAAAAAGCCTTC-GAGAGCTTTTTGATGTT
1 CATCTGTAAGACCTACAGTGCATG-ATGTTTT--C-AAAAAGCCTTCGGA-AGCTTTTTGATGTT
*
75275 GTTTAAAGCCTTC-GGGT
61 TTTTAAAGCC-TCAGGGT
* *
75292 CATCTGTAAGACCTACAGTGCATGATG--TTCAAAAATCCTTCGGGAGCTTTTTGATGTTTTTTA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTTTA
75355 AAGCCTCAGGGT
66 AAGCCTCAGGGT
* *
75367 CATCTGTAAAACCTACAGTGCATGATGTTTTCAAAAAGTCTTCGGAAGCTTTTTGAT-TTTTTTA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTTTA
75431 AAGCCTCAGGGT
66 AAGCCTCAGGGT
* * * * **
75443 CATCTGTAGGACCTACAGTGCATAATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGA---CATTTA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTTTA
75505 AAGCCTCAGGGT
66 AAGCCTCAGGGT
*
75517 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
75544 ATAAGACCTC
Statistics
Matches: 228, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
74 42 0.18
75 63 0.28
76 71 0.31
77 25 0.11
78 2 0.01
80 24 0.11
81 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (77 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTTTA
AAGCCTCAGGGT
Found at i:75551 original size:22 final size:21
Alignment explanation
Indices: 75523--75580 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
75513 GGGTCATCTG
75523 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGCAAGAT-A
* * **
75545 TAAGACCT-CAGGGCCATCTA
1 TAAGACCTACAGTGCAAGATA
75565 TAAGACCTACAGTGCA
1 TAAGACCTACAGTGCA
75581 GAATGTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
TAAGACCTACAGTGCAAGATA
Found at i:75876 original size:16 final size:16
Alignment explanation
Indices: 75851--75884 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
75841 ATTTTATTAT
*
75851 TATTATTATTAATATA
1 TATTAGTATTAATATA
*
75867 TATTAGTATTATTATA
1 TATTAGTATTAATATA
75883 TA
1 TA
75885 AATAATTTTA
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:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TATTAGTATTAATATA
Found at i:81145 original size:55 final size:55
Alignment explanation
Indices: 81050--81158 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
81040 TTTTACAGTA
* * ** *
81050 AGAGAATCTACACTATTGACGTCTTTTGCTTTTTAGTGACAGTTCACATTAACTC
1 AGAGAATATACACTATTCACGTCTTTTGCTTTGCAGTGACAGTTCACAATAACTC
* *
81105 AGAGAATATACACTATTCACGTCTTTTGCTTTGCATTGACATTTCACAATAACT
1 AGAGAATATACACTATTCACGTCTTTTGCTTTGCAGTGACAGTTCACAATAACT
81159 TAGATAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (55 bp):
AGAGAATATACACTATTCACGTCTTTTGCTTTGCAGTGACAGTTCACAATAACTC
Found at i:84445 original size:29 final size:28
Alignment explanation
Indices: 84406--84465 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
84396 CACACCTAAA
84406 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
84434 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
84463 TTA
1 TTA
84466 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:86407 original size:15 final size:14
Alignment explanation
Indices: 86373--86407 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
86363 CAAGCTAAGT
86373 GTGATGGTGAAAAA
1 GTGATGGTGAAAAA
86387 GTGATGGTGAAAAA
1 GTGATGGTGAAAAA
86401 GTCGATG
1 GT-GATG
86408 CTTAAGGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.37, C:0.03, G:0.37, T:0.23
Consensus pattern (14 bp):
GTGATGGTGAAAAA
Found at i:89140 original size:29 final size:29
Alignment explanation
Indices: 89101--89189 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
89091 CACACCTAAA
89101 TTAA-TTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
89129 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
89158 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
89187 TTA
1 TTA
89190 GTTAGGTGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 4 0.07
29 56 0.93
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (29 bp):
TTAATTTTGATGTCATTGCTTACATCAAT
Found at i:89513 original size:24 final size:23
Alignment explanation
Indices: 89468--89513 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
89458 AACTTAGTAT
*
89468 CAAAACAAACAAAGAATCGAATC
1 CAAAACAAACAAAGAATAGAATC
* *
89491 CAAAACTAACCAACGAATAGAAT
1 CAAAAC-AAACAAAGAATAGAAT
89514 AAAGATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.11
Consensus pattern (23 bp):
CAAAACAAACAAAGAATAGAATC
Found at i:91428 original size:15 final size:15
Alignment explanation
Indices: 91408--91438 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
91398 AGGGGTCGAG
91408 AGAGATTCACAATAA
1 AGAGATTCACAATAA
91423 AGAGATTCACAATAA
1 AGAGATTCACAATAA
91438 A
1 A
91439 CACTAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (15 bp):
AGAGATTCACAATAA
Found at i:91803 original size:19 final size:19
Alignment explanation
Indices: 91771--91807 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
91761 AAATGACATT
91771 TAAAAAAAAGGCTTAAATA
1 TAAAAAAAAGGCTTAAATA
* *
91790 TAAAATAAATGCTTAAAT
1 TAAAAAAAAGGCTTAAAT
91808 TATATCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (19 bp):
TAAAAAAAAGGCTTAAATA
Found at i:98637 original size:33 final size:33
Alignment explanation
Indices: 98599--98663 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
98589 TGATATCTAC
*
98599 TAATAACTGAAATTTATTTTATTAATATTTTAT
1 TAATAACTCAAATTTATTTTATTAATATTTTAT
98632 TAATAACTCAAATTTATTTTATTAATATTTTA
1 TAATAACTCAAATTTATTTTATTAATATTTTA
98664 ATAACTCCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (33 bp):
TAATAACTCAAATTTATTTTATTAATATTTTAT
Found at i:100802 original size:24 final size:24
Alignment explanation
Indices: 100761--100817 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
100751 TATTTGGATG
*
100761 GCGACGGTCCCCTGGATCTGTTAT
1 GCGACCGTCCCCTGGATCTGTTAT
* *
100785 GTGACCGTCCCCTTGATCTGTTAT
1 GCGACCGTCCCCTGGATCTGTTAT
100809 GCGACCGTC
1 GCGACCGTC
100818 GAGTGGCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.32, G:0.26, T:0.30
Consensus pattern (24 bp):
GCGACCGTCCCCTGGATCTGTTAT
Found at i:112944 original size:16 final size:17
Alignment explanation
Indices: 112916--112950 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
112906 TCTCTTCAAT
112916 TAAATTAAAAAAATATA
1 TAAATTAAAAAAATATA
112933 TAAATT-AAAAAATATA
1 TAAATTAAAAAAATATA
112949 TA
1 TA
112951 CATTTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATTAAAAAAATATA
Found at i:123867 original size:8 final size:8
Alignment explanation
Indices: 123854--123878 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
123844 ATAAAAGTAG
123854 AATAGTTT
1 AATAGTTT
123862 AATAGTTT
1 AATAGTTT
123870 AATAGTTT
1 AATAGTTT
123878 A
1 A
123879 TGTGGGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (8 bp):
AATAGTTT
Found at i:124597 original size:20 final size:20
Alignment explanation
Indices: 124572--124680 Score: 218
Period size: 20 Copynumber: 5.5 Consensus size: 20
124562 TTCAGTGTGT
124572 ATCGATGCACACAGGTAGGC
1 ATCGATGCACACAGGTAGGC
124592 ATCGATGCACACAGGTAGGC
1 ATCGATGCACACAGGTAGGC
124612 ATCGATGCACACAGGTAGGC
1 ATCGATGCACACAGGTAGGC
124632 ATCGATGCACACAGGTAGGC
1 ATCGATGCACACAGGTAGGC
124652 ATCGATGCACACAGGTAGGC
1 ATCGATGCACACAGGTAGGC
124672 ATCGATGCA
1 ATCGATGCA
124681 TGGGAATTTC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 89 1.00
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (20 bp):
ATCGATGCACACAGGTAGGC
Found at i:125698 original size:31 final size:30
Alignment explanation
Indices: 125597--125724 Score: 87
Period size: 31 Copynumber: 4.1 Consensus size: 30
125587 AGAGTCGAGG
*
125597 GTTTACCTATGCTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATAT-GACA
* * * * *
125628 GAATTACCTATG-TCTTTCGGGACAGATGAACC
1 G-TTTACCTATGTTC-TACGGAACATATG-ACA
* *
125660 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTTTACCTATGTTCTACGGAACATAT-GACA
* * * *
125691 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATAT-GACA
125722 GTT
1 GTT
125725 GTCGAGGTTC
Statistics
Matches: 73, Mismatches: 19, Indels: 10
0.72 0.19 0.10
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (30 bp):
GTTTACCTATGTTCTACGGAACATATGACA
Found at i:130247 original size:31 final size:31
Alignment explanation
Indices: 130212--130273 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
130202 ATGAACCGTA
*
130212 TACCTATGTTC-TAAGGAACATATGGACAGTT
1 TACCTAGGTTCTTAAGG-ACATATGGACAGTT
*
130243 TACCTAGGTTCTTCAGGACATATGGACAGTT
1 TACCTAGGTTCTTAAGGACATATGGACAGTT
130274 GTCGAGGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTAGGTTCTTAAGGACATATGGACAGTT
Found at i:131347 original size:21 final size:22
Alignment explanation
Indices: 131323--131363 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
131313 AGATGTTTAT
131323 AAAAGAATAAA-TT-GAATTTCG
1 AAAAG-ATAAACTTGGAATTTCG
131344 AAAAGATAAACTTGGAATTT
1 AAAAGATAAACTTGGAATTT
131364 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (22 bp):
AAAAGATAAACTTGGAATTTCG
Found at i:132718 original size:23 final size:23
Alignment explanation
Indices: 132692--132751 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
132682 CAGCTTCAAC
132692 CCACTTGGTGAAATAGTCGATTG
1 CCACTTGGTGAAATAGTCGATTG
* * *
132715 CCACGTAGTGAAATAGTTGATTG
1 CCACTTGGTGAAATAGTCGATTG
*
132738 CCACTAGGATGAAA
1 CCACTTGG-TGAAA
132752 CAATGTCCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (23 bp):
CCACTTGGTGAAATAGTCGATTG
Found at i:139178 original size:14 final size:16
Alignment explanation
Indices: 139161--139192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
139151 ATTATTTTTT
139161 TGAAT-TTTA-CTTAA
1 TGAATGTTTATCTTAA
139175 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
139191 TG
1 TG
139193 TAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:143186 original size:2 final size:2
Alignment explanation
Indices: 143179--143219 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
143169 TAAAGTAAAC
143179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
143220 GGTCTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143323 original size:19 final size:21
Alignment explanation
Indices: 143299--143339 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
143289 CCTCTTTCTT
143299 AATATTAA-AAAAATA-AATA
1 AATATTAATAAAAATATAATA
*
143318 AATATTAATTAAAATATAATA
1 AATATTAATAAAAATATAATA
143339 A
1 A
143340 TTTTTCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATATTAATAAAAATATAATA
Found at i:143379 original size:2 final size:2
Alignment explanation
Indices: 143372--143414 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
143362 AATTAAAGTG
*
143372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
143414 T
1 T
143415 CATAAAAGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:144864 original size:3 final size:3
Alignment explanation
Indices: 144858--144897 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
144848 ATTTATTATT
*
144858 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
144898 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:146280 original size:21 final size:20
Alignment explanation
Indices: 146256--146297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
146246 GTCATACAAC
*
146256 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
146277 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
146297 T
1 T
146298 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:170298 original size:2 final size:2
Alignment explanation
Indices: 170291--170315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
170281 AAGATATAAC
170291 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
170316 ATAAAATGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184586 original size:22 final size:23
Alignment explanation
Indices: 184560--184602 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
184550 ACTTATTTCA
*
184560 AAAATCAA-AGTAAAAAAGGACT
1 AAAATCAAGAGAAAAAAAGGACT
*
184582 AAAATGAAGAGAAAAAAAGGA
1 AAAATCAAGAGAAAAAAAGGA
184603 AGAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.19, T:0.09
Consensus pattern (23 bp):
AAAATCAAGAGAAAAAAAGGACT
Found at i:195769 original size:43 final size:43
Alignment explanation
Indices: 195708--195794 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
195698 TTGATTTTCG
195708 TTAACTCCTTTTATTCAAGTCTTTTTTACTTGAATCCCAAACA
1 TTAACTCCTTTTATTCAAGTCTTTTTTACTTGAATCCCAAACA
195751 TTAACTCCTTTTATTCAAGTCTTTTTTACTTGAATCCCAAACA
1 TTAACTCCTTTTATTCAAGTCTTTTTTACTTGAATCCCAAACA
195794 T
1 T
195795 AACCGAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (43 bp):
TTAACTCCTTTTATTCAAGTCTTTTTTACTTGAATCCCAAACA
Found at i:196282 original size:41 final size:40
Alignment explanation
Indices: 196225--196350 Score: 207
Period size: 41 Copynumber: 3.1 Consensus size: 40
196215 GAGTGCCGTT
196225 TTGGTCTCGATCGAGGCATAAATACTCTTCACCGCACTGG
1 TTGGTCTCGATCGAGGCATAAATACTCTTCACCGCACTGG
*
196265 ATTGGTCTCGATCGAGGCATAAATACTCTTCACCGGACTGG
1 -TTGGTCTCGATCGAGGCATAAATACTCTTCACCGCACTGG
* *
196306 TTTGGTCTAGATCGAGGCATAAATAATCTTCACCGCACTGG
1 -TTGGTCTCGATCGAGGCATAAATACTCTTCACCGCACTGG
196347 TTGG
1 TTGG
196351 CACACCAAAC
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 4 0.05
41 76 0.95
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (40 bp):
TTGGTCTCGATCGAGGCATAAATACTCTTCACCGCACTGG
Found at i:206580 original size:58 final size:58
Alignment explanation
Indices: 206490--206605 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
206480 GGAAAAATAA
*
206490 AAGGGATAAAATTACATGAAAGACGAGTGTAATTTCACAAATAACAAAGAATCCAACT
1 AAGGGATAAAATTACATGAAAGACGAGTGTAATTTCACAAATAACAAAGAACCCAACT
206548 AAGGGATAAAATTACATGAAAGACGAGTGTAATTTCACAAATAACAAAGAACCCAACT
1 AAGGGATAAAATTACATGAAAGACGAGTGTAATTTCACAAATAACAAAGAACCCAACT
206606 TTATCCACGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.20
Consensus pattern (58 bp):
AAGGGATAAAATTACATGAAAGACGAGTGTAATTTCACAAATAACAAAGAACCCAACT
Found at i:220938 original size:23 final size:23
Alignment explanation
Indices: 220912--220958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
220902 AAATTAAACT
* *
220912 TTAAATATAATTTTTAAAAAAAA
1 TTAAATATAAATATTAAAAAAAA
* *
220935 TTAAATTTAAATATTAAAATAAA
1 TTAAATATAAATATTAAAAAAAA
220958 T
1 T
220959 CAAAATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAATATAAATATTAAAAAAAA
Found at i:220963 original size:29 final size:30
Alignment explanation
Indices: 220886--220967 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 30
220876 AATATCATGG
220886 TATTAAAATGAAATAAAAATTAAACTTTAAA
1 TATTAAAAT-AAATAAAAATTAAACTTTAAA
**
220917 TA-TAATTTTTAAA-AAAAATTAAA-TTTAAA
1 TATTAA--AATAAATAAAAATTAAACTTTAAA
*
220946 TATTAAAATAAATCAAAATTAA
1 TATTAAAATAAATAAAAATTAA
220968 TAGTTTATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
28 4 0.10
29 16 0.38
30 16 0.38
31 5 0.12
32 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (30 bp):
TATTAAAATAAATAAAAATTAAACTTTAAA
Found at i:221901 original size:39 final size:39
Alignment explanation
Indices: 221847--221924 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
221837 GCAAAATGAT
*
221847 TATTACATTCATTGAATTGTTACAAAATGATCATTGCAC
1 TATTACATTCATTGAATTGTTACAAAACGATCATTGCAC
221886 TATTACATTCATTGAATTGTTACAAAACGATCATTGCAC
1 TATTACATTCATTGAATTGTTACAAAACGATCATTGCAC
221925 GTTGTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (39 bp):
TATTACATTCATTGAATTGTTACAAAACGATCATTGCAC
Found at i:221908 original size:17 final size:17
Alignment explanation
Indices: 221849--221909 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
221839 AAAATGATTA
221849 TTACATTCATTGAATTG
1 TTACATTCATTGAATTG
* * *
221866 TTACAAAATGATCATTGCACTA
1 TTAC---AT--TCATTGAATTG
221888 TTACATTCATTGAATTG
1 TTACATTCATTGAATTG
221905 TTACA
1 TTACA
221910 AAACGATCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 17 0.52
19 2 0.06
20 2 0.06
22 12 0.36
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
TTACATTCATTGAATTG
Found at i:227712 original size:22 final size:22
Alignment explanation
Indices: 227687--227729 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
227677 TGTTCCTTGA
227687 GATTCGGCCATTGATT-TGGTTC
1 GATTCGG-CATTGATTCTGGTTC
*
227709 GATTTGGCATTGATTCTGGTT
1 GATTCGGCATTGATTCTGGTT
227730 TGTTTTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (22 bp):
GATTCGGCATTGATTCTGGTTC
Found at i:228235 original size:14 final size:14
Alignment explanation
Indices: 228218--228294 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
228208 AATCAAAATA
228218 ATAAATAAATATAT
1 ATAAATAAATATAT
228232 AT-AATAAATATA-
1 ATAAATAAATATAT
228244 AT-AATATAATATA-
1 ATAAATA-AATATAT
* *
228257 ATACATATACTATACT
1 ATAAATA-AATATA-T
* *
228273 ATATATATATATAT
1 ATAAATAAATATAT
*
228287 ATATATAA
1 ATAAATAA
228295 CACCATGATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 6 0.11
13 18 0.34
14 19 0.36
15 4 0.08
16 6 0.11
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAATAAATATAT
Found at i:228311 original size:2 final size:2
Alignment explanation
Indices: 228226--228293 Score: 65
Period size: 2 Copynumber: 35.5 Consensus size: 2
228216 TAATAAATAA
* *
228226 AT AT AT AT A- AT AA AT AT A- AT A- AT AT A- AT AT A- AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228263 AT ACT AT ACT AT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT A
228294 ACACCATGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
1 5 0.09
2 46 0.84
3 4 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:229297 original size:20 final size:20
Alignment explanation
Indices: 229260--229298 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
229250 GGTTTACATT
* *
229260 TATAATTATAATTTTTTTAA
1 TATAATTATAAATATTTTAA
*
229280 TATAATTTTAAATATTTTA
1 TATAATTATAAATATTTTA
229299 CCTTCTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATTATAAATATTTTAA
Found at i:230158 original size:60 final size:60
Alignment explanation
Indices: 230092--230218 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
230082 TAAAGTATAT
*
230092 AAATGATCCATC-GACTACATG-GTATTATTTTCTTAAGTCCCTCGACTATTAAAAGTTACA
1 AAATGAT-CATCTGACTACA-GAGTATTACTTTCTTAAGTCCCTCGACTATTAAAAGTTACA
* * * * * * * *
230152 AAATGATCTTCTGATTATAGAGTGTTGCTTTGTTAAGTCTCTCGACTATTAAAAGTTATA
1 AAATGATCATCTGACTACAGAGTATTACTTTCTTAAGTCCCTCGACTATTAAAAGTTACA
230212 AAATGAT
1 AAATGAT
230219 TACTCATCTA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (60 bp):
AAATGATCATCTGACTACAGAGTATTACTTTCTTAAGTCCCTCGACTATTAAAAGTTACA
Found at i:239786 original size:7 final size:8
Alignment explanation
Indices: 239769--239793 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
239759 TTTACAGAAA
239769 TTTATTTT
1 TTTATTTT
239777 TTTATTTT
1 TTTATTTT
239785 TTTATTTT
1 TTTATTTT
239793 T
1 T
239794 CAGCTGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:241925 original size:15 final size:15
Alignment explanation
Indices: 241905--241935 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
241895 TCTTGTTTGA
*
241905 TTCTAAACTATCATC
1 TTCTAAAATATCATC
241920 TTCTAAAATATCATC
1 TTCTAAAATATCATC
241935 T
1 T
241936 CCATCTCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
TTCTAAAATATCATC
Found at i:246754 original size:16 final size:17
Alignment explanation
Indices: 246733--246771 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
246723 TGATTTGATA
246733 TGAAAATTT-AGATATC
1 TGAAAATTTCAGATATC
*
246749 TGAAAATTTCGGATATC
1 TGAAAATTTCAGATATC
246766 T-AAAAT
1 TGAAAAT
246772 AGTTATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (17 bp):
TGAAAATTTCAGATATC
Found at i:247018 original size:16 final size:16
Alignment explanation
Indices: 246993--247038 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
246983 ATACTCTAAT
*
246993 TTTTATTGAGTTAGAG
1 TTTTAATGAGTTAGAG
247009 TTTTAATGAGTTAGAG
1 TTTTAATGAGTTAGAG
*
247025 TTTTAATGGGTTAG
1 TTTTAATGAGTTAG
247039 TGGGTTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTAATGAGTTAGAG
Found at i:250207 original size:60 final size:60
Alignment explanation
Indices: 250098--250213 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
250088 TCGAGTGATT
** * *
250098 ATTTTATAACTTTTAATAGTTGAAGGACTTGACAAAACAACATTCTATAATCAGAAGATC
1 ATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAACAACATTCTATAATCAGAAGATC
* * * * * *
250158 ATTTTATAATTTTTAATAGTCAAATAACTTAATAAAATAATATTTTATAATCAGAA
1 ATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAACAACATTCTATAATCAGAA
250214 AAACATTTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAACAACATTCTATAATCAGAAGATC
Found at i:262313 original size:21 final size:21
Alignment explanation
Indices: 262287--262326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
262277 TCAACCCTAT
* *
262287 ACTATCATATCAGTACCGTGA
1 ACTATCACATCAATACCGTGA
262308 ACTATCACATCAATACCGT
1 ACTATCACATCAATACCGT
262327 AACGGTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (21 bp):
ACTATCACATCAATACCGTGA
Found at i:266665 original size:48 final size:48
Alignment explanation
Indices: 266596--266706 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
266586 AAATATTTTA
* * *
266596 TCTGATTTCCGACT-TGAATTCTGTTCTGAT-ACATTACCTGAATTTTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCTGATGAC-TGACCTGAATTCTGT
* * *
266644 TCTGATTTCTGATATGGATTCTGTTCTGATGTCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCTGATGACTGACCTGAATTCTGT
*
266692 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
266707 CTCTGGTTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCTGATGACTGACCTGAATTCTGT
Found at i:266668 original size:24 final size:24
Alignment explanation
Indices: 266634--266706 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
266624 ATACATTACC
*
266634 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * *
266658 TGGATTCTGTTCTGATGTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
*
266682 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
266706 T
1 T
266707 CTCTGGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Done.