Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011126.1 Kokia drynarioides strain JFW-HI SEQ_126099, 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: 150859
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 222 characters in sequence are not A, C, G, or T
Found at i:1267 original size:18 final size:18
Alignment explanation
Indices: 1246--1307 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1236 CATATTGGGT
*
1246 TGAGCTTGCATCTTTTGA
1 TGAGCTTGCAGCTTTTGA
* *
1264 TGAGCTCGTAGCTTTTGA
1 TGAGCTTGCAGCTTTTGA
* * *
1282 TAAGCTTGTAG-TTTTGTT
1 TGAGCTTGCAGCTTTTG-A
1300 TGAGCTTG
1 TGAGCTTG
1308 TAGTAATGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 5 0.14
18 31 0.86
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (18 bp):
TGAGCTTGCAGCTTTTGA
Found at i:1308 original size:18 final size:18
Alignment explanation
Indices: 1282--1325 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1272 TAGCTTTTGA
**
1282 TAAGCTTGTAGTTTTGTT
1 TAAGCTTGTAGTAATGTT
*
1300 TGAGCTTGTAGTAATGTT
1 TAAGCTTGTAGTAATGTT
1318 TAAGCTTG
1 TAAGCTTG
1326 CAACTTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (18 bp):
TAAGCTTGTAGTAATGTT
Found at i:3879 original size:24 final size:24
Alignment explanation
Indices: 3821--3879 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3811 ATGGGTGTTC
*
3821 AACCTTTCATCTTCCTTGACCTTT
1 AACCTTTCATCTTCCTTAACCTTT
* * *
3845 GATCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTTCCTTAACCTTT
*
3869 AACCTTCCATC
1 AACCTTTCATC
3880 CTTTAATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.03, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTTCCTTAACCTTT
Found at i:4181 original size:20 final size:21
Alignment explanation
Indices: 4158--4202 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4148 AAAATTAAAT
*
4158 AATAAAAATTT-TAATTTTTA
1 AATAAAAATTTAAAATTTTTA
**
4178 AATAAAGGTTTAAAATTTTTA
1 AATAAAAATTTAAAATTTTTA
4199 AATA
1 AATA
4203 CTATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
AATAAAAATTTAAAATTTTTA
Found at i:5258 original size:55 final size:55
Alignment explanation
Indices: 5149--5265 Score: 177
Period size: 55 Copynumber: 2.1 Consensus size: 55
5139 CTCTTTTAGG
* *
5149 TTTTTCTT-TTTTATAGTTCTTGAGTTGTGCTGGGAAGTTTTAGGGACGGTCATT
1 TTTTTTTTCTTTTATAGTTCTTGAGTTGTGCTGGGAAGTTTTAGGGACGATCATT
5203 TTCTTTTTTCTTTT-TAGTTCTTGAGTTGTGCTGGGAAGTTTTAGGGAC-ATCCATT
1 TT-TTTTTTCTTTTATAGTTCTTGAGTTGTGCTGGGAAGTTTTAGGGACGAT-CATT
5258 TTTTTTTT
1 TTTTTTTT
5266 AGGTTTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
54 9 0.16
55 45 0.78
56 4 0.07
ACGTcount: A:0.14, C:0.10, G:0.22, T:0.54
Consensus pattern (55 bp):
TTTTTTTTCTTTTATAGTTCTTGAGTTGTGCTGGGAAGTTTTAGGGACGATCATT
Found at i:11935 original size:16 final size:16
Alignment explanation
Indices: 11914--11945 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11904 ATATTAAAAA
*
11914 TATATTAAAAAGTATT
1 TATATTAAAAAATATT
11930 TATATTAAAAAATATT
1 TATATTAAAAAATATT
11946 ACCATAAATA
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:0.03, T:0.44
Consensus pattern (16 bp):
TATATTAAAAAATATT
Found at i:12134 original size:29 final size:31
Alignment explanation
Indices: 12072--12155 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
12062 TTGCTATTGG
*
12072 ATTATTGATTTAATATAAATATAAATATATATA
1 ATTATT-ATTTAACAT-AATATAAATATATATA
*
12105 ATTATTATTTAACAT-ATATAATTA-ATATA
1 ATTATTATTTAACATAATATAAATATATATA
*
12134 ATTATTTTTATAACATAATATA
1 ATTATTATT-TAACATAATATA
12156 TTCTAATCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.28
30 14 0.30
31 5 0.11
32 8 0.17
33 6 0.13
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
ATTATTATTTAACATAATATAAATATATATA
Found at i:12330 original size:19 final size:20
Alignment explanation
Indices: 12306--12344 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12296 TAAATAATGA
12306 ATATGA-ATATTTTAAAATT
1 ATATGATATATTTTAAAATT
* *
12325 ATATGATATGTTTTATAATT
1 ATATGATATATTTTAAAATT
12345 CATTCAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATATGATATATTTTAAAATT
Found at i:18903 original size:2 final size:2
Alignment explanation
Indices: 18896--18929 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18886 AAGGTATATT
18896 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18930 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19979 original size:15 final size:15
Alignment explanation
Indices: 19959--19987 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19949 AATTTCATTT
19959 CCTTTTTAATTTAAA
1 CCTTTTTAATTTAAA
19974 CCTTTTTAATTTAA
1 CCTTTTTAATTTAA
19988 TCAAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
CCTTTTTAATTTAAA
Found at i:21545 original size:30 final size:29
Alignment explanation
Indices: 21511--21647 Score: 105
Period size: 30 Copynumber: 4.6 Consensus size: 29
21501 TGTTTCATTT
* *
21511 AAAATTATATTTTGACCTCTGAACTTCCCA
1 AAAATTACATTTTGACC-CTAAACTTCCCA
* * *
21541 AAAATCACATTTTAACCTTAAACTTTCCC-
1 AAAATTACATTTTGACCCTAAAC-TTCCCA
* * * *
21570 AAAATCACATTTTGTCCCTCCAACTTTCCA
1 AAAATTACATTTTGACCCT-AAACTTCCCA
* **
21600 AAAATTACATTTTGACCCTTAAATTTTTCA
1 AAAATTACATTTTGACCC-TAAACTTCCCA
* *
21630 AAAATTATATTTTAACCC
1 AAAATTACATTTTGACCC
21648 CAAATTCTTC
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
29 24 0.28
30 61 0.71
31 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTAAACTTCCCA
Found at i:29023 original size:17 final size:17
Alignment explanation
Indices: 29003--29047 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
28993 TAAAACAAAA
*
29003 AAAACAAAAAAAAAAGG
1 AAAAGAAAAAAAAAAGG
*
29020 AAAAGAAAAAGAAAAGG
1 AAAAGAAAAAAAAAAGG
29037 AAAAGAAAAAA
1 AAAAGAAAAAA
29048 GAAGGAGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGG
Found at i:29923 original size:50 final size:50
Alignment explanation
Indices: 29859--30618 Score: 602
Period size: 50 Copynumber: 15.3 Consensus size: 50
29849 TGATACCCTA
* * * * *
29859 AAGATATGAAGGGAAAGGTTGAGGCCACAACGGCAAACCCGGTACCTTAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * * ** *
29909 AAGATGTGATGGGAAATGTTGAGGCCACAATGGTGAACCTAGTACCAT-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * * *
29958 AAGATATGAAGGGAAAGGTTGTGGCCGTAACGGCGAACCCGATATCCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTA-CCTTAG
* * *
30009 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCAT-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * * * * * * ** *
30058 AAGATATAAAGGGAAAGGTTAAGGCCGTAATGGTGTACTTGGTACCTTAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* ** * *
30108 AAGATGCGATGGGAAAGGTTGAGGTTGCAACGGTGAACTCGGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* *
30158 AAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGGTACC-T-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * ** ** *
30206 AAGATATGAAGGGAAAGGTTAAGGTGGCAACGGCGAGTCCAGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * ** **
30256 AAGATGTGATGGGAAAGGTTGATGTCGCAATGATGAACCCAATACCATT--
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC-TTAG
* * ** * * *
30305 AAGATATGAAGGGAAAGGTTGAGGCTACAACGGTGAACTCGATACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
** ** *
30355 AAGATGTGATGGGAAAGGTTGAGGCCATAACGGCGAACCCAATACCAT-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * * * ** *
30404 AATATATGAAGGGAAAAGTTGAGGCCGCAACGACGAATGCAGTATCCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTA-CCTTAG
* * * * * *
30455 AAGATGTGAT-GGAAAGGTTGAGGCCGCAACGACAAACTCGATACCTCAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * * ** *
30504 AAGATGTAATGGGAAAGGTTAAAGCTGCAACGGCGAACCCAATACCTTGG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* * * *
30554 AAGATGTGATGGGAAAGGTTAAGGCCTCAACGGCGAACTCGGTACCATA-
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
* *
30603 AAGATATGAAGGGAAA
1 AAGATGTGATGGGAAA
30619 CCCTTAGAAG
Statistics
Matches: 557, Mismatches: 142, Indels: 23
0.77 0.20 0.03
Matches are distributed among these distances:
48 41 0.07
49 169 0.30
50 299 0.54
51 48 0.09
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.19
Consensus pattern (50 bp):
AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAG
Found at i:30361 original size:99 final size:98
Alignment explanation
Indices: 30118--30618 Score: 490
Period size: 99 Copynumber: 5.1 Consensus size: 98
30108 AAGATGCGAT
* * * *
30118 GGGAAAGGTTGAGGTTGCAACGGTGAACTCGGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGC
1 GGGAAAGGTTGAGGCTGCAACGGCGAACTCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
** **
30183 CGCAACGGTGAACCCGGTACCTGAAGATATGAA
66 CGCAACGACGAACCCAATACCTGAAGATATGAA
* * * *
30216 GGGAAAGGTTAAGG-TGGCAACGGCG-AGTCCAGTACCTTAGAAGATGTGATGGGAAAGGTTGAT
1 GGGAAAGGTTGAGGCT-GCAACGGCGAACTCGA-TACCTTAGAAGATGTGATGGGAAAGGTTGAG
* * * *
30279 GTCGCAATGATGAACCCAATACCATTAAGATATGAA
64 GCCGCAACGACGAACCCAATACC-TGAAGATATGAA
* *
30315 GGGAAAGGTTGAGGCTACAACGGTGAACTCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
1 GGGAAAGGTTGAGGCTGCAACGGCGAACTCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
** * *
30380 CATAACGGCGAACCCAATACCATGAATATATGAA
66 CGCAACGACGAACCCAATACC-TGAAGATATGAA
* * *
30414 GGGAAAAGTTGAGGCCGCAACGACGAA-T-GCAGTATCCTTAGAAGATGTGAT-GGAAAGGTTGA
1 GGGAAAGGTTGAGGCTGCAACGGCGAACTCG-A-TA-CCTTAGAAGATGTGATGGGAAAGGTTGA
* * * * * *
30476 GGCCGCAACGACAAACTCGATACCTCAAAAGATGTAA
63 GGCCGCAACGACGAACCCAATACCTGAAGATATG-AA
* * * * * *
30513 TGGGAAAGGTTAAAGCTGCAACGGCGAACCCAATACCTTGGAAGATGTGATGGGAAAGGTTAAGG
1 -GGGAAAGGTTGAGGCTGCAACGGCGAACTCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGG
* * * ** *
30578 CCTCAACGGCGAACTCGGTACCATAAAGATATGAA
65 CCGCAACGACGAACCCAATACC-TGAAGATATGAA
30613 GGGAAA
1 GGGAAA
30619 CCCTTAGAAG
Statistics
Matches: 332, Mismatches: 57, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
97 5 0.02
98 77 0.23
99 165 0.50
100 77 0.23
101 8 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (98 bp):
GGGAAAGGTTGAGGCTGCAACGGCGAACTCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
CGCAACGACGAACCCAATACCTGAAGATATGAA
Found at i:30469 original size:149 final size:149
Alignment explanation
Indices: 29859--30590 Score: 582
Period size: 149 Copynumber: 4.9 Consensus size: 149
29849 TGATACCCTA
* * * * * *
29859 AAGATATGAAGGGAAAGGTTGAGGCCACAACGGCAAACCCGGTACCTTAAAAGATGTGATGGGAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
* * * * * * * * *
29924 ATGTTGAGGCCACAATGGTGAACCTAGTACCATGAAGATATGAAGGGAAAGGTTGTGGCCGTAAC
66 AGGTTAAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGATGGGAAAGGTTGAGGCCGCAAC
*
29989 GGCGAA-CCCGATATCCTTAG
131 GGCGAATCCAG-TA-CCTTAG
* * * * *
30009 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCC-AGTACCAT-GAAGATATAAAGGGA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGA-TACCTTAGAAGATGTGATGGGA
* * * * *** * * ** **
30072 AAGGTTAAGGCCGTAATGGTGTACTTGGTACCTTAAAAGATGCGATGGGAAAGGTTGAGGTTGCA
65 AAGGTTAAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGATGGGAAAGGTTGAGGCCGCA
* *
30137 ACGGTGAA-CTCGGTACCTTAG
129 ACGGCGAATC-CAGTACCTTAG
* * * * *
30158 AAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTGAACCCGGTACC-T-GAAGATATGAAGGGAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
** ** * * * *
30221 AGGTTAAGGTGGCAACGGCGAGTCCAGTACCTTAGAAGATGTGATGGGAAAGGTTGATGTCGCAA
66 AGGTTAAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGATGGGAAAGGTTGAGGCCGCAA
* ** * *
30286 TGATGAACCCAATACCATT--
130 CGGCGAATCCAGTACC-TTAG
* * ** * *
30305 AAGATATGAAGGGAAAGGTTGAGGCTACAACGGTGAACTCGATACCTTAGAAGATGTGATGGGAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
* ** * * * *
30370 AGGTTGAGGCCATAACGGCGAACCCAATACCATGAATATATGAAGGGAAAAGTTGAGGCCGCAAC
66 AGGTTAAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGATGGGAAAGGTTGAGGCCGCAAC
* *
30435 GACGAATGCAGTATCCTTAG
131 GGCGAATCCAGTA-CCTTAG
* * * * * *
30455 AAGATGTGAT-GGAAAGGTTGAGGCCGCAACGACAAACTCGATACCTCAAAAGATGTAATGGGAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
* * * * * * *
30519 AGGTTAAAGCTGCAACGGCGAACCCAATACCTTGGAAGATGTGATGGGAAAGGTTAAGGCCTCAA
66 AGGTTAAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGATGGGAAAGGTTGAGGCCGCAA
30584 CGGCGAA
130 CGGCGAA
30591 CTCGGTACCA
Statistics
Matches: 465, Mismatches: 105, Indels: 24
0.78 0.18 0.04
Matches are distributed among these distances:
147 39 0.08
148 113 0.24
149 200 0.43
150 111 0.24
151 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (149 bp):
AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
AGGTTAAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGATGGGAAAGGTTGAGGCCGCAAC
GGCGAATCCAGTACCTTAG
Found at i:30657 original size:72 final size:73
Alignment explanation
Indices: 30548--30691 Score: 182
Period size: 72 Copynumber: 2.0 Consensus size: 73
30538 GAACCCAATA
* * * * *
30548 CCTTGGAAGATGTGATGGGAAAGGTTAAGGCCTCAACGGCGAACTCGGTACCAT-AAAGATATGA
1 CCTTAGAAGATGTGATAGGAAAGGTTAAGGCCGCAACGACGAACCCGGTACCATAAAAGATATGA
30612 AGGGAAAC
66 AGGGAAAC
* * * * *
30620 CCTTAGAAGATGTGATAGGAAAGGTTGAGGTCGCAACGACGAACCCTGTACCTTAAAAGATGTGA
1 CCTTAGAAGATGTGATAGGAAAGGTTAAGGCCGCAACGACGAACCCGGTACCATAAAAGATATGA
*
30685 TGGGAAA
66 AGGGAAA
30692 GGTTGAGGCT
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
72 45 0.75
73 15 0.25
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (73 bp):
CCTTAGAAGATGTGATAGGAAAGGTTAAGGCCGCAACGACGAACCCGGTACCATAAAAGATATGA
AGGGAAAC
Found at i:30713 original size:50 final size:50
Alignment explanation
Indices: 30620--30774 Score: 154
Period size: 50 Copynumber: 3.1 Consensus size: 50
30610 GAAGGGAAAC
* * *
30620 CCTTAGAAGATGTGATAGGAAAGGTTGAGG-TCGCAAC-GACGAACCCTGTA
1 CCTTAAAAGATGTGATGGGAAAGGTTGAGGCT-GCAACAG-CGAACCCAGTA
* * *
30670 CCTTAAAAGATGTGATGGGAAAGGTTGAGGCTGTAACAGCGAACTCGGTA
1 CCTTAAAAGATGTGATGGGAAAGGTTGAGGCTGCAACAGCGAACCCAGTA
* * * * * * *
30720 CCAT-GAAGATATGAAGGGAAAGCTTGAGGCTGCAATAGCGAACCCAATA
1 CCTTAAAAGATGTGATGGGAAAGGTTGAGGCTGCAACAGCGAACCCAGTA
30769 CCTTAA
1 CCTTAA
30775 GAAAACATGA
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
49 39 0.46
50 44 0.52
51 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (50 bp):
CCTTAAAAGATGTGATGGGAAAGGTTGAGGCTGCAACAGCGAACCCAGTA
Found at i:30721 original size:122 final size:122
Alignment explanation
Indices: 30504--30740 Score: 325
Period size: 122 Copynumber: 1.9 Consensus size: 122
30494 GATACCTCAA
* * **
30504 AAGATGTAATGGGAAAGGTTAAAGCTGCAACGGCGAACCCAATACCTTGGAAGATGTGATGGGAA
1 AAGATGTAATAGGAAAGGTTAAAGCTGCAACGACGAACCCAATACCTTAAAAGATGTGATGGGAA
*
30569 AGGTTAAGGCCTCAACGGCGAACTCGGTACCATAAAGATATGAAGGGAAACCCTTAG
66 AGGTTAAGGCCTCAACAGCGAACTCGGTACCATAAAGATATGAAGGGAAACCCTTAG
* * * **
30626 AAGATGTGATAGGAAAGGTT-GAGGTCGCAACGACGAACCCTGTACCTTAAAAGATGTGATGGGA
1 AAGATGTAATAGGAAAGGTTAAAGCT-GCAACGACGAACCCAATACCTTAAAAGATGTGATGGGA
* * *
30690 AAGGTTGAGG-CTGTAACAGCGAACTCGGTACCATGAAGATATGAAGGGAAA
65 AAGGTTAAGGCCT-CAACAGCGAACTCGGTACCATAAAGATATGAAGGGAAA
30741 GCTTGAGGCT
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
121 5 0.05
122 95 0.95
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (122 bp):
AAGATGTAATAGGAAAGGTTAAAGCTGCAACGACGAACCCAATACCTTAAAAGATGTGATGGGAA
AGGTTAAGGCCTCAACAGCGAACTCGGTACCATAAAGATATGAAGGGAAACCCTTAG
Found at i:30847 original size:40 final size:40
Alignment explanation
Indices: 30803--31016 Score: 181
Period size: 40 Copynumber: 5.3 Consensus size: 40
30793 ATGAAGCATT
*
30803 CAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACACAC
1 CAATCTCTTACCCTAGTCAGAGGGCAGATTGAAGACACAC
* *
30843 CAATCTCTTACCC-AGATCATG-GGGTAGATTGAAG-CA-TC
1 CAATCTCTTACCCTAG-TCA-GAGGGCAGATTGAAGACACAC
* * *
30881 CAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACACAC
1 CAATCTCTTACCCTAGTCAGAGGGCAGATTGAAGACACAC
* * *
30921 CAATCTCTTACCC-CGATCATGGGGGCAGATTGAAG-CA-TC
1 CAATCTCTTACCCTAG-TCA-GAGGGCAGATTGAAGACACAC
* * * * *
30960 CAATCTCTTACCCTAATCAAACGACAAATTGAAGACATCATC
1 CAATCTCTTACCCTAGTCAGAGGGCAGATTGAAGACA-CA-C
*
31002 CAAATCTTTTACCCT
1 C-AATCTCTTACCCT
31017 TAAAGATAAG
Statistics
Matches: 137, Mismatches: 23, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
38 37 0.27
39 28 0.20
40 45 0.33
41 13 0.09
42 2 0.01
43 12 0.09
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (40 bp):
CAATCTCTTACCCTAGTCAGAGGGCAGATTGAAGACACAC
Found at i:30923 original size:78 final size:79
Alignment explanation
Indices: 30794--31015 Score: 311
Period size: 78 Copynumber: 2.8 Consensus size: 79
30784 ACGGGAGAGA
* * *
30794 TGAAGCATTCAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCAGA
1 TGAAGCATCCAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACACACCAATCTCTTACCCAGA
*
30859 TCAT-GGGGTAGAT
66 TCATGGGGGCAGAT
*
30872 TGAAGCATCCAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACACACCAATCTCTTACCCCGA
1 TGAAGCATCCAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACACACCAATCTCTTACCCAGA
30937 TCATGGGGGCAGAT
66 TCATGGGGGCAGAT
* * * * * *
30951 TGAAGCATCCAATCTCTTACCCTAATCAAACGACAAATTGAAGACATCATCCAAATCTTTTACCC
1 TGAAGCATCCAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACA-CA-CC-AATCTCTTACCC
31016 TTAAAGATAA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
78 65 0.50
79 49 0.38
80 2 0.02
81 2 0.02
82 11 0.09
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (79 bp):
TGAAGCATCCAATCTTTTACCCTAGTCAAAAGGCAGATTGAAGACACACCAATCTCTTACCCAGA
TCATGGGGGCAGAT
Found at i:31669 original size:35 final size:35
Alignment explanation
Indices: 31630--31700 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
31620 CTTGCCCACT
* *
31630 CATCAACAATGGCCACCCATCATCTGCCACTACCA
1 CATCAACAATGGCCACCCATCATCTACCACCACCA
*
31665 CATCAGCAATGGCCACCCATCATCTACCACCACCA
1 CATCAACAATGGCCACCCATCATCTACCACCACCA
31700 C
1 C
31701 CAGTAACTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.45, G:0.08, T:0.15
Consensus pattern (35 bp):
CATCAACAATGGCCACCCATCATCTACCACCACCA
Found at i:32057 original size:11 final size:11
Alignment explanation
Indices: 32041--32066 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32031 ACATACATTT
32041 AATACATAATA
1 AATACATAATA
32052 AATACATAATA
1 AATACATAATA
32063 AATA
1 AATA
32067 AAAAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
AATACATAATA
Found at i:33141 original size:29 final size:29
Alignment explanation
Indices: 33063--33198 Score: 166
Period size: 30 Copynumber: 4.6 Consensus size: 29
33053 TGTTTCATTT
* *
33063 AAATCACATTTTGACCTCTAAACTTTCCAA
1 AAATCACATTTTAACC-CTAAACTTTCTAA
*
33093 AAATCACATTTTGACCCCTAAACTTTCTAA
1 AAATCACATTTT-AACCCTAAACTTTCTAA
* *
33123 AAATCACATTTTAACCCTAAACTTTTTTA
1 AAATCACATTTTAACCCTAAACTTTCTAA
*
33152 AAATAACATTTTAACCCTTAAACTTTGC-AA
1 AAATCACATTTTAACCC-TAAACTTT-CTAA
*
33182 AAATTACATTTTAACCC
1 AAATCACATTTTAACCC
33199 CTAATTTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
29 30 0.32
30 61 0.66
31 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATCACATTTTAACCCTAAACTTTCTAA
Found at i:33145 original size:59 final size:59
Alignment explanation
Indices: 33063--33198 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
33053 TGTTTCATTT
* * *
33063 AAATCACATTTTGACCTCTAAACTTTCCAAAAATCACATTTTGACCCCTAAACTTT-CTAA
1 AAATCACATTTTAACC-CTAAACTTTCCAAAAATAACATTTTAACCCCTAAACTTTGC-AA
*** *
33123 AAATCACATTTTAACCCTAAACTTTTTTAAAATAACATTTTAACCCTTAAACTTTGCAA
1 AAATCACATTTTAACCCTAAACTTTCCAAAAATAACATTTTAACCCCTAAACTTTGCAA
*
33182 AAATTACATTTTAACCC
1 AAATCACATTTTAACCC
33199 CTAATTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 51 0.76
60 16 0.24
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (59 bp):
AAATCACATTTTAACCCTAAACTTTCCAAAAATAACATTTTAACCCCTAAACTTTGCAA
Found at i:33208 original size:59 final size:60
Alignment explanation
Indices: 33063--33229 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 60
33053 TGTTTCATTT
* * * *
33063 AAATCACATTTTGACCTCTAAAC--TTTCCAAAAATCACATTTTGACCCCTAAACTTTCTAA
1 AAATCACATTTTAACC-CTAAACTTTTTTC-AAAATAACATTTTAACCCCTAAACTTTCTAA
*
33123 AAATCACATTTTAACCCTAAACTTTTTT-AAAATAACATTTTAACCCTTAAACTTTGC-AA
1 AAATCACATTTTAACCCTAAACTTTTTTCAAAATAACATTTTAACCCCTAAACTTT-CTAA
* * * **
33182 AAATTACATTTTAACCCCT-AATTTTTTTCAAGATTGCATTTTAACCCC
1 AAATCACATTTTAA-CCCTAAACTTTTTTCAAAATAACATTTTAACCCC
33230 AAATTCTTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
59 53 0.58
60 35 0.38
61 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (60 bp):
AAATCACATTTTAACCCTAAACTTTTTTCAAAATAACATTTTAACCCCTAAACTTTCTAA
Found at i:43248 original size:19 final size:18
Alignment explanation
Indices: 43217--43253 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
43207 AAATTTATCG
43217 ATATTTAAAAAATATTTA
1 ATATTTAAAAAATATTTA
*
43235 ATATTTATATAAATATTTA
1 ATATTTA-AAAAATATTTA
43254 CAATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTAAAAAATATTTA
Found at i:48492 original size:18 final size:17
Alignment explanation
Indices: 48450--48492 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
48440 GAGTTAAGTT
*
48450 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
48467 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
48485 TATAATTT
1 TATAATTT
48493 AGAATACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:48983 original size:13 final size:13
Alignment explanation
Indices: 48967--48991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48957 ACCAAAAAGG
48967 TTTTACTAAAATA
1 TTTTACTAAAATA
48980 TTTTACTAAAAT
1 TTTTACTAAAAT
48992 TATGATTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTACTAAAATA
Found at i:65941 original size:48 final size:48
Alignment explanation
Indices: 65870--65966 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
65860 TATTGGTTAT
65870 TTCAGAAAAAAATTTAACCCTCGAGGGTGTTTAGTTCAAAATGGTAAA
1 TTCAGAAAAAAATTTAACCCTCGAGGGTGTTTAGTTCAAAATGGTAAA
65918 TTCAGAAAAAAATTTAACCCTCGAGGGTGTTTAGTTCAAAATGGTAAA
1 TTCAGAAAAAAATTTAACCCTCGAGGGTGTTTAGTTCAAAATGGTAAA
65966 T
1 T
65967 ATCTTCATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (48 bp):
TTCAGAAAAAAATTTAACCCTCGAGGGTGTTTAGTTCAAAATGGTAAA
Found at i:68204 original size:417 final size:417
Alignment explanation
Indices: 67430--68265 Score: 1584
Period size: 417 Copynumber: 2.0 Consensus size: 417
67420 AAAAAATGGA
67430 TACAAATGGAAAATACTAAAAAATGACATTTTAATTATGTGTTAATTTCAAGACTTATGTAGTGT
1 TACAAATGGAAAATACTAAAAAATGACATTTTAATTATGTGTTAATTTCAAGACTTATGTAGTGT
*
67495 TTTTCATTATGTAGTGATATAATACTTTAATTCGGTTAATTCGGGTAATTTTTATACCAAAAATA
66 TTTTCATTATGTAGTGATATAATACTTTAATTCGGTTAATTCAGGTAATTTTTATACCAAAAATA
67560 AAAAAAACATAATTTTCGGTTAATTCAGTTAACCAGTCGAATTAACCAAAAAATTTCGGCTCGTT
131 AAAAAAACATAATTTTCGGTTAATTCAGTTAACCAGTCGAATTAACCAAAAAATTTCGGCTCGTT
67625 TAATTTTTTTTTGGAAAATTTTTGATTCAGTTAATGGTTAAGGATTTAAAGGGGTCGATTAATTC
196 TAATTTTTTTTTGGAAAATTTTTGATTCAGTTAATGGTTAAGGATTTAAAGGGGTCGATTAATTC
**
67690 AATTAATGATGGTTTGGGTCAGAATCGATTAAACACCCTTATGCGGAGGGTCTCAGCTTCTTCTC
261 AATTAATGATGGTTTGGGTCAGAATCGATTAAACACCCTTATGCGGAGAATCTCAGCTTCTTCTC
*
67755 GCCAACAATTTCTTATTATTATCGTTTTATTTTATTAAGAATCGTGGTGTGAGACAATTATTTTT
326 GCCAACAATTTCTTATTATTATCGTTTTATTTTATTAAGAATCGTGGTATGAGACAATTATTTTT
*
67820 AATTACGTCACTTAGATGCATTTTATT
391 AATTACGTCACTTAGATGCATGTTATT
67847 TACAAATGGAAAATACTAAAAAATGACATTTTAATTATGTGTTAATTTCAAGACTTATGTAGTGT
1 TACAAATGGAAAATACTAAAAAATGACATTTTAATTATGTGTTAATTTCAAGACTTATGTAGTGT
67912 TTTTCATTATGTAGTGATATAATACTTTAATTCGGTTAATTCAGGTAATTTTTATACCAAAAATA
66 TTTTCATTATGTAGTGATATAATACTTTAATTCGGTTAATTCAGGTAATTTTTATACCAAAAATA
* * *
67977 AAAAAACATATAATTTTCGGTTAATTCAGTTAACCAGTTGAATTAACCAAAAAATTTCGGTTCGT
131 AAAAAA-ACATAATTTTCGGTTAATTCAGTTAACCAGTCGAATTAACCAAAAAATTTCGGCTCGT
68042 TTAATTTTTTTTTGGAAAATTTTTGATTCAGTTAATGGTTAAGGATTTAAAGGGGTCGATTAATT
195 TTAATTTTTTTTTGGAAAATTTTTGATTCAGTTAATGGTTAAGGATTTAAAGGGGTCGATTAATT
68107 CAATTAATGATGGTTTGGGTCAGAATCGATTAAACACCCTTATGCGGAGAATCTCAGCTTCTTCT
260 CAATTAATGATGGTTTGGGTCAGAATCGATTAAACACCCTTATGCGGAGAATCTCAGCTTCTTCT
68172 C-CCAACAATTTCTTATTATTATCGTTTTATTTTATTAAGAATCGTGGTATGAGACAATTATTTT
325 CGCCAACAATTTCTTATTATTATCGTTTTATTTTATTAAGAATCGTGGTATGAGACAATTATTTT
68236 TAATTACGTCACTTAGATGCATGTTATT
390 TAATTACGTCACTTAGATGCATGTTATT
68264 TA
1 TA
68266 TTAATGTTAT
Statistics
Matches: 410, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
417 226 0.55
418 184 0.45
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (417 bp):
TACAAATGGAAAATACTAAAAAATGACATTTTAATTATGTGTTAATTTCAAGACTTATGTAGTGT
TTTTCATTATGTAGTGATATAATACTTTAATTCGGTTAATTCAGGTAATTTTTATACCAAAAATA
AAAAAAACATAATTTTCGGTTAATTCAGTTAACCAGTCGAATTAACCAAAAAATTTCGGCTCGTT
TAATTTTTTTTTGGAAAATTTTTGATTCAGTTAATGGTTAAGGATTTAAAGGGGTCGATTAATTC
AATTAATGATGGTTTGGGTCAGAATCGATTAAACACCCTTATGCGGAGAATCTCAGCTTCTTCTC
GCCAACAATTTCTTATTATTATCGTTTTATTTTATTAAGAATCGTGGTATGAGACAATTATTTTT
AATTACGTCACTTAGATGCATGTTATT
Found at i:72064 original size:50 final size:50
Alignment explanation
Indices: 71989--72092 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
71979 TTTCTGTAAT
71989 TTCTTGTAATATATCATCGTCTTGATCAGCATTCAAGAGAATGTTTAGTC
1 TTCTTGTAATATATCATCGTCTTGATCAGCATTCAAGAGAATGTTTAGTC
72039 TTCTTGTAATATATCATCGTCTTGATCAGCATTCAAGAGAATGTTTAGTC
1 TTCTTGTAATATATCATCGTCTTGATCAGCATTCAAGAGAATGTTTAGTC
72089 TTCT
1 TTCT
72093 AGTTAAACTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (50 bp):
TTCTTGTAATATATCATCGTCTTGATCAGCATTCAAGAGAATGTTTAGTC
Found at i:74957 original size:58 final size:58
Alignment explanation
Indices: 74862--74975 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
74852 TCATCTTGGA
*
74862 GATGAATATAATCTTTCTAAATCGAGTTTACCATCTAGATCGAGTTGAAGAGATTACT
1 GATGAATATAATCTTTCCAAATCGAGTTTACCATCTAGATCGAGTTGAAGAGATTACT
* * * *
74920 GATGAATATAGTCTTTCCGAATCG-GATTTACCGTCTAGATCGAGTTGAGGAGATTA
1 GATGAATATAATCTTTCCAAATCGAG-TTTACCATCTAGATCGAGTTGAAGAGATTA
74976 TAGTCTTGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 1 0.02
58 49 0.98
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (58 bp):
GATGAATATAATCTTTCCAAATCGAGTTTACCATCTAGATCGAGTTGAAGAGATTACT
Found at i:76917 original size:9 final size:9
Alignment explanation
Indices: 76799--76947 Score: 63
Period size: 9 Copynumber: 15.7 Consensus size: 9
76789 AAAAAGGTTT
76799 TTTTTTATA
1 TTTTTTATA
*
76808 GTTTTTATA
1 TTTTTTATA
76817 TATTTTTA-A
1 T-TTTTTATA
76826 TTTGTTTTATAA
1 -TT-TTTTAT-A
*
76838 TTGTTATATA
1 TT-TTTTATA
**
76848 TTTTAAATA
1 TTTTTTATA
* *
76857 TTTTGTAAA
1 TTTTTTATA
76866 TTTTGTTA-A
1 TTTT-TTATA
*
76875 ATTTTTATA
1 TTTTTTATA
76884 GTTTTTT-TCA
1 -TTTTTTAT-A
*
76894 TTTTTCTAAA
1 TTTTT-TATA
*
76904 ATTTTTATA
1 TTTTTTATA
76913 TTTTTCTA-A
1 TTTTT-TATA
*
76922 TTTTTAATGA
1 TTTTTTAT-A
*
76932 TTTTCTTAAA
1 TTTT-TTATA
76942 TTTTTT
1 TTTTTT
76948 TTTTAATGAA
Statistics
Matches: 108, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
8 4 0.04
9 52 0.48
10 41 0.38
11 10 0.09
12 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (9 bp):
TTTTTTATA
Found at i:76934 original size:19 final size:18
Alignment explanation
Indices: 76893--76946 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
76883 AGTTTTTTTC
76893 ATTTTTCTAAAATTTTTAT
1 ATTTTTCT-AAATTTTTAT
76912 ATTTTTCT-AATTTTTA-
1 ATTTTTCTAAATTTTTAT
76928 ATGATTTTCTTAAATTTTT
1 AT--TTTTC-TAAATTTTT
76947 TTTTTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.06
17 8 0.26
18 5 0.16
19 9 0.29
20 7 0.23
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTCTAAATTTTTAT
Found at i:77477 original size:17 final size:18
Alignment explanation
Indices: 77455--77488 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
77445 TAATAATTTC
77455 AAAAAAAATAAA-AAATT
1 AAAAAAAATAAACAAATT
*
77472 AAAAAATATAAACAAAT
1 AAAAAAAATAAACAAAT
77489 CTTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAAAATAAACAAATT
Found at i:88647 original size:21 final size:22
Alignment explanation
Indices: 88608--88650 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
88598 GTTCAAAAAT
*
88608 TGTGCAGATTTCTACCGATACA
1 TGTGCAGAGTTCTACCGATACA
*
88630 TGTGCA-AGTTCTATCGATACA
1 TGTGCAGAGTTCTACCGATACA
88651 AGTATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTGCAGAGTTCTACCGATACA
Found at i:96326 original size:744 final size:750
Alignment explanation
Indices: 93874--98416 Score: 5046
Period size: 744 Copynumber: 6.0 Consensus size: 750
93864 ACAAAACCCA
* * * *
93874 ACTCAAAGGTAAAGGATTGTTCCTTTCCCCTAGAATATACAAAAAGCTTAAAATATAAAACAACA
1 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
* * * * **
93939 CAAAATCAGAATTTGTATAACAGTAAGAAGAAAAAAACAAAAACAAATGGCTATTTACCGTACTA
66 CAAAATCAGAATCTGTATAACATTAGGAAGAAAAGAACAAAAACAAATGGCTATTTGTCGTACTA
* * *
94004 TTCTTTCATTTACAAGAAATAAAACCCACATTACAAGATTTGCTTGAGTTGAACCAGATTAAAAT
131 TTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAAAAC
* * * * * * *
94069 CAAACAAATAACATATAGTTCCCCAAAAACACTAAACGTTTAAAGTAAAAACACACCCCAAAATC
196 CAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAAACACAACCCAAAATC
* * * *
94134 CATTACATCTTTATTTTTTGATTCTTTTTTTTATCTTGTTTCTAATGTAAAAAGAGAACCATTGA
261 CATTACCTCTTTATTTTTCGATTC--TTTTTTATCTTGTTTCTAATGCAAAAATAGAACCATTGA
* * * *
94199 TTTTTTTTCTTTAATAGTAAGGGTTGAAATTTGGGAATAGGATGTAGAGGAGGGTTGGAGAAGTA
324 TTTTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTAGA-GA--G--GGAGAAG--
* *
94264 AAAAAGTTAGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGTTTTTCTTTTTCTTTC
382 ---AAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTG-CTTT-TTTTTCTTTC
* * * * * *
94329 CTATTAAGAAACTTCAGTCGAAAACATAAGTAAATGTATTCGTATTGATATTCCTATTTTCAAAA
442 TTATTATGAAACTTCAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAAAG
* * * *
94394 AAAGCATAATTGTACT-AATTCCAAAAAATTTCAAAATTGTTCAGCCTAAATGCTCATATGGACA
507 AATGCATAATTGTACTGAA-TCCCAAAATTTTCAAAATTGTTCAGCCCAAATGCTCATATGGACA
* *
94458 TGGTTCATCTAAGTTAAACAGTTAGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAATCAT
571 TGGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAATCAT
* * * * *
94523 TCATTGGTTATTTTATTATTAATGAGAACAGTTGAAATTTTTTTCAGAAATAATGGCCTCCTTCC
636 TCATTGGTTATTTTATTGTTAATGAGAAAAGCT-AAAATTTTTTCAGAAATAATGGGC-CCTTCC
* * * * * * * *
94588 AGTTTTGGGCCATGGACGATTGCACTACTAGACTACCCTTAGGGCCGAGCCTG
699 AGTTTTGGGCCTTGGGCGGTTGCACTCCTAGACTACCC-CAAGGTCGAGCCCG
* * *
94641 ACTCGAAGGTAAAAGATTGCTCCCTTTCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
1 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
* *
94706 CAAAATCAAAATCTGTATAACATTAGGAAGAAAA-AGACAAAAACAAATGGCTATTTGTCATACT
66 CAAAATCAGAATCTGTATAACATTAGGAAGAAAAGA-ACAAAAACAAATGGCTATTTGTCGTACT
* * *
94770 ATTCTTTCATTTACAAGAAACAAAATCCACATTACAAAATTTGCTCGAGTTGAGCCAGATTAAAA
130 ATTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAAAA
*
94835 CCAACCAAACAACATATAGTTCCACAAGAATAC-ACAAAGCTTAAAGTAAAAACACAACCCAAAA
195 CCAACCAAACAACATATAGTTCCCCAAGAATACTA-AAAGCTTAAAGTAAAAACACAACCCAAAA
* * *
94899 TTCATTACCTCTTTATTTTTCGATTATTTTTTTTATCTTGTTCCTAATGCAAAAATAGAACCATT
259 TCCATTACCTCTTTATTTTTCGA-T-TCTTTTTTATCTTGTTTCTAATGCAAAAATAGAACCATT
* * *
94964 GA-TTTCTTGCTTTAATAGT-CGAGGTTGGAATTTGGGAATGGGATGTAGGGGAGAGTTGGAGAA
322 GATTTTTTTGCTTTAACAGTAAG-GGTTGGAATTTGGGAATGGGATGTA---GAGAG--GGAGAA
* *
95027 GTCAAAAAGTTGGAGACGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGTTTTTTTTTCTTT
381 G-----AAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGCTTTTTTTTCTTT
* *
95092 -TCTATTATGAAACTTCAGTCGAAAACATAAGCACACATATTCGTATTGGTATTCCTATTTTCAA
441 CT-TATTATGAAACTTCAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAA
95156 AGAATGCATAATTGTACT-AATTCCCAAAATTTTCAAAATT-TTCAGCCCAAATGC-CTATAT-G
505 AGAATGCATAATTGTACTGAA-TCCCAAAATTTTCAAAATTGTTCAGCCCAAATGCTC-ATATGG
* *
95217 AGCATGGTT-ATCTAAGTTGAACAGTTGGGCCCAATAATAAGTTATGTTGGATTGTTGCCCTTAA
568 A-CATGGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAA
* ** * * *
95281 TCATTCATT-GTTATTTTATTGTTAATGAAAAAAG-TTGATTTCTTTTCAAAAATATTGGGCGCC
632 TCATTCATTGGTTATTTTATTGTTAATGAGAAAAGCTAAAATT-TTTTCAGAAATAATGGGC-CC
* * * * * * *
95344 TTCCAATTTTGGGCCCTAGGCGGTTGCACTCTTAGACTACCTCATGGTCGAGTCTC-
695 TTCCAGTTTTGGGCCTTGGGCGGTTGCACTCCTAGACTACCCCAAGGTCGAG-CCCG
* * * * * * **
95400 ACTCAAAGATAAAAGGTTATTCTCTTCCCTAAGAATATACTAAAAACTTAAAATATAAGGCAACA
1 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
* *
95465 CAAAATCAAAATCTGTATAACATTAGGAAGAAAAGAACAAAATCAAATGGCTATTTGTCGTACTA
66 CAAAATCAGAATCTGTATAACATTAGGAAGAAAAGAACAAAAACAAATGGCTATTTGTCGTACTA
* * ** * *
95530 TTTTTTCATTTACAGGAAACAAAATTCACATTACAAGATTTGCTCGAGTTGAACTAGAATAAAAC
131 TTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAAAAC
** *
95595 CAACCAAACAGTATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTACAAACACAACCCAAAATC
196 CAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAAACACAACCCAAAATC
* ** *
95660 TATTACCTCTTTATTTACCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAAACATTGA-T
261 CATTACCTCTTTATTTTTCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAACCATTGATT
* *
95724 TTTTTGCTTTAACGGTAAGGGTTGAAATTTGGGAATGGGATG-A-A-A-GG-G-AG-AGTTGGAG
326 TTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTAGAGAGGGAGAAGAAGTTGGAG
** * *
95782 ACAAAAAGGGAAGAAATGAAAGCATTTTTTATTTTCTGCCTTTTGTTCTTTCTTA-TATGAAACT
391 ATGAAAAGGGAAGAAATGAAAGCA-TTTTTATTTTCTGCTTTTTTTTCTTTCTTATTATGAAACT
* * * *
95846 TCAGTTGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAACGAATGCATATTTGC
455 TCAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAAAGAATGCATAATTGT
** * * * * *
95911 ACTGAATCCCAAAATTTTCAATGTTATTCAGCCTAAATACTCGTATTGACATGGTTCATCTAAGT
520 ACTGAATCCCAAAATTTTCAAAATTGTTCAGCCCAAATGCTCATATGGACATGGTTCATCTAAGT
* * * * *
95976 TGAATAGTTGAGTCCAATAATGAGTTATGTTGGATGGTTACCCTTAATCATTCATTGGTTATATT
585 TGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAATCATTCATTGGTTATTTT
* * * * *
96041 CTTGTTAATGAGAAAAGCTAAATATTTTTTAAAAAAATAATGGG-CCTTCTAGTTTGGGGCCTTG
650 ATTGTTAATGAGAAAAGCTAAA-ATTTTTT-CAGAAATAATGGGCCCTTCCAGTTTTGGGCCTTG
* * * *
96105 GGCGGTTGCACTCCAAGACAACCCCTAAGTTCAAGCCCG
713 GGCGGTTGCACTCCTAGACTACCCC-AAGGTCGAGCCCG
* *
96144 ACTCAAAGGTAAAAGATTATTCCCTTCCCCCCAA-AA-ATACTAAAAGCTTATAATATAAAACAA
1 ACTCAAAGGTAAAAGATTGTTCCCTT--CCCCAAGAATATACTAAAAGCTTAAAATATAAAACAA
* * *
96207 TACGAAATCAGAATATGTATAACATTAGGAAGAAAAGAACAAAAACAAATGG-TCATTTGTCGTA
64 CACAAAATCAGAATCTGTATAACATTAGGAAGAAAAGAACAAAAACAAATGGCT-ATTTGTCGTA
* * * * **
96271 CCATTCTTTCATTTATAGGAAACAAAACTCATGTTACAAGATTTGCTCGAGTTGAACCAGATTAA
128 CTATTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAA
* * * *
96336 AACCAACCAAACAGCATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAGACGCAACCCCAA
193 AACCAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAAACACAACCCAAA
* * * *
96401 ATCCATTACCTCTTTATTTGTCGATTCTTTTTTATCATGTTTCTAATGCAAAAATAGAACCGTTA
258 ATCCATTACCTCTTTATTTTTCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAACCATTG
* * *
96466 ATTTTTTTTTACTTTAACAGTAAGGGTTGGAATTTAGGAATAGGATGTA-ATGAAGGGTTAGAGA
323 A--TTTTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTAGA-G-A-GG---GAGA
*
96530 AGTAAAAAAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTACTTTTTTTTTCT
380 AG-----AAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGC-TTTTTTTTCT
* * * * *
96595 TTCCTATTATGAAACTTCAGTCGAAAACGTAAGCAAATGTATTCGTATTGGTATTCTTATTTTTA
439 TTCTTATTATGAAACTTCAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCA
* * * * * *
96660 ATGAATGCTTAATTTTACTGATTCCCAAAATTTTAAAAATTGTTTAGCCCAAATGAC-CATATGG
504 AAGAATGCATAATTGTACTGAATCCCAAAATTTTCAAAATTGTTCAGCCCAAATG-CTCATATGG
* *
96724 ACATGGTTCATCTAAGTTGAACAATTGGGCCCAATAATGAGTTATGTTGGATAGTTGCCCTTAAT
568 ACATGGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAAT
* * ****
96789 CATTCATTAGTTATTTTATTGTTACTGAGAAAAGCTAAAAAAAATTCAGAAATAATGGGCCCCCT
633 CATTCATTGGTTATTTTATTGTTAATGAGAAAAGCTAAAATTTTTTCAGAAATAATGGG--CCCT
* * * * ** * * * * *
96854 TCTAATTTTTGGCCCTCAGTGGTTGCACTCCTTGACTACCTTCAAAG-CTGGGCCCG
696 TCCAGTTTTGGGCCTTGGGCGGTTGCACTCCTAGACTACC-CCAAGGTC-GAGCCCG
* * *
96910 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTACATTATTAAACAACA
1 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAAC-
* * * * *
96975 AAAAAATCAGAATCTATATAACATTAGGAAGAACAAG-ATAAAAACAACTAGCTATTTG-CTGTA
65 ACAAAATCAGAATCTGTATAACATTAGGAAGAA-AAGAACAAAAACAAATGGCTATTTGTC-GTA
* * *
97038 CTATTCTTTCATTTACAGGAAACAAAACCCACAGTACAAGATTTGCTCGAGTTGAACCATATTAA
128 CTATTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAA
* ** * * * * ** *
97103 AACAAAAAAAATAGCATATAGTTTCCCAAGAATATTGGAAGCTTAAAGTAAAAAACGCAACCCAA
193 AACCAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGT-AAAAACACAACCCAA
* *
97168 AATCCATTACCTCTTTATTTTTTGATTCTTTTTTATCTTGTTTCTAATACAAAAATAGAACCGTT
257 AATCCATTACCTCTTTATTTTTCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAACC---
* * * * * *
97233 GATTTTTTTATTTTTTTTTGCTTTAGCAGTAGGGGTTGGGATTTGGGAATGGAATGTAGGGGAAG
319 -A----TTGA--TTTTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTA-GAG-A-
* *
97298 GTTGGAGAAGTAAAAAATTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTTCTTT
374 G--GGAGAAG-----AAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGCTTT
* * * *
97363 TGTTTCTTTCTTATTATGAAA-TTCAGTCGAAAACGTAAGCAAACGTATTTGTATTGGTATTCTT
432 TTTTTCTTTCTTATTATGAAACTTCAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCT
* * *
97427 ATTTTCAAAGAATGCATTATTGTATTGATTCCCAAAATTTTCAAAATTGTTCAGCCCAAATG-TC
497 ATTTTCAAAGAATGCATAATTGTACTGAATCCCAAAATTTTCAAAATTGTTCAGCCCAAATGCT-
* * * *
97491 CGTATGGACATAGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTCGT
561 CATATGGACATGGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGC
* * *
97556 CGTTAATCATTCATTGATTATTTTATTGTTAATGAGAAAAGCTGAAAATGTTTTCTAGAAATAAT
626 CCTTAATCATTCATTGGTTATTTTATTGTTAATGAGAAAAGCT-AAAATTTTTTC-AGAAATAAT
* * * **
97621 GGGCCCCTTCTAGTTTTGGG-CTT-----G--G-A---CT--AC--CCCCAAGATCG-GATCTA
689 GGG-CCCTTCCAGTTTTGGGCCTTGGGCGGTTGCACTCCTAGACTACCCCAAGGTCGAG-CCCG
* * *
97668 ACTCAAAGGTAAAAGATTGTCCCCTTCTCTAAGAATATACTAAAAGCTTAAAATATAAAACAACA
1 ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
* *
97733 CAAAATTAGAATCTGTATAACTTTAGGAAGAAAA-AGACAAAAACAAATGGCTATTTGTCGTACT
66 CAAAATCAGAATCTGTATAACATTAGGAAGAAAAGA-ACAAAAACAAATGGCTATTTGTCGTACT
* * *
97797 ATACTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTAG-TCGAGTTAAATCAGATTAAA
130 ATTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTT-GCTCGAGTTGAACCAGATTAAA
* * * *
97861 ACCAACCAAACAACATATAATTCCCTAATAATACTAAAAGCTTAAAGTAAAAACACAATCCAAAA
194 ACCAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAAACACAACCCAAAA
* ** * **
97926 TTCATTACCTCTTTATTAGTCGATTCTTTTTTATCTTGTTTCTAATGTAAAAATA-AATCTGTTG
259 TCCATTACCTCTTTATTTTTCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAA-CCATTG
* * * * * *
97990 TTTTTTTTGCTTTAGCAATAGGGGTTGGAATTTGGGAATGGGATGTAGGGGGTTGGAGAAGTCAA
323 ATTTTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTAGAGAG--GGAGAAG----
* * *
98055 AAAGTTGGAGATGAAAAGGGAATAAATGAAAGCATTTTTA-TTTCTGCTTTTTTTTTCTTTCCTG
382 -AAGTTGGAGATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGC-TTTTTTTTCTTTCTTA
* * *
98119 TTATGAAACTTTAG-CTGAAAACGTAATCAAACGTATTCGTATTGGTATTCCTATTTTCAACA-A
445 TTATGAAACTTCAGTC-GAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAA-AGA
* * *
98182 ATGCATAATTGTACTGATTCTCAAAAATTTT-AGAAA-TGTTCAGCCCAAATGCCCATATGGACA
508 ATGCATAATTGTACTGAATC-CCAAAATTTTCA-AAATTGTTCAGCCCAAATGCTCATATGGACA
* * * * * *
98245 TGGTTCAACTAAGTTGAATAGTTGGACCCAATAATGAGTTATGTTGGATTGTTGACCTAAATCAT
571 TGGTTCATCTAAGTTGAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAATCAT
* * * *
98310 TCATTGATTATTTTATTTTTAATGTGAAAAGCTGAAATTTTTTCAGAAATAATGGGTCCCTTCCA
636 TCATTGGTTATTTTATTGTTAATGAGAAAAGCTAAAATTTTTTCAGAAATAATGGG-CCCTTCCA
* *
98375 GTTTTGGGCCTTGGGCAGTTGCACTCCTAGATTACCTCCAAG
700 GTTTTGGGCCTTGGGCGGTTGCACTCCTAGACTACC-CCAAG
98417 ATTGGGCCTG
Statistics
Matches: 3249, Mismatches: 413, Indels: 236
0.83 0.11 0.06
Matches are distributed among these distances:
740 119 0.04
741 49 0.02
742 95 0.03
743 146 0.04
744 467 0.14
745 31 0.01
746 50 0.02
747 39 0.01
748 7 0.00
750 1 0.00
751 3 0.00
752 1 0.00
753 1 0.00
754 2 0.00
755 2 0.00
756 70 0.02
757 220 0.07
758 71 0.02
759 268 0.08
760 55 0.02
761 24 0.01
762 63 0.02
763 50 0.02
764 153 0.05
765 202 0.06
766 190 0.06
767 431 0.13
768 78 0.02
769 4 0.00
774 195 0.06
775 44 0.01
776 112 0.03
777 5 0.00
779 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (750 bp):
ACTCAAAGGTAAAAGATTGTTCCCTTCCCCAAGAATATACTAAAAGCTTAAAATATAAAACAACA
CAAAATCAGAATCTGTATAACATTAGGAAGAAAAGAACAAAAACAAATGGCTATTTGTCGTACTA
TTCTTTCATTTACAAGAAACAAAACCCACATTACAAGATTTGCTCGAGTTGAACCAGATTAAAAC
CAACCAAACAACATATAGTTCCCCAAGAATACTAAAAGCTTAAAGTAAAAACACAACCCAAAATC
CATTACCTCTTTATTTTTCGATTCTTTTTTATCTTGTTTCTAATGCAAAAATAGAACCATTGATT
TTTTTGCTTTAACAGTAAGGGTTGGAATTTGGGAATGGGATGTAGAGAGGGAGAAGAAGTTGGAG
ATGAAAAGGGAAGAAATGAAAGCATTTTTATTTTCTGCTTTTTTTTCTTTCTTATTATGAAACTT
CAGTCGAAAACATAAGCAAACGTATTCGTATTGGTATTCCTATTTTCAAAGAATGCATAATTGTA
CTGAATCCCAAAATTTTCAAAATTGTTCAGCCCAAATGCTCATATGGACATGGTTCATCTAAGTT
GAACAGTTGGGCCCAATAATGAGTTATGTTGGATGGTTGCCCTTAATCATTCATTGGTTATTTTA
TTGTTAATGAGAAAAGCTAAAATTTTTTCAGAAATAATGGGCCCTTCCAGTTTTGGGCCTTGGGC
GGTTGCACTCCTAGACTACCCCAAGGTCGAGCCCG
Found at i:100034 original size:24 final size:24
Alignment explanation
Indices: 100006--100064 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
99996 TAGACTAATA
100006 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
100030 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
100054 AGAGTTTAACT
1 AGAGTTTAACT
100065 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:103172 original size:17 final size:16
Alignment explanation
Indices: 103146--103180 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
103136 ATATCATGGG
103146 AATATCATTAAATTGTT
1 AATATCATTAAATT-TT
*
103163 AATATGATTAAATTTT
1 AATATCATTAAATTTT
103179 AA
1 AA
103181 ATTTTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (16 bp):
AATATCATTAAATTTT
Found at i:103613 original size:54 final size:52
Alignment explanation
Indices: 103530--103663 Score: 216
Period size: 53 Copynumber: 2.6 Consensus size: 52
103520 AAAATTATTA
*
103530 AAAGTTAATTAGTTTTTTATGATTCTAAAATTAAAATATTTTTGAAAAAAATT
1 AAAGTTAATTAGTTTTTTATGATTTTAAAATTAAAATA-TTTTGAAAAAAATT
* *
103583 AAAGTTAATTAGTTTATATATGATTTTAAAATTTAAATATTTTGAAAAAAATT
1 AAAGTTAATTAGTTT-TTTATGATTTTAAAATTAAAATATTTTGAAAAAAATT
103636 -AAGTTAATTAGTTTTTTATGATTTTAAA
1 AAAGTTAATTAGTTTTTTATGATTTTAAA
103664 TTTTATTATT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
51 13 0.17
52 14 0.18
53 29 0.38
54 20 0.26
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (52 bp):
AAAGTTAATTAGTTTTTTATGATTTTAAAATTAAAATATTTTGAAAAAAATT
Found at i:103687 original size:14 final size:13
Alignment explanation
Indices: 103649--103691 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
103639 TTAATTAGTT
*
103649 TTTTATGATTTTAAA
1 TTTTATTATTTT--A
103664 TTTTATTATTTTA
1 TTTTATTATTTTA
103677 TTTTAATTATTTTA
1 TTTT-ATTATTTTA
103691 T
1 T
103692 GATTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 11 0.42
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:122945 original size:56 final size:56
Alignment explanation
Indices: 122859--122970 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
122849 GAAAGAGTCG
122859 AAGATAATCCATCCAGAGCTGACTACTGGTTGAAAAAATACTTTACGGGTCTTGAA
1 AAGATAATCCATCCAGAGCTGACTACTGGTTGAAAAAATACTTTACGGGTCTTGAA
* *
122915 AAGATAATCCATCCAGAGCTGAGTACTGGTTGGAAAAATACTTTACGGGTCTTGAA
1 AAGATAATCCATCCAGAGCTGACTACTGGTTGAAAAAATACTTTACGGGTCTTGAA
122971 TGAGATGGCC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (56 bp):
AAGATAATCCATCCAGAGCTGACTACTGGTTGAAAAAATACTTTACGGGTCTTGAA
Found at i:132457 original size:30 final size:30
Alignment explanation
Indices: 132404--132462 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
132394 ATGAGGCAGT
* * *
132404 AGAAGAAGATGACCAAGAGAAAGAGAATGA
1 AGAAGAAGAAGAACAAGAAAAAGAGAATGA
* *
132434 AGAAGAAGAAGAAGAAGAAAAAGATAATG
1 AGAAGAAGAAGAACAAGAAAAAGAGAATG
132463 CACTGAAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.61, C:0.03, G:0.29, T:0.07
Consensus pattern (30 bp):
AGAAGAAGAAGAACAAGAAAAAGAGAATGA
Found at i:133558 original size:11 final size:11
Alignment explanation
Indices: 133509--133564 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
133499 TAGTCACTTA
*
133509 AAAAGAAAAAA
1 AAAAGAAAAAG
133520 AAATGAGAAAAAG
1 AAA--AGAAAAAG
* *
133533 -AGAGAAATGAG
1 AAAAGAAA-AAG
133544 AAAAGAAAAAG
1 AAAAGAAAAAG
133555 AAAAGAAAAA
1 AAAAGAAAAA
133565 AAATTATGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 5 0.14
11 17 0.47
12 7 0.19
13 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:137673 original size:52 final size:52
Alignment explanation
Indices: 137593--137830 Score: 165
Period size: 52 Copynumber: 4.6 Consensus size: 52
137583 CTTCATTCAT
* * * ** * *
137593 ATACTCACAATGACACATAGCCACCGGACCT-TATAATCCGCAAGGGATTCGC
1 ATACTCACGATGACACATAGTCATCGGACCTCT-TAATCCGCAAAAGATCCAC
* * * *
137645 ATACTCACGATGACACAGATTCATCGGACCTCTTAATCCGTAAAAGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGCAAAAGATCCAC
* ** * * ** *
137697 ATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGGTTAAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGCAAAAGATCCAC
* * ** *** * * *
137749 ATACTCACGAGGACACTTAGTCATCAAACCT-TATAATCCATGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCT-TAATCCGCAAAAGATCCAC
* *
137801 ATACTCACGATGACACTTAGTCATCAGACC
1 ATACTCACGATGACACATAGTCATCGGACC
137831 CTTTTTCATT
Statistics
Matches: 157, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
51 1 0.01
52 155 0.99
53 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGCAAAAGATCCAC
Found at i:144263 original size:18 final size:18
Alignment explanation
Indices: 144240--144309 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
144230 GACGCGAAAG
*
144240 TTTGAGCATATTGGCTCA
1 TTTGAGCATACTGGCTCA
144258 TTTGAGCATACTGGCTC-
1 TTTGAGCATACTGGCTCA
* *
144275 TTTGACCATACTAGCTCA
1 TTTGAGCATACTGGCTCA
*
144293 TTAGAGCATACTGGCTC
1 TTTGAGCATACTGGCTC
144310 GTAAGAGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.33
18 30 0.67
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (18 bp):
TTTGAGCATACTGGCTCA
Done.