Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002950.1 Hibiscus syriacus cultivar Beakdansim tig00006089_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: 129564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2158 original size:101 final size:100
Alignment explanation
Indices: 2035--2232 Score: 387
Period size: 101 Copynumber: 2.0 Consensus size: 100
2025 TTCATGGAAT
2035 TTGAGTGTGAATCCAGTCCACTGAGATATAGAAGTCTGTAGTTGAATGACGCTGTGTTATGATAC
1 TTGAGTGTGAATCCAGTCCACTGAGATATAGAAGTCTGTAGTTGAATGACGCTGTGTTATGATAC
2100 AGCAAGAGACGTTTGCAAACAGCCATTGCCATTGAA
66 AGCAAGAGACGTTTGCAAACAGCCA-TGCCATTGAA
2136 TTGAGTGTGAATCCAGTCCACTGAGATATAGAAGTCTGTAGTTGAATGACGCTGTGTTATGATAC
1 TTGAGTGTGAATCCAGTCCACTGAGATATAGAAGTCTGTAGTTGAATGACGCTGTGTTATGATAC
2201 AGCAAGAGACGTTTGCAAACAGCCATGCCATT
66 AGCAAGAGACGTTTGCAAACAGCCATGCCATT
2233 TGCAGAATGT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 7 0.07
101 90 0.93
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (100 bp):
TTGAGTGTGAATCCAGTCCACTGAGATATAGAAGTCTGTAGTTGAATGACGCTGTGTTATGATAC
AGCAAGAGACGTTTGCAAACAGCCATGCCATTGAA
Found at i:4149 original size:24 final size:26
Alignment explanation
Indices: 4101--4152 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 26
4091 TGATTCTCGC
4101 GCTTGATTCAAACACTCGATTATCCAT
1 GCTTGATTCAAACAC-CGATTATCCAT
4128 GCTTGATTC-AACA-CGATTATCCAT
1 GCTTGATTCAAACACCGATTATCCAT
4152 G
1 G
4153 TTTGTGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.48
26 4 0.16
27 9 0.36
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (26 bp):
GCTTGATTCAAACACCGATTATCCAT
Found at i:6126 original size:39 final size:38
Alignment explanation
Indices: 5986--6126 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 38
5976 GGTCTACCCT
* * * *
5986 GCACAAAGCAGAGGAGCCT-ACGGTAAGGTCTTATCATGT
1 GCACAAAGCAGAGGAGCCTGA--GTAAGGACTTACCCTGA
* *
6025 GCACAAAGCAGAGGAGCAT--GTAAGGACTTACTCTGA
1 GCACAAAGCAGAGGAGCCTGAGTAAGGACTTACCCTGA
* *
6061 GCACAAAATC-GAGGAGCCTGAGGTAAGGACTTACCCTAA
1 GCAC-AAAGCAGAGGAGCCTGA-GTAAGGACTTACCCTGA
*
6100 GCACAAAGCCGAGGAGCCTGCAGTAAG
1 GCACAAAGCAGAGGAGCCTG-AGTAAG
6127 CATTAAGGTC
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
36 24 0.28
37 4 0.05
38 4 0.05
39 52 0.61
40 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16
Consensus pattern (38 bp):
GCACAAAGCAGAGGAGCCTGAGTAAGGACTTACCCTGA
Found at i:7266 original size:18 final size:18
Alignment explanation
Indices: 7243--7290 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
7233 TTTGTTTCTA
7243 AAAGAGGAAATATTAAGG
1 AAAGAGGAAATATTAAGG
7261 AAAGAGGAAATATTAAGG
1 AAAGAGGAAATATTAAGG
* *
7279 AGAGAGAAAATA
1 AAAGAGGAAATA
7291 AATAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (18 bp):
AAAGAGGAAATATTAAGG
Found at i:8016 original size:16 final size:16
Alignment explanation
Indices: 7991--8032 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
7981 CGGCGTTTCG
*
7991 ACCGAGGCTAAGGTTA
1 ACCGAAGCTAAGGTTA
8007 ACCGAAGCTAAGGTTA
1 ACCGAAGCTAAGGTTA
8023 ACCGAAGCTA
1 ACCGAAGCTA
8033 CTCAAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (16 bp):
ACCGAAGCTAAGGTTA
Found at i:8654 original size:41 final size:41
Alignment explanation
Indices: 8608--8826 Score: 146
Period size: 41 Copynumber: 5.3 Consensus size: 41
8598 AAAATGATAC
* *
8608 TTTAGCGGCGTTTTTTAAACAAACACTGTAATAGAG-GGTAA
1 TTTAGCGGCG-TTTTTAAACAAACGCCGTAATAGAGAGGTAA
* ** *
8649 TTTAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGATGT--
1 TTTAGCGGCGTTTTTA-AACAAACGCCGTAATAGAGAGGTAA
* * * *
8689 TTATAGTGGTGTTTTTTTAACAAACGCCGTAATAGAGTGGTAA
1 TT-TAGCGGCG-TTTTTAAACAAACGCCGTAATAGAGAGGTAA
* * **
8732 TTTAGTGGCGTTTTTAAACAAACGCCGCT-ATAGTGTTGT--
1 TTTAGCGGCGTTTTTAAACAAACGCCG-TAATAGAGAGGTAA
* * * *
8771 TTATAGTGGCGTTTTTTCAACAAACGACGCT-ATAGAGAAGTAA
1 TT-TAGCGGCG-TTTTTAAACAAACGCCG-TAATAGAGAGGTAA
*
8814 TTTCGCGGCGTTT
1 TTTAGCGGCGTTT
8827 AATAAAAAAT
Statistics
Matches: 142, Mismatches: 25, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
39 2 0.01
40 15 0.11
41 101 0.71
42 20 0.14
43 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAACAAACGCCGTAATAGAGAGGTAA
Found at i:8778 original size:40 final size:41
Alignment explanation
Indices: 8668--8796 Score: 156
Period size: 41 Copynumber: 3.1 Consensus size: 41
8658 GTTTATAGCT
* * *
8668 CAAACGCCGTAATAGAGATGTTTATAGTGGTGTTTTTTTAA
1 CAAACGCCGTAATAGAGTTGTTTATAGTGGCGTTTTTTAAA
*
8709 CAAACGCCGTAATAGAGTGGTAATT-TAGTGGCG-TTTTTAAA
1 CAAACGCCGTAATAGAGTTGT--TTATAGTGGCGTTTTTTAAA
* *
8750 CAAACGCCGCT-ATAGTGTTGTTTATAGTGGCGTTTTTTCAA
1 CAAACGCCG-TAATAGAGTTGTTTATAGTGGCGTTTTTTAAA
8791 CAAACG
1 CAAACG
8797 ACGCTATAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
39 2 0.03
40 8 0.11
41 56 0.74
42 8 0.11
43 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (41 bp):
CAAACGCCGTAATAGAGTTGTTTATAGTGGCGTTTTTTAAA
Found at i:8847 original size:82 final size:82
Alignment explanation
Indices: 8614--8864 Score: 246
Period size: 82 Copynumber: 3.1 Consensus size: 82
8604 ATACTTTAGC
* * **
8614 GGCGTTTTTTAAACAAAC-ACTGTAATAGAG-GGTAATTTAGCGGCGTTTATAGCTCAAACGCCG
1 GGCGTTTTTTCAACAAACGAC-GTAATAGAGAAGTAATTTAGCGGCGTTTATA-AACAAACGCCG
* *
8677 TAATAG-AGATGTTTATAGT
64 CAATAGTA-TTGTTTATAGT
* * * ** * * *
8696 GGTGTTTTTTTAACAAACGCCGTAATAGAGTGGTAATTTAGTGGCGTTTTTAAACAAACGCCGCT
1 GGCGTTTTTTCAACAAACGACGTAATAGAGAAGTAATTTAGCGGCGTTTATAAACAAACGCCGCA
*
8761 ATAGTGTTGTTTATAGT
66 ATAGTATTGTTTATAGT
* *
8778 GGCGTTTTTTCAACAAACGACGCT-ATAGAGAAGTAATTTCGCGGCGTTTAATAAA-AAATGCCG
1 GGCGTTTTTTCAACAAACGACG-TAATAGAGAAGTAATTTAGCGGCGTTT-ATAAACAAACGCCG
*
8841 CAATAGTATT-ATT-TAGT
64 CAATAGTATTGTTTATAGT
8858 GGCGTTT
1 GGCGTTT
8865 GTGCAAAAAA
Statistics
Matches: 141, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
80 11 0.08
81 2 0.01
82 103 0.73
83 25 0.18
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (82 bp):
GGCGTTTTTTCAACAAACGACGTAATAGAGAAGTAATTTAGCGGCGTTTATAAACAAACGCCGCA
ATAGTATTGTTTATAGT
Found at i:9326 original size:22 final size:22
Alignment explanation
Indices: 9278--9329 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
9268 GTTTTTTTTT
* *
9278 CTTTCGAATAGAAAAATAATTG
1 CTTTTGAATAGAAAAATAATAG
*
9300 CTTTTGAATAGGAAAATAATAG
1 CTTTTGAATAGAAAAATAATAG
9322 CTTTTGAA
1 CTTTTGAA
9330 AACGTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
CTTTTGAATAGAAAAATAATAG
Found at i:10529 original size:41 final size:42
Alignment explanation
Indices: 10461--10539 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 42
10451 TTTGGTTAAT
* ** *
10461 AAACGCCACAAAATATTTATATTTTAGCGACGTTTTTTCAAA
1 AAACGCCACAAAATATTTACACATTAGCGACATTTTTTCAAA
* *
10503 AAACGCTAC-AAATATTTACACATTAGCGGCATTTTTT
1 AAACGCCACAAAATATTTACACATTAGCGACATTTTTT
10540 GTACAAACGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 23 0.74
42 8 0.26
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (42 bp):
AAACGCCACAAAATATTTACACATTAGCGACATTTTTTCAAA
Found at i:10675 original size:42 final size:41
Alignment explanation
Indices: 10628--10709 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
10618 TTTTTTACCT
* * *
10628 AAACGCCGCGATATATATGCACTATAGAGGCATTTTGTTTAA
1 AAACGCCACAATATATAGGCACTATAGAGGCATTTT-TTTAA
* *
10670 AAACGCCACAATATATCGGCATTATAGAGGCATTTTTTTA
1 AAACGCCACAATATATAGGCACTATAGAGGCATTTTTTTA
10710 TAATGTCGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
AAACGCCACAATATATAGGCACTATAGAGGCATTTTTTTAA
Found at i:12441 original size:36 final size:36
Alignment explanation
Indices: 12394--12464 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
12384 CGATTATTAT
12394 ATATAGTTTACCTAGAATAATTAACTACACCAATGA
1 ATATAGTTTACCTAGAATAATTAACTACACCAATGA
* *
12430 ATATAGTTTACCTAGAATAATTAGCTACACTAATG
1 ATATAGTTTACCTAGAATAATTAACTACACCAATG
12465 TCGATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (36 bp):
ATATAGTTTACCTAGAATAATTAACTACACCAATGA
Found at i:15579 original size:21 final size:21
Alignment explanation
Indices: 15553--15638 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
15543 AGAGCAGCAA
* *
15553 CAGCGGAAGCAAAGAGAGTAG
1 CAGCGGAAGCACAGAGAGAAG
* *
15574 CAGCGGAAGCAGAGAAAGAAG
1 CAGCGGAAGCACAGAGAGAAG
15595 CAGCGGCAA-CACAGAGAGAAG
1 CAGCGG-AAGCACAGAGAGAAG
*
15616 CAGCGGCAGCACAGAGAGAAG
1 CAGCGGAAGCACAGAGAGAAG
15637 CA
1 CA
15639 ACATATAAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.95
22 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.36, T:0.01
Consensus pattern (21 bp):
CAGCGGAAGCACAGAGAGAAG
Found at i:15910 original size:43 final size:43
Alignment explanation
Indices: 15802--15954 Score: 146
Period size: 43 Copynumber: 3.6 Consensus size: 43
15792 CCCGCAAAAT
* * *
15802 ATCAACACCTACTGTGGCGTTTGTAAGTAAAACGTCGCTAAATC
1 ATCAACACCTACTGCGGCGTTTTTAAGAAAAACGTCGCTAAA-C
** *
15846 -TCAACACCTACTGCGATGTTTTTAGGAAAAACGTCGCTAAAC
1 ATCAACACCTACTGCGGCGTTTTTAAGAAAAACGTCGCTAAAC
* ** * * * *
15888 ATCAACACCTATTGCGGCGTTTTTCTGATAAACGCCTCTAAAT
1 ATCAACACCTACTGCGGCGTTTTTAAGAAAAACGTCGCTAAAC
* * *
15931 AACAACACCTATTACGGCGTTTTT
1 ATCAACACCTACTGCGGCGTTTTT
15955 TGTTCAAAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 90 0.99
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
ATCAACACCTACTGCGGCGTTTTTAAGAAAAACGTCGCTAAAC
Found at i:22216 original size:251 final size:252
Alignment explanation
Indices: 21765--22250 Score: 857
Period size: 251 Copynumber: 1.9 Consensus size: 252
21755 ATTAAAATCA
* *
21765 ATGCCACCGCAGATTAAACAAGGTTAAAGAAGAAAAAATTGATCAAATCTGTAGCGAGAATCTAC
1 ATGCCACCGCAGATTAAACAAAGTTAAAGAAGAAAAAATTGATCAAATCTGTAGCGAGAATATAC
* *
21830 TAGCCCATTTAGATGAGAGAAAGATTATTAGTATTTCTCTGGTAGTAGAATCTTAATAATTATTT
66 TAACCCATTTAGATGAGAGAAAGATTATCAGTATTTCTCTGGTAGTAGAATCTTAATAATTATTT
*
21895 GTCAATAAATTAAGAAAATTTTAAATAGTTATTATTTTATAACCACTCTAAATTATTAAAAAATA
131 GTCAATAAATTAAGAAAATTTTAAATAGTTATTATTTTATAACCACTCTAAATTATTAAAAAAAA
21960 TATAAATAATTTTTATATTGATAATTATATTTTATAAATTTGTATTGATAATTATCG
196 TATAAATAATTTTTATATTGATAATTATATTTTATAAATTTGTATTGATAATTATCG
*
22017 ATGCTACCGCAGATTAAACAAAGTTAAAGAAG-AAAAATTGATCAAATCTGTAGCGAGAATATAC
1 ATGCCACCGCAGATTAAACAAAGTTAAAGAAGAAAAAATTGATCAAATCTGTAGCGAGAATATAC
* * * *
22081 TAACCCATTTAGATGAGAGAAAGATTGTCAGTATTTCTCTTGTCGTAGAATCTTGATAATTATTT
66 TAACCCATTTAGATGAGAGAAAGATTATCAGTATTTCTCTGGTAGTAGAATCTTAATAATTATTT
* *
22146 GTCAATAAATTAAGAAAATTTTGAATAGTTATTATTTTATAATCACTCTAAATTATTAAAAAAAA
131 GTCAATAAATTAAGAAAATTTTAAATAGTTATTATTTTATAACCACTCTAAATTATTAAAAAAAA
22211 TATAAATAATTTTTATATTGATAATTATATTTTATAAATT
196 TATAAATAATTTTTATATTGATAATTATATTTTATAAATT
22251 AAAATTGAAT
Statistics
Matches: 222, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
251 192 0.86
252 30 0.14
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (252 bp):
ATGCCACCGCAGATTAAACAAAGTTAAAGAAGAAAAAATTGATCAAATCTGTAGCGAGAATATAC
TAACCCATTTAGATGAGAGAAAGATTATCAGTATTTCTCTGGTAGTAGAATCTTAATAATTATTT
GTCAATAAATTAAGAAAATTTTAAATAGTTATTATTTTATAACCACTCTAAATTATTAAAAAAAA
TATAAATAATTTTTATATTGATAATTATATTTTATAAATTTGTATTGATAATTATCG
Found at i:23380 original size:16 final size:17
Alignment explanation
Indices: 23361--23392 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23351 TAAATAATAA
23361 TTTT-AAAAAAAATTAC
1 TTTTCAAAAAAAATTAC
23377 TTTTCAAAAAAAATTA
1 TTTTCAAAAAAAATTA
23393 AAAATCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTCAAAAAAAATTAC
Found at i:25244 original size:21 final size:21
Alignment explanation
Indices: 25192--25238 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
25182 GTTTCCAGAT
*
25192 TCGCAACGTGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
25213 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
25234 TCGCA
1 TCGCA
25239 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:25284 original size:21 final size:21
Alignment explanation
Indices: 25257--25617 Score: 551
Period size: 21 Copynumber: 17.2 Consensus size: 21
25247 TATATATTCA
25257 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
* *
25278 TGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTT
*
25299 CGTTGCGATAGTCTCCAAGTA
1 CGTTGCGATAGTCTCCAAGTT
* *
25320 CGTTACGATAGTCTCCAAGTG
1 CGTTGCGATAGTCTCCAAGTT
* *
25341 CATTGCGATAGACTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
25362 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
25383 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
* *
25404 CGTTGCGATAATCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTT
25425 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
* *
25446 CATTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
*
25467 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
*
25488 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
*
25509 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
* *
25530 CGTTGTGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
*
25551 CGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTT
*
25572 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTT
*
25593 CGTTGTGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
25614 CGTT
1 CGTT
25618 ATTGCATTTG
Statistics
Matches: 314, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 314 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCTCCAAGTT
Found at i:26200 original size:6 final size:6
Alignment explanation
Indices: 26191--26221 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
26181 CGTCTCTCGC
*
26191 TCGTGC TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
26222 AATACGTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:26538 original size:21 final size:21
Alignment explanation
Indices: 26314--26523 Score: 327
Period size: 21 Copynumber: 10.0 Consensus size: 21
26304 TGCGATTTTG
*
26314 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
26335 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
26356 GACTATCGCAACGCACTTGGA
1 GACTATCGCAACGAACTTGGA
26377 GACTATCGCAAC-ACACTTGGA
1 GACTATCGCAACGA-ACTTGGA
26398 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
26419 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
26440 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
26461 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
26482 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
26503 -A-AATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
26524 CTATCACAAT
Statistics
Matches: 179, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
19 7 0.04
20 1 0.01
21 170 0.95
22 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:29835 original size:20 final size:20
Alignment explanation
Indices: 29791--30068 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 20
29781 AATGACCAAT
** *
29791 AAAATCGCAACGCGAAAT-C
1 AAAATCGCAACGCGATTTAG
29810 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
29830 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
29850 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
29870 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
29891 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
29914 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
29934 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
29954 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
29974 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
29994 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
30017 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
30037 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
30057 AAAATCGCAACG
1 AAAATCGCAACG
30069 GTCAAAAGAA
Statistics
Matches: 205, Mismatches: 42, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
19 16 0.08
20 145 0.71
21 15 0.07
22 1 0.00
23 28 0.14
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:30001 original size:63 final size:63
Alignment explanation
Indices: 29934--30058 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 63
29924 TGCGATTGAT
* * * * *
29934 AGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAG
1 AGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAG
29997 AGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAA
1 AGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAA
30059 AATCGCAACG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (63 bp):
AGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAG
Found at i:30006 original size:83 final size:83
Alignment explanation
Indices: 29895--30068 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
29885 GCTTCCAAGT
* * * * *
29895 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * *
29960 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
*
29978 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
30043 GCAACGCGATTTAGAAAA
66 GCAACGCGATTGAGAAAA
30061 TCGCAACG
1 TCGCAACG
30069 GTCAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:30063 original size:40 final size:40
Alignment explanation
Indices: 29916--30066 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
29906 TTTAGAAGAA
* * *
29916 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
29956 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* *
29999 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
30039 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
30067 CGGTCAAAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
40 58 0.61
41 3 0.03
42 1 0.01
43 33 0.35
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:30167 original size:6 final size:6
Alignment explanation
Indices: 30156--30278 Score: 246
Period size: 6 Copynumber: 20.5 Consensus size: 6
30146 GACACGTATT
30156 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
30204 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
30252 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
30279 CGAGACGAGA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 117 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:30990 original size:6 final size:6
Alignment explanation
Indices: 30969--31005 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
30959 TCTCGTCTCA
30969 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
31006 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:31127 original size:20 final size:20
Alignment explanation
Indices: 31117--31254 Score: 159
Period size: 20 Copynumber: 6.8 Consensus size: 20
31107 CGATTTTATA
31117 AATCGCATTGCGATTCTCTC
1 AATCGCATTGCGATTCTCTC
* * *
31137 AGTCGCGTTGCGATTTTCTTCTA
1 AATCGCATTGCGA--TTC-TCTC
* *
31160 AATCGCGTTGCGACTCTCTC
1 AATCGCATTGCGATTCTCTC
* *
31180 AATCGCGTTGCGACTCTCTC
1 AATCGCATTGCGATTCTCTC
* *
31200 AATCGCATTGCGATTATATC
1 AATCGCATTGCGATTCTCTC
*
31220 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTCTC
31240 AATCGCATTGCGATT
1 AATCGCATTGCGATT
31255 TTCTTCTAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
20 84 0.81
21 2 0.02
22 3 0.03
23 15 0.14
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTCTCTC
Found at i:31146 original size:40 final size:40
Alignment explanation
Indices: 31102--31275 Score: 177
Period size: 40 Copynumber: 4.2 Consensus size: 40
31092 TTATTTTCAA
* *
31102 CGTTGCGATTTTATAAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * *
31142 CGTTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
1 CGTTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCG
* * * * *
31185 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * *
31225 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGA--TTC-TCTCAATCG
31268 CGTTGCGA
1 CGTTGCGA
31276 ACTTGGAAGC
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
40 57 0.52
41 2 0.02
42 4 0.04
43 47 0.43
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
Found at i:31316 original size:20 final size:20
Alignment explanation
Indices: 31291--31342 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
31281 GAAGCTCGCA
*
31291 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
31311 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
31331 TTGCGATTTTCT
1 TTGCGATTTTCT
31343 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:31369 original size:19 final size:20
Alignment explanation
Indices: 31329--31379 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
31319 TTCTTTTTAA
*
31329 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
31349 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
31368 CGTTGCGATTTT
1 CGTTGCGATTTT
31380 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:31700 original size:17 final size:16
Alignment explanation
Indices: 31674--31710 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
31664 TGATATAAAA
*
31674 AATACAAAAAATTATT
1 AATACAAAAAAATATT
31690 AATACCAAAAAAATATT
1 AATA-CAAAAAAATATT
31707 AATA
1 AATA
31711 TATGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
AATACAAAAAAATATT
Found at i:37686 original size:12 final size:11
Alignment explanation
Indices: 37629--37686 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
37619 ATCATGTATC
37629 TCATATCAC-T
1 TCATATCACAT
*
37639 TCATATCATATT
1 TCATATCACA-T
*
37651 CTCATATCACAGG
1 -TCATATCACA-T
37664 TCATATCACAT
1 TCATATCACAT
37675 ATCATATCACAT
1 -TCATATCACAT
37687 GAACATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 8 0.21
12 22 0.56
13 9 0.23
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (11 bp):
TCATATCACAT
Found at i:38197 original size:64 final size:64
Alignment explanation
Indices: 38065--38199 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 64
38055 TGGGATACAT
* * * * *
38065 CGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAATGGGATGCAT
1 CGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGAGATGCAC
* * *
38129 CGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-AGAGTGCA
1 CGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGT-TTCACTATTAAAGAGA-TGCA
38192 C
64 C
38193 CGATGCA
1 CGATGCA
38200 TTACCAATGC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 56 0.92
65 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (64 bp):
CGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGAGATGCAC
Found at i:38213 original size:64 final size:64
Alignment explanation
Indices: 38065--38219 Score: 154
Period size: 64 Copynumber: 2.4 Consensus size: 64
38055 TGGGATACAT
* * * *
38065 CGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAATGGGATGCAT
1 CGATGCACTACC-AATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGAGATGCAC
** * * * *
38129 CGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-AGAGTGCA
1 CGATGCACTACCAATGCATCGATGCACCAATTGCATTCGATGT-TTCACTATTAAAGAGA-TGCA
38192 C
64 C
* *
38193 CGATGCATTACCAATGCATCGGTGCAC
1 CGATGCACTACCAATGCATCGATGCAC
38220 ATTCAAACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.03
64 69 0.92
65 4 0.05
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (64 bp):
CGATGCACTACCAATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGAGATGCAC
Found at i:44430 original size:12 final size:12
Alignment explanation
Indices: 44396--44430 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
44386 TATCATGTTC
**
44396 TCATATCACAGG
1 TCATATCACATA
44408 TCATATCACATA
1 TCATATCACATA
44420 TCATATCACAT
1 TCATATCACAT
44431 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:44848 original size:64 final size:64
Alignment explanation
Indices: 44779--44915 Score: 204
Period size: 64 Copynumber: 2.1 Consensus size: 64
44769 CATAAAAGGT
* * *
44779 ATTCGATGTAGT-ATTATTGATGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTAC
1 ATTCGATGT-GTCACTATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTAC
* * *
44843 ATTCGATGTTTCACTATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGC
1 ATTCGATGTGTCACTATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTAC
44907 ATTCGATGT
1 ATTCGATGT
44916 CTTTATTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.02
64 65 0.98
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (64 bp):
ATTCGATGTGTCACTATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTAC
Found at i:44936 original size:64 final size:64
Alignment explanation
Indices: 44802--44963 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
44792 TTATTGATGG
* * *
44802 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCACTATTAAAGA
* * * *
44866 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGT-TTCACTATTAAAGA
* ** *
44929 GAGTGCATCGATGCATTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
44964 ATTCAAACAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 80 0.94
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCACTATTAAAGA
Found at i:45022 original size:21 final size:21
Alignment explanation
Indices: 44996--45049 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
44986 AACCTTGATA
44996 CATCGATGCACTATGAATGTG
1 CATCGATGCACTATGAATGTG
45017 CATCGATGCACTATGAATGTG
1 CATCGATGCACTATGAATGTG
45038 CATCGATGCACT
1 CATCGATGCACT
45050 CTGCACAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (21 bp):
CATCGATGCACTATGAATGTG
Found at i:51476 original size:109 final size:109
Alignment explanation
Indices: 51285--51611 Score: 600
Period size: 109 Copynumber: 3.0 Consensus size: 109
51275 GTAAACCTAG
*
51285 TTTTTAACCTAATCTGAGCTCAACCAACCAACTCGTAGTAGAGGTGGGCTACAAGGAATTCAAGC
1 TTTTTAACCTAATCTGAGCTCAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTCAAGC
51350 CTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGCTTCA
66 CTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGCTTCA
51394 TTTTTAACCTAATCTGAGCTCAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTCAAGC
1 TTTTTAACCTAATCTGAGCTCAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTCAAGC
51459 CTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGCTTCA
66 CTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGCTTCA
51503 TTTTTAACCTAATCTGAGCTCAACCAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTC
1 TTTTTAACCTAATCTGAGCT----CAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTC
*
51568 AAGCCTTGGAGGAGAAGAAAAGTGTGAGACACTAACCCCTTGGC
62 AAGCCTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGC
51612 ATCAATCAAG
Statistics
Matches: 212, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
109 128 0.60
113 84 0.40
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (109 bp):
TTTTTAACCTAATCTGAGCTCAACCAACCAACTCGTAGTTGAGGTGGGCTACAAGGAATTCAAGC
CTTGGAGGAGAAGAGAAGTGTGAGACACTAACCCCTTGGCTTCA
Found at i:54504 original size:17 final size:18
Alignment explanation
Indices: 54482--54518 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54472 TCTTATGCAC
54482 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
54499 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
54517 AT
1 AT
54519 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:57125 original size:16 final size:17
Alignment explanation
Indices: 57099--57130 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
57089 AAAAATAAAT
57099 GAACATAAAACGAACAC
1 GAACATAAAACGAACAC
57116 GAACAT-AAACGAACA
1 GAACATAAAACGAACA
57131 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACATAAAACGAACAC
Found at i:57221 original size:16 final size:16
Alignment explanation
Indices: 57200--57264 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
57190 TAATAAATAA
**
57200 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
57216 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
57232 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
57248 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
57264 A
1 A
57265 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:57515 original size:11 final size:11
Alignment explanation
Indices: 57499--57550 Score: 86
Period size: 11 Copynumber: 4.6 Consensus size: 11
57489 TCGAGACTTG
*
57499 AGCTCGATTGA
1 AGCTCGATTCA
57510 AGCTCGATTCA
1 AGCTCGATTCA
57521 AGCTCGATTCTA
1 AGCTCGATTC-A
57533 AGCTCGATTCA
1 AGCTCGATTCA
57544 AGCTCGA
1 AGCTCGA
57551 CATTGCCCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 28 0.72
12 11 0.28
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:57539 original size:23 final size:22
Alignment explanation
Indices: 57499--57550 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
57489 TCGAGACTTG
57499 AGCTCGATTGAAGCTCGATTCA
1 AGCTCGATTGAAGCTCGATTCA
*
57521 AGCTCGATTCTAAGCTCGATTCA
1 AGCTCGATT-GAAGCTCGATTCA
57544 AGCTCGA
1 AGCTCGA
57551 CATTGCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
AGCTCGATTGAAGCTCGATTCA
Found at i:58395 original size:14 final size:14
Alignment explanation
Indices: 58376--58427 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
58366 AACATAAACA
58376 AACATAACCGAACG
1 AACATAACCGAACG
58390 AACAT-A---AACG
1 AACATAACCGAACG
*
58400 AACATAACAGAACG
1 AACATAACCGAACG
58414 AACATAACCGAACG
1 AACATAACCGAACG
58428 TTCACGAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.08
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:58425 original size:24 final size:24
Alignment explanation
Indices: 58352--58426 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
58342 GATTGGGTTA
* *
58352 AACATAA-ATGAATGAACATAAACA
1 AACATAACA-GAACGAACATAAACG
*
58376 AACATAACCGAACGAACATAAACG
1 AACATAACAGAACGAACATAAACG
*
58400 AACATAACAGAACGAACATAACCG
1 AACATAACAGAACGAACATAAACG
58424 AAC
1 AAC
58427 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAACAGAACGAACATAAACG
Found at i:60599 original size:42 final size:42
Alignment explanation
Indices: 60551--60635 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
60541 AAGGAGAAGG
* *
60551 GAAATTGAACAGTCAGCCGGACATAGGAGATGGAGATGAAAA
1 GAAATTGAACAGTCAGCCGGAAATAGGAGATGAAGATGAAAA
*
60593 GAAATTGAACAGTCAGTCGGAAATAGGAGATGAAGATGAAAA
1 GAAATTGAACAGTCAGCCGGAAATAGGAGATGAAGATGAAAA
60635 G
1 G
60636 GAAGAACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.09, G:0.31, T:0.15
Consensus pattern (42 bp):
GAAATTGAACAGTCAGCCGGAAATAGGAGATGAAGATGAAAA
Found at i:62482 original size:15 final size:15
Alignment explanation
Indices: 62462--62495 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
62452 TGCAATTTAC
62462 CCAATAATTTATAAT
1 CCAATAATTTATAAT
62477 CCAATAATTTATAAT
1 CCAATAATTTATAAT
62492 CCAA
1 CCAA
62496 ATACGTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (15 bp):
CCAATAATTTATAAT
Found at i:67968 original size:2 final size:2
Alignment explanation
Indices: 67961--68001 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
67951 TACCAGTGAT
67961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68002 CTTCTTTATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68335 original size:2 final size:2
Alignment explanation
Indices: 68328--68420 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
68318 TTTGATTCAT
68328 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68412 TA TA TA TA T
1 TA TA TA TA T
68421 TTCATAAAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68646 original size:16 final size:16
Alignment explanation
Indices: 68625--68662 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
68615 ACAAAGGCCT
68625 GATATTTTAAAAAAAA
1 GATATTTTAAAAAAAA
*
68641 GATATTTTTAAATAAAA
1 GATA-TTTTAAAAAAAA
68658 -ATATT
1 GATATT
68663 AAATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 7 0.35
17 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
GATATTTTAAAAAAAA
Found at i:69668 original size:28 final size:28
Alignment explanation
Indices: 69636--69692 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
69626 CTCTTCATTT
*
69636 ACATTATATCGTCGAGTAAGTGCTTGAA
1 ACATTATATCGTCGAGCAAGTGCTTGAA
*
69664 ACATTATATCGTCGAGCCAGTGCTTGAA
1 ACATTATATCGTCGAGCAAGTGCTTGAA
69692 A
1 A
69693 ACAACGACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (28 bp):
ACATTATATCGTCGAGCAAGTGCTTGAA
Found at i:77660 original size:21 final size:21
Alignment explanation
Indices: 77630--77670 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
77620 CGAACTGTCG
*
77630 TAAATTTTTAA-AAATAAAAT
1 TAAATTTTTAATAAACAAAAT
77650 TAAAGTTTTTAATAAACAAAA
1 TAAA-TTTTTAATAAACAAAA
77671 AGATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATTTTTAATAAACAAAAT
Found at i:86672 original size:2 final size:2
Alignment explanation
Indices: 86665--86700 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
86655 TATTTTTGAA
86665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86701 TAGTCGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88257 original size:13 final size:13
Alignment explanation
Indices: 88236--88265 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
88226 ATTTTTGGTT
*
88236 TTTTTTTATTTTC
1 TTTTGTTATTTTC
88249 TTTTGTTATTTTC
1 TTTTGTTATTTTC
88262 TTTT
1 TTTT
88266 TTTGTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTGTTATTTTC
Found at i:90257 original size:15 final size:15
Alignment explanation
Indices: 90237--90270 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
90227 TTTAACTGGG
90237 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
*
90252 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGA
90267 CGGG
1 CGGG
90271 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.65, T:0.06
Consensus pattern (15 bp):
CGGGCGGATGCGGGA
Found at i:92596 original size:21 final size:21
Alignment explanation
Indices: 92566--92611 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
92556 CCCTAAATTG
92566 ATAACCCTAAACCAT-AACCC
1 ATAACCCTAAACCATAAACCC
92586 ATAACCTCTAAACCATAAACCC
1 ATAACC-CTAAACCATAAACCC
92608 -TAAC
1 ATAAC
92612 TTAAAACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 13 0.54
22 5 0.21
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAACCCTAAACCATAAACCC
Found at i:99572 original size:62 final size:64
Alignment explanation
Indices: 99489--99663 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 64
99479 TAAAATAAAT
* *
99489 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCG-TGCAT-CCATTAATAAGGA-A
1 ACATCGAATGCAATTAGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAA-GACA
* *
99551 ACATCGAATGCAATTAGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACA
1 ACATCGAATGCAATTAGTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCAGTAATAAGACA
* * * *
99615 ACATCGAATACATTTTA-TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCA-ATTAGTGCATCGATGCATAAGTAGTGCATCGATGCAT
99664 ACCTTCATTA
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
62 38 0.39
63 10 0.10
64 47 0.48
65 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
ACATCGAATGCAATTAGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAGACA
Found at i:100534 original size:103 final size:102
Alignment explanation
Indices: 100410--100631 Score: 426
Period size: 103 Copynumber: 2.2 Consensus size: 102
100400 GTCGAGGGTC
100410 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
100475 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAG-AAATGTATATGATTCTTAAGGAGTGA
100513 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
100578 TTGATCCCTAGAAATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGAAATGTATATGATTCTTAAGGAGTGA
100615 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
100632 CATTATTATA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 42 0.36
103 76 0.64
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGAAATGTATATGATTCTTAAGGAGTGA
Found at i:100680 original size:23 final size:23
Alignment explanation
Indices: 100643--100705 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
100633 ATTATTATAT
*
100643 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
100666 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
*
100689 GGCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
100706 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:105248 original size:64 final size:64
Alignment explanation
Indices: 105180--105404 Score: 267
Period size: 64 Copynumber: 3.5 Consensus size: 64
105170 TTGTTTGAAG
** **
105180 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATTCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATTCAATT
105243 T
64 T
** *
105244 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATTCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATTCAATTT
* * * * *
105308 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATTCAATTT
* * *
105372 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
105405 ACCTTCATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 129 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATTCAATTT
Found at i:106280 original size:103 final size:103
Alignment explanation
Indices: 106156--106378 Score: 446
Period size: 103 Copynumber: 2.2 Consensus size: 103
106146 GTCGAGGGTC
106156 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
106221 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
106259 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
106324 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
106362 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
106379 CATTATTATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 120 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:106423 original size:23 final size:23
Alignment explanation
Indices: 106392--106452 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
106382 TATTATATGG
*
106392 CACTACGGTGCAATTTTACGCGA
1 CACTACGGTGCAATTCTACGCGA
* * *
106415 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGA
*
106438 CACTTCGGTGCAATT
1 CACTACGGTGCAATT
106453 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGA
Found at i:110616 original size:18 final size:19
Alignment explanation
Indices: 110593--110632 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
110583 TTTAACCATA
*
110593 TATTTGAAT-TAAATTAAT
1 TATTTGAATAAAAATTAAT
110611 TATTTGAATAAAAATTAAT
1 TATTTGAATAAAAATTAAT
110630 TAT
1 TAT
110633 AGTGATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TATTTGAATAAAAATTAAT
Found at i:110782 original size:10 final size:9
Alignment explanation
Indices: 110766--110808 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
110756 AAATTGTTTG
110766 TTTTTATAT
1 TTTTTATAT
110775 TATTTTATGAT
1 T-TTTTAT-AT
110786 TTTTTAATAT
1 TTTTT-ATAT
110796 TTTTT-TAT
1 TTTTTATAT
110804 TTTTT
1 TTTTT
110809 CGTGTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
9 1 0.03
10 17 0.55
11 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:116027 original size:50 final size:51
Alignment explanation
Indices: 115965--116073 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
115955 ACAAATGTTA
* * *
115965 TTATTGCA-TTGT-GCAATAGTCAAATATATGTCTAAGAATATATGAATCAT
1 TTATTG-ATTTGTGGCAACAGTCAAATATATGTCTAAGAACACATGAATCAT
*
116015 TTATTGATTTGTGGCAACAGTCAAATATATGTCTAAGAACACATGAATCGT
1 TTATTGATTTGTGGCAACAGTCAAATATATGTCTAAGAACACATGAATCAT
116066 TTATTGAT
1 TTATTGAT
116074 CCTTCTTCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 1 0.02
50 10 0.19
51 42 0.79
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (51 bp):
TTATTGATTTGTGGCAACAGTCAAATATATGTCTAAGAACACATGAATCAT
Found at i:121761 original size:19 final size:20
Alignment explanation
Indices: 121723--121762 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
121713 GTTTCGAAAG
*
121723 TTATAAAATGATTATTAAAT
1 TTATAAAATGATTATAAAAT
*
121743 TTATTAAAT-ATTATAAAAT
1 TTATAAAATGATTATAAAAT
121762 T
1 T
121763 ATCATTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATAAAATGATTATAAAAT
Found at i:121826 original size:31 final size:31
Alignment explanation
Indices: 121790--121863 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
121780 AATAGTGATA
* ** *
121790 CGATAAGTTTAAGGTTCATTTTGTAATAGTT
1 CGATAAGTTTAACGACCATTTTATAATAGTT
121821 CGATAAGTTTAACGACCATTTTATAATAGTT
1 CGATAAGTTTAACGACCATTTTATAATAGTT
*
121852 TGATAAAGTTTA
1 CGAT-AAGTTTA
121864 GTGATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 30 0.81
32 7 0.19
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (31 bp):
CGATAAGTTTAACGACCATTTTATAATAGTT
Found at i:121874 original size:32 final size:31
Alignment explanation
Indices: 121790--121878 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
121780 AATAGTGATA
* * *
121790 CGATAAGTTTAAGGTTC-ATTTTGTAATAGTT
1 CGATAAGTTTAACG-ACAATTTTATAATAGTT
*
121821 CGATAAGTTTAACGACCATTTTATAATAGTT
1 CGATAAGTTTAACGACAATTTTATAATAGTT
* ** *
121852 TGATAAAGTTTAGTGATAATTTTATAA
1 CGAT-AAGTTTAACGACAATTTTATAA
121879 CGTTTTGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 29 0.60
32 18 0.38
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CGATAAGTTTAACGACAATTTTATAATAGTT
Found at i:126409 original size:30 final size:29
Alignment explanation
Indices: 126357--126418 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
126347 TAAATTCATA
**
126357 AATATTTAATAATTATTTAATTTAGATAAT
1 AATATTTAATAATTATAAAATTTAGA-AAT
*
126387 AATATTTAATTAATT-TAAAATTTTGAAAT
1 AATATTTAA-TAATTATAAAATTTAGAAAT
126416 AAT
1 AAT
126419 TAAAAACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 17 0.61
31 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
AATATTTAATAATTATAAAATTTAGAAAT
Done.