Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 89
Found at i:497 original size:183 final size:183
Alignment explanation
Indices: 187--532 Score: 629
Period size: 183 Copynumber: 1.9 Consensus size: 183
177 GGTTTAACTA
187 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATTGCCA
* ** *
252 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
317 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCATTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCATTAGAGGGACAAATCACTG
* *
370 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATTGCCA
*
435 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
500 CTATAACCAATTGCCTTAGTGGAATAGCTCAGC
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGC
533 TTTACGGATT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 156 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCATTAGAGGGACAAATCACTG
Found at i:4525 original size:21 final size:21
Alignment explanation
Indices: 4487--4537 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
4477 ACATAGTATT
4487 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
4507 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
4528 ATATATAGAA
1 AAATA-AGAA
4538 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:4961 original size:75 final size:74
Alignment explanation
Indices: 4776--4981 Score: 263
Period size: 74 Copynumber: 2.7 Consensus size: 74
4766 CAAAGTCAAA
* * **
4776 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
4841 TTTGGCTCCGAG
63 TTTGGCTCCGAG
* *
4853 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
4917 TTGTTCCGAG
65 TGGCTCCGAG
* *
4927 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
4982 CTTGTACAAC
Statistics
Matches: 114, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 62 0.54
75 27 0.24
76 1 0.01
77 23 0.20
78 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:10683 original size:20 final size:20
Alignment explanation
Indices: 10655--10732 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
10645 TTGGTGCAGA
*
10655 GGAATCGATCCCCCCCTGAG
1 GGAACCGATCCCCCCCTGAG
**
10675 GGAACCGATTCCCCCTTTGAATG
1 GGAACCGA-TCCCCCCCTG-A-G
* **
10698 GGAACCGATTCCCCCCACAG
1 GGAACCGATCCCCCCCTGAG
*
10718 GGAATCGATACCCCC
1 GGAACCGAT-CCCCC
10733 TGGGGTTCTG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
20 16 0.36
21 13 0.30
22 6 0.14
23 9 0.20
ACGTcount: A:0.23, C:0.38, G:0.22, T:0.17
Consensus pattern (20 bp):
GGAACCGATCCCCCCCTGAG
Found at i:12657 original size:17 final size:17
Alignment explanation
Indices: 12635--12668 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12625 ACATTATATT
*
12635 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
12652 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
12669 GATTATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:13405 original size:72 final size:74
Alignment explanation
Indices: 13257--13460 Score: 234
Period size: 72 Copynumber: 2.8 Consensus size: 74
13247 CAAAGTCAAA
* * * * **
13257 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCTATAGGAGGAATCGATTCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCTATAGGAGGAACCGATTCCCCCTAAACAGT
13322 TTGGCTCCGAG
64 TTGGCTCCGAG
*
13333 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCC-ATAGGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCTATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
13396 TGTTCCGAG
66 GGCTCCGAG
* * * * *
13405 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCTATAGGAGGAACCGATTCCCCCT
13461 TGTATAACGG
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
72 60 0.54
73 3 0.03
74 21 0.19
75 1 0.01
76 26 0.23
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCTATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:14305 original size:2 final size:2
Alignment explanation
Indices: 14298--14324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14288 ATATTCTTAA
14298 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
14325 AAATTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16426 original size:45 final size:45
Alignment explanation
Indices: 16376--16526 Score: 182
Period size: 45 Copynumber: 3.4 Consensus size: 45
16366 GTAGACCTAG
*
16376 GTCACACAACATC-AGCATCTCCCAAGTATCTCAGGTGAGGTCTGA
1 GTCACACAGCATCGA-CATCTCCCAAGTATCTCAGGTGAGGTCTGA
* * *
16421 GTCACAGAGCATCGACATCTCCCAAGTATCTCAGGCGAGGTCCGA
1 GTCACACAGCATCGACATCTCCCAAGTATCTCAGGTGAGGTCTGA
* * * * *
16466 GTCACATAGCATCGACACCTCCCAAG-ACCTTAGGCT-AGGTCTGG
1 GTCACACAGCATCGACATCTCCCAAGTATCTCAGG-TGAGGTCTGA
16510 GTCACACAGCATCGACA
1 GTCACACAGCATCGACA
16527 CCATGCTTGG
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 28 0.30
45 63 0.68
46 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (45 bp):
GTCACACAGCATCGACATCTCCCAAGTATCTCAGGTGAGGTCTGA
Found at i:17590 original size:41 final size:41
Alignment explanation
Indices: 17539--17617 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
17529 CAAAGAAGGG
*
17539 ATCGATCATTTTCT-CCAAGTGATCGATCCTTTTGAAAAGAT
1 ATCGATCA-TTTCTGCCAAGGGATCGATCCTTTTGAAAAGAT
* * *
17580 ATCGATCATTTCTGTCGAGGGATCGATTCTTTTGAAAA
1 ATCGATCATTTCTGCCAAGGGATCGATCCTTTTGAAAA
17618 TGTATTGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
ATCGATCATTTCTGCCAAGGGATCGATCCTTTTGAAAAGAT
Found at i:17662 original size:31 final size:31
Alignment explanation
Indices: 17627--17694 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
17617 ATGTATTGAT
17627 CCTTTGCTGGATAGAAACTTTGGGATCGATC
1 CCTTTGCTGGATAGAAACTTTGGGATCGATC
17658 CCTTTGCTGGATAGAAACTTTGGGATCGATC
1 CCTTTGCTGGATAGAAACTTTGGGATCGATC
17689 CCTTTG
1 CCTTTG
17695 GTCGAGGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (31 bp):
CCTTTGCTGGATAGAAACTTTGGGATCGATC
Found at i:17695 original size:15 final size:15
Alignment explanation
Indices: 17644--17695 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
17634 TGGATAGAAA
17644 CTTTGGGATCGATCC
1 CTTTGGGATCGATCC
* **
17659 CTTTGCTGGATAGA-AA
1 CTTTG--GGATCGATCC
17675 CTTTGGGATCGATCC
1 CTTTGGGATCGATCC
17690 CTTTGG
1 CTTTGG
17696 TCGAGGGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 6 0.21
15 11 0.39
16 5 0.18
17 6 0.21
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (15 bp):
CTTTGGGATCGATCC
Found at i:19359 original size:27 final size:26
Alignment explanation
Indices: 19315--19395 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
19305 TTCATAATCA
*
19315 TTTATATT-ACTAACTTAAAAAATATTT
1 TTTATATTAACTTA-TT-AAAAATATTT
*
19342 TTTATATTAACTTATTAAATATATTT
1 TTTATATTAACTTATTAAAAATATTT
*
19368 TAT-TATTAACTTAATTTAAAAATATTT
1 TTTATATTAACTT-A-TTAAAAATATTT
19395 T
1 T
19396 CATTTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.19
26 12 0.26
27 22 0.47
28 4 0.09
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTATATTAACTTATTAAAAATATTT
Found at i:19374 original size:25 final size:25
Alignment explanation
Indices: 19314--19395 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 25
19304 ATTCATAATC
* **
19314 ATTTATATTACTAACTTAAAAAATAT
1 ATTT-TATTATTAACTTATTAAATAT
*
19340 TTTTTA-TATTAACTTATTAAATAT
1 ATTTTATTATTAACTTATTAAATAT
*
19364 ATTTTATTATTAACTTAATTTAAAAAT
1 ATTTTATTATTAACTT-A-TTAAATAT
19391 ATTTT
1 ATTTT
19396 CATTTAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
24 20 0.43
25 11 0.23
26 4 0.09
27 12 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTATTATTAACTTATTAAATAT
Found at i:19422 original size:20 final size:21
Alignment explanation
Indices: 19386--19424 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
19376 ACTTAATTTA
19386 AAAATATTTTCATTTAAAAAT
1 AAAATATTTTCATTTAAAAAT
19407 AAAA-ATTTT-ATGTTAAAA
1 AAAATATTTTCAT-TTAAAA
19425 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 11 0.65
21 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAATATTTTCATTTAAAAAT
Found at i:19648 original size:17 final size:16
Alignment explanation
Indices: 19617--19667 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 16
19607 TTTTTAGTAA
*
19617 TTTA-ATTTTTTTATT
1 TTTATATTTTTATATT
19632 TTTATATTTTGTATATT
1 TTTATATTTT-TATATT
* *
19649 TTAATATTTTTTTATT
1 TTTATATTTTTATATT
19665 TTT
1 TTT
19668 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 4 0.13
16 12 0.40
17 14 0.47
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATATTTTTATATT
Found at i:19668 original size:9 final size:8
Alignment explanation
Indices: 19617--19667 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
19607 TTTTTAGTAA
19617 TTTA-ATT
1 TTTATATT
*
19624 TTTTTATT
1 TTTATATT
19632 TTTATATT
1 TTTATATT
19640 TTGTATATT
1 TT-TATATT
*
19649 TTAATATT
1 TTTATATT
*
19657 TTTTTATT
1 TTTATATT
19665 TTT
1 TTT
19668 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 3 0.08
8 26 0.70
9 8 0.22
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTATATT
Found at i:20705 original size:27 final size:27
Alignment explanation
Indices: 20666--20727 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
20656 ATTTTAAGTT
*
20666 AAAAATATGAATTCAAAAATAAAAA-ATA
1 AAAAAT-TAAATT-AAAAATAAAAATATA
** *
20694 AAAAATTAAATTATTAATAAAAATATT
1 AAAAATTAAATTAAAAATAAAAATATA
20721 AAAAATT
1 AAAAATT
20728 TGAAGTACGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.31
27 14 0.48
28 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAATTAAATTAAAAATAAAAATATA
Found at i:20834 original size:6 final size:6
Alignment explanation
Indices: 20823--20848 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20813 ATAAAATTTT
20823 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
20849 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:24869 original size:54 final size:54
Alignment explanation
Indices: 24782--25139 Score: 459
Period size: 54 Copynumber: 6.6 Consensus size: 54
24772 TGAACGACCG
* *
24782 ATGAACGACCATATC-AGCACTAAATGTGCAACCCACAAAATTCATAATAAGTTT
1 ATGAACGACCGTATCGA-CACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * * * * *
24836 ATGAATGACCGTATTGGCACTAAATGTGTAACCCACAGAATTCATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * *
24890 ATGAACGATCGTATCGACACTAAGTGTGCAACCCCCAAAATTTATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * * * *
24944 ATGAGCGACCGTATCGACACTAAGTATGCAACACACGAAATTTATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * **
24998 ATGAATGACCGTATCGGCACTAAGTGTGCAACCCATGAAATTCATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * * *
25052 ATTAACGACTGTATCGACACTAAGTGTGCAACCCACATAATTCATAATGAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* *
25106 ATGAACGACCGTATTGACACTACGTGTGC-ACCCA
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCA
25140 AAAGAACTTA
Statistics
Matches: 263, Mismatches: 40, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
53 5 0.02
54 258 0.98
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (54 bp):
ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
Found at i:31761 original size:54 final size:53
Alignment explanation
Indices: 31676--31862 Score: 293
Period size: 54 Copynumber: 3.5 Consensus size: 53
31666 CTATGTGTAC
* *
31676 TATCGACACTAAGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCAA-TAATTCATAATAAGTTTATGAACGACCG
*
31730 TATCGACACTAAGTGTGCAACTCACATAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCA-ATAATTCATAATAAGTTTATGAACGACCG
*
31784 TATCGACACTAAGTGTGCAACCCATATAATTCATAATGAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCA-ATAATTCATAATAAGTTTATGAACGACCG
* *
31838 TATCGACACTATGTGTGCACCCCAA
1 TATCGACACTAAGTGTGCAACCCAA
31863 AGAACTTATA
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.01
54 122 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (53 bp):
TATCGACACTAAGTGTGCAACCCAATAATTCATAATAAGTTTATGAACGACCG
Found at i:40347 original size:21 final size:21
Alignment explanation
Indices: 40321--40360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40311 CTGTAGTAGT
40321 ACTGTAACAGTGCATCGATGC
1 ACTGTAACAGTGCATCGATGC
*
40342 ACTGTAGCAGTGCATCGAT
1 ACTGTAACAGTGCATCGAT
40361 ACGCAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAACAGTGCATCGATGC
Found at i:43788 original size:32 final size:32
Alignment explanation
Indices: 43747--43843 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
43737 GAGTCGAGGG
*
43747 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTAAGGAACATATGGACAGT
***
43779 TTTACCTATG-TCTTTTGAGACATATGGACAG-
1 TTTACCTATGTTCTAAGGA-ACATATGGACAGT
* *
43810 TATACCTATGTTCTAAGGAACATATAGACAGT
1 TTTACCTATGTTCTAAGGAACATATGGACAGT
43842 TT
1 TT
43844 ACATAGGTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 25 0.47
32 28 0.53
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTCTAAGGAACATATGGACAGT
Found at i:43833 original size:31 final size:31
Alignment explanation
Indices: 43749--43841 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
43739 GTCGAGGGTT
* *
43749 TACCTATGTTCTACGGAACATATGGACAGTTT
1 TACCTATGTTCTAAGGAACATATGGACAG-TA
***
43781 TACCTATG-TCTTTTGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTA
*
43812 TACCTATGTTCTAAGGAACATATAGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
43842 TTACATAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:44621 original size:11 final size:11
Alignment explanation
Indices: 44599--44632 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
44589 TTACGAAAGT
44599 TACTGTAGCAG
1 TACTGTAGCAG
* *
44610 TATTGTATCAG
1 TACTGTAGCAG
44621 TACTGTAGCAG
1 TACTGTAGCAG
44632 T
1 T
44633 GCATCGATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (11 bp):
TACTGTAGCAG
Found at i:47227 original size:13 final size:13
Alignment explanation
Indices: 47209--47234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47199 TCCAAACACT
47209 GAGGCGAGCATTC
1 GAGGCGAGCATTC
47222 GAGGCGAGCATTC
1 GAGGCGAGCATTC
47235 AAAGCTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
GAGGCGAGCATTC
Found at i:49075 original size:21 final size:23
Alignment explanation
Indices: 49048--49104 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 23
49038 TTGCAGCTGC
49048 CAATTTGGACTTTAAC-AGCTCT
1 CAATTTGGACTTTAACAAGCTCT
* *
49070 -AATTTGGACTTTTACAAGCTGT
1 CAATTTGGACTTTAACAAGCTCT
*
49092 CAATTTAGACTTT
1 CAATTTGGACTTT
49105 TTAACAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.47
22 5 0.17
23 11 0.37
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (23 bp):
CAATTTGGACTTTAACAAGCTCT
Found at i:52608 original size:16 final size:16
Alignment explanation
Indices: 52589--52623 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52579 GATATAAGAC
*
52589 AATTTAAATTTAAATT
1 AATTTAAATTTAAAAT
*
52605 AATTTAATTTTAAAAT
1 AATTTAAATTTAAAAT
52621 AAT
1 AAT
52624 GTTTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:55979 original size:30 final size:29
Alignment explanation
Indices: 55943--56017 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
55933 GTAATTGATT
55943 TTCTAGAAAATGAATTACTCG-AATTTAAA
1 TTCTAGAAAATGAATTACT-GAAATTTAAA
*
55972 TTACTAGAAAATGAATTACTGAAATTTGAA
1 TT-CTAGAAAATGAATTACTGAAATTTAAA
*
56002 TTCTGGAAAATGAATT
1 TTCTAGAAAATGAATT
56018 TTATTTCTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (29 bp):
TTCTAGAAAATGAATTACTGAAATTTAAA
Found at i:55988 original size:15 final size:15
Alignment explanation
Indices: 55945--56017 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
55935 AATTGATTTT
55945 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
* ** *
55960 CTCGAATTTAAATTA
1 CTAGAAAATGAATTA
55975 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
*
55990 CT-GAAATTTGAATT-
1 CTAGAAA-ATGAATTA
*
56004 CTGGAAAATGAATT
1 CTAGAAAATGAATT
56018 TTATTTCTAG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
14 12 0.26
15 34 0.74
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (15 bp):
CTAGAAAATGAATTA
Found at i:56046 original size:14 final size:14
Alignment explanation
Indices: 56027--56061 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56017 TTTATTTCTA
*
56027 GAAAATGTTTTTCG
1 GAAAATGTTTTCCG
56041 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
56055 TAAAATG
1 GAAAATG
56062 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:56456 original size:26 final size:25
Alignment explanation
Indices: 56413--56507 Score: 77
Period size: 26 Copynumber: 3.6 Consensus size: 25
56403 AAATTATTAT
*
56413 TATTATATAATTAA-ATATAATAATAC
1 TATTAT-T-ATTAATATATAATAATAA
* *
56439 TATTCATTATTAATATATAAAAATAT
1 TATT-ATTATTAATATATAATAATAA
* *
56465 TATATATTTATTAAAATAAAAATAATAA
1 TAT-TA-TTATTAATAT-ATAATAATAA
56493 TATTATTA-TAATATA
1 TATTATTATTAATATA
56508 ATTATTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
24 1 0.02
25 10 0.18
26 22 0.39
27 14 0.25
28 10 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTATTATTAATATATAATAATAA
Found at i:56501 original size:53 final size:54
Alignment explanation
Indices: 56391--56614 Score: 143
Period size: 53 Copynumber: 4.3 Consensus size: 54
56381 TTAAATATCT
* * ** *
56391 TTATTAA-ATATTAAATTATTAT-TATTATATAATTA-AATATAATAATACTATTCA
1 TTATTAATATATAAAAATATTATATATT-TATAAAGATAA-ATAATAATAATATT-A
56445 TTATTAATATATAAAAATATTATATATTTATTAAA-ATAAA-AATAATAATATTA
1 TTATTAATATATAAAAATATTATATATTTA-TAAAGATAAATAATAATAATATTA
* ** * *
56498 TTA-TAATATAATTATTATTTTATATATTTATAAAGATAAATATTAATAATA-TA
1 TTATTAATAT-ATAAAAATATTATATATTTATAAAGATAAATAATAATAATATTA
*** * * *
56551 TT-TTAA-ATATTTTAATAATTA-ATATTT-TGATGA-AAATGATAATAAATATT-
1 TTATTAATATATAAAAAT-ATTATATATTTATAAAGATAAATAATAAT-AATATTA
56601 TTATTAATAT-TAAA
1 TTATTAATATATAAA
56615 TTCATAAATA
Statistics
Matches: 138, Mismatches: 19, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
49 8 0.06
50 10 0.07
51 18 0.13
52 17 0.12
53 32 0.23
54 27 0.20
55 17 0.12
56 9 0.07
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (54 bp):
TTATTAATATATAAAAATATTATATATTTATAAAGATAAATAATAATAATATTA
Found at i:56505 original size:23 final size:24
Alignment explanation
Indices: 56444--56505 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
56434 AATACTATTC
*
56444 ATTATTAATATATAAAAATATTATAT
1 ATTATT-ATA-ATAAAAATAATATAT
*
56470 ATTTATTAAAATAAAAATAATA-AT
1 A-TTATTATAATAAAAATAATATAT
56494 ATTATTATAATA
1 ATTATTATAATA
56506 TAATTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 10 0.31
24 3 0.09
25 11 0.34
26 3 0.09
27 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTATTATAATAAAAATAATATAT
Found at i:63914 original size:5 final size:6
Alignment explanation
Indices: 63891--63927 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
63881 ATTTTGTTAC
*
63891 ATTTTT ATTTTT CGTTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT -ATTTTT ATTTTT ATTTTT ATTTTT
63928 TTGATCGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:63928 original size:13 final size:13
Alignment explanation
Indices: 63891--63928 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
63881 ATTTTGTTAC
*
63891 ATTTTTATTTTTC
1 ATTTTTATTTTTT
*
63904 GTTTTTA-TTTTT
1 ATTTTTATTTTTT
63916 ATTTTTATTTTTT
1 ATTTTTATTTTTT
63929 TGATCGAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:63928 original size:19 final size:19
Alignment explanation
Indices: 63891--63927 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
63881 ATTTTGTTAC
*
63891 ATTTTTATTTTTCGTTTTT
1 ATTTTTATTTTTAGTTTTT
63910 ATTTTTATTTTTA-TTTTT
1 ATTTTTATTTTTAGTTTTT
63928 TTGATCGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (19 bp):
ATTTTTATTTTTAGTTTTT
Found at i:73481 original size:30 final size:33
Alignment explanation
Indices: 73427--73492 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
73417 TGCGCAGAAA
73427 CAAAAGCTCCTCAACAACCATATCA-CCGA-AC
1 CAAAAGCTCCTCAACAACCATATCACCCGAGAC
73458 CAAAAGC-CTCTCAACAA-CATATCACCCGAGAC
1 CAAAAGCTC-CTCAACAACCATATCACCCGAGAC
73490 CAA
1 CAA
73493 CTCAATAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 8 0.25
31 19 0.59
32 5 0.16
ACGTcount: A:0.42, C:0.38, G:0.08, T:0.12
Consensus pattern (33 bp):
CAAAAGCTCCTCAACAACCATATCACCCGAGAC
Found at i:77067 original size:23 final size:23
Alignment explanation
Indices: 77023--77070 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
77013 GGTGGGGTGA
*
77023 TTTAATGGTTGTTTAAACTTTAT
1 TTTAATGGTTATTTAAACTTTAT
*
77046 TTTAATGGTATATTT-AAGTTTAT
1 TTTAATGGT-TATTTAAACTTTAT
77069 TT
1 TT
77071 GGTTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (23 bp):
TTTAATGGTTATTTAAACTTTAT
Found at i:99177 original size:16 final size:15
Alignment explanation
Indices: 99153--99186 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
99143 AAACTTGGTT
*
99153 GAAGGAAGAAGATGAA
1 GAAGAAAGAAGAT-AA
99169 GAAGAAAGAAGATAA
1 GAAGAAAGAAGATAA
99184 GAA
1 GAA
99187 AGCAATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.06
Consensus pattern (15 bp):
GAAGAAAGAAGATAA
Found at i:104738 original size:32 final size:32
Alignment explanation
Indices: 104685--104765 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
104675 TTATGCATAG
104685 ACTAAAATTTTCTCAACATGCTTATGTCATGACA
1 ACTAAAA-TTT-TCAACATGCTTATGTCATGACA
104719 ACTAAAATTTTCAACATGCTTATGTCATGACA
1 ACTAAAATTTTCAACATGCTTATGTCATGACA
104751 ACTAAAATTTTCAAC
1 ACTAAAATTTTCAAC
104766 CAATTATCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 37 0.79
33 3 0.06
34 7 0.15
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (32 bp):
ACTAAAATTTTCAACATGCTTATGTCATGACA
Found at i:109842 original size:416 final size:417
Alignment explanation
Indices: 109063--109887 Score: 1418
Period size: 416 Copynumber: 2.0 Consensus size: 417
109053 TGGAAGATAG
* *
109063 CTGGAGCATTACACAGCCCGAACAACATTCGTCTAAATGCATAGGTACCATAAGGGCATGTGAAA
1 CTGGAGCATTACACACCCCGAACAACATTCGTCTAAATACATAGGTACCATAAGGGCATGTGAAA
*
109128 GTGGTTTTCTCTTGATCCTCTGGTGCTATGGCTATTTGATTATATCCTAAGTATCCATTAAGGAA
66 GTGGTTTTCTCTTGATCCTCCGGTGCTATGGCTATTTGATTATATCCTAAGTATCCATTAAGGAA
**
109193 GCAAAAGAATGCTTTTCCCGCTAACCTATCAAGCATTTGGTCGATAAAATGGAGGGGAAAATGAC
131 GCAAAAGAATGCTTTTCCCGCTAACCTATCAAGCATTTGGTCGATAAAAAAGAGGGGAAAATGAC
*
109258 CTTTATTTGTGGCTTTATTAAGCTTCTTGTAATCCATACATATACGCCAGCCCGTGATTGTTCTA
196 CTTTATTTGTGGCTTTATTAAGCTTCCTGTAATCCATACATATACGCCAGCCCGTGATTGTTCTA
* * *
109323 GTGGTGAGGAGTTCGTTATGTTCGCTTTTAACCACTGTCACACCACCCTTCTTTGGCACACACTA
261 GTGGTGAGGAGTTCATCATGTTCGCTTTTAACCACGGTCACACCACCCTTCTTTGGCACACACTA
109388 CACCGGGCTGACCCATGAACTATAGGATATAGGATAAATCACTCTCGCATCCAACCATTTTATAA
326 CACCGGGCTGACCCATGAACTATAGGATATAGGATAAATCACTCTCGCATCCAACCATTTTATAA
*
109453 TTTACTTCATGAATACCTTATTTATGA
391 TTTACTTCATCAATACCTTATTTATGA
* * * *
109480 CTGGAGTATTACACACCCCGAACGACATTCGTCTAAATACATATGTATCATAAGGGCATGTGAAA
1 CTGGAGCATTACACACCCCGAACAACATTCGTCTAAATACATAGGTACCATAAGGGCATGTGAAA
*
109545 GTGGTTTTCTCTTGATCCTCCGGTGCTAT-GCTATTTGATTATATCCTGAGTATCCATTAAGGAA
66 GTGGTTTTCTCTTGATCCTCCGGTGCTATGGCTATTTGATTATATCCTAAGTATCCATTAAGGAA
* *
109609 GCAATAGAATGCTTTTCCCGCTAACCTATCAAGCATTTGGTCGATAAAAAAGAGGGGAAAATGAT
131 GCAAAAGAATGCTTTTCCCGCTAACCTATCAAGCATTTGGTCGATAAAAAAGAGGGGAAAATGAC
*
109674 CTTTATTTGTGGCTTTATTAAGCTTCCTGTAATCCATACATATACGCCAGCCCGTGATTGTTCTG
196 CTTTATTTGTGGCTTTATTAAGCTTCCTGTAATCCATACATATACGCCAGCCCGTGATTGTTCTA
* *
109739 GTGGTGAGGATTTCATCATGTTTGCTTTTAACCACGGTCACACCACCCTTCTTTGGCACACACTA
261 GTGGTGAGGAGTTCATCATGTTCGCTTTTAACCACGGTCACACCACCCTTCTTTGGCACACACTA
* * * *
109804 CACCGGGTTGAGCCATGAACTATCGGATATAGGATAAATCACTCTTGCATCCAACCATTTTATAA
326 CACCGGGCTGACCCATGAACTATAGGATATAGGATAAATCACTCTCGCATCCAACCATTTTATAA
*
109869 TTTCCTTCATCAATACCTT
391 TTTACTTCATCAATACCTT
109888 CTTCATGATT
Statistics
Matches: 383, Mismatches: 25, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
416 296 0.77
417 87 0.23
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (417 bp):
CTGGAGCATTACACACCCCGAACAACATTCGTCTAAATACATAGGTACCATAAGGGCATGTGAAA
GTGGTTTTCTCTTGATCCTCCGGTGCTATGGCTATTTGATTATATCCTAAGTATCCATTAAGGAA
GCAAAAGAATGCTTTTCCCGCTAACCTATCAAGCATTTGGTCGATAAAAAAGAGGGGAAAATGAC
CTTTATTTGTGGCTTTATTAAGCTTCCTGTAATCCATACATATACGCCAGCCCGTGATTGTTCTA
GTGGTGAGGAGTTCATCATGTTCGCTTTTAACCACGGTCACACCACCCTTCTTTGGCACACACTA
CACCGGGCTGACCCATGAACTATAGGATATAGGATAAATCACTCTCGCATCCAACCATTTTATAA
TTTACTTCATCAATACCTTATTTATGA
Found at i:111611 original size:21 final size:20
Alignment explanation
Indices: 111586--111624 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
111576 CATCAAGGTC
*
111586 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
111607 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
111625 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:120266 original size:3 final size:3
Alignment explanation
Indices: 120260--120294 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
120250 AAGTGTTGTT
*
120260 ATA ATA ATA ATA ATA ATA AGA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
120295 TTGAGAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:121031 original size:20 final size:20
Alignment explanation
Indices: 121006--121043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
120996 TGATCGATAG
* *
121006 AAAATATAAAGAAAAATTTT
1 AAAATACAAAAAAAAATTTT
121026 AAAATACAAAAAAAAATT
1 AAAATACAAAAAAAAATT
121044 AAAATTCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAATACAAAAAAAAATTTT
Found at i:139030 original size:12 final size:12
Alignment explanation
Indices: 139013--139037 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
139003 AGCTTCTTCA
139013 TATAATACTAAT
1 TATAATACTAAT
139025 TATAATACTAAT
1 TATAATACTAAT
139037 T
1 T
139038 CCTTGGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATACTAAT
Found at i:159684 original size:21 final size:22
Alignment explanation
Indices: 159653--159707 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
159643 TGATGGAAGG
* *
159653 GGTATCGATACCTGTATGAAT-A
1 GGTATCAATACCTCTATG-ATGA
159675 -GTATCAATACC-CTATGATGA
1 GGTATCAATACCTCTATGATGA
159695 GGTATCAATACCT
1 GGTATCAATACCT
159708 ATGTGGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 5 0.18
21 21 0.75
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (22 bp):
GGTATCAATACCTCTATGATGA
Found at i:159726 original size:21 final size:21
Alignment explanation
Indices: 159675--159726 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
159665 TGTATGAATA
159675 GTATCAATACCCTATGAT-GA-G
1 GTATCAATA-CCTATG-TGGAGG
159696 GTATCAATACCTATGTGGAGG
1 GTATCAATACCTATGTGGAGG
*
159717 GTATCGATAC
1 GTATCAATAC
159727 AAGGGGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 8 0.29
21 19 0.68
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (21 bp):
GTATCAATACCTATGTGGAGG
Found at i:162094 original size:45 final size:43
Alignment explanation
Indices: 162011--162094 Score: 96
Period size: 45 Copynumber: 1.9 Consensus size: 43
162001 TAAATAAATA
* ** * *
162011 AAAGGGGTTCAAGATAAAAATCTGTAAAGGGCGTCTTGAAACC
1 AAAGGGGTTCAAGATAAAAACCTACAAAGAGCGGCTTGAAACC
*
162054 AAAGGAGGTCTCAAGCTAAAAACCTACAAAGAGCGGCTTGA
1 AAAGG-GGT-TCAAGATAAAAACCTACAAAGAGCGGCTTGA
162095 TAATCATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 5 0.15
44 3 0.09
45 25 0.76
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (43 bp):
AAAGGGGTTCAAGATAAAAACCTACAAAGAGCGGCTTGAAACC
Found at i:163553 original size:133 final size:133
Alignment explanation
Indices: 163300--163657 Score: 386
Period size: 133 Copynumber: 2.7 Consensus size: 133
163290 AATCGAACTA
* * *
163300 GATTCAATCTTCCCT-AAGAATAGTGGAATGAATCAACGTTTCTAGAAT-TGATTTT-CCTGAAG
1 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAG-ATCTAATTTTCCCTGAAG
** * * * *
163362 AAGCAGCGGAGTAGATCCCTTGTTTTTTCAGATTTAATCTTCACTGAGGAATAATGGAACAAGTT
65 AAGCAGCGGAACAGATCCC-T-TTTTTTCAGATTTAATCTTCACTAAAGAAGAATGGAACAAGTC
*
163427 TGTCTC
128 TGCCTC
** * *
163433 GATTCAATCTTCCCTGTTGAATAGTGGAATGAATCAACATCTCCAGATCTTATTTTCCCTGAAGA
1 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTGAAGA
* * * * *
163498 AGCAGTGGAACATATTCC-TTTTTTCAGATTTGATCTTCCCTAAAGAAGAAGTGGAACAAGTCTG
66 AGCAGCGGAACAGATCCCTTTTTTTCAGATTTAATCTTCACTAAAGAAGAA-TGGAACAAGTCTG
163562 CCTC
130 CCTC
* * * *
163566 GATTCAATATTCCCTGAAGAACAGTGGAATGAAT-AGACATTTCCAGATCTAATCTACCCTGAAG
1 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCA-ACATTTCCAGATCTAATTTTCCCTGAAG
* * *
163630 AAGCAAC-GAAGCAGATCTCTTTTCTTCA
65 AAGCAGCGGAA-CAGATCCCTTTTTTTCA
163658 AAAATCTCTC
Statistics
Matches: 186, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
132 31 0.17
133 96 0.52
134 38 0.20
135 21 0.11
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (133 bp):
GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTGAAGA
AGCAGCGGAACAGATCCCTTTTTTTCAGATTTAATCTTCACTAAAGAAGAATGGAACAAGTCTGC
CTC
Found at i:163856 original size:5 final size:5
Alignment explanation
Indices: 163846--163896 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
163836 TTTTATTAAT
* *
163846 TTTTA TTTTA TTTTTA TTTTA TTATA TATTTA TATTA TCTTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA TTTTA T-TTTA TTTTA T-TTTA TTTTA
163894 TTT
1 TTT
163897 CTGCAAGCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 26 0.67
6 13 0.33
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:163860 original size:11 final size:11
Alignment explanation
Indices: 163844--163896 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 11
163834 AATTTTATTA
163844 ATTTTTATTTT
1 ATTTTTATTTT
163855 ATTTTTATTTT
1 ATTTTTATTTT
*
163866 ATTATATATTTAT
1 ATT-TTTATTT-T
163879 ATTATCTTTATTTT
1 A-T-T-TTTATTTT
163893 ATTT
1 ATTT
163897 CTGCAAGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
11 15 0.43
12 7 0.20
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:163888 original size:27 final size:26
Alignment explanation
Indices: 163835--163895 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
163825 ATCATGTTAA
* * *
163835 ATTTTATTAATTTTTATTTTATTTTT
1 ATTTTATTAATATTTATATTATCTTT
163861 ATTTTATTATATATTTATATTATCTTT
1 ATTTTATTA-ATATTTATATTATCTTT
163888 ATTTTATT
1 ATTTTATT
163896 TCTGCAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
ATTTTATTAATATTTATATTATCTTT
Found at i:170330 original size:18 final size:18
Alignment explanation
Indices: 170308--170350 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
170298 CTTAAAATTA
170308 AATATTATTTTA-AATAAT
1 AATATT-TTTTACAATAAT
*
170326 TATATTTTTTACAATAAT
1 AATATTTTTTACAATAAT
170344 AATATTT
1 AATATTT
170351 CACCTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTTTACAATAAT
Found at i:171044 original size:2 final size:2
Alignment explanation
Indices: 171037--171361 Score: 298
Period size: 2 Copynumber: 175.5 Consensus size: 2
171027 ACACAATTAG
* * *
171037 TA TA TA TA -A TA TA TA GTG TA T- TG TA TA T- TA TA GA -A TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
171075 TA TA TA CTA TA TA TA T- TA T- TA TA -A TA TG T- TA TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
171113 TA T- TA T- TA TA GTG TA TA TT TA TA TA TA T- 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
* *
171153 TA TA T- TA TA TA GT- TA CA TA T- TA T- TA T- TA TA TA TA TA TC
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
171191 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
171232 T- TA TA T- TA TA TA TA GA TA TA TA TA TA TA TA T- TA GTA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
171271 T- TA TA TA T- TA TA T- TA TA TA TA TA T- 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
171309 T- TA T- TA TA TA -A 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
171348 T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
171362 TAGTATTGAC
Statistics
Matches: 270, Mismatches: 17, Indels: 72
0.75 0.05 0.20
Matches are distributed among these distances:
1 31 0.11
2 232 0.86
3 7 0.03
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:172803 original size:13 final size:13
Alignment explanation
Indices: 172785--172840 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
172775 ACACCTATCA
172785 AGTATTATATTAT
1 AGTATTATATTAT
172798 AGTA-T-TATTAT
1 AGTATTATATTAT
172809 A--A-TATATTATT
1 AGTATTATATTA-T
*
172820 ATTATT-TATTAT
1 AGTATTATATTAT
172832 AGTATTATA
1 AGTATTATA
172841 GTATTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
9 2 0.06
10 5 0.14
11 9 0.25
12 7 0.19
13 12 0.33
14 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
AGTATTATATTAT
Found at i:172805 original size:8 final size:7
Alignment explanation
Indices: 172790--172861 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
172780 TATCAAGTAT
172790 TATATTA
1 TATATTA
172797 TAGTATTA
1 TA-TATTA
*
172805 T-TATAA
1 TATATTA
172811 TATATTA
1 TATATTA
172818 T-TATTA
1 TATATTA
*
172824 TTTATTA
1 TATATTA
172831 TAGTATTA
1 TA-TATTA
172839 TAGTATTTTA
1 TA-TA--TTA
172849 TATATTA
1 TATATTA
*
172856 TTTATT
1 TATATT
172862 CATTCATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 11 0.20
7 21 0.38
8 16 0.29
9 2 0.04
10 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:172808 original size:16 final size:16
Alignment explanation
Indices: 172787--172861 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
172777 ACCTATCAAG
172787 TATTATATTATAGTAT
1 TATTATATTATAGTAT
* *
172803 TATTATAATATATTAT
1 TATTATATTATAGTAT
172819 TATTATTTATTATAGTAT
1 TATTA--TATTATAGTAT
*
172837 TATAGTATTTTATA-TAT
1 TAT--TATATTATAGTAT
172854 TATT-TATT
1 TATTATATT
172862 CATTCATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 19 0.39
17 6 0.12
18 18 0.37
20 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
TATTATATTATAGTAT
Found at i:177708 original size:17 final size:19
Alignment explanation
Indices: 177686--177720 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
177676 CGAGTGGACA
177686 ATATAT-TA-TTTTAATAT
1 ATATATCTATTTTTAATAT
177703 ATATATCTATTTTTAATA
1 ATATATCTATTTTTAATA
177721 ACTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATCTATTTTTAATAT
Found at i:177753 original size:17 final size:17
Alignment explanation
Indices: 177732--177771 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
177722 CTTAAAATTA
177732 AATATATTTTA-AATAAT
1 AATAT-TTTTACAATAAT
*
177749 TATATTTTTACAATAAT
1 AATATTTTTACAATAAT
177766 AATATT
1 AATATT
177772 CACCTCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTTACAATAAT
Found at i:178454 original size:2 final size:2
Alignment explanation
Indices: 178447--178707 Score: 212
Period size: 2 Copynumber: 140.5 Consensus size: 2
178437 ACACAATTAG
* *
178447 TA TA TA TA -A TA TA TA GTA TA T- TG TA TA T- TA TA GA 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
178487 TA CTA TA T- TA TA T- TA T- TA TA -A TA TA TA TA T- TA -A TA T-
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
178523 TA TA GTG TA -A TA TA TA TA T- TC TA TC TA TA TA T- TA T- TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
178561 TA CA -A T- TA T- TA TA T- TA TA GTA 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
* *
178600 TA T- TA TA TA TT TA TA TA TA TA TA TA TA TA T- TA TA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
178640 TT TA TA TA TA GTA TA T- TA T- TA TA TA TA -A 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
*
178680 TA TA TA TA TA TA TT TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
178708 TAGATTGACT
Statistics
Matches: 212, Mismatches: 17, Indels: 60
0.73 0.06 0.21
Matches are distributed among these distances:
1 25 0.12
2 178 0.84
3 9 0.04
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:178488 original size:27 final size:26
Alignment explanation
Indices: 178447--178705 Score: 229
Period size: 27 Copynumber: 10.0 Consensus size: 26
178437 ACACAATTAG
*
178447 TATATATAATATATAGTATATTGTATAT
1 TATATAT-ATATATA-TATATTATATAT
*
178475 TATAGATATATATACTATA-T-TATAT
1 TATATATATATATA-TATATTATATAT
178500 TAT-TATA-ATATATATATTA-ATAT
1 TATATATATATATATATATTATATAT
* * *
178523 TATAGTGTA-ATATATATATTCTAT-C
1 TATA-TATATATATATATATTATATAT
*
178548 TATATAT-TAT-TATTACAATTATTATAT
1 TATATATATATATA-TA-TATTA-TATAT
178575 TATAGTATATATATATATATATATATAT
1 TATA-TATATATATATATAT-TATATAT
*
178603 TATATATTTATATATATATATATATAT
1 TATATATATATATATATAT-TATATAT
* *
178630 TATATAGATATTTATATA-TAGTATAT
1 TATATATATATATATATATTA-TATAT
178656 TAT-TATATATA-ATATA-TATATAT
1 TATATATATATATATATATTATATAT
*
178679 ATATATATATATATTTATATTATATAT
1 -TATATATATATATATATATTATATAT
178706 ATTAGATTGA
Statistics
Matches: 194, Mismatches: 18, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
22 4 0.02
23 20 0.10
24 19 0.10
25 45 0.23
26 18 0.09
27 59 0.30
28 20 0.10
29 7 0.04
30 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATATATATATATATATATTATATAT
Found at i:178498 original size:25 final size:24
Alignment explanation
Indices: 178447--178709 Score: 184
Period size: 23 Copynumber: 11.1 Consensus size: 24
178437 ACACAATTAG
*
178447 TATATATAATATATAGTATATTGTA-
1 TATATAT-ATATATA-TATATTATAT
* *
178472 TAT-TATAGATATATATACTATAT
1 TATATATATATATATATATTATAT
178495 TATATTATTATAATATATATATTAATAT
1 TATA-TA-TAT-ATATATATATT-ATAT
* *
178523 TATAGTGTA-ATATATATATTCTAT
1 TATA-TATATATATATATATTATAT
**
178547 CTATATAT-TAT-TAT-TACAATTAT
1 -TATATATATATATATATATTA-TAT
178570 TATAT-TATAGTATATATA-TATA-
1 TATATATATA-TATATATATTATAT
178592 TATATATATAT-TATATATT-TAT
1 TATATATATATATATATATTATAT
*
178614 ATATATATATATATATTATATAGATAT
1 -TATATATATATATA-TATAT-TATAT
178641 T-TATATATAGTATAT-TATTATA-
1 TATATATATA-TATATATATTATAT
178663 TATA-ATATATATATATA-TATA-
1 TATATATATATATATATATTATAT
*
178684 TATATATATTTATAT-TATATATAT
1 TATATATATATATATATAT-TATAT
178708 TA
1 TA
178710 GATTGACTAG
Statistics
Matches: 194, Mismatches: 16, Indels: 57
0.73 0.06 0.21
Matches are distributed among these distances:
21 24 0.12
22 40 0.21
23 42 0.22
24 21 0.11
25 36 0.19
26 7 0.04
27 15 0.08
28 9 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATATATATATATATATTATAT
Found at i:178691 original size:67 final size:67
Alignment explanation
Indices: 178444--178708 Score: 226
Period size: 69 Copynumber: 3.9 Consensus size: 67
178434 CGGACACAAT
* * * * *
178444 TAGTATA-TATAATATATAGTATATTGTATATTATAGATATATATACTATATTATAT--TA-TTA
1 TAGTATATTATTATATATAATATA-TATATA-TATATATATATATATTATATTATATAATATTTA
178505 TAATA
64 T-ATA
* * * * * * *
178510 TA-TATATTAATAT-TATAGTGTAATATATATATTCTATCTATATATTATTATTACA-ATTA-TT
1 TAGTATATTATTATATATAATAT-ATATATATA-TATATATATATATTA-TATTATATAATATTT
178571 ATATTA
63 ATA-TA
*
178577 TAGTATA-TATATATATATATATATATTATATATTTATATATATATATATATATTATATAGATAT
1 TAGTATATTAT-TATATATA-ATATA-TATATATATATATATATATAT-TATATTATATA-ATAT
178641 TTATATA
61 TTATATA
178648 TAGTATATTATTATATATAATATATATATATATATATATATATATTTATATTATAT-ATATT
1 TAGTATATTATTATATATAATATATATATATATATATATATATA-TTATATTATATAATATT
178709 AGATTGACTA
Statistics
Matches: 163, Mismatches: 18, Indels: 35
0.75 0.08 0.16
Matches are distributed among these distances:
64 2 0.01
65 27 0.17
66 14 0.09
67 17 0.10
68 7 0.04
69 51 0.31
70 18 0.11
71 19 0.12
72 8 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (67 bp):
TAGTATATTATTATATATAATATATATATATATATATATATATATTATATTATATAATATTTATA
TA
Found at i:178931 original size:13 final size:13
Alignment explanation
Indices: 178913--178938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
178903 GAATTGTTTT
178913 TTAAAATAAAATA
1 TTAAAATAAAATA
178926 TTAAAATAAAATA
1 TTAAAATAAAATA
178939 AAAGACAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATAAAATA
Found at i:178972 original size:19 final size:18
Alignment explanation
Indices: 178931--178966 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
178921 AAATATTAAA
*
178931 ATAAAATAAAAGACAAAG
1 ATAAAATAAAAAACAAAG
178949 ATAAAATAAATAAACAAA
1 ATAAAATAAA-AAACAAA
178967 TTTAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
ATAAAATAAAAAACAAAG
Found at i:180172 original size:8 final size:7
Alignment explanation
Indices: 180157--180212 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 7
180147 TATCAAGTAT
180157 TATATTA
1 TATATTA
180164 TAGTATTA
1 TA-TATTA
*
180172 T-TATAA
1 TATATTA
180178 TATATTA
1 TATATTA
180185 T-TATTA
1 TATATTA
*
180191 TTTATTA
1 TATATTA
180198 TAGTATTA
1 TA-TATTA
180206 TAGTATT
1 TA-TATT
180213 TTTATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 11 0.26
7 13 0.31
8 18 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:180175 original size:16 final size:16
Alignment explanation
Indices: 180154--180206 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
180144 ACCTATCAAG
180154 TATTATATTATAGTAT
1 TATTATATTATAGTAT
* *
180170 TATTATAATATATTAT
1 TATTATATTATAGTAT
180186 TATTATTTATTATAGTAT
1 TATTA--TATTATAGTAT
180204 TAT
1 TAT
180207 AGTATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 19 0.61
18 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTATATTATAGTAT
Found at i:180196 original size:26 final size:27
Alignment explanation
Indices: 180154--180225 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
180144 ACCTATCAAG
180154 TATTA-TATTATAGTATTATTA-TAATA
1 TATTATTATTATA-TATTATTAGTAATA
* *
180180 TATTATTATTATTTATTA-TAGTATTA
1 TATTATTATTATATATTATTAGTAATA
* *
180206 TAGTATTTTTATATATTATT
1 TATTATTATTATATATTATT
180226 TATTCATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.05
26 29 0.76
27 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TATTATTATTATATATTATTAGTAATA
Found at i:180210 original size:42 final size:45
Alignment explanation
Indices: 180159--180241 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 45
180149 TCAAGTATTA
180159 TATTATAGTATTATTATA-A-TATATTATT-ATT-ATTTATTATAG
1 TATTATAGTATTATTATATATTAT-TTATTCATTCATTTATTATAG
*
180201 TATTATAGTATTTTTATATATTATTTATTCATTCATTTATT
1 TATTATAGTATTATTATATATTATTTATTCATTCATTTATT
180242 TATTTTTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
42 17 0.47
43 6 0.17
44 6 0.17
45 7 0.19
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (45 bp):
TATTATAGTATTATTATATATTATTTATTCATTCATTTATTATAG
Found at i:180226 original size:13 final size:13
Alignment explanation
Indices: 180154--180225 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
180144 ACCTATCAAG
180154 TATTA-TATTATA
1 TATTATTATTATA
*
180166 GTATTATTATAATA
1 -TATTATTATTATA
*
180180 TATTATTATTATT
1 TATTATTATTATA
*
180193 TATTA-TAGTATTA
1 TATTATTATTA-TA
* *
180206 TAGTATTTTTATA
1 TATTATTATTATA
180219 TATTATT
1 TATTATT
180226 TATTCATTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
12 4 0.09
13 34 0.72
14 9 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:184630 original size:29 final size:29
Alignment explanation
Indices: 184587--184669 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
184577 CTCACCTAAC
184587 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
184617 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
184646 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
184670 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:189321 original size:29 final size:29
Alignment explanation
Indices: 189278--189360 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
189268 CTCGTCTAAC
189278 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
189308 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
189337 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
189361 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:190183 original size:18 final size:18
Alignment explanation
Indices: 190161--190203 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
190151 CTTAAAATTA
190161 AATATTATTTTA-AATAAT
1 AATATT-TTTTACAATAAT
*
190179 TATATTTTTTACAATAAT
1 AATATTTTTTACAATAAT
190197 AATATTT
1 AATATTT
190204 CACCTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTTTACAATAAT
Found at i:190886 original size:2 final size:2
Alignment explanation
Indices: 190879--191179 Score: 232
Period size: 2 Copynumber: 162.5 Consensus size: 2
190869 ACACAATTAG
* *
190879 TA TA TA TA -A TA TA TA GTA TA T- TG TA TA T- TA TA GA -A TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
190917 TA TA TA CTA TA TA TA TA TA TA -A TA TG T- TA TA TA T- TA TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
190956 TA T- TA TA GTG TA TA TT TA TA TA T- TA TA T- 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
*
190996 TA T- TA T- TA GT- TA CA TA T- TA T- TA T- TA T- TA TA GTA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
191033 TA TA TC TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- 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
* *
191073 TT TA TA TA GTA TT TA TA TA T- TA T- TA TA T- TA TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191112 GTA TA -A TA TA TA TA TA TA TA TA TA T- TA TA -A 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
*
191152 TA TA TA T- TA TA T- TT TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
191180 TAGTATTGAC
Statistics
Matches: 245, Mismatches: 16, Indels: 76
0.73 0.05 0.23
Matches are distributed among these distances:
1 31 0.13
2 202 0.82
3 12 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:191177 original size:51 final size:51
Alignment explanation
Indices: 190880--191179 Score: 255
Period size: 51 Copynumber: 5.8 Consensus size: 51
190870 CACAATTAGT
* *
190880 ATATATAATATATAGTATATTGTATATTATAGAATATTATATACTATATATATATATA
1 ATATAT-ATATATA-TATA-T-TATATTTTA-TATATTATATA-TATATATAT-TATA
* ** *
190938 ATATGT-TATATATTATATTATTATAGTGTATATT-TATATAT-TATATTAT-
1 ATATATATATATA-TATATTA-TATTTTATATATTATATATATATATATTATA
190987 ATATATATATAT-TATTAGTTACATATTATTAT-TATTATAGTATATATATATCTAT-
1 ATATATATATATATA-TA-TT--ATATT-TTATATATTATA-TATATATATAT-TATA
* *
191042 ATATATATATATATATATTATATATTATATATT-TATATAGTATTTA-TATA
1 ATATATATATATATATATTATATTTTATATATTATATATA-TATATATTATA
* * *
191092 TTAT-TATAT-TATATATTATAGTATA-ATATATATATATATATATATTATA
1 ATATATATATATATATATTATATTTTATATAT-TATATATATATATATTATA
191141 ATATATATATATATATATTATATTTTATATATTATATAT
1 ATATATATATATATATATTATATTTTATATATTATATAT
191180 TAGTATTGAC
Statistics
Matches: 201, Mismatches: 20, Indels: 49
0.74 0.07 0.18
Matches are distributed among these distances:
47 4 0.02
48 21 0.10
49 28 0.14
50 22 0.11
51 44 0.22
52 20 0.10
53 9 0.04
54 14 0.07
55 22 0.11
56 12 0.06
58 5 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (51 bp):
ATATATATATATATATATTATATTTTATATATTATATATATATATATTATA
Found at i:191404 original size:13 final size:13
Alignment explanation
Indices: 191386--191411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191376 GAATTGTTTT
191386 TTAAAATAAAATA
1 TTAAAATAAAATA
191399 TTAAAATAAAATA
1 TTAAAATAAAATA
191412 AAAGACAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATAAAATA
Found at i:191445 original size:19 final size:18
Alignment explanation
Indices: 191404--191439 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
191394 AAATATTAAA
*
191404 ATAAAATAAAAGACAAAG
1 ATAAAATAAAAAACAAAG
191422 ATAAAATAAATAAACAAA
1 ATAAAATAAA-AAACAAA
191440 TTTAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
ATAAAATAAAAAACAAAG
Found at i:192643 original size:13 final size:13
Alignment explanation
Indices: 192625--192680 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
192615 ACACCTATCA
192625 AGTATTATATTAT
1 AGTATTATATTAT
192638 AGTA-T-TATTAT
1 AGTATTATATTAT
192649 A--A-TATATTATT
1 AGTATTATATTA-T
*
192660 ATTATT-TATTAT
1 AGTATTATATTAT
192672 AGTATTATA
1 AGTATTATA
192681 GTATTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
9 2 0.06
10 5 0.14
11 9 0.25
12 7 0.19
13 12 0.33
14 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
AGTATTATATTAT
Found at i:192645 original size:8 final size:7
Alignment explanation
Indices: 192630--192696 Score: 57
Period size: 7 Copynumber: 9.1 Consensus size: 7
192620 TATCAAGTAT
192630 TATATTA
1 TATATTA
192637 TAGTATTA
1 TA-TATTA
*
192645 T-TATAA
1 TATATTA
192651 TATATTA
1 TATATTA
192658 T-TATTA
1 TATATTA
*
192664 TTTATTA
1 TATATTA
192671 TAGTATTA
1 TA-TATTA
192679 TAGTATTTTA
1 TA-TA--TTA
192689 TATATTA
1 TATATTA
192696 T
1 T
192697 TCATTCATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 11 0.22
7 17 0.33
8 16 0.31
9 2 0.04
10 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:193295 original size:130 final size:130
Alignment explanation
Indices: 193043--193286 Score: 294
Period size: 129 Copynumber: 1.9 Consensus size: 130
193033 AACATTAGAG
* * * * *
193043 TTAATATTGAATTTTAGGATAAAATAGTAATATCTCTTCATTTTGATTTGAGTAATAAATGACTG
1 TTAATATTGAATTTTAGGAGAAAATAATAATATCTCTTCATTTTGATTGGAGTAAGAAATGACTA
* ** * **
193108 CTTTAAGATATGAGAGGTTATTTCTTCTTGTCGGAAATAATTGGATATTATTGTTTTCTCACTGA
66 CTTTAAGAGATGAGAGGTTATTTCTTCTAATCAGAAATAATTAAATATTATTGTTTTCTCACTGA
* * * *
193173 TTAATATTTAATTTTAGGAGGAAATAATAATAT-TTTTTATTTTGATTGGAGTAAGAAATGACTA
1 TTAATATTGAATTTTAGGAGAAAATAATAATATCTCTTCATTTTGATTGGAGTAAGAAATGACTA
* * *
193237 CTTTAAGGGATGATAGGTTGTTTCTTCTCAAT-AGAATATAATTAAATATT
66 CTTTAAGAGATGAGAGGTTATTTCTTCT-AATCAGAA-ATAATTAAATATT
193287 TCCTTTTTCC
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
129 53 0.56
130 41 0.44
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (130 bp):
TTAATATTGAATTTTAGGAGAAAATAATAATATCTCTTCATTTTGATTGGAGTAAGAAATGACTA
CTTTAAGAGATGAGAGGTTATTTCTTCTAATCAGAAATAATTAAATATTATTGTTTTCTCACTGA
Found at i:194481 original size:14 final size:14
Alignment explanation
Indices: 194462--194493 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
194452 ACTCCTTTTA
194462 ATTTAATATTATTT
1 ATTTAATATTATTT
*
194476 ATTTAATTTTATTT
1 ATTTAATATTATTT
194490 ATTT
1 ATTT
194494 TTCATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTAATATTATTT
Found at i:194523 original size:5 final size:5
Alignment explanation
Indices: 194473--194538 Score: 62
Period size: 5 Copynumber: 12.6 Consensus size: 5
194463 TTTAATATTA
* *
194473 TTTAT TTAAT TTTA- TTTATT TTTCAT TTTCAT TTTCAT TTTGT TTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTT-AT TTT-AT TTT-AT TTTAT TTTAT
*
194521 TTTAT TTTAT CTTAT TTT
1 TTTAT TTTAT TTTAT TTT
194539 TATTATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
4 4 0.08
5 28 0.54
6 19 0.37
7 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:198473 original size:19 final size:20
Alignment explanation
Indices: 198451--198493 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
198441 ATAATCCTAT
*
198451 TATTT-CAAATTTATTAATA
1 TATTTACAAATATATTAATA
*
198470 TATTTAAGAAATATATTAATA
1 TATTT-ACAAATATATTAATA
198491 TAT
1 TAT
198494 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
21 15 0.75
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTTACAAATATATTAATA
Found at i:198877 original size:15 final size:15
Alignment explanation
Indices: 198850--198881 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
198840 TGACTACATA
198850 ATAATAATTAAATAT
1 ATAATAATTAAATAT
198865 ATAA-AATTAAA-AT
1 ATAATAATTAAATAT
198878 ATAA
1 ATAA
198882 ATAAACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATTAAATAT
Found at i:198881 original size:13 final size:14
Alignment explanation
Indices: 198850--198882 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
198840 TGACTACATA
198850 ATAATAATTAAATAT
1 ATAA-AATTAAATAT
198865 ATAAAATTAAA-AT
1 ATAAAATTAAATAT
198878 ATAAA
1 ATAAA
198883 TAAACAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATTAAATAT
Found at i:200185 original size:5 final size:5
Alignment explanation
Indices: 200177--200237 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 5
200167 CTGAAATATA
* *
200177 AAAAT AAAAAT ATAAT AATAAT AAATAAT AAATAT AATAT AATAAT AAAAT
1 AAAAT -AAAAT AAAAT AA-AAT -AA-AAT AAA-AT AAAAT AA-AAT AAAAT
200228 AAAAT AAAAT
1 AAAAT AAAAT
200238 TAATAGTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
5 23 0.49
6 18 0.38
7 6 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (5 bp):
AAAAT
Found at i:200189 original size:14 final size:14
Alignment explanation
Indices: 200170--200226 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
200160 GTTGGGTCTG
200170 AAATATAAAAATAA
1 AAATATAAAAATAA
*
200184 AAATATAATAATAA
1 AAATATAAAAATAA
*
200198 TAAATA-ATAAAT-A
1 -AAATATAAAAATAA
* *
200211 TAATATAATAATAA
1 AAATATAAAAATAA
200225 AA
1 AA
200227 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 4 0.12
13 5 0.15
14 19 0.58
15 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATATAAAAATAA
Found at i:200196 original size:3 final size:3
Alignment explanation
Indices: 200174--200271 Score: 59
Period size: 3 Copynumber: 34.0 Consensus size: 3
200164 GGTCTGAAAT
* *
200174 ATA AAA ATA AAA AT- ATA ATA ATA ATAA ATA ATA A-A TATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA
* *
200218 ATA ATA A-A ATA A-A ATA A-A ATTA ATA GT- ATAA ATG A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA
*
200260 TTA ATA ATA ATA
1 ATA ATA ATA ATA
200272 TAAAAAACAA
Statistics
Matches: 73, Mismatches: 10, Indels: 24
0.68 0.09 0.22
Matches are distributed among these distances:
2 13 0.18
3 52 0.71
4 8 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:200233 original size:27 final size:27
Alignment explanation
Indices: 200185--200274 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
200175 TAAAAATAAA
*
200185 AATATAATAATAATAA-ATAATAAATAT
1 AATATAATAATAA-AATAAAATAAATAT
200212 AATATAATAATAAAATAAAATAAA-ATT
1 AATATAATAATAAAATAAAATAAATA-T
* * *
200239 AATAGT-ATAAATGAAATAATATTAATAAT
1 AATA-TAAT-AATAAAATAAAATAAAT-AT
200268 AATATAA
1 AATATAA
200275 AAAACAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
26 3 0.06
27 27 0.52
28 15 0.29
29 6 0.12
30 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AATATAATAATAAAATAAAATAAATAT
Found at i:200806 original size:19 final size:20
Alignment explanation
Indices: 200745--200806 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 20
200735 GTTGAACAAG
*
200745 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACGTC
**
200765 TTCTTCCTC-TTCA-G-ACGAG
1 TTCTT-CTCATT-ATGAACGTC
200784 TTCTTCTCATTATGAAC-TC
1 TTCTTCTCATTATGAACGTC
200803 TTCT
1 TTCT
200807 GGAAATGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 11
0.67 0.10 0.23
Matches are distributed among these distances:
18 4 0.12
19 14 0.44
20 10 0.31
21 4 0.12
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (20 bp):
TTCTTCTCATTATGAACGTC
Found at i:201134 original size:122 final size:122
Alignment explanation
Indices: 200868--201318 Score: 565
Period size: 122 Copynumber: 3.8 Consensus size: 122
200858 GATGAATTCA
* * *
200868 AGCAAAAGGTTAAATAAGTTCTTCTCATTCTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAGATGAGTTCTTCT
*
200933 CATTATGAACTCTTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTC-
66 CATTATGAACTC-TTCTGGAAATGTTGATGTT-ATCTATCTCCTTCTGTGATAGAATCG
*
200991 ATGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTC
1 A-GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAGATGAGTTCTTC
*
201054 TCATTATGGACTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTGTGATAGAATCG
65 TCATTATGAACTCTTCTGGAAATGTTGATGTT-ATCTATCTCCTTCTGTGATAGAATCG
* * * *
201113 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTC-TCTTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAGATGAGTTCTTCT
* * * **
201177 CATTATGAACTCTACCTGGCAATG-T--TG--ATCCA--T-C--GAGTGAT-GAATTCG
66 CATTATGAACTCT-TCTGGAAATGTTGATGTTATCTATCTCCTTCTGTGATAGAA-TCG
201225 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTTCTTCAGATGAGTTCTTC
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTC-TCTTCAGATGAGTTCTTC
* *
201289 TCATTATGAACTATTGTTGGAAATGTTGAT
65 TCATTATGAACTCTT-CTGGAAATGTTGAT
201319 CCATTGAATG
Statistics
Matches: 292, Mismatches: 24, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
111 3 0.01
112 46 0.16
113 40 0.14
114 2 0.01
115 1 0.00
116 1 0.00
117 4 0.01
120 2 0.01
121 47 0.16
122 98 0.34
123 46 0.16
124 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (122 bp):
AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAGATGAGTTCTTCT
CATTATGAACTCTTCTGGAAATGTTGATGTTATCTATCTCCTTCTGTGATAGAATCG
Found at i:201176 original size:264 final size:260
Alignment explanation
Indices: 200649--201120 Score: 729
Period size: 264 Copynumber: 1.8 Consensus size: 260
200639 GTTGTTCTCA
200649 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAATATTGATGTTGATCTATCTCCTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAATATTGATGTTGATCTATCTCCTT
200714 CTATGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
66 CTATGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
*
200779 ACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGGCAATG
131 ACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTGG-AAT-
* * ** * * * *
200844 CTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTAAATAAGTTCTTCTCATTCTGAACTTCTTC
194 CAGA--CATCGAGTCAAAAATTCAAGCAAAACGTTAAATAACTTCTTCTCATTCTCAACTACTTC
200909 TTCT
257 TTCT
* *
200913 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCTGGAAATGTTGATGTTGATCTATCTCCT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTAGAAATATTGATGTTGATCTATCTCCT
*
200977 TCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
65 TCTATGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
* *
201042 GATGAGTTCTTCTCATTATGGACTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTGTG-AT
130 GACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTG-GAAT
201106 -AGA-ATCGAG-CAAAAA
194 CAGACATCGAGTCAAAAA
201121 GTTGAACAAG
Statistics
Matches: 196, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
257 3 0.02
258 6 0.03
261 2 0.01
263 2 0.01
264 180 0.92
265 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (260 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAATATTGATGTTGATCTATCTCCTT
CTATGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
ACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTGGAATCA
GACATCGAGTCAAAAATTCAAGCAAAACGTTAAATAACTTCTTCTCATTCTCAACTACTTCTTCT
Found at i:201241 original size:112 final size:113
Alignment explanation
Indices: 201101--201338 Score: 345
Period size: 113 Copynumber: 2.1 Consensus size: 113
201091 ATCTCCTTCT
* * *
201101 GTGATAGAA-TCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTC-TCTTTCTTCA
1 GTGAT-GAATTCGAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
201164 GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGA
65 GATGAGTTCTTCTCATTATGAACTATACCTGGAAATGTTGATCCATCGA
*
201213 GTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCGAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*** *
201278 ATGAGTTCTTCTCATTATGAACTATTGTTGGAAATGTTGATCCATTGA
66 ATGAGTTCTTCTCATTATGAACTATACCTGGAAATGTTGATCCATCGA
* *
201326 ATGATGGATTCGA
1 GTGATGAATTCGA
201339 ATCTTTTCTA
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
111 3 0.03
112 46 0.41
113 63 0.56
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (113 bp):
GTGATGAATTCGAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTATACCTGGAAATGTTGATCCATCGA
Found at i:201923 original size:20 final size:20
Alignment explanation
Indices: 201898--201943 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
201888 ATCGCAACAT
201898 TGGTTCAGCACCATAATTAC
1 TGGTTCAGCACCATAATTAC
201918 TGGTTCAGCACCATAATTAC
1 TGGTTCAGCACCATAATTAC
201938 TGGTTC
1 TGGTTC
201944 GTAAAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
TGGTTCAGCACCATAATTAC
Found at i:202220 original size:18 final size:17
Alignment explanation
Indices: 202199--202240 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
202189 TATATGAAAG
202199 AATAAATTTAATTTCGAA
1 AATAAATTTAATTTC-AA
202217 AATAAATTTAATTTCAA
1 AATAAATTTAATTTCAA
202234 AGATAAA
1 A-ATAAA
202241 CTTGGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (17 bp):
AATAAATTTAATTTCAA
Found at i:210489 original size:15 final size:15
Alignment explanation
Indices: 210462--210493 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
210452 TGACTACATA
210462 ATAATAATTAAATAT
1 ATAATAATTAAATAT
210477 ATAA-AATTAAA-AT
1 ATAATAATTAAATAT
210490 ATAA
1 ATAA
210494 ATAAACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATTAAATAT
Found at i:210493 original size:13 final size:14
Alignment explanation
Indices: 210462--210494 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
210452 TGACTACATA
210462 ATAATAATTAAATAT
1 ATAA-AATTAAATAT
210477 ATAAAATTAAA-AT
1 ATAAAATTAAATAT
210490 ATAAA
1 ATAAA
210495 TAAACAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATTAAATAT
Found at i:211451 original size:3 final size:3
Alignment explanation
Indices: 211443--211526 Score: 52
Period size: 3 Copynumber: 28.3 Consensus size: 3
211433 GAAATGTAAA
* * *
211443 AAT AAT AAT ATT AAT ATT AAT AAAT AAT -AT AAT ATAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* *
211489 AA- AAT AAT AGT -AT AAAT GA- AAT AAT -AT AAAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT A
211527 TAAAAAACAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
2 8 0.13
3 45 0.73
4 9 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:211465 original size:15 final size:14
Alignment explanation
Indices: 211454--211527 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
211444 ATAATAATAT
211454 TAATATTAATA-AA
1 TAATATTAATATAA
211467 TAATA-TAATATATTA
1 TAATATTAATATA--A
* *
211482 TAATAATAAAATAA
1 TAATATTAATATAA
* *
211496 TAGTATAAATGA-AA
1 TAATATTAAT-ATAA
211510 TAATA-TAA-ATAA
1 TAATATTAATATAA
211522 TAATAT
1 TAATAT
211528 AAAAAACAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
11 1 0.02
12 12 0.26
13 8 0.17
14 13 0.28
15 7 0.15
16 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATATTAATATAA
Found at i:211493 original size:26 final size:26
Alignment explanation
Indices: 211444--211523 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
211434 AAATGTAAAA
*
211444 ATAATAATATTAATATTAAT-AAATAAT
1 ATAAT-ATATT-ATAATAATAAAATAAT
211471 ATAATATATTATAATAATAAAATAAT
1 ATAATATATTATAATAATAAAATAAT
* *
211497 AGT-ATAAATGA-AATAATATAAATAAT
1 A-TAATATATTATAATAATA-AAATAAT
211523 A
1 A
211524 ATATAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 14 0.30
26 27 0.57
27 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
ATAATATATTATAATAATAAAATAAT
Found at i:215176 original size:19 final size:19
Alignment explanation
Indices: 215152--215226 Score: 141
Period size: 19 Copynumber: 3.9 Consensus size: 19
215142 ATGACCAACA
215152 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
215171 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
215190 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
215209 AAATCGCAACGCAATCTC
1 AAATCGCAACGCGATCTC
215227 CAGTATCGCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:215296 original size:21 final size:21
Alignment explanation
Indices: 215272--215328 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
215262 ATTTTGACTA
*
215272 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
215293 TCGCGTTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
215314 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
215329 AGAAAATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:215338 original size:21 final size:21
Alignment explanation
Indices: 215271--215345 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
215261 GATTTTGACT
*
215271 ATCGCATTGCGATTTTTCAAA
1 ATCGCATTGCGATTTTACAAA
* * * *
215292 TTCGCGTTGTGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* *
215313 TTCGCATTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
215334 ATCGCAATGCGA
1 ATCGCATTGCGA
215346 ATATGTAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:215377 original size:20 final size:20
Alignment explanation
Indices: 215354--215439 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
215344 GAATATGTAA
215354 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
215374 ATCGCAACGCGA-T-AAACAT
1 ATCGCAACGCGATTCTGAC-T
*
215393 AATCGCAACTCGATTC-GACT
1 -ATCGCAACGCGATTCTGACT
215413 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
215433 GTCGCAA
1 ATCGCAA
215440 TGCTGAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 16 0.29
20 34 0.62
21 3 0.05
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:216507 original size:14 final size:13
Alignment explanation
Indices: 216488--216522 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
216478 CGAAAAAGAA
216488 GAAGAAAAATCCCC
1 GAAGAAAAAT-CCC
*
216502 GAAGAAAAGTCCC
1 GAAGAAAAATCCC
216515 GAAGAAAA
1 GAAGAAAA
216523 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.54, C:0.20, G:0.20, T:0.06
Consensus pattern (13 bp):
GAAGAAAAATCCC
Found at i:218535 original size:11 final size:11
Alignment explanation
Indices: 218519--218543 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
218509 TGGTGTCAAA
218519 AAAAGGCAATC
1 AAAAGGCAATC
218530 AAAAGGCAATC
1 AAAAGGCAATC
218541 AAA
1 AAA
218544 TCAAAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAGGCAATC
Found at i:218875 original size:20 final size:20
Alignment explanation
Indices: 218850--218998 Score: 157
Period size: 20 Copynumber: 7.8 Consensus size: 20
218840 TTACACATTC
* *
218850 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
218870 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
218890 ATTTGACTATCGGAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
218910 ATATGACTATCGTAACGC-A
1 ATTTGACTATCGCAACGCGA
*
218929 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
218944 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* ** *
218964 ATTTGATTATTACAACGGGA
1 ATTTGACTATCGCAACGCGA
218984 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
218999 TGAGAAAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.08
15 3 0.03
19 3 0.03
20 92 0.86
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:218991 original size:74 final size:74
Alignment explanation
Indices: 218858--219049 Score: 217
Period size: 74 Copynumber: 2.6 Consensus size: 74
218848 TCATTTGAAT
* ** *
218858 ATCGCAATGCGAATTTGACTATCGCAACGCGAATTTGACTATCGGAACGCGAATATGACTATCGT
1 ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATATGACTATCGC
218923 AACGCA-AAA
66 AACG-AGAAA
* * * * * *
218932 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATTACAACGGGAATTTGACTATCGC
1 ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATATGACTATCGC
*
218997 AATGAGAAA
66 AACGAGAAA
* * * * *
219006 ATTGCAAATCGTATTAGACTATCGCAACGCGAA-TTGACTTTCAC
1 ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCAC
219050 GTTGCGATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
73 9 0.09
74 89 0.91
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (74 bp):
ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATATGACTATCGC
AACGAGAAA
Found at i:219078 original size:20 final size:20
Alignment explanation
Indices: 219039--219116 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
219029 GCAACGCGAA
* *
219039 TTGACTTTCACGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
219059 TT-AGCTTTCGCATTGTGATT
1 TTGA-CTTTCGCATTGCGATT
219079 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
219099 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
219117 AAGTGTACCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:220688 original size:21 final size:21
Alignment explanation
Indices: 220628--220745 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
220618 GTGAATCGGG
* * * *
220628 CTCTTGAATGGTGGGAGAGAC
1 CTCTTGAACGATGGGAGGGGC
* * **
220649 CTCTTCAACAATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
220670 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** **
220691 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
220712 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
220733 CTCTTGAACGATG
1 CTCTTGAACGATG
220746 AAAGGTGAGT
Statistics
Matches: 72, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:220695 original size:42 final size:42
Alignment explanation
Indices: 220641--220746 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
220631 TTGAATGGTG
* * *
220641 GGAGA-GACCTCTTCAACAATGACAGGGGCCTCTTGAACGATG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** *
220683 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
220725 GGAGAGGCCTCTTGAACGATGA
1 GGAGAGGACTCTTGAACGATGA
220747 AAGGTGAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 50 0.96
43 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:222721 original size:31 final size:31
Alignment explanation
Indices: 222678--222744 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
222668 ATAATTATTT
* * *
222678 ATAGTGGTGTTTTATCAACAAACTCCGTAAA
1 ATAGTGGCGTTTTATCAACAAACGCCATAAA
*
222709 ATAGTGGCGTTTTATCAATAAACGCCATAAA
1 ATAGTGGCGTTTTATCAACAAACGCCATAAA
222740 ATAGT
1 ATAGT
222745 AGTACTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (31 bp):
ATAGTGGCGTTTTATCAACAAACGCCATAAA
Found at i:223462 original size:22 final size:22
Alignment explanation
Indices: 223432--223473 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
223422 GTTTTTCTAC
223432 TTTCAAATA-GAAAAGTAATAGT
1 TTTCAAATAGGAAAA-TAATAGT
*
223454 TTTCGAATAGGAAAATAATA
1 TTTCAAATAGGAAAATAATA
223474 CCTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (22 bp):
TTTCAAATAGGAAAATAATAGT
Found at i:223479 original size:23 final size:22
Alignment explanation
Indices: 223432--223479 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
223422 GTTTTTCTAC
*
223432 TTTCAAATAGAAAAGTAATAGT
1 TTTCAAATAGAAAAGTAATACT
*
223454 TTTCGAATAGGAAAA-TAATACCT
1 TTTCAAATA-GAAAAGTAATA-CT
223477 TTT
1 TTT
223480 GAAAACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
TTTCAAATAGAAAAGTAATACT
Found at i:233488 original size:28 final size:28
Alignment explanation
Indices: 233448--233501 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
233438 ATGAAAACTT
*
233448 TTGTTCATTATATTG-GATTTGATGTTGC
1 TTGTTCATTATATAGAG-TTTGATGTTGC
233476 TTGTT-ATTGATATAGAGTTTGATGTT
1 TTGTTCATT-ATATAGAGTTTGATGTT
233502 ATGTCTGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 3 0.13
28 19 0.83
29 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.54
Consensus pattern (28 bp):
TTGTTCATTATATAGAGTTTGATGTTGC
Found at i:233788 original size:44 final size:44
Alignment explanation
Indices: 233679--234000 Score: 425
Period size: 44 Copynumber: 7.4 Consensus size: 44
233669 AAATATTAAC
* *
233679 ACCTATTGCGGCGTTTGTAT-C-AAGAAATGCCGCTATATACCA-
1 ACCTATAGCGGCGTTTGTATCCTAA-AAACGCCGCTATATACCAG
* * * *
233721 ACTTTTAGCGGCGTTTGTATCCTAAAAATGCCTCTATATACCAG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
* *
233765 ACCTATAGCGACGTTTGTGTCCTAAAAACGCCGCTATATACCAG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
* *
233809 ACCTATAGCGGCGTTTGTATCCTAAAAACACCGTTATATACCAG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
* * * * * *
233853 ACCCATAGCAGTGTTTATATCCTAAAAACGCTGCTATATACCAA
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
*
233897 ACCTATAGCGGTGTTTGTATCCTAAAAACGCCGCTATATACCAG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
** *
233941 ACCTATAGCGGCGTTTGTATCCTAAAAATACCGCTAAATACCAG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
*
233985 ACCTATTGCGGCGTTT
1 ACCTATAGCGGCGTTT
234001 TCATAAAAAA
Statistics
Matches: 245, Mismatches: 32, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
42 17 0.07
43 18 0.07
44 210 0.86
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
Found at i:234012 original size:44 final size:44
Alignment explanation
Indices: 233642--234056 Score: 185
Period size: 44 Copynumber: 9.4 Consensus size: 44
233632 ATACATTTAA
* * * ** *
233642 CGGCGTTTGTATCAAAAAAACACCGCGAAATATTAACACCTATTG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATA-CCAGACCTATTG
* * * * *
233687 CGGCGTTTGTAT-CAAGAAATGCCGCTATATACCA-A-CTTTTAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATT-G
*** * * * *
233729 CGGCGTTTGTATCCTAAAAATGCCTCTATATACCAGACCTATAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
* * *** ** * *
233773 CGACGTTTGTGTCCTAAAAACGCCGCTATATACCAGACCTATAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
*** * * * * *
233817 CGGCGTTTGTATCCTAAAAACACCGTTATATACCAGACCCATAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
* * * *** ** * * * *
233861 CAGTGTTTATATCCTAAAAACGCTGCTATATACCAAACCTATAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
* *** ** * *
233905 CGGTGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATAG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
***
233949 CGGCGTTTGTATCCTAAAAATACCGCTAAATACCAGACCTATTG
1 CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
*
233993 CGGCGTTT-TCATAAAAAAAAATACCGCGAAAT-CTCA-ACACTTATTG
1 CGGCGTTTGT-AT-AAAAAAAATACCGCTAAATAC-CAGAC-C-TATTG
234039 CGGCGTTTGTGATAAAAA
1 CGGCGTTTGT-ATAAAAA
234057 CGCCACTAAA
Statistics
Matches: 315, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.01
42 14 0.04
43 21 0.07
44 222 0.70
45 33 0.10
46 18 0.06
47 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (44 bp):
CGGCGTTTGTATAAAAAAAATACCGCTAAATACCAGACCTATTG
Found at i:234055 original size:132 final size:130
Alignment explanation
Indices: 233758--234060 Score: 317
Period size: 132 Copynumber: 2.3 Consensus size: 130
233748 ATGCCTCTAT
* * *
233758 ATACCAGACCTATAGCGACGTTTGTGTCCTAAAAACGCCGCTATATACCAGACCTATAGCGGCGT
1 ATACCAAACCTATAGCGGCG-TT-TGTACTAAAAACGCCGCTATATACCAGACCTATAGCGGCGT
* * * **** *
233823 TTGTATCCTAAAAACACCGTTATATACCAGACCCATAGCAGTGTTTATATCCTAAAAACGCTGCT
64 TTGTATCCTAAAAACACCGCTAAATACCAGACCCATAGCAGCGTTTATAAAAAAAAAACGCTGCG
*
233888 AT
129 AA
*
233890 ATACCAAACCTATAGCGGTGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATAGCGGCGT
1 ATACCAAACCTATAGCGGCGTTTGTA--CTAAAAACGCCGCTATATACCAGACCTATAGCGGCGT
* * * *
233955 TTGTATCCTAAAAATACCGCTAAATACCAGACCTATTGCGGCGTTTTCATAAAAAAAAATAC-C-
64 TTGTATCCTAAAAACACCGCTAAATACCAGACCCATAGCAGCG-TTT-ATAAAAAAAAA-ACGCT
234018 GCGAA
126 GCGAA
* *
234023 AT-CTCAACACTTATTGCGGCGTTTGTGA-TAAAAACGCC
1 ATAC-CAA-ACCTATAGCGGCGTTTGT-ACTAAAAACGCC
234061 ACTAAATATT
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
130 3 0.02
131 2 0.01
132 101 0.71
133 11 0.08
134 23 0.16
135 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (130 bp):
ATACCAAACCTATAGCGGCGTTTGTACTAAAAACGCCGCTATATACCAGACCTATAGCGGCGTTT
GTATCCTAAAAACACCGCTAAATACCAGACCCATAGCAGCGTTTATAAAAAAAAAACGCTGCGAA
Found at i:234081 original size:43 final size:43
Alignment explanation
Indices: 234021--234133 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
234011 AAATACCGCG
* * * *
234021 AAATCTCAACACTTATTGCGGCGTTTGTGATAAAAACGCCACT
1 AAATATCAACACCTATTGCGGCGTTTGTAAGAAAAACGCCACT
* * * *
234064 AAATATTAACACCTATTGCGGCGTTTTTAAGACAAACGCCGCT
1 AAATATCAACACCTATTGCGGCGTTTGTAAGAAAAACGCCACT
** *
234107 AAATATCAGTACCTATTGCGGTGTTTG
1 AAATATCAACACCTATTGCGGCGTTTG
234134 CGGCGTTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
AAATATCAACACCTATTGCGGCGTTTGTAAGAAAAACGCCACT
Found at i:237221 original size:11 final size:11
Alignment explanation
Indices: 237205--237236 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
237195 GCTAAGCATT
237205 CATACGCAGTG
1 CATACGCAGTG
*
237216 CATACGTAGTG
1 CATACGCAGTG
237227 CATACGCAGT
1 CATACGCAGT
237237 ACGGGCACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (11 bp):
CATACGCAGTG
Done.