Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011701.1 Kokia drynarioides strain JFW-HI SEQ_126695, 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: 550108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:11116 original size:21 final size:21
Alignment explanation
Indices: 11090--11137 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
11080 GACTTGAGTT
11090 GTATCGGTAGATACATGATAA
1 GTATCGGTAGATACATGATAA
*
11111 GTATCGGTAGATGCATGATAA
1 GTATCGGTAGATACATGATAA
11132 GTATCG
1 GTATCG
11138 ATAGTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGATACATGATAA
Found at i:19671 original size:37 final size:37
Alignment explanation
Indices: 19630--19702 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
19620 GCTGTCGCCG
**
19630 CATGAGCACTTTTAGAATGCACCCAAAACTGTCACTA
1 CATGAGCACTTCCAGAATGCACCCAAAACTGTCACTA
* *
19667 CATGAGCACTTCCAGATTGTACCCAAAACTGTCACT
1 CATGAGCACTTCCAGAATGCACCCAAAACTGTCACT
19703 GCAGGAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.25
Consensus pattern (37 bp):
CATGAGCACTTCCAGAATGCACCCAAAACTGTCACTA
Found at i:19743 original size:38 final size:38
Alignment explanation
Indices: 19682--19799 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 38
19672 GCACTTCCAG
* * * *
19682 ATTGTACCCAAAACTGTCACTGCAGGAATATT-TTCAA
1 ATTGCACCTAAAACTGTCGCTGCAGAAATATTCTTCAA
*
19719 ATTTGCACCTAAAACTGTCGCTGCATAAATATTCTTCAA
1 A-TTGCACCTAAAACTGTCGCTGCAGAAATATTCTTCAA
* * * * *
19758 ATTGCATCTAGAACTATCGCTGCATAAGTATTCTT-AA
1 ATTGCACCTAAAACTGTCGCTGCAGAAATATTCTTCAA
19795 ATTGC
1 ATTGC
19800 TCCCAAGAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 8 0.11
38 56 0.80
39 6 0.09
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (38 bp):
ATTGCACCTAAAACTGTCGCTGCAGAAATATTCTTCAA
Found at i:22274 original size:12 final size:11
Alignment explanation
Indices: 22255--22300 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
22245 TGGCAATATA
22255 TTTCTTTTCTT
1 TTTCTTTTCTT
22266 TTATCTTTTCTT
1 TT-TCTTTTCTT
*
22278 CTTC-TTTCTT
1 TTTCTTTTCTT
*
22288 TTT-ATTTCTT
1 TTTCTTTTCTT
22298 TTT
1 TTT
22301 GTGATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 17 0.55
11 4 0.13
12 10 0.32
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:35270 original size:15 final size:15
Alignment explanation
Indices: 35250--35283 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35240 AGTAGAAATA
35250 AAAACAAAAAAAGAC
1 AAAACAAAAAAAGAC
* *
35265 AAAACAAATAATGAC
1 AAAACAAAAAAAGAC
35280 AAAA
1 AAAA
35284 AATTCCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAACAAAAAAAGAC
Found at i:47385 original size:12 final size:12
Alignment explanation
Indices: 47370--47394 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47360 TTGTTTGTGT
47370 CTCTTGTTGTAC
1 CTCTTGTTGTAC
47382 CTCTTGTTGTAC
1 CTCTTGTTGTAC
47394 C
1 C
47395 GGTGTGTCTC
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:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (12 bp):
CTCTTGTTGTAC
Found at i:55896 original size:18 final size:18
Alignment explanation
Indices: 55873--55907 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55863 AATTCATATT
55873 ACTTTCAATTCCAATTTC
1 ACTTTCAATTCCAATTTC
* *
55891 ACTTTCACTTTCAATTT
1 ACTTTCAATTCCAATTT
55908 TGATCACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTC
Found at i:62430 original size:23 final size:23
Alignment explanation
Indices: 62380--62430 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
62370 TTGATTGTGC
*
62380 ATTTAGGAATAGAATTTGGTTTT
1 ATTTTGGAATAGAATTTGGTTTT
*
62403 ATTTTGGAATAGGATTTGGTTTT
1 ATTTTGGAATAGAATTTGGTTTT
*
62426 CTTTT
1 ATTTT
62431 TATTTTCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.53
Consensus pattern (23 bp):
ATTTTGGAATAGAATTTGGTTTT
Found at i:63234 original size:31 final size:31
Alignment explanation
Indices: 63196--63258 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
63186 TGTCTCTCCC
63196 ATTGGTTACTTCCTTATAACTTGAGTAAAAA
1 ATTGGTTACTTCCTTATAACTTGAGTAAAAA
** *
63227 ATTGGTTACTTCCTTATGGCTTGAGTCAAAA
1 ATTGGTTACTTCCTTATAACTTGAGTAAAAA
63258 A
1 A
63259 GGTCAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (31 bp):
ATTGGTTACTTCCTTATAACTTGAGTAAAAA
Found at i:67372 original size:62 final size:63
Alignment explanation
Indices: 67282--67411 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 63
67272 CGAGGTTGGT
* * * *
67282 TTCAATTCGCATTTGATAACTCACGATGACACGGAGTCATC-AGACCT-TTAATTCGTAATAGGA
1 TTCAATTCGCATTTAATAACTCACGATGACACAGAGTCATCGA-ACCTCATAATCCGTAA-AGGA
* * * *
67345 TTCATTTCTCATTTAAT-ACTCATGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
1 TTCAATTCGCATTTAATAACTCACGATGACACAGAGTCATCGAACCTCATAATCCGTAAAGGA
67407 TTCAA
1 TTCAA
67412 ATACTCACGA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
62 32 0.57
63 24 0.43
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (63 bp):
TTCAATTCGCATTTAATAACTCACGATGACACAGAGTCATCGAACCTCATAATCCGTAAAGGA
Found at i:67437 original size:52 final size:52
Alignment explanation
Indices: 67360--67651 Score: 397
Period size: 52 Copynumber: 5.6 Consensus size: 52
67350 TTCTCATTTA
* * *
67360 ATACTCATGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAA
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCAT
* *
67412 ATACTCACGATGACACATAATCATCGGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCAT
* * *
67464 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTACAAGATTCGT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCAT
* * * *
67516 ATACTCACAATGACACATAGTCATCAAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCAT
* *
67568 ATACTCACGATGACATATAGTCATCGAAACTCGA-AATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTC-ATAATCCGTAAAAGATTCAT
** * *
67620 ATAACTCACGGCGACACAGAGTCATCAAACCT
1 AT-ACTCACGATGACACATAGTCATCGAACCT
67652 TTTGCATTTA
Statistics
Matches: 211, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
52 187 0.89
53 24 0.11
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCAT
Found at i:71445 original size:54 final size:55
Alignment explanation
Indices: 71349--71454 Score: 123
Period size: 54 Copynumber: 1.9 Consensus size: 55
71339 CAAACAGAAA
*
71349 AAAAAAAGTTTAAACCTCAATATGAAAACAATTGTCAAATTT-AAGAACTAACTTG
1 AAAAAAAGTTTAAACCTCAATATGAAAACAATTATCAAATTTAAAG-ACTAACTTG
*
71404 AAAAAAAG-TTAAA-TTCTAATAT-AAGAACAATTAT-AATATTTAAAGACTAAC
1 AAAAAAAGTTTAAACCTC-AATATGAA-AACAATTATCAA-ATTTAAAGACTAAC
71455 GTTAACAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
53 6 0.13
54 28 0.62
55 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (55 bp):
AAAAAAAGTTTAAACCTCAATATGAAAACAATTATCAAATTTAAAGACTAACTTG
Found at i:76206 original size:28 final size:28
Alignment explanation
Indices: 76166--76306 Score: 133
Period size: 28 Copynumber: 5.1 Consensus size: 28
76156 GCTAGAAGTG
* *
76166 AAATGAAAGTCTTTGTGGCGAACGTCTA
1 AAATGAAAGCCTTTGTGGCGAACCTCTA
* * *
76194 AAATGAAAGTCTTTGTGACGAACCTTTA
1 AAATGAAAGCCTTTGTGGCGAACCTCTA
* *
76222 AAAGGAAAGCCTTTGTGGCAAACCTCTGA
1 AAATGAAAGCCTTTGTGGCGAACCTCT-A
* *
76251 AAA-GAAAGCCCTTGTGGCGAATCTCTA
1 AAATGAAAGCCTTTGTGGCGAACCTCTA
* * * * *
76278 AAAGGAAGGCCTATATGGTGAA-CTCTA
1 AAATGAAAGCCTTTGTGGCGAACCTCTA
76305 AA
1 AA
76307 GAATATTAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.12
28 80 0.84
29 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (28 bp):
AAATGAAAGCCTTTGTGGCGAACCTCTA
Found at i:82888 original size:15 final size:16
Alignment explanation
Indices: 82870--82907 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
82860 AAAGGGAGTA
82870 GAAGAAAAACAAAAG-
1 GAAGAAAAACAAAAGT
* *
82885 GAAGAAAAAGAAACGT
1 GAAGAAAAACAAAAGT
82901 GAAGAAA
1 GAAGAAA
82908 GTGAGGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (16 bp):
GAAGAAAAACAAAAGT
Found at i:97571 original size:3 final size:3
Alignment explanation
Indices: 97549--97617 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
97539 CCTCGGTAGG
* * *
97549 TTC TTT TTC TTC TT- TCTC TTC TTCC TT- TCC TTG TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC T-TC TTC TT-C TTC TTC TTC TTC TTC TTC TTC
* *
97594 TTG TTCC TTG TTC TTC TTC TTC TT
1 TTC TT-C TTC TTC TTC TTC TTC TT
97618 AATCCTTCCC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:97603 original size:22 final size:21
Alignment explanation
Indices: 97565--97617 Score: 88
Period size: 22 Copynumber: 2.5 Consensus size: 21
97555 TTCTTCTTTC
*
97565 TCTTCTTCCTTTCCTTGTTCT
1 TCTTCTTCTTTTCCTTGTTCT
97586 TCTTCTTCTTGTTCCTTGTTCT
1 TCTTCTTCTT-TTCCTTGTTCT
97608 TCTTCTTCTT
1 TCTTCTTCTT
97618 AATCCTTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.00, C:0.30, G:0.06, T:0.64
Consensus pattern (21 bp):
TCTTCTTCTTTTCCTTGTTCT
Found at i:97623 original size:22 final size:22
Alignment explanation
Indices: 97576--97624 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
97566 CTTCTTCCTT
**
97576 TCCTTGTTCTTCTTCTTCTTGT
1 TCCTTGTTCTTCTTCTTCTTAA
97598 TCCTTGTTCTTCTTCTTCTTAA
1 TCCTTGTTCTTCTTCTTCTTAA
97620 TCCTT
1 TCCTT
97625 CCCCTTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.04, C:0.29, G:0.06, T:0.61
Consensus pattern (22 bp):
TCCTTGTTCTTCTTCTTCTTAA
Found at i:108254 original size:27 final size:27
Alignment explanation
Indices: 108212--108266 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
108202 TGGTATAAAG
* *
108212 AAAGCTATGTGTGATTTAAGAGCATCC
1 AAAGCCATGTGCGATTTAAGAGCATCC
108239 AAAGCCATGTGCGATTTAAGAGCATCC
1 AAAGCCATGTGCGATTTAAGAGCATCC
108266 A
1 A
108267 TTAATGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
AAAGCCATGTGCGATTTAAGAGCATCC
Found at i:114611 original size:16 final size:17
Alignment explanation
Indices: 114587--114619 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
114577 AGCAATTTTA
114587 TTCTCTTTTTCTTTTCT
1 TTCTCTTTTTCTTTTCT
*
114604 TTCT-TTTTTTTTTTCT
1 TTCTCTTTTTCTTTTCT
114620 CATTTTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTCTCTTTTTCTTTTCT
Found at i:121946 original size:18 final size:18
Alignment explanation
Indices: 121913--121948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
121903 TTGCAAGCTT
*
121913 GATTGTGGTAGTAATTGA
1 GATTGTGGTAGCAATTGA
*
121931 GATTGTGGTTGCAATTGA
1 GATTGTGGTAGCAATTGA
121949 CTATGTGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.39
Consensus pattern (18 bp):
GATTGTGGTAGCAATTGA
Found at i:124072 original size:34 final size:34
Alignment explanation
Indices: 124029--124130 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
124019 GCAATGTAAA
124029 GTAAGAATCAAAATGATATAACATTAAAAGATAC
1 GTAAGAATCAAAATGATATAACATTAAAAGATAC
124063 GTAAGAATCAAAATGATATAACATTAAAAGATAC
1 GTAAGAATCAAAATGATATAACATTAAAAGATAC
124097 GTAAGAATCAAAATGATATAACATTAAAAGATAC
1 GTAAGAATCAAAATGATATAACATTAAAAGATAC
124131 TATCGTATTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (34 bp):
GTAAGAATCAAAATGATATAACATTAAAAGATAC
Found at i:130359 original size:5 final size:5
Alignment explanation
Indices: 130349--130393 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
130339 TTGCAACAAA
* * *
130349 ATTTT ATTTT ACTTT ATTTT ATTTT ATTTT GTTTT GTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
130394 TAGTTTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:134304 original size:201 final size:198
Alignment explanation
Indices: 133992--134414 Score: 522
Period size: 201 Copynumber: 2.1 Consensus size: 198
133982 ATCGAGCACT
* * * * * *
133992 ATTTATTTTAAATGAAACTAGACTTCTGTACGATTATATAGATAGAAGGTTCGCTTCCTATTTTA
1 ATTTATTCTAAACGAAACTAGACTTCTGTACGATTATAGAGATAGAAGGCTCACTTCCTATTTAA
* * * * * * * *
134057 TCTTTTGTAATTTTTGGTGATTTTTCAAAGTCATTACTAAATCTGTTATATAATAATTCTGCTGC
66 TCTTGTGCAATTTTTAGTGATTTGTCAAAATCAATACTAAATCTGTTATATAAGAACTCTGCTGC
* * * **
134122 CAGATTTTTTTGACCTTTCAACATTAAAAAATTCATATATATTTTAAACTGCAAATCAAAAATAA
131 CAGATTTTTATGACCTTTCAACACTAAAAAATTC--ATATATTTCAAACCACAAATC-AAAATAA
134187 ATCTCC
193 ATCTCC
* * * * * *
134193 GTTTATTCTAAACGAAACTAGACTTTTGTATGGTTATAGGGATATAAGGCTCACTTCCTATTTAA
1 ATTTATTCTAAACGAAACTAGACTTCTGTACGATTATAGAGATAGAAGGCTCACTTCCTATTTAA
* *
134258 TCTTGTGCAGTTTTTAGTGATTTGTCAAAATCAATACTAAATCTGTTTTATAAGAACTCTGCTGC
66 TCTTGTGCAATTTTTAGTGATTTGTCAAAATCAATACTAAATCTGTTATATAAGAACTCTGCTGC
* * *
134323 TAGATTTTTATGACCTTTCAACACTAAAAAATTCATATATTTCAAACCATAAATCAAAATCAATC
131 CAGATTTTTATGACCTTTCAACACTAAAAAATTCATATATTTCAAACCACAAATCAAAATAAATC
*
134388 TCT
196 TCC
* *
134391 ATTTCTTCTAAACAAAACTAGACT
1 ATTTATTCTAAACGAAACTAGACT
134415 GACTCATAGT
Statistics
Matches: 188, Mismatches: 34, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
198 32 0.17
199 17 0.09
201 139 0.74
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (198 bp):
ATTTATTCTAAACGAAACTAGACTTCTGTACGATTATAGAGATAGAAGGCTCACTTCCTATTTAA
TCTTGTGCAATTTTTAGTGATTTGTCAAAATCAATACTAAATCTGTTATATAAGAACTCTGCTGC
CAGATTTTTATGACCTTTCAACACTAAAAAATTCATATATTTCAAACCACAAATCAAAATAAATC
TCC
Found at i:141005 original size:21 final size:21
Alignment explanation
Indices: 140979--141031 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
140969 TAGTACAGAT
* *
140979 TTCTATCGATACAAGTGA-TAG
1 TTCTATCGATACAAGAGACT-C
141000 TTCTATCGATACAAGAGACTC
1 TTCTATCGATACAAGAGACTC
141021 TTCTATCGATA
1 TTCTATCGATA
141032 TAGGTTTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCTATCGATACAAGAGACTC
Found at i:141923 original size:52 final size:52
Alignment explanation
Indices: 141827--142109 Score: 424
Period size: 52 Copynumber: 5.4 Consensus size: 52
141817 TGATATTCAT
* * ** * *
141827 GATGACACAGAGTCATCGGACC-CTTAATCCGTATTGAAAATCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAG-GATTCATATACTCAC
*
141879 GATGACACATAGTCATCGGACCTCATAATCCGTAAATGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
*
141931 GATGACACATAGTCATCGGACCTCATAATCCGTAGAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* ** * *
141983 GATGACACATAATCATCAAACCTCATAATCCATAAAGGATTTATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
*
142035 GATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
142087 GATGACACATAGTCATCGGACCT
1 GATGACACATAGTCATCGGACCT
142110 ATTTCATTCA
Statistics
Matches: 208, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 198 0.95
53 10 0.05
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (52 bp):
GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
Found at i:160659 original size:7 final size:6
Alignment explanation
Indices: 160637--160670 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
160627 CAACAATTTA
160637 TTCTTT TTCTTT TTCTTT CTTCTTT TCTCTTT TT
1 TTCTTT TTCTTT TTCTTT -TTCTTT T-TCTTT TT
160671 TTTGCTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:166189 original size:33 final size:33
Alignment explanation
Indices: 166145--166210 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
166135 AATAAGGATT
* *
166145 AAGGAGTGCTGACTTAACAGATGCAGCTTGTTC
1 AAGGAGAGCTGACTTAACAAATGCAGCTTGTTC
*
166178 AAGGAGAGCTGACTTAACAAATGCAGTTTGTTC
1 AAGGAGAGCTGACTTAACAAATGCAGCTTGTTC
166211 TAAAACATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (33 bp):
AAGGAGAGCTGACTTAACAAATGCAGCTTGTTC
Found at i:171146 original size:21 final size:21
Alignment explanation
Indices: 171122--171161 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
171112 GAGAAGGAAA
171122 CTGAGAAGGA-ACAGTCTGAAT
1 CTGA-AAGGATACAGTCTGAAT
*
171143 CTGAAAGGATAGAGTCTGA
1 CTGAAAGGATACAGTCTGA
171162 TAATGCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (21 bp):
CTGAAAGGATACAGTCTGAAT
Found at i:172438 original size:24 final size:25
Alignment explanation
Indices: 172378--172442 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
172368 TACATTATAA
172378 TCACTTTATTTTTCCTTCTTTTTCT
1 TCACTTTATTTTTCCTTCTTTTTCT
* *
172403 TCATTTTGTTTTT-CTT-TTCTTTCT
1 TCACTTTATTTTTCCTTCTT-TTTCT
*
172427 TCCCTTTA-TTTTCCTT
1 TCACTTTATTTTTCCTT
172443 AGCAAGCCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 6 0.18
24 16 0.48
25 11 0.33
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.69
Consensus pattern (25 bp):
TCACTTTATTTTTCCTTCTTTTTCT
Found at i:172954 original size:17 final size:17
Alignment explanation
Indices: 172919--172954 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
172909 TGTATTTTAT
172919 TTGTTCTAGCATTTGCA
1 TTGTTCTAGCATTTGCA
* *
172936 TTGTTGTAGCATTTTCA
1 TTGTTCTAGCATTTGCA
172953 TT
1 TT
172955 ATTATTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (17 bp):
TTGTTCTAGCATTTGCA
Found at i:173923 original size:20 final size:21
Alignment explanation
Indices: 173900--173939 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
173890 GCATATATTT
*
173900 TTTGCATTTTGT-ACTTAGTA
1 TTTGCATTTTCTAACTTAGTA
173920 TTTGCATTTTCTAACTTAGT
1 TTTGCATTTTCTAACTTAGT
173940 GTTGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTGCATTTTCTAACTTAGTA
Found at i:176336 original size:52 final size:51
Alignment explanation
Indices: 176260--176469 Score: 208
Period size: 52 Copynumber: 4.1 Consensus size: 51
176250 TTGACTTTGT
* * * * *
176260 TGAGTATATAAATCAATTAAGGATTATGAGGTACGATGATTATTTGTCATCG
1 TGAGTATATGAATCATTTACGGATTATGAGGTCCGATGA-TATGTGTCATCG
* * * *
176312 TGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGA-CTGTGTCATCA
1 TGAGTATATGAATCATTTACGGATTATGAGGTCCGATGATATGTGTCATCG
*
176362 TGAGTATATGAATCATTTACGAATTATGAGGTCCGATGACTATGTGTCATCG
1 TGAGTATATGAATCATTTACGGATTATGAGGTCCGATGA-TATGTGTCATCG
* * * * * * * *
176414 TAAGTATATGATTCCTAATACAGATTAAG-GGTCCAATGACTCTGTGTCATCG
1 TGAGTATATGAATCAT-TTACGGATTATGAGGTCCGATGA-TATGTGTCATCG
176466 TGAG
1 TGAG
176470 CATTAAAAGT
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
50 44 0.34
52 79 0.60
53 8 0.06
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (51 bp):
TGAGTATATGAATCATTTACGGATTATGAGGTCCGATGATATGTGTCATCG
Found at i:176372 original size:50 final size:50
Alignment explanation
Indices: 176304--176469 Score: 199
Period size: 50 Copynumber: 3.2 Consensus size: 50
176294 GATGATTATT
176304 TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGACTG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGACTG
* * * *
176354 TGTCATCATGAGTATATGAATCATTTACGAATTATGAGGTCCGATGACTATG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGAC--TG
* * * * *
176406 TGTCATCGTAAGTATATGATTCCTAATACAGATTAAG-GGTCCAATGACTCTG
1 TGTCATCGTGAGTATATGAATCCT-TTACGGATTATGAGGTCCAATGA--CTG
176458 TGTCATCGTGAG
1 TGTCATCGTGAG
176470 CATTAAAAGT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
50 44 0.45
52 44 0.45
53 8 0.08
54 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (50 bp):
TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGACTG
Found at i:176447 original size:102 final size:103
Alignment explanation
Indices: 176260--176469 Score: 271
Period size: 102 Copynumber: 2.0 Consensus size: 103
176250 TTGACTTTGT
* * * *
176260 TGAGTATATAAATCAATTAAGGATTATGAGGTACGATGATTATTTGTCATCGTGAGTATATGAAT
1 TGAGTATATAAATCAATTAAGAATTATGAGGTACGATGACTATGTGTCATCGTAAGTATATGAAT
* * *
176325 CCTTTACGGATTATGAGGTCCAATGA-CTGTGTCATCA
66 CCTATACAGATTAAGAGGTCCAATGACCTGTGTCATCA
* * * * *
176362 TGAGTATATGAATCATTTACGAATTATGAGGTCCGATGACTATGTGTCATCGTAAGTATATGATT
1 TGAGTATATAAATCAATTAAGAATTATGAGGTACGATGACTATGTGTCATCGTAAGTATATGAAT
*
176427 CCTAATACAGATTAAG-GGTCCAATGACTCTGTGTCATCG
66 CCT-ATACAGATTAAGAGGTCCAATGAC-CTGTGTCATCA
176466 TGAG
1 TGAG
176470 CATTAAAAGT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
102 69 0.75
103 9 0.10
104 14 0.15
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (103 bp):
TGAGTATATAAATCAATTAAGAATTATGAGGTACGATGACTATGTGTCATCGTAAGTATATGAAT
CCTATACAGATTAAGAGGTCCAATGACCTGTGTCATCA
Found at i:184381 original size:18 final size:17
Alignment explanation
Indices: 184355--184398 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
184345 ATGCATAGCA
* *
184355 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
*
184373 TTTATTTGTTACTGCAT
1 TTTATTTGTCACTGCAT
184390 TTTATTTGT
1 TTTATTTGT
184399 TAGTACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:184394 original size:17 final size:18
Alignment explanation
Indices: 184367--184400 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
184357 TAGTTGTCAT
184367 TGCATTTTTATTTGTTAC
1 TGCATTTTTATTTGTTAC
184385 TGCA-TTTTATTTGTTA
1 TGCATTTTTATTTGTTA
184401 GTACATTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.62
Consensus pattern (18 bp):
TGCATTTTTATTTGTTAC
Found at i:184407 original size:17 final size:17
Alignment explanation
Indices: 184372--184408 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
184362 GTCATTGCAT
*
184372 TTTTATTTGTTACTGCA
1 TTTTATTTGTTACTACA
*
184389 TTTTATTTGTTAGTACA
1 TTTTATTTGTTACTACA
184406 TTT
1 TTT
184409 GCATTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (17 bp):
TTTTATTTGTTACTACA
Found at i:189182 original size:16 final size:16
Alignment explanation
Indices: 189158--189204 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
189148 ATGATGCGAT
189158 AACAAAAT-AAAATGC
1 AACAAAATAAAAATGC
189173 AACAATAATAAAAATGC
1 AACAA-AATAAAAATGC
**
189190 ATTAAAACTAAAAAT
1 AACAAAA-TAAAAAT
189205 TTTGTACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
17 17 0.63
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (16 bp):
AACAAAATAAAAATGC
Found at i:209586 original size:23 final size:23
Alignment explanation
Indices: 209560--209604 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
209550 TATTACATTT
* *
209560 TAATTATTGTGTTTAAAATGTCC
1 TAATGATTGTGTTCAAAATGTCC
209583 TAATGATTGTGTTCAAAATGTC
1 TAATGATTGTGTTCAAAATGTC
209605 TTAGGTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (23 bp):
TAATGATTGTGTTCAAAATGTCC
Found at i:220532 original size:24 final size:24
Alignment explanation
Indices: 220504--220555 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
220494 TTCATAAGTC
* *
220504 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
220528 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
220552 AAAT
1 AAAT
220556 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:222411 original size:29 final size:30
Alignment explanation
Indices: 222348--222437 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
222338 ATCAAATACC
* * * *
222348 AAGATTAAATAAATAATAAAAT-GATTTAA
1 AAGATTAAAAAAATAAGAAAATAGAATAAA
*
222377 AGGATTAAAAAAAT-AGAAAATAGAATAAA
1 AAGATTAAAAAAATAAGAAAATAGAATAAA
* *
222406 AAGATTAAAAATATAAGAAAGATAAAATAAA
1 AAGATTAAAAAAATAAGAAA-ATAGAATAAA
222437 A
1 A
222438 GAACATAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 6 0.12
29 29 0.58
30 5 0.10
31 10 0.20
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (30 bp):
AAGATTAAAAAAATAAGAAAATAGAATAAA
Found at i:223915 original size:13 final size:13
Alignment explanation
Indices: 223897--223921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223887 TAAATGGACA
223897 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
223910 TTTTTTCTTTTT
1 TTTTTTCTTTTT
223922 AATTTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:224362 original size:100 final size:100
Alignment explanation
Indices: 224239--224479 Score: 315
Period size: 100 Copynumber: 2.4 Consensus size: 100
224229 ACTTGTCATT
* * * *
224239 TTAGCTTTAATCCGACCCACTACAACTTTAGAG-TATAGGACTTGATGTTGTAGCTTCATCTTGC
1 TTAGTTTTAATCCGATCC-CTACAACTTTAGAGATATAGGACTTGATGTTGTAGCTTAATCTTAC
* ** * * *
224303 TTCACTGTAACTTTAGGGAGATAAAGATTTGCTACTG
65 TCCACTACAACTTCA-AGAGATAAAGATTTGCCACTG
* * *
224340 TTAGTTTTTATCCGATCCCTACAACTTTAGAGATATAGGATTTGGTGTTGTAGCTTAATCTTACT
1 TTAGTTTTAATCCGATCCCTACAACTTTAGAGATATAGGACTTGATGTTGTAGCTTAATCTTACT
224405 CCACTACAACTTCAAGAGATAAAGATTTGCCACTG
66 CCACTACAACTTCAAGAGATAAAGATTTGCCACTG
*
224440 TTAGTTTTAATTCGATCCCTACAACTTTA-AGGATATAGGA
1 TTAGTTTTAATCCGATCCCTACAACTTTAGA-GATATAGGA
224480 TTTAAGGTGG
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
99 1 0.01
100 69 0.56
101 53 0.43
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (100 bp):
TTAGTTTTAATCCGATCCCTACAACTTTAGAGATATAGGACTTGATGTTGTAGCTTAATCTTACT
CCACTACAACTTCAAGAGATAAAGATTTGCCACTG
Found at i:224482 original size:50 final size:51
Alignment explanation
Indices: 224311--224482 Score: 151
Period size: 50 Copynumber: 3.4 Consensus size: 51
224301 GCTTCACTGT
* * * *
224311 AACTTTAGGGAGATA-AAGATTTGCTACTGTTAGTTTTTATCCGATCCCTAC
1 AACTTTA-AGAGATATAGGATTTGCTACTGTTAGTTTTAATTCGATCCCTAC
* ** * *
224362 AACTTT-AGAGATATAGGATTTGGTGTTG-TAG-CTTAA-TCTTACTCCACTAC
1 AACTTTAAGAGATATAGGATTTGCTACTGTTAGTTTTAATTC-GA-TCC-CTAC
* * *
224412 AACTTCAAGAGATA-AAGATTTGCCACTGTTAGTTTTAATTCGATCCCTAC
1 AACTTTAAGAGATATAGGATTTGCTACTGTTAGTTTTAATTCGATCCCTAC
224462 AACTTTAAG-GATATAGGATTT
1 AACTTTAAGAGATATAGGATTT
224483 AAGGTGGCTT
Statistics
Matches: 93, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
47 1 0.01
48 4 0.04
49 16 0.17
50 46 0.49
51 19 0.20
52 5 0.05
53 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (51 bp):
AACTTTAAGAGATATAGGATTTGCTACTGTTAGTTTTAATTCGATCCCTAC
Found at i:224596 original size:99 final size:99
Alignment explanation
Indices: 224490--225160 Score: 428
Period size: 99 Copynumber: 6.9 Consensus size: 99
224480 TTTAAGGTGG
* *
224490 CTTCACTCCATTCCACTAGAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCCGCTTCA
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCTGCTTCA
* * *
224555 TTGCAAC-TCAAGAAGATAGGATTAGGGGCGTTAA
66 CTGCAACTTCAGGAAGATAGGATTTGGGG-GTTAA
* * * * * *
224589 CTTCACTCCATTCCATTGCAAATTC-----AG--TGAG--TTA---CTTGTTTCAATCTGATCCA
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCTGCTTCA
* * * * * * **
224642 CTACAACTTCATGG-ATATAAGATTAGAGGTTGTGG
66 CTGCAACTTCA-GGAAGATAGGATTTGGGGGT-TAA
* * * * * *
224677 C-TCTACTCCATTCCACTGCAACTTCAGTGTAGATTGAGATCTACTACTTGTTGTAATCTACTTC
1 CTTC-ACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCTGCTTC
* *
224741 ACTTCAACTTCAGGAAGATAGGATTTGGGGTGGTAA
65 ACTGCAACTTCAGGAAGATAGGATTTGGGG-GTTAA
* * * *
224777 CTTCACTCCATTCAACTACAACTTCA-AGGAGATT--GATGTT-CGTTACTTGTTTTAATATG-A
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGAT-TTAC-TT-CTTGTTTTAATCTGCT
* * * * *
224837 TCTACTGTAACTTCATGG-ATATAGGATTTGAGGTTGTAG
63 TC-ACTGCAACTTCA-GGAAGATAGGATTTGGGGGT-TAA
* * * *
224876 CTTCACTTCATTCCACTACAATTTCAGTGGAG-TTGAGATATACTAT-TTGTTTTAATCCGCTTC
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACT-TCTTGTTTTAATCTGCTTC
*
224939 ACTGCAACTTCAGGAAGATAGGATTTGGGGTGGTAA
65 ACTGCAACTTCAGGAAGATAGGATTTGGGG-GTTAA
* * * * * * *
224975 CTTCGCTTCATTCCACTACAACTTCAG-CGAGATTGAGATCT-GTTACTTGTTTTAATCTGATCC
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTT-CTTGTTTTAATCTGCTTC
* * * * *
225038 ACTGTAACTTCAGGGATATAGGATTT-GAGGTTATGG
65 ACTGCAACTTCAGGAAGATAGGATTTGGGGGTTA--A
* * * ** * *
225074 CTTTACTCTATTCCATTGTAACTTCAGTGGAGATTGAGA--T-CTACTAGTTTTAATCTGCTTCA
1 CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCTGCTTCA
* * *
225136 CTACAACTTTAGGAAGATAAGATTT
66 CTGCAACTTCAGGAAGATAGGATTT
225161 TGTGCTGTAT
Statistics
Matches: 435, Mismatches: 98, Indels: 80
0.71 0.16 0.13
Matches are distributed among these distances:
87 23 0.05
88 36 0.08
89 1 0.00
90 3 0.01
92 4 0.01
93 2 0.00
94 2 0.00
95 4 0.01
97 45 0.10
98 14 0.03
99 217 0.50
100 77 0.18
101 7 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (99 bp):
CTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATTTACTTCTTGTTTTAATCTGCTTCA
CTGCAACTTCAGGAAGATAGGATTTGGGGGTTAA
Found at i:224978 original size:198 final size:198
Alignment explanation
Indices: 224619--225160 Score: 720
Period size: 198 Copynumber: 2.7 Consensus size: 198
224609 AATTCAGTGA
* ** * *
224619 GTTACTTGTTTCAATCTGATCCACTACAACTTCATGGATATAAGATTAGAGGTTGTGGC-TCTAC
1 GTTACTTGTTTTAATCTGATCCACTGTAACTTCATGGATATAGGATTTGAGGTTGTGGCTTC-AC
* * * * *
224683 TCCATTCCACTGCAACTTCAGTGTAGATTGAGATCTACTACTTGTTGTAATCTACTTCACTTCAA
65 TTCATTCCACTGCAACTTCAGTGGAGATTGAGATCTACTA-TTGTTTTAATCTGCTTCACTACAA
224748 CTTCAGGAAGATAGGATTTGGGGTGGTAACTTCACTCCATTCAACTACAACTTCAAG-GAGATTG
129 CTTCAGGAAGATAGGATTTGGGGTGGTAACTTCACTCCATTCAACTACAACTTC-AGCGAGATTG
*
224812 ATGTTC-
193 A-GATCT
* * *
224818 GTTACTTGTTTTAATATGATCTACTGTAACTTCATGGATATAGGATTTGAGGTTGTAGCTTCACT
1 GTTACTTGTTTTAATCTGATCCACTGTAACTTCATGGATATAGGATTTGAGGTTGTGGCTTCACT
* * * * *
224883 TCATTCCACTACAATTTCAGTGGAG-TTGAGATATACTATTTGTTTTAATCCGCTTCACTGCAAC
66 TCATTCCACTGCAACTTCAGTGGAGATTGAGATCTACTA-TTGTTTTAATCTGCTTCACTACAAC
* * *
224947 TTCAGGAAGATAGGATTTGGGGTGGTAACTTCGCTTCATTCCACTACAACTTCAGCGAGATTGAG
130 TTCAGGAAGATAGGATTTGGGGTGGTAACTTCACTCCATTCAACTACAACTTCAGCGAGATTGAG
225012 ATCT
195 ATCT
* * *
225016 GTTACTTGTTTTAATCTGATCCACTGTAACTTCAGGGATATAGGATTTGAGGTTATGGCTTTAC-
1 GTTACTTGTTTTAATCTGATCCACTGTAACTTCATGGATATAGGATTTGAGGTTGTGGCTTCACT
* *
225080 TCTATTCCATTGTAACTTCAGTGGAGATTGAGATCTACTA--GTTTTAATCTGCTTCACTACAAC
66 TC-ATTCCACTGCAACTTCAGTGGAGATTGAGATCTACTATTGTTTTAATCTGCTTCACTACAAC
* *
225143 TTTAGGAAGATAAGATTT
130 TTCAGGAAGATAGGATTT
225161 TGTGCTGTAT
Statistics
Matches: 301, Mismatches: 37, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
196 37 0.12
197 7 0.02
198 168 0.56
199 87 0.29
200 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (198 bp):
GTTACTTGTTTTAATCTGATCCACTGTAACTTCATGGATATAGGATTTGAGGTTGTGGCTTCACT
TCATTCCACTGCAACTTCAGTGGAGATTGAGATCTACTATTGTTTTAATCTGCTTCACTACAACT
TCAGGAAGATAGGATTTGGGGTGGTAACTTCACTCCATTCAACTACAACTTCAGCGAGATTGAGA
TCT
Found at i:230759 original size:29 final size:29
Alignment explanation
Indices: 230724--230790 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
230714 ATAAAATACC
* *
230724 AAGATTAAATAAATAATAAAAT-GATTTAA
1 AAGATTAAATAAAT-AGAAAATAGATTAAA
* *
230753 AGGATTAAATAAGTAGAAAATAGATTAAA
1 AAGATTAAATAAATAGAAAATAGATTAAA
230782 AAGATTAAA
1 AAGATTAAA
230791 AATTTAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (29 bp):
AAGATTAAATAAATAGAAAATAGATTAAA
Found at i:231817 original size:2 final size:2
Alignment explanation
Indices: 231807--231840 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
231797 AAAAAAAACA
231807 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
231841 ACTGCAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:250946 original size:12 final size:11
Alignment explanation
Indices: 250926--250959 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
250916 ATTTCCCCTA
250926 AAAAAAGAAAG
1 AAAAAAGAAAG
250937 AAACAAAGAAAG
1 AAA-AAAGAAAG
250949 AAAAAA-AAAG
1 AAAAAAGAAAG
250959 A
1 A
250960 GAGGCCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 6 0.27
12 11 0.50
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:251944 original size:50 final size:49
Alignment explanation
Indices: 251777--252195 Score: 199
Period size: 50 Copynumber: 8.4 Consensus size: 49
251767 GATGAATTCG
* * *
251777 ATACCCTAAAGATGTAA-AGGGAAAGATTGAAGCCGTAAAGGTGAATCTT
1 ATACCCTAAAGCTG-AAGAGGGAAAGATTGAAGCCATAAAGGTGAATCTA
** *** * *** *** *
251826 ATACCCTAAAGAC-GTCGACAAAAAGATTAAAGCTGCAAAGACAAATCTT
1 ATACCCTAAAG-CTGAAGAGGGAAAGATTGAAGCCATAAAGGTGAATCTA
* * *
251875 ATACCCTAAAGAT-ATAGAGGGAAAGATTGAAGTCATATAGGTGAATCTA
1 ATACCCTAAAGCTGA-AGAGGGAAAGATTGAAGCCATAAAGGTGAATCTA
* *
251924 ATAACCCTAAAGCTGAAGA-GGAGAAGATTAAAGTCGA-AAAGGCT-AATCTA
1 AT-ACCCTAAAGCTGAAGAGGGA-AAGATTGAAG-CCATAAAGG-TGAATCTA
* * * *
251974 ATACTTCTAAAGTTTAGAGAGGGGCAA-ATTGAAGCCATAAAGGTGAATCTA
1 ATAC-CCTAAAGCTGA-AGA-GGGAAAGATTGAAGCCATAAAGGTGAATCTA
* * ** * ** *
252025 ATACTCCTAAAGTTAAAGAGGGTCATATTGAAGCCACGAAGGTGAATCTT
1 ATAC-CCTAAAGCTGAAGAGGGAAAGATTGAAGCCATAAAGGTGAATCTA
* * ** ** *
252075 ATACCCTTGAAGCTGAAGAGGAGCAA-ATTGAAGCCGCAAAGGCAAATATA
1 ATACCC-TAAAGCTGAAGAGG-GAAAGATTGAAGCCATAAAGGTGAATCTA
* * * * * * *
252125 ATTCTCCTAAAGTTGCAGAGGGTCAA-ATTGAAGCCGTAAAGGCGAATCTT
1 ATAC-CCTAAAGCTGAAGAGGG-AAAGATTGAAGCCATAAAGGTGAATCTA
*
252175 ATACCCCTGAAGCTGAAGAGG
1 ATA-CCCTAAAGCTGAAGAGG
252196 AGCATATTGA
Statistics
Matches: 280, Mismatches: 69, Indels: 41
0.72 0.18 0.11
Matches are distributed among these distances:
49 80 0.29
50 154 0.55
51 42 0.15
52 2 0.01
53 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (49 bp):
ATACCCTAAAGCTGAAGAGGGAAAGATTGAAGCCATAAAGGTGAATCTA
Found at i:252132 original size:100 final size:100
Alignment explanation
Indices: 251991--252236 Score: 294
Period size: 100 Copynumber: 2.5 Consensus size: 100
251981 TAAAGTTTAG
* * ** * *
251991 AGAGGGGCAAATTGAAGCCATAAAGGTGAATCTAATACTCCTAAAGTTAAAGAGGGTCATATTGA
1 AGAGGAGCAAATTGAAGCCACAAAGGCAAATATAATACTCCTAAAGTTAAAGAGGGTCAAATTGA
* * *
252056 AGCCACGAAGGTGAATCTTATACCCTTGAAGCTGA
66 AGCCACAAAGGCGAATCTTATACCCCTGAAGCTGA
* * **
252091 AGAGGAGCAAATTGAAGCCGCAAAGGCAAATATAATTCTCCTAAAGTTGCAGAGGGTCAAATTGA
1 AGAGGAGCAAATTGAAGCCACAAAGGCAAATATAATACTCCTAAAGTTAAAGAGGGTCAAATTGA
**
252156 AGCCGTAAAGGCGAATCTTATACCCCTGAAGCTGA
66 AGCCACAAAGGCGAATCTTATACCCCTGAAGCTGA
* * * * * * *
252191 AGAGGAGCATATTGAGGCCAAAAAAGCAAATCTTATACCCCTAAAG
1 AGAGGAGCAAATTGAAGCCACAAAGGCAAATATAATACTCCTAAAG
252237 CTATAGAGAA
Statistics
Matches: 122, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 122 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (100 bp):
AGAGGAGCAAATTGAAGCCACAAAGGCAAATATAATACTCCTAAAGTTAAAGAGGGTCAAATTGA
AGCCACAAAGGCGAATCTTATACCCCTGAAGCTGA
Found at i:252202 original size:150 final size:151
Alignment explanation
Indices: 251913--252210 Score: 363
Period size: 150 Copynumber: 2.0 Consensus size: 151
251903 GAAGTCATAT
* * *
251913 AGGTGAATCTAATAACCCTAAAGCTGAAGAGGAGAAGATTAAAGTCGAAAAGGCTAATCTAATAC
1 AGGTGAATCTAATAACCCTAAAGCTGAAGAGGAGAAGATTAAAGCCGAAAAGGCAAATATAATAC
* * * *
251978 TTCTAAAGTTTAGAGAGGGGCAAATTGAAGCCATAAAGGTGAATCTAATACTCCTAAAGTTAAAG
66 TCCTAAAGTTTAGAGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTAAAG
252043 AGGGTCATATTGAAGCCACGA
131 AGGGTCATATTGAAGCCACGA
* * * *
252064 AGGTGAATCTTAT-ACCCTTGAAGCTGAAGAGGAGCAA-ATTGAAGCCGCAAAGGCAAATATAAT
1 AGGTGAATCTAATAACCC-TAAAGCTGAAGAGGAG-AAGATTAAAGCCGAAAAGGCAAATATAAT
* * * * * *
252127 TCTCCTAAAG-TT-GCAGAGGGTCAAATTGAAGCCGTAAAGGCGAATCTTATACCCCTGAAGCTG
64 ACTCCTAAAGTTTAG-AGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTA
*
252190 AAGAGGAG-CATATTGAGGCCA
128 AAGAGG-GTCATATTGAAGCCA
252211 AAAAAGCAAA
Statistics
Matches: 125, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
149 1 0.01
150 65 0.52
151 57 0.46
152 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (151 bp):
AGGTGAATCTAATAACCCTAAAGCTGAAGAGGAGAAGATTAAAGCCGAAAAGGCAAATATAATAC
TCCTAAAGTTTAGAGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTAAAG
AGGGTCATATTGAAGCCACGA
Found at i:252205 original size:50 final size:50
Alignment explanation
Indices: 251917--252238 Score: 236
Period size: 50 Copynumber: 6.4 Consensus size: 50
251907 TCATATAGGT
* * * *
251917 GAATCTAATAACCCTAAAGCTGAAGAGGAG-AAGATTAAAGTCGAAAAGGC
1 GAATCTAATACCCCTAAAGCTGAAGAGGAGCAA-ATTGAAGCCAAAAAGGC
* ** * * * * *
251967 TAATCTAATACTTCTAAAGTTTAGAGAGGGGCAAATTGAAGCCATAAAGGT
1 GAATCTAATACCCCTAAAGCTGA-AGAGGAGCAAATTGAAGCCAAAAAGGC
* * * * ** *
252018 GAATCTAATACTCCTAAAGTTAAAGAGG-GTCATATTGAAGCCACGAAGGT
1 GAATCTAATACCCCTAAAGCTGAAGAGGAG-CAAATTGAAGCCAAAAAGGC
* * * **
252068 GAATCTTATACCCTTGAAGCTGAAGAGGAGCAAATTGAAGCCGCAAAGGC
1 GAATCTAATACCCCTAAAGCTGAAGAGGAGCAAATTGAAGCCAAAAAGGC
* * * * * * **
252118 AAATATAATTCTCCTAAAGTTGCAGAGG-GTCAAATTGAAGCCGTAAAGGC
1 GAATCTAATACCCCTAAAGCTGAAGAGGAG-CAAATTGAAGCCAAAAAGGC
* * * * *
252168 GAATCTTATACCCCTGAAGCTGAAGAGGAGCATATTGAGGCCAAAAAAGC
1 GAATCTAATACCCCTAAAGCTGAAGAGGAGCAAATTGAAGCCAAAAAGGC
* *
252218 AAATCTTATACCCCTAAAGCT
1 GAATCTAATACCCCTAAAGCT
252239 ATAGAGAAGT
Statistics
Matches: 213, Mismatches: 53, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
49 2 0.01
50 169 0.79
51 40 0.19
52 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (50 bp):
GAATCTAATACCCCTAAAGCTGAAGAGGAGCAAATTGAAGCCAAAAAGGC
Found at i:252262 original size:150 final size:150
Alignment explanation
Indices: 251991--252271 Score: 332
Period size: 150 Copynumber: 1.9 Consensus size: 150
251981 TAAAGTTTAG
* * *
251991 AGAGGGGCAAATTGAAGCCATAAAGGTGAATCTAATACTCCTAAAGTTAAAGAGGGTCATATTGA
1 AGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTAAAGAGGGTCATATTGA
** * ** * * * * *
252056 AGCCACGAAGGTGAATCTTATACCCTTGAAGCTGAAGAGGAGCAAATTGAAGCCGCAAAGGCAAA
66 AGCCAAAAAAGCAAATCTTATACCCCTAAAGCTGAAGAGAAGCAAATAGAAGCCGCAAAGACAAA
252121 TATAATTCTCCTAAAGTTGC
131 TATAATTCTCCTAAAGTTGC
* * * * *
252141 AGAGGGTCAAATTGAAGCCGTAAAGGCGAATCTTATACCCCTGAAGCTGAAGAGGAG-CATATTG
1 AGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTAAAGAGG-GTCATATTG
* * * *
252205 AGGCCAAAAAAGCAAATCTTATACCCCTAAAGCT-ATAGAGAAGTAGATAGAGGCCGCAAAGACA
65 AAGCCAAAAAAGCAAATCTTATACCCCTAAAGCTGA-AGAGAAGCAAATAGAAGCCGCAAAGACA
252269 AAT
129 AAT
252272 CCTAAATCTA
Statistics
Matches: 107, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
149 1 0.01
150 105 0.98
151 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.20
Consensus pattern (150 bp):
AGAGGGGCAAATTGAAGCCATAAAGGCGAATCTAATACCCCTAAAGCTAAAGAGGGTCATATTGA
AGCCAAAAAAGCAAATCTTATACCCCTAAAGCTGAAGAGAAGCAAATAGAAGCCGCAAAGACAAA
TATAATTCTCCTAAAGTTGC
Found at i:259969 original size:20 final size:19
Alignment explanation
Indices: 259931--259976 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
259921 TTATTTACAT
259931 TTGTGTTATTTACTTTTAG
1 TTGTGTTATTTACTTTTAG
* *
259950 TTGTTTTATTTATGTTTTAG
1 TTGTGTTATTTA-CTTTTAG
*
259970 TTTTGTT
1 TTGTGTT
259977 TATTAGTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (19 bp):
TTGTGTTATTTACTTTTAG
Found at i:259988 original size:21 final size:20
Alignment explanation
Indices: 259931--259989 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
259921 TTATTTACAT
*
259931 TTGTGTTATTTA-CTTTTAG
1 TTGTTTTATTTATCTTTTAG
*
259950 TTGTTTTATTTATGTTTTAG
1 TTGTTTTATTTATCTTTTAG
*
259970 TTTTGTTTA-TTAGTCTTTTA
1 TTGT-TTTATTTA-TCTTTTA
259990 CAAGAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.33
20 12 0.36
21 10 0.30
ACGTcount: A:0.15, C:0.03, G:0.14, T:0.68
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTAG
Found at i:275534 original size:16 final size:16
Alignment explanation
Indices: 275507--275553 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
275497 TTTATTTTCT
*
275507 TTTCTCTTTTCTTCTTC
1 TTTCT-TTTTCTTATTC
275524 TTTCTTTTTCTTATTC
1 TTTCTTTTTCTTATTC
*
275540 ATTCATTTTT-TTAT
1 TTTC-TTTTTCTTAT
275554 ATATGTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTTTTTCTTATTC
Found at i:276149 original size:17 final size:17
Alignment explanation
Indices: 276101--276167 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
276091 GATAAGAATG
276101 GAAATGCAACT-AC-AAT
1 GAAATGCAA-TGACAAAT
* *
276117 GCAAATGCACTAACAAAT
1 G-AAATGCAATGACAAAT
*
276135 GAAATGCAGTGACAAAT
1 GAAATGCAATGACAAAT
*
276152 AAAAATGCAATGACAA
1 -GAAATGCAATGACAA
276168 CTAAATAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
16 2 0.05
17 23 0.55
18 17 0.40
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.16
Consensus pattern (17 bp):
GAAATGCAATGACAAAT
Found at i:276159 original size:18 final size:18
Alignment explanation
Indices: 276136--276172 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
276126 CTAACAAATG
*
276136 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
276154 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
276172 A
1 A
276173 TAAGATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:276297 original size:3 final size:3
Alignment explanation
Indices: 276251--276277 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
276241 CTACTTTGTC
276251 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
276278 TGGGCGCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:284931 original size:26 final size:27
Alignment explanation
Indices: 284902--284984 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 27
284892 AAAAATTTTG
* *
284902 AAAA-AAGAAAAAATTGAAATATTG-AA
1 AAAAGAAGAAAAAATTCAAAT-GTGAAA
*
284928 AAAATAA-AAAAAATTCAAAGTGTGAAA
1 AAAAGAAGAAAAAATTCAAA-TGTGAAA
*
284955 AAAAGAAGAAAAAATTCAAAT-TAAAA
1 AAAAGAAGAAAAAATTCAAATGTGAAA
284981 AAAA
1 AAAA
284985 ACTTTGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 25 0.51
27 12 0.24
28 12 0.24
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (27 bp):
AAAAGAAGAAAAAATTCAAATGTGAAA
Found at i:284985 original size:27 final size:27
Alignment explanation
Indices: 284926--284984 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
284916 TGAAATATTG
* *
284926 AAAAAATAAAAAAAATTCAAAGTGTGA
1 AAAAAAGAAAAAAAATTCAAAGTGTAA
284953 AAAAAAGAAGAAAAAATTCAAA-T-TAA
1 AAAAAAGAA-AAAAAATTCAAAGTGTAA
284979 AAAAAA
1 AAAAAA
284985 ACTTTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 9 0.31
28 12 0.41
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAAGAAAAAAAATTCAAAGTGTAA
Found at i:289248 original size:62 final size:64
Alignment explanation
Indices: 289125--289282 Score: 225
Period size: 62 Copynumber: 2.5 Consensus size: 64
289115 AAATGATTAT
* * *
289125 AAATAAT-AATGTAATAAATATTTTAATACATATATATATACAAAACATCCCGAATATTAAAGG
1 AAATAATAAATGTATTAAATATATTAATACATATATATATACAAAACATCCCGAATAATAAAGG
* * *
289188 AAATAATAAATGCATTAAATATATTAATACATATATATA-A-AAAACGTCTCGAATAATAAAGG
1 AAATAATAAATGTATTAAATATATTAATACATATATATATACAAAACATCCCGAATAATAAAGG
*
289250 AAATAATAAATGTATTAAATATA-TAATAAATAT
1 AAATAATAAATGTATTAAATATATTAATACATAT
289283 CAAATAAATA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
61 9 0.10
62 41 0.48
63 8 0.09
64 28 0.33
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (64 bp):
AAATAATAAATGTATTAAATATATTAATACATATATATATACAAAACATCCCGAATAATAAAGG
Found at i:289281 original size:11 final size:11
Alignment explanation
Indices: 289252--289296 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
289242 AATAAAGGAA
*
289252 ATAATAAATGT
1 ATAATAAATAT
289263 AT--TAAATAT
1 ATAATAAATAT
289272 ATAATAAATAT
1 ATAATAAATAT
289283 CA-AATAAATAT
1 -ATAATAAATAT
289294 ATA
1 ATA
289297 CTATTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 19 0.66
12 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
ATAATAAATAT
Found at i:289839 original size:6 final size:6
Alignment explanation
Indices: 289830--289952 Score: 71
Period size: 6 Copynumber: 21.3 Consensus size: 6
289820 GGACATTACT
* * *
289830 AATTTA AATTT- AGTATA AATTTA AATTTA GGAA--TA AATTTA AACTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA --AATTTA AATTTA AATTTA
* * * * *
289877 AA-TTA AATTTA AA-TTA AA-ATA AATTTA AACTGA AACTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* ** *
289921 ATTTTA AATTTA AAAATA AATTTA AACTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
289953 ATAAATCTAA
Statistics
Matches: 90, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
4 2 0.02
5 20 0.22
6 66 0.73
8 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:289927 original size:39 final size:41
Alignment explanation
Indices: 289870--289948 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 41
289860 GAATAAATTT
*
289870 AAACTTAAATTAAATTTAAA-TT-AAAATAAATTTAAACTG
1 AAACTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTG
*
289909 AAACTTAAAATAATTTTAAATTTAAAAATAAATTTAAACT
1 AAACTTAAAATAAATTTAAATTTAAAAATAAATTTAAACT
289949 TAAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 18 0.50
40 2 0.06
41 16 0.44
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (41 bp):
AAACTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTG
Found at i:289940 original size:23 final size:23
Alignment explanation
Indices: 289875--289940 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
289865 AATTTAAACT
289875 TAAA-TTAAATTT-AAATTAAAA
1 TAAATTTAAATTTAAAATTAAAA
* * *
289896 TAAATTTAAACTGAAACTTAAAA
1 TAAATTTAAATTTAAAATTAAAA
* *
289919 TAATTTTAAATTTAAAAATAAA
1 TAAATTTAAATTTAAAATTAAA
289941 TTTAAACTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 25 0.71
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATTAAAA
Found at i:289965 original size:18 final size:17
Alignment explanation
Indices: 289830--289963 Score: 108
Period size: 17 Copynumber: 7.5 Consensus size: 17
289820 GGACATTACT
* **
289830 AATTTAAATTTAGTATA
1 AATTTAAACTTAAAATA
* *
289847 AATTTAAATTTAGGAATA
1 AATTTAAACTTA-AAATA
*
289865 AATTTAAACTTAAATTA
1 AATTTAAACTTAAAATA
289882 AATTTAAA-TTAAAATA
1 AATTTAAACTTAAAATA
289898 AATTTAAACTGAAACTTAAAATA
1 AA-TT----T-AAACTTAAAATA
* *
289921 ATTTTAAATTTAAAAATA
1 AATTTAAACTT-AAAATA
289939 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
289956 AATCTAAA
1 AATTTAAA
289964 ACAAAATGGG
Statistics
Matches: 98, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.09
17 43 0.44
18 31 0.32
21 1 0.01
22 5 0.05
23 9 0.09
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:290693 original size:39 final size:39
Alignment explanation
Indices: 290637--291015 Score: 241
Period size: 39 Copynumber: 9.8 Consensus size: 39
290627 AATGATCGCC
* *
290637 ATCTGCCCCATGATCGGGGTAAGAGATTGGCTGATTGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * ** * *
290676 ATCTGCCTCAGGCTCGGGGTAAGAGATAGAATGGCTT-TA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATTGTG
* * ** * ** **
290715 ATTTGCCCCAGGCTCGGGGTAAGATATCAGATGGCTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * *
290754 ATCTG-CCCAGGCTCAGGGTAAGAGATTGGCTAATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * * *
290792 ATCTGCCCCAGGCTTGGGGTAAGAGA-T--CTAATGGCTACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTG-T--G
* * **
290831 ATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATAATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * **
290870 ATC-GACCCCAAGCTCGGGGTAAGAGATTGACTGATAATG
1 ATCTG-CCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * * * ** ***
290909 ATCTACCCCAAGCTCGAGGTAAGAGATTGGATGGCTACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* *
290948 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
* * * *
290987 ATCT-ACCTAGCCTCGGGGTAAAAGATTGG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGG
291016 AATCTTCATT
Statistics
Matches: 266, Mismatches: 63, Indels: 23
0.76 0.18 0.07
Matches are distributed among these distances:
36 7 0.03
37 1 0.00
38 51 0.19
39 198 0.74
40 4 0.02
41 1 0.00
42 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATTGTG
Found at i:290934 original size:117 final size:117
Alignment explanation
Indices: 290759--290982 Score: 306
Period size: 117 Copynumber: 1.9 Consensus size: 117
290749 CTGCAATCTG
* * ** * * * *
290759 CCCAGGCTCAGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAGGCTTGGGGTAAGAGATCT-AA
1 CCCAAGCTCAGGGTAAGAGATTGACTAATAATGATCTACCCCAAGCTCGAGGTAAGAGAT-TGAA
* *
290823 TGGCTACAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATAATGATCGAC
65 TGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATAATGATCGAC
* * *
290876 CCCAAGCTCGGGGTAAGAGATTGACTGATAATGATCTACCCCAAGCTCGAGGTAAGAGATTGGAT
1 CCCAAGCTCAGGGTAAGAGATTGACTAATAATGATCTACCCCAAGCTCGAGGTAAGAGATTGAAT
*
290941 GGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGAT
66 GGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGAT
290983 GGTGATCTAC
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 1 0.01
117 91 0.99
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (117 bp):
CCCAAGCTCAGGGTAAGAGATTGACTAATAATGATCTACCCCAAGCTCGAGGTAAGAGATTGAAT
GGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATAATGATCGAC
Found at i:291050 original size:41 final size:41
Alignment explanation
Indices: 291002--291096 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
290992 CCTAGCCTCG
* * * *
291002 GGGTAAAAGATTGGAATCTTCATTCTGCCCTTCTTGATTAA
1 GGGTAAAAGACTGGAATCTTCAATCTACCCTTCTTGACTAA
*
291043 TGGTAAAAGACTGGAATCTTCAATCTACCCTTCTTGACTAA
1 GGGTAAAAGACTGGAATCTTCAATCTACCCTTCTTGACTAA
291084 GGGTAAAAGACTG
1 GGGTAAAAGACTG
291097 AATGATGATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (41 bp):
GGGTAAAAGACTGGAATCTTCAATCTACCCTTCTTGACTAA
Found at i:291610 original size:49 final size:49
Alignment explanation
Indices: 291372--291613 Score: 175
Period size: 50 Copynumber: 4.9 Consensus size: 49
291362 AATCCTTCAA
* * * * *
291372 ATCTTCATGGTACCGGGTTCGCCGTTACGGCCTCAACCTTTCTCGTGAC
1 ATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTAC
* * ** ** * ** * * *
291421 ATCTTCTAAGATACCAAGTTCGTAGTTGTGGGCTCAATCTTTCCTTTTAA
1 ATCTTC-ATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTAC
* *
291471 ATCTTCATGGT-CCTGGGTTTGTCGTTGCGACCTCAACCTTT--CTTGTCAC
1 ATCTTCATGGTACC-GGGTTCGCCGTTGCGACCTCAACCTTTCCCTT-T-AC
* * * **
291520 ATCTTCTTAGGTACCGAGTTCGCTGTTGCGGTCTCAACCTTTCCCTTTAC
1 ATCTTCAT-GGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTAC
* * *
291570 ATCTTCATGGTATCGGGTTCGCCATTGCGACCTCAGCCTTTCCC
1 ATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCC
291614 ATCACGTCTT
Statistics
Matches: 143, Mismatches: 42, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
47 2 0.01
48 3 0.02
49 65 0.45
50 67 0.47
51 3 0.02
52 3 0.02
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (49 bp):
ATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTAC
Found at i:291629 original size:99 final size:99
Alignment explanation
Indices: 291365--291632 Score: 306
Period size: 99 Copynumber: 2.7 Consensus size: 99
291355 CGACCTCAAT
* * * * *
291365 CCTTCAAATCTTCATGGTACCGGGTTCGCCGTTACGGCCTCAACCTTTCTCGTGACATCTTCTAA
1 CCTTTAAATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCTCGTCACATCTTCTTA
* * *
291430 GATACCAAGTTCGTAGTTGTGGGCTCAATCTTTC
66 GGTACCAAGTTCGTAGTTGCGGGCTCAACCTTTC
* * * *
291464 CTTTTAAATCTTCATGGT-CCTGGGTTTGTCGTTGCGACCTCAACCTTTCTTGTCACATCTTCTT
1 CCTTTAAATCTTCATGGTACC-GGGTTCGCCGTTGCGACCTCAACCTTTCTCGTCACATCTTCTT
* *
291528 AGGTACCGAGTTCGCT-GTTGCGGTCTCAACCTTTC
65 AGGTACCAAGTTCG-TAGTTGCGGGCTCAACCTTTC
* * * * * * * *
291563 CCTTTACATCTTCATGGTATCGGGTTCGCCATTGCGACCTCAGCCTTTCCCATCACGTCTTTTTA
1 CCTTTAAATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCTCGTCACATCTTCTTA
291628 GGTAC
66 GGTAC
291633 TGGGCTCACC
Statistics
Matches: 140, Mismatches: 26, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
98 2 0.01
99 136 0.97
100 2 0.01
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (99 bp):
CCTTTAAATCTTCATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCTCGTCACATCTTCTTA
GGTACCAAGTTCGTAGTTGCGGGCTCAACCTTTC
Found at i:291647 original size:99 final size:99
Alignment explanation
Indices: 291365--291662 Score: 231
Period size: 99 Copynumber: 3.0 Consensus size: 99
291355 CGACCTCAAT
* * * * * * * *
291365 CCTTCAAATCTTCATGGTACC-GGGTTCGCCGTTACGGCCTCAACCTTTCTCGTGACATCTTCTA
1 CCTTTAAATCTTCATGGT-CCTGGGTTCGCCATTGCGACCTCAACCTTTCCCATCACATCTTCTT
* * * *** * ** *
291429 AGATACCAAGTTCGTAGTTGTGGGCTCAATCTTTC
65 AGGTACCGAGCTCACCGTTGCGATCTCAACCTTTC
* * * * ***
291464 CTTTTAAATCTTCATGGTCCTGGGTTTGTCGTTGCGACCTCAACCTTTCTTGTCACATCTTCTTA
1 CCTTTAAATCTTCATGGTCCTGGGTTCGCCATTGCGACCTCAACCTTTCCCATCACATCTTCTTA
* * * *
291529 GGTACCGAGTTCGCTGTTGCGGTCTCAACCTTTC
66 GGTACCGAGCTCACCGTTGCGATCTCAACCTTTC
* * * * *
291563 CCTTTACATCTTCATGGT-ATCGGGTTCGCCATTGCGACCTCAGCCTTTCCCATCACGTCTTTTT
1 CCTTTAAATCTTCATGGTCCT-GGGTTCGCCATTGCGACCTCAACCTTTCCCATCACATCTTCTT
* *
291627 AGGTACTGGGCTCACCGTTGCGATCTCAACCCTTTC
65 AGGTACCGAGCTCACCGTTGCGATCTCAA-CCTTTC
291663 TTATCAAACC
Statistics
Matches: 162, Mismatches: 34, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
98 3 0.02
99 153 0.94
100 6 0.04
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.36
Consensus pattern (99 bp):
CCTTTAAATCTTCATGGTCCTGGGTTCGCCATTGCGACCTCAACCTTTCCCATCACATCTTCTTA
GGTACCGAGCTCACCGTTGCGATCTCAACCTTTC
Found at i:306455 original size:49 final size:49
Alignment explanation
Indices: 306391--306498 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
306381 GTGTGTGCAA
* * ** * *
306391 GCACACGACCGTGTGGGTTTTTAC-AGTCCATGTGTGCAGGCCGTGTGTG
1 GCACACGCCCCTGTGGCCTTTTACAAGT-CATGTGTGCAGCCCGTATGTG
* *
306440 GCACATGCCCCTGTGGCCTTTTACAAGTCATGTGTGTAGCCCGTATGTG
1 GCACACGCCCCTGTGGCCTTTTACAAGTCATGTGTGCAGCCCGTATGTG
306489 GCACACGCCC
1 GCACACGCCC
306499 GTGTAGCTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.27
Consensus pattern (49 bp):
GCACACGCCCCTGTGGCCTTTTACAAGTCATGTGTGCAGCCCGTATGTG
Found at i:309132 original size:17 final size:17
Alignment explanation
Indices: 309110--309147 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
309100 ACGGGCGAGT
*
309110 AACTAAATTGAGCTACA
1 AACTAAATTAAGCTACA
*
309127 AACTAAATTAAGCTTCA
1 AACTAAATTAAGCTACA
309144 AACT
1 AACT
309148 GGACTACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (17 bp):
AACTAAATTAAGCTACA
Found at i:310435 original size:19 final size:19
Alignment explanation
Indices: 310413--310455 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
310403 AAATAATTGA
*
310413 CAAAAATAGTAATATGAAC
1 CAAAAATAGTAATAAGAAC
* * *
310432 CAAAATTGGTAATAAGAAT
1 CAAAAATAGTAATAAGAAC
310451 CAAAA
1 CAAAA
310456 TTGATTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (19 bp):
CAAAAATAGTAATAAGAAC
Found at i:310456 original size:19 final size:19
Alignment explanation
Indices: 310421--310458 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
310411 GACAAAAATA
*
310421 GTAATATGAACCAAAATTG
1 GTAATAAGAACCAAAATTG
*
310440 GTAATAAGAATCAAAATTG
1 GTAATAAGAACCAAAATTG
310459 ATTATATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (19 bp):
GTAATAAGAACCAAAATTG
Found at i:310719 original size:28 final size:25
Alignment explanation
Indices: 310658--310720 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 25
310648 TCGTACTTAA
* *
310658 ACTTAATATTTTTTTTTAATTTGGT
1 ACTTAATTTTTTTTTTTAATTTGAT
*
310683 ATTTAAATTTTTTTTTATTGAATTTGAT
1 ACTT-AATTTTTTTTT-TT-AATTTGAT
310711 ACTTGAATTT
1 ACTT-AATTT
310721 GACATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 3 0.10
26 10 0.33
27 2 0.07
28 15 0.50
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (25 bp):
ACTTAATTTTTTTTTTTAATTTGAT
Found at i:311090 original size:31 final size:31
Alignment explanation
Indices: 311037--311099 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
311027 ATGTACCGAC
* * * *
311037 TTAAAAAAAAGTGTTAAATTTAAATATCAAA
1 TTAAAAAAAAATATCAAATTTAAATAACAAA
*
311068 TTAAAAAAAAATATCAAGTTTAAATAACAAA
1 TTAAAAAAAAATATCAAATTTAAATAACAAA
311099 T
1 T
311100 ATTATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (31 bp):
TTAAAAAAAAATATCAAATTTAAATAACAAA
Found at i:319096 original size:25 final size:24
Alignment explanation
Indices: 319063--319124 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
319053 ATTCTCCCCT
*
319063 TTATGTCTCATTCCATCTCACC-TCC
1 TTATTTCTCATT-C-TCTCACCTTCC
*
319088 TTATTTCTCCTTCTCTCACCTTCC
1 TTATTTCTCATTCTCTCACCTTCC
319112 TTATTTCTTCATT
1 TTATTTC-TCATT
319125 TTAGGAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.22
24 11 0.34
25 14 0.44
ACGTcount: A:0.13, C:0.35, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATTTCTCATTCTCTCACCTTCC
Found at i:321291 original size:150 final size:147
Alignment explanation
Indices: 321034--321359 Score: 379
Period size: 150 Copynumber: 2.2 Consensus size: 147
321024 TTTAATCTTG
* * *
321034 AGAAAAGTTTTGATTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAATATATTTTTA
1 AGAAAAGTTTT-A-TTTTTTAAAAAAAAGAAAGTTTAGATTTTAAAAAAATAAAATATATTTTTA
* * * *
321099 GTAATTTTAAAAGAAAAGGCTTGAATTTTTAAAAACAAAGTTTTGATTTTTTTAACTGTTTCGAA
64 GTAATTTTAAAAGAAAAAGCTTAAATTTTTAAAAACAAAGTTTTGAATTTTTTAACTATTTCGAA
*
321164 ACAAAAACTTTAATCTTTA
129 ACAAAAACTTTAATATTTA
* * *
321183 ATAAAAGTTTTATTTTTTAAAAAAAAGAGAGTTTAGATTTTAAAAAAATAAAAATATGTTTTTTT
1 AGAAAAGTTTTATTTTTTAAAAAAAAGAAAGTTTAGATTTTAAAAAAAT-AAAATA--TATTTTT
** * *
321248 TTTCATTTT-AAAGAAAAAAG-TTCAAATTTTTAAAAACAAAGTTTTGAATTTTTTAACTATTTT
63 AGTAATTTTAAAAG-AAAAAGCTT-AAATTTTTAAAAACAAAGTTTTGAATTTTTTAACTATTTC
* * *
321311 GAAATAAAAGCTTTGATATTTA
126 GAAACAAAAACTTTAATATTTA
*
321333 AGAAAAGTAATTA-TTTTTAAAAGAAAA
1 AGAAAAGT-TTTATTTTTTAAAA-AAAA
321360 CTTTTGATTT
Statistics
Matches: 150, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
147 33 0.22
148 7 0.05
149 16 0.11
150 87 0.58
151 7 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (147 bp):
AGAAAAGTTTTATTTTTTAAAAAAAAGAAAGTTTAGATTTTAAAAAAATAAAATATATTTTTAGT
AATTTTAAAAGAAAAAGCTTAAATTTTTAAAAACAAAGTTTTGAATTTTTTAACTATTTCGAAAC
AAAAACTTTAATATTTA
Found at i:323053 original size:20 final size:22
Alignment explanation
Indices: 323012--323061 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
323002 GGTTTTTTAG
323012 TATTTGTGCATATTAGATTTATT
1 TATTTGTGCA-ATTAGATTTATT
323035 TATTTGTGC-ATTA-ATTTATT
1 TATTTGTGCAATTAGATTTATT
*
323055 TAATTGT
1 TATTTGT
323062 CTAATTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
23 9 0.35
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (22 bp):
TATTTGTGCAATTAGATTTATT
Found at i:328158 original size:26 final size:26
Alignment explanation
Indices: 328118--328199 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 26
328108 ATATACTGGT
* *
328118 TAAACTCTATCTGGGCTCGTAAGAGC
1 TAAACTCTGTTTGGGCTCGTAAGAGC
328144 TAAACTCTGTTTGGGCTCGTAAGAGC
1 TAAACTCTGTTTGGGCTCGTAAGAGC
* * * *
328170 TAAACTTTGATTGGGCTCGTAGGAAC
1 TAAACTCTGTTTGGGCTCGTAAGAGC
328196 TAAA
1 TAAA
328200 GTTCTGGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (26 bp):
TAAACTCTGTTTGGGCTCGTAAGAGC
Found at i:338386 original size:17 final size:18
Alignment explanation
Indices: 338362--338409 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
338352 ATATATATGC
*
338362 AAATGCAATGACAAT-AT
1 AAATGCAATGACAATAAA
* *
338379 AGATGCAACGACAATAAA
1 AAATGCAATGACAATAAA
338397 AAATGCAATGACA
1 AAATGCAATGACA
338410 TTAATAATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.17
Consensus pattern (18 bp):
AAATGCAATGACAATAAA
Found at i:340274 original size:122 final size:122
Alignment explanation
Indices: 340057--340298 Score: 475
Period size: 122 Copynumber: 2.0 Consensus size: 122
340047 AGCTATACAC
*
340057 TCACGTTGATCTGGTGTGATCTTCATAAATCTGTAGATTGTCGCCGCATCTCTGGTCACGATCTG
1 TCACGTTGATCTGGTGTGATCTTCATAAATCTGCAGATTGTCGCCGCATCTCTGGTCACGATCTG
340122 AAATCTTTAGTTACGGCGACAACGTGTGAAATTCCTGTTCTGGTGCTTCTAGATAAA
66 AAATCTTTAGTTACGGCGACAACGTGTGAAATTCCTGTTCTGGTGCTTCTAGATAAA
340179 TCACGTTGATCTGGTGTGATCTTCATAAATCTGCAGATTGTCGCCGCATCTCTGGTCACGATCTG
1 TCACGTTGATCTGGTGTGATCTTCATAAATCTGCAGATTGTCGCCGCATCTCTGGTCACGATCTG
340244 AAATCTTTAGTTACGGCGACAACGTGTGAAATTCCTGTTCTGGTGCTTCTAGATA
66 AAATCTTTAGTTACGGCGACAACGTGTGAAATTCCTGTTCTGGTGCTTCTAGATA
340299 TACTTGTAGC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (122 bp):
TCACGTTGATCTGGTGTGATCTTCATAAATCTGCAGATTGTCGCCGCATCTCTGGTCACGATCTG
AAATCTTTAGTTACGGCGACAACGTGTGAAATTCCTGTTCTGGTGCTTCTAGATAAA
Found at i:354122 original size:12 final size:12
Alignment explanation
Indices: 354105--354129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
354095 GCAATCCTAT
354105 CTTTGTATGATA
1 CTTTGTATGATA
354117 CTTTGTATGATA
1 CTTTGTATGATA
354129 C
1 C
354130 AGTTTCAAGC
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (12 bp):
CTTTGTATGATA
Found at i:368894 original size:23 final size:23
Alignment explanation
Indices: 368864--368913 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
368854 TTAAATCAAG
368864 AAAAAAACACACAAAAAAG-AGAA
1 AAAAAAACA-ACAAAAAAGAAGAA
*
368887 AAAAAAACAACAAAAAGGAAGAA
1 AAAAAAACAACAAAAAAGAAGAA
368910 AAAA
1 AAAA
368914 TAGAGAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAACAACAAAAAAGAAGAA
Found at i:369435 original size:42 final size:42
Alignment explanation
Indices: 369318--369611 Score: 375
Period size: 42 Copynumber: 7.1 Consensus size: 42
369308 ATGGAAAACA
* * *
369318 TTCATTGCATTT--A-GCCCAGGTGTGGAGGTGCATTTACCT
1 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
* *
369357 TTCATTACATTTAGAGGT-CAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
* *
369398 TTCATTACATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
* * * *
369440 TTCGTTGCATTTAGAGG-CTCAAGTGTGAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGTC-CAGGTGTGGAGGTCCATTTACTT
369482 TTCATTGCATTTAGAGG-CCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGTCC-AGGTGTGGAGGTCCATTTACTT
*
369524 TTCATTGCATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
* ** * *
369566 TTCATTGCATTTAGAGGTCAAATTGTGGAGGTCTATTTATTT
1 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
369608 TTCA
1 TTCA
369612 CTACATATAG
Statistics
Matches: 225, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
39 11 0.05
41 41 0.18
42 171 0.76
43 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.40
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
Found at i:369561 original size:126 final size:125
Alignment explanation
Indices: 369337--369626 Score: 431
Period size: 126 Copynumber: 2.3 Consensus size: 125
369327 TTTAGCCCAG
* * * *
369337 GTGTGGAGGTGCATTTACCTTTCATTACATTTAGAGGTCAGGTGTGGAGGTTCATTTACTTTTCA
1 GTGTGGAGGTTCATTTACTTTTCATTACATTTAGAGGCCAGGTGTGGAGGTCCATTTACTTTTCA
*
369402 TTACATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTTTTCGTTGCATTTAGAGGCTC-AA
66 TTACATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGG-TCAAA
* *
369462 GTGTGAAGGTTCATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTC
1 GTGTGGAGGTTCATTTACTTTTCATTACATTTAGAGGCC-AGGTGTGGAGGTCCATTTACTTTTC
*
369527 ATTGCATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCAAA
65 ATTACATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCAAA
* * * *
369588 TTGTGGAGG-TCTATTTATTTTTCACTACATATAGAGGCC
1 GTGTGGAGGTTC-ATTTACTTTTCATTACATTTAGAGGCC
369627 GCATAGAGGT
Statistics
Matches: 148, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
125 38 0.26
126 110 0.74
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (125 bp):
GTGTGGAGGTTCATTTACTTTTCATTACATTTAGAGGCCAGGTGTGGAGGTCCATTTACTTTTCA
TTACATTTAAAGGTCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCAAA
Found at i:370330 original size:18 final size:19
Alignment explanation
Indices: 370287--370323 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
370277 ATTATTTCGA
370287 AATAAAAGTTTTGATTTTT
1 AATAAAAGTTTTGATTTTT
*
370306 AAGAAAAG-TTTGATTTTT
1 AATAAAAGTTTTGATTTTT
370324 TTTAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (19 bp):
AATAAAAGTTTTGATTTTT
Found at i:370350 original size:157 final size:155
Alignment explanation
Indices: 370000--370425 Score: 602
Period size: 151 Copynumber: 2.8 Consensus size: 155
369990 TTGATTATGG
* * * *
370000 GAAAAGTTTTGATTTTTTTTAAAAAAGAAAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTT
1 GAAAAGCTTTGATTTTTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAAACTATTTTT
370065 TAATCATTTTAAAGGAAAATGTTTAAATTTTTAAAAAAAATGTTTTG----A--TTTTTTAACTA
66 TAATCATTTTAAAGGAAAA-GTTTAAATTTTTAAAAAAAA-GTTTTGATTTATTTTTTTTAACTA
370124 TTTCGAAATAAAAGCTTTGATCTTTAA
129 TTTCGAAATAAAAGCTTTGATCTTTAA
*
370151 GAAAAGCTTTGATTTTTTTTAGAAAAGAGAATA-TTTAGATTTTTAAAAAATAAAAAACTATTTT
1 GAAAAGCTTTGATTTTTTTTAAAAAAGAGAA-AGTTTAGATTTTTAAAAAATAAAAAACTATTTT
* * *
370215 TTAGTCATTTTAAAGGACAAAGTTTAAATTTTTAAAAATGAAGTTTTGATTTATTTTTTTTAATT
65 TTAATCATTTTAAAGGA-AAAGTTTAAATTTTTAAAAA-AAAGTTTTGATTTATTTTTTTTAACT
* *
370280 ATTTCGAAATAAAAGTTTTGATTTTTAA
128 ATTTCGAAATAAAAGCTTTGATCTTTAA
370308 GAAAAG-TTTGATTTTTTTTAAAAAAGGAGAAAGTTTAGATTTTTAAAAAAT-AAAAA-TATTTT
1 GAAAAGCTTTGATTTTTTTTAAAAAA-GAGAAAGTTTAGATTTTTAAAAAATAAAAAACTATTTT
* *
370370 TTATTAATTTTAAAGGAAAAAGTTTAAATTTTTAAAAACAAAGTTTTGATTTATTT
65 TTAATCATTTTAAAGG-AAAAGTTTAAATTTTTAAAAA-AAAGTTTTGATTTATTT
370426 AACTGTCGAA
Statistics
Matches: 248, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
151 96 0.39
152 6 0.02
155 57 0.23
156 25 0.10
157 64 0.26
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (155 bp):
GAAAAGCTTTGATTTTTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAAACTATTTTT
TAATCATTTTAAAGGAAAAGTTTAAATTTTTAAAAAAAAGTTTTGATTTATTTTTTTTAACTATT
TCGAAATAAAAGCTTTGATCTTTAA
Found at i:371635 original size:86 final size:87
Alignment explanation
Indices: 371524--372114 Score: 432
Period size: 86 Copynumber: 6.8 Consensus size: 87
371514 AACGGAGTCA
* *
371524 AAAAT-GTAATTTTTAGATGCTCAGGGGTAAAATAGTAATTTTT-GAAAGTTTAGGG-CAAAAAT
1 AAAATGGTAA-TTTTGGATGTTCAGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAAT
* * * * *
371586 GCAATTTTTAGATACTCGAGGGC
65 GTAATTTTTGGACATTCGAGGGT
* * * * * ** *
371609 AAAATGGTAATTTTGGGATGATCAGGGGTAAAACAATAATTTTTGGATACTCAAAGG-C-AAAAT
1 AAAATGGTAATTTT-GGATGTTCAGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAAT
371672 GGTAATTTTTGG--ATGTCTGAGGGT
65 -GTAATTTTTGGACAT-TC-GAGGGT
* * * ** ** *
371696 AAAACGATAATTTTTGGATATTCAGGGGTAAAATAGTTTTTTTTTTAAA-TTTAGGGTCAAAAGT
1 AAAATGGTAA-TTTTGGATGTTCAGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAAT
* *
371760 GTATTTTTTGGACA-TCTAGGGGT
65 GTAATTTTTGGACATTCGA-GGGT
* * * * * *
371783 AAAATGGTAATTTTGGATGTTTAGGTGTAAAATGGAAATTTATGAAAAGTTTAGGGTCAAAAATG
1 AAAATGGTAATTTTGGATGTTCAGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAATG
* *
371848 TAAATTTTGGACATTCG-GAGT
66 TAATTTTTGGACATTCGAGGGT
**
371869 AAAATGGTAATTTTGGATGTTC-GAGGGTAAAAT-GCTAATTTTTGGAAAGTTCGGGGTCAAAAA
1 AAAATGGTAATTTTGGATGTTCAG-GGGTAAAATAG-TAATTTTTGGAAAGTTTAGGGTCAAAAA
*
371932 TATAATTTTTGGACATTCTGA-GGT
64 TGTAATTTTTGGACATTC-GAGGGT
* * * * *
371956 AAAATGATAATTTTGGATGTTC-GAGGGT-ACATGGTAATTTTTGGAAAGTGTGGGGTCAAAAAT
1 AAAATGGTAATTTTGGATGTTCAG-GGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAAT
* * *
372019 GTGATTTTTGGA-AGTTTGGGGGT
65 GTAATTTTTGGACA-TTCGAGGGT
* * * * * *
372042 AAAAAT-GTAATTTTTGAGAAGTT-TGAGGTTAAAAT-GTGAGTTTTGG-AAGTTTGGGGGT-AA
1 -AAAATGGTAA-TTTTG-GATGTTCAG-GGGTAAAATAGTAATTTTTGGAAAGTTT-AGGGTCAA
372102 AAATGTAATTTTT
61 AAATGTAATTTTT
372115 AGGAAGTTCG
Statistics
Matches: 406, Mismatches: 73, Indels: 52
0.76 0.14 0.10
Matches are distributed among these distances:
85 14 0.03
86 188 0.46
87 166 0.41
88 34 0.08
89 4 0.01
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (87 bp):
AAAATGGTAATTTTGGATGTTCAGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTCAAAAATG
TAATTTTTGGACATTCGAGGGT
Found at i:371659 original size:58 final size:58
Alignment explanation
Indices: 371588--371715 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 58
371578 GCAAAAATGC
* * *
371588 AATTTTTAGATACTCGAGGGCAAAATGGTAATTTTGGGATGATCAG-GGGTAAAACAAT
1 AATTTTTGGATACTCAAAGGCAAAATGGTAATTTTGGGATG-TCAGAGGGTAAAACAAT
* * *
371646 AATTTTTGGATACTCAAAGGCAAAATGGTAATTTTTGGATGTCTGAGGGTAAAACGAT
1 AATTTTTGGATACTCAAAGGCAAAATGGTAATTTTGGGATGTCAGAGGGTAAAACAAT
371704 AATTTTTGGATA
1 AATTTTTGGATA
371716 TTCAGGGGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.05
58 60 0.95
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (58 bp):
AATTTTTGGATACTCAAAGGCAAAATGGTAATTTTGGGATGTCAGAGGGTAAAACAAT
Found at i:371729 original size:58 final size:57
Alignment explanation
Indices: 371530--371729 Score: 183
Period size: 58 Copynumber: 3.5 Consensus size: 57
371520 GTCAAAAATG
* * * * * * *
371530 TAATTTTTAGATGCTCAGGGGTAAAATAGTAATTTTTGAAAGT-TTAGGGCAAAA-A
1 TAATTTTTAGATACTCAGGGGCAAAATGGTAATTTTTGGATGTCTGAGGGTAAAACA
* *
371585 TGCAATTTTTAGATACTC-GAGGGCAAAATGGTAATTTTGGGATGATCAG-GGGTAAAACAA
1 T--AATTTTTAGATACTCAG-GGGCAAAATGGTAATTTTTGGATG-TCTGAGGGTAAAAC-A
* **
371645 TAATTTTTGGATACTCAAAGGCAAAATGGTAATTTTTGGATGTCTGAGGGTAAAACGA
1 TAATTTTTAGATACTCAGGGGCAAAATGGTAATTTTTGGATGTCTGAGGGTAAAAC-A
* * *
371703 TAATTTTTGGATATTCAGGGGTAAAAT
1 TAATTTTTAGATACTCAGGGGCAAAAT
371730 AGTTTTTTTT
Statistics
Matches: 117, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
55 1 0.01
56 1 0.01
57 36 0.31
58 77 0.66
60 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.33
Consensus pattern (57 bp):
TAATTTTTAGATACTCAGGGGCAAAATGGTAATTTTTGGATGTCTGAGGGTAAAACA
Found at i:371984 original size:28 final size:28
Alignment explanation
Indices: 371779--371984 Score: 122
Period size: 28 Copynumber: 7.2 Consensus size: 28
371769 GGACATCTAG
* *
371779 GGGTAAAATGGTAATTTTGGATGTT-TA
1 GGGTAAAATGATAATTTTGGATGTTCGA
* * *
371806 GGTGTAAAATGGA-AATTTATGAAAAGTT-TA
1 GG-GTAAAAT-GATAATTT-TG-GATGTTCGA
**
371836 GGGTCAAAAATG-TAAATTTTGGACATTCG-
1 GGGT--AAAATGAT-AATTTTGGATGTTCGA
* *
371865 GAGTAAAATGGTAATTTTGGATGTTCGA
1 GGGTAAAATGATAATTTTGGATGTTCGA
* *
371893 GGGTAAAATGCTAATTTTTGGAAAGTTCG-
1 GGGTAAAATGATAA-TTTTGG-ATGTTCGA
**
371922 GGGTCAAAAAT-ATAATTTTTGGACATTCTGA
1 GGGT--AAAATGATAA-TTTTGGATGTTC-GA
371953 -GGTAAAATGATAATTTTGGATGTTCGA
1 GGGTAAAATGATAATTTTGGATGTTCGA
371980 GGGTA
1 GGGTA
371985 CATGGTAATT
Statistics
Matches: 142, Mismatches: 18, Indels: 37
0.72 0.09 0.19
Matches are distributed among these distances:
27 23 0.16
28 44 0.31
29 29 0.20
30 31 0.22
31 15 0.11
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGATAATTTTGGATGTTCGA
Found at i:371997 original size:28 final size:29
Alignment explanation
Indices: 371524--372125 Score: 159
Period size: 29 Copynumber: 20.9 Consensus size: 29
371514 AACGGAGTCA
* *
371524 AAAATG-TAATTTTTAGATGCTC-AGGGGT
1 AAAATGATAATTTTTGGATGTTCGA-GGGT
* * * *
371552 AAAAT-AGTAATTTTTGAAAGTT-TAGGGCA
1 AAAATGA-TAATTTTTGGATGTTCGAGGG-T
* * ** *
371581 AAAATG-CAATTTTTAGATACTCGAGGGC
1 AAAATGATAATTTTTGGATGTTCGAGGGT
* * *
371609 AAAATGGTAATTTTGGGATGATC-AGGGGT
1 AAAATGATAATTTTTGGATGTTCGA-GGGT
** ** * * *
371638 AAAACAATAATTTTTGGATACTCAAAGGC
1 AAAATGATAATTTTTGGATGTTCGAGGGT
*
371667 AAAATGGTAATTTTTGGATG-TCTGAGGGT
1 AAAATGATAATTTTTGGATGTTC-GAGGGT
* *
371696 AAAACGATAATTTTTGGATATTC-AGGGGT
1 AAAATGATAATTTTTGGATGTTCGA-GGGT
* ** **
371725 AAAATAGTTTTTTTTTTAAAT-TT--AGGGT
1 AAAAT-G-ATAATTTTTGGATGTTCGAGGGT
* ** *
371753 CAAAAGTG-TATTTTTTGGA-CATCTAGGGGT
1 -AAAA-TGATAATTTTTGGATGTTCGA-GGGT
* *
371783 AAAATGGTAA-TTTTGGATGTT-TAGGTGT
1 AAAATGATAATTTTTGGATGTTCGAGG-GT
* * * *
371811 AAAATGGA-AATTTATGAAAAGTT-TAGGGT
1 AAAAT-GATAATTTTTG-GATGTTCGAGGGT
* ** *
371840 CAAAAATG-TAAATTTTGGACATTCG-GAGT
1 --AAAATGATAATTTTTGGATGTTCGAGGGT
*
371869 AAAATGGTAA-TTTTGGATGTTCGAGGGT
1 AAAATGATAATTTTTGGATGTTCGAGGGT
* *
371897 AAAATGCTAATTTTTGGAAAGTTCG-GGGT
1 AAAATGATAATTTTTGG-ATGTTCGAGGGT
**
371926 CAAAAAT-ATAATTTTTGGACATTCTGA-GGT
1 --AAAATGATAATTTTTGGATGTTC-GAGGGT
371956 AAAATGATAA-TTTTGGATGTTCGAGGGT
1 AAAATGATAATTTTTGGATGTTCGAGGGT
* * *
371984 -ACATGGTAATTTTTGGAAAGTGT-G-GGGT
1 AAAATGATAATTTTTGG-ATGT-TCGAGGGT
* * * *
372012 CAAAAATG-TGATTTTTGGAAGTTTGGGGGT
1 --AAAATGATAATTTTTGGATGTTCGAGGGT
* * *
372042 AAAAATG-TAATTTTTGAGAAGTTTGAGGTT
1 -AAAATGATAATTTTTG-GATGTTCGAGGGT
* * * * *
372072 AAAATG-TGAGTTTTGGAAGTTTGGGGGT
1 AAAATGATAATTTTTGGATGTTCGAGGGT
*
372100 AAAAATG-TAATTTTTAGGAAGTTCGA
1 -AAAATGATAATTTTT-GGATGTTCGA
372126 TGTCAAAAAA
Statistics
Matches: 436, Mismatches: 87, Indels: 100
0.70 0.14 0.16
Matches are distributed among these distances:
27 37 0.08
28 106 0.24
29 192 0.44
30 79 0.18
31 22 0.05
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGATAATTTTTGGATGTTCGAGGGT
Found at i:372038 original size:29 final size:29
Alignment explanation
Indices: 371829--372194 Score: 208
Period size: 29 Copynumber: 12.6 Consensus size: 29
371819 AATTTATGAA
* *
371829 AAGTTTAGGGTCAAAAATGTAAATTTTGG
1 AAGTTTGGGGTCAAAAATGTAATTTTTGG
* *
371858 ACA-TTCGGAGT--AAAATGGTAA-TTTTGG
1 A-AGTTTGGGGTCAAAAAT-GTAATTTTTGG
* *
371885 ATGTTCGAGGGT--AAAATGCTAATTTTTGG
1 AAGTTTG-GGGTCAAAAATG-TAATTTTTGG
* *
371914 AAAGTTCGGGGTCAAAAATATAATTTTTGG
1 -AAGTTTGGGGTCAAAAATGTAATTTTTGG
*
371944 ACA-TTCTGAGGT--AAAATGATAA-TTTTGG
1 A-AGTT-TGGGGTCAAAAATG-TAATTTTTGG
* * *
371972 ATGTTCGAGGGT---ACATGGTAATTTTTGG
1 AAGTTTG-GGGTCAAAAAT-GTAATTTTTGG
* *
372000 AAAGTGTGGGGTCAAAAATGTGATTTTTGG
1 -AAGTTTGGGGTCAAAAATGTAATTTTTGG
372030 AAGTTTGGGGGT-AAAAATGTAATTTTTGAG
1 AAGTTT-GGGGTCAAAAATGTAATTTTTG-G
* * * *
372060 AAGTTTGAGGT-TAAAATGTGAGTTTTGG
1 AAGTTTGGGGTCAAAAATGTAATTTTTGG
372088 AAGTTTGGGGGT-AAAAATGTAATTTTTAGG
1 AAGTTT-GGGGTCAAAAATGTAATTTTT-GG
* ** **
372118 AAGTTCGATGTCAAAAAATGTAATTTTTTAA
1 AAGTTTGGGGTC-AAAAATGTAA-TTTTTGG
* *
372149 AAGTTTAGGGGTC-AAAATATAATTTTTATG
1 AAGTTT-GGGGTCAAAAATGTAATTTTT-GG
*
372179 AAGTTCGGGGTCAAAA
1 AAGTTTGGGGTCAAAA
372195 TATGATTTTG
Statistics
Matches: 266, Mismatches: 41, Indels: 59
0.73 0.11 0.16
Matches are distributed among these distances:
27 24 0.09
28 50 0.19
29 93 0.35
30 67 0.25
31 23 0.09
32 9 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
AAGTTTGGGGTCAAAAATGTAATTTTTGG
Found at i:372057 original size:87 final size:87
Alignment explanation
Indices: 371548--372114 Score: 375
Period size: 87 Copynumber: 6.6 Consensus size: 87
371538 AGATGCTCAG
* * * * * * * *
371548 GGGTAAAATAGTAATTTTT-GAAAGTTT-AGGG-CAAAAATGCAATTTTTAGATACTCGAGGGCA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACATTTG-GGGTA
*
371610 AAATGGTAATTTTGGGATGATC-A
65 AAATGGTAATTTT-GGATGTTCGA
*** * * ** ** *
371633 GGGGTAAAACAATAATTTTTGGATA--CTCAAAGG-C-AAAATGGTAATTTTTGGATGTCTGAGG
1 -GGGTAAAATGGTAATTTTTGGAAAGTTTC-GGGGTCAAAAAT-GTAATTTTTGGACATTTG-GG
* * *
371694 GTAAAACGATAATTTTTGGATATTC-A
62 GTAAAATGGTAA-TTTTGGATGTTCGA
* ** ** * * * *
371720 GGGGTAAAATAGTTTTTTTTTTAAA-TTT-AGGGTCAAAAGTGTATTTTTTGGACATCTAGGGGT
1 -GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACAT-TTGGGGT
*
371783 AAAATGGTAATTTTGGATGTT-TA
64 AAAATGGTAATTTTGGATGTTCGA
* * * * * * *
371806 GGTGTAAAATGGAAATTTATGAAAAGTTT-AGGGTCAAAAATGTAAATTTTGGACATTCGGAGTA
1 GG-GTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACATTTGGGGTA
371870 AAATGGTAATTTTGGATGTTCGA
65 AAATGGTAATTTTGGATGTTCGA
* * *
371893 GGGTAAAATGCTAATTTTTGGAAAG-TTCGGGGTCAAAAATATAATTTTTGGACATTCTGAGGTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACATT-TGGGGTA
*
371957 AAATGATAATTTTGGATGTTCGA
65 AAATGGTAATTTTGGATGTTCGA
* * *
371980 GGGT-ACATGGTAATTTTTGGAAAGTGT-GGGGTCAAAAATGTGATTTTTGGA-AGTTTGGGGGT
1 GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACA-TTT-GGGGT
* *
372042 AAAAAT-GTAATTTTTGAGAAGTTTGA
64 -AAAATGGTAA-TTTTG-GATGTTCGA
* * * *
372068 GGTTAAAAT-GTGAGTTTTGG-AAGTTTGGGGGT-AAAAATGTAATTTTT
1 GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTT
372115 AGGAAGTTCG
Statistics
Matches: 385, Mismatches: 73, Indels: 45
0.77 0.15 0.09
Matches are distributed among these distances:
85 7 0.02
86 170 0.44
87 171 0.44
88 34 0.09
89 3 0.01
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (87 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTCGGGGTCAAAAATGTAATTTTTGGACATTTGGGGTAA
AATGGTAATTTTGGATGTTCGA
Found at i:372211 original size:29 final size:29
Alignment explanation
Indices: 372156--372211 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
372146 TAAAAGTTTA
* **
372156 GGGGTCAAAATATAATTTTTATGAAGTTC
1 GGGGTCAAAATATAATTTTGACAAAGTTC
* *
372185 GGGGTCAAAATATGATTTTGGCAAAGT
1 GGGGTCAAAATATAATTTTGACAAAGT
372212 GTAAAGGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (29 bp):
GGGGTCAAAATATAATTTTGACAAAGTTC
Found at i:373401 original size:15 final size:15
Alignment explanation
Indices: 373381--373411 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
373371 AAATATAAAT
*
373381 ATTATATATTTATTA
1 ATTATACATTTATTA
373396 ATTATACATTTATTA
1 ATTATACATTTATTA
373411 A
1 A
373412 CCTGAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATACATTTATTA
Found at i:374078 original size:17 final size:17
Alignment explanation
Indices: 374056--374112 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
374046 TCTTTCAAAT
374056 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
**
374073 TTTAAATTTAAAATAGT
1 TTTAAATTTAAAATAAA
*
374090 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
374107 TTTAAA
1 TTTAAA
374113 ATAAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:374119 original size:17 final size:17
Alignment explanation
Indices: 374056--374124 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
374046 TCTTTCAAAT
*
374056 TTTAAATTTAAAATAAA
1 TTTAAAATTAAAATAAA
* **
374073 TTTAAATTTAAAATAGT
1 TTTAAAATTAAAATAAA
*
374090 TTTAAACTTAAAATAAA
1 TTTAAAATTAAAATAAA
*
374107 TTTAAAATAAAAAATAAA
1 TTTAAAAT-TAAAATAAA
374125 AAGTGGGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
TTTAAAATTAAAATAAA
Found at i:374569 original size:48 final size:48
Alignment explanation
Indices: 374505--374612 Score: 189
Period size: 48 Copynumber: 2.2 Consensus size: 48
374495 CTTCTTCCCT
374505 GTATCTCATCAGGAAGACGATCATTTTATTACGTCGACCTGCTTCTCA
1 GTATCTCATCAGGAAGACGATCATTTTATTACGTCGACCTGCTTCTCA
* * *
374553 GTATCTTATCAGGAAGACGATCATTTTATTGCTTCGACCTGCTTCTCA
1 GTATCTCATCAGGAAGACGATCATTTTATTACGTCGACCTGCTTCTCA
374601 GTATCTCATCAG
1 GTATCTCATCAG
374613 AAAGCTGGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (48 bp):
GTATCTCATCAGGAAGACGATCATTTTATTACGTCGACCTGCTTCTCA
Found at i:374710 original size:123 final size:124
Alignment explanation
Indices: 374546--374816 Score: 388
Period size: 123 Copynumber: 2.2 Consensus size: 124
374536 CGTCGACCTG
* *
374546 CTTCTCAGTATCTTATCAGGAAGACGATCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* **
374611 -AGAAAGCTGGGGTTCGAAGATTT-GCTCACTTTGAGC-CTGGTTTCATTGATTTGGTCTA
66 AAG-AAGCTGGGGTTCGAAG-TTTCGCTCACATCAAGCTCTGGTTTCATTGATTTGGTCTA
* **
374669 CTTCTCAGTATCTCATCAGGAATACGACCATTTTATTGCTTCGAGTTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * *
374734 AAGAAGTTGGGGTTTGAAGTTTCGCTCACATCAAGCTTTGGTTTCATTGATTTGGTCTA
66 AAGAAGCTGGGGTTCGAAGTTTCGCTCACATCAAGCTCTGGTTTCATTGATTTGGTCTA
374793 CTTCTCAGTATCTCAT-ATGGAAGA
1 CTTCTCAGTATCTCATCA-GGAAGA
374817 TGGCCGCATC
Statistics
Matches: 132, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
122 3 0.02
123 85 0.64
124 44 0.33
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (124 bp):
CTTCTCAGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
AAGAAGCTGGGGTTCGAAGTTTCGCTCACATCAAGCTCTGGTTTCATTGATTTGGTCTA
Found at i:375520 original size:210 final size:210
Alignment explanation
Indices: 374700--376368 Score: 2386
Period size: 210 Copynumber: 8.0 Consensus size: 210
374690 ATACGACCAT
** * * *
374700 TTTATTGCTTCGAGTTGCTTCTCAGTATCTCATCAAGAAGTTGGGGTTTGAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* *
374765 CAAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCAT-ATGGAAGATGGCCGCATCAC
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCA-GGAAGATGACCGCATCAC
* * *
374829 TTGTTTTGATCCACTTCTCTGTGTC-CTATTAGAAAGACGGATCTGGTTCACCTCTCTGTATCTC
130 TTGTTTTGATCCACTTCTCTGTGTCTC-ATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTC
*
374893 ATCAATAAGGTAACCGC
194 ATCAAGAAGGTAACCGC
* * * *
374910 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCACT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAG-TTTCGCTCACA
* * * * * * * *
374974 TTGAG-TCTAGTTTTATTAATTTGGTCTACTTCTCAGTATCTCATTAGGAAGACGGCCGCATCAC
65 TCGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC
* * *
375038 TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAGGATGGATCTAGTTCACTTCTCTGTATCTCA
130 TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCA
*
375103 TCAAGAAGGTAACTGC
195 TCAAGAAGGTAACCGC
*
375119 TTTATTGCTTCGACCTACTTCTCAGTA-C-C-TC----A-------TTCGAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* *
375170 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCATTAGGAAGATGACCGCATCACT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
* * *
375235 TGTTTTGATTCACTTCTCTATGTCTCATCAGGAAGACGGATATGGTTCACTTCTCTGTATCTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
375300 CAAGAAGGTAACCGC
196 CAAGAAGGTAACCGC
* *
375315 TTTATTGCTTCGACCTGCTTCTCAGTACTTCATCAGGAAGTTGGGGTTCGAAGTTTCACTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* * * * *
375380 CGAGCTTTGGTTTCATTGATTTGATCCACTTCTCAGTATCTCATCAAGAAGATGACCACATCGCT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
* *
375445 TGTTTTGATCCACTTCTCTGTCTCTCATCAGGAAGACGGATCTGGTTCTCTTCTCTGTATCTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
* *
375510 CAAAAAGGTAACCAC
196 CAAGAAGGTAACCGC
* ** *
375525 TTTATTGCTTCGACCTGCTTCTCAATACCTCATCAATAAGCTGGGGTTCGAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* *
375590 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCATTAGGAAGATGACCGCATCACT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
*
375655 TGTTTTGATCCACTTCTCTATGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
*
375720 CAGGAAGGTAACCGC
196 CAAGAAGGTAACCGC
*
375735 TGTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* * * * * *
375800 CGAGCTTTGGTTTCATTGATTTGATCCACTTCTGAGTATTTCATCAGGAAGATGATCGCATCGCT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
*
375865 TGTTTTGATCCACTTCTATGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
*
375930 CAGGAAGGTAACCGC
196 CAAGAAGGTAACCGC
*
375945 TTTATTGCTTCGACCTACTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* *
376010 CGAGCTTTGGTTTCAATGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
* * * * * * *
376075 TATTTTGATTCACTTCTTTGTGTCTCATCAGGAAGATGGATCTAGTTCACTTCTCTATATTTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
* *
376140 CAGGAAGGTAA-CAC
196 CAAGAAGGTAACCGC
* * *
376154 TTTATTGCTTTGACCTGCTTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTTGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
* * * * *
376219 CGAGCTTTTGTTTCATTGATTTGGTCCACTTCTCAGTTTCTCATCAAGAAGATGACCGCATCGCT
66 CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
** * * *
376284 TGTTTCAATCCGCTTCTCTGTATCTCATCATGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
131 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
* *
376349 CAGGAAGGTAATCGC
196 CAAGAAGGTAACCGC
376364 TTTAT
1 TTTAT
376369 CGTTTTGGAT
Statistics
Matches: 1308, Mismatches: 131, Indels: 40
0.88 0.09 0.03
Matches are distributed among these distances:
194 3 0.00
195 17 0.01
196 152 0.12
198 1 0.00
199 2 0.00
202 1 0.00
203 1 0.00
206 2 0.00
207 1 0.00
208 1 0.00
209 333 0.25
210 791 0.60
211 3 0.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (210 bp):
TTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGTTGGGGTTCGAAGTTTCGCTCACAT
CGAGCTTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCAT
CAAGAAGGTAACCGC
Found at i:377086 original size:50 final size:50
Alignment explanation
Indices: 376922--377323 Score: 286
Period size: 50 Copynumber: 8.1 Consensus size: 50
376912 TGCGACCTTA
* *
376922 ATCTTCTTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTTAC
1 ATCTTATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
* * ** * *
376972 ATCTTTTTAAGGTATCGAATTCACCGTTACAGCCTCAATCC-TCCCCTGTCATC
1 ATCTTATT-AGGTACCGGGTTCGCCGTTACAGCCTCAA-CCTTTCCCT-TCA-C
* * * *
377025 -TCTTCA-T-GGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCAC
1 ATCTT-ATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
* ** * *
377073 ATCTTATTAGGTACTGGGTTCATCGTTATAGCCTCAACCTTTCCCATCAC
1 ATCTTATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
** ** * * *
377123 AT-TTCA-T-GGTACCGAATTCTTCGTTGCAGCCTCAATCTTTCCCATCAC
1 ATCTT-ATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
* *
377171 AT-TT-TTGAGGTACCAGGTTCGCCGTTACAGCATCAACCTTTCCCTTCAC
1 ATCTTATT-AGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
* * * * * * * *
377220 AT-TTCTGAGGTACCAGGTTCGTCGTTGCGGCATCAACCTTTCCCTTCAA
1 ATCTTATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
* ** ** * *
377269 ATCTTCTTAGGTACTAGGTTCATCGTTGC-GACCTCAACCTTTCCCTTCAA
1 ATCTTATTAGGTACCGGGTTCGCCGTTACAG-CCTCAACCTTTCCCTTCAC
377319 ATCTT
1 ATCTT
377324 CATGTTTTTC
Statistics
Matches: 288, Mismatches: 48, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
47 1 0.00
48 40 0.14
49 90 0.31
50 117 0.41
51 30 0.10
52 9 0.03
53 1 0.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (50 bp):
ATCTTATTAGGTACCGGGTTCGCCGTTACAGCCTCAACCTTTCCCTTCAC
Found at i:377154 original size:48 final size:49
Alignment explanation
Indices: 377046--377313 Score: 181
Period size: 49 Copynumber: 5.4 Consensus size: 49
377036 CTGGGTTCGC
* * * **
377046 CGTTGCGGCCTCAACCTTTCCCGTCACATCTTATTAGGTACTGGGTTCAT
1 CGTTGCAGCCTCAACCTTTCCCATCACAT-TTATTAGGTACCGAATTCAT
** *
377096 CGTTATAGCCTCAACCTTTCCCATCACATTTCA-T-GGTACCGAATTCTT
1 CGTTGCAGCCTCAACCTTTCCCATCACATTT-ATTAGGTACCGAATTCAT
* * **
377144 CGTTGCAGCCTCAATCTTTCCCATCACATTT-TTGAGGTACC-AGGTTCGC
1 CGTTGCAGCCTCAACCTTTCCCATCACATTTATT-AGGTACCGA-ATTCAT
* * * * * * *
377193 CGTTACAGCATCAACCTTTCCCTTCACATTTCTGAGGTACC-AGGTTCGT
1 CGTTGCAGCCTCAACCTTTCCCATCACATTTATTAGGTACCGA-ATTCAT
* * * * * * *
377242 CGTTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTA-CTAGGTTCAT
1 CGTTGCAGCCTCAACCTTTCCCATCACAT-TTATTAGGTACCGA-ATTCAT
377292 CGTTGC-GACCTCAACCTTTCCC
1 CGTTGCAG-CCTCAACCTTTCCC
377314 TTCAAATCTT
Statistics
Matches: 183, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.01
48 39 0.21
49 81 0.44
50 62 0.34
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (49 bp):
CGTTGCAGCCTCAACCTTTCCCATCACATTTATTAGGTACCGAATTCAT
Found at i:377223 original size:97 final size:98
Alignment explanation
Indices: 376945--377327 Score: 269
Period size: 98 Copynumber: 3.9 Consensus size: 98
376935 CCGGGTTCGC
* * * * * * *
376945 CGTTACAGCCTCAACCTTTCCCTTTACATCTTTTTAAGGTATC-GAATTCACCGTTACAGCCTCA
1 CGTTGCAGCCTCAACCTTTCCCATCACATCTTATT-AGGTACCAG-GTTCACCGTTACAGCATCA
* * * ** **
377009 ATCC-TCCCCTGTCATC-TCTTCATGGTACTGGGTTCGC
64 A-CCTTTCCC-ATCA-CAT-TTCATGGTACCGAATTCTT
* * ** * * *
377046 CGTTGCGGCCTCAACCTTTCCCGTCACATCTTATTAGGTACTGGGTTCATCGTTATAGCCTCAAC
1 CGTTGCAGCCTCAACCTTTCCCATCACATCTTATTAGGTACCAGGTTCACCGTTACAGCATCAAC
377111 CTTTCCCATCACATTTCATGGTACCGAATTCTT
66 CTTTCCCATCACATTTCATGGTACCGAATTCTT
* *
377144 CGTTGCAGCCTCAATCTTTCCCATCACAT-TT-TTGAGGTACCAGGTTCGCCGTTACAGCATCAA
1 CGTTGCAGCCTCAACCTTTCCCATCACATCTTATT-AGGTACCAGGTTCACCGTTACAGCATCAA
* * *
377207 CCTTTCCCTTCACATTTC-TGAGGTACC-AGGTTCGT
65 CCTTTCCCATCACATTTCAT--GGTACCGA-ATTCTT
* * * * * * * * *
377242 CGTTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACTAGGTTCATCGTTGC-GACCTCAA
1 CGTTGCAGCCTCAACCTTTCCCATCACATCTTATTAGGTACCAGGTTCACCGTTACAG-CATCAA
* *
377306 CCTTTCCCTTCAAATCTTCATG
65 CCTTTCCCATCACAT-TTCATG
377328 TTTTTCTCAG
Statistics
Matches: 230, Mismatches: 40, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
96 3 0.01
97 43 0.19
98 76 0.33
99 45 0.20
100 31 0.13
101 32 0.14
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.34
Consensus pattern (98 bp):
CGTTGCAGCCTCAACCTTTCCCATCACATCTTATTAGGTACCAGGTTCACCGTTACAGCATCAAC
CTTTCCCATCACATTTCATGGTACCGAATTCTT
Found at i:378318 original size:9 final size:10
Alignment explanation
Indices: 378282--378332 Score: 63
Period size: 9 Copynumber: 5.4 Consensus size: 10
378272 CTTTTTTCTA
378282 TTTT-TTTCC
1 TTTTCTTTCC
*
378291 TTTCCTTTCC
1 TTTTCTTTCC
*
378301 TTTTATTT-C
1 TTTTCTTTCC
378310 TTTTCTTT-C
1 TTTTCTTTCC
378319 TTTTCTTTCC
1 TTTTCTTTCC
378329 TTTT
1 TTTT
378333 TATTTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:383640 original size:28 final size:29
Alignment explanation
Indices: 383598--383726 Score: 111
Period size: 29 Copynumber: 4.5 Consensus size: 29
383588 AAACGGAGTA
* * *
383598 AAAAAT-GCAATTTTTGGATGCCCGAGGG
1 AAAAATGGTAATTTTTAGATGCTCGAGGG
* * *
383626 TAAAATGGTAATTTTTAGAAGTTC-AGGG
1 AAAAATGGTAATTTTTAGATGCTCGAGGG
*
383654 CAAAAAT-GTAATTTTTAGATGCTTGAGGG
1 -AAAAATGGTAATTTTTAGATGCTCGAGGG
** **
383683 AAAAATGGTAATTTTGGGATAATCGAGGG
1 AAAAATGGTAATTTTTAGATGCTCGAGGG
* *
383712 TAAAACGGTAATTTT
1 AAAAATGGTAATTTT
383727 AGTACACCCG
Statistics
Matches: 80, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 29 0.36
29 51 0.64
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.32
Consensus pattern (29 bp):
AAAAATGGTAATTTTTAGATGCTCGAGGG
Found at i:383909 original size:29 final size:29
Alignment explanation
Indices: 383821--384098 Score: 141
Period size: 29 Copynumber: 9.5 Consensus size: 29
383811 ACTCGGGGGA
*
383821 AAAATGGTAA-TTTTAAAAAGTTT-GAGGT
1 AAAATGGTAATTTTTGAAAAGTTTAG-GGT
* *
383849 CAAAAAT-GTAATTTTTTG-ACA-TTCAGGGT
1 --AAAATGGTAA-TTTTTGAAAAGTTTAGGGT
*
383878 AAAATGGTAATTTTTGAAAAGTTTAGTGT
1 AAAATGGTAATTTTTGAAAAGTTTAGGGT
* * *
383907 AAAAAAAT-GTAATTTTTGGATA-TTCGAGGGT
1 ---AAAATGGTAATTTTTGAAAAGTT-TAGGGT
* *
383938 AAAATGGTAATTTTTG-GATGTTTAAGGGT
1 AAAATGGTAATTTTTGAAAAGTTT-AGGGT
**
383967 AAAATGGTAATTTTTG-AAAGTTCGGGGT
1 AAAATGGTAATTTTTGAAAAGTTTAGGGT
* * ***
383995 CAAAAAT-GTAATTTTTGGACA-TCCGGGGGGT
1 --AAAATGGTAATTTTTGAAAAGT--TTAGGGT
*
384026 AAAATGGTAATTTTTGGAAAGTTTAGGGTT
1 AAAATGGTAATTTTTGAAAAGTTTAGGG-T
* *
384056 AAAAT-GTGATTTTTG-GAAGTTTGAGGGT
1 AAAATGGTAATTTTTGAAAAGTTT-AGGGT
* *
384084 AAAATTGTATTTTTT
1 AAAATGGTAATTTTT
384099 CTAAAAAATA
Statistics
Matches: 196, Mismatches: 29, Indels: 47
0.72 0.11 0.17
Matches are distributed among these distances:
27 11 0.06
28 27 0.14
29 91 0.46
30 36 0.18
31 26 0.13
32 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAAAAGTTTAGGGT
Found at i:383922 original size:59 final size:59
Alignment explanation
Indices: 383793--383953 Score: 204
Period size: 58 Copynumber: 2.7 Consensus size: 59
383783 ACCCAGGGGC
* * * * *
383793 AAAATGGTAA-TTTTGGACACTCGGGGGAAAAATGGTAA-TTTTAAAAAGTTTGAGGTCA
1 AAAAT-GTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGTAA
*
383851 AAAATGTAATTTTTTGACATTC-AGGGTAAAATGGTAATTTTTGAAAAGTTT-AGTGTAAA
1 AAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTTGAG-GT-AA
*
383910 AAAATGTAATTTTTGGATATTCGAGGGTAAAATGGTAATTTTTG
1 AAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTG
383954 GATGTTTAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
57 19 0.21
58 29 0.32
59 21 0.23
60 21 0.23
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGTAA
Found at i:384098 original size:88 final size:88
Alignment explanation
Indices: 383873--384098 Score: 262
Period size: 88 Copynumber: 2.6 Consensus size: 88
383863 TTTGACATTC
** * * * * *
383873 AGGGTAAAATGGTAATTTTTGAAAAGTTTAGTGTAAAAAAATGTAATTTTTGGATATTC-GAGGG
1 AGGGTAAAATGGTAATTTTTG-AAAGTTCGGGGT-CAAAAATGTAATTTTTGGACATCCGGGGGG
*
383937 TAAAATGGTAATTTTTGGATGTTTA
64 TAAAATGGTAATTTTTGGAAGTTTA
383962 AGGGTAAAATGGTAATTTTTGAAAGTTCGGGGTCAAAAATGTAATTTTTGGACATCCGGGGGGTA
1 AGGGTAAAATGGTAATTTTTGAAAGTTCGGGGTCAAAAATGTAATTTTTGGACATCCGGGGGGTA
384027 AAATGGTAATTTTTGGAAAGTTT-
66 AAATGGTAATTTTTGG-AAGTTTA
* * * * *
384050 AGGGTTAAAAT-GTGATTTTTGGAAGTTTGAGGGT-AAAATTGTATTTTTT
1 AGGG-TAAAATGGTAATTTTTGAAAGTTCG-GGGTCAAAAATGTAATTTTT
384099 CTAAAAAATA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
87 21 0.17
88 63 0.52
89 36 0.30
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (88 bp):
AGGGTAAAATGGTAATTTTTGAAAGTTCGGGGTCAAAAATGTAATTTTTGGACATCCGGGGGGTA
AAATGGTAATTTTTGGAAGTTTA
Found at i:385369 original size:15 final size:15
Alignment explanation
Indices: 385349--385379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
385339 AAATAAAAAG
*
385349 ATTATATATTTATTA
1 ATTATACATTTATTA
385364 ATTATACATTTATTA
1 ATTATACATTTATTA
385379 A
1 A
385380 CTTGAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATACATTTATTA
Found at i:387150 original size:49 final size:50
Alignment explanation
Indices: 387089--387210 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 50
387079 AAATAAAATA
* * *
387089 ATCTGAACAAAACAATATAAATAAATA-TTATGTCTATGCAAAACATGAT
1 ATCTAAACAAAACAATATAAATAAATATTTATATCTATGCAAAACATCAT
* **
387138 ATCTAAACAAAACAA-ATTAAATAAATATTTATATTTATTTAAAACATCAT
1 ATCTAAACAAAACAATA-TAAATAAATATTTATATCTATGCAAAACATCAT
* *
387188 ATC-AGA-AAAACAATTTAAATAAA
1 ATCTAAACAAAACAATATAAATAAA
387211 CAAGATCTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
48 16 0.26
49 26 0.42
50 20 0.32
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (50 bp):
ATCTAAACAAAACAATATAAATAAATATTTATATCTATGCAAAACATCAT
Found at i:389895 original size:77 final size:77
Alignment explanation
Indices: 389752--390084 Score: 287
Period size: 82 Copynumber: 4.2 Consensus size: 77
389742 TTAAAATTCT
* * * * ** * *
389752 GAAACAAAATCAAAATCAATTCTGTTGAACAGTAGAAATAAATCCTTAAACAGAATTATTTTATT
1 GAAACAAAATCAAAATCAATTCTATTGAACGGCAGGAATAAATCCAAAAACAGAATTAATTAATT
389817 AATTCTTGTTTG
66 AATTCTTGTTTG
* *
389829 GAAAGAAAAGCAAAATCAATTCTATTGAACGGCAGGAATAAATCCAAAAACAGAATTAATTAATT
1 GAAACAAAATCAAAATCAATTCTATTGAACGGCAGGAATAAATCCAAAAACAGAATTAATTAATT
389894 AATTCTTGTTTG
66 AATTCTTGTTTG
* * * *
389906 GAAACAAAATCAAAATAGAATAAAACCTATTGAATGGC-GAGAATAAATCCCAAAACAGAATT-A
1 GAAACAAAATCAAAAT-CAAT----TCTATTGAACGGCAG-GAATAAATCCAAAAACAGAATTAA
**
389969 TTCAATTAATTCTTACTTG
60 TT-AATTAATTCTTGTTTG
* * * * ** *
389988 GAAACAAAATCAAAATAGAAAAAAATT-TGTTGTACGGTAGGAATAAATCCCGAAATAGAATT-A
1 GAAACAAAATCAAAAT------CAATTCTATTGAACGGCAGGAATAAATCCAAAAACAGAATTAA
*
390051 TTCAATTAATCCTTGTTTG
60 TT-AATTAATTCTTGTTTG
*
390070 GAAACAAAATTAAAA
1 GAAACAAAATCAAAA
390085 CAGAATAAAA
Statistics
Matches: 213, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
77 81 0.38
78 3 0.01
81 4 0.02
82 120 0.56
83 1 0.00
87 4 0.02
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (77 bp):
GAAACAAAATCAAAATCAATTCTATTGAACGGCAGGAATAAATCCAAAAACAGAATTAATTAATT
AATTCTTGTTTG
Found at i:389963 original size:82 final size:82
Alignment explanation
Indices: 389788--390218 Score: 477
Period size: 82 Copynumber: 5.4 Consensus size: 82
389778 GAACAGTAGA
** ** * * *
389788 AATAAATCCTTAAACAGAATTATTTTATTAATTCTTGTTTGGAAAGAAAAGCAAAAT-CAAT---
1 AATAAATCCCAAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAA
389849 -TCTATTGAACGGCAGG
66 ATCTATTGAACGGCAGG
*
389865 AATAAATCCAAAAACAGAATTAATT-AATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
1 AATAAATCCCAAAACAGAATT-ATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* *
389929 AACCTATTGAATGGC-GAG
65 AATCTATTGAACGGCAG-G
** *
389947 AATAAATCCCAAAACAGAATTATTCAATTAATTCTTACTTGGAAACAAAATCAAAATAGAAAAAA
1 AATAAATCCCAAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAA
* * * *
390012 ATTTGTTGTACGGTAGG
66 ATCTATTGAACGGCAGG
* * * * *
390029 AATAAATCCCGAAATAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATTAAAACAGAATAAA
1 AATAAATCCCAAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAA
* ***
390094 ATCTGTTGAACGATGGG
66 ATCTATTGAACGGCAGG
* * * *
390111 AATAAATCTCGAAACAG-A-TATTCAATTAATCCTTGTTT-GAAACAAAATCAAAATAAAATAAA
1 AATAAATCCCAAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAA
* *
390173 ATATATTGAACGACAGG
66 ATCTATTGAACGGCAGG
*
390190 AATAAATCCCAAAACAGATTTATTCAATT
1 AATAAATCCCAAAACAGAATTATTCAATT
390219 TTAATTTTTA
Statistics
Matches: 301, Mismatches: 42, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
77 48 0.16
78 6 0.02
79 49 0.16
80 20 0.07
81 14 0.05
82 163 0.54
83 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (82 bp):
AATAAATCCCAAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAA
ATCTATTGAACGGCAGG
Found at i:390731 original size:50 final size:50
Alignment explanation
Indices: 390659--390774 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
390649 TAAATTTAAA
** * * * * *
390659 ATATTTATAAAAAATACAAGATCTGAATAAAATAATATAAACAAATATTT
1 ATATTTATGTAAAACACCAGATCTGAACAAAACAAAATAAACAAATATTT
* *
390709 ATGTTTATGTAAAACACCAGATCTGAACAAAACAAAATAAATAAATATTT
1 ATATTTATGTAAAACACCAGATCTGAACAAAACAAAATAAACAAATATTT
*
390759 ATATTTATTTAAAACA
1 ATATTTATGTAAAACA
390775 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (50 bp):
ATATTTATGTAAAACACCAGATCTGAACAAAACAAAATAAACAAATATTT
Found at i:391052 original size:22 final size:21
Alignment explanation
Indices: 391023--391065 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
391013 CGAAACGTTT
*
391023 GAAAAAATTGGAGAGAAAAAA
1 GAAAAAATTCGAGAGAAAAAA
391044 GAAAGAAATTCGAGAGAAAAAA
1 GAAA-AAATTCGAGAGAAAAAA
391066 TAAACTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.09
Consensus pattern (21 bp):
GAAAAAATTCGAGAGAAAAAA
Done.