Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015343.1 Kokia drynarioides strain JFW-HI SEQ_130390, 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: 430638
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 147 characters in sequence are not A, C, G, or T
Found at i:260 original size:23 final size:23
Alignment explanation
Indices: 214--281 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
204 TAAACGGAAC
*
214 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGTACACAAAGTACT
* *
236 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACT
259 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGTACACAAAGTACT
282 GAGCACACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGTACACAAAGTACT
Found at i:320 original size:23 final size:23
Alignment explanation
Indices: 282--331 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
272 ACAAAGTACT
282 GAGCACACACAATGCTAATCAGA
1 GAGCACACACAATGCTAATCAGA
* *
305 GAGCACATACAGTGCTAATCAGA
1 GAGCACACACAATGCTAATCAGA
328 GAGC
1 GAGC
332 GCGCTAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (23 bp):
GAGCACACACAATGCTAATCAGA
Found at i:432 original size:24 final size:26
Alignment explanation
Indices: 394--441 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
384 TTTGCATGGG
394 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
420 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
442 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:2552 original size:10 final size:10
Alignment explanation
Indices: 2522--2555 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2512 TACCATACCA
2522 ATTTTTCTAAT
1 ATTTTT-TAAT
2533 ATTATTTTAAT
1 ATT-TTTTAAT
2544 ATTTTTTAAT
1 ATTTTTTAAT
2554 AT
1 AT
2556 AAAAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 10 0.45
12 3 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:11473 original size:2 final size:2
Alignment explanation
Indices: 11466--11500 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11456 GATCCGTGCT
11466 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11501 TAATGATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:14788 original size:72 final size:72
Alignment explanation
Indices: 14671--14814 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
14661 TTTTTCATGC
14671 TTATTTTACAATATTGGAGTAGAACCATTTTCATGTTTTTCTTTTAAAATTTCAATGGAGTTACG
1 TTATTTTACAATATTGGAGTAGAACCATTTTCATGTTTTTCTTTTAAAATTTCAATGGAGTTACG
14736 ATACCCA
66 ATACCCA
*
14743 TTATTTTACAATATTGGAGTAGAACCATTTTCATGTTTTTCTTTTAAAATTTCAGTGGAGTTACG
1 TTATTTTACAATATTGGAGTAGAACCATTTTCATGTTTTTCTTTTAAAATTTCAATGGAGTTACG
14808 ATACCCA
66 ATACCCA
14815 AACCAAACTG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (72 bp):
TTATTTTACAATATTGGAGTAGAACCATTTTCATGTTTTTCTTTTAAAATTTCAATGGAGTTACG
ATACCCA
Found at i:30216 original size:180 final size:180
Alignment explanation
Indices: 29965--30304 Score: 423
Period size: 180 Copynumber: 1.9 Consensus size: 180
29955 GTAAAAATAA
** * * *
29965 ATTTCTTTCTTAAATATTTGAATTAAATTCAAATTTTAAAATTAACATTATTAGAAGAATTTTAT
1 ATTTCTTTCTTAAATATTTGAATTAAATTCAAAACTTAAAATCAACATTATTAGAAGAACTTTAC
* * *
30030 TTAAATATCACTATCAACCCAAATAAAATTAGATTTAGATTACAAAACGGATGAAAATATATGTA
66 TTAAATATCACTATCAACCCAAATAAAATTAGACTCAAATTACAAAACGGATGAAAATATATGTA
* * *
30095 TTTG-ATTCACGCTTGTAAATGGTGCAATGGTTAGAAGAATCGGAAATTG
131 GTTGAATTCACACTTGTAAATGATGCAATGGTTAGAAGAATCGGAAATTG
* * * * *
30144 ATTTCTTTCTTAAATTATTTGGATTAAATTTAAAACTTAAAATCGATATTGTT-GAAAGAACTTT
1 ATTTCTTTCTTAAA-TATTTGAATTAAATTCAAAACTTAAAATCAACATTATTAG-AAGAACTTT
* ** ** * * *
30208 ACTTAAATATCACTTTTGACCTGAATAAAATTAGACTCAAATTATAAAACGGGTGAAAATATTTG
64 ACTTAAATATCACTATCAACCCAAATAAAATTAGACTCAAATTACAAAACGGATGAAAATATATG
*
30273 TAGTTGAATTCACACTTGTGAATGATGCAATG
129 TAGTTGAATTCACACTTGTAAATGATGCAATG
30305 TGTAACACCC
Statistics
Matches: 133, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
179 15 0.11
180 96 0.72
181 22 0.17
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (180 bp):
ATTTCTTTCTTAAATATTTGAATTAAATTCAAAACTTAAAATCAACATTATTAGAAGAACTTTAC
TTAAATATCACTATCAACCCAAATAAAATTAGACTCAAATTACAAAACGGATGAAAATATATGTA
GTTGAATTCACACTTGTAAATGATGCAATGGTTAGAAGAATCGGAAATTG
Found at i:31024 original size:23 final size:22
Alignment explanation
Indices: 30998--31068 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
30988 AAACAGTAAA
*
30998 CACACATAGTGCAATCTAGTAGG
1 CACACATAATGCAATC-AGTAGG
*
31021 CACACACAATGCAATCAGTAGG
1 CACACATAATGCAATCAGTAGG
* * *
31043 CGCACATAACGCAAATCAGTAAG
1 CACACATAATGC-AATCAGTAGG
31066 CAC
1 CAC
31069 GTGAAGTGCG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.38
23 25 0.62
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.15
Consensus pattern (22 bp):
CACACATAATGCAATCAGTAGG
Found at i:33194 original size:6 final size:6
Alignment explanation
Indices: 33183--33210 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33173 CTGTTCTCCA
33183 TTCATC TTCATC TTCATC TTCATC TTCA
1 TTCATC TTCATC TTCATC TTCATC TTCA
33211 AGAAGAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCATC
Found at i:54543 original size:28 final size:25
Alignment explanation
Indices: 54508--54574 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 25
54498 TCACTTAACT
*
54508 ATTA-TTAAATTTCTTTTTTATCATTCA
1 ATTATTTAAATTTATTTTTT-T-A-TCA
*
54535 ATTATTTAATTTTATTTTTTTATCA
1 ATTATTTAAATTTATTTTTTTATCA
54560 ATTTATCTTAAATTT
1 A-TTAT-TTAAATTT
54575 TTTATCACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 5 0.15
27 12 0.35
28 13 0.38
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTATTTAAATTTATTTTTTTATCA
Found at i:62039 original size:16 final size:15
Alignment explanation
Indices: 62018--62061 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
62008 TATATTTTCA
62018 TATAATAAATTATTAT
1 TATAATAAATTATT-T
*
62034 TATAATTAATTA-TT
1 TATAATAAATTATTT
62048 T-TAATAAATTATTT
1 TATAATAAATTATTT
62062 AATATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 1 0.04
16 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATAAATTATTT
Found at i:62073 original size:29 final size:30
Alignment explanation
Indices: 62020--62085 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
62010 TATTTTCATA
*
62020 TAATAAATTATTATTATAATTAA-TTATTT
1 TAATAAATTATTATAATAATTAATTTATTT
*
62049 TAATAAATTATT-TAATATTTCAATTTTATTT
1 TAATAAATTATTATAATAATT-AA-TTTATTT
62080 TAATAA
1 TAATAA
62086 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 14 0.44
31 12 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TAATAAATTATTATAATAATTAATTTATTT
Found at i:62092 original size:13 final size:14
Alignment explanation
Indices: 62076--62117 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
62066 TTTCAATTTT
62076 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
62089 ATTTTAAGAATAATA
1 ATTTTAATAAT-ATA
62104 ATTTTAAATAATAT
1 ATTTT-AATAATAT
62118 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:62108 original size:15 final size:16
Alignment explanation
Indices: 62081--62110 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62071 ATTTTATTTT
62081 AATAATAAATTTTAAG
1 AATAATAAATTTTAAG
62097 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
62111 ATAATATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAG
Found at i:62434 original size:18 final size:18
Alignment explanation
Indices: 62413--62459 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
62403 TAATATATTA
62413 TTTAATTAAAAAATAA-T
1 TTTAATTAAAAAATAAGT
*
62430 GTTTATTTAAAAAATAAGT
1 -TTTAATTAAAAAATAAGT
62449 TCTTAATTAAA
1 T-TTAATTAAA
62460 TATATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
TTTAATTAAAAAATAAGT
Found at i:62493 original size:20 final size:19
Alignment explanation
Indices: 62460--62506 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
62450 CTTAATTAAA
62460 TATATATTAAATTTTATTAG
1 TATAT-TTAAATTTTATTAG
*
62480 TATATTTAATATTTTATTAT
1 TATATTTAA-ATTTTATTAG
62500 TATATTT
1 TATATTT
62507 TAAAAAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATTTAAATTTTATTAG
Found at i:62644 original size:19 final size:20
Alignment explanation
Indices: 62612--62650 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
62602 TAAGTTCTTA
62612 ATTATATATATTAAT-TTTT
1 ATTATATATATTAATATTTT
62631 ATTAGTATAT-TTAATATTTT
1 ATTA-TATATATTAATATTTT
62651 TTGAACGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTATATATATTAATATTTT
Found at i:74578 original size:19 final size:18
Alignment explanation
Indices: 74533--74584 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
74523 TTTTGATGTT
*
74533 TTTTAATTTTTATTTATC
1 TTTTAATTTTTATTTATA
*
74551 TTGTT-ATTTTTCTGTTATA
1 TT-TTAATTTTTAT-TTATA
74570 TTTTAA-TTTTATTTA
1 TTTTAATTTTTATTTA
74585 GAATGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 3 0.11
18 16 0.57
19 9 0.32
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTTATTTATA
Found at i:77755 original size:33 final size:32
Alignment explanation
Indices: 77718--77782 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
77708 CTCTAGGTTG
*
77718 ATAGCGGATTACTTTTAGAATGGATCAAACTTT
1 ATAGCAGATTACTTTTAGAATGGATC-AACTTT
77751 ATAGCAGATTACTTTTAGAATGGATCAACTTT
1 ATAGCAGATTACTTTTAGAATGGATCAACTTT
77783 TTTTTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
ATAGCAGATTACTTTTAGAATGGATCAACTTT
Found at i:77783 original size:17 final size:17
Alignment explanation
Indices: 77728--77783 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
77718 ATAGCGGATT
77728 ACTTTTAGAATGGATCAA
1 ACTTTTAGAATGGATC-A
* *
77746 ACTTTATAGCA--GAT-T
1 ACTTT-TAGAATGGATCA
77761 ACTTTTAGAATGGATCA
1 ACTTTTAGAATGGATCA
77778 ACTTTT
1 ACTTTT
77784 TTTTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 3 0.10
17 9 0.30
18 5 0.17
19 4 0.13
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (17 bp):
ACTTTTAGAATGGATCA
Found at i:101160 original size:27 final size:27
Alignment explanation
Indices: 101122--101176 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
101112 TAAGAAACCA
101122 TGAAATTTCTTAAAACAACTTCATAAG
1 TGAAATTTCTTAAAACAACTTCATAAG
101149 TGAAATTTCTTAAAACAACTTCATAAG
1 TGAAATTTCTTAAAACAACTTCATAAG
101176 T
1 T
101177 TTTCTAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (27 bp):
TGAAATTTCTTAAAACAACTTCATAAG
Found at i:105431 original size:3 final size:3
Alignment explanation
Indices: 105423--105455 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
105413 TTTTGTTTTG
105423 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
105456 ACAGCGCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:107407 original size:14 final size:14
Alignment explanation
Indices: 107388--107427 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
107378 AAACGGGAAA
107388 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
*
107402 AAAAGAAAGAAAGG
1 AAAAGAAAGAAAAG
* *
107416 AGAGGAAAGAAA
1 AAAAGAAAGAAA
107428 GAAGAAGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAG
Found at i:107412 original size:18 final size:18
Alignment explanation
Indices: 107384--107430 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
107374 AAATAAACGG
107384 GAAAA-AAAGAAAGAAAA
1 GAAAAGAAAGAAAGAAAA
* *
107401 GAAAAGAAAGAAAGGAGA
1 GAAAAGAAAGAAAGAAAA
*
107419 GGAAAGAAAGAA
1 GAAAAGAAAGAA
107431 GAAGGAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
GAAAAGAAAGAAAGAAAA
Found at i:107428 original size:14 final size:14
Alignment explanation
Indices: 107392--107444 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
107382 GGGAAAAAAA
* * *
107392 GAAAGAAAAGAAAA
1 GAAAGAAAGGAGAG
107406 GAAAGAAAGGAGAG
1 GAAAGAAAGGAGAG
*
107420 GAAAGAAAGAAGAAG
1 GAAAGAAAGGAG-AG
*
107435 GAGAGAAAGG
1 GAAAGAAAGG
107445 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGGAGAG
Found at i:110285 original size:26 final size:27
Alignment explanation
Indices: 110248--110301 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
110238 ATGAATTTGA
*
110248 AATTAATTATTTCAATATTTGCA-TTT
1 AATTAATAATTTCAATATTTGCACTTT
**
110274 AATTAATAATTTTTATATTTGCACTTT
1 AATTAATAATTTCAATATTTGCACTTT
110301 A
1 A
110302 GTTTTGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (27 bp):
AATTAATAATTTCAATATTTGCACTTT
Found at i:110442 original size:7 final size:7
Alignment explanation
Indices: 110432--110513 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
110422 ATGTATAGGA
*
110432 TTTATGG
1 TTTAAGG
110439 TTTAAGG
1 TTTAAGG
110446 TTTTAA-G
1 -TTTAAGG
*
110453 TCTAAGG
1 TTTAAGG
110460 TTTAAGG
1 TTTAAGG
**
110467 TTTATCG
1 TTTAAGG
110474 TTCTAA-G
1 TT-TAAGG
*
110481 TTTAGGG
1 TTTAAGG
**
110488 TTTTGGG
1 TTTAAGG
110495 TTT-AGG
1 TTTAAGG
110501 TTTTAAGG
1 -TTTAAGG
110509 TTTAA
1 TTTAA
110514 AGTTATGAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
6 8 0.13
7 42 0.70
8 10 0.17
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:110759 original size:21 final size:21
Alignment explanation
Indices: 110733--110776 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
110723 TAGGGTCCAT
*
110733 TTGCCCTGG-AGGAGTAGAGTA
1 TTGCCC-GGAAGGAGTAAAGTA
110754 TTGCCCGGAAGGAGTAAAGTA
1 TTGCCCGGAAGGAGTAAAGTA
110775 TT
1 TT
110777 ACGGTGGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (21 bp):
TTGCCCGGAAGGAGTAAAGTA
Found at i:110835 original size:45 final size:45
Alignment explanation
Indices: 110771--110906 Score: 218
Period size: 45 Copynumber: 3.0 Consensus size: 45
110761 GAAGGAGTAA
* *
110771 AGTATTACGGTGGCTCGTCAAACTCAGCCTGATATCCTTGGCTTG
1 AGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
*
110816 AGTATTACGGTGACTCGTCAAACTGAGGCTGATATCCTTGGCTTG
1 AGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
* * *
110861 AGTATTGCGGTGGCTCGTCAAAGTGAGGCTGATATCTTTGGCTTG
1 AGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
110906 A
1 A
110907 TGATCTAGAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (45 bp):
AGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
Found at i:112935 original size:133 final size:133
Alignment explanation
Indices: 112695--112961 Score: 498
Period size: 133 Copynumber: 2.0 Consensus size: 133
112685 AATATAATAC
*
112695 AAAAATAATAATTAAATATCAAAATGGATTATTTACTAAAATGGTACAAAATATATATTTATATA
1 AAAAATAATAATTAAATACCAAAATGGATTATTTACTAAAATGGTACAAAATATATATTTATATA
* *
112760 CCAAAATGATGTTCACACACCATTATTTACCAAAATGGTACAAAATAAATTTATTTTGTATATTT
66 CCAAAATGATGTCCACACACCATTATTTACCAAAATGATACAAAATAAATTTATTTTGTATATTT
112825 TGT
131 TGT
112828 AAAAATAATAATTAAATACCAAAATGGATTATTTACTAAAATGGTACAAAATATATATTTATATA
1 AAAAATAATAATTAAATACCAAAATGGATTATTTACTAAAATGGTACAAAATATATATTTATATA
*
112893 CCAAAATGGTGTCCACACACCATTATTTACCAAAATGATACAAAATAAATTTATTTTGTATATTT
66 CCAAAATGATGTCCACACACCATTATTTACCAAAATGATACAAAATAAATTTATTTTGTATATTT
112958 TGT
131 TGT
112961 A
1 A
112962 CCATTTTGGT
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (133 bp):
AAAAATAATAATTAAATACCAAAATGGATTATTTACTAAAATGGTACAAAATATATATTTATATA
CCAAAATGATGTCCACACACCATTATTTACCAAAATGATACAAAATAAATTTATTTTGTATATTT
TGT
Found at i:113011 original size:16 final size:16
Alignment explanation
Indices: 112990--113039 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
112980 TGATGGAGAT
112990 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
113006 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
*
113021 A-TACTTTGGTAATTA
1 ATTATTTTGGTAATTA
113036 ATTA
1 ATTA
113040 GCTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.30
15 6 0.22
16 13 0.48
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:113774 original size:20 final size:21
Alignment explanation
Indices: 113749--113793 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
113739 CTTACTTACT
113749 ATTACTAA-TAACAAAATAAA
1 ATTACTAACTAACAAAATAAA
*
113769 ATTACTAACTAACAAAATTAA
1 ATTACTAACTAACAAAATAAA
113790 ATTA
1 ATTA
113794 AAGTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTACTAACTAACAAAATAAA
Found at i:113919 original size:23 final size:23
Alignment explanation
Indices: 113886--113929 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
113876 ACAAATCAAT
*
113886 AAAAAAATTAAATTAAACAAAAC
1 AAAAAAATTAAAATAAACAAAAC
* *
113909 AAAAAACTTAAAATAATCAAA
1 AAAAAAATTAAAATAAACAAA
113930 TTAACTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAAAATTAAAATAAACAAAAC
Found at i:114168 original size:4 final size:4
Alignment explanation
Indices: 114159--114195 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
114149 TACTCCTTCG
*
114159 TCTT TCTT TCTT TCTT TTTT TCTT TCTT T-TT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
114196 AAATCACGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:116330 original size:16 final size:19
Alignment explanation
Indices: 116298--116335 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
116288 AATAAATAAC
116298 ATATTATAAAACTCTTA-A
1 ATATTATAAAACTCTTATA
116316 ATATTA-AAAAC-CTTATA
1 ATATTATAAAACTCTTATA
116333 ATA
1 ATA
116336 CAACCCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 9 0.47
18 6 0.32
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATTATAAAACTCTTATA
Found at i:116550 original size:2 final size:2
Alignment explanation
Indices: 116543--116577 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
116533 CAATCTAATC
116543 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116578 ATCTAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:119102 original size:16 final size:16
Alignment explanation
Indices: 119048--119102 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
119038 TATGTAGAAA
*
119048 TATATTATTTTATGGT
1 TATATTATTTTATGAT
* *
119064 TATCTTATTTTTTGCAT
1 TATATTATTTTATG-AT
119081 AATATATTATTTTATGAT
1 --TATATTATTTTATGAT
119099 TATA
1 TATA
119103 ATTTGCTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 16 0.52
17 1 0.03
18 2 0.06
19 12 0.39
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (16 bp):
TATATTATTTTATGAT
Found at i:127925 original size:2 final size:2
Alignment explanation
Indices: 127918--127945 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
127908 ATTATTTTTA
127918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127946 TATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134294 original size:14 final size:14
Alignment explanation
Indices: 134275--134301 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
134265 TCAGAATTGG
134275 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
134289 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
134302 GAGAAGCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:148811 original size:2 final size:2
Alignment explanation
Indices: 148806--148832 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
148796 CGCGCGCGCG
148806 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
148833 GAGTAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:152489 original size:14 final size:14
Alignment explanation
Indices: 152470--152496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
152460 AGATTGATTG
152470 CTCTTTTCTTTTTC
1 CTCTTTTCTTTTTC
152484 CTCTTTTCTTTTT
1 CTCTTTTCTTTTT
152497 TTAAGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
CTCTTTTCTTTTTC
Found at i:154148 original size:18 final size:18
Alignment explanation
Indices: 154125--154159 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
154115 TTAACTTGAT
154125 ATTAAAT-TTAATATTAAA
1 ATTAAATATTAA-ATTAAA
154143 ATTAAATATTAAATTAA
1 ATTAAATATTAAATTAA
154160 GATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAATATTAAATTAAA
Found at i:154150 original size:13 final size:12
Alignment explanation
Indices: 154123--154159 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
154113 GTTTAACTTG
*
154123 ATATTAAATTTA
1 ATATTAAATTAA
154135 ATATTAAAATTAA
1 ATATT-AAATTAA
154148 ATATTAAATTAA
1 ATATTAAATTAA
154160 GATAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTAAATTAA
Found at i:154176 original size:26 final size:25
Alignment explanation
Indices: 154123--154182 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
154113 GTTTAACTTG
* ** *
154123 ATATTAAATTTAATATTAAAATTAA
1 ATATTAAATTAAATAAAAAAAATAA
154148 ATATTAAATTAAGATAAAAAAAATAA
1 ATATTAAATTAA-ATAAAAAAAATAA
*
154174 ATATCAAAT
1 ATATTAAAT
154183 CGAATATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATTAAATTAAATAAAAAAAATAA
Found at i:161470 original size:2 final size:2
Alignment explanation
Indices: 161463--161505 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
161453 TTTTAAGAAC
161463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
161505 A
1 A
161506 AGAACCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:168361 original size:18 final size:18
Alignment explanation
Indices: 168338--168390 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
168328 CAAACACTTA
168338 ATTTAATTACAGAGATAG
1 ATTTAATTACAGAGATAG
168356 ATTTAA--AC----ATA-
1 ATTTAATTACAGAGATAG
168367 ATTTAATTACAGAGATAG
1 ATTTAATTACAGAGATAG
168385 ATTTAA
1 ATTTAA
168391 ACATGCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 2 0.07
16 2 0.07
17 3 0.11
18 12 0.43
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
ATTTAATTACAGAGATAG
Found at i:168400 original size:29 final size:29
Alignment explanation
Indices: 168336--168394 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
168326 AACAAACACT
168336 TAATTTAATTACAGAGATAGATTTAAACA
1 TAATTTAATTACAGAGATAGATTTAAACA
168365 TAATTTAATTACAGAGATAGATTTAAACA
1 TAATTTAATTACAGAGATAGATTTAAACA
168394 T
1 T
168395 GCTTTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (29 bp):
TAATTTAATTACAGAGATAGATTTAAACA
Found at i:189691 original size:21 final size:21
Alignment explanation
Indices: 189666--189706 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
189656 CCCTCCTCCG
*
189666 TCAACTCCTTCAACCCCACCC
1 TCAACTCCGTCAACCCCACCC
*
189687 TCAACTCCGTCGACCCCACC
1 TCAACTCCGTCAACCCCACC
189707 GTCTCCGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.56, G:0.05, T:0.17
Consensus pattern (21 bp):
TCAACTCCGTCAACCCCACCC
Found at i:199754 original size:3 final size:3
Alignment explanation
Indices: 199746--199776 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
199736 ATGCATACAT
199746 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
199777 ACATAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:201115 original size:18 final size:18
Alignment explanation
Indices: 201092--201135 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
201082 GATCAGTAAG
201092 GAGATCACATATCCCTAA
1 GAGATCACATATCCCTAA
201110 GAGATCACATATCCCTAA
1 GAGATCACATATCCCTAA
201128 GAGATCAC
1 GAGATCAC
201136 TTTGTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (18 bp):
GAGATCACATATCCCTAA
Found at i:213652 original size:21 final size:20
Alignment explanation
Indices: 213623--213663 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
213613 AAAAGATTGC
*
213623 TGATGATGATCATTATCATCA
1 TGATGATGATC-TAATCATCA
*
213644 TGATTATGATCTAATCATCA
1 TGATGATGATCTAATCATCA
213664 AGGAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
TGATGATGATCTAATCATCA
Found at i:213764 original size:4 final size:4
Alignment explanation
Indices: 213755--213780 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
213745 AAAATGGAAG
213755 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
213781 TTCAATCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:245733 original size:30 final size:30
Alignment explanation
Indices: 245699--245756 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
245689 AATAATCTAC
*
245699 ATATACTTCATA-AAATTTCAAAAAATATAT
1 ATATACTTCA-ACAAATTTAAAAAAATATAT
* *
245729 ATATATTTCAACACATTTAAAAAAATAT
1 ATATACTTCAACAAATTTAAAAAAATAT
245757 CCATGTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (30 bp):
ATATACTTCAACAAATTTAAAAAAATATAT
Found at i:245811 original size:23 final size:22
Alignment explanation
Indices: 245771--245819 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
245761 GTCAACATAT
*
245771 AAATATATGTTAATTACTTAATA
1 AAATATATGTCAATTAC-TAATA
*
245794 AAATATTATGTCAA-TACTATTA
1 AAATA-TATGTCAATTACTAATA
245816 AAAT
1 AAAT
245820 TTTAACGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATATATGTCAATTACTAATA
Found at i:251082 original size:8 final size:8
Alignment explanation
Indices: 251069--251095 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
251059 TTTAATTAAT
251069 TTTTAAAA
1 TTTTAAAA
251077 TTTTAAAA
1 TTTTAAAA
251085 TTTTAAAA
1 TTTTAAAA
251093 TTT
1 TTT
251096 AAGAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:257678 original size:50 final size:50
Alignment explanation
Indices: 257598--257698 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
257588 GTTACGAAAT
* *
257598 GATCATTCTACCGTTAAATTCCGTTCTCTCCCTGACGGTAATCCTACATG
1 GATCATTCTACCGTTAAATTCCGTTATCTCCCTAACGGTAATCCTACATG
* * *
257648 GATCATTCTGCCGTTAAGTTCCGTTATCTCCCTAACGGTAATCTTACATG
1 GATCATTCTACCGTTAAATTCCGTTATCTCCCTAACGGTAATCCTACATG
257698 G
1 G
257699 CAGTCCAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.35
Consensus pattern (50 bp):
GATCATTCTACCGTTAAATTCCGTTATCTCCCTAACGGTAATCCTACATG
Found at i:279195 original size:859 final size:847
Alignment explanation
Indices: 277633--279195 Score: 1942
Period size: 859 Copynumber: 1.8 Consensus size: 847
277623 ATCGTAACTT
* * *
277633 CATATCAGCAAAATGTTTTTATGAACAAAATATTATAAGTTAGTGTAAATTGTGACATTTAATAG
1 CATATCAACAAAACGTTTTTATGAACAAAATATTATAAGTTAGTGTAAAATGTGACATTTAATAG
* *
277698 TAGAAGTGATTCTAGGGTTATTAATGATGTGCTATTGAAGATAGTGAAACTTTGTTGAAATAGAG
66 TAGAAATAATTCTAGGGTTATTAATGATGTGCTATTGAAGATAGTGAAACTTTGTTGAAATAGAG
277763 TAAGATATAATGATCTTAAAGAAAAATCATGAGTTCAATAAATTGTGAAATTTAATATTAAAAGT
131 TAAGATATAATGATCTTAAAGAAAAATCATGAGTTCAATAAA-T-TG------AATATTAAAAGT
* * * *
277828 ATTTTTATGAACAAAACAGTGAGATTCAATAAATTGAAACTCAATTTTAATAGGTGGCGTAGTCA
188 ATTTTTATGAACAAAACAGTGAGATTCAATAAATTGAAACACAACTTTAACAGGT-GCGTACTCA
* * ** *
277893 ATTTAAAAACAAAACAAGGTAGATTTAGAGTTTTATTGAGAAGATAAGCAAAGGAGGATGTAGCT
252 ATTTAAAAACAAAAAAAGGTAGATGTAGAGACTTATTGAGAAGAGAAGCAAAGGAGGATGTAGCT
** * * ** *
277958 CAAATGGTAGAGTGCTCGCTTTGCATGTGAGAGGCACGGGGTTCGATCCCTTGCATCTCCATTTT
317 CAAATGGTAGAGCACTCGCTTTGCATGCGAGAGGCACGAGGTTCGATCCCCGGCATCTCCATTGT
* *
278023 GTTATTTTTTTCATTTTTCATGAAGATTCTCTTTTCTCCATGACAGCGTCGTTTTTAGTTTTGCC
382 GTTATTTTTTTCATTTTTCATGAAGATTCTATTCTCTCCATGACAGCGTCGTTTTTAGTTTTGCC
* * * * *
278088 TCTCAACAAGTGTGGTCTCCATCTCTCTTCTTTCTAACTTATTGTCATCCTCAAATTCTTATCTC
447 TCTCAACAAGTGTGGTCTCCATCTCTCTTCTCTCTAACTTACTGTCATCCTCAAATACTCACCTC
* * *
278153 TCTTTGCGGCGCTTATTATTTTTATTATTATTCAAAAGGTACGTTCTCGTCAATGGCGACCTTTT
512 TCTTTGCGGCGC----------TATTATTATTCAAAAGGTACGTCCTCGCCAATGGCGACCCTTT
** * * * * * * * **
278218 GTTTCAGAATATTTCAAATCCAGTCGAAATGTTTCTAGTGAAGTCTAAATTTTACTTCGATTGAA
567 GCCTCAGAACACTTCAAACCCAGTCGAAACGCTCCTAGTAAAGTCTAAATCCTACTTCGATTGAA
* * *
278283 TCTAATCCTAGTTTTAATTCCCTCTCTTTCATCTCGTTGCAAAAAGATATATATCCCGAGGACTG
632 CCCAACCCTAGTTTTAATTCCCTCTCTTTCATCTCGTTGCAAAAAGATATATATCCCGAGGACTG
278348 ATGAAGAAGGGATCAATCTTTTAACATCCTACAATTACTCTAAGCAATTGTCTTCTTGATCAGTT
697 ATGAAGAAGGGATCAATCTTTTAACATCCTACAATTACTCTAAGCAATTGTCTTCTTGATCAGTT
278413 TGTCCCTACTCTCAGTCTCTATATATGAACCGAACTCCGTTACACCACCTTGATCTCCTCTTTGT
762 TGTCCCTACTCTCAGTCTCTATATATGAACCGAACTCCGTTACACCACCTTGATCTCCTCTTTGT
278478 TCTCTTTCCCTATTAAAATTC
827 TCTCTTTCCCTATTAAAATTC
* * *
278499 CATATCAACAAAGCGTTTTTATGAACAATATATTATAAGTTAGTGTAAAATGTGACATTTAATAT
1 CATATCAACAAAACGTTTTTATGAACAAAATATTATAAGTTAGTGTAAAATGTGACATTTAATAG
* * * * * ** *
278564 TAGAAATAATTTTAGGGTTATTAATTATGTGGTATTGAAGATGGTGGATGTTTGTTGAAAATGGA
66 TAGAAATAATTCTAGGGTTATTAATGATGTGCTATTGAAGATAGTGAAACTTTGTTG-AAATAGA
* * * *
278629 GTAAGATGTAATGATCTTAAAGAAGAATTATGAGTTCAAT-AA-TG-ATCTT-AAAGTATTTTTA
130 GTAAGATATAATGATCTTAAAGAAAAATCATGAGTTCAATAAATTGAATATTAAAAGTATTTTTA
* ** * *
278690 TGAACAAAACCGTGAGATTCAATAAATTGATGCACGACTTT-GCA-GT-CG-ACTCAATTTAAAA
195 TGAACAAAACAGTGAGATTCAATAAATTGAAACACAACTTTAACAGGTGCGTACTCAATTTAAAA
* **
278751 ACAAAAAAAATGTAGATGTAGAGACTTATTGAGAAGAGAAGCGTCGAGG-GGATGTAGCTCAAAT
260 AC-AAAAAAAGGTAGATGTAGAGACTTATTGAGAAGAGAAGC--AAAGGAGGATGTAGCTCAAAT
278815 GGTAGAGCACTCGCTTTGCATGCGAGAGGCACGAGGTTCGATCCCCGGCATCTCCACTTCGTGTT
322 GGTAGAGCACTCGCTTTGCATGCGAGAGGCACGAGGTTCGATCCCCGGCATCTCCA-TT-GTGTT
*
278880 ATTCTTTTCATTTTTCATTTTCTAGCGTGAACTGTAAAGATTCTATTCTCTCCATGACATCGTCG
385 A-----TT--TTTTTCATTTT-T--C----A-TG--AAGATTCTATTCTCTCCATGACAGCGTCG
* * *
278945 TTTTTAGTTTTGCCTCTCGACAAGTGTGGTCTCGATCTCTCTTCTCTCTACCTTACTGTCATCCT
433 TTTTTAGTTTTGCCTCTCAACAAGTGTGGTCTCCATCTCTCTTCTCTCTAACTTACTGTCATCCT
* * *
279010 CGAATACTCGCCTCTCTTTGCGGCGC-A-TATTATTCAAAAGGTACGTCCTCGCCGATGGCGACC
498 CAAATACTCACCTCTCTTTGCGGCGCTATTATTATTCAAAAGGTACGTCCTCGCCAATGGCGACC
* * *
279073 CTTTGCCTCGGAACGCTTCAAACCCAGTCGAAGCGCTCCTAGTAAAGTCTAAATCCTACTTCGAT
563 CTTTGCCTCAGAACACTTCAAACCCAGTCGAAACGCTCCTAGTAAAGTCTAAATCCTACTTCGAT
* * *
279138 TGGACCCAACCCTGGTTTTAATTCCCTCTCTTTCATCTCGTTGCAAAAAGGTATATAT
628 TGAACCCAACCCTAGTTTTAATTCCCTCTCTTTCATCTCGTTGCAAAAAGATATATAT
279196 ATTTCTTCTA
Statistics
Matches: 593, Mismatches: 81, Indels: 53
0.82 0.11 0.07
Matches are distributed among these distances:
850 14 0.02
851 35 0.06
852 65 0.11
853 7 0.01
854 6 0.01
855 47 0.08
856 4 0.01
859 137 0.23
860 1 0.00
861 11 0.02
862 1 0.00
863 2 0.00
864 1 0.00
866 109 0.18
867 43 0.07
868 1 0.00
869 2 0.00
871 107 0.18
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (847 bp):
CATATCAACAAAACGTTTTTATGAACAAAATATTATAAGTTAGTGTAAAATGTGACATTTAATAG
TAGAAATAATTCTAGGGTTATTAATGATGTGCTATTGAAGATAGTGAAACTTTGTTGAAATAGAG
TAAGATATAATGATCTTAAAGAAAAATCATGAGTTCAATAAATTGAATATTAAAAGTATTTTTAT
GAACAAAACAGTGAGATTCAATAAATTGAAACACAACTTTAACAGGTGCGTACTCAATTTAAAAA
CAAAAAAAGGTAGATGTAGAGACTTATTGAGAAGAGAAGCAAAGGAGGATGTAGCTCAAATGGTA
GAGCACTCGCTTTGCATGCGAGAGGCACGAGGTTCGATCCCCGGCATCTCCATTGTGTTATTTTT
TTCATTTTTCATGAAGATTCTATTCTCTCCATGACAGCGTCGTTTTTAGTTTTGCCTCTCAACAA
GTGTGGTCTCCATCTCTCTTCTCTCTAACTTACTGTCATCCTCAAATACTCACCTCTCTTTGCGG
CGCTATTATTATTCAAAAGGTACGTCCTCGCCAATGGCGACCCTTTGCCTCAGAACACTTCAAAC
CCAGTCGAAACGCTCCTAGTAAAGTCTAAATCCTACTTCGATTGAACCCAACCCTAGTTTTAATT
CCCTCTCTTTCATCTCGTTGCAAAAAGATATATATCCCGAGGACTGATGAAGAAGGGATCAATCT
TTTAACATCCTACAATTACTCTAAGCAATTGTCTTCTTGATCAGTTTGTCCCTACTCTCAGTCTC
TATATATGAACCGAACTCCGTTACACCACCTTGATCTCCTCTTTGTTCTCTTTCCCTATTAAAAT
TC
Found at i:287950 original size:46 final size:46
Alignment explanation
Indices: 287883--288000 Score: 209
Period size: 46 Copynumber: 2.6 Consensus size: 46
287873 TTGAACCATT
* *
287883 TCGGGTTTAAGTCTTTTCAAGTTTAGGTCTCAAATTTTGCATCAAA
1 TCGGGTTTAAATCTTTTCAAGTTTAAGTCTCAAATTTTGCATCAAA
287929 TCGGGTTTAAATCTTTTCAAGTTTAAGTCTCAAATTTTGCATCAAA
1 TCGGGTTTAAATCTTTTCAAGTTTAAGTCTCAAATTTTGCATCAAA
*
287975 TCGGGTTTAAATCTTTTCAAGCTTAA
1 TCGGGTTTAAATCTTTTCAAGTTTAA
288001 ACAAATTTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (46 bp):
TCGGGTTTAAATCTTTTCAAGTTTAAGTCTCAAATTTTGCATCAAA
Found at i:289329 original size:16 final size:16
Alignment explanation
Indices: 289308--289338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
289298 ATTCCAACAT
*
289308 AATATTTTCATATTCG
1 AATATTTTCAAATTCG
289324 AATATTTTCAAATTC
1 AATATTTTCAAATTC
289339 AACTCGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (16 bp):
AATATTTTCAAATTCG
Found at i:294503 original size:13 final size:14
Alignment explanation
Indices: 294478--294512 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
294468 AGTAAAGAGG
294478 TATATGATGATATA
1 TATATGATGATATA
294492 TATATG-TGATATA
1 TATATGATGATATA
*
294505 TACATGAT
1 TATATGAT
294513 ATTGTGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (14 bp):
TATATGATGATATA
Found at i:294672 original size:23 final size:23
Alignment explanation
Indices: 294658--294746 Score: 110
Period size: 23 Copynumber: 3.9 Consensus size: 23
294648 TATTGTTCAA
*
294658 CACTGTGTGTGCTTAATGATTC-G
1 CACTGTGTGTGCTTACTG-TTCTG
* *
294681 CACTATGTGTGCTTACTGTTTTG
1 CACTGTGTGTGCTTACTGTTCTG
*
294704 CACTGTGTGTGCCTACTGATT-TG
1 CACTGTGTGTGCTTACTG-TTCTG
294727 CACTGTGTGTGCTTACTGTT
1 CACTGTGTGTGCTTACTGTT
294747 TCTCCAGCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
22 4 0.07
23 52 0.90
24 2 0.03
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (23 bp):
CACTGTGTGTGCTTACTGTTCTG
Found at i:294730 original size:46 final size:46
Alignment explanation
Indices: 294658--294747 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
294648 TATTGTTCAA
*
294658 CACTGTGTGTGCTTAATGATTCGCACTATGTGTGCTTACTGTTTTG
1 CACTGTGTGTGCCTAATGATTCGCACTATGTGTGCTTACTGTTTTG
* * *
294704 CACTGTGTGTGCCTACTGATTTGCACTGTGTGTGCTTACTGTTT
1 CACTGTGTGTGCCTAATGATTCGCACTATGTGTGCTTACTGTTT
294748 CTCCAGCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.43
Consensus pattern (46 bp):
CACTGTGTGTGCCTAATGATTCGCACTATGTGTGCTTACTGTTTTG
Found at i:295691 original size:26 final size:26
Alignment explanation
Indices: 295662--295713 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
295652 TATAAAATTT
*
295662 GTAACTTATTTACTTATTTCTCAAAC
1 GTAACTTATTTACTTAGTTCTCAAAC
* *
295688 GTAATTTATTTTCTTAGTTCTCAAAC
1 GTAACTTATTTACTTAGTTCTCAAAC
295714 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (26 bp):
GTAACTTATTTACTTAGTTCTCAAAC
Found at i:297293 original size:24 final size:24
Alignment explanation
Indices: 297265--297315 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
297255 AGAAATAATC
* * *
297265 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
297289 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
297313 TTT
1 TTT
297316 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:299135 original size:23 final size:23
Alignment explanation
Indices: 299109--299247 Score: 132
Period size: 23 Copynumber: 6.3 Consensus size: 23
299099 ACACTAGCGC
*
299109 GCTCTCTAATTAGCA-TTGTGTGT
1 GCTCTCTGATTAGCACTT-TGTGT
* *
299132 GCTCTCTGATTAACACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
299155 GCTCTCTGTTTTGCACTTCGTGT
1 GCTCTCTGATTAGCACTTTGTGT
299178 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
299201 -C-CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
299217 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
299240 GCTCTCTG
1 GCTCTCTG
299248 TTGCCCAGCA
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
16 11 0.12
17 1 0.01
18 3 0.03
21 3 0.03
22 1 0.01
23 74 0.79
24 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:307710 original size:100 final size:100
Alignment explanation
Indices: 307537--307737 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
307527 AACAATATCG
307537 AGATGATACATGTTTGACGAAAATTTAAGGGAATAACTTATGTAAGGATAATCTTAAAGCCTAAG
1 AGATGATACATGTTTGACGAAAATTTAAGGGAATAACTTATGTAAGGATAATCTTAAAGCCTAAG
*
307602 GTTTTTAGGTACTAATAAAATTTTGTCACACCATC
66 GCTTTTAGGTACTAATAAAATTTTGTCACACCATC
307637 AGATGATACATGTTTGACGAAAATTTAAGGGAATAACTTATGTAAGGATAATCTTAAAGCCTAAG
1 AGATGATACATGTTTGACGAAAATTTAAGGGAATAACTTATGTAAGGATAATCTTAAAGCCTAAG
307702 GCTTTTAGGTACTAATAAAATTTTGTCACACCATC
66 GCTTTTAGGTACTAATAAAATTTTGTCACACCATC
307737 A
1 A
307738 AATTTTAAAT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (100 bp):
AGATGATACATGTTTGACGAAAATTTAAGGGAATAACTTATGTAAGGATAATCTTAAAGCCTAAG
GCTTTTAGGTACTAATAAAATTTTGTCACACCATC
Found at i:330175 original size:18 final size:17
Alignment explanation
Indices: 330145--330178 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
330135 CTCGTAACTA
*
330145 AAAAAGAAAAAGGCAAT
1 AAAAACAAAAAGGCAAT
330162 AAAAACAAATAAGGCAA
1 AAAAACAAA-AAGGCAA
330179 GTAGAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.09, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAACAAAAAGGCAAT
Found at i:330190 original size:18 final size:17
Alignment explanation
Indices: 330145--330193 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
330135 CTCGTAACTA
*
330145 AAAAAGAAAAAGGCAAT
1 AAAAAGAATAAGGCAAT
*
330162 AAAAACAAATAAGGCAAGT
1 AAAAA-GAATAAGGCAA-T
*
330181 AGAAAGAATAAGG
1 AAAAAGAATAAGG
330194 AACAACTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.65, C:0.06, G:0.20, T:0.08
Consensus pattern (17 bp):
AAAAAGAATAAGGCAAT
Found at i:347954 original size:25 final size:25
Alignment explanation
Indices: 347917--347967 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
347907 CCATGCAGTT
347917 TGGTTCTTCACTAATATTGATTGTA
1 TGGTTCTTCACTAATATTGATTGTA
*
347942 TGGTTCTTTACTAATATTGATTGTA
1 TGGTTCTTCACTAATATTGATTGTA
347967 T
1 T
347968 AGAAGGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.51
Consensus pattern (25 bp):
TGGTTCTTCACTAATATTGATTGTA
Found at i:349532 original size:19 final size:20
Alignment explanation
Indices: 349500--349537 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
349490 ACATAAAAAA
*
349500 AAAAAAAATTAATT-TTTTC
1 AAAAAAAATGAATTATTTTC
*
349519 AAAAAAGATGAATTATTTT
1 AAAAAAAATGAATTATTTT
349538 TTAAAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAAAAAATGAATTATTTTC
Found at i:375542 original size:25 final size:25
Alignment explanation
Indices: 375509--375574 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
375499 TCCCAATAAA
375509 TTCTATTTTATTTAAAATAATTTTTT
1 TTCT-TTTTATTTAAAATAATTTTTT
* * *
375535 TTCTTTTTAATTAAATTGATTTTTT
1 TTCTTTTTATTTAAAATAATTTTTT
*
375560 TTATTTTT-TTTAAAA
1 TTCTTTTTATTTAAAA
375575 AAAATTAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 5 0.15
25 25 0.74
26 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (25 bp):
TTCTTTTTATTTAAAATAATTTTTT
Found at i:384659 original size:7 final size:8
Alignment explanation
Indices: 384645--384674 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
384635 CGTACGTTAG
384645 ATTTTTTT
1 ATTTTTTT
384653 ATTTTTTT
1 ATTTTTTT
384661 ATTTTTTT
1 ATTTTTTT
384669 ATTTTT
1 ATTTTT
384675 GTTTTGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
ATTTTTTT
Found at i:391276 original size:58 final size:57
Alignment explanation
Indices: 391212--391358 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 57
391202 TTTGTCATAT
391212 AAAAAA-TATAATTTTTTTGTGTTGGCCATGCAATGGTCGACATCCCC-TGTTTGAGAAA
1 AAAAAATTA-AATTTTTTTGTGTTGGCCATGC-ATGGTCGACA-CCCCTTGTTTGAGAAA
** * *
391270 AAAAAATTGCATTTTTTGGTGTTGGTCATTGCATGGTCGACACCCCTTGTTTGAGAAA
1 AAAAAATTAAATTTTTTTGTGTTGGCCA-TGCATGGTCGACACCCCTTGTTTGAGAAA
391328 AAAAAATTCAAATTTTTTTTGTGTTGGCCAT
1 AAAAAATT-AAA-TTTTTTTGTGTTGGCCAT
391359 TTTAGGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
57 4 0.05
58 51 0.67
59 6 0.08
60 15 0.20
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (57 bp):
AAAAAATTAAATTTTTTTGTGTTGGCCATGCATGGTCGACACCCCTTGTTTGAGAAA
Found at i:404057 original size:23 final size:23
Alignment explanation
Indices: 404031--404118 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
404021 TCTCTGTTTT
404031 GCACGTTT-CGTGCCCTCTGATCA
1 GCAC-TTTGCGTGCCCTCTGATCA
* * *
404054 GCACTTTGTGTGCTCTCTGATTA
1 GCACTTTGCGTGCCCTCTGATCA
* * * *
404077 GTACTTTGTGTGCTCTCTGATTA
1 GCACTTTGCGTGCCCTCTGATCA
* * *
404100 GCACTGTGTGTGCTCTCTG
1 GCACTTTGCGTGCCCTCTG
404119 TTTGTTCTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 3 0.05
23 55 0.95
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (23 bp):
GCACTTTGCGTGCCCTCTGATCA
Found at i:404086 original size:21 final size:24
Alignment explanation
Indices: 404040--404118 Score: 110
Period size: 23 Copynumber: 3.4 Consensus size: 24
404030 TGCACGTTTC
* *
404040 GTGCCCTCTGATCAGCACTT-TGT
1 GTGCTCTCTGATTAGCACTTGTGT
*
404063 GTGCTCTCTGATTAGTACTT-TGT
1 GTGCTCTCTGATTAGCACTTGTGT
404086 GTGCTCTCTGATTAGCAC-TGTGT
1 GTGCTCTCTGATTAGCACTTGTGT
404109 GTGCTCTCTG
1 GTGCTCTCTG
404119 TTTGTTCTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.02
23 50 0.98
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (24 bp):
GTGCTCTCTGATTAGCACTTGTGT
Found at i:407318 original size:27 final size:26
Alignment explanation
Indices: 407239--407318 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 26
407229 AAACAATGGA
407239 TAATTATCTTTTATTACAAGTAAAACC
1 TAATTAT-TTTTATTACAAGTAAAACC
** * *
407266 T-ATT-TTAAT-TTACAAAT-AGA--
1 TAATTATTTTTATTACAAGTAAAACC
407286 TAATTATGTTTTATTACAAGTAAAACC
1 TAATTAT-TTTTATTACAAGTAAAACC
407313 TAATTA
1 TAATTA
407319 ACATGACTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 3 0.08
23 9 0.24
24 9 0.24
25 3 0.08
26 3 0.08
27 7 0.18
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (26 bp):
TAATTATTTTTATTACAAGTAAAACC
Found at i:412094 original size:20 final size:19
Alignment explanation
Indices: 412040--412096 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
412030 CTCAATAAAC
*
412040 TTTAATA-AAATTAGATATT
1 TTTAATATAAACTA-ATATT
*
412059 TTTAATTTAAACTAATATT
1 TTTAATATAAACTAATATT
412078 TTATAATAATAAA-TAATAT
1 TT-TAAT-ATAAACTAATAT
412097 GTAATTATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 13 0.41
20 15 0.47
21 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAATATAAACTAATATT
Found at i:414469 original size:13 final size:13
Alignment explanation
Indices: 414451--414480 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
414441 GAACAAACAA
*
414451 AAACTCAAGTATC
1 AAACTCAAGAATC
414464 AAACTCAAGAATC
1 AAACTCAAGAATC
414477 AAAC
1 AAAC
414481 ATAGCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (13 bp):
AAACTCAAGAATC
Found at i:414930 original size:26 final size:25
Alignment explanation
Indices: 414901--414953 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
414891 TATATTTTTT
* *
414901 ATTTTATTTCTTAAATATCAATTAAA
1 ATTTTAATTCATAAATA-CAATTAAA
*
414927 ATTTTAATTCATAAATAGAATTAAA
1 ATTTTAATTCATAAATACAATTAAA
414952 AT
1 AT
414954 ATTTTCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTTAATTCATAAATACAATTAAA
Found at i:415636 original size:19 final size:19
Alignment explanation
Indices: 415593--415636 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
415583 TTTTAAGTTT
* *
415593 TAAAGAATTCAAAAATTTTA
1 TAAA-AATTAAAAAATTATA
*
415613 AAAAAATTAAAAAATTATA
1 TAAAAATTAAAAAATTATA
415632 TAAAA
1 TAAAA
415637 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAATTAAAAAATTATA
Found at i:418388 original size:16 final size:16
Alignment explanation
Indices: 418367--418403 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
418357 ATTTGAACTC
418367 AAAATGATTCGAAATT
1 AAAATGATTCGAAATT
* *
418383 AAAATGGTTCGAATTT
1 AAAATGATTCGAAATT
418399 AAAAT
1 AAAAT
418404 AAGTTGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (16 bp):
AAAATGATTCGAAATT
Found at i:418630 original size:17 final size:16
Alignment explanation
Indices: 418599--418638 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
418589 GCTAGAACTC
*
418599 AAAATTATTCGAACCA
1 AAAATTATTCAAACCA
*
418615 AAAATTGATTCAAACCC
1 AAAATT-ATTCAAACCA
418632 AAAATTA
1 AAAATTA
418639 AAATGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (16 bp):
AAAATTATTCAAACCA
Found at i:429473 original size:22 final size:22
Alignment explanation
Indices: 429423--429502 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 22
429413 GCTGGGGAAA
*
429423 CAGTAAGCACACACAGTGCAATT
1 CAGTAGGCACACACAGTGCAA-T
429446 CAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
* * *
429468 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
429491 CAGTAGGCACAC
1 CAGTAGGCACAC
429503 GAGGTGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 17 0.33
23 34 0.67
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:429567 original size:23 final size:22
Alignment explanation
Indices: 429420--429567 Score: 98
Period size: 23 Copynumber: 6.5 Consensus size: 22
429410 AGAGCTGGGG
*
429420 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACAAAGTGC
* * *
429442 AATTCAGTAGGCACACACAGTGC
1 AA-ACAGTAAGCACACAAAGTGC
* * * * *
429465 AATCAGTAGGCGCACATAGCGC
1 AAACAGTAAGCACACAAAGTGC
* * *
429487 AAATCAGTAGGCACACGAGGTGC
1 AAA-CAGTAAGCACACAAAGTGC
* * *
429510 GAAATAATAAGCACACGAAGTGC
1 -AAACAGTAAGCACACAAAGTGC
* *
429533 GAAATAGAAAGCACACAAAGTGC
1 -AAACAGTAAGCACACAAAGTGC
429556 TAAACAGTAAGC
1 -AAACAGTAAGC
429568 GCGCTAGCGT
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
22 21 0.21
23 78 0.76
24 3 0.03
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (22 bp):
AAACAGTAAGCACACAAAGTGC
Found at i:429658 original size:10 final size:10
Alignment explanation
Indices: 429645--429674 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
429635 TCTCTCATAT
*
429645 TCATCATTTC
1 TCATAATTTC
429655 TCATAATTTC
1 TCATAATTTC
429665 TCATAATTTC
1 TCATAATTTC
429675 ATATATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (10 bp):
TCATAATTTC
Done.