Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003496.1 Hibiscus syriacus cultivar Beakdansim tig00007392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 159022
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9644 original size:16 final size:16
Alignment explanation
Indices: 9625--9668 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
9615 TAATAATTTT
9625 ATAATGTAATCATTGA
1 ATAATGTAATCATTGA
* * *
9641 ATAATGTAACCGTTGG
1 ATAATGTAATCATTGA
*
9657 ATAATATAATCA
1 ATAATGTAATCA
9669 CATTATTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (16 bp):
ATAATGTAATCATTGA
Found at i:10589 original size:57 final size:57
Alignment explanation
Indices: 10517--10644 Score: 170
Period size: 57 Copynumber: 2.2 Consensus size: 57
10507 AAACGGTCGA
* * * *
10517 TGATCAACTAAAAAGCACCGCTGTCACT-GCTTAATATTAGAGAAA-TGAAACAATCAG
1 TGATCAATTAAAAAGCACCACTGTC-CTCGCTCAATATTAAAGAAACT-AAACAATCAG
*
10574 TGATCAATTAAAAAGCACCACTGTCGTCGCTCAATATTAAAGAAACTAAACAATCAG
1 TGATCAATTAAAAAGCACCACTGTCCTCGCTCAATATTAAAGAAACTAAACAATCAG
*
10631 TGATAAATTAAAAA
1 TGATCAATTAAAAA
10645 AACACTGTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
56 1 0.02
57 61 0.97
58 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (57 bp):
TGATCAATTAAAAAGCACCACTGTCCTCGCTCAATATTAAAGAAACTAAACAATCAG
Found at i:11001 original size:57 final size:56
Alignment explanation
Indices: 10759--11276 Score: 376
Period size: 56 Copynumber: 9.3 Consensus size: 56
10749 GATATAACCT
* * * * * * * * *
10759 CTTAATATTAAAGAAACGAAATGATCATTGATTAATTAAAAATAC-CATCATCACCA
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAA-ACATATTATCATCG
* * * * * ** *
10815 TTTAATATTAAAGAAACGAAATGATCGGTGATCAA-TTAAAAACATTAACATCACCG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACA-TATTATCATCG
* * * * *
10871 CTTAATATTAAAGAAACGAAACGATCGGTGATCAACTAAAAAA-ATCACTATCACCA
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACAT-ATTATCATCG
* *
10927 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACATAGTTGTCATTG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACATA-TTATCATCG
* * * *
10984 CTTAGTATTAAAGAAACAAAATGATCATTGATCAACTAAAAAACACTATTGTCATCG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACA-TATTATCATCG
* * * *
11041 TTTAATATTAAAGAAACAAAAGGATCAGTG----ACTAAAAAACACTATTAACACCG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACA-TATTATCATCG
* * * * * ** ** * *
11094 TTTAATATTAAAGAAA-AAAACGGTAAGTGGTTAACTAAAGTACCGA-AATCACCG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACATATTATCATCG
** * * * ** *
11148 CTTAATATTAAAGAAATGAAACAAT-TGATAATCAACTAAAAAATTC-CGTTATCATTG
1 CTTAATATTAAAGAAACAAAACGATCAG-TGATCAACTAAAAAA--CATATTATCATCG
* * *
11205 CTTAATATTAAA-AATCAAAACGATCAGTGATCAACTAAAAAATATTATTGTCATCG
1 CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACA-TATTATCATCG
11261 CTTAATATTAAAGAAA
1 CTTAATATTAAAGAAA
11277 TGAAATGATC
Statistics
Matches: 374, Mismatches: 68, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
52 10 0.03
53 36 0.10
54 24 0.06
55 22 0.06
56 171 0.46
57 109 0.29
58 2 0.01
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (56 bp):
CTTAATATTAAAGAAACAAAACGATCAGTGATCAACTAAAAAACATATTATCATCG
Found at i:11038 original size:27 final size:26
Alignment explanation
Indices: 10955--11038 Score: 69
Period size: 30 Copynumber: 3.0 Consensus size: 26
10945 AAACGATCAG
10955 TGATCAACTAAAAAACATAGTTGTCAT
1 TGATCAACTAAAAAACATA-TTGTCAT
* * * * *
10982 TGCTTAGTATTAAAGAAACAAAATGATCAT
1 TGATCA--ACTAAA-AAACATATTG-TCAT
11012 TGATCAACTAAAAAACACTATTGTCAT
1 TGATCAACTAAAAAACA-TATTGTCAT
11039 CGTTTAATAT
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
27 13 0.31
28 8 0.19
29 7 0.17
30 14 0.33
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (26 bp):
TGATCAACTAAAAAACATATTGTCAT
Found at i:12377 original size:21 final size:22
Alignment explanation
Indices: 12348--12409 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
12338 GCCATCGACG
12348 TCATCCCCGGATTCGATGCCA-
1 TCATCCCCGGATTCGATGCCAT
* *
12369 TCTTCCCCGGATTCGATG-GAT
1 TCATCCCCGGATTCGATGCCAT
12390 TCATCCCCGGATTCGATGCC
1 TCATCCCCGGATTCGATGCC
12410 GCATTCCCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.16, C:0.35, G:0.21, T:0.27
Consensus pattern (22 bp):
TCATCCCCGGATTCGATGCCAT
Found at i:12417 original size:21 final size:21
Alignment explanation
Indices: 12351--12424 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
12341 ATCGACGTCA
12351 TCCCCGGATTCGATGCCATC-T
1 TCCCCGGATTCGATGCC-TCAT
**
12372 TCCCCGGATTCGATGGATTCA-
1 TCCCCGGATTCGAT-GCCTCAT
*
12393 TCCCCGGATTCGATGCCGCAT
1 TCCCCGGATTCGATGCCTCAT
*
12414 TCCCCGCATTC
1 TCCCCGGATTC
12425 TATTTTCCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.07
21 40 0.91
22 1 0.02
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.27
Consensus pattern (21 bp):
TCCCCGGATTCGATGCCTCAT
Found at i:17520 original size:23 final size:23
Alignment explanation
Indices: 17494--17539 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
17484 AAATATGTTC
17494 TAAAAATAATATTAGAT-ACACCA
1 TAAAAATAATATTA-ATAACACCA
*
17517 TAAATATAATATTAATAACACCA
1 TAAAAATAATATTAATAACACCA
17540 ATGGCATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAAATAATATTAATAACACCA
Found at i:31676 original size:72 final size:72
Alignment explanation
Indices: 31559--31706 Score: 296
Period size: 72 Copynumber: 2.1 Consensus size: 72
31549 TAGCTTGTGA
31559 CTTAGCATTCAACAAGTAGATCCATGCATGCTCACAATGACAGAGTAAATGATTTATTGATTCCG
1 CTTAGCATTCAACAAGTAGATCCATGCATGCTCACAATGACAGAGTAAATGATTTATTGATTCCG
31624 GTTCTTT
66 GTTCTTT
31631 CTTAGCATTCAACAAGTAGATCCATGCATGCTCACAATGACAGAGTAAATGATTTATTGATTCCG
1 CTTAGCATTCAACAAGTAGATCCATGCATGCTCACAATGACAGAGTAAATGATTTATTGATTCCG
31696 GTTCTTT
66 GTTCTTT
31703 CTTA
1 CTTA
31707 CACACAATAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (72 bp):
CTTAGCATTCAACAAGTAGATCCATGCATGCTCACAATGACAGAGTAAATGATTTATTGATTCCG
GTTCTTT
Found at i:32360 original size:133 final size:132
Alignment explanation
Indices: 32094--32360 Score: 400
Period size: 133 Copynumber: 2.0 Consensus size: 132
32084 CCCGTTTTAT
* * *
32094 ATAATAATATAGTTGTCGATTTTAAATTTATTTTTTTAATGACAAAACAAAATTAAAATCAATAT
1 ATAATAATATAGTTGTCGATTTAAAATTGATTTTGTTAATGACAAAACAAAATTAAAATCAATAT
*
32159 ATTATGTATATTCATTAGTATATAGATTTATTTATTTATTACTTTATTTATATTGTCATTTTATA
66 ATTATGTATATTCATTAGTATAGAGATTTATTTATTTATTACTTTATTTATATTGTCATTTTATA
32224 TA
131 TA
* **
32226 ATAATTAATATATTTGTCGATTTAAAATTGATTTTGTTAAT-ATCTGAACAAAATTAAAATCAAT
1 ATAA-TAATATAGTTGTCGATTTAAAATTGATTTTGTTAATGA-CAAAACAAAATTAAAATCAAT
*
32290 ATA-T-TGTATATTCATTAGTATAGAG-TTTATTTATATT-TTACTTTATTTATATTTTCATTTT
64 ATATTATGTATATTCATTAGTATAGAGATTTATTTAT-TTATTACTTTATTTATATTGTCATTTT
32351 ATATA
128 ATATA
32356 ATAAT
1 ATAAT
32361 TAGTGTATAT
Statistics
Matches: 124, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
129 1 0.01
130 41 0.33
131 22 0.18
132 6 0.05
133 54 0.44
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.50
Consensus pattern (132 bp):
ATAATAATATAGTTGTCGATTTAAAATTGATTTTGTTAATGACAAAACAAAATTAAAATCAATAT
ATTATGTATATTCATTAGTATAGAGATTTATTTATTTATTACTTTATTTATATTGTCATTTTATA
TA
Found at i:32784 original size:2 final size:2
Alignment explanation
Indices: 32779--32820 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
32769 ACCACACACG
32779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32821 ACTATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33197 original size:2 final size:2
Alignment explanation
Indices: 33185--33227 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
33175 TTAACCAAAA
33185 AT AT GAT 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
33228 TTATTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33982 original size:16 final size:17
Alignment explanation
Indices: 33958--33992 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
33948 CCATTACTTA
33958 ATTTATCACTGT-ATTT
1 ATTTATCACTGTGATTT
*
33974 ATTTGTCACTGTGATTT
1 ATTTATCACTGTGATTT
33991 AT
1 AT
33993 GTTGAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (17 bp):
ATTTATCACTGTGATTT
Found at i:41539 original size:35 final size:35
Alignment explanation
Indices: 41491--41558 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
41481 ATTATTTTTG
* * *
41491 ATTATTTTGGAATTTGGGGTTTAGAATGTAATTGA
1 ATTATTTTAGAATTTAGGGTTTAGAATGAAATTGA
41526 ATTATTTTAGAATTTAGGGTTTAGAATGAAATT
1 ATTATTTTAGAATTTAGGGTTTAGAATGAAATT
41559 AAGTATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (35 bp):
ATTATTTTAGAATTTAGGGTTTAGAATGAAATTGA
Found at i:44009 original size:16 final size:16
Alignment explanation
Indices: 43987--44034 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
43977 TTTACTTCTT
43987 TATTATTATTTATTTAC
1 TATTATTATTTATTT-C
44004 -ATTATTTATTT-TTTC
1 TATTA-TTATTTATTTC
44019 TATTATTATTATATTT
1 TATTATTATT-TATTT
44035 TTTCCTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.22
16 12 0.44
17 9 0.33
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTATTTATTTC
Found at i:55355 original size:1 final size:1
Alignment explanation
Indices: 55349--55373 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
55339 GAGCATCTTC
55349 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
55374 TCATCAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56070 original size:105 final size:105
Alignment explanation
Indices: 55565--56076 Score: 922
Period size: 105 Copynumber: 4.9 Consensus size: 105
55555 GGTTTTACCC
*
55565 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
55630 CGAAGGGACCGCTGGTTGTC-ACCAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
55669 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
55734 CGAAGGGACCGCTGGTTGTC-ACTAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAAC-AAACATTTCTCAAATTT
55774 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
55839 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
55879 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
55944 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
* * *
55983 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCGCG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
56048 ACGAAGGGACCGCTGGTTGTCAATAAACA
65 ACGAAGGGACCGCTGGTTGTCAACAAACA
56077 ATTACCCAAT
Statistics
Matches: 397, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
104 91 0.23
105 305 0.77
106 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
Found at i:56174 original size:20 final size:20
Alignment explanation
Indices: 56149--56190 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
56139 CCAGAACTCT
56149 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAATTTCAC
56169 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAATTTCAC
56189 GA
1 GA
56191 CGAAGGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAATTTCAC
Found at i:57664 original size:8 final size:8
Alignment explanation
Indices: 57629--57666 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
57619 TTATTTCACT
57629 TATATGT-
1 TATATGTA
57636 TATAT-TA
1 TATATGTA
*
57643 TATATATA
1 TATATGTA
57651 TATATGTA
1 TATATGTA
57659 TATATGTA
1 TATATGTA
57667 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:62262 original size:29 final size:29
Alignment explanation
Indices: 62227--62294 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
62217 CATTTTACAC
* * *
62227 AAATAGCACCCTTTTTAAAATATTTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
62256 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
62285 GAATAGCACC
1 AAATAGCACC
62295 AAAACCGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:62303 original size:29 final size:29
Alignment explanation
Indices: 62247--62352 Score: 131
Period size: 29 Copynumber: 3.7 Consensus size: 29
62237 CTTTTTAAAA
* * ***
62247 TATTTACCAAAATAGCACCCATTTCGAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
*
62276 TAATTACCAGAATAGCACCAAAACCGAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
* **
62305 TATTTACCATAATAGCACCAAAACTAAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
62334 TATTTACCAGAATAGCACC
1 TATTTACCAGAATAGCACC
62353 GGTCAACGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (29 bp):
TATTTACCAGAATAGCACCAAAACCGAAT
Found at i:62392 original size:18 final size:18
Alignment explanation
Indices: 62360--62412 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
62350 ACCGGTCAAC
*
62360 GGTCAACA-ATCGGGTCG
1 GGTCAACAGGTCGGGTCG
62377 GGTCAACAGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
* *
62395 GGTAAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
62413 CGACGGTCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 8 0.25
18 24 0.75
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Found at i:69259 original size:47 final size:47
Alignment explanation
Indices: 69206--69298 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
69196 TAAATGTTAA
69206 AATACTGAGAAGTTCTCATTCTATATATTAGTAAGGGTCTATTTGAC
1 AATACTGAGAAGTTCTCATTCTATATATTAGTAAGGGTCTATTTGAC
69253 AATACTGAGAAGTTCTCATTCTATATATTAGTAAGGGTCTATTTGA
1 AATACTGAGAAGTTCTCATTCTATATATTAGTAAGGGTCTATTTGA
69299 TCCTTATGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (47 bp):
AATACTGAGAAGTTCTCATTCTATATATTAGTAAGGGTCTATTTGAC
Found at i:82844 original size:29 final size:29
Alignment explanation
Indices: 82790--82845 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
82780 CTGAAAATGA
* * *
82790 TTTAAAAGTTTAGTGACTATATTACAAGT
1 TTTAAAAGTTGAGTGACTAAAATACAAGT
*
82819 TTTAAAAGTTGGGTGACTAAAATACAA
1 TTTAAAAGTTGAGTGACTAAAATACAA
82846 ATGCTCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTAAAAGTTGAGTGACTAAAATACAAGT
Found at i:86358 original size:2 final size:2
Alignment explanation
Indices: 86351--86390 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
86341 TCTCTAACTC
86351 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
86391 GAATATGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88653 original size:2 final size:2
Alignment explanation
Indices: 88646--88677 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88636 CGATTGCCAA
88646 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
88678 CGGATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89160 original size:19 final size:18
Alignment explanation
Indices: 89136--89171 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
89126 ATCTTCAAAG
*
89136 ATAAAAGTTTTATGCTTTT
1 ATAAAACTTTTAT-CTTTT
89155 ATAAAACTTTTATCTTT
1 ATAAAACTTTTATCTTT
89172 GTGTCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (18 bp):
ATAAAACTTTTATCTTTT
Found at i:96827 original size:35 final size:34
Alignment explanation
Indices: 96786--96998 Score: 157
Period size: 35 Copynumber: 6.1 Consensus size: 34
96776 AAAAAAATCA
* *
96786 TGAGCTCGATTGAAGCTCGAGACTCGAGCTCGA-T
1 TGAGCTCGATTGAAGCTCGA-ACTCAAACTCGATT
*
96820 TGAAGCTCGATTTTG-AGCTCG-ATTCAAACTCGATT
1 TG-AGCTCGA--TTGAAGCTCGAACTCAAACTCGATT
* * *
96855 TCAAGCTCGATTTTG-AGCTCG-ATTCAAGCTCGATTT
1 T-GAGCTCGA--TTGAAGCTCGAACTCAAACTCGA-TT
* ** ** *
96891 TGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTT
1 TGAGCTCGATTGAAGCTCGAACTCAAACTCGA-TT
*
96926 TGAGCTCGATTCAAGCTCGAACTCAAACTCGAATT
1 TGAGCTCGATTGAAGCTCGAACTCAAACTCG-ATT
* *
96961 TGAGCTCGATTTAAGCTCGAACTCGAACTCGAATT
1 TGAGCTCGATTGAAGCTCGAACTCAAACTCG-ATT
96996 TGA
1 TGA
96999 ACCTACAAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.01
34 17 0.11
35 121 0.79
36 10 0.07
37 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (34 bp):
TGAGCTCGATTGAAGCTCGAACTCAAACTCGATT
Found at i:96841 original size:23 final size:23
Alignment explanation
Indices: 96787--96945 Score: 130
Period size: 23 Copynumber: 6.8 Consensus size: 23
96777 AAAAAATCAT
**
96787 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-TTTC
*
96811 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTC
* *
96834 GAGCTCGATTCAAACTCGATTTC
1 GAGCTCGATTGAAGCTCGATTTC
*
96857 AAGCTCGATTTTG-AGCTCGA-TTC
1 GAGCTCGA--TTGAAGCTCGATTTC
*
96880 AAGCTCGATTTTG-AGCTCGA-TTC
1 GAGCTCGA--TTGAAGCTCGATTTC
* *
96903 AAGCTCGATTTTG-AGCTCGATTTT
1 GAGCTCGA--TTGAAGCTCGATTTC
*
96927 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTGAAGCTCGA
96946 ACTCAAACTC
Statistics
Matches: 119, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.02
23 81 0.68
24 34 0.29
25 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTC
Found at i:96979 original size:23 final size:23
Alignment explanation
Indices: 96848--96981 Score: 144
Period size: 23 Copynumber: 5.7 Consensus size: 23
96838 TCGATTCAAA
*
96848 CTCGATTTCAAGCTCGATTTTGAG
1 CTCGA-TTCAAGCTCGAATTTGAG
*
96872 CTCGATTCAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGAATTTGAG
*
96895 CTCGATTCAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGAATTTGAG
** **
96918 CTCGATTTTGAGCTCG-ATTCAAG
1 CTCGA-TTCAAGCTCGAATTTGAG
* *
96941 CTCGAACTCAAACTCGAATTTGAG
1 CTCG-ATTCAAGCTCGAATTTGAG
*
96965 CTCGATTTAAGCTCGAA
1 CTCGATTCAAGCTCGAA
96982 CTCGAACTCG
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
23 70 0.75
24 23 0.25
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (23 bp):
CTCGATTCAAGCTCGAATTTGAG
Found at i:96992 original size:58 final size:57
Alignment explanation
Indices: 96788--96992 Score: 212
Period size: 58 Copynumber: 3.5 Consensus size: 57
96778 AAAAATCATG
* *
96788 AGCTCGATTGAAGCTCGAGACTCGAGCTCGATTGAAGCTCGATTTTGAGCTCGATTCA
1 AGCTCGATTTAAGCTCGA-ACTCGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTCA
* ** *
96846 AACTCGATTTCAAGCTCGATTTTGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTCA
1 AGCTCGATTT-AAGCTCGAACTCGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTCA
* ** * ** ** * **
96904 AGCTCGATTTTGAGCTCGATTTTGAGCTCGATTCAAGCTCGAACTCAAACTCGAATTTG
1 AGCTCGA-TTTAAGCTCGAACTCGAGCTCGATTCAAGCTCGATTTTGAGCTCG-ATTCA
*
96963 AGCTCGATTTAAGCTCGAACTCGAACTCGA
1 AGCTCGATTTAAGCTCGAACTCGAGCTCGA
96993 ATTTGAACCT
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
58 103 0.83
59 21 0.17
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (57 bp):
AGCTCGATTTAAGCTCGAACTCGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTCA
Found at i:97000 original size:12 final size:12
Alignment explanation
Indices: 96951--97000 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
96941 CTCGAACTCA
96951 AACTCGAATTTG
1 AACTCGAATTTG
*
96963 AGCTCG-ATTT-
1 AACTCGAATTTG
* *
96973 AAGCTCGAACTCG
1 AA-CTCGAATTTG
96986 AACTCGAATTTG
1 AACTCGAATTTG
96998 AAC
1 AAC
97001 CTACAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
12 18 0.62
13 2 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (12 bp):
AACTCGAATTTG
Found at i:97857 original size:12 final size:12
Alignment explanation
Indices: 97840--97864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
97830 TTATTTAAAG
97840 ATAAACAAACTC
1 ATAAACAAACTC
97852 ATAAACAAACTC
1 ATAAACAAACTC
97864 A
1 A
97865 CCACAGGGGA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAACAAACTC
Found at i:98734 original size:35 final size:35
Alignment explanation
Indices: 98688--98767 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
98678 GGAATGCTTG
98688 AATAATAATCTGCCCATACAAATTACAAAGCATTA
1 AATAATAATCTGCCCATACAAATTACAAAGCATTA
*
98723 AATAATAATCTGCCCATACAAATTACAAAGCATTG
1 AATAATAATCTGCCCATACAAATTACAAAGCATTA
98758 AATAATAATC
1 AATAATAATC
98768 GTTGAAAAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (35 bp):
AATAATAATCTGCCCATACAAATTACAAAGCATTA
Found at i:99043 original size:21 final size:21
Alignment explanation
Indices: 99019--99075 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
99009 TGTTTAAAAT
99019 TATAAACACTAAACCATAA-AC
1 TATAAAC-CTAAACCATAATAC
99040 TATAAATCCT-AACACATAATAC
1 TATAAA-CCTAAAC-CATAATAC
99062 -ATAAACCCTAAACC
1 TATAAA-CCTAAACC
99076 TTACACCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.10
21 22 0.71
22 6 0.19
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (21 bp):
TATAAACCTAAACCATAATAC
Found at i:99086 original size:35 final size:35
Alignment explanation
Indices: 99060--99234 Score: 179
Period size: 35 Copynumber: 4.8 Consensus size: 35
99050 AACACATAAT
* * *
99060 ACATAAACCCTAAACCTTACACCCTAAATCCTATC
1 ACATAAACCCTAAACCCTAAACCCTAAATCATATC
*
99095 ACATAAACCCTAACCCCTAAACCCTAAATCATATC
1 ACATAAACCCTAAACCCTAAACCCTAAATCATATC
* *
99130 ATATAAACCCTAAACCCTAAACCTTAAATCATATC
1 ACATAAACCCTAAACCCTAAACCCTAAATCATATC
* * *
99165 ATATAAACTATAACCCTTAAATCCTAAACCTTAAATCATATC
1 ----ACA-TA-AACCC-TAAACCCTAAACCCTAAATCATATC
* * *
99207 ATATAAACTCTAAAACCTAAACCCTAAA
1 ACATAAACCCTAAACCCTAAACCCTAAA
99235 CCTTAAATCA
Statistics
Matches: 120, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
35 79 0.66
36 4 0.03
37 2 0.02
38 2 0.02
39 2 0.02
40 2 0.02
41 5 0.04
42 24 0.20
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (35 bp):
ACATAAACCCTAAACCCTAAACCCTAAATCATATC
Found at i:99114 original size:7 final size:7
Alignment explanation
Indices: 99063--99122 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
99053 ACATAATACA
99063 TAAACCC
1 TAAACCC
*
99070 TAAACCT
1 TAAACCC
*
99077 TACACCC
1 TAAACCC
*
99084 TAAATCC
1 TAAACCC
* *
99091 T-ATCACA
1 TAAAC-CC
99098 TAAACCC
1 TAAACCC
*
99105 TAACCCC
1 TAAACCC
99112 TAAACCC
1 TAAACCC
99119 TAAA
1 TAAA
99123 TCATATCATA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
6 1 0.03
7 36 0.92
8 2 0.05
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:99144 original size:42 final size:42
Alignment explanation
Indices: 99098--99283 Score: 217
Period size: 42 Copynumber: 4.6 Consensus size: 42
99088 TCCTATCACA
* *
99098 TAAACCCTAACCCCTAAACCCTAAATCATATC--AT--A---
1 TAAACCCTAAACCCTAAACCTTAAATCATATCATATAAACTC
*
99133 TAAACCCTAAACCCTAAACCTTAAATCATATCATATAAACTA
1 TAAACCCTAAACCCTAAACCTTAAATCATATCATATAAACTC
*
99175 T-AACCCTTAAATCCTAAACCTTAAATCATATCATATAAACTC
1 TAAACCC-TAAACCCTAAACCTTAAATCATATCATATAAACTC
* * * *
99217 TAAAACCTAAACCCTAAACCTTAAATCACATCACATAAATTC
1 TAAACCCTAAACCCTAAACCTTAAATCATATCATATAAACTC
* *
99259 TAAACTCTAAACCCTAAACCCTAAA
1 TAAACCCTAAACCCTAAACCTTAAA
99284 CTTTATCGCA
Statistics
Matches: 130, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
35 30 0.23
37 2 0.02
39 1 0.01
41 5 0.04
42 88 0.68
43 4 0.03
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (42 bp):
TAAACCCTAAACCCTAAACCTTAAATCATATCATATAAACTC
Found at i:99475 original size:42 final size:42
Alignment explanation
Indices: 99365--99476 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
99355 AATCTAAATC
* *
99365 ATAAACCCTAAACCCTAAACTTTAAACCATAACTCCTAACAT
1 ATAAACCCTAAACCCTAAACTATAAACCATAACTCATAACAT
* * * *
99407 ATAAAACCTAAACCCTAAA-TCCTAAACCA-CATTACATAA-ACT
1 ATAAACCCTAAACCCTAAACT-ATAAACCATAACT-CATAACA-T
*
99449 CTAAACCCTAAACCCTAAACTATAAACC
1 ATAAACCCTAAACCCTAAACTATAAACC
99477 TTAAATCCTG
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 4 0.07
42 53 0.91
43 1 0.02
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (42 bp):
ATAAACCCTAAACCCTAAACTATAAACCATAACTCATAACAT
Found at i:99481 original size:7 final size:7
Alignment explanation
Indices: 99366--99468 Score: 52
Period size: 7 Copynumber: 14.7 Consensus size: 7
99356 ATCTAAATCA
99366 TAAACCC
1 TAAACCC
99373 TAAACCC
1 TAAACCC
**
99380 TAAACTT
1 TAAACCC
*
99387 TAAACCA
1 TAAACCC
99394 T-AACTCC
1 TAAAC-CC
**
99401 T-AACATA
1 TAAAC-CC
*
99408 TAAAACC
1 TAAACCC
99415 TAAACCC
1 TAAACCC
*
99422 TAAATCC
1 TAAACCC
99429 TAAACCAC
1 TAAACC-C
* *
99437 -ATTA-CA
1 TA-AACCC
*
99443 TAAACTC
1 TAAACCC
99450 TAAACCC
1 TAAACCC
99457 TAAACCC
1 TAAACCC
99464 TAAAC
1 TAAAC
99469 TATAAACCTT
Statistics
Matches: 70, Mismatches: 20, Indels: 12
0.69 0.20 0.12
Matches are distributed among these distances:
6 4 0.06
7 62 0.89
8 4 0.06
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:99481 original size:28 final size:27
Alignment explanation
Indices: 99366--99481 Score: 60
Period size: 28 Copynumber: 4.1 Consensus size: 27
99356 ATCTAAATCA
* *
99366 TAAACCCTAAACCCTAAACTTTAAACCA
1 TAAACCCTAAACCCTAAAC-ATAAACCT
** * *
99394 T-AACTCCT-AACATATAAAACCTAAACCC
1 TAAAC-CCTAAAC-CCT-AAACATAAACCT
* *
99422 TAAATCCTAAACCAC-ATTACATAAA-CT
1 TAAACCCTAAACC-CTA-AACATAAACCT
99449 CTAAACCCTAAACCCTAAACTATAAACCT
1 -TAAACCCTAAACCCTAAAC-ATAAACCT
99478 TAAA
1 TAAA
99482 TCCTGTCACT
Statistics
Matches: 65, Mismatches: 12, Indels: 22
0.66 0.12 0.22
Matches are distributed among these distances:
27 11 0.17
28 43 0.66
29 11 0.17
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.22
Consensus pattern (27 bp):
TAAACCCTAAACCCTAAACATAAACCT
Found at i:99999 original size:14 final size:14
Alignment explanation
Indices: 99982--100022 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
99972 TTTATTCATC
99982 AATAATGTATTTTT
1 AATAATGTATTTTT
99996 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
100007 AATAATGTAATTTT
1 AATAATGTATTTTT
100021 AA
1 AA
100023 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:100509 original size:12 final size:12
Alignment explanation
Indices: 100492--100538 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
100482 CAGGTTTTTT
*
100492 AACCGGATAAAA
1 AACCGGTTAAAA
100504 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
100519 AACCGGTTAAAA
1 AACCGGTTAAAA
100531 AACCGGTT
1 AACCGGTT
100539 TTTATCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:102857 original size:21 final size:21
Alignment explanation
Indices: 102833--102872 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
102823 TTTATTTTAT
102833 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
102854 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
102873 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:102909 original size:33 final size:33
Alignment explanation
Indices: 102867--102966 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
102857 TTTGTTTCAA
102867 TTATCGAACTT-GAAGTTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAG-TTTTTAAGTATTTGAAT
102900 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
* * * *
102933 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
102966 T
1 T
102967 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 58 0.94
34 4 0.06
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
Found at i:102995 original size:13 final size:13
Alignment explanation
Indices: 102952--103006 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
102942 TTGGAAGTAT
102952 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
102965 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
102979 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
102992 TTAAGTATTTGAA
1 TTAAGTATTTCAA
103005 TT
1 TT
103007 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:103429 original size:15 final size:15
Alignment explanation
Indices: 103404--103459 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
103394 ATCTGGAATA
*
103404 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
103419 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
103434 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
103451 TTAAAACCG
1 TTAAAACCG
103460 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:103468 original size:21 final size:18
Alignment explanation
Indices: 103423--103456 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
103413 GTTTTTTTAT
103423 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
103440 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
103457 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:103576 original size:15 final size:17
Alignment explanation
Indices: 103550--103581 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
103540 TTCTATGGGA
103550 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
103566 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
103582 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:105715 original size:12 final size:12
Alignment explanation
Indices: 105698--105722 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105688 TTAAAAAATG
105698 TGTTATTAATTT
1 TGTTATTAATTT
105710 TGTTATTAATTT
1 TGTTATTAATTT
105722 T
1 T
105723 TTAATAAAAT
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:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TGTTATTAATTT
Found at i:107746 original size:17 final size:16
Alignment explanation
Indices: 107724--107758 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
107714 TTAATGAGAT
107724 AAAATTATAATTCATAA
1 AAAATTATAATTC-TAA
*
107741 AAAATTATATTTCTAA
1 AAAATTATAATTCTAA
107757 AA
1 AA
107759 CTTATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTATAATTCTAA
Found at i:110220 original size:10 final size:10
Alignment explanation
Indices: 110205--110248 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
110195 TATTTAAATG
110205 ATAAACGAAC
1 ATAAACGAAC
110215 ATAAACGAAC
1 ATAAACGAAC
*
110225 ATAAAAAAGGAAC
1 AT---AAACGAAC
110238 ATAAACGAAC
1 ATAAACGAAC
110248 A
1 A
110249 ACACAAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 20 0.69
13 9 0.31
ACGTcount: A:0.64, C:0.16, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:111481 original size:12 final size:12
Alignment explanation
Indices: 111466--111490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111456 CTCCACGCAT
111466 AGTTCCACACAA
1 AGTTCCACACAA
111478 AGTTCCACACAA
1 AGTTCCACACAA
111490 A
1 A
111491 TAATACGCTC
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:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
AGTTCCACACAA
Found at i:111957 original size:24 final size:25
Alignment explanation
Indices: 111901--111957 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
111891 TTTAATTTAC
* *
111901 AAATTAAAAGTGAGTTTATTTGATT
1 AAATTAAAAGTGAATTTATTAGATT
111926 AAATTAAAA-TGAATTT-TTAGATAT
1 AAATTAAAAGTGAATTTATTAGAT-T
111950 AAATTAAA
1 AAATTAAA
111958 TATTTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 15 0.52
25 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (25 bp):
AAATTAAAAGTGAATTTATTAGATT
Found at i:119146 original size:10 final size:10
Alignment explanation
Indices: 119131--119205 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
119121 CATTTAATAA
119131 ATAAACGAAC
1 ATAAACGAAC
119141 ATAAACGAAC
1 ATAAACGAAC
119151 ----ACGAAC
1 ATAAACGAAC
119157 ATAAACGAAC
1 ATAAACGAAC
** *
119167 ACGAAC-ATAA
1 ATAAACGA-AC
119177 ATGAACACGAAC
1 AT-AA-ACGAAC
*
119189 ATAAAGGAAC
1 ATAAACGAAC
119199 ATAAACG
1 ATAAACG
119206 TTGGAGGCCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 33 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:119156 original size:16 final size:16
Alignment explanation
Indices: 119135--119199 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
119125 TAATAAATAA
119135 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
119151 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
119167 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
119183 ACGAACATAAAGGAAC
1 ACGAACATAAACGAAC
119199 A
1 A
119200 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.22, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:121112 original size:23 final size:22
Alignment explanation
Indices: 121060--121114 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
121050 AATTAATAAC
*
121060 ATTTTAAATATATTATACAAATA
1 ATTTTAAA-ATATTAAACAAATA
** *
121083 AAATTAAAAGTATTAAAGAAATA
1 ATTTTAAAA-TATTAAACAAATA
121106 ATTTTAAAA
1 ATTTTAAAA
121115 AATCAAGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
ATTTTAAAATATTAAACAAATA
Found at i:124948 original size:18 final size:20
Alignment explanation
Indices: 124911--124948 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
124901 ATTAAGCTTC
*
124911 ATAGATGCCATATGAATAGG
1 ATAGATGCCATATAAATAGG
124931 ATAGATG-C-TATAAATAGG
1 ATAGATGCCATATAAATAGG
124949 CAGTTGTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (20 bp):
ATAGATGCCATATAAATAGG
Found at i:132570 original size:68 final size:68
Alignment explanation
Indices: 132490--132893 Score: 557
Period size: 68 Copynumber: 6.1 Consensus size: 68
132480 GGAAGGAGAT
*
132490 TGCAATTGAAATATAAATGCAAATCGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132555 TGA
66 TGA
* * * *
132558 TGCAATTGAAATATAAATGCAAATTGATCCCATAAATTAAAATAGATAGTTCAACTACAAATTTA
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132623 TGA
66 TGA
* * *
132626 GGCAATTGAAATATAAATGCAAATTGGT--C-TAAA--AAATTA-ATAGCTCAACTAC-AATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132684 TGA
66 TGA
* * * * *
132687 TACAGTTGAAATATAAATGCAAATCGATCCCAAAAATTAAATTAGATAGCTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132752 TGA
66 TGA
*
132755 TGCAATTGAAATATAAATGTAAATTGGTCCCAAAAA-T----TA-ATAGCTCAACTAC-AATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132813 TGA
66 TGA
* * *
132816 TACAGTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTA
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
132881 TGA
66 TGA
132884 TGCAATTGAA
1 TGCAATTGAA
132894 GTATCATGCA
Statistics
Matches: 295, Mismatches: 27, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
61 73 0.25
62 26 0.09
63 8 0.03
64 3 0.01
65 4 0.01
66 9 0.03
67 27 0.09
68 145 0.49
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (68 bp):
TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
TGA
Found at i:132716 original size:129 final size:129
Alignment explanation
Indices: 132490--132893 Score: 610
Period size: 129 Copynumber: 3.1 Consensus size: 129
132480 GGAAGGAGAT
* *
132490 TGCAATTGAAATATAAATGCAAATCGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGT--C-AAAA--AAATTA-ATAGCTCAACTAC-AATTTC
* * * *
132555 TGATGCAATTGAAATATAAATGCAAATTGATCCCATAAATTAAAATAGATAGTTCAACTACAAAT
59 TGATACAGTTGAAATATAAATGCAAATTGATCCCAAAAATTAAAATAGATAGCTCAACTACAAAT
132620 TTATGA
124 TTATGA
* *
132626 GGCAATTGAAATATAAATGCAAATTGGTCTAAAAAATTAATAGCTCAACTACAATTTCTGATACA
1 TGCAATTGAAATATAAATGCAAATTGGTCAAAAAAATTAATAGCTCAACTACAATTTCTGATACA
* * *
132691 GTTGAAATATAAATGCAAATCGATCCCAAAAATTAAATTAGATAGCTCAACTACAAATTTCTGA
66 GTTGAAATATAAATGCAAATTGATCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTATGA
* **
132755 TGCAATTGAAATATAAATGTAAATTGGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATACA
1 TGCAATTGAAATATAAATGCAAATTGGTCAAAAAAATTAATAGCTCAACTACAATTTCTGATACA
*
132820 GTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTATGA
66 GTTGAAATATAAATGCAAATTGATCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTATGA
132884 TGCAATTGAA
1 TGCAATTGAA
132894 GTATCATGCA
Statistics
Matches: 249, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
129 201 0.81
130 13 0.05
131 5 0.02
133 3 0.01
134 1 0.00
136 26 0.10
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (129 bp):
TGCAATTGAAATATAAATGCAAATTGGTCAAAAAAATTAATAGCTCAACTACAATTTCTGATACA
GTTGAAATATAAATGCAAATTGATCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTATGA
Found at i:135138 original size:68 final size:66
Alignment explanation
Indices: 135023--135290 Score: 358
Period size: 68 Copynumber: 4.2 Consensus size: 66
135013 GACCGGTGAA
* *
135023 TTCAATTGCATCAGAAA-TTGTAG-T--CGAGCTA-TTAATTTTTGGGACCAATTTGCATTTATA
1 TTCAATTGCATCAGAAATTTGTAGTTGACTATCTATTTAATTTTTGGGACCAATTTGCATTTATA
135083 T
66 T
135084 TTCAATTGCATCAGAAATTTGTAGTTGAACTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTG-ACTATCTA-TTTAATTTTTGGGACCAATTTGCATTTA
135149 TAT
64 TAT
* * * *
135152 TTCAACTGTATCAGAAA-TTGTAGTTG---AGCTA-TTAATTTTTGGGACAAATTTGCATTTATA
1 TTCAATTGCATCAGAAATTTGTAGTTGACTATCTATTTAATTTTTGGGACCAATTTGCATTTATA
135212 T
66 T
* *
135213 TTCAATTGCATCAGAAATTTGAAGTTGAGCTATCTATCTTAATTTTTGGGACCAATTTACATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGA-CTATCTAT-TTAATTTTTGGGACCAATTTGCATTTA
135278 TAT
64 TAT
135281 TTCAATTGCA
1 TTCAATTGCA
135291 ATCTCCTTCC
Statistics
Matches: 181, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
61 61 0.34
62 14 0.08
63 5 0.03
66 9 0.05
67 9 0.05
68 83 0.46
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (66 bp):
TTCAATTGCATCAGAAATTTGTAGTTGACTATCTATTTAATTTTTGGGACCAATTTGCATTTATA
T
Found at i:135255 original size:129 final size:129
Alignment explanation
Indices: 135023--135290 Score: 455
Period size: 129 Copynumber: 2.1 Consensus size: 129
135013 GACCGGTGAA
* *
135023 TTCAATTGCATCAGAAATTGTAGTCGAGCTATTAATTTTTGGGACCAATTTGCATTTATATTTCA
1 TTCAACTGCATCAGAAATTGTAGTCGAGCTATTAATTTTTGGGACAAATTTGCATTTATATTTCA
* * *
135088 ATTGCATCAGAAATTTGTAGTTGAACTATCTATTTTAATTTTTGGGACCAATTTGCATTTATAT
66 ATTGCATCAGAAATTTGAAGTTGAACTATCTATCTTAATTTTTGGGACCAATTTACATTTATAT
* *
135152 TTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACAAATTTGCATTTATATTTCA
1 TTCAACTGCATCAGAAATTGTAGTCGAGCTATTAATTTTTGGGACAAATTTGCATTTATATTTCA
*
135217 ATTGCATCAGAAATTTGAAGTTGAGCTATCTATCTTAATTTTTGGGACCAATTTACATTTATAT
66 ATTGCATCAGAAATTTGAAGTTGAACTATCTATCTTAATTTTTGGGACCAATTTACATTTATAT
*
135281 TTCAATTGCA
1 TTCAACTGCA
135291 ATCTCCTTCC
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (129 bp):
TTCAACTGCATCAGAAATTGTAGTCGAGCTATTAATTTTTGGGACAAATTTGCATTTATATTTCA
ATTGCATCAGAAATTTGAAGTTGAACTATCTATCTTAATTTTTGGGACCAATTTACATTTATAT
Found at i:135651 original size:68 final size:68
Alignment explanation
Indices: 135571--135974 Score: 566
Period size: 68 Copynumber: 6.1 Consensus size: 68
135561 GGAAGGAGAT
* * *
135571 TGCAATTGAAATATAAATGCAAATCGGTCTCAAAAATTAAAATAGATAACTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135636 TGA
66 TGA
* *
135639 TGCAATTGAAATATAAATGCAAATTGGTCCCATAAATTAAAATAGATAGTTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135704 TGA
66 TGA
* * *
135707 GGCAATTGAAATATAAATGCAAATTGGTCTCAAAAA-T----TA-ATAGCTCAACTAC-AATTTT
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135765 TGA
66 TGA
** * * *
135768 TATAGTTGAAATATAAATGCAAATTGATCCCAAAAATTAAATTAGATAGCTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135833 TGA
66 TGA
*
135836 TGCAATTGAAATATAAATGTAAATTGGTCCCAAAAA-T----TA-ATAGCTCAACTAC-AATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135894 TGA
66 TGA
* *
135897 TACAGTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
135962 TGA
66 TGA
135965 TGCAATTGAA
1 TGCAATTGAA
135975 GTATCATGCA
Statistics
Matches: 295, Mismatches: 27, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
61 80 0.27
62 27 0.09
63 4 0.01
66 4 0.01
67 28 0.09
68 152 0.52
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (68 bp):
TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTC
TGA
Found at i:135814 original size:129 final size:129
Alignment explanation
Indices: 135571--135974 Score: 637
Period size: 129 Copynumber: 3.1 Consensus size: 129
135561 GGAAGGAGAT
*
135571 TGCAATTGAAATATAAATGCAAATCGGTCTCAAAAATTAAAATAGATAACTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCTCAAAAATT--AATAG----CTCAACTAC-AATTTC
* * * *
135636 TGATGCAATTGAAATATAAATGCAAATTGGTCCCATAAATTAAAATAGATAGTTCAACTACAAAT
59 TGATACAGTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAAT
135701 TTCTGA
124 TTCTGA
* * *
135707 GGCAATTGAAATATAAATGCAAATTGGTCTCAAAAATTAATAGCTCAACTACAATTTTTGATATA
1 TGCAATTGAAATATAAATGCAAATTGGTCTCAAAAATTAATAGCTCAACTACAATTTCTGATACA
* *
135772 GTTGAAATATAAATGCAAATTGATCCCAAAAATTAAATTAGATAGCTCAACTACAAATTTCTGA
66 GTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTGA
* *
135836 TGCAATTGAAATATAAATGTAAATTGGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATACA
1 TGCAATTGAAATATAAATGCAAATTGGTCTCAAAAATTAATAGCTCAACTACAATTTCTGATACA
135901 GTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTGA
66 GTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTGA
135965 TGCAATTGAA
1 TGCAATTGAA
135975 GTATCATGCA
Statistics
Matches: 251, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
129 201 0.80
130 9 0.04
134 5 0.02
136 36 0.14
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (129 bp):
TGCAATTGAAATATAAATGCAAATTGGTCTCAAAAATTAATAGCTCAACTACAATTTCTGATACA
GTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTGA
Found at i:144186 original size:20 final size:20
Alignment explanation
Indices: 144163--144200 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
144153 AATATAAAAT
144163 TATTATATATTTTATATTTA
1 TATTATATATTTTATATTTA
*
144183 TATTATATATTTTTTATT
1 TATTATATATTTTATATT
144201 AAAAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTATATATTTTATATTTA
Found at i:151504 original size:15 final size:14
Alignment explanation
Indices: 151474--151507 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
151464 CTGAATTGTC
*
151474 TATTAAATATTAAG
1 TATTAAATAATAAG
151488 TATTAATATAATAAG
1 TATTAA-ATAATAAG
151503 TATTA
1 TATTA
151508 TTAATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
TATTAAATAATAAG
Found at i:153418 original size:61 final size:61
Alignment explanation
Indices: 153314--153436 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 61
153304 GCATCACATG
* * * ** * *
153314 CTCTTAAATTATGACCTTCATTTTAAATTAGTACTTAAATTTTTAAATATTTTAATTTCAT
1 CTCTAAAACTATGACCTTCATTCTAAATTAGTACCCAAATTTTTAAACATTTGAATTTCAT
*
153375 CTCTAAAACTATGACCTTCATTCTAAATTAGT-CCCAAACTTTTTGAACATTTGAATTTCAT
1 CTCTAAAACTATGACCTTCATTCTAAATTAGTACCCAAA-TTTTTAAACATTTGAATTTCAT
153436 C
1 C
153437 CCATCTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 4 0.08
61 49 0.92
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (61 bp):
CTCTAAAACTATGACCTTCATTCTAAATTAGTACCCAAATTTTTAAACATTTGAATTTCAT
Found at i:154399 original size:17 final size:15
Alignment explanation
Indices: 154377--154420 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
154367 GACTGTTTAC
154377 ATTATAAATTATAATAT
1 ATTATAAATTAT-A-AT
*
154394 ATTATAATTTATAAT
1 ATTATAAATTATAAT
154409 ATTATAAATTAT
1 ATTATAAATTAT
154421 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
17 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAATTATAAT
Found at i:155643 original size:2 final size:2
Alignment explanation
Indices: 155636--155663 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
155626 AACACGTATC
155636 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
155664 TTATTTAACT
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
Done.