Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003329.1 Kokia drynarioides strain JFW-HI SEQ_116030, 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: 129022
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:492 original size:3 final size:3
Alignment explanation
Indices: 484--629 Score: 94
Period size: 3 Copynumber: 46.0 Consensus size: 3
474 GGGTTTTTTG
* * * *
484 TTA TTA TTA TTA TTA TTAA TTA TTA TAA TTA CTA TTA TTAA TTA ATG
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA
* * * *
531 TCA TTA GTA TTA TCCTA TTA TTA ATA TTA TTA TTAA TTA TTA TAA TTA
1 TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * * * * *
579 CTA TTA TTAA TTA ATG TCA TTA GTA TTA TCCTA TTA TTA ATA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA
627 TTA
1 TTA
630 AGGCTATTTA
Statistics
Matches: 107, Mismatches: 28, Indels: 16
0.71 0.19 0.11
Matches are distributed among these distances:
3 89 0.83
4 12 0.11
5 6 0.06
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:514 original size:22 final size:22
Alignment explanation
Indices: 484--591 Score: 107
Period size: 22 Copynumber: 5.0 Consensus size: 22
474 GGGTTTTTTG
* *
484 TTATTATTATTATTATTAATTA
1 TTATAATTACTATTATTAATTA
506 TTATAATTACTATTATTAATTA
1 TTATAATTACTATTATTAATTA
* * * *
528 ATGTCATTAGTATTATCCT-ATTA
1 TTATAATTACTATTAT--TAATTA
*
551 -T-TAA-TATTATTATTAATTA
1 TTATAATTACTATTATTAATTA
570 TTATAATTACTATTATTAATTA
1 TTATAATTACTATTATTAATTA
592 ATGTCATTAG
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 9 0.13
21 5 0.07
22 47 0.66
23 4 0.06
24 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATAATTACTATTATTAATTA
Found at i:583 original size:64 final size:64
Alignment explanation
Indices: 484--630 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
474 GGGTTTTTTG
*
484 TTATTATTATTATTATTAATTATTATAATTACTATTATTAATTAATGTCATTAGTATTATCCTA
1 TTATTAATATTATTATTAATTATTATAATTACTATTATTAATTAATGTCATTAGTATTATCCTA
548 TTATTAATATTATTATTAATTATTATAATTACTATTATTAATTAATGTCATTAGTATTATCCTA
1 TTATTAATATTATTATTAATTATTATAATTACTATTATTAATTAATGTCATTAGTATTATCCTA
612 TTATTAATATTATTATTAA
1 TTATTAATATTATTATTAA
631 GGCTATTTAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 82 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (64 bp):
TTATTAATATTATTATTAATTATTATAATTACTATTATTAATTAATGTCATTAGTATTATCCTA
Found at i:600 original size:22 final size:22
Alignment explanation
Indices: 489--607 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 22
479 TTTTGTTATT
* *
489 ATTATTATTATTAATTATTATA
1 ATTACTATTATTAATTAATATA
* *
511 ATTACTATTATTAATTAATGTC
1 ATTACTATTATTAATTAATATA
*
533 ATTAGTATTATCCT-ATT-AT-TA
1 ATTACTATTAT--TAATTAATATA
* *
554 A-TATTATTATTAATTATTATA
1 ATTACTATTATTAATTAATATA
* *
575 ATTACTATTATTAATTAATGTC
1 ATTACTATTATTAATTAATATA
*
597 ATTAGTATTAT
1 ATTACTATTAT
608 CCTATTATTA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 9 0.12
21 5 0.06
22 56 0.72
23 3 0.04
24 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTACTATTATTAATTAATATA
Found at i:1312 original size:14 final size:15
Alignment explanation
Indices: 1289--1317 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1279 AATTTGGACA
1289 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
1304 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
1318 ATAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:1365 original size:17 final size:17
Alignment explanation
Indices: 1329--1408 Score: 88
Period size: 17 Copynumber: 4.4 Consensus size: 17
1319 TAATAATTTT
1329 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
1347 TTTAAATTTAAAATTAATTTAA
1 TTTAAATTTAAAA-T-A---AA
*
1369 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
1386 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
1403 TTTAAA
1 TTTAAA
1409 AGGGGCCGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
17 26 0.49
18 10 0.19
19 1 0.02
20 1 0.02
21 1 0.02
22 14 0.26
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1366 original size:39 final size:39
Alignment explanation
Indices: 1332--1407 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1322 TAATTTTTTT
*
1332 AAATTTGAAAATAAATTTAAATTTAAAATTAATTTAATTC
1 AAATTT-AAAATAAATCTAAATTTAAAATTAATTTAATTC
*
1372 AAATTTAAAATAAATCTAAATTTAAAATAAATTTAA
1 AAATTTAAAATAAATCTAAATTTAAAATTAATTTAA
1408 AAGGGGCCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 28 0.82
40 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (39 bp):
AAATTTAAAATAAATCTAAATTTAAAATTAATTTAATTC
Found at i:1370 original size:5 final size:6
Alignment explanation
Indices: 1329--1408 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
1319 TAATAATTTT
* * *
1329 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA ATT-AA TTT-AA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
1375 TTTAAA -ATAAA TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1409 AGGGGCCGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 19 0.33
6 36 0.62
7 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:1370 original size:22 final size:23
Alignment explanation
Indices: 1343--1397 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1333 AATTTGAAAA
*
1343 TAAATTTAAATTTAAAATTAAT-
1 TAAATTTAAATTTAAAATAAATC
* *
1365 TTAATTCAAATTTAAAATAAATC
1 TAAATTTAAATTTAAAATAAATC
1388 TAAATTTAAA
1 TAAATTTAAA
1398 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATC
Found at i:5024 original size:27 final size:27
Alignment explanation
Indices: 4989--5053 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
4979 ATGGATTTTG
*
4989 AAAAATTAAAAGGAAAATTGATTAATA
1 AAAAATTAAAAGGAAAATTAATTAATA
*
5016 AAAAATTAAAAGGAAAATTAATTAATT
1 AAAAATTAAAAGGAAAATTAATTAATA
*
5043 AAAAGTTAAAA
1 AAAAATTAAAA
5054 TGATAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (27 bp):
AAAAATTAAAAGGAAAATTAATTAATA
Found at i:5483 original size:18 final size:18
Alignment explanation
Indices: 5460--5502 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
5450 ATTAACACAA
5460 TTCAAACTTAAACTATAC
1 TTCAAACTTAAACTATAC
5478 TTCAAACTTAAACTATAC
1 TTCAAACTTAAACTATAC
5496 TTCAAAC
1 TTCAAAC
5503 GGTAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (18 bp):
TTCAAACTTAAACTATAC
Found at i:5608 original size:5 final size:5
Alignment explanation
Indices: 5598--5627 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5588 TTTCTCGTAC
5598 ATATT ATATT ATATT ATATT AT-TT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT A
5628 CAAGTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:5983 original size:31 final size:31
Alignment explanation
Indices: 5948--6044 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 31
5938 AATATTTGAC
*
5948 ACTTGAACATGATA-CTTTTTTCTAATTTGGT
1 ACTTGAACATGACATCTTTTTT-TAATTTGGT
**
5979 ACTTGAATTTGACATCTTTTTTTAATTTGGT
1 ACTTGAACATGACATCTTTTTTTAATTTGGT
* ** *
6010 A-TCTAAATTTGGCAT-TTTTTCTTAATTTGGT
1 ACT-TGAACATGACATCTTTTT-TTAATTTGGT
6041 ACTT
1 ACTT
6045 AATTTTTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
30 6 0.11
31 43 0.75
32 8 0.14
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (31 bp):
ACTTGAACATGACATCTTTTTTTAATTTGGT
Found at i:14414 original size:22 final size:22
Alignment explanation
Indices: 14389--14445 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
14379 AATTTTACAA
*
14389 TAACCAAGCAATAAAAAAATAG
1 TAACCAAACAATAAAAAAATAG
* *
14411 TAA-CAATATAATAGAAAAATAG
1 TAACCAA-ACAATAAAAAAATAG
*
14433 TAACAAAACAATA
1 TAACCAAACAATA
14446 TTAAAATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 3 0.11
22 23 0.82
23 2 0.07
ACGTcount: A:0.65, C:0.11, G:0.07, T:0.18
Consensus pattern (22 bp):
TAACCAAACAATAAAAAAATAG
Found at i:14452 original size:22 final size:22
Alignment explanation
Indices: 14397--14445 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
14387 AATAACCAAG
* *
14397 CAATAAAAAAATAGTAACAATA
1 CAATAGAAAAATAGTAACAAAA
*
14419 TAATAGAAAAATAGTAACAAAA
1 CAATAGAAAAATAGTAACAAAA
14441 CAATA
1 CAATA
14446 TTAAAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (22 bp):
CAATAGAAAAATAGTAACAAAA
Found at i:21967 original size:30 final size:30
Alignment explanation
Indices: 21932--22025 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
21922 CAAAACAGGT
** *
21932 TGAGAAGATTGTAAGGTTGACGAAGGTGCA
1 TGAGAAGATTGTACTGTTGATGAAGGTGCA
* *
21962 TGAGAAGATTGGACTGTTGATGAAGGCGCA
1 TGAGAAGATTGTACTGTTGATGAAGGTGCA
21992 TGAGAAGATTGTACTGTTGATGAAGGTGCA
1 TGAGAAGATTGTACTGTTGATGAAGGTGCA
22022 TGAG
1 TGAG
22026 CTGTCAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.31, C:0.07, G:0.36, T:0.26
Consensus pattern (30 bp):
TGAGAAGATTGTACTGTTGATGAAGGTGCA
Found at i:32517 original size:18 final size:18
Alignment explanation
Indices: 32483--32521 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
32473 CTATTTTTAA
*
32483 AAATTAAATATACTATTT
1 AAATTAAATATAATATTT
32501 AAATTGAAATA-AATATTT
1 AAATT-AAATATAATATTT
32519 AAA
1 AAA
32522 AATGCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTAAATATAATATTT
Found at i:37139 original size:595 final size:596
Alignment explanation
Indices: 35004--37946 Score: 4559
Period size: 596 Copynumber: 4.9 Consensus size: 596
34994 TTTAGTCTCA
* * *
35004 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTCGTGTTATTCGTCAAAACTTAGTGTTTATAG
1 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
* * * * * * *
35069 GTTAAGTGTTCAGTGTGGTAAGACCCAAGATTTGAATTCGATGAATTAGATTGAGTTGAGGGTTT
66 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
* * *
35134 TACAGTAGCTAAATCAAGTTCTCAATTGAAGGAAGTA-AACTGCTTTACCAATAGTTGAGACTCA
131 TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACCCA
* * * *
35198 ATCAGAAGAAGTTTCGACGTATATTCCTAATAATGTGATTTCTATTACAAATGGACAAATATTCT
196 ATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATTCT
* * *
35263 TATTCGTCGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGAGGATTTTCATCTCT-AG
261 TATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTCATCTCTAAG
* * *
35327 AGTAGGACCCACAACTTAAATTAAAGTTATAAAACAAGTGGTTGGTAAATCAAAATTGGAATTAA
326 -GTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATTAA
* * * *
35392 TCTAATTCGTCGAATTAAAAACTTTTGTATTGCGAATCTCGATAAAGCTACTCAAAATTAGTTGG
390 CCTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTTGG
35457 CACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACAG
455 CACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACAG
* * * * *
35522 TTATTAAACA-CATAATGAAATTTAACAGATAGTTTAATTAAATTGAAATCAAATTTATCTAACG
520 TTATTAAA-AGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACG
**
35586 ATATTTAGTGTTG
584 ATATTTAGTCCTG
* *
35599 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTTGCCAAAACTTAGTGTTTATAA
1 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
* * * * * * * * *
35664 GTTATGTGTTCGGTGTGGTAAGACTCAAGATTCGGATTCGATGCATCAGATCAAGTTGAGAGCGT
66 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
*
35729 TACATTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACCCA
131 TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACCCA
*
35794 ATCAGGAGAAATTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAAT-AGACAAATATTC
196 ATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGA-ACAAATATTC
* * * * *
35858 TTATCCGTTGATCTATTCAATGATGGAATCAGGCTTGATATTAATAAGGGGATTTTCGTCTCTAA
260 TTATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTCATCTCTAA
* * *
35923 AGTAGGACCCCCGACTTAAATTAAAGTTATAAAACAAGTTGCTAGTAAATCAAAATTGGAATTAA
325 GGTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATTAA
* *
35988 CCTAATTCGTCGAATAAGGAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTTGG
390 CCTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTTGG
36053 CACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACAG
455 CACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACAG
*
36118 TTATTAAACGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACGA
520 TTATTAAAAGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACGA
*
36183 TAATTAGTCCTG
585 TATTTAGTCCTG
*
36195 GAATGTAATTTTAAATTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
1 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
* * * * *
36260 GTTATGTGTTATGTGTGGTAAGACCCATGATTCGGATTAGATGAATTAA-ATCGAGTTGAA-GAT
66 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAA-TAAGATCGAGTT-AAGGGT
* * *
36323 GTTACAGTCGCTAAATCAAATTCTCAATTGTAGGAAGTATAACCGCTTTACTAATAGTTGAGACC
129 GTTACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACC
* * * *
36388 CAATCAGGAGAAGTTTCGACGTATATTCCTACAAATGTTATTTCCATTACAAATGGACAAATATC
194 CAATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATT
* * * *
36453 CTTATCCGTCGATCTATTCAATGTTGGAATCAGACTTGATATTAATAAGGGAATTTTCATCTCT-
259 CTTATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTCATCTCTA
* * * *
36517 AGAGTTGGACCCACGACTTAAATTAAAGTTATAAAACAAGTAGTTGGTAAATCAAAATTGAAATT
324 AG-GTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATT
*
36582 AACCTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGTTAAAGCTACTCAAAATTAGTT
388 AACCTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTT
*
36647 GGCACGTGAAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTAT
453 GGCACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTA-
*
36712 C-GTTATTAAAAGCATAATGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAA
517 CAGTTATTAAAAGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAA
*
36776 CGATATTTAGTCCTA
582 CGATATTTAGTCCTG
36791 GAATGTAATTTT-AACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
1 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
36855 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
66 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
* * *
36920 TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAATATATA-TGCTTTACTAATAGTTGAAACTC
131 TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATA-ACTGCTTTACTAATAGTTGAGACCC
* *
36984 AATCAGGAGAAGTTTCAACATATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATTC
195 AATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATTC
* * * *
37049 TTATCCGTAGATCTATTCAGTACTGGAATCAGACTTGATATTAACGAGGGGA-TTTCTGTCTCTA
260 TTATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTC-ATCTCTA
*
37113 AGGTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTATATCAAAATTGGAATTA
324 AGGTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATTA
* *
37178 ACCTAATTCGTCGAATTAAAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAGATTAGTTG
389 ACCTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTTG
*
37243 GCACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTAATTAAAATTATTTACA
454 GCACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACA
* *
37308 GTTATTAAACGCATAACGAAATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACG
519 GTTATTAAAAGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACG
37373 ATATTTAGTCCTG
584 ATATTTAGTCCTG
*
37386 GAATGTAATTTTAAATTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
1 GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
* *
37451 G-T-TGTGTTCTATGTGGTAAGACTCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
66 GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
* * * *
37514 TACAGTCGCTAAATCAAGTTCTCAATTAAAAGAAATATAACTGCTTTACTAATAGTTGAAACCCA
131 TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACCCA
* ** *
37579 ATCAGGAGAAGTTTCAATATATATTCCTACTAATGTGATTTCCATTACAAATGAATAAATATTCT
196 ATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATTCT
*
37644 TATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGA-GGGATTTTCATCTCTAGG
261 TATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTCATCTCTAAG
*
37708 GTAGGACCTGC-CGACTTAAATTAAAGTTATAAAACAAGTTGCTAGTAAATCAAAATTGGAATTA
326 GTAGGACC--CACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATTA
** * * * *
37772 ACCTAATTCG-CTGAATTAGAAACTTTTGCGCTTCTAGTCTTGATAAAGCTACTCAAAATTAATT
389 ACCTAATTCGTC-GAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTT
* *
37836 GGCACGTGAAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAACTATTTAC
453 GGCACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTAC
* * *
37901 AGTTATTATATGCATAACGATATTTAACGAATAGTTTAGTTAAATT
518 AGTTATTAAAAGCATAACGATATTTAACGGATAGTTTAGTTAAATT
37947 TTGTTCAAAT
Statistics
Matches: 2159, Mismatches: 168, Indels: 43
0.91 0.07 0.02
Matches are distributed among these distances:
593 21 0.01
594 448 0.21
595 687 0.32
596 998 0.46
597 5 0.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (596 bp):
GAATGTAATTTTAAACTAGGATTGTTTGTAATTTGGTGTTGTTCGCCAAAACTTAGTGTTTATAG
GTTATGTGTTCTGTGTGGTAAGACCCAAGATTTGGATTCGATGAATAAGATCGAGTTAAGGGTGT
TACAGTCGCTAAATCAAGTTCTCAATTGAAGGAAGTATAACTGCTTTACTAATAGTTGAGACCCA
ATCAGGAGAAGTTTCGACGTATATTCCTACTAATGTGATTTCCATTACAAATGAACAAATATTCT
TATCCGTAGATCTATTCAATGCTGGAATCAGACTTGATATTAATGAGGGGATTTTCATCTCTAAG
GTAGGACCCACGACTTAAATTAAAGTTATAAAACAAGTTGCTGGTAAATCAAAATTGGAATTAAC
CTAATTCGTCGAATTAGAAACTTTTGTACTGCTAATCTCGATAAAGCTACTCAAAATTAGTTGGC
ACGTGGAAAACAAGTTTGTTTATACATTTTACTTTTTAAAGTTGTTATTTAAAATTATTTACAGT
TATTAAAAGCATAACGATATTTAACGGATAGTTTAGTTAAATTGAAATCAGATTTATCTAACGAT
ATTTAGTCCTG
Found at i:41912 original size:93 final size:93
Alignment explanation
Indices: 41753--41930 Score: 277
Period size: 93 Copynumber: 1.9 Consensus size: 93
41743 TGCTGCTTCT
** * * *
41753 TGTGTGAATGTTGATGATGAGAAGACTCCTGTTGCATATCCAACAGGTTCATCTGCTGAAAGGAA
1 TGTGTGAATGTTGATGATGAGAAGAAGCCAGTGGCATATCCAACAGGTTCATCAGCTGAAAGGAA
*
41818 GTTAACTCCTGTAGTTGGTGGTTCATCA
66 GTTAACTCCTGTAGCTGGTGGTTCATCA
*
41846 TGTGTGAATGTTGATGATG-GAATGAAGCCAGTGGCATCTCCAACAGGTTCATCAGCTGAAAGGA
1 TGTGTGAATGTTGATGATGAGAA-GAAGCCAGTGGCATATCCAACAGGTTCATCAGCTGAAAGGA
41910 AGTTAACTCCTGTAGCTGGTG
65 AGTTAACTCCTGTAGCTGGTG
41931 AGGTTTTGTC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 3 0.04
93 74 0.96
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (93 bp):
TGTGTGAATGTTGATGATGAGAAGAAGCCAGTGGCATATCCAACAGGTTCATCAGCTGAAAGGAA
GTTAACTCCTGTAGCTGGTGGTTCATCA
Found at i:55391 original size:58 final size:58
Alignment explanation
Indices: 55301--55422 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 58
55291 TTAAGAGAGG
*
55301 TCATTATGACCTCAAATGTATACTCAAAGCGAAAACTTCATTTATGACTACGTGTACA
1 TCATTATGACCTCAAATGTATACTCAAAGCGAAAACTTCATTTATGACTACATGTACA
* *
55359 TCATTGTGACCTCAAATGTATACTCAAAGCGAAAACTTCATTTATGGCTACATGTACA
1 TCATTATGACCTCAAATGTATACTCAAAGCGAAAACTTCATTTATGACTACATGTACA
55417 T-ATTAT
1 TCATTAT
55423 CATACATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 4 0.07
58 56 0.93
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (58 bp):
TCATTATGACCTCAAATGTATACTCAAAGCGAAAACTTCATTTATGACTACATGTACA
Found at i:55778 original size:18 final size:18
Alignment explanation
Indices: 55748--55782 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55738 ATTTCCCACA
55748 TTATCATATTATAATCAT
1 TTATCATATTATAATCAT
55766 TTAT-ATATATATAATCA
1 TTATCATAT-TATAATCA
55783 ATTTCACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATCATATTATAATCAT
Found at i:58464 original size:52 final size:51
Alignment explanation
Indices: 58378--58625 Score: 253
Period size: 52 Copynumber: 4.8 Consensus size: 51
58368 ATTTCACTTT
* * * ** *
58378 ATTCATATACTCACAATGACACATAGCCACCGGACCTTATAATCCACGAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTT-TAATCCATAAAGG
* * * *
58430 ATTCGTATACTCACGATGACACAGAATCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT-TTAATCCATAAAGG
* * * * *
58482 ATCCATATACTTACAATGACACTTAGTCATCGGACCTTTAAATTCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTT-AATCCATAAAGG
* * * * *
58534 ATTTCATGTACTCATGATGACACAGAGTCATCGGACCTCGTAATCCTTAAAGG
1 A-TTCATATACTCACGATGACACATAGTCATCGGACCT-TTAATCCATAAAGG
* *
58587 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTT
58626 TTTCATTTAC
Statistics
Matches: 158, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
51 3 0.02
52 113 0.72
53 41 0.26
54 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTTTAATCCATAAAGG
Found at i:58578 original size:105 final size:105
Alignment explanation
Indices: 58381--58625 Score: 314
Period size: 105 Copynumber: 2.3 Consensus size: 105
58371 TCACTTTATT
* * * * ** * * *
58381 CATATACTCACAATGACACATAGCCACCGGACC-TTATAATCCACGAGGGA-TTCGTATACTCAC
1 CATATACTCACAATGACACTTAGTCATCGGACCTTTA-AATTCATAAAGGATTTCATGTACTCAC
*
58444 GATGACACAGAATCATCGGACCTCTTAATCCGTAAAGGATC
65 GATGACACAGAATCATCGGACCTCGTAATCCGTAAAGGATC
* *
58485 CATATACTTACAATGACACTTAGTCATCGGACCTTTAAATTCATAAAGGATTTCATGTACTCATG
1 CATATACTCACAATGACACTTAGTCATCGGACCTTTAAATTCATAAAGGATTTCATGTACTCACG
* * *
58550 ATGACACAGAGTCATCGGACCTCGTAATCCTTAAAGGATT
66 ATGACACAGAATCATCGGACCTCGTAATCCGTAAAGGATC
* *
58590 CATTTACTCACGATGACACTTAGTCATCGGACCTTT
1 CATATACTCACAATGACACTTAGTCATCGGACCTTT
58626 TTTCATTTAC
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
104 38 0.31
105 83 0.69
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (105 bp):
CATATACTCACAATGACACTTAGTCATCGGACCTTTAAATTCATAAAGGATTTCATGTACTCACG
ATGACACAGAATCATCGGACCTCGTAATCCGTAAAGGATC
Found at i:60836 original size:20 final size:21
Alignment explanation
Indices: 60799--60841 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
60789 CTAAATTAAC
* *
60799 AAAAACTATAAATTTATA-AA
1 AAAAAATATAAATATATATAA
*
60819 AAAAAATATAAGTATATATAA
1 AAAAAATATAAATATATATAA
60840 AA
1 AA
60842 CAACTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAATATAAATATATATAA
Found at i:61561 original size:19 final size:20
Alignment explanation
Indices: 61537--61575 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61527 TTTAAAGACT
61537 CAATTTAC-TAAAAAAATTC
1 CAATTTACTTAAAAAAATTC
*
61556 CAATTTACTTAAAGAAATTC
1 CAATTTACTTAAAAAAATTC
61576 AAAATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (20 bp):
CAATTTACTTAAAAAAATTC
Found at i:70685 original size:45 final size:45
Alignment explanation
Indices: 70620--70707 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
70610 CTAGAATTTT
* * *
70620 ATATGTATATATAAATATAAACTTTAGAGAAATTTTGTAAACATC
1 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACATC
70665 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACA
1 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACA
70708 ACCCATTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (45 bp):
ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACATC
Found at i:70722 original size:47 final size:45
Alignment explanation
Indices: 70620--70729 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 45
70610 CTAGAATTTT
* * * *
70620 ATATGTATATATAAATATAAACTTTAGAGAAATTTTGTAAACATC
1 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACACC
70665 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACAACCC
1 ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAAC-A-CC
70712 AT-TGATATATA-AAATATA
1 ATAT-ATATATATAAATATA
70730 TACTCTTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
45 39 0.67
46 9 0.16
47 10 0.17
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (45 bp):
ATATATATATATAAATATAAACTTGAGAGAAACTTTGTAAACACC
Found at i:71289 original size:47 final size:46
Alignment explanation
Indices: 71209--71298 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
71199 GAATGTAAAT
* *
71209 ATAATAAAAAAGACTAAAGGAAATAATCGTCGACATGATAAGTGGC
1 ATAATAAAAAAAACTAAAGGAAATAATCATCGACATGATAAGTGGC
* * * *
71255 ATAATAAAAATAAATTAAATGATATAATCATCGACGTGATAAGT
1 ATAATAAAAA-AAACTAAAGGAAATAATCATCGACATGATAAGT
71299 TATATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 10 0.27
47 27 0.73
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (46 bp):
ATAATAAAAAAAACTAAAGGAAATAATCATCGACATGATAAGTGGC
Found at i:71306 original size:47 final size:46
Alignment explanation
Indices: 71207--71308 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
71197 GTGAATGTAA
* *
71207 ATATAATAAAAAAGACTAAAGGAAATAATCGTCGACATGATAAGTG
1 ATATAATAAAAAAAACTAAAGGAAATAATCATCGACATGATAAGTG
** * * * * *
71253 GCATAATAAAAATAAATTAAATGATATAATCATCGACGTGATAAGTT
1 ATATAATAAAAA-AAACTAAAGGAAATAATCATCGACATGATAAGTG
71300 ATATAATAA
1 ATATAATAA
71309 CCACTAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
46 10 0.23
47 34 0.77
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (46 bp):
ATATAATAAAAAAAACTAAAGGAAATAATCATCGACATGATAAGTG
Found at i:71870 original size:3 final size:3
Alignment explanation
Indices: 71862--71904 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
71852 ACCAGGACAT
71862 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
71905 GATTTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:71989 original size:6 final size:7
Alignment explanation
Indices: 71970--71995 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
71960 ATGGAAGATT
71970 ATAAAAA
1 ATAAAAA
71977 ATAAAAA
1 ATAAAAA
71984 ATAAAAA
1 ATAAAAA
71991 ATAAA
1 ATAAA
71996 TCTAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:72724 original size:23 final size:23
Alignment explanation
Indices: 72694--72781 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
72684 TTAATGCTCA
*
72694 CGAACATGTTCATGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
* *
72717 CGAACATGTTCACGAACAATAAA
1 CGAACATGTTCACGAACATTAAT
*
72740 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* *
72764 TGAACACGTTCACGAACA
1 CGAACATGTTCACGAACA
72782 ATGTTAATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
23 37 0.67
24 18 0.33
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:72900 original size:12 final size:12
Alignment explanation
Indices: 72873--72919 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
72863 TCATTAATAA
72873 ATAAACGAGC-T
1 ATAAACGAGCTT
72884 ATAAACGAGCTT
1 ATAAACGAGCTT
* *
72896 ATAAATGAGCTA
1 ATAAACGAGCTT
72908 ATAAACGAGCTT
1 ATAAACGAGCTT
72920 GTTCGTGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:72916 original size:24 final size:23
Alignment explanation
Indices: 72873--72919 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
72863 TCATTAATAA
72873 ATAAACGAGCTATAAACGAGCTT
1 ATAAACGAGCTATAAACGAGCTT
*
72896 ATAAATGAGCTAATAAACGAGCTT
1 ATAAACGAGCT-ATAAACGAGCTT
72920 GTTCGTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (23 bp):
ATAAACGAGCTATAAACGAGCTT
Found at i:74348 original size:7 final size:7
Alignment explanation
Indices: 74336--74366 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
74326 AACAAAAATC
74336 ATATTAA
1 ATATTAA
74343 ATATTAA
1 ATATTAA
74350 ATATTAA
1 ATATTAA
*
74357 ACATTAA
1 ATATTAA
74364 ATA
1 ATA
74367 AAAAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATTAA
Found at i:92046 original size:19 final size:19
Alignment explanation
Indices: 92010--92051 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
92000 GTATACTTTT
*
92010 TTTTTTAAAATTTATGAAC
1 TTTTTTAAAATTTATGAAA
*
92029 TTTTTT-AAATTTGTTGAAA
1 TTTTTTAAAATTT-ATGAAA
92048 TTTT
1 TTTT
92052 AAAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAATTTATGAAA
Found at i:92577 original size:15 final size:16
Alignment explanation
Indices: 92557--92586 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
92547 TATCAAAGTG
92557 TAATTTT-AATTTTAT
1 TAATTTTAAATTTTAT
92572 TAATTTTAAATTTTA
1 TAATTTTAAATTTTA
92587 AATGACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTAAATTTTAT
Found at i:95165 original size:19 final size:19
Alignment explanation
Indices: 95132--95170 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
95122 TTTATTTATC
*
95132 ATTTTTTTCGATAAATTTT
1 ATTTTTTTCGATAAAATTT
95151 ATTTTTTTACG-TAAAATTT
1 ATTTTTTT-CGATAAAATTT
95170 A
1 A
95171 CGTATTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTTTTCGATAAAATTT
Found at i:99677 original size:2 final size:2
Alignment explanation
Indices: 99670--99709 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
99660 AATCAAAACA
*
99670 AT AT AT AT AC 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
99710 TTAAGGGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:101342 original size:35 final size:35
Alignment explanation
Indices: 101246--101328 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
101236 TGTTTGCAGT
* * *
101246 TGTGATATGAAATTGAATAAGTATATGGGTATAAA
1 TGTGGTATGAAATTGAATAAGTATATGCGTACAAA
* *
101281 TGTGGTATAAAATTTAATAAGTATATGCGTACAAA
1 TGTGGTATGAAATTGAATAAGTATATGCGTACAAA
101316 TGTGGTATGAAAT
1 TGTGGTATGAAAT
101329 GATTATGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (35 bp):
TGTGGTATGAAATTGAATAAGTATATGCGTACAAA
Found at i:120211 original size:23 final size:24
Alignment explanation
Indices: 120160--120213 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
120150 ACATTGTTTG
*
120160 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTATATGCTCA
**
120184 TGAACATGTTCGTTTA-ATGCTCA
1 TGAACATGTTCAATTATATGCTCA
120207 TGAACAT
1 TGAACAT
120214 TAAACAAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (24 bp):
TGAACATGTTCAATTATATGCTCA
Found at i:120253 original size:30 final size:30
Alignment explanation
Indices: 120213--120286 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
120203 CTCATGAACA
* *
120213 TTAAACAAACGAACATGAACACATATAATT
1 TTAAATAAACGAACATGAACACACATAATT
120243 TTAAATAAACGAACATGAACACACATAATT
1 TTAAATAAACGAACATGAACACACATAATT
120273 TTAAATAAACGAAC
1 TTAAATAAACGAAC
120287 TGACCAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (30 bp):
TTAAATAAACGAACATGAACACACATAATT
Found at i:123283 original size:18 final size:19
Alignment explanation
Indices: 123262--123297 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
123252 ATATTTATGA
123262 ATAAAAAACT-GTAAAAAT
1 ATAAAAAACTAGTAAAAAT
*
123280 ATAAAAAATTAGTAAAAA
1 ATAAAAAACTAGTAAAAA
123298 AATTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (19 bp):
ATAAAAAACTAGTAAAAAT
Found at i:123408 original size:20 final size:19
Alignment explanation
Indices: 123383--123440 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
123373 ATTAAATAAC
*
123383 TTAAAAAATGTGAAAA-GCA
1 TTAAAAAATGTAAAAATG-A
*
123402 TTCAAAAATTGTAAAAATGA
1 TT-AAAAAATGTAAAAATGA
*
123422 TTAAAAAAT-TAAAATTGA
1 TTAAAAAATGTAAAAATGA
123440 T
1 T
123441 AAGAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
20 15 0.45
21 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (19 bp):
TTAAAAAATGTAAAAATGA
Found at i:123600 original size:21 final size:20
Alignment explanation
Indices: 123574--123623 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
123564 AAATATTTTG
123574 AATAAATTTTATACATTTTAA
1 AATAAATTTTA-ACATTTTAA
* * *
123595 AATAAACTTTAATATTTTTA
1 AATAAATTTTAACATTTTAA
123615 AAT-AATTTT
1 AATAAATTTT
123624 TTTACTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 10 0.40
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAAATTTTAACATTTTAA
Found at i:123611 original size:20 final size:19
Alignment explanation
Indices: 123565--123619 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
123555 AATTTAAATA
* *
123565 AATATTTTGAATAAATTTT
1 AATATTTTAAATAAACTTT
*
123584 ATACATTTTAAAATAAACTTT
1 A-ATATTTT-AAATAAACTTT
123605 AATATTTTTAAATAA
1 AATA-TTTTAAATAA
123620 TTTTTTTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 14 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (19 bp):
AATATTTTAAATAAACTTT
Found at i:124410 original size:19 final size:20
Alignment explanation
Indices: 124388--124430 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
124378 TAAATACTTG
* *
124388 TTTTTAATTTTTATA-ATTA
1 TTTTCAATTTATATATATTA
124407 TTTTCAATTTATATATATTA
1 TTTTCAATTTATATATATTA
124427 TTTT
1 TTTT
124431 GGCTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCAATTTATATATATTA
Found at i:124469 original size:23 final size:22
Alignment explanation
Indices: 124435--124508 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
124425 TATTTTGGCT
124435 TTTTAAAATTTATAATTATATA
1 TTTTAAAATTTATAATTATATA
* *
124457 TTTTAAAATTTTATAA-AAAATCA
1 TTTTAAAA-TTTATAATTATAT-A
* *
124480 TTTTAAAAAATTATAGATTATATG
1 TTTT-AAAATTTATA-ATTATATA
124504 TTTTA
1 TTTTA
124509 CATTTTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 11 0.27
23 18 0.44
24 9 0.22
25 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (22 bp):
TTTTAAAATTTATAATTATATA
Found at i:128723 original size:61 final size:59
Alignment explanation
Indices: 128632--128828 Score: 222
Period size: 61 Copynumber: 3.3 Consensus size: 59
128622 AAAAATCAAA
* *
128632 TTTTTTTGTGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTTAGATGAAAAATTTAAT
1 TTTTTTTGTGTTGGCCATGCCATGGCCGACACCCCTTTTTT-TTAGATGAAAAATTTAAT
* *
128692 TTTTTTTGGTGTTAGCCATGCCATGGCCGACACCTCC-TTTTTTCAGATGAAAAATTTTCAAAT
1 TTTTTTT-GTGTTGGCCATGCCATGGCCGACACC-CCTTTTTTTTAGATGAAAAA-TTT--AAT
* *
128755 TTTTTTTATGTTGGCCATTG-CATGGCCGACACCCCTTTTTATTT-GAAT-AAAAAATTAAT
1 TTTTTTTGTGTTGGCCA-TGCCATGGCCGACACCCCTTTTT-TTTAG-ATGAAAAATTTAAT
*
128814 TTTTTTGGTGTTGGC
1 TTTTTTTGTGTTGGC
128829 GGATTTTTTA
Statistics
Matches: 118, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
59 16 0.14
60 18 0.15
61 35 0.30
62 33 0.28
63 16 0.14
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (59 bp):
TTTTTTTGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTTTAGATGAAAAATTTAAT
Found at i:128807 original size:62 final size:60
Alignment explanation
Indices: 128572--128828 Score: 214
Period size: 62 Copynumber: 4.3 Consensus size: 60
128562 TGATAAATTT
* * * * *
128572 TTTTTTTTGGTGTTGACCATTACA-GGTCGACACTCCCTTTTAATCTGAT-AAAAA-ATCAAA
1 TTTTTTTTGGTGTTGGCCA-TGCATGGCCGACAC-CCCTTTT-TTCTGATGAAAAATTTCAAA
* *
128632 -TTTTTTT-GTGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTTAGATGAAAAATTT--AA
1 TTTTTTTTGGTGTTGGCCATGC-ATGGCCGACACCCCTTTTTT-CT-GATGAAAAATTTCAAA
* *
128691 TTTTTTTTGGTGTTAGCCATGCCATGGCCGACACCTCCTTTTTTCAGATGAAAAATTTTCAAA
1 TTTTTTTTGGTGTTGGCCATG-CATGGCCGACACC-CCTTTTTTCTGATGAAAAA-TTTCAAA
* * *
128754 TTTTTTTT-ATGTTGGCCATTGCATGGCCGACACCCCTTTTTATTTGAAT-AAAAAATT--AA
1 TTTTTTTTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTT-TCTG-ATGAAAAATTTCAAA
128813 -TTTTTTTGGTGTTGGC
1 TTTTTTTTGGTGTTGGC
128829 GGATTTTTTA
Statistics
Matches: 165, Mismatches: 15, Indels: 35
0.77 0.07 0.16
Matches are distributed among these distances:
57 3 0.02
58 25 0.15
59 30 0.18
60 21 0.13
61 35 0.21
62 37 0.22
63 14 0.08
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (60 bp):
TTTTTTTTGGTGTTGGCCATGCATGGCCGACACCCCTTTTTTCTGATGAAAAATTTCAAA
Done.