Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003916.1 Hibiscus syriacus cultivar Beakdansim tig00008467_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: 72941
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1190 original size:18 final size:17
Alignment explanation
Indices: 1163--1197 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1153 AATGAGTAAA
1163 ATATTTTAAAAAATAAT
1 ATATTTTAAAAAATAAT
*
1180 ATATATTTAAAGAATAAT
1 ATAT-TTTAAAAAATAAT
1198 TTCATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATTTTAAAAAATAAT
Found at i:11261 original size:2 final size:2
Alignment explanation
Indices: 11240--11293 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
11230 TCAATTGGTA
* * *
11240 AT AT AT AA AT AA AT AA 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
11282 AT AT AT AT AT AT
1 AT AT AT AT AT AT
11294 GAATAGTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13974 original size:2 final size:2
Alignment explanation
Indices: 13969--13998 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13959 ATTTTTTAAA
13969 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
13999 TAATAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14715 original size:20 final size:20
Alignment explanation
Indices: 14690--14754 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
14680 TACAAAATTG
*
14690 AAAAGATAAATAGATTTAAT
1 AAAAGATAAATAGGTTTAAT
14710 AAAAGATAAATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
*
14730 AAAAGATATATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
14750 AAAAG
1 AAAAG
14755 GGTAAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAAGATAAATAGGTTTAAT
Found at i:18131 original size:19 final size:19
Alignment explanation
Indices: 18107--18168 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
18097 AACACGGAAA
18107 TCGGTTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
*
18126 TCGGTTTTTT---TAACGGT
1 TCGGTTTTTTCGGT-TCGGT
*
18143 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
18162 TCGGTTT
1 TCGGTTT
18169 ATCGGTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTCGGTTCGGT
Found at i:18320 original size:12 final size:12
Alignment explanation
Indices: 18303--18327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18293 TGAAGCCTTT
18303 AAACCGAACCGA
1 AAACCGAACCGA
18315 AAACCGAACCGA
1 AAACCGAACCGA
18327 A
1 A
18328 CCGTTTTACT
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:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:21399 original size:30 final size:29
Alignment explanation
Indices: 21358--21430 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
21348 AAAATGTTTG
* **
21358 AATATTTTAGGTACCTA-TTTGATTAAAA
1 AATACTTTAGGTACCTATTTTGACCAAAA
**
21386 AGATAACTTTAGGTATTTATTTTGACCAAAA
1 A-AT-ACTTTAGGTACCTATTTTGACCAAAA
21417 AATACTTTAGGTAC
1 AATACTTTAGGTAC
21431 TCAAATGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 1 0.03
29 12 0.33
30 13 0.36
31 10 0.28
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
AATACTTTAGGTACCTATTTTGACCAAAA
Found at i:23420 original size:2 final size:2
Alignment explanation
Indices: 23413--23441 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23403 TTCAGCCATG
23413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23442 GAAAATCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25745 original size:21 final size:20
Alignment explanation
Indices: 25707--25745 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
25697 TATCCACCAT
* *
25707 ACGGTGTGAATTTGAAAAGA
1 ACGGTGTAAATTTAAAAAGA
25727 ACGGTGATAAATTTAAAAA
1 ACGGTG-TAAATTTAAAAA
25746 TATTAGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (20 bp):
ACGGTGTAAATTTAAAAAGA
Found at i:30482 original size:2 final size:2
Alignment explanation
Indices: 30475--30505 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30465 AATAATAATA
30475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30506 GTCAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31810 original size:15 final size:16
Alignment explanation
Indices: 31779--31811 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31769 AAAAATTTAT
*
31779 TTTTATATCTTTTAAA
1 TTTTATATCTTTCAAA
31795 TTTTATATC-TTCAAA
1 TTTTATATCTTTCAAA
31810 TT
1 TT
31812 CATTCATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATATCTTTCAAA
Found at i:32559 original size:2 final size:2
Alignment explanation
Indices: 32552--32582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32542 ATATTTTATT
32552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32583 TATGTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38568 original size:15 final size:15
Alignment explanation
Indices: 38548--38576 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38538 CAAAATACAA
38548 TATTCCTAGTAATCC
1 TATTCCTAGTAATCC
38563 TATTCCTAGTAATC
1 TATTCCTAGTAATC
38577 TTTTATTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (15 bp):
TATTCCTAGTAATCC
Found at i:40055 original size:22 final size:22
Alignment explanation
Indices: 40014--40055 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40004 AGTTCAGAGG
* *
40014 TTAAATTTTTTTTACCTTTTCA
1 TTAAATCTTTTTTACATTTTCA
*
40036 TTAAATCTTTTTTATATTTT
1 TTAAATCTTTTTTACATTTT
40056 TAATTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAAATCTTTTTTACATTTTCA
Found at i:40129 original size:37 final size:36
Alignment explanation
Indices: 40054--40129 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
40044 TTTTTATATT
*
40054 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
40090 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
40127 TTT
1 TTT
40130 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:40311 original size:20 final size:20
Alignment explanation
Indices: 40275--40312 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40265 ATCCTATTCT
**
40275 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
40295 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
40313 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:40365 original size:131 final size:131
Alignment explanation
Indices: 40204--40465 Score: 488
Period size: 131 Copynumber: 2.0 Consensus size: 131
40194 TCCTTTAACC
* *
40204 AAACACGGTAATCTTACATTCTTGCTAAACCAACCAAACACAAAATACAACATTCTCGGTAATCC
1 AAACACGGTAATCTTACATTCTTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCC
*
40269 TATTCTCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAG
66 TATTCCCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAG
40334 G
131 G
*
40335 AAACACGGTAATCTTACATTCTTGCTAAACCAACCAAACACAAAATATAACATTCCCAGTAATCC
1 AAACACGGTAATCTTACATTCTTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCC
40400 TATTCCCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAG
66 TATTCCCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAG
40465 G
131 G
40466 TGTGTTTTGG
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (131 bp):
AAACACGGTAATCTTACATTCTTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCC
TATTCCCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAG
G
Found at i:40442 original size:20 final size:20
Alignment explanation
Indices: 40406--40443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40396 ATCCTATTCC
**
40406 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
40426 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
40444 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:45409 original size:73 final size:75
Alignment explanation
Indices: 45285--45433 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 75
45275 AATGCCAAAG
*
45285 ACAAATGACAGGCATATCTTGCAGCACAGATACACTTGCTACTTACAGGAATAAGTACAAAGCTA
1 ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
45350 ATATGAAGAA
66 ATATGAAGAA
* *
45360 ACAAATGACA-G-ATATCTTGCAGCACAGATAAATTTGCTACTTACCGGAATAAGTACAAAGCTA
1 ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
45423 ATATGAAGAA
66 ATATGAAGAA
45433 A
1 A
45434 TTATAAGTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 60 0.85
74 1 0.01
75 10 0.14
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (75 bp):
ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
ATATGAAGAA
Found at i:49465 original size:17 final size:16
Alignment explanation
Indices: 49434--49467 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
49424 CACGTGAGGA
49434 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
49450 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
49467 T
1 T
49468 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:55851 original size:19 final size:21
Alignment explanation
Indices: 55814--55856 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
55804 TAACTTTTTC
55814 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
55834 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
55854 TTT
1 TTT
55857 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:55862 original size:19 final size:20
Alignment explanation
Indices: 55813--55862 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
55803 TTAACTTTTT
*
55813 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
55833 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
55852 CTTTTACCTTT
1 CTTTTACCTTT
55863 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:59702 original size:16 final size:16
Alignment explanation
Indices: 59681--59713 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59671 CACGTGAGGA
59681 TTATTT-TCTTCTTATT
1 TTATTTATCTT-TTATT
59697 TTATTTATCTTTTATT
1 TTATTTATCTTTTATT
59713 T
1 T
59714 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTATCTTTTATT
Found at i:65209 original size:21 final size:21
Alignment explanation
Indices: 65176--65244 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
65166 GTCCTCATCC
*
65176 GAGTAGGACTGACTACC-CTTG
1 GAGTTGGACTGAC-ACCTCTTG
*
65197 GAGTTGGATTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
65218 GAGTTGGACTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
*
65239 AAGTTG
1 GAGTTG
65245 AACTAAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 3 0.07
21 40 0.93
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
GAGTTGGACTGACACCTCTTG
Found at i:65508 original size:81 final size:81
Alignment explanation
Indices: 65405--65568 Score: 222
Period size: 81 Copynumber: 2.0 Consensus size: 81
65395 TTGATGAGGT
* ** * * *
65405 GGATGTCCTCATCCGGGTTGGACTAAGTACTCTTGGAGCTGAGCTGAGGACTGAAGTTGAG-CTA
1 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGAC-A
**
65469 TGGGATTGACTTGATGA
65 TGGGATTGACAGGATGA
* *
65486 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGTTGAACTGAGAATTGAAGTTGAGACAT
1 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGACAT
65551 GGGATTGACAGGATGA
66 GGGATTGACAGGATGA
65567 GG
1 GG
65569 CGGATATTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 71 0.99
82 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.27
Consensus pattern (81 bp):
GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGACAT
GGGATTGACAGGATGA
Found at i:65587 original size:33 final size:34
Alignment explanation
Indices: 65550--65634 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 34
65540 AGTTGAGACA
65550 TGGGATTGAC-AGGATGAGGCGGATATTGAGCTT
1 TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
* *
65583 TGGGATTG-CTTGGATGAGGCGGATGTTGAGCTT
1 TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
65616 TGGGATTGACTA-GATGAGG
1 TGGGATTGACTAGGATGAGG
65635 TCGATGTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 44 0.94
34 2 0.04
ACGTcount: A:0.21, C:0.08, G:0.41, T:0.29
Consensus pattern (34 bp):
TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
Found at i:65824 original size:33 final size:33
Alignment explanation
Indices: 65757--65824 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
65747 GAGAATTGAA
*
65757 GTTGAGCTACGGAATTGACTGAATGAGTTAGAT
1 GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
* * * * *
65790 GTTGAGCTATGGGATTGATTGGATGAGGTGGAT
1 GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
65823 GT
1 GT
65825 CCTCATTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.32
Consensus pattern (33 bp):
GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
Found at i:66059 original size:84 final size:84
Alignment explanation
Indices: 65918--66084 Score: 280
Period size: 84 Copynumber: 2.0 Consensus size: 84
65908 TCCCACTCGT
* * * * *
65918 AGTTGGACTGAGAACTGGAGTTGAGCTATGGGATTGACTTGATGAGGTGGATGTCCTCATCCGAG
1 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
65983 TTGGACTGACTACCCTTGG
66 TTGGACTGACTACCCTTGG
66002 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
1 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
*
66067 TTGGACTGACTCCCCTTG
66 TTGGACTGACTACCCTTG
66085 AAGTATGATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (84 bp):
AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
TTGGACTGACTACCCTTGG
Found at i:66069 original size:147 final size:147
Alignment explanation
Indices: 65790--66075 Score: 366
Period size: 147 Copynumber: 1.9 Consensus size: 147
65780 TGAGTTAGAT
* *
65790 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATTCGAGTTGGGCTGACAACCCTTGC
1 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTGC
* * * * * * *
65855 AGTTGAATTGATAACTGATGTTGAGCTATAGGATAGACTCGATGTGGTGGATGTCCCACTCGTAG
66 AGTTGAACTGAGAACGGATGTCGAGCTATAGGATAGACTCGATGAGGTAGAAGTCCCACTCGTAG
65920 TTGGACTGAGAACTGGA
131 TTGGACTGAGAACTGGA
*
65937 GTTGAGCTATGGGATTGACTT-GATGAGGTGGATGTCCTCATCCGAGTTGGACTGACTACCCTTG
1 GTTGAGCTATGGGATTGA-TTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTG
* * * *
66001 GAGTTGGACTGAGAACCGGA-GTCGAGCTAT-GAGATTGACTTGATGAGGTAGAAGTCCTCA-TC
65 CAGTTGAACTGAGAA-CGGATGTCGAGCTATAG-GATAGACTCGATGAGGTAGAAGTCC-CACT-
66063 CG-AGTTGGACTGA
126 CGTAGTTGGACTGA
66076 CTCCCCTTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
146 1 0.01
147 110 0.92
148 9 0.08
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (147 bp):
GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTGC
AGTTGAACTGAGAACGGATGTCGAGCTATAGGATAGACTCGATGAGGTAGAAGTCCCACTCGTAG
TTGGACTGAGAACTGGA
Found at i:66112 original size:42 final size:42
Alignment explanation
Indices: 66066--66203 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
66056 CCTCATCCGA
*
66066 GTTGGACTGACTCCCCTTGAAGTATGATTGGCTCCTCTTGCG
1 GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
* ** * *
66108 GTTGGAGTTGGACT--GATTGAAGTATGACTGGATCCTCTTACTGTTGG
1 GTTGGA-CT-GACTCCCCTTGAAGTATGACTGGCTCCTC-T--TG--CG
*
66155 AGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCA
1 -GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
66198 GTTGGA
1 GTTGGA
66204 GTGGAAGGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
42 31 0.42
43 2 0.03
44 4 0.05
45 4 0.05
46 4 0.05
47 3 0.04
48 26 0.35
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.33
Consensus pattern (42 bp):
GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
Found at i:66121 original size:48 final size:48
Alignment explanation
Indices: 66064--66205 Score: 197
Period size: 48 Copynumber: 3.1 Consensus size: 48
66054 GTCCTCATCC
* *
66064 GAGTTGGACTGACTCCCCTTGAAGTATGATTGGCTCCTCTTGCGGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
* * *
66112 GAGTTGGACTGA------TTGAAGTATGACTGGATCCTCTTACTGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
66154 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
66202 GAGT
1 GAGT
66206 GGAAGGTCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
42 38 0.47
48 43 0.53
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (48 bp):
GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
Found at i:69229 original size:45 final size:46
Alignment explanation
Indices: 69165--69259 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 46
69155 TACTTCATAC
*
69165 AAAAATAAATATTTAAATTATATATTCAATTAATTTATGATGTCTA
1 AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCTA
* * * *
69211 AAAAAT-ATTATTTAAATTATATCTTAAATTAATTTTTGATGTTTA
1 AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCTA
69256 AAAA
1 AAAA
69260 GTTTTTCCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 38 0.86
46 6 0.14
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (46 bp):
AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCTA
Found at i:71225 original size:12 final size:11
Alignment explanation
Indices: 71202--71235 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
71192 ATCGGATGGA
*
71202 CTCGAATCGAG
1 CTCGACTCGAG
71213 CTCGAGCTCGAG
1 CTCGA-CTCGAG
71225 CTCGACTCGAG
1 CTCGACTCGAG
71236 TTCTTAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (11 bp):
CTCGACTCGAG
Found at i:71508 original size:31 final size:29
Alignment explanation
Indices: 71473--71562 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 29
71463 GCTGTTCATG
* *
71473 AGCTTCAGTTCAGAATTTCGAGTTCGAGTCT
1 AGCTTCAATTCAG-ATTTCGAG-TCGAGTCA
*
71504 AGCTTAAAATT-AG-TGTTCGAGTCGAGTCA
1 AGCTT-CAATTCAGAT-TTCGAGTCGAGTCA
*
71533 AGCTTCATTTCAGAGTTTTCGAGTCGAGTC
1 AGCTTCAATTCAGA--TTTCGAGTCGAGTC
71563 GAACTCAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 6 0.12
31 20 0.42
32 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (29 bp):
AGCTTCAATTCAGATTTCGAGTCGAGTCA
Done.