Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008712.1 Hibiscus syriacus cultivar Beakdansim tig00111764_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: 93006
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3505 original size:17 final size:17
Alignment explanation
Indices: 3483--3515 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3473 AGATTCTCAT
3483 AGTTTCTCATTTAATGA
1 AGTTTCTCATTTAATGA
*
3500 AGTTTCTCGTTTAATG
1 AGTTTCTCATTTAATG
3516 TTTTCACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (17 bp):
AGTTTCTCATTTAATGA
Found at i:3613 original size:33 final size:34
Alignment explanation
Indices: 3528--3627 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 34
3518 TTCACTCAAG
* *
3528 ATTTTATCTCACTTGAAATTATTTCCTTAAAACA
1 ATTTTATCTCACTTGAGATTATTTTCTTAAAACA
*
3562 TATTTTATCTCACTTGAGATTATTTTCTTGAAAC-
1 -ATTTTATCTCACTTGAGATTATTTTCTTAAAACA
* *
3596 ATTTTATCTTACATGAGA-TAGTTTTCTTAAAA
1 ATTTTATCTCACTTGAGATTA-TTTTCTTAAAA
3628 ACAAATTTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.03
33 26 0.45
35 30 0.52
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (34 bp):
ATTTTATCTCACTTGAGATTATTTTCTTAAAACA
Found at i:5540 original size:29 final size:29
Alignment explanation
Indices: 5508--5571 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
5498 TCAAATTTTA
* * *
5508 CTTTATTTTTTTCTA-TTTACATTTATGTC
1 CTTTAATTTTATCTACTTTA-ATTCATGTC
*
5537 CTTTAATTTTATGTACTTTAATTCATGTC
1 CTTTAATTTTATCTACTTTAATTCATGTC
5566 CTTTAA
1 CTTTAA
5572 ATTTCTAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.22, C:0.14, G:0.05, T:0.59
Consensus pattern (29 bp):
CTTTAATTTTATCTACTTTAATTCATGTC
Found at i:5547 original size:15 final size:14
Alignment explanation
Indices: 5523--5571 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
5513 TTTTTTTCTA
5523 TTTACATTTATGTCC
1 TTTA-ATTTATGTCC
*
5538 TTTAATTTTATGTAC
1 TTTAA-TTTATGTCC
*
5553 TTTAATTCATGTCC
1 TTTAATTTATGTCC
5567 TTTAA
1 TTTAA
5572 ATTTCTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTAATTTATGTCC
Found at i:5596 original size:30 final size:28
Alignment explanation
Indices: 5528--5599 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
5518 TTCTATTTAC
*
5528 ATTTATGTCCTTTAATTTTATGTACTTT
1 ATTTCTGTCCTTTAATTTTATGTACTTT
* *
5556 AATTCATGTCCTTTAAATTTCTA-GTATTTGT
1 ATTTC-TGTCCTTT-AATTT-TATGTACTT-T
5587 ATTTCTGTCCTTT
1 ATTTCTGTCCTTT
5600 TTTTAATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.08
29 8 0.22
30 18 0.50
31 7 0.19
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (28 bp):
ATTTCTGTCCTTTAATTTTATGTACTTT
Found at i:6407 original size:20 final size:22
Alignment explanation
Indices: 6373--6431 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 22
6363 TTTTAAAATT
6373 ATTAAATAATATATTTTT-ATA
1 ATTAAATAATATATTTTTAATA
* *
6394 A-TAATTATTATATTTTTAATA
1 ATTAAATAATATATTTTTAATA
6415 ATTAAATAATATATTTT
1 ATTAAATAATATATTTT
6432 AACATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 14 0.44
21 5 0.16
22 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAAATAATATATTTTTAATA
Found at i:6415 original size:18 final size:20
Alignment explanation
Indices: 6382--6431 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
6372 TATTAAATAA
6382 TATATTTTTATAATAATTAT
1 TATATTTTTATAATAATTAT
* *
6402 TATATTTTTAATAATTAAATAA
1 TATATTTTT-ATAA-TAATTAT
6424 TATATTTT
1 TATATTTT
6432 AACATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.35
21 4 0.15
22 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATTTTTATAATAATTAT
Found at i:6438 original size:20 final size:20
Alignment explanation
Indices: 6373--6444 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
6363 TTTTAAAATT
*
6373 ATTAAATAATATATTTTTATA
1 ATTAAATAATATA-TTTTAAA
* *
6394 A-TAATTATTATATTTTTAATA
1 ATTAAATAATATA-TTTTAA-A
*
6415 ATTAAATAATATATTTTAAC
1 ATTAAATAATATATTTTAAA
6435 ATTAAA-AATA
1 ATTAAATAATA
6445 AAAATATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.09
20 21 0.49
21 9 0.21
22 9 0.21
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAATAATATATTTTAAA
Found at i:12035 original size:21 final size:21
Alignment explanation
Indices: 12010--12052 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12000 CAAATAACTG
*
12010 AAAACGTG-TCATAAAGACAGA
1 AAAACGTGCT-ATAAAGAAAGA
12031 AAAACGTGCTATAAAGAAAGA
1 AAAACGTGCTATAAAGAAAGA
12052 A
1 A
12053 GAATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.14
Consensus pattern (21 bp):
AAAACGTGCTATAAAGAAAGA
Found at i:12101 original size:16 final size:17
Alignment explanation
Indices: 12082--12113 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12072 CATAATTATT
12082 AAAAATAAAAA-ACAAA
1 AAAAATAAAAATACAAA
12098 AAAAATAAAAATACAA
1 AAAAATAAAAATACAA
12114 TGAGTATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.09
Consensus pattern (17 bp):
AAAAATAAAAATACAAA
Found at i:16650 original size:200 final size:201
Alignment explanation
Indices: 16293--16775 Score: 538
Period size: 201 Copynumber: 2.4 Consensus size: 201
16283 AATCGCAAGT
* * * * *
16293 GTTT-ATAGGCA-AGTTCCAGGGGTACTTTT-GGGTAGTTAATCTAAAAAATTTTGTAATTTACA
1 GTTTGATAGGCATA-TTCGAGGGATA-TTTTCGGGTAGTTAATCTGAAAATTTTTGTAATTTATA
* * * *
16355 ATG-TTAGAGG-GTAGTATTGGAATCTATCTTTCAGTTGAAGCCAATATCGACACATACGAGATA
64 A-GATTAGAGGCGTAGTATTGGAATCTATCTTTCAATTGAAGCCAATACCGACACATACAAGACA
* * * *
16418 TTGTAAGTGGGTTAAAAATCGCGTTGAAAATGGTTCCAAAGCTT-GTTTTGCGCATGAAGAA-AC
128 CTGTAAGTGGGTTAAAAATCACATTCAAAATGGTTCCAAAGCTTGGTTTTGCGCATGAAGAAGA-
16481 AACTAAAATA
192 AACTAAAATA
**
16491 GTTTGATAGGCATATTCGAGGGATATTTTCGGGTAGTTAATCTGAATTTTTTTGTAATTTATAAG
1 GTTTGATAGGCATATTCGAGGGATATTTTCGGGTAGTTAATCTGAAAATTTTTGTAATTTATAAG
* * * **
16556 ATTAGAGGCATAGTATTGTAATTTATCTTTCAATTG-AGTGTAATACC-AGCACATACAAGACAC
66 ATTAGAGGCGTAGTATTGGAATCTATCTTTCAATTGAAG-CCAATACCGA-CACATACAAGACAC
* * *
16619 TGTAAGTGAGG-TAAAAATTACATTCAAAATGGTTCCAAAGCTTGGTTTTGTGCATGGAGAAGAA
129 TGTAAGTG-GGTTAAAAATCACATTCAAAATGGTTCCAAAGCTTGGTTTTGCGCATGAAGAAGAA
*
16683 GCTAAAATA
193 ACTAAAATA
* * ** * *
16692 GCTTGATAGACATATTCG-GGGACTATTTTCATGAAGTTAATCTGAAAATTTTTGTGATTTATAA
1 GTTTGATAGGCATATTCGAGGGA-TATTTTCGGGTAGTTAATCTGAAAATTTTTGTAATTTATAA
*
16756 GATTAAAGGCGTAGTATTGG
65 GATTAGAGGCGTAGTATTGG
16776 TACTTACGTT
Statistics
Matches: 239, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
198 9 0.04
199 55 0.23
200 80 0.33
201 94 0.39
202 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (201 bp):
GTTTGATAGGCATATTCGAGGGATATTTTCGGGTAGTTAATCTGAAAATTTTTGTAATTTATAAG
ATTAGAGGCGTAGTATTGGAATCTATCTTTCAATTGAAGCCAATACCGACACATACAAGACACTG
TAAGTGGGTTAAAAATCACATTCAAAATGGTTCCAAAGCTTGGTTTTGCGCATGAAGAAGAAACT
AAAATA
Found at i:16837 original size:201 final size:200
Alignment explanation
Indices: 16444--16854 Score: 483
Period size: 201 Copynumber: 2.0 Consensus size: 200
16434 AATCGCGTTG
* *
16444 AAAATGGTTCCAAAGCTTGTTTTGCGCATGAAGAAACAACTAAAATAGTTTGATAGGCATATTCG
1 AAAATGGTTCCAAAGCTTGTTTTGCGCATGAAGAAACAACTAAAATAGCTTGATAGACATATTCG
* * ** *
16509 AGGGATATTTTCGGGTAGTTAATCTGAATTTTTTTGTAATTTATAAGATTAGAGGCATAGTATTG
66 AGGGATATTTTCAGGAAGTTAATCTGAAAATTTTTGTAATTTATAAGATTAAAGGCATAGTATTG
* * * *
16574 TAATTTATCTTTCAATTGAGTGTAATACCAGCACATACAAGACACTGTAAGTGAGGTAAAAATTA
131 TAACTTATCTTTCAATTGAGTGTAATACCAGCACATACAAGACACTATAAGTCAGATAAAAATTA
16639 CATTC
196 CATTC
* * *
16644 AAAATGGTTCCAAAGCTTGGTTTTGTGCATGGAGAAGA-AGCTAAAATAGCTTGATAGACATATT
1 AAAATGGTTCCAAAGCTT-GTTTTGCGCATGAAGAA-ACAACTAAAATAGCTTGATAGACATATT
* * *
16708 CG-GGGACTATTTTCATGAAGTTAATCTGAAAATTTTTGTGATTTATAAGATTAAAGGCGTAGTA
64 CGAGGGA-TATTTTCAGGAAGTTAATCTGAAAATTTTTGTAATTTATAAGATTAAAGGCATAGTA
* *** * *
16772 TTGGT-ACTTA-CGTTTCAATTGAG-GCTAGTATTGGCACATACGAGACATTATAAG-CAGTATA
128 TT-GTAACTTATC-TTTCAATTGAGTG-TAATACCAGCACATACAAGACACTATAAGTCAG-ATA
* * *
16833 AAAATTGCGTTG
189 AAAATTACATTC
16845 AAAATGGTTC
1 AAAATGGTTC
16855 GGAACAAAAA
Statistics
Matches: 178, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
200 26 0.15
201 149 0.84
202 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (200 bp):
AAAATGGTTCCAAAGCTTGTTTTGCGCATGAAGAAACAACTAAAATAGCTTGATAGACATATTCG
AGGGATATTTTCAGGAAGTTAATCTGAAAATTTTTGTAATTTATAAGATTAAAGGCATAGTATTG
TAACTTATCTTTCAATTGAGTGTAATACCAGCACATACAAGACACTATAAGTCAGATAAAAATTA
CATTC
Found at i:17668 original size:21 final size:21
Alignment explanation
Indices: 17624--17664 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17614 CATTTCCCAT
17624 TTCTCTTCTCTTAATTTCTTC
1 TTCTCTTCTCTTAATTTCTTC
* *
17645 TTCTTTTCTCTT-CTTTCTTC
1 TTCTCTTCTCTTAATTTCTTC
17665 CTTCCCTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTCTTCTCTTAATTTCTTC
Found at i:21990 original size:17 final size:18
Alignment explanation
Indices: 21968--22001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21958 AAAAACAAAA
21968 TAAAAA-TAATCATAAAT
1 TAAAAATTAATCATAAAT
*
21985 TAAAAATTTATCATAAA
1 TAAAAATTAATCATAAA
22002 AATTTACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTAATCATAAAT
Found at i:22950 original size:22 final size:23
Alignment explanation
Indices: 22920--22974 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
22910 GGCCTCAAGC
*
22920 CCAAACCAAACTA-ACCCCCAAA
1 CCAACCCAAACTAGACCCCCAAA
*
22942 CCAACCC-AACTAGAGCCCCAAA
1 CCAACCCAAACTAGACCCCCAAA
22964 CCTAAACCCAA
1 CC--AACCCAA
22975 CTGAAACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 16 0.59
24 5 0.19
25 1 0.04
ACGTcount: A:0.45, C:0.45, G:0.04, T:0.05
Consensus pattern (23 bp):
CCAACCCAAACTAGACCCCCAAA
Found at i:23908 original size:23 final size:23
Alignment explanation
Indices: 23878--23923 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
23868 ACCTATAGGG
23878 ACCAAAACTGATATTTTTCCTTT
1 ACCAAAACTGATATTTTTCCTTT
23901 ACCAAAACTGATATTTTTCCTTT
1 ACCAAAACTGATATTTTTCCTTT
23924 TTTGTGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (23 bp):
ACCAAAACTGATATTTTTCCTTT
Found at i:24255 original size:24 final size:25
Alignment explanation
Indices: 24228--24281 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
24218 TAGGTCCCTG
24228 TAGTTTCT-ATATGTTTTTATATTT
1 TAGTTTCTAATATGTTTTTATATTT
** * *
24252 TAGTCCCTAATCTGTTTTTTTATTT
1 TAGTTTCTAATATGTTTTTATATTT
24277 T-GTTT
1 TAGTTT
24282 AGATTTAGCC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (25 bp):
TAGTTTCTAATATGTTTTTATATTT
Found at i:24408 original size:21 final size:22
Alignment explanation
Indices: 24383--24424 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
24373 AATTTAGTCC
24383 TTGTGTTTTTTAT-TTTTTATG
1 TTGTGTTTTTTATGTTTTTATG
*
24404 TTGTGTTTTTTCTGTTTTTAT
1 TTGTGTTTTTTATGTTTTTAT
24425 TATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.07, C:0.02, G:0.14, T:0.76
Consensus pattern (22 bp):
TTGTGTTTTTTATGTTTTTATG
Found at i:29962 original size:23 final size:23
Alignment explanation
Indices: 29928--29972 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29918 TTTTAATGAG
29928 TCTGTCTGTATGACACGTTTTCA
1 TCTGTCTGTATGACACGTTTTCA
* * *
29951 TCTGTCTTTATGATACTTTTTC
1 TCTGTCTGTATGACACGTTTTC
29973 TTTTTTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (23 bp):
TCTGTCTGTATGACACGTTTTCA
Found at i:35159 original size:18 final size:20
Alignment explanation
Indices: 35116--35155 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
35106 ATATAATGAA
35116 TCTCAGGGCTGGTTGATTGACT
1 TCTCAGGGCTGGTTGATT-A-T
35138 TCTCAGGGCTGGTTGATT
1 TCTCAGGGCTGGTTGATT
35156 TCTCGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (20 bp):
TCTCAGGGCTGGTTGATTAT
Found at i:44966 original size:13 final size:13
Alignment explanation
Indices: 44948--44975 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44938 ACATCTATAG
44948 AAATAAATAATGA
1 AAATAAATAATGA
44961 AAATAAATAATGA
1 AAATAAATAATGA
44974 AA
1 AA
44976 CAAGAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATAAATAATGA
Found at i:45779 original size:21 final size:21
Alignment explanation
Indices: 45727--45779 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
45717 AACTTATAAT
*
45727 TATAAATTAGTTAAAAATTAAA
1 TATAAATTA-TTAAAAATAAAA
* *
45749 TATAATTTATTTAAAATAAAA
1 TATAAATTATTAAAAATAAAA
45770 GT-TAAATTAT
1 -TATAAATTAT
45780 ATCAGTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TATAAATTATTAAAAATAAAA
Found at i:48336 original size:6 final size:6
Alignment explanation
Indices: 48325--48368 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
48315 TCTCGTCTCG
48325 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
48369 AGAAAATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:48453 original size:20 final size:20
Alignment explanation
Indices: 48428--48544 Score: 164
Period size: 20 Copynumber: 5.7 Consensus size: 20
48418 CTCATTTTCT
48428 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
48448 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
48468 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
48488 GAATATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
48510 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
48530 GAAGATCGCGTTGCG
1 G-A-ATCGCGTTGCG
48545 CTCTTCTTTT
Statistics
Matches: 87, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
20 55 0.63
21 7 0.08
22 25 0.29
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:48514 original size:42 final size:40
Alignment explanation
Indices: 48421--48544 Score: 178
Period size: 42 Copynumber: 3.0 Consensus size: 40
48411 GAATTTACTC
48421 ATTTTCTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
*
48461 ATTCTTGGAATCGCGTTGCGATTCTTGGAATATCGCGTTGCG
1 ATT-TTTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
*
48503 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG
48545 CTCTTCTTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
40 24 0.32
41 5 0.07
42 47 0.62
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (40 bp):
ATTTTTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCG
Found at i:48581 original size:20 final size:19
Alignment explanation
Indices: 48558--48609 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
48548 TTCTTTTCAA
* *
48558 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
* *
48578 CGTTGCGGTTTTGATATCG
1 CGTTGCGATTTTGAAATCG
48597 CGTTGCGATTTTG
1 CGTTGCGATTTTG
48610 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:58188 original size:11 final size:13
Alignment explanation
Indices: 58156--58185 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58146 TGGCCAAAGA
58156 TGAAAAGGTATGT
1 TGAAAAGGTATGT
58169 TGAAAAGGTATG-
1 TGAAAAGGTATGT
58181 TGAAA
1 TGAAA
58186 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:63507 original size:23 final size:23
Alignment explanation
Indices: 63477--63531 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
63467 TGTATTCTTA
*
63477 TAAAAAAAAATGATGCTCTAAAT
1 TAAAAAAAAATGAAGCTCTAAAT
63500 TAAAAAAAAATGAAGCTCTAAAT
1 TAAAAAAAAATGAAGCTCTAAAT
63523 TAAAAAAAA
1 TAAAAAAAA
63532 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (23 bp):
TAAAAAAAAATGAAGCTCTAAAT
Found at i:70169 original size:21 final size:22
Alignment explanation
Indices: 70134--70176 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
70124 TGTCCAGGAC
70134 AATGAGTATCAGTACT-CCTTT
1 AATGAGTATCAGTACTACCTTT
**
70155 AATGAGTATTGGTACTACCTTT
1 AATGAGTATCAGTACTACCTTT
70177 GTAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (22 bp):
AATGAGTATCAGTACTACCTTT
Found at i:77101 original size:18 final size:17
Alignment explanation
Indices: 77069--77105 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
77059 GAATATATGT
*
77069 TTAATTTTTTAAATTAA
1 TTAATTTTTAAAATTAA
77086 TTAATTTTTAATAATTAA
1 TTAATTTTTAA-AATTAA
77104 TT
1 TT
77106 TGTTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATTTTTAAAATTAA
Found at i:77102 original size:14 final size:16
Alignment explanation
Indices: 77069--77106 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
77059 GAATATATGT
77069 TTAATTTTTTAAATTAA
1 TTAA-TTTTTAAATTAA
77086 TTAATTTTT-AA-TAA
1 TTAATTTTTAAATTAA
77100 TTAATTT
1 TTAATTT
77107 GTTTAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
16 5 0.24
17 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTTTAAATTAA
Found at i:77718 original size:23 final size:22
Alignment explanation
Indices: 77668--77718 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
77658 TGTAATGCAA
* *
77668 TGTATTTAAAAGCATATTAGAT
1 TGTATTTAAAAGAATATTAAAT
77690 TGTATTTAAAAGAAATATTAAAT
1 TGTATTTAAAAG-AATATTAAAT
*
77713 TTTATT
1 TGTATT
77719 ATTTGAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
TGTATTTAAAAGAATATTAAAT
Found at i:79412 original size:17 final size:18
Alignment explanation
Indices: 79379--79412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
79369 CCGCTATTAG
79379 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
79397 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
79413 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:86402 original size:12 final size:12
Alignment explanation
Indices: 86385--86418 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
86375 TTGAGATTAG
86385 CATCCTTCTAAT
1 CATCCTTCTAAT
86397 CATCCTTCTAAT
1 CATCCTTCTAAT
86409 CATCCTTCTA
1 CATCCTTCTA
86419 CCCTCAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (12 bp):
CATCCTTCTAAT
Found at i:87052 original size:23 final size:22
Alignment explanation
Indices: 87020--87068 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
87010 ACACATTTTT
87020 TTTACA-TTTTCTCTCTCTCTTAA
1 TTTACATTTTTCTC-CTCT-TTAA
* *
87043 TTTACTTTTTTTTCCTCTTTAA
1 TTTACATTTTTCTCCTCTTTAA
87065 TTTA
1 TTTA
87069 TTTAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTACATTTTTCTCCTCTTTAA
Done.