Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009441.1 Hibiscus syriacus cultivar Beakdansim tig00113505_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: 72929
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:89 original size:24 final size:24
Alignment explanation
Indices: 62--135 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
52 AATTAGACAA
*
62 AATTCAGATCATATATCATAACAG
1 AATTCAGATCAGATATCATAACAG
* * *
86 AATTCATATTAGATATCATAATAG
1 AATTCAGATCAGATATCATAACAG
* * *
110 AATCCGGATCAGAAATCATAACAG
1 AATTCAGATCAGATATCATAACAG
134 AA
1 AA
136 ATCATATAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (24 bp):
AATTCAGATCAGATATCATAACAG
Found at i:2733 original size:27 final size:27
Alignment explanation
Indices: 2676--2733 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
2666 ACTTTAAGCT
* *
2676 ATTTTACACTTTAGGGGTATTTTGGTC
1 ATTTTACACTTTAGGGGCATTTTGGTA
2703 ATTTTACACTTTAGGGGCATTATT-GTA
1 ATTTTACACTTTAGGGGCATT-TTGGTA
2730 ATTT
1 ATTT
2734 ATGCATGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.48
Consensus pattern (27 bp):
ATTTTACACTTTAGGGGCATTTTGGTA
Found at i:3362 original size:18 final size:18
Alignment explanation
Indices: 3341--3375 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3331 GTCGGCTTGG
3341 CTCGACTCAGTGGCTCAA
1 CTCGACTCAGTGGCTCAA
* *
3359 CTCGGCTCGGTGGCTCA
1 CTCGACTCAGTGGCTCA
3376 CCAAGCTGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (18 bp):
CTCGACTCAGTGGCTCAA
Found at i:5184 original size:29 final size:27
Alignment explanation
Indices: 5142--5204 Score: 92
Period size: 29 Copynumber: 2.3 Consensus size: 27
5132 TAATATACTG
*
5142 ATTTATATGCATTTATCCTTTATTTTTTT
1 ATTTATATGCATTTAT-CTTT-TTTTTAT
5171 ATTTATATGCATTTATCTTTTTTTTAT
1 ATTTATATGCATTTATCTTTTTTTTAT
5198 -TTTATAT
1 ATTTATAT
5205 TGTAATTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 7 0.21
27 6 0.18
28 4 0.12
29 16 0.48
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67
Consensus pattern (27 bp):
ATTTATATGCATTTATCTTTTTTTTAT
Found at i:25363 original size:24 final size:24
Alignment explanation
Indices: 25336--25381 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25326 GTCAATTTCC
25336 TTTTAATAATATTATTAGGTTAGA
1 TTTTAATAATATTATTAGGTTAGA
* **
25360 TTTTAGTTGTATTATTAGGTTA
1 TTTTAATAATATTATTAGGTTA
25382 ATTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (24 bp):
TTTTAATAATATTATTAGGTTAGA
Found at i:25396 original size:24 final size:24
Alignment explanation
Indices: 25344--25397 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
25334 CCTTTTAATA
25344 ATATTATTAGGTTAGATTTTAGTT
1 ATATTATTAGGTTAGATTTTAGTT
*
25368 GTATTATTAGGTTA-ATTATT-GATT
1 ATATTATTAGGTTAGATT-TTAG-TT
25392 ATATTA
1 ATATTA
25398 ATATTGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (24 bp):
ATATTATTAGGTTAGATTTTAGTT
Found at i:26882 original size:118 final size:118
Alignment explanation
Indices: 26673--26896 Score: 306
Period size: 118 Copynumber: 1.9 Consensus size: 118
26663 CCTAAACTTT
* ** *
26673 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTACAATGATTGAGGGACCATTTTAATTCTTT
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
* *
26738 GACTAAATAATTGGTTAAAATGAATTATGATTAATATTAGACACTTTAGTCCC
66 GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
* * ** * * *
26791 TTAATTAGGGAATGATTTGATTTGGCTCTCGCATTAAAATGCTCAAGGGACCATTTTGATTATTC
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATT-
*
26856 T-ACTTAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
65 TGACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
26897 GCTTTCATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 90 0.99
119 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (118 bp):
TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
Found at i:29706 original size:35 final size:35
Alignment explanation
Indices: 29664--29733 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
29654 GCGATAATGC
*
29664 CTAAGGTGATGATGTTGAATGAAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
* *
29699 CTAAGGTGAGGATGTTGAGTGCAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
29734 ACACTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.31, T:0.27
Consensus pattern (35 bp):
CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
Found at i:31330 original size:36 final size:36
Alignment explanation
Indices: 31290--31484 Score: 173
Period size: 36 Copynumber: 5.4 Consensus size: 36
31280 CACTAAAGTT
* *
31290 TTTATCTCGCTTGAGATTGTTTTTCTTAAAGCATAC
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
** * * *
31326 TTTATCTTGCTTAAGATTGTTTTCCTTAAAACATAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
* * * * *
31362 TTTATCTCAATTGAGATTATTTTTTTTCTAAA-ATAGA
1 TTTATCTCACTTGAGATTGTTTTTCTT-AAAACATA-C
* *
31399 TCTTATTTCACTTGAGA-T-TTTTTATTAAAACATAC
1 T-TTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
* * *
31434 CTTATCTCACTTGAGATTG-TTTTCTTAAAATATAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
*
31469 TTTATCTCATTTGAGA
1 TTTATCTCACTTGAGA
31485 ATTGAGATTT
Statistics
Matches: 127, Mismatches: 26, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
34 14 0.11
35 31 0.24
36 64 0.50
37 5 0.04
38 13 0.10
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (36 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
Found at i:31428 original size:34 final size:34
Alignment explanation
Indices: 31351--31484 Score: 124
Period size: 35 Copynumber: 3.8 Consensus size: 34
31341 ATTGTTTTCC
* * * *
31351 TTAAAACATATTTTATCTCAATTGAGATTATTTTTTT
1 TTAAAATATATCTTATCTCACTTGAG---ATTTTTTA
* *
31388 TCTAAAATAGATCTTATTTCACTTGAGATTTTTTA
1 T-TAAAATATATCTTATCTCACTTGAGATTTTTTA
* * *
31423 TTAAAACATACCTTATCTCACTTGAGATTGTTTTC
1 TTAAAATATATCTTATCTCACTTGAGATT-TTTTA
* *
31458 TTAAAATATATTTTATCTCATTTGAGA
1 TTAAAATATATCTTATCTCACTTGAGA
31485 ATTGAGATTT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
34 24 0.30
35 35 0.44
37 1 0.01
38 20 0.25
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (34 bp):
TTAAAATATATCTTATCTCACTTGAGATTTTTTA
Found at i:31514 original size:108 final size:109
Alignment explanation
Indices: 31299--31499 Score: 255
Period size: 108 Copynumber: 1.8 Consensus size: 109
31289 TTTTATCTCG
* * * **
31299 CTTGAGATTGTTTTTCTTAAAGCATACTTTATCTTGCTTAAGATTGTTTTCCTTAAAACATATTT
1 CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
** *
31364 TATCTCAATTGAGATTATTTTTTTTCTAAAATAGATCTTATTTCA
66 TATCTCAATTGAGATTAGATTTTATCTAAAATAGA-CTTATTTCA
* *
31409 CTTGAGA-T-TTTTTATTAAAACATACCTTATCTCACTTGAGATTGTTTT-CTTAAAATATATTT
1 CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
*
31471 TATCTCATTTGAGAATTGAGATTTTATCT
66 TATCTCAATTGAG-ATT-AGATTTTATCT
31500 TACTTGAGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 25 0.32
108 37 0.47
109 9 0.12
110 7 0.09
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (109 bp):
CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
TATCTCAATTGAGATTAGATTTTATCTAAAATAGACTTATTTCA
Found at i:31551 original size:36 final size:36
Alignment explanation
Indices: 31501--31633 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 36
31491 ATTTTATCTT
*
31501 ACTTGAGATTATTTTTCTTAAAACATATAATATATC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** *
31537 ACTTGAGATAATTTTTATTAAAATAGATTTTATCTC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** * *
31573 ACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTT
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* *
31609 ACTTGAAATTGTTTTTCTTAAAACA
1 ACTTGAGATTATTTTTCTTAAAACA
31634 AATTTGTTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (36 bp):
ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
Found at i:31619 original size:131 final size:131
Alignment explanation
Indices: 31360--31619 Score: 301
Period size: 131 Copynumber: 2.0 Consensus size: 131
31350 CTTAAAACAT
* * ** *
31360 ATTTTATCTCAATTGAGATTATTTTTTTTCTAAAATAGATCTTATTTCACTTGAGATTTTTTATT
1 ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATT
* * * * *
31425 AAAACATACCTTATCTCACTTGAGATTGTTTTCTTAAAATATATTTTATCTCATTTGAGAATTGA
66 AAAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGA
31490 G
131 G
* * *
31491 ATTTTATCTTACTTGAGATTA-TTTTTCT-TAAAACATATAATATATCACTTGAGATAATTTTTA
1 ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGAT--TTTTTA
* ** * * *
31554 TTAAAATAGATTTTATCTCACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTTACTTGA-AAT
64 TTAAAACAGACCTTATCTCACTGGAGATTG-TTTTCTTAAAACAGATTTTATCTCACTTGAGAAT
31618 TG
128 TG
31620 TTTTTCTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
129 22 0.21
130 6 0.06
131 55 0.51
132 24 0.22
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (131 bp):
ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATT
AAAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGA
G
Found at i:31622 original size:167 final size:168
Alignment explanation
Indices: 31326--31631 Score: 384
Period size: 167 Copynumber: 1.8 Consensus size: 168
31316 TAAAGCATAC
* * ** * * *
31326 TTTATCTTGCTTAAGATTGTTTTCCTTAAAACATATTTTATCTCAATTGAGATTATTTTTTTTCT
1 TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
* * * *
31391 AAAATAGATCTTATTTCACTTGAGATTTTTTATTAAAACATACCTTATCTCACTTGAGATTG-TT
66 AAAATAGATCTTATCTCACTGGAGATTTTTTATTAAAACAGACCTTATCTCACTTGAAATTGTTT
31455 TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
131 TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
* * *
31493 TTTATCTTACTTGAGATTATTTTTCTTAAAACATATAATATATCACTTGAGA-TAATTTTTAT-T
1 TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
* * *** * *
31556 AAAATAGATTTTATCTCACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTTACTTGAAATTGT
66 AAAATAGATCTTATCTCACTGGAGA-T-TTTTTATTAAAACAGACCTTATCTCACTTGAAATTGT
31621 TTTTCTTAAAA
129 TTTTCTTAAAA
31632 CAAATTTGTT
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
165 23 0.20
166 9 0.08
167 72 0.63
168 11 0.10
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (168 bp):
TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
AAAATAGATCTTATCTCACTGGAGATTTTTTATTAAAACAGACCTTATCTCACTTGAAATTGTTT
TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
Found at i:31788 original size:13 final size:12
Alignment explanation
Indices: 31766--31799 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31756 CCTTTTACTA
31766 ATATTATTAGTTT
1 ATATTATTAG-TT
*
31779 ATATTTTTAGTT
1 ATATTATTAGTT
31791 ATATTATTA
1 ATATTATTA
31800 ATTTAACTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
ATATTATTAGTT
Found at i:31794 original size:12 final size:13
Alignment explanation
Indices: 31766--31804 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
31756 CCTTTTACTA
31766 ATATTATTAGTTT
1 ATATTATTAGTTT
*
31779 ATATTTTTAG-TT
1 ATATTATTAGTTT
*
31791 ATATTATTAATTT
1 ATATTATTAGTTT
31804 A
1 A
31805 ACTGTTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATATTATTAGTTT
Found at i:45752 original size:20 final size:19
Alignment explanation
Indices: 45723--45763 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
45713 TACATTCGAA
45723 ATATGGAGTGTATCGATAC
1 ATATGGAGTGTATCGATAC
*
45742 ATATAGGAGTGTATCGGTAC
1 ATAT-GGAGTGTATCGATAC
45762 AT
1 AT
45764 CCCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (19 bp):
ATATGGAGTGTATCGATAC
Found at i:46192 original size:23 final size:24
Alignment explanation
Indices: 46160--46205 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
46150 ATGAAGAGAG
46160 AAAATTAAAATAAGGAAA-TAAAAT
1 AAAATTAAAATAA-GAAATTAAAAT
46184 AAAA-TAAAATAAGAAATTAAAA
1 AAAATTAAAATAAGAAATTAAAA
46206 AGAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAATTAAAATAAGAAATTAAAAT
Found at i:54283 original size:24 final size:24
Alignment explanation
Indices: 54256--54301 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54246 GTCAATTTCC
54256 TTTTACTAATATTATTAGGTTAGA
1 TTTTACTAATATTATTAGGTTAGA
* **
54280 TTTTAGTTGTATTATTAGGTTA
1 TTTTACTAATATTATTAGGTTA
54302 ATTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.54
Consensus pattern (24 bp):
TTTTACTAATATTATTAGGTTAGA
Found at i:54316 original size:24 final size:24
Alignment explanation
Indices: 54264--54317 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
54254 CCTTTTACTA
54264 ATATTATTAGGTTAGATTTTAGTT
1 ATATTATTAGGTTAGATTTTAGTT
*
54288 GTATTATTAGGTTA-ATTATT-GATT
1 ATATTATTAGGTTAGATT-TTAG-TT
54312 ATATTA
1 ATATTA
54318 ATATTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (24 bp):
ATATTATTAGGTTAGATTTTAGTT
Found at i:55801 original size:118 final size:118
Alignment explanation
Indices: 55592--55815 Score: 306
Period size: 118 Copynumber: 1.9 Consensus size: 118
55582 CCTAAACTTT
* ** *
55592 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTACAATGATTGAGGGACCATTTTAATTCTTT
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
* *
55657 GACTAAATAATTGGTTAAAATGAATTATGATTAATATTAGACACTTTAGTCCC
66 GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
* * ** * * *
55710 TTAATTAGGGAATGATTTGATTTGGCTCTCGCATTAAAATGCTCAAGGGACCATTTTGATTATTC
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATT-
*
55775 T-ACTTAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
65 TGACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
55816 GCTTTCATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 90 0.99
119 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (118 bp):
TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
Found at i:58628 original size:35 final size:35
Alignment explanation
Indices: 58586--58655 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
58576 GCGATAATGC
*
58586 CTAAGGTGATGATGTTGAATGAAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
* *
58621 CTAAGGTGAGGATGTTGAGTGCAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
58656 ACACTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.31, T:0.27
Consensus pattern (35 bp):
CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
Found at i:60252 original size:36 final size:36
Alignment explanation
Indices: 60212--60406 Score: 173
Period size: 36 Copynumber: 5.4 Consensus size: 36
60202 CACTAAAGTT
* *
60212 TTTATCTCGCTTGAGATTGTTTTTCTTAAAGCATAC
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
** * * *
60248 TTTATCTTGCTTAAGATTGTTTTCCTTAAAACATAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
* * * * *
60284 TTTATCTCAATTGAGATTATTTTTTTTCTAAA-ATAGA
1 TTTATCTCACTTGAGATTGTTTTTCTT-AAAACATA-C
* *
60321 TCTTATTTCACTTGAGA-T-TTTTTATTAAAACATAC
1 T-TTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
* * *
60356 CTTATCTCACTTGAGATTG-TTTTCTTAAAATATAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
*
60391 TTTATCTCATTTGAGA
1 TTTATCTCACTTGAGA
60407 ATTGAGATTT
Statistics
Matches: 127, Mismatches: 26, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
34 14 0.11
35 31 0.24
36 64 0.50
37 5 0.04
38 13 0.10
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (36 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
Found at i:60350 original size:34 final size:34
Alignment explanation
Indices: 60273--60406 Score: 124
Period size: 35 Copynumber: 3.8 Consensus size: 34
60263 ATTGTTTTCC
* * * *
60273 TTAAAACATATTTTATCTCAATTGAGATTATTTTTTT
1 TTAAAATATATCTTATCTCACTTGAG---ATTTTTTA
* *
60310 TCTAAAATAGATCTTATTTCACTTGAGATTTTTTA
1 T-TAAAATATATCTTATCTCACTTGAGATTTTTTA
* * *
60345 TTAAAACATACCTTATCTCACTTGAGATTGTTTTC
1 TTAAAATATATCTTATCTCACTTGAGATT-TTTTA
* *
60380 TTAAAATATATTTTATCTCATTTGAGA
1 TTAAAATATATCTTATCTCACTTGAGA
60407 ATTGAGATTT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
34 24 0.30
35 35 0.44
37 1 0.01
38 20 0.25
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (34 bp):
TTAAAATATATCTTATCTCACTTGAGATTTTTTA
Found at i:60436 original size:108 final size:109
Alignment explanation
Indices: 60221--60421 Score: 255
Period size: 108 Copynumber: 1.8 Consensus size: 109
60211 TTTTATCTCG
* * * **
60221 CTTGAGATTGTTTTTCTTAAAGCATACTTTATCTTGCTTAAGATTGTTTTCCTTAAAACATATTT
1 CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
** *
60286 TATCTCAATTGAGATTATTTTTTTTCTAAAATAGATCTTATTTCA
66 TATCTCAATTGAGATTAGATTTTATCTAAAATAGA-CTTATTTCA
* *
60331 CTTGAGA-T-TTTTTATTAAAACATACCTTATCTCACTTGAGATTGTTTT-CTTAAAATATATTT
1 CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
*
60393 TATCTCATTTGAGAATTGAGATTTTATCT
66 TATCTCAATTGAG-ATT-AGATTTTATCT
60422 TACTTGAGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 25 0.32
108 37 0.47
109 9 0.12
110 7 0.09
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (109 bp):
CTTGAGATTGTTTTTATTAAAACATACCTTATCTCACTTAAGATTGTTTTCCTTAAAACATATTT
TATCTCAATTGAGATTAGATTTTATCTAAAATAGACTTATTTCA
Found at i:60473 original size:36 final size:36
Alignment explanation
Indices: 60423--60555 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 36
60413 ATTTTATCTT
*
60423 ACTTGAGATTATTTTTCTTAAAACATATAATATATC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** *
60459 ACTTGAGATAATTTTTATTAAAATAGATTTTATCTC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** * *
60495 ACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTT
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* *
60531 ACTTGAAATTGTTTTTCTTAAAACA
1 ACTTGAGATTATTTTTCTTAAAACA
60556 AATTTGTTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (36 bp):
ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
Found at i:60541 original size:131 final size:131
Alignment explanation
Indices: 60282--60541 Score: 301
Period size: 131 Copynumber: 2.0 Consensus size: 131
60272 CTTAAAACAT
* * ** *
60282 ATTTTATCTCAATTGAGATTATTTTTTTTCTAAAATAGATCTTATTTCACTTGAGATTTTTTATT
1 ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATT
* * * * *
60347 AAAACATACCTTATCTCACTTGAGATTGTTTTCTTAAAATATATTTTATCTCATTTGAGAATTGA
66 AAAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGA
60412 G
131 G
* * *
60413 ATTTTATCTTACTTGAGATTA-TTTTTCT-TAAAACATATAATATATCACTTGAGATAATTTTTA
1 ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGAT--TTTTTA
* ** * * *
60476 TTAAAATAGATTTTATCTCACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTTACTTGA-AAT
64 TTAAAACAGACCTTATCTCACTGGAGATTG-TTTTCTTAAAACAGATTTTATCTCACTTGAGAAT
60540 TG
128 TG
60542 TTTTTCTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
129 22 0.21
130 6 0.06
131 55 0.51
132 24 0.22
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (131 bp):
ATTTTATCTCAATTGAGATTATTTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATT
AAAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGA
G
Found at i:60544 original size:167 final size:168
Alignment explanation
Indices: 60248--60553 Score: 384
Period size: 167 Copynumber: 1.8 Consensus size: 168
60238 TAAAGCATAC
* * ** * * *
60248 TTTATCTTGCTTAAGATTGTTTTCCTTAAAACATATTTTATCTCAATTGAGATTATTTTTTTTCT
1 TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
* * * *
60313 AAAATAGATCTTATTTCACTTGAGATTTTTTATTAAAACATACCTTATCTCACTTGAGATTG-TT
66 AAAATAGATCTTATCTCACTGGAGATTTTTTATTAAAACAGACCTTATCTCACTTGAAATTGTTT
60377 TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
131 TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
* * *
60415 TTTATCTTACTTGAGATTATTTTTCTTAAAACATATAATATATCACTTGAGA-TAATTTTTAT-T
1 TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
* * *** * *
60478 AAAATAGATTTTATCTCACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTTACTTGAAATTGT
66 AAAATAGATCTTATCTCACTGGAGA-T-TTTTTATTAAAACAGACCTTATCTCACTTGAAATTGT
60543 TTTTCTTAAAA
129 TTTTCTTAAAA
60554 CAAATTTGTT
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
165 23 0.20
166 9 0.08
167 72 0.63
168 11 0.10
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (168 bp):
TTTATCTTACTTAAGATTATTTTCCTTAAAACATATAATATATCAATTGAGATTAATTTTTATCT
AAAATAGATCTTATCTCACTGGAGATTTTTTATTAAAACAGACCTTATCTCACTTGAAATTGTTT
TTCTTAAAATATATTTTATCTCATTTGAGAATTGAGAT
Found at i:60710 original size:13 final size:12
Alignment explanation
Indices: 60688--60721 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
60678 CCTTTTACTA
60688 ATATTATTAGTTT
1 ATATTATTAG-TT
*
60701 ATATTTTTAGTT
1 ATATTATTAGTT
60713 ATATTATTA
1 ATATTATTA
60722 ATTTAACTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
ATATTATTAGTT
Found at i:60716 original size:12 final size:13
Alignment explanation
Indices: 60688--60726 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
60678 CCTTTTACTA
60688 ATATTATTAGTTT
1 ATATTATTAGTTT
*
60701 ATATTTTTAG-TT
1 ATATTATTAGTTT
*
60713 ATATTATTAATTT
1 ATATTATTAGTTT
60726 A
1 A
60727 ACTGTTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATATTATTAGTTT
Found at i:65055 original size:3 final size:3
Alignment explanation
Indices: 65047--65174 Score: 204
Period size: 3 Copynumber: 42.7 Consensus size: 3
65037 TTTTTATCCA
*
65047 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
65095 TAT TAT CAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
65141 TAT TAT TAT TA- TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
65175 ATTTATATTA
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.02
3 110 0.96
4 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:67265 original size:28 final size:28
Alignment explanation
Indices: 67230--67314 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 28
67220 AATTTATATA
*
67230 TTTA-ATTTTAATTTTTCTTTTCAAATT
1 TTTATATTTTAATTTTTATTTTCAAATT
* * *
67257 TTTATA-TTTACTTATTATTTTCATAATA
1 TTTATATTTTAATTTTTATTTTCA-AATT
* *
67285 TTTATATGTTTTA-TTTTATTTGCAAATT
1 TTTATAT-TTTAATTTTTATTTTCAAATT
67313 TT
1 TT
67315 ATTTCAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
27 18 0.40
28 15 0.33
29 9 0.20
30 3 0.07
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTATATTTTAATTTTTATTTTCAAATT
Done.