Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002540.1 Hibiscus syriacus cultivar Beakdansim tig00005157_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: 91687
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3460 original size:18 final size:18
Alignment explanation
Indices: 3439--3476 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3429 TTAAACATCA
3439 AATGATAAATTTA-GAAAC
1 AATGATAAA-TTACGAAAC
*
3457 AATGTTAAATTACGAAAC
1 AATGATAAATTACGAAAC
3475 AA
1 AA
3477 AACTAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (18 bp):
AATGATAAATTACGAAAC
Found at i:5063 original size:2 final size:2
Alignment explanation
Indices: 5058--5113 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
5048 AATTAAAATA
5058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5100 AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
5114 ATAAATTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8368 original size:12 final size:12
Alignment explanation
Indices: 8351--8376 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8341 AAGTCTGCAA
8351 GAGATGGAACTG
1 GAGATGGAACTG
8363 GAGATGGAACTG
1 GAGATGGAACTG
8375 GA
1 GA
8377 TATGATCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.42, T:0.15
Consensus pattern (12 bp):
GAGATGGAACTG
Found at i:10663 original size:10 final size:10
Alignment explanation
Indices: 10647--10686 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
10637 ATCTATTTTG
10647 TAATTTAATC
1 TAATTTAATC
*
10657 TATTTTAATC
1 TAATTTAATC
*
10667 TACTTTAATC
1 TAATTTAATC
10677 TAATTTAATC
1 TAATTTAATC
10687 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (10 bp):
TAATTTAATC
Found at i:10793 original size:20 final size:20
Alignment explanation
Indices: 10768--10817 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
10758 ATCTATCTTG
10768 TAATTTAATCTACTTCAATA
1 TAATTTAATCTACTTCAATA
* * *
10788 TAATTTAATATACTTTAATC
1 TAATTTAATCTACTTCAATA
10808 TAATTTAATC
1 TAATTTAATC
10818 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTTAATCTACTTCAATA
Found at i:10817 original size:10 final size:10
Alignment explanation
Indices: 10768--10817 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
10758 ATCTATCTTG
10768 TAATTTAATC
1 TAATTTAATC
* * *
10778 TACTTCAATA
1 TAATTTAATC
*
10788 TAATTTAATA
1 TAATTTAATC
*
10798 TACTTTAATC
1 TAATTTAATC
10808 TAATTTAATC
1 TAATTTAATC
10818 ATTAAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATTTAATC
Found at i:11361 original size:135 final size:138
Alignment explanation
Indices: 11197--11457 Score: 411
Period size: 135 Copynumber: 1.9 Consensus size: 138
11187 ATAGCCACAG
* * *
11197 AAATTATATTTATATATTTTATTATTATATGTAAGTTGCGTTAAATTATCGGTAAATAAAGAAAT
1 AAATTAAATTTATATATTTTATTATTATATGTAAGTTGCGTGAAATAATCGGTAAATAAAGAAAT
11262 TAGATGAA-TTTTA-T-TTTTTTATGTGAATGGATGAATTTTAACAATTTGTAAATTATAAGGAT
66 TAGATGAATTTTTATTATTTTTTATGTGAATGGATGAATTTTAACAATTTGTAAATTATAAGGAT
11324 TTATTATA
131 TTATTATA
11332 AAATTAAATTTATATATTTTATTATTATATGTAAGTTGCGTGAAATAATCGGTAAATAAAGAAAT
1 AAATTAAATTTATATATTTTATTATTATATGTAAGTTGCGTGAAATAATCGGTAAATAAAGAAAT
11397 TAGATGAATTTTTTTATTTTTTTATTTTTTATGTGAATGGATGAATTTTAACAATTTGTAA
66 TAGATGAA--TTTTTA-----TTATTTTTTATGTGAATGGATGAATTTTAACAATTTGTAA
11458 TTTTTTCTTT
Statistics
Matches: 113, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
135 70 0.62
138 5 0.04
144 1 0.01
145 37 0.33
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (138 bp):
AAATTAAATTTATATATTTTATTATTATATGTAAGTTGCGTGAAATAATCGGTAAATAAAGAAAT
TAGATGAATTTTTATTATTTTTTATGTGAATGGATGAATTTTAACAATTTGTAAATTATAAGGAT
TTATTATA
Found at i:11714 original size:24 final size:24
Alignment explanation
Indices: 11687--11738 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11677 TATTTAATTT
* **
11687 TTTTGATGTAATTAAATGTCTAAC
1 TTTTAATGTAATTAAATACCTAAC
11711 TTTTAATGTAATTAAATACCTAAC
1 TTTTAATGTAATTAAATACCTAAC
11735 TTTT
1 TTTT
11739 TTTATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTTAATGTAATTAAATACCTAAC
Found at i:40541 original size:20 final size:19
Alignment explanation
Indices: 40516--40568 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
40506 CTGCACATGT
40516 AGTTTCAAAACTTTGAAGAA
1 AGTTTCAAAACTTTGAA-AA
*
40536 AGTTTCAAAACTTTGTAAA
1 AGTTTCAAAACTTTGAAAA
*
40555 AGTATCAAAACTTT
1 AGTTTCAAAACTTT
40569 TAAACACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (19 bp):
AGTTTCAAAACTTTGAAAA
Found at i:40562 original size:19 final size:19
Alignment explanation
Indices: 40520--40572 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
40510 ACATGTAGTT
* *
40520 TCAAAACTTTGAAGAAAGTT
1 TCAAAACTTTGTA-AAAGTA
40540 TCAAAACTTTGTAAAAGTA
1 TCAAAACTTTGTAAAAGTA
40559 TCAAAACTTT-TAAA
1 TCAAAACTTTGTAAA
40573 CACATTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.13
19 15 0.48
20 12 0.39
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (19 bp):
TCAAAACTTTGTAAAAGTA
Found at i:46615 original size:15 final size:15
Alignment explanation
Indices: 46595--46623 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46585 ACAATTTAGG
46595 TTGTAAATTAACTAA
1 TTGTAAATTAACTAA
46610 TTGTAAATTAACTA
1 TTGTAAATTAACTA
46624 CGCTTATATG
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:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
TTGTAAATTAACTAA
Found at i:50110 original size:35 final size:34
Alignment explanation
Indices: 50066--50143 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
50056 GGTAAGAAAT
* * * *
50066 TTATTTTTATGTTAGTAT-TTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
50100 TTATATTTTATATTAATATATTTATGTAAATATTA
1 TTAT-TTTTATATTAATATATTTATGTAAATATTA
50135 TT-TTTTTAT
1 TTATTTTTAT
50144 TAAAATAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 6 0.16
34 5 0.13
35 17 0.45
36 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:50332 original size:31 final size:33
Alignment explanation
Indices: 50284--50362 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
50274 TTTAAATAGT
* *
50284 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
50316 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
50350 TATTATTTATTTA
1 TATTATTTTTTTA
50363 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:50354 original size:34 final size:31
Alignment explanation
Indices: 50274--50362 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
50264 TTAGTATTTT
* * *
50274 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
50306 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
50340 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
50363 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:50523 original size:17 final size:17
Alignment explanation
Indices: 50501--50554 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
50491 AATGTTAATA
50501 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
50518 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
50535 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
50552 TTT
1 TTT
50555 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:52075 original size:21 final size:21
Alignment explanation
Indices: 52051--52111 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
52041 ACCAGTTTAT
*
52051 ATTCCGAGCCCGCAAGGTTAC
1 ATTCCTAGCCCGCAAGGTTAC
*
52072 ATTCCTAGCCCGCCAGGTTAC
1 ATTCCTAGCCCGCAAGGTTAC
* *
52093 ATGCCTAGCCCGCAGGGTT
1 ATTCCTAGCCCGCAAGGTT
52112 TTATACCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (21 bp):
ATTCCTAGCCCGCAAGGTTAC
Found at i:52738 original size:34 final size:34
Alignment explanation
Indices: 52633--52739 Score: 153
Period size: 34 Copynumber: 3.1 Consensus size: 34
52623 ATAAATGTTT
*
52633 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
52667 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
52701 TTAAAATATAAATTATAGTT-TTCGAAATTTAACA
1 TTAAAATAAAAATTATA-TTATTCGAAATTTAAAA
52735 TTAAA
1 TTAAA
52740 TTTCAACTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 63 0.97
35 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:52867 original size:14 final size:14
Alignment explanation
Indices: 52848--52877 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52838 TTTTATCATT
*
52848 AACATATATATTAA
1 AACATATACATTAA
52862 AACATATACATTAA
1 AACATATACATTAA
52876 AA
1 AA
52878 TCAACTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:53742 original size:8 final size:8
Alignment explanation
Indices: 53729--53769 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
53719 TCACAAGCTT
53729 TCAAATTC
1 TCAAATTC
53737 TCAAATTC
1 TCAAATTC
* *
53745 CCAAACTC
1 TCAAATTC
53753 T-AAATTC
1 TCAAATTC
53760 TCAAATTC
1 TCAAATTC
53768 TC
1 TC
53770 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:57645 original size:13 final size:14
Alignment explanation
Indices: 57610--57644 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
57600 CCGAAAAATT
57610 ATATTTTTCATTTA
1 ATATTTTTCATTTA
57624 ATATTTTTCATTTA
1 ATATTTTTCATTTA
57638 ATATTTT
1 ATATTTT
57645 CGATCAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTCATTTA
Found at i:57777 original size:19 final size:19
Alignment explanation
Indices: 57733--57777 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
57723 TGATTTGGTA
*
57733 CCACGTGTGGTAAGGCACG
1 CCACGTGGGGTAAGGCACG
57752 -CACCGTGGGGTAAGGCACG
1 CCA-CGTGGGGTAAGGCACG
57771 CCACGTG
1 CCACGTG
57778 AGGCGCGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.13
Consensus pattern (19 bp):
CCACGTGGGGTAAGGCACG
Found at i:58076 original size:9 final size:9
Alignment explanation
Indices: 58064--58097 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
58054 TAATATTTTA
58064 TATTTAATT
1 TATTTAATT
*
58073 TATTTAA-G
1 TATTTAATT
58081 TATTTAATT
1 TATTTAATT
58090 TATTTAAT
1 TATTTAAT
58098 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:58108 original size:16 final size:16
Alignment explanation
Indices: 58057--58101 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
58047 ATATTTTTAA
*
58057 TATTTTATATTTAATT
1 TATTTAATATTTAATT
58073 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
58090 TATTTAATATTT
1 TATTTAATATTT
58102 TACTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:59789 original size:23 final size:23
Alignment explanation
Indices: 59754--59829 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
59744 GATTCATCCT
*
59754 CAGCTGCACCAGCAGGACCTTCA
1 CAGCAGCACCAGCAGGACCTTCA
*
59777 CAGCAGCAACAGCAGGACCTTCA
1 CAGCAGCACCAGCAGGACCTTCA
59800 CAGCAGCACCAGCAGGACCTTCA
1 CAGCAGCACCAGCAGGACCTTCA
59823 CAGCAGC
1 CAGCAGC
59830 TAGCGTATCC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.30, C:0.38, G:0.22, T:0.09
Consensus pattern (23 bp):
CAGCAGCACCAGCAGGACCTTCA
Found at i:65476 original size:3 final size:3
Alignment explanation
Indices: 65468--65495 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
65458 ACTCAATTGT
65468 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
65496 GGTTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:81808 original size:2 final size:2
Alignment explanation
Indices: 81801--81829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
81791 CTCATTTAAT
81801 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
81830 GATTTTATTA
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:82727 original size:53 final size:53
Alignment explanation
Indices: 82634--82736 Score: 131
Period size: 53 Copynumber: 1.9 Consensus size: 53
82624 GGCACGTGTC
*
82634 CACCCTGAAATCCAGATTTTCTTCGATTAGTCACCTATTTT-ATTGATGGTGCT
1 CACCCTGAAATCCAGATTTTATTCGATTAGTCACCTATTTTGA-TGATGGTGCT
* *
82687 CACCCTGAAAT-CTGAATTTTATTCGATTAGTGATCC-ATTTTGATGATGGT
1 CACCCTGAAATCCAG-ATTTTATTCGATTAGTCA-CCTATTTTGATGATGGT
82737 TTCCATCCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 2 0.05
53 39 0.89
54 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (53 bp):
CACCCTGAAATCCAGATTTTATTCGATTAGTCACCTATTTTGATGATGGTGCT
Found at i:89175 original size:184 final size:186
Alignment explanation
Indices: 88815--89178 Score: 588
Period size: 184 Copynumber: 2.0 Consensus size: 186
88805 CTTCATAGGA
* *
88815 GTGTGTGTATGTAGATGCATCCTCAATGAAAAGGAAGTAAGACAGTAACTGGAATGCTAGACTGT
1 GTGTGTATATGTAGATGCATCCTCAATGAAAAGGAAGTAAGACAATAACTGGAATGCTAGACTGT
* * *
88880 ACTCGATCCATGTAATCATAAAAATAAAAATAAAAAATACCATAGTGTCTTTGGAAACTGCAGGA
66 ACTCGATCCATG-AAGCATAAAAATAAAAATAAAAAATACCATAGTGTCCTTAGAAACTGCAGGA
88945 TCATTTGCAACTGGATTTTTCTGCTTCGCCTGACTTCCAAAATTCAAGGGAGTGTGT
130 TCATTTGCAACTGGATTTTTCTGCTTCGCCTGACTTCCAAAATTCAAGGGAGTGTGT
* *
89002 GTGTGTATATGTAGATGCATCCTCAGTGAAAAGGAAGTAAGACAATTACTGGAATGCTAGACTGT
1 GTGTGTATATGTAGATGCATCCTCAATGAAAAGGAAGTAAGACAATAACTGGAATGCTAGACTGT
* ** *
89067 ATTCGATCCATG-AGCATAATCATAAAAAT-AAAAATACCATAGTGTCCTTAGCAACTGCAGGAT
66 ACTCGATCCATGAAGCATAAAAATAAAAATAAAAAATACCATAGTGTCCTTAGAAACTGCAGGAT
* *
89130 CATTTGCAACTGGATTTTTCTGCTTCGCCTGAGTTCCAGAATTCAAGGG
131 CATTTGCAACTGGATTTTTCTGCTTCGCCTGACTTCCAAAATTCAAGGG
89179 TCCTGATGTT
Statistics
Matches: 164, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 78 0.48
185 14 0.09
187 72 0.44
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (186 bp):
GTGTGTATATGTAGATGCATCCTCAATGAAAAGGAAGTAAGACAATAACTGGAATGCTAGACTGT
ACTCGATCCATGAAGCATAAAAATAAAAATAAAAAATACCATAGTGTCCTTAGAAACTGCAGGAT
CATTTGCAACTGGATTTTTCTGCTTCGCCTGACTTCCAAAATTCAAGGGAGTGTGT
Found at i:89732 original size:11 final size:11
Alignment explanation
Indices: 89682--89824 Score: 103
Period size: 11 Copynumber: 12.6 Consensus size: 11
89672 TAACTCATCC
89682 TCGAGCTT-AA
1 TCGAGCTTGAA
89692 GTCGAGCTTGAA
1 -TCGAGCTTGAA
*
89704 TTGAGCTT-AA
1 TCGAGCTTGAA
*
89714 GTCAAGCTTGAA
1 -TCGAGCTTGAA
*
89726 TTGAGC-TGACAA
1 TCGAGCTTG--AA
89738 TCGAGCTTGAA
1 TCGAGCTTGAA
**
89749 TCGAGCTCACAA
1 TCGAGCT-TGAA
89761 TCGAGCTTGAA
1 TCGAGCTTGAA
* **
89772 TCAAGCTCACAA
1 TCGAGCT-TGAA
89784 TCGAGCTTGAA
1 TCGAGCTTGAA
* **
89795 TCAAGCTCACAA
1 TCGAGCT-TGAA
89807 TCGAGCTTGAA
1 TCGAGCTTGAA
89818 TCGAGCT
1 TCGAGCT
89825 CATAATTGAG
Statistics
Matches: 101, Mismatches: 22, Indels: 18
0.72 0.16 0.13
Matches are distributed among these distances:
10 4 0.04
11 59 0.58
12 36 0.36
13 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:89748 original size:23 final size:23
Alignment explanation
Indices: 89693--89837 Score: 193
Period size: 23 Copynumber: 6.3 Consensus size: 23
89683 CGAGCTTAAG
* * *
89693 TCGAGCTTGAATTGAGCTTA-AG
1 TCGAGCTTGAATCGAGCTCACAA
* * *
89715 TCAAGCTTGAATTGAGCTGACAA
1 TCGAGCTTGAATCGAGCTCACAA
89738 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
89761 TCGAGCTTGAATCAAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
89784 TCGAGCTTGAATCAAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
89807 TCGAGCTTGAATCGAGCTCATAA
1 TCGAGCTTGAATCGAGCTCACAA
*
89830 TTGAGCTT
1 TCGAGCTT
89838 CAATTGACTT
Statistics
Matches: 112, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
22 18 0.16
23 94 0.84
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:91556 original size:21 final size:21
Alignment explanation
Indices: 91530--91571 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
91520 CATGTTATTT
91530 TATAATAAAACGCTTGTAATC
1 TATAATAAAACGCTTGTAATC
91551 TATAATAAAACGCTTGTAATC
1 TATAATAAAACGCTTGTAATC
91572 AGAATGAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
TATAATAAAACGCTTGTAATC
Done.