Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001108.1 Hibiscus syriacus cultivar Beakdansim tig00002190_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: 65125
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:3291 original size:36 final size:37
Alignment explanation
Indices: 3227--3311 Score: 136
Period size: 36 Copynumber: 2.3 Consensus size: 37
3217 ATGCTTAACT
*
3227 CTCTCGAACATTAAGCAAACAACTAAGTGATAGCCAA
1 CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
*
3264 CTCTCGAAGGTTAAGC-AACAACTAAGTGATAGCCAA
1 CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
*
3300 ATCTCGAAGATT
1 CTCTCGAAGATT
3312 TTCTCTTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 30 0.68
37 14 0.32
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (37 bp):
CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
Found at i:5671 original size:57 final size:57
Alignment explanation
Indices: 5604--5805 Score: 291
Period size: 57 Copynumber: 3.5 Consensus size: 57
5594 GAATTTACCT
*
5604 ACTTATTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* * *
5661 ACTTGGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATATGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* *
5718 ACTTAGTATAAATTTCTTAGCTTTTTGCACACAAAGTGCCCATAC-AGAAATAT-ATAA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGA-AAAT-TCATAC
* * *
5775 ACTAATTATGAATTTCTTAACTTTTTGCACA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACA
5806 ATCAATGTCA
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 129 0.99
58 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (57 bp):
ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
Found at i:6266 original size:20 final size:21
Alignment explanation
Indices: 6230--6280 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
6220 GATATCAATG
*
6230 GTATCGATAC-CTTCCTTATA
1 GTATCGATACTCTCCCTTATA
*
6250 GTATCGATACTC-CCCTTTTA
1 GTATCGATACTCTCCCTTATA
*
6270 GTGTCGATACT
1 GTATCGATACT
6281 GCTTGCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (21 bp):
GTATCGATACTCTCCCTTATA
Found at i:8958 original size:42 final size:42
Alignment explanation
Indices: 8911--8996 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
8901 AAAGTAAAAC
8911 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
1 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
8953 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
1 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
8995 AA
1 AA
8997 GCAACACGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (42 bp):
AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
Found at i:9705 original size:24 final size:24
Alignment explanation
Indices: 9673--9721 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
9663 AGTCTTCCTG
*
9673 ATGATGTATAAAGCATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
9697 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
9721 A
1 A
9722 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:12347 original size:18 final size:18
Alignment explanation
Indices: 12324--12358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12314 GTTTAATTGT
*
12324 ATTTTAAACCCTTAAAAA
1 ATTTTAAACCATTAAAAA
12342 ATTTTAAACCATTAAAA
1 ATTTTAAACCATTAAAA
12359 TTAAGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTTTAAACCATTAAAAA
Found at i:16319 original size:18 final size:19
Alignment explanation
Indices: 16296--16333 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
16286 CCCAGTAATC
16296 TTATTCC-CTGGTAATCTT
1 TTATTCCACTGGTAATCTT
16314 TTATTCCTACTGGTAATCTT
1 TTATTCC-ACTGGTAATCTT
16334 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (19 bp):
TTATTCCACTGGTAATCTT
Found at i:16339 original size:20 final size:20
Alignment explanation
Indices: 16303--16340 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16293 ATCTTATTCC
**
16303 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
16323 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
16341 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:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:18707 original size:14 final size:14
Alignment explanation
Indices: 18688--18726 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18678 TAATGGGAAT
18688 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
18702 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
18716 GAATCTCTGCA
1 TAATCCCTGCA
18727 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:23506 original size:19 final size:20
Alignment explanation
Indices: 23465--23506 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
23455 AGCTTAATAC
* *
23465 TTATGTGTGTATTTCTTGATT
1 TTATGTGGGCATTTCTT-ATT
23486 TTATGTGGGCATTTCTT-TT
1 TTATGTGGGCATTTCTTATT
23505 TT
1 TT
23507 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.12, C:0.07, G:0.19, T:0.62
Consensus pattern (20 bp):
TTATGTGGGCATTTCTTATT
Found at i:30478 original size:96 final size:96
Alignment explanation
Indices: 30311--30490 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 96
30301 CAATAGATCC
* * * * **
30311 CATGATCCATAAATCAGGAAATATTGTATTTTCCAGTGAAAATAGGAAACCATATAGCACATTTC
1 CATGATCCATAAATCAGGAAATATTATATTTTCCAGTGAAAACAGGAAACCAGATAACACATACC
30376 AGGTAACCATAGTTCATAAACTAGTAGATTT
66 AGGTAACCATAGTTCATAAACTAGTAGATTT
* ** * *
30407 CATGATCCATAAATTAGG-AATGATTATATTTTTTAGTGAAAACAGGTAACCAGATAACATATAC
1 CATGATCCATAAATCAGGAAAT-ATTATATTTTCCAGTGAAAACAGGAAACCAGATAACACATAC
* *
30471 CATGTAACTATAGTTCATAA
65 CAGGTAACCATAGTTCATAA
30491 GCCAATAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
95 3 0.04
96 67 0.96
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (96 bp):
CATGATCCATAAATCAGGAAATATTATATTTTCCAGTGAAAACAGGAAACCAGATAACACATACC
AGGTAACCATAGTTCATAAACTAGTAGATTT
Found at i:31410 original size:23 final size:22
Alignment explanation
Indices: 31384--31426 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
31374 ACATAAAACT
* *
31384 TGTCCCGAAGGACCTCATGTATA
1 TGTCCCAAAAGACCT-ATGTATA
31407 TGTCCCAAAAGACCTATGTA
1 TGTCCCAAAAGACCTATGTA
31427 ACCCTCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
TGTCCCAAAAGACCTATGTATA
Found at i:34298 original size:22 final size:22
Alignment explanation
Indices: 34266--34307 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34256 TCCATTTCAA
34266 CATCAACACCATCAACATCCTC
1 CATCAACACCATCAACATCCTC
* *
34288 CATCAAGACCATCATCATCC
1 CATCAACACCATCAACATCC
34308 ACTTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (22 bp):
CATCAACACCATCAACATCCTC
Found at i:42546 original size:12 final size:12
Alignment explanation
Indices: 42502--42569 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
42492 TTTATACATA
42502 TTAAAT-TTATT
1 TTAAATATTATT
*
42513 TTAAAATATTGAAT
1 TT-AAATATT-ATT
*
42527 TT-ATTATTATT
1 TTAAATATTATT
*
42538 TTAAATATTATA
1 TTAAATATTATT
*
42550 TTAACTA-TATT
1 TTAAATATTATT
42561 TTAATATAT
1 TTAA-ATAT
42570 ATATATATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
11 13 0.30
12 24 0.56
13 2 0.05
14 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAAATATTATT
Found at i:42569 original size:24 final size:23
Alignment explanation
Indices: 42499--42585 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 23
42489 TTTTTTATAC
*
42499 ATATTAAATTTATTTTAAAATATT
1 ATATTAAATATATTTT-AAATATT
* *
42523 GA-ATTTATTATTATTTTAAATATT
1 -ATATTAAATA-TATTTTAAATATT
*
42547 ATATTAACTATATTTTAATATATAT
1 ATATTAAATATATTTTAA-ATAT-T
*
42572 ATATATATATATAT
1 ATAT-TAAATATAT
42586 ATATATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
23 9 0.18
24 22 0.44
25 12 0.24
26 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
ATATTAAATATATTTTAAATATT
Found at i:42571 original size:2 final size:2
Alignment explanation
Indices: 42564--42608 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
42554 CTATATTTTA
*
42564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42606 AT A
1 AT A
42609 AATCACTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:45934 original size:186 final size:185
Alignment explanation
Indices: 45618--45996 Score: 636
Period size: 186 Copynumber: 2.0 Consensus size: 185
45608 ATTAAATTTT
* * * * *
45618 AAATATTAAATATATTATATATAACATATGGGGTCAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTACATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
45683 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
45748 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTCTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTT-TTGAATTAAA
*
45804 AAATATTAAATATATTACATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTACATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
45869 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
45934 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
45989 AAAT-TTAA
1 AAATATTAA
45997 TTTTTATATA
Statistics
Matches: 182, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
184 6 0.03
185 16 0.09
186 160 0.88
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (185 bp):
AAATATTAAATATATTACATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:51046 original size:2 final size:2
Alignment explanation
Indices: 51039--51136 Score: 80
Period size: 2 Copynumber: 49.0 Consensus size: 2
51029 TAGGTGGTTT
*
51039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TT TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
51082 TA AA GTA TA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
51124 TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA
51137 AGTATAATTA
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
1 5 0.06
2 68 0.86
3 6 0.08
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:51125 original size:23 final size:23
Alignment explanation
Indices: 51099--51148 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
51089 TATATATACA
51099 TATATAATA-ATATAAAGTATAAG
1 TATATAATATATAT-AAGTATAAG
* *
51122 TATATTATATATATAAGTATAAT
1 TATATAATATATATAAGTATAAG
51145 TATA
1 TATA
51149 AGACTAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (23 bp):
TATATAATATATATAAGTATAAG
Found at i:51125 original size:29 final size:30
Alignment explanation
Indices: 51039--51143 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 30
51029 TAGGTGGTTT
*
51039 TATATATATATA-TATATA-TATATATAT-A
1 TATATATATA-AGTATAAAGTATATATATAA
* *
51067 TATATAGTTTTAGTATAAAGTATATATATACA
1 TATATA-TATAAGTATAAAGTATATATATA-A
*
51099 TATATA-ATAA-TATAAAGTATA-AGTATAT
1 TATATATATAAGTATAAAGTATATA-TATAA
51127 TATATATATAAGTATAA
1 TATATATATAAGTATAA
51144 TTATAAGACT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
28 14 0.22
29 26 0.41
30 16 0.25
32 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.44
Consensus pattern (30 bp):
TATATATATAAGTATAAAGTATATATATAA
Found at i:51133 original size:42 final size:43
Alignment explanation
Indices: 51039--51136 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
51029 TAGGTGGTTT
* * * *
51039 TATATATATATATATATATATATATATATATATAGTTTTAGTA
1 TATATATATATATACATATATATATATATATAAAGTATAAGTA
*
51082 TAAAGTATATATATACATATATA-ATA-ATATAAAGTATAAGTA
1 TATA-TATATATATACATATATATATATATATAAAGTATAAGTA
51124 TAT-TATATATATA
1 TATATATATATATA
51137 AGTATAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
40 10 0.21
42 15 0.31
43 6 0.12
44 17 0.35
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (43 bp):
TATATATATATATACATATATATATATATATAAAGTATAAGTA
Found at i:51184 original size:14 final size:16
Alignment explanation
Indices: 51165--51200 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
51155 AAGTGTATAT
51165 GTATATAA-TA-TAAA
1 GTATATAAGTATTAAA
51179 GTATATAAGTATTAAA
1 GTATATAAGTATTAAA
51195 GTATAT
1 GTATAT
51201 GTTGAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (16 bp):
GTATATAAGTATTAAA
Found at i:51440 original size:20 final size:20
Alignment explanation
Indices: 51415--51466 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
51405 CAAAGGTATG
*
51415 AGAAGTATTGATCCTCACTA
1 AGAAGTATCGATCCTCACTA
51435 AGAAGTATCGATCCTCACTA
1 AGAAGTATCGATCCTCACTA
* *
51455 GGTAGTATCGAT
1 AGAAGTATCGAT
51467 ACTACCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
AGAAGTATCGATCCTCACTA
Found at i:51631 original size:45 final size:45
Alignment explanation
Indices: 51561--51697 Score: 224
Period size: 45 Copynumber: 3.0 Consensus size: 45
51551 TGATACCATC
51561 AGGCCCAACAGCTAGTCAC-AGCTAGTTTTATTTAAAAATAACAAA
1 AGGCCCAACAGCTAGTCACGA-CTAGTTTTATTTAAAAATAACAAA
*
51606 AGGCCCAACACCTAGTCACGACTAGTTTTATTTAAAAATAACAAA
1 AGGCCCAACAGCTAGTCACGACTAGTTTTATTTAAAAATAACAAA
*
51651 AGGCCCAACAGCTAGTCAAGGA-TAGTTTTATTTAAAAATAACAAA
1 AGGCCCAACAGCTAGTC-ACGACTAGTTTTATTTAAAAATAACAAA
51696 AG
1 AG
51698 TAGTACCGAT
Statistics
Matches: 87, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
45 83 0.95
46 4 0.05
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (45 bp):
AGGCCCAACAGCTAGTCACGACTAGTTTTATTTAAAAATAACAAA
Found at i:52990 original size:87 final size:86
Alignment explanation
Indices: 52800--53278 Score: 574
Period size: 87 Copynumber: 5.5 Consensus size: 86
52790 GAGCATGCAA
* * * * * *
52800 AAACGGTAAGGTCTTACCCTTTCACATAGT-AAAAGAGCCT-GGGAAACGGTAAGGTCTTACCCT
1 AAACTGTAAGG-CTTACCCTTGCACACA-TCAAAGGAACCTGGGGAAACTGTAAGG-CTTACCCT
*
52863 TTCACACA-ACAAAGGAACCTGGGG
63 TGCACACAGA-AAAGGAACCTGGGG
* *
52887 AAAACTGTAAGGCTTACCCTTGCATACATCAAAGGAACCTTGGGGAAAATGTAAGGCTTACCCTT
1 -AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACC-TGGGGAAACTGTAAGGCTTACCCTT
* *
52952 GCACATAGAAAAGGAACCTGTGG
64 GCACACAGAAAAGGAACCTGGGG
* *
52975 AAACTGTAAGGCTTACCATTGCACACAGCAAAGGAACCTAGGGGAAACTGTAAGGCTTACCCTTG
1 AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCT-GGGGAAACTGTAAGGCTTACCCTTG
* *
53040 CACACAGCAAAGGAACCTTGGG
65 CACACAGAAAAGGAACCTGGGG
* * * * * *
53062 AAACTATAAGGCTTACCTTTCCACACAACAAATGAACCTGAGGAAACTGTAAGGCTTACCCTTGC
1 AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
*
53127 ACACA-ACAAAGGAACTTGGGGG
66 ACACAGA-AAAGGAACCT-GGGG
* *
53149 AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGAGGAAACT-TAAGGCTTACCCATGC
1 AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
* * *
53213 ACAAAGCAAAGGAACTTGGGG
66 ACACAGAAAAGGAACCTGGGG
*
53234 AAACTGTAAGGCTTACCCTTGCACACGGT-AAAGGAACCTGGGGAA
1 AAACTGTAAGGCTTACCCTTGCACAC-ATCAAAGGAACCTGGGGAA
53279 CCTGGGGATT
Statistics
Matches: 344, Mismatches: 38, Indels: 21
0.85 0.09 0.05
Matches are distributed among these distances:
85 45 0.13
86 71 0.21
87 177 0.51
88 38 0.11
89 13 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (86 bp):
AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
ACACAGAAAAGGAACCTGGGG
Found at i:53276 original size:43 final size:43
Alignment explanation
Indices: 52800--53278 Score: 602
Period size: 43 Copynumber: 11.0 Consensus size: 43
52790 GAGCATGCAA
* * * * * *
52800 AAACGGTAAGGTCTTACCCTTTCACATAGTAAAAGAGCCT-GGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * *
52843 AAACGGTAAGGTCTTACCCTTTCACACAACAAAGGAACCTGGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
52887 AAAACTGTAAGGCTTACCCTTGCATACATCAAAGGAACCTTGGGG
1 -AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACC-TGGGG
* * * *
52932 AAAATGTAAGGCTTACCCTTGCACATAGAAAAGGAACCTGTGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
*
52975 AAACTGTAAGGCTTACCATTGCACACAGCAAAGGAACCTAGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGG
*
53019 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * * * *
53062 AAACTATAAGGCTTACCTTTCCACACAACAAATGAACCTGAGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
53105 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACTTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGG
* *
53149 AAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGAGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * *
53192 AAACT-TAAGGCTTACCCATGCACAAAGCAAAGGAACTTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
53234 AAACTGTAAGGCTTACCCTTGCACACGGTAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
53277 AA
1 AA
53279 CCTGGGGATT
Statistics
Matches: 382, Mismatches: 48, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
42 37 0.10
43 189 0.49
44 141 0.37
45 15 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (43 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
Found at i:55236 original size:19 final size:20
Alignment explanation
Indices: 55196--55237 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
55186 GTTAACTAAC
*
55196 TAAAAAGGAAATAAACAGAA
1 TAAAAAGGAAATAAACACAA
55216 TAAAAA-GAAAT-AACAACAA
1 TAAAAAGGAAATAAAC-ACAA
55235 TAA
1 TAA
55238 CACCTGTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (20 bp):
TAAAAAGGAAATAAACACAA
Found at i:60618 original size:19 final size:19
Alignment explanation
Indices: 60594--60634 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
60584 TCAACACAAC
*
60594 ATATGCACTAAACGAAGGT
1 ATATGCACCAAACGAAGGT
60613 ATATGCACCAAACGAAGGT
1 ATATGCACCAAACGAAGGT
60632 ATA
1 ATA
60635 AATATTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (19 bp):
ATATGCACCAAACGAAGGT
Done.