Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007236.1 Hibiscus syriacus cultivar Beakdansim tig00019159_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: 81344
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9453 original size:18 final size:18
Alignment explanation
Indices: 9421--9455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9411 TTCTTAATTG
* *
9421 AGTAGAGTCGGATTTTGA
1 AGTAGAGTAGAATTTTGA
9439 AGTAGAGTAGAATTTTG
1 AGTAGAGTAGAATTTTG
9456 TTATTCGCTA
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:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (18 bp):
AGTAGAGTAGAATTTTGA
Found at i:10319 original size:23 final size:23
Alignment explanation
Indices: 10292--10338 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
10282 TATAAAATAT
10292 ATAAAACTCATT-TGTGTATATAA
1 ATAAAACTC-TTCTGTGTATATAA
*
10315 ATAAATCTCTTCTGTGTATATAA
1 ATAAAACTCTTCTGTGTATATAA
10338 A
1 A
10339 ATGGACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
ATAAAACTCTTCTGTGTATATAA
Found at i:18460 original size:38 final size:38
Alignment explanation
Indices: 18415--18509 Score: 172
Period size: 38 Copynumber: 2.5 Consensus size: 38
18405 TGATTTAATT
18415 AGTATTACTATTGTTTTCATTCTTTCTTTTTAATAGAA
1 AGTATTACTATTGTTTTCATTCTTTCTTTTTAATAGAA
*
18453 ATTATTACTATTGTTTTCATTCTTTCTTTTTAATAGAA
1 AGTATTACTATTGTTTTCATTCTTTCTTTTTAATAGAA
*
18491 AGTATTAGTATTGTTTTCA
1 AGTATTACTATTGTTTTCA
18510 ATTTATATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.56
Consensus pattern (38 bp):
AGTATTACTATTGTTTTCATTCTTTCTTTTTAATAGAA
Found at i:19505 original size:55 final size:55
Alignment explanation
Indices: 19444--19547 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
19434 TGCATAGTAG
*** *
19444 ATAGATGAGGAGGGATTGATAGTGCGATTATCCTATTTTTAAAAGATGATAGCAA
1 ATAGATGAGGAGGGACCAATAGTGCGATTATACTATTTTTAAAAGATGATAGCAA
*
19499 ATAGATGAGGAGGTACCAATAGTGCGATTATACTATTTTTAAAAGATGA
1 ATAGATGAGGAGGGACCAATAGTGCGATTATACTATTTTTAAAAGATGA
19548 GAGCTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (55 bp):
ATAGATGAGGAGGGACCAATAGTGCGATTATACTATTTTTAAAAGATGATAGCAA
Found at i:21325 original size:32 final size:32
Alignment explanation
Indices: 21289--21403 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 32
21279 AAATATTAGT
* * *
21289 AGTGTTACATTCAAATAATGCATATCAATGTC
1 AGTGTCACATTCAGATAATGCATAACAATGTC
** * * *
21321 AGTGTTGCATTTAGATAATACATAACAGTGTC
1 AGTGTCACATTCAGATAATGCATAACAATGTC
* * *
21353 AGTGTCACTTTTAGATAATGCACAACAATGTC
1 AGTGTCACATTCAGATAATGCATAACAATGTC
* *
21385 ATTGTCGCATTCAGATAAT
1 AGTGTCACATTCAGATAAT
21404 ACGCAACAGT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
AGTGTCACATTCAGATAATGCATAACAATGTC
Found at i:21395 original size:64 final size:64
Alignment explanation
Indices: 21303--21422 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 64
21293 TTACATTCAA
* * * * *
21303 ATAATGCATATCAATGTCAGTGTTGCATTTAGATAATACATAACAGTGTCAGTGTCACTTTTAG
1 ATAATGCACAACAATGTCAGTGTCGCATTCAGATAATACACAACAGTGTCAGTGTCACTTTTAG
* * *
21367 ATAATGCACAACAATGTCATTGTCGCATTCAGATAATACGCAACAGTGTTAGTGTC
1 ATAATGCACAACAATGTCAGTGTCGCATTCAGATAATACACAACAGTGTCAGTGTC
21423 GCATTGAACG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (64 bp):
ATAATGCACAACAATGTCAGTGTCGCATTCAGATAATACACAACAGTGTCAGTGTCACTTTTAG
Found at i:21411 original size:32 final size:32
Alignment explanation
Indices: 21314--21427 Score: 129
Period size: 32 Copynumber: 3.6 Consensus size: 32
21304 TAATGCATAT
* *
21314 CAATGTCAGTGTTGCATTTAGATAATACATAA
1 CAATGTCAGTGTCGCATTTAGATAATACACAA
* * * *
21346 CAGTGTCAGTGTCACTTTTAGATAATGCACAA
1 CAATGTCAGTGTCGCATTTAGATAATACACAA
* * *
21378 CAATGTCATTGTCGCATTCAGATAATACGCAA
1 CAATGTCAGTGTCGCATTTAGATAATACACAA
* *
21410 CAGTGTTAGTGTCGCATT
1 CAATGTCAGTGTCGCATT
21428 GAACGTTTAT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
CAATGTCAGTGTCGCATTTAGATAATACACAA
Found at i:22087 original size:31 final size:31
Alignment explanation
Indices: 22047--22132 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
22037 AATTAACGTG
22047 TTTAATACCTAAACTATCAATTTTGATTCAT
1 TTTAATACCTAAACTATCAATTTTGATTCAT
* * * *
22078 TTTAGTACCTAAACTATTAGTTTTGATTCGT
1 TTTAATACCTAAACTATCAATTTTGATTCAT
* *
22109 TTTAATACCTAAACTTTCATTTTT
1 TTTAATACCTAAACTATCAATTTT
22133 TTCAAAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTAATACCTAAACTATCAATTTTGATTCAT
Found at i:28256 original size:26 final size:24
Alignment explanation
Indices: 28227--28299 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 24
28217 TTAAAATCAT
28227 AATATTGTATATATATTAACTTAAAA
1 AATATT-T-TATATATTAACTTAAAA
*
28253 AATATTTTTTATATTAACTTATTAAA
1 AATATTTTATATATTAACTTA--AAA
*
28279 TATATTTTAT-TATTAACTTAA
1 AATATTTTATATATTAACTTAA
28300 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.02
24 13 0.31
25 11 0.26
26 17 0.40
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (24 bp):
AATATTTTATATATTAACTTAAAA
Found at i:28336 original size:54 final size:53
Alignment explanation
Indices: 28241--28364 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 53
28231 TTGTATATAT
* ** *
28241 ATTAACTTAAAAAATATTTTTTATATTAACTTATTAAATATATTTTAT-TATTAA
1 ATTAA-TTTAAAAATATTTTTTATATTAACTTAAAAAATATATTTTATGT-TAAA
* * * *
28295 CTTAATTTAAAAATATTTTTTATTTTCATTTAAAAATATATATTTTATGTTAAA
1 ATTAATTTAAAAATATTTTTTATATTAACTTAAAAA-ATATATTTTATGTTAAA
*
28349 ATTTATTTAAAAATAT
1 ATTAATTTAAAAATAT
28365 GACTAAATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
53 25 0.43
54 32 0.55
55 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (53 bp):
ATTAATTTAAAAATATTTTTTATATTAACTTAAAAAATATATTTTATGTTAAA
Found at i:28352 original size:27 final size:23
Alignment explanation
Indices: 28250--28353 Score: 64
Period size: 27 Copynumber: 4.0 Consensus size: 23
28240 TATTAACTTA
*
28250 AAAAATATTTTTTATATTAACTTATT
1 AAAAATATTTTTTAT-TTAA-AT-TT
* *
28276 AAATATATTTTATTATTAACTTAATTT
1 AAAAATATTTT-TTATT---TAAATTT
**
28303 AAAAATATTTTTTATTTTCATTT
1 AAAAATATTTTTTATTTAAATTT
28326 AAAAATATATATTTTATGTTAAAATTT
1 AAAAATAT-T-TTTTAT-TT-AAATTT
28353 A
1 A
28354 TTTAAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
23 14 0.22
24 1 0.02
25 6 0.10
26 18 0.29
27 21 0.33
28 1 0.02
29 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (23 bp):
AAAAATATTTTTTATTTAAATTT
Found at i:34283 original size:14 final size:14
Alignment explanation
Indices: 34264--34302 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
34254 TAATGGGAAT
34264 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
34278 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
34292 GAATCTCTGCA
1 TAATCCCTGCA
34303 TATAGACATA
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:46735 original size:44 final size:44
Alignment explanation
Indices: 46672--46759 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
46662 GTAAGAAAAA
*
46672 ACAAAAAAGACAGATTACCAAAACTTATGTACAAATACATATCT
1 ACAAAAAAGACAGATTACCAAAACTTATGCACAAATACATATCT
*
46716 ACAAAAAAGACAGATTACCAAAACTTGTGCACAAATACATATCT
1 ACAAAAAAGACAGATTACCAAAACTTATGCACAAATACATATCT
46760 TTGTTCACAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (44 bp):
ACAAAAAAGACAGATTACCAAAACTTATGCACAAATACATATCT
Found at i:48792 original size:26 final size:26
Alignment explanation
Indices: 48758--48810 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
48748 TTGGGGTCTA
48758 TCATCTATGTTACTTAGATTAGGGTG
1 TCATCTATGTTACTTAGATTAGGGTG
48784 TCATCTATGTTACTTAGATTAGGGTG
1 TCATCTATGTTACTTAGATTAGGGTG
48810 T
1 T
48811 AAGTGTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (26 bp):
TCATCTATGTTACTTAGATTAGGGTG
Found at i:50573 original size:2 final size:2
Alignment explanation
Indices: 50566--50591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50556 ATTTTATCTA
50566 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
50592 GAGTTAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53188 original size:19 final size:21
Alignment explanation
Indices: 53160--53199 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
53150 TATATAACAT
*
53160 TTAATTTTAA-ATT-TGAATA
1 TTAATATTAATATTATGAATA
53179 TTAATATTAATATTATGAATA
1 TTAATATTAATATTATGAATA
53200 AAGTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTAATATTAATATTATGAATA
Found at i:54173 original size:40 final size:40
Alignment explanation
Indices: 54117--54196 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
54107 TAAATTTGTG
54117 TAAAACTAAAGAGTTTTATATTATATAACAATATCATATC
1 TAAAACTAAAGAGTTTTATATTATATAACAATATCATATC
* * *
54157 TAAAACTAAAGTGTTTTATATTGTGTAACAATATCATATC
1 TAAAACTAAAGAGTTTTATATTATATAACAATATCATATC
54197 CCATATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (40 bp):
TAAAACTAAAGAGTTTTATATTATATAACAATATCATATC
Found at i:55717 original size:20 final size:20
Alignment explanation
Indices: 55692--55735 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
55682 TATTGCTTGG
55692 GGATGATGGAGAACAATGGA
1 GGATGATGGAGAACAATGGA
55712 GGATGATGGAGAACAATGGA
1 GGATGATGGAGAACAATGGA
55732 GGAT
1 GGAT
55736 CAGTGGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.41, T:0.16
Consensus pattern (20 bp):
GGATGATGGAGAACAATGGA
Found at i:68167 original size:17 final size:18
Alignment explanation
Indices: 68147--68180 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
68137 AAATATTTAA
*
68147 TTTGTAAGTTA-ATTTTC
1 TTTGAAAGTTACATTTTC
68164 TTTGAAAGTTACATTTT
1 TTTGAAAGTTACATTTT
68181 TTGAGAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (18 bp):
TTTGAAAGTTACATTTTC
Found at i:70709 original size:18 final size:20
Alignment explanation
Indices: 70659--70709 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
70649 TTTTATTATT
70659 TTATTTTATTA-TTTAGAGA
1 TTATTTTATTATTTTAGAGA
* *
70678 TTAATTTATGATTTTAGA-A
1 TTATTTTATTATTTTAGAGA
70697 -TATTTTATTATTT
1 TTATTTTATTATTT
70710 ATTGACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.41
19 10 0.37
20 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TTATTTTATTATTTTAGAGA
Found at i:71540 original size:19 final size:19
Alignment explanation
Indices: 71516--71555 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
71506 AATAAACTTC
71516 ATCTTGATTAGTTATAACG
1 ATCTTGATTAGTTATAACG
71535 ATCTTGATTAGTTATAACG
1 ATCTTGATTAGTTATAACG
71554 AT
1 AT
71556 GCCAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (19 bp):
ATCTTGATTAGTTATAACG
Found at i:72396 original size:29 final size:29
Alignment explanation
Indices: 72351--72408 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
72341 GTGTTGGCCG
*
72351 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
72380 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
72409 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:72470 original size:14 final size:14
Alignment explanation
Indices: 72451--72478 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
72441 CGCTGGGCAT
72451 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
72465 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
72479 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:72490 original size:20 final size:20
Alignment explanation
Indices: 72465--72519 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
72455 GGCCATCCGA
72465 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
72485 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
72505 CCAAGGCCATCCGAA
1 CCGAGGCCATCCGAA
72520 CGAGCTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.36, G:0.25, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:72544 original size:10 final size:10
Alignment explanation
Indices: 72445--72585 Score: 66
Period size: 10 Copynumber: 13.1 Consensus size: 10
72435 CCAACACGCT
72445 GGGCATCCGA
1 GGGCATCCGA
*
72455 GGCCATCCGA
1 GGGCATCCGA
72465 CCGAGGCCATCCGA
1 --G-GG-CATCCGA
**
72479 AAGCATCCGA
1 GGGCATCCGA
*
72489 GGCCATCCGA
1 GGGCATCCGA
* *
72499 GAGCATCCAA
1 GGGCATCCGA
*
72509 GGCCATCCGAA
1 GGGCATCCG-A
* *
72520 CGAGCTATGCGA
1 -GGGC-ATCCGA
72532 GGGCATCCGA
1 GGGCATCCGA
*
72542 GGGCAACCGA
1 GGGCATCCGA
**
72552 GTGAGCTATGTGA
1 G-G-GC-ATCCGA
*
72565 GGGAATCCGA
1 GGGCATCCGA
*
72575 GGGCAACCGA
1 GGGCATCCGA
72585 G
1 G
72586 CGAGGGTAGG
Statistics
Matches: 94, Mismatches: 27, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
10 64 0.68
11 7 0.07
12 7 0.07
13 9 0.10
14 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.33, T:0.11
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:72558 original size:33 final size:33
Alignment explanation
Indices: 72521--72585 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
72511 CCATCCGAAC
*
72521 GAGCTATGCGAGGGCATCCGAGGGCAACCGAGT
1 GAGCTATGCGAGGGAATCCGAGGGCAACCGAGT
*
72554 GAGCTATGTGAGGGAATCCGAGGGCAACCGAG
1 GAGCTATGCGAGGGAATCCGAGGGCAACCGAG
72586 CGAGGGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.40, T:0.12
Consensus pattern (33 bp):
GAGCTATGCGAGGGAATCCGAGGGCAACCGAGT
Found at i:72625 original size:29 final size:29
Alignment explanation
Indices: 72591--72647 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
72581 CCGAGCGAGG
*
72591 GTAGGTCGCCCGGAGTGCATGGCGACCTT
1 GTAGGTCGCCCGGAGGGCATGGCGACCTT
72620 GTAGGTCGCCCGGAGGGCATGGCGACCT
1 GTAGGTCGCCCGGAGGGCATGGCGACCT
72648 ATGTGTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.18
Consensus pattern (29 bp):
GTAGGTCGCCCGGAGGGCATGGCGACCTT
Found at i:72753 original size:29 final size:29
Alignment explanation
Indices: 72707--72763 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
72697 GAGCAAGGGT
72707 AGGTCGCCCGGAGTGCATGACGACCTACA
1 AGGTCGCCCGGAGTGCATGACGACCTACA
*
72736 AGGTCGCCCGGAAG-GCATGTCGACCTAC
1 AGGTCGCCCGG-AGTGCATGACGACCTAC
72764 GACCAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGACGACCTACA
Found at i:73544 original size:2 final size:2
Alignment explanation
Indices: 73537--73570 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
73527 TCTGACCTAA
73537 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
73571 TATTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74781 original size:35 final size:36
Alignment explanation
Indices: 74733--74813 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
74723 AACACAATCA
* *
74733 TCAATTATATTCTAAACCTCAAATTCC-AAAATGCT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
*
74768 TTAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
74804 TCAATTACAT
1 TCAATTACAT
74814 GCCCAACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 25 0.61
36 16 0.39
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
Found at i:74827 original size:36 final size:35
Alignment explanation
Indices: 74746--74829 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 35
74736 ATTATATTCT
* * * *
74746 AAACCTCAAATTCCAAAATGCTTTAATTACATTCT
1 AAACCTCAAATTCCAAAATACTTCAATTACATGCC
74781 AAACCTCAAATTCCAAAAATACTTCAATTACATGCC
1 AAACCTCAAATTCC-AAAATACTTCAATTACATGCC
* *
74817 CAACCCCAAATTC
1 AAACCTCAAATTC
74830 ATAATCCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 14 0.33
36 28 0.67
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (35 bp):
AAACCTCAAATTCCAAAATACTTCAATTACATGCC
Found at i:75491 original size:147 final size:147
Alignment explanation
Indices: 75311--75601 Score: 492
Period size: 147 Copynumber: 2.0 Consensus size: 147
75301 AAACTATTTA
*
75311 AATTAGAATCAAATAATATTATAATATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
*
75376 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTCGAGTCAACTA
66 AATTCAATTCAATTAGACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTCGAGTCAACTA
75441 TTTTATAAACTGAACTG
131 TTTTATAAACTGAACTG
* * *
75458 AATTATAATCACATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* ** * *
75523 AATTCAATTCAATTAGATTTGATTTAAATTTTATAAACTCAAATCGAAAAATTTTGAGTCAACTA
66 AATTCAATTCAATTAGACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTCGAGTCAACTA
75588 TTTTATAAACTGAA
131 TTTTATAAACTGAA
75602 TTGAGTATTT
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 134 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (147 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTAGACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTCGAGTCAACTA
TTTTATAAACTGAACTG
Found at i:75797 original size:35 final size:35
Alignment explanation
Indices: 75758--75834 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
75748 GTTGGTTATG
75758 TAATTGAAATATTTTGGGAT-TTGAGGTTTAGAATA
1 TAATTGAAATATTTT-GGATCTTGAGGTTTAGAATA
* * * *
75793 TAATTTAAGTATTTTGGATCTTGATGTTTAGAATG
1 TAATTGAAATATTTTGGATCTTGAGGTTTAGAATA
75828 TAATTGA
1 TAATTGA
75835 TGAATGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (35 bp):
TAATTGAAATATTTTGGATCTTGAGGTTTAGAATA
Found at i:76709 original size:2 final size:2
Alignment explanation
Indices: 76704--76734 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76694 TGAAATAACC
76704 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
76735 GAAATATCCA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.