Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009409.1 Hibiscus syriacus cultivar Beakdansim tig00113344_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: 23053
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2019 original size:2 final size:2
Alignment explanation
Indices: 2012--2057 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2002 TTAATAATAC
2012 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
2054 AT AT
1 AT AT
2058 TCAATTACCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3646 original size:179 final size:178
Alignment explanation
Indices: 3339--3695 Score: 477
Period size: 179 Copynumber: 2.0 Consensus size: 178
3329 TGCCTATGCT
* *
3339 CGTGCCTTCAAAACTTTGTGTGATCAACTACATGCAATCGGTCGTCCAGTTGATGGAACCGATAA
1 CGTGCCTTCAAAACTTTGTGTGACCAACTACATGCAATCGGTCGTCCAGTTAATGGAACCGATAA
** * * *
3404 AGTCCATTGGTTCTTGTGTGGTTTCGGTCCCGATTTATCCAGCTTCTCTACTGCCCAGATGGCAC
66 AGTCCATTGGTTCTTACGTGGTCTCGGTCCAGATTTATCCAGCTTCTCCACTGCCCAGATGGCAC
* * ** *
3469 ATACCCTATCTCCTATTTTTCT-GATCTTGTGTCTAAAGCAGAGAGTTTTGA
131 AAACCC-ATCCCCTATTTTT-TGGATC-T-TAACTAAAGCAAAGAGTTTTGA
* * * * *
3520 CGTGTCTTCAAAACTTTGTGTGACCAACTACATGTAATCGGTCG-CCGGTTAATGGAACTGA-CA
1 CGTGCCTTCAAAACTTTGTGTGACCAACTACATGCAATCGGTCGTCCAGTTAATGGAACCGATAA
* *
3583 AGTCTATTGGTTCTTACGTGGTCTCGGTCCAGATTTCTCCAGCTTCTCCACTGCCCAGATGGCAC
66 AGTCCATTGGTTCTTACGTGGTCTCGGTCCAGATTTATCCAGCTTCTCCACTGCCCAGATGGCAC
*
3648 AAACCCCTCCCCTATTTTTTGGATCTTAACTAAAGCAAAGAGTTTTGA
131 AAACCCATCCCCTATTTTTTGGATCTTAACTAAAGCAAAGAGTTTTGA
3696 AATTTTTCAA
Statistics
Matches: 155, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
176 19 0.12
177 2 0.01
178 15 0.10
179 64 0.41
180 14 0.09
181 41 0.26
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (178 bp):
CGTGCCTTCAAAACTTTGTGTGACCAACTACATGCAATCGGTCGTCCAGTTAATGGAACCGATAA
AGTCCATTGGTTCTTACGTGGTCTCGGTCCAGATTTATCCAGCTTCTCCACTGCCCAGATGGCAC
AAACCCATCCCCTATTTTTTGGATCTTAACTAAAGCAAAGAGTTTTGA
Found at i:4614 original size:21 final size:21
Alignment explanation
Indices: 4588--4641 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
4578 TACACTACAT
4588 GAACCGATTCCCTATGAGGGG
1 GAACCGATTCCCTATGAGGGG
*
4609 GAACCGATTCCTTATGAGGGG
1 GAACCGATTCCCTATGAGGGG
*
4630 GTACCGATTCCC
1 GAACCGATTCCC
4642 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (21 bp):
GAACCGATTCCCTATGAGGGG
Found at i:10287 original size:23 final size:23
Alignment explanation
Indices: 10247--10328 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
10237 TCTGGCGGGA
*
10247 GGAATCGA-TACCCCTTTGAAGG
1 GGAATCGATTCCCCCTTTGAAGG
*
10269 GGAA-CTGATTCCCCCTTTGAATG
1 GGAATC-GATTCCCCCTTTGAAGG
** *
10292 GGAATCGATTCCCCCCCTGTA-G
1 GGAATCGATTCCCCCTTTGAAGG
*
10314 GGAATCGATACCCCC
1 GGAATCGATTCCCCC
10329 CCACGGGGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 21 0.41
23 28 0.55
24 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (23 bp):
GGAATCGATTCCCCCTTTGAAGG
Found at i:14359 original size:20 final size:20
Alignment explanation
Indices: 14336--14387 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
14326 AACGCGATCC
14336 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
14356 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
14376 CCAAAATCGCAA
1 CCAGAATCGCAA
14388 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:14404 original size:21 final size:20
Alignment explanation
Indices: 14377--14475 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
14367 AATCAGTTTC
14377 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
14398 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
14419 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
14439 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
14460 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
14476 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:14504 original size:20 final size:20
Alignment explanation
Indices: 14442--14635 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
14432 CGATTTTCCA
* ** *
14442 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
14462 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
14482 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
14502 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
14522 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
14542 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
14562 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
14582 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
14602 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
14623 AAATCGCAACGCG
1 AAATCGCAACGCG
14636 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:14526 original size:60 final size:60
Alignment explanation
Indices: 14442--14635 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
14432 CGATTTTCCA
* ** * *
14442 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
14502 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
14562 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
14623 AAATCGCAACGCG
1 AAATCGCAACGCG
14636 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:15056 original size:32 final size:33
Alignment explanation
Indices: 15014--15083 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
15004 TTCACTTAGA
15014 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
15047 TTTCA-TTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
15079 TTTCA
1 TTTCA
15084 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:15223 original size:14 final size:14
Alignment explanation
Indices: 15204--15257 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
15194 AGAATGACTG
15204 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
15218 TCGCAACGCGAAATGGAA
1 TCGCAA--CGAGA--GAA
*
15236 TTGCAACGAGAGAA
1 TCGCAACGAGAGAA
15250 TCGCAACG
1 TCGCAACG
15258 CGAAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 16 0.50
16 8 0.25
18 8 0.25
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:15291 original size:19 final size:19
Alignment explanation
Indices: 15269--15366 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
15259 GAAACCAAAA
*
15269 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
15288 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
15302 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
15321 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
15335 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
15354 TCGCGTTGCGATT
1 TCGCGTTGCGATT
15367 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:15310 original size:14 final size:14
Alignment explanation
Indices: 15291--15380 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
15281 TTTCATTTCG
15291 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
15305 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
15324 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
15338 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
15355 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
15371 CGTTGCGATT
1 CGTTGCGATT
15381 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:15316 original size:33 final size:33
Alignment explanation
Indices: 15274--15388 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
15264 CAAAATCGCA
15274 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
15307 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
15340 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
15373 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
15389 AACCAAAGAC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:15499 original size:45 final size:45
Alignment explanation
Indices: 15450--15535 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
15440 TTTTTATGTT
15450 TATCTAACTTGGTATGTTTATTGTTTTTGTAGAAATTTTTTGGTA
1 TATCTAACTTGGTATGTTTATTGTTTTTGTAGAAATTTTTTGGTA
15495 TATCTAACTTGGTATGTTTATTGTTTTTGTAGAAATTTTTT
1 TATCTAACTTGGTATGTTTATTGTTTTTGTAGAAATTTTTT
15536 TCGGCTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (45 bp):
TATCTAACTTGGTATGTTTATTGTTTTTGTAGAAATTTTTTGGTA
Found at i:17222 original size:92 final size:93
Alignment explanation
Indices: 17064--17436 Score: 690
Period size: 92 Copynumber: 4.1 Consensus size: 93
17054 TAGATTGCTT
17064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
17128 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
17156 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
17220 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
17247 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
17309 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
17336 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC-CTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
17400 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
17428 AGTAAATTT
1 AGTAAATTT
17437 ATCCATTCAA
Statistics
Matches: 275, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
88 11 0.04
89 76 0.28
90 3 0.01
91 79 0.29
92 90 0.33
93 16 0.06
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:17369 original size:180 final size:184
Alignment explanation
Indices: 17064--17436 Score: 686
Period size: 180 Copynumber: 2.0 Consensus size: 184
17054 TAGATTGCTT
17064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
17129 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
17194 TGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 TGTATTCTTTAAC-CTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
17247 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
17309 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
17373 GTGTATTCTTTAACCTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACCTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
17428 AGTAAATTT
1 AGTAAATTT
17437 ATCCATTCAA
Statistics
Matches: 187, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
179 10 0.05
180 87 0.47
181 31 0.17
182 1 0.01
183 47 0.25
184 11 0.06
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACCTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:17503 original size:20 final size:20
Alignment explanation
Indices: 17478--17575 Score: 90
Period size: 19 Copynumber: 5.4 Consensus size: 20
17468 ATAGTTACTT
* *
17478 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
17498 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
17517 TCGC-ACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
*
17535 TCGCAA--CG--A--CAGAA
1 TCGCAACGCGAAACTCAAAA
17549 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
17568 TCGCAACG
1 TCGCAACG
17576 ACAAGATCGC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 17 0.26
19 21 0.32
20 13 0.20
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:17518 original size:19 final size:19
Alignment explanation
Indices: 17478--17604 Score: 107
Period size: 18 Copynumber: 7.3 Consensus size: 19
17468 ATAGTTACTT
* *
17478 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
17498 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
17517 TCGC-ACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
17535 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
17549 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
17568 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
17582 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
17600 TCGCA
1 TCGCA
17605 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 24
0.73 0.08 0.20
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 25 0.29
19 20 0.23
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:17568 original size:33 final size:32
Alignment explanation
Indices: 17514--17604 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
17504 CGCGAAACCA
**
17514 AAATCGC-ACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
17545 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
17578 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
17605 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 15 0.27
33 39 0.71
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:17627 original size:19 final size:19
Alignment explanation
Indices: 17600--17732 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
17590 CGAAACCAAA
*
17600 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17619 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
17635 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
17652 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
17668 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
17685 TCGCGTTGCGATTTT-GTT
1 TCGCGTTGCGATTTTCATT
17703 TCGCGTTGCGATTTT-AGTT
1 TCGCGTTGCGATTTTCA-TT
*
17722 TCGTGTTGCGA
1 TCGCGTTGCGA
17733 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 17 0.18
19 41 0.43
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:17641 original size:14 final size:14
Alignment explanation
Indices: 17622--17678 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
17612 TTTCATTTCG
17622 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
17636 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
17653 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
17669 CGTTGCGATT
1 CGTTGCGATT
17679 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:17647 original size:33 final size:33
Alignment explanation
Indices: 17605--17732 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
17595 CCAAATCGCA
17605 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
17638 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
17671 TTGCGATTTTCATTTCGCGTTGCGATTTTGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTCTTT--CG
*
17708 TTGCGATTTT-AGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
17733 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
33 55 0.65
35 4 0.05
36 1 0.01
37 24 0.29
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:19531 original size:33 final size:37
Alignment explanation
Indices: 19502--19570 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
19492 TATTGATTGT
19502 TTTTTGA-T-TTT-TTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTATTGATTTGTAAAAGTTGATTCAA
*
19536 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTT-ATTGATTTGTAAAAGTTGATT
19571 TGTAAAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 7 0.23
35 1 0.03
36 3 0.10
38 19 0.63
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (37 bp):
TTTTTGATTGTTTATTGATTTGTAAAAGTTGATTCAA
Found at i:19571 original size:14 final size:14
Alignment explanation
Indices: 19552--19587 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
19542 ATTGTTTAAT
19552 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
19566 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
19580 TGATTTGT
1 TGATTTGT
19588 GTTATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:19710 original size:19 final size:19
Alignment explanation
Indices: 19694--19795 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
19684 AAAAATGACT
19694 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
19713 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
19732 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
19746 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
19765 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
19785 ATCGCAATGCG
1 ATCGCAATGCG
19796 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:19844 original size:33 final size:33
Alignment explanation
Indices: 19802--20128 Score: 201
Period size: 33 Copynumber: 9.5 Consensus size: 33
19792 TGCGTTTATA
19802 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
19835 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
19872 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* * *
19907 ATTTCGTATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
19945 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
19978 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
20018 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
20049 A-TTCGCATTGCGA-T-TCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
20079 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
20113 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
20129 GTATTTCCGT
Statistics
Matches: 248, Mismatches: 20, Indels: 52
0.77 0.06 0.16
Matches are distributed among these distances:
30 22 0.09
31 6 0.02
32 11 0.04
33 55 0.22
34 44 0.18
35 16 0.06
36 22 0.09
37 8 0.03
38 52 0.21
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:19848 original size:19 final size:19
Alignment explanation
Indices: 19824--20128 Score: 340
Period size: 19 Copynumber: 17.4 Consensus size: 19
19814 GATTATCTCG
19824 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19843 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19862 TTGCGA-TTTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
19877 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
19896 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
19915 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
19934 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
19953 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
19968 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19986 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
20005 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
20019 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
20038 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
20056 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
20068 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
20088 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
20102 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
20121 TTGCGATT
1 TTGCGATT
20129 GTATTTCCGT
Statistics
Matches: 248, Mismatches: 11, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.02
14 26 0.10
15 8 0.03
16 23 0.09
17 26 0.10
18 21 0.08
19 126 0.51
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:19864 original size:52 final size:52
Alignment explanation
Indices: 19802--20063 Score: 232
Period size: 52 Copynumber: 4.9 Consensus size: 52
19792 TGCGTTTATA
19802 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
19854 ATTTCGCATTGCGATTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATTTC--TCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
* *
19907 ATTTCGTATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTATGTC
1 ATTTCG-ATTGCGA-TTTC---TCG--TTGCGATTTTCATTTCGCATTGCGATTATCTC
** * * * *
19966 GGTTCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
* * * * *
20018 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCA-TTCGCATTGCGATT
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATT
20064 CTCGTTGCGA
Statistics
Matches: 189, Mismatches: 12, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
51 16 0.08
52 75 0.40
53 46 0.24
54 5 0.03
55 5 0.03
57 30 0.16
58 3 0.02
59 9 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
Found at i:22633 original size:24 final size:23
Alignment explanation
Indices: 22593--22638 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
22583 CTGAAACATC
22593 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGTGTATTG-CCAAT
*
22617 ATCAAAGTCCG-GATATTGCCAA
1 ATCAAAATCCGTG-TATTGCCAA
22639 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGTGTATTGCCAAT
Done.