Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000171.1 Hibiscus syriacus cultivar Beakdansim tig00000300_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: 63674
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4146 original size:10 final size:10
Alignment explanation
Indices: 4131--4181 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
4121 ACACGCTGGG
4131 CATCCGAGGC
1 CATCCGAGGC
4141 CATCCGACTGAGGC
1 CAT-C--C-GAGGC
4155 CATCCGAGAG-
1 CATCCGAG-GC
4165 CATCCGAGGC
1 CATCCGAGGC
4175 CATCCGA
1 CATCCGA
4182 ACGAGCTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 21 0.60
11 3 0.09
13 2 0.06
14 8 0.23
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.12
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:4221 original size:33 final size:34
Alignment explanation
Indices: 4165--4252 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 34
4155 CATCCGAGAG
* * *
4165 CATCCGAGGCCATCCGAACGAGCTATGCGA-GGA
1 CATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
*
4198 CATCCGAGGGCAACCGAGTGAGCTATGCGAGGGA
1 CATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
4232 -ATCCGAGGG-AAGCCGAGCGAG
1 CATCCGAGGGCAA-CCGAGCGAG
4253 GGTAGGTCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 43 0.90
34 3 0.06
ACGTcount: A:0.27, C:0.26, G:0.36, T:0.10
Consensus pattern (34 bp):
CATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:4289 original size:29 final size:28
Alignment explanation
Indices: 4256--4310 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
4246 GAGCGAGGGT
* *
4256 AGGTCTCCCAGAGTGCATGGCGACCTACA
1 AGGTCGCCCAGAGGGCATGGCG-CCTACA
*
4285 AGGTCGCCCGGAGGGCATGGCGCCTA
1 AGGTCGCCCAGAGGGCATGGCGCCTA
4311 TGTGTTGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.15
Consensus pattern (28 bp):
AGGTCGCCCAGAGGGCATGGCGCCTACA
Found at i:4431 original size:29 final size:29
Alignment explanation
Indices: 4388--4444 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4378 GAGCAAGGGT
*
4388 AGGTTGCCCGAAGTGCATGGCGACCTACA
1 AGGTCGCCCGAAGTGCATGGCGACCTACA
*
4417 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGAAGTGCATGGCGACCTAC
4445 GGTCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGAAGTGCATGGCGACCTACA
Found at i:5503 original size:58 final size:60
Alignment explanation
Indices: 5441--5573 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 60
5431 ATTGTTTTCT
* *
5441 GACTATAGA-ATGTTGTTTTGTTGAGTCT-TCGA-TAATTAAAAGTTACAAAATAGTC-TCC
1 GACTATA-ATATGTTGTTTTGTTGAATCTCTCGACT-ATTAAAAGTTACAAAATAGTCACCC
* * *
5499 GACTATAATATGTTGTTTTGTTGAATCTCTTGACTCTTGAAAGTTACAAAATAGTCACCC
1 GACTATAATATGTTGTTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATAGTCACCC
*
5559 GACTATTCATATGTT
1 GACTA-TAATATGTT
5574 TTAAACTCGT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.02
58 25 0.39
59 22 0.34
60 8 0.12
61 8 0.12
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (60 bp):
GACTATAATATGTTGTTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATAGTCACCC
Found at i:11106 original size:17 final size:17
Alignment explanation
Indices: 11081--11119 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11071 AGGAAAAGTG
*
11081 AGAAGGAAAGATGGAGA
1 AGAAGGAAAGAAGGAGA
* *
11098 AGAATGAAATAAGGAGA
1 AGAAGGAAAGAAGGAGA
11115 AGAAG
1 AGAAG
11120 ATAAATGATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (17 bp):
AGAAGGAAAGAAGGAGA
Found at i:15392 original size:20 final size:20
Alignment explanation
Indices: 15367--15406 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15357 ATGTTTTACA
15367 TATGTTT-TAGATTCATTTAT
1 TATGTTTGTAGA-TCATTTAT
*
15387 TATGTTTGTATATCATTTAT
1 TATGTTTGTAGATCATTTAT
15407 ATATCATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TATGTTTGTAGATCATTTAT
Found at i:15462 original size:20 final size:21
Alignment explanation
Indices: 15436--15485 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
15426 TCATTCATTC
15436 ATTAGCTCATGTCATG-TTAT
1 ATTAGCTCATGTCATGTTTAT
* *
15456 TTTAGCTCATGTTATGTTTAT
1 ATTAGCTCATGTCATGTTTAT
15477 ATTAGCTCA
1 ATTAGCTCA
15486 CTAGCTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
ATTAGCTCATGTCATGTTTAT
Found at i:18284 original size:20 final size:20
Alignment explanation
Indices: 18259--18308 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
18249 TCTAAGTCAT
18259 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
18279 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
18299 TTTTCAAAAT
1 TTTTCAAAAT
18309 CAACTCTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGA
Found at i:20700 original size:19 final size:20
Alignment explanation
Indices: 20673--20718 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
20663 GGCCAAGAGT
* *
20673 ATGTGTTTTCATT-AAAGTC
1 ATGTATTTTCATTAAAAATC
20692 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATC
20712 ATGTATT
1 ATGTATT
20719 GTCAAAGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATC
Found at i:21565 original size:32 final size:32
Alignment explanation
Indices: 21492--21594 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 32
21482 CCCGAACCCG
* *
21492 ACCCGACCCGACCCGAATATCATACTTAAAAAA
1 ACCCGACTCGACCCGAATATCACACTT-AAAAA
*
21525 ACCTGACTCGACCCGAATATCACACTTAAAAA
1 ACCCGACTCGACCCGAATATCACACTTAAAAA
21557 ACCCGACTCGACCCGAATATCACACTT-AAAA
1 ACCCGACTCGACCCGAATATCACACTTAAAAA
21588 ACCCGAC
1 ACCCGAC
21595 CCGAACAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
31 11 0.17
32 31 0.47
33 24 0.36
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.16
Consensus pattern (32 bp):
ACCCGACTCGACCCGAATATCACACTTAAAAA
Found at i:24623 original size:18 final size:18
Alignment explanation
Indices: 24597--24633 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24587 GCCTGATTAA
* *
24597 TATTTATTTATTTTATTT
1 TATTAATTTATATTATTT
24615 TATTAATTTATATTATTT
1 TATTAATTTATATTATTT
24633 T
1 T
24634 TTTACAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTAATTTATATTATTT
Found at i:24889 original size:19 final size:21
Alignment explanation
Indices: 24853--24895 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
24843 GGGGTAAAAT
*
24853 AATTTTAAAATTAGAAATGAA
1 AATTTTAAAATTAGAAATAAA
*
24874 AATTTT-AATTTA-AAATAAA
1 AATTTTAAAATTAGAAATAAA
24893 AAT
1 AAT
24896 AGTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
AATTTTAAAATTAGAAATAAA
Found at i:27267 original size:45 final size:44
Alignment explanation
Indices: 27217--27447 Score: 189
Period size: 45 Copynumber: 5.1 Consensus size: 44
27207 TAATCCAAGG
* *
27217 CTTTTGATTATTGGATTCCTAAAAGTAAAATAAAAAGATTAGTTC
1 CTTTTGATTATTGGGTTCC-AAAAGTAAAATAAAAGGATTAGTTC
* * * *
27262 ATTTTGATTATTGTGGTGCCAAAAGTAAAATTAAAGGATTAGTCC
1 CTTTTGATTATTG-GGTTCCAAAAGTAAAATAAAAGGATTAGTTC
* * *
27307 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAATTC
1 CTTTTGATTATTGGGTT-CCAAAAGTAAAATAAAAGGATTAGTTC
* * * *
27352 CTTTCGATTACTT--GTTGCAGAAATTAAAATCAAATATGATTAGTTC
1 CTTTTGATTA-TTGGGTTCCA-AAAGTAAAAT-AAA-AGGATTAGTTC
* * * * *
27398 TTTTTGATTATTGGGATGCAAAAATTAAATTCAAAAGG-TTAGTTC
1 CTTTTGATTATTGGG-TTCCAAAAGTAAAAT-AAAAGGATTAGTTC
*
27443 TTTTT
1 CTTTT
27448 TTTTATTATT
Statistics
Matches: 153, Mismatches: 24, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
43 2 0.01
44 16 0.10
45 94 0.61
46 25 0.16
47 14 0.09
48 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (44 bp):
CTTTTGATTATTGGGTTCCAAAAGTAAAATAAAAGGATTAGTTC
Found at i:27336 original size:90 final size:91
Alignment explanation
Indices: 27217--27447 Score: 238
Period size: 91 Copynumber: 2.5 Consensus size: 91
27207 TAATCCAAGG
* * *
27217 CTTTTGATTATTGGATT-CCTAAAAGTAAAATAAAAAGATTAGTTCATTTTGATTA-TTGTGGTG
1 CTTTTGATTATTGGGTTGCC-AAAATTAAAATCAAAAGATTAGTTCATTTTGATTACTTGT--TG
*
27280 CCA-AAAGTAAAAT-TAA-AGGATTAGTCC
63 -CAGAAAGTAAAATCAAATAGGATTAGTCC
* * * *
27307 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAATTCCTTTCGATTACTTGTTGCAG
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAAGATTAGTTCATTTTGATTACTTGTTGCAG
* * *
27372 AAATTAAAATCAAATATGATTAGTTC
66 AAAGTAAAATCAAATAGGATTAGTCC
* * * * * *
27398 TTTTTGATTATTGGGATGCAAAAATTAAATTCAAAAGGTTAGTTCTTTTT
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAAGATTAGTTCATTTT
27448 TTTTATTATT
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
88 2 0.02
89 11 0.09
90 47 0.41
91 56 0.48
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (91 bp):
CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAAGATTAGTTCATTTTGATTACTTGTTGCAG
AAAGTAAAATCAAATAGGATTAGTCC
Found at i:33002 original size:57 final size:58
Alignment explanation
Indices: 32864--33589 Score: 490
Period size: 58 Copynumber: 12.4 Consensus size: 58
32854 TTTGTAAGGG
* * * *
32864 AAATAAATCGTTGAATTTATTTTCTTAAGAATCTCGAATGATTTTATCTTT-TAAAA-A
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTAT-TTTGTAAAAGA
* * * * * *
32921 GAGATAACTTATTGAATTT-GTTTCTTGAGAATCTTGAATGATTCTATTTTATAAAATA
1 -AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
* ** * * * ** *
32979 AAAT-ATTTTTTTAATTTATTTTCTTGAGAATCTTAAATGAATCTATCGTGTAAAAGG
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
* * * * * * * **
33036 AAGT-AATCGTTGAATTTATTTTATAGTGGATCTT-ACATGATTTTGGTTTGTAAAA-A
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGA-ATGATTCTATTTTGTAAAAGA
* * * *
33092 TAAATAAATCATTTAATTTATTTTCTT-ATAAATCTTAAATGATTCTATTTTTTCTATTTTGTAT
1 -AAATAAATCATTGAATTTATTTTCTTGA-GAATCTTGAATG-----A----TTCTATTTTGTAA
33156 AAGA
55 AAGA
* * * **
33160 AAATAAATCATTTAATTTATTTTCATGTGAATCTT-ATATGATTCTAACTTGTAAAAGGA
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGA-ATGATTCTATTTTGTAAAA-GA
* * * * * * * *
33219 AAA-AAGTCGTCGAATTTATTTTCTTGGGAATATTGAATCATTTTTATTTTATAAAATG-
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGA-TTCTATTTTGTAAAA-GA
* ** * * * * * * *
33277 AAATAATTTGTT-AAGTTTATTTTCCTGCGAAT-TTTATATGTTTTTAGTTTGTAAAAGG
1 AAATAAATCATTGAA-TTTATTTTCTTGAGAATCTTGA-ATGATTCTATTTTGTAAAAGA
** *
33335 AAATAAATCATCAAATTTATTTTCTTGAGAATCTTGAATGATTATATTTTGTAAAAGA
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
* * * * * * *
33393 AAATAAATCGTTTAATTTATTTTCTTAAGAATCTTTAATTATTATATTTTGTAAAATA
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
* * * * *
33451 AAATAAATCATTGAATTTATTTTCTTAAGAATCCTAAATTATTCTATTTTGTAAAAGG
1 AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
* * * *
33509 AAATAAAT-AGTTGAATTTATTTTCTTAAGAATCTTGAATTATCCTATTTTGTAAAAGG
1 AAATAAATCA-TTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
*
33567 GAATAAATCATTGAATTTATTTT
1 AAATAAATCATTGAATTTATTTT
33590 ACTATAAATC
Statistics
Matches: 531, Mismatches: 106, Indels: 62
0.76 0.15 0.09
Matches are distributed among these distances:
56 14 0.03
57 106 0.20
58 315 0.59
59 47 0.09
62 1 0.00
63 1 0.00
66 1 0.00
67 45 0.08
68 1 0.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (58 bp):
AAATAAATCATTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTTTGTAAAAGA
Found at i:33533 original size:174 final size:175
Alignment explanation
Indices: 32864--33626 Score: 583
Period size: 174 Copynumber: 4.3 Consensus size: 175
32854 TTTGTAAGGG
* *
32864 AAATAAATCGTTGAATTTATTTTCTTAAGAATCTCGAATGATTTTATCTTT-TAAAAAGAGATAA
1 AAATAAATCGTTGAATTTATTTTCTTAAGAATCTTGAATGATTTTAT-TTTGTAAAAAGAAATAA
* * * * * * * * * **
32928 CTTATTGAATTT-GTTTCTTGAGAATCTTGAAT-GATTCTATTTTATAAAATAAAAT-ATTTTTT
65 ATCATTGAATTTATTTTCTTAAGAATCTTAAATCTATTCTATTTTGTAAAAGAAAATAAATCATT
* * * *
32990 TAATTTATTTTCTTGAGAATCTTAAATGAATCTATCGTGTAAAAGG
130 TAATTTATTTTCTTGAGAATCTTGAATGATTCTATCTTGTAAAAGA
* * * * ** *
33036 AAGT-AATCGTTGAATTTATTTT-ATAGTGGATCTT-ACATGATTTTGGTTTGTAAAAATAAATA
1 AAATAAATCGTTGAATTTATTTTCTTA-AGAATCTTGA-ATGATTTTATTTTGTAAAAAGAAATA
* *
33098 AATCATTTAATTTATTTTCTTATA-AATCTTAAATGATTCTATTTTTTCTATTTTGTATAAGAAA
64 AATCATTGAATTTATTTTCTTA-AGAATCTT-AA--A-TCTA----TTCTATTTTGTAAAAGAAA
* * *
33162 ATAAATCATTTAATTTATTTTCATGTGAATCTT-ATATGATTCTAACTTGTAAAAGGA
120 ATAAATCATTTAATTTATTTTCTTGAGAATCTTGA-ATGATTCTATCTTGTAAAA-GA
* * ** * * * *
33219 AAA-AAGTCGTCGAATTTATTTTCTTGGGAATATTGAATCATTTTTATTTTATAAAATGAAATAA
1 AAATAAATCGTTGAATTTATTTTCTTAAGAATCTTGAATGA-TTTTATTTTGTAAAAAGAAATAA
* ** * ** * * * * * *
33283 TTTGTT-AAGTTTATTTTCCTGCGAATTTTATATGT-TTTTAGTTTGTAAAAGGAAATAAATCAT
65 ATCATTGAA-TTTATTTTCTTAAGAATCTTAAATCTATTCTATTTTGTAAAAGAAAATAAATCAT
** * *
33346 CAAATTTATTTTCTTGAGAATCTTGAATGATTATATTTTGTAAAAGA
129 TTAATTTATTTTCTTGAGAATCTTGAATGATTCTATCTTGTAAAAGA
* * * *
33393 AAATAAATCGTTTAATTTATTTTCTTAAGAATCTTTAATTATTATATTTTGTAAAATA-AAATAA
1 AAATAAATCGTTGAATTTATTTTCTTAAGAATCTTGAATGATTTTATTTTGTAAAA-AGAAATAA
* *
33457 ATCATTGAATTTATTTTCTTAAGAATCCTAAAT-TATTCTATTTTGTAAAAGGAAATAAAT-AGT
65 ATCATTGAATTTATTTTCTTAAGAATCTTAAATCTATTCTATTTTGTAAAAGAAAATAAATCA-T
* * * * * *
33520 TGAATTTATTTTCTTAAGAATCTTGAATTATCCTATTTTGTAAAAGG
129 TTAATTTATTTTCTTGAGAATCTTGAATGATTCTATCTTGTAAAAGA
* * * *
33567 GAATAAATCATTGAATTTATTTTAC-TATA-AATCTT-ATATGATTTT-TTTTGTTAAAGGAAA
1 AAATAAATCGTTGAATTTATTTT-CTTA-AGAATCTTGA-ATGATTTTATTTTGTAAAAAGAAA
33627 AGAATTTTTT
Statistics
Matches: 460, Mismatches: 98, Indels: 65
0.74 0.16 0.10
Matches are distributed among these distances:
170 6 0.01
171 51 0.11
172 15 0.03
173 17 0.04
174 143 0.31
175 94 0.20
176 2 0.00
177 1 0.00
180 2 0.00
181 20 0.04
182 41 0.09
183 30 0.07
184 38 0.08
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (175 bp):
AAATAAATCGTTGAATTTATTTTCTTAAGAATCTTGAATGATTTTATTTTGTAAAAAGAAATAAA
TCATTGAATTTATTTTCTTAAGAATCTTAAATCTATTCTATTTTGTAAAAGAAAATAAATCATTT
AATTTATTTTCTTGAGAATCTTGAATGATTCTATCTTGTAAAAGA
Found at i:36989 original size:34 final size:30
Alignment explanation
Indices: 36951--37019 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
36941 TTGATATAAA
36951 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
36985 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
37014 AATTTA
1 AATTTA
37020 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:37030 original size:29 final size:30
Alignment explanation
Indices: 36960--37019 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
36950 AAATTTAAGG
36960 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
36991 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
37020 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:37127 original size:21 final size:20
Alignment explanation
Indices: 37101--37197 Score: 106
Period size: 21 Copynumber: 4.7 Consensus size: 20
37091 GGTGTCAAAA
37101 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCA-CCCTGCAG
*
37122 TGCATCCATGCATCTCTGCAG
1 TGCATCCATGCA-CCCTGCAG
37143 TGCATCCATGCA-CCTGCACTAG
1 TGCATCCATGCACCCTG--C-AG
* *
37165 TGCATCAATGCACCATGCAG
1 TGCATCCATGCACCCTGCAG
*
37185 TGTATCCATGCAC
1 TGCATCCATGCAC
37198 TCAAACACCA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.05
20 13 0.20
21 33 0.51
22 13 0.20
23 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.24
Consensus pattern (20 bp):
TGCATCCATGCACCCTGCAG
Found at i:37243 original size:20 final size:19
Alignment explanation
Indices: 37218--37291 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
37208 AATGCAATTA
37218 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTT-T
**
37238 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC--CTTT
*
37259 GTACATCGATGCATCCTATT
1 GTGCATCGATGCATCCT-TT
*
37279 GTGCATCCATGCA
1 GTGCATCGATGCA
37292 CGAAGGCTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 28 0.64
21 15 0.34
22 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:40553 original size:34 final size:30
Alignment explanation
Indices: 40515--40583 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
40505 TTGATATAAC
*
40515 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAATT-AATTG
40549 AATTT-ACAAAATGTTTTTGGAATTAATTG
1 AATTTAACAAAATGTTTTTGGAATTAATTG
40578 AATTTA
1 AATTTA
40584 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGAATTAATTG
Found at i:40594 original size:29 final size:30
Alignment explanation
Indices: 40524--40583 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
40514 CAATTTAAGG
*
40524 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
40555 CAAAATGTTTTTGGAATT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
40584 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:40689 original size:21 final size:20
Alignment explanation
Indices: 40663--40761 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
40653 AGGGTGTCAA
*
40663 AGTGCATCCATGCACCGCTGC
1 AGTGCATCCATGCACC-CTAC
*
40684 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCC-TAC
*
40705 AGTGAATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCT--AC
* *
40726 TAGTGCATCGATGCACCATAC
1 -AGTGCATCCATGCACCCTAC
40747 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
40762 TCAAACACCG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.01
20 17 0.25
21 35 0.52
22 12 0.18
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTAC
Found at i:40750 original size:42 final size:42
Alignment explanation
Indices: 40663--40761 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
40653 AGGGTGTCAA
* * *
40663 AGTGCATCCATGCACCGCTGCAGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCGCTACAGTGCATCCATGCACCCATAC
* *
40705 AGTGAATCCATGCACCTGC-ACTAGTGCATCGATGCA-CCATAC
1 AGTGCATCCATGCACC-GCTAC-AGTGCATCCATGCACCCATAC
40747 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
40762 TCAAACACCG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.21
Consensus pattern (42 bp):
AGTGCATCCATGCACCGCTACAGTGCATCCATGCACCCATAC
Found at i:40807 original size:20 final size:19
Alignment explanation
Indices: 40782--40855 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
40772 AATGCAATTA
40782 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTT-T
***
40802 GTGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC--CTTT
40823 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCT-TT
*
40843 GTGCATCCATGCA
1 GTGCATCGATGCA
40856 CGAAGGCTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:42219 original size:15 final size:16
Alignment explanation
Indices: 42177--42219 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
42167 TTTCACCTCA
42177 TAAAATTATAAATGAT
1 TAAAATTATAAATGAT
*
42193 TAACA-TACTAAAT-AT
1 TAAAATTA-TAAATGAT
42208 TAAAATTATAAA
1 TAAAATTATAAA
42220 AATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAATTATAAATGAT
Found at i:42692 original size:20 final size:20
Alignment explanation
Indices: 42667--42709 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42657 GAACATAAAC
* * *
42667 AAACGAATATAAATAAATAT
1 AAACGAACATAAACAAACAT
42687 AAACGAACATAAACAAACAT
1 AAACGAACATAAACAAACAT
42707 AAA
1 AAA
42710 ATTGAACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.16
Consensus pattern (20 bp):
AAACGAACATAAACAAACAT
Found at i:42824 original size:40 final size:40
Alignment explanation
Indices: 42748--42825 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
42738 AACGAGTCAT
*
42748 TTGTTCATATTCGTTCATTTAATTAAACGAACATAAAATC
1 TTGTTCATATTCGTTCATTTAATTAAACAAACATAAAATC
* * * *
42788 TTGTTTATGTTCGTTCGTTTAA-TAAATAAACGATAAAA
1 TTGTTCATATTCGTTCATTTAATTAAACAAAC-ATAAAA
42826 GAACTTCCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (40 bp):
TTGTTCATATTCGTTCATTTAATTAAACAAACATAAAATC
Found at i:43970 original size:15 final size:15
Alignment explanation
Indices: 43952--43985 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
43942 GTGAAATTCT
43952 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
43967 AATTATTTATATAAA
1 AATTATTTAAATAAA
43982 AATT
1 AATT
43986 CATCGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:47867 original size:3 final size:3
Alignment explanation
Indices: 47853--47902 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
47843 AACATTGAAT
* *
47853 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47901 TT
1 TT
47903 TAAATATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:48999 original size:2 final size:2
Alignment explanation
Indices: 48990--49034 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48980 ATGAAAAAAC
48990 AT AT -T 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
49031 AT AT
1 AT AT
49035 TGTTGCTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:49383 original size:19 final size:20
Alignment explanation
Indices: 49359--49401 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
49349 TAAGTTTACA
* *
49359 ATTATACTTGTAAAT-TTTT
1 ATTATAATTCTAAATATTTT
49378 ATTATAATTCTAAATATTTT
1 ATTATAATTCTAAATATTTT
49398 -TTAT
1 ATTAT
49402 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTATAATTCTAAATATTTT
Found at i:49997 original size:21 final size:21
Alignment explanation
Indices: 49973--50014 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49963 GAAGATAAAA
*
49973 TTATTTTTTATTAT-ATTATTT
1 TTATTTTATATT-TAATTATTT
49994 TTATTTTATATTTAATTATTT
1 TTATTTTATATTTAATTATTT
50015 GACCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTTATATTTAATTATTT
Found at i:50002 original size:16 final size:15
Alignment explanation
Indices: 49972--50005 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
49962 CGAAGATAAA
49972 ATTATTTTTTATTAT
1 ATTATTTTTTATTAT
*
49987 ATTATTTTTATTTTAT
1 ATTATTTTT-TATTAT
50003 ATT
1 ATT
50006 TAATTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATTTTTTATTAT
Found at i:53303 original size:16 final size:16
Alignment explanation
Indices: 53282--53313 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53272 TTTTTAGTTA
53282 ATGTGCTACTCAAGTG
1 ATGTGCTACTCAAGTG
53298 ATGTGCTACTCAAGTG
1 ATGTGCTACTCAAGTG
53314 CAAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (16 bp):
ATGTGCTACTCAAGTG
Found at i:53420 original size:24 final size:24
Alignment explanation
Indices: 53385--53469 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 24
53375 TCAAACAATT
53385 AAATAATAAAAACATTAAGAAACA
1 AAATAATAAAAACATTAAGAAACA
* ** * **
53409 AAATCAATAAAAA-GTCCA-TAATT
1 AAAT-AATAAAAACATTAAGAAACA
53432 AAATAATAAAAACATTAAGAAACA
1 AAATAATAAAAACATTAAGAAACA
53456 AAATAAATAAAAAC
1 AAAT-AATAAAAAC
53470 TTCATAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
22 8 0.18
23 8 0.18
24 12 0.27
25 17 0.38
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.19
Consensus pattern (24 bp):
AAATAATAAAAACATTAAGAAACA
Found at i:53487 original size:43 final size:44
Alignment explanation
Indices: 53389--53555 Score: 273
Period size: 43 Copynumber: 3.8 Consensus size: 44
53379 ACAATTAAAT
*
53389 AATAAAAACATTAAGAAACAAAATCAATAAAAAGTCCATAATTAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATT--A
* *
53435 TAATAAAAACATTAAGAAACAAAATAAATAAAAACTTCATAATTA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
53480 AAT-AAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
53523 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
53556 TAAGTCTATC
Statistics
Matches: 114, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
43 41 0.36
44 32 0.28
45 1 0.01
47 40 0.35
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
Found at i:53501 original size:90 final size:87
Alignment explanation
Indices: 53393--53555 Score: 290
Period size: 90 Copynumber: 1.8 Consensus size: 87
53383 TTAAATAATA
*
53393 AAAACATTAAGAAACAAAATCAATAAAAAGTCCATAATTAAATAATAAAAACATTAAGAAACAAA
1 AAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATT--A-AATAAAAACATTAAGAAACAAA
53458 ATAAATAAAAACTTCATAATTAAAT
63 ATAAATAAAAACTTCATAATTAAAT
53483 AAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAGAAACAAAATA
1 AAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAGAAACAAAATA
53548 AATAAAAA
66 AATAAAAA
53556 TAAGTCTATC
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
87 33 0.46
88 1 0.01
90 38 0.53
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (87 bp):
AAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAGAAACAAAATA
AATAAAAACTTCATAATTAAAT
Found at i:53983 original size:21 final size:21
Alignment explanation
Indices: 53959--54040 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
53949 AAACCCAGCG
53959 GTGGTGGCATATGAAATGGTT
1 GTGGTGGCATATGAAATGGTT
* *
53980 GTGGTGACATCA-GAAACGGTT
1 GTGGTGGCAT-ATGAAATGGTT
* * *
54001 GTGATGCCATCTGAAATGGTT
1 GTGGTGGCATATGAAATGGTT
*
54022 GTGGTGGCATCTGAAATGG
1 GTGGTGGCATATGAAATGG
54041 CTGCGGAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 50 0.98
22 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.29
Consensus pattern (21 bp):
GTGGTGGCATATGAAATGGTT
Found at i:59849 original size:20 final size:20
Alignment explanation
Indices: 59824--59865 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
59814 TATATATGTT
59824 ATGACTTGCTTTGAATATGA
1 ATGACTTGCTTTGAATATGA
*
59844 ATGACTTGTTTTGAATATGA
1 ATGACTTGCTTTGAATATGA
59864 AT
1 AT
59866 TGTGATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (20 bp):
ATGACTTGCTTTGAATATGA
Found at i:61708 original size:18 final size:18
Alignment explanation
Indices: 61685--61720 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
61675 CAACAGATTC
61685 CTAAGAAGTTGAGCATGA
1 CTAAGAAGTTGAGCATGA
61703 CTAAGAAGTTGAGCATGA
1 CTAAGAAGTTGAGCATGA
61721 TTTAAGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
CTAAGAAGTTGAGCATGA
Found at i:63404 original size:12 final size:12
Alignment explanation
Indices: 63379--63442 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
63369 ACGGAGATAT
*
63379 CAGAAATCAAAA
1 CAGAAATCAGAA
*
63391 CAGAATTCAGAA
1 CAGAAATCAGAA
* *
63403 CAGATATTAGAA
1 CAGAAATCAGAA
** *
63415 CAG-AATCCTAT
1 CAGAAATCAGAA
63426 CAGAAATCAGAA
1 CAGAAATCAGAA
63438 CAGAA
1 CAGAA
63443 CAGGTCATGT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
11 6 0.16
12 32 0.84
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Done.