Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006991.1 Hibiscus syriacus cultivar Beakdansim tig00018028_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: 38180
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:654 original size:14 final size:14
Alignment explanation
Indices: 635--662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
625 TTTGGGTTAT
635 TTTAGATATTGTAG
1 TTTAGATATTGTAG
649 TTTAGATATTGTAG
1 TTTAGATATTGTAG
663 CGTAATCAAA
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:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTAGATATTGTAG
Found at i:12553 original size:35 final size:35
Alignment explanation
Indices: 12490--12589 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
12480 TTTCGTCTTA
*
12490 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
12527 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
12562 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
12590 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:16515 original size:13 final size:13
Alignment explanation
Indices: 16497--16539 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
16487 CAATCAGAAT
16497 AAAAAAGGCAAAA
1 AAAAAAGGCAAAA
16510 AAAAAAGAAGCAAAA
1 AAAAAAG--GCAAAA
16525 AACAAAA-GCAAAA
1 AA-AAAAGGCAAAA
16538 AA
1 AA
16540 GAACAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
15 8 0.30
16 4 0.15
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGGCAAAA
Found at i:16524 original size:14 final size:13
Alignment explanation
Indices: 16497--16539 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
16487 CAATCAGAAT
*
16497 AAAAAAGGCAAAAA
1 AAAAAAAGC-AAAA
16511 AAAAAGAAGCAAAA
1 AAAAA-AAGCAAAA
*
16525 AACAAAAGCAAAA
1 AAAAAAAGCAAAA
16538 AA
1 AA
16540 GAACAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 13 0.50
15 3 0.12
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGCAAAA
Found at i:16544 original size:16 final size:15
Alignment explanation
Indices: 16521--16576 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
16511 AAAAAGAAGC
16521 AAAA-AACAAAAGCAA
1 AAAAGAACAAAAG-AA
16536 AAAAGAACAAAAAGAA
1 AAAAGAAC-AAAAGAA
*
16552 AAAAGAA-AAAGGGACA
1 AAAAGAACAAA-AGA-A
16568 AAAAGAACA
1 AAAAGAACA
16577 TGCAAAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 3 0.09
15 6 0.17
16 20 0.57
17 6 0.17
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAACAAAAGAA
Found at i:16568 original size:23 final size:24
Alignment explanation
Indices: 16510--16574 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
16500 AAAGGCAAAA
*
16510 AAAAAAGAAGCAAAAA-ACAAAAGC
1 AAAAAAGAA-CAAAAAGAAAAAAGC
16534 AAAAAAGAACAAAAAGAAAAAAG-
1 AAAAAAGAACAAAAAGAAAAAAGC
* *
16557 AAAAAGGGACAAAAAGAA
1 AAAAAAGAACAAAAAGAA
16575 CATGCAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.59
24 15 0.41
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAGAACAAAAAGAAAAAAGC
Found at i:17188 original size:22 final size:22
Alignment explanation
Indices: 17160--17203 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17150 AGCTACCCCA
17160 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
17182 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
17204 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:17661 original size:18 final size:18
Alignment explanation
Indices: 17638--17673 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17628 TCAACATCAA
*
17638 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
17656 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
17674 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:18204 original size:36 final size:36
Alignment explanation
Indices: 18154--18535 Score: 282
Period size: 36 Copynumber: 10.9 Consensus size: 36
18144 ACTAGAAGAG
18154 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
*
18190 TTTTGTCTCC-CTTGAGACAGTTTCTCTTGAAACATAA
1 TTTTGTC-CCTCTTGAGACAGTTTCCCTTGAAACA-AA
* * * *
18227 -------AC-ATTGAAAACA-TTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTG-AGACAGTTTCCCTTGAAACAAA
* * *
18255 TTTTCGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
1 TTTT-GTCCCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
18293 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-TAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
18328 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
*
18364 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * * *
18400 ----AT--AT-TT-AAATATGTTTTCTTTGAAACAAA
1 TTTTGTCCCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
18429 TTTCGTCCCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
18466 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
18502 TTTTGTCTCC-CTTGAGACAGTTACTCTTGAAACA
1 TTTTGTC-CCTCTTGAGACAGTTTCCCTTGAAACA
18536 CAAAATCTTC
Statistics
Matches: 279, Mismatches: 41, Indels: 52
0.75 0.11 0.14
Matches are distributed among these distances:
28 5 0.02
29 33 0.12
30 5 0.02
32 1 0.00
33 1 0.00
35 33 0.12
36 115 0.41
37 79 0.28
38 7 0.03
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:18301 original size:37 final size:36
Alignment explanation
Indices: 18238--18401 Score: 231
Period size: 37 Copynumber: 4.5 Consensus size: 36
18228 CATTGAAAAC
* *
18238 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAAAAAATTTT-GTCTCTCTTGAGACA
18275 ATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAA-AAAATTTTGTCTCTCTTGAGACA
* *
18312 GTTTCCCTTG-AAATAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACA
* *
18347 TTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACA
*
18383 GTTTCCCTTGAAACAAAAT
1 ATTTCCCTTGAAA-AAAAT
18402 ATTTAAATAT
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
35 31 0.27
36 37 0.32
37 40 0.35
38 7 0.06
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (36 bp):
ATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACA
Found at i:18342 original size:174 final size:174
Alignment explanation
Indices: 18154--18535 Score: 498
Period size: 174 Copynumber: 2.2 Consensus size: 174
18144 ACTAGAAGAG
* *
18154 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * * *
18219 AAACATAAACATTGAAA-ACATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAATTTCCCT
66 AAACA-AAACATTGAAATACATTTCCCTTGAAACAAA-TTTCGTCCCCCTTGAGACAATTTCCCT
*
18283 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-TAA
129 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
18328 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * ** * * * **
18393 AAACAAAATATTTAAATATGTTTTCTTTGAAACAAATTTCGTCCCCCTTGAGACAGTTTCTTTTG
66 AAACAAAACATTGAAATACATTTCCCTTGAAACAAATTTCGTCCCCCTTGAGACAATTTCCCTTG
* * * *
18458 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
131 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
18502 TTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
18536 CAAAATCTTC
Statistics
Matches: 178, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
173 68 0.38
174 110 0.62
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (174 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
AAACAAAACATTGAAATACATTTCCCTTGAAACAAATTTCGTCCCCCTTGAGACAATTTCCCTTG
AAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:18470 original size:138 final size:137
Alignment explanation
Indices: 18282--18535 Score: 375
Period size: 138 Copynumber: 1.8 Consensus size: 137
18272 ATAATTTCCC
* * *
18282 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAATTTTGTCTCTCTTGAGACA
1 TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGAAATAATTTTGTCTCTCTTGAGACA
* * * *
18347 TTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTAAATAT
66 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATAT
18412 GTTTTCT
131 GTTTTCT
** *
18419 TTGAAAC-AAATTTCGTCCCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTT-GAAATAA-TTTTGTCTCTCTTGAGA
* *
18483 CAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
64 CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACA
18536 CAAAATCTTC
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
136 26 0.25
137 13 0.13
138 64 0.62
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (137 bp):
TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGAAATAATTTTGTCTCTCTTGAGACA
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATAT
GTTTTCT
Found at i:19435 original size:105 final size:105
Alignment explanation
Indices: 19208--20179 Score: 1089
Period size: 105 Copynumber: 9.3 Consensus size: 105
19198 GCCATCCGCG
* * *
19208 ATTTCAACTCCAC-GACGGAGGATATTGTGGCACTCGAGACAACGCAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATA-T-TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGA
* * *
19272 AGGGACGGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACGGCTGCTTGTCAA-CAACAACTTCCCAATTTCAGAGCCA
* * * * *
19317 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
19382 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
19422 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
19486 GATC-GCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
65 GA-CGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * ** * *
19527 ATTTCAACTTCACAACGAAGGAAATTGGACTTGAGACAATGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
19592 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
19632 ATTTCAACTTCATAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
19697 ACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * * *
19737 ATTTCAACTTCAGAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
19802 GCGGCTGAC-TGT---CGACAA----GCAATTTC-GAAGCCA
66 ACGGCTG-CTTGTCAACAACAACTTCCCAATTTCAG-AGCCA
*
19835 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * ** * *
19900 ATGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
66 ACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
**
19941 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
20006 ACGGCTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * *
20041 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * * *
20106 GCGACTGAC-TGTCAACAAACAATTTCCCAGTTCCAAAACCA
66 ACGGCTG-CTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
20147 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
20180 GAACAATATT
Statistics
Matches: 748, Mismatches: 91, Indels: 51
0.84 0.10 0.06
Matches are distributed among these distances:
97 1 0.00
98 76 0.10
100 79 0.11
101 3 0.00
102 8 0.01
103 4 0.01
104 3 0.00
105 376 0.50
106 173 0.23
107 4 0.01
108 1 0.00
109 20 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:20702 original size:35 final size:35
Alignment explanation
Indices: 20639--20738 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
20629 TTTCGTCCTA
* *
20639 CTAGGATTCAAACTCTCAAAAATAGGATAGACTTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
20676 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
20711 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
20739 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:21145 original size:18 final size:17
Alignment explanation
Indices: 21106--21148 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
21096 GTTATATGGA
21106 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
21122 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
21140 TATTATTAT
1 TATTATTAT
21149 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:21702 original size:9 final size:9
Alignment explanation
Indices: 21681--21714 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
21671 TTTTTTTTCC
21681 TTTATCTTA-
1 TTTAT-TTAT
21690 TTTATTTAT
1 TTTATTTAT
21699 TTTATTTAT
1 TTTATTTAT
21708 TTTATTT
1 TTTATTT
21715 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:21703 original size:13 final size:14
Alignment explanation
Indices: 21681--21715 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
21671 TTTTTTTTCC
*
21681 TTTATCTTATTTA-
1 TTTATTTTATTTAT
21694 TTTATTTTATTTAT
1 TTTATTTTATTTAT
21708 TTTATTTT
1 TTTATTTT
21716 TCCCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:25552 original size:17 final size:17
Alignment explanation
Indices: 25532--25573 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
25522 AGGGAAGTAG
25532 TTCATTAAACTAGTTCA
1 TTCATTAAACTAGTTCA
* *
25549 TTCATCAAACTAGTTTA
1 TTCATTAAACTAGTTCA
*
25566 TTTATTAA
1 TTCATTAA
25574 CTTAACTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (17 bp):
TTCATTAAACTAGTTCA
Found at i:30250 original size:90 final size:90
Alignment explanation
Indices: 30097--30263 Score: 275
Period size: 90 Copynumber: 1.9 Consensus size: 90
30087 CCTAACACAC
* * *
30097 CCTTTTATAGTCAAGTTACCCTAATTATATTAGGATATTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGTCAAGTTACCCTAATCATATTAGGATATTTACTATTTCAAATTAAATAAATCTAT
30162 ATTTAATTAATTAGAATTTAACAAT
66 ATTTAATTAATTAGAATTTAACAAT
30187 CCTTTTATA-TCCAAGTTACCCTAATCATATTAAGGAT-TTTACTATTTCAAATTAAATAAATCT
1 CCTTTTATAGT-CAAGTTACCCTAATCATATT-AGGATATTTACTATTTCAAATTAAATAAATCT
30250 ATATTTAATTAATT
64 ATATTTAATTAATT
30264 GAGATTAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
89 1 0.01
90 66 0.92
91 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGTCAAGTTACCCTAATCATATTAGGATATTTACTATTTCAAATTAAATAAATCTAT
ATTTAATTAATTAGAATTTAACAAT
Found at i:35245 original size:90 final size:90
Alignment explanation
Indices: 35092--35269 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
35082 CATAACACAC
*
35092 CCTTTTATAGCCAAGTTACCATAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCATAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
35157 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * * *
35182 CCTTTTATATCCAAGTTACCCTAATTATATTAGGGATTTTATTATTTCAAATTAATTGAATCTAT
1 CCTTTTATAGCCAAGTTACCATAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
35247 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
35270 TTCAGGATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCATAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Done.