Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007296.1 Corchorus capsularis cultivar CVL-1 contig07317, 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: 32215
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:243 original size:42 final size:40
Alignment explanation
Indices: 182--266 Score: 143
Period size: 42 Copynumber: 2.1 Consensus size: 40
172 AAGGTTCACT
182 TTTAATAATTTTAAATTAACCTATTTGTCTATGCAAACTG
1 TTTAATAATTTTAAATTAACCTATTTGTCTATGCAAACTG
*
222 TTTAATAATTTTTTAAATTAACCTATTTGTCTATGCAAGCTG
1 TTTAATAA--TTTTAAATTAACCTATTTGTCTATGCAAACTG
264 TTT
1 TTT
267 TAGATTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 8 0.19
42 34 0.81
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (40 bp):
TTTAATAATTTTAAATTAACCTATTTGTCTATGCAAACTG
Found at i:4698 original size:20 final size:20
Alignment explanation
Indices: 4670--4714 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4660 TTTCCGTTGT
* * *
4670 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACACAACGAA
4690 TTAAGATCTAACACAACGAA
1 TTAAGATCTAACACAACGAA
4710 TTAAG
1 TTAAG
4715 TGTCCACTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.24
Consensus pattern (20 bp):
TTAAGATCTAACACAACGAA
Found at i:5361 original size:36 final size:35
Alignment explanation
Indices: 5321--5429 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 35
5311 TAGATTAAGC
*
5321 TCTTTATTGACTTCACTTAATTACCTTGAATTAAAT
1 TCTTTATTGAC-TCACTTAATTACCCTGAATTAAAT
* *
5357 TCTTTATT--CT-ACTTAATTACCCTCAATT-AAG
1 TCTTTATTGACTCACTTAATTACCCTGAATTAAAT
*
5388 TCTTTTATTGACCTCACTTAATTACCCTGAATTAAGT
1 TC-TTTATTGA-CTCACTTAATTACCCTGAATTAAAT
5425 TCTTT
1 TCTTT
5430 GTTTTACTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.07
32 22 0.36
33 1 0.02
34 1 0.02
35 2 0.03
36 28 0.46
37 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.47
Consensus pattern (35 bp):
TCTTTATTGACTCACTTAATTACCCTGAATTAAAT
Found at i:5376 original size:32 final size:32
Alignment explanation
Indices: 5335--5442 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 32
5325 TATTGACTTC
*
5335 ACTTAATTACCTTGAATTAAATTCTTTATTCT
1 ACTTAATTACCCTGAATTAAATTCTTTATTCT
* *
5367 ACTTAATTACCCTCAATT-AAGTCTTTTATTGACCT
1 ACTTAATTACCCTGAATTAAATTC-TTTATT---CT
* * *
5402 CACTTAATTACCCTGAATTAAGTTCTTTGTTTT
1 -ACTTAATTACCCTGAATTAAATTCTTTATTCT
5435 ACTTAATT
1 ACTTAATT
5443 TCCTTTCCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
31 4 0.06
32 30 0.48
33 1 0.02
35 2 0.03
36 22 0.35
37 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAATTCTTTATTCT
Found at i:5395 original size:68 final size:68
Alignment explanation
Indices: 5314--5442 Score: 197
Period size: 68 Copynumber: 1.9 Consensus size: 68
5304 TCTTTTCTAG
* *
5314 ATTAAGCTCTTTATTGACTTCACTTAATTACCTTGAATTAAATTCTTTATTCTACTTAATTACCC
1 ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAATTCTTTATTCTACTTAATTACCC
5379 TCA
66 TCA
* * *
5382 ATTAAG-TCTTTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTGTTTTACTTAATT
1 ATTAAGCTC-TTTATTGACCTCACTTAATTACCCTGAATTAAATTCTTTATTCTACTTAATT
5443 TCCTTTCCTG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 2 0.04
68 53 0.96
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAATTCTTTATTCTACTTAATTACCC
TCA
Found at i:5458 original size:37 final size:37
Alignment explanation
Indices: 5413--5485 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
5403 ACTTAATTAC
*
5413 CCTGAATTAAGTTCT-T-TGTTTTACTTAATTTCCTTT
1 CCTGAATTAAG-CCTATGTGTTTTACTTAATTTCCTTT
*
5449 CCTGAAATTAAGCCTATGTTTTTTACTTAATTTCCTT
1 CCTG-AATTAAGCCTATGTGTTTTACTTAATTTCCTT
5486 GAAATTAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.19
37 8 0.25
38 18 0.56
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.52
Consensus pattern (37 bp):
CCTGAATTAAGCCTATGTGTTTTACTTAATTTCCTTT
Found at i:5728 original size:71 final size:71
Alignment explanation
Indices: 5618--6285 Score: 816
Period size: 71 Copynumber: 9.4 Consensus size: 71
5608 TCCTTACTAG
* *
5618 TTTCCTTGAAA-TTAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTAT-CTT
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
*
5681 TACCTAG
65 TACCTAA
* * * *
5688 TTTTCTTGAAACTAAGCCAGCCTTTCCTTTACCTAATTTCCTTGAAACTAAGCCAGCCTTTCCTT
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
* *
5753 TACTTAG
65 TACCTAA
* *
5760 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTAT-CTT
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
*
5824 TACCTAG
65 TACCTAA
* * *
5831 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAACTAAGCCAGCCTTTCCTT
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
* *
5896 TACTTAG
65 TACCTAA
* * *
5903 TTTCCTTGAAATTAAGCCAAGTCTTTTCTTTACCTAGTTTCCTTGAAAATAAGCCAGTCTAT-CT
1 TTTCCTTGAAACTAAGCC-AGTC-TTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCT
*
5967 TTACCTAG
64 TTACCTAA
* *
5975 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAACTAAGCCAGT-TTT-CTT
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
* *
6038 TACTTAG
65 TACCTAA
* * *
6045 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTATCTAGTTTCCTTGAAACTAAGCCAGTCTAT-CTT
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
*
6109 TACCTAG
65 TACCTAA
* *
6116 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAACTAAGCCAGTC-TT-CTT
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
* *
6179 TACTTAG
65 TACCTAA
* * * * * * *
6186 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAATTTCCATGAAATTAAACTAGTCTTTTCTT
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTT
6251 TACCTAA
65 TACCTAA
6258 TTTCCTTGAAACTAAGCCAGTC-TTCTTT
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTT
6286 CAGTCTAATT
Statistics
Matches: 530, Mismatches: 54, Indels: 28
0.87 0.09 0.05
Matches are distributed among these distances:
70 148 0.28
71 202 0.38
72 139 0.26
73 38 0.07
74 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (71 bp):
TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTCCTTT
ACCTAA
Found at i:6291 original size:11 final size:11
Alignment explanation
Indices: 6283--6363 Score: 117
Period size: 11 Copynumber: 7.4 Consensus size: 11
6273 GCCAGTCTTC
6283 TTTCAGTCTAA
1 TTTCAGTCTAA
*
6294 TTTCAGTCTAG
1 TTTCAGTCTAA
6305 TTTCAGTCTAA
1 TTTCAGTCTAA
**
6316 TTTCAGTCTTC
1 TTTCAGTCTAA
6327 TTTCAGTCTAA
1 TTTCAGTCTAA
**
6338 TTTCAGTCTTC
1 TTTCAGTCTAA
6349 TTTCAGTCTAA
1 TTTCAGTCTAA
6360 TTTC
1 TTTC
6364 TTTTGCCTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 60 1.00
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.49
Consensus pattern (11 bp):
TTTCAGTCTAA
Found at i:6297 original size:36 final size:35
Alignment explanation
Indices: 5446--6285 Score: 1068
Period size: 36 Copynumber: 23.8 Consensus size: 35
5436 CTTAATTTCC
* * * *
5446 TTTCC-TGAAATTAAGCCTA-TGTTT-TTTACTTAA
1 TTTCCTTGAAACTAAGCC-AGTCTTTCTTTACCTAG
* *
5479 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
* *
5515 TTTCCTTGAAACTAAGTCAGT-TTTCTTTACTTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* * * *
5549 TTTTCTTGAAACTAAGCCAGCCCTTCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
5584 TTTCCTTGAAACTAAGCCAGCCTTTCCTTA-CTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
*
5618 TTTCCTTGAAA-TTAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAG
*
5653 TTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* * *
5688 TTTTCTTGAAACTAAGCCAGCCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
* *
5724 TTTCCTTGAAACTAAGCCAGCCTTTCCTTTACTTAG
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
*
5760 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAG
*
5796 TTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
5831 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
* *
5867 TTTCCTTGAAACTAAGCCAGCCTTTCCTTTACTTAG
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
*
5903 TTTCCTTGAAATTAAGCCAAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCC-AGTC-TTTCTTTACCTAG
* *
5940 TTTCCTTGAAAATAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
5975 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
*
6011 TTTCCTTGAAACTAAGCCAGT-TTTCTTTACTTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
6045 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTATCTAG
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAG
*
6081 TTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
6116 TTTTCTTGAAACTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
*
6152 TTTCCTTGAAACTAAGCCAGTC-TTCTTTACTTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
* *
6186 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTT-CTTTACCTAG
* * * * *
6222 TTTCCATGAAATTAAACTAGTCTTTTCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTC-TTTCTTTACCTAG
6258 TTTCCTTGAAACTAAGCCAGTC-TTCTTT
1 TTTCCTTGAAACTAAGCCAGTCTTTCTTT
6286 CAGTCTAATT
Statistics
Matches: 713, Mismatches: 74, Indels: 39
0.86 0.09 0.05
Matches are distributed among these distances:
33 14 0.02
34 126 0.18
35 199 0.28
36 336 0.47
37 35 0.05
38 3 0.00
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (35 bp):
TTTCCTTGAAACTAAGCCAGTCTTTCTTTACCTAG
Found at i:6300 original size:22 final size:22
Alignment explanation
Indices: 6275--6363 Score: 160
Period size: 22 Copynumber: 4.0 Consensus size: 22
6265 GAAACTAAGC
6275 CAGTCTTCTTTCAGTCTAATTT
1 CAGTCTTCTTTCAGTCTAATTT
**
6297 CAGTCTAGTTTCAGTCTAATTT
1 CAGTCTTCTTTCAGTCTAATTT
6319 CAGTCTTCTTTCAGTCTAATTT
1 CAGTCTTCTTTCAGTCTAATTT
6341 CAGTCTTCTTTCAGTCTAATTT
1 CAGTCTTCTTTCAGTCTAATTT
6363 C
1 C
6364 TTTTGCCTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.48
Consensus pattern (22 bp):
CAGTCTTCTTTCAGTCTAATTT
Found at i:6524 original size:35 final size:36
Alignment explanation
Indices: 6422--6540 Score: 161
Period size: 36 Copynumber: 3.3 Consensus size: 36
6412 TCATCTATGG
* *
6422 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAA
* *
6458 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAG
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAA
* *
6494 ATTATA-TCTTTGCT-AGTTTACTTAAATCTTGTGAA
1 ATTA-AGTCTTTGCTAACTTTACTTAATTCTTGTGAA
6529 ATTAAGTCTTTG
1 ATTAAGTCTTTG
6541 AACTTGCTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.01
35 28 0.38
36 44 0.59
37 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.49
Consensus pattern (36 bp):
ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAA
Found at i:11107 original size:2 final size:2
Alignment explanation
Indices: 11100--11127 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11090 TAAATTTGTT
11100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11128 GGCAGTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11684 original size:13 final size:13
Alignment explanation
Indices: 11644--11692 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
11634 TCACATAATA
*
11644 TATAGTAATTATTT
1 TATA-TAATTATAT
* *
11658 TATTTAA-TAGAT
1 TATATAATTATAT
11670 TATATAATTATAT
1 TATATAATTATAT
11683 TATATAATTA
1 TATATAATTA
11693 ATTTTCGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 9 0.31
13 17 0.59
14 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (13 bp):
TATATAATTATAT
Found at i:11791 original size:15 final size:15
Alignment explanation
Indices: 11771--11801 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11761 ATCCTACTTA
11771 TATTAAATTTTAGTT
1 TATTAAATTTTAGTT
*
11786 TATTAATTTTTAGTT
1 TATTAAATTTTAGTT
11801 T
1 T
11802 TATGTTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATTAAATTTTAGTT
Found at i:12630 original size:19 final size:19
Alignment explanation
Indices: 12595--12632 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12585 TAATATTGAT
*
12595 TTTTTATTTATATATTATA
1 TTTTTATTTATAAATTATA
12614 TTTTTATTT-TAAAATTATA
1 TTTTTATTTAT-AAATTATA
12633 CTTAATCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATTTATAAATTATA
Found at i:13504 original size:75 final size:75
Alignment explanation
Indices: 13327--13628 Score: 279
Period size: 75 Copynumber: 4.0 Consensus size: 75
13317 TCCAAATTAG
* ** * *
13327 TAAATATCTTGAAGAGACGTTACAAACATTTGTAACTG-CCGAAATATGATGTTTTGCATGTAAC
1 TAAATACCTTGAAGAGACGTTACAAGTATTTGTAACTGTCC-AAATATGATGTTATGCATATAAC
* * *
13391 TTC-AAAATCGC
65 CTCTAAACT-AC
* * * ** * *
13402 TGAATAACTTAAATCGAGGTTACAAGTATTTGTAACTGTCCAAATATGATGTTGTGCATATAACC
1 TAAATACCTTGAAGAGACGTTACAAGTATTTGTAACTGTCCAAATATGATGTTATGCATATAACC
*
13467 TCT-AATTAC
66 TCTAAACTAC
* * * *
13476 TAAATACCTTGAAGAGGCGTTTATAAGTATTTGAAACTGCCCAAATATGATGTTATGCATATAAC
1 TAAATACCTTGAAGAGACG-TTACAAGTATTTGTAACTGTCCAAATATGATGTTATGCATATAAC
*
13541 CTCTAAACTAT
65 CTCTAAACTAC
* * * * * *
13552 TAAATACCTTGAATAGACGTTACAAGTACTTGTAAAC-GTCCAAATATAATGTCATTCATGTAAC
1 TAAATACCTTGAAGAGACGTTACAAGTATTTGT-AACTGTCCAAATATGATGTTATGCATATAAC
* *
13616 CTCAAAATTAC
65 CTCTAAACTAC
13627 TA
1 TA
13629 TAGATTTGTA
Statistics
Matches: 183, Mismatches: 39, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
74 13 0.07
75 144 0.79
76 26 0.14
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (75 bp):
TAAATACCTTGAAGAGACGTTACAAGTATTTGTAACTGTCCAAATATGATGTTATGCATATAACC
TCTAAACTAC
Found at i:13593 original size:150 final size:149
Alignment explanation
Indices: 13321--13603 Score: 336
Period size: 150 Copynumber: 1.9 Consensus size: 149
13311 TGTTGCTCCA
* * * * *
13321 AATTAGTAAATATCTTGAAGAGACGTTACAAACATTTGTAACTGCCGAAATATGATGTTTTGCAT
1 AATTACTAAATACCTTGAAGAGACGTTACAAACATTTGAAACTGCCCAAATATGATGTTATGCAT
* * * * * * * *
13386 GTAACTTCAAAATCGCTGAATAACTTAAATCGAGGTTACAAGTATTTGTAACTGTCCAAATATGA
66 ATAACCTCAAAATCACTAAATAACTTAAATAGACGTTACAAGTACTTGTAACTGTCCAAATATAA
13451 TGTTGTGCATATAACCTCT
131 TGTTGTGCATATAACCTCT
* * **
13470 AATTACTAAATACCTTGAAGAGGCGTTTATAAGTATTTGAAACTGCCCAAATATGATGTTATGCA
1 AATTACTAAATACCTTGAAGAGACG-TTACAAACATTTGAAACTGCCCAAATATGATGTTATGCA
* * * *
13535 TATAACCTCTAAA-CTATTAAATACCTTGAATAGACGTTACAAGTACTTGTAAAC-GTCCAAATA
65 TATAACCTCAAAATC-ACTAAATAACTTAAATAGACGTTACAAGTACTTGT-AACTGTCCAAATA
13598 TAATGT
128 TAATGT
13604 CATTCATGTA
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
149 23 0.21
150 84 0.76
151 3 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (149 bp):
AATTACTAAATACCTTGAAGAGACGTTACAAACATTTGAAACTGCCCAAATATGATGTTATGCAT
ATAACCTCAAAATCACTAAATAACTTAAATAGACGTTACAAGTACTTGTAACTGTCCAAATATAA
TGTTGTGCATATAACCTCT
Found at i:14478 original size:12 final size:12
Alignment explanation
Indices: 14461--14491 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
14451 TATGGCTTGA
14461 TTTTTCTTTTTT
1 TTTTTCTTTTTT
14473 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
14485 GTTTTCT
1 TTTTTCT
14492 AATTGTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:24298 original size:31 final size:31
Alignment explanation
Indices: 24274--24350 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
24264 TTTTTTTGTT
24274 TTTAGGCTCAAATTGAGCAATTTTTGAAATG
1 TTTAGGCTCAAATTGAGCAATTTTTGAAATG
* * *
24305 TTTAGGCTCAAATTGAGCAACTTTGGAAAGG
1 TTTAGGCTCAAATTGAGCAATTTTTGAAATG
*
24336 TTTAGCCTCAAATTG
1 TTTAGGCTCAAATTG
24351 GTAATTTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTAGGCTCAAATTGAGCAATTTTTGAAATG
Found at i:28863 original size:21 final size:19
Alignment explanation
Indices: 28818--28916 Score: 56
Period size: 21 Copynumber: 4.7 Consensus size: 19
28808 ACTCTTTGAA
* *
28818 TTACTGATCACCTTTTACTC
1 TTACTGATTA-CTTTGACTC
28838 TTTACTGATTACTAATTGACTC
1 -TTACTGATTACT--TTGACTC
*
28860 TTACTAATCATCACTTTG-CTC
1 TTACTGAT--T-ACTTTGACTC
* *
28881 TTACTGGTTACTGTTTTACTC
1 TTACTGATTAC--TTTGACTC
28902 TTACTGATTATCTTT
1 TTACTGATTA-CTTT
28917 TATCGATTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 8 0.13
21 37 0.60
22 10 0.16
23 1 0.02
24 3 0.05
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.48
Consensus pattern (19 bp):
TTACTGATTACTTTGACTC
Found at i:28950 original size:16 final size:16
Alignment explanation
Indices: 28929--28962 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28919 TCGATTACTT
*
28929 TTTTACTCTTTGCTGA
1 TTTTACTCTTTACTGA
28945 TTTTACTCTTTACTGA
1 TTTTACTCTTTACTGA
28961 TT
1 TT
28963 ACCTTCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTTACTCTTTACTGA
Found at i:29049 original size:35 final size:34
Alignment explanation
Indices: 29027--29093 Score: 75
Period size: 35 Copynumber: 2.0 Consensus size: 34
29017 TCTTTACTTT
* *
29027 TTTTTCTTTACTGATTATTCTTTTACTTTTTAC-CA
1 TTTTACTTTACTGATTACTC-TTTAC-TTTTACTCA
*
29062 TTTTACTTTGCTGATTACTCTTTA-TTTTACTC
1 TTTTACTTTACTGATTACTCTTTACTTTTACTC
29094 TCTACTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
32 6 0.21
33 1 0.04
34 4 0.14
35 17 0.61
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.61
Consensus pattern (34 bp):
TTTTACTTTACTGATTACTCTTTACTTTTACTCA
Found at i:29182 original size:22 final size:21
Alignment explanation
Indices: 29154--29488 Score: 145
Period size: 22 Copynumber: 15.5 Consensus size: 21
29144 TTACTTTTTC
29154 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
29176 TTTACTGATTACCATTTTACTCT
1 TTTACTGATTACC-TTTTACT-T
* * *
29199 TTT-CTAATTACTATTTTACCT
1 TTTACTGATTAC-CTTTTACTT
29220 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACC-TTTTACTT
*
29242 TTTACCAT-TTTACCTTTTTAC-T
1 TTTA-C-TGATTACC-TTTTACTT
** *
29264 CGTACT-ATTACTCTTTCTTTATCAT
1 TTTACTGATTAC-C--T-TTTA-CTT
*
29289 TTT--TGTATTTA-CTGATTACTCT
1 TTTACTG-A-TTACCT-TTTACT-T
** *
29311 TCCACTGATTA-CTCTTTACTC
1 TTTACTGATTACCT-TTTACTT
* * * **
29332 TTTACTAATTGTCATTTTACCC
1 TTTACTGATT-ACCTTTTACTT
*
29354 TTT-CAGA-TACCTTTTCACTT
1 TTTACTGATTACCTTTT-ACTT
29374 TTTACTGATTACCTTTTACTT
1 TTTACTGATTACCTTTTACTT
* *
29395 TTTACTGTTTA-CTATTACTT
1 TTTACTGATTACCTTTTACTT
* * * *
29415 CTTACTGATT-TCTATTACTC
1 TTTACTGATTACCTTTTACTT
*
29435 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACC-TTTTACTT
* * *
29457 TTTACTGATTGCCATTATACCT
1 TTTACTGATTACC-TTTTACTT
29479 TTTACTGATT
1 TTTACTGATT
29489 GCATCTTTCT
Statistics
Matches: 242, Mismatches: 45, Indels: 52
0.71 0.13 0.15
Matches are distributed among these distances:
19 5 0.02
20 44 0.18
21 35 0.14
22 123 0.51
23 24 0.10
24 5 0.02
25 3 0.01
26 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:29201 original size:8 final size:7
Alignment explanation
Indices: 29137--29263 Score: 55
Period size: 7 Copynumber: 17.6 Consensus size: 7
29127 CTTGTATGAA
29137 TACTCTTT
1 TACT-TTT
29145 TACTTTT
1 TACTTTT
29152 T-C--TT
1 TACTTTT
**
29156 TACTGAT
1 TACTTTT
29163 TACTCTTT
1 TACT-TTT
29171 TACTTTT
1 TACTTTT
**
29178 TACTGAT
1 TACTTTT
*
29185 TACCATTT
1 TA-CTTTT
29193 TACTCTTT
1 TACT-TTT
**
29201 T-CTAAT
1 TACTTTT
29207 TACTATTT
1 TACT-TTT
*
29215 TACCTTT
1 TACTTTT
**
29222 TACTGAT
1 TACTTTT
29229 TACCTTTT
1 TA-CTTTT
29237 TACTTTT
1 TACTTTT
*
29244 TACCATTT
1 TA-CTTTT
29252 TACCTTTT
1 TA-CTTTT
29260 TACT
1 TACT
29264 CGTACTATTA
Statistics
Matches: 88, Mismatches: 21, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
6 3 0.03
7 42 0.48
8 39 0.44
ACGTcount: A:0.19, C:0.20, G:0.02, T:0.58
Consensus pattern (7 bp):
TACTTTT
Found at i:29392 original size:14 final size:13
Alignment explanation
Indices: 29373--29424 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
29363 CCTTTTCACT
29373 TTTTACTGATTACC
1 TTTTACTGATTA-C
**
29387 TTTTACTTTTTAC
1 TTTTACTGATTAC
29400 TGTTTACT-ATTAC
1 T-TTTACTGATTAC
29413 TTCTTACTGATT
1 TT-TTACTGATT
29425 TCTATTACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.03
13 12 0.38
14 19 0.59
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.58
Consensus pattern (13 bp):
TTTTACTGATTAC
Found at i:29412 original size:20 final size:20
Alignment explanation
Indices: 29370--29466 Score: 104
Period size: 20 Copynumber: 4.7 Consensus size: 20
29360 ATACCTTTTC
*
29370 ACTTTTTACTGATTACCTTTT
1 ACTTTTTACTGATTA-CTATT
*
29391 ACTTTTTACTGTTTACTATT
1 ACTTTTTACTGATTACTATT
* *
29411 ACTTCTTACTGATTTCTATT
1 ACTTTTTACTGATTACTATT
* *
29431 ACTCTTTACTGATTACCATTTT
1 ACTTTTTACTGATTA-C-TATT
*
29453 ACTCTTTACTGATT
1 ACTTTTTACTGATT
29467 GCCATTATAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
20 33 0.51
21 15 0.23
22 17 0.26
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.55
Consensus pattern (20 bp):
ACTTTTTACTGATTACTATT
Done.