Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015631.1 Corchorus capsularis cultivar CVL-1 contig15652, 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: 64369
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:98 original size:60 final size:60
Alignment explanation
Indices: 1--332 Score: 504
Period size: 60 Copynumber: 5.5 Consensus size: 60
* *
1 TTCAGTATCGCTATAAAGACGAACGTCTCCTTGGAGACCGTTTTACTTTAAAATAAACGA
1 TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
61 TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
1 TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
* *
121 TTCAGTATCGTTATAAAGACAAACGTCTCTTTTGAGACCGTTTTACTTTAAAATAAACGA
1 TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
* * *
181 TT-ACGTATCGTTATAAAGACGATCGCCTCTTTTGAGACCGTTTTACTTTAAAATAAACGA
1 TTCA-GTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
* * * * *
241 TTCAGTATCGTTATAAAGGCGAACGCCTCTTTTGAGACCCTTTTACTTTAAAACTTAAAAGA
1 TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAA--TAAACGA
* *
303 TTCAGTATCGTTATAAAGATGTACGTCTCC
1 TTCAGTATCGTTATAAAGACGAACGTCTCC
333 GACAAGACCA
Statistics
Matches: 252, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.00
60 219 0.87
61 1 0.00
62 31 0.12
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (60 bp):
TTCAGTATCGTTATAAAGACGAACGTCTCCTTTGAGACCGTTTTACTTTAAAATAAACGA
Found at i:3845 original size:17 final size:17
Alignment explanation
Indices: 3808--3845 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3798 GGACTTTAAT
*
3808 TAAA-CAAGGTCCAACC
1 TAAATCAAGGTCCAAAC
*
3824 CAAATCAAGGTCCAAAC
1 TAAATCAAGGTCCAAAC
3841 TAAAT
1 TAAAT
3846 AATTAACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (17 bp):
TAAATCAAGGTCCAAAC
Found at i:4150 original size:23 final size:23
Alignment explanation
Indices: 4124--4170 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4114 GTTGTGCGCG
* *
4124 GATGCCCCATGTGATGGCTGGTT
1 GATGCCCCATGCGATGGCCGGTT
4147 GATGCCCCATGCGATGGCCGGTT
1 GATGCCCCATGCGATGGCCGGTT
4170 G
1 G
4171 TGGCCGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.36, T:0.26
Consensus pattern (23 bp):
GATGCCCCATGCGATGGCCGGTT
Found at i:10715 original size:23 final size:23
Alignment explanation
Indices: 10689--10733 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
10679 GTTGTGCGCG
10689 GATGCCCCATGCGATGGCCGGTT
1 GATGCCCCATGCGATGGCCGGTT
*
10712 GATGCCCCATGCGATGTCCGGT
1 GATGCCCCATGCGATGGCCGGT
10734 CAAGTGGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.22
Consensus pattern (23 bp):
GATGCCCCATGCGATGGCCGGTT
Found at i:14659 original size:85 final size:85
Alignment explanation
Indices: 14511--14677 Score: 253
Period size: 85 Copynumber: 2.0 Consensus size: 85
14501 ATGTACATTT
** * *
14511 AATTTTAGCACTTAGGGTTACAAAAATTGATAGTAAGTAGTAACTAGTTAATTAGTGCTCAATTT
1 AATTTTAGCACTTAACGTTACAAAAATTGATAGTAAGTAGTAACTAGCTAATTAGTGCCCAATTT
* *
14576 GCTATAAGTTGTAGCACATA
66 GCAATAAGTTATAGCACATA
* * *
14596 AATTTTAGCACTTAACGTTGCCAAAATTGATAGTAAGTAGTAACTAGCTAGTTAGTGCCCAATTT
1 AATTTTAGCACTTAACGTTACAAAAATTGATAGTAAGTAGTAACTAGCTAATTAGTGCCCAATTT
14661 GCAATAAGTTATAGCAC
66 GCAATAAGTTATAGCAC
14678 GTAGGGTACT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (85 bp):
AATTTTAGCACTTAACGTTACAAAAATTGATAGTAAGTAGTAACTAGCTAATTAGTGCCCAATTT
GCAATAAGTTATAGCACATA
Found at i:14978 original size:67 final size:67
Alignment explanation
Indices: 14901--15034 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
14891 TGAGAGATAC
14901 TCAATTCTCAACCTTTAGTATCTAAAATAATATTATAGAAAAAGGAAAAAGAGAAGTAAAACAAT
1 TCAATTCTCAACCTTTAGTATCTAAAATAATATTATAGAAAAAGGAAAAAGAGAAGTAAAACAAT
14966 CT
66 CT
14968 TCAATTCTCAACCTTTAGTATCTAAAATAATATTATAGAAAAAGGAAAAAGAGAAGTAAAACAAT
1 TCAATTCTCAACCTTTAGTATCTAAAATAATATTATAGAAAAAGGAAAAAGAGAAGTAAAACAAT
15033 CT
66 CT
15035 ACGAAGGGGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (67 bp):
TCAATTCTCAACCTTTAGTATCTAAAATAATATTATAGAAAAAGGAAAAAGAGAAGTAAAACAAT
CT
Found at i:18778 original size:36 final size:35
Alignment explanation
Indices: 18737--18855 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 35
18727 TTTTTTCTAG
*
18737 ATTAAGCTCTTTATTAACTTCACTTAATTACCTTGA
1 ATTAAGCTCTTTATT-ACTTCACTTAATTACCCTGA
*
18773 ATTAAGTTCTTTATT-C-T-ACTTAATTACCCTGA
1 ATTAAGCTCTTTATTACTTCACTTAATTACCCTGA
18805 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGA
1 ATTAAGCTC-TTTATT-ACTTCACTTAATTACCCTGA
*
18841 ATTAAGTTCTTTATT
1 ATTAAGCTCTTTATT
18856 TTACTTAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
33 1 0.01
34 2 0.03
35 1 0.01
36 41 0.56
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (35 bp):
ATTAAGCTCTTTATTACTTCACTTAATTACCCTGA
Found at i:18799 original size:32 final size:32
Alignment explanation
Indices: 18758--18865 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
18748 TATTAACTTC
*
18758 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCT
*
18790 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT--C-T
*
18825 CACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCT
18858 ACTTAATT
1 ACTTAATT
18866 TCCTTTCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 34 0.52
33 1 0.02
34 1 0.02
35 1 0.02
36 27 0.41
37 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCT
Found at i:18818 original size:68 final size:68
Alignment explanation
Indices: 18737--18865 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
18727 TTTTTTCTAG
*
18737 ATTAAGCTCTTTATTAACTTCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
1 ATTAAGCTCTTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
18802 TGA
66 TGA
* *
18805 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGCTC-TTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATT
18866 TCCTTTCCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 1 0.02
68 56 0.98
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:18941 original size:36 final size:36
Alignment explanation
Indices: 18869--19251 Score: 527
Period size: 36 Copynumber: 10.7 Consensus size: 36
18859 CTTAATTTCC
* * * * * *
18869 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
18903 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
*
18939 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * * *
18975 TTTTCTTGAAACTAAGCCAGTTCTTTTTTTTACTTAA
1 TTTCCTTGAAACTAAGCCAG-TCTTTTCTTTACCTAG
* * *
19012 TTTCCTTGAAATTAAGTCAGTCTATTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
19048 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
19084 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACTTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
19120 TTTCCTTGAAATTAAGTCAGTCTATTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
*
19156 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTATCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
19192 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
19228 TTTCCTTGAAACTAAGCCAGTCTT
1 TTTCCTTGAAACTAAGCCAGTCTT
19252 CTTTCAGTCT
Statistics
Matches: 312, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
34 5 0.02
35 16 0.05
36 261 0.84
37 30 0.10
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
Found at i:19172 original size:108 final size:108
Alignment explanation
Indices: 18869--19250 Score: 590
Period size: 108 Copynumber: 3.5 Consensus size: 108
18859 CTTAATTTCC
* * * *
18869 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCT-TTCCT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATT-CT
* *
18931 TTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
65 TTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
18975 TTTTCTTGAAACTAAGCCAGTTCTTTTTTTTACTTAATTTCCTTGAAATTAAGTCAGTCTATTCT
1 TTTCCTTGAAACTAAGCCAG-TCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTCT
19040 TTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
65 TTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* *
19084 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGTCAGTCTATTCTT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTCTT
*
19149 TACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTATCTAG
66 TACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
19192 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCT
19251 TCTTTCAGTC
Statistics
Matches: 255, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
106 4 0.02
107 12 0.05
108 144 0.56
109 93 0.36
110 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (108 bp):
TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTCTT
TACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
Found at i:19261 original size:11 final size:11
Alignment explanation
Indices: 19245--19404 Score: 142
Period size: 11 Copynumber: 14.5 Consensus size: 11
19235 GAAACTAAGC
*
19245 CAGTCTTCTTT
1 CAGTCTTATTT
*
19256 CAGTCTTCTTT
1 CAGTCTTATTT
*
19267 CAGTCTTCTTT
1 CAGTCTTATTT
* *
19278 CAGTATTCTTT
1 CAGTCTTATTT
*
19289 CAGTCTGATTT
1 CAGTCTTATTT
*
19300 CAGT-TTAATAT
1 CAGTCTT-ATTT
*
19311 CAGTCTTATAT
1 CAGTCTTATTT
*
19322 CAGTCTAATTT
1 CAGTCTTATTT
* *
19333 CAGTCTAATAT
1 CAGTCTTATTT
*
19344 CAGTCTTATAT
1 CAGTCTTATTT
*
19355 CAGTCTAATTT
1 CAGTCTTATTT
* *
19366 CAGTCTAATAT
1 CAGTCTTATTT
* *
19377 CAGTCTTCTAT
1 CAGTCTTATTT
*
19388 CAGTCTAATTT
1 CAGTCTTATTT
19399 CAGTCT
1 CAGTCT
19405 AACTTTGCCT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
10 1 0.01
11 126 0.98
12 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (11 bp):
CAGTCTTATTT
Found at i:19314 original size:33 final size:33
Alignment explanation
Indices: 19245--19406 Score: 216
Period size: 33 Copynumber: 4.9 Consensus size: 33
19235 GAAACTAAGC
* ** ** *
19245 CAGTCTTCTTTCAGTCTTCTTTCAGTCTTCTTT
1 CAGTCTTCTATCAGTCTAATTTCAGTCTAATAT
* * * *
19278 CAGTATTCTTTCAGTCTGATTTCAGTTTAATAT
1 CAGTCTTCTATCAGTCTAATTTCAGTCTAATAT
*
19311 CAGTCTTATATCAGTCTAATTTCAGTCTAATAT
1 CAGTCTTCTATCAGTCTAATTTCAGTCTAATAT
*
19344 CAGTCTTATATCAGTCTAATTTCAGTCTAATAT
1 CAGTCTTCTATCAGTCTAATTTCAGTCTAATAT
19377 CAGTCTTCTATCAGTCTAATTTCAGTCTAA
1 CAGTCTTCTATCAGTCTAATTTCAGTCTAA
19407 CTTTGCCTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 116 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (33 bp):
CAGTCTTCTATCAGTCTAATTTCAGTCTAATAT
Found at i:19609 original size:42 final size:42
Alignment explanation
Indices: 19548--19643 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
19538 CTGAATTAGG
19548 ACTATGTTTG-CTTTTCTTAATCACCATGGATTACAACTTCA
1 ACTATGTTTGACTTTTCTTAATCACCATGGATTACAACTTCA
* *
19589 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCATGGATTACAACTTCA
19631 ACTATGTTTGACT
1 ACTATGTTTGACT
19644 ATCCAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
41 10 0.19
42 42 0.81
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (42 bp):
ACTATGTTTGACTTTTCTTAATCACCATGGATTACAACTTCA
Found at i:23386 original size:22 final size:22
Alignment explanation
Indices: 23361--23429 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
23351 CTTGCCCTGG
* *
23361 GAAATTCTGCCCTAAGACGCTT
1 GAAAGTCTGCCCTGAGACGCTT
*
23383 GAAAGTCTGCCCTGAGACACTT
1 GAAAGTCTGCCCTGAGACGCTT
*
23405 AAAAGTCTGCCCTTGAGACGCTT
1 GAAAGTCTGCCC-TGAGACGCTT
23428 GA
1 GA
23430 GAAAGACCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (22 bp):
GAAAGTCTGCCCTGAGACGCTT
Found at i:27374 original size:33 final size:33
Alignment explanation
Indices: 27332--27402 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
27322 GTGTTTTAGA
* * *
27332 TGTTGTTTGCGATGATGCTAAACCTAATTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
* **
27365 TGTTGTTTGCAATAATACTAAATCTGTTTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
27398 TGTTG
1 TGTTG
27403 ATAGAGATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGCAATAATACTAAACCTAATTTGAG
Found at i:27517 original size:33 final size:33
Alignment explanation
Indices: 27431--27569 Score: 244
Period size: 33 Copynumber: 4.2 Consensus size: 33
27421 TCTTATTAGA
27431 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
27464 TGCAAATAA-TCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
27496 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
27529 TGAAAATAATTCTGTTTTTGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
27562 TGAAAATA
1 TGAAAATA
27570 GGACTGTTTC
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.31
33 69 0.69
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:27536 original size:65 final size:66
Alignment explanation
Indices: 27431--27569 Score: 244
Period size: 65 Copynumber: 2.1 Consensus size: 66
27421 TCTTATTAGA
*
27431 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAA-TCTGTTTTGGTTGATCATAGCA
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGAAAATAATTCTGTTTTGGTTGATCATAGCA
27495 T
66 T
* *
27496 TGAAAATAATTTTGTTTTGGTTGATCATAGCATTGAAAATAATTCTGTTTTTGTTGATCATAGCA
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGAAAATAATTCTGTTTTGGTTGATCATAGCA
27561 T
66 T
27562 TGAAAATA
1 TGAAAATA
27570 GGACTGTTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
65 40 0.57
66 30 0.43
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (66 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGAAAATAATTCTGTTTTGGTTGATCATAGCA
T
Found at i:30117 original size:15 final size:16
Alignment explanation
Indices: 30092--30125 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30082 AATAAAATAA
*
30092 TAAATTTAAACTAGAC
1 TAAATTTAAACTAAAC
30108 TAAA-TTAAACTAAAC
1 TAAATTTAAACTAAAC
30123 TAA
1 TAA
30126 GAGAAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAATTTAAACTAAAC
Found at i:30351 original size:19 final size:21
Alignment explanation
Indices: 30322--30363 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
30312 ATAAACTATG
30322 AACTAAAATTG-AAATAATTA
1 AACTAAAATTGCAAATAATTA
*
30342 AACT-AAATTGCAAGTAATTA
1 AACTAAAATTGCAAATAATTA
30362 AA
1 AA
30364 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGCAAATAATTA
Found at i:36450 original size:30 final size:30
Alignment explanation
Indices: 36416--36476 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
36406 TGAAAAAGTG
36416 TTGTAAAACCCGAAAAAC-TTTTGCCCTTAT
1 TTGTAAAACCCG-AAAACGTTTTGCCCTTAT
**
36446 TTGTAAAATTCGAAAACGTTTTGCCCTTAT
1 TTGTAAAACCCGAAAACGTTTTGCCCTTAT
36476 T
1 T
36477 CGCTCATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (30 bp):
TTGTAAAACCCGAAAACGTTTTGCCCTTAT
Found at i:38698 original size:13 final size:13
Alignment explanation
Indices: 38680--38704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38670 AAAAAAAAAA
38680 AGGGGGGGGGGGT
1 AGGGGGGGGGGGT
38693 AGGGGGGGGGGG
1 AGGGGGGGGGGG
38705 GATTGTGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.88, T:0.04
Consensus pattern (13 bp):
AGGGGGGGGGGGT
Found at i:44644 original size:2 final size:2
Alignment explanation
Indices: 44639--44674 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
44629 TCCCTTGTAG
*
44639 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44675 ATTTAGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47617 original size:20 final size:21
Alignment explanation
Indices: 47594--47632 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47584 ACGTGATTGC
47594 TAAATACC-GCCCCTTTTTGT
1 TAAATACCAGCCCCTTTTTGT
*
47614 TAAATACCATCCCCTTTTT
1 TAAATACCAGCCCCTTTTT
47633 TACACTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.31, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAATACCAGCCCCTTTTTGT
Found at i:47763 original size:24 final size:25
Alignment explanation
Indices: 47703--47761 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
47693 TTCAAACCCT
* *
47703 AAACTTCATTTCTAACAACTTTTTC
1 AAACTTCATTTCTAACAACATCTTC
47728 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
47752 AAA-TTCATTT
1 AAACTTCATTT
47762 TCCTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:47800 original size:26 final size:26
Alignment explanation
Indices: 47771--47838 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
47761 TTCCTTTATT
47771 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
47797 TTAATCATAAACTAATTAGATATTAA
1 TTAATCATAAACTAATTAAATACTAA
*
47823 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
47839 AAACTAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:47801 original size:15 final size:15
Alignment explanation
Indices: 47771--47814 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
47761 TTCCTTTATT
47771 TTAATCATAAACTAA
1 TTAATCATAAACTAA
47786 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
47797 TTAATCATAAACTAA
1 TTAATCATAAACTAA
47812 TTA
1 TTA
47815 GATATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:53582 original size:16 final size:16
Alignment explanation
Indices: 53561--53604 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
53551 AAGGAATAGG
53561 TAATCAATCAAAGCAA
1 TAATCAATCAAAGCAA
*
53577 TAATCATTCAAAGCAA
1 TAATCAATCAAAGCAA
53593 -AA-CAATGCAAAG
1 TAATCAAT-CAAAG
53605 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 7 0.28
16 15 0.60
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (16 bp):
TAATCAATCAAAGCAA
Found at i:56619 original size:19 final size:19
Alignment explanation
Indices: 56595--56636 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
56585 CCTAAATTAA
56595 TTTTCGACACAATTTTTTT
1 TTTTCGACACAATTTTTTT
*
56614 TTTTCGACGCAATTTTTTT
1 TTTTCGACACAATTTTTTT
56633 TTTT
1 TTTT
56637 TAGAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTCGACACAATTTTTTT
Found at i:58348 original size:11 final size:10
Alignment explanation
Indices: 58305--58351 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
58295 TTGAAATAAT
* *
58305 TCTTCAATTG
1 TCTTCAAATA
58315 TCTTC-AAT-
1 TCTTCAAATA
58323 TCTTCAAATA
1 TCTTCAAATA
58333 TCTTCAAATAA
1 TCTTCAAAT-A
58344 TCTTCAAA
1 TCTTCAAA
58352 CACGAACTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
8 5 0.15
9 5 0.15
10 14 0.42
11 9 0.27
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (10 bp):
TCTTCAAATA
Found at i:58349 original size:21 final size:21
Alignment explanation
Indices: 58293--58351 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 21
58283 AATTCTTGCT
* * *
58293 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAAATA
58315 TCTTC-AAT--TCTTCAAATA
1 TCTTCAAATAATCTTCAAATA
58333 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
58352 CACGAACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 13 0.42
19 3 0.10
21 11 0.35
22 4 0.13
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAAATA
Found at i:60693 original size:28 final size:28
Alignment explanation
Indices: 60626--60697 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
60616 GTTACGGGGT
* * *
60626 TTTTGTAATTTTGGCTAGTTGCGGCAAA
1 TTTTGCAATTTTGGGTACTTGCGGCAAA
* *
60654 TTTTGGAATTTTGGGTACTTGTGGC-AA
1 TTTTGCAATTTTGGGTACTTGCGGCAAA
60681 TTTTGCAATTTTTGGGT
1 TTTTGCAA-TTTTGGGT
60698 TGCTGCGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.47
Consensus pattern (28 bp):
TTTTGCAATTTTGGGTACTTGCGGCAAA
Found at i:61064 original size:12 final size:11
Alignment explanation
Indices: 61047--61076 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
61037 CTCTCTTTTC
61047 TTTTTTTCTTCT
1 TTTTTTTCTT-T
61059 TTTTTTTCTTT
1 TTTTTTTCTTT
61070 TTTTTTT
1 TTTTTTT
61077 AAAAAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:61784 original size:2 final size:2
Alignment explanation
Indices: 61777--61806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61767 TGCTAGTCTC
61777 TA 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 TA
61807 ATGTGCTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64154 original size:11 final size:11
Alignment explanation
Indices: 64138--64203 Score: 96
Period size: 11 Copynumber: 6.0 Consensus size: 11
64128 TATACTATAT
64138 CTAATTAATAA
1 CTAATTAATAA
*
64149 CTAATTAATAT
1 CTAATTAATAA
64160 CTAATTAATAA
1 CTAATTAATAA
*
64171 CTAATTAATAT
1 CTAATTAATAA
*
64182 CTAATTAATAG
1 CTAATTAATAA
*
64193 TTAATTAATAA
1 CTAATTAATAA
64204 TGAATAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 49 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:64159 original size:22 final size:22
Alignment explanation
Indices: 64134--64202 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
64124 CCATTATACT
64134 ATATCTAATTAATAACTAATTA
1 ATATCTAATTAATAACTAATTA
64156 ATATCTAATTAATAACTAATTA
1 ATATCTAATTAATAACTAATTA
**
64178 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAACTAATTA
64200 ATA
1 ATA
64203 ATGAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Found at i:64175 original size:33 final size:33
Alignment explanation
Indices: 64138--64203 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
64128 TATACTATAT
64138 CTAATTAATAACTAATTAATA-TCTAATTAATAA
1 CTAATTAATAACTAATTAATAGT-TAATTAATAA
*
64171 CTAATTAATATCTAATTAATAGTTAATTAATAA
1 CTAATTAATAACTAATTAATAGTTAATTAATAA
64204 TGAATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (33 bp):
CTAATTAATAACTAATTAATAGTTAATTAATAA
Done.