Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005959.1 Corchorus capsularis cultivar CVL-1 contig05977, 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: 104253
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:722 original size:3 final size:3
Alignment explanation
Indices: 707--739 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
697 TCGAGCTTGG
*
707 GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
740 ATTAGCAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:16727 original size:22 final size:22
Alignment explanation
Indices: 16701--16750 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
16691 TACTCGATTA
* *
16701 ATGTTCGTTTAGTA-TTCGTTT
1 ATGTTCGTTTAATAGCTCGTTT
16722 ATTGTTCGTTTAATAGCTCGTTT
1 A-TGTTCGTTTAATAGCTCGTTT
16745 ATGTTC
1 ATGTTC
16751 ATTATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 7 0.28
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (22 bp):
ATGTTCGTTTAATAGCTCGTTT
Found at i:20518 original size:31 final size:29
Alignment explanation
Indices: 20480--20679 Score: 147
Period size: 31 Copynumber: 6.6 Consensus size: 29
20470 ATTGGCTAAT
20480 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTT-TCAAAA
* * **
20511 TGCTCAAATAAGGGTCTGATCTTTT-AATT
1 TGCTCAAATAAGGGCCT-AACTTTTCAAAA
* *
20540 TGGC-CAAATAAGGGTCTAACCTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAA-CTTTTC-AAAA
* * **
20571 TGCTCAAATAAGGGCCCGATCTTTT-AATT
1 TGCTCAAATAAGGG-CCTAACTTTTCAAAA
*
20600 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTTC-AAAA
*
20631 TGCTCAAATAAGGGCCTAACGTTATTAAAAAA
1 TGCTCAAATAAGGGCCTAAC-TT-TT-CAAAA
20663 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
20680 GTTGTCAGTT
Statistics
Matches: 134, Mismatches: 21, Indels: 27
0.74 0.12 0.15
Matches are distributed among these distances:
28 5 0.04
29 36 0.27
30 9 0.07
31 58 0.43
32 26 0.19
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACTTTTCAAAA
Found at i:20577 original size:60 final size:60
Alignment explanation
Indices: 20484--20646 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
20474 GCTAATTGCT
* * * *
20484 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-CTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
20544 CAAATAAGGGTCTAACCTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACCTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
20604 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACCTTATCGAAAATGCTCAAATAAGGGCC
20647 TAACGTTATT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 4 0.04
60 91 0.96
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACCTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:20668 original size:32 final size:31
Alignment explanation
Indices: 20604--20679 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 31
20594 TTAATTTGGC
**
20604 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATAAAAAATGCT
20635 CAAATAAGGGCCTAACGTTATTAAAAAATGCT
1 CAAATAAGGGCCTAACGTTA-TAAAAAATGCT
20667 CAAATAAGGGCCT
1 CAAATAAGGGCCT
20680 GTTGTCAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 20 0.48
32 22 0.52
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATAAAAAATGCT
Found at i:20787 original size:60 final size:60
Alignment explanation
Indices: 20709--20867 Score: 264
Period size: 60 Copynumber: 2.6 Consensus size: 60
20699 CATGAGACAA
* * **
20709 ACCCATATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
1 ACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
*
20769 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
1 ACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
*
20829 ACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTAT
1 ACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTAT
20868 CTGAGCAATT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (60 bp):
ACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
Found at i:20806 original size:31 final size:30
Alignment explanation
Indices: 20714--20874 Score: 127
Period size: 31 Copynumber: 5.3 Consensus size: 30
20704 GACAAACCCA
20714 TATTTGAGCATTTTGGCAAACGTTAGGCCCT
1 TATTTGAGCATTTT-GCAAACGTTAGGCCCT
** **
20745 TATTTG-GCCAAATT-CAAA-GATGGGGCCCT
1 TATTTGAG-CATTTTGCAAACG-TTAGGCCCT
20774 TATTTGAGCATTTTGGCAAACGTTAGGCCCT
1 TATTTGAGCATTTT-GCAAACGTTAGGCCCT
** * * *
20805 TATTTG-GCCAAATT--AAAAGATCAGACCCT
1 TATTTGAG-CATTTTGCAAACG-TTAGGCCCT
20834 TATTTGAGCATTTTGACAAACGTTAGGCCCT
1 TATTTGAGCATTTTG-CAAACGTTAGGCCCT
*
20865 TATCTGAGCA
1 TATTTGAGCA
20875 ATTAGCCAAA
Statistics
Matches: 99, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.05
29 38 0.38
30 4 0.04
31 47 0.47
32 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (30 bp):
TATTTGAGCATTTTGCAAACGTTAGGCCCT
Found at i:29175 original size:156 final size:155
Alignment explanation
Indices: 28786--29175 Score: 431
Period size: 156 Copynumber: 2.5 Consensus size: 155
28776 TCACCTCAAA
* *
28786 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGAGGTGTGAAG-TCGG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTG-GAAGCTCGG
* *
28850 TTCACTACCAAGG-GAAGCTCGGTTTTACTTAGAAAGTTTTCCATAGTCTTATGGAGATAATCTA
65 TTCACTATCAAGGAGAAGCTCGGTTTTAATTAGAAAGTTTTCCATAGTCTTATGGAGATAATCTA
**
28914 AGCCTACTGGTGGAAAATTAGCCTTGTT
130 AGCC-ACT-GTGGAAAATTAGCCTCATT
* * * *
28942 GA-ACTTAGAATGAAAAACTTATGCTAGTTCTTCATTTAAGGACAACTCATG-GGTGGAAAC-CT
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAA-T-TTGAGGTGGAAGCTC-
* * * ** *
29004 AGTTCACCATCAAGGAG-AGCTCGGTTTTAATTATAATTTTTTCCATAGTCTTATGTG-GATATT
63 GGTTCACTATCAAGGAGAAGCTCGGTTTTAATTAGAAAGTTTTCCATAGTCTTATG-GAGATAAT
29067 CTAAGTCC-CT-TGGAAAAATTTCAG-CTCATT
127 CTAAG-CCACTGTGG-AAAA-TT-AGCCTCATT
*
29097 CAGACTTAGAATGAAGAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAGCTCGG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTG-GAAGCTCGG
* *
29162 TTTACTATGAAGGA
65 TTCACTATCAAGGA
29176 AGGCTCAGAA
Statistics
Matches: 195, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
153 3 0.02
154 6 0.03
155 58 0.30
156 121 0.62
157 7 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (155 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGGAAGCTCGGT
TCACTATCAAGGAGAAGCTCGGTTTTAATTAGAAAGTTTTCCATAGTCTTATGGAGATAATCTAA
GCCACTGTGGAAAATTAGCCTCATT
Found at i:33617 original size:12 final size:12
Alignment explanation
Indices: 33600--33624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33590 CAAATTTAAA
33600 TAAATAATGAAT
1 TAAATAATGAAT
33612 TAAATAATGAAT
1 TAAATAATGAAT
33624 T
1 T
33625 TTAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAATAATGAAT
Found at i:45553 original size:37 final size:38
Alignment explanation
Indices: 45495--45566 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
45485 CTTGATCAAC
* *
45495 ATACATGATCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGATCTTTCCAAATAGACATAACTTTATGATCA
45533 ATACATG-TCTTTCCAAATAGACATAACTTTATGA
1 ATACATGATCTTTCCAAATAGACATAACTTTATGA
45567 ATAATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (38 bp):
ATACATGATCTTTCCAAATAGACATAACTTTATGATCA
Found at i:46810 original size:31 final size:32
Alignment explanation
Indices: 46762--46823 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
46752 CATCATAGTG
46762 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
* *
46794 ATATATCTC-TTTGTTTCTTTAAGAAACCAA
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAA
46824 GACACCCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
Found at i:48405 original size:35 final size:37
Alignment explanation
Indices: 48338--48406 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
48328 CTTGATCAAC
*
48338 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTTCATAAAGACATAACTTTATGATCA
*
48375 ATACATGTC-TTTC-TAAAGTCATAACTTTATGA
1 ATACATGTCTTTTCATAAAGACATAACTTTATGA
48407 ATAATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 17 0.57
36 4 0.13
37 9 0.30
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (37 bp):
ATACATGTCTTTTCATAAAGACATAACTTTATGATCA
Found at i:48463 original size:388 final size:388
Alignment explanation
Indices: 47747--48516 Score: 1432
Period size: 388 Copynumber: 2.0 Consensus size: 388
47737 ATTTGAATTA
* *
47747 TGAGAAAATTTCTAATTAAGAAAATATTGAAACAAGACTTTGAGGCGCCAAGCTTTCTCAAATAC
1 TGAGAAAATTTCTAATTAAGAAAATATTGAAACAAGACTTTGAGGCACCAAGATTTCTCAAATAC
47812 AATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTCA
66 AATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTCA
* * *
47877 GAGAGAAGTAGAATTATTGGTTCTCTCTCTTTTAAAATGTTTATGTGAAAGCTACCTTATATATT
131 GAGAGAAGTAGAATTATTGGTTCTATCTCTTTTAAAATGTTTATGTGAAAGCCACCTTATATACT
47942 TGATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCAATAAATGTCTTTCTAAAGAC
196 TGATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCAATAAATGTCTTTCTAAAGAC
*
48007 ATAACTTTATGAATAATTATATTATAAAGATACCTATTATAGACAAATAAGTCTCTTCATAATTG
261 ATAACTTTATGAATAATTATATCATAAAGATACCTATTATAGACAAATAAGTCTCTTCATAATTG
48072 TTCACTTATGAACAAATGCATTCAATAAACATCAACATTCAAAAAATATCCAACAATATATTG
326 TTCACTTATGAACAAATGCATTCAATAAACATCAACATTCAAAAAATATCCAACAATATATTG
48135 TGAGAAAATTTCTAATTAAGAAAATATTGAAACAAGACTTTGAGGCACCAAGATTTCTCAAATAC
1 TGAGAAAATTTCTAATTAAGAAAATATTGAAACAAGACTTTGAGGCACCAAGATTTCTCAAATAC
*
48200 AATATTGCTTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTCA
66 AATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTCA
48265 GAGAGAAGTAGAATTATTGGTTCTATCTCTTTTAAAATGTTTATGTGAAAGCCACCTTATATACT
131 GAGAGAAGTAGAATTATTGGTTCTATCTCTTTTAAAATGTTTATGTGAAAGCCACCTTATATACT
* *
48330 TGATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCAATACATGTCTTTCTAAAGTC
196 TGATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCAATAAATGTCTTTCTAAAGAC
* *
48395 ATAACTTTATGAATAATTATATCATAAAGATACCTTTTATAGAGAAATAAGTCTCTTCATAATTG
261 ATAACTTTATGAATAATTATATCATAAAGATACCTATTATAGACAAATAAGTCTCTTCATAATTG
*
48460 TTCACTTATGAACAAATGCTTTCAATAAACATCAACATTCAAAAAATATCCAACAAT
326 TTCACTTATGAACAAATGCATTCAATAAACATCAACATTCAAAAAATATCCAACAAT
48517 CCCCCACTAT
Statistics
Matches: 370, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
388 370 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (388 bp):
TGAGAAAATTTCTAATTAAGAAAATATTGAAACAAGACTTTGAGGCACCAAGATTTCTCAAATAC
AATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTCA
GAGAGAAGTAGAATTATTGGTTCTATCTCTTTTAAAATGTTTATGTGAAAGCCACCTTATATACT
TGATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCAATAAATGTCTTTCTAAAGAC
ATAACTTTATGAATAATTATATCATAAAGATACCTATTATAGACAAATAAGTCTCTTCATAATTG
TTCACTTATGAACAAATGCATTCAATAAACATCAACATTCAAAAAATATCCAACAATATATTG
Found at i:50200 original size:26 final size:25
Alignment explanation
Indices: 50162--50213 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
50152 TTTCTCACAA
50162 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * *
50188 AAATAATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
50213 A
1 A
50214 TCTCATTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:50913 original size:35 final size:37
Alignment explanation
Indices: 50849--50917 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
50839 CTTGATCAAC
*
50849 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTTCATAAAGACATAACTTTATGATCA
50886 ATACATGTC-TTTC-TAAAGACATAACTTTATGA
1 ATACATGTCTTTTCATAAAGACATAACTTTATGA
50918 ATAATCATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 18 0.58
36 4 0.13
37 9 0.29
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (37 bp):
ATACATGTCTTTTCATAAAGACATAACTTTATGATCA
Found at i:52801 original size:31 final size:31
Alignment explanation
Indices: 52777--52855 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 31
52767 TAAATCTTTT
52777 ATTTTAG-GAGGGTCAATGTGATAAAACTTCA
1 ATTTTAGTG-GGGTCAATGTGATAAAACTTCA
52808 ATTTTAGTGGGGTCAATGTGATAAAACTTCA
1 ATTTTAGTGGGGTCAATGTGATAAAACTTCA
52839 ATTTTAGTGGGGTCAAT
1 ATTTTAGTGGGGTCAAT
52856 TGGTAATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 46 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (31 bp):
ATTTTAGTGGGGTCAATGTGATAAAACTTCA
Found at i:56413 original size:21 final size:21
Alignment explanation
Indices: 56389--56464 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
56379 AAAGCTGTAA
*
56389 AGAACAGCCGCCTACACCTAG
1 AGAACAGCCGCCTACCCCTAG
*
56410 AGAACAACCGCCTACCCCTAG
1 AGAACAGCCGCCTACCCCTAG
*
56431 AGAACAGCCGACTACCCCTAG
1 AGAACAGCCGCCTACCCCTAG
*
56452 AGAACAGCGGCCT
1 AGAACAGCCGCCT
56465 CCTCCACTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.09
Consensus pattern (21 bp):
AGAACAGCCGCCTACCCCTAG
Found at i:59698 original size:27 final size:26
Alignment explanation
Indices: 59651--59719 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
59641 CATCAGTGGA
* *
59651 TACCGCAGGAAAATCTGGAGAATTAAT-
1 TACCGCAGGAAAAACTAGAG-A-TAATC
* *
59678 TATCGCAGGAAAAACTAGAGATGATC
1 TACCGCAGGAAAAACTAGAGATAATC
59704 TACCGCAGGAAAAACT
1 TACCGCAGGAAAAACT
59720 TGATATGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.08
26 16 0.44
27 17 0.47
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (26 bp):
TACCGCAGGAAAAACTAGAGATAATC
Found at i:63510 original size:1 final size:1
Alignment explanation
Indices: 63474--63498 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
63464 ATTTTGTTGC
63474 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
63499 GTGAATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:64661 original size:5 final size:5
Alignment explanation
Indices: 64651--64675 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
64641 ACTTTTTATT
64651 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
64676 TTTAGGTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:67391 original size:17 final size:16
Alignment explanation
Indices: 67357--67393 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
67347 TTAGAATGCC
*
67357 AAAAAAAAATTAACCA
1 AAAAAAAAATTAAACA
67373 AAAAAAAAATTAAAACA
1 AAAAAAAAATT-AAACA
67390 AAAA
1 AAAA
67394 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAAAAAATTAAACA
Found at i:77681 original size:38 final size:39
Alignment explanation
Indices: 77589--77700 Score: 145
Period size: 38 Copynumber: 2.8 Consensus size: 39
77579 ACGTTTTCTA
*
77589 TTTAAACAATTCCAAGAGAAGACTTTTGGAAAATAAATGTCT
1 TTTAAA-AAATCCAAGAGAAGACTTTTGG-AAATAAATG-CT
** *
77631 TTTAGCAAATCCAAAAGAAGACTTTTGGAAATAAATG-T
1 TTTAAAAAATCCAAGAGAAGACTTTTGGAAATAAATGCT
*
77669 TTTAAAAAATCCAAGAGAAGACTTTTAGAAAT
1 TTTAAAAAATCCAAGAGAAGACTTTTGGAAAT
77701 TAATAAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 29 0.47
40 9 0.15
41 20 0.32
42 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (39 bp):
TTTAAAAAATCCAAGAGAAGACTTTTGGAAATAAATGCT
Found at i:91677 original size:88 final size:89
Alignment explanation
Indices: 91501--91680 Score: 353
Period size: 88 Copynumber: 2.0 Consensus size: 89
91491 AAAATTGCAT
91501 GTGCATGGCTAGAGCTTTGAGTTGAGAGATGTCTATATTGAATTTTTATATCCCCTTTTTGCAAA
1 GTGCATGGCTAGAGCTTTGAGTTGAGAGATGTCTATATTGAATTTTTATATCCCCTTTTTGCAAA
91566 TCCAAGTTGATTTTATTCTCTAAA
66 TCCAAGTTGATTTTATTCTCTAAA
91590 GTGCATGGCTAGAGCTTTGAGTTGAGAGATGTCTATATTGAA-TTTTATATCCCCTTTTTGCAAA
1 GTGCATGGCTAGAGCTTTGAGTTGAGAGATGTCTATATTGAATTTTTATATCCCCTTTTTGCAAA
91654 TCCAAGTTGATTTTATTCTCTAAA
66 TCCAAGTTGATTTTATTCTCTAAA
91678 GTG
1 GTG
91681 TTCTAAAGTT
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 49 0.54
89 42 0.46
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (89 bp):
GTGCATGGCTAGAGCTTTGAGTTGAGAGATGTCTATATTGAATTTTTATATCCCCTTTTTGCAAA
TCCAAGTTGATTTTATTCTCTAAA
Found at i:99582 original size:2 final size:2
Alignment explanation
Indices: 99577--99607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
99567 AGTTGAGAGA
99577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
99608 CACACTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100399 original size:66 final size:65
Alignment explanation
Indices: 100323--100449 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 65
100313 AAAGAATTAC
* * **
100323 AAATAAAATATAGTCTATGGCAATACTTAATATTTTTTTGTTTTGTAATTAGAATATCTAATATA
1 AAATAAAATATAATCTATGGCAATACTTAATATTTTTATGTTTAAT-ATTAGAATATCTAATATA
100388 G
65 G
100389 AAATAAAATATAATCTATGGCAATACTTAATATTTTTATGTTTAATATTAGAATATCTAAT
1 AAATAAAATATAATCTATGGCAATACTTAATATTTTTATGTTTAATATTAGAATATCTAAT
100450 TTTTTTTGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 15 0.26
66 42 0.74
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (65 bp):
AAATAAAATATAATCTATGGCAATACTTAATATTTTTATGTTTAATATTAGAATATCTAATATAG
Found at i:100597 original size:21 final size:21
Alignment explanation
Indices: 100571--100612 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
100561 GTTCTTCTTT
100571 AAGGTTACTAAAAAA-GTTATA
1 AAGGTTA-TAAAAAATGTTATA
100592 AAGGTTATAAAAAATGTTATA
1 AAGGTTATAAAAAATGTTATA
100613 GTATTATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (21 bp):
AAGGTTATAAAAAATGTTATA
Found at i:100779 original size:2 final size:2
Alignment explanation
Indices: 100774--100799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
100764 TTGTGAAGAT
100774 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
100800 AAGTTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100940 original size:21 final size:20
Alignment explanation
Indices: 100898--100941 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
100888 TCTTGTAATC
*
100898 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
100918 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
100939 TAA
1 TAA
100942 TGCTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:102789 original size:3 final size:3
Alignment explanation
Indices: 102775--102826 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
102765 TCAACAAATT
*
102775 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
102823 TTA T
1 TTA T
102827 ATTTTGATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:103128 original size:21 final size:21
Alignment explanation
Indices: 103104--103149 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
103094 CTCTACCAAA
*
103104 CTAATGAATGATCTATGTGAT
1 CTAATGAATGATCAATGTGAT
103125 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATGTGAT
103146 CTAA
1 CTAA
103150 AATAACATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
CTAATGAATGATCAATGTGAT
Done.