Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013762.1 Corchorus olitorius cultivar O-4 contig13795, 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: 26706
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:7 original size:1 final size:1
Alignment explanation
Indices: 2--27 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1 C
2 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
28 CACTGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:779 original size:29 final size:29
Alignment explanation
Indices: 737--809 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
727 ACTAAAAGAC
737 TTTATAAGTTTTTTTTTTGGCACACAAAT
1 TTTATAAGTTTTTTTTTTGGCACACAAAT
766 TTTATAAGTTTTTTTTTTGGCACACAAAT
1 TTTATAAGTTTTTTTTTTGGCACACAAAT
*
795 TTTATAAGTTATTTT
1 TTTATAAGTTTTTTT
810 AAGAAACAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (29 bp):
TTTATAAGTTTTTTTTTTGGCACACAAAT
Found at i:5290 original size:22 final size:22
Alignment explanation
Indices: 5243--5290 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5233 GCTTACAAGA
*
5243 TTAC-AAAAATTTTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
* *
5264 CTACTAAAAATTGTAATAAGGG
1 TTACTAAAAATTGTAATAAAGG
5286 TTACT
1 TTACT
5291 GAAACGTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
TTACTAAAAATTGTAATAAAGG
Found at i:5606 original size:22 final size:20
Alignment explanation
Indices: 5581--5627 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5571 AAAACACTCA
*
5581 ATAAGGTTGCTAAAAAAACTTC
1 ATAAGGTTACT-AAAAAA-TTC
*
5603 ATAAGGTTACTATAAAATTC
1 ATAAGGTTACTAAAAAATTC
5623 ATAAG
1 ATAAG
5628 TTAACTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 10 0.43
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (20 bp):
ATAAGGTTACTAAAAAATTC
Found at i:5625 original size:20 final size:21
Alignment explanation
Indices: 5581--5638 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
5571 AAAACACTCA
* *
5581 ATAAGGTTGCTAAAAAAACTTC
1 ATAAGGTTACT-ATAAAACTTC
5603 ATAAGGTTACTATAAAA-TTC
1 ATAAGGTTACTATAAAACTTC
5623 ATAA-GTTAACTATAAA
1 ATAAGGTT-ACTATAAA
5639 TCTTACAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 5 0.15
22 10 0.30
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (21 bp):
ATAAGGTTACTATAAAACTTC
Found at i:5682 original size:21 final size:20
Alignment explanation
Indices: 5658--5711 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
5648 GTCACTAAAC
* *
5658 AAAAACTTAAGTAAGGTCTCT
1 AAAAACTTAA-TAAGATCACT
5679 AAAACACGTTAATAAGATCACT
1 AAAA-AC-TTAATAAGATCACT
5701 AAAAATCTTAA
1 AAAAA-CTTAA
5712 ACGAGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 9 0.32
22 15 0.54
23 4 0.14
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAAACTTAATAAGATCACT
Found at i:5750 original size:45 final size:45
Alignment explanation
Indices: 5700--5838 Score: 115
Period size: 45 Copynumber: 3.1 Consensus size: 45
5690 ATAAGATCAC
5700 TAAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAACTATT
1 TAAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAACTATT
* ** * * * * * **
5745 TAAAAAGCTTTTA--AGTTTAATGAA-AAATTTTA-TAAGCTTACCA
1 TAAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAAC-TA-TT
* * *
5788 AAAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATT
1 TAAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAACTATT
5833 TAAAAA
1 TAAAAA
5839 ACTTTTAAGT
Statistics
Matches: 65, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
41 3 0.05
42 9 0.14
43 18 0.28
45 23 0.35
46 9 0.14
47 3 0.05
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.32
Consensus pattern (45 bp):
TAAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAACTATT
Found at i:5795 original size:88 final size:86
Alignment explanation
Indices: 5701--5881 Score: 299
Period size: 88 Copynumber: 2.1 Consensus size: 86
5691 TAAGATCACT
* *
5701 AAAAATCTTAAACGAGATTATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGATGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAGTTTAAT
*
5766 GAAAAATTTTATAAGCTTACCAA
66 G-AAAACTTTATAAGCTTA-CAA
*
5789 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGATGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAGTTTAAT
5854 GAAAACTTTATAAGCTTACAA
66 GAAAACTTTATAAGCTTACAA
5875 AGAAAAT
1 A-AAAAT
5882 TTACAAGGTT
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
86 4 0.05
87 21 0.24
88 63 0.72
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (86 bp):
AAAAATCTTAAACGAGATGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAGTTTAAT
GAAAACTTTATAAGCTTACAA
Found at i:5965 original size:21 final size:20
Alignment explanation
Indices: 5920--5962 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
5910 TTACAGTAAT
*
5920 AAGTTAAATAGTTTACTAAA
1 AAGTTAAATAGATTACTAAA
5940 AAGTTAAATAAGATTACCTAAA
1 AAGTTAAAT-AGATTA-CTAAA
5962 A
1 A
5963 GTTTTCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (20 bp):
AAGTTAAATAGATTACTAAA
Found at i:10377 original size:26 final size:28
Alignment explanation
Indices: 10341--10392 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
10331 TAAGGTGACT
10341 AAAAAACTTT-ATAAGG-CCAAAAAAGG
1 AAAAAACTTTAATAAGGTCCAAAAAAGG
*
10367 AAAAAAGTTTAATAAGGTCCAAAAAA
1 AAAAAACTTTAATAAGGTCCAAAAAA
10393 AAGATCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAAAACTTTAATAAGGTCCAAAAAAGG
Found at i:11257 original size:3 final size:3
Alignment explanation
Indices: 11239--11271 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
11229 TTATTCCAAA
11239 ATT ATTT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11272 TTCCTCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:11299 original size:26 final size:27
Alignment explanation
Indices: 11270--11333 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
11260 ATTATTATTA
11270 TTTTCCTCCTAATTCTCTT-ATTTTCC
1 TTTTCCTCCTAATTCTCTTCATTTTCC
* ** * *
11296 TTTTCTTCCTTTTTCTTTTCTTTTTCC
1 TTTTCCTCCTAATTCTCTTCATTTTCC
11323 TTCTTCCTCCT
1 TT-TTCCTCCT
11334 TATATTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 15 0.50
27 8 0.27
28 7 0.23
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTCCTCCTAATTCTCTTCATTTTCC
Found at i:11615 original size:27 final size:28
Alignment explanation
Indices: 11568--11642 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
11558 CCCTTATTGG
*
11568 TAAAATTA-CGATTTTACCCCTATCAT-GAA
1 TAAAATTACCG-TTTT-GCCCT-TCATCGAA
**
11597 -AAAATTACCGTTTTGCCCTTTGTCGAA
1 TAAAATTACCGTTTTGCCCTTCATCGAA
11624 TAAAATTACCGTTTTGCCC
1 TAAAATTACCGTTTTGCCC
11643 CTGTAGACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.05
27 7 0.17
28 29 0.73
29 2 0.05
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (28 bp):
TAAAATTACCGTTTTGCCCTTCATCGAA
Found at i:11657 original size:28 final size:28
Alignment explanation
Indices: 11597--11649 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
11587 CTATCATGAA
* *
11597 AAAATTACCGTTTTGCCCTTTGTCGAAT
1 AAAATTACCGTTTTGCCCTCTGTAGAAT
11625 AAAATTACCGTTTTGCCC-CTGTAGA
1 AAAATTACCGTTTTGCCCTCTGTAGA
11650 CCTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (28 bp):
AAAATTACCGTTTTGCCCTCTGTAGAAT
Found at i:13504 original size:16 final size:16
Alignment explanation
Indices: 13483--13513 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13473 TCTACAAATT
13483 ATAAAGACTTAGTAAA
1 ATAAAGACTTAGTAAA
*
13499 ATAAAGATTTAGTAA
1 ATAAAGACTTAGTAA
13514 TATTTTCAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAAAGACTTAGTAAA
Found at i:17948 original size:27 final size:27
Alignment explanation
Indices: 17916--17973 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
17906 ATTTCAATTC
17916 CAAATTTATTTCTCAAATGTGGGTTCA
1 CAAATTTATTTCTCAAATGTGGGTTCA
17943 CAAATTTATTTCTCAAATGTGGGTTCA
1 CAAATTTATTTCTCAAATGTGGGTTCA
17970 CAAA
1 CAAA
17974 CGGACCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (27 bp):
CAAATTTATTTCTCAAATGTGGGTTCA
Found at i:20714 original size:91 final size:91
Alignment explanation
Indices: 20555--20738 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
20545 ATGTATAAGT
*
20555 AAACATCTCTAGGACCTAACATGTTTATATTACGTCAAAATTCAAATAACCACATTCGAAGGAGA
1 AAACATCTCTAGGACCTAACATGTTTATATTACGTCAAAATTCAAATAACCACATTCGAAGGAAA
20620 ACAGAAAATTGGAACAAGAAAACAGA
66 ACAGAAAATTGGAACAAGAAAACAGA
20646 AAACATCTCTAGGACCTAACATGTTTATATTACGTCAAAATTCAAATAACCACATTCGAAGGAAA
1 AAACATCTCTAGGACCTAACATGTTTATATTACGTCAAAATTCAAATAACCACATTCGAAGGAAA
20711 ACAGAAAATTGGAACAAGAAAACAGA
66 ACAGAAAATTGGAACAAGAAAACAGA
20737 AA
1 AA
20739 GCATTGGAGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (91 bp):
AAACATCTCTAGGACCTAACATGTTTATATTACGTCAAAATTCAAATAACCACATTCGAAGGAAA
ACAGAAAATTGGAACAAGAAAACAGA
Found at i:22247 original size:3 final size:3
Alignment explanation
Indices: 22193--22232 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
22183 CAAAAAAAAA
*
22193 AAG AAA AAG AAG AAG AAG AAG AAG AAG -AG ACAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG A
22233 GCAAAGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Done.