Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011236.1 Corchorus capsularis cultivar CVL-1 contig11257, 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: 6391
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
44 T
1 T
45 TATTTTTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:199 original size:11 final size:11
Alignment explanation
Indices: 183--225 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
173 TATACTATAT
183 CTAATTAATAG
1 CTAATTAATAG
*
194 CTAATTAATAT
1 CTAATTAATAG
205 CTAATTAATAG
1 CTAATTAATAG
*
216 TTAATTAATA
1 CTAATTAATA
226 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:204 original size:22 final size:22
Alignment explanation
Indices: 179--225 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
169 CCATTATACT
179 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
201 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
223 ATA
1 ATA
226 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:2031 original size:108 final size:107
Alignment explanation
Indices: 1874--2196 Score: 391
Period size: 107 Copynumber: 3.0 Consensus size: 107
1864 GGTGGATAGC
*
1874 CTGTATATAAGGCATTCAGTCATGTCACACTTATACGATGTGGGATATTATTACTCTAACATGCC
1 CTGTATATAAGGCAATCAGTCATGTCACACTTATACGATGTGGGATATTATTACTCTAACAT-CC
* * *
1939 CCTTACATGTAATCCGGAACAACACATCGGGTCTATACGTGGA
65 CCTCACGTGTAGTCCGGAACAACACATCGGGTCTATACGTGGA
* * * * * *
1982 CTGTATATAAGGCACTCAGTCATGTCACACTTGTACGATGTGCGATATTATCACT-AACACACCC
1 CTGTATATAAGGCAATCAGTCATGTCACACTTATACGATGTGGGATATTATTACTCTA-ACATCC
* * * *
2046 CCTCACGTGTAGCCCGGAACAGCACCTCGGGTCTACACGTGGA
65 CCTCACGTGTAGTCCGGAACAACACATCGGGTCTATACGTGGA
* * * * *
2089 CTATATATAAGGCAATCAGTAATGTAACACTTATACGATGTGGGATATTATCACT-AATACATCC
1 CTGTATATAAGGCAATCAGTCATGTCACACTTATACGATGTGGGATATTATTACTCTA-ACATCC
* * *
2153 CCTCACGTGTAGGT-CAGAACAACACATCAGGTTTATACGTGGA
65 CCTCACGTGTA-GTCCGGAACAACACATCGGGTCTATACGTGGA
2196 C
1 C
2197 AACCGAGTCT
Statistics
Matches: 185, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
107 130 0.70
108 55 0.30
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (107 bp):
CTGTATATAAGGCAATCAGTCATGTCACACTTATACGATGTGGGATATTATTACTCTAACATCCC
CTCACGTGTAGTCCGGAACAACACATCGGGTCTATACGTGGA
Found at i:2727 original size:31 final size:31
Alignment explanation
Indices: 2689--2787 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
2679 TTAATTTGGC
2689 CAAATAAGGGCCTAACGTTTGGCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGGCAAAATGCT
* * **
2720 CAAATAAGGGCCCATC-TTT-G-AATTTGGC-
1 CAAATAAGGGCCTAACGTTTGGCAAAAT-GCT
*
2748 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGGCAAAATGCT
2779 CAAATAAGG
1 CAAATAAGG
2788 ACTTATCTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 17 0.31
29 6 0.11
30 5 0.09
31 26 0.48
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGGCAAAATGCT
Found at i:2749 original size:59 final size:59
Alignment explanation
Indices: 2656--2787 Score: 210
Period size: 59 Copynumber: 2.2 Consensus size: 59
2646 ATAGGCTAAT
* ** * *
2656 TGCTCAAATAAGAGTCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGGCAAAA
1 TGCTCAAATAAG-GGCCCATCTTTGAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAA
2716 TGCTCAAATAAGGGCCCATCTTTGAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCCATCTTTGAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAA
2775 TGCTCAAATAAGG
1 TGCTCAAATAAGG
2788 ACTTATCTCT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 55 0.82
60 12 0.18
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (59 bp):
TGCTCAAATAAGGGCCCATCTTTGAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:2759 original size:28 final size:28
Alignment explanation
Indices: 2674--2759 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
2664 TAAGAGTCTG
* *
2674 ATCTTTTAATTTGGCCAAATAAGGGCCT
1 ATCTTTGAATTTGGCCAAATAAGGGCCC
* **
2702 AACGTTTGGCAAAAT-GCTCAAATAAGGGCCC
1 ATC-TTT-G-AATTTGGC-CAAATAAGGGCCC
2733 ATCTTTGAATTTGGCCAAATAAGGGCC
1 ATCTTTGAATTTGGCCAAATAAGGGCC
2760 TAACGTTTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
28 17 0.38
29 6 0.13
30 5 0.11
31 17 0.38
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (28 bp):
ATCTTTGAATTTGGCCAAATAAGGGCCC
Found at i:2857 original size:31 final size:31
Alignment explanation
Indices: 2822--2893 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
2812 TGACACCAAG
2822 CCCTTATTTGAGCATTTTCAATAACGTTAGA
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA
* *
2853 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA
*
2884 TCCTTATTTG
1 CCCTTATTTG
2894 GCCAAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGA
Found at i:5684 original size:438 final size:437
Alignment explanation
Indices: 4796--5654 Score: 1081
Period size: 438 Copynumber: 2.0 Consensus size: 437
4786 TGCGTTGCCT
* * *
4796 TTTA-TTTTTGTATTTTTTTTCTATTTGTCTGAGTAAGGTGATTCAAGTGTCTATTAAAATGTAA
1 TTTACTTTTT-TATTTTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* * * * * *
4860 TTTCATTATCTACAATTTTCATGCAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAAAAT
65 TTTAATGATCTACAACTTTCATGAAGAACTCAAAAGTCAATTTTAATGTTTTAATTCAAAAAAAT
* * * * *
4925 GCTTCCGAAATTTTGTGGTTTTGATTGCTGGTCAATTTAATTTCGTATAATTTTTCGTCCACATG
130 GCTTCCGAAATTTGGTCGTTTCGATTGCTGGTCAATTTAATATCATATAATTTTTCGTCCACATG
* * * *
4990 TCCAATTGAAATTATTGAAATGTCAGTTAAAAGATTATTGCATGATTTACGACTGTCATGAAGGA
195 TCCAATTGAAATTATTCAAATGTCAGTTAAAAGATTACTGCATGATCTACGACTGTCATGAAGAA
* * *
5055 CCAGAAAGCTAAATTTGATTTGCGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAT
260 CCAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAG
* * * *
5120 ATCTCCATTAATAAACATTTTCGTATTTCGATTATTTATCAAATGACCGTCATATATTTCTACTT
325 ATATCCATTAAGAAACATTTTCGTATTTCGATTAGTTATCAAATGACCCTCATATATTTCTACTT
*
5185 TATACTACTTAGTACTTTACAAATTCTATCTTAATCTAACGTCTAAGA
390 TATACTACTTAGTACTTTACAAATTCTATCTTAATCTAACGTCTAACA
* * * * *
5233 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTTATGTGTCTATTAAAAGGTAA
1 TTTACTTTTTTATT-TTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
*
5298 TTTAATGATCTACAACTTTCATGAATG-ACTCAAAAG-CAAATTTTTATGTTTTAATTCAAAAAA
65 TTTAATGATCTACAACTTTCATGAA-GAACTCAAAAGTC-AATTTTAATGTTTTAATTCAAAAAA
* * * *
5361 ATGCTTCCTAAATTTGGTCGTTTCGATTGTTTGTCTATTTAATATCATATAA-TTTTCGATCCAC
128 ATGCTTCCGAAATTTGGTCGTTTCGATTGCTGGTCAATTTAATATCATATAATTTTTCG-TCCAC
* * * * * * *
5425 ATTTCCGATT-AAAGTTATTCAATTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGA
192 ATGTCCAATTGAAA-TTATTCAAATGTCAGTTAAAAGATTACTGCATGATCTACGACTGTCATGA
* * *
5489 AGAATCC-GAAAG-TTAATTTGATCTACGAGTTTCATGAAGGGTTTAAAAGGGAATTTTTATGTT
256 AGAA-CCAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCT
* * *
5552 TCAAGATATCCATTAAGAAATATTTTCTTATTT-GAATTAGTTATCAAATGACCCTCATGCT-TT
320 TCAAGATATCCATTAAGAAACATTTTCGTATTTCG-ATTAGTTATCAAATGACCCTCAT-ATATT
* * * *
5615 TTTATTTTATGCTACTTAGT-CATTTTCAAATTCTATCTTA
383 TCTACTTTATACTACTTAGTAC-TTTACAAATTCTATCTTA
5655 TTCGATTTAA
Statistics
Matches: 361, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
436 2 0.01
437 149 0.41
438 207 0.57
439 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (437 bp):
TTTACTTTTTTATTTTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
TTAATGATCTACAACTTTCATGAAGAACTCAAAAGTCAATTTTAATGTTTTAATTCAAAAAAATG
CTTCCGAAATTTGGTCGTTTCGATTGCTGGTCAATTTAATATCATATAATTTTTCGTCCACATGT
CCAATTGAAATTATTCAAATGTCAGTTAAAAGATTACTGCATGATCTACGACTGTCATGAAGAAC
CAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGA
TATCCATTAAGAAACATTTTCGTATTTCGATTAGTTATCAAATGACCCTCATATATTTCTACTTT
ATACTACTTAGTACTTTACAAATTCTATCTTAATCTAACGTCTAACA
Done.