Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014070.1 Corchorus capsularis cultivar CVL-1 contig14091, 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: 25923
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:229 original size:6 final size:6
Alignment explanation
Indices: 196--227 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
186 GTGGACAATA
196 TTTGTT TTTGTT TTTGTT TTTGTT TTT-TT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
228 TTGGCAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTGTT
Found at i:2514 original size:7 final size:7
Alignment explanation
Indices: 2502--2527 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2492 TAAGTAACTA
2502 GGAACAC
1 GGAACAC
2509 GGAACAC
1 GGAACAC
2516 GGAACAC
1 GGAACAC
2523 GGAAC
1 GGAAC
2528 CCACCTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.31, T:0.00
Consensus pattern (7 bp):
GGAACAC
Found at i:16772 original size:36 final size:36
Alignment explanation
Indices: 16732--16807 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
16722 TGTAGTAGGT
16732 GGTGCTTCATT-AGCTGTAGGTGCTTCATTACTTGCA
1 GGTGCTTC-TTCAGCTGTAGGTGCTTCATTACTTGCA
* *
16768 GGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCC
1 GGTGCTTCTTCAGCTGTAGGTGCTTCATTACTTGCA
16804 GGTG
1 GGTG
16808 TTGTATCTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.13, C:0.20, G:0.28, T:0.39
Consensus pattern (36 bp):
GGTGCTTCTTCAGCTGTAGGTGCTTCATTACTTGCA
Found at i:16807 original size:18 final size:18
Alignment explanation
Indices: 16732--16807 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
16722 TGTAGTAGGT
*
16732 GGTGCTTCATTAGC-TGTA
1 GGTGCTTCATTA-CTTGCA
16750 GGTGCTTCATTACTTGCA
1 GGTGCTTCATTACTTGCA
* *
16768 GGTGCTTC-TTCAGTTGTA
1 GGTGCTTCATT-ACTTGCA
*
16786 GGTGCTTCATTACTTGCC
1 GGTGCTTCATTACTTGCA
16804 GGTG
1 GGTG
16808 TTGTATCTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.06
18 44 0.90
19 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.28, T:0.39
Consensus pattern (18 bp):
GGTGCTTCATTACTTGCA
Found at i:17005 original size:18 final size:18
Alignment explanation
Indices: 16948--17005 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
16938 TGTAGTAGGT
**
16948 GGTGCTTCAAAACTTGCA
1 GGTGCTTCATTACTTGCA
* *
16966 GGTGCTTC-TTCAGTTGTA
1 GGTGCTTCATT-ACTTGCA
*
16984 GGTGCTTCATTACTTGCC
1 GGTGCTTCATTACTTGCA
17002 GGTG
1 GGTG
17006 TTGTATCTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.36
Consensus pattern (18 bp):
GGTGCTTCATTACTTGCA
Found at i:17088 original size:198 final size:198
Alignment explanation
Indices: 16750--17129 Score: 697
Period size: 198 Copynumber: 1.9 Consensus size: 198
16740 ATTAGCTGTA
**
16750 GGTGCTTCATTACTTGCAGGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCCGGTGTTGTATC
1 GGTGCTTCAAAACTTGCAGGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCCGGTGTTGTATC
* *
16815 TGCAGTTTTCTTATTTGGACAAGCAGATGACAAATGACCCTTTTGTCCACACTCGTAGCATGTTC
66 TGCAGTTTTCGTATTTGGACAAGCAGACGACAAATGACCCTTTTGTCCACACTCGTAGCATGTTC
*
16880 TTCTCCTCATCTTGCCACTGCTGACATTCGAATTACCACCATTATCAGCTTCGCTAACTGTAGTA
131 TTCTCCTCATCTTGCCACTGCTGACATTAGAATTACCACCATTATCAGCTTCGCTAACTGTAGTA
16945 GGT
196 GGT
16948 GGTGCTTCAAAACTTGCAGGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCCGGTGTTGTATC
1 GGTGCTTCAAAACTTGCAGGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCCGGTGTTGTATC
* *
17013 TGCAGTTTTCGTATTTGGACAAGCAGACGACAAGTGGCCCTTTTGTCCACACTCGTAGCATGTTC
66 TGCAGTTTTCGTATTTGGACAAGCAGACGACAAATGACCCTTTTGTCCACACTCGTAGCATGTTC
17078 TTCTCCTCATCTTGCCACTGCTGACATTAGAATTACCACCATTATCAGCTTC
131 TTCTCCTCATCTTGCCACTGCTGACATTAGAATTACCACCATTATCAGCTTC
17130 ATCACCAGTG
Statistics
Matches: 175, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 175 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (198 bp):
GGTGCTTCAAAACTTGCAGGTGCTTCTTCAGTTGTAGGTGCTTCATTACTTGCCGGTGTTGTATC
TGCAGTTTTCGTATTTGGACAAGCAGACGACAAATGACCCTTTTGTCCACACTCGTAGCATGTTC
TTCTCCTCATCTTGCCACTGCTGACATTAGAATTACCACCATTATCAGCTTCGCTAACTGTAGTA
GGT
Found at i:19062 original size:29 final size:30
Alignment explanation
Indices: 19030--19091 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
19020 CCTCATCTCT
* * *
19030 CTTCCTCTTTTTTTTCTTCCCCT-TTTCAA
1 CTTCCTCATTCTTTTCTTCCCCTCCTTCAA
*
19059 CTTCCTCATTCTTTTCTTCTCCTCCTTCAA
1 CTTCCTCATTCTTTTCTTCCCCTCCTTCAA
19089 CTT
1 CTT
19092 TTTCCCCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.55
Consensus pattern (30 bp):
CTTCCTCATTCTTTTCTTCCCCTCCTTCAA
Found at i:20627 original size:287 final size:286
Alignment explanation
Indices: 20014--20962 Score: 1442
Period size: 290 Copynumber: 3.3 Consensus size: 286
20004 GGAATTTCCA
* **
20014 GGTAAGGAAGAGGAAACGAATTTTACTTTATGATATCTTCAAAATATTAAGAATATTAACCCTAA
1 GGTAAAGAAGAGGAAAAAAATTTTACTTTATGATATCTTCAAAATATTAAGAATATT-ACCCTAA
* *
20079 TGAGATTAACAATTGAT-AAAAAAAAAGAATTTTACTCTATGATATGTT--A-ATATGAATATTG
65 TGAGATTAACATTTGATAAAAAAAAAAGAATTTTACTTTATGATATGTTCAAGATATGAATATTG
* * * * *
20140 ACACTTTCTTAATTCATGTTTATTTTGTCATGAGTAAATAGAAAGAAAGGAACATGCATGAGACA
130 ACCCTTTCTTAATCCATGTTTACTTTGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGGACA
* * *
20205 TATAAAGTATAACTTGAACGGAT-GGCTCATCTTTTGGACATGTTTAGTTGAACATTTTTATTCT
195 TATAAAGTATAACTTGAACGGATAAG---A-------GACAGGTTTAGTTGAACATTTTTCTTCT
*
20269 TTCTTTTACTTTTCAGAATTTCCACATTTTAAAAATG
250 TTCTTTTACTTTTCAGAATTTCCACATTTTAAGAATG
* *
20306 GGTATAGAAGAGGAAAAGAATTTTACTTTATGATATCTTCAAAATATTAAGAATATTAACCCTAA
1 GGTAAAGAAGAGGAAAAAAATTTTACTTTATGATATCTTCAAAATATTAAGAATATT-ACCCTAA
20371 TGAGATTAACATTTGATAAAAAAAAAAGAATTTTACTTTATGATATGTTCAAGATATGAATATTG
65 TGAGATTAACATTTGATAAAAAAAAAAGAATTTTACTTTATGATATGTTCAAGATATGAATATTG
*
20436 ACCCTTTCTTAATCCATGTTTACTTCGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGGACA
130 ACCCTTTCTTAATCCATGTTTACTTTGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGGACA
* * * *
20501 TATTAAGTATAACTTGAATGAATAAGAGCCAGGTTTAGTTGAACATTTTTCTTCTTTCTTTTACT
195 TATAAAGTATAACTTGAACGGATAAGAGACAGGTTTAGTTGAACATTTTTCTTCTTTCTTTTACT
20566 TTTCAGAATTTCCACATTTTAAGAATG
260 TTTCAGAATTTCCACATTTTAAGAATG
* *
20593 GGTAAAAAAGAGGAAAAAAAATTTACTTTATGATATCTTCAAAATATTAAGAATATTACCCTAAT
1 GGTAAAGAAGAGGAAAAAAATTTTACTTTATGATATCTTCAAAATATTAAGAATATTACCCTAAT
*
20658 GAGATTAACATTTGATAAAAAAAAAGAAAAGAATTTTACTTTATGACATGTTCAAGATATGAATA
66 GAGATTAACATTTGAT---AAAAAA-AAAAGAATTTTACTTTATGATATGTTCAAGATATGAATA
*
20723 TTGACCCTTTCTTAATCTATGTTTACTTTGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGG
127 TTGACCCTTTCTTAATCCATGTTTACTTTGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGG
* *
20788 ACATAAAAAGTATAACTTGAACGGATAAGAGTCAGGTTTAGTTGAACATTTTTCTTCTTTCTTTT
192 ACATATAAAGTATAACTTGAACGGATAAGAGACAGGTTTAGTTGAACATTTTTCTTCTTTCTTTT
20853 ACTTTTCAGAATTTCCACATTTTAAGAATG
257 ACTTTTCAGAATTTCCACATTTTAAGAATG
** *
20883 GGTAAAGAAGAGG-AAAATTTTTTACTTTATGATATCTTCAAAATATTAAGAATATTATCCTAAT
1 GGTAAAGAAGAGGAAAAAAATTTTACTTTATGATATCTTCAAAATATTAAGAATATTACCCTAAT
20947 GAGATTAACATTTGAT
66 GAGATTAACATTTGAT
20963 TCGAATCAAA
Statistics
Matches: 612, Mismatches: 36, Indels: 21
0.91 0.05 0.03
Matches are distributed among these distances:
286 24 0.04
287 114 0.19
289 69 0.11
290 203 0.33
292 78 0.13
293 30 0.05
294 1 0.00
295 1 0.00
296 91 0.15
297 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (286 bp):
GGTAAAGAAGAGGAAAAAAATTTTACTTTATGATATCTTCAAAATATTAAGAATATTACCCTAAT
GAGATTAACATTTGATAAAAAAAAAAGAATTTTACTTTATGATATGTTCAAGATATGAATATTGA
CCCTTTCTTAATCCATGTTTACTTTGTCATGAGTAAATAGAAAGGAAGGAACATGCATGGGACAT
ATAAAGTATAACTTGAACGGATAAGAGACAGGTTTAGTTGAACATTTTTCTTCTTTCTTTTACTT
TTCAGAATTTCCACATTTTAAGAATG
Done.