Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017622.1 Corchorus olitorius cultivar O-4 contig17655, 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: 17984
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5951 original size:30 final size:29
Alignment explanation
Indices: 5908--5964 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
5898 TTAGGATTAG
5908 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
5936 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
5965 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:7512 original size:19 final size:18
Alignment explanation
Indices: 7488--7523 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7478 TGAAGACTTA
7488 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
7507 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
7524 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:12614 original size:9 final size:9
Alignment explanation
Indices: 12596--12626 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12586 CACTCGGGGT
*
12596 CATATGACC
1 CATATAACC
12605 CATATAACC
1 CATATAACC
12614 CATATAACC
1 CATATAACC
12623 CATA
1 CATA
12627 CCTTCCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.32, G:0.03, T:0.23
Consensus pattern (9 bp):
CATATAACC
Found at i:16337 original size:70 final size:70
Alignment explanation
Indices: 16223--16431 Score: 337
Period size: 70 Copynumber: 3.0 Consensus size: 70
16213 ATGAATTCAG
16223 CTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCATAAGC
1 CTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCATAAGC
16288 CAAAA
66 CAAAA
* * *
16293 TTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTCCATCCAAGCACCATGGGCTTTTCCATAAGC
1 CTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCATAAGC
*
16358 CAAAG
66 CAAAA
* * * *
16363 CTCGTTTCCATACGAGTCAGTTTAAACCTTGGTTCCACCCAAGCATCAGGGGGCTTTTCCATAAG
1 CTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACA-TGGGCTTTTCCATAAG
16428 CCAA
65 CCAA
16432 GTTTTCCACA
Statistics
Matches: 128, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 109 0.85
71 19 0.15
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (70 bp):
CTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCATAAGC
CAAAA
Found at i:16672 original size:128 final size:128
Alignment explanation
Indices: 16444--16682 Score: 469
Period size: 128 Copynumber: 1.9 Consensus size: 128
16434 TTTCCACATG
16444 AATTCAGTCTTTCAAGAGCAAACTCGTTTCCATACGAGTTAGTTTAAACTTTGGTTCCATCCAAG
1 AATTCAGTCTTTCAAGAGCAAACTCGTTTCCATACGAGTTAGTTTAAACTTTGGTTCCATCCAAG
16509 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGAT
66 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGAT
*
16572 AATTCAGTCTTTCAAGAGCAAACTCGTTTCCATACGAGTTAGTTTAAGCTTTGGTTCCATCCAAG
1 AATTCAGTCTTTCAAGAGCAAACTCGTTTCCATACGAGTTAGTTTAAACTTTGGTTCCATCCAAG
16637 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATA
66 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATA
16683 GTTTAAGCTT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 110 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (128 bp):
AATTCAGTCTTTCAAGAGCAAACTCGTTTCCATACGAGTTAGTTTAAACTTTGGTTCCATCCAAG
CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGAT
Found at i:16711 original size:70 final size:70
Alignment explanation
Indices: 16599--16752 Score: 283
Period size: 70 Copynumber: 2.2 Consensus size: 70
16589 GCAAACTCGT
*
16599 TTCCATACGAGT-TAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
1 TTCCATGCGAGTATAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
16663 TTCGC
66 TTCGC
*
16668 TTCCATGCGAGTATAGTTTAAGCTTTGGTTTCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
1 TTCCATGCGAGTATAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
16733 TTCGC
66 TTCGC
16738 TTCCATGCGAGTATA
1 TTCCATGCGAGTATA
16753 CAATTTGATT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
69 11 0.13
70 71 0.87
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (70 bp):
TTCCATGCGAGTATAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
TTCGC
Found at i:16864 original size:198 final size:197
Alignment explanation
Indices: 16471--16933 Score: 705
Period size: 198 Copynumber: 2.3 Consensus size: 197
16461 GCAAACTCGT
*
16471 TTCCATACGAGTTAGTTTAAACTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAGT
1 TTCCATACGAGTTAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAGT
16536 TCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAATTCAGTCTTTCAAGAGCAAACTCGTTT
66 TCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAATTCAGTCTTTCAAGAGCAAACTCGTTT
** * * * *
16601 CCATACGAGTTAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAGTTC
131 CCATACGAGTTAGTTTAAGCTTCAGTTCCATCCAAGCATCTGAGGCGTTTCCATAAACCAAGTTC
16666 GC
196 GC
* *
16668 TTCCATGCGAGTATAGTTTAAGCTTTGGTTTCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
1 TTCCATACGAGT-TAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAG
*
16733 TTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAGTTCAGTCTTT-AAGAGCAAACTCGTT
65 TTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAATTCAGTCTTTCAAGAGCAAACTCGTT
16797 TCCATACGAGTTAGTTTAAGCTTCAGTTCCATCCAAGCATCTGAGGCGTTTCCATAAACCAAAGT
130 TCCATACGAGTTAGTTTAAGCTTCAGTTCCATCCAAGCATCTGAGGCGTTTCCATAAACC-AAGT
*
16862 TCGT
194 TCGC
* * * * ****
16866 TTCCATATGAGTCACTTTAAG-TCTTGGTTCCACCCAAGCACAAAAGGGCTTTTCCATAAGCCAA
1 TTCCATACGAGTTAGTTTAAGCT-TTGGTTCCATCCAAGCA-TTTGGGGCTTTTCCATAAGCCAA
16930 GTTC
64 GTTC
16934 AATGAGGTTT
Statistics
Matches: 241, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
196 1 0.00
197 102 0.42
198 138 0.57
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (197 bp):
TTCCATACGAGTTAGTTTAAGCTTTGGTTCCATCCAAGCATTTGGGGCTTTTCCATAAGCCAAGT
TCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAATTCAGTCTTTCAAGAGCAAACTCGTTT
CCATACGAGTTAGTTTAAGCTTCAGTTCCATCCAAGCATCTGAGGCGTTTCCATAAACCAAGTTC
GC
Found at i:17284 original size:43 final size:43
Alignment explanation
Indices: 17226--17317 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
17216 TTTCATTCAA
*
17226 TTTCAGGAATCTATGTTGATTCT-TGAATCGTCTTCTTGTTAAT
1 TTTCAGGAATCTATGTTGA-TCTGCGAATCGTCTTCTTGTTAAT
* * *
17269 TTTC-GGAGATCTATGTTGATCTGCGAATTGTCTTCTTGTCAAC
1 TTTCAGGA-ATCTATGTTGATCTGCGAATCGTCTTCTTGTTAAT
17312 TTTCAG
1 TTTCAG
17318 AGGTCTGCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 6 0.14
43 35 0.83
44 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (43 bp):
TTTCAGGAATCTATGTTGATCTGCGAATCGTCTTCTTGTTAAT
Found at i:17375 original size:43 final size:43
Alignment explanation
Indices: 17328--17421 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
17318 AGGTCTGCGA
* * ** *
17328 TGATCTTCGAGTTGTCATTTTA-ATAATATTCGGAGATCTAGGC
1 TGATCTTCGAATTATC-TTTTAGATAATATTCAAAGATCTAAGC
* *
17371 TGATCTTCGAATTATCTTTTAGTTAATTTTCAAAGATCTAAGC
1 TGATCTTCGAATTATCTTTTAGATAATATTCAAAGATCTAAGC
17414 TGATCTTC
1 TGATCTTC
17422 CAAAAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (43 bp):
TGATCTTCGAATTATCTTTTAGATAATATTCAAAGATCTAAGC
Found at i:17508 original size:18 final size:19
Alignment explanation
Indices: 17437--17529 Score: 104
Period size: 18 Copynumber: 4.9 Consensus size: 19
17427 AAAACAAATC
17437 AAAACAAAAAC-AAAAACA
1 AAAACAAAAACAAAAAACA
17455 AAAACAAAAAC-AAAAACA
1 AAAACAAAAACAAAAAACA
17473 AAAACAAAAACAAAAAA-A
1 AAAACAAAAACAAAAAACA
*
17491 TAAAA-ATAAAACAAAAAAATA
1 -AAAACA-AAAAC-AAAAAACA
*
17512 AAAATAAAAACAGAAAAA
1 AAAACAAAAACA-AAAAA
17530 ATTAATAAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
18 31 0.46
19 15 0.22
20 20 0.29
21 2 0.03
ACGTcount: A:0.84, C:0.11, G:0.01, T:0.04
Consensus pattern (19 bp):
AAAACAAAAACAAAAAACA
Found at i:17521 original size:6 final size:6
Alignment explanation
Indices: 17437--17507 Score: 108
Period size: 6 Copynumber: 11.7 Consensus size: 6
17427 AAAACAAATC
17437 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
*
17485 AAAA-A ATAAAAA TAAAACA AAAA
1 AAAACA A-AAACA -AAAACA AAAA
17508 AATAAAAATA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
5 2 0.03
6 53 0.87
7 5 0.08
8 1 0.02
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACA
Found at i:17530 original size:1 final size:1
Alignment explanation
Indices: 17423--17521 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
17413 CTGATCTTCC
* ** * * * * * * * *
17423 AAAAAAAACAAATCAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
17488 AAATAAAAATAAAACAAAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17522 CAGAAAAAAT
Statistics
Matches: 67, Mismatches: 31, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:17537 original size:25 final size:25
Alignment explanation
Indices: 17422--17523 Score: 102
Period size: 25 Copynumber: 4.1 Consensus size: 25
17412 GCTGATCTTC
* *
17422 CAAAA-AAAACAAATCAAAACAAAAA
1 CAAAACAAAA-AAATAAAAATAAAAA
* * *
17447 CAAAA-ACAAAAACAAAAACAAAAA
1 CAAAACAAAAAAATAAAAATAAAAA
17471 CAAAAACAAAAACAA-AAAAATAAAAA
1 C-AAAACAAAAA-AATAAAAATAAAAA
*
17497 TAAAACAAAAAAATAAAAATAAAAA
1 CAAAACAAAAAAATAAAAATAAAAA
17522 CA
1 CA
17524 GAAAAAATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
24 16 0.24
25 34 0.52
26 14 0.21
27 2 0.03
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (25 bp):
CAAAACAAAAAAATAAAAATAAAAA
Done.