Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018323.1 Corchorus olitorius cultivar O-4 contig18356, 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: 35104
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 19--51 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9 TTAATTACTA
19 AT 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 AT A
52 ATTGACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273 original size:22 final size:22
Alignment explanation
Indices: 176--482 Score: 182
Period size: 22 Copynumber: 14.1 Consensus size: 22
166 TCACACTAAC
*
176 AAATTTTGATAACC-CCCT-TG
1 AAATTTTGATAACCTCACTATG
*
196 TAAGATTTTGATAACCACAC--TG
1 -AA-ATTTTGATAACCTCACTATG
* *
218 AAATTTTCATAATCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATG
* * * * *
240 AAATCTTAATAACCACACAATT
1 AAATTTTGATAACCTCACTATG
* *
262 AAATTTTGATAATCGCACTATG
1 AAATTTTGATAACCTCACTATG
* * *
284 ATATGTTGGTAACCTC-CTATG
1 AAATTTTGATAACCTCACTATG
305 AAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATG
* *
327 AAGTTTTGATAATCTCACTATG
1 AAATTTTGATAACCTCACTATG
* * * *
349 AAATTTTGATTACCTCCCAATA
1 AAATTTTGATAACCTCACTATG
371 AAATTTTGATAACCAT-ACTATG
1 AAATTTTGATAACC-TCACTATG
* * * * *
393 AAATTTTAATAATCTCGCCAAG
1 AAATTTTGATAACCTCACTATG
* * *
415 AAATATAGGTAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATG
* * **
437 ATATTGTGATAACCTCTTTATG
1 AAATTTTGATAACCTCACTATG
* * *
459 AAATTTTAATTAGCTCACTATG
1 AAATTTTGATAACCTCACTATG
481 AA
1 AA
483 TTATATATAT
Statistics
Matches: 213, Mismatches: 61, Indels: 23
0.72 0.21 0.08
Matches are distributed among these distances:
19 1 0.00
20 11 0.05
21 25 0.12
22 171 0.80
23 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:491 original size:2 final size:2
Alignment explanation
Indices: 484--513 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
474 CACTATGAAT
484 TA TA 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 TA TA
514 ACCAGAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1865 original size:14 final size:14
Alignment explanation
Indices: 1846--1874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1836 CTTTGAGAAA
1846 TTAATGTGCCAAGT
1 TTAATGTGCCAAGT
1860 TTAATGTGCCAAGT
1 TTAATGTGCCAAGT
1874 T
1 T
1875 ATATGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TTAATGTGCCAAGT
Found at i:2026 original size:69 final size:72
Alignment explanation
Indices: 1948--2082 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 72
1938 AGAAACGTTA
*
1948 TATAGACCACAATATTTAATTGTTAACG-T-T-TTATTTAATTGATTCTTAACGTCATATGAATA
1 TATAGACCACAATATTTAATTGTTAACGTTATATTATTTAATTAATTCTTAACGTCATATGAATA
2010 TTAACGT
66 TTAACGT
* *
2017 TATAGACCACAATATTTAATTGTTAATGTTATATTTTTTAATTAATTCTTAACGTCATATGAATA
1 TATAGACCACAATATTTAATTGTTAACGTTATATTATTTAATTAATTCTTAACGTCATATGAATA
2082 T
66 T
2083 AAAATTGTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
69 27 0.45
70 1 0.02
71 1 0.02
72 31 0.52
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (72 bp):
TATAGACCACAATATTTAATTGTTAACGTTATATTATTTAATTAATTCTTAACGTCATATGAATA
TTAACGT
Found at i:2108 original size:69 final size:72
Alignment explanation
Indices: 1948--2121 Score: 180
Period size: 69 Copynumber: 2.5 Consensus size: 72
1938 AGAAACGTTA
* * * *
1948 TATAGACCACAATATTTAATTGTTAACGTT---TTATTTAATTGATTCTTAACGTCATATGAATA
1 TATAGACCACAAAAATTAATTGTTAACGTTACATTTTTTAATTAATTCTTAACGTCATATGAATA
**
2010 TTAACGT
66 TTAAAAT
* * * *
2017 TATAGACCACAATATTTAATTGTTAATGTTATATTTTTTAATTAATTCTTAACGTCATATGAATA
1 TATAGACCACAAAAATTAATTGTTAACGTTACATTTTTTAATTAATTCTTAACGTCATATGAATA
2082 -TAAAAT
66 TTAAAAT
* ** *
2088 TGTA-TTCA-AAAAATTCATTGTTAACGTTACATTT
1 TATAGACCACAAAAATTAATTGTTAACGTTACATTT
2122 GATTATTAAC
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 50 0.56
70 2 0.02
71 7 0.08
72 30 0.34
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (72 bp):
TATAGACCACAAAAATTAATTGTTAACGTTACATTTTTTAATTAATTCTTAACGTCATATGAATA
TTAAAAT
Found at i:3527 original size:128 final size:128
Alignment explanation
Indices: 3287--3542 Score: 440
Period size: 128 Copynumber: 2.0 Consensus size: 128
3277 ACAAATTACA
*
3287 AAATTGTAATTAGAATTAAGAAATTTATATAATAAATTAATTCCATAATTACATATATTATAAAG
1 AAATTGTAATTAGAATTAAGAAATTGATATAATAAATTAATTCCATAATTACATATATTATAAAG
** *
3352 GCATATATATAATTAAAACGATATGTTTAAAATTCAGTTTCCGATTCAAACACTGTTCAAGAG
66 GCATATATATAATTAAAACGATATGTTTAAAATTCAGTACCCCATTCAAACACTGTTCAAGAG
* *
3415 AAATTGTAATTAGAATTAAGAAATTGATATAATTAATTAATTCCATAATTACATATATTGTAAAG
1 AAATTGTAATTAGAATTAAGAAATTGATATAATAAATTAATTCCATAATTACATATATTATAAAG
* *
3480 GCATATATATAATTAAAACGATATGTTTAAGATTTAGTACCCCATTCAAACACTGTTCAAGAG
66 GCATATATATAATTAAAACGATATGTTTAAAATTCAGTACCCCATTCAAACACTGTTCAAGAG
3543 TATTGGAAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 120 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (128 bp):
AAATTGTAATTAGAATTAAGAAATTGATATAATAAATTAATTCCATAATTACATATATTATAAAG
GCATATATATAATTAAAACGATATGTTTAAAATTCAGTACCCCATTCAAACACTGTTCAAGAG
Found at i:8209 original size:17 final size:16
Alignment explanation
Indices: 8179--8235 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
8169 CGTTCAAATG
8179 TCGGGTCA-TTTGGGT
1 TCGGGTCATTTTGGGT
8194 TCGGGTCAATTTTGGGT
1 TCGGGTC-ATTTTGGGT
* *
8211 T-GGGTCGTTTTCGGTT
1 TCGGGTCATTTT-GGGT
8227 TCGGGTCAT
1 TCGGGTCAT
8236 ACGGTTCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 14 0.40
ACGTcount: A:0.07, C:0.14, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCATTTTGGGT
Found at i:9848 original size:16 final size:17
Alignment explanation
Indices: 9821--9865 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
9811 GTCGGGTTGA
9821 TCGGGTTCGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
9838 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
9854 TCGGGTTCGGGT
1 TCGGGTTCGGGT
9866 ACCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.04, C:0.13, G:0.40, T:0.42
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:9914 original size:17 final size:17
Alignment explanation
Indices: 9874--9914 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
9864 GTACCTAAAA
9874 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
9891 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
9907 TTTCGGGT
1 TTTCGGGT
9915 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:16654 original size:61 final size:61
Alignment explanation
Indices: 16581--16703 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
16571 AATAAAACTC
16581 TTCATGAGGGAGTCTGCAAATTACCATCTGCTTTGTGTACTATGGCAGCGAGATTAGTTAG
1 TTCATGAGGGAGTCTGCAAATTACCATCTGCTTTGTGTACTATGGCAGCGAGATTAGTTAG
16642 TTCATGAGGGAGTCTGCAAATTACCATCTGCTTTGTGTACTATGGCAGCGAGATTAGTTAG
1 TTCATGAGGGAGTCTGCAAATTACCATCTGCTTTGTGTACTATGGCAGCGAGATTAGTTAG
16703 T
1 T
16704 GAAGTTGAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (61 bp):
TTCATGAGGGAGTCTGCAAATTACCATCTGCTTTGTGTACTATGGCAGCGAGATTAGTTAG
Found at i:19317 original size:21 final size:21
Alignment explanation
Indices: 19279--19318 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19269 GGTGCCCACA
* *
19279 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
19300 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
19319 GGTAAGCTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:19318 original size:76 final size:76
Alignment explanation
Indices: 19181--19321 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 76
19171 TGGCTGTCCC
* * *
19181 CGACTCTACCTGGGCGCCCACATGGTTGTTCTGAACACCCATGTGGTCTGCTTGAGGACCCAGGT
1 CGACTCTACCAGGGCGCCCACATGGTTGTTCTGAACACCCATGTGGTCTGCCTGAGCACCCAGGT
19246 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * *
19257 CGACTCTAGCAGGGTGCCCACATGGTT-TGTCTGAAGACCCATGTGGTTTGCCTGATCACCCAGG
1 CGACTCTACCAGGGCGCCCACATGGTTGT-TCTGAACACCCATGTGGTCTGCCTGAGCACCCAGG
19321 T
65 T
19322 AAGCTGTGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 1 0.02
76 55 0.98
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCTACCAGGGCGCCCACATGGTTGTTCTGAACACCCATGTGGTCTGCCTGAGCACCCAGGT
GGGCAGTGTCA
Found at i:25618 original size:15 final size:16
Alignment explanation
Indices: 25588--25627 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
25578 TTACTTTGTT
25588 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
25604 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
25619 TTATTTTCT
1 TTGTTTTCT
25628 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:26057 original size:18 final size:19
Alignment explanation
Indices: 26034--26072 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
26024 TTTTTGTGAT
26034 TTTGCGTCA-AAAAAAAAA
1 TTTGCGTCATAAAAAAAAA
26052 TTTGCGTCATAAAAAAAAA
1 TTTGCGTCATAAAAAAAAA
26071 TT
1 TT
26073 GTTTCTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
TTTGCGTCATAAAAAAAAA
Found at i:28821 original size:21 final size:21
Alignment explanation
Indices: 28781--28822 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28771 CCGAGCCGCG
*
28781 CCGAGCTACCTGCCCGGCCAC
1 CCGAGCTACCTGCCCAGCCAC
* *
28802 CCGAGCTATCTGTCCAGCCAC
1 CCGAGCTACCTGCCCAGCCAC
28823 TAGCGCCACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (21 bp):
CCGAGCTACCTGCCCAGCCAC
Found at i:32416 original size:15 final size:16
Alignment explanation
Indices: 32386--32425 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
32376 TTACTTTGTT
32386 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
32402 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
32417 TTGCTTTCT
1 TTGTTTTCT
32426 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:33507 original size:28 final size:28
Alignment explanation
Indices: 33436--33500 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
33426 GGGGACATAT
33436 TGGTAATTTAGACCAATCAAGGGTAACA
1 TGGTAATTTAGACCAATCAAGGGTAACA
33464 TGGTAATTTAGACCAATCAAGGGTAACA
1 TGGTAATTTAGACCAATCAAGGGTAACA
33492 TGGTAATTT
1 TGGTAATTT
33501 TACCCAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (28 bp):
TGGTAATTTAGACCAATCAAGGGTAACA
Found at i:34669 original size:19 final size:18
Alignment explanation
Indices: 34645--34693 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
34635 TCCTTTTTTA
34645 TTTCCTTATTTCTTCTTAT
1 TTTCCTTATTTCTTCTT-T
34664 TTTCCTTA-TTCTCTCTTT
1 TTTCCTTATTTCT-TCTTT
34682 TTT-CTT-TTTCTT
1 TTTCCTTATTTCTT
34694 TACATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.25
18 8 0.29
19 12 0.43
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCCTTATTTCTTCTTT
Done.