Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014015.1 Corchorus olitorius cultivar O-4 contig14048, 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: 48625
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2327 original size:21 final size:20
Alignment explanation
Indices: 2294--2334 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2284 TTGACACAAG
2294 CAAGAAGAAAAAAACTTTGA
1 CAAGAAGAAAAAAACTTTGA
*
2314 CAAGCAAGAGAAAAACTTTGA
1 CAAG-AAGAAAAAAACTTTGA
2335 AACTCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (20 bp):
CAAGAAGAAAAAAACTTTGA
Found at i:5486 original size:25 final size:25
Alignment explanation
Indices: 5435--5482 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5425 ATTGGAGTAT
5435 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGTTTCTTAATTTTA
* *
5460 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTTCTTAATTTT
5483 TATTGTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTCTTAATTTTA
Found at i:5903 original size:14 final size:15
Alignment explanation
Indices: 5884--5913 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5874 AACTAGGAAA
5884 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
5898 AATAAATAAACAAGG
1 AATAAATAAACAAGG
5913 A
1 A
5914 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:10552 original size:33 final size:31
Alignment explanation
Indices: 10474--10554 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 31
10464 AGATCACAAG
**
10474 GATACAGAAAATCACCACCAAGTGTTTGAAT
1 GATACAGAAAATCACCACCAAGTGTTCAAAT
* **
10505 CAGT-C-GAAGCTCACCACCAAGTGATTCAAATT
1 GA-TACAGAAAATCACCACCAAGTG-TTCAAA-T
10537 GATACAGAAAATCACCAC
1 GATACAGAAAATCACCAC
10555 AACTTGAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
30 16 0.43
31 7 0.19
32 4 0.11
33 10 0.27
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.20
Consensus pattern (31 bp):
GATACAGAAAATCACCACCAAGTGTTCAAAT
Found at i:13776 original size:15 final size:15
Alignment explanation
Indices: 13743--13784 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
13733 TTACTTTGCT
*
13743 TTGTTTTCTAGTTTCA
1 TTGTTTTCT-GTTTAA
13759 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
13774 TTGCTTTCTGT
1 TTGTTTTCTGT
13785 CAACCTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:20055 original size:46 final size:45
Alignment explanation
Indices: 19933--20063 Score: 113
Period size: 46 Copynumber: 2.9 Consensus size: 45
19923 GATAATTTTT
* * * * * *
19933 TTTTTCCAAAACGCCCTTCCCGAACGAAAGGCGCTAATTTTTCTA
1 TTTTTCCAAAACACCCTTTCCGGACGAAAGGTGCCAATTTTTATA
* * ** * *
19978 CTTTTCCTAAAACACCTTTTCTAGACAAAAGGTGCCAATTTTTATGG
1 TTTTTCC-AAAACACCCTTTCCGGACGAAAGGTGCCAATTTTTAT-A
*
20025 TTTTTCCAAAATACCCTTTCCGGACGAAAGGT--CAATTTT
1 TTTTTCCAAAACACCCTTTCCGGACGAAAGGTGCCAATTTT
20064 ATTTTGTTTA
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
44 7 0.11
45 6 0.09
46 47 0.71
47 6 0.09
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (45 bp):
TTTTTCCAAAACACCCTTTCCGGACGAAAGGTGCCAATTTTTATA
Found at i:29291 original size:30 final size:30
Alignment explanation
Indices: 29246--29548 Score: 444
Period size: 30 Copynumber: 10.0 Consensus size: 30
29236 ATTTTTTTTT
* * *
29246 TCTTACAAATGACACCAGAAGTTGTCATAA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29276 TCTTGCAATTGACACCAGAAGTTGTCATGC
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
29306 TCTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29336 TTTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29366 TTTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29396 TGTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29426 TGTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
29456 TCTTGCAATTGACACCATAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* ** * *
29486 TCTTGCAATTGATACTTGAAGATGTCATAA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
29516 TTTTATTCAATTGACACCAGAAGTTGTCATGA
1 -TCT-TGCAATTGACACCAGAAGTTGTCATGA
29548 T
1 T
29549 AAATTTCCAA
Statistics
Matches: 249, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
30 225 0.90
31 3 0.01
32 21 0.08
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (30 bp):
TCTTGCAATTGACACCAGAAGTTGTCATGA
Found at i:29408 original size:90 final size:90
Alignment explanation
Indices: 29255--29616 Score: 463
Period size: 90 Copynumber: 3.9 Consensus size: 90
29245 TTCTTACAAA
* *
29255 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGACA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACA
29320 CCAGAAGTTGTCATGATTTTGCAAT
66 CCAGAAGTTGTCATGATTTTGCAAT
* *
29345 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATGTTGCAATTGACA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACA
*
29410 CCAGAAGTTGTCATGATGTTGCAAT
66 CCAGAAGTTGTCATGATTTTGCAAT
* *
29435 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCATAAGTTGTCATGATCTTGCAATTGATA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACA
** * * *
29500 CTTGAAGATGTCATAATTTTATTCAAT
66 CCAGAAGTTGTCATGA-TTT-TGCAAT
* * * *** * * * *
29527 TGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TGCAAT
29592 TGACACCAGAAGTTGTCATGATTTT
61 TGACACCAGAAGTTGTCATGATTTT
29617 ACCTTTCAAA
Statistics
Matches: 234, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
90 158 0.68
91 2 0.01
92 27 0.12
95 21 0.09
96 5 0.02
97 21 0.09
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (90 bp):
TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACA
CCAGAAGTTGTCATGATTTTGCAAT
Found at i:29528 original size:32 final size:32
Alignment explanation
Indices: 29255--29617 Score: 193
Period size: 30 Copynumber: 11.8 Consensus size: 32
29245 TTCTTACAAA
* * *
29255 TGACACCAGAAGTTGTCATAA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* ** * *
29285 TGACACCAGAAGTTGTCAT-GCTCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
29315 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
29345 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * *
29375 TGACACCAGAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * *
29405 TGACACCAGAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * *
29435 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * * *
29465 TGACACCATAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* **
29495 TGATACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* ** *
29527 TGACACCAGAAGTTGTCATGATAAATT-TCCAAT
1 TGACACCAGAAGATGTCAT-A-ATTTTATTCAAT
* ***
29560 AGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* *
29592 TGACACCAGAAGTTGTCATGATTTTA
1 TGACACCAGAAGATGTCATAATTTTA
29618 CCTTTCAAAA
Statistics
Matches: 291, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
30 217 0.75
31 5 0.02
32 46 0.16
33 20 0.07
34 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
TGACACCAGAAGATGTCATAATTTTATTCAAT
Found at i:29590 original size:65 final size:62
Alignment explanation
Indices: 29281--29613 Score: 309
Period size: 60 Copynumber: 5.4 Consensus size: 62
29271 CATAATCTTG
* * * ** * * *
29281 CAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * * *
29341 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * * *
29401 CAATTGACACCAGAAGTTGTCATGATGTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * *
29461 CAATTGACACCATAAGTTGTCATGATCTTGCAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* *
29523 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTATT
29588 CAATTGACACCAGAAGTTGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
29614 TTTACCTTTC
Statistics
Matches: 248, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
60 163 0.66
61 2 0.01
62 26 0.10
65 57 0.23
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
Found at i:34693 original size:18 final size:18
Alignment explanation
Indices: 34670--34719 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
34660 TTTAGGTTTT
34670 AATTATTGGAAATAATTA
1 AATTATTGGAAATAATTA
** *
34688 AATTATTAAAAATAATTT
1 AATTATTGGAAATAATTA
34706 AATTATTGGAAATA
1 AATTATTGGAAATA
34720 TTATTGGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (18 bp):
AATTATTGGAAATAATTA
Found at i:36171 original size:14 final size:14
Alignment explanation
Indices: 36152--36182 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
36142 AAGAATTTAA
36152 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
36166 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
36180 TTT
1 TTT
36183 CTCTCCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:37562 original size:29 final size:27
Alignment explanation
Indices: 37519--37574 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
37509 AAAAAAAAAA
37519 GTTGAAAAAAGGAAAAGGTTTAAAAACAT
1 GTTGAAAAAAGG-AAA-GTTTAAAAACAT
** *
37548 GTTGAAAAATTGAAAGTTTAGAAACAT
1 GTTGAAAAAAGGAAAGTTTAAAAACAT
37575 CAAACATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.46
28 3 0.12
29 10 0.42
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.25
Consensus pattern (27 bp):
GTTGAAAAAAGGAAAGTTTAAAAACAT
Found at i:41859 original size:27 final size:27
Alignment explanation
Indices: 41821--41873 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
41811 AAGATGAGCC
*
41821 AAAAATGGCCAAAATACCCCTGAATGT
1 AAAAATGACCAAAATACCCCTGAATGT
*
41848 AAAAATGACCAAAATGCCCCTGAATG
1 AAAAATGACCAAAATACCCCTGAATG
41874 ACCTTAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATACCCCTGAATGT
Found at i:42101 original size:29 final size:31
Alignment explanation
Indices: 42035--42101 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
42025 TCTAATTGAC
42035 TATATCCTTAATTGCTCCATTTTCGTAACGT
1 TATATCCTTAATTGCTCCATTTTCGTAACGT
* **
42066 TATATCCTTGATTGCT-TGTTTT-GTAACGT
1 TATATCCTTAATTGCTCCATTTTCGTAACGT
42095 TATATCC
1 TATATCC
42102 CAAATTGCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 4 0.12
31 15 0.45
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCCATTTTCGTAACGT
Found at i:42532 original size:31 final size:31
Alignment explanation
Indices: 42461--42539 Score: 133
Period size: 30 Copynumber: 2.6 Consensus size: 31
42451 ACTTTTAGGA
* *
42461 TCAAGCAATTAAGGATATGACGTTTTTGATT
1 TCAAGCAATTAAGGATATGACGGTTTCGATT
42492 TC-AGCAATTAAGGATATGACGGTTTCGATT
1 TCAAGCAATTAAGGATATGACGGTTTCGATT
42522 TCAAGCAATTAAGGATAT
1 TCAAGCAATTAAGGATAT
42540 ACTCAATTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 28 0.62
31 17 0.38
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (31 bp):
TCAAGCAATTAAGGATATGACGGTTTCGATT
Found at i:45893 original size:30 final size:30
Alignment explanation
Indices: 45858--45916 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
45848 AATTAAATTT
* * *
45858 AATG-AAATTAGAACTAAATTTAATAAAAAG
1 AATGAAAATTA-AAATAAAATTAAAAAAAAG
45888 AATGAAAATTAAAATAAAATTAAAAAAAA
1 AATGAAAATTAAAATAAAATTAAAAAAAA
45917 AGCCAAGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.24
Consensus pattern (30 bp):
AATGAAAATTAAAATAAAATTAAAAAAAAG
Done.