Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012693.1 Corchorus olitorius cultivar O-4 contig12726, 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: 16705
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:140 original size:16 final size:16
Alignment explanation
Indices: 119--150 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
109 AAATAACTAA
119 ATAAAAATAATAAATC
1 ATAAAAATAATAAATC
135 ATAAAAATAATAAATC
1 ATAAAAATAATAAATC
151 GCATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAAAATAATAAATC
Found at i:897 original size:272 final size:271
Alignment explanation
Indices: 398--940 Score: 1023
Period size: 272 Copynumber: 2.0 Consensus size: 271
388 CTAACTTGGC
*
398 TTTTCTTGCAACTCTTTTTCTTTTTGGTTTTTCATATGCTTGGCTTGGCAAATCATCCATCGAGC
1 TTTTCTTGCAACTCTTTTTCGTTTTGGTTTTTCATATGCTTGGCTTGGCAAATCATCCATCGAGC
463 ATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAACTT
66 ATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAACTT
528 TCTCTTTTCCACGAAAATGTTGAGATGTGCCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
131 TCTCTTTTCCACGAAAATGTTGAGATGTGCCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
*
593 AATTTCTTTGATTAACTCGGCATTTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTG
196 AATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTG
658 TAGATATCAGT
261 TAGATATCAGT
*
669 TTTTCTTGCAACTCCTTTTTCGTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGAG
1 TTTTCTTGCAACT-CTTTTTCGTTTTGGTTTTTCATATGCTTGGCTTGGCAAATCATCCATCGAG
* *
734 CATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTTTTCTTGAGCT
65 CATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAACT
*
799 TTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTTG
130 TTCTCTTTTCCACGAAAATGTTGAGATGTGCCAACATTTTCTTCATCTTCAAATTTGTAATTTTG
864 CAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTT
195 CAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTT
929 GTAGATATCAGT
260 GTAGATATCAGT
941 GCTAGTTCCA
Statistics
Matches: 265, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
271 13 0.05
272 252 0.95
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (271 bp):
TTTTCTTGCAACTCTTTTTCGTTTTGGTTTTTCATATGCTTGGCTTGGCAAATCATCCATCGAGC
ATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAACTT
TCTCTTTTCCACGAAAATGTTGAGATGTGCCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
AATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTG
TAGATATCAGT
Found at i:2188 original size:26 final size:24
Alignment explanation
Indices: 2133--2182 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2123 AGTAATGATC
2133 TATTGATATATTTCAAAGAAAAAT
1 TATTGATATATTTCAAAGAAAAAT
2157 TATTGATATATTTCAAAGAAAAAT
1 TATTGATATATTTCAAAGAAAAAT
2181 TA
1 TA
2183 AATTGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
TATTGATATATTTCAAAGAAAAAT
Found at i:3387 original size:30 final size:30
Alignment explanation
Indices: 3305--3388 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
3295 ATACCACTAA
* *
3305 TAATTATTATTATTATAATAATAATAAGTT
1 TAATAATTATTATAATAATAATAATAAGTT
* ** *
3335 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATAATAATAATAATAAGTT
3365 TAATAATTATTATAATAATAATAA
1 TAATAATTATTATAATAATAATAA
3389 ATCTAAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (30 bp):
TAATAATTATTATAATAATAATAATAAGTT
Found at i:3476 original size:12 final size:11
Alignment explanation
Indices: 3459--3504 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
3449 AAGTAAAACG
3459 TAATTATATATA
1 TAATTATATA-A
3471 TAATTA-ATAA
1 TAATTATATAA
3481 TAATT-T-TAA
1 TAATTATATAA
3490 TAATTATAATAA
1 TAATTAT-ATAA
3502 TAA
1 TAA
3505 GTTGTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.27
10 7 0.23
11 3 0.10
12 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATTATATAA
Found at i:4515 original size:1 final size:1
Alignment explanation
Indices: 4509--4536 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4499 CATGTGGTTC
4509 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
4537 AATGAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6655 original size:17 final size:17
Alignment explanation
Indices: 6635--6667 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6625 TCTTGAATGA
6635 ATTATGAATTATGAATT
1 ATTATGAATTATGAATT
*
6652 ATTATGGATTATGAAT
1 ATTATGAATTATGAAT
6668 GGATGGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTATGAATTATGAATT
Found at i:16493 original size:7 final size:7
Alignment explanation
Indices: 16481--16513 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16471 TTTTTTAAAT
16481 TTATTTA
1 TTATTTA
16488 TTATTTA
1 TTATTTA
16495 TTTATTTA
1 -TTATTTA
16503 TT-TTTA
1 TTATTTA
16509 TTATT
1 TTATT
16514 ATCATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATTTA
Found at i:16499 original size:15 final size:14
Alignment explanation
Indices: 16479--16510 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
16469 TCTTTTTTAA
16479 ATTTATTTATTATTT
1 ATTTATTTATT-TTT
16494 ATTTATTTATTTTT
1 ATTTATTTATTTTT
16508 ATT
1 ATT
16511 ATTATCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTATTTATTTTT
Done.