Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023259.1 Corchorus olitorius cultivar O-4 contig23292, 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: 27714
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4177 original size:66 final size:66
Alignment explanation
Indices: 4105--4228 Score: 95
Period size: 66 Copynumber: 1.9 Consensus size: 66
4095 GGTTGCTTGC
* * * * * * * *
4105 TTGAGTCTGAATTCTCATAAATGATGAACGGACTTATCGGAGAATTTATACCTTTCGATTCTTTG
1 TTGAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTG
*
4170 C
66 T
* ** * * * * *
4171 TCGAGTCAGCATTTTCATAAATAATGAATGGACTTATTGGAGAATTCACTCCTTTGGA
1 TTGAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGA
4229 ATTTTTTATG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 47 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (66 bp):
TTGAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTG
T
Found at i:4345 original size:66 final size:66
Alignment explanation
Indices: 4251--4633 Score: 457
Period size: 66 Copynumber: 5.8 Consensus size: 66
4241 TTTTTTACCA
* * * * * **
4251 GAGTTTGCATTGTCGTATATTATGAATGGACTGATTGGAGAATTCACACTTTTGGATT-TCTTAC
1 GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCT-TTTT
*
4315 TC
65 TT
* * * * * * *
4317 GAGTTTGGATCCTCATAAATGATAAATGGGCTAATCGGAGAGTTCACACCTTTGGATTCTTTTTT
1 GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTTTT
4382 T
66 T
* * * * *
4383 GAGTTTGGATTCTCGTAAATTATGAAGGGACTAATAGGAGAATTCACACCTTTGGATTCTTTTTT
1 GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTTTT
4448 T
66 T
* *
4449 GAGTTTACTTTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTTTT
1 GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTTTT
4514 T
66 T
* * * * *
4515 GAGTTTGTATTCTCATAAATTATGAACGGGCTTATCGGAGAATTCACAACTTTGGATT-TCTTTT
1 GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCT-TTTT
4579 TT
65 TT
* *
4581 GAGTCAT-CATTCTCATAAATTATGAATGGACTGATCGGAGAATTAACACCTTT
1 GAGT-TTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTT
4634 CTTGTGTAAG
Statistics
Matches: 270, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
65 1 0.00
66 267 0.99
67 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (66 bp):
GAGTTTGCATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGATTCTTTTTT
T
Found at i:4623 original size:198 final size:202
Alignment explanation
Indices: 4104--4633 Score: 543
Period size: 198 Copynumber: 2.6 Consensus size: 202
4094 TGGTTGCTTG
* * * * *
4104 CTTGAGTCTGAATTCTCATAAATGATGAACGGACTTATCGGAGAATTTATACCTTTCGATTCTTT
1 CTTGAGTTTGAATTCTCATAAATGATGAACGGGCTTATCGGAGAATTCACACCTTTGGATTCTTT
* * * * * * * *
4169 GCTCGAGTCAGCATTTTCATAAATAATGAATGGACTTATTGGAGAATTCACTCCTTTGGAATTTT
66 -TTTGAGTCATCATTCTCATAAATTATGAATGGACTAATAGGAGAATTCACACCTTTGGAA----
* * * * * *
4234 TTATGGTTTTTTTACCAGAGTTTGCATTGTCGTATATTATGAATGGACTGATTGGAGAATTCACA
126 TTATGCTTTTTTT---AGAGTTTACATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACA
*
4299 CTTTTGGATTTCTTA
188 CCTTTGGATTTCTTA
* * * * * * *
4314 CTCGAGTTTGGATCCTCATAAATGATAAATGGGCTAATCGGAGAGTTCACACCTTTGGATTCTTT
1 CTTGAGTTTGAATTCTCATAAATGATGAACGGGCTTATCGGAGAATTCACACCTTTGGATTC-TT
* * * *
4379 TTTTGAGT-TTGGATTCTCGTAAATTATGAAGGGACTAATAGGAGAATTCACACCTTTGG-A-T-
65 TTTTGAGTCAT-CATTCTCATAAATTATGAATGGACTAATAGGAGAATTCACACCTTTGGAATTA
*
4440 T-CTTTTTTT-GAGTTTACTTTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTG
129 TGCTTTTTTTAGAGTTTACATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTG
*
4503 GA-TTCTTTT
194 GATTTC-TTA
* * * *
4512 TTTGAGTTTGTATTCTCATAAATTATGAACGGGCTTATCGGAGAATTCACAACTTTGGATTTCTT
1 CTTGAGTTTGAATTCTCATAAATGATGAACGGGCTTATCGGAGAATTCACACCTTTGGA-TTCTT
* * *
4577 TTTTGAGTCATCATTCTCATAAATTATGAATGGACTGATCGGAGAATTAACACCTTT
65 TTTTGAGTCATCATTCTCATAAATTATGAATGGACTAATAGGAGAATTCACACCTTT
4634 CTTGTGTAAG
Statistics
Matches: 265, Mismatches: 50, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
197 3 0.01
198 150 0.57
199 4 0.02
202 7 0.03
203 1 0.00
204 1 0.00
209 1 0.00
210 95 0.36
211 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (202 bp):
CTTGAGTTTGAATTCTCATAAATGATGAACGGGCTTATCGGAGAATTCACACCTTTGGATTCTTT
TTTGAGTCATCATTCTCATAAATTATGAATGGACTAATAGGAGAATTCACACCTTTGGAATTATG
CTTTTTTTAGAGTTTACATTCTCATAAATTATGAATGGACTGATCGGAGAATTCACACCTTTGGA
TTTCTTA
Found at i:7688 original size:30 final size:30
Alignment explanation
Indices: 7652--7712 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
7642 TTAGTAAGAT
7652 ATTAAAATTTGAGGGTATAAGA-AGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGA-AAAGTC
7682 ATTAAAATTTGAGGGTATAAGAGAAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGAAAAGTC
7712 A
1 A
7713 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGAAAAGTC
Found at i:12078 original size:29 final size:29
Alignment explanation
Indices: 12035--12090 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
12025 TTTAGCGAAA
* *
12035 TGCTCAATTCGGTACCAAACCTTTTAACT
1 TGCTCAAATCAGTACCAAACCTTTTAACT
12064 TGCTCAAATCAGTACCAAACCTTTTAA
1 TGCTCAAATCAGTACCAAACCTTTTAA
12091 AATTGGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (29 bp):
TGCTCAAATCAGTACCAAACCTTTTAACT
Found at i:13368 original size:29 final size:30
Alignment explanation
Indices: 13298--13370 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
13288 TTATAAATGT
* *
13298 TACCAAATTGAACCAATTTTGAAAGGTTTGG
1 TACCAAATTG-AGCAATGTTGAAAGGTTTGG
*** *
13329 TATTGATTTGAGCAA-GTTGAAAGGTTTGG
1 TACCAAATTGAGCAATGTTGAAAGGTTTGG
13358 TACCAAATTGAGC
1 TACCAAATTGAGC
13371 TTTTAGCCAA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
29 22 0.69
30 4 0.12
31 6 0.19
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (30 bp):
TACCAAATTGAGCAATGTTGAAAGGTTTGG
Found at i:14225 original size:5 final size:5
Alignment explanation
Indices: 14215--14245 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
14205 TCAAGTTTTT
*
14215 AAAGG AAAGG AAGGG AAAGG AAAGG AAAGG A
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG A
14246 GAATGAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:15479 original size:25 final size:24
Alignment explanation
Indices: 15451--15503 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
15441 TTACAAGTAG
*
15451 ATTACCTGGAAGCTTCTCTAAGTTT
1 ATTACCTGGAAGCTTCTCT-AGATT
*
15476 ATTACCTGTAAGCTTCTCTAGATT
1 ATTACCTGGAAGCTTCTCTAGATT
15500 ATTA
1 ATTA
15504 TTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (24 bp):
ATTACCTGGAAGCTTCTCTAGATT
Found at i:17878 original size:20 final size:20
Alignment explanation
Indices: 17853--17895 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17843 GGTTATTGCT
17853 TTTGTTGATTCTTCCCTTTG
1 TTTGTTGATTCTTCCCTTTG
* * *
17873 TTTGTTGTTTCTTGCTTTTG
1 TTTGTTGATTCTTCCCTTTG
17893 TTT
1 TTT
17896 TTCTATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.14, G:0.16, T:0.67
Consensus pattern (20 bp):
TTTGTTGATTCTTCCCTTTG
Found at i:18062 original size:39 final size:41
Alignment explanation
Indices: 18008--18087 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 41
17998 TTTGTATGGT
*
18008 TGGGAAATAAAATTAAAAATTGGAGATAC-AA-GAATTGAA
1 TGGGAAACAAAATTAAAAATTGGAGATACAAATGAATTGAA
18047 TGGGAAACAAAATTAAAAATTGGAGATACAAATGAATTGAA
1 TGGGAAACAAAATTAAAAATTGGAGATACAAATGAATTGAA
18088 GAGGAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 28 0.74
40 2 0.05
41 8 0.21
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.23
Consensus pattern (41 bp):
TGGGAAACAAAATTAAAAATTGGAGATACAAATGAATTGAA
Found at i:26899 original size:8 final size:8
Alignment explanation
Indices: 26886--26910 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
26876 AAATAATATA
26886 ATCTTACT
1 ATCTTACT
26894 ATCTTACT
1 ATCTTACT
26902 ATCTTACT
1 ATCTTACT
26910 A
1 A
26911 CTATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (8 bp):
ATCTTACT
Found at i:27562 original size:1 final size:1
Alignment explanation
Indices: 27556--27586 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
27546 CTAATCCAGC
*
27556 TTTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27587 ATCCTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:27593 original size:17 final size:17
Alignment explanation
Indices: 27557--27593 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27547 TAATCCAGCT
* *
27557 TTTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTATCC
27574 TTTTTTTTTTTTTATCC
1 TTTTTTTTTTTTTATCC
27591 TTT
1 TTT
27594 GCATTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTTTTATCC
Done.