Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017061.1 Corchorus olitorius cultivar O-4 contig17094, 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: 20635
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3471 original size:22 final size:22
Alignment explanation
Indices: 3436--3477 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3426 TTCCCGCAAC
*
3436 AACTCCTGGACAGGACTTGTGT
1 AACTCCTGCACAGGACTTGTGT
* *
3458 AACTCCTGCCCAGGTCTTGT
1 AACTCCTGCACAGGACTTGT
3478 CCTGTATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (22 bp):
AACTCCTGCACAGGACTTGTGT
Found at i:8447 original size:19 final size:18
Alignment explanation
Indices: 8414--8449 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8404 TGGAAATAAT
8414 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
8432 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
8450 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:9315 original size:30 final size:30
Alignment explanation
Indices: 9215--9343 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
9205 TAGTTACGTT
* *
9215 CGTCCTGGACCTTGGTACAA-GAACGACGAG
1 CGTCCTGGACATTGGTA-AATGAACGACGAA
**
9245 CGTCCTGGACCA-TGGTAAATGAACGAC-TT
1 CGTCCTGGA-CATTGGTAAATGAACGACGAA
* *
9274 CGTCTTGGACATTGGTACATGAACGACGAA
1 CGTCCTGGACATTGGTAAATGAACGACGAA
**
9304 CGTCCTGGACATTGCCAAATGAAC-ACGAA
1 CGTCCTGGACATTGGTAAATGAACGACGAA
9333 C-TCCCTGGACA
1 CGT-CCTGGACA
9344 ATGCCATCGG
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
28 3 0.04
29 38 0.46
30 41 0.49
31 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (30 bp):
CGTCCTGGACATTGGTAAATGAACGACGAA
Found at i:9324 original size:59 final size:59
Alignment explanation
Indices: 9213--9327 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
9203 ATTAGTTACG
* * **
9213 TTCGTCCTGGACCTTGGTACAAGAACGACGAGCGTCCTGGACCATGGTAAATGAACGAC
1 TTCGTCCTGGACATTGGTACAAGAACGACGAACGTCCTGGACCATGCCAAATGAACGAC
* *
9272 TTCGTCTTGGACATTGGTACATGAACGACGAACGTCCTGGA-CATTGCCAAATGAAC
1 TTCGTCCTGGACATTGGTACAAGAACGACGAACGTCCTGGACCA-TGCCAAATGAAC
9328 ACGAACTCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 2 0.04
59 47 0.96
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (59 bp):
TTCGTCCTGGACATTGGTACAAGAACGACGAACGTCCTGGACCATGCCAAATGAACGAC
Found at i:9341 original size:29 final size:30
Alignment explanation
Indices: 9235--9349 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 30
9225 CTTGGTACAA
* * **
9235 GAACGACGAGCGTCCTGGACCATGGTAAAT
1 GAACGACGAACGTCCTGGACAATGCCAAAT
** * * ** *
9265 GAACGAC-TTCGTCTTGGACATTGGTACAT
1 GAACGACGAACGTCCTGGACAATGCCAAAT
*
9294 GAACGACGAACGTCCTGGACATTGCCAAAT
1 GAACGACGAACGTCCTGGACAATGCCAAAT
9324 GAAC-ACGAAC-TCCCTGGACAATGCCA
1 GAACGACGAACGT-CCTGGACAATGCCA
9350 TCGGAACACG
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 42 0.60
30 27 0.39
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.19
Consensus pattern (30 bp):
GAACGACGAACGTCCTGGACAATGCCAAAT
Found at i:12407 original size:15 final size:15
Alignment explanation
Indices: 12387--12421 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12377 CTAGCCCAAA
*
12387 AATTAAAACCAATTT
1 AATTAAAACCAACTT
*
12402 AATTAAATCCAACTT
1 AATTAAAACCAACTT
12417 AATTA
1 AATTA
12422 GCCTCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTAAAACCAACTT
Found at i:14127 original size:22 final size:22
Alignment explanation
Indices: 14096--14623 Score: 100
Period size: 22 Copynumber: 23.6 Consensus size: 22
14086 GTATAGCTAC
*
14096 CAAAAATTCATATGGAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
* *
14118 CAACACTTCAT-TGTGTA-GTTAT
1 CAAAATTTCATATG-G-AGGTTAT
**
14140 CAAAATTTCATACAGAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
*** **
14162 CAAAATTTCATAAAAACTTTAT
1 CAAAATTTCATATGGAGGTTAT
* *
14184 CAAAATTTC-TTTGGGAGGTTAA
1 CAAAATTTCATAT-GGAGGTTAT
* * * *
14206 CAAAATCTCATACGAATGTTAT
1 CAAAATTTCATATGGAGGTTAT
** *
14228 TGAAATCTT-ATA-GTGTGGTTAT
1 CAAAAT-TTCATATG-GAGGTTAT
*
14250 CAAAATTTCATAGGAAGGGAGGTTAT
1 CAAAATTTCAT----ATGGAGGTTAT
* *
14276 CAAAA--T--T-T-GTGCTTAT
1 CAAAATTTCATATGGAGGTTAT
*
14292 CAAAATTTCATAGGGAGGTTAATT
1 CAAAATTTCATATGGAGGTT-A-T
*
14316 AACCAAATTTCATATGGAGGTTAT
1 --CAAAATTTCATATGGAGGTTAT
*
14340 GAAAATTT--TATGGAGAGGTTAT
1 CAAAATTTCATAT-G-GAGGTTAT
* *
14362 CAAAATTACATA-GAGAGGATATT
1 CAAAATTTCATATG-GAGGTTA-T
** * *
14385 ACAGTTTTATTCTCATAAGAAGGTTAT
1 -CA---AAATT-TCATATGGAGGTTAT
* *
14412 CGAAATTTC--ATGGTGTGTTTAT
1 CAAAATTTCATATGGAG-G-TTAT
* **
14434 CATAATTTTTTGA-GGAGGTTAT
1 CAAAATTTCAT-ATGGAGGTTAT
**
14456 CAAAATTTTCAT-TGTGTTGTTA-
1 CAAAA-TTTCATATG-GAGGTTAT
* * *
14478 CCAAATTT-ATA-GTATGATTAT
1 CAAAATTTCATATGGA-GGTTAT
*
14499 CAAAATTTTCATA-GGGGGATTAT
1 CAAAA-TTTCATATGGAGG-TTAT
** *
14522 CAAAAATTTCATACAGAGATTAT
1 C-AAAATTTCATATGGAGGTTAT
* *
14545 CGAAATTTCATA-GTGTGGTTAT
1 CAAAATTTCATATG-GAGGTTAT
*
14567 -AAAATTTTCATAGGGAGGTTAT
1 CAAAA-TTTCATATGGAGGTTAT
***
14589 TGGAATTTCATAAT-GAGGTTAT
1 CAAAATTTCAT-ATGGAGGTTAT
*
14611 CAATATTTC-TATG
1 CAAAATTTCATATG
14624 TTAGAGCATG
Statistics
Matches: 359, Mismatches: 90, Indels: 115
0.64 0.16 0.20
Matches are distributed among these distances:
16 11 0.03
18 1 0.00
20 15 0.04
21 20 0.06
22 204 0.57
23 43 0.12
24 16 0.04
25 2 0.01
26 32 0.09
27 5 0.01
28 9 0.03
29 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATATGGAGGTTAT
Found at i:14128 original size:44 final size:44
Alignment explanation
Indices: 14070--14173 Score: 109
Period size: 44 Copynumber: 2.4 Consensus size: 44
14060 CATAGGAAGA
* * **
14070 TTATTAAAATTTCATAGTATAGCTACCAAAAATTCATATGGAGG
1 TTATCAAAACTTCATAGTATAGCTACCAAAAATTCATACAGAGG
* * * * * *
14114 TTATCAACACTTCATTGTGTAGTTATCAAAATTTCATACAGAGG
1 TTATCAAAACTTCATAGTATAGCTACCAAAAATTCATACAGAGG
*
14158 TTATCAAAATTTCATA
1 TTATCAAAACTTCATA
14174 AAAACTTTAT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (44 bp):
TTATCAAAACTTCATAGTATAGCTACCAAAAATTCATACAGAGG
Found at i:14485 original size:44 final size:43
Alignment explanation
Indices: 14405--14510 Score: 101
Period size: 43 Copynumber: 2.4 Consensus size: 43
14395 TCTCATAAGA
* * *
14405 AGGTTATCGAAA-TTTCATGGTGTGTTTATCATAATTTTTTGAGG
1 AGGTTATCAAAATTTTCATGGTGTGTTTACCATAA-TTTAT-AGG
* *
14449 AGGTTATCAAAATTTTCATTGTGT-TGTTACCA-AATTTATAGT
1 AGGTTATCAAAATTTTCATGGTGTGT-TTACCATAATTTATAGG
*
14491 ATGATTATCAAAATTTTCAT
1 A-GGTTATCAAAATTTTCAT
14511 AGGGGGATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 3 0.06
43 21 0.40
44 14 0.26
45 15 0.28
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.45
Consensus pattern (43 bp):
AGGTTATCAAAATTTTCATGGTGTGTTTACCATAATTTATAGG
Found at i:14519 original size:23 final size:23
Alignment explanation
Indices: 14493--14581 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
14483 TTTATAGTAT
14493 GATTATCAAAATTTTCATAGGGG
1 GATTATCAAAATTTTCATAGGGG
* ** *
14516 GATTATCAAAAATTTCATACAGA
1 GATTATCAAAATTTTCATAGGGG
* *
14539 GATTATCGAAA-TTTCATAGTGTG
1 GATTATCAAAATTTTCATAG-GGG
14562 G-TTAT-AAAATTTTCATAGGG
1 GATTATCAAAATTTTCATAGGG
14582 AGGTTATTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
21 4 0.08
22 19 0.36
23 30 0.57
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
GATTATCAAAATTTTCATAGGGG
Found at i:14555 original size:45 final size:45
Alignment explanation
Indices: 14493--14578 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
14483 TTTATAGTAT
14493 GATTATCAAAATTTTCATAG-GGGGATTATCAAAAATTTCATACAGA
1 GATTATCAAAATTTTCATAGTGGGG-TTAT-AAAAATTTCATACAGA
* * *
14539 GATTATCGAAA-TTTCATAGTGTGGTTATAAAATTTTCATA
1 GATTATCAAAATTTTCATAGTGGGGTTATAAAAATTTCATA
14579 GGGAGGTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 11 0.31
45 12 0.33
46 13 0.36
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (45 bp):
GATTATCAAAATTTTCATAGTGGGGTTATAAAAATTTCATACAGA
Found at i:18355 original size:21 final size:21
Alignment explanation
Indices: 18330--18400 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
18320 GAGACAAGAG
18330 GAGAGTGCTCGTCATGAAGCA
1 GAGAGTGCTCGTCATGAAGCA
*
18351 GAGAGTGCTCGTCATGAACCA
1 GAGAGTGCTCGTCATGAAGCA
18372 GAGAGTGCTCGTCATGAAGCA
1 GAGAGTGCTCGTCATGAAGCA
*
18393 GAGCGTGC
1 GAGAGTGC
18401 ACGAATGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.27, C:0.21, G:0.34, T:0.18
Consensus pattern (21 bp):
GAGAGTGCTCGTCATGAAGCA
Done.