Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011272.1 Corchorus capsularis cultivar CVL-1 contig11293, 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: 26295
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4543 original size:3 final size:3
Alignment explanation
Indices: 4535--4578 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4525 ATATATATAT
4535 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4579 TCAATTGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4620 original size:9 final size:10
Alignment explanation
Indices: 4599--4631 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4589 TAATCATGAC
4599 AAAA-AAAGA
1 AAAAGAAAGA
4608 AAAAGAAAGA
1 AAAAGAAAGA
*
4618 AAAAGAAGGA
1 AAAAGAAAGA
4628 AAAA
1 AAAA
4632 ATCTAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:23660 original size:178 final size:181
Alignment explanation
Indices: 23306--23661 Score: 560
Period size: 178 Copynumber: 2.0 Consensus size: 181
23296 TTCATGAAAG
*
23306 TTGTAGACCATGGAATTACCTTTAAATAGACACTTGAATCACCTTGATCGGTCAATAGAAAAAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAATAG-AAAAAA
* **
23371 ATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAGTGATTAAATAGTAAA
65 ATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAAA
23436 AATTATAAAAGTATAATGATCATTTAATAAATAATCCAACAAAAAAATATGA
130 AATTATAAAAGTATAATGATCATTTAATAAATAATCCAACAAAAAAATATGA
* *
23488 TTGTAGACCATGGAATTATCTTTAAATAGACACCTGAATCACCTTGATTGGTCAAATAG-AAAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTC-AATAGAAAAAA
* * *
23552 A-AAAA-CATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAACATA
65 ATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAAA
*
23614 AATTATAAAAGTATGA-GAATCATTTAATAAATAATCCAACAAAAAAAT
130 AATTATAAAAGTATAATG-ATCATTTAATAAATAATCCAACAAAAAAAT
23662 GATTTGCTTA
Statistics
Matches: 162, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
177 1 0.01
178 56 0.35
179 40 0.25
180 4 0.02
181 6 0.04
182 50 0.31
183 5 0.03
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (181 bp):
TTGTAGACCATGGAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAATAGAAAAAAA
TAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAAAA
ATTATAAAAGTATAATGATCATTTAATAAATAATCCAACAAAAAAATATGA
Found at i:24359 original size:2 final size:2
Alignment explanation
Indices: 24300--24340 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
24290 AATGTATTGT
* *
24300 TA TA GA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
24341 AAATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:24364 original size:10 final size:10
Alignment explanation
Indices: 24333--24366 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
24323 ATATCTATAC
24333 TATATATAAAA
1 TATATA-AAAA
24344 TATAATAAAAA
1 TAT-ATAAAAA
24355 TATATAAAAA
1 TATATAAAAA
24365 TA
1 TA
24367 CGAATAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 10 0.45
12 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:24430 original size:31 final size:30
Alignment explanation
Indices: 24395--24456 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
24385 ATGTTTTCCG
**
24395 ATTGTACCCTTATTTTTAAAACATATTTCTA
1 ATTGTA-CCTTATTTAAAAAACATATTTCTA
*
24426 ATTGTACCTTGTTTAAAAAACATATTTCTA
1 ATTGTACCTTATTTAAAAAACATATTTCTA
24456 A
1 A
24457 ATTGCAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
ATTGTACCTTATTTAAAAAACATATTTCTA
Found at i:24671 original size:37 final size:36
Alignment explanation
Indices: 24577--24671 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
24567 AATTTGGTTT
24577 TTTGTTTCCAACGTCATATTTAATTTGTCTTTTGTC
1 TTTGTTTCCAACGTCATATTTAATTTGTCTTTTGTC
* **
24613 TTTGTTTCGAATCGTTGTATTTAATTT-TACTTTTTGTC
1 TTTGTTTCCAA-CGTCATATTTAATTTGT-C-TTTTGTC
* *
24651 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCATATTT
24672 GGACTTAGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
36 11 0.22
37 22 0.45
38 16 0.33
ACGTcount: A:0.16, C:0.17, G:0.12, T:0.56
Consensus pattern (36 bp):
TTTGTTTCCAACGTCATATTTAATTTGTCTTTTGTC
Found at i:24946 original size:22 final size:22
Alignment explanation
Indices: 24918--25123 Score: 96
Period size: 22 Copynumber: 9.3 Consensus size: 22
24908 TGTCTCTATG
24918 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
24940 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
24963 -GATTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
24984 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAAGA
** ** *
25006 AAGTTATCAAAATCCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
25028 TGGTTACCAAATTTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
25050 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
25072 TCAGATTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
25096 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
25118 TGGTTA
1 TGGTTA
25124 ATTATCACAA
Statistics
Matches: 136, Mismatches: 38, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 110 0.81
23 5 0.04
24 18 0.13
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:24988 original size:44 final size:44
Alignment explanation
Indices: 24950--25046 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
24940 TGGTTATTAT
*
24950 AATTTCATGAGGAGA-TTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAAGTTATCAAAATTCCATAGTGTGGTTACCAA
* *
24994 AATTTCATATGAAAGTTATCAAAATCCCATAGTGTGGTTACCAA
1 AATTTCATAGGAAAGTTATCAAAATTCCATAGTGTGGTTACCAA
*
25038 ATTTTCATA
1 AATTTCATA
25047 ATGTGGTTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (44 bp):
AATTTCATAGGAAAGTTATCAAAATTCCATAGTGTGGTTACCAA
Found at i:25069 original size:44 final size:44
Alignment explanation
Indices: 24969--25069 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
24959 AGGAGATTAT
*
24969 CAAAATTCCATAGTGTGGTTACCAAAATTTCATATGAAAGTTAT
1 CAAAATTCCATAGTGTGGTTACCAAAATTTCATATGAAAGTTAC
* * **
25013 CAAAATCCCATAGTGTGGTTACCAAATTTTCATAATG-TGGTTAC
1 CAAAATTCCATAGTGTGGTTACCAAAATTTCAT-ATGAAAGTTAC
*
25057 CAAAATTTCATAG
1 CAAAATTCCATAG
25070 GATCAGATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 46 0.94
45 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (44 bp):
CAAAATTCCATAGTGTGGTTACCAAAATTTCATATGAAAGTTAC
Found at i:25454 original size:44 final size:45
Alignment explanation
Indices: 25361--25554 Score: 193
Period size: 44 Copynumber: 4.4 Consensus size: 45
25351 ATAGAGATCA
* *
25361 GATTATCAAAATTT-ATAAGA-AGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-T
* *
25405 G-TTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * *
25448 GATTATCAGAATTTCAT-AGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
* * *
25492 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
**
25536 GATTAAGAAAATTTCATAA
1 GATTATCAAAATTTCATAA
25555 TGGTATTTCT
Statistics
Matches: 119, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
43 17 0.14
44 101 0.85
45 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (45 bp):
GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:25461 original size:66 final size:66
Alignment explanation
Indices: 25382--25529 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
25372 TTTATAAGAA
* ** * * *
25382 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
25446 GT
65 GT
* * * *
25448 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
*
25513 A
66 T
* *
25514 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
25530 AAATGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Found at i:25517 original size:22 final size:22
Alignment explanation
Indices: 25363--25529 Score: 142
Period size: 22 Copynumber: 7.6 Consensus size: 22
25353 AGAGATCAGA
*
25363 TTATCAAAATTT-AT-AAGAAGA
1 TTATCAAAATTTCATAAAG-AGG
** **
25384 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
25406 TTATCAAAATTTCA-AAGTGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
25428 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* * *
25450 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * *
25472 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
25494 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
25516 TTATCAAATTTTCA
1 TTATCAAAATTTCA
25530 AAATGTGATT
Statistics
Matches: 115, Mismatches: 27, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
21 13 0.11
22 99 0.86
23 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:25660 original size:20 final size:20
Alignment explanation
Indices: 25635--25684 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
25625 TTATGGAGTA
25635 ATCAAAATTTCAGAGAAGAT
1 ATCAAAATTTCAGAGAAGAT
* * *
25655 ATCAAAATTTTAGGGAGGAT
1 ATCAAAATTTCAGAGAAGAT
25675 ATCAAAATTT
1 ATCAAAATTT
25685 AATAGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAAGAT
Found at i:25768 original size:22 final size:22
Alignment explanation
Indices: 25741--26196 Score: 232
Period size: 22 Copynumber: 20.6 Consensus size: 22
25731 TAGTATATAG
*
25741 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
25763 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
25785 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
25807 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
25823 ATC-AAGTTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
25844 ATCAAAATTTTATAGGGAGATTGATTT
1 ATCAAAATTTCATAGGGAG---G--TT
* *
25871 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
25894 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
25916 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
25938 ATCAAAATTTCAGAGTATGGAGGTT
1 ATCAAAATTTC--A-TAGGGAGGTT
* * * ** *
25963 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
25985 ATCAATATATCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
26007 ATCAACATCTCATAGAGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
26030 AGCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
26052 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
26075 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
26096 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
26118 A-AAAACAATT-ATAAAAAGGTT
1 ATCAAA-ATTTCATAGGGAGGTT
* * * * *
26139 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
26161 ATTAAAATTTCGTAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
26183 ATCAAAATTTCATA
1 ATCAAAATTTCATA
26197 AAGAGGTCAT
Statistics
Matches: 323, Mismatches: 88, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
15 2 0.01
16 8 0.02
17 2 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 24 0.07
22 206 0.64
23 40 0.12
24 2 0.01
25 15 0.05
27 20 0.06
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Done.