Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013050.1 Corchorus capsularis cultivar CVL-1 contig13071, 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: 3865
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:126 original size:22 final size:21
Alignment explanation
Indices: 87--130 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
77 AAATAGGACC
*
87 TGAAACATTGAAGAATTGCAAT
1 TGAAACATCGAAGAATTG-AAT
109 TGAAACATCGAA-AGATTGAAT
1 TGAAACATCGAAGA-ATTGAAT
130 T
1 T
131 TGAAGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (21 bp):
TGAAACATCGAAGAATTGAAT
Found at i:135 original size:36 final size:36
Alignment explanation
Indices: 94--184 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
84 ACCTGAAACA
*
94 TTGAAGAATTGCAATTGAAACATCGAAAGATTGAAT
1 TTGAAGAATTGAAATTGAAACATCGAAAGATTGAAT
* *** * *
130 TTGAAGAATTGGAATTGGGGCATTGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATCGAAAGATTGAAT
*
166 TTGGAGAATTGAAATTGAA
1 TTGAAGAATTGAAATTGAA
185 GCGTCATTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACATCGAAAGATTGAAT
Found at i:169 original size:22 final size:22
Alignment explanation
Indices: 130--178 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
120 AAGATTGAAT
* *
130 TTGAAGAATTGGAATTGGGGCA
1 TTGAAGAATTGGAATTGGAGAA
*
152 TTGAAGGATT-GAATTTGGAGAA
1 TTGAAGAATTGGAA-TTGGAGAA
174 TTGAA
1 TTGAA
179 ATTGAAGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.31
Consensus pattern (22 bp):
TTGAAGAATTGGAATTGGAGAA
Found at i:260 original size:16 final size:16
Alignment explanation
Indices: 239--289 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
229 CATTCAAGTA
*
239 AATTGAAGCATTGAAT
1 AATTGAAGGATTGAAT
255 AATTGAAGGATTGAAT
1 AATTGAAGGATTGAAT
*
271 --TTGAAGGATTGAAG
1 AATTGAAGGATTGAAT
285 AATTG
1 AATTG
290 CATTTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.42
16 18 0.58
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.31
Consensus pattern (16 bp):
AATTGAAGGATTGAAT
Found at i:303 original size:22 final size:22
Alignment explanation
Indices: 249--311 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
239 AATTGAAGCA
* *
249 TTGAATAATTGAAGGATTGAAT
1 TTGAAAAATTGAAGAATTGAAT
** *
271 TTGAAGGATTGAAGAATTGCAT
1 TTGAAAAATTGAAGAATTGAAT
293 TTGAAAAATTG--GAATTGAA
1 TTGAAAAATTGAAGAATTGAA
312 ACATTGAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 7 0.21
22 27 0.79
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (22 bp):
TTGAAAAATTGAAGAATTGAAT
Found at i:340 original size:21 final size:21
Alignment explanation
Indices: 306--361 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
296 AAAAATTGGA
306 ATTGAAACATTGAAATTAAAGC
1 ATTGAAA-ATTGAAATTAAAGC
* *
328 ATTGAAAATTGAAATTGAGGC
1 ATTGAAAATTGAAATTAAAGC
349 ATTGAATAATTGA
1 ATTGAA-AATTGA
362 GGAACGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.30
Consensus pattern (21 bp):
ATTGAAAATTGAAATTAAAGC
Found at i:451 original size:58 final size:59
Alignment explanation
Indices: 340--471 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 59
330 TGAAAATTGA
* * * *
340 AATTGAGGCATTGAATAATTGAGGAACGGAATAAAGACCACCATGTATTATTG-AAGCC
1 AATTGAAGCATTGAATAATTGAGAAACGGAAGAAAGACCACCATGTATCATTGAAAGCC
* **
398 AATTGAAGCATTGAATAATTGAAGAAAC-GAAGAAAGACCACCCTGGT-TCATTGAAAGTG
1 AATTGAAGCATTGAATAATTG-AGAAACGGAAGAAAGACCACCAT-GTATCATTGAAAGCC
*
457 AATTGAAGAATTGAA
1 AATTGAAGCATTGAA
472 GCATTGACTA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
58 39 0.62
59 24 0.38
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (59 bp):
AATTGAAGCATTGAATAATTGAGAAACGGAAGAAAGACCACCATGTATCATTGAAAGCC
Found at i:469 original size:8 final size:8
Alignment explanation
Indices: 456--558 Score: 81
Period size: 8 Copynumber: 13.2 Consensus size: 8
446 CATTGAAAGT
456 GAATTGAA
1 GAATTGAA
464 GAATTGAA
1 GAATTGAA
* *
472 GCATTGAC
1 GAATTGAA
*
480 TAATTGAA
1 GAATTGAA
488 GAATTGAA
1 GAATTGAA
496 GCAA-T-AA
1 G-AATTGAA
503 GTAATTGAA
1 G-AATTGAA
*
512 GAATGGAA
1 GAATTGAA
*
520 GAAAT--A
1 GAATTGAA
526 -AATTGAA
1 GAATTGAA
*
533 GTATTGAA
1 GAATTGAA
541 GAATTGAA
1 GAATTGAA
* *
549 TAATTAAA
1 GAATTGAA
557 GA
1 GA
559 GTCGAAGAGG
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
5 3 0.04
6 1 0.01
7 6 0.08
8 58 0.79
9 5 0.07
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (8 bp):
GAATTGAA
Found at i:486 original size:24 final size:23
Alignment explanation
Indices: 457--558 Score: 91
Period size: 24 Copynumber: 4.4 Consensus size: 23
447 ATTGAAAGTG
* *
457 AATTGAAGAATTGAAGCATTGACT
1 AATTGAAGAATTGAAGAAATGA-T
* *
481 AATTGAAGAATTGAAGCAATAAGT
1 AATTGAAGAATTGAAGAAATGA-T
*
505 AATTGAAGAATGGAAGAAAT-A-
1 AATTGAAGAATTGAAGAAATGAT
* *
526 AATTGAAGTATTGAAGAATTGAAT
1 AATTGAAGAATTGAAGAAATG-AT
*
550 AATTAAAGA
1 AATTGAAGA
559 GTCGAAGAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
21 17 0.26
23 2 0.03
24 46 0.71
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (23 bp):
AATTGAAGAATTGAAGAAATGAT
Found at i:553 original size:45 final size:44
Alignment explanation
Indices: 481--603 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 44
471 AGCATTGACT
* *
481 AATTGAAGAATTGAAGCAAT-AAGTAATTGAAGAATGGAAGAAATA
1 AATTGAAGTATTGAAG-AATGAA-TAATTGAAGAATCGAAGAAATA
* * **
526 AATTGAAGTATTGAAGAATTGAATAATTAAAGAGTCGAAGAGGTA
1 AATTGAAGTATTGAAGAA-TGAATAATTGAAGAATCGAAGAAATA
* * *
571 ATTTAAAGTATTGAAGAACTGAATAATGGAAGA
1 AATTGAAGTATTGAAGAA-TGAATAATTGAAGA
604 TTTGAAACAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.03
45 61 0.94
46 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.25
Consensus pattern (44 bp):
AATTGAAGTATTGAAGAATGAATAATTGAAGAATCGAAGAAATA
Found at i:1602 original size:16 final size:16
Alignment explanation
Indices: 1581--1611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1571 TCTTTTCCAT
1581 TCATTTTTTCATTTTC
1 TCATTTTTTCATTTTC
*
1597 TCATTTTTTTATTTT
1 TCATTTTTTCATTTT
1612 TCCATCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (16 bp):
TCATTTTTTCATTTTC
Found at i:1619 original size:19 final size:18
Alignment explanation
Indices: 1573--1625 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1563 CCTAGAGCTC
*
1573 TTTTCCATTCATTTTTTCA
1 TTTTCCA-TCATTTTTTTA
1592 TTTT-C-TCATTTTTTTA
1 TTTTCCATCATTTTTTTA
1608 TTTTTCCATCATTTTTTT
1 -TTTTCCATCATTTTTTT
1626 TCTTCATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.33
17 4 0.13
18 2 0.07
19 14 0.47
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCCATCATTTTTTTA
Found at i:2334 original size:14 final size:15
Alignment explanation
Indices: 2315--2343 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2305 CTCTCTTTTG
2315 AAACA-TTTTGAAAA
1 AAACATTTTTGAAAA
2329 AAACATTTTTGAAAA
1 AAACATTTTTGAAAA
2344 CTATGACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (15 bp):
AAACATTTTTGAAAA
Done.