Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010064.1 Corchorus capsularis cultivar CVL-1 contig10085, 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: 10268
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Found at i:104 original size:54 final size:54
Alignment explanation
Indices: 1--337 Score: 385
Period size: 54 Copynumber: 6.3 Consensus size: 54
** * * * * *
1 AAACTTCTTTAAATGACCGCACCGG-CCCATTCGAGATCAACTCTAACCACTGA
1 AAACTTCTTGGAATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
* * * * *
54 AAATTTCTT-GAGACGACCACACCGGATCAATTGGGGGTCAACTCTGACCACCG-
1 AAACTTCTTGGA-ATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
*
107 AAACTTCTTGGAATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGA
1 AAACTTCTTGGAATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
* * * *
161 AAACTTCTTGGAATGACCGCACTGGATCAATTGGAGATCAACTCTGAACTCCAA
1 AAACTTCTTGGAATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
* * * * *
215 AAACTTCTTGGAATGACCGCACTGGGTCAATTGGAGATCAACTCTGAACTCCAA
1 AAACTTCTTGGAATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
* * **
269 AAACTTCTTGGAATGACCACACCGGATCAATCT-GAGATCAACTCTGATCATTGA
1 AAACTTCTTGGAATGACCGCACCGGATCAAT-TGGAGATCAACTCTGACCACCGA
*
323 AAACTTCTTGAAATG
1 AAACTTCTTGGAATG
338 TGATCAACTC
Statistics
Matches: 247, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
52 1 0.00
53 63 0.26
54 182 0.74
55 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (54 bp):
AAACTTCTTGGAATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGA
Found at i:350 original size:35 final size:35
Alignment explanation
Indices: 304--372 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
294 ATCAATCTGA
304 GATCAACTCTGATCATTGAAAACTTCTTGAAATGT
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATGT
* *
339 GATCAACTCTGATCGTTGAAAACTTCTTGGAATG
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATG
373 ACCACATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (35 bp):
GATCAACTCTGATCATTGAAAACTTCTTGAAATGT
Found at i:401 original size:89 final size:89
Alignment explanation
Indices: 268--462 Score: 354
Period size: 89 Copynumber: 2.2 Consensus size: 89
258 CTGAACTCCA
*
268 AAAACTTCTTGGAATGACCACACCGGATCAATCTGAGATCAACTCTGATCATTGAAAACTTCTTG
1 AAAACTTCTTGGAATGACCACACCAGATCAATCTGAGATCAACTCTGATCATTGAAAACTTCTTG
* *
333 AAATGTGATCAACTCTGATCGTTG
66 AAATGAGATCAACTCTGATCATTG
*
357 AAAACTTCTTGGAATGACCACATCAGATCAATCTGAGATCAACTCTGATCATTGAAAACTTCTTG
1 AAAACTTCTTGGAATGACCACACCAGATCAATCTGAGATCAACTCTGATCATTGAAAACTTCTTG
422 AAATGAGATCAACTCTGATCATTG
66 AAATGAGATCAACTCTGATCATTG
446 AAAACTTCTTGGAATGA
1 AAAACTTCTTGGAATGA
463 GATCAACTCT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 102 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (89 bp):
AAAACTTCTTGGAATGACCACACCAGATCAATCTGAGATCAACTCTGATCATTGAAAACTTCTTG
AAATGAGATCAACTCTGATCATTG
Found at i:436 original size:35 final size:34
Alignment explanation
Indices: 390--691 Score: 426
Period size: 35 Copynumber: 8.7 Consensus size: 34
380 CAGATCAATC
*
390 TGAGATCAACTCTGATCATTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
425 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
*
460 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAG
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
* *
495 TGAGATCAACTCTGATCTTCGAAAACTTTTTAGAA
1 TGAGATCAACTCTGATCTT-GAAAACTTCTTGGAA
* *
530 TGAGATCAACTCTGATCGTTG-GAACTTTTTGGAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
* *
564 TGAGATCAACTCTGATCGTTGGAAACTTCTTGAAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
**
599 TGAGATCAACTCTGATCTTCCAAACTTCTTGGAA
1 TGAGATCAACTCTGATCTTGAAAACTTCTTGGAA
*
633 TGAGATCAACTCTGATCTTCGAAAACTTCTTGGGA
1 TGAGATCAACTCTGATCTT-GAAAACTTCTTGGAA
668 TGAGATCAACTCTGATCTTCGAAA
1 TGAGATCAACTCTGATCTT-GAAA
692 CTTTGAAAGA
Statistics
Matches: 247, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
34 67 0.27
35 178 0.72
36 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (34 bp):
TGAGATCAACTCTGATCTTGAAAACTTCTTGGAA
Found at i:590 original size:69 final size:70
Alignment explanation
Indices: 390--684 Score: 436
Period size: 69 Copynumber: 4.2 Consensus size: 70
380 CAGATCAATC
*
390 TGAGATCAACTCTGATCATTGAAAACTTCTTGAAATGAGATCAACTCTGATCATT-GAAAACTTC
1 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGAGATCAACTCTGATC-TTCGAAAACTTC
454 TTGGAA
65 TTGGAA
* *
460 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAGTGAGATCAACTCTGATCTTCGAAAACTTTT
1 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCTTCGAAAACTTCT
*
525 TAGAA
66 TGGAA
* * * *
530 TGAGATCAACTCTGATCGTTG-GAACTTTTTGGAATGAGATCAACTCTGATCGTT-GGAAACTTC
1 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGAGATCAACTCTGATC-TTCGAAAACTTC
*
593 TTGAAA
65 TTGGAA
**
599 TGAGATCAACTCTGATC-TTCCAAACTTCTTGGAATGAGATCAACTCTGATCTTCGAAAACTTCT
1 TGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCTTCGAAAACTTCT
*
663 TGGGA
66 TGGAA
668 TGAGATCAACTCTGATC
1 TGAGATCAACTCTGATC
685 TTCGAAACTT
Statistics
Matches: 203, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
68 4 0.02
69 114 0.56
70 85 0.42
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (70 bp):
TGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCTTCGAAAACTTCT
TGGAA
Found at i:604 original size:104 final size:102
Alignment explanation
Indices: 390--694 Score: 427
Period size: 104 Copynumber: 2.9 Consensus size: 102
380 CAGATCAATC
390 TGAGATCAACTCTGATCATT-GAAAACTTCTTGAAATGAGATCAACTCTGATCATTGAAAACTTC
1 TGAGATCAACTCTGATC-TTCGAAAACTTCTTG-AATGAGATCAACTCTGATC-TTGAAAACTTC
* * *
454 TTGGAATGAGATCAACTCTGATCATTGAAAACTTCTTGGAG
63 TTGGAATGAGATCAACTCTGATC-TTGGAAACTTCTTGAAA
* * *
495 TGAGATCAACTCTGATCTTCGAAAACTTTTTAGAATGAGATCAACTCTGATCGTTG-GAACTTTT
1 TGAGATCAACTCTGATCTTCGAAAACTTCTT-GAATGAGATCAACTCTGATC-TTGAAAACTTCT
559 TGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGAAA
64 TGGAATGAGATCAACTCTGATC-TTGGAAACTTCTTGAAA
*
599 TGAGATCAACTCTGATCTTC-CAAACTTCTTGGAATGAGATCAACTCTGATCTTCGAAAACTTCT
1 TGAGATCAACTCTGATCTTCGAAAACTTCTT-GAATGAGATCAACTCTGATCTT-GAAAACTTCT
* *
663 TGGGATGAGATCAACTCTGATCTTCGAAACTT
64 TGGAATGAGATCAACTCTGATCTTGGAAACTT
695 TGAAAGATCA
Statistics
Matches: 181, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
102 2 0.01
103 38 0.21
104 91 0.50
105 49 0.27
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (102 bp):
TGAGATCAACTCTGATCTTCGAAAACTTCTTGAATGAGATCAACTCTGATCTTGAAAACTTCTTG
GAATGAGATCAACTCTGATCTTGGAAACTTCTTGAAA
Found at i:1224 original size:17 final size:16
Alignment explanation
Indices: 1202--1235 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1192 ATTATTAATA
1202 AATAAGGAAATATGTAC
1 AATAA-GAAATATGTAC
*
1219 AATAAGACATATGTAC
1 AATAAGAAATATGTAC
1235 A
1 A
1236 GAGAAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (16 bp):
AATAAGAAATATGTAC
Found at i:1652 original size:14 final size:15
Alignment explanation
Indices: 1635--1674 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1625 TTTAGAAACC
*
1635 TTTTTTTTTTG-TTT
1 TTTTTTTTTTGCTCT
1649 TTTTTTTTTTGCTCT
1 TTTTTTTTTTGCTCT
*
1664 TTTTTGTTTTG
1 TTTTTTTTTTG
1675 GACTTTACGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTGCTCT
Found at i:8912 original size:21 final size:21
Alignment explanation
Indices: 8865--8912 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
8855 GGCCTTACTC
* *
8865 CTGCCTCATTTCTTCTTGCGA
1 CTGCCTCATTTCTCCCTGCGA
* *
8886 CGGCCTCATTTCTCCCTGTGA
1 CTGCCTCATTTCTCCCTGCGA
8907 CTGCCT
1 CTGCCT
8913 TAACTGTTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.08, C:0.38, G:0.17, T:0.38
Consensus pattern (21 bp):
CTGCCTCATTTCTCCCTGCGA
Done.