Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007408.1 Corchorus capsularis cultivar CVL-1 contig07429, 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: 34626
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:138 original size:2 final size:2
Alignment explanation
Indices: 131--167 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
121 GAACAGCAGA
131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
168 CAAAAAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9376 original size:11 final size:11
Alignment explanation
Indices: 9360--9390 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9350 GAAGTTCGTG
*
9360 TTTGAAGATCA
1 TTTGAAGATAA
9371 TTTGAAGATAA
1 TTTGAAGATAA
9382 TTTGAAGAT
1 TTTGAAGAT
9391 TTGAAGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:9394 original size:19 final size:18
Alignment explanation
Indices: 9370--9407 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
9360 TTTGAAGATC
*
9370 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
9389 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
9407 A
1 A
9408 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:10769 original size:6 final size:6
Alignment explanation
Indices: 10758--10787 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10748 TAATTGCCAC
10758 AGATTT AGATTT AGATTT AGATTT A-ATTT A
1 AGATTT AGATTT AGATTT AGATTT AGATTT A
10788 CTTTGCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:12283 original size:15 final size:15
Alignment explanation
Indices: 12263--12303 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
12253 CCTTGCTAAG
12263 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
12278 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
12293 -CATGAAGATGA
1 CCA-GAAGATGA
12304 ACAAACTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.10
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:12829 original size:6 final size:6
Alignment explanation
Indices: 12808--12845 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
12798 AACATTGTAA
*
12808 TTTTCT TTTTAGT TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT TTTTCT T
12846 ATTAGGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:12835 original size:18 final size:19
Alignment explanation
Indices: 12808--12845 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12798 AACATTGTAA
*
12808 TTTTCTTTTTAGTTTTTCT
1 TTTTCTTTTTACTTTTTCT
12827 TTTTCTTTTT-CTTTTTCT
1 TTTTCTTTTTACTTTTTCT
12845 T
1 T
12846 ATTAGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTCTTTTTACTTTTTCT
Found at i:14178 original size:23 final size:20
Alignment explanation
Indices: 14151--14202 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
14141 ATTAATTGAT
14151 TGATTTGATTTTTGATTGAAGAA
1 TGATTTGATTTTT--TT-AAGAA
* *
14174 TGATTAGAATTTTTTAAGAA
1 TGATTTGATTTTTTTAAGAA
14194 TG-TTTGATT
1 TGATTTGATT
14203 CATTGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 2 0.08
23 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (20 bp):
TGATTTGATTTTTTTAAGAA
Found at i:15324 original size:11 final size:11
Alignment explanation
Indices: 15308--15338 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15298 GAAGTTCGTG
*
15308 TTTGAAGATCA
1 TTTGAAGATAA
15319 TTTGAAGATAA
1 TTTGAAGATAA
15330 TTTGAAGAT
1 TTTGAAGAT
15339 TTGAAGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:15342 original size:19 final size:18
Alignment explanation
Indices: 15318--15355 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
15308 TTTGAAGATC
*
15318 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
15337 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
15355 A
1 A
15356 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:16717 original size:6 final size:6
Alignment explanation
Indices: 16706--16741 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
16696 TAATTGCCAC
*
16706 AGATTT AGATTT AGATTT AGATTT AAATTT A-ATTT A
1 AGATTT AGATTT AGATTT AGATTT AGATTT AGATTT A
16742 CTTTGCTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:19338 original size:27 final size:27
Alignment explanation
Indices: 19308--19382 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
19298 AAGTGGACTC
*
19308 AAAATGATCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
* * *
19335 AAAATGACCTAAATGCTCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
*
19362 AAAATGACCATAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
19383 GATAACCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:19626 original size:28 final size:28
Alignment explanation
Indices: 19567--19638 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
19557 CTAGGACGTC
* * *
19567 TCCCTCTGGTGTATCAGGCGGAAATTTG
1 TCCCTCTGATGTATCAGGCGAAAATCTG
19595 TCCCTCTGATGTATCAGGCGTAAAATCT-
1 TCCCTCTGATGTATCAGGCG-AAAATCTG
*
19623 TCCCTCGGATGTATCA
1 TCCCTCTGATGTATCA
19639 CATGGCATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGAAAATCTG
Found at i:20510 original size:156 final size:154
Alignment explanation
Indices: 19984--20489 Score: 683
Period size: 156 Copynumber: 3.2 Consensus size: 154
19974 TTCACACCCC
* * * *
19984 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCTGATTGAGATCAAATTTCGTCAAGGGACT
1 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTT-GCCAAGAGACT
**
20049 TAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACAAAACTCTCCTTCATAGTGAAG
65 TAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCTCCTTCATAGTGAA-
*
20114 TTGGTTTCTCACCCCAAACTGTCCTT
129 CTGGTTTCTCACCCCAAACTGTCCTT
* * * ** * *
20140 AACTGAAAAACGTGCATAAGTTTTTCATCTTAAGTCCAATAAAGCTG-AATTT-CCACCAGTAGG
1 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTGCCA--AG-AGA
* *
20203 CTTAGATTATCTCCATAAGACTATGGAAAAAAATCTAAGTAAAACCGAACTCTCCTTGATAGTGA
63 CTTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCTCCTTCATAGTGA
*
20268 ACTGGTTTTCTCACCCCAAATTGTCCTT
128 ACTGG-TTTCTCACCCCAAACTGTCCTT
* * * * **
20296 AACTAAAAAACATGCATAAGTTTTTCATCCTAAGTTTGATTGAGATGAAATTTGGCCAAGAGACT
1 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTT-GCCAAGAGACT
* * *
20361 TAGATTATCTCCATAAAACTATAGGAAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAA
65 TAGATTATCTCCATAAGACTAT-GGAAAAAATTCTAAGTAAAACCGAACTCTCCTTCATAGTGAA
*
20426 CTGGTTTCTCACCTCAAACTGTCCTT
129 CTGGTTTCTCACCCCAAACTGTCCTT
20452 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCG
1 AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCG
20490 TTTTGGATGA
Statistics
Matches: 302, Mismatches: 40, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
153 2 0.01
155 10 0.03
156 238 0.79
157 49 0.16
159 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (154 bp):
AAATGAAAAACTTGCATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTGCCAAGAGACTT
AGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCTCCTTCATAGTGAACT
GGTTTCTCACCCCAAACTGTCCTT
Found at i:33513 original size:12 final size:12
Alignment explanation
Indices: 33496--33534 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
33486 CCCAATTCCC
33496 TTTTGTTTTTTT
1 TTTTGTTTTTTT
33508 TTTTGTTTTTTT
1 TTTTGTTTTTTT
33520 TTATT-TTTTTATT
1 TT-TTGTTTTT-TT
33533 TT
1 TT
33535 AGCATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.05, C:0.00, G:0.05, T:0.90
Consensus pattern (12 bp):
TTTTGTTTTTTT
Done.