Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016375.1 Corchorus capsularis cultivar CVL-1 contig16396, 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: 31233
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:302 original size:24 final size:24
Alignment explanation
Indices: 270--326 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
260 CTTGGCTGTC
270 GTTGCAATCTTGGATTTGA-TAGAG
1 GTTGCAATCTTGGATTTGACT-GAG
294 GTTGCAATCTTGGATTTGACTGAG
1 GTTGCAATCTTGGATTTGACTGAG
*
318 GTTGGAATC
1 GTTGCAATC
327 CTCTACTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.37
Consensus pattern (24 bp):
GTTGCAATCTTGGATTTGACTGAG
Found at i:2340 original size:16 final size:16
Alignment explanation
Indices: 2319--2349 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2309 GAGGAAGAAC
2319 TCTGTTCGACGAGAGT
1 TCTGTTCGACGAGAGT
2335 TCTGTTCGACGAGAG
1 TCTGTTCGACGAGAG
2350 AGAAGCGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29
Consensus pattern (16 bp):
TCTGTTCGACGAGAGT
Found at i:7898 original size:30 final size:30
Alignment explanation
Indices: 7862--7924 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
7852 TCTTCAAGGG
7862 GGAGGGAATGATCCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATCCG-CCAAGGACTTATCAT
*
7892 GGAGGGAATGATGCGCCAAGGACTTATCAT
1 GGAGGGAATGATCCGCCAAGGACTTATCAT
7922 GGA
1 GGA
7925 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATCCGCCAAGGACTTATCAT
Found at i:10409 original size:10 final size:11
Alignment explanation
Indices: 10393--10421 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
10383 CATCTTCCTT
10393 CAAAACAAAAG
1 CAAAACAAAAG
10404 -AAAACAAAAG
1 CAAAACAAAAG
10414 CAAAACAA
1 CAAAACAA
10422 GATCAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAG
Found at i:12957 original size:16 final size:16
Alignment explanation
Indices: 12936--12967 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12926 TCAGCCCTAA
12936 ACCGCCCTATCTATGT
1 ACCGCCCTATCTATGT
12952 ACCGCCCTATCTATGT
1 ACCGCCCTATCTATGT
12968 TCCTCCACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (16 bp):
ACCGCCCTATCTATGT
Found at i:13774 original size:15 final size:16
Alignment explanation
Indices: 13754--13787 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13744 GATTGCTTTC
*
13754 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
13769 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
13785 TTA
1 TTA
13788 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:21256 original size:29 final size:29
Alignment explanation
Indices: 21222--21284 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
21212 GAATGTTTAG
21222 AATTTTTAATAATGTTTTATTCTTTGATT
1 AATTTTTAATAATGTTTTATTCTTTGATT
21251 AATTTTTAATAATGTTTTATTCTTTGATT
1 AATTTTTAATAATGTTTTATTCTTTGATT
21280 AATTT
1 AATTT
21285 ATAGTAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (29 bp):
AATTTTTAATAATGTTTTATTCTTTGATT
Found at i:22350 original size:19 final size:18
Alignment explanation
Indices: 22326--22361 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22316 TGAAGATTTC
22326 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
22345 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
22362 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23663 original size:15 final size:16
Alignment explanation
Indices: 23643--23676 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23633 GATTGCTTTC
*
23643 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
23658 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
23674 TTA
1 TTA
23677 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:25819 original size:60 final size:60
Alignment explanation
Indices: 25715--25863 Score: 217
Period size: 60 Copynumber: 2.5 Consensus size: 60
25705 TAGTAGTTAT
* * **
25715 GCAACATGCTTTCTGATGAGTGTAGCTATTATATTATATCAAAGTGGTAAAGGTAATTAA
1 GCAACATGCTTTCTGATGAGTGTAGTTATTATATTAGATCAAAGTAATAAAGGTAATTAA
* * * *
25775 GCATCATGCTTTTTGATGAGTGTAGTTATTATATTAGATTAAAGTAATAAAGGTAATTAT
1 GCAACATGCTTTCTGATGAGTGTAGTTATTATATTAGATCAAAGTAATAAAGGTAATTAA
*
25835 GCAACATGCTTTCTGATGAGTGTAATTAT
1 GCAACATGCTTTCTGATGAGTGTAGTTAT
25864 CTGAGATCTC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (60 bp):
GCAACATGCTTTCTGATGAGTGTAGTTATTATATTAGATCAAAGTAATAAAGGTAATTAA
Done.