Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008219.1 Corchorus capsularis cultivar CVL-1 contig08240, 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: 58060
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Found at i:1129 original size:25 final size:26
Alignment explanation
Indices: 1084--1136 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
1074 AGCCCTTAAT
1084 AACAACTGCATTTTTTAGTAACCTTG
1 AACAACTGCATTTTTTAGTAACCTTG
1110 AACAACTGCA-TTTTTAGTAACCTTG
1 AACAACTGCATTTTTTAGTAACCTTG
1135 AA
1 AA
1137 TAAGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (26 bp):
AACAACTGCATTTTTTAGTAACCTTG
Found at i:3406 original size:2 final size:2
Alignment explanation
Indices: 3394--3429 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3384 GTATTTTACG
3394 AT AT A- 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
3430 CCTAAAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6486 original size:18 final size:18
Alignment explanation
Indices: 6458--6508 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
6448 TTTCCTTTAG
6458 TTTTG-TTTTGTTTCGTA
1 TTTTGTTTTTGTTTCGTA
*
6475 TTTTGTTTTTGTTTTTCGTT
1 TTTTGTTTTTG--TTTCGTA
6495 TTTGTGTTTTTGTT
1 TTT-TGTTTTTGTT
6509 AATTTTGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 2 0.07
20 9 0.31
21 8 0.28
ACGTcount: A:0.02, C:0.04, G:0.18, T:0.76
Consensus pattern (18 bp):
TTTTGTTTTTGTTTCGTA
Found at i:11583 original size:92 final size:92
Alignment explanation
Indices: 11424--11672 Score: 462
Period size: 92 Copynumber: 2.7 Consensus size: 92
11414 AAACTAGCTC
* * *
11424 TCAGCCCGCGCTTCGCCGCGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAATCTATGTTT
1 TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
*
11489 TTTGCAAGAATGTTCATTTGAGTGTTA
66 TTTGAAAGAATGTTCATTTGAGTGTTA
11516 TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
1 TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
11581 TTTGAAAGAATGTTCATTTGAGTGTTA
66 TTTGAAAGAATGTTCATTTGAGTGTTA
11608 TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
1 TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
11673 AGAATAACGT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 153 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (92 bp):
TCAGCCCGCGCTTCGCCGTGGGCGAGGGATTTGCAAACACGTTAATTATGAAAAAGTCTATGCTT
TTTGAAAGAATGTTCATTTGAGTGTTA
Found at i:12842 original size:80 final size:80
Alignment explanation
Indices: 12709--12864 Score: 258
Period size: 80 Copynumber: 1.9 Consensus size: 80
12699 CCAATCTGAC
* * * *
12709 CATACTGTGCCCAAAGGATGACATCATTAGCACATGTTTTCCTAATTGTTCCACTTCTAAGTAAG
1 CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTAAGTAAG
12774 AAAACAATTCTAGAG
66 AAAACAATTCTAGAG
*
12789 CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTATGTAAG
1 CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTAAGTAAG
*
12854 AAAACATTTCT
66 AAAACAATTCT
12865 GACAGTCGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (80 bp):
CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTAAGTAAG
AAAACAATTCTAGAG
Found at i:15962 original size:34 final size:34
Alignment explanation
Indices: 15922--15996 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
15912 TAACCTTATT
15922 CAAGACAACCTAACAGTAACAAAATAAAAAATCA
1 CAAGACAACCTAACAGTAACAAAATAAAAAATCA
15956 CAAGACAACCTAACAGTAACAAAATAAAAAATCA
1 CAAGACAACCTAACAGTAACAAAATAAAAAATCA
15990 -AAG-CAAC
1 CAAGACAAC
15997 AAAAATCACT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 4 0.10
33 3 0.07
34 34 0.83
ACGTcount: A:0.61, C:0.21, G:0.07, T:0.11
Consensus pattern (34 bp):
CAAGACAACCTAACAGTAACAAAATAAAAAATCA
Found at i:16562 original size:45 final size:45
Alignment explanation
Indices: 16511--16600 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
16501 GGAAGACCCT
* * ** *
16511 AAAATCCTAAAACCATTCAATAGTACAAACATTAGGAAATCATGC
1 AAAATCCAAAAACCATTCAACAACACAAACATTAAGAAATCATGC
* * *
16556 AAAATCCAAAAACTATTGAACAACACAAATATTAAGAAATCATGC
1 AAAATCCAAAAACCATTCAACAACACAAACATTAAGAAATCATGC
16601 GATCATCACT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (45 bp):
AAAATCCAAAAACCATTCAACAACACAAACATTAAGAAATCATGC
Found at i:19295 original size:33 final size:32
Alignment explanation
Indices: 19258--19319 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
19248 GATCAAGGCA
* *
19258 CAAAATCAGGGATAAAGTCGAAAAGCAGCAACG
1 CAAAAT-AGGGAGAAAGTCAAAAAGCAGCAACG
* *
19291 CAAAATGGGGCGAAAGTCAAAAAGCAGCA
1 CAAAATAGGGAGAAAGTCAAAAAGCAGCA
19320 TCTGCAATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.48, C:0.18, G:0.26, T:0.08
Consensus pattern (32 bp):
CAAAATAGGGAGAAAGTCAAAAAGCAGCAACG
Found at i:19672 original size:20 final size:21
Alignment explanation
Indices: 19647--19688 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
19637 ATGAAGGTAA
*
19647 TTACTAAATACCG-TCCCCTT
1 TTACTAAACACCGCTCCCCTT
*
19667 TTACTAAGCACCGCTCCCCTT
1 TTACTAAACACCGCTCCCCTT
19688 T
1 T
19689 GGACTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.33
Consensus pattern (21 bp):
TTACTAAACACCGCTCCCCTT
Found at i:20032 original size:21 final size:23
Alignment explanation
Indices: 19995--20040 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
19985 GCGGGTCATG
19995 CGCGACCCACACCATGG-CTGGT
1 CGCGACCCACACCATGGCCTGGT
*
20017 CGCGACCCA-TCCATGGCCTGGT
1 CGCGACCCACACCATGGCCTGGT
20039 CG
1 CG
20041 TGATCCGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.15, C:0.41, G:0.28, T:0.15
Consensus pattern (23 bp):
CGCGACCCACACCATGGCCTGGT
Found at i:35431 original size:21 final size:22
Alignment explanation
Indices: 35405--35449 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
35395 GAGAAAGGTG
35405 TTGCTAAACACCGCCCC-CTTT
1 TTGCTAAACACCGCCCCACTTT
**
35426 TTGCTATTCACCGCCCCACTTT
1 TTGCTAAACACCGCCCCACTTT
35448 TT
1 TT
35450 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.16, C:0.40, G:0.09, T:0.36
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Done.