Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014237.1 Corchorus capsularis cultivar CVL-1 contig14258, 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: 15527
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1114 original size:20 final size:20
Alignment explanation
Indices: 1073--1115 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1063 TTCTCACAAG
* *
1073 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
1093 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
1113 TTT
1 TTT
1116 TCCACATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:1354 original size:104 final size:104
Alignment explanation
Indices: 1174--1408 Score: 337
Period size: 104 Copynumber: 2.3 Consensus size: 104
1164 CTGTCAGAAA
* *
1174 AGTATTAGTCGATGAAAACTCAAGTTTTAATTCCAGTGTTATCGACTAAAACTCCAAGTCTCCAC
1 AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATTATCGACTAAAACTCCAAGTCTCCAC
**
1239 TTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGT
66 TTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * ** *
1278 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATT-ATCGACTAAAACTCCAAGTCTCCA
1343 CTTTT-AAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
65 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
** * *
1382 AGTATTAATTAATGAATACTTAAGTTT
1 AGTATTAATCGATGAAAACTCAAGTTT
1409 CATGTTTCAA
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
104 88 0.76
105 28 0.24
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (104 bp):
AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATTATCGACTAAAACTCCAAGTCTCCAC
TTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:1434 original size:105 final size:105
Alignment explanation
Indices: 1174--1436 Score: 296
Period size: 104 Copynumber: 2.5 Consensus size: 105
1164 CTGTCAGAAA
* * * * * ***
1174 AGTATTAGTCGATGAAAACTCAAGTTTTAATTCCAGTGTT-ATCGACTAAAACTCCAAGTCTCCA
1 AGTATTAATCAATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
**
1238 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGT
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * * ** *
1278 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCAATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
1343 CTTTT-AAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * * * *
1382 AGTATTAATTAATGAATACTTAAGTTTCATGTTTCAACGTTCATCGATTAAAACT
1 AGTATTAATCAATGAAAACTCAAGTTTCA-GTTTCAACATTAATCGACTAAAACT
1437 TTCTTTAATT
Statistics
Matches: 136, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
104 89 0.65
105 47 0.35
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (105 bp):
AGTATTAATCAATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:7287 original size:12 final size:12
Alignment explanation
Indices: 7270--7297 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7260 ACCTGACAAT
7270 TCGTGTTTCGTG
1 TCGTGTTTCGTG
7282 TCGTGTTTCGTG
1 TCGTGTTTCGTG
7294 TCGT
1 TCGT
7298 ATAAACGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:8542 original size:15 final size:15
Alignment explanation
Indices: 8522--8575 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
8512 AGTAATTAAT
*
8522 AATAATTATGCTAAA
1 AATAATTATGCAAAA
*
8537 AATAATTATGCCAAA
1 AATAATTATGCAAAA
8552 AATAATTATGCAAAA
1 AATAATTATGCAAAA
8567 AATAATTAT
1 AATAATTAT
8576 TATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (15 bp):
AATAATTATGCAAAA
Found at i:12320 original size:29 final size:28
Alignment explanation
Indices: 12288--12344 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
12278 TCCAAATTGC
12288 AAGTTCATGGGG-CAAAACGTCCAAAATTA
1 AAGTTCA-GGGGACAAAACGT-CAAAATTA
*
12317 AAGTTTAGGGGACAAAACGTCAAAATTA
1 AAGTTCAGGGGACAAAACGTCAAAATTA
12345 TACAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (28 bp):
AAGTTCAGGGGACAAAACGTCAAAATTA
Found at i:12358 original size:31 final size:28
Alignment explanation
Indices: 12296--12364 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 28
12286 GCAAGTTCAT
*
12296 GGGGCAAAACGTCCAAAATTAAAGTTTA
1 GGGGCAAAACGTCCAAAATTAAAATTTA
12324 GGGGACAAAACGT-CAAAATTATACAAATTTA
1 GGGG-CAAAACGTCCAAAA-T-TA-AAATTTA
12355 GGGGGCAAAA
1 -GGGGCAAAA
12365 AGGCATTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
28 9 0.26
29 9 0.26
30 2 0.06
31 11 0.31
32 4 0.11
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (28 bp):
GGGGCAAAACGTCCAAAATTAAAATTTA
Found at i:14671 original size:19 final size:20
Alignment explanation
Indices: 14630--14674 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
14620 CCCTAACGTG
*
14630 TAATTATTTTATTTGACTTA
1 TAATTAATTTATTTGACTTA
14650 TAATTAATTT-TTTG-CTTGA
1 TAATTAATTTATTTGACTT-A
14669 TAATTA
1 TAATTA
14675 TAACTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (20 bp):
TAATTAATTTATTTGACTTA
Found at i:15341 original size:17 final size:17
Alignment explanation
Indices: 15319--15353 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15309 GTCACGCGCG
*
15319 ACGCCACGTGGAAGTGA
1 ACGCCACATGGAAGTGA
15336 ACGCCACATGGAAGTGA
1 ACGCCACATGGAAGTGA
15353 A
1 A
15354 GACTAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.31, T:0.11
Consensus pattern (17 bp):
ACGCCACATGGAAGTGA
Done.