Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014842.1 Corchorus olitorius cultivar O-4 contig14875, 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: 63703
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1488 original size:101 final size:101
Alignment explanation
Indices: 1313--1512 Score: 357
Period size: 101 Copynumber: 2.0 Consensus size: 101
1303 TAAAAAATCT
*
1313 AGGGAAAAATATTGAATGGTTATCGTATAAATTTAACTTTCGTTGAATTCATGTGATAGAGAGGT
1 AGGGAAAAATATTGAATGGTTATCGTATAAATTTAACTTTCATTGAATTCATGTGATAGAGAGGT
1378 GTGTGACCTTAAAAGCCTCATAATAAACATGTTTCA
66 GTGTGACCTTAAAAGCCTCATAATAAACATGTTTCA
* *
1414 AGGGAAAAATATTGAATGGTTATTGTATTAATTTAACTTTCATTGAATTCATGTGATAGA-AGAG
1 AGGGAAAAATATTGAATGGTTATCGTATAAATTTAACTTTCATTGAATTCATGTGATAGAGAG-G
1478 TGTGTGACCTTAAAAGCCTCATAATAAACATGTTT
65 TGTGTGACCTTAAAAGCCTCATAATAAACATGTTT
1513 TAATTACATG
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
100 2 0.02
101 93 0.98
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (101 bp):
AGGGAAAAATATTGAATGGTTATCGTATAAATTTAACTTTCATTGAATTCATGTGATAGAGAGGT
GTGTGACCTTAAAAGCCTCATAATAAACATGTTTCA
Found at i:3535 original size:24 final size:24
Alignment explanation
Indices: 3492--3539 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3482 AATTGTATAC
3492 GTACAAAATTAGGTGATTAATTAT
1 GTACAAAATTAGGTGATTAATTAT
* * *
3516 GTACAAATTTATGTGGTTAATTAT
1 GTACAAAATTAGGTGATTAATTAT
3540 ATTAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (24 bp):
GTACAAAATTAGGTGATTAATTAT
Found at i:5141 original size:22 final size:22
Alignment explanation
Indices: 5113--5158 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5103 CTTTAATCAA
5113 TACAAAAGATATGTACAGAGTT
1 TACAAAAGATATGTACAGAGTT
5135 TACAAAAGATATGTACAGAGTT
1 TACAAAAGATATGTACAGAGTT
5157 TA
1 TA
5159 GAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (22 bp):
TACAAAAGATATGTACAGAGTT
Found at i:5204 original size:29 final size:29
Alignment explanation
Indices: 5149--5221 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
5139 AAAGATATGT
5149 ACAGAGTTTAGAA-TTTTTTTTGAAGTAA
1 ACAGAGTTTAGAATTTTTTTTTGAAGTAA
5177 ACAGAGTTTAGAATTTTTTTTTGAAGTAA
1 ACAGAGTTTAGAATTTTTTTTTGAAGTAA
5206 ACAGAGTTTAGAATTT
1 ACAGAGTTTAGAATTT
5222 GAATGTTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 13 0.30
29 31 0.70
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (29 bp):
ACAGAGTTTAGAATTTTTTTTTGAAGTAA
Found at i:30647 original size:13 final size:13
Alignment explanation
Indices: 30629--30653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30619 CTTCTAAATT
30629 AGACTGCATAATC
1 AGACTGCATAATC
30642 AGACTGCATAAT
1 AGACTGCATAAT
30654 TTTTTTGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
AGACTGCATAATC
Found at i:37251 original size:21 final size:21
Alignment explanation
Indices: 37225--37274 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
37215 CTTACTTGAA
37225 GCATCACCGTTGCCATAGAAC
1 GCATCACCGTTGCCATAGAAC
37246 GCATCACCGTTGCCATAGAAC
1 GCATCACCGTTGCCATAGAAC
*
37267 TCATCACC
1 GCATCACC
37275 CACTCTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (21 bp):
GCATCACCGTTGCCATAGAAC
Found at i:58639 original size:15 final size:16
Alignment explanation
Indices: 58616--58657 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
58606 CATCTTCTTA
*
58616 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
58631 TTATTATTATTATAAC
1 TTATTATTATTATAAC
*
58647 -AATTATTATTA
1 TTATTATTATTA
58658 GTTACATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:58652 original size:18 final size:18
Alignment explanation
Indices: 58613--58657 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
58603 AAACATCTTC
* *
58613 TTATTATAATTATTAAAC
1 TTATTATTATTATTAAAA
58631 TTATTATTATTA-TAACAA
1 TTATTATTATTATTAA-AA
58649 TTATTATTA
1 TTATTATTA
58658 GTTACATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTATTATTATTAAAA
Found at i:60071 original size:22 final size:22
Alignment explanation
Indices: 60041--60082 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
60031 GAGATAATAA
* *
60041 TATAGTTTTTAAAATAATCACT
1 TATACTTTTTAAAACAATCACT
*
60063 TATACTTTTTAGAACAATCA
1 TATACTTTTTAAAACAATCA
60083 TTGAAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAAAACAATCACT
Done.