Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011459.1 Corchorus capsularis cultivar CVL-1 contig11480, 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: 33963
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:947 original size:30 final size:33
Alignment explanation
Indices: 897--982 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
887 GCCGCGCAAC
*
897 ACCGGCCACATGATCGGCCATCGCATGG-G-A-CA
1 ACCGGCCACA--ACCGGCCATCGCATGGTGCACCA
*
929 ACCGGCCACAACCGGCCATCGCTTGGTGCACCA
1 ACCGGCCACAACCGGCCATCGCATGGTGCACCA
*
962 ACCGGCCACAACCGGACATCG
1 ACCGGCCACAACCGGCCATCG
983 ATTGGGTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 14 0.29
31 1 0.02
32 11 0.23
33 22 0.46
ACGTcount: A:0.24, C:0.40, G:0.26, T:0.10
Consensus pattern (33 bp):
ACCGGCCACAACCGGCCATCGCATGGTGCACCA
Found at i:969 original size:33 final size:30
Alignment explanation
Indices: 897--1010 Score: 104
Period size: 30 Copynumber: 3.6 Consensus size: 30
887 GCCGCGCAAC
* *
897 ACCGGCCACATGATCGGCCATCGCATGGGACA
1 ACCGGCCACA--ACCGGCCATCGCTTGGGACA
929 ACCGGCCACAACCGGCCATCGCTTGGTGCACCA
1 ACCGGCCACAACCGGCCATCGCTTGG-G-A-CA
* * *
962 ACCGGCCACAACCGGACATCGATTGGGTCA
1 ACCGGCCACAACCGGCCATCGCTTGGGACA
* *
992 TCCGGACA-AGACCGGCCAT
1 ACCGGCCACA-ACCGGCCAT
1011 TTGATCCTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
29 1 0.01
30 30 0.43
31 1 0.01
32 12 0.17
33 26 0.37
ACGTcount: A:0.25, C:0.37, G:0.26, T:0.12
Consensus pattern (30 bp):
ACCGGCCACAACCGGCCATCGCTTGGGACA
Found at i:7968 original size:72 final size:72
Alignment explanation
Indices: 7851--7994 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
7841 ACCAATATGT
7851 TTATAGTTTTTCACTAACCTATGAGTCTATCGAGTCAGTCTTAAACATGTTTGTGGGTATCGTCT
1 TTATAGTTTTTCACTAACCTATGAGTCTATCGAGTCAGTCTTAAACATGTTTGTGGGTATCGTCT
7916 TAGTTAA
66 TAGTTAA
7923 TTATAGTTTTTCACTAACCTATGAGTCTATCGAGTCAGTCTTAAACATGTTTGTGGGTATCGTCT
1 TTATAGTTTTTCACTAACCTATGAGTCTATCGAGTCAGTCTTAAACATGTTTGTGGGTATCGTCT
7988 TAGTTAA
66 TAGTTAA
7995 GAAAACCCTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (72 bp):
TTATAGTTTTTCACTAACCTATGAGTCTATCGAGTCAGTCTTAAACATGTTTGTGGGTATCGTCT
TAGTTAA
Found at i:15029 original size:89 final size:89
Alignment explanation
Indices: 14878--15058 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
14868 CACATCCATA
* *
14878 TGTCGAACTTGCAAGATATGCCTGATTGGGATTAAACCGTGAAACAATTGCCAAATAAAAAATTT
1 TGTCGAACTCGCAAGATATGCCTGATTGGGATTAAACCGTGAAACAATCGCCAAATAAAAAATTT
*
14943 CACCTTTGGGTTTGTTCTTGATAT
66 CACCTTTGGGTTTGTCCTTGATAT
*
14967 TGTCGAGCTCGCAAGATATGCCTGATTGGGATTAAACCGTGAAACAATCGCCAAATAAAAAATTT
1 TGTCGAACTCGCAAGATATGCCTGATTGGGATTAAACCGTGAAACAATCGCCAAATAAAAAATTT
15032 CACCTTTGGGTTTGTCCTTGATAT
66 CACCTTTGGGTTTGTCCTTGATAT
15056 TGT
1 TGT
15059 TGTTGGATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (89 bp):
TGTCGAACTCGCAAGATATGCCTGATTGGGATTAAACCGTGAAACAATCGCCAAATAAAAAATTT
CACCTTTGGGTTTGTCCTTGATAT
Found at i:15886 original size:107 final size:104
Alignment explanation
Indices: 15653--15890 Score: 338
Period size: 107 Copynumber: 2.3 Consensus size: 104
15643 ATTTTAATTT
**
15653 TAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTATTTCTTAAACCTTATAACAATATT
1 TAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTTAAACCCAATAACAATATT
* * *
15716 ATTAGTTATGGAATTTACCCTTAAAATAAAAAAAAAATT
66 ATTAATTATGAAATTTACCCTTAAAATAAAAAAAAAATA
* * *
15755 TAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT-TTAAAACCCAATAACAATAA
1 TAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTT-AAACCCAATAACAAT--
*
15819 ATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAAATA
63 ATTATTAATTATGAAATTTACCCTTAAAATAAAAA-AAAAATA
15862 TAATTTGGGGCTAAACTTAGTGAAATTAA
1 TAATTTGGGGCTAAACTTAGTGAAATTAA
15891 GGCTAAACTT
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 6 0.05
103 17 0.14
104 31 0.26
106 32 0.27
107 34 0.28
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (104 bp):
TAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTTAAACCCAATAACAATATT
ATTAATTATGAAATTTACCCTTAAAATAAAAAAAAAATA
Found at i:25388 original size:19 final size:19
Alignment explanation
Indices: 25332--25390 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
25322 AAACTATTCT
25332 TAATCATTATTCAT-TA-A
1 TAATCATTATTCATATATA
25349 TAAT-ATATATACTC-TAT-TA
1 TAATCAT-TAT--TCATATATA
25368 TAATCATTATTCATATATA
1 TAATCATTATTCATATATA
25387 TAAT
1 TAAT
25391 AATGCCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 4 0.12
19 17 0.50
20 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATCATTATTCATATATA
Found at i:26501 original size:31 final size:31
Alignment explanation
Indices: 26458--26519 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
26448 ACATTAAAAA
*
26458 CACATCCTACTCAAGCTTGATTCCTACTAGC
1 CACAACCTACTCAAGCTTGATTCCTACTAGC
*
26489 CACAACCTACTCAATCTTGATTCCTACTAGC
1 CACAACCTACTCAAGCTTGATTCCTACTAGC
26520 TTGATTCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.29
Consensus pattern (31 bp):
CACAACCTACTCAAGCTTGATTCCTACTAGC
Found at i:26524 original size:15 final size:15
Alignment explanation
Indices: 26504--26537 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
26494 CCTACTCAAT
26504 CTTGATTCCTACTAG
1 CTTGATTCCTACTAG
26519 CTTGATTCCTACTAG
1 CTTGATTCCTACTAG
26534 CTTG
1 CTTG
26538 CCACTCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (15 bp):
CTTGATTCCTACTAG
Found at i:28723 original size:17 final size:16
Alignment explanation
Indices: 28697--28730 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
28687 TTCTTCAAAA
28697 AAATAAGATATTAATG
1 AAATAAGATATTAATG
28713 AAATGAAGATATTAATG
1 AAAT-AAGATATTAATG
28730 A
1 A
28731 CGTACACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (16 bp):
AAATAAGATATTAATG
Found at i:31298 original size:20 final size:22
Alignment explanation
Indices: 31273--31327 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
31263 ATGGAAACGG
31273 AATGGAGAAATGGAAG-GCA-A
1 AATGGAGAAATGGAAGAGCACA
*
31293 AATGGAGATATGG-AGAGCACA
1 AATGGAGAAATGGAAGAGCACA
*
31314 AATGGAGGAATGGA
1 AATGGAGAAATGGA
31328 GTAAGCGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.13
Consensus pattern (22 bp):
AATGGAGAAATGGAAGAGCACA
Found at i:32073 original size:17 final size:17
Alignment explanation
Indices: 32047--32096 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
32037 TTTTTGATGT
*
32047 AATTAAGAAAATTTTGA
1 AATTACGAAAATTTTGA
32064 AATTACGAAAATTTTGA
1 AATTACGAAAATTTTGA
*
32081 AATTACAAAAATTTTG
1 AATTACGAAAATTTTG
32097 CATTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (17 bp):
AATTACGAAAATTTTGA
Done.