Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022457.1 Corchorus olitorius cultivar O-4 contig22490, 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: 23103
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4157 original size:23 final size:24
Alignment explanation
Indices: 4116--4164 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
4106 TTATTGTAGC
*
4116 AAGTGGTGGTATTGAAAGGGGGCA
1 AAGTGATGGTATTGAAAGGGGGCA
*
4140 AAGTGATGGTATTGAAGGGGGGCA
1 AAGTGATGGTATTGAAAGGGGGCA
4164 A
1 A
4165 TGTCATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.45, T:0.20
Consensus pattern (24 bp):
AAGTGATGGTATTGAAAGGGGGCA
Found at i:5431 original size:22 final size:23
Alignment explanation
Indices: 5403--5461 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
5393 TTCTTCATAG
*
5403 TACAACTCTCCAATTTA-CGATC
1 TACAACTCTCCAATTTAGAGATC
5425 TACAACTCTCCAA-TTAGAGATC
1 TACAACTCTCCAATTTAGAGATC
*
5447 TACAACTCCCCAATT
1 TACAACTCTCCAATT
5462 CGTTACCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 29 0.88
23 1 0.03
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (23 bp):
TACAACTCTCCAATTTAGAGATC
Found at i:13131 original size:60 final size:60
Alignment explanation
Indices: 13063--13226 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 60
13053 GGCTAATTGC
* * *** *
13063 TCAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGTTCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCAATATTTTAATTTGG
* *
13123 TCAAATAAGGACCTAACGTTATCGAAAATGCTAAAATAAGGGCCCAATATTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCAATATTTTAATTTGG
* * *
13183 TCGAATAAGGGCCTAACATTATCGAAAGTGCTCAAATAAGGGCC
1 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
13227 TGGTCAGTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCAATATTTTAATTTGG
Found at i:13224 original size:31 final size:31
Alignment explanation
Indices: 13060--13227 Score: 112
Period size: 31 Copynumber: 5.5 Consensus size: 31
13050 ATAGGCTAAT
* *
13060 TGCTCAAATAAGGGTCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACATTATCGAAAA
* ** * **
13091 TGCTCAAATAAGGGTCTGTTC-TT-T-TAATT
1 TGCTCAAATAAGGGCCT-AACATTATCGAAAA
* * *
13120 TGGTCAAATAAGGACCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACATTATCGAAAA
* * * * **
13151 TGCTAAAATAAGGGCCCAATATT-T-TAATT
1 TGCTCAAATAAGGGCCTAACATTATCGAAAA
* * *
13180 TGGTCGAATAAGGGCCTAACATTATCGAAAG
1 TGCTCAAATAAGGGCCTAACATTATCGAAAA
13211 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
13228 GGTCAGTTTG
Statistics
Matches: 99, Mismatches: 32, Indels: 12
0.69 0.22 0.08
Matches are distributed among these distances:
28 1 0.01
29 38 0.38
30 4 0.04
31 55 0.56
32 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACATTATCGAAAA
Found at i:13368 original size:31 final size:31
Alignment explanation
Indices: 13330--13434 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
13320 AAAGACCGGG
13330 CCCTTATTTGAGCATTTTGGCAAATGTTAGA
1 CCCTTATTTGAGCATTTTGGCAAATGTTAGA
* ** * *
13361 CCCTTATTTGACCAAATT---AAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAATG-TTAGA
* * * *
13390 CCTTTATTTGAACTTTTTGGCAAATGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAATGTTAGA
13421 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
13435 ATTAGCCTTG
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
28 4 0.07
29 17 0.31
31 29 0.54
32 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTGGCAAATGTTAGA
Found at i:13379 original size:60 final size:60
Alignment explanation
Indices: 13268--13431 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 60
13258 GACGCCAAGG
* * * *
13268 CCTTATTTGAGCATTTTGGCAAACATAATTAGACCCTTATTTGGCCAAATTAAAAGACCGGGC
1 CCTTATTTGAGCATTTTGGC-AA-AT-GTTAGACCCTTATTTGACCAAATTAAAAGACCAGAC
*
13331 CCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGACCAAATTAAAAGATCAGAC
1 CCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGACCAAATTAAAAGACCAGAC
* * * *
13391 CTTTATTTGAACTTTTTGGCAAATGTTAGGCCCTTATTTGA
1 CCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGA
13432 GCAATTAGCC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 68 0.74
61 2 0.02
62 2 0.02
63 20 0.22
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGACCAAATTAAAAGACCAGAC
Found at i:14739 original size:21 final size:21
Alignment explanation
Indices: 14701--14740 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14691 AATCATATTC
*
14701 ATAGTATAAATTAGTTAATAT
1 ATAGTATAAATTAATTAATAT
**
14722 ATAGTATAGTTTAATTAAT
1 ATAGTATAAATTAATTAAT
14741 TGAAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAGTATAAATTAATTAATAT
Found at i:23035 original size:3 final size:3
Alignment explanation
Indices: 23027--23068 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
23017 CCCAGTCAAC
**
23027 TTA TTA TTA TTA TTA ACA TTA TTA TTA TTAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
23069 TTCATTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:23082 original size:2 final size:2
Alignment explanation
Indices: 23075--23103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23065 TATTTTCATT
23075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.