Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010428.1 Corchorus capsularis cultivar CVL-1 contig10449, 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: 35377
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1344 original size:29 final size:30
Alignment explanation
Indices: 1312--1378 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
1302 CCTTTTTAGT
*
1312 TTTTGCCTCATGAACT-TTAATTTTGGACA
1 TTTTGCCTCATAAACTCTTAATTTTGGACA
* *
1341 TTTTGCCCCATAAACTCTTAATTTTGGACG
1 TTTTGCCTCATAAACTCTTAATTTTGGACA
1371 TTTTGCCT
1 TTTTGCCT
1379 TTTCTCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (30 bp):
TTTTGCCTCATAAACTCTTAATTTTGGACA
Found at i:1560 original size:29 final size:28
Alignment explanation
Indices: 1527--1602 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
1517 TGTTTGAGAG
* * *
1527 GGGGCAAAACATCCAATATTGAGAGTTCA
1 GGGGCAAAACGTCCAAAATT-AAAGTTCA
*
1556 GGGGCAAAACGTCCAAAATTAAAGTTTA
1 GGGGCAAAACGTCCAAAATTAAAGTTCA
1584 GGAGGCAAAACGTCCAAAA
1 GG-GGCAAAACGTCCAAAA
1603 GCTACAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (28 bp):
GGGGCAAAACGTCCAAAATTAAAGTTCA
Found at i:3444 original size:157 final size:157
Alignment explanation
Indices: 3158--3469 Score: 570
Period size: 157 Copynumber: 2.0 Consensus size: 157
3148 AAAAAAAAAC
*
3158 CACTACTGCCAAATAAGAATTGATTTGCTCCAATGTTATTGTCAATATTCAAATAATTTGTATCA
1 CACTACTGCCAAATAAGAATTGATTTGCTCCAATGTTATTGTCAATATTCAAATAATTTGTAGCA
* *
3223 CAACCTTTATCACCAATCAACATTTTAATTAACAACTTTGCCACTGCAACAGAGATTTATTGTGG
66 CAACCTTTATCACAAATCAACATTTTAATTAACAACTTTGCCACTACAACAGAGATTTATTGTGG
3288 GCATGCTCATGTCACAAAAGCTGAAAT
131 GCATGCTCATGTCACAAAAGCTGAAAT
*
3315 CACTACTGCCAAATAAGAATTGATTTGCTCCAATGTTATTGTCAATCTTCAAATAATTTGTAGCA
1 CACTACTGCCAAATAAGAATTGATTTGCTCCAATGTTATTGTCAATATTCAAATAATTTGTAGCA
3380 CAACCTTTATCACAAATCAACATTTTAATTAACAACTTTGCCACTACAACAGAGATTTATTGTGG
66 CAACCTTTATCACAAATCAACATTTTAATTAACAACTTTGCCACTACAACAGAGATTTATTGTGG
* *
3445 GTATGCTCATGTCACAAAAGTTGAA
131 GCATGCTCATGTCACAAAAGCTGAA
3470 CTGTTTGCGG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (157 bp):
CACTACTGCCAAATAAGAATTGATTTGCTCCAATGTTATTGTCAATATTCAAATAATTTGTAGCA
CAACCTTTATCACAAATCAACATTTTAATTAACAACTTTGCCACTACAACAGAGATTTATTGTGG
GCATGCTCATGTCACAAAAGCTGAAAT
Found at i:6754 original size:21 final size:21
Alignment explanation
Indices: 6729--6772 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6719 TAAAACTGGA
6729 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
6750 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
6771 TT
1 TT
6773 TACGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:7108 original size:32 final size:33
Alignment explanation
Indices: 7067--7147 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
7057 AAAATGGTCT
*
7067 AGCCGCCCCA-TGAGGGCGGCCTG-CCGTGGCGA
1 AGCCGCCCCAGTG-GGGCGGCCTGCCCATGGCGA
*
7099 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGCGA
*
7132 AGCTGCCCCAGTGGGG
1 AGCCGCCCCAGTGGGG
7148 AGGCTCCGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 20 0.45
33 24 0.55
ACGTcount: A:0.12, C:0.36, G:0.41, T:0.11
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCATGGCGA
Found at i:26128 original size:72 final size:72
Alignment explanation
Indices: 26011--26153 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
26001 GTCATTGGTT
*
26011 TTTCGCTCAATTATGGGTCACTTTTTGTCCCAGGCATACAAATTGAAAGGCAAATGACAAAATTA
1 TTTCGCTCAATTATGGGTCACTTTTTGTCCCAAGCATACAAATTGAAAGGCAAATGACAAAATTA
26076 GAAGTTC
66 GAAGTTC
* *
26083 TTTCGTTCAATTATGGGTCACTTTTTGTCCCAAGCATATAAATTGAAAGGCAAATGACAAAATTA
1 TTTCGCTCAATTATGGGTCACTTTTTGTCCCAAGCATACAAATTGAAAGGCAAATGACAAAATTA
26148 GAAGTT
66 GAAGTT
26154 GAGGGGCTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (72 bp):
TTTCGCTCAATTATGGGTCACTTTTTGTCCCAAGCATACAAATTGAAAGGCAAATGACAAAATTA
GAAGTTC
Found at i:30166 original size:12 final size:13
Alignment explanation
Indices: 30143--30171 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30133 TCTTTTCCCA
30143 TTTTGTCATAGAT
1 TTTTGTCATAGAT
30156 TTTTGTC-TAGAT
1 TTTTGTCATAGAT
30168 TTTT
1 TTTT
30172 AGATGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (13 bp):
TTTTGTCATAGAT
Done.