Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009476.1 Corchorus capsularis cultivar CVL-1 contig09497, 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: 10039
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:924 original size:2 final size:2
Alignment explanation
Indices: 888--914 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
878 TCCTTTAATT
888 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 T
915 TCCCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3810 original size:170 final size:169
Alignment explanation
Indices: 3524--3857 Score: 578
Period size: 170 Copynumber: 2.0 Consensus size: 169
3514 CATAAACTAT
* *
3524 TAGAGTTAATGTGATAATTAAATTAGAATTAATTTAGTTAGGAATCATGGCTAATTTAGGAGTTG
1 TAGAGTTAATGTGATAATGAAATTAGAATTAATTTAGTTAGGAATCATGGCTAATTTAGAAGTTG
* * *
3589 ACTAAAGTAATTCAAAGGATAGGAAACGTAACTTTTAATGGACAAATGGCTAGCCAATGTTCAAT
66 ACTAAAGTAATTCAAAGGATAAGAAACGTAACTTTTAATGGACAAATGGCTAGCAAATGATCAAT
*
3654 AAGGATTGACTTTAGTTTCGGTCAAAAATAAAAAATTTGC
131 AAGGATTGACTTTAATTTCGGTC-AAAATAAAAAATTTGC
3694 TAGAGTTAATGTGATAATGAAATTAGAATTAATTTAGTTAGGAATCATGGCTAATTTAGAAGTTG
1 TAGAGTTAATGTGATAATGAAATTAGAATTAATTTAGTTAGGAATCATGGCTAATTTAGAAGTTG
* *
3759 ACTAAAGTAATTCAAAGGATAAGAAACGTAACTTTTAATGGAGAGATGGCTAGCAAATGATCAAT
66 ACTAAAGTAATTCAAAGGATAAGAAACGTAACTTTTAATGGACAAATGGCTAGCAAATGATCAAT
*
3824 TAGGATTGACTTTAATTTCGGTCAAAATAAAAAA
131 AAGGATTGACTTTAATTTCGGTCAAAATAAAAAA
3858 AATTGCTTTT
Statistics
Matches: 155, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
169 11 0.07
170 144 0.93
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (169 bp):
TAGAGTTAATGTGATAATGAAATTAGAATTAATTTAGTTAGGAATCATGGCTAATTTAGAAGTTG
ACTAAAGTAATTCAAAGGATAAGAAACGTAACTTTTAATGGACAAATGGCTAGCAAATGATCAAT
AAGGATTGACTTTAATTTCGGTCAAAATAAAAAATTTGC
Found at i:6443 original size:32 final size:33
Alignment explanation
Indices: 6384--6445 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6374 AACTTGTTAA
*
6384 GGCGCGATGAAGGCCCGTGAACTTCATTGTAAC
1 GGCGCGATGAAGGCACGTGAACTTCATTGTAAC
*
6417 GGCGTGATGAAGGCACGT-AACTTCATTGT
1 GGCGCGATGAAGGCACGTGAACTTCATTGT
6446 TTGTAAGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (33 bp):
GGCGCGATGAAGGCACGTGAACTTCATTGTAAC
Found at i:6919 original size:6 final size:6
Alignment explanation
Indices: 6903--6933 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6893 CAAAGCAAAA
6903 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
6934 TAGCAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:8300 original size:18 final size:19
Alignment explanation
Indices: 8277--8315 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8267 TTCTTGAAAT
*
8277 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
8295 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
8314 AA
1 AA
8316 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:8314 original size:11 final size:11
Alignment explanation
Indices: 8298--8327 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
8288 TGTCTTCAAT
*
8298 TCTTCAAATTA
1 TCTTCAAATAA
8309 TCTTCAAATAA
1 TCTTCAAATAA
8320 TCTTCAAA
1 TCTTCAAA
8328 CACGAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:8326 original size:22 final size:22
Alignment explanation
Indices: 8268--8327 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
8258 AATTCTTGCT
* *
8268 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
8290 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
8309 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
8328 CACGAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 3 0.09
21 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Done.