Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012586.1 Corchorus capsularis cultivar CVL-1 contig12607, 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: 14292
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:367 original size:166 final size:165
Alignment explanation
Indices: 72--510 Score: 576
Period size: 166 Copynumber: 2.6 Consensus size: 165
62 ATGAGGAGTG
* * * * *
72 AGAGAACTAATTTTTTTCGTTTTTTCCCACTTGACCGATTACTTAAATGCCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * *
137 TTGAGGTGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAATAGACTAGTGGAAT
66 TTGAGGGGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATGGACTTGAATAGACTAGTGGAAT
* * * * ** *
202 TACTAAAAGATCCCTACCAAGGCTTGCTTTTGAAGTT
130 TAATAAAAGATCCCCACCAAGGATTGATGATG-AGCT
*
239 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTT-AATGTCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * * *
303 TTGAGGGGATTAAAAAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTGGTGGAAT
66 TTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATGGACTTGAATAGACTAGTGGAAT
*
368 TAATAAAAGATCCCCATCAAGGATTGATGATGAGCT
130 TAATAAAAGATCCCCACCAAGGATTGATGATGAGCT
* * * * *
404 AGAAAACTAATCTTTTCCGTCTTTACCTACTTAGCAGATTA-TTAAAATGTCCTAACTTTTGATT
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTT-AAATGTCCTAACTTTTGATT
*
468 CTTAAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
65 CTTGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTCAAT
511 TGACAAATGA
Statistics
Matches: 238, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
164 2 0.01
165 39 0.16
166 156 0.66
167 41 0.17
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (165 bp):
AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
TTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATGGACTTGAATAGACTAGTGGAATT
AATAAAAGATCCCCACCAAGGATTGATGATGAGCT
Found at i:899 original size:27 final size:27
Alignment explanation
Indices: 868--921 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
858 AAACTAATTA
868 TACTTAATGTTTGTAACCATATAGGGG
1 TACTTAATGTTTGTAACCATATAGGGG
*
895 TACTTAATGTTTGTAAGCATATAGGGG
1 TACTTAATGTTTGTAACCATATAGGGG
922 GTGATTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (27 bp):
TACTTAATGTTTGTAACCATATAGGGG
Found at i:3199 original size:18 final size:17
Alignment explanation
Indices: 3176--3234 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
3166 AATTAAATGA
3176 AAATTAAAATAGTGATTG
1 AAATTAAAATA-TGATTG
* *
3194 AAATT-AAAT-TAAATG
1 AAATTAAAATATGATTG
3209 AAAATTAAAATAATGATTG
1 -AAATTAAAAT-ATGATTG
3228 AAATTAA
1 AAATTAA
3235 TTATATATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 8 0.24
18 12 0.36
19 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (17 bp):
AAATTAAAATATGATTG
Found at i:3201 original size:34 final size:34
Alignment explanation
Indices: 3163--3234 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
3153 ATACTCATAT
*
3163 TTAAATTAAATGAAAATTAAAATAGTGATTGAAA
1 TTAAATTAAATGAAAATTAAAATAATGATTGAAA
3197 TTAAATTAAATGAAAATTAAAATAATGATTGAAA
1 TTAAATTAAATGAAAATTAAAATAATGATTGAAA
3231 TTAA
1 TTAA
3235 TTATATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (34 bp):
TTAAATTAAATGAAAATTAAAATAATGATTGAAA
Found at i:3992 original size:25 final size:25
Alignment explanation
Indices: 3943--3993 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3933 TTAGTAGAAT
*
3943 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
3968 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
3994 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:7931 original size:67 final size:66
Alignment explanation
Indices: 7813--7974 Score: 184
Period size: 67 Copynumber: 2.4 Consensus size: 66
7803 GCTCCAACGT
* * *
7813 AGAAATGTTGATAACAACACTGTAAAATTTTGATAAGCTCATCATGAAATTTCGATAA-CTTCCC
1 AGAAATTTTTATAACCACACTGTAAAATTTTGATAAGCTCATCATGAAATTTCGATAATC-TCCC
7877 TA
65 TA
* * * *
7879 AGAAAATTTTTATAACCACACTGTAAAATTTTGATAATCTCAGT-GTGAAATTTTGATTATCTCC
1 AG-AAATTTTTATAACCACACTGTAAAATTTTGATAAGCTCA-TCATGAAATTTCGATAATCTCC
7943 CTA
64 CTA
* * * *
7946 CGAATTTTTTATAATCACACTATAAAATT
1 AGAAATTTTTATAACCACACTGTAAAATT
7975 GGTAACCACA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
66 26 0.32
67 54 0.66
68 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (66 bp):
AGAAATTTTTATAACCACACTGTAAAATTTTGATAAGCTCATCATGAAATTTCGATAATCTCCCT
A
Found at i:8038 original size:22 final size:22
Alignment explanation
Indices: 7814--8057 Score: 102
Period size: 22 Copynumber: 11.1 Consensus size: 22
7804 CTCCAACGTA
* * *
7814 GAAATGTTGATAACAACACTGT
1 GAAATTTTGATAACCACACTAT
* * *
7836 AAAATTTTGATAAGCTCA-TCAT
1 GAAATTTTGATAACCACACT-AT
* ** * *
7858 GAAATTTCGATAACTTCCCTAA
1 GAAATTTTGATAACCACACTAT
* *
7880 GAAAATTTTTATAACCACACTGT
1 G-AAATTTTGATAACCACACTAT
* * * * *
7903 AAAATTTTGATAATCTCAGTGT
1 GAAATTTTGATAACCACACTAT
* * * * *
7925 GAAATTTTGATTATCTCCCTAC
1 GAAATTTTGATAACCACACTAT
* * *
7947 GAATTTTTTATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* *
7969 -AAA-ATTGGTAACCACAC-ATT
1 GAAATTTTGATAACCACACTA-T
**
7989 GAAAATTTTGATAACC-TTCTCAT
1 G-AAATTTTGATAACCACACT-AT
*
8012 AAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
8034 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
8056 GA
1 GA
8058 GAATGAAACT
Statistics
Matches: 160, Mismatches: 52, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
19 1 0.01
20 11 0.07
21 3 0.02
22 118 0.74
23 26 0.16
24 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:8097 original size:22 final size:22
Alignment explanation
Indices: 8060--8295 Score: 131
Period size: 22 Copynumber: 10.5 Consensus size: 22
8050 CCCTATGAGA
* * *
8060 ATGAAACTGTGATATCCTCTCT
1 ATGAAATTTTGATAACCTCTCT
* * *
8082 ATGTAATTTTGATATCCTCTCC
1 ATGAAATTTTGATAACCTCTCT
* * *
8104 ATAAAATTTTCATAACCTCCCT
1 ATGAAATTTTGATAACCTCTCT
*
8126 AGGAAATTTTGATAACCTCCTTTCCT
1 ATGAAATTTTGATAACCT-C--T-CT
* *
8152 ATGAATTAATTTTGTTAACAT-TCTT
1 ATG-A--AATTTTGATAACCTCTC-T
*
8177 ATGAAATTTTGATAA-C-CAC-
1 ATGAAATTTTGATAACCTCTCT
**
8196 AAAAAATTTTTGATAACCT-TCGT
1 ATGAAA-TTTTGATAACCTCTC-T
* * *
8219 ATGAAATTTGGTTAACCTCCCT
1 ATGAAATTTTGATAACCTCTCT
* * * *
8241 AAGAAATTTTGACAACCTTTTT
1 ATGAAATTTTGATAACCTCTCT
* *
8263 ATGAAATTTTGGTAACCTCTTT
1 ATGAAATTTTGATAACCTCTCT
8285 ATGAAATTTTG
1 ATGAAATTTTG
8296 GAAACAACAC
Statistics
Matches: 160, Mismatches: 39, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
19 4 0.03
20 9 0.06
21 3 0.02
22 114 0.71
23 6 0.04
24 2 0.01
25 5 0.03
26 4 0.03
27 1 0.01
29 12 0.08
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCTCT
Done.