Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006896.1 Corchorus olitorius cultivar O-4 contig06921, 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, 753
Length: 1256
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Found at i:206 original size:22 final size:22
Alignment explanation
Indices: 137--537 Score: 123
Period size: 22 Copynumber: 18.6 Consensus size: 22
127 TAACATTCTT
*
137 ATGAAATTTTGTTAACCTCCCTA
1 ATGAAATTTTGATAACCTCCC-A
* * *
160 A-GGAATTTTGA-AGACCTCACT
1 ATGAAATTTTGATA-ACCTCCCA
*
181 ATGAAATTTTGATAACTTCCCA
1 ATGAAATTTTGATAACCTCCCA
**
203 ATGAAATTTTGATAACC-AACA
1 ATGAAATTTTGATAACCTCCCA
* * *
224 ATGAGATGTTGATAACCTCCAA
1 ATGAAATTTTGATAACCTCCCA
* * * * ***
246 ATCATATATTGATAACCACGTT
1 ATGAAATTTTGATAACCTCCCA
* * *
268 ATGAAAATTTAAAAACCT-CCA
1 ATGAAATTTTGATAACCTCCCA
* * * *
289 TATG-AATTGTT-AGTAATCACACT
1 -ATGAAATT-TTGA-TAACCTCCCA
* * * * *
312 CTGAAATTTTGATAATCACACT
1 ATGAAATTTTGATAACCTCCCA
* * ***
334 ATGAAATTGTAATAACCTCGTT
1 ATGAAATTTTGATAACCTCCCA
* *
356 ATGAAATTTTGATAAACCTTCCT
1 ATGAAATTTTGAT-AACCTCCCA
* *
379 ATAAAATTTTGATAAACCTCCCT
1 ATGAAATTTTGAT-AACCTCCCA
*
402 ATAAAATTTTGATAACCT--C-
1 ATGAAATTTTGATAACCTCCCA
* *
421 ATGAAATCTTGATAA-CT-ACA
1 ATGAAATTTTGATAACCTCCCA
** ***
441 A--ATTTTTTGATAACCTCATT
1 ATGAAATTTTGATAACCTCCCA
* * *
461 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAACCTCCCA
* ** *
483 ATGAAATTTTGA-AAACTAAACT
1 ATGAAATTTTGATAACCT-CCCA
*
505 ATGAAATTTTGATATCCTCCC-
1 ATGAAATTTTGATAACCTCCCA
*
526 -TCAAATTTTGAT
1 ATGAAATTTTGAT
538 TACTTCATAA
Statistics
Matches: 283, Mismatches: 76, Indels: 41
0.71 0.19 0.10
Matches are distributed among these distances:
18 11 0.04
19 16 0.06
20 15 0.05
21 27 0.10
22 163 0.58
23 51 0.18
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCA
Found at i:227 original size:21 final size:20
Alignment explanation
Indices: 181--240 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
171 AGACCTCACT
*
181 ATGAAATTTTGATAACTTCCCA
1 ATGAAATTTTGATAAC--CACA
203 ATGAAATTTTGATAACCAACA
1 ATGAAATTTTGATAACC-ACA
* *
224 ATGAGATGTTGATAACC
1 ATGAAATTTTGATAACC
241 TCCAAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 17 0.50
22 16 0.47
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGAAATTTTGATAACCACA
Found at i:385 original size:23 final size:23
Alignment explanation
Indices: 359--420 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
349 CCTCGTTATG
*
359 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
382 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
405 AAATTTTGAT-AACCTC
1 AAATTTTGATAAACCTC
421 ATGAAATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 6 0.16
23 32 0.84
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:691 original size:21 final size:22
Alignment explanation
Indices: 664--722 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
654 TAACCTCTTT
664 ATGAAATTTTGATAATCCCTCG
1 ATGAAATTTTGATAATCCCTCG
* * * *
686 AT-AAATTTTGTTGACCCCTCT
1 ATGAAATTTTGATAATCCCTCG
*
707 ATGAAATTCTGATAAT
1 ATGAAATTTTGATAAT
723 AAGATTATGT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAATCCCTCG
Found at i:758 original size:22 final size:21
Alignment explanation
Indices: 733--786 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
723 AAGATTATGT
*
733 AATTTTGATAACCT-CGCTTTGA
1 AATTTTGATAACCTAC-CTAT-A
*
755 AATTTTGATAATCTACCTATA
1 AATTTTGATAACCTACCTATA
776 AATTTTGATAA
1 AATTTTGATAA
787 TCCGATCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 16 0.55
23 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
AATTTTGATAACCTACCTATA
Found at i:946 original size:22 final size:22
Alignment explanation
Indices: 886--948 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
876 ATAACCTTCA
886 TATGAAATTTTAATAACCACAC
1 TATGAAATTTTAATAACCACAC
**
908 TAAAAAATTTTTAATAACCACAC
1 TATGAAA-TTTTAATAACCACAC
* *
931 TATGGAATTTTGATAACC
1 TATGAAATTTTAATAACC
949 TCCCCATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.33
Consensus pattern (22 bp):
TATGAAATTTTAATAACCACAC
Found at i:1090 original size:22 final size:22
Alignment explanation
Indices: 1065--1130 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
1055 TATAATTGTG
*
1065 ATAACC-ACACTATGAAATTTCA
1 ATAACCTAC-CTAAGAAATTTCA
* *
1087 ATAACCTTCCTAAGAAATTTTA
1 ATAACCTACCTAAGAAATTTCA
*
1109 ATAACCTGATCCTATGAAATTT
1 ATAACCT-A-CCTAAGAAATTT
1131 AGGTAAGCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 24 0.67
23 1 0.03
24 11 0.31
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAACCTACCTAAGAAATTTCA
Found at i:1127 original size:24 final size:22
Alignment explanation
Indices: 1074--1130 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
1064 GATAACCACA
1074 CTATGAAATTTCAATAACCTTC
1 CTATGAAATTTCAATAACCTTC
* *
1096 CTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTCAATAACCT--TC
1120 CTATGAAATTT
1 CTATGAAATTT
1131 AGGTAAGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTCAATAACCTTC
Found at i:1158 original size:65 final size:66
Alignment explanation
Indices: 1066--1245 Score: 181
Period size: 65 Copynumber: 2.7 Consensus size: 66
1056 ATAATTGTGA
** *
1066 TAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCC-TATGAAATT
1 TAACCACACTA-G-AATTTTGATAACCTTCCTATGAAATTTTAATAACC-GATCCATATGAAATT
1130 TAGG
63 TAGG
* * * * * *
1134 TAAGCACACTA-ATTTTTGATAACCTTCCCATGAAATTTTGATAA--GTTCCATATGAAATTTTG
1 TAACCACACTAGAATTTTGATAACCTTCCTATGAAATTTTAATAACCGATCCATATGAAATTTAG
1196 G
66 G
*
1197 TAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACC
1 TAACCACACTA--GAATTTTGATAACCTTCCT-ATGAAATTTTAATAACC
1246 ATCTTATGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
62 4 0.04
63 22 0.24
65 30 0.33
66 25 0.27
68 10 0.11
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (66 bp):
TAACCACACTAGAATTTTGATAACCTTCCTATGAAATTTTAATAACCGATCCATATGAAATTTAG
G
Found at i:1174 original size:22 final size:22
Alignment explanation
Indices: 1147--1245 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
1137 GCACACTAAT
1147 TTTTGATAACCTTCC-CATGAAA
1 TTTTGATAACC-TCCACATGAAA
** *
1169 TTTTGATAAGTTCCATATGAAA
1 TTTTGATAACCTCCACATGAAA
* * *
1191 TTTTGGTAACC-ACACTATGGAA
1 TTTTGATAACCTCCAC-ATGAAA
*
1213 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCCACATGAAA
* *
1235 TTATAATAACC
1 TTTTGATAACC
1246 ATCTTATGAA
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
21 5 0.08
22 52 0.88
23 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTCCACATGAAA
Done.