Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015067.1 Corchorus capsularis cultivar CVL-1 contig15088, 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: 38266
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:204 original size:49 final size:49
Alignment explanation
Indices: 12--460 Score: 417
Period size: 50 Copynumber: 9.1 Consensus size: 49
2 AGGTCCTTAG
** * ** *
12 TTTCTTTAATTGTTTCCCAAAATGCCGTTTCCCGGTCGGAAGGTCCTTGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-AGT
* *
62 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCACACT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC-CAGT
** * *
112 TTTCTTCATTT-ATTCC-AAAA-GCCCCTTCCCAGTCGGAAGGTCACAGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC-CAGT
* * *
159 TTTCTTCT-CTT-ATTCCAAAAATGCCCCTTCCCGGTCTGAAGGTCACAGT
1 TTTCTT-TGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC-CAGT
* * * * * * **
208 TCTCTCCT-CTT-ATTCAAAAAATGCCCCTTCCCGGTCTGAAGGTCCCTCT
1 TTTCT-TTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCAGT
* ** * *
257 TTTTTTTGTTTGTTTCCAAAAATGCCCCTTCGTGGTTGGAAGGTCCCTGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCAGT
* * * **
307 TCTCTTTATTTGTTTCCCAAAATGCCCCTTCCTAGTCGGAAGGTCCTAGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-AGT
* **
357 TTTCTTTGTTTGTTTCCCAAAATGCCCCTTCCTAGTCGGAAGGTCCTAGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-AGT
* *
407 TTTCTTTGTTTGTTTCCCAAAATACCCCTTCCCGGTCGGAAGGTCCAGT
1 TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAGT
456 TTTCT
1 TTTCT
461 CTTCACATTT
Statistics
Matches: 343, Mismatches: 47, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
47 37 0.11
48 9 0.03
49 85 0.25
50 211 0.62
51 1 0.00
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.38
Consensus pattern (49 bp):
TTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAGT
Found at i:1195 original size:21 final size:21
Alignment explanation
Indices: 1170--1209 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1160 GTTTATTAAT
1170 ATATATAATTAAATATATTAG
1 ATATATAATTAAATATATTAG
*
1191 ATATATAATTATATATATT
1 ATATATAATTAAATATATT
1210 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
ATATATAATTAAATATATTAG
Found at i:3890 original size:25 final size:25
Alignment explanation
Indices: 3857--3906 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3847 GTCATCAAGC
3857 TATATTTGATTACATGAATAAAAAA
1 TATATTTGATTACATGAATAAAAAA
3882 TATATTTGATTACATGAATAAAAAA
1 TATATTTGATTACATGAATAAAAAA
3907 CAAAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (25 bp):
TATATTTGATTACATGAATAAAAAA
Found at i:23729 original size:12 final size:13
Alignment explanation
Indices: 23714--23747 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
23704 AATCTAAATC
23714 TAAAGCAAATT-A
1 TAAAGCAAATTAA
*
23726 TAAAACAAATTAA
1 TAAAGCAAATTAA
23739 TAAAGCAAA
1 TAAAGCAAA
23748 CAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:23735 original size:23 final size:23
Alignment explanation
Indices: 23692--23735 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
23682 AAAATAAAGC
* *
23692 AAAGCAAATCTAAATCTAAATCT
1 AAAGCAAATATAAAACTAAATCT
23715 AAAGCAAATTATAAAAC-AAAT
1 AAAGCAAA-TATAAAACTAAAT
23736 TAATAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAGCAAATATAAAACTAAATCT
Found at i:30092 original size:12 final size:13
Alignment explanation
Indices: 30077--30110 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
30067 AATCTAAATC
30077 TAAAGCAAATT-A
1 TAAAGCAAATTAA
*
30089 TAAAACAAATTAA
1 TAAAGCAAATTAA
30102 TAAAGCAAA
1 TAAAGCAAA
30111 CAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:30098 original size:23 final size:23
Alignment explanation
Indices: 30055--30098 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
30045 AAAATAAAGC
* *
30055 AAAGCAAATCTAAATCTAAATCT
1 AAAGCAAATATAAAACTAAATCT
30078 AAAGCAAATTATAAAAC-AAAT
1 AAAGCAAA-TATAAAACTAAAT
30099 TAATAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAGCAAATATAAAACTAAATCT
Found at i:31039 original size:10 final size:10
Alignment explanation
Indices: 31024--31048 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31014 GAGGACTCTA
31024 GAATTTTCTG
1 GAATTTTCTG
31034 GAATTTTCTG
1 GAATTTTCTG
31044 GAATT
1 GAATT
31049 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:34234 original size:23 final size:23
Alignment explanation
Indices: 34204--34250 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
34194 CAACCGGCCA
*
34204 CAACCGGCCATCACATGGGGCAT
1 CAACCGGCAATCACATGGGGCAT
34227 CAACCGGCAATCACATGGGGCAT
1 CAACCGGCAATCACATGGGGCAT
34250 C
1 C
34251 CGCGCACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.34, G:0.26, T:0.13
Consensus pattern (23 bp):
CAACCGGCAATCACATGGGGCAT
Found at i:35903 original size:12 final size:12
Alignment explanation
Indices: 35886--35916 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35876 TACTAAACCA
35886 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
35898 ATCCTCTTCAAT
1 ATCCTCCTCAAT
35910 ATCCTCC
1 ATCCTCC
35917 AAAACTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:36225 original size:87 final size:87
Alignment explanation
Indices: 36033--36236 Score: 252
Period size: 87 Copynumber: 2.3 Consensus size: 87
36023 TCACAAAATC
* * * * *
36033 CTCCACCAAATCAGTTTCCCAAGATTTTGCATCATTACTAACCATAACTCCATTAGGAAGATCAC
1 CTCCACCTAATCAGTTTCCAAAGATTTTGCACCATAACCAACCATAACTCCATTAGGAAGATCAC
36098 TAAAATTTGAATTCAAACTATT
66 TAAAATTTGAATTCAAACTATT
* * *
36120 CTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTAGGAAGATCA
1 CTCCACC-TAATCAGTTTCCAAAGATTTTGCACCATAACCAACCATAACTCCATTAGGAAGATCA
*
36184 C-AATCAA-TTGAATTCAAATTATT
65 CTAA--AATTTGAATTCAAACTATT
* * *
36207 CTCCACCTTATCAGTTTCCACAGAATTTGC
1 CTCCACCTAATCAGTTTCCAAAGATTTTGC
36237 GCCTAAAGAA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
86 5 0.05
87 89 0.90
88 5 0.05
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (87 bp):
CTCCACCTAATCAGTTTCCAAAGATTTTGCACCATAACCAACCATAACTCCATTAGGAAGATCAC
TAAAATTTGAATTCAAACTATT
Found at i:37194 original size:2 final size:2
Alignment explanation
Indices: 37187--37233 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
37177 CCAATAGCAA
37187 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37229 AG AG A
1 AG AG A
37234 TTGCTACAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.