Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000628.1 Corchorus capsularis cultivar CVL-1 contig00628, 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: 39190
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5391 original size:2 final size:2
Alignment explanation
Indices: 5380--5412 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5370 TTTGTTGGGG
5380 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5413 TTTCTGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11851 original size:2 final size:2
Alignment explanation
Indices: 11844--11874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11834 TCCTACCTGC
11844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11875 ATTAATCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15081 original size:42 final size:41
Alignment explanation
Indices: 15009--15099 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
14999 AGTCCATTGC
* * *
15009 CTAA-ATTCTACTTCATCTCTAGGTAATTCATCAAAATAAA
1 CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAA
*
15049 GCTAATATTATACTCCATCTCTAGATAATTCATTAAAATAAA
1 -CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAA
*
15091 CCAATATTA
1 CTAATATTA
15100 ATTGTTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 12 0.27
42 32 0.73
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (41 bp):
CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAA
Found at i:17422 original size:26 final size:21
Alignment explanation
Indices: 17372--17448 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
17362 GTTTCACAGA
17372 CTTTTCTTTTCCTTGCACAAC
1 CTTTTCTTTTCCTTGCACAAC
17393 CTTTTCTTTTCCTTGCACAAC
1 CTTTTCTTTTCCTTGCACAAC
**
17414 CAATTCTTTTCCTTGCACAAC
1 CTTTTCTTTTCCTTGCACAAC
17435 CTTTTCTTTTCCTT
1 CTTTTCTTTTCCTT
17449 TCCTGCCCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.14, C:0.32, G:0.04, T:0.49
Consensus pattern (21 bp):
CTTTTCTTTTCCTTGCACAAC
Found at i:22489 original size:28 final size:29
Alignment explanation
Indices: 22435--22490 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
22425 AAACGTTCGT
*
22435 CATGTTAGTTTATACTCAATTGCGGAGTC
1 CATGTTAGTTTATACTCAATCGCGGAGTC
*
22464 CATG-TAGTTTATACTCAATCGTGGAGT
1 CATGTTAGTTTATACTCAATCGCGGAGT
22491 TATTGCCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (29 bp):
CATGTTAGTTTATACTCAATCGCGGAGTC
Found at i:24235 original size:27 final size:27
Alignment explanation
Indices: 24193--24248 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
24183 TAATATCATA
* * *
24193 TATATATTAAACCTTATTTGAGTGGGC
1 TATATACTAAACCTTATTCGAGTGAGC
*
24220 TATATACTAAATCTTATTCGAGTGAGC
1 TATATACTAAACCTTATTCGAGTGAGC
24247 TA
1 TA
24249 ATGAAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (27 bp):
TATATACTAAACCTTATTCGAGTGAGC
Found at i:24553 original size:29 final size:28
Alignment explanation
Indices: 24510--24577 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
24500 TCATTCTGAC
*
24510 AAAAGAAATTCGTTTATG-ATCCTATTTGA
1 AAAAGAAATTTGTTTATGAAT-CTATTT-A
*
24539 AAAAGAAATTTGTTTATGAATCTCTTTA
1 AAAAGAAATTTGTTTATGAATCTATTTA
24567 AAAA-AAATTTG
1 AAAAGAAATTTG
24578 ATATCGGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 7 0.19
28 5 0.14
29 22 0.61
30 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (28 bp):
AAAAGAAATTTGTTTATGAATCTATTTA
Found at i:27008 original size:2 final size:2
Alignment explanation
Indices: 26987--27039 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
26977 AATATTAATA
* *
26987 AT AT AA AT AT AA AT -T AT AT AT AT CAT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
27028 AT AT -T AT AT AT A
1 AT AT AT AT AT AT A
27040 AAAATTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27028 original size:31 final size:33
Alignment explanation
Indices: 26978--27039 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
26968 TATATTATTA
26978 ATATTAATAATATAAATATAAATTATATATATC
1 ATATTAATAATATAAATATAAATTATATATATC
* *
27011 ATATT-AT-ATATATATATATATTATATATA
1 ATATTAATAATATAAATATAAATTATATATA
27040 AAAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 20 0.74
32 2 0.07
33 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATTAATAATATAAATATAAATTATATATATC
Found at i:32099 original size:2 final size:2
Alignment explanation
Indices: 32092--32148 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
32082 ACGTTATCAG
32092 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
32134 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
32149 TATAGATTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33234 original size:380 final size:380
Alignment explanation
Indices: 32533--33241 Score: 1337
Period size: 380 Copynumber: 1.9 Consensus size: 380
32523 ACGAGTCAAA
32533 GAATGAGTAAGAGGAAGCACACCCTCTTCTCAACGAACCAGAACAATTTTTGGAACACTTAAAAC
1 GAATGAGTAAGAGGAAGCACACCCTCTTCTCAACGAACCAGAACAATTTTTGGAACACTTAAAAC
32598 TAATGCAGAGAAAGAAAAGAGAGAAAGAGCTTTTGTTGCTTTTCGTTGTGTTTAATGCAGAAGGG
66 TAATGCAGAGAAAGAAAAGAGAGAAAGAGCTTTTGTTGCTTTTCGTTGTGTTTAATGCAGAAGGG
* *
32663 AAAGTCTCTATTTATATGCCAATGATAGGGTTAAAATTGGAAAGTAAATTAGAAATATCAGTCCA
131 AAAGTCTCTATTTATAGGCCAATGATAGGGTTAAAATTGGAAAGTAAATTAGAAATATCAGCCCA
32728 AATATCAGATTTAGAGATATTATTGGTGATTTTTATTTACCAAACTTCCCATGATCTGAGTGGTT
196 AATATCAGATTTAGAGATATTATTGGTGATTTTTATTTACCAAACTTCCCATGATCTGAGTGGTT
*
32793 GAGATATTTTCTCAACCACTTGGACTTGACATTTTTTACCAATTTGACTTGGTAAAATGCCACAT
261 GAGATATTTTCTCAACCACTTGAACTTGACATTTTTTACCAATTTGACTTGGTAAAATGCCACAT
32858 GTTTTTCTATTCATGGTTTCATCCTTGAGCACGGAGGCAGACAATCTGTTTTAAG
326 GTTTTTCTATTCATGGTTTCATCCTTGAGCACGGAGGCAGACAATCTGTTTTAAG
*
32913 GAATGAGTAAGAGGAAGCACACCCTCTTTTCAACGAACCAGAACAATTTTTGGAACACTTAAAAC
1 GAATGAGTAAGAGGAAGCACACCCTCTTCTCAACGAACCAGAACAATTTTTGGAACACTTAAAAC
*
32978 TAATGCAGAGAAAGAAAAGAGAGAAGGAGCTTTTGTTGCTTTTCGTTGTGTTTAATGCAGAAGGG
66 TAATGCAGAGAAAGAAAAGAGAGAAAGAGCTTTTGTTGCTTTTCGTTGTGTTTAATGCAGAAGGG
* * *
33043 AAAGTCTCTATTTATAGGCCAATGGTAGGGTTAGAATTGGAAAGTAAATTAGAAATATTAGCCCA
131 AAAGTCTCTATTTATAGGCCAATGATAGGGTTAAAATTGGAAAGTAAATTAGAAATATCAGCCCA
33108 AATATCAGATTTAGAGATATTATTGGTGATTTTTATTTACCAAACTTCCCATGATCTGAGTGGTT
196 AATATCAGATTTAGAGATATTATTGGTGATTTTTATTTACCAAACTTCCCATGATCTGAGTGGTT
*
33173 GAGATATTTTCTCAACCACTTGAACTTGGCATTTTTTACCAATTTGACTTGGTAAAATGCCACAT
261 GAGATATTTTCTCAACCACTTGAACTTGACATTTTTTACCAATTTGACTTGGTAAAATGCCACAT
33238 GTTT
326 GTTT
33242 CCATTCAAAC
Statistics
Matches: 320, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
380 320 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (380 bp):
GAATGAGTAAGAGGAAGCACACCCTCTTCTCAACGAACCAGAACAATTTTTGGAACACTTAAAAC
TAATGCAGAGAAAGAAAAGAGAGAAAGAGCTTTTGTTGCTTTTCGTTGTGTTTAATGCAGAAGGG
AAAGTCTCTATTTATAGGCCAATGATAGGGTTAAAATTGGAAAGTAAATTAGAAATATCAGCCCA
AATATCAGATTTAGAGATATTATTGGTGATTTTTATTTACCAAACTTCCCATGATCTGAGTGGTT
GAGATATTTTCTCAACCACTTGAACTTGACATTTTTTACCAATTTGACTTGGTAAAATGCCACAT
GTTTTTCTATTCATGGTTTCATCCTTGAGCACGGAGGCAGACAATCTGTTTTAAG
Found at i:34931 original size:27 final size:27
Alignment explanation
Indices: 34850--34932 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 27
34840 CAATGCCAAG
* *
34850 GATGTTGGTGCCGAAGTGGAGATTGAA
1 GATGTTGATGCTGAAGTGGAGATTGAA
* *
34877 AATGTTGATGCTAAAGTGGAGATTGAA
1 GATGTTGATGCTGAAGTGGAGATTGAA
* *
34904 GATGTTGCTGCTGAAGTGGAGATCGAA
1 GATGTTGATGCTGAAGTGGAGATTGAA
34931 GA
1 GA
34933 AGAATGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.36, T:0.27
Consensus pattern (27 bp):
GATGTTGATGCTGAAGTGGAGATTGAA
Found at i:35048 original size:13 final size:13
Alignment explanation
Indices: 35030--35054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35020 CGGCAAGTGC
35030 TACCTCAACCTCT
1 TACCTCAACCTCT
35043 TACCTCAACCTC
1 TACCTCAACCTC
35055 AACTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (13 bp):
TACCTCAACCTCT
Found at i:36429 original size:27 final size:28
Alignment explanation
Indices: 36374--36430 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
36364 ATCATTATTA
**
36374 TTTTCTTTTCCTTTTCTTTTTATGTAAC
1 TTTTCTTTTCCTTTTCTTTTTATCCAAC
*
36402 TTTT-TTTTCCTTTTCTTTTTCTCCAAC
1 TTTTCTTTTCCTTTTCTTTTTATCCAAC
36429 TT
1 TT
36431 GTCAAGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (28 bp):
TTTTCTTTTCCTTTTCTTTTTATCCAAC
Done.