Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007940.1 Corchorus capsularis cultivar CVL-1 contig07961, 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: 41163
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:361 original size:24 final size:24
Alignment explanation
Indices: 334--390 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
324 TCAAGTAGAG
* **
334 GATTCCAACCTCAGTCAAATCCAA
1 GATTGCAACCTCTATCAAATCCAA
358 GATTGCAACCTCTATCAAATCCAA
1 GATTGCAACCTCTATCAAATCCAA
382 GATTGCAAC
1 GATTGCAAC
391 GACAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.23
Consensus pattern (24 bp):
GATTGCAACCTCTATCAAATCCAA
Found at i:1518 original size:12 final size:12
Alignment explanation
Indices: 1501--1527 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1491 AAATGTTTAC
1501 ATATTTTGTCTT
1 ATATTTTGTCTT
1513 ATATTTTGTCTT
1 ATATTTTGTCTT
1525 ATA
1 ATA
1528 CTGAATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (12 bp):
ATATTTTGTCTT
Found at i:2166 original size:29 final size:30
Alignment explanation
Indices: 2092--2174 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
2082 GTTGAAATCT
* *
2092 CAATTTGGTACCAAACCTTTATGTTTAATAG
1 CAATTTGGTACCAAACCTTT-TATTTAATAC
* **
2123 TAATTTGGTACCAAACCTTTTATTTCGT-C
1 CAATTTGGTACCAAACCTTTTATTTAATAC
*
2152 CAATTTGGTACCAAACGTTTTAT
1 CAATTTGGTACCAAACCTTTTAT
2175 AAATAGTCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.47
30 5 0.11
31 19 0.42
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (30 bp):
CAATTTGGTACCAAACCTTTTATTTAATAC
Found at i:2187 original size:31 final size:30
Alignment explanation
Indices: 2092--2188 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 30
2082 GTTGAAATCT
*
2092 CAATTTGGTACCAAACCTTTATGTTTAATAGT-
1 CAATTTGGTACCAAACC-TT-T-TATAATAGTC
* *
2124 -AATTTGGTACCAAACCTTTTAT-TTCGTC
1 CAATTTGGTACCAAACCTTTTATAATAGTC
*
2152 CAATTTGGTACCAAACGTTTTATAAATAGTC
1 CAATTTGGTACCAAACCTTTTAT-AATAGTC
2183 CAATTT
1 CAATTT
2189 AATACTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
27 3 0.05
28 2 0.04
29 22 0.40
30 2 0.04
31 26 0.47
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (30 bp):
CAATTTGGTACCAAACCTTTTATAATAGTC
Found at i:4088 original size:5 final size:6
Alignment explanation
Indices: 4073--4149 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
4063 GAAAGATGAG
** *
4073 AAAAAT AAAAAT AAAAAT --ATTT AAAAAT AAAAATAT AAAAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAA-AT AAAAAT AAAAAT
* * *
4121 AAATATT AAAAAT ACAAA- AATAAT AAAAA
1 AAA-AAT AAAAAT AAAAAT AAAAAT AAAAA
4150 AAAGCCACAT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
4 2 0.04
5 3 0.06
6 33 0.62
7 13 0.25
8 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:4099 original size:16 final size:16
Alignment explanation
Indices: 4078--4139 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
4068 ATGAGAAAAA
4078 TAAAAATAAAAATATT
1 TAAAAATAAAAATATT
*
4094 TAAAAATAAAAATATA
1 TAAAAATAAAAATATT
*
4110 AAAATAATAATAAATA-T
1 TAAA-AATAA-AAATATT
4127 TAAAAATACAAAA
1 TAAAAATA-AAAA
4140 ATAATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 25 0.64
17 9 0.23
18 5 0.13
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAAATATT
Found at i:4116 original size:36 final size:33
Alignment explanation
Indices: 4073--4152 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
4063 GAAAGATGAG
4073 AAAAATAAAAATAAAAAT--AT-TTAAAAATA-
1 AAAAATAAAAATAAAAATAAATATTAAAAATAC
*
4102 AAAATATAAAAATAATAATAAATATTAAAAATAC
1 AAAA-ATAAAAATAAAAATAAATATTAAAAATAC
4136 AAAAATAATAAA-AAAAA
1 AAAAATAA-AAATAAAAA
4153 GCCACATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 4 0.09
30 13 0.30
32 2 0.05
33 17 0.40
34 7 0.16
ACGTcount: A:0.76, C:0.01, G:0.00, T:0.23
Consensus pattern (33 bp):
AAAAATAAAAATAAAAATAAATATTAAAAATAC
Found at i:4118 original size:27 final size:27
Alignment explanation
Indices: 4073--4146 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
4063 GAAAGATGAG
* *
4073 AAAAATAAAAATAAAAATATTTAAA-AAT
1 AAAAATAAAAA-AATAATA-ATAAATAAT
* *
4101 AAAAATATAAAAATAATAATAAATATT
1 AAAAATAAAAAAATAATAATAAATAAT
*
4128 AAAAATACAAAAATAATAA
1 AAAAATAAAAAAATAATAA
4147 AAAAAAGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 4 0.10
27 26 0.65
28 10 0.25
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAAATAAAAAAATAATAATAAATAAT
Found at i:6808 original size:3 final size:3
Alignment explanation
Indices: 6800--6829 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6790 ATATATATAT
6800 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6830 TAGATAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8067 original size:134 final size:134
Alignment explanation
Indices: 7825--8085 Score: 323
Period size: 134 Copynumber: 1.9 Consensus size: 134
7815 TCCGCCGCCT
* * * * ** * *
7825 CCGCCTGAACCCTAGCCATCGTGCCGGAATCCTCCAACAATCATCAAGGTGCTTCGTTTTCTCTT
1 CCGCCTGAACCCTAGCCACCGTACCGGAATCCTCCAACAACCACCAAGGTGCTTCGTTCCCCCTC
**
7890 CTAAGCTCTTTTAGTCTTGAAATTTCTTGATTCAACCTTCAAAT-CTCTGGAATCCGAGTTACAA
66 CTAAGCTCTTTTAGTCTTGAAATTTCTTGATTCAACCACCAAATCCT-TGGAATCCGAGTTACAA
7954 GAAAC
130 GAAAC
* * *
7959 CCGCCTGAACCCTAGCCACCGTACCGGAGTCCTCCGAA-AGCCACCAAGGT-TTTCGTTCCCCCT
1 CCGCCTGAACCCTAGCCACCGTACCGGAATCCTCC-AACAACCACCAAGGTGCTTCGTTCCCCCT
* *
8022 CCTAAGCTCTTATTTAGTCTTG-ATTTTCTTGATTCAACCACCAAATCCTTGGAATCTGAGTTAC
65 CCTAAGCTC-T-TTTAGTCTTGAAATTTCTTGATTCAACCACCAAATCCTTGGAATCCGAGTTAC
8086 CAGACACCAA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
133 17 0.16
134 77 0.71
135 14 0.13
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (134 bp):
CCGCCTGAACCCTAGCCACCGTACCGGAATCCTCCAACAACCACCAAGGTGCTTCGTTCCCCCTC
CTAAGCTCTTTTAGTCTTGAAATTTCTTGATTCAACCACCAAATCCTTGGAATCCGAGTTACAAG
AAAC
Found at i:18295 original size:306 final size:307
Alignment explanation
Indices: 17741--18351 Score: 1152
Period size: 306 Copynumber: 2.0 Consensus size: 307
17731 GGTCGGGTTA
* *
17741 GATTTGGGTTAAAGAAATTTTGGCTTATATGGGTTCGGTTAATTTTCAGTTTTAAGTTGGGTTGG
1 GATTTGGGTTAAAGAAATTTTGCCTTATATGGGTTCGGTTAATTTTCAGTTTCAAGTTGGGTTGG
17806 GTTCGGATCGATTGCTCAAATGTCGAGTCATTTGGGTTTTGGTCAATTTTAGTTCGGGTCTTTTT
66 GTTCGGATCGATTGCTCAAATGTCGAGTCATTTGGGTTTTGGTCAATTTTAGTTCGGGTCTTTTT
*
17871 TCGGTTTCGTGTCATATGGTTCTGATAATTTCGGGTTTGAGCCTTCGATTTTCAAGTTCAGGTCT
131 TCGGTTTCGGGTCATATGGTTCTGATAATTTCGGGTTTGAGCCTTCGATTTTCAAGTTCAGGTCT
17936 TTTCAAATTCGGGTCATTTAAATATAATTAATCTCGATTCAGGTAATTTCGGATTAATCTCTCGG
196 TTTCAAATTCGGGTCATTTAAATATAATTAATCTCGATTCAGGTAATTTCGGATTAATCTCTCGG
18001 GTTGATCGGGTTCGGGTCATAAGGATTTGGGTTAGGTCATTTCGGCG
261 GTTGATCGGGTTCGGGTCATAAGGATTTGGGTTAGGTCATTTCGGCG
*
18048 GATTTGGGTTAAGGAAATTTTGCCTTATATGGGTTCGGTTAATTTTCAGTTTCAAGTTGGGTTGG
1 GATTTGGGTTAAAGAAATTTTGCCTTATATGGGTTCGGTTAATTTTCAGTTTCAAGTTGGGTTGG
18113 GTTCGGATCGATTGCTCAAATGTCGAGTCATTT-GGTTTTGGTCAATTTTAGTTCGGGTCTTTTT
66 GTTCGGATCGATTGCTCAAATGTCGAGTCATTTGGGTTTTGGTCAATTTTAGTTCGGGTCTTTTT
* *
18177 TCGGTTTCGGGTCATATGGTTCTGATAATTTCGGGTTTGAGCCTTCGATTTTTAGGTTCAGGTCT
131 TCGGTTTCGGGTCATATGGTTCTGATAATTTCGGGTTTGAGCCTTCGATTTTCAAGTTCAGGTCT
18242 TTTCAAATTCGGGTCATTTAAATATAATTAATCTCGATTCAGGTAATTTCGGATTAATCTCTCGG
196 TTTCAAATTCGGGTCATTTAAATATAATTAATCTCGATTCAGGTAATTTCGGATTAATCTCTCGG
*
18307 GTTGATCGGGTTCGGGTTATAAGGATTTGGGTTAGGTCATTTCGG
261 GTTGATCGGGTTCGGGTCATAAGGATTTGGGTTAGGTCATTTCGG
18352 TTTCGGATTG
Statistics
Matches: 297, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
306 202 0.68
307 95 0.32
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (307 bp):
GATTTGGGTTAAAGAAATTTTGCCTTATATGGGTTCGGTTAATTTTCAGTTTCAAGTTGGGTTGG
GTTCGGATCGATTGCTCAAATGTCGAGTCATTTGGGTTTTGGTCAATTTTAGTTCGGGTCTTTTT
TCGGTTTCGGGTCATATGGTTCTGATAATTTCGGGTTTGAGCCTTCGATTTTCAAGTTCAGGTCT
TTTCAAATTCGGGTCATTTAAATATAATTAATCTCGATTCAGGTAATTTCGGATTAATCTCTCGG
GTTGATCGGGTTCGGGTCATAAGGATTTGGGTTAGGTCATTTCGGCG
Found at i:19214 original size:2 final size:2
Alignment explanation
Indices: 19170--19238 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
19160 TATCTAGTAA
* * * *
19170 AT AT AA AT AT AT A- AT A- AT AT ACT AT GT AT AT TT A- AG A- AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
19209 AT 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
19239 CTAAATCAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
1 4 0.07
2 50 0.89
3 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22401 original size:156 final size:156
Alignment explanation
Indices: 22177--22488 Score: 597
Period size: 156 Copynumber: 2.0 Consensus size: 156
22167 TGATAAAATG
* *
22177 GTGAACAGCTAACAATTATAGTTAGGGAAAGCCAAATGCAACCAATTTCGAACGTTTATAATCAA
1 GTGAACAGCTAACAATTATAGTCAGGGAAAGCCAAATGCAACCAATTTCAAACGTTTATAATCAA
*
22242 GGTAATGAAATATATAAAGCCTTTTCCAGATAAGGATAATAACAAATTCTTACACTTCTTTCCAA
66 GGTAATGAAATATATAAAGCCTTTTCCAGATAAGGATAATAACAAATCCTTACACTTCTTTCCAA
22307 GGCCTTGGCGAACTAATAGTTTATTT
131 GGCCTTGGCGAACTAATAGTTTATTT
22333 GTGAACAGCTAACAATTATAGTCAGGGAAAGCCAAATGCAACCAATTTCAAACGTTTATAATCAA
1 GTGAACAGCTAACAATTATAGTCAGGGAAAGCCAAATGCAACCAATTTCAAACGTTTATAATCAA
22398 GGTAATGAAATATATAAAGCCTTTTCCAGATAAGGATAATAACAAATCCTTACACTTCTTTCCAA
66 GGTAATGAAATATATAAAGCCTTTTCCAGATAAGGATAATAACAAATCCTTACACTTCTTTCCAA
22463 GGCCTTGGCGAACTAATAGTTTATTT
131 GGCCTTGGCGAACTAATAGTTTATTT
22489 CTTATGCAAT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (156 bp):
GTGAACAGCTAACAATTATAGTCAGGGAAAGCCAAATGCAACCAATTTCAAACGTTTATAATCAA
GGTAATGAAATATATAAAGCCTTTTCCAGATAAGGATAATAACAAATCCTTACACTTCTTTCCAA
GGCCTTGGCGAACTAATAGTTTATTT
Found at i:33642 original size:10 final size:10
Alignment explanation
Indices: 33629--33664 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
33619 AAATCTCGAT
33629 ATATCCGTAA
1 ATATCCGTAA
33639 ATATCCGTAA
1 ATATCCGTAA
* *
33649 AGATCCATAA
1 ATATCCGTAA
33659 ATATCC
1 ATATCC
33665 ACATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (10 bp):
ATATCCGTAA
Done.