Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012308.1 Corchorus capsularis cultivar CVL-1 contig12329, 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: 14299
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Found at i:8503 original size:4 final size:4
Alignment explanation
Indices: 8496--8546 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
8486 TGTTTGCATA
*
8496 TATT TATT TATT TATT TATT TATT TATT TATT CATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
8544 TAT
1 TAT
8547 ACTTTATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:13125 original size:63 final size:63
Alignment explanation
Indices: 13035--13295 Score: 168
Period size: 63 Copynumber: 4.2 Consensus size: 63
13025 CTGTTTTAGT
* * *
13035 TCTCTAGTTGAGAGTCTTTTGTATCAA-TCTA-AATC-CAGTTTC-ATTTCCAAATCCTAATTGA
1 TCTCTAGTCGAGAGTCTCTAGTATCAATTC-AGAATCTC-GTTTCTA-TT-CAAATCCTAATTGA
13096 GG
62 GG
* * * **
13098 TCTCTAGTCGAGGGTCTCTAGTGTCAATTCAGAGTCTCGTTTCTATTCAAATCCTGCTTGAGG
1 TCTCTAGTCGAGAGTCTCTAGTATCAATTCAGAATCTCGTTTCTATTCAAATCCTAATTGAGG
* * * * **
13161 TCTCTAGTCGAGAGTTTCTTGT-T---TTAAG-ATCAT-GTTTGT-TTCAAATCCTGTTTGAGG
1 TCTCTAGTCGAGAGTCTCTAGTATCAATTCAGAATC-TCGTTTCTATTCAAATCCTAATTGAGG
* * * * * ** * **
13218 TTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGT-TTCAAACCCTGGTTGAGG
1 TCTCTAGTCGAGAGTCTCTAGTATCAA-TTCAGAATCTCGTTTCTATTCAAATCCTAATTGAGG
13281 TCTCTAGTCGAGAGT
1 TCTCTAGTCGAGAGT
13296 TTCTTGTTTC
Statistics
Matches: 164, Mismatches: 22, Indels: 24
0.78 0.10 0.11
Matches are distributed among these distances:
57 38 0.23
58 8 0.05
59 5 0.03
62 5 0.03
63 94 0.57
64 12 0.07
65 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (63 bp):
TCTCTAGTCGAGAGTCTCTAGTATCAATTCAGAATCTCGTTTCTATTCAAATCCTAATTGAGG
Found at i:13267 original size:120 final size:120
Alignment explanation
Indices: 13082--13304 Score: 313
Period size: 120 Copynumber: 1.9 Consensus size: 120
13072 GTTTCATTTC
* * * *
13082 CAAATCCTAATTGAGGTCTCTAGTCGAGGGTCTCTAGTGTCAATTCAGAGTCTCGTTTCTATTCA
1 CAAATCCTAATTGAGGTCTCTAGTCGAGAGTCTCTAGTGTCAATTCAAAATCTCGTTGCTATTCA
*
13147 AATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGATCATGTTTGTTT
66 AACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGATCATGTTTGTTT
** * * * * *
13202 CAAATCCTGTTTGAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGT-TTC
1 CAAATCCTAATTGAGGTCTCTAGTCGAGAGTCTCTAGTGTCAA-TTCAAAATCTCGTTGCTATTC
*
13266 AAACCCTGGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTT
65 AAACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTT
13305 CGATTCCAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
120 76 0.85
121 13 0.15
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (120 bp):
CAAATCCTAATTGAGGTCTCTAGTCGAGAGTCTCTAGTGTCAATTCAAAATCTCGTTGCTATTCA
AACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGATCATGTTTGTTT
Found at i:13297 original size:63 final size:63
Alignment explanation
Indices: 13082--13359 Score: 241
Period size: 63 Copynumber: 4.5 Consensus size: 63
13072 GTTTCATTTC
** * * * * * ** **
13082 CAAATCCTAATTGAGGTCTCTAGTCGAGGGTCTCTAGTGTCAATT-CAGAGTCTCGTTTCTATT
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAACCTCGTTAGT-TT
* * *
13145 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-TT---TT--AAGATCAT-GTTTGTTT
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAA-AACCTCGTTAGTTT
* * * * *
13202 CAAATCCTGTTTGAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGTTT
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAACCTCGTTAGTTT
* * * * *
13265 CAAACCCTGGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCGATTCCAAAGCCTTGTTAGTTT
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAACCTCGTTAGTTT
* *
13328 CTAATCCTGCTTGAGGTCTCTGGTCGAG-GTTT
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT
13360 GTCAATTCCA
Statistics
Matches: 177, Mismatches: 30, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
57 37 0.21
58 8 0.05
59 4 0.02
61 2 0.01
62 7 0.04
63 119 0.67
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (63 bp):
CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAACCTCGTTAGTTT
Found at i:13365 original size:120 final size:118
Alignment explanation
Indices: 13082--13371 Score: 268
Period size: 120 Copynumber: 2.4 Consensus size: 118
13072 GTTTCATTTC
** * * * * **
13082 CAAATCCTAATTGAGGTCTCTAGTCGAGGGTCTCTAGTGTCAATT-CAGAGTCTCGTTTCTATTC
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGT-TCTTGT-TCAATTCCAAAATCTCGTTGGT-TTC
* * *
13146 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGATCATGTTTGTTT
63 AAACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGACCATGTTAGTTT
* * *
13202 CAAATCCTGTTTGAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGTTTCA
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TTCTTG-TTCAATTCCAAAATCTCGTTGGTTTCA
* *
13267 AACCCTGGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCGATTCCAA-AGCCTTGTTAGTTT
64 AACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-TT---TT--AAGA-CCATGTTAGTTT
* *
13328 CTAATCCTGCTTGAGGTCTCTGGTCGAG-G-T-TTG-TCAATTCCAAA
1 CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTCTTGTTCAATTCCAAA
13372 TCATGTTTCA
Statistics
Matches: 141, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
120 83 0.59
121 15 0.11
122 3 0.02
123 1 0.01
124 2 0.01
125 2 0.01
126 35 0.25
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (118 bp):
CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTCTTGTTCAATTCCAAAATCTCGTTGGTTTCAAA
CCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTAAGACCATGTTAGTTT
Found at i:13683 original size:27 final size:29
Alignment explanation
Indices: 13653--13725 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 29
13643 GGTCATCTAG
*
13653 GGGCATTTTGGTCATTTTTTACACT-A-A
1 GGGCATTTTGGTCATTTTTCACACTCAGA
*
13680 GGGCATTTTGGTCA-TTTTCACATTCAGA
1 GGGCATTTTGGTCATTTTTCACACTCAGA
*
13708 GGGCATTTAGGTCATTTT
1 GGGCATTTTGGTCATTTT
13726 GAGTCCACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.20
27 15 0.38
28 14 0.35
29 3 0.08
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTCACACTCAGA
Found at i:13720 original size:28 final size:26
Alignment explanation
Indices: 13653--13725 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 26
13643 GGTCATCTAG
*
13653 GGGCATTTTGGTCATTTTTTACACTAA
1 GGGCATTTTGGTCA-TTTTCACACTAA
*
13680 GGGCATTTTGGTCATTTTCACATTCAGA
1 GGGCATTTTGGTCATTTTCACACT-A-A
*
13708 GGGCATTTAGGTCATTTT
1 GGGCATTTTGGTCATTTT
13726 GAGTCCACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 8 0.20
27 15 0.37
28 18 0.44
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTCACACTAA
Found at i:13860 original size:24 final size:24
Alignment explanation
Indices: 13833--13880 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13823 ATTGTTGCAT
13833 ATTCCATGGCATTTTCATTTAGTA
1 ATTCCATGGCATTTTCATTTAGTA
13857 ATTCCATGGCATTTTCATTTAGTA
1 ATTCCATGGCATTTTCATTTAGTA
13881 TTGTTGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (24 bp):
ATTCCATGGCATTTTCATTTAGTA
Found at i:14060 original size:16 final size:17
Alignment explanation
Indices: 14024--14063 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
14014 TGTGAAAAAT
14024 ACAAAA-AAAAAAGTAG
1 ACAAAAGAAAAAAGTAG
*
14040 A-AAAAGAAAAAAG-GG
1 ACAAAAGAAAAAAGTAG
14055 ACAAAAGAA
1 ACAAAAGAA
14064 TAAGAGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (17 bp):
ACAAAAGAAAAAAGTAG
Done.