Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013549.1 Corchorus capsularis cultivar CVL-1 contig13570, 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: 26165
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2128 original size:32 final size:32
Alignment explanation
Indices: 2092--2180 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
2082 CGAGTCACTC
* * *
2092 GGGTTACGTGTCATTCGGGTTTCGGATCATTT
1 GGGTTACGGGTCATTCGGGTCTCGGATCATCT
*
2124 GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
1 GGGTTACGGGTCATTCGGGTCTCGGATCATCT
* * *
2156 GGGTTGCGGGTCACTCAGGTCTCGG
1 GGGTTACGGGTCATTCGGGTCTCGG
2181 GTCGGACGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.33
Consensus pattern (32 bp):
GGGTTACGGGTCATTCGGGTCTCGGATCATCT
Found at i:2149 original size:16 final size:16
Alignment explanation
Indices: 2047--2183 Score: 75
Period size: 16 Copynumber: 8.6 Consensus size: 16
2037 CGGGTTAACT
* *
2047 TCTCGGGTTATTCGAG
1 TCTCGGGTCATTCGGG
* * **
2063 TTTCGGGTCATACAAG
1 TCTCGGGTCATTCGGG
* * *
2079 TCACGAGTCACTCGGG
1 TCTCGGGTCATTCGGG
*
2095 T-TACGTGTCATTCGGG
1 TCT-CGGGTCATTCGGG
* * *
2111 TTTCGGATCATTTGGG
1 TCTCGGGTCATTCGGG
2127 T-TACGGGTCATTCGGG
1 TCT-CGGGTCATTCGGG
2143 TCTCGGGTCA-TCTGGG
1 TCTCGGGTCATTC-GGG
* *
2159 T-TGCGGGTCACTCAGG
1 TCT-CGGGTCATTCGGG
2175 TCTCGGGTC
1 TCTCGGGTC
2184 GGACGAGTTC
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
15 4 0.04
16 84 0.90
17 5 0.05
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.32
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:2234 original size:15 final size:15
Alignment explanation
Indices: 2211--2253 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2201 TTACTTTTTC
2211 ATTGAACGGATTCGG
1 ATTGAACGGATTCGG
* *
2226 ATTGGACGGGTTCGG
1 ATTGAACGGATTCGG
*
2241 GTTGAACGGATTC
1 ATTGAACGGATTC
2254 TCGAGTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.28
Consensus pattern (15 bp):
ATTGAACGGATTCGG
Found at i:20244 original size:26 final size:26
Alignment explanation
Indices: 20208--20262 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
20198 GGATGGTACT
20208 ATAGAAATTGAATTTTTCTAAATAAA
1 ATAGAAATTGAATTTTTCTAAATAAA
20234 ATAGAAATTGAATTTTTCTAAATAAA
1 ATAGAAATTGAATTTTTCTAAATAAA
20260 ATA
1 ATA
20263 TTTTAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (26 bp):
ATAGAAATTGAATTTTTCTAAATAAA
Found at i:20436 original size:25 final size:27
Alignment explanation
Indices: 20384--20449 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
20374 AAAAATACAC
*
20384 AAAATTATATTTTAATAGTGACATAA-TT
1 AAAA-TATATTTTAATAATGACA-AATTT
*
20412 AAAATATTTTTTAATAATGAC-AATTT
1 AAAATATATTTTAATAATGACAAATTT
20438 AGAAATATATTT
1 A-AAATATATTT
20450 GGAAAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 24 0.73
28 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGACAAATTT
Found at i:20554 original size:23 final size:23
Alignment explanation
Indices: 20528--20576 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
20518 AGATAGATAT
20528 AAATATATTTCTAAATTAATAAG
1 AAATATATTTCTAAATTAATAAG
* *
20551 AAATGTATTTCTAAATTGATAAG
1 AAATATATTTCTAAATTAATAAG
20574 AAA
1 AAA
20577 ATGAAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (23 bp):
AAATATATTTCTAAATTAATAAG
Found at i:21548 original size:350 final size:350
Alignment explanation
Indices: 20906--21703 Score: 1179
Period size: 350 Copynumber: 2.3 Consensus size: 350
20896 CAATCAGTAA
* * **
20906 TTATGTTTATCTCGAGACCTAATTCTGCAGTTCCGGTGGATGATTTTGCCCTTGAAATTTCTATA
1 TTATGTTTATCTCGAGACCTAATTCTGCAGTTCTGGTGGACGATTTTGCCCTTGAAATTTCTGGA
* *
20971 TAGAATTGATCTTCTCCTAAACCGACTTAGAGAGCCAGATGTCTTGAACCCTAAATTCGATACTA
66 TATAATTGATCTTCTCCTAAACCGACTTGGAGAGCCAGATGTCTTGAACCCTAAATTCGATACTA
* * * **
21036 TTAGATCCAATTCGTTAACATGGAAGCCAAATAAGGAGTCCAAGTCCAATCAGTAATTATGATGC
131 TTAGAGCCAATTCGTTAACATGGAAGCCAAAGAAGGAGTCCAAGTCCAACCAGTAATTATGAAAC
* *
21101 AATAATGATTCAGCATTGATGCAACATTGTTAAATCCTATTCAAAAGAGGACTTCACAAGAGCAG
196 AATAATGATTCAACACTGATGCAACATTGTTAAATCCTATTCAAAAGAGGACTTCACAAGAGCAG
* * *
21166 TTTTGGAAGAAAATTCATAACTTTTTATCTAGAGCTCAGAAAAATGCAAATGAGGTACCGTTGGA
261 TTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTCAGAAAAATACAAATGAGGTACCGTTAGA
*
21231 AAGAGGATTCCAATATCTACAACTT
326 AAGAAGATTCCAATATCTACAACTT
* * *
21256 TTATG-TTACCTCGAGACCTAATTCTGCAGTTCTAGTGGACGATTTTGCCCTTAAAATTTCTGGA
1 TTATGTTTATCTCGAGACCTAATTCTGCAGTTCTGGTGGACGATTTTGCCCTTGAAATTTCTGGA
* * * ** *
21320 CATAATTGATCTTCTCCTGAACCGACTTGGAGGGCCAGATGTCTTGAAGTCTAAA-TCTGATATT
66 TATAATTGATCTTCTCCTAAACCGACTTGGAGAGCCAGATGTCTTGAACCCTAAATTC-GATACT
* * **
21384 CTTAG-GCCTAATTCGTTAATATGGAAGCCCAAAGAAGGAGTTTAAGTCCAACCAGTAATTATGA
130 ATTAGAGCC-AATTCGTTAACATGGAAG-CCAAAGAAGGAGTCCAAGTCCAACCAGTAATTATGA
* * * * **
21448 AATAGTAATGATTCAACCCTGATGCATCATTGTTAAATCCTATTCAAAAGAGGACTTCACAATTG
193 AACAATAATGATTCAACACTGATGCAACATTGTTAAATCCTATTCAAAAGAGGACTTCACAAGAG
21513 CAGTTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTCAGAAAAATACAAATGAGGTACCGTT
258 CAGTTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTCAGAAAAATACAAATGAGGTACCGTT
21578 AGAAAGAAGATTCCAATATCTACAACTT
323 AGAAAGAAGATTCCAATATCTACAACTT
* * *
21606 TTATGTTTATCTAGAGACCTAATTCTGCAGTTCTGGTGGACAATTTTGCCCTTGAAATTTATGGA
1 TTATGTTTATCTCGAGACCTAATTCTGCAGTTCTGGTGGACGATTTTGCCCTTGAAATTTCTGGA
* *
21671 TATAATTGATCTTTTCTTAAACCGACTTGGAGA
66 TATAATTGATCTTCTCCTAAACCGACTTGGAGA
21704 ATGTTTTGGA
Statistics
Matches: 397, Mismatches: 47, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
348 4 0.01
349 126 0.32
350 186 0.47
351 81 0.20
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (350 bp):
TTATGTTTATCTCGAGACCTAATTCTGCAGTTCTGGTGGACGATTTTGCCCTTGAAATTTCTGGA
TATAATTGATCTTCTCCTAAACCGACTTGGAGAGCCAGATGTCTTGAACCCTAAATTCGATACTA
TTAGAGCCAATTCGTTAACATGGAAGCCAAAGAAGGAGTCCAAGTCCAACCAGTAATTATGAAAC
AATAATGATTCAACACTGATGCAACATTGTTAAATCCTATTCAAAAGAGGACTTCACAAGAGCAG
TTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTCAGAAAAATACAAATGAGGTACCGTTAGA
AAGAAGATTCCAATATCTACAACTT
Found at i:22028 original size:22 final size:22
Alignment explanation
Indices: 21986--22029 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21976 TATTCATATG
*
21986 AAATTATGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
22008 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
22030 TTCGATGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:22066 original size:23 final size:21
Alignment explanation
Indices: 22027--22211 Score: 79
Period size: 22 Copynumber: 8.5 Consensus size: 21
22017 TAATTACACT
*
22027 ATTTTCGATGACCTCCTTAT-AA
1 ATTTT-GATAACCTCC-TATGAA
22049 GATTTTGATAACCTTCCTATGAA
1 -ATTTTGATAACC-TCCTATGAA
* * * *
22072 ATTTTAATAACGATACTATGGA
1 ATTTTGATAAC-CTCCTATGAA
* * **
22094 ATTTCGAGAACCTTTTTAT-AA
1 ATTTTGATAACC-TCCTATGAA
* * * ** *
22115 TTTTTTAAAATTTCTTATGAA
1 ATTTTGATAACCTCCTATGAA
* * *
22136 ATTTTGTTAACCTCCCTAAGGA
1 ATTTTGATAACCT-CCTATGAA
22158 ATTTTGA-AGACCTCACTATGAA
1 ATTTTGATA-ACCTC-CTATGAA
* *
22180 ATTTTGATAACATCCCAATGAA
1 ATTTTGATAACCT-CCTATGAA
22202 ATTTTGATAA
1 ATTTTGATAA
22212 ACAACACTAT
Statistics
Matches: 119, Mismatches: 33, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
20 5 0.04
21 18 0.15
22 84 0.71
23 12 0.10
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
ATTTTGATAACCTCCTATGAA
Found at i:22075 original size:22 final size:22
Alignment explanation
Indices: 22050--22211 Score: 89
Period size: 22 Copynumber: 7.5 Consensus size: 22
22040 TCCTTATAAG
22050 ATTTTGATAACCTTCCTATGAA
1 ATTTTGATAACCTTCCTATGAA
* ** * *
22072 ATTTTAATAACGATACTATGGA
1 ATTTTGATAACCTTCCTATGAA
* * **
22094 ATTTCGAGAACCTTTTTAT-AA
1 ATTTTGATAACCTTCCTATGAA
* * ** *
22115 TTTTTTA-AAATTTCTTATGAA
1 ATTTTGATAACCTTCCTATGAA
* * * *
22136 ATTTTGTTAACCTCCCTAAGGA
1 ATTTTGATAACCTTCCTATGAA
22158 ATTTTGA-AGACC-TCACTATGAA
1 ATTTTGATA-ACCTTC-CTATGAA
* * *
22180 ATTTTGATAACATCCCAATGAA
1 ATTTTGATAACCTTCCTATGAA
22202 ATTTTGATAA
1 ATTTTGATAA
22212 ACAACACTAT
Statistics
Matches: 99, Mismatches: 35, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
20 8 0.08
21 13 0.13
22 76 0.77
23 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
ATTTTGATAACCTTCCTATGAA
Found at i:22223 original size:23 final size:22
Alignment explanation
Indices: 22171--22224 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
22161 TTGAAGACCT
*
22171 CACTATGAAATTTTGATAACAT
1 CACTATGAAATTTTGATAACAA
* *
22193 CCCAATGAAATTTTGATAAACAA
1 CACTATGAAATTTTGAT-AACAA
22216 CACTATGAA
1 CACTATGAA
22225 GTGTTAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACAA
Found at i:25141 original size:33 final size:33
Alignment explanation
Indices: 25104--25208 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
25094 CTAATTGTGA
*
25104 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGATCATAGCAT
* *
25137 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGATCATAGCAT
25170 TGAAAACAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGATCATAGCAT
25203 TGAAAA
1 TGAAAA
25209 TAGGACTGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (33 bp):
TGAAAACAATTCTGTTTTGGTTGATCATAGCAT
Done.