Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015017.1 Corchorus capsularis cultivar CVL-1 contig15038, 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: 20861
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:1170 original size:214 final size:214
Alignment explanation
Indices: 732--1753 Score: 1533
Period size: 211 Copynumber: 4.8 Consensus size: 214
722 TTAAGAAACT
* * * * *
732 TCAA-TTTAAAAAAGAGTCGCAAGATACTGCGACGTATATTAAAATGTCACATATTAAAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
* * * *
796 TTTCC-AAAACGTTGTTATAAATGTCGGAAAAGTCCATCTTAAAGCGGCGTTTGTTAAAAAATGT
66 TTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTTAAAAAATGT
* * ** * *
860 CGCATGATTGAACGACGTTTGAGAAAAACGTCTTTACAAATGTCGTAAAAGCATAAACAAGAGCG
131 CACATGATTGAACGACGTTTGA-AAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCG
*
925 ACGTTATTAAAAAACGTCAC
195 ACGTAATTAAAAAACGTCAC
*
945 TCAA-TTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGATG
1 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
1009 TTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTTAAAAAATGT
66 TTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTTAAAAAATGT
1074 CACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCGA
131 CACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCGA
1139 CGTAATTAAAAAACGTCAC
196 CGTAATTAAAAAACGTCAC
*
1158 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTAATATATTAAAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
1223 TTTCCGAAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTT----AATG
66 TTTCCG-AAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTTAAAAAATG
*
1284 TCACATGATTGAACGACGTTTGAGAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCG
130 TCACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCG
1349 ACGTAATTAAAAAACGTCAC
195 ACGTAATTAAAAAACGTCAC
*
1369 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGCCATATATTAAAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
* *
1434 TTTCTGAAAAACGTTGTTATAAATGTTGGAAAAATTTATCTTAAAGCGACGTTTGTTAAAAAAAT
66 TTTCCG-AAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTT-AAAAAAT
* *
1499 GTCACATGATTGAACGACGTTGGAAAAAACGTCTCTACAAGCGTTGCAAAAGTATAAACAAGAGC
129 GTCACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGC
* * *
1564 GACGCAATTAAAAAACTTCAT
194 GACGTAATTAAAAAACGTCAC
* ** * * * *
1585 TCAATTTTAAAAAAGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCATTTATT-AAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
* * * *
1649 TTTCCTTAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAAACGA-GTTTTGTT-AAAAA
66 TTTCC-GAAAACGTTGTTATAAATGTTGGAAAAATCTATCTT-AAAGCGACG-TTTGTTAAAAAA
* * *
1712 TGTCGCATGATTGAACGACGTTTGACAAAAATGTCTTTACAA
128 TGTCACATGATTGAACGACGTTTGA-AAAAACGTCTCTACAA
1754 ATGTCGTAAA
Statistics
Matches: 749, Mismatches: 48, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
211 206 0.28
213 123 0.16
214 168 0.22
215 109 0.15
216 143 0.19
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (214 bp):
TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTCATATATTAAAACGACG
TTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTTAAAAAATGT
CACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCGA
CGTAATTAAAAAACGTCAC
Found at i:1527 original size:427 final size:423
Alignment explanation
Indices: 732--1766 Score: 1574
Period size: 427 Copynumber: 2.4 Consensus size: 423
722 TTAAGAAACT
* *
732 TCAA-TTTAAAAAAGAGTCGCAAGATACTGCGACGTATATTAAAATGTCACATATTAAAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGATACTGCGACGTTTATTAAAATGTCATATATTAAAACGACG
* *
796 TTTCCAAAACGTTGTTATAAATGTCGGAAAAGTCCATCTTAAAGCGGCGTTTGTTAAAAAATGTC
66 TTTCCAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTT---AAATGTC
* * *
861 GCATGATTGAACGACGTTTGAGAAAAACGTCTTTACAAATGTCGTAAAAGCATAAACAAGAGCGA
128 GCATGATTGAACGACGTTTGAG-AAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGA
*
926 CGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATG
192 CGTAATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATG
* *
991 TCATATATTAAAACGATGTTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCG
257 CCATATATTAAAACGACGTTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCG
*
1056 ACGTTTGTTAAAAAATGTCACATGATTGAACGACGTTTGAAAAAACGTCTCTACAAGCGTCGCAA
322 ACGTTTGTTAAAAAATGTCACATGATTGAACGACGTTGGAAAAAACGTCTCTACAAGCGTCGCAA
*
1121 AAGTATAAACAAGAGCGACGTAATTAAAAAACGTCAC
387 AAGTATAAACAAGAGCGACGCAATTAAAAAACGTCAC
* * * *
1158 TCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGTAATATATTAAAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGATACTGCGACGTTTATTAAAATGTCATATATTAAAACGACG
* * *
1223 TTTCCGAAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGTTTGTT-AATGTCA
66 TTTCC--AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAATGTCG
* *
1287 CATGATTGAACGACGTTTGAGAAAACGTCTCTACAAGCGTCGCAAAAGTATAAACAAGAGCGACG
129 CATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACG
1352 TAATTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGC
194 TAATTAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGC
* *
1417 CATATATTAAAACGACGTTTCTGAAAAACGTTGTTATAAATGTTGGAAAAATTTATCTTAAAGCG
258 CATATATTAAAACGACGTTTCCG-AAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCG
*
1482 ACGTTTGTTAAAAAAATGTCACATGATTGAACGACGTTGGAAAAAACGTCTCTACAAGCGTTGCA
322 ACGTTTGTT-AAAAAATGTCACATGATTGAACGACGTTGGAAAAAACGTCTCTACAAGCGTCGCA
* *
1547 AAAGTATAAACAAGAGCGACGCAATTAAAAAACTTCAT
386 AAAGTATAAACAAGAGCGACGCAATTAAAAAACGTCAC
** * *
1585 TCAATTTTAAAAAAGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCATTTATT-AAACGACG
1 TCAATTTTAAAAAAGAGTCGCAAGATACTGCGACGTTTATTAAAATGTCATATATTAAAACGACG
*
1649 TTTCCTTAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAAACGA-GTTTTGTTAAAAAT
66 TTTCC--AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTT-AAAGCGACG-TTTGTT--AAAT
* * * * *
1713 GTCGCATGATTGAACGACGTTTGACAAAAATGTCTTTACAAATGTCGTAAAAGC
125 GTCGCATGATTGAACGACGTTTGA-GAAAACGTCTCTACAAACGTCGCAAAAGC
1767 GTGAGCAATA
Statistics
Matches: 550, Mismatches: 47, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
424 59 0.11
425 90 0.16
426 100 0.18
427 207 0.38
429 46 0.08
430 26 0.05
431 22 0.04
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (423 bp):
TCAATTTTAAAAAAGAGTCGCAAGATACTGCGACGTTTATTAAAATGTCATATATTAAAACGACG
TTTCCAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAATGTCGCA
TGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTA
ATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTACTGCGACGTTTCTTAACATGCCAT
ATATTAAAACGACGTTTCCGAAAACGTTGTTATAAATGTTGGAAAAATCTATCTTAAAGCGACGT
TTGTTAAAAAATGTCACATGATTGAACGACGTTGGAAAAAACGTCTCTACAAGCGTCGCAAAAGT
ATAAACAAGAGCGACGCAATTAAAAAACGTCAC
Found at i:6029 original size:33 final size:33
Alignment explanation
Indices: 5987--6049 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
5977 TGAAAAGGAG
*
5987 AAAATAAAAAGATGGGGTAATGGGTTTTTGGAC
1 AAAATAAAAAGATGGAGTAATGGGTTTTTGGAC
6020 AAAATAAAAAGATGGAGTAATGGGTTTTTG
1 AAAATAAAAAGATGGAGTAATGGGTTTTTG
6050 TGATGAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.29, T:0.29
Consensus pattern (33 bp):
AAAATAAAAAGATGGAGTAATGGGTTTTTGGAC
Found at i:8372 original size:5 final size:5
Alignment explanation
Indices: 8362--8404 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
8352 CTTATATATA
*
8362 ATCAT ATCAT ATCATT AT-AT ATAAT GATCAT ATCAT ATCAT AT
1 ATCAT ATCAT ATCA-T ATCAT ATCAT -ATCAT ATCAT ATCAT AT
8405 GACAAATGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
4 3 0.09
5 24 0.71
6 7 0.21
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (5 bp):
ATCAT
Found at i:8381 original size:21 final size:21
Alignment explanation
Indices: 8353--8397 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
8343 GCCTACCACC
*
8353 TTATATATAATCATATCATATCA
1 TTATATATAAT--GATCATATCA
8376 TTATATATAATGATCATATCA
1 TTATATATAATGATCATATCA
8397 T
1 T
8398 ATCATATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATATATAATGATCATATCA
Found at i:8398 original size:26 final size:25
Alignment explanation
Indices: 8354--8402 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
8344 CCTACCACCT
8354 TATATATAATCATATCATATCATTA
1 TATATATAATCATATCATATCATTA
*
8379 TATATAATGATCATATCATATCAT
1 TATAT-ATAATCATATCATATCAT
8403 ATGACAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (25 bp):
TATATATAATCATATCATATCATTA
Found at i:10383 original size:29 final size:30
Alignment explanation
Indices: 10351--10419 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
10341 GCTTAATTAG
*
10351 GGGGGCAAAATATCCAAA-AT-TAAAGTTCA
1 GGGGGCAAAACATCCAAACATAT-AAGTTCA
*
10380 GGGGGCAAAACGTCCAAACCATATAAGTTCA
1 GGGGGCAAAACATCCAAA-CATATAAGTTCA
10411 -GGGGCAAAA
1 GGGGGCAAAA
10420 AGGGCATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 16 0.46
30 9 0.26
31 9 0.26
32 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.16
Consensus pattern (30 bp):
GGGGGCAAAACATCCAAACATATAAGTTCA
Found at i:11146 original size:22 final size:22
Alignment explanation
Indices: 11121--11165 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11111 CAAAAGCCTC
*
11121 AAGAATTTCGCGGGTCGCTAGT
1 AAGAATTTCGCGCGTCGCTAGT
11143 AAGAATTTCGCGCGTCGCTAGT
1 AAGAATTTCGCGCGTCGCTAGT
11165 A
1 A
11166 GATATCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (22 bp):
AAGAATTTCGCGCGTCGCTAGT
Found at i:16625 original size:150 final size:148
Alignment explanation
Indices: 16288--16698 Score: 677
Period size: 150 Copynumber: 2.8 Consensus size: 148
16278 TCTATAAGCC
* * *
16288 AACATCTAAACGAGAATTCAACCCAAACTAGAAA--ACCATAAATAAACTACATACTTACAAAAT
1 AACATCTAAATGAGAATTCAACCCAAACTAGAAACTACCATAAATAAACTAC-TACCTACCAAAT
16351 AAACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCC-AAATCTCATTACAATTC
65 AAACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCCAAAATCTCATTACAATTC
16415 AAATAAATATTTATGCTCA
130 AAATAAATATTTATGCTCA
*
16434 AACATCTAAATGAGAATTCAACCTAAACTAGAAACATACCATAAATAAACTATCTACCTACCAAA
1 AACATCTAAATGAGAATTCAACCCAAACTAGAAAC-TACCATAAATAAACTA-CTACCTACCAAA
16499 TAAACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCCAAAATCTCATTACAATT
64 TAAACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCCAAAATCTCATTACAATT
16564 CAAATAAATATTTATG-TCCA
129 CAAATAAATATTTATGCT-CA
*
16584 AACATCTAAATGAGAATTAAACCCAAACTAGAAACCTACCATAAATAAACTACCTACCTACCAAA
1 AACATCTAAATGAGAATTCAACCCAAACTAGAAA-CTACCATAAATAAACTA-CTACCTACCAAA
* *
16649 TAAACAAACAAATTATAAACAAACTCACATTCTGTGAGAGTTGAACCCAA
64 TAAACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCCAA
16699 GACCACCCAA
Statistics
Matches: 249, Mismatches: 9, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
146 32 0.13
149 73 0.29
150 143 0.57
151 1 0.00
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.22
Consensus pattern (148 bp):
AACATCTAAATGAGAATTCAACCCAAACTAGAAACTACCATAAATAAACTACTACCTACCAAATA
AACAAACAAATTACAAACAAACTCACATTCCGTGAGAGTTGAACCCAAAATCTCATTACAATTCA
AATAAATATTTATGCTCA
Found at i:20050 original size:184 final size:184
Alignment explanation
Indices: 19741--20107 Score: 680
Period size: 184 Copynumber: 2.0 Consensus size: 184
19731 TCTCCAAATG
* *
19741 TATGGCATATCTCATTTTCAAACACCACTGCATACACCAGAACACAATGGTGTCTCTGATAGAAA
1 TATGGCATATCTCATTTTCAAACACCACTGCATACACCAGAACACAACGGTGTCTCTGAAAGAAA
19806 ACATCGTCATATAGTTGAGACTAGTCTTGCCTTGCTTTACCATGCTAAACTGCCTTCAAAGTTTT
66 ACATCGTCATATAGTTGAGACTAGTCTTGCCTTGCTTTACCATGCTAAACTGCCTTCAAAGTTTT
*
19871 AGACCTTGGCTTTTCAAACTGCCGTTTACTTAATAAACAGGTTACCCACTCCTA
131 AGACCTTGGCTTTTCAAACTGCCGTTTACTTAATAAACAGGTTACCCAATCCTA
19925 TATGGCATATCTCATTTTCAAACACCACTGCATACACCAGAACACAACGGTGTCTCTGAAAGAAA
1 TATGGCATATCTCATTTTCAAACACCACTGCATACACCAGAACACAACGGTGTCTCTGAAAGAAA
* * *
19990 ATATCGTCATATATTTGAGACTGGTCTTGCCTTGCTTTACCATGCTAAACTGCCTTCAAAGTTTT
66 ACATCGTCATATAGTTGAGACTAGTCTTGCCTTGCTTTACCATGCTAAACTGCCTTCAAAGTTTT
20055 AGACCTTGGCTTTTCAAACTGCCGTTTACTTAATAAACAGGTTACCCAATCCT
131 AGACCTTGGCTTTTCAAACTGCCGTTTACTTAATAAACAGGTTACCCAATCCT
20108 GTCTTAAATA
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 177 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (184 bp):
TATGGCATATCTCATTTTCAAACACCACTGCATACACCAGAACACAACGGTGTCTCTGAAAGAAA
ACATCGTCATATAGTTGAGACTAGTCTTGCCTTGCTTTACCATGCTAAACTGCCTTCAAAGTTTT
AGACCTTGGCTTTTCAAACTGCCGTTTACTTAATAAACAGGTTACCCAATCCTA
Found at i:20538 original size:27 final size:26
Alignment explanation
Indices: 20508--20569 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 26
20498 GTACAGCCAC
20508 CGGTAAGTTCATCT-CAAGTTTTTCCTG
1 CGGTAA-TTCATCTCCAA-TTTTTCCTG
20535 CGGTGAATTCATCTCCAATTTTTCCTG
1 CGGT-AATTCATCTCCAATTTTTCCTG
20562 CGGTAATT
1 CGGTAATT
20570 GATTCTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.12
27 24 0.73
28 5 0.15
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (26 bp):
CGGTAATTCATCTCCAATTTTTCCTG
Found at i:20579 original size:26 final size:26
Alignment explanation
Indices: 20515--20579 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 26
20505 CACCGGTAAG
20515 TTCATCTCAAGTTTTTCCTGCGGTGAA
1 TTCATCTCAA-TTTTTCCTGCGGTGAA
20542 TTCATCTCCAATTTTTCCTGCGGT-AA
1 TTCATCT-CAATTTTTCCTGCGGTGAA
*
20568 TTGATTCTCAAT
1 TTCA-TCTCAAT
20580 ATATACCTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 9 0.26
27 23 0.66
28 3 0.09
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (26 bp):
TTCATCTCAATTTTTCCTGCGGTGAA
Done.