Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010315.1 Corchorus olitorius cultivar O-4 contig10347, 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: 2031
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Found at i:70 original size:46 final size:46
Alignment explanation
Indices: 1--160 Score: 238
Period size: 46 Copynumber: 3.5 Consensus size: 46
* *
1 TTTCTGGAGAAGGGTGCTCACATAAGAGCTACTTTATAGAGTATTC
1 TTTCTGAAGAAGGGTGCTCACATAAGAGCTACTATATAGAGTATTC
* *
47 TTTCTGAATG-AGGGTGCTTACATAAGAGCTACCATATAGAGTATTC
1 TTTCTGAA-GAAGGGTGCTCACATAAGAGCTACTATATAGAGTATTC
*
93 TTTCTGAAGAAGGGTGCTCACATAAGAGCTACTGTATAGAGTATTC
1 TTTCTGAAGAAGGGTGCTCACATAAGAGCTACTATATAGAGTATTC
139 TTTCT---GAAGGGTGCTCACATAA
1 TTTCTGAAGAAGGGTGCTCACATAA
161 AATGCATCTC
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
43 17 0.16
45 1 0.01
46 86 0.82
47 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (46 bp):
TTTCTGAAGAAGGGTGCTCACATAAGAGCTACTATATAGAGTATTC
Found at i:377 original size:36 final size:36
Alignment explanation
Indices: 334--491 Score: 217
Period size: 36 Copynumber: 4.4 Consensus size: 36
324 AAGGCTAGTA
334 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
* * * *
370 GCTTTATAGCCAATTATTGGGCGACTTAGGCCATCG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
*
406 GCATTATAGCCAAGTATTGGGCGACTAAGGCCAGCG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
* * * * *
442 GCTTTATAGCCAATTATTAGGCGACTTAGGCCATCG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
*
478 ACATTATAGCCAAA
1 GCATTATAGCCAAA
492 GACGAAGCAA
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 106 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (36 bp):
GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCG
Found at i:451 original size:72 final size:72
Alignment explanation
Indices: 334--491 Score: 289
Period size: 72 Copynumber: 2.2 Consensus size: 72
324 AAGGCTAGTA
*
334 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAATTATTGGGCGACTTAG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAATTATTAGGCGACTTAG
399 GCCATCG
66 GCCATCG
*
406 GCATTATAGCCAAGTATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAATTATTAGGCGACTTAG
1 GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAATTATTAGGCGACTTAG
471 GCCATCG
66 GCCATCG
*
478 ACATTATAGCCAAA
1 GCATTATAGCCAAA
492 GACGAAGCAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 82 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (72 bp):
GCATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAATTATTAGGCGACTTAG
GCCATCG
Found at i:861 original size:30 final size:30
Alignment explanation
Indices: 805--862 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
795 CAGGACGTTG
* * *
805 GAAGGAGGTGAGACTTCGCTAGCACCATTA
1 GAAGGAGGTGAGACTTCACAAACACCATTA
*
835 GAAGGAGGTGATACTTCACAAACACCAT
1 GAAGGAGGTGAGACTTCACAAACACCAT
863 ATGCTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (30 bp):
GAAGGAGGTGAGACTTCACAAACACCATTA
Found at i:941 original size:34 final size:34
Alignment explanation
Indices: 898--962 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
888 ATAGTTTCGT
898 AAACACCATATGCCTTTGACATTGAAAGAGGCAC
1 AAACACCATATGCCTTTGACATTGAAAGAGGCAC
* *
932 AAACACCATATGTCTTTGATATTGAAAGAGG
1 AAACACCATATGCCTTTGACATTGAAAGAGG
963 GTGATAGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (34 bp):
AAACACCATATGCCTTTGACATTGAAAGAGGCAC
Found at i:981 original size:78 final size:78
Alignment explanation
Indices: 851--1000 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 78
841 GGTGATACTT
* * *
851 CACAAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGTAAACACCATATGCCTTTG
1 CACAAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATACCTTTG
916 ACATTGAAAGAGG
66 ACATTGAAAGAGG
* *
929 CACAAACACCATATG-TCTTTGATATTGAAAGAGGGTGATAGTCTCGCGAACACCATATACCTTT
1 CACAAACACCATATGCT-TTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATACCTTT
993 GACATTGA
65 GACATTGA
1001 CATTGAAAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 1 0.02
78 65 0.98
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (78 bp):
CACAAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATACCTTTG
ACATTGAAAGAGG
Found at i:1482 original size:25 final size:25
Alignment explanation
Indices: 1445--1642 Score: 112
Period size: 25 Copynumber: 7.6 Consensus size: 25
1435 GAATACCATA
*
1445 TCGCGAATGCCACATGCATTTGACG
1 TCGCGAATACCACATGCATTTGACG
*** *
1470 TCGCGAATACCACATTGCAAATACCACA
1 TCGCGAATACCACA-TGC--ATTTGACG
* *
1498 TCGTGAATGCCACATGTC-TTTGACG
1 TCGCGAATACCACATG-CATTTGACG
** *
1523 TCGCGAATACCACATTGCAAAT-ACCATA
1 TCGCGAATACCACA-TGCATTTGA-C--G
* *
1551 TCGCGAATGCCACATGCCTTTGACG
1 TCGCGAATACCACATGCATTTGACG
**** *
1576 TCGCGAATACCACATTGCAGAACCACA
1 TCGCGAATACCACA-TGCA-TTTGACG
* *
1603 TCGCGAATGCCACATGCCTTTGACG
1 TCGCGAATACCACATGCATTTGACG
*
1628 TCTCGAATACCACAT
1 TCGCGAATACCACAT
1643 TGCAAATACC
Statistics
Matches: 124, Mismatches: 37, Indels: 24
0.67 0.20 0.13
Matches are distributed among these distances:
25 58 0.47
26 13 0.10
27 22 0.18
28 31 0.25
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (25 bp):
TCGCGAATACCACATGCATTTGACG
Found at i:1497 original size:39 final size:39
Alignment explanation
Indices: 1415--1498 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
1405 GAAGCGAATG
* * * *
1415 CCACATGCTTTTGACGTCACGAATACCATATCGCGAATG
1 CCACATGCATTTGACGTCACGAATACCACATCGCAAATA
* *
1454 CCACATGCATTTGACGTCGCGAATACCACATTGCAAATA
1 CCACATGCATTTGACGTCACGAATACCACATCGCAAATA
1493 CCACAT
1 CCACAT
1499 CGTGAATGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (39 bp):
CCACATGCATTTGACGTCACGAATACCACATCGCAAATA
Found at i:1520 original size:53 final size:53
Alignment explanation
Indices: 1436--1653 Score: 366
Period size: 53 Copynumber: 4.1 Consensus size: 53
1426 TGACGTCACG
* *
1436 AATACCATATCGCGAATGCCACATGCATTTGACGTCGCGAATACCACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
* *
1489 AATACCACATCGTGAATGCCACATGTCTTTGACGTCGCGAATACCACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
*
1542 AATACCATATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
* *
1595 GA-ACCACATCGCGAATGCCACATGCCTTTGACGTCTCGAATACCACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
1647 AATACCA
1 AATACCA
1654 TCACATGCCT
Statistics
Matches: 153, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
52 49 0.32
53 104 0.68
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (53 bp):
AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
Found at i:1651 original size:105 final size:106
Alignment explanation
Indices: 1436--1654 Score: 386
Period size: 105 Copynumber: 2.1 Consensus size: 106
1426 TGACGTCACG
1436 AATACCATATCGCGAATGCCACATGCATTTGACGTCGCGAATACCACATTGCAAATACCACATCG
1 AATACCATATCGCGAATGCCACATGCATTTGACGTCGCGAATACCACATTGCAAATACCACATCG
* *
1501 TGAATGCCACATGTCTTTGACGTCGCGAATACCACATTGCA
66 CGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
* *
1542 AATACCATATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAGA-ACCACATCG
1 AATACCATATCGCGAATGCCACATGCATTTGACGTCGCGAATACCACATTGCAAATACCACATCG
*
1606 CGAATGCCACATGCCTTTGACGTCTCGAATACCACATTGCA
66 CGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
1647 AATACCAT
1 AATACCAT
1655 CACATGCCTT
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 55 0.51
106 53 0.49
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (106 bp):
AATACCATATCGCGAATGCCACATGCATTTGACGTCGCGAATACCACATTGCAAATACCACATCG
CGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
Done.