Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018452.1 Corchorus olitorius cultivar O-4 contig18485, 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: 57146
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Found at i:1476 original size:27 final size:27
Alignment explanation
Indices: 1408--1477 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1398 TTACTATTTT
*
1408 ACCCTTTGATGGA-TAAAGTACTAAATC
1 ACCCTTTGAT-GATTAAAGTACGAAATC
* * *
1435 ACCC-TTAAGTTATTAAATTACGAAATC
1 ACCCTTTGA-TGATTAAAGTACGAAATC
1462 ACCCTTTGATGATTAA
1 ACCCTTTGATGATTAA
1478 TTTTAAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.12
27 27 0.79
28 3 0.09
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (27 bp):
ACCCTTTGATGATTAAAGTACGAAATC
Found at i:5691 original size:3 final size:3
Alignment explanation
Indices: 5683--5748 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
5673 CATATTATAT
5683 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5731 ATA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA
5749 CCTGAGAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7326 original size:19 final size:20
Alignment explanation
Indices: 7296--7359 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
7286 TTGACACTAT
7296 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
* *
7317 TTA-CACTGTATAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
7336 TTAGGTACTATACAGATGAGA
1 TTA-GCACTGTACAGATGAGA
7357 TTA
1 TTA
7360 TTAGAGCAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:7434 original size:19 final size:19
Alignment explanation
Indices: 7410--7457 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
7400 TTTGGTCCCA
7410 AAACGGTGATAAAACAATC
1 AAACGGTGATAAAACAATC
* * *
7429 AAACGGTGGTCAAACAGTC
1 AAACGGTGATAAAACAATC
*
7448 AAACGATGAT
1 AAACGGTGAT
7458 CTAGGTGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (19 bp):
AAACGGTGATAAAACAATC
Found at i:7669 original size:7 final size:6
Alignment explanation
Indices: 7638--7667 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
7628 AAAAAATAAA
7638 TAAAAT TAAAAAT TAAAAT TAAAAT TAAAA
1 TAAAAT T-AAAAT TAAAAT TAAAAT TAAAA
7668 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAAAT
Found at i:8608 original size:18 final size:18
Alignment explanation
Indices: 8585--8630 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
8575 TCTTACCTAG
* *
8585 TACTATATATATAGTGTA
1 TACTATATATATACTATA
8603 TACTATATATATACTATA
1 TACTATATATATACTATA
8621 TACTATATAT
1 TACTATATAT
8631 GTCAAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (18 bp):
TACTATATATATACTATA
Found at i:13725 original size:30 final size:31
Alignment explanation
Indices: 13686--13757 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
13676 ATGTGACATG
13686 TGGCATGCCACATGTC-CTTTTTTGTACACA
1 TGGCATGCCACATGTCACTTTTTTGTACACA
* * * *
13716 TGGCGTGCCACATGTCATTTTTTTGTTCACG
1 TGGCATGCCACATGTCACTTTTTTGTACACA
13747 TGGCATGCCAC
1 TGGCATGCCAC
13758 GTCAGATGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 15 0.42
31 21 0.58
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTTGTACACA
Found at i:38645 original size:13 final size:13
Alignment explanation
Indices: 38627--38651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38617 GGTCGTCTGT
38627 TAAGCCCTATTGC
1 TAAGCCCTATTGC
38640 TAAGCCCTATTG
1 TAAGCCCTATTG
38652 TGTAGGCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (13 bp):
TAAGCCCTATTGC
Found at i:39215 original size:631 final size:631
Alignment explanation
Indices: 38009--39257 Score: 2203
Period size: 631 Copynumber: 2.0 Consensus size: 631
37999 TTCTTCTTGT
* * *
38009 TAAGCCCTATTGTGTAGGCTTGGACGATCTCTGATTCGGGCACTCCTTTTACTTCCGTGCAGGCA
1 TAAGCCCTATTGTGTAGGCTTGGACAATCTCTGATTCGGGCACTCCTTCTACTTCCATGCAGGCA
* *
38074 TTCTAGAAGCGCTTGGCGTAACCCTCTAGGGGCTCCTCCAATCCTTGCCGTATGCTTAGGAGGTG
66 TTCTAGAAACACTTGGCGTAACCCTCTAGGGGCTCCTCCAATCCTTGCCGTATGCTTAGGAGGTG
* *
38139 CAGGCTTATTTTTCCTACTGCCATCCGGCTGTGGAAGCCTGAGAGGAATTGTCGAGCCAATTGCT
131 CAGGCTTATTTTTCCTACTGCCATACGGCTGTGGAAGCCTGAGAAGAATTGTCGAGCCAATTGCT
*
38204 CAAAACTTGTGATGGAGAGATCCTCTAATTTGTGATACCATGTCAGAGTTGGTCCGACGAGTGTC
196 CAAAACTTGTGATGGAGAGATCCTCTAATTTGTGATACCATGTCAGAGCTGGTCCGACGAGTGTC
*
38269 AATGTGAAGGCTCTGCAATACATGGAATCTGTAGCAAGCTGCATTTACATGGTGGCCTTAAAATG
261 AATGGGAAGGCTCTGCAATACATGGAATCTGTAGCAAGCTGCATTTACATGGTGGCCTTAAAATG
* *
38334 AGAGAGGTGCTCTCTGGGGTTTTTGGTTCCATTGTACTTCATTTTTGGTACCTTAAAGTTTAGAG
326 AGAGAGGTGCTCTCTGGGGTCTTCGGTTCCATTGTACTTCATTTTTGGTACCTTAAAGTTTAGAG
38399 GGGCCTGCTCTCTCTGAATTTCTACTGACAAGGGGCAGCTGTGGGAGTTCATGAATTCCCAAACA
391 GGGCCTGCTCTCTCTGAATTTCTACTGACAAGGGGCAGCTGTGGGAGTTCATGAATTCCCAAACA
* * *
38464 TCTGTATCGCCCCTTGCCCTTGCCTCACGCTCTCGGCGTGCGTCTTCTTCCATCTCGGCGAGCTT
456 TCCGTATCGCCCCTTGCCCTTGCCTCACGCTCTCGGCGTGCGCCTTCCTCCATCTCGGCGAGCTT
* *
38529 ATGTTCAAGTCTATTGATTTTGTTGAGCAATGGGGCGGCCATTGCCTCTGTTAGATTCTGTGATG
521 ATGTTCAAGTCTATTGATTTTGTCGAGCAATGGGGCGGCCATTGCCTCCGTTAGATTCTGTGATG
*
38594 CATTCTCAGTCAAGTTTTCCCTCGGTCGTCTGTTAAGCCCTATTGC
586 CATTCTCAGTCAAGTTTTCCCTCGGTCCTCTGTTAAGCCCTATTGC
* *
38640 TAAGCCCTATTGTGTAGGCTTGGACAATTTTTGATTCGGGCACTCCTTCTACTTCCATGCAGGCA
1 TAAGCCCTATTGTGTAGGCTTGGACAATCTCTGATTCGGGCACTCCTTCTACTTCCATGCAGGCA
* *
38705 TTCTGGAAACACTTGGCGTAACCCTCTAGGGGCTCCTCCAATCCTTGTCGTATGCTTAGGAGGTG
66 TTCTAGAAACACTTGGCGTAACCCTCTAGGGGCTCCTCCAATCCTTGCCGTATGCTTAGGAGGTG
* * *
38770 CAGGCTTGTTTTTCCTACTGTCATACGGCTGTGGAAGCCTGAGAAGAATTGTCGGGCCAATTGCT
131 CAGGCTTATTTTTCCTACTGCCATACGGCTGTGGAAGCCTGAGAAGAATTGTCGAGCCAATTGCT
38835 CAAAACTTGTGATGGAGAGATCCTCTAATTTGTGATACCATGTCAGAGCTGGTCCGACGAGTGTC
196 CAAAACTTGTGATGGAGAGATCCTCTAATTTGTGATACCATGTCAGAGCTGGTCCGACGAGTGTC
* * *
38900 AATGGGAAGGCTTTGCAATACATGGAATCTGTAGCAAGCTGCATTTGCATGGTGGCCTTGAAATG
261 AATGGGAAGGCTCTGCAATACATGGAATCTGTAGCAAGCTGCATTTACATGGTGGCCTTAAAATG
38965 AGAGAGGTGCTCTCTGGGGTCTTCGGTTCCATTGTACTTCATTTTTGGTACCTTAAAGTTTAGAG
326 AGAGAGGTGCTCTCTGGGGTCTTCGGTTCCATTGTACTTCATTTTTGGTACCTTAAAGTTTAGAG
*
39030 GGGCGC-GCTCTCTCTGAATTTCTACTGACAAGGGGCAGCTGTGGGAGTTCATGGATTCCCAAAC
391 GGGC-CTGCTCTCTCTGAATTTCTACTGACAAGGGGCAGCTGTGGGAGTTCATGAATTCCCAAAC
*
39094 ATCCGTATCGCCTCTTGCCCTTGCCTCACGCTCTCGGCGTGCGCCTTCCTCCATCTCGGCGAGCT
455 ATCCGTATCGCCCCTTGCCCTTGCCTCACGCTCTCGGCGTGCGCCTTCCTCCATCTCGGCGAGCT
* *
39159 TCTGTTCAGGTCTATTGATTTTGTCGAGCAATGGGGCGGCCATTGCCTCCGTTAGATTCTGTGAT
520 TATGTTCAAGTCTATTGATTTTGTCGAGCAATGGGGCGGCCATTGCCTCCGTTAGATTCTGTGAT
39224 GCATTCTCAGTCAAGTTTTCCCTCGGTCCTCTGT
585 GCATTCTCAGTCAAGTTTTCCCTCGGTCCTCTGT
39258 CAGCTGTTCG
Statistics
Matches: 586, Mismatches: 31, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
631 585 1.00
632 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (631 bp):
TAAGCCCTATTGTGTAGGCTTGGACAATCTCTGATTCGGGCACTCCTTCTACTTCCATGCAGGCA
TTCTAGAAACACTTGGCGTAACCCTCTAGGGGCTCCTCCAATCCTTGCCGTATGCTTAGGAGGTG
CAGGCTTATTTTTCCTACTGCCATACGGCTGTGGAAGCCTGAGAAGAATTGTCGAGCCAATTGCT
CAAAACTTGTGATGGAGAGATCCTCTAATTTGTGATACCATGTCAGAGCTGGTCCGACGAGTGTC
AATGGGAAGGCTCTGCAATACATGGAATCTGTAGCAAGCTGCATTTACATGGTGGCCTTAAAATG
AGAGAGGTGCTCTCTGGGGTCTTCGGTTCCATTGTACTTCATTTTTGGTACCTTAAAGTTTAGAG
GGGCCTGCTCTCTCTGAATTTCTACTGACAAGGGGCAGCTGTGGGAGTTCATGAATTCCCAAACA
TCCGTATCGCCCCTTGCCCTTGCCTCACGCTCTCGGCGTGCGCCTTCCTCCATCTCGGCGAGCTT
ATGTTCAAGTCTATTGATTTTGTCGAGCAATGGGGCGGCCATTGCCTCCGTTAGATTCTGTGATG
CATTCTCAGTCAAGTTTTCCCTCGGTCCTCTGTTAAGCCCTATTGC
Found at i:41815 original size:2 final size:2
Alignment explanation
Indices: 41808--41833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41798 TAATATTTAG
41808 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41834 CCCAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42291 original size:55 final size:56
Alignment explanation
Indices: 42207--42314 Score: 173
Period size: 55 Copynumber: 1.9 Consensus size: 56
42197 ATGGATATGC
* * *
42207 CCATTCCTAAATTGACACAAATTAATAACTTGGTGT-CCCTTAGAGATTGAGATGG
1 CCATTCCTAAATTAACACAAACTAATAACTTGGTGTCCCCTAAGAGATTGAGATGG
*
42262 CCATTCCTAAATTAACACAAACTAATAACTTGGTGTCCCCTAAGAGCTTGAGA
1 CCATTCCTAAATTAACACAAACTAATAACTTGGTGTCCCCTAAGAGATTGAGA
42315 GATTAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
55 34 0.71
56 14 0.29
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (56 bp):
CCATTCCTAAATTAACACAAACTAATAACTTGGTGTCCCCTAAGAGATTGAGATGG
Found at i:54603 original size:19 final size:19
Alignment explanation
Indices: 54579--54617 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54569 GCTAAGATAG
54579 GCTTTAGGTTGTTGTGAGA
1 GCTTTAGGTTGTTGTGAGA
54598 GCTTTAGGTTGTTGTGAGA
1 GCTTTAGGTTGTTGTGAGA
54617 G
1 G
54618 AATCACCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.38, T:0.41
Consensus pattern (19 bp):
GCTTTAGGTTGTTGTGAGA
Found at i:54816 original size:2 final size:2
Alignment explanation
Indices: 54809--54843 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54799 AAACATGATT
54809 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54844 GCTTGATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55901 original size:198 final size:198
Alignment explanation
Indices: 55623--56025 Score: 779
Period size: 198 Copynumber: 2.0 Consensus size: 198
55613 AATATATTAT
* *
55623 ATAATATCTATATACTATATAAGTTTAAACTTAAAAAATCTTGACCTGAAATATCTGAAATATCC
1 ATAA-ATCTATATACTATATAAGTCTAAACTTAAAAAACCTTGACCTGAAATATCTGAAATATCC
55688 TTCTTTATCTTTAACTTTTAAGGTTTAATATGTAATTTTATTTATCAATTAAATATATTAAAAAT
65 TTCTTTATCTTTAACTTTTAAGGTTTAATATGTAATTTTATTTATCAATTAAATATATTAAAAAT
55753 TCTAATTTCCTTACACGAAGTCTTCCTCTAATGATAAATTTCTTACTTTTGCTTCATCCGTAAAT
130 TCTAATTTCCTTACACGAAGTCTTCCTCTAATGATAAATTTCTTACTTTTGCTTCATCCGTAAAT
55818 AATA
195 AATA
55822 ATAAATCTATATACTATATAAGTCTAAACTTAAAAAACCTTGACCTGAAATATCTGAAATATCCT
1 ATAAATCTATATACTATATAAGTCTAAACTTAAAAAACCTTGACCTGAAATATCTGAAATATCCT
55887 TCTTTATCTTTAACTTTTAAGGTTTAATATGTAATTTTATTTATCAATTAAATATATTAAAAATT
66 TCTTTATCTTTAACTTTTAAGGTTTAATATGTAATTTTATTTATCAATTAAATATATTAAAAATT
55952 CTAATTTCCTTACACGAAGTCTTCCTCTAATGATAAATTTCTTACTTTTGCTTCATCCGTAAATA
131 CTAATTTCCTTACACGAAGTCTTCCTCTAATGATAAATTTCTTACTTTTGCTTCATCCGTAAATA
56017 ATA
196 ATA
56020 ATAAAT
1 ATAAAT
56026 AAATAAGGTA
Statistics
Matches: 202, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
198 198 0.98
199 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.42
Consensus pattern (198 bp):
ATAAATCTATATACTATATAAGTCTAAACTTAAAAAACCTTGACCTGAAATATCTGAAATATCCT
TCTTTATCTTTAACTTTTAAGGTTTAATATGTAATTTTATTTATCAATTAAATATATTAAAAATT
CTAATTTCCTTACACGAAGTCTTCCTCTAATGATAAATTTCTTACTTTTGCTTCATCCGTAAATA
ATA
Done.