Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013949.1 Corchorus olitorius cultivar O-4 contig13982, 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: 16311
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:3422 original size:24 final size:25
Alignment explanation
Indices: 3386--3433 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3376 AGTAACAATA
*
3386 AAAATAAATAAACAAGA-AAATAAT
1 AAAATAAAGAAACAAGATAAATAAT
*
3410 AAAATTAAGAAACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
3434 ATACTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAT
Found at i:5840 original size:29 final size:31
Alignment explanation
Indices: 5800--5861 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
5790 ACGGAGACTC
5800 AAATTGAAAATTTA-AGGGGCAAAATGTCCA
1 AAATTGAAAATTTAGAGGGGCAAAATGTCCA
* *
5830 AAATTG-AAATTTAGGGGGGCAAAGTGTCCA
1 AAATTGAAAATTTAGAGGGGCAAAATGTCCA
5860 AA
1 AA
5862 TGCTATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (31 bp):
AAATTGAAAATTTAGAGGGGCAAAATGTCCA
Found at i:9460 original size:878 final size:878
Alignment explanation
Indices: 7611--9914 Score: 3800
Period size: 878 Copynumber: 2.6 Consensus size: 878
7601 AATTAAAAAT
** * * * * *
7611 AATTGTTGTATTCCGGATATCCCAAATTATAATCTACTAAATTGATCATGTAAGTGGAAGCAACT
1 AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGCAACT
* * *
7676 AAAATAATAAATCATTCACGTAAAAAAAAAAAGAATTTACGTGGTTCGTCACTGAACTTGCCTAC
66 AAAACAATAAATCATCCAC---AAAAAAAAAAGAATTTACGTGGTTCGGCACTGAACTTGCCTAC
*
7741 GTCCACGAAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAA
128 GTCCACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAA
*
7806 CTCTCACTCAATCTCTCAACCCAATCTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGT
193 CTCTCACTCAATCTCTCAACCCAATCTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGC
* *
7871 ACTCTCGCTCGATCTCTATTTGAGCACTCTTGCTCGGTCTATACAAACGAATAATCACACACACA
258 ACTCTCGCTCGGTCTCTATTTGAGCACTCTTGCTCGGTCTATACAAACGAACAATCACACACACA
7936 CCCATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATC
323 CCCATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATC
*
8001 TTTTCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATATTAGTACAAACTTAGCCTC
388 TTTTCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATACTAGTACAAACTTAGCCTC
* *
8066 CAAGAATCCCTTTCCTACTAGGATTCTTGATTACCAAATCATTTTATCCAACAAGCAATAGGCCT
453 CAAGAATCCCTTTCCTACTAGGATTCTTGATTACCAAGTCTTTTTATCCAACAAGCAATAGGCCT
*
8131 AAAAAAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAATCTCCACTTTGGC
518 -AAAAAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAATCTCCACCTTGGC
*
8196 TCAAATTCCATCAAATCTTCGATCTTCAATCAATCTTCAAGGACATGCATGGCTCCACCTACGAT
582 TCAAATTCCATCAAATCTTCAATCTTCAATCAATCTTCAAGGACATGCATGGCTCCACCTACGAT
*
8261 GAAAGTCTAACAATCTTCAAGCAATCTTCTCTTGTGTGTCTTCATCTTCGCTGCATCATCTTCAA
647 GAAAGTCTAACAATCTTCAAGCAATCTTCTCTTGTGTGTCTTCATCTTCACTGCATCATCTTCAA
8326 CTTTAATTCCGAATCCGATCTTGCTTTCCATCCAAATCTGAGCAATCTTCAAAACAATCATCAAG
712 CTTTAATTCCGAATCCGATCTTGCTTTCCATCCAAATCTGAGCAATCTTCAAAACAATCATCAAG
8391 CAGCACAATTTGGCAATCTCCACGACAACAAATCTGACGAACCATATCACAAGTTTAGACTACCG
777 CAGCACAATTTGGCAATCTCCACGACAACAAATCTGACGAACCATATCACAAGTTTAGACTACCG
* * * *
8456 GGTAATCTCCAATCCATTCAACCTGAGTTCGGATACC
842 GGCAACCTCCAATCCATTCAACCTAAGCTCGGATACC
*
8493 AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGTAACT
1 AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGCAACT
*
8558 AAAACAAAAAATCATCCA-AAAAAAAAAAGAATTTACGTGGTTCGGCACTGAACTTGCCTACGTC
66 AAAACAATAAATCATCCACAAAAAAAAAAGAATTTACGTGGTTCGGCACTGAACTTGCCTACGTC
8622 CACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAACTC
131 CACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAACTC
* *
8687 TCGCTCAATCTCTCAACCCAATTTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGCACT
196 TCACTCAATCTCTCAACCCAATCTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGCACT
*
8752 CTCGCTCGGTTTCTATTTGAGCACTCTTGCTCGGTCTATACAAACGAACAATCACACACACACCC
261 CTCGCTCGGTCTCTATTTGAGCACTCTTGCTCGGTCTATACAAACGAACAATCACACACACACCC
8817 ATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATCTTT
326 ATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATCTTT
8882 TCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATACTAGTACAAACTTAGCCTCCAA
391 TCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATACTAGTACAAACTTAGCCTCCAA
* *
8947 GAATCACTTCCCTACTAGGATTCTTGATTACCAAGTCTTTTTATCCAACAAGCAATAGGCCTAAA
456 GAATCCCTTTCCTACTAGGATTCTTGATTACCAAGTCTTTTTATCCAACAAGCAATAGGCCTAAA
9012 AAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAATCTCCACCTTGGCTCAA
521 AAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAATCTCCACCTTGGCTCAA
9077 ATTCCATCAAATCTTCAATCTTCAATCAATCTTCAAGGACATGCATGGCTCCACCTACGATGAAA
586 ATTCCATCAAATCTTCAATCTTCAATCAATCTTCAAGGACATGCATGGCTCCACCTACGATGAAA
*
9142 GTCTAACAATCTTCAAGCAATCTTCTCTTGTGTGTTTTCATCTTCACTGCATCATCTTCAACTTT
651 GTCTAACAATCTTCAAGCAATCTTCTCTTGTGTGTCTTCATCTTCACTGCATCATCTTCAACTTT
9207 AATTCCGAATCCGATCTTGCTTTCCATCCAAATCTGAGCAATCTTCAAAACAATCATCAAGCAGC
716 AATTCCGAATCCGATCTTGCTTTCCATCCAAATCTGAGCAATCTTCAAAACAATCATCAAGCAGC
*
9272 ACAATTTGGCAATCTCTACGACAACAAATCTGACGAACCATATCACAAGTTTAGACTACCGGGCA
781 ACAATTTGGCAATCTCCACGACAACAAATCTGACGAACCATATCACAAGTTTAGACTACCGGGCA
*
9337 ACCTCCAATCCATTCAA-TTCAAGCTCGGATACC
846 ACCTCCAATCCATTCAACCT-AAGCTCGGATACC
9370 AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGCAACT
1 AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGCAACT
*
9435 AAAACAATAAATCATCCACAAAAAAATAAGAATTTACGTGGTTCGGCACTGAACTTGCCTACGTC
66 AAAACAATAAATCATCCACAAAAAAAAAAGAATTTACGTGGTTCGGCACTGAACTTGCCTACGTC
9500 CACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAACTC
131 CACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAACTC
* * * *
9565 TCACTCAATCTCTCAACCCAATCTAACAATCAATCCTAAACCAAATCCAAATAATCTTGAGCACT
196 TCACTCAATCTCTCAACCCAATCTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGCACT
*** * ** * * * * *
9630 CTCGCTCGGTCTCTA-CAAACCAAC-AAT-CAC-ATCAAT-CAAAACAAACAATTACACACACAC
261 CTCGCTCGGTCTCTATTTGAGC-ACTCTTGCTCGGTCTATAC-AAACGAACAATCACACACACAC
* * *
9690 CCAT----A--A------------GTGGGGTGTCTCCACGCAAATCTAACACTTAGACTACATCT
324 CCATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATCT
* * * *
9737 TTTCTCAAAGCATA-AAAAAATTATAAAGAAACTCTCTATTTATACTAGCACAAACTTAGCCTCT
389 TTTCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATACTAGTACAAACTTAGCCTCC
*
9801 AAGAATCCCTTTCCTACTAGGATTCTTGATTACCAAGTCTTTTTGTCCAACAAGCAATAGGCCTA
454 AAGAATCCCTTTCCTACTAGGATTCTTGATTACCAAGTCTTTTTATCCAACAAGCAATAGGCCTA
* * *
9866 AAAAAATCCCAATCCAAATTTAATTAGGA-TT-ACTCAAAATCTTAACAAT
519 AAAAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAAT
9915 AATTGCCTAG
Statistics
Matches: 1350, Mismatches: 68, Indels: 36
0.93 0.05 0.02
Matches are distributed among these distances:
854 16 0.01
855 2 0.00
856 136 0.10
857 52 0.04
869 1 0.00
871 1 0.00
874 1 0.00
875 28 0.02
876 3 0.00
877 433 0.32
878 605 0.45
882 72 0.05
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (878 bp):
AATTGTTGTAACCCGGATATCCCAAACTATAATCTACCAAATTAATCATGCAAGCGGAAGCAACT
AAAACAATAAATCATCCACAAAAAAAAAAGAATTTACGTGGTTCGGCACTGAACTTGCCTACGTC
CACGGAGGAGAAGAGAAATCCACTAGTTATAGAAAATTACATCAACACATAATTATCAATAACTC
TCACTCAATCTCTCAACCCAATCTAACGATCAATTCTAAACCAAACCCAAACAATCTTGAGCACT
CTCGCTCGGTCTCTATTTGAGCACTCTTGCTCGGTCTATACAAACGAACAATCACACACACACCC
ATGAGGACCATCCTTTTCTCCTATGGGGTGCCTCCACCCAAATCTAACACTTAGACTACATCTTT
TCTCAAAGCATACAAAAAACTATAGAGAAACTCTCTATTTATACTAGTACAAACTTAGCCTCCAA
GAATCCCTTTCCTACTAGGATTCTTGATTACCAAGTCTTTTTATCCAACAAGCAATAGGCCTAAA
AAAATCCCAATCCAAATCTAATTAGGATTTGAGTCAAAATCCTAACAATCTCCACCTTGGCTCAA
ATTCCATCAAATCTTCAATCTTCAATCAATCTTCAAGGACATGCATGGCTCCACCTACGATGAAA
GTCTAACAATCTTCAAGCAATCTTCTCTTGTGTGTCTTCATCTTCACTGCATCATCTTCAACTTT
AATTCCGAATCCGATCTTGCTTTCCATCCAAATCTGAGCAATCTTCAAAACAATCATCAAGCAGC
ACAATTTGGCAATCTCCACGACAACAAATCTGACGAACCATATCACAAGTTTAGACTACCGGGCA
ACCTCCAATCCATTCAACCTAAGCTCGGATACC
Found at i:11274 original size:24 final size:25
Alignment explanation
Indices: 11225--11274 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
11215 ATTTTTCCTC
* *
11225 TTAATTTTTATTCATAAGTTAAAAA
1 TTAATTTTAATTCATAAGTGAAAAA
*
11250 TTAATTTTAATT-ATAAGTGATAAA
1 TTAATTTTAATTCATAAGTGAAAAA
11274 T
1 T
11275 GTATTAGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
TTAATTTTAATTCATAAGTGAAAAA
Found at i:12223 original size:16 final size:15
Alignment explanation
Indices: 12201--12244 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
12191 TTAAAGTTTG
*
12201 AATTCAGTACTTATGA
1 AATTCAGTACTTA-AA
*
12217 GATTCAGTA-TTAAA
1 AATTCAGTACTTAAA
12231 AATTCAGTACTTAA
1 AATTCAGTACTTAA
12245 TCTTTTAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AATTCAGTACTTAAA
Found at i:12541 original size:2 final size:2
Alignment explanation
Indices: 12530--12558 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12520 TTTTCTAAAC
12530 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12559 AGTTTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:15758 original size:60 final size:60
Alignment explanation
Indices: 15665--15826 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
15655 GCTAATTGCT
* * * * * **
15665 CAAATAAGGGCCTCACGTTTTCTAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTCGAATTTGGC
* *
15725 CAAATAAGGGTCTAACGTTTACCAAAATACTCAAATAAGGGCCCGATCTTCGAATTTGGC
1 CAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTCGAATTTGGC
* *
15785 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGC
15827 TTGGCGTCGA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTCGAATTTGGC
Found at i:15823 original size:31 final size:30
Alignment explanation
Indices: 15661--15826 Score: 97
Period size: 31 Copynumber: 5.5 Consensus size: 30
15651 AGAGGCTAAT
* * *
15661 TGCTCAAATAAGGGCCTCACGTTTTCTAAAA
1 TGCTCAAATAAGGGCCTAATG-TTTCCAAAA
* * * * **
15692 TGCTCAAATAAGGGTCTGATCTTT-TAATT
1 TGCTCAAATAAGGGCCTAATGTTTCCAAAA
* *
15721 TGGC-CAAATAAGGGTCTAACGTTTACCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTT-CCAAAA
* ** * * **
15752 TACTCAAATAAGGGCCCGAT-CTTCGAATT
1 TGCTCAAATAAGGGCCTAATGTTTCCAAAA
15781 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTT-CCAAAA
15812 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
15827 TTGGCGTCGA
Statistics
Matches: 99, Mismatches: 28, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
29 39 0.39
30 13 0.13
31 47 0.47
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAATGTTTCCAAAA
Found at i:15903 original size:31 final size:31
Alignment explanation
Indices: 15865--15958 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
15855 AACTGACGTA
15865 AGGCCCTTATTTGAGCATTTTCGATAAAGTT
1 AGGCCCTTATTTGAGCATTTTCGATAAAGTT
** *
15896 AGGCCCTTATTTG-GTCAAATT--A-AAAGAT
1 AGGCCCTTATTTGAG-CATTTTCGATAAAGTT
* * *
15924 CGGACCCTTATTAGAGCATTTTCGATAACGTT
1 AGG-CCCTTATTTGAGCATTTTCGATAAAGTT
15956 AGG
1 AGG
15959 TTCTCATTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
28 7 0.15
29 14 0.30
30 2 0.04
31 18 0.38
32 6 0.13
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAAAGTT
Found at i:15968 original size:60 final size:60
Alignment explanation
Indices: 15868--16028 Score: 234
Period size: 60 Copynumber: 2.7 Consensus size: 60
15858 TGACGTAAGG
* * *
15868 CCCTTATTTGAGCATTTTCGATAAAGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA
* * * *
15928 CCCTTATTAGAGCATTTTCGATAACGTTAGGTTCTCATTTGGCCAAATTAAAGGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA
*
15988 CCCTTATTTGAGCATTTTGGCA-AACGTTAGGCTCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCTCTTATTTG
16029 AACAATTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:16291 original size:2 final size:2
Alignment explanation
Indices: 16284--16311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16274 GTTCCACCTT
16284 TA 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 TA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.