Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024495.1 Corchorus olitorius cultivar O-4 contig24528, 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: 8741
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1435 original size:21 final size:21
Alignment explanation
Indices: 1411--1586 Score: 259
Period size: 21 Copynumber: 8.4 Consensus size: 21
1401 CTTAGGCAAT
*
1411 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
1432 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
1453 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
1474 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
1495 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
*
1516 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
1537 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
1558 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
1579 TCCAATGA
1 TCCAATGA
1587 ACTTCTAGCA
Statistics
Matches: 146, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.04
21 137 0.94
22 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:1495 original size:63 final size:63
Alignment explanation
Indices: 1411--1590 Score: 301
Period size: 63 Copynumber: 2.9 Consensus size: 63
1401 CTTAGGCAAT
* *
1411 TCCAATGAGCTTGAAACCTTCTCCAATGATCTTGGAACCTT-CTCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAACCTTC
*
1474 TCCAATGAACTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
1537 TCCAATGAGCTTGGAA-CTTGCTCCAATGAGCTTGGAACTTGCTCCAATGAACTT
1 TCCAATGAGCTTGGAACCTT-CTCCAATGAGCTTGGAACTTGCTCCAATGAACTT
1591 CTAGCATCTT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
62 6 0.05
63 105 0.95
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (63 bp):
TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
Found at i:1807 original size:68 final size:68
Alignment explanation
Indices: 1694--1893 Score: 314
Period size: 68 Copynumber: 3.0 Consensus size: 68
1684 GGCGCATCAT
* * * *
1694 TTTC-CACAAGCCAAACTCGTTTCAACATGAGCCAGTTAAGTCTTGGTTCCATCCAAGCATCAGG
1 TTTCTCACAAGCCAAACTCGTTTCCACACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGG
*
1758 GGC
66 AGC
1761 TTTCTCACAAGCCAAACTCGTTTCCACACGAGCCTA-TTAAGCCTTGGTTCCATCCAAGCAGCAG
1 TTTCTCACAAGCCAAACTCGTTTCCACACGAGCC-AGTTAAGCCTTGGTTCCATCCAAGCAGCAG
1825 GAGC
65 GAGC
* *
1829 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTAGTTCCATCCAAGCAGCAGG
1 TTTCTCACAAGCCAAACTCGTTTCCACACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGG
1894 CGTGATACGA
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
67 5 0.04
68 117 0.95
69 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (68 bp):
TTTCTCACAAGCCAAACTCGTTTCCACACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGG
AGC
Found at i:3146 original size:47 final size:47
Alignment explanation
Indices: 3026--3469 Score: 444
Period size: 47 Copynumber: 9.4 Consensus size: 47
3016 ATCCAGGTAA
* * * *
3026 TCTTCTCTCACTTCCATGCGAGTCTACAATTTAATGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* ** *** * *
3073 GCTTTTCTCATTTCTGTGCGAATCTACAAGTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* * * *
3120 TCTTTTCTCGCTTCCACACGAGTCTACGATTTGGCGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* * *
3167 TCTTTGCTCGCTTCCACGCGAGTCTA-AGATTTGGCGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACA-ATTTAGTGACCAAAGTTGG
* * * * * *
3214 TCGTTTCTCACTTCCACGTGAGTTTGCAATATAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* *
3261 TCTTTTCTCGCTTCCATGCGAGTCTACAGTTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
** * * * *
3308 TCTTTTCTCGCTTCCACATGAGTTTGCAATATAGTGACCAAAGTTTG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* * * *
3355 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGCGACCAAAGTTGC
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* ** * * * *
3402 TCTTTTCTCACTTCCACGTAAGTTTGCAATATCT-TTGACAAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAAT-T-TAGTGACCAAAGTTGG
3450 T-TTTTCTCGCTTCCACGCGA
1 TCTTTTCTCGCTTCCACGCGA
3470 ATCTCAAGTT
Statistics
Matches: 322, Mismatches: 71, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
47 308 0.96
48 13 0.04
49 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
Found at i:3349 original size:188 final size:188
Alignment explanation
Indices: 3031--3479 Score: 598
Period size: 188 Copynumber: 2.4 Consensus size: 188
3021 GGTAATCTTC
* * * * * * ** **
3031 TCTCACTTCCATGCGAGTCTACAATTTAATGACCAAAGTTGGGCTTTTCTCATTTCTGTGCGAAT
1 TCTCACTTCCACGTGAGTTTGCAATATAATGACCAAAGTTGGTCTTTTCTCGCTTCCATGCGAAT
* * *
3096 CTACAAGTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACACGAGTCTACGATTTGGCGACCAA
66 CTACAAGTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACACGAGTCTACAATATAGCGACCAA
*
3161 AGTTGGTCTTTGCTCGCTTCCACGCGAGTCTAAGATTTGGCGACCAAAGTTGGTCGTT
131 AGTTGGTCTTTGCTCGCTTCCACGCGAGTCTAAGATTTGGCGACCAAAGTTGCTCGTT
* *
3219 TCTCACTTCCACGTGAGTTTGCAATATAGTGACCAAAGTTGGTCTTTTCTCGCTTCCATGCGAGT
1 TCTCACTTCCACGTGAGTTTGCAATATAATGACCAAAGTTGGTCTTTTCTCGCTTCCATGCGAAT
* * * *
3284 CTAC-AGTTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACATGAGTTTGCAATATAGTGACCA
66 CTACAAG-TTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACACGAGTCTACAATATAGCGACCA
* * * *
3348 AAGTTTGTCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGCGACCAAAGTTGCTCTTT
130 AAGTTGGTCTTTGCTCGCTTCCACGCGAGTCTAAGATTTGGCGACCAAAGTTGCTCGTT
* ** * *
3407 TCTCACTTCCACGTAAGTTTGCAATATCTTTGACAAAAGTTGGT-TTTTCTCGCTTCCACGCGAA
1 TCTCACTTCCACGTGAGTTTGCAATAT-AATGACCAAAGTTGGTCTTTTCTCGCTTCCATGCGAA
3471 TCT-CAAGTT
65 TCTACAAGTT
3480 GACCTCAGAA
Statistics
Matches: 228, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
187 5 0.02
188 210 0.92
189 13 0.06
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (188 bp):
TCTCACTTCCACGTGAGTTTGCAATATAATGACCAAAGTTGGTCTTTTCTCGCTTCCATGCGAAT
CTACAAGTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACACGAGTCTACAATATAGCGACCAA
AGTTGGTCTTTGCTCGCTTCCACGCGAGTCTAAGATTTGGCGACCAAAGTTGCTCGTT
Found at i:3670 original size:21 final size:21
Alignment explanation
Indices: 3644--3756 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
3634 TGCTAGAAGT
3644 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
3665 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
3686 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
3707 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
3728 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
3749 TCATTGGA
1 TCATTGGA
3757 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:4957 original size:37 final size:40
Alignment explanation
Indices: 4885--4963 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 40
4875 CCCACTTTAT
*
4885 CATTTAATTGAGCCCAAACTTATTAAGCTTTAGTCCA-TTTTC
1 CATTTAATTGAGCCCAAACTTATT-A--TTAAGTCCAGTTTTC
4927 CATTTAATTGAGCCCAAACTTA-T-TTAAGTCCAGTTTT
1 CATTTAATTGAGCCCAAACTTATTATTAAGTCCAGTTTT
4964 GCAAGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
37 8 0.23
38 4 0.11
41 1 0.03
42 22 0.63
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (40 bp):
CATTTAATTGAGCCCAAACTTATTATTAAGTCCAGTTTTC
Done.