Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017998.1 Corchorus olitorius cultivar O-4 contig18031, 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: 31489
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8583 original size:51 final size:52
Alignment explanation
Indices: 8482--8583 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
8472 GTTCATCAAA
* **
8482 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
8534 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
8584 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:10819 original size:112 final size:113
Alignment explanation
Indices: 10652--10905 Score: 314
Period size: 112 Copynumber: 2.3 Consensus size: 113
10642 GCGTTCCTAA
* * * * * *
10652 TCCAAAACGCCACTATATAGGGGTGTTTCAGGCTAAAAAAGCCACCATGTTTAATTTTTTCCTAG
1 TCCAAAACGCCACTATATGGGGGTGTTTAAGGATAAAAAAGCCACAATATATAATTTTTTCCTAG
* * * * *
10717 AAAT-TGAAATTTGGTAAGAATAAAGGCTAAAATTAGTGG-ATTTTTTT
66 AAATAT-AAATTTGGTAAAAATAAAGACTAAAATTAATGGCATTTCTAT
* * * *
10764 TCCAAAATGCCACTATATGGGGGCGTTTAAGGATAAAAACGCCACAATATATAATTTTTTCTTAG
1 TCCAAAACGCCACTATATGGGGGTGTTTAAGGATAAAAAAGCCACAATATATAATTTTTTCCTAG
* *
10829 AAATATAAATTTGGTAAAAATAACGACTAAAATTAATGGCGTTTCTAT
66 AAATATAAATTTGGTAAAAATAAAGACTAAAATTAATGGCATTTCTAT
* *
10877 TCAAAAACGCCACTATATGGAGGTGTTTA
1 TCCAAAACGCCACTATATGGGGGTGTTTA
10906 TGAGTAAATC
Statistics
Matches: 119, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
112 88 0.74
113 31 0.26
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (113 bp):
TCCAAAACGCCACTATATGGGGGTGTTTAAGGATAAAAAAGCCACAATATATAATTTTTTCCTAG
AAATATAAATTTGGTAAAAATAAAGACTAAAATTAATGGCATTTCTAT
Found at i:11001 original size:96 final size:96
Alignment explanation
Indices: 10824--11003 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 96
10814 ATAATTTTTT
* * *
10824 CTTAGAAATATAAATTTGGTAAAAATAACGACTAAAATTAATGGCGTTTCTATTCAAAAACGCCA
1 CTTAAAAATATAAATTTAGTAAAAATAAAGACTAAAATTAATGGCGTTTCTATTCAAAAACGCCA
*
10889 CTATATGGAGGTGTTTATGAGTAAATCTTTC
66 CTATATGGAGGCGTTTATGAGTAAATCTTTC
* * *
10920 CTTAAAAATATAAATTTAGTAAAAATAAAGACTAAAATTAGTGGCGTTTCTTTTTC-AAAATGCC
1 CTTAAAAATATAAATTTAGTAAAAATAAAGACTAAAATTAATGGCGTTTC-TATTCAAAAACGCC
*
10984 ACTATATGGGGGCGTTTATG
65 ACTATATGGAGGCGTTTATG
11004 GATAAAAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
96 71 0.95
97 4 0.05
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (96 bp):
CTTAAAAATATAAATTTAGTAAAAATAAAGACTAAAATTAATGGCGTTTCTATTCAAAAACGCCA
CTATATGGAGGCGTTTATGAGTAAATCTTTC
Found at i:11178 original size:111 final size:113
Alignment explanation
Indices: 10916--11194 Score: 409
Period size: 111 Copynumber: 2.5 Consensus size: 113
10906 TGAGTAAATC
* * *
10916 TTTCCTTAAAAATATAAATTTAGTAAAAATAAAGACTAAAATTAGTGGCGTTTCTTTTTCAAAAT
1 TTTCC-TAAAAATATAAATTTAATAAAAATAAAGACTAAAATTAGTGGCGTTTCTTTTCCAAAAC
* *
10981 GCCACTATATGGGGGCGTTTATGGATAAAAACACCACTATATATAATTT
65 GCCACTATATGGAGGCGTTTATGGATAAAAACACCACTATATATAACTT
* * *
11030 TTTCCTATAAATATAAATATAATAAAAATAAAGACTAAAATTAGTGGTGTTTCTTTTCCAAAACG
1 TTTCCTAAAAATATAAATTTAATAAAAATAAAGACTAAAATTAGTGGCGTTTCTTTTCCAAAACG
***
11095 CCACTATAT-GAGGCGTTTAT-GATAAAAATGGCACTATATATAACTT
66 CCACTATATGGAGGCGTTTATGGATAAAAACACCACTATATATAACTT
* * *
11141 TTTCCTAGAAATATAAATTTAATAAAAATAAATACTAAAATCAGTGGCGTTTCT
1 TTTCCTAAAAATATAAATTTAATAAAAATAAAGACTAAAATTAGTGGCGTTTCT
11195 ATTAAAAAAA
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
111 71 0.48
112 10 0.07
113 63 0.42
114 5 0.03
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (113 bp):
TTTCCTAAAAATATAAATTTAATAAAAATAAAGACTAAAATTAGTGGCGTTTCTTTTCCAAAACG
CCACTATATGGAGGCGTTTATGGATAAAAACACCACTATATATAACTT
Found at i:14544 original size:19 final size:18
Alignment explanation
Indices: 14493--14545 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
14483 AATTTTTTTT
*
14493 CTTCTTCTTCTTCTCGCG
1 CTTCTTCCTCTTCTCGCG
*
14511 CTTCTCCCTCATTCTCGAC-
1 CTTCTTCCTC-TTCTCG-CG
14530 CTTCTTCCTGCTTCTC
1 CTTCTTCCT-CTTCTC
14546 ATTATGCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.28
19 19 0.66
20 2 0.07
ACGTcount: A:0.04, C:0.43, G:0.08, T:0.45
Consensus pattern (18 bp):
CTTCTTCCTCTTCTCGCG
Found at i:22852 original size:23 final size:22
Alignment explanation
Indices: 22792--22877 Score: 104
Period size: 23 Copynumber: 3.9 Consensus size: 22
22782 TCTCACAGAG
* *
22792 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATTAAAATTTCATAGGA
* *
22813 AGGTTA-CAGAATTTCATAGGA
1 AGGTTATTAAAATTTCATAGGA
22834 AGGTTTATTAAAATTTCATAGGA
1 AGG-TTATTAAAATTTCATAGGA
22857 AGGCTTATTAAAATTTCATAG
1 AGG-TTATTAAAATTTCATAG
22878 TTAAGTTATC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 4 0.07
21 17 0.30
22 3 0.05
23 33 0.58
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.33
Consensus pattern (22 bp):
AGGTTATTAAAATTTCATAGGA
Found at i:22927 original size:29 final size:29
Alignment explanation
Indices: 22869--22927 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
22859 GCTTATTAAA
* * * *
22869 ATTTCATAGTTAAGTTATCAAAGTTTCAT
1 ATTTCATAGATAAATTATCAAAATTCCAT
22898 ATTTCATAGATAAATTATCAAAATTCCAT
1 ATTTCATAGATAAATTATCAAAATTCCAT
22927 A
1 A
22928 ACGTGGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (29 bp):
ATTTCATAGATAAATTATCAAAATTCCAT
Found at i:22937 original size:22 final size:22
Alignment explanation
Indices: 22898--23007 Score: 109
Period size: 22 Copynumber: 5.0 Consensus size: 22
22888 AAAGTTTCAT
*
22898 ATTTCAT-AGATAAATTATCAAA
1 ATTTCATAAGAT-AGTTATCAAA
* *
22920 ATTCCATAACG-TGGTTATCAAA
1 ATTTCATAA-GATAGTTATCAAA
*
22942 ATTTAATAAGATAGTTATCAAA
1 ATTTCATAAGATAGTTATCAAA
* *
22964 ATTTCATAAAGCTAATCTATCAAA
1 ATTTCAT-AAGATAGT-TATCAAA
22988 ATTTCAT-AGATAGTTATCAA
1 ATTTCATAAGATAGTTATCAA
23008 CATCCACCTG
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
21 7 0.10
22 42 0.58
23 8 0.11
24 15 0.21
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (22 bp):
ATTTCATAAGATAGTTATCAAA
Found at i:22972 original size:44 final size:45
Alignment explanation
Indices: 22898--23007 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 45
22888 AAAGTTTCAT
* * * **
22898 ATTTCATAGATAAATTATCAAAATTCCATAACG-TGGT-TATCAAA
1 ATTTAATAGAT-AGTTATCAAAATTCCATAAAGCTAATCTATCAAA
*
22942 ATTTAATAAGATAGTTATCAAAATTTCATAAAGCTAATCTATCAAA
1 ATTTAAT-AGATAGTTATCAAAATTCCATAAAGCTAATCTATCAAA
*
22988 ATTTCATAGATAGTTATCAA
1 ATTTAATAGATAGTTATCAA
23008 CATCCACCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
44 24 0.43
45 19 0.34
46 13 0.23
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (45 bp):
ATTTAATAGATAGTTATCAAAATTCCATAAAGCTAATCTATCAAA
Found at i:23045 original size:2 final size:2
Alignment explanation
Indices: 23032--23099 Score: 63
Period size: 2 Copynumber: 36.0 Consensus size: 2
23022 CTAAAACTAG
* * * * *
23032 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TT TC GA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23074 TA T- TA TA TA -A TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23100 GTAATACGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
1 4 0.08
2 49 0.92
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25728 original size:2 final size:2
Alignment explanation
Indices: 25721--25759 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
25711 GTCTCCACCC
25721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25760 AAGAAACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25774 original size:17 final size:17
Alignment explanation
Indices: 25754--25789 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25744 ATATATATAT
25754 ATTATAAAGAAACAATA
1 ATTATAAAGAAACAATA
25771 ATTATAAAGAAACAATA
1 ATTATAAAGAAACAATA
25788 AT
1 AT
25790 AGTAGGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (17 bp):
ATTATAAAGAAACAATA
Found at i:26827 original size:435 final size:433
Alignment explanation
Indices: 26075--27098 Score: 1104
Period size: 435 Copynumber: 2.3 Consensus size: 433
26065 CGCTTTACCT
* * * *
26075 TTTATTTTTGTATT-TTTTTTACTATTTGTCCGATTAAGGTGATTCAAGCGTCTATTAAAAGGTA
1 TTTATTTTTTTATTCTTTGTT-CTATTTGTCCAATTAA-GTGATTCAAGTGTCTATTAAAAGGTA
* * * *
26139 ATTTCATGATCTACAAATTTCATTTAAAACTCAAAAGTC-AATTTTAATGTTTTAATTGATCTAA
64 ATTTCATGATCTACAAATTTCA-TGAAGACTCAAAAG-CAAATTTTTATG--TCAATT--TCTAA
* * * * * *
26203 AAAATGCTTTTGAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCC
123 AAAATGCTTCTGAAATTTGGTCGTTTTGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCC
* * * * * *
26268 ACATCTCCGATTGAAGTTATTGAAGTGTTGGTTAAAATGTTATTTCATGATTTACGACTTTCATA
188 ACATCTCCAATTAAAGTTATTCAAGTGTTGGTTAAAATGTTATTTCATAATCTACGACTTTAATA
* ** ** *
26333 AAGGACCCGAAAGCTAAATTTGATCTATGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTT
253 AAGGACCCGAAAGCTAAATTTGATCTACGAGTTTAATGAAGAATTCAAAAGGAAATTTTTATGTT
* * * *
26398 TCAAGATCTCC-ATTAACAAAAATTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTT
318 TCAAGATCTCCAATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATCACCCT-ATACTTTT
* *
26462 CTACTTTA-GACTACTTAGTTCTTTACAAATTCTATC-TAATCAAACATTTAA-GC
382 CTACTTTATG-CTACTTAGTCCTTTACAAATTCTATCTTAATC---CATTTAACAC
*
26515 TTTATTTTTTTATTCTTTGTTCTATTTGTCCAATTAAGTTGATTCATGTGTCTATTAAAAGGTAA
1 TTTATTTTTTTATTCTTTGTTCTATTTGTCCAATTAAG-TGATTCAAGTGTCTATTAAAAGGTAA
*
26580 TTTCATGATCTACAAATTTCATGAAGGACTCAAAAGCAAATTTTTATGTCAA-TTCAAAAAAATG
65 TTTCATGATCTACAAATTTCATGAA-GACTCAAAAGCAAATTTTTATGTCAATTTCTAAAAAATG
** *
26644 CTTCCT-AAATTTGGTCGTTTTGATTGTTGGTTTATTTAATACCATATAA-TTTTCGATCCACAT
129 CTT-CTGAAATTTGGTCGTTTTGATTGCCGGTTAATTTAATACCATATAATTTTTCG-TCCACAT
* *
26707 GTCCAATTAAAGTTATTCAAGTGTTGGTTAACAGAT-TT-TTGT-ATAATCTACGACTTTAAT-G
192 CTCCAATTAAAGTTATTCAAGTGTTGGTTAA-A-ATGTTATT-TCATAATCTACGACTTTAATAA
** * *
26768 AGGAACCCGAAAG-TTTATTTGATTTACGAGTTTAATGAAGAATTGAAAAGGAAAATTTTTATGT
254 AGG-ACCCGAAAGCTAAATTTGATCTACGAGTTTAATGAAGAATTCAAAAGG-AAATTTTTATGT
*
26832 TTCAAGATCTCCATTAATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTATACT
317 TTCAAGATCTCC---AATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATCACCCTATACT
* * * *
26897 TTTCTATTTTATGCTACTTAGTCCTTTATAAATTCTATCTTACTCGATTTAACAC
379 TTTCTACTTTATGCTACTTAGTCCTTTACAAATTCTATCTTAATCCATTTAACAC
* * * *
26952 TTCATTTTTTTAATTTTCTTTGTTTTATTTTTGTCCAATTCAAGTAATTCAGGTGTCTATTAAAA
1 TTTATTTTTTT-A--TTCTTTGTTCTA--TTTGTCCAATT-AAGTGATTCAAGTGTCTATTAAAA
* * * * * * *
27017 GGTAATTTTATAATCTACAATTTTCAAGAAAGACTCAAAAACTAATTTTTATATTTCAATTTCTA
60 GGTAATTTCATGATCTACAAATTTCATG-AAGACTCAAAAGC-AAATTTT-TATGTCAATTTCTA
*
27082 AAAAATGCTTTTGAAAT
122 AAAAATGCTTCTGAAAT
27099 ATTGTGATTT
Statistics
Matches: 494, Mismatches: 61, Indels: 53
0.81 0.10 0.09
Matches are distributed among these distances:
434 37 0.07
435 132 0.27
436 11 0.02
437 14 0.03
438 42 0.09
439 50 0.10
440 102 0.21
441 5 0.01
442 64 0.13
443 11 0.02
444 8 0.02
445 18 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (433 bp):
TTTATTTTTTTATTCTTTGTTCTATTTGTCCAATTAAGTGATTCAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAAATTTCATGAAGACTCAAAAGCAAATTTTTATGTCAATTTCTAAAAAATGCT
TCTGAAATTTGGTCGTTTTGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCCACATCTCC
AATTAAAGTTATTCAAGTGTTGGTTAAAATGTTATTTCATAATCTACGACTTTAATAAAGGACCC
GAAAGCTAAATTTGATCTACGAGTTTAATGAAGAATTCAAAAGGAAATTTTTATGTTTCAAGATC
TCCAATTAACAAAAATTTTCTTATTTGAATTAGTTATCAAATCACCCTATACTTTTCTACTTTAT
GCTACTTAGTCCTTTACAAATTCTATCTTAATCCATTTAACAC
Found at i:29413 original size:22 final size:21
Alignment explanation
Indices: 29390--29440 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29380 ATAATTTCTA
*
29390 AAATCAGGGGTCAAATTGAAT
1 AAATCAGGGATCAAATTGAAT
* *
29411 AAAGCAGGGATCAAATTGCATT
1 AAATCAGGGATCAAATTG-AAT
29433 AAATCAGG
1 AAATCAGG
29441 AAATATACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (21 bp):
AAATCAGGGATCAAATTGAAT
Done.