Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012748.1 Corchorus olitorius cultivar O-4 contig12781, 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: 22509
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:430 original size:154 final size:154
Alignment explanation
Indices: 1--1031 Score: 1471
Period size: 154 Copynumber: 6.7 Consensus size: 154
*
1 CCAAAATAAACAAGTTTTCCTAAATAGAGCTAAAAACTTACACAGTGGACGTAATCTCACCAAAA
1 CCAAAAT-AACAAGTGTTCC-AAAT-GAGCTAAAAACTT-CACAGTGGAC-TAATCTCACCAAAA
* ** * *
66 TAGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGATTTGCCAAAT-TATGGACGA
61 T-GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGA-AGACGA
* * *
130 TTCAAAATGTCACTAATGGGCCCCGATAGAC
124 TTCAAAACGTCACTAAAGGGCCCCGATAGGC
* * *
161 CCAAAATAACAAGTGTTCTAATTGAGCT-AAAACTTCACAGTGGACTAATCTCACCAAAATGGTT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * * *
225 ATACTTTGGCCATAAACAATGGAGAGAAAAGCATAGA-GGTTAGGCAAATCGAAGACGATTCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT-GCCAAATCGAAGACGATTCAAA
*
289 ACGTCACTAAAGGCCCCCGATAGGC
130 ACGTCACTAAAGGGCCCCGATAGGC
*
314 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAGTCTCTA-CAAAATGAT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC-ACCAAAATGAT
* * * * *
378 TATAGTTAGACCATAAACAGTGGCAAGAAAAGCATCGAGGGTTGTCAAATCGAAGACGATTCAAA
65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
** * *
443 ACGGGACTAATGGGCCCCGATATG-
130 ACGTCACTAAAGGGCCCCGATAGGC
*
467 CCAAAATAACAAGTGTTCCAAATGATGCTATAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCAAAATAACAAGTGTTCCAAATGA-GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
532 TATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
*
597 ATGTCACTAAAGGGCCCCGATAGGC
130 ACGTCACTAAAGGGCCCCGATAGGC
* * * * *
622 CCAAAATAACAAGTTTTCCAAATCAGCTAAAAACTTCACTGTGGACTTATCTCACCAAATTGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* *
687 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAGTCGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
752 CGTCACTAAAGGGCCCCGATAGGC
131 CGTCACTAAAGGGCCCCGATAGGC
* *
776 CCAAAATAACAAGTGTTCCAAATGAGCT-AAAACATCACAGTGGACTAATCTCACCAAAATGATA
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * *
840 ATAGTTAGGTCATAATCAATGGAAAGAAAAGCATCGAGGGTTGCTAAATCGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
** *
905 CGGAACTAAATGGGCCCCGATAGTC
131 CGTCACTAAA-GGGCCCCGATAGGC
*
930 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTATTCTCACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
995 ATAGTTTGGCCATAAACAATGGAAAGAAAAGCATTGA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
1032 AGACGATTCA
Statistics
Matches: 780, Mismatches: 81, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
152 2 0.00
153 223 0.29
154 419 0.54
155 104 0.13
156 7 0.01
157 5 0.01
158 3 0.00
159 10 0.01
160 7 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
CGTCACTAAAGGGCCCCGATAGGC
Found at i:1840 original size:33 final size:32
Alignment explanation
Indices: 1802--1882 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 32
1792 ATTTCAAGTT
* *
1802 GTGGTGATTTTCTGTATCAATTTGAATCACTTG
1 GTGGTGATTTTCTGTATCAA-TTCAAACACTTG
* * *
1835 GTGGTGAGTTTC-G-ACCGATTCAAACACTTG
1 GTGGTGATTTTCTGTATCAATTCAAACACTTG
*
1865 GTGGTGATTTTCTCTATC
1 GTGGTGATTTTCTGTATC
1883 CTTGTGATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
30 21 0.55
31 3 0.08
32 3 0.08
33 11 0.29
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (32 bp):
GTGGTGATTTTCTGTATCAATTCAAACACTTG
Found at i:8404 original size:22 final size:22
Alignment explanation
Indices: 8379--8425 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
8369 AAATTTTGTT
8379 AAATAAA-TATTAAAGAT-ATAAA
1 AAATAAATTA-TAAA-ATAATAAA
8401 AAATAAATTATAAAATAATAAA
1 AAATAAATTATAAAATAATAAA
8423 AAA
1 AAA
8426 ATCAACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAAATTATAAAATAATAAA
Found at i:10095 original size:19 final size:20
Alignment explanation
Indices: 10059--10096 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10049 TCTCTTTATA
* *
10059 TACATATAAAAACTTAAATC
1 TACAAATAAAAACATAAATC
10079 TACAAATAAAAA-ATAAAT
1 TACAAATAAAAACATAAAT
10097 TTAACTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (20 bp):
TACAAATAAAAACATAAATC
Found at i:10764 original size:2 final size:2
Alignment explanation
Indices: 10759--10834 Score: 56
Period size: 2 Copynumber: 40.0 Consensus size: 2
10749 AAAGTTATTT
* * *
10759 TA TA TA TA TA TA TA TA TA TA TA TA TT TGA TT TGA TA TA -A TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA
*
10802 TA AA TA TA -A TA TA T- TA T- TA TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10835 CAATTATGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
1 6 0.10
2 50 0.86
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16365 original size:21 final size:21
Alignment explanation
Indices: 16324--16373 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
16314 TTTACCAGCA
* *
16324 TTATAAAGTTTTTTAATAACC
1 TTATTAAGTTTTTTAAGAACC
*
16345 TTATTAAGTTTTTTAGGAACC
1 TTATTAAGTTTTTTAAGAACC
*
16366 ATATTAAG
1 TTATTAAG
16374 GTCTTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (21 bp):
TTATTAAGTTTTTTAAGAACC
Found at i:16380 original size:21 final size:21
Alignment explanation
Indices: 16341--16380 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16331 GTTTTTTAAT
* * *
16341 AACCTTATTAAGTTTTTTAGG
1 AACCATATTAAGGTCTTTAGG
16362 AACCATATTAAGGTCTTTA
1 AACCATATTAAGGTCTTTA
16381 ATATATAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
AACCATATTAAGGTCTTTAGG
Found at i:18560 original size:2 final size:2
Alignment explanation
Indices: 18553--18667 Score: 194
Period size: 2 Copynumber: 56.5 Consensus size: 2
18543 CTCTCAAATA
*
18553 GT GT GT GT GT GT GT GT GT GT GT CCT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT -GT GT GT GT GT GT GT GT GT GT
18596 GT GT GT GT GT GT GT GT GT GT GCT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT G-T GT GT GT GT GT GT GT GT GT GT
*
18639 GT GT GT GT GT GT GT GT GT GT GT GT TT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
18668 ATTACCATAA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
2 104 0.97
3 3 0.03
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.50
Consensus pattern (2 bp):
GT
Found at i:19185 original size:21 final size:21
Alignment explanation
Indices: 19159--19203 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
19149 TCCAATCAAC
19159 CAAGAACCCTAATTTTGAACT
1 CAAGAACCCTAATTTTGAACT
*
19180 CAAGAACCCTAATTTTGAATT
1 CAAGAACCCTAATTTTGAACT
19201 CAA
1 CAA
19204 TGAGCTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (21 bp):
CAAGAACCCTAATTTTGAACT
Found at i:21250 original size:18 final size:18
Alignment explanation
Indices: 21227--21262 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21217 AAGTTGAGTC
*
21227 CTTTCCCAGGCCAAATGT
1 CTTTCCCAAGCCAAATGT
21245 CTTTCCCAAGCCAAATGT
1 CTTTCCCAAGCCAAATGT
21263 TTTGCACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (18 bp):
CTTTCCCAAGCCAAATGT
Found at i:22222 original size:21 final size:21
Alignment explanation
Indices: 22198--22294 Score: 142
Period size: 21 Copynumber: 4.6 Consensus size: 21
22188 CTTAGGCAAT
* *
22198 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
22219 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
22240 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
22261 TCCAATGAACTTGGAA-CTTGT
1 TCCAATGAACTTGGAACCTT-C
22282 TCCAATGAACTTG
1 TCCAATGAACTTG
22295 ATGAGTTCTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 3 0.04
21 68 0.96
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Done.