Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020997.1 Corchorus olitorius cultivar O-4 contig21030, 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: 6963
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Found at i:2034 original size:39 final size:39
Alignment explanation
Indices: 1923--2359 Score: 359
Period size: 39 Copynumber: 11.2 Consensus size: 39
1913 AAAGAAGGAG
* * * *
1923 CTAAGCGGGTTTACATAAATAGGAAC-TCTAAGCAGAGAC
1 CTAAGCAGGTTTACTTAAA-CGAAACTTCTAAGCAGAGAC
* * * * *
1962 CTAAACAGTTTTACTCAGACGAAAC-TCTAAGCAGAGAA
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
* * *
2000 CTAAGCAGTTTTTTCTTAAACGAAACTTC-AAGCAGAGGC
1 CTAAGCAG-GTTTACTTAAACGAAACTTCTAAGCAGAGAC
* ** * *
2039 CTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGA-C
* * * *
2079 CTAAGCAGGTTTTTCTTAAACGAAA-GTCTAAGCAAAGGC
1 CTAAGCAGG-TTTACTTAAACGAAACTTCTAAGCAGAGAC
* ** * *
2118 CTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGA-C
*
2158 CTAAGCAGGTTTTTCTTAAACGAAAC-TCTAAGCAGATG-C
1 CTAAGCAGG-TTTACTTAAACGAAACTTCTAAGCAGA-GAC
* * * * *
2197 CTGAGCATGTCTACTTAAAGGCAAC-TCTAAGCAGAGAC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
* * * *
2235 CTAAGCAAGTTTTCTTAAACGAAAATTCTAAACAGAGAC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
* * *
2274 CTAAGCAGGTTTACCTAAACGAAACTT-TAAGCAGCGCC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
* * * **
2312 CTAAGCAGGTTTACTCAAACGAAAATTCCAAATAGAGAC
1 CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
2351 CTAAGCAGG
1 CTAAGCAGG
2360 CTTGATGGAA
Statistics
Matches: 312, Mismatches: 74, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
37 1 0.00
38 123 0.39
39 125 0.40
40 39 0.12
41 24 0.08
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (39 bp):
CTAAGCAGGTTTACTTAAACGAAACTTCTAAGCAGAGAC
Found at i:2102 original size:79 final size:78
Alignment explanation
Indices: 1949--2323 Score: 382
Period size: 79 Copynumber: 4.8 Consensus size: 78
1939 AAATAGGAAC
* * * * ** *
1949 TCTAAGCAGAGACCTAAACAGTTTTACTCAGACGAAACTCTAAGCAGAGAA-CTAAGCAGTTTTT
1 TCTAAGCAGAGGCCTAAACAGGTTTACTTAAAAAAAACTCTAAGCAGA-AACCTAAGCAGGTTTT
2013 TCTTAAACGAAACT
65 TCTTAAACGAAACT
*
2027 TC-AAGCAGAGGCCTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATCCTAAGCAGGTTT
1 TCTAAGCAGAGGCCTAAACAGGTTTACTTAAA-AAAAACTCTAAGCAGAAA-CCTAAGCAGGTTT
*
2091 TTCTTAAACGAAA-G
64 TTCTTAAACGAAACT
* *
2105 TCTAAGCAAAGGCCTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATCCTAAGCAGGTTT
1 TCTAAGCAGAGGCCTAAACAGGTTTACTTAAA-AAAAACTCTAAGCAGAAA-CCTAAGCAGGTTT
2170 TTCTTAAACGAAAC-
64 TTCTTAAACGAAACT
* * * * * *** * *
2184 TCTAAGCAGATGCCTGAGCATGTCTACTTAAAGGCAACTCTAAGCAGAGACCTAAGCAAG-TTTT
1 TCTAAGCAGAGGCCTAAACAGGTTTACTTAAAAAAAACTCTAAGCAGAAACCTAAGCAGGTTTTT
*
2248 CTTAAACGAAAAT
66 CTTAAACGAAACT
* * * * ** * ***
2261 TCTAAACAGAGACCTAAGCAGGTTTACCTAAACGAAACTTTAAGCAGCGCCCTAAGCAGGTTT
1 TCTAAGCAGAGGCCTAAACAGGTTTACTTAAAAAAAACTCTAAGCAGAAACCTAAGCAGGTTT
2324 ACTCAAACGA
Statistics
Matches: 254, Mismatches: 36, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
76 15 0.06
77 83 0.33
78 32 0.13
79 124 0.49
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (78 bp):
TCTAAGCAGAGGCCTAAACAGGTTTACTTAAAAAAAACTCTAAGCAGAAACCTAAGCAGGTTTTT
CTTAAACGAAACT
Found at i:2315 original size:77 final size:78
Alignment explanation
Indices: 1949--2359 Score: 384
Period size: 77 Copynumber: 5.3 Consensus size: 78
1939 AAATAGGAAC
* * * * * *
1949 TCTAAGCAGAGACCTAAACAGTTTTACTCAGACGAAACTCTAAGCAGAGAACTAAGCAGTTTTTT
1 TCTAAGCAGAGACCTAAACAGGTTTACTTAAACGAAACTTTAAGCAGAGACCTAAGCAGGTTTTT
*
2014 CTTAAACGAAACT
66 CTTAAACGAAAAT
* ** * *
2027 TC-AAGCAGAGGCCTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATCCTAAGCAGGTTT
1 TCTAAGCAGAGACCTAAACAGGTTTACTTAAACGAAACTT-TAAGCAGAGA-CCTAAGCAGGTTT
*
2091 TTCTTAAACG-AAAG
64 TTCTTAAACGAAAAT
* * ** * *
2105 TCTAAGCAAAGGCCTAAACAGGTTTACTTAAATAAAAATTCTAAGCAGAAATCCTAAGCAGGTTT
1 TCTAAGCAGAGACCTAAACAGGTTTACTTAAACGAAACTT-TAAGCAGAGA-CCTAAGCAGGTTT
*
2170 TTCTTAAACG-AAAC
64 TTCTTAAACGAAAAT
* * * * * * * *
2184 TCTAAGCAGATG-CCTGAGCATGTCTACTTAAAGGCAACTCTAAGCAGAGACCTAAGCAAG-TTT
1 TCTAAGCAGA-GACCTAAACAGGTTTACTTAAACGAAACTTTAAGCAGAGACCTAAGCAGGTTTT
2247 TCTTAAACGAAAAT
65 TCTTAAACGAAAAT
* * * * * *
2261 TCTAAACAGAGACCTAAGCAGGTTTACCTAAACGAAACTTTAAGCAGCGCCCTAAGCAGG-TTTA
1 TCTAAGCAGAGACCTAAACAGGTTTACTTAAACGAAACTTTAAGCAGAGACCTAAGCAGGTTTTT
*
2325 CTCAAACGAAAAT
66 CTTAAACGAAAAT
* ** *
2338 TCCAAATAGAGACCTAAGCAGG
1 TCTAAGCAGAGACCTAAACAGG
2360 CTTGATGGAA
Statistics
Matches: 284, Mismatches: 43, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
76 13 0.05
77 123 0.43
78 24 0.08
79 123 0.43
80 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (78 bp):
TCTAAGCAGAGACCTAAACAGGTTTACTTAAACGAAACTTTAAGCAGAGACCTAAGCAGGTTTTT
CTTAAACGAAAAT
Found at i:2619 original size:31 final size:31
Alignment explanation
Indices: 2581--2641 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2571 AAACTTCTAA
*
2581 ACAGAGACCTAAGCAGGTTTACTTGAACGGG
1 ACAGAGACCTAAGCAGGTTTACTTAAACGGG
*
2612 ACAGAGACCTAAGCAGGTTTGCTTAAACGG
1 ACAGAGACCTAAGCAGGTTTACTTAAACGG
2642 AAATTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (31 bp):
ACAGAGACCTAAGCAGGTTTACTTAAACGGG
Found at i:2684 original size:39 final size:40
Alignment explanation
Indices: 2612--2709 Score: 137
Period size: 39 Copynumber: 2.5 Consensus size: 40
2602 CTTGAACGGG
* *
2612 ACAGAGACCTAAGCAGG-TTTGCTTAAACGGAAATTCTAA
1 ACAGGGACCTAAGCAGGTTTTACTTAAACGGAAATTCTAA
* *
2651 ACAGGGACCTAAGCAGGTTTTACTTATAC-GAAATTCTGA
1 ACAGGGACCTAAGCAGGTTTTACTTAAACGGAAATTCTAA
*
2690 ACGGGGACCTAAGCAGGTTT
1 ACAGGGACCTAAGCAGGTTT
2710 GCTATGATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 44 0.83
40 9 0.17
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (40 bp):
ACAGGGACCTAAGCAGGTTTTACTTAAACGGAAATTCTAA
Done.