Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016395.1 Corchorus olitorius cultivar O-4 contig16428, 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: 51991
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:997 original size:31 final size:31
Alignment explanation
Indices: 962--1024 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
952 TATAATTCAA
962 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
1 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
993 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
1 CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
1024 C
1 C
1025 TAATATTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (31 bp):
CGCAAAAAGCATTGAAGGGTTTTTCACGCTT
Found at i:2009 original size:333 final size:332
Alignment explanation
Indices: 560--3027 Score: 3345
Period size: 333 Copynumber: 7.3 Consensus size: 332
550 GATTTCGGTT
* * * * * *
560 AAAAACTGACACGAAAAATTTTTTCTCAATGTTTTTTGCCACAACAGACATAAAAAATATATAAT
1 AAAAACTGACCCGAAAAATTTTTCCTC-AT-TGTTTTGCCACAACGGTCAGAAAAAATATATAAT
* * * *
625 TCAACACCAAAAAG-ATTGAAGGGTTTTTAACGCTTCTAATATTGTTTTTCCTTATATTT-CTGA
64 TCAAC-GCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTT-TTTTTCCTGA
* *
688 ATATATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAAACCTTAAATCAAATT
127 ATATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATT
*
753 TGGCTGAGATTTGGTTAGACTAATATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAA
192 TGGCTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAA
* * * *
818 ACTGAGCCGGGGCCCCGGAACGCGTTTTTATCCCGAAAATCGTGAAGGTTAGTACACGATTTCGG
257 ACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAA-CGTGATGGTCAGTACACGATTTCGG
883 CTAAAATTTTGC
321 CTAAAATTTTGC
* * * *
895 AAAAACTAACCCGAAAACTTTTTCCTCATTCTTTAGCCACAACGGTCAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
*
960 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCGCAAAAAGCATTGAAGGGTTTTTCACGCTTC
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTT---------C--T-AA-----TAT--CG----
* * * *
1025 TAATATTGTTTTTCTTTTTATTTCTGAATATATTTCTAATTAAATCGAAAAAATATTTAGATGCT
108 T--T-T----TTCCTTTTT-TTCCTGAATATATTTCTAATTAAATCGAAACAAGATTTAGATGCT
* *
1090 TGTAAAAACAAATTCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAACATAGATATTTTAAG
165 CGTAAAAACAAATCCTTAAATCAAATTTGGCTGAGATTTGGTTAGACTAACATAGATATTTTAAG
*
1155 GAGTCTTTCTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAAGCGTTTTTAGCCCGAAA
230 GAGTCTTTCTGTTAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAA
*
1220 ACCGTGATGGTCAGTACACGATTTCGGCTAAAATTTCGC
295 A-CGTGATGGTCAGTACACGATTTCGGCTAAAATTTTGC
* * *
1259 AAAAACTGACCCGAAAAATTCTTCCTCATTGTTTTGCCCCAACGGTCAGAAATAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
* *
1324 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTCCCGAATTT
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCTGAATAT
* * *
1388 ATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAAACCTTAAATCAAATTTGAC
131 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGGC
*
1453 TTAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAATATCATGCAAAACT
196 TGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAA-ATCATGCAAAACT
* ** * *
1518 GAGCCGAGGCCCCGAAACTTGTTTTTAGCCCGAAATC-CGA--G--A-TACACGATTTCGGCTAA
260 GAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACGTGATGGTCAGTACACGATTTCGGCTAA
1577 AATTTTGC
325 AATTTTGC
* * *
1585 ATAAACAGACCCAAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
* *
1650 AACGCAAAAAGCATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCTTTTTTTCCTGAATTT
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCTGAATAT
* * * * *
1715 ATTTCTAATTTAATCGAAACAAGATTTAGATGCTCCTAAAAACAAATCCTCAAATCCAATGTGGC
131 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGGC
* * * *
1780 TGGGATTTGGTTACA-TGAATATAGATATTTTAAGGAGTCTTTTTGTTAAAAATCATGCAAAACT
196 TGAGATTTGGTTAGACT-AACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAACT
* * * *
1844 GAGCCGGGGCCCTGGAACGCGTTTTTAGCCCGAAAATCGTGAAGGTTAGTACACGATTTCGGCTA
260 GAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAA-CGTGATGGTCAGTACACGATTTCGGCTA
1909 AAATTTTGC
324 AAATTTTGC
* * * *
1918 AAAAACTAACCCGAAAAGTTTTTCCTCATTCTTTAGCCACAACGGTCAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
* * *
1983 AATGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATTGTTTTT-CTTTTTATTTCTGAATA
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTT-TTCCTGAATA
* * *
2047 TATTTCTAATTAAATCGAAAAAATATTTAGATGCTCGTAAAAACAAATTCTTAAATCAAATTTGG
130 TATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGG
2112 CTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAACT
195 CTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAACT
** * *
2177 GAGCCGGGGCCCCGAAAATCGTTTTTAGCCCGAAAACCGTGATGGTCAGTAAACTATTTCGGCTA
260 GAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAA-CGTGATGGTCAGTACACGATTTCGGCTA
2242 AAATTTTGC
324 AAATTTTGC
* * *
2251 AAAAATTGACCTGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTTAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
*
2316 AACGCAAAAAGCATTGAAGGGTTTTTTACGCTTCTAATA------TTCCTTTTATTT-CTGAATA
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTT-TTTCCTGAATA
2374 TATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGG
130 TATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGG
*
2439 CTGAGATTTTGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAAAATCATGCAAAAC
195 CTGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTT-AAAAATCATGCAAAAC
** ** * *
2504 TGAATCGGGGCCCCGAAACTTGTTTGTAGCCCGAAAACTGTGATGGTAAGTACACGATTTCGGCT
259 TGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC-GTGATGGTCAGTACACGATTTCGGCT
2569 AAAATTTTGC
323 AAAATTTTGC
* * * *
2579 AAAAACTGACCCAAAAAATTTTTCCTCATTGATTTGCCACAACGGTCATAAAAAATGTATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
*
2644 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCCCCGAAT
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTT--CCTGAAT
* * * ** *
2709 TTATTTCTAATTAAATCGAAAGAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCGATGTG
129 ATATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTG
* * * * * * *
2774 GCTGGGATTTGGTTACA-TGAATATAGATATTTTAGGGAGTCTTTTTGTTACAAATCATTCAAAA
194 GCTGAGATTTGGTTAGACT-AACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAA
** * *
2838 CTGAGCCGGGGCCCCGAAACGCGTTTTTAGCTTGAAAACTGTGATGGTTAGTACACTATTTCGGC
258 CTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAAC-GTGATGGTCAGTACACGATTTCGGC
2903 TAAAATTTTGC
322 TAAAATTTTGC
* * *
2914 AAAAACTGATCCGAAAAATTTTTCCTCATTGTTTTGCCACAATGGTCAAAAAAAATATATAATTC
1 AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
*
2979 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCC
66 AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
3028 ATTTAATTTA
Statistics
Matches: 1897, Mismatches: 177, Indels: 118
0.87 0.08 0.05
Matches are distributed among these distances:
326 175 0.09
327 236 0.12
328 186 0.10
329 2 0.00
330 1 0.00
331 2 0.00
332 131 0.07
333 516 0.27
334 14 0.01
335 211 0.11
336 105 0.06
338 1 0.00
339 1 0.00
341 1 0.00
342 1 0.00
344 1 0.00
345 4 0.00
347 2 0.00
350 2 0.00
352 3 0.00
353 1 0.00
355 1 0.00
356 1 0.00
358 1 0.00
359 1 0.00
362 2 0.00
363 7 0.00
364 288 0.15
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
AAAAACTGACCCGAAAAATTTTTCCTCATTGTTTTGCCACAACGGTCAGAAAAAATATATAATTC
AACGCAAAAAGCATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCTGAATAT
ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCAAATTTGGC
TGAGATTTGGTTAGACTAACATAGATATTTTAAGGAGTCTTTCTGTTAAAAATCATGCAAAACTG
AGCCGGGGCCCCGAAACGCGTTTTTAGCCCGAAAACGTGATGGTCAGTACACGATTTCGGCTAAA
ATTTTGC
Found at i:37245 original size:18 final size:18
Alignment explanation
Indices: 37218--37259 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
37208 AGTTTATGAG
*
37218 TTTTATTTTA-AAATTTT
1 TTTTAATTTATAAATTTT
*
37235 ATTTTAATTTATATATTTT
1 -TTTTAATTTATAAATTTT
37254 TTTTAA
1 TTTTAA
37260 AAAATAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTAATTTATAAATTTT
Found at i:38035 original size:24 final size:23
Alignment explanation
Indices: 37981--38055 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
37971 CCCTTCCACA
*
37981 ATTTTTATTTTCTAATTTAGTCCCTT
1 ATTTTT-TTTT-TAATTT-GTCCCAT
*
38007 CTTTTTTTTTTAATTTGTCCCCAT
1 ATTTTTTTTTTAATTTGT-CCCAT
*
38031 ATTTTTTTATTTTAATTTGGCCCAT
1 A-TTTTTT-TTTTAATTTGTCCCAT
38056 TGATAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.05
24 10 0.24
25 15 0.36
26 15 0.36
ACGTcount: A:0.17, C:0.16, G:0.05, T:0.61
Consensus pattern (23 bp):
ATTTTTTTTTTAATTTGTCCCAT
Done.