Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017578.1 Corchorus olitorius cultivar O-4 contig17611, 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: 12166
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:986 original size:331 final size:330
Alignment explanation
Indices: 26--2216 Score: 2765
Period size: 331 Copynumber: 6.6 Consensus size: 330
16 TGGTTAGTTT
*
26 ACGATTTCGGCTAAAATTTTG-AAAAAAGTGA-CACGAAAAATTTTTCCGTCAA-TTTTGGCTAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAA-TGACCA-AAAAAATTTTTCCGTCAATTTTTGGCTAA
* *
88 AATACTCATAAAATACATATAATTTATCGCCAAAAATATTGGAGGACTCTTCACGCTTTTAATAT
64 AATACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATAT
*
153 CGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCGAAACAAGATTTAGATGCTCGTAAAA
129 CGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAA
* *
218 ACAAATCCTTAAATTCAATGTGGGT-GTTATTTGATTAGATGAATATAGATATTTCATGGAGTCT
194 ACAAATCCTTAAATTCAATGT-GGTAG-AAATTGATTAGATGAATATAGATATTTCATGGAGTCT
* *
282 CGGTGCCAAAAGTCATGCAAAACGAAGCTGGGGCCCTGAAACGCCTTTTTAGCCAAAATCTGTGA
257 CGGTGCCAAAA-TCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCCAAAATCTGTGA
347 T--TTAACGTAC
321 TAGTT-A-GTAC
* * **
357 ACGATTTCGGCTAAAATTTTACAAAAAATGACCAAAAAATATTTTTCTGTCAATTTTTGTATAAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAA-ATTTTTCCGTCAATTTTTGGCTAAA
* * * * * * *
422 ATACTCATAAAATATATATAATTAAATGTCAAAAAAAGATTGGAGTATTTTTCACGCTTTTAATA
65 ATACTCATAAAATACATATAATTTAACG-C-CAAAAATATTGGAGGACTTTTCACGCTTTTAATA
* ** * * *
487 TAGTTTTTCATATTTTTTTGAATTAAACTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
128 TCGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAA
* * * *
552 AACAAATACTTAAATTCAATGTGGCAGAAATTGATTAGATGAATATAGATATTTCATGGAGTATT
193 AACAAATCCTTAAATTCAATGTGGTAGAAATTGATTAGATGAATATAGATATTTCATGGAGTCTC
* * * *
617 GGTGCCGAAAATCATGCAAAATTAAGTTGGGACCCCGAAACGCCTTTTTAGCCAAAATTTGTGAT
258 GGTGCC-AAAATCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCCAAAATCTGTGAT
682 AGTTAGTAC
322 AGTTAGTAC
* ** * *
691 ACGATTTCGGCTAAAATTTTGCAAAAAGTGACCCGAAAAATTATTCCGTCAATTTTTGGTTAAAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAAATTTTTCCGTCAATTTTTGGCTAAAA
* * *
756 TACTCATGAAATACATATAATTTAACGCCAAAAATATTGGAGGGCTTTTAACGCTTTTAATATCG
66 TACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCG
* *
821 TTTTTCATA-TTTTTTGAATTAATTTATAATCAAATCAAAAAAAGATTTAGATACTCGTAAAAAC
131 TTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAAAC
* * * *
885 AAATCCTTAAATTCAATGTGGTTGATATTTGATTAGATGAATATAGATATTTCATGGAGTGTCAG
196 AAATCCTTAAATTCAATGTGGTAGA-AATTGATTAGATGAATATAGATATTTCATGGAGTCTCGG
* * * * * *
950 TGCCACAAATAATACAAAACTAAGCCGGGGCCCCGAAACGTCTTTTTAGTCAAAATCTGTGACAG
260 TGCCA-AAATCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCCAAAATCTGTGATAG
1015 TTAGTAC
324 TTAGTAC
* * * ***
1022 ACGATTTCGGCTAAAGTTTTACAAAAAATGACCAAAAAAACTTTTCTACCAATTTTTGGCTAAAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAAATTTTTCCGTCAATTTTTGGCTAAAA
* * * * * * **
1087 TACTCATAAAATATATATAATTAAATGTCAAAAAAAGAGTGGAATACTTTTCACGCTTTTAATAT
66 TACTCATAAAATACATATAATTTAACG-C-CAAAAATATTGGAGGACTTTTCACGCTTTTAATAT
* * *
1152 CGTTTTTCATA-TTTTTTGAATTTATTTCTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAA
129 CGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAA
* * *
1216 A-AAATACTTAAATTCAATGTGGTAGAAATTGATAAGATGAATATAGATATTTCTTGGAGTCTCG
194 ACAAATCCTTAAATTCAATGTGGTAGAAATTGATTAGATGAATATAGATATTTCATGGAGTCTCG
* ** * * * * **
1280 GCGGTAAAAATCATGCAAAACTAAGCGGGGGTCCCGAAACGCGTTTTTAGCCAAAAAACCATGAT
259 G-TGCCAAAATCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCC-AAAATCTGTGAT
*
1345 GGTTAGTAC
322 AGTTAGTAC
* * *
1354 ATGATTTCGACT-AAATTTTGCAAAAAGTGACCAAAAAAATTTTTCCGTCAATTTTTGG------
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAAATTTTTCCGTCAATTTTTGGCTAAAA
*
1412 ----C-TAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACACTTTTAATATCG
66 TACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCG
* *
1472 TTTTTTCATATTTTTTTGAATTATTTTATAATCAAATCGAAACAAGATTTAGATGCTCGTAAAAA
131 -TTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAAA
* * * *
1537 CAAATCCTTAAATTTAATGTGGTTGATATTTTATTAGATGAATATAGATATTTCATGGAGTCTCG
195 CAAATCCTTAAATTCAATGTGGTAGA-AATTGATTAGATGAATATAGATATTTCATGGAGTCTCG
* * *
1602 GTGCCGAAAATCATGTAAAACTAAGCTGGTG-TCCGAAACGCCTTTTTAGCCAAAATCTGTGATA
259 GTGCC-AAAATCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCCAAAATCTGTGATA
1666 GTTAGTAC
323 GTTAGTAC
* * * * *
1674 ATGATTTCGGCTAAAGTTTTACAAAAAACGACCAAAAAATATTTTTCTGTCAATTTTTGGCTAAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAA-ATTTTTCCGTCAATTTTTGGCTAAA
** * * * * *
1739 ATACTCATAAAATATGTATAATTAAATGTCAGAAAAAGATTGGAGTACTTTTCACGCTTTTAATA
65 ATACTCATAAAATACATATAATTTAACG-C-CAAAAATATTGGAGGACTTTTCACGCTTTTAATA
* * * * * *
1804 TAGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAA
128 TCGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAA
* * * *
1869 AACAAATACTTAAATTCAATGTGGCAGAAATTGATTTGATGAATATAGATATTTCAAGGAGTCTC
193 AACAAATCCTTAAATTCAATGTGGTAGAAATTGATTAGATGAATATAGATATTTCATGGAGTCTC
* * * *
1934 GGCGCCAAAAATCATGCAAAACTAAG-TCGGGGTCCCGAAACGCGTTTTTAGCCAAAAAAAATCC
258 GGTGCC-AAAATCATGCAAAACTAAGCT-GGGGCCCCGAAACGCCTTTTTAGCC----AAAATCT
* *
1998 ATGATGGTTAGTAC
317 GTGATAGTTAGTAC
* * *
2012 ACGATTTTCGGGTAATATTTTGCAAAAAATGTACC-GAAAAATTTTTCCGTCAATTTTTGGCTAA
1 ACGA-TTTCGGCTAAAATTTTGCAAAAAATG-ACCAAAAAAATTTTTCCGTCAATTTTTGGCTAA
*
2076 AATACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATAT
64 AATACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATAT
* *
2141 CGTTTTTCATAGTTATTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAA
129 CGTTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAA
2206 ACAAATCCTTA
194 ACAAATCCTTA
2217 GACCTTTCGT
Statistics
Matches: 1585, Mismatches: 231, Indels: 83
0.83 0.12 0.04
Matches are distributed among these distances:
318 31 0.02
319 10 0.01
320 95 0.06
321 64 0.04
322 76 0.05
330 71 0.04
331 349 0.22
332 75 0.05
333 242 0.15
334 228 0.14
335 146 0.09
336 100 0.06
337 1 0.00
338 69 0.04
339 25 0.02
340 3 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (330 bp):
ACGATTTCGGCTAAAATTTTGCAAAAAATGACCAAAAAAATTTTTCCGTCAATTTTTGGCTAAAA
TACTCATAAAATACATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCG
TTTTTCATATTTTTTTGAATTAATTTATAATCAAATCAAAACAAGATTTAGATGCTCGTAAAAAC
AAATCCTTAAATTCAATGTGGTAGAAATTGATTAGATGAATATAGATATTTCATGGAGTCTCGGT
GCCAAAATCATGCAAAACTAAGCTGGGGCCCCGAAACGCCTTTTTAGCCAAAATCTGTGATAGTT
AGTAC
Found at i:3415 original size:31 final size:31
Alignment explanation
Indices: 3379--3455 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
3369 ACGTGGCATG
* * *
3379 CCACGTGTACAAAAAAGCGACATATGGTACG
1 CCACGTGTACCAAAAAGCGACATATGGCACA
* *
3410 GCACGTGTACCAAAAAGCGACATGTGGCACA
1 CCACGTGTACCAAAAAGCGACATATGGCACA
3441 CCACGTGTACCAAAA
1 CCACGTGTACCAAAA
3456 GGTGACACGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (31 bp):
CCACGTGTACCAAAAAGCGACATATGGCACA
Found at i:4111 original size:45 final size:45
Alignment explanation
Indices: 4059--4148 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4049 TATTGTTTTT
*
4059 TTGTTAATCTCTTTGTTCTAATCTTTCTCTTGAGAATAGAAATTG
1 TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
4104 TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
1 TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
4149 CTGCGTATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (45 bp):
TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
Found at i:11015 original size:20 final size:20
Alignment explanation
Indices: 10970--11338 Score: 229
Period size: 20 Copynumber: 18.5 Consensus size: 20
10960 CATTGAGGGC
10970 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGCAAGTT
* *
10991 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGCAAGTT
* *
11011 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGCAAGTT
* *
11031 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGCAAGTT
* *
11051 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGCAAGTT
* * * * *
11072 CAATGTTATTTGGGAAATTT
1 CAATGTGAATTAGGCAAGTT
* *
11092 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGCAAGTT
* *
11112 CAATGTCAATT-GGGAATGTT
1 CAATGTGAATTAGGCAA-GTT
* *
11132 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGCAAGTT
*
11152 CAATGTGAATT-GGAAAAG-T
1 CAATGTGAATTAGG-CAAGTT
**
11171 GGATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGCAAGTT
* *
11192 C-ATGT-CATT-GGGAA-TT
1 CAATGTGAATTAGGCAAGTT
* *
11208 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGCAAGTT
*
11229 CAATGTCAATT-GG-AATGTT
1 CAATGTGAATTAGGCAA-GTT
*
11248 GAATGTG-ATTAAGGCAAGTT
1 CAATGTGAATT-AGGCAAGTT
* * *
11268 CAATGTCAATT-GGAAAATTT
1 CAATGTGAATTAGG-CAAGTT
* *
11288 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGCAAGTT
* * *
11309 CAATGTCAATTGGGAAAGTT
1 CAATGTGAATTAGGCAAGTT
**
11329 TTATGTGAAT
1 CAATGTGAAT
11339 GCGCTGCGTA
Statistics
Matches: 257, Mismatches: 71, Indels: 41
0.70 0.19 0.11
Matches are distributed among these distances:
16 2 0.01
17 8 0.03
18 7 0.03
19 31 0.12
20 148 0.58
21 59 0.23
22 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (20 bp):
CAATGTGAATTAGGCAAGTT
Found at i:11028 original size:40 final size:40
Alignment explanation
Indices: 10971--11338 Score: 514
Period size: 40 Copynumber: 9.2 Consensus size: 40
10961 ATTGAGGGCC
*
10971 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11012 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* * *
11052 AATGTGAATCAAGGCAAGTTCAATGTTATTTGGGAAATTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11093 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
11133 AATGTGAATAAGGCAAGTTCAATGTGAATTGGAAAAG-TG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11172 GATGTGAATTAAGGCAAGTTC-ATGTC-ATTGGG-AA-TTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11209 AATGTGAATCAAGGCAAGTTCAATGTCAATT-GGAATGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* * *
11249 AATGTGATTAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11289 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
11330 TATGTGAAT
1 AATGTGAAT
11339 GCGCTGCGTA
Statistics
Matches: 293, Mismatches: 24, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
36 1 0.00
37 22 0.08
38 12 0.04
39 38 0.13
40 139 0.47
41 81 0.28
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Done.