Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010980.1 Corchorus olitorius cultivar O-4 contig11012, 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, 829
Length: 1383
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Found at i:485 original size:155 final size:154
Alignment explanation
Indices: 1--1135 Score: 1682
Period size: 155 Copynumber: 7.3 Consensus size: 154
* *
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
* *
66 ATTGTAGTTAGTCCATAAACAATGGAAAG-AAAGACTTTGAGCTTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAG-CTTTGAGGTTTGCCAAATCGAAGACGATTC
**
130 -AAACGGAACTAATGGGCCCCGATA
130 AAAACGTCACTAATGGGCCCCGATA
* * *
154 GGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATCATAGTGGACCTAATCCCTCACCAAA
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGA-CTAAT--CTCACCAAA
* *
219 ATCGTAGTTATAGTTAGTCCATAAA-AATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGTAGAC
63 AT-G-A-TTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
283 GATTCAAAACGTCACTAATGGGCCCCGATA
125 GATTCAAAACGTCACTAATGGGCCCCGATA
* *
313 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
* * *
378 ATTGTAGTTAGTCCATAAACAATGGAAAGAATAGACTTTGAGCTTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAG-CTTTGAGGTTTGCCAAATCGAAGACGATTC
**
443 AAAACGGAACTAATGGGCCCCGATA
130 AAAACGTCACTAATGGGCCCCGATA
* * *
468 GGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATCATAGTGGACTAATCTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
* *
533 ATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGTAGACGATTCA
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
598 AAACGTCACTAATGGGGCCCCGGATA
131 AAACGTCACTAAT-GGGCCCC-GATA
* *
624 GGCCCGAAAATAACCAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
1 GGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAAT
*
689 GATTATAGTTAGTCCTATAAACAATGGAAAGTAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
65 GATTATAGTTAGTCC-ATAAACAATGGAAAG-AAAAGCTTTGAGGTTTGCCAAATCGAAGACGAT
* ** *
754 TCAAAATGGAACTAGTGGGCCCCGATA
128 TCAAAACGTCACTAATGGGCCCCGATA
* * *
781 GGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAGCTTCACAGTGGACTAATCTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
* * * *
846 ATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCA
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
911 AAACGTCACTAATGGGCCCCGATA
131 AAACGTCACTAATGGGCCCCGATA
* * * * *
935 GGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTAGCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
* * * * *
1000 ATTATAGTTAGCCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCA
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
1065 AGAACGTCACTAATGGGCCCCGATA
131 A-AACGTCACTAATGGGCCCCGATA
* *
1090 GGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTG
1136 CCATCTCCAT
Statistics
Matches: 899, Mismatches: 67, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
153 62 0.07
154 232 0.26
155 233 0.26
156 99 0.11
157 79 0.09
158 64 0.07
159 130 0.14
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (154 bp):
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
AAACGTCACTAATGGGCCCCGATA
Found at i:755 original size:313 final size:309
Alignment explanation
Indices: 1--1118 Score: 1735
Period size: 313 Copynumber: 3.6 Consensus size: 309
*
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* *
66 ATTGTAGTTAGTCCATAAACAATGGAAAG-AAAGACTTTGAGCTTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGACATTGAGCTTTGCCAAATCGAAGACGATTC
130 -AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
131 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
*
194 ATAGTGGACCTAATCCCTCACCAAAATCGTAGTTATAGTTAGTCCAT-AAAAATGGAAAGAAAAA
196 ATAGTGGA-CTAAT--CTCACCAAAAT-G-A-TTATAGTTAGTCCATAAAAAATGGAAAGAAAAG
258 CTTTGAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGCCCCGATA
255 CTTTGAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGCCCCGATA
*
313 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* * *
378 ATTGTAGTTAGTCCATAAACAATGGAAAGAATAGACTTTGAGCTTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGACATTGAGCTTTGCCAAATCGAAGACGATTC
443 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
131 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
508 ATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGA
196 ATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGA
573 GGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGGCCCCGGATA
261 GGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAAT-GGGCCCC-GATA
* * *
624 GGCCCGAAAATAACCAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
1 GGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAAT
*
689 GATTATAGTTAGTCCTATAAACAATGGAAAGTAAAAG-CATTGAGGTTTGCCAAATCGAAGACGA
65 GATTATAGTTAGTCC-ATAAACAATGGAAAG-AAAAGACATTGAGCTTTGCCAAATCGAAGACGA
* * * *
753 TTCAAAATGGAACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAA-AAG
128 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAA-
* * * * * *
817 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCA
192 CATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCT
* *
882 TTGAGGTTTCCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATA
257 TTGAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGCCCCGATA
* * * * * *
935 GGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTAGCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* * * **
1000 ATTATAGTTAGCCCATAAACAATGGAAACAAAAG-CATCGAGGGTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGACATTGAGCTTTGCCAAATCGAAGACGATTC
** *
1064 AAGAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
131 AA-AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAG
1119 TTAAAAACTT
Statistics
Matches: 760, Mismatches: 36, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
308 50 0.07
309 122 0.16
310 77 0.10
311 28 0.04
312 172 0.23
313 235 0.31
314 76 0.10
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (309 bp):
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGACATTGAGCTTTGCCAAATCGAAGACGATTC
AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
ATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGA
GGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGCCCCGATA
Found at i:907 original size:467 final size:467
Alignment explanation
Indices: 1--1135 Score: 1701
Period size: 467 Copynumber: 2.4 Consensus size: 467
*
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* *
66 ATTGTAGTTAGTCCATAAACAATGGAAAG-AAAGACTTTGAGCTTTGCCAAATCGAAGACGATTC
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAG-CTTTGAGGTTTGCCAAATCGAAGACGATTC
** * * *
130 -AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATC
130 AAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
194 ATAGTGGACCTAATCCCTCACCAAAATCGTAGTTATAGTTAGTCCATAAAAATGGAAAGAAAAAC
195 ACAGTGGACCTAAT-CCTCACCAAAATCGTAGTTATAGTTAGTCCATAAAAATGGAAAGAAAAAC
* * **
259 TTTGAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATA
259 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* * *
324 ACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATGTCACCAAAATGATTGTAGTTAG
324 ACAAGTGTTCCAAATAAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* * * * *
389 TCCATAAACAATGGAAAGAATAGACTTTGAGCTTTGCCAAATCGAAGACGATTCAAAACGGAACT
389 GCCATAAACAATCGAAAGAAAAGACATTGAGCTTTCCCAAATCGAAGACGATTCAAAACGGAACT
454 AATGGGCCCCGATA
454 AATGGGCCCCGATA
* * *
468 GGCCCAAAATAACAAGTGTACCAAATGAGCTAAGAACATCATAGTGGACTAATCTCACCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* *
533 ATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGTAGACGATTCA
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
*
598 AAACGTCACTAATGGGGCCCCGGATAGGCCCGAAAATAACCAGTGTTCCAAATGAGCTAAAAACT
131 AAACGTCACTAAT-GGGCCCC-GATAGGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACT
663 TCACAGTGGA-CTAAT-CTCACCAAAAT-G-A-TTATAGTTAGTCCTATAAACAATGGAAAGTAA
193 TCACAGTGGACCTAATCCTCACCAAAATCGTAGTTATAGTTAGTCC-ATAAA-AATGGAAAG-AA
* * *
723 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAGTGGGCCCCGATAGGCCCAA
255 AAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* * *
788 AATAACAAGTGTTCCAAATAAGCTAAAAGCTTCACAGTGGACTAATCTCACCAAAATGATTATAG
320 AATAACAAGTGTTCCAAATAAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATGATTATAG
* *
853 TTAGGCCATAAACAATCGAAAGAAAAG-CATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGT
385 TTAGGCCATAAACAATCGAAAGAAAAGACATTGAGCTTTCCCAAATCGAAGACGATTCAAAACGG
*
917 CACTAATGGGCCCCGATA
450 AACTAATGGGCCCCGATA
* * * * * *
935 GGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTAGCAAAATG
1 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
* * * * *
1000 ATTATAGTTAGCCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCA
66 ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
*
1065 AGAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC
131 A-AACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
1130 ACAGTG
195 ACAGTG
1136 CCATCTCCAT
Statistics
Matches: 606, Mismatches: 53, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
465 52 0.09
466 15 0.02
467 299 0.49
468 181 0.30
469 7 0.01
470 14 0.02
471 38 0.06
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (467 bp):
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCA
AAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACCTAATCCTCACCAAAATCGTAGTTATAGTTAGTCCATAAAAATGGAAAGAAAAACAT
TGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC
AAGTGTTCCAAATAAGCTAAAAACATCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATCGAAAGAAAAGACATTGAGCTTTCCCAAATCGAAGACGATTCAAAACGGAACTAA
TGGGCCCCGATA
Done.