Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009710.1 Corchorus olitorius cultivar O-4 contig09742, 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: 6411
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2014 original size:275 final size:269
Alignment explanation
Indices: 1516--2803 Score: 1828
Period size: 275 Copynumber: 4.7 Consensus size: 269
1506 CTCTTCTTTA
*
1516 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGATATATT
1 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGAAATATT
*
1581 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGAAAAAGAACATCAAATTCAACATACA
66 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATT--ACATAC-
1646 ATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCCACC
128 A-ATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCCACC
1711 AATGTGACCTTTTTCTTTTTTTAAAAAAAAAAAACTTAAAGGTTAAA-AATTTTTCTAAAAAAAA
192 AATGTGACCTTTTTC-TTTTTT-AAAAAAAAAAACTTAAAGGTTAAATAA-TTTTCTAAAAAAAA
*
1775 GGTTGTTAACATGGTG
254 GGTTGTTAACATGGCG
1791 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGAAATATT
1 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGAAATATT
* * *
1856 CCCCACGTACTTTATATACAAAATCTAAAGTGAAATTTGGAAAAGAACATTAAATT-CA-AC-AT
66 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATTACATACAAT
* *
1918 AGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCTACCAACG
131 AGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCCACCAATG
*
1983 TGACCTAGCTTTTCTTTTTTTTAAAAAAAAAAACAAAAACTTAAAAGGTTAAATAATTTTTTAAA
196 TGACCT---TTTTC--TTTTTT-----AAAAAA-AAAAACTT-AAAGGTTAAATAATTTTCTAAA
* *
2048 ATAAAGGTTGTTAATATGGCG
249 AAAAAGGTTGTTAACATGGCG
* *
2069 TATAACACTGTCAATAATATTTAGCTTTACTAAAAAAAAATACGAAAATTTAGCAAATAAGAAAT
1 TATAACACTGTCAATAATATGTAGCTTTACT--AAAAAAA-ACGAAATTTTAGCAAATAAGAAAT
* *
2134 ATTCTCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAAAAACATCAAATTCAACA
63 ATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGG-AAAAGAACATCAAATT--ACA
2199 TACAATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATATATAAGGC
125 TAC-A-ATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGA-T--TA-ATAAGGC
*
2264 -TCCCACCAATGTGACCTTTTTC-TTTTT---AAAAAAAACTTAAAGGTTAAATAATTTTCT-AA
184 GCCCCACCAATGTGACCTTTTTCTTTTTTAAAAAAAAAAACTTAAAGGTTAAATAATTTTCTAAA
*
2323 AAAGAGGTTGTTAACATGGCG
249 AAAAAGGTTGTTAACATGGCG
*
2344 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAAAACTGAAATTTTAACAAATAAGAAAT
1 TATAACACTGTCAATAATATGTAGCTTTACT--AAAAAAAAC-GAAATTTTAGCAAATAAGAAAT
2409 ATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATTCAACAT
63 ATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATT--ACAT
*
2474 ACAATATAGAAGTAGAAAATTTTCGATCCACCAAATTCTTGTTGACGTGATTAATAAGGCGCCCC
126 AC-A-ATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCC
*
2539 ACCAATGTGACCTTTTTCTTTTTTAAACAAAAAAACTTAAAGGTTAAATAATTTTCTAAAAAAAA
189 ACCAATGTGACCTTTTTCTTTTTTAAAAAAAAAAACTTAAAGGTTAAATAATTTTCTAAAAAAAA
*
2604 GGTTGTTAACATGTCG
254 GGTTGTTAACATGGCG
* *
2620 TATAACACTGTCAATAATATATAGCTTTACT-AAAAAAACGAAAATTTAGCAAATAAGAAATATT
1 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGAAATATT
* * * *
2684 CCCCACGTACTTTATA-A-AAAATCTAAACTAAAATTTTGAAAAAAACCTCAAATTCAACATACA
66 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATT--ACATAC-
* * * *
2747 ATATAGAATTAGAAAATTTTTGATCCACCAAATTTATGTTGACGTAATTAATAAGGC
128 A-ATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGC
2804 TTGAAAGAGG
Statistics
Matches: 933, Mismatches: 47, Indels: 71
0.89 0.04 0.07
Matches are distributed among these distances:
268 71 0.08
270 101 0.11
271 31 0.03
272 53 0.06
273 9 0.01
274 72 0.08
275 266 0.29
276 76 0.08
277 16 0.02
278 69 0.07
279 2 0.00
280 7 0.01
281 63 0.07
282 14 0.02
285 2 0.00
286 7 0.01
289 50 0.05
290 1 0.00
292 16 0.02
293 7 0.01
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (269 bp):
TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGAAATATT
CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACATCAAATTACATACAAT
AGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCGCCCCACCAATG
TGACCTTTTTCTTTTTTAAAAAAAAAAACTTAAAGGTTAAATAATTTTCTAAAAAAAAGGTTGTT
AACATGGCG
Found at i:2852 original size:556 final size:547
Alignment explanation
Indices: 1516--2814 Score: 1760
Period size: 556 Copynumber: 2.4 Consensus size: 547
1506 CTCTTCTTTA
* * *
1516 TATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTAGCAAATAAGATATATT
1 TATAACACTGTCAATAATATATAGCTTTACTAAAAAAAACGAAAATTTAGCAAATAAGAAATATT
1581 CCCCACGTACTTTATACACAAAATCTAAACTGAAA-TTTGAAAAAGAACATCAAATTCAACATAC
66 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTTGAAAAA-AACATCAAATTCAACATAC
***
1645 AATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGC-GCCCCA
130 AATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCTG-AAAA
*** ** *
1709 ---CCAATGTGACCTTTTTCTTTTTTTAAAA--AAAAAAAACTTAAAGGTTAAAAATTTTTCTAA
194 GGTCCAAT-T-A-AAGTAAC-CTTTTTAAAATTAAAAAAAACTTAAAGGTTAAAAATTTTTCTAA
*
1769 AAAAAAGGTTGTTAACATGGTGTATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAA
255 AAAAAAGGTTGTTAACATGGCGTATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAA
* * *
1834 ATTTTAGCAAATAAGAAATATTCCCCACGTACTTTATATACAAAATCTAAAGTGAAATTTGGAAA
320 ATTTTAACAAATAAGAAATATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAA
*
1899 AGAACATTAAATTCAACATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTA
385 AGAACATCAAATTCAACATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTA
*
1964 ATAAGGCGCCCTACCAACGTGACCTAGCTTTTCTTTTTTTTAAAAAAAAAAACAAAAACTTAAAA
450 ATAAGGCGCCCCACCAACGTGACCTA--TTTTC-TTTTTTT----AAAAAAACAAAAACTTAAAA
* * *
2029 GGTTAAATAATTTTTTAAAATAAAGGTTGTTAATATGGCG
508 GGTTAAATAATTTTCTAAAAAAAAGGTTGTTAACATGGCG
*
2069 TATAACACTGTCAATAATATTTAGCTTTACTAAAAAAAAATACGAAAATTTAGCAAATAAGAAAT
1 TATAACACTGTCAATAATATATAGCTTTACT--AAAAAAA-ACGAAAATTTAGCAAATAAGAAAT
* *
2134 ATTCTCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAAAAACATCAAATTCAACA
63 ATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTTG-AAAAAAACATCAAATTCAACA
*
2199 TACAATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAAT-A---T-AT
127 TACAATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCTGAA
* ** * * ****
2259 AAGGCTCCCACCAATGTGACCTTTTTCTTTTTAAAAAAAACTTAAAGGTTAAATAA-TTTTCT-A
192 AAGG-TCCAATTAAAGTAACCTTTTTAAAATTAAAAAAAACTTAAAGGTTAAA-AATTTTTCTAA
*
2322 AAAAGAGGTTGTTAACATGGCGTATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAAAACT
255 AAAAAAGGTTGTTAACATGGCGTATAACACTGTCAATAATATGTAGCTTTACT--AAAAAAAAC-
2387 GAAATTTTAACAAATAAGAAATATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGG
317 GAAATTTTAACAAATAAGAAATATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGG
*
2452 AAAAGAACATCAAATTCAACATACAATATAGAAGTAGAAAATTTTCGATCCACCAAATTCTTGTT
382 AAAAGAACATCAAATT---CA-AC---ATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTT
* *
2517 GACGTGATTAATAAGGCGCCCCACCAATGTGACCT-TTTTC-TTTTTT-AAACAA-AAAAACTT-
440 GACGTGATTAATAAGGCGCCCCACCAACGTGACCTATTTTCTTTTTTTAAAAAAACAAAAACTTA
*
2577 AAAGGTTAAATAATTTTCTAAAAAAAAGGTTGTTAACATGTCG
505 AAAGGTTAAATAATTTTCTAAAAAAAAGGTTGTTAACATGGCG
2620 TATAACACTGTCAATAATATATAGCTTTACT-AAAAAAACGAAAATTTAGCAAATAAGAAATATT
1 TATAACACTGTCAATAATATATAGCTTTACTAAAAAAAACGAAAATTTAGCAAATAAGAAATATT
* *
2684 CCCCACGTACTTTATA-A-AAAATCTAAACTAAAATTTTGAAAAAAACCTCAAATTCAACATACA
66 CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTTGAAAAAAACATCAAATTCAACATACA
* * * *
2747 ATATAGAATTAGAAAATTTTTGATCCACCAAATTTATGTTGACGTAATTAATAAGGCTTGAAAGA
131 ATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGC-TGAAA-A
2812 GGT
194 GGT
2815 TTAAATTAAA
Statistics
Matches: 672, Mismatches: 44, Indels: 63
0.86 0.06 0.08
Matches are distributed among these distances:
544 72 0.11
545 20 0.03
546 1 0.00
547 42 0.06
548 6 0.01
549 1 0.00
550 3 0.00
551 72 0.11
552 14 0.02
553 90 0.13
554 28 0.04
555 18 0.03
556 140 0.21
557 75 0.11
558 11 0.02
559 2 0.00
560 7 0.01
563 70 0.10
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (547 bp):
TATAACACTGTCAATAATATATAGCTTTACTAAAAAAAACGAAAATTTAGCAAATAAGAAATATT
CCCCACGTACTTTATACACAAAATCTAAACTGAAATTTTGAAAAAAACATCAAATTCAACATACA
ATATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGGCTGAAAAGG
TCCAATTAAAGTAACCTTTTTAAAATTAAAAAAAACTTAAAGGTTAAAAATTTTTCTAAAAAAAA
GGTTGTTAACATGGCGTATAACACTGTCAATAATATGTAGCTTTACTAAAAAAAACGAAATTTTA
ACAAATAAGAAATATTCCCCACGTACTTTATACACAAAATCTAAACTGAAATTTGGAAAAGAACA
TCAAATTCAACATAGAAGTAGAAAATTTTCGATCCACCAAATTCATGTTGACGTGATTAATAAGG
CGCCCCACCAACGTGACCTATTTTCTTTTTTTAAAAAAACAAAAACTTAAAAGGTTAAATAATTT
TCTAAAAAAAAGGTTGTTAACATGGCG
Found at i:3253 original size:114 final size:114
Alignment explanation
Indices: 2929--3255 Score: 539
Period size: 115 Copynumber: 2.9 Consensus size: 114
2919 TCCTAGCATT
2929 TGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCATAGAAGCGCCACTAATTTAGGGCGTTTCA
1 TGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCATAGAAGCGCCACTAATTTAGGGCGTTTCA
* * * * *
2994 GAATATAAACGCCGCCATATATAGTCTATTCCTACAAATACAAATTTAG
66 GCATAAAAACGCCGCCATATATAATCTGTTCCTAAAAATACAAATTTAG
*
3043 TGAAAATAAAGACTAAAATTAGCAGCGTTTTTCTCATTAGAAGCGCCACTAATTTAGGGCGTTTC
1 TGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCA-TAGAAGCGCCACTAATTTAGGGCGTTTC
* *
3108 AACATAAAAACGCCGCCATATATAATTTGTTCCTAAAAATACAAATTTAG
65 AGCATAAAAACGCCGCCATATATAATCTGTTCCTAAAAATACAAATTTAG
*
3158 TGAAAATAAAGACTAAAATTAGCGGTGTTTTTCTCATAGAAGCGCCACTAATTT-GAGGCGTTTC
1 TGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCATAGAAGCGCCACTAATTTAG-GGCGTTTC
*
3222 AGCATAAAAACACCGCCATATATAATCTGTTCCT
65 AGCATAAAAACGCCGCCATATATAATCTGTTCCT
3256 TATTTTGCCT
Statistics
Matches: 198, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 92 0.46
115 105 0.53
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (114 bp):
TGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCATAGAAGCGCCACTAATTTAGGGCGTTTCA
GCATAAAAACGCCGCCATATATAATCTGTTCCTAAAAATACAAATTTAG
Done.