Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015671.1 Corchorus olitorius cultivar O-4 contig15704, 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: 30331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1937 original size:334 final size:332
Alignment explanation
Indices: 4--2680 Score: 1081
Period size: 333 Copynumber: 8.1 Consensus size: 332
1 CAA
* * * ** *
4 ATGCTCCTAAAAACAAATCCTTAAATCCGATGTGGCTAAAGATTTGGCTAGATGACTATAGATAT
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT-AAGATTTGATTAGATGAATATAGATAT
* * * * * * * *
69 TTTAACGAATGTTGC--CACTAAAAATCATGCAAAACTAACCC-GAGACCCC-AGAACGCGTTTT
65 CTCAATG-AGGCT-CAACGCCAAAAATCATGCAAAACTAACCCAGAG-CCCCGA-AACGCATTTT
* * * * * * **
130 TAGCCAAAAAACCGTGATG----GTACACGATTTCGACTAAAATTTT-CCAAAAATTGACCCGAA
126 TAGCAAAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAAT-ACCAAAA
*** * * * * * * *** * *
190 ATTTTTTCCTCCATTTTTAGCCACAATACTCAT--AGAATATATATAACTAAAAGCCAAAAAGAT
190 AAAGTTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATATAA-TTCTATCCAAAAATAT
* * * * *
253 TGAAGAACTCTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGTATTAATTTCTAATTAGATC
254 TGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATC
* *
318 GAAACAAGATTAAG
319 GAAATAAGATTTAG
* *
332 ATGCTCGTAAAAAGAAATCCTTAAATTG-AATGTGGCTAAGATTTGATTAGATAAATATAGATAT
1 ATGCTCGTAAAAACAAATCCTTAAA-TGCAATGTGGCTAAGATTTGATTAGATGAATATAGATAT
* * * ** * * * * *
396 TTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTAAGCCGGTGTCCCGAAACGCGTTTTTAGC
65 CTCAATGAGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGAGCCCCGAAACGCATTTTTAG-
* **
461 CAAAAAAAAAAAAGCCGTGATGATTAATACACGATTTCGGCTAAAATTTT-GTAAAAAATGACCC
129 C----AAAAAAAA--CGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAAT-A-CC
* ** * *
525 GAAAAATTTTTCTGTCAATTTTTGGCATAAATACTCATAATATACATACATACATATATATATAT
186 AAAAAAAGTTTC-CTCAAATTTTGG--------CT-A-AA-ATAC-T-CATA-A-A-A-A-ATAT
* * ** *
590 ATATATATAATTTAACGCCAAAAGGATTGGAGGACTTTTCACGTTTTATAATATCGTTTTTCATA
232 ATATA-AT--TCT-A-TCCAAAAATATTGGAGGACTTTTCACGCTTT-TAATATCGTTTTTCATA
* * *
655 TTTTTCTGAATCAATTTCTAATTAAATCGAAACAAGATTCAG
291 TTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTTAG
** * * * * * *
697 ATAATCGTAAAATCAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATC
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
** *** **** * * * * * * *
762 TCAAACATTTTTGGTGCCAAAAATCATGCAAAACTTAGCTAGGGCCTCGGAACGCGTTTTTAGC-
66 TCAATGAGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGAGCCCCGAAACGCATTTTTAGCA
* * * * * * ***
826 CAAAAACCGTGATGATTATTACACGATTTCGGC-AAGAATTTTGC-AAAAATTGACTCGAAAGTT
131 AAAAAAACGTGATGATTAATACACGATTTCGCCTAA-AATTTTACAAAAAAAT-AC-C-AAAAAA
* * * *** * * * *
889 A-TTTTCTCAAGTTTTAGCCGCAATACTCAGT--AAAAT-CACATAATTCAATGCCAAAAAGATT
192 AGTTTCCTCAAATTTTGGCTAAAATACTCA-TAAAAAATATATATAATTCTAT-CCAAAAATATT
* * * *
950 GAATGG-CTTTTCATGCTTTTAGA-ATCGTTTTTCCTATTATTT-TCAAGATTAATTTCTAATTA
255 GGA-GGACTTTTCACGCTTTTA-ATATCGTTTTTCATATT-TTTCT-GA-ATTAATTTCTAATTA
* * * * *
1012 ACTTGAAACATGATTCAG
315 AATCGAAATAAGATTTAG
* *** * ** * * * * * * * *
1030 ATGCTTGT-TTTACAAATCTTTAAATTTATTATGGATGAGATTTGGTTAAATTAATATAGATATT
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
* * ** * * * * * * * * *
1094 TCAAGGAGTCTCGGCGCAAAAAATCATGCAACACTGAA-CCGGGGCCCTGGATCTCGTTTTTAGG
66 TCAATGAGGCTCAACGCCAAAAATCATGCAAAACT-AACCCAGAGCCCCGAAACGCATTTTTA-G
** * * * * *
1158 GGAAAAAAAC-CG-TGATT--T---CGA------CTAATATTTTGCAAAAATTAA-A-CATAAAT
129 CAAAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAA--AATACCAAAAAA
* * * * * * *
1208 AGTTTACCTCAATTTTTGTCGAAAATTCCCAT--AATATATATATAATTCAACTCCAAAAATATT
192 AGTTT-CCTCAAATTTTGGCTAAAATACTCATAAAAAATATATATAATTCTA-TCCAAAAATATT
* **
1271 AGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAAAATCTAATTAAATCG
255 GGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCG
*
1336 AAATAAGGTTTAG
320 AAATAAGATTTAG
* * *
1349 ATGCTCGTAAAAACAAAT-CTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATATATATT
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
* * ** * * *
1413 TCAATGAGGCTCAATGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTTGCA
66 TCAATGAGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGAGCCCCGAAACGCATTTTTAGC-
*
1478 AAAAAAAAAAAACGTGATGGTTAATACACGATTTCGCCTAAAATTTTACAAAAAAATACCAAAAA
130 ----AAAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAATACCAAAAA
* * * *
1543 AAGTTTCCTCAAATTTTGGCTAAAATACTCATGAAATATATATATAATT-TAACACCAAAAAGAT
191 AAGTTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATATAATTCT-A-TCCAAAAATAT
* * * * *
1607 TGGAGAACGTTTCACGATTTTCATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTTAA
254 TGGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT-A-TTTTTCTGAATTAATTTCTAATTAAA
1672 TCGAAATAAGATTTAG
317 TCGAAATAAGATTTAG
* * ** * * *
1688 ATGCTCATAAAAACGAATCCGCAAATGCAATGTGTCTAAGATTTGATTATATGAATATGGATATC
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
* * * * * ** *
1753 TCAA-GTAGTCTTAGCGCCAAAAATCATGCCAAATTAACCCA-AGGCCTGGGAACGCATTTTTAG
66 TCAATG-AGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGA-GCCCCGAAACGCATTTTTAG
* * * * * *
1816 C-CAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAAAATGACCGGAAAGA
129 CAAAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAAT-ACC--AAAAA
* * * *
1880 TA-TTTCTTCAATTTTTTGCTAAAATA-TCATAAAAAATA-ATATAATTCTATGCCAAAAATATT
191 AAGTTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATATAATTCTAT-CCAAAAATATT
* * * * * * * *
1942 GAAGGATTTTTTACGCTTCTAATATAGTTTCT-ACTACTATTTCTGAATAAATTTCTAATTAAAT
255 GGAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TA-TTTTTCTGAATTAATTTCTAATTAAAT
*
2006 CGAAAGAAGATTTAG
318 CGAAATAAGATTTAG
* * * * *
2021 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTCGATTCGTTTAATATAGATAGT
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATA-T
* * ** * * * * * * * * *
2086 -TCAAGGAGTCTTGATGCCGAAAATCATGCAATACTGACCCGGGGTCCTGGAACGCATTTTTAGA
65 CTCAATGAGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGAGCCCCGAAACGCATTTTTAG-
* * * * * *
2150 AGAAAAAAAATCGTGATG--T--TGCACGATTTCGACTAATATTTTGCAAAAAAATGTCGC-AAA
129 -CAAAAAAAA-CGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAAT-AC-CAAAA
* * * * * * ** * *
2210 ATATTCTTCGTCAACTTTTAG-TCACAATACTCAT--AAAA-ATATATAATTGAACGCCAAAAAG
190 AAAGT-TTCCTCAAATTTTGGCT-AAAATACTCATAAAAAATATATATAATTCTA-TCCAAAAAT
* * ** * * *
2271 ATTGAAGGGCTTTTCGTGCTTCTAATA-CTGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAA
252 ATTGGAGGACTTTTCACGCTTTTAATATC-GTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
** * * * *
2335 AAAGAAACATGATTCAA
316 ATCGAAATAAGATTTAG
* * * * *
2352 ATGCT--T----A-TAA-----AAA--CAA--TGGCTGAGATTTGGTTAGATGAATATAGACATT
1 ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
* * * * * * * * * *
2401 TCCAGGAGTCTCAGCGCCAAAAATCATTCAAATCTGAA---ATGGGCCTCGGAATGCATTTTTAG
66 TCAATGAGGCTCAACGCCAAAAATCATGCAAAACT-AACCCA-GAGCCCCGAAACGCATTTTTAG
* ** * * * *
2463 C----CAAACCCG-TGATTATTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCAAAAGA
129 CAAAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAAT-A-CCAAAA-A
* ** * ** * * *
2522 TA-TTTCCTC-AATTGTTATCCATGATATTCAT-AAAAATATATATAATTC-AACGTCAAAAAGA
191 AAGTTTCCTCAAATT-TTGGCTAAAATACTCATAAAAAATATATATAATTCTATC--CAAAAATA
* * * * *
2583 TTGAAGGGCTTTTGACACTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAAT
253 TTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAT
* * *
2648 CGAAACATGATTCAG
318 CGAAATAAGATTTAG
2663 ATGCTCGTTAAAAACAAA
1 ATGCTCG-TAAAAACAAA
2681 AAAAAAATCT
Statistics
Matches: 1808, Mismatches: 394, Indels: 303
0.72 0.16 0.12
Matches are distributed among these distances:
306 2 0.00
307 2 0.00
308 7 0.00
309 25 0.01
310 32 0.02
311 93 0.05
312 1 0.00
314 20 0.01
315 50 0.03
316 1 0.00
317 3 0.00
318 3 0.00
319 122 0.07
320 22 0.01
321 74 0.04
322 8 0.00
323 8 0.00
324 4 0.00
325 5 0.00
326 2 0.00
327 71 0.04
328 35 0.02
329 2 0.00
330 4 0.00
331 61 0.03
332 175 0.10
333 227 0.13
334 110 0.06
335 39 0.02
336 55 0.03
337 71 0.04
338 32 0.02
339 68 0.04
340 93 0.05
343 2 0.00
344 2 0.00
345 4 0.00
346 1 0.00
348 2 0.00
349 1 0.00
350 1 0.00
351 4 0.00
352 1 0.00
353 3 0.00
356 12 0.01
357 44 0.02
358 2 0.00
359 6 0.00
360 10 0.01
361 1 0.00
363 1 0.00
364 28 0.02
365 156 0.09
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (332 bp):
ATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATC
TCAATGAGGCTCAACGCCAAAAATCATGCAAAACTAACCCAGAGCCCCGAAACGCATTTTTAGCA
AAAAAAACGTGATGATTAATACACGATTTCGCCTAAAATTTTACAAAAAAATACCAAAAAAAGTT
TCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATATAATTCTATCCAAAAATATTGGAGGA
CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAATAA
GATTTAG
Found at i:4253 original size:37 final size:37
Alignment explanation
Indices: 4191--4269 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
4181 AGCACAGTCA
4191 TAAGAACCAACAAAACAAATACCAACTAAACAACAGC
1 TAAGAACCAACAAAACAAATACCAACTAAACAACAGC
* * *
4228 TAAGAACCAACAGAACATATGCCAACTAAACAACAGC
1 TAAGAACCAACAAAACAAATACCAACTAAACAACAGC
*
4265 AAAGA
1 TAAGA
4270 GAAAAAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.57, C:0.25, G:0.09, T:0.09
Consensus pattern (37 bp):
TAAGAACCAACAAAACAAATACCAACTAAACAACAGC
Found at i:18461 original size:27 final size:28
Alignment explanation
Indices: 18430--18495 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
18420 TGAGTACATA
* *
18430 ATGTAAATTGTTTTGGTGATCT-C-CTAC
1 ATGTAAATTGTTTTAGTCAT-TACACTAC
*
18457 ATGT-AA-TATTTTAGTCATTACACTAC
1 ATGTAAATTGTTTTAGTCATTACACTAC
18483 ATGTAAATTGTTT
1 ATGTAAATTGTTT
18496 GGCAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 10 0.32
27 6 0.19
28 4 0.13
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (28 bp):
ATGTAAATTGTTTTAGTCATTACACTAC
Found at i:21009 original size:31 final size:31
Alignment explanation
Indices: 20969--21047 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
20959 ATTTTTAGCC
20969 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
* *
21000 -CTCAATTTGAGTCTAAACCTTTTAAAGGTTG
1 AC-CAATTTGAGTCTAAACCTTTCAAAAGTTG
*
21031 ACCAATTTGAGCCTAAA
1 ACCAATTTGAGTCTAAA
21048 AACAGATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 41 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (31 bp):
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
Done.