Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006365.1 Corchorus capsularis cultivar CVL-1 contig06386, 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: 2592
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Found at i:1547 original size:324 final size:323
Alignment explanation
Indices: 314--2132 Score: 1260
Period size: 324 Copynumber: 5.4 Consensus size: 323
304 TGAGGCTCAA
* * * * * * * *
314 TTTTGCATGATTTTTGGCGTCC-AGACTCCTTAAAATAACTATATTCATCTAACCAAATCTCATC
1 TTTTGCATGATTTTTGGCG-CCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACC
* * * ** *
378 CATATTGGATTTACGGATTT-TTTTATACGAGCATC-CGAATTTTGTTTTGATTTAATTAGAAAT
65 CACATTGGATTTAAGGATTTGTTTT-TACGAGCATCTTG-A-TCCGTTTCGATTTAATTAGAAAT
** * * * * *
441 TAATTAAGAAAAAAAATAAGTAAAACGATATTAGAAGCGTGAAAAACCCTTT-AATCTTTTTCGC
127 TAATTCGGAAAAAAAAT-AGAAAAACAATATTAGAAGCGTG-AGAAGCCTTTCAATCTTTTTGGC
* * * * * *
505 ATTGAATTATATATATTCTATGAGTATTGTGACTAAAAATTGAGAGAAAAACTTTTGGAGAGAAA
190 ATTGAGTTATATATTTTTTATGAGTATTGTGCCCAAAAATT-AG-GAGAAA----T-----G---
** * * * * *
570 ATTTTCAAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTACTAACCATTACGACTTTTGACTAA
241 --TTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCAT-GTCACC---A--ATTTTTGACTAA
* *
635 AAACACGTTCCGGGGC-CCTGATTCTG
298 AAACGCGTTCCGGGGCACC-GACTCTG
* * ** * * * *
661 TTTTGCACGATTTTTAGCGTGAAG--TCATTGAAATATCTATATTCATTTAACCAAATCTCACGC
1 TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACCC
**
724 ACATTGGATTTAAGGATTTGTTTTTACGAGCATC-TGAATTATGTTTCGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTG-A-TCCGTTTCGATTTAATTAGAAATTA
** * * ** *
788 ATTCGG---AAAAATAGAAAAATCGGTATTAGAAGCGTTAGTAGTTTTTCAATCTTTTTGGTATT
129 ATTCGGAAAAAAAATAGAAAAA-CAATATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCATT
* * * * * *
850 GAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTAAGAAAAACTTTTTCAG-GTCAATTTT
193 GAGTTATATATTTTTTATGAGTATTGTGCCCAAAAATTAGGAGAAA-TGTTTC-GTGTCAATTTT
* * * *
914 TGTAAAATTTTAGCCGAAATCGTGT-ACCAAGTTTTTTG-CTAAAAACGCGTTCCGGGGCCCCGG
256 TGCAAAATTTTAGCCGAAATCATGTCACCAA--TTTTTGACTAAAAACGCGTTCCGGGGCACCGA
*
977 CTCAG
319 CTCTG
* * * ** *
982 TTTTGCATGATTTTTTGGCGCCAAGACTTATTGAAATATCTATATTCATATAATGAAATCTCAGC
1 TTTTGCATGA-TTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACC
* **
1047 CACATTGGATTTAAGGATTTATTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTT
65 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTGATCC-GTTTCGATTTAATTAGAAA-TT
* * * *
1112 AATTCGGAAAAAAATTGGTAAAACAATATTAGAAGCGTGAGAAACCTTTCAATCTTTTTGGCATT
128 AATTCGGAAAAAAAATAGAAAAACAATATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCATT
1177 GAGTTATATATTTTTTATGAGTATTGTGCCCAAAAATTGAGGAGAAATGTTTCGTGTCAATTTTT
193 GAGTTATATATTTTTTATGAGTATTGTGCCCAAAAATT-AGGAGAAATGTTTCGTGTCAATTTTT
* * * * *
1242 ACAAAATTTTAGTCGAAATTATGTCA-CAATTTTTGACTAAAAACGCATTCCGGGGCACCGGCTC
257 GCAAAATTTTAGCCGAAATCATGTCACCAATTTTTGACTAAAAACGCGTTCCGGGGCACCGACTC
1306 TG
322 TG
* * * **
1308 TTTTGTATGATTTTTGGCGCCAAGTCTCTTTGAAATATTTATATCCATATAACAAAATAACACCC
1 TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACCC
* *
1373 CCATTGGATTTAAGGATTTGTTTTTATGAGCATCTTGATCCGATTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTGATCCG-TTTCGATTTAATTAGAAATTAA
* * * * *
1438 TTCGGAAAAAAAAAAGAAAAACAATATTAGAAGCGTGAGAAGCCCTTCAATGTTTTTGACGTTGA
130 TTCGGAAAAAAAATAGAAAAACAATATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCATTGA
* * * *
1503 GTTATATATTTTTTATGAGTATTGTGCCCAAAAATATTGGAGAAATGTTTCATGTCAAATTTCGC
195 GTTATATATTTTTTATGAGTATTGTGCCCAAAAAT-TAGGAGAAATGTTTCGTGTCAATTTTTGC
* * ** *
1568 AAAGTTTTAACCGAAATCATGTACTAACCATCAAAGTTTGACTAAAAACGCGTTCCGGGGCATCG
259 AAAATTTTAGCCGAAATCATGT-C--A-C--CAATTTTTGACTAAAAACGCGTTCCGGGGCACCG
1633 ACTCTG
318 ACTCTG
* * *
1639 TTTTGCATGATTTTTTGTGCCAAGTTTCATTGAAATATCTATATCCATCTATTGGACAAAAAAAA
1 TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATAT-C--C-A-T-----------A
* * * *
1704 TATATCTATATCCATCTAACCAAATTTTACCCACATTGGATTGAAGGA-TTATTTATACGAGCAT
50 TA-A-C-A-A--AATCT---C--A-----CCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * *
1768 C-TGAATCATGTTTCGACTTAATTAGAAATTAATTC--AGAAAAATTAGGAAAACCGATATTAGA
99 CTTG-ATC-CGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATA-GAAAAACAATATTAGA
** * * * *
1830 AGCGTGA-ATAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTTGA-GAGTATCGTGGCG
161 AGCGTGAGA-AGCCTTTCAATCTTTTTGGCATTGAGTTATATATTTTTT-ATGAGTATTGTGCCC
* * * * *
1893 AAAAATT-GAGAAAAACTCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAAC
224 AAAAATTAG-GAGAAA-TGTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCATG---T--C
** * * *
1957 TATCACGGTTTTTTTG-CTAAAAACACGTTCC-GGG-ATCCCAGCTCAG
282 -A-C-C--AATTTTTGACTAAAAACGCGTTCCGGGGCA-CCGA-CTCTG
* ** * ** * * *
2003 TTTTACATGATTTTTGGCGCCAAGAGTCATTGAAATATATATATTTATCTAACGAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACCC
** *
2068 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGA-ATAATTAGAAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTGATCC-GTTTCGATTTAATTAGAAATTAA
2132 T
130 T
2133 CCGGTGTTTG
Statistics
Matches: 1200, Mismatches: 192, Indels: 175
0.77 0.12 0.11
Matches are distributed among these distances:
320 1 0.00
321 32 0.03
322 19 0.02
323 1 0.00
324 223 0.19
325 119 0.10
326 38 0.03
327 141 0.12
328 17 0.01
331 73 0.06
332 33 0.03
333 25 0.02
334 1 0.00
335 1 0.00
336 1 0.00
337 2 0.00
339 1 0.00
340 6 0.00
341 12 0.01
342 70 0.06
344 1 0.00
345 91 0.08
346 5 0.00
347 23 0.02
348 3 0.00
349 1 0.00
350 1 0.00
351 1 0.00
353 2 0.00
356 1 0.00
358 1 0.00
359 2 0.00
360 15 0.01
361 105 0.09
362 43 0.04
363 24 0.02
364 59 0.05
365 6 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (323 bp):
TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATATAACAAAATCTCACCC
ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTGATCCGTTTCGATTTAATTAGAAATTAAT
TCGGAAAAAAAATAGAAAAACAATATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCATTGAG
TTATATATTTTTTATGAGTATTGTGCCCAAAAATTAGGAGAAATGTTTCGTGTCAATTTTTGCAA
AATTTTAGCCGAAATCATGTCACCAATTTTTGACTAAAAACGCGTTCCGGGGCACCGACTCTG
Found at i:2463 original size:16 final size:16
Alignment explanation
Indices: 2442--2488 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
2432 GTGAATATCT
*
2442 CACCAGATGAGTATTA
1 CACCAGGTGAGTATTA
2458 CACCAGGTGAGTATTA
1 CACCAGGTGAGTATTA
2474 CACCAGGTGAGTATT
1 CACCAGGTGAGTATT
2489 GTACTGGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (16 bp):
CACCAGGTGAGTATTA
Found at i:2483 original size:74 final size:73
Alignment explanation
Indices: 2400--2545 Score: 222
Period size: 74 Copynumber: 2.0 Consensus size: 73
2390 AGCATGGCCT
* *
2400 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGGTGAA-TATCTCACCAGATGAGTATTACACCAG
1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGAT-AAGTATCTCACCAGATGAGTATT-CACCAA
2464 GTGAGTATTA
64 GTGAGTATTA
* * *
2474 CACCAGGTGAGTATTGTACTGGGTGAGTGTGGATAAGTATCTCACCAGGTGAGTATTTACCAAGT
1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGATAAGTATCTCACCAGATGAGTATTCACCAAGT
2539 GAGTATT
66 GAGTATT
2546 TGTATTGGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 15 0.23
74 51 0.77
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (73 bp):
CACCAGGTGAGTATTGTACTGGGAGAGTGTGGATAAGTATCTCACCAGATGAGTATTCACCAAGT
GAGTATTA
Found at i:2540 original size:15 final size:15
Alignment explanation
Indices: 2517--2546 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2507 TAAGTATCTC
*
2517 ACCAGGTGAGTATTT
1 ACCAAGTGAGTATTT
2532 ACCAAGTGAGTATTT
1 ACCAAGTGAGTATTT
2547 GTATTGGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (15 bp):
ACCAAGTGAGTATTT
Done.