Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001884.1 Corchorus capsularis cultivar CVL-1 contig01886, 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: 1732
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Found at i:1225 original size:319 final size:320
Alignment explanation
Indices: 111--1696 Score: 1403
Period size: 334 Copynumber: 4.9 Consensus size: 320
101 TGGGGTCAGT
* * * *
111 TTTTGTCAAATTTTGGACGAAATCTTGTGCTAACCATCACAGTTTTTGGCTGAAAATGCGTTTCG
1 TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAATG-GTTCCG
* * * * * *
176 AGGCCCCAGTTGAGTTTTGCATGATTTTTG-TGCCAAGAGTAATTGAAAAATATATATTCATCTA
65 AGGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAGA-TAATTGAAATATCTATATTCATCTA
* ** * * * *
240 ACCAAATTTCATTCAAATTGGATTGAAGGA-TTCGTTTTTACGAGCATTTGAATCATGTTTCGAG
129 ACCAAATCTCAGCCACATTGGATTGAAGGATTTC-TTTTTACGAGCATTTCAATCATGTTTCAAT
* * * * *
304 TTAATTAGAAATTAATTCGG-AAAATGAGAAAAATGATATTAGAAGCATGAAAAT-CCTTTTTTT
193 TTAATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTTGAAGCGTG--AATGCCATTTTTT
* * * ** * * *
367 CTTTTCGGCATTGAATTATATATCATTTAATAGTATTGTAGCCAAAAATTGAGGAAAACATTTTC
256 CTTTTTGACGTTGAATTATATATC-TTT--TA-TACAGTAG----GAATTGAGAAAAAAATTTTC
* **
432 GAGTCAGT
313 GGGTCAAC
* * * * *
440 TTTTGCCAAATTTTGGACGAATTCGTGTGCTAATCATCACGGTTTTTTTGCTAAAAATGCATTCC
1 TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGG-TTTTTGGCTGAAAATG-GTTCC
* * * * ** *
505 GGGGACCCGGCTGAGTTTTGAATGATTTTAGGTGCCAAGAGTAATTGAAATATCTATATTCATCT
64 GAGGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAGA-TAATTGAAATATCTATATTCATCT
* * * *
570 AATCAAATCTCATCCACATTGGAGTGAAGGATTTCTTTTTACGAGCATTTGAATCATG-------
128 AACCAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAAT
* **
628 ----TTAGAAATTAATTCGGAAAAATAAGAAAAA-ACGATATTAGAAGCGTGAAAAGTGCTGTTT
193 TTAATTAGAAATTAATTCGGAAAAATAAGAAAAATA--ATATTTGAAGCGTG--AA-TGC--CAT
* *
688 TTTCTTCTTTTTGTAAGTTGAATTATATATCTTTTATGAGCATTGT-GGCCAAAATTTGAGGAAA
251 TTT-TTCTTTTTG-ACGTTGAATTATATATCTTTTAT-A-CA--GTAGG----AA-TTGAGAAAA
* * **
752 AATTTTTTGGGTCAGT
305 AAATTTTCGGGTCAAC
* *
768 TTTTGCTAAAATTTGGACGAAATC--GT-C--A-C-T----GTTTTTGGCTGAAAATGTGTTCCG
1 TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAATG-GTTCCG
* * *
822 AGGCCCCGGCTGAGTTTTGCATGATTTTTGCAC--CAAGGATAATTGAAATCTCTATACTCATCA
65 AGGCCCCGGCTGAGTTTTGCATGATTTTTGC-CGTCAA-GATAATTGAAATATCTATATTCATCT
* * * * * * **
885 AACCAAATCTCAGCCACATTGGGTTTAAGAATTTGTTTTTATGAGCATTTCAATTATGTTTTGAT
128 AACCAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAAT
*
950 TTAATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTTGAAGCGTGATATGCCCTTTTTTC
193 TTAATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTTGAAGCGTGA-ATGCCATTTTTTC
1015 TTTTTGACGTTGAATTATATATCTTTTATA-AG-A-G-ATTGAGAAAAAAAATTTT-GGGTCAAC
257 TTTTTGACGTTGAATTATATATCTTTTATACAGTAGGAATTGAG-AAAAAAATTTTCGGGTCAAC
* *
1075 TTTTGCCAATTTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAATGCATTCCG
1 TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAATG-GTTCCG
* *
1140 GGGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAAACTAATTGAAATATCTATATTCATCTA
65 AGGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAGA-TAATTGAAATATCTATATTCATCTA
* *
1205 ACCAAATATCAGTCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAATT
129 ACCAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAATT
** * * * *
1270 TAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGACGCATGAATAGCCTTTTTTTTT
194 TAATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTTGAAGCGTGAAT-GCC---ATTTTT
* * * * *
1335 TCTTTTCGGCATTGAATTATATATCATTTA-ACAGTATTGCGGCCCAAAATTGAGGAAAAAATTT
255 TCTTTTTGACGTTGAATTATATATCTTTTATACAGTA----GG-----AATTGAGAAAAAAATTT
**
1399 TCGGGTCAGT
311 TCGGGTCAAC
* * * *
1409 TTTTGCCAAATTTTGGACTAAATCGTGTGTTAACCATCACGGTTTTTGCCTGAAAATAGGTTCCA
1 TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAAT-GGTTCCG
* ** * * * * *
1474 AGGACTAGGTTGAGTTTTGCATGATTTTTGGCGTCGAGAGTAATTGAAAAATCTATATTTATCTA
65 AGGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAGA-TAATTGAAATATCTATATTCATCTA
*
1539 ACCAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTGAATCATGTTTCAATT
129 ACCAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAATT
* * *
1604 TAATTAGTAATTAATTCAGAAAAATAAGAAAAATAAT-TTTAGAAGCGTGAAAAGCCATTTTTT-
194 TAATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTT-GAAGCGTG-AATGCCATTTTTTC
*
1667 TCTTTTGATGTTGAATTATATATCTTTTAT
257 T-TTTTGACGTTGAATTATATATCTTTTAT
1697 GAGCATTGTG
Statistics
Matches: 1044, Mismatches: 138, Indels: 147
0.79 0.10 0.11
Matches are distributed among these distances:
307 32 0.03
308 10 0.01
309 2 0.00
310 1 0.00
312 1 0.00
313 2 0.00
314 2 0.00
315 72 0.07
316 48 0.05
317 2 0.00
318 56 0.05
319 150 0.14
320 25 0.02
321 18 0.02
322 51 0.05
323 7 0.01
324 3 0.00
325 17 0.02
326 37 0.04
327 15 0.01
328 59 0.06
329 37 0.04
330 44 0.04
331 108 0.10
332 3 0.00
333 12 0.01
334 227 0.22
335 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (320 bp):
TTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCTGAAAATGGTTCCGA
GGCCCCGGCTGAGTTTTGCATGATTTTTGCCGTCAAGATAATTGAAATATCTATATTCATCTAAC
CAAATCTCAGCCACATTGGATTGAAGGATTTCTTTTTACGAGCATTTCAATCATGTTTCAATTTA
ATTAGAAATTAATTCGGAAAAATAAGAAAAATAATATTTGAAGCGTGAATGCCATTTTTTCTTTT
TGACGTTGAATTATATATCTTTTATACAGTAGGAATTGAGAAAAAAATTTTCGGGTCAAC
Done.