Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006677.1 Corchorus capsularis cultivar CVL-1 contig06698, 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: 3176
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Found at i:678 original size:28 final size:28
Alignment explanation
Indices: 646--702 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
636 TAAAATTTTA
646 AATTATGGAAAGATATTAATAATCTACT
1 AATTATGGAAAGATATTAATAATCTACT
674 AATTATGGAAAGATATTAATAATCTACT
1 AATTATGGAAAGATATTAATAATCTACT
702 A
1 A
703 TAATTGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (28 bp):
AATTATGGAAAGATATTAATAATCTACT
Found at i:2354 original size:329 final size:327
Alignment explanation
Indices: 739--2754 Score: 1584
Period size: 329 Copynumber: 6.1 Consensus size: 327
729 ATAATTATTT
* * *
739 CATCTGAATCCTGTTTGGATTTAATTAGAAATAAATTCGAG-AAAAAATGG-AAAACGATATTAG
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAATGGAAAAACGATATTAG
* * *
802 AAGTGTGAAAAGCCCGTCAATCTTTTTGGAATTGAATTAAATATTTTTTTCTTACTATTGTGGCA
66 AAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATA-TTTTTTCTTACTATTGTGGC-
* ** * * *
867 AAAAAAATTGAGGAAAACTTTTTCAGGTCAGTTTTTGTAAAATTTTAG-CTGAAATCGTGTACTT
129 -AAAAAATTGAGAAAAAAATTTTCAGGTCAGTTTTTGCAAAATTTTAGTC-GAAATC--GTCCAT
* * * *
931 CATGA--TTTTTTGCTAAAAAAACGCGTTCCGGAGTCCCGACTTAGTTTTGCATGATTTTTGGCG
190 CACGATTTTTTTTGCT--AAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCA
* * * * * * *
994 TAAAGACTTCTTGCAATATCTATATTTATCGAACCGAATCTCACCCACATT--A---AA-TATAT
253 TAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA-GCACATTGGATTTAAGGAT-T
1053 TG--TTTACGAG
316 TGTTTTTACGAG
* **
1063 CATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTC--G-AAAAAATGGAAAAATTATATTAG
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAATGGAAAAACGATATTAG
** * * * *
1125 -AGACGTGAAAAGTTCGTCAATCTTTTTGGCATTGAATTATATA-TATTT-TAAATATTGTCGCA
66 AAG-CGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTTACTATTGTGGC-
* * * *
1187 AAAAAATATATTAAAAAAAAAGGAGAAATTTCGGGTCAGTTTTTAGCTGAAAATTGAAATT-GT-
129 --AAAA-A-ATT--GAGAAAA--A-AATTTTCAGGTCAGTTTTT-GC--AAAATT----TTAGTC
* * ** * * *** ** * *
1250 GTACT-AACCATCATG-GTTTTGGGGCTAAAAACGCGTTTTGG-G-TCCGTCTCAGTTTTGCATG
178 GAAATCGTCCATCACGATTTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATG
* * * *
1311 ATTTTTGGCATAAAGACTCCTTGAAATATATATATTCATCTAACTAAATCTCAGCCACATTCGAT
243 ATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAG-CACATTGGAT
* * **
1376 TTAAGAATGTTTTTTTTTGTGAG
307 TTAAGGA--TTTGTTTTTACGAG
* * * * *
1399 CATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGAGAAAAAAATGGGAAAATGATATTTG
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAATGGAAAAACGATATTAG
** * * * * *
1464 AAATGTGAAAAACCCCTTCAAT-TTTTTTGCATTGCATTATATATTTTTTCTGACTATTGTGGCA
66 AAGCGTG-AAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTTACTATTGTGGC-
* * * * *
1528 AAAAAAAGTGAG-GAAAAATTTTTAGATCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACCCA
129 -AAAAAATTGAGAAAAAAATTTTCAGGTCAGTTTTTGCAAAATTTTAGTCGAAATC--GT--CCA
* * * * *
1592 TCAC--TGTTTTTTGCTAAAAACGCGTTCCGGAGGCCCGGCTCAGTTTTACATGATTTTTGGCGT
189 TCACGATTTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCAT
* * *
1655 AAAGACTTCTTGAAATATCTATATTCATCAAACCAAATCTCAACCACATTGGATATAAGGATTTG
254 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC-AGCACATTGGATTTAAGGATTTG
1720 TTTTTACGAG
318 TTTTTACGAG
* * *
1730 CAACTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-G--AAAAATGGGAAAACGATACTAG
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAATGGAAAAACGATATTAG
* * * *
1792 AAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTT-TTGAGTAATGTGGTA
66 AAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTT-ACTATTGTGGCA
* * * * * * * * *
1856 TAAATTTCAGAAAAAAAAATTTC-GAGTCAGCTTTTAGCCGAAA---TCGT-G-TA-CGT-TATC
130 AAAAATTGAG-AAAAAAATTTTCAG-GTCAG-TTTTTG-CAAAATTTTAGTCGAAATCGTCCATC
* * * * * * * * *
1913 A-TA-GTTTTTGGTCTAAAAACGCGTTCCGGGGTCCTGTCTCAGTTTTGCATTATTTTTGGCAAA
191 ACGATTTTTTTTG-CTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCATA
* * * *
1976 AAGACACCTTGAAATATCTATATTCATCTAACCAAATTTCAGCCACATTGGATTTAAGGATTTAT
255 AAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAG-CACATTGGATTTAAGGATTTGT
***
2041 TTTTGTTAG
319 TTTTACGAG
* * * *
2050 CATCTAAATCTTGTTTCTATTTAATTAGAAATAAATTCGAGAAAAAAAATGGAAAAACAATATTA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAG-AAAAAAATGGAAAAACGATATTA
* * * ** *
2115 GAAGCGTGAAAA-CCCTTCAATTTTTTTTGTGTTGAATTATATATTTTTTCTTACTATTTTGGCA
65 GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTTACTATTGTGGCA
* * *
2179 AAGAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTCCATCACGA
130 AAAAATTGAGAAAAAAATTTTCAGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTCCATCACGA
* * * * *
2244 TTTTTTTTGCTAAAAAATGCGTTCTGGAGCCCCGACTCAGTTTTGAATGATTTTTGGCGTAAGGA
195 TTTTTTTTGCT-AAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGA
* * * *
2309 CTTCTTGCAATATCTATATTTATCAAACCAAATCTCAAGCACATTGGATCTAAGGATTTGTTTTT
259 CTCCTTGAAATATCTATATTCATCAAACCAAATCTC-AGCACATTGGATTTAAGGATTTGTTTTT
2374 ACGAG
323 ACGAG
***
2379 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAGAAAAATGAAAAAAAAAAACGATA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAG-AAAA--AAATGGAAAAACGATA
** * * * ** * *
2444 TTAGAAGCGTGAAAAGCCAATAAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGAAATATG
62 TTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTTACTATTGTG
** * * * ** *
2509 GCAAAATTTTCAGAAAAAAATTTTTCATGTCAGTTTTTAGCTGAAATCGT-GTAC-TAA----CC
127 GCAAAAAATTGAGAAAAAAA-TTTTCAGGTCAGTTTTT-GC-AAAATTTTAGT-CGAAATCGTCC
* ** * * * *
2568 ATCACGGTTTTTGGT-CTAAAAACGCGTTCTGG-GACCCCGGCTCAGTTTTGCCTGATTTTTGGA
188 ATCACGATTTTTTTTGCTAAAAACGCGTTCCGGAG-CCCCGACTCAGTTTTGCATGATTTTTGGC
* * * *
2631 AAAAAGACACCTTGAAATATCTATATTCAT-AGAACCAAATCTCAACCACATTGGATATAAGGAT
252 ATAAAGACTCCTTGAAATATCTATATTCATCA-AACCAAATCTC-AGCACATTGGATTTAAGGAT
2695 TTGTTTTTACGAG
315 TTGTTTTTACGAG
* * *
2708 TATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCG-GAAAAAAA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAA
2755 ATTGAGAAAA
Statistics
Matches: 1352, Mismatches: 254, Indels: 172
0.76 0.14 0.10
Matches are distributed among these distances:
319 12 0.01
320 154 0.11
321 16 0.01
322 30 0.02
323 100 0.07
324 71 0.05
325 8 0.01
326 16 0.01
327 92 0.07
328 90 0.07
329 305 0.23
330 23 0.02
331 94 0.07
332 51 0.04
333 135 0.10
334 19 0.01
335 11 0.01
336 48 0.04
338 3 0.00
339 43 0.03
340 21 0.02
341 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (327 bp):
CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAATGGAAAAACGATATTAG
AAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTTACTATTGTGGCAA
AAAATTGAGAAAAAAATTTTCAGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTCCATCACGAT
TTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACT
CCTTGAAATATCTATATTCATCAAACCAAATCTCAGCACATTGGATTTAAGGATTTGTTTTTACG
AG
Done.