Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005567.1 Corchorus capsularis cultivar CVL-1 contig05585, 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: 2032
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:929 original size:322 final size:322
Alignment explanation
Indices: 342--1907 Score: 2131
Period size: 322 Copynumber: 4.9 Consensus size: 322
332 ATCGGGCTTC
*
342 GTTAGTACACGATTTTGGCAAAAAATTGACCCGAAAATTTTTTTCTCAATTTTTTCGCCAAAATA
1 GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTCAA-TTTTTCGCCAAAATA
*
407 CACAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
65 CTCAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
* * * ** *
472 TACCCA-TTTTTTCCTAATTAA-TTCTAATTAAACCGAAATC-AAATTGAGATGCTCAAAAAAAT
130 TACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA-CAAAATTCAGATGCTCGTAAAAAG
*
534 AAATCTGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTA
194 AAATCT-TAAATTCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTA
599 CGCAAAAAATTAGGCAAAACTGAGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
258 CGCAAAAAATTAGGCAAAACTGAGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
*
664 GTTAGTACACGATTTCGGCAAGAAATTGACCCGAAAATTTTTTTCTCAATTTTTCGCCAAAATAC
1 GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTCAATTTTTCGCCAAAATAC
* * * * *
729 TCAGCAAAAATAAATAATTCAATGTCAAAAAAATTGAAA-GCTTTTCACCCTTTTAATATCGTTT
66 TCAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTT
793 ACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAA
131 ACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAA
* * *
858 ATCTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGTGTTTACA
196 ATCTTAA-ATTCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACG
*
923 CAAAAAATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
260 CAAAAAATTAGGCAAAACTGAGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
* * * *
986 GTTAGTACACGATTTCGGCAAAAAATTGTCCCGAAAACTTTATTCTCAAATTTCTCGCCAAAATA
1 GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTC-AATTTTTCGCCAAAATA
* * *
1051 CACAGAAAAAATNTATAATTCAATGT-AAAAAAATTAAAAGGTTTTTCACGCTTCTAATATCGTT
65 CTCAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
** *
1115 TACAAACTTTTTTTTTCCGAATTAATTT-TCAATTAAATCGAAACAAAATTCAGATGCTTGTAAA
130 TAC---CCATTTTTTTCCGAATTAATTTCT-AATTAAATCGAAACAAAATTCAGATGCTCGTAAA
* * * * *
1179 AAGAAATCTTTAATTCTAATGAGGTTGAGATCTGGTTCAATAAATATAGATAACTCAAGGAGTCT
191 AAGAAATCTTAAATTC-AATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCT
* * * * *** **
1244 TTACGCTAAAAATCAGGCAAAACTGAATCAGGGTTTTC-GACTGCGTTTTTAGCAAAAACCAATG
255 TTACGCAAAAAATTAGGCAAAACTG-AGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTG
*
1308 AT-G
319 ATAT
* * *
1311 GTTAATACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTCTCTCAAATTTTTCGCAAAAATA
1 GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTC-AATTTTTCGCCAAAATA
* * * *
1376 CTCAGAAAAAAAATATAATTCAATGCCAAAAAAAATTGAAAGGTTTTTAACGCTTCTAATATCAT
65 CTCAGAAAAAATATATAATTCAATGTC-AAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGT
* *
1441 TTAACCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGCTCGTAAAAAG
129 TTACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAG
* *
1506 AAATCTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGTGTTTA
194 AAATCTTAA-ATTCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTA
* * *
1571 CGCAAAATATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCTGTGATA-
258 CGCAAAAAATTAGGCAAAACTGAGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
* * * *
1635 GTTAATACAAGATTT---C--AGAA---A----AAAA--TTATTCTCAATTTTTTCGCCAAAATA
1 GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTCAA-TTTTTCGCCAAAATA
*
1686 CTCAGGAAAAATATATAATTCAATG-CAAAAATAATTGAAAGGTTTTTCACGCTTCTAATATCGT
65 CTCAGAAAAAATATATAATTCAATGTCAAAAA-AATTGAAAGGTTTTTCACGCTTCTAATATCGT
* * * ***
1750 TTACCCATTTTTTTCCCAATTAA-TTCTAATTAAACCGAAATC-AAATTGAGATGCTTAAAAAAA
129 TTACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA-CAAAATTCAGATGCTCGTAAAAA
* * *
1813 TAAATCTGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTATTT
193 GAAATCT-TAAATTCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTT
*
1878 ATGCAAAAAATTAGGCAAAACTGAGCCGGG
257 ACGCAAAAAATTAGGCAAAACTGAGCCGGG
1908 ATGTAGTTCA
Statistics
Matches: 1107, Mismatches: 115, Indels: 58
0.86 0.09 0.05
Matches are distributed among these distances:
308 122 0.11
309 57 0.05
310 43 0.04
312 4 0.00
316 1 0.00
319 3 0.00
320 27 0.02
321 71 0.06
322 257 0.23
323 68 0.06
324 167 0.15
325 90 0.08
326 154 0.14
327 43 0.04
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (322 bp):
GTTAGTACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTTTCTCAATTTTTCGCCAAAATAC
TCAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTT
ACCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAA
ATCTTAAATTCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACGC
AAAAAATTAGGCAAAACTGAGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATAT
Found at i:1585 original size:650 final size:640
Alignment explanation
Indices: 342--1901 Score: 2308
Period size: 650 Copynumber: 2.4 Consensus size: 640
332 ATCGGGCTTC
*
342 GTTAGTACACGATTTTGGCAAAAAATTGACCCGAAAATTTTTTTCTCAATTTTTTCGCCAAAATA
1 GTTAGTACACGA-TTTGGCAAAAAATTG-CCCGAAAA-TTTATTCTCAATTTTTTCGCCAAAATA
407 CACAGAAAAAATATATAATTCAATGTCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
63 CACAGAAAAAATATATAATTCAATGT-AAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
* *
472 TACCCA-TTTTTTCCTAATTAATTCTAATTAAACCGAAATCAAATTGAGATGCTCAAAAAAATAA
127 TA-CCATTTTTTTCCCAATTAATTCTAATTAAACCGAAATCAAATTGAGATGCTTAAAAAAATAA
536 ATCTGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACG
191 ATCTGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACG
* ** *
601 CAAAAAATTAGGCAAAACTG-AGCCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATATG
256 CAAAAAATTAGGCAAAACTGAAGCAGGGGCATCGGACTGCGTTTTTAGCAAAAACCAATGATAGG
* * * *
665 TTAGTACACGATTTCGGCAAGAAATTGACCCGAAAATTTTTTTCTCAATTTTTCGCCAAAATACT
321 TTAATACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTCTCTCAATTTTTCGCAAAAATACT
* * * * * *
730 CAGCAAAAATAAATAATTCAATGTCAAAAAAATTGAAAGCTTTTCACCCTTTTAATATCGTTTAC
386 CAGCAAAAAAAAATAATTCAATGCCAAAAAAATTGAAAGCTTTTAACCCTTCTAATATCATTTAA
*
795 CCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAAT
451 CCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGCTCGTAAAAAGAAAT
860 CTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGTGTTTACACA
516 CTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGTGTTTACACA
925 AAAAATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATA
581 AAAAATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATA
* *
985 TGTTAGTACACGATTTCGGCAAAAAATTGTCCCGAAAACTTTATTCTCAAATTTCTCGCCAAAAT
1 -GTTAGTACACGATTT-GGCAAAAAATTG-CCCGAAAA-TTTATTCTCAATTTTTTCGCCAAAAT
* *
1050 ACACAGAAAAAATNTATAATTCAATGTAAAAAAATTAAAAGGTTTTTCACGCTTCTAATATCGTT
62 ACACAGAAAAAATATATAATTCAATGTAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTT
* * * * * **
1115 TACAAACTTTTTTTTTCCGAATTAATTTTCAATTAAATCGAAA-CAAAATTCAGATGCTTGTAAA
127 TAC---C-ATTTTTTTCCCAATTAATTCT-AATTAAACCGAAATC-AAATTGAGATGCTTAAAAA
* * * * * * * *
1179 AAGAAATCTTTAATTCTAATGAGGTTGAGATCTGGTTCAATAAATATAGATAACTCAAGGAGTCT
186 AATAAATCTGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCT
* * * ***
1244 TTACGCTAAAAATCAGGCAAAACTGAATCAGGGTTTTC-GACTGCGTTTTTAGCAAAAACCAATG
251 TTACGCAAAAAATTAGGCAAAACTGAAGCAGGGGCATCGGACTGCGTTTTTAGCAAAAACCAATG
1308 AT-GGTTAATACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTCTCTCAAATTTTTCGCAAA
316 ATAGGTTAATACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTCTCTC-AATTTTTCGCAAA
* *
1372 AATACTCAG-AAAAAAAATATAATTCAATGCCAAAAAAAATTGAAAGGTTTTTAACGCTTCTAAT
380 AATACTCAGCAAAAAAAA-ATAATTCAATGCC-AAAAAAATTGAAA-GCTTTTAACCCTTCTAAT
1436 ATCATTTAACCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGCTCGTA
442 ATCATTTAACCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGCTCGTA
1501 AAAAGAAATCTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGT
507 AAAAGAAATCTTAATATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGT
* * *
1566 GTTTACGCAAAATATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCTGT
572 GTTTACACAAAAAATTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGT
1631 GATA
637 GATA
* * * *
1635 GTTAATACAAGATTT--C-AGAAA-------AAAA-TTATTCTCAATTTTTTCGCCAAAATACTC
1 GTTAGTACACGATTTGGCAAAAAATTGCCCGAAAATTTATTCTCAATTTTTTCGCCAAAATACAC
* *
1689 AGGAAAAATATATAATTCAATGCAAAAATAATTGAAAGGTTTTTCACGCTTCTAATATCGTTTAC
66 AGAAAAAATATATAATTCAATGTAAAAA-AATTGAAAGGTTTTTCACGCTTCTAATATCGTTTA-
1754 CCATTTTTTTCCCAATTAATTCTAATTAAACCGAAATCAAATTGAGATGCTTAAAAAAATAAATC
129 CCATTTTTTTCCCAATTAATTCTAATTAAACCGAAATCAAATTGAGATGCTTAAAAAAATAAATC
* *
1819 TGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTATTTATGCAA
194 TGTAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACGCAA
1884 AAAATTAGGCAAAACTGA
259 AAAATTAGGCAAAACTGA
1902 GCCGGGATGT
Statistics
Matches: 822, Mismatches: 78, Indels: 44
0.87 0.08 0.05
Matches are distributed among these distances:
632 107 0.13
633 19 0.02
634 1 0.00
635 51 0.06
636 34 0.04
637 5 0.01
642 1 0.00
643 42 0.05
644 81 0.10
645 5 0.01
646 1 0.00
647 69 0.08
648 166 0.20
649 33 0.04
650 207 0.25
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (640 bp):
GTTAGTACACGATTTGGCAAAAAATTGCCCGAAAATTTATTCTCAATTTTTTCGCCAAAATACAC
AGAAAAAATATATAATTCAATGTAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTTACC
ATTTTTTTCCCAATTAATTCTAATTAAACCGAAATCAAATTGAGATGCTTAAAAAAATAAATCTG
TAAATCCAATGTGGTTGAGATTTGGTTCGATAAATATAGATATCTCAAGGAGTCTTTACGCAAAA
AATTAGGCAAAACTGAAGCAGGGGCATCGGACTGCGTTTTTAGCAAAAACCAATGATAGGTTAAT
ACACGATTTCGGCAAAAAATTGACCCGAAAATTTTTCTCTCAATTTTTCGCAAAAATACTCAGCA
AAAAAAAATAATTCAATGCCAAAAAAATTGAAAGCTTTTAACCCTTCTAATATCATTTAACCATT
TTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGCTCGTAAAAAGAAATCTTAA
TATTCAATGTGGTTGAGATTTAGTTCGATAAATATAGATATCTCAAGGAGTGTTTACACAAAAAA
TTAGGCAAAACTGAGTCGGGGCATCGGACTGCGTTTTTAGCAAAAACCCGTGATA
Done.