Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020867.1 Corchorus olitorius cultivar O-4 contig20900, 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: 11337
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:766 original size:42 final size:42
Alignment explanation
Indices: 707--789 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
697 GATGGGCTTT
707 TCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATTAGG
1 TCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATTAGG
*
749 TCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCGAATTAG
1 TCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATTAG
790 TTTCTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.48
Consensus pattern (42 bp):
TCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATTAGG
Found at i:1805 original size:41 final size:42
Alignment explanation
Indices: 1748--1833 Score: 156
Period size: 41 Copynumber: 2.0 Consensus size: 42
1738 TGACGGGTTT
1748 TTCACTCTTCTAAAATCGTTTTTCCA-TTTTTTCCGAATTAG
1 TTCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCGAATTAG
1789 TTCACTCTTCTAAAATCGTTTTTCCATTTTTTTTCCGAATTAG
1 TTCACTCTTCTAAAATCGTTTTTCCA-TTTTTTTCCGAATTAG
1832 TT
1 TT
1834 TCTAATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 26 0.60
43 17 0.40
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (42 bp):
TTCACTCTTCTAAAATCGTTTTTCCATTTTTTTCCGAATTAG
Found at i:3217 original size:662 final size:651
Alignment explanation
Indices: 1795--3601 Score: 2504
Period size: 662 Copynumber: 2.7 Consensus size: 651
1785 TTAGTTCACT
* * ** *
1795 CTTCTAAAATCGTTTTTCCATTTTTTTTCCGAA-TTAGTTTCTAATTAAATCGAATCAAGATTCA
1 CTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTA-TTTCAAATTAAATCGAAAGAAGATACA
* * * * * * * *
1859 GATGCTCGTAAAAACAAATCGTTACATCGAATTTGTCTGGAT-TTTGGTTCGACGAATATAGGTA
65 GATGCTCGTAAAAATAAATCCTTAAATCCAATTTGGCT-GATATTTGGTTAGATGAATATAGATA
* * * * * * * * *
1923 TTTCAAGGAGTCTTTACGCGAAAAATCATGCAAAACTGAGCCGGAACCCCGGAAA-GTGTTTTTA
129 TTTCAAAGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTCGG-GCCCC-GAAACGCGATTTTA
* ** * *
1987 G-CAAAAACCGTGATGGTTAGTATACGGTTTCGGCTAAAATTTTGAAAAAATTGACCCG-AAAA-
192 GCCAAAAACCGTGATGGTTAGTACACAATTTCGGC--------T--AAAAACTGGCCCGCAAAAT
* * * *
2049 TTTTTTCCTCAATTATT-TTACGACAATACTCAG-AAAAATATATAATT-ATCACCAAAAATATT
247 TTTTTTCCTAAATT-TTCCT-CCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATT
* *
2111 GACGGGCTTTTCACTCTTCTAAAATCGTTTTTCCA-TTTTTTCCGAATTAGTTTCTAATTAAATC
310 GACGGGCTTTTCACTCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATC
*
2175 GAAACAAGATTCATATGCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGA
375 GAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGA
* *
2240 TGAATATAGGTATTTCAAGTAGTCTTTACGCCAAAAATCATACAAAACTGAGCCGGGACCCCGGA
440 TGAATATAGGTATTTCAAGCAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGA
*
2305 ACGTGTTTTTAGCAAAAAACCGTGATGGTTACGGTTTCGGCTAAAATTTTGAAAAAATTCACCCG
505 ACGTGTTTTTAGAAAAAAACCGTGATGGTTACGGTTTCGGCTAAAATTTTGAAAAAATTCACCCG
* * *
2370 AAAATTTTATTCCTCAATTATTTTGCGACAATAGTGAGGAAAATATATAATTCAACCGAAAAATA
570 AAAATTTTATTCCTCAATTATTTTGCGAAAATAGTCAGGAAAATATATAATTCAACCGAAAAAAA
2435 TTGAAGGGTTTTACACG
635 TTGAAGGGTTTTACACG
* *
2452 CTTCTAATACCGTTTTTCCTTTTTTTTTCCGAATTTATTTCAAATTAAATCGAAAGAAGATACAG
1 CTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCAAATTAAATCGAAAGAAGATACAG
* *
2517 ATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGATATTTGGTTAGATAAATATAGATATT
66 ATGCTCGTAAAAATAAATCCTTAAATCCAATTTGGCTGATATTTGGTTAGATGAATATAGATATT
*
2582 TCAATGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTCAGGGCCCCGAAACGCGATTTTAGCC
131 TCAAAGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTC-GGGCCCCGAAACGCGATTTTAGCC
2647 AAAAAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGGCCCGCAAAATTTTTTTCCT
195 ----AAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGGCCCGCAAAATTTTTTTCCT
2712 AAATTTTCCTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTT
256 AAATTTTCCTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTT
*
2777 CACTCTTCTAATATCGTTTTTCCATTTTTTTCCGACTTAATTTCTAATTAAATCGAAACAAGATT
321 CACTCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
2842 CAGATGCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGATGAATATAGGT
386 CAGATGCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGATGAATATAGGT
*
2907 ATTTCAAGCAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGTGTTTTTA
451 ATTTCAAGCAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGTGTTTTTA
* *
2972 GGAAAAAAACCGTGATGTTAGTATATGGTTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAATT
516 -GAAAAAAACCGTGATG---GT-TACGGTTTCGGCTAAAATTTTGAAAAAATTCACCCGAAAATT
*
3037 TTTTTCCTCAATTATTTTGCGAAAATAGTCAGGAAAAATATATAATTCAACCGAAAAAAATTGAA
576 TTATTCCTCAATTATTTTGCGAAAATAGTCAGG-AAAATATATAATTCAACCGAAAAAAATTGAA
*
3102 GGGTTTTTCACG
640 GGGTTTTACACG
* * *
3114 CTTTTATTATCGTTTTTCAATTTTTTTTCCGAATTTATTTCAAATTAAATCGAAAGAAGATACAG
1 CTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCAAATTAAATCGAAAGAAGATACAG
* *
3179 ATTCTCGTAAAAATAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATT
66 ATGCTCGTAAAAATAAATCCTTAAATCCAATTTGGCTGATATTTGGTTAGATGAATATAGATATT
* *
3244 TCAAAGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTCGTGGCCCCAAAACGCGGTTTTAGCC
131 TCAAAGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTCG-GGCCCCGAAACGCGATTTTAG-C
* * * * *
3309 CAAAAACCGTGATGGTTAGAACATAATTTCGGCTAAAAACAGAG-TCGCAAAATTTTTTTTCCTG
194 CAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTG-GCCCGCAAAA-TTTTTTTCCTA
* * *
3373 AATTTTCCGCCACAATA-TTAGAAAAAATATATAATTCAACACCAAAAATATTGGCGGGCTTTTC
257 AATTTTCCTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTTC
* * ** *
3437 ACTCTTCTAATATCGTTTTTCCATTTTTGTCTGAATTAATTTCTAATTAAATCTTAAGAAGATTC
322 ACTCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * * * * *
3502 GGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGATA
387 AGATGCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGATGAATATAGGTA
* * * *
3567 TTTCAAGGAGTCTTTGCCCCAAAAACCATGCAAAA
452 TTTCAAGCAGTCTTTACGCCAAAAATCATGCAAAA
3602 TTTTGTCGGT
Statistics
Matches: 1037, Mismatches: 88, Indels: 48
0.88 0.08 0.04
Matches are distributed among these distances:
652 11 0.01
653 18 0.02
654 29 0.03
655 48 0.05
656 171 0.16
657 166 0.16
658 6 0.01
659 237 0.23
660 29 0.03
661 71 0.07
662 249 0.24
663 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (651 bp):
CTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCAAATTAAATCGAAAGAAGATACAG
ATGCTCGTAAAAATAAATCCTTAAATCCAATTTGGCTGATATTTGGTTAGATGAATATAGATATT
TCAAAGAGTCTTTATGCCAAAACTCATCCAAAACTGAGTCGGGCCCCGAAACGCGATTTTAGCCA
AAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGGCCCGCAAAATTTTTTTCCTAAATT
TTCCTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTTCACTC
TTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
GCTCGTAAAAACAAATCGTTACATCGAATTTGGCTGGGATTTGGTTCGATGAATATAGGTATTTC
AAGCAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGTGTTTTTAGAAAA
AAACCGTGATGGTTACGGTTTCGGCTAAAATTTTGAAAAAATTCACCCGAAAATTTTATTCCTCA
ATTATTTTGCGAAAATAGTCAGGAAAATATATAATTCAACCGAAAAAAATTGAAGGGTTTTACAC
G
Found at i:8045 original size:21 final size:20
Alignment explanation
Indices: 8001--8055 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
7991 TTTAACAATG
8001 GTACAGATGAGATT-ATAAT
1 GTACAGATGAGATTAATAAT
* *
8020 GTACAGATTAGATTAGATACT
1 GTACAGATGAGATTA-ATAAT
*
8041 GTACATATGAGATTA
1 GTACAGATGAGATTA
8056 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (20 bp):
GTACAGATGAGATTAATAAT
Done.