Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009267.1 Corchorus capsularis cultivar CVL-1 contig09288, 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: 4708
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:746 original size:50 final size:49
Alignment explanation
Indices: 618--1000 Score: 382
Period size: 49 Copynumber: 7.8 Consensus size: 49
608 TTTCACTCGC
* * *
618 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTG-T
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
* * * *
666 TTTTCTCAGAACGCCCTTCCCGGATGGAAGGCACTGAGTTTTACCTGTT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
* * **
715 TTTTCCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATCTTCAAATGTT
1 TTTT-CCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
*
765 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCATTGATTTTTACCTGTT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
* * ** * **
814 TTCTT---AAAACGCCCTTCCCGGA-GGAAAGGCATTAATCCTTACTTGCA
1 TT-TTCCCAAAACGCCCTTCCCGGACGG-AAGGCACTGATTTTTACCTGTT
* * * * *
861 TTTACCCAAAACGCCCTTCCCGGATGGAAGGCACTAATTTTTACTTGCT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
* * * ** *
910 TTTTCCTAAAATGCCTTTCCCGGACGGAAGGCACCAACTTTTA-CTCGCTT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCT-G-TT
* * *
960 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCGCTAATTTT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTT
1001 ACTCGCTTTT
Statistics
Matches: 280, Mismatches: 45, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
46 3 0.01
47 35 0.12
48 41 0.15
49 119 0.43
50 82 0.29
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (49 bp):
TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
Found at i:930 original size:145 final size:147
Alignment explanation
Indices: 618--988 Score: 426
Period size: 145 Copynumber: 2.5 Consensus size: 147
608 TTTCACTCGC
* * *
618 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCTCAGAACGCCCT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTAATTTTTACCTG-TTTTCTTAAAACGCCCT
* * * ** *
683 TCCCGGATGG-AAGGCACTGAGTTTTACCTGTTTTTTCCCCAAAACGCCCTTCCCGGACGGAAGG
65 TCCCGGACGGAAAGGCACTGAATCTTACCTGTCATTTACCCAAAACGCCCTTCCCGGACGGAAGG
* *
747 CACTGATCTTCAAATGTT
130 CACTAATCTTCAAATGCT
* *
765 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCATTGATTTTTACCTGTTTTCTTAAAACGCCCTT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTAATTTTTACCTGTTTTCTTAAAACGCCCTT
* * *
830 CCCGGA-GGAAAGGCA-TTAATCCTTACTTG-CATTTACCCAAAACGCCCTTCCCGGATGGAAGG
66 CCCGGACGGAAAGGCACTGAAT-CTTACCTGTCATTTACCCAAAACGCCCTTCCCGGACGGAAGG
* * **
892 CACTAATTTTTACTTGCT
130 CACTAATCTTCAAATGCT
* * ** * * *
910 TTTTCCTAAAATGCCTTTCCCGGACGGAAGGCACCAACTTTTACTCGCTTTTTTCCTAAAACGCC
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTAATTTTTA--C-CTGTTTTCTTAAAACGCC
975 CTTCCCGGACGGAA
63 CTTCCCGGACGGAA
989 GGCGCTAATT
Statistics
Matches: 191, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
145 82 0.43
146 34 0.18
147 46 0.24
148 25 0.13
149 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (147 bp):
TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTAATTTTTACCTGTTTTCTTAAAACGCCCTT
CCCGGACGGAAAGGCACTGAATCTTACCTGTCATTTACCCAAAACGCCCTTCCCGGACGGAAGGC
ACTAATCTTCAAATGCT
Found at i:1001 original size:98 final size:99
Alignment explanation
Indices: 618--1012 Score: 366
Period size: 99 Copynumber: 4.1 Consensus size: 99
608 TTTCACTCGC
* * * * * *
618 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTA--C-CTGTTTTTCTCAGAACGC
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAACTTTTACTCGCT-TTTTTCCCAAAACGC
* * *
680 CCTTCCCGGATGGAAGGCACTGAGTTTTACCTGTT
65 CCTTCCCGGACGGAAGGCACTGAATTTTACCTGCT
* ** *
715 TTTTCCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATCTTCAAAT-G-TTTTTTCCCAAAACG
1 TTTT-CCCAAAACGCCCTTCCCGGACGGAAGGCACT-AACTTTTACTCGCTTTTTTCCCAAAACG
* *
778 CCCTTCCCGGACGGAAGGCATTGATTTTTACCTG--
64 CCCTTCCCGGACGGAAGGCACTGAATTTTACCTGCT
** * * * * *
812 TTTTCTTAAAACGCCCTTCCCGGA-GGAAAGGCATTAA-TCCTTACTTGC-ATTTACCCAAAACG
1 TTTTCCCAAAACGCCCTTCCCGGACGG-AAGGCACTAACT-TTTACTCGCTTTTTTCCCAAAACG
* *
874 CCCTTCCCGGATGGAAGGCACT-AATTTTTACTTGCT
64 CCCTTCCCGGACGGAAGGCACTGAA-TTTTACCTGCT
* * * * *
910 TTTTCCTAAAATGCCTTTCCCGGACGGAAGGCACCAACTTTTACTCGCTTTTTTCCTAAAACGCC
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAACTTTTACTCGCTTTTTTCCCAAAACGCC
*
975 CTTCCCGGACGGAAGGCGCT-AATTTTA-CTCGCT
66 CTTCCCGGACGGAAGGCACTGAATTTTACCT-GCT
1008 TTTTC
1 TTTTC
1013 TTGAAGTGCC
Statistics
Matches: 243, Mismatches: 39, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
94 1 0.00
95 6 0.02
96 66 0.27
97 9 0.04
98 78 0.32
99 82 0.34
100 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (99 bp):
TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAACTTTTACTCGCTTTTTTCCCAAAACGCC
CTTCCCGGACGGAAGGCACTGAATTTTACCTGCT
Done.