Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016637.1 Corchorus olitorius cultivar O-4 contig16670, 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: 21701
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1541 original size:22 final size:22
Alignment explanation
Indices: 1477--1541 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
1467 ATCTCGATTA
1477 ATCTGAGATTT-ATCGTG---G
1 ATCTGAGATTTAATCGTGTTAG
* * *
1495 ATCT-ATATTAAATCTTGATTA-
1 ATCTGAGATTTAATCGTG-TTAG
1516 ATCTGAGATTTAATCGTGTTAG
1 ATCTGAGATTTAATCGTGTTAG
1538 ATCT
1 ATCT
1542 CAATTGAGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 4 0.12
18 9 0.26
21 7 0.21
22 14 0.41
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (22 bp):
ATCTGAGATTTAATCGTGTTAG
Found at i:7882 original size:19 final size:19
Alignment explanation
Indices: 7860--7920 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
7850 ATGTGTTTGT
7860 ATGTATTCGAACTGTTTAG
1 ATGTATTCGAACTGTTTAG
* *
7879 ATG--TTCGAAATGTGTTTG
1 ATGTATTCGAACTGT-TTAG
*
7897 TATGTATTCGAACTGTTTGG
1 -ATGTATTCGAACTGTTTAG
7917 ATGT
1 ATGT
7921 TCGAGATGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 9 0.26
18 3 0.09
19 10 0.29
20 3 0.09
21 9 0.26
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (19 bp):
ATGTATTCGAACTGTTTAG
Found at i:7887 original size:17 final size:17
Alignment explanation
Indices: 7865--7924 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
7855 TTTGTATGTA
7865 TTCGAACTGTTTAGATG
1 TTCGAACTGTTTAGATG
* *
7882 TTCGAAATGTGTTTGTATG
1 TTCGAACTGT-TTAG-ATG
*
7901 TATTCGAACTGTTTGGATG
1 --TTCGAACTGTTTAGATG
7920 TTCGA
1 TTCGA
7925 GATGGAAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 14 0.40
18 3 0.09
19 6 0.17
20 3 0.09
21 9 0.26
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (17 bp):
TTCGAACTGTTTAGATG
Found at i:7901 original size:38 final size:38
Alignment explanation
Indices: 7850--7924 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
7840 TTTTAATACC
7850 ATGTGTTTGTATGTATTCGAACTGTTTAGATGTTCGAA
1 ATGTGTTTGTATGTATTCGAACTGTTTAGATGTTCGAA
*
7888 ATGTGTTTGTATGTATTCGAACTGTTTGGATGTTCGA
1 ATGTGTTTGTATGTATTCGAACTGTTTAGATGTTCGA
7925 GATGGAAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (38 bp):
ATGTGTTTGTATGTATTCGAACTGTTTAGATGTTCGAA
Found at i:9534 original size:66 final size:66
Alignment explanation
Indices: 9439--9833 Score: 763
Period size: 66 Copynumber: 6.0 Consensus size: 66
9429 GTCCTTCCAT
*
9439 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGAAAGTTGGACTGCTGGTGTCCGGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9504 A
66 A
*
9505 TTGTGAAGTTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9570 A
66 A
9571 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9636 A
66 A
9637 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9702 A
66 A
9703 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9768 A
66 A
*
9769 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCTGCCA
1 TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
9834 TCTGAAGAGA
Statistics
Matches: 325, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 325 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (66 bp):
TTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCGGCCA
A
Found at i:12269 original size:17 final size:16
Alignment explanation
Indices: 12229--12271 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
12219 CATGTAATCT
*
12229 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
12245 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
12262 TTAGATCACT
1 TT-GATCACT
12272 AGTAATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:12279 original size:17 final size:16
Alignment explanation
Indices: 12222--12279 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
12212 ATAAACCCAT
*
12222 GTAATCTTTGATCACCG
1 GTAATC-TTGATCACTG
*
12239 GTGATCTTGCATCACTG
1 GTAATCTTG-ATCACTG
* *
12256 GTGATCTTAGATCACTA
1 GTAATCTT-GATCACTG
12273 GTAATCT
1 GTAATCT
12280 GGGGGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.09
17 31 0.89
18 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (16 bp):
GTAATCTTGATCACTG
Found at i:20149 original size:13 final size:13
Alignment explanation
Indices: 20119--20159 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
20109 AAGAAATATA
20119 TATATCTTA-T-C
1 TATATCTTACTAC
20130 T-TATCTTACTAC
1 TATATCTTACTAC
20142 TATATCTTACTAC
1 TATATCTTACTAC
20155 TATAT
1 TATAT
20160 AAAATCACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
12 2 0.07
13 16 0.59
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATCTTACTAC
Found at i:20724 original size:2 final size:2
Alignment explanation
Indices: 20717--20743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20707 TCACCGCCTG
20717 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20744 TCCTTACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21649 original size:2 final size:2
Alignment explanation
Indices: 21642--21691 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
21632 TGTCCAACCA
*
21642 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21684 AT AT AT AT
1 AT AT AT AT
21692 TGGAAAAGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.