Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020258.1 Corchorus olitorius cultivar O-4 contig20291, 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: 22914
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:774 original size:25 final size:24
Alignment explanation
Indices: 729--779 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
719 CTTGAATTTC
*
729 TTAATGCTTAATTCTTAAATTTAT
1 TTAATGCTTAATTATTAAATTTAT
*
753 TTAATGTCTTAATTATTCAATTTAT
1 TTAATG-CTTAATTATTAAATTTAT
778 TT
1 TT
780 TACAATCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAATGCTTAATTATTAAATTTAT
Found at i:1567 original size:17 final size:17
Alignment explanation
Indices: 1537--1571 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1527 TAAGATACGG
1537 TGTACATATAAATTATA
1 TGTACATATAAATTATA
1554 TGTA-ATATATAATTATA
1 TGTACATATA-AATTATA
1571 T
1 T
1572 ATTATATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (17 bp):
TGTACATATAAATTATA
Found at i:1578 original size:17 final size:17
Alignment explanation
Indices: 1542--1580 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1532 TACGGTGTAC
*
1542 ATATA-AATTATATGTA
1 ATATATAATTATATATA
*
1558 ATATATAATTATATATT
1 ATATATAATTATATATA
1575 ATATAT
1 ATATAT
1581 CAACAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATATAATTATATATA
Found at i:2029 original size:2 final size:2
Alignment explanation
Indices: 2022--2062 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2012 CAAATCAAAT
2022 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
2063 GATTCCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4704 original size:4 final size:4
Alignment explanation
Indices: 4695--4739 Score: 81
Period size: 4 Copynumber: 11.0 Consensus size: 4
4685 AAAAGGGGTG
4695 AATT AATT AATT AATT AATAT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AAT-T AATT AATT AATT AATT AATT AATT
4740 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:4747 original size:2 final size:2
Alignment explanation
Indices: 4740--4769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4730 TTAATTAATT
4740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4770 GTAACAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11798 original size:37 final size:38
Alignment explanation
Indices: 11723--11806 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 38
11713 TTTGGCATGC
11723 ATCTATATAGACAATACATTATTTCTCTTTATTTATTTATATT
1 ATCTATATAGACAATACATTA----T-TTTATTTATTTATATT
11766 ATCTATATAGACAATACATTA-TTTATTTATTTATATT
1 ATCTATATAGACAATACATTATTTTATTTATTTATATT
11803 -TCTA
1 ATCTA
11807 ATTAGCCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
36 4 0.10
37 16 0.39
43 21 0.51
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (38 bp):
ATCTATATAGACAATACATTATTTTATTTATTTATATT
Found at i:12178 original size:6 final size:6
Alignment explanation
Indices: 12167--12192 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12157 TTGAATGATC
12167 AAACCA AAACCA AAACCA AAACCA AA
1 AAACCA AAACCA AAACCA AAACCA AA
12193 TCCCAAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:15954 original size:12 final size:12
Alignment explanation
Indices: 15937--15961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15927 ATTTACTGAT
15937 TATGCTCTATGC
1 TATGCTCTATGC
15949 TATGCTCTATGC
1 TATGCTCTATGC
15961 T
1 T
15962 CTATCACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TATGCTCTATGC
Found at i:18362 original size:8 final size:7
Alignment explanation
Indices: 18315--18365 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
18305 TTTCTTAATT
18315 TTTTTTC
1 TTTTTTC
18322 TTTTTTAC
1 TTTTTT-C
*
18330 GTTTTTC
1 TTTTTTC
*
18337 TCTTTTC
1 TTTTTTC
*
18344 TTCTTTC
1 TTTTTTC
18351 -TTTTTC
1 TTTTTTC
*
18357 TGTTTTC
1 TTTTTTC
18364 TT
1 TT
18366 CCTTTCTTCC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 5 0.15
7 23 0.68
8 6 0.18
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:20344 original size:69 final size:69
Alignment explanation
Indices: 20229--20367 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
20219 CCACCGCCCT
* *
20229 TCCGATTCCGACATCATCATAAATCACAGACGAATCCTCATTGTAATTCCTGATCTGTTGCGCAA
1 TCCGATTCCGACATCATCATAAATCACAGACGAATCCTCATCGTAATTCCTGATCTGTTGCACAA
20294 TAGG
66 TAGG
* *
20298 TCCGATTCCGACATCATCATAAATTACAGACGAATCCTCATCGTAATTCGTGATCTGTTGCACAA
1 TCCGATTCCGACATCATCATAAATCACAGACGAATCCTCATCGTAATTCCTGATCTGTTGCACAA
20363 TAGG
66 TAGG
20367 T
1 T
20368 GGTGATTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (69 bp):
TCCGATTCCGACATCATCATAAATCACAGACGAATCCTCATCGTAATTCCTGATCTGTTGCACAA
TAGG
Found at i:20902 original size:36 final size:36
Alignment explanation
Indices: 20862--20937 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
20852 TTGTTGCGTC
20862 AGATGGACGCTTTGTGTTTGAAAATATGCGTGAGTG
1 AGATGGACGCTTTGTGTTTGAAAATATGCGTGAGTG
20898 AGATGGACGCTTTGTGTTTGAAAATATGCGTGAGTG
1 AGATGGACGCTTTGTGTTTGAAAATATGCGTGAGTG
20934 AGAT
1 AGAT
20938 CAAGACTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.33
Consensus pattern (36 bp):
AGATGGACGCTTTGTGTTTGAAAATATGCGTGAGTG
Done.