Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007468.1 Corchorus capsularis cultivar CVL-1 contig07489, 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: 11894
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2137 original size:43 final size:43
Alignment explanation
Indices: 2053--2148 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 43
2043 TGATTTTTTT
2053 ACTCAAATAAATGCCGCCTATTTTTTATTTAACAAAATTTTCCC
1 ACTCAAATAAA-GCCGCCTATTTTTTATTTAACAAAATTTTCCC
** *
2097 ACTCAAATAAA-CCTGCCTA-TTTTTATTTTCCAAAATTTTTCC
1 ACTCAAATAAAGCC-GCCTATTTTTTATTTAACAAAATTTTCCC
2139 -CTCTAAATAA
1 ACTC-AAATAA
2149 TTGTTACAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 3 0.06
42 28 0.60
43 5 0.11
44 11 0.23
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (43 bp):
ACTCAAATAAAGCCGCCTATTTTTTATTTAACAAAATTTTCCC
Found at i:5680 original size:12 final size:13
Alignment explanation
Indices: 5651--5691 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
5641 TTTACTTTTC
5651 CTTTGCATTGATTTG
1 CTTTG-ATTGA-TTG
5666 CTTTGATT-ATTG
1 CTTTGATTGATTG
5678 CTTTGATTGATTG
1 CTTTGATTGATTG
5691 C
1 C
5692 CTATTCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.44
13 6 0.24
14 3 0.12
15 5 0.20
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.54
Consensus pattern (13 bp):
CTTTGATTGATTG
Found at i:8020 original size:18 final size:17
Alignment explanation
Indices: 7993--8028 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
7983 TTTCTCTTCA
7993 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
8010 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
8028 T
1 T
8029 TTAGGTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:8869 original size:17 final size:17
Alignment explanation
Indices: 8833--8870 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
8823 TTTTTGAGTG
*
8833 ATTCTTAGATAAGATTT
1 ATTCTTAGATAAGATCT
8850 ATTCTTTAGATAAG-TCT
1 ATTC-TTAGATAAGATCT
8867 ATTC
1 ATTC
8871 CCCTTCTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (17 bp):
ATTCTTAGATAAGATCT
Found at i:11084 original size:24 final size:24
Alignment explanation
Indices: 11057--11106 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
11047 AAAAATATTA
*
11057 TTAATAAT-ATATTTAAATTAAAAT
1 TTAATAATGATATAT-AATTAAAAT
*
11081 TTAATTATGATATATAATTAAAAT
1 TTAATAATGATATATAATTAAAAT
11105 TT
1 TT
11107 TACAACGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAATAATGATATATAATTAAAAT
Found at i:11329 original size:19 final size:18
Alignment explanation
Indices: 11283--11322 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
11273 TTTTGGTCAG
*
11283 TTTTACATTCGGGGGCAT
1 TTTTACATTCAGGGGCAT
11301 TTTTACATTCAGGGGCAT
1 TTTTACATTCAGGGGCAT
11319 TTTT
1 TTTT
11323 GTCATTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (18 bp):
TTTTACATTCAGGGGCAT
Done.