Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023655.1 Corchorus olitorius cultivar O-4 contig23688, 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: 32182
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7077 original size:11 final size:11
Alignment explanation
Indices: 7061--7085 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7051 ATTTTAGATC
7061 TTTTCTTCTAG
1 TTTTCTTCTAG
7072 TTTTCTTCTAG
1 TTTTCTTCTAG
7083 TTT
1 TTT
7086 AGGCAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:10707 original size:19 final size:18
Alignment explanation
Indices: 10683--10718 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10673 TGAAGACTTA
10683 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10702 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10719 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:13169 original size:46 final size:46
Alignment explanation
Indices: 13102--13189 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
13092 GTTACCAATT
13102 TTTATTTAATTCAAATATCAATTAAATTAATTAAGGTCTTTCCAAG
1 TTTATTTAATTCAAATATCAATTAAATTAATTAAGGTCTTTCCAAG
*
13148 TTTATTTAATTCAAATATCAATTAAATTATTTAAGGTCTTTC
1 TTTATTTAATTCAAATATCAATTAAATTAATTAAGGTCTTTC
13190 AAGAAATTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.47
Consensus pattern (46 bp):
TTTATTTAATTCAAATATCAATTAAATTAATTAAGGTCTTTCCAAG
Found at i:14093 original size:7 final size:7
Alignment explanation
Indices: 14083--14118 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
14073 TTTTTTTTTC
14083 CTTGTTA
1 CTTGTTA
14090 CTTGTTA
1 CTTGTTA
14097 CTTGTTA
1 CTTGTTA
14104 CTTGTTA
1 CTTGTTA
*
14111 GTTGTTA
1 CTTGTTA
14118 C
1 C
14119 CCAATACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.56
Consensus pattern (7 bp):
CTTGTTA
Found at i:22744 original size:19 final size:19
Alignment explanation
Indices: 22720--22756 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
22710 TGTTTATTGG
22720 TACATTATCATTTGATTAA
1 TACATTATCATTTGATTAA
22739 TACATTATCATTTGATTA
1 TACATTATCATTTGATTA
22757 GTGTCGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (19 bp):
TACATTATCATTTGATTAA
Found at i:22935 original size:42 final size:44
Alignment explanation
Indices: 22884--22977 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
22874 AAAGTATTAC
* *
22884 CTAA-ATTCTA-T-TCCATCTTTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTATTCTCCATCTCTAGATAATTCATCAAAATAAAG
22925 CTAATATTCTATTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTATT-CTCCATCTCTAGATAATTCATCAAAATAAAG
*
22970 TTAATATT
1 CTAATATT
22978 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
43 1 0.02
45 35 0.76
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (44 bp):
CTAATATTCTATTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:24639 original size:7 final size:7
Alignment explanation
Indices: 24627--24655 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
24617 CATAACTCCC
24627 TCAACAA
1 TCAACAA
24634 TCAACAA
1 TCAACAA
24641 TCAACAA
1 TCAACAA
24648 TCAACAA
1 TCAACAA
24655 T
1 T
24656 AATAACGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (7 bp):
TCAACAA
Found at i:24775 original size:2 final size:2
Alignment explanation
Indices: 24768--24813 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
24758 TTCAACTTTA
* * *
24768 AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT AT GT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24808 AT AT AT
1 AT AT AT
24814 GCAAGTGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (2 bp):
AT
Found at i:24814 original size:14 final size:16
Alignment explanation
Indices: 24769--24814 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
24759 TCAACTTTAA
*
24769 TATATATATATATATAT
1 TATAT-TATATATATGT
24786 TATATTATATATATGT
1 TATATTATATATATGT
24802 T-TATT-TATATATG
1 TATATTATATATATG
24815 CAAGTGCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
16 11 0.39
17 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TATATTATATATATGT
Found at i:26739 original size:2 final size:2
Alignment explanation
Indices: 26726--26757 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
26716 TCTATGAAGC
26726 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
26758 GAGATAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.