Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020693.1 Corchorus olitorius cultivar O-4 contig20726, 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: 7753
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1581 original size:51 final size:52
Alignment explanation
Indices: 1480--1581 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
1470 GTTCTTCATA
* * **
1480 TTCTCCTTGTTTAGATCTTGTCTTCGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
*
1532 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
1582 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
Found at i:3675 original size:30 final size:30
Alignment explanation
Indices: 3599--3692 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 30
3589 AAGGGACTAA
*
3599 TTTGTCCCAAAA-AAAACATAAGGGACTTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTTT
3628 TTTGTCCCAAAAGGAAAACATAAGGGATTTT
1 TTTGTCCCAAAA-GAAAACATAAGGGATTTT
*
3659 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAG-AAAACATAAGGGATTTT
3690 TTT
1 TTT
3693 AGTATTTAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.20
30 1 0.02
31 47 0.78
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAACATAAGGGATTTT
Found at i:4070 original size:153 final size:154
Alignment explanation
Indices: 3836--4249 Score: 573
Period size: 154 Copynumber: 2.7 Consensus size: 154
3826 AATTCCCTAA
* * * * *
3836 AAAAAGGTAAAGACAAAATAGTTATAAA-ATATT-GAATTTAATTAAATAAAAATAGAATTTTTG
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAG-ATTTAATTAAATAAAAATAGAGTTTTTA
** * * **
3899 GTAAAATAAAACTATAAAAGTTTAAATAATTTCATTTAAGAAATATATTTAAAAAATTCCAATAC
65 GTTGAGTAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCCAATAC
*
3964 ATCTAA-TTTTTTAATTAAAATAGT
130 ATCGAAGTTTTTTAATTAAAATAGT
* * *
3988 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGCTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
* * * * * * *
4053 TTGAGTAAAATTGTAAAAGTTAAAACAATGGCATTTAAAAAATATATTTAAAAAATTCTAATATA
66 TTGAGTAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCCAATACA
4118 TCGAAGTTTTTTAATTAAAATAGT
131 TCGAAGTTTTTTAATTAAAATAGT
* *
4142 AAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAG
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
*
4207 TTGAGTAAAACTATAAAAATTTAAACAATGACATTTAAGAAAT
66 TTGAGTAAAACTATAAAAGTTTAAACAATGACATTTAAGAAAT
4250 TTAATCGAAA
Statistics
Matches: 227, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
152 25 0.11
153 86 0.38
154 116 0.51
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (154 bp):
AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
TTGAGTAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCCAATACA
TCGAAGTTTTTTAATTAAAATAGT
Found at i:4204 original size:75 final size:75
Alignment explanation
Indices: 3971--4205 Score: 203
Period size: 75 Copynumber: 3.1 Consensus size: 75
3961 TACATCTAAT
* **
3971 TTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAAT
1 TTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAAT
4036 AAAAATAGAG
66 AAAAATAGAG
* * * *** * * *
4046 CTTTTAATTGAGTAAAATTGTAAAA-GTTAAAACAATGGCAT-TTAAAAAATATATTTA-A-AAA
1 TTTTTAA-T---TAAAATAGTAAAATGGT-AAA-AATAAAATATTTATAAATATA-TTAGATTAA
* * *
4107 ATT--CTAATATATCGAAG
59 ATTAAATAA-AAATAG-AG
4124 TTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAA
1 -TTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAA
4189 TAAAAATAGAG
65 TAAAAATAGAG
4200 TTTTTA
1 TTTTTA
4206 GTTGAGTAAA
Statistics
Matches: 117, Mismatches: 27, Indels: 32
0.66 0.15 0.18
Matches are distributed among these distances:
74 8 0.07
75 38 0.32
76 13 0.11
77 8 0.07
78 11 0.09
79 31 0.26
80 8 0.07
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (75 bp):
TTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAAT
AAAAATAGAG
Found at i:4739 original size:28 final size:30
Alignment explanation
Indices: 4696--4787 Score: 134
Period size: 28 Copynumber: 3.1 Consensus size: 30
4686 AAAAAAATCA
* * *
4696 CTTATGTTTTTCTTTTGGGACAAAATAATCC
1 CTTATGTTTTT-TTATGGGACAAATTAGTCC
4727 CTTATGTTTTTTTATGGGAC--ATTAGTCC
1 CTTATGTTTTTTTATGGGACAAATTAGTCC
4755 CTTATGTTTTTTTATGGGACAAATTAGTCC
1 CTTATGTTTTTTTATGGGACAAATTAGTCC
4785 CTT
1 CTT
4788 GCTAACGTGG
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
28 26 0.46
30 19 0.34
31 11 0.20
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (30 bp):
CTTATGTTTTTTTATGGGACAAATTAGTCC
Found at i:4962 original size:29 final size:30
Alignment explanation
Indices: 4920--4998 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
4910 CTTATTTTTG
* * *
4920 AAACGTAAGGGATTGA-TTTGTCTCAAAA-A
1 AAACATAAGGGATT-ATTTTATCCCAAAACA
4949 AAACATAAGGGATTATTTTATCCCAAAAGCA
1 AAACATAAGGGATTATTTTATCCCAAAA-CA
*
4980 AAACATAAGGGATTTTTTT
1 AAACATAAGGGATTATTTT
4999 GGGTATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.02
29 23 0.53
31 19 0.44
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTATCCCAAAACA
Done.