Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009586.1 Corchorus olitorius cultivar O-4 contig09618, 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: 14254
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Found at i:1103 original size:66 final size:66
Alignment explanation
Indices: 1020--1153 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
1010 AATATGTGTC
*
1020 ACTAAATCTATATGGTTAATGAGCAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
1 ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
1085 A
66 A
*
1086 ACTAAATGTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
1 ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
1151 A
66 A
1152 AC
1 AC
1154 ACGAATATGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (66 bp):
ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
A
Found at i:1757 original size:57 final size:57
Alignment explanation
Indices: 1632--2129 Score: 682
Period size: 57 Copynumber: 8.7 Consensus size: 57
1622 AGCTTGAATT
* * * *
1632 GAAAACTCTCGAACAGAGACCTCGAAGC-GGATTTAAAGAAGAATGAA-ATTTTAAAGCA
1 GAAAACTCTCTACCAGAGACCTC-AACCAGGATTTAAA-AAGAA-CAATATTTTAAAGCA
*
1690 GAAAATTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
1747 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAAGAACAATATTTTAAAGCA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTT-AAAAAGAACAATATTTTAAAGCA
* *
1805 GAAAACTCTCTACCAGAGGCCTCAACCGGGATTTAAAAAGAACAATATTTTAAAGCA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* * * *
1862 GAAAACTCTCTACCAGAGACCTCAGCCAGGATTTAAAAAGAATAACATTTTAAAACA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* * *
1919 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAATAACATTTTAAAACA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* * *
1976 GAAAAATCTCTACCATAGACCTCAACCAGGATTTAAAAAGAATAATATTTTAAAGCA
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* * ** **
2033 GAAAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGATTTTGGA-TT
1 GAAAACTCTCTACCAGAGACCTC-AACCAGGATTTAAAAA-GA-ACAATATTTTAAAGCA
2091 GAAAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAA
1 GAAAACTCTCTACCAGAGACCTC-AACCAGGATTTAAAAA
2130 AAGAACGGGG
Statistics
Matches: 406, Mismatches: 28, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
56 2 0.00
57 269 0.66
58 126 0.31
59 9 0.02
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (57 bp):
GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
Found at i:1768 original size:115 final size:114
Alignment explanation
Indices: 1632--2129 Score: 700
Period size: 115 Copynumber: 4.3 Consensus size: 114
1622 AGCTTGAATT
* * *
1632 GAAAACTCTCGAACAGAGACCTCGAAGC-GGATTTAAAGAAGAATGAA-ATTTTAAAGCAGAAAA
1 GAAAACTCTCTACCAGAGACCTC-AACCAGGATTTAAA-AAGAAT-AATATTTTAAAGCAGAAAA
*
1695 TTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
63 CTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
*
1747 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAAGAACAATATTTTAAAGCAGAAAACT
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTT-AAAAAGAATAATATTTTAAAGCAGAAAACT
* *
1812 CTCTACCAGAGGCCTCAACCGGGATTTAAAAAGAACAATATTTTAAAGCA
65 CTCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* * *
1862 GAAAACTCTCTACCAGAGACCTCAGCCAGGATTTAAAAAGAATAACATTTTAAAACAGAAAACTC
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAATAATATTTTAAAGCAGAAAACTC
* * *
1927 TCTACCAGAGACCTCAACCAGGATTTAAAAAGAATAACATTTTAAAACA
66 TCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
* *
1976 GAAAAATCTCTACCATAGACCTCAACCAGGATTTAAAAAGAATAATATTTTAAAGCAGAAAACTC
1 GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAATAATATTTTAAAGCAGAAAACTC
* * ** **
2041 TCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGATTTTGGA-TT
66 TCTACCAGAGACCTC-AACCAGGATTTAAAAA-GA-ACAATATTTTAAAGCA
2091 GAAAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAA
1 GAAAACTCTCTACCAGAGACCTC-AACCAGGATTTAAAAA
2130 AAGAACGGGG
Statistics
Matches: 346, Mismatches: 30, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
114 165 0.48
115 167 0.48
116 14 0.04
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (114 bp):
GAAAACTCTCTACCAGAGACCTCAACCAGGATTTAAAAAGAATAATATTTTAAAGCAGAAAACTC
TCTACCAGAGACCTCAACCAGGATTTAAAAAGAACAATATTTTAAAGCA
Found at i:2155 original size:58 final size:58
Alignment explanation
Indices: 1578--2133 Score: 190
Period size: 57 Copynumber: 9.7 Consensus size: 58
1568 TTTAAAACAG
* * ** * * *
1578 AAACTCTCGACCAGAGACCTCGAATAGGATTTTTAAACAGGACAAG--CTTGAATTGA
1 AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAACAAGACAAGAATTTGGATTGA
* * * * ** **
1634 AAACTCTCGAACAGAGACCTCGAAGC-GGATTTAAAGAAGAATG--AA-ATTTTAAAGCAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAA-AACAA-GACAAGAATTTGGA-TTGA
* * * * ** **
1692 AAATTCTCTACCAGAGACCTC-AACCAGGATTTAAAAA-GA-ACAATATTTTAAAGCAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGAATTTGGA-TTGA
* * ** **
1749 AAACTCTCTACCAGAGACCTC-AACCAGGATTT-AAAA-AAGAACAATATTTTAAAGCAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAG-ACAAGAATTTGGA-TTGA
* * * * * ** **
1807 AAACTCTCTACCAGAGGCCTC-AACCGGGATTTAAAAA-GA-ACAATATTTTAAAGCAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGAATTTGGA-TTGA
* * * * * ** **
1864 AAACTCTCTACCAGAGACCTC-AGCCAGGATTTAAAAA-GA-ATAACATTTTAAAACAGA
1 AAACTCTCTACCAGAGACCTCGA-ACAGGATTTAAAAACAAGACAAGAATTT-GGATTGA
* * * * ** **
1921 AAACTCTCTACCAGAGACCTC-AACCAGGATTTAAAAA-GA-ATAACATTTTAAAACAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGAATTT-GGATTGA
* * * * * * ** **
1978 AAAATCTCTACCATAGACCTC-AACCAGGATTTAAAAA-GA-ATAATATTTTAAAGCAGA
1 AAACTCTCTACCAGAGACCTCGAA-CAGGATTTAAAAACAAGACAAGAATTTGGA-TTGA
*
2035 AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAACAAGACAAGATTTTGGATTGA
1 AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAACAAGACAAGAATTTGGATTGA
2093 AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAA-AAGA
1 AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAACAAGA
2134 ACGGGGAATT
Statistics
Matches: 442, Mismatches: 38, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
56 43 0.10
57 262 0.59
58 123 0.28
59 14 0.03
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (58 bp):
AAACTCTCTACCAGAGACCTCGAACAGGATTTAAAAACAAGACAAGAATTTGGATTGA
Found at i:2193 original size:17 final size:18
Alignment explanation
Indices: 2155--2193 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2145 GATTTAAAAC
*
2155 TGAAACTCAATAGTGATA
1 TGAAACTCAATAGTCATA
2173 -GAAACTCAATA-TCATA
1 TGAAACTCAATAGTCATA
2189 TGAAA
1 TGAAA
2194 ATCATCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (18 bp):
TGAAACTCAATAGTCATA
Found at i:3037 original size:37 final size:37
Alignment explanation
Indices: 2989--3091 Score: 181
Period size: 37 Copynumber: 2.8 Consensus size: 37
2979 TTTTTTTCTT
*
2989 ACCTCTTTCTATTTTAGG-CCAAGTTTTTTCTTTTTCG
1 ACCTCTCTCTATTTTAGGTCC-AGTTTTTTCTTTTTCG
3026 ACCTCTCTCTATTTTAGGTCCAGTTTTTTCTTTTTCG
1 ACCTCTCTCTATTTTAGGTCCAGTTTTTTCTTTTTCG
3063 ACCTCTCTCTATTTTAGGTCCAGTTTTTT
1 ACCTCTCTCTATTTTAGGTCCAGTTTTTT
3092 TTTATATTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
37 62 0.97
38 2 0.03
ACGTcount: A:0.13, C:0.23, G:0.11, T:0.53
Consensus pattern (37 bp):
ACCTCTCTCTATTTTAGGTCCAGTTTTTTCTTTTTCG
Done.