Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015368.1 Corchorus olitorius cultivar O-4 contig15401, 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: 15765
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:674 original size:16 final size:15
Alignment explanation
Indices: 636--677 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
626 ACAGAGATTG
*
636 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
651 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
666 ACTAGAAAACAA
1 AC-AGAAAACAA
678 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:2108 original size:29 final size:29
Alignment explanation
Indices: 2052--2109 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2042 CTTGAAATAA
* *
2052 ATCTTCAATGGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGACACCAATTT
*
2081 ATCTTCAAATGGTCTTCAA-ACACGAATTT
1 ATCTTC-AATGGTCTTCAAGACACCAATTT
2110 CGAATTTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCTTCAATGGTCTTCAAGACACCAATTT
Found at i:7292 original size:24 final size:25
Alignment explanation
Indices: 7244--7314 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 25
7234 AAGAAAACTC
7244 TTTTTTTTATGACGCAGAAACAAAGT-TT
1 TTTTTTTTATGACGC---AA-AAAGTATT
7272 TTTTTTTTATGACGCAAAAAGTATT
1 TTTTTTTTATGACGCAAAAAGTATT
* *
7297 TTATTTTT-CGACGCAAAA
1 TTTTTTTTATGACGCAAAA
7315 CACAAAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.35
25 11 0.28
28 15 0.38
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (25 bp):
TTTTTTTTATGACGCAAAAAGTATT
Found at i:7706 original size:16 final size:15
Alignment explanation
Indices: 7668--7709 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7658 ACAGAGATAG
*
7668 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
7683 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7698 ACTAGAAAACAA
1 AC-AGAAAACAA
7710 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:12652 original size:53 final size:53
Alignment explanation
Indices: 12509--12644 Score: 193
Period size: 54 Copynumber: 2.5 Consensus size: 53
12499 TTCTTCAATA
*
12509 TTTTCTTGTTTCAATCCTGGCTCCGGACACCCAAACACTCTTTTAGTGTTTTT
1 TTTTCTTGTTTCAATCCTGACTCCGGACACCCAAACACTCTTTTAGTGTTTTT
* *
12562 TTTTCCTTGTTTCAATCCTGACTCCGGACACCCAAACATTTTTTTAGTG-TTTT
1 TTTT-CTTGTTTCAATCCTGACTCCGGACACCCAAACACTCTTTTAGTGTTTTT
* * *
12615 TTTTCTTTGATTCAATCTTGTCTCCGGACA
1 TTTTC-TTGTTTCAATCCTGACTCCGGACA
12645 TAAAAACACT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
52 1 0.01
53 33 0.44
54 41 0.55
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCTTGTTTCAATCCTGACTCCGGACACCCAAACACTCTTTTAGTGTTTTT
Found at i:14201 original size:2 final size:2
Alignment explanation
Indices: 14194--14238 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
14184 TTACAAAATA
* *
14194 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14236 AT A
1 AT A
14239 CTAGGTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14756 original size:29 final size:31
Alignment explanation
Indices: 14699--14754 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 31
14689 GGGCAAAATG
14699 TTTAAGTTTCGGTCTAATTTGGGATAAACCT
1 TTTAAGTTTCGGTCTAATTTGGGATAAACCT
*
14730 TTTAA-TTT-GGTCT-ATTTGGGGTAAA
1 TTTAAGTTTCGGTCTAATTTGGGATAAA
14755 ACGTTCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 11 0.46
29 5 0.21
30 3 0.12
31 5 0.21
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (31 bp):
TTTAAGTTTCGGTCTAATTTGGGATAAACCT
Found at i:14970 original size:15 final size:16
Alignment explanation
Indices: 14950--14987 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
14940 ACCGTTAATT
14950 TAATTTAAAT-AATAA
1 TAATTTAAATAAATAA
14965 TAATTT-AATAAATAA
1 TAATTTAAATAAATAA
*
14980 TAAATTAA
1 TAATTTAA
14988 TTTTTTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 16 0.80
16 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTTAAATAAATAA
Found at i:14978 original size:18 final size:19
Alignment explanation
Indices: 14945--14982 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
14935 TCTATACCGT
14945 TAATTTAATTTAAATAATAA
1 TAATTTAA-TTAAATAATAA
14965 TAATTTAA-TAAATAATAA
1 TAATTTAATTAAATAATAA
14983 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTAATTAAATAATAA
Found at i:14988 original size:20 final size:20
Alignment explanation
Indices: 14944--14990 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
14934 ATCTATACCG
14944 TTAATTTAATTTAAATAATAA
1 TTAATTTAA-TTAAATAATAA
14965 -TAATTTAA-TAAATAATAAA
1 TTAATTTAATTAAATAAT-AA
14984 TTAATTT
1 TTAATTT
14991 TTTGACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 2 0.08
20 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTTAATTAAATAATAA
Found at i:15181 original size:30 final size:31
Alignment explanation
Indices: 15147--15208 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
15137 CCTTATCAAT
* * *
15147 CTAGACAAATATGAACATTATAAGAA-AACA
1 CTAGACAAACATGAACATCATAAAAATAACA
15177 CTAGACAAACATGAACATCATAAAAATAACA
1 CTAGACAAACATGAACATCATAAAAATAACA
15208 C
1 C
15209 CAGAAAGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (31 bp):
CTAGACAAACATGAACATCATAAAAATAACA
Found at i:15636 original size:15 final size:15
Alignment explanation
Indices: 15616--15644 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15606 GCTATATACC
15616 ACTAGAAGGGGAAGA
1 ACTAGAAGGGGAAGA
15631 ACTAGAAGGGGAAG
1 ACTAGAAGGGGAAG
15645 CAGAAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.41, T:0.07
Consensus pattern (15 bp):
ACTAGAAGGGGAAGA
Done.