Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012197.1 Corchorus olitorius cultivar O-4 contig12230, 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: 25154
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3464 original size:2 final size:2
Alignment explanation
Indices: 3457--3485 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3447 TAACCGAAAG
3457 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3486 AAAATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5114 original size:19 final size:20
Alignment explanation
Indices: 5073--5114 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5063 TGATTAAATG
*
5073 AACTCTAGAAAGTGTATTCA
1 AACTCTAGAAACTGTATTCA
5093 AACTCT-GAAACTCGTATT-A
1 AACTCTAGAAACT-GTATTCA
5112 AAC
1 AAC
5115 CCTATAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
AACTCTAGAAACTGTATTCA
Found at i:5278 original size:13 final size:13
Alignment explanation
Indices: 5260--5311 Score: 77
Period size: 13 Copynumber: 3.8 Consensus size: 13
5250 TATACTCTGG
*
5260 TTTATGACTTTGA
1 TTTATGATTTTGA
5273 TTTATGATTTTGA
1 TTTATGATTTTGA
5286 TTTATGATTTTGA
1 TTTATGATTTTGA
5299 TTTTAATGATTTT
1 -TTT-ATGATTTT
5312 CTTGTGTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 25 0.69
14 3 0.08
15 8 0.22
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (13 bp):
TTTATGATTTTGA
Found at i:5288 original size:6 final size:6
Alignment explanation
Indices: 5268--5302 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
5258 GGTTTATGAC
5268 TTTGAT TTATGAT TTTGAT TTATGAT TTTGAT TTT
1 TTTGAT TT-TGAT TTTGAT TT-TGAT TTTGAT TTT
5303 AATGATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:8157 original size:11 final size:11
Alignment explanation
Indices: 8141--8165 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8131 TTAGACTTAT
8141 ATAATATAAAG
1 ATAATATAAAG
8152 ATAATATAAAG
1 ATAATATAAAG
8163 ATA
1 ATA
8166 TACTAGTAAT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
ATAATATAAAG
Found at i:9658 original size:206 final size:205
Alignment explanation
Indices: 9285--9698 Score: 693
Period size: 206 Copynumber: 2.0 Consensus size: 205
9275 GAACTTGACG
*
9285 AAAATCTCCTCCAAAAAAATTACTTTTCCTCCAAAAATTTCAGAACTGTTTGTGGTCTCGTAAAC
1 AAAATCTCCTCCAAAAAAATTACTTTTCCTCCAAAAATTTCAGAACTGGTTGTGGTCTCGTAAAC
* *
9350 TTCGATCCAAAGTCTCAATTGAAAATCTTTTAGACATCAGAGCTTCATCCCATATGATAAGCCAT
66 TTCAACCCAAAGTCTCAATTGAAAATCTTTTAGACATCAGAGCTTCATCCCATATGATAAGCCAT
* * *
9415 GCTTTTCTTAATAGATGTGCAGTACCATCTTGTTTTGAATAGCCATATAAAGATGTCTCAGTTGG
131 GCTTTTCTTAATAGATGTGCAATACCATCTTGTTTTGAATAGCCATATAAAGATATCTCAATTGG
9480 GTTTAGTGGC
196 GTTTAGTGGC
* *
9490 AAAATCTCCTCCAAAAACAGTTACTTTTCCTCCAAAAATTTCAGAATTGGTTGTGGTCTCGTAAA
1 AAAATCTCCTCCAAAAA-AATTACTTTTCCTCCAAAAATTTCAGAACTGGTTGTGGTCTCGTAAA
** * * * *
9555 CTTCAACCCAAAGTCTCAATTGAAAATCTTTTAGACATTGGAGTTTCATCCTATATGATAAGTCG
65 CTTCAACCCAAAGTCTCAATTGAAAATCTTTTAGACATCAGAGCTTCATCCCATATGATAAGCCA
9620 TGCTTTTCTTAATAGATGTGCAATACCATCTTGTTTTGAATAGCCATATAAAGATATCTCAATTG
130 TGCTTTTCTTAATAGATGTGCAATACCATCTTGTTTTGAATAGCCATATAAAGATATCTCAATTG
9685 GGTTTAGTGGC
195 GGTTTAGTGGC
9696 AAA
1 AAA
9699 GCGAACCTTG
Statistics
Matches: 194, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
205 17 0.09
206 177 0.91
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (205 bp):
AAAATCTCCTCCAAAAAAATTACTTTTCCTCCAAAAATTTCAGAACTGGTTGTGGTCTCGTAAAC
TTCAACCCAAAGTCTCAATTGAAAATCTTTTAGACATCAGAGCTTCATCCCATATGATAAGCCAT
GCTTTTCTTAATAGATGTGCAATACCATCTTGTTTTGAATAGCCATATAAAGATATCTCAATTGG
GTTTAGTGGC
Found at i:18612 original size:26 final size:27
Alignment explanation
Indices: 18580--18631 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
18570 GTAAAATTGG
*
18580 TAATAAAATTGG-AAGATTTTGGAAAT
1 TAATAAAATTGGTAAGATTTTAGAAAT
*
18606 TAATAAAATTGGTAAGTTTTTAGAAA
1 TAATAAAATTGGTAAGATTTTAGAAA
18632 AAATCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATAAAATTGGTAAGATTTTAGAAAT
Found at i:18640 original size:26 final size:27
Alignment explanation
Indices: 18581--18645 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
18571 TAAAATTGGT
* *
18581 AATAAAATTGG-AAGATTTTGGAAATT
1 AATAAAATTGGTAAGATTTTAGAAATA
*
18607 AATAAAATTGGTAAGTTTTTAGAAA-A
1 AATAAAATTGGTAAGATTTTAGAAATA
*
18633 AATCAAA-TGGTAA
1 AATAAAATTGGTAA
18646 AAAGATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.18
26 17 0.50
27 11 0.32
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (27 bp):
AATAAAATTGGTAAGATTTTAGAAATA
Found at i:21970 original size:12 final size:12
Alignment explanation
Indices: 21953--21983 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21943 GGATTTTTTA
21953 TTTTTATTATTT
1 TTTTTATTATTT
21965 TTTTTATTATTT
1 TTTTTATTATTT
21977 TTTTTAT
1 TTTTTAT
21984 ACAGAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTATTATTT
Done.