Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022376.1 Corchorus olitorius cultivar O-4 contig22409, 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: 21379
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4544 original size:17 final size:16
Alignment explanation
Indices: 4510--4541 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4500 ACTACTAATA
4510 GTGATGATTTGCTTTT
1 GTGATGATTTGCTTTT
*
4526 GTGATGATTTGGTTTT
1 GTGATGATTTGCTTTT
4542 TGTTGTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.28, T:0.56
Consensus pattern (16 bp):
GTGATGATTTGCTTTT
Found at i:8217 original size:29 final size:29
Alignment explanation
Indices: 8127--8345 Score: 311
Period size: 29 Copynumber: 7.7 Consensus size: 29
8117 GGTCACTTAA
8127 AGGGGCATTTTGGTCA-TTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
8155 AGGGGCATTTTGGTCA-TTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* *
8183 ATGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
*
8212 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* *
8241 AGGGGACATTTTAGTCACTTTTGCATATCC
1 AGGGG-CATTTTGGTCATTTTTGCATATCC
8271 AGGGGCATTTTGGTCA-TTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* *
8299 -GGGGCATTTTGGTCATTTTTGCACATCT
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* * *
8327 AAGGGTATTTCGGTCATTT
1 AGGGGCATTTTGGTCATTT
8346 CAAGTGCACT
Statistics
Matches: 175, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
27 15 0.09
28 65 0.37
29 69 0.39
30 26 0.15
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATCC
Found at i:8313 original size:86 final size:86
Alignment explanation
Indices: 8127--8325 Score: 323
Period size: 86 Copynumber: 2.3 Consensus size: 86
8117 GGTCACTTAA
* * *
8127 AGGGGCATTTTGGTCA-TTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCATGGGCAT
1 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTAGTCATTTTGCATATCCAGGGGCAT
8191 TTTGGTCATTTTTGCACATCC
66 TTTGGTCATTTTTGCACATCC
8212 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGACATTTTAGTCACTTTTGCATATCCAGGGGC
1 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGG-CATTTTAGTCA-TTTTGCATATCCAGGGGC
*
8277 ATTTTGGTCA-TTTTGCATATCC
64 ATTTTGGTCATTTTTGCACATCC
8299 -GGGGCATTTTGGTCATTTTTGCACATC
1 AGGGGCATTTTGGTCATTTTTGCACATC
8326 TAAGGGTATT
Statistics
Matches: 107, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
85 16 0.15
86 43 0.40
87 21 0.20
88 27 0.25
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (86 bp):
AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTAGTCATTTTGCATATCCAGGGGCAT
TTTGGTCATTTTTGCACATCC
Found at i:8345 original size:115 final size:114
Alignment explanation
Indices: 8127--8345 Score: 359
Period size: 115 Copynumber: 1.9 Consensus size: 114
8117 GGTCACTTAA
* *
8127 AGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCATGGGCATT
1 AGGGGCATTTTAGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATT
* *
8192 TTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTTTGCACATCC
66 TTGGTCATTTTTGCACATCCAAGGGCATTTCGGTCATTTTTGCACATCC
8241 AGGGGACATTTTAGTCACTTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCC-GGGGCA
1 AGGGG-CATTTTAGTCA-TTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGGGCA
* *
8305 TTTTGGTCATTTTTGCACATCTAAGGGTATTTCGGTCATTT
64 TTTTGGTCATTTTTGCACATCCAAGGGCATTTCGGTCATTT
8346 CAAGTGCACT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
114 5 0.05
115 52 0.54
116 40 0.41
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (114 bp):
AGGGGCATTTTAGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATT
TTGGTCATTTTTGCACATCCAAGGGCATTTCGGTCATTTTTGCACATCC
Found at i:15794 original size:11 final size:11
Alignment explanation
Indices: 15760--15807 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
15750 TTGAAATAAT
15760 TCTTCAAA-AG
1 TCTTCAAATAG
15770 TCTTC--A-AG
1 TCTTCAAATAG
15778 TCTTCAAATTA-
1 TCTTCAAA-TAG
15789 TCTTCAAATAG
1 TCTTCAAATAG
15800 TCTTCAAA
1 TCTTCAAA
15808 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (11 bp):
TCTTCAAATAG
Done.