Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018560.1 Corchorus olitorius cultivar O-4 contig18593, 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: 10464
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 10--48 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 TACTACTAC
10 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49 GTTAAATTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:789 original size:50 final size:50
Alignment explanation
Indices: 734--911 Score: 259
Period size: 50 Copynumber: 3.5 Consensus size: 50
724 AGATATCCAG
*
734 AAGAGTGAATTGGAAGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
784 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * * *
834 AAGATTAAAATGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * *
884 TATATTTGAATTGGAAGAC-GATTCAAAG
1 AAGA-GTGAATTGGAAGACAG-TTCAAAG
912 AAGTTGATTC
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 98 0.84
51 19 0.16
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.24
Consensus pattern (50 bp):
AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:925 original size:26 final size:26
Alignment explanation
Indices: 896--983 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
886 TATTTGAATT
896 GGAAGACGATTCAAAGAAGTTGATTC
1 GGAAGACGATTCAAAGAAGTTGATTC
***
922 GGAAGACGATTCCCCGAAGATTGAATT-
1 GGAAGACGATTCAAAGAAG-TTG-ATTC
* **
949 GGAAGACAATTTGAAGAAGTTGA-TC
1 GGAAGACGATTCAAAGAAGTTGATTC
*
974 GGGAGACGAT
1 GGAAGACGAT
984 CCATTTCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
24 1 0.02
25 9 0.18
26 19 0.39
27 17 0.35
28 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (26 bp):
GGAAGACGATTCAAAGAAGTTGATTC
Found at i:1224 original size:28 final size:28
Alignment explanation
Indices: 1184--1306 Score: 149
Period size: 28 Copynumber: 4.4 Consensus size: 28
1174 TTTACTTCTT
1184 ATTTTGGTCATTTTGCATATCCAGGGGC
1 ATTTTGGTCATTTTGCATATCCAGGGGC
* * * *
1212 ATTTTGGTCATTTCGAATGTCCAAGGGC
1 ATTTTGGTCATTTTGCATATCCAGGGGC
* *
1240 ATTTTGGTCATTTTGCATGTCCAGTGGC
1 ATTTTGGTCATTTTGCATATCCAGGGGC
* *
1268 ATTTTGGTCA-TTTGCACATCCGGGGGGGC
1 ATTTTGGTCATTTTGCATATCC--AGGGGC
1297 ATTTTGGTCA
1 ATTTTGGTCA
1307 CTCCAAGTAC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
27 9 0.11
28 58 0.72
29 14 0.17
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATATCCAGGGGC
Found at i:2940 original size:29 final size:29
Alignment explanation
Indices: 2907--3103 Score: 306
Period size: 29 Copynumber: 6.8 Consensus size: 29
2897 CACGACTTAG
2907 GGGCATTTTGGTCATTTTTGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCATATCCAA
2936 GGGCATTTTGGTCATTTTTGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCATATCCAA
*
2965 GGGCATTTTGGTCCTTTTTGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCATATCCAA
* * *
2994 GGGAATTTTGGTCCTTTTTGCATATCCAG
1 GGGCATTTTGGTCATTTTTGCATATCCAA
3023 GGGCATTTTGGTCATTTTTGCATATCC-A
1 GGGCATTTTGGTCATTTTTGCATATCCAA
* * *
3051 GGGCACTTTGGTCATTTTTGCACATCCAG
1 GGGCATTTTGGTCATTTTTGCATATCCAA
* *
3080 GGGCAGTTTGGTTATTTTTGCATA
1 GGGCATTTTGGTCATTTTTGCATA
3104 CTCTAGGTTC
Statistics
Matches: 155, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
28 25 0.16
29 130 0.84
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCATATCCAA
Found at i:7216 original size:16 final size:16
Alignment explanation
Indices: 7195--7225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7185 AACAAAAGCA
7195 TTTTTTAAAAGTGTTT
1 TTTTTTAAAAGTGTTT
*
7211 TTTTTTAAATGTGTT
1 TTTTTTAAAAGTGTT
7226 CTCTTATTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTTTTAAAAGTGTTT
Done.