Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016696.1 Corchorus olitorius cultivar O-4 contig16729, 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: 64119
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8928 original size:20 final size:21
Alignment explanation
Indices: 8903--8945 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
8893 CATATCAAGG
8903 AATAGGCAAGC-AAGCAAAGC
1 AATAGGCAAGCAAAGCAAAGC
* *
8923 AATAGGCAATCAAAGCAATGC
1 AATAGGCAAGCAAAGCAAAGC
8944 AA
1 AA
8946 AGAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (21 bp):
AATAGGCAAGCAAAGCAAAGC
Found at i:12281 original size:18 final size:19
Alignment explanation
Indices: 12258--12297 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
12248 AATTGTTTTT
12258 AATTTTATTTT-AAAACGC
1 AATTTTATTTTAAAAACGC
*
12276 AATTTTTTTTTCAAAAACGC
1 AATTTTATTTT-AAAAACGC
12296 AA
1 AA
12298 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (19 bp):
AATTTTATTTTAAAAACGC
Found at i:21508 original size:31 final size:34
Alignment explanation
Indices: 21450--21514 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
21440 TTCGGAGTAT
21450 AAACTATCAAGCTTCTTTTTGGTGCCAAAAAAAA
1 AAACTATCAAGCTTCTTTTTGGTGCCAAAAAAAA
21484 AAACTATCAAGCTT-TTTTT-G-GCCAAAAAAAA
1 AAACTATCAAGCTTCTTTTTGGTGCCAAAAAAAA
21515 GTTTGATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 11 0.35
32 1 0.03
33 5 0.16
34 14 0.45
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (34 bp):
AAACTATCAAGCTTCTTTTTGGTGCCAAAAAAAA
Found at i:30999 original size:54 final size:54
Alignment explanation
Indices: 30918--31026 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
30908 ATCCCTGTAT
* *
30918 ATTCAATTCTATTGGTAATGAAATAGCTTTGAAGGAAATATTGAATTGGCTTAA
1 ATTCAATTCTATTAGTAATGAAATAGCTTTGAAGGAAATATTGAATTAGCTTAA
*
30972 ATTCAATTCTATTAGTAATGAAATAGCTTTGAAGGACATATTGAATTAGCTTAA
1 ATTCAATTCTATTAGTAATGAAATAGCTTTGAAGGAAATATTGAATTAGCTTAA
31026 A
1 A
31027 AGCATTCGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (54 bp):
ATTCAATTCTATTAGTAATGAAATAGCTTTGAAGGAAATATTGAATTAGCTTAA
Found at i:39039 original size:42 final size:40
Alignment explanation
Indices: 38977--39057 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 40
38967 CCACCAAGAG
38977 GCCGATGCAAAGGTAAAGGGCGATAAAAAAAATCAACCCCGC
1 GCCGATGCAAAGGTAAAGGGCGAT--AAAAAATCAACCCCGC
* *
39019 GCCGATGCAAAGGTAGAGGGCGATAAGAAATCAACCCCG
1 GCCGATGCAAAGGTAAAGGGCGATAAAAAATCAACCCCG
39058 TCAAGACGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 14 0.38
42 23 0.62
ACGTcount: A:0.40, C:0.23, G:0.27, T:0.10
Consensus pattern (40 bp):
GCCGATGCAAAGGTAAAGGGCGATAAAAAATCAACCCCGC
Found at i:39346 original size:15 final size:15
Alignment explanation
Indices: 39326--39357 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39316 AAATTGTCTA
39326 TTGTGGGTAGTGTTG
1 TTGTGGGTAGTGTTG
39341 TTGTGGGTAGTGTTG
1 TTGTGGGTAGTGTTG
39356 TT
1 TT
39358 CGAAGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (15 bp):
TTGTGGGTAGTGTTG
Found at i:39885 original size:2 final size:2
Alignment explanation
Indices: 39878--39910 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39868 AAAAGAAAGA
39878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39911 CACACACGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56433 original size:38 final size:38
Alignment explanation
Indices: 56337--56485 Score: 228
Period size: 38 Copynumber: 3.9 Consensus size: 38
56327 GGCTGTGCAT
*
56337 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
56376 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
56414 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
56452 AGTGGACCCGTGCCTCAAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTC-AGGGGGTTAAACTGTTGG
56486 CTAGACTCGA
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 63 0.61
39 40 0.39
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:56473 original size:77 final size:76
Alignment explanation
Indices: 56337--56485 Score: 228
Period size: 77 Copynumber: 1.9 Consensus size: 76
56327 GGCTGTGCAT
56337 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAGAGTGGACCCATACCACAGGGGGTTAA
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAGAGTGGACCCATACCACAGGGGGTT-A
56402 ACTGTTGGTAAG
65 ACTGTTGGTAAG
* * * * *
56414 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGT-AAGAGTGGACCCGTGCCTCAAGGGGGTTA
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAGAGTGGACCCATACCAC-AGGGGGTTA
56478 ACTGTTGG
65 ACTGTTGG
56486 CTAGACTCGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
76 25 0.38
77 41 0.62
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (76 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAGAGTGGACCCATACCACAGGGGGTTAA
CTGTTGGTAAG
Found at i:56526 original size:6 final size:6
Alignment explanation
Indices: 56515--56540 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56505 CGTTAACGGA
56515 TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TG
56541 GTGCAGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:60201 original size:2 final size:2
Alignment explanation
Indices: 60194--60224 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60184 AAAAGGACAT
60194 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 T
60225 TAAACAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60461 original size:29 final size:29
Alignment explanation
Indices: 60405--60462 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
60395 TATTAACTAA
* **
60405 TGGACAATTTGCATCCTGAACTTTAATTT
1 TGGACAATTTGCATCCTAAACTAAAATTT
*
60434 TGGAGAATTTGCATCCTAAACTAAAATTT
1 TGGACAATTTGCATCCTAAACTAAAATTT
60463 ACAGACAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (29 bp):
TGGACAATTTGCATCCTAAACTAAAATTT
Found at i:63603 original size:11 final size:12
Alignment explanation
Indices: 63576--63608 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
63566 ATAGCCTTCA
63576 AGTCTTCAAATT
1 AGTCTTCAAATT
63588 AGTCTTCAAA-T
1 AGTCTTCAAATT
63599 AGTCTTCAAA
1 AGTCTTCAAA
63609 CACGAGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (12 bp):
AGTCTTCAAATT
Done.