Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024365.1 Corchorus olitorius cultivar O-4 contig24398, 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: 4721
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42 AT A
1 AT A
45 GGAATTTGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:292 original size:43 final size:42
Alignment explanation
Indices: 152--399 Score: 292
Period size: 41 Copynumber: 5.8 Consensus size: 42
142 CATAAGGAAA
*
152 AATG-CCTCTGTGTTATATATGTGTTTGTGGACTTT-GATATAG
1 AATGCCCT-TGTGTTATATATGTGTTTGGGGACTTTGGA-ATAG
*
194 -ATG-CCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCT-TGTGTTATATATGTGTTTGGGGAC-TTTGGAATAG
* * *
236 ATTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
1 A-ATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
* *
279 AATTGCCCTTGTGTTATATATGTGTTTGGGGACTTGGGTATAG
1 AA-TGCCCTTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
*
322 -ATG-CCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCT-TGTGTTATATATGTGTTTGGGGAC-TTTGGAATAG
*
364 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 -AATGCCCTTGTGTTATATATGTGTTTGGGGACTTT
400 TTGGTTATTG
Statistics
Matches: 180, Mismatches: 15, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
40 3 0.02
41 55 0.31
42 16 0.09
43 51 0.28
44 51 0.28
45 4 0.02
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.43
Consensus pattern (42 bp):
AATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
Found at i:297 original size:128 final size:128
Alignment explanation
Indices: 160--399 Score: 435
Period size: 128 Copynumber: 1.9 Consensus size: 128
150 AAAATGCCTC
* *
160 TGTGTTATATATGTGTTTGTGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
1 TGTGTTATATATGTGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
**
225 TTTTGGAATAGATTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCT
66 TTTTGGAATAGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCT
*
288 TGTGTTATATATGTGTTTGGGGACTTGGGTATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
1 TGTGTTATATATGTGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
353 TTTTGGAATAGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
66 TTTTGGAATAGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
400 TTGGTTATTG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 107 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (128 bp):
TGTGTTATATATGTGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
TTTTGGAATAGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCT
Found at i:390 original size:85 final size:84
Alignment explanation
Indices: 153--398 Score: 336
Period size: 85 Copynumber: 2.9 Consensus size: 84
143 ATAAGGAAAA
* *
153 ATGCCTCTGTGTTATATATGTGTTTGTGGACTTT-GATATAG--ATGCCTCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAAATGCCCCTGTGTTATATATGT
* *
215 GTTTGAGGACTTTTGGAATAG
65 GTTTGGGGAC-TTGGGAATAG
* * * * *
236 ATTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCTTGTGTTATATATG
1 A--TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATG
*
301 TGTTTGGGGACTTGGGTATAG
64 TGTTTGGGGACTTGGGAATAG
322 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAAATGCCCCTGTGTTATATATGT
387 GTTTGGGGACTT
65 GTTTGGGGACTT
399 TTTGGTTATT
Statistics
Matches: 143, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
83 1 0.01
84 28 0.20
85 77 0.54
86 10 0.07
87 27 0.19
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATGTG
TTTGGGGACTTGGGAATAG
Found at i:1269 original size:16 final size:15
Alignment explanation
Indices: 1231--1269 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1221 ACAGAGATTG
*
1231 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
1246 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
1261 ACTAGAAAA
1 AC-AGAAAA
1270 TAAAGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:2885 original size:22 final size:23
Alignment explanation
Indices: 2839--2898 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
2829 AATATTAATA
* *
2839 AAATA-GCATATAATTA-AGCAT
1 AAATAGGCATAAAAATATAGCAT
*
2860 AAATGGGTC-TAAAAATATAGCA-
1 AAATAGG-CATAAAAATATAGCAT
2882 AAATAGGCATAAAAATA
1 AAATAGGCATAAAAATA
2899 GGGTCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 5 0.16
22 21 0.68
23 5 0.16
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.23
Consensus pattern (23 bp):
AAATAGGCATAAAAATATAGCAT
Done.