Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020611.1 Corchorus olitorius cultivar O-4 contig20644, 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: 28359
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:219 original size:25 final size:24
Alignment explanation
Indices: 191--284 Score: 63
Period size: 25 Copynumber: 4.0 Consensus size: 24
181 AAAAAAAATA
191 CATGACATGAAACTCAAACCCTAAC
1 CATGACATGAAAC-CAAACCCTAAC
*
216 CATGAAATG--A-CAAACCCTAA-
1 CATGACATGAAACCAAACCCTAAC
* * ***
236 -GTGAGATGAAGGTTAAACCCTAAC
1 CATGACATGAA-ACCAAACCCTAAC
*
260 CATGGCATGAAAGCCAAACCCTAAC
1 CATGACATGAAA-CCAAACCCTAAC
285 ATGTCATCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 14
0.67 0.14 0.18
Matches are distributed among these distances:
19 6 0.12
21 10 0.20
23 10 0.20
25 25 0.49
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.16
Consensus pattern (24 bp):
CATGACATGAAACCAAACCCTAAC
Found at i:221 original size:20 final size:20
Alignment explanation
Indices: 196--235 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
186 AAATACATGA
196 CATGAAACT-CAAACCCTAAC
1 CATGAAA-TACAAACCCTAAC
216 CATGAAATGACAAACCCTAA
1 CATGAAAT-ACAAACCCTAA
236 GTGAGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 7 0.39
21 10 0.56
ACGTcount: A:0.47, C:0.30, G:0.07, T:0.15
Consensus pattern (20 bp):
CATGAAATACAAACCCTAAC
Found at i:297 original size:25 final size:25
Alignment explanation
Indices: 250--297 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
240 GATGAAGGTT
*
250 AAACCCTAACCATGGCATGAAAGCC
1 AAACCCTAACCATGGCATCAAAGCC
*
275 AAACCCTAA-CATGTCATCCAAAG
1 AAACCCTAACCATGGCAT-CAAAG
298 TGAAGGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (25 bp):
AAACCCTAACCATGGCATCAAAGCC
Found at i:493 original size:60 final size:60
Alignment explanation
Indices: 400--519 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
390 AAAACCATGC
400 GCAAAAAGACACAAAAACCATGCAAATAGTACCCCAAATGAATGTGGTGAGAGAATAAGG
1 GCAAAAAGACACAAAAACCATGCAAATAGTACCCCAAATGAATGTGGTGAGAGAATAAGG
460 GCAAAAAGACACAAAAACCATGCAAATAGTACCCCAAATGAATGTGGTGAGAGAATAAGG
1 GCAAAAAGACACAAAAACCATGCAAATAGTACCCCAAATGAATGTGGTGAGAGAATAAGG
520 TTGCCCTTGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (60 bp):
GCAAAAAGACACAAAAACCATGCAAATAGTACCCCAAATGAATGTGGTGAGAGAATAAGG
Found at i:2685 original size:2 final size:2
Alignment explanation
Indices: 2678--2706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2668 ACAAAAAGAG
2678 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 A
2707 AGAACATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5303 original size:21 final size:21
Alignment explanation
Indices: 5278--5329 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
5268 AATTATTTAC
* **
5278 ATGTACATGTCATAGAGTATT
1 ATGTACATGTCATACAAAATT
* *
5299 ATGTATATATCATACAAAATT
1 ATGTACATGTCATACAAAATT
5320 ATGTACATGT
1 ATGTACATGT
5330 ATTATATTGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (21 bp):
ATGTACATGTCATACAAAATT
Found at i:22817 original size:24 final size:24
Alignment explanation
Indices: 22758--22821 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
22748 TGGTGCTTGA
*
22758 CTTCTGCGGTAGAATAGTGATTGG
1 CTTCTGCGGTAGAATAGTGATTAG
* * *
22782 CTTC-GACAGTAGAATGGTGGTTAG
1 CTTCTG-CGGTAGAATAGTGATTAG
22806 CTTCTGCGGTAGAATA
1 CTTCTGCGGTAGAATA
22822 CTAGTTGGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.03
24 30 0.94
25 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.31
Consensus pattern (24 bp):
CTTCTGCGGTAGAATAGTGATTAG
Found at i:23024 original size:23 final size:23
Alignment explanation
Indices: 22987--23046 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 23
22977 CTTTTCACCC
22987 TTTGTCTTTTCTTTTTTGG-AAAT
1 TTTGTCTTTT-TTTTTTGGAAAAT
23010 TTTGCTCTTTTTTTTTTGGAAAAT
1 TTTG-TCTTTTTTTTTTGGAAAAT
*
23034 TTTGGTCATTTTT
1 TTT-GTCTTTTTT
23047 GCCGCAACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 12 0.36
24 20 0.61
25 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.65
Consensus pattern (23 bp):
TTTGTCTTTTTTTTTTGGAAAAT
Found at i:23369 original size:27 final size:26
Alignment explanation
Indices: 23267--23503 Score: 230
Period size: 27 Copynumber: 9.0 Consensus size: 26
23257 CTATGCAGCT
* *
23267 TCCGCGGTTGGGACTCATTCTGAAGC
1 TCCGCAGTTGGGACTCATGCTGAAGC
* * * *
23293 TCTCGTAGTTGGGACTCACGCTATAAAAC
1 TC-CGCAGTTGGGACTCATGC--TGAAGC
* *
23322 TCC-CA--TAGGACTCATGGTGAAGC
1 TCCGCAGTTGGGACTCATGCTGAAGC
*
23345 TCCTGCAGTTGGGACTCATGTTGAAGC
1 TCC-GCAGTTGGGACTCATGCTGAAGC
**
23372 TCCCGCAGTTGGGACTCATGCCAAAGCC
1 T-CCGCAGTTGGGACTCATGCTGAAG-C
*
23400 TCCGCAGTTGGGGCTCATGCTGAAGC
1 TCCGCAGTTGGGACTCATGCTGAAGC
* *
23426 TCCCGCAGTCGGGACTCATGCCGAAGCC
1 T-CCGCAGTTGGGACTCATGCTGAAG-C
*
23454 TCCGCAGTT-GGACTCATGCTGAAGA
1 TCCGCAGTTGGGACTCATGCTGAAGC
*
23479 TCCGCAGTTTGGACTCATGCTGAAG
1 TCCGCAGTTGGGACTCATGCTGAAG
23504 GACTCATGTC
Statistics
Matches: 173, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
23 7 0.04
25 20 0.12
26 33 0.19
27 100 0.58
28 7 0.04
29 6 0.03
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.24
Consensus pattern (26 bp):
TCCGCAGTTGGGACTCATGCTGAAGC
Found at i:23538 original size:41 final size:40
Alignment explanation
Indices: 23463--23545 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 40
23453 CTCCGCAGTT
* *
23463 GGACTCATGCTGAAGATCCGCAGTTTGGACTCATGCTGAA
1 GGACTCATGCTGAAGATCCGCAGTTGGGACTCATGCTAAA
* *
23503 GGACTCATG-TCGAAGCTCCCGTAGTTGGGACTCATGCTAAA
1 GGACTCATGCT-GAAGAT-CCGCAGTTGGGACTCATGCTAAA
23544 GG
1 GG
23546 TCCCGCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.03
40 14 0.38
41 22 0.59
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
GGACTCATGCTGAAGATCCGCAGTTGGGACTCATGCTAAA
Done.