Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021650.1 Corchorus olitorius cultivar O-4 contig21683, 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: 36108
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:5018 original size:29 final size:29
Alignment explanation
Indices: 4976--5035 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
4966 TACGATAAAT
4976 GATTACTTAAGCAAGCAATTGGATTTGAA
1 GATTACTTAAGCAAGCAATTGGATTTGAA
* *
5005 GATTACTTAAGCAAGCTATTTGATTTGAA
1 GATTACTTAAGCAAGCAATTGGATTTGAA
5034 GA
1 GA
5036 CAGTACTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (29 bp):
GATTACTTAAGCAAGCAATTGGATTTGAA
Found at i:9077 original size:30 final size:30
Alignment explanation
Indices: 9036--9139 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
9026 AATAGCCAGC
*
9036 TGTAAATCCTGCGACAATGGAATATCTGTT
1 TGTAAATCCTGCGACAATGGAACATCTGTT
* *
9066 TGTACATCCTGC-AGCGGAA--GAACATCAGTT
1 TGTAAATCCTGCGA-C--AATGGAACATCTGTT
* * **
9096 TGTAAATCCTGCGGCAGTGGAACATCTGCC
1 TGTAAATCCTGCGACAATGGAACATCTGTT
*
9126 TGTACATCCTGCGA
1 TGTAAATCCTGCGA
9140 TGGAGCCGGA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 53 0.93
32 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (30 bp):
TGTAAATCCTGCGACAATGGAACATCTGTT
Found at i:25309 original size:44 final size:44
Alignment explanation
Indices: 25259--25388 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 44
25249 AAGGAGGATT
* *
25259 ATTGAAAGAAGATCCACATATGTGGAGGATTTTTATCAAAGAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAA
* * * *
25303 ATTGAAAGAAAATCCACGTATGTGGAAGA--ATTATTAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAA
25345 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAA-AAA
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAA
25388 A
1 A
25389 GGTTCAAGGA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 37 0.50
43 3 0.04
44 34 0.46
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.25
Consensus pattern (44 bp):
ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAA
Found at i:25662 original size:62 final size:58
Alignment explanation
Indices: 25559--25682 Score: 185
Period size: 62 Copynumber: 2.1 Consensus size: 58
25549 AAGACCATCG
* * *
25559 AATCAAATCAAACTCCCAACTCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA
1 AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCA
25617 AATCAAATCAAACTCTCAAATTATCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAAGCA
1 AATCAAATCAAACTC-CAAA--ATCATCAA-TTCAAGATCAAGTCATTCGACCCTTGAAGCA
25679 AATC
1 AATC
25683 TTGAAGCATA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 15 0.25
59 3 0.05
61 7 0.12
62 34 0.58
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (58 bp):
AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCA
Found at i:28300 original size:44 final size:44
Alignment explanation
Indices: 28200--28378 Score: 263
Period size: 44 Copynumber: 4.0 Consensus size: 44
28190 AAGGAGGATT
** *
28200 ATTGAAAGAAGATCCATATATGTGGGGGATTATCATCATCAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTAT--T-ATCAAAGAAG
*
28247 ATTGAAAGAAGATCCACGTATGTGGAGGATTTTTATCAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAG
* *
28291 ATTGAAAGAAGATCCACGTATGTGGAGGA--ACTATTAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAG
28333 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAG
28377 AT
1 AT
28379 CCAAGGAGGA
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
42 39 0.32
44 52 0.43
45 1 0.01
47 29 0.24
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (44 bp):
ATTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAG
Found at i:28617 original size:58 final size:61
Alignment explanation
Indices: 28546--28669 Score: 155
Period size: 62 Copynumber: 2.1 Consensus size: 61
28536 AAGACCATCG
* * * *
28546 AATCAAATCAAACT-CCCAA-GTCATTAA-TTCAAGATCAAGTTATTCAACCCTTGAATCA
1 AATCAAATCAAACTGCCAAATATCATTAAGTTCAAGATCAAGTCATTCAACCCTTGAAGCA
* * *
28604 AATCAAATCAAACTGTCAAATTATCATTAAGTTGAAGATCAAGTCATTCGACCCTTGAAGCA
1 AATCAAATCAAACTGCCAAA-TATCATTAAGTTCAAGATCAAGTCATTCAACCCTTGAAGCA
28666 AATC
1 AATC
28670 TTAAAGCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 14 0.25
59 3 0.05
61 7 0.13
62 31 0.56
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (61 bp):
AATCAAATCAAACTGCCAAATATCATTAAGTTCAAGATCAAGTCATTCAACCCTTGAAGCA
Found at i:32855 original size:16 final size:15
Alignment explanation
Indices: 32834--32881 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
32824 CAAAAAAGCT
32834 CAAACCCGAAAAAAC
1 CAAACCCGAAAAAAC
* *
32849 CAGAACCCGAATAATAT
1 CA-AACCCGAA-AAAAC
*
32866 GAAACCCGAAAAAAC
1 CAAACCCGAAAAAAC
32881 C
1 C
32882 CGAATGTGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.54, C:0.29, G:0.10, T:0.06
Consensus pattern (15 bp):
CAAACCCGAAAAAAC
Found at i:33121 original size:32 final size:32
Alignment explanation
Indices: 33083--33185 Score: 145
Period size: 32 Copynumber: 3.2 Consensus size: 32
33073 AACCCAACCG
* *
33083 AACCCGAACCCGAATTATCCTGACCCAAAATT
1 AACCCGAACCCGAATAATCCTGACCCAAATTT
* * *
33115 GACCCGAACCCGAATCAGCCTGACCCAAATTT
1 AACCCGAACCCGAATAATCCTGACCCAAATTT
33147 AACCCGAACCCGAATCAATCC-GACCCAAATTT
1 AACCCGAACCCGAAT-AATCCTGACCCAAATTT
33179 AACCCGA
1 AACCCGA
33186 CCTGACTCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
32 60 0.95
33 3 0.05
ACGTcount: A:0.36, C:0.37, G:0.12, T:0.16
Consensus pattern (32 bp):
AACCCGAACCCGAATAATCCTGACCCAAATTT
Found at i:33185 original size:16 final size:16
Alignment explanation
Indices: 33136--33187 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
33126 GAATCAGCCT
33136 GACCCAAATTTAACCC
1 GACCCAAATTTAACCC
* * *
33152 GAACCCGAA-TCAATCC
1 G-ACCCAAATTTAACCC
33168 GACCCAAATTTAACCC
1 GACCCAAATTTAACCC
33184 GACC
1 GACC
33188 TGACTCAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 6 0.21
16 16 0.57
17 6 0.21
ACGTcount: A:0.37, C:0.38, G:0.10, T:0.15
Consensus pattern (16 bp):
GACCCAAATTTAACCC
Found at i:33976 original size:31 final size:30
Alignment explanation
Indices: 33941--34053 Score: 142
Period size: 28 Copynumber: 3.7 Consensus size: 30
33931 TAAAATTTAA
33941 TTGACACCAGAAGTTGTCATATTAAATTATC
1 TTGACACCAGAAGTTGTCATA-TAAATTATC
33972 TTGACACCAGAAGTTGTCATGA-AAATTA--
1 TTGACACCAGAAGTTGTCAT-ATAAATTATC
34000 TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATAT--AA--ATTATC
*
34034 TTGATACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
34054 GCTGAGGAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
30 8 0.11
31 20 0.27
32 5 0.07
34 19 0.26
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (30 bp):
TTGACACCAGAAGTTGTCATATAAATTATC
Found at i:34027 original size:59 final size:63
Alignment explanation
Indices: 33940--34086 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 63
33930 TTAAAATTTA
*
33940 ATTGACACCAGAAGTTGTCATAT-TAA-ATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
1 ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
*
33999 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGATACCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAA-TATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAA
34064 TT
62 TT
34066 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
34087 CCCAAGATTG
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
59 23 0.29
60 2 0.03
62 24 0.31
65 3 0.04
67 26 0.33
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (63 bp):
ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
Done.