Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022762.1 Corchorus olitorius cultivar O-4 contig22795, 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: 42246
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5673 original size:29 final size:30
Alignment explanation
Indices: 5631--5687 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
5621 TCGATATGAG
*
5631 ATGTAATACTAGGT-ATGTACAAGTTTGCA
1 ATGTAAGACTAGGTAATGTACAAGTTTGCA
*
5660 ATGTAAGACTAGGTAATGTCCAAGTTTG
1 ATGTAAGACTAGGTAATGTACAAGTTTG
5688 TTCATGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (30 bp):
ATGTAAGACTAGGTAATGTACAAGTTTGCA
Found at i:8129 original size:3 final size:3
Alignment explanation
Indices: 8121--8160 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
8111 TTTTTATCCA
8121 ATT ATT ATT ATT ATTT ATTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT AT
8161 ATATCTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:8134 original size:17 final size:17
Alignment explanation
Indices: 8109--8151 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
8099 ATGTTATGAA
*
8109 TATTTTTATCCAATTAT
1 TATTATTATCCAATTAT
** *
8126 TATTATTATTTATTTAT
1 TATTATTATCCAATTAT
8143 TATTATTAT
1 TATTATTAT
8152 TATTATTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATCCAATTAT
Found at i:12111 original size:3 final size:3
Alignment explanation
Indices: 12103--12165 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
12093 AATAGAGATG
12103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12151 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
12166 ATAGTGAGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16367 original size:5 final size:5
Alignment explanation
Indices: 16357--16385 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
16347 CATATGGTTA
16357 TATAT TATAT TATAT TATAT TATA- TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
16386 AGACATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:33043 original size:2 final size:2
Alignment explanation
Indices: 33036--33060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33026 TGAACTTTTA
33036 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 A
33061 GTTAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34396 original size:13 final size:13
Alignment explanation
Indices: 34378--34402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34368 AAGTGGCCGC
34378 ATTAATTAAACAA
1 ATTAATTAAACAA
34391 ATTAATTAAACA
1 ATTAATTAAACA
34403 GCAGTGAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAACAA
Found at i:41091 original size:165 final size:165
Alignment explanation
Indices: 40781--41224 Score: 674
Period size: 165 Copynumber: 2.7 Consensus size: 165
40771 AGTCAGTTAT
* * * * *
40781 AACTTTGATTGGCAAAGTTAACTAATGACTAACTTGATTCATTTGTCTATTTAGCATGTTCAATA
1 AACTTTGATTGACAAAATTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATA
* * *
40846 ATTAATTTTTTTGGTAACATAATCACTAATTGATTGATTTATTTATGGTAATTTTTTTGGTAGCG
66 ATTAATTTTTTTGGTAACATAATTACT-ATTGATTCATTTATTTATAGTAATTTTTTTGGTAGCG
* *
40911 ATTTATGGTAAAATTAAATAATTATCAATCAATTAA
130 ATTTATGATAAAATTAAATAATCATCAATCAATTAA
*
40947 AACTTTGATTGACAAAATTAACTAACGACTAACTTGGATTCATTTATTTATTTACCATGTTCAAT
1 AACTTTGATTGACAAAATTAACTAACGACTAACTT-GATTCATTTATTTATTTAGCATGTTCAAT
*
41012 AATTAATTTTTTTGGTAACATAATTACT-TTGATTTATTTATTTATAGTAATTTTTTTGGTAGCG
65 AATTAATTTTTTTGGTAACATAATTACTATTGATTCATTTATTTATAGTAATTTTTTTGGTAGCG
*
41076 ATTTATGATAAAATTAAATAATCATCAATCAATTAC
130 ATTTATGATAAAATTAAATAATCATCAATCAATTAA
*
41112 AACTTTGATTGACAAAATTAACTAACGGCTAACTTGATTCATTTATTTATTTAGCATGTTCAATC
1 AACTTTGATTGACAAAATTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT-
* * * *
41177 AATTTTATTTTTTTGCTAACGTAATTACTAATTGATTCGTTTATTTAT
65 AA-TTAATTTTTTTGGTAACATAATTACT-ATTGATTCATTTATTTAT
41225 GGCAAAATTA
Statistics
Matches: 254, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
164 28 0.11
165 103 0.41
166 55 0.22
167 53 0.21
168 15 0.06
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (165 bp):
AACTTTGATTGACAAAATTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATA
ATTAATTTTTTTGGTAACATAATTACTATTGATTCATTTATTTATAGTAATTTTTTTGGTAGCGA
TTTATGATAAAATTAAATAATCATCAATCAATTAA
Found at i:41514 original size:142 final size:140
Alignment explanation
Indices: 41241--41516 Score: 356
Period size: 140 Copynumber: 2.0 Consensus size: 140
41231 ATTATAGGAG
* * ** * * *
41241 TAACTTTTATTGGCAAAGTTGACTTGGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAAT
1 TAACTTTGATTGGCAAAGTTGAATTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
* * ** *
41306 CAGTTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGAAAAATTTAATAATCAT
66 CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAACCAT
41371 CAATTAGTTA
131 CAATTAGTTA
* * *
41381 TAACTTTGATTGGCAAAGTT-AATTAACGACTAATTTGATTTATTTATTTATTTAGTATGTTCAA
1 TAACTTTGATTGGCAAAGTTGAATT-ACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* * *
41445 TCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCAC
65 TCAATTTA--TTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAAC
41510 CATCAAT
128 CATCAAT
41517 CAATTATATA
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
139 3 0.03
140 57 0.50
142 55 0.48
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (140 bp):
TAACTTTGATTGGCAAAGTTGAATTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAACCAT
CAATTAGTTA
Found at i:41524 original size:142 final size:140
Alignment explanation
Indices: 41241--41524 Score: 354
Period size: 142 Copynumber: 2.0 Consensus size: 140
41231 ATTATAGGAG
* * ** * * *
41241 TAACTTTTATTGGCAAAGTTGACTTGGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAAT
1 TAACTTTGATTGGCAAAGTTGAATTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
* * ** *
41306 CAGTTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGAAAAATTTAATAATCAT
66 CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAACCAT
* *
41371 CAATTAGTTA
131 CAATCAATTA
* * *
41381 TAACTTTGATTGGCAAAGTT-AATTAACGACTAATTTGATTTATTTATTTATTTAGTATGTTCAA
1 TAACTTTGATTGGCAAAGTTGAATT-ACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* * *
41445 TCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCAC
65 TCAATTTA--TTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAAC
41510 CATCAATCAATTA
128 CATCAATCAATTA
41523 TA
1 TA
41525 TAATTATGAA
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
139 3 0.02
140 57 0.47
142 61 0.50
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (140 bp):
TAACTTTGATTGGCAAAGTTGAATTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGAAAAATCAAATAACCAT
CAATCAATTA
Done.