Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020103.1 Corchorus olitorius cultivar O-4 contig20136, 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: 28874
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1940 original size:2 final size:2
Alignment explanation
Indices: 1928--1979 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1918 GTTTCAAATA
* * * *
1928 AT AT TT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1970 AT TT AT AT AT
1 AT AT AT AT AT
1980 TTAGTAACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (2 bp):
AT
Found at i:8289 original size:31 final size:30
Alignment explanation
Indices: 8246--8313 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
8236 AAAAAGTCAA
*
8246 GGACCCAATTGCTAAATTA-ACTTCACTTCAG
1 GGACCCAATTGCT-AACTACA-TTCACTTCAG
* *
8277 GGACTCAATTGCTCACTACATTCACTTCAG
1 GGACCCAATTGCTAACTACATTCACTTCAG
8307 GGACCCA
1 GGACCCA
8314 TTTACACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (30 bp):
GGACCCAATTGCTAACTACATTCACTTCAG
Found at i:9197 original size:20 final size:19
Alignment explanation
Indices: 9168--9221 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
9158 TCACCCAAAT
*
9168 TTTTTTAA-AAAATATATA
1 TTTTTTAATAAAAAATATA
*
9186 TATTTTAA-AAAAAATAT-
1 TTTTTTAATAAAAAATATA
9203 TTTTTTAATAAAAAA-ATA
1 TTTTTTAATAAAAAATATA
9221 T
1 T
9222 GACGTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTTTAATAAAAAATATA
Found at i:10131 original size:108 final size:107
Alignment explanation
Indices: 9865--10184 Score: 358
Period size: 107 Copynumber: 3.0 Consensus size: 107
9855 AAAGTCAATT
* * * * *
9865 AATTTCACTAAATTTAGCCTTAAATTGTAAAAA-GTAATTCATTTTAAGGGTAAATTATGAAATT
1 AATTTCACTAAGTTTAGCCTTAAA-TG-AAAAATTTAATTCATTTCAAGGGTAAGTTATCAAATT
** * * *
9929 AAAGATTTATTCGTATAGGGTTCTAGAAAAAATAGAAT-TAACC
64 AAAGATTTATTATTATAGGGTTTTAGAAAAAATAAAATAAAACC
** * * *
9972 AATTTCACTAAGTTTAGCCCCAAATTAAAAAATTTAATTTATCTCAAGGGTAAGTTATCAAATTA
1 AATTTCACTAAGTTTAGCCTTAAA-TGAAAAATTTAATTCATTTCAAGGGTAAGTTATCAAATTA
* **
10037 AAGATTTATTATTATAGTGTTTTAGAAAAAATAAAATAAAATG
65 AAGATTTATTATTATAGGGTTTTAGAAAAAATAAAATAAAACC
** *
10080 AATTTCACTAAGTTTAGTTTTAAATGAAAACATTTAATTCATTTCAAGGGTAAGTTGTCAAATTA
1 AATTTCACTAAGTTTAGCCTTAAATGAAAA-ATTTAATTCATTTCAAGGGTAAGTTATCAAATTA
* *
10145 AA-ATTTTTTTTATTATAGGGTTTTAGTAAAAATAAAATAA
65 AAGA--TTTATTATTATAGGGTTTTAGAAAAAATAAAATAA
10185 TCAATTTCAT
Statistics
Matches: 179, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
106 5 0.03
107 87 0.49
108 55 0.31
109 32 0.18
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (107 bp):
AATTTCACTAAGTTTAGCCTTAAATGAAAAATTTAATTCATTTCAAGGGTAAGTTATCAAATTAA
AGATTTATTATTATAGGGTTTTAGAAAAAATAAAATAAAACC
Found at i:12965 original size:11 final size:11
Alignment explanation
Indices: 12951--12988 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12941 ATTCATAACA
12951 AATTTATAATT
1 AATTTATAATT
12962 AATTTATAATT
1 AATTTATAATT
12973 -ATTTGATAATT
1 AATTT-ATAATT
*
12984 TATTT
1 AATTT
12989 TATATAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15297 original size:27 final size:27
Alignment explanation
Indices: 15264--15321 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
15254 TGCTGTTTAG
15264 TTTCCTTTGCCTCTGGTTTAGAAGTTA
1 TTTCCTTTGCCTCTGGTTTAGAAGTTA
* *
15291 TTTCCTTTGCTTCTGGTTTAGAATTTA
1 TTTCCTTTGCCTCTGGTTTAGAAGTTA
15318 TTTC
1 TTTC
15322 AACATCAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.17, G:0.16, T:0.53
Consensus pattern (27 bp):
TTTCCTTTGCCTCTGGTTTAGAAGTTA
Found at i:22606 original size:13 final size:13
Alignment explanation
Indices: 22588--22612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22578 GGTAGCAACA
22588 AAAAATCATCACC
1 AAAAATCATCACC
22601 AAAAATCATCAC
1 AAAAATCATCAC
22613 TCATGCCAAA
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATCATCACC
Found at i:28304 original size:33 final size:33
Alignment explanation
Indices: 28206--28336 Score: 145
Period size: 33 Copynumber: 3.8 Consensus size: 33
28196 AAAAACTGAA
* ****
28206 TGGGAACTTTCCCAATTTGAAAACTTAAAAGTTAA
1 TGGGAACTTTCCCAA-TTAAAAACTTAAAA-CCGG
28241 TGGGAACTTTCCCAATTTTTAAAAACTTAAAACCGG
1 TGGGAACTTTCCCAA---TTAAAAACTTAAAACCGG
* * *
28277 TGGGAACTTTCCCGATTAAAAATTTAAAACTGG
1 TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
28310 TGGGAACTTTCCCAATTAAAAACTTAA
1 TGGGAACTTTCCCAATTAAAAACTTAA
28337 TGAAATTCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 41 0.49
35 15 0.18
36 14 0.17
37 14 0.17
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
Done.