Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012163.1 Corchorus olitorius cultivar O-4 contig12196, 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: 6619
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Found at i:265 original size:22 final size:22
Alignment explanation
Indices: 220--299 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
210 CATAGGGAGA
* * **
220 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCTCAGTGTGG
**
242 TTATCAAAATTTCTTTGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
264 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
286 TTATCCAAATTTCT
1 TTATCAAAATTTCT
300 ATGTTGGAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCTCAGTGTGG
Found at i:288 original size:44 final size:44
Alignment explanation
Indices: 122--298 Score: 153
Period size: 44 Copynumber: 4.0 Consensus size: 44
112 AGTTTCATTA
* * *
122 TCATAGGGAGGTTATCGAAATTTCAAAGTATGGTTATCAAAATTT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAA-TT
* * * * *
167 TCATAGTGCA-GCTATC-AACTTT-ATAGTGTGATTATCAAAATT
1 TCATAGTG-AGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
* * * * *
209 CCATAGGGAGATTATCAAAATTTCACACTAAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
* * * * *
253 TCTTTGTGTGGTTATCAAAATTTCACAGTGTGGTTATCCAAATT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
297 TC
1 TC
299 TATGTTGGAG
Statistics
Matches: 102, Mismatches: 26, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 12 0.12
43 20 0.20
44 56 0.55
45 12 0.12
46 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (44 bp):
TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
Found at i:1222 original size:38 final size:38
Alignment explanation
Indices: 1171--1247 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
1161 TTGACAAATG
*
1171 ATATAATGAATGGTTTTAAATTTTTTCG-TAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTT-GATAAATATATA
1209 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
1247 A
1 A
1248 ATTATTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
Found at i:4740 original size:19 final size:19
Alignment explanation
Indices: 4687--4740 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
4677 CTTATTAAGC
* *
4687 TTTTTAATAACTTTATAGG
1 TTTTTAATAACCTTAGAGG
*
4706 TTTTTCAATAATCTTAGAGG
1 TTTTT-AATAACCTTAGAGG
*
4726 TTTTTAGTAACCTTA
1 TTTTTAATAACCTTA
4741 ATAATTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTTTAATAACCTTAGAGG
Found at i:4752 original size:19 final size:20
Alignment explanation
Indices: 4730--4775 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4720 TAGAGGTTTT
4730 TAGTAACCTTAATAAT-TTG
1 TAGTAACCTTAATAATATTG
** *
4749 TAGTAATGTTATTAATATTG
1 TAGTAACCTTAATAATATTG
4769 TAGTAAC
1 TAGTAAC
4776 TTTATTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (20 bp):
TAGTAACCTTAATAATATTG
Found at i:4771 original size:20 final size:19
Alignment explanation
Indices: 4730--4783 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4720 TAGAGGTTTT
* *
4730 TAGTAACCTTAATAATTTG
1 TAGTAACTTTATTAATTTG
4749 TAGTAA-TGTTATTAATATTG
1 TAGTAACT-TTATTAAT-TTG
4769 TAGTAACTTTATTAA
1 TAGTAACTTTATTAA
4784 ACTTTTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 13 0.43
20 16 0.53
21 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (19 bp):
TAGTAACTTTATTAATTTG
Found at i:6235 original size:37 final size:37
Alignment explanation
Indices: 6188--6272 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
6178 AATAATTTAT
* * *
6188 TAAAATATTTTATTAAGCATTTAAATAAAATCAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
6225 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
6262 TAAAACATTTT
1 TAAAACATTTT
6273 CCTCAACGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (37 bp):
TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
Done.