Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012475.1 Corchorus olitorius cultivar O-4 contig12508, 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: 22059
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1103 original size:18 final size:19
Alignment explanation
Indices: 1067--1104 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1057 ATCAAACACA
*
1067 TGAAGAATTTTCAATAGTT
1 TGAAGAATTTTCAACAGTT
*
1086 TGAA-AATTTTTAACAGTT
1 TGAAGAATTTTCAACAGTT
1104 T
1 T
1105 ATCAAACAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
TGAAGAATTTTCAACAGTT
Found at i:20040 original size:22 final size:22
Alignment explanation
Indices: 19988--20443 Score: 244
Period size: 22 Copynumber: 20.9 Consensus size: 22
19978 TTGACCTTCT
* *
19988 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTCAC
* * *
20010 TAAGGAATTTTGAAAACCTCAC
1 TATGAAATTTTGATAACCTCAC
* * *
20032 TATGAAATTTTAATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
20054 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
20077 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * **
20098 ATATGATATATTGATAACCAT-GT
1 -TATGAAATTTTGATAACC-TCAC
* * * * *
20121 TTTGAAAATTTAAAAATCTCTA-
1 TATGAAATTTTGATAACCTC-AC
* *
20143 TATG-AATTGTT-ATTAATCACAC
1 TATGAAATT-TTGA-TAACCTCAC
** * *
20165 CCT-AAACTTTTGATAATCACAC
1 TATGAAA-TTTTGATAACCTCAC
* *
20187 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
20209 TATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
* *
20232 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
*
20255 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
20276 TTATGAAATCTTGAT-A----AC
1 -TATGAAATTTTGATAACCTCAC
*
20294 TAT-AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** * *
20315 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTCAC
* * *
20337 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
20359 TATGAAATTTTGATCTACAT-AT
1 TATGAAATTTTGAT-AACCTCAC
*
20381 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
20403 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
20425 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
20444 TCATTTTGAT
Statistics
Matches: 331, Mismatches: 73, Indels: 59
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
18 1 0.00
20 2 0.01
21 16 0.05
22 229 0.69
23 68 0.21
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:20093 original size:45 final size:45
Alignment explanation
Indices: 20015--20117 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
20005 CTCTCTAAGG
* * * *
20015 AATTTTGAAAACC-TCACTATGAAATTTTAATAACTTCCCA-ATGA
1 AATTTTGATAACCAACACTATGAAATGTTAATAACCT-CCATATGA
* *
20059 AATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGA
1 AATTTTGATAACCAACACTATGAAATGTTAATAACCTCCATATGA
* *
20104 TATATTGATAACCA
1 AATTTTGATAACCA
20118 TGTTTTGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 15 0.31
45 34 0.69
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (45 bp):
AATTTTGATAACCAACACTATGAAATGTTAATAACCTCCATATGA
Done.