Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019663.1 Corchorus olitorius cultivar O-4 contig19696, 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: 11294
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6906 original size:64 final size:64
Alignment explanation
Indices: 6805--6932 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
6795 TATCTGCTTC
6805 TGCTTGATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGT
1 TGCTTGATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGT
*
6869 TGCTTGATCAAGTAATTCTCTCATGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGT
1 TGCTTGATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGT
6933 AGGAGGATTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.45
Consensus pattern (64 bp):
TGCTTGATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGT
Found at i:6951 original size:64 final size:64
Alignment explanation
Indices: 6810--6953 Score: 218
Period size: 64 Copynumber: 2.2 Consensus size: 64
6800 GCTTCTGCTT
* **
6810 GATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGTTGCTT
1 GATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGTAGCAG
* *
6874 GATCAAGTAATTCTCTCATGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGTAGGAG
1 GATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGTAGCAG
*
6938 GATTC-AGTTATTCTCT
1 GA-TCAAGTAATTCTCT
6954 GTCTAATCTC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
64 71 0.97
65 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (64 bp):
GATCAAGTAATTCTCTCACGATCATAGTTGTCTGCCGTTACTTTTTACTGTTTCAGTGTAGCAG
Found at i:8128 original size:102 final size:103
Alignment explanation
Indices: 8015--8212 Score: 265
Period size: 102 Copynumber: 1.9 Consensus size: 103
8005 ACTCCCTTAA
** * *
8015 TTAATTAACTAGGTTTGACATGGCTCGACTCCAA-ATTAATAGGGACCCAATATGATATCCAACC
1 TTAATTAACTAGGTCCGACATGGCTCGA-TCCAAGATTAATAGGAACCCAATATAATATCCAACC
*
8079 AAAAGAG-AAGAGACGAACAAAAATTCTCTTAAATTCCC
65 AAAAGAGAAAGAGACGAACAAAAACTCTCTTAAATTCCC
** * * *
8117 TTAATTAACTAGGTCCGACATGGCTCGATTTAAGATTAGTCGGAACTCAATATAATATCCAACCA
1 TTAATTAACTAGGTCCGACATGGCTCGATCCAAGATTAATAGGAACCCAATATAATATCCAACCA
*
8182 AAAGAGAAAAGAGATGAACAAAAACTCTCTT
66 AAAGAG-AAAGAGACGAACAAAAACTCTCTT
8213 GATGGTCCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 3 0.04
102 58 0.71
104 21 0.26
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (103 bp):
TTAATTAACTAGGTCCGACATGGCTCGATCCAAGATTAATAGGAACCCAATATAATATCCAACCA
AAAGAGAAAGAGACGAACAAAAACTCTCTTAAATTCCC
Found at i:8248 original size:14 final size:15
Alignment explanation
Indices: 8229--8260 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
8219 CCGATGCGAC
8229 TCGACTCCA-ATTAA
1 TCGACTCCATATTAA
8243 TCGACTCCATATTAA
1 TCGACTCCATATTAA
8258 TCG
1 TCG
8261 GGACCGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (15 bp):
TCGACTCCATATTAA
Found at i:10067 original size:27 final size:27
Alignment explanation
Indices: 10025--10123 Score: 108
Period size: 27 Copynumber: 3.4 Consensus size: 27
10015 ATGAGTGACC
10025 TGTAAGTATATCAGTGATATATATCAT
1 TGTAAGTATATCAGTGATATATATCAT
* * *
10052 TGTAAGTATATTAGTGATCTGTTAGTGAGTGACT
1 TGTAAGTATATCAGTGA--T-ATA-T-A-TCA-T
10086 TGTAAGTATATCAGTGATATATATCAT
1 TGTAAGTATATCAGTGATATATATCAT
10113 TGTAAGTATAT
1 TGTAAGTATAT
10124 TAATGATCTA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
27 28 0.47
28 2 0.03
29 2 0.03
30 3 0.05
31 3 0.05
32 2 0.03
33 2 0.03
34 17 0.29
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.41
Consensus pattern (27 bp):
TGTAAGTATATCAGTGATATATATCAT
Found at i:10081 original size:61 final size:61
Alignment explanation
Indices: 10011--10132 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
10001 AATGATTTTC
*
10011 GTTAATGAGTGACCTGTAAGTATATCAGTGATATATATCATTGTAAGTATATTAGTGATCT
1 GTTAATGAGTGACCTGTAAGTATATCAGTGATATATATCATTGTAAGTATATTAATGATCT
* *
10072 GTTAGTGAGTGACTTGTAAGTATATCAGTGATATATATCATTGTAAGTATATTAATGATCT
1 GTTAATGAGTGACCTGTAAGTATATCAGTGATATATATCATTGTAAGTATATTAATGATCT
10133 ATAAGTACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (61 bp):
GTTAATGAGTGACCTGTAAGTATATCAGTGATATATATCATTGTAAGTATATTAATGATCT
Done.