Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014182.1 Corchorus olitorius cultivar O-4 contig14215, 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: 7958
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:779 original size:15 final size:15
Alignment explanation
Indices: 749--790 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
739 TTACTTTGCT
749 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
765 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
780 TTGCTTTCTGT
1 TTGTTTTCTGT
791 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:1165 original size:24 final size:24
Alignment explanation
Indices: 1136--1207 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
1126 AATTGTTTTG
1136 TGTTTTGCGTCGAAAAAAAAAAATA
1 TGTTTTGCGTC-AAAAAAAAAAATA
* * *
1161 T-TTTTGCGTCATAAAAAAAATTT
1 TGTTTTGCGTCAAAAAAAAAAATA
1184 TGTTTCTGCGTCATAAAAAAAAAA
1 TGTTT-TGCGTCA-AAAAAAAAAA
1208 GTTTTCTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 11 0.28
24 12 0.31
25 8 0.21
26 8 0.21
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
TGTTTTGCGTCAAAAAAAAAAATA
Found at i:1176 original size:25 final size:25
Alignment explanation
Indices: 1138--1207 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
1128 TTGTTTTGTG
*
1138 TTTTGCGTC-GAAAAAAAAAAATAT
1 TTTTGCGTCATAAAAAAAAAAATAT
*** *
1162 TTTTGCGTCATAAAAAAAATTTTGT
1 TTTTGCGTCATAAAAAAAAAAATAT
*
1187 TTCTGCGTCATAAAAAAAAAA
1 TTTTGCGTCATAAAAAAAAAA
1208 GTTTTCTTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 9 0.24
25 28 0.76
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (25 bp):
TTTTGCGTCATAAAAAAAAAAATAT
Found at i:1218 original size:25 final size:25
Alignment explanation
Indices: 1140--1219 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
1130 GTTTTGTGTT
1140 TTGCGTCGA-AAAAAAAAAATATTT-
1 TTGCGTC-ATAAAAAAAAAATATTTC
** *
1164 TTGCGTCATAAAAAAAATTTTGTTTC
1 TTGCGTCATAAAAAAAA-AATATTTC
1190 -TGCGTCATAAAAAAAAAAGT-TTTC
1 TTGCGTCATAAAAAAAAAA-TATTTC
1214 TTGCGT
1 TTGCGT
1220 TTTTAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.02
24 19 0.41
25 26 0.57
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (25 bp):
TTGCGTCATAAAAAAAAAATATTTC
Found at i:3496 original size:24 final size:24
Alignment explanation
Indices: 3462--3519 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
3452 AGATTGATGT
*
3462 ATTCGATGGTTCAATGACCATGGA
1 ATTCGACGGTTCAATGACCATGGA
*
3486 ATTCGACGGTTCACTGACCATGGA
1 ATTCGACGGTTCAATGACCATGGA
3510 ATTCGACGGT
1 ATTCGACGGT
3520 GATATAATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (24 bp):
ATTCGACGGTTCAATGACCATGGA
Found at i:4545 original size:21 final size:21
Alignment explanation
Indices: 4490--4549 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
4480 CCAAGCCATT
* *
4490 ACCGGCCATTCACCGTGACACC
1 ACCGGCCATGC-CCGTGCCACC
** *
4512 ACCGGTTAAGCCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
4533 ACCGGCCATGCCCGTGC
1 ACCGGCCATGCCCGTGC
4550 AATCACCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.13
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Found at i:4928 original size:15 final size:14
Alignment explanation
Indices: 4908--4937 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4898 ATCTCTTTAA
4908 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
4923 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
4937 T
1 T
4938 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Done.