Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013028.1 Corchorus olitorius cultivar O-4 contig13061, 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: 36413
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1018 original size:24 final size:21
Alignment explanation
Indices: 963--1017 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
953 CGCCCATTCA
*
963 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
984 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
1005 CCGTGCCATCACC
1 CCGTGCCACCACC
1018 ATTCACTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:1392 original size:15 final size:14
Alignment explanation
Indices: 1372--1401 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1362 ATCTTTTTAA
1372 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
1387 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
1401 T
1 T
1402 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
Found at i:4277 original size:15 final size:15
Alignment explanation
Indices: 4247--4288 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4237 TTACTTTGTT
4247 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
4263 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
4278 TTGTTTTCTGT
1 TTGTTTTCTGT
4289 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:9895 original size:33 final size:33
Alignment explanation
Indices: 9856--9923 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
9846 TTAAATTAAA
*
9856 TAGAACTTTGCATTAAGAAGTGAAATTAATAGT
1 TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
*
9889 TAGAACTTTGCATAAAGAAGTGAATTTAATAGT
1 TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
9922 TA
1 TA
9924 CTTAGTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (33 bp):
TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
Found at i:10176 original size:18 final size:18
Alignment explanation
Indices: 10155--10193 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
10145 AAATATAATA
10155 AATTTTAGATCATGTTGT
1 AATTTTAGATCATGTTGT
10173 AATTTTAGATCATGTTGT
1 AATTTTAGATCATGTTGT
10191 AAT
1 AAT
10194 AGAAGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (18 bp):
AATTTTAGATCATGTTGT
Found at i:14556 original size:15 final size:16
Alignment explanation
Indices: 14523--14562 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
14513 TTACTTTGCT
14523 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
14539 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
14554 TTGCTTTCT
1 TTGTTTTCT
14563 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:25031 original size:43 final size:43
Alignment explanation
Indices: 24973--25061 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
24963 AGAGCTTCTC
* * *
24973 CCTGCTTTCATCAAAGGGTTCTTGTCTAATGTTTCTATTATCT
1 CCTGCTTTCATCAAAGAGTTCTTGGCTAAGGTTTCTATTATCT
25016 CCTGCTTTCATCAAAGAGTTCTTGGCTAAGGTTTCTATTATCT
1 CCTGCTTTCATCAAAGAGTTCTTGGCTAAGGTTTCTATTATCT
25059 CCT
1 CCT
25062 TCAATTCCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (43 bp):
CCTGCTTTCATCAAAGAGTTCTTGGCTAAGGTTTCTATTATCT
Found at i:36191 original size:15 final size:17
Alignment explanation
Indices: 36159--36195 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
36149 CTAGGGAATT
*
36159 CTTTTTTTCTTTTATTA
1 CTTTTTTTCTTGTATTA
36176 CTTTTTTTC-TGT-TTA
1 CTTTTTTTCTTGTATTA
36191 CTTTT
1 CTTTT
36196 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (17 bp):
CTTTTTTTCTTGTATTA
Done.