Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021405.1 Corchorus olitorius cultivar O-4 contig21438, 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: 35712
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3367 original size:30 final size:30
Alignment explanation
Indices: 3333--3390 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3323 TTTTATCTTG
*
3333 ACTTTCCTCTTATATCCTCAAATTTTAAGA
1 ACTTTCCTCTTATACCCTCAAATTTTAAGA
*
3363 ACTTTTCTCTTATACCCTCAAATTTTAA
1 ACTTTCCTCTTATACCCTCAAATTTTAA
3391 TGGCTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAAGA
Found at i:3880 original size:7 final size:7
Alignment explanation
Indices: 3868--3901 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
3858 GACTTGAGAA
3868 TTTTGTT
1 TTTTGTT
3875 TTTTGTTTT
1 TTTTG--TT
3884 TTTTGTT
1 TTTTGTT
3891 TTTTGTT
1 TTTTGTT
3898 TTTT
1 TTTT
3902 TTGTCAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:3887 original size:9 final size:9
Alignment explanation
Indices: 3873--3905 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3863 GAGAATTTTG
3873 TTTTTTGTT
1 TTTTTTGTT
3882 TTTTTTG--
1 TTTTTTGTT
3889 TTTTTTGTT
1 TTTTTTGTT
3898 TTTTTTGT
1 TTTTTTGT
3906 CAATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:3889 original size:16 final size:16
Alignment explanation
Indices: 3868--3905 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3858 GACTTGAGAA
3868 TTTTGTTTTTTGTTTT
1 TTTTGTTTTTTGTTTT
3884 TTTTGTTTTTTGTTTT
1 TTTTGTTTTTTGTTTT
3900 TTTTGT
1 TTTTGT
3906 CAATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTTTGTTTT
Found at i:10805 original size:86 final size:86
Alignment explanation
Indices: 10657--10835 Score: 218
Period size: 86 Copynumber: 2.1 Consensus size: 86
10647 AATGTATGGA
* * * *
10657 TTTCTTAACTATAATTTGGTTAAAAGTGATCAATTGGAGATTACAATATTAATGATGTATCCACT
1 TTTCTTAACAATAATTTGGTTAAAAGTGACCAATTGGAGATTACAATATTAACGATGAATCCACT
* * *
10722 CCTTGATCTCGTGCCTTTTTG
66 CATTAATCTCGTGCCTTTGTG
* * * *
10743 TTTCTTAACAATAATTTGGTTAAGAGTTG-CCAATTGGAGATTACGATTTTAACGGTGAATCCAC
1 TTTCTTAACAATAATTTGGTTAAAAG-TGACCAATTGGAGATTACAATATTAACGATGAATCCAC
* *
10807 TCATTAATTTCGTGTCTTTGTG
65 TCATTAATCTCGTGCCTTTGTG
10829 TTT-TTAA
1 TTTCTTAA
10836 GTGTCTGTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 4 0.05
86 73 0.92
87 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (86 bp):
TTTCTTAACAATAATTTGGTTAAAAGTGACCAATTGGAGATTACAATATTAACGATGAATCCACT
CATTAATCTCGTGCCTTTGTG
Found at i:11996 original size:20 final size:20
Alignment explanation
Indices: 11971--12049 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
11961 TCTCTGATCT
*
11971 CGTCTCTCTCGAATTTCTTC
1 CGTCTCTCTCAAATTTCTTC
11991 CGTCTCTCTCAAATTTCTTC
1 CGTCTCTCTCAAATTTCTTC
* *
12011 TC-TCTCTCTCGATTTTCTTC
1 -CGTCTCTCTCAAATTTCTTC
**
12031 TATCTCTCTCAAATTTCTT
1 CGTCTCTCTCAAATTTCTT
12050 TTGATTGTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.13, C:0.33, G:0.05, T:0.49
Consensus pattern (20 bp):
CGTCTCTCTCAAATTTCTTC
Found at i:12028 original size:40 final size:41
Alignment explanation
Indices: 11968--12049 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 41
11958 CTCTCTCTGA
*
11968 TCTCGTCTCTCTCGAATTTCTTCCGTCTCTCTCAAATTTCT
1 TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT
* *
12009 TCTC-TCTCTCTCGATTTTCTTCTATCTCTCTCAAATTTCT
1 TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT
12049 T
1 T
12050 TTGATTGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.12, C:0.33, G:0.05, T:0.50
Consensus pattern (41 bp):
TCTCGTCTCTCTCGAATTTCTTCCATCTCTCTCAAATTTCT
Found at i:22416 original size:2 final size:2
Alignment explanation
Indices: 22409--22452 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
22399 CGACTTGGCA
22409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22451 AT
1 AT
22453 TAGACAGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25272 original size:35 final size:36
Alignment explanation
Indices: 25226--25297 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
25216 TTAAGATTCG
*
25226 AACCCTTCTTATACCAAACTTAAGTTCGAGT-CTTT
1 AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTTT
25261 AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTTT
1 AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTTT
25297 A
1 A
25298 TCTATAGGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (36 bp):
AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTTT
Found at i:34411 original size:2 final size:2
Alignment explanation
Indices: 34406--34520 Score: 230
Period size: 2 Copynumber: 57.5 Consensus size: 2
34396 AAAAAAGTCA
34406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34521 CCTTATAATG
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.