Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009830.1 Corchorus olitorius cultivar O-4 contig09862, 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: 17610
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2926 original size:17 final size:17
Alignment explanation
Indices: 2904--2936 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2894 TTTGAATGGA
2904 ATGCTTTGAAGTTTTGC
1 ATGCTTTGAAGTTTTGC
*
2921 ATGCTTTGTAGTTTTG
1 ATGCTTTGAAGTTTTG
2937 AATTCCTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.24, T:0.52
Consensus pattern (17 bp):
ATGCTTTGAAGTTTTGC
Found at i:3291 original size:48 final size:48
Alignment explanation
Indices: 3236--3387 Score: 245
Period size: 48 Copynumber: 3.2 Consensus size: 48
3226 ATACCTATTT
*
3236 AGGAAGGCACGTGAGAGAATGAGTTGTATTGTGTAAAAGTTCCTAATA
1 AGGAAGGCACGTGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
* *
3284 AGGAAGGCACATGAGAGAACGAGTTGTATCGTGTAAAAGTTCCTAATA
1 AGGAAGGCACGTGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
*
3332 AGGAAGGCACGT--GAGAATGAATTTGTATCGTGTAAAAGTTCCTAATA
1 AGGAAGGCACGTGAGAGAATG-AGTTGTATCGTGTAAAAGTTCCTAATA
3379 AGGAAGGCA
1 AGGAAGGCA
3388 TGATAGATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
46 6 0.06
47 35 0.36
48 56 0.58
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (48 bp):
AGGAAGGCACGTGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
Found at i:5842 original size:15 final size:15
Alignment explanation
Indices: 5821--5985 Score: 294
Period size: 15 Copynumber: 11.0 Consensus size: 15
5811 GCCTTTGAAG
5821 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
*
5836 GAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
*
5851 AAGCAAAAGGATGAC
1 AAGCAAGAGGATGAC
5866 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
*
5881 AAGCAAAAGGATGAC
1 AAGCAAGAGGATGAC
5896 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
5911 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
5926 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
5941 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
*
5956 AAGCAAGAGGATGAA
1 AAGCAAGAGGATGAC
5971 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
5986 CACCTTGCTG
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 142 1.00
ACGTcount: A:0.48, C:0.13, G:0.33, T:0.07
Consensus pattern (15 bp):
AAGCAAGAGGATGAC
Found at i:6673 original size:117 final size:117
Alignment explanation
Indices: 6521--6884 Score: 658
Period size: 117 Copynumber: 3.1 Consensus size: 117
6511 GAAGGGACAC
6521 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
* *
6586 GATAATGTGCCTGCTAATGTAGATGAAACTAAGAAAGAAAGTGGC-TTAGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACT-GCGA
*
6638 GTGATTCAGAAGCAAAAACAAACAGACGCTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
* *
6703 GATAATTTGCCCACTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
*
6755 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCATTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
6820 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
6872 GTGATTCAGAAGC
1 GTGATTCAGAAGC
6885 GAAGTCACTG
Statistics
Matches: 237, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
117 236 1.00
118 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (117 bp):
GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
Found at i:11414 original size:61 final size:59
Alignment explanation
Indices: 11339--11532 Score: 245
Period size: 61 Copynumber: 3.3 Consensus size: 59
11329 ATCTGATAAT
* * *
11339 CACATTGAGCTCCGATTAATCCGGAGTCGAGTTGTATAGGACCCTAAATGAAGTAACCA
1 CACATTGAGCTCCGACTAATCCGGAGTCGAGTTGCATAGGACCCTAAATGAGGTAACCA
* * *
11398 TGCACATTGAACTCCGACTAATCCGGGGTCGAGTTGCATAAGACCCTAAATGAGGTAACCA
1 --CACATTGAGCTCCGACTAATCCGGAGTCGAGTTGCATAGGACCCTAAATGAGGTAACCA
* * *
11459 -A-ATTGAGCT-CTACAAATCCGAAGTCGAGTTGCATAGGACCCTAAATGAGGTAA-C-
1 CACATTGAGCTCCGACTAATCCGGAGTCGAGTTGCATAGGACCCTAAATGAGGTAACCA
*
11513 CACATTGAACTCCGACTAAT
1 CACATTGAGCTCCGACTAAT
11533 TCGGTATCAG
Statistics
Matches: 115, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
55 2 0.02
56 46 0.40
57 13 0.11
58 1 0.01
61 53 0.46
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (59 bp):
CACATTGAGCTCCGACTAATCCGGAGTCGAGTTGCATAGGACCCTAAATGAGGTAACCA
Done.