Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023059.1 Corchorus olitorius cultivar O-4 contig23092, 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: 36013
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:69 original size:24 final size:24
Alignment explanation
Indices: 3--74 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
1 TT
3 TTCTTTTTTATCAGATAAGTTACA
1 TTCTTTTTTATCAGATAAGTTACA
* * *
27 TTATTTTTAAAC-G-TCAAGTTACA
1 TTCTTTTTTATCAGAT-AAGTTACA
50 TTCTTTTTTATCAGATAAGTTACA
1 TTCTTTTTTATCAGATAAGTTACA
74 T
1 T
75 CAATAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 18 0.46
24 19 0.49
25 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
TTCTTTTTTATCAGATAAGTTACA
Found at i:8245 original size:6 final size:6
Alignment explanation
Indices: 8234--8262 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8224 TTGAACTAGG
8234 GCTCGA GCTCGA GCTCGA GCTCG- GCTCGA
1 GCTCGA GCTCGA GCTCGA GCTCGA GCTCGA
8263 AATTTCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.14, C:0.34, G:0.34, T:0.17
Consensus pattern (6 bp):
GCTCGA
Found at i:15493 original size:18 final size:17
Alignment explanation
Indices: 15463--15498 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
15453 GTCTCTACCC
15463 CCTTTTACTCTCTCCTT
1 CCTTTTACTCTCTCCTT
*
15480 CCTTTTATCTCTCTTCTT
1 CCTTTTA-CTCTCTCCTT
15498 C
1 C
15499 TCTCATCCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (17 bp):
CCTTTTACTCTCTCCTT
Found at i:31842 original size:32 final size:32
Alignment explanation
Indices: 31806--32087 Score: 356
Period size: 32 Copynumber: 8.8 Consensus size: 32
31796 TCTTGTTCTG
31806 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
* * *
31838 AAGACGCCGCTAAATAAGGGCATTTCGTTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
* * *
31870 AAGACGCCGCTAAATAATGGCG-TTTCGTTCTG
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTT-TT
* *
31902 AAGACGCCGCTAAATAAGGGCGTTTCGTTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
* *
31934 AAGACGCCGCTAAATAAGGGCGTTTCGTTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
* * *
31966 AAGACGCCGCTAAATAATGGCG-TTTCGTTCT
1 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
* *
31997 ATAGACGCCGCCAAATAAGGGCGTTTT-GTTCT
1 A-AGACGCCGCTAAATAAGGGCGTTTTGGTTTT
*
32029 ACAGACGCCGCTAAATAAGGGCGTTTT-GTTGT
1 A-AGACGCCGCTAAATAAGGGCGTTTTGGTTTT
32061 ATAGACGCCGCTAAATAAGGGCGTTTT
1 A-AGACGCCGCTAAATAAGGGCGTTTT
32088 CTTTTCACAC
Statistics
Matches: 221, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.05
32 204 0.92
33 7 0.03
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (32 bp):
AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
Found at i:31900 original size:96 final size:96
Alignment explanation
Indices: 31787--32086 Score: 455
Period size: 96 Copynumber: 3.1 Consensus size: 96
31777 GCAGTTAAAT
*
31787 ATAACGGCGTCTT-GTTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAA
1 ATAATGGCGT-TTCGTTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAA
*
31851 ATAAGGGCATTTCGTTTTTAAGACGCCGCTAA
65 ATAAGGGCGTTTCGTTTTTAAGACGCCGCTAA
* *
31883 ATAATGGCGTTTCGTTCTGAAGACGCCGCTAAATAAGGGCGTTTCGTTTTTAAGACGCCGCTAAA
1 ATAATGGCGTTTCGTTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAA
31948 TAAGGGCGTTTCGTTTTTAAGACGCCGCTAA
66 TAAGGGCGTTTCGTTTTTAAGACGCCGCTAA
* *
31979 ATAATGGCGTTTCGTTCT-ATAGACGCCGCCAAATAAGGGCGTTTT-GTTCTACAGACGCCGCTA
1 ATAATGGCGTTTCGTTCTGA-AGACGCCGCTAAATAAGGGCGTTTTGGTTTTA-AGACGCCGCTA
* *
32042 AATAAGGGCGTTTTG-TTGTATAGACGCCGCTAA
64 AATAAGGGCGTTTCGTTTTTA-AGACGCCGCTAA
*
32075 ATAAGGGCGTTT
1 ATAATGGCGTTT
32087 TCTTTTCACA
Statistics
Matches: 189, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
95 11 0.06
96 178 0.94
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (96 bp):
ATAATGGCGTTTCGTTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAA
TAAGGGCGTTTCGTTTTTAAGACGCCGCTAA
Found at i:34513 original size:27 final size:27
Alignment explanation
Indices: 34483--34599 Score: 180
Period size: 27 Copynumber: 4.3 Consensus size: 27
34473 AAGTAACTGT
*
34483 ATCCACTGCTGGGGTCGAAGTGTGAGG
1 ATCCACTGCTGGGGTCGAAGTGGGAGG
*
34510 ATCCACTGCTGGGATCGAAGTGGGAGG
1 ATCCACTGCTGGGGTCGAAGTGGGAGG
34537 ATCCACTGCTGGGGTCGAAGTGGGAGG
1 ATCCACTGCTGGGGTCGAAGTGGGAGG
* ** *
34564 ATCCACTACTGGGGTCGAAGCAGAAGG
1 ATCCACTGCTGGGGTCGAAGTGGGAGG
34591 ATCCACTGC
1 ATCCACTGC
34600 GGTAACAGTC
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (27 bp):
ATCCACTGCTGGGGTCGAAGTGGGAGG
Found at i:35208 original size:3 final size:3
Alignment explanation
Indices: 35200--35279 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
35190 AACTATATAT
35200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
35248 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
35280 GGCTAATGGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Done.