Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4879
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: 13047
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Found at i:3389 original size:15 final size:16
Alignment explanation
Indices: 3371--3401 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3361 GACATTCATG
3371 CATTCATTCA-TGCAT
1 CATTCATTCATTGCAT
3386 CATTCATTCATTGCAT
1 CATTCATTCATTGCAT
3402 ATCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
CATTCATTCATTGCAT
Found at i:11966 original size:141 final size:137
Alignment explanation
Indices: 11696--12716 Score: 1367
Period size: 141 Copynumber: 7.4 Consensus size: 137
11686 TAAGCCTTTT
* * *
11696 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGA-ATGAGTTGAGCCTCA-GACACGCTGAGG
** *
11761 TAATTTCAATTTCTTTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
63 T-ATTTCAATTTCTTTT--TCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
11826 GCTGAGGTAATTTC
125 GCTGAGGT-ATTTC
11840 AATTT-TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTGAGGT
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAG-AATGAGTTGAGCCTCAGACACGCTGAGGT
11904 AATTTCAATTTC-TTTTCAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
64 -ATTTCAATTTCTTTTTC-AAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
11968 CTGAGGTATTTC
126 CTGAGGTATTTC
* *
11980 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAG-GTGAGTTGAGCCTCAAGACACGTTGAGGT
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAATGAGTTGAGCCTC-AGACACGCTGAGGT
* *
12044 ATTTCAATTTCTGTTTCAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTCAAGACAC-TTG
64 ATTTCAATTTCTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTG
12106 AGGTATTTC
129 AGGTATTTC
*
12115 AATTT-TGTTTTCAAAATCAACTCATATT--GAGAATGAGTTGAGCCTCAGACACGTTGAGGTAT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAGACACGCTGAGGTAT
* *
12177 TTCAATTTCTTTATGTTTTCAAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAGGACAC
66 TTCAATTTC----T-TTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
12241 GCTGAGGTATTTC
125 GCTGAGGTATTTC
12254 AATTTCT-TTTTCAAAATCAACTCATATTGCGAG-ATGAGTTGAGCCTC-G-CACGCTGAGGTAT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAGACACGCTGAGGTA-
*
12315 TTTCAA-TTCTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC---ACACGTTGA
65 TTTCAATTTCTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
12376 GG-ATTTC
130 GGTATTTC
12383 AATTTTTTCTG-TTTCAAAATCAACTCATATTGCGAG--TGAGTTGAGCCTCAAGACA--C-GAG
1 AA---TTTCTGTTTTCAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTC-AGACACGCTGAG
12442 GTATTTCAATTTTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
62 GTATTTCAA--TTTCT-TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
*
12507 ACGTTGAGGTATTTC
123 ACGCTGAGGTATTTC
12522 AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAGACACGCTGAGGT
1 AATTTCTG-TTTTCAAAA-TCAACTCATATTGCGAGAATGAGTTGAGCCTCAGACACGCTGAGGT
12587 ATTTCAATTTCTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACG
64 ATTTCAATTTC-T-TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
12651 CTGAGGTAATTTC
126 CTGAGGT-ATTTC
*
12664 AATTTCTG-TTTCAAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAG
1 AATTTCTGTTTTC--AAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTCAG
12717 TTCACATGTT
Statistics
Matches: 808, Mismatches: 19, Indels: 102
0.87 0.02 0.11
Matches are distributed among these distances:
129 7 0.01
130 16 0.02
131 47 0.06
132 65 0.08
133 36 0.04
134 23 0.03
135 50 0.06
136 31 0.04
137 21 0.03
138 69 0.09
139 96 0.12
140 55 0.07
141 130 0.16
142 112 0.14
143 44 0.05
144 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (137 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAGACACGCTGAGGTAT
TTCAATTTCTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
GTATTTC
Found at i:12006 original size:71 final size:70
Alignment explanation
Indices: 11696--12715 Score: 1339
Period size: 71 Copynumber: 14.7 Consensus size: 70
11686 TAAGCCTTTT
* * ** *
11696 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
11761 TAATTTC
65 T-ATTTC
** *
11768 AATTTCT-TTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTT--TCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
11832 GTAATTTC
64 GT-ATTTC
11840 AATTT-TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCTGAGG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
11903 TAATTTC
65 T-ATTTC
11910 AATTTC--TTTTCAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
1 AATTTCTGTTTTC-AAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
11973 GTATTTC
64 GTATTTC
* *
11980 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAG--GTGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
12043 TATTTC
65 TATTTC
*
12049 AATTTCTG-TTTCAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTCAAGACAC-TTGAGGT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
12110 ATTTC
66 ATTTC
*
12115 AATTT-TGTTTTCAAAATCAACTCATATT--GAG-AATGAGTTGAGCCTC-AGACACGTTGAGGT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
12175 ATTTC
66 ATTTC
* *
12180 AATTTCTTTATGTTTTCAAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAGGACACGCT
1 AATTTC----TGTTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCT
12244 GAGGTATTTC
61 GAGGTATTTC
12254 AATTTCT-TTTTCAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTC--G-CACGCTGAGGT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
12313 ATTTTC
66 A-TTTC
*
12319 AA-TTCT-TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC---ACACGTTGAGG-
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
12378 ATTTC
66 ATTTC
12383 AATTTTTTCTG-TTTCAAAATCAACTCATATTGCGAG---TGAGTTGAGCCTCAAGACA--C-GA
1 AA---TTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
12441 GGTATTTC
63 GGTATTTC
*
12449 AATTTTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
1 AA--TTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
12514 GGTATTTC
63 GGTATTTC
12522 AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTC-AGACACGCTGAG
1 AATTTCTG-TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
12585 GTATTTC
64 GTATTTC
12592 AATTTCTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCTGAG
1 AATTTC-TGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
12656 GTAATTTC
64 GT-ATTTC
12664 AATTTCTG-TTTCAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 AATTTCTGTTTTC--AAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
12716 GTTCACATGT
Statistics
Matches: 878, Mismatches: 20, Indels: 100
0.88 0.02 0.10
Matches are distributed among these distances:
64 57 0.06
65 66 0.08
66 75 0.09
67 67 0.08
68 61 0.07
69 50 0.06
70 165 0.19
71 169 0.19
72 116 0.13
73 29 0.03
74 23 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (70 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
ATTTC
Done.