Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold43
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 889
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.22
Found at i:210 original size:39 final size:39
Alignment explanation
Indices: 163--267 Score: 167
Period size: 39 Copynumber: 2.7 Consensus size: 39
153 GAGTCGTAGG
163 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGT
* * *
202 GCCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTAGTAGGCGTAGTCTGAGT
241 ACCAGTGGTGTGCAGCGACGTAGTAGG
1 ACCAGTGGTGTGCAGCGACGTAGTAGG
268 ACCAGTAGAC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 1 0.02
39 57 0.97
40 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.41, T:0.22
Consensus pattern (39 bp):
ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGT
Left flanking sequence: Indices 1 -- 162
AGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCC
ACGTGGTGATAGTCACTGTTATACACGACAGGGGCGGAGGTGTGGAGGTGGTGGAAGACTCTGAT
GTAGGACCGGTGGACGTAGTCAGAGTCGTAGG
Right flanking sequence: Indices 268 -- 767
ACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGG
TACCGGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGGTCAGCGACGTCGTA
GGCGTAGTCTGGGTACCGGTAGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTGGTGTG
CAGCGACGTAGTAGGACCTGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGTCGGCGACGTCG
TAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGTG
TGCAGCGAAGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTGGTCAGCGACGT
GGTAGGCGTAGTCTGGGTACCGGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGG
TGTGCAGCGACGTGGTTGGCGTAGTCTGAGTACCAGTGGTGTGCA
Found at i:300 original size:132 final size:126
Alignment explanation
Indices: 145--889 Score: 511
Period size: 132 Copynumber: 5.9 Consensus size: 126
135 GACCGGTGGA
*
145 CGTAGTCAGAGTCGTAGGACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTGCCAGTGG
1 CGTAGTC-GAGTCGT-GGACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGG
* *
210 TG-GTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGT
64 TGTG-CAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAGTAGG--C-GT
274 AG
125 AG
* * * *
276 ACGTAGTCAGAGTCGTAGGACCAGTGGTAGT-CGGCGACGTCGTAGGCGTAGTCTGGGTACCGGT
1 -CGTAGTC-GAGTCGT-GGACCAGTGGT-GTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGT
* * *
340 GGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTG-GTCAGCGACGTCGTAGGCGTA
62 GGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTGGTGTG-CAGCGACGTAGTAGGCGTA
404 -
126 G
* * * * *
404 -GT-CT-G-G--GT--ACCGGTAGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTGGTG
1 CGTAGTCGAGTCGTGGACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGGTG
* * ** * *
461 TGCAGCGACGTAGTAGGACCTGTAGAC-GTAGTCAGCGACGTGG-GACCAGTG--GTAGTCGGCG
66 TGCAGCGACGTAGTAGG--C-GTAGTCTG-AGT-A-CCA-GTGGTGTGCAGCGACGTAGTAGGCG
522 -ACG
124 TA-G
* *
525 TCGTAGGCGTAGTC-TGGGTACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGT
1 -CGTAGTCG-AGTCGT-GG-ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGT
* * * * * *
589 GGTGTGCAGCGAAGTAGTAGGACCAGTAGAC-GTAGT-CAGAGTCGTAG-GACCAGTG--GTGGT
62 GGTGTGCAGCGACGTAGTAGG--C-GTAGTCTG-AGTAC-CAGTGGT-GTG--CAGCGACGTAGT
649 CAGCGACGT-G
119 -AG-G-CGTAG
* * *
659 -GTAGGCGTAGTC-TGGGTACCGGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTG
1 CGTAGTCG-AGTCGT-GG-ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTG
* *
722 GTGTGCAGCGACGTGGTTGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTA-
63 GTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTAG
* * *
785 -GT-CT-G-G--GT-G-CCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGT
1 CGTAGTCGAGTCGTGGACCAGTGGTGTG-CAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGGT
* * * *
841 G-GTCAGCGACGTCGTAGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGAC
65 GTG-CAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGAC
Statistics
Matches: 514, Mismatches: 55, Indels: 103
0.76 0.08 0.15
Matches are distributed among these distances:
116 4 0.01
117 139 0.27
119 4 0.01
120 17 0.03
121 2 0.00
122 9 0.02
123 7 0.01
124 1 0.00
125 2 0.00
126 7 0.01
127 6 0.01
128 4 0.01
129 25 0.05
130 6 0.01
131 2 0.00
132 271 0.53
133 4 0.01
134 2 0.00
135 2 0.00
ACGTcount: A:0.18, C:0.19, G:0.41, T:0.22
Consensus pattern (126 bp):
CGTAGTCGAGTCGTGGACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGGTG
TGCAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTAG
Left flanking sequence: Indices 1 -- 144
AGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCC
ACGTGGTGATAGTCACTGTTATACACGACAGGGGCGGAGGTGTGGAGGTGGTGGAAGACTCTGAT
GTAGGACCGGTGGA
Right flanking sequence: None
Found at i:317 original size:27 final size:26
Alignment explanation
Indices: 241--321 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
231 TAGTCTGGGT
*
241 ACCAGTGGT-GTGCAGCGACGTAGTAGG
1 ACCAGTGGTAGT-C-GCGACGTCGTAGG
*
268 ACCAGTAGACGTAGTC-AGA-GTCGTAGG
1 ACCAGT-G--GTAGTCGCGACGTCGTAGG
295 ACCAGTGGTAGTCGGCGACGTCGTAGG
1 ACCAGTGGTAGTC-GCGACGTCGTAGG
322 CGTAGTCTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
24 6 0.14
26 3 0.07
27 27 0.61
28 3 0.07
30 3 0.07
31 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.38, T:0.19
Consensus pattern (26 bp):
ACCAGTGGTAGTCGCGACGTCGTAGG
Left flanking sequence: Indices 1 -- 240
AGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCC
ACGTGGTGATAGTCACTGTTATACACGACAGGGGCGGAGGTGTGGAGGTGGTGGAAGACTCTGAT
GTAGGACCGGTGGACGTAGTCAGAGTCGTAGGACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGT
CTGAGTGCCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGGT
Right flanking sequence: Indices 322 -- 821
CGTAGTCTGGGTACCGGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGGTCA
GCGACGTCGTAGGCGTAGTCTGGGTACCGGTAGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTG
CCAGTGGTGTGCAGCGACGTAGTAGGACCTGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGT
CGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAG
TGCCAGTGGTGTGCAGCGAAGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTG
GTCAGCGACGTGGTAGGCGTAGTCTGGGTACCGGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTG
AGTGCCAGTGGTGTGCAGCGACGTGGTTGGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAG
TAGGCGTAGTCTGGGTGCCAGTGGTGGTCAGCGACGTCGTAGGCG
Found at i:342 original size:39 final size:39
Alignment explanation
Indices: 295--609 Score: 296
Period size: 39 Copynumber: 7.7 Consensus size: 39
285 GAGTCGTAGG
*
295 ACCAGTGGTAGT-CGGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGT-GTGCAGCGACGTCGTAGGCGTAGTCTGGGT
* *
334 ACCGGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
373 ACCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTCGTAGGCGTAGTCTGGGT
* * *
412 ACCGGTAGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
* * *
451 GCCAGTGGTGTGCAGCGACGTAGTAGGACCTGTAGACGTAGTCAGCG-
1 ACCAGTGGTGTGCAGCGACGTCGTAGG--C-GTAGTC-T-G---G-GT
*
498 ACGTGGGACCAGTGGTAGT-CGGCGACGTCGTAGGCGTAGTCTGGGT
1 AC-------CAGTGGT-GTGCAGCGACGTCGTAGGCGTAGTCTGGGT
* *
544 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
* * *
583 GCCAGTGGTGTGCAGCGAAGTAGTAGG
1 ACCAGTGGTGTGCAGCGACGTCGTAGG
610 ACCAGTAGAC
Statistics
Matches: 231, Mismatches: 23, Indels: 44
0.78 0.08 0.15
Matches are distributed among these distances:
38 5 0.02
39 180 0.78
40 1 0.00
41 1 0.00
42 5 0.02
43 1 0.00
44 1 0.00
45 1 0.00
46 3 0.01
47 2 0.01
48 1 0.00
49 1 0.00
50 1 0.00
51 5 0.02
52 1 0.00
54 20 0.09
55 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.22
Consensus pattern (39 bp):
ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
Left flanking sequence: Indices 1 -- 294
AGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCC
ACGTGGTGATAGTCACTGTTATACACGACAGGGGCGGAGGTGTGGAGGTGGTGGAAGACTCTGAT
GTAGGACCGGTGGACGTAGTCAGAGTCGTAGGACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGT
CTGAGTGCCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACG
TAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGG
Right flanking sequence: Indices 610 -- 889
ACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGG
TACCGGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTGGTT
GGCGTAGTCTGAGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGGGTGCCAGTGGTGGT
CAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGG
TGCCAGTAGTGTGCAGCGAC
Found at i:525 original size:210 final size:210
Alignment explanation
Indices: 163--889 Score: 844
Period size: 210 Copynumber: 3.5 Consensus size: 210
153 GAGTCGTAGG
* *
163 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTGCCAGTGGTGGTCAGCGACGTCGTAG
1 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTAGTGGTCAGCGACGTCGTAG
*
228 GCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTA
66 GCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGACGTA
*
293 GGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGGTACCGGTGGTGTGCAGCGACGTGGT
131 GGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGT
*
358 AGGCGTAGTCTGGGT
196 AGGCGTAGTCTGAGT
* * * *
373 ACCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGTACCGGTAGT-GTGCAGCGACGTGGT
1 ACCAGTGGTGTG-CAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTAGTGGT-CAGCGACGTCGT
* * *
436 AGGCGTAGTCTGGGTGCCAGTGGTGTGCAGCGACGTAGTAGGACCTGTAGACGTAGTCAGCGACG
64 AGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGACG
*
501 TGGGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTG
129 TAGGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTG
566 GTAGGCGTAGTCTGAGT
194 GTAGGCGTAGTCTGAGT
* * * *
583 GCCAGTGGTGTGCAGCGAAGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTGG
1 ACCAGTGGTGTGCAGCGACGTAGT------AG--G-CGTAGTC----T-G-AGTACCAGTAGTGG
* * * *
648 TCAGCGACGTGGTAGGCGTAGTCTGGGTACCGGTAGTGTGCAGCGAC---GT-----C-GTAGGC
51 TCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGAC
* * * * *
704 GTAGTC--TGA-GT--G-CCAGTGGT-GTGCAGCGACGTGGTTGGCGTAGTCTGAGTACCAGTGG
116 GTAGTCAGAGACGTAGGACCAGTGGTAGT-CGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGG
* *
762 TGTGCAGCGACGTAGTAGGCGTAGTCTGGGT
180 TGTGCAGCGACGTGGTAGGCGTAGTCTGAGT
* * * *
793 GCCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGGTCAGCGACGTCGTA
1 ACCAGTGGTGTG-CAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTAGTGGTCAGCGACGTCGTA
* *
857 GGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGAC
65 GGCGTAGTCTGGGTACCAGTGGTGTGCAGCGAC
Statistics
Matches: 458, Mismatches: 38, Indels: 57
0.83 0.07 0.10
Matches are distributed among these distances:
195 56 0.12
196 1 0.00
197 1 0.00
201 7 0.02
202 1 0.00
204 2 0.00
209 6 0.01
210 299 0.65
211 2 0.00
213 2 0.00
214 2 0.00
216 13 0.03
217 1 0.00
218 1 0.00
219 7 0.02
222 2 0.00
223 1 0.00
224 1 0.00
225 51 0.11
226 2 0.00
ACGTcount: A:0.18, C:0.19, G:0.41, T:0.22
Consensus pattern (210 bp):
ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTACCAGTAGTGGTCAGCGACGTCGTAG
GCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGACGTA
GGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGT
AGGCGTAGTCTGAGT
Left flanking sequence: Indices 1 -- 162
AGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCC
ACGTGGTGATAGTCACTGTTATACACGACAGGGGCGGAGGTGTGGAGGTGGTGGAAGACTCTGAT
GTAGGACCGGTGGACGTAGTCAGAGTCGTAGG
Right flanking sequence: None
Found at i:692 original size:39 final size:39
Alignment explanation
Indices: 637--889 Score: 350
Period size: 39 Copynumber: 6.5 Consensus size: 39
627 GAGTCGTAGG
*
637 ACCAGTGGTG-GTCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTCGTAGGCGTAGTCTGGGT
* * *
676 ACCGGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
* * * *
715 GCCAGTGGTGTGCAGCGACGTGGTTGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
*
754 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
*
793 GCCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTCGTAGGCGTAGTCTGGGT
832 ACCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTCGTAGGCGTAGTCTGGGT
* *
871 GCCAGTAGTGTGCAGCGAC
1 ACCAGTGGTGTGCAGCGAC
Statistics
Matches: 193, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 190 0.98
40 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.23
Consensus pattern (39 bp):
ACCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
Left flanking sequence: Indices 137 -- 636
CCGGTGGACGTAGTCAGAGTCGTAGGACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGT
GCCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAG
GACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTAGTCGGCGACGTCGTAGGCGTAGTCTGG
GTACCGGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGGTCAGCGACGTCGT
AGGCGTAGTCTGGGTACCGGTAGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTGGTGT
GCAGCGACGTAGTAGGACCTGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGTCGGCGACGTC
GTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGT
GTGCAGCGAAGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGG
Right flanking sequence: None
Done.