Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3721
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, 406
Length: 678
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:154 original size:88 final size:87
Alignment explanation
Indices: 1--678 Score: 715
Period size: 88 Copynumber: 7.8 Consensus size: 87
* * * **
1 TCAACCAGCTCCATCACAACCGAGGGAGGCAAAGTTTGTGTGTTCGATCTAATTCGCTG-CAAAT
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGT-CTCGACCTGCTTCGCTGTC-AAT
*
65 GCAGGAAGGCAAGATCT-TCTGTCC
64 GCAGGAAGGCAAGATCTGT-TGTCT
*
89 TCAACTAGCTCCATC-CTAACCGAGAGAGGCAAAGTTTGTGTCTCGGACCTGCTTCGCTGTCAAT
1 TCAACCAGCTCCATCAC-AACCGAGAGAGGCAAAGTTTGTGTCTC-GACCTGCTTCGCTGTCAAT
153 GCAGGAAGGCAAGATCTGTTGTCT
64 GCAGGAAGGCAAGATCTGTTGTCT
* * * *
177 TCAACAAGCTCAATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTC-TCGACCTGCTTCGCTGTCAATG
* *
242 TAGGATGGCAAGATCTGTTGTCT
65 CAGGAAGGCAAGATCTGTTGTCT
* * * *
265 TCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCACTGTCAACG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTC-TCGACCTGCTTCGCTGTCAATG
*
330 CAGGAAGGCAAAATCTGTTGTCT
65 CAGGAAGGCAAGATCTGTTGTCT
* * * *****
353 TAAACTAGCTCCATCACAACCGAGGGAGGC--AG---G-G-CT---TNNNNTTCGCTGTCAATGC
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTCTCGACCTGCTTCGCTGTCAATGC
408 AGGAAGGCAAGATCTTGCTT-TCT
66 AGGAAGGCAAGATC-TG-TTGTCT
* * * *
431 TC-ACCAGCTCTATCACAACCGAGAGAGGCGAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTC-TCGACCTGCTTCGCTGTCAATG
* *
495 CATGAAGGTAAGAT-TGGTTGTCT
65 CAGGAAGGCAAGATCT-GTTGTCT
* *
518 TCAACCAGCCCCATCACAACCGAGAGAGGCAACA-TTTGTGTCTTTGACCTGCTTCGCTGTCAAT
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAA-AGTTTGTGTC-TCGACCTGCTTCGCTGTCAAT
*
582 GCAGGAAGGCAAGATCGGTTGTCT
64 GCAGGAAGGCAAGATCTGTTGTCT
* * ** * * * * *
606 TCAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTTGTGTCTTCGATCTGATTCACTGTCGATG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTC-TCGACCTGCTTCGCTGTCAATG
671 CAGGAAGG
65 CAGGAAGG
Statistics
Matches: 500, Mismatches: 65, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
77 49 0.10
78 6 0.01
79 3 0.01
80 1 0.00
81 1 0.00
82 2 0.00
83 2 0.00
84 1 0.00
85 1 0.00
86 4 0.01
87 9 0.02
88 417 0.83
89 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (87 bp):
TCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTCTCGACCTGCTTCGCTGTCAATGC
AGGAAGGCAAGATCTGTTGTCT
Found at i:207 original size:44 final size:44
Alignment explanation
Indices: 159--383 Score: 129
Period size: 44 Copynumber: 5.1 Consensus size: 44
149 CAATGCAGGA
*
159 AGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCAATCACAACCGAGAG
* * ** * ** ** *
203 AGGCAAGGTTTG-TGTCTTTGACCTGCTTCGCTGTCAA-TGTAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGC-TCAATCACAACCG-AGAG
*
246 ATGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 A-GGCAAGATCTGTTGTCTTCAACCAGCTCAATCACAACCGAGAG
* * ** * * **
291 AGGCAAGGTTTG-TGTCTTTGACCTGCTTCACTGTCAA-CGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGC-TCAATCACAACCG-AGAG
* * * * *
334 AAGGCAAAATCTGTTGTCTTAAACTAGCTCCATCACAACCGAGGG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCAATCACAACCGAGAG
379 AGGCA
1 AGGCA
384 GGGCTTNNNN
Statistics
Matches: 128, Mismatches: 41, Indels: 24
0.66 0.21 0.12
Matches are distributed among these distances:
43 27 0.21
44 74 0.58
45 27 0.21
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCAATCACAACCGAGAG
Found at i:307 original size:176 final size:175
Alignment explanation
Indices: 1--678 Score: 805
Period size: 176 Copynumber: 3.9 Consensus size: 175
* * * * **
1 TCAACCAGCTCCATCACAACCGAGGGAGGCAAAGTTTGTGTGTTCGATCTAATTCGCTG-CAAAT
1 TCAACCAGCTCCATCACAACCGAGAGAGGC-AAGTTTGTGTCTTTGACCTGCTTCGCTGTC-AAT
* * *
65 GCAGGAAGGCAAGATCT-TCTGTCCTCAACTAGCTCCATC-CTAACCGAGAGAGGCAAAGTTTGT
64 GCAGGAAGGCAAGATCTGT-TGTCTTCAACCAGCTCCATCAC-AACCGAGAGAGGCAAGGTTTGT
*
128 GTC-TCGGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCT
127 GTCTTC-GACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCT
* *
177 TCAACAAGCTCAATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAA-GTTTGTGTCTTTGACCTGCTTCGCTGTCAATG
* *
242 TAGGATGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
65 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
* * *
307 TTTGACCTGCTTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCT
130 TTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCT
* * * ****
353 TAAACTAGCTCCATCACAACCGAGGGAGGC-AG---G-G-C-TT---NNNNTTCGCTGTCAATGC
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAAGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGC
* *
408 AGGAAGGCAAGATCTTGCTT-TCTTC-ACCAGCTCTATCACAACCGAGAGAGGCGAGGTTTGTGT
66 AGGAAGGCAAGATC-TG-TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGT
* *
471 CTTCGACCTGCTTCACTGTCAATGCATGAAGGTAAGAT-TGGTTGTCT
129 CTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT-GTTGTCT
* *
518 TCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCAATG
1 TCAACCAGCTCCATCACAACCGAGAGAGGCAA-GTTTGTGTCTTTGACCTGCTTCGCTGTCAATG
* * * * *
583 CAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTTGTGTC
65 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
* * *
648 TTCGATCTGATTCACTGTCGATGCAGGAAGG
130 TTCGACCTGCTTCACTGTCAATGCAGGAAGG
Statistics
Matches: 427, Mismatches: 54, Indels: 42
0.82 0.10 0.08
Matches are distributed among these distances:
164 1 0.00
165 128 0.30
166 8 0.02
167 2 0.00
168 2 0.00
169 1 0.00
170 2 0.00
171 2 0.00
172 1 0.00
173 2 0.00
174 3 0.01
175 9 0.02
176 262 0.61
177 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (175 bp):
TCAACCAGCTCCATCACAACCGAGAGAGGCAAGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGC
AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
TCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCT
Found at i:492 original size:253 final size:249
Alignment explanation
Indices: 141--642 Score: 749
Period size: 253 Copynumber: 2.0 Consensus size: 249
131 TCGGACCTGC
141 TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCGAGAGAGG
1 TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCGAGAGAGG
* * * *
206 CAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGTAGGATGGCAAGATCT-GTTGTCTTCAAC
66 CAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGAT-TGGTTGTCTTCAAC
* **
270 CAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCACTGTCAACGCAGGA
130 CAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCACTGTCAACGCAGGA
* * *
335 AGGCAAAATCTGTTGTCTTAAACTAGCTCCATCACAACCGAGGGAGGCAGGGCTT
195 AGGCAAAATCGGTTGTCTTAAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTT
* *
390 NNNNTTCGCTGTCAATGCAGGAAGGCAAGATCTTGCTT-TCTTC-ACCAGCTCTATCACAACCGA
1 ----TTCGCTGTCAATGCAGGAAGGCAAGATC-TG-TTGTCTTCAACAAGCTCAATCACAACCGA
* * *
453 GAGAGGCGAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCATGAAGGTAAGATTGGTTGTCT
60 GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATTGGTTGTCT
* *
518 TCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCAATG
125 TCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCACTGTCAACG
* *
583 CAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTT
190 CAGGAAGGCAAAATCGGTTGTCTTAAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTT
643 GTGTCTTCGA
Statistics
Matches: 227, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
252 1 0.00
253 217 0.96
254 7 0.03
255 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (249 bp):
TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCGAGAGAGG
CAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATTGGTTGTCTTCAACC
AGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCACTGTCAACGCAGGAA
GGCAAAATCGGTTGTCTTAAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTT
Found at i:517 original size:165 final size:161
Alignment explanation
Indices: 229--678 Score: 474
Period size: 165 Copynumber: 2.7 Consensus size: 161
219 TTTGACCTGC
* *
229 TTCGCTGTCAATGTAGGATGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
1 TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
* *
294 CAAGGTTTGTGTCTTTGACCTGCTTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACT
66 CAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACC
* *
359 AGCTCCATCACAACCGAGGGAGGCAGGGCTT
131 AGCCCCATCACAACCGAGAGAGGCAGGGCTT
*
390 NNNNTTCGCTGTCAATGCAGGAAGGCAAGATCTTGCTT-TCTTC-ACCAGCTCTATCACAACCGA
1 ----TTCGCTGTCAATGCAGGAAGGCAAGATC-TG-TTGTCTTCAACCAGCTCCATCACAACCGA
* * * * *
453 GAGAGGCGAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCATGAAGGTAAGAT-TGGTTGTC
60 GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAACGCAGGAAGGCAAAATCT-GTTGTC
* *
517 TTCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGC
124 TTAAACCAGCCCCATCACAACCGAGAGAGG---CA---G-G-----G--CT-T
* * *
570 TTCGCTGTCAATGCAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGGGAGG
1 TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
* * * * * *
635 CAGGGCTTGTGTCTTCGATCTGATTCACTGTCGATGCAGGAAGG
66 CAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAACGCAGGAAGG
Statistics
Matches: 240, Mismatches: 25, Indels: 29
0.82 0.09 0.10
Matches are distributed among these distances:
164 1 0.00
165 127 0.53
166 7 0.03
167 2 0.01
168 2 0.01
171 1 0.00
172 1 0.00
174 2 0.01
175 6 0.03
176 88 0.37
177 1 0.00
179 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (161 bp):
TTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
CAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACC
AGCCCCATCACAACCGAGAGAGGCAGGGCTT
Found at i:676 original size:341 final size:337
Alignment explanation
Indices: 53--678 Score: 902
Period size: 341 Copynumber: 1.8 Consensus size: 337
43 TTCGATCTAA
*
53 TTCGCTGCAAATGCAGGAAGGCAAGATCTTCTGTCCTCAACTAGCTCCATCCTAACCGAGAGAGG
1 TTCGCTGCAAATGCAGGAAGGCAAGATCTTCTGTCCTCAACCAGCTCCATCCTAACCGAGAGAGG
*
118 CAAAGTTTGTGTCTCGGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACA
66 CAAAGTTTGTGTCTCGGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACA
* ** * *
183 AGCTCAATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGTAGGAT
131 AGCCCAATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCAATGCAGGAA
* * * *
248 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGAC
196 GGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGAGAGGCAAGGCTTGTGTCTTCGAC
*
313 CTGCTTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACTAGCTCCATCACAACCGAGG
261 CTGATTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACTAGCTCCATCACAACCGAGG
378 GAGGCAGGGCTT
326 GAGGCAGGGCTT
* * *
390 NNNNTTCGCTGTC-AATGCAGGAAGGCAAGATCTTGCTTTCTTC-ACCAGCTCTATCAC-AACCG
1 ----TTCGCTG-CAAATGCAGGAAGGCAAGATCTT-CTGTCCTCAACCAGCTCCATC-CTAACCG
* * * *
452 AGAGAGGCGAGGTTTGTGTCTTC-GACCTGCTTCACTGTCAATGCATGAAGGTAAGAT-TGGTTG
59 AGAGAGGCAAAGTTTGTGTC-TCGGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT-GTTG
* *
515 TCTTCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCA
122 TCTTCAACAAGCCCAATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCA
* *
580 ATGCAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGGGAGGCAGGGCTTGT
187 ATGCAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGAGAGGCAAGGCTTGT
* * *
645 GTCTTCGATCTGATTCACTGTCGATGCAGGAAGG
252 GTCTTCGACCTGATTCACTGTCAACGCAGGAAGG
Statistics
Matches: 254, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
340 1 0.00
341 243 0.96
342 10 0.04
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (337 bp):
TTCGCTGCAAATGCAGGAAGGCAAGATCTTCTGTCCTCAACCAGCTCCATCCTAACCGAGAGAGG
CAAAGTTTGTGTCTCGGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACA
AGCCCAATCACAACCGAGAGAGGCAACATTTGTGTCTTTGACCTGCTTCGCTGTCAATGCAGGAA
GGCAAGATCGGTTGTCTTCAACCAGCTCCATCACAACCAAGAGAGGCAAGGCTTGTGTCTTCGAC
CTGATTCACTGTCAACGCAGGAAGGCAAAATCTGTTGTCTTAAACTAGCTCCATCACAACCGAGG
GAGGCAGGGCTT
Done.