Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold346
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: 475321
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:471637 original size:175 final size:175
Alignment explanation
Indices: 471319--472204 Score: 1157
Period size: 175 Copynumber: 5.0 Consensus size: 175
471309 TCTTCTAAGT
* * * ** **
471319 CCAATGTCGTTGGCCTTGAATCGGCGCATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
* * * *
471384 TGAATCAGTACATTGGGACAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT-T
66 TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCT
* *
471448 TCTAAGACCAATGTCGCTGGCCTTGAATCAACACATTAGCACAAGC
131 T-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
** * *
471494 CCAATATCGCAAGCCTTAAATCAACATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
* * * *
471559 TGAATCAGGACATTGGCATAAGCCCAATATCGCTGGCCTTGAATTAACATATTGGCACCTTATCT
66 TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCT
*
471624 TTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGA
131 TTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
471669 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTCTAAGACCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
* *
471733 TGAATCAGCACGTTGGCATAAGCCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTTGTC
66 TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTC
* *
471798 TTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGCCACAAGC
130 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
471844 CCAATATTGCTGGCCTTGAATTAGCATATTGGCACC-TTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
* * *
471908 TGAATCAGCACATTGGCAAAAGCCAAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTGTCT
66 TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCT
* * * *
471973 TTAAGACCAATGTCTCTAGCCTTCAATCAGCACATTGGCACAAGT
131 TTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * * * *
472018 CCAGTATGGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG---TCTTTAAGACCAATGTCGCTGG
* ** * *
472083 CCTTGAATCAGTACATTGGCAACTTTATTTTTAAATCCAATATTGTTGGCCTTGAATCAGCATAT
63 CCTTGAATCAGCACATTGG---C---A----TAAGCCCAATATCGCTGGCCTTGAATCAGCATAT
472148 TGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
118 TGGCACCTT-G---TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
472205 TCTTCAGCTT
Statistics
Matches: 624, Mismatches: 67, Indels: 23
0.87 0.09 0.03
Matches are distributed among these distances:
174 158 0.25
175 347 0.56
176 2 0.00
178 38 0.06
181 1 0.00
184 1 0.00
188 36 0.06
189 1 0.00
192 40 0.06
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (175 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCT
TTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:471823 original size:262 final size:263
Alignment explanation
Indices: 471346--472204 Score: 1211
Period size: 262 Copynumber: 3.2 Consensus size: 263
471336 GAATCGGCGC
* * *
471346 ATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGTACATTGGGACAAGCCTAA
1 ATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCAAA
*
471411 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTTTCTAAGACCAATGTCGCTGGCCTTGAAT
66 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAAT
* * ** * *
471476 CAACACATTAGCACAAGCCCAATATCGCAAGCCTTAAATCAACATATTGGCACCTTTGTCTTTAA
131 CAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAA
* * * *
471541 GACCAATGTCGCTGGCCTTGAATCAGGACATTGGCATAAGCCCAATATCGCTGGCCTTGAATTAA
196 GACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTGGCCTTGAATTAG
471606 CAT
261 CAT
471609 ATTGGCACCTT-ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGACC-A
1 ATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAG-CCAA
*
471672 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATATCGCTGGCCTTGAA
65 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
* * *
471737 TCAGCACGTTGGCATAAGCCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTTGTCTTTA
130 TCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTA
* *
471802 AGACCAATGTCACTGGCCTTGAATCAGCACATTGCCACAAGCCCAATATTGCTGGCCTTGAATTA
195 AGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTGGCCTTGAATTA
471867 GCAT
260 GCAT
* *
471871 ATTGGCACCTT-GTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAAAAGCCAAA
1 ATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCAAA
* * * * *
471935 TATCGCTGGCCTTGAATCAGTATATTGGCACCTTGTCTTTAAGACCAATGTCTCTAGCCTTCAAT
66 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAAT
* * * *
472000 CAGCACATTGGCACAAGTCCAGTATGGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
131 CAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG---TCTT
* * ** *
472065 TAAGTCCAATGTCACTGGCCTTGAATCAGTACATTGGCAACTTTATTTTTAAATCCAATATTGTT
193 TAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG---C---A----TAAGCCCAATATTGCT
*
472130 GGCCTTGAATCAGCAT
248 GGCCTTGAATTAGCAT
472146 ATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ATTGGCACC-T--TCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
472205 TCTTCAGCTT
Statistics
Matches: 534, Mismatches: 43, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
261 2 0.00
262 398 0.75
263 13 0.02
265 38 0.07
268 1 0.00
271 1 0.00
275 36 0.07
276 1 0.00
278 1 0.00
279 43 0.08
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (263 bp):
ATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCAAA
TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAAT
CAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAA
GACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTGGCCTTGAATTAG
CAT
Found at i:472092 original size:52 final size:51
Alignment explanation
Indices: 472014--472289 Score: 247
Period size: 52 Copynumber: 5.4 Consensus size: 51
472004 ACATTGGCAC
* * *
472014 AAGTCCAGTATGGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTT
* * * * * *
472066 AAGTCCAATGTCACTGGCCTTGAATCAGTACATTGGCAAC-TTT-ATTTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTT
* * * *
472115 AAATCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TTCATCTTT
* * * * *
472167 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--TCTTCAGCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTT
* * * * * *
472216 AAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCATCTTTAACAT-TCCT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCT-TT
* *
472268 AAGCCCAATGTCGCTGGCCTTG
1 AAGTCCAATATCGCTGGCCTTG
472290 TCTCAGCACA
Statistics
Matches: 175, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
49 76 0.43
50 3 0.02
51 6 0.03
52 90 0.51
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (51 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTT
Found at i:472203 original size:101 final size:101
Alignment explanation
Indices: 472028--472302 Score: 354
Period size: 101 Copynumber: 2.7 Consensus size: 101
472018 CCAGTATGGC
* * *
472028 TGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGGCCTTGAATCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
* * ** *
472093 GTACATTGGCAACTTTATTTTTAAATCCAATATTGT
66 GCACATTGGCAACTTCAGCTTTAAATCCAATATCGT
*
472129 TGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
* * *
472194 GCACATTGGCATCTTCAGCTTTAAGTCCGATATCGT
66 GCACATTGGCAACTTCAGCTTTAAATCCAATATCGT
* * ** * * **
472230 TGGCCTTGAATCAACATATTGGCATCTTTAACAT-TCCTAAGCCCAATGTCGCTGGCCTTGTCTC
1 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT-TTAAGACCAATGTCGCTGGCCTTGAATC
472294 AGCACATTG
65 AGCACATTG
472303 AATTCTTCTT
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 1 0.01
101 151 0.99
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (101 bp):
TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
GCACATTGGCAACTTCAGCTTTAAATCCAATATCGT
Found at i:474001 original size:9 final size:9
Alignment explanation
Indices: 473987--474017 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
473977 TTTTAGGATT
473987 ATTTTGATG
1 ATTTTGATG
473996 ATTTTGATG
1 ATTTTGATG
474005 ATTTTGATG
1 ATTTTGATG
474014 ATTT
1 ATTT
474018 GAAGTCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (9 bp):
ATTTTGATG
Done.