Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00766.F2
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: 4406
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:1084 original size:15 final size:16
Alignment explanation
Indices: 1051--1085 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1041 AAACAAGTGC
*
1051 TTATCCAGTTTGACAT
1 TTATCCAGATTGACAT
1067 TTATCCAGATTG-CAT
1 TTATCCAGATTGACAT
1082 TTAT
1 TTAT
1086 GAAGTGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (16 bp):
TTATCCAGATTGACAT
Found at i:2289 original size:213 final size:213
Alignment explanation
Indices: 1922--2674 Score: 1454
Period size: 213 Copynumber: 3.5 Consensus size: 213
1912 AGGGAAAACA
*
1922 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGA
1 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
1987 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
66 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
2052 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
131 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
2117 GGGAGATTTGATCTTAAC
196 GGGAGATTTGATCTTAAC
2135 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
1 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
*
2200 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATC
66 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
2265 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
131 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
*
2330 GAGAGATTTGATCTTGAA-
196 GGGAGATTTGATCTT-AAC
*
2348 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGA
1 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
2413 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
66 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
2478 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
131 TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
2543 GGGAGATTTGATCTTAAC
196 GGGAGATTTGATCTTAAC
2561 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
1 GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
2626 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTT
66 TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTT
2675 TTTAAATTGA
Statistics
Matches: 531, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
212 2 0.00
213 527 0.99
214 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (213 bp):
GGTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGA
TTTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATC
TGAGATTGAACAACTGTAAAAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTT
GGGAGATTTGATCTTAAC
Found at i:2978 original size:354 final size:359
Alignment explanation
Indices: 2302--3028 Score: 1198
Period size: 354 Copynumber: 2.0 Consensus size: 359
2292 TTTCCCTTCC
* *
2302 TGACAACCTTTATAAATTGAAATCTCTTGAGAGATTTGATCTTGAAGGTTGCTCGAGATTGGAGA
1 TGACAATCTTTATAAATTGAAATCTCTTGAGAGATTTAATCTTGAAGGTTGCTCGAGATTGGAGA
* *
2367 TTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCTTTG
66 TTTTTCCAG-AA---TAGAGACCATAGAGAGGTTGAGCTTTCTTGATTTAAGCGGAACGGCTTTG
2432 AAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATCTGAGATTGAACAACTGTAA
127 AAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATCTGAGATTGAACAACTGTAA
* *
2497 AAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTTGGGAGATTTGATCTTAACG
192 AAACCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTTAGGAGATTTAATCTTAACG
*
2562 GTTGCTCGAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGAT
257 GTTGCTCAAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGAT
2627 TTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAAT
322 TTAAGCGGAACGGCTTTGAAGGAATTACCATCCTCAAT
* * * *
2665 TGACAATCTTTTTAAATTGAAATCTCTTGAGCGTTTTAATCTTAGCAGG-TGCTCGAGATTGGAG
1 TGACAATCTTTATAAATTGAAATCTCTTGAGAGATTTAATCTT-GAAGGTTGCTCGAGATTGGAG
2729 ATTTTTCC-G-A-AG-G-CCATAGAGAGGTTGAGCTTTCTTGATTTAAGCGGAACGGCTTTGAAG
65 ATTTTTCCAGAATAGAGACCATAGAGAGGTTGAGCTTTCTTGATTTAAGCGGAACGGCTTTGAAG
* *
2789 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTGTGAAAA
130 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATCTGAGATTGAACAACTGTAAAAA
* * *
2854 CCTTGTTTGCTTTCCTGACAACCTTTATAAATTGAAATCTCTTAGGATATTTAATCTTGAA-GGT
195 CCTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTTAGGAGATTTAATCTT-AACGGT
*
2918 TGCTCAAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTT
259 TGCTCAAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGATTT
2983 AAGCGGAACGGCTTTGAAGGAATTACCATCCTCAAT
324 AAGCGGAACGGCTTTGAAGGAATTACCATCCTCAAT
3019 TGACAATCTT
1 TGACAATCTT
3029 ATTGGTCTTG
Statistics
Matches: 345, Mismatches: 17, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
354 273 0.79
355 3 0.01
356 2 0.01
360 1 0.00
362 1 0.00
363 61 0.18
364 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (359 bp):
TGACAATCTTTATAAATTGAAATCTCTTGAGAGATTTAATCTTGAAGGTTGCTCGAGATTGGAGA
TTTTTCCAGAATAGAGACCATAGAGAGGTTGAGCTTTCTTGATTTAAGCGGAACGGCTTTGAAGG
AATTACCATCCTCAATTGACAATCTTATTGGTCTTGATGATCTGAGATTGAACAACTGTAAAAAC
CTTGTTTCCCTTCCTGACAACCTTTATAAATTGAAATCTCTTAGGAGATTTAATCTTAACGGTTG
CTCAAGATTGGAGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGCTTTCTTGATTTAA
GCGGAACGGCTTTGAAGGAATTACCATCCTCAAT
Found at i:3035 original size:213 final size:214
Alignment explanation
Indices: 2665--3250 Score: 912
Period size: 213 Copynumber: 2.8 Consensus size: 214
2655 CATCCTCAAT
* * * * *
2665 TGACAATCTTTTTAAATTGAAATCTCTT-GAGCGT-TTTAATCTTAGCAGG-TGCTCGAGATTGG
1 TGACAACCTTTATAAATTGAAATCTCTTAGAG-ATATTTAATCTT-GAAGGTTGCTCAAGATTGG
* *
2727 AGATTTTTCC-G--A----AG-G-CCATAGAGAGGTTGAGCTTTCTTGATTTAAGCGGAACGGCT
64 AGATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCT
2783 TTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTG
129 TTGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTG
*
2848 TGAAAACCTTGTTTGCTTTCC
194 TGAAAACCTTGTTTGCCTTCC
2869 TGACAACCTTTATAAATTGAAATCTCTTAG-GATATTTAATCTTGAAGGTTGCTCAAGATTGGAG
1 TGACAACCTTTATAAATTGAAATCTCTTAGAGATATTTAATCTTGAAGGTTGCTCAAGATTGGAG
2933 ATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCTTT
66 ATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCTTT
2998 GAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTGTG
131 GAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTGTG
3063 AAAACCTTGTTTGCCTTCC
196 AAAACCTTGTTTGCCTTCC
* * *
3082 TGACAACCTTTATAAATTGAAATCTCTT-GAGAGATTTGATCTTAAAGGTTGCTCAAGATTGGAG
1 TGACAACCTTTATAAATTGAAATCTCTTAGAGATATTTAATCTTGAAGGTTGCTCAAGATTGGAG
* *** *
3146 ATTTTTCCAGAAATCTTAGAGACCATGGAGATGTTGAGGGAGCTTGATTTAAGCGGAACAGCTTT
66 ATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCTTT
3211 GAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTT
131 GAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTT
3251 CGAAGCTTGA
Statistics
Matches: 353, Mismatches: 16, Indels: 17
0.91 0.04 0.04
Matches are distributed among these distances:
203 5 0.01
204 58 0.16
205 2 0.01
207 1 0.00
211 2 0.01
212 2 0.01
213 283 0.80
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (214 bp):
TGACAACCTTTATAAATTGAAATCTCTTAGAGATATTTAATCTTGAAGGTTGCTCAAGATTGGAG
ATTTTTCCAGAAATCTTAGAGACCATGGAGAGGTTGAGGTTTCTTGATTTAAGCGGAACGGCTTT
GAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGATTATCTGAGATTGAACAACTGTG
AAAACCTTGTTTGCCTTCC
Done.