Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g02538.F3
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: 3928
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:40 original size:7 final size:7
Alignment explanation
Indices: 30--59 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20 AGAAAAAAAG
30 GAAAACA
1 GAAAACA
37 GAAAACA
1 GAAAACA
44 GAAAACA
1 GAAAACA
51 GAAAACA
1 GAAAACA
58 GA
1 GA
60 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAACA
Found at i:205 original size:14 final size:14
Alignment explanation
Indices: 168--195 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
158 CCCATTATTT
168 CTTTCATTTTTTCC
1 CTTTCATTTTTTCC
182 CTTTCATTTTTTCC
1 CTTTCATTTTTTCC
196 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
CTTTCATTTTTTCC
Found at i:2473 original size:132 final size:132
Alignment explanation
Indices: 2231--3001 Score: 675
Period size: 120 Copynumber: 6.0 Consensus size: 132
2221 AACATGCTGT
** **
2231 CACTGCCA-ATGGGCTTCAGTCTCAAGTGTTGAGCAATGCAAGTGGAACTGTGGCTCCGGCAAAA
1 CACTG-CAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAA
* * * *
2295 AGCAGCCCAGCGTGGGATGAAGCCTGGGGCTCTGCCCACAGAGGAGCTGCCAATGCCACTGCCAC
65 AGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTGCCAC
2360 TAC
130 TAC
* ** * * *
2363 CACTGCAGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAGCCGTGGCTCTGGCAAAAA
1 CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAAA
* * * *
2428 GCAGCCCAGCATGGGACGAAGAGTGGGGCTCTGCCAAC-----AG-TG--GA-G---CTGCCACT
66 GCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTGCCACT
2481 AC
131 AC
* * * *
2483 CACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAGCTGTGGCTCCT-GCAAAA
1 CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCT-CTAGCAAAA
* * * ** * * *
2547 AGCAACCCAGAATGGGATGAAGAGTGGGGCTCTACCTCCAGCA-GAACTTCCAATGCCACTACCA
65 AGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCAACAG-AGGAGCTGCCAATGCCACTGCCA
2611 CTAC
129 CTAC
* * * *
2615 CGCCGCAGATGGGCTTCAGTCTCAAGCCTTGAGCTATACAAGTGGAACTGTGGCTCTAGCAAAAA
1 CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAAA
* * * ** *
2680 GCGGCCCAGCAT-GGATGAAAACTGGGGCTCTACCACCTGCAGAGCTGCTAATGCCAATGCCAAT
66 GCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCA---ACAGAGGAGC---TGCCAATGCCACT
*
2744 GTCACTAC
125 GCCACTAC
* * * * * * **
2752 CACTGGAGATGGGCTTCGGTCTCAAGCCTTCAGCAATGTAAGTGGAACTGTGGCACCAGCGGAAA
1 CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAAA
* * *
2817 GCAGCTCATCATGGGATGAAGACAGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTG-----
66 GCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTGCCACT
2877 --
131 AC
* * *
2877 CA--G--G-TGGGGTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGCGGCTCCAGCAAAAA
1 CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAAA
* * ** * * *
2937 GCTGCTCTCCATGGGGTGAAGAC-GGAGACTCTACCAACCA-AGGAGCTGCCACTGCCACTGCCA
66 GCAGCCCAGCATGGGATGAAGACTGG-GGCTCTACCAA-CAGAGGAGCTGCCAATGCCACTGCCA
3000 CT
129 CT
3002 GCCCACCAGC
Statistics
Matches: 525, Mismatches: 84, Indels: 67
0.78 0.12 0.10
Matches are distributed among these distances:
119 2 0.00
120 197 0.38
121 5 0.01
123 2 0.00
124 1 0.00
125 3 0.01
126 3 0.01
127 2 0.00
128 1 0.00
129 1 0.00
131 24 0.05
132 172 0.33
133 1 0.00
134 4 0.01
135 7 0.01
137 79 0.15
138 21 0.04
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (132 bp):
CACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTAGCAAAAA
GCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTGCCACT
AC
Found at i:2602 original size:252 final size:251
Alignment explanation
Indices: 2231--2710 Score: 667
Period size: 252 Copynumber: 1.9 Consensus size: 251
2221 AACATGCTGT
* * ** *
2231 CACTGCCAATGGGCTTCAGTCTCAAGTGTTGAGCAATGCAAGTGGAACTGTGGCTCCGGCAAAAA
1 CACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCCGGCAAAAA
* ** * * * *
2296 GCAGCCCAGCGTGGGATGAAGCCTGGGGCTCTGCCCACAGAGGAGCTGCCAATGCCACTGCCACT
66 GCAACCCAGAATGGGATGAAGACTGGGGCTCTACCCACAGAGGAACTGCCAATGCCACTACCACT
* * *
2361 ACCACTGCAGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAGCCGTGGCTCTGGCAAA
131 ACCACCGCAGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAACCGTGGCTCTAGCAAA
* *
2426 AAGCAGCCCAGCATGGGACGAAGAGTGGGGCTCTGCCAACAGTGGAGCTGCCACTAC
196 AAGCAGCCCAGCAT-GGACGAAAACTGGGGCTCTGCCAACAGTGGAGCTGCCACTAC
* *
2483 CACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAGCTGTGGCTCCTGCAAAAA
1 CACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCCGGCAAAAA
* *
2548 GCAACCCAGAATGGGATGAAGAGTGGGGCTCTACCTC-CAGCA-GAACTTCCAATGCCACTACCA
66 GCAACCCAGAATGGGATGAAGACTGGGGCTCTACC-CACAG-AGGAACTGCCAATGCCACTACCA
* * * * *
2611 CTACCGCCGCAGATGGGCTTCAGTCTCAAGCCTTGAGCTATACAAGTGGAACTGTGGCTCTAGCA
129 CTACCACCGCAGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAACCGTGGCTCTAGCA
* *
2676 AAAAGCGGCCCAGCATGGATGAAAACTGGGGCTCT
194 AAAAGCAGCCCAGCATGGACGAAAACTGGGGCTCT
2711 ACCACCTGCA
Statistics
Matches: 198, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
251 16 0.08
252 180 0.91
253 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (251 bp):
CACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCCGGCAAAAA
GCAACCCAGAATGGGATGAAGACTGGGGCTCTACCCACAGAGGAACTGCCAATGCCACTACCACT
ACCACCGCAGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAACCGTGGCTCTAGCAAA
AAGCAGCCCAGCATGGACGAAAACTGGGGCTCTGCCAACAGTGGAGCTGCCACTAC
Found at i:2780 original size:137 final size:132
Alignment explanation
Indices: 2476--2938 Score: 423
Period size: 137 Copynumber: 3.6 Consensus size: 132
2466 AGTGGAGCTG
* * * *
2476 CCACTACCACTGCAAATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAGCTGTGGCTCCT
1 CCACTACCACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCT-CT
* * * *
2541 -GCAAAAAGCAACCCAGAATGGGATGAAGAGTGGGGCTCTACCTCCAGCAGAACTTCCAATGCCA
65 AGCAAAAAGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCACCAGCAGAACTTCCAATGCCA
*
2605 CTA
130 ATA
* * * *
2608 CCACTACCGCCGCAGATGGGCTTCAGTCTCAAGCCTTGAGCTATACAAGTGGAACTGTGGCTCTA
1 CCACTACCACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTA
* * * *
2673 GCAAAAAGCGGCCCAGCAT-GGATGAAAACTGGGGCTCTACCACCTGCAGAGCTGCTAATGCCAA
66 GCAAAAAGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCACCAGCAGA---ACT--T-CCAA
*
2737 TGCCAATG
125 TGCCAATA
* * * * * * *
2745 TCACTACCACTGGAGATGGGCTTCGGTCTCAAGCCTTCAGCAATGTAAGTGGAACTGTGGCACCA
1 CCACTACCACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTA
** * * * * * *
2810 GCGGAAAGCAGCTCATCATGGGATGAAGACAGGGGCTCTACCAACAG-AGGA---GC--TGCC--
66 GCAAAAAGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCACCAGCAGAACTTCCAATGCCAA
2867 -A
131 TA
* * * * *
2868 --A-TGCCACTGCAGGTGGGGTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGCGGCTCCA
1 CCACTACCACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTA
2930 GCAAAAAGC
66 GCAAAAAGC
2939 TGCTCTCCAT
Statistics
Matches: 270, Mismatches: 53, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
120 59 0.22
121 1 0.00
126 4 0.01
128 1 0.00
131 29 0.11
132 70 0.26
134 2 0.01
136 1 0.00
137 80 0.30
138 23 0.09
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (132 bp):
CCACTACCACTGCAGATGGGCTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGTGGCTCTA
GCAAAAAGCAGCCCAGCATGGGATGAAGACTGGGGCTCTACCACCAGCAGAACTTCCAATGCCAA
TA
Found at i:2971 original size:389 final size:384
Alignment explanation
Indices: 2239--2938 Score: 898
Period size: 389 Copynumber: 1.8 Consensus size: 384
2229 GTCACTGCCA
** * *
2239 ATGGGCTTCAGTCTCAAGTGTTGAGCAATGCAAGTGGAACTGTGGCTCCGGCAAAAAGCAGCCCA
1 ATGGGCTTCAGTCTCAAGCCTTGAGCAATACAAGTGGAACTGTGGCTCCAGCAAAAAGCAGCCCA
* ** * * *
2304 GCGTGGGATGAAGCCTGGGGCTCTGCCCACAGAGGAGCTGCCAATGCCACTGCCACTACCACTGC
66 GCATGGGATGAAAACTGGGGCTCTCCCCACAGAGCAGCTGCCAATGCCAATGCCACTACCACTGC
* * * **
2369 AGATGGGATTCAGTCTCAAGCCTTGAGCAACACAAGTGGAGCCGTGGCTCTGGCAAAAAGCAGCC
131 AGATGGGATTCAGTCTCAAGCCTTCAGCAACACAAGTGGAACCGTGGCACCAGCAAAAAGCAGCC
** * * *
2434 CAGCATGGGACGAAGAGTGGGGCTCTGCCAACAGTGGAGCTGCCACTACCACTGCAAATGGGATT
196 CAGCATGGGACGAAGACAGGGGCTCTACCAACAGAGGAGCTGCCAATACCACTGCAAATGGGATT
* * * *
2499 CAGTCTCAAGCCTTGAGCAACGCAAGTGGAGCTGTGGCTCCTGCAAAAAGCAACCCAGAATGGGA
261 CAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGCGGCTCCAGCAAAAAGCAACCCACAATGGGA
* *
2564 TGAAGAGTGGGGCTCTACCTCCAGCAGAACTTCCAATGCCACTACCACTACCGCCGCAG
326 TGAAGAGTGAGACTCTACCTCCAGCAGAACTTCCAATGCCACTACCACTACCGCCGCAG
* * *
2623 ATGGGCTTCAGTCTCAAGCCTTGAGCTATACAAGTGGAACTGTGGCTCTAGCAAAAAGCGGCCCA
1 ATGGGCTTCAGTCTCAAGCCTTGAGCAATACAAGTGGAACTGTGGCTCCAGCAAAAAGCAGCCCA
* * *
2688 GCAT-GGATGAAAACTGGGGCTCTACCACCTGCAGAGCTGCTAATGCCAATGCCAATGTCACTAC
66 GCATGGGATGAAAACTGGGGCTCT-CC-CC-ACAGAGCAGC---TGCCAATGCCAATGCCACTAC
* * * *** * **
2752 CACTGGAGATGGGCTTCGGTCTCAAGCCTTCAGCAATGTAAGTGGAACTGTGGCACCAGCGGAAA
125 CACTGCAGATGGGATTCAGTCTCAAGCCTTCAGCAACACAAGTGGAACCGTGGCACCAGCAAAAA
* * * * **
2817 GCAGCTCATCATGGGATGAAGACAGGGGCTCTACCAACAGAGGAGCTGCCAATGCCACTGCAGGT
190 GCAGCCCAGCATGGGACGAAGACAGGGGCTCTACCAACAGAGGAGCTGCCAATACCACTGCAAAT
* *
2882 GGGGTTCAGTCTCAAGCCTTGAGCAATGCAAGTGGAACTGCGGCTCCAGCAAAAAGC
255 GGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGCGGCTCCAGCAAAAAGC
2939 TGCTCTCCAT
Statistics
Matches: 264, Mismatches: 46, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
383 17 0.06
384 62 0.23
385 2 0.01
386 7 0.03
389 176 0.67
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (384 bp):
ATGGGCTTCAGTCTCAAGCCTTGAGCAATACAAGTGGAACTGTGGCTCCAGCAAAAAGCAGCCCA
GCATGGGATGAAAACTGGGGCTCTCCCCACAGAGCAGCTGCCAATGCCAATGCCACTACCACTGC
AGATGGGATTCAGTCTCAAGCCTTCAGCAACACAAGTGGAACCGTGGCACCAGCAAAAAGCAGCC
CAGCATGGGACGAAGACAGGGGCTCTACCAACAGAGGAGCTGCCAATACCACTGCAAATGGGATT
CAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGCGGCTCCAGCAAAAAGCAACCCACAATGGGA
TGAAGAGTGAGACTCTACCTCCAGCAGAACTTCCAATGCCACTACCACTACCGCCGCAG
Done.