Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01543.F1
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: 3397
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:287 original size:101 final size:100
Alignment explanation
Indices: 142--740 Score: 564
Period size: 101 Copynumber: 6.1 Consensus size: 100
132 TAATTGCCTT
* ** * * *
142 CCAATTTGAATGCTTAAAGAAATGTATTCTTAATTTTGCATTCAATCTAATTTTGGTAGGACAGT
1 CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTT-GCAGGGCAGT
* *
207 TTGGCTGGGTAGTTTGGCATTACAGTCCATTTCGTC
65 TTGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
* * *
243 CCAATTTGAATGCTTACAGAAATGTCGTCTTAATTTTTCATTCAATCAAATTTT--A--GC-G--
1 CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTGCAGGGCAGTT
301 -GAG-T---T-GTTTGGCATGACAATCCATTTCGTC
66 TG-GCTGGGTAGTTTGGCATGACAATCCATTTCGTC
* * * * * **
331 CCAATTTAAATGCTAATAGAAATGTTCTCTTAATTTTGCATTTAAGCAAATATTTGCAGGGTGGT
1 CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAAT-TTTGCAGGGCAGT
* * * * * *
396 TTGGCAGAGTAGTTTGACATGACAATCTACTTCATC
65 TTGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
* *
432 CCAAATTGAATGCTTATAGTAATGTCCTCTTAATTTTGCATTCAATCAAATTTTGGCAGGGCAGT
1 CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTT-GCAGGGCAGT
* * * ** *
497 TTGGTTGTGTAGTTTGGCATGACAGTTTATTTTGTC
65 TTGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
* * * * * * * *
533 GCAATTTGAATCCTTATATAAATGTCATCTTATTTTTGCTTTCAATC-AATTTTGTCAGAGTAGT
1 CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTG-CAGGGCAGT
* * * * * *
597 TTAGCTGGGTAGTTTGGCTTGATAGTCCATTTTGTT
65 TTGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
*
633 CCAATTTGAATGCTTATA-AAATTGTCCTCTT-ATATTTGCATTCAACCAAATTTTGGCAGGGCA
1 CCAATTTGAATGCTTATAGAAA-TGTCCTCTTAAT-TTTGCATTCAATCAAATTTT-GCAGGGCA
* * *
696 GTTTGGCTGGTTAGTTTGGCATGATAATCGATTTCGTC
63 GTTTGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
734 CCAATTT
1 CCAATTT
741 AGCACTTACA
Statistics
Matches: 404, Mismatches: 73, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
88 66 0.16
89 4 0.01
91 1 0.00
92 2 0.00
93 2 0.00
94 1 0.00
95 1 0.00
96 2 0.00
97 1 0.00
98 1 0.00
99 5 0.01
100 80 0.20
101 237 0.59
102 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (100 bp):
CCAATTTGAATGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTGCAGGGCAGTT
TGGCTGGGTAGTTTGGCATGACAATCCATTTCGTC
Found at i:367 original size:88 final size:88
Alignment explanation
Indices: 218--381 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 88
208 TGGCTGGGTA
* * * * *
218 GTTTGGCATTACAGTCCATTTCGTCCCAATTTGAATGCTTACAGAAATGTCGTCTTAATTTTTCA
1 GTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATGTCGTCTTAATTTTGCA
*
283 TTCAATCAAATTTTAGCGGAGTT
66 TTCAAGCAAATTTTAGCGGAGTT
*
306 GTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAATAGAAATGTTC-TCTTAATTTTGC
1 GTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATG-TCGTCTTAATTTTGC
*
370 ATTTAAGCAAAT
65 ATTCAAGCAAAT
382 ATTTGCAGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 65 0.97
89 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (88 bp):
GTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATGTCGTCTTAATTTTGCA
TTCAAGCAAATTTTAGCGGAGTT
Found at i:398 original size:88 final size:87
Alignment explanation
Indices: 213--401 Score: 238
Period size: 88 Copynumber: 2.1 Consensus size: 87
203 CAGTTTGGCT
* * * *
213 GGGTAGTTTGGCATTACAGTCCATTTCGTCCCAATTTGAATGCTTACAGAAATGTCGTCTTAATT
1 GGGTAGTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATGTCGTCTTAATT
* *
278 TTTCATTCAATCAAATTTTAGC
66 TTGCATTCAAGCAAATTTTAGC
* *
300 GGAGTTGTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAATAGAAATGTTC-TCTTAA
1 GG-GTAGTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATG-TCGTCTTAA
*
364 TTTTGCATTTAAGCAAATATTT-GC
64 TTTTGCATTCAAGCAAAT-TTTAGC
*
388 AGGGTGGTTTGGCA
1 -GGGTAGTTTGGCA
402 GAGTAGTTTG
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
87 2 0.02
88 79 0.90
89 7 0.08
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (87 bp):
GGGTAGTTTGGCATGACAATCCATTTCGTCCCAATTTAAATGCTAACAGAAATGTCGTCTTAATT
TTGCATTCAAGCAAATTTTAGC
Found at i:443 original size:189 final size:188
Alignment explanation
Indices: 1--498 Score: 565
Period size: 189 Copynumber: 2.6 Consensus size: 188
* * * *
1 AAATTTTGGTAGGGCAATTTGGCTAGGTAGTTTGGCATGACAATCCATTTCATCTCAATTTGAAT
1 AAATTTTGGCAGGACAGTTTGGC-AGGTAGTTTGGCATGACAATCCATTTCATCCCAATTTGAAT
* *
66 GCTTATAGAAATTTCCTCTTAATTTTGCATTCAATC-AATTTTAGCAGGGTAGTTTAGCCTAACA
65 GCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTAGCAGGGTAGTTTAGCATAACA
* * * * *
130 GTTAATTGCCTTCCAATTTGAATGCTTAAAGAAATGTATTCTTAATTTTGCATTCAATC
130 ATCAATTGCCTCCCAATTTAAATGCTTAAAGAAATGTATTCTTAATTTTGCATTCAAGC
* * * * * *
189 TAATTTTGGTAGGACAGTTTGGCTGGGTAGTTTGGCATTACAGTCCATTTCGTCCCAATTTGAAT
1 AAATTTTGGCAGGACAGTTTGGC-AGGTAGTTTGGCATGACAATCCATTTCATCCCAATTTGAAT
* * * * * *
254 GCTTACAGAAATGTCGTCTTAATTTTTCATTCAATCAAATTTTAGC-GGAGTTGTTTGGCATGAC
65 GCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTAGCAGG-GTAGTTTAGCATAAC
* * * *
318 AATCCATTTCGTCCCAATTTAAATGC-TAATAGAAATGT-TCTCTTAATTTTGCATTTAAGC
129 AATCAATTGCCTCCCAATTTAAATGCTTAA-AGAAATGTAT-TCTTAATTTTGCATTCAAGC
*** * * * *
378 AAATATTT-GCAGGGTGGTTTGGCAGAGTAGTTTGACATGACAATCTACTTCATCCCAAATTGAA
1 AAAT-TTTGGCAGGACAGTTTGGCAG-GTAGTTTGGCATGACAATCCATTTCATCCCAATTTGAA
* * *
442 TGCTTATAGTAATGTCCTCTTAATTTTGCATTCAATCAAATTTTGGCAGGGCAGTTT
64 TGCTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTAGCAGGGTAGTTT
499 GGTTGTGTAG
Statistics
Matches: 258, Mismatches: 45, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
188 96 0.37
189 157 0.61
190 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (188 bp):
AAATTTTGGCAGGACAGTTTGGCAGGTAGTTTGGCATGACAATCCATTTCATCCCAATTTGAATG
CTTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTTAGCAGGGTAGTTTAGCATAACAA
TCAATTGCCTCCCAATTTAAATGCTTAAAGAAATGTATTCTTAATTTTGCATTCAAGC
Done.