Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00814.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: 4098
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Found at i:2893 original size:150 final size:150
Alignment explanation
Indices: 2459--2886 Score: 547
Period size: 150 Copynumber: 2.9 Consensus size: 150
2449 AATCGTGATT
* * * * *
2459 GTTCCAATAATCAAGAACCTATAGGTTGGCCTTTGCTCGGGCATCGTTTACTAGGACCCGAATCT
1 GTTCTAATAATCAAGAACCTTTAGGTTGGCCTTTGCTCAGGCATCATTTACTAGGAGCCGAATCT
* * *
2524 GTAAATAATCCCCTTGAGTC-TCTTCGAGGGCGTAGAAGCCATAGTTTTGATGGAAATGAAATTA
66 GTAAATAATCCCCTTGAG-CATCGTCGAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATTA
2588 GAGAACAAGAACCTGCACAAC
130 GAGAACAAGAACCTGCACAAC
* * * * * *
2609 GTTTTGATAATCAAGAACCTTTAGGTTGGCCGTTGCTCA-GAAGTCATTTACTGGGAGCCGAATT
1 GTTCTAATAATCAAGAACCTTTAGGTTGGCCTTTGCTCAGGCA-TCATTTACTAGGAGCCGAATC
* * ** *
2673 TGTAAATAATCCCCTGGAGCATCGTCGAAGGTGTAGAAGCCATAGTTCCCATGGAAGTGAAATTA
65 TGTAAATAATCCCCTTGAGCATCGTCGAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATTA
*
2738 GAGAACAAGAACAC-GTACAAC
130 GAGAACAAGAAC-CTGCACAAC
* * * * *
2759 GTTCTAATAATCAAGAATCTTTAGGTTGGCCTTTCCTCAGGCATCATTTCCTAGAAGTCGAATCT
1 GTTCTAATAATCAAGAACCTTTAGGTTGGCCTTTGCTCAGGCATCATTTACTAGGAGCCGAATCT
* * * *
2824 ATAAGTGATCCCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATT
66 GTAAATAATCCCCTTGAGCATCGTCGAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATT
2887 CAAGAACCTT
Statistics
Matches: 234, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
149 3 0.01
150 228 0.97
151 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (150 bp):
GTTCTAATAATCAAGAACCTTTAGGTTGGCCTTTGCTCAGGCATCATTTACTAGGAGCCGAATCT
GTAAATAATCCCCTTGAGCATCGTCGAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATTAG
AGAACAAGAACCTGCACAAC
Found at i:2975 original size:117 final size:117
Alignment explanation
Indices: 2769--3234 Score: 505
Period size: 117 Copynumber: 4.0 Consensus size: 117
2759 GTTCTAATAA
* * * * * *
2769 TCAAGAATCTTTAGGTTGGCCTTTCCTCAGGCATCATTTCCTAGAAGTC-GAATCTATAAGTGAT
1 TCAAGAACCTTTAGGCTGGCCTTTCCTCAGGCATCATTTCTTGGGAG-CAGAATCTATAAGTAAT
*
2833 CCCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAAT
65 CCCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATGGAAATGAAAT
* * * *
2886 TCAAGAACCTTTAGGTTGGCCTTTCCTCGGGCGTTATTTCTTGGGAGCAGAATCTATAAGTAATC
1 TCAAGAACCTTTAGGCTGGCCTTTCCTCAGGCATCATTTCTTGGGAGCAGAATCTATAAGTAATC
* * * *
2951 ACCTTGAGCATCGTCAAAGGCGTAGAAGCTATGGTTCCAATGGAAATGAAAT
66 CCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATGGAAATGAAAT
* * * * * *
3003 TCTAGAATCTTTAGGCCGGCCTTTCCTCAGGCGTCATTT-TCTGGGAGCTGAATCTGTAAGTAAT
1 TCAAGAACCTTTAGGCTGGCCTTTCCTCAGGCATCATTTCT-TGGGAGCAGAATCTATAAGTAAT
* *** * ** *
3067 CCCCTTGAGCATCGTCAAAGGTGTAGCTTCCATAGTTCCGGTCAAAATGAAAA
65 CCCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATGGAAATGAAAT
* * *
3120 TCAAGAACCTTTCGGCTGGCCTCTT-CTCAGGCATCATTTCTTGGGAGCTAG-ATCTGTAAGTGA
1 TCAAGAACCTTTAGGCTGGCCT-TTCCTCAGGCATCATTTCTTGGGAGC-AGAATCTATAAGTAA
* ** * * *
3183 TCCCTTTGAGCATCGTGGAAGGCATAG-A--CTTAGTTCCGATGAAAATGAAAT
64 TCCCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATGGAAATGAAAT
3234 T
1 T
3235 AGAGAACAAG
Statistics
Matches: 294, Mismatches: 50, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
114 20 0.07
116 2 0.01
117 268 0.91
118 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (117 bp):
TCAAGAACCTTTAGGCTGGCCTTTCCTCAGGCATCATTTCTTGGGAGCAGAATCTATAAGTAATC
CCCTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATGGAAATGAAAT
Found at i:3194 original size:234 final size:234
Alignment explanation
Indices: 2772--3198 Score: 574
Period size: 234 Copynumber: 1.8 Consensus size: 234
2762 CTAATAATCA
** *
2772 AGAATCTTTAGGTTGGCCTTTCCTCAGGCATCATTTCCTAGAAGTCGAATCTATAAGTGATCCCC
1 AGAATCTTTAGGCCGGCCTTTCCTCAGGCATCATTTCCTAGAAGTCGAATCTATAAGTAATCCCC
* ** * *
2837 TTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCTGATGGAAATGAAATTCAAGAACCTTTAGGT
66 TTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATCAAAATGAAAATCAAGAACCTTTAGGC
* * *
2902 TGGCCTTTCCTCGGGCGTTATTTCTTGGGAGCAGAATCTATAAGTAATCACCTTGAGCATCGTCA
131 TGGCCTTTCCTCAGGCATCATTTCTTGGGAGCAGAATCTATAAGTAATCACCTTGAGCATCGTCA
2967 AAGGCGTAGAAGCTATGGTTCCAATGGAAATGAAATTCT
196 AAGGCGTAGAAGCTATGGTTCCAATGGAAATGAAATTCT
* * * * *
3006 AGAATCTTTAGGCCGGCCTTTCCTCAGGCGTCATTTTCTGGGAG-CTGAATCTGTAAGTAATCCC
1 AGAATCTTTAGGCCGGCCTTTCCTCAGGCATCATTTCCTAGAAGTC-GAATCTATAAGTAATCCC
* *** * *
3070 CTTGAGCATCGTCAAAGGTGTAGCTTCCATAGTTCCGGTCAAAATGAAAATCAAGAACCTTTCGG
65 CTTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATCAAAATGAAAATCAAGAACCTTTAGG
* *
3135 CTGGCCTCTT-CTCAGGCATCATTTCTTGGGAGCTAG-ATCTGTAAGTGATC-CCTTTGAGCATC
130 CTGGCCT-TTCCTCAGGCATCATTTCTTGGGAGC-AGAATCTATAAGTAATCACC-TTGAGCATC
3197 GT
192 GT
3199 GGAAGGCATA
Statistics
Matches: 165, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
233 3 0.02
234 158 0.96
235 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (234 bp):
AGAATCTTTAGGCCGGCCTTTCCTCAGGCATCATTTCCTAGAAGTCGAATCTATAAGTAATCCCC
TTGAGCATCGTCAAAGGCGTAGAAGCCATAGTTCCGATCAAAATGAAAATCAAGAACCTTTAGGC
TGGCCTTTCCTCAGGCATCATTTCTTGGGAGCAGAATCTATAAGTAATCACCTTGAGCATCGTCA
AAGGCGTAGAAGCTATGGTTCCAATGGAAATGAAATTCT
Done.