Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00813.F4
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: 3352
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Found at i:2264 original size:117 final size:117
Alignment explanation
Indices: 2067--2532 Score: 505
Period size: 117 Copynumber: 4.0 Consensus size: 117
2057 CTTGTTCTCT
* * * ** *
2067 AATTTCATTTTCATCGGAACTA-AG--TCTATGCCTTCCACGATGCTCAAAGGGATCACTTACAG
1 AATTTCATTTCCATCGGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTACAG
* * * *
2129 A-TCTAGCTCCCAAGAAATGATGCCTGA-GAAGAGGCCAGCCGAAAGGTTCTTG
66 ATTC-AGCTCCCAAGAAATGACGCCTGAGGAA-AGGCCAACCTAAAGATTCTTG
* ** * *** * *
2181 ATTTTCATTTTGACCGGAACTATGGAAGCTACACCTTTGACGATGCTCAAGGGGATTACTTACAG
1 AATTTCATTTCCATCGGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTACAG
** *
2246 ATTCAGCTCCC-AGAAAATGACGCCTGAGGAAAGGCCGGCCTAAAGATTCTAG
66 ATTCAGCTCCCAAG-AAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTTG
* * * * * *
2298 AATTTCATTTCCATTGGAACCATAGCTTCTACGCCTTTGACGATGCTCAAGGTGATTACTTATAG
1 AATTTCATTTCCATCGGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTACAG
* * * *
2363 ATTCTGCTCCCAAGAAATAACGCCCGAGGAAAGGCCAACCTAAAGGTTCTTG
66 ATTCAGCTCCCAAGAAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTTG
* *
2415 AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTATAG
1 AATTTCATTTCCATCGGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTACAG
* * * *
2480 ATTC-GACTTCTAGGAAATGATGCCTGAGGAAAGGCCAACCTAAAGATTCTTG
66 ATTCAG-CTCCCAAGAAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTTG
2532 A
1 A
2533 TTATTAGAAC
Statistics
Matches: 295, Mismatches: 49, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
114 19 0.06
115 1 0.00
116 3 0.01
117 265 0.90
118 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (117 bp):
AATTTCATTTCCATCGGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTACAG
ATTCAGCTCCCAAGAAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTTG
Found at i:2512 original size:234 final size:234
Alignment explanation
Indices: 2103--2529 Score: 574
Period size: 234 Copynumber: 1.8 Consensus size: 234
2093 TATGCCTTCC
* * * *
2103 ACGATGCTCAAAGGGATCACTTACAGATCTAGCTCCCAAGAAATGATGCCTGAGAAGAGGCCAGC
1 ACGATGCTCAAAGGGATCACTTACAGATCTAGCTCCCAAGAAATAACGCCCGAGAAGAGGCCAAC
* ** *
2168 CGAAAGGTTCTTGATTTTCATTTTGACCGGAACTATGGAAGCTACACCTTTGACGATGCTCAAGG
66 CGAAAGGTTCTTGAATTTCATTTCCACCAGAACTATGGAAGCTACACCTTTGACGATGCTCAAGG
* **
2233 GGATTACTTACAGATTCAGCTCCCAGAAAATGACGCCTGAGGAAAGGCCGGCCTAAAGATTCTAG
131 GGATCACTTACAGATTCAGCTCCCAGAAAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTAG
2298 AATTTCATTTCCATTGGAACCATAGCTTCTACGCCTTTG
196 AATTTCATTTCCATTGGAACCATAGCTTCTACGCCTTTG
* *
2337 ACGATGCTC-AAGGTGATTACTTATAGATTCT-GCTCCCAAGAAATAACGCCCGAGGAA-AGGCC
1 ACGATGCTCAAAGG-GATCACTTACAGA-TCTAGCTCCCAAGAAATAACGCCCGA-GAAGAGGCC
* * *** *
2399 AACCTAAAGGTTCTTGAATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTTGACGATGCTCA
63 AACCGAAAGGTTCTTGAATTTCATTTCCACCAGAACTATGGAAGCTACACCTTTGACGATGCTCA
* * * * *
2464 AGGGGATCACTTATAGATTC-GACTTCTAGGAAATGATGCCTGAGGAAAGGCCAACCTAAAGATT
128 AGGGGATCACTTACAGATTCAG-CTCCCAGAAAATGACGCCTGAGGAAAGGCCAACCTAAAGATT
2528 CT
192 CT
2530 TGATTATTAG
Statistics
Matches: 165, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
233 5 0.03
234 154 0.93
235 6 0.04
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (234 bp):
ACGATGCTCAAAGGGATCACTTACAGATCTAGCTCCCAAGAAATAACGCCCGAGAAGAGGCCAAC
CGAAAGGTTCTTGAATTTCATTTCCACCAGAACTATGGAAGCTACACCTTTGACGATGCTCAAGG
GGATCACTTACAGATTCAGCTCCCAGAAAATGACGCCTGAGGAAAGGCCAACCTAAAGATTCTAG
AATTTCATTTCCATTGGAACCATAGCTTCTACGCCTTTG
Found at i:2680 original size:150 final size:150
Alignment explanation
Indices: 2415--2842 Score: 547
Period size: 150 Copynumber: 2.9 Consensus size: 150
2405 AAGGTTCTTG
* * * *
2415 AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTTGACGATGCTCAAGGGGATCACTTATAG
1 AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTCGACGATGCTCAAGGGGATTATTTACAG
* * * * *
2480 ATTCGACTTCTAGGAAATGATGCCTGAGGAAAGGCCAACCTAAAGATTCTTGATTATTAGAACGT
66 ATTCGGCTCCTAGTAAATGATGCCTGAGCAAAGGCCAACCTAAAGGTTCTTGATTATTAGAACGT
2545 TGTAC-GTGTTCTTGTTCTCT
131 TGTACAG-GTTCTTGTTCTCT
* ** * * *
2565 AATTTCACTTCCATGGGAACTATGGCTTCTACACCTTCGACGATGCTCCAGGGGATTATTTACAA
1 AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTCGACGATGCTCAAGGGGATTATTTACAG
* * * * *
2630 ATTCGGCTCCCAGTAAATGACT-TCTGAGCAACGGCCAACCTAAAGGTTCTTGATTATCAAAACG
66 ATTCGGCTCCTAGTAAATGA-TGCCTGAGCAAAGGCCAACCTAAAGGTTCTTGATTATTAGAACG
*
2694 TTGTGCAGGTTCTTGTTCTCT
130 TTGTACAGGTTCTTGTTCTCT
* * *
2715 AATTTCATTTCCATCAAAACTATGGCTTCTACGCCCTCGAAGA-GACTCAAGGGGATTATTTACA
1 AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTCGACGATG-CTCAAGGGGATTATTTACA
* * * * *
2779 GATTCGGGTCCTAGTAAACGATGCCCGAGCAAAGGCCAACCTATAGGTTCTTGATTATTGGAAC
65 GATTCGGCTCCTAGTAAATGATGCCTGAGCAAAGGCCAACCTAAAGGTTCTTGATTATTAGAAC
2843 AATCACGATT
Statistics
Matches: 234, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
149 2 0.01
150 230 0.98
151 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (150 bp):
AATTTCATTTCCATCAGAACTATGGCTTCTACGCCTTCGACGATGCTCAAGGGGATTATTTACAG
ATTCGGCTCCTAGTAAATGATGCCTGAGCAAAGGCCAACCTAAAGGTTCTTGATTATTAGAACGT
TGTACAGGTTCTTGTTCTCT
Done.