Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01862.C1
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: 5329
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Found at i:546 original size:127 final size:127
Alignment explanation
Indices: 393--813 Score: 743
Period size: 127 Copynumber: 3.3 Consensus size: 127
383 GGTGGAAGTT
393 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* * *
458 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGACTGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* * *
520 AGAGAGAAACGCTGATTTTGTGTTTGTTGAATTATATTTGTTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
*
585 TTTCTAGTTCAATTTAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* *
647 AGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATTTGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* *
712 TTTCTAGTTCAGTTAAAACAGTCTTATTTTATTTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
774 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAG
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAG
814 ATGACTCCTA
Statistics
Matches: 281, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 281 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (127 bp):
AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
Found at i:1495 original size:369 final size:365
Alignment explanation
Indices: 812--2237 Score: 2156
Period size: 369 Copynumber: 3.9 Consensus size: 365
802 GAATTATATT
* *
812 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * * * *
877 CCCTTTCCCAAAATTGGTTCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCTATGCCGAT
* *
942 TTTAGTTTACAGGAGGAAGAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACT
131 TTTAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGTGCTAGCGCTGTTGTTGCCAACT
* * * * *
1007 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAAT
196 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTGTTAGTTCTGAT
*
1072 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGCAACAAA
261 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
*
1137 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC
326 GATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GC
*
1178 AGATGATTCCTAAATGTGATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCT
* *
1242 TCCCTTACCCAAAACTGGTTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGA
65 TCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCTATGCCGA
* * * *
1307 TTTCAGTTTACAGTAGGGGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCTCTGTTGTTGCC
130 TTTTAGTTTAC---AGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGTGCTAGCGCTGTTGTTGCC
* * *
1372 AACTTTTATGCACGGGAGCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTT
192 AACTTTTGTGCACAGGAGC-TGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTGTTAGTT
* *
1436 CTGATGCACTTTCGGAGGCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCA
256 CTGATGCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCA
1501 ACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGC
321 ACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGC
1546 AAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCT
1 -AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCT
* * *
1611 TCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTAAGTATGAGGTTTGAAAGTCCTATTCCGA
65 TCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCTATGCCGA
* * * * *
1676 TCTTAATTTACAGGATGAAGAAACGGTGGGGCAGAAGCAGCAGTGCTAACGCTGTTGTTGCCAAC
130 TTTTAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGTGCTAGCGCTGTTGTTGCCAAC
*
1741 TTTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGA
195 TTTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTGTTAGTTCTGA
* * *
1806 TGCGCTTTCAGAGGCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAA
260 TGCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAA
* * *
1871 AGATTTCTTTATGTGATTGGATATCTGATAATGAAACTTTCC
325 AGATTTCTTTATGTGATTGGATGTCTGGTAATGAAAC-TTGC
* * ** *
1913 GGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGTAAAGAGGCTGAGGATTCACGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * * *
1978 CCCTTACCCGAAACTGGTTCTCAGCGGTTATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGAT
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCTATGCCGAT
* * *
2043 TTTAGTTTACAGTAGGAGGAAAAAACGGTGGGGCAGCAGCAGCATTGCTAGCGCTGCTGTTGCCA
131 TTTAGTTTAC---AGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGTGCTAGCGCTGTTGTTGCCA
* * *
2108 ACTTTTGTGCACAGGAGCCGGTTAATTCAAAGAGAAGCACAGATTGTCTTTCTGTTGTTAGTTCT
193 ACTTTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTGTTAGTTCT
** * * *
2173 GATGTGCTTTCAGAGGCAGTTATGG-GACAAAAGGGAGTTCCTCGAGTTGAACATGAAATTGCAA
258 GATGCACTTTCAGAGGCAGTTATGGAG-CAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAA
2237 C
322 C
2238 TGTTAGAGCT
Statistics
Matches: 965, Mismatches: 82, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
365 4 0.00
366 455 0.47
367 3 0.00
368 3 0.00
369 496 0.51
370 4 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (365 bp):
AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCTATGCCGAT
TTTAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGTGCTAGCGCTGTTGTTGCCAACT
TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTGTTAGTTCTGAT
GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
GATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGC
Found at i:2223 original size:735 final size:735
Alignment explanation
Indices: 812--2237 Score: 2280
Period size: 735 Copynumber: 1.9 Consensus size: 735
802 GAATTATATT
* *
812 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * * *
877 CCCTTTCCCAAAATTGGTTCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
66 CCCTTACCCAAAACTGGTTCTCAACAGTCATCTGTAAGTATGAGGTTTGAAAGTCCAACGCCGAT
* * * * **
942 TTTAGTTTACAGGAGGAAGAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACT
131 CTTAATTTACAGGAGGAAGAAACGGTGGGGCAGAAGCAGCAGTGCTAACGCTGTTGTTGCCAACT
* * *
1007 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAAT
196 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTCTTAGTTCTAAT
*
1072 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGCAACAAA
261 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
* * * * *
1137 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGATTCCTAAATGTGATGGTA
326 GACTTCTTTATGTGATTGGATATCTGATAATGAAACTTGCCAGATGACTCCTAAATGTGATAGTA
* *
1202 CTTCACAAGCTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAG
391 CTTCACAACCTGGATGTAAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAG
* *
1267 CAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGGGGAAGAA
456 CAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGAGGAAAAA
* * * *
1332 ACGGTGGGGCAGCAGCAGCAGCGCTAGCTCTGTTGTTGCCAACTTTTATGCACGGGAGCATGTTA
521 ACGGTGGGGCAGCAGCAGCAGCGCTAGCGCTGCTGTTGCCAACTTTTATGCACAGGAGCAGGTTA
** * *
1397 ATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGTTATG
586 ATTCAAAGAGAAGCACAGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCAGAGGCAGTTATG
* *
1462 GAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATTGGAT
651 GAGCAAAAGGGAGTTCCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATTGGAT
1527 GTCTGGTAATGAAACTTGCA
716 GTCTGGTAATGAAACTTGCA
1547 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * **
1612 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTAAGTATGAGGTTTGAAAGTCCTATTCCGAT
66 CCCTTACCCAAAACTGGTTCTCAACAGTCATCTGTAAGTATGAGGTTTGAAAGTCCAACGCCGAT
*
1677 CTTAATTTACAGGATGAAGAAACGGTGGGGCAGAAGCAGCAGTGCTAACGCTGTTGTTGCCAACT
131 CTTAATTTACAGGAGGAAGAAACGGTGGGGCAGAAGCAGCAGTGCTAACGCTGTTGTTGCCAACT
*
1742 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTG-TCGTTAGTTCTGA
196 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTC-TTAGTTCTAA
* * *
1806 TGCGCTTTCAGAGGCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAA
260 TGCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAA
* * *
1871 AGATTTCTTTATGTGATTGGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGT
325 AGACTTCTTTATGTGATTGGATATCTGATAATGAAACTTGCCAGATGACTCCTAAATGTGATAGT
*
1936 ACTTCACAACCTGGATGTAAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCA
390 ACTTCACAACCTGGATGTAAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCA
* ** *
2001 GCGGTTATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTTAGTTTACAGTAGGAGGAAAA
455 GCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGAGGAAAA
** * *
2066 AACGGTGGGGCAGCAGCAGCATTGCTAGCGCTGCTGTTGCCAACTTTTGTGCACAGGAGCCGGTT
520 AACGGTGGGGCAGCAGCAGCAGCGCTAGCGCTGCTGTTGCCAACTTTTATGCACAGGAGCAGGTT
**
2131 AATTCAAAGAGAAGCACAGATTGTCTTTCTGTTGTTAGTTCTGATGTGCTTTCAGAGGCAGTTAT
585 AATTCAAAGAGAAGCACAGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCAGAGGCAGTTAT
* *
2196 GG-GACAAAAGGGAGTTCCTCGAGTTGAACATGAAATTGCAAC
650 GGAG-CAAAAGGGAGTTCCTCAAGTTGAACATGAAACTGCAAC
2238 TGTTAGAGCT
Statistics
Matches: 629, Mismatches: 60, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
734 3 0.00
735 626 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (735 bp):
AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
CCCTTACCCAAAACTGGTTCTCAACAGTCATCTGTAAGTATGAGGTTTGAAAGTCCAACGCCGAT
CTTAATTTACAGGAGGAAGAAACGGTGGGGCAGAAGCAGCAGTGCTAACGCTGTTGTTGCCAACT
TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTTCTTAGTTCTAAT
GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
GACTTCTTTATGTGATTGGATATCTGATAATGAAACTTGCCAGATGACTCCTAAATGTGATAGTA
CTTCACAACCTGGATGTAAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAG
CAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGAGGAAAAA
ACGGTGGGGCAGCAGCAGCAGCGCTAGCGCTGCTGTTGCCAACTTTTATGCACAGGAGCAGGTTA
ATTCAAAGAGAAGCACAGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCAGAGGCAGTTATG
GAGCAAAAGGGAGTTCCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATTGGAT
GTCTGGTAATGAAACTTGCA
Done.