Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01532.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: 2972
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Found at i:1996 original size:369 final size:364
Alignment explanation
Indices: 991--2173 Score: 1130
Period size: 369 Copynumber: 3.2 Consensus size: 364
981 CGATAAAAAT
* * * * * * * * * **
991 AAGCTTGTCGTTGACACAACATACAATGAGGTCATCAATGGC-GACGTATTAGTAGCTGAACCTG
1 AAGCTTGTCATTGACACAGCTTATAATGAAGTCACCAATGGCAG-CGTATCAATAGCGGAAATTG
* * * * * * *
1055 AGGATATCGAAGCAAAGCTCCCCAAAGAATCCTTTAATGTTGGGC---ATGAT---GGAAAGTTT
65 AGCAAAACGAAGCAAAGCT-CCCAGAGAATCCTTCAATGTTGGGCAGGATGATAAGGGAAACTTC
* * * * *
1114 GTCATTTACTCGACTTATAATGAAGTCATTAATGACGGTGTATCAGTAGTGGAAACTAAGCAAAA
129 GACA-TTA-ACGACTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAACTGAGCAAAA
* * * * ** *
1179 CGAAGCAAAGCTCTCCAGAGAATACTTTAATGTTGGGCATGATGATGATGGAAAGTTTGACATTG
192 CGAAGCGAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATAACAGAAAGTTTGTCATTG
* * * * *
1244 ACATAGCTTATAATGA-AGTCATCAATGGCTG-CATATCAGTAGCGGAAACTGAGCAAAATGAAG
257 ACACA-CTTACAATGAGA-TCATCAATGGC-GACATATTAGTAGCTGAAACTGAGCATAATGAAG
* * * * *
1307 CAAAGCTCCCCAGAGAATCCTTCAATGTTGGGCAGGATGATGATGGA
319 TAAAGCTCCCCACAGAATCCTT-AATGTTGGGCATGATGATAATGAA
* * * * ** * * * *
1354 AAGTTTGACATTAACGCAGCTTATAATGAAGTCATGAATGACGGCGTATCAATAGTGGAAATGGA
1 AAGCTTGTCATTGACACAGCTTATAATGAAGTCACCAATGGCAGCGTATCAATAGCGGAAATTGA
* * * * * *
1419 GCAAAACGTAGCGAAGCTCCCAGAGAATCCTTCAATGTTGGGCAGGATGATGATGGAAAGTTTGA
66 GCAAAACGAAGCAAAGCTCCCAGAGAATCCTTCAATGTTGGGCAGGATGATAAGGGAAACTTCGA
* *
1484 CATTAACGCAGCTTATAATGAAGTCATGAATGACGGCGTATCAATAGTGGAAA-TGGAGCAAAAC
131 CATTAACG-A-CTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAACT-GAGCAAAAC
* * * * *
1548 GTAGCGAAGCTCCCCAGAGAATCCCTTAATGTTGGGCATGACGATAACAAAAAGTTTGTCACTGA
193 GAAGCGAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATAACAGAAAGTTTGTCATTGA
* *
1613 CACGACTTACAATGAGATCATCAATGGCGACGTATTAGTAGCTGAAGCTGAGCATAATGAAGTAA
258 CAC-ACTTACAATGAGATCATCAATGGCGACATATTAGTAGCTGAAACTGAGCATAATGAAGTAA
* *
1678 AGCTCCCCACAGAATCCCTTAATGTTCGGCATGATGATAATCAA
322 AGCTCCCCACAGAAT-CCTTAATGTTGGGCATGATGATAATGAA
* * * * * * *
1722 AAACTTGTCTTTGACACAACTTACAATGATGTCACCAATGGCAGCCTATCAGTAGCGGAAATTGA
1 AAGCTTGTCATTGACACAGCTTATAATGAAGTCACCAATGGCAGCGTATCAATAGCGGAAATTGA
* * * * *
1787 GAAAAAAGAAGCAAAGCTCGCCAGTA-AATCTCTT-AATGTTGGGTATGATGATAAGGGGAACTT
66 GCAAAACGAAGCAAAGCTC-CCAG-AGAATC-CTTCAATGTTGGGCAGGATGATAAGGGAAACTT
* * * * *
1850 CGTCATTGATACGACTTGTAATGAAGTCATCAATGATGGCATATCAGTAGCGGAAACTGAGCAAA
128 CGACATT-A-ACGACTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAACTGAGCAAA
* * * * * * * *
1915 ACAAAGTGAAGCTCCCCACAGAATCCTTTAATATTGAGCATGATGGTAACAGAAAGCTTGTCGTT
191 ACGAAGCGAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATAACAGAAAGTTTGTCATT
* * * * *
1980 TACACACCTTACAATGAGGTCATCAATGGCGACATATTAATAGTTGAAACTGAGCATAACGAAGT
256 GACACA-CTTACAATGAGATCATCAATGGCGACATATTAGTAGCTGAAACTGAGCATAATGAAGT
** * * *
2045 AAAGCTCCCCGTAGAATTCTTTAATATTGGGCATGATGACAATGAA
320 AAAGCTCCCCACAGAA-TCCTTAATGTTGGGCATGATGATAATGAA
* * * * *
2091 AAGCTTGTCAATGACACAGCTTATAATGAGGTCACTAATGGCCGCGTATCAATAGCGGAAACTGA
1 AAGCTTGTCATTGACACAGCTTATAATGAAGTCACCAATGGCAGCGTATCAATAGCGGAAATTGA
*
2156 GCAAAACGAAGTAAAGCT
66 GCAAAACGAAGCAAAGCT
2174 TCCTACAAAC
Statistics
Matches: 665, Mismatches: 133, Indels: 38
0.80 0.16 0.05
Matches are distributed among these distances:
362 23 0.03
363 58 0.09
364 1 0.00
365 5 0.01
366 2 0.00
367 6 0.01
368 260 0.39
369 299 0.45
370 8 0.01
371 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (364 bp):
AAGCTTGTCATTGACACAGCTTATAATGAAGTCACCAATGGCAGCGTATCAATAGCGGAAATTGA
GCAAAACGAAGCAAAGCTCCCAGAGAATCCTTCAATGTTGGGCAGGATGATAAGGGAAACTTCGA
CATTAACGACTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAACTGAGCAAAACGAA
GCGAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATAACAGAAAGTTTGTCATTGACAC
ACTTACAATGAGATCATCAATGGCGACATATTAGTAGCTGAAACTGAGCATAATGAAGTAAAGCT
CCCCACAGAATCCTTAATGTTGGGCATGATGATAATGAA
Found at i:2202 original size:123 final size:122
Alignment explanation
Indices: 677--2173 Score: 1009
Period size: 123 Copynumber: 12.3 Consensus size: 122
667 GGCAATGTGC
* * * * ** * *
677 CAGTAGCTGAAACTGAGCATAACGAAGCAAAGCTCCCCACAGAATCCCCTAACATTAGGCATGAC
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAAT-CCTTAATGTTGGGCATGAT
** * * * * * * * **
742 GATAACAAAAAGCTTGTCGTTGACACAACTTACAAT-CAG--GTCAACGGTGATGTAT
65 GATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* ** * * * * * *
797 CAGTAGCGCG-AACTGACCGGAACAAAGCAAAAC-CCTCCACAGAATCGATTAATGTTAGGCACG
1 CAGTAGCG-GAAACTGAGCAAAACGAAGCAAAGCTCC-CCAGAGAATC-CTTAATGTTGGGCATG
** * * * * *
860 ATGATAACAAAAAGCTTGTCATCGGA-AAAGTTTATAA-CAAG--GTCAATGGCGGCGTAT
63 ATGATAATGAAAAGCTTGTCAT-TGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * ** * * * * * *
917 CAATAGCGGAAACTAAGCCGAACGAAGTAAAGC-CCTCCATAAAATCCCTTGATGTTGGACATTA
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCC-CCAGAGAAT-CCTTAATGTTGGGCATGA
* * * * * * * *
981 CGATAA-AAATAAGCTTGTCGTTGACACAACATACAATGAGGTCATCAATGGCGACGTAT
64 TGATAATGAA-AAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * * * * * *
1040 TAGTAGCTGAACCTGAGGATATCGAAGCAAAGCTCCCCAAAGAATCCTTTAATGTTGGGCATGAT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAATCC-TTAATGTTGGGCATGAT
* * * * * *
1105 G-----G-AAAGTTTGTCATTTACTC-GACTTATAATGAAGTCATTAATGACGGTGTAT
65 GATAATGAAAAGCTTGTCATTGACACAG-CTTATAATGAAGTCATCAATGGCGGCGTAT
* * * *
1157 CAGTAGTGGAAACTAAGCAAAACGAAGCAAAGCTCTCCAGAGAATACTTTAATGTTGGGCATGAT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAAT-CCTTAATGTTGGGCATGAT
* * * * * * *
1222 GATGATGGAAAGTTTGACATTGACATAGCTTATAATGAAGTCATCAATGGCTGCATAT
65 GATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* *
1280 CAGTAGCGGAAACTGAGCAAAATGAAGCAAAGCTCCCCAGAGAATCCTTCAATGTTGGGCAGGAT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAATCCTT-AATGTTGGGCATGAT
* * * * * * * *
1345 GATGATGGAAAGTTTGACATTAACGCAGCTTATAATGAAGTCATGAATGACGGCGTAT
65 GATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * * * *
1403 CAATAGTGGAAA-TGGAGCAAAACGTAGCGAAGCT-CCCAGAGAATCCTTCAATGTTGGGCAGGA
1 CAGTAGCGGAAACT-GAGCAAAACGAAGCAAAGCTCCCCAGAGAATCCTT-AATGTTGGGCATGA
* * * * * * * *
1466 TGATGATGGAAAGTTTGACATTAACGCAGCTTATAATGAAGTCATGAATGACGGCGTAT
64 TGATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * * *
1525 CAATAGTGGAAA-TGGAGCAAAACGTAGCGAAGCTCCCCAGAGAATCCCTTAATGTTGGGCATGA
1 CAGTAGCGGAAACT-GAGCAAAACGAAGCAAAGCTCCCCAGAGAAT-CCTTAATGTTGGGCATGA
* ** * * * *
1589 CGATAACAAAAAGTTTGTCACTGACAC-GACTTACAATG-AGATCATCAATGGCGACGTAT
64 TGATAATGAAAAGCTTGTCATTGACACAG-CTTATAATGAAG-TCATCAATGGCGGCGTAT
* * * * * * * *
1648 TAGTAGCTGAAGCTGAGCATAATGAAGTAAAGCTCCCCACAGAATCCCTTAATGTTCGGCATGAT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAAT-CCTTAATGTTGGGCATGAT
* * * * * * * * *
1713 GATAATCAAAAACTTGTCTTTGACACAACTTACAATGATGTCACCAATGGCAGCCTAT
65 GATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * * * *
1771 CAGTAGCGGAAATTGAGAAAAAAGAAGCAAAGCTCGCCAGTA-AATCTCTTAATGTTGGGTATGA
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAG-AGAATC-CTTAATGTTGGGCATGA
* ** * * ** *
1835 TGATAAGGGGAA-CTTCGTCATTGATAC-GACTTGTAATGAAGTCATCAATGATGGCATAT
64 TGATAATGAAAAGCTT-GTCATTGACACAG-CTTATAATGAAGTCATCAATGGCGGCGTAT
* ** * * *
1894 CAGTAGCGGAAACTGAGCAAAACAAAGTGAAGCTCCCCACAGAATCCTTTAATATTGAGCATGAT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAATCC-TTAATGTTGGGCATGAT
* * * * * * * * *
1959 GGTAA-CAGAAAGCTTGTCGTTTACACACCTTACAATGAGGTCATCAATGGCGACATAT
65 GATAATGA-AAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
* * ** * * * *
2017 TAATAGTTGAAACTGAGCATAACGAAGTAAAGCTCCCC-GTAGAATTCTTTAATATTGGGCATGA
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAG-AGAA-TCCTTAATGTTGGGCATGA
* * * *
2081 TGACAATGAAAAGCTTGTCAATGACACAGCTTATAATGAGGTCA-CTAATGGCCGCGTAT
64 TGATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATC-AATGGCGGCGTAT
* *
2140 CAATAGCGGAAACTGAGCAAAACGAAGTAAAGCT
1 CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCT
2174 TCCTACAAAC
Statistics
Matches: 1099, Mismatches: 233, Indels: 87
0.77 0.16 0.06
Matches are distributed among these distances:
117 89 0.08
118 2 0.00
119 9 0.01
120 152 0.14
121 6 0.01
122 139 0.13
123 686 0.62
124 16 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (122 bp):
CAGTAGCGGAAACTGAGCAAAACGAAGCAAAGCTCCCCAGAGAATCCTTAATGTTGGGCATGATG
ATAATGAAAAGCTTGTCATTGACACAGCTTATAATGAAGTCATCAATGGCGGCGTAT
Done.