Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g01435.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: 4521
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Found at i:1326 original size:123 final size:122
Alignment explanation
Indices: 1130--1350 Score: 275
Period size: 123 Copynumber: 1.8 Consensus size: 122
1120 TCCGACTAAT
* * ** * * *
1130 ATAGAAAAATATAAACTTGTTTGAGGACTTGAAATAGGCTTTTACTTTCTTCATTATTATTCGAT
1 ATAGAAAAAGATAAACTTGTTTGAGGACGTGAAATAGGAATTTACCTTCTTCATTATCATCCGAT
*
1195 CACGTGAAT-TTTGGATTTAATTCATGATCAAGCTCCCCGAATCCTGAGCCTGAGTAAG
66 CACATGAATATTT-GATTT-ATTCATGATCAAGCTCCCCGAATCCTGAGCCTGAGTAAG
* * *
1253 ATAGAAGAAGATAAACTTGTTTGAGGACGTGAAATGGGAATTTACCTTCTTCATTATCA-CCTAT
1 ATAGAAAAAGATAAACTTGTTTGAGGACGTGAAATAGGAATTTACCTTCTTCATTATCATCCGA-
** *
1317 TTGCATGAATATTTGATTTATTCATGATCTAGCT
65 TCACATGAATATTTGATTTATTCATGATCAAGCT
1351 ATTTGCATGG
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
122 16 0.20
123 63 0.77
124 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (122 bp):
ATAGAAAAAGATAAACTTGTTTGAGGACGTGAAATAGGAATTTACCTTCTTCATTATCATCCGAT
CACATGAATATTTGATTTATTCATGATCAAGCTCCCCGAATCCTGAGCCTGAGTAAG
Found at i:1660 original size:154 final size:155
Alignment explanation
Indices: 1260--1973 Score: 640
Period size: 154 Copynumber: 4.6 Consensus size: 155
1250 AAGATAGAAG
* * *
1260 AAGATAAACTTGTTTGAGGACGTGAAATGGGAATTTACCTTCTTCATTATCACCTATTTGCATGA
1 AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCATGA
* * ** * * * *
1325 ATATTTGATTT-ATTCATGATCTAGCTATTTGCATGGTTCCGTTTTATCGAGTACAAACATGTAC
66 ATATTAGATTTAATTCATGATCAAGCTATCCGGATGGTTCTGTTTTATTGAGTACAAACACGTAC
* * *
1389 CCTAATCACA-AATCCACTTAAGGTAGAA
131 CCTAATCA-AGAGTCCACATAA-G-A-TA
* * * * * * * **
1417 GAAGATAAACTTGTTTGAGGACTTGCAATAGGCTTTTCCCTTTTTCATTGTCATCTCTCCGCATG
1 -AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCATG
* * * *
1482 ACTATTAGATTTAATTCATTATCAAGCTATCCGGATGGTTCTGTTTTATTGAGTAGAAACACGGA
65 AATATTAGATTTAATTCATGATCAAGCTATCCGGATGGTTCTGTTTTATTGAGTACAAACACGTA
* * * *
1547 -CTTGAATTATGGGTCCACATAAGAT-
130 CCCT-AATCAAGAGTCCACATAAGATA
* * *
1572 AAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATCATCACCTATTTGCATGA
1 AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCATGA
* * * * * * *
1637 ATATTTGATTTCATTAATGATCAAGCTAGT-CGGATGATTTTGTTTTATTGAGTACAATCATGTA
66 ATATTAGATTTAATTCATGATCAAGCTA-TCCGGATGGTTCTGTTTTATTGAGTACAAACACGTA
*
1701 CCCTAATCAAGAGTCCACTTAAGATAGAA
130 CCCTAATCAAGAGTCCACATAAGAT---A
* * * * *
1730 GAAGATAAACTTGTTTGAGGACTTGAAATAGGCTTTTTCCTTCTTCATTGTTATCT-TTT-CACT
1 -AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCA--
* * * * *
1793 TGACTATTAG-TTTAATTCATCATCAAGCTATCC-AATGGTTC-ATTTTATTGAGTAGAAACACG
63 TGAATATTAGATTTAATTCATGATCAAGCTATCCGGATGGTTCTGTTTTATTGAGTACAAACACG
* *
1855 TA-CCTGAATCAGGGGTCCACATAAGATA
128 TACCCT-AATCAAGAGTCCACATAAGATA
** * * *** * *
1883 GAAGATAAGTTTGTTTGAGGGCTTGAAATAGGATTTTACCTTCTTCATTGTTTTCTATTTGCGTC
1 -AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCATG
*
1948 AATATTAGATATAATTCATGATCAAG
65 AATATTAGATTTAATTCATGATCAAG
1974 TTACTCTGAT
Statistics
Matches: 446, Mismatches: 93, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
153 59 0.13
154 139 0.31
155 7 0.02
156 37 0.08
157 9 0.02
158 86 0.19
159 109 0.24
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (155 bp):
AAGATAAACTTGTTTGAGGACTTGAAATAGGATTTTACCTTCTTCATTATCACCTATTTGCATGA
ATATTAGATTTAATTCATGATCAAGCTATCCGGATGGTTCTGTTTTATTGAGTACAAACACGTAC
CCTAATCAAGAGTCCACATAAGATA
Found at i:1943 original size:312 final size:314
Alignment explanation
Indices: 1258--2003 Score: 1000
Period size: 312 Copynumber: 2.4 Consensus size: 314
1248 GTAAGATAGA
* * *
1258 AGAAGATAAACTTGTTTGAGGACGTGAAATGGGAATTTACCTTCTTCATTATCACCTATTTGCAT
1 AGAAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATTATCACCTATTTGCAT
* * * * * *
1323 GAATATTTGATTTATTCATGATCTAGCTATTTGCATGGTTCCGTTTTATCGAGTACAAACATGTA
66 GAATATTTGATTTATTCATGATCAAGCTACTCGGATGATTCTGTTTTATCGAGTACAAACATGTA
* *
1388 CCCTAATCACAAATCCACTTAAGGTAGAAGAAGATAAACTTGTTTGAGGACTTGCAATAGGCTTT
131 CCCTAATCACAAATCCACTTAAGATAGAAGAAGATAAACTTGTTTGAGGACTTGAAATAGGCTTT
* * * *
1453 TCCCTTTTTCATTGTCATCTCTCCGCATGACTATTAGATTTAATTCATTATCAAGCTATCCGGAT
196 TCCCTTCTTCATTGTCATCTCTCCACATGACTATTAGATTTAATTCATCATCAAGCTATCCGAAT
* * * *
1518 GGTTCTGTTTTATTGAGTAGAAACACGGACTTGAATTATGGGTCCACATAAGAT
261 GGTTCTATTTTATTGAGTAGAAACACGGACCTGAATCAGGGGTCCACATAAGAT
*
1572 --AAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATCATCACCTATTTGCAT
1 AGAAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATTATCACCTATTTGCAT
* * * * *
1635 GAATATTTGATTTCATTAATGATCAAGCTAGTCGGATGATTTTGTTTTATTGAGTACAATCATGT
66 GAATATTTGATTT-ATTCATGATCAAGCTACTCGGATGATTCTGTTTTATCGAGTACAAACATGT
*
1700 ACCCTAATCA-AGAGTCCACTTAAGATAGAAGAAGATAAACTTGTTTGAGGACTTGAAATAGGCT
130 ACCCTAATCACA-AATCCACTTAAGATAGAAGAAGATAAACTTGTTTGAGGACTTGAAATAGGCT
* * * * *
1764 TTTTCCTTCTTCATTGTTATCTTTTCACTTGACTATTAG-TTTAATTCATCATCAAGCTATCC-A
194 TTTCCCTTCTTCATTGTCATCTCTCCACATGACTATTAGATTTAATTCATCATCAAGCTATCCGA
*
1827 ATGGTTC-ATTTTATTGAGTAGAAACACGTACCTGAATCAGGGGTCCACATAAGAT
259 ATGGTTCTATTTTATTGAGTAGAAACACGGACCTGAATCAGGGGTCCACATAAGAT
** * * *** *
1882 AGAAGATAAGTTTGTTTGAGGGCTTGAAATAGGATTTTACCTTCTTCATTGTTTTCTATTTGCGT
1 AGAAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATTATCACCTATTTGCAT
* * * * * * *
1947 CAATATTAGATATAATTCATGATCAAGTTACTCTGATCATTCTGTTTTATCAAGTAC
66 GAATATTTGAT-TTATTCATGATCAAGCTACTCGGATGATTCTGTTTTATCGAGTAC
2004 TATGTTGTTG
Statistics
Matches: 376, Mismatches: 51, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
310 43 0.11
311 7 0.02
312 193 0.51
313 133 0.35
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (314 bp):
AGAAGATAAACTTGTTTGAGGGCTTGAAATGGGATTTTACCTTCTTCATTATCACCTATTTGCAT
GAATATTTGATTTATTCATGATCAAGCTACTCGGATGATTCTGTTTTATCGAGTACAAACATGTA
CCCTAATCACAAATCCACTTAAGATAGAAGAAGATAAACTTGTTTGAGGACTTGAAATAGGCTTT
TCCCTTCTTCATTGTCATCTCTCCACATGACTATTAGATTTAATTCATCATCAAGCTATCCGAAT
GGTTCTATTTTATTGAGTAGAAACACGGACCTGAATCAGGGGTCCACATAAGAT
Done.