Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g00662.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: 3181
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Found at i:710 original size:123 final size:123
Alignment explanation
Indices: 492--1138 Score: 729
Period size: 123 Copynumber: 5.3 Consensus size: 123
482 GAATTCTTCC
* * *
492 GAGTCTAGTAGCGAGGAAGATTCATCTTCTGACGAAGAAGCT-C--CTCAGAATAAAAAACCTGT
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
* * * *
554 TGTTTCTAAAAATGGCC-CTGTTCCAGCTGCCAAGACAGTGAAAGATGATAGTAGTTCT
66 AGTTGCTAAAAA-GGCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
* *
612 GAGTCTAGCAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAATCCTGT
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
* * *
677 AGTTGCTAAAAAGGCCTGTGTTCCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTCT
66 AGTTGCTAAAAAGGCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
* * *
735 ---TCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGCTCCTGCTCAGAATAAAAAACCTGT
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
* * ** * * *
797 AGCTGC-AAAAACTGG-CTCTATTCTGGCTGCTAAGACTGTTAAAGCTGGTAGTAGTTCT
66 AGTTGCTAAAAA--GGCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
* * * * * * *
855 GAGTCTAGTAGTGAAGAAGACTCATCCTCTGATGAAGAAGCTACTGCACAGAATAAAAAATCTGT
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
*** ** ** * * *
920 AGCCACTAAAACTGTATCTGTTCCAGATGCTAAGGCTGTGAAAGCTGATAGTAGTTCT
66 AGTTGCTAAAAAGGCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
* * **
978 GAGTCTAGTAGTGAGGAAGGTTCATCCTCTGACGAAGAAGTTCCTGCTCAGAAGAAAAAACCCAT
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
* * * * * *
1043 AGTTGCT-AAAAGTGGCTCTATACTAGCTGCTAAGACAGTGAAGGCTGATAGTAGTTCA
66 AGTTGCTAAAAAG-GCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
* *
1101 GAGTCTAGTAGTGAGGAAGATTCATCCTCCGATGAAGA
1 GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGA
1139 GCGTGTTGCA
Statistics
Matches: 443, Mismatches: 72, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
119 5 0.01
120 135 0.30
121 3 0.01
122 8 0.02
123 288 0.65
124 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (123 bp):
GAGTCTAGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAAACCTGT
AGTTGCTAAAAAGGCCTCTGTTCCAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCT
Found at i:944 original size:243 final size:243
Alignment explanation
Indices: 498--1138 Score: 779
Period size: 243 Copynumber: 2.6 Consensus size: 243
488 TTCCGAGTCT
* * * *
498 AGTAGCGAGGAAGATTCATCTTCTGACGAAGAAGCT-C--CTCAGAATAAAAAACCTGTTGTTTC
1 AGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAATAAAAAACCTGTAGTTGC
* * * * * *
560 TAAAAATGGCCCTGTTCCAGCTGCCAAGACAGTGAAAGATGATAGTAGTTCTGAGTCTAGCAGTG
66 -AAAAATGGCTCTATTCTAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTG
* * * * ***
625 AGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAATCCTGTAGTTGCTAAAAAG
130 AGGAAGATTCATCCTCTGATGAAGAAGCTACTGCACAGAAAAAAAATCCTGTAGCCACTAAAAAG
* * *
690 GCCTGTGTTCCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTCT-TCA
195 GCATCTGTTCCAGATGCCAAGACAGTGAAAGCTGATAGCAGTTCTGTCA
* *
738 AGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGCTCCTGCTCAGAATAAAAAACCTGTAGCTGC
1 AGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAATAAAAAACCTGTAGTTGC
* * * *
803 AAAAACTGGCTCTATTCTGGCTGCTAAGACTGTTAAAGCTGGTAGTAGTTCTGAGTCTAGTAGTG
66 AAAAA-TGGCTCTATTCTAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTG
* * *
868 AAGAAGACTCATCCTCTGATGAAGAAGCTACTGCACAGAATAAAAAAT-CTGTAGCCACTAAAAC
130 AGGAAGATTCATCCTCTGATGAAGAAGCTACTGCACAGAA-AAAAAATCCTGTAGCCACTAAAAA
* * * * * * *
932 TGTATCTGTTCCAGATGCTAAGGCTGTGAAAGCTGATAGTAGTTCTGAGTCT
194 GGCATCTGTTCCAGATGCCAAGACAGTGAAAGCTGATAGCAGTTCT--GTCA
* * * **
984 AGTAGTGAGGAAGGTTCATCCTCTGACGAAGAAGTTCCTGCTCAGAAGAAAAAACCCATAGTTGC
1 AGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAATAAAAAACCTGTAGTTGC
* * * *
1049 TAAAAGTGGCTCTATACTAGCTGCTAAGACAGTGAAGGCTGATAGTAGTTCAGAGTCTAGTAGTG
66 -AAAAATGGCTCTATTCTAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTG
*
1114 AGGAAGATTCATCCTCCGATGAAGA
130 AGGAAGATTCATCCTCTGATGAAGA
1139 GCGTGTTGCA
Statistics
Matches: 338, Mismatches: 54, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
240 33 0.10
241 1 0.00
242 5 0.01
243 155 0.46
244 6 0.02
246 134 0.40
247 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (243 bp):
AGTAGTGAGGAAGATTCATCCTCTGACGAAGAAGCTCCTGCTCAGAATAAAAAACCTGTAGTTGC
AAAAATGGCTCTATTCTAGCTGCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGA
GGAAGATTCATCCTCTGATGAAGAAGCTACTGCACAGAAAAAAAATCCTGTAGCCACTAAAAAGG
CATCTGTTCCAGATGCCAAGACAGTGAAAGCTGATAGCAGTTCTGTCA
Found at i:2920 original size:3 final size:3
Alignment explanation
Indices: 2912--2947 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2902 TTTGTGCTAG
2912 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2948 GTTTTGGGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.