Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01760.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: 2190
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Found at i:894 original size:132 final size:135
Alignment explanation
Indices: 499--934 Score: 406
Period size: 132 Copynumber: 3.2 Consensus size: 135
489 TTTACGCCTA
* * * * *
499 TACCTTAGATGGGGATCTGATAGGGAAG-AGTAGTCATAGGCTACACAATGTAAATTCCTATGCT
1 TACCTTTGATGGGGATTTGATAGGGAAGAACTAGTCATA----ACACCATATAAATTCCTATGCT
*
563 TTTCAATGAA--TGTGAATGCACTCTGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTG
62 TTTCAA-GAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTG
626 CTTATGCCCT
126 CTTATGCCCT
* * * * **
636 TACCTTTGATGGGGATTTGATAGGGAAG-AGTAGTCATAAGCTACCCGATGTCAATTTCTAACCT
1 TACCTTTGATGGGGATTTGATAGGGAAGAACTAGTCATAA-C-A-CC-ATATAAATTCCTATGCT
* * * * * * * * * * * *
700 TTTAAATAATTTGTGACTGCACAATGGCAGATTCTCGGTAGTGGGATTTAATAG-TTCGATTGTG
62 TTTCAAGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACT-GCTTCCATTGTG
*
764 CTT-TACACCTT
126 CTTATGC-CC-T
* * * * *
775 TGCCATAGATGGAGATTTGATAGGGAAGAACT-GTGATAA-A-C-TATAAATTCCTATGCTTTTC
1 TACCTTTGATGGGGATTTGATAGGGAAGAACTAGTCATAACACCATATAAATTCCTATGCTTTTC
* *
836 AAGAATTTGTGAATGCACTATGGCAGGTTTTCTGAATTAGGAGTTGCTGCTTCCATTGTGCTTAT
66 AAGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTGCTTAT
901 GCCCT
131 GCCCT
906 TACCTTTGATGGGGATTTGATAGGGAAGA
1 TACCTTTGATGGGGATTTGATAGGGAAGA
935 GTTGTCATAG
Statistics
Matches: 236, Mismatches: 51, Indels: 30
0.74 0.16 0.09
Matches are distributed among these distances:
131 27 0.11
132 64 0.27
133 3 0.01
134 2 0.01
135 1 0.00
136 4 0.02
137 56 0.24
138 45 0.19
139 32 0.14
140 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (135 bp):
TACCTTTGATGGGGATTTGATAGGGAAGAACTAGTCATAACACCATATAAATTCCTATGCTTTTC
AAGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTGCTTAT
GCCCT
Found at i:980 original size:270 final size:263
Alignment explanation
Indices: 549--1270 Score: 891
Period size: 270 Copynumber: 2.7 Consensus size: 263
539 CTACACAATG
*
549 TAAATTCCTATGCTTTTCAATGAA--TGTGAATGCACTCTGGCAGGTTTTCTGAAGTAGGAGTTA
1 TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTA
* *
612 CTGCTTCCATTGTGCTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTAGTCATAAGC
66 CTGCTTCCATTGTGCTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCATAGGC
* * * * ** **
677 TACCCGATGTCAATTTCTAACCTTTTAAATAATTTGTGACTGCACAATGGCAGATTCTCGGTAGT
131 TACCCAATGTGAATTTCTAAGCTTTTCAATAATTTGTGAAAGCACAATGGCAGATTCTCGAAAGT
* *
742 GGGATTTAATAGTTCGATTGTGC-TTTACACCTTTGCCA-TAGATGGAGATTTGATAGGGAAGAA
196 AGGA--T--T--TTC---TGTGCTTTTACACATTT-CCATTAGATGGAGATTTGATAGGGAAGAA
* *
805 CTGTGATAAACTA
251 CCGTAATAAACTA
* *
818 TAAATTCCTATGCTTTTCAA-GAATTTGTGAATGCACTATGGCAGGTTTTCTGAATTAGGAGTTG
1 TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTA
*
882 CTGCTTCCATTGTGCTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCATAGGT
66 CTGCTTCCATTGTGCTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCATAGGC
*
947 TACCCAATGTGAA-TTCATAAGCTTTTCAATAATTTGTGAAAGCACAATGTCAGATTCTCGAAAG
131 TACCCAATGTGAATTTC-TAAGCTTTTCAATAATTTGTGAAAGCACAATGGCAGATTCTCGAAAG
* * *
1011 TAGGATTTTCTGTGCTTTTACACATTTTCATTAGGTGGAGATTTGATAGGGAAGAACCGTAATAG
195 TAGGATTTTCTGTGCTTTTACACATTTCCATTAGATGGAGATTTGATAGGGAAGAACCGTAATAA
1076 ACTA
260 ACTA
* * * * *
1080 TAAATTCCTAATATGGTTTTCAATG-ATTTGTGAATGCACTGTGACAGATTTTCTGAAGTAGGAT
1 TAAATTCC---TATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAG
* * * * * *
1144 TTATTGGTTCCGTTGTGCTTTATGCTCTTACCTTTGATGGGAATTTGATAGGGAAGAGTTGTAAT
63 TTACTGCTTCCATTGTGC-TTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCAT
* * * ** * * *
1209 TGGCTACCCAAAGTGAATTTCCAAGCTTCACAATAATTTGTGAAGGCACAACGGCTGATTCT
127 AGGCTACCCAATGTGAATTTCTAAGCTTTTCAATAATTTGTGAAAGCACAATGGCAGATTCT
1271 TAGAAGTGGG
Statistics
Matches: 397, Mismatches: 45, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
261 7 0.02
262 52 0.13
264 3 0.01
265 59 0.15
266 93 0.23
267 3 0.01
268 4 0.01
269 23 0.06
270 153 0.39
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (263 bp):
TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTA
CTGCTTCCATTGTGCTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCATAGGC
TACCCAATGTGAATTTCTAAGCTTTTCAATAATTTGTGAAAGCACAATGGCAGATTCTCGAAAGT
AGGATTTTCTGTGCTTTTACACATTTCCATTAGATGGAGATTTGATAGGGAAGAACCGTAATAAA
CTA
Found at i:983 original size:138 final size:138
Alignment explanation
Indices: 499--1257 Score: 518
Period size: 138 Copynumber: 5.6 Consensus size: 138
489 TTTACGCCTA
* * *
499 TACCTTAGATGGGGATCTGATAGGGAAGAGTAGTCATAGGCTACACAATGTAAATTCCTATGCTT
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGTAAATTCCTAAGCTT
*
564 TTCAATGAA--TGTGAATGCACTCTGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTGC
66 TTCAAT-AATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTGC
627 TTATGCCCT
130 TTATGCCCT
* * * * * *
636 TACCTTTGATGGGGATTTGATAGGGAAGAGTAGTCATAAGCTACCCGATGTCAATTTCTAACCTT
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGTAAATTCCTAAGCTT
* * * * * * * * * * *
701 TTAAATAATTTGTGACTGCACAATGGCAGATTCTCGGTAGTGGGATTTAATAG-TTCGATTGTGC
66 TTCAATAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACT-GCTTCCATTGTGC
*
765 TT-TACACCTT
130 TTATGC-CC-T
* * * * * *
775 TGCCATAGATGGAGATTTGATAGGGAAGA--A--C-T-GTGATA---AACTATAAATTCCTATGC
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAG-GCTACCCAA-TGTAAATTCCTAAGC
* * *
831 TTTTCAAGAATTTGTGAATGCACTATGGCAGGTTTTCTGAATTAGGAGTTGCTGCTTCCATTGTG
64 TTTTCAATAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTG
896 CTTATGCCCT
129 CTTATGCCCT
* * * * *
906 TACCTTTGATGGGGATTTGATAGGGAAGAGTTGTCATAGGTTACCCAATGTGAATTCATAAGCTT
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGTAAATTCCTAAGCTT
* * * * *
971 TTCAATAATTTGTGAAAGCACAATGTCAGATTCTC-GAAAGTAGGA--T--T--TT-C--TGTGC
66 TTCAATAATTTGTGAATGCACTATGGCAGGTTTTCTG-AAGTAGGAGTTACTGCTTCCATTGTGC
* * *
1026 TTTTACACATT
130 TTATGC-C-CT
* * * * *** * *
1037 TTCATTAGGTGGAGATTTGATAGGGAAGAACCGTAATA-G--A--C--TATAAATTCCTAATATG
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGTAAATTCCT-A-A-G
* * * * * * * * *
1095 GTTTTCAATGATTTGTGAATGCACTGTGACAGATTTTCTGAAGTAGGATTTATTGGTTCCGTTGT
63 CTTTTCAATAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGT
*
1160 GCTTTATGCTCT
128 GC-TTATGCCCT
* * * * * * *
1172 TACCTTTGATGGGAATTTGATAGGGAAGAGTTGTAATTGGCTACCCAAAGTGAATTTCC-AAGCT
1 TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGT-AAATTCCTAAGCT
** *
1236 TCACAATAATTTGTGAAGGCAC
65 TTTCAATAATTTGTGAATGCAC
1258 AACGGCTGAT
Statistics
Matches: 469, Mismatches: 110, Indels: 84
0.71 0.17 0.13
Matches are distributed among these distances:
124 8 0.02
125 1 0.00
126 2 0.00
127 40 0.09
128 2 0.00
129 10 0.02
130 2 0.00
131 60 0.13
132 66 0.14
133 4 0.01
134 6 0.01
135 31 0.07
136 13 0.03
137 70 0.15
138 95 0.20
139 49 0.10
140 2 0.00
141 1 0.00
142 1 0.00
143 6 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (138 bp):
TACCTTAGATGGGGATTTGATAGGGAAGAGTAGTCATAGGCTACCCAATGTAAATTCCTAAGCTT
TTCAATAATTTGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGAGTTACTGCTTCCATTGTGCT
TATGCCCT
Done.