Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A04G115100.1.v1.1
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, 666
Length: 1110
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Found at i:173 original size:33 final size:33
Alignment explanation
Indices: 122--213 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 33
112 CCAAAGCCTG
** *
122 AAATGCCAGAAATCCCAAAACCTGAAATACCTA
1 AAATGCCAGAGTTGCCAAAACCTGAAATACCTA
* * *
155 AAATGCCTGAGTTGCCAAAACCTGAATTGCCTA
1 AAATGCCAGAGTTGCCAAAACCTGAAATACCTA
* * *
188 AAGTTCCAGAGTTGCCAAAGCCTGAA
1 AAATGCCAGAGTTGCCAAAACCTGAA
214 TTGCCTAAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (33 bp):
AAATGCCAGAGTTGCCAAAACCTGAAATACCTA
Found at i:214 original size:33 final size:33
Alignment explanation
Indices: 136--233 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 33
126 GCCAGAAATC
* * * * *
136 CCAAAACCTGAAATACCTAAAATGCCTGAGTTG
1 CCAAAACCTGAATTGCCTAAAGTTCCAGAGTTG
169 CCAAAACCTGAATTGCCTAAAGTTCCAGAGTTG
1 CCAAAACCTGAATTGCCTAAAGTTCCAGAGTTG
* * *
202 CCAAAGCCTGAATTGCCTAAGGTTCCCGAGTT
1 CCAAAACCTGAATTGCCTAAAGTTCCAGAGTT
234 TTCGAAAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (33 bp):
CCAAAACCTGAATTGCCTAAAGTTCCAGAGTTG
Found at i:248 original size:51 final size:51
Alignment explanation
Indices: 187--335 Score: 217
Period size: 51 Copynumber: 2.9 Consensus size: 51
177 TGAATTGCCT
* *
187 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCTAAGGTTCCCGAGTTTTCG
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTACCTAAGGTTCCCGAGTTTCCG
* * * *
238 AAAGTTCCAGAGTTGCCAAAACCGGAATTACCCAAGGTTCCTGAGTTTCCG
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTACCTAAGGTTCCCGAGTTTCCG
* * *
289 AAAGTGCCAGAGTTGCCAAAGCCTGAATTTCCTAAGATTCCCGAGTT
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTACCTAAGGTTCCCGAGTT
336 GAAAAAACCT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (51 bp):
AAAGTTCCAGAGTTGCCAAAGCCTGAATTACCTAAGGTTCCCGAGTTTCCG
Found at i:505 original size:99 final size:99
Alignment explanation
Indices: 402--686 Score: 286
Period size: 99 Copynumber: 2.9 Consensus size: 99
392 AATCTGAAGC
* * * * *
402 ACCAAAAGTTCCGGAGTTACCAAATCTAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAAT
1 ACCAAAAGTTCCCGAGTTACCAAAACTAGAATTACCTAAAGTTCCTGAAGTACCCAAGCCGGAAT
467 TACCCAAAGCTCCCG-AGTTGCCAAAACCTGAATT
66 TACCCAAAGCTCCCGAAG-TGCCAAAACCTGAATT
* * * * * * *
501 ACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTACCTAAGTCGGAAT
1 ACCAAAAGTTCCCGAGTTACCAAAACTAGAATTACCTAAAGTTCCTGAAGTACCCAAGCCGGAAT
* * * *
566 TGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATT
66 TACCCAAAGCTCCCGAAGTGCCAAAACCTGAATT
* * * * * * * *
600 ACCCAAAGCTCCCGAGTTGCCAAAACTTGAATCACCAAAAGTTCCTG-AGTTACCAAAGCCAGAA
1 ACCAAAAGTTCCCGAGTTACCAAAACTAGAATTACCTAAAGTTCCTGAAG-TACCCAAGCCGGAA
* * * *
664 TTGCCTAAAGTTCCTGAAGTGCC
65 TTACCCAAAGCTCCCGAAGTGCC
687 TAAGCCAGAA
Statistics
Matches: 155, Mismatches: 29, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
98 1 0.01
99 152 0.98
100 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (99 bp):
ACCAAAAGTTCCCGAGTTACCAAAACTAGAATTACCTAAAGTTCCTGAAGTACCCAAGCCGGAAT
TACCCAAAGCTCCCGAAGTGCCAAAACCTGAATT
Found at i:589 original size:18 final size:18
Alignment explanation
Indices: 566--611 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
556 AAGTCGGAAT
566 TGCCCAAAGCTCCTGAAG
1 TGCCCAAAGCTCCTGAAG
*
584 TGCCC-AAG--CCTGAAT
1 TGCCCAAAGCTCCTGAAG
*
599 TACCCAAAGCTCC
1 TGCCCAAAGCTCC
612 CGAGTTGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 3 0.13
18 7 0.30
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17
Consensus pattern (18 bp):
TGCCCAAAGCTCCTGAAG
Found at i:643 original size:132 final size:132
Alignment explanation
Indices: 429--719 Score: 492
Period size: 132 Copynumber: 2.2 Consensus size: 132
419 TACCAAATCT
* * *
429 AGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
1 AGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
* *
494 CTGAATTACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTACCTAAG
66 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAG
*
559 TC
131 CC
*
561 GGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
1 AGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
* *
626 TTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAG
66 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAG
691 CC
131 CC
*
693 AGAATTGCCCAAAGCTCCTGAATTGCC
1 AGAATTGCCCAAAGCTCCTGAAGTGCC
720 AAAAATTCCT
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 148 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (132 bp):
AGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAG
CC
Found at i:678 original size:33 final size:33
Alignment explanation
Indices: 406--722 Score: 235
Period size: 33 Copynumber: 9.6 Consensus size: 33
396 TGAAGCACCA
* * * * * *
406 AAAGTTCCGGAGTTACCAAATCTAGAATTTCCT
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* *
439 AAAGTTCCTGAAG-TGCCCAAGCCTGAATTACCC
1 AAAGTTCCTG-AGTTGCCAAAGCCAGAATTACCC
* * * * *
472 AAAGCTCCCGAGTTGCCAAAACCTGAATTACCA
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* * *
505 AAAGTTCCTGAGTTACCAAAGCCAGAATTGCCT
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* * * * * *
538 AAAGTTCCTGAGGTACCTAAGTCGGAATTGCCC
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* * *
571 AAAGCTCCTGAAG-TGCCCAAGCCTGAATTACCC
1 AAAGTTCCTG-AGTTGCCAAAGCCAGAATTACCC
* * * ** * *
604 AAAGCTCCCGAGTTGCCAAAACTTGAATCACCA
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* * *
637 AAAGTTCCTGAGTTACCAAAGCCAGAATTGCCT
1 AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
* *
670 AAAGTTCCTGAAG-TGCCTAAGCCAGAATTGCCC
1 AAAGTTCCTG-AGTTGCCAAAGCCAGAATTACCC
* *
703 AAAGCTCCTGAATTGCCAAA
1 AAAGTTCCTGAGTTGCCAAA
723 AATTCCTGAG
Statistics
Matches: 226, Mismatches: 52, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
32 5 0.02
33 215 0.95
34 6 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (33 bp):
AAAGTTCCTGAGTTGCCAAAGCCAGAATTACCC
Found at i:692 original size:99 final size:99
Alignment explanation
Indices: 439--723 Score: 302
Period size: 99 Copynumber: 2.9 Consensus size: 99
429 AGAATTTCCT
* * * * * * * *
439 AAAGTTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTGCCAAAACCTGAATTAC
1 AAAGTTCCTGAGGTACCAAAGCCAGAATTGCCCAAAGCTCCTGAAG-TGCCCAAGCCTGAATTAC
* * * * ** *
503 CAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCT
65 CCAAAGCTCCTGAGTTGCCAAAACCAGAATCACCA
* * *
538 AAAGTTCCTGAGGTACCTAAGTCGGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACC
1 AAAGTTCCTGAGGTACCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACC
* **
603 CAAAGCTCCCGAGTTGCCAAAACTTGAATCACCA
66 CAAAGCTCCTGAGTTGCCAAAACCAGAATCACCA
* * * * * *
637 AAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCC
1 AAAGTTCCTGAGGTACCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACC
*
702 CAAAGCTCCTGAATTGCCAAAA
66 CAAAGCTCCTGAGTTGCCAAAA
724 ATTCCTGAGT
Statistics
Matches: 155, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
99 153 0.99
100 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (99 bp):
AAAGTTCCTGAGGTACCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACC
CAAAGCTCCTGAGTTGCCAAAACCAGAATCACCA
Found at i:722 original size:84 final size:84
Alignment explanation
Indices: 634--807 Score: 242
Period size: 84 Copynumber: 2.1 Consensus size: 84
624 ACTTGAATCA
* * * * * * *
634 CCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAGCCAGAATT
1 CCAAAAATTCCTGAGTTAACAAAACCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATT
*
699 GCCCAAAGCT-CCTGAATTG
66 GCCCAAAG-TGACTGAATTG
*
718 CCAAAAATTCCTGAGTTAACAAAACCAGAATTGCCTAAAATTCCTGAGGTACCAAAACCAGAATT
1 CCAAAAATTCCTGAGTTAACAAAACCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATT
*
783 GCCCAAAGTGACTGAGTTG
66 GCCCAAAGTGACTGAATTG
802 CCAAAA
1 CCAAAA
808 CCTGAATTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 1 0.01
84 78 0.99
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (84 bp):
CCAAAAATTCCTGAGTTAACAAAACCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATT
GCCCAAAGTGACTGAATTG
Found at i:752 original size:132 final size:131
Alignment explanation
Indices: 429--757 Score: 392
Period size: 132 Copynumber: 2.5 Consensus size: 131
419 TACCAAATCT
* * * * * * * *
429 AGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
1 AGAATTGCCCAAAGCTCCTGAAGTGCCAAAGCCTGAATTACACAAA-CACCAGAATTGCCAAAAC
* *
494 CTGAATTACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTACCTAAG
65 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAG
*
559 TC
130 CC
* * * * * *
561 GGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
1 AGAATTGCCCAAAGCTCCTGAAGTGCCAAAGCCTGAATTACACAAA-CACCAGAATTGCCAAAAC
* *
626 TTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAG
65 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAG
691 CC
130 CC
* * *
693 AGAATTGCCCAAAGCTCCTGAATTGCCAAAAATTCCTGAGTTA-ACAAA-ACCAGAATTGCCTAA
1 AGAATTGCCCAAAGCTCCTGAAGTGCC--AAA-GCCTGAATTACACAAACACCAGAATTGCC-AA
756 AA
62 AA
758 TTCCTGAGGT
Statistics
Matches: 175, Mismatches: 18, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
132 157 0.90
133 4 0.02
134 6 0.03
135 8 0.05
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (131 bp):
AGAATTGCCCAAAGCTCCTGAAGTGCCAAAGCCTGAATTACACAAACACCAGAATTGCCAAAACC
TGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTACCTAAGC
C
Found at i:830 original size:84 final size:84
Alignment explanation
Indices: 642--1003 Score: 230
Period size: 84 Copynumber: 4.4 Consensus size: 84
632 CACCAAAAGT
* * * *
642 TCCTGAGTTACC-AAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCCCAAA
1 TCCTGAGTTACCAAAAGCCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATTGCCCAAA
*
706 GCTCCTGAATTGCCAAAAA
66 GCTACTGAATTGCCAAAAA
* *
725 TTCCTGAGTTAACAAAA-CCAGAATTGCCTAAAATTCCTGAGGTACCAAAACCAGAATTGCCCAA
1 -TCCTGAGTTACCAAAAGCCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATTGCCCAA
*
789 AG-TGACTGAGTTGCC-AAAA
65 AGCT-ACTGAATTGCCAAAAA
* ** * * * * * *
808 -CCTGAATTACCAAAAGTTCCAGAGGTGCCT--AA-GCCAGAATTGCCAAAAGCTCCTGAATT-A
1 TCCTGAGTTACCAAAAG--CCAGAATTGCCTAAAATTCCTGAAGTACCAAAA---CCAGAATTGC
* * * *
868 CCAAAAC--CTCAATTACCTAAAAT
61 CCAAAGCTACTGAATTGCC-AAAAA
* * * * * * *
891 TCCCGGGTTAACAAAA-CCAGAATTGCCTAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAA
1 TCCTGAGTTACCAAAAGCCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATTGCCCAAA
* * *
955 ACTCCTGAGTTGCC-AAAA
66 GCTACTGAATTGCCAAAAA
* * *
973 -CCTGAATTACCTAAAGTTCCTGAATTGCCTA
1 TCCTGAGTTACCAAAAG--CCAGAATTGCCTA
1004 GCATGCCTAA
Statistics
Matches: 209, Mismatches: 48, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
81 58 0.28
82 12 0.06
83 14 0.07
84 122 0.58
85 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (84 bp):
TCCTGAGTTACCAAAAGCCAGAATTGCCTAAAATTCCTGAAGTACCAAAACCAGAATTGCCCAAA
GCTACTGAATTGCCAAAAA
Found at i:906 original size:99 final size:99
Alignment explanation
Indices: 803--992 Score: 274
Period size: 99 Copynumber: 1.9 Consensus size: 99
793 ACTGAGTTGC
* * * *
803 CAAAACCTGAATTACCAAAAGTTCCAGAGGTGCCTAAGCCAGAATTG-CCAAAAGCTCCTGAATT
1 CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAA-CTCCTGAATT
867 ACCAAAACCTCAATTACCTAAAATTCCCGGGTTAA
65 ACCAAAACCTCAATTACCTAAAATTCCCGGGTTAA
* * * *
902 CAAAACCAGAATTGCCTAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTGAGTTG
1 CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTGAATTA
* *
967 CCAAAACCTGAATTACCTAAAGTTCC
66 CCAAAACCTCAATTACCTAAAATTCC
993 TGAATTGCCT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 74 0.93
100 6 0.08
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (99 bp):
CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTGAATTA
CCAAAACCTCAATTACCTAAAATTCCCGGGTTAA
Found at i:1001 original size:33 final size:33
Alignment explanation
Indices: 712--995 Score: 244
Period size: 33 Copynumber: 8.6 Consensus size: 33
702 CAAAGCTCCT
* * *
712 GAATTGCCAAAAATTCCTGAGTTAACAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* *
745 GAATTGCCTAAAATTCCTGAGGTACCAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* ** * *
778 GAATTGCCCAAAGTGACTGAGTTGCCAAAACCT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * * * * *
811 GAATTACCAAAAGTTCCAGAGGTGCCTAAGCCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * *
844 GAATTGCCAAAAGCTCCTGAATTACCAAAACCT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * * * *
877 CAATTACCTAAAATTCCCGGGTTAACAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * *
910 GAATTGCCTAAAGTTCCAGAGGTACCGAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* ** * *
943 GAATTGCCCAAAACTCCTGAGTTGCCAAAACCT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
*
976 GAATTACCTAAAGTTCCTGA
1 GAATTGCCTAAAGTTCCTGA
996 ATTGCCTAGC
Statistics
Matches: 193, Mismatches: 58, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 193 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (33 bp):
GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
Done.