Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01203.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: 5488
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Found at i:4669 original size:44 final size:44
Alignment explanation
Indices: 4606--5223 Score: 221
Period size: 44 Copynumber: 14.0 Consensus size: 44
4596 TATGGCGGAT
* * * * * *
4606 CTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAACCACCAGC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * *
4650 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA-TAGCAAAC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAA-ACTA-CAAGC
* * ** * *
4695 CTTATCTTCCTGAAGTTACAGTGAAACA-AGTTAAAATTACTAAGC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGA-TTGAAACTAC-AAGC
* * * * * **
4740 CTTATCTCCTTGAAATTCCAGCGGAGTAGATTGAAGCTACAAAT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * * *
4784 CTCT-TCTCCCTGAAATTACATTAGAGTAGATTGAAACCACCAGC
1 CT-TATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * * * **
4828 CTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAAT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * * * * * *
4872 CTCT-TCTCCCTTAAATTACATTGGAATGGGTCGAATAC-ACAAAC
1 CT-TATCTCCCTGAAGTTACAGTGGAGTAGATTGAA-ACTACAAGC
* * * * **
4916 TTTATCTTCCTGAAGTTATAGTGGAGTA-AGTTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGA-TTGAAACTA-CAAGC
* * * * * * * **
4961 TTTGTCTCCTTGAAGTTCCAGTAGAGTAGATCGAAGCTACAAAT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * * * * *
5005 C-TATTTTCCCTAAAATTACATTGGAGCAGATTGAAGCTACCAGC
1 CTTA-TCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * ** **
5049 CTTATCT-CTTGGAAGTTCCAGTGGAGTAGATCGAAGGTACAAAT
1 CTTATCTCCCT-GAAGTTACAGTGGAGTAGATTGAAACTACAAGC
* * * ** * * * *
5093 CTTTTCTCCCTGAAATTACATTGGAGCGGGTCGAATA-AACAAAC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAA-ACTACAAGC
* * * * **
5137 CTTATCTCCCTGAAGTTATAGTGGAGCAGGTTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTA-CAAGC
* * * * *
5182 CTTATCTCCTTAAAGTT-CTAGCGGAGTAGATCGAAGCTACAA
1 CTTATCTCCCTGAAGTTAC-AGTGGAGTAGATTGAAACTACAA
5224 ATCTCTTCTC
Statistics
Matches: 412, Mismatches: 139, Indels: 46
0.69 0.23 0.08
Matches are distributed among these distances:
43 7 0.02
44 271 0.66
45 132 0.32
46 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAACTACAAGC
Found at i:4729 original size:143 final size:143
Alignment explanation
Indices: 4454--4716 Score: 341
Period size: 143 Copynumber: 1.8 Consensus size: 143
4444 TAGATCGAAG
* * * * *
4454 ATGGTGGATCTTATCTTCTTGACGTCGCAGTGGAGTAGATTGAAGACGCTAGCCTTATCTCCCTG
1 ATGGCGGATCTTATCTTCTTGAAGTCGCAGTGGAGCAGATTGAAGACACCAGCCTTATCTCCCTG
* * * * * **
4519 AAGTTGCAGCGTAGCAGATTGAAAACAGCGAATCTTATTTTCCTGATATTGTAGTAGAACAGATT
66 AAGTTGCAGCGGAGCAGACTGAAAACAGCAAACCTTATCTTCCTGATATTACAGTAGAACAGATT
4584 AAAGTTAAAAGTT
131 AAAGTTAAAAGTT
*
4597 ATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAA-ACCACCAGCCTTATCTCCCT
1 ATGGCGGATCTTATCTTCTTGAAGTCGCAGTGGAGCAGATTGAAGA-CACCAGCCTTATCTCCCT
* * * *
4661 GAAGTTGCAGTGGAGTAGACTGAAGATAGCAAACCTTATCTTCCTGA-AGTTACAGT
65 GAAGTTGCAGCGGAGCAGACTGAAAACAGCAAACCTTATCTTCCTGATA-TTACAGT
4717 GAAACAAGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
142 2 0.02
143 99 0.98
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (143 bp):
ATGGCGGATCTTATCTTCTTGAAGTCGCAGTGGAGCAGATTGAAGACACCAGCCTTATCTCCCTG
AAGTTGCAGCGGAGCAGACTGAAAACAGCAAACCTTATCTTCCTGATATTACAGTAGAACAGATT
AAAGTTAAAAGTT
Found at i:4838 original size:88 final size:88
Alignment explanation
Indices: 4633--4893 Score: 301
Period size: 88 Copynumber: 2.9 Consensus size: 88
4623 GCAGTGGAGC
* * * * * *
4633 AGATTGAAACCACCAGCCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAACCT-
1 AGATTGAAACCACCAGCCTTATCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGCTA-CAAATCTC
* * *
4697 TATCTTCCTGAAGTTACAGTGAAACA
65 T-TCTCCCTGAAATTACA-TTAAACA
* ** * *
4723 AG-TTAAAATTACTAAGCCTTATCTCCTTGAAATTCCAGCGGAGTAGATTGAAGCTACAAATCTC
1 AGATTGAAACCAC-CAGCCTTATCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGCTACAAATCTC
* **
4787 TTCTCCCTGAAATTACATTAGAGT
65 TTCTCCCTGAAATTACATTAAACA
*
4811 AGATTGAAACCACCAGCCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCT
1 AGATTGAAACCACCAGCCTTATCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGCTACAAATCTCT
*
4876 TCTCCCTTAAATTACATT
66 TCTCCCTGAAATTACATT
4894 GGAATGGGTC
Statistics
Matches: 144, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
88 71 0.49
89 34 0.24
90 39 0.27
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (88 bp):
AGATTGAAACCACCAGCCTTATCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGCTACAAATCTCT
TCTCCCTGAAATTACATTAAACA
Found at i:4921 original size:88 final size:88
Alignment explanation
Indices: 4739--4932 Score: 257
Period size: 88 Copynumber: 2.2 Consensus size: 88
4729 AATTACTAAG
* *
4739 CCTTATCTCCTTGAAATTCCAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATTACA
1 CCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACA
* * * *
4804 TTAGAGTAGATTGAAACCACCAG
66 TTAGAATAGATCGAAACCACAAA
*
4827 CCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTTAAATTACA
1 CCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACA
* * *
4892 TTGGAATGGGTCGAATA-CACAAA
66 TTAGAATAGATCGAA-ACCACAAA
*
4915 CTTTATCTTCC-TGAAGTT
1 CCTTATC-TCCTTGAAGTT
4933 ATAGTGGAGT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 89 0.96
89 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (88 bp):
CCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACA
TTAGAATAGATCGAAACCACAAA
Found at i:4999 original size:221 final size:221
Alignment explanation
Indices: 4690--5252 Score: 804
Period size: 221 Copynumber: 2.5 Consensus size: 221
4680 CTGAAGATAG
* * * * * ** *
4690 CAAACCTTATCTTCCTGAAGTTACAGTGAAACAAGTTAAAATTACTAAGCCTTATCTCCTTGAAA
1 CAAACCTTATCTTCCTGAAGTTATAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAG
* *
4755 TTCCAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGTAGATTGAAA
66 TTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAGATTGAAA
*
4820 CCACCAGCCTTATCTCCTT-GAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTT
131 CCACCAGCCTTATCT-CTTGGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTG
* *
4884 AAATTACATTGGAATGGGTCGAATACA
195 AAATTACATTGGAACGGGTCGAATAAA
* * * *
4911 CAAACTTTATCTTCCTGAAGTTATAGTGGAGTAAGTTGAAATTACCAATTTTTGTCTCCTTGAAG
1 CAAACCTTATCTTCCTGAAGTTATAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAG
** * * * * *
4976 TTCCAGTAGAGTAGATCGAAGCTACAAATCTATTTTCCCTAAAATTACATTGGAGCAGATTGAAG
66 TTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAGATTGAAA
* * * *
5041 CTACCAGCCTTATCTCTTGGAAGTTCCAGTGGAGTAGATCGAAGGTACAAATCTTTTCTCCCTGA
131 CCACCAGCCTTATCTCTTGGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGA
*
5106 AATTACATTGGAGCGGGTCGAATAAA
196 AATTACATTGGAACGGGTCGAATAAA
* * *
5132 CAAACCTTATCTCCCTGAAGTTATAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAG
1 CAAACCTTATCTTCCTGAAGTTATAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAG
* *
5197 TTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCTTGAAATTACATTGGAGT
66 TTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGT
5253 GGATCGAAGC
Statistics
Matches: 297, Mismatches: 44, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
220 3 0.01
221 294 0.99
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (221 bp):
CAAACCTTATCTTCCTGAAGTTATAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAG
TTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAGATTGAAA
CCACCAGCCTTATCTCTTGGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGA
AATTACATTGGAACGGGTCGAATAAA
Found at i:5252 original size:44 final size:44
Alignment explanation
Indices: 4744--5262 Score: 225
Period size: 44 Copynumber: 11.8 Consensus size: 44
4734 CTAAGCCTTA
* * *
4744 TCTCCTTGAAATTCCAGCGGAGTAGATTGAAGCTACAAATCTCT
1 TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * * * * * * **
4788 TCTCCCTGAAATTACATTAGAGTAGATTGAAACCACCAGCCT-T
1 TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * *
4831 ATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCT
1 -TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * * * * *
4876 TCTCCCTT-AAATTACATTGGAATGGGTCGAA--TACACAAACTTT
1 TCT-CCTTGAAATTACAGTGGAGTAGATCGAAGCTACA-AATCTCT
* * * ** * * *
4919 ATCTTCC-TGAAGTTATAGTGGAGTA-AGTTGAAATTACCAATTTTT
1 -TC-TCCTTGAAATTACAGTGGAGTAGA-TCGAAGCTACAAATCTCT
* * * *
4964 GTCTCCTTGAAGTTCCAGTAGAGTAGATCGAAGCTACAAATCTAT
1 -TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * * * * * * *
5009 TTTCCCTAAAATTACATTGGAGCAGATTGAAGCTAC-CAGC-CT
1 TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * * * *
5051 TATCTCTTGGAAGTTCCAGTGGAGTAGATCGAAGGTACAAATCTTT
1 TCTC-CTT-GAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * ** * *** *
5097 TCTCCCTGAAATTACATTGGAGCGGGTCGAATAAACAAACCT-T
1 TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
* * * * * * ** *
5140 ATCTCCCTGAAGTTATAGTGGAGCAGGTTGAAATTACCAAT-TCTT
1 -TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTC-T
*
5185 ATCTCCTT-AAAGTT-CTAGCGGAGTAGATCGAAGCTACAAATCTCT
1 -TCTCCTTGAAA-TTAC-AGTGGAGTAGATCGAAGCTACAAATCTCT
* *
5230 TCTCCTTGAAATTACATTGGAGTGGATCGAAGC
1 TCTCCTTGAAATTACAGTGGAGTAGATCGAAGC
5263 ACCAATTCCT
Statistics
Matches: 341, Mismatches: 110, Indels: 48
0.68 0.22 0.10
Matches are distributed among these distances:
42 8 0.02
43 13 0.04
44 233 0.68
45 77 0.23
46 10 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (44 bp):
TCTCCTTGAAATTACAGTGGAGTAGATCGAAGCTACAAATCTCT
Done.