Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2518
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: 14870
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Found at i:13830 original size:44 final size:43
Alignment explanation
Indices: 13763--14870 Score: 962
Period size: 44 Copynumber: 25.5 Consensus size: 43
13753 AAGTCATTAA
* *
13763 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * * *
13807 AGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-CGGAAGTAGATCGAAGAT
* * * *
13851 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
13895 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * * *
13939 AGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-CGGAAGTAGATCGAAGAT
* * * *
13983 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
14027 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * * *
14071 AGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-CGGAAGTAGATCGAAGAT
* * *
14115 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-AGAA
1 AGCAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
14158 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-T
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * *
14201 AGCAGGTC-TATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-CGGAAGTAGATCGAAGAT
* * * *
14244 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
14288 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * ** * *
14332 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTG-GCGGAAGTAGATCGAAGAT
* * *
14376 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-AGAA
1 AGCAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
14419 AGCAGATCTTG-CTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * ** * *
14462 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTG-GCGGAAGTAGATCGAAGAT
* *
14506 -GCAGATCTTGTCTTCC-ATATTGGTGGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGCGGAAGTAGATCGAAGAT
* * *
14547 AGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * *
14590 AGCAGATC-TATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-CGGAAGTAGATCGAAGAT
* * *
14633 -GCAGATCTTGTCCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGT-CTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* *
14678 AGCAGA--TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* * * * * *
14720 AGCAGGTCCTATCTTCCTATATT-GAGGAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCGGAAGTAGATCGAAGAT
* * * *
14762 -GCCAGATCTTGTC-TCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AG-CAGATCTTGTCTTCCTATATTGG-CG-GAAGTAGATCGAAGAT
* * *
14806 AGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
* *
14850 AGCAG-TCCTATCTTCCTATAT
1 AGCAGATCTTGTCTTCCTATAT
Statistics
Matches: 848, Mismatches: 177, Indels: 79
0.77 0.16 0.07
Matches are distributed among these distances:
41 23 0.03
42 129 0.15
43 230 0.27
44 370 0.44
45 91 0.11
46 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
AGCAGATCTTGTCTTCCTATATTGGCGGAAGTAGATCGAAGAT
Found at i:13998 original size:132 final size:132
Alignment explanation
Indices: 13761--14870 Score: 2000
Period size: 132 Copynumber: 8.5 Consensus size: 132
13751 TGAAGTCATT
13761 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
13826 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
13891 AG
131 AG
13893 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
13958 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
14023 AG
131 AG
14025 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14090 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
14154 AG
131 AG
14156 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-TAGCAGGT-CTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14219 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
14284 AG
131 AG
14286 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
14351 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
14415 AG
131 AG
14417 AAAGCAGATCTTG-CTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * *
14481 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTT-CCATATTGGT-G-GAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
14543 AG
131 AG
* *
14545 AAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCGAAGGTAGCAGAT-CTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14608 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCCTTCCCATATTGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGT-CTTCCCATATTGGTGGCGAAGTAGATCG
*
14673 AAG
130 CAG
14676 AAAGCAGA--TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
14739 TATT-G-AGGAAGTGGATCCAAGATGCCAGATCTTGTC-TCCCATATTGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGATG-CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
14801 CAG
130 CAG
*
14804 AAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA-GTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14868 TAT
66 TAT
Statistics
Matches: 953, Mismatches: 11, Indels: 31
0.96 0.01 0.03
Matches are distributed among these distances:
127 56 0.06
128 80 0.08
129 157 0.16
130 220 0.23
131 106 0.11
132 334 0.35
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
AG
Found at i:14336 original size:261 final size:264
Alignment explanation
Indices: 13761--14870 Score: 2000
Period size: 261 Copynumber: 4.3 Consensus size: 264
13751 TGAAGTCATT
13761 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
13826 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
13891 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
131 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
*
13956 TATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
196 TATATTGGTAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
14021 GCAG
261 GCAG
14025 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14090 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
14154 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-TAGCAGGT-CTATCTTCC
131 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
*
14217 TATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
196 TATATTGGTAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
14282 GCAG
261 GCAG
14286 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
14351 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
14415 AGAAAGCAGATCTTG-CTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
131 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
*
14479 TATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTT-CCATATTGGT-G-GAAGTAGATC
196 TATATTGGTAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
*
14541 GAAG
261 GCAG
* *
14545 AAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCGAAGGTAGCAGAT-CTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14608 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCCTTCCCATATTGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGT-CTTCCCATATTGGTGGCGAAGTAGATCG
14673 AAGAAAGCAGA--TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTC
130 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTC
14736 CTATATT-G-AGGAAGTGGATCCAAGATGCCAGATCTTGTC-TCCCATATTGGTGGCGAAGTAGA
195 CTATATTGGTAGGAAGTGGATCCAAGATG-CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGA
14798 TCGCAG
259 TCGCAG
*
14804 AAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA-GTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
14868 TAT
66 TAT
Statistics
Matches: 821, Mismatches: 14, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
256 20 0.02
257 69 0.08
258 109 0.13
259 86 0.10
260 68 0.08
261 238 0.29
262 56 0.07
263 46 0.06
264 129 0.16
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (264 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
TATATTGGTAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
GCAG
Done.