Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9322.1
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, 1000
Length: 4481
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:353 original size:86 final size:86
Alignment explanation
Indices: 219--654 Score: 674
Period size: 86 Copynumber: 5.1 Consensus size: 86
209 AAATCTGCCA
* * * * * * *
219 TCTTTGATCTGCTTCGCTGCCAAATACAGAAAAGCAAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTA
* *
284 CAAACGAGAGAGGCAAGGTTTG
65 CGACCGAGAGAGGCAAGGTTTG
* * * * *
306 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
* * * *
371 AAACGAGAGTGGCAAGGTTTT
66 GACCGAGAGAGGCAAGGTTTG
392 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
457 GACCGAGAGAGGCAAGGTTTG
66 GACCGAGAGAGGCAAGGTTTG
*
478 TCTTCGATCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
543 GACCGAGAGAGGCAAGGTTTG
66 GACCGAGAGAGGCAAGGTTTG
*
564 TCTTCGATCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
*
629 GACCGAGAGAGGCAAGGTTTA
66 GACCGAGAGAGGCAAGGTTTG
650 TCTTC
1 TCTTC
655 AATTTTTACT
Statistics
Matches: 328, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
86 309 0.94
87 19 0.06
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAGCTTCAACTAGCTCTGCTAC
GACCGAGAGAGGCAAGGTTTG
Found at i:514 original size:42 final size:41
Alignment explanation
Indices: 381--600 Score: 114
Period size: 42 Copynumber: 5.1 Consensus size: 41
371 AAACGAGAGT
*
381 GGCAAGGTTTTTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCG-TGTCAATGCAGGAA
* * * * * *
423 GGCAAGATCTGATAGCTTC-AACTAGC-TC-TG-CTACGACCGAGAGA
1 GGCAAGGTTTG-T--CTTCGATCT-GCTTCGTGTCAATG-CAG-GA-A
467 GGCAAGGTTTGTCTTCGATCTGCTTCGTTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCG-TGTCAATGCAGGAA
* * * * * *
509 GGCAAGATCTGATAGCTTC-AACTAGC-TC-TG-CTACGACCGAGAGA
1 GGCAAGGTTTG-T--CTTCGATCT-GCTTCGTGTCAATG-CAG-GA-A
553 GGCAAGGTTTGTCTTCGATCTGCTTCGTTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCG-TGTCAATGCAGGAA
595 GGCAAG
1 GGCAAG
601 ATCTGATAGC
Statistics
Matches: 129, Mismatches: 25, Indels: 48
0.64 0.12 0.24
Matches are distributed among these distances:
41 18 0.14
42 43 0.33
43 12 0.09
44 38 0.29
45 18 0.14
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
GGCAAGGTTTGTCTTCGATCTGCTTCGTGTCAATGCAGGAA
Found at i:1268 original size:108 final size:108
Alignment explanation
Indices: 1079--1274 Score: 293
Period size: 108 Copynumber: 1.8 Consensus size: 108
1069 GAAAAATGCT
* **
1079 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTATAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGCCGAGAGCAAAGCTATAAACAAACAAAT
*
1144 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
66 CAATCAAGATAGCAAATGTTGCTGAGATACGAGATGTATAAGA
* * * * **
1187 TGAAAAAGATTATCACAATGGATAAGATGAAAATTTGCCGAGAGCAAAGCTCTAAATGAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGCCGAGAGCAAAGCTATAAACAAACAAAT
*
1252 TAATCAAGATAGCAAATGTTGCT
66 CAATCAAGATAGCAAATGTTGCT
1275 AGAATACAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 77 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGCCGAGAGCAAAGCTATAAACAAACAAAT
CAATCAAGATAGCAAATGTTGCTGAGATACGAGATGTATAAGA
Found at i:1646 original size:20 final size:20
Alignment explanation
Indices: 1617--1662 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1607 CTCCTTTTTC
*
1617 TTTTTC-TTTTTTTTTTCAT
1 TTTTTCATTTTTATTTTCAT
*
1636 TTTTTCATTTTTATTTTCGT
1 TTTTTCATTTTTATTTTCAT
1656 TTTTTCA
1 TTTTTCA
1663 AGTGAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTCATTTTTATTTTCAT
Found at i:2130 original size:15 final size:15
Alignment explanation
Indices: 2087--2148 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
2077 CCAATAGAGG
* *
2087 TTTTTCTTTTATTTGT
1 TTTTTATTTT-TTTGC
*
2103 TTATTTGTTTTTTTGC
1 TT-TTTATTTTTTTGC
**
2119 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTGC
2134 TTTTTATTTTTTTGC
1 TTTTTATTTTTTTGC
2149 CTCCACTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 23 0.61
16 8 0.21
17 7 0.18
ACGTcount: A:0.08, C:0.05, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTATTTTTTTGC
Found at i:4238 original size:57 final size:57
Alignment explanation
Indices: 4150--4263 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
4140 CATTATAGGC
4150 TCATACGGACTGAGTTCGTTTCAGGGGAATACATTTCCCTATGGCCATGCGGAGATG
1 TCATACGGACTGAGTTCGTTTCAGGGGAATACATTTCCCTATGGCCATGCGGAGATG
4207 TCATACGGACTGAGTTCAG-TTCAGGGGAATACATTTCCCTATGGCCATGCGGAGATG
1 TCATACGGACTGAGTTC-GTTTCAGGGGAATACATTTCCCTATGGCCATGCGGAGATG
4264 AAAATCTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 55 0.98
58 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (57 bp):
TCATACGGACTGAGTTCGTTTCAGGGGAATACATTTCCCTATGGCCATGCGGAGATG
Done.