Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold888
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: 4654
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.30
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:747 original size:219 final size:219
Alignment explanation
Indices: 360--771 Score: 612
Period size: 219 Copynumber: 1.9 Consensus size: 219
350 CATACTTTGA
* *
360 AAACAATACCAAATGAGTTCAACACATAAACAATAACAAAGCATGTGTTCTGTACCTTCAGAACG
1 AAACAATACCAAATGAGTTCAACAAATAAACAATAACAAAGCATGTGTTCTGTACCTTAAGAACG
* * * *
425 ATGACGAAAACTGAAATGAAAGCAATGAAATGGATTGACCAAAATCTGGAGAAGAAAAACAAAAT
66 ATGAAGAAAACTGAAATGAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAAAAAAACAAAAG
* * * *
490 TTAAAATCAGTTCCTAACAAATTAAACCGCAGACAAAAACAGTAA-TGAACAATAGAAGCAGTAC
131 TTAAAATCAATTCCTAACAAACTAAACCACACACAAAAACAG-AAGTGAACAATAGAAGCAGTAC
554 CAAATTGACTGAAAATAACCATGTC
195 CAAATTGACTGAAAATAACCATGTC
* * *
579 AAACAGTACCAAATGAGTTCCACAAATAAACAGTAACAAAGCATGTGTTCTGTACCTTAAGAACG
1 AAACAATACCAAATGAGTTCAACAAATAAACAATAACAAAGCATGTGTTCTGTACCTTAAGAACG
644 ATGAAGAAAACTGAAATGAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAAAAAAACAAAAG
66 ATGAAGAAAACTGAAATGAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAAAAAAACAAAAG
* ** ** **
709 TTAAACA-CAATTTCTAACACCCTAAACCATTCACAAAAACAGAAGTTCACAATAGAAGCAGTA
131 TTAAA-ATCAATTCCTAACAAACTAAACCACACACAAAAACAGAAGTGAACAATAGAAGCAGTA
772 ACTAACCTTC
Statistics
Matches: 171, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
218 2 0.01
219 168 0.98
220 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (219 bp):
AAACAATACCAAATGAGTTCAACAAATAAACAATAACAAAGCATGTGTTCTGTACCTTAAGAACG
ATGAAGAAAACTGAAATGAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAAAAAAACAAAAG
TTAAAATCAATTCCTAACAAACTAAACCACACACAAAAACAGAAGTGAACAATAGAAGCAGTACC
AAATTGACTGAAAATAACCATGTC
Found at i:3783 original size:114 final size:112
Alignment explanation
Indices: 3629--4108 Score: 479
Period size: 113 Copynumber: 4.2 Consensus size: 112
3619 AAAACGAAAC
* **** *
3629 CGTTTTGGTTAAGATATTTGCGACGCTT-TTTGTAATACGCCGCTAAT-ACTGTTC-TTTAGCGG
1 CGTTTTGGTTAAGATATTTGCGGCGCTTACAAATAA-ACGCCACTAATGA-TGTTCTTTTA-CGG
* ** * **
3691 CGTTTTATCGTAAATGCCACTAATTCTAATATACCTCAA-AGCCAAACGCTG
63 AGTTTT-TAATAAACGCCACTAAAACTAATATACCTCAAGA-CCAAACGCTG
*
3742 CGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG
1 CGTTTTGGTTAAGATA-TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG
* * * *
3807 TTTTTAATAAGCGCCACTAAAACTAATCTACCTCAGGACCAAACGGTG
65 TTTTTAATAAACGCCACTAAAACTAATATACCTCAAGACCAAACGCTG
* * **** *
3855 CGTTTTGGTTAAGATATTTGTGACGCTT-TTTGTAATACGCCGCTAAT-ACTGTTC-TTTAGCGG
1 CGTTTTGGTTAAGATATTTGCGGCGCTTACAAATAA-ACGCCACTAATGA-TGTTCTTTTA-CGG
* ** ** * *
3917 CGTTTTATCGTAAACGCCACTAATTCTAATATATCTCAAAACCAAACGCTG
63 AGTTTT-TAATAAACGCCACTAAAACTAATATACCTCAAGACCAAACGCTG
* *
3968 CGTTTTGGTTAAGGTATTTTGCGGCACTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG
1 CGTTTTGGTTAAGATA-TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG
* * * *
4033 TTTTTAATAAGCGCCACTAAAACTAATCTACCTCAGGACCAAACGGTG
65 TTTTTAATAAACGCCACTAAAACTAATATACCTCAAGACCAAACGCTG
4081 CGTTTTGGTTAAGATATTTGCGGCGCTT
1 CGTTTTGGTTAAGATATTTGCGGCGCTT
4109 TTTGTAATAC
Statistics
Matches: 296, Mismatches: 58, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
111 8 0.03
112 44 0.15
113 161 0.54
114 67 0.23
115 16 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (112 bp):
CGTTTTGGTTAAGATATTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGT
TTTTAATAAACGCCACTAAAACTAATATACCTCAAGACCAAACGCTG
Found at i:3849 original size:113 final size:112
Alignment explanation
Indices: 3706--4108 Score: 481
Period size: 113 Copynumber: 3.6 Consensus size: 112
3696 TATCGTAAAT
** *
3706 GCCACTAATTCTAATATACCTCA-AAGCCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCT
1 GCCACTAAAACTAATATACCTCAGAA-CCAAACGCTGCGTTTTGGTTAAGATA-TTTGCGGCGCT
3770 TACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGC
64 TACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGC
* * * * *
3819 GCCACTAAAACTAATCTACCTCAGGACCAAACGGTGCGTTTTGGTTAAGATATTTGTGACGCTT-
1 GCCACTAAAACTAATATACCTCAGAACCAAACGCTGCGTTTTGGTTAAGATATTTGCGGCGCTTA
**** * * ** *
3883 TTTGTAATACGCCGCTAAT-ACTGTTC-TTTAGCGGCGTTTTATCGTAAAC
66 CAAATAA-ACGCCACTAATGA-TGTTCTTTTA-CGGAGTTTT-TAATAAGC
** * * * *
3932 GCCACTAATTCTAATATATCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCACTT
1 GCCACTAAAACTAATATACCTCAGAACCAAACGCTGCGTTTTGGTTAAGATA-TTTGCGGCGCTT
3997 ACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGC
65 ACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGC
* * *
4045 GCCACTAAAACTAATCTACCTCAGGACCAAACGGTGCGTTTTGGTTAAGATATTTGCGGCGCTT
1 GCCACTAAAACTAATATACCTCAGAACCAAACGCTGCGTTTTGGTTAAGATATTTGCGGCGCTT
4109 TTTGTAATAC
Statistics
Matches: 235, Mismatches: 46, Indels: 19
0.78 0.15 0.06
Matches are distributed among these distances:
111 8 0.03
112 44 0.19
113 142 0.60
114 33 0.14
115 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (112 bp):
GCCACTAAAACTAATATACCTCAGAACCAAACGCTGCGTTTTGGTTAAGATATTTGCGGCGCTTA
CAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGC
Found at i:4023 original size:226 final size:226
Alignment explanation
Indices: 3629--4120 Score: 930
Period size: 226 Copynumber: 2.2 Consensus size: 226
3619 AAAACGAAAC
3629 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
* *
3694 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAGCCAAACGCTGCGTTTTGGTTAAGGTAT
66 TTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
*
3759 TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCAC
131 TTTGCGGCACTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCAC
3824 TAAAACTAATCTACCTCAGGACCAAACGGTG
196 TAAAACTAATCTACCTCAGGACCAAACGGTG
*
3855 CGTTTTGGTTAAGATATTTGTGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
*
3920 TTTATCGTAAACGCCACTAATTCTAATATATCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
66 TTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
3985 TTTGCGGCACTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCAC
131 TTTGCGGCACTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCAC
4050 TAAAACTAATCTACCTCAGGACCAAACGGTG
196 TAAAACTAATCTACCTCAGGACCAAACGGTG
*
4081 CGTTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGC
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGC
4121 NNNNNNNNNN
Statistics
Matches: 259, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
226 259 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (226 bp):
CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
TTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
TTTGCGGCACTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCAC
TAAAACTAATCTACCTCAGGACCAAACGGTG
Done.