Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold995
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: 3486
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.28
Warning! 131 characters in sequence are not A, C, G, or T
Found at i:3213 original size:339 final size:338
Alignment explanation
Indices: 2534--3486 Score: 1031
Period size: 339 Copynumber: 2.8 Consensus size: 338
2524 CAAGCGGACT
* * * * * * *
2534 AGCGGGTCAATACCAAGCGAGCTTACTTTG-TTCCGACCCGATCGGGGAACTATCTATTTTGACG
1 AGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCCG-CCCGATCGGCGAACTTTCGATTTTGACG
* * * *
2598 CTAAAAATTTAGTCCAAGTAA-TCCTAGTCGATTTTCCTCGATTTGGGACTGAGAAAAAAATGTC
65 CTAAAAATTTAGTCCATGTAACCCCT-GTCGATTTTACTCGATTTGGGACTGAGAAAAAAATTTC
* * * *
2662 GAGA-TACAGTCGCATCCTACGCATTTTG-AGGCGTAGAATCAATTCCGCACGGTCCCGA--CTC
129 GAGATTTCAGTCGCATCCTACGTA-GTTGAAGGCGTAGAATCGATTCCGCACGGT-CCGACTCTC
* * * * *
2723 --AGAAACAGTCGCTGAACGAAACGCTCCCGAAACAG--TCAGAAACTGGTCAAAAACCAGCTTT
192 GGCGAGAC-TTC-CTG-A-G---C-CT--AGAAACAGAAT-A-AAACTGGTCAAAAACGAGCTTT
*
2784 TCAGACCGATTTTTTACTCTTTCTCTAGAGCGTTTTCAGCGGAAAGCTCGAAGCGAGGGACTCGC
245 TCAGACCAATTTTTTACTCTTTCTCTAGAGCGTTTTCAGCGGAAAGCTCGAAGCGAGGGACTCGC
2849 GGAGCTTTACCGAATGGAAAATCGCACTC
310 GGAGCTTTACCGAATGGAAAATCGCACTC
* * * *
2878 AGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCTGCCCGATCAGCGAATTTTCGATTTTGATGC
1 AGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCCGCCCGATCGGCGAACTTTCGATTTTGACGC
* ** *
2943 TAAAAATTTGGTCCATGTAACCCCTGTCGATTTTTTTCGATTTGGGACTGAGAAAAAAATTTCAA
66 TAAAAATTTAGTCCATGTAACCCCTGTCGATTTTACTCGATTTGGGACTGAGAAAAAAATTTCGA
3008 GATTTCAGTCGCATCCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTCTCGACTCTCGGC
131 GATTTCAGTCGCATCCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTC-CGACTCTCGGC
*
3073 GAGACTTCCTGAGCCTAGAAACAGAATAAAACTGGTCAAACACGAGCTTTTCAGACCAATTTTTT
195 GAGACTTCCTGAGCCTAGAAACAGAATAAAACTGGTCAAAAACGAGCTTTTCAGACCAATTTTTT
* **
3138 ACTCTTTCTCTGGAGCGTGTTT-AGC-GAATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTTCGA
260 ACTCTTTCTCTAGAGCGT-TTTCAGCGGAA-AGCTCGAAGCGAGGGACTCGCGGAGCTTTACCGA
* *
3201 CTGGAGAATCGCACTC
323 ATGGAAAATCGCACTC
* * * * *
3217 AGCGGGTCATTTCCAAGCGGCATAACTT-GCTTCCGGCTCGATCGGCGAACTTTCGATTTTGACG
1 AGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCC-GCCCGATCGGCGAACTTTCGATTTTGACG
* ** ** *
3281 CTTAAAATTTAGTTAATGTAACGACTGTTC-ATTTTACTCGATTTTGGACTGAGAAAAATAA-TT
65 CTAAAAATTTAGTCCATGTAACCCCTG-TCGATTTTACTCGATTTGGGACTGAGAAAAA-AATTT
* * * * *
3344 CGAGATTTCAGTCGCATTCTACGTTGCTGGAA-GCGTAGAATCGATTCAGCACGGTCCTAACTCT
128 CGAGATTTCAGTCGCATCCTACGTAG-TTGAAGGCGTAGAATCGATTCCGCACGGTCC-GACTCT
* * * * * * *
3408 TGGCGAGGCTTCCTGAACCGAGAAACAGTAA-AAAACTAGTCAAAAACGAGCTTTTCTGACCACT
191 CGGCGAGACTTCCTGAGCCTAGAAACAG-AATAAAACTGGTCAAAAACGAGCTTTTCAGACCAAT
*
3472 TTTTGACTCTTTCTC
255 TTTTTACTCTTTCTC
Statistics
Matches: 523, Mismatches: 67, Indels: 43
0.83 0.11 0.07
Matches are distributed among these distances:
338 8 0.02
339 323 0.62
340 14 0.03
341 3 0.01
342 1 0.00
344 109 0.21
345 52 0.10
346 1 0.00
347 6 0.01
348 2 0.00
349 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (338 bp):
AGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCCGCCCGATCGGCGAACTTTCGATTTTGACGC
TAAAAATTTAGTCCATGTAACCCCTGTCGATTTTACTCGATTTGGGACTGAGAAAAAAATTTCGA
GATTTCAGTCGCATCCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTCCGACTCTCGGCG
AGACTTCCTGAGCCTAGAAACAGAATAAAACTGGTCAAAAACGAGCTTTTCAGACCAATTTTTTA
CTCTTTCTCTAGAGCGTTTTCAGCGGAAAGCTCGAAGCGAGGGACTCGCGGAGCTTTACCGAATG
GAAAATCGCACTC
Done.