Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1295
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: 2107
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:410 original size:11 final size:11
Alignment explanation
Indices: 372--410 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
362 ACGTGAAAAC
*
372 AATGTTTTTAA
1 AATGTTTTCAA
*
383 AATGTGTTCAA
1 AATGTTTTCAA
394 AATGTTTTCAA
1 AATGTTTTCAA
*
405 ATTGTT
1 AATGTT
411 CTACTATCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (11 bp):
AATGTTTTCAA
Found at i:767 original size:197 final size:195
Alignment explanation
Indices: 432--832 Score: 705
Period size: 197 Copynumber: 2.0 Consensus size: 195
422 TTTTAAAAAC
* * *
432 GTTTTCAACACATCTCCAACATGTTCTCAGATACTTCTAATTTCGAAGTGTTTGGTGAAATGTTT
1 GTTTTCAACACATCTCCAACACGTTCTCAGAAACTTCCAATTTCGAAGTGTTTGGTGAAATGTTT
*
497 TGGAAATATTCTGAAAATGTTTCGAATGAATCTACAGCTTGTTTCAAGCAACTTCTCAAAGTGCT
66 TCGAAATATTCTGAAAATGTTTCGAATGAATCTACAGC-TGTTTCAAGCAACTTCTCAAAGTGCT
*
562 GTCAGATACTTTTCCTGCACGACTCAACAACACCTCCCAGCAACCTATCTGACACATTTTGGATT
130 GTCAGATACTTTTCCTGCACGACTCAACAACACCTCCCAGCAACCTATCTGACACATTTTAGA-T
627 AT
194 AT
629 GTTTTCAACACATCTCCAACACGTTCTCAGAAACTTCCAATTTCGAAGTGTTTGGTGAAATGTTT
1 GTTTTCAACACATCTCCAACACGTTCTCAGAAACTTCCAATTTCGAAGTGTTTGGTGAAATGTTT
*
694 TCGAAATATTTTGAAAATGTTTCGAATGAAAATCTACAGC-GTTTCAAGCAACTTCTCAAAGTGC
66 TCGAAATATTCTGAAAATGTTTCGAATG--AATCTACAGCTGTTTCAAGCAACTTCTCAAAGTGC
758 TGTCAGATACTTTTCCTGCACGACTCAACAACACCTCCCAGCAACCTATCTGACACATTTTAGAT
129 TGTCAGATACTTTTCCTGCACGACTCAACAACACCTCCCAGCAACCTATCTGACACATTTTAGAT
823 AT
194 AT
825 GTTTTCAA
1 GTTTTCAA
833 TTATTAATAA
Statistics
Matches: 196, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
196 11 0.06
197 175 0.89
199 10 0.05
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (195 bp):
GTTTTCAACACATCTCCAACACGTTCTCAGAAACTTCCAATTTCGAAGTGTTTGGTGAAATGTTT
TCGAAATATTCTGAAAATGTTTCGAATGAATCTACAGCTGTTTCAAGCAACTTCTCAAAGTGCTG
TCAGATACTTTTCCTGCACGACTCAACAACACCTCCCAGCAACCTATCTGACACATTTTAGATAT
Done.