Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4049
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, 358
Length: 598
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Found at i:209 original size:46 final size:46
Alignment explanation
Indices: 159--350 Score: 132
Period size: 46 Copynumber: 4.3 Consensus size: 46
149 ATCTGCTTCG
159 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
* * * * *
205 CTGCCAAATACAGG-GAG-ATAGAGT-TATCGA-CTTCAATGTACTCCA
1 CTGCCAAATACAGGAAAGCA-AGA-TCT-GCAATCTTCAATCTATTCCA
* * * * * * * ** * *
250 CTG--TAGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CG
1 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCT-ATTCCA
293 CTGCCAAATACA-GAAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAA-GCAAGATCTGCAATCTTCAATCTATTCCA
339 CTGCCAAATACA
1 CTGCCAAATACA
351 TGGAGATAGA
Statistics
Matches: 104, Mismatches: 29, Indels: 26
0.65 0.18 0.16
Matches are distributed among these distances:
42 7 0.07
43 16 0.15
44 3 0.03
45 28 0.27
46 50 0.48
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:294 original size:134 final size:135
Alignment explanation
Indices: 54--464 Score: 672
Period size: 134 Copynumber: 3.1 Consensus size: 135
44 ACAATTTTTT
*
54 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
117 TAGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGA
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGA
182 TCTGCA
130 TCTGCA
*
188 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
253 TAGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACA-GAAAGGCAAGA
66 TAGTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAA-GCAAGA
316 TCTGCA
130 TCTGCA
* *
322 ATCTTCAATCTATTCCACTGCCAAATACATGGAGATAGAGTTATTGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
387 TAGTCACAGGGAGGTAAAA-CTGCCAT-TTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTT-GATCTGCTTCGCTGCCAAATACAGGAAAGCAAG
450 ATCTGCA
129 ATCTGCA
*
457 ATCCTCAA
1 ATCTTCAA
465 CCAGCTCTGC
Statistics
Matches: 261, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
133 4 0.02
134 149 0.57
135 51 0.20
136 57 0.22
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (135 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGAT
CTGCA
Found at i:560 original size:86 final size:86
Alignment explanation
Indices: 439--598 Score: 268
Period size: 86 Copynumber: 1.9 Consensus size: 86
429 TGCCAAATAC
439 AGGAAGGCAAGATCTGCAATCCTCAACCAGCTCTGCTAC-AATCGAGAGAGGCAAGGTTTGTCTT
1 AGGAAGGCAAGATCTGCAATCCTCAACCAGCTCTGCTACGAAT-GAGAGAGGCAAGGTTTGTCTT
503 CGATCCGCTTCGCTGTTAATGT
65 CGATCCGCTTCGCTGTTAATGT
** *
525 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACGAATGAGAGAGGCAAGGTTTGTCTTC
1 AGGAAGGCAAGATCTGCAATCCTCAACCAGCTCTGCTACGAATGAGAGAGGCAAGGTTTGTCTTC
*
590 GATCTGCTT
66 GATCCGCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
86 66 0.96
87 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (86 bp):
AGGAAGGCAAGATCTGCAATCCTCAACCAGCTCTGCTACGAATGAGAGAGGCAAGGTTTGTCTTC
GATCCGCTTCGCTGTTAATGT
Done.