Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold612
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: 19093
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:339 original size:6 final size:6
Alignment explanation
Indices: 322--365 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
312 TTACCAGAGG
* * * *
322 CACCTC CTCCTC CGCCTC CTCCTC CACCTC CACCTC CCCCTC CA
1 CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CA
366 GCACCACCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.09, C:0.68, G:0.02, T:0.20
Consensus pattern (6 bp):
CACCTC
Found at i:341 original size:12 final size:12
Alignment explanation
Indices: 322--364 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
312 TTACCAGAGG
322 CACCTCCTCCTC
1 CACCTCCTCCTC
*
334 CGCCTCCTCCTC
1 CACCTCCTCCTC
*
346 CACCTCCACCTC
1 CACCTCCTCCTC
*
358 CCCCTCC
1 CACCTCC
365 AGCACCACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.70, G:0.02, T:0.21
Consensus pattern (12 bp):
CACCTCCTCCTC
Found at i:5157 original size:18 final size:21
Alignment explanation
Indices: 5118--5158 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5108 GATGTAAAAT
5118 AATAATAATGATGACAATGTA
1 AATAATAATGATGACAATGTA
5139 AATAA-AATGAT-ACAA-GTA
1 AATAATAATGATGACAATGTA
5157 AA
1 AA
5159 ACAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 6 0.30
21 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (21 bp):
AATAATAATGATGACAATGTA
Found at i:7066 original size:50 final size:50
Alignment explanation
Indices: 7006--7979 Score: 627
Period size: 50 Copynumber: 19.5 Consensus size: 50
6996 ATCGAGAAAA
* * ** *
7006 TAAGATTCGCCATCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * **
7056 TAAGATTCGCCGTTGTGGCCTCAATCT-TTTAATTGCAAT-GTC-GAGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGC-ATCGTCTG-GGAAG
** * * * *
7105 CGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCAGAGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
** * ** * *
7155 TAAGATTCGCCGTTG--GCTTTGATCTTTTAAATTGTAAT-GTCGGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTG-CATCGTCTGGGAAG
* * ** * *
7203 TGAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGCAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * ** **
7253 TAAGATCCGCTGTTGTAGCTTCAATCCT-TTTAATTGCAAT-GTCAAGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAAT-CTGTTCCATTGC-ATCGTCTGGGAAG
* * * *
7303 TAAGATCCGCTGTTGTAGCTTCAATCTGTTCCATTGCAACGT-TAGGAAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCT-GGGAAG
* * * ** *
7353 TAAGATTCGCCGTTGTGGCATCAATCTTTTGAATTGCAAT-GTCGGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGC-ATCGTCTGGGAAG
* * * ** * *
7403 TGAGATTCACCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * ** **
7453 TAAGATCCGCTGTTGTAGCTTCAATCCT-TTTAATTGCAAT-GTCAAGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAAT-CTGTTCCATTGC-ATCGTCTGGGAAG
* * * * *
7503 TAAGATCCACTGTTGTAGCTTCAATCTGTTCCATTGCAACG-CTAGGAAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCT-GGGAAG
** * * * ** *
7553 TAAGATTTTCCGTTGTGGCCTCAATCTTTTGAATTGCAAT-GTCGGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGC-ATCGTCTGGGAAG
* * ** **
7603 TGAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCTGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * * * * ** * *
7653 TAAGATTTGCCATTGTGGCTTCAATATTTTAAATTGTAAT-GTCAGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTG-CATCGTCTGGGAAG
* * ** * *
7703 TAAGATTCACCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * ** *
7753 TAAGATCCGCTGTTGTAGCTTCAATCAT-TTTAATTGCAAT-GTCAGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATC-TGTTCCATTGC-ATCGTCTGGGAAG
* * * *
7803 TAAGATTCACCGTCGTAGCTTCAATCTGTTCCATTGCAACG-CTAGGAAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCT-GGGAAG
* * * * ** *
7853 TAAGATTCACCGTTGTGGCCTCAATCTTTTGAATTGCAAT-GTCGGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGC-ATCGTCTGGGAAG
* * * ** *
7903 TGAGATTCGCTGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAG
1 TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
* * *
7953 TAAGATTTGCCATTGTGGCTTCAATCT
1 TAAGATTCGCCGTTGTAGCTTCAATCT
7980 TTTGAATTGC
Statistics
Matches: 681, Mismatches: 208, Indels: 70
0.71 0.22 0.07
Matches are distributed among these distances:
48 34 0.05
49 59 0.09
50 569 0.84
51 19 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
TAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCATCGTCTGGGAAG
Found at i:7332 original size:100 final size:100
Alignment explanation
Indices: 6953--7991 Score: 1222
Period size: 100 Copynumber: 10.4 Consensus size: 100
6943 GTCTCGCCGA
* * * * * * * * *
6953 GGAAA-TAAGATTCGCCATTGCGGCTTCAATC-TTT-AGTTGTAATATCGAGAAAATAAGATTCG
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCG
*
7015 CCATCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
66 CCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * * *
7050 GGGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCGAGGAAGCGAGATTCG
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCG
* *
7114 CCGTTGTAGCTTCAATCTGTTCCACTGCATCGCC-
66 CCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* ** * *
7148 AGAGAAGTAAGATTCGCCG-T-TGGCTTTGATCTTTTAAATTGTAATGTCGGGGAAGTGAGATTC
1 GGA-AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
7211 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * * * ** * *
7247 GGCAAGTAAGATCCGCTGTTGTAGCTTCAATCCTTTT-AATTGCAATGTCAAGGAAGTAAGATCC
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAAT-CTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
* * ** * *
7311 GCTGTTGTAGCTTCAATCTGTTCCATTGCAACG-TT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
*
7346 AGGAAAGTAAGATTCGCCGTTGTGGCATCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
1 -GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
*
7411 ACCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * * ** * *
7447 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCCTTTT-AATTGCAATGTCAAGGAAGTAAGATCC
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAAT-CTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
* * * ** *
7511 ACTGTTGTAGCTTCAATCTGTTCCATTGCAACG-CT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
** *
7546 AGGAAAGTAAGATTTTCCGTTGTGGCCTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
1 -GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
*
7611 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * * * * * * * *
7647 GGGAAGTAAGATTTGCCATTGTGGCTTCAATATTTTAAATTGTAATGTCAGGGAAGTAAGATTCA
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCG
7712 CCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
66 CCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * * * *
7747 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCATTTT-AATTGCAATGTCAGGGAAGTAAGATTC
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATC-TTTTGAATTGCAATGTCGGGGAAGTGAGATTC
* ** *
7811 ACCGTCGTAGCTTCAATCTGTTCCATTGCAACG-CT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* *
7846 AGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
1 -GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTC
*
7911 GCTGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
65 GCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
* * *
7947 GGGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTGAATTGCAA
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAA
7992 ACCATGGTTT
Statistics
Matches: 796, Mismatches: 127, Indels: 35
0.83 0.13 0.04
Matches are distributed among these distances:
97 16 0.02
98 95 0.12
99 91 0.11
100 575 0.72
101 19 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCG
CCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT
Done.