Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1668
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: 2890
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Found at i:638 original size:37 final size:37
Alignment explanation
Indices: 577--724 Score: 228
Period size: 37 Copynumber: 4.0 Consensus size: 37
567 TACGTATGAT
* *
577 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
612 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
649 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
686 TATCTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CA-CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
724 C
1 C
725 GAAAGCTATC
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 57 0.55
38 34 0.33
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:709 original size:75 final size:72
Alignment explanation
Indices: 577--724 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 72
567 TACGTATGAT
*
577 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATAA
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGATAA
642 GTGTAGC
66 GTGTAGC
* * * *
649 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTATCTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCCA-CCTATCACTTTGTCTCTTGATCAGA
714 TAAGTGTAGC
63 TAAGTGTAGC
724 C
1 C
725 GAAAGCTATC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 10 0.15
73 3 0.04
74 21 0.31
75 34 0.50
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (72 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGATAA
GTGTAGC
Found at i:734 original size:45 final size:45
Alignment explanation
Indices: 683--998 Score: 345
Period size: 45 Copynumber: 6.7 Consensus size: 45
673 AGATAAGTGT
* *
683 AGCTAT-CTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAA
1 AGCTATACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCG-A
*
728 AGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGA
1 AGCTAT-ACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
774 AGCTATCACTTATCACTTT-TCACTTGATCAGATAAGTATAGCCGA
1 AGCTAT-ACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
*
819 AGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCC-A
1 AGCTAT-ACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGA
870 AGCTATCACTTATCACTTTGTCACTTGATCAGA-AAGTATAGCCGA
1 AGCTAT-ACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
* **
915 AGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAA
1 AGCTA-TACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGA
* *
967 AGCTACCACTTATCACTTTAT-ACTTGATCAGA
1 AGCTA-TACTTATCACTTTGTCACTTGATCAGA
999 AGTACTCAAT
Statistics
Matches: 243, Mismatches: 10, Indels: 36
0.84 0.03 0.12
Matches are distributed among these distances:
44 9 0.04
45 89 0.37
46 24 0.10
47 38 0.16
49 1 0.00
50 1 0.00
51 35 0.14
52 46 0.19
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
AGCTATACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
Found at i:849 original size:52 final size:51
Alignment explanation
Indices: 777--985 Score: 279
Period size: 52 Copynumber: 4.2 Consensus size: 51
767 TAGCCGAAGC
*
777 TATCACTTATCACTTTTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTT-TCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
829 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCC-AAGCTATCACT
1 TATCACTTT-CACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
880 TATCAC--T---TTGTCACTTGATCAGA-AAGTATAGCCGAAGCTATTACT
1 TATCACTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* ** *
925 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
977 TATCACTTT
1 TATCACTTT
986 ATACTTGATC
Statistics
Matches: 139, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
44 9 0.06
45 32 0.23
47 1 0.01
49 1 0.01
51 34 0.24
52 62 0.45
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
TATCACTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:920 original size:96 final size:97
Alignment explanation
Indices: 689--998 Score: 458
Period size: 96 Copynumber: 3.3 Consensus size: 97
679 GTGTAGCTAT
* *
689 CTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAAGCTATCACTTATCAC--T----TTG
1 CTTATCACTTTGTCACTTGATCAGATAAGTATAGCCG-AAGCTATCACTTATCACTTTCCACTTG
* *
748 TCTCTTGATCAGATAAGTATAGCCGAAGCTATCA
65 TCACTTGATCAGATAAGTGTAGCC-AAGCTATCA
782 CTTATCACTTT-TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGT
1 CTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGT
846 CACTTGATCAGATAAGTGTAGCCAAGCTATCA
66 CACTTGATCAGATAAGTGTAGCCAAGCTATCA
*
878 CTTATCACTTTGTCACTTGATCAGA-AAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGT
1 CTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGT
* *
942 CACTTGATCAGATAAGTGTAGCTAAAGCTACCA
66 CACTTGATCAGATAAGTGTAGC-CAAGCTATCA
*
975 CTTATCACTTTAT-ACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
999 AGTACTCAAT
Statistics
Matches: 201, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
91 17 0.08
92 23 0.11
93 12 0.06
96 91 0.45
97 58 0.29
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (97 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGT
CACTTGATCAGATAAGTGTAGCCAAGCTATCA
Done.