Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold585
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: 28300
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.33
Warning! 1001 characters in sequence are not A, C, G, or T
Found at i:10243 original size:18 final size:18
Alignment explanation
Indices: 10220--10262 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
10210 GAATATGTTT
10220 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
10238 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
10256 TTAATTA
1 TTAATTA
10263 CACCTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:11366 original size:28 final size:29
Alignment explanation
Indices: 11330--11395 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
11320 AATTATGAAA
11330 AAAACTTTTC-AAAATAAATAAAAAAACT-T
1 AAAA-TTTTCTAAAA-AAATAAAAAAACTAT
* * *
11359 AAAATTTTCTTAAAAAATAAAATAATTAT
1 AAAATTTTCTAAAAAAATAAAAAAACTAT
11388 AAAATTTT
1 AAAATTTT
11396 TTATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATTTTCTAAAAAAATAAAAAAACTAT
Found at i:12410 original size:9 final size:9
Alignment explanation
Indices: 12384--12413 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12374 TATACTTTTT
*
12384 ATTTTTAAT
1 ATTTTTAAA
12393 ATTTTTAAA
1 ATTTTTAAA
12402 ATTTTTAAA
1 ATTTTTAAA
12411 ATT
1 ATT
12414 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:13335 original size:9 final size:9
Alignment explanation
Indices: 13318--13371 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
13308 TAAAATTAAA
13318 AATATTTTT
1 AATATTTTT
13327 AATAATTTTT
1 AAT-ATTTTT
*
13337 -ATACTTTT
1 AATATTTTT
13345 --TATTTTT
1 AATATTTTT
13352 AATATTTTT
1 AATATTTTT
*
13361 AAAATTTTT
1 AATATTTTT
13370 AA
1 AA
13372 AATTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 5 0.13
9 22 0.56
10 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:13358 original size:24 final size:25
Alignment explanation
Indices: 13320--13370 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
13310 AAATTAAAAA
* *
13320 TATTTTTAATAATTTTTATACTTTT
1 TATTTTTAATAATTTTTAAAATTTT
13345 TATTTTTAAT-ATTTTTAAAATTTT
1 TATTTTTAATAATTTTTAAAATTTT
13369 TA
1 TA
13371 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTTAATAATTTTTAAAATTTT
Found at i:14807 original size:17 final size:19
Alignment explanation
Indices: 14767--14801 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
14757 AAAGTTTTAC
14767 AAGATTGTTTGAATGGTAA
1 AAGATTGTTTGAATGGTAA
14786 AAGATT-TTTG-ATGGTA
1 AAGATTGTTTGAATGGTA
14802 CTAGATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (19 bp):
AAGATTGTTTGAATGGTAA
Found at i:24441 original size:15 final size:15
Alignment explanation
Indices: 24421--24467 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
24411 TGGTTACTAG
*
24421 TAATAATAAGGTTAA
1 TAATAATAAGGATAA
*
24436 TAATAATAATGATAA
1 TAATAATAAGGATAA
* *
24451 TAATAATGATGATAA
1 TAATAATAAGGATAA
24466 TA
1 TA
24468 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATAATAAGGATAA
Found at i:24450 original size:12 final size:12
Alignment explanation
Indices: 24435--24467 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
24425 AATAAGGTTA
24435 ATAATAATAATG
1 ATAATAATAATG
24447 ATAATAATAATG
1 ATAATAATAATG
*
24459 ATGATAATA
1 ATAATAATA
24468 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:26258 original size:46 final size:46
Alignment explanation
Indices: 26190--27089 Score: 1472
Period size: 46 Copynumber: 19.8 Consensus size: 46
26180 AAATCTCTGG
* * *
26190 CTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26236 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26282 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26328 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26374 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26420 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26466 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26512 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26558 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26604 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26650 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26696 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26742 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26788 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
26834 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
*
26880 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGACCTG-----
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
* * * * * *
26921 GTGCGATCTCCTCTACTGTAA-CTTC-AGAGAGATAAGATCCT--TATT
1 CTTCGATCTGCTCCACTATAATC-TCAAG-GAGATAAGAT-CTGAAATT
* * * *
26966 -TT-AATCCGCTCCACTATAA-CTTCAGGGAGATAGGAT-T---ATGT
1 CTTCGATCTGCTCCACTATAATC-TCAAGGAGATAAGATCTGAAAT-T
* * * *
27007 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATT
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
*
27053 CTTCGGTCTGCTCCACTATAATCTCAAGGAGATAAGA
1 CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGA
27090 CCTGGTGCGA
Statistics
Matches: 810, Mismatches: 28, Indels: 32
0.93 0.03 0.04
Matches are distributed among these distances:
40 5 0.01
41 29 0.04
42 4 0.00
43 52 0.06
44 4 0.00
46 714 0.88
47 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (46 bp):
CTTCGATCTGCTCCACTATAATCTCAAGGAGATAAGATCTGAAATT
Found at i:26995 original size:84 final size:84
Alignment explanation
Indices: 26889--27170 Score: 318
Period size: 84 Copynumber: 3.3 Consensus size: 84
26879 TCTTCGATCT
*
26889 GCTCCACTATAATCTCAAGGAGATAAGACCTGGTGCGATCTCCTCTACTGTAACTTCAGAGAGAT
1 GCTCCACTATAATCTCAAGGAGATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGAT
26954 AAGATCCTTATTTTAATCC
66 AAGATCCTTATTTTAATCC
* * ** * * * ** * *
26973 GCTCCACTATAA-CTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGA
1 GCTCCACTATAATC-TCAAGGAGATAAGA-CCTG-GTGCGATCTACTCTACTGTAACTTCAGAGA
* ** *
27037 GATAAGAT-CTGAAATTCTTCGGTCT
63 GATAAGATCCT--TATT-TT-AATCC
27062 GCTCCACTATAATCTCAAGGAGATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGAT
1 GCTCCACTATAATCTCAAGGAGATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGAT
27127 AAGATCCTTATTTTAATCC
66 AAGATCCTTATTTTAATCC
*
27146 GCTCCACTATAA-CTTCAGGGAGATA
1 GCTCCACTATAATC-TCAAGGAGATA
27171 GGATTATGTC
Statistics
Matches: 157, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
83 2 0.01
84 48 0.31
85 6 0.04
86 34 0.22
87 34 0.22
88 6 0.04
89 26 0.17
90 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (84 bp):
GCTCCACTATAATCTCAAGGAGATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGAT
AAGATCCTTATTTTAATCC
Done.