Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2207
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: 33464
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Found at i:1823 original size:31 final size:33
Alignment explanation
Indices: 1787--1854 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
1777 CTTAAATAAT
**
1787 AATATTATA-TTT-TTATATTATTTTTATTAAA
1 AATATTATATTTTATTATATTATAATTATTAAA
1818 AATATTATATTTTAATTATATTATAATTATTAAA
1 AATATTATATTTT-ATTATATTATAATTATTAAA
1852 AAT
1 AAT
1855 TATTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 9 0.28
32 3 0.09
34 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATATTATATTTTATTATATTATAATTATTAAA
Found at i:1848 original size:34 final size:33
Alignment explanation
Indices: 1787--1866 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 33
1777 CTTAAATAAT
**
1787 AATATTATA-TTT--TTATATTATTTTTATTAAA
1 AATATTATATTTTAATTATATTATAATTATT-AA
1818 AATATTATATTTTAATTATATTATAATTATTAA
1 AATATTATATTTTAATTATATTATAATTATTAA
1851 AA-ATTAT-TTTTAATTA
1 AATATTATATTTTAATTA
1867 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
31 18 0.41
32 8 0.18
33 4 0.09
34 14 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
AATATTATATTTTAATTATATTATAATTATTAA
Found at i:1869 original size:16 final size:16
Alignment explanation
Indices: 1803--1870 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
1793 ATATTTTTAT
1803 ATTATTTTTATTAAAA
1 ATTATTTTTATTAAAA
*
1819 A-TATTATATT-TTAATTAT
1 ATTATT-T-TTATTAA--AA
**
1837 ATTATAATTATTAAAA
1 ATTATTTTTATTAAAA
1853 ATTATTTTTAATTAAAA
1 ATTATTTTT-ATTAAAA
1870 A
1 A
1871 AATAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
15 4 0.10
16 14 0.36
17 12 0.31
18 6 0.15
19 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATTTTTATTAAAA
Found at i:3017 original size:32 final size:32
Alignment explanation
Indices: 2955--3046 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
2945 TCAATTCAAT
*
2955 ATTACGTCTCTTAT-AAAA-AATATAAAGAAG
1 ATTACGTCTCTTATAAAAATAAAATAAAGAAG
*
2985 ATTATGTCTCTTATAAAAATAAAATAAAGAAG
1 ATTACGTCTCTTATAAAAATAAAATAAAGAAG
3017 ATTACGTCTCTTATAAAAATAAAATAAAGA
1 ATTACGTCTCTTATAAAAATAAAATAAAGA
3047 TTACGTCTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 13 0.23
31 4 0.07
32 40 0.70
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (32 bp):
ATTACGTCTCTTATAAAAATAAAATAAAGAAG
Found at i:6350 original size:17 final size:18
Alignment explanation
Indices: 6323--6356 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6313 AATAAAAAAT
6323 TTTAATAAAAAAATAAAC
1 TTTAATAAAAAAATAAAC
6341 TTTAAT-AAAAAATAAA
1 TTTAATAAAAAAATAAA
6357 TTAAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTAATAAAAAAATAAAC
Found at i:6436 original size:10 final size:10
Alignment explanation
Indices: 6421--6488 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 10
6411 TTATTTACTT
6421 ATAAATATT-A
1 ATAAAT-TTAA
6431 ATAAATTTAA
1 ATAAATTTAA
6441 ATAAAATTTAAA
1 AT-AAATTT-AA
*
6453 ATTTATATGTTAA
1 A--TAAAT-TTAA
6466 ATTAAATTTAA
1 A-TAAATTTAA
6477 ATAAA-TTAA
1 ATAAATTTAA
6486 ATA
1 ATA
6489 TAAATAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
9 9 0.18
10 13 0.26
11 11 0.22
12 8 0.16
13 6 0.12
14 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
ATAAATTTAA
Found at i:6483 original size:15 final size:15
Alignment explanation
Indices: 6463--6495 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6453 ATTTATATGT
*
6463 TAAATTAAATTTAAA
1 TAAATTAAATATAAA
6478 TAAATTAAATATAAA
1 TAAATTAAATATAAA
6493 TAA
1 TAA
6496 TTTTATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATTAAATATAAA
Found at i:7084 original size:3 final size:3
Alignment explanation
Indices: 7071--7105 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
7061 AAAGCTTGAA
*
7071 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7106 AGGTAGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7292 original size:17 final size:17
Alignment explanation
Indices: 7266--7298 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7256 AAACATAATT
7266 AATAAATATAATATAAA
1 AATAAATATAATATAAA
*
7283 AATAATTATAATATAA
1 AATAAATATAATATAA
7299 TATAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATATAATATAAA
Found at i:7311 original size:24 final size:24
Alignment explanation
Indices: 7248--7304 Score: 82
Period size: 22 Copynumber: 2.4 Consensus size: 24
7238 TCTAGAATTA
*
7248 ATAATATTAAACATAATTAATAAAT
1 ATAATA-TAAAAATAATTAATAAAT
7273 ATAATATAAAAATAATT-AT-AAT
1 ATAATATAAAAATAATTAATAAAT
7295 ATAATATAAA
1 ATAATATAAA
7305 TTTATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 13 0.42
23 2 0.06
24 10 0.32
25 6 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATATAAAAATAATTAATAAAT
Found at i:7373 original size:24 final size:23
Alignment explanation
Indices: 7346--7416 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
7336 AATTATTTAT
7346 ATATTAAATGTATATAAATATAAA
1 ATATTAAAT-TATATAAATATAAA
** * *
7370 ATATTTTATT-TATAATTATAAT
1 ATATTAAATTATATAAATATAAA
* *
7392 ATAATAAAATATATAAATTATAAA
1 ATATTAAATTATATAAA-TATAAA
7416 A
1 A
7417 CCTTTCGTTG
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 16 0.46
23 6 0.17
24 13 0.37
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
ATATTAAATTATATAAATATAAA
Found at i:7379 original size:37 final size:38
Alignment explanation
Indices: 7338--7409 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
7328 ATAATAAAAA
*
7338 TTATTTATATATTA-AATGT-ATATAAATATA-AAATATT
1 TTATTTATA-ATTATAATATAATA-AAATATATAAATATT
7375 TTATTTATAATTATAATATAATAAAATATATAAAT
1 TTATTTATAATTATAATATAATAAAATATATAAAT
7410 TATAAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 4 0.13
37 20 0.65
38 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (38 bp):
TTATTTATAATTATAATATAATAAAATATATAAATATT
Found at i:7659 original size:26 final size:26
Alignment explanation
Indices: 7607--7659 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
7597 AGTTCAGTTT
**
7607 TTTTAATTAATAAAAATATTTTTAAA
1 TTTTAATTAATAAAAATATTTAAAAA
7633 TTTTAATT-ATAAAAATATATTAAAAA
1 TTTTAATTAATAAAAATAT-TTAAAAA
7659 T
1 T
7660 ATAAATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTTAATTAATAAAAATATTTAAAAA
Found at i:10216 original size:2 final size:2
Alignment explanation
Indices: 10211--10248 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
10201 ATATATATAT
*
10211 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10249 TCCATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11364 original size:19 final size:20
Alignment explanation
Indices: 11342--11395 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
11332 AAAGTTGTAA
*
11342 TACATAAATTTATTAT-ATT
1 TACATAAATTTATTATAAGT
*
11361 TACATAAAATT-TTATAAGT
1 TACATAAATTTATTATAAGT
* *
11380 TAAATAAATATATTAT
1 TACATAAATTTATTAT
11396 CAAAAGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
TACATAAATTTATTATAAGT
Found at i:11529 original size:21 final size:20
Alignment explanation
Indices: 11504--11548 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11494 AAAATATTTT
11504 TTATCAAAAT-AATATAAAACA
1 TTATC-AAATGAATA-AAAACA
*
11525 TTATCAATTGAATAAAAACA
1 TTATCAAATGAATAAAAACA
11545 TTAT
1 TTAT
11549 TAATTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (20 bp):
TTATCAAATGAATAAAAACA
Found at i:11544 original size:20 final size:21
Alignment explanation
Indices: 11514--11562 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
11504 TTATCAAAAT
11514 AATATAAAACATTATCAATTG
1 AATATAAAACATTATCAATTG
*
11535 AATA-AAAACATTATTAATT-
1 AATATAAAACATTATCAATTG
11554 -ATATAAAAC
1 AATATAAAAC
11563 GAAATCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 14 0.54
21 4 0.15
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (21 bp):
AATATAAAACATTATCAATTG
Found at i:11740 original size:57 final size:57
Alignment explanation
Indices: 11672--11805 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 57
11662 AGTTACATTT
11672 AAACATTACCAATTATATAAAATATT-T-TTGAACAATAATTTTTATCAAAATTACATA
1 AAACATTACCAATTATATAAAATATTATCTT-AA-AATAATTTTTATCAAAATTACATA
* * * ** *
11729 ATACATTACCAATTACATAAAAATATTATCTTTAGTTAATTTTTATCAAAATTACGTA
1 AAACATTACCAATTATAT-AAAATATTATCTTAAAATAATTTTTATCAAAATTACATA
11787 AAACATTACCAATTATATA
1 AAACATTACCAATTATATA
11806 TAAGTTGATA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 17 0.26
58 45 0.68
59 2 0.03
60 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (57 bp):
AAACATTACCAATTATATAAAATATTATCTTAAAATAATTTTTATCAAAATTACATA
Found at i:12140 original size:14 final size:15
Alignment explanation
Indices: 12121--12153 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12111 TATTAATTTT
12121 TAAAAA-TATTTTAA
1 TAAAAATTATTTTAA
12135 TAAAAATTATTTTAA
1 TAAAAATTATTTTAA
12150 -AAAA
1 TAAAA
12154 TAAAAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAATTATTTTAA
Found at i:14318 original size:2 final size:2
Alignment explanation
Indices: 14311--14347 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
14301 AATTTTAAGA
14311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14348 CTGTGTGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16121 original size:13 final size:13
Alignment explanation
Indices: 16075--16124 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
16065 AAAAATATAT
16075 AAATATTAATTT-
1 AAATATTAATTTA
*
16087 AAAT-TTATTTTA
1 AAATATTAATTTA
*
16099 AAATAATAATTTA
1 AAATATTAATTTA
*
16112 AAATTTTAATTTA
1 AAATATTAATTTA
16125 TCGAATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 6 0.19
12 8 0.26
13 17 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTAATTTA
Found at i:16655 original size:2 final size:2
Alignment explanation
Indices: 16643--16677 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16633 GTAAAGTGAG
16643 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16678 CTCCTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18038 original size:18 final size:18
Alignment explanation
Indices: 17976--18039 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
17966 ATTTATATAA
*
17976 TATAAATTATTA-ATATAT
1 TATAAATTATTATA-AAAT
*
17994 TA-AAATTAATTTTAAAA-
1 TATAAATT-ATTATAAAAT
*
18011 TAAAATATTATTATAAAAT
1 TATAA-ATTATTATAAAAT
18030 TATAAATTAT
1 TATAAATTAT
18040 AATATTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 7 0.19
18 22 0.59
19 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAATTATTATAAAAT
Found at i:18051 original size:33 final size:34
Alignment explanation
Indices: 18014--18089 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 34
18004 TTTAAAATAA
* *
18014 AATATTATTATAAAATTATAAAT-TA-TAATAT-TT
1 AATATT-TTATAAAA-TAAAAATATATTAATATATC
18047 AATATTTTAATAAAATAAAAATATATTAATATATC
1 AATATTTT-ATAAAATAAAAATATATTAATATATC
18082 AATATTTT
1 AATATTTT
18090 TATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
32 8 0.22
33 14 0.38
34 6 0.16
35 9 0.24
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AATATTTTATAAAATAAAAATATATTAATATATC
Found at i:20623 original size:23 final size:24
Alignment explanation
Indices: 20597--20642 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20587 TATTATAATT
* *
20597 TTTTTA-ACATATAAAGTAAAAAC
1 TTTTTACACAAATAAAATAAAAAC
20620 TTTTTACACAAATAAAATAAAAA
1 TTTTTACACAAATAAAATAAAAA
20643 GATGTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTTTACACAAATAAAATAAAAAC
Found at i:21840 original size:18 final size:17
Alignment explanation
Indices: 21817--21858 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
21807 AATAAATTGG
21817 ATATTTATATATTTTT-TA
1 ATATTTA-A-ATTTTTATA
21835 ATATTTAAATTTTTATA
1 ATATTTAAATTTTTATA
21852 AGTATTT
1 A-TATTT
21859 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATTTAAATTTTTATA
Found at i:21900 original size:25 final size:25
Alignment explanation
Indices: 21875--21933 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
21865 TTAAATTTAT
*
21875 TTATTATTT--ATATTAAATTATATA
1 TTATTATTTGAAT-TTAAATTAAATA
21899 TTATTATTTGAATTTAAATTAAATA
1 TTATTATTTGAATTTAAATTAAATA
*
21924 ATATTATTTG
1 TTATTATTTG
21934 TTAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 9 0.29
25 20 0.65
26 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TTATTATTTGAATTTAAATTAAATA
Found at i:22087 original size:13 final size:14
Alignment explanation
Indices: 22060--22107 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
22050 TTATCCATAA
22060 AAATAATATAAATTT
1 AAATAATA-AAATTT
22075 AAATAA-AAAATTT
1 AAATAATAAAATTT
*
22088 AAAAAATAAATATTT
1 AAATAATAAA-ATTT
22103 AAATA
1 AAATA
22108 TTTATATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 11 0.38
14 4 0.14
15 14 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAATAAAATTT
Found at i:22205 original size:16 final size:17
Alignment explanation
Indices: 22173--22205 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22163 CTAAATTCAC
22173 TTTATAAAATTAAAATTT
1 TTTATAAAA-TAAAATTT
22191 TTTATAAAA-AAAATT
1 TTTATAAAATAAAATT
22206 AAATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAAAATAAAATTT
Found at i:23330 original size:2 final size:2
Alignment explanation
Indices: 23323--23351 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23313 AATACCTATG
23323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23352 TTAGATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25999 original size:17 final size:17
Alignment explanation
Indices: 25974--26013 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
25964 AACGGTCCTA
* *
25974 CTGGCCTGAATAGTTAT
1 CTGGGCTGAATACTTAT
25991 CTGGGCTGAATACTTAT
1 CTGGGCTGAATACTTAT
26008 CTGGGC
1 CTGGGC
26014 ATGAGCTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (17 bp):
CTGGGCTGAATACTTAT
Found at i:27110 original size:6 final size:6
Alignment explanation
Indices: 27065--27266 Score: 53
Period size: 6 Copynumber: 33.0 Consensus size: 6
27055 TTTATGGTTT
* * *
27065 TATTTG TATTAA TAATTA TATTTAA TAATTTA TA-TTA TATTTA TATTTAAAA
1 TATTTA TATTTA TATTTA TATTT-A T-ATTTA TATTTA TATTTA TATTT---A
* * * * ***
27117 TATTT- TATATA AATTT- TA-TAA TATTAA TAATTTA TA-TTA TAAAAA
1 TATTTA TATTTA TATTTA TATTTA TATTTA T-ATTTA TATTTA TATTTA
* * * * *
27162 T-TTTAA TATATA TAATTA TATTTA TATTTA TATTAA TTTTTA AATGTTA
1 TATTT-A TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT-TTA
** * *
27211 TTATGTT- T-TAAA TTTTTA TATTATCA TATTTA TATTATA TAATTA T-TTTA
1 -TAT-TTA TATTTA TATTTA TATT-T-A TATTTA TATT-TA TATTTA TATTTA
27261 TATTTA
1 TATTTA
27267 AAATGATTAA
Statistics
Matches: 142, Mismatches: 33, Indels: 42
0.65 0.15 0.19
Matches are distributed among these distances:
4 1 0.01
5 23 0.16
6 77 0.54
7 21 0.15
8 14 0.10
9 6 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (6 bp):
TATTTA
Found at i:27125 original size:27 final size:26
Alignment explanation
Indices: 27066--27155 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 26
27056 TTATGGTTTT
*
27066 ATTTGTATTAATAATTATATTTAATA
1 ATTTATATTAATAATTATATTTAATA
*
27092 ATTTATATT-ATATTTATATTTAAAATA
1 ATTTATATTAATAATTATATTT--AATA
* * *
27119 TTTTATATAAAT-TTTATAATATTAATA
1 ATTTATATTAATAATTAT-AT-TTAATA
27146 ATTTATATTA
1 ATTTATATTA
27156 TAAAAATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 11 0.21
26 8 0.15
27 28 0.53
28 4 0.08
29 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
ATTTATATTAATAATTATATTTAATA
Found at i:27152 original size:16 final size:16
Alignment explanation
Indices: 27071--27170 Score: 59
Period size: 17 Copynumber: 6.2 Consensus size: 16
27061 GTTTTATTTG
27071 TATTAATAA-TTAT-A
1 TATTAATAATTTATAA
27085 T-TTAATAATTTATATTA
1 TATTAATAATTTATA--A
* *
27102 TATTTAT-ATTTAAAA
1 TATTAATAATTTATAA
27117 TATTTTATATAAATTTTATAA
1 TA--TTA-AT-AA-TTTATAA
*
27138 TATTAATAATTTATAT
1 TATTAATAATTTATAA
*
27154 TA-TAAAAATTT-TAA
1 TATTAATAATTTATAA
27168 TAT
1 TAT
27171 ATATAATTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
13 7 0.10
14 9 0.13
15 11 0.16
16 8 0.12
17 12 0.18
18 8 0.12
19 3 0.04
20 1 0.01
21 8 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAATAATTTATAA
Found at i:27187 original size:30 final size:31
Alignment explanation
Indices: 27120--27187 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
27110 TTTAAAATAT
*
27120 TTTATATAAATTTTATAATATTAATAATTTA
1 TTTATAAAAATTTTATAATATTAATAATTTA
27151 TATTATAAAAA-TTT-TAATA-TATATAATTATA
1 T-TTATAAAAATTTTATAATATTA-ATAATT-TA
27182 TTTATA
1 TTTATA
27188 TTTATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
29 2 0.06
30 16 0.48
31 7 0.21
32 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTATAAAAATTTTATAATATTAATAATTTA
Found at i:27195 original size:54 final size:55
Alignment explanation
Indices: 27079--27198 Score: 129
Period size: 54 Copynumber: 2.2 Consensus size: 55
27069 TGTATTAATA
*** * * *
27079 ATTATATTTAATAATTTATATTATATTTATATTTAAAATATTTTATATAAATTT-T
1 ATTATA-TTAATAATTTATATTATAAAAATATTTAAAATATATAATATATATTTAT
* *
27134 ATAATATTAATAATTTATATTATAAAAAT-TTTAATATATATAAT-TATATTTAT
1 ATTATATTAATAATTTATATTATAAAAATATTTAAAATATATAATATATATTTAT
27187 ATTTATATTAAT
1 A-TTATATTAAT
27199 TTTTAAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
52 6 0.11
53 14 0.26
54 29 0.54
55 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (55 bp):
ATTATATTAATAATTTATATTATAAAAATATTTAAAATATATAATATATATTTAT
Found at i:27203 original size:12 final size:12
Alignment explanation
Indices: 27065--27195 Score: 61
Period size: 12 Copynumber: 10.3 Consensus size: 12
27055 TTTATGGTTT
*
27065 TATTTGTATTAA
1 TATTTATATTAA
*
27077 TAATTATATTTAA
1 TATTTATA-TTAA
27090 TAATTTATATT-A
1 T-ATTTATATTAA
27102 TATTTATATTTAAAA
1 TATTTATA-TT--AA
*
27117 TATTTTATATAAA
1 TA-TTTATATTAA
*
27130 TTTTATAATATTAA
1 TATT-T-ATATTAA
27144 TAATTTATATT-A
1 T-ATTTATATTAA
*** *
27156 TAAAAATTTTAA
1 TATTTATATTAA
*
27168 TATATATAATT-A
1 TATTTAT-ATTAA
*
27180 TATTTATATTTA
1 TATTTATATTAA
27192 TATT
1 TATT
27196 AATTTTTAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
11 15 0.16
12 32 0.35
13 18 0.20
14 14 0.15
15 6 0.07
16 6 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:27244 original size:14 final size:13
Alignment explanation
Indices: 27225--27266 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
27215 GTTTTAAATT
27225 TTTATATTATCATA
1 TTTATATTAT-ATA
27239 TTTATATTATATA
1 TTTATATTATATA
*
27252 ATTAT-TT-TATA
1 TTTATATTATATA
27263 TTTA
1 TTTA
27267 AAATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 7 0.27
12 2 0.08
13 7 0.27
14 10 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:27358 original size:20 final size:20
Alignment explanation
Indices: 27335--27373 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27325 ACTCTTTGCT
*
27335 ACATTTAATAAAGATTCTGG
1 ACATTTAATAAAGAGTCTGG
27355 ACATTTAATAAAGAGTCTG
1 ACATTTAATAAAGAGTCTG
27374 TACAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
ACATTTAATAAAGAGTCTGG
Found at i:27383 original size:20 final size:20
Alignment explanation
Indices: 27340--27385 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
27330 TTGCTACATT
* **
27340 TAATAAAGATTCTGGACATT
1 TAATAAAGAGTCTGGACAAA
*
27360 TAATAAAGAGTCTGTACAAA
1 TAATAAAGAGTCTGGACAAA
27380 TAATAA
1 TAATAA
27386 TTTTTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (20 bp):
TAATAAAGAGTCTGGACAAA
Found at i:27715 original size:24 final size:24
Alignment explanation
Indices: 27665--27726 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
27655 GATGACATAA
* * *
27665 TTTTATTATTTTATATTTTTAAAT
1 TTTTATTATTTTAAATATATAAAT
*
27689 TTTTATTATTTTAAATATAT-ATT
1 TTTTATTATTTTAAATATATAAAT
*
27712 TTTTGACTATTTTAA
1 TTTT-ATTATTTTAA
27727 TTTTTTAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTATTATTTTAAATATATAAAT
Found at i:29843 original size:15 final size:14
Alignment explanation
Indices: 29821--29853 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29811 CTTCTTTTTA
29821 TTTT-TTAAAATAAT
1 TTTTATTAAAAT-AT
29835 TTTTATTAAAATAT
1 TTTTATTAAAATAT
29849 TTTTA
1 TTTTA
29854 AAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTATTAAAATAT
Found at i:29867 original size:27 final size:27
Alignment explanation
Indices: 29819--29870 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29809 TTCTTCTTTT
* *
29819 TATTTTTTAAAATAATTTTTATTAAAA
1 TATTTTTAAAAATAATTATTATTAAAA
29846 TATTTTTAAAAATTAA-TATTATTAA
1 TATTTTTAAAAA-TAATTATTATTAA
29871 TTATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTTTTAAAAATAATTATTATTAAAA
Found at i:30281 original size:58 final size:57
Alignment explanation
Indices: 30169--30300 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 57
30159 TATCAACTTA
*
30169 TATATAATTGGTAATGTTTTACGTAATTTTGATAAAAATTAACTAAAGATAATATTTT
1 TATATAATTGGTAATGTATTACGTAATTTTGATAAAAATTAACTAAAGATAATA-TTT
* * ** *
30227 TATGTAATTGGTAATGTATTATGTAATTTTGATAAAAATTATTGTTCAA-A-AATATTT
1 TATATAATTGGTAATGTATTACGTAATTTTGATAAAAATTA--ACTAAAGATAATATTT
30284 TATATAATTGGTAATGT
1 TATATAATTGGTAATGT
30301 TTAAATGTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
57 19 0.29
58 42 0.65
59 1 0.02
60 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (57 bp):
TATATAATTGGTAATGTATTACGTAATTTTGATAAAAATTAACTAAAGATAATATTT
Found at i:30438 original size:20 final size:20
Alignment explanation
Indices: 30412--30459 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
30402 TAAAGATTTC
30412 GTTTTATAT-AATTAATAAT
1 GTTTTATATCAATTAATAAT
*
30431 GTTTT-TATTCAATTGATAAT
1 GTTTTATA-TCAATTAATAAT
30451 GTTTTATAT
1 GTTTTATAT
30460 TATTTTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 15 0.60
21 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
GTTTTATATCAATTAATAAT
Found at i:30629 original size:19 final size:20
Alignment explanation
Indices: 30580--30633 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
30570 TTGTCTTTTG
* * *
30580 ATAATATATTTATTTAACTT
1 ATAATAAATTTATGTAACAT
*
30600 ATAA-AATTTTATGTAA-AT
1 ATAATAAATTTATGTAACAT
30618 ATAATAAATTTATGTA
1 ATAATAAATTTATGTA
30634 TTACAACTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
ATAATAAATTTATGTAACAT
Found at i:31735 original size:2 final size:2
Alignment explanation
Indices: 31730--31769 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
31720 TATATATGGA
*
31730 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31770 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Done.