Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1483
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: 87939
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:547 original size:19 final size:20
Alignment explanation
Indices: 512--559 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
502 AAACGTTCAG
512 ATATGAATATAAAATATAATA
1 ATATG-ATATAAAATATAATA
*
533 ATATGATAT-AAATATAATG
1 ATATGATATAAAATATAATA
552 ATATGATA
1 ATATGATA
560 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 17 0.65
20 4 0.15
21 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (20 bp):
ATATGATATAAAATATAATA
Found at i:955 original size:20 final size:20
Alignment explanation
Indices: 922--961 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
912 TATTTATATT
922 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
942 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
962 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:1591 original size:2 final size:2
Alignment explanation
Indices: 1584--1655 Score: 78
Period size: 2 Copynumber: 36.5 Consensus size: 2
1574 ATTGAATTGC
* * *
1584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AG AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1625 A- AGT CA- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1656 AATAAGAGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 10
0.85 0.01 0.13
Matches are distributed among these distances:
1 3 0.05
2 60 0.94
4 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1646 original size:39 final size:39
Alignment explanation
Indices: 1592--1670 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 39
1582 GCATATATAT
1592 ATATATATATATATATATATATATATAA-AAGAGAAGTCA
1 ATATATATATATATATATATATATA-AATAAGAGAAGTCA
1631 ATATATATATATATATATATATATAAATAAGAGAAGTCA
1 ATATATATATATATATATATATATAAATAAGAGAAGTCA
1670 A
1 A
1671 AGTCAGGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 2 0.05
39 37 0.95
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (39 bp):
ATATATATATATATATATATATATAAATAAGAGAAGTCA
Found at i:3872 original size:25 final size:26
Alignment explanation
Indices: 3843--3898 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3833 TTAAATTTTT
* **
3843 AAATTATATAAAA-ATAATTTATATA
1 AAATTATATAAAATAAAAAATATATA
3868 AAATTATATAAAATAAAAAATATATA
1 AAATTATATAAAATAAAAAATATATA
3894 AAATT
1 AAATT
3899 TTAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTATATAAAATAAAAAATATATA
Found at i:3891 original size:16 final size:16
Alignment explanation
Indices: 3867--3897 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3857 TAATTTATAT
*
3867 AAAATTATATAAAATA
1 AAAAATATATAAAATA
3883 AAAAATATATAAAAT
1 AAAAATATATAAAAT
3898 TTTAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATATATAAAATA
Found at i:3903 original size:24 final size:25
Alignment explanation
Indices: 3853--3927 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
3843 AAATTATATA
3853 AAAATAATTTATATAAAATTATATAAAAT
1 AAAATAA--TATATAAAATT-T-TAAAAT
*
3882 AAAA-AATATATAAAATTTTAAATTT
1 AAAATAATATATAAAATTTTAAA-AT
3907 AAAATAAT-T-T-AAATTTTAAAA
1 AAAATAATATATAAAATTTTAAAA
3928 AATTTAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 10 0.24
24 5 0.12
25 7 0.17
26 14 0.33
28 2 0.05
29 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATAATATATAAAATTTTAAAAT
Found at i:3917 original size:16 final size:16
Alignment explanation
Indices: 3893--3935 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3883 AAAAATATAT
*
3893 AAAATTTTAAA-TTTA
1 AAAAATTTAAATTTTA
3908 AAATAATTTAAATTTTA
1 AAA-AATTTAAATTTTA
3925 AAAAATTTAAA
1 AAAAATTTAAA
3936 CTCAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 15 0.60
17 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATTTAAATTTTA
Found at i:18350 original size:27 final size:27
Alignment explanation
Indices: 18285--18355 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
18275 AAACAAGCCT
* *
18285 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
18313 CCATTTTTGACAAACACAAA-ATAACTA
1 CCATTTTTGACAAACACAAAGA-AACCA
18340 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
18356 AATGGGTAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:20275 original size:21 final size:22
Alignment explanation
Indices: 20237--20282 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
20227 ATCTGTTGAA
* **
20237 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
20258 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
20280 ACT
1 ACT
20283 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:24078 original size:22 final size:24
Alignment explanation
Indices: 24027--24079 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
24017 TTTTCATGAG
* *
24027 TTAATTATAAAATTAATTTTTATA
1 TTAAATATTAAATTAATTTTTATA
24051 TT--ATATTAAATT-ATTTTTAT-
1 TTAAATATTAAATTAATTTTTATA
24071 TTAAATATT
1 TTAAATATT
24080 TTTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 13 0.52
24 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAAATATTAAATTAATTTTTATA
Found at i:24079 original size:14 final size:16
Alignment explanation
Indices: 24051--24083 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
24041 AATTTTTATA
24051 TTATATTAAATTATTT
1 TTATATTAAATTATTT
24067 TTAT-TTAAA-TATTT
1 TTATATTAAATTATTT
24081 TTA
1 TTA
24084 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTAAATTATTT
Found at i:24095 original size:23 final size:24
Alignment explanation
Indices: 24064--24119 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
24054 TATTAAATTA
24064 TTTTTATTTAAAT-ATT-TTTAAT
1 TTTTTATTTAAATAATTATTTAAT
*
24086 TTTTTAATTTAAATAATTATTTAAA
1 TTTTT-ATTTAAATAATTATTTAAT
*
24111 TTGTTATTT
1 TTTTTATTT
24120 TTATTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 8 0.28
24 7 0.24
25 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTATTTAAATAATTATTTAAT
Found at i:24407 original size:49 final size:46
Alignment explanation
Indices: 24329--24516 Score: 149
Period size: 49 Copynumber: 4.0 Consensus size: 46
24319 TAGACTTAAA
* * * *
24329 ATTTAAATATT-TACATTTTATTTTTATATTTTTATGTATTATGATTAT
1 ATTTAAATATTATATA-TTTATATTAATATTTATAT-TATTAT-ATTAT
24377 ATTTAAAATATTATATATTTATATTAATATTTATATTATTA-ATTTAT
1 ATTT-AAATATTATATATTTATATTAATATTTATATTATTATA-TTAT
* **
24424 ATTATATAAATTTTAATATATTTATA-TCGTATTTATATTATTTATATTAT
1 A-T-T-TAAATATT-ATATATTTATATTAATATTTATATTA-TTATATTAT
*
24474 A-TTATAT-TTATATATTTATATT-ATA-TTATATT-TATATATTAT
1 ATTTAAATATTATATATTTATATTAATATTTATATTAT-TATATTAT
24516 A
1 A
24517 AAATTATATC
Statistics
Matches: 120, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
41 1 0.01
42 9 0.08
43 7 0.06
44 13 0.11
45 3 0.03
46 5 0.04
47 6 0.05
48 10 0.08
49 42 0.35
50 23 0.19
51 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.60
Consensus pattern (46 bp):
ATTTAAATATTATATATTTATATTAATATTTATATTATTATATTAT
Found at i:24428 original size:38 final size:35
Alignment explanation
Indices: 24384--24516 Score: 135
Period size: 38 Copynumber: 3.6 Consensus size: 35
24374 TATATTTAAA
24384 ATATTATATATTTATATTAATATTTATATTATTAATTT
1 ATATTATATATTTATATT-ATATTTATA-TATT-ATTT
* **
24422 ATATTATATAAATTT-TAATATATTTATATCGTATTT
1 ATATTATAT--ATTTATATTATATTTATATATTATTT
*
24458 ATATTATTTATATTATATTATATTTATATATTTATATT
1 ATATTATATAT-TTATATTATATTTATATA-TTAT-TT
24496 ATATTATAT-TTATATATTATA
1 ATATTATATATT-TATATTATA
24517 AAATTATATC
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
34 2 0.03
35 2 0.03
36 26 0.32
37 15 0.19
38 28 0.35
39 3 0.04
40 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
ATATTATATATTTATATTATATTTATATATTATTT
Found at i:24458 original size:11 final size:9
Alignment explanation
Indices: 24387--24515 Score: 89
Period size: 8 Copynumber: 15.0 Consensus size: 9
24377 ATTTAAAATA
24387 TTATA-TAT
1 TTATATTAT
24395 TTATATTA-
1 TTATATTAT
*
24403 ATAT-TTAT
1 TTATATTAT
*
24411 ATTAT-TAAT
1 -TTATATTAT
24420 TTATATTAT
1 TTATATTAT
* *
24429 ATAAATT-T
1 TTATATTAT
*
24437 TAATA-TAT
1 TTATATTAT
24445 TTATATCGTAT
1 TTATAT--TAT
24456 TTATATTAT
1 TTATATTAT
24465 TTATATTAT
1 TTATATTAT
*
24474 AT-TA-TAT
1 TTATATTAT
24481 TTATA-TAT
1 TTATATTAT
24489 TTATATTAT
1 TTATATTAT
24498 ATTATATT-T
1 -TTATATTAT
*
24507 ATATATTAT
1 TTATATTAT
24516 AAAATTATAT
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
7 8 0.08
8 38 0.40
9 34 0.35
10 7 0.07
11 9 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (9 bp):
TTATATTAT
Found at i:24458 original size:36 final size:33
Alignment explanation
Indices: 24418--24499 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 33
24408 TATATTATTA
*
24418 ATTTATATTATATAAATTTTAATATATTTATATCGT
1 ATTTATATTATATAAATTATAATATATTTATA---T
* * *
24454 ATTTATATTATTTATATTATATTATATTTATAT
1 ATTTATATTATATAAATTATAATATATTTATAT
24487 ATTTATATTATAT
1 ATTTATATTATAT
24500 TATATTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 13 0.32
36 28 0.68
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (33 bp):
ATTTATATTATATAAATTATAATATATTTATAT
Found at i:24494 original size:24 final size:24
Alignment explanation
Indices: 24387--24513 Score: 140
Period size: 24 Copynumber: 5.4 Consensus size: 24
24377 ATTTAAAATA
24387 TTATATATTTATATTAATATT-TAT
1 TTATATATTTATATT-ATATTATAT
*
24411 ATTAT-TAATTTATATTATA-TAAAT
1 -TTATAT-ATTTATATTATATTATAT
* **
24435 TT-TA-ATATAT-TTATATCGTAT
1 TTATATATTTATATTATATTATAT
24456 TTATATTATTTATATTATATTATAT
1 TTATA-TATTTATATTATATTATAT
24481 TTATATATTTATATTATATTATAT
1 TTATATATTTATATTATATTATAT
24505 TTATATATT
1 TTATATATT
24514 ATAAAATTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
20 5 0.06
21 9 0.10
22 3 0.03
23 3 0.03
24 39 0.45
25 27 0.31
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (24 bp):
TTATATATTTATATTATATTATAT
Found at i:24523 original size:50 final size:51
Alignment explanation
Indices: 24366--24525 Score: 154
Period size: 50 Copynumber: 3.1 Consensus size: 51
24356 ATTTTTATGT
24366 ATTATGATTATATTTAAAATATTATATATTTATATTA-ATATT-TATATTATTAA
1 ATTAT-ATTATATTT-AAATATTATATATTTATATTATAT-TTATATATTA-TAA
* * ** *
24419 TTTATATTATA--TAAATTTTAATATATTTATATCGTATTTATATTATT-TAT
1 ATTATATTATATTTAAATATT-ATATATTTATATTATATTTATA-TATTATAA
*
24469 ATTATATTATATTTATATATT-TATA-TTATATTATATTTATATATTATAAA
1 ATTATATTATATTTAAATATTATATATTTATATTATATTTATATATTAT-AA
24519 ATTATAT
1 ATTATAT
24526 CGTAGGTCTA
Statistics
Matches: 88, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
48 4 0.05
49 21 0.24
50 39 0.44
51 4 0.05
52 16 0.18
53 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (51 bp):
ATTATATTATATTTAAATATTATATATTTATATTATATTTATATATTATAA
Found at i:24622 original size:18 final size:18
Alignment explanation
Indices: 24599--24633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24589 AGTCAAAGCT
* *
24599 TTTTGATGTTTTTGATAC
1 TTTTGAAGTTTTGGATAC
24617 TTTTGAAGTTTTGGATA
1 TTTTGAAGTTTTGGATA
24634 TGGCTGAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (18 bp):
TTTTGAAGTTTTGGATAC
Found at i:24892 original size:28 final size:28
Alignment explanation
Indices: 24854--24916 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
24844 GAATGTGTTT
24854 TATATATTATAAATTATTAAAATTTATA
1 TATATATTATAAATTATTAAAATTTATA
24882 TATATATTATAAATTATTAAAATTTATA
1 TATATATTATAAATTATTAAAATTTATA
*
24910 TAGATAT
1 TATATAT
24917 GTAATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TATATATTATAAATTATTAAAATTTATA
Found at i:26067 original size:13 final size:13
Alignment explanation
Indices: 26049--26082 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
26039 ACGGGGAGAG
26049 AAAAAAAGGAAAA
1 AAAAAAAGGAAAA
* *
26062 AAAAAAAAGAAAG
1 AAAAAAAGGAAAA
26075 AAAAAAAG
1 AAAAAAAG
26083 AGAGAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGAAAA
Found at i:26068 original size:14 final size:14
Alignment explanation
Indices: 26049--26101 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
26039 ACGGGGAGAG
26049 AAAAAAAGGAAAAA
1 AAAAAAAGGAAAAA
26063 AAAAAAA-GAAAGAA
1 AAAAAAAGGAAA-AA
26077 AAAAAGAGAGAGAAAAA
1 AAAAA-A-AG-GAAAAA
26094 AGAAAAAA
1 A-AAAAAA
26102 ATTACGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.12
14 14 0.42
15 1 0.03
16 2 0.06
17 4 0.12
18 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAAAAA
Found at i:26161 original size:19 final size:17
Alignment explanation
Indices: 26123--26167 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
26113 GTATTATTTT
26123 TTTAT-TATTTAAAATA
1 TTTATATATTTAAAATA
26139 -TTATATATTTATATAATA
1 TTTATATATTTA-A-AATA
26157 TTTATATATTT
1 TTTATATATTT
26168 TATGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 1 0.04
18 4 0.16
19 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTTAAAATA
Found at i:26238 original size:23 final size:22
Alignment explanation
Indices: 26172--26248 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
26162 ATATTTTATG
26172 TTTTTATAATCGTG-TTATATTTA
1 TTTTTAT-ATCGTGTTTATA-TTA
* * *
26195 TTTTTGTGTTGAT-TTTA-ATTAA
1 TTTTTATATCG-TGTTTATATT-A
26217 TTTTTATATCGTGTTTATATTA
1 TTTTTATATCGTGTTTATATTA
26239 TTTTTCATAT
1 TTTTT-ATAT
26249 ATTTAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 3 0.07
22 22 0.52
23 17 0.40
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTTATATCGTGTTTATATTA
Found at i:27834 original size:22 final size:22
Alignment explanation
Indices: 27801--27843 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
27791 CCTTATTCTA
27801 AATATAAATTTAAATATTTATTT
1 AATATAAATTT-AATATTTATTT
*
27824 AATA-AAATTTAATTTTTATT
1 AATATAAATTTAATATTTATT
27844 AAAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATAAATTTAATATTTATTT
Found at i:30003 original size:9 final size:11
Alignment explanation
Indices: 29978--30006 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
29968 AAGTTTTTAG
29978 GAAAAATATTT
1 GAAAAATATTT
29989 GAAAAAT-TTT
1 GAAAAATATTT
29999 GAAAAATA
1 GAAAAATA
30007 ATCTAGTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (11 bp):
GAAAAATATTT
Found at i:32250 original size:95 final size:95
Alignment explanation
Indices: 32122--32395 Score: 458
Period size: 95 Copynumber: 2.9 Consensus size: 95
32112 AGAGGAGTGC
** * * * *
32122 CAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAAGGAAAAATGGACAATGTGGTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGACAATGTGCTGATTCAAG
32187 GCCAGCGACATTGAGCTAAAGGAAAATGGA
66 GCCAGCGACATTGAGCTAAAGGAAAATGGA
* *
32217 CAATTTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAGTGGACAATGTGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGACAATGTGCTGATTCAAG
* *
32282 GCCAGCGACATTGAGCTAAGGGAAAATGTA
66 GCCAGCGACATTGAGCTAAAGGAAAATGGA
32312 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGACAATGTGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGACAATGTGCTGATTCAAG
32377 GCCAGCGACATTGAGCTAA
66 GCCAGCGACATTGAGCTAA
32396 TAAAGGTGCC
Statistics
Matches: 167, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 167 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (95 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGACAATGTGCTGATTCAAG
GCCAGCGACATTGAGCTAAAGGAAAATGGA
Found at i:32396 original size:48 final size:48
Alignment explanation
Indices: 32122--32396 Score: 437
Period size: 48 Copynumber: 5.8 Consensus size: 48
32112 AGAGGAGTGC
** * * *
32122 CAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAAGGAAAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
* *
32170 CAATGTGGTGATTCAAGGCCAGCGACATTGAGCTAAAGG-AAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
* *
32217 CAATTTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
* *
32265 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-GGGAAAATGTA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
32312 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
32360 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAT
32397 AAAGGTGCCA
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 88 0.42
48 122 0.58
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGGAAAAATGGA
Found at i:32692 original size:32 final size:32
Alignment explanation
Indices: 32648--33413 Score: 863
Period size: 32 Copynumber: 24.9 Consensus size: 32
32638 TTGGAAAAGA
*
32648 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
32680 TGCCACCAACTTGTGTGGGCTATGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
32712 TGCCACCAACTTGTGTGGGCTATAAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
32744 TGCCACCAACTTGTGTGGGCATTGAAA--GGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
**
32774 TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
** * *
32802 TGCCACTGAC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
32830 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
32862 TACCACCAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
**
32894 TGCCACCAACTTGTGTGGGAATTGAAA--GGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
32924 TGCCACTAAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
** ** *
32952 TGCCACTGAC-T-TGTGGGCTTT-AAA-AAGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
32980 TGCCACCGACTTGTATGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
33012 TGCCACCAACTTGTGTGCGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33044 TGCCACCAACTTGTGTGGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33076 TGCCACCAACTTGTGTGGGCTTTGAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33108 TGCCACCAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33140 TGCCACCAACTTGTATGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
** * *
33170 TGCCACTGAC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
33198 TGCTACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
33230 TACCACCAACTTGTGTGGACTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * * *
33262 TGCAACCGACTTATGTGGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
33294 TGCCACCAACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
33324 TGCTACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33354 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
33386 TGCCACTAACTTGTGTGGGCTTTGAAAT
1 TGCCACCAACTTGTGTGGGCTTTGAAAT
33414 AAGTTGTCAC
Statistics
Matches: 641, Mismatches: 74, Indels: 38
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.01
28 109 0.17
29 10 0.02
30 119 0.19
31 11 0.02
32 386 0.60
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
Found at i:32727 original size:64 final size:64
Alignment explanation
Indices: 32506--33413 Score: 904
Period size: 64 Copynumber: 14.9 Consensus size: 64
32496 AAAAAAAAGG
* * * * * *
32506 TGCCACTAACTTCTGTGGGCTTTG-AA-GAGATGCCACTGAC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * * * *
32564 TGCCACTAAC-T-TGTGGGCTTTGGAA-G-GATGCCACTGAC-T-CGTCGGCTTTGAAA--AGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * *
32620 TGCCACTGAC-T-TGTGGGCTTGGAAA--AGATGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * *
32680 TGCCACCAACTTGTGTGGGCTATGAAATGAGTTGCCACCAACTTGTGTGGGCTATAAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * *
32744 TGCCACCAACTTGTGTGGGCATTGAAA-G-GATGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** *
32802 TGCCACTGAC-T-TGTGGGCTTTGAAA--AGATGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * **
32862 TACCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCAACTTGTGTGGGAATTGAAA--GGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * ** *
32924 TGCCACTAAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T-TGTGGGCTTT-AAA-AAGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * *
32980 TGCCACCGACTTGTATGGGCTTTGAAATGAGTTGCCACCAACTTGTGTGCGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * *
33044 TGCCACCAACTTGTGTGGGCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
33108 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCAACTTGTATGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * *
33170 TGCCACTGAC-T-TGTGGGCTTTGAAA--AGATGCTACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * *
33230 TACCACCAACTTGTGTGGACTTTGAAATGAGTTGCAACCGACTTATGTGGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
33294 TGCCACCAACTTGTGTGGGCTTTGAAA-G-GGTGCTACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * **
33354 TGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTAACTTGTGTGGGCTTTGAAAT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAAT
33414 AAGTTGTCAC
Statistics
Matches: 721, Mismatches: 92, Indels: 69
0.82 0.10 0.08
Matches are distributed among these distances:
55 3 0.00
56 112 0.16
57 9 0.01
58 92 0.13
59 10 0.01
60 99 0.14
61 11 0.02
62 126 0.17
63 7 0.01
64 252 0.35
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
Found at i:32868 original size:150 final size:154
Alignment explanation
Indices: 32607--33412 Score: 912
Period size: 150 Copynumber: 5.3 Consensus size: 154
32597 CTGACTCGTC
* * * * *
32607 GGCTTTGAAA-AGTTGCCACTGACTTGTGGGCTTGGAAAAGATGCCACCGACTTGTGTGGGCTTT
1 GGCTTTGAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTT
* * * * *
32671 GAAATGGGTTGCCACCAACTTGTGTGGGCTATGAAATGAGTTGCCACCAACTTGTGTGGGCTATA
66 GAAA-GAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTG
32736 AAATGAGTTGCCACCAACTTGTGTG
130 AAATGAGTTGCCACCAACTTGTGTG
* * * *
32761 GGCATTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTT
1 GGCTTTGAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTT
* * *
32823 GAAA-AGATGCCACCGACTTGTGTGGGCTTTGAAATGGGTTACCACCAACTTGTGTGGGCTTTGA
66 GAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGA
32887 AATGAGTTGCCACCAACTTGTGTG
131 AATGAGTTGCCACCAACTTGTGTG
** *
32911 GGAATTGAAA-GGTTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTT
1 GGCTTTGAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTT
* * * * * *
32973 -AAAAAGATGCCACCGACTTGTATGGGCTTTGAAATGAGTTGCCACCAACTTGTGTGCGCTTTGA
66 GAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGA
33037 AATGAGTTGCCACCAACTTGTGTG
131 AATGAGTTGCCACCAACTTGTGTG
* * * *
33061 GGCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTGTGTGG
1 GGCTTTGAAA-GGGTTGCCACTAAC-T-TGTGGGCTTTG-AA-AGGGTGCCACCGACTTGTGTGG
* **
33126 GCTTTGAAATGAGTTGCCACCAACTTGTATGGGCTTTGAAA-GGG-TGCCACTGAC-T-TGTGGG
61 GCTTTGAAA-GAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGG
* * *
33187 CTTTGAAA--AGATGCTACCGACTTGTGTG
125 CTTTGAAATGAGTTGCCACCAACTTGTGTG
* * * * *
33215 GGCTTTGAAATGGGTTACCACCAACTTGTGTGGACTTTGAAATGAGTTGCAACCGACTTATGTGG
1 GGCTTTGAAA-GGGTTGCCACTAACTTGTG-GG-CTTTGAAA-G-GGTGCCACCGACTTGTGTGG
* * * *
33280 GCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAA-GGG-TGCTACCGACTTGTGTGGG
61 GCTTTGAAA-GAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGG
* *
33343 CTTTGAAA-G-GGTGCCACCGACTTGTGTG
125 CTTTGAAATGAGTTGCCACCAACTTGTGTG
33371 GGCTTTGAAATGGGTTGCCACTAACTTGTGTGGGCTTTGAAA
1 GGCTTTGAAA-GGGTTGCCACTAAC-T-TGTGGGCTTTGAAA
33413 TAAGTTGTCA
Statistics
Matches: 579, Mismatches: 53, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
149 3 0.01
150 222 0.38
152 31 0.05
153 8 0.01
154 166 0.29
155 3 0.01
156 86 0.15
157 5 0.01
158 22 0.04
159 5 0.01
160 28 0.05
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (154 bp):
GGCTTTGAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTT
GAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGA
AATGAGTTGCCACCAACTTGTGTG
Found at i:46273 original size:2 final size:2
Alignment explanation
Indices: 46266--46295 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46256 TCGAATTTTA
46266 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
46296 GTATGTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47798 original size:18 final size:17
Alignment explanation
Indices: 47771--47804 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47761 TTAAAAAGTT
47771 AAAAAATAATAATTTTA
1 AAAAAATAATAATTTTA
*
47788 AAAATAATAATTATTTT
1 AAAA-AATAATAATTTT
47805 TAATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAAATAATAATTTTA
Found at i:49088 original size:29 final size:28
Alignment explanation
Indices: 49034--49089 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
49024 ATTAATATAA
* *
49034 AAATAAAAATTTTATTTTTATTATTTAT
1 AAATAAAAATTTAATTTTTATAATTTAT
49062 AAATAATAAATATTAATTTTTA-AATTTA
1 AAATAA-AAAT-TTAATTTTTATAATTTA
49090 AATGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATAAAAATTTAATTTTTATAATTTAT
Found at i:52858 original size:28 final size:27
Alignment explanation
Indices: 52804--52874 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
52794 GTCACCCATT
*
52804 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
52831 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
52859 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
52875 AGGCTTGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:57426 original size:28 final size:27
Alignment explanation
Indices: 57371--57441 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
57361 GCCACCCATT
57371 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
57398 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
57426 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
57442 AGGCTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:61109 original size:27 final size:26
Alignment explanation
Indices: 61073--61144 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
61063 AAAGTTACCT
* * *
61073 TTTGTGTTTGTCAACAATGGTGGTTAC
1 TTTGTATTTGTCAAAAATGATGGTT-C
61100 TTTGTATTTGTCAAAAATGATGGTTC
1 TTTGTATTTGTCAAAAATGATGGTTC
*
61126 TTTTTAGTTTGTCAAAAAT
1 TTTGTA-TTTGTCAAAAAT
61145 TATGACTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (26 bp):
TTTGTATTTGTCAAAAATGATGGTTC
Found at i:61247 original size:13 final size:13
Alignment explanation
Indices: 61229--61301 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 13
61219 AGGCTCCCTC
61229 ATCCCTCTCAAGT
1 ATCCCTCTCAAGT
* *
61242 ATCCCTCTTAAGC
1 ATCCCTCTCAAGT
* * *
61255 ATCTCTTTCAAGC
1 ATCCCTCTCAAGT
**
61268 ATCCCTCTCTTGT
1 ATCCCTCTCAAGT
* **
61281 ATCCTTCTCTTGT
1 ATCCCTCTCAAGT
61294 ATCCCTCT
1 ATCCCTCT
61302 TCAATTCTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.16, C:0.37, G:0.07, T:0.40
Consensus pattern (13 bp):
ATCCCTCTCAAGT
Found at i:63018 original size:204 final size:204
Alignment explanation
Indices: 62668--63049 Score: 710
Period size: 204 Copynumber: 1.9 Consensus size: 204
62658 CCAGTTTGAA
* *
62668 GAAAAATCTCATCTTGTTGGGAGCCTTAGAATCCAAAGGCTCAATCATCACTTTAAGTGATGGAG
1 GAAAAATCTCATCTCGTTGGGAGCCTTAGAATCCAAAGGCTCAATCATCACTTTAAGAGATGGAG
*
62733 TTTTGAAGGTCACATCTGGCGCACTTGTGATAATGAAGAGCATAAAAAAAAATAACTTGTATTAC
66 TTTTGAAGGTCACATCTGGCGCACTCGTGATAATGAAGAGCATAAAAAAAAATAACTTGTATTAC
62798 TATCAGGATAGTACAGTTATTGGAGCAGTAGCAGCAGCTTCCGATGGTCACATCTGGCGCACTCG
131 TATCAGGATAGTACAGTTATTGGAGCAGTAGCAGCAGCTTCCGATGGTCACATCTGGCGCACTCG
62863 TGACAATTT
196 TGACAATTT
62872 GAAAAATCTCATCTCGTTGGGAGCCTTAGAATCCAAAGGCTCAATCATCACTTTAAGAGATGGAG
1 GAAAAATCTCATCTCGTTGGGAGCCTTAGAATCCAAAGGCTCAATCATCACTTTAAGAGATGGAG
* *
62937 TTTTGAAGGTCACATCTGGCGCACTCGTGATAATGAAGGGCATCAAAAAAAATAACTTGTATTAC
66 TTTTGAAGGTCACATCTGGCGCACTCGTGATAATGAAGAGCATAAAAAAAAATAACTTGTATTAC
*
63002 TATCAGGGTAGTACAGTTATTGGAGCAGTAGCAGCAGCTTCCGATGGT
131 TATCAGGATAGTACAGTTATTGGAGCAGTAGCAGCAGCTTCCGATGGT
63050 GATAATTTGA
Statistics
Matches: 172, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
204 172 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (204 bp):
GAAAAATCTCATCTCGTTGGGAGCCTTAGAATCCAAAGGCTCAATCATCACTTTAAGAGATGGAG
TTTTGAAGGTCACATCTGGCGCACTCGTGATAATGAAGAGCATAAAAAAAAATAACTTGTATTAC
TATCAGGATAGTACAGTTATTGGAGCAGTAGCAGCAGCTTCCGATGGTCACATCTGGCGCACTCG
TGACAATTT
Found at i:65901 original size:27 final size:27
Alignment explanation
Indices: 65864--65941 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
65854 AAAAGCCACC
* *
65864 CTTTGTGTTTGTCAACAATGATGGTTA
1 CTTTGTATTTGTCAAAAATGATGGTTA
*
65891 CTTTGTATTTGTCAAAAATGATGGTTC
1 CTTTGTATTTGTCAAAAATGATGGTTA
*
65918 CTTT-TAGTTTGTCAAAAATTATGG
1 CTTTGTA-TTTGTCAAAAATGATGG
65942 CTTATTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (27 bp):
CTTTGTATTTGTCAAAAATGATGGTTA
Found at i:65956 original size:24 final size:25
Alignment explanation
Indices: 65870--65958 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 25
65860 CACCCTTTGT
*
65870 GTTTGTCAACAATGATGGTTACTTTGTA
1 GTTTGTCAAAAATGATGG-T-CTTT-TA
65898 -TTTGTCAAAAATGATGGTTCCTTTTA
1 GTTTGTCAAAAATGATGG-T-CTTTTA
*
65924 GTTTGTCAAAAATTATGG-CTTATT-
1 GTTTGTCAAAAATGATGGTCTT-TTA
65948 GTTTGTCAAAA
1 GTTTGTCAAAA
65959 TTGGTGGCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
24 14 0.25
25 2 0.04
26 2 0.04
27 38 0.68
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (25 bp):
GTTTGTCAAAAATGATGGTCTTTTA
Found at i:67022 original size:17 final size:17
Alignment explanation
Indices: 66996--67032 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
66986 CATGCTACGC
66996 TTGAAGTCACAAGCCAT
1 TTGAAGTCACAAGCCAT
* *
67013 TTGAATTCACGAGCCAT
1 TTGAAGTCACAAGCCAT
67030 TTG
1 TTG
67033 GGGCTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (17 bp):
TTGAAGTCACAAGCCAT
Found at i:69711 original size:16 final size:16
Alignment explanation
Indices: 69684--69723 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
69674 CGCGCTGTTT
69684 GTTTCA-CCTTATAAA
1 GTTTCAGCCTTATAAA
69699 GTTTCAGCCTTATAAA
1 GTTTCAGCCTTATAAA
*
69715 GTTGCAGCC
1 GTTTCAGCC
69724 AAACTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (16 bp):
GTTTCAGCCTTATAAA
Found at i:70163 original size:14 final size:14
Alignment explanation
Indices: 70144--70266 Score: 70
Period size: 14 Copynumber: 9.3 Consensus size: 14
70134 TAGACATTAA
70144 ATATTAATATATTT
1 ATATTAATATATTT
70158 ATATTAATAT-TTAT
1 ATATTAATATATT-T
* *
70172 ATGTTATTA-ATTT
1 ATATTAATATATTT
*
70185 ATATT-ATATA--A
1 ATATTAATATATTT
*
70196 ATTTTAATATATTT
1 ATATTAATATATTT
70210 AT-TTAATTATATTAT
1 ATATTAA-TATATT-T
*
70225 ATTTTAAT-TATTT
1 ATATTAATATATTT
70238 -TATT--TATA-TT
1 ATATTAATATATTT
* *
70248 ATATTTATGTATATT
1 ATATTAATATAT-TT
70263 ATAT
1 ATAT
70267 ATAGCCGTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
10 3 0.04
11 10 0.12
12 10 0.12
13 16 0.19
14 32 0.38
15 10 0.12
16 4 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATATTAATATATTT
Found at i:70168 original size:20 final size:18
Alignment explanation
Indices: 70151--70255 Score: 68
Period size: 15 Copynumber: 6.2 Consensus size: 18
70141 TAAATATTAA
70151 TATATTTATATTAATATT
1 TATATTTATATTAATATT
*
70169 TATATGT-TATT-A-ATT
1 TATATTTATATTAATATT
* *
70184 TATA-TTATATAAATTTT
1 TATATTTATATTAATATT
70201 AATATATTTAT-TTAATTATAT
1 --TATATTTATATTAA-TAT-T
*
70222 TATATTT-TA--ATTATT
1 TATATTTATATTAATATT
70237 T-TATTTATATT-ATATT
1 TATATTTATATTAATATT
70253 TAT
1 TAT
70256 GTATATTATA
Statistics
Matches: 66, Mismatches: 8, Indels: 27
0.65 0.08 0.27
Matches are distributed among these distances:
14 6 0.09
15 14 0.21
16 10 0.15
17 8 0.12
18 7 0.11
19 14 0.21
20 6 0.09
21 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (18 bp):
TATATTTATATTAATATT
Found at i:70212 original size:33 final size:32
Alignment explanation
Indices: 70145--70226 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 32
70135 AGACATTAAA
* *
70145 TATTAATATAT-TTATATTAATATTTATATGT
1 TATTAATTTATATTATATAAATATTTATATGT
*
70176 TATTAATTTATATTATATAAAT-TTTAATATATT
1 TATTAATTTATATTATATAAATATTT-ATAT-GT
70209 TATTTAA-TTATATTATAT
1 TA-TTAATTTATATTATAT
70227 TTTAATTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.30
32 13 0.30
33 14 0.32
34 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TATTAATTTATATTATATAAATATTTATATGT
Found at i:70264 original size:20 final size:18
Alignment explanation
Indices: 70151--70266 Score: 71
Period size: 20 Copynumber: 6.3 Consensus size: 18
70141 TAAATATTAA
*
70151 TATATTTATATTAATAT-T
1 TATATTTAT-TTATTATAT
*
70169 TATATGTTATTAATTTATAT
1 TATAT-TTATTTA-TTATAT
* *
70189 TATA-TAAATT-TTA-A-
1 TATATTTATTTATTATAT
70203 TATATTTATTTAATTATAT
1 TATATTTATTT-ATTATAT
* *
70222 TATATTTTAATTATTTTATT
1 TATA-TTTATTTATTATA-T
70242 TATATTATATTTATGTATAT
1 TATATT-TATTTAT-TATAT
70262 TATAT
1 TATAT
70267 ATAGCCGTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
14 4 0.05
15 5 0.07
16 3 0.04
17 3 0.04
18 11 0.15
19 18 0.24
20 28 0.37
21 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATATTTATTTATTATAT
Found at i:70607 original size:23 final size:24
Alignment explanation
Indices: 70581--70635 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
70571 ATATTTTTTT
*
70581 AATTTATTTT-AT-TATACGTAAAA
1 AATTTATTTTGATGTATA-ATAAAA
70604 AA-TTATTTTGATGTATAATAAAA
1 AATTTATTTTGATGTATAATAAAA
70627 AATATTATT
1 AAT-TTATT
70636 AAAAAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 4 0.15
25 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (24 bp):
AATTTATTTTGATGTATAATAAAA
Found at i:75487 original size:27 final size:27
Alignment explanation
Indices: 75452--75551 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
75442 AAGTACCCAT
*
75452 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
75479 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* * *
75506 TGTTTGTCAAAAATGGTGATTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
75533 TATTTGCCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
75552 CATGTTGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:76079 original size:23 final size:23
Alignment explanation
Indices: 76053--76117 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
76043 TTGATGATTG
76053 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
* *
76076 ATTGAG-TT-T-GA--TGA-TTG
1 ATTGAGTTTATAGATTTTATTTT
76093 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
76116 AT
1 AT
76118 GTTAAAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 8 0.25
18 4 0.12
19 1 0.03
20 4 0.12
21 1 0.03
22 4 0.12
23 10 0.31
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (23 bp):
ATTGAGTTTATAGATTTTATTTT
Found at i:76086 original size:40 final size:40
Alignment explanation
Indices: 76026--76117 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
76016 AATCTTTGAT
* *
76026 ATTTCATTTTAGTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
76066 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
76106 ATTTTATTTTAT
1 ATTTTATTTTAT
76118 GTTAAAAGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.18, T:0.55
Consensus pattern (40 bp):
ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
Found at i:76108 original size:17 final size:17
Alignment explanation
Indices: 76038--76101 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
76028 TTCATTTTAG
76038 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
* *
76055 TGAGTTTATAGATTTTATTTTAT
1 TGAG-TT-T-GA--TGA-TTGAT
76078 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
76095 TGAGTTT
1 TGAGTTT
76102 ATAGATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 15 0.41
18 4 0.11
19 1 0.03
20 4 0.11
21 1 0.03
22 4 0.11
23 8 0.22
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (17 bp):
TGAGTTTGATGATTGAT
Found at i:76208 original size:21 final size:20
Alignment explanation
Indices: 76168--76208 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
76158 GATTTTAATG
**
76168 ATTTATTTAATTTTTGTTAT
1 ATTTATTTAATTTTCATTAT
76188 ATTTATGTTAATTTTCATTAT
1 ATTTAT-TTAATTTTCATTAT
76209 GATGATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTATTTAATTTTCATTAT
Found at i:77970 original size:154 final size:153
Alignment explanation
Indices: 77593--78088 Score: 409
Period size: 153 Copynumber: 3.2 Consensus size: 153
77583 GGCCATCGAA
* * * * * *
77593 TCGCTTCTACGCCAAAGGTATAGT-TTTAGG-GTAGGTTTATCTTTTTCTTGTTATTTTTAC-GC
1 TCGCTTCTATGCCAAAGGTATA-TATTTAGGAATAGATTTATCTTTTTCTTATCA-TTTTACATC
* * * * * *
77655 TCTTTAGGGTTACCAAGATACTTTCACATCG-AAG-ATATACCTTAA-AGGCATTTTCGTAACTT
64 T-TTTAAGATTATCGAGATACTTTCACGTCGAAAGTAT-TACC-TAAGA-GCATTTTCTTAA-TT
* * * * *
77717 TTCTAAAATCGAGTGCTAGATAGTTACCAGG
124 TTCTAAAACCAAGTCCTAGATAGTCA-CAAG
* * * * * * * *
77748 TCGTTTCTATGCCAATGGTGTATATTTATG-ATAGGTTTGTCTTTTTCTTATCATTTTGCGTCTT
1 TCGCTTCTATGCCAAAGGTATATATTTAGGAATAGATTTATCTTTTTCTTATCATTTTACATCTT
*
77812 TTAAGATTATCGGGATACTTTCACGTCGAAAGTATTACCTAAGAGCATTTTCTTAATTTTCTAAA
66 TTAAGATTATCGAGATACTTTCACGTCGAAAGTATTACCTAAGAGCATTTTCTTAATTTTCTAAA
*
77877 ACCAAGTCCTAGATAGTCACTAG
131 ACCAAGTCCTAGATAGTCACAAG
* * * * * *
77900 ATCGCTTCTGTGCCAAAAGTATATATTTA-GAATAGATTTATTTTTTTATTTATTATTTTATATC
1 -TCGCTTCTATGCCAAAGGTATATATTTAGGAATAGATTTATCTTTTT-CTTATCATTTTACATC
* * * * **
77964 TTTTAAGATTATCGAGATACTTTTACGTCGAAGGTA-TACCCCAAG-GCATTTTGTTAATTCACT
64 TTTTAAGATTATCGAGATACTTTCACGTCGAAAGTATTA-CCTAAGAGCATTTTCTTAATTTTCT
* * *
78027 ATAACCAAATCCTAAATAGTCAACAAG
128 AAAACCAAGTCCTAGATAGTC-ACAAG
* * *
78054 TCACTTTTATGCCAAAGGTATGTATTTAGGAATAG
1 TCGCTTCTATGCCAAAGGTATATATTTAGGAATAG
78089 GTTCGTCATT
Statistics
Matches: 277, Mismatches: 53, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
152 3 0.01
153 118 0.43
154 102 0.37
155 52 0.19
156 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (153 bp):
TCGCTTCTATGCCAAAGGTATATATTTAGGAATAGATTTATCTTTTTCTTATCATTTTACATCTT
TTAAGATTATCGAGATACTTTCACGTCGAAAGTATTACCTAAGAGCATTTTCTTAATTTTCTAAA
ACCAAGTCCTAGATAGTCACAAG
Found at i:86768 original size:20 final size:20
Alignment explanation
Indices: 86694--86768 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
86684 ACCCAGAATA
* *
86694 TATCGATACAATGAGAAATG
1 TATCGATACATTTAGAAATG
* *
86714 TATCGATTCATTTGAAAACATG
1 TATCGATACATTT-AGAA-ATG
* *
86736 TATCGATATATTTAGTAATG
1 TATCGATACATTTAGAAATG
86756 TATCGATACATTT
1 TATCGATACATTT
86769 CCTTAGCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 25 0.57
21 5 0.11
22 14 0.32
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
TATCGATACATTTAGAAATG
Done.