Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold189
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: 2243555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:2730 original size:26 final size:26
Alignment explanation
Indices: 2696--2748 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2686 CTAGGGTTTA
2696 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
2722 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
2748 T
1 T
2749 CAGAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTATTACTTTATTATAACAAGT
Found at i:6419 original size:12 final size:12
Alignment explanation
Indices: 6402--6428 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6392 GGTCACTTAA
6402 AAATCTTTGACT
1 AAATCTTTGACT
6414 AAATCTTTGACT
1 AAATCTTTGACT
6426 AAA
1 AAA
6429 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:7247 original size:18 final size:17
Alignment explanation
Indices: 7213--7289 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 17
7203 TTATGTTTAA
*
7213 ATATTTAAATAT-CTTT
1 ATATTTAAATATATTTT
*
7229 A-A-TTATAT-TATTTT
1 ATATTTAAATATATTTT
*
7243 AT-TTAAAATATATTTT
1 ATATTTAAATATATTTT
*
7259 ATATTTAAATTAAAATTTT
1 ATATTTAAA-T-ATATTTT
7278 A-ATTTAAATATA
1 ATATTTAAATATA
7290 AATAAATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
13 1 0.02
14 9 0.19
15 5 0.11
16 11 0.23
17 6 0.13
18 8 0.17
19 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTAAATATATTTT
Found at i:7292 original size:18 final size:18
Alignment explanation
Indices: 7238--7292 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
7228 TAATTATATT
*
7238 ATTTT-ATTTAAA-ATAT
1 ATTTTAATTTAAATATAA
7254 ATTTTATATTTAAAT-TAAA
1 ATTTTA-ATTTAAATAT-AA
7273 ATTTTAATTTAAATATAA
1 ATTTTAATTTAAATATAA
7291 AT
1 AT
7293 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.15
18 20 0.61
19 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTTAAATATAA
Found at i:7384 original size:21 final size:20
Alignment explanation
Indices: 7335--7389 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
7325 TGGACTTATT
7335 AAATATAATT-ATAAAATATA
1 AAAT-TAATTAATAAAATATA
7355 AAATCTTAATTAATAAAATAATA
1 AAA--TTAATTAATAAAAT-ATA
*
7378 AAATTAAATAAT
1 AAATTAATTAAT
7390 TTTTATCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 13 0.43
22 8 0.27
23 6 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTAATTAATAAAATATA
Found at i:8190 original size:19 final size:19
Alignment explanation
Indices: 8166--8202 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8156 AGCTTTATTA
8166 TTGATTAAGATTTTTGATG
1 TTGATTAAGATTTTTGATG
8185 TTGATTAAGATTTTTGAT
1 TTGATTAAGATTTTTGAT
8203 ATTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (19 bp):
TTGATTAAGATTTTTGATG
Found at i:15172 original size:103 final size:102
Alignment explanation
Indices: 14983--15173 Score: 283
Period size: 103 Copynumber: 1.9 Consensus size: 102
14973 GATGACTACG
* * *
14983 CTGCAACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
* * *
15048 GATGGACTCTTTTAACCAAAAAATCTGAAAAAATATC
66 AATAGACTATTTTAACCAAAAAATCTGAAAAAATATC
* * *
15085 CTGCAACCAAAACATATTTGAGACACTAGTCATTATTTTACAGGAAATGGAATAAGATAAGATGC
1 CTGCAACC-AAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATAC
*
15150 CAATATACTATTTTAACCAAAAAA
65 CAATAGACTATTTTAACCAAAAAA
15174 ATACTAACAA
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 8 0.10
103 70 0.90
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
AATAGACTATTTTAACCAAAAAATCTGAAAAAATATC
Found at i:16494 original size:2 final size:2
Alignment explanation
Indices: 16489--16543 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
16479 CACATACACA
16489 TG TG TG TG T- TG -G TG TG T- TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16528 TG TG TG -G TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
16544 ATATATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:16530 original size:27 final size:25
Alignment explanation
Indices: 16489--16543 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
16479 CACATACACA
*
16489 TGTGTGTGTTGGTGTGTTGTGTGTG
1 TGTGTGTGTTGGTGTGTGGTGTGTG
16514 TGTGTGTGTGTGTGTGTGTGGTGTGTG
1 TGTGTGTGT-TG-GTGTGTGGTGTGTG
16541 TGT
1 TGT
16544 ATATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (25 bp):
TGTGTGTGTTGGTGTGTGGTGTGTG
Found at i:19526 original size:2 final size:2
Alignment explanation
Indices: 19458--19513 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
19448 CAGAACGCAA
19458 AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19499 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
19514 CGTTGGAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19780 original size:28 final size:28
Alignment explanation
Indices: 19716--19826 Score: 80
Period size: 28 Copynumber: 3.9 Consensus size: 28
19706 ATATTTTTAT
*
19716 ATTTAAATTAAAAATTTATTTAAATATAA
1 ATTTAAA-TAAAAATTTATTTAAATACAA
** *
19745 ATAAAAATAAAAATTTATTTTAATACAA
1 ATTTAAATAAAAATTTATTTAAATACAA
* * * *
19773 TTTTAAATTTAAATTTTATTTAATTA-AA
1 ATTTAAA-TAAAAATTTATTTAAATACAA
* ** *
19801 ATTAAAATTATTAACTTATTTAAATA
1 ATTTAAA-TAAAAATTTATTTAAATA
19827 TTATCACAAA
Statistics
Matches: 62, Mismatches: 19, Indels: 3
0.74 0.23 0.04
Matches are distributed among these distances:
28 43 0.69
29 19 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTAAATAAAAATTTATTTAAATACAA
Found at i:19820 original size:57 final size:57
Alignment explanation
Indices: 19717--19826 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
19707 TATTTTTATA
* *
19717 TTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAATTTATTTTAATACAAT
1 TTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAACTTATTTAAATACAAT
* * * * **
19774 TTTAAATTTAAATTTTATTTAATTA-AAATTAAAATTATTAACTTATTTAAATA
1 TTTAAATTAAAAATTTATTTAAATATAAA-TAAAAATAAAAACTTATTTAAATA
19827 TTATCACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 3 0.07
57 41 0.93
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (57 bp):
TTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAACTTATTTAAATACAAT
Found at i:20118 original size:22 final size:22
Alignment explanation
Indices: 20058--20131 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
20048 TTTATTTTAC
*
20058 ATAATTTTTAATTATGA-TAT--
1 ATAATTTTTATTTAT-ATTATAA
* *
20078 ATAATTTAT-TTTATATTATTA
1 ATAATTTTTATTTATATTATAA
*
20099 ATAATTTTTATTTATTTTATAA
1 ATAATTTTTATTTATATTATAA
*
20121 ATAATATTTAT
1 ATAATTTTTAT
20132 ATTACATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 7 0.16
20 8 0.18
21 8 0.18
22 20 0.45
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
ATAATTTTTATTTATATTATAA
Found at i:20129 original size:41 final size:41
Alignment explanation
Indices: 20050--20157 Score: 97
Period size: 41 Copynumber: 2.8 Consensus size: 41
20040 CCCTTTACTT
*
20050 TATT-TTACATAATTTTTAATTATGATATATAATTTATTTTA
1 TATTATTACATAATTTTTAATTATGATATATAATATA-TTTA
* **
20091 TATTATTA-ATAATTTTTATTTATTTTATA-AATA-ATATT-
1 TATTATTACATAATTTTTAATTATGATATATAATATAT-TTA
20129 TA-TATTACATAA-TTTTAATATAT-ATATAT
1 TATTATTACATAATTTTTAAT-TATGATATAT
20158 TTTAATAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
37 15 0.27
38 10 0.18
39 3 0.05
40 3 0.05
41 22 0.39
42 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (41 bp):
TATTATTACATAATTTTTAATTATGATATATAATATATTTA
Found at i:20174 original size:14 final size:16
Alignment explanation
Indices: 20140--20174 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20130 ATATTACATA
20140 ATTTTAATATATATAT
1 ATTTTAATATATATAT
20156 ATTTTAATA-ATAT-T
1 ATTTTAATATATATAT
20170 ATTTT
1 ATTTT
20175 TATTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 4 0.21
16 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATATATATAT
Found at i:20461 original size:54 final size:55
Alignment explanation
Indices: 20340--20462 Score: 136
Period size: 53 Copynumber: 2.3 Consensus size: 55
20330 ATTACTATCA
20340 TTTATATTTTA-AA-AAATAATTTAATAAAAAAATGATACTTCAAAATTTATTAAT
1 TTTATATTTTATAATAAATAATTTAATAAAAAAATGATACTT-AAAATTTATTAAT
* *
20394 TATA-ATTAT-TAATAAATACATTTAATAATAAAAAT-ATA--TATAAATTT-TTAAT
1 TTTATATTTTATAATAAATA-ATTTAATAA-AAAAATGATACTTA-AAATTTATTAAT
20446 TTTATATTTTATAATAA
1 TTTATATTTTATAATAA
20463 TAAAAAAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
52 9 0.16
53 17 0.29
54 14 0.24
55 12 0.21
56 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (55 bp):
TTTATATTTTATAATAAATAATTTAATAAAAAAATGATACTTAAAATTTATTAAT
Found at i:22996 original size:32 final size:32
Alignment explanation
Indices: 22955--23019 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
22945 AACACAAATT
*
22955 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
22987 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
1 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
23019 A
1 A
23020 AATCCTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (32 bp):
AGCAGAACCAAGATAAAACAAAACAGGTCCAC
Found at i:25406 original size:2 final size:2
Alignment explanation
Indices: 25399--25434 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25389 ATGAAGAAAT
25399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25435 AAGAAGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34134 original size:12 final size:12
Alignment explanation
Indices: 34117--34143 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34107 GGTCACTTAA
34117 AAATCTTTGACT
1 AAATCTTTGACT
34129 AAATCTTTGACT
1 AAATCTTTGACT
34141 AAA
1 AAA
34144 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:34974 original size:18 final size:18
Alignment explanation
Indices: 34947--35004 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
34937 TTTAAATATC
*
34947 TTTAATTATATTATTTTA
1 TTTAAATATATTATTTTA
*
34965 TTTAAATATATT-TTAATA
1 TTTAAATATATTATT-TTA
34983 TTT-AA-AT-TTATTTTA
1 TTTAAATATATTATTTTA
34998 TTTAAAT
1 TTTAAAT
35005 TAAAGTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 4 0.12
18 16 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATATATTATTTTA
Found at i:35005 original size:15 final size:15
Alignment explanation
Indices: 34957--35005 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
34947 TTTAATTATA
34957 TTATTTTATTTAAAT
1 TTATTTTATTTAAAT
*
34972 ATATTTTAATATTTAAAT
1 TTA-TTT--TATTTAAAT
34990 TTATTTTATTTAAAT
1 TTATTTTATTTAAAT
35005 T
1 T
35006 AAAGTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 12 0.41
16 3 0.10
17 3 0.10
18 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTTATTTAAAT
Found at i:35008 original size:38 final size:37
Alignment explanation
Indices: 34929--35008 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 37
34919 ATTTTTATGT
* * *
34929 TTAAAATATTTAAATATCTTTAATTATATTATTTTAT
1 TTAAAATATTTAAATATCTTAAATTATATTATTTAAA
* *
34966 TTAAATATATTTTAATAT-TTAAATTTATTTTATTTAAA
1 TTAAA-ATATTTAAATATCTTAAA-TTATATTATTTAAA
35004 TTAAA
1 TTAAA
35009 GTTATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 9 0.25
38 27 0.75
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (37 bp):
TTAAAATATTTAAATATCTTAAATTATATTATTTAAA
Found at i:35656 original size:2 final size:2
Alignment explanation
Indices: 35651--35678 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35641 AAAAAAAAAA
35651 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
35679 GATTATTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37414 original size:102 final size:102
Alignment explanation
Indices: 37238--37425 Score: 286
Period size: 102 Copynumber: 1.8 Consensus size: 102
37228 GATGACTACG
* * *
37238 CTGCAAGCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
* * *
37303 GATGGACTATTTTAACCAAAAAATCTGAAAAAATATC
66 AATAGACTATTTGAACCAAAAAATCTGAAAAAATATC
* * *
37340 CTGCAACCAAACATATTTGAGACGCTAGTCATTATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
*
37405 AATATACTATTTGAACCAAAA
66 AATAGACTATTTGAACCAAAA
37426 TATACTAACA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 76 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
AATAGACTATTTGAACCAAAAAATCTGAAAAAATATC
Found at i:38746 original size:2 final size:2
Alignment explanation
Indices: 38741--38770 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38731 ACACATACAC
38741 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
38771 ATAATAAGCC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:41952 original size:15 final size:15
Alignment explanation
Indices: 41916--41957 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
41906 CCCACCACTA
* *
41916 AAAGCCCAACTCTTC
1 AAAGCCTAACTCTGC
41931 AAAGCCTAACTCTGC
1 AAAGCCTAACTCTGC
41946 AAAGCCT-ACTCT
1 AAAGCCTAACTCT
41958 AAAAGCCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.33, C:0.36, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAGCCTAACTCTGC
Found at i:41974 original size:32 final size:33
Alignment explanation
Indices: 41937--42001 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
41927 CTTCAAAGCC
*
41937 TAACTCTGCAAAGCCTACTCTAAAAGCC-AACA
1 TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
* * *
41969 TAACTCTTCAAAGCCCATTTTAAAAGCCGAACA
1 TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
42002 CAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (33 bp):
TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
Found at i:42137 original size:3 final size:3
Alignment explanation
Indices: 42129--42167 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
42119 ATTTATCTTA
*
42129 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42168 AAAGATGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:45515 original size:32 final size:32
Alignment explanation
Indices: 45474--45538 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
45464 AACACAAATT
45474 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCATGATAAAACAAAACAGGTCCAC
45506 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCATGATAAAACAAAACAGGTCCAC
45538 A
1 A
45539 AATCCTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.09
Consensus pattern (32 bp):
AGCAGAACCATGATAAAACAAAACAGGTCCAC
Found at i:49644 original size:19 final size:19
Alignment explanation
Indices: 49620--49657 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
49610 GATAGTTGCC
49620 TCATAAAGTTGCTCCCGAA
1 TCATAAAGTTGCTCCCGAA
*
49639 TCATAAAGTTTCTCCCGAA
1 TCATAAAGTTGCTCCCGAA
49658 GTACATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (19 bp):
TCATAAAGTTGCTCCCGAA
Found at i:50041 original size:22 final size:22
Alignment explanation
Indices: 50016--50090 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
50006 TATATATATA
*
50016 TATATGTATGTATGTATATACG
1 TATATATATGTATGTATATACG
* *
50038 TATATATGTGTGTGTATATACG
1 TATATATATGTATGTATATACG
* *
50060 TATATATCTGTATATGTATATATG
1 TATATATATG--TATGTATATACG
50084 TATATAT
1 TATATAT
50091 GTATATATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 28 0.62
24 17 0.38
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (22 bp):
TATATATATGTATGTATATACG
Found at i:50093 original size:22 final size:22
Alignment explanation
Indices: 50008--50096 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
49998 AAATTTTATA
* * *
50008 TATATATATATATGTATGTATG
1 TATATATGTATATATATATATG
* * * *
50030 TATATACGTATATATGTGTGTG
1 TATATATGTATATATATATATG
* *
50052 TATATACGTATATATCTGTATATG
1 TATATATGTATATA--TATATATG
*
50076 TATATATGTATATATGTATAT
1 TATATATGTATATATATATAT
50097 ATCTACATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
22 38 0.67
24 19 0.33
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (22 bp):
TATATATGTATATATATATATG
Found at i:50097 original size:24 final size:24
Alignment explanation
Indices: 50014--50098 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
50004 TATATATATA
*
50014 TATATATGTATGTATGTATATACG
1 TATATATGTATATATGTATATACG
* *
50038 TATATATG--TGTGTGTATATACG
1 TATATATGTATATATGTATATACG
* * *
50060 TATATATCTGTATATGTATATATG
1 TATATATGTATATATGTATATACG
50084 TATATATGTATATAT
1 TATATATGTATATAT
50099 CTACATACAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 20 0.38
24 32 0.62
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (24 bp):
TATATATGTATATATGTATATACG
Found at i:54971 original size:102 final size:102
Alignment explanation
Indices: 54795--54982 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 102
54785 GATGACTACG
* * *
54795 CTGCAACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
**
54860 GAAGGACTATTTAAACCAAAAAATCTGAAAAAATATC
66 GAAACACTATTTAAACCAAAAAATCTGAAAAAATATC
* * *
54897 CTGCAACCAAACATATTTGAGACACTAGTCATTATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
*
54962 -AATACACTATTTTAACCAAAA
66 GAA-ACACTATTTAAACCAAAA
54983 TATACTAACA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
101 2 0.03
102 74 0.97
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
GAAACACTATTTAAACCAAAAAATCTGAAAAAATATC
Found at i:55990 original size:303 final size:305
Alignment explanation
Indices: 55439--56045 Score: 1164
Period size: 303 Copynumber: 2.0 Consensus size: 305
55429 GAAAAATTAA
*
55439 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAAAGCATTTTTCTTCACAGTT
1 TATCAACCATGAACGGTAGTTATGGCTCTAAC--AAAAAAAAAAAAAGCATTCTTCTTCACAGTT
55504 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
64 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
55569 TCTTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAAT
129 TCTTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAAT
55634 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
194 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
55699 TTTGGGCCAAAGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
259 TTTGGGCCAAAGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
55746 TATCAACCATGAACGGTAGTTATGGCTCTAAC-AAAAAAAAAAAAGCATTCTTCTTCACAGTTGT
1 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTCTTCTTCACAGTTGT
55810 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATC-TTTTAAGGTAGCGCAACATC
66 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
55874 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAATAT
131 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAATAT
55939 GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
196 GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
*
56004 TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAA
261 TGGGCCAAAGTCATTTTATAACGGCCAAAAACTGAGTGACAA
56046 ATGTTGACAT
Statistics
Matches: 298, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
303 191 0.64
304 75 0.25
307 32 0.11
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (305 bp):
TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTCTTCTTCACAGTTGT
TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAATAT
GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
TGGGCCAAAGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
Found at i:57475 original size:2 final size:2
Alignment explanation
Indices: 57468--57495 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57458 GCAGAAATTT
57468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57496 CGTATAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60659 original size:26 final size:26
Alignment explanation
Indices: 60620--60672 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
60610 CTAGGGTTTA
*
60620 TTAATGATTGCTTTACTATAACAAGT
1 TTAATGATTACTTTACTATAACAAGT
* *
60646 TTAATTATTACTTTATTATAACAAGT
1 TTAATGATTACTTTACTATAACAAGT
60672 T
1 T
60673 CAGAAAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (26 bp):
TTAATGATTACTTTACTATAACAAGT
Found at i:62921 original size:20 final size:20
Alignment explanation
Indices: 62896--62936 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
62886 TCATGATAGA
62896 AGAAAACGTTAAAAAGAAAG
1 AGAAAACGTTAAAAAGAAAG
*
62916 AGAAAATGTTAAAAAGAAAG
1 AGAAAACGTTAAAAAGAAAG
62936 A
1 A
62937 CTCATGCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.20, T:0.12
Consensus pattern (20 bp):
AGAAAACGTTAAAAAGAAAG
Found at i:64421 original size:12 final size:12
Alignment explanation
Indices: 64404--64430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64394 GGTCACTTAA
64404 AAATCTTTGACT
1 AAATCTTTGACT
64416 AAATCTTTGACT
1 AAATCTTTGACT
64428 AAA
1 AAA
64431 GTCTACGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:65462 original size:28 final size:28
Alignment explanation
Indices: 65415--65485 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
65405 ATTTCAAATA
* *
65415 AAATTTTTAAAAATTTAAAATATAATTTTT
1 AAATTTATAAAAA-TTAAAATA-AATTTTC
*
65445 GAATTTATAAAAA-TAAAATAAATTTTC
1 AAATTTATAAAAATTAAAATAAATTTTC
65472 AAATTTTATAAAAA
1 AAA-TTTATAAAAA
65486 ATTTAAACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.22
28 17 0.47
30 11 0.31
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
AAATTTATAAAAATTAAAATAAATTTTC
Found at i:68232 original size:102 final size:102
Alignment explanation
Indices: 68052--68235 Score: 260
Period size: 102 Copynumber: 1.8 Consensus size: 102
68042 ACTACGCTGG
* * * * ** *
68052 AACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACTGATG
1 AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
*
68117 GACTATTTTAACCAAAAAATCTGAAAAAATATCCTGC
66 GACTATTTGAACCAAAAAATCTGAAAAAATATCCTGC
* * *
68154 AACCAAACATATTTGAGACACTAGTCATTATTTTACAGGAAATGGAATAAGATAAAATGCCAATA
1 AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
*
68219 TACTATTTGAACCAAAA
66 GACTATTTGAACCAAAA
68236 TATACTAACA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
102 70 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (102 bp):
AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
GACTATTTGAACCAAAAAATCTGAAAAAATATCCTGC
Found at i:69561 original size:2 final size:2
Alignment explanation
Indices: 69556--69587 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69546 ACACATACAC
69556 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
69588 ATAATAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:71841 original size:96 final size:96
Alignment explanation
Indices: 71731--71922 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
71721 AAAAGAGACC
*
71731 TTAGAATTCAGAAGAACAAAATGAGGTTGGAAATTGGTATAAAAAGAGAAAGGAGGAAAGTTTAA
1 TTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTTTAA
71796 GGCGGTTTGAGAGTACAGCTAAGCACTAACG
66 GGCGGTTTGAGAGTACAGCTAAGCACTAACG
71827 TTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTTTAA
1 TTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTTTAA
71892 GGCGGTTTGAGAGTACAGCTAAGCACTAACG
66 GGCGGTTTGAGAGTACAGCTAAGCACTAACG
71923 GTCACTTAAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.20
Consensus pattern (96 bp):
TTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTTTAA
GGCGGTTTGAGAGTACAGCTAAGCACTAACG
Found at i:84405 original size:12 final size:12
Alignment explanation
Indices: 84388--84414 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
84378 GGTCACTTAA
84388 AAATCTTTGACT
1 AAATCTTTGACT
84400 AAATCTTTGACT
1 AAATCTTTGACT
84412 AAA
1 AAA
84415 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:85248 original size:18 final size:18
Alignment explanation
Indices: 85221--85263 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
85211 TTAAAATATC
*
85221 TTTAATTATATCATTT-TA
1 TTTAAATATAT-ATTTATA
*
85239 TTTAAATATATTTTTATA
1 TTTAAATATATATTTATA
85257 TTTAAAT
1 TTTAAAT
85264 TAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAATATATATTTATA
Found at i:85274 original size:15 final size:16
Alignment explanation
Indices: 85254--85283 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
85244 ATATATTTTT
85254 ATATTTAAAT-TAAAA
1 ATATTTAAATATAAAA
85269 ATATTTAAATATAAA
1 ATATTTAAATATAAA
85284 TAAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTTAAATATAAAA
Found at i:86742 original size:21 final size:21
Alignment explanation
Indices: 86700--86744 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
86690 GCTTTGAATG
*
86700 TAATAAAGATTGATGCTCTAA
1 TAATAAAGATTGATGATCTAA
* * *
86721 TAATACAGATTTATGATGTAA
1 TAATAAAGATTGATGATCTAA
86742 TAA
1 TAA
86745 AGCAATCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (21 bp):
TAATAAAGATTGATGATCTAA
Found at i:89048 original size:12 final size:12
Alignment explanation
Indices: 89031--89057 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
89021 GGTTACTTGA
89031 AAATCTTTGACT
1 AAATCTTTGACT
89043 AAATCTTTGACT
1 AAATCTTTGACT
89055 AAA
1 AAA
89058 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:89928 original size:18 final size:17
Alignment explanation
Indices: 89901--89963 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
89891 TTAAAATATC
*
89901 TTTAATTATATCATTTTA
1 TTTAAATATAT-ATTTTA
*
89919 TTTAAATATATTTTTATA
1 TTTAAATATATATTT-TA
*
89937 TTTAAAT-TAAAATTTTA
1 TTTAAATAT-ATATTTTA
89954 TTTAAATATA
1 TTTAAATATA
89964 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 14 0.37
18 24 0.63
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATATATATTTTA
Found at i:89966 original size:17 final size:17
Alignment explanation
Indices: 89913--89966 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
89903 TAATTATATC
*
89913 ATTTTATTTAAATATAT
1 ATTTTATTTAAATATAA
*
89930 TTTTATATTTAAAT-TAAA
1 ATTT-TATTTAAATAT-AA
89948 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
89965 AT
1 AT
89967 AAAAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:89995 original size:24 final size:23
Alignment explanation
Indices: 89940--89997 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
89930 TTTTATATTT
* *
89940 AAATTAAAATTTTATTTAAATAT
1 AAATTAAAAATTTATTTAAATAC
* *
89963 AAATAAAAAATTTATTTTAATAC
1 AAATTAAAAATTTATTTAAATAC
*
89986 AAATTCAAAATT
1 AAATTAAAAATT
89998 AAGTGTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTAAAAATTTATTTAAATAC
Found at i:90325 original size:40 final size:39
Alignment explanation
Indices: 90280--90374 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 39
90270 TAAAAAAATA
*
90280 TATATTACTAATTTTTTTA-ATTATGATAT-ATATTTTATTT
1 TATATTACTAATTTTTTTATA-TATGATATGA-ATATTA-TT
* ** *
90320 TATATTATTAATAATTTTATATATTATATGAATATTATT
1 TATATTACTAATTTTTTTATATATGATATGAATATTATT
90359 TATATTACATAATTTT
1 TATATTAC-TAATTTT
90375 AATACATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
39 9 0.20
40 33 0.75
41 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (39 bp):
TATATTACTAATTTTTTTATATATGATATGAATATTATT
Found at i:90326 original size:24 final size:22
Alignment explanation
Indices: 90294--90348 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
90284 TTACTAATTT
90294 TTTTA-ATTATGATATATATTTTA
1 TTTTATATTATGA-ATA-ATTTTA
*
90317 TTTTATATTATTAATAATTTTA
1 TTTTATATTATGAATAATTTTA
90339 TATATTATAT
1 T-T-TTATAT
90349 GAATATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.25
23 9 0.32
24 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATATTATGAATAATTTTA
Found at i:90360 original size:22 final size:20
Alignment explanation
Indices: 90314--90363 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
90304 GATATATATT
90314 TTATTT-TATATTATTAATA
1 TTATTTATATATTATTAATA
*
90333 AT-TTTATATATTATATGAATA
1 TTATTTATATATTAT-T-AATA
90354 TTATTTATAT
1 TTATTTATAT
90364 TACATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 9 0.36
20 1 0.04
21 5 0.20
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTTATATATTATTAATA
Found at i:90399 original size:26 final size:26
Alignment explanation
Indices: 90370--90422 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
90360 ATATTACATA
90370 ATTTTAATACATA-TACAAATTTTTTT
1 ATTTTAATA-ATATTACAAATTTTTTT
* *
90396 ATTTTAATATTATTACTAATTTTTTT
1 ATTTTAATAATATTACAAATTTTTTT
90422 A
1 A
90423 CCTGCACTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTTAATAATATTACAAATTTTTTT
Found at i:93787 original size:48 final size:48
Alignment explanation
Indices: 93712--93808 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
93702 AGCAAATGTC
*
93712 AGACTTTTCGTCCTTTTATCTGTCTTCCTTCGACCCAAGAGCATGTTT
1 AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
*
93760 AGACTTTTCGTCTTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
1 AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
93808 A
1 A
93809 ACGTAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (48 bp):
AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
Found at i:93977 original size:17 final size:18
Alignment explanation
Indices: 93933--93986 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
93923 TTATTTTTTA
* *
93933 AAATTA-TTTAAATAATAA
1 AAATTATTTTTAA-AATAT
93951 AAATTATTTTT-AAATAT
1 AAATTATTTTTAAAATAT
93968 AAATTATTTTTAAAATAT
1 AAATTATTTTTAAAATAT
93986 A
1 A
93987 TAATATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 14 0.44
19 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTTTTAAAATAT
Found at i:93978 original size:18 final size:17
Alignment explanation
Indices: 93933--94000 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
93923 TTATTTTTTA
* *
93933 AAATTATTTAAATAATAA
1 AAATTATTTTAA-AATAT
*
93951 AAATTATTTTTAAATAT
1 AAATTATTTTAAAATAT
93968 AAATTATTTTTAAAATAT
1 AAATTA-TTTTAAAATAT
*
93986 ATAATATATGTTAAA
1 A-AAT-TATTTTAAA
94001 TTATTTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.24
18 21 0.50
19 9 0.21
20 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
AAATTATTTTAAAATAT
Found at i:94450 original size:31 final size:31
Alignment explanation
Indices: 94405--94464 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
94395 TTTTAAAAGG
* * *
94405 TTTATAATTGTAGTTCAATTGAAAATATTAC
1 TTTAAAATTATAGTTCAATTAAAAATATTAC
* *
94436 TTTAAAATTATAGTTTATTTAAAAATATT
1 TTTAAAATTATAGTTCAATTAAAAATATT
94465 CAAATAACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (31 bp):
TTTAAAATTATAGTTCAATTAAAAATATTAC
Found at i:94602 original size:32 final size:35
Alignment explanation
Indices: 94535--94604 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 35
94525 AGAATCGTAT
*
94535 TTAAAATATTATATATTTTATAAAAATTTTAACATA
1 TTAAAATATTATATAATTTAT-AAAATTTTAACATA
*
94571 TTAAAA-ATT-TATAATTTAT-AAATTTTGACATA
1 TTAAAATATTATATAATTTATAAAATTTTAACATA
94603 TT
1 TT
94605 TATCTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.44
34 9 0.28
35 3 0.09
36 6 0.19
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAAAATATTATATAATTTATAAAATTTTAACATA
Found at i:94657 original size:15 final size:16
Alignment explanation
Indices: 94637--94679 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
94627 AAATTTATAT
*
94637 TATAATATAA-TAAAA
1 TATAATAAAATTAAAA
94652 TATAATAAAATTAAAA
1 TATAATAAAATTAAAA
* *
94668 TTTATTAAAATT
1 TATAATAAAATT
94680 TTAATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAATAAAATTAAAA
Found at i:94872 original size:209 final size:205
Alignment explanation
Indices: 94517--94918 Score: 642
Period size: 209 Copynumber: 1.9 Consensus size: 205
94507 ATATTATGTT
*
94517 TTTATGTCAGAATCGTATTTAAAATATTATATATTTTATAAAAATTTTAACATATTAAAAATTTA
1 TTTATGTCAGAATCGTATTCAAAATATTATATATTTTATAAAAATTTTAACATATTAAAAATTTA
* * *
94582 TAATTTATAAATTTTGACATATTTATCTCTTCTTATTATATAATTAAATTTATATTATAATATAA
66 TAATTTATAAATTTTGACATATTTATCTATTCTTATTATATAATTAAATTTAGATTATAATACAA
*
94647 TAAAATATAATAAAATTAAAATTTATTAAAATTTTAATTATTAAAAATTTACTTTTACAATAACA
131 TAAAATATAATAAAATT---ATTT-TTAAAATTTTAATTATTAAAAATTTACTTTTACAACAACA
94712 CATAAATTTATCTA
192 CATAAATTTATCTA
* * * *
94726 TTTATGTCATAATCGTATTCAAAATATTATATATTTTATACAATTTTTAACATGTTAAAAATTTA
1 TTTATGTCAGAATCGTATTCAAAATATTATATATTTTATAAAAATTTTAACATATTAAAAATTTA
* * * *
94791 TTATTTATAAATTTTGACATATTTATTTATTCTTATTATATCATTAAATTTAGATTATAATACAC
66 TAATTTATAAATTTTGACATATTTATCTATTCTTATTATATAATTAAATTTAGATTATAATACAA
*
94856 TAAAATATAATAAAATTATTTTTTAAATTTTAATTATTAAAAATTTACTTTTACAACAACACA
131 TAAAATATAATAAAATTATTTTTAAAATTTTAATTATTAAAAATTTACTTTTACAACAACACA
94919 CAACTAAAAA
Statistics
Matches: 179, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
205 40 0.22
206 4 0.02
209 135 0.75
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (205 bp):
TTTATGTCAGAATCGTATTCAAAATATTATATATTTTATAAAAATTTTAACATATTAAAAATTTA
TAATTTATAAATTTTGACATATTTATCTATTCTTATTATATAATTAAATTTAGATTATAATACAA
TAAAATATAATAAAATTATTTTTAAAATTTTAATTATTAAAAATTTACTTTTACAACAACACATA
AATTTATCTA
Found at i:94985 original size:21 final size:21
Alignment explanation
Indices: 94960--95003 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
94950 AATCAATAAT
94960 TATTTATTAACAAT-ATTATTA
1 TATTTATTAA-AATCATTATTA
* *
94981 TATTTTTTAAAATCATTTTTA
1 TATTTATTAAAATCATTATTA
95002 TA
1 TA
95004 ACAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTATTAAAATCATTATTA
Found at i:95869 original size:54 final size:54
Alignment explanation
Indices: 95809--95919 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
95799 TAAAATTAAC
*
95809 ATAATGAAATTGAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
1 ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
* *
95863 ATAATGAAATTAAAATTATATAGCAATCCAATATTCAATAAAATTTAACGTGAA
1 ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
95917 ATA
1 ATA
95920 TAGACAATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (54 bp):
ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
Found at i:98100 original size:17 final size:18
Alignment explanation
Indices: 98078--98111 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
98068 AAATAAGAAC
98078 CATCAAAGA-AATTTATT
1 CATCAAAGATAATTTATT
*
98095 CATCAATGATAATTTAT
1 CATCAAAGATAATTTAT
98112 CAAAATCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
CATCAAAGATAATTTATT
Found at i:111142 original size:20 final size:20
Alignment explanation
Indices: 111105--111142 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
111095 ATTACGTGTC
**
111105 TATATATATACATGTATATA
1 TATATATATACACATATATA
111125 TATATATATACACATATA
1 TATATATATACACATATA
111143 AAAAAAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATATATACACATATATA
Found at i:114258 original size:2 final size:2
Alignment explanation
Indices: 114251--114296 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
114241 CTACTCAGAA
114251 AT AT AT AT AT AT 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 AT AT AT
114293 AT AT
1 AT AT
114297 CAAACAAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114599 original size:31 final size:31
Alignment explanation
Indices: 114563--114630 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
114553 CAACAAAGCA
* *
114563 TGAAAAATATCA-AAACAAATAAATGAAAAAT
1 TGAAAAATAGCATAAA-AAAGAAATGAAAAAT
* *
114594 TGAAAAATAGCATAAAAAAGGAATTAAAAAT
1 TGAAAAATAGCATAAAAAAGAAATGAAAAAT
114625 TGAAAA
1 TGAAAA
114631 TAATGAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.66, C:0.04, G:0.10, T:0.19
Consensus pattern (31 bp):
TGAAAAATAGCATAAAAAAGAAATGAAAAAT
Found at i:114843 original size:38 final size:39
Alignment explanation
Indices: 114768--114845 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
114758 CAAAAAGAAA
114768 AACTAAAAACGAAAGAAAGAAAAAATTTCACTTACGTTT
1 AACTAAAAACGAAAGAAAGAAAAAATTTCACTTACGTTT
*
114807 AACTAAAAACGAAAGAAAG-AAATATTTCACTTACGTTT
1 AACTAAAAACGAAAGAAAGAAAAAATTTCACTTACGTTT
114845 A
1 A
114846 TCTTTGTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 19 0.50
39 19 0.50
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (39 bp):
AACTAAAAACGAAAGAAAGAAAAAATTTCACTTACGTTT
Found at i:119140 original size:22 final size:24
Alignment explanation
Indices: 119109--119152 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
119099 AGAAATCATA
119109 AAAAAGAAT-AAA-AAGAAAATTG
1 AAAAAGAATAAAATAAGAAAATTG
*
119131 AAAAATAATAAAATAAGAAAAT
1 AAAAAGAATAAAATAAGAAAAT
119153 ATCTCACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (24 bp):
AAAAAGAATAAAATAAGAAAATTG
Found at i:120696 original size:36 final size:38
Alignment explanation
Indices: 120633--120705 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
120623 CATTAGCAAA
120633 AATCCATAAAAATATAAAAATATATATAATAATTCATG
1 AATCCATAAAAATATAAAAATATATATAATAATTCATG
120671 AATCCATAAAAATA-AAATAA-A-ATATAATAATTCAT
1 AATCCATAAAAATATAAA-AATATATATAATAATTCAT
120706 AAGTGGTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 14 0.41
37 4 0.12
38 16 0.47
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.30
Consensus pattern (38 bp):
AATCCATAAAAATATAAAAATATATATAATAATTCATG
Found at i:121758 original size:103 final size:103
Alignment explanation
Indices: 121579--121773 Score: 293
Period size: 103 Copynumber: 1.9 Consensus size: 103
121569 ACAAAGTATG
* ** *
121579 AATATCCTGCAACCAAACATACTCGAGGCACTAGTCATCATCTTGTAGGAAATAGAATAAGCTAA
1 AATATCCTGCAACCAAACATACTCGAGACACTAGTCATCATCTTACAGGAAAAAGAATAAGCTAA
*
121644 GATACCAATAGACTATTTTAACCAAAAAAATCAGAAGA
66 GATACCAATAGACTATTTTAAACAAAAAAATCAGAAGA
* * * *
121682 AATATCCTGCAATCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAAAAGAATAAGCTAA
1 AATATCCTGCAACCAAACATACTCGAGACACTAGTCATCATCTTACAGGAAAAAGAATAAGCTAA
121747 GATA-CAGATAGACTATTTTAAACAAAA
66 GATACCA-ATAGACTATTTTAAACAAAA
121774 TGTACTGACC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 2 0.02
103 80 0.98
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (103 bp):
AATATCCTGCAACCAAACATACTCGAGACACTAGTCATCATCTTACAGGAAAAAGAATAAGCTAA
GATACCAATAGACTATTTTAAACAAAAAAATCAGAAGA
Found at i:123529 original size:23 final size:22
Alignment explanation
Indices: 123492--123560 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
123482 AAATAAAATA
* *
123492 TTTTTATTAACTTTATATTTTAAT
1 TTTTTATT-ATTTTA-AATTTAAT
* *
123516 TTTTTATTATTTTAAATATATT
1 TTTTTATTATTTTAAATTTAAT
*
123538 TTTTTATATATTTTAACTTTAAT
1 TTTTTAT-TATTTTAAATTTAAT
123561 CACTTTCTCG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 12 0.32
23 17 0.46
24 8 0.22
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTATTATTTTAAATTTAAT
Found at i:132827 original size:23 final size:22
Alignment explanation
Indices: 132777--132827 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
132767 ATTTTTAGAT
*
132777 ATAAAAAATTAAAATTTATCTAA
1 ATAAAAAATTAAAATTTA-CAAA
132800 A-AAAAAATATAAAACTTTA-AAA
1 ATAAAAAAT-TAAAA-TTTACAAA
132822 ATAAAA
1 ATAAAA
132828 TTATAATCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
22 10 0.42
23 10 0.42
24 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAAAATTAAAATTTACAAA
Found at i:134360 original size:22 final size:20
Alignment explanation
Indices: 134335--134378 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
134325 TTATATATTT
*
134335 TATTATATTATTATTTATAAAA
1 TATTAT-TTATTAATT-TAAAA
*
134357 TATTATTTTTTAATTTAAAA
1 TATTATTTATTAATTTAAAA
134377 TA
1 TA
134379 AATAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 7 0.35
22 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTATTAATTTAAAA
Found at i:135078 original size:26 final size:26
Alignment explanation
Indices: 135049--135104 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
135039 TTAATATAAT
** *
135049 AAATAATAAAATAAAATTTTAAAATA
1 AAATAATAAAATAAAAAATTAAAAAA
**
135075 AAATAATTTAATAAAAAATTAAAAAA
1 AAATAATAAAATAAAAAATTAAAAAA
135101 AAAT
1 AAAT
135105 TAAATCATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATAATAAAATAAAAAATTAAAAAA
Found at i:135087 original size:31 final size:31
Alignment explanation
Indices: 135018--135090 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
135008 ATTATTATTT
* * *
135018 AATAATAAAAATAATATTTTATTAATATAATA
1 AATAAT-AAAATAAAATTTTATAAATAAAATA
135050 AATAATAAAATAAAATTTTA-AAATAAAATA
1 AATAATAAAATAAAATTTTATAAATAAAATA
*
135080 ATTTAATAAAA
1 A-ATAATAAAA
135091 AATTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 9 0.25
31 21 0.58
32 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AATAATAAAATAAAATTTTATAAATAAAATA
Found at i:146784 original size:22 final size:23
Alignment explanation
Indices: 146757--146817 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
146747 AAATTAATTT
146757 TTATATTATATTATATTTTTA-A
1 TTATATTATATTATATTTTTATA
*
146779 TTATATT-TA-AATTATTTTTATA
1 TTATATTATATTA-TATTTTTATA
*
146801 TTA-AATA-ATTATATTTT
1 TTATATTATATTATATTTT
146818 ATTTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 19 0.59
22 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATATTATATTATATTTTTATA
Found at i:146826 original size:20 final size:19
Alignment explanation
Indices: 146748--146824 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 19
146738 ATATAAATAA
*
146748 AATTAATTTTTATATTATAT
1 AATT-ATTTTTATATTAAAT
* *
146768 TA-TATTTTTA-ATTATATTT
1 AATTATTTTTATATTA-A-AT
146787 AAATTATTTTTATATTAAAT
1 -AATTATTTTTATATTAAAT
146807 AATTATATTTTAT-TTAAA
1 AATTAT-TTTTATATTAAA
146825 ATTACTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 13 0.28
20 9 0.20
21 9 0.20
22 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTATTTTTATATTAAAT
Found at i:148724 original size:27 final size:27
Alignment explanation
Indices: 148677--148730 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
148667 AATAAAATTT
*
148677 ATTTATTATAAATTATAAATATATTAAA
1 ATTTATTATAAATCATAAATAT-TTAAA
148705 ATTTA-TATAAATACAT-AATATTTAAA
1 ATTTATTATAAAT-CATAAATATTTAAA
148731 TATAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 12 0.50
28 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTTATTATAAATCATAAATATTTAAA
Found at i:148774 original size:30 final size:29
Alignment explanation
Indices: 148719--148775 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
148709 ATATAAATAC
*
148719 ATAATATTTAAATATAATTATAATAAAAA
1 ATAATATTTAAATATAATTAAAATAAAAA
148748 ATAATAATTTAAATATAA-TACAAATAAA
1 ATAAT-ATTTAAATATAATTA-AAATAAA
148776 TCATAGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAATATTTAAATATAATTAAAATAAAAA
Found at i:149150 original size:20 final size:20
Alignment explanation
Indices: 149127--149169 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
149117 CTTTATAATA
*
149127 ATATGAAAAATATTATTTTT
1 ATATGAAAAATAATATTTTT
* * *
149147 ATATTAATATTAATATTTTT
1 ATATGAAAAATAATATTTTT
149167 ATA
1 ATA
149170 ATTAATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATGAAAAATAATATTTTT
Found at i:149182 original size:21 final size:20
Alignment explanation
Indices: 149140--149179 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
149130 TGAAAAATAT
149140 TATTTTTATATTAATATTAA
1 TATTTTTATATTAATATTAA
149160 TATTTTTATAATTAAT-TTAA
1 TATTTTTAT-ATTAATATTAA
149180 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTATATTAATATTAA
Found at i:149200 original size:22 final size:24
Alignment explanation
Indices: 149150--149223 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
149140 TATTTTTATA
* *
149150 TTAATATTAATATTTTTATAATTAAT
1 TTAACATTAAAATTTTT-TAA-TAAT
149176 TTAA-A-TAAAATTTTTTAATAAT
1 TTAACATTAAAATTTTTTAATAAT
**
149198 TTAACATTAATTTTTTTTAA-AAT
1 TTAACATTAAAATTTTTTAATAAT
149221 TTA
1 TTA
149224 TATTTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.19
23 10 0.23
24 20 0.47
25 1 0.02
26 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAACATTAAAATTTTTTAATAAT
Found at i:149235 original size:23 final size:24
Alignment explanation
Indices: 149150--149223 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 24
149140 TATTTTTATA
* *
149150 TTAATATTAATATTTTTATAATTAAT
1 TTAACATTAA-ATTTTTTTAA-TAAT
*
149176 TTAA-A-TAAAATTTTTTAATAAT
1 TTAACATTAAATTTTTTTAATAAT
*
149198 TTAACATTAATTTTTTTTAA-AAT
1 TTAACATTAAATTTTTTTAATAAT
149221 TTA
1 TTA
149224 TATTTAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.19
23 15 0.36
24 14 0.33
25 1 0.02
26 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAACATTAAATTTTTTTAATAAT
Found at i:149253 original size:15 final size:17
Alignment explanation
Indices: 149218--149257 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
149208 TTTTTTTTAA
149218 AATTTATATTTAAATTTT
1 AATTTATA-TTAAATTTT
149236 AATTTATA-TAAA-TTT
1 AATTTATATTAAATTTT
149251 AATTTAT
1 AATTTAT
149258 CAATAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
18 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTATATTAAATTTT
Found at i:149678 original size:14 final size:14
Alignment explanation
Indices: 149661--149694 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
149651 TTTAAATTAA
149661 ATTAATTAATTTA-T
1 ATTAATT-ATTTATT
149675 ATTAATTATTTATT
1 ATTAATTATTTATT
149689 ATTAAT
1 ATTAAT
149695 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTATTTATT
Found at i:149704 original size:50 final size:46
Alignment explanation
Indices: 149650--149772 Score: 121
Period size: 47 Copynumber: 2.6 Consensus size: 46
149640 TTTTATTTAG
149650 ATTTAAATTAAATTAATTAATTTATATTAATTATTTAT-TATTAATAA-AAA
1 ATTTAAA-TAAATT-ATT--TTTATATTAA-TATTTATATATT-ATAATAAA
*
149700 ATTT-AA-AAATTATTTTTATATTAATATTTATATATTATAATTAA
1 ATTTAAATAAATTATTTTTATATTAATATTTATATATTATAATAAA
*
149744 ATTTAAATAAAAATATTTTT-TAATTAATA
1 ATTTAAAT-AAATTATTTTTAT-ATTAATA
149773 AATATTAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
43 11 0.17
44 20 0.31
45 2 0.03
46 4 0.06
47 22 0.34
49 2 0.03
50 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (46 bp):
ATTTAAATAAATTATTTTTATATTAATATTTATATATTATAATAAA
Found at i:149711 original size:43 final size:44
Alignment explanation
Indices: 149664--149750 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
149654 AAATTAAATT
149664 AATTA-ATTTATATTAATTATTTAT-TATTAATAA-AAAATTTAAA
1 AATTATATTTATATTAA-TATTTATATATT-ATAATAAAATTTAAA
* *
149707 AATTATTTTTATATTAATATTTATATATTATAATTAAATTTAAA
1 AATTATATTTATATTAATATTTATATATTATAATAAAATTTAAA
149751 TAAAAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 16 0.41
44 23 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (44 bp):
AATTATATTTATATTAATATTTATATATTATAATAAAATTTAAA
Found at i:149777 original size:18 final size:17
Alignment explanation
Indices: 149745--149778 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
149735 TATAATTAAA
149745 TTTAAATAAAAATATTT
1 TTTAAATAAAAATATTT
*
149762 TTTAATTAATAAATATT
1 TTTAAATAA-AAATATT
149779 AATTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAATAAAAATATTT
Found at i:149825 original size:22 final size:22
Alignment explanation
Indices: 149800--149847 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
149790 TATCAAATCG
**
149800 ATTTAAATTGATAAAAAAATTT
1 ATTTAAATACATAAAAAAATTT
*
149822 ATTTAAATACATAAATAAATTT
1 ATTTAAATACATAAAAAAATTT
149844 ATTT
1 ATTT
149848 GATATGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTAAATACATAAAAAAATTT
Found at i:150219 original size:2 final size:2
Alignment explanation
Indices: 150209--150241 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
150199 AAAATATAGA
*
150209 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150242 TGAAAAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:158990 original size:20 final size:21
Alignment explanation
Indices: 158965--159006 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
158955 TAAAAAATTC
158965 ATAATTATATA-AATTTTAAA
1 ATAATTATATATAATTTTAAA
*
158985 ATAATTATATATATTTTTAAA
1 ATAATTATATATAATTTTAAA
159006 A
1 A
159007 AACTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTATATATAATTTTAAA
Found at i:159013 original size:24 final size:22
Alignment explanation
Indices: 158965--159034 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 22
158955 TAAAAAATTC
*
158965 ATAATTATATA-AATTTT-AAA
1 ATAATTATATATATTTTTAAAA
158985 ATAATTATATATATTTTTAAAAA
1 ATAATTATATATATTTTT-AAAA
* *
159008 ACTAATTACAATTTATTTTTTAAAA
1 A-TAATTA-TATATA-TTTTTAAAA
159033 AT
1 AT
159035 TTTTTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 11 0.27
21 5 0.12
23 4 0.10
24 7 0.17
25 9 0.22
26 5 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATTATATATATTTTTAAAA
Found at i:163128 original size:18 final size:18
Alignment explanation
Indices: 163101--163145 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
163091 AATTTATTTT
163101 TAAAAA-TTAT-TAAAATA
1 TAAAAATTTATAT-AAATA
*
163118 TCAAAATTTATATAAATA
1 TAAAAATTTATATAAATA
163136 TAAAAATTTA
1 TAAAAATTTA
163146 GAAACGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 18 0.75
19 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATTTATATAAATA
Found at i:164970 original size:22 final size:22
Alignment explanation
Indices: 164950--165004 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 22
164940 TTTAAATTAT
164950 TTTAAATATTAAATAAAATTAAA
1 TTTAAAT-TTAAATAAAATTAAA
164973 TTTAAATTTAAATAATAATTTAATA
1 TTTAAATTTAAATAA-AA-TTAA-A
164998 TTTAAAT
1 TTTAAAT
165005 AAATATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.28
23 9 0.31
24 4 0.14
25 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATTTAAATAAAATTAAA
Found at i:165002 original size:19 final size:18
Alignment explanation
Indices: 164971--165006 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
164961 AATAAAATTA
164971 AATTTAAATTTAAATAAT
1 AATTTAAATTTAAATAAT
164989 AATTTAATATTTAAATAA
1 AATTTAA-ATTTAAATAA
165007 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAAATTTAAATAAT
Found at i:165012 original size:25 final size:24
Alignment explanation
Indices: 164950--165017 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
164940 TTTAAATTAT
*
164950 TTTAAATATTAAAT-AAAA-TTAAA
1 TTTAAAT-TAAAATAAAAATTTAAA
* *
164973 TTTAAATTTAAATAATAATTTAATA
1 TTTAAATTAAAATAAAAATTTAA-A
164998 TTTAAA-TAAATATAAAAATT
1 TTTAAATTAAA-ATAAAAATT
165018 CATATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.16
23 10 0.26
24 7 0.18
25 15 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATTAAAATAAAAATTTAAA
Found at i:165205 original size:16 final size:16
Alignment explanation
Indices: 165165--165220 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 16
165155 AAATTTAAAA
165165 TTAAA-AATAAAAATT
1 TTAAATAATAAAAATT
165180 AATTATAATAATAAAAATT
1 --TTA-AATAATAAAAATT
* *
165199 TTAAATAACATAAA-T
1 TTAAATAATAAAAATT
165214 TTAAATA
1 TTAAATA
165221 TACAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.23
16 9 0.26
17 6 0.17
18 2 0.06
19 10 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAATAATAAAAATT
Found at i:167061 original size:19 final size:19
Alignment explanation
Indices: 167037--167075 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
167027 TCTTTAGGTG
167037 CATGCATATACAATTCTGT
1 CATGCATATACAATTCTGT
167056 CATGCATATACAATTCTGT
1 CATGCATATACAATTCTGT
167075 C
1 C
167076 CTTGAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (19 bp):
CATGCATATACAATTCTGT
Found at i:169015 original size:2 final size:2
Alignment explanation
Indices: 169008--169044 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
168998 TTAAATAAGA
169008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
169045 GGAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:174115 original size:22 final size:20
Alignment explanation
Indices: 174090--174187 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 20
174080 AAACATAATT
*
174090 AAAACTATATGAAAAATTATC
1 AAAATTATAT-AAAAATTATC
174111 AAAAATTATATTAAAAATTATC
1 -AAAATTATA-TAAAAATTATC
174133 AAAATTATTATAAATAA-TATC
1 AAAATTA-TATAAA-AATTATC
174154 AAAATTATATAAAAAATTA-C
1 AAAATTATAT-AAAAATTATC
174174 AAAATTATAATAAA
1 AAAATTAT-ATAAA
174188 TGTTATCAAG
Statistics
Matches: 69, Mismatches: 1, Indels: 14
0.82 0.01 0.17
Matches are distributed among these distances:
20 17 0.25
21 29 0.42
22 22 0.32
23 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (20 bp):
AAAATTATATAAAAATTATC
Found at i:174128 original size:12 final size:12
Alignment explanation
Indices: 174090--174172 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 12
174080 AAACATAATT
* *
174090 AAAACTATATGA
1 AAAATTATATCA
174102 AAAA-T-TATCA
1 AAAATTATATCA
*
174112 AAAATTATATTA
1 AAAATTATATCA
174124 AAAA-T-TATC-
1 AAAATTATATCA
174133 AAAATTAT-T-A
1 AAAATTATATCA
* *
174143 TAAATAATATC-
1 AAAATTATATCA
*
174154 AAAATTATATAA
1 AAAATTATATCA
174166 AAAATTA
1 AAAATTA
174173 CAAAATTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
9 4 0.07
10 19 0.35
11 13 0.24
12 19 0.35
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (12 bp):
AAAATTATATCA
Found at i:174179 original size:41 final size:43
Alignment explanation
Indices: 174107--174188 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
174097 TATGAAAAAT
* *
174107 TATCAAAAATTATATTAAAAATTATCAAAATTATTATAAATAA
1 TATCAAAAATTATATAAAAAATTATCAAAATTATAATAAATAA
174150 TATC-AAAATTATATAAAAAATTA-CAAAATTATAATAAAT
1 TATCAAAAATTATATAAAAAATTATCAAAATTATAATAAAT
174189 GTTATCAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 15 0.41
42 18 0.49
43 4 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (43 bp):
TATCAAAAATTATATAAAAAATTATCAAAATTATAATAAATAA
Found at i:174195 original size:41 final size:42
Alignment explanation
Indices: 174105--174196 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 42
174095 TATATGAAAA
* *
174105 ATTATCAAAAATTATATTAAAAATTATCAAAATTATTATAAAT
1 ATTATC-AAAATTATATAAAAAATTATCAAAATTATAATAAAT
*
174148 AATATCAAAATTATATAAAAAATTA-CAAAATTATAATAAAT
1 ATTATCAAAATTATATAAAAAATTATCAAAATTATAATAAAT
*
174189 GTTATCAA
1 ATTATCAA
174197 GATTTTTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 21 0.48
42 18 0.41
43 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (42 bp):
ATTATCAAAATTATATAAAAAATTATCAAAATTATAATAAAT
Found at i:187131 original size:18 final size:17
Alignment explanation
Indices: 187094--187143 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
187084 AAATTTTATT
187094 TAAATTTAATTAAAATA
1 TAAATTTAATTAAAATA
187111 TAAATATTAATATAAAA-A
1 TAAAT-TTAAT-TAAAATA
187129 T-AATTT--TTAAAATA
1 TAAATTTAATTAAAATA
187143 T
1 T
187144 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
16 2 0.07
17 8 0.27
18 7 0.23
19 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAATTAAAATA
Found at i:189371 original size:15 final size:16
Alignment explanation
Indices: 189343--189379 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
189333 ACATCAATAA
*
189343 TAAATTATATAATATT
1 TAAATTATAAAATATT
189359 TAAATTA-AAAATATT
1 TAAATTATAAAATATT
189374 TAAATT
1 TAAATT
189380 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTATAAAATATT
Found at i:189490 original size:58 final size:55
Alignment explanation
Indices: 189389--189500 Score: 129
Period size: 58 Copynumber: 2.0 Consensus size: 55
189379 TTTTTATTTT
* *
189389 TAAAATTAACTATTTATTATTTTTACTCAATGTCATTAATTTTA-ATAATATAATA
1 TAAAATTAACTATTTATTATTTTTACTAAATATCATTAATTTTACA-AATATAATA
* *
189444 TAAAATTAATTAATTTATATATTTTTA-TAAATTAATCATTGATTTTACAAATATAAT
1 TAAAATTAACT-ATTTAT-TATTTTTACTAAA-T-ATCATTAATTTTACAAATATAAT
189501 TACGATGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
55 10 0.21
56 9 0.19
57 9 0.19
58 19 0.40
59 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (55 bp):
TAAAATTAACTATTTATTATTTTTACTAAATATCATTAATTTTACAAATATAATA
Found at i:196571 original size:6 final size:6
Alignment explanation
Indices: 196560--196587 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
196550 TATTTTTTAT
196560 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
196588 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:196940 original size:19 final size:18
Alignment explanation
Indices: 196906--196950 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
196896 TTTATTAGAC
196906 TAATATT-ATGAATTAAA
1 TAATATTAATGAATTAAA
196923 TAATATTAATGTAATTAAA
1 TAATATTAATG-AATTAAA
*
196942 AAATATTAA
1 TAATATTAA
196951 AAAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TAATATTAATGAATTAAA
Found at i:196994 original size:29 final size:31
Alignment explanation
Indices: 196951--197014 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
196941 AAAATATTAA
196951 AAAAATATTTAAAAA-TAATTATTATTT-TTT
1 AAAAATATTTAAAAATTAATTATT-TTTATTT
*
196981 AAAAA-ATTTAAAAATTATTTATTTTTATTT
1 AAAAATATTTAAAAATTAATTATTTTTATTT
197011 AAAA
1 AAAA
197015 TTTACTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AAAAATATTTAAAAATTAATTATTTTTATTT
Found at i:210636 original size:35 final size:35
Alignment explanation
Indices: 210590--210659 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
210580 CCAATTATTG
210590 AGGCAGAGAGTTACTCATGGTGATAACATTGGCTT
1 AGGCAGAGAGTTACTCATGGTGATAACATTGGCTT
210625 AGGCAGAGAGTTACTCATGGTGATAACATTGGCTT
1 AGGCAGAGAGTTACTCATGGTGATAACATTGGCTT
210660 TACTGTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (35 bp):
AGGCAGAGAGTTACTCATGGTGATAACATTGGCTT
Found at i:214565 original size:18 final size:19
Alignment explanation
Indices: 214521--214565 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
214511 CAAATTGATC
*
214521 AAAAATT-TTAATTATTAT
1 AAAAATTATTAAATATTAT
214539 AAAAA-TATTAAATATTA-
1 AAAAATTATTAAATATTAT
214556 AAAAATTATT
1 AAAAATTATT
214566 CTTATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTATTAAATATTAT
Found at i:214603 original size:23 final size:22
Alignment explanation
Indices: 214562--214605 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
214552 ATTAAAAAAT
*
214562 TATTCTTATATTAATATTTAAG
1 TATTCTTATATTAAAATTTAAG
*
214584 TATTTTTATAATTAAAATTTAA
1 TATTCTTAT-ATTAAAATTTAA
214606 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTCTTATATTAAAATTTAAG
Found at i:214963 original size:2 final size:2
Alignment explanation
Indices: 214956--214982 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
214946 TTTGAAAATC
214956 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
214983 CATGGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219645 original size:4 final size:4
Alignment explanation
Indices: 219638--219664 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
219628 ATTTATTTAA
219638 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
219665 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:220362 original size:2 final size:2
Alignment explanation
Indices: 220355--220388 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
220345 AATTTAACCA
220355 AT AT 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
220389 TTAACATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220583 original size:2 final size:2
Alignment explanation
Indices: 220576--220609 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
220566 TGCTAAACCC
220576 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
220610 AGAAACCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:222050 original size:2 final size:2
Alignment explanation
Indices: 222043--222073 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
222033 TTGGGGAGTT
222043 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
222074 GGGTTTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:238654 original size:2 final size:2
Alignment explanation
Indices: 238642--238672 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
238632 AATTTAGGTG
*
238642 TA TA CA 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 TA T
238673 TGTGATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.