Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003876.1 Hibiscus syriacus cultivar Beakdansim tig00008351_pilon, whole genome shotgun sequence
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: 70408
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1958 original size:49 final size:49
Alignment explanation
Indices: 1903--2087 Score: 210
Period size: 49 Copynumber: 3.6 Consensus size: 49
1893 TAGTATGATT
*
1903 TAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1952 TAGTAATGATTAGTAATAATGAAATTA-TATTAATATTTAATGATTTGATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG--A
* *
2002 GTAATGCTTTGGTAATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTAA
1 -T-A-------GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * *
2060 AAGTAATGATTAGTAATCATGCAATTAT
1 TAGTAATGATTAGTAATAATGAAATTAT
2088 AATAATGATT
Statistics
Matches: 119, Mismatches: 5, Indels: 24
0.80 0.03 0.16
Matches are distributed among these distances:
48 20 0.17
49 51 0.43
50 1 0.01
51 1 0.01
52 1 0.01
56 1 0.01
58 1 0.01
59 24 0.20
60 19 0.16
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:1962 original size:108 final size:109
Alignment explanation
Indices: 1844--2087 Score: 384
Period size: 108 Copynumber: 2.3 Consensus size: 109
1834 AATAATTATT
* *
1844 TAGTCATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-ATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* *
1908 ATGATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGA
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAA
* *
1952 TAGTAATGATTAGTAATAATGAAATTA-TATTAATATTTAATGATTTGATAGTAATGCTTTGGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
2016 ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTAA
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAA
* * *
2060 AAGTAATGATTAGTAATCATGCAATTAT
1 TAGTAATGATTAGTAATAATGAAATTAT
2088 AATAATGATT
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
107 25 0.20
108 99 0.80
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (109 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAA
Found at i:2066 original size:60 final size:59
Alignment explanation
Indices: 1954--2067 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 59
1944 TGATTTGATA
* *
1954 GTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTGATAGTAATGCTTTG
1 GTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTAAAAGTAATGCTTTG
*
2013 GTAATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTAAAAGTAATG
1 GTAATGATTAGTAATAATGAAATTA-TATTAATATTTAATGATTTAAAAGTAATG
2068 ATTAGTAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 24 0.47
60 27 0.53
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (59 bp):
GTAATGATTAGTAATAATGAAATTATATTAATATTTAATGATTTAAAAGTAATGCTTTG
Found at i:2076 original size:59 final size:58
Alignment explanation
Indices: 1843--2076 Score: 290
Period size: 59 Copynumber: 4.1 Consensus size: 58
1833 TAATAATTAT
* *
1843 TTAGTCATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTATGA
*
1901 TTTAGTAATGATTAGTAATAATTAAATTATTATTAATATTT-A--A--TGAT--T-TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTATGA
*
1952 -TAGTAATGATTAGTAATAATGAAATTA-TATTAATATTTAATGATTTGATAGTAATGCT
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-ATG-A
* * * *
2010 TTGGTAATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTAAAAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-ATGA
2069 TTAGTAAT
1 TTAGTAAT
2077 CATGCAATTA
Statistics
Matches: 152, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
48 11 0.07
49 27 0.18
51 4 0.03
52 1 0.01
53 4 0.03
54 4 0.03
55 1 0.01
56 1 0.01
57 2 0.01
58 1 0.01
59 69 0.45
60 27 0.18
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.45
Consensus pattern (58 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTATGA
Found at i:2116 original size:49 final size:50
Alignment explanation
Indices: 1882--2116 Score: 126
Period size: 49 Copynumber: 4.5 Consensus size: 50
1872 TATTAATATT
* * * *
1882 TAATGATTTGATAGT-ATGATTTAGTAATGATTAGTAATAATTAAATTATTAT
1 TAATGATTTGATACTAATGA-TT--TAATGATTAGTAATCATGAAATTATTAA
* * * *
1934 TAAT-ATTTAATGA-T-TTGATAGTAATGATTAGTAATAATGAAATTATATTAATA
1 TAATGATTTGAT-ACTAATGAT-TTAATGATTAGTAATCATGAAA-T-TATT-A-A
* * *
1987 TTTAATGATTTGATAGTAATGCTTTGGTAATGATTAGTAATCATGAAATTATTAT
1 --TAATGATTTGATACTAATG-ATT--TAATGATTAGTAATCATGAAATTATTAA
* * ** *
2042 TAAT-ATTTAATGATTTAA--AAGTAATGATTAGTAATCATGCAATTA-TAA
1 TAATGATTTGAT-A-CTAATGATTTAATGATTAGTAATCATGAAATTATTAA
2090 TAATGATTTGATACTAATGATTTAATG
1 TAATGATTTGATACTAATGATTTAATG
2117 GGGTGATAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
47 3 0.02
48 7 0.05
49 55 0.39
50 2 0.01
51 14 0.10
52 12 0.08
53 5 0.04
54 3 0.02
55 5 0.04
56 8 0.06
57 6 0.04
58 2 0.01
59 20 0.14
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (50 bp):
TAATGATTTGATACTAATGATTTAATGATTAGTAATCATGAAATTATTAA
Found at i:2295 original size:14 final size:14
Alignment explanation
Indices: 2276--2364 Score: 61
Period size: 14 Copynumber: 6.9 Consensus size: 14
2266 CAATTAACCA
2276 TAATAATGATTTAG
1 TAATAATGATTTAG
**
2290 TAATAACCA--TA-
1 TAATAATGATTTAG
2301 TAATAATGATTT-G
1 TAATAATGATTTAG
2314 ATAATAATGATTTAG
1 -TAATAATGATTTAG
*
2329 TAAT--T-A-TTAT
1 TAATAATGATTTAG
*
2339 TAATAATGATTTAT
1 TAATAATGATTTAG
*
2353 TATTAAT-ATTTA
1 TAATAATGATTTA
2365 ATGATTTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.12
11 8 0.13
12 4 0.07
13 7 0.12
14 33 0.55
15 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (14 bp):
TAATAATGATTTAG
Found at i:2345 original size:24 final size:23
Alignment explanation
Indices: 2315--2395 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
2305 AATGATTTGA
2315 TAATAATGATTTAGTAATTATTAT
1 TAATAATGATTTA-TAATTATTAT
* *
2339 TAATAATGATTTATTATTAATAT
1 TAATAATGATTTATAATTATTAT
*
2362 T--TAATGATTT-TATATTAATGAT
1 TAATAATGATTTATA-ATT-ATTAT
2384 TAAGTAATGATT
1 TAA-TAATGATT
2396 AGTAATAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 4 0.09
23 9 0.19
24 13 0.28
25 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
TAATAATGATTTATAATTATTAT
Found at i:2368 original size:21 final size:22
Alignment explanation
Indices: 2317--2395 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 22
2307 TGATTTGATA
* *
2317 ATAATGATTTAGTAATTATTATT
1 ATAATGATTTA-TTATTAATATT
2340 AATAATGATTTATTATTAATATT
1 -ATAATGATTTATTATTAATATT
2363 -TAATGATTT-TATATTAATGATT
1 ATAATGATTTAT-TATTAAT-ATT
2385 AAGTAATGATT
1 -A-TAATGATT
2396 AGTAATAATG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
20 1 0.02
21 16 0.33
22 3 0.06
23 9 0.19
24 11 0.23
25 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
ATAATGATTTATTATTAATATT
Found at i:2378 original size:38 final size:38
Alignment explanation
Indices: 2275--2384 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 38
2265 GCAATTAACC
* * **
2275 ATAATAATGATTTAGTAATAACCATATAATAATGATTTG
1 ATAATAATGATTTAATAATTATTAT-TAATAATGATTTG
*
2314 ATAATAATGATTTAGTAATTATTATTAATAATGATTT-
1 ATAATAATGATTTAATAATTATTATTAATAATGATTTG
* * *
2351 ATTATTAAT-ATTTAATGATT-TTA-TATTAATGATT
1 A-TAATAATGATTTAATAATTATTATTAATAATGATT
2385 AAGTAATGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 10 0.16
36 3 0.05
37 10 0.16
38 18 0.29
39 22 0.35
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (38 bp):
ATAATAATGATTTAATAATTATTATTAATAATGATTTG
Found at i:2685 original size:11 final size:11
Alignment explanation
Indices: 2669--2835 Score: 100
Period size: 11 Copynumber: 14.1 Consensus size: 11
2659 TAATATTGAC
2669 AATAATGATTT
1 AATAATGATTT
2680 AATAATGATTTT
1 AATAATGA-TTT
* * *
2692 AATATTTAATGT
1 AATA-ATGATTT
* *
2704 ACTGATGATTT
1 AATAATGATTT
*
2715 AGTAATGATTGAT
1 AATAATGATT--T
*
2728 AATAATCATTAT
1 AATAATGATT-T
2740 AATAATGATTTAGT
1 AATAATGA-TT--T
*
2754 AATAATTATTAT
1 AATAATGATT-T
2766 AATAATGATTT
1 AATAATGATTT
* * *
2777 GATAATAATGAT
1 AATAATGAT-TT
*
2789 ATTAATGATTT
1 AATAATGATTT
2800 AATAATGATTT
1 AATAATGATTT
* *
2811 AGTAATTATTATT
1 AATAATGA-T-TT
2824 AATAATGATTT
1 AATAATGATTT
2835 A
1 A
2836 TTATTAATAT
Statistics
Matches: 118, Mismatches: 29, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
11 48 0.41
12 39 0.33
13 23 0.19
14 8 0.07
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (11 bp):
AATAATGATTT
Found at i:2695 original size:23 final size:23
Alignment explanation
Indices: 2669--2834 Score: 93
Period size: 23 Copynumber: 7.0 Consensus size: 23
2659 TAATATTGAC
2669 AATAATGATTTAATAATGATTTT
1 AATAATGATTTAATAATGATTTT
* * * * *
2692 AATATTTAATGTACTGATGA-TTT
1 AATA-ATGATTTAATAATGATTTT
* * *
2715 AGTAATGATTGATAATAATCATTAT
1 AATAATGATT--TAATAATGATTTT
* *
2740 AATAATGATTTAGTAATAATTATTAT
1 AATAATGA-TT--TAATAATGATTTT
* * **
2766 AATAATGATTTGATAATAATGAT
1 AATAATGATTTAATAATGATTTT
*
2789 ATTAATGATTTAATAATGA-TTT
1 AATAATGATTTAATAATGATTTT
* *
2811 AGTAATTATTATTAATAATGATTT
1 AATAATGA-T-TTAATAATGATTT
2835 ATTATTAATA
Statistics
Matches: 108, Mismatches: 27, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
22 10 0.09
23 37 0.34
24 26 0.24
25 13 0.12
26 22 0.20
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (23 bp):
AATAATGATTTAATAATGATTTT
Found at i:2764 original size:26 final size:26
Alignment explanation
Indices: 2717--2805 Score: 98
Period size: 26 Copynumber: 3.6 Consensus size: 26
2707 GATGATTTAG
*
2717 TAATGATTGA-TAATAATCATTATAA
1 TAATGATTTAGTAATAATCATTATAA
*
2742 TAATGATTTAGTAATAATTATTATAA
1 TAATGATTTAGTAATAATCATTATAA
*
2768 TAATGATTT-GATAATAATGA-TAT--
1 TAATGATTTAG-TAATAATCATTATAA
*
2791 TAATGATTTAATAAT
1 TAATGATTTAGTAAT
2806 GATTTAGTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
23 13 0.23
25 13 0.23
26 31 0.54
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (26 bp):
TAATGATTTAGTAATAATCATTATAA
Found at i:2825 original size:24 final size:23
Alignment explanation
Indices: 2789--2855 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
2779 TAATAATGAT
2789 ATTAATGATTTAATAATGATTTAGTA
1 ATTAAT-A-TTAATAATGATTTA-TA
* *
2815 ATTATTATTAATAATGATTTATT
1 ATTAATATTAATAATGATTTATA
2838 ATTAATATT--TAATGATTT
1 ATTAATATTAATAATGATTT
2856 GATACTAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 9 0.24
23 9 0.24
24 14 0.37
25 1 0.03
26 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
ATTAATATTAATAATGATTTATA
Found at i:5465 original size:39 final size:39
Alignment explanation
Indices: 5363--5486 Score: 110
Period size: 44 Copynumber: 3.1 Consensus size: 39
5353 CAAATATAAC
* *
5363 TTAACTATTTAACTATC--ACAAACTAATTAAATATTTT
1 TTAACTATATAACTATCAAACAAACTAATTAATTATTTT
* *
5400 TTTA-TATAACTAACGACTAATAAAACAAACTAATTAATTATTTT
1 TTAACTAT-A-T-A--ACT-ATCAAACAAACTAATTAATTATTTT
* *
5444 TTAACTATATAACTATCAAACATACTAATTAAATAATTTT
1 TTAACTATATAACTATCAAACAAACTAATT-AATTATTTT
5484 TTA
1 TTA
5487 TTTCTGTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
36 3 0.04
37 3 0.04
38 1 0.01
39 15 0.22
40 14 0.20
41 3 0.04
42 3 0.04
43 1 0.01
44 23 0.33
45 3 0.04
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (39 bp):
TTAACTATATAACTATCAAACAAACTAATTAATTATTTT
Found at i:5674 original size:13 final size:13
Alignment explanation
Indices: 5635--5681 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5625 CTCACAAGTG
5635 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
5649 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
5663 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
5676 -CTTTCT
1 CCTTTCT
5682 TTCTCGGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:6088 original size:11 final size:11
Alignment explanation
Indices: 6064--6107 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
6054 GGCTCATGCA
6064 AACTCTCG--T
1 AACTCTCGTAT
6073 AACTCTCGTAT
1 AACTCTCGTAT
6084 AACTCTCGTAT
1 AACTCTCGTAT
6095 AACTCTCGTAT
1 AACTCTCGTAT
6106 AA
1 AA
6108 GGTTGCCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 8 0.24
11 25 0.76
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (11 bp):
AACTCTCGTAT
Found at i:16050 original size:51 final size:51
Alignment explanation
Indices: 15958--16065 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
15948 TAAAACATGT
* * * * *
15958 TATGAATGATTAGGAGCTATGACTCACTTGGTATGTCAAGATGAGAAACTA
1 TATGAATGATAAGGAGCTACGACTCACTTAGTACGTCAAGATAAGAAACTA
* *
16009 TATGAATGATAAGGAGCTACGACTCATTTATTACG-CAAAGATAAGAAACTA
1 TATGAATGATAAGGAGCTACGACTCACTTAGTACGTC-AAGATAAGAAACTA
*
16060 TGTGAA
1 TATGAA
16066 AAATATGTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 47 0.98
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (51 bp):
TATGAATGATAAGGAGCTACGACTCACTTAGTACGTCAAGATAAGAAACTA
Found at i:17923 original size:20 final size:19
Alignment explanation
Indices: 17891--17937 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
17881 TGATAATGTC
*
17891 GATGATGTGATTTGAATTTT
1 GATGATTTGATTT-AATTTT
* *
17911 GATTATTTGATTTAGTTTT
1 GATGATTTGATTTAATTTT
17930 GATGATTT
1 GATGATTT
17938 TACGTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.55
Consensus pattern (19 bp):
GATGATTTGATTTAATTTT
Found at i:21005 original size:32 final size:32
Alignment explanation
Indices: 20964--21027 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
20954 TCGAATTACA
*
20964 TAGTTCAACATCCAAACATAATTAA-AAAATGT
1 TAGTCCAACATCCAAACATAA-TAATAAAATGT
20996 TAGTCCAACATCCAAACATAATAATAAAATGT
1 TAGTCCAACATCCAAACATAATAATAAAATGT
21028 CATGTTAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATAATAAAATGT
Found at i:21243 original size:37 final size:37
Alignment explanation
Indices: 21200--21305 Score: 91
Period size: 37 Copynumber: 3.0 Consensus size: 37
21190 ATTATATTAG
21200 ATAATAAATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATAAATAAGTGACCAAATAGGTAGTTTACCCTAA
* * *** *
21237 ATAAT-AATCGAGTGACCAAA-A---A--ATAAATTAG
1 ATAATAAAT-AAGTGACCAAATAGGTAGTTTACCCTAA
*
21268 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATAAATAAGTGACCAAATAGGTAGTTTACCCTAA
21305 A
1 A
21306 AAATCCCTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 16
0.62 0.17 0.21
Matches are distributed among these distances:
31 19 0.40
32 3 0.06
33 1 0.02
35 1 0.02
36 4 0.08
37 20 0.42
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (37 bp):
ATAATAAATAAGTGACCAAATAGGTAGTTTACCCTAA
Found at i:21283 original size:68 final size:68
Alignment explanation
Indices: 21108--21305 Score: 264
Period size: 68 Copynumber: 3.0 Consensus size: 68
21098 ATTTAAAAAA
* *
21108 AATAATCGAGTGACCAAAACATAAATTAGATAATTTATAAGTGACCAAATCA-GTAGTTTACCCT
1 AATAATCGAGTGACCAAAAAATAAATTAGATAATATATAAGTGACCAAAT-AGGTAGTTTACCCT
21172 AAAT
65 AAAT
* * ** * * *
21176 AAAAAT--A-T-A-TATGAATTATATTAGATAATAAATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
21236 AAT
66 AAT
21239 AATAATCGAGTGACCAAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
21304 AA
66 AA
21306 AAATCCCTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 49 0.45
64 1 0.01
65 2 0.02
66 2 0.02
67 1 0.01
68 52 0.48
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (68 bp):
AATAATCGAGTGACCAAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
AAT
Found at i:21762 original size:14 final size:14
Alignment explanation
Indices: 21743--21803 Score: 70
Period size: 15 Copynumber: 4.2 Consensus size: 14
21733 CTAATTTTTC
21743 ATTTTACTT-TTATT
1 ATTTTA-TTATTATT
21757 ATTTTATTATTATT
1 ATTTTATTATTATT
* *
21771 ATTATAAATATTATT
1 ATT-TTATTATTATT
21786 ATTGTTATTATTATT
1 ATT-TTATTATTATT
21801 ATT
1 ATT
21804 AAATAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
13 2 0.05
14 14 0.35
15 24 0.60
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:21766 original size:3 final size:3
Alignment explanation
Indices: 21752--21804 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
21742 CATTTTACTT
* * *
21752 TTA TTA TT- TTA TTA TTA TTA TTA TAA ATA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21799 TTA TTA
1 TTA TTA
21805 AATAAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:23298 original size:3 final size:3
Alignment explanation
Indices: 23290--23319 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
23280 TTTACTCTTA
*
23290 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23320 TAGTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:23655 original size:16 final size:17
Alignment explanation
Indices: 23625--23661 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
23615 ATATTTTATT
23625 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
23642 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
23658 TATA
1 TATA
23662 ACTTTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:23660 original size:26 final size:26
Alignment explanation
Indices: 23611--23661 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
23601 TTCTAAATAA
* *
23611 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
23637 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
23662 ACTTTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:24163 original size:28 final size:26
Alignment explanation
Indices: 24132--24190 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
24122 TAATTCTTTC
*
24132 TTTTTAAAATTTTTATATATACTTATTA
1 TTTTTAAAATATTTATATATA--TATTA
* * *
24160 TTTTCATAATATTTATATGTATATTA
1 TTTTTAAAATATTTATATATATATTA
24186 TTTTT
1 TTTTT
24191 TATATATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTAAAATATTTATATATATATTA
Found at i:24191 original size:28 final size:30
Alignment explanation
Indices: 24140--24201 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
24130 TCTTTTTAAA
*
24140 ATTTTTATATATACTTATTATTTTCATA-AT
1 ATTTATATATATACTTATTATTTT-ATATAT
*
24170 ATTTATATGTATA-TTATT-TTTTATATAT
1 ATTTATATATATACTTATTATTTTATATAT
24198 ATTT
1 ATTT
24202 TATTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 10 0.34
29 5 0.17
30 11 0.38
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTTATATATATACTTATTATTTTATATAT
Found at i:24192 original size:18 final size:18
Alignment explanation
Indices: 24171--24207 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24161 TTTCATAATA
*
24171 TTTATATGTATATTATTT
1 TTTATATATATATTATTT
*
24189 TTTATATATATTTTATTT
1 TTTATATATATATTATTT
24207 T
1 T
24208 AATTTCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTATATATATATTATTT
Found at i:28527 original size:18 final size:18
Alignment explanation
Indices: 28504--28555 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
28494 ATTATACTTG
*
28504 AAAAAAAACACAAAAAGAA
1 AAAAAAAAGA-AAAAAGAA
28523 AAAAAAAAGAAAAAAGAA
1 AAAAAAAAGAAAAAAGAA
*
28541 AAAAAAAGGAAAAAA
1 AAAAAAAAGAAAAAA
28556 AGGGAGAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.87, C:0.04, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAGAA
Found at i:28528 original size:10 final size:10
Alignment explanation
Indices: 28515--28556 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
28505 AAAAAAACAC
28515 AAAAAG-AAA
1 AAAAAGAAAA
*
28524 AAAAA-AAGA
1 AAAAAGAAAA
28533 AAAAAGAAAA
1 AAAAAGAAAA
28543 AAAAAGGAAAA
1 AAAAA-GAAAA
28554 AAA
1 AAA
28557 GGGAGAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.43
10 8 0.29
11 8 0.29
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:28529 original size:11 final size:11
Alignment explanation
Indices: 28504--28556 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
28494 ATTATACTTG
* *
28504 AAAAAAAACAC
1 AAAAAAAAAAG
*
28515 AAAAAGAAAAAA
1 AAAAA-AAAAAG
28527 AAAAGAAAAAAG
1 AAAA-AAAAAAG
*
28539 AAAAAAAAAGG
1 AAAAAAAAAAG
28550 AAAAAAA
1 AAAAAAA
28557 GGGAGAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 18 0.50
12 17 0.47
13 1 0.03
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:30869 original size:114 final size:114
Alignment explanation
Indices: 30669--30891 Score: 365
Period size: 114 Copynumber: 2.0 Consensus size: 114
30659 TGCCATGTGA
* * *
30669 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * *
30734 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGC
* *
30783 TCATAGTAGAAATAAGGAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
30848 TTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
30892 CTGCATGATC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGC
Found at i:33251 original size:22 final size:22
Alignment explanation
Indices: 33196--33277 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
33186 TACATCAACA
* * *
33196 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGAAAAATTCT
** * *
33218 CACTTCAGAGATGAAAAATTTT
1 CTTTTCAAAGATGAAAAATTCT
* * *
33240 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGAAAAATTCT
33262 CTTTTCAAAGATGAAA
1 CTTTTCAAAGATGAAA
33278 GCTTTATGGG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
CTTTTCAAAGATGAAAAATTCT
Found at i:34079 original size:76 final size:76
Alignment explanation
Indices: 33953--34791 Score: 1651
Period size: 76 Copynumber: 11.0 Consensus size: 76
33943 CTATTTCCCA
33953 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34018 ATCCTCAGGGT
66 ATCCTCAGGGT
34029 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34094 ATCCTCAGGGT
66 ATCCTCAGGGT
34105 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34170 ATCCTCAGGGT
66 ATCCTCAGGGT
34181 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34246 ATCCTCAGGGT
66 ATCCTCAGGGT
34257 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34322 ATCCTCAGGGT
66 ATCCTCAGGGT
34333 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34398 ATCCTCAGGGT
66 ATCCTCAGGGT
34409 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34474 ATCCTCAGGGT
66 ATCCTCAGGGT
34485 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34550 ATCCTCAGGGT
66 ATCCTCAGGGT
*
34561 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34626 ATCCTCAGGGT
66 ATCCTCAGGGT
34637 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
34702 ATCCTCAGGGT
66 ATCCTCAGGGT
34713 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
34778 ACCCCCAGGGT
66 ATCCTCAGGGT
34789 CAT
1 CAT
34792 TCATAAGATC
Statistics
Matches: 759, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 759 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTCAGGGT
Found at i:34957 original size:14 final size:14
Alignment explanation
Indices: 34938--35001 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 14
34928 CTAATTTTTC
34938 ATTTTACTT-TTATT
1 ATTTTA-TTATTATT
34952 ATTTTATTATTATT
1 ATTTTATTATTATT
34966 ATTATTATAAATATTATT
1 ATT-TTAT---TATTATT
34984 ATTGTTATTATTATT
1 ATT-TTATTATTATT
34999 ATT
1 ATT
35002 AAATAAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
13 2 0.05
14 14 0.32
15 14 0.32
18 14 0.32
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:34961 original size:3 final size:3
Alignment explanation
Indices: 34947--35002 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
34937 CATTTTACTT
* * *
34947 TTA TTA TT- TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34994 TTA TTA TTA
1 TTA TTA TTA
35003 AATAAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:36519 original size:3 final size:3
Alignment explanation
Indices: 36511--36540 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
36501 TTTACTCTTA
*
36511 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36541 TAGTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:36858 original size:17 final size:17
Alignment explanation
Indices: 36836--36873 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
36826 ATATTTTATT
36836 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
36853 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
36870 TATA
1 TATA
36874 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:37892 original size:21 final size:20
Alignment explanation
Indices: 37810--37912 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
37800 AGCAAATCAG
37810 TTTCCAAAATCGCAACGCGAT
1 TTTCC-AAATCGCAACGCGAT
* *
37831 TCTT-GACAATCGCAATGCGAT
1 T-TTCCA-AATCGCAACGCGAT
** * **
37852 AGTACAAATTCGCATTGCGAT
1 TTTCCAAA-TCGCAACGCGAT
*
37873 TTTCCAGAATCGCAACGCGAA
1 TTTCCA-AATCGCAACGCGAT
* **
37894 TATGAAAATCGCAACGCGA
1 TTTCCAAATCGCAACGCGA
37913 ACACATAAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
20 17 0.27
21 41 0.66
22 4 0.06
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
TTTCCAAATCGCAACGCGAT
Found at i:37905 original size:20 final size:20
Alignment explanation
Indices: 37880--38052 Score: 206
Period size: 20 Copynumber: 8.6 Consensus size: 20
37870 GATTTTCCAG
* ** *
37880 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
37900 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37920 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37940 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37960 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37980 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
38000 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
38020 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
38041 AATCGCAACGCG
1 AATCGCAACGCG
38053 ATTTTTAAAG
Statistics
Matches: 133, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 118 0.89
21 14 0.11
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38471 original size:33 final size:33
Alignment explanation
Indices: 38432--38502 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
38422 TTCACTTAGA
38432 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
38465 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
38498 TTTCA
1 TTTCA
38503 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:38608 original size:21 final size:20
Alignment explanation
Indices: 38582--38688 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
38572 TGCAGAAGAG
38582 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
38603 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
38623 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
38645 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
38659 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
38678 TCGCAACGAGA
1 TCGCAACGAGA
38689 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:38662 original size:14 final size:14
Alignment explanation
Indices: 38643--38699 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38633 GAAAAATGAA
38643 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38657 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38676 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38690 AATCGCAACG
1 AATCGCAACG
38700 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38674 original size:33 final size:33
Alignment explanation
Indices: 38636--38715 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
38626 GCAACGAGAA
38636 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
38669 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
38702 AAACCAAAATCGCA
1 AAATGAAAATCGCA
38716 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:38752 original size:14 final size:14
Alignment explanation
Indices: 38733--38770 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
38723 TTTCATTTCG
38733 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
38747 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
38761 CGTTGCGATT
1 CGTTGCGATT
38771 TTCATTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:38781 original size:21 final size:21
Alignment explanation
Indices: 38755--38819 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
38745 CTCGTTGCGA
38755 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
38776 TTCTCTTGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
38796 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
38817 TTC
1 TTC
38820 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:38816 original size:20 final size:20
Alignment explanation
Indices: 38754--38817 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
38744 TCTCGTTGCG
38754 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
38774 ATTTCTCTTGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
38795 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
38815 ATT
1 ATT
38818 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.12, C:0.23, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:40662 original size:93 final size:93
Alignment explanation
Indices: 40503--40725 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
40493 TAGATTGCTT
*
40503 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40568 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40596 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40661 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40689 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
40726 AATACCCTGA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:40860 original size:14 final size:14
Alignment explanation
Indices: 40841--40897 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40831 CGAAACTTAA
40841 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40855 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
40874 AATCGCAACGACAG
1 AATCGCAACGAGAG
40888 AATCGCAACG
1 AATCGCAACG
40898 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40879 original size:19 final size:18
Alignment explanation
Indices: 40855--40946 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
40845 GCAACGAGAG
40855 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
40874 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
40888 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
40907 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
40921 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
40940 AATCGCA
1 AATCGCA
40947 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:40881 original size:33 final size:33
Alignment explanation
Indices: 40823--40946 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
40813 TAGTTTACTT
* * *
40823 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
40857 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
40890 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
40923 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
40947 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:40923 original size:14 final size:14
Alignment explanation
Indices: 40872--40930 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
40862 ACGCGAAATG
40872 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40886 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
40905 AAAATCGCAACGAC
1 AAAATCGCAACGAC
40919 AAAATCGCAACG
1 AAAATCGCAACG
40931 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40964 original size:19 final size:19
Alignment explanation
Indices: 40942--41114 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
40932 GAAACCAAAA
*
40942 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40961 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
40975 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
40994 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
**
41010 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
41027 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
41046 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
41065 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
41084 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
41104 TCGTGTTGCGA
1 TCGCGTTGCGA
41115 AAGTAAACTA
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 7 0.06
17 8 0.06
19 83 0.65
20 12 0.09
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:40983 original size:14 final size:14
Alignment explanation
Indices: 40964--41020 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40954 TTTCATTTCG
40964 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40978 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
40995 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
41011 CGTTGCGATT
1 CGTTGCGATT
41021 TTGGTTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41062 original size:38 final size:38
Alignment explanation
Indices: 40942--41114 Score: 150
Period size: 33 Copynumber: 4.8 Consensus size: 38
40932 GAAACCAAAA
* **
40942 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTCATT
** * *
40977 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTCATT
* **
41010 T--CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTCATT
*
41046 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTCATT
* *
41084 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT-GGTTTCGCGTTGCGA
41115 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 50 0.43
34 1 0.01
35 2 0.02
36 2 0.02
38 46 0.40
39 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTCATT
Found at i:43051 original size:14 final size:14
Alignment explanation
Indices: 43032--43067 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43022 ATTGTTTAAT
43032 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
43046 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
43060 TGATTTGT
1 TGATTTGT
43068 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:43182 original size:19 final size:19
Alignment explanation
Indices: 43158--43245 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
43148 GCATTATGTT
43158 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
43177 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
43194 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
43210 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
43229 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
43246 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:43277 original size:53 final size:53
Alignment explanation
Indices: 43158--43264 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
43148 GCATTATGTT
43158 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
43210 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
43263 GA
1 GA
43265 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:43282 original size:19 final size:19
Alignment explanation
Indices: 43254--43514 Score: 294
Period size: 19 Copynumber: 14.7 Consensus size: 19
43244 AACGAGAGAA
*
43254 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
43273 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
43292 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
43309 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
43325 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
43344 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
43360 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
43377 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
43396 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
*
43413 TCG--TTGAGATTTTCATT
1 TCGCATTGCGATTTTCATT
43430 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
43449 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
43468 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
43486 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
43502 TCGCATTGCGATT
1 TCGCATTGCGATT
43515 CTCTCGTTGC
Statistics
Matches: 208, Mismatches: 11, Indels: 46
0.78 0.04 0.17
Matches are distributed among these distances:
14 27 0.13
15 3 0.01
16 21 0.10
17 16 0.08
18 14 0.07
19 92 0.44
20 35 0.17
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:43326 original size:33 final size:34
Alignment explanation
Indices: 43278--43547 Score: 234
Period size: 33 Copynumber: 7.8 Consensus size: 34
43268 TCATTTCGCA
43278 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
43312 TTGCGA-TTTCATTT-CGCATTGCGATT-T-TCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* * *
43342 TTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TC-CGCATTGCGA--TTC-TCTCG
43380 CATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* *
43416 TTGAGATTTTCATTT-CGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCCGCATTGCGA--TTC-TCTCG
* *
43452 CATTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 --TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
43488 TTGGGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* * **
43521 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCCGCATTGCGAT
43548 AGTCAAATGC
Statistics
Matches: 193, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
30 6 0.03
31 5 0.03
32 15 0.08
33 53 0.27
34 43 0.22
35 7 0.04
36 11 0.06
37 8 0.04
38 18 0.09
39 20 0.10
40 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:43425 original size:53 final size:52
Alignment explanation
Indices: 43260--43528 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
43250 AGAATCGCAA
43260 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
43313 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
43364 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
43417 TGAGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
43475 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
43522 TGCGATT
1 TGCGATT
43529 GTAATTTCCG
Statistics
Matches: 203, Mismatches: 5, Indels: 22
0.88 0.02 0.10
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 27 0.13
52 64 0.32
53 80 0.39
54 3 0.01
55 3 0.01
56 4 0.02
58 10 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:43439 original size:72 final size:72
Alignment explanation
Indices: 43363--43514 Score: 277
Period size: 72 Copynumber: 2.1 Consensus size: 72
43353 GATTCTCTCG
43363 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGAGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGAGATTTTCA
43428 TTTCGCA
66 TTTCGCA
* * *
43435 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGAGATTTTCA
43500 TTTCGCA
66 TTTCGCA
43507 TTGCGATT
1 TTGCGATT
43515 CTCTCGTTGC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGAGATTTTCA
TTTCGCA
Found at i:45829 original size:12 final size:12
Alignment explanation
Indices: 45812--45836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45802 TCTTCGGGGA
45812 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45824 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45836 C
1 C
45837 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:46045 original size:24 final size:24
Alignment explanation
Indices: 46011--46057 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
46001 CTGAAACATC
46011 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
46035 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
46058 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:46778 original size:20 final size:20
Alignment explanation
Indices: 46750--46978 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
46740 AAATTTCAGT
* * *
46750 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
46770 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
46790 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
46810 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
46830 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
46850 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
46870 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
46890 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
46910 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
46930 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
46950 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
46970 GTTGCGATT
1 GTTGCGATT
46979 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:47031 original size:21 final size:20
Alignment explanation
Indices: 46946--47043 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
46936 ATTTATGTGT
* *
46946 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
46966 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
46987 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
47008 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
47029 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
47044 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:47039 original size:42 final size:43
Alignment explanation
Indices: 46946--47044 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
46936 ATTTATGTGT
* *
46946 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
46987 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
47029 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
47045 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:47291 original size:32 final size:32
Alignment explanation
Indices: 47255--47328 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
47245 CTTTAGGTGG
* *
47255 TGTGACACATACTACATCATTACTTTAGATAA
1 TGTGACACATACGACAACATTACTTTAGATAA
* * * *
47287 TGTGACATATACGCCAACATTATTTTAGGTAA
1 TGTGACACATACGACAACATTACTTTAGATAA
*
47319 TATGACACAT
1 TGTGACACAT
47329 GACGCGACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
TGTGACACATACGACAACATTACTTTAGATAA
Found at i:47480 original size:7 final size:8
Alignment explanation
Indices: 47461--47485 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47451 TATTTTAACA
47461 AAAAAATT
1 AAAAAATT
47469 AAAAAATT
1 AAAAAATT
47477 AAAAAATT
1 AAAAAATT
47485 A
1 A
47486 GAGTCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAAATT
Found at i:47824 original size:23 final size:23
Alignment explanation
Indices: 47777--47824 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
47767 AATGACATAT
**
47777 TAGGTAGAGCTTATATAATGTAA
1 TAGGTAGAGCTTATATAATAAAA
*
47800 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAGCTTATATAATAAAA
47823 TA
1 TA
47825 AGTATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAATAAAA
Found at i:47887 original size:87 final size:87
Alignment explanation
Indices: 47741--47989 Score: 426
Period size: 87 Copynumber: 2.9 Consensus size: 87
47731 ATGTTATATC
* * *
47741 ATTTAACCGGAAATATTATCAAGTAAAATGACATATTAGGTAGAGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
47806 GCGCTTATATAATAAAATAAGT
66 GCGCTTATATAATAAAATAAGT
*
47828 ATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
*
47893 GTGCTTATATAATAAAATAAGT
66 GCGCTTATATAATAAAATAAGT
* *
47915 ATTTAACCGGAAATATTATCAAGTACAATAACATATTACGTAGCGCTTATATAATTTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
*
47980 ACGCTTATAT
66 GCGCTTATAT
47990 TGACATATTT
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 152 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAAGT
Found at i:47911 original size:23 final size:23
Alignment explanation
Indices: 47864--47911 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
47854 AATAACATAT
**
47864 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
47887 TAGGTAGTGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
47910 TA
1 TA
47912 AGTATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:48289 original size:15 final size:15
Alignment explanation
Indices: 48269--48297 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48259 ATCGTTTTCG
48269 ATGTTTTTGGGATCA
1 ATGTTTTTGGGATCA
48284 ATGTTTTTGGGATC
1 ATGTTTTTGGGATC
48298 GATACTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
ATGTTTTTGGGATCA
Found at i:49106 original size:126 final size:125
Alignment explanation
Indices: 48848--49341 Score: 548
Period size: 126 Copynumber: 3.9 Consensus size: 125
48838 ACCGGTAAAA
* * * *
48848 AATAACAAAACTGGTAGCGTTTTTACCGGTTTTGTTAAGAAACCCGGTAAAATGCCAAAATAATA
1 AATAACAAAACCGATAGCGCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCCAAAATAATA
* * * *
48913 AAAA-ATC-AGTAGAAATAATGATGTTTTCGGTAATTTTTACCGGTTTTGTTATACACAAC
66 AAAATATCGA-TAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAAC
*** *
48972 AATAACAAAACCGATAGTTTTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGTCAAAATAATA
1 AATAACAAAACCGATAGCGCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCCAAAATAAT-
* * * *
49037 AAAAATATCGGTAGAAATAATTATGTTTTCGGTAATTTTTACCGATTTTATTATACACAAC
65 AAAAATATCGATAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAAC
* * * * *
49098 CATAACAAAACTAGA-AGCGCTTTTACCCGTTTTGCTAAGAAA-CCTATTAAAATGCCAAAATAA
1 AATAACAAAAC-CGATAGCGCTTTTACCGGTTTTGTTAAGAAACCCGA-TAAAATGCCAAAATAA
* *
49161 TAAAAAAAATCGATAGAAATAATGATATTTTCGATAATTTTTATCGATTTTATTATACACAAC
64 T-AAAAATATCGATAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAAC
* ** ** * * * * **
49224 AATAACAAAATCGATAGTACTTTTATTGATTTTATTAAAAAATCCGATAAAATATCAAAATAATA
1 AATAACAAAACCGATAGCGCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCCAAAATAATA
* * * * *
49289 AAAAT-TCTGATAAAAATAATAATATTTTTGATAAATTTTACTGATTTTATTAT
66 AAAATATC-GATAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTAT
49342 GCACCGATTT
Statistics
Matches: 315, Mismatches: 47, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
124 60 0.19
125 54 0.17
126 196 0.62
127 5 0.02
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (125 bp):
AATAACAAAACCGATAGCGCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCCAAAATAATA
AAAATATCGATAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAAC
Found at i:49292 original size:252 final size:249
Alignment explanation
Indices: 48849--49341 Score: 648
Period size: 252 Copynumber: 2.0 Consensus size: 249
48839 CCGGTAAAAA
* * * * * *
48849 ATAACAAAACTGGTAGCGTTTTTACCGGTTTTGTTAAGAAACCCGGTAAAATGCCAAAATAATAA
1 ATAACAAAACTAGAAGCGCTTTTACCCGTTTTGCTAAGAAACCCAGTAAAATGCCAAAATAATAA
* * * *
48914 AAAATCAGTAGAAATAATGATGTTTTCGGTAATTTTTACCGGTTTTGTTATACACAACAATAACA
66 AAAATCAGTAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAACAATAACA
** * * * *
48979 AAACCGATAGTTTTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGTCAAAATAATAAAAAATA
131 AAACCGATAGTACTTTTACCGATTTTATTAAAAAACCCGATAAAATATCAAAATAAT-AAAAAT-
* * * * * *
49044 TC-GGTAGAAATAATTATGTTTTCGGTAATTTTTACCGATTTTATTATACACAACC
194 TCTGATAAAAATAATAATATTTTCGATAAATTTTACCGATTTTATTATACACAACC
* *
49099 ATAACAAAACTAGAAGCGCTTTTACCCGTTTTGCTAAGAAACCTATTAAAATGCCAAAATAATAA
1 ATAACAAAACTAGAAGCGCTTTTACCCGTTTTGCTAAGAAACCCAGTAAAATGCCAAAATAAT--
*
49164 AAAAAATC-GATAGAAATAATGATATTTTCGATAATTTTTATCGATTTTATTATACACAACAATA
64 AAAAAATCAG-TAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAACAATA
* ** *
49228 ACAAAATCGATAGTACTTTTATTGATTTTATTAAAAAATCCGATAAAATATCAAAATAATAAAAA
128 ACAAAACCGATAGTACTTTTACCGATTTTATTAAAAAACCCGATAAAATATCAAAATAATAAAAA
* *
49293 TTCTGATAAAAATAATAATATTTTTGATAAATTTTACTGATTTTATTAT
193 TTCTGATAAAAATAATAATATTTTCGATAAATTTTACCGATTTTATTAT
49342 GCACCGATTT
Statistics
Matches: 208, Mismatches: 31, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
250 57 0.27
251 44 0.21
252 107 0.51
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (249 bp):
ATAACAAAACTAGAAGCGCTTTTACCCGTTTTGCTAAGAAACCCAGTAAAATGCCAAAATAATAA
AAAATCAGTAGAAATAATGATATTTTCGATAATTTTTACCGATTTTATTATACACAACAATAACA
AAACCGATAGTACTTTTACCGATTTTATTAAAAAACCCGATAAAATATCAAAATAATAAAAATTC
TGATAAAAATAATAATATTTTCGATAAATTTTACCGATTTTATTATACACAACC
Found at i:54089 original size:13 final size:13
Alignment explanation
Indices: 54071--54095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54061 GTTAATCCAA
54071 TATATATATATAT
1 TATATATATATAT
54084 TATATATATATA
1 TATATATATATA
54096 ACAATTCTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:54675 original size:36 final size:36
Alignment explanation
Indices: 54628--54706 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
54618 AAGTGAAACC
54628 GCAAATCTTGATGAGATATCAGGAGCTGAAGAAAAT
1 GCAAATCTTGATGAGATATCAGGAGCTGAAGAAAAT
54664 GCAAATCTTGATGAGATATCAGGAGCTGAAGAAAAT
1 GCAAATCTTGATGAGATATCAGGAGCTGAAGAAAAT
54700 GCAAATC
1 GCAAATC
54707 CGGAGGAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (36 bp):
GCAAATCTTGATGAGATATCAGGAGCTGAAGAAAAT
Found at i:56983 original size:21 final size:21
Alignment explanation
Indices: 56959--57008 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
56949 TGTGACCAAA
56959 TCAATTTTGGAGTTTAAAGTT
1 TCAATTTTGGAGTTTAAAGTT
*
56980 TCAATTTTGTAGTTTAAAGTT
1 TCAATTTTGGAGTTTAAAGTT
*
57001 TCATTTTT
1 TCAATTTT
57009 TTGGTTGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (21 bp):
TCAATTTTGGAGTTTAAAGTT
Found at i:60388 original size:38 final size:37
Alignment explanation
Indices: 60307--60397 Score: 148
Period size: 37 Copynumber: 2.4 Consensus size: 37
60297 ACCTAAATCC
60307 GACCCGACCCAAACTTATCTTCTAAAAAATCTGACAT
1 GACCCGACCCAAACTTATCTTCTAAAAAATCTGACAT
60344 GACCCGACCCAAACTTATCTTCTAAAAAATCTGATC-T
1 GACCCGACCCAAACTTATCTTCTAAAAAATCTGA-CAT
*
60381 GATCCCGACTCAAACTT
1 GA-CCCGACCCAAACTT
60398 TATTTTTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
37 37 0.73
38 14 0.27
ACGTcount: A:0.35, C:0.31, G:0.09, T:0.25
Consensus pattern (37 bp):
GACCCGACCCAAACTTATCTTCTAAAAAATCTGACAT
Found at i:61779 original size:19 final size:19
Alignment explanation
Indices: 61755--61793 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
61745 CTAGATGAAT
61755 ATTCCAAGCATTGGGATTC
1 ATTCCAAGCATTGGGATTC
61774 ATTCCAAGCATTGGGATTC
1 ATTCCAAGCATTGGGATTC
61793 A
1 A
61794 GTTGGTTGGT
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:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (19 bp):
ATTCCAAGCATTGGGATTC
Found at i:64646 original size:3 final size:3
Alignment explanation
Indices: 64638--64710 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
64628 AATATATATT
64638 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64685 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
64711 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:65369 original size:231 final size:229
Alignment explanation
Indices: 64855--65605 Score: 1102
Period size: 231 Copynumber: 3.3 Consensus size: 229
64845 ATGCTTCTCT
* ** * *
64855 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCAAATGATGAA
1 TTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGCTGATCCATCAAATGATGAA
64920 TTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
65 TTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
* * * * *
64985 TTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCA-AGCAAAAGA
130 TTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCAGA-AAAAAGG
*
65049 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
194 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
65085 TTCTTCAGATGACGAGTTCTTCTCA-TATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGAT
1 TTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGAT
65148 GAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
62 GAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65213 GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAA
127 GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAA-TTGATGAATTCAGAAAAA
65278 AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
191 AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* *
65317 TTCTTCAGATAAGTTCTTCTCATTATGAAGTTTCTCTGGAAAAGACTGATCCATCAAATGATGGA
1 TTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATCAAATGATGAA
** * * *
65382 TTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAG
65 TTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
* * **
65444 TTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAG
130 TTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAA-TTGATGAATTCAGAAAAAAG
65508 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
193 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * **
65545 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGAT
1 TTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGAT
65606 AGCTTTGAAT
Statistics
Matches: 479, Mismatches: 32, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
227 17 0.04
228 137 0.29
229 13 0.03
230 25 0.05
231 204 0.43
232 69 0.14
233 14 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (229 bp):
TTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAAT
TCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGT
TCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCAGAAAAAAGGTT
GAACAAATTCTTCTCATTATGAACTTCTTCTTCC
Found at i:65594 original size:114 final size:113
Alignment explanation
Indices: 64855--65588 Score: 1001
Period size: 114 Copynumber: 6.4 Consensus size: 113
64845 ATGCTTCTCT
** *
64855 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCAAATGATGAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATGATCCATCAAATGATGAA
*
64920 TTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
65 TTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
64969 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGAT
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGAT
*
65033 GAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
62 GAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
65085 TTCTTCAGATGACGAGTTCTTCTCA-TATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGAT
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGAT
*
65148 GAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
62 GAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * * *
65200 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAACTTGA
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAA-ATGA
* *
65264 TGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
61 TGAATTCAAG-CAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
65317 TTCTTCAGATAAGTTCTTCTCATTATGAAGTTTCTCTGGAAAAGACTGATCCATCAAATGATGGA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA-TGATCCATCAAATGATGAA
** * *
65382 TTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
65 TTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
65431 TTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA-ATGATGAA
* * *
65496 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
65 TTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
65545 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
65589 CTAATCTTTC
Statistics
Matches: 581, Mismatches: 28, Indels: 22
0.92 0.04 0.03
Matches are distributed among these distances:
113 12 0.02
114 228 0.39
115 126 0.22
116 132 0.23
117 81 0.14
118 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (113 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAAT
TCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
Found at i:66493 original size:115 final size:114
Alignment explanation
Indices: 66292--66512 Score: 379
Period size: 115 Copynumber: 1.9 Consensus size: 114
66282 GATCATGCAG
* * *
66292 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
66357 ACACTTCCAGAAAATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAAATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
66406 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATCGG-TTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
*
66471 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
65 AACACTTCCAGAAAATGCTATTGGGTCTCCTTATTTCTACTA
66513 CGAGAACATG
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 23 0.23
115 77 0.77
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAAATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:67634 original size:8 final size:7
Alignment explanation
Indices: 67618--67703 Score: 72
Period size: 7 Copynumber: 12.1 Consensus size: 7
67608 CTTGACCCCC
67618 TTTTTCT
1 TTTTTCT
67625 TTTTTCCT
1 TTTTT-CT
67633 TTTTTCT
1 TTTTTCT
67640 TTTTT-T
1 TTTTTCT
67646 TCTCTTT-T
1 T-T-TTTCT
67654 TATTTTCT
1 T-TTTTCT
*
67662 TTTTTTT
1 TTTTTCT
67669 TATTTTCT
1 T-TTTTCT
*
67677 TTATT-T
1 TTTTTCT
*
67683 TCTTT-T
1 TTTTTCT
67689 TTTTTCT
1 TTTTTCT
67696 TTTTTCT
1 TTTTTCT
67703 T
1 T
67704 CAAGCATAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
6 11 0.17
7 34 0.52
8 21 0.32
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:67638 original size:15 final size:15
Alignment explanation
Indices: 67618--67690 Score: 60
Period size: 16 Copynumber: 4.8 Consensus size: 15
67608 CTTGACCCCC
67618 TTTTTCTTTTTTCCT
1 TTTTTCTTTTTTCCT
*
67633 TTTTTCTTTTTTTTCT
1 TTTTTC-TTTTTTCCT
* *
67649 CTTTT-TATTTT-CT
1 TTTTTCTTTTTTCCT
* *
67662 TTTTTTTTATTTTCTT
1 TTTTTCTT-TTTTCCT
67678 TATTTTCTTTTTT
1 T-TTTTCTTTTTT
67691 TTTCTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.13
14 6 0.13
15 10 0.22
16 18 0.39
17 6 0.13
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTCCT
Found at i:67645 original size:24 final size:23
Alignment explanation
Indices: 67618--67703 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 23
67608 CTTGACCCCC
67618 TTTTTCTTTTTTCCTTTTTTCTTT
1 TTTTTCTTTTTT-CTTTTTTCTTT
* *
67642 TTTTTCTCTTTT-TATTTTCTTT
1 TTTTTCTTTTTTCTTTTTTCTTT
*
67664 TTTTT-TATTTTCTTTATTTTCTTTT
1 TTTTTCTTTTTTC-TT-TTTTC-TTT
67689 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
67704 CAAGCATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
21 5 0.10
22 14 0.27
23 1 0.02
24 16 0.31
25 10 0.19
26 6 0.12
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTTTCTTTTTTCTTT
Found at i:67660 original size:37 final size:35
Alignment explanation
Indices: 67618--67701 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 35
67608 CTTGACCCCC
*
67618 TTTTTCTTTTTTCCTT-TTTTCTTTTTTTTCTCTTTT
1 TTTTTCTTTTTTCCTTATTTTC-TTTATTT-TCTTTT
*
67654 TATTTTCTTTTTT-TTTATTTTCTTTATTTTCTTTT
1 T-TTTTCTTTTTTCCTTATTTTCTTTATTTTCTTTT
67689 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
67702 TTCAAGCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 11 0.26
35 7 0.16
36 9 0.21
37 16 0.37
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (35 bp):
TTTTTCTTTTTTCCTTATTTTCTTTATTTTCTTTT
Found at i:67698 original size:15 final size:15
Alignment explanation
Indices: 67618--67703 Score: 77
Period size: 15 Copynumber: 5.5 Consensus size: 15
67608 CTTGACCCCC
*
67618 TTTTTCTTTTTTCCT
1 TTTTTCTTTTTTTCT
67633 TTTTTCTTTTTTTTCT
1 TTTTTC-TTTTTTTCT
*
67649 CTTTTTATTTTCTTT-T
1 -TTTTTCTTTT-TTTCT
* *
67665 TTTTTATTTTCTTTAT
1 TTTTTCTTTT-TTTCT
67681 TTTCTT-TTTTTTTCT
1 TTT-TTCTTTTTTTCT
67696 TTTTTCTT
1 TTTTTCTT
67704 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
14 2 0.03
15 29 0.47
16 21 0.34
17 10 0.16
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Done.