Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015308.1 Kokia drynarioides strain JFW-HI SEQ_130353, 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: 468748
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 814 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5118 original size:18 final size:18
Alignment explanation
Indices: 5061--5112 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
5051 TAGATGCAGT
*
5061 CACATACTCAGATGCAAC
1 CACATACTCAAATGCAAC
* *
5079 CATATAATCAAATGCAAC
1 CACATACTCAAATGCAAC
*
5097 CACATGCTCAAATGCA
1 CACATACTCAAATGCA
5113 GTCACAATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (18 bp):
CACATACTCAAATGCAAC
Found at i:11208 original size:15 final size:16
Alignment explanation
Indices: 11184--11222 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11174 GGTATTGCAG
*
11184 TAGAACAAGA-AGAAA
1 TAGAAGAAGAGAGAAA
11199 TAGAAGAAGAGAGAAA
1 TAGAAGAAGAGAGAAA
11215 -AGAAGAAG
1 TAGAAGAAG
11223 GAATTGCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.64, C:0.03, G:0.28, T:0.05
Consensus pattern (16 bp):
TAGAAGAAGAGAGAAA
Found at i:11659 original size:17 final size:17
Alignment explanation
Indices: 11628--11669 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
11618 TAATTATCAT
*
11628 TGCATTTTTTATTGTCTC
1 TGCATTTTATATTGT-TC
11646 TGCATTTTAT-TTGTTC
1 TGCATTTTATATTGTTC
11662 TAGCATTT
1 T-GCATTT
11670 GAATTGTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (17 bp):
TGCATTTTATATTGTTC
Found at i:24050 original size:27 final size:28
Alignment explanation
Indices: 24000--24053 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
23990 AAAAACATAA
*
24000 TAAAGTCCCAAAATAATAACAAAGTCCT
1 TAAAGTCCCAAAATAATAAAAAAGTCCT
24028 TAAAGT-CCAAAAT-ATAATAAAAGTCC
1 TAAAGTCCCAAAATAATAA-AAAAGTCC
24054 ATAGTTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 14 0.58
28 6 0.25
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (28 bp):
TAAAGTCCCAAAATAATAAAAAAGTCCT
Found at i:24504 original size:48 final size:47
Alignment explanation
Indices: 24452--24550 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 47
24442 AATCATATAT
*
24452 TCACTTTGCA-ATTAAACTACCACATAATCGCCATAAATGGCCACATAA
1 TCACTTTGCAGA-TAAACTACCACATAATCACCATAAATGGCCACAT-A
*
24500 TCACTTTGCAGATAAACTACCACATAATTACCATAAATGGCCACATA
1 TCACTTTGCAGATAAACTACCACATAATCACCATAAATGGCCACATA
24547 TCAC
1 TCAC
24551 ATAATTGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 5 0.10
48 42 0.88
49 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (47 bp):
TCACTTTGCAGATAAACTACCACATAATCACCATAAATGGCCACATA
Found at i:24565 original size:28 final size:28
Alignment explanation
Indices: 24520--24573 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
24510 GATAAACTAC
*
24520 CACATAATTACCATAAATGGCCACATAT
1 CACATAATTACCAAAAATGGCCACATAT
*
24548 CACATAATTGCCAAAAATGGCCACAT
1 CACATAATTACCAAAAATGGCCACAT
24574 CTTCCACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (28 bp):
CACATAATTACCAAAAATGGCCACATAT
Found at i:46313 original size:64 final size:64
Alignment explanation
Indices: 46212--46354 Score: 241
Period size: 64 Copynumber: 2.2 Consensus size: 64
46202 TCGAGACATG
*
46212 TTGGTGTGTTGGAGAGTGTTAGATTTATGCTACGCTTATGGGATATGTTAAACTCTTTGAGTCA
1 TTGGTGTGTTGGAGAATGTTAGATTTATGCTACGCTTATGGGATATGTTAAACTCTTTGAGTCA
* * *
46276 TTGGTGTGTTGGAGAATGTTAGCTTTATGCTACGCTTATGGGATATGTTAGACTTTTTGAGTCA
1 TTGGTGTGTTGGAGAATGTTAGATTTATGCTACGCTTATGGGATATGTTAAACTCTTTGAGTCA
*
46340 TTGGTGTGATGGAGA
1 TTGGTGTGTTGGAGA
46355 TCCATGTATT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 74 1.00
ACGTcount: A:0.21, C:0.08, G:0.30, T:0.41
Consensus pattern (64 bp):
TTGGTGTGTTGGAGAATGTTAGATTTATGCTACGCTTATGGGATATGTTAAACTCTTTGAGTCA
Found at i:46902 original size:3 final size:3
Alignment explanation
Indices: 46894--46927 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
46884 TATTTATTGT
46894 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
46928 GTTTTAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47647 original size:27 final size:27
Alignment explanation
Indices: 47624--47701 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 27
47614 GTTCGTCAGA
*
47624 ACAGTAAACACGAGGGAGTCCGTCGAG
1 ACAGTAAACACGAGGTAGTCCGTCGAG
* *
47651 ATAGTAAAAACACGAGGTAGTCCATCGAG
1 ACAGT--AAACACGAGGTAGTCCGTCGAG
* *
47680 ACATTAAACATGAGGTAGTCCG
1 ACAGTAAACACGAGGTAGTCCG
47702 CCAGGAGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 19 0.45
29 23 0.55
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (27 bp):
ACAGTAAACACGAGGTAGTCCGTCGAG
Found at i:54876 original size:24 final size:25
Alignment explanation
Indices: 54832--54879 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
54822 GTTGGATCCA
*
54832 AATTAAATTTTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
54857 AATTAAA-TCTAAACAA-ATAATTT
1 AATTAAATTCTAAA-AAGATAATTT
54880 CATAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:55931 original size:22 final size:21
Alignment explanation
Indices: 55904--55961 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
55894 GCTCAAATTT
55904 TTTTCTTCTATTTTTTTCTGAA
1 TTTTCTTCTATTTTTTTC-GAA
* *
55926 TTTTCTTTTTTTTTTTTCGAA
1 TTTTCTTCTATTTTTTTCGAA
*
55947 TTTTTTTC-ATTTTTT
1 TTTTCTTCTATTTTTT
55962 CGACTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 6 0.19
21 9 0.29
22 16 0.52
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTCTTCTATTTTTTTCGAA
Found at i:55940 original size:21 final size:22
Alignment explanation
Indices: 55904--55961 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
55894 GCTCAAATTT
55904 TTTTCTTCTA-TTTTTTTCTGAA
1 TTTTCTTCTATTTTTTTTC-GAA
*
55926 TTTTCTT-TTTTTTTTTTCGAA
1 TTTTCTTCTATTTTTTTTCGAA
*
55947 TTTTTTTC-ATTTTTT
1 TTTTCTTCTATTTTTT
55962 CGACTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTCTTCTATTTTTTTTCGAA
Found at i:55953 original size:19 final size:19
Alignment explanation
Indices: 55914--55980 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
55904 TTTTCTTCTA
55914 TTTTTTTCTGAATTTTCTTTTT
1 TTTTTTTC-GAA-TTT-TTTTT
*
55936 TTTTTTTCGAATTTTTTTC
1 TTTTTTTCGAATTTTTTTT
*
55955 ATTTTTTCGACTATTTTTTTCT
1 TTTTTTTCGA--ATTTTTTT-T
55977 TTTT
1 TTTT
55981 ATAAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 13 0.34
20 3 0.08
21 11 0.29
22 11 0.29
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTTTCGAATTTTTTTT
Found at i:55970 original size:21 final size:18
Alignment explanation
Indices: 55931--55980 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
55921 CTGAATTTTC
55931 TTTTTT-TTTTTTCGAAT
1 TTTTTTCTTTTTTCGAAT
55948 TTTTTTCATTTTTTCGACTAT
1 TTTTTTC-TTTTTTCGA--AT
55969 TTTTTTCTTTTT
1 TTTTTTCTTTTT
55981 ATAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.21
19 9 0.31
20 5 0.17
21 9 0.31
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTTTCTTTTTTCGAAT
Found at i:56899 original size:16 final size:15
Alignment explanation
Indices: 56878--56913 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
56868 ATAATAACTA
56878 AAAAACCCATAAGAAT
1 AAAAA-CCATAAGAAT
56894 AAAAACCATAAGAAT
1 AAAAACCATAAGAAT
56909 AAAAA
1 AAAAA
56914 TAGTGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAACCATAAGAAT
Found at i:56996 original size:20 final size:19
Alignment explanation
Indices: 56957--57017 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
56947 ATAAATATAC
*
56957 TAATTTTTTTTTGAACTTTT
1 TAATTTTTTTTTTAA-TTTT
56977 TAAATTTTTTTTTTAATTTT
1 T-AATTTTTTTTTTAATTTT
*
56997 TTATTTTTTTTTTCAATTTT
1 TAATTTTTTTTTT-AATTTT
57017 T
1 T
57018 TTTAAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.30
20 13 0.35
21 13 0.35
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (19 bp):
TAATTTTTTTTTTAATTTT
Found at i:57018 original size:21 final size:20
Alignment explanation
Indices: 56959--57019 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
56949 AAATATACTA
* **
56959 ATTTTTTTTTGAACTTTTTAA
1 ATTTTTTTTTTAA-TTTTTTT
56980 ATTTTTTTTTTAA-TTTTTT
1 ATTTTTTTTTTAATTTTTTT
56999 ATTTTTTTTTTCAATTTTTTT
1 ATTTTTTTTTT-AATTTTTTT
57020 TAAAAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.43
20 2 0.06
21 18 0.51
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTAATTTTTTT
Found at i:64929 original size:2 final size:2
Alignment explanation
Indices: 64924--64949 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64914 TATATATATA
64924 TG TG 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
64950 ATTTGGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:72238 original size:24 final size:24
Alignment explanation
Indices: 72209--72291 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
72199 TAGACTAATA
*
72209 AAAGTTTAACTGAAACAAATAAAC
1 AAAGTTTAATTGAAACAAATAAAC
*
72233 AAAGTTTAATTGAAA-AAAAAAAC
1 AAAGTTTAATTGAAACAAATAAAC
*
72256 AAAATTTAATTGAAACAAATAAAC
1 AAAGTTTAATTGAAACAAATAAAC
72280 AGAA-TTTAATTG
1 A-AAGTTTAATTG
72292 GAAGATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.40
24 30 0.57
25 2 0.04
ACGTcount: A:0.59, C:0.07, G:0.08, T:0.25
Consensus pattern (24 bp):
AAAGTTTAATTGAAACAAATAAAC
Found at i:74201 original size:24 final size:24
Alignment explanation
Indices: 74162--74228 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
74152 AATCTAAACT
*
74162 AATAAGAGTTTGATTGAAACAAATA
1 AATAA-AGTTTAATTGAAACAAATA
74187 AATAAAGTTTAATTGAAACAAATA
1 AATAAAGTTTAATTGAAACAAATA
* *
74211 AACAGAGTTTAATTGAAA
1 AATAAAGTTTAATTGAAA
74229 GATTATTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 34 0.87
25 5 0.13
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.28
Consensus pattern (24 bp):
AATAAAGTTTAATTGAAACAAATA
Found at i:79586 original size:21 final size:21
Alignment explanation
Indices: 79553--79614 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
79543 CAGCAAATGA
*
79553 TTTTAAAATTATAAAAATTATT
1 TTTTTAAA-TATAAAAATTATT
*
79575 TTTTTAAATAT-AAAATTA-A
1 TTTTTAAATATAAAAATTATT
79594 TTTTTAAATA-ATAAAATTATT
1 TTTTTAAATATA-AAAATTATT
79615 AAATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 10 0.29
20 14 0.41
21 3 0.09
22 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTTAAATATAAAAATTATT
Found at i:80561 original size:31 final size:31
Alignment explanation
Indices: 80526--80585 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
80516 ATGATGATTT
*
80526 AATAATTTTATATTTTAAAAATTAATTTTAA
1 AATAATTTTATATTTTAAAAAATAATTTTAA
80557 AATAATTTTATATTTTAAAAAATAATTTT
1 AATAATTTTATATTTTAAAAAATAATTTT
80586 TATAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAATTTTATATTTTAAAAAATAATTTTAA
Found at i:80580 original size:20 final size:22
Alignment explanation
Indices: 80548--80598 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
80538 TTTTAAAAAT
80548 TAATTTT--AAAATAA-TTTTA
1 TAATTTTAAAAAATAATTTTTA
80567 T-ATTTTAAAAAATAATTTTTA
1 TAATTTTAAAAAATAATTTTTA
80588 TAATTTTAAAA
1 TAATTTTAAAA
80599 TTATTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.18
19 1 0.04
20 7 0.25
21 6 0.21
22 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTTTAAAAAATAATTTTTA
Found at i:80599 original size:20 final size:20
Alignment explanation
Indices: 80548--80604 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
80538 TTTTAAAAAT
80548 TAATTTTAAAATAA-TTTTA
1 TAATTTTAAAATAATTTTTA
80567 T-ATTTTAAAAAATAATTTTTA
1 TAATTTT--AAAATAATTTTTA
*
80588 TAATTTTAAAATTATTT
1 TAATTTTAAAATAATTT
80605 GTTGATGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 16 0.48
21 6 0.18
22 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTTAAAATAATTTTTA
Found at i:88818 original size:16 final size:16
Alignment explanation
Indices: 88797--88827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88787 GCAAGGTTAC
88797 GAAATGACAGTATTGT
1 GAAATGACAGTATTGT
*
88813 GAAATGACATTATTG
1 GAAATGACAGTATTG
88828 CATATCATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (16 bp):
GAAATGACAGTATTGT
Found at i:93560 original size:12 final size:12
Alignment explanation
Indices: 93527--93574 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
93517 TCAGTTGAAG
**
93527 GAGAAAGATTAA
1 GAGAAAGAAGAA
*
93539 GAAAAAGAAGAA
1 GAGAAAGAAGAA
93551 G-GAAAGGAAGAA
1 GAGAAA-GAAGAA
93563 GAGAAAGAAGAA
1 GAGAAAGAAGAA
93575 AAAGAACCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.77
13 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (12 bp):
GAGAAAGAAGAA
Found at i:98532 original size:51 final size:49
Alignment explanation
Indices: 98469--98599 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 49
98459 TCAGATTTGA
* * * *
98469 TATTTTAAATAAATATGAATATTTATTTA-ATGTGA-TTTGTTTAAATCT
1 TATTTTATATAAATATAAATATTTATTTATAT-TAATTTTGTTGAAATCT
* *
98517 AATGATTTTATATAAATATAAATAATTATTTATATTAATTTTGTTGAGATCT
1 --T-ATTTTATATAAATATAAATATTTATTTATATTAATTTTGTTGAAATCT
**
98569 TATTTTAATATAAATATTTATATTTATTTAT
1 TATTTT-ATATAAATATAAATATTTATTTAT
98600 GTTCACCAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 5 0.07
50 23 0.34
51 27 0.40
52 13 0.19
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (49 bp):
TATTTTATATAAATATAAATATTTATTTATATTAATTTTGTTGAAATCT
Found at i:101700 original size:21 final size:20
Alignment explanation
Indices: 101654--101705 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
101644 AATAGTGCAG
* * *
101654 ACTTCTACCGATACAAGTGA
1 ACTTCTACCGAAACAAATCA
101674 AGCTTCTACCGAAACAAATCA
1 A-CTTCTACCGAAACAAATCA
101695 TACTTCTACCG
1 -ACTTCTACCG
101706 GTACTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (20 bp):
ACTTCTACCGAAACAAATCA
Found at i:102522 original size:52 final size:52
Alignment explanation
Indices: 102440--102627 Score: 234
Period size: 52 Copynumber: 3.6 Consensus size: 52
102430 TTCTCATTTA
* * *
102440 ATACTCATGATGACACATAGTCATCAGACCTCTTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* * *
102492 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATGCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* * ** *
102544 ATACTCATGATGGCACA-ATGTCATCGGATTTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATA-GTCATCGGACCTCATAATCCGTAAAAGATTCAT
* *
102596 ATAAGTCACGATGACACAGAGTCATCGGACCT
1 AT-ACTCACGATGACACATAGTCATCGGACCT
102628 TTTGCATTTA
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
51 1 0.01
52 90 0.79
53 22 0.19
54 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
Found at i:112547 original size:17 final size:18
Alignment explanation
Indices: 112525--112559 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
112515 ACTTAGTTGA
*
112525 TTTCTT-CTTTCCCTTAG
1 TTTCTTGCTTCCCCTTAG
112542 TTTCTTGCTTCCCCTTAG
1 TTTCTTGCTTCCCCTTAG
112560 AGGATGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.06, C:0.31, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTCTTGCTTCCCCTTAG
Found at i:125132 original size:21 final size:21
Alignment explanation
Indices: 125092--125132 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
125082 ATTTCAGCAA
*
125092 TTTATTCTTCTTTTTCTTTTC
1 TTTATTCTTCTTTCTCTTTTC
125113 TTTATTCTT-TTTCTCATTTT
1 TTTATTCTTCTTTCTC-TTTT
125133 TTTTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTCTTCTTTCTCTTTTC
Found at i:159728 original size:15 final size:15
Alignment explanation
Indices: 159708--159748 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
159698 AAGAGAAAAG
*
159708 AAAAGAATAAGGAAA
1 AAAAGAAGAAGGAAA
159723 AAAAG-AGAAGGAAA
1 AAAAGAAGAAGGAAA
159737 AAGAAGAAGAAG
1 AA-AAGAAGAAG
159749 TTGTCTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AAAAGAAGAAGGAAA
Found at i:162321 original size:23 final size:24
Alignment explanation
Indices: 162294--162340 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
162284 CACAACAATT
* *
162294 CATTTTCTATTA-ATTTGCTCTAA
1 CATTTTATATTATATTTGCACTAA
*
162317 CATTTTATGTTATATTTGCACTAA
1 CATTTTATATTATATTTGCACTAA
162341 TAGATTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (24 bp):
CATTTTATATTATATTTGCACTAA
Found at i:181043 original size:22 final size:22
Alignment explanation
Indices: 181002--181046 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
180992 ATTAATTAAG
*
181002 AAAGAAATTTATATGTATATTA
1 AAAGAAATTTAAATGTATATTA
181024 AAAGAAATTTAAATAGATATATT
1 AAAGAAATTTAAAT-G-TATATT
181047 CCTAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
AAAGAAATTTAAATGTATATTA
Found at i:182981 original size:41 final size:41
Alignment explanation
Indices: 182924--183004 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
182914 ATGCTTCTAT
182924 TTTCTAGTGAGTCAACAAATAAGATGCGTCGACAAGGAGCC
1 TTTCTAGTGAGTCAACAAATAAGATGCGTCGACAAGGAGCC
182965 TTTCTAGTGAGTCAACAAATAAGATGCGTCGACAAGGAGC
1 TTTCTAGTGAGTCAACAAATAAGATGCGTCGACAAGGAGC
183005 TTGGCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (41 bp):
TTTCTAGTGAGTCAACAAATAAGATGCGTCGACAAGGAGCC
Found at i:194374 original size:17 final size:18
Alignment explanation
Indices: 194326--194376 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 18
194316 GAGTTGGTTT
194326 TAAATAGCATAAAATAAAACG
1 TAAA-AGCA-AAAA-AAAACG
**
194347 TAAAATAAAAAAAAAAC-
1 TAAAAGCAAAAAAAAACG
194364 TAAAAGCAAAAAA
1 TAAAAGCAAAAAA
194377 TTGAGATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 4 0.15
20 2 0.08
21 4 0.15
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.14
Consensus pattern (18 bp):
TAAAAGCAAAAAAAAACG
Found at i:197325 original size:19 final size:18
Alignment explanation
Indices: 197303--197342 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
197293 CTTCTATTTC
197303 CTTCTCTTCTCTTCTTTGT
1 CTTCTCTTCTC-TCTTTGT
* *
197322 CTTCTCTTTTCTCTTTTT
1 CTTCTCTTCTCTCTTTGT
197340 CTT
1 CTT
197343 TAACACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.68
Consensus pattern (18 bp):
CTTCTCTTCTCTCTTTGT
Found at i:201654 original size:218 final size:218
Alignment explanation
Indices: 201271--201709 Score: 761
Period size: 218 Copynumber: 2.0 Consensus size: 218
201261 CCTCAACTTT
* * *
201271 GTGGCCACATTCAGATAAGGCATTATCTTCCAATGTCACCGCATATTCCTCTAGTACTACTGAAC
1 GTGGCCACATTCAGATAAGGCACTATCTTCCAATGTCACCGAATATTCCTCTAGTACTACTAAAC
* *
201336 TTCGTTCATTAAATTCCTCTATATTTAACTTGTCTAGAACATCAATGTGATGATATTGTTCCTTA
66 TTCATTCATTAAATTCCTCTATATTTAACTTGTCCAGAACATCAATGTGATGATATTGTTCCTTA
* * *
201401 CTTCGTGATGGAGATGCTTCGAAAACACTAAAGGTTACATGTTCATCGTTATGGCACATAATCAA
131 CTTCGTGATAGAGATGCTTCAAAAACACTAAAGGTTACATGTTCATCATTATGGCACATAATCAA
201466 CTCACCCTTGAAAACATCTATGA
196 CTCACCCTTGAAAACATCTATGA
* * *
201489 GTGGTCACATTCAGGTAGGGCACTATCTTCCAATGTCACCGAATATTCCTCTAGTACTACTAAAC
1 GTGGCCACATTCAGATAAGGCACTATCTTCCAATGTCACCGAATATTCCTCTAGTACTACTAAAC
201554 TTCATTCATTAAATTCCTCTATATTTAACTTGTCCAGAACATCAATGTGATGATATTGTTCCTTA
66 TTCATTCATTAAATTCCTCTATATTTAACTTGTCCAGAACATCAATGTGATGATATTGTTCCTTA
* *
201619 CTTCGTGATAGAGATGCTTCAAAAACATTAAAGGTTACATGTTCATCATTATGGCACATGATCAA
131 CTTCGTGATAGAGATGCTTCAAAAACACTAAAGGTTACATGTTCATCATTATGGCACATAATCAA
201684 CTCACCCTTGAAAACATCTATGA
196 CTCACCCTTGAAAACATCTATGA
201707 GTG
1 GTG
201710 TGCATCTCGT
Statistics
Matches: 208, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
218 208 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (218 bp):
GTGGCCACATTCAGATAAGGCACTATCTTCCAATGTCACCGAATATTCCTCTAGTACTACTAAAC
TTCATTCATTAAATTCCTCTATATTTAACTTGTCCAGAACATCAATGTGATGATATTGTTCCTTA
CTTCGTGATAGAGATGCTTCAAAAACACTAAAGGTTACATGTTCATCATTATGGCACATAATCAA
CTCACCCTTGAAAACATCTATGA
Found at i:202793 original size:18 final size:18
Alignment explanation
Indices: 202762--202806 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
202752 CATATTTGGT
* * *
202762 TGCATTTGATTATATGAC
1 TGCATCTGAGTATATGAA
202780 TGCATCTGAGTATATGAA
1 TGCATCTGAGTATATGAA
202798 TGCATCTGA
1 TGCATCTGA
202807 TCAGGTTGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (18 bp):
TGCATCTGAGTATATGAA
Found at i:205823 original size:100 final size:100
Alignment explanation
Indices: 205700--206596 Score: 810
Period size: 100 Copynumber: 8.9 Consensus size: 100
205690 AGTAAAAACA
* *
205700 AGTAGCAGATCTCAATCTCCACTGAAGTTGCGGTGGAATAGAGTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
*
205765 TCCCTGAAGATGCAGTGGATCAGATT-AAACTTAAC
66 TCCCTGAAGTTGCAGTGGATCAGATTAAAAC-TAAC
* * ** * *
205800 AGTAGCGGATCTCAACCTCCACTGAAGTTGCAAAGAAATGGAGTGAAGCCACACCAAATTCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* ** * * * *
205865 TCCTTGAAGAAGAAGTGGAAC-GCATTCAAACTAAT
66 TCCCTGAAGTTGCAGTGGATCAG-ATTAAAACTAAC
** * * * *
205900 AGTAGCAGGCCTCAATCTCCACTGGAGTTGCAATGGAATGCACTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* *
205965 TCCCTGAAGATGCAGTGGATTAGATTAAAACTAAC
66 TCCCTGAAGTTGCAGTGGATCAGATTAAAACTAAC
* * *
206000 AGTAGTAGATCTCAATCTCAACTGAAGTTGTAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * * *
206065 -CCTCTAAATTTGTAG-AGAGGCGGATTAAAACTAAC
66 TCC-CTGAAGTTGCAGTGGA-TCAGATTAAAACTAAC
* ** * * * * * * *
206100 AATAAAAGATCTCAATCTCCATTAAAGTTGTAGCGAAATGGAGTGAAGTCAGACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * *
206165 TCCCTAAAGTTGTAGTAGATCAGACTAAAACTAAT
66 TCCCTGAAGTTGCAGTGGATCAGATTAAAACTAAC
* * * * *
206200 AGTAGCAGATCTCAATCTCAATTGAAGTTGCAGTGGAATTGAGTGAAGCCATACAAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * * *
206265 -CCTCTAAAGTTGTAGTGGGGT-GGATTAAAGCTAAT
66 TCC-CTGAAGTTGCAGT-GGATCAGATTAAAACTAAC
* * * * * *
206300 AGTAGCAAATCTTAATTTTCATTGAAGTTGTAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * *
206365 -CCTCTAAAGTTGTAGAGGGT-GGATTAAAACTAAC
66 TCC-CTGAAGTTGCAGTGGATCAGATTAAAACTAAC
* * * * **
206399 AATAGCAGATCTCAATCTCCACTAAAGTTACAGTAGAATAAAGTGAAGCCACAACCTCAAATCCT
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCAC-A-C-CAAATCCT
* ** *
206464 ATATCCCTGAAGTTACAGTGGATTGGATTAAAACTCAC
63 ATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAAC
* * * *
206502 AGTAAC-GAATCTCAATCTCC-CTGAAGTTGTAGTGGAATGGAGTGAAGTTACAGACCCAAATCC
1 AGTAGCAG-ATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAG--CCACA-CCAAATCC
*
206565 TATAT-CCTAGAAGTTGCA-AGGATCAGATTAAA
62 TATATCCCT-GAAGTTGCAGTGGATCAGATTAAA
206597 GATACGGTAG
Statistics
Matches: 656, Mismatches: 123, Indels: 35
0.81 0.15 0.04
Matches are distributed among these distances:
99 63 0.10
100 465 0.71
101 27 0.04
102 65 0.10
103 34 0.05
104 2 0.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (100 bp):
AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
TCCCTGAAGTTGCAGTGGATCAGATTAAAACTAAC
Found at i:206514 original size:103 final size:102
Alignment explanation
Indices: 206384--206579 Score: 236
Period size: 102 Copynumber: 1.9 Consensus size: 102
206374 TTGTAGAGGG
*
206384 TGGATTAAAACTAACAATAGCAGATCTCAATCTCCACTAAAGTTACAGTAGAATAAAGTGAAGCC
1 TGGATTAAAACTAACAATAACAGATCTCAATCTCC-CTAAAGTTACAGTAGAATAAAGTGAAGCC
206449 ACA-ACCTCAAATCCTATATCCCT-GAAGTTACAGTGGAT
65 ACAGACC-CAAATCCTATAT-CCTAGAAGTTACAGTGGAT
* * * ** * ** **
206487 TGGATTAAAACTCACAGTAAC-GAATCTCAATCTCCCTGAAGTTGTAGTGGAATGGAGTGAAGTT
1 TGGATTAAAACTAACAATAACAG-ATCTCAATCTCCCTAAAGTTACAGTAGAATAAAGTGAAGCC
206551 ACAGACCCAAATCCTATATCCTAGAAGTT
65 ACAGACCCAAATCCTATATCCTAGAAGTT
206580 GCAAGGATCA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
101 3 0.04
102 43 0.54
103 33 0.42
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (102 bp):
TGGATTAAAACTAACAATAACAGATCTCAATCTCCCTAAAGTTACAGTAGAATAAAGTGAAGCCA
CAGACCCAAATCCTATATCCTAGAAGTTACAGTGGAT
Found at i:208241 original size:23 final size:23
Alignment explanation
Indices: 208174--208241 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
208164 ATATTTCAGC
*
208174 TGTTCATGTATTAGATGATTTAT
1 TGTTCATGTATTAGATGATTTGT
* * *
208197 TGTTCTTGAAATT-GA-AACTTTGT
1 TGTTCATG-TATTAGATGA-TTTGT
*
208220 TGTTCCTGTATTAGATGATTTG
1 TGTTCATGTATTAGATGATTTG
208242 CAGCTAGGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (23 bp):
TGTTCATGTATTAGATGATTTGT
Found at i:215130 original size:27 final size:27
Alignment explanation
Indices: 215074--215132 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
215064 GATGAGGAGA
*
215074 AAGAAGAAGGAAAAGAAGAAGAACGAG
1 AAGAAGAAGGAAAAGAAGAAGAAAGAG
* *
215101 AAGAGGAAGGGAAAGAAGAAAGAAAG-G
1 AAGAAGAAGGAAAAGAAG-AAGAAAGAG
215128 AAGAA
1 AAGAA
215133 CCTACTATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.63, C:0.02, G:0.36, T:0.00
Consensus pattern (27 bp):
AAGAAGAAGGAAAAGAAGAAGAAAGAG
Found at i:216575 original size:20 final size:21
Alignment explanation
Indices: 216550--216589 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
216540 TGTATTTTTA
*
216550 GCATTTT-TAACTTAGTAATT
1 GCATTTTCTAACTCAGTAATT
216570 GCATTTTCTAACTCAGTAAT
1 GCATTTTCTAACTCAGTAAT
216590 GCTAGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTAATT
Found at i:224596 original size:21 final size:21
Alignment explanation
Indices: 224553--224598 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
224543 ACGGTTGCTA
*
224553 TTTTTTACCAACATTAGCCAT
1 TTTTTTACCAACATTAGCAAT
** *
224574 TTTTTTACCAATGTTTGCAAT
1 TTTTTTACCAACATTAGCAAT
224595 TTTT
1 TTTT
224599 GGCCATTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTTTACCAACATTAGCAAT
Found at i:226777 original size:16 final size:16
Alignment explanation
Indices: 226756--226786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
226746 TTTATAAAAA
*
226756 TTTCTTTCTTTTTCTT
1 TTTCTTCCTTTTTCTT
226772 TTTCTTCCTTTTTCT
1 TTTCTTCCTTTTTCT
226787 CATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTCCTTTTTCTT
Found at i:229661 original size:20 final size:21
Alignment explanation
Indices: 229636--229674 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
229626 GCAAGGAATT
229636 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
229656 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
229675 TAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:234934 original size:13 final size:14
Alignment explanation
Indices: 234916--234945 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
234906 TTCAATGCAA
234916 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
234929 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
234943 TCA
1 TCA
234946 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:236660 original size:100 final size:100
Alignment explanation
Indices: 236439--236665 Score: 350
Period size: 100 Copynumber: 2.3 Consensus size: 100
236429 CAAGTAGCAT
** * * * *
236439 ATCTCAATCTCCACTGAAGTTACAGTGGAATGAAGTGAAGCCACACCAAATCCTATATCCTTGAA
1 ATCTCAATCTCCACTGAAGTTGTAGTGAAATGAAGTGAAGCCACACAAAATCCTATATCCCTAAA
236504 GATGCAATGGATCAGATTAAAACTAACAGTAGTAG
66 GATGCAATGGATCAGATTAAAACTAACAGTAGTAG
* *
236539 ATTTCAATCTCCACTGAAGTTGTAGTGAAATGGAGTGAAGCCACACAAAATCCTATATCCCTAAA
1 ATCTCAATCTCCACTGAAGTTGTAGTGAAATGAAGTGAAGCCACACAAAATCCTATATCCCTAAA
236604 GATG-AAGTGGATC-GAATTAAAACTAACAGTAGTAG
66 GATGCAA-TGGATCAG-ATTAAAACTAACAGTAGTAG
236639 ATCTCAATCTCCACTGAAGTTGTAGTG
1 ATCTCAATCTCCACTGAAGTTGTAGTG
236666 GATCGGATTA
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
99 3 0.03
100 113 0.97
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (100 bp):
ATCTCAATCTCCACTGAAGTTGTAGTGAAATGAAGTGAAGCCACACAAAATCCTATATCCCTAAA
GATGCAATGGATCAGATTAAAACTAACAGTAGTAG
Found at i:238616 original size:22 final size:19
Alignment explanation
Indices: 238591--238659 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 19
238581 CCTTTTCCCT
238591 TTTTTGTTTATTTTTGTATTGA
1 TTTTT-TTTATTTTT-TATT-A
238613 TTTTTTTATATTTTTTA-TA
1 TTTTTTT-TATTTTTTATTA
238632 TTTTTATTTTATTATTTTATTA
1 -TTTT-TTTTATT-TTTTATTA
238654 TTTTTT
1 TTTTTT
238660 GTCATTTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 16 0.38
22 14 0.33
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTTTATTTTTTATTA
Found at i:238616 original size:23 final size:20
Alignment explanation
Indices: 238590--238659 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 20
238580 TCCTTTTCCC
238590 TTTTTTGTTTATTTTTGTATTGA
1 TTTTTT-TTTATTTTT-TATT-A
*
238613 TTTTTTTATATTTTTTA-TA
1 TTTTTTTTTATTTTTTATTA
238632 TTTTTATTTTATTATTTTATTA
1 TTTTT-TTTTATT-TTTTATTA
238654 TTTTTT
1 TTTTTT
238660 GTCATTTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.14
20 7 0.17
21 8 0.19
22 15 0.36
23 6 0.14
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTATTTTTTATTA
Found at i:238626 original size:8 final size:7
Alignment explanation
Indices: 238597--238659 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 7
238587 CCCTTTTTTG
238597 TTTATTT
1 TTTATTT
*
238604 TTGTATTGA
1 TT-TATT-T
238613 TTT-TTT
1 TTTATTT
*
238619 TATATTT
1 TTTATTT
238626 TTTATATT
1 TTTAT-TT
238634 TTTATTT
1 TTTATTT
238641 TATTATTT
1 T-TTATTT
238649 TATTATTT
1 T-TTATTT
238657 TTT
1 TTT
238660 GTCATTTACA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
6 2 0.04
7 16 0.34
8 27 0.57
9 2 0.04
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTATTT
Found at i:238646 original size:16 final size:15
Alignment explanation
Indices: 238616--238659 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
238606 GTATTGATTT
238616 TTTTA-TATTTTTTA
1 TTTTATTATTTTTTA
238630 TATTT-TTATTTTATTA
1 T-TTTATTATTTT-TTA
238646 TTTTATTATTTTTT
1 TTTTATTATTTTTT
238660 GTCATTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 14 0.54
16 11 0.42
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTATTTTTTA
Found at i:238731 original size:19 final size:19
Alignment explanation
Indices: 238709--238747 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
238699 AATTTTGTCC
238709 TTTATTCATTCTT-TTTATT
1 TTTA-TCATTCTTATTTATT
*
238728 TTTATCATTTTTATTTATT
1 TTTATCATTCTTATTTATT
238747 T
1 T
238748 ATTTTTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATCATTCTTATTTATT
Found at i:238749 original size:23 final size:23
Alignment explanation
Indices: 238722--238766 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
238712 ATTCATTCTT
* *
238722 TTTATTTTTATCATTTTTATTTA
1 TTTATTTTTAGCACTTTTATTTA
238745 TTTATTTTTAGCACTTTTATTT
1 TTTATTTTTAGCACTTTTATTT
238767 TTCCGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTATTTTTAGCACTTTTATTTA
Found at i:238861 original size:43 final size:40
Alignment explanation
Indices: 238803--238881 Score: 95
Period size: 43 Copynumber: 1.9 Consensus size: 40
238793 TTTATTGTTG
* *
238803 TTTATTTTACTTTATTGTGTAGTATATACATATTATTATTTGT
1 TTTATTTTACATTATTAT-TAGTAT-TACAT-TTATTATTTGT
* *
238846 TTTATTTTCCATTATTATTTGTATTACATTTATTAT
1 TTTATTTTACATTATTATTAGTATTACATTTATTAT
238882 ATTTGCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.22
41 5 0.16
42 5 0.16
43 15 0.47
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (40 bp):
TTTATTTTACATTATTATTAGTATTACATTTATTATTTGT
Found at i:238886 original size:20 final size:19
Alignment explanation
Indices: 238833--238907 Score: 55
Period size: 22 Copynumber: 3.8 Consensus size: 19
238823 AGTATATACA
* *
238833 TATTATTATTTGTTTTATTT
1 TATTA-TATTTGTATTACTT
238853 TCCATTATTATTTGTATTACATT
1 T--ATTA-TATTTGTATTAC-TT
* *
238876 TATTATATTTGCATTTCTT
1 TATTATATTTGTATTACTT
238895 TATT-TATTT-TATT
1 TATTATATTTGTATT
238908 TTATCATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.06
18 5 0.11
19 6 0.13
20 11 0.23
21 4 0.09
22 15 0.32
23 3 0.06
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
TATTATATTTGTATTACTT
Found at i:238907 original size:5 final size:5
Alignment explanation
Indices: 238893--238942 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
238883 TTTGCATTTC
*
238893 TTTA- TTTAT TTTAT TTTAT CATTTAT TTTGTT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT --TTTAT TTT-AT TTTAT TTTAT TTTAT
238940 TTT
1 TTT
238943 GCTTTAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.10
5 27 0.68
6 4 0.10
7 5 0.12
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:238955 original size:21 final size:22
Alignment explanation
Indices: 238914--238964 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
238904 TATTTTATCA
* *
238914 TTTATTTTGTTTTTATTTTA-T
1 TTTATTTTGTCTTTATATTATT
238935 TTTATTTTG-CTTTAGTATTATT
1 TTTATTTTGTCTTTA-TATTATT
238957 TTTATTTT
1 TTTATTTT
238965 CGAATGTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 13 0.50
22 9 0.35
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTATTTTGTCTTTATATTATT
Found at i:238959 original size:32 final size:33
Alignment explanation
Indices: 238893--238964 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
238883 TTTGCATTTC
* * *
238893 TTTA-TTTATTTTATTTTATCATTTATTTTGTT
1 TTTATTTTATTTTATTTTAGCATTTATATTATT
238925 TTTATTTTATTTTATTTT-GC-TTTAGTATTATT
1 TTTATTTTATTTTATTTTAGCATTTA-TATTATT
238957 TTTATTTT
1 TTTATTTT
238965 CGAATGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 4 0.11
32 18 0.51
33 13 0.37
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (33 bp):
TTTATTTTATTTTATTTTAGCATTTATATTATT
Found at i:246432 original size:27 final size:27
Alignment explanation
Indices: 246402--246533 Score: 99
Period size: 27 Copynumber: 4.9 Consensus size: 27
246392 AAACACGAAA
* *
246402 TCTGAAAGAACAACCTTTATGGCAAAC
1 TCTGAAAGAACTACCTTTGTGGCAAAC
*
246429 TCTGAAAGGAA-TGCCTTTGTGGCGAAA-
1 TCTGAAA-GAACTACCTTTGTGGC-AAAC
* * *
246456 TATGGAAGAACTACCTTCGTGGCAAAC
1 TCTGAAAGAACTACCTTTGTGGCAAAC
* *
246483 TCTGAAAAGAA-TGCCTATGTGGCAAAC
1 TCTG-AAAGAACTACCTTTGTGGCAAAC
* * * * *
246510 TTTAAAAGAAATGCCTTTGCGGCA
1 TCTGAAAGAACTACCTTTGTGGCA
246534 TGTCATAATA
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
26 12 0.14
27 60 0.72
28 11 0.13
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
TCTGAAAGAACTACCTTTGTGGCAAAC
Found at i:246465 original size:54 final size:54
Alignment explanation
Indices: 246397--246505 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
246387 ATCATAAACA
* * * *
246397 CGAAATCTGAAAGAACAACCTTTATGGCAAACTCTGAAAGGAATGCCTTTGTGG
1 CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
* * *
246451 CGAAATATGGAAGAACTACCTTCGTGGCAAACTCTGAAAAGAATGCCTATGTGG
1 CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
246505 C
1 C
246506 AAACTTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (54 bp):
CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
Found at i:246519 original size:54 final size:54
Alignment explanation
Indices: 246397--246519 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
246387 ATCATAAACA
* * * * *
246397 CGAAATCTGAAAGAACAACCTTTATGGCAAACTCTGAAAGGAATGCCTTTGTGG
1 CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
** * *
246451 CGAAATATGGAAGAACTACCTTCGTGGCAAACTCTGAAAAGAATGCCTATGTGG
1 CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
*
246505 C-AAACTTTAAAAGAA
1 CGAAA-TATAAAAGAA
246520 ATGCCTTTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.05
54 55 0.95
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (54 bp):
CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
Found at i:247082 original size:23 final size:24
Alignment explanation
Indices: 247056--247100 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
247046 TTTACTTTCA
*
247056 TAATAA-CATTTATAAATTAATAG
1 TAATAACCATTTATAAAATAATAG
247079 TAATAACCATTTATAAAATAAT
1 TAATAACCATTTATAAAATAAT
247101 CAGAATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATAACCATTTATAAAATAATAG
Found at i:247672 original size:29 final size:29
Alignment explanation
Indices: 247630--247687 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
247620 CAAACATGAA
247630 AATTTCAATTTAGGGGAATGGTACAAGCC
1 AATTTCAATTTAGGGGAATGGTACAAGCC
247659 AATTTCAATTTAGGGGAATGGTACAAGCC
1 AATTTCAATTTAGGGGAATGGTACAAGCC
247688 TTGGTTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (29 bp):
AATTTCAATTTAGGGGAATGGTACAAGCC
Found at i:247973 original size:21 final size:22
Alignment explanation
Indices: 247948--247996 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
247938 AAATTGTAAC
*
247948 CTTAATATTTA-TCAAATTTAT
1 CTTAATATTAATTCAAATTTAT
* *
247969 CTTAATCTTAATTCATATTTAT
1 CTTAATATTAATTCAAATTTAT
247991 -TTAATA
1 CTTAATA
247997 ATAAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (22 bp):
CTTAATATTAATTCAAATTTAT
Found at i:253081 original size:9 final size:9
Alignment explanation
Indices: 253069--253093 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
253059 AAAATAAAAA
253069 ATATTTTAT
1 ATATTTTAT
253078 ATATTTTAT
1 ATATTTTAT
253087 ATATTTT
1 ATATTTT
253094 TTTATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTAT
Found at i:253098 original size:100 final size:101
Alignment explanation
Indices: 252960--253163 Score: 356
Period size: 100 Copynumber: 2.0 Consensus size: 101
252950 GGGATACGAC
*
252960 AATAAAAAATATTTTTTATATTTTTATATATTTTTTTATGTTAAAATACTTACATTCAATTGATT
1 AATAAAAAATATTTTATATATTTTTATATATTTTTTTATGTTAAAATACTTACATTCAATTGATT
253025 TAAACTTTCATATTTGTTGAAACTTGAAAATAAAAA
66 TAAACTTTCATATTTGTTGAAACTTGAAAATAAAAA
* * *
253061 AATAAAAAATATTTTATATA-TTTTATATATTTTTTTATGTTAAAATGCTTACCTTCAATTGTTT
1 AATAAAAAATATTTTATATATTTTTATATATTTTTTTATGTTAAAATACTTACATTCAATTGATT
*
253125 TAAACTTTCATATTTGTTGAAACTTGAAAATAGAAA
66 TAAACTTTCATATTTGTTGAAACTTGAAAATAAAAA
253161 AAT
1 AAT
253164 GGAAATAAAC
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 79 0.81
101 19 0.19
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (101 bp):
AATAAAAAATATTTTATATATTTTTATATATTTTTTTATGTTAAAATACTTACATTCAATTGATT
TAAACTTTCATATTTGTTGAAACTTGAAAATAAAAA
Found at i:254919 original size:23 final size:25
Alignment explanation
Indices: 254893--254938 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
254883 CCAATTAGGA
254893 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
254916 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
254939 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:256042 original size:13 final size:14
Alignment explanation
Indices: 256025--256056 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
256015 TATTATTTGC
256025 ATTTTTC-A-TTTA
1 ATTTTTCTATTTTA
256037 ATTTTTCTATTTTA
1 ATTTTTCTATTTTA
256051 ATTTTT
1 ATTTTT
256057 TTCCTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTTCTATTTTA
Found at i:261534 original size:24 final size:24
Alignment explanation
Indices: 261495--261557 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
261485 TAGACTAATA
* * *
261495 AGAGTTTGACTCAAACAACTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
261519 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
261543 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
261558 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:263535 original size:24 final size:24
Alignment explanation
Indices: 263477--263535 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
263467 TAGACTAATA
* *
263477 AGAGTTTAACTCAAACAACTAAAC
1 AGAGTTTAATTCAAACAAATAAAC
*
263501 ATAGTTTAATT-ACAACAAATAAAC
1 AGAGTTTAATTCA-AACAAATAAAC
263525 AGAGTTTAATT
1 AGAGTTTAATT
263536 GAAATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:264875 original size:3 final size:3
Alignment explanation
Indices: 264850--264993 Score: 109
Period size: 3 Copynumber: 47.7 Consensus size: 3
264840 TTACTTTTTG
* * *
264850 TTA TT- TTA ATA TTA TT- TTC TTA TTA TTA TTTG TTA TTTA GTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA -TTA TTA
* * *
264895 TTA TTG TTA TTA TTT TTA TTA TTA TTG TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
264942 TTT TTA TTA CTA TTA TTTA TTA TTT TTA TTA TTT TTA CTTA TTTA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA
264989 TTA TT
1 TTA TT
264994 TGTTATTTGT
Statistics
Matches: 111, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
2 10 0.09
3 85 0.77
4 16 0.14
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:265001 original size:26 final size:26
Alignment explanation
Indices: 264901--265000 Score: 115
Period size: 23 Copynumber: 4.1 Consensus size: 26
264891 TTTATTATTG
264901 TTATTATT-TTTATTATTA-TTGTTA
1 TTATTATTATTTATTATTATTTGTTA
264925 TTATTATTA-TT-TTATTATTT-TTA
1 TTATTATTATTTATTATTATTTGTTA
* *
264948 TTACTATTATTTATTATT-TTTATTA
1 TTATTATTATTTATTATTATTTGTTA
*
264973 TTTTTACTTATTTATT-TTATTTGTTA
1 TTATTA-TTATTTATTATTATTTGTTA
264999 TT
1 TT
265001 TGTCTACTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
23 17 0.26
24 17 0.26
25 14 0.22
26 17 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (26 bp):
TTATTATTATTTATTATTATTTGTTA
Found at i:267535 original size:16 final size:16
Alignment explanation
Indices: 267452--267544 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 16
267442 TTTTTTGTTT
*
267452 AGAAAAAGAAGAAAAA
1 AGAAAAAGAAAAAAAA
*
267468 AGAAAAA-AAAAGTCGAAA
1 AGAAAAAGAAAA---AAAA
267486 AGAAAAATTGAAAAAAAA
1 AGAAAAA--GAAAAAAAA
* ** *
267504 TA-ATATTGAGAAAAAA
1 -AGAAAAAGAAAAAAAA
267520 AGAAAAAGAAAAAAAA
1 AGAAAAAGAAAAAAAA
267536 AGACAAAAG
1 AGA-AAAAG
267545 TATGTTCGAG
Statistics
Matches: 57, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
15 4 0.07
16 28 0.49
17 5 0.09
18 15 0.26
19 1 0.02
21 4 0.07
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAA
Found at i:269947 original size:28 final size:27
Alignment explanation
Indices: 269899--269976 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
269889 CCGGTTCAAA
*
269899 AAAAAAAGAAACAATAAAAAATAGATTT
1 AAAAAAAGAAA-AATAAAAAATAGATCT
**
269927 AAAAAAAGAAAAAGTGCAAAATAGATCT
1 AAAAAAAGAAAAA-TAAAAAATAGATCT
*
269955 AAAAGGAAGAAAAATACAAAAA
1 AAAA-AAAGAAAAATA-AAAAA
269977 AAGGTTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 2 0.05
28 27 0.66
29 12 0.29
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.13
Consensus pattern (27 bp):
AAAAAAAGAAAAATAAAAAATAGATCT
Found at i:270880 original size:30 final size:29
Alignment explanation
Indices: 270842--270949 Score: 153
Period size: 30 Copynumber: 3.6 Consensus size: 29
270832 ACCCCCGAAC
270842 TTTCCTAAAATTACATTTTAACCCTTAAA
1 TTTCCTAAAATTACATTTTAACCCTTAAA
* *
270871 TTTCTCTAAAATTACATTTTGACCCTCAAA
1 TTTC-CTAAAATTACATTTTAACCCTTAAA
* *
270901 CTTCTCTAAAATTACTTTTTAACCCTTAAA
1 TTTC-CTAAAATTACATTTTAACCCTTAAA
270931 GTTTCCTAAAATTACATTT
1 -TTTCCTAAAATTACATTT
270950 CACCCCTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 4 0.06
30 62 0.90
31 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTCCTAAAATTACATTTTAACCCTTAAA
Found at i:270966 original size:30 final size:30
Alignment explanation
Indices: 270842--270979 Score: 124
Period size: 30 Copynumber: 4.6 Consensus size: 30
270832 ACCCCCGAAC
*
270842 TTTCCTAAAATTACATTTTAACCCTTAAA-
1 TTTCCTAAAATTACATTTTAACCCCTAAAT
*
270871 TTTCTCTAAAATTACATTTTGA-CCCTCAAA-
1 TTTC-CTAAAATTACATTTTAACCCCT-AAAT
* * * *
270901 CTTCTCTAAAATTACTTTTTAACCCTTAAAG
1 TTTC-CTAAAATTACATTTTAACCCCTAAAT
*
270932 TTTCCTAAAATTACA-TTTCACCCCTAAACT
1 TTTCCTAAAATTACATTTTAACCCCTAAA-T
* *
270962 TTTCC-AAATTTACGTTTT
1 TTTCCTAAAATTACATTTT
270980 GATCCCGTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
29 25 0.28
30 59 0.66
31 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTCCTAAAATTACATTTTAACCCCTAAAT
Found at i:282578 original size:39 final size:38
Alignment explanation
Indices: 282524--283095 Score: 310
Period size: 39 Copynumber: 14.7 Consensus size: 38
282514 CCATCAGCCA
* *
282524 ATCTCTTACGCCGAGCCTGGGGCAGCTTGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* * *
282563 ATCTTTTACCCCGAGCCTGGGGCCGA-TCA-CCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCATC---CG
* * * *
282602 ATCTCTTACCCCAAGCCTGAGGCAGATTGTAGCCAACCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* ** * *
282641 ATCTTTTACCCCGAGCCTAAGGTAGA-TCA-CCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCAT---CCG
* * * *** *
282680 ATCTCTTACCCCGAGCTTGAGGCATATTGCAATTATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* * * * * *
282719 ATCTTTTACCCCGAGCCTGAGGTAGA-TCACCGTCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCA--GCCATCCG
* * * *
282758 ATATCTTACCCTGAGCCTGGGGCAAATTGCAGCCATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* * *
282797 ATCTTTTACCCCGAGCCTAGGGCAGA-TCA-CCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCAT---CCG
* ** * *
282836 ATCCCTTACCCCGAGCCTAAGGCAGATTGTAGCCATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* * * * *
282875 ATCTTTTACCCCGAGCTTGGGACA-AATCA-CCATCAGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCATC--C-G
* *
282914 ACCTCTTACCCCGAGCCTGGGGCAAATTACAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* * *
282953 ATCTTTTACCCCGAGCTTGGGGCAGA-TCA-CCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCAT---CCG
* *
282992 ATCCCTTA-CCCGAGCCTGGGGCAGATTACAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATCCG
* *
283030 ATCTTTTACCCCGAGCCT-GGGCAGA-TCA-CCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCAT---CCG
*
283068 ATCTCTTACCCCGAACCTGGGGCAGATT
1 ATCTCTTACCCCGAGCCTGGGGCAGATT
283096 GTAATCATTC
Statistics
Matches: 401, Mismatches: 92, Indels: 79
0.70 0.16 0.14
Matches are distributed among these distances:
35 4 0.01
36 23 0.06
37 11 0.03
38 54 0.13
39 272 0.68
40 10 0.02
41 12 0.03
42 15 0.04
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCATCCG
Found at i:282591 original size:78 final size:78
Alignment explanation
Indices: 282446--283156 Score: 814
Period size: 78 Copynumber: 9.1 Consensus size: 78
282436 GAAGATTTTG
* ** * ** * * * * **
282446 ATCTCTTACCCCGATCAAGGGGCGGATCACAGTCATCCGATCTTTTACTCCAAGCTTGGGATAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
282511 TCACCATCAGCCA
66 TCACCATCAGCCA
* * *
282524 ATCTCTTACGCCGAGCCTGGGGCAGCTTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCCGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
*
282589 TCACCATCAGTCA
66 TCACCATCAGCCA
* * * * ** *
282602 ATCTCTTACCCCAAGCCTGAGGCAGATTGTAGCCAACCGATCTTTTACCCCGAGCCTAAGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
*
282667 TCACCATCAACCA
66 TCACCATCAGCCA
* * * *** * * *
282680 ATCTCTTACCCCGAGCTTGAGGCATATTGCAATTATCTGATCTTTTACCCCGAGCCTGAGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
*
282745 TCACCGTCAGCCA
66 TCACCATCAGCCA
* * * * *
282758 ATATCTTACCCTGAGCCTGGGGCAAATTGCAGCCATCTGATCTTTTACCCCGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
282823 TCACCATCAGCCA
66 TCACCATCAGCCA
* ** * * * * *
282836 ATCCCTTACCCCGAGCCTAAGGCAGATTGTAGCCATCTGATCTTTTACCCCGAGCTTGGGACAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
*
282901 TCACCATCAGCAA
66 TCACCATCAGCCA
* * * *
282914 ACCTCTTACCCCGAGCCTGGGGCAAATTACAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
282979 TCACCATCAGCCA
66 TCACCATCAGCCA
* * *
282992 ATCCCTTA-CCCGAGCCTGGGGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCT-GGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
283055 TCACCATCAGCCA
66 TCACCATCAGCCA
* * ** * * * * *
283068 ATCTCTTACCCCGAACCTGGGGCAGATTGTAATCATTCGATCTTTTACCTCGATCATGGGGCAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* *
283133 TCACCGTCAGTCA
66 TCACCATCAGCCA
283146 ATCTCTTACCC
1 ATCTCTTACCC
283157 TGCAAAAGGG
Statistics
Matches: 539, Mismatches: 92, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
76 27 0.05
77 85 0.16
78 427 0.79
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:283621 original size:86 final size:86
Alignment explanation
Indices: 283472--283629 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 86
283462 GCAAGCACCA
* ** *
283472 TCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGTAATAAAGCGGTCACCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTGGATCAAACCAATAAAGCGGTCACCTTCCTAATAAGATAC
283537 AGAGAAGTAGACCAAAATCTG
66 AGAGAAGTAGACCAAAATCTG
* * * * *
283558 TCTTCTTGATGAGATACAGAGAAA-TGGATTAAACCAATGAAGCGGTCATCTTCCTGATAAGATA
1 TCTTCCTGATGAGATACAGA-AAAGTGGATCAAACCAATAAAGCGGTCACCTTCCTAATAAGATA
283622 CAGAGAAG
65 CAGAGAAG
283630 AAGGCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
86 59 0.95
87 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (86 bp):
TCTTCCTGATGAGATACAGAAAAGTGGATCAAACCAATAAAGCGGTCACCTTCCTAATAAGATAC
AGAGAAGTAGACCAAAATCTG
Found at i:285797 original size:60 final size:60
Alignment explanation
Indices: 285688--285810 Score: 178
Period size: 60 Copynumber: 2.0 Consensus size: 60
285678 TCACAAGAGG
*
285688 CCCTCGAACTTTCCAAAAATCACATTTTAACCCCCAAATTTCTCTAAAATTAGATTTTCA
1 CCCTCGAACTTTCCAAAAATCACATTTTAACCCCCAAATTTCTCTAAAATTACATTTTCA
* **
285748 CCCTCGAACTTCTCC-AAAATTACATTTTAACCCTTAAACTTTCTC-AAAATTACATTTTCA
1 CCCTCGAACTT-TCCAAAAATCACATTTTAACCCCCAAA-TTTCTCTAAAATTACATTTTCA
285808 CCC
1 CCC
285811 CCTAAACTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 48 0.84
61 9 0.16
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (60 bp):
CCCTCGAACTTTCCAAAAATCACATTTTAACCCCCAAATTTCTCTAAAATTACATTTTCA
Found at i:285817 original size:31 final size:31
Alignment explanation
Indices: 285694--285818 Score: 123
Period size: 30 Copynumber: 4.1 Consensus size: 31
285684 GAGGCCCTCG
* *
285694 AACTTTC-CAAAAATCACATTTTAACCCCCA
1 AACTTTCTCAAAAATTACATTTTCACCCCCA
* * * *
285724 AA-TTTCTCTAAAATTAGATTTTCACCCTCG
1 AACTTTCTCAAAAATTACATTTTCACCCCCA
* * **
285754 AAC-TTCTCCAAAATTACATTTTAACCCTTA
1 AACTTTCTCAAAAATTACATTTTCACCCCCA
285784 AACTTTCTC-AAAATTACATTTTCACCCCCTA
1 AACTTTCTCAAAAATTACATTTTCACCCCC-A
285815 AACT
1 AACT
285819 ATTCCAATTT
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 4 0.05
30 63 0.82
31 10 0.13
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (31 bp):
AACTTTCTCAAAAATTACATTTTCACCCCCA
Found at i:293180 original size:75 final size:75
Alignment explanation
Indices: 293064--293215 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 75
293054 GACATAGGCA
* * ** * *
293064 TGTGAGTGACCATGTGTCTACTAGAGCTTAATTTCACAAAATTTTGAAATGACACACGTCTTATA
1 TGTGACTGACCATGTGTCTACTAGAGCTTAATTTCACAAAATTTCGAAACAACACACATCTTACA
293129 GACACGAGCG
66 GACACGAGCG
* *** *
293139 TGTGACTGACCGTGTGTCTACTAGAGCTTAATTTTGTAAAATTTCGAAACAACACACATCTTACC
1 TGTGACTGACCATGTGTCTACTAGAGCTTAATTTCACAAAATTTCGAAACAACACACATCTTACA
*
293204 GACACGGGCG
66 GACACGAGCG
293214 TG
1 TG
293216 GGAGAACAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (75 bp):
TGTGACTGACCATGTGTCTACTAGAGCTTAATTTCACAAAATTTCGAAACAACACACATCTTACA
GACACGAGCG
Found at i:294031 original size:3 final size:3
Alignment explanation
Indices: 294014--294158 Score: 77
Period size: 3 Copynumber: 47.7 Consensus size: 3
294004 TCTTTACTTT
* * * *
294014 TTA TTA TTTA ATA TTA TT- TTC TAA TTA TTA TTTG TTA TTTA GTT- TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA -TTA TTA
* * *
294061 TTA TT- TTA TGA TTA ATA TTT TTA TTA TTA TTTA TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
294104 TTA TTT TTA TTA TTA TTTA TTA TTT TTA TTT TTA TTT TTA TTTA TTTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
294152 TT- TTA TT
1 TTA TTA TT
294159 TGTTATTTGT
Statistics
Matches: 108, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
2 12 0.11
3 73 0.68
4 23 0.21
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:294065 original size:44 final size:38
Alignment explanation
Indices: 294012--294165 Score: 130
Period size: 41 Copynumber: 3.7 Consensus size: 38
294002 CTTCTTTACT
294012 TTTTATTATTTAATATTATTTTCTAATTATTATTTGTTATTTA
1 TTTTATTATTT-ATATTATTTT-T-ATTATTATTT-TT-TTTA
*
294055 GTTTTATTATTTTATGATTAATATTTTTATTATTATTTATTTTA
1 -TTTTATTA-TTTAT-A-T--TATTTTTATTATTATTTTTTTTA
*
294099 TTTTATTATTTTTATTATTATTTATTATT-TTTATTTTTA
1 TTTTATTATTTATATTATT-TTTATTATTATTT-TTTTTA
*
294138 TTTTTATTTATTTATTTTATTTGTTATT
1 -TTTTA-TTATTTATATTATTT-TTATT
294166 TGTCTACTGT
Statistics
Matches: 95, Mismatches: 5, Indels: 23
0.77 0.04 0.19
Matches are distributed among these distances:
38 7 0.07
39 14 0.15
40 7 0.07
41 18 0.19
42 4 0.04
43 8 0.08
44 14 0.15
45 5 0.05
46 11 0.12
47 1 0.01
48 6 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.72
Consensus pattern (38 bp):
TTTTATTATTTATATTATTTTTATTATTATTTTTTTTA
Found at i:294099 original size:9 final size:9
Alignment explanation
Indices: 294048--294159 Score: 79
Period size: 10 Copynumber: 11.7 Consensus size: 9
294038 TTATTATTTG
294048 TTATTTAGTT
1 TTATTTA-TT
294058 TTA-TTATT
1 TTATTTATT
*
294066 TTATGATTAATA
1 TTAT--TT-ATT
294078 TT-TTTATT
1 TTATTTATT
294086 ATTATTTATT
1 -TTATTTATT
294096 TTATTTTATT
1 TTA-TTTATT
294106 ATT-TTTATT
1 -TTATTTATT
294115 ATTATTTATT
1 -TTATTTATT
294125 ATT-TTTATTT
1 -TTATTTA-TT
*
294135 TTATTTTTAT
1 TTATTTAT-T
294145 TTATTTATT
1 TTATTTATT
294154 TTATTT
1 TTATTT
294160 GTTATTTGTC
Statistics
Matches: 86, Mismatches: 4, Indels: 25
0.75 0.03 0.22
Matches are distributed among these distances:
8 7 0.08
9 33 0.38
10 37 0.43
11 5 0.06
12 4 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
TTATTTATT
Found at i:294144 original size:25 final size:24
Alignment explanation
Indices: 294078--294166 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 24
294068 ATGATTAATA
* *
294078 TTTTTATTATTATTTAT-TTTATT
1 TTTTTATTTTTATTTTTATTTATT
* *
294101 TTATTATTTTTATTATTATTTATT
1 TTTTTATTTTTATTTTTATTTATT
294125 ATTTTTATTTTTATTTTTATTTATT
1 -TTTTTATTTTTATTTTTATTTATT
294150 TATTTTATTTGTTATTT
1 T-TTTTATTT-TTATTT
294167 GTCTACTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
23 13 0.23
24 7 0.12
25 30 0.54
26 6 0.11
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTTATTTTTATTTTTATTTATT
Found at i:294151 original size:29 final size:31
Alignment explanation
Indices: 294017--294153 Score: 124
Period size: 29 Copynumber: 4.4 Consensus size: 31
294007 TTACTTTTTA
* *
294017 TTATTTA-ATATTATTTTCTAATTATTATTT
1 TTATTTATTTATTATTTTATAATTATTATTT
* *
294047 GTTATTTAGTTTTATTATTTTATGATTAATATTT
1 -TTATTTA--TTTATTATTTTATAATTATTATTT
*
294081 TTA-TTA-TTATTTATTTTAT-TTTATTATTT
1 TTATTTATTTA-TTATTTTATAATTATTATTT
*
294110 TTATTATTATTTATTATTTT-T-ATTTTTATTT
1 TTA-T-TTATTTATTATTTTATAATTATTATTT
294141 TTATTTATTTATT
1 TTATTTATTTATT
294154 TTATTTGTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 18
0.78 0.07 0.16
Matches are distributed among these distances:
29 23 0.26
30 10 0.11
31 19 0.21
32 13 0.14
33 6 0.07
34 19 0.21
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.72
Consensus pattern (31 bp):
TTATTTATTTATTATTTTATAATTATTATTT
Found at i:294166 original size:45 final size:45
Alignment explanation
Indices: 294011--294155 Score: 129
Period size: 44 Copynumber: 3.1 Consensus size: 45
294001 CCTTCTTTAC
*
294011 TTTTTATTATTTAATATTATTTTCTAATTATTATTTGTTATTTAGTTTTATTA
1 TTTTTATTA-TT-AT-TTATTTT-T-ATTATTATTT-AT-TTTA-TTTTATTA
* *
294064 -TTTTATGATTA-ATATTTTTATTATTATTTATTTTATTTTATTA
1 TTTTTATTATTATTTATTTTTATTATTATTTATTTTATTTTATTA
294107 TTTTTATTATTATTTATTATTT-TTATT-TTTATTTT-TATTTATTTA
1 TTTTTATTATTATTTATT-TTTATTATTATTTATTTTAT-TTTA-TTA
294152 TTTT
1 TTTT
294156 ATTTGTTATT
Statistics
Matches: 82, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
43 9 0.11
44 26 0.32
45 17 0.21
46 13 0.16
47 1 0.01
48 6 0.07
50 1 0.01
51 2 0.02
52 7 0.09
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (45 bp):
TTTTTATTATTATTTATTTTTATTATTATTTATTTTATTTTATTA
Found at i:296849 original size:23 final size:25
Alignment explanation
Indices: 296823--296868 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
296813 CCAATTAGGA
296823 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
296846 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
296869 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:301068 original size:15 final size:16
Alignment explanation
Indices: 301044--301073 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
301034 TTTTTATTTC
301044 ATTTTAATTTAGTTTA
1 ATTTTAATTTAGTTTA
301060 ATTTT-ATTTAGTTT
1 ATTTTAATTTAGTTT
301074 TTGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (16 bp):
ATTTTAATTTAGTTTA
Found at i:301256 original size:20 final size:20
Alignment explanation
Indices: 301192--301262 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 20
301182 TTAGTCCCTG
*
301192 TTATTTTTA-TTATTT-GTA
1 TTATTTTTATTTATTTATTA
*
301210 TT-TATTTATTT-TTTAATGT-
1 TTATTTTTATTTATTT-AT-TA
*
301229 TTAATTTTATTTATTTATTA
1 TTATTTTTATTTATTTATTA
*
301249 TTATTTTTACTTAT
1 TTATTTTTATTTAT
301263 ATGTTGTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 3 0.08
20 22 0.55
21 3 0.08
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (20 bp):
TTATTTTTATTTATTTATTA
Found at i:301262 original size:24 final size:23
Alignment explanation
Indices: 301192--301262 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
301182 TTAGTCCCTG
*
301192 TTATTTTTATTATTTGTATTTAT
1 TTATTTTTATTATTTTTATTTAT
* *
301215 TTATTTTT-TAATGTTTAATTTTAT
1 TTATTTTTATTAT-TTTTA-TTTAT
*
301239 TTATTTATTATTATTTTTACTTAT
1 TTATTT-TTATTATTTTTATTTAT
301263 ATGTTGTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 3 0.08
23 11 0.29
24 15 0.39
25 6 0.16
26 3 0.08
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (23 bp):
TTATTTTTATTATTTTTATTTAT
Found at i:301300 original size:25 final size:26
Alignment explanation
Indices: 301272--301326 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
301262 TATGTTGTTA
*
301272 TTTTATGTCATTTT-TTT-ATTTTCAT
1 TTTTATG-CATTTTATTTAATTTACAT
* *
301297 TTTTTTGCCTTTTATTTAATTTACAT
1 TTTTATGCATTTTATTTAATTTACAT
301323 TTTT
1 TTTT
301327 TTATTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 9 0.36
26 11 0.44
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTATGCATTTTATTTAATTTACAT
Found at i:302323 original size:20 final size:20
Alignment explanation
Indices: 302277--302324 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
302267 ATTTTTTTTT
*
302277 ATATATGTTGCTTTGATAAC
1 ATATATGTTGATTTGATAAC
*
302297 A-ATATGTTGATATTGCTAA-
1 ATATATGTTGAT-TTGATAAC
302316 ATATATGTT
1 ATATATGTT
302325 TACATTTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (20 bp):
ATATATGTTGATTTGATAAC
Found at i:305658 original size:22 final size:21
Alignment explanation
Indices: 305611--305658 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
305601 AACTTTCATC
* *
305611 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATCAATCATATT
*
305632 TTTAACCTTAATCAATCATATT
1 ATTAA-CTTAATCAATCATATT
305654 ATTAA
1 ATTAA
305659 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAACTTAATCAATCATATT
Found at i:310336 original size:7 final size:7
Alignment explanation
Indices: 310326--310355 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
310316 CTTCTTTCTT
310326 TTTTCCC
1 TTTTCCC
310333 TTTTCCC
1 TTTTCCC
*
310340 TTTTTCC
1 TTTTCCC
310347 TTTTCCC
1 TTTTCCC
310354 TT
1 TT
310356 GTCATTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (7 bp):
TTTTCCC
Found at i:324489 original size:24 final size:24
Alignment explanation
Indices: 324461--324511 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
324451 GGGGTTATAA
324461 TGTTTGGAAGTTGTGGGTTCTTAC
1 TGTTTGGAAGTTGTGGGTTCTTAC
324485 TGTTTGGAAGTTGTGGGTTCTTAC
1 TGTTTGGAAGTTGTGGGTTCTTAC
324509 TGT
1 TGT
324512 CGCATTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.08, G:0.33, T:0.47
Consensus pattern (24 bp):
TGTTTGGAAGTTGTGGGTTCTTAC
Found at i:331195 original size:18 final size:18
Alignment explanation
Indices: 331172--331207 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
331162 TTACGAGCCG
*
331172 CCGTAAAGTCTTCCTTCA
1 CCGTAAAGCCTTCCTTCA
331190 CCGTAAAGCCTTCCTTCA
1 CCGTAAAGCCTTCCTTCA
331208 TTATAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.36, G:0.11, T:0.31
Consensus pattern (18 bp):
CCGTAAAGCCTTCCTTCA
Found at i:332402 original size:106 final size:105
Alignment explanation
Indices: 332245--332434 Score: 285
Period size: 106 Copynumber: 1.8 Consensus size: 105
332235 GTGTGTTAGA
* * *
332245 CTGAGTAACCAGGATGGAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGGT-TAACACTTTC
1 CTGAGTAACCAAGATAGAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAA-GGTCTAACACATTC
332309 TTAAAAAAGAAAAAGAAAAAAAATGATTGGGAGCATGTTGGG
65 TTAAAAAA-AAAAAGAAAAAAAATGATTGGGAGCATGTTGGG
* *
332351 CTGAGTAACCAAGATAGAGTGTTTGAG-TGTCATTTCATTTCGCGTCAAAAGGTCTAATACATTC
1 CTGAGTAACCAAGATAGAGTGCTTG-GTTGTCATTTCATTTCGCGTCAAAAGGTCTAACACATTC
*
332415 TTAAAGAAAAAAAGAAAAAA
65 TTAAAAAAAAAAAGAAAAAA
332435 TCGACAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
105 15 0.20
106 60 0.79
107 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (105 bp):
CTGAGTAACCAAGATAGAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGTCTAACACATTCT
TAAAAAAAAAAAGAAAAAAAATGATTGGGAGCATGTTGGG
Found at i:332937 original size:14 final size:14
Alignment explanation
Indices: 332886--332929 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
332876 ATATATTTAA
*
332886 TTTATATTTATCTT
1 TTTAGATTTATCTT
332900 TTTAGATTTATCTT
1 TTTAGATTTATCTT
332914 TTTAGATTTATCTT
1 TTTAGATTTATCTT
332928 TT
1 TT
332930 AGAGTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (14 bp):
TTTAGATTTATCTT
Found at i:350235 original size:15 final size:14
Alignment explanation
Indices: 350215--350245 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
350205 GGGTAGTGGT
350215 AACAGAAAAGTTCTA
1 AACAGAAAAGTT-TA
350230 AACAGAAAAGTTTA
1 AACAGAAAAGTTTA
350244 AA
1 AA
350246 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (14 bp):
AACAGAAAAGTTTA
Found at i:350813 original size:21 final size:21
Alignment explanation
Indices: 350787--350841 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
350777 TGGCTTGAAT
*
350787 TGTATCGATCGTTGCATAGTA
1 TGTATCGATAGTTGCATAGTA
* *
350808 TGTATCGGTAGTTTCATAGTA
1 TGTATCGATAGTTGCATAGTA
* *
350829 GGTATCGGTAGTT
1 TGTATCGATAGTT
350842 TTGCTCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (21 bp):
TGTATCGATAGTTGCATAGTA
Found at i:350842 original size:21 final size:21
Alignment explanation
Indices: 350801--350842 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
350791 TCGATCGTTG
*
350801 CATAGTATGTATCGGTAGTTT
1 CATAGTAGGTATCGGTAGTTT
350822 CATAGTAGGTATCGGTAGTTT
1 CATAGTAGGTATCGGTAGTTT
350843 TGCTCACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (21 bp):
CATAGTAGGTATCGGTAGTTT
Found at i:352327 original size:12 final size:12
Alignment explanation
Indices: 352310--352335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
352300 AAAATGATTG
352310 AAATATATATAT
1 AAATATATATAT
352322 AAATATATATAT
1 AAATATATATAT
352334 AA
1 AA
352336 TTGACTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATATAT
Found at i:359061 original size:8 final size:8
Alignment explanation
Indices: 359048--359072 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
359038 ATAAAAATTG
359048 AAATAATA
1 AAATAATA
359056 AAATAATA
1 AAATAATA
359064 AAATAATA
1 AAATAATA
359072 A
1 A
359073 GAGTTGATAA
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):
AAATAATA
Found at i:361756 original size:4 final size:4
Alignment explanation
Indices: 361749--361787 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
361739 TTAGTATATA
361749 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
361788 AATTACTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:379275 original size:41 final size:41
Alignment explanation
Indices: 379225--379419 Score: 236
Period size: 41 Copynumber: 4.8 Consensus size: 41
379215 ACTCAATATT
* *
379225 TAAATGGAAGACTCATTTCTCAGAATGAGAATGAGATCATAC
1 TAAA-GGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
379267 TAAAGGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
1 TAAAGGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
* * *
379308 T--A--AAGACTCATGTCTCGGGATGAGAATGATATCATCC
1 TAAAGGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
** ** *
379345 TAAAGGAAGACTCATGTCTCGGGGTGAGAATGAGATTTTAT
1 TAAAGGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
** *
379386 TAAAGGAAGACTCATGTCTCATAATGAGCATGAG
1 TAAAGGAAGACTCATGTCTCGGAATGAGAATGAG
379420 GTTTGTTTGT
Statistics
Matches: 133, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
37 33 0.25
39 2 0.02
41 94 0.71
42 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGGAATGAGAATGAGATCATAC
Found at i:379390 original size:78 final size:78
Alignment explanation
Indices: 379232--379380 Score: 235
Period size: 78 Copynumber: 1.9 Consensus size: 78
379222 ATTTAAATGG
*
379232 AAGACTCATTTCTCAGAATGAGAATGAGATCATACTAAAGGAAGACTCATGTCTCGGAATGAGAA
1 AAGACTCATGTCTCAGAATGAGAATGAGATCATACTAAAGGAAGACTCATGTCTCGGAATGAGAA
379297 TGAGATCATACTA
66 TGAGATCATACTA
* * * * **
379310 AAGACTCATGTCTCGGGATGAGAATGATATCATCCTAAAGGAAGACTCATGTCTCGGGGTGAGAA
1 AAGACTCATGTCTCAGAATGAGAATGAGATCATACTAAAGGAAGACTCATGTCTCGGAATGAGAA
379375 TGAGAT
66 TGAGAT
379381 TTTATTAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (78 bp):
AAGACTCATGTCTCAGAATGAGAATGAGATCATACTAAAGGAAGACTCATGTCTCGGAATGAGAA
TGAGATCATACTA
Found at i:386457 original size:41 final size:41
Alignment explanation
Indices: 386388--386531 Score: 198
Period size: 41 Copynumber: 3.5 Consensus size: 41
386378 ACTCGATATT
* * *
386388 TAAATGGAAGACTCATGTCCCGAAATGAGAATGAGATCATAC
1 TAAA-GGAAGACTAATGTCTCGAGATGAGAATGAGATCATAC
* * *
386430 TAAAGGAAGACTCATGTCTTGGGATGAGAATGAGATCATAC
1 TAAAGGAAGACTAATGTCTCGAGATGAGAATGAGATCATAC
* *
386471 TAAAGGAAGACTAATGTCTCGAGATGAGAATGAGATTATAT
1 TAAAGGAAGACTAATGTCTCGAGATGAGAATGAGATCATAC
*
386512 TAAAGGAAAACTAATGTCTC
1 TAAAGGAAGACTAATGTCTC
386532 ATAATGAGCA
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 88 0.96
42 4 0.04
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.24
Consensus pattern (41 bp):
TAAAGGAAGACTAATGTCTCGAGATGAGAATGAGATCATAC
Found at i:388337 original size:25 final size:25
Alignment explanation
Indices: 388266--388330 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
388256 GATTTGAAAA
388266 GTGAGGTTGAGGGGTCTATTTATAG
1 GTGAGGTTGAGGGGTCTATTTATAG
388291 GTGAGGTTGAGGGGTCTATTTATAG
1 GTGAGGTTGAGGGGTCTATTTATAG
*
388316 GTGAGGTTAAGGGGT
1 GTGAGGTTGAGGGGT
388331 GAGTTTACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.20, C:0.03, G:0.43, T:0.34
Consensus pattern (25 bp):
GTGAGGTTGAGGGGTCTATTTATAG
Found at i:389593 original size:43 final size:42
Alignment explanation
Indices: 389497--389722 Score: 199
Period size: 43 Copynumber: 5.3 Consensus size: 42
389487 TTTTTTTGGG
* * *
389497 GCTATAGAACGTGGTCATTAGCGGCG-TTTTCCCATAAACGTA-
1 GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAA-G-AC
* *
389539 GCTATAGAACATGGTCATTAGCGACGCTTTTCCCACAAAGACC
1 GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAAGA-C
* * * **
389582 GCTAAATAACATGGTCTTTAGTGGCATTTTTCCCACAAA-AGC
1 GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAAGA-C
* *
389624 TGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACAC
1 -GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAAGAC
** * * *
389667 AGCTAAAGAACATGGTTTTTAGCGGTGCTTTACCAACAAACGTA-
1 -GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAA-G-AC
389711 GCTAAAGAACAT
1 GCTAAAGAACAT
389723 ATTTTTATTA
Statistics
Matches: 156, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 27 0.17
43 126 0.81
44 1 0.01
45 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
GCTAAAGAACATGGTCATTAGCGGCGCTTTTCCCACAAAGAC
Found at i:389706 original size:86 final size:86
Alignment explanation
Indices: 389536--389722 Score: 232
Period size: 86 Copynumber: 2.2 Consensus size: 86
389526 TCCCATAAAC
* * * *
389536 GTAGCTATAGAACATGGTCATTAGCGACGCTTTTCCCACAAAGACCGCTAAATAACATGGTCTTT
1 GTAGCTAAAGAACATGGTCATTAGCGACGCTTTTCCCACAAACACAGCTAAAGAACATGGTCTTT
* * * *
389601 AGTGGCATTTTTCCCACAAAA
66 AGCGGCACTTTACCAACAAAA
* * *
389622 GCT-GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACACAGCTAAAGAACATGGTTTT
1 G-TAGCTAAAGAACATGGTCATTAGCGACGCTTTTCCCACAAACACAGCTAAAGAACATGGTCTT
** *
389686 TAGCGGTGCTTTACCAACAAAC
65 TAGCGGCACTTTACCAACAAAA
389708 GTAGCTAAAGAACAT
1 GTAGCTAAAGAACAT
389723 ATTTTTATTA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
85 1 0.01
86 83 0.98
87 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (86 bp):
GTAGCTAAAGAACATGGTCATTAGCGACGCTTTTCCCACAAACACAGCTAAAGAACATGGTCTTT
AGCGGCACTTTACCAACAAAA
Found at i:390450 original size:20 final size:20
Alignment explanation
Indices: 390427--390466 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
390417 TTAATGAACA
390427 ATTAAGTTAATATAATTAAG
1 ATTAAGTTAATATAATTAAG
*
390447 ATTAAGTTAATTTAATTAAG
1 ATTAAGTTAATATAATTAAG
390467 TAATTAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
ATTAAGTTAATATAATTAAG
Found at i:391542 original size:41 final size:41
Alignment explanation
Indices: 391480--391798 Score: 365
Period size: 41 Copynumber: 7.8 Consensus size: 41
391470 TAGTTCTCTA
* *
391480 CGCCACTAATGCTCTGACCTTTAGCGGCGTTTATGAGACAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
* *
391521 CGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTGAGAAAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
* *
391562 CACCGCTAATGATCTGACCTTTAGCGGCGTTTATGAGAAAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
* * * * *
391603 AGCCGCTAATGC-CTAGACCTTTAACGACGTTTAAGATG-AAC
1 CGCCGCTAATGCTCT-GACCTTTAGCGGCGTTTATGA-GAAAG
* *
391644 CGCCGTTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
* * * ***
391685 CGCCACTAATGCTCTAACCTTTAGTGGCGTTT-TCCCACAAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGA-AAG
* * * *
391726 CACCGCTAATGCTCTGACTTTTAGCAGCGTTTATGATAAAG
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
* *
391767 CACCGCTAATGCTCAGACCTTTAGCGGCGTTT
1 CGCCGCTAATGCTCTGACCTTTAGCGGCGTTT
391799 TTTCTATAAA
Statistics
Matches: 231, Mismatches: 41, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
40 4 0.02
41 222 0.96
42 5 0.02
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (41 bp):
CGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAG
Found at i:391857 original size:40 final size:40
Alignment explanation
Indices: 391783--391919 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
391773 TAATGCTCAG
* * * * * *
391783 ACCTTTAGCGGCGTTTTTTCTATAAATGCCGCTATTGGTTT
1 ACCTTTTGCGGCG-TTTATCCAAAAACGCCGCTATTGCTTT
* * * *
391824 AGCTTTTACGGCGTTTATGCAAAAACGCCGCTATTGCTTA
1 ACCTTTTGCGGCGTTTATCCAAAAACGCCGCTATTGCTTT
* *
391864 ACCTTTTGCAGCGTTTATCCAAAAACGCGGCTATTGCTTT
1 ACCTTTTGCGGCGTTTATCCAAAAACGCCGCTATTGCTTT
*
391904 ACCTTTTGTGGCGTTT
1 ACCTTTTGCGGCGTTT
391920 TCTATCCAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
40 68 0.87
41 10 0.13
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (40 bp):
ACCTTTTGCGGCGTTTATCCAAAAACGCCGCTATTGCTTT
Found at i:396671 original size:28 final size:28
Alignment explanation
Indices: 396631--396687 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
396621 TGTAATTCTT
396631 TTTACAAATCTACAAACCTTTCGTACTA
1 TTTACAAATCTACAAACCTTTCGTACTA
396659 TTTACAAATCTACAAACCTTTCGTACTA
1 TTTACAAATCTACAAACCTTTCGTACTA
396687 T
1 T
396688 CTTGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTACAAATCTACAAACCTTTCGTACTA
Found at i:398551 original size:2 final size:2
Alignment explanation
Indices: 398544--398608 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
398534 GCTTGTTGCA
* *
398544 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT GT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
398586 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
398609 GTAGATTCTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.51
Consensus pattern (2 bp):
CT
Found at i:402829 original size:23 final size:23
Alignment explanation
Indices: 402785--402829 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
402775 GGATTAAAAC
*
402785 TTAATTAACTTAATTAACCATTG
1 TTAATTAACTTAATTAAACATTG
*
402808 TTAATTATC-TAATTAAGACATT
1 TTAATTAACTTAATTAA-ACATT
402830 TTTATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (23 bp):
TTAATTAACTTAATTAAACATTG
Done.