Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015149.1 Kokia drynarioides strain JFW-HI SEQ_130193, 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: 348839
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 434 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:381 original size:17 final size:17
Alignment explanation
Indices: 326--396 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
316 AATAAGTTTG
* *
326 AATTTATTTTAAATTCA
1 AATTTACTTTAAATTTA
* * *
343 AATTCACTTTGAGTTTA
1 AATTTACTTTAAATTTA
360 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTTA
** *
377 AATTTTTTTTAAATTAA
1 AATTTACTTTAAATTTA
394 AAT
1 AAT
397 AAAATTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTACTTTAAATTTA
Found at i:1309 original size:5 final size:5
Alignment explanation
Indices: 1288--1327 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
1278 CAATTTGATC
*
1288 TTTTA TTTATC TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1328 CAAATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:9492 original size:125 final size:125
Alignment explanation
Indices: 9270--9523 Score: 499
Period size: 125 Copynumber: 2.0 Consensus size: 125
9260 TCGGAATGTA
9270 ATTAGAAAGTTTTGAAGTTTGTAGACCAATTTGAAATGAGTGTTATAGTTTAGGGATGTTTGATG
1 ATTAGAAAGTTTTGAAGTTTGTAGACCAATTTGAAATGAGTGTTATAGTTTAGGGATGTTTGATG
9335 AATTAACTCAATTTCTTTTTATTACATTTAAGAAGAGGCTTGGATGGTACTGGTTCTGTG
66 AATTAACTCAATTTCTTTTTATTACATTTAAGAAGAGGCTTGGATGGTACTGGTTCTGTG
*
9395 ATTAGAAAGTTTTGAAGTTTGTAGACCAATTTGAAATGAGTGTTATAGTTTTGGGATGTTTGATG
1 ATTAGAAAGTTTTGAAGTTTGTAGACCAATTTGAAATGAGTGTTATAGTTTAGGGATGTTTGATG
9460 AATTAACTCAATTTCTTTTTATTACATTTAAGAAGAGGCTTGGATGGTACTGGTTCTGTG
66 AATTAACTCAATTTCTTTTTATTACATTTAAGAAGAGGCTTGGATGGTACTGGTTCTGTG
9520 ATTA
1 ATTA
9524 TATATGCATG
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 128 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (125 bp):
ATTAGAAAGTTTTGAAGTTTGTAGACCAATTTGAAATGAGTGTTATAGTTTAGGGATGTTTGATG
AATTAACTCAATTTCTTTTTATTACATTTAAGAAGAGGCTTGGATGGTACTGGTTCTGTG
Found at i:23979 original size:32 final size:32
Alignment explanation
Indices: 23943--24007 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
23933 ATATGAACAT
23943 ATACTACCATGTAATCACACCAATATATTAAA
1 ATACTACCATGTAATCACACCAATATATTAAA
23975 ATACTACCATGTAATCACACCAATATATTAAA
1 ATACTACCATGTAATCACACCAATATATTAAA
24007 A
1 A
24008 AACATGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.28
Consensus pattern (32 bp):
ATACTACCATGTAATCACACCAATATATTAAA
Found at i:24802 original size:21 final size:21
Alignment explanation
Indices: 24778--24830 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
24768 ACGAGAACTT
*
24778 TTAAAAATTTTGAGAATCTAA
1 TTAAAAATTTTAAGAATCTAA
** *
24799 TTAAATTTTTTAAGGATCTAA
1 TTAAAAATTTTAAGAATCTAA
**
24820 CAAAAAATTTT
1 TTAAAAATTTT
24831 CATAACTTTG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (21 bp):
TTAAAAATTTTAAGAATCTAA
Found at i:32109 original size:12 final size:12
Alignment explanation
Indices: 32090--32140 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
32080 GCAAAGTCCA
32090 AAGT-CGAACCT
1 AAGTCCGAACCT
32101 AAGTCCGAACCT
1 AAGTCCGAACCT
32113 AAGTCCGAACCT
1 AAGTCCGAACCT
* * *
32125 GAGTCCAAAGCT
1 AAGTCCGAACCT
32137 AAGT
1 AAGT
32141 GCGTTGAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 4 0.11
12 31 0.89
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (12 bp):
AAGTCCGAACCT
Found at i:33835 original size:24 final size:25
Alignment explanation
Indices: 33785--33835 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
33775 GAATTTGATA
* *
33785 AAAGTATTAATAATGTTATCATATT
1 AAAGTATTAATAATGCTAACATATT
* *
33810 AAAG-ATTAATAGTGCTAACATTTT
1 AAAGTATTAATAATGCTAACATATT
33834 AA
1 AA
33836 CCACATTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (25 bp):
AAAGTATTAATAATGCTAACATATT
Found at i:36523 original size:16 final size:16
Alignment explanation
Indices: 36502--36533 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36492 CAATCAATTG
*
36502 AAAATTTTAATTTTTA
1 AAAATTTCAATTTTTA
36518 AAAATTTCAATTTTTA
1 AAAATTTCAATTTTTA
36534 GTATGCTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTCAATTTTTA
Found at i:38808 original size:13 final size:13
Alignment explanation
Indices: 38788--38825 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
38778 AAATTTGTGA
38788 TTGAAGATAATTT
1 TTGAAGATAATTT
*
38801 TT-AGAGATAATAT
1 TTGA-AGATAATTT
38814 TTGAAGATAATT
1 TTGAAGATAATT
38826 CCTAGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (13 bp):
TTGAAGATAATTT
Found at i:47290 original size:84 final size:82
Alignment explanation
Indices: 47202--47407 Score: 206
Period size: 84 Copynumber: 2.5 Consensus size: 82
47192 GGTGCTGGTA
* * *
47202 GTGGTGGCGGGTATGGAGAAGTCGGTGGACATGGAGGTGGTG-GGGGA-GGTAGTGCAGGTGGA-
1 GTGGTGG-GGCTATGGAGGAGTCGGTGGACAAGGAGGTGGTGCGGGGACGGTAGTGCAGGTGGAG
**
47264 CATGGTGGTGGAGCTTCTGGAG
65 C-TGGTGAAGGAG---CTGGAG
* * * *
47286 GTGGT--GGTTATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGTGACGGTAGTGTAGGTGGAG
1 GTGGTGGGGCTATGGAGGAGTCGGTGGACAAGGAGGTGGTGC-GGGGACGGTAGTGCAGGTGGAG
*
47349 CTGGTGAAGGAGGTGGAG
65 CTGGTGAAGGAGCTGGAG
* *
47367 CTGGTGGTGCCTATGGAGGAGTCGGTGGACAAGGAGGTGGT
1 GTGGTGG-GGCTATGGAGGAGTCGGTGGACAAGGAGGTGGT
47408 TCTGGTGGAG
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
81 39 0.38
83 4 0.04
84 58 0.57
85 1 0.01
ACGTcount: A:0.17, C:0.09, G:0.52, T:0.21
Consensus pattern (82 bp):
GTGGTGGGGCTATGGAGGAGTCGGTGGACAAGGAGGTGGTGCGGGGACGGTAGTGCAGGTGGAGC
TGGTGAAGGAGCTGGAG
Found at i:47447 original size:84 final size:82
Alignment explanation
Indices: 47285--47448 Score: 197
Period size: 84 Copynumber: 2.0 Consensus size: 82
47275 AGCTTCTGGA
** *
47285 GGTGGTGGTTATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGTGACGGTAGTGTAGGTGGAGC
1 GGTGGTGCCTATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGTGACGGTAGTGTAGGCGGAGC
*
47350 TGGTGAAGGAGGTGGAGCT
66 TAGT--AGGAGGTGGAGCT
* *
47369 GGTGGTGCCTATGGAGGAGTCGGTGGACAAGGAGGTGGTTCTGGTGGA-GGTAGTGGTGGAGGCG
1 GGTGGTGCCTATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGT-GACGGTAGT-GT--AGGCG
*
47433 GAGCTAGT-GTAGGTGG
62 GAGCTAGTAGGAGGTGG
47449 TGCTTCTGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
84 54 0.78
85 4 0.06
87 11 0.16
ACGTcount: A:0.17, C:0.09, G:0.52, T:0.22
Consensus pattern (82 bp):
GGTGGTGCCTATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGTGACGGTAGTGTAGGCGGAGC
TAGTAGGAGGTGGAGCT
Found at i:47570 original size:48 final size:45
Alignment explanation
Indices: 47513--47643 Score: 120
Period size: 51 Copynumber: 2.8 Consensus size: 45
47503 AACCAATGGG
*
47513 CATGGAGGTGGTGTTGGTGGCGGCAGTGGTGGAGGCGAAGGTGGA
1 CATGCAGGTGGTGTTGGTGGCGGCAGTGGTGGAGGCGAAGGTGGA
** * * *
47558 GCTACTGCAGGTGGTGCTTCTGG-GTATGGCAATGGAGGAGGCGCAGGTGGA
1 -C-A-TGCAGGTGGTG--T-TGGTG-GCGGCAGTGGTGGAGGCGAAGGTGGA
* *
47609 CATGGAGGTGGTGCTGGTGGCGGCAGTGGTGGAGG
1 CATGCAGGTGGTGTTGGTGGCGGCAGTGGTGGAGG
47644 TGGAGCTAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
45 15 0.23
46 2 0.03
47 1 0.02
48 20 0.30
49 1 0.02
50 3 0.05
51 24 0.36
ACGTcount: A:0.15, C:0.12, G:0.52, T:0.21
Consensus pattern (45 bp):
CATGCAGGTGGTGTTGGTGGCGGCAGTGGTGGAGGCGAAGGTGGA
Found at i:47690 original size:96 final size:93
Alignment explanation
Indices: 47513--47685 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 93
47503 AACCAATGGG
* *
47513 CATGGAGGTGGTGTTGGTGGCGGCAGTGGTGGAGGCGAAGGTGGAGCTACTGCAGGTGGTGCTTC
1 CATGGAGGTGGTGCTGGTGGCGGCAGTGGT---GGCGAAGGTGGAGCTACTGCAGGTGGCGCTTC
*
47578 TGGGTATGGCAATGGAGGAGGCGCAGGTGGA
63 TGGGTATGGAAATGGAGGAGGCGCAGGTGGA
*
47609 CATGGAGGTGGTGCTGGTGGCGGCAGTGGT-G-G-AGGTGGAGCTAGTGCAGGTGGCGCTTCTGG
1 CATGGAGGTGGTGCTGGTGGCGGCAGTGGTGGCGAAGGTGGAGCTACTGCAGGTGGCGCTTCTGG
47671 GTATGGAAATGGAGG
66 GTATGGAAATGGAGG
47686 TGGAGCTGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
90 42 0.58
91 1 0.01
92 1 0.01
96 29 0.40
ACGTcount: A:0.16, C:0.12, G:0.50, T:0.21
Consensus pattern (93 bp):
CATGGAGGTGGTGCTGGTGGCGGCAGTGGTGGCGAAGGTGGAGCTACTGCAGGTGGCGCTTCTGG
GTATGGAAATGGAGGAGGCGCAGGTGGA
Found at i:53534 original size:28 final size:29
Alignment explanation
Indices: 53485--53552 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
53475 ATTTGATTCA
*
53485 ATTTTCATA-AATCATTAATACAGTTA-TT
1 ATTTT-ATACAATCATTAATACAGTTACAT
* *
53513 ATTTATATACAATCATT-TTACATTTACAT
1 ATTT-TATACAATCATTAATACAGTTACAT
53542 ATTTTATACAA
1 ATTTTATACAA
53553 AAATAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTTTATACAATCATTAATACAGTTACAT
Found at i:55423 original size:66 final size:66
Alignment explanation
Indices: 55213--55429 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 66
55203 GGAGTTGGTG
* * * * * *
55213 GTGCCGGTGGGTATGGAGGAGCTAGTGGACATGGAGGTGGTGCTGGTAGTGGTGGTGGCGGAGCA
1 GTGCAGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGGTGGTAGTGGTGGCGGAGGAGCT
55278 A
66 A
* ** * * * * * * *
55279 GTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTGG-GGAAGGAGGCGGAGC
1 GTGCAGGTGGATA---TGGAGGAGCTAGTGGACATGGAGGTGGTGGTGGTAG-TGGTGGCGGAGG
* * *
55343 TGGTG
62 AGCTA
* *
55348 GTGTC-GGTGGATATGGAGGAGCTGGTGGACATGGAGGTGGTGGTGGTAGTGGTGGCGGTGGAGC
1 GTG-CAGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGGTGGTAGTGGTGGCGGAGGAGC
55412 TA
65 TA
55414 GTGCAGGTGGATATGG
1 GTGCAGGTGGATATGG
55430 TGGTGGAGGT
Statistics
Matches: 111, Mismatches: 33, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
65 1 0.01
66 62 0.56
67 1 0.01
68 1 0.01
69 45 0.41
70 1 0.01
ACGTcount: A:0.16, C:0.08, G:0.53, T:0.23
Consensus pattern (66 bp):
GTGCAGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGGTGGTAGTGGTGGCGGAGGAGCT
A
Found at i:55435 original size:135 final size:135
Alignment explanation
Indices: 55127--55437 Score: 514
Period size: 135 Copynumber: 2.3 Consensus size: 135
55117 GAGGTGGCAA
* *
55127 TGGTGGCGGTGGAGCTAGTGTAGGTGGATATGGTGGTGAAGCTTCTGGATATGGTGGTGGAGGTG
1 TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
* * *
55192 GCGAAGGAGGTGGAGTTGGTGGTGCCGGTGGGTATGGAGGAGCTAGTGGACATGGAGGTGGTGCT
66 GCGAAGGAGGCGGAGCTGGTGGTGCCGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGCT
55257 GGTAG
131 GGTAG
* * *
55262 TGGTGGTGGCGGAGCAAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
1 TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
* * * *
55327 GGGAAGGAGGCGGAGCTGGTGGTGTCGGTGGATATGGAGGAGCTGGTGGACATGGAGGTGGTGGT
66 GCGAAGGAGGCGGAGCTGGTGGTGCCGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGCT
55392 GGTAG
131 GGTAG
55397 TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAG
1 TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAG
55438 GTGGCGAAAG
Statistics
Matches: 161, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 161 1.00
ACGTcount: A:0.16, C:0.07, G:0.52, T:0.24
Consensus pattern (135 bp):
TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
GCGAAGGAGGCGGAGCTGGTGGTGCCGGTGGATATGGAGGAGCTAGTGGACATGGAGGTGGTGCT
GGTAG
Found at i:55699 original size:30 final size:30
Alignment explanation
Indices: 55663--55733 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
55653 GTGGTGGAAG
*
55663 TGGTGGTGGAGGTGC-AAGTGCAGGAGGATA
1 TGGTGGTGGAGGGGCTAA-TGCAGGAGGATA
* *
55693 TGGTGGTGGAGGGGCTCATGCAGGTGGATA
1 TGGTGGTGGAGGGGCTAATGCAGGAGGATA
*
55723 TGGCGGTGGAG
1 TGGTGGTGGAG
55734 AAGGAGCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.18, C:0.08, G:0.52, T:0.21
Consensus pattern (30 bp):
TGGTGGTGGAGGGGCTAATGCAGGAGGATA
Found at i:55789 original size:12 final size:12
Alignment explanation
Indices: 55772--55814 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
55762 AGGCGATCAC
55772 GGTGGTGGAGGT
1 GGTGGTGGAGGT
***
55784 GGTGGTGGCTCT
1 GGTGGTGGAGGT
55796 GGTGGTGGAGGT
1 GGTGGTGGAGGT
*
55808 GCTGGTG
1 GGTGGTG
55815 TATATGGTGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.07, G:0.60, T:0.28
Consensus pattern (12 bp):
GGTGGTGGAGGT
Found at i:55822 original size:24 final size:24
Alignment explanation
Indices: 55772--55833 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
55762 AGGCGATCAC
* * *
55772 GGTGGTGGAGGTGGTGGTGGCTCT
1 GGTGGTGGAGGTGCTGGTGGATAT
*
55796 GGTGGTGGAGGTGCTGGTGTATAT
1 GGTGGTGGAGGTGCTGGTGGATAT
**
55820 GGTGCAGGAGGTGC
1 GGTGGTGGAGGTGC
55834 ACATGCAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.10, C:0.08, G:0.55, T:0.27
Consensus pattern (24 bp):
GGTGGTGGAGGTGCTGGTGGATAT
Found at i:56936 original size:16 final size:16
Alignment explanation
Indices: 56911--56941 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56901 AAAATTAAAC
*
56911 TGAAATTAATCCAAAT
1 TGAAAATAATCCAAAT
56927 TGAAAATAATCCAAA
1 TGAAAATAATCCAAA
56942 CCCAAATGTT
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:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (16 bp):
TGAAAATAATCCAAAT
Found at i:62092 original size:16 final size:17
Alignment explanation
Indices: 62054--62086 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62044 AAATTCACAT
*
62054 AAAATAAAATCAAATAA
1 AAAAGAAAATCAAATAA
62071 AAAAGAAAAT-AAATAA
1 AAAAGAAAATCAAATAA
62087 CCAAGACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAGAAAATCAAATAA
Found at i:64932 original size:6 final size:6
Alignment explanation
Indices: 64913--64949 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
64903 GTACTTATAC
*
64913 ACATAT ACACAT ACATAT ACATAT --ATAT ACATAT ACA
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACA
64950 CCAAAGGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.15
6 23 0.85
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (6 bp):
ACATAT
Found at i:64940 original size:10 final size:10
Alignment explanation
Indices: 64908--64947 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
64898 TATACGTACT
*
64908 TATACACATA
1 TATACATATA
* *
64918 TACACATACA
1 TATACATATA
64928 TATACATATA
1 TATACATATA
64938 TATACATATA
1 TATACATATA
64948 CACCAAAGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (10 bp):
TATACATATA
Found at i:65142 original size:6 final size:6
Alignment explanation
Indices: 65131--65161 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
65121 TTCACTCCTA
65131 ACATAC ACATAC ACATAC ACATAC ACATAC A
1 ACATAC ACATAC ACATAC ACATAC ACATAC A
65162 AAAGGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:67320 original size:20 final size:22
Alignment explanation
Indices: 67281--67324 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
67271 CATTTTTTTC
67281 TATGTATACATATGTATTTGTA
1 TATGTATACATATGTATTTGTA
*
67303 TATGTATAC-TCT-TATTTGTA
1 TATGTATACATATGTATTTGTA
67323 TA
1 TA
67325 ACTAATTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (22 bp):
TATGTATACATATGTATTTGTA
Found at i:67492 original size:68 final size:66
Alignment explanation
Indices: 67391--67590 Score: 221
Period size: 68 Copynumber: 3.0 Consensus size: 66
67381 TATGTATATA
* * *
67391 TATTCTCCTATTTGTGTTACTACTGGCCTTTAAGTTATATAATGGAGATGTATGTCTATGTGTAT
1 TATTCTCTTATTTGTGTAACTACTGGCC-TTAAGTTATATAATGGAGATGTATGTATAT-TGTAT
67456 GTG
64 GTG
* * *
67459 TATTCTCTTATTTGTGTAACTGCTGATCCTTAAGTTTTATAAT-GA-A-G-ATGTATATT-TATG
1 TATTCTCTTATTTGTGTAACTACTG-GCCTTAAGTTATATAATGGAGATGTATGTATATTGTATG
67519 TG
65 TG
* * * * * *
67521 TATCCTCTTGTTTGTGTAACTATTGGCCTTAAGCTATATAATGGAGATGTATGTGTATATGTATA
1 TATTCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAATGGAGATGTATGTATAT-TGTATG
67586 TG
65 TG
67588 TAT
1 TAT
67591 ATGTATATGT
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
61 14 0.13
62 29 0.26
63 2 0.02
64 8 0.07
65 8 0.07
66 2 0.02
67 10 0.09
68 35 0.32
69 2 0.02
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.46
Consensus pattern (66 bp):
TATTCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAATGGAGATGTATGTATATTGTATGT
G
Found at i:67641 original size:6 final size:6
Alignment explanation
Indices: 67567--67634 Score: 127
Period size: 6 Copynumber: 11.3 Consensus size: 6
67557 TATAATGGAG
*
67567 ATGTAT GTGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
67615 ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT AT
67635 TTGTATTCTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:74200 original size:31 final size:31
Alignment explanation
Indices: 74162--74220 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
74152 CAACTTGGTG
*
74162 ACTTAAATAAAAAATTTTGAATAGTTCAGTA
1 ACTTAAATAAAAAATTTCGAATAGTTCAGTA
* *
74193 ACTTAAATGAAAACTTTCGAATAGTTCA
1 ACTTAAATAAAAAATTTCGAATAGTTCA
74221 ATGATCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCGAATAGTTCAGTA
Found at i:75328 original size:6 final size:6
Alignment explanation
Indices: 75313--75344 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
75303 TCGTATTCGG
75313 AAAA-A AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAA
75345 GAGAGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:77204 original size:83 final size:83
Alignment explanation
Indices: 77063--77234 Score: 272
Period size: 83 Copynumber: 2.1 Consensus size: 83
77053 ACTAATGAGT
* *
77063 AGTCTTCGAATAGTTTAAAGACTAGGTAAAAATAATCAAGTACAATCCTCTTCTTTTTTAACTTC
1 AGTC-TCGAATAGTTTAAAGACTAGGTAAAAATAATCAAGTACAACCCTCTTCCTTTTTAACTTC
* *
77128 CGTTACGTGTTGTCGATTG
65 CGCTACGTATTGTCGATTG
* * *
77147 AGTCTCGAATAGTTTAAAGACTAGGTAAAAATACTCAAGTACAACCCTCTTCCTTTTTAATTTCT
1 AGTCTCGAATAGTTTAAAGACTAGGTAAAAATAATCAAGTACAACCCTCTTCCTTTTTAACTTCC
77212 GCTACGTATTGTCGATTG
66 GCTACGTATTGTCGATTG
77230 AGTCT
1 AGTCT
77235 TAGATCGATT
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 77 0.95
84 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (83 bp):
AGTCTCGAATAGTTTAAAGACTAGGTAAAAATAATCAAGTACAACCCTCTTCCTTTTTAACTTCC
GCTACGTATTGTCGATTG
Found at i:80408 original size:2 final size:2
Alignment explanation
Indices: 80403--80446 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
80393 ATAAAAAAAA
80403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80445 AT
1 AT
80447 TTACAACCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83244 original size:21 final size:22
Alignment explanation
Indices: 83220--83272 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
83210 TTTTAAGATT
*
83220 TTTTAAATTAGAGTTT-TGGTA
1 TTTTAAATTAGAGTTTAGGGTA
* *
83241 TTTTAAATAAGGGTTTAGGGTA
1 TTTTAAATTAGAGTTTAGGGTA
83263 TTTTAAATTA
1 TTTTAAATTA
83273 ATAGTTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (22 bp):
TTTTAAATTAGAGTTTAGGGTA
Found at i:88185 original size:51 final size:52
Alignment explanation
Indices: 88105--88231 Score: 150
Period size: 51 Copynumber: 2.4 Consensus size: 52
88095 ATATATATAT
* * * *
88105 ATAATTTATTGCTTGAAGACTTTAACATAGCATAACAAAA-G-CATGGCATGC
1 ATAATTCATTCCTTGAACAC-TTAACATAGCATAACAAAAGGCCATAGCATGC
* * *
88156 ATAATTCCTTTCTTGATCACTTAAGCATAGCATAACAAAAGTGCCATAGCATGC
1 ATAATTCATTCCTTGAACACTTAA-CATAGCATAACAAAAG-GCCATAGCATGC
88210 ATAATTCATTCCTTGAACACTT
1 ATAATTCATTCCTTGAACACTT
88232 CAACTTATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
50 4 0.06
51 30 0.48
53 1 0.02
54 28 0.44
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (52 bp):
ATAATTCATTCCTTGAACACTTAACATAGCATAACAAAAGGCCATAGCATGC
Found at i:88656 original size:18 final size:20
Alignment explanation
Indices: 88628--88678 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
88618 CTTATGGAAG
88628 CTTTCTCTCTCTATCTCCAA
1 CTTTCTCTCTCTATCTCCAA
88648 CTTTCTCTCTCTATCTCCAA
1 CTTTCTCTCTCTATCTCCAA
88668 CTTTCTCTCTC
1 CTTTCTCTCTC
88679 AAGAACCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.41, G:0.00, T:0.47
Consensus pattern (20 bp):
CTTTCTCTCTCTATCTCCAA
Found at i:88853 original size:17 final size:18
Alignment explanation
Indices: 88816--88854 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
88806 AAAAAGCAAG
*
88816 AAAAATGAAAAAAAAATA
1 AAAAATGAAAAAAAAAGA
*
88834 AAAAAT-AAAAAAAAGGA
1 AAAAATGAAAAAAAAAGA
88851 AAAA
1 AAAA
88855 GGGAGAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAATGAAAAAAAAAGA
Found at i:90254 original size:51 final size:51
Alignment explanation
Indices: 90178--90276 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
90168 CATATGAAAT
*
90178 TAGTTATTTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTTAA
1 TAGTTAATTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTTAA
90229 TAGTTAATTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATT
1 TAGTTAATTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATT
90277 CAAGAGGTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.44
Consensus pattern (51 bp):
TAGTTAATTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTTAA
Found at i:90288 original size:51 final size:51
Alignment explanation
Indices: 90185--90288 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
90175 AATTAGTTAT
* * *
90185 TTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTTAATAGTTAA
1 TTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTCAAGAGGTAA
90236 TTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTCAAGAGGTAA
1 TTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTCAAGAGGTAA
90287 TT
1 TT
90289 CATTGAAACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (51 bp):
TTGACTCAGTCTCCTCTTATACTATATATTAATGCAATATTCAAGAGGTAA
Found at i:93577 original size:51 final size:54
Alignment explanation
Indices: 93522--93623 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
93512 AAGACTCTAA
* * * *
93522 CATAGCATAACAA-AG-G-CGTGGCATGCATAATTCCTTTCTTGAACACTTAAG
1 CATAGCATAACAATAGTGCCATAGCATGCATAATTCATTCCTTGAACACTTAAG
93573 CATAGCATAACAATAGTGCCATAGCATGCATAATTCATTCCTTGAACACTT
1 CATAGCATAACAATAGTGCCATAGCATGCATAATTCATTCCTTGAACACTT
93624 TAACTTATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 13 0.30
52 2 0.05
53 1 0.02
54 28 0.64
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (54 bp):
CATAGCATAACAATAGTGCCATAGCATGCATAATTCATTCCTTGAACACTTAAG
Found at i:99322 original size:17 final size:17
Alignment explanation
Indices: 99300--99335 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
99290 AATTAAAAAT
99300 ATTTTTTGAATAGTGCA
1 ATTTTTTGAATAGTGCA
99317 ATTTTTTGAATAGTGCA
1 ATTTTTTGAATAGTGCA
99334 AT
1 AT
99336 GGACTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (17 bp):
ATTTTTTGAATAGTGCA
Found at i:110809 original size:21 final size:22
Alignment explanation
Indices: 110785--110827 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
110775 TTATGTGTCT
110785 ATATTATATATT-ATAA-AAATA
1 ATATT-TATATTCATAATAAATA
*
110806 ATATTTTTATTCATAATAAATA
1 ATATTTATATTCATAATAAATA
110828 TTATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTATATTCATAATAAATA
Found at i:110824 original size:24 final size:23
Alignment explanation
Indices: 110797--110847 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
110787 ATTATATATT
110797 ATAAAAATAAT-ATTTTTATTCATA
1 ATAAAAATAATAATTTTT-TT-ATA
* *
110821 ATAAATATTATAATTTTTTTATA
1 ATAAAAATAATAATTTTTTTATA
110844 ATAA
1 ATAA
110848 CTTAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAAAATAATAATTTTTTTATA
Found at i:118119 original size:102 final size:100
Alignment explanation
Indices: 117977--118174 Score: 299
Period size: 102 Copynumber: 2.0 Consensus size: 100
117967 AAAATATGAT
*
117977 CAACTGAGTTTTAATTTGAATAATATCAATATTATTTTCAGTACAAAAAA-ACGTAAATTCAACT
1 CAACTGAATTTTAATTTGAATAATATCAATATTATTTTCAGTA-AAAAAATA--TAAATTCAACT
**
118041 ATTTTTAAATGCATTATTTTTTTATTTAAAAATTGAAA
63 ATAATTAAATGCATTATTTTTTTATTTAAAAATTGAAA
* * * *
118079 CAACTGAATTTTAATTTGAATAATATCGATATTATTTTCAGTAAAAAAATATAGATTCGATTATA
1 CAACTGAATTTTAATTTGAATAATATCAATATTATTTTCAGTAAAAAAATATAAATTCAACTATA
118144 ATTAAATGCATTATTTTTTTATTTAAAAATT
66 ATTAAATGCATTATTTTTTTATTTAAAAATT
118175 AAAAAAAATT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
100 40 0.45
101 6 0.07
102 42 0.48
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (100 bp):
CAACTGAATTTTAATTTGAATAATATCAATATTATTTTCAGTAAAAAAATATAAATTCAACTATA
ATTAAATGCATTATTTTTTTATTTAAAAATTGAAA
Found at i:118194 original size:100 final size:101
Alignment explanation
Indices: 117988--118183 Score: 261
Period size: 100 Copynumber: 1.9 Consensus size: 101
117978 AACTGAGTTT
**
117988 TAATTTGAATAATATCAATATTATTTTCAGTACAAAAAAACGTAAATTCAACTATTTTTAAATGC
1 TAATTTGAATAATATCAATATTATTTTCAGTACAAAAAAAC-TAAATTCAACTATAATTAAATGC
* * * **
118053 ATTATTTTTTTATTTAAAAATTGAAACAACTGAATTT
65 ATTATTTTTTTATTTAAAAATTAAAAAAAATGAATAA
* * * *
118090 TAATTTGAATAATATCGATATTATTTTCAGTA-AAAAAATA-TAGATTCGATTATAATTAAATGC
1 TAATTTGAATAATATCAATATTATTTTCAGTACAAAAAA-ACTAAATTCAACTATAATTAAATGC
118153 ATTATTTTTTTATTTAAAAATTAAAAAAAAT
65 ATTATTTTTTTATTTAAAAATTAAAAAAAAT
118184 TATGAATAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 46 0.55
101 6 0.07
102 32 0.38
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (101 bp):
TAATTTGAATAATATCAATATTATTTTCAGTACAAAAAAACTAAATTCAACTATAATTAAATGCA
TTATTTTTTTATTTAAAAATTAAAAAAAATGAATAA
Found at i:125533 original size:9 final size:8
Alignment explanation
Indices: 125518--125559 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
125508 AAAATAAAAA
125518 TATATTTT
1 TATATTTT
125526 TCATATTTT
1 T-ATATTTT
125535 TATGATTTT
1 TAT-ATTTT
125544 TAT-TTTT
1 TATATTTT
125551 TATAATTTT
1 TAT-ATTTT
125560 GATTTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
8 3 0.10
9 20 0.67
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:125552 original size:16 final size:16
Alignment explanation
Indices: 125521--125564 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
125511 ATAAAAATAT
*
125521 ATTTTTCATATTTTTATG
1 ATTTTT-AT-TTTTTATA
125539 ATTTTTATTTTTTATA
1 ATTTTTATTTTTTATA
*
125555 ATTTTGATTT
1 ATTTTTATTT
125565 GAATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 2 0.08
18 6 0.25
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (16 bp):
ATTTTTATTTTTTATA
Found at i:127354 original size:6 final size:6
Alignment explanation
Indices: 127345--127369 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
127335 TTTATTTTAT
127345 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
127370 GAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:129080 original size:20 final size:21
Alignment explanation
Indices: 129057--129099 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
129047 AAATAAATTT
129057 AAAATCCAAAAAAATT-ATAA
1 AAAATCCAAAAAAATTAATAA
* *
129077 AAAATTCATAAAAATTAATAA
1 AAAATCCAAAAAAATTAATAA
129098 AA
1 AA
129100 TAACATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATCCAAAAAAATTAATAA
Found at i:129143 original size:91 final size:91
Alignment explanation
Indices: 129038--129219 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
129028 TTAATTTTTA
129038 AAAAAATAAAAATAAATTTAAAATCCAAAAAAATTATAAAAAATTCATAAAAATTAATAAAATAA
1 AAAAAATAAAAATAAATTTAAAATCCAAAAAAATTATAAAAAATTCATAAAAATTAATAAAATAA
* *
129103 CATGAAATACATGTGGATTGTCATTT
66 CATGAAATACATGTGAATTCTCATTT
129129 AAAAAATAAAAATAAATTTAAAATCCAAAAAAATTATAAAAAATTCATAAAAATTAATAAAATAA
1 AAAAAATAAAAATAAATTTAAAATCCAAAAAAATTATAAAAAATTCATAAAAATTAATAAAATAA
129194 CATGAAATACATGTGAATTCTCATTT
66 CATGAAATACATGTGAATTCTCATTT
129220 CAACTATCAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (91 bp):
AAAAAATAAAAATAAATTTAAAATCCAAAAAAATTATAAAAAATTCATAAAAATTAATAAAATAA
CATGAAATACATGTGAATTCTCATTT
Found at i:129171 original size:20 final size:21
Alignment explanation
Indices: 129148--129190 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
129138 AAATAAATTT
129148 AAAATCCAAAAAAATT-ATAA
1 AAAATCCAAAAAAATTAATAA
* *
129168 AAAATTCATAAAAATTAATAA
1 AAAATCCAAAAAAATTAATAA
129189 AA
1 AA
129191 TAACATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATCCAAAAAAATTAATAA
Found at i:132347 original size:31 final size:31
Alignment explanation
Indices: 132285--132360 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
132275 ACTAAATTTG
* * *
132285 AGTACAAGGACTAAATTTATAATTTACATAT
1 AGTACAAGGACTAAATTCAAAATCTACATAT
* * *
132316 AGTACAAGGAGTATATTCAAAATCTATATAT
1 AGTACAAGGACTAAATTCAAAATCTACATAT
* *
132347 AATATAAGGACTAA
1 AGTACAAGGACTAA
132361 TAGTAGAACT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (31 bp):
AGTACAAGGACTAAATTCAAAATCTACATAT
Found at i:134373 original size:6 final size:6
Alignment explanation
Indices: 134362--134386 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
134352 TGAATGCAAT
134362 TGTGTA TGTGTA TGTGTA TGTGTA T
1 TGTGTA TGTGTA TGTGTA TGTGTA T
134387 TCGTGCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTGTA
Found at i:137120 original size:126 final size:127
Alignment explanation
Indices: 136895--137147 Score: 463
Period size: 126 Copynumber: 2.0 Consensus size: 127
136885 ATGAAAATGG
*
136895 AACGTAATACCACTCTGCACGCCATCTACGATCCTCTTGTTTTGCTCTTTTTTCTTCTTTGAATT
1 AACGTAATACCACTCTGCACGCCATCTACGATCCTCTTGTTTTGCTCTGTTTTCTTCTTTGAATT
* *
136960 TATTCCAATCTTTTGGTGTTTCCTTTATATATATGAAGGCTTTGTTCGTT-AATTAACGATA
66 TATTCCAATCTTTAGGCGTTTCCTTTATATATATGAAGGCTTTGTTCGTTAAATTAACGATA
*
137021 AACGTAATACCACTCTGCACGCCATCTCCGATCCTCTTGTTTTGCTCTGTTTTCTTCTTTGAATT
1 AACGTAATACCACTCTGCACGCCATCTACGATCCTCTTGTTTTGCTCTGTTTTCTTCTTTGAATT
137086 TATTCCAATCTTTAGGCGTTTCCTTTATATATATGAAGGCTTTGTTCGTTAAATTAACGATA
66 TATTCCAATCTTTAGGCGTTTCCTTTATATATATGAAGGCTTTGTTCGTTAAATTAACGATA
137148 TTTTTTCTCT
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 111 0.91
127 11 0.09
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (127 bp):
AACGTAATACCACTCTGCACGCCATCTACGATCCTCTTGTTTTGCTCTGTTTTCTTCTTTGAATT
TATTCCAATCTTTAGGCGTTTCCTTTATATATATGAAGGCTTTGTTCGTTAAATTAACGATA
Found at i:148353 original size:20 final size:19
Alignment explanation
Indices: 148314--148353 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
148304 AAATAAATTT
*
148314 AAAAAAAAAAGAAAATAAA
1 AAAAAAAAAAGAAAAGAAA
*
148333 AAAAAAAAGAAGAAGAGAAA
1 AAAAAAAA-AAGAAAAGAAA
148353 A
1 A
148354 TTAAAAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAGAAA
Found at i:151585 original size:15 final size:15
Alignment explanation
Indices: 151565--151615 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
151555 TCCACATTTC
151565 TTATTTTTATATTAT
1 TTATTTTTATATTAT
*
151580 TTATTTTTAATATCA-
1 TTATTTTT-ATATTAT
* *
151595 TTATTTTTCTTTTAT
1 TTATTTTTATATTAT
151610 TT-TTTT
1 TTATTTT
151616 AACTTAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.23
15 18 0.60
16 5 0.17
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTTTTATATTAT
Found at i:155655 original size:10 final size:10
Alignment explanation
Indices: 155626--155660 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
155616 TTAAAATATT
155626 AATTATATAA
1 AATTATATAA
*
155636 AAAT-TATAA
1 AATTATATAA
155645 AATTATATAA
1 AATTATATAA
155655 AATTAT
1 AATTAT
155661 TTTAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTATATAA
Found at i:175177 original size:29 final size:29
Alignment explanation
Indices: 175138--175193 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
175128 TTAGTACATG
* *
175138 ATAAAATTTCACTTTAATCTTTTAAAATA
1 ATAAAATTTCAATTTAATCCTTTAAAATA
* *
175167 ATAAATTTTCAATTTAGTCCTTTAAAA
1 ATAAAATTTCAATTTAATCCTTTAAAA
175194 AACTATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (29 bp):
ATAAAATTTCAATTTAATCCTTTAAAATA
Found at i:176566 original size:262 final size:262
Alignment explanation
Indices: 176101--176627 Score: 1036
Period size: 262 Copynumber: 2.0 Consensus size: 262
176091 AAGTCAATTT
*
176101 CATGTATTACCCACAATTGGACTAACTTATCACATTTTATAAAGAGTTAATATAACTTTTAGTCC
1 CATGTATTACCCACAATTGGACTAACTTATCACATTTTATAAAGAGTTAATATAACTTTTAATCC
176166 CTAAACTTGGCAATTATATCCACTTTGATACCTATACTTTTTTTGTTCATTTTGATACCTGAACT
66 CTAAACTTGGCAATTATATCCACTTTGATACCTATACTTTTTTTGTTCATTTTGATACCTGAACT
176231 TGGATCCATCATGATTTGATGATGCGGTACTCTAAGATTGCCATATGATCAAACTTTTACATTTT
131 TGGATCCATCATGATTTGATGATGCGGTACTCTAAGATTGCCATATGATCAAACTTTTACATTTT
*
176296 GCCAAGTTCATGGGCCAAAATGAACATAATTGTCATGTTCAAATACCAAATAGAGAATAAAAAAA
196 GCCAAGTTCATGGGCCAAAATGAACATAATTGTCATGTTCAAATACCAAATAGAGAAAAAAAAAA
176361 GA
261 GA
176363 CATGTATTACCCACAATTGGACTAACTTATCACATTTTATAAAGAGTTAATATAACTTTTAATCC
1 CATGTATTACCCACAATTGGACTAACTTATCACATTTTATAAAGAGTTAATATAACTTTTAATCC
176428 CTAAACTTGGCAATTATATCCACTTTGATACCTATACTTTTTTTGTTCATTTTGATACCTGAACT
66 CTAAACTTGGCAATTATATCCACTTTGATACCTATACTTTTTTTGTTCATTTTGATACCTGAACT
176493 TGGATCCATCATGATTTGATGATGCGGTACTCTAAGATTGCCATATGATCAAACTTTTACATTTT
131 TGGATCCATCATGATTTGATGATGCGGTACTCTAAGATTGCCATATGATCAAACTTTTACATTTT
176558 GCCAAGTTCATGGGCCAAAATGAACATAATTGTCATGTTCAAATACCAAATAGAGAAAAAAAAAA
196 GCCAAGTTCATGGGCCAAAATGAACATAATTGTCATGTTCAAATACCAAATAGAGAAAAAAAAAA
176623 GA
261 GA
176625 CAT
1 CAT
176628 TTACCTAAAT
Statistics
Matches: 263, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
262 263 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (262 bp):
CATGTATTACCCACAATTGGACTAACTTATCACATTTTATAAAGAGTTAATATAACTTTTAATCC
CTAAACTTGGCAATTATATCCACTTTGATACCTATACTTTTTTTGTTCATTTTGATACCTGAACT
TGGATCCATCATGATTTGATGATGCGGTACTCTAAGATTGCCATATGATCAAACTTTTACATTTT
GCCAAGTTCATGGGCCAAAATGAACATAATTGTCATGTTCAAATACCAAATAGAGAAAAAAAAAA
GA
Found at i:180894 original size:16 final size:16
Alignment explanation
Indices: 180873--180907 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
180863 AATCATTTAA
180873 AAATTATAAAAAATAT
1 AAATTATAAAAAATAT
* *
180889 AAATTATTAAAATTAT
1 AAATTATAAAAAATAT
180905 AAA
1 AAA
180908 ATTAGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTATAAAAAATAT
Found at i:183116 original size:21 final size:21
Alignment explanation
Indices: 183090--183132 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
183080 TTTAAGGGGG
183090 TCGAAGTTAAATTATAATTTT
1 TCGAAGTTAAATTATAATTTT
183111 TCGAAGTTAAATTATAATTTT
1 TCGAAGTTAAATTATAATTTT
183132 T
1 T
183133 ACGATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (21 bp):
TCGAAGTTAAATTATAATTTT
Found at i:189918 original size:4 final size:4
Alignment explanation
Indices: 189909--189963 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
189899 TTATCAATAT
189909 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
189957 ATAC ATA
1 ATAC ATA
189964 TAGCACTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:191022 original size:2 final size:2
Alignment explanation
Indices: 191017--191051 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
191007 TATATATATA
*
191017 TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
191052 AAATTTCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:197271 original size:21 final size:22
Alignment explanation
Indices: 197232--197273 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
197222 TCAATAATAA
197232 TTAATTAAATATTTCATAAATT
1 TTAATTAAATATTTCATAAATT
*
197254 TTAATTAAA-ATTTTATAAAT
1 TTAATTAAATATTTCATAAAT
197274 CTGTTCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATTAAATATTTCATAAATT
Found at i:197831 original size:20 final size:20
Alignment explanation
Indices: 197808--197845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
197798 ATATTTTCTA
*
197808 AATATATTTTAAAATAAAAT
1 AATATATATTAAAATAAAAT
*
197828 AATATATATTAAATTAAA
1 AATATATATTAAAATAAA
197846 TTAGAGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATATATTAAAATAAAAT
Found at i:198632 original size:12 final size:12
Alignment explanation
Indices: 198615--198644 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
198605 CATGGTAATA
198615 GAATTTCTATGG
1 GAATTTCTATGG
198627 GAATTTCTATGG
1 GAATTTCTATGG
198639 GAATTT
1 GAATTT
198645 GAGAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (12 bp):
GAATTTCTATGG
Found at i:205053 original size:17 final size:16
Alignment explanation
Indices: 205013--205055 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
205003 AAGAAAAAAT
*
205013 AGTTATAAGAATATGAA
1 AGTTA-AAGAAGATGAA
205030 AGATTAAAGAAGATGAAA
1 AG-TTAAAGAAGATG-AA
205048 AGTTAAAG
1 AGTTAAAG
205056 GTCAAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (16 bp):
AGTTAAAGAAGATGAA
Found at i:209900 original size:38 final size:38
Alignment explanation
Indices: 209849--209924 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
209839 ATTTAGGAAA
*
209849 TTTACCCTTGGATATGCAAGAAATTATAGTTGTGATAG
1 TTTACCCCTGGATATGCAAGAAATTATAGTTGTGATAG
209887 TTTACCCCTGGATATGCAAGAAATTATAGTTGTGATAG
1 TTTACCCCTGGATATGCAAGAAATTATAGTTGTGATAG
209925 GAATCAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (38 bp):
TTTACCCCTGGATATGCAAGAAATTATAGTTGTGATAG
Found at i:213068 original size:25 final size:25
Alignment explanation
Indices: 213019--213068 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
213009 GTAAAAAGGG
*
213019 AGGGAAAGTAAAAAAAATTTGAAGAA
1 AGGGAAAG-AAAAAAAATTTAAAGAA
213045 AGGGAAAG-AAAAAAATGTTAAAGA
1 AGGGAAAGAAAAAAAAT-TTAAAGA
213069 GAGTTGGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 6 0.27
26 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (25 bp):
AGGGAAAGAAAAAAAATTTAAAGAA
Found at i:226868 original size:21 final size:20
Alignment explanation
Indices: 226827--226876 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
226817 ATTAATTTCA
226827 ATTTATTTAATTATTTATAAT
1 ATTT-TTTAATTATTTATAAT
226848 -TTGTTTTAATTTATTCT-TAAT
1 ATT-TTTTAA-TTATT-TATAAT
226869 ATTTTTTA
1 ATTTTTTA
226877 TAATCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTTAATTATTTATAAT
Found at i:230854 original size:9 final size:9
Alignment explanation
Indices: 230842--230894 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
230832 TTTTAGAAAA
230842 TTTAAATTT
1 TTTAAATTT
*
230851 TTTAACTTT
1 TTTAAATTT
*
230860 CTTTATATTT
1 -TTTAAATTT
*
230870 TTTGAATTT
1 TTTAAATTT
230879 TTTATAATTT
1 TTTA-AATTT
230889 TTTAAA
1 TTTAAA
230895 AAAATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTAAATTT
Found at i:230869 original size:19 final size:17
Alignment explanation
Indices: 230842--230893 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
230832 TTTTAGAAAA
*
230842 TTTAAATTTTTTAACTTT
1 TTTATATTTTTTAA-TTT
230860 CTTTATATTTTTTGAATTT
1 -TTTATATTTTTT-AATTT
230879 TTTATAATTTTTTAA
1 TTTAT-ATTTTTTAA
230894 AAAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 21 0.70
20 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTTTTTAATTT
Found at i:230920 original size:18 final size:17
Alignment explanation
Indices: 230899--230942 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
230889 TTTAAAAAAA
230899 TATAAATTTTAGAATATT
1 TATAAATTTTAGAA-ATT
*
230917 TATAAATATTTTGAAATT
1 TATAAAT-TTTAGAAATT
*
230935 TAAAAATT
1 TATAAATT
230943 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TATAAATTTTAGAAATT
Found at i:230951 original size:18 final size:18
Alignment explanation
Indices: 230904--230952 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
230894 AAAAATATAA
*
230904 ATTTTAGAATATTTATAAAT
1 ATTTT-GAA-ATTTAAAAAT
230924 ATTTTGAAATTTAAAAATT
1 ATTTTGAAATTTAAAAA-T
230943 ATTTT-AAATT
1 ATTTTGAAATT
230953 ATTTTGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 13 0.48
19 9 0.33
20 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTTTGAAATTTAAAAAT
Found at i:234091 original size:22 final size:23
Alignment explanation
Indices: 234049--234093 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
234039 TATATATTAA
234049 ATTTAAAAGTAAATTGATCATTTT
1 ATTTAAAAG-AAATTGATCATTTT
234073 ATTTAAAA-AAATT-ATTCATTT
1 ATTTAAAAGAAATTGA-TCATTT
234094 ATACTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
24 8 0.40
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTAAAAGAAATTGATCATTTT
Found at i:248444 original size:12 final size:12
Alignment explanation
Indices: 248427--248461 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
248417 GTCCTTCCAC
248427 TCTTATTCTTCT
1 TCTTATTCTTCT
248439 TCTTATTCTTCT
1 TCTTATTCTTCT
*
248451 TCTTGTTCTTC
1 TCTTATTCTTC
248462 GAAGTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.66
Consensus pattern (12 bp):
TCTTATTCTTCT
Found at i:250165 original size:31 final size:32
Alignment explanation
Indices: 250078--250153 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
250068 TTACAAAATG
* *
250078 GTCACTGAAC-ATTCAAAAG-TTTTTATTGAA
1 GTCATTGAACTATTTAAAAGTTTTTTATTGAA
* *
250108 GTCGTTGAACTATTTAAAAGTTTTTTATTTAA
1 GTCATTGAACTATTTAAAAGTTTTTTATTGAA
*
250140 GTCATTGGACTATT
1 GTCATTGAACTATT
250154 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 8 0.21
31 8 0.21
32 22 0.58
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (32 bp):
GTCATTGAACTATTTAAAAGTTTTTTATTGAA
Found at i:250588 original size:9 final size:9
Alignment explanation
Indices: 250576--250602 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
250566 TAATTTTTGA
250576 ATTTTTAAT
1 ATTTTTAAT
250585 ATTTTTAAT
1 ATTTTTAAT
250594 ATTTTTAAT
1 ATTTTTAAT
250603 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:252130 original size:8 final size:8
Alignment explanation
Indices: 252117--252142 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
252107 CCTTATATTC
252117 TTTAAAAT
1 TTTAAAAT
252125 TTTAAAAT
1 TTTAAAAT
252133 TTTAAAAT
1 TTTAAAAT
252141 TT
1 TT
252143 AATCTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTAAAAT
Found at i:255113 original size:147 final size:146
Alignment explanation
Indices: 254787--255247 Score: 624
Period size: 147 Copynumber: 3.1 Consensus size: 146
254777 CAGTAGGTTT
*
254787 GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCGTATACTGCTGCAAAGA
1 GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCGTATGCTGCTGCAAAGA
** * *
254852 TCCGGTGAAACCGGATAATTTGAGAAGAACT--GAGTTTAA-CTCGGTTGGTTTATTCAACCACC
66 TATGCTGAAACCGGATAATTTGAGAAGAACTCGGAG-TTAAGCTCAGTTGGTTTATTCAACCA-C
254914 CCGATATGCAGCAAGTTC
129 CCGATATGCAGCAAGTTC
* ***
254932 GGGATTCGAATCCCAACATCTGCAACCATTTTCCCTATGTCTTGAGAAGTATGCTGCTGCAAAGA
1 GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCGTATGCTGCTGCAAAGA
*
254997 TATGCTGAAACCGGATAATTTGAGAAGAACTCGGAGTTAAGCTCAGTTGGTTTATTCAATCACCT
66 TATGCTGAAACCGGATAATTTGAGAAGAACTCGGAGTTAAGCTCAGTTGGTTTATTCAACCACC-
* *
255062 CGATCTGCAGCAACTTC
130 CGATATGCAGCAAGTTC
* *
255079 GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCCTATGCTGCTGCTGCAA
1 GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCGTATGCTGCTGC--AAA
* * * * * *
255144 G-GATCCAATGAAACCGGATAATTTGATAAGAGCCCGGAGTTAAGCTAAGTTGGTTTATTCAACC
64 GATATGC--TGAAACCGGATAATTTGAGAAGAACTCGGAGTTAAGCTCAGTTGGTTTATTCAACC
* *
255208 ACCCTGATATGCAGTAGGTTC
127 ACCC-GATATGCAGCAAGTTC
255229 GGGATTCGAATCCCAACAT
1 GGGATTCGAATCCCAACAT
255248 CTATAACCAT
Statistics
Matches: 278, Mismatches: 29, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
145 88 0.32
146 6 0.02
147 92 0.33
148 3 0.01
149 4 0.01
150 85 0.31
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (146 bp):
GGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGATCCGTATGCTGCTGCAAAGA
TATGCTGAAACCGGATAATTTGAGAAGAACTCGGAGTTAAGCTCAGTTGGTTTATTCAACCACCC
GATATGCAGCAAGTTC
Found at i:260664 original size:20 final size:19
Alignment explanation
Indices: 260624--260666 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
260614 AAAAAATATT
*
260624 TAAATTAAAATTCAGTTGA
1 TAAATTAAAATTCAATTGA
*
260643 TAAATTAAAATTTTAATTGA
1 TAAATTAAAA-TTCAATTGA
260663 TAAA
1 TAAA
260667 ATTGATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (19 bp):
TAAATTAAAATTCAATTGA
Found at i:261414 original size:13 final size:13
Alignment explanation
Indices: 261396--261432 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
261386 TTGTTTCACT
261396 GAAAATGATTTCG
1 GAAAATGATTTCG
261409 GAAAATGATTTCG
1 GAAAATGATTTCG
*
261422 GAAAATAATTT
1 GAAAATGATTT
261433 ACTTTATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (13 bp):
GAAAATGATTTCG
Found at i:261917 original size:15 final size:15
Alignment explanation
Indices: 261899--261972 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 15
261889 CTACAAAACA
*
261899 TTATTATTAATATATT
1 TTATTATTAAAATA-T
*
261915 TATAATTATAACAAATAT
1 T-T-ATTATTA-AAATAT
261933 TTATTATTAAAATA-
1 TTATTATTAAAATAT
*
261947 TTAATATT-AAATAT
1 TTATTATTAAAATAT
261961 TT-TTATATAAAA
1 TTATTAT-TAAAA
261973 AAATTAACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 8 0.17
14 10 0.21
15 8 0.17
16 7 0.15
17 2 0.04
18 8 0.17
19 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTATTAAAATAT
Found at i:263884 original size:23 final size:23
Alignment explanation
Indices: 263858--263902 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
263848 AGAAATCAAA
263858 TTATAATTTTACTATGTTTTAAT
1 TTATAATTTTACTATGTTTTAAT
* *
263881 TTATAATTTTATTATTTTTTAA
1 TTATAATTTTACTATGTTTTAA
263903 AAGAATTAAA
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:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATAATTTTACTATGTTTTAAT
Found at i:266483 original size:30 final size:31
Alignment explanation
Indices: 266414--266486 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
266404 ATATTCTTTA
*
266414 TTAGTGACTATTTTGTCACTTTTCAATAACG
1 TTAGTGACTGTTTTGTCACTTTTCAATAACG
266445 TTAGTGACTGTTTTGTCACATTTTC-A-AA-G
1 TTAGTGACTGTTTTGTCAC-TTTTCAATAACG
266474 TTGAGTGACTGTT
1 TT-AGTGACTGTT
266487 GTGTTAAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 3 0.08
30 12 0.31
31 19 0.49
32 5 0.13
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCACTTTTCAATAACG
Found at i:268863 original size:3 final size:3
Alignment explanation
Indices: 268855--268894 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
268845 TTGTTAATGC
268855 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
268895 TTGTTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:269001 original size:3 final size:3
Alignment explanation
Indices: 268995--269033 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
268985 CAATTTAACA
* * *
268995 AAT AAT AAT AAT AAC AAC AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
269034 GTTAACAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:270219 original size:18 final size:19
Alignment explanation
Indices: 270188--270225 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
270178 AATTCCTCAA
*
270188 TTATATTAACATTTGAAAT
1 TTATAATAACATTTGAAAT
*
270207 TTATAATAA-ATTTTAAAT
1 TTATAATAACATTTGAAAT
270225 T
1 T
270226 ACATCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTATAATAACATTTGAAAT
Found at i:274247 original size:10 final size:10
Alignment explanation
Indices: 274234--274305 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
274224 TATTAAAAAT
274234 TAAAAATATA
1 TAAAAATATA
**
274244 TAAAAACGTA
1 TAAAAATATA
*
274254 -AAAGAT-TA
1 TAAAAATATA
274262 TAAAACA-A-A
1 TAAAA-ATATA
274271 TAAAAATATA
1 TAAAAATATA
*
274281 TAAAGATATA
1 TAAAAATATA
*
274291 TAAAAAAATA
1 TAAAAATATA
274301 TAAAA
1 TAAAA
274306 TTCATAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.06
9 14 0.29
10 32 0.65
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (10 bp):
TAAAAATATA
Found at i:274515 original size:19 final size:19
Alignment explanation
Indices: 274488--274524 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
274478 ATAACTTTTT
*
274488 TTTATAATTTTTATAAAAG
1 TTTACAATTTTTATAAAAG
274507 TTTACAATTTTTATAAAA
1 TTTACAATTTTTATAAAA
274525 AAATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTACAATTTTTATAAAAG
Found at i:279508 original size:29 final size:31
Alignment explanation
Indices: 279451--279508 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
279441 AATTATCATT
*
279451 AAACTATTCTAAAGTTTTCATTTAAGTCACA
1 AAACTATTCTAAAGTATTCATTTAAGTCACA
*
279482 AAACTATTC-AAA-TATTCTTTTAAGTCA
1 AAACTATTCTAAAGTATTCATTTAAGTCA
279509 TTGGTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 3 0.12
31 9 0.36
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (31 bp):
AAACTATTCTAAAGTATTCATTTAAGTCACA
Found at i:279993 original size:93 final size:96
Alignment explanation
Indices: 279882--280056 Score: 241
Period size: 93 Copynumber: 1.9 Consensus size: 96
279872 TAACTCAACA
* * * * * *
279882 TTTTGATGTTTGGGACTAAATTAA-AATTTTA-TTATAGTTTGAGGG-TGTTTAGTG-AATTAAT
1 TTTTGAAGTTTGAGACTAAATTAAGAATTTTAGTTATAATTTG-GGGCTGTTTAATGCAAATAAA
* *
279943 TCTTTTTTATTGCATATTTTGGAAAGTCGAAG
65 TATTTTTCATTGCATATTTTGGAAAGTCGAAG
279975 TTTTGAAGTTTGAGACTAAATTAAGAATTTTAGTTATAATTTGGGGCTGTTTAATGCAAATAAAT
1 TTTTGAAGTTTGAGACTAAATTAAGAATTTTAGTTATAATTTGGGGCTGTTTAATGCAAATAAAT
280040 ATTTTTCATTGCATATT
66 ATTTTTCATTGCATATT
280057 CATAGTTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 22 0.31
94 10 0.14
95 17 0.24
96 21 0.30
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.46
Consensus pattern (96 bp):
TTTTGAAGTTTGAGACTAAATTAAGAATTTTAGTTATAATTTGGGGCTGTTTAATGCAAATAAAT
ATTTTTCATTGCATATTTTGGAAAGTCGAAG
Found at i:281724 original size:18 final size:18
Alignment explanation
Indices: 281701--281745 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
281691 TATTAAAAAT
281701 ATTTTTATATTTTTAATA
1 ATTTTTATATTTTTAATA
* *
281719 ATTTTTA-ATTTTTTATG
1 ATTTTTATATTTTTAATA
*
281736 ATTTGTATAT
1 ATTTTTATAT
281746 ATATTAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTTTTATATTTTTAATA
Found at i:281899 original size:18 final size:19
Alignment explanation
Indices: 281872--281907 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
281862 ATTTTAAGGG
281872 TTAAAAAAAGG-TAAAATA
1 TTAAAAAAAGGCTAAAATA
*
281890 TTAAATAAAGGCTAAAAT
1 TTAAAAAAAGGCTAAAAT
281908 GATTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.25
Consensus pattern (19 bp):
TTAAAAAAAGGCTAAAATA
Found at i:296538 original size:269 final size:260
Alignment explanation
Indices: 295993--296773 Score: 930
Period size: 270 Copynumber: 2.9 Consensus size: 260
295983 GTAGCTCGAC
* * *
295993 CTGTTGAACTGGTCGAATTTGAGTGT--TAATACTTTATTTGAGTAGCTTATCAGTTTAATGCAG
1 CTGTTGAACTGGTCGAATTTGAGTATACTAATACTTTATTTGAGTAGCTTATCAATTTAATCCAG
* * * * *
296056 CTTTTTTCTATTCTTAATGAGTATTG-GAAAACTTCAAGTTAAACCTTTAAACACGTGTTTGAGT
66 CTTTTTTCTATTTTTAATGAGTATTGAG-AAACTTCAATTTAAACATTTAAACACGAGTTT-AGC
** * * * *
296120 TTGAGCACTAATCATTGAGCTTGAAATCGAGCATGGGAGTTGAGCTTTAAACATGGAACTCGATT
129 TCAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTGAGTTTTAAA-GTGGAACTCGATT
* * * *
296185 GAGCTTCTGTTGAGTTGT-AGGCTTCTGAGTTTCAAGTCAAACTTGAGCTCAATCTTCTTATGGC
193 GAGCTTCTGTTGAGTT-TCAAGCTT-TGAATTTCAAGTCAAACTTGAGCTCAACCTTCTTAGGGC
296249 TTGAG
256 TTGAG
* *
296254 CTGTTGAACTGGTCG-ATTTCGAGTATACTAATACTTTATTTGAGTAGCTTATCAACTTAATTCA
1 CTGTTGAACTGGTCGAATTT-GAGTATACTAATACTTTATTTGAGTAGCTTATCAATTTAATCCA
** *
296318 GCTTTTTTTTTTTTCTATTTTTAATGAGTATTGAGAAACTTCAATTTTGGACAATTAAACACGAG
65 GC------TTTTTTCTATTTTTAATGAGTATTGAGAAACTTCAA-TTTAAACATTTAAACACGAG
296383 TTTAAGCTCAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTGAGTTTTAAATGTGGAA
123 TTT-AGCTCAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTGAGTTTTAAA-GTGGAA
296448 CTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGAATTTCAAGTCAAACTTGAGCTCAAGCCTT-T
186 CTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGAATTTCAAGTCAAACTTGAGCTCAA-CCTTCT
296512 TAGGGCTTGAG
250 TAGGGCTTGAG
* * *
296523 CTGTTGAAGTGGTCGAATTTGAGTATACTAATACTTTATTTGAGTATCGTATC-ATTGTAATCCA
1 CTGTTGAACTGGTCGAATTTGAGTATACTAATACTTTATTTGAGTAGCTTATCAATT-TAATCCA
* * * *
296587 GCTTTTTTCTATATTTAATGAGTATTGA-AAACCTTCAATATAAATATTTAAACACTGAATTCTA
65 GCTTTTTTCTATTTTTAATGAGTATTGAGAAA-CTTCAATTTAAACATTTAAACAC-GAGTT-TA
* * * * *
296651 GCTCCAGTACTAATAATTGAGCTTGAAATCGAGCATTAGAGTTAAGCTTTTAAAGTGGAACTCAA
127 GCTCAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTGAG-TTTTAAAGTGGAACTCGA
*
296716 TCGAGCTTCTGTTGAGTTTCAACTTTCAAGCTTTGAATTTCAAGTCAAACTTGAGCTC
191 TTGAGCTTCTGTTGAG-------TTTCAAGCTTTGAATTTCAAGTCAAACTTGAGCTC
296774 GAGCTTAGCT
Statistics
Matches: 452, Mismatches: 42, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
260 4 0.01
261 20 0.04
262 15 0.03
263 138 0.31
264 8 0.02
268 2 0.00
269 124 0.27
270 141 0.31
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (260 bp):
CTGTTGAACTGGTCGAATTTGAGTATACTAATACTTTATTTGAGTAGCTTATCAATTTAATCCAG
CTTTTTTCTATTTTTAATGAGTATTGAGAAACTTCAATTTAAACATTTAAACACGAGTTTAGCTC
AAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTGAGTTTTAAAGTGGAACTCGATTGAG
CTTCTGTTGAGTTTCAAGCTTTGAATTTCAAGTCAAACTTGAGCTCAACCTTCTTAGGGCTTGAG
Found at i:298651 original size:14 final size:14
Alignment explanation
Indices: 298632--298659 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
298622 TCTTTGGAAG
298632 GCCATATTCTCATA
1 GCCATATTCTCATA
298646 GCCATATTCTCATA
1 GCCATATTCTCATA
298660 CTCATGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
GCCATATTCTCATA
Found at i:300366 original size:31 final size:31
Alignment explanation
Indices: 300325--300384 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
300315 TAATCTTTGT
* *
300325 ACTAGGTAATTGTTCTT-ATATTGGGGTTTAA
1 ACTAGATAATTGTT-TTCAAATTGGGGTTTAA
300356 ACTAGATAATTGTTTTCAAATTGGGGTTT
1 ACTAGATAATTGTTTTCAAATTGGGGTTT
300385 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.45
Consensus pattern (31 bp):
ACTAGATAATTGTTTTCAAATTGGGGTTTAA
Found at i:302457 original size:22 final size:23
Alignment explanation
Indices: 302415--302458 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
302405 GTTTCCCCAA
302415 TTGAAAGTAGTGATTTATTTTTC
1 TTGAAAGTAGTGATTTATTTTTC
* *
302438 TTGAAATTATTGA-TTATTTTT
1 TTGAAAGTAGTGATTTATTTTT
302459 ATTATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTGAAAGTAGTGATTTATTTTTC
Found at i:307768 original size:154 final size:155
Alignment explanation
Indices: 307486--307768 Score: 435
Period size: 154 Copynumber: 1.8 Consensus size: 155
307476 TATATTGCAT
**
307486 TAACTTATATATTTTTTGAGAGTCAAAGTGTGATTTTATACATCGTAACTTTTAATTCTGTTATT
1 TAACTTATATATTTTTTGAGAGTCAAAGTGTGATTTTATACATAATAAC-TTTAATTCTGTTATT
* *
307551 TATTAAGGGATTAAAAGAAAAATTTTCCATTTGAGGGAGTCAAGCACCTGTCTGCCGCCTTTAAT
65 TATTAAGGGACTAAAAGAAAAATTTTCCATTTGAGGGAGTCAAGCACCTGTCCGCCGCCTTTAAT
307616 TTTAATCATAGTAACTTATGATTTCA
130 TTTAATCATAGTAACTTATGATTTCA
** * * *
307642 TAACTTATATATTTTTTTTGAGTCGAAGTGTGATTTTATATATAATAAC-TTAATTTTGTTATTT
1 TAACTTATATATTTTTTGAGAGTCAAAGTGTGATTTTATACATAATAACTTTAATTCTGTTATTT
* *
307706 ATT-AGCGGACTAAAAGACAATTTTTCCATTTGAGGGAGTCAAGCACCTGTCCGCCGCCTTTAA
66 ATTAAG-GGACTAAAAGAAAAATTTTCCATTTGAGGGAGTCAAGCACCTGTCCGCCGCCTTTAA
307769 ATTTCATCTA
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
153 2 0.02
154 70 0.61
156 43 0.37
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (155 bp):
TAACTTATATATTTTTTGAGAGTCAAAGTGTGATTTTATACATAATAACTTTAATTCTGTTATTT
ATTAAGGGACTAAAAGAAAAATTTTCCATTTGAGGGAGTCAAGCACCTGTCCGCCGCCTTTAATT
TTAATCATAGTAACTTATGATTTCA
Found at i:308712 original size:11 final size:12
Alignment explanation
Indices: 308689--308713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
308679 TTAAATTTAT
308689 AAAAATTTAAAA
1 AAAAATTTAAAA
308701 AAAAATTTAAAA
1 AAAAATTTAAAA
308713 A
1 A
308714 TTTAAGAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTTAAAA
Found at i:309685 original size:10 final size:10
Alignment explanation
Indices: 309667--309700 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
309657 GTATATTTTC
*
309667 TTTAAAATTT
1 TTTATAATTT
309677 TTTATAATTT
1 TTTATAATTT
309687 TTTATAATTT
1 TTTATAATTT
309697 TTTA
1 TTTA
309701 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATAATTT
Found at i:309708 original size:26 final size:26
Alignment explanation
Indices: 309686--309748 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
309676 TTTTATAATT
*
309686 TTTTATAATTTTT-TAAAAATATAAA
1 TTTTAGAATTTTTATAAAAATATAAA
* *
309711 TTTTAGAATTTTTATAAATATTTTAAA
1 TTTTAGAATTTTTATAAA-AATATAAA
*
309738 TTTTAAAATTT
1 TTTTAGAATTT
309749 ATTTTGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 12 0.38
26 4 0.12
27 16 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTAGAATTTTTATAAAAATATAAA
Found at i:311520 original size:30 final size:30
Alignment explanation
Indices: 311474--311556 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 30
311464 TTTTTTCTTG
* **
311474 AAATTTATTG-AAATTTTAATT-TGTCTCTC
1 AAATTTTTTGAAAATTTTAATTATACCT-TC
* *
311503 AAATTTTTTGAAAATTTTCATTATACCTTT
1 AAATTTTTTGAAAATTTTAATTATACCTTC
*
311533 TAATTTCTTTGAAAATTTTAATTA
1 AAATTT-TTTGAAAATTTTAATTA
311557 AGCTCTTCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 9 0.20
30 16 0.36
31 19 0.43
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (30 bp):
AAATTTTTTGAAAATTTTAATTATACCTTC
Found at i:312003 original size:14 final size:16
Alignment explanation
Indices: 311975--312005 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
311965 ATTGTCACTT
311975 ATTTAAAAAATATATA
1 ATTTAAAAAATATATA
311991 ATTTAAAAAATATAT
1 ATTTAAAAAATATAT
312006 TTGTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAAAAAATATATA
Found at i:314820 original size:36 final size:36
Alignment explanation
Indices: 314780--314862 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
314770 ATATATTAAT
314780 TAATTATTATAATATATACAATACATCTATATAAGA
1 TAATTATTATAATATATACAATACATCTATATAAGA
314816 TAATTATTATAATATATACAATACATCTATATAAGA
1 TAATTATTATAATATATACAATACATCTATATAAGA
314852 TAATTATTATA
1 TAATTATTATA
314863 TATTGTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (36 bp):
TAATTATTATAATATATACAATACATCTATATAAGA
Found at i:315045 original size:13 final size:13
Alignment explanation
Indices: 315027--315051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315017 GAGATTATTG
315027 AAATTTTTAAATC
1 AAATTTTTAAATC
315040 AAATTTTTAAAT
1 AAATTTTTAAAT
315052 TTATCATTTT
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:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTTTTAAATC
Found at i:315356 original size:15 final size:15
Alignment explanation
Indices: 315318--315356 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
315308 CAAATAATAA
*
315318 TTATAATATTTAAAT
1 TTATATTATTTAAAT
315333 TTA-ATTATTTAAAT
1 TTATATTATTTAAAT
315347 TTATATTATT
1 TTATATTATT
315357 CGAATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTATTTAAAT
Found at i:320524 original size:15 final size:16
Alignment explanation
Indices: 320497--320527 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
320487 AGAAAACCAT
320497 AAATACATAAAAAAAA
1 AAATACATAAAAAAAA
320513 AAATAC-TAAAAAAAA
1 AAATACATAAAAAAAA
320528 TCGAAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
AAATACATAAAAAAAA
Found at i:322278 original size:143 final size:143
Alignment explanation
Indices: 321963--322565 Score: 566
Period size: 143 Copynumber: 4.3 Consensus size: 143
321953 CTGAAGAACA
* * * *
321963 AAGCGAACATATCGATTACAAGTATATACAAGCATAAACAAGTGTTTACAGAAAAA--GGGAGCA
1 AAGCTAACATATCGATTACAAGTATATACAAGCATGAACAAGTGCTTACACAAAAACTGGGAGCA
* * * * *
322026 TGTATGTTACATCAACGGTTACA--AGGATCAGCGAACCTATGTTACAATTCGCATCAAGCTCAC
66 TGTATGTTACATCAATGGTTACAGCAGGATCAGCAAACCTATGTTACAATTTGCATCTAGCTCAT
* *
322089 ATATGCCCCCATTAC
131 ATATG--CCTATTAT
* *
322104 AACCTAACATATCGATTACAAGTATATACAAGCATGAATAAGTGCTTACACAAAAACTGGGGAGC
1 AAGCTAACATATCGATTACAAGTATATACAAGCATGAACAAGTGCTTACACAAAAACT-GGGAGC
* * *
322169 ATTTATG-TACATCCATGGTTACAGCAGGATCAG-AAACACTATGTTACAATTTGTATCTAGCTC
65 ATGTATGTTACATCAATGGTTACAGCAGGATCAGCAAAC-CTATGTTACAATTTGCATCTAGCTC
322232 ATATATGCCTATTAT
129 ATATATGCCTATTAT
** * *
322247 AAATTAACATATTGATTACAAGTATATACAAGCATGAACAAGTGCTTACACGAAAACTGGGA--A
1 AAGCTAACATATCGATTACAAGTATATACAAGCATGAACAAGTGCTTACACAAAAACTGGGAGCA
* *
322310 -GTATG-----T--AT-GTTACATCA--A-CAGCAAACCTATGCTACAATTTGCATCTAAGCTCA
66 TGTATGTTACATCAATGGTTACAGCAGGATCAGCAAACCTATGTTACAATTTGCATCT-AGCTCA
* *
322363 TCTATGCCTATTCT
130 TATATGCCTATTAT
* * * * * * *
322377 ATGCTAACATATTGGTTACAAGTGA-ATACAAGCATGAGCAAGTGCTTAAACAGAAACCGGGGAG
1 AAGCTAACATATCGATTACAAGT-ATATACAAGCATGAACAAGTGCTTACACA-AAAACTGGGAG
** * ** ** *
322441 TGTGCATGTTACATCAATGGTTACAGTTGGAT-AGGTGATCCTATGTTACAATTTGCATCTAGCT
64 CATGTATGTTACATCAATGGTTACAGCAGGATCA-GCAAACCTATGTTACAATTTGCATCTAGCT
* *
322505 CATCTATGCCTATTCT
128 CATATATGCCTATTAT
* * * *
322521 ACGCTAACAAATCAATTACAAGTGTATACATAGCATGAACAAGTG
1 AAGCTAACATATCGATTACAAGTATATACA-AGCATGAACAAGTG
322566 TTCACCTCGA
Statistics
Matches: 383, Mismatches: 52, Indels: 50
0.79 0.11 0.10
Matches are distributed among these distances:
129 21 0.05
130 66 0.17
131 9 0.02
132 8 0.02
133 2 0.01
134 4 0.01
135 1 0.00
139 5 0.01
140 1 0.00
141 52 0.14
142 10 0.03
143 73 0.19
144 60 0.16
145 71 0.19
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (143 bp):
AAGCTAACATATCGATTACAAGTATATACAAGCATGAACAAGTGCTTACACAAAAACTGGGAGCA
TGTATGTTACATCAATGGTTACAGCAGGATCAGCAAACCTATGTTACAATTTGCATCTAGCTCAT
ATATGCCTATTAT
Found at i:322450 original size:130 final size:130
Alignment explanation
Indices: 322202--322457 Score: 338
Period size: 130 Copynumber: 2.0 Consensus size: 130
322192 GCAGGATCAG
* * *
322202 AAACACTATGTTACAATTTGTATCTAGCTCATATATGCCTATTATAAATTAACATATTGATTACA
1 AAACACTATGCTACAATTTGCATCTAGCTCATATATGCCTATTATAAACTAACATATTGATTACA
* * *
322267 AGTATATACAAGCATGAACAAGTGCTTACACGAAAACTGGGAAGTATGTATGTTACATCAACAGC
66 AGTATATACAAGCATGAACAAGTGCTTAAACGAAAACCGGGAAGTATGCATGTTACATCAACAGC
* * ** *
322332 AAAC-CTATGCTACAATTTGCATCTAAGCTCATCTATGCCTATTCTATGCTAACATATTGGTTAC
1 AAACACTATGCTACAATTTGCATCT-AGCTCATATATGCCTATTATAAACTAACATATTGATTAC
* * *
322396 AAGTGA-ATACAAGCATGAGCAAGTGCTTAAAC-AGAAACCGGGGAGTGTGCATGTTACATCAA
65 AAGT-ATATACAAGCATGAACAAGTGCTTAAACGA-AAACCGGGAAGTATGCATGTTACATCAA
322458 TGGTTACAGT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
129 19 0.17
130 89 0.82
131 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (130 bp):
AAACACTATGCTACAATTTGCATCTAGCTCATATATGCCTATTATAAACTAACATATTGATTACA
AGTATATACAAGCATGAACAAGTGCTTAAACGAAAACCGGGAAGTATGCATGTTACATCAACAGC
Found at i:328607 original size:31 final size:29
Alignment explanation
Indices: 328527--328607 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
328517 GAATTTAATC
328527 AAACCAAAAATTCATATATAAAATTATACA
1 AAACC-AAAATTCATATATAAAATTATACA
** * * *
328557 AAATTAAAATTTATGTATAAAATTATATA
1 AAACCAAAATTCATATATAAAATTATACA
*
328586 TTAGACCAAAATTCATATATAA
1 --AAACCAAAATTCATATATAA
328608 TTTTGAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 21 0.54
30 3 0.08
31 15 0.38
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACCAAAATTCATATATAAAATTATACA
Found at i:330706 original size:3 final size:3
Alignment explanation
Indices: 330698--330730 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
330688 GCCTTTACAA
330698 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
330731 TCACTCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:332101 original size:200 final size:200
Alignment explanation
Indices: 331744--332141 Score: 679
Period size: 200 Copynumber: 2.0 Consensus size: 200
331734 TATTGAACAT
** *
331744 ATATTGTATTAAGAGCCAATGAGGTACGAAGTTAATCAATATTGTATTAAATTATTTGTATTTTT
1 ATATTGTATTAAGAGCCAATGAGGTACGAAGTTAATCAATATTGTATTAAATTATTTGTACCTCT
* * *
331809 AGGAATGTTCAAATTTCGATTAAAATCGAATTAATCGATCGAATCAGTCTAATTCGGTTAATCGG
66 AGGAATGTTCAAATTTCGATTAAAACCGAATTAATCGATCAAATCAGTCTAATTCGATTAATCGG
* *
331874 TCAGTTAATCGATTTAATTGAATCGGAGGTCGGTTAATAATTTTTTTGAAGTTTAGTTATCAGTT
131 TCAGTTAATCGATCTAATTGAATCGGAGGTCGGTTAATAATTTTTTAGAAGTTTAGTTATCAGTT
331939 AATCA
196 AATCA
331944 ATATTGTATTAAGAGCCAATGAGGTACGAAGTTAATCAATATTGTATTAAATTATTTGTACCTCT
1 ATATTGTATTAAGAGCCAATGAGGTACGAAGTTAATCAATATTGTATTAAATTATTTGTACCTCT
* *
332009 AGGAATGTTCAAATTTTGATTAAAACCGAATTAATCGATCAAATCGGTCTAATTCGATTAATCGG
66 AGGAATGTTCAAATTTCGATTAAAACCGAATTAATCGATCAAATCAGTCTAATTCGATTAATCGG
* * *
332074 TCAGTTAATCGATCTAATTGGATCGGAGGTCGGTTAATGATTTTTTAGAAGTTTGGTTATCAGTT
131 TCAGTTAATCGATCTAATTGAATCGGAGGTCGGTTAATAATTTTTTAGAAGTTTAGTTATCAGTT
332139 AAT
196 AAT
332142 TCGATTTGAA
Statistics
Matches: 185, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
200 185 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (200 bp):
ATATTGTATTAAGAGCCAATGAGGTACGAAGTTAATCAATATTGTATTAAATTATTTGTACCTCT
AGGAATGTTCAAATTTCGATTAAAACCGAATTAATCGATCAAATCAGTCTAATTCGATTAATCGG
TCAGTTAATCGATCTAATTGAATCGGAGGTCGGTTAATAATTTTTTAGAAGTTTAGTTATCAGTT
AATCA
Found at i:332483 original size:21 final size:22
Alignment explanation
Indices: 332443--332483 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
332433 AACATACATG
*
332443 AATATATTTTTAACAGTAAACA
1 AATATATTTTTAACAATAAACA
*
332465 AATAT-TTTTTAATAATAAA
1 AATATATTTTTAACAATAAA
332484 TAGTCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTTTTAACAATAAACA
Found at i:332978 original size:3 final size:3
Alignment explanation
Indices: 332970--333018 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
332960 GAACACAAAG
332970 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
333018 A
1 A
333019 GAAGAAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:333023 original size:3 final size:3
Alignment explanation
Indices: 333017--333052 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
333007 TAATAATAAT
333017 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
333053 GAGGTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:334085 original size:17 final size:17
Alignment explanation
Indices: 334063--334095 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
334053 TTTAAAATTA
334063 AAAACT-AAAAATAAAGT
1 AAAACTGAAAAA-AAAGT
334080 AAAACTGAAAAAAAAG
1 AAAACTGAAAAAAAAG
334096 ATAGTAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAACTGAAAAAAAAGT
Found at i:337801 original size:21 final size:21
Alignment explanation
Indices: 337776--337828 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
337766 TTATTTAAAT
337776 TTAATTATAA-AAATATAATTA
1 TTAATTATAATAAATAT-ATTA
*
337797 TTAA-TATAATTAATATATTA
1 TTAATTATAATAAATATATTA
*
337817 TATAATTTTAAT
1 T-TAATTATAAT
337829 TTTTAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTATAATAAATATATTA
Found at i:337819 original size:16 final size:16
Alignment explanation
Indices: 337791--337823 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
337781 TATAAAAATA
337791 TAATTATTAATATAAT
1 TAATTATTAATATAAT
337807 TAATATATT-ATATAAT
1 TAAT-TATTAATATAAT
337823 T
1 T
337824 TTAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTATTAATATAAT
Found at i:341515 original size:15 final size:16
Alignment explanation
Indices: 341490--341527 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
341480 TGAGGATAAA
*
341490 AAATATTTTTTGT-ATT
1 AAAT-TTTTTTATAATT
341506 AAATTTTTTTATAATT
1 AAATTTTTTTATAATT
341522 AAATTT
1 AAATTT
341528 AGGGTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
AAATTTTTTTATAATT
Found at i:341955 original size:29 final size:30
Alignment explanation
Indices: 341899--341959 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
341889 GTCGAACTTA
* * * *
341899 AAAAATATTTAATAATTTAGTGATTTAAAT
1 AAAAATATTAAATAATTTAATAACTTAAAT
341929 AAAAA-ATTAAATAATTTAATAACTTAAAT
1 AAAAATATTAAATAATTTAATAACTTAAAT
341958 AA
1 AA
341960 TTTTTCGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAAATATTAAATAATTTAATAACTTAAAT
Found at i:342509 original size:107 final size:109
Alignment explanation
Indices: 342349--342559 Score: 293
Period size: 114 Copynumber: 1.9 Consensus size: 109
342339 AATTCCAAAC
* *
342349 AAAAAATTCATTTGTAGAATCATAAAATAACTTTCAAAAATATTAGCTCAG-T-T-AATGATAAA
1 AAAAAATTCATTTGTAAAATCATAAAAAAACTTTCAAAAATATTAGCTCAGTTATAAATGATAAA
342411 TTTTAAACAATAAATAATAACTCTATTAAAATTTGGACTTATTA
66 TTTTAAACAATAAATAATAACTCTATTAAAATTTGGACTTATTA
*
342455 AAAAAATTCATTTGTAAAATCATAAAAAAAACTTTCAAAAATATTAGCTTAGTTAGCAGTAAATG
1 AAAAAATTCATTTGTAAAATCAT-AAAAAAACTTTCAAAAATATTAGCTCAGTT---A-TAAATG
* * * *
342520 ATAATTTTTAAATAATAAATACTAACTTTATTAAAATTTG
61 ATAAATTTTAAACAATAAATAATAACTCTATTAAAATTTG
342560 AATTTATTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
106 22 0.24
107 26 0.29
108 1 0.01
113 1 0.01
114 40 0.44
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (109 bp):
AAAAAATTCATTTGTAAAATCATAAAAAAACTTTCAAAAATATTAGCTCAGTTATAAATGATAAA
TTTTAAACAATAAATAATAACTCTATTAAAATTTGGACTTATTA
Done.