Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014907.1 Kokia drynarioides strain JFW-HI SEQ_129950, 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: 425439
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 158 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:461 original size:15 final size:15
Alignment explanation
Indices: 441--481 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
431 AAATTTAGAT
441 AATATTTAATTTTCA
1 AATATTTAATTTTCA
456 AATATTTAATTTTCA
1 AATATTTAATTTTCA
*
471 AATATTCAATT
1 AATATTTAATT
482 AGCTTCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTTAATTTTCA
Found at i:869 original size:1 final size:1
Alignment explanation
Indices: 863--889 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
853 AAAATTTTGA
863 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
890 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8673 original size:20 final size:20
Alignment explanation
Indices: 8648--8725 Score: 93
Period size: 20 Copynumber: 3.6 Consensus size: 20
8638 GGAAGGGGAA
8648 TTAGGGATTGGGGAAAGGAG
1 TTAGGGATTGGGGAAAGGAG
*
8668 TTAGGGATTGGGAAAGGAAAGGGGAA
1 TTAGGGATT-GG---GGAAA--GGAG
8694 TTAGGGATTGGGGAAAGGAG
1 TTAGGGATTGGGGAAAGGAG
8714 TTAGGGATTGGG
1 TTAGGGATTGGG
8726 AAGGGAAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
20 24 0.48
21 2 0.04
22 5 0.10
24 5 0.10
25 2 0.04
26 12 0.24
ACGTcount: A:0.31, C:0.00, G:0.49, T:0.21
Consensus pattern (20 bp):
TTAGGGATTGGGGAAAGGAG
Found at i:8680 original size:26 final size:26
Alignment explanation
Indices: 8651--8726 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
8641 AGGGGAATTA
8651 GGGATTGGGGAAAGGAGTTAGGGATT
1 GGGATTGGGGAAAGGAGTTAGGGATT
** *
8677 GGGA--AAGGAAA-G-G---GGAATT
1 GGGATTGGGGAAAGGAGTTAGGGATT
8696 AGGGATTGGGGAAAGGAGTTAGGGATT
1 -GGGATTGGGGAAAGGAGTTAGGGATT
8723 GGGA
1 GGGA
8727 AGGGAAAGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
22 6 0.17
23 2 0.06
24 6 0.17
26 8 0.22
27 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (26 bp):
GGGATTGGGGAAAGGAGTTAGGGATT
Found at i:8693 original size:46 final size:46
Alignment explanation
Indices: 8640--8735 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
8630 ACTTAGGGGG
8640 AAGGGGAATTAGGGATTGGGGAAAGGAGTTAGGGATTGGGAAAGGA
1 AAGGGGAATTAGGGATTGGGGAAAGGAGTTAGGGATTGGGAAAGGA
*
8686 AAGGGGAATTAGGGATTGGGGAAAGGAGTTAGGGATTGGGAAGGGA
1 AAGGGGAATTAGGGATTGGGGAAAGGAGTTAGGGATTGGGAAAGGA
8732 AAGG
1 AAGG
8736 CTGGGTTCGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.00, G:0.49, T:0.17
Consensus pattern (46 bp):
AAGGGGAATTAGGGATTGGGGAAAGGAGTTAGGGATTGGGAAAGGA
Found at i:12241 original size:31 final size:30
Alignment explanation
Indices: 12205--12289 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
12195 GATTAAATCA
*
12205 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * * * * *
12235 ACAATTAGAGTTTTACGTGTATAATTGCATC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
12266 AAATTAAAG-TTCAAGTATACAATT
1 AAATTAAAGTTTCAAGTATACAATT
12290 ACACATTAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
29 11 0.27
30 8 0.20
31 22 0.54
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:15252 original size:29 final size:29
Alignment explanation
Indices: 15220--15285 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
15210 TTAATTTGAA
15220 AAAAATGATAGTCAATAAGCTTAGATTGT
1 AAAAATGATAGTCAATAAGCTTAGATTGT
15249 AAAAATGATAGTCAATAAGCTTAGATTGT
1 AAAAATGATAGTCAATAAGCTTAGATTGT
15278 AAAAATGA
1 AAAAATGA
15286 CTAAATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (29 bp):
AAAAATGATAGTCAATAAGCTTAGATTGT
Found at i:36351 original size:2 final size:2
Alignment explanation
Indices: 36346--36373 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36336 GATCGAGTAA
36346 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
36374 CCTCGAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:44306 original size:16 final size:18
Alignment explanation
Indices: 44279--44312 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44269 TATTAAAATT
44279 TTAAATTAA-TTTCTCAA
1 TTAAATTAATTTTCTCAA
44296 TTAAA-TAATTTTCTCAA
1 TTAAATTAATTTTCTCAA
44313 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAATTTTCTCAA
Found at i:53855 original size:19 final size:19
Alignment explanation
Indices: 53840--53879 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53830 TAATAATATT
53840 AAATAATTAAAATAATAAG
1 AAATAATTAAAATAATAAG
*
53859 AAATAATTAAAA-AAAAAG
1 AAATAATTAAAATAATAAG
53877 AAA
1 AAA
53880 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATAATTAAAATAATAAG
Found at i:60371 original size:16 final size:16
Alignment explanation
Indices: 60347--60378 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60337 TATTTTTAAT
60347 TAATAAAATAAATAAA
1 TAATAAAATAAATAAA
*
60363 TAATTAAATAAATAAA
1 TAATAAAATAAATAAA
60379 ACTAAAAGTA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAAATAAATAAA
Found at i:62677 original size:18 final size:19
Alignment explanation
Indices: 62651--62694 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
62641 ATGAAATAAT
62651 TTAA-ATATAAAATATTCA
1 TTAATATATAAAATATTCA
62669 TTAATTATATAAAATATTCA
1 TTAA-TATATAAAATATTCA
62689 TTAATA
1 TTAATA
62695 AACTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 18 0.75
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATATATAAAATATTCA
Found at i:62680 original size:20 final size:20
Alignment explanation
Indices: 62655--62693 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
62645 AATAATTTAA
62655 ATATAAAATATTCATTAATT
1 ATATAAAATATTCATTAATT
62675 ATATAAAATATTCATTAAT
1 ATATAAAATATTCATTAAT
62694 AAACTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAAAATATTCATTAATT
Found at i:68671 original size:3 final size:3
Alignment explanation
Indices: 68663--68717 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
68653 AGTCAAACAA
* *
68663 AGT AGT AGT CGT AGT AGT AAT AGT AGT AGT AGT AGT AGT AGT AGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
68711 AGT AGT A
1 AGT AGT A
68718 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:85404 original size:55 final size:55
Alignment explanation
Indices: 85338--85447 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
85328 GTAGAGAAAC
*
85338 GAATTTGAAAATCTCTCGACTTTTTAGATGGAGGAGTCAGGAAAGATCTGGTCAT
1 GAATTTGAAAATCTCTCGACTTTTTAGATGGAGGAGTCAAGAAAGATCTGGTCAT
*
85393 GAATTTGAAAATCTTTCGACTTTTTAGATGGAGGAGTCAAGAAAGATCTGGTCAT
1 GAATTTGAAAATCTCTCGACTTTTTAGATGGAGGAGTCAAGAAAGATCTGGTCAT
85448 ACTCCGCTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (55 bp):
GAATTTGAAAATCTCTCGACTTTTTAGATGGAGGAGTCAAGAAAGATCTGGTCAT
Found at i:98499 original size:46 final size:46
Alignment explanation
Indices: 98431--98522 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
98421 ACGATACAAT
98431 ATTAAGAATAAGAGATTAGGGTAATACCGTTCAAACCCTTATCAAA
1 ATTAAGAATAAGAGATTAGGGTAATACCGTTCAAACCCTTATCAAA
*
98477 ATTAAGAATAAGAGATTGGGGTAATACCGTTCAAACCCTTATCAAA
1 ATTAAGAATAAGAGATTAGGGTAATACCGTTCAAACCCTTATCAAA
98523 CACGAATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.26
Consensus pattern (46 bp):
ATTAAGAATAAGAGATTAGGGTAATACCGTTCAAACCCTTATCAAA
Found at i:106131 original size:16 final size:17
Alignment explanation
Indices: 106101--106134 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
106091 ACTGGTTACC
106101 AAAAATAAGAACAAATTA
1 AAAAATAAG-ACAAATTA
106119 AAAAATAAG-CAAATTA
1 AAAAATAAGACAAATTA
106135 TACCCACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAATAAGACAAATTA
Found at i:109261 original size:27 final size:27
Alignment explanation
Indices: 109231--109297 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
109221 ATTTAAATTT
*
109231 TATTTTTATAATAAATTTTAAAAATAA
1 TATTTTTATAATAAATTTAAAAAATAA
* *
109258 TATTTTTTTTGA-AAATTTAAAAAATAA
1 TA-TTTTTATAATAAATTTAAAAAATAA
*
109285 TAATTTTA-AATAA
1 TATTTTTATAATAA
109298 CATTCTTCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 1 0.03
26 6 0.19
27 18 0.56
28 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
TATTTTTATAATAAATTTAAAAAATAA
Found at i:109840 original size:13 final size:14
Alignment explanation
Indices: 109805--109839 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
109795 AAAAAGTAAG
109805 TCATTTTTCAAAGA
1 TCATTTTTCAAAGA
109819 TCATTTTTCGAAA-A
1 TCATTTTTC-AAAGA
109833 TCATTTT
1 TCATTTT
109840 CAGTGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (14 bp):
TCATTTTTCAAAGA
Found at i:110573 original size:27 final size:28
Alignment explanation
Indices: 110518--110576 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
110508 AAATGCAATT
* *
110518 TTTTTATGCTTTGAAGTAGCATTTTTTC
1 TTTTTATGCTCTGAAGTAGCATTTGTTC
*
110546 TTTTTATGCTCTGAGGTAGCA-TTGTTC
1 TTTTTATGCTCTGAAGTAGCATTTGTTC
110573 TTTT
1 TTTT
110577 GACTTCTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (28 bp):
TTTTTATGCTCTGAAGTAGCATTTGTTC
Found at i:116061 original size:37 final size:38
Alignment explanation
Indices: 115989--116066 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 38
115979 GTTTTTTGGG
* *
115989 TTTCATTTATTTTTCTGGTGTCTGCTTTTAATGTGGGTT
1 TTTCATTTATTTTTCTGATGTCAGCTTTT-ATGTGGGTT
*
116028 TTTCATTTATTTTTCTGATTTCAG-TTGTT-TGTGGGTT
1 TTTCATTTATTTTTCTGATGTCAGCTT-TTATGTGGGTT
116065 TT
1 TT
116067 CTTGTTGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 10 0.29
38 2 0.06
39 23 0.66
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.62
Consensus pattern (38 bp):
TTTCATTTATTTTTCTGATGTCAGCTTTTATGTGGGTT
Found at i:121791 original size:17 final size:18
Alignment explanation
Indices: 121752--121793 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
121742 TTTCATTAGT
*
121752 TTTATATTTAAGATTTCGG
1 TTTA-ATTTAAGATTTCGA
*
121771 TTTAATTTAA-ATTTTGA
1 TTTAATTTAAGATTTCGA
121788 TTTAAT
1 TTTAAT
121794 GTCTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.52
18 6 0.29
19 4 0.19
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTAATTTAAGATTTCGA
Found at i:126928 original size:22 final size:23
Alignment explanation
Indices: 126902--126960 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
126892 ATATCCAAAC
126902 AATAACAACAAAATAG-TAGCAA
1 AATAACAACAAAATAGATAGCAA
* * *
126924 TATAATAGCAAAAT-GATAGCAA
1 AATAACAACAAAATAGATAGCAA
* *
126946 AACAACAACACAATA
1 AATAACAACAAAATA
126961 AAATTTAGGC
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.61, C:0.15, G:0.08, T:0.15
Consensus pattern (23 bp):
AATAACAACAAAATAGATAGCAA
Found at i:127718 original size:28 final size:28
Alignment explanation
Indices: 127686--127811 Score: 73
Period size: 29 Copynumber: 4.5 Consensus size: 28
127676 TCTCTACTTG
127686 ATTTTATAATTTTTATAATATTTT-TACA
1 ATTTTATAATTTTTATAATATTTTATA-A
* *
127714 ATTTTAT--TTTTTTTACTATTTTATAA
1 ATTTTATAATTTTTATAATATTTTATAA
** * * *
127740 AAATTATAATTTTT-TCTATATTACTATAT
1 ATTTTATAATTTTTAT-AATATT-TTATAA
* **
127769 ATTTTATAATCTTTACGAT-TTTTATAAAA
1 ATTTTATAATTTTTATAATATTTTAT--AA
*
127798 ATTTTACAATTTTT
1 ATTTTATAATTTTT
127812 TTTTATAACT
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
26 19 0.26
27 6 0.08
28 18 0.25
29 30 0.41
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTTATAATTTTTATAATATTTTATAA
Found at i:127860 original size:29 final size:29
Alignment explanation
Indices: 127828--127943 Score: 80
Period size: 28 Copynumber: 4.0 Consensus size: 29
127818 AACTTTTGTG
127828 ATTTTTATATTTTTTTCTATTTTTAGTCA
1 ATTTTTATATTTTTTTCTATTTTTAGTCA
* * *
127857 A-TTTTAAATATTTTTCTTAGTTTTTAAT-A
1 ATTTTTATATTTTTTTC-TA-TTTTTAGTCA
* * **
127886 ATTTTTTTATATTTTTCTATATTTTTA-TTG
1 A--TTTTTATATTTTTTTCTATTTTTAGTCA
*
127916 ATTTTTAT-TATTTTAT-TATTTTTAGTCA
1 ATTTTTATAT-TTTTTTCTATTTTTAGTCA
127944 CACGTTGTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
27 9 0.13
28 26 0.38
29 6 0.09
30 14 0.21
31 2 0.03
32 11 0.16
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.68
Consensus pattern (29 bp):
ATTTTTATATTTTTTTCTATTTTTAGTCA
Found at i:127881 original size:30 final size:29
Alignment explanation
Indices: 127828--127939 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 29
127818 AACTTTTGTG
* *
127828 ATTTTTATATTTTTTTC-TATTTTTAGTCA
1 ATTTTTATATATTTTTCTTATTTTTAAT-A
*
127857 A-TTTTAAATATTTTTCTTAGTTTTTAATA
1 ATTTTTATATATTTTTCTTA-TTTTTAATA
* * *
127886 ATTTTTTTATATTTTTCTATATTTTTATTG
1 ATTTTTATATATTTTTCT-TATTTTTAATA
*
127916 ATTTTTAT-TA-TTTTATTATTTTTA
1 ATTTTTATATATTTTTCTTATTTTTA
127940 GTCACACGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
27 8 0.11
28 18 0.26
29 7 0.10
30 35 0.50
31 2 0.03
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (29 bp):
ATTTTTATATATTTTTCTTATTTTTAATA
Found at i:127900 original size:19 final size:21
Alignment explanation
Indices: 127857--127900 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
127847 TTTTTAGTCA
127857 ATTTTAAATATTTTTCTTAGT
1 ATTTTAAATATTTTTCTTAGT
127878 -TTTT-AATAATTTTT-TTA-T
1 ATTTTAAAT-ATTTTTCTTAGT
127896 ATTTT
1 ATTTT
127901 TCTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.05
19 10 0.48
20 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTTTAAATATTTTTCTTAGT
Found at i:127919 original size:10 final size:9
Alignment explanation
Indices: 127828--127939 Score: 66
Period size: 10 Copynumber: 11.8 Consensus size: 9
127818 AACTTTTGTG
127828 ATTTTTA-T
1 ATTTTTATT
*
127836 ATTTTTTTCT
1 ATTTTTAT-T
*
127846 ATTTTTAGTCA
1 ATTTTTA-T-T
* *
127857 ATTTTAAAT
1 ATTTTTATT
*
127866 ATTTTTCTT
1 ATTTTTATT
*
127875 AGTTTTTAATA
1 A-TTTTT-ATT
*
127886 ATTTTTTTAT
1 ATTTTTAT-T
*
127896 ATTTTTCTAT
1 ATTTTTAT-T
127906 ATTTTTATT
1 ATTTTTATT
127915 GATTTTTATT
1 -ATTTTTATT
127925 A-TTTTATT
1 ATTTTTATT
127933 ATTTTTA
1 ATTTTTA
127940 GTCACACGTT
Statistics
Matches: 81, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
8 14 0.17
9 15 0.19
10 42 0.52
11 10 0.12
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (9 bp):
ATTTTTATT
Found at i:128671 original size:40 final size:40
Alignment explanation
Indices: 128625--128730 Score: 144
Period size: 40 Copynumber: 2.6 Consensus size: 40
128615 AAAAACCCCC
*
128625 CAAAAAGTAAATCAATAGCGGCGTTTTT-CTATAAA-TGCCG
1 CAAAAAGTAAAGCAATAGCGGCGTTTTTAC-ATAAACT-CCG
* *
128665 CAAAAAGTAAAGCAACAACGGCGTTTTTACATAAACTCCG
1 CAAAAAGTAAAGCAATAGCGGCGTTTTTACATAAACTCCG
*
128705 CAAAAAGTAAAGCAATAGCGTCGTTT
1 CAAAAAGTAAAGCAATAGCGGCGTTT
128731 GTAGGAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 56 0.97
41 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (40 bp):
CAAAAAGTAAAGCAATAGCGGCGTTTTTACATAAACTCCG
Found at i:128772 original size:42 final size:41
Alignment explanation
Indices: 128697--128944 Score: 173
Period size: 41 Copynumber: 6.0 Consensus size: 41
128687 GTTTTTACAT
* * * * * *
128697 AAACTCCGCAAAAAGT-AAAGCAATAGCGTCGTTTGTAGGAA
1 AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTAT-GGAA
* *
128738 AAACGCTGCTAAAAGTCAGAGCATTAGCGGCGTTTATGGGA
1 AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTATGGAA
* *
128779 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCATTTATGTG-A
1 AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTATG-GAA
* * * * * * *
128820 AACCGTCACTAAAGGTCAGAGCATTAGCGACATTTATATGAA
1 AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTAT-GGAA
* * * * *
128862 AGTA--CCGCTAAAGGTTACAGAATTAGCGGCGTTTATGAGAA
1 A-AACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTATG-GAA
* * * *
128903 AAA-ACCGTTAAAGGTCAGAGCATTAGCGACGTTTATGTGAA
1 AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTATG-GAA
128944 A
1 A
128945 GTGCCGCTAA
Statistics
Matches: 167, Mismatches: 33, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 147 0.88
42 19 0.11
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (41 bp):
AAACGCCGCTAAAAGTCAGAGCATTAGCGGCGTTTATGGAA
Found at i:128782 original size:41 final size:41
Alignment explanation
Indices: 128737--128970 Score: 234
Period size: 41 Copynumber: 5.7 Consensus size: 41
128727 GTTTGTAGGA
* * *
128737 AAAACGCTGCTAAAAGTCAGAGCATTAGCGGCGTTTATGGG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
*
128778 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCATTTATGTG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
* * * * * *
128819 AAACCGTCACTAAAGGTCAGAGCATTAGCGACATTTATATG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
*** * * * *
128860 AAAGTACCGCTAAAGGTTACAGAATTAGCGGCGTTTATGAG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
** * *
128901 AAAAAACCGTTAAAGGTCAGAGCATTAGCGACGTTTATGTG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
** * * *
128942 AAAGTGCCGCTAAAGATAAGAGAATTAGC
1 AAAACGCCGCTAAAGGTCAGAGCATTAGC
128971 ATGTTATACT
Statistics
Matches: 157, Mismatches: 36, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 157 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (41 bp):
AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGTG
Found at i:128845 original size:82 final size:81
Alignment explanation
Indices: 128746--128970 Score: 265
Period size: 82 Copynumber: 2.8 Consensus size: 81
128736 AAAAACGCTG
* * * ** * *
128746 CTAAAAGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAAAGGTCAGAGCATTAGCGGCA
1 CTAAAGGTCAGAGCATTAGCGACGTTTATGTGAAAGTGCCGCTAAAGGTAAGAGAATTAGCGGCA
*
128811 TTTATGTG-AAACCGT
66 TTTATGAGAAAACCGT
* * * * *
128826 CACTAAAGGTCAGAGCATTAGCGACATTTATATGAAAGTACCGCTAAAGGTTACAGAATTAGCGG
1 --CTAAAGGTCAGAGCATTAGCGACGTTTATGTGAAAGTGCCGCTAAAGGTAAGAGAATTAGCGG
*
128891 CGTTTATGAGAAAAAACCGT
64 CATTTATGAG--AAAACCGT
*
128911 -TAAAGGTCAGAGCATTAGCGACGTTTATGTGAAAGTGCCGCTAAAGATAAGAGAATTAGC
1 CTAAAGGTCAGAGCATTAGCGACGTTTATGTGAAAGTGCCGCTAAAGGTAAGAGAATTAGC
128971 ATGTTATACT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
82 114 0.94
85 7 0.06
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (81 bp):
CTAAAGGTCAGAGCATTAGCGACGTTTATGTGAAAGTGCCGCTAAAGGTAAGAGAATTAGCGGCA
TTTATGAGAAAACCGT
Found at i:142243 original size:23 final size:22
Alignment explanation
Indices: 142201--142245 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
142191 TAATATATAT
* *
142201 ATATATATATATATTAGTGTTA
1 ATATATATAAATAATAGTGTTA
142223 ATATATGATAAATAATAGTGTTA
1 ATATAT-ATAAATAATAGTGTTA
142246 TAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (22 bp):
ATATATATAAATAATAGTGTTA
Found at i:143100 original size:17 final size:17
Alignment explanation
Indices: 143078--143111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
143068 AGTTGACATG
*
143078 GAAAATGTTATTGAAAT
1 GAAAATGCTATTGAAAT
143095 GAAAATGCTATTGAAAT
1 GAAAATGCTATTGAAAT
143112 AGCGAGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (17 bp):
GAAAATGCTATTGAAAT
Found at i:152320 original size:14 final size:15
Alignment explanation
Indices: 152301--152334 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
152291 TTCCTACAAA
152301 TAATAAAC-AATATT
1 TAATAAACTAATATT
152315 TAAT-AACTAATATT
1 TAATAAACTAATATT
152329 TAATAA
1 TAATAA
152335 CTTGAGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 14 0.78
15 1 0.06
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAAACTAATATT
Found at i:152335 original size:14 final size:14
Alignment explanation
Indices: 152309--152336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
152299 AATAATAAAC
152309 AATATTTAATAACT
1 AATATTTAATAACT
152323 AATATTTAATAACT
1 AATATTTAATAACT
152337 TGAGCAGTTG
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATTTAATAACT
Found at i:172375 original size:20 final size:19
Alignment explanation
Indices: 172331--172375 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
172321 TTATGCTTTC
172331 AAAATTAAGTTTTGACATT
1 AAAATTAAGTTTTGACATT
* *
172350 AGAAATTAATTTTTGATATAT
1 A-AAATTAAGTTTTGACAT-T
172371 AAAAT
1 AAAAT
172376 ATTACTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.86
21 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (19 bp):
AAAATTAAGTTTTGACATT
Found at i:175573 original size:20 final size:20
Alignment explanation
Indices: 175548--175588 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
175538 TTCTAAATTT
175548 AATACTGAATATGATTTGCC
1 AATACTGAATATGATTTGCC
175568 AATACTGAATATGATTTGCC
1 AATACTGAATATGATTTGCC
175588 A
1 A
175589 TTTACGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
AATACTGAATATGATTTGCC
Found at i:177585 original size:28 final size:28
Alignment explanation
Indices: 177554--177615 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
177544 AAAATGAGAC
177554 TTTGGA-TACTCTAGGGCAAAAAGGTAAT
1 TTTGGACT-CTCTAGGGCAAAAAGGTAAT
* * *
177582 TTTGGACTTTCTGGGGCAAAACGGTAAT
1 TTTGGACTCTCTAGGGCAAAAAGGTAAT
177610 TTTGGA
1 TTTGGA
177616 GAAGTTCGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.32
Consensus pattern (28 bp):
TTTGGACTCTCTAGGGCAAAAAGGTAAT
Found at i:177758 original size:58 final size:58
Alignment explanation
Indices: 177605--177763 Score: 169
Period size: 58 Copynumber: 2.7 Consensus size: 58
177595 GGGCAAAACG
* * * *
177605 GTAATTTTGGAGAAGTTCGGGGTTAAAAATGGAATTTTTAGACACTCGAGGGTAAAATG
1 GTAATTTTAGA-AAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
* * * * * *
177664 GTAATTTTTAGGAAA-ATCAAGATAAAAAATGGAATTTTTGGACA-TCGGGGGTGAAATA
1 GTAA-TTTTA-GAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
*
177722 GTAATTTTAGAAAGTTTCGAGGTTAAAAATGAAATTTTTGGA
1 GTAATTTTAGAAAG-TTCGAGGTTAAAAATGGAATTTTTGGA
177764 AAAGTGTAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.05
57 5 0.06
58 37 0.46
59 27 0.33
60 6 0.07
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (58 bp):
GTAATTTTAGAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
Found at i:177827 original size:30 final size:30
Alignment explanation
Indices: 177791--177911 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
177781 AGTTTGGGGT
*
177791 AAAATGGAATTTTTTGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
* * *
177821 AAAATGGAATTTTTGGGAGTTTGAGGG-TA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
* *
177850 AAAATGTG-ATTTTTAGAAGTTTTAGGGTTT
1 AAAATG-GAATTTTTTGAAGTTTTAGGGTTA
177880 AAAATGGAATTTTTTGAAG-TTTAGGGTTA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
177909 AAA
1 AAA
177912 TATAATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
29 36 0.46
30 42 0.54
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.40
Consensus pattern (30 bp):
AAAATGGAATTTTTTGAAGTTTTAGGGTTA
Found at i:177833 original size:29 final size:31
Alignment explanation
Indices: 177791--177911 Score: 139
Period size: 29 Copynumber: 4.1 Consensus size: 31
177781 AGTTTGGGGT
*
177791 AAAATGGAATTTTTT-GAAGTTTTAGGGTCA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
* * *
177821 AAAATGGAA-TTTTTGGGAGTTTGAGGG-TA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
*
177850 AAAATGTG-A-TTTTTAGAAGTTTTAGGGTTT
1 AAAATG-GAATTTTTTAGAAGTTTTAGGGTTA
177880 AAAATGGAATTTTTT-GAAG-TTTAGGGTTA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
177909 AAA
1 AAA
177912 TATAATTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
29 41 0.53
30 32 0.41
31 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.40
Consensus pattern (31 bp):
AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
Found at i:177869 original size:59 final size:58
Alignment explanation
Indices: 177771--177934 Score: 183
Period size: 59 Copynumber: 2.8 Consensus size: 58
177761 GGAAAAGTGT
*
177771 AATTTTTAGGAGTTTG-GGGTAAAATG-GAATTTTTTGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTAGGAGTTTGAGGGTAAAATGTG-ATTTTTAGAAGTTTTAGGGTCAAAAATGG
* **
177828 AATTTTTGGGAGTTTGAGGGTAAAAATGTGATTTTTAGAAGTTTTAGGGTTTAAAATGG
1 AATTTTTAGGAGTTTGAGGGT-AAAATGTGATTTTTAGAAGTTTTAGGGTCAAAAATGG
* * * * *
177887 AATTTTTTGAAGTTT-AGGGTTAAAATATAATTTTTGGACAG-TTTAGGG
1 AATTTTTAGGAGTTTGAGGG-TAAAATGTGATTTTTAGA-AGTTTTAGGG
177935 ACCTCTAGGG
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
57 15 0.16
58 29 0.31
59 48 0.52
60 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (58 bp):
AATTTTTAGGAGTTTGAGGGTAAAATGTGATTTTTAGAAGTTTTAGGGTCAAAAATGG
Found at i:177921 original size:29 final size:28
Alignment explanation
Indices: 177770--177934 Score: 120
Period size: 29 Copynumber: 5.7 Consensus size: 28
177760 TGGAAAAGTG
* *
177770 TAATTTTTAGG-AGTTT-GGGGTAAAATG
1 TAATTTTT-GGAAGTTTAGGGTTAAAATA
* * *
177797 GAATTTTTTGAAGTTTTAGGGTCAAAA-A
1 TAATTTTTGGAAG-TTTAGGGTTAAAATA
* * *
177825 TGGAATTTTTGGGAGTTTGAGGGTAAAAATG
1 T--AATTTTTGGAAGTTT-AGGGTTAAAATA
* * *
177856 TGATTTTTAGAAGTTTTAGGGTTTAAAATG
1 TAATTTTTGGAAG-TTTAGGG-TTAAAATA
* *
177886 GAATTTTTTGAAGTTTAGGGTTAAAATA
1 TAATTTTTGGAAGTTTAGGGTTAAAATA
177914 TAATTTTTGGACAGTTTAGGG
1 TAATTTTTGGA-AGTTTAGGG
177935 ACCTCTAGGG
Statistics
Matches: 108, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.01
27 9 0.08
28 19 0.18
29 39 0.36
30 39 0.36
31 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (28 bp):
TAATTTTTGGAAGTTTAGGGTTAAAATA
Found at i:179011 original size:3 final size:3
Alignment explanation
Indices: 179003--179089 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
178993 ATATTAATGT
* ** * * * *
179003 TTA TTA TTA TTA TTG TCG TCA TTA ATA TTA TTAA TGA -TA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* ** *
179048 ATA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
179090 AAGCCTTATT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
2 1 0.02
3 62 0.95
4 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:179810 original size:6 final size:6
Alignment explanation
Indices: 179793--179830 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
179783 GTCTTAAGTC
**
179793 AATTTA AA-TTA AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
179831 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:179825 original size:18 final size:17
Alignment explanation
Indices: 179793--179830 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
179783 GTCTTAAGTC
*
179793 AATTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
179810 AATTTAAAAATAAATTTA
1 AATTT-AAAATAAATTTA
179828 AAT
1 AAT
179831 CAATTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:179850 original size:39 final size:40
Alignment explanation
Indices: 179770--179850 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
179760 TTGGGCTTTT
* * * * *
179770 AATTTAAAATTAAGTCTTAAGTCAATTTAAATTAAATTTA
1 AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
*
179810 AATTTAAAAATAAAT-TTAAATCAATTTAAACTCAACTTA
1 AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
179849 AA
1 AA
179851 ATAAAAGGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
Found at i:183849 original size:20 final size:20
Alignment explanation
Indices: 183824--183864 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
183814 TTCTAAATTT
183824 AATACTGAATATGATTTGCC
1 AATACTGAATATGATTTGCC
183844 AATACTGAATATGATTTGCC
1 AATACTGAATATGATTTGCC
183864 A
1 A
183865 TTTACGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
AATACTGAATATGATTTGCC
Found at i:185861 original size:28 final size:28
Alignment explanation
Indices: 185830--185891 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
185820 AAAATGAGAC
185830 TTTGGA-TACTCTAGGGCAAAAAGGTAAT
1 TTTGGACT-CTCTAGGGCAAAAAGGTAAT
* * *
185858 TTTGGACTTTCTGGGGCAAAACGGTAAT
1 TTTGGACTCTCTAGGGCAAAAAGGTAAT
185886 TTTGGA
1 TTTGGA
185892 GAAGTTCGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.32
Consensus pattern (28 bp):
TTTGGACTCTCTAGGGCAAAAAGGTAAT
Found at i:186034 original size:58 final size:58
Alignment explanation
Indices: 185881--186039 Score: 169
Period size: 58 Copynumber: 2.7 Consensus size: 58
185871 GGGCAAAACG
* * * *
185881 GTAATTTTGGAGAAGTTCGGGGTTAAAAATGGAATTTTTAGACACTCGAGGGTAAAATG
1 GTAATTTTAGA-AAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
* * * * * *
185940 GTAATTTTTAGGAAA-ATCAAGATAAAAAATGGAATTTTTGGACA-TCGGGGGTGAAATA
1 GTAA-TTTTA-GAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
*
185998 GTAATTTTAGAAAGTTTCGAGGTTAAAAATGAAATTTTTGGA
1 GTAATTTTAGAAAG-TTCGAGGTTAAAAATGGAATTTTTGGA
186040 AAAGTGTAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.05
57 5 0.06
58 37 0.46
59 27 0.33
60 6 0.07
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (58 bp):
GTAATTTTAGAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCGAGGGTAAAATA
Found at i:186103 original size:30 final size:30
Alignment explanation
Indices: 186067--186187 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
186057 AGTTTGGGGT
*
186067 AAAATGGAATTTTTTGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
* * *
186097 AAAATGGAATTTTTGGGAGTTTGAGGG-TA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
* *
186126 AAAATGTG-ATTTTTAGAAGTTTTAGGGTTT
1 AAAATG-GAATTTTTTGAAGTTTTAGGGTTA
186156 AAAATGGAATTTTTTGAAG-TTTAGGGTTA
1 AAAATGGAATTTTTTGAAGTTTTAGGGTTA
186185 AAA
1 AAA
186188 TATAATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
29 36 0.46
30 42 0.54
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.40
Consensus pattern (30 bp):
AAAATGGAATTTTTTGAAGTTTTAGGGTTA
Found at i:186109 original size:29 final size:31
Alignment explanation
Indices: 186067--186187 Score: 139
Period size: 29 Copynumber: 4.1 Consensus size: 31
186057 AGTTTGGGGT
*
186067 AAAATGGAATTTTTT-GAAGTTTTAGGGTCA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
* * *
186097 AAAATGGAA-TTTTTGGGAGTTTGAGGG-TA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
*
186126 AAAATGTG-A-TTTTTAGAAGTTTTAGGGTTT
1 AAAATG-GAATTTTTTAGAAGTTTTAGGGTTA
186156 AAAATGGAATTTTTT-GAAG-TTTAGGGTTA
1 AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
186185 AAA
1 AAA
186188 TATAATTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
29 41 0.53
30 32 0.41
31 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.40
Consensus pattern (31 bp):
AAAATGGAATTTTTTAGAAGTTTTAGGGTTA
Found at i:186145 original size:59 final size:58
Alignment explanation
Indices: 186047--186210 Score: 183
Period size: 59 Copynumber: 2.8 Consensus size: 58
186037 GGAAAAGTGT
*
186047 AATTTTTAGGAGTTTG-GGGTAAAATG-GAATTTTTTGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTAGGAGTTTGAGGGTAAAATGTG-ATTTTTAGAAGTTTTAGGGTCAAAAATGG
* **
186104 AATTTTTGGGAGTTTGAGGGTAAAAATGTGATTTTTAGAAGTTTTAGGGTTTAAAATGG
1 AATTTTTAGGAGTTTGAGGGT-AAAATGTGATTTTTAGAAGTTTTAGGGTCAAAAATGG
* * * * *
186163 AATTTTTTGAAGTTT-AGGGTTAAAATATAATTTTTGGACAG-TTTAGGG
1 AATTTTTAGGAGTTTGAGGG-TAAAATGTGATTTTTAGA-AGTTTTAGGG
186211 ACCTCTAGGG
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
57 15 0.16
58 29 0.31
59 48 0.52
60 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (58 bp):
AATTTTTAGGAGTTTGAGGGTAAAATGTGATTTTTAGAAGTTTTAGGGTCAAAAATGG
Found at i:186197 original size:29 final size:28
Alignment explanation
Indices: 186046--186210 Score: 120
Period size: 29 Copynumber: 5.7 Consensus size: 28
186036 TGGAAAAGTG
* *
186046 TAATTTTTAGG-AGTTT-GGGGTAAAATG
1 TAATTTTT-GGAAGTTTAGGGTTAAAATA
* * *
186073 GAATTTTTTGAAGTTTTAGGGTCAAAA-A
1 TAATTTTTGGAAG-TTTAGGGTTAAAATA
* * *
186101 TGGAATTTTTGGGAGTTTGAGGGTAAAAATG
1 T--AATTTTTGGAAGTTT-AGGGTTAAAATA
* * *
186132 TGATTTTTAGAAGTTTTAGGGTTTAAAATG
1 TAATTTTTGGAAG-TTTAGGG-TTAAAATA
* *
186162 GAATTTTTTGAAGTTTAGGGTTAAAATA
1 TAATTTTTGGAAGTTTAGGGTTAAAATA
186190 TAATTTTTGGACAGTTTAGGG
1 TAATTTTTGGA-AGTTTAGGG
186211 ACCTCTAGGG
Statistics
Matches: 108, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.01
27 9 0.08
28 19 0.18
29 39 0.36
30 39 0.36
31 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.41
Consensus pattern (28 bp):
TAATTTTTGGAAGTTTAGGGTTAAAATA
Found at i:187287 original size:3 final size:3
Alignment explanation
Indices: 187279--187365 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
187269 ATATTAATGT
* ** * * * *
187279 TTA TTA TTA TTA TTG TCG TCA TTA ATA TTA TTAA TGA -TA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* ** *
187324 ATA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
187366 AAGCCTTATT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
2 1 0.02
3 62 0.95
4 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:188086 original size:6 final size:6
Alignment explanation
Indices: 188069--188106 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
188059 GTCTTAAGTC
**
188069 AATTTA AA-TTA AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
188107 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:188101 original size:18 final size:17
Alignment explanation
Indices: 188069--188106 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
188059 GTCTTAAGTC
*
188069 AATTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
188086 AATTTAAAAATAAATTTA
1 AATTT-AAAATAAATTTA
188104 AAT
1 AAT
188107 CAATTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:188126 original size:39 final size:40
Alignment explanation
Indices: 188046--188126 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
188036 TTGGGCTTTT
* * * * *
188046 AATTTAAAATTAAGTCTTAAGTCAATTTAAATTAAATTTA
1 AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
*
188086 AATTTAAAAATAAAT-TTAAATCAATTTAAACTCAACTTA
1 AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
188125 AA
1 AA
188127 ATAAAAGGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
AATTTAAAAATAAATCTTAAATCAATTTAAACTAAACTTA
Found at i:193651 original size:27 final size:27
Alignment explanation
Indices: 193621--193675 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
193611 ATATATTATG
*
193621 GATCCGAAACAAAGTTCTATAACTTAA
1 GATCCAAAACAAAGTTCTATAACTTAA
*
193648 GATCCAAAACAAAGTTCTATAATTTAA
1 GATCCAAAACAAAGTTCTATAACTTAA
193675 G
1 G
193676 TTATGATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (27 bp):
GATCCAAAACAAAGTTCTATAACTTAA
Found at i:206152 original size:48 final size:48
Alignment explanation
Indices: 206068--206164 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
206058 GATGGGCTCA
* * *
206068 CAAGATTTGACTCCATAAACAGTAGCAAGGATTTTGGCAGCGGGTTTT
1 CAAGATTTGACTCCATAAACAGTAGCAAAGACTTTGGCAGCGGATTTT
*
206116 CAAGGTTTGACTCCATAAACAGTAGCAAAGACTTTGGCAGCGGATTTT
1 CAAGATTTGACTCCATAAACAGTAGCAAAGACTTTGGCAGCGGATTTT
206164 C
1 C
206165 CCCACAACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (48 bp):
CAAGATTTGACTCCATAAACAGTAGCAAAGACTTTGGCAGCGGATTTT
Found at i:206955 original size:2 final size:2
Alignment explanation
Indices: 206950--206979 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
206940 AAAAAAAAAA
206950 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
206980 TTCTTATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:227943 original size:50 final size:50
Alignment explanation
Indices: 227857--227952 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
227847 TGTTTAATTT
* *
227857 AGACTTCTTTCTGTAACTTGAAACCAAATTTTGCTCTATGGACCATATTG
1 AGACTTCTTTCCGTAACTTGAAACCAAATTTCGCTCTATGGACCATATTG
* *
227907 AGACTTGTTTCCGTAACTTGAAA-CAAAGTTTCGCTCTTTGGACCAT
1 AGACTTCTTTCCGTAACTTGAAACCAAA-TTTCGCTCTATGGACCAT
227953 GTCTTTGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 4 0.10
50 37 0.90
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
AGACTTCTTTCCGTAACTTGAAACCAAATTTCGCTCTATGGACCATATTG
Found at i:233288 original size:2 final size:2
Alignment explanation
Indices: 233281--233320 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
233271 CTTTGCCTTC
233281 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
233321 TCTTTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238853 original size:53 final size:53
Alignment explanation
Indices: 238790--238898 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
238780 AAAATCCCAT
*
238790 TCGCTCCATCAGTAATTGGATAAATGATCACATCACCCGATCGTAAGCTTTAC
1 TCGCTCCATCAGTAATTGGATAAATGATCACACCACCCGATCGTAAGCTTTAC
* * *
238843 TCGCTTCATCATTAATTGGATAAATGATCACACCACCCGATCGTAATCTTTAC
1 TCGCTCCATCAGTAATTGGATAAATGATCACACCACCCGATCGTAAGCTTTAC
238896 TCG
1 TCG
238899 TATTCACCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (53 bp):
TCGCTCCATCAGTAATTGGATAAATGATCACACCACCCGATCGTAAGCTTTAC
Found at i:242878 original size:21 final size:20
Alignment explanation
Indices: 242854--242899 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
242844 TAAAGACTTA
* *
242854 AATGAAGTATTATGTGATAGT
1 AATGAAGTATAAAGTGATA-T
*
242875 AATGAAGTGTAAAGTGATAT
1 AATGAAGTATAAAGTGATAT
242895 AATGA
1 AATGA
242900 TTATTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
AATGAAGTATAAAGTGATAT
Found at i:244493 original size:52 final size:52
Alignment explanation
Indices: 244415--244520 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
244405 TTATATGAAC
244415 CTAGTTTTCCCGAGCTCAATAGCTAGCTTTTGGAGTGTGATTCTTCAAAGGA
1 CTAGTTTTCCCGAGCTCAATAGCTAGCTTTTGGAGTGTGATTCTTCAAAGGA
244467 CTAGTTTTCCCGAGCTCAATAGCTAGCTTTTGGAGTGTGATTCTTCAAAGGA
1 CTAGTTTTCCCGAGCTCAATAGCTAGCTTTTGGAGTGTGATTCTTCAAAGGA
244519 CT
1 CT
244521 CTATCAATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (52 bp):
CTAGTTTTCCCGAGCTCAATAGCTAGCTTTTGGAGTGTGATTCTTCAAAGGA
Found at i:245459 original size:18 final size:18
Alignment explanation
Indices: 245427--245464 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
245417 AAACGAATTT
*
245427 AATTAAAGGATAAA-TGA
1 AATTAAAGAATAAATTGA
245444 AATTAAAGTAATAAATTGA
1 AATTAAAG-AATAAATTGA
245463 AA
1 AA
245465 AGTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (18 bp):
AATTAAAGAATAAATTGA
Found at i:246115 original size:16 final size:16
Alignment explanation
Indices: 246096--246126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
246086 TATTTTTTAA
*
246096 AAAAATTTAAAATTTC
1 AAAAATATAAAATTTC
246112 AAAAATATAAAATTT
1 AAAAATATAAAATTT
246127 ATTAAATTTA
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:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATATAAAATTTC
Found at i:263679 original size:6 final size:6
Alignment explanation
Indices: 263668--263693 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
263658 CTTCATACTA
263668 ATGATT ATGATT ATGATT ATGATT AT
1 ATGATT ATGATT ATGATT ATGATT AT
263694 AACCTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATGATT
Found at i:275435 original size:18 final size:19
Alignment explanation
Indices: 275414--275451 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
275404 AATTTTCATT
275414 ATTTATAAAA-ATAT-TCAA
1 ATTTA-AAAATATATATCAA
275432 ATTTAAAAATATATATCAA
1 ATTTAAAAATATATATCAA
275451 A
1 A
275452 ATAAATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAATATATATCAA
Found at i:275740 original size:54 final size:55
Alignment explanation
Indices: 275629--275742 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 55
275619 TGAAAATTTG
* *
275629 AAAAAAATTTGGTGTTGGCCATGTAATGGTCGACACCCCCTTTTTTATCTGACAA
1 AAAAAAATTTGGTGTTGGCCATGTAATGGTCAACACCCCCTTTTTAATCTGACAA
* * * *
275684 AAAAAAATTTGGTGTTGGCTAT-TGCATGGTCAACACTCCC-TTTTAATCTGATAA
1 AAAAAAATTTGGTGTTGGCCATGT-AATGGTCAACACCCCCTTTTTAATCTGACAA
275738 AAAAA
1 AAAAA
275743 TCAAATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 18 0.35
55 34 0.65
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (55 bp):
AAAAAAATTTGGTGTTGGCCATGTAATGGTCAACACCCCCTTTTTAATCTGACAA
Found at i:275773 original size:60 final size:59
Alignment explanation
Indices: 275636--276176 Score: 260
Period size: 60 Copynumber: 9.1 Consensus size: 59
275626 TTGAAAAAAA
* * * * *
275636 TTTGGTGTTGGCCATGTAATGGTCGACACCCCCTTTTTTATCTGA-CAAAAAA--AAA---
1 TTTGGTGTTAGTCATGCAATGGTCGACACTCCC--TTTTATCTGATAAAAAAATCAAATTT
* *
275691 TTTGGTGTT-GGCTATTGC-ATGGTCAACACTCCCTTTTAATCTGATAAAAAAATCAAATTT
1 TTTGGTGTTAGTC-A-TGCAATGGTCGACACTCCCTTTT-ATCTGATAAAAAAATCAAATTT
* * * ** * *
275751 TTTGGTGTTCGTCATGCAATGGTCGACACTTCCTTTTTGTCAAATAAAAAATTCAATTTT
1 TTTGGTGTTAGTCATGCAATGGTCGACAC-TCCCTTTTATCTGATAAAAAAATCAAATTT
* * * * *
275811 TTTTGTGTTGGCCATGCAATGGCCGACA-TCCCTATTTATATGATAAAAAAAATCAAATTT
1 TTTGGTGTTAGTCATGCAATGGTCGACACTCCCT-TTTATCTGAT-AAAAAAATCAAATTT
* * * * * *
275871 TTGGGTATTAGTCATGCAATGGTCAACACCCCCTTTT-TCCAGATAAAAAAATTTTAAAATTT
1 TTTGGTGTTAGTCATGCAATGGTCGACACTCCCTTTTAT-CTGATAAAAAAA---TCAAATTT
* *
275933 TTTTGTGTTAGCCATTGC-ATGGTCGACAC-CCCTTTTTATCTGA-ATAAAAAATCAAATTT
1 TTTGGTGTTAGTCA-TGCAATGGTCGACACTCCC-TTTTATCTGATA-AAAAAATCAAATTT
* * * * * * * * *
275992 TTGGGTGTTGGTCATGTC-ATGGCCGATA-TCCCCATATTGTCAGATAAAAAATTCGAATTT
1 TTTGGTGTTAGTCATG-CAATGGTCGACACT-CCC-TTTTATCTGATAAAAAAATCAAATTT
* * * * ** *
276052 TTTTGTGTT-GATCATGTC-ATGGCCTATAAC-CTTTTTTATCTGAT-AAAAAAT-TAATTT
1 TTTGGTGTTAG-TCATG-CAATGGTCGA-CACTCCCTTTTATCTGATAAAAAAATCAAATTT
* * * * * * ** *
276109 TTTTGTATTTGTCATGCAATGGCCGACAC-CCTTTTTTTTCAAATAAAAAATTCAAATTTT
1 TTTGGTGTTAGTCATGCAATGGTCGACACTCC-CTTTTATCTGATAAAAAAATCAAA-TTT
276169 TTTGGTGT
1 TTTGGTGT
276177 CGACCATTCC
Statistics
Matches: 374, Mismatches: 76, Indels: 67
0.72 0.15 0.13
Matches are distributed among these distances:
53 4 0.01
54 8 0.02
55 29 0.08
56 6 0.02
57 37 0.10
58 19 0.05
59 54 0.14
60 154 0.41
61 19 0.05
62 40 0.11
63 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (59 bp):
TTTGGTGTTAGTCATGCAATGGTCGACACTCCCTTTTATCTGATAAAAAAATCAAATTT
Found at i:275857 original size:59 final size:59
Alignment explanation
Indices: 275720--276172 Score: 289
Period size: 60 Copynumber: 7.6 Consensus size: 59
275710 TGGTCAACAC
* * * * * *
275720 TCCCTTTTAATCTGATAAAAAAATCAAATTTTTTGGTGTTCGTCATGCAATGGTCGACA
1 TCCCTTTTTATATGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA
* * * * *
275779 CTTCCTTTTTGTCA-AATAAAAAATTCAATTTTTTTTGTGTTGGCCATGCAATGGCCGACA
1 -TCCCTTTTTAT-ATGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA
* * ** * * * *
275839 TCCCTATTTATATGATAAAAAAAATCAAATTTTTGGGTATTAGTCATGCAATGGTCAACA
1 TCCCTTTTTATATGAT-AAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA
* ** * * * *
275899 CCCCCTTTTTCCA-GATAAAAAAATTTTAAAATTTTTTTGTGTTAGCCATTGC-ATGGTCGACA
1 -TCCCTTTTTATATGAT-AAAAAA--TTCAAATTTTTTTGTGTTGGTCA-TGCAATGGCCGACA
* * ** *
275961 CCCCTTTTTATCTGAATAAAAAA-TCAAATTTTTGGGTGTTGGTCATGTC-ATGGCCGATA
1 TCCCTTTTTATATG-ATAAAAAATTCAAATTTTTTTGTGTTGGTCATG-CAATGGCCGACA
* * * * * * *
276020 TCCCCATATTGTCA-GATAAAAAATTCGAATTTTTTTGTGTTGATCATGTC-ATGGCCTATA
1 T-CCCTTTTTAT-ATGATAAAAAATTCAAATTTTTTTGTGTTGGTCATG-CAATGGCCGACA
* * * * *
276080 ACCTTTTTTATCTGATAAAAAATT--AATTTTTTTGTATTTGTCATGCAATGGCCGACA
1 TCCCTTTTTATATGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA
* *
276137 -CCCTTTTT-TTTCAAATAAAAAATTCAAATTTTTTTG
1 TCCCTTTTTATAT--GATAAAAAATTCAAATTTTTTTG
276173 GTGTCGACCA
Statistics
Matches: 305, Mismatches: 69, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
55 2 0.01
56 8 0.03
57 36 0.12
58 3 0.01
59 71 0.23
60 130 0.43
61 17 0.06
62 33 0.11
63 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (59 bp):
TCCCTTTTTATATGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA
Found at i:276036 original size:122 final size:118
Alignment explanation
Indices: 275695--276172 Score: 380
Period size: 120 Copynumber: 4.0 Consensus size: 118
275685 AAAAAATTTG
* * * *
275695 GTGTTGGCTATTGCATGGTCAACACTCCCTTTTAATCTG-ATAAAAAAATCAAATTTTTTGGTGT
1 GTGTTGGCCATTGCATGGTCGACAC-CCCTTTTTATCTGAAT-AAAAAATCAAATTTTTGGGTGT
* ** * * *
275759 TCGTCATGCAATGGTCGACACTTCCTTTTTGTCAAAT-AAAAAATTCAATTTTTTTT
64 TAGTCATGCAATGGTCGACAC--CCCATTTGTCAGATAAAAAAATTAAAATTTTTTT
* * * * * *
275815 GTGTTGGCCA-TGCAATGGCCGACATCCCTATTTATATGATAAAAAAAATCAAATTTTTGGGTAT
1 GTGTTGGCCATTGC-ATGGTCGACACCCCTTTTTATCTGA-ATAAAAAATCAAATTTTTGGGTGT
* * *
275879 TAGTCATGCAATGGTCAACACCCCCTTTTTCCAGATAAAAAAATTTTAAAATTTTTTT
64 TAGTCATGCAATGGTCGACACCCCATTTGT-CAGATAAAAAAA--TTAAAATTTTTTT
* *
275937 GTGTTAGCCATTGCATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGGGTGTTG
1 GTGTTGGCCATTGCATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGGGTGTTA
* * **
276002 GTCATGTC-ATGGCCGATATCCCCATATTGTCAGAT-AAAAAATTCGAATTTTTTT
66 GTCATG-CAATGGTCGACA-CCCCAT-TTGTCAGATAAAAAAATTAAAATTTTTTT
** * * * * * * ** *
276056 GTGTTGATCA-TGTCATGGCCTATAACCTTTTTTATCTG-ATAAAAAAT-TAATTTTTTTGTATT
1 GTGTTGGCCATTG-CATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGGGTGTT
* * ** * * *
276118 TGTCATGCAATGGCCGACACCCTTTTTTTTCAAAT-AAAAAATTCAAATTTTTTT
65 AGTCATGCAATGGTCGACACCC-CATTTGTCAGATAAAAAAATTAAAATTTTTTT
276172 G
1 G
276173 GTGTCGACCA
Statistics
Matches: 292, Mismatches: 52, Indels: 32
0.78 0.14 0.09
Matches are distributed among these distances:
116 30 0.10
117 27 0.09
118 17 0.06
119 55 0.19
120 62 0.21
121 43 0.15
122 52 0.18
123 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (118 bp):
GTGTTGGCCATTGCATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGGGTGTTA
GTCATGCAATGGTCGACACCCCATTTGTCAGATAAAAAAATTAAAATTTTTTT
Found at i:276098 original size:241 final size:239
Alignment explanation
Indices: 275695--276158 Score: 544
Period size: 241 Copynumber: 1.9 Consensus size: 239
275685 AAAAAATTTG
* * *
275695 GTGTTGGCTATTGCATGGTCAACACTCCCTTTTAATCTGATAAAAAAATCAAATTTTTTGGTGTT
1 GTGTTAGCCATTGCATGGTCAACACTCCCTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTT
* * * * *
275760 CGTCATGCAATGGTCGACACTTCCTTTTTGTCAAATAAAAAATTCAATTTTTTTTGTGTTGGCCA
66 CGTCATGCAATGGCCGACACTCCCATATTGTCAAATAAAAAATTCAATTTTTTTTGTGTTGACCA
*
275825 TGCAATGGCCGACATCCCTATTTATATGATAAAAAAAATCAAATTTTTGGGTATTAGTCATGCAA
131 TGCAATGGCCGACAACCCTATTTATATGAT--AAAAAAT-AAATTTTTGGGTATTAGTCATGCAA
* *
275890 TGGTCAACACCCCCTTTTTCCAGATAAAAAAATTTTAAAATTTTTTT
193 TGGCCAACACCCCCTTTTTCCAAATAAAAAAATTTTAAAATTTTTTT
* *
275937 GTGTTAGCCATTGCATGGTCGACAC-CCCTTTTTATCTGA-ATAAAAAATCAAATTTTTGGGTGT
1 GTGTTAGCCATTGCATGGTCAACACTCCCTTTTAATCTGATA-AAAAAATCAAATTTTTGGGTGT
* * *
276000 TGGTCATGTC-ATGGCCGATA-TCCCCATATTGTCAGATAAAAAATTCGAA-TTTTTTTGTGTTG
65 TCGTCATG-CAATGGCCGACACT-CCCATATTGTCAAATAAAAAATTC-AATTTTTTTTGTGTTG
* * * * * * * ** *
276062 ATCATGTC-ATGGCCTATAACCTTTTTTATCTGATAAAAAATTAATTTTTTTGTATTTGTCATGC
127 ACCATG-CAATGGCCGACAACCCTATTTATATGATAAAAAATAAATTTTTGGGTATTAGTCATGC
* ** *
276126 AATGGCCGACACCCTTTTTTTTCAAATAAAAAA
191 AATGGCCAACACCCCCTTTTTCCAAATAAAAAA
276159 TTCAAATTTT
Statistics
Matches: 187, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
238 46 0.25
239 7 0.04
240 2 0.01
241 106 0.57
242 26 0.14
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (239 bp):
GTGTTAGCCATTGCATGGTCAACACTCCCTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTT
CGTCATGCAATGGCCGACACTCCCATATTGTCAAATAAAAAATTCAATTTTTTTTGTGTTGACCA
TGCAATGGCCGACAACCCTATTTATATGATAAAAAATAAATTTTTGGGTATTAGTCATGCAATGG
CCAACACCCCCTTTTTCCAAATAAAAAAATTTTAAAATTTTTTT
Found at i:276109 original size:57 final size:57
Alignment explanation
Indices: 275928--276172 Score: 201
Period size: 59 Copynumber: 4.2 Consensus size: 57
275918 AAAATTTTAA
* * * * *
275928 AATTTTTTTGTGTTAGCCAT-TGCATGGTCGACACCCCTTTTTATCTGAATAAAAAA-TC
1 AATTTTTTTGTGTT-GTCATGT-CATGGCCGATACCCTTTTTTATCAG-ATAAAAAATTC
** ** * *
275986 AAATTTTTGGGTGTTGGTCATGTCATGGCCGATATCCCCATATTGTCAGATAAAAAATTC
1 -AATTTTTTTGTGTT-GTCATGTCATGGCCGATA-CCCTTTTTTATCAGATAAAAAATTC
* * *
276046 GAATTTTTTTGTGTTGATCATGTCATGGCCTATAACCTTTTTTATCTGATAAAAAATT-
1 -AATTTTTTTGTGTTG-TCATGTCATGGCCGATACCCTTTTTTATCAGATAAAAAATTC
* * * *
276104 AATTTTTTTGTATTTGTCATG-CAATGGCCGACACCCTTTTTTTTCAAATAAAAAATTC
1 AATTTTTTTGT-GTTGTCATGTC-ATGGCCGATACCCTTTTTTATCAGATAAAAAATTC
276162 AAATTTTTTTG
1 -AATTTTTTTG
276173 GTGTCGACCA
Statistics
Matches: 151, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.01
57 44 0.29
58 3 0.02
59 62 0.41
60 41 0.27
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (57 bp):
AATTTTTTTGTGTTGTCATGTCATGGCCGATACCCTTTTTTATCAGATAAAAAATTC
Found at i:277051 original size:30 final size:29
Alignment explanation
Indices: 277016--277126 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 29
277006 AAAAAATAAT
*
277016 AATTAGAAATGAAATTTAAAAGACAAACGA
1 AATTAGAAATGAAATTTAAAATA-AAACGA
* * * * *
277046 AATTAGAAATTAAAATAAAAATATACAGGA
1 AATTAGAAATGAAATTTAAAATA-AAACGA
* *
277076 AATTAAAAATTAAATTTAAAATAAAATCGA
1 AATTAGAAATGAAATTTAAAATAAAA-CGA
*
277106 AATTACAAATTG-AATTTAAAA
1 AATTAGAAA-TGAAATTTAAAA
277127 AGTTAAAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
29 2 0.03
30 62 0.95
31 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (29 bp):
AATTAGAAATGAAATTTAAAATAAAACGA
Found at i:278279 original size:21 final size:21
Alignment explanation
Indices: 278228--278281 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
278218 TTTTTTTGTA
*
278228 AAAAAAATATTTCTAAAATGT
1 AAAAAAATATTTCAAAAATGT
*****
278249 ATTTTTATATTTCAAAAATGT
1 AAAAAAATATTTCAAAAATGT
278270 AAAAAAATATTT
1 AAAAAAATATTT
278282 GTAAAAAATA
Statistics
Matches: 22, Mismatches: 11, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAAAAATATTTCAAAAATGT
Found at i:278340 original size:20 final size:20
Alignment explanation
Indices: 278315--278404 Score: 85
Period size: 20 Copynumber: 5.0 Consensus size: 20
278305 TTTTTAAAAA
278315 TTCGAAAATATAAAAAATAT
1 TTCGAAAATATAAAAAATAT
*
278335 TTCGAAAATAGAAAAAATA-
1 TTCGAAAATATAAAAAATAT
278354 -T------TAT-AAAAA-A-
1 TTCGAAAATATAAAAAATAT
278364 TTCGAAAATATAAAAAATAT
1 TTCGAAAATATAAAAAATAT
*
278384 TTCGAAAATAAAAAAAATAT
1 TTCGAAAATATAAAAAATAT
278404 T
1 T
278405 ATAAAAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
10 1 0.02
11 6 0.11
12 2 0.04
17 3 0.05
18 6 0.11
19 1 0.02
20 38 0.67
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (20 bp):
TTCGAAAATATAAAAAATAT
Found at i:278365 original size:49 final size:49
Alignment explanation
Indices: 278310--278424 Score: 221
Period size: 49 Copynumber: 2.3 Consensus size: 49
278300 TTATTTTTTT
*
278310 AAAAATTCGAAAATATAAAAAATATTTCGAAAATAGAAAAAATATTATA
1 AAAAATTCGAAAATATAAAAAATATTTCGAAAATAAAAAAAATATTATA
278359 AAAAATTCGAAAATATAAAAAATATTTCGAAAATAAAAAAAATATTATA
1 AAAAATTCGAAAATATAAAAAATATTTCGAAAATAAAAAAAATATTATA
278408 AAAAATTCGAAAATATA
1 AAAAATTCGAAAATATA
278425 TCTTACATCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.26
Consensus pattern (49 bp):
AAAAATTCGAAAATATAAAAAATATTTCGAAAATAAAAAAAATATTATA
Found at i:278384 original size:29 final size:30
Alignment explanation
Indices: 278319--278384 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
278309 TAAAAATTCG
278319 AAAATA-TAAAAAATATTTCGAAAATAGAA
1 AAAATATTAAAAAATATTTCGAAAATAGAA
*
278348 AAAATATTATAAAAA-A-TTCGAAAATATAA
1 AAAATATTA-AAAAATATTTCGAAAATAGAA
278377 AAAATATT
1 AAAATATT
278385 TCGAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 26 0.76
30 3 0.09
31 5 0.15
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAATATTAAAAAATATTTCGAAAATAGAA
Found at i:279737 original size:45 final size:45
Alignment explanation
Indices: 279677--279820 Score: 112
Period size: 45 Copynumber: 3.4 Consensus size: 45
279667 TTAAATATTT
*
279677 AAAATTAGTAAATAATGTATTGTCAAATTAACACATTATTTGATA
1 AAAATTAGTAAATAATGTATTGTCAAATTAACAAATTATTTGATA
* * *
279722 AAAATT-GTAATATAATAATAATT-T----TTATCAAAATA-TT--T-
1 AAAATTAGTAA-ATAAT-GT-ATTGTCAAATTAACAAATTATTTGATA
* * *
279760 AAATTTAGTAAATAATGTATTGTCAAATCAACATATTATTTGATA
1 AAAATTAGTAAATAATGTATTGTCAAATTAACAAATTATTTGATA
279805 AAAATT-GTAATATAAT
1 AAAATTAGTAA-ATAAT
279821 AATAATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
36 3 0.04
37 2 0.03
38 10 0.14
39 5 0.07
41 9 0.12
42 10 0.14
44 9 0.12
45 21 0.28
46 2 0.03
47 3 0.04
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (45 bp):
AAAATTAGTAAATAATGTATTGTCAAATTAACAAATTATTTGATA
Found at i:279779 original size:83 final size:83
Alignment explanation
Indices: 279630--280009 Score: 537
Period size: 83 Copynumber: 4.5 Consensus size: 83
279620 TAAATTTAAA
*
279630 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTTAAATTTAGTAAATAATGT
279695 ATTGTCAAATTAACACATT
65 ATTGTCAAATTAACACATT
**
279714 ATTTGATAAAAATTGTAATATAATAATAATTTTTATCAAAATATTTAAATTTAGTAAATAATGTA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* *
279779 TTGTCAAATCAACATATT
66 TTGTCAAATTAACACATT
*
279797 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATAATTAAATTTAGTAAATAATGTA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
*
279862 TTGTCAAATTAACACACT
66 TTGTCAAATTAACACATT
* * ** *
279880 ATTTAATAAAAATTGTAATATAATAATAATTTGTAATTTAAATATGAAAATTT-GATATATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTT-TTATTTAAATATTTAAATTTAG-TAAATAATG
* * *
279944 TATTGTCAAATGAATACAAT
64 TATTGTCAAATTAACACATT
* **
279964 ATTTGATATAAATTAAAATATAATAATAATCTTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAA---TTTTTATTTAAATA
280010 ATGTTAACTT
Statistics
Matches: 266, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
83 158 0.59
84 95 0.36
86 10 0.04
87 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (83 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
TTGTCAAATTAACACATT
Found at i:279905 original size:17 final size:18
Alignment explanation
Indices: 279883--279916 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
279873 ACACACTATT
279883 TAATAA-AAATTGTAATA
1 TAATAATAAATTGTAATA
*
279900 TAATAATAATTTGTAAT
1 TAATAATAAATTGTAAT
279917 TTAAATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
TAATAATAAATTGTAATA
Found at i:279948 original size:167 final size:167
Alignment explanation
Indices: 279630--280011 Score: 561
Period size: 167 Copynumber: 2.3 Consensus size: 167
279620 TAAATTTAAA
*
279630 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAATTAAAATTAGTAAATAATGT
* * * **
279695 ATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTATCAAAATATTT
66 ATTGTCAAATTAACACACTATTTAATAAAAATTGTAATATAATAATAATTTTAATCAAAATATGA
* *
279760 AAATTTAGTAAATAATGTATTGTCAAATCAACATATT
131 AAATTTAGTAAATAATGTATTGTCAAATCAACACAAT
*
279797 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATAATTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAATTAAAATTAGTAAATAATGT
**
279861 ATTGTCAAATTAACACACTATTTAATAAAAATTGTAATATAATAATAATTTGTAATTTAAATATG
66 ATTGTCAAATTAACACACTATTTAATAAAAATTGTAATATAATAATAATTT-TAATCAAAATATG
* * *
279926 AAAATTT-GATATATAATGTATTGTCAAATGAATACAAT
130 AAAATTTAG-TAAATAATGTATTGTCAAATCAACACAAT
* **
279964 ATTTGATATAAATTAAAATATAATAATAATCTTTTTTATTTAAATAAT
1 ATTTGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATAAT
280012 GTTAACTTAA
Statistics
Matches: 193, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
166 83 0.43
167 94 0.49
170 16 0.08
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (167 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAATTAAAATTAGTAAATAATGT
ATTGTCAAATTAACACACTATTTAATAAAAATTGTAATATAATAATAATTTTAATCAAAATATGA
AAATTTAGTAAATAATGTATTGTCAAATCAACACAAT
Found at i:280180 original size:28 final size:28
Alignment explanation
Indices: 280126--280180 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
280116 CATGTACATC
**
280126 AATTTTCAAATTAATTTCAACTTAAATT
1 AATTTTCAAATTAATTTCAACACAAATT
* **
280154 AATTTTCAAATTAGTTTTTACACAAAT
1 AATTTTCAAATTAATTTCAACACAAAT
280181 ATTCTTCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (28 bp):
AATTTTCAAATTAATTTCAACACAAATT
Found at i:283907 original size:60 final size:62
Alignment explanation
Indices: 283830--284064 Score: 236
Period size: 60 Copynumber: 3.9 Consensus size: 62
283820 AGGAAAAATT
* * * *
283830 GGTGTCGGCTATTGCATGGCCAACACAAAAAAATTT-ATTTTTTTTACCAGATAAAAAAGGG
1 GGTGTCGGCCATGGCATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAAAAGGG
* * * *
283891 GGTGTC-GCCATGGCATGACCAATACAAAAAAATTTCGA-TTTTTTTATCTGA-CAAAAAGAG
1 GGTGTCGGCCATGGCATGACCAACACAAAAAAATTT-GATTTTTTTTATCAGATAAAAAAGGG
* * ** *
283951 GATGTCGGCTATGGCATGACCAACACCCAAAAATTTGATTTTTTAT-TCAGAT-AAAAA-GG
1 GGTGTCGGCCATGGCATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAAAAGGG
** * *
284010 GGTGTCGGCCAT-GCAATGACCAACACCCAAAAATTT-AATTTTTTTATCTGATAAA
1 GGTGTCGGCCATGGC-ATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAA
284065 TAGGCAATGG
Statistics
Matches: 145, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
58 9 0.06
59 37 0.26
60 50 0.34
61 48 0.33
62 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (62 bp):
GGTGTCGGCCATGGCATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAAAAGGG
Found at i:284158 original size:46 final size:45
Alignment explanation
Indices: 284084--284176 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 45
284074 GCCGACACCA
* * * *
284084 AAAAATTAAATTTTTTATCTGACAAAAAGGGGGTGTTGGCCATGC
1 AAAAATTAAATTTTTTATCAGACAAAAAGAGAGTGTCGGCCATGC
* ** *
284129 AAAAATTTAATGTTTTTATCAGATTAAAAGAGAGTGTCGGTCATGC
1 AAAAATTAAAT-TTTTTATCAGACAAAAAGAGAGTGTCGGCCATGC
284175 AA
1 AA
284177 TGGCCAACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 10 0.26
46 29 0.74
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAAATTAAATTTTTTATCAGACAAAAAGAGAGTGTCGGCCATGC
Found at i:286413 original size:29 final size:29
Alignment explanation
Indices: 286339--286415 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
286329 TCTCAAATTG
*
286339 CATTTTAGTCATTTATATTTAAAATGTTA
1 CATTTTAGTCATTTATGTTTAAAATGTTA
* *
286368 CGTTTTAGTCATTTATGTTTAACATGTTA
1 CATTTTAGTCATTTATGTTTAAAATGTTA
286397 CATTTTAGTCATTTATGTT
1 CATTTTAGTCATTTATGTT
286416 ATCGTTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.53
Consensus pattern (29 bp):
CATTTTAGTCATTTATGTTTAAAATGTTA
Found at i:294455 original size:3 final size:3
Alignment explanation
Indices: 294443--294473 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
294433 GTCCATTGAG
294443 TGA T-A TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
294474 GTGAGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:302017 original size:13 final size:13
Alignment explanation
Indices: 301999--302025 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
301989 GATTTGAAGG
301999 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
302012 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
302025 A
1 A
302026 GAAGGAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:302251 original size:16 final size:16
Alignment explanation
Indices: 302232--302264 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
302222 CTTCTCATTC
302232 TTCTTTCTTTATTTTT
1 TTCTTTCTTTATTTTT
302248 TTCTTTCTTTATTTTT
1 TTCTTTCTTTATTTTT
302264 T
1 T
302265 CATTCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTTTCTTTATTTTT
Found at i:306270 original size:29 final size:30
Alignment explanation
Indices: 306222--306596 Score: 325
Period size: 30 Copynumber: 12.5 Consensus size: 30
306212 ATGAAAATAA
* * *
306222 AATTTTAGAGAAGTTTGAGGGTCAAAATGT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* * * *
306252 GATTTT-GAAAAGTTTGAGGGTTAAAATAT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* * *
306281 GATTTTGGAAAAGTTTAAGGGTTAAAATAT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* *
306311 AATTTTGAAAAAGTTTAAGGGTCAAAATAT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* ** *
306341 GATTTTGGAAAAAAATTAGGGGTCAAAATGT
1 AATTTTGG-AAAAGTTTAAGGGTCAAAATGT
* *
306372 AATTTTAAGAAAAGTTTAAGGGTCAAAATAT
1 AATTTT-GGAAAAGTTTAAGGGTCAAAATGT
* *
306403 GATTTTGGAAAAGTTT-GGGAGTCAAAATGT
1 AATTTTGGAAAAGTTTAAGG-GTCAAAATGT
* *
306433 AATTTTGGGGAAAGTTTGAA-AGTC-AAATGT
1 AATTTT-GGAAAAGTTT-AAGGGTCAAAATGT
***
306463 AATTTCAAAAAAGTTTAAGGGAT-AAAATGT
1 AATTTTGGAAAAGTTTAAGGG-TCAAAATGT
* * *
306493 TATTTTGGAAAAGTTT-AGTGGTTAAAATAT
1 AATTTTGGAAAAGTTTAAG-GGTCAAAATGT
* *
306523 AATTTTAGAAAAGTTT-AGGGTCTAAATGT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* *
306552 AATCTTGAAAAAGTTTAAGGGTC-AAATGT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATGT
* *
306581 AGTTTTTGAAAAGTTT
1 AATTTTGGAAAAGTTT
306597 GGGGACCTCT
Statistics
Matches: 282, Mismatches: 50, Indels: 27
0.79 0.14 0.08
Matches are distributed among these distances:
28 2 0.01
29 78 0.28
30 143 0.51
31 58 0.21
32 1 0.00
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTAAGGGTCAAAATGT
Found at i:309007 original size:98 final size:98
Alignment explanation
Indices: 308896--310128 Score: 1546
Period size: 98 Copynumber: 12.6 Consensus size: 98
308886 TTGCGGTCGT
* * * *
308896 AACCTTTCCCTCCATATCTTCGTGGTATTGGATTCGCCTTTACGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
*
308961 CTT-TCGAGGTACAAGGTTCGTCGTTGCGACTTA
66 CTTCT-GAGGTACAAGGTTCGCCGTTGCGACTTA
* * * *
308994 AACCTTTCTCTCCATATCCTTGTGGTACTGGATTCGTCGTTGCAGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* ***
309059 CTTCTAAGGTACAAGGTTTATCGTTGCGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * * *
309092 AACATTTCCCTCCATATCTTTGTGATACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* *
309157 CTT-TCGAGGTACAAGGTTCCCCATTGCGACTTA
66 CTTCT-GAGGTACAAGGTTCGCCGTTGCGACTTA
** * * * * *
309190 AACAGTTCCCTCCATATCTTCGTGGTTCTGGATTCGCCATTGCGACTTAAATTTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * *
309255 TTTCTAAGATACAAGGTTCGCCGTTGTGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * * * * *
309288 AACCCTTCCTTCTATATCCTTGTGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCTCTTCATT
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* *
309353 CTTCTAAGGTACAAGGTTCGCCGTTGTGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* ** * * *
309386 CACCATTT-CCTCCATATCCTCGTGGTACTAAACTCGTCGTTACGGCTTAAAT-TCTTCCCTTCA
1 AACC-TTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCT-TTCCCTTCA
* *
309449 TGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTA
64 TGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * *
309484 AACCATTCCCTCCATGTCCTCATGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
**
309549 CTTCTGAGGTACAAGGTTCATCGTTGCGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * *
309582 AACCTTTCCCTCCATGTCCACGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
*
309647 CTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * *
309680 AACCTTTGCCTCCATGTCCTCGTGGTACTGGATTTGCCGTTGCGACTTAAAT-TCTTCCCTTCAT
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCT-TTCCCTTCAT
* *
309744 GCTTTTGAGGTACAAGGTTCGCCGTTACGACTTA
65 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * * * *
309778 AACCATTCCTTCCA-AGTCCTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCTTTCAC
1 AACCTTTCCCTCCATA-TCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* *
309842 GCTTCTAAGGTACAAGGTTCACCGTTGCGACTTA
65 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * *
309876 AACCTTTCCCTCCATGTCCTCGTGGTACTAGATTCGCCTTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * *
309941 CTTCTTAGGTACAAGGTTCGCAGTTGC-AGTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * ** *
309973 AACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCCGTTACGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * * *
310038 TTTCAGAGGTACAATGTTCACCATTGCGACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* *
310071 AACCTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
1 AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
310129 ATCTCATCTT
Statistics
Matches: 986, Mismatches: 137, Indels: 25
0.86 0.12 0.02
Matches are distributed among these distances:
97 133 0.13
98 847 0.86
99 6 0.01
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (98 bp):
AACCTTTCCCTCCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
Found at i:310009 original size:48 final size:49
Alignment explanation
Indices: 309872--310125 Score: 150
Period size: 49 Copynumber: 5.2 Consensus size: 49
309862 ACCGTTGCGA
* * ** *
309872 CTTAAACCTTTCCCTCCATGTCCTCGTGGTACTAGATTCGCCTTTGCGG
1 CTTAAACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCAGTTGCAG
* * * *
309921 CTTAAA-TCTTTCCCTTCATG-CTTCTTAGGTAC-AAGGTTCGCAGTTGCAG
1 CTTAAACT-TTTCCCTCCATGTCCTCGT-GGTACTAA-ATTCGCAGTTGCAG
* * *
309970 -TTAAACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCCGTTACGG
1 CTTAAACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCAGTTGCAG
* * * * *
310018 CTTAAA-TCTTTCCCTTCATGT-TTCAGAGGTAC-AATGTTCACCA-TTGC-G
1 CTTAAACT-TTTCCCTCCATGTCCTC-GTGGTACTAA-ATTC-GCAGTTGCAG
* * * * * *
310066 ACTTAAACCTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGG
1 -CTTAAACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCAGTTGCAG
310115 CTTAAATCTTT
1 CTTAAA-CTTT
310126 CCCATCTCAT
Statistics
Matches: 156, Mismatches: 31, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
47 1 0.01
48 65 0.42
49 89 0.57
50 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (49 bp):
CTTAAACTTTTCCCTCCATGTCCTCGTGGTACTAAATTCGCAGTTGCAG
Found at i:312051 original size:15 final size:14
Alignment explanation
Indices: 312003--312057 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 14
311993 TCATCTTGAC
312003 TTTTTTTTTCTTCCT
1 TTTTTTTTTCTT-CT
*
312018 TTTTCTTTTCTTCT
1 TTTTTTTTTCTTCT
312032 TTTTTATTTTCTTTTCT
1 TTTTT-TTTTC--TTCT
312049 TTTTTTTTT
1 TTTTTTTTT
312058 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 16 0.46
16 4 0.11
17 9 0.26
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTCTTCT
Found at i:312056 original size:20 final size:20
Alignment explanation
Indices: 312018--312055 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
312008 TTTTCTTCCT
312018 TTTTCTTTTCTTCTTTTTTA
1 TTTTCTTTTCTTCTTTTTTA
312038 TTTTCTTTTCTT-TTTTTT
1 TTTTCTTTTCTTCTTTTTT
312056 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTCTTCTTTTTTA
Found at i:316355 original size:60 final size:59
Alignment explanation
Indices: 316290--316663 Score: 412
Period size: 60 Copynumber: 6.3 Consensus size: 59
316280 ATGAAAATGA
* * * * *
316290 AATTTTAGAGAAGTTTGAGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
* * *
316350 GATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAATAGTTTAGTGGTCAAAATAT
1 AATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
* * * * *
316410 GATTTTGGAAAAGTTTAGAGGTCAAAATGTAATTTTGGGAAAGTTTA-GGGTTAAAATAT
1 AATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
* * * *
316469 GATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATGT
1 AATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
* ** * * * **
316529 AATTTTAGAAAAAAAATTAAGGTTAAAATATAATTAT-GAACAAGTTTA-GGGTTTAAATAT
1 AATTTT-G-GAAAAGTTTAGGGTTAAAATGTAATTTTAGAA-AAGTTTAGGGGTCAAAATAT
* * *
316589 AATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
316648 AATTTTGGAAAAGTTT
1 AATTTTGGAAAAGTTT
316664 GAGGACCGCT
Statistics
Matches: 265, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
58 28 0.11
59 83 0.31
60 125 0.47
61 22 0.08
62 7 0.03
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.36
Consensus pattern (59 bp):
AATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATAT
Found at i:316502 original size:119 final size:117
Alignment explanation
Indices: 316283--316667 Score: 463
Period size: 119 Copynumber: 3.2 Consensus size: 117
316273 ACTCGGAATG
* * * * * *
316283 AAAATGAAATTTTAGAGAAGTTT-GAGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAA
1 AAAATGTAATTTTGGAAAAGTTTAGA-GGTCAAAATATAATTTTGGAAAAGTTTA-GGGTTAAAA
*
316347 TATGATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAATAGTTTAGTGGTC
64 TATGATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAG-GGTC
* * * *
316403 AAAATATGATTTTGGAAAAGTTTAGAGGTCAAAATGTAATTTTGGGAAAGTTTAGGGTTAAAATA
1 AAAATGTAATTTTGGAAAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATA
*
316468 TGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTC
66 TGATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTAGAAAAGTTT-AGGGTC
* ** * * *
316522 AAAATGTAATTTTAGAAAAAAAATTA-AGGTTAAAATATAATTAT-GAACAAGTTTAGGGTTTAA
1 AAAATGTAATTTT-G-GAAAAGTTTAGAGGTCAAAATATAATTTTGGAA-AAGTTTAGGGTTAAA
* * *
316585 ATATAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTT
63 ATATGATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTA-GGGTC
316641 AAAATGTAATTTTGGAAAAGTTT-GAGG
1 AAAATGTAATTTTGGAAAAGTTTAGAGG
316668 ACCGCTCGAG
Statistics
Matches: 228, Mismatches: 29, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
117 9 0.04
118 3 0.01
119 114 0.50
120 93 0.41
121 9 0.04
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.36
Consensus pattern (117 bp):
AAAATGTAATTTTGGAAAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATA
TGATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTC
Found at i:316520 original size:149 final size:148
Alignment explanation
Indices: 316283--316663 Score: 507
Period size: 149 Copynumber: 2.6 Consensus size: 148
316273 ACTCGGAATG
* * * *
316283 AAAATGAAATTTT-AGAGAAGTTTGAGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAA
1 AAAATGTAATTTTGGGA-AAGTTT-AGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAA
* * * * ** * *
316347 TATGATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAG-AATAGTTTAGTGGTCAAAATATG
64 TGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAAAATTA-AGGTCAAAATATA
*
316411 ATTTTGGAA-AAGTTTAGAGGTC
128 ATTAT-GAACAAGTTTAG-GGTC
316433 AAAATGTAATTTTGGGAAAGTTTAGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATG
1 AAAATGTAATTTTGGGAAAGTTTAGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATG
* *
316498 TAATTTTAGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAAAAATTAAGGTTAAAATATAAT
66 TAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAG-AAAAAAATTAAGGTCAAAATATAAT
*
316563 TATGAACAAGTTTAGGGTT
130 TATGAACAAGTTTAGGGTC
* * * *
316582 TAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATG
1 AAAATGTAATTTTGGGAAAGTTTAGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATG
316647 TAATTTTGGAAAAGTTT
66 TAATTTTGGAAAAGTTT
316664 GAGGACCGCT
Statistics
Matches: 206, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
149 158 0.77
150 40 0.19
151 8 0.04
ACGTcount: A:0.41, C:0.01, G:0.22, T:0.36
Consensus pattern (148 bp):
AAAATGTAATTTTGGGAAAGTTTAGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATG
TAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAAAATTAAGGTCAAAATATAATT
ATGAACAAGTTTAGGGTC
Found at i:316563 original size:31 final size:29
Alignment explanation
Indices: 316290--316663 Score: 318
Period size: 30 Copynumber: 12.6 Consensus size: 29
316280 ATGAAAATGA
* *
316290 AATTTTAGAGAAGTTTGAGGGTTAAAATAT
1 AATTTTAGAAAAGTTT-AAGGTTAAAATAT
* * * *
316320 GATTTTGGAAAAGTTTAGGGGTCAAAATAT
1 AATTTTAGAAAAGTTTA-AGGTTAAAATAT
* * *
316350 GATTTTGGAAAAGTTTAAGGGTTAAAATGT
1 AATTTTAGAAAAGTTTAA-GGTTAAAATAT
* * *
316380 AATTTTAGAATAGTTTAGTGGTCAAAATAT
1 AATTTTAGAAAAGTTTA-AGGTTAAAATAT
* * * *
316410 GATTTTGGAAAAGTTTAGAGGTCAAAATGT
1 AATTTTAGAAAAGTTTA-AGGTTAAAATAT
* * *
316440 AATTTTGGGAAAGTTTAGGGTTAAAATAT
1 AATTTTAGAAAAGTTTAAGGTTAAAATAT
* * *
316469 GATTTTAGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTAGAAAAGTTTA-AGGTTAAAATAT
* *
316499 AATTTTAGAAAAGTTTAAGGGTCAAAATGT
1 AATTTTAGAAAAGTTTAA-GGTTAAAATAT
**
316529 AATTTTAGAAAAAAAATTAAGGTTAAAATAT
1 AATTTTAG--AAAAGTTTAAGGTTAAAATAT
* * *
316560 AATTAT-GAACAAGTTTAGGGTTTAAATAT
1 AATTTTAGAA-AAGTTTAAGGTTAAAATAT
* * *
316589 AATTTTGGAAAAGTTTAGGGTTAAAATGT
1 AATTTTAGAAAAGTTTAAGGTTAAAATAT
* * *
316618 GATTTTAGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTAGAAAAGTTTA-AGGTTAAAATAT
*
316648 AATTTTGGAAAAGTTT
1 AATTTTAGAAAAGTTT
316664 GAGGACCGCT
Statistics
Matches: 288, Mismatches: 46, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.01
29 76 0.26
30 188 0.65
31 14 0.05
32 8 0.03
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.36
Consensus pattern (29 bp):
AATTTTAGAAAAGTTTAAGGTTAAAATAT
Found at i:320937 original size:18 final size:17
Alignment explanation
Indices: 320893--320937 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
320883 TTTTAATTTT
* *
320893 TAAAAAATTAAAAAATT
1 TAAAATATTAAAAAATA
320910 TAAAATTATTAAAAAAATA
1 TAAAA-TATT-AAAAAATA
320929 TAAAATATT
1 TAAAATATT
320938 TTGTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 7 0.29
19 12 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATATTAAAAAATA
Found at i:321430 original size:21 final size:21
Alignment explanation
Indices: 321404--321444 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
321394 TAATTAGAAA
*
321404 ATTTAATATATAATT-AAATTT
1 ATTTAA-AAATAATTGAAATTT
321425 ATTTAAAAATAATTGAAATT
1 ATTTAAAAATAATTGAAATT
321445 GGAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTAAAAATAATTGAAATTT
Found at i:328476 original size:6 final size:6
Alignment explanation
Indices: 328425--328501 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
328415 CATCCATCCC
* * * * * *
328425 CTACAT -TACAT CTACAAA CCACAT TTACAT TTACAT CTACAC CTACGT
1 CTACAT CTACAT CTAC-AT CTACAT CTACAT CTACAT CTACAT CTACAT
*
328473 CTACGT CTACAT CTACAT CTACAT CTACA
1 CTACAT CTACAT CTACAT CTACAT CTACA
328502 GACATGTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
5 5 0.08
6 50 0.85
7 4 0.07
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (6 bp):
CTACAT
Found at i:331087 original size:2 final size:2
Alignment explanation
Indices: 331080--331114 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
331070 TCCTTACTTT
331080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
331115 TCTTTGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:336675 original size:24 final size:24
Alignment explanation
Indices: 336636--336698 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
336626 TAGACTAATA
* * *
336636 AGAGTTTGACTCAAACAACTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
336660 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
336684 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
336699 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:337062 original size:47 final size:47
Alignment explanation
Indices: 337008--337102 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
336998 GAATTAATAT
*
337008 TAAAAAAAATTAGGTACCAAATCAAGAAAAATAATCAAGTTCAAGTA
1 TAAAAAAAATTAAGTACCAAATCAAGAAAAATAATCAAGTTCAAGTA
* * * *
337055 TAAAAAAAATTAAGTACCAAATTAGGAAAAATAGTCAAGTTCAGGTA
1 TAAAAAAAATTAAGTACCAAATCAAGAAAAATAATCAAGTTCAAGTA
337102 T
1 T
337103 CAAATTGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (47 bp):
TAAAAAAAATTAAGTACCAAATCAAGAAAAATAATCAAGTTCAAGTA
Found at i:337084 original size:25 final size:24
Alignment explanation
Indices: 337009--337085 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 24
336999 AATTAATATT
* *
337009 AAAAAAAATTAGGTACCAAATCAAG
1 AAAAAAAATTAAGTACCAAAT-TAG
* * * * *
337034 AAAAATAATCAAGT-TC-AAGTAT
1 AAAAAAAATTAAGTACCAAATTAG
337056 AAAAAAAATTAAGTACCAAATTAG
1 AAAAAAAATTAAGTACCAAATTAG
*
337080 GAAAAA
1 AAAAAA
337086 TAGTCAAGTT
Statistics
Matches: 37, Mismatches: 13, Indels: 5
0.67 0.24 0.09
Matches are distributed among these distances:
22 13 0.35
23 3 0.08
24 10 0.27
25 11 0.30
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.19
Consensus pattern (24 bp):
AAAAAAAATTAAGTACCAAATTAG
Found at i:341632 original size:69 final size:69
Alignment explanation
Indices: 341553--341691 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
341543 CCACCTCCCA
341553 AACAAACAAAATTGGAGTACTTCATCCCATCTAATGTAACGAGTACTCACCTCATTTCCATAATA
1 AACAAACAAAATTGGAGTACTTCATCCCATCTAATGTAACGAGTACTCACCTCATTTCCATAATA
341618 ACTT
66 ACTT
341622 AACAAACAAAATTGGAGTACTTCATCCCATCTAATGTAACGAGTACTCACCTCATTTCCATAATA
1 AACAAACAAAATTGGAGTACTTCATCCCATCTAATGTAACGAGTACTCACCTCATTTCCATAATA
341687 ACTT
66 ACTT
341691 A
1 A
341692 TGCTTCATGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (69 bp):
AACAAACAAAATTGGAGTACTTCATCCCATCTAATGTAACGAGTACTCACCTCATTTCCATAATA
ACTT
Found at i:349924 original size:42 final size:43
Alignment explanation
Indices: 349846--349931 Score: 156
Period size: 42 Copynumber: 2.0 Consensus size: 43
349836 CGAGTGGCTG
349846 TTATATTTATTTCATAAAAATATATTAAATAGTTTGTTTCGTT
1 TTATATTTATTTCATAAAAATATATTAAATAGTTTGTTTCGTT
*
349889 TTATATTTATTTCAT-AAAATATATTAAATATTTTGTTTCGTT
1 TTATATTTATTTCATAAAAATATATTAAATAGTTTGTTTCGTT
349931 T
1 T
349932 AGTAATGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 27 0.64
43 15 0.36
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.56
Consensus pattern (43 bp):
TTATATTTATTTCATAAAAATATATTAAATAGTTTGTTTCGTT
Found at i:355230 original size:2 final size:2
Alignment explanation
Indices: 355225--355269 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
355215 TGGGGAAAAA
*
355225 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
355267 AG A
1 AG A
355270 ATGCAACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:361432 original size:21 final size:20
Alignment explanation
Indices: 361384--361437 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
361374 AATAAAGGGG
361384 GAAAAGAAAGAAAAAAAGAA
1 GAAAAGAAAGAAAAAAAGAA
* *
361404 GAAGAAGAAAGGAAGAAAAGGA
1 GAA-AAGAAA-GAAAAAAAGAA
*
361426 GCAAAGAGAAGA
1 GAAAAGA-AAGA
361438 GAGGAGAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.11
21 12 0.43
22 13 0.46
ACGTcount: A:0.69, C:0.02, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAAGAAAGAAAAAAAGAA
Found at i:361692 original size:23 final size:25
Alignment explanation
Indices: 361666--361718 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
361656 AATATTTATT
361666 TTTTCATTCA-T-AAAATTCCAACA
1 TTTTCATTCATTAAAAATTCCAACA
* *
361689 TTTTCTTTGATTAAAAAATTCCAACA
1 TTTTCATTCATT-AAAAATTCCAACA
361715 TTTT
1 TTTT
361719 TATTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 1 0.04
26 16 0.64
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTCATTCATTAAAAATTCCAACA
Found at i:361729 original size:26 final size:26
Alignment explanation
Indices: 361677--361729 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
361667 TTTCATTCAT
* *
361677 AAAATTCCAACATTTTCTTTGATTAA
1 AAAATTCCAACATTTTCTTTAAATAA
361703 AAAATTCCAACATTTT-TATTAAATAA
1 AAAATTCCAACATTTTCT-TTAAATAA
361729 A
1 A
361730 CATTCAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (26 bp):
AAAATTCCAACATTTTCTTTAAATAA
Found at i:365018 original size:44 final size:44
Alignment explanation
Indices: 364969--365054 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
364959 GATCAGTCTA
* *
364969 CATCAAGAAAATTTGCATCAATCAGGAAATATAATAAAACAATG
1 CATCAAGAAAATTTGCATCAATCAGAAAATAGAATAAAACAATG
* *
365013 CATCAATAATATTTGCATCAATCAGAAAATAGAATAAAACAA
1 CATCAAGAAAATTTGCATCAATCAGAAAATAGAATAAAACAA
365055 CAATCAGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.23
Consensus pattern (44 bp):
CATCAAGAAAATTTGCATCAATCAGAAAATAGAATAAAACAATG
Found at i:366747 original size:18 final size:17
Alignment explanation
Indices: 366721--366754 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
366711 TTGCTATTTG
366721 TTTTCTTTCCTTTTTTTT
1 TTTTCTTT-CTTTTTTTT
*
366739 TTTTTTTTCTTTTTTT
1 TTTTCTTTCTTTTTTT
366755 GCTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTCTTTCTTTTTTTT
Found at i:366760 original size:18 final size:17
Alignment explanation
Indices: 366717--366761 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
366707 GGCATTGCTA
366717 TTTGTTTTCTTTCCTTTT
1 TTTGTTTT-TTTCCTTTT
* *
366735 TTTTTTTTTTTTCTTTT
1 TTTGTTTTTTTCCTTTT
366752 TTTGCTTTTT
1 TTTG-TTTTT
366762 AAAGTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.84
Consensus pattern (17 bp):
TTTGTTTTTTTCCTTTT
Found at i:367302 original size:13 final size:13
Alignment explanation
Indices: 367284--367348 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
367274 TTAAACCAAG
*
367284 CTTTTCAAAAGTA
1 CTTTTCAAAAGCA
*
367297 CTTTTCAAAATCA
1 CTTTTCAAAAGCA
*
367310 CTTTTCCAAAGCA
1 CTTTTCAAAAGCA
367323 C-TTTCTAAAAGCA
1 CTTTTC-AAAAGCA
*
367336 CTTCTCAAAAGCA
1 CTTTTCAAAAGCA
367349 ATGCTAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
12 4 0.09
13 37 0.84
14 3 0.07
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:370002 original size:12 final size:12
Alignment explanation
Indices: 369985--370011 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
369975 ATGAGCTCAT
369985 CAACTTTGTGCC
1 CAACTTTGTGCC
369997 CAACTTTGTGCC
1 CAACTTTGTGCC
370009 CAA
1 CAA
370012 AACAGAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (12 bp):
CAACTTTGTGCC
Done.