Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 36 of 47
Found at i:5851328 original size:21 final size:21
Alignment explanation
Indices: 5851302--5851350 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5851292 TATTATTAAT
5851302 TTTAATATTAGCAATATAA-AA
1 TTTAAT-TTAGCAATATAATAA
* *
5851323 TTTAATTTATCATTATAATAA
1 TTTAATTTAGCAATATAATAA
5851344 -TTAATTT
1 TTTAATTT
5851351 TATAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAATTTAGCAATATAATAA
Found at i:5851352 original size:21 final size:20
Alignment explanation
Indices: 5851316--5851359 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5851306 ATATTAGCAA
*
5851316 TATAAAATTTAATTTATCAT
1 TATAAAATTTAATTTATAAT
5851336 TATAATAA-TTAATTTTATAAT
1 TATAA-AATTTAA-TTTATAAT
5851357 TAT
1 TAT
5851360 TATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAAAATTTAATTTATAAT
Found at i:5852554 original size:19 final size:20
Alignment explanation
Indices: 5852530--5852577 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5852520 AATTAAATAA
5852530 ATAAAAATTTAAAA-CATAT
1 ATAAAAATTTAAAATCATAT
* **
5852549 ATAAAAAATTAAAATTTTAT
1 ATAAAAATTTAAAATCATAT
5852569 ATAAAAATT
1 ATAAAAATT
5852578 AAACTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATTTAAAATCATAT
Found at i:5852588 original size:19 final size:18
Alignment explanation
Indices: 5852517--5852588 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
5852507 TTAAATTTTA
5852517 AAAAATTAAATAA-ATA-
1 AAAAATTAAATAATATAT
*
5852533 AAAATTTAAA-ACATATAT
1 AAAAATTAAATA-ATATAT
**
5852551 AAAAAATTAAAATTTTATAT
1 -AAAAATT-AAATAATATAT
5852571 AAAAATTAAACTAATATA
1 AAAAATTAAA-TAATATA
5852589 ATATTAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
15 1 0.02
16 10 0.23
17 3 0.07
18 3 0.07
19 18 0.42
20 8 0.19
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTAAATAATATAT
Found at i:5852773 original size:56 final size:56
Alignment explanation
Indices: 5852696--5852816 Score: 206
Period size: 56 Copynumber: 2.2 Consensus size: 56
5852686 CAATTGGTAG
*
5852696 GGGAACATCTTTTACACAGAAAACATAAATAAAAAGGAAGAAAAAACAAGGAAAGT
1 GGGAAAATCTTTTACACAGAAAACATAAATAAAAAGGAAGAAAAAACAAGGAAAGT
* *
5852752 GGGAAAATCTTTTACATAGAAAACATAAATAAATAGGAAGAAAAAACAAGGAAAGT
1 GGGAAAATCTTTTACACAGAAAACATAAATAAAAAGGAAGAAAAAACAAGGAAAGT
*
5852808 GAGAAAATC
1 GGGAAAATC
5852817 ACAAGAAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.57, C:0.09, G:0.18, T:0.16
Consensus pattern (56 bp):
GGGAAAATCTTTTACACAGAAAACATAAATAAAAAGGAAGAAAAAACAAGGAAAGT
Found at i:5852884 original size:2 final size:2
Alignment explanation
Indices: 5852861--5852918 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
5852851 TTTCAACGGT
*
5852861 TA TA T- TA TA -A TA T- TA T- TA TA TA TA TA TA TA TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5852898 TA TA -A TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
5852919 AAAATTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
1 6 0.13
2 40 0.87
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5852887 original size:22 final size:24
Alignment explanation
Indices: 5852861--5852916 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
5852851 TTTCAACGGT
5852861 TATAT-TATAATATTAT-T-ATATA
1 TATATATATAA-ATTATATAATATA
5852883 TATATATATAAATTATATAATATA
1 TATATATATAAATTATATAATATA
*
5852907 TATAAATATA
1 TATATATATA
5852917 TAAAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 10 0.33
23 6 0.20
24 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATATATAAATTATATAATATA
Found at i:5852888 original size:24 final size:22
Alignment explanation
Indices: 5852861--5852910 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
5852851 TTTCAACGGT
5852861 TATAT-TATAATATTAT-TATATA
1 TATATATATAA-ATTATATA-ATA
5852883 TATATATATAAATTATATAATA
1 TATATATATAAATTATATAATA
5852905 TATATA
1 TATATA
5852911 AATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATATATAAATTATATAATA
Found at i:5852927 original size:26 final size:26
Alignment explanation
Indices: 5852869--5852921 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
5852859 GTTATATTAT
* *
5852869 AATAT-TATTATATATATATATATAA
1 AATATATAATATATATAAATATATAA
*
5852894 ATTATATAATATATATAAATATATAA
1 AATATATAATATATATAAATATATAA
5852920 AA
1 AA
5852922 ATTATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATATATAATATATATAAATATATAA
Found at i:5852932 original size:26 final size:26
Alignment explanation
Indices: 5852870--5852932 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
5852860 TTATATTATA
* *
5852870 ATATTATTATATATATATATATAAATT
1 ATATTA-TATATAAATATATAAAAATT
5852897 ATATAATATATATAAATATATAAAAATT
1 ATAT--TATATATAAATATATAAAAATT
5852925 ATATTATA
1 ATATTATA
5852933 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 4 0.12
28 22 0.69
29 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTATATATAAATATATAAAAATT
Found at i:5853006 original size:25 final size:25
Alignment explanation
Indices: 5852978--5853026 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5852968 TTAAAATGTG
5852978 AATTTT-TTAATTTATTTTTTAAATA
1 AATTTTATT-ATTTATTTTTTAAATA
*
5853003 AATTTTATTTTTTATTTTTTAAAT
1 AATTTTATTATTTATTTTTTAAAT
5853027 TGAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
AATTTTATTATTTATTTTTTAAATA
Found at i:5854359 original size:19 final size:19
Alignment explanation
Indices: 5854332--5854380 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
5854322 GTAAAATAAT
5854332 ATTTAAAAATTA-AATAAAAA
1 ATTT-AAAATTACAA-AAAAA
5854352 ATTTAAAATATACAAAAAAA
1 ATTTAAAAT-TACAAAAAAA
5854372 A-TTAAAATT
1 ATTTAAAATT
5854381 TTATATCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 12 0.44
20 12 0.44
21 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTAAAATTACAAAAAAA
Found at i:5854773 original size:16 final size:16
Alignment explanation
Indices: 5854752--5854800 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
5854742 TTTTTATTTA
5854752 TTTTTTAAATTTAAAT
1 TTTTTTAAATTTAAAT
*
5854768 TTTTTTAATATTTAAAG
1 TTTTTTAA-ATTTAAAT
* *
5854785 TATTTTAGATTTAAAT
1 TTTTTTAAATTTAAAT
5854801 AAATTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
TTTTTTAAATTTAAAT
Found at i:5855016 original size:16 final size:16
Alignment explanation
Indices: 5854995--5855038 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5854985 TATTATATTT
5854995 ATTTATTTATTTTTAA
1 ATTTATTTATTTTTAA
* *
5855011 ATTTATTTGTATTTAA
1 ATTTATTTATTTTTAA
*
5855027 TTTATATTTATT
1 ATT-TATTTATT
5855039 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTATTTATTTTTAA
Found at i:5856492 original size:15 final size:15
Alignment explanation
Indices: 5856474--5856514 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5856464 AATTTAAAAT
5856474 TTTTTAATATTGTAA
1 TTTTTAATATTGTAA
* *
5856489 TTTTTAATATTTTTA
1 TTTTTAATATTGTAA
*
5856504 TTTTGAATATT
1 TTTTTAATATT
5856515 ATTAAACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTTTAATATTGTAA
Found at i:5856569 original size:27 final size:27
Alignment explanation
Indices: 5856536--5856600 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
5856526 AATTTTTTAT
*
5856536 TTTTATAATAT-ATAATCAATATTATTA
1 TTTTATAATATAATAA-AAATATTATTA
* *
5856563 TTTTATATTTTAATAAAAATATTATTA
1 TTTTATAATATAATAAAAATATTATTA
5856590 TTTTAATAATA
1 TTTT-ATAATA
5856601 AATTATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATAATATAATAAAAATATTATTA
Found at i:5856786 original size:32 final size:33
Alignment explanation
Indices: 5856749--5856828 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
5856739 TAAAATATTT
5856749 ATATTTTAATAATA-TA-AATATTAAGAAAAATA
1 ATATTTTAATAATATTATAATATT-AGAAAAATA
** *
5856781 ATATTTTAATAATTATTATAATATTTTAAAATTA
1 ATATTTTAATAA-TATTATAATATTAGAAAAATA
*
5856815 ATGTTTTAATAATA
1 ATATTTTAATAATA
5856829 AATAGTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.29
33 4 0.10
34 19 0.46
35 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (33 bp):
ATATTTTAATAATATTATAATATTAGAAAAATA
Found at i:5857110 original size:17 final size:19
Alignment explanation
Indices: 5857071--5857115 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
5857061 TTTATAAAAA
*
5857071 AATATCATATTAAGTATTT
1 AATATAATATTAAGTATTT
5857090 AATATAATATTAA-TA-TT
1 AATATAATATTAAGTATTT
5857107 AATATAATA
1 AATATAATA
5857116 ATTTACTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.44
18 2 0.08
19 12 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AATATAATATTAAGTATTT
Found at i:5857909 original size:32 final size:32
Alignment explanation
Indices: 5857866--5857927 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5857856 TAAGTTTATA
* * *
5857866 TATATAAATTTTTATTTGTTAATAATTTATTT
1 TATATAAATTTTGATATATTAATAATTTATTT
* *
5857898 TATATATATTTTGATATATTTATAATTTAT
1 TATATAAATTTTGATATATTAATAATTTAT
5857928 AATATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
TATATAAATTTTGATATATTAATAATTTATTT
Found at i:5858225 original size:16 final size:16
Alignment explanation
Indices: 5858204--5858237 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5858194 AGTATTTTAA
5858204 ATTTAAATAAATTTTT
1 ATTTAAATAAATTTTT
5858220 ATTTAAATAAATTTTT
1 ATTTAAATAAATTTTT
5858236 AT
1 AT
5858238 ATATTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATAAATTTTT
Found at i:5860092 original size:17 final size:17
Alignment explanation
Indices: 5860072--5860120 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5860062 AAATTTGAGT
5860072 TTATTTTTTTATTATAA
1 TTATTTTTTTATTATAA
*
5860089 TTATTTTTATATT-TAA
1 TTATTTTTTTATTATAA
5860105 TT-TTTTATTATATTAT
1 TTATTTT-TT-TATTAT
5860121 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 6 0.22
17 16 0.59
18 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTTTATTATAA
Found at i:5860097 original size:15 final size:15
Alignment explanation
Indices: 5860077--5860123 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
5860067 TGAGTTTATT
5860077 TTTTTATTATAATTA
1 TTTTTATTATAATTA
*
5860092 TTTTTATATTTAA-T-
1 TTTTTAT-TATAATTA
5860106 TTTTTATTAT-ATTA
1 TTTTTATTATAATTA
5860120 TTTT
1 TTTT
5860124 AAAAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 3 0.11
14 11 0.41
15 8 0.30
16 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTATAATTA
Found at i:5860131 original size:29 final size:29
Alignment explanation
Indices: 5860071--5860133 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
5860061 TAAATTTGAG
* * *
5860071 TTTATTTTTTTATTATAATTATTTTTATA
1 TTTAATTTTTTATTATAATTATTTTAAAA
5860100 TTTAATTTTTTATTAT-ATTATTTTAAAAA
1 TTTAATTTTTTATTATAATTATTTT-AAAA
5860129 TTTAA
1 TTTAA
5860134 AAATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTAATTTTTTATTATAATTATTTTAAAA
Found at i:5860251 original size:22 final size:21
Alignment explanation
Indices: 5860160--5860252 Score: 53
Period size: 22 Copynumber: 4.1 Consensus size: 21
5860150 ATTTCTTGAA
5860160 TATTATTAAAT-ATAAATATT
1 TATTATTAAATAATAAATATT
* *
5860180 TTTATATTTTAATAATAAATTATT
1 TAT-TA-TTAAATAATAAA-TATT
** * * *
5860204 AATATTAACAAAAAATATATTTTT
1 --TATTATTAAATAATA-AATATT
5860228 TATTATTTAAATAATAAATATT
1 TATTA-TTAAATAATAAATATT
5860250 TAT
1 TAT
5860253 AAATATTGTT
Statistics
Matches: 51, Mismatches: 14, Indels: 14
0.65 0.18 0.18
Matches are distributed among these distances:
20 2 0.04
21 2 0.04
22 17 0.33
23 12 0.24
24 13 0.25
25 3 0.06
26 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATTAAATAATAAATATT
Found at i:5862893 original size:22 final size:21
Alignment explanation
Indices: 5862843--5862893 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
5862833 TCAAGTTATT
*
5862843 TTAGGTTTAGGGTTGAATCAA
1 TTAGGTTTAGAGTTGAATCAA
* *
5862864 TCATGTTTAGCAGTTGAATTC-A
1 TTAGGTTTAG-AGTTGAA-TCAA
5862886 TTAGGTTT
1 TTAGGTTT
5862894 GATCGTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 8 0.35
22 13 0.57
23 2 0.09
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (21 bp):
TTAGGTTTAGAGTTGAATCAA
Found at i:5864055 original size:48 final size:48
Alignment explanation
Indices: 5863981--5864124 Score: 150
Period size: 48 Copynumber: 3.0 Consensus size: 48
5863971 TAATTATTCG
* * *
5863981 AGTCATTTCGAGTTTG-GATTACTTCGAATTCAGGTCATTTTGGGTTTA
1 AGTCATTTCGAATTTGAG-TTATTTCGAGTTCAGGTCATTTTGGGTTTA
* * *
5864029 AGTCATTTCGAATTTGAGTTATTTCGAGTTCAGGTCAATTCGGGTTTG
1 AGTCATTTCGAATTTGAGTTATTTCGAGTTCAGGTCATTTTGGGTTTA
* * *
5864077 TGTCATTTTGAATTT-AGGTTATTT-TAGGTTCAGGTCATTTATGGGTTT
1 AGTCATTTCGAATTTGA-GTTATTTCGA-GTTCAGGTCATTT-TGGGTTT
5864125 GGATTAATCG
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.02
48 72 0.89
49 7 0.09
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (48 bp):
AGTCATTTCGAATTTGAGTTATTTCGAGTTCAGGTCATTTTGGGTTTA
Found at i:5865163 original size:25 final size:26
Alignment explanation
Indices: 5865135--5865191 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
5865125 TTTTTATTTA
* *
5865135 AACCCAAATCCAAACCTAT-ACTCAT
1 AACCCAAACCCAAACCTATAACACAT
* *
5865160 AA-CCTAACCCATACCTATAACACAT
1 AACCCAAACCCAAACCTATAACACAT
5865185 AACCCAA
1 AACCCAA
5865192 TACATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 13 0.52
25 9 0.36
26 3 0.12
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.18
Consensus pattern (26 bp):
AACCCAAACCCAAACCTATAACACAT
Found at i:5865189 original size:20 final size:20
Alignment explanation
Indices: 5865164--5865239 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
5865154 ACTCATAACC
5865164 TAACCCATACCTATAACACA
1 TAACCCATACCTATAACACA
*
5865184 TAACCCAATACATAATAAAAAAACACA
1 TAACCC-ATACCT-AT-----AACACA
*
5865211 TAACCCATACCAATAACACA
1 TAACCCATACCTATAACACA
*
5865231 TAACTCATA
1 TAACCCATA
5865240 ACCGATAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
20 20 0.44
21 5 0.11
22 2 0.04
25 2 0.04
26 4 0.09
27 12 0.27
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (20 bp):
TAACCCATACCTATAACACA
Found at i:5866633 original size:51 final size:50
Alignment explanation
Indices: 5866570--5866735 Score: 219
Period size: 51 Copynumber: 3.3 Consensus size: 50
5866560 AAATAATAGG
* *
5866570 GTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGAAAATAAAATCAGA
* *
5866621 GTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAAATAAAGTCAGA
1 GTTGGAGTATCCCCGATTATGA-AAATTGGTGTTTTGAAAATAAAATCAGA
* * *
5866672 GTTGGAATATCCCCGATTGTGAAAAATTGGTATTTT-AGAAATAAAATCAG-
1 GTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTGA-AAATAAAATCAGA
5866722 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
5866736 TCGAAAATAA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
50 15 0.15
51 86 0.84
52 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGAAAATAAAATCAGA
Found at i:5866866 original size:28 final size:28
Alignment explanation
Indices: 5866825--5866898 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
5866815 GATATATAGC
5866825 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
* * *
5866853 TGGGGTTGGAGTATCCCCGATGAAGTAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
5866881 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
5866899 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:5866940 original size:107 final size:106
Alignment explanation
Indices: 5866672--5866949 Score: 319
Period size: 107 Copynumber: 2.6 Consensus size: 106
5866662 TAAAGTCAGA
* *
5866672 GTTGGAATATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGTTGGAGTATCCCCT
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGGTTGGAGTATCCCCT
* *
5866737 CGAAAATAACGAGATTGGAGTATCCTCGATGACATATCGGG
66 CGAAAATAACGAGATTGGAGTATCCCCGATGACATAACGGG
* * *** * * **
5866778 GTTGGAGTACCCCCGATTATGAAAAATCAATATTTTAGATATATAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATC-GGGTTGGAGTATCCCC
* * *
5866843 TC-AGAAATAATGGGGTTGGAGTATCCCCGATGA-AGTAACGGG
65 TCGA-AAATAACGAGATTGGAGTATCCCCGATGACA-TAACGGG
* * *
5866885 GTTGGAGTATCCCCAATTGTGAAAATTTGGTGTTTT-GAAAATAAAATCGGAGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAG-AAATAAAATCGG-GTTGGAGTATCCC
5866949 C
64 C
5866950 GATTGCGATA
Statistics
Matches: 139, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
106 43 0.31
107 96 0.69
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (106 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGGTTGGAGTATCCCCT
CGAAAATAACGAGATTGGAGTATCCCCGATGACATAACGGG
Found at i:5867028 original size:51 final size:51
Alignment explanation
Indices: 5866885--5867028 Score: 189
Period size: 51 Copynumber: 2.8 Consensus size: 51
5866875 AAGTAACGGG
* * * * *
5866885 GTTGGAGTATCCCCAATTGTGAAAATTTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * * *
5866936 GTTGGAGTATCCCCGATTGCGATAAATCGATGCTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
*
5866987 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAAT
5867029 GGAACCGGGA
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:5869393 original size:33 final size:33
Alignment explanation
Indices: 5869351--5869420 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
5869341 AAAATGCCTG
*
5869351 AATGTATCGATACAATTAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
5869384 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
5869417 AATG
1 AATG
5869421 CAAAATGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:5869419 original size:13 final size:13
Alignment explanation
Indices: 5869370--5869400 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5869360 ATACAATTAG
5869370 CAATGTATCGATA
1 CAATGTATCGATA
5869383 CAATGTATCGATA
1 CAATGTATCGATA
5869396 CAATG
1 CAATG
5869401 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:5869420 original size:20 final size:20
Alignment explanation
Indices: 5869351--5869420 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
5869341 AAAATGCCTG
*
5869351 AATGTATCGATACAATTAGC
1 AATGTATCGATACAATGAGC
5869371 AATGTATCG-----AT-A-C
1 AATGTATCGATACAATGAGC
5869384 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
5869404 AATGTATCGATACAATG
1 AATGTATCGATACAATG
5869421 CAAAATGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
15 2 0.05
18 2 0.05
19 1 0.02
20 27 0.63
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:5869427 original size:20 final size:20
Alignment explanation
Indices: 5869384--5869437 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
5869374 GTATCGATAC
*
5869384 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
5869404 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
*
5869424 AATGTATCAATACA
1 AATGTATCGATACA
5869438 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:5869471 original size:13 final size:13
Alignment explanation
Indices: 5869453--5869482 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5869443 GTAAACCCAG
5869453 AATGTATCGATAC
1 AATGTATCGATAC
5869466 AATGTATCGATAC
1 AATGTATCGATAC
5869479 AATG
1 AATG
5869483 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:5869489 original size:20 final size:20
Alignment explanation
Indices: 5869464--5869520 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
5869454 ATGTATCGAT
5869464 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
5869484 ACAATGTATCGATATAATGA
1 ACAATGTATCGATACAATGA
*
5869504 ACAATGTATTGATACAA
1 ACAATGTATCGATACAA
5869521 ATTGTGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:5876251 original size:20 final size:20
Alignment explanation
Indices: 5876226--5876276 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5876216 TTACCACTGT
5876226 TTGTATCGATACATAGTACA
1 TTGTATCGATACATAGTACA
* *
5876246 TTGTATTGATACATGGTACA
1 TTGTATCGATACATAGTACA
5876266 TTGTATCGATA
1 TTGTATCGATA
5876277 AATGATGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATAGTACA
Found at i:5877925 original size:21 final size:21
Alignment explanation
Indices: 5877899--5877940 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5877889 AATCAACCAC
* *
5877899 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
5877920 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
5877941 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:5878386 original size:21 final size:21
Alignment explanation
Indices: 5878362--5878405 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5878352 TAATATTCTT
* *
5878362 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
5878383 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
5878404 GA
1 GA
5878406 GGAGCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:5878418 original size:21 final size:21
Alignment explanation
Indices: 5878362--5878420 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
5878352 TAATATTCTT
** *
5878362 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAAGAAATGAATTA
*
5878383 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAAGAAATGAATTA
** *
5878404 GAGGAGCAAAGAAATGA
1 GAAAAGAAAAGAAATGA
5878421 GTTGCAACTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAAGAAATGAATTA
Found at i:5881777 original size:20 final size:20
Alignment explanation
Indices: 5881754--5881807 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5881744 CACACCTAGA
5881754 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
5881774 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
5881794 TGCATCGATACATT
1 TGTATCGATACATT
5881808 GTATCGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:5881849 original size:20 final size:19
Alignment explanation
Indices: 5881803--5881858 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
5881793 TTGCATCGAT
*
5881803 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
5881822 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
5881841 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
5881859 AAAACTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:5881925 original size:13 final size:13
Alignment explanation
Indices: 5881904--5881933 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5881894 CGATACATGG
*
5881904 TACATTGTATCGA
1 TACAATGTATCGA
5881917 TACAATGTATCGA
1 TACAATGTATCGA
5881930 TACA
1 TACA
5881934 TTGCTTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:5883775 original size:32 final size:33
Alignment explanation
Indices: 5883715--5883776 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
5883705 TTCAACGATT
5883715 TGTATCGATACATAAAATGTTGTATCGATATAA
1 TGTATCGATACATAAAATGTTGTATCGATATAA
* * *
5883748 TGTATTGATACAT-AAGTTTTGTATCGATA
1 TGTATCGATACATAAAATGTTGTATCGATA
5883777 CAATTTAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATATAA
Found at i:5883839 original size:13 final size:13
Alignment explanation
Indices: 5883821--5883845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5883811 ATTACTCAAA
5883821 TGTATCGATACAT
1 TGTATCGATACAT
5883834 TGTATCGATACA
1 TGTATCGATACA
5883846 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5883897 original size:52 final size:53
Alignment explanation
Indices: 5883834--5883979 Score: 181
Period size: 52 Copynumber: 2.8 Consensus size: 53
5883824 ATCGATACAT
***
5883834 TGTATCGATACACCGAT-CTTTGTATCAATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
** *
5883886 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
* * * *
5883938 TGTATCCATACA-CTATTAAATGTATCGATACATGCAGGCAAA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCAGGCAAA
5883980 ATTTCATATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (53 bp):
TGTATCGATACACCGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
Found at i:5896620 original size:15 final size:15
Alignment explanation
Indices: 5896594--5896643 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5896584 TAAAAATGCT
5896594 AAAAAAGCAAAAGCAC
1 AAAAAAG-AAAAGCAC
*
5896610 AAAAAAGAAAAACAC
1 AAAAAAGAAAAGCAC
*
5896625 AATAAAA-AAAAGAAC
1 AA-AAAAGAAAAGCAC
5896640 AAAA
1 AAAA
5896644 TGAAAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 17 0.57
16 11 0.37
ACGTcount: A:0.78, C:0.12, G:0.08, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAGCAC
Found at i:5898163 original size:31 final size:31
Alignment explanation
Indices: 5898060--5898183 Score: 130
Period size: 31 Copynumber: 4.1 Consensus size: 31
5898050 AGTAAAATAA
* **
5898060 CCTT-TTAAAAGTCCACGACTTAGTGTTATC
1 CCTTCTTAAAAGTCCACGACTCAGTGGCATC
* * *
5898090 CCCTC-TAAAAGTCCACAACTCAG-CGCAT-
1 CCTTCTTAAAAGTCCACGACTCAGTGGCATC
* *
5898118 CCTTTTTTAAAGTCCACGACTCAGTGGCATC
1 CCTTCTTAAAAGTCCACGACTCAGTGGCATC
* *
5898149 CCTTCTTCAAAGTCCACGACTCAGTGGCACC
1 CCTTCTTAAAAGTCCACGACTCAGTGGCATC
5898180 CCTT
1 CCTT
5898184 TCTAAAGTTC
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
28 3 0.04
29 18 0.24
30 23 0.30
31 32 0.42
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (31 bp):
CCTTCTTAAAAGTCCACGACTCAGTGGCATC
Found at i:5898237 original size:29 final size:29
Alignment explanation
Indices: 5898200--5898362 Score: 118
Period size: 29 Copynumber: 5.7 Consensus size: 29
5898190 GTTCATAACC
5898200 TTTTAAAGTCCACAACTCTATGGCACCTT
1 TTTTAAAGTCCACAACTCTATGGCACCTT
* * *
5898229 TTTTAAAGTCTACAACTCTGTAGCACCTT
1 TTTTAAAGTCCACAACTCTATGGCACCTT
* * * * *
5898258 TTTT-AAGTCTATAACTTTGTGGCATCTT
1 TTTTAAAGTCCACAACTCTATGGCACCTT
* * * * *
5898286 TTTCAATGTCCATAACT-TAGTGGCAATCTC
1 TTTTAAAGTCCACAACTCTA-TGGC-ACCTT
* * *
5898316 TTTCAAAGTCCATAACTCCATGGCA--TT
1 TTTTAAAGTCCACAACTCTATGGCACCTT
*
5898343 CTTTTAAAGTCTACAACTCT
1 -TTTTAAAGTCCACAACTCT
5898363 GTTGCGTCTT
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
27 1 0.01
28 39 0.35
29 45 0.41
30 24 0.22
31 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTTAAAGTCCACAACTCTATGGCACCTT
Found at i:5898327 original size:30 final size:29
Alignment explanation
Indices: 5898262--5898353 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 29
5898252 CACCTTTTTT
* * *
5898262 AAGTCTATAACTTTGTGGCATCTTTTTCA
1 AAGTCCATAACTTAGTGGCATCTCTTTCA
*
5898291 ATGTCCATAACTTAGTGGCAATCTCTTTCA
1 AAGTCCATAACTTAGTGGC-ATCTCTTTCA
* *
5898321 AAGTCCATAACTCCA-TGGCAT-TCTTTTA
1 AAGTCCATAACT-TAGTGGCATCTCTTTCA
5898349 AAGTC
1 AAGTC
5898354 TACAACTCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 11 0.20
29 18 0.33
30 24 0.44
31 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (29 bp):
AAGTCCATAACTTAGTGGCATCTCTTTCA
Found at i:5898460 original size:29 final size:29
Alignment explanation
Indices: 5898200--5898515 Score: 152
Period size: 28 Copynumber: 11.0 Consensus size: 29
5898190 GTTCATAACC
* * *
5898200 TTTTAAAGTCCACAACTCTATGGCACCTT
1 TTTTAAAGTCTACAACTCTGTGGCACCCT
*
5898229 TTTTAAAGTCTACAACTCTGTAGCA-CCT
1 TTTTAAAGTCTACAACTCTGTGGCACCCT
* * * *
5898257 TTTTTAAGTCTATAACTTTGTGGCA-TCT
1 TTTTAAAGTCTACAACTCTGTGGCACCCT
* * * **
5898285 TTTTCAATGTCCATAACT-TAGTGGCAATCT
1 TTTT-AAAGTCTACAACTCT-GTGGCACCCT
* * * ** **
5898315 CTTTCAAAGTCCATAACTCCATGGCATTC-
1 -TTTTAAAGTCTACAACTCTGTGGCACCCT
* **
5898344 TTTTAAAGTCTACAACTCTGTTGC-GTCT
1 TTTTAAAGTCTACAACTCTGTGGCACCCT
* * *
5898372 TTTTAAAATCTACAA-TTTCATGGCACCC-
1 TTTTAAAGTCTACAACTCT-GTGGCACCCT
* *
5898400 TCTTAAAGTC--C-ACTCTGTGACACTCCT
1 TTTTAAAGTCTACAACTCTGTGGCAC-CCT
* *
5898427 TTTTAAAGTCTACAACTCCGTAGCACCCT
1 TTTTAAAGTCTACAACTCTGTGGCACCCT
* * *
5898456 TTTTAAAGT-TCACAAGTCAGTGGTATCCCT
1 TTTTAAAGTCT-ACAACTCTGTGGCA-CCCT
* * *
5898486 TTTCAAAG-CTCACAAGTCTGTGGCATCCT
1 TTTTAAAGTCT-ACAACTCTGTGGCACCCT
5898515 T
1 T
5898516 CTCAAAGCTC
Statistics
Matches: 223, Mismatches: 47, Indels: 34
0.73 0.15 0.11
Matches are distributed among these distances:
25 6 0.03
26 5 0.02
27 13 0.06
28 74 0.33
29 66 0.30
30 56 0.25
31 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (29 bp):
TTTTAAAGTCTACAACTCTGTGGCACCCT
Found at i:5898521 original size:29 final size:29
Alignment explanation
Indices: 5898460--5898578 Score: 150
Period size: 29 Copynumber: 4.1 Consensus size: 29
5898450 CACCCTTTTT
* * *
5898460 AAAGTTCACAAGTCAGTGGTATCCCTTTTC
1 AAAGCTCACAAGTCAGTGGCAT-CCTTCTC
*
5898490 AAAGCTCACAAGTCTGTGGCATCCTTCTC
1 AAAGCTCACAAGTCAGTGGCATCCTTCTC
5898519 AAAGCTCACAAGTCAGTGGCATCCTT-TC
1 AAAGCTCACAAGTCAGTGGCATCCTTCTC
* * * *
5898547 CAAGCCCACAAGTCAGTGGTAACCTTCTC
1 AAAGCTCACAAGTCAGTGGCATCCTTCTC
5898576 AAA
1 AAA
5898579 AGCCCACATA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 24 0.31
29 35 0.45
30 19 0.24
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
AAAGCTCACAAGTCAGTGGCATCCTTCTC
Found at i:5898574 original size:57 final size:59
Alignment explanation
Indices: 5898460--5898578 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 59
5898450 CACCCTTTTT
* * * * *
5898460 AAAGTTCACAAGTCAGTGGTATCCCTTTTCAAAGCTCACAAGTCTGTGGCATCCTTCTC
1 AAAGCTCACAAGTCAGTGGCATCCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCTC
* *
5898519 AAAGCTCACAAGTCAGTGGCAT-CC-TTTCCAAGCCCACAAGTCAGTGGTAACCTTCTC
1 AAAGCTCACAAGTCAGTGGCATCCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCTC
5898576 AAA
1 AAA
5898579 AGCCCACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 31 0.58
58 2 0.04
59 20 0.38
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAGCTCACAAGTCAGTGGCATCCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCTC
Found at i:5898952 original size:156 final size:155
Alignment explanation
Indices: 5898684--5899883 Score: 537
Period size: 156 Copynumber: 7.8 Consensus size: 155
5898674 AATGTCGATA
* * * * * * * *
5898684 GCCTTGAATCAGCACATTGGCACTCTTCTCTTCTTTAAGTCCAATATTGATGGCCCTGGATCAGC
1 GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
* * * * * * * * * * *
5898749 ATATTAGCAC-CCTCATCATTTTTAAGCCTGATATCGCTGGCCTTAAATCAGCATATTAGCACAT
66 ACATTGGCACTCTTC-TCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCAC-T
* * *
5898813 TTCTCATCTTTAAGTCCAATATTACTG
129 TTCTCATTTTTAAGCCCAATATTGCTG
* * * *
5898840 GCTTTAAATCAGCATATTGGCACCCTTATCATCTTTAAGTCCAATGTCGTTGGCCTTGAATAAGC
1 GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
* * * *
5898905 ACATTGGCACTATTCTCATCTTTAAGTCTAATGTCGCTGGTCATAAATTAACACATTGGTACTCT
66 ACATTGGCACTCTTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCACT-T
* * *
5898970 TATCATTTTTAAGCCCAATATCGTTG
130 TCTCATTTTTAAGCCCAATATTGCTG
* * * * * *
5898996 GCCTTGAATCAACATATTAAG-ACCTTTCTCATTTTTAAGTCCAATGTCGTTGGCCTTGAATCAG
1 GCCTTAAATCAGCATATT-GGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAG
* * * * * * * **
5899060 CACATTGGCACTTTTCTTATTTTTAAGTCCAATGTTGCTAGTCTTGAATTAGCACATTGGCACCC
65 CACATTGGCACTCTTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCACTT
*
5899125 TCATCATTTTTAAGCCCAATATTGCTA
130 TC-TCATTTTTAAGCCCAATATTGCTG
* ** * * * * *
5899152 GCCTTAAATCAGCTTATTGGCACATTTCTAATCTTTAAGTTCGATATCACTT-GCCTTGAATTAG
1 GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATC-GTTGGCCTTGAATCAG
* * * *
5899216 CATATTGGCACCCTTATTATCTTTAAGTCTAATGT---T-G-C------TAGC-C-TTGGCACTC
65 CACATTGGCACTCTTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCACT-
** * * * ***
5899268 TTCTCATCCTTAAGTCTAATGTCATTG
129 TTCTCATTTTTAAGCCCAATATTGCTG
* * * * * * *
5899295 GTCTTGAATCAGCACATTGGCACCC-TCATCATTTTTAAG-CCTGATATCGCTAGCCTTGAATCA
1 GCCTTAAATCAGCATATTGGCACCCTTC-TCATCTTTAAGTCC-AATATCGTTGGCCTTGAATCA
* * * * * * * * ** * * *
5899358 GCATATTAGCAC-CTTTCTCATCTTGAAGTCCAATATCACTAGCCTCGAATCAGTATATTGGCAC
64 GCACATTGGCACTC-TTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCA-
* * * * *
5899422 CCTTATCATCTTTAAGTCCAATATTGCTA
127 CTTTCTCATTTTTAAGCCCAATATTGCTG
* * ** * * * * * *
5899451 GCCTTGAATCAGCACATTGGTTCCC-TCATTATCTTTAACTACGATATC-TCT-ACCTTAAATCA
1 GCCTTAAATCAGCATATTGGCACCCTTC-TCATCTTTAAGTCCAATATCGT-TGGCCTTGAATCA
* * * * * * * * * * * * ** * *
5899513 ACATAGTGACAC-CTTCATCATTTTTAA-ACTCGATATAGCTGGCCTTGAATCAAAATATTGACA
64 GCACATTGGCACTCTTC-TCATCTTTAAGTCT-AATGTCGCTGGTCTTAAATTAGCACATTGGCA
* * ** **
5899576 CCTTTCTCATCTTTAAGTCTGATATCACTG
127 -CTTTCTCATTTTTAAGCCCAATATTGCTG
* * * * ** * *
5899606 ACCTTGAATCCGCATATTAGCACATTTCTCATCTTTAAGTCCAATATCGTTGGCCTTAAATTAGC
1 GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
* * *** * * *
5899671 -CAATTGGCACT-TTCATCATCTTTAAGTCTGATATCGCTAAACTTGAATCAGCATATTGGCACC
66 AC-ATTGGCACTCTTC-TCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCA-C
* * * ** **
5899734 TTTCTCATCTTTAAGTCTAACGTCACTG
128 TTTCTCATTTTTAAGCCCAATATTGCTG
* * ** ** * *
5899762 GCCTTGAATCAGTATATTGGCACTTTTCTCATCTTTAAGTCCAATATCACTAGCATTGAATC-GC
1 GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
* * * * * * * * * *
5899826 ATATTGGCACTTTTATCATCTTCAAATCTAAGGTCGCTGGCCTTGAATCAACACATTG
66 ACATTGGCACTCTTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTG
5899884 ACACCCTTAT
Statistics
Matches: 805, Mismatches: 202, Indels: 75
0.74 0.19 0.07
Matches are distributed among these distances:
142 5 0.01
143 94 0.12
144 3 0.00
145 4 0.00
146 1 0.00
147 1 0.00
148 1 0.00
151 1 0.00
152 1 0.00
153 1 0.00
154 6 0.01
155 154 0.19
156 524 0.65
157 9 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (155 bp):
GCCTTAAATCAGCATATTGGCACCCTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
ACATTGGCACTCTTCTCATCTTTAAGTCTAATGTCGCTGGTCTTAAATTAGCACATTGGCACTTT
CTCATTTTTAAGCCCAATATTGCTG
Found at i:5899132 original size:104 final size:104
Alignment explanation
Indices: 5898667--5900102 Score: 602
Period size: 104 Copynumber: 13.9 Consensus size: 104
5898657 CATGTCTTTC
* *
5898667 TAAGTCCAATGTCGA-TAGCCTTGAATCAGCACATTGGCACTCTTC-TC-TTCTTTAAGTCCAAT
1 TAAGTCCAATATC-ACTAGCCTTGAATCAGCACATTGGCAC-CCTCATCATT-TTTAAGTCCAAT
* * * * * * * ** *
5898729 ATTGATGGCCCTGGATCAGCATATTAGCAC-CCTCATCATTTT
63 ATCGCTAGCCTTGAATCAGCACATTGGCACTTTTC-TCATCTT
* * * * * * ** *
5898771 TAAG-CCTGATATCGCTGGCCTTAAATCAGCATATTAGCACATTTC-TCATCTTTAAGTCCAATA
1 TAAGTCC-AATATCACTAGCCTTGAATCAGCACATTGGCAC-CCTCATCATTTTTAAGTCCAATA
** * * * * ** *
5898834 TTACTGGCTTTAAATCAGCATATTGGCACCCTTATCATCTT
64 TCGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* ** * * ** * * *
5898875 TAAGTCCAATGTCGTTGGCCTTGAATAAGCACATTGGCACTATTC-TCATCTTTAAGTCTAATGT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCAC-CCTCATCATTTTTAAGTCCAATAT
* * * * * * * * * *
5898939 CGCTGGTCATAAATTAACACATTGGTACTCTTATCATTTT
65 CGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* ** * * * * * *
5898979 TAAGCCCAATATCGTTGGCCTTGAATCAACATATTAAG-ACCTTTC-TCATTTTTAAGTCCAATG
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATT-GGCACC-CTCATCATTTTTAAGTCCAATA
* * * *
5899042 TCGTTGGCCTTGAATCAGCACATTGGCACTTTTCTTATTTT
64 TCGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* ** * * * *
5899083 TAAGTCCAATGTTGCTAGTCTTGAATTAGCACATTGGCACCCTCATCATTTTTAAGCCCAATATT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCCAATATC
* ** * *
5899148 GCTAGCCTTAAATCAGCTTATTGGCACATTTCTAATCTT
66 GCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* * * * * * * *
5899187 TAAGTTCGATATCACTTGCCTTGAATTAGCATATTGGCACCCTTATTATCTTTAAGT-C--TA--
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCCAATATC
* * * *
5899247 -AT-G--TTG-CT-AGC-C-TTGGCACTCTTCTCATCCT
66 GCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* * * * * *
5899278 TAAGTCTAATGTCATTGGTCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAG-CCTGATAT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCC-AATAT
* * *
5899342 CGCTAGCCTTGAATCAGCATATTAGCACCTTTCTCATCTT
65 CGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* * * * * * *
5899382 GAAGTCCAATATCACTAGCCTCGAATCAGTATATTGGCACCCTTATCATCTTTAAGTCCAATATT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCCAATATC
* **
5899447 GCTAGCCTTGAATCAGCACATTGGTTCCCTCAT-T-ATCTT
66 GCTAGCCTTGAATCAGCACATTGG--CACTTTTCTCATCTT
* * * * * * * * * * * *
5899486 TAACTACGATATCTCTA-CCTTAAATCAACATAGTGACACCTTCATCATTTTTAA-ACTCGATAT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTC-CAATAT
* * ** * * *
5899549 AGCTGGCCTTGAATCAAAATATTGACACCTTTCTCATCTT
65 CGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
** * * * ** *
5899589 TAAGTCTGATATCACT-GACCTTGAATCCGCATATTAGCACATTTC-TCATCTTTAAGTCCAATA
1 TAAGTCCAATATCACTAG-CCTTGAATCAGCACATTGGCAC-CCTCATCATTTTTAAGTCCAATA
* * * *
5899652 TCGTTGGCCTTAAATTAGC-CAATTGGCAC-TTTCATCATCTT
64 TCGCTAGCCTTGAATCAGCAC-ATTGGCACTTTTC-TCATCTT
** * ** * * * * **
5899693 TAAGTCTGATATCGCTAAACTTGAATCAGCATATTGGCACCTTTC-TCATCTTTAAGTCTAACGT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACC-CTCATCATTTTTAAGTCCAATAT
* * * *
5899757 CACTGGCCTTGAATCAGTATATTGGCACTTTTCTCATCTT
65 CGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* * ** * * * * * **
5899797 TAAGTCCAATATCACTAGCATTGAATC-GCATATTGGCACTTTTATCATCTTCAAATCTAAGGTC
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCCAATATC
* * * ** *
5899861 GCTGGCCTTGAATCAACACATTGACACCCTTATCATCTT
66 GCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
** * ** * ** * * *
5899900 TAAGTCTGATTTCACTAGCCTTGAATCAGCATGTTGACACTTGTCAAAACCTTCTTTCCAAAGCC
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCAC-CCTC--ATCATT-TTT---AAGTC
* * * * *
5899965 CAATGTCACTAGCCTTGAATCAGCACATTGGCACCTTTATCATATT
59 CAATATCGCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
* * ** * * * * * * *
5900011 TAAATCCAATGTTGCTGGCCTTGAATCAGCACTTTGACACCC-CTATCATCTTTAAGTCTAGTGT
1 TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTC-ATCATTTTTAAGTCCAATAT
* *
5900075 CGCAAGCCTTGAAT-ATACACATTGGCAC
65 CGCTAGCCTTGAATCA-GCACATTGGCAC
5900103 ATTTGTCAAG
Statistics
Matches: 1017, Mismatches: 266, Indels: 98
0.74 0.19 0.07
Matches are distributed among these distances:
91 60 0.06
93 3 0.00
94 3 0.00
95 2 0.00
97 2 0.00
98 2 0.00
100 3 0.00
101 6 0.01
102 7 0.01
103 163 0.16
104 660 0.65
105 19 0.02
106 3 0.00
107 6 0.01
108 5 0.00
109 1 0.00
111 72 0.07
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (104 bp):
TAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGTCCAATATC
GCTAGCCTTGAATCAGCACATTGGCACTTTTCTCATCTT
Found at i:5899261 original size:52 final size:52
Alignment explanation
Indices: 5898667--5899244 Score: 417
Period size: 52 Copynumber: 11.1 Consensus size: 52
5898657 CATGTCTTTC
* * * * * *
5898667 TAAGTCCAATGTCGATAGCCTTGAATCAGCACATTGGCACTCTTCTCTTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * * *
5898719 TAAGTCCAATATTGATGGCCCTGGATCAGCATATTAGCACCC-TCATCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTC-TCATCTT
* * * **
5898771 TAAG-CCTGATATCGCTGGCCTTAAATCAGCATATTAGCACATTTCTCATCTT
1 TAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
** * * *
5898823 TAAGTCCAATATTACTGGCTTTAAATCAGCATATTGGCACCCTTATCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * **
5898875 TAAGTCCAATGTCGTTGGCCTTGAATAAGCACATTGGCACTATTCTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * * * * * * * * *
5898927 TAAGTCTAATGTCGCTGGTCATAAATTAACACATTGGTACTCTTATCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * * *
5898979 TAAGCCCAATATCGTTGGCCTTGAATCAACATATTAAG-ACCTTTCTCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-GGCACCCTTCTCATCTT
* * * ** * *
5899031 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTTTTCTTATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * * * *
5899083 TAAGTCCAATGTTGCTAGTCTTGAATTAGCACATTGGCACCC-TCATCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTC-TCATCTT
* * * * * ** *
5899135 TAAGCCCAATATTGCTAGCCTTAAATCAGCTTATTGGCACATTTCTAATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
* * * * * * *
5899187 TAAGTTCGATATCACTTGCCTTGAATTAGCATATTGGCACCCTTATTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
5899239 TAAGTC
1 TAAGTC
5899245 TAATGTTGCT
Statistics
Matches: 416, Mismatches: 102, Indels: 16
0.78 0.19 0.03
Matches are distributed among these distances:
51 7 0.02
52 402 0.97
53 7 0.02
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (52 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTCATCTT
Found at i:5899353 original size:52 final size:52
Alignment explanation
Indices: 5899297--5900088 Score: 411
Period size: 52 Copynumber: 15.1 Consensus size: 52
5899287 TGTCATTGGT
* * * *
5899297 CTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCTGATATCGCTAGC
1 CTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGCCTAATATCGCTAGC
* * *
5899349 CTTGAATCAGCATATTAGCACCTTTC-TCATCTTGAAGTCC-AATATCACTAGC
1 CTTGAATCAGCATATTGGCACC-TTCATCATCTTTAAG-CCTAATATCGCTAGC
* * *
5899401 CTCGAATCAGTATATTGGCACCCTT-ATCATCTTTAAGTCC-AATATTGCTAGC
1 CTTGAATCAGCATATTGGCA-CCTTCATCATCTTTAAG-CCTAATATCGCTAGC
* ** * * *
5899453 CTTGAATCAGCACATTGGTTCCCTCATTATCTTTAA--CTACGATATCTCTA-C
1 CTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGCCTA--ATATCGCTAGC
* * * * * * * * *
5899504 CTTAAATCAACATAGTGACACCTTCATCATTTTTAA-ACTCGATATAGCTGGC
1 CTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGCCT-AATATCGCTAGC
** * * * *
5899556 CTTGAATCAAAATATTGACACCTTTC-TCATCTTTAAGTCTGATATCACT-GAC
1 CTTGAATCAGCATATTGGCACC-TTCATCATCTTTAAGCCTAATATCGCTAG-C
* * * * *
5899608 CTTGAATCCGCATATTAGCACATTTC-TCATCTTTAAGTCC-AATATCGTTGGC
1 CTTGAATCAGCATATTGGCAC-CTTCATCATCTTTAAG-CCTAATATCGCTAGC
* * * * * **
5899660 CTTAAATTAGCCA-ATTGGCACTTTCATCATCTTTAAGTCTGATATCGCTAAA
1 CTTGAATCAG-CATATTGGCACCTTCATCATCTTTAAGCCTAATATCGCTAGC
* ** * *
5899712 CTTGAATCAGCATATTGGCACCTTTC-TCATCTTTAAGTCTAACGTCACTGGC
1 CTTGAATCAGCATATTGGCACC-TTCATCATCTTTAAGCCTAATATCGCTAGC
* * *
5899764 CTTGAATCAGTATATTGGCACTTTTC-TCATCTTTAAGTCC-AATATCACTAGC
1 CTTGAATCAGCATATTGGCAC-CTTCATCATCTTTAAG-CCTAATATCGCTAGC
* * * * ** ** *
5899816 ATTGAATC-GCATATTGGCACTTTTATCATCTTCAAATCTAAGGTCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGCCTAATATCGCTAGC
* * * * * * *
5899867 CTTGAATCAACACATTGACACCCTT-ATCATCTTTAAGTCTGATTTCACTAGC
1 CTTGAATCAGCATATTGGCA-CCTTCATCATCTTTAAGCCTAATATCGCTAGC
* * * * * * * *
5899919 CTTGAATCAGCATGTTGACACTTGTCAAAACCTTCTTTCCAAAGCCCAATGTCACTAGC
1 CTTGAATCAGCATATTGGCACCT-TC---ATCATCTTT---AAGCCTAATATCGCTAGC
* * * * * * *
5899978 CTTGAATCAGCACATTGGCACCTTTATCATATTTAAATCC-AATGTTGCTGGC
1 CTTGAATCAGCATATTGGCACCTTCATCATCTTT-AAGCCTAATATCGCTAGC
* * * * * *
5900030 CTTGAATCAGCACT-TTGACACC-CCTATCATCTTTAAGTCTAGTGTCGCAAGC
1 CTTGAATCAGCA-TATTGGCACCTTC-ATCATCTTTAAGCCTAATATCGCTAGC
5900082 CTTGAAT
1 CTTGAAT
5900089 ATACACATTG
Statistics
Matches: 567, Mismatches: 134, Indels: 78
0.73 0.17 0.10
Matches are distributed among these distances:
49 1 0.00
50 5 0.01
51 84 0.15
52 403 0.71
53 27 0.05
55 6 0.01
56 7 0.01
58 1 0.00
59 33 0.06
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (52 bp):
CTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGCCTAATATCGCTAGC
Found at i:5899396 original size:195 final size:195
Alignment explanation
Indices: 5899100--5899456 Score: 543
Period size: 195 Copynumber: 1.8 Consensus size: 195
5899090 AATGTTGCTA
* *
5899100 GTCTTGAATTAGCACATTGGCACCCTCATCATTTTTAAGCCCAATATTGCTAGCCTTAAATCAGC
1 GTCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCCAATATCGCTAGCCTTAAATCAGC
* * * * * * * *
5899165 TTATTGGCACATTTCTAATCTTTAAGTTCGATATCACTTGCCTTGAATTAGCATATTGGCACCCT
66 ATATTAGCACATTTCTAATCTTGAAGTCCAATATCACTAGCCTCGAATCAGCATATTGGCACCCT
* * *
5899230 TATTATCTTTAAGTCTAATGTTGCTAGCCTTGGCACTCTTCTCATCCTTAAGTCTAATGTCATTG
131 TATCATCTTTAAGTCCAATATTGCTAGCCTTGGCACTCTTCTCATCCTTAAGTCTAATGTCATTG
** *
5899295 GTCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCTGATATCGCTAGCCTTGAATCAGC
1 GTCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCCAATATCGCTAGCCTTAAATCAGC
* * *
5899360 ATATTAGCACCTTTCTCATCTTGAAGTCCAATATCACTAGCCTCGAATCAGTATATTGGCACCCT
66 ATATTAGCACATTTCTAATCTTGAAGTCCAATATCACTAGCCTCGAATCAGCATATTGGCACCCT
5899425 TATCATCTTTAAGTCCAATATTGCTAGCCTTG
131 TATCATCTTTAAGTCCAATATTGCTAGCCTTG
5899457 AATCAGCACA
Statistics
Matches: 143, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
195 143 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (195 bp):
GTCTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCCAATATCGCTAGCCTTAAATCAGC
ATATTAGCACATTTCTAATCTTGAAGTCCAATATCACTAGCCTCGAATCAGCATATTGGCACCCT
TATCATCTTTAAGTCCAATATTGCTAGCCTTGGCACTCTTCTCATCCTTAAGTCTAATGTCATTG
Found at i:5899925 original size:207 final size:205
Alignment explanation
Indices: 5899297--5899931 Score: 618
Period size: 207 Copynumber: 3.1 Consensus size: 205
5899287 TGTCATTGGT
* * * ** * * *
5899297 CTTGAATCAGCACATTGGCACCCTCATCATTTTTAAGCCTGATATCGCTAGCCTTGAATCAGCAT
1 CTTGAATCAGCATATTGGCACCTTCATCATTTTTAAGACT-ACGTCACTGGCCTTGAATCAGAAT
* * * * **
5899362 ATTAGCACCTTTCTCATCTTGAAGTCCAATATCACTAGCCTCGAATCAGTATATTGGCACCCTTA
65 ATTGGCACCTTTCTCATCTTTAAGTCCAATATCACTAGCCTTGAATC-GCATATTGGCACATTTA
* * ** * * *
5899427 TCATCTTTAAGTCCAATATTGCTAGCCTTGAATCAGCACATTGGTTCCCTCATTATCTTTAACTA
129 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTTATCATCTTTAAGT-
*
5899492 C-GATATCTCTAC
193 CTGATATCACTAC
* * * * * *
5899504 CTTAAATCAACATAGTGACACCTTCATCATTTTTAA-ACT-CGATATAGCTGGCCTTGAATCAAA
1 CTTGAATCAGCATATTGGCACCTTCATCATTTTTAAGACTACG-T-CA-CTGGCCTTGAATCAGA
* ** *
5899567 ATATTGACACCTTTCTCATCTTTAAGTCTGATATCACT-GACCTTGAATCCGCATATTAGCACAT
63 ATATTGGCACCTTTCTCATCTTTAAGTCCAATATCACTAG-CCTTGAAT-CGCATATTGGCACAT
* * * * *
5899631 TTCTCATCTTTAAGTCCAATATCGTTGGCCTTAAATTAGC-CAATTGGCA-CTTTCATCATCTTT
126 TTATCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAC-ATTGGCACCCTT-ATCATCTTT
* *
5899694 AAGTCTGATATCGCTAAA
189 AAGTCTGATATCACT-AC
* * *
5899712 CTTGAATCAGCATATTGGCACCTTTC-TCATCTTTAAGTCTAACGTCACTGGCCTTGAATCAGTA
1 CTTGAATCAGCATATTGGCACC-TTCATCATTTTTAAGACT-ACGTCACTGGCCTTGAATCAGAA
* * *
5899776 TATTGGCACTTTTCTCATCTTTAAGTCCAATATCACTAGCATTGAATCGCATATTGGCACTTTTA
64 TATTGGCACCTTTCTCATCTTTAAGTCCAATATCACTAGCCTTGAATCGCATATTGGCACATTTA
* * * ** * *
5899841 TCATCTTCAAATCTAAGGTCGCTGGCCTTGAATCAACACATTGACACCCTTATCATCTTTAAGTC
129 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTTATCATCTTTAAGTC
*
5899906 TGATTTCACTAGC
194 TGATATCACTA-C
5899919 CTTGAATCAGCAT
1 CTTGAATCAGCAT
5899932 GTTGACACTT
Statistics
Matches: 342, Mismatches: 69, Indels: 34
0.77 0.16 0.08
Matches are distributed among these distances:
205 1 0.00
206 8 0.02
207 235 0.69
208 88 0.26
209 7 0.02
210 1 0.00
211 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (205 bp):
CTTGAATCAGCATATTGGCACCTTCATCATTTTTAAGACTACGTCACTGGCCTTGAATCAGAATA
TTGGCACCTTTCTCATCTTTAAGTCCAATATCACTAGCCTTGAATCGCATATTGGCACATTTATC
ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTTATCATCTTTAAGTCTG
ATATCACTAC
Found at i:5900732 original size:19 final size:19
Alignment explanation
Indices: 5900708--5900749 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5900698 TGAATGTATT
5900708 GATACATATAAAATATATC
1 GATACATATAAAATATATC
*
5900727 GATACATGTAAAATATATC
1 GATACATATAAAATATATC
5900746 GATA
1 GATA
5900750 TAGGATCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
GATACATATAAAATATATC
Found at i:5904759 original size:22 final size:21
Alignment explanation
Indices: 5904734--5904774 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5904724 ATTAAATCTG
5904734 AAAAATTAAATAACTATTTGAT
1 AAAAATTAAATAA-TATTTGAT
*
5904756 AAAAATTTAATAATATTTG
1 AAAAATTAAATAATATTTG
5904775 CATGAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAATTAAATAATATTTGAT
Found at i:5906359 original size:157 final size:156
Alignment explanation
Indices: 5906132--5906449 Score: 397
Period size: 157 Copynumber: 2.0 Consensus size: 156
5906122 TTTTTTAAAT
* * * *
5906132 TTTAATGTCTTAAAATATTGTTTTGGGGAAATACTTTCCTGAATGGTTTAGGAAGTATTACATGC
1 TTTAATGTCTTAAAATATTGTTTTGGGAAAAAACTTTCCTAAATGGTTTAGGAAATATTACATGC
* *
5906197 TAAATAATTTG-TCCAAGTTAAAAAAAAAATATCTAAAAGTTAAATAATATCTTAATTAAGACAA
66 TAAATAATTTGTTCCAA-TTAAAAAAAAAATATCTAAAAATTAAATAATATCCTAATTAAGACAA
*
5906261 ACT-ACCTAAAAGTTAGGTAATGTCCAA
130 A-TAACATAAAAGTTAGGTAATGTCCAA
* * * *
5906288 TTTAATGTCTTAAAATGTTGTTTTTGGAAAACAAGTTTCTTAAATGGTTTAGGAAATATTACATG
1 TTTAATGTCTTAAAATATTGTTTTGGGAAAA-AACTTTCCTAAATGGTTTAGGAAATATTACATG
* * * * * * * * *
5906353 CTAAATAGTTTGTTCCAATTAAGATAAAATTTTTTAAAAATTAGATAATGTCCTAATTAAGTCAA
65 CTAAATAATTTGTTCCAATTAAAAAAAAAATATCTAAAAATTAAATAATATCCTAATTAAGACAA
**
5906418 ATAACATAAAAGTTAGGTAATGTTTAA
130 ATAACATAAAAGTTAGGTAATGTCCAA
5906445 TTTAA
1 TTTAA
5906450 GACAAACTTC
Statistics
Matches: 137, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
156 29 0.21
157 103 0.75
158 5 0.04
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.37
Consensus pattern (156 bp):
TTTAATGTCTTAAAATATTGTTTTGGGAAAAAACTTTCCTAAATGGTTTAGGAAATATTACATGC
TAAATAATTTGTTCCAATTAAAAAAAAAATATCTAAAAATTAAATAATATCCTAATTAAGACAAA
TAACATAAAAGTTAGGTAATGTCCAA
Found at i:5907324 original size:156 final size:156
Alignment explanation
Indices: 5907035--5907346 Score: 520
Period size: 156 Copynumber: 2.0 Consensus size: 156
5907025 TGTTAAATTT
* * *
5907035 ATTTTTGAATTTATATATGAGTGATATATAATTGAATAAATGCTATGCATGCTAATTAAACAAAA
1 ATTTTTGAACTTATAAATGAGTGATATATAATTGAATAAATGCTATGAATGCTAATTAAACAAAA
*
5907100 CAATGAAACCTAATTTAAATGATAAAAATCCATCATAAAATATTGTGTCCATACCTAAGTATAAC
66 CAATGAAACCTAATTTAAATGATAAAAATCCATCATAAAATATTGAGTCCATACCTAAGTATAAC
5907165 TAGTTGCCTTCCATCATTCATAACAA
131 TAGTTGCCTTCCATCATTCATAACAA
5907191 ATTTTTGAACTTATAAATGTA-TGATATATAATTGAATAAATGCTAT-AAGTGCTAATTAAACAA
1 ATTTTTGAACTTATAAATG-AGTGATATATAATTGAATAAATGCTATGAA-TGCTAATTAAACAA
* * *
5907254 AACAATGAAACCTAATTTAAATGATAAAAATCCATTATAAAATATTGAGTTCATACCTAAGTATG
64 AACAATGAAACCTAATTTAAATGATAAAAATCCATCATAAAATATTGAGTCCATACCTAAGTATA
*
5907319 GCTAGTTGCCTTCCATCATTCATAACAA
129 ACTAGTTGCCTTCCATCATTCATAACAA
5907347 GATACATAAG
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
155 1 0.01
156 144 0.99
157 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (156 bp):
ATTTTTGAACTTATAAATGAGTGATATATAATTGAATAAATGCTATGAATGCTAATTAAACAAAA
CAATGAAACCTAATTTAAATGATAAAAATCCATCATAAAATATTGAGTCCATACCTAAGTATAAC
TAGTTGCCTTCCATCATTCATAACAA
Found at i:5909361 original size:34 final size:34
Alignment explanation
Indices: 5909318--5909385 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
5909308 AGACTGTTAA
*
5909318 AAGTTGAATAATCTTGTTCAAAGTAAAAGAATAT
1 AAGTTGAATAATCTTATTCAAAGTAAAAGAATAT
5909352 AAGTTGAATAATCTTATTCAAAGTAAAAGAATAT
1 AAGTTGAATAATCTTATTCAAAGTAAAAGAATAT
5909386 TATGCAGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (34 bp):
AAGTTGAATAATCTTATTCAAAGTAAAAGAATAT
Found at i:5909425 original size:2 final size:2
Alignment explanation
Indices: 5909418--5909448 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5909408 AAATGTTCAA
5909418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5909449 AATGTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5912224 original size:29 final size:28
Alignment explanation
Indices: 5912176--5912243 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
5912166 TATTATTTAT
*
5912176 TATATTTAA-TATTTATTATTAAAATAA
1 TATATTTAATTATTTAATATTAAAATAA
5912203 TATATTTTAATTATTTAATATTAAAATAA
1 TATA-TTTAATTATTTAATATTAAAATAA
5912232 TATAATTTAATT
1 TAT-ATTTAATT
5912244 GAATAATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 4 0.11
28 5 0.14
29 27 0.73
30 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATTTAATTATTTAATATTAAAATAA
Found at i:5912250 original size:18 final size:18
Alignment explanation
Indices: 5912227--5912267 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5912217 TTAATATTAA
*
5912227 AATAATATAATTTAATTG
1 AATAATATAATTAAATTG
*
5912245 AATAATCTAATTAAATTG
1 AATAATATAATTAAATTG
5912263 -ATAAT
1 AATAAT
5912268 TGAAATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
AATAATATAATTAAATTG
Found at i:5912620 original size:2 final size:2
Alignment explanation
Indices: 5912613--5912645 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5912603 CAGGTTGAGG
5912613 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5912646 CAACGTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5916444 original size:23 final size:23
Alignment explanation
Indices: 5916401--5916445 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5916391 ACCTTTTAAT
* *
5916401 TTTATATTTATTTTAATAATTTA
1 TTTAAATTTATTTTAAAAATTTA
5916424 TTTAAATTT-TTTTATAAAATTT
1 TTTAAATTTATTTTA-AAAATTT
5916446 TTAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAATTTATTTTAAAAATTTA
Found at i:5923799 original size:13 final size:13
Alignment explanation
Indices: 5923781--5923807 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5923771 TATAATAAAC
5923781 ATGTATCGATACA
1 ATGTATCGATACA
5923794 ATGTATCGATACA
1 ATGTATCGATACA
5923807 A
1 A
5923808 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5924625 original size:20 final size:20
Alignment explanation
Indices: 5924602--5924639 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5924592 TATATGTATA
*
5924602 AATGTATTGATACATTCTTC
1 AATGTATTAATACATTCTTC
5924622 AATGTATTAATACATTCT
1 AATGTATTAATACATTCT
5924640 ATCTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (20 bp):
AATGTATTAATACATTCTTC
Found at i:5932938 original size:52 final size:53
Alignment explanation
Indices: 5932857--5932978 Score: 221
Period size: 52 Copynumber: 2.3 Consensus size: 53
5932847 GAAAATTTAT
*
5932857 CTGCATGTATCGATAC-ATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTTAATAATGTATCGATACATCTGGGCAAATTTGC
5932909 CTGCATGTATCGATACAATTT-ATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTTAATAATGTATCGATACATCTGGGCAAATTTGC
5932961 CTGCATGTATCGATACAA
1 CTGCATGTATCGATACAA
5932979 AGATCAGTGT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 64 0.94
53 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (53 bp):
CTGCATGTATCGATACAATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:5932990 original size:52 final size:50
Alignment explanation
Indices: 5932857--5932997 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
5932847 GAAAATTTAT
*
5932857 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
5932909 CTGCATGTATCGATACAATTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAA--AATAGTGTATCGATACATCTGGGCAAATTTGC
5932961 CTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
5932998 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (50 bp):
CTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:5933004 original size:13 final size:13
Alignment explanation
Indices: 5932986--5933010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5932976 CAAAGATCAG
5932986 TGTATCGATACAA
1 TGTATCGATACAA
5932999 TGTATCGATACA
1 TGTATCGATACA
5933011 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5933096 original size:13 final size:13
Alignment explanation
Indices: 5933078--5933102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5933068 CAAAAAAATA
5933078 TGTATCGATACAT
1 TGTATCGATACAT
5933091 TGTATCGATACA
1 TGTATCGATACA
5933103 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5933098 original size:33 final size:33
Alignment explanation
Indices: 5933056--5933122 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5933046 AGTAGCTTAA
5933056 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5933089 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5933122 A
1 A
5933123 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5937799 original size:33 final size:33
Alignment explanation
Indices: 5937762--5937828 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
5937752 CACATGCAGA
* * * *
5937762 TGTATCAATGCAAGTTGTAATTTATCGATACAT
1 TGTATCAATACAAATTGCAATATATCGATACAT
*
5937795 TGTATCAATACAAATTGCAATATATCTATACAT
1 TGTATCAATACAAATTGCAATATATCGATACAT
5937828 T
1 T
5937829 ATGATAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (33 bp):
TGTATCAATACAAATTGCAATATATCGATACAT
Found at i:5937920 original size:21 final size:23
Alignment explanation
Indices: 5937872--5937929 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
5937862 GCTATCCTTC
5937872 GAATGTATCGATAC-ATACATAG
1 GAATGTATCGATACAATACATAG
*
5937894 GAATGTATCGATACAATTC-TA-
1 GAATGTATCGATACAATACATAG
5937915 GAATGTATCGATACA
1 GAATGTATCGATACA
5937930 TCCAGAAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.44
22 16 0.47
23 3 0.09
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (23 bp):
GAATGTATCGATACAATACATAG
Found at i:5944751 original size:32 final size:32
Alignment explanation
Indices: 5944714--5944789 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
5944704 CATTTCATAG
* *
5944714 TGTATCGATACATCTGGGCAAATTTGCCTGTA
1 TGTATCGATACATCTGGGCAAAGTTGCCTGCA
5944746 TGTATCGATACATCTGGGCAAAGTTGCCTGCA
1 TGTATCGATACATCTGGGCAAAGTTGCCTGCA
5944778 TGTATCGATACA
1 TGTATCGATACA
5944790 AAGATCAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATCTGGGCAAAGTTGCCTGCA
Found at i:5944816 original size:13 final size:13
Alignment explanation
Indices: 5944798--5944822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5944788 CAAAGATCAG
5944798 TGTATCGATACAA
1 TGTATCGATACAA
5944811 TGTATCGATACA
1 TGTATCGATACA
5944823 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5944889 original size:19 final size:19
Alignment explanation
Indices: 5944865--5944914 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
5944855 TAGCTTACAT
5944865 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
5944884 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
5944903 TGTATCGATACA
1 TGTATCGATACA
5944915 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:5944921 original size:13 final size:13
Alignment explanation
Indices: 5944903--5944927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5944893 ACAACACTTA
5944903 TGTATCGATACAT
1 TGTATCGATACAT
5944916 TGTATCGATACA
1 TGTATCGATACA
5944928 AATCGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5947406 original size:6 final size:6
Alignment explanation
Indices: 5947397--5947530 Score: 178
Period size: 6 Copynumber: 22.3 Consensus size: 6
5947387 TCTCTCTCTT
* * *
5947397 TATATA TATATA TATATA TATGTA TATATA CATATA TATATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
5947445 TGTATA TATACA TATATA TATATA CATATA TATATA CATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
5947493 TACATA TATATA TATGTA TATATA CATATA TATATA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TA
5947531 CACAAACCTC
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 110 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:5947416 original size:14 final size:14
Alignment explanation
Indices: 5947397--5947530 Score: 178
Period size: 14 Copynumber: 9.6 Consensus size: 14
5947387 TCTCTCTCTT
5947397 TATATATATATATA
1 TATATATATATATA
*
5947411 TATATATGTATATA
1 TATATATATATATA
*
5947425 TACATATATATATA
1 TATATATATATATA
* *
5947439 TGTATATGTATATA
1 TATATATATATATA
*
5947453 TACATATATATATA
1 TATATATATATATA
*
5947467 TACATATATATATA
1 TATATATATATATA
*
5947481 CATATATATATATA
1 TATATATATATATA
* *
5947495 CATATATATATATG
1 TATATATATATATA
*
5947509 TATATATACATATA
1 TATATATATATATA
5947523 TATATATA
1 TATATATA
5947531 CACAAACCTC
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 105 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (14 bp):
TATATATATATATA
Found at i:5947422 original size:22 final size:22
Alignment explanation
Indices: 5947397--5947529 Score: 176
Period size: 22 Copynumber: 6.0 Consensus size: 22
5947387 TCTCTCTCTT
*
5947397 TATATATATATATATATATATG
1 TATATATACATATATATATATG
5947419 TATATATACATATATATATATG
1 TATATATACATATATATATATG
* * *
5947441 TATATGTATATATACATATATATA
1 TATA--TATACATATATATATATG
* * * *
5947465 TATACATATATATATACATATA
1 TATATATACATATATATATATG
5947487 TATATATACATATATATATATG
1 TATATATACATATATATATATG
5947509 TATATATACATATATATATAT
1 TATATATACATATATATATAT
5947530 ACACAAACCT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
22 79 0.81
24 19 0.19
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (22 bp):
TATATATACATATATATATATG
Found at i:5950034 original size:9 final size:10
Alignment explanation
Indices: 5950009--5950043 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5949999 TATTAATGAT
*
5950009 TTATTATTAA
1 TTATTTTTAA
5950019 TTATTTTTAA
1 TTATTTTTAA
5950029 -TATTTTTAA
1 TTATTTTTAA
5950038 TTATTT
1 TTATTT
5950044 ATTTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTTTAA
Found at i:5950629 original size:13 final size:13
Alignment explanation
Indices: 5950611--5950654 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5950601 ATTTAATACG
5950611 ACAAAAAATATAT
1 ACAAAAAATATAT
* *
5950624 ACAAAATATAAAT
1 ACAAAAAATATAT
*
5950637 ACAAAAAATTTAT
1 ACAAAAAATATAT
5950650 A-AAAA
1 ACAAAA
5950655 TCTCACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
ACAAAAAATATAT
Found at i:5951771 original size:2 final size:2
Alignment explanation
Indices: 5951766--5951794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5951756 GTGTGTGTGT
5951766 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5951795 GACAGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5955588 original size:1 final size:1
Alignment explanation
Indices: 5955553--5955579 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5955543 TTTTTTTTTT
5955553 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
5955580 AGAGGGGGGC
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:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:5956636 original size:39 final size:39
Alignment explanation
Indices: 5956593--5956689 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
5956583 AATTATTTTT
*
5956593 AATATTATTTATAAATAAGT-TTGAAATAAAATATATTAA
1 AATATTA-TTATAAATAAGTATTGAAATAAAATATAATAA
** *
5956632 AATATTATTATAAATATTTATTTAAATAAAATATAATAA
1 AATATTATTATAAATAAGTATTGAAATAAAATATAATAA
*
5956671 AACATT-TTA-AAATAA-TATT
1 AATATTATTATAAATAAGTATT
5956690 TTAGATGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 4 0.08
37 5 0.10
38 13 0.25
39 29 0.57
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (39 bp):
AATATTATTATAAATAAGTATTGAAATAAAATATAATAA
Found at i:5963582 original size:15 final size:15
Alignment explanation
Indices: 5963552--5963598 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5963542 TCAAATGTAT
*
5963552 ATTTAATATTAAAATA
1 ATTTAA-ATAAAAATA
5963568 ATTTAAATAAAAAT-
1 ATTTAAATAAAAATA
*
5963582 ATTAAAATTAAAAATA
1 ATTTAAA-TAAAAATA
5963598 A
1 A
5963599 AGTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 14 0.52
16 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTAAATAAAAATA
Found at i:5963690 original size:23 final size:26
Alignment explanation
Indices: 5963664--5963714 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
5963654 ATATAATAAT
5963664 TTTA-TATTTAT-ATATATAT-TTTA
1 TTTACTATTTATAATATATATATTTA
*
5963687 TTTATCTATTTATAATCTATATATTTA
1 TTTA-CTATTTATAATATATATATTTA
5963714 T
1 T
5963715 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
25 7 0.30
26 7 0.30
27 5 0.22
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTACTATTTATAATATATATATTTA
Found at i:5963850 original size:18 final size:18
Alignment explanation
Indices: 5963827--5963865 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5963817 TATTTATAAA
5963827 TAAAAA-TTTTAATTTTAT
1 TAAAAAGTTTTAA-TTTAT
*
5963845 TAAAAAGTTTTGATTTAT
1 TAAAAAGTTTTAATTTAT
5963863 TAA
1 TAA
5963866 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TAAAAAGTTTTAATTTAT
Found at i:5964849 original size:19 final size:20
Alignment explanation
Indices: 5964802--5964849 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
5964792 TCACTTTCAT
** *
5964802 GTATCGATACAATTGAGTAT
1 GTATCGATACAATTGAACAG
*
5964822 GTATTGATACAA-TGAACAG
1 GTATCGATACAATTGAACAG
5964841 GTATCGATA
1 GTATCGATA
5964850 TAAAGGATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
GTATCGATACAATTGAACAG
Found at i:5965516 original size:17 final size:16
Alignment explanation
Indices: 5965478--5965509 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5965468 TATATTCAAT
*
5965478 ATATAAAAATTTTATA
1 ATATAAAAATTTCATA
5965494 ATATAAAAATTTCATA
1 ATATAAAAATTTCATA
5965510 TCTATAACAT
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAAAATTTCATA
Found at i:5966376 original size:29 final size:30
Alignment explanation
Indices: 5966326--5966391 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
5966316 CAACTTAATT
5966326 TTATTTTCAAAATAAATTATCAAAATATTA
1 TTATTTTCAAAATAAATTATCAAAATATTA
* *
5966356 TTATTTT-AAAATTATTTATCAAAATATTA
1 TTATTTTCAAAATAAATTATCAAAATATTA
*
5966385 CTATTTT
1 TTATTTT
5966392 TACATACATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.79
30 7 0.21
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (30 bp):
TTATTTTCAAAATAAATTATCAAAATATTA
Found at i:5967908 original size:13 final size:13
Alignment explanation
Indices: 5967890--5967916 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5967880 ACAATTGTGC
5967890 ATGTATCGATACA
1 ATGTATCGATACA
5967903 ATGTATCGATACA
1 ATGTATCGATACA
5967916 A
1 A
5967917 AGCATTATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5975043 original size:21 final size:21
Alignment explanation
Indices: 5975017--5975060 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5975007 ATTAATAGGA
*
5975017 TTAGTTCAA-AACTAAGCCTAT
1 TTAGTTAAATAACTAAGCC-AT
*
5975038 TTAGTTAAATAAGTAAGCCAT
1 TTAGTTAAATAACTAAGCCAT
5975059 TT
1 TT
5975061 GAATAATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (21 bp):
TTAGTTAAATAACTAAGCCAT
Found at i:5975135 original size:20 final size:21
Alignment explanation
Indices: 5975110--5975152 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5975100 TTAATTAAAT
5975110 TTTTATTTCAAATAAA-ATAA
1 TTTTATTTCAAATAAATATAA
*
5975130 TTTTATTTCATATAAATATAA
1 TTTTATTTCAAATAAATATAA
5975151 TT
1 TT
5975153 AAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATTTCAAATAAATATAA
Found at i:5982355 original size:2 final size:2
Alignment explanation
Indices: 5982348--5982379 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5982338 ACTCTTCAGG
5982348 TC TC 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 TC TC
5982380 ATTTTCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5984253 original size:14 final size:14
Alignment explanation
Indices: 5984234--5984262 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5984224 ATGGTTTAGT
5984234 TGGTTTCTCTCAAG
1 TGGTTTCTCTCAAG
5984248 TGGTTTCTCTCAAG
1 TGGTTTCTCTCAAG
5984262 T
1 T
5984263 AATGCCAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (14 bp):
TGGTTTCTCTCAAG
Found at i:5985103 original size:32 final size:32
Alignment explanation
Indices: 5985067--5985137 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
5985057 ATTACTCATG
*
5985067 AATTTGATGAATATTAAACAAAATTACGT-GTA
1 AATTTGATGAATATTAAACAAAATAAC-TCGTA
* *
5985099 AATTTGATGAATATTAGACATAATAACTCGTA
1 AATTTGATGAATATTAAACAAAATAACTCGTA
5985131 AATTTGA
1 AATTTGA
5985138 CAGTTATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 34 0.97
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (32 bp):
AATTTGATGAATATTAAACAAAATAACTCGTA
Found at i:5987845 original size:2 final size:2
Alignment explanation
Indices: 5987838--5987865 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5987828 GGGTGTCATA
5987838 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
5987866 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5988423 original size:93 final size:93
Alignment explanation
Indices: 5988264--5988448 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 93
5988254 TCAAAAATTA
5988264 TACCAAACACTACTCATGGGGAAGGCTTATTTTGCGTCAATGGTGTATCAAGGACATTAGAGATG
1 TACCAAACACTACTCATGGGGAAGGCTTATTTTGCGTCAATGGTGTATCAAGGACATTAGAGATG
5988329 ATGCCTATGCCTGCTTATCTAAAGATCC
66 ATGCCTATGCCTGCTTATCTAAAGATCC
* * ***
5988357 TACCAAACACTACTCATGGGGAAGGCTTATTTTGTGTCAATGGTGTGTTGGGGACATTAGAGATG
1 TACCAAACACTACTCATGGGGAAGGCTTATTTTGCGTCAATGGTGTATCAAGGACATTAGAGATG
5988422 ATGCCTATGCCTGCTTATCTAAAGATC
66 ATGCCTATGCCTGCTTATCTAAAGATC
5988449 ACGCAACTGA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (93 bp):
TACCAAACACTACTCATGGGGAAGGCTTATTTTGCGTCAATGGTGTATCAAGGACATTAGAGATG
ATGCCTATGCCTGCTTATCTAAAGATCC
Found at i:5992426 original size:13 final size:12
Alignment explanation
Indices: 5992404--5992433 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5992394 TATATCATTC
5992404 TTTTTTTTTTAT
1 TTTTTTTTTTAT
5992416 TTTTTTATTTTAT
1 TTTTTT-TTTTAT
5992429 TTTTT
1 TTTTT
5992434 GTCAAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:5993677 original size:29 final size:28
Alignment explanation
Indices: 5993594--5993755 Score: 90
Period size: 29 Copynumber: 5.8 Consensus size: 28
5993584 ATCTTATCAT
* * *
5993594 TTTATCTAATTAAATTTTTAAATTTTTATTA
1 TTTATATAAATAAATTATT-AATTTTTA--A
* *
5993625 TTT-T-TAAATAAGTTAATAA-TTTTAA
1 TTTATATAAATAAATTATTAATTTTTAA
5993650 TTTATAATAAATAAATTATTAATTTTTAA
1 TTTAT-ATAAATAAATTATTAATTTTTAA
* *
5993679 TTTGT-GAAATAAA--ATTAA-TTTTAA
1 TTTATATAAATAAATTATTAATTTTTAA
* * *
5993703 TTCATATAAAATAAAATT-TTTATTTTTTA
1 TTTATAT-AAAT-AAATTATTAATTTTTAA
5993732 TTTATATTTAAATAAAATT-TTAAT
1 TTTATA--TAAAT-AAATTATTAAT
5993756 ATAAATAAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 25
0.72 0.10 0.17
Matches are distributed among these distances:
24 9 0.09
25 9 0.09
26 5 0.05
27 15 0.14
28 18 0.17
29 29 0.28
30 15 0.14
31 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTATATAAATAAATTATTAATTTTTAA
Found at i:5993751 original size:17 final size:17
Alignment explanation
Indices: 5993732--5993779 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
5993722 TTATTTTTTA
5993732 TTTATATTTAAATAAAAT
1 TTTA-ATTTAAATAAAAT
*
5993750 TTTAATATAAATAAAAT
1 TTTAATTTAAATAAAAT
5993767 TTTAATTTAAATA
1 TTTAATTTAAATA
5993780 TAAAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATTTAAATAAAAT
Found at i:5994930 original size:2 final size:2
Alignment explanation
Indices: 5994923--5994963 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5994913 CTTATTCAAA
5994923 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5994964 GTGGACATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5998011 original size:2 final size:2
Alignment explanation
Indices: 5998006--5998035 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5997996 AATCTCTCAT
*
5998006 TC TC TC TC TC TC TC TC TC GC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5998036 ACATTGGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:6002566 original size:2 final size:2
Alignment explanation
Indices: 6002559--6002585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6002549 GAAAGGAAAT
6002559 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6002586 AGGGTGGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6010098 original size:7 final size:7
Alignment explanation
Indices: 6010086--6010121 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
6010076 AACATTAAAG
6010086 AGCAACC
1 AGCAACC
6010093 AGCAACC
1 AGCAACC
6010100 AGCAACC
1 AGCAACC
6010107 AGCAACC
1 AGCAACC
6010114 AGCAACC
1 AGCAACC
6010121 A
1 A
6010122 ACATCCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.42, G:0.14, T:0.00
Consensus pattern (7 bp):
AGCAACC
Found at i:6010134 original size:21 final size:21
Alignment explanation
Indices: 6010089--6010136 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6010079 ATTAAAGAGC
* *
6010089 AACCAGCAACCAGCAACCAGC
1 AACCAGCAACCAACAACCAGA
* *
6010110 AACCAGCAACCAACATCCATA
1 AACCAGCAACCAACAACCAGA
6010131 AACCAG
1 AACCAG
6010137 TAACTCTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.40, G:0.10, T:0.04
Consensus pattern (21 bp):
AACCAGCAACCAACAACCAGA
Found at i:6011527 original size:52 final size:52
Alignment explanation
Indices: 6011450--6011552 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
6011440 GTATTGACAC
* * * *
6011450 ATTTCTCATTTGTATCAATATAATCAAGTAAACATGCCTAATGTATAAATAT
1 ATTTCCCATTTGTATCAATACAATCAAGCAAAAATGCCTAATGTATAAATAT
** *
6011502 ATTTCCCATTTGTATTGATACAATCAAGCAAAAATGCCTAATGTATCAATA
1 ATTTCCCATTTGTATCAATACAATCAAGCAAAAATGCCTAATGTATAAATA
6011553 CAATTCCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (52 bp):
ATTTCCCATTTGTATCAATACAATCAAGCAAAAATGCCTAATGTATAAATAT
Found at i:6011581 original size:52 final size:52
Alignment explanation
Indices: 6011456--6011574 Score: 132
Period size: 52 Copynumber: 2.3 Consensus size: 52
6011446 ACACATTTCT
* * * * * * *
6011456 CATTTGTATCAATATAATCAAGTAAACATGCCTAATGTATAAATATATTTCC
1 CATTTATATCGATACAATCAAGCAAAAATGCCTAATGTATAAATAAATTCCC
* * *
6011508 CATTTGTATTGATACAATCAAGCAAAAATGCCTAATGTATCAATACAATTCCC
1 CATTTATATCGATACAATCAAGCAAAAATGCCTAATGTATAAATA-AATTCCC
6011561 CA-TTATATCGATAC
1 CATTTATATCGATAC
6011575 GTTCAAGTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 49 0.88
53 7 0.12
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (52 bp):
CATTTATATCGATACAATCAAGCAAAAATGCCTAATGTATAAATAAATTCCC
Found at i:6012436 original size:38 final size:38
Alignment explanation
Indices: 6012394--6012543 Score: 216
Period size: 38 Copynumber: 3.9 Consensus size: 38
6012384 ATATTTATCC
6012394 TTGAATGATATTTATCCTTTATCATTTATGTTTAATAT
1 TTGAATGATATTTATCCTTTATCATTTATGTTTAATAT
*
6012432 TTGAATGATATTTATCCTTCATCATTTATGTTTAATAT
1 TTGAATGATATTTATCCTTTATCATTTATGTTTAATAT
6012470 TTGAATGATATTTAT-CTTTCATCATTTATGTTTAATAT
1 TTGAATGATATTTATCCTTT-ATCATTTATGTTTAATAT
* * *
6012508 TTG-ATGATATATATGCTTATTTCA-TTATGCTTTAAT
1 TTGAATGATATTTATCCTT-TATCATTTATG-TTTAAT
6012544 GTGGTTATGT
Statistics
Matches: 104, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
37 18 0.17
38 85 0.82
39 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (38 bp):
TTGAATGATATTTATCCTTTATCATTTATGTTTAATAT
Found at i:6023318 original size:27 final size:27
Alignment explanation
Indices: 6023288--6023341 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6023278 ATAGGTAAAG
6023288 AATTTTTGAACTTCAATACGATAATCT
1 AATTTTTGAACTTCAATACGATAATCT
6023315 AATTTTTGAACTTCAATACGATAATCT
1 AATTTTTGAACTTCAATACGATAATCT
6023342 TTTCACCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (27 bp):
AATTTTTGAACTTCAATACGATAATCT
Found at i:6023981 original size:22 final size:22
Alignment explanation
Indices: 6023930--6023979 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
6023920 CGTTACCTTC
*
6023930 ATTTTTCATGGTAACACACATT
1 ATTTTTCATGGTAACACAAATT
6023952 ATTTTTCATGGTATGACA-AAATT
1 ATTTTTCATGGTA--ACACAAATT
6023975 ATTTT
1 ATTTT
6023980 CAAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 9 0.36
24 3 0.12
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (22 bp):
ATTTTTCATGGTAACACAAATT
Found at i:6028429 original size:27 final size:27
Alignment explanation
Indices: 6028391--6028444 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6028381 CTGATCATTA
* *
6028391 GAGGAAGTGGATATAATAAGAGACTTC
1 GAGGAAATGGATACAATAAGAGACTTC
6028418 GAGGAAATGGATACAATAAGAGACTTC
1 GAGGAAATGGATACAATAAGAGACTTC
6028445 TTCTATGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.20
Consensus pattern (27 bp):
GAGGAAATGGATACAATAAGAGACTTC
Done.