Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 18 of 38
Found at i:2796474 original size:140 final size:139
Alignment explanation
Indices: 2796319--2796570 Score: 371
Period size: 140 Copynumber: 1.8 Consensus size: 139
2796309 AAAATAACTT
* * *
2796319 TTATAAAAAAATTTAAATAAAATATTTTTATTATTAAATTATAATTTCAATTAAACCTT-CTCTA
1 TTATAAAAAAATTTAAATAAAATATTTTTATTAATAAATCATAATTTCAATTAAA-CTTACTCAA
* * * *
2796383 ATTTAAAAAAAAACATATCTCTTATAAAACTCTCTCTACTATTGTTATACTCTAATTTGAAAAAA
65 ATTCAAAAAAAAACATACCTCTTA-AAAACTCTCCCTACTATTATTATACTCTAATTTGAAAAAA
2796448 AACAATAGATC
129 AACAATAGATC
* * **
2796459 TTATAAAAAATTTTAAATAAAATATTTTTATTAATATATCATAATTTGGATTAAACTTACTCAAA
1 TTATAAAAAAATTTAAATAAAATATTTTTATTAATAAATCATAATTTCAATTAAACTTACTCAAA
*
2796524 TTCAAAAAAAACCATACCTCTTAAAAACTCTCCCTACTATTATTATA
66 TTCAAAAAAAAACATACCTCTTAAAAACTCTCCCTACTATTATTATA
2796571 ATCATCATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
139 25 0.25
140 74 0.75
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (139 bp):
TTATAAAAAAATTTAAATAAAATATTTTTATTAATAAATCATAATTTCAATTAAACTTACTCAAA
TTCAAAAAAAAACATACCTCTTAAAAACTCTCCCTACTATTATTATACTCTAATTTGAAAAAAAA
CAATAGATC
Found at i:2796954 original size:2 final size:2
Alignment explanation
Indices: 2796947--2796984 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2796937 AGAAATTAAA
2796947 AG AG 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
2796985 GGGTTTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2797993 original size:20 final size:21
Alignment explanation
Indices: 2797955--2798003 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2797945 AAAGAAATAT
* *
2797955 TTAAATAAGATTATTTAGATA
1 TTAAATTAGATTATATAGATA
2797976 TTAAATTAG-TTATATAGATA
1 TTAAATTAGATTATATAGATA
*
2797996 TTCAATTA
1 TTAAATTA
2798004 CCCATATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (21 bp):
TTAAATTAGATTATATAGATA
Found at i:2798062 original size:38 final size:38
Alignment explanation
Indices: 2798020--2798104 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
2798010 TCTATTTAAC
2798020 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
1 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
2798058 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
1 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
*
2798096 TTAATTTAA
1 TTAAATTAA
2798105 ATTATTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.41
Consensus pattern (38 bp):
TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
Found at i:2798114 original size:38 final size:38
Alignment explanation
Indices: 2798020--2798114 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
2798010 TCTATTTAAC
*
2798020 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
1 TTAAATTAATTATCTTATTTACCAAAAGATAAATATAA
*
2798058 TTAAATTAATTCTCTTATTTACCAAAAGATAAATATAA
1 TTAAATTAATTATCTTATTTACCAAAAGATAAATATAA
*
2798096 TTAATTTAAATTAT-TTATT
1 TTAAATT-AATTATCTTATT
2798115 CTTGTCTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 49 0.91
39 5 0.09
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (38 bp):
TTAAATTAATTATCTTATTTACCAAAAGATAAATATAA
Found at i:2798774 original size:19 final size:19
Alignment explanation
Indices: 2798750--2798788 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2798740 TGGAATATCA
2798750 AAGCATACAAGTTATAAAT
1 AAGCATACAAGTTATAAAT
2798769 AAGCATACAAGTTATAAAT
1 AAGCATACAAGTTATAAAT
2798788 A
1 A
2798789 TGAAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
AAGCATACAAGTTATAAAT
Found at i:2800408 original size:17 final size:17
Alignment explanation
Indices: 2800386--2800418 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2800376 TTGGGGCATA
2800386 GACCAATTCAGATCATT
1 GACCAATTCAGATCATT
*
2800403 GACCAATTCGGATCAT
1 GACCAATTCAGATCAT
2800419 GTGAAGCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (17 bp):
GACCAATTCAGATCATT
Found at i:2801550 original size:13 final size:13
Alignment explanation
Indices: 2801532--2801571 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2801522 ATAGTAACCC
2801532 ATGTATCGATACA
1 ATGTATCGATACA
** *
2801545 ATGTATTAATATA
1 ATGTATCGATACA
2801558 ATGTATCGATACA
1 ATGTATCGATACA
2801571 A
1 A
2801572 AGAACATTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2807831 original size:19 final size:19
Alignment explanation
Indices: 2807787--2807842 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2807777 CTGCCAATTT
* **
2807787 CATGTATCGATACAGTTGTG
1 CATGTATCGATACA-ATGAA
2807807 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
2807826 CATGTATCGATATAATG
1 CATGTATCGATACAATG
2807843 TATCGATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2808229 original size:12 final size:13
Alignment explanation
Indices: 2808204--2808254 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2808194 TATTTTGAAT
2808204 ATTATATATTAAA
1 ATTATATATTAAA
*
2808217 ATTTTAT-TTAAA
1 ATTATATATTAAA
*
2808229 AATATATATTAAA
1 ATTATATATTAAA
2808242 ATATAATATATTA
1 AT-T-ATATATTA
2808255 TATAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 10 0.32
13 12 0.39
14 1 0.03
15 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATATATTAAA
Found at i:2809776 original size:20 final size:20
Alignment explanation
Indices: 2809751--2809804 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2809741 GTTAGAAGAA
* *
2809751 ATGTATCGATATAAT-TCATC
1 ATGTATCGATACAATGT-ACC
2809771 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
2809791 ATGTATCGATACAA
1 ATGTATCGATACAA
2809805 ACCGTGGTAG
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:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:2809871 original size:13 final size:13
Alignment explanation
Indices: 2809853--2809884 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2809843 TACAATGAAC
2809853 ATGTATCGATACA
1 ATGTATCGATACA
2809866 ATGTATCGATACA
1 ATGTATCGATACA
*
2809879 AAGTAT
1 ATGTAT
2809885 AATGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2810487 original size:17 final size:17
Alignment explanation
Indices: 2810453--2810485 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2810443 AAAGCTCTCA
2810453 TTAAAGAAAATTTTCCC
1 TTAAAGAAAATTTTCCC
*
2810470 TTAAA-AAATTTTTCCC
1 TTAAAGAAAATTTTCCC
2810486 CTCGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (17 bp):
TTAAAGAAAATTTTCCC
Found at i:2818019 original size:33 final size:33
Alignment explanation
Indices: 2817972--2818036 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2817962 TGTTAGAAGC
*
2817972 AATGTATCGATACAAT-TCATCATGTATCGATAT
1 AATGTATCGATACAATGT-ACCATGTATCGATAT
2818005 AATGTATC-AGTACAATGTACCATGTATCGATA
1 AATGTATCGA-TACAATGTACCATGTATCGATA
2818037 CAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 27 0.93
34 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACAATGTACCATGTATCGATAT
Found at i:2818112 original size:19 final size:20
Alignment explanation
Indices: 2818068--2818120 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
2818058 CTGTCAGTTT
* **
2818068 CATGTATAGATACAATTGTC
1 CATGTATCGATACAATTGAA
2818088 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
2818107 CATGTATCGATACA
1 CATGTATCGATACA
2818121 TTTGGGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2822389 original size:20 final size:19
Alignment explanation
Indices: 2822363--2822413 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2822353 CTGCCAGTTT
*
2822363 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-GGAG
* *
2822383 TATGTATCAATACAAGGAG
1 CATGTATCGATACAAGGAG
2822402 CATGTATCGATA
1 CATGTATCGATA
2822414 TAAAGTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAAGGAG
Found at i:2822408 original size:19 final size:20
Alignment explanation
Indices: 2822363--2822409 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2822353 CTGCCAGTTT
* *
2822363 CATGTATCGATACAATTGAG
1 CATGTATCAATACAATGGAG
*
2822383 TATGTATCAATACAA-GGAG
1 CATGTATCAATACAATGGAG
2822402 CATGTATC
1 CATGTATC
2822410 GATATAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCAATACAATGGAG
Found at i:2831130 original size:13 final size:13
Alignment explanation
Indices: 2831112--2831136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2831102 CAAAGATTAG
2831112 TGTATCGATACAA
1 TGTATCGATACAA
2831125 TGTATCGATACA
1 TGTATCGATACA
2831137 TTGGAGTAAT
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:2834670 original size:13 final size:13
Alignment explanation
Indices: 2834652--2834681 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2834642 GCATTTCATC
*
2834652 ATGTATTGATACA
1 ATGTATCGATACA
2834665 ATGTATCGATACA
1 ATGTATCGATACA
2834678 ATGT
1 ATGT
2834682 CCCATGTATC
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:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2834820 original size:86 final size:86
Alignment explanation
Indices: 2834721--2834891 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
2834711 AGCTACTGCT
* * * *
2834721 AGTTTCATGTATCGATACAATTGAGTATGTATCGATACAAAGAGCTTGTATTGATACAATGTATC
1 AGTTTCATGTATCGATACAATTGAGTATCTATCGATACAAAGAGCATATATCGATACAATGTATC
2834786 GATACAAAGCATAATGTATCC
66 GATACAAAGCATAATGTATCC
*
2834807 AGTTTCATGTATCGATACAATTGAGTATCTATTGATACAAAGAGCATATATCGATACAATGTATC
1 AGTTTCATGTATCGATACAATTGAGTATCTATCGATACAAAGAGCATATATCGATACAATGTATC
2834872 GATACAAAGCATAATGTATC
66 GATACAAAGCATAATGTATC
2834892 GATACAATGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (86 bp):
AGTTTCATGTATCGATACAATTGAGTATCTATCGATACAAAGAGCATATATCGATACAATGTATC
GATACAAAGCATAATGTATCC
Found at i:2834864 original size:19 final size:20
Alignment explanation
Indices: 2834816--2834866 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2834806 CAGTTTCATG
* * *
2834816 TATCGATACAATTGAGTATC
1 TATCGATACAATAGAGCATA
*
2834836 TATTGATACAA-AGAGCATA
1 TATCGATACAATAGAGCATA
2834855 TATCGATACAAT
1 TATCGATACAAT
2834867 GTATCGATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
TATCGATACAATAGAGCATA
Found at i:2834873 original size:13 final size:13
Alignment explanation
Indices: 2834855--2834944 Score: 78
Period size: 13 Copynumber: 7.8 Consensus size: 13
2834845 AAAGAGCATA
2834855 TATCGATACAATG
1 TATCGATACAATG
2834868 TATCGATACAA--
1 TATCGATACAATG
*
2834879 -AGC-AT--AATG
1 TATCGATACAATG
2834888 TATCGATACAATG
1 TATCGATACAATG
2834901 TATCGATACAA--
1 TATCGATACAATG
*
2834912 -AGC-AT--AATG
1 TATCGATACAATG
2834921 TATCGATACAATG
1 TATCGATACAATG
2834934 TATCGATACAA
1 TATCGATACAA
2834945 AGCATAATGT
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
7 4 0.07
9 4 0.07
10 8 0.13
11 4 0.07
13 41 0.67
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:2834889 original size:20 final size:20
Alignment explanation
Indices: 2834864--2834984 Score: 144
Period size: 20 Copynumber: 6.8 Consensus size: 20
2834854 ATATCGATAC
2834864 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
2834884 AATGTATCGAT----A-C--
1 AATGTATCGATACAAAGCAT
2834897 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
2834917 AATGTATCGAT----A-C--
1 AATGTATCGATACAAAGCAT
2834930 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
2834950 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
2834970 AATGTATCGATACAA
1 AATGTATCGATACAA
2834985 TGTATCGATA
Statistics
Matches: 87, Mismatches: 0, Indels: 28
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.25
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
20 57 0.66
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAAGCAT
Found at i:2834896 original size:33 final size:33
Alignment explanation
Indices: 2834855--2834964 Score: 220
Period size: 33 Copynumber: 3.3 Consensus size: 33
2834845 AAAGAGCATA
2834855 TATCGATACAATGTATCGATACAAAGCATAATG
1 TATCGATACAATGTATCGATACAAAGCATAATG
2834888 TATCGATACAATGTATCGATACAAAGCATAATG
1 TATCGATACAATGTATCGATACAAAGCATAATG
2834921 TATCGATACAATGTATCGATACAAAGCATAATG
1 TATCGATACAATGTATCGATACAAAGCATAATG
2834954 TATCGATACAA
1 TATCGATACAA
2834965 AGCATAATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
TATCGATACAATGTATCGATACAAAGCATAATG
Found at i:2834988 original size:13 final size:13
Alignment explanation
Indices: 2834970--2834994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2834960 TACAAAGCAT
2834970 AATGTATCGATAC
1 AATGTATCGATAC
2834983 AATGTATCGATA
1 AATGTATCGATA
2834995 TTTTCTAGGG
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2836377 original size:2 final size:2
Alignment explanation
Indices: 2836370--2836408 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2836360 TGGTCTTTGT
2836370 TA TA 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 TA TA T
2836409 GTCCATGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2839495 original size:33 final size:33
Alignment explanation
Indices: 2839458--2839554 Score: 178
Period size: 33 Copynumber: 3.0 Consensus size: 33
2839448 TTCAACGATC
2839458 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2839491 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*
2839524 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAATGTTGTATCGATACA
2839555 TAAGTTTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 17 0.27
33 46 0.73
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2839496 original size:13 final size:13
Alignment explanation
Indices: 2839478--2839535 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
2839468 CATAAAATGT
2839478 TGTATCGATACAA
1 TGTATCGATACAA
2839491 TGTATCGATACATAAAA
1 TGTATCGATAC----AA
2839508 TGTTGTATCGATACAA
1 ---TGTATCGATACAA
2839524 TGTATCGATACA
1 TGTATCGATACA
2839536 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 23 0.61
16 2 0.05
17 2 0.05
20 11 0.29
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2839548 original size:19 final size:18
Alignment explanation
Indices: 2839458--2839573 Score: 99
Period size: 19 Copynumber: 6.7 Consensus size: 18
2839448 TTCAACGATC
2839458 TGTATCGATACATAAAATGT
1 TGTATCGATACAT--AATGT
2839478 TGTATCGATAC--AA---
1 TGTATCGATACATAATGT
2839491 TGTATCGATACATAAAATGT
1 TGTATCGATACAT--AATGT
2839511 TGTATCGATAC--AA---
1 TGTATCGATACATAATGT
2839524 TGTATCGATACATAAGTGT
1 TGTATCGATACATAA-TGT
*
2839543 TGTATCGATACATAAGTTT
1 TGTATCGATACATAA-TGT
2839562 TGTATCGATACA
1 TGTATCGATACA
2839574 ATGTAAGCTA
Statistics
Matches: 82, Mismatches: 1, Indels: 27
0.75 0.01 0.25
Matches are distributed among these distances:
13 22 0.27
15 2 0.02
16 4 0.05
17 2 0.02
19 30 0.37
20 22 0.27
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAATGT
Found at i:2839664 original size:20 final size:20
Alignment explanation
Indices: 2839612--2839664 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2839602 ATACATCAAA
*
2839612 TGTATCGATACACTGATCTT
1 TGTATCGATACATTGATCTT
2839632 TGTATCGATACATTGATCTT
1 TGTATCGATACATTGATCTT
2839652 TGTATCGATACAT
1 TGTATCGATACAT
2839665 GCAGGCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGATCTT
Found at i:2839708 original size:52 final size:52
Alignment explanation
Indices: 2839652--2839751 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
2839642 CATTGATCTT
2839652 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
*
2839704 TGTATCGATACATGTAGGCAAATTTGCCTAGATGTATCGATACACTAT
1 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTAT
2839752 TGTCGTAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
Found at i:2841924 original size:20 final size:19
Alignment explanation
Indices: 2841897--2841940 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
2841887 ATGGAGGTGT
2841897 TGAACATA-TCATAAATGCA
1 TGAACATACTCA-AAATGCA
2841916 TGAAGCATAGCTCAAAATGCA
1 TGAA-CATA-CTCAAAATGCA
2841937 TGAA
1 TGAA
2841941 TCATGGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 11 0.50
22 3 0.14
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (19 bp):
TGAACATACTCAAAATGCA
Found at i:2842957 original size:19 final size:19
Alignment explanation
Indices: 2842933--2843017 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
2842923 TAGCTTACAT
2842933 TGTATCGATACAAAATTTA
1 TGTATCGATACAAAATTTA
2842952 TGTATCGATACAAAATTTA
1 TGTATCGATACAAAATTTA
2842971 TGTATCGATAC---A---A
1 TGTATCGATACAAAATTTA
*
2842984 TGTATCGATACAATATTTTA
1 TGTATCGATACAA-AATTTA
2843004 TGTATCGATACAAA
1 TGTATCGATACAAA
2843018 TCGTTGAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
13 12 0.21
16 1 0.02
19 31 0.53
20 14 0.24
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAATTTA
Found at i:2842988 original size:13 final size:13
Alignment explanation
Indices: 2842970--2842997 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2842960 TACAAAATTT
2842970 ATGTATCGATACA
1 ATGTATCGATACA
2842983 ATGTATCGATACA
1 ATGTATCGATACA
2842996 AT
1 AT
2842998 ATTTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2842992 original size:32 final size:33
Alignment explanation
Indices: 2842951--2843016 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2842941 TACAAAATTT
2842951 ATGTATCGATACAA-AATTTATGTATCGATACA
1 ATGTATCGATACAATAATTTATGTATCGATACA
*
2842983 ATGTATCGATACAATATTTTATGTATCGATACA
1 ATGTATCGATACAATAATTTATGTATCGATACA
2843016 A
1 A
2843017 ATCGTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACAATAATTTATGTATCGATACA
Found at i:2843868 original size:21 final size:20
Alignment explanation
Indices: 2843801--2843869 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
2843791 AAAGATGGAA
2843801 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
2843822 AAGGCTAGCTATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
2843844 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
2843865 AAGGT
1 AAGGT
2843870 CAACTACATT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 14 0.38
22 9 0.24
23 5 0.14
24 2 0.05
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:2843966 original size:48 final size:47
Alignment explanation
Indices: 2843756--2844033 Score: 294
Period size: 48 Copynumber: 5.8 Consensus size: 47
2843746 AAAAGGATGT
* *
2843756 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-T-G---AGGTGC
* *
2843808 CAATATGCTGATTCAAGGCTAGCTATATTGGACTT-AA---AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGAGGTGC
* * *
2843851 CAATGTGCTGATTCAAGGTCAACTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-TG-AGGTGC
* * * *
2843900 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAAGTGAGGTAC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGTGAGGTGC
* **
2843948 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACATGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGA-GGTGC
* * *
2843996 CGATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAA
2844034 AGGAGATGCC
Statistics
Matches: 191, Mismatches: 27, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
43 36 0.19
44 2 0.01
47 5 0.03
48 74 0.39
49 37 0.19
50 4 0.02
51 2 0.01
52 31 0.16
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (47 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGAGGTGC
Found at i:2844104 original size:30 final size:30
Alignment explanation
Indices: 2844053--2844309 Score: 157
Period size: 30 Copynumber: 8.5 Consensus size: 30
2844043 CACCAACTTG
*
2844053 TGTGGGCTTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
*
2844081 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
* ** * ** * *
2844111 TATGGGCTTAAAAGGAAAAAGAGTGCTTCAGAGT
1 TGTGGGCTT---TTG-AAAAGGGTGCCACTGACT
* ** * * *
2844145 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTG-AAAAGGGTGCCACTGACT
** * * *
2844180 TGTGAACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
** *
2844209 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
*
2844239 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
*
2844266 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
2844296 TGTGGGCTTTTGAA
1 TGTGGGCTTTTGAA
2844310 GGGTGAGGAA
Statistics
Matches: 181, Mismatches: 37, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
27 21 0.12
28 16 0.09
29 24 0.13
30 71 0.39
31 1 0.01
33 1 0.01
34 19 0.10
35 28 0.15
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.28
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGGTGCCACTGACT
Found at i:2844180 original size:35 final size:34
Alignment explanation
Indices: 2844116--2844184 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
2844106 TAACTTATGG
* **
2844116 GCTTAAAAGGAAAAAGAGTGCTTCAGAGTTGTGA
1 GCTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGA
*
2844150 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGA
1 GCTTA-AAAAGAAAAAGAGTGCCACAGAGTTGTGA
2844185 ACTTTGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (34 bp):
GCTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGA
Found at i:2844281 original size:57 final size:58
Alignment explanation
Indices: 2844198--2844311 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
2844188 TTGGAAAAGA
* *
2844198 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGGT
1 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGT
* **
2844255 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGG
1 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGG
2844312 GTGAGGAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 43 0.84
58 8 0.16
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.30
Consensus pattern (58 bp):
TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGT
Found at i:2845199 original size:33 final size:33
Alignment explanation
Indices: 2845162--2845228 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2845152 TTCAACGATC
2845162 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2845195 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2845228 T
1 T
2845229 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2845200 original size:13 final size:13
Alignment explanation
Indices: 2845182--2845206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2845172 CATAAAATGT
2845182 TGTATCGATACAA
1 TGTATCGATACAA
2845195 TGTATCGATACA
1 TGTATCGATACA
2845207 TATTTTTTTG
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:2847875 original size:14 final size:14
Alignment explanation
Indices: 2847856--2847896 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2847846 CTTTTTGTTG
2847856 TTGTTTTGTTTTTT
1 TTGTTTTGTTTTTT
2847870 TTGTTTTGTTTTTT
1 TTGTTTTGTTTTTT
*
2847884 TT-TTCTGTTTTTT
1 TTGTTTTGTTTTTT
2847897 ATTATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (14 bp):
TTGTTTTGTTTTTT
Found at i:2847883 original size:13 final size:13
Alignment explanation
Indices: 2847856--2847896 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
2847846 CTTTTTGTTG
2847856 TTGTTTTGTTTTTT
1 TTGTTTTG-TTTTT
2847870 TTGTTTTGTTTTT
1 TTGTTTTGTTTTT
2847883 TT-TTTCTGTTTTT
1 TTGTTT-TGTTTTT
2847896 T
1 T
2847897 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.12
13 15 0.58
14 8 0.31
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (13 bp):
TTGTTTTGTTTTT
Found at i:2847885 original size:18 final size:19
Alignment explanation
Indices: 2847847--2847894 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
2847837 ATCTGGACCC
2847847 TTTTTGTTGTTGTTTTGTTT
1 TTTTTGTT-TTGTTTTGTTT
2847867 TTTTTGTTTTGTTTT-TTT
1 TTTTTGTTTTGTTTTGTTT
*
2847885 TTTCTGTTTT
1 TTTTTGTTTT
2847895 TTATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.44
19 7 0.26
20 8 0.30
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (19 bp):
TTTTTGTTTTGTTTTGTTT
Found at i:2847887 original size:25 final size:25
Alignment explanation
Indices: 2847848--2847896 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2847838 TCTGGACCCT
* *
2847848 TTTTGTTGTTGTTTTGTTTTTTTTG
1 TTTTGTTGTTGTTTTCTGTTTTTTG
* *
2847873 TTTTGTTTTTTTTTTCTGTTTTTT
1 TTTTGTTGTTGTTTTCTGTTTTTT
2847897 ATTATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (25 bp):
TTTTGTTGTTGTTTTCTGTTTTTTG
Found at i:2847895 original size:19 final size:19
Alignment explanation
Indices: 2847847--2847895 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2847837 ATCTGGACCC
*
2847847 TTTTTGTTGTTGTTTTGTT
1 TTTTTGTTTTTGTTTTGTT
2847866 TTTTT-TGTTTTGTTTT-TT
1 TTTTTGT-TTTTGTTTTGTT
2847884 TTTTCTGTTTTT
1 TTTT-TGTTTTT
2847896 TATTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTTGTTTTTGTTTTGTT
Found at i:2849614 original size:14 final size:14
Alignment explanation
Indices: 2849595--2849625 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2849585 TAACAGCCCA
2849595 TGATTCATGCATTT
1 TGATTCATGCATTT
2849609 TGATTCATGCATTT
1 TGATTCATGCATTT
2849623 TGA
1 TGA
2849626 GCTATGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (14 bp):
TGATTCATGCATTT
Found at i:2853580 original size:10 final size:10
Alignment explanation
Indices: 2853565--2853590 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2853555 ATTTTCACCC
2853565 AAAAAAAAGA
1 AAAAAAAAGA
2853575 AAAAAAAAGA
1 AAAAAAAAGA
2853585 AAAAAA
1 AAAAAA
2853591 TTTAGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2854792 original size:112 final size:112
Alignment explanation
Indices: 2854602--2854910 Score: 352
Period size: 112 Copynumber: 2.7 Consensus size: 112
2854592 ATTTGTTTGA
* * * * *
2854602 TTTTCAAAGAAATCCATATTTTATACGACCTAATCTATTTGTACCTA-AGAAAATGGGGCATATA
1 TTTTCAAAGAAATTCATATTTTATACGACATGATCCATTCGTACCTAGA-AAAATGGGGCATATA
** * *
2854666 TCCTATTGGATTTGAAATTTTTTATCCAACAACATCAAATTTGTC-TAG
65 TCCTATCAG-TTTGAAATTTTTGATCCAACAACATCAAATTTATCTTAG
* ** *
2854714 TTTTCAAAGAAATTCATATTTTATACAATTTGATCCATTCGTACCTAGAAAAATGGGGCATGTAT
1 TTTTCAAAGAAATTCATATTTTATACGACATGATCCATTCGTACCTAGAAAAATGGGGCATATAT
* * * *
2854779 CTTATCAGTTTTGAAAATTTTGATCCAAGAACATCAAATTTATCTTAT
66 CCTATCAG-TTTGAAATTTTTGATCCAACAACATCAAATTTATCTTAG
* ** * * * *
2854827 TTTTCAAAGAAATTAATGGTTTATACGACATGATTCATTCGTGCCTAGAAAAATGGAGCATCTAT
1 TTTTCAAAGAAATTCATATTTTATACGACATGATCCATTCGTACCTAGAAAAATGGGGCATATAT
2854892 CCTATCAAGTTTGAAATTT
66 CCTATC-AGTTTGAAATTT
2854911 GAGCTAACCA
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
112 91 0.55
113 72 0.44
114 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (112 bp):
TTTTCAAAGAAATTCATATTTTATACGACATGATCCATTCGTACCTAGAAAAATGGGGCATATAT
CCTATCAGTTTGAAATTTTTGATCCAACAACATCAAATTTATCTTAG
Found at i:2855525 original size:86 final size:87
Alignment explanation
Indices: 2855341--2855654 Score: 229
Period size: 86 Copynumber: 3.6 Consensus size: 87
2855331 CTATCATTTG
* *
2855341 CATTTGCATCGTTTCACGCACATCTACACTTTAGATTGACATTGGTATTTGAATCGTATCATATG
1 CATTTGCATCATTTCACGCACATCTACACTTTAGA-TGACA-TGGCATTTGAATCGTATCATATG
* *
2855406 CATTTATCTCTTTATCAATGCTCG
64 CATTTACCTCTTTATCAATGCTCA
* * * * * *
2855430 CATTAGCATCTTTTCACGCACGTCTGCACTTTAGATGACAT-GCATTT-ACATCGTATTATGTGC
1 CATTTGCATCATTTCACGCACATCTACACTTTAGATGACATGGCATTTGA-ATCGTATCATATGC
* * ** *
2855493 TTTTGCCTCTTTATTGATGCTTA
65 ATTTACCTCTTTATCAATGCTCA
* * * * * * * * *
2855516 CATTTGCATCATTTCATGTACATCTACATTTTAGATGACATTAGTATTTGCATCATTTCACATGC
1 CATTTGCATCATTTCACGCACATCTACACTTTAGATGACA-TGGCATTTGAATCGTATCATATGC
* * **
2855581 ATTTTCCAT-TTTATTAATGCTTG
65 ATTTACC-TCTTTATCAATGCTCA
* ** * ** *
2855604 CATTTACATTGTTTCATGTGCATCTACATTATTAGATGACATTGGCATTTG
1 CATTTGCATCATTTCACGCACATCTACACT-TTAGATGACA-TGGCATTTG
2855655 CCTTGTTTCG
Statistics
Matches: 181, Mismatches: 38, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
85 1 0.01
86 66 0.36
87 2 0.01
88 62 0.34
89 50 0.28
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (87 bp):
CATTTGCATCATTTCACGCACATCTACACTTTAGATGACATGGCATTTGAATCGTATCATATGCA
TTTACCTCTTTATCAATGCTCA
Found at i:2855619 original size:88 final size:88
Alignment explanation
Indices: 2855497--2855751 Score: 237
Period size: 89 Copynumber: 2.9 Consensus size: 88
2855487 ATGTGCTTTT
* * * * ** *
2855497 GCCTCTTTATTGATGCTTACATTTGCATCATTTCATGTACATCTACATTTTAGATGACATTAGTA
1 GCCTGTTTATTAATGCTTGCATTTACATTGTTTCATGTACATCTACATTTTAGATGACATTAGCA
*
2855562 TTTGCATCATTTC-ACATGCATTT
66 TTTGCATCATTTCGA-ATGCATTC
* * *
2855585 TCCAT-TTTATTAATGCTTGCATTTACATTGTTTCATGTGCATCTACATTATTAGATGACATTGG
1 GCC-TGTTTATTAATGCTTGCATTTACATTGTTTCATGTACATCTACATT-TTAGATGACATTAG
* **
2855649 CATTTGCCTTGTTTCGAATGCATTC
64 CATTTGCATCATTTCGAATGCATTC
* ** * * * * *
2855674 GCCTGTTTACTAATTTTTGCA-TTAGCATTGTTTCATGTAAATCTACAATTTAGGTAACATTTGC
1 GCCTGTTTATTAATGCTTGCATTTA-CATTGTTTCATGTACATCTACATTTTAGATGACATTAGC
* *
2855738 ATTAGCATCGTTTC
65 ATTTGCATCATTTC
2855752 ATGAAGTTTT
Statistics
Matches: 136, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
88 67 0.49
89 68 0.50
90 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (88 bp):
GCCTGTTTATTAATGCTTGCATTTACATTGTTTCATGTACATCTACATTTTAGATGACATTAGCA
TTTGCATCATTTCGAATGCATTC
Found at i:2856509 original size:60 final size:60
Alignment explanation
Indices: 2856052--2856775 Score: 565
Period size: 60 Copynumber: 12.1 Consensus size: 60
2856042 TTTCATATAT
* * * ** * *
2856052 AGTCATGGTTTAGGTTTCTAGTTTTATCTAGATCATTTCTTTGAATCTTGGTTTCGCCTA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
* * * *
2856112 AGTTATTGTTTAAGG-TTCTAGTTTCATCTAGGCCATTTCTTTAAGTCTTGGTTTT-ACTCA
1 AGTCATTGTTT-AGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCT-A
* * * * * *
2856172 AGTCTTTGTTT-GGATTTCTAGTTTTATCTAGGCTATTTCCTTGAGTCTTGGTTTTACCTA
1 AGTCATTGTTTAGG-TTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
* * * * * * *
2856232 AGTTATTGTTTATGTTTCTGGTTTTATCTTGGCCATTTCTTTGAGTTTTGATTTTACCTA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
* * * * * * *
2856292 AGTCATTGTTTAGGGTTCTGGTTTCATCTCGACCGTTATGTTT-AGTCTTGGTTTTTCCCA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATT-TCTTTGAGTCTTGGTTTTGCCTA
* * * * * * *
2856352 AGTCATTATTTAGGTTTCTGGTTTCATCTAAGCTAGTTCCTTGACTCTTGGTTTTACCTA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
* * * * * *
2856412 AGTGATTAG-TTACGTTTCAGGTTTAATGTAGGCCATTTCTTTAAGTCTTGGTTTTGCCTA
1 AGTCATT-GTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
* * * * * *
2856472 AGTCATTGTTTAGGTTTATGGGTTCATCCAGGTCATTT-GTTGAGTCTTAGTTTTG-CTCA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCT-A
* * * * * *
2856531 AGTCATTGTTTAGGTTTTTGGTTTCATCCAGGCCGTTT-TGTTAAGTCTTAGTTTTGCCCA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCT-TTGAGTCTTGGTTTTGCCTA
* * * * * * *
2856591 AGTCATTATTTAGGTTT-TAGTTTCGTCAATGCCATTT-TATTGAGTTTTGGTTTTGCCCGA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCT-TTGAGTCTTGGTTTTG-CCTA
* * * * * **
2856651 AGTCATTG-TTAGGTTTCTAGTTTTACCCAAGCCATTT-TGTTGAGTCTTGGTTACGCCTA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCT-TTGAGTCTTGGTTTTGCCTA
* * * * * * * *
2856710 AGTCATTG-TTAGGTTTTTGGTTTTATCCAAGTCATTTCCTCGAGTCTTGGTTTTACCTA
1 AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
2856769 AGTCATT
1 AGTCATT
2856776 ATTTCTAATT
Statistics
Matches: 535, Mismatches: 113, Indels: 33
0.79 0.17 0.05
Matches are distributed among these distances:
58 4 0.01
59 151 0.28
60 369 0.69
61 11 0.02
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.48
Consensus pattern (60 bp):
AGTCATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTCTTTGAGTCTTGGTTTTGCCTA
Found at i:2857996 original size:65 final size:67
Alignment explanation
Indices: 2857909--2858146 Score: 202
Period size: 66 Copynumber: 3.6 Consensus size: 67
2857899 TGGTTAACTT
** **
2857909 TTTTGGACTTAAGTTCTGTCTTGGTCATTTTTAGTTGACTTTATCAGTTTTGACC-TGGTCAACC
1 TTTT-GACTTAAGTTCCATCTTGGTCACCTTTAGTTGACTTTATCAGTTTTGACCTTGGTCAACC
2857973 C-C
65 CTC
* * * * *
2857975 TTTTGACTTAGGTTCCATCTTGGTCACCCTTAGTTGACTTTATTA-ATTTCACCTTGGTCAACCC
1 TTTTGACTTAAGTTCCATCTTGGTCACCTTTAGTTGACTTTATCAGTTTTGACCTTGGTCAACCC
*
2858039 TT
66 TC
* * * * * * * *
2858041 TTTTGACTTACGTTTCACCTTAGTCACCTTTAGTTGTCTTTAACGGTTTTG-CCTTAGTCAACCC
1 TTTTGACTTAAGTTCCATCTTGGTCACCTTTAGTTGACTTTATCAGTTTTGACCTTGGTCAACCC
2858105 T-
66 TC
* * *
2858106 TTGTCT-ACTT-AGATTTCATCTTAGTCACCTTTTGTTGACTT
1 TT-T-TGACTTAAG-TTCCATCTTGGTCACCTTTAGTTGACTT
2858147 GTCGATTTTG
Statistics
Matches: 140, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
64 6 0.04
65 47 0.34
66 83 0.59
67 4 0.03
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (67 bp):
TTTTGACTTAAGTTCCATCTTGGTCACCTTTAGTTGACTTTATCAGTTTTGACCTTGGTCAACCC
TC
Found at i:2858101 original size:66 final size:65
Alignment explanation
Indices: 2857938--2858146 Score: 217
Period size: 66 Copynumber: 3.2 Consensus size: 65
2857928 CTTGGTCATT
* * *
2857938 TTTAGTTGACTTTATCAGTTTTGACC-TGGTCAACCC-CTTTTGACTTAGGTTCCATCTTGGTCA
1 TTTAGTTGACTTTATCAGTTTTG-CCTTGGTCAACCCTTTTTTGACTTA-GTTTCATCTTAGTCA
2858001 CC
64 CC
* * * ** *
2858003 CTTAGTTGACTTTATTAATTTCACCTTGGTCAACCCTTTTTTGACTTACGTTTCACCTTAGTCAC
1 TTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCTTTTTTGACTTA-GTTTCATCTTAGTCAC
2858068 C
65 C
* * * * *
2858069 TTTAGTTGTCTTTAACGGTTTTGCCTTAGTCAACCCTTTGTCT-ACTTAGATTTCATCTTAGTCA
1 TTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCTTT-TTTGACTTAG-TTTCATCTTAGTCA
2858133 CC
64 CC
*
2858135 TTTTGTTGACTT
1 TTTAGTTGACTT
2858147 GTCGATTTTG
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
64 2 0.02
65 29 0.25
66 84 0.72
67 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (65 bp):
TTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCTTTTTTGACTTAGTTTCATCTTAGTCACC
Found at i:2858284 original size:64 final size:64
Alignment explanation
Indices: 2858180--2858322 Score: 148
Period size: 64 Copynumber: 2.2 Consensus size: 64
2858170 CTTTAACTCT
* * **
2858180 TTAACTTATCTGTTTCGCCCTAGTCAATCTTTTCTAACTTA-AGTTTTTTCCTAATCACCCTTTG
1 TTAACTTATCGGTTTCGACCTAGTCAATCTTTTCTAACTTAGA-TTTCATCCTAATCACCCTTTG
* * * *
2858244 TTAACTTATCGGTTTC-ACCTTGTCAACCTCTTTT-TGACTTAGATTTCATCCTAGTTACCCTTT
1 TTAACTTATCGGTTTCGACCTAGTCAA--TCTTTTCTAACTTAGATTTCATCCTAATCACCCTTT
2858307 G
64 G
* *
2858308 TTGATTTATCGGTTT
1 TTAACTTATCGGTTT
2858323 TGTCCCAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 8 0.12
64 51 0.77
65 7 0.11
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (64 bp):
TTAACTTATCGGTTTCGACCTAGTCAATCTTTTCTAACTTAGATTTCATCCTAATCACCCTTTG
Found at i:2858388 original size:168 final size:169
Alignment explanation
Indices: 2858102--2858493 Score: 407
Period size: 168 Copynumber: 2.3 Consensus size: 169
2858092 CCTTAGTCAA
* * * * * * * *
2858102 CCCTTTGTCTACTTAGATTTCATCTTAGTCACCTTTTGTTGACTTGTCGATTTTGTCCTAGTGAA
1 CCCTTT-TCAACTTAGATTTCATCTTAGTTACCCTTTGTTGATTTATCGATTTTGTCCCAATCAA
* *
2858167 CCCCTTTAACTCTTTAACTTATCTGTTTCGCCCTAGTCAATCTTTTCTAACTTAAGTTTTTTCCT
65 CCCCTTTAACTCTTTAACTTATCTGTTTCGCCCTAGTCAATCTTTTCTAACTTAAGCTTTATCCT
* * *
2858232 AATCACCCTTTGTTAACTTATCGGTTTCA-CCTTGTCAAC
130 AATCACCCTTTGTTAACTTATAGGTTTCACCCTAGTAAAC
* ** * *
2858271 CTCTTTTTGACTTAGATTTCATCCTAGTTACCCTTTGTTGATTTATCGGTTTTGTCCCAATCAAC
1 CCCTTTTCAACTTAGATTTCATCTTAGTTACCCTTTGTTGATTTATCGATTTTGTCCCAATCAAC
* * * * ** * * * *
2858336 CTCTTTAACTTTTTGACTTATC-GATTTTGCTTTGGTTAATCCTTTT-TAACTTAGGCTTTATCT
66 CCCTTTAACTCTTTAACTTATCTG-TTTCGCCCTAGTCAAT-CTTTTCTAACTTAAGCTTTATCC
* *
2858399 TAGTCACCCTTTGTTGACTTATAGGTTTCACCCTAGTAAAC
129 TAATCACCCTTTGTTAACTTATAGGTTTCACCCTAGTAAAC
* *
2858440 CCCTTTTCAACTTAGATTTTATCTTAG-T-CGCCTTTAGTTGATTTTATCAATTTT
1 CCCTTTTCAACTTAGATTTCATCTTAGTTAC-CCTTT-GTTGA-TTTATCGATTTT
2858494 ACCATGGTAA
Statistics
Matches: 181, Mismatches: 36, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
167 2 0.01
168 124 0.69
169 45 0.25
170 10 0.06
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (169 bp):
CCCTTTTCAACTTAGATTTCATCTTAGTTACCCTTTGTTGATTTATCGATTTTGTCCCAATCAAC
CCCTTTAACTCTTTAACTTATCTGTTTCGCCCTAGTCAATCTTTTCTAACTTAAGCTTTATCCTA
ATCACCCTTTGTTAACTTATAGGTTTCACCCTAGTAAAC
Found at i:2858609 original size:65 final size:66
Alignment explanation
Indices: 2858470--2858617 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 66
2858460 ATCTTAGTCG
* * * *
2858470 CCTTTAGTTGATTTTATCAATTTTACCATGGTAAACCCTTTTTTGACTTAAGTTTCATCCTAGTA
1 CCTTTAGTTGACTTTATCAATTTTACCATGATAAACCCTTTTTCGACTTAAGGTTCATCCTAGTA
2858535 A
66 A
* * * *
2858536 CCCTTAGTTGACTTTATCAATTTTACCCT-ATCAACCCTTTTTCGACTT-AGGTT-ATGCCTCGG
1 CCTTTAGTTGACTTTATCAATTTTACCATGATAAACCCTTTTTCGACTTAAGGTTCAT-CCT-AG
*
2858598 TTA
64 TAA
*
2858601 TCTTTAGTTGACTTTAT
1 CCTTTAGTTGACTTTAT
2858618 TAGTTTCACC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.03
64 7 0.10
65 34 0.49
66 26 0.38
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (66 bp):
CCTTTAGTTGACTTTATCAATTTTACCATGATAAACCCTTTTTCGACTTAAGGTTCATCCTAGTA
A
Found at i:2858732 original size:109 final size:108
Alignment explanation
Indices: 2858538--2858734 Score: 259
Period size: 109 Copynumber: 1.8 Consensus size: 108
2858528 CCTAGTAACC
* * ** *
2858538 CTTAGTTGACTTTATCAATTTTACCCTATCAACCCTTTTTCGACTTAGGTTATGCCTCGGTTATC
1 CTTAGTTGACTTTATCAATTTCACCCTATCAAACCTTTTTCGACTTAGGTTACACCTCGGTCATC
* ** *
2858603 TTTAGTTGACTTTATTAGTTTCACCCTAATTAACCCTATTTAA
66 CTTAGTCAACTTTATCAGTTTCACCCTAATTAACCCTATTTAA
* * * *
2858646 CTTAGTTGACTTTATCAATTTCACCCTGGTCAAACCTTTTTTGACTTAGGTTCCACCTTGGTCAT
1 CTTAGTTGACTTTATCAATTTCACCCT-ATCAAACCTTTTTCGACTTAGGTTACACCTCGGTCAT
*
2858711 CCTTAGTCAACTTTGTCAGTTTCA
65 CCTTAGTCAACTTTATCAGTTTCA
2858735 TCTTGGTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
108 26 0.35
109 48 0.65
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (108 bp):
CTTAGTTGACTTTATCAATTTCACCCTATCAAACCTTTTTCGACTTAGGTTACACCTCGGTCATC
CTTAGTCAACTTTATCAGTTTCACCCTAATTAACCCTATTTAA
Found at i:2859620 original size:20 final size:20
Alignment explanation
Indices: 2859595--2859647 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2859585 ACACATGTAG
* * *
2859595 ATGTATCAATATAAGTTGCT
1 ATGTATCAATACAAATTGCA
*
2859615 ATGTATCGATACAAATTGCA
1 ATGTATCAATACAAATTGCA
2859635 ATGTATCAATACA
1 ATGTATCAATACA
2859648 CCATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCAATACAAATTGCA
Found at i:2863032 original size:47 final size:47
Alignment explanation
Indices: 2862978--2863084 Score: 160
Period size: 47 Copynumber: 2.3 Consensus size: 47
2862968 TTTTTTAAAA
2862978 TGTATCGATACAAAGGAAAATGTATCAATACATCTAGGTTTCTAGAC
1 TGTATCGATACAAAGGAAAATGTATCAATACATCTAGGTTTCTAGAC
**** * *
2863025 TGTATCGATACAATTTTAAATGTATCAATACATTTAGGTTTCTAGAT
1 TGTATCGATACAAAGGAAAATGTATCAATACATCTAGGTTTCTAGAC
2863072 TGTATCGATACAA
1 TGTATCGATACAA
2863085 TTTTAAATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (47 bp):
TGTATCGATACAAAGGAAAATGTATCAATACATCTAGGTTTCTAGAC
Found at i:2863036 original size:27 final size:26
Alignment explanation
Indices: 2862996--2863083 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
2862986 TACAAAGGAA
2862996 AATGTATCAATACATCTAGGTTTCTAG
1 AATGTATCAATACAT-TAGGTTTCTAG
* *
2863023 ACTGTATCGATACA--A--TTT-TA-
1 AATGTATCAATACATTAGGTTTCTAG
2863043 AATGTATCAATACATTTAGGTTTCTAG
1 AATGTATCAATACA-TTAGGTTTCTAG
* *
2863070 ATTGTATCGATACA
1 AATGTATCAATACA
2863084 ATTTTAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
20 12 0.25
21 2 0.04
22 3 0.06
23 1 0.02
24 1 0.02
25 3 0.06
26 2 0.04
27 24 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (26 bp):
AATGTATCAATACATTAGGTTTCTAG
Found at i:2863050 original size:20 final size:20
Alignment explanation
Indices: 2863025--2863103 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
2863015 GTTTCTAGAC
2863025 TGTATCGATACAATTTTAAA
1 TGTATCGATACAATTTTAAA
* *
2863045 TGTATCAATACATTTAGGTTTCTAGAT
1 TGTATCGATACA---A--TTT-TA-AA
2863072 TGTATCGATACAATTTTAAA
1 TGTATCGATACAATTTTAAA
*
2863092 TGTATTGATACA
1 TGTATCGATACA
2863104 TATCACGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
20 23 0.49
21 2 0.04
22 3 0.06
23 1 0.02
24 1 0.02
25 3 0.06
26 2 0.04
27 12 0.26
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATTTTAAA
Found at i:2863104 original size:47 final size:47
Alignment explanation
Indices: 2862995--2863096 Score: 186
Period size: 47 Copynumber: 2.2 Consensus size: 47
2862985 ATACAAAGGA
2862995 AAATGTATCAATACATCTAGGTTTCTAGACTGTATCGATACAATTTT
1 AAATGTATCAATACATCTAGGTTTCTAGACTGTATCGATACAATTTT
* *
2863042 AAATGTATCAATACATTTAGGTTTCTAGATTGTATCGATACAATTTT
1 AAATGTATCAATACATCTAGGTTTCTAGACTGTATCGATACAATTTT
2863089 AAATGTAT
1 AAATGTAT
2863097 TGATACATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (47 bp):
AAATGTATCAATACATCTAGGTTTCTAGACTGTATCGATACAATTTT
Found at i:2866089 original size:18 final size:18
Alignment explanation
Indices: 2866063--2866097 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2866053 TAGCTAGTAG
2866063 GTGGAGGATTCGACCTAT
1 GTGGAGGATTCGACCTAT
*
2866081 GTGGGGGATTCGACCTA
1 GTGGAGGATTCGACCTA
2866098 AAAATGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (18 bp):
GTGGAGGATTCGACCTAT
Found at i:2866413 original size:13 final size:13
Alignment explanation
Indices: 2866395--2866419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2866385 ATTACTCAAA
2866395 TGTATCGATACAT
1 TGTATCGATACAT
2866408 TGTATCGATACA
1 TGTATCGATACA
2866420 CTGATCTTTG
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:2866484 original size:52 final size:52
Alignment explanation
Indices: 2866428--2866608 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
2866418 CACTGATCTT
*
2866428 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2866480 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
2866532 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2866584 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2866609 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2870742 original size:10 final size:10
Alignment explanation
Indices: 2870727--2870753 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2870717 TGCTAACTAA
2870727 GTTTTTGTTT
1 GTTTTTGTTT
2870737 GTTTTTGTTT
1 GTTTTTGTTT
2870747 GTTTTTG
1 GTTTTTG
2870754 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:2880437 original size:1 final size:1
Alignment explanation
Indices: 2880431--2880529 Score: 81
Period size: 1 Copynumber: 99.0 Consensus size: 1
2880421 GGCGTCCTCC
** ** * * **
2880431 AAAAAAAAAAAAAAAAACGAAAAAAAATGAAAAAAAAAAAACAAAAAAAAAACAAAAGGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
2880496 AAAAACAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2880530 GGGGGTCCGG
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:2880467 original size:30 final size:29
Alignment explanation
Indices: 2880431--2880515 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
2880421 GGCGTCCTCC
* *
2880431 AAAAAAAAAAAAAAAAACGAAAA-AAAATG
1 AAAAAAAAAAAAAAAAA-AAAAACAAAAGG
2880460 AAAAAAAAAAAACAAAAAAAAAACAAAAGG
1 AAAAAAAAAAAA-AAAAAAAAAACAAAAGG
* *
2880490 AAAAAAAAAAACAATAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAACAAA
2880516 CAAAAACAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 29 0.58
30 21 0.42
ACGTcount: A:0.87, C:0.06, G:0.05, T:0.02
Consensus pattern (29 bp):
AAAAAAAAAAAAAAAAAAAAAACAAAAGG
Found at i:2880493 original size:40 final size:40
Alignment explanation
Indices: 2880433--2880526 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
2880423 CGTCCTCCAA
*
2880433 AAAAAAAAAAAAAAACGAAAAAAAATGAAA-AA-AAAAAAAC
1 AAAAAAAAAACAAAACGAAAAAAAA--AAACAATAAAAAAAC
*
2880473 AAAAAAAAAACAAAAGGAAAAAAAAAAACAATAAAAAAAC
1 AAAAAAAAAACAAAACGAAAAAAAAAAACAATAAAAAAAC
*
2880513 -AAACAAAAACAAAA
1 AAAAAAAAAACAAAA
2880527 AAAGGGGGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 3 0.06
39 15 0.31
40 31 0.63
ACGTcount: A:0.86, C:0.07, G:0.04, T:0.02
Consensus pattern (40 bp):
AAAAAAAAAACAAAACGAAAAAAAAAAACAATAAAAAAAC
Found at i:2880526 original size:29 final size:27
Alignment explanation
Indices: 2880430--2880529 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 27
2880420 CGGCGTCCTC
*
2880430 CAAAAAAAAAAAAAAA-AACGAAAAAAA
1 CAAAAAAAAAAAAAAACAA-AAAAAAAA
**
2880457 -ATGAAAAAAAAAAAACAAAAAAAAAA
1 CAAAAAAAAAAAAAAACAAAAAAAAAA
*
2880483 CAAAAGGAAAAAAAAAAACAATAAAAAAA
1 CAAAA--AAAAAAAAAAACAAAAAAAAAA
2880512 CAAACAAAAACAAAAAAA
1 CAAA-AAAAA-AAAAAAA
2880530 GGGGGTCCGG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
26 20 0.33
27 4 0.07
28 4 0.07
29 32 0.52
30 1 0.02
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (27 bp):
CAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:2882075 original size:27 final size:27
Alignment explanation
Indices: 2882033--2882085 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2882023 ATTTTTTTCG
*
2882033 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
2882060 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
2882086 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:2882280 original size:28 final size:29
Alignment explanation
Indices: 2881970--2882380 Score: 205
Period size: 30 Copynumber: 13.9 Consensus size: 29
2881960 TTCATCACCC
* ***
2881970 TTCAAAAGTCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* * ***
2882000 TTC-AAATCCCACAAGTCAATGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
*
2882029 TTCGAAAGCCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
2882057 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * *
2882086 TTCCGAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* * * *
2882115 TTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * *
2882146 TTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTCTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCAAC-C-T
* *
2882180 TTC---AGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
**
2882207 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
*
2882237 TTCAAAAGCCCACAAGTTAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
2882266 TT-AAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* **
2882294 GTTCAAAAGCCCACAAGTCAATGGCATATTTTTT
1 -TTCAAAAGCCCACAAGTCAGTGGCA-A---CCT
*
2882328 TTTAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
2882357 TT-TAAAGCCCACAACTCCGTGGCA
1 TTCAAAAGCCCACAAGTCAGTGGCA
2882381 CTTTTTTCTT
Statistics
Matches: 305, Mismatches: 52, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
26 1 0.00
27 40 0.13
28 49 0.16
29 59 0.19
30 104 0.34
31 4 0.01
32 1 0.00
33 23 0.08
34 6 0.02
35 18 0.06
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:2882288 original size:88 final size:89
Alignment explanation
Indices: 2882183--2882370 Score: 306
Period size: 88 Copynumber: 2.1 Consensus size: 89
2882173 CACTCTTTTC
* *
2882183 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATA-TTTTTCAAAAGCC
1 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATATTTTTTCAAAAGCC
*
2882247 CACAAGTTAGTGGCAACCTTTAAA
66 CACAAGTCAGTGGCAACCTTTAAA
*
2882271 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATATTTTTTTTTAAAAG
1 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATA--TTTTTTCAAAAG
*
2882336 CCCACAAGTCAGTGGCAACCTTTTAA
64 CCCACAAGTCAGTGGCAACCTTTAAA
2882362 AGCCCACAA
1 AGCCCACAA
2882371 CTCCGTGGCA
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
88 49 0.53
91 43 0.47
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (89 bp):
AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATATTTTTTCAAAAGCC
CACAAGTCAGTGGCAACCTTTAAA
Found at i:2882299 original size:58 final size:60
Alignment explanation
Indices: 2882183--2882352 Score: 200
Period size: 58 Copynumber: 2.8 Consensus size: 60
2882173 CACTCTTTTC
* * * *
2882183 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCACACTGTTCAAA
* *
2882243 AGCCCACAAGTTAGTGGCAACC-TTT-AAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCACACTGTTCAAA
* * ** *
2882301 AGCCCACAAGTCAATGGCATATTTTTTTTTAAAAGCCCACAAGTCAGTGGCA
1 AGCCCACAAGTTAGTGGCA-A--CCTTTTCAAAAGCCCACAAGTCAGTGGCA
2882353 ACCTTTTAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 45 0.48
59 4 0.04
60 21 0.22
62 3 0.03
63 21 0.22
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (60 bp):
AGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCACACTGTTCAAA
Found at i:2882387 original size:28 final size:28
Alignment explanation
Indices: 2882325--2882421 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 28
2882315 TGGCATATTT
* *
2882325 TTTTTTAAAAGCCCACAAGTCAGTGGCAAC
1 TTTTTT-AAAGCCCACAACTCCGTGGC-AC
*
2882355 -CTTTTAAAGCCCACAACTCCGTGGCAC
1 TTTTTTAAAGCCCACAACTCCGTGGCAC
2882382 TTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC
1 ----TT-TTTTAAAGCCCACAACTCCGTGGCAC
2882415 TCTTTTT
1 T-TTTTT
2882422 TCCCTTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.04
28 18 0.32
29 9 0.16
30 1 0.02
33 26 0.46
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (28 bp):
TTTTTTAAAGCCCACAACTCCGTGGCAC
Found at i:2882421 original size:91 final size:88
Alignment explanation
Indices: 2882183--2882381 Score: 281
Period size: 91 Copynumber: 2.2 Consensus size: 88
2882173 CACTCTTTTC
* * *
2882183 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAACTCAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
*
2882248 ACAAGTTAGTGGCAACCTTTAAA
66 ACAAGTCAGTGGCAACCTTTAAA
* * * *
2882271 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATATTTTTTTTTAAAAG
1 AGCCCACAACTCAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATA---TTTTTCAAAAG
*
2882336 CCCACAAGTCAGTGGCAACCTTTTAA
63 CCCACAAGTCAGTGGCAACCTTTAAA
*
2882362 AGCCCACAACTCCGTGGCAC
1 AGCCCACAACTCAGTGGCAC
2882382 TTTTTTCTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 49 0.49
91 51 0.51
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (88 bp):
AGCCCACAACTCAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
ACAAGTCAGTGGCAACCTTTAAA
Found at i:2882673 original size:141 final size:141
Alignment explanation
Indices: 2882354--2882780 Score: 569
Period size: 141 Copynumber: 3.0 Consensus size: 141
2882344 TCAGTGGCAA
2882354 CCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
* * *
2882418 TTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGG
66 TTTTT-CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCCTT-CTAAAGCCCACACAACTCCG
2882483 TGGCAACCTTCTT
129 TGGCAACCTTCTT
* * **
2882496 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
* * * *
2882560 TTTTTCCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCCGTT-TAAAG-CC-CACAACTCCG
66 TTTTTCCTTTT--AAGTCCACAACTCCGTGGCATCTTTTTCCCTTCTAAAGCCCACACAACTCCG
*
2882622 TGGC-ACTCTTTTT
129 TGGCAAC-CTTCTT
**
2882635 CCCTTTTCAAAGCCCACAACTCCGTGATACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 -CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
* * * * *
2882700 TTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTTTCCTTCCCAAAGCCCACACAAGTCG
65 TTTTTTCCTTTTAAGTCCACAACTCCGTGGCATC-TTTTTCCCTT-CTAAAGCCCACACAACTCC
2882765 GTGGCAACCTTCTT
128 GTGGCAACCTTCTT
2882779 CC
1 CC
2882781 AAAGCCCACA
Statistics
Matches: 245, Mismatches: 28, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
138 2 0.01
139 36 0.15
140 10 0.04
141 84 0.34
142 63 0.26
143 31 0.13
144 17 0.07
145 2 0.01
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (141 bp):
CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
TTTTTCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCCTTCTAAAGCCCACACAACTCCGTG
GCAACCTTCTT
Found at i:2882741 original size:70 final size:69
Alignment explanation
Indices: 2882354--2882739 Score: 467
Period size: 70 Copynumber: 5.5 Consensus size: 69
2882344 TCAGTGGCAA
2882354 CCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC-T
2882419 TTTTC
65 TTTTC
* ** * * *
2882424 CCTTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCA
1 CCTTTTAAAGCCCACAACTCCGTGGCA-CTTT-TTTCTT-TTAAAG-CC-CACAACTCCGTGGC-
*
2882488 AC-CTTCTT-
60 ACTCTTTTTC
* * **
2882496 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 CCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
*
2882560 TTTTT
65 TTTTC
* * *
2882565 CCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 CCTTTT-AAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
2882630 TTTTTC
64 TTTTTC
**
2882636 CCTTTTCAAAGCCCACAACTCCGTGATACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 CCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
2882701 TTTTC
65 TTTTC
*
2882706 CCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTT
1 CCTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTT
2882740 TCCTTCCCAA
Statistics
Matches: 270, Mismatches: 33, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
67 2 0.01
68 33 0.12
69 28 0.10
70 87 0.32
71 72 0.27
72 8 0.03
73 25 0.09
74 13 0.05
75 2 0.01
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.34
Consensus pattern (69 bp):
CCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTC
Found at i:2882778 original size:105 final size:102
Alignment explanation
Indices: 2882355--2882757 Score: 315
Period size: 105 Copynumber: 3.8 Consensus size: 102
2882345 CAGTGGCAAC
* *
2882355 CTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTC-T
** *
2882419 TTTTCCCTT--TTAAGTCCACAACTCCGTGGCAT-CT-TT
65 TTTTCCCTTCCCAAAGCCCACAACTCCGT-G-ATACTCTT
* * * *
2882455 CTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT-CTTTTCAAAGCCCACAACTCCGT
1 CT---TT--TAAAG-CC-CACAACTCCGTGGC-ACCTTTTTCCCTTT-AAAGCCCACAACTCCGT
* ** ** **
2882519 GGCAC-CTTCTT--CTT-TTAAAGCCCACAACTTTGTGGCACTCTTTTTT
57 GGCACTCTTTTTCCCTTCCCAAAGCCCACAACTCCGTGATACTC----TT
* *
2882565 CCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 -CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTC
** *
2882630 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGATACTTTTTT
64 TTTTTCCCTTCCCAAAGCCCACAACTCCGTGATAC--TCTT
* *
2882671 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCT
1 CTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTC-
*
2882735 TTTTTTCCTTCCCAAAGCCCACA
64 TTTTTCCCTTCCCAAAGCCCACA
2882758 CAAGTCGGTG
Statistics
Matches: 247, Mismatches: 28, Indels: 51
0.76 0.09 0.16
Matches are distributed among these distances:
100 2 0.01
103 2 0.01
104 52 0.21
105 87 0.35
106 21 0.09
107 23 0.09
108 28 0.11
109 27 0.11
110 3 0.01
111 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.34
Consensus pattern (102 bp):
CTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTCCCTTCCCAAAGCCCACAACTCCGTGATACTCTT
Found at i:2882929 original size:49 final size:49
Alignment explanation
Indices: 2882808--2883378 Score: 725
Period size: 49 Copynumber: 11.7 Consensus size: 49
2882798 GTGGCAACCC
* *
2882808 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
2882860 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
2882909 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
2882961 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2883010 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2883059 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2883108 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2883157 CTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
2883200 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2883249 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2883292 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CAT
* *
2883344 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
2883379 GTTGACATCC
Statistics
Matches: 454, Mismatches: 47, Indels: 36
0.85 0.09 0.07
Matches are distributed among these distances:
43 75 0.17
45 2 0.00
47 1 0.00
49 253 0.56
50 5 0.01
51 2 0.00
52 116 0.26
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:2882983 original size:101 final size:100
Alignment explanation
Indices: 2882808--2883547 Score: 895
Period size: 98 Copynumber: 7.3 Consensus size: 100
2882798 GTGGCAACCC
*
2882808 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTTTAAGTCCAAT
2882873 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
65 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2882909 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTTTAAGTCCAAT
2882974 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
65 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* *
2883010 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-TCTT-CATCTTTAAGTCCAATG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTTTAAGTCCAATG
2883073 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* * *
2883108 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-TCTT-CATCTTGAAGTCCAATG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTTTAAGTCCAATG
2883171 TAGCTGGCCTTGACTCAGCACATTGGCA----C--
66 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* * *
2883200 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTA-TCTT-CATCTTTAAGTCCAATG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTTTAAGTCCAATG
* *
2883263 TAGCTGGCCTTGAATCAACACATTGGCA----C--
66 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
*
2883292 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTTTCCATCTTTAAGTCCAAT
* * *
2883357 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
65 GTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TCAT
* * * * *
2883399 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG---------CAC-TTT-TC--CATC
* * * * *
2883464 ATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
53 --TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* *
2883514 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
2883548 CGTTGACATC
Statistics
Matches: 575, Mismatches: 35, Indels: 44
0.88 0.05 0.07
Matches are distributed among these distances:
92 128 0.22
94 4 0.01
95 41 0.07
98 142 0.25
99 3 0.01
101 141 0.25
105 1 0.00
107 35 0.06
115 31 0.05
116 7 0.01
117 2 0.00
119 4 0.01
120 1 0.00
121 35 0.06
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (100 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTTTAAGTCCAATG
TAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
Found at i:2883222 original size:43 final size:43
Alignment explanation
Indices: 2883161--2883334 Score: 222
Period size: 43 Copynumber: 3.9 Consensus size: 43
2883151 CTTCATCTTG
* * *
2883161 AAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
* *
2883204 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTATCTTCATCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG------CACCTTT
* * *
2883253 AAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCACCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
2883296 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
2883335 ATTTTCCATC
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
43 74 0.66
49 38 0.34
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
Found at i:2883228 original size:92 final size:92
Alignment explanation
Indices: 2883108--2883378 Score: 452
Period size: 92 Copynumber: 2.9 Consensus size: 92
2883098 GCACCTTCAT
*
2883108 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2883173 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
2883200 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2883265 GCTGGCCTTGAATCAACACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
2883292 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
2883357 GTAGCTGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGAATCAGCAC
2883379 GTTGACATCC
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 127 0.76
94 4 0.02
95 36 0.22
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2883316 original size:22 final size:22
Alignment explanation
Indices: 2883249--2883316 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
2883239 GTATCTTCAT
*
2883249 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
2883271 CTTGAA-T-CAACACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
2883292 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
2883314 CTT
1 CTT
2883317 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:2883581 original size:170 final size:170
Alignment explanation
Indices: 2883293--2884535 Score: 2387
Period size: 170 Copynumber: 7.3 Consensus size: 170
2883283 CATTGGCACC
* *
2883293 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAATG
*
2883358 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
63 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCA
2883423 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
128 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2883466 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
2883531 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
2883596 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2883636 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
2883701 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
2883766 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2883806 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
2883871 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
2883936 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2883976 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
2884041 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
2884106 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2884146 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
2884211 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
2884276 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
2884316 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
*
2884381 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTGGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
*
2884446 ATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2884486 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
2884536 ATCTCTAAAA
Statistics
Matches: 1062, Mismatches: 7, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
170 972 0.92
171 52 0.05
173 38 0.04
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (170 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2885299 original size:33 final size:33
Alignment explanation
Indices: 2885262--2885328 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2885252 TTCAACGATT
2885262 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2885295 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2885328 T
1 T
2885329 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2885300 original size:13 final size:13
Alignment explanation
Indices: 2885282--2885306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2885272 CATAAAATGT
2885282 TGTATCGATACAA
1 TGTATCGATACAA
2885295 TGTATCGATACA
1 TGTATCGATACA
2885307 TATTTTTTTG
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:2886186 original size:28 final size:27
Alignment explanation
Indices: 2886119--2886186 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2886109 CTTCACAATC
**
2886119 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* * *
2886146 GGGGATACTCCAACCCTGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
2886174 GGGGATACTCCAA
1 GGGGATACTCCAA
2886187 TCCCAGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:2886238 original size:52 final size:52
Alignment explanation
Indices: 2886174--2886342 Score: 175
Period size: 52 Copynumber: 3.2 Consensus size: 52
2886164 TTATTTCCGA
* *
2886174 GGGGATACTCCAATCCCAGTTTTATCGCT-AAAACACTAATTTTTCCATAATC
1 GGGGATACTCCAATCCCAGTTTTAT-TCTAAAAACACCAATTTTTCCATAATC
* * * * *
2886226 GGGGATACTCCAATCCCGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAATCCCAGTTTTATTCTAAAAACACCAATTTTTCC-ATAATC
* * *
2886278 GGGGATACTCCAACTCCGA-TTTTATTTCTAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAA-TCCCAGTTTTA-TTCTAAAAACACCAATTTTTCCATAATC
*
2886330 GAGGATACTCCAA
1 GGGGATACTCCAA
2886343 CCTCGTTATT
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
51 7 0.07
52 71 0.73
53 15 0.15
54 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAATCCCAGTTTTATTCTAAAAACACCAATTTTTCCATAATC
Found at i:2886330 original size:104 final size:103
Alignment explanation
Indices: 2886007--2886344 Score: 267
Period size: 104 Copynumber: 3.2 Consensus size: 103
2885997 CTCAATTCTC
* * * * * *
2886007 CACAATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCAGGGAT
1 CACAATCGGGGATACTCCAAC-CCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
* * *
2886071 TCTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTT-CTAAAAACACCAATTT-TT
* * ** * * * * *
2886112 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA---CCCTGTTATTTCCG
1 CACAATCGGGGATACTCCAACCCGGTTTTATTTTC---AAAACACCAATTTTCCT-TTA-AT-C-
* ** *
2886173 AGGGGATACTCCAA-TCCCAGTTTTATCGCT-AAAACACTAATTTTT
59 -GGGGATACTCCAACTCCGA-TTTTATTTCTAAAAACACCAATTTTT
* *
2886218 CCATAATCGGGGATACTCCAATCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
2886283 TACTCCAACTCCGATTTTATTTCTAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTT
*
2886323 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
2886345 TCGTTATTTC
Statistics
Matches: 176, Mismatches: 39, Indels: 38
0.70 0.15 0.15
Matches are distributed among these distances:
103 8 0.05
104 43 0.24
105 38 0.22
106 17 0.10
107 33 0.19
108 12 0.07
109 25 0.14
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTT
Found at i:2886363 original size:28 final size:28
Alignment explanation
Indices: 2886327--2886398 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
2886317 ATTTTTCACA
* *
2886327 ATCGAGGATACTCCAA-CCTCGTTATTTC
1 ATCGGGGATACTCCAACCCT-GTTACTTC
2886355 ATCGGGGATACTCCAACCCTGTTACTTC
1 ATCGGGGATACTCCAACCCTGTTACTTC
***
2886383 CGAGGGGATACTCCAA
1 ATCGGGGATACTCCAA
2886399 TCCCGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTGTTACTTC
Found at i:2886400 original size:212 final size:212
Alignment explanation
Indices: 2886005--2886402 Score: 604
Period size: 212 Copynumber: 1.9 Consensus size: 212
2885995 TTCTCAATTC
* *
2886005 TCCACAATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGA
1 TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGA
* * *
2886070 TTCTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
2886135 CGTTAATCATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAATCCCAGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAATCCCAGTTTTATC
2886200 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * * * *
2886217 TCCATAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCAGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCAGG
* *
2886281 GATACTCCAACTCCGATTTTATTT-CTAAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
2886344 CTCGTTATTTCATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAATCCC
129 CCCGTTA-ATCATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAATCCC
2886403 GATTTTTTTT
Statistics
Matches: 167, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
211 29 0.17
212 107 0.64
213 31 0.19
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAATCCCAGTTTTATC
GCTAAAACACTAATTTT
Found at i:2898909 original size:19 final size:18
Alignment explanation
Indices: 2898865--2898922 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
2898855 ACATTCTCTT
2898865 CAAAAAAAAAAAGAAGCAAAA
1 CAAAAAAAAAAA-AAG--AAA
*
2898886 AAAAAAAAAACAAAAGAAA
1 CAAAAAAAAA-AAAAGAAA
*
2898905 CAAAACAAAGAAAAAGAA
1 CAAAA-AAAAAAAAAGAA
2898923 GAGAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
21 12 0.38
22 2 0.06
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAAAGAAA
Found at i:2900225 original size:55 final size:54
Alignment explanation
Indices: 2899932--2900542 Score: 692
Period size: 55 Copynumber: 11.0 Consensus size: 54
2899922 GATGCCTTTT
* * * * *
2899932 CCTTTTAAAGCCCACACGAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
* * *
2899987 CCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGAC-
1 CC---TTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
*
2900043 CCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGC-GAGATGCTTTT
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAG-GA--C---A
* * *
2900107 TCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
* *
2900161 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGTCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGACA
** *
2900216 CCACTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
* * *
2900271 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
*
2900326 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
*
2900381 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
* * *
2900436 TCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
* * * * * *
2900491 CCTTTCAAAGCCTACACGAG-TAGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGA
2900543 TACACTTTAT
Statistics
Matches: 487, Mismatches: 45, Indels: 49
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.00
54 66 0.14
55 265 0.54
56 13 0.03
57 22 0.05
58 71 0.15
59 43 0.09
60 2 0.00
63 3 0.01
64 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (54 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
Found at i:2900275 original size:26 final size:26
Alignment explanation
Indices: 2900243--2900387 Score: 71
Period size: 26 Copynumber: 5.3 Consensus size: 26
2900233 AAGTTGGTGG
2900243 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * * **
2900269 CACCTTTCAAAGCCCACCCAAGTTGGTGG-
1 CACCTTTC--AGTCC-CCAAAG-AGCAGGA
** * *
2900298 CATTTTTCAGTCCTCAAAGAGTAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
2900324 CACCTCTTAAAG-CCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGCAGGA
2900353 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
2900379 CACCTTTCA
1 CACCTTTCA
2900388 AAGCCCACAC
Statistics
Matches: 83, Mismatches: 24, Indels: 24
0.63 0.18 0.18
Matches are distributed among these distances:
25 6 0.07
26 27 0.33
27 12 0.14
28 13 0.16
29 19 0.23
30 6 0.07
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:2900275 original size:110 final size:110
Alignment explanation
Indices: 2899932--2900542 Score: 779
Period size: 110 Copynumber: 5.5 Consensus size: 110
2899922 GATGCCTTTT
* * * * * *
2899932 CCTTTTAAAGCCCACACGAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTTTTA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACC---TCTTA
*
2899997 AAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGAC-
63 AAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
*
2900043 CCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGC-GAGATGCTTT
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAG-GA--C---
** *
2900106 TTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACA
55 ACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * *
2900161 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGTCACCACTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTCTTAAAG
*
2900226 CCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* *
2900271 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTT-TCAGTCCTCAAAGAGTAGGACACCTCTTAAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT-AGTCCTCAAAGAGCAGGACACCTCTTAAA
*
2900335 GCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
65 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* *
2900381 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACATCTCTTAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTCTTAAAG
* *
2900446 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * * * *
2900491 CCTTTCAAAGCCTACACGAG-TAGTGGCACTTTT-TACTCCTCAATGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGA
2900543 TACACTTTAT
Statistics
Matches: 450, Mismatches: 32, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
109 51 0.11
110 249 0.55
111 2 0.00
112 4 0.01
113 27 0.06
114 16 0.04
115 17 0.04
116 26 0.06
117 55 0.12
118 2 0.00
120 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (110 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTCTTAAAG
CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
Found at i:2900868 original size:21 final size:21
Alignment explanation
Indices: 2900842--2900939 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
2900832 AAATTATCCA
*
2900842 AATGTATGGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
2900863 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2900884 AATGTATCGATACAATTGT-G
1 AATGTATCGATACATTTGTAG
* * *
2900904 TAATGTATCAATACA-TTCTACA
1 -AATGTATCGATACATTTGTA-G
2900926 AATGTATCGATACA
1 AATGTATCGATACA
2900940 GGGTCCCAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.06
21 64 0.94
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2900999 original size:19 final size:19
Alignment explanation
Indices: 2900975--2901042 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2900965 AATTCAACAA
2900975 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2900994 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2901009 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2901026 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2901043 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2901014 original size:13 final size:13
Alignment explanation
Indices: 2900996--2901020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2900986 ACATAAGTTT
2900996 TGTATCGATACAA
1 TGTATCGATACAA
2901009 TGTATCGATACA
1 TGTATCGATACA
2901021 TAAGTATTGT
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:2901018 original size:32 final size:32
Alignment explanation
Indices: 2900977--2901039 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2900967 TTCAACAATT
*
2900977 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2901009 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2901040 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2901100 original size:13 final size:13
Alignment explanation
Indices: 2901082--2901107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2901072 CATTTTTCTG
2901082 TGTATCGATACAT
1 TGTATCGATACAT
2901095 TGTATCGATACAT
1 TGTATCGATACAT
2901108 AGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2901104 original size:33 final size:33
Alignment explanation
Indices: 2901062--2901128 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2901052 GCCAAGGAAA
***
2901062 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
*
2901095 TGTATCGATACATAGATCTTTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
2901128 T
1 T
2901129 TGGAAATTTT
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:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATAGATCTGTGTATCGATACAT
Found at i:2903714 original size:52 final size:51
Alignment explanation
Indices: 2903639--2903809 Score: 159
Period size: 52 Copynumber: 3.3 Consensus size: 51
2903629 TTATTTCCGA
* * * *
2903639 GGGGATACTTCAACCCCGGTTTTATCGCT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAA-CCCGATTTTAT-TCTAAAAACACCAATTTTTCCACAATC
* * * * **
2903691 GGGGATACTCCAATCCCAATTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTCTAAAAACACCAATTTTTCC-ACAATC
*
2903743 GGGGATACTCCAACTCCGATTTTATTTCTAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGATTTTA-TTCTAAAAACACCAATTTTTCCACAATC
*
2903795 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2903810 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
51 9 0.09
52 71 0.74
53 12 0.12
54 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCGATTTTATTCTAAAAACACCAATTTTTCCACAATC
Found at i:2903792 original size:104 final size:101
Alignment explanation
Indices: 2903472--2903809 Score: 284
Period size: 104 Copynumber: 3.2 Consensus size: 101
2903462 CTCAATTCTC
* ** *
2903472 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCAATAATCGGGGATA
1 CACAATCGGGGATACTCCAAC-CC-ATTTTATTTTCAAAACACCAATTTTCATTAATCGGGGATA
* *
2903537 CTCTAACTCCGATTTTATTTCCACAAAACACCAATTTCTT
64 CTCCAACTCCGATTTTATTTCTA-AAAACACCAATTT-TT
** * ** * * * * * *
2903577 CACAATCGGGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAA-CTTCGTTATTTCCGAGG
1 CACAATCGGGGATACTCCAACCCATTTTATTTTC---AAAACACCAATTTTCATTA-AT-C--GG
* * * ** *
2903641 GGATACTTCAACCCCGGTTTTATCGCT-AAAACACTAATTTTT
59 GGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTT
* *
2903683 CCACAATCGGGGATACTCCAATCCCAATTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAA-CCC-ATTTTATTTTCAAAACACCAATTTT-CATTAATCGGGGA
*
2903748 TACTCCAACTCCGATTTTATTTCTAAAAATACCAATTTTT
62 TACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTT
*
2903788 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
2903810 TCGTTATTTC
Statistics
Matches: 178, Mismatches: 42, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
103 8 0.04
104 45 0.25
105 38 0.21
106 16 0.09
107 36 0.20
108 7 0.04
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (101 bp):
CACAATCGGGGATACTCCAACCCATTTTATTTTCAAAACACCAATTTTCATTAATCGGGGATACT
CCAACTCCGATTTTATTTCTAAAAACACCAATTTTT
Found at i:2903828 original size:28 final size:30
Alignment explanation
Indices: 2903792--2903868 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 30
2903782 ATTTTTCACA
* *
2903792 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2903820 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
*
2903850 A--GGGGATACTCCAATCCCG
1 ATCGGGGATACTCCAACCCCG
2903869 ATTTTTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 39 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:2903854 original size:212 final size:212
Alignment explanation
Indices: 2903470--2903873 Score: 582
Period size: 212 Copynumber: 1.9 Consensus size: 212
2903460 TTCTCAATTC
* * **
2903470 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCAATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCAATTTTATTTTCAAAACACCAATTTTCAATAATCGGGGA
* *
2903535 TACTCTAACTCCGATTTTATTTCCACAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCACAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
** * *
2903600 CGTTAATCATCGGGGATACTCCAACTTCGTTATTTCCGAGGGGATACTTCAACCCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATC
2903665 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* **
2903682 TCCACAATCGGGGATACTCCAA-TCCCAATTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCAATTTTATTTTCAAAACACCAATTTT-CAATAATCGGG
* *
2903746 GATACTCCAACTCCGATTTTATTTCTA-AAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCACAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
2903809 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTT-CGAGGGGATACTCCAATCCCGATTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTTCCGAGGGGATACTCCAACCCCGATTT
2903873 T
192 T
2903874 TTTTCTTCTA
Statistics
Matches: 170, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
211 29 0.17
212 104 0.61
213 37 0.22
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCAATTTTATTTTCAAAACACCAATTTTCAATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCACAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATC
GCTAAAACACTAATTTT
Found at i:2905973 original size:52 final size:52
Alignment explanation
Indices: 2905823--2905953 Score: 226
Period size: 52 Copynumber: 2.5 Consensus size: 52
2905813 CCCAAAATAT
2905823 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* * *
2905875 GAAAATTTTCCTGCATTTATCGATACATTTTATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
2905927 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
2905954 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:2906065 original size:32 final size:33
Alignment explanation
Indices: 2906024--2906092 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
2906014 GGCAGTAGCT
2906024 TACATTGTATCGATACAAAAC-CTATGTATCGA
1 TACATTGTATCGATACAAAACTCTATGTATCGA
* *
2906056 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTCTATGTATCGA
2906089 TACA
1 TACA
2906093 AATCATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTCTATGTATCGA
Found at i:2906066 original size:13 final size:13
Alignment explanation
Indices: 2906048--2906072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2906038 ACAAAACCTA
2906048 TGTATCGATACAT
1 TGTATCGATACAT
2906061 TGTATCGATACA
1 TGTATCGATACA
2906073 ACACTTTATG
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:2906547 original size:33 final size:33
Alignment explanation
Indices: 2906502--2906564 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2906492 ATGCAGATTT
* *
2906502 ATCGATATAAGTTGCTATGTATCGATACATTGG
1 ATCGATACAAGTTGCAATGTATCGATACATTGG
2906535 ATCGATACAAGTTGCAATGTATCGATACAT
1 ATCGATACAAGTTGCAATGTATCGATACAT
2906565 GAAACTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
ATCGATACAAGTTGCAATGTATCGATACATTGG
Found at i:2906560 original size:20 final size:19
Alignment explanation
Indices: 2906501--2906563 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
2906491 CATGCAGATT
*
2906501 TATCGATATAAGTTGCTATG
1 TATCGATACAAGTTGC-ATG
2906521 TATCGATAC-A-TTG---G
1 TATCGATACAAGTTGCATG
2906535 -ATCGATACAAGTTGCAATG
1 TATCGATACAAGTTGC-ATG
2906554 TATCGATACA
1 TATCGATACA
2906564 TGAAACTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
13 8 0.23
14 2 0.06
15 3 0.09
18 3 0.09
19 2 0.06
20 17 0.49
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (19 bp):
TATCGATACAAGTTGCATG
Found at i:2906616 original size:22 final size:22
Alignment explanation
Indices: 2906588--2906685 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 22
2906578 GTTACCCTTT
2906588 GACTGTATCGATACAACTATGA
1 GACTGTATCGATACAACTATGA
2906610 GACTGTATCGAT---AC-ATGA
1 GACTGTATCGATACAACTATGA
* * * * * *
2906628 AACTAGCAGTAGTTAC-CCT-T-T
1 GACT-GTA-TCGATACAACTATGA
2906649 GACTGTATCGATACAACTATGA
1 GACTGTATCGATACAACTATGA
2906671 GACTGTATCGATACA
1 GACTGTATCGATACA
2906686 TGTTTAAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
18 7 0.12
19 9 0.16
20 7 0.12
21 4 0.07
22 29 0.52
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (22 bp):
GACTGTATCGATACAACTATGA
Found at i:2906628 original size:61 final size:61
Alignment explanation
Indices: 2906552--2906687 Score: 272
Period size: 61 Copynumber: 2.2 Consensus size: 61
2906542 CAAGTTGCAA
2906552 TGTATCGATACATGAAACTAGCAGTAGTTACCCTTTGACTGTATCGATACAACTATGAGAC
1 TGTATCGATACATGAAACTAGCAGTAGTTACCCTTTGACTGTATCGATACAACTATGAGAC
2906613 TGTATCGATACATGAAACTAGCAGTAGTTACCCTTTGACTGTATCGATACAACTATGAGAC
1 TGTATCGATACATGAAACTAGCAGTAGTTACCCTTTGACTGTATCGATACAACTATGAGAC
2906674 TGTATCGATACATG
1 TGTATCGATACATG
2906688 TTTAAATTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (61 bp):
TGTATCGATACATGAAACTAGCAGTAGTTACCCTTTGACTGTATCGATACAACTATGAGAC
Found at i:2907787 original size:10 final size:11
Alignment explanation
Indices: 2907764--2907788 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2907754 AATTTTTTTA
2907764 TTTTAAAGATT
1 TTTTAAAGATT
2907775 TTTTAAAGATT
1 TTTTAAAGATT
2907786 TTT
1 TTT
2907789 CTATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTTAAAGATT
Found at i:2909842 original size:13 final size:13
Alignment explanation
Indices: 2909824--2909853 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2909814 ACTTTTTACT
2909824 ATGTATCGATACA
1 ATGTATCGATACA
*
2909837 ATGTATTGATACA
1 ATGTATCGATACA
2909850 ATGT
1 ATGT
2909854 CCCATGTATC
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:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2912272 original size:31 final size:31
Alignment explanation
Indices: 2912237--2912301 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2912227 TTACAAAGAT
2912237 TTTGAAGAAAAATG-AAAGGAAATGATGTAAA
1 TTTGAAGAAAAATGAAAAGGAAATGATG-AAA
* **
2912268 TTTGATGAAATTTGAAAAGGAAATGATGAAA
1 TTTGAAGAAAAATGAAAAGGAAATGATGAAA
2912299 TTT
1 TTT
2912302 CAGATTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (31 bp):
TTTGAAGAAAAATGAAAAGGAAATGATGAAA
Found at i:2916080 original size:20 final size:20
Alignment explanation
Indices: 2916057--2916129 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2916047 ACAACTCAAA
2916057 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2916077 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2916098 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2916118 GTATCGATACAT
1 GTATCGATACAT
2916130 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2916108 original size:41 final size:42
Alignment explanation
Indices: 2916057--2916151 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2916047 ACAACTCAAA
*
2916057 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2916098 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2916140 GTATCGATACAT
1 GTATCGATACAT
2916152 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Done.