Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 1 of 54
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--45 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1 TAACCCC
1 TAACCCC
8 TAACCCC
1 TAACCCC
15 TAACCCC
1 TAACCCC
22 TAACCCC
1 TAACCCC
*
29 TAAACCC
1 TAACCCC
*
36 TAAACCC
1 TAACCCC
43 TAA
1 TAA
46 ACCAAAACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.36, C:0.49, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:6767 original size:7 final size:7
Alignment explanation
Indices: 6757--6925 Score: 256
Period size: 7 Copynumber: 24.7 Consensus size: 7
6747 AAAAAAAAAA
6757 AAACCCT
1 AAACCCT
6764 AAACCCT
1 AAACCCT
6771 AAACCCT
1 AAACCCT
6778 AAACCCT
1 AAACCCT
6785 AAACCCT
1 AAACCCT
6792 AAACCCT
1 AAACCCT
*
6799 AAACCCG
1 AAACCCT
*
6806 AAACCCG
1 AAACCCT
*
6813 AAACCCG
1 AAACCCT
*
6820 AAACCCG
1 AAACCCT
6827 AAACCCT
1 AAACCCT
6834 AAACCCT
1 AAACCCT
6841 AAACCCT
1 AAACCCT
6848 AAACCCT
1 AAACCCT
6855 AAACCCT
1 AAACCCT
6862 AAACCCT
1 AAACCCT
6869 AAACCCT
1 AAACCCT
6876 AAACCCT
1 AAACCCT
6883 AAACCCT
1 AAACCCT
6890 AAA-CCT
1 AAACCCT
*
6896 AAA-CCA
1 AAACCCT
6902 AAACCCT
1 AAACCCT
6909 AAA-CC-
1 AAACCCT
*
6914 AAAACCT
1 AAACCCT
6921 AAACC
1 AAACC
6926 AAAAAAAAAA
Statistics
Matches: 154, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
5 3 0.02
6 15 0.10
7 136 0.88
ACGTcount: A:0.46, C:0.41, G:0.02, T:0.11
Consensus pattern (7 bp):
AAACCCT
Found at i:14296 original size:7 final size:7
Alignment explanation
Indices: 14286--14493 Score: 193
Period size: 7 Copynumber: 28.9 Consensus size: 7
14276 AAAAAAAAAA
*
14286 AAACCCT
1 AAACCCC
*
14293 AAA-CCT
1 AAACCCC
*
14299 AAACCCT
1 AAACCCC
*
14306 AAACCCTT
1 AAACCC-C
*
14314 AAACCCT
1 AAACCCC
14321 AAACCCC
1 AAACCCC
*
14328 AAACCCTA
1 AAACCC-C
*
14336 AAACCCT
1 AAACCCC
*
14343 AAACCCTA
1 AAACCC-C
*
14351 AAACCCTAAA
1 AAACCC---C
*
14361 AAACCCT
1 AAACCCC
*
14368 AAACCCT
1 AAACCCC
14375 AAACCCC
1 AAACCCC
14382 AAACCCC
1 AAACCCC
*
14389 CAACCCC
1 AAACCCC
*
14396 CAACCCC
1 AAACCCC
14403 AAACCCC
1 AAACCCC
14410 AAACCCC
1 AAACCCC
*
14417 AAAACCTC
1 -AAACCCC
14425 AAACCCC
1 AAACCCC
*
14432 AACCCCC
1 AAACCCC
14439 AAACCCC
1 AAACCCC
14446 AAACCCC
1 AAACCCC
14453 AAACCCC
1 AAACCCC
*
14460 AACCCCC
1 AAACCCC
14467 AAACCCC
1 AAACCCC
14474 AAACCCC
1 AAACCCC
*
14481 AAAACCC
1 AAACCCC
14488 AAACCC
1 AAACCC
14494 TAANNNNNNN
Statistics
Matches: 177, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
6 6 0.03
7 139 0.79
8 25 0.14
10 7 0.04
ACGTcount: A:0.43, C:0.50, G:0.00, T:0.06
Consensus pattern (7 bp):
AAACCCC
Found at i:15588 original size:7 final size:7
Alignment explanation
Indices: 15573--15668 Score: 129
Period size: 7 Copynumber: 13.6 Consensus size: 7
15563 NNNNNNNNNN
*
15573 CTAACCC
1 CTAAACC
15580 CTAAACC
1 CTAAACC
*
15587 CTAACCC
1 CTAAACC
15594 CTAAACC
1 CTAAACC
15601 CTAAACC
1 CTAAACC
*
15608 CTAACCC
1 CTAAACC
*
15615 CTAACCC
1 CTAAACC
*
15622 CTAACCC
1 CTAAACC
*
15629 CTAACCC
1 CTAAACC
15636 CTAAACC
1 CTAAACC
15643 CTAAACC
1 CTAAACC
15650 CTAAACC
1 CTAAACC
15657 CTAAAACC
1 CT-AAACC
15665 CTAA
1 CTAA
15669 CCAACCCAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
7 76 0.92
8 7 0.08
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:15602 original size:21 final size:21
Alignment explanation
Indices: 15573--15668 Score: 147
Period size: 21 Copynumber: 4.5 Consensus size: 21
15563 NNNNNNNNNN
*
15573 CTAACCCCTAAACCCTAACCC
1 CTAAACCCTAAACCCTAACCC
15594 CTAAACCCTAAACCCTAACCC
1 CTAAACCCTAAACCCTAACCC
* *
15615 CTAACCCCTAACCCCTAACCC
1 CTAAACCCTAAACCCTAACCC
*
15636 CTAAACCCTAAACCCTAAACC
1 CTAAACCCTAAACCCTAACCC
15657 CTAAAACCCTAA
1 CT-AAACCCTAA
15669 CCAACCCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
21 59 0.87
22 9 0.13
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.15
Consensus pattern (21 bp):
CTAAACCCTAAACCCTAACCC
Found at i:24977 original size:7 final size:7
Alignment explanation
Indices: 24967--25072 Score: 99
Period size: 7 Copynumber: 14.9 Consensus size: 7
24957 TCCTTCTTCN
24967 TAACCCC
1 TAACCCC
24974 TAACCCC
1 TAACCCC
24981 TAACCCC
1 TAACCCC
24988 TAACCCC
1 TAACCCC
24995 TAAACCCC
1 T-AACCCC
*
25003 CAA-CCC
1 TAACCCC
25009 TCAACCCC
1 T-AACCCC
**
25017 CCACCCC
1 TAACCCC
25024 TAACCCC
1 TAACCCC
*
25031 CAACCCCC
1 TAA-CCCC
*
25039 AAACCCC
1 TAACCCC
*
25046 AAACCCC
1 TAACCCC
25053 -AACCCC
1 TAACCCC
*
25059 TGACCCC
1 TAACCCC
25066 TGAACCC
1 T-AACCC
25073 TGAACGCTGA
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
6 9 0.11
7 55 0.66
8 19 0.23
ACGTcount: A:0.29, C:0.60, G:0.02, T:0.08
Consensus pattern (7 bp):
TAACCCC
Found at i:24993 original size:21 final size:21
Alignment explanation
Indices: 24967--25072 Score: 99
Period size: 22 Copynumber: 5.0 Consensus size: 21
24957 TCCTTCTTCN
24967 TAACCCCTAACCCCTAACCCC
1 TAACCCCTAACCCCTAACCCC
*
24988 TAACCCCTAAACCCCCAA-CCC
1 TAACCCCT-AACCCCTAACCCC
**
25009 TCAACCCCCCACCCCTAACCCC
1 T-AACCCCTAACCCCTAACCCC
* * *
25031 CAACCCCCAAACCCCAAACCCC
1 TAA-CCCCTAACCCCTAACCCC
*
25053 -AACCCCTGACCCCTGAACCC
1 TAACCCCTAACCCCT-AACCC
25073 TGAACGCTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
20 9 0.13
21 28 0.41
22 32 0.46
ACGTcount: A:0.29, C:0.60, G:0.02, T:0.08
Consensus pattern (21 bp):
TAACCCCTAACCCCTAACCCC
Found at i:25014 original size:29 final size:28
Alignment explanation
Indices: 24967--25058 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
24957 TCCTTCTTCN
* * *
24967 TAACCCCTAACCCCTAACCCCTAACCCC
1 TAACCCCCAACCCCAAACCCCAAACCCC
**
24995 TAAACCCCCAACCCTC-AACCCCCCACCCC
1 T-AACCCCCAACCC-CAAACCCCAAACCCC
25024 TAACCCCCAACCCCCAAACCCCAAACCCC
1 TAACCCCCAA-CCCCAAACCCCAAACCCC
25053 -AACCCC
1 TAACCCC
25059 TGACCCCTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 17 0.31
29 37 0.67
30 1 0.02
ACGTcount: A:0.30, C:0.62, G:0.00, T:0.08
Consensus pattern (28 bp):
TAACCCCCAACCCCAAACCCCAAACCCC
Found at i:32741 original size:7 final size:7
Alignment explanation
Indices: 32731--32849 Score: 97
Period size: 7 Copynumber: 17.7 Consensus size: 7
32721 TAAAAAAAAA
*
32731 AAACTCT
1 AAACCCT
32738 AAACCCT
1 AAACCCT
32745 AAACCCT
1 AAACCCT
32752 -AACACCT
1 AAAC-CCT
*
32759 AACCCCT
1 AAACCCT
*
32766 AACCCCT
1 AAACCCT
32773 AAACCCT
1 AAACCCT
*
32780 AACCCCT
1 AAACCCT
*
32787 AAACCCC
1 AAACCCT
* *
32794 GAACCCC
1 AAACCCT
*
32801 AAACCCG
1 AAACCCT
32808 AAACCCT
1 AAACCCT
*
32815 GAA-CCT
1 AAACCCT
*
32821 TAA-CCT
1 AAACCCT
32827 AAA-CCT
1 AAACCCT
32833 AAA-CCT
1 AAACCCT
32839 AAA-CCT
1 AAACCCT
32845 AAACC
1 AAACC
32850 AAAAAACCTA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
6 31 0.32
7 63 0.66
8 2 0.02
ACGTcount: A:0.40, C:0.44, G:0.03, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:32831 original size:6 final size:6
Alignment explanation
Indices: 32816--32878 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
32806 CGAAACCCTG
* *
32816 AACCTT AACCTA AACCTA AACCTA AACCTA AACCAAAA AACCTA AA--TA
1 AACCTA AACCTA AACCTA AACCTA AACCTA AACC--TA AACCTA AACCTA
*
32864 AACC-A AACCAA AACC
1 AACCTA AACCTA AACC
32879 AAAAAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 35 0.71
8 5 0.10
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.13
Consensus pattern (6 bp):
AACCTA
Found at i:38988 original size:12 final size:12
Alignment explanation
Indices: 38971--38996 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38961 TTTAAATCCC
38971 CAACATGTTTCT
1 CAACATGTTTCT
38983 CAACATGTTTCT
1 CAACATGTTTCT
38995 CA
1 CA
38997 CATTTTATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (12 bp):
CAACATGTTTCT
Found at i:40106 original size:21 final size:21
Alignment explanation
Indices: 40066--40409 Score: 181
Period size: 20 Copynumber: 16.4 Consensus size: 21
40056 AAAAAACCTT
* *
40066 AAACCCTAACCCCTAA-CCCC
1 AAACCCCAACCCCCAACCCCC
40086 AAACCCCAACCCCCAACCCCC
1 AAACCCCAACCCCCAACCCCC
**
40107 AAAACCCCAA-CCCTGACCCCC
1 -AAACCCCAACCCCCAACCCCC
*
40128 AAACCCCAAACCCTCAA--CCC
1 AAACCCC-AACCCCCAACCCCC
* * *
40148 TAACCCCTAAACCCCAAACCCC
1 AAACCCC-AACCCCCAACCCCC
* * * *
40170 AAA--CCTACACCCTAAACCCT
1 AAACCCCAAC-CCCCAACCCCC
*
40190 AACCCCCAA-CCCCAACCCCC
1 AAACCCCAACCCCCAACCCCC
*
40210 AAACCCCTAACCCCTCAACACCC
1 AAACCCC-AACCCC-CAACCCCC
* * *
40233 -AACCCCCACACCTCAAACCCC
1 AAACCCCAAC-CCCCAACCCCC
* **
40254 ACACCCTCAACCCTAAACCCCC
1 AAACCC-CAACCCCCAACCCCC
* **
40276 -AACCCCTA-CCCCAAATCCC
1 AAACCCCAACCCCCAACCCCC
*
40295 AAACCCCTAA-CCCCAAACCCC
1 AAACCCC-AACCCCCAACCCCC
** * * *
40316 AAACCTTAACCCCTAAACCCT
1 AAACCCCAACCCCCAACCCCC
* **
40337 AACCCCCAAACCCTTAACCCCC
1 AAACCCC-AACCCCCAACCCCC
*
40359 AAACCCCTACCCCCAA-CCCC
1 AAACCCCAACCCCCAACCCCC
** *
40379 AAATCCAAAACCCCCAACCCCT
1 AAA-CCCCAACCCCCAACCCCC
40401 AAACCCCAA
1 AAACCCCAA
40410 ATCCAAACCC
Statistics
Matches: 244, Mismatches: 59, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
19 8 0.03
20 81 0.33
21 78 0.32
22 67 0.27
23 10 0.04
ACGTcount: A:0.35, C:0.57, G:0.00, T:0.08
Consensus pattern (21 bp):
AAACCCCAACCCCCAACCCCC
Found at i:40412 original size:29 final size:27
Alignment explanation
Indices: 40357--40429 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
40347 CCCTTAACCC
* *
40357 CCAAACCCCTACCCC-CAACCCCAAAT
1 CCAAACCCCAACCCCTAAACCCCAAAT
40383 CCAAAACCCCCAACCCCTAAACCCCAAAT
1 CC-AAA-CCCCAACCCCTAAACCCCAAAT
40412 CCAAACCCCAACCCCTAA
1 CCAAACCCCAACCCCTAA
40430 TCGCTAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 16 0.38
28 12 0.29
29 12 0.29
ACGTcount: A:0.38, C:0.55, G:0.00, T:0.07
Consensus pattern (27 bp):
CCAAACCCCAACCCCTAAACCCCAAAT
Found at i:40655 original size:7 final size:7
Alignment explanation
Indices: 40073--40664 Score: 264
Period size: 7 Copynumber: 84.7 Consensus size: 7
40063 CTTAAACCCT
*
40073 AACCCCT
1 AACCCCA
40080 AACCCCA
1 AACCCCA
40087 AACCCCA
1 AACCCCA
*
40094 ACCCCCA
1 AACCCCA
*
40101 ACCCCCAA
1 AACCCC-A
40109 AACCCC-
1 AACCCCA
**
40115 AACCCTG
1 AACCCCA
*
40122 ACCCCCA
1 AACCCCA
40129 AACCCCA
1 AACCCCA
40136 AACCCTC-
1 AACCC-CA
*
40143 AA-CCCT
1 AACCCCA
40149 AACCCCTA
1 AACCCC-A
40157 AACCCCA
1 AACCCCA
40164 AACCCCA
1 AACCCCA
*
40171 AA-CCTA
1 AACCCCA
* *
40177 CACCCTA
1 AACCCCA
*
40184 AA-CCCT
1 AACCCCA
*
40190 AACCCCC
1 AACCCCA
40197 AACCCCA
1 AACCCCA
*
40204 ACCCCCA
1 AACCCCA
*
40211 AACCCCT
1 AACCCCA
*
40218 AACCCCTC
1 AACCCC-A
40226 AACACCCA
1 AAC-CCCA
*
40234 ACCCCCA
1 AACCCCA
* *
40241 CACCTCA
1 AACCCCA
40248 AACCCCA
1 AACCCCA
*
40255 CACCCTC-
1 AACCC-CA
*
40262 AACCCTA
1 AACCCCA
*
40269 AACCCCC
1 AACCCCA
40276 AACCCC-
1 AACCCCA
*
40282 TACCCCA
1 AACCCCA
*
40289 AATCCCA
1 AACCCCA
*
40296 AACCCCT
1 AACCCCA
40303 AACCCCA
1 AACCCCA
40310 AACCCCA
1 AACCCCA
**
40317 AA-CCTT
1 AACCCCA
40323 AACCCCTA
1 AACCCC-A
*
40331 AACCCTA
1 AACCCCA
*
40338 ACCCCCA
1 AACCCCA
*
40345 AACCCTTA
1 AACCC-CA
*
40353 ACCCCCA
1 AACCCCA
40360 AACCCC-
1 AACCCCA
* *
40366 TACCCCC
1 AACCCCA
40373 AACCCCA
1 AACCCCA
* *
40380 AATCCAA
1 AACCCCA
*
40387 AACCCCC
1 AACCCCA
40394 AACCCCTA
1 AACCCC-A
40402 AACCCCA
1 AACCCCA
*
40409 AA-TCCA
1 AACCCCA
40415 AACCCC-
1 AACCCCA
40421 AACCCCTA
1 AACCCC-A
* * *
40429 ATCGCTA
1 AACCCCA
*
40436 AA-CCCT
1 AACCCCA
*
40442 AA-CCCT
1 AACCCCA
40448 AACCCCAA
1 AACCCC-A
**
40456 AACCCTT
1 AACCCCA
* *
40463 AAGCCTA
1 AACCCCA
40470 AACCCCTA
1 AACCCC-A
*
40478 AA-CCCT
1 AACCCCA
*
40484 AACCCTTA
1 AACCC-CA
*
40492 AACCCTA
1 AACCCCA
* *
40499 AA-CTCT
1 AACCCCA
* *
40505 AGCCCCT
1 AACCCCA
**
40512 AACCTTTA
1 AACC-CCA
*
40520 AA-CCCT
1 AACCCCA
40526 AACCCCA
1 AACCCCA
* *
40533 AAACCCT
1 AACCCCA
*
40540 AATCCCA
1 AACCCCA
40547 AATCCCCA
1 AA-CCCCA
* *
40555 AACTCTA
1 AACCCCA
*
40562 AACCCCC
1 AACCCCA
*
40569 AACCTCA
1 AACCCCA
**
40576 AACCTTA
1 AACCCCA
40583 AACCCCA
1 AACCCCA
40590 AA-CCCA
1 AACCCCA
40596 AACCCCA
1 AACCCCA
* *
40603 AACCTCG
1 AACCCCA
*
40610 AACCCCG
1 AACCCCA
40617 AACCCCGA
1 AACCCC-A
* *
40625 AACTCAA
1 AACCCCA
*
40632 AACCCGA
1 AACCCCA
***
40639 AACTAAA
1 AACCCCA
40646 AACCCCA
1 AACCCCA
40653 AACCCCA
1 AACCCCA
40660 AACCC
1 AACCC
40665 TAAAAAAATA
Statistics
Matches: 433, Mismatches: 120, Indels: 64
0.70 0.19 0.10
Matches are distributed among these distances:
5 1 0.00
6 63 0.15
7 303 0.70
8 63 0.15
9 3 0.01
ACGTcount: A:0.37, C:0.52, G:0.01, T:0.10
Consensus pattern (7 bp):
AACCCCA
Found at i:48834 original size:26 final size:26
Alignment explanation
Indices: 48798--48957 Score: 169
Period size: 26 Copynumber: 6.5 Consensus size: 26
48788 ACTGACTTTG
* *
48798 GGCATTGCGTGACTAGTTTTTTATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
48824 GGCATTGCGTGACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
48850 GGCATTGCGTGACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
* **
48876 GGTATTGTATGACTAG--T-TGAT-A
1 GGCATTGCGTGACTAGTTTCTGATAA
* * *
48898 GGCATTGCGTAACTTG-TT-AG-TAA
1 GGCATTGCGTGACTAGTTTCTGATAA
48921 GGCATTGCGTGACTAG-TTC-G-TAA
1 GGCATTGCGTGACTAGTTTCTGATAA
*
48944 GGCATTGTGTGACT
1 GGCATTGCGTGACT
48958 TAAGCATTGC
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
22 13 0.11
23 40 0.34
24 1 0.01
26 63 0.54
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (26 bp):
GGCATTGCGTGACTAGTTTCTGATAA
Found at i:49010 original size:22 final size:21
Alignment explanation
Indices: 48985--49047 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
48975 TCAGTCATGC
48985 AATGTATAAAAACTAGTCACGT
1 AATG-ATAAAAACTAGTCACGT
* * *
49007 AATGCCT-AAAACCAATCACGT
1 AATG-ATAAAAACTAGTCACGT
49028 AATGACTAAAAACTAGTCAC
1 AATGA-TAAAAACTAGTCAC
49048 ACGGTGATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (21 bp):
AATGATAAAAACTAGTCACGT
Found at i:51364 original size:100 final size:102
Alignment explanation
Indices: 51217--51403 Score: 263
Period size: 101 Copynumber: 1.9 Consensus size: 102
51207 TTAGGGCCAT
*
51217 TTGAGTCCAAGTCCCAACTAAAAATAAGCTTCCAAGGTTTGGGAAAAGCCTTATT-AGGGCCAAA
1 TTGAGTCCAAGTCCCAACTAAAAATAAGCTTCCAAGGTTTGGGAAAAGCCTAATTAAGGGCCAAA
51281 AAGATTTAACCAGTCCATTAAAAATTTTCCTTGCACA
66 AAGATTTAACCAGTCCATTAAAAATTTTCCTTGCACA
* * * * * *
51318 TTGAGTCCAAGTCCCGAC-AAACAA-AGGTTTTCAAGGTTTGTGAAAAGCCTAATTAAGGGCCTA
1 TTGAGTCCAAGTCCCAACTAAA-AATAAGCTTCCAAGGTTTGGGAAAAGCCTAATTAAGGGCCAA
* *
51381 AAGGATTTAACTAGTCCATTAAA
65 AAAGATTTAACCAGTCCATTAAA
51404 GAATATCCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
100 28 0.37
101 47 0.63
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (102 bp):
TTGAGTCCAAGTCCCAACTAAAAATAAGCTTCCAAGGTTTGGGAAAAGCCTAATTAAGGGCCAAA
AAGATTTAACCAGTCCATTAAAAATTTTCCTTGCACA
Found at i:59622 original size:3 final size:3
Alignment explanation
Indices: 59610--59652 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
59600 TATCACGCTG
*
59610 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT GCT TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
59653 CTCTCATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:60666 original size:46 final size:46
Alignment explanation
Indices: 60599--60690 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
60589 GAAAATGACA
60599 ATGAAAGATACATAGCACTAGAAGGATGCAATAAGTTTGGATCATT
1 ATGAAAGATACATAGCACTAGAAGGATGCAATAAGTTTGGATCATT
*
60645 ATGAAAGATATATAGCACTAGAAGGATGCAATAAGTTTGGATCATT
1 ATGAAAGATACATAGCACTAGAAGGATGCAATAAGTTTGGATCATT
60691 TTGCTTCTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (46 bp):
ATGAAAGATACATAGCACTAGAAGGATGCAATAAGTTTGGATCATT
Found at i:61479 original size:18 final size:18
Alignment explanation
Indices: 61448--61485 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
61438 ATATTTTCCC
* *
61448 GAATGCGAATGGGAATGG
1 GAATGAGAACGGGAATGG
61466 GAATGAGAACGGGAATGG
1 GAATGAGAACGGGAATGG
61484 GA
1 GA
61486 TCTATTGCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.45, T:0.13
Consensus pattern (18 bp):
GAATGAGAACGGGAATGG
Found at i:68657 original size:3 final size:3
Alignment explanation
Indices: 68651--68675 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
68641 AGAAGAGAGG
68651 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
68676 CAGAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:69723 original size:26 final size:26
Alignment explanation
Indices: 69694--69790 Score: 73
Period size: 26 Copynumber: 3.8 Consensus size: 26
69684 ATAAATTATT
*
69694 TATAAAAATATTAAATATTAATATAA
1 TATAATAATATTAAATATTAATATAA
*
69720 TATATATAAT-TTAAACATT-AT-TAA
1 TATA-ATAATATTAAATATTAATATAA
*
69744 TATTAATAAGATTAAAATATTAA-AT-A
1 TA-TAATAATATT-AAATATTAATATAA
*
69770 T-TAAT-ATTTTAAACTATTAAT
1 TATAATAATATTAAA-TATTAAT
69791 GTTTTATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
22 3 0.05
23 9 0.16
24 13 0.23
25 6 0.11
26 20 0.35
27 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (26 bp):
TATAATAATATTAAATATTAATATAA
Found at i:69752 original size:24 final size:24
Alignment explanation
Indices: 69717--69788 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
69707 AATATTAATA
69717 TAATA-TATATAATTTAAACATTAT
1 TAATATTA-ATAATTTAAACATTAT
*
69741 TAATATTAATAAGATTAAA-A-TAT
1 TAATATTAATAA-TTTAAACATTAT
*
69764 TAAATATTAATATTTTAAACTATTA
1 T-AATATTAATAATTTAAAC-ATTA
69789 ATGTTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 9 0.23
24 20 0.51
25 8 0.21
26 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (24 bp):
TAATATTAATAATTTAAACATTAT
Found at i:69781 original size:23 final size:23
Alignment explanation
Indices: 69755--69827 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
69745 ATTAATAAGA
69755 TTAAAATATTAAATATTAATATT
1 TTAAAATATTAAATATTAATATT
* * *
69778 TTAAACTATT-AATGTT-TTATTT
1 TTAAAATATTAAATATTAATA-TT
*
69800 ATTAAATTATTAATATATTAAT-TT
1 -TTAAAATATTAA-ATATTAATATT
69824 TTAA
1 TTAA
69828 TGAATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
21 2 0.05
22 7 0.18
23 22 0.56
24 3 0.08
25 4 0.10
26 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TTAAAATATTAAATATTAATATT
Found at i:69789 original size:16 final size:15
Alignment explanation
Indices: 69763--69827 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
69753 GATTAAAATA
69763 TTAAATATTAATATT
1 TTAAATATTAATATT
*
69778 TTAAACTATTAATGTT
1 TTAAA-TATTAATATT
**
69794 TTATTTATTAA-ATT
1 TTAAATATTAATATT
69808 ATTAATATATTAAT-TT
1 -TTAA-ATATTAATATT
69824 TTAA
1 TTAA
69828 TGAATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 2 0.05
15 18 0.45
16 20 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAAATATTAATATT
Found at i:69803 original size:31 final size:30
Alignment explanation
Indices: 69768--69826 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
69758 AAATATTAAA
69768 TATTAATATT-TTAA-ACTATTAATGTTTTATT
1 TATTAA-ATTATTAATA-TATTAAT-TTTTATT
69799 TATTAAATTATTAATATATTAATTTTTA
1 TATTAAATTATTAATATATTAATTTTTA
69827 ATGAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TATTAAATTATTAATATATTAATTTTTATT
Found at i:69822 original size:15 final size:15
Alignment explanation
Indices: 69702--69828 Score: 54
Period size: 15 Copynumber: 8.5 Consensus size: 15
69692 TTTATAAAAA
69702 TATTAA-ATATTAA-
1 TATTAATATATTAAT
69715 TA-TAATATATATAAT
1 TATTAATATAT-TAAT
* *
69730 T-TAAACATTATTAA-
1 TATTAATA-TATTAAT
* *
69744 TATTAATAAGATTAAAA
1 TATTAAT-ATATT-AAT
69761 TATTAA-ATATTAAT
1 TATTAATATATTAAT
*
69775 ATTTTAA-ACTATTAAT
1 -TATTAATA-TATTAAT
* *
69791 GT-TTTATTTATTAAAT
1 -TATTAATATATT-AAT
69807 TATTAATATATTAAT
1 TATTAATATATTAAT
*
69822 TTTTAAT
1 TATTAAT
69829 GAATATAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
12 3 0.03
13 6 0.07
14 6 0.07
15 40 0.47
16 25 0.29
17 6 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TATTAATATATTAAT
Found at i:69890 original size:15 final size:15
Alignment explanation
Indices: 69870--69912 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
69860 AAATTATACA
69870 TAAAATATTATTAAT
1 TAAAATATTATTAAT
* *
69885 TAAAATATAAGTAAT
1 TAAAATATTATTAAT
*
69900 TAAATTA-TATTAA
1 TAAAATATTATTAA
69913 AATATTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TAAAATATTATTAAT
Found at i:69916 original size:25 final size:24
Alignment explanation
Indices: 69879--69930 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
69869 ATAAAATATT
69879 ATTAATTAAAATA-TAAGTAATTAA
1 ATTAATTAAAATATTAA-TAATTAA
*
69903 ATTATATTAAAATATTAATATTTAA
1 ATTA-ATTAAAATATTAATAATTAA
69928 ATT
1 ATT
69931 TTTAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 18 0.72
26 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTAATTAAAATATTAATAATTAA
Found at i:69953 original size:25 final size:26
Alignment explanation
Indices: 69916--69967 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
69906 ATATTAAAAT
* * *
69916 ATTAATATTTAAATTTTTAATTTTTA
1 ATTAATATATAAATTATTAATATTTA
69942 ATTAAT-TATAAATTATTAATATTTA
1 ATTAATATATAAATTATTAATATTTA
69967 A
1 A
69968 AAATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTAATATATAAATTATTAATATTTA
Found at i:70593 original size:7 final size:7
Alignment explanation
Indices: 70581--70610 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
70571 AATATGCACC
70581 ACTTGGA
1 ACTTGGA
70588 ACTTGGA
1 ACTTGGA
70595 ACTTGGA
1 ACTTGGA
70602 ACTTGGA
1 ACTTGGA
70609 AC
1 AC
70611 ATCCCTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (7 bp):
ACTTGGA
Found at i:70637 original size:3 final size:3
Alignment explanation
Indices: 70629--70658 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
70619 CTATAAATTA
*
70629 ACT ACT ACT ACT ACT ACT ACC ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
70659 TAAATTAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ACT
Found at i:78328 original size:2 final size:2
Alignment explanation
Indices: 78313--78354 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
78303 GGTAGAGTAC
78313 AT AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78353 AT
1 AT
78355 TTGTAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78407 original size:2 final size:2
Alignment explanation
Indices: 78394--78425 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
78384 GACCTAAGAA
*
78394 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78426 TTGTAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:78438 original size:71 final size:71
Alignment explanation
Indices: 78322--78465 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 71
78312 CATATATAAT
*
78322 AATATATATATATATATATATATATATATATATTTGTAAATGATTTGGTAAAAGTATGTTATGAC
1 AATATATAAATATATATATATATATATATATATTTGTAAATGATTTGGTAAAAGTATGTTATGAC
78387 CTAAGA
66 CTAAGA
78393 AATATATAAATATATATATATATATATATATATTTGTAAATGATTTGGTAAAAGTATGTTATGAC
1 AATATATAAATATATATATATATATATATATATTTGTAAATGATTTGGTAAAAGTATGTTATGAC
*
78458 TTAAGA
66 CTAAGA
78464 AA
1 AA
78466 ATAGACGACT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (71 bp):
AATATATAAATATATATATATATATATATATATTTGTAAATGATTTGGTAAAAGTATGTTATGAC
CTAAGA
Found at i:79396 original size:4 final size:4
Alignment explanation
Indices: 79387--79413 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
79377 AAAAAAGGCA
79387 GGAG GGAG GGAG GGAG GGAG GGAG GGA
1 GGAG GGAG GGAG GGAG GGAG GGAG GGA
79414 CACATTAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:80383 original size:2 final size:2
Alignment explanation
Indices: 80376--80411 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
80366 AGTTTACCCC
*
80376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
80412 ATTGATAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:90473 original size:2 final size:2
Alignment explanation
Indices: 90466--90501 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
90456 AAATATACAC
90466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90502 TCACATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90553 original size:71 final size:70
Alignment explanation
Indices: 90472--90613 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 70
90462 ACACATATAT
90472 ATATATATATATATATATATATATATATATTCACATAGTTAAGTAACAAATCTAAAAATAGAAGA
1 ATATATATATATATATATATATATATATATTCACATAGTTAAGTAACAAATCTAAAAATAGAAGA
90537 GGAAA
66 GGAAA
*
90542 NATATTTATATATATATATATATATATATATTCACATAGTTAAGTAACAAATCTAAAAATAGAAG
1 -ATATATATATATATATATATATATATATATTCACATAGTTAAGTAACAAATCTAAAAATAGAAG
90607 AGGAAA
65 AGGAAA
90613 A
1 A
90614 AACTACATAT
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 1 0.01
71 69 0.99
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (70 bp):
ATATATATATATATATATATATATATATATTCACATAGTTAAGTAACAAATCTAAAAATAGAAGA
GGAAA
Found at i:90555 original size:2 final size:2
Alignment explanation
Indices: 90543--90572 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
90533 AAGAGGAAAN
*
90543 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90573 TCACATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:95900 original size:104 final size:104
Alignment explanation
Indices: 95717--95924 Score: 265
Period size: 104 Copynumber: 2.0 Consensus size: 104
95707 ATAGAAGCAT
* * * * *
95717 TTATGTTTCAAATATATAAATGAGCGTTTCATCAGTGCTCGATCTTCCTTGTTATTCTATTGATT
1 TTATGTTTCAAATATATAAAAGAGCATCTCATCAGTGCTCGATCTTCCTTATTATTCTATTAATT
*
95782 TTTGGTGACATGAACATAAGTTGAAATTGTTACGAGAGA
66 TTTAGTGACATGAACATAAGTTGAAATTGTTACGAGAGA
* * *
95821 TTATGTTTCGAATATATAAAAGAGCATCTCATCAGTGCTCGGTC-TCCTTAATTATTCTTTTAAT
1 TTATGTTTCAAATATATAAAAGAGCATCTCATCAGTGCTCGATCTTCCTT-ATTATTCTATTAAT
* * * ** *
95885 TTTTATTGGCTTGAACATAAGTTGATGTTGTTATGAGAGA
65 TTTTAGTGACATGAACATAAGTTGAAATTGTTACGAGAGA
95925 GACTATACCT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
103 5 0.06
104 83 0.94
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (104 bp):
TTATGTTTCAAATATATAAAAGAGCATCTCATCAGTGCTCGATCTTCCTTATTATTCTATTAATT
TTTAGTGACATGAACATAAGTTGAAATTGTTACGAGAGA
Found at i:97252 original size:2 final size:2
Alignment explanation
Indices: 97245--97271 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
97235 TTTAAAACAT
97245 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
97272 CTGGAGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:104976 original size:24 final size:24
Alignment explanation
Indices: 104934--104997 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
104924 CAATCCTCAT
* * *
104934 CCCT-TGCAAAATGAAAACATTAA
1 CCCTCTGCAGAATGAGAACATCAA
*
104957 CCCTCTGCAGACTGAGAACATCAA
1 CCCTCTGCAGAATGAGAACATCAA
* *
104981 TCCTTTGCAGAATGAGA
1 CCCTCTGCAGAATGAGA
104998 TGGGCCTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (24 bp):
CCCTCTGCAGAATGAGAACATCAA
Found at i:108221 original size:2 final size:2
Alignment explanation
Indices: 108214--108247 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
108204 CCTAAATCAC
*
108214 AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
108248 CAGTGGCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:110451 original size:16 final size:16
Alignment explanation
Indices: 110418--110456 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
110408 ACATCTTTCC
* *
110418 TTGCTGGTTATGTTCT
1 TTGCTTGTTATGTGCT
*
110434 TTGCTTGTTTTGTGCT
1 TTGCTTGTTATGTGCT
110450 TTGCTTG
1 TTGCTTG
110457 ATCAATCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.59
Consensus pattern (16 bp):
TTGCTTGTTATGTGCT
Found at i:117678 original size:5 final size:5
Alignment explanation
Indices: 117668--117703 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
117658 TGGTTGTGGT
* *
117668 AAGAG AAGAG AAGAG AAGAG AAGAG AGGAG AGGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG A
117704 TGGCCGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:117781 original size:4 final size:4
Alignment explanation
Indices: 117774--117806 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
117764 TGGATGGATG
*
117774 GATA GATA GATA GATA GAAA GA-A GATA GATA GA
1 GATA GATA GATA GATA GATA GATA GATA GATA GA
117807 GAGTGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (4 bp):
GATA
Found at i:118340 original size:3 final size:3
Alignment explanation
Indices: 118332--118358 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
118322 TTAATACTTT
118332 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
118359 GCTCTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:133460 original size:2 final size:2
Alignment explanation
Indices: 133453--133485 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
133443 CCTATTTATG
133453 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 T
133486 TAATAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140836 original size:13 final size:13
Alignment explanation
Indices: 140818--140852 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
140808 AAAAAAATGT
140818 AAAATTTGACTAC
1 AAAATTTGACTAC
* *
140831 ATAATTTTACTAC
1 AAAATTTGACTAC
140844 AAAATTTGA
1 AAAATTTGA
140853 GTTAATAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (13 bp):
AAAATTTGACTAC
Found at i:173796 original size:16 final size:16
Alignment explanation
Indices: 173775--173827 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
173765 ATTTTTAAGA
*
173775 TAATTTTATTAATTAT
1 TAATTTTATAAATTAT
173791 TAATTTTA-AAATTTAT
1 TAATTTTATAAA-TTAT
*
173807 T-ATTATATAAATTA-
1 TAATTTTATAAATTAT
173821 TAATTTT
1 TAATTTT
173828 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.03
15 14 0.45
16 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTTATAAATTAT
Found at i:173825 original size:22 final size:22
Alignment explanation
Indices: 173774--173841 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
173764 TATTTTTAAG
*
173774 ATAATTTTATTAATTAT-TAATTTT
1 ATAA-TTTATT-ATTATATAA-ATT
*
173798 AAAATTTATTATTATATAAATT
1 ATAATTTATTATTATATAAATT
*
173820 ATAATTTTTTATT-TA-AAATT
1 ATAATTTATTATTATATAAATT
173840 AT
1 AT
173842 TTTTAAGGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.18
21 2 0.05
22 18 0.46
23 9 0.23
24 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATTTATTATTATATAAATT
Found at i:174788 original size:16 final size:16
Alignment explanation
Indices: 174767--174815 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
174757 CATTNTATTA
174767 ATATTAATATTTA-AAT
1 ATATTAA-ATTTATAAT
*
174783 ATATTAAAATTAATAAT
1 ATATT-AAATTTATAAT
*
174800 ATATTAAATTTTTAAT
1 ATATTAAATTTATAAT
174816 GAATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTAAATTTATAAT
Found at i:174889 original size:22 final size:25
Alignment explanation
Indices: 174836--174891 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
174826 ATAAAATTAT
*
174836 TATATATTATTAATATTTTAACTAAA
1 TATAAATTATTAATATTTTAAC-AAA
174862 TTATAAATTATTAATA-TTTAA-AAA
1 -TATAAATTATTAATATTTTAACAAA
174886 -ATAAAT
1 TATAAAT
174892 AAAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.21
24 3 0.11
26 5 0.18
27 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAAATTATTAATATTTTAACAAA
Found at i:176580 original size:14 final size:14
Alignment explanation
Indices: 176561--176589 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
176551 AATCGAGTGA
176561 TTGAGTCATACACT
1 TTGAGTCATACACT
176575 TTGAGTCATACACT
1 TTGAGTCATACACT
176589 T
1 T
176590 CTTTTTCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (14 bp):
TTGAGTCATACACT
Found at i:179903 original size:2 final size:2
Alignment explanation
Indices: 179896--179920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
179886 TCTCTGCTCG
179896 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
179921 TACGTTCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:187047 original size:2 final size:2
Alignment explanation
Indices: 187040--187070 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
187030 TGTTCCTTCC
187040 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
187071 NGTTAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:187106 original size:2 final size:2
Alignment explanation
Indices: 187099--187134 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
187089 TTTCTTCCTC
*
187099 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
187135 TTGTGACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:203872 original size:2 final size:2
Alignment explanation
Indices: 203867--203900 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
203857 ACACACACAC
203867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203901 CCTGTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213915 original size:15 final size:17
Alignment explanation
Indices: 213890--213927 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
213880 TGATTTGTCA
213890 TTTGCTTTTT-CCTTTT
1 TTTGCTTTTTCCCTTTT
213906 TTTG-TTTTTCCCTTTT
1 TTTGCTTTTTCCCTTTT
213922 TGTTGC
1 T-TTGC
213928 ATCAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.26
16 11 0.58
17 3 0.16
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.71
Consensus pattern (17 bp):
TTTGCTTTTTCCCTTTT
Found at i:220710 original size:47 final size:47
Alignment explanation
Indices: 220652--220749 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
220642 TTTTTGTGAA
220652 TTCTGATCGACTTATCTTATACTACATACATTAAAGACAGAAGATTT
1 TTCTGATCGACTTATCTTATACTACATACATTAAAGACAGAAGATTT
220699 TTCTGATCGACTTATCTTATACTACATACATTAAAGACAGAAGATTT
1 TTCTGATCGACTTATCTTATACTACATACATTAAAGACAGAAGATTT
220746 TTCT
1 TTCT
220750 TACATTCCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (47 bp):
TTCTGATCGACTTATCTTATACTACATACATTAAAGACAGAAGATTT
Found at i:224977 original size:40 final size:39
Alignment explanation
Indices: 224884--224983 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 39
224874 ACCCTTCGTA
*
224884 TTTGAAGTATTTTTTACTATAAAGAAAAACCTTTAAGCAT
1 TTTGAAGTA-TTTTTACTACAAAGAAAAACCTTTAAGCAT
** * *
224924 TTTGAAACAATTTTTACTACACGAAGAAAAATCTTTGAGCAT
1 TTTG-AAGTATTTTTACTACA--AAGAAAAACCTTTAAGCAT
224966 TTTG-AGTATTTTTA-TACA
1 TTTGAAGTATTTTTACTACA
224984 TTTTCGAGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
39 4 0.08
40 22 0.44
41 3 0.06
42 21 0.42
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (39 bp):
TTTGAAGTATTTTTACTACAAAGAAAAACCTTTAAGCAT
Found at i:225285 original size:22 final size:23
Alignment explanation
Indices: 225235--225286 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
225225 ATATTGCATT
* *
225235 ATTGGTTGATATGGTATTACGTG
1 ATTGGTTGATATGGCATTACGTA
*
225258 ACTGGTTGATAT-GCATTACGTA
1 ATTGGTTGATATGGCATTACGTA
225280 ATTGGTT
1 ATTGGTT
225287 AGTAAAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (23 bp):
ATTGGTTGATATGGCATTACGTA
Found at i:225300 original size:23 final size:23
Alignment explanation
Indices: 225271--225324 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
225261 GGTTGATATG
* *
225271 CATTACGTAATTGGTTAGTAAAA
1 CATTACGTAAATAGTTAGTAAAA
*
225294 CATTACGTAAATAGTTAGTAAGA
1 CATTACGTAAATAGTTAGTAAAA
225317 CATTACGT
1 CATTACGT
225325 GACTTAAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
CATTACGTAAATAGTTAGTAAAA
Found at i:225386 original size:21 final size:21
Alignment explanation
Indices: 225337--225388 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
225327 CTTAAGGCAT
*
225337 TACCTAAAAATTAGTCACGCAA
1 TACCT-AAAATCAGTCACGCAA
* *
225359 TATCTAAAATCAGTTACGCAA
1 TACCTAAAATCAGTCACGCAA
*
225380 TGCCTAAAA
1 TACCTAAAA
225389 ATTAGATACG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (21 bp):
TACCTAAAATCAGTCACGCAA
Found at i:225398 original size:22 final size:21
Alignment explanation
Indices: 225337--225399 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
225327 CTTAAGGCAT
225337 TACCTAAAAATTAGTCACGCAA
1 TACCTAAAAATTAGT-ACGCAA
* *
225359 TATCT-AAAATCAGTTACGCAA
1 TACCTAAAAATTAG-TACGCAA
*
225380 TGCCTAAAAATTAGATACGC
1 TACCTAAAAATTAG-TACGC
225400 TATAATTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (21 bp):
TACCTAAAAATTAGTACGCAA
Found at i:225875 original size:23 final size:23
Alignment explanation
Indices: 225841--225887 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
225831 TTATGAAAAA
225841 ATAACTTAAAAGAACAAATAAAG
1 ATAACTTAAAAGAACAAATAAAG
* * *
225864 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTAAAAGAACAAATAAAG
225887 A
1 A
225888 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAG
Found at i:250877 original size:2 final size:2
Alignment explanation
Indices: 250870--250914 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
250860 GAACTTGAAT
250870 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
250912 AC A
1 AC A
250915 TATTAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:252357 original size:22 final size:21
Alignment explanation
Indices: 252325--252365 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
252315 TTATAAATTT
252325 ATTATTTTA-TTATATATTTGA
1 ATTATTTTATTTAT-TATTTGA
252346 ATTATTTTTATTTATTATTT
1 ATTA-TTTTATTTATTATTT
252366 TTATCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTATTTTATTTATTATTTGA
Found at i:252362 original size:13 final size:13
Alignment explanation
Indices: 252346--252410 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
252336 ATATATTTGA
252346 ATTATTTTTATTT
1 ATTATTTTTATTT
*
252359 ATTATTTTTATCCT
1 ATTATTTTTAT-TT
* *
252373 CTT-TTTTTATCT
1 ATTATTTTTATTT
*
252385 ATTGTTATTTATTT
1 ATTATT-TTTATTT
*
252399 GTTATTTTTATT
1 ATTATTTTTATT
252411 GAATAACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 4 0.09
13 26 0.60
14 13 0.30
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.72
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:252623 original size:15 final size:14
Alignment explanation
Indices: 252603--252658 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
252593 AATATAATGG
252603 TATTTTTGTATTTAT
1 TATTTTT-TATTTAT
252618 TATTTTTTA--T-T
1 TATTTTTTATTTAT
* *
252629 TATTTTTAAATTAT
1 TATTTTTTATTTAT
252643 TATTATTTTATTTAT
1 TATT-TTTTATTTAT
252658 T
1 T
252659 TGTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 9 0.26
12 1 0.03
13 1 0.03
14 7 0.21
15 16 0.47
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTTAT
Found at i:253765 original size:13 final size:12
Alignment explanation
Indices: 253748--253778 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
253738 TTTAAAAAAA
253748 TTATTTATATAT
1 TTATTTATATAT
253760 TATATTTATATAT
1 T-TATTTATATAT
253773 TTATTT
1 TTATTT
253779 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTATATAT
Found at i:253775 original size:21 final size:19
Alignment explanation
Indices: 253747--253792 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
253737 TTTTAAAAAA
253747 ATTATTTATATATTATATTT
1 ATTATTTATATATTAT-TTT
* *
253767 ATATATTTATTTTTTATTTT
1 AT-TATTTATATATTATTTT
253787 ATTATT
1 ATTATT
253793 ATTTTTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 7 0.30
21 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATTTATATATTATTTT
Found at i:254900 original size:19 final size:19
Alignment explanation
Indices: 254866--254903 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
254856 CCATTTGACT
*
254866 TATTGGAGTAGGATTTGAG
1 TATTGGAGTAGAATTTGAG
*
254885 TATTGGAGTATAATTTGAG
1 TATTGGAGTAGAATTTGAG
254904 GTTTGACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (19 bp):
TATTGGAGTAGAATTTGAG
Found at i:255109 original size:28 final size:29
Alignment explanation
Indices: 255068--255127 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
255058 GTCTATGGGC
*
255068 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
255096 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
255126 AA
1 AA
255128 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:274585 original size:52 final size:52
Alignment explanation
Indices: 274511--274624 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 52
274501 AAGCGTGGTG
* *
274511 GAATAGAAGAAATCAAGTAAGGTAAAAGTAACATGGACAAATTACGGTATCATA
1 GAATA-AA-AAATCAAGAAAGGTAAAAGTAAAATGGACAAATTACGGTATCATA
*
274565 GAATAAAAAATCGAGAAAGGTAAAAGTAAAATGGACAAATTACGGTATCATA
1 GAATAAAAAATCAAGAAAGGTAAAAGTAAAATGGACAAATTACGGTATCATA
*
274617 GAAGAAAA
1 GAATAAAA
274625 GGGTAAAGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
52 49 0.88
53 2 0.04
54 5 0.09
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (52 bp):
GAATAAAAAATCAAGAAAGGTAAAAGTAAAATGGACAAATTACGGTATCATA
Found at i:287113 original size:12 final size:12
Alignment explanation
Indices: 287069--287116 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
287059 TGAGATTGAA
287069 TGTTGTAAAATT
1 TGTTGTAAAATT
* *
287081 TGTTGCTATATACT
1 TGTTG-TA-AAATT
287095 T-TTGTAAAATT
1 TGTTGTAAAATT
287106 TGTTGTAAAAT
1 TGTTGTAAAAT
287117 CAAAGTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 4 0.14
12 16 0.55
13 5 0.17
14 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (12 bp):
TGTTGTAAAATT
Found at i:294758 original size:314 final size:309
Alignment explanation
Indices: 294180--294811 Score: 1075
Period size: 314 Copynumber: 2.0 Consensus size: 309
294170 ATATAATTAT
* *
294180 TAAAAAGTAATTTATATATTAAGATTTAAATATTACATGGAAAGATAAAAAAATTTCCTTCTATA
1 TAAAAAATAATTTATATATTAAGATTTAAATATTACATGAAAAGATAAAAAAATTTCCTTCTATA
* **
294245 ATTTAAGGTTTTATTAAAAAGGTCAAAACCTAAACTACTCTCCCTTTCCAAAAATTCAAGTATAA
66 ATTTAAGATTTTATTAAAAAAATCAAAACCTAAACTACTCTCCCTTTCCAAAAATTCAAGTATAA
294310 GACCTGTAGTGACATTTCCTTTTCTCGATCCTTGGTTGTGTTTTTCACTCTCTCAAAACAACTCA
131 GACCTGTAGTGACATTTCCTTTTCTCGATCCTTGGTTGTGTTTTTCACTCTCTCAAAACAACTCA
* *
294375 TCTAGGCTTTAATTGTAAGTAATTTTCAATCTAAATTAAGTTTTTAAATATTTTATGTCTAAATA
196 TCTAGGCTTTAATTGTAAGTAATTTTCAATCTAAATTAAGTTTTTAAATACTTCATGTCTAAATA
294440 TTTTTTTGATTTATTTGATTGTTTGGGTTCATAATTATAATCTAAATAA
261 TTTTTTTGATTTATTTGATTGTTTGGGTTCATAATTATAATCTAAATAA
* *
294489 TAAAAAATAATATNTATATATTAATATTTAAATATTACATGAAAAGATAAAAAAAACTTTCTTTC
1 TAAAAAATAAT-T-TATATATTAAGATTTAAATATTACATGAAAAGAT-AAAAAAA-TTTCCTTC
* *
294554 TATGATTTAAGATTTTATTTAAAAAAATTAAAACCTAAACTACTCTCCCTTTCCAAAAATTCAAG
62 TATAATTTAAGATTTTA-TTAAAAAAATCAAAACCTAAACTACTCTCCCTTTCCAAAAATTCAAG
294619 TATAAGACCTGTAGTGACATTTCCTTTTCTCGATCCTTGGTTGTGTTTTTCACTCTCTCAAAACA
126 TATAAGACCTGTAGTGACATTTCCTTTTCTCGATCCTTGGTTGTGTTTTTCACTCTCTCAAAACA
* *
294684 ACTCATCTAGGCTTTAATTGTAAGTAATTTTCAATCTACATTAAGTTTTTAAATGCTTCATGTCT
191 ACTCATCTAGGCTTTAATTGTAAGTAATTTTCAATCTAAATTAAGTTTTTAAATACTTCATGTCT
**
294749 AAATATTTTTTTGATTTATTTGATTGTTTGGGTTCATAATTATAATCTAGCTAA
256 AAATATTTTTTTGATTTATTTGATTGTTTGGGTTCATAATTATAATCTAAATAA
*
294803 TAGAAAATA
1 TAAAAAATA
294812 GTATTGTACA
Statistics
Matches: 302, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
309 10 0.03
310 1 0.00
311 32 0.11
312 7 0.02
313 22 0.07
314 230 0.76
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (309 bp):
TAAAAAATAATTTATATATTAAGATTTAAATATTACATGAAAAGATAAAAAAATTTCCTTCTATA
ATTTAAGATTTTATTAAAAAAATCAAAACCTAAACTACTCTCCCTTTCCAAAAATTCAAGTATAA
GACCTGTAGTGACATTTCCTTTTCTCGATCCTTGGTTGTGTTTTTCACTCTCTCAAAACAACTCA
TCTAGGCTTTAATTGTAAGTAATTTTCAATCTAAATTAAGTTTTTAAATACTTCATGTCTAAATA
TTTTTTTGATTTATTTGATTGTTTGGGTTCATAATTATAATCTAAATAA
Found at i:309972 original size:30 final size:30
Alignment explanation
Indices: 309938--309997 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
309928 ATCCCTTATG
*
309938 ATTATATAAACT-TTCATACATATAAACTTT
1 ATTAT-TAAACTATTCATAAATATAAACTTT
* *
309968 ATTATTCATCTATTCATAAATATAAACTTT
1 ATTATTAAACTATTCATAAATATAAACTTT
309998 GTACACATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTATTAAACTATTCATAAATATAAACTTT
Found at i:324255 original size:839 final size:833
Alignment explanation
Indices: 322638--324255 Score: 2289
Period size: 839 Copynumber: 1.9 Consensus size: 833
322628 AATTAATATA
* *
322638 TCTTGAATTTGGAAAGAATAGTCCATTATTATGTAAAAACATTTTTTAAAATAAAAATTTAACTA
1 TCTTGAATTTGGAAAGAATAGTACATTAATATGTAAAAACATTTTTTAAAATAAAAATTTAACTA
322703 ACCCTAACAAGTGTTTATAGGCACCTATTAACTAAATCTTTTTTTTCTTCAATGCATAACTAATT
66 ACCCTAACAAGTGTTTATAGGCACCTATTAACTAAATCTTTTTTTTCTTCAATGCATAACTAATT
*
322768 AACATAAAAGTATAAATTTCCAATCCAAGTTAATTTTTTCATGGATTTTTTCTTAATGGAGATCC
131 AACATAAAAGTATAAATTTCCAATCCAAGTTAATTTTTTCATGAATTTTTTCTTAATGGAGATCC
* * * *
322833 AAGAAATCTCGTGAATTCAACAATAATTAAGAAAGTCATGATTTCATAGTTTTAACACCCACATT
196 AACAAATCACGTAAATTCAACAATAATTAAGAAAGTCATGATTTCATAGTTTTAACACCCACACT
* * * *
322898 TATAATAAATTTGAAATTTAAATATTTGTTTTCTAAATTCAAGTTTTCAATTTCAACCTAAACTA
261 TATAATAAATTTGAAATTTAAATATCTGTCTTCTAAATTAAAGTTTTCAATTTCAAACTAAACTA
* * *
322963 GAATCATATATATGAAATTACAAATAAATATAAATTGACAACTAATCAGTTTAATTTGTTTAAAG
326 AAATCATAAATATGAAATTACAAATAAAAATAAATTGACAACTAATCAGTTTAATTTGTTTAAAG
* ** * * * ***
323028 GGAGACCATGTCAAATATACCTGTTAAGTTGTTTCTATTGAGATACAACTGGTTTAATCTAGTCA
391 GAAGACCAACTCAAACATACCTCTTAAGTTGTTACTATTGAGATACAACTCACTTAATCTAGTCA
* * * * * *
323093 AATTCTTGATTTCTTGAGGCACACTTCCCTCCAAAGCATTGTTAGATAGATATAAAATTTCTAAC
456 AATTCCTGACTTCTTGAGACACAATTCCCTCCAAAGCATTGTTAGATAAAGATAAAATTTCTAAC
* * *
323158 TCTTGGCACTTGAATAAAGTTGATGGAAGTTGACCCCACAATGAGATTATTAGTGTTGAAATCAA
521 TCTCGGCACTTGAATAAAGCTGATGGAAGTTGACCCCACAATGAGATTATTAGTGTCGAAATCAA
** *
323223 TATTTGCAATAAAGATATATTGATGATTGAAAGCAAGCTGATTATTATGCAACCTGAAAACTTAT
586 TATTTGCAATAAAGATATATTGATGATCAAAAGCAAGCTGATCATTATGCAACCTGAAAACTTAT
* * *
323288 TATTGTTCAAATATAACCATTTCAGGTTGGAAAGATTTTCAATTGCTATAGGAATATTCCCATTC
651 TATTGTCCAAATACAACCATTTCAAGTTGGAAAGATTTTCAATTGCTATAGGAATATTCCCATTC
** ** * * * *
323353 AGATCATTGTCATACAAGATCAACTTCTTGAGATTTGATAGAGAACCCAAAGAAGATGGGATAAT
716 AGATCATTGTCATACAAGATCAACACCTCAAGATTTGACAAAGAACCCAAAGAACACGGGATAAT
323418 ATATGTTAAGGTGATATCTGTAAAAAGATTTTTGTAATTAATATATTGTCTTT
781 ATATGTTAAGGTGATATCTGTAAAAAGATTTTTGTAATTAATATATTGTCTTT
*
323471 TCTTGAATTTGGAAAGAATAGTACATTAATATGTAAAAACATTTTTT-AAATAAAAGTTTAACTA
1 TCTTGAATTTGGAAAGAATAGTACATTAATATGTAAAAACATTTTTTAAAATAAAAATTTAACTA
** * *
323535 ACTGTAACAAGTGTTTCTAGGCACCTATTAGCTAAATCTTTTTTTATCTTCAATGCATAACTAAT
66 ACCCTAACAAGTGTTTATAGGCACCTATTAACTAAATCTTTTTTT-TCTTCAATGCATAACTAAT
** *
323600 TAACATAAAAGTATAAATTTTTAATCCAAGTTAATTTTTTCATGAATTTTTTCTTAATGTAGATC
130 TAACATAAAAGTATAAATTTCCAATCCAAGTTAATTTTTTCATGAATTTTTTCTTAATGGAGATC
* * * * * *
323665 TAACAAATCAGGTAAATTCCAA-AATAATTAAGAAAGTCATGTTTTCATGGGTTTTATCACTCAC
195 CAACAAATCACGTAAATT-CAACAATAATTAAGAAAGTCATGATTTCAT-AGTTTTAACACCCAC
* * *
323729 ACTTGTACTAAATTTGAAATTTAAATATCT-TCTTCTAAATTAAAGTTTTCAACTGCAATTTAAA
258 ACTTATAATAAATTTGAAATTTAAATATCTGTCTTCTAAATTAAAGTTTTCAA-T----TTCAAA
* * * * * *
323793 TTAAAACTAAAATCATAAATCTGAACTTACGAATAAAAATAAATTGTCAACTAATCATTTTAATT
318 CT-AAACTAAAATCATAAATATGAAATTACAAATAAAAATAAATTGACAACTAATCAGTTTAATT
* * * * * * *
323858 T-TTCTCAAGGAAGGCCCACACT-AAGCATACTTCTTAGGTTGTTAGTATTGAGGTACAACTCAC
382 TGTT-TAAAGGAA-GACCA-ACTCAAACATACCTCTTAAGTTGTTACTATTGAGATACAACTCAC
323921 TTAATCTAGTCAAATTCCTGACTTCTTGAGACACAATTCCCTCCAAAGCATTGTTAGATAAAGAT
444 TTAATCTAGTCAAATTCCTGACTTCTTGAGACACAATTCCCTCCAAAGCATTGTTAGATAAAGAT
** * *
323986 AAAATTTCTAACTCTCGGCACTTGAATAGCGCTGCTGGAAGTTGA-CCTACAATGAGATTATTAG
509 AAAATTTCTAACTCTCGGCACTTGAATAAAGCTGATGGAAGTTGACCCCACAATGAGATTATTAG
324050 TGTCGAAATCAATATTTGCAATAAAGATATATTGATGATCAAAAGCAAGCTGATCATTATGCAAC
574 TGTCGAAATCAATATTTGCAATAAAGATATATTGATGATCAAAAGCAAGCTGATCATTATGCAAC
*
324115 CTGAAAA-TTGATTATTGTCCAAATACAACCATTTCAAGTTGGAAAGATTTTCTATTGCTATAGG
639 CTGAAAACTT-ATTATTGTCCAAATACAACCATTTCAAGTTGGAAAGATTTTCAATTGCTATAGG
* * * *
324179 AAT-TTGCCCCTTCAGATCATTGTTATACAAGATCAACACCTCAAGGTTTGACAAAGAGCCCAAA
703 AATATT-CCCATTCAGATCATTGTCATACAAGATCAACACCTCAAGATTTGACAAAGAACCCAAA
324243 GAACACGGGATAA
767 GAACACGGGATAA
324256 CACCAAAGAA
Statistics
Matches: 686, Mismatches: 85, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
832 57 0.08
833 183 0.27
834 42 0.06
838 11 0.02
839 259 0.38
840 133 0.19
841 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (833 bp):
TCTTGAATTTGGAAAGAATAGTACATTAATATGTAAAAACATTTTTTAAAATAAAAATTTAACTA
ACCCTAACAAGTGTTTATAGGCACCTATTAACTAAATCTTTTTTTTCTTCAATGCATAACTAATT
AACATAAAAGTATAAATTTCCAATCCAAGTTAATTTTTTCATGAATTTTTTCTTAATGGAGATCC
AACAAATCACGTAAATTCAACAATAATTAAGAAAGTCATGATTTCATAGTTTTAACACCCACACT
TATAATAAATTTGAAATTTAAATATCTGTCTTCTAAATTAAAGTTTTCAATTTCAAACTAAACTA
AAATCATAAATATGAAATTACAAATAAAAATAAATTGACAACTAATCAGTTTAATTTGTTTAAAG
GAAGACCAACTCAAACATACCTCTTAAGTTGTTACTATTGAGATACAACTCACTTAATCTAGTCA
AATTCCTGACTTCTTGAGACACAATTCCCTCCAAAGCATTGTTAGATAAAGATAAAATTTCTAAC
TCTCGGCACTTGAATAAAGCTGATGGAAGTTGACCCCACAATGAGATTATTAGTGTCGAAATCAA
TATTTGCAATAAAGATATATTGATGATCAAAAGCAAGCTGATCATTATGCAACCTGAAAACTTAT
TATTGTCCAAATACAACCATTTCAAGTTGGAAAGATTTTCAATTGCTATAGGAATATTCCCATTC
AGATCATTGTCATACAAGATCAACACCTCAAGATTTGACAAAGAACCCAAAGAACACGGGATAAT
ATATGTTAAGGTGATATCTGTAAAAAGATTTTTGTAATTAATATATTGTCTTT
Found at i:332721 original size:23 final size:23
Alignment explanation
Indices: 332691--332751 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
332681 GTGACTTAAA
*
332691 AACCAGTCACATAATACCCTATC
1 AACCAGTCACACAATACCCTATC
** *
332714 AACCAGTCATGCAATACCTTATC
1 AACCAGTCACACAATACCCTATC
* *
332737 AACCAATCACGCAAT
1 AACCAGTCACACAAT
332752 GCCTAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.33, G:0.07, T:0.21
Consensus pattern (23 bp):
AACCAGTCACACAATACCCTATC
Found at i:332840 original size:22 final size:21
Alignment explanation
Indices: 332809--332872 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
332799 GTTATCAACT
*
332809 AGTTACGCAATGCCTAAATATC
1 AGTTACGCAAAGCCTAAA-ATC
*
332831 AGTTATGCAACA-CCTTACAAATC
1 AGTTACGCAA-AGCC-TA-AAATC
332854 AGTTACGCAAAGCCTAAAA
1 AGTTACGCAAAGCCTAAAA
332873 ATTAGTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 3 0.09
22 14 0.40
23 16 0.46
24 2 0.06
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
AGTTACGCAAAGCCTAAAATC
Found at i:332847 original size:68 final size:68
Alignment explanation
Indices: 332718--332851 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 68
332708 CCTATCAACC
* * **
332718 AGTCATGCAATACCTTATCAACCAATCACGCAATGCCTAAAAATCAATCATGTAATGCCTTACAA
1 AGTCACGCAATACCTTATCAACCAATCACGCAATGCCTAAAAATCAATCATGCAACACCTTACAA
332783 ACT
66 ACT
* * * * * * * *
332786 AGTCACGCAATGCGTTATCAACTAGTTACGCAATGCCTAAATATCAGTTATGCAACACCTTACAA
1 AGTCACGCAATACCTTATCAACCAATCACGCAATGCCTAAAAATCAATCATGCAACACCTTACAA
332851 A
66 A
332852 TCAGTTACGC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (68 bp):
AGTCACGCAATACCTTATCAACCAATCACGCAATGCCTAAAAATCAATCATGCAACACCTTACAA
ACT
Found at i:332860 original size:45 final size:45
Alignment explanation
Indices: 332809--332915 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
332799 GTTATCAACT
* * *
332809 AGTTACGCAATGCCTAAATATCAGT-TATGCAACACCTTACAAATC
1 AGTTACGCAATGCCTAAAAATCAGTCT-TGCAACACCCTACAAACC
* * *
332854 AGTTACGCAAAGCCTAAAAATTAGTCTTGCAATACCCTACAAACC
1 AGTTACGCAATGCCTAAAAATCAGTCTTGCAACACCCTACAAACC
* *
332899 AGTCACGCAATACCTAA
1 AGTTACGCAATGCCTAA
332916 GTCACACAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.23
Consensus pattern (45 bp):
AGTTACGCAATGCCTAAAAATCAGTCTTGCAACACCCTACAAACC
Found at i:333291 original size:49 final size:49
Alignment explanation
Indices: 333166--333291 Score: 123
Period size: 49 Copynumber: 2.5 Consensus size: 49
333156 ACCTAGTGAG
*
333166 AAATG-CTCAAAATGCTAAAAGTTTTTTGTTGTGTATAAAAAATCATTCCA
1 AAATGCCT-AAAATGCTAAAAG-TTTTTGTTGTGTATAAAAAACCATTCCA
* * * * * *
333216 AAATACTTAAAACGCTCAAA-TTTTTTTGTGTGTATCAAAAACCACTT-CA
1 AAATGCCTAAAATGCTAAAAGTTTTTGT-TGTGTATAAAAAACCA-TTCCA
333265 AAATGCCTAAAATGCTGAAAAGTTTTT
1 AAATGCCTAAAATGCT-AAAAGTTTTT
333292 CTTCCTAGTG
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
48 6 0.10
49 29 0.48
50 19 0.32
51 6 0.10
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (49 bp):
AAATGCCTAAAATGCTAAAAGTTTTTGTTGTGTATAAAAAACCATTCCA
Found at i:333291 original size:50 final size:50
Alignment explanation
Indices: 333166--333291 Score: 141
Period size: 50 Copynumber: 2.5 Consensus size: 50
333156 ACCTAGTGAG
*
333166 AAATG-CTCAAAATGCTAAAAGTTTTTTGTTGTGTATAAAAAATCATTCCA
1 AAATGCCT-AAAATGCTAAAAGTTTTTTGTTGTGTATAAAAAACCATTCCA
* * * * * *
333216 AAATACTTAAAACGCTCAAATTTTTTTG-TGTGTATCAAAAACCACTT-CA
1 AAATGCCTAAAATGCTAAAAGTTTTTTGTTGTGTATAAAAAACCA-TTCCA
333265 AAATGCCTAAAATGCTGAAAAGTTTTT
1 AAATGCCTAAAATGCT-AAAAGTTTTT
333292 CTTCCTAGTG
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
49 29 0.48
50 31 0.51
51 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (50 bp):
AAATGCCTAAAATGCTAAAAGTTTTTTGTTGTGTATAAAAAACCATTCCA
Found at i:336781 original size:18 final size:18
Alignment explanation
Indices: 336758--336803 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
336748 CTTTAATGCA
*
336758 TTTTCTTTTGATTTAT-TT
1 TTTTCTTTT-ATTAATATT
336776 TTTTC-TTTATTAATATT
1 TTTTCTTTTATTAATATT
336793 TTTTCTTTTAT
1 TTTTCTTTTAT
336804 CAAATTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTATTAATATT
Found at i:349206 original size:24 final size:26
Alignment explanation
Indices: 349179--349237 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
349169 TTTTTTTCAC
* *
349179 AAAATATAGATAGA-G-AAAAAATAA
1 AAAATATAGACAGATGAAAAAAAGAA
*
349203 AAAATAAAGACAGATTGAAAAAAAGAA
1 AAAATATAGACAGA-TGAAAAAAAGAA
349230 AAAATATA
1 AAAATATA
349238 AATAAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 12 0.43
26 1 0.04
27 15 0.54
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (26 bp):
AAAATATAGACAGATGAAAAAAAGAA
Found at i:361208 original size:19 final size:20
Alignment explanation
Indices: 361184--361224 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
361174 GAGCCCATTG
361184 ACTTTGTTATGACT-AAAGA
1 ACTTTGTTATGACTAAAAGA
361203 ACTTTGTTATGACTAAAAGA
1 ACTTTGTTATGACTAAAAGA
361223 AC
1 AC
361225 CTTGGCTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (20 bp):
ACTTTGTTATGACTAAAAGA
Found at i:362888 original size:29 final size:29
Alignment explanation
Indices: 362833--362890 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
362823 GTGACGCCGG
*
362833 GGCGTTGTAAAGGCACATGGGCGTTATGA
1 GGCGTTGTAAAGGCACATGGGCATTATGA
* * *
362862 GGCGTTGTAAAGGTACTTGGGTATTATGA
1 GGCGTTGTAAAGGCACATGGGCATTATGA
362891 AAGACACCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.29
Consensus pattern (29 bp):
GGCGTTGTAAAGGCACATGGGCATTATGA
Found at i:362953 original size:40 final size:40
Alignment explanation
Indices: 362895--362973 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
362885 TTATGAAAGA
*
362895 CACCAATCGTGACGAGGTTGAAAACCCCACTAAGGTGAAT
1 CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAAT
* * *
362935 CACCAATCTTGGCAAGGTTGAAAACCTCACTAAGGTGAA
1 CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAA
362974 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (40 bp):
CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAAT
Found at i:369191 original size:14 final size:14
Alignment explanation
Indices: 369174--369203 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
369164 TAAATATCTT
369174 TTTTCAAATTAAAA
1 TTTTCAAATTAAAA
*
369188 TTTTCAAGTTAAAA
1 TTTTCAAATTAAAA
369202 TT
1 TT
369204 GAATGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTCAAATTAAAA
Found at i:376220 original size:292 final size:294
Alignment explanation
Indices: 375650--376224 Score: 782
Period size: 292 Copynumber: 2.0 Consensus size: 294
375640 GAAGATTTTT
* * * *
375650 GTAATTAATATATTGACTTTTGTTGAATTTGTTAAGTATAGTATATTAATATATAAAAACATTTT
1 GTAATTAATATATTAACTTTTCTTGAATTTGGTAAGAATAGTATATTAATATATAAAAACATTTT
* * * ** *
375715 TCAAATAAAAATTTAACAAACTTTAACAAGTATTTATATGCATGTCTCAACGAAATCTTTTTTTT
66 TCAAATAAAAATTTAACAAACCTTAACAAGTACTTATAGGCAACTCTCAACGAAATCTTTATTTT
* *
375780 TTTCTATAATGCATAACTAATTAACTAACATAAAAGTATAAATTTCCTATCCAAATTATTTTTTC
131 TTTCTATAATGCATAACTAATT-A-TAACATAAAAGTATAAATCTCCAATCCAAATTATTTTTTC
* * * *
375845 ATGAATTTTTTCTAAATGGACAAGTAACAAGACCAGCGGATTATAAACTAATTAAGAAAGTTACG
194 ATGAAGTTTTTCTAAATGGACAACTAACAAGACCAGCGAATTATAAACTAATTAAGAAAGTCACG
*
375910 GTTTCATGAGTCTTATCACCCACGTTTTGAAATTTG
259 ATTTCATGAGTCTTATCACCCACGTTTTGAAATTTG
* *
375946 GTAATTAATATATTAATTTTTCTTGAATTTGGTAAGAATAGTATATTAAATATATAAAAGCATTT
1 GTAATTAATATATTAACTTTTCTTGAATTTGGTAAGAATAGTATATT-AATATATAAAAACATTT
* * *
376011 TTCAAATAAAAATTTAACAAACCTTAACAAGTGCTTATAGGCAACTTTTAACGAAATC-TTATTT
65 TTCAAATAAAAATTTAACAAACCTTAACAAGTACTTATAGGCAACTCTCAACGAAATCTTTATTT
* *
376075 TTTTCTTTAATGCATAACTAA-T-TAACATAAAAGTATAAATCTCCAATCCAAGTTATTTTTTCA
130 TTTTCTATAATGCATAACTAATTATAACATAAAAGTATAAATCTCCAATCCAAATTATTTTTTCA
* * * * * * *
376138 TGAAGTTTTTCGT-AATGGAGATCTAATAA-ATCCGGTGAATTTTAAACTAATTAAGAAAGTCAT
195 TGAAGTTTTTC-TAAATGGACAACTAACAAGA-CCAGCGAATTATAAACTAATTAAGAAAGTCAC
*
376201 GATTTCATGAGTTTTATCACCCAC
258 GATTTCATGAGTCTTATCACCCAC
376225 ATTTATATTA
Statistics
Matches: 244, Mismatches: 32, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
291 1 0.00
292 108 0.44
293 1 0.00
295 1 0.00
296 67 0.27
297 66 0.27
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (294 bp):
GTAATTAATATATTAACTTTTCTTGAATTTGGTAAGAATAGTATATTAATATATAAAAACATTTT
TCAAATAAAAATTTAACAAACCTTAACAAGTACTTATAGGCAACTCTCAACGAAATCTTTATTTT
TTTCTATAATGCATAACTAATTATAACATAAAAGTATAAATCTCCAATCCAAATTATTTTTTCAT
GAAGTTTTTCTAAATGGACAACTAACAAGACCAGCGAATTATAAACTAATTAAGAAAGTCACGAT
TTCATGAGTCTTATCACCCACGTTTTGAAATTTG
Found at i:378163 original size:14 final size:14
Alignment explanation
Indices: 378146--378175 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
378136 TAAATATCTT
378146 TTTTCAAATTAAAA
1 TTTTCAAATTAAAA
*
378160 TTTTCAAGTTAAAA
1 TTTTCAAATTAAAA
378174 TT
1 TT
378176 AAATGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTCAAATTAAAA
Found at i:380139 original size:31 final size:31
Alignment explanation
Indices: 380098--380163 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
380088 CAGTTCACAT
* * *
380098 TTGAATTTTCCTTTTTTCGTCCATGATACGG
1 TTGAACTTTCCTTTTGTCGTCCATGACACGG
380129 TTGAACTTTCCTTTTGTCGTCCATGACACGG
1 TTGAACTTTCCTTTTGTCGTCCATGACACGG
380160 TTGA
1 TTGA
380164 GCTATCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (31 bp):
TTGAACTTTCCTTTTGTCGTCCATGACACGG
Found at i:401108 original size:3 final size:3
Alignment explanation
Indices: 401100--401124 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
401090 AGAGAGCTGG
401100 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
401125 AGAGGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:403140 original size:170 final size:171
Alignment explanation
Indices: 402831--403171 Score: 535
Period size: 170 Copynumber: 2.0 Consensus size: 171
402821 AGATCAAAAC
* *
402831 CATGGTGCAGTTTCTTGCAGCAAATGAGATCAGAAAAAAGAGAAGTGGGGGAGGTGGTATATTCT
1 CATGGTGCACTTTCTTGCAGCAAATGAGAACAGAAAAAAGAGAAGTGGGGGAGGTGGTATATTCT
* * * ** **
402896 AAAAAGGGGGTGAATGGGATTTGCATACACATACTTAGGCTTCAGGGCATCAACTGGACATTCCA
66 AAAAAGAGAGTGAATGGAATTTGCATACACATACTTAGGCTGAAGCACATCAACTGGACATTCCA
402961 TAGATTAAATCATGAGGTTTCAAATAATTTCTTTACAAGTA
131 TAGATTAAATCATGAGGTTTCAAATAATTTCTTTACAAGTA
*
403002 CATGGTGCACTTTCTTGCAGCAAATGTGAACAGAAAAAAGAGAAG-GGGGGAGGTGGTATATTCT
1 CATGGTGCACTTTCTTGCAGCAAATGAGAACAGAAAAAAGAGAAGTGGGGGAGGTGGTATATTCT
*
403066 -AAAAGAGAGTGAATGGAATTTGCATACACATACTTCAGGCTGAAGCACCTCAACTAGG-CATTC
66 AAAAAGAGAGTGAATGGAATTTGCATACACATACTT-AGGCTGAAGCACATCAACT-GGACATTC
*
403129 CATAGATTAAATCATGAGGTTTCAAATGATTTCTTTACAAGTA
129 CATAGATTAAATCATGAGGTTTCAAATAATTTCTTTACAAGTA
403172 TATGTTTCTA
Statistics
Matches: 156, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
169 32 0.21
170 80 0.51
171 44 0.28
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (171 bp):
CATGGTGCACTTTCTTGCAGCAAATGAGAACAGAAAAAAGAGAAGTGGGGGAGGTGGTATATTCT
AAAAAGAGAGTGAATGGAATTTGCATACACATACTTAGGCTGAAGCACATCAACTGGACATTCCA
TAGATTAAATCATGAGGTTTCAAATAATTTCTTTACAAGTA
Found at i:414012 original size:2 final size:2
Alignment explanation
Indices: 414005--414036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
413995 TTGTTAACTA
414005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414037 GAACAAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:418751 original size:2 final size:2
Alignment explanation
Indices: 418744--418773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
418734 TCNCTTCCTC
418744 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
418774 GTTTCTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:429710 original size:18 final size:18
Alignment explanation
Indices: 429687--429724 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
429677 TAAGGGGATA
429687 AGGCATTATTCTTTGGAG
1 AGGCATTATTCTTTGGAG
429705 AGGCATTATTCTTTGGAG
1 AGGCATTATTCTTTGGAG
429723 AG
1 AG
429725 AGAACCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.37
Consensus pattern (18 bp):
AGGCATTATTCTTTGGAG
Found at i:432766 original size:21 final size:21
Alignment explanation
Indices: 432742--432786 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
432732 TTTCATCTTG
*
432742 TTTCTCATCTTTTTTCTCCTC
1 TTTCTCATCCTTTTTCTCCTC
** *
432763 TTTCTTTTCCTTTTTCTTCTC
1 TTTCTCATCCTTTTTCTCCTC
432784 TTT
1 TTT
432787 GACGCTCAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCTCATCCTTTTTCTCCTC
Found at i:442800 original size:26 final size:26
Alignment explanation
Indices: 442767--442927 Score: 159
Period size: 26 Copynumber: 6.3 Consensus size: 26
442757 ACGTGACCAA
*
442767 TTTTTGATAAGGCATTGCATCACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
* * *
442793 TTTCTGATAAGGTATTGCTTGACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
* *
442819 TTTTTTATATGGCATTGCATGACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
* * *
442845 TTTTTGATAAGACATTGCGTAACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
*
442871 ---TTGAT-AGGCATTGCGTGACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
* * * *
442893 TTTTTGATAAAGTATTACTTGACTAG
1 TTTTTGATAAGGCATTGCATGACTAG
*
442919 TTTCTGATA
1 TTTTTGATA
442928 TGACATTACG
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
22 15 0.14
23 5 0.05
25 5 0.05
26 85 0.77
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (26 bp):
TTTTTGATAAGGCATTGCATGACTAG
Found at i:442833 original size:52 final size:51
Alignment explanation
Indices: 442767--442927 Score: 184
Period size: 52 Copynumber: 3.2 Consensus size: 51
442757 ACGTGACCAA
* *
442767 TTTTTGATAAGGCATTGCATCACTAGTTTCTGATAAGGTATTGCTTGACTAG
1 TTTTTGAT-AGGCATTGCATGACTAGTTTTTGATAAGGTATTGCTTGACTAG
* ** * *
442819 TTTTTTATATGGCATTGCATGACTAGTTTTTGATAAGACATTGCGTAACTAG
1 TTTTTGATA-GGCATTGCATGACTAGTTTTTGATAAGGTATTGCTTGACTAG
* * *
442871 ---TTGATAGGCATTGCGTGACTAGTTTTTGATAAAGTATTACTTGACTAG
1 TTTTTGATAGGCATTGCATGACTAGTTTTTGATAAGGTATTGCTTGACTAG
*
442919 TTTCTGATA
1 TTTTTGATA
442928 TGACATTACG
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
48 35 0.39
49 5 0.06
51 6 0.07
52 43 0.48
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (51 bp):
TTTTTGATAGGCATTGCATGACTAGTTTTTGATAAGGTATTGCTTGACTAG
Found at i:442884 original size:22 final size:23
Alignment explanation
Indices: 442848--442894 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
442838 TGACTAGTTT
442848 TTGATAAGACATTGCGTAACTAG
1 TTGATAAGACATTGCGTAACTAG
* *
442871 TTGAT-AGGCATTGCGTGACTAG
1 TTGATAAGACATTGCGTAACTAG
442893 TT
1 TT
442895 TTTGATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (23 bp):
TTGATAAGACATTGCGTAACTAG
Found at i:442894 original size:74 final size:74
Alignment explanation
Indices: 442752--442982 Score: 237
Period size: 74 Copynumber: 3.1 Consensus size: 74
442742 TAGTTTTTAG
* * * * * * *
442752 GCATTACGTGACCAATTTTTGATAAGGCATTGCATCACTAGTTTCTGATAAGGTATTGCTTGACT
1 GCATTACATGACTAGTTTTTGATAAGACATTGCGTAACTAG--T-TGAT-AGGTATTGCGTGACT
* **
442817 AGTTTTTTATATG
62 AGTTTTTGATAAA
* *
442830 GCATTGCATGACTAGTTTTTGATAAGACATTGCGTAACTAGTTGATAGGCATTGCGTGACTAGTT
1 GCATTACATGACTAGTTTTTGATAAGACATTGCGTAACTAGTTGATAGGTATTGCGTGACTAGTT
442895 TTTGATAAA
66 TTTGATAAA
* * * * * * *
442904 GTATTACTTGACTAGTTTCTGATATGACATTACGTTATTAGTTGATAGGTATTGCGTGACTAGTT
1 GCATTACATGACTAGTTTTTGATAAGACATTGCGTAACTAGTTGATAGGTATTGCGTGACTAGTT
*
442969 TCTGATAAA
66 TTTGATAAA
*
442978 ACATT
1 GCATT
442983 GAGTAACTAG
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
74 90 0.70
75 4 0.03
76 1 0.01
78 34 0.26
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (74 bp):
GCATTACATGACTAGTTTTTGATAAGACATTGCGTAACTAGTTGATAGGTATTGCGTGACTAGTT
TTTGATAAA
Found at i:442935 original size:26 final size:25
Alignment explanation
Indices: 442737--442994 Score: 120
Period size: 26 Copynumber: 10.4 Consensus size: 25
442727 TGAGAATTAT
* *
442737 GTGACTAG-TTTT--TAGGCATTAC
1 GTGACTAGTTTTTGATAGACATTGC
* * *
442759 GTGACCAATTTTTGATAAGGCATTGC
1 GTGACTAGTTTTTGAT-AGACATTGC
* * * **
442785 ATCACTAGTTTCTGATAAGGTATTGC
1 GTGACTAGTTTTTGAT-AGACATTGC
* * *
442811 TTGACTAGTTTTTTATATGGCATTGC
1 GTGACTAGTTTTTGATA-GACATTGC
*
442837 ATGACTAGTTTTTGATAAGACATTGC
1 GTGACTAGTTTTTGAT-AGACATTGC
* *
442863 GTAACTAG---TTGATAGGCATTGC
1 GTGACTAGTTTTTGATAGACATTGC
* * *
442885 GTGACTAGTTTTTGATAAAGTATTAC
1 GTGACTAGTTTTTGATAGA-CATTGC
* * *
442911 TTGACTAGTTTCTGATATGACATTAC
1 GTGACTAGTTTTTGATA-GACATTGC
* * **
442937 GTTATTAG---TTGATAGGTATTGC
1 GTGACTAGTTTTTGATAGACATTGC
* * *
442959 GTGACTAGTTTCTGATAAAACATTGA
1 GTGACTAGTTTTTGAT-AGACATTGC
*
442985 GTAACTAGTT
1 GTGACTAGTT
442995 GATAGGCATT
Statistics
Matches: 177, Mismatches: 44, Indels: 26
0.72 0.18 0.11
Matches are distributed among these distances:
22 32 0.18
23 14 0.08
25 12 0.07
26 117 0.66
27 2 0.01
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (25 bp):
GTGACTAGTTTTTGATAGACATTGC
Found at i:442982 original size:48 final size:48
Alignment explanation
Indices: 442912--443012 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
442902 AAGTATTACT
** * * * *
442912 TGACTAGTTTCTGATATGACATT-ACGTTATTAGTTGATAGGTATTGCG
1 TGACTAGTTTCTGATAAAACATTGA-GTAACTAGTTGATAGGCATTGCA
442960 TGACTAGTTTCTGATAAAACATTGAGTAACTAGTTGATAGGCATTGCA
1 TGACTAGTTTCTGATAAAACATTGAGTAACTAGTTGATAGGCATTGCA
443008 TGACT
1 TGACT
443013 TGTAAGGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (48 bp):
TGACTAGTTTCTGATAAAACATTGAGTAACTAGTTGATAGGCATTGCA
Found at i:445571 original size:71 final size:71
Alignment explanation
Indices: 445441--445572 Score: 228
Period size: 71 Copynumber: 1.9 Consensus size: 71
445431 ATTCTAATGG
* **
445441 GGTTTGATTCCAAAGAAGGAGTCTGGGAAACGACTACTACATCTAAGGAGTCTGGGAAAAGACTG
1 GGTTTGATTCCAAAGAAGGAGTCTGGGAAACAACTACTACATCTAAGGAGTCTAAGAAAAGACTG
445506 TAACAA
66 TAACAA
*
445512 GGTTTGATTCCAGAGAAGGAGTCTGGGAAACAACTACTACATCTAAGGAGTCTAAGAAAAG
1 GGTTTGATTCCAAAGAAGGAGTCTGGGAAACAACTACTACATCTAAGGAGTCTAAGAAAAG
445573 GGAATTGAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (71 bp):
GGTTTGATTCCAAAGAAGGAGTCTGGGAAACAACTACTACATCTAAGGAGTCTAAGAAAAGACTG
TAACAA
Found at i:448027 original size:14 final size:16
Alignment explanation
Indices: 448008--448039 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
447998 AAGTGGACCT
448008 ATGTATT-TTTT-TAA
1 ATGTATTATTTTATAA
448022 ATGTATTATTTTATAA
1 ATGTATTATTTTATAA
448038 AT
1 AT
448040 TTAATGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATGTATTATTTTATAA
Found at i:456128 original size:15 final size:15
Alignment explanation
Indices: 456108--456138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
456098 AGGCGACGAA
*
456108 CTTGAACTTCGTCAT
1 CTTGAACTTCCTCAT
456123 CTTGAACTTCCTCAT
1 CTTGAACTTCCTCAT
456138 C
1 C
456139 ACTTGACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (15 bp):
CTTGAACTTCCTCAT
Found at i:458824 original size:24 final size:23
Alignment explanation
Indices: 458785--458852 Score: 93
Period size: 22 Copynumber: 2.9 Consensus size: 23
458775 AAATTTTAAT
* *
458785 TTTTTTATTTTATTTTTTAAAAC
1 TTTTATATTTTATTTTTTAAAAA
458808 TTTTAT-TTTTATTTTTTAAAAA
1 TTTTATATTTTATTTTTTAAAAA
458830 TTTTATAATTTTATTTTATTAAA
1 TTTTAT-ATTTTATTTT-TTAAA
458853 TATTAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 21 0.52
23 5 0.12
24 9 0.22
25 5 0.12
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTATATTTTATTTTTTAAAAA
Found at i:461125 original size:2 final size:2
Alignment explanation
Indices: 461118--461158 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
461108 TGATGCATAC
461118 TA 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 TA T
461159 CATCAGCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:463595 original size:6 final size:6
Alignment explanation
Indices: 463559--463593 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
463549 GCTTTCCCTC
*
463559 CCACCT CCACCT CCACCT CCACCT CCACCA CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
463594 ACTACCGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.20, C:0.69, G:0.00, T:0.11
Consensus pattern (6 bp):
CCACCT
Found at i:491420 original size:20 final size:20
Alignment explanation
Indices: 491361--491422 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
491351 ATTATTTTTA
*
491361 TAATTATAAAT-TTTAAATT
1 TAATTATAAATATTTATATT
*
491380 TAAATAATAAA-A-TTATATT
1 T-AATTATAAATATTTATATT
*
491399 TAATTATAAATATTTTTATT
1 TAATTATAAATATTTATATT
491419 TAAT
1 TAAT
491423 CATGTTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 8 0.23
19 9 0.26
20 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTATAAATATTTATATT
Found at i:511711 original size:147 final size:147
Alignment explanation
Indices: 511385--511756 Score: 471
Period size: 147 Copynumber: 2.5 Consensus size: 147
511375 ACCCGGATTA
* * * *
511385 CATGGGAGGACAATGGAAGTACCCTTTGATCAAATCCTTCCACCTGGATTCAAACTTGCATGGCA
1 CATGGGAGGACAATGGGAGTACCCTTTGATC-AATACTTTCACCCGGATTCAAACTTGCATGGCA
* * * *
511450 TGGATTCATTTCTTCTTCTGAAGACCAACAACCTGGTTTTGATATCTGCTACAGAGTTTCTCCCT
65 TGGATTCA--TCTTCTTCTAAAGACCAACAACCTGGTTTTGACATCTGCTACAGAGCTTCTCCAT
* * *
511515 GTTTAAAATGTTTCATTTTT
128 GTTTAAAATGTTTAAATTTG
* * * *
511535 CATGAGAGGGCAATGGGAGTACCCATTGATCGAATACTTTTACCCGGATTCAAACTTGCATGGCA
1 CATGGGAGGACAATGGGAGTACCCTTTGATC-AATACTTTCACCCGGATTCAAACTTGCATGGCA
* *
511600 TGGATTCA-CTTCTTCTAAAGAGCAACAA-CTGGTTTTGACATCTGCTAGACG-GCTTCTCCATG
65 TGGATTCATCTTCTTCTAAAGACCAACAACCTGGTTTTGACATCTGCTACA-GAGCTTCTCCATG
511662 TTTAAAAATGTTTAAATTTG
129 TTT-AAAATGTTTAAATTTG
* *
511682 CATGGGAGGACAATGGGAGTACCCTTTGATCAATTACATTCACCCGGATTCAAGCTTGCATGGCA
1 CATGGGAGGACAATGGGAGTACCCTTTGATCAA-TACTTTCACCCGGATTCAAACTTGCATGGC-
511747 TATGGATTCA
64 -ATGGATTCA
511757 AACTCTCACT
Statistics
Matches: 193, Mismatches: 24, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
146 33 0.17
147 87 0.45
149 9 0.05
150 64 0.33
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (147 bp):
CATGGGAGGACAATGGGAGTACCCTTTGATCAATACTTTCACCCGGATTCAAACTTGCATGGCAT
GGATTCATCTTCTTCTAAAGACCAACAACCTGGTTTTGACATCTGCTACAGAGCTTCTCCATGTT
TAAAATGTTTAAATTTG
Found at i:515186 original size:30 final size:27
Alignment explanation
Indices: 515145--515215 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
515135 GTCCTCCAAA
* * *
515145 ATTTCAAAATTTTATATATTGTTTTGTTTT
1 ATTTTAAAATTTTATAGA-T-TTTT-TTAT
515175 ATTTTAAAATTTTA-AGATTTTTTTAT
1 ATTTTAAAATTTTATAGATTTTTTTAT
515201 -TTTTAAAATTTTATA
1 ATTTTAAAATTTTATA
515216 AATTCATCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 13 0.35
26 4 0.11
27 4 0.11
28 1 0.03
29 2 0.05
30 13 0.35
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTTAAAATTTTATAGATTTTTTTAT
Found at i:522401 original size:15 final size:16
Alignment explanation
Indices: 522374--522403 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
522364 TGATCTCTTG
522374 TATCCTATCTTTCCTC
1 TATCCTATCTTTCCTC
522390 TATCCT-TCTTTCCT
1 TATCCTATCTTTCCT
522404 TTGTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (16 bp):
TATCCTATCTTTCCTC
Found at i:524071 original size:12 final size:12
Alignment explanation
Indices: 524054--524078 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
524044 TTTTATTATA
524054 AAAAAATAAAAT
1 AAAAAATAAAAT
524066 AAAAAATAAAAT
1 AAAAAATAAAAT
524078 A
1 A
524079 TGTAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:527430 original size:30 final size:30
Alignment explanation
Indices: 527391--527470 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
527381 GAGGAGTGGA
527391 TTCCTCCACCTCCTCCTGATAATGAACAAG
1 TTCCTCCACCTCCTCCTGATAATGAACAAG
* *
527421 TTCCACCACCTCCTCCTGATAATGAACAGG
1 TTCCTCCACCTCCTCCTGATAATGAACAAG
* *
527451 TTCCTCCACCACCACCTGAT
1 TTCCTCCACCTCCTCCTGAT
527471 GAGCCTCCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.25, C:0.40, G:0.10, T:0.25
Consensus pattern (30 bp):
TTCCTCCACCTCCTCCTGATAATGAACAAG
Found at i:534828 original size:57 final size:57
Alignment explanation
Indices: 534718--534900 Score: 221
Period size: 57 Copynumber: 3.2 Consensus size: 57
534708 TTTACATGGT
* * *
534718 AACGCGTATTTGACTCAATGATTAGTACAGGATTTATTTACTTAAAAAAGCAGATTCGG
1 AACGCG-ATTTGACTCAATAATTAGTACATGATTT-TTTACTTAAAAGAGCAGATTCGG
*
534777 ATACGC-ATTTGACTCAATAATTAATACATGATTTTTTACTTAAAAGAGCAGATTC-G
1 A-ACGCGATTTGACTCAATAATTAGTACATGATTTTTTACTTAAAAGAGCAGATTCGG
* * *
534833 AACGCGTATTTGA-TCCAATAATTAGTATATGATTTTTTACTTAATAGAGGAGATTCGG
1 AACGCG-ATTTGACT-CAATAATTAGTACATGATTTTTTACTTAAAAGAGCAGATTCGG
534891 -ACGCGTATTT
1 AACGCG-ATTT
534901 ATTAATATAT
Statistics
Matches: 111, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
55 4 0.04
56 3 0.03
57 73 0.66
58 26 0.23
59 1 0.01
60 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (57 bp):
AACGCGATTTGACTCAATAATTAGTACATGATTTTTTACTTAAAAGAGCAGATTCGG
Done.