Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold301
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: 1013018
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32220 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:874586 original size:5 final size:5
Alignment explanation
Indices: 874576--874676 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
874566 GAAAAAAATT
* *
874576 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
874628 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
874677 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:874594 original size:30 final size:30
Alignment explanation
Indices: 874552--874676 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
874542 TATTAGGAAA
874552 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
874580 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
874610 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
874643 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
874671 AAATGA
1 AAATGA
874677 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:874597 original size:12 final size:12
Alignment explanation
Indices: 874578--874647 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
874568 AAAAAATTAA
874578 TGAAATGAAATG
1 TGAAATGAAATG
* *
874590 TTAAATGAAATA
1 TGAAATGAAATG
874602 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
874613 TGAAATGTAATT
1 TGAAATGAAATG
* *
874625 TGTAATG-AATA
1 TGAAATGAAATG
874636 TGAAATGAAATG
1 TGAAATGAAATG
874648 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:874615 original size:35 final size:33
Alignment explanation
Indices: 874578--874648 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
874568 AAAAAATTAA
*
874578 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
874613 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
874646 TGA
1 TGA
874649 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:874659 original size:28 final size:27
Alignment explanation
Indices: 874601--874676 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
874591 TAAATGAAAT
*
874601 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
874629 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
874657 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
874677 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:874765 original size:20 final size:20
Alignment explanation
Indices: 874711--874810 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
874701 AAATGAAAAT
*
874711 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
874729 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
874748 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
874768 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
874790 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
874809 AA
1 AA
874811 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:874786 original size:21 final size:21
Alignment explanation
Indices: 874742--874808 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
874732 TCAAAAACTG
874742 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
874761 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
874783 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
874803 AAATGA
1 AAATGA
874809 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:874825 original size:19 final size:17
Alignment explanation
Indices: 874776--874838 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
874766 GAGAAATAAT
874776 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
874793 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
874806 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
874825 TTAATTTAAATGGA
1 TAAATTTAAATGGA
874839 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:874834 original size:29 final size:30
Alignment explanation
Indices: 874777--874836 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
874767 AGAAATAATT
874777 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
874808 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
874837 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:874874 original size:5 final size:5
Alignment explanation
Indices: 874864--874925 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
874854 ATGTAGATGT
* * *
874864 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
874913 AAATG AAATG AAA
1 AAATG AAATG AAA
874926 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:874877 original size:22 final size:22
Alignment explanation
Indices: 874863--874926 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
874853 AATGTAGATG
874863 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
874885 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
874906 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
874927 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:874894 original size:27 final size:27
Alignment explanation
Indices: 874864--874925 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
874854 ATGTAGATGT
*
874864 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
874891 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
874918 AAATGAAA
1 AAATGAAA
874926 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:874909 original size:11 final size:11
Alignment explanation
Indices: 874864--874922 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
874854 ATGTAGATGT
874864 AAATG-AAATG
1 AAATGCAAATG
* *
874874 AAATGAAAATAT
1 AAATGCAAAT-G
874886 AAATG-AAATG
1 AAATGCAAATG
*
874896 AAATGCAAAGG
1 AAATGCAAATG
*
874907 AAATACAAATG
1 AAATGCAAATG
874918 AAATG
1 AAATG
874923 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:875324 original size:19 final size:18
Alignment explanation
Indices: 875302--875340 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
875292 GTATATTAGG
*
875302 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
875321 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
875339 AA
1 AA
875341 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:875339 original size:5 final size:5
Alignment explanation
Indices: 875329--875429 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
875319 GAAAAAAATT
* *
875329 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
875381 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
875430 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:875347 original size:30 final size:30
Alignment explanation
Indices: 875305--875429 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
875295 TATTAGGAAA
875305 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
875333 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
875363 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
875396 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
875424 AAATGA
1 AAATGA
875430 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:875350 original size:12 final size:12
Alignment explanation
Indices: 875331--875400 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
875321 AAAAAATTAA
875331 TGAAATGAAATG
1 TGAAATGAAATG
* *
875343 TTAAATGAAATA
1 TGAAATGAAATG
875355 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
875366 TGAAATGTAATT
1 TGAAATGAAATG
* *
875378 TGTAATG-AATA
1 TGAAATGAAATG
875389 TGAAATGAAATG
1 TGAAATGAAATG
875401 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:875368 original size:35 final size:33
Alignment explanation
Indices: 875331--875401 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
875321 AAAAAATTAA
*
875331 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
875366 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
875399 TGA
1 TGA
875402 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:875412 original size:28 final size:27
Alignment explanation
Indices: 875354--875429 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
875344 TAAATGAAAT
*
875354 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
875382 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
875410 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
875430 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:875518 original size:20 final size:20
Alignment explanation
Indices: 875464--875563 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
875454 AAATGAAAAT
*
875464 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
875482 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
875501 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
875521 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
875543 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
875562 AA
1 AA
875564 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:875539 original size:21 final size:21
Alignment explanation
Indices: 875495--875561 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
875485 TCAAAAACTG
875495 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
875514 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
875536 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
875556 AAATGA
1 AAATGA
875562 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:875578 original size:19 final size:17
Alignment explanation
Indices: 875529--875591 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
875519 GAGAAATAAT
875529 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
875546 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
875559 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
875578 TTAATTTAAATGGA
1 TAAATTTAAATGGA
875592 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:875587 original size:29 final size:30
Alignment explanation
Indices: 875530--875589 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
875520 AGAAATAATT
875530 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
875561 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
875590 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:875627 original size:5 final size:5
Alignment explanation
Indices: 875617--875678 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
875607 ATGTAGATGT
* * *
875617 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
875666 AAATG AAATG AAA
1 AAATG AAATG AAA
875679 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:875630 original size:22 final size:22
Alignment explanation
Indices: 875616--875679 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
875606 AATGTAGATG
875616 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
875638 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
875659 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
875680 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:875647 original size:27 final size:27
Alignment explanation
Indices: 875617--875678 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
875607 ATGTAGATGT
*
875617 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
875644 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
875671 AAATGAAA
1 AAATGAAA
875679 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:875662 original size:11 final size:11
Alignment explanation
Indices: 875617--875675 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
875607 ATGTAGATGT
875617 AAATG-AAATG
1 AAATGCAAATG
* *
875627 AAATGAAAATAT
1 AAATGCAAAT-G
875639 AAATG-AAATG
1 AAATGCAAATG
*
875649 AAATGCAAAGG
1 AAATGCAAATG
*
875660 AAATACAAATG
1 AAATGCAAATG
875671 AAATG
1 AAATG
875676 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:876077 original size:19 final size:18
Alignment explanation
Indices: 876055--876093 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
876045 GTATATTAGG
*
876055 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
876074 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
876092 AA
1 AA
876094 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:876092 original size:5 final size:5
Alignment explanation
Indices: 876082--876182 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
876072 GAAAAAAATT
* *
876082 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
876134 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
876183 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:876100 original size:30 final size:30
Alignment explanation
Indices: 876058--876182 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
876048 TATTAGGAAA
876058 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
876086 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
876116 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
876149 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
876177 AAATGA
1 AAATGA
876183 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:876103 original size:12 final size:12
Alignment explanation
Indices: 876084--876153 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
876074 AAAAAATTAA
876084 TGAAATGAAATG
1 TGAAATGAAATG
* *
876096 TTAAATGAAATA
1 TGAAATGAAATG
876108 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
876119 TGAAATGTAATT
1 TGAAATGAAATG
* *
876131 TGTAATG-AATA
1 TGAAATGAAATG
876142 TGAAATGAAATG
1 TGAAATGAAATG
876154 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:876121 original size:35 final size:33
Alignment explanation
Indices: 876084--876154 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
876074 AAAAAATTAA
*
876084 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
876119 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
876152 TGA
1 TGA
876155 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:876165 original size:28 final size:27
Alignment explanation
Indices: 876107--876182 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
876097 TAAATGAAAT
*
876107 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
876135 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
876163 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
876183 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:876771 original size:29 final size:30
Alignment explanation
Indices: 876724--876781 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
876714 TTGGCTTTGA
876724 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
1 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
876754 CATT-TCCTTAGGCTTTGCCTTAGACTTA
1 CATTGTCCTTAGGCTTTGCCTTAGACTTA
876782 ACAATTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (30 bp):
CATTGTCCTTAGGCTTTGCCTTAGACTTAG
Found at i:878343 original size:16 final size:17
Alignment explanation
Indices: 878310--878343 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
878300 TCGGGCTATA
*
878310 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
878327 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
878343 A
1 A
878344 TAGTATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:879791 original size:11 final size:11
Alignment explanation
Indices: 879775--879799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
879765 TCCATTTGAG
879775 TTTTTCTTTGC
1 TTTTTCTTTGC
879786 TTTTTCTTTGC
1 TTTTTCTTTGC
879797 TTT
1 TTT
879800 ATTAGTTGAA
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:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTGC
Found at i:882685 original size:18 final size:17
Alignment explanation
Indices: 882663--882702 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
882653 AAAAATTAGA
*
882663 TAAATGATATACTTTAT
1 TAAATGATACACTTTAT
*
882680 TCAAATTATACACTTTAT
1 T-AAATGATACACTTTAT
882698 TAAAT
1 TAAAT
882703 ATAATACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATGATACACTTTAT
Found at i:882822 original size:22 final size:24
Alignment explanation
Indices: 882767--882822 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
882757 ACGATGAGAG
*
882767 AAATTTTAATATGAAAAAAAATGT
1 AAATTTAAATATGAAAAAAAATGT
*
882791 AAATTAAAATA-GAAAAAAAA-G-
1 AAATTTAAATATGAAAAAAAATGT
882812 ATAATTTAAAT
1 A-AATTTAAAT
882823 GACAAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
23 9 0.32
24 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATTTAAATATGAAAAAAAATGT
Found at i:882834 original size:26 final size:27
Alignment explanation
Indices: 882797--882869 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
882787 ATGTAAATTA
**
882797 AAAT-AGAAAAAAAAGATAATTTAAATG
1 AAATGAGAAAAAAATTA-AATTTAAATG
*
882824 ACAA-GAGAAAAAAATTAAATTTAAGTG
1 A-AATGAGAAAAAAATTAAATTTAAATG
882851 AAATGAGAAAAAAATTAAA
1 AAATGAGAAAAAAATTAAA
882870 ATGGAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 26 0.65
28 12 0.30
ACGTcount: A:0.66, C:0.01, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATGAGAAAAAAATTAAATTTAAATG
Found at i:882834 original size:27 final size:27
Alignment explanation
Indices: 882780--882869 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
882770 TTTTAATATG
* *
882780 AAAAA-AAATGTAAATTAAAAT-AGAAA
1 AAAAATAAATTTAAA-TGAAATGAGAAA
*
882806 AAAAAGATAATTTAAATGACAA-GAGAAA
1 AAAAATA-AATTTAAATGA-AATGAGAAA
* *
882834 AAAATTAAATTTAAGTGAAATGAGAAA
1 AAAAATAAATTTAAATGAAATGAGAAA
*
882861 AAAATTAAA
1 AAAAATAAA
882870 ATGGAAAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 7 0.13
27 28 0.52
28 19 0.35
ACGTcount: A:0.67, C:0.01, G:0.11, T:0.21
Consensus pattern (27 bp):
AAAAATAAATTTAAATGAAATGAGAAA
Found at i:882880 original size:27 final size:27
Alignment explanation
Indices: 882828--882881 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
882818 TAAATGACAA
** *
882828 GAGAAAAAAATTAAATTTAAGTGAAAT
1 GAGAAAAAAATTAAATGGAAGAGAAAT
882855 GAGAAAAAAATTAAAATGGAA-AGAAAT
1 GAGAAAAAAATT-AAATGGAAGAGAAAT
882882 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (27 bp):
GAGAAAAAAATTAAATGGAAGAGAAAT
Found at i:882896 original size:43 final size:45
Alignment explanation
Indices: 882832--882959 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 45
882822 TGACAAGAGA
*
882832 AAAAAATTAAATTTAAGTGAAATGAGAAAAAAATTAAAATGGAAA-G
1 AAAAAA-T-AATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
* * **
882878 -AAATATAATTTAAATGAAATGAGGAAGAAATTAAATTTAAATTTAAATG
1 AAAAAATAATTTAAATGAAATGA-G-A-AAA--AAATTAAAATGGAAATG
882927 AAAAAAATAATTTAAATGAAATGAGAAAAAAAT
1 -AAAAAATAATTTAAATGAAATGAGAAAAAAAT
882960 AAATTTAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
43 15 0.22
44 2 0.03
45 5 0.07
46 7 0.10
48 15 0.22
49 2 0.03
50 1 0.01
51 21 0.31
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (45 bp):
AAAAAATAATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
Found at i:882909 original size:70 final size:71
Alignment explanation
Indices: 882791--882947 Score: 192
Period size: 70 Copynumber: 2.2 Consensus size: 71
882781 AAAAAAATGT
882791 AAATTAAAATAGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTT-AAGTGAAAT
1 AAATTAAAAT-GAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAAT
*
882855 GAGAAAA
65 GAAAAAA
* * * * * * *
882862 AAATTAAAATGGAAAGAAATATAATTTAAATGA-AATGAGGAAGAAATTAAATTTAAATTTAAAT
1 AAATTAAAATGAAAAAAAAGATAATTTAAATGACAA-GAGAAAAAAATTAAATTTAAAGTGAAAT
882926 GAAAAAA
65 GAAAAAA
*
882933 ATAATTTAAATGAAA
1 A-AATTAAAATGAAA
882948 TGAGAAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
69 2 0.03
70 36 0.49
71 24 0.33
72 11 0.15
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (71 bp):
AAATTAAAATGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAATG
AAAAAA
Found at i:882947 original size:51 final size:53
Alignment explanation
Indices: 882862--882969 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 53
882852 AATGAGAAAA
* *
882862 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGGAAGAAATTAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGA-GAAAAAAATAAATTT
*
882916 AAATTTAAAT-GAAA-AAA-ATAATTTAAATGAAATGAGAAAAAAATAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
882966 AAAT
1 AAAT
882970 AGAAAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 17 0.33
51 18 0.35
52 3 0.06
53 4 0.08
54 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (53 bp):
AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
Found at i:883402 original size:19 final size:18
Alignment explanation
Indices: 883380--883418 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
883370 GTATATTAGG
*
883380 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
883399 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
883417 AA
1 AA
883419 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:883417 original size:5 final size:5
Alignment explanation
Indices: 883407--883507 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
883397 GAAAAAAATT
* *
883407 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
883459 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
883508 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:883425 original size:30 final size:30
Alignment explanation
Indices: 883383--883507 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
883373 TATTAGGAAA
883383 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
883411 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
883441 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
883474 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
883502 AAATGA
1 AAATGA
883508 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:883428 original size:12 final size:12
Alignment explanation
Indices: 883409--883478 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
883399 AAAAAATTAA
883409 TGAAATGAAATG
1 TGAAATGAAATG
* *
883421 TTAAATGAAATA
1 TGAAATGAAATG
883433 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
883444 TGAAATGTAATT
1 TGAAATGAAATG
* *
883456 TGTAATG-AATA
1 TGAAATGAAATG
883467 TGAAATGAAATG
1 TGAAATGAAATG
883479 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:883446 original size:35 final size:33
Alignment explanation
Indices: 883409--883479 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
883399 AAAAAATTAA
*
883409 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
883444 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
883477 TGA
1 TGA
883480 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:883490 original size:28 final size:27
Alignment explanation
Indices: 883432--883507 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
883422 TAAATGAAAT
*
883432 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
883460 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
883488 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
883508 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:883596 original size:20 final size:20
Alignment explanation
Indices: 883542--883641 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
883532 AAATGAAAAT
*
883542 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
883560 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
883579 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
883599 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
883621 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
883640 AA
1 AA
883642 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:883617 original size:21 final size:21
Alignment explanation
Indices: 883573--883639 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
883563 TCAAAAACTG
883573 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
883592 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
883614 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
883634 AAATGA
1 AAATGA
883640 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:883656 original size:19 final size:17
Alignment explanation
Indices: 883607--883669 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
883597 GAGAAATAAT
883607 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
883624 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
883637 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
883656 TTAATTTAAATGGA
1 TAAATTTAAATGGA
883670 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:883665 original size:29 final size:30
Alignment explanation
Indices: 883608--883667 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
883598 AGAAATAATT
883608 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
883639 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
883668 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:883705 original size:5 final size:5
Alignment explanation
Indices: 883695--883756 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
883685 ATGTAGATGT
* * *
883695 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
883744 AAATG AAATG AAA
1 AAATG AAATG AAA
883757 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:883708 original size:22 final size:22
Alignment explanation
Indices: 883694--883757 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
883684 AATGTAGATG
883694 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
883716 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
883737 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
883758 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:883725 original size:27 final size:27
Alignment explanation
Indices: 883695--883756 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
883685 ATGTAGATGT
*
883695 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
883722 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
883749 AAATGAAA
1 AAATGAAA
883757 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:883740 original size:11 final size:11
Alignment explanation
Indices: 883695--883753 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
883685 ATGTAGATGT
883695 AAATG-AAATG
1 AAATGCAAATG
* *
883705 AAATGAAAATAT
1 AAATGCAAAT-G
883717 AAATG-AAATG
1 AAATGCAAATG
*
883727 AAATGCAAAGG
1 AAATGCAAATG
*
883738 AAATACAAATG
1 AAATGCAAATG
883749 AAATG
1 AAATG
883754 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:884174 original size:23 final size:23
Alignment explanation
Indices: 884131--884174 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
884121 GTATATTAGG
*
884131 AAAAAAGTAATAAATTTAAATGA
1 AAAAAAGTAATAAATTCAAATGA
*
884154 AAAAAATTAATGAAA-TCAAAT
1 AAAAAAGTAAT-AAATTCAAAT
884175 ATTAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAAAAGTAATAAATTCAAATGA
Found at i:884205 original size:23 final size:23
Alignment explanation
Indices: 884172--884232 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
884162 AATGAAATCA
*
884172 AATATTAAATGAAATATG-AATAAG
1 AATATGAAATGAAATATGTAAT--G
* *
884196 AA-ATGAAATGTAATTTGTAATG
1 AATATGAAATGAAATATGTAATG
884218 AATATGAAATGAAAT
1 AATATGAAATGAAAT
884233 GAAATAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 3 0.10
23 23 0.74
24 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (23 bp):
AATATGAAATGAAATATGTAATG
Found at i:884292 original size:18 final size:18
Alignment explanation
Indices: 884269--884309 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
884259 TTATAAATGA
* *
884269 AAATGAAAAGAAGAACTG
1 AAATGAAAAAAAAAACTG
*
884287 AAATGAAAAAAAAAATTG
1 AAATGAAAAAAAAAACTG
884305 AAATG
1 AAATG
884310 GTAAATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (18 bp):
AAATGAAAAAAAAAACTG
Found at i:889833 original size:12 final size:11
Alignment explanation
Indices: 889802--889840 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
889792 TTGTTTTAAG
889802 TTTTATTATTA
1 TTTTATTATTA
889813 TTATTATTATTA
1 TT-TTATTATTA
*
889825 TTTTAATTAATA
1 TTTT-ATTATTA
889837 TTTT
1 TTTT
889841 TAGAAGGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:894527 original size:8 final size:8
Alignment explanation
Indices: 894516--894559 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
894506 TTTATTCAAT
894516 TATTTTAC
1 TATTTTAC
*
894524 TATTTTAT
1 TATTTTAC
894532 TATTTTAC
1 TATTTTAC
894540 TATTTT-C
1 TATTTTAC
*
894547 -ATTTTAT
1 TATTTTAC
894554 TATTTT
1 TATTTT
894560 CATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
6 5 0.16
7 1 0.03
8 25 0.81
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAC
Found at i:894533 original size:16 final size:16
Alignment explanation
Indices: 894514--894545 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
894504 AATTTATTCA
894514 ATTATTTTACTATTTT
1 ATTATTTTACTATTTT
894530 ATTATTTTACTATTTT
1 ATTATTTTACTATTTT
894546 CATTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTATTTTACTATTTT
Found at i:898140 original size:28 final size:28
Alignment explanation
Indices: 898104--898158 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
898094 CCACATGCTA
* *
898104 GTGTAGCCCTATGGCCTAACACACGCCC
1 GTGTAGCCCCACGGCCTAACACACGCCC
*
898132 GTGTGGCCCCACGGCCTAACACACGCC
1 GTGTAGCCCCACGGCCTAACACACGCC
898159 AACCCGTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.15
Consensus pattern (28 bp):
GTGTAGCCCCACGGCCTAACACACGCCC
Found at i:904686 original size:21 final size:21
Alignment explanation
Indices: 904661--904701 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
904651 ATATGACCAC
904661 AAAAATCACTTTTTCACTTTA
1 AAAAATCACTTTTTCACTTTA
*
904682 AAAAATCAGTTTTTCACTTT
1 AAAAATCACTTTTTCACTTT
904702 GGCATGCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAATCACTTTTTCACTTTA
Found at i:904790 original size:2 final size:2
Alignment explanation
Indices: 904783--904821 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
904773 ATATTTACAC
904783 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
904822 CAATATTTCA
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:905923 original size:21 final size:21
Alignment explanation
Indices: 905898--905938 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
905888 ATATGACCAC
905898 AAAAATCACTTTTTCACTTTA
1 AAAAATCACTTTTTCACTTTA
*
905919 AAAAATCAGTTTTTCACTTT
1 AAAAATCACTTTTTCACTTT
905939 GGCATGCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAATCACTTTTTCACTTTA
Found at i:911057 original size:38 final size:38
Alignment explanation
Indices: 911015--911096 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
911005 TCTTTTAATA
* * *
911015 TTTTTGTTTCAAC-CAATTGTCATTGGGGTTAATTGTGG
1 TTTTTGTTTCAACTC-ATTGCCACTGGGGTTAATTATGG
*
911053 TTTTTGTTTCGACTCATTGCCACTGGGGTTAATTATGG
1 TTTTTGTTTCAACTCATTGCCACTGGGGTTAATTATGG
911091 TTTTTG
1 TTTTTG
911097 ATATTTATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (38 bp):
TTTTTGTTTCAACTCATTGCCACTGGGGTTAATTATGG
Found at i:911215 original size:341 final size:342
Alignment explanation
Indices: 910674--911704 Score: 1638
Period size: 342 Copynumber: 3.0 Consensus size: 342
910664 TGAATTGTGG
* * * * *
910674 TTTTTATTCCAACCAATTATCATTGGGGTTAATTGCGGTTTATGTTTCGACCCATTGTCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* * *
910739 GTTAATTGTGG-TTTTGACATTTGTCATCGGGGTTAAGGGATAAAAAAAAGGAGTTGTTATTTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGA-GAGTTGTTATTTTT
* * * * *
910803 TTTATCTATCAATATTTTAGAAATTATTGATTTGTCTTTATCATAGTTTTGACACAGAATATGAT
130 TTTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCT
910868 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
195 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
* * *
910933 CT-ATGCTTTTGTGCTTGCTTAACTAAACCAAGGGAAATTCTAGTTACTTACTGTGTAGTAAAAC
260 CTAATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAAC
*
910997 TAACTCCATCTTTTAATA
325 TCACTCCATCTTTTAATA
* *
911015 TTTTTGTTTCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACTCATTGCCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* *
911080 GTTAATTATGGTTTTTGATATTTATCATCGGGGTTAAAGGATAAAAAAGAGAGTTGTTATTTTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGAGAGTTGTTATTTTTT
* *
911145 TTATCTATCAGTATTTAAGAAATTATTGAATTATCTTTATCACAGTTTTGACACGGAATATGCTT
131 TTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCTT
*
911210 TGAATTATTTATTGTGGTATAATCATAAATTTTACAACTATGGATTTTTTACTAAATATTTAGCC
196 TGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGCC
* *
911275 TAAATGCTTTTGTGCTTGCTTAACTCAACTAAGGGAAATGCTAGTTACTTACTTTGTAGTTAAAC
261 T-AATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAAC
*
911340 TCACTCTATCTTTTAATA
325 TCACTCCATCTTTTAATA
* * *
911358 ATTTTGTTCCAACCAATTGCCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGGCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* * * *
911423 GTTAATTATGATTTTTGACATTTTTCATCGAGGTTAAGGGAGAAAAAATG-GAGTTGTTA-TTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAA-GAGAGTTGTTATTTTT
* *
911486 TTTATCTATCAGTATTTCAGAAATTATTGATTTGTCTTTACCACAGTTTTGACACGGAATATGCT
130 TTTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCT
* * *
911551 TTGAATTATTTATTGTGGTATAATCATAAATTTTAAAATTATGGGTTTTTTACTAGATATTTAGC
195 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
*
911616 CTAAATGCTTTTGTGCTTGCTTAACCCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAA
260 CT-AATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAA
911681 CTCACTCCATCTTTTAATA
324 CTCACTCCATCTTTTAATA
911700 TTTTT
1 TTTTT
911705 ACAGGTTTTG
Statistics
Matches: 635, Mismatches: 51, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
341 206 0.32
342 244 0.38
343 184 0.29
344 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (342 bp):
TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGAGAGTTGTTATTTTTT
TTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCTT
TGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGCC
TAATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAACT
CACTCCATCTTTTAATA
Found at i:911401 original size:38 final size:38
Alignment explanation
Indices: 911359--911439 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
911349 CTTTTAATAA
* * *
911359 TTTTGTTCCAACCAATTGCCATTGGGGTTAATTGTGGT
1 TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
* * * *
911397 TTTTGTTTCGACCCATTGGCACTGGGGTTAATTATGAT
1 TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
911435 TTTTG
1 TTTTG
911440 ACATTTTTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (38 bp):
TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
Found at i:918056 original size:20 final size:21
Alignment explanation
Indices: 918023--918061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
918013 TTAATTTCAA
*
918023 TTTTTTAATATTATTTAATAT
1 TTTTTTAATATTATGTAATAT
*
918044 TTTTTTCAT-TTATGTAAT
1 TTTTTTAATATTATGTAAT
918062 TTTAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTTAATATTATGTAATAT
Found at i:918081 original size:26 final size:23
Alignment explanation
Indices: 918036--918088 Score: 54
Period size: 26 Copynumber: 2.1 Consensus size: 23
918026 TTTAATATTA
918036 TTTAATATTTTTTTCATTTATGTAAT
1 TTTAATATTTTTTT-ATTTA-G-AAT
918062 TTTAAT-TATTTTTTATTTTAGAAT
1 TTTAATAT-TTTTTTA-TTTAGAAT
918086 TTT
1 TTT
918089 TTATAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 16 0.64
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTAATATTTTTTTATTTAGAAT
Found at i:925860 original size:34 final size:34
Alignment explanation
Indices: 925812--925912 Score: 154
Period size: 34 Copynumber: 3.1 Consensus size: 34
925802 TATTATTTTT
925812 AAAAC-CTAAACCCTAATTTAATTAATTTTCTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
*
925845 AAAACTCTAAACCCTAATTTAATTAATTTACTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
* *
925879 AAACCTCTAAAACCTAATTTAATT-ATTTT-TTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
925911 AA
1 AA
925913 TTCTAAACCT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 5 0.08
33 9 0.14
34 49 0.78
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
Found at i:926394 original size:34 final size:34
Alignment explanation
Indices: 926346--926442 Score: 151
Period size: 34 Copynumber: 2.9 Consensus size: 34
926336 TATTATTTTT
*
926346 AAAAC-CTAAACCCTAATATAATTAATTTTCTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
*
926379 AAAACTCTAAACCCTAATTTAATTAATTTACTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
* *
926413 AAACCTCTAAAACCTAATTTAATTAATTTT
1 AAAACTCTAAACCCTAATTTAATTAATTTT
926443 AAAAAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 5 0.09
34 53 0.91
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (34 bp):
AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
Found at i:926456 original size:34 final size:34
Alignment explanation
Indices: 926346--926459 Score: 142
Period size: 34 Copynumber: 3.4 Consensus size: 34
926336 TATTATTTTT
* *
926346 AAAAC-CTAAACCCTAATATAATTAATTTTCTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTATTA
926379 AAAACTCTAAACCCTAATTTAATTAA-TTTACTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTA-TTA
* * **
926413 AAACCTCTAAAACCTAATTTAATTAATTTTAAAA
1 AAAACTCTAAACCCTAATTTAATTAATTTTATTA
*
926447 AAAATTCTAAACC
1 AAAACTCTAAACC
926460 TTGATTTATT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 8 0.12
34 57 0.83
35 4 0.06
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (34 bp):
AAAACTCTAAACCCTAATTTAATTAATTTTATTA
Found at i:929301 original size:20 final size:20
Alignment explanation
Indices: 929276--929316 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
929266 CACATGGTAG
*
929276 TGTGTTTGAAAACCATAACT
1 TGTGTTGGAAAACCATAACT
*
929296 TGTGTTGGAAAACCGTAACT
1 TGTGTTGGAAAACCATAACT
929316 T
1 T
929317 TGCTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTGTTGGAAAACCATAACT
Found at i:931962 original size:24 final size:23
Alignment explanation
Indices: 931913--931970 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
931903 CAATAATAGA
* *
931913 AATATTAAAATATATTCAAAATT
1 AATATTAAAATATATTAAAAAAT
931936 AATATTGAAAATAT-TTAATAAAAT
1 AATATT-AAAATATATTAA-AAAAT
931960 AAT-TTATAAAT
1 AATATTA-AAAT
931971 TTTTGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 14 0.47
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATTAAAATATATTAAAAAAT
Found at i:933359 original size:32 final size:32
Alignment explanation
Indices: 933264--933362 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
933254 AGCCTTTAAT
*
933264 AATTTTTAAAAT--TTTTAATTAGAC-CCCCA
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
* * * * * * *
933293 ATTTTTTTAGA-AATTCTCATTAGGCT-TCTAA
1 AATTTTTAAAATAATTTTAATTAGACTCTC-CA
933324 AATTTTTAAAATAATTTTAATTAGACTCTCCA
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
933356 AATTTTT
1 AATTTTT
933363 TGGAGATCCT
Statistics
Matches: 49, Mismatches: 15, Indels: 9
0.67 0.21 0.12
Matches are distributed among these distances:
29 8 0.16
30 10 0.20
31 9 0.18
32 20 0.41
33 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (32 bp):
AATTTTTAAAATAATTTTAATTAGACTCTCCA
Found at i:933387 original size:63 final size:60
Alignment explanation
Indices: 933248--933388 Score: 147
Period size: 63 Copynumber: 2.3 Consensus size: 60
933238 TGAAAAGTTA
** * *
933248 TCATTAAGCCTTTAATAATTTTTAAAATTTTTAATTAGACCCCCAATTTTTTTAGAAATTC
1 TCATTAAGCCCCTAA-AATTTTTAAAATTTTTAATTAGACCCCCAAATTTTTTAGAAATCC
* ** * * *
933309 TCATTAGGCTTCTAAAATTTTTAAAATAATTTTAATTAGACTCTCCAAATTTTTTGGAGATCC
1 TCATTAAGCCCCTAAAATTTTTAAAAT--TTTTAATTAGAC-CCCCAAATTTTTTAGAAATCC
*
933372 TCATTAATCCCCTAAAA
1 TCATTAAGCCCCTAAAA
933389 GTTCTAAGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 12 0.18
61 12 0.18
62 12 0.18
63 29 0.45
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (60 bp):
TCATTAAGCCCCTAAAATTTTTAAAATTTTTAATTAGACCCCCAAATTTTTTAGAAATCC
Found at i:934761 original size:27 final size:27
Alignment explanation
Indices: 934719--934856 Score: 109
Period size: 27 Copynumber: 5.1 Consensus size: 27
934709 AACACGTCAA
**
934719 GAAAGGAAAGTTTTTGTGGTGAAATAT
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
***
934746 GAAAGGAAAGCCTTTGTGACAAAATA-
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
* * * *
934772 CAAGAGAAAAGCCTTTGTAGCGAAATAT
1 GAA-AGGAAAGCCTTTGTGGTGAAATAT
* *
934800 GAAAAGAAAGTCTTTGTGGTG-AATCAT
1 GAAAGGAAAGCCTTTGTGGTGAAAT-AT
* * * *
934827 GAAAGAAAAGCTTTTATGGTGAATTAT
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
934854 GAA
1 GAA
934857 TGGATAGTCT
Statistics
Matches: 85, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
26 5 0.06
27 76 0.89
28 4 0.05
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (27 bp):
GAAAGGAAAGCCTTTGTGGTGAAATAT
Found at i:942333 original size:24 final size:24
Alignment explanation
Indices: 942297--942352 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
942287 AAGGAAAAAA
* *
942297 ATAT-AATATTATTTTATATGTTT
1 ATATAAATAATATTATATATGTTT
*
942320 ATATAAATAATATTATATGTGTTT
1 ATATAAATAATATTATATATGTTT
942344 ATATTAAAT
1 ATA-TAAAT
942353 TATAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (24 bp):
ATATAAATAATATTATATATGTTT
Found at i:944674 original size:27 final size:27
Alignment explanation
Indices: 944635--944784 Score: 205
Period size: 27 Copynumber: 5.6 Consensus size: 27
944625 ACATAATCAT
*
944635 ACAGCCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* *
944662 ACTGTCATTTTATAACATAGGGGTATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
944689 ACAGTCATTTTATAACATAGGGGCTTA
1 ACAGTCATTTTATAACATAGGGGCATA
*
944716 ACAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* *
944743 ATAGTCATTTTACT-ACGT-GAGGGCATA
1 ACAGTCATTTTA-TAACATAG-GGGCATA
944770 ACAGTCATTTTATAA
1 ACAGTCATTTTATAA
944785 TAGTTTAGGG
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 105 0.97
28 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGCATA
Found at i:952278 original size:27 final size:27
Alignment explanation
Indices: 952242--952307 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
952232 CATAAATCAT
952242 ACAGTCATTTTATAACATAGGGGAATA
1 ACAGTCATTTTATAACATAGGGGAATA
* * *
952269 ATAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGAATA
952296 ACAGTCATTTTA
1 ACAGTCATTTTA
952308 CCACGTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGAATA
Found at i:960512 original size:19 final size:19
Alignment explanation
Indices: 960488--960528 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
960478 AACTAACTAA
960488 AAAAAGAAAAATTAAAAA-G
1 AAAAAG-AAAATTAAAAATG
960507 AAAAAGAAAATTAAAAATG
1 AAAAAGAAAATTAAAAATG
960526 AAA
1 AAA
960529 CTGAAACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAGAAAATTAAAAATG
Found at i:963963 original size:20 final size:20
Alignment explanation
Indices: 963930--963968 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
963920 CGGCACCGAT
963930 TCTGTAAGTGTTTTAAAAAC
1 TCTGTAAGTGTTTTAAAAAC
963950 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTTTAAAAA
963969 TATGAGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TCTGTAAGTGTTTTAAAAAC
Found at i:972681 original size:21 final size:21
Alignment explanation
Indices: 972635--972674 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
972625 TTCGTTTGAT
972635 AAGGGAAGAAGAAGGAAAGGA
1 AAGGGAAGAAGAAGGAAAGGA
972656 AAGGGAAGAAG-A-GAAAGGA
1 AAGGGAAGAAGAAGGAAAGGA
972675 GGAAGGGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (21 bp):
AAGGGAAGAAGAAGGAAAGGA
Found at i:979180 original size:24 final size:24
Alignment explanation
Indices: 979135--979180 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
979125 TTCACTTTGC
** * *
979135 GCCACCCCTGCGCCGTTGTCGAAT
1 GCCACCCCCACGCCGCTATCGAAT
979159 GCCACCCCCACGCCGCTATCGA
1 GCCACCCCCACGCCGCTATCGA
979181 CACCAATACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.48, G:0.22, T:0.15
Consensus pattern (24 bp):
GCCACCCCCACGCCGCTATCGAAT
Found at i:982184 original size:14 final size:14
Alignment explanation
Indices: 982165--982195 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
982155 TTGAATGCTT
982165 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
982179 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
982193 TGA
1 TGA
982196 CTGCTTATGT
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:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (14 bp):
TGAGTGAACCTTAG
Found at i:992465 original size:43 final size:43
Alignment explanation
Indices: 992390--992533 Score: 211
Period size: 43 Copynumber: 3.3 Consensus size: 43
992380 GCGTCGCAAA
* *
992390 CTTTAGCGGCG-TTTCCACAAAAAAACGCCGCTAAAGATCAAGAC
1 CTTTAGCGGCGCTTTCCAC--ACAAACGCCGCTAAAGACCAAGAC
992434 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
* *
992477 CTTTAGCTGCGCTTCTCC-CACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTT-TCCACACAAACGCCGCTAAAGACCAAGAC
992520 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
992534 CTTTTACAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
43 72 0.77
44 14 0.15
45 7 0.08
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
Found at i:992534 original size:43 final size:43
Alignment explanation
Indices: 992412--992554 Score: 216
Period size: 43 Copynumber: 3.3 Consensus size: 43
992402 TTCCACAAAA
*
992412 AAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTT-TCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCC-CAC
*
992455 AAACGCCGCTAAAGACCAAGACCTTTAGCTGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* ***
992498 AAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTTTTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
992541 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
992555 GTTCTTCTCC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 88 0.97
44 3 0.03
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
Found at i:995447 original size:25 final size:25
Alignment explanation
Indices: 995419--995828 Score: 220
Period size: 25 Copynumber: 16.3 Consensus size: 25
995409 TATATATTTC
* **
995419 TGTATTAAGTAAATTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
995444 TGTATTATATAAGTTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
995469 CGTATTATGTGAGCTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
995494 CGTATTATGTGAGCTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* * *
995519 TTTAGTATGTAAGCTATGTAAGTTG
1 TGTATTATGTAAGCTATGTAAGTTA
995544 TGTATTATGTAAGCTATGT-A-TTA
1 TGTATTATGTAAGCTATGTAAGTTA
** * *
995567 TGTTAGTTATGTCGGTTATAT-A-TTA
1 TG-TA-TTATGTAAGCTATGTAAGTTA
*
995592 TGTATGTTATGTAAG-T-TGTTCAGTTA
1 TGTA--TTATGTAAGCTATG-TAAGTTA
* * * *
995618 T-AAGCTATGTAAGTTATGTGAGTTA
1 TGTA-TTATGTAAGCTATGTAAGTTA
*
995643 --TA-TATGTAAGTTATGTATAAGTTTAA
1 TGTATTATGTAAGCTATG--TAAG-TT-A
*
995669 T-T-TGTAT-TAAGCTATGTAAGTTG
1 TGTAT-TATGTAAGCTATGTAAGTTA
* * * *
995692 TGAATAATGTAAGTTATGAAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
995717 TGTATTATGTTAAGTTATGAAAGTTA
1 TGTATTATG-TAAGCTATGTAAGTTA
* * *
995743 TGTATTAAGTTGTGTA-TTATGTAAGTTG
1 TGTATT-A--TGT-AAGCTATGTAAGTTA
* * *
995771 TGAATAATGTAAGTTATG-AACGTTA
1 TGTATTATGTAAGCTATGTAA-GTTA
* *
995796 TGTATTATGTTAAGTTATGAAAGTTA
1 TGTATTATG-TAAGCTATGTAAGTTA
995822 TGTATTA
1 TGTATTA
995829 AGTTGTGTAT
Statistics
Matches: 313, Mismatches: 45, Indels: 53
0.76 0.11 0.13
Matches are distributed among these distances:
22 13 0.04
23 6 0.02
24 27 0.09
25 184 0.59
26 49 0.16
27 13 0.04
28 18 0.06
29 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (25 bp):
TGTATTATGTAAGCTATGTAAGTTA
Found at i:995450 original size:16 final size:17
Alignment explanation
Indices: 995430--995825 Score: 109
Period size: 16 Copynumber: 24.1 Consensus size: 17
995420 GTATTAAGTA
995430 AATTATGTAAGTTATGT
1 AATTATGTAAGTTATGT
*
995447 -ATTATATAAGTTATGT
1 AATTATGTAAGTTATGT
*
995463 AAGTTACGT-A-TTATGT
1 AA-TTATGTAAGTTATGT
** *
995479 GAGCTATGTAAGTTACGT
1 -AATTATGTAAGTTATGT
* *
995497 -ATTATGTGAGCTATGT
1 AATTATGTAAGTTATGT
*
995513 AAGTTAT-TTAG-TATGT
1 AA-TTATGTAAGTTATGT
* *
995529 AAGCTATGTAAGTTGTGT
1 AA-TTATGTAAGTTATGT
*
995547 -ATTATGTAAGCTATGT
1 AATTATGTAAGTTATGT
*
995563 -ATTATGTTAGTTATGT
1 AATTATGTAAGTTATGT
** *
995579 CGGTTATAT-A-TTATGT
1 -AATTATGTAAGTTATGT
* *
995595 ATGTTATGTAAGTTGT-T
1 A-ATTATGTAAGTTATGT
* *
995612 CAGTTA--TAAGCTATGT
1 -AATTATGTAAGTTATGT
*
995628 AAGTTATGTGAGTTA--T
1 AA-TTATGTAAGTTATGT
995644 -A-TATGTAAGTTATGT
1 AATTATGTAAGTTATGT
* * *
995659 -ATAAGTTTAATTTGTAT-T
1 AATTA-TGTAA-GT-TATGT
* *
995677 AAGCTATGTAAGTTGTG-
1 AA-TTATGTAAGTTATGT
* *
995694 AATAATGTAAGTTATGA
1 AATTATGTAAGTTATGT
995711 AAGTTATGT-A-TTATGTT
1 AA-TTATGTAAGTTATG-T
*
995728 AAGTTATGAAAGTTATG-
1 AA-TTATGTAAGTTATGT
*
995745 ---TAT-TAAGTTGTGT
1 AATTATGTAAGTTATGT
*
995758 -ATTATGTAAGTTGTG-
1 AATTATGTAAGTTATGT
*
995773 AATAATGTAAGTTATG-
1 AATTATGTAAGTTATGT
995789 AACGTTATGT-A-TTATGTT
1 AA--TTATGTAAGTTATG-T
*
995807 AAGTTATGAAAGTTATGT
1 AA-TTATGTAAGTTATGT
995825 A
1 A
995826 TTAAGTTGTG
Statistics
Matches: 283, Mismatches: 52, Indels: 87
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.02
13 13 0.05
15 13 0.05
16 136 0.48
17 45 0.16
18 50 0.18
19 18 0.06
20 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (17 bp):
AATTATGTAAGTTATGT
Found at i:995465 original size:9 final size:9
Alignment explanation
Indices: 995427--995825 Score: 170
Period size: 9 Copynumber: 47.3 Consensus size: 9
995417 TCTGTATTAA
*
995427 GTAAATTAT
1 GTAAGTTAT
995436 GTAAGTTAT
1 GTAAGTTAT
995445 GT-A-TTAT
1 GTAAGTTAT
*
995452 ATAAGTTAT
1 GTAAGTTAT
*
995461 GTAAGTTAC
1 GTAAGTTAT
995470 GT-A-TTAT
1 GTAAGTTAT
* *
995477 GTGAGCTAT
1 GTAAGTTAT
*
995486 GTAAGTTAC
1 GTAAGTTAT
995495 GT-A-TTAT
1 GTAAGTTAT
* *
995502 GTGAGCTAT
1 GTAAGTTAT
995511 GTAAGTTAT
1 GTAAGTTAT
*
995520 -TTAG-TAT
1 GTAAGTTAT
*
995527 GTAAGCTAT
1 GTAAGTTAT
*
995536 GTAAGTTGT
1 GTAAGTTAT
995545 GT-A-TTAT
1 GTAAGTTAT
*
995552 GTAAGCTAT
1 GTAAGTTAT
995561 GT-A-TTAT
1 GTAAGTTAT
*
995568 GTTAGTTAT
1 GTAAGTTAT
**
995577 GTCGGTTAT
1 GTAAGTTAT
*
995586 AT-A-TTAT
1 GTAAGTTAT
*
995593 GTATGTTAT
1 GTAAGTTAT
*
995602 GTAAGTTGT
1 GTAAGTTAT
*
995611 -TCAGTTA-
1 GTAAGTTAT
*
995618 -TAAGCTAT
1 GTAAGTTAT
995626 GTAAGTTAT
1 GTAAGTTAT
*
995635 GTGAGTTA-
1 GTAAGTTAT
995643 -T-A--TAT
1 GTAAGTTAT
995648 GTAAGTTAT
1 GTAAGTTAT
995657 GTATAAG-T-T
1 G--TAAGTTAT
*
995666 -TAATTTGTAT
1 GTAA-GT-TAT
*
995676 -TAAGCTAT
1 GTAAGTTAT
*
995684 GTAAGTTGT
1 GTAAGTTAT
*
995693 G-AA-TAAT
1 GTAAGTTAT
995700 GTAAGTTAT
1 GTAAGTTAT
*
995709 GAAAGTTAT
1 GTAAGTTAT
995718 GT-A-TTAT
1 GTAAGTTAT
995725 GTTAAGTTAT
1 G-TAAGTTAT
*
995735 GAAAGTTAT
1 GTAAGTTAT
*
995744 GTATTAAGTTGT
1 G---TAAGTTAT
995756 GT-A-TTAT
1 GTAAGTTAT
*
995763 GTAAGTTGT
1 GTAAGTTAT
*
995772 G-AA-TAAT
1 GTAAGTTAT
995779 GTAAGTTAT
1 GTAAGTTAT
995788 G-AACGTTAT
1 GTAA-GTTAT
995797 GT-A-TTAT
1 GTAAGTTAT
995804 GTTAAGTTAT
1 G-TAAGTTAT
*
995814 GAAAGTTAT
1 GTAAGTTAT
995823 GTA
1 GTA
995826 TTAAGTTGTG
Statistics
Matches: 291, Mismatches: 54, Indels: 90
0.67 0.12 0.21
Matches are distributed among these distances:
4 2 0.01
6 5 0.02
7 61 0.21
8 39 0.13
9 158 0.54
10 15 0.05
11 4 0.01
12 7 0.02
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:995553 original size:41 final size:41
Alignment explanation
Indices: 995508--995604 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
995498 TTATGTGAGC
* * *
995508 TATGTAAGTTATTTAGTATGTAAGCTATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
* * * * **
995549 TATGTAAGCTATGTATTATGTTAGTTATGTCGGTTATATAT
1 TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
*
995590 TATGTATGTTATGTA
1 TATGTAAGTTATGTA
995605 AGTTGTTCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (41 bp):
TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
Found at i:995737 original size:26 final size:26
Alignment explanation
Indices: 995675--995828 Score: 159
Period size: 26 Copynumber: 5.9 Consensus size: 26
995665 TTAATTTGTA
* * * * *
995675 TTAAGCTATGTAAGTTGTGAATAATG
1 TTAAGTTATGAAAGTTATGTATTATG
995701 -TAAGTTATGAAAGTTATGTATTATG
1 TTAAGTTATGAAAGTTATGTATTATG
*
995726 TTAAGTTATGAAAGTTATGTATTAAG
1 TTAAGTTATGAAAGTTATGTATTATG
** * * * *
995752 TTGTGTATTATGTAAGTTGTGAATAATG
1 TTAAG--TTATGAAAGTTATGTATTATG
*
995780 -TAAGTTATGAACGTTATGTATTATG
1 TTAAGTTATGAAAGTTATGTATTATG
995805 TTAAGTTATGAAAGTTATGTATTA
1 TTAAGTTATGAAAGTTATGTATTA
995829 AGTTGTGTAT
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
25 36 0.35
26 49 0.48
27 2 0.02
28 16 0.16
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (26 bp):
TTAAGTTATGAAAGTTATGTATTATG
Found at i:995777 original size:79 final size:79
Alignment explanation
Indices: 995681--995848 Score: 318
Period size: 79 Copynumber: 2.1 Consensus size: 79
995671 TGTATTAAGC
995681 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
1 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
995746 ATTAAGTTGTGTAT
66 ATTAAGTTGTGTAT
*
995760 TATGTAAGTTGTGAATAATGTAAGTTATGAACGTTATGTATTATGTTAAGTTATGAAAGTTATGT
1 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
995825 ATTAAGTTGTGTAT
66 ATTAAGTTGTGTAT
*
995839 TATGTTAGTT
1 TATGTAAGTT
995849 ATTTAAGCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (79 bp):
TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
ATTAAGTTGTGTAT
Found at i:995955 original size:37 final size:36
Alignment explanation
Indices: 995914--996009 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 36
995904 TAGAAACTGA
995914 TATGTAATTAGAAATTGTATCTTAATATTATATAAGT
1 TATGTAATTAGAAATT-TATCTTAATATTATATAAGT
*
995951 TATGTAATGAG-AA---A--TTAATATTATATAAGT
1 TATGTAATTAGAAATTTATCTTAATATTATATAAGT
*
995981 TATGTAATTCGAAATTTTATCTTAATATT
1 TATGTAATTAGAAA-TTTATCTTAATATT
996010 TGTATAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
30 25 0.51
31 2 0.04
32 1 0.02
35 1 0.02
36 2 0.04
37 18 0.37
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
TATGTAATTAGAAATTTATCTTAATATTATATAAGT
Found at i:996090 original size:94 final size:94
Alignment explanation
Indices: 995965--996172 Score: 262
Period size: 94 Copynumber: 2.2 Consensus size: 94
995955 TAATGAGAAA
* * * **
995965 TTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTTGTATAA-TTATCTAAATA-
1 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAA-AATAATATAACTTATCTAAATAT
* *
996028 TATA-AATTTAAGTGTACTTAGAAATTACAAT-
65 TATAGAAGTT-A-TGTAATTAGAAATT-CAATC
*
996059 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTTAATATT
1 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTAAATATT
**
996124 ATAGAAGTTATGTAATTAGAAATTTTATC
66 ATAGAAGTTATGTAATTAGAAATTCAATC
996153 TTAATATTATATAAGTTATG
1 TTAATATTATATAAGTTATG
996173 AAGTGTCCTG
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
93 9 0.09
94 82 0.82
95 5 0.05
96 4 0.04
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (94 bp):
TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTAAATATT
ATAGAAGTTATGTAATTAGAAATTCAATC
Found at i:996120 original size:57 final size:57
Alignment explanation
Indices: 996059--996171 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
996049 AAATTACAAT
* *
996059 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATC
1 TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAACTTATC
* * * * *
996116 TTAATATTATAGAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTAT
1 TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAACTTAT
996172 GAAGTGTCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (57 bp):
TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAACTTATC
Found at i:1003102 original size:228 final size:228
Alignment explanation
Indices: 1002692--1003110 Score: 545
Period size: 228 Copynumber: 1.8 Consensus size: 228
1002682 GTGAAGCCGA
* *
1002692 AACGATGCATTTTGGTCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCCACTAAAAGCTGATATAT
1 AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATAT
* * *
1002757 AGCGGCGTTTACGGGTACGCGTCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
66 AGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
* * ** * * *
1002822 TTAAAAATTTTCAGTGTTTTTTAGTTAAACGCCACTATTTATGGGATATAGCGGCATTTTCAGGT
131 TTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGGT
1002887 AAGCACCACTAATGCCTTTATACGTCAAACCCG
196 AAGCACCACTAATGCCTTTATACGTCAAACCCG
** * * *
1002920 AACGATGTGTTTTGTTCAAAATATTTGCGGCGATTCAGGA-ATAGCGCCACTAAAAGCTGATATA
1 AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGA-AGCGCCACTAAAAGCTGATATA
* * * * *
1002984 TAGCGGCGTTTTCGGCTAAGCGCCGCTAAAGGCTCTATAGCTCAAGACGAAACGTTGCGTTTTGG
65 TAGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGG
* * * ** * *
1003049 TTTCAAAAGTTCCGGCATTTTTCGGTTACGCGCCGCTA-ATAGCGGGCTATAGCGGCATTTTC
130 TTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATA-CGGGATATAGCGGCATTTTC
1003111 CACAAGCGCC
Statistics
Matches: 160, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
227 3 0.02
228 157 0.98
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (228 bp):
AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATAT
AGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
TTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGGT
AAGCACCACTAATGCCTTTATACGTCAAACCCG
Found at i:1003177 original size:228 final size:227
Alignment explanation
Indices: 1002691--1003179 Score: 531
Period size: 228 Copynumber: 2.1 Consensus size: 227
1002681 CGTGAAGCCG
*
1002691 AAACGATGCATTTTGG-TCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCCACTAAAAGCTGATAT
1 AAACGATGCATTTTGGTTCAAAA-TTTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATAT
* * *
1002755 ATAGCGGCGTTTACGGGTACGCGTCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCG
65 ATAGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCG
* * ** * * *
1002820 GTTTAAAAATTTTCAGTGTTTTTTAGTTAAACGCCACTATTTATGGGATATAGCGGCATTTTCAG
130 GTTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCA-
* * *
1002885 GTAAGCACCACTAATGCCTTTATACGTCAAACCC
194 GCAAGCACCACTAATGCCTCTATACCTCAAACCC
* ** * *
1002919 GAACGATGTGTTTT-GTTCAAAATATTTGCGGCGATTCAGGA-ATAGCGCCACTAAAAGCTGATA
1 AAACGATGCATTTTGGTTCAAAAT-TTTGCGGCGATTAAGCAGA-AGCGCCACTAAAAGCTGATA
* * * * *
1002982 TATAGCGGCGTTTTCGGCTAAGCGCCGCTAAAGGCTCTATAGCTCAAGACGAAACGTTGCGTTTT
64 TATAGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTC
* * * ** * *
1003047 GGTTTCAAAAGTTCCGGCATTTTTCGGTTACGCGCCGCTA-ATAGCGGGCTATAGCGGCATTTTC
129 GGTTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATA-CGGGATATAGCGGCATTTT-
* * * *
1003111 CA-CAAGCGCCACTATTGGCTCTATGCCTCAATA-CC
192 CAGCAAGCACCACTAATGCCTCTATACCTCAA-ACCC
* *
1003146 AAACGTTGCATTTTGGTTCAGATATTTTGCGGCG
1 AAACGATGCATTTTGGTTCA-AAATTTTGCGGCG
1003180 CTTGTACTAT
Statistics
Matches: 213, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
227 39 0.18
228 169 0.79
229 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (227 bp):
AAACGATGCATTTTGGTTCAAAATTTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATA
TAGCGGCGTTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGG
TTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGC
AAGCACCACTAATGCCTCTATACCTCAAACCC
Found at i:1005259 original size:38 final size:38
Alignment explanation
Indices: 1005192--1005297 Score: 139
Period size: 38 Copynumber: 2.8 Consensus size: 38
1005182 CAAGTGTTTC
*
1005192 AAAATATTT--AATAAA-TTAGAAATGTGATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
*
1005227 AAAATATTTACAATAAATTTAGAAACGAGATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
*
1005265 AAAATA-TCAGCAAATAAATTTAGAAATGAGATT
1 AAAATATTTA-C-AATAAATTTAGAAATGAGATT
1005298 TTTTACCCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 9 0.15
37 8 0.13
38 25 0.40
39 20 0.32
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (38 bp):
AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
Found at i:1008067 original size:15 final size:15
Alignment explanation
Indices: 1008047--1008076 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1008037 ATGTAGGAGG
*
1008047 GATAAATCATATCCT
1 GATAAATCAAATCCT
1008062 GATAAATCAAATCCT
1 GATAAATCAAATCCT
1008077 ACTACATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (15 bp):
GATAAATCAAATCCT
Done.