Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 424860
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 46523 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1895 original size:22 final size:22
Alignment explanation
Indices: 1867--1910 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1857 TTTTGAACCA
1867 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
1889 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
1911 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:2481 original size:21 final size:20
Alignment explanation
Indices: 2436--2483 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2426 TGCAAGCGAG
*
2436 AAAGAGAAATTGAAAGAAAA
1 AAAGAAAAATTGAAAGAAAA
*
2456 GAAGAAAAGATTGAAA-AAGAA
1 AAAGAAAA-ATTGAAAGAA-AA
2477 AAAGAAA
1 AAAGAAA
2484 TCCAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAGAAAAATTGAAAGAAAA
Found at i:5856 original size:45 final size:45
Alignment explanation
Indices: 5807--6129 Score: 565
Period size: 45 Copynumber: 7.2 Consensus size: 45
5797 TCGGCCATGG
* * * *
5807 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
5852 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
5897 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
5942 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
5987 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6032 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
6077 TGCTTCCTCAAATTCTCCCATGAATTATGCTTGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6122 TGCTTCCT
1 TGCTTCCT
6130 TAATTTCATG
Statistics
Matches: 268, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 268 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:14174 original size:20 final size:20
Alignment explanation
Indices: 14128--14174 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14118 AGCTCGTTTC
*
14128 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14148 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14168 CAGCTCA
1 CAGCTCA
14175 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15681 original size:31 final size:32
Alignment explanation
Indices: 15643--15721 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 32
15633 GTATTGGAGT
* *
15643 AAAAAAAAAAAAAATTCGAAAAAAAATTGAA-A
1 AAAAAAAAAAAAAAGT-GAAAAAAAATCGAAGA
15675 AAAAAAAAAAAAAAGTGAAAAAAAATCG-AGA
1 AAAAAAAAAAAAAAGTGAAAAAAAATCGAAGA
15706 AAAAAAAGAGAAAAAA
1 AAAAAAA-A-AAAAAA
15722 AAAGAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 1 0.02
31 19 0.45
32 16 0.38
33 6 0.14
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.08
Consensus pattern (32 bp):
AAAAAAAAAAAAAAGTGAAAAAAAATCGAAGA
Found at i:15740 original size:12 final size:11
Alignment explanation
Indices: 15648--15741 Score: 79
Period size: 11 Copynumber: 8.4 Consensus size: 11
15638 GGAGTAAAAA
15648 AAAAAAAAATTCG
1 AAAAAAAAA-T-G
*
15661 AAAAAAAATTG
1 AAAAAAAAATG
15672 AAAAAAAAA--
1 AAAAAAAAATG
*
15681 AAAAAAAAGTG
1 AAAAAAAAATG
15692 -AAAAAAAATCG
1 AAAAAAAAAT-G
15703 AGAAAAAAAA-G
1 A-AAAAAAAATG
*
15714 AGAAAAAAAAAG
1 A-AAAAAAAATG
15726 AAAAAAAAAGTG
1 AAAAAAAAA-TG
15738 AAAA
1 AAAA
15742 GTCTTGCGAG
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
9 8 0.12
10 8 0.12
11 29 0.42
12 8 0.12
13 16 0.23
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:16840 original size:48 final size:47
Alignment explanation
Indices: 16761--16866 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
16751 GAGTGTCATG
*
16761 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
16809 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
16857 GAAAAAGAAA
1 GAAAAAGAAA
16867 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:18582 original size:20 final size:20
Alignment explanation
Indices: 18536--18582 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18526 AGCTCGTTTC
*
18536 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18556 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18576 CAGCTCA
1 CAGCTCA
18583 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25861 original size:15 final size:15
Alignment explanation
Indices: 25841--25880 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
25831 CTTCTTCTTC
25841 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
25856 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
25871 TTTTTTTTCA
1 TTTTTTTTCA
25881 ACTTGATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:25942 original size:22 final size:22
Alignment explanation
Indices: 25917--25960 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25907 AAAGGAAACC
* *
25917 AATTTTTTTTTGAATTTTTTTT
1 AATTTTTTTTTCAAATTTTTTT
25939 AATTTTTTTTTCAAATTTTTTT
1 AATTTTTTTTTCAAATTTTTTT
25961 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
AATTTTTTTTTCAAATTTTTTT
Found at i:25948 original size:10 final size:11
Alignment explanation
Indices: 25920--25963 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
25910 GGAAACCAAT
25920 TTTTTTTTGAA
1 TTTTTTTTGAA
25931 TTTTTTTT-AA
1 TTTTTTTTGAA
*
25941 TTTTTTTTTCAA
1 -TTTTTTTTGAA
*
25953 ATTTTTTTGAA
1 TTTTTTTTGAA
25964 GAAACTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:26999 original size:21 final size:23
Alignment explanation
Indices: 26954--27000 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26944 TCACCTGCAA
* *
26954 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
26977 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
26998 TAA
1 TAA
27001 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:32911 original size:25 final size:22
Alignment explanation
Indices: 32870--32926 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 22
32860 AGTAGATTCG
32870 TGAAAAAAAATAAAAAAAAAAT
1 TGAAAAAAAATAAAAAAAAAAT
32892 TGAAAAAAAATCAAAGAAAAGAAAT
1 TGAAAAAAAAT-AAA-AAAA-AAAT
32917 TGAAAAAAAA
1 TGAAAAAAAA
32927 AATTGTATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.34
23 3 0.09
24 4 0.12
25 14 0.44
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (22 bp):
TGAAAAAAAATAAAAAAAAAAT
Found at i:38645 original size:27 final size:29
Alignment explanation
Indices: 38590--38662 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
38580 TCATGAGATT
* *
38590 GGCACGAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGAGTTTAAA-TGTACA
*
38620 -GCACTATGTGTGCGAGTTTAAA-GTACA
1 GGCACTAAGTGTGCGAGTTTAAATGTACA
38647 TGGCACTAAGTGTGCG
1 -GGCACTAAGTGTGCG
38663 CGGTTGATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
29 32 0.86
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGTTTAAATGTACA
Found at i:38917 original size:173 final size:174
Alignment explanation
Indices: 38621--38946 Score: 546
Period size: 173 Copynumber: 1.9 Consensus size: 174
38611 AATTGTACAG
* * * *
38621 CACTATGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGT
1 CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC
* *
38686 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGAT
66 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
38751 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
131 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
* * * *
38795 CACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATGC
1 CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC
*
38860 GTGC-AACCCTATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
66 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
38924 TTTGGACAGCGGAAAAGGTAAGT
131 TTTGGACAGCGGAAAAGGTAAGT
38947 ACCTTGAGTT
Statistics
Matches: 141, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
173 80 0.57
174 61 0.43
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (174 bp):
CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC
GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
Found at i:45158 original size:30 final size:30
Alignment explanation
Indices: 45124--45211 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
45114 TAAACTAAAA
*
45124 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
45154 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
45184 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
45212 TATGAGCAAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:45218 original size:30 final size:29
Alignment explanation
Indices: 45118--45218 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 29
45108 CGAGTTTAAA
* *
45118 CTAAAATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
45147 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
45177 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
45207 CTAAATATGAGC
1 CTAAAT-TGAGC
45219 AAGAAGTGAG
Statistics
Matches: 53, Mismatches: 16, Indels: 5
0.72 0.22 0.07
Matches are distributed among these distances:
29 8 0.15
30 43 0.81
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:48771 original size:20 final size:20
Alignment explanation
Indices: 48748--48793 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
48738 CCAGCTCGAA
*
48748 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
48768 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
48788 TTAGCT
1 TTAGCT
48794 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:48775 original size:30 final size:30
Alignment explanation
Indices: 48740--48813 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
48730 AGTTTTTCCC
48740 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
48770 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
48800 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
48814 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:50432 original size:19 final size:19
Alignment explanation
Indices: 50393--50434 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
50383 TATTATTGAG
* *
50393 AAAATTCAAAAAATTTAAA
1 AAAATTCAAAAAAATCAAA
50412 AAAATTCAAAAAAATCGAAA
1 AAAATTCAAAAAAATC-AAA
50432 AAA
1 AAA
50435 GGAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATTCAAAAAAATCAAA
Found at i:50434 original size:10 final size:10
Alignment explanation
Indices: 50393--50426 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
50383 TATTATTGAG
50393 AAAATTC-AA
1 AAAATTCAAA
*
50402 AAAATTTAAA
1 AAAATTCAAA
50412 AAAATTCAAA
1 AAAATTCAAA
50422 AAAAT
1 AAAAT
50427 CGAAAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATTCAAA
Found at i:51465 original size:12 final size:12
Alignment explanation
Indices: 51448--51612 Score: 52
Period size: 12 Copynumber: 13.8 Consensus size: 12
51438 CGAGAAAAGG
*
51448 AAAAGAGATTGA
1 AAAAGAAATTGA
51460 AAAAGAAATTG-
1 AAAAGAAATTGA
**
51471 -AAAGAAA-ACA
1 AAAAGAAATTGA
**
51481 AAAAGAAAACGA
1 AAAAGAAATTGA
**
51493 AAAAGAAAAAGA
1 AAAAGAAATTGA
** *
51505 AATTGCAAA-AGA
1 AAAAG-AAATTGA
*
51517 AAAAGAAATCGA
1 AAAAGAAATTGA
** **
51529 AAAAGTGAGAGA
1 AAAAGAAATTGA
*
51541 AAAAGAAAATGAA
1 AAAAGAAATTG-A
*
51554 GAAAAAAAATTGA
1 -AAAAGAAATTGA
**
51567 AAAAGAAAAAGCGA
1 AAAAG--AAATTGA
51581 AAAAGAAATTGA
1 AAAAGAAATTGA
* **
51593 AAGAGAGCTTG-
1 AAAAGAAATTGA
51604 AAAAGAAAT
1 AAAAGAAAT
51613 CAAGTGAAAA
Statistics
Matches: 112, Mismatches: 32, Indels: 19
0.69 0.20 0.12
Matches are distributed among these distances:
10 7 0.06
11 16 0.14
12 65 0.58
13 5 0.04
14 19 0.17
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:51503 original size:6 final size:6
Alignment explanation
Indices: 51471--51588 Score: 78
Period size: 6 Copynumber: 19.2 Consensus size: 6
51461 AAAGAAATTG
* * ** *
51471 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * *
51518 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAA GAAA-AA AAATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAA--GAA
51568 AAAGAA AAAGCGAA AAAGAA A
1 AAAGAA AAA--GAA AAAGAA A
51589 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
5 6 0.07
6 65 0.77
7 2 0.02
8 11 0.13
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:51568 original size:26 final size:26
Alignment explanation
Indices: 51539--51594 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
51529 AAAAGTGAGA
*
51539 GAAAAAGAAAATGAAGAAAAA-AAATT
1 GAAAAAGAAAAAG-AGAAAAAGAAATT
*
51565 GAAAAAGAAAAAGCGAAAAAGAAATT
1 GAAAAAGAAAAAGAGAAAAAGAAATT
51591 GAAA
1 GAAA
51595 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAAGAGAAAAAGAAATT
Found at i:51632 original size:33 final size:33
Alignment explanation
Indices: 51591--51653 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
51581 AAAAGAAATT
51591 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
51624 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
51654 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:53449 original size:20 final size:20
Alignment explanation
Indices: 53426--53479 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
53416 AGTTTTTCCC
*
53426 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
53446 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
53466 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
53480 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:53461 original size:30 final size:30
Alignment explanation
Indices: 53426--53499 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
53416 AGTTTTTCCC
53426 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
53456 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
53486 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
53500 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:53489 original size:20 final size:20
Alignment explanation
Indices: 53426--53490 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
53416 AGTTTTTCCC
* * * *
53426 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
53446 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
53465 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
53486 AGCTC
1 AGCTC
53491 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:57411 original size:4 final size:4
Alignment explanation
Indices: 57402--57437 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
57392 TTAAACTAAG
57402 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
57438 AATAAAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:59152 original size:11 final size:11
Alignment explanation
Indices: 59136--59160 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59126 TATACCTATA
59136 TTGTAGAATTT
1 TTGTAGAATTT
59147 TTGTAGAATTT
1 TTGTAGAATTT
59158 TTG
1 TTG
59161 GTCTGGCCAA
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:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (11 bp):
TTGTAGAATTT
Found at i:73025 original size:20 final size:20
Alignment explanation
Indices: 73002--73048 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
72992 TGGTTAAGAT
*
73002 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
73022 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
73042 TGAGCTG
1 TGAGCTG
73049 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:73638 original size:14 final size:14
Alignment explanation
Indices: 73614--73665 Score: 90
Period size: 14 Copynumber: 3.9 Consensus size: 14
73604 GGATATCAAG
73614 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
73628 TT-TG-AAAAAAAA
1 TTGTGAAAAAAAAA
73640 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
73654 TTGTGAAAAAAA
1 TTGTGAAAAAAA
73666 GAGAGAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.28
13 4 0.11
14 22 0.61
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:73643 original size:26 final size:27
Alignment explanation
Indices: 73614--73665 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
73604 GGATATCAAG
73614 TTGTGAAAAAAAAATT-TGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
73640 TTGTGAAAAAAAAATTGTGAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAA
73666 GAGAGAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAA
Found at i:78645 original size:19 final size:18
Alignment explanation
Indices: 78609--78648 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
78599 TTTCCACTCG
*
78609 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
78627 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
78646 TTT
1 TTT
78649 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:78747 original size:18 final size:17
Alignment explanation
Indices: 78722--78764 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
78712 CACTCTTTCT
78722 TTTCTTTTCCAATCTTT-
1 TTTCTTTTCCAAT-TTTG
*
78739 TTCTCTTTTTCAATTTTG
1 TT-TCTTTTCCAATTTTG
78757 TTTCTTTT
1 TTTCTTTT
78765 TGGTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTCTTTTCCAATTTTG
Found at i:78748 original size:19 final size:17
Alignment explanation
Indices: 78722--78765 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
78712 CACTCTTTCT
*
78722 TTTCTTTTCCAATCTTT-
1 TTTCTTTTTCAAT-TTTG
78739 TTCTCTTTTTCAATTTTG
1 TT-TCTTTTTCAATTTTG
78757 TTTCTTTTT
1 TTTCTTTTT
78766 GGTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTCTTTTTCAATTTTG
Found at i:79774 original size:12 final size:12
Alignment explanation
Indices: 79757--79801 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
79747 GGAAACTAAA
79757 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
79769 TTTTTTTTCAAAAT
1 TTTTTTTT--GAAT
79783 TTTTTTTTGAAT
1 TTTTTTTTGAAT
79795 TTTTTTT
1 TTTTTTT
79802 CGAAGATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 18 0.62
14 11 0.38
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:91501 original size:22 final size:22
Alignment explanation
Indices: 91471--91514 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
91461 TTTGGTATTT
91471 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
91493 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
91515 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:96771 original size:19 final size:18
Alignment explanation
Indices: 96735--96774 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
96725 TTTCCACTCG
*
96735 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
96753 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
96772 TTT
1 TTT
96775 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:96885 original size:19 final size:18
Alignment explanation
Indices: 96858--96907 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
96848 TTTCTTTCTC
*
96858 CAATCTTTTTCTCTTTTT
1 CAATTTTTTTCTCTTTTT
96876 CAATTTTTTT-TCTTTTT
1 CAATTTTTTTCTCTTTTT
**
96893 CGGTTTTTTTTCTCT
1 C-AATTTTTTTCTCT
96908 CGTCACTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.30
18 16 0.59
19 3 0.11
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.70
Consensus pattern (18 bp):
CAATTTTTTTCTCTTTTT
Found at i:96899 original size:17 final size:17
Alignment explanation
Indices: 96847--96905 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
96837 GCACTCTTTC
*
96847 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
96866 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
**
96883 TTTTCTTTTTCGGTTTT
1 TTTTCTTTTTCAATTTT
96900 TTTTCT
1 TTTTCT
96906 CTCGTCACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 23 0.66
18 5 0.14
19 7 0.20
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:97870 original size:26 final size:26
Alignment explanation
Indices: 97829--97879 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
97819 ACTAGCTCTC
97829 TTTTTTTTAAATTTTTTTTTCACAAT
1 TTTTTTTTAAATTTTTTTTTCACAAT
97855 TTTTTTTTCAAA-TTTTTTTTCACAA
1 TTTTTTTT-AAATTTTTTTTTCACAA
97880 CTTGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTTTTTAAATTTTTTTTTCACAAT
Found at i:97876 original size:12 final size:13
Alignment explanation
Indices: 97829--97874 Score: 76
Period size: 14 Copynumber: 3.5 Consensus size: 13
97819 ACTAGCTCTC
97829 TTTTTTTT-AAAT
1 TTTTTTTTCAAAT
97841 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
97855 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
97868 TTTTTTT
1 TTTTTTT
97875 CACAACTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.25
13 11 0.34
14 13 0.41
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:104607 original size:20 final size:20
Alignment explanation
Indices: 104584--104637 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
104574 AGTTTTTCCC
*
104584 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
104604 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
104624 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
104638 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:104619 original size:30 final size:30
Alignment explanation
Indices: 104584--104657 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
104574 AGTTTTTCCC
104584 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
104614 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
104644 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
104658 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:104647 original size:20 final size:20
Alignment explanation
Indices: 104584--104648 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
104574 AGTTTTTCCC
* * * *
104584 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
104604 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
104623 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
104644 AGCTC
1 AGCTC
104649 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:107998 original size:20 final size:20
Alignment explanation
Indices: 107973--108019 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
107963 AGCTCGTTTC
*
107973 CAGCTCACTCGAGTTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
107993 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
108013 CAGCTCA
1 CAGCTCA
108020 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:109510 original size:27 final size:27
Alignment explanation
Indices: 109472--109526 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
109462 CTTTAATGAT
109472 GGGCTGGTTCATGAATGGAAGCATGTA
1 GGGCTGGTTCATGAATGGAAGCATGTA
109499 GGGCTGGTTCATGAATGGAAGCATGTA
1 GGGCTGGTTCATGAATGGAAGCATGTA
109526 G
1 G
109527 CTTGTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.25
Consensus pattern (27 bp):
GGGCTGGTTCATGAATGGAAGCATGTA
Found at i:110158 original size:20 final size:19
Alignment explanation
Indices: 110135--110199 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
110125 AAGCTCAAAC
110135 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
110155 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
110175 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
110195 GAGCT
1 GAGCT
110200 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:112007 original size:33 final size:33
Alignment explanation
Indices: 111969--112031 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
111959 GATTACTCAC
111969 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
112002 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
112032 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:112063 original size:14 final size:13
Alignment explanation
Indices: 112028--112084 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
112018 TCAAGCTCTC
112028 TTTCAA-TTTCTT
1 TTTCAATTTTCTT
**
112040 TTTCGCTTTTTCTT
1 TTTC-AATTTTCTT
112054 TTTCAATTTTCTTT
1 TTTCAATTTTC-TT
112068 TCTTC-ATTTTCTT
1 T-TTCAATTTTCTT
112081 TTTC
1 TTTC
112085 TCTCACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.19
13 8 0.22
14 19 0.51
15 3 0.08
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTCAATTTTCTT
Found at i:112165 original size:6 final size:6
Alignment explanation
Indices: 112034--112152 Score: 60
Period size: 6 Copynumber: 19.2 Consensus size: 6
112024 TCTCTTTCAA
* * *
112034 TTTCTT TTTCGCTT TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC
1 TTTCTT TTT--CTT TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT
** ** * ** * *
112087 TCACTT TTTCGA TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT CTTCAT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *
112135 TTTGTT TTT-GT TTTCTT T
1 TTTCTT TTTCTT TTTCTT T
112153 CAATTTCTTT
Statistics
Matches: 80, Mismatches: 28, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
5 4 0.05
6 58 0.73
7 9 0.11
8 9 0.11
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:115515 original size:40 final size:40
Alignment explanation
Indices: 115389--115598 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
115379 TCTTCGGAAT
* * *
115389 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
115428 TTAGCCCGGAT-ATATCAACTCGCA-AAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
*
115467 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * * *
115507 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCAGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
115547 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
115587 TTAGCCCGGATA
1 TTAGCCCGGATA
115599 TCATTCAAAT
Statistics
Matches: 142, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 41 0.29
40 98 0.69
41 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:115515 original size:79 final size:80
Alignment explanation
Indices: 115389--115599 Score: 327
Period size: 80 Copynumber: 2.7 Consensus size: 80
115379 TCTTCGGAAT
* * * * *
115389 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCA-
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
*
115452 AAATGCCTTCGGGTC
66 AAATGCCTTCAGGTC
* *
115467 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
115532 AAATGCCTTCAGGTC
66 AAATGCCTTCAGGTC
*
115547 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
115600 CATTCAAATG
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 4 0.03
79 52 0.43
80 64 0.53
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCAGGTC
Found at i:123476 original size:40 final size:40
Alignment explanation
Indices: 123427--123638 Score: 273
Period size: 40 Copynumber: 5.3 Consensus size: 40
123417 TTCTTCGAAT
*
123427 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
123466 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
123506 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * * *
123546 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * *
123586 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
123626 TTAGCCCGGATAT
1 TTAGCCCGGATAT
123639 CATTCAAATG
Statistics
Matches: 144, Mismatches: 28, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 4 0.03
40 140 0.97
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
Found at i:123565 original size:80 final size:80
Alignment explanation
Indices: 123427--123638 Score: 345
Period size: 80 Copynumber: 2.7 Consensus size: 80
123417 TTCTTCGAAT
* * * * *
123427 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
123491 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
123506 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
123571 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
123586 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
123639 CATTCAAATG
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
79 4 0.03
80 118 0.97
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:180380 original size:30 final size:30
Alignment explanation
Indices: 180346--180442 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
180336 TAAACTAAAA
*
180346 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
180376 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
180406 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
180435 ATGAGCTA
1 -TGAGCTA
180443 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:182573 original size:12 final size:12
Alignment explanation
Indices: 182558--182588 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
182548 TTCTTTTTGC
182558 TTTTCAAAGGCT
1 TTTTCAAAGGCT
182570 TTTTCAAAGGCT
1 TTTTCAAAGGCT
182582 TTTTCAA
1 TTTTCAA
182589 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:182646 original size:5 final size:5
Alignment explanation
Indices: 182636--182696 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
182626 CTCTTGCCTC
* * *
182636 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTCTT GCTTT TTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCT-TT TCTTT TCTTT
182682 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
182697 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.09
5 33 0.73
6 7 0.16
7 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:182659 original size:16 final size:14
Alignment explanation
Indices: 182636--182703 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 14
182626 CTCTTGCCTC
182636 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
182651 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
*
182666 TCTCTTGCTTTTTTTT
1 TCT-TTTC-TTTTTTT
*
182682 TCTTTTCTTTTCTT
1 TCTTTTCTTTTTTT
*
182696 TGTTTTCT
1 TCTTTTCT
182704 CTTTACAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 14 0.32
15 11 0.25
16 19 0.43
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:183630 original size:13 final size:12
Alignment explanation
Indices: 183610--183644 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
183600 TCAAAAAAAA
183610 AATTTTTTTTTG
1 AATTTTTTTTTG
183622 AATTTTTTTTTG
1 AATTTTTTTTTG
183634 AATTTTTTTTT
1 AATTTTTTTTT
183645 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:183650 original size:13 final size:12
Alignment explanation
Indices: 183609--183651 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
183599 TTCAAAAAAA
183609 AAATTTTTTTTT
1 AAATTTTTTTTT
*
183621 GAATTTTTTTTT
1 AAATTTTTTTTT
*
183633 GAATTTTTTTTT
1 AAATTTTTTTTT
183645 CAAATTT
1 -AAATTT
183652 CCTCTTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (12 bp):
AAATTTTTTTTT
Found at i:185384 original size:30 final size:30
Alignment explanation
Indices: 185350--185446 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
185340 TAAACTAAAA
*
185350 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
185380 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
185410 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
185439 ATGAGCTA
1 -TGAGCTA
185447 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:187367 original size:9 final size:9
Alignment explanation
Indices: 187353--187387 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
187343 GCAAAAAAGC
187353 AGTCAAAAA
1 AGTCAAAAA
187362 AGTCAAAAA
1 AGTCAAAAA
*
187371 AGTGAAAAA
1 AGTCAAAAA
187380 A-TCAAAAA
1 AGTCAAAAA
187388 TACGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:189519 original size:22 final size:22
Alignment explanation
Indices: 189491--189534 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
189481 TTTTGAACCA
189491 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
189513 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
189535 AAATACCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:190321 original size:27 final size:27
Alignment explanation
Indices: 190291--190343 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
190281 ACAAGTGAGG
190291 AAAAAGAAAAAGAGAATGAAAAAGAAC
1 AAAAAGAAAAAGAGAATGAAAAAGAAC
* ** *
190318 AAAAAGAGATTGAGAGTGAAAAAGAA
1 AAAAAGAAAAAGAGAATGAAAAAGAA
190344 ATTGAAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAAC
Found at i:193816 original size:453 final size:456
Alignment explanation
Indices: 192959--193859 Score: 1422
Period size: 453 Copynumber: 2.0 Consensus size: 456
192949 AAGGGGGGAG
*
192959 TGATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAA
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGC-C--ATC---AAAATCAA
* * * * *
193024 GATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCTAATTTTGCTGTTCGGAG
60 GATTCACTTTCTTGTTTTCAAGAAAATCAAGAAACCCAATCTTGGCCCAATTATGCTGTTCGAAG
* *
193089 TGATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTAGAAATCTTGGTCCAAGAAACCGAATC
125 AGATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTAGAAATCTTGGTCCAAGAAACCAAATC
* * *
193154 TTGCAGCCAAAGCGCGTTGGGTCTCCATTACGAGCGTCAACGACCCAATTTCGGTAAGAGATGGA
190 TTGCAGCCAAAGCGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAAGAGATGGA
*
193219 TCACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCA
255 TCACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAACCAAATTCCCAGCCCAATCAAGAAATCCA
* * *
193284 TACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTGTAAACATTTTAGTTGTT
320 TACATACTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTATAAACATTTTAATTGTT
* * *
193349 TAAGTTAATTTTTAAGTTTTAGGAATATCACATGTTAAATTCGGCCC-AAAACAGCCCAATAGGA
385 TAAGTTAATTTTTAAGCTTTAGGAACAT-ACATGTAAAATTCGGCCCAAAAACAGCCCAATAGGA
193413 TGCATGGC
449 TGCATGGC
193421 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGG-C-TC-AAATCAAGATTCA
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCCATCAAAATCAAGATTCA
193483 CTTTCTTGTTTTCAAGAAAATCAAGAAACCCAATCTTGGCCCAATTATGCTGTTCGAAGAGATTT
66 CTTTCTTGTTTTCAAGAAAATCAAGAAACCCAATCTTGGCCCAATTATGCTGTTCGAAGAGATTT
*
193548 CAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCAG
131 CAAGAATCAAGAAAATCAAGATTTCAAATCTTAGAAATCTTGGTCCAAGAAACCAAATCTTGCAG
*
193613 CCAACA-CGCATTGGATCTCCATTACGAGCATCAACGACCTAATTTCGG-AAGGAGATGGATCAC
196 CCAA-AGCGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAA-GAGATGGATCAC
* * *
193676 GAGCCCAAATTCTTGAAGGCAAGGCCCAATAACCAAATT-CCAGCCCAATCAAGAAATTCC-TTC
259 AAGCCCAAATTCTTAAAGGCAAGGCCCAATAACCAAATTCCCAGCCCAATCAAGAAA-TCCATAC
*
193739 ATACTTAGTTGAAAATCAGGCCAAAATGTCAAATGGCCCAATTTATAAACATTTTAATTGTTTAA
323 ATACTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTATAAACATTTTAATTGTTTAA
*
193804 TTTAATTTTTTAAGCTTTAGGAACATACATGTAAAATTCGGCCCAAAAACAGCCCA
388 GTTAA-TTTTTAAGCTTTAGGAACATACATGTAAAATTCGGCCCAAAAACAGCCCA
193860 TATATATGCT
Statistics
Matches: 409, Mismatches: 25, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
452 103 0.25
453 257 0.63
454 1 0.00
457 2 0.00
460 1 0.00
462 45 0.11
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (456 bp):
TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCCATCAAAATCAAGATTCA
CTTTCTTGTTTTCAAGAAAATCAAGAAACCCAATCTTGGCCCAATTATGCTGTTCGAAGAGATTT
CAAGAATCAAGAAAATCAAGATTTCAAATCTTAGAAATCTTGGTCCAAGAAACCAAATCTTGCAG
CCAAAGCGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAAGAGATGGATCACAA
GCCCAAATTCTTAAAGGCAAGGCCCAATAACCAAATTCCCAGCCCAATCAAGAAATCCATACATA
CTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTATAAACATTTTAATTGTTTAAGTT
AATTTTTAAGCTTTAGGAACATACATGTAAAATTCGGCCCAAAAACAGCCCAATAGGATGCATGG
C
Found at i:202493 original size:21 final size:21
Alignment explanation
Indices: 202448--202510 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
202438 TTTGAACCAT
* *
202448 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
202470 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
202491 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
202511 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:204637 original size:19 final size:19
Alignment explanation
Indices: 204613--204650 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
204603 TGGCTTAGAA
204613 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
204632 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
204651 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:205121 original size:37 final size:37
Alignment explanation
Indices: 205075--205152 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
205065 TTAAATGAAC
205075 TTAACTCATGCATCAATAAATAATCCTAGGAACTAGA
1 TTAACTCATGCATCAATAAATAATCCTAGGAACTAGA
205112 TTAACTCATGCATCAATAAATAATCCTAGGAACTAGA
1 TTAACTCATGCATCAATAAATAATCCTAGGAACTAGA
205149 TTAA
1 TTAA
205153 TTAAGAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (37 bp):
TTAACTCATGCATCAATAAATAATCCTAGGAACTAGA
Found at i:207065 original size:19 final size:18
Alignment explanation
Indices: 207029--207068 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
207019 TTTCCACTCG
*
207029 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
207047 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
207066 TTT
1 TTT
207069 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:207196 original size:10 final size:11
Alignment explanation
Indices: 207172--207198 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
207162 TCTTTTTCAA
207172 TTTTCGTTTCT
1 TTTTCGTTTCT
207183 TTTTCGTTTCT
1 TTTTCGTTTCT
207194 TTTTC
1 TTTTC
207199 TCTCGTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTCGTTTCT
Found at i:208155 original size:15 final size:14
Alignment explanation
Indices: 208119--208152 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
208109 TAGCTTCTTC
208119 TTTTTTCACGAATT
1 TTTTTTCACGAATT
208133 TTTTTTCACGAATT
1 TTTTTTCACGAATT
208147 TTTTTT
1 TTTTTT
208153 TCAACTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTTCACGAATT
Found at i:208212 original size:13 final size:12
Alignment explanation
Indices: 208192--208249 Score: 98
Period size: 12 Copynumber: 4.8 Consensus size: 12
208182 AATGGAAACC
208192 AATTTTTTTTTG
1 AATTTTTTTTTG
208204 AATTTTTTTTTG
1 AATTTTTTTTTG
208216 AATTTTTTTTTG
1 AATTTTTTTTTG
208228 AATTTTTTTTTCG
1 AATTTTTTTTT-G
*
208241 AGTTTTTTT
1 AATTTTTTT
208250 CGAGAAACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
12 35 0.80
13 9 0.20
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:208962 original size:19 final size:19
Alignment explanation
Indices: 208938--208975 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
208928 TGGCTTAGAA
208938 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
208957 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
208976 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:213152 original size:13 final size:12
Alignment explanation
Indices: 213126--213166 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
213116 ACGGTATTGT
213126 AAAAAAA-T-AA
1 AAAAAAATTCAA
* *
213136 AAAAAACTTGAA
1 AAAAAAATTCAA
213148 AAAAAAATTCAA
1 AAAAAAATTCAA
213160 AAAAAAA
1 AAAAAAA
213167 AGTTTGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 19 0.73
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:213255 original size:29 final size:29
Alignment explanation
Indices: 213212--213279 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
213202 AGTATTGAAG
**
213212 GAAAAAAAAAGAAGAAAAAAATTCGGAATT
1 GAAAAAAAAAGAAGAAAAAAA-TCAAAATT
213242 -AAAAAAAAAGAAGAAAAAAATCAAAATT
1 GAAAAAAAAAGAAGAAAAAAATCAAAATT
213270 GAAAAAAAAA
1 GAAAAAAAAA
213280 AGAGTGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (29 bp):
GAAAAAAAAAGAAGAAAAAAATCAAAATT
Found at i:214153 original size:17 final size:15
Alignment explanation
Indices: 214133--214171 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
214123 GCGAGTGAGA
214133 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
214150 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
214165 AAGATGA
1 AA-ATGA
214172 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:217698 original size:20 final size:19
Alignment explanation
Indices: 217675--217739 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
217665 AAGCTCAAAC
217675 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
217695 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
217715 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
217735 GAGCT
1 GAGCT
217740 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:219553 original size:33 final size:33
Alignment explanation
Indices: 219515--219577 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
219505 GATTACTCAC
219515 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
219548 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
219578 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:219604 original size:21 final size:21
Alignment explanation
Indices: 219575--219711 Score: 53
Period size: 21 Copynumber: 6.7 Consensus size: 21
219565 CAAGCTCTCT
*
219575 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
219596 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
219617 TTCATTTTCTTTTTCTCTCACTTT-
1 TTCATTTTC-TTTT-T-TC-CTTTC
219641 TTCGA-TTTC-TTTTT-CTTT-
1 TTC-ATTTTCTTTTTTCCTTTC
* *
219659 TGCAATTTC-TTTTT-CTTT-
1 TTCATTTTCTTTTTTCCTTTC
219677 TTCATTTTCTTTTTGT--TTTC
1 TTCATTTTCTTTTT-TCCTTTC
*
219697 TTTCAATTTCTTTTT
1 -TTCATTTTCTTTTT
219712 CAATCTCTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
17 1 0.01
18 26 0.28
19 7 0.08
20 5 0.05
21 34 0.37
22 5 0.05
23 1 0.01
24 9 0.10
25 4 0.04
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:219623 original size:14 final size:14
Alignment explanation
Indices: 219574--219630 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
219564 TCAAGCTCTC
219574 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
219587 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
219601 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
219615 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
219629 TT
1 TT
219631 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:219690 original size:18 final size:18
Alignment explanation
Indices: 219592--219695 Score: 93
Period size: 18 Copynumber: 5.6 Consensus size: 18
219582 TCTTTTTTCG
219592 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
219611 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
219631 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
219649 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
219667 CTTTTTCTTTTTCATTTT
1 CTTTTTCTTTTTCATTTT
*
219685 CTTTTTGTTTT
1 CTTTTTCTTTT
219696 CTTTCAATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
17 1 0.01
18 47 0.70
19 3 0.04
20 8 0.12
21 8 0.12
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:219695 original size:11 final size:12
Alignment explanation
Indices: 219594--219713 Score: 81
Period size: 12 Copynumber: 10.0 Consensus size: 12
219584 TTTTTTCGCT
219594 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
219607 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
219621 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
219632 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
219646 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
219656 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
219669 TTTTCTTTTTCA
1 TTTTCTTTTTCA
*
219681 TTTTCTTTTT-G
1 TTTTCTTTTTCA
219692 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
219702 ATTTCTTTTTCA
1 TTTTCTTTTTCA
219714 ATCTCTTTCT
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 9 0.11
12 44 0.52
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:219712 original size:6 final size:6
Alignment explanation
Indices: 219592--219699 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
219582 TCTTTTTTCG
* * * **
219592 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
219643 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CATTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
219691 -GTTTT CTTT
1 CTTTTT CTTT
219700 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:223018 original size:12 final size:12
Alignment explanation
Indices: 223001--223038 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
222991 AAAAGAGAAG
223001 AAATTCAAAAAA
1 AAATTCAAAAAA
223013 AAATTCAAAAAA
1 AAATTCAAAAAA
*
223025 AAAATCAAAAAA
1 AAATTCAAAAAA
223037 AA
1 AA
223039 GAAGTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:223025 original size:13 final size:13
Alignment explanation
Indices: 223001--223053 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 13
222991 AAAAGAGAAG
223001 AAATTC-AAAAAA
1 AAATTCAAAAAAA
223013 AAATTCAAAAAAA
1 AAATTCAAAAAAA
223026 AAA-TCAAAAAAA
1 AAATTCAAAAAAA
* *
223038 AGAAGTGAAAAAAA
1 A-AATTCAAAAAAA
223052 AA
1 AA
223054 GAAGTGACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 16 0.43
13 12 0.32
14 9 0.24
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:223065 original size:14 final size:15
Alignment explanation
Indices: 223031--223109 Score: 83
Period size: 16 Copynumber: 5.2 Consensus size: 15
223021 AAAAAAAATC
223031 AAAAAAAAGAAGTGA
1 AAAAAAAAGAAGTGA
223046 AAAAAAAAGAAGTGA
1 AAAAAAAAGAAGTGA
*
223061 CAAAAAAAATCG-AGTTA
1 -AAAAAAAA--GAAGTGA
223078 AAAAAAAAGAA--GA
1 AAAAAAAAGAAGTGA
*
223091 AAGAAAAAAAAAGTGA
1 AA-AAAAAAGAAGTGA
223107 AAA
1 AAA
223110 GTCTTGCGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
13 3 0.06
14 9 0.17
15 17 0.31
16 20 0.37
17 4 0.07
18 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (15 bp):
AAAAAAAAGAAGTGA
Found at i:224738 original size:20 final size:20
Alignment explanation
Indices: 224691--224738 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
224681 AGTAAGCTCG
224691 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
224711 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
224731 GTTGAGCT
1 GTTGAGCT
224739 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:226406 original size:11 final size:12
Alignment explanation
Indices: 226376--226407 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
226366 TTTCACTCTT
226376 CTCTTTTTCAAA
1 CTCTTTTTCAAA
226388 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
226400 TTCTTTTT
1 CTCTTTTT
226408 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:226419 original size:27 final size:27
Alignment explanation
Indices: 226389--226450 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
226379 TTTTTCAAAC
*
226389 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
226416 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
226443 TCTTTTTC
1 TCTTTTTC
226451 TTTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:226429 original size:13 final size:12
Alignment explanation
Indices: 226413--226532 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
226403 TTTTTTCGCT
226413 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
226426 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
226440 TTTTCTTTTTC-
1 TTTTCTTTTTCA
* *
226451 TTTCACTTTTTTGA
1 TTT-TC-TTTTTCA
226465 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
226475 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
226488 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
226500 TTTTCTTTTT-G
1 TTTTCTTTTTCA
226511 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
226521 ATTTCTTTTTCA
1 TTTTCTTTTTCA
226533 ATCTCTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 17 0.20
12 30 0.35
13 19 0.22
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:226442 original size:14 final size:14
Alignment explanation
Indices: 226391--226449 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
226381 TTTCAAACTC
*
226391 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
226404 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
226417 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
226432 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
226446 TTTT
1 TTTT
226450 CTTTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:226449 original size:15 final size:15
Alignment explanation
Indices: 226413--226452 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
226403 TTTTTTCGCT
226413 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTAA
*
226426 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTAA
226440 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
226453 TCACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 6 0.26
15 7 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCTTAA
Found at i:226531 original size:6 final size:6
Alignment explanation
Indices: 226411--226518 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
226401 TCTTTTTTCG
* * **
226411 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
226462 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
226510 -GTTTT CTTT
1 CTTTTT CTTT
226519 CAATTTCTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 5 0.07
6 58 0.76
7 10 0.13
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:229792 original size:20 final size:20
Alignment explanation
Indices: 229745--229792 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
229735 AGTAAGCTCG
229745 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
229765 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
229785 GTTGAGCT
1 GTTGAGCT
229793 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:230697 original size:18 final size:18
Alignment explanation
Indices: 230676--230710 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
230666 AGAAAAGAAA
230676 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
230694 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
230711 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:242849 original size:20 final size:20
Alignment explanation
Indices: 242826--242890 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
242816 AAGCTCAAAC
*
242826 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTGAGCTAAATT
242846 GAGCTCAAAG-GAGCTAAATT
1 GAGCT-AAAGTGAGCTAAATT
* * * *
242866 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGTGAGCTAAATT
242886 GAGCT
1 GAGCT
242891 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.05
20 31 0.84
21 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (20 bp):
GAGCTAAAGTGAGCTAAATT
Found at i:246330 original size:21 final size:21
Alignment explanation
Indices: 246304--246347 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
246294 TTGGTATTTG
246304 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
246325 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
246346 GG
1 GG
246348 TATTAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:246335 original size:11 final size:11
Alignment explanation
Indices: 246315--246347 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
246305 GAATTGGTAC
246315 GAAATGGTATG
1 GAAATGGTATG
*
246326 GAATTGGTAT-
1 GAAATGGTATG
246336 GAAATGGTATG
1 GAAATGGTATG
246347 G
1 G
246348 TATTAAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:247437 original size:10 final size:10
Alignment explanation
Indices: 247422--247463 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
247412 TTTGCAAGTT
247422 TTGAGCTAAA
1 TTGAGCTAAA
* *
247432 TTGAGCTGAT
1 TTGAGCTAAA
*
247442 TTGAGCT-CA
1 TTGAGCTAAA
247451 TTGAGCTAAA
1 TTGAGCTAAA
247461 TTG
1 TTG
247464 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:250507 original size:20 final size:20
Alignment explanation
Indices: 250480--250524 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
250470 TTATTCATTC
*
250480 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTTAATTTTCTTT
*
250499 TCTTTTTTTTATTTTTCTTT
1 TCTTTTTTTTAATTTTCTTT
250519 TCTTTT
1 TCTTTT
250525 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (20 bp):
TCTTTTTTTTAATTTTCTTT
Found at i:250539 original size:36 final size:37
Alignment explanation
Indices: 250466--250545 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 37
250456 GCTTTTCTCA
**
250466 TTTTTTATTCATTCTCTTTTTTTGAATTTTCTTTCTT
1 TTTTTTATTCATTCTCTTTTTTTGAATTTTCGCTCTT
* *
250503 TTTTTTATT-TTTCT-TTTCTTTTGTATTTTCGCTCTT
1 TTTTTTATTCATTCTCTTT-TTTTGAATTTTCGCTCTT
250539 TTCTTTT
1 TT-TTTT
250546 TCTCTCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 3 0.08
36 21 0.57
37 13 0.35
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (37 bp):
TTTTTTATTCATTCTCTTTTTTTGAATTTTCGCTCTT
Found at i:255045 original size:21 final size:21
Alignment explanation
Indices: 255000--255062 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
254990 TTTGAACCAT
* *
255000 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
255022 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
255043 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
255063 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:256288 original size:21 final size:21
Alignment explanation
Indices: 256262--256305 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
256252 TTGGTATTTG
256262 GGAATTGGTACT-AAATGGTAT
1 GGAATTGGTA-TGAAATGGTAT
256283 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
256304 GG
1 GG
256306 TATTAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:258585 original size:21 final size:21
Alignment explanation
Indices: 258559--258602 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
258549 CTCTTTAATA
258559 CCATACCATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
258580 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
258601 CC
1 CC
258603 CAAATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:259008 original size:10 final size:10
Alignment explanation
Indices: 258993--259034 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
258983 TTTGCAAGTT
258993 TTGAGCTAAA
1 TTGAGCTAAA
*
259003 TTGAGCTAAT
1 TTGAGCTAAA
* *
259013 TTGAGAT-CA
1 TTGAGCTAAA
259022 TTGAGCTAAA
1 TTGAGCTAAA
259032 TTG
1 TTG
259035 GAAGTTAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:261118 original size:21 final size:23
Alignment explanation
Indices: 261073--261119 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
261063 TCACCTGCAA
* *
261073 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
261096 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
261117 TAA
1 TAA
261120 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:263364 original size:29 final size:30
Alignment explanation
Indices: 263285--263366 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
263275 AAAGTCATAC
*
263285 ATTATGTAACTTTCATGTTAGTTAAGTTTGC
1 ATTATGTAACTTTCATGTTAGTT-AGTTTGA
* * *
263316 ATCAT-TAA-ATT-AAGTCTAGTTAGTTT-A
1 ATTATGTAACTTTCATGT-TAGTTAGTTTGA
263343 ATTATGTAACTTTCATGTTAGTTA
1 ATTATGTAACTTTCATGTTAGTTA
263367 AATTTGCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 15 0.38
30 6 0.15
31 4 0.10
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (30 bp):
ATTATGTAACTTTCATGTTAGTTAGTTTGA
Found at i:264358 original size:46 final size:46
Alignment explanation
Indices: 264306--264399 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
264296 ATAGTGTGGC
*
264306 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
264352 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
264398 GT
1 GT
264400 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:267823 original size:19 final size:18
Alignment explanation
Indices: 267787--267826 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
267777 TTTCCACTCG
*
267787 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
267805 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
267824 TTT
1 TTT
267827 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:268897 original size:14 final size:13
Alignment explanation
Indices: 268879--268930 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
268869 ACTAGCTCTT
268879 TTTTTTTTCACAA
1 TTTTTTTTCACAA
268892 TTTTTTTTCACAA
1 TTTTTTTTCACAA
268905 TTTTTTTTTCA-AA
1 -TTTTTTTTCACAA
268918 TTTTTTTTCACAA
1 TTTTTTTTCACAA
268931 CTTGATATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.27
13 17 0.46
14 10 0.27
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:268919 original size:26 final size:27
Alignment explanation
Indices: 268878--268930 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
268868 AACTAGCTCT
268878 TTTTTTTTTCACAATTTTTTTTCACAA
1 TTTTTTTTTCACAATTTTTTTTCACAA
268905 TTTTTTTTTCA-AATTTTTTTTCACAA
1 TTTTTTTTTCACAATTTTTTTTCACAA
268931 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTTTTCACAATTTTTTTTCACAA
Found at i:268989 original size:12 final size:12
Alignment explanation
Indices: 268972--269014 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
268962 AACCAAAAGT
268972 TTTTTTTTTGAA
1 TTTTTTTTTGAA
268984 TTTTTTTTTGAA
1 TTTTTTTTTGAA
* *
268996 TTTTTTTTCGAG
1 TTTTTTTTTGAA
269008 TTTTTTT
1 TTTTTTT
269015 GAGAAACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:270831 original size:10 final size:10
Alignment explanation
Indices: 270816--270853 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
270806 ATTTGGGAAT
270816 TGGTATGAAA
1 TGGTATGAAA
*
270826 TGGTATGGAAT
1 TGGTAT-GAAA
270837 TGGTATGAAA
1 TGGTATGAAA
270847 TGGTATG
1 TGGTATG
270854 GTATTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (10 bp):
TGGTATGAAA
Found at i:270837 original size:21 final size:21
Alignment explanation
Indices: 270811--270873 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
270801 TTGGTATTTG
270811 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
270832 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* * *
270853 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
270874 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:273614 original size:20 final size:21
Alignment explanation
Indices: 273580--273637 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
273570 AGGTGGAATT
* **
273580 GAGCTC-AAGTGAGCTGATTG
1 GAGCTCGAATTGAGCTGAAGG
273600 GAG-TCGAATTGAGCT-AAGG
1 GAGCTCGAATTGAGCTGAAGG
*
273619 GAGCTGGAATTGAGCTGAA
1 GAGCTCGAATTGAGCTGAA
273638 ATTAGCTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 7 0.23
20 22 0.71
21 2 0.06
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.22
Consensus pattern (21 bp):
GAGCTCGAATTGAGCTGAAGG
Found at i:274547 original size:20 final size:20
Alignment explanation
Indices: 274522--274564 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
274512 AAAAGAAAAG
274522 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
274542 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
274562 AAA
1 AAA
274565 ACAAGATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:276188 original size:13 final size:13
Alignment explanation
Indices: 276167--276201 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
276157 ATAAGTTGCT
*
276167 GTTAGTTAAATAA
1 GTTAATTAAATAA
276180 GTTAATTAAATAA
1 GTTAATTAAATAA
276193 GTTAATTAA
1 GTTAATTAA
276202 TTTGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:276458 original size:23 final size:23
Alignment explanation
Indices: 276428--276490 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
276418 TTTTCCAGAT
276428 GAATTTAATGTATGTCTT-TGGCC
1 GAATTTAATGTATGT-TTCTGGCC
276451 GAATTTAATGTATGTTTCTGGCC
1 GAATTTAATGTATGTTTCTGGCC
*
276474 GAATTTAATGCATGTTT
1 GAATTTAATGTATGTTT
276491 TAAAGGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (23 bp):
GAATTTAATGTATGTTTCTGGCC
Done.