Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004255.1 Hibiscus syriacus cultivar Beakdansim tig00009326_pilon, whole genome shotgun sequence
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: 170008
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:713 original size:41 final size:41
Alignment explanation
Indices: 592--718 Score: 114
Period size: 42 Copynumber: 3.0 Consensus size: 41
582 TACATTTGTA
* * * * *
592 GCGTTTGTTTCCAGAACGCCACTAATGAACTGATCTTTTGTG
1 GCGTTTGTTT-CAAAACGCCGCTAATGACCTGACCTTTTGCG
* * *
634 ACGTTTG-TTCAAACAACGCCGCTAATGACATAACCTTTTGCG
1 GCGTTTGTTTC-AA-AACGCCGCTAATGACCTGACCTTTTGCG
* *
676 GCGTTTGTTTCAAAAGGCCGCTAAATGACCTGA-CTTTTACG
1 GCGTTTGTTTCAAAACGCCGCT-AATGACCTGACCTTTTGCG
717 GC
1 GC
719 ATTTATACGA
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 20 0.29
42 44 0.65
43 3 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (41 bp):
GCGTTTGTTTCAAAACGCCGCTAATGACCTGACCTTTTGCG
Found at i:936 original size:106 final size:103
Alignment explanation
Indices: 736--940 Score: 347
Period size: 106 Copynumber: 2.0 Consensus size: 103
726 CGAAAAGTGC
*
736 CGCTAATATCATGGTATATAGCGGGTTTTATTTACAAACGTCGCTAAATGACCAACCTATGCGGC
1 CGCTAATATCATGGTATATAGCGGGTTTTATTTACAAACGTCACTAAATGACCAACCTATGCGGC
*
801 ATTTGGAAAATAAACGCTGCTAAATGTCCTAATTGGTT
66 ATTTGGAAAATAAACGCCGCTAAATGTCCTAATTGGTT
*
839 CGCTACATATCATGGTATATAGCGGCGTTTTATTTACAAACGTCACTAAATGACTAACCTATTGC
1 CGCTA-ATATCATGGTATATAGCGG-GTTTTATTTACAAACGTCACTAAATGACCAACCTA-TGC
*
904 GGCATTTGGGAAATAAACGCCGCTAAATGTCCTAATT
63 GGCATTTGGAAAATAAACGCCGCTAAATGTCCTAATT
941 TGTTGGGGCG
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
103 5 0.05
104 19 0.20
105 33 0.35
106 38 0.40
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (103 bp):
CGCTAATATCATGGTATATAGCGGGTTTTATTTACAAACGTCACTAAATGACCAACCTATGCGGC
ATTTGGAAAATAAACGCCGCTAAATGTCCTAATTGGTT
Found at i:7598 original size:22 final size:23
Alignment explanation
Indices: 7558--7601 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
7548 AATTAGTAAT
*
7558 AAAATATTTAATAATTTAATATA
1 AAAATATTTAATAAGTTAATATA
*
7581 AAAATATTT-TTAAGTTAATAT
1 AAAATATTTAATAAGTTAATAT
7602 GTATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAATATTTAATAAGTTAATATA
Found at i:7609 original size:25 final size:24
Alignment explanation
Indices: 7556--7610 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
7546 TAAATTAGTA
*
7556 ATAAAATATTTAATAATTTAATAT
1 ATAAAATATTTAATAAGTTAATAT
*
7580 A-AAAATATTT-TTAAGTTAATATGT
1 ATAAAATATTTAATAAGTTAATA--T
7604 ATAAAAT
1 ATAAAAT
7611 TATGAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.35
23 9 0.35
24 3 0.12
25 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
ATAAAATATTTAATAAGTTAATAT
Found at i:8636 original size:31 final size:31
Alignment explanation
Indices: 8588--8681 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
8578 TTTTGGTCAC
*
8588 ACATTATTGTTTTTATTAAATTTT-GATCGCTT
1 ACATTATTG-TTTTATTAAATTTTAG-TCACTT
*
8620 ACATTATTGTTTTATTAAGTTTTAGTCACTT
1 ACATTATTGTTTTATTAAATTTTAGTCACTT
* * **
8651 ACGTTATCGTTTTATTAAGCTTTAGTCACTT
1 ACATTATTGTTTTATTAAATTTTAGTCACTT
8682 CACTTGGATA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
31 46 0.82
32 10 0.18
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (31 bp):
ACATTATTGTTTTATTAAATTTTAGTCACTT
Found at i:12694 original size:15 final size:15
Alignment explanation
Indices: 12670--12706 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12660 AGCCGAAGAT
* *
12670 TCAATTGCATCATCA
1 TCAATAGCATCAACA
12685 TCAATAGCATCAACA
1 TCAATAGCATCAACA
12700 TCAATAG
1 TCAATAG
12707 TTGCAGGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (15 bp):
TCAATAGCATCAACA
Found at i:13579 original size:21 final size:21
Alignment explanation
Indices: 13553--13601 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
13543 TACCATATTG
*
13553 AGATTAATTACCATAATAGGT
1 AGATTAATTACCATAATAGGA
**
13574 AGATTAATTACCATGGTAGGA
1 AGATTAATTACCATAATAGGA
13595 AGATTAA
1 AGATTAA
13602 GTGTTAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
AGATTAATTACCATAATAGGA
Found at i:19136 original size:18 final size:19
Alignment explanation
Indices: 19096--19139 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
19086 TTTGGTTCAC
*
19096 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
19116 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
19134 GGAATA
1 GGAATA
19140 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:19910 original size:114 final size:114
Alignment explanation
Indices: 19739--19963 Score: 432
Period size: 114 Copynumber: 2.0 Consensus size: 114
19729 CACCCTAAGG
*
19739 GTCTCACCATGAGTACAACTCTATTGTGTATCTACCCACACTAATTGTAACTACTTTATATTATC
1 GTCTCACCATGAGTACAACTCTATTGTGTATCTACCCACACTAACTGTAACTACTTTATATTATC
19804 TAAATGTAACACTAACTGTAACATTAAAACTACTGCACATTTTCTGCAT
66 TAAATGTAACACTAACTGTAACATTAAAACTACTGCACATTTTCTGCAT
19853 GTCTCACCATGAGTACAACTCTATTGTGTATCTACCCACACTAACTGTAACTACTTTATATTATC
1 GTCTCACCATGAGTACAACTCTATTGTGTATCTACCCACACTAACTGTAACTACTTTATATTATC
*
19918 TAAATGTAACACTAACTGTAACATTAACACTACTGCACATTTTCTG
66 TAAATGTAACACTAACTGTAACATTAAAACTACTGCACATTTTCTG
19964 AATTGTTGTG
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (114 bp):
GTCTCACCATGAGTACAACTCTATTGTGTATCTACCCACACTAACTGTAACTACTTTATATTATC
TAAATGTAACACTAACTGTAACATTAAAACTACTGCACATTTTCTGCAT
Found at i:21872 original size:21 final size:20
Alignment explanation
Indices: 21825--21864 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
21815 GATTGCTCAG
*
21825 AGGGAACCGATTCCCCCCCA
1 AGGGTACCGATTCCCCCCCA
21845 AGGGGGTACCGATTCCCCCC
1 A--GGGTACCGATTCCCCCC
21865 TGAAGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
22 16 0.94
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (20 bp):
AGGGTACCGATTCCCCCCCA
Found at i:29733 original size:17 final size:17
Alignment explanation
Indices: 29708--29741 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29698 TTGAATATTT
*
29708 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
29725 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
29742 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:34888 original size:21 final size:20
Alignment explanation
Indices: 34844--34917 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
34834 GCAGCCTTTG
*
34844 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
**
34864 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
34885 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACA-ACAGGA
34905 TGCATCGATGCAC
1 TGCATCGATGCAC
34918 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:35002 original size:13 final size:14
Alignment explanation
Indices: 34975--35007 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
34965 GATGCACTAG
*
34975 TGCATGTGCATGGA
1 TGCATGTGCAGGGA
34989 TGCAT-TGCAGGGA
1 TGCATGTGCAGGGA
35002 TGCATG
1 TGCATG
35008 GATGCACTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.27
Consensus pattern (14 bp):
TGCATGTGCAGGGA
Found at i:35007 original size:21 final size:21
Alignment explanation
Indices: 34938--35057 Score: 129
Period size: 21 Copynumber: 5.7 Consensus size: 21
34928 CGGTGTTTGA
*
34938 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * *
34958 GTACATCGATGCACT--AGTGCAT
1 GTGCATGGATGCACTGCAG-G--G
*
34980 GTGCATGGATGCATTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
35001 ATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
35022 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
35043 GTGCATGAATGCACT
1 GTGCATGGATGCACT
35058 TTGACACCCT
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
18 1 0.01
20 13 0.16
21 53 0.65
22 12 0.15
23 1 0.01
24 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:35158 original size:29 final size:29
Alignment explanation
Indices: 35126--35188 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
35116 GAAACCTTTT
35126 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
35156 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
35186 AAA
1 AAA
35189 TCATTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:35184 original size:30 final size:30
Alignment explanation
Indices: 35137--35196 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
35127 AAACTTTGAA
35137 TAAATTCAATTAAGTCCAAAAAT-ATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
35166 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
35197 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:38465 original size:20 final size:20
Alignment explanation
Indices: 38436--38505 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
38426 GCAGCCTTCG
* *
38436 TGCATGGATGCACATCAGGA
1 TGCATCGATGCACACCAGGA
**
38456 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-ACCAGGA
***
38477 TGCATCGATGCACGGAAGGA
1 TGCATCGATGCACACCAGGA
38497 TGCATCGAT
1 TGCATCGAT
38506 ACACTAAGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACACCAGGA
Found at i:38577 original size:22 final size:23
Alignment explanation
Indices: 38544--38586 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
38534 ATGGATGCAC
*
38544 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCCATGCACTAG
38567 TGCA-GGTGCATCCATGCACT
1 TGCATGGTGCATCCATGCACT
38587 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCCATGCACTAG
Found at i:38604 original size:21 final size:20
Alignment explanation
Indices: 38533--38628 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 20
38523 TGTTTGAGTA
*
38533 CATGGATGCACTGCATGGTG
1 CATGGATGCACTGCAGGGTG
*
38553 CATCGATGCACTAGTGCA-GGTG
1 CATGGATGCAC---TGCAGGGTG
**
38575 CATCCATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGG-TG
38596 CATGGATGCACTGCAGGGGTG
1 CATGGATGCACTGCA-GGGTG
38617 CATGGATGCACT
1 CATGGATGCACT
38629 TTGACACCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.06
20 12 0.18
21 29 0.44
22 17 0.26
23 4 0.06
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (20 bp):
CATGGATGCACTGCAGGGTG
Found at i:38729 original size:29 final size:29
Alignment explanation
Indices: 38708--38765 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
38698 AAACTTTGAA
*
38708 TAAATTCAATT-AAATCTAAAAACATTTTG
1 TAAATTCAATTCAAATCCAAAAACA-TTTG
38737 TAAATTCAATTCAAATCCAAAAACCATTT
1 TAAATTCAATTCAAATCCAAAAA-CATTT
38766 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAATCCAAAAACATTTG
Found at i:38759 original size:30 final size:30
Alignment explanation
Indices: 38708--38767 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
38698 AAACTTTGAA
*
38708 TAAATTCAATTAAATCTAAAAA-CATTTTG
1 TAAATTCAATTAAATCCAAAAACCATTTTG
38737 TAAATTCAATTCAAATCCAAAAACCATTTTG
1 TAAATTCAATT-AAATCCAAAAACCATTTTG
38768 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAATCCAAAAACCATTTTG
Found at i:45565 original size:15 final size:15
Alignment explanation
Indices: 45545--45576 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
45535 ACACAAGACT
45545 AAGATTAAGACAATG
1 AAGATTAAGACAATG
*
45560 AAGATTAAGATAATG
1 AAGATTAAGACAATG
45575 AA
1 AA
45577 AATAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (15 bp):
AAGATTAAGACAATG
Found at i:48177 original size:34 final size:34
Alignment explanation
Indices: 48130--48197 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
48120 GTATTAACAT
* **
48130 TTCTAAATCGAGTGATTATAGGTTTAAAAAAATG
1 TTCTAAATAGAGTGACCATAGGTTTAAAAAAATG
*
48164 TTCTAGATAGAGTGACCATAGGTTTAAAAAAATG
1 TTCTAAATAGAGTGACCATAGGTTTAAAAAAATG
48198 AAACACTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (34 bp):
TTCTAAATAGAGTGACCATAGGTTTAAAAAAATG
Found at i:59671 original size:21 final size:22
Alignment explanation
Indices: 59645--59741 Score: 87
Period size: 21 Copynumber: 4.6 Consensus size: 22
59635 ATGAATAAGT
59645 AAATCGCAATGCGAAT-TTGGA
1 AAATCGCAATGCGAATATTGGA
*
59666 AAATCGCAATGCG-ATACT-GA
1 AAATCGCAATGCGAATATTGGA
** * * **
59686 CTATCGCAACGCG-ATAATACA
1 AAATCGCAATGCGAATATTGGA
59707 AAATCGCAATGCGAAT-TTGGA
1 AAATCGCAATGCGAATATTGGA
*
59728 AAATTGCAATGCGA
1 AAATCGCAATGCGA
59742 TACTGACTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 18 0.30
21 40 0.67
22 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.22
Consensus pattern (22 bp):
AAATCGCAATGCGAATATTGGA
Found at i:59711 original size:62 final size:62
Alignment explanation
Indices: 59645--59823 Score: 263
Period size: 62 Copynumber: 2.9 Consensus size: 62
59635 ATGAATAAGT
59645 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
*
59707 AAATCGCAATGCGAATTTGGAAAATTGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
* * *** * *
59769 AAATCGCAACGCG-ATACT-GACTTTCGCAACGCGATACTGACTTTCGCAACGCGAT
1 AAATCGCAATGCGAAT-TTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGAT
59824 TCTGACTTTC
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
61 33 0.31
62 74 0.69
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (62 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
Found at i:59761 original size:20 final size:20
Alignment explanation
Indices: 59733--59864 Score: 149
Period size: 20 Copynumber: 6.5 Consensus size: 20
59723 TTGGAAAATT
*
59733 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* *
59753 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
*
59774 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
*
59794 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
* *
59814 GCAACGCGATTCTGACTTTC
1 GCAACGCGATACTGACTATC
* *
59834 GCAACGAGATTCTGACTATC
1 GCAACGCGATACTGACTATC
*
59854 GCAACGAGATA
1 GCAACGCGATA
59865 ATACAGAATC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 80 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:59776 original size:21 final size:21
Alignment explanation
Indices: 59688--59784 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
59678 GATACTGACT
59688 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
59709 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-ATACAAA
* * * *
59730 ATTGCAATGCGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
59750 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
59771 ATCGCAACGCGATA
1 ATCGCAACGCGATA
59785 CTGACTTTCG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.03
20 14 0.24
21 41 0.71
22 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:59803 original size:41 final size:42
Alignment explanation
Indices: 59727--59839 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 42
59717 GCGAATTTGG
* * *
59727 AAAATTGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
*
59768 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
59810 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
59840 AGATTCTGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
40 27 0.42
41 35 0.55
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:60629 original size:24 final size:24
Alignment explanation
Indices: 60602--60655 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
60592 GTATTCGAAA
*
60602 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
60626 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
60650 TTTGAT
1 TTTGAT
60656 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:60847 original size:12 final size:12
Alignment explanation
Indices: 60830--60854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60820 ATATAATCCT
60830 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60842 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60854 G
1 G
60855 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:63178 original size:20 final size:19
Alignment explanation
Indices: 63150--63204 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
63140 CAATCATCTT
*
63150 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
63170 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
63189 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
63205 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:63192 original size:19 final size:17
Alignment explanation
Indices: 63157--63260 Score: 76
Period size: 19 Copynumber: 6.1 Consensus size: 17
63147 CTTAATGTCT
*
63157 ATCGCAACGCGGAAATGA
1 ATCGCAATGC-GAAATGA
63175 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
63196 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
63210 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
63229 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
63243 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
63260 A
1 A
63261 AATCGTAACG
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.23
16 10 0.14
17 12 0.17
19 21 0.30
20 9 0.13
21 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:63214 original size:14 final size:14
Alignment explanation
Indices: 63195--63249 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
63185 GCGAAATGAA
63195 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
63209 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
63228 AATCGCAACGAGAG
1 AATCGCAACGAGAG
63242 AATCGCAA
1 AATCGCAA
63250 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:63219 original size:33 final size:33
Alignment explanation
Indices: 63177--63303 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
63167 GGAAATGACT
63177 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
63210 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
63243 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
63276 ATCGCAAAGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
63304 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:63345 original size:19 final size:19
Alignment explanation
Indices: 63303--63379 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
63293 AAATTGCAAC
* *
63303 GCGAATTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
63322 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
63341 GCGATTTT-G--T--CGTA
1 GCGATTTTAGTTTCGCGTT
63355 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
63374 GCGATT
1 GCGATT
63380 CTCTCGTTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.23
16 1 0.02
17 1 0.02
18 1 0.02
19 34 0.71
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:63369 original size:33 final size:33
Alignment explanation
Indices: 63319--63444 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
63309 TTAGTTTCGT
* *
63319 GTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
*
63352 GTAGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
63385 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
**
63418 GTTGCGATTTTCATTTCGTATTGCGAT
1 GTTGCGATTTTCATTTCGCGTTGCGAT
63445 AGTCATTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
Found at i:63408 original size:19 final size:19
Alignment explanation
Indices: 63313--63435 Score: 80
Period size: 19 Copynumber: 7.3 Consensus size: 19
63303 GCGAATTTAG
*
63313 TTTCGTGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
63331 GTTTCGCGTTGCGA-TTT--
1 -TTTCGCGTTGCGATTTTCA
* *
63348 TGT--CGTAGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
63365 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
63381 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
63398 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
63414 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
63431 TTTCG
1 TTTCG
63436 TATTGCGATA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 27 0.34
15 3 0.04
16 8 0.10
17 8 0.10
18 3 0.04
19 31 0.39
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:63444 original size:19 final size:17
Alignment explanation
Indices: 63350--63436 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 17
63340 TGCGATTTTG
*
63350 TCGTAGCGATTTTCATT
1 TCGTTGCGATTTTCATT
*
63367 TCGCGTTGCGA--TTC-TC
1 T--CGTTGCGATTTTCATT
63383 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
*
63400 TCGCGTTGCGA--TTC-TC
1 T--CGTTGCGATTTTCATT
63416 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
63433 TCGT
1 TCGT
63437 ATTGCGATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 16 0.29
16 10 0.18
17 14 0.25
19 15 0.27
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (17 bp):
TCGTTGCGATTTTCATT
Found at i:63570 original size:14 final size:15
Alignment explanation
Indices: 63551--63588 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
63541 CATCAATTAA
63551 ACAAATCAA-CTTTT
1 ACAAATCAATCTTTT
63565 ACAAAT-AATCTTTT
1 ACAAATCAATCTTTT
63579 ACAAATCAAT
1 ACAAATCAAT
63589 TAAACAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCTTTT
Found at i:65003 original size:21 final size:21
Alignment explanation
Indices: 64937--65003 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
64927 GTGAATCGGG
*
64937 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
64957 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
64979 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
65000 CTCT
1 CTCT
65004 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:65585 original size:94 final size:94
Alignment explanation
Indices: 65448--65751 Score: 485
Period size: 94 Copynumber: 3.3 Consensus size: 94
65438 GAATAGTTTC
* * *
65448 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAATTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTC
65513 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
65542 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTC
65607 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
65636 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGAAAAATAC-AACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGAAAAATACTAACTT
*
65699 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
65725 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
65752 AAGCAATCTA
Statistics
Matches: 201, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
89 41 0.20
93 33 0.16
94 127 0.63
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:67452 original size:20 final size:20
Alignment explanation
Indices: 67427--67489 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
67417 TTTTGGTTGA
67427 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
67447 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
67466 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
67487 AAT
1 AAT
67490 CGCAACGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:67493 original size:14 final size:14
Alignment explanation
Indices: 67474--67510 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
67464 GGAAATGACT
67474 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
67488 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
67502 ATCGCAACG
1 ATCGCAACG
67511 CGAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:67561 original size:33 final size:34
Alignment explanation
Indices: 67487--67563 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
67477 GCAACGAGAG
* *
67487 AATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 AATCGCAATGAGAGAATCGCAACACGAAATGAAA
67521 AATCGCAATGAGAGAATCGCAACACGAAATG-AA
1 AATCGCAATGAGAGAATCGCAACACGAAATGAAA
67554 AATCGCAATG
1 AATCGCAATG
67564 CGATTTTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 12 0.29
34 29 0.71
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (34 bp):
AATCGCAATGAGAGAATCGCAACACGAAATGAAA
Found at i:67664 original size:20 final size:19
Alignment explanation
Indices: 67562--67665 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
67552 AAAATCGCAA
** *
67562 TGCGATTTTGGTTTCGCGA
1 TGCGATTTTCATTTCGCGT
*
67581 TCCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
67600 TGGGATTTTCATTTCGTGT
1 TGCGATTTTCATTTCGCGT
*
67619 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
67633 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
67653 TGCGATTTTCATT
1 TGCGATTTTCATT
67666 CTCGAAACTA
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.14
16 2 0.03
17 3 0.05
19 36 0.55
20 15 0.23
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:68234 original size:20 final size:19
Alignment explanation
Indices: 68222--68313 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 19
68212 ATTCGTATTG
68222 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGA-TTACGTAT
* *
68242 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTACGT-AT
*
68263 TCGCATTGCGATTTACTTAAT
1 TCGCATTGCGA-TTACGT-AT
*
68284 T-GCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TTACGTAT
68303 TCGCATTGCGA
1 TCGCATTGCGA
68314 ATTATGAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 3 0.05
20 38 0.60
21 22 0.35
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (19 bp):
TCGCATTGCGATTACGTAT
Found at i:68292 original size:41 final size:40
Alignment explanation
Indices: 68222--68313 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
68212 ATTCGTATTG
*
68222 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACCT-AT
* * *
68263 TCGCATTGCGATTTACTTAATT-GCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACCTAT
68303 TCGCATTGCGA
1 TCGCATTGCGA
68314 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 13 0.28
41 30 0.65
42 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTAT
Found at i:68334 original size:21 final size:21
Alignment explanation
Indices: 68310--68365 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
68300 TATTCGCATT
*
68310 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
68331 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
68351 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
68366 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:68374 original size:21 final size:21
Alignment explanation
Indices: 68303--68375 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
68293 ATTTACGTAT
* *
68303 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
68324 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
68344 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
68365 TTGCATTGCGA
1 TCGCAATGCGA
68376 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:68388 original size:41 final size:42
Alignment explanation
Indices: 68281--68461 Score: 119
Period size: 41 Copynumber: 4.4 Consensus size: 42
68271 CGATTTACTT
* * *
68281 AATTGCGTTGCGAT--TTACGTATTCGCATTGCGAATTATGAA
1 AATTGCATTGCGATAGTCACGTA-TCGCATTGCGAATTAGGAA
* ** *
68322 AATCGCAACGCGA-A-T-ACGTAAATCGCAATGCGAATTAGGAA
1 AATTGCATTGCGATAGTCACGT--ATCGCATTGCGAATTAGGAA
****
68363 AATTGCATTGCGATAGTCA-GTATCGCATTGC-AATTTTCCA
1 AATTGCATTGCGATAGTCACGTATCGCATTGCGAATTAGGAA
* * *
68403 AATTCGCATTGCGAT--TTACTTATTCGCATTGCGAATTGGGAA
1 AATT-GCATTGCGATAGTCACGTA-TCGCATTGCGAATTAGGAA
*
68445 AATCGCATTGCGATAGT
1 AATTGCATTGCGATAGT
68462 AATAATCGCG
Statistics
Matches: 107, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
39 2 0.02
40 15 0.14
41 75 0.70
42 10 0.09
43 4 0.04
44 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
AATTGCATTGCGATAGTCACGTATCGCATTGCGAATTAGGAA
Found at i:68389 original size:82 final size:83
Alignment explanation
Indices: 68303--68479 Score: 191
Period size: 82 Copynumber: 2.2 Consensus size: 83
68293 ATTTACGTAT
*
68303 TCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAAT
1 TCGCATTGCGAATTATCCAAAATCGCAACGCGATATAC-TAAATCGCAATGCGAATTAGGAAAAT
* *
68366 TGCATTGCGATAGTCAGT-A
65 CGCATTGCGATAGT-AATAA
* * ** * * * * *
68385 TCGCATTGC-AATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATC
1 TCGCATTGCGAATTATCCAAAATCGCAACGCGATATACTAAATCGCAATGCGAATTAGGAAAATC
68449 GCATTGCGATAGTAATAA
66 GCATTGCGATAGTAATAA
*
68467 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
68480 CTGGAAACTG
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
81 7 0.09
82 65 0.83
83 6 0.08
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (83 bp):
TCGCATTGCGAATTATCCAAAATCGCAACGCGATATACTAAATCGCAATGCGAATTAGGAAAATC
GCATTGCGATAGTAATAA
Found at i:68476 original size:41 final size:41
Alignment explanation
Indices: 68303--68479 Score: 139
Period size: 41 Copynumber: 4.3 Consensus size: 41
68293 ATTTACGTAT
* **
68303 TCGCATTGCGAATTATGAAAATCGCAACGCGAATACGT-A-AA
1 TCGCATTGCGAATTAGGAAAATCGCATTGCG-ATA-GTAATAA
* * *
68344 TCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGT-A
1 TCGCATTGCGAATTAGGAAAATCGCATTGCGATAGT-AATAA
*** * * * *
68385 TCGCATTGC-AATTTTCCAAATTCGCATTGCGAT-TTACTTAT
1 TCGCATTGCGAA-TTAGGAAAATCGCATTGCGATAGTA-ATAA
*
68426 TCGCATTGCGAATTGGGAAAATCGCATTGCGATAGTAATAA
1 TCGCATTGCGAATTAGGAAAATCGCATTGCGATAGTAATAA
*
68467 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
68480 CTGGAAACTG
Statistics
Matches: 105, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
39 3 0.03
40 7 0.07
41 91 0.87
42 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (41 bp):
TCGCATTGCGAATTAGGAAAATCGCATTGCGATAGTAATAA
Found at i:71379 original size:3 final size:3
Alignment explanation
Indices: 71368--71431 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
71358 TTTTTTATCG
** *
71368 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
71413 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
71432 CATATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:71400 original size:32 final size:32
Alignment explanation
Indices: 71362--71429 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
71352 CGGGTTTTTT
*
71362 TTATCGTTATTTTATTATTATTATTATTA-TTA
1 TTATCGTTATCTTATTATT-TTATTATTATTTA
71394 TTATCGTTATCTTATTATTTTATTATTATTTA
1 TTATCGTTATCTTATTATTTTATTATTATTTA
71426 TTAT
1 TTAT
71430 TACATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.66
Consensus pattern (32 bp):
TTATCGTTATCTTATTATTTTATTATTATTTA
Found at i:71437 original size:28 final size:28
Alignment explanation
Indices: 71377--71442 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
71367 GTTATTTTAT
* *
71377 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
71406 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
71434 TATTTTTTT
1 TATTATTTT
71443 GCAGGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:75332 original size:31 final size:32
Alignment explanation
Indices: 75296--75357 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
75286 ATTTTACATG
75296 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
75327 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
75358 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:77435 original size:12 final size:11
Alignment explanation
Indices: 77420--77489 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 11
77410 AAAATCAAAG
77420 AGAAAAGAGCAA
1 AGAAAA-AGCAA
77432 AG-AAAA--AA
1 AGAAAAAGCAA
* *
77440 ACAAAGAGCAA
1 AGAAAAAGCAA
*
77451 AGAGAAAATCAA
1 AGA-AAAAGCAA
*
77463 AGCAAAAATCAA
1 AG-AAAAAGCAA
77475 AGAAAAAGCAA
1 AGAAAAAGCAA
77486 AGAA
1 AGAA
77490 CAAAAAGAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 1 0.02
11 19 0.40
12 20 0.43
13 1 0.02
ACGTcount: A:0.70, C:0.10, G:0.17, T:0.03
Consensus pattern (11 bp):
AGAAAAAGCAA
Found at i:77444 original size:26 final size:27
Alignment explanation
Indices: 77402--77454 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
77392 CAATCAAAAA
77402 CAAAGAAAAAAATCAAAGAGAAAAGAG
1 CAAAGAAAAAAATCAAAGAGAAAAGAG
*
77429 CAAAGAAAAAAA-CAAAGAGCAAAGAG
1 CAAAGAAAAAAATCAAAGAGAAAAGAG
77455 AAAATCAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.70, C:0.09, G:0.19, T:0.02
Consensus pattern (27 bp):
CAAAGAAAAAAATCAAAGAGAAAAGAG
Found at i:77447 original size:19 final size:19
Alignment explanation
Indices: 77423--77464 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
77413 ATCAAAGAGA
77423 AAAGAGCAAAGAAAAAAAC
1 AAAGAGCAAAGAAAAAAAC
* *
77442 AAAGAGCAAAGAGAAAATC
1 AAAGAGCAAAGAAAAAAAC
77461 AAAG
1 AAAG
77465 CAAAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.69, C:0.10, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAGAGCAAAGAAAAAAAC
Found at i:77480 original size:11 final size:11
Alignment explanation
Indices: 77448--77489 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
77438 AAACAAAGAG
77448 CAAAGAGAAAAT
1 CAAAGA-AAAAT
77460 CAAAGCAAAAAT
1 CAAAG-AAAAAT
*
77472 CAAAGAAAAAG
1 CAAAGAAAAAT
77483 CAAAGAA
1 CAAAGAA
77490 CAAAAAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.69, C:0.12, G:0.14, T:0.05
Consensus pattern (11 bp):
CAAAGAAAAAT
Found at i:78682 original size:12 final size:12
Alignment explanation
Indices: 78665--78739 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 12
78655 GATTGAGAAA
78665 CATACATCAACT
1 CATACATCAACT
*
78677 CATACATACATATAT
1 CATACAT-CA-A-CT
78692 ACATACATCAACT
1 -CATACATCAACT
*
78705 CATACATACATATAT
1 CATACAT-CA-A-CT
78720 ACATACATCAACT
1 -CATACATCAACT
78733 CATACAT
1 CATACAT
78740 ATATATATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
12 21 0.41
13 6 0.12
14 4 0.08
15 6 0.12
16 14 0.27
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (12 bp):
CATACATCAACT
Found at i:78695 original size:28 final size:28
Alignment explanation
Indices: 78664--78767 Score: 190
Period size: 28 Copynumber: 3.7 Consensus size: 28
78654 AGATTGAGAA
78664 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
78692 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
*
78720 ACATACATCAACTCATACATATATATAT
1 ACATACATCAACTCATACATACATATAT
*
78748 ACATACATCAACACATACAT
1 ACATACATCAACTCATACAT
78768 GCATGTTACA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 74 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (28 bp):
ACATACATCAACTCATACATACATATAT
Found at i:78749 original size:12 final size:12
Alignment explanation
Indices: 78678--78755 Score: 75
Period size: 12 Copynumber: 5.8 Consensus size: 12
78668 ACATCAACTC
78678 ATACATACATAT
1 ATACATACATAT
78690 ATACATACATCAACT
1 ATACATACAT--A-T
78705 CATACATACATAT
1 -ATACATACATAT
78718 ATACATACATCAACT
1 ATACATACAT--A-T
*
78733 CATACATATATAT
1 -ATACATACATAT
78746 ATACATACAT
1 ATACATACAT
78756 CAACACATAC
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
12 29 0.52
13 2 0.04
14 4 0.07
15 2 0.04
16 19 0.34
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (12 bp):
ATACATACATAT
Found at i:78767 original size:4 final size:4
Alignment explanation
Indices: 78677--78755 Score: 66
Period size: 4 Copynumber: 21.8 Consensus size: 4
78667 TACATCAACT
* *
78677 CATA CATA CATA TATA CATA CAT- CA-A C-T- CATA CATA CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
78721 CATA CAT- CA-A C-T- CATA CATA TATA TATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
78756 CAACACATAC
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
2 2 0.03
3 8 0.13
4 51 0.84
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:79178 original size:36 final size:35
Alignment explanation
Indices: 79123--79259 Score: 161
Period size: 36 Copynumber: 3.9 Consensus size: 35
79113 TTTTGAGAAT
79123 TTTAAAACAAATTTTTGTCTCGCTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* *
79159 TTTCAAAGCAAATTTTGTCTCGCTTGAGACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
79196 -TAAAAAC-AATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* *
79229 TCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACA
79260 TTTTTCCTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
33 3 0.04
34 20 0.24
35 10 0.12
36 41 0.48
37 11 0.13
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:79210 original size:70 final size:72
Alignment explanation
Indices: 79126--79259 Score: 193
Period size: 70 Copynumber: 1.9 Consensus size: 72
79116 TGAGAATTTT
* * * *
79126 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCAAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
79190 GCTTTCTA
65 GCTTTCTA
*
79198 AAAAC-AA-TTTTGTCTCGTTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
79260 TTTTTCCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 47 0.84
71 4 0.07
72 5 0.09
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTA
Found at i:79351 original size:105 final size:103
Alignment explanation
Indices: 79226--79471 Score: 293
Period size: 105 Copynumber: 2.4 Consensus size: 103
79216 TTGAGACAAA
* * * *
79226 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTG
1 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
* *
79291 ATTCAC-TTAAAACAAAATTAATCTCACCTT-AGATTGTTGT
66 ATTCACACT-AAACAAAATTAATCTCA-CTTGAGATCG-T-T
* *
79331 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
* * *
79396 TTTCACACTAAACAAAGTTGATCTCACTTGAGATCGTT
66 ATTCACACTAAACAAAATTAATCTCACTTGAGATCGTT
** *
79434 TTC-TCAAAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 TTCTTTTAAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
79472 TCTAAAAACA
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
102 27 0.22
103 7 0.06
104 4 0.03
105 84 0.68
106 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (103 bp):
TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
ATTCACACTAAACAAAATTAATCTCACTTGAGATCGTT
Found at i:79462 original size:36 final size:36
Alignment explanation
Indices: 79417--79536 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
79407 ACAAAGTTGA
**
79417 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
*
79453 TCTCGCTTGAGACAATTTCTCTAAAAACAAACTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
79489 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
79523 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
79537 TCATTTTCTC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 41 0.58
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:79829 original size:29 final size:26
Alignment explanation
Indices: 79795--79862 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 26
79785 CTCTTGAGAT
79795 AAATCTTTGAGTCTGTTCCTTTTGAATAA
1 AAATCTTTGAGTCTGTTCCTTTTG---AA
*
79824 AAATCTTTGAGT-TGTTTCTTTTGAA
1 AAATCTTTGAGTCTGTTCCTTTTGAA
79849 AAATCTTTGAGTCT
1 AAATCTTTGAGTCT
79863 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 14 0.38
26 1 0.03
28 10 0.27
29 12 0.32
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (26 bp):
AAATCTTTGAGTCTGTTCCTTTTGAA
Found at i:79856 original size:25 final size:26
Alignment explanation
Indices: 79781--79875 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 26
79771 TCTGGAGACA
*
79781 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGA-A-AAATCTTTGAGTCT
*
79809 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTG---AAAAATCTTTGAGTCT
79837 GTTTCTTTTGAAAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAATCTTTGAGTCT
* *
79863 ATTTATTTTGAAA
1 GTTTCTTTTGAAA
79876 CAAAGTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 14 0.24
26 12 0.21
28 18 0.31
29 12 0.21
30 1 0.02
31 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (26 bp):
GTTTCTTTTGAAAAATCTTTGAGTCT
Found at i:79992 original size:27 final size:27
Alignment explanation
Indices: 79962--80013 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
79952 ATTTTGTGAA
79962 AAAAAATCTTTGAGATTGTTTCTTTTC
1 AAAAAATCTTTGAGATTGTTTCTTTTC
*
79989 AAAAAATCTTTGAGTTTGTTTCTTT
1 AAAAAATCTTTGAGATTGTTTCTTT
80014 GGAAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (27 bp):
AAAAAATCTTTGAGATTGTTTCTTTTC
Found at i:80056 original size:37 final size:37
Alignment explanation
Indices: 80006--80127 Score: 123
Period size: 37 Copynumber: 3.5 Consensus size: 37
79996 CTTTGAGTTT
80006 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
80043 GTTTCTTTTGAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
80073 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * *
80110 ATTTCTTTTGAAAAAAAA
1 GTTTCTTTGGAAACAAAA
80128 ATCTTTGAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
30 22 0.34
31 3 0.05
36 3 0.05
37 37 0.57
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:80065 original size:67 final size:67
Alignment explanation
Indices: 79989--80187 Score: 278
Period size: 67 Copynumber: 3.0 Consensus size: 67
79979 GTTTCTTTTC
79989 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGA
80054 AA
66 AA
* *
80056 CAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGA
80121 AA
66 AA
* * * * * * *
80123 AAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCTTGAGACAGTCTCTTTT
1 AAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCTTAAGATAGTTTCTTTT
80185 GAA
64 GAA
80188 GTAAATCCTT
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 31 0.26
67 85 0.71
68 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (67 bp):
AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGA
AA
Found at i:80669 original size:15 final size:15
Alignment explanation
Indices: 80646--80704 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
80636 TTTTGAGTCG
*
80646 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
80661 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
80676 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
80691 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
80705 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:81110 original size:28 final size:28
Alignment explanation
Indices: 81039--81120 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
81029 TAAAAATATC
* * *
81039 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
81067 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
81095 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
81121 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:81284 original size:46 final size:45
Alignment explanation
Indices: 81156--81501 Score: 162
Period size: 43 Copynumber: 8.1 Consensus size: 45
81146 TCCTCATTAT
* *
81156 GTAGGAACCGTGTCATC-CC-CAGA---CCAGATCTCTTCATCAC
1 GTAGGAACCGTGTCATCACCTTAGATGGCCAGAACTCTTCATCAC
* * * ** * *
81196 GTATGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTCATCAC
1 GTAGGAACCGTGTCATCACCTTAGATGGCCAGAAC-TCTTCATCAC
*
81239 GTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCAC
1 GTAGGAACCGTGTCATCACC-TTAGATGGCCAGAACTCTTCATCAC
* * * *
81285 GTATGAGCCGTGTCATTC-CC-CAGA---CCAGATCTCTTCATCAC
1 GTAGGAACCGTGTCA-TCACCTTAGATGGCCAGAACTCTTCATCAC
* * * ** * * * *
81326 GTAGGAGCTGTGTCA--ACCGTAGATAACCAG-CCGTCCTCATTAT
1 GTAGGAACCGTGTCATCACCTTAGATGGCCAGAAC-TCTTCATCAC
*
81369 GTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCAC
1 GTAGGAACCGTGTCATCACCTT-AGATGGCC-AGAACTCTTCATCAC
* * * * ** *
81416 GTATGAGCAGTGTCAAC-CCTT-GA---CCAGATTTCCTCATCAC
1 GTAGGAACCGTGTCATCACCTTAGATGGCCAGAACTCTTCATCAC
* * * *
81456 GTAGGAACCATGTCA-C-CCTTAGACGACCCGAACTCTTCATCAC
1 GTAGGAACCGTGTCATCACCTTAGATGGCCAGAACTCTTCATCAC
81499 GTA
1 GTA
81502 TGAGCAGTGT
Statistics
Matches: 229, Mismatches: 51, Indels: 49
0.70 0.16 0.15
Matches are distributed among these distances:
39 9 0.04
40 44 0.19
41 31 0.14
42 2 0.01
43 64 0.28
44 5 0.02
45 7 0.03
46 42 0.18
47 24 0.10
48 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (45 bp):
GTAGGAACCGTGTCATCACCTTAGATGGCCAGAACTCTTCATCAC
Found at i:81295 original size:89 final size:83
Alignment explanation
Indices: 81139--81299 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
81129 CTAAAGATGG
* * *
81139 CCAGCCGTCCTCATTATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
81204 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
81222 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
81287 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
81300 TTCCCCAGAC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 31 0.46
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:81365 original size:130 final size:130
Alignment explanation
Indices: 81163--81470 Score: 474
Period size: 130 Copynumber: 2.4 Consensus size: 130
81153 TATGTAGGAA
*
81163 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCC
1 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
*
81228 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAG
66 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGAG
* *
81292 CCGTGTCATTCCCCAGACCAGATCTCTTCATCACGTAGGAGCTGTGTCAACCGTAGATAACCAGC
1 CCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGC
* *
81357 CGTCCTCATTATGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGA
65 CGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGA
81422 G
130 G
* * ** * * * *
81423 CAGTGTCAACCCTTGACCAGATTTCCTCATCACGTAGGAACCATGTCA
1 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA
81471 CCCTTAGACG
Statistics
Matches: 162, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
129 8 0.05
130 125 0.77
131 29 0.18
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (130 bp):
CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGAG
Found at i:81683 original size:3 final size:3
Alignment explanation
Indices: 81672--81735 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
81662 TTTTTTATCG
** *
81672 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81717 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
81736 CATATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:81704 original size:32 final size:32
Alignment explanation
Indices: 81666--81733 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
81656 CGGGTTTTTT
*
81666 TTATCGTTATTTTATTATTATTATTATTA-TTA
1 TTATCGTTATCTTATTATT-TTATTATTATTTA
81698 TTATCGTTATCTTATTATTTTATTATTATTTA
1 TTATCGTTATCTTATTATTTTATTATTATTTA
81730 TTAT
1 TTAT
81734 TACATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.66
Consensus pattern (32 bp):
TTATCGTTATCTTATTATTTTATTATTATTTA
Found at i:81741 original size:28 final size:28
Alignment explanation
Indices: 81681--81746 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
81671 GTTATTTTAT
* *
81681 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
81710 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
81738 TATTTTTTT
1 TATTATTTT
81747 GCAGGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:85678 original size:117 final size:117
Alignment explanation
Indices: 85535--85752 Score: 341
Period size: 116 Copynumber: 1.9 Consensus size: 117
85525 ATTTTTAGAG
* * *
85535 GGTGACCAAAATGAATAAAAATATAATATTTGGGTATTAAATGTGTAATTTACCCTAAAATAATC
1 GGTGACCAAAATGAATAAAAATATAATAATTGGGTACTAAATGCGTAATTTACCCT-AAATAATC
*
85600 ACTCCCTTTATAATTATTAAAATTATCCATTATTAATGCTGAATTTTTATTGA
65 AATCCCTTTATAATTATTAAAATTATCCATTATTAATGCTGAATTTTTATTGA
* *
85653 GGTGACTAAAATGGAAT-AAAA-ATAATAATTGGGTACTAAATGCGTAATTTACCCTAAATAGTC
1 GGTGACCAAAAT-GAATAAAAATATAATAATTGGGTACTAAATGCGTAATTTACCCTAAATAATC
*
85716 AATCCCTTTATAATTATTAAAATTGTCCATTATTAAT
65 AATCCCTTTATAATTATTAAAATTATCCATTATTAAT
85753 TTTTTAAAAG
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
116 42 0.46
117 31 0.34
118 15 0.16
119 4 0.04
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (117 bp):
GGTGACCAAAATGAATAAAAATATAATAATTGGGTACTAAATGCGTAATTTACCCTAAATAATCA
ATCCCTTTATAATTATTAAAATTATCCATTATTAATGCTGAATTTTTATTGA
Found at i:90703 original size:65 final size:65
Alignment explanation
Indices: 90599--90729 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
90589 GATTTTCTCT
90599 ATATATCACCGTCTACGATCAGGTACCGTTTAGATTATATTTTTTGATCTAACACCATTTACAAA
1 ATATATCACCGTCTACGATCAGGTACCGTTTAGATTATATTTTTTGATCTAACACCATTTACAAA
* **
90664 ATATATTACCGTCTACGATCAGGTGTCGTTTAGATTATATTTTTTGATCTAACACCATTTACAAA
1 ATATATCACCGTCTACGATCAGGTACCGTTTAGATTATATTTTTTGATCTAACACCATTTACAAA
90729 A
1 A
90730 AGGTGTGCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (65 bp):
ATATATCACCGTCTACGATCAGGTACCGTTTAGATTATATTTTTTGATCTAACACCATTTACAAA
Found at i:91114 original size:21 final size:21
Alignment explanation
Indices: 91090--91130 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
91080 TATTTTAAAT
* *
91090 ATATTGTATTTAATTTATTTA
1 ATATTGTACTTAATTAATTTA
*
91111 ATATTTTACTTAATTAATTT
1 ATATTGTACTTAATTAATTT
91131 TTTTGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATTGTACTTAATTAATTTA
Found at i:93393 original size:13 final size:13
Alignment explanation
Indices: 93352--93395 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
93342 TATTTAGTAC
93352 TTTTTATTGTAAT
1 TTTTTATTGTAAT
* * *
93365 TGTTTATTGGACT
1 TTTTTATTGTAAT
93378 TTTTTATTGTAAT
1 TTTTTATTGTAAT
93391 TTTTT
1 TTTTT
93396 TTTATTTATC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.02, G:0.11, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:94112 original size:22 final size:23
Alignment explanation
Indices: 94068--94112 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
94058 TTAATATTGA
*
94068 AAAATAAATATTAAAATATGATT
1 AAAATAAATATTAAAATAGGATT
94091 AAAAT-AAT-TTATAAATAGGATT
1 AAAATAAATATTA-AAATAGGATT
94113 TTAATAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
AAAATAAATATTAAAATAGGATT
Found at i:94218 original size:15 final size:15
Alignment explanation
Indices: 94200--94237 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
94190 TAATAATAAT
94200 TAAATATATTAAAA-A
1 TAAATATA-TAAAATA
*
94215 TAAACATATAAAATA
1 TAAATATATAAAATA
94230 TAAATATA
1 TAAATATA
94238 AATAAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAATATATAAAATA
Found at i:94953 original size:50 final size:51
Alignment explanation
Indices: 94837--94953 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
94827 AATGTACCTT
** * * *
94837 CTGCACCGCGTTATACGATGATTTGGCGTCACGTGAGGTATAGTGTGCCCC
1 CTGCACCGCGTTATACGATGAGCTGGCATCACGTGAGGTATAGCGCGCCCC
* *
94888 CTGCACCGCGTTATACGGTGAGCTGGCATCACGTG-GGTATAGCGCGGCCC
1 CTGCACCGCGTTATACGATGAGCTGGCATCACGTGAGGTATAGCGCGCCCC
*
94938 CTGCACCGCGCTATAC
1 CTGCACCGCGTTATAC
94954 CTGTATATCT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 27 0.47
51 31 0.53
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (51 bp):
CTGCACCGCGTTATACGATGAGCTGGCATCACGTGAGGTATAGCGCGCCCC
Found at i:95154 original size:13 final size:14
Alignment explanation
Indices: 95126--95154 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95116 ATATTTTATA
95126 ATATTTTTACTATT
1 ATATTTTTACTATT
95140 ATATTTTTACT-TT
1 ATATTTTTACTATT
95153 AT
1 AT
95155 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:96853 original size:18 final size:18
Alignment explanation
Indices: 96830--96868 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
96820 CCAGCAGCCA
*
96830 CCGCAGCTATATATGATG
1 CCGCAGCCATATATGATG
96848 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
96866 CCG
1 CCG
96869 ACATCGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:112111 original size:106 final size:106
Alignment explanation
Indices: 110813--112095 Score: 2004
Period size: 106 Copynumber: 12.2 Consensus size: 106
110803 ATTTTGCTCG
* * *
110813 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
110878 CGAAGGGACCGCTGGTTGTCAATAAACTATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
110919 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
110984 CGAAGGGACCGCTGGTTGTCAAAAAATAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
111025 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111090 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
111131 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111196 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
111237 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAGAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111302 CGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
**
111343 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111408 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
111449 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
111514 CGAAGGGACCGCTGGTTATCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
111555 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
111620 CGAAGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
111661 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111726 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * *
111767 AGAGCCAATTTCGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACG
* * * *
111831 ACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * * *
111867 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACATCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-G
* *
111932 ACGAAGGGACGGCTGGTTGTCAAAAAACAACTTCCCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * *
111974 AGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGGCAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * * ** *
112039 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCTCGGTTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
112080 AGAGCCAATTTCAACT
1 AGAGCCAATTTCAACT
112096 CCACGACGGA
Statistics
Matches: 1092, Mismatches: 76, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
100 56 0.05
101 23 0.02
102 3 0.00
103 4 0.00
104 4 0.00
105 5 0.00
106 936 0.86
107 61 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:123830 original size:10 final size:10
Alignment explanation
Indices: 123824--123848 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
123814 GAAAATATTT
123824 TAAAATAATA
1 TAAAATAATA
123834 TAAAATAATA
1 TAAAATAATA
123844 TAAAA
1 TAAAA
123849 ATAACATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAATAATA
Found at i:126788 original size:6 final size:6
Alignment explanation
Indices: 126777--126808 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
126767 GACACGTATT
126777 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
126809 CGAGAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:127327 original size:6 final size:6
Alignment explanation
Indices: 127306--127346 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
127296 TCTCGTCTCG
127306 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
127347 ATAATACGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:127524 original size:41 final size:41
Alignment explanation
Indices: 127479--127699 Score: 415
Period size: 41 Copynumber: 5.4 Consensus size: 41
127469 ACAACTGTAG
*
127479 ACTATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
127520 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
127561 ACTATCGCAACACGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
127602 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
127643 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
127684 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
127700 TTTGCGATAG
Statistics
Matches: 175, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 175 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:128312 original size:37 final size:36
Alignment explanation
Indices: 128237--128313 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
128227 AATGTTAAAT
* * *
128237 AAAT-GAAAAAAGAAAAGAAAAAAAGAATAATAATA
1 AAATAGAAAAAAGAAAAGAAAAAAAGAAAAAAAACA
*
128272 AAATAGAAAATAAG-AAAGTAAAAAAGTAAAAAAAACA
1 AAATAGAAAA-AAGAAAAGAAAAAAAG-AAAAAAAACA
128309 AAATA
1 AAATA
128314 CTAAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 4 0.11
36 16 0.46
37 15 0.43
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.12
Consensus pattern (36 bp):
AAATAGAAAAAAGAAAAGAAAAAAAGAAAAAAAACA
Found at i:129532 original size:21 final size:20
Alignment explanation
Indices: 129483--129534 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
129473 GGACCGAAGG
129483 AAAA-AATAA-AAAAAATAA
1 AAAAGAATAATAAAAAATAA
*
129501 AAAAGATTAATAAACAAATAA
1 AAAAGAATAATAAA-AAATAA
* *
129522 ATAATAATAATAA
1 AAAAGAATAATAA
129535 TAATAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 3 0.11
21 16 0.59
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAGAATAATAAAAAATAA
Found at i:129605 original size:36 final size:36
Alignment explanation
Indices: 129565--129907 Score: 384
Period size: 36 Copynumber: 9.5 Consensus size: 36
129555 AGAAATTTAC
* *
129565 AACTATATATTATATATAATTTTTTAAAA-GTTTT-CA
1 AACTATATA-TATATAT-ATTTTTCAAAATGTTTTAAA
*
129601 AACTATATAT-TATATAGTTTTCAAAATGTTTTAAA
1 AACTATATATATATATATTTTTCAAAATGTTTTAAA
* *
129636 AACCATATAT-TATATA-TTTTCAAAATATTTTTAAA
1 AACTATATATATATATATTTTTCAAAAT-GTTTTAAA
*
129671 AACTATATAT-TATATAATTTTCAAAATGTTTTAAA
1 AACTATATATATATATATTTTTCAAAATGTTTTAAA
*
129706 AACTATATAT-TATGTATATTTTCAAAATGTTTTAAA
1 AACTATATATATATATAT-TTTTCAAAATGTTTTAAA
*
129742 AACTATATAT-TATATAAGTTTTCAAAATGTTTTAAA
1 AACTATATATATATAT-ATTTTTCAAAATGTTTTAAA
*
129778 AACTATATAT-TATATATATTTCCAAAATGTTTTAAA
1 AACTATATATATATATAT-TTTTCAAAATGTTTTAAA
*
129814 AACTATATA-ATATATATGTTTCCAAAATGTTTTCAAA
1 AACTATATATATATATAT-TTTTCAAAATGTTTT-AAA
* **
129851 AACTATATATTATATATATATTTCAAAAAT-TATTTGCA
1 AACTATATA-TATATATATTTTTC-AAAATGT-TTTAAA
129889 AACTATATAATATATATAT
1 AACTATAT-ATATATATAT
129908 ATATATATAT
Statistics
Matches: 275, Mismatches: 18, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
33 9 0.03
34 20 0.07
35 62 0.23
36 132 0.48
37 13 0.05
38 22 0.08
39 17 0.06
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
AACTATATATATATATATTTTTCAAAATGTTTTAAA
Found at i:129651 original size:35 final size:34
Alignment explanation
Indices: 129565--129867 Score: 403
Period size: 36 Copynumber: 8.5 Consensus size: 34
129555 AGAAATTTAC
* *
129565 AACTATATATTATATATAATTTTTTAAAA-GTTTT-CA
1 AACTATATA-T-TATAT-A-TTTTCAAAATGTTTTAAA
129601 AACTATATATTATATAGTTTTCAAAATGTTTTAAA
1 AACTATATATTATATA-TTTTCAAAATGTTTTAAA
* *
129636 AACCATATATTATATATTTTCAAAATATTTTTAAA
1 AACTATATATTATATATTTTCAAAAT-GTTTTAAA
129671 AACTATATATTATATAATTTTCAAAATGTTTTAAA
1 AACTATATATTATAT-ATTTTCAAAATGTTTTAAA
129706 AACTATATATTATGTATATTTTCAAAATGTTTTAAA
1 AACTATATATTA--TATATTTTCAAAATGTTTTAAA
129742 AACTATATATTATATAAGTTTTCAAAATGTTTTAAA
1 AACTATATATTATAT-A-TTTTCAAAATGTTTTAAA
129778 AACTATATATTATATATATTTCCAAAATGTTTTAAA
1 AACTATATATTATATAT-TTT-CAAAATGTTTTAAA
*
129814 AACTATATAATATATATGTTTCCAAAATGTTTTCAAA
1 AACTATATATTATATAT-TTT-CAAAATGTTTT-AAA
129851 AACTATATATTATATAT
1 AACTATATATTATATAT
129868 ATATTTCAAA
Statistics
Matches: 246, Mismatches: 10, Indels: 21
0.89 0.04 0.08
Matches are distributed among these distances:
33 9 0.04
34 24 0.10
35 62 0.25
36 129 0.52
37 22 0.09
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (34 bp):
AACTATATATTATATATTTTCAAAATGTTTTAAA
Found at i:129770 original size:72 final size:72
Alignment explanation
Indices: 129565--129904 Score: 460
Period size: 72 Copynumber: 4.7 Consensus size: 72
129555 AGAAATTTAC
* *
129565 AACTATATATTATATATAATTTTTTAAAA-GTTTT-CAAACTATATATTATAT-AGTTTTCAAAA
1 AACTATATATTATATAT-A-TTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAA
129627 TGTTTTAAA
64 TGTTTTAAA
* *
129636 AACCATATA-T-TATATATTTTCAAAATATTTTTAAAAACTATATATTATATAA-TTTTCAAAAT
1 AACTATATATTATATATATTTTCAAAAT-GTTTTAAAAACTATATATTATATAAGTTTTCAAAAT
129698 GTTTTAAA
65 GTTTTAAA
*
129706 AACTATATATTATGTATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
1 AACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
129771 TTTTAAA
66 TTTTAAA
* * * *
129778 AACTATATATTATATATATTTCCAAAATGTTTTAAAAACTATATAATATATATGTTTCCAAAATG
1 AACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
129843 TTTTCAAA
66 TTTT-AAA
** *
129851 AACTATATATTATATATATATTTCAAAAAT-TATTTGCAAACTATATAATATATA
1 AACTATATATTATATATAT-TTTC-AAAATGT-TTTAAAAACTATATATTATATA
129905 TATATATATA
Statistics
Matches: 243, Mismatches: 15, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
67 8 0.03
68 1 0.00
69 9 0.04
70 43 0.18
71 34 0.14
72 97 0.40
73 22 0.09
74 4 0.02
75 25 0.10
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
AACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
TTTTAAA
Found at i:129903 original size:2 final size:2
Alignment explanation
Indices: 129892--129925 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
129882 ATTTGCAAAC
129892 TA TA TA -A 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 T
129926 GAAGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:130246 original size:20 final size:20
Alignment explanation
Indices: 130223--130273 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
130213 CACGGAATGT
130223 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
130243 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
130263 AAGATTACCAG
1 AAGATTACCAG
130274 GGAATAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:130433 original size:17 final size:18
Alignment explanation
Indices: 130395--130433 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
130385 AAATTGTCCT
* *
130395 TATTACATATTCGTATAA
1 TATTACAAATTCGTAAAA
130413 TATTACAAATT-GTAAAA
1 TATTACAAATTCGTAAAA
130430 TATT
1 TATT
130434 TATATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (18 bp):
TATTACAAATTCGTAAAA
Found at i:132225 original size:20 final size:20
Alignment explanation
Indices: 132200--132245 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
132190 ACTTTTAATT
*
132200 GTATTTTTACTTTACGTTCA
1 GTATTTTCACTTTACGTTCA
132220 GTATTTTCACTTTACGTTCA
1 GTATTTTCACTTTACGTTCA
*
132240 GAATTT
1 GTATTT
132246 GGGTCTCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (20 bp):
GTATTTTCACTTTACGTTCA
Found at i:132272 original size:82 final size:82
Alignment explanation
Indices: 132177--132371 Score: 311
Period size: 82 Copynumber: 2.4 Consensus size: 82
132167 GCCTTAAGTT
* * *
132177 CATAATTTGAGTCACTTTTAATTGTATTTTTACTTTACGTTCAGTATTTTCACTTTACGTTCAGA
1 CATAATTTGAGTCACTTTTAATTGCATTTTTAATTTACGTTCAGTATTTTCACTTTACATTCAGA
132242 ATTTGGGTCTCCAGTAC
66 ATTTGGGTCTCCAGTAC
* *
132259 CATAATTTGAGTCACTTTTAATTGCATTTTCAATTTACGTTCAGTATTTTCACTTTACATTCAGT
1 CATAATTTGAGTCACTTTTAATTGCATTTTTAATTTACGTTCAGTATTTTCACTTTACATTCAGA
*
132324 ATTTGGGTCTCCAGTAT
66 ATTTGGGTCTCCAGTAC
*
132341 CAT-ATTCTGAGTCACTTTTAACTGCATTTTT
1 CATAATT-TGAGTCACTTTTAATTGCATTTTT
132372 CTCCTTTAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 3 0.03
82 101 0.97
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (82 bp):
CATAATTTGAGTCACTTTTAATTGCATTTTTAATTTACGTTCAGTATTTTCACTTTACATTCAGA
ATTTGGGTCTCCAGTAC
Found at i:132309 original size:20 final size:20
Alignment explanation
Indices: 132284--132327 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
132274 TTTTAATTGC
*
132284 ATTTTCAATTTACGTTCAGT
1 ATTTTCAATTTACATTCAGT
*
132304 ATTTTCACTTTACATTCAGT
1 ATTTTCAATTTACATTCAGT
132324 ATTT
1 ATTT
132328 GGGTCTCCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTCAATTTACATTCAGT
Found at i:135295 original size:2 final size:2
Alignment explanation
Indices: 135288--135337 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
135278 ATTTACTAAT
135288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
135331 -A TA TA TA
1 TA TA TA TA
135338 GAATGCATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:137011 original size:19 final size:19
Alignment explanation
Indices: 136984--137033 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
136974 TTATCACAAT
* *
136984 AAATGTTATCACTATAATTA
1 AAAT-TTATCACTACAAGTA
*
137004 AAATTTATAACTACAAGTA
1 AAATTTATCACTACAAGTA
*
137023 TAATTTATCAC
1 AAATTTATCAC
137034 AAAAATGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATTTATCACTACAAGTA
Found at i:137201 original size:19 final size:20
Alignment explanation
Indices: 137159--137201 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
137149 TCTTTACGAC
* * *
137159 AATATATTTTGTTACTATAT
1 AATATATTTTGATACTAAAA
137179 AATAT-TTTTGATACTAAAA
1 AATATATTTTGATACTAAAA
137198 AATA
1 AATA
137202 AGGATAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
AATATATTTTGATACTAAAA
Found at i:137537 original size:420 final size:416
Alignment explanation
Indices: 136791--137597 Score: 1064
Period size: 420 Copynumber: 1.9 Consensus size: 416
136781 AAATACAGAG
* * *
136791 AAATGTTTATGATATTATAATTTTACATAATGATTAAAATATATAACTACAAAAAATAATTTATT
1 AAATGGTTATGATAGTATAATTTTACATAATGATTAAAATATATAACTACAAAAAATAATTGATT
* * *
136856 ACAAAAAACTTAAATTTTTATTGTCTGGTATGATAATTTTTTTATAACAATAATTATAAATTATA
66 ACAAAAAACCTAAATTTTTATTATCTGATATGATAATTTTTTTATAACAATAATTATAAATTATA
* *
136921 ATTACAAAACTTATGAATATAACTTTTTGAAACAAAAAAATGAAGAAAAATATTTATCACAATAA
131 ATTACAAAAATTATGAATATAACTTTTTGAAACAAAAAAATGAAGAAAAATAATTATCACAATAA
* * * *
136986 ATGTTATCACTATAATTAAAATTTATAACTACAAGTATAATTTATCACAAAAATGTGAATACCAC
196 ATGCTATCACTATAATTAAAATTTATAACTACAAATATAATTTATCACAAAAACGTAAATACCAC
* * * *
137051 TATTTTTGTGACCATATTTTTTGTAATAATTATAAATACTTATAGTTACAAAATTGTTACTATAT
261 TATTTTTGTGACAATATTTTCTATAATAATTATAAATACTTATAGTTACAAAATTGTCACTATAT
** * * *
137116 GATTTTTTTGACGCAATAAAATATGGAGGAAAATCTTTACGACAATATATTTTGTTACTATATAA
326 GACCTTTTTGACGCAAAAAAATATGGAGGAAAATCTTCACGACAATATATTTTGTCACTATATAA
137181 TATTTTTGATACTAAAAAATAAGGAT
391 TATTTTTGATACTAAAAAATAAGGAT
* * *
137207 AAATGGTTCTGATAGTATAATTTTTCATAATGATTAAAATATATAAGTA-AAAAAATAATTGATT
1 AAATGGTTATGATAGTATAATTTTACATAATGATTAAAATATATAACTACAAAAAATAATTGATT
* * *
137271 ACAAAAAACCTGAA-TTTTATTATTTGATGTGATAATTTTTTCTATAACAATAACAATAACTATA
66 ACAAAAAACCTAAATTTTTATTATCTGATATGATAATTTTTT-TATAACAAT---AAT---TATA
* * * * * * *
137335 AATTATAATTATAAAAATTGTTAATATAAC-TTTTGAAACAAAAAAGTGGAGAAACATAATTATG
124 AATTATAATTACAAAAATTATGAATATAACTTTTTGAAACAAAAAAATGAAGAAAAATAATTATC
** * * * *
137399 ATGATATATGCTATCACTATAGTTAAAATTTATAATTACAAATATAATTTGTCACAAAAACGTAA
189 ACAATAAATGCTATCACTATAATTAAAATTTATAACTACAAATATAATTTATCACAAAAACGTAA
* * * *
137464 ATATCA-TTTTTTTGTGACAATGTTTTCTATAATAATTATTAATACTTATAGTTACAAAATTTGT
254 ATACCACTATTTTTGTGACAATATTTTCTATAATAATTATAAATACTTATAGTTACAAAA-TTGT
* * * * **
137528 CATTATATGACCTTTTTGGCGCAAAAAAATTTGGAGGGAAATCTTCGTGACAATATATTTTGTCA
318 CACTATATGACCTTTTTGACGCAAAAAAATATGGAGGAAAATCTTCACGACAATATATTTTGTCA
137593 CTATA
383 CTATA
137598 ATTAAAACAT
Statistics
Matches: 333, Mismatches: 50, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
414 23 0.07
415 35 0.11
416 44 0.13
418 3 0.01
419 47 0.14
420 151 0.45
421 30 0.09
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (416 bp):
AAATGGTTATGATAGTATAATTTTACATAATGATTAAAATATATAACTACAAAAAATAATTGATT
ACAAAAAACCTAAATTTTTATTATCTGATATGATAATTTTTTTATAACAATAATTATAAATTATA
ATTACAAAAATTATGAATATAACTTTTTGAAACAAAAAAATGAAGAAAAATAATTATCACAATAA
ATGCTATCACTATAATTAAAATTTATAACTACAAATATAATTTATCACAAAAACGTAAATACCAC
TATTTTTGTGACAATATTTTCTATAATAATTATAAATACTTATAGTTACAAAATTGTCACTATAT
GACCTTTTTGACGCAAAAAAATATGGAGGAAAATCTTCACGACAATATATTTTGTCACTATATAA
TATTTTTGATACTAAAAAATAAGGAT
Found at i:138073 original size:23 final size:21
Alignment explanation
Indices: 138017--138068 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
138007 GGTTTTAGGT
138017 TTTTTTTCAA-AATTGTATATA
1 TTTTTTT-AATAATTGTATATA
138038 TTTTTTTAATAATTGTATATA
1 TTTTTTTAATAATTGTATATA
138059 TTTTTTTAAT
1 TTTTTTTAAT
138069 TTAATGCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTTTAATAATTGTATATA
Found at i:147150 original size:19 final size:19
Alignment explanation
Indices: 147126--147164 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
147116 TCGAATGCAT
147126 TCCATGCAC-CGATGCACTC
1 TCCATGC-CTCGATGCACTC
147145 TCCATGCCTCGATGCACTC
1 TCCATGCCTCGATGCACTC
147164 T
1 T
147165 GAATATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.18, C:0.41, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCCTCGATGCACTC
Found at i:147265 original size:64 final size:65
Alignment explanation
Indices: 147112--147272 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
147102 GAATTAATTG
* * *** * *
147112 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCCTCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
147177 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
147240 A
65 A
147241 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
147273 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:147287 original size:64 final size:65
Alignment explanation
Indices: 147112--147289 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 65
147102 GAATTAATTG
* * * *
147112 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGC-CTCGATGCACTCTGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCAC-CGATGCACTCAGAATATTTTCA
147176 A
65 A
* ** * **
147177 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCACCGATGCACTCAGAATA-TTTTCA
147240 A
65 A
***
147241 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCACCGATGCA
147290 TCAAGTGTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
64 47 0.50
65 47 0.50
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCACCGATGCACTCAGAATATTTTCAA
Found at i:153115 original size:44 final size:42
Alignment explanation
Indices: 153059--153182 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
153049 TTTGTGCTTC
* * *
153059 ATGCACCGATGCATTTAACAATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCA-TAAACAATGCACCGATGCATCCC-TTGAAT
* * * * *
153103 ATGTATCGATGCATCACCATGATGCACCAATGCATGCCTTGAAT
1 ATGCATCGATGCATAAACA--ATGCACCGATGCATCCCTTGAAT
*
153147 ATGCATCGATGCATAAGACCATGCACCGATGCATCC
1 ATGCATCGATGCATAA-ACAATGCACCGATGCATCC
153183 GTCGGGTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
43 18 0.28
44 31 0.48
45 15 0.23
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCATCGATGCATAAACAATGCACCGATGCATCCCTTGAAT
Found at i:154764 original size:21 final size:21
Alignment explanation
Indices: 154721--154764 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
154711 ACTCCGGGAG
**
154721 CTAGTTCTTCTCGAGCTGTTC
1 CTAGTTCTTCTCGAGCTCCTC
*
154742 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTCGAGCTCCTC
154763 CT
1 CT
154765 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.34, G:0.16, T:0.43
Consensus pattern (21 bp):
CTAGTTCTTCTCGAGCTCCTC
Found at i:155852 original size:19 final size:19
Alignment explanation
Indices: 155828--155866 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
155818 TCGAATGCAT
155828 TCCATGCAC-CGATGCACTC
1 TCCATGC-CTCGATGCACTC
155847 TCCATGCCTCGATGCACTC
1 TCCATGCCTCGATGCACTC
155866 T
1 T
155867 GAATATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.18, C:0.41, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCCTCGATGCACTC
Found at i:155967 original size:64 final size:65
Alignment explanation
Indices: 155814--155974 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
155804 GAATTAATTG
* * *** * ***
155814 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCCTCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACGAGGAATATTTTCAA
* *
155879 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACGAGG-CTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACGAGGAATA-TTTTCA
155942 A
65 A
155943 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
155975 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACGAGGAATATTTTCAA
Found at i:157778 original size:23 final size:23
Alignment explanation
Indices: 157747--157801 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
157737 TAAGCTACAG
*
157747 AAAGCCAGAAAAAAACGTGTCAT
1 AAAGACAGAAAAAAACGTGTCAT
* * *
157770 AAAGACAGATATAAACGTGTTAT
1 AAAGACAGAAAAAAACGTGTCAT
157793 AAAGACAGA
1 AAAGACAGA
157802 GAACATGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (23 bp):
AAAGACAGAAAAAAACGTGTCAT
Found at i:166586 original size:93 final size:92
Alignment explanation
Indices: 166473--166652 Score: 222
Period size: 93 Copynumber: 1.9 Consensus size: 92
166463 TGAACATCGA
* *
166473 ATGCATTTCATGCATGGATGCA-CATACTATACATAGATGCACTCAGAG-T-TTTATGAAAACAT
1 ATGCATTTCATGCATCGATGCACCA-ACCATACATAGATGCACTCAG-GCTATTT-TG-AAACAT
*
166535 CGAATGCATTTGATGCATCGATGCACAAGTT
62 CGAATGCATTTCATGCATCGATGCACAAGTT
* * * * * *
166566 ATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAATATCGAA
1 ATGCATTTCATGCATCGATGCACCAACCATACATAGATGCACTCAGGCTATTTTGAAACATCGAA
166631 TGCATTTCATGCATCGATGCAC
66 TGCATTTCATGCATCGATGCAC
166653 TCTTAGTGCA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
92 31 0.41
93 39 0.52
94 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (92 bp):
ATGCATTTCATGCATCGATGCACCAACCATACATAGATGCACTCAGGCTATTTTGAAACATCGAA
TGCATTTCATGCATCGATGCACAAGTT
Done.