Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005819.1 Hibiscus syriacus cultivar Beakdansim tig00013636_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: 637054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:5860 original size:90 final size:89
Alignment explanation
Indices: 5708--5880 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
5698 ACACACCCTT
* *
5708 TTATAGCCAAGTTATCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
5773 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
5797 TTATATCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTATATTT
5862 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
5881 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 27 0.35
90 51 0.65
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:7164 original size:90 final size:90
Alignment explanation
Indices: 6983--7214 Score: 288
Period size: 90 Copynumber: 2.6 Consensus size: 90
6973 CCTGAAAATG
** ** * ** * * * *
6983 AGGCTTAGTTTCTAAAAAATCATTTGAAAACATATTTC-CCGAAGGTCTTATGGATGACCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTAAAGATCTTACGAATGGCCCGAAG
* * *
7047 GATTTAGAAATCAAGAAACCTCCGA
66 GACTTACAAATAAAGAAACCTCCGA
*
7072 AGGCTTAGTTTCTACAATCTCATTTGAAAACATCCTGCACTAAAGATCTTACGAATGGCCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTAAAGATCTTACGAATGGCCCGAAG
7137 GACTTACAAATAAAGAAACC-CTCGA
66 GACTTACAAATAAAGAAACCTC-CGA
* *
7162 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTACG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTAAAGATCTTACG
7215 GATTGCATGA
Statistics
Matches: 123, Mismatches: 18, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
89 33 0.27
90 90 0.73
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (90 bp):
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTAAAGATCTTACGAATGGCCCGAAG
GACTTACAAATAAAGAAACCTCCGA
Found at i:10212 original size:45 final size:45
Alignment explanation
Indices: 10163--10263 Score: 184
Period size: 45 Copynumber: 2.2 Consensus size: 45
10153 ATATTACTTA
*
10163 ATTGTTTTATTTTTTTTAACATGTGGTATACTGAAATCTATGGTT
1 ATTGTTTTATTTGTTTTAACATGTGGTATACTGAAATCTATGGTT
10208 ATTGTTTTATTTGTTTTAACATGTGGTATACTGAAATCTATGGTT
1 ATTGTTTTATTTGTTTTAACATGTGGTATACTGAAATCTATGGTT
*
10253 ATTTTTTTATT
1 ATTGTTTTATT
10264 GATGCACCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (45 bp):
ATTGTTTTATTTGTTTTAACATGTGGTATACTGAAATCTATGGTT
Found at i:10519 original size:31 final size:31
Alignment explanation
Indices: 10484--10558 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
10474 CTTAAGATCA
* **
10484 TTCTTGGGTAGGCCCTGTGGCC-CTGAGATTT
1 TTCTTGGGTAGGCCCCGTGGCCTC-GAGAACT
**
10515 TTCTTATGTAGGCCCCGTGGCCTCGAGAACT
1 TTCTTGGGTAGGCCCCGTGGCCTCGAGAACT
10546 TTCTTGGGTAGGC
1 TTCTTGGGTAGGC
10559 TCTTAGGTCC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.33
Consensus pattern (31 bp):
TTCTTGGGTAGGCCCCGTGGCCTCGAGAACT
Found at i:12073 original size:13 final size:12
Alignment explanation
Indices: 12043--12086 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
12033 AATAGACAAG
*
12043 TACCTAACTCTC
1 TACCTAACTTTC
12055 -ACCTAACTTTC
1 TACCTAACTTTC
12066 ATACCTAACTTT-
1 -TACCTAACTTTC
12078 TACCTAACT
1 TACCTAACT
12087 AAATTGATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (12 bp):
TACCTAACTTTC
Found at i:15536 original size:24 final size:24
Alignment explanation
Indices: 15481--15536 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
15471 TTGTTGTAAT
*
15481 TCTAGCCTCGTCCATGACCGCAACT
1 TCTA-CCTCGTCCATGACCGCAACC
* * * *
15506 TCCACCTCGTCCATGGCCTCTACC
1 TCTACCTCGTCCATGACCGCAACC
15530 TCTACCT
1 TCTACCT
15537 AGGCCATGCT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.16, C:0.45, G:0.12, T:0.27
Consensus pattern (24 bp):
TCTACCTCGTCCATGACCGCAACC
Found at i:19541 original size:17 final size:17
Alignment explanation
Indices: 19519--19558 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
19509 CTTATCGATG
19519 TGAGTTATCGGTAACTT
1 TGAGTTATCGGTAACTT
19536 TGAGTTATCGGTAACTT
1 TGAGTTATCGGTAACTT
19553 TGAGTT
1 TGAGTT
19559 GTAAGCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (17 bp):
TGAGTTATCGGTAACTT
Found at i:21086 original size:29 final size:29
Alignment explanation
Indices: 21044--21152 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
21034 ATTTTCACCT
*
21044 AACTAAACTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
21073 AACTAAATTGATGTAAGCAATTACAT---
1 AACTAAATTGATGTAAGCAATGACATCAA
21099 --C-AAATT--TGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
21123 AACTAAATTGATGTAAGCAATTACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
21152 A
1 A
21153 TTAATTCAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
21 14 0.21
23 5 0.07
24 1 0.01
26 1 0.01
27 5 0.07
29 42 0.62
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.26
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:21109 original size:21 final size:21
Alignment explanation
Indices: 21084--21123 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21074 ACTAAATTGA
*
21084 TGTAAGCAATTACATCAAATT
1 TGTAAGCAATGACATCAAATT
21105 TGTAAGCAATGACATCAAA
1 TGTAAGCAATGACATCAAA
21124 ACTAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (21 bp):
TGTAAGCAATGACATCAAATT
Found at i:21130 original size:50 final size:50
Alignment explanation
Indices: 21055--21154 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
21045 ACTAAACTGA
21055 TGTAAGCAATGACATCAAAACTAAATTGATGTAAGCAATTACATCAAATT
1 TGTAAGCAATGACATCAAAACTAAATTGATGTAAGCAATTACATCAAATT
21105 TGTAAGCAATGACATCAAAACTAAATTGATGTAAGCAATTACATCAAATT
1 TGTAAGCAATGACATCAAAACTAAATTGATGTAAGCAATTACATCAAATT
21155 AATTCAAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (50 bp):
TGTAAGCAATGACATCAAAACTAAATTGATGTAAGCAATTACATCAAATT
Found at i:26787 original size:31 final size:31
Alignment explanation
Indices: 26722--26780 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
26712 CTAATGTGAC
*
26722 TCTTGGGTAGCCTCTGCGGCCCTGAGATCAT
1 TCTTGGGTAGCATCTGCGGCCCTGAGATCAT
*
26753 TCTTGGGTATGCAT-TGTGGCCCTGAGAT
1 TCTTGGGTA-GCATCTGCGGCCCTGAGAT
26781 TTTTCTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.14, C:0.24, G:0.31, T:0.32
Consensus pattern (31 bp):
TCTTGGGTAGCATCTGCGGCCCTGAGATCAT
Found at i:26803 original size:31 final size:32
Alignment explanation
Indices: 26768--26861 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 32
26758 GGTATGCATT
*
26768 GTGGCCCTGAGATTTTTCTTAGGTAGG-TCTC
1 GTGGCCCTAAGATTTTTCTTAGGTAGGCTCTC
* ** *
26799 GTGGCCCCAAGAACTTTCTTGGGTAGGCTCTC
1 GTGGCCCTAAGATTTTTCTTAGGTAGGCTCTC
* * *
26831 -AGGCCCTAAGATGTTCTCTTAGGTTGGCTCT
1 GTGGCCCTAAGAT-TTTTCTTAGGTAGGCTCT
26862 TTATATAATG
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
31 31 0.63
32 18 0.37
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.34
Consensus pattern (32 bp):
GTGGCCCTAAGATTTTTCTTAGGTAGGCTCTC
Found at i:30060 original size:137 final size:136
Alignment explanation
Indices: 29815--30078 Score: 363
Period size: 137 Copynumber: 1.9 Consensus size: 136
29805 TTGATTGACC
* *
29815 GTTGACCTTGACAAAAAAGTAAAATTTTTTGAAAAATCATATTTTATGTTTTTTGACGTTCTGAG
1 GTTGACCTTGACAAAAAAGTAAAATTTTTCGAAAAATCATATTTTATGTTTTTTGACGTCCTGAG
*
29880 TCTGATTCGGAAGTCTGTTTTGCGAAATTCCAACCCGAAAGCCTCCAAATTTTCAGTCAAACCCG
66 TCTGATTCGGAAGTCTGTTTTGCGAAATTCAAACCCGAAAGCCTCCAAATTTTCAGTCAAACCCG
29945 TTGAAA
131 TTGAAA
* * * *
29951 GTTGA-CTATGACAAAAAATTCAAAA-TTTTCGAAAAGTTATATTTTATGTTTTTTTACGTCCTG
1 GTTGACCT-TGACAAAAAAGT-AAAATTTTTCGAAAAATCATATTTTATGTTTTTTGACGTCCTG
* * * * *
30014 AATGTC-GATTCTGAAGTTTGTTTTTCTAAATTCAAACTCGAAAGCCTCCAAATTTTCAGTCAAA
64 -A-GTCTGATTCGGAAGTCTGTTTTGCGAAATTCAAACCCGAAAGCCTCCAAATTTTCAGTCAAA
30078 C
127 C
30079 ACGAACATGC
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
135 2 0.02
136 49 0.44
137 58 0.52
138 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (136 bp):
GTTGACCTTGACAAAAAAGTAAAATTTTTCGAAAAATCATATTTTATGTTTTTTGACGTCCTGAG
TCTGATTCGGAAGTCTGTTTTGCGAAATTCAAACCCGAAAGCCTCCAAATTTTCAGTCAAACCCG
TTGAAA
Found at i:32258 original size:11 final size:11
Alignment explanation
Indices: 32242--32284 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
32232 ATAGACCAAT
32242 ACCTAACTTTC
1 ACCTAACTTTC
32253 ACCTAACTTTC
1 ACCTAACTTTC
*
32264 ATGTCTAACTTTC
1 A--CCTAACTTTC
32277 ACCTAACT
1 ACCTAACT
32285 AAATTGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (11 bp):
ACCTAACTTTC
Found at i:36948 original size:11 final size:11
Alignment explanation
Indices: 36908--36950 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
36898 ATAGACAAAT
*
36908 ACCTAACTCTC
1 ACCTAACTTTC
*
36919 ACTTAACTTTC
1 ACCTAACTTTC
36930 ATACCTAACTTTC
1 --ACCTAACTTTC
36943 ACCTAACT
1 ACCTAACT
36951 AAGTTGATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (11 bp):
ACCTAACTTTC
Found at i:38057 original size:148 final size:148
Alignment explanation
Indices: 37789--38085 Score: 531
Period size: 148 Copynumber: 2.0 Consensus size: 148
37779 CCTCAATGTT
37789 AGCCCCCATTCTTTGAATCACGCCAAGCTGACGACATAAATGTTCAAACTTTCCAACACTCAAGC
1 AGCCCCCATTCTTTGAATCACGCCAAGCTGACGACATAAATGTTCAAACTTTCCAACACTCAAGC
* * *
37854 TTTTTGTAAACAAGTCAGCAATTTGCTCATATGTCTTGATTTTCCTCATCTCAATCCCTTCTTGC
66 TTTTTGTAAACAAGTCAACAATTTACTCATATGTCTTGATTTGCCTCATCTCAATCCCTTCTTGC
37919 AAAACTTTTTCCCTAATA
131 AAAACTTTTTCCCTAATA
* **
37937 AGCCCCTATTCTTTGAATCACGCCAAGCTGACGACATACGTGTTCAAACTTTCCAACACTCAAGC
1 AGCCCCCATTCTTTGAATCACGCCAAGCTGACGACATAAATGTTCAAACTTTCCAACACTCAAGC
*
38002 TTTTTGTAAACAAGTCAACAATTTACTCATATGTCTTGATTTGCCTCATCTCAATCTCTTCTTGC
66 TTTTTGTAAACAAGTCAACAATTTACTCATATGTCTTGATTTGCCTCATCTCAATCCCTTCTTGC
38067 AAAACTTTTTCCCTAATA
131 AAAACTTTTTCCCTAATA
38085 A
1 A
38086 AGTAGTGATG
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 142 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (148 bp):
AGCCCCCATTCTTTGAATCACGCCAAGCTGACGACATAAATGTTCAAACTTTCCAACACTCAAGC
TTTTTGTAAACAAGTCAACAATTTACTCATATGTCTTGATTTGCCTCATCTCAATCCCTTCTTGC
AAAACTTTTTCCCTAATA
Found at i:44994 original size:29 final size:29
Alignment explanation
Indices: 44952--45010 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
44942 AATTTTCACT
44952 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
44981 AACTAAATTGATGTAAGCAATTACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
45010 A
1 A
45011 TTAATTCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:46741 original size:2 final size:2
Alignment explanation
Indices: 46734--46779 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
46724 CATGAGTTTT
46734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46775 TA TA T
1 TA TA T
46780 TCATATGACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50678 original size:27 final size:27
Alignment explanation
Indices: 50640--50700 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
50630 GTCGATACGC
50640 CATCATTTGTTAGGACAAACAATGAAG
1 CATCATTTGTTAGGACAAACAATGAAG
50667 CATCATTTGTTAGGACAAACAATGAAG
1 CATCATTTGTTAGGACAAACAATGAAG
50694 CATCATT
1 CATCATT
50701 CGTGGTGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (27 bp):
CATCATTTGTTAGGACAAACAATGAAG
Found at i:52441 original size:10 final size:10
Alignment explanation
Indices: 52426--52485 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
52416 CCGGTTTTCA
52426 ACCGGTTCTG
1 ACCGGTTCTG
52436 ACCGGTTC-G
1 ACCGGTTCTG
52445 AACCGGTT-TG
1 -ACCGGTTCTG
52455 ACCGG-TCTG
1 ACCGGTTCTG
52464 AACCGGTT-TG
1 -ACCGGTTCTG
*
52474 ACTGG-TCTG
1 ACCGGTTCTG
52483 ACC
1 ACC
52486 CGACCCGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
8 2 0.05
9 16 0.38
10 23 0.55
11 1 0.02
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:52458 original size:19 final size:19
Alignment explanation
Indices: 52425--52483 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
52415 ACCGGTTTTC
52425 AACCGGTTCTGACCGGT-TCG
1 AACCGGTT-TGACCGGTCT-G
52445 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
52464 AACCGGTTTGACTGGTCTG
1 AACCGGTTTGACCGGTCTG
52483 A
1 A
52484 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 28 0.76
20 9 0.24
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:52510 original size:22 final size:22
Alignment explanation
Indices: 52482--52524 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
52472 TGACTGGTCT
52482 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
52504 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
52525 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:59735 original size:5 final size:5
Alignment explanation
Indices: 59725--59776 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
59715 CGGTCTGATT
* *
59725 CGACC CGACC CGACC CGACC CGACC CGACC GTTGACC CGACT CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC CGACC --CGACC CGACC CGACC CGACC
59777 GTTGATCGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 37 0.90
7 4 0.10
ACGTcount: A:0.19, C:0.54, G:0.21, T:0.06
Consensus pattern (5 bp):
CGACC
Found at i:59764 original size:22 final size:22
Alignment explanation
Indices: 59736--59781 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
59726 GACCCGACCC
59736 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
*
59758 GACCCGACTCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
59780 GA
1 GA
59782 TCGTTAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.46, G:0.24, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:59791 original size:7 final size:7
Alignment explanation
Indices: 59776--59816 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
59766 TCGACCCGAC
59776 CGTTGAT
1 CGTTGAT
*
59783 CGTTAAT
1 CGTTGAT
59790 CGTTGAT
1 CGTTGAT
*
59797 CGTTGAC
1 CGTTGAT
*
59804 CGTTGAC
1 CGTTGAT
59811 CGTTGA
1 CGTTGA
59817 CTTTCTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.37
Consensus pattern (7 bp):
CGTTGAT
Found at i:59815 original size:14 final size:14
Alignment explanation
Indices: 59773--59817 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
59763 GACTCGACCC
59773 GACCGTTGATCGTT
1 GACCGTTGATCGTT
* *
59787 AATCGTTGATCGTT
1 GACCGTTGATCGTT
*
59801 GACCGTTGACCGTT
1 GACCGTTGATCGTT
59815 GAC
1 GAC
59818 TTTCTTTGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (14 bp):
GACCGTTGATCGTT
Found at i:64249 original size:30 final size:29
Alignment explanation
Indices: 64211--64273 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
64201 GAAGAGTGGC
64211 TTTTATATCAACTAGACATCAAAAATACA
1 TTTTATATCAACTAGACATCAAAAATACA
*
64240 TTTTCATATCAACTAGACATCAATAATACA
1 TTTT-ATATCAACTAGACATCAAAAATACA
64270 TTTT
1 TTTT
64274 TAAATGAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTATATCAACTAGACATCAAAAATACA
Found at i:67312 original size:2 final size:2
Alignment explanation
Indices: 67305--67370 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
67295 AACTAGTTTG
67305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67347 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
67371 TTCACTAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72311 original size:23 final size:24
Alignment explanation
Indices: 72265--72328 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
72255 TGTTAAAACA
72265 TTTTGAATGTTTTGGATTTGTTTG
1 TTTTGAATGTTTTGGATTTGTTTG
*
72289 TTTTGGATG-TTTGGATATT-TTTG
1 TTTTGAATGTTTTGGAT-TTGTTTG
*
72312 -TTTGAAT-TTTTGAATTT
1 TTTTGAATGTTTTGGATTT
72329 TTAATTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 12 0.34
23 11 0.31
24 10 0.29
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (24 bp):
TTTTGAATGTTTTGGATTTGTTTG
Found at i:75105 original size:18 final size:18
Alignment explanation
Indices: 75082--75126 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
75072 AAAGGCGGTT
75082 TTGACTCAAGCACCAGTG
1 TTGACTCAAGCACCAGTG
75100 TTGACTCAAGCACCAGTG
1 TTGACTCAAGCACCAGTG
75118 TTGACTCAA
1 TTGACTCAA
75127 CTTGAGTCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (18 bp):
TTGACTCAAGCACCAGTG
Found at i:79837 original size:43 final size:42
Alignment explanation
Indices: 79775--79980 Score: 190
Period size: 42 Copynumber: 4.8 Consensus size: 42
79765 CTATACACCA
*
79775 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTTAACCT-TGCACAAAGCAAAGGGA-CCT-GGAAAACT
* * * *
79819 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTAACCTTGCACAAAGCAAAGGGACCTGGAAAACT
* * *
79861 GTAAGGCTTACCCTTGCACACAA-CAAAGGGACCTAGTAAACT
1 GTAAGGCTTAACCTTGCACA-AAGCAAAGGGACCTGGAAAACT
* *
79903 GTAAGGCTT-ACTTTCGCACACAA-CAAAGGGACCTGGGAAACT
1 GTAAGGCTTAACCTT-GCACA-AAGCAAAGGGACCTGGAAAACT
*
79945 GTAAGGCTT-ACATTCGCA-AACAGCAAAAGGGACCTG
1 GTAAGGCTTAACCTT-GCACAA-AGC-AAAGGGACCTG
79981 ATAATACTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
40 1 0.01
41 5 0.04
42 94 0.67
43 26 0.18
44 15 0.11
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (42 bp):
GTAAGGCTTAACCTTGCACAAAGCAAAGGGACCTGGAAAACT
Found at i:79866 original size:42 final size:42
Alignment explanation
Indices: 79814--79980 Score: 221
Period size: 42 Copynumber: 4.0 Consensus size: 42
79804 GAGCCTAGGA
* *
79814 AAACTGTAAGGTTTATCCTT-GCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
* *
79856 AAACTGTAAGGCTTACCCTT-GCACACAACAAAGGGACCTAGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
*
79898 AAACTGTAAGGCTTACTTTCGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
* * *
79940 AAACTGTAAGGCTTACATTCGCAAACAGCAAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTCGCACACAAC-AAAGGGACCTG
79981 ATAATACTTC
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
41 3 0.03
42 98 0.88
43 11 0.10
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
Found at i:79922 original size:84 final size:86
Alignment explanation
Indices: 79775--79955 Score: 246
Period size: 84 Copynumber: 2.1 Consensus size: 86
79765 CTATACACCA
* * *
79775 GTAAGGCTTAACCTGTGCACAAAGCAGAGGAGCCTAGGAAAACTGTAAGGTTTATCCTTGCACAC
1 GTAAGGCTTACCCTGTGCACAAAGCAAAGGAGCCTAGGAAAACTGTAAGGCTTATCCTTGCACAC
*
79840 AGCAAAGGGACCTGGGAAACT
66 AACAAAGGGACCTGGGAAACT
* *
79861 GTAAGGCTTACCCT-TGCACACAA-CAAAGG-GACCTA-GTAAACTGTAAGGCTTA-CTTTCGCA
1 GTAAGGCTTACCCTGTGCACA-AAGCAAAGGAG-CCTAGGAAAACTGTAAGGCTTATCCTT-GCA
79921 CACAACAAAGGGACCTGGGAAACT
63 CACAACAAAGGGACCTGGGAAACT
79945 GTAAGGCTTAC
1 GTAAGGCTTAC
79956 ATTCGCAAAC
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
83 3 0.03
84 53 0.62
85 15 0.17
86 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (86 bp):
GTAAGGCTTACCCTGTGCACAAAGCAAAGGAGCCTAGGAAAACTGTAAGGCTTATCCTTGCACAC
AACAAAGGGACCTGGGAAACT
Found at i:80403 original size:11 final size:11
Alignment explanation
Indices: 80387--80423 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
80377 ATAAATAATC
80387 TAAATATTATT
1 TAAATATTATT
*
80398 TAAATA--ATC
1 TAAATATTATT
80407 TAAATATTATT
1 TAAATATTATT
80418 TAAATA
1 TAAATA
80424 ATATACGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATATTATT
Found at i:80403 original size:20 final size:20
Alignment explanation
Indices: 80378--80425 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
80368 AATCCTAATA
80378 TAAATAATCTAAATATTATT
1 TAAATAATCTAAATATTATT
80398 TAAATAATCTAAATATTATT
1 TAAATAATCTAAATATTATT
80418 TAAATAAT
1 TAAATAAT
80426 ATACGGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATAATCTAAATATTATT
Found at i:80958 original size:29 final size:29
Alignment explanation
Indices: 80922--81106 Score: 201
Period size: 29 Copynumber: 6.3 Consensus size: 29
80912 CATTTTACAG
* * * *
80922 AAATAGCACCTTTTTTAAAATAATTACCA
1 AAATAGCACCTATTTCAAATTAATTCCCA
* **
80951 AAATAGCACCCTTTTTTGAATTAATTCCCA
1 AAATAGCA-CCTATTTCAAATTAATTCCCA
*
80981 AAATAGCA-ATCATTTCAAATTAATTCCCA
1 AAATAGCACCT-ATTTCAAATTAATTCCCA
* *
81010 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCTATTTCAAATTAATTCCCA
* * *
81039 AAATAGCACCCATTTCGAATTAATTCCTA
1 AAATAGCACCTATTTCAAATTAATTCCCA
* * *
81068 AAATAGCACCCATTTCGAATAAATTCCCA
1 AAATAGCACCTATTTCAAATTAATTCCCA
81097 AAATAGCACC
1 AAATAGCACC
81107 GGTCAACGGT
Statistics
Matches: 140, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
28 1 0.01
29 113 0.81
30 26 0.19
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCTATTTCAAATTAATTCCCA
Found at i:81053 original size:58 final size:58
Alignment explanation
Indices: 80922--81106 Score: 253
Period size: 58 Copynumber: 3.2 Consensus size: 58
80912 CATTTTACAG
** * * * * *
80922 AAATAGCACCTTTTTTAAAATAATTACCAAAATAGCACCCTTTTTTGAATTAATTCCCA
1 AAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCC-ATTTCGAATTAATTCCCA
**
80981 AAATAGCAATCATTTCAAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTCCCA
* * *
81039 AAATAGCACCCATTTCGAATTAATTCCTAAAATAGCACCCATTTCGAATAAATTCCCA
1 AAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTCCCA
81097 AAATAGCACC
1 AAATAGCACC
81107 GGTCAACGGT
Statistics
Matches: 112, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
58 79 0.71
59 33 0.29
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (58 bp):
AAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTCCCA
Found at i:81093 original size:87 final size:88
Alignment explanation
Indices: 80942--81106 Score: 251
Period size: 87 Copynumber: 1.9 Consensus size: 88
80932 TTTTTTAAAA
* * * *
80942 TAATTACCAAAATAGCACCCTTTTTTGAATTAATTCCCAAAATAGCAATCATTTCAAATTAATTC
1 TAATTACCAAAATAGCACCCTATTTCGAATTAATTCCCAAAATAGCAACCATTTCAAATAAATTC
81007 CCAAAATAGCACCCATTTCGAAT
66 CCAAAATAGCACCCATTTCGAAT
* * * *
81030 TAATTCCCAAAATAGCACCC-ATTTCGAATTAATTCCTAAAATAGCACCCATTTCGAATAAATTC
1 TAATTACCAAAATAGCACCCTATTTCGAATTAATTCCCAAAATAGCAACCATTTCAAATAAATTC
81094 CCAAAATAGCACC
66 CCAAAATAGCACC
81107 GGTCAACGGT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
87 50 0.72
88 19 0.28
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (88 bp):
TAATTACCAAAATAGCACCCTATTTCGAATTAATTCCCAAAATAGCAACCATTTCAAATAAATTC
CCAAAATAGCACCCATTTCGAAT
Found at i:81132 original size:13 final size:13
Alignment explanation
Indices: 81114--81156 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
81104 ACCGGTCAAC
81114 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
81127 GGTCAACGAGTCG
1 GGTCAACGGGTCG
81140 GGTCAACGGGTCG
1 GGTCAACGGGTCG
81153 GGTC
1 GGTC
81157 GGGTCGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:81797 original size:13 final size:13
Alignment explanation
Indices: 81781--81805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81771 TTAATTATAT
81781 TTATTATTATTTA
1 TTATTATTATTTA
81794 TTATTATTATTT
1 TTATTATTATTT
81806 TCAAATTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:93308 original size:11 final size:13
Alignment explanation
Indices: 93276--93305 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
93266 TGGACAAAGA
93276 TGAAAAGGTATGT
1 TGAAAAGGTATGT
93289 TGAAAAGGTATG-
1 TGAAAAGGTATGT
93301 TGAAA
1 TGAAA
93306 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:102403 original size:108 final size:108
Alignment explanation
Indices: 102214--102411 Score: 315
Period size: 108 Copynumber: 1.8 Consensus size: 108
102204 ACCAAAATAA
* *
102214 AAAATGAGTTAGTATCAATGAGATAATCAACAAAATAGTAAGAATTATCTTTAATGAATAAAATC
1 AAAATGAGTTAGTATCAAAGAGATAATCAACAAAATAGTAAGAACTATCTTTAATGAATAAAATC
102279 TACCCTAACATGTTGTCTATACAAATACAAGAAAAAAAAGTAG
66 TACCCTAACATGTTGTCTATACAAATACAAGAAAAAAAAGTAG
* * * *
102322 AAAATGAGTTCGTATCAAAGAGATAATCAATAAAGTAGTAAGAACTATCTTTAATTAATAAAATC
1 AAAATGAGTTAGTATCAAAGAGATAATCAACAAAATAGTAAGAACTATCTTTAATGAATAAAATC
* * *
102387 TACTCTCACATGTTGTCTATCCAAA
66 TACCCTAACATGTTGTCTATACAAA
102412 CATGGTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 81 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (108 bp):
AAAATGAGTTAGTATCAAAGAGATAATCAACAAAATAGTAAGAACTATCTTTAATGAATAAAATC
TACCCTAACATGTTGTCTATACAAATACAAGAAAAAAAAGTAG
Found at i:103360 original size:90 final size:89
Alignment explanation
Indices: 103204--103369 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 89
103194 CCTAACACAC
* *
103204 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCATAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
103269 TTTAATTAATTATAATTTAATAAT
66 TTTAATTAATTATAATTTAATAAT
* *
103293 CCTTTTATATCCAAGTTACCATAATCATATTAGAGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCATAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTAT
103358 ATTTAATTAATT
65 ATTTAATTAATT
103370 GAAATTAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.43
90 41 0.57
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCATAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTATAATTTAATAAT
Found at i:106608 original size:23 final size:24
Alignment explanation
Indices: 106580--106645 Score: 118
Period size: 23 Copynumber: 2.8 Consensus size: 24
106570 TTGATTTTCT
106580 GGAAAATGAATTAATATTTT-CCA
1 GGAAAATGAATTAATATTTTGCCA
106603 GGAAAATGAATTAATATTTTGCCA
1 GGAAAATGAATTAATATTTTGCCA
106627 GGAAAATGAATT-ATATTTT
1 GGAAAATGAATTAATATTTT
106646 TCTGAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 27 0.64
24 15 0.36
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (24 bp):
GGAAAATGAATTAATATTTTGCCA
Found at i:106790 original size:3 final size:3
Alignment explanation
Indices: 106784--106808 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
106774 TATCATAAAA
106784 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
106809 AAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:106914 original size:31 final size:29
Alignment explanation
Indices: 106778--106915 Score: 71
Period size: 27 Copynumber: 4.8 Consensus size: 29
106768 ATTATTTATC
* *
106778 ATAAAAATTATT-ATTATTAT-TATTATT-
1 ATAAAAA-TATTAATAATTATATTTTATTA
*
106805 ATTAAAATATTTAAATAATT-TA-TTTATT-
1 ATAAAAATA-TT-AATAATTATATTTTATTA
* *
106833 AT-TAAATATT--TATTTATAATTTTATTA
1 ATAAAAATATTAATAATTAT-ATTTTATTA
*
106860 ATAAAAATATTAATATTGGTATATTTTATTGAA
1 ATAAAAATATTAATAAT--TATATTTTATT--A
106893 ATAAAAATATT-ATAAATTATATT
1 ATAAAAATATTAAT-AATTATATT
106916 AATTATTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 28
0.72 0.06 0.23
Matches are distributed among these distances:
23 4 0.05
24 1 0.01
25 1 0.01
26 10 0.11
27 15 0.17
28 15 0.17
29 5 0.06
30 4 0.05
31 14 0.16
32 5 0.06
33 14 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATAAAAATATTAATAATTATATTTTATTA
Found at i:117593 original size:19 final size:19
Alignment explanation
Indices: 117537--117597 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
117527 CTATTATTAG
*
117537 AATATAAATAATAA-AATA
1 AATATAAATATTAATAATA
* * *
117555 ATTCTAAAATTATTAGTAATA
1 AATAT-AAA-TATTAATAATA
117576 AATATAAATATTAATAATA
1 AATATAAATATTAATAATA
117595 AAT
1 AAT
117598 TAGTTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.09
19 16 0.48
20 7 0.21
21 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
AATATAAATATTAATAATA
Found at i:119142 original size:32 final size:32
Alignment explanation
Indices: 119101--119208 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 32
119091 GGGGCTTGAA
** *
119101 AGCCTACCCAAGAGTGTACCTTAGGTCCTAAG
1 AGCCTACCCAAGAGAATACCTTAGGGCCTAAG
* *
119133 AGCCTACCCAAGGGAATACCTTAGGGCCTTAG
1 AGCCTACCCAAGAGAATACCTTAGGGCCTAAG
* * * *
119165 AGCCTACCCAAG-GAAATAACTTGGGGCTTCAG
1 AGCCTACCCAAGAG-AATACCTTAGGGCCTAAG
*
119197 AACCTACCCAAG
1 AGCCTACCCAAG
119209 TGTCACCTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 1 0.02
32 64 0.98
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (32 bp):
AGCCTACCCAAGAGAATACCTTAGGGCCTAAG
Found at i:123726 original size:20 final size:20
Alignment explanation
Indices: 123701--123745 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
123691 TTAAAATGCT
*
123701 CATTTAACTACATATAGTTG
1 CATTTAACTACATAAAGTTG
* *
123721 CATTTAAGTCCATAAAGTTG
1 CATTTAACTACATAAAGTTG
123741 CATTT
1 CATTT
123746 GGTGGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (20 bp):
CATTTAACTACATAAAGTTG
Found at i:124106 original size:39 final size:39
Alignment explanation
Indices: 124052--124140 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
124042 ATGGGGGAAT
* * *
124052 TTAAGAGTCTCTTGGGAGGTAGAGTGTTTTATTCTGAAA
1 TTAAGATTCTCTTGGGAGGTAGAGTATTTTACTCTGAAA
* * *
124091 TTAAGATTCTCTTGGGAGTTAGAGTATTTTACTGTGAAT
1 TTAAGATTCTCTTGGGAGGTAGAGTATTTTACTCTGAAA
124130 TTAAGAGTTCT
1 TTAAGA-TTCT
124141 TGGAAGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 39 0.91
40 4 0.09
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (39 bp):
TTAAGATTCTCTTGGGAGGTAGAGTATTTTACTCTGAAA
Found at i:127756 original size:39 final size:40
Alignment explanation
Indices: 127696--127791 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 40
127686 CTGAGCTTAT
* * * * * *
127696 GGTAAGAACTTA-CCAAGTGCACAAGGCAAAGGAGTCTGC
1 GGTAAGGACTTACCCTAGTGCACAAAGCAAAAGAGCCTGA
127735 GGTAAGGACTTACCCTA-TGCACAAAGCAAAAGAGCCTGA
1 GGTAAGGACTTACCCTAGTGCACAAAGCAAAAGAGCCTGA
*
127774 GATAAGGACTTACCCTAG
1 GGTAAGGACTTACCCTAG
127792 CTATAGTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 45 0.94
40 3 0.06
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (40 bp):
GGTAAGGACTTACCCTAGTGCACAAAGCAAAAGAGCCTGA
Found at i:128857 original size:27 final size:27
Alignment explanation
Indices: 128823--128889 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
128813 TTCAAAGCTC
** * *
128823 AGGGTATTTTGGTTATTTTA-ATGTTTA
1 AGGGTATTTCAGTAATTTTAGA-GTTCA
128850 AGGGTATTTCAGTAATTTTAGAGTTCA
1 AGGGTATTTCAGTAATTTTAGAGTTCA
128877 AGGGTATTTCAGT
1 AGGGTATTTCAGT
128890 CATATCATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.46
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTAGAGTTCA
Found at i:130077 original size:44 final size:42
Alignment explanation
Indices: 130029--130155 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 42
130019 AAATCCTAAT
130029 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAA
1 TAAAATACTAAAA--TATTTAAACTAAAATACCTAAAACAAAAA
*
130073 TAAAATA-TAAAA-A--T-AA-T---AT-CCTAAAA-AATAAT
1 TAAAATACTAAAATATTTAAACTAAAATACCTAAAACAA-AAA
*
130105 TAAAATACTAAAATATATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACT-AAA-ATATTTAAACTAAAATACCTAAAACAAAAA
130149 TAAAATA
1 TAAAATA
130156 TAATGTTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 28
0.68 0.03 0.29
Matches are distributed among these distances:
31 2 0.03
32 16 0.24
33 3 0.05
34 3 0.05
35 1 0.02
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 7 0.11
44 22 0.33
45 2 0.03
ACGTcount: A:0.63, C:0.11, G:0.01, T:0.25
Consensus pattern (42 bp):
TAAAATACTAAAATATTTAAACTAAAATACCTAAAACAAAAA
Found at i:130097 original size:32 final size:32
Alignment explanation
Indices: 130056--130117 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
130046 TTTAAACTAA
130056 AATACCTAAAACAA-AAATAAAATA-TAAAAAT
1 AATACCTAAAA-AATAAATAAAATACTAAAAAT
*
130087 AATATCCTAAAAAATAATTAAAATACTAAAA
1 AATA-CCTAAAAAATAAATAAAATACTAAAA
130118 TATATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 6 0.22
32 16 0.59
33 5 0.19
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (32 bp):
AATACCTAAAAAATAAATAAAATACTAAAAAT
Found at i:130105 original size:76 final size:75
Alignment explanation
Indices: 129967--130158 Score: 250
Period size: 76 Copynumber: 2.6 Consensus size: 75
129957 ATTAATCACT
* * * * ***
129967 TAAAACTATTTAAACTAAAATACCT---A-AAAACTAATAT-TTAAAATAATATTCTAAATCCTA
1 TAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAAAATA
130027 ATTAAAATAC
66 ATTAAAATAC
130037 TAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAAAAT
1 TAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAAAAT
130102 AATTAAAATAC
65 AATTAAAATAC
* *
130113 TAAAATATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
130159 TGTTTAAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
70 5 0.05
71 20 0.19
74 1 0.01
75 9 0.08
76 71 0.67
ACGTcount: A:0.60, C:0.11, G:0.01, T:0.28
Consensus pattern (75 bp):
TAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAAAATA
ATTAAAATAC
Found at i:131962 original size:13 final size:14
Alignment explanation
Indices: 131940--131970 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
131930 TAAACCAAAT
*
131940 CTGTTTTTTTTGCA
1 CTGTTTTTTCTGCA
131954 CTGTTTTTTCTGCA
1 CTGTTTTTTCTGCA
131968 CTG
1 CTG
131971 CATTGTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.16, T:0.58
Consensus pattern (14 bp):
CTGTTTTTTCTGCA
Found at i:132145 original size:11 final size:11
Alignment explanation
Indices: 132129--132153 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
132119 TTGTTCAGAG
132129 AAAAATAAAAT
1 AAAAATAAAAT
132140 AAAAATAAAAT
1 AAAAATAAAAT
132151 AAA
1 AAA
132154 TAGAATGAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:135909 original size:12 final size:11
Alignment explanation
Indices: 135892--135964 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 11
135882 TTATTATACA
135892 TAATATATACTT
1 TAATATATA-TT
*
135904 TAATATATATA
1 TAATATATATT
135915 T-ATATATATT
1 TAATATATATT
*
135925 TAATATTTAATAT
1 TAATATAT-AT-T
* *
135938 TAAAATATAAT
1 TAATATATATT
135949 TAATA-ATATT
1 TAATATATATT
135959 T-ATATA
1 TAATATA
135965 AAATATTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 3 0.06
10 15 0.31
11 12 0.24
12 12 0.24
13 7 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATATATATT
Found at i:140002 original size:44 final size:42
Alignment explanation
Indices: 139918--140072 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 42
139908 GATCCATTCT
* *
139918 TGCATAAAGCAGTAAGGTTTTACCCTTGCACA-TAGCAAAGGAGCC
1 TGCAGAAA-CAGTAAGGTCTTACCCTT--ACATTAG-AAAGGAGCC
139963 TGCAGAAACAGTAAGGTCTTACCCTTACATGTAGAAAAGGAGCC
1 TGCAGAAACAGTAAGGTCTTACCCTTACAT-TAG-AAAGGAGCC
* *
140007 TGCAGAAA-AGGTAAGGTCTTACCCTTGCACATAAGAGAGGAGCC
1 TGCAGAAACA-GTAAGGTCTTACCCTT--ACATTAGAAAGGAGCC
**
140051 TGCAGAAATGGTAAGGTCTTAC
1 TGCAGAAACAGTAAGGTCTTAC
140073 AAGTTATAGA
Statistics
Matches: 98, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
42 3 0.03
43 1 0.01
44 81 0.83
45 9 0.09
46 4 0.04
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (42 bp):
TGCAGAAACAGTAAGGTCTTACCCTTACATTAGAAAGGAGCC
Found at i:144934 original size:29 final size:32
Alignment explanation
Indices: 144902--144972 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
144892 ACTACTAAAC
*
144902 AATTATAC-AATCA-T-TCACAACTTTTCCAA
1 AATTATACGAATCAGTCTCACAACTTTTCAAA
*
144931 AATTAT-CGAATTAGTCTCACAACTTTTCAAA
1 AATTATACGAATCAGTCTCACAACTTTTCAAA
144962 AATTATA-GAAT
1 AATTATACGAAT
144973 GGTCCCTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 10 0.28
30 1 0.03
31 24 0.67
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.35
Consensus pattern (32 bp):
AATTATACGAATCAGTCTCACAACTTTTCAAA
Found at i:147615 original size:32 final size:32
Alignment explanation
Indices: 147579--147681 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 32
147569 ATCGTTCATC
147579 TTCTT-TTTTTTCTTTTTCTTTTTTTCTTCTTT
1 TTCTTCTTTTTTCTTTTTCTTTTTTTCTT-TTT
*
147611 TTCTTCTTTCTT-TTTTTCTTCTTTCTT-TTTTT
1 TTCTTCTTTTTTCTTTTTCTT-TTT-TTCTTTTT
* *
147643 TTCTTCTTTTTTC-ATGT-TTTTTTTCTTTTT
1 TTCTTCTTTTTTCTTTTTCTTTTTTTCTTTTT
*
147673 TCCTT-TTTT
1 TTCTTCTTTT
147682 CCTTCTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
29 6 0.10
30 12 0.20
31 2 0.03
32 29 0.48
33 10 0.16
34 2 0.03
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.82
Consensus pattern (32 bp):
TTCTTCTTTTTTCTTTTTCTTTTTTTCTTTTT
Found at i:147625 original size:38 final size:39
Alignment explanation
Indices: 147582--147688 Score: 130
Period size: 39 Copynumber: 2.7 Consensus size: 39
147572 GTTCATCTTC
*
147582 TTTTTTTTCTTTTTCTTTTTTTCTTCTT-TTTCTTC-TT
1 TTTTTTTTCTTTTTCTTTTTTTCTTCTTCTTTCTTCATG
*
147619 TCTTTTTTTCTTCTTTCTTTTTTT-TTCTTCTTTTTTCATG
1 T-TTTTTTTCTT-TTTCTTTTTTTCTTCTTCTTTCTTCATG
*
147659 TTTTTTTTCTTTTTTCCTTTTTTCCTTCTT
1 TTTTTTTTC-TTTTT-CTTTTTTTCTTCTT
147689 ATTTTTTAGC
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
37 1 0.02
38 15 0.25
39 28 0.47
40 11 0.18
41 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (39 bp):
TTTTTTTTCTTTTTCTTTTTTTCTTCTTCTTTCTTCATG
Found at i:147666 original size:41 final size:40
Alignment explanation
Indices: 147573--147688 Score: 118
Period size: 41 Copynumber: 3.0 Consensus size: 40
147563 TTAAGCATCG
147573 TTCATC-TTC-TTTTTTTTCTTTTTCTTTTTTTCTTCTTT
1 TTCATCTTTCTTTTTTTTTCTTTTTCTTTTTTTCTTCTTT
*
147611 TTCTTCTTTCTTTTTTTCTTCTTTCTT-TTTTTTTCTTCTTTT
1 TTCATCTTTCTTTTTTT-TTCTTT-TTCTTTTTTTCTTC-TTT
* * * *
147653 TTCAT-GTT-TTTTTTCTT-TTTTCCTTTTTTCCTTCTT
1 TTCATCTTTCTTTTTTTTTCTTTTTCTTTTTTTCTTCTT
147689 ATTTTTTAGC
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
37 3 0.05
38 18 0.27
39 5 0.08
40 12 0.18
41 19 0.29
42 9 0.14
ACGTcount: A:0.02, C:0.19, G:0.01, T:0.78
Consensus pattern (40 bp):
TTCATCTTTCTTTTTTTTTCTTTTTCTTTTTTTCTTCTTT
Found at i:152508 original size:31 final size:31
Alignment explanation
Indices: 152462--152529 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
152452 TTAGTCCCTA
*
152462 AACTTTTTTAAAGTTTATACTTTGGTCACTT
1 AACTTTTCTAAAGTTTATACTTTGGTCACTT
*
152493 AACTTTTCTATAGTTTATACTTTGGTCACTT
1 AACTTTTCTAAAGTTTATACTTTGGTCACTT
152524 AACTTT
1 AACTTT
152530 AAAATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (31 bp):
AACTTTTCTAAAGTTTATACTTTGGTCACTT
Found at i:152548 original size:29 final size:31
Alignment explanation
Indices: 152462--152548 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
152452 TTAGTCCCTA
**
152462 AACTTTTTTAAAGTTTATACTTTGGTCACTT
1 AACTTTTCAAAAGTTTATACTTTGGTCACTT
* *
152493 AACTTTTCTATAGTTTATACTTTGGTCACTT
1 AACTTTTCAAAAGTTTATACTTTGGTCACTT
* *
152524 AAC-TTT-AAAATTTTATATTTTGGTC
1 AACTTTTCAAAAGTTTATACTTTGGTC
152549 CCTGGCCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.30
30 3 0.06
31 32 0.64
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (31 bp):
AACTTTTCAAAAGTTTATACTTTGGTCACTT
Found at i:161041 original size:2 final size:2
Alignment explanation
Indices: 161034--161122 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
161024 CAATGGAACC
161034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
161076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
161118 TA TA T
1 TA TA T
161123 CTCATCAAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:161375 original size:3 final size:3
Alignment explanation
Indices: 161369--161460 Score: 175
Period size: 3 Copynumber: 30.7 Consensus size: 3
161359 ATTATTGTAT
161369 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
161417 CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
161461 GGTAAAGTAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:165472 original size:20 final size:20
Alignment explanation
Indices: 165447--165487 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
165437 ACATGAGGTT
165447 CTAAAAGTGCTCTTTCAATC
1 CTAAAAGTGCTCTTTCAATC
165467 CTAAAAGTGCTCTTTCAATC
1 CTAAAAGTGCTCTTTCAATC
165487 C
1 C
165488 ATATATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (20 bp):
CTAAAAGTGCTCTTTCAATC
Found at i:167258 original size:14 final size:15
Alignment explanation
Indices: 167215--167250 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
167205 TTTAAAATAA
167215 TTAA-AATAATATAT
1 TTAATAATAATATAT
167229 TTAATAATAATATAT
1 TTAATAATAATATAT
167244 TT-ATAAT
1 TTAATAAT
167251 CATTTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATAATAATATAT
Found at i:171268 original size:39 final size:39
Alignment explanation
Indices: 171211--171318 Score: 189
Period size: 39 Copynumber: 2.8 Consensus size: 39
171201 TAATAAATGT
*
171211 ACCAATCTGTCCAGGCTACTCATAAATGTAAGGATGAGC
1 ACCAATCTGTCCAGGCTACTCATAAATGTAAGGAAGAGC
*
171250 ACTAATCTGTCCAGGCTACTCATAAATGTAAGGAAGAGC
1 ACCAATCTGTCCAGGCTACTCATAAATGTAAGGAAGAGC
*
171289 ACCAGTCTGTCCAGGCTACTCATAAATGTA
1 ACCAATCTGTCCAGGCTACTCATAAATGTA
171319 TGTATCCCGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (39 bp):
ACCAATCTGTCCAGGCTACTCATAAATGTAAGGAAGAGC
Found at i:176108 original size:14 final size:15
Alignment explanation
Indices: 176084--176115 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
176074 ACATTAAAAA
176084 TTCTGAAAAACATTT
1 TTCTGAAAAACATTT
176099 TTCT-AAAAACATTT
1 TTCTGAAAAACATTT
176113 TTC
1 TTC
176116 AGTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (15 bp):
TTCTGAAAAACATTT
Found at i:177667 original size:28 final size:28
Alignment explanation
Indices: 177619--177725 Score: 117
Period size: 28 Copynumber: 3.8 Consensus size: 28
177609 ACAGTCAACT
* *
177619 ATTACAAAAATAACACCTTTTTT-TAATA
1 ATTACAAAAATATCA-CTTTTTTAAAATA
* *
177647 AATACAAAAATATCATTTTTTTCAAAATA
1 ATTACAAAAATATCACTTTTTT-AAAATA
* *
177676 ATTACCAAAATATCACTTTTTTGAAATA
1 ATTACAAAAATATCACTTTTTTAAAATA
* *
177704 ATTACCAAAATATCATTTTTTT
1 ATTACAAAAATATCACTTTTTT
177726 CGAAATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 6 0.09
28 39 0.57
29 23 0.34
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.41
Consensus pattern (28 bp):
ATTACAAAAATATCACTTTTTTAAAATA
Found at i:177675 original size:29 final size:29
Alignment explanation
Indices: 177643--177744 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
177633 ACCTTTTTTT
* *
177643 AATAAATACAAAAATATCATTTTTTTCAA
1 AATAAATACCAAAATATCATTTTTTTCGA
* *
177672 AATAATTACCAAAATATCACTTTTTT-GA
1 AATAAATACCAAAATATCATTTTTTTCGA
*
177700 AATAATTACCAAAATATCATTTTTTTCGA
1 AATAAATACCAAAATATCATTTTTTTCGA
* *
177729 AATATATACTAAAATA
1 AATAAATACCAAAATA
177745 ACACCTTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.41
29 38 0.59
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (29 bp):
AATAAATACCAAAATATCATTTTTTTCGA
Found at i:177697 original size:57 final size:57
Alignment explanation
Indices: 177619--177751 Score: 169
Period size: 57 Copynumber: 2.3 Consensus size: 57
177609 ACAGTCAACT
**
177619 ATTACAAAAATAACACCTTTTTTTAATAAATACAAAAATATCATTTTTTTCAAAATA
1 ATTACAAAAATAACACCTTTTTGAAATAAATACAAAAATATCATTTTTTTCAAAATA
* * * * * *
177676 ATTACCAAAATATCACTTTTTTGAAATAATTACCAAAATATCATTTTTTTCGAAAT-
1 ATTACAAAAATAACACCTTTTTGAAATAAATACAAAAATATCATTTTTTTCAAAATA
*
177732 ATATACTAAAATAACACCTT
1 AT-TACAAAAATAACACCTT
177752 ATTAATAGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 2 0.03
57 62 0.97
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (57 bp):
ATTACAAAAATAACACCTTTTTGAAATAAATACAAAAATATCATTTTTTTCAAAATA
Found at i:181043 original size:29 final size:29
Alignment explanation
Indices: 180913--181031 Score: 195
Period size: 29 Copynumber: 4.1 Consensus size: 29
180903 ACATTTTTTT
*
180913 AATAATTACAAAAATATCATTTTTTTCGA
1 AATAATTACCAAAATATCATTTTTTTCGA
180942 AATAATTACCAAAATATCATTTTTTTCGA
1 AATAATTACCAAAATATCATTTTTTTCGA
180971 AATAATTACCAAAATATCA-TTTTTTCGA
1 AATAATTACCAAAATATCATTTTTTTCGA
* * *
180999 ACTAATTATCAAAATATCATTTTTTTTGA
1 AATAATTACCAAAATATCATTTTTTTCGA
181028 AATA
1 AATA
181032 TATACGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
28 26 0.31
29 58 0.69
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (29 bp):
AATAATTACCAAAATATCATTTTTTTCGA
Found at i:181043 original size:57 final size:58
Alignment explanation
Indices: 180913--181031 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 58
180903 ACATTTTTTT
*
180913 AATAATTACAAAAATATCATTTTTTTCGAAATAATTACCAAAATATCATTTTTTTCGA
1 AATAATTACCAAAATATCATTTTTTTCGAAATAATTACCAAAATATCATTTTTTTCGA
* * *
180971 AATAATTACCAAAATATCA-TTTTTTCGAACTAATTATCAAAATATCATTTTTTTTGA
1 AATAATTACCAAAATATCATTTTTTTCGAAATAATTACCAAAATATCATTTTTTTCGA
181028 AATA
1 AATA
181032 TATACGAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 39 0.68
58 18 0.32
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (58 bp):
AATAATTACCAAAATATCATTTTTTTCGAAATAATTACCAAAATATCATTTTTTTCGA
Found at i:181060 original size:29 final size:29
Alignment explanation
Indices: 181028--181099 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
181018 TTTTTTTTGA
*
181028 AATATATACGAAAATAACACCTTCTTAAC
1 AATATTTACGAAAATAACACCTTCTTAAC
* ** *
181057 AATATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACGAAAATAACACCTTCTTAAC
*
181086 AATATTTACAAAAA
1 AATATTTACGAAAA
181100 ATACCACCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (29 bp):
AATATTTACGAAAATAACACCTTCTTAAC
Found at i:181078 original size:86 final size:84
Alignment explanation
Indices: 180889--181081 Score: 185
Period size: 86 Copynumber: 2.2 Consensus size: 84
180879 ACAGTCAACT
* *
180889 ATTACGAAAATAACACATTTTTTTAATAATTACAAAAATATCATTTTTTTCGAAATAATTACCAA
1 ATTACCAAAAT-A-ACATTTTTTGAATAATTACAAAAATATCATTTTTTTCGAAATAATTACCAA
* ** * *
180954 AATATCATTTTTTTCGAAATA
64 AATAACACCTTCTTCAAAATA
* * *
180975 ATTACCAAAATATCATTTTTTCGAACTAATTATC-AAAATATCATTTTTTTTGAAAT-ATATACG
1 ATTACCAAAATAACATTTTTT-GAA-TAATTA-CAAAAATATCATTTTTTTCGAAATAAT-TACC
181038 AAAATAACACCTTCTT-AACAATA
62 AAAATAACACCTTCTTCAA-AATA
* * *
181061 TTTACGAAACTAACATTTTTT
1 ATTACCAAAATAACATTTTTT
181082 TAACAATATT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
84 8 0.09
85 6 0.07
86 73 0.83
87 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (84 bp):
ATTACCAAAATAACATTTTTTGAATAATTACAAAAATATCATTTTTTTCGAAATAATTACCAAAA
TAACACCTTCTTCAAAATA
Found at i:181978 original size:17 final size:19
Alignment explanation
Indices: 181956--181991 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
181946 TCATGCATCA
181956 TGCATTTT-TTT-CATTTT
1 TGCATTTTATTTACATTTT
181973 TGCATTTTATTTACATTTT
1 TGCATTTTATTTACATTTT
181992 CATTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.67
Consensus pattern (19 bp):
TGCATTTTATTTACATTTT
Found at i:190282 original size:13 final size:13
Alignment explanation
Indices: 190264--190300 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
190254 AGTAAACTAT
190264 AAATAATAATTAA
1 AAATAATAATTAA
*
190277 AAATAATAATGAA
1 AAATAATAATTAA
*
190290 AAATAAAAATT
1 AAATAATAATT
190301 CCTACCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAATAATAATTAA
Found at i:196692 original size:19 final size:19
Alignment explanation
Indices: 196662--196712 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
196652 TTTTTTCTTA
*
196662 TTTTCTTA-T-TTTTCCCT
1 TTTTCTTATTCTTTTTCCT
*
196679 TTTT-TTATTCTTTTTTCT
1 TTTTCTTATTCTTTTTCCT
*
196697 TTTTCTTTTTCTTTTT
1 TTTTCTTATTCTTTTT
196713 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 5 0.18
18 10 0.36
19 10 0.36
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTATTCTTTTTCCT
Found at i:196701 original size:6 final size:6
Alignment explanation
Indices: 196677--196783 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
196667 TTATTTTTCC
* *
196677 CTTTTT -TTATT CTTTTTT CTTTTT CTTTTT C--TTT -TTTTT CATTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* * *
196722 CATTTT CTTCTTT CATTTT -TTTTT CTTCTTTT CTTTTT CTGTTT CTTTTT
1 CTTTTT CTT-TTT CTTTTT CTTTTT C-T-TTTT CTTTTT CTTTTT CTTTTT
196772 -TTTTT CTATTTT
1 CTTTTT CT-TTTT
196784 TTAACTCTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
4 3 0.04
5 16 0.20
6 42 0.51
7 16 0.20
8 5 0.06
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:196711 original size:30 final size:29
Alignment explanation
Indices: 196650--196784 Score: 132
Period size: 29 Copynumber: 4.5 Consensus size: 29
196640 GCATCTCTCA
* **
196650 TTTTTTTTCTTATTTTCTTATT-TTTCCCT
1 TTTTTTTTCTT-TTTTCTTTTTCTTTTTCT
196679 TTTTTTATTCTTTTTTCTTTTTCTTTTTC-
1 TTTTTT-TTCTTTTTTCTTTTTCTTTTTCT
* *
196708 TTTTTTTTC-ATTTTCATTTTCTTCTTTCAT
1 TTTTTTTTCTTTTTTCTTTTTCTT-TTTC-T
*
196738 TTTTTTTTCTTCTTTTCTTTTTCTGTTTCTT
1 TTTTTTTTCTT-TTTTCTTTTTCTTTTTC-T
196769 TTTTTTTTCTATTTTT
1 TTTTTTTTCT-TTTTT
196785 TAACTCTTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
27 12 0.13
28 7 0.08
29 21 0.24
30 18 0.20
31 19 0.21
32 12 0.13
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (29 bp):
TTTTTTTTCTTTTTTCTTTTTCTTTTTCT
Found at i:196743 original size:31 final size:30
Alignment explanation
Indices: 196691--196776 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 30
196681 TTTTATTCTT
*
196691 TTTTC-TTTT-TCTTT-TTCTTTTTTTTCA
1 TTTTCATTTTCTCTTTCTTTTTTTTTTTCA
196718 TTTTCATTTTCTTCTTTCATTTTTTTTTCTTC-
1 TTTTCATTTTC-TCTTTC-TTTTTTTTT-TTCA
* *
196750 TTTTCTTTTTCTGTTTCTTTTTTTTTT
1 TTTTCATTTTCTCTTTCTTTTTTTTTT
196777 CTATTTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.10
28 4 0.08
29 1 0.02
30 14 0.28
31 5 0.10
32 18 0.36
33 3 0.06
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (30 bp):
TTTTCATTTTCTCTTTCTTTTTTTTTTTCA
Found at i:196754 original size:47 final size:42
Alignment explanation
Indices: 196650--196785 Score: 114
Period size: 43 Copynumber: 3.1 Consensus size: 42
196640 GCATCTCTCA
* *
196650 TTTTTTTTCTTATTTTCTTATTTTTCCCTTTTTTTATTCTTTT
1 TTTTTTTTCTT-TTTTCTTTTTTTTCACTTTTTTTATTCTTTT
* * *
196693 TTCTTTTTC-TTTTTCTTTTTTTTCATTTTCATTTTCTTCTTTCAT
1 TTTTTTTTCTTTTTTCTTTTTTTTCACTTT--TTTTATTCTTT--T
* * *
196738 TTTTTTTTCTTCTTTTCTTTTTCTGTT-TCTTTTTTTTTTCTATT
1 TTTTTTTTCTT-TTTTCTTTTT-T-TTCACTTTTTTTATTCTTTT
196782 TTTT
1 TTTT
196786 AACTCTTATG
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
41 16 0.21
42 1 0.01
43 18 0.24
44 5 0.07
45 9 0.12
46 10 0.13
47 10 0.13
48 4 0.05
49 2 0.03
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (42 bp):
TTTTTTTTCTTTTTTCTTTTTTTTCACTTTTTTTATTCTTTT
Found at i:203020 original size:17 final size:16
Alignment explanation
Indices: 203000--203032 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
202990 TTTTGAAACT
203000 ATATGTTTTTTAAAAAA
1 ATAT-TTTTTTAAAAAA
203017 ATATTTTTTTAAAAAA
1 ATATTTTTTTAAAAAA
203033 TTACATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTTTTTTAAAAAA
Found at i:203093 original size:37 final size:36
Alignment explanation
Indices: 203037--203201 Score: 153
Period size: 36 Copynumber: 4.6 Consensus size: 36
203027 AAAAAATTAC
203037 ATAT-TATATGTTTTC-AAAAAACATTTTAAAAACT
1 ATATATATATGTTTTCAAAAAAACATTTTAAAAACT
* * *
203071 ATATACTATAAGTTTTCAAAAAAA-A-ATTAAACACT
1 ATATA-TATATGTTTTCAAAAAAACATTTTAAAAACT
* * *
203106 ATATATTATATTTTTTTCAAAAATACGTTTTCAAAAACT
1 ATATA-TATA-TGTTTTCAAAAAAACATTTT-AAAAACT
*
203145 ATATTATATATACGTTTTC--AAAAATATTTTAAAAACT
1 ATA-TATATAT--GTTTTCAAAAAAACATTTTAAAAACT
*
203182 ATATATTTATGTTTTCAAAA
1 ATATATATATGTTTTCAAAA
203202 CTATATATTA
Statistics
Matches: 104, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
34 10 0.10
35 17 0.16
36 30 0.29
37 16 0.15
38 11 0.11
39 13 0.12
40 7 0.07
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (36 bp):
ATATATATATGTTTTCAAAAAAACATTTTAAAAACT
Found at i:203142 original size:111 final size:112
Alignment explanation
Indices: 202999--203201 Score: 261
Period size: 111 Copynumber: 1.8 Consensus size: 112
202989 CTTTTGAAAC
** * *
202999 TATATGTTTTTTAAAAAAATATTTTTTTAAAAAAT-TACATAT-TATATGTTTTCAAAAAACATT
1 TATATGTTTTTTAAAAAAATACGTTTTCAAAAAATATA-ATATATATACGTTTTC-AAAAACATT
203062 TTAAAAACTATATACTATAAGTTTTCAAAAAAAAATTAAACACTATATAT
64 TTAAAAACTATATA-TATAAGTTTTCAAAAAAAAATTAAACACTATATAT
* * * *
203112 TATAT-TTTTTT-CAAAAATACGTTTTCAAAAACTATATTATATATACGTTTTCAAAAATATTTT
1 TATATGTTTTTTAAAAAAATACGTTTTCAAAAAATATAATATATATACGTTTTCAAAAACATTTT
* *
203175 AAAAACTATATATTTATGTTTTCAAAA
66 AAAAACTATATATATAAGTTTTCAAAA
203202 CTATATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
110 13 0.17
111 42 0.54
112 18 0.23
113 5 0.06
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (112 bp):
TATATGTTTTTTAAAAAAATACGTTTTCAAAAAATATAATATATATACGTTTTCAAAAACATTTT
AAAAACTATATATATAAGTTTTCAAAAAAAAATTAAACACTATATAT
Found at i:203162 original size:76 final size:71
Alignment explanation
Indices: 203028--203201 Score: 208
Period size: 76 Copynumber: 2.4 Consensus size: 71
203018 TATTTTTTTA
* *
203028 AAAAATTACATATTATATGTTTTCAAAAAACATTTTAAAAACTATATACTATAAGTTTTCAAAAA
1 AAAAACTATATATTATATGTTTTCAAAAAACATTTTAAAAACTATATACTATAAGTTTTCAAAAA
203093 AAAATT
66 AAAATT
* * *
203099 AAACACTATATATTATATTTTTTTCAAAAATACGTTTTCAAAAACTATATTA-TATATACGTTTT
1 AAAAACTATATATTATA-TGTTTTCAAAAA-ACATTTT-AAAAACTATA-TACTATA-A-GTTTT
* **
203163 CAAAAATATTTT
60 CAAAAAAAAATT
203175 AAAAACTATATATT-TATGTTTTCAAAA
1 AAAAACTATATATTATATGTTTTCAAAA
203202 CTATATATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
71 14 0.16
72 11 0.13
73 6 0.07
74 24 0.28
75 5 0.06
76 27 0.31
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (71 bp):
AAAAACTATATATTATATGTTTTCAAAAAACATTTTAAAAACTATATACTATAAGTTTTCAAAAA
AAAATT
Found at i:203201 original size:22 final size:23
Alignment explanation
Indices: 203171--203227 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
203161 TTCAAAAATA
*
203171 TTTTAAAAACTATATATT-TATG
1 TTTTCAAAACTATATATTATATG
203193 TTTTCAAAACTATATATTATATG
1 TTTTCAAAACTATATATTATATG
203216 TTTTCCAAAACT
1 TTTT-CAAAACT
203228 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 17 0.53
23 8 0.25
24 7 0.22
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTCAAAACTATATATTATATG
Found at i:203546 original size:13 final size:12
Alignment explanation
Indices: 203526--203681 Score: 77
Period size: 13 Copynumber: 13.2 Consensus size: 12
203516 GTATATTAAA
203526 TATATTATAT-T
1 TATATTATATAT
203537 ATAGTATTATATAT
1 -TA-TATTATATAT
203551 TATTATTATATAT
1 TA-TATTATATAT
*
203564 TATAATATATTATAG
1 TAT-AT-TA-TATAT
203579 TATTATTATATAT
1 TA-TATTATATAT
*
203592 TATTGTTATATAT
1 TA-TATTATATAT
*
203605 TATATTA-A-AG
1 TATATTATATAT
* *
203615 TATATTCTTAAAT
1 TATATT-ATATAT
203628 T-TATT-T-T-T
1 TATATTATATAT
203636 TATA-TATATA-
1 TATATTATATAT
*
203646 CA-ATT-TATAT
1 TATATTATATAT
203656 TATTATTAT-TAT
1 TA-TATTATATAT
203668 TATATTAT-TAT
1 TATATTATATAT
203679 TAT
1 TAT
203682 TAATATTTTC
Statistics
Matches: 115, Mismatches: 11, Indels: 37
0.71 0.07 0.23
Matches are distributed among these distances:
8 3 0.03
9 8 0.07
10 12 0.10
11 13 0.11
12 20 0.17
13 45 0.39
14 5 0.04
15 8 0.07
16 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (12 bp):
TATATTATATAT
Found at i:203549 original size:10 final size:9
Alignment explanation
Indices: 203526--203609 Score: 71
Period size: 10 Copynumber: 8.6 Consensus size: 9
203516 GTATATTAAA
203526 TATATTATAT
1 TATA-TATAT
*
203536 TATA-GTAT
1 TATATATAT
203544 TATATATTAT
1 TATATA-TAT
203554 TATTATATAT
1 TA-TATATAT
203564 TATAATATAT
1 TAT-ATATAT
203574 TATAGTATTAT
1 TATA-TA-TAT
203585 TATATATTAT
1 TATATA-TAT
*
203595 TGTTATATAT
1 T-ATATATAT
203605 TATAT
1 TATAT
203610 TAAAGTATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.11
9 5 0.08
10 36 0.57
11 15 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (9 bp):
TATATATAT
Found at i:203556 original size:3 final size:3
Alignment explanation
Indices: 203528--203688 Score: 65
Period size: 3 Copynumber: 54.3 Consensus size: 3
203518 ATATTAAATA
* *
203528 TAT TA- TAT TA- TAG TAT TAT ATAT TAT TAT TAT ATAT TAT AAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT -TAT
* * * *
203574 TA- TAG TAT TAT TAT ATAT TAT TGT TAT ATAT TA- TAT TA- AAG TA-
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * *
203617 TAT TCT TA- AATT TAT T-T T-T TAT ATAT ATAC AAT T-T ATAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT -TAT -TAT TAT TAT -TAT TAT TAT
*
203662 TAT TAT TA- TAT TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
203689 TTCTTTTTTA
Statistics
Matches: 122, Mismatches: 18, Indels: 36
0.69 0.10 0.20
Matches are distributed among these distances:
2 19 0.16
3 81 0.66
4 22 0.18
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:203577 original size:28 final size:28
Alignment explanation
Indices: 203531--203688 Score: 94
Period size: 28 Copynumber: 6.0 Consensus size: 28
203521 TTAAATATAT
*
203531 TATATTATAGTAT-TATATATTATTATTA
1 TATATTATAATATAT-TATATTATTATTA
*
203559 TATATTATAATATATTATAGTATTATTA
1 TATATTATAATATATTATATTATTATTA
**
203587 TATATTATTGT-TA-TATATTA-TATTAAA
1 TATATTATAATATATTATATTATTATT--A
* *
203614 GTATATTCT--TAAATT-TATT-TT-TTA
1 -TATATTATAATATATTATATTATTATTA
203638 TATA-TATACA-AT-TTATATTATTATTA
1 TATATTATA-ATATATTATATTATTATTA
*
203664 T-TATTAT-AT-TATTATTATTAATATT
1 TATATTATAATATATTA-TATTATTATT
203689 TTCTTTTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
22 2 0.02
23 6 0.06
24 8 0.08
25 11 0.11
26 25 0.24
27 9 0.09
28 41 0.40
29 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.58
Consensus pattern (28 bp):
TATATTATAATATATTATATTATTATTA
Found at i:203601 original size:41 final size:42
Alignment explanation
Indices: 203517--203608 Score: 143
Period size: 41 Copynumber: 2.2 Consensus size: 42
203507 AATAGTAGTG
*
203517 TATATTA-AATATATTATATTATAGTATTATATATTATTATTA
1 TATATTATAATATATTATAGTATA-TATTATATATTATTATTA
*
203559 TATATTATAATATATTATAGTAT-TATTATATATTATTGTTA
1 TATATTATAATATATTATAGTATATATTATATATTATTATTA
203600 TATATTATA
1 TATATTATA
203609 TTAAAGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 26 0.55
42 7 0.15
43 14 0.30
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (42 bp):
TATATTATAATATATTATAGTATATATTATATATTATTATTA
Found at i:203679 original size:23 final size:23
Alignment explanation
Indices: 203529--203688 Score: 85
Period size: 23 Copynumber: 7.3 Consensus size: 23
203519 TATTAAATAT
*
203529 ATTA-TATTATAGTATTATATATT
1 ATTATTATTATATTATTAT-TATT
*
203552 ATTATTA-TATATTATAATATATT
1 ATTATTATTATATTATTAT-TATT
*
203575 ATAGTATTATTATA-TATTATTGTT
1 AT--TATTATTATATTATTATTATT
* *
203599 A-TA-TATTATATTA-AAGTA-T
1 ATTATTATTATATTATTATTATT
* *
203618 ATTCTTA-AAT-TTATT-TT-TT
1 ATTATTATTATATTATTATTATT
**
203637 ATATATATACAAT-TTA-TATTATT
1 AT-TAT-TATTATATTATTATTATT
203660 ATTATTATTATATTATTATTATT
1 ATTATTATTATATTATTATTATT
*
203683 AATATT
1 ATTATT
203689 TTCTTTTTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
19 9 0.08
20 14 0.13
21 13 0.12
22 14 0.13
23 36 0.34
24 6 0.06
25 10 0.09
26 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (23 bp):
ATTATTATTATATTATTATTATT
Found at i:204227 original size:10 final size:10
Alignment explanation
Indices: 204212--204240 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
204202 CAAGGAATAC
204212 ATAGCAAAAT
1 ATAGCAAAAT
204222 ATAGCAAAAT
1 ATAGCAAAAT
204232 ATAGCAAAA
1 ATAGCAAAA
204241 CCCTAAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (10 bp):
ATAGCAAAAT
Found at i:204916 original size:7 final size:7
Alignment explanation
Indices: 204904--204928 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
204894 ATTTCTTTTA
204904 ATTTAAT
1 ATTTAAT
204911 ATTTAAT
1 ATTTAAT
204918 ATTTAAT
1 ATTTAAT
204925 ATTT
1 ATTT
204929 TTCATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:214179 original size:15 final size:16
Alignment explanation
Indices: 214156--214195 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
214146 ATATTAGTAT
214156 TTTAA-AATAAT-ATA
1 TTTAATAATAATAATA
214170 TTTAATAATAATAATA
1 TTTAATAATAATAATA
214186 TTTATATAAT
1 TTTA-ATAAT
214196 CATTTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 6 0.26
16 7 0.30
17 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAATAATAATAATA
Found at i:215372 original size:3 final size:3
Alignment explanation
Indices: 215364--215426 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
215354 ATATATATAT
215364 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
215412 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
215427 TGATAGTGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:221174 original size:13 final size:13
Alignment explanation
Indices: 221156--221182 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
221146 TGGTGAGCTG
221156 ACTATTATGAATA
1 ACTATTATGAATA
221169 ACTATTATGAATA
1 ACTATTATGAATA
221182 A
1 A
221183 AATCTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ACTATTATGAATA
Found at i:222173 original size:40 final size:40
Alignment explanation
Indices: 222128--222207 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
222118 CATTTGTTTG
*
222128 TGTTCATTCATTTAATTAAACGAACAGAAAACTTTATTCA
1 TGTTCATTCATTTAATTAAACGAACAGAAAACATTATTCA
**
222168 TGTTCATTCATTTAATTAAACGAACCTAAAACATTATTCA
1 TGTTCATTCATTTAATTAAACGAACAGAAAACATTATTCA
222208 CGAATTTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (40 bp):
TGTTCATTCATTTAATTAAACGAACAGAAAACATTATTCA
Found at i:233170 original size:60 final size:60
Alignment explanation
Indices: 233085--233218 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 60
233075 TCTTGGTAAA
* * ** **
233085 TTATACAAATGATCCCTCAATTATAGGGTGTTACTTTGTTGAGTCTCTTGTTTATTAAAAG
1 TTATA-AAATGATCCCTCAACTATAGGGTATTACTTTGTTGAGTCTCCCGACTATTAAAAG
* * *
233146 TTATAAAATGGTCCTTCAACTATAGGGTATTATTTTGTTGAGTCTCCCGACTATTAAAAG
1 TTATAAAATGATCCCTCAACTATAGGGTATTACTTTGTTGAGTCTCCCGACTATTAAAAG
*
233206 TTACAAAATGATC
1 TTATAAAATGATC
233219 ATTCGACTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 57 0.92
61 5 0.08
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (60 bp):
TTATAAAATGATCCCTCAACTATAGGGTATTACTTTGTTGAGTCTCCCGACTATTAAAAG
Found at i:235928 original size:29 final size:29
Alignment explanation
Indices: 235896--235963 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
235886 TGTCAACACT
*
235896 AAAAAGTAAAGG-CACAAAT-TAAAATAAC
1 AAAAAATAAAGGTCACAAATGT-AAATAAC
* * *
235924 AAAAATTTAAAGGTTAGAAATGTAAATAAC
1 AAAAA-ATAAAGGTCACAAATGTAAATAAC
235954 AAAAAATAAA
1 AAAAAATAAA
235964 TCGATCGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 5 0.15
29 10 0.30
30 17 0.52
31 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (29 bp):
AAAAAATAAAGGTCACAAATGTAAATAAC
Found at i:245837 original size:170 final size:170
Alignment explanation
Indices: 245555--245894 Score: 680
Period size: 170 Copynumber: 2.0 Consensus size: 170
245545 AGTCCACTCT
245555 TGAATAGCTTGAATCATGGAAGAATCTGTAACTACTCCATGTTGAGAAATAGTATGTCCGAGATA
1 TGAATAGCTTGAATCATGGAAGAATCTGTAACTACTCCATGTTGAGAAATAGTATGTCCGAGATA
245620 TTCCACTTCTGTTTGCCCGAAAAATCATTTACTCCGCTTAGCAAAAAGCTGATTTGTCCTTACAA
66 TTCCACTTCTGTTTGCCCGAAAAATCATTTACTCCGCTTAGCAAAAAGCTGATTTGTCCTTACAA
245685 TCTGTAAAACAGTTCTCAATTGCTGCACATGACTAAGCAA
131 TCTGTAAAACAGTTCTCAATTGCTGCACATGACTAAGCAA
245725 TGAATAGCTTGAATCATGGAAGAATCTGTAACTACTCCATGTTGAGAAATAGTATGTCCGAGATA
1 TGAATAGCTTGAATCATGGAAGAATCTGTAACTACTCCATGTTGAGAAATAGTATGTCCGAGATA
245790 TTCCACTTCTGTTTGCCCGAAAAATCATTTACTCCGCTTAGCAAAAAGCTGATTTGTCCTTACAA
66 TTCCACTTCTGTTTGCCCGAAAAATCATTTACTCCGCTTAGCAAAAAGCTGATTTGTCCTTACAA
245855 TCTGTAAAACAGTTCTCAATTGCTGCACATGACTAAGCAA
131 TCTGTAAAACAGTTCTCAATTGCTGCACATGACTAAGCAA
245895 ATCAGAATTG
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (170 bp):
TGAATAGCTTGAATCATGGAAGAATCTGTAACTACTCCATGTTGAGAAATAGTATGTCCGAGATA
TTCCACTTCTGTTTGCCCGAAAAATCATTTACTCCGCTTAGCAAAAAGCTGATTTGTCCTTACAA
TCTGTAAAACAGTTCTCAATTGCTGCACATGACTAAGCAA
Found at i:246963 original size:40 final size:40
Alignment explanation
Indices: 246908--246987 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
246898 AGTGACAAAA
246908 CTATGAGTACTGCCACTGTTAATCAATATACTGAGTGGTT
1 CTATGAGTACTGCCACTGTTAATCAATATACTGAGTGGTT
246948 CTATGAGTACTGCCACTGTTAATCAATATACTGAGTGGTT
1 CTATGAGTACTGCCACTGTTAATCAATATACTGAGTGGTT
246988 TCCCTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (40 bp):
CTATGAGTACTGCCACTGTTAATCAATATACTGAGTGGTT
Found at i:247779 original size:28 final size:28
Alignment explanation
Indices: 247747--247833 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
247737 TAGTATTTTA
247747 AAATTATTAAAATAATATATTTAATAAT
1 AAATTATTAAAATAATATATTTAATAAT
* * * **
247775 AAATTATCTATAATCATTTA-TTATATTTT
1 AAATTAT-TAAAATAATATATTTA-ATAAT
* *
247804 AAATGATTAAAATAATATATTTTATAAT
1 AAATTATTAAAATAATATATTTAATAAT
247832 AA
1 AA
247834 TTTGTTATAT
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 24 0.55
29 20 0.45
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (28 bp):
AAATTATTAAAATAATATATTTAATAAT
Found at i:248352 original size:30 final size:31
Alignment explanation
Indices: 248318--248390 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
248308 GAAATTAGAC
*
248318 AAAATATTAATTTGAC-CTTAAACTTTACAT
1 AAAATATTAATTTAACTCTTAAACTTTACAT
* * *
248348 AAAATACTAATCTAACTCTTAAACTTTATAT
1 AAAATATTAATTTAACTCTTAAACTTTACAT
*
248379 AAAATATGAATT
1 AAAATATTAATT
248391 GACTCCTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (31 bp):
AAAATATTAATTTAACTCTTAAACTTTACAT
Found at i:250144 original size:15 final size:16
Alignment explanation
Indices: 250124--250159 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
250114 ATTTAAATCG
250124 ATTTATTA-TTTTATA
1 ATTTATTATTTTTATA
250139 ATTTATTATTTTTATA
1 ATTTATTATTTTTATA
250155 ATTTA
1 ATTTA
250160 AACACTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTATTTTTATA
Found at i:258415 original size:13 final size:13
Alignment explanation
Indices: 258399--258424 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
258389 TTTTCCGTTA
258399 AATTTTTATTTTT
1 AATTTTTATTTTT
258412 AATTTTTATTTTT
1 AATTTTTATTTTT
258425 GTTCGACCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
AATTTTTATTTTT
Found at i:263474 original size:18 final size:18
Alignment explanation
Indices: 263451--263490 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
263441 CGGGGTCGTA
263451 GGAGCAGGATCATCTATC
1 GGAGCAGGATCATCTATC
263469 GGAGCAGGATCATCTATC
1 GGAGCAGGATCATCTATC
263487 GGAG
1 GGAG
263491 GTGGGGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (18 bp):
GGAGCAGGATCATCTATC
Found at i:265292 original size:129 final size:129
Alignment explanation
Indices: 265062--265322 Score: 380
Period size: 129 Copynumber: 2.0 Consensus size: 129
265052 TATGCATGTT
* * * * * *
265062 CGGGTTTGACTGATAATTTGGAGGCTTTTGAGTTCGAATTTGGCAAAACGGACTTCAGATTCAAA
1 CGGGTTTGACTAATAATTTCGAGGCTTTTGAGATCAAATTTGGCAAAACAGACTTCAGAATCAAA
* *
265127 CTCAGGACGTCGAAAAACACAAAATATGACTTTTTGAAATTTTTGACTTTTTGGTCAAAGTCAA
66 CTCAGGACGTCGAAAAACACAAAATATGACTTTTTGAAAATTTTAACTTTTTGGTCAAAGTCAA
**
265191 CGGGTTTGACTAATAATTTCGAGG-TTTTCGAGATCAAATTTGGCAAAACAGACTTCAGAATCGG
1 CGGGTTTGACTAATAATTTCGAGGCTTTT-GAGATCAAATTTGGCAAAACAGACTTCAGAATCAA
* * * *
265255 ACTCAGGACGTCGAAAAATATAAAATATGATTTTTTGAAAATTTTAACTTTTTGGTCAAAGTCGA
65 ACTCAGGACGTCGAAAAACACAAAATATGACTTTTTGAAAATTTTAACTTTTTGGTCAAAGTCAA
265320 CGG
1 CGG
265323 TAAACGGTCG
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
128 4 0.03
129 113 0.97
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (129 bp):
CGGGTTTGACTAATAATTTCGAGGCTTTTGAGATCAAATTTGGCAAAACAGACTTCAGAATCAAA
CTCAGGACGTCGAAAAACACAAAATATGACTTTTTGAAAATTTTAACTTTTTGGTCAAAGTCAA
Found at i:269368 original size:14 final size:14
Alignment explanation
Indices: 269315--269371 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
269305 CAAATGGCTC
*
269315 GTTCGTTCATTTAC
1 GTTCGTTCATTTAT
269329 GTTCG---ATTATAT
1 GTTCGTTCATT-TAT
*
269341 GTTCATTCATTTAT
1 GTTCGTTCATTTAT
269355 GTTCGTTCATTTAT
1 GTTCGTTCATTTAT
269369 GTT
1 GTT
269372 GGAACAGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 3 0.08
12 6 0.17
14 24 0.67
15 3 0.08
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (14 bp):
GTTCGTTCATTTAT
Found at i:269650 original size:10 final size:10
Alignment explanation
Indices: 269635--269702 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
269625 GTGTTTGTGT
269635 TGTTCGTTTA
1 TGTTCGTTTA
269645 TGTTCGTTTA
1 TGTTCGTTTA
*
269655 TTGTGTTCGTTAA
1 ---TGTTCGTTTA
*
269668 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
269682 TGTTCGTTTA
1 TGTTCGTTTA
269692 TGTTCGTTTA
1 TGTTCGTTTA
269702 T
1 T
269703 TATTTAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 27 0.57
11 3 0.06
13 11 0.23
14 6 0.13
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:277284 original size:16 final size:18
Alignment explanation
Indices: 277255--277295 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
277245 AACTATTTTT
277255 TCTCTCACTCGACCACTC
1 TCTCTCACTCGACCACTC
**
277273 TCTCTC-CT-GACCGTTC
1 TCTCTCACTCGACCACTC
277289 TCTCTCA
1 TCTCTCA
277296 TCTTTTACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.12, C:0.46, G:0.07, T:0.34
Consensus pattern (18 bp):
TCTCTCACTCGACCACTC
Found at i:277957 original size:28 final size:29
Alignment explanation
Indices: 277912--277978 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
277902 AGCGCATTTA
* *
277912 GCAGCCTGATGCAGTAGGGG-TACATAAT
1 GCAGTCTGATACAGTAGGGGATACATAAT
* *
277940 GCGGTCTGATACAGTAGGGGATACATAGT
1 GCAGTCTGATACAGTAGGGGATACATAAT
277969 GCAGTCTGAT
1 GCAGTCTGAT
277979 TTGATTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GCAGTCTGATACAGTAGGGGATACATAAT
Found at i:285559 original size:47 final size:47
Alignment explanation
Indices: 285505--285639 Score: 234
Period size: 47 Copynumber: 2.9 Consensus size: 47
285495 ACCATTTATC
*
285505 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAAATT
285552 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAAATT
* * *
285599 CCATAAGCTCATAAGCTTATTTTATCAATATACTTGCCATT
1 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATT
285640 ATTCCATAAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (47 bp):
CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAAATT
Found at i:285670 original size:20 final size:20
Alignment explanation
Indices: 285645--285687 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
285635 CCATTATTCC
* *
285645 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
*
285665 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
285685 ATA
1 ATA
285688 GCCCAATATA
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:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:285841 original size:59 final size:59
Alignment explanation
Indices: 285749--285877 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
285739 CGTAGTGCTA
* * * **
285749 TCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
285808 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
285867 TCCCGAATATG
1 TCCCGAATATG
285878 TAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:288057 original size:23 final size:24
Alignment explanation
Indices: 288031--288078 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
288021 TGTATATAGA
288031 AGAT-ATAATAAAT-TTTATATCTT
1 AGATAATAA-AAATATTTATATCTT
288054 AGATAATAAAAATAATTTATATCTT
1 AGATAATAAAAAT-ATTTATATCTT
288079 TTTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
AGATAATAAAAATATTTATATCTT
Done.