Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013444.1 Kokia drynarioides strain JFW-HI SEQ_128470, 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: 131314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:5456 original size:13 final size:13
Alignment explanation
Indices: 5438--5488 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
5428 CTTAACTCAA
5438 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
5451 ACTTTTC-AAAAT
1 ACTTTTCAAAAAT
* **
5463 CACTTTTTAAAAGC
1 -ACTTTTCAAAAAT
*
5477 ACTTATCAAAAA
1 ACTTTTCAAAAA
5489 CAATGCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.17
13 22 0.73
14 3 0.10
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:5632 original size:24 final size:25
Alignment explanation
Indices: 5604--5657 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
5594 TTGTTTTTAA
*
5604 AATTTATTAAATA-ATATATTT-TT
1 AATTTATCAAATATATATATTTGTT
*
5627 ATATTT-TCAAATATATGTATTTGTT
1 A-ATTTATCAAATATATATATTTGTT
5652 AATTTA
1 AATTTA
5658 AGGGTTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 7 0.28
24 15 0.60
25 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
AATTTATCAAATATATATATTTGTT
Found at i:5865 original size:18 final size:18
Alignment explanation
Indices: 5826--5865 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5816 TTTAGTAATA
* **
5826 TTTTTATCTCAAAAGTGT
1 TTTTTATCCCAAAAGTAC
5844 TTTTTATCCCAAAAGTAC
1 TTTTTATCCCAAAAGTAC
5862 TTTT
1 TTTT
5866 GAAAAGCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTTTATCCCAAAAGTAC
Found at i:7782 original size:13 final size:13
Alignment explanation
Indices: 7764--7790 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7754 ATATACCAAT
7764 TATTAATATAACA
1 TATTAATATAACA
7777 TATTAATATAACA
1 TATTAATATAACA
7790 T
1 T
7791 TTACCTTTAT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTAATATAACA
Found at i:9720 original size:22 final size:22
Alignment explanation
Indices: 9692--9735 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9682 AATATGATTT
*
9692 ATTAATTAATTTAATTAGATAA
1 ATTAATTAATTTAATTAAATAA
**
9714 ATTAATTTTTTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
9736 TTTTCTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATTAATTTAATTAAATAA
Found at i:9738 original size:17 final size:18
Alignment explanation
Indices: 9711--9744 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9701 TTTAATTAGA
*
9711 TAAATTAATTTTTTTAAT
1 TAAATTAATTTTCTTAAT
9729 TAAA-TAATTTTCTTAA
1 TAAATTAATTTTCTTAA
9745 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTAATTTTCTTAAT
Found at i:10368 original size:30 final size:30
Alignment explanation
Indices: 10332--10396 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
10322 ACTTATTTTA
*
10332 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTACTATTTTAGAGGCAT
*
10362 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTATTACTATTTTAGAGGCAT
10392 TTGTT
1 TTGTT
10397 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATTTTAGAGGCAT
Found at i:12753 original size:23 final size:23
Alignment explanation
Indices: 12723--12780 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
12713 GAGCAAAAAA
* *
12723 TGCTAAATCCAGGAGCATCAAAG
1 TGCTAAATACAGGAGCACCAAAG
* *
12746 TGTTAAATACGGGAGCACCAAAG
1 TGCTAAATACAGGAGCACCAAAG
12769 TGCTAAATACAG
1 TGCTAAATACAG
12781 AACCACTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (23 bp):
TGCTAAATACAGGAGCACCAAAG
Found at i:15582 original size:97 final size:97
Alignment explanation
Indices: 15416--15609 Score: 277
Period size: 97 Copynumber: 2.0 Consensus size: 97
15406 AACCTTGAAA
* * **
15416 AAGGGTATTCTATTATCACGGTTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAATTTTTCA
1 AAGGGTATTCGATTATCACGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAATTTTTCA
*
15481 AAACC-CGAAATAAAGGAATATTGCCTCAATTT
66 AAACCTC-AAATAAAAGAATATTGCCTCAATTT
15513 AAGGGTATTCGATTATC-CTGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACGAA-TTTT
1 AAGGGTATTCGATTATCAC-GGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCAC-AATTTTT
* *
15576 CAAAACCTCAAATAAAATAATATTGCCTCGATTT
64 CAAAACCTCAAATAAAAGAATATTGCCTCAATTT
15610 TAAATATTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
96 1 0.01
97 83 0.95
98 3 0.03
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGGTATTCGATTATCACGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAATTTTTCA
AAACCTCAAATAAAAGAATATTGCCTCAATTT
Found at i:15752 original size:14 final size:14
Alignment explanation
Indices: 15733--15773 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
15723 AAGAATGAAC
15733 AAATATACGAAAAT
1 AAATATACGAAAAT
15747 AAATATGA-GAAAAAT
1 AAATAT-ACG-AAAAT
15762 AAA-ATACGAAAA
1 AAATATACGAAAA
15774 AATAAACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.21
14 10 0.42
15 9 0.38
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (14 bp):
AAATATACGAAAAT
Found at i:15774 original size:14 final size:15
Alignment explanation
Indices: 15733--15779 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
15723 AAGAATGAAC
15733 AAATATACG-AAAAT
1 AAATATACGAAAAAT
15747 AAATATGA-GAAAAAT
1 AAATAT-ACGAAAAAT
15762 AAA-ATACGAAAAAAT
1 AAATATACG-AAAAAT
15777 AAA
1 AAA
15780 CGAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 18 0.62
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (15 bp):
AAATATACGAAAAAT
Found at i:16054 original size:30 final size:29
Alignment explanation
Indices: 15912--16311 Score: 370
Period size: 29 Copynumber: 13.8 Consensus size: 29
15902 AAAATTTTAG
* * *
15912 GGGTAAAAATGTCATTTTAGGAAAATTCGA
1 GGGTAAAAATGTAATTTTTGG-AAGTTCGA
* *
15942 -GGTGAAAATGTGATTTTTGGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTTCGA
* *
15970 GAGTAAAAATGTGATTTTTGGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTTCGA
* **
15999 GGGCAAAAATGTAATTTTTAAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTTCGA
* *
16028 GGGCAAAAATGTAAATTTTGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTG-GAAGTTCGA
* * *
16058 GGGTCAAAATGTGATTTTTTGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTTCGA
*
16087 GGGAAAAAAATGTAATTTTTGAGAAGTT-GA
1 GGG-TAAAAATGTAATTTTTG-GAAGTTCGA
* * *
16117 GGGTCAAGATGTAATTTTTGGAAGTCCG-
1 GGGTAAAAATGTAATTTTTGGAAGTTCGA
* *
16145 GGG--GAAATATAATTTTTGAGAAGTTCG-
1 GGGTAAAAATGTAATTTTTG-GAAGTTCGA
* * * * *
16172 GAGGTTAATATGTGATTTTTGTAAGTT-TA
1 G-GGTAAAAATGTAATTTTTGGAAGTTCGA
*
16201 GGGGTAAAAATGTAATTTTTGGAAGTTTGA
1 -GGGTAAAAATGTAATTTTTGGAAGTTCGA
*
16231 GGGGTAAAAATGTAATTTTTGGAA-TTCAA
1 -GGGTAAAAATGTAATTTTTGGAAGTTCGA
16260 GGGTAAAAAAT-TAATTTTTGAGAAGTTCGA
1 GGGT-AAAAATGTAATTTTTG-GAAGTTCGA
* *
16290 GGGTTAAAATGTGA-TTTTGGAA
1 GGGTAAAAATGTAATTTTTGGAA
16312 AAGTGTAAGG
Statistics
Matches: 307, Mismatches: 47, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
26 12 0.04
27 8 0.03
28 33 0.11
29 160 0.52
30 88 0.29
31 6 0.02
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCGA
Found at i:16075 original size:59 final size:59
Alignment explanation
Indices: 15937--16311 Score: 380
Period size: 59 Copynumber: 6.5 Consensus size: 59
15927 TTTAGGAAAA
* * * *
15937 TTCGA-GGTGAAAATGTGATTTTTGGAAGTTCGAGAGTAAAAATGTGATTTTTG-GAAG
1 TTCGAGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAG
* ** * *
15994 TTCGAGGG-CAAAAATGTAATTTTTAAAAGTTCGAGGGCAAAAATGTAAATTTTGAGAAG
1 TTCGAGGGTC-AAAATGTGATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAG
*
16053 TTCGAGGGTCAAAATGTGATTTTTTGAAGTTCGAGGGAAAAAAATGTAATTTTTGAGAAG
1 TTCGAGGGTCAAAATGTGATTTTTGGAAGTTCGAGGG-AAAAAATGTAATTTTTGAGAAG
* * * * *
16113 TT-GAGGGTCAAGATGTAATTTTTGGAAGTCCG-GGG--GAAATATAATTTTTGAGAAG
1 TTCGAGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAG
* * * * *
16168 TTCG-GAGGTTAATATGTGATTTTTGTAAGTT-TAGGGGTAAAAATGTAATTTTTG-GAAG
1 TTCGAG-GGTCAAAATGTGATTTTTGGAAGTTCGA-GGGAAAAAATGTAATTTTTGAGAAG
* * * *
16226 TTTGAGGGGTAAAAATGTAATTTTTGGAA-TTCAAGGGTAAAAAAT-TAATTTTTGAGAAG
1 TTCGA-GGGTCAAAATGTGATTTTTGGAAGTTCGAGGG-AAAAAATGTAATTTTTGAGAAG
*
16285 TTCGAGGGTTAAAATGTGA-TTTTGGAA
1 TTCGAGGGTCAAAATGTGATTTTTGGAA
16312 AAGTGTAAGG
Statistics
Matches: 265, Mismatches: 37, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
55 21 0.08
56 21 0.08
57 16 0.06
58 75 0.28
59 108 0.41
60 24 0.09
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
TTCGAGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAG
Found at i:17511 original size:18 final size:19
Alignment explanation
Indices: 17481--17529 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
17471 ACATTTAGAA
17481 ATAATAAATAATAATGGTAAT
1 ATAATAAATAAT-A-GGTAAT
17502 ATAATAAATAAATAGGT-AT
1 ATAATAAAT-AATAGGTAAT
17521 -TAATAAATA
1 ATAATAAATA
17530 TAGAGGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 2 0.07
20 3 0.11
21 10 0.37
22 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
ATAATAAATAATAGGTAAT
Found at i:18138 original size:6 final size:6
Alignment explanation
Indices: 18127--18226 Score: 77
Period size: 6 Copynumber: 17.3 Consensus size: 6
18117 GGACATTATT
* *
18127 AATTTA AATTTA GAA--TA AATTTA AATTTA AGA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA
* * * *
18174 AA-ATA AATTTA AATTTA AA-ATA AATTTA AACTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
18219 AACTTA AA
1 AATTTA AA
18227 ATAAATCTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
4 2 0.03
5 15 0.20
6 55 0.73
7 3 0.04
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:18149 original size:17 final size:17
Alignment explanation
Indices: 18127--18237 Score: 168
Period size: 17 Copynumber: 6.5 Consensus size: 17
18117 GGACATTATT
* *
18127 AATTTAAATTTAGAATA
1 AATTTAAACTTAAAATA
*
18144 AATTTAAATTTAAGAATA
1 AATTTAAACTTAA-AATA
18162 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
18179 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
18196 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
18213 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
18230 AATCTAAA
1 AATTTAAA
18238 AAAAATGGGT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
17 72 0.82
18 16 0.18
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:18699 original size:39 final size:39
Alignment explanation
Indices: 18651--19224 Score: 247
Period size: 39 Copynumber: 14.7 Consensus size: 39
18641 AATGATTGCA
* * *
18651 ATCTGCCCCATGATCGGGATAAGAGATTGGCTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * ** * *
18690 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATTACT-A-C
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGA-TGATG
* * * *
18728 ATTATGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTA
1 A-TCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * *
18768 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGATG--GCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
18805 CAATCTGCCCTATGATCGGGGTAAGAGATTTACTGAATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTG-ATGATG
* *
18847 ATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
18886 ATCTACCTC-AGTCTCGGGGCAAGAGATTGAATGCTGCA--
1 ATCTGCCCCAAG-CTCGGGGTAAGAGATTGGCTGATG-ATG
* * * * * * *
18924 ATTTACCCGATGGTCGGGGTAAGAGATTTGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * ** *
18963 ATCTGCCTCAAGCTCGAGGTAAAAGATCGAATG--GTTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * *
19000 CAATCTACCCTAGGCTCGGGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
19041 ATCTGCCCCAATCTCGGGGTAAAAGATCGAATG--GTTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * *
19078 CAATTTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * * *
19119 ATCTGCCTCAGGCTCGGGATAAGAGATCGAACGGCT--TG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTG-GCTGATGATG
* *** * *
19157 CAATCTGCCTCAAGCTCAAAGTAAGAGATTGGCTAATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* * *
19198 ATTTGCCCCAGGCTCGGGGTAAAAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
19225 CGAATCTTCA
Statistics
Matches: 381, Mismatches: 127, Indels: 54
0.68 0.23 0.10
Matches are distributed among these distances:
37 8 0.02
38 30 0.08
39 275 0.72
40 57 0.15
41 8 0.02
42 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
Found at i:18910 original size:118 final size:116
Alignment explanation
Indices: 18732--18989 Score: 329
Period size: 118 Copynumber: 2.2 Consensus size: 116
18722 TACTACATTA
* * *
18732 TGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAGCTCGAGGTAAGAGATTG
1 TGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATAATCTGACCTAAGCTCGAGGCAAGAGATTG
* * *
18797 GATGGCTGCAATCTGCCCTATGATCGGGGTAAGAGATTTACTGAATGGTGATC
66 AAT-GCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTG-ATGGTGATC
* * * * * *
18850 TGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATGATCT-ACCTCAGTCTCGGGGCAAGAGATT
1 TGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATAATCTGACCTAAG-CTCGAGGCAAGAGATT
* * *
18914 GAATGCTGCAATTTACCCGATGGTCGGGGTAAGAGATTTGCTGATGGTGATC
65 GAATGCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTGATGGTGATC
* *
18966 TGCCTCAAGCTCGAGGTAAAAGAT
1 TGCCTCAAGCTCGGGGTAAGAGAT
18990 CGAATGGTTG
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
116 29 0.24
117 39 0.32
118 52 0.43
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (116 bp):
TGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATAATCTGACCTAAGCTCGAGGCAAGAGATTG
AATGCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTGATGGTGATC
Found at i:19006 original size:116 final size:117
Alignment explanation
Indices: 18732--19029 Score: 293
Period size: 118 Copynumber: 2.5 Consensus size: 117
18722 TACTACATTA
* * * * * * * * *
18732 TGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAGCTCGAGGTAAGAGATTG
1 TGCCCCAAGCTCGAGGTAAAAGATT-GCTGATGATGATCTACCCTAGGCTCGGGGCAAGAGATTG
* * *
18797 GATGGCTGCAATCTGCCCTATGATCGGGGTAAGAGATTTACTGAATGGTGATC
65 AATGGCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTGAATGGTGATC
* * * *
18850 TGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATGATCTA-CCTCAGTCTCGGGGCAAGAGATT
1 TGCCCCAAGCTCGAGGTAAAAGA-TTGCTGATGATGATCTACCCT-AGGCTCGGGGCAAGAGATT
* * *
18914 GAAT-GCTGCAATTTACCCGATGGTCGGGGTAAGAGATTTGCTG-ATGGTGATC
64 GAATGGCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTGAATGGTGATC
* * *
18966 TGCCTCAAGCTCGAGGTAAAAGA-T-C-GAATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGA
1 TGCCCCAAGCTCGAGGTAAAAGATTGCTG-AT-GATG--ATCTACCCTAGGCTCGGGGCAAGAGA
19028 TT
62 TT
19030 TGCTGATGAT
Statistics
Matches: 151, Mismatches: 22, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
112 1 0.01
113 3 0.02
114 4 0.03
116 50 0.33
117 40 0.26
118 51 0.34
119 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (117 bp):
TGCCCCAAGCTCGAGGTAAAAGATTGCTGATGATGATCTACCCTAGGCTCGGGGCAAGAGATTGA
ATGGCTGCAATCTACCCGATGATCGGGGTAAGAGATTTACTGAATGGTGATC
Found at i:19036 original size:78 final size:78
Alignment explanation
Indices: 18862--19229 Score: 402
Period size: 78 Copynumber: 4.7 Consensus size: 78
18852 CCCCAAGCTT
* * * * * *
18862 GGGGTAAGAGATTTGCTGATGATGATCTACCTC-AGTCTCGGGGCAAGAGATTGAAT-GCTGCAA
1 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAG-CTCGGGGTAAAAGATCGAATGGTTGCAA
* *
18925 TTTACCCGATGG-TC
65 TCTACCCTA-GGCTC
*
18939 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGAGGTAAAAGATCGAATGGTTGCAAT
1 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGTTGCAAT
19004 CTACCCTAGGCTC
66 CTACCCTAGGCTC
* * *
19017 GGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGTAAAAGATCGAATGGTTGCAAT
1 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGTTGCAAT
* * * *
19082 TTGCCCCAGGCTT
66 CTACCCTAGGCTC
* * * *
19095 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAGGCTCGGGATAAGAGATCGAACGGCTTGCAA
1 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGG-TTGCAA
* *
19160 TCT-GCCTCAAGCTC
65 TCTACCCT-AGGCTC
*** * * * * *
19174 AAAGTAAGAGATTGGCTAATGGTGATTTGCCCCAGGCTCGGGGTAAAAGATCGAAT
1 GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAAT
19230 CTTCAATCTG
Statistics
Matches: 247, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
77 49 0.20
78 140 0.57
79 58 0.23
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (78 bp):
GGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGTTGCAAT
CTACCCTAGGCTC
Found at i:19145 original size:195 final size:193
Alignment explanation
Indices: 18651--19067 Score: 448
Period size: 195 Copynumber: 2.1 Consensus size: 193
18641 AATGATTGCA
* * * * * * * *
18651 ATCTGCCCCATGATCGGGATAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATT-GCTGATGATGATCTACCCCAGGCTCGGGGCAAGAGA
* * * *
18716 TCGAATTACT-ACATTATGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAG
65 TTGAA-TGCTGA-A-TCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAG
* * * * * *
18780 CTCGAGGTAAGAGATTGGATGGCTGCAATCTGCCCTATGATCGGGGTAAGAGATTTACTGAATGG
127 CTCGAGGTAAAAGATCGAATGGCTGCAATCTACCCTAGGATCGGGGTAAGAGATTTACTGAATGA
18845 TG
192 TG
* * * *
18847 ATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCTCAGTCTCGGGGCAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-TTGCTGATGATGATCTACCCCAGGCTCGGGGCAAGAGA
* * * *
18912 TTGAATGCTGCAATTTACC-CGATGG-TCGGGGTAAGAGATTTGCTGATGGTGATCTG-CCTCAA
65 TTGAATGCTG-AATCTGCCTC-A-GGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCT-AA
* * *
18974 GCTCGAGGTAAAAGATCGAATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTTGCTG-ATG
126 GCTCGAGGTAAAAGATCGAATGGCTGCAATCTACCCTAGGATCGGGGTAAGAGATTTACTGAATG
19038 ATG
191 ATG
*
19041 ATCTGCCCCAATCTCGGGGTAAAAGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGAT
19068 CGAATGGTTG
Statistics
Matches: 186, Mismatches: 29, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
193 1 0.01
194 32 0.17
195 92 0.49
196 58 0.31
197 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (193 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGCTGATGATGATCTACCCCAGGCTCGGGGCAAGAGAT
TGAATGCTGAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAGCTCG
AGGTAAAAGATCGAATGGCTGCAATCTACCCTAGGATCGGGGTAAGAGATTTACTGAATGATG
Found at i:30442 original size:116 final size:115
Alignment explanation
Indices: 30279--30556 Score: 350
Period size: 116 Copynumber: 2.4 Consensus size: 115
30269 TGTAGGGGTT
* * * *
30279 AAAATGTGACTTTTG-GAAGTTCGAGGGT-AAAATGTAAATTTTGGAAGTTCAAGGGCAAAAATG
1 AAAATGTAATTTTTGAGAAGTT-AAGGGTCAAAATGT-GATTTTGGAAGTTCAAGGGCAAAAATG
* *
30342 TAATTTTTGAGAAG-TTAAGGGTCAAAATGT-TATTTTTG-GAAGTTTAGGGG
64 TAATTTTT-AGAAGTTTAAGGGTAAAAATGTATATTTTTGAGAAATTTAGGGG
* *
30392 CAAAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAAT
1 --AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGA-TTTTGGAAGTTCAAGGGCAAAAAT
* *
30457 GTAATTTTTAGATGTTTAAGGGTAAAAATGTATTTTTTTGAGAAATTTAGGGG
63 GTAATTTTTAGAAGTTTAAGGGTAAAAATGTATATTTTTGAGAAATTTAGGGG
* *
30510 AAAATGTAATTTTTGAGAAGTTTAGGGGTCAAATTGTGATTTTGGAA
1 AAAATGTAATTTTTGAGAAG-TTAAGGGTCAAAATGTGATTTTGGAA
30557 TAGTGTAGGG
Statistics
Matches: 144, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
115 23 0.16
116 87 0.60
117 23 0.16
118 11 0.08
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (115 bp):
AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTGGAAGTTCAAGGGCAAAAATGTA
ATTTTTAGAAGTTTAAGGGTAAAAATGTATATTTTTGAGAAATTTAGGGG
Found at i:30448 original size:28 final size:28
Alignment explanation
Indices: 30185--30583 Score: 244
Period size: 29 Copynumber: 13.9 Consensus size: 28
30175 AGTTTCGGAG
* * * *
30185 AGTTTGGGGTAAAAATGTCATTTTGGGAA
1 AGTTTAGGGTCAAAATGTGATTTTTGG-A
*
30214 AATTTAGGGT-AAAATGTGATTTTTGGA
1 AGTTTAGGGTCAAAATGTGATTTTTGGA
**
30241 AGTTCGGGGGT---AA-GTGA-TTTTGGAAA
1 AGTT-TAGGGTCAAAATGTGATTTTTGG--A
* * * *
30267 ACTGTAGGGGTTAAAATGTGACTTTTGGA
1 AGTTTA-GGGTCAAAATGTGATTTTTGGA
* * *
30296 AGTTCGAGGGT-AAAATGTAAATTTTGGA
1 AGTT-TAGGGTCAAAATGTGATTTTTGGA
* *
30324 AGTTCAAGGG-CAAAAATGTAATTTTTGAGA
1 AGTT-TAGGGTC-AAAATGTGATTTTTG-GA
* *
30354 AGTTAAGGGTCAAAATGTTATTTTTGGA
1 AGTTTAGGGTCAAAATGTGATTTTTGGA
* *
30382 AGTTTAGGGGCAAAAATGTAATTTTTGAGA
1 AGTTTAGGGTC-AAAATGTGATTTTTG-GA
*
30412 AGTTAAGGGTCAAAATGTGATTTTTGGA
1 AGTTTAGGGTCAAAATGTGATTTTTGGA
* * *
30440 AGTTTAGGGGCAAAAATGTAATTTTTAGA
1 AGTTTAGGGTC-AAAATGTGATTTTTGGA
* *
30469 TGTTTAAGGGTAAAAATGT-ATTTTTTTGAGA
1 AGTTT-AGGGTCAAAATGTGA--TTTTTG-GA
* * *
30500 AATTTAGGG-GAAAATGTAATTTTTGAGA
1 AGTTTAGGGTCAAAATGTGATTTTTG-GA
*
30528 AGTTTAGGGGTCAAATTGTGA-TTTTGGAA
1 AGTTTA-GGGTCAAAATGTGATTTTTGG-A
* *
30557 TAGTGTAGGGTTCAAAATATGATTTTT
1 -AGTTTAGGG-TCAAAATGTGATTTTT
30584 AGATAGTTCA
Statistics
Matches: 299, Mismatches: 43, Indels: 54
0.76 0.11 0.14
Matches are distributed among these distances:
24 6 0.02
25 4 0.01
26 9 0.03
27 4 0.01
28 80 0.27
29 123 0.41
30 58 0.19
31 15 0.05
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
AGTTTAGGGTCAAAATGTGATTTTTGGA
Found at i:30553 original size:29 final size:30
Alignment explanation
Indices: 30271--30596 Score: 261
Period size: 29 Copynumber: 11.2 Consensus size: 30
30261 TGGAAAACTG
* * *
30271 TAGGGGTTAAAATGTGACTTTTG-GAAG-T
1 TAGGGGTCAAAATGTAATTTTTGAGAAGTT
* *
30299 TCGAGGGT-AAAATGTAAATTTTG-GAAGTT
1 TAG-GGGTCAAAATGTAATTTTTGAGAAGTT
* *
30328 CAAGGG-CAAAAATGTAATTTTTGAGAAG-T
1 TAGGGGTC-AAAATGTAATTTTTGAGAAGTT
* *
30357 TAAGGGTCAAAATGTTATTTTTG-GAAGTT
1 TAGGGGTCAAAATGTAATTTTTGAGAAGTT
30386 TAGGGG-CAAAAATGTAATTTTTGAGAAG-T
1 TAGGGGTC-AAAATGTAATTTTTGAGAAGTT
* *
30415 TAAGGGTCAAAATGTGATTTTTG-GAAGTT
1 TAGGGGTCAAAATGTAATTTTTGAGAAGTT
*
30444 TAGGGG-CAAAAATGTAATTTTT-AGATGTT
1 TAGGGGTC-AAAATGTAATTTTTGAGAAGTT
* * * *
30473 TAAGGGTAAAAATGTATTTTTTTGAGAAATT
1 TAGGGGTCAAAATGTA-ATTTTTGAGAAGTT
30504 TAGGGG--AAAATGTAATTTTTGAGAAGTT
1 TAGGGGTCAAAATGTAATTTTTGAGAAGTT
* * * *
30532 TAGGGGTCAAATTGTGATTTTGGA-ATAGTG
1 TAGGGGTCAAAATGTAATTTTTGAGA-AGTT
* * *
30562 TAGGGTTCAAAATATGATTTTT-AGATAGTT
1 TAGGGGTCAAAATGTAATTTTTGAGA-AGTT
*
30592 CAGGG
1 TAGGG
30597 ACCTTCTAAG
Statistics
Matches: 244, Mismatches: 34, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
28 50 0.20
29 126 0.52
30 58 0.24
31 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
TAGGGGTCAAAATGTAATTTTTGAGAAGTT
Found at i:30566 original size:58 final size:57
Alignment explanation
Indices: 30279--30556 Score: 316
Period size: 58 Copynumber: 4.8 Consensus size: 57
30269 TGTAGGGGTT
* * * * * * *
30279 AAAATGTGACTTTTG-GAAGTTCGAGGGT-AAAATGTAAATTTTGGAAGTTCAAGGGCA
1 AAAATGTAATTTTTGAGAAGTT-AAGGGTCAAAATGTGATTTTTGGAAGTT-TAGGGGA
*
30336 AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTTATTTTTGGAAGTTTAGGGGCA
1 AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTTGGAAGTTTAGGGG-A
30394 AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTTGGAAGTTTAGGGGCA
1 AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTTGGAAGTTTAGGGG-A
* * *
30452 AAAATGTAATTTTT-AGATGTTTAAGGGTAAAAATGT-ATTTTTTTGAGAAATTTAGGGG-
1 AAAATGTAATTTTTGAGAAG-TTAAGGGTCAAAATGTGA--TTTTTG-GAAGTTTAGGGGA
* *
30510 AAAATGTAATTTTTGAGAAGTTTAGGGGTCAAATTGTGA-TTTTGGAA
1 AAAATGTAATTTTTGAGAAG-TTAAGGGTCAAAATGTGATTTTTGGAA
30557 TAGTGTAGGG
Statistics
Matches: 197, Mismatches: 15, Indels: 19
0.85 0.06 0.08
Matches are distributed among these distances:
56 3 0.02
57 32 0.16
58 126 0.64
59 24 0.12
60 12 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTTGAGAAGTTAAGGGTCAAAATGTGATTTTTGGAAGTTTAGGGGA
Found at i:31676 original size:16 final size:16
Alignment explanation
Indices: 31651--31681 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31641 TAAGACTTTT
*
31651 TTATTTATTATTATTA
1 TTATTAATTATTATTA
31667 TTATTAATTATTATT
1 TTATTAATTATTATT
31682 TATTTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTAATTATTATTA
Found at i:31694 original size:10 final size:10
Alignment explanation
Indices: 31651--31694 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
31641 TAAGACTTTT
31651 TTATTTATTA
1 TTATTTATTA
31661 TTA-TTATTA
1 TTATTTATTA
*
31670 TTAATTATTA
1 TTATTTATTA
*
31680 TTTATTTAATA
1 -TTATTTATTA
31691 TTAT
1 TTAT
31695 AATTAATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.30
10 13 0.43
11 8 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:31770 original size:21 final size:21
Alignment explanation
Indices: 31724--31770 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
31714 TACGTTTAGA
31724 AATAATAAATAATAATGGTAAT
1 AATAATAAATAATAA-GGTAAT
*
31746 -ATAATAAATAAATAA-GTATT
1 AATAATAAAT-AATAAGGTAAT
31766 AATAA
1 AATAA
31771 ATATATGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (21 bp):
AATAATAAATAATAAGGTAAT
Found at i:32375 original size:6 final size:6
Alignment explanation
Indices: 32364--32429 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
32354 AGACATTATT
* *
32364 AATTTA AATTTA GAA--TA AATTTA AATTTA AGA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA
*
32411 AA-ATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
32430 AACAAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
4 2 0.04
5 7 0.14
6 37 0.76
7 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:32386 original size:17 final size:17
Alignment explanation
Indices: 32364--32458 Score: 127
Period size: 17 Copynumber: 5.5 Consensus size: 17
32354 AGACATTATT
*
32364 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
32381 AATTTAAATTTAAGAATA
1 AATTTAAATTTAA-AATA
*
32399 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
32416 AATTTAAATTTAAAAACA
1 AATTTAAATTT-AAAATA
*
32434 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
32451 AATCTAAA
1 AATTTAAA
32459 AATTTGAGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
17 38 0.55
18 31 0.45
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:32403 original size:35 final size:35
Alignment explanation
Indices: 32364--32458 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
32354 AGACATTATT
* * * *
32364 AATTTAAATTTAGAATAAATTTAAATTTAAGAATA
1 AATTTAAACTTAAAATAAATTTAAATTTAAAAACA
32399 AATTTAAACTTAAAATAAATTTAAATTTAAAAACA
1 AATTTAAACTTAAAATAAATTTAAATTTAAAAACA
*
32434 AATTTAAACTTAAAATAAATCTAAA
1 AATTTAAACTTAAAATAAATTTAAA
32459 AATTTGAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (35 bp):
AATTTAAACTTAAAATAAATTTAAATTTAAAAACA
Found at i:35533 original size:20 final size:20
Alignment explanation
Indices: 35496--35533 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35486 TGAATTCTCT
*
35496 TAATTAAAGGTATTAAGTGC
1 TAATTAAAGGTATAAAGTGC
35516 TAATTCAAAGGTA-AAAGT
1 TAATT-AAAGGTATAAAGT
35534 AGTTAGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (20 bp):
TAATTAAAGGTATAAAGTGC
Found at i:37162 original size:52 final size:52
Alignment explanation
Indices: 36934--37166 Score: 308
Period size: 52 Copynumber: 4.5 Consensus size: 52
36924 TAAATGAAAA
* * *
36934 AGGTCTGATGGCTATGTGCCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
36986 AGGTTCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
37038 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CTCTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTATGGATTATG
** * * * * * *
37090 AGGTTTGATGATTCTGTGTCATCGTGAGTATATGATTCCTTTACGGATGAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
*
37142 AGGTCCGATG-CTTATATGTCATCGT
1 AGGTCCGATGAC-TATGTGTCATCGT
37167 AGGAATTAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
51 2 0.01
52 154 0.97
53 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
Found at i:37939 original size:21 final size:21
Alignment explanation
Indices: 37913--37959 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
37903 TTAGTATCAA
*
37913 TAGAAGCATA-ACTTGTTTCGG
1 TAGAAG-ATACACTTGTATCGG
*
37934 TAGAAGTTACACTTGTATCGG
1 TAGAAGATACACTTGTATCGG
37955 TAGAA
1 TAGAA
37960 CTTTTCCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (21 bp):
TAGAAGATACACTTGTATCGG
Found at i:46743 original size:10 final size:10
Alignment explanation
Indices: 46728--46753 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46718 CTAAAAAGAA
46728 AAAGAAGTCC
1 AAAGAAGTCC
46738 AAAGAAGTCC
1 AAAGAAGTCC
46748 AAAGAA
1 AAAGAA
46754 AGAGAAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.19, T:0.08
Consensus pattern (10 bp):
AAAGAAGTCC
Found at i:55778 original size:20 final size:21
Alignment explanation
Indices: 55742--55780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55732 GCATTTTTTA
*
55742 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
55763 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
55781 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:58208 original size:25 final size:27
Alignment explanation
Indices: 58175--58226 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
58165 TTAGAAAAGG
58175 AAAATGAGAAAA-AGAAAGAA-AAAAAT
1 AAAATGAGAAAAGA-AAAGAAGAAAAAT
58201 AAAA-GAGAAAAGAAAAGAAGAAAAAT
1 AAAATGAGAAAAGAAAAGAAGAAAAAT
58227 TGTTTGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAATGAGAAAAGAAAAGAAGAAAAAT
Found at i:58211 original size:12 final size:13
Alignment explanation
Indices: 58167--58224 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
58157 TCAGCCACTT
58167 AGAAAAGGAAAATG-
1 AGAAAA-GAAAA-GA
58181 AGAAAA-AGAAAGA
1 AGAAAAGA-AAAGA
* *
58194 AAAAAATAAAAG-
1 AGAAAAGAAAAGA
58206 AGAAAAGAAAAGA
1 AGAAAAGAAAAGA
58219 AGAAAA
1 AGAAAA
58225 ATTGTTTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 12 0.32
13 18 0.49
14 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
AGAAAAGAAAAGA
Found at i:58224 original size:20 final size:19
Alignment explanation
Indices: 58167--58225 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
58157 TCAGCCACTT
58167 AGAAAAGGAAAATG-AGAAAA
1 AGAAAA-GAAAA-GAAGAAAA
* *
58187 AG-AAAGAAAAAAATAAAA
1 AGAAAAGAAAAGAAGAAAA
58205 GAGAAAAGAAAAGAAGAAAA
1 -AGAAAAGAAAAGAAGAAAA
58225 A
1 A
58226 TTGTTTGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 10 0.31
19 6 0.19
20 16 0.50
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AGAAAAGAAAAGAAGAAAA
Found at i:61787 original size:23 final size:23
Alignment explanation
Indices: 61755--61802 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
61745 AAATTTATAA
61755 TTTTAAAATTTT-TT-ATAACTTT
1 TTTTAAAATTTTATTCATAA-TTT
61777 TTTTATAAATTTTATTCATAATTT
1 TTTTA-AAATTTTATTCATAATTT
61801 TT
1 TT
61803 AAGTAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 7 0.30
24 7 0.30
25 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAAAATTTTATTCATAATTT
Found at i:61955 original size:31 final size:31
Alignment explanation
Indices: 61917--61988 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
61907 AATAGAATAG
*
61917 GGGTCAAATTAAATAAATATGTAAATATTAA
1 GGGTCAAATTAAATAAATATATAAATATTAA
* *
61948 GGGTCAAATTAAATAATTATATAAATATTGA
1 GGGTCAAATTAAATAAATATATAAATATTAA
*
61979 GGGTTAAATT
1 GGGTCAAATT
61989 TATTATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (31 bp):
GGGTCAAATTAAATAAATATATAAATATTAA
Found at i:64769 original size:17 final size:17
Alignment explanation
Indices: 64747--64780 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
64737 CAAAGCAAAA
64747 CGGTTTAAAATTATTTT
1 CGGTTTAAAATTATTTT
**
64764 CGGTTTTCAATTATTTT
1 CGGTTTAAAATTATTTT
64781 TGTTCAACTC
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:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (17 bp):
CGGTTTAAAATTATTTT
Found at i:66752 original size:17 final size:17
Alignment explanation
Indices: 66702--66753 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
66692 AGTATGGGAA
*
66702 GTAATCTTCA-AATATAT
1 GTAATCTT-AGAATATTT
* **
66719 GCAATCTTAGAGGATTT
1 GTAATCTTAGAATATTT
66736 GTAATCTTAGAATATTT
1 GTAATCTTAGAATATTT
66753 G
1 G
66754 ATTCTGTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 1 0.04
17 26 0.96
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (17 bp):
GTAATCTTAGAATATTT
Found at i:76332 original size:1 final size:1
Alignment explanation
Indices: 76328--76389 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
76318 TTTTTCACCC
* * * * * * * *
76328 AAAAAGAAAAAGAAAAAAAAAAAGAAAAAAAGAAAAGAAAAGAAAAAAAAAAGAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
76390 GGGACAGGTC
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:76351 original size:18 final size:18
Alignment explanation
Indices: 76328--76383 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
76318 TTTTTCACCC
76328 AAAAAGAAAAAGAAAAAA-
1 AAAAAGAAAAA-AAAAAAG
76346 AAAAAGAAAAAAAGAAAAG
1 AAAAAGAAAAAAA-AAAAG
76365 -AAAAG-AAAAAAAAAAG
1 AAAAAGAAAAAAAAAAAG
76381 AAA
1 AAA
76384 CAAAAAGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.14
17 10 0.29
18 20 0.57
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAAG
Found at i:76357 original size:26 final size:26
Alignment explanation
Indices: 76328--76390 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
76318 TTTTTCACCC
76328 AAAAAGAAAAAGAAAA-AAAAAAAGAA
1 AAAAAGAAAAAGAAAAGAAAAAAA-AA
76354 AAAAAG-AAAAGAAAAGAAAAAAAAA
1 AAAAAGAAAAAGAAAAGAAAAAAAAA
* *
76379 AGAAACAAAAAG
1 AAAAAGAAAAAG
76391 GGACAGGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.86, C:0.02, G:0.13, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAGAAAAAAAAA
Found at i:76388 original size:25 final size:25
Alignment explanation
Indices: 76335--76388 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
76325 CCCAAAAAGA
*
76335 AAAAGAAAAAAAAAAAGAAAAAAAG
1 AAAAGAAAAAAAAAAAGAAAAAAAC
*
76360 AAAAGAAAAGAAAAAAA-AAAGAAAC
1 AAAAGAAAA-AAAAAAAGAAAAAAAC
76385 AAAA
1 AAAA
76389 AGGGACAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (25 bp):
AAAAGAAAAAAAAAAAGAAAAAAAC
Found at i:76390 original size:31 final size:31
Alignment explanation
Indices: 76329--76388 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
76319 TTTTCACCCA
76329 AAAAGAAAAAGAAAAAAAAAAAGAAAAAAAG
1 AAAAGAAAAAGAAAAAAAAAAAGAAAAAAAG
76360 AAAAG-AAAAG-AAAAAAAAAAGAAACAAAA
1 AAAAGAAAAAGAAAAAAAAAAAGAAA-AAAA
76389 AGGGACAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 14 0.50
30 9 0.32
31 5 0.18
ACGTcount: A:0.87, C:0.02, G:0.12, T:0.00
Consensus pattern (31 bp):
AAAAGAAAAAGAAAAAAAAAAAGAAAAAAAG
Found at i:77621 original size:46 final size:45
Alignment explanation
Indices: 77521--78043 Score: 420
Period size: 46 Copynumber: 11.9 Consensus size: 45
77511 TTGCAGTCAT
* * * *
77521 TCCAATCTTTTATCCCTAA-TCAAGAGGGACAAATTGAAGAC-CT
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * ** *
77564 TCTAATCTTTTACCCCAAAGTCAAGAGGGGCAGATAAAAGTCGTCA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGAC-TCA
* *
77610 TCCAATCTTTTACCCCTAAGTCAAGAGGGGTAGATTGAAGCCATCA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGAC-TCA
* * * *
77656 TCCAATATTTTACCCCTAA-TCAAGAAGGGTAGATTGAAGAC-CT
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * * * *
77699 TCCGATCTTTTACCCCTAAGTCAAGAAGGGCAAATTGATGACACA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* *
77744 TTCCAATCTTTTACCCCTAAGTCAAAAGGGGCAGATTGAAGTCGTCA
1 -TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGAC-TCA
* * * * *
77791 TCCAATCTTTTACCCCTAAGTAAAAAAGGACAGACTGAAG--TCA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * * *
77834 TTTCAATCTTTTACCCCTAA-TTAAAAGGGGCAGATTAAAGACT--
1 -TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * *
77877 T-CAATCTTCTATCCCTAA-TCAAGAGGGGCAAATTGAAGA-T--
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * * *
77917 TCTAATCTTTTACCCCTAA-TCAAAAAGGGTAGATTGAAG-CT-A
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
* * * *
77959 TTCCAATCTTTTACCTCTAA-TCAATAGGGGTAGATTGAAGACCTTTA
1 -TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGA-C-TCA
* * **
78006 T--AATCTTTTACCCTTAAGTCAAGATGGAAAGATTGAAG
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAG
78044 CCATCTTCCT
Statistics
Matches: 395, Mismatches: 66, Indels: 36
0.79 0.13 0.07
Matches are distributed among these distances:
40 2 0.01
41 63 0.16
42 1 0.00
43 87 0.22
44 68 0.17
45 39 0.10
46 132 0.33
47 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (45 bp):
TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACTCA
Found at i:77627 original size:89 final size:89
Alignment explanation
Indices: 77521--78027 Score: 454
Period size: 89 Copynumber: 5.8 Consensus size: 89
77511 TTGCAGTCAT
* * *
77521 TCCAATCTTTTATCCCTAA-TCAAGAGGGACAAATTGAAGACC-TTCTAATCTTTTACCCCAAAG
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCATTCTAATCTTTTACCCCTAA-
* ** *
77584 TCAAGAGGGGCAGATAAAAGTCGTCA
65 TCAAAAGGGGCAGATTGAAGAC-TCA
* * * *
77610 TCCAATCTTTTACCCCTAAGTCAAGAGGGGTAGATTGAAG-CCATCATCCAATATTTTACCCCTA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCAT--TCTAATCTTTTACCCCTA
* *
77674 ATCAAGAA-GGGTAGATTGAAGAC-CT
64 ATCAA-AAGGGGCAGATTGAAGACTCA
* * * *
77699 TCCGATCTTTTACCCCTAAGTCAAGAAGGGCAAATTGATGACACATTCCAATCTTTTACCCCTAA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGAC-CATTCTAATCTTTTACCCCTAA
*
77764 GTCAAAAGGGGCAGATTGAAGTCGTCA
65 -TCAAAAGGGGCAGATTGAAGAC-TCA
* * * * * * *
77791 TCCAATCTTTTACCCCTAAGTAAAAAAGGACAGACTGAAG-TCATT-TCAATCTTTTACCCCTAA
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCATTCT-AATCTTTTACCCCTAA
* *
77854 TTAAAAGGGGCAGATTAAAGACT--
65 TCAAAAGGGGCAGATTGAAGACTCA
* *
77877 T-CAATCTTCTATCCCTAA-TCAAGAGGGGCAAATTGAAG---ATTCTAATCTTTTACCCCTAAT
1 TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCATTCTAATCTTTTACCCCTAAT
* *
77937 CAAAAAGGGTAGATTGAAG-CT-A
66 CAAAAGGGGCAGATTGAAGACTCA
* * * * * * *
77959 TTCCAATCTTTTACCTCTAA-TCAATAGGGGTAGATTGAAGACCTTTATAATCTTTTACCCTTAA
1 -TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCATTCTAATCTTTTACCCCTAA
78023 GTCAA
65 -TCAA
78028 GATGGAAAGA
Statistics
Matches: 343, Mismatches: 55, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
81 2 0.01
82 35 0.10
83 2 0.01
84 45 0.13
85 15 0.04
86 1 0.00
87 18 0.05
88 5 0.01
89 95 0.28
90 56 0.16
91 18 0.05
92 51 0.15
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (89 bp):
TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGACCATTCTAATCTTTTACCCCTAAT
CAAAAGGGGCAGATTGAAGACTCA
Found at i:77677 original size:135 final size:133
Alignment explanation
Indices: 77521--78044 Score: 466
Period size: 135 Copynumber: 4.0 Consensus size: 133
77511 TTGCAGTCAT
* * *
77521 TCCAATCTTTTATCCCTAATCAAGAGGGACAAATTGAAGACCTTCTAATCTTTTACCCCAAAGTC
1 TCCAATCTTTTACCCCTAATCAAGAGGGACAGATTGAAGACCTTCTAATCTTTTACCCCTAAGTC
* * *
77586 AAGAGGGGCAGATAAAAGTCGTCATCCAATCTTTTACCCCTAAGTCAAGAGGGGTAGATTGAAGC
66 AAGAGGGGCAGATTAAAGAC-TCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAG-
77651 CATCA
129 CATCA
* * **
77656 TCCAATATTTTACCCCTAATCAAGAAGGG-TAGATTGAAGACCTTCCGATCTTTTACCCCTAAGT
1 TCCAATCTTTTACCCCTAATCAAG-AGGGACAGATTGAAGACCTTCTAATCTTTTACCCCTAAGT
* * * * * *
77720 CAAGAAGGGCAAATTGATGACACATTCCAATCTTTTACCCCTAAGTCAAAAGGGGCAGATTGAAG
65 CAAGAGGGGCAGATTAAAGACTCA-TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAG
*
77785 TCGTCA
129 -CATCA
* * * * * *
77791 TCCAATCTTTTACCCCTAAGTAAAAAAGGACAGACTGAAGTCATT-TCAATCTTTTACCCCTAA-
1 TCCAATCTTTTACCCCTAA-TCAAGAGGGACAGATTGAAGACCTTCT-AATCTTTTACCCCTAAG
* * * * *
77854 TTAAAAGGGGCAGATTAAAGACT--T-CAATCTTCTATCCCTAA-TCAAGAGGGGCAAATTGAAG
64 TCAAGAGGGGCAGATTAAAGACTCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAG
77915 -AT--
129 CATCA
* * * * * *
77917 TCTAATCTTTTACCCCTAATCAAAAAGGG-TAGATTGAAG-CTATTCCAATCTTTTACCTCTAA-
1 TCCAATCTTTTACCCCTAATC-AAGAGGGACAGATTGAAGAC-CTTCTAATCTTTTACCCCTAAG
* * * * * * **
77979 TCAATAGGGGTAGATTGAAGACCTTTAT--AATCTTTTACCCTTAAGTCAAGATGGAAAGATTGA
64 TCAAGAGGGGCAGATTAAAGA-C-TCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGA
78042 AGC
127 AGC
78045 CATCTTCCTA
Statistics
Matches: 317, Mismatches: 58, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
124 1 0.00
125 44 0.14
126 25 0.08
127 1 0.00
128 14 0.04
129 17 0.05
130 18 0.06
131 15 0.05
132 1 0.00
134 2 0.01
135 146 0.46
136 33 0.10
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (133 bp):
TCCAATCTTTTACCCCTAATCAAGAGGGACAGATTGAAGACCTTCTAATCTTTTACCCCTAAGTC
AAGAGGGGCAGATTAAAGACTCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCA
TCA
Found at i:78345 original size:123 final size:123
Alignment explanation
Indices: 78123--78667 Score: 627
Period size: 123 Copynumber: 4.4 Consensus size: 123
78113 CAGTGGAGTA
* * * * *
78123 GAGTGAGACTTCA-AATCCCATCTTCCTAGTGAGGTACAGAGAAGTAGGTCAAATAATGAAATGG
1 GAGTGAAACTTCAGACT-CCATCTTCCTGGTGAGGTACAGAGAAGTAGGTCAAACAATGAAGTGG
* * * *
78187 TCATCTTCTTGGTGAGATACATAGAAGTGTGCCAAAATAATGAGGAGAAGCTCAAATGT
65 TCATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGAGAAGCTCAAATAT
*
78246 GAGTGAAACTTCAGACTCCATCTTCCTGGTGAGGTACAAAGAAGTAGGTCAAACAATGAAGTGGT
1 GAGTGAAACTTCAGACTCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTCAAACAATGAAGTGGT
* * *
78311 CATCTTCCTAGTGAGATACAGAGAAGTGTACCAAAATAATGAAGAGAAGCTCAAATGT
66 CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGAGAAGCTCAAATAT
* * * * *
78369 GAGTGAAACTTCAGACCCCATCTTCTTGGTGAGGTAAAAAGAAGTAGGTCAAACAATGAGGTGGT
1 GAGTGAAACTTCAGACTCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTCAAACAATGAAGTGGT
* * * * *
78434 TATCTTCCTTGTGATATACAGAGAAGTGTACCAAAATAATAAGGTGAAGCTCAAATAT
66 CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGAGAAGCTCAAATAT
* * * * * * * *
78492 AAGTGAAACTTCAAACCCCATCTTCTTGGTGAGATACAGAGAAGTGGGTCAGACAATGAAGTGAT
1 GAGTGAAACTTCAGACTCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTCAAACAATGAAGTGGT
* * *
78557 CATCTTCCTGGTAAGGTACAGAGAAGTAG-ACC-AAATCAATGAAGTAG-AGCTC--ATAT
66 CATCTTCCTGGTGAGATACAGAGAAGT-GTACCAAAAT-AATG-AGGAGAAGCTCAAATAT
* * * * *
78613 GAGTAAAACTTC-GAAATCCCATTTTCCTGGTAAGGTACAGAGAAGTGGGTTCAAA
1 GAGTGAAACTTCAG-ACT-CCATCTTCCTGGTGAGGTACAGAGAAGTAGG-TCAAA
78668 ACAGTGTATT
Statistics
Matches: 366, Mismatches: 49, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
121 15 0.04
122 31 0.08
123 314 0.86
124 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (123 bp):
GAGTGAAACTTCAGACTCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTCAAACAATGAAGTGGT
CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGAGAAGCTCAAATAT
Found at i:80520 original size:24 final size:24
Alignment explanation
Indices: 80477--80529 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
80467 AATCATTTTA
80477 TTTAAAATTATTACTTTATTATT-AT
1 TTTAAAATTATTAC-TTATT-TTGAT
80502 TTTAAAATTGATTAC-TATTTTGAT
1 TTTAAAATT-ATTACTTATTTTGAT
80526 TTTA
1 TTTA
80530 TTTTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 2 0.08
24 10 0.38
25 9 0.35
26 5 0.19
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTAAAATTATTACTTATTTTGAT
Found at i:81451 original size:21 final size:21
Alignment explanation
Indices: 81421--81461 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
81411 TTATATATGA
81421 TTTTATTTG-TTTTTCAAAAC
1 TTTTATTTGATTTTTCAAAAC
81441 TTTTACTTTGTATTTTTCAAA
1 TTTTA-TTTG-ATTTTTCAAA
81462 GATTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
23 9 0.50
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTATTTGATTTTTCAAAAC
Found at i:85296 original size:69 final size:69
Alignment explanation
Indices: 85178--85314 Score: 193
Period size: 69 Copynumber: 2.0 Consensus size: 69
85168 GGTAGGCCAG
* * * * * *
85178 CACTCCTAGTGGGTCGATTGTGAGGAGTGGATTTAATCAACCCAGTACAAATTATATGGAATATG
1 CACTCCTAGTGGGTCAATTGTAAGAAGTGGATTTAATCAACCAAATACAAATTATATGAAATATG
85243 GTAA
66 GTAA
* * *
85247 CACTCCTAGTGGGTCAATTGTAAGAAGTGGATTTGATCTACCAAATACAAATTATGTGAAATATG
1 CACTCCTAGTGGGTCAATTGTAAGAAGTGGATTTAATCAACCAAATACAAATTATATGAAATATG
85312 GTA
66 GTA
85315 GAGTTACAAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (69 bp):
CACTCCTAGTGGGTCAATTGTAAGAAGTGGATTTAATCAACCAAATACAAATTATATGAAATATG
GTAA
Found at i:93840 original size:20 final size:18
Alignment explanation
Indices: 93806--93852 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
93796 TAAAATTAGT
**
93806 TTTATTTTATTATTTTGAA
1 TTTATTTTAAAATTTT-AA
93825 TATTATTTTAAAATTTTAA
1 T-TTATTTTAAAATTTTAA
93844 TTT-TTTTAA
1 TTTATTTTAA
93853 TAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 4 0.16
20 13 0.52
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATTTTAAAATTTTAA
Found at i:93850 original size:29 final size:28
Alignment explanation
Indices: 93809--93878 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
93799 AATTAGTTTT
* * *
93809 ATTTTATTATTTTGAAT-ATTATTTTAAA
1 ATTTTATT-TTTTTAATAAATATTTAAAA
93837 ATTTTAATTTTTTTAATAAATATTTAAAA
1 ATTTT-ATTTTTTTAATAAATATTTAAAA
93866 ATATTTATTTTTT
1 AT-TTTATTTTTT
93879 ATTTTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.33
29 21 0.58
30 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
ATTTTATTTTTTTAATAAATATTTAAAA
Found at i:100384 original size:24 final size:24
Alignment explanation
Indices: 100289--100400 Score: 116
Period size: 24 Copynumber: 4.7 Consensus size: 24
100279 GAATGGTTAA
* * * *
100289 CTCTTATGAGCCCAAAATGATTAG
1 CTCTTACGAGCCCAGAGTGTTTAG
* *
100313 CTCTTATGAGCCCAAAGTGTTTAG
1 CTCTTACGAGCCCAGAGTGTTTAG
* * *
100337 CTCTTACGAACCCAGAATGGTTAG
1 CTCTTACGAGCCCAGAGTGTTTAG
* *
100361 CTCTTACGAGCCTAGAGTATTTAG
1 CTCTTACGAGCCCAGAGTGTTTAG
*
100385 CTCTTACGAGTCCAGA
1 CTCTTACGAGCCCAGA
100401 CAGAGTTTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
CTCTTACGAGCCCAGAGTGTTTAG
Found at i:100400 original size:48 final size:48
Alignment explanation
Indices: 100289--100400 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
100279 GAATGGTTAA
* * * *
100289 CTCTTATGAGCCCAAAATGATTAGCTCTTATGAGCCCAAAGTGTTTAG
1 CTCTTACGAGCCCAGAATGATTAGCTCTTACGAGCCCAAAGTATTTAG
* * * *
100337 CTCTTACGAACCCAGAATGGTTAGCTCTTACGAGCCTAGAGTATTTAG
1 CTCTTACGAGCCCAGAATGATTAGCTCTTACGAGCCCAAAGTATTTAG
*
100385 CTCTTACGAGTCCAGA
1 CTCTTACGAGCCCAGA
100401 CAGAGTTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (48 bp):
CTCTTACGAGCCCAGAATGATTAGCTCTTACGAGCCCAAAGTATTTAG
Found at i:101785 original size:29 final size:30
Alignment explanation
Indices: 101753--101815 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
101743 TGAAAATGGG
* * *
101753 ATTTTTGGATACTCG-GGGGTGAAATGGTA
1 ATTTTTGGACACTCGAGGGGTAAAATGCTA
*
101782 A-TTTTGGACACTTGAGGGGTAAAATGCTA
1 ATTTTTGGACACTCGAGGGGTAAAATGCTA
101811 ATTTT
1 ATTTT
101816 AGGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.39
29 14 0.50
30 3 0.11
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (30 bp):
ATTTTTGGACACTCGAGGGGTAAAATGCTA
Found at i:101786 original size:28 final size:29
Alignment explanation
Indices: 101745--101873 Score: 84
Period size: 28 Copynumber: 4.5 Consensus size: 29
101735 TCGGAGTTTG
* * *
101745 AAAATGGGATTTTTGGATACTCG-GGGGT
1 AAAATGGTAATTTTGGACACTCGAGGGGT
* *
101773 GAAATGGTAATTTTGGACACTTGAGGGGT
1 AAAATGGTAATTTTGGACACTCGAGGGGT
* * * *
101802 AAAATGCTAATTTTAGGAAAGTTC-AGGGTT
1 AAAATGGTAATTTT-GGACA-CTCGAGGGGT
* * * ** *
101832 AAAAGGGGAATTTTAGACA-TTTAAGGGT
1 AAAATGGTAATTTTGGACACTCGAGGGGT
101860 AAAATGGTAATTTT
1 AAAATGGTAATTTT
101874 TAGAAAAAAA
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
27 1 0.01
28 34 0.45
29 20 0.26
30 20 0.26
31 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGACACTCGAGGGGT
Found at i:101830 original size:29 final size:28
Alignment explanation
Indices: 101769--101879 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 28
101759 GGATACTCGG
* * * * *
101769 GGGTGAAATGGTAATTTTGGACACTTGAG
1 GGGTAAAATGGTAATTTTAGAAAGTT-AA
* *
101798 GGGTAAAATGCTAATTTTAGGAAAGTTCA
1 GGGTAAAATGGTAATTTTA-GAAAGTTAA
* * * *
101827 GGGTTAAAAGGGGAATTTTAGACATTTAA
1 GGG-TAAAATGGTAATTTTAGAAAGTTAA
101856 GGGTAAAATGGTAATTTTTAGAAA
1 GGGTAAAATGGTAA-TTTTAGAAA
101880 AAAATCGGGA
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
28 9 0.14
29 36 0.57
30 18 0.29
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGAAAGTTAA
Found at i:101974 original size:58 final size:59
Alignment explanation
Indices: 101860--101997 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 59
101850 ATTTAAGGGT
*
101860 AAAATGGTAATTTTTAGAAAAAAATCGGGATCAAAAACTGAATTTTTGGACATTCGAAGGC
1 AAAATGGTAATTTTTAG--AAAAATCGGGATCAAAAACTGAATTTTTGAACATTCGAAGGC
* *
101921 AAAATGGTAATTTTTAGAAAAAT-GGGATCAAAAA-TGGAATTTTCT-AACATTCGAGGGT
1 AAAATGGTAATTTTTAGAAAAATCGGGATCAAAAACT-GAATTTT-TGAACATTCGAAGGC
*
101979 AAAATTGTAATTTTT-GAAA
1 AAAATGGTAATTTTTAGAAA
101998 GTTTTGGGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
57 5 0.07
58 42 0.59
59 7 0.10
61 17 0.24
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAAAATCGGGATCAAAAACTGAATTTTTGAACATTCGAAGGC
Found at i:102007 original size:29 final size:29
Alignment explanation
Indices: 101975--102242 Score: 110
Period size: 29 Copynumber: 9.1 Consensus size: 29
101965 TAACATTCGA
101975 GGGTAAAATTGTAATTTTTGAAAGTTTTG
1 GGGTAAAATTGTAATTTTTGAAAGTTTTG
* *
102004 GGGTTAAATT-TAGGATATTTTG-AAG-TTCG
1 GGGTAAAATTGTA--AT-TTTTGAAAGTTTTG
* **
102033 AGGGTAAAATGGTAATTTTT-AGAAGTTTCA
1 -GGGTAAAATTGTAATTTTTGA-AAGTTTTG
* * *
102063 AGGTCAAAATTGGAATTTTTTG-AAG-TTCG
1 GGGT-AAAATTGTAA-TTTTTGAAAGTTTTG
* *
102092 GAGGTAAAAATGTAATTTTT-AGAAGTTTCG
1 G-GGTAAAATTGTAATTTTTGA-AAGTTTTG
* * * *
102122 AGGTCAAAA-AGGAACTTTT-AGAAG-TTTG
1 GGGT-AAAATTGTAATTTTTGA-AAGTTTTG
* **
102150 AGGGTAAAAATGTAATTTTTTTAAGTTTTG
1 -GGGTAAAATTGTAATTTTTGAAAGTTTTG
* *
102180 GGGTCAAAAATAG-AATTTTTTGGAAG-TTTG
1 GGGT--AAAATTGTAA-TTTTTGAAAGTTTTG
* *
102210 AGGGTAAAAATGTAATTTTTAGATAGTTTTG
1 -GGGTAAAATTGTAATTTTT-GAAAGTTTTG
102241 GG
1 GG
102243 ACCTCCAGGG
Statistics
Matches: 182, Mismatches: 30, Indels: 53
0.69 0.11 0.20
Matches are distributed among these distances:
28 18 0.10
29 76 0.42
30 55 0.30
31 33 0.18
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (29 bp):
GGGTAAAATTGTAATTTTTGAAAGTTTTG
Found at i:102041 original size:59 final size:59
Alignment explanation
Indices: 101970--102242 Score: 256
Period size: 59 Copynumber: 4.6 Consensus size: 59
101960 TTTTCTAACA
* * *
101970 TTCGAGGGTAAAATTGTAATTTTTGAAAGTTTTGGGGTTAAATTTAGGATATTTT-GAAG
1 TTCGAGGGTAAAAATGTAATTTTT-AAAGTTTTGGGGTCAAAATTAGGATATTTTAGAAG
*** *
102029 TTCGAGGGT-AAAATGGTAATTTTTAGAAGTTTCAAGGTCAAAATT-GGA-ATTTTTTGAAG
1 TTCGAGGGTAAAAAT-GTAATTTTTA-AAGTTTTGGGGTCAAAATTAGGATA-TTTTAGAAG
* *
102088 TTCG-GAGGTAAAAATGTAATTTTTAGAAGTTTCGAGGTCAAAA--AGGA-ACTTTTAGAAG
1 TTCGAG-GGTAAAAATGTAATTTTTA-AAGTTTTGGGGTCAAAATTAGGATA-TTTTAGAAG
* * * * * *
102146 TTTGAGGGTAAAAATGTAATTTTTTTAAGTTTTGGGGTCAAAAATAGAATTTTTTGGAAG
1 TTCGAGGGTAAAAATGTAA-TTTTTAAAGTTTTGGGGTCAAAATTAGGATATTTTAGAAG
*
102206 TTTGAGGGTAAAAATGTAATTTTTAGATAGTTTTGGG
1 TTCGAGGGTAAAAATGTAATTTTTA-A-AGTTTTGGG
102243 ACCTCCAGGG
Statistics
Matches: 183, Mismatches: 17, Indels: 26
0.81 0.08 0.12
Matches are distributed among these distances:
57 1 0.01
58 56 0.31
59 81 0.44
60 36 0.20
61 9 0.05
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGTAATTTTTAAAGTTTTGGGGTCAAAATTAGGATATTTTAGAAG
Found at i:102080 original size:30 final size:29
Alignment explanation
Indices: 102038--102238 Score: 154
Period size: 29 Copynumber: 6.8 Consensus size: 29
102028 GTTCGAGGGT
102038 AAAATGGTAATTTTTAGAAGTTTCAAGGTCA
1 AAAATGG-AATTTTTAGAAGTTTCAAGGT-A
* * *
102069 AAATTGGAATTTTTTGAAG-TTCGGAGGTA
1 AAAATGGAATTTTTAGAAGTTTC-AAGGTA
* *
102098 AAAATGTAATTTTTAGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGAAGTTTCAAGGT-A
* * *
102128 AAAA-GGAACTTTTAGAAGTTTGAGGGTA
1 AAAATGGAATTTTTAGAAGTTTCAAGGTA
* ** ***
102156 AAAATGTAATTTTTTTAAGTTTTGGGGTCA
1 AAAATGGAATTTTTAGAAGTTTCAAGGT-A
* * * *
102186 AAAATAGAATTTTTTGGAAGTTTGAGGGTA
1 AAAATGGAA-TTTTTAGAAGTTTCAAGGTA
*
102216 AAAATGTAATTTTTAGATAGTTT
1 AAAATGGAATTTTTAGA-AGTTT
102239 TGGGACCTCC
Statistics
Matches: 137, Mismatches: 26, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.04
29 67 0.49
30 44 0.32
31 21 0.15
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTAGAAGTTTCAAGGTA
Found at i:102200 original size:31 final size:30
Alignment explanation
Indices: 101973--102229 Score: 157
Period size: 30 Copynumber: 8.7 Consensus size: 30
101963 TCTAACATTC
* *
101973 GAGGGTAAAATTGTAA-TTTTTGAAAGTTTT
1 GAGGGTAAAAATGTAATTTTTTGGAAG-TTT
* * * *
102003 G-GGGT-TAAATTTAGGATATTTT-GAAGTTC
1 GAGGGTAAAAATGTA--ATTTTTTGGAAGTTT
*
102032 GAGGGT-AAAATGGTAA-TTTTTAGAAGTTT
1 GAGGGTAAAAAT-GTAATTTTTTGGAAGTTT
* * * * *
102061 CAAGGTCAAAATTGGAATTTTTT-GAAGTTC
1 GAGGGT-AAAAATGTAATTTTTTGGAAGTTT
*
102091 G-GAGGTAAAAATGTAA-TTTTTAGAAGTTT
1 GAG-GGTAAAAATGTAATTTTTTGGAAGTTT
* * *
102120 CGA-GGTCAAAAA-GGAA-CTTTTAGAAGTTT
1 -GAGGGT-AAAAATGTAATTTTTTGGAAGTTT
*
102149 GAGGGTAAAAATGTAATTTTTT-TAAGTTTT
1 GAGGGTAAAAATGTAATTTTTTGGAAG-TTT
102179 G-GGGTCAAAAATAG-AATTTTTTGGAAGTTT
1 GAGGGT-AAAAAT-GTAATTTTTTGGAAGTTT
102209 GAGGGTAAAAATGTAATTTTT
1 GAGGGTAAAAATGTAATTTTT
102230 AGATAGTTTT
Statistics
Matches: 178, Mismatches: 26, Indels: 46
0.71 0.10 0.18
Matches are distributed among these distances:
28 21 0.12
29 64 0.36
30 70 0.39
31 23 0.13
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (30 bp):
GAGGGTAAAAATGTAATTTTTTGGAAGTTT
Found at i:104407 original size:17 final size:17
Alignment explanation
Indices: 104385--104453 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
104375 AAGTTTGAGT
*
104385 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
*
104402 TTTAAACTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
104419 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
*
104436 TTTAGAAATAAATCTAAA
1 TTTA-AAATAAATTTAAA
104454 GTAATTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 29 0.66
18 15 0.34
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:111748 original size:19 final size:18
Alignment explanation
Indices: 111702--111748 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
111692 CTATATTATC
111702 ATTTTATATATTATTTAAT
1 ATTTTAT-TATTATTTAAT
*
111721 ATCTATATTATTATTTAAGT
1 AT-TTTATTATTATTTAA-T
111741 ATTTTATT
1 ATTTTATT
111749 GCGTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTATTATTATTTAAT
Found at i:112424 original size:8 final size:8
Alignment explanation
Indices: 112404--112441 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
112394 AAATAAAAAT
112404 AATTTTTA
1 AATTTTTA
112412 TAATTTTTA
1 -AATTTTTA
112421 AATTTTTA
1 AATTTTTA
112429 AATTTTTA
1 AATTTTTA
112437 AATTT
1 AATTT
112442 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
AATTTTTA
Found at i:118211 original size:17 final size:18
Alignment explanation
Indices: 118175--118213 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
118165 TTTGTTTTTC
* *
118175 AAAAATATTTTTGGATTA
1 AAAAATATTTTTGAAGTA
118193 AAAAATATTTTT-AAGTA
1 AAAAATATTTTTGAAGTA
118210 AAAA
1 AAAA
118214 TTAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
AAAAATATTTTTGAAGTA
Found at i:118331 original size:18 final size:19
Alignment explanation
Indices: 118299--118334 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
118289 AAAGTGATTT
118299 TTTTAAATTTAATAATAAA
1 TTTTAAATTTAATAATAAA
*
118318 TTTT-AATTTTATAATAA
1 TTTTAAATTTAATAATAA
118335 CATTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAATTTAATAATAAA
Found at i:119090 original size:20 final size:20
Alignment explanation
Indices: 119065--119130 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
119055 TGAATCAATT
*
119065 TTTTATATATTAAAATGGGG
1 TTTTATTTATTAAAATGGGG
*** *
119085 TTTTATTTATTAGTTTGGAG
1 TTTTATTTATTAAAATGGGG
*
119105 -TTTATTTATAAAAATGGGG
1 TTTTATTTATTAAAATGGGG
119124 TTTTATT
1 TTTTATT
119131 AATTCATCCC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
19 14 0.40
20 21 0.60
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTTATTTATTAAAATGGGG
Found at i:119126 original size:19 final size:19
Alignment explanation
Indices: 119066--119126 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
119056 GAATCAATTT
*
119066 TTTATATATTAAAATGGGG
1 TTTATTTATTAAAATGGGG
*** *
119085 TTTTATTTATTAGTTTGGAG
1 -TTTATTTATTAAAATGGGG
*
119105 TTTATTTATAAAAATGGGG
1 TTTATTTATTAAAATGGGG
119124 TTT
1 TTT
119127 TATTAATTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTATTTATTAAAATGGGG
Found at i:120665 original size:22 final size:23
Alignment explanation
Indices: 120631--120674 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
120621 ACATAGGTAA
*
120631 AAAAATATTATTTGT-AATTTTTC
1 AAAAATATCATTT-TCAATTTTTC
120654 AAAAAT-TCATTTTCAATTTTT
1 AAAAATATCATTTTCAATTTTT
120675 ATCAGTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 12 0.63
23 6 0.32
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
AAAAATATCATTTTCAATTTTTC
Found at i:120972 original size:17 final size:17
Alignment explanation
Indices: 120935--121027 Score: 96
Period size: 17 Copynumber: 5.4 Consensus size: 17
120925 CCAAACTCCC
* *
120935 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
120953 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
120970 TTTAAATTTGTCTTGAA
1 TTTAAATTTATTTTAAA
* *
120987 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
121004 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
121022 TTTAAA
1 TTTAAA
121028 AAAAATTATT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 41 0.68
18 19 0.32
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:120978 original size:23 final size:23
Alignment explanation
Indices: 120950--120997 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
120940 ATTTGTTTAA
* *
120950 AAATTTGAATTTATTTTAAATTT
1 AAATTTGAATTGAATTTAAATTT
**
120973 AAATTTGTCTTGAATTTAAATTT
1 AAATTTGAATTGAATTTAAATTT
120996 AA
1 AA
120998 TTTAAGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (23 bp):
AAATTTGAATTGAATTTAAATTT
Found at i:121011 original size:23 final size:23
Alignment explanation
Indices: 120964--121013 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
120954 TTGAATTTAT
*
120964 TTTAAATTTAAATTTGTCTTGAA
1 TTTAAATTTAAATTTGTCTTAAA
120987 TTTAAATTT-AATTTAAGT-TTAAA
1 TTTAAATTTAAATTT--GTCTTAAA
121010 TTTA
1 TTTA
121014 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTGTCTTAAA
Found at i:121766 original size:13 final size:13
Alignment explanation
Indices: 121748--121786 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
121738 TATTTATAAC
*
121748 TATTAATAATTAT
1 TATTAATAATTAA
*
121761 TATTAATAATCAA
1 TATTAATAATTAA
*
121774 TATTAATTATTAA
1 TATTAATAATTAA
121787 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTAATAATTAA
Found at i:122953 original size:59 final size:59
Alignment explanation
Indices: 122793--123173 Score: 532
Period size: 59 Copynumber: 6.5 Consensus size: 59
122783 GGAGGTCCCT
* *
122793 GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * ** *
122852 GAACTTTCT-AAAATTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
122910 GACCCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
122969 GAACCTTCTAAAATTTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * ** *
123028 AAACCTTCTAAAATTTACCATTTTACCCTTGAACTTCC-AAAATCTCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * *
123086 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTTACTCT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
123145 GAACCTTCTAAAAACTACCATTTTGCCCC
1 GAACCTTCTAAAAATTACCATTTTACCCC
123174 GTGCATCCGA
Statistics
Matches: 286, Mismatches: 34, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
58 100 0.35
59 186 0.65
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:123041 original size:117 final size:116
Alignment explanation
Indices: 122793--123173 Score: 523
Period size: 117 Copynumber: 3.2 Consensus size: 116
122783 GGAGGTCCCT
* * *
122793 GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAACTT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
122858 TCTAAAATTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCC
66 TCTAAAATTACCATTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCTC
* *
122910 GACCCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
122975 TCTAAAATTTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC
66 TCTAAAA-TTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCTC
* * ** *
123028 AAACCTTCTAAAATTTACCATTTTACCCTTGAACTTCC-AAAATCTCATTTTTGACCCCGAACCT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
123092 TCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTTA-CTC
66 T-CTAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* *
123144 TGAACCTTCTAAAAACTACCATTTTGCCCC
1 -GAACCTTCTAAAAATTACCATTTTACCCC
123174 GTGCATCCGA
Statistics
Matches: 235, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
116 3 0.01
117 152 0.65
118 79 0.34
119 1 0.00
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (116 bp):
GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
TCTAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCTC
Found at i:123087 original size:176 final size:176
Alignment explanation
Indices: 122793--123173 Score: 575
Period size: 176 Copynumber: 2.2 Consensus size: 176
122783 GGAGGTCCCT
* * *
122793 GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAACTT
1 GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
* *
122858 TCTAAAATTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGACCCTTCTAAAA
66 TCTAAAATTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAA
122923 ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
131 ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
** * *
122969 GAACCTTCTAAAATTTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAACCT
1 GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
* * *
123034 TCTAAAATTTACCATTTTACCCTTGAACTTCC-AAAATCTCATTTTTGACCCCGAACCTTCCAAA
66 TCTAAAA-TTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAA
* * * * *
123098 AATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTTACTCT
130 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* *
123145 GAACCTTCTAAAAACTACCATTTTGCCCC
1 GAACCTTCTAAAAAATACCATTTTACCCC
123174 GTGCATCCGA
Statistics
Matches: 183, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
176 162 0.89
177 21 0.11
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (176 bp):
GAACCTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
TCTAAAATTACAATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAA
ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
Done.