Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000293.1 Hibiscus syriacus cultivar Beakdansim tig00000538_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: 557133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4519 original size:16 final size:16
Alignment explanation
Indices: 4487--4534 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
4477 ATTCAAGTCA
* *
4487 TTTTATGTTCAGTTTG
1 TTTTATGTTCGGATTG
4503 TTTTATGTTCGGATTG
1 TTTTATGTTCGGATTG
* *
4519 TTTCAAGTTCGGATTG
1 TTTTATGTTCGGATTG
4535 CTTCAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTTATGTTCGGATTG
Found at i:4539 original size:16 final size:16
Alignment explanation
Indices: 4509--4545 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
4499 TTTGTTTTAT
*
4509 GTTCGGATTGTTTCAA
1 GTTCGGATTGCTTCAA
4525 GTTCGGATTGCTTCAA
1 GTTCGGATTGCTTCAA
4541 GTTCG
1 GTTCG
4546 AATCATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (16 bp):
GTTCGGATTGCTTCAA
Found at i:10891 original size:18 final size:19
Alignment explanation
Indices: 10843--10891 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
10833 CCGTTTGCTC
* *
10843 ATTGCATGTTTGTGCTTGT
1 ATTGCATGTTTTTGCTTAT
* *
10862 AATGCTTGTTTTTG-TTAT
1 ATTGCATGTTTTTGCTTAT
10880 ATTGCATGTTTT
1 ATTGCATGTTTT
10892 ACTCGTATGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.14, C:0.08, G:0.20, T:0.57
Consensus pattern (19 bp):
ATTGCATGTTTTTGCTTAT
Found at i:15049 original size:265 final size:266
Alignment explanation
Indices: 14538--15049 Score: 963
Period size: 266 Copynumber: 1.9 Consensus size: 266
14528 TTATATTAAA
* * *
14538 ATTTTTGAGGGAGCACAATTAAATAATTAATAGAAAATACAAATAAAAATTTAAAATAAAACATT
1 ATTTTAGAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
*
14603 TCATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
66 TCATAATTTATTAACCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
14668 GTTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
131 GTTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
*
14733 ATAAACTTATTTTTATTTTTATTTATTTATTTGTTTGTCTTCTCAATTTCCTTAAAAATTTAGAG
196 ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCTTAAAAATTTAGAG
14798 TTATAT
261 TTATAT
*
14804 ATTTTAGAGGGTGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
1 ATTTTAGAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
14869 TCATAATTTATTAACCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
66 TCATAATTTATTAACCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
14934 G-TTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
131 GTTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
14998 ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCT
196 ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCT
15050 AGGATTTTTT
Statistics
Matches: 240, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
265 114 0.47
266 126 0.52
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (266 bp):
ATTTTAGAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
TCATAATTTATTAACCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
GTTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCTTAAAAATTTAGAG
TTATAT
Found at i:27024 original size:31 final size:32
Alignment explanation
Indices: 26955--27027 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
26945 GGCCTGCGAC
*
26955 CCTACCCAAGAAAATTATCAGGGTCACGGAGG
1 CCTACCCAAGAAAAATATCAGGGTCACGGAGG
* *
26987 CCTACCCAAGAAAAATCTCAGGG-C-CGTAGAG
1 CCTACCCAAGAAAAATATCAGGGTCACGGAG-G
27018 CCTACCCAAG
1 CCTACCCAAG
27028 GGTCATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 12 0.32
32 21 0.57
ACGTcount: A:0.34, C:0.30, G:0.22, T:0.14
Consensus pattern (32 bp):
CCTACCCAAGAAAAATATCAGGGTCACGGAGG
Found at i:27196 original size:12 final size:12
Alignment explanation
Indices: 27171--27226 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
27161 ACAGAGATAT
*
27171 CAGAAATCATAA
1 CAGAAATCAGAA
*
27183 CAGAATTCAGAA
1 CAGAAATCAGAA
*
27195 CAGAATTCAGAA
1 CAGAAATCAGAA
*
27207 CATAAATCAGAA
1 CAGAAATCAGAA
*
27219 CATAAATC
1 CAGAAATC
27227 GGATGAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:30189 original size:20 final size:20
Alignment explanation
Indices: 30164--30237 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
30154 AACACGATCT
* **
30164 CAATTTCGCAACGCAAATTC
1 CAATTTCGCAACTCAGTTTC
30184 CAATTTCGCAACTCAGTTTC
1 CAATTTCGCAACTCAGTTTC
*
30204 CAATTTCACAACTCAGTTTC
1 CAATTTCGCAACTCAGTTTC
30224 CAATTTCGCAACTC
1 CAATTTCGCAACTC
30238 GAATATGTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (20 bp):
CAATTTCGCAACTCAGTTTC
Found at i:30345 original size:19 final size:19
Alignment explanation
Indices: 30287--30354 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
30277 GCTATTTTCC
* *
30287 AAATTTGCAATGCGAAAGTT
1 AAATTCGCAATGCG-AATTT
30307 AAATTCGCAA--CTGAATTTT
1 AAATTCGCAATGC-GAA-TTT
30326 AAATTCGCAATGCGAATTT
1 AAATTCGCAATGCGAATTT
*
30345 AATTTCGCAA
1 AAATTCGCAA
30355 CAGGTTTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.07
19 25 0.61
20 12 0.29
21 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (19 bp):
AAATTCGCAATGCGAATTT
Found at i:31281 original size:24 final size:24
Alignment explanation
Indices: 31247--31300 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31237 GTATTCGAAA
31247 TTTGATATTGGTCAATACTCAGAC
1 TTTGATATTGGTCAATACTCAGAC
* * *
31271 TTTGATCTTGGTCAATATTCAGAT
1 TTTGATATTGGTCAATACTCAGAC
31295 TTTGAT
1 TTTGAT
31301 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCAGAC
Found at i:33583 original size:18 final size:18
Alignment explanation
Indices: 33560--33595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33550 AAGCAAAAGG
*
33560 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
33578 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
33596 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:33942 original size:20 final size:20
Alignment explanation
Indices: 33914--33975 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
33904 CACGAAATAA
33914 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
33934 GCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
33954 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
33974 GC
1 GC
33976 AACGCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:33993 original size:34 final size:38
Alignment explanation
Indices: 33914--34000 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 38
33904 CACGAAATAA
* *
33914 GCGTTGCGAATTTGACTATCGCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATCGCG-AACG-ACTTGACTTTC
33954 GCGTTGCGAATTTGACTATCGC-AACG-CTT-A-TTTC
1 GCGTTGCGAATTTGACTATCGCGAACGACTTGACTTTC
*
33988 GCGTTGCAAATTT
1 GCGTTGCGAATTT
34001 ACCTTCAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
36 2 0.05
38 3 0.07
40 22 0.50
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (38 bp):
GCGTTGCGAATTTGACTATCGCGAACGACTTGACTTTC
Found at i:35487 original size:22 final size:22
Alignment explanation
Indices: 35457--35503 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
35447 GATGGAGATA
*
35457 GACAGATTTCGTCGGAAATGGG
1 GACAAATTTCGTCGGAAATGGG
*
35479 GACAAATTTCGTCGGAGATGGG
1 GACAAATTTCGTCGGAAATGGG
35501 GAC
1 GAC
35504 GGATGTTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (22 bp):
GACAAATTTCGTCGGAAATGGG
Found at i:35688 original size:21 final size:21
Alignment explanation
Indices: 35673--35716 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
35663 TTCGCGTTGT
35673 GAATTTGGAAAATCGCAACGC
1 GAATTTGGAAAATCGCAACGC
*
35694 GAATTTGGAAAATCGCAATGC
1 GAATTTGGAAAATCGCAACGC
35715 GA
1 GA
35717 TTTACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGC
Found at i:41918 original size:23 final size:23
Alignment explanation
Indices: 41892--41937 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
41882 AATATTTGGG
41892 AGAACAAAATACTTTAAAAAAAT
1 AGAACAAAATACTTTAAAAAAAT
*
41915 AGAACAAAATGCTTTAAAAAAAT
1 AGAACAAAATACTTTAAAAAAAT
41938 TAGATAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
AGAACAAAATACTTTAAAAAAAT
Found at i:58923 original size:13 final size:13
Alignment explanation
Indices: 58905--58938 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
58895 CATAGTTAAA
58905 CAGTCTTCATATG
1 CAGTCTTCATATG
58918 CAGTCTTCATATG
1 CAGTCTTCATATG
58931 CACGTCTT
1 CA-GTCTT
58939 TAATGGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:61931 original size:2 final size:2
Alignment explanation
Indices: 61924--61958 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61914 TTGAATTTGA
61924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61959 AACATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63855 original size:16 final size:18
Alignment explanation
Indices: 63823--63856 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
63813 TATTAATGTA
63823 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
63841 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
63857 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:64559 original size:130 final size:130
Alignment explanation
Indices: 64326--64573 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
64316 ATTTTTCTTC
* *
64326 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
64391 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
64456 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
64521 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
64574 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:65020 original size:35 final size:35
Alignment explanation
Indices: 64970--65045 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
64960 AATTGAATTT
* *
64970 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
65005 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
65040 AATTGA
1 AATTGA
65046 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:76045 original size:43 final size:43
Alignment explanation
Indices: 75968--76081 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
75958 GAATTGACGT
* * *
75968 TGATCCAGCTCCTTCTGTGAAAAACCAAGCGAAAGACTT-TCAC
1 TGATCCAACTCCTTCTGTGAAAGATCAAGCGAAAG-CTTGTCAC
* * *
76011 TGATCCAACTCCTTCTGTGAAAGATCAAGTGAAAGGTTGTTAC
1 TGATCCAACTCCTTCTGTGAAAGATCAAGCGAAAGCTTGTCAC
** * *
76054 TGATCCAACTTATTATGTGGAAGATCAA
1 TGATCCAACTCCTTCTGTGAAAGATCAA
76082 ACAACACGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.03
43 58 0.97
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (43 bp):
TGATCCAACTCCTTCTGTGAAAGATCAAGCGAAAGCTTGTCAC
Found at i:76276 original size:43 final size:42
Alignment explanation
Indices: 76186--76351 Score: 154
Period size: 43 Copynumber: 3.8 Consensus size: 42
76176 AAGGTTACGT
* * *
76186 TGATCCAACTCCTTATGTGAAGAATCAAGCAAAAAGATACCAT-
1 TGATCCAACTCCTTCTGTGAAGAATCAAGCAAAATG-T-CTATG
*
76229 TGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTCTATG
1 TGATCCAACTCCTTCTGTGAAGAATCAAGCAAAATGTCTATG
* * * ** *
76271 ATGATCTACCTCGTTCTGTGATAGAATCCGGCAAAATAAGTTTATG
1 -TGATCCAACTCCTTCTGTGA-AGAATCAAGCAAAAT--GTCTATG
* *
76317 CTGATTCAACTCCTTCTGTGAAGAATCGAGCAAAA
1 -TGATCCAACTCCTTCTGTGAAGAATCAAGCAAAA
76352 AATTGACACT
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 50 0.50
44 12 0.12
45 12 0.12
46 22 0.22
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (42 bp):
TGATCCAACTCCTTCTGTGAAGAATCAAGCAAAATGTCTATG
Found at i:76881 original size:9 final size:9
Alignment explanation
Indices: 76861--76913 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
76851 TTCACTTTAA
76861 TTTTTCTCTC
1 TTTTTCT-TC
76871 TTTTTCTTC
1 TTTTTCTTC
*
76880 TTCTTCTTC
1 TTTTTCTTC
76889 TTTTTC--C
1 TTTTTCTTC
*
76896 TTTTTATTTC
1 TTTTT-CTTC
76906 TTTTTCTT
1 TTTTTCTT
76914 TTCAAAACTG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 6 0.17
9 17 0.47
10 13 0.36
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:76911 original size:6 final size:6
Alignment explanation
Indices: 76869--76915 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
76859 AATTTTTCTC
* * * *
76869 TCTTTT TCTTCT TCTTCT TCTTTT TCCTTT T-TATT TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
76916 CAAAACTGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:82095 original size:2 final size:2
Alignment explanation
Indices: 82083--82126 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
82073 GACCAACCGA
* *
82083 AT AT AT GT AT AT AT AT AT AT AT AT AT AT GT -T AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
82125 AT
1 AT
82127 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86570 original size:170 final size:168
Alignment explanation
Indices: 86251--86592 Score: 582
Period size: 170 Copynumber: 2.0 Consensus size: 168
86241 TCACATATTG
*
86251 TTAAATCTCCTTTTCGGTAAAAATTGTTCGCCGATATAATCAATTGTAGCCCAACAATTTACCAA
1 TTAAATCTCCTTTTCGGTAAAAATTGTTCACCGATATAATCAATTGTAGCCCAACAATTTACCAA
*
86316 ATTGTTTGATTCGCTTATCATTCCTTATCACTTTGTAAAGTGTCTTGTTCGACATAGACAAAAAG
66 ATTGTTTGATTCG--TATCATTCCTTATCACTTTGTAAAGCGTCTTGTTCGACATAGACAAAAAG
86381 TCTTATAAAGGTTATTGGTTCTTTTGATGTTAGACGTCAT
129 TCTTATAAAGGTTATTGGTTCTTTTGATGTTAGACGTCAT
86421 TTAAATCTCC-TTTCGGTAAAAATTTGTTCACCGATATAATCAAAATTGTGTAGCCCAACAATTT
1 TTAAATCTCCTTTTCGGTAAAAA-TTGTTCACCGATATAATC--AA-T-TGTAGCCCAACAATTT
86485 ACCAAATTGTTTGATTCG-ATCATTCCTTATCACTTTGTAAAGCGTCTTGTTCGACATAGACAAA
61 ACCAAATTGTTTGATTCGTATCATTCCTTATCACTTTGTAAAGCGTCTTGTTCGACATAGACAAA
86549 AA-TCTTATAAAGGTTATTGGTTCTTTTGATGTTAGACGTCAT
126 AAGTCTTATAAAGGTTATTGGTTCTTTTGATGTTAGACGTCAT
86591 TT
1 TT
86593 TCAGTGGAAT
Statistics
Matches: 165, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
169 12 0.07
170 69 0.42
171 47 0.28
172 2 0.01
173 1 0.01
174 34 0.21
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (168 bp):
TTAAATCTCCTTTTCGGTAAAAATTGTTCACCGATATAATCAATTGTAGCCCAACAATTTACCAA
ATTGTTTGATTCGTATCATTCCTTATCACTTTGTAAAGCGTCTTGTTCGACATAGACAAAAAGTC
TTATAAAGGTTATTGGTTCTTTTGATGTTAGACGTCAT
Found at i:96555 original size:31 final size:31
Alignment explanation
Indices: 96517--96579 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
96507 CCCGAAGGAC
*
96517 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
96548 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
96579 C
1 C
96580 CCTCGACCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:107635 original size:16 final size:16
Alignment explanation
Indices: 107614--107653 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
107604 AAAACCCATC
107614 AGAAAGAAGAAAAAAA
1 AGAAAGAAGAAAAAAA
* *
107630 AGAAAGAAGTAAAGAA
1 AGAAAGAAGAAAAAAA
*
107646 AGGAAGAA
1 AGAAAGAA
107654 AAAGCCTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (16 bp):
AGAAAGAAGAAAAAAA
Found at i:115350 original size:24 final size:24
Alignment explanation
Indices: 115264--115350 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 24
115254 ATTTCCGACT
*
115264 TGAATTCTGTTCTGATA-CATTACC
1 TGAATTCTGTTCTGATATC-TTATC
* * *
115288 TGAATTTTGTTCTGATTTCTGT-TA
1 TGAATTCTGTTCTGATATCT-TATC
*
115312 TG-ATTATGTTCTGATATCTTATC
1 TGAATTCTGTTCTGATATCTTATC
*
115335 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
115351 CTGTGGGGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
22 1 0.02
23 18 0.36
24 29 0.58
25 2 0.04
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATC
Found at i:119351 original size:29 final size:26
Alignment explanation
Indices: 119301--119358 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
119291 GCTATTTGTC
* *
119301 ATTATGCCAAAAAGAAATTAGACGTG
1 ATTATGCCAAAAAAAAATTAGAAGTG
119327 ATTATGCCAAAAAAAATTAATTAGAAGTG
1 ATTATGCC-AAAAAAA--AATTAGAAGTG
119356 ATT
1 ATT
119359 TGATTCAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 6 0.22
29 13 0.48
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.28
Consensus pattern (26 bp):
ATTATGCCAAAAAAAAATTAGAAGTG
Found at i:129933 original size:27 final size:27
Alignment explanation
Indices: 129903--129964 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
129893 TAAGATAATA
129903 TCACATCATCTTTGAAGATAAAAAATG
1 TCACATCATCTTTGAAGATAAAAAATG
129930 TCACATCATCTTTGAAGATAAAAAATG
1 TCACATCATCTTTGAAGATAAAAAATG
*
129957 TAACATCA
1 TCACATCA
129965 ATAGTCCTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (27 bp):
TCACATCATCTTTGAAGATAAAAAATG
Found at i:132153 original size:32 final size:32
Alignment explanation
Indices: 132109--132173 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
132099 TTTGTTTAAT
*
132109 TGATGACGTGATATGTATCATGTCACCCAAAA
1 TGATGACATGATATGTATCATGTCACCCAAAA
* *
132141 TGATGACATGATATTTATCATGTCACTCAAAA
1 TGATGACATGATATGTATCATGTCACCCAAAA
132173 T
1 T
132174 AATAAAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
TGATGACATGATATGTATCATGTCACCCAAAA
Found at i:135107 original size:20 final size:20
Alignment explanation
Indices: 135063--135114 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
135053 AAATCGGTTT
* *
135063 GAGTTGACTCAGGTCGGTTC
1 GAGTTGACTCAGGTCAGTCC
* *
135083 AAGTTGACTCAGTTCAGTCC
1 GAGTTGACTCAGGTCAGTCC
*
135103 GAGTTAACTCAG
1 GAGTTGACTCAG
135115 ACCTGTTCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (20 bp):
GAGTTGACTCAGGTCAGTCC
Found at i:140009 original size:164 final size:167
Alignment explanation
Indices: 139737--140067 Score: 641
Period size: 164 Copynumber: 2.0 Consensus size: 167
139727 CTTTTTCCTC
139737 AACTTTTTCTCGTTATAGGTTAGAGTCTGTAGGGAGAAGGCAAACCGGTCATGTTTATGCTATGA
1 AACTTTTTCTCGTTATAGGTTAGAGTCTGTAGGGAGAAGGCAAACCGGTCATGTTTATGCTATGA
139802 AGAAGCTGAAGAAGTCAGAGATGCTTCGTAGAGGCCAGGTACACAA-TTTGAATCA-CTATGTAG
66 AGAAGCTGAAGAAGTCAGAGATGCTTCGTAGAGGCCAGGTACACAATTTTGAATCAGCTATGTAG
139865 TTTCGTTAATTTGTTTTGTGCCATGATGCTAACTTGT
131 TTTCGTTAATTTGTTTTGTGCCATGATGCTAACTTGT
139902 AACTTTTTCTCGTTATAGGTTAGAGTCTGTAGGGAGAAGGC-AACCGGTCATGTTTATGCTATGA
1 AACTTTTTCTCGTTATAGGTTAGAGTCTGTAGGGAGAAGGCAAACCGGTCATGTTTATGCTATGA
139966 AGAAGCTGAAGAAGTCAGAGATGCTTCGTAGAGGCCAGGTACACAATTTTGAATCAGCTATGTAG
66 AGAAGCTGAAGAAGTCAGAGATGCTTCGTAGAGGCCAGGTACACAATTTTGAATCAGCTATGTAG
140031 TTTCGTTAATTTGTTTTGTGCCATGATGCTAACTTGT
131 TTTCGTTAATTTGTTTTGTGCCATGATGCTAACTTGT
140068 TAGCTTGCAT
Statistics
Matches: 164, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
164 69 0.42
165 50 0.30
166 45 0.27
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (167 bp):
AACTTTTTCTCGTTATAGGTTAGAGTCTGTAGGGAGAAGGCAAACCGGTCATGTTTATGCTATGA
AGAAGCTGAAGAAGTCAGAGATGCTTCGTAGAGGCCAGGTACACAATTTTGAATCAGCTATGTAG
TTTCGTTAATTTGTTTTGTGCCATGATGCTAACTTGT
Found at i:153430 original size:2 final size:2
Alignment explanation
Indices: 153423--153458 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
153413 AACACGATTT
153423 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
153459 CACCGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:158602 original size:338 final size:339
Alignment explanation
Indices: 157981--158655 Score: 1254
Period size: 338 Copynumber: 2.0 Consensus size: 339
157971 TTCATGCACA
*
157981 ATGTGATTCTAGGGGTATGAGGGGTATTTTGCACCCAACAATATTCAACAACATCATCATTACCC
1 ATGTGATTCTAGGGGTATGAGGGGTATTTTGCACCCAACAATATCCAACAACATCATCATTACCC
158046 CTAGATATTTTTATTATATATTACACCTCACAAGAGAGAGTGTGTGGAAGAAAGGAGACGCATAT
66 CTAGATATTTTTATTATATATTACACCTCACAAGAGAGAGTGTGTGGAAGAAAGGAGACGCATAT
158111 TGTAGCAGAAAAATCATATTTTTATTTTCCCTTTTCCTTTTTCTTCCTTGGGTTTTCCTCATTGA
131 TGTAGCAGAAAAATCATATTTTTATTTTCCCTTTTCCTTTTTCTTCCTTGGGTTTTCCTCATTGA
158176 TAAAACTTCAGGAGTGGCGAGCTAGGTGCCGAGAGGAGCTAGCGAGCTAAGGCGGTTCGTGGTGG
196 TAAAACTTCAGGAGTGGCGAGCTAGGTGCCGAGAGGAGCTAGCGAGCTAAGGCGGTTCGTGGTGG
158241 CCGAGGAGACCTCCGGTGGCGCGCGTCGAAGGCTCTTTCTCAATTCCCTTTACTGTTATTTTTA-
261 CCGAGGAGACCTCCGGTGGCGCGCGTCGAAGGCTCTTTCTCAATTCCCTTTACTGTTATTTTTAT
158305 TT-TTTTATTTGAC
326 TTATTTTATTTGAC
158318 ATGTGATTCTAGGGGTATGAGGGGTATTTTGCACCCCAACAATATCCAACAACATCATCATTACC
1 ATGTGATTCTAGGGGTATGAGGGGTATTTTGCA-CCCAACAATATCCAACAACATCATCATTACC
158383 CCTAGATATTTTTATTATATATTACACCTCACAAGAGAGAGTGTGTGGAAGAAAGGAGACGCATA
65 CCTAGATATTTTTATTATATATTACACCTCACAAGAGAGAGTGTGTGGAAGAAAGGAGACGCATA
158448 TTGTAGCAGAAAAATCATATTTTT-TTTTCCCTTTTCCTTTATTCTTCCTTGGGTTTTCCTCCAC
130 TTGTAGCAGAAAAATCATATTTTTATTTTCCCTTTTCCTTT-TTCTTCCTTGGGTTTTCCT-CA-
158512 TTGATAAAACTTCAAGGAGTGGCGAGCTAGGTGCCGAGAGGAGCTAGCGAGCTAAGGCGGTTCGT
192 TTGATAAAACTTC-AGGAGTGGCGAGCTAGGTGCCGAGAGGAGCTAGCGAGCTAAGGCGGTTCGT
158577 GGTGGCCGA-GAGACCTCC-G-GGCGCGCGTCGAAGGCTCTTTCTCAATTCCCTTTACTGTTATT
256 GGTGGCCGAGGAGACCTCCGGTGGCGCGCGTCGAAGGCTCTTTCTCAATTCCCTTTACTGTTATT
158639 TTTATTTATTTTATTTG
321 TTTATTTATTTTATTTG
158656 TGGGTTGTTG
Statistics
Matches: 330, Mismatches: 1, Indels: 11
0.96 0.00 0.03
Matches are distributed among these distances:
337 49 0.15
338 185 0.56
339 5 0.02
340 31 0.09
341 60 0.18
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (339 bp):
ATGTGATTCTAGGGGTATGAGGGGTATTTTGCACCCAACAATATCCAACAACATCATCATTACCC
CTAGATATTTTTATTATATATTACACCTCACAAGAGAGAGTGTGTGGAAGAAAGGAGACGCATAT
TGTAGCAGAAAAATCATATTTTTATTTTCCCTTTTCCTTTTTCTTCCTTGGGTTTTCCTCATTGA
TAAAACTTCAGGAGTGGCGAGCTAGGTGCCGAGAGGAGCTAGCGAGCTAAGGCGGTTCGTGGTGG
CCGAGGAGACCTCCGGTGGCGCGCGTCGAAGGCTCTTTCTCAATTCCCTTTACTGTTATTTTTAT
TTATTTTATTTGAC
Found at i:161690 original size:15 final size:15
Alignment explanation
Indices: 161666--161708 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
161656 TGAGTGTTTG
161666 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
161680 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
161694 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
161709 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:161791 original size:55 final size:54
Alignment explanation
Indices: 161708--161812 Score: 201
Period size: 55 Copynumber: 1.9 Consensus size: 54
161698 TTTTAATTTT
161708 AATATTTTTTTAGGACAAAGGGTGTTTTGAAGGATGAATATGATGAAATCACGA
1 AATATTTTTTTAGGACAAAGGGTGTTTTGAAGGATGAATATGATGAAATCACGA
161762 AATATTTTTTTTAGGACAAAGGGTGTTTTGAAGGATGAATATGATGAAATC
1 AATA-TTTTTTTAGGACAAAGGGTGTTTTGAAGGATGAATATGATGAAATC
161813 TCACGATGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 4 0.08
55 46 0.92
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (54 bp):
AATATTTTTTTAGGACAAAGGGTGTTTTGAAGGATGAATATGATGAAATCACGA
Found at i:163891 original size:24 final size:24
Alignment explanation
Indices: 163846--163895 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
163836 TGGTGGTTGG
*
163846 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
163870 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
163894 TT
1 TT
163896 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:179237 original size:153 final size:155
Alignment explanation
Indices: 178956--179264 Score: 561
Period size: 153 Copynumber: 2.0 Consensus size: 155
178946 ATGAATGACT
178956 TACTCATAATTGTTTATGATTTCAACTTCACTTGAATGATTTGCTTATATATACACACACAAACT
1 TACTCATAATTGTTTATGATTTCAACTTCACTTGAATGATTTGCTTATATATA-ACACACAAACT
179021 GGATAAAAGAGAGATCGAGTTCAAATGATTTAATGGATTGTTAAACAAGAAGACTATGGAAATCG
65 GGATAAAAGAGAGATCGAGTTCAAATGATTTAATGGATTGTTAAACAAGAAGACTATGGAAATCG
*
179086 AGTTTAAATCCATAACCAGAAGAAGA
130 AGCTTAAATCCATAACCAGAAGAAGA
179112 TACTCATAATTGTTTATGATTTCAACTTCACTTGAATGA-TTGCTTATATAT-ACACACAAAC-G
1 TACTCATAATTGTTTATGATTTCAACTTCACTTGAATGATTTGCTTATATATAACACACAAACTG
*
179174 GATGAAAAGAGAGATCGAGTTCAAATGATTTAATGGCTTGTTAAACAAGAAGACTATGGAAATCG
66 GAT-AAAAGAGAGATCGAGTTCAAATGATTTAATGGATTGTTAAACAAGAAGACTATGGAAATCG
179239 AGCTTAAATCCATAACCAGAAGAAGA
130 AGCTTAAATCCATAACCAGAAGAAGA
179265 CGCACTGAAT
Statistics
Matches: 150, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
152 4 0.03
153 95 0.63
155 12 0.08
156 39 0.26
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (155 bp):
TACTCATAATTGTTTATGATTTCAACTTCACTTGAATGATTTGCTTATATATAACACACAAACTG
GATAAAAGAGAGATCGAGTTCAAATGATTTAATGGATTGTTAAACAAGAAGACTATGGAAATCGA
GCTTAAATCCATAACCAGAAGAAGA
Found at i:179495 original size:15 final size:15
Alignment explanation
Indices: 179460--179503 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
179450 CTTGTTTTCC
*
179460 AGTGGAGTCAACGGT
1 AGTGGAGTCAATGGT
* *
179475 AATGGAGTCAATTGT
1 AGTGGAGTCAATGGT
*
179490 AGTGGACTCAATGG
1 AGTGGAGTCAATGG
179504 AAGATGATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (15 bp):
AGTGGAGTCAATGGT
Found at i:180513 original size:21 final size:21
Alignment explanation
Indices: 180488--180529 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
180478 ATTCATTCTC
*
180488 GTCGCCATTATGATCCCTCGA
1 GTCGCCATTACGATCCCTCGA
180509 GTCGCCATTACGATCCCTCGA
1 GTCGCCATTACGATCCCTCGA
180530 ACTGCATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (21 bp):
GTCGCCATTACGATCCCTCGA
Found at i:188395 original size:32 final size:32
Alignment explanation
Indices: 188359--188420 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
188349 TCATTCAATG
188359 TGATGACAT-AGTATATGTCACATTACCTAATA
1 TGATGACATGA-TATATGTCACATTACCTAATA
* *
188391 TGATGACGTGATATGTGTCACATTACCTAA
1 TGATGACATGATATATGTCACATTACCTAA
188421 GATAATGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
TGATGACATGATATATGTCACATTACCTAATA
Found at i:188438 original size:32 final size:32
Alignment explanation
Indices: 188369--188439 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
188359 TGATGACATA
* * *
188369 GTATATGTCACATTACCTAATATGATGACGTG
1 GTATGTGTCACATTACCTAAGATAATGACGTG
* *
188401 ATATGTGTCACATTACCTAAGATAATGATGTG
1 GTATGTGTCACATTACCTAAGATAATGACGTG
188433 GTATGTG
1 GTATGTG
188440 ATACATCAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
GTATGTGTCACATTACCTAAGATAATGACGTG
Found at i:189497 original size:48 final size:47
Alignment explanation
Indices: 189414--189515 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 47
189404 GTCATGTCAA
189414 AAGATCGTGACTTCTTTATATCTAGTTCTCCAAAGATCTTATGTGTG
1 AAGATCGTGACTTCTTTATATCTAGTTCTCCAAAGATCTTATGTGTG
*
189461 AAGATCGTGACTTCTTTTATATCTAGTTCTCTAAAGATCTTATGTGTG
1 AAGATCGTGACTTC-TTTATATCTAGTTCTCCAAAGATCTTATGTGTG
189509 AAGATCG
1 AAGATCG
189516 ATACGATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 14 0.26
48 39 0.74
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (47 bp):
AAGATCGTGACTTCTTTATATCTAGTTCTCCAAAGATCTTATGTGTG
Found at i:192783 original size:2 final size:2
Alignment explanation
Indices: 192776--192802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
192766 TAGAGTCATC
192776 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
192803 AAAAATGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:192847 original size:25 final size:24
Alignment explanation
Indices: 192801--192856 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
192791 TATATATATA
* * *
192801 TAAAAAATGTTAATTCATAATATC
1 TAAAATATGTTAATTCAGAATAAC
192825 GTAAAATAT-TTAATTACAGAATAAC
1 -TAAAATATGTTAATT-CAGAATAAC
192850 TAAAATA
1 TAAAATA
192857 ATAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (24 bp):
TAAAATATGTTAATTCAGAATAAC
Found at i:196041 original size:22 final size:22
Alignment explanation
Indices: 196013--196063 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
196003 TTTCTAATTT
196013 TTATTATTACTT-TATGTCATTA
1 TTATTATTACTTCTAT-TCATTA
**
196035 TTATTATTTTTTCTATTCATTA
1 TTATTATTACTTCTATTCATTA
196057 -TATTATT
1 TTATTATT
196064 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 16 0.62
23 3 0.12
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (22 bp):
TTATTATTACTTCTATTCATTA
Found at i:197318 original size:62 final size:61
Alignment explanation
Indices: 197221--197587 Score: 475
Period size: 62 Copynumber: 5.9 Consensus size: 61
197211 TCTTGTTTCC
* * *
197221 TAGAGTCAATTTCTGACTTTCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
1 TAGAGTCAATTT-TGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
** * * **
197283 TAGAGTTTATTTCTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTGG
1 TAGAGTCAATTT-TGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
** * * *
197345 TAGAGTTTATTTTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAG
1 TAGAGTCAATTTTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
* *
197406 TAGAGTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAATATTTATTATTTCTGACTCCTCAG
1 TAGAGTCAATTT-TGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
* * *
197468 TAGAGTCAATATTTGAC-TCCTTCGCGAAGAGAAGTCAACATTTGTTATTTTTGACTCCTCAG
1 TAGAGTCAAT-TTTGACTTCC-TCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
* * *
197530 TAGAGTCAATCATTGACTTCCTCGTGAATAGAAGTCAACATTTATTATTCCTGACTCC
1 TAGAGTCAAT-TTTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCC
197588 CAGCAAAGTC
Statistics
Matches: 276, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
61 60 0.22
62 211 0.76
63 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (61 bp):
TAGAGTCAATTTTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
Found at i:197453 original size:123 final size:123
Alignment explanation
Indices: 197221--197587 Score: 504
Period size: 123 Copynumber: 3.0 Consensus size: 123
197211 TCTTGTTTCC
*
197221 TAGAGTCAATTTCTGACTTTCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAG
1 TAGAGTCAATTT-TGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAG
** * * **
197286 AGTTTATTTCTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTGG
65 AGTCAATTTCTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
** *
197345 TAGAGTTTATTTTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAGTAGA
1 TAGAGTCAATTTTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGA
* *
197410 GTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAATATTTATTATTTCTGACTCCTCAG
66 GTCAATTTCTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
** * * *
197468 TAGAGTCAATATTTGAC-TCCTTCGCGAAGAGAAGTCAACATTTGTTATTTTTGACTCCTCAGTA
1 TAGAGTCAAT-TTTGACTTCC-TCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTA
* * *
197532 GAGTCAATCAT-TGACTTCCTCGTGAATAGAAGTCAACATTTATTATTCCTGACTCC
64 GAGTCAAT-TTCTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCC
197588 CAGCAAAGTC
Statistics
Matches: 215, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
123 112 0.52
124 102 0.47
125 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (123 bp):
TAGAGTCAATTTTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGA
GTCAATTTCTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAG
Found at i:197535 original size:185 final size:186
Alignment explanation
Indices: 197221--197587 Score: 506
Period size: 185 Copynumber: 2.0 Consensus size: 186
197211 TCTTGTTTCC
** * *
197221 TAGAGTCAATTTCTGACTTTCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAG
1 TAGAGTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAG
** ** * **
197286 AGTTTATTTCTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTGGTAGAGT
66 AGTCAATTTCTGACTTCCTCGCGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAGAGT
** * * * *
197351 TTAT-TTTGACTTCCTCTTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAG
131 CAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCTTAG
*
197406 TAGAGTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAATATTTATTATTTCTGACTCCTCAGTAG
1 TAGAGTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAG
* *
197471 AGTCAATATT-TGAC-TCCTTCGCGAAGAGAAGTCAACATTTGTTATTTTTGACTCCTCAGTAGA
66 AGTCAAT-TTCTGACTTCC-TCGCGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAGA
*
197534 GTCAATCATTGACTTCCTCGTGAATAGAAGTCAACATTTATTATTCCTGACTCC
129 GTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCC
197588 CAGCAAAGTC
Statistics
Matches: 158, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
184 3 0.02
185 111 0.70
186 44 0.28
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (186 bp):
TAGAGTCAATTTCTGACTCCCTCGTGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAG
AGTCAATTTCTGACTTCCTCGCGAAGAGAAGTCAACATTTATTATTTCTGACTCCTCAGTAGAGT
CAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCTTAG
Found at i:198278 original size:9 final size:9
Alignment explanation
Indices: 198250--198282 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
198240 ATATTATTCT
198250 TTAATTAAA
1 TTAATTAAA
*
198259 TT-ATAAAA
1 TTAATTAAA
198267 TTAATTAAA
1 TTAATTAAA
198276 TTAATTA
1 TTAATTA
198283 GCATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:198747 original size:24 final size:26
Alignment explanation
Indices: 198681--198747 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
198671 TTTTTCAATT
198681 TTTTATTATTATT-TTTAATAATGGAA
1 TTTTATTATTATTATTTAATAAT-GAA
* * *
198707 TTATTTTTGTTATTATTTAATTAT-AA
1 TT-TTATTATTATTATTTAATAATGAA
198733 TTTTATT-TTATTATT
1 TTTTATTATTATTATT
198748 ATCTTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 8 0.23
25 4 0.11
26 6 0.17
27 9 0.26
28 8 0.23
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTATTATTATTATTTAATAATGAA
Found at i:201600 original size:24 final size:24
Alignment explanation
Indices: 201555--201616 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
201545 TACCTCTTCT
** * *
201555 CTTACAACATTGAAATAACTTCACT
1 CTTACAATGTTGAGATAACTTC-CC
*
201580 CTTAC-ATGTTGAGATACCTTCCC
1 CTTACAATGTTGAGATAACTTCCC
201603 CTTACAATGTTGAG
1 CTTACAATGTTGAG
201617 GTGCCCCCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.19
24 20 0.65
25 5 0.16
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (24 bp):
CTTACAATGTTGAGATAACTTCCC
Found at i:202659 original size:22 final size:22
Alignment explanation
Indices: 202608--202651 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
202598 CGGAAGCTTT
*
202608 AACACCAACGTGGCTACTCCAA
1 AACACCAACGTGACTACTCCAA
202630 AACACCAACGTGACTACTCCAA
1 AACACCAACGTGACTACTCCAA
202652 GCCACCAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (22 bp):
AACACCAACGTGACTACTCCAA
Found at i:210385 original size:24 final size:24
Alignment explanation
Indices: 210353--210408 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
210343 CTATTCTTTC
*
210353 GCTTTAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
210377 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
210401 GCTTCAAT
1 GCTTCAAT
210409 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:211395 original size:59 final size:60
Alignment explanation
Indices: 211318--211449 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 60
211308 TGTTTAAATC
* * *
211318 ATTTC-AATTCATCTTTAAACTATGACTCTTATTCTAAATAGAT-TCCAAACTTTTCAAT
1 ATTTCAAATTCATCCTTAAACTATGACCCTTATTCTAAATAGATCTCCAAAATTTTCAAT
* * * * *
211376 ATTTCAAATTCATCCTTAAATTATGACCCTTATTCTATATTGGTCTCCAAAATTTTGAAT
1 ATTTCAAATTCATCCTTAAACTATGACCCTTATTCTAAATAGATCTCCAAAATTTTCAAT
* *
211436 ATTCCAATTTCATC
1 ATTTCAAATTCATC
211450 TCAAACTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
58 5 0.08
59 32 0.52
60 25 0.40
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTCAAATTCATCCTTAAACTATGACCCTTATTCTAAATAGATCTCCAAAATTTTCAAT
Found at i:211912 original size:15 final size:15
Alignment explanation
Indices: 211880--211913 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
211870 TTATAATTGA
*
211880 TAATAACATAATTTT
1 TAATAACATAATTAT
*
211895 TAATGACATAATTAT
1 TAATAACATAATTAT
211910 TAAT
1 TAAT
211914 TATATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TAATAACATAATTAT
Found at i:212644 original size:175 final size:171
Alignment explanation
Indices: 212314--212662 Score: 617
Period size: 175 Copynumber: 2.0 Consensus size: 171
212304 CCACACTCGG
*
212314 GCTCGTGATTTCGGTTATGATCTTCTTAGCCGGCACCCTGTTTTATCGGCACCGGGTGCCCACCG
1 GCTCGTGATTTCGGTTATGATCTTCTTAGCCGGCACCCCGTTTTATCGGCACCGGGTGCCCACCG
*
212379 AGAGTCCGTTCACGTGGCTACGGTCATAGTGGCCGCCATTAGGAAATGGAGGGTGCCACTTCCTA
66 AGAGTCCGTTCACGTGGCTACAGTCATAGTGGCCGCCATTAGGAAATGGAGGGTGCCACTTCCTA
* *
212444 GTGACCCTAAGGCACTTCATGAACTTGACTTTGAAGAGTAT
131 GTGACCCTAAGGAACTTCATGAACTTGACTTGGAAGAGTAT
212485 GCTCGTGATTTCGGTTATGATCTTCTTAGCCGGCACCCCGTTTTATCGGCACCGGGTGCCCACCG
1 GCTCGTGATTTCGGTTATGATCTTCTTAGCCGGCACCCCGTTTTATCGGCACCGGGTGCCCACCG
*
212550 AGAGTCCGTTCGCGAGAATGGCTACAGTCATAGTGGCCGCCATTAGGAAATGGAGGGTGCCACTT
66 AGAGTCCGTTCAC--G--TGGCTACAGTCATAGTGGCCGCCATTAGGAAATGGAGGGTGCCACTT
212615 CCTAGTGACCCTAAGGAACTTCATGAACTTGACTTGGAAGAGTAT
127 CCTAGTGACCCTAAGGAACTTCATGAACTTGACTTGGAAGAGTAT
212660 GCT
1 GCT
212663 TGGAATGGGA
Statistics
Matches: 169, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
171 76 0.45
173 1 0.01
175 92 0.54
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.27
Consensus pattern (171 bp):
GCTCGTGATTTCGGTTATGATCTTCTTAGCCGGCACCCCGTTTTATCGGCACCGGGTGCCCACCG
AGAGTCCGTTCACGTGGCTACAGTCATAGTGGCCGCCATTAGGAAATGGAGGGTGCCACTTCCTA
GTGACCCTAAGGAACTTCATGAACTTGACTTGGAAGAGTAT
Found at i:230740 original size:113 final size:108
Alignment explanation
Indices: 230507--230751 Score: 319
Period size: 108 Copynumber: 2.2 Consensus size: 108
230497 TTTTGATAGG
* * * *
230507 AAGAGAAACAGAACATCAAAGCATGATACCCTGTCAGCAATTCAATCTGTATTCTCTAATAAATG
1 AAGAGAAACAGAACATCAAAGCACGATACCCCGTCAACAATTCAATCTGTATTCTCTAATAAATA
**
230572 GTCAGTAGCCTTAGGACATACTTGGATAGCCAGATGCCAAGCT
66 GTCAGTAGCCTTACAACATACTTGGATAGCCAGATGCCAAGCT
* * *
230615 AAGAGAAACAGAACATCATAGCACGATACCCCGTCAACAGTTCAGTCTGTATTCTCTAATATATA
1 AAGAGAAACAGAACATCAAAGCACGATACCCCGTCAACAATTCAATCTGTATTCTCTAATA-A-A
* * * *
230680 TAGTCAGTAGTTGCGTTTCAACATACTTGGGTAGCTAGATGCCAAGCT
64 TAGTCAGTA---GCCTTACAACATACTTGGATAGCCAGATGCCAAGCT
*
230728 AAGAGAAACAGAACATAAAAGCAC
1 AAGAGAAACAGAACATCAAAGCAC
230752 ATATGCCCCC
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
108 55 0.47
109 1 0.01
110 9 0.08
113 52 0.44
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (108 bp):
AAGAGAAACAGAACATCAAAGCACGATACCCCGTCAACAATTCAATCTGTATTCTCTAATAAATA
GTCAGTAGCCTTACAACATACTTGGATAGCCAGATGCCAAGCT
Found at i:242032 original size:15 final size:15
Alignment explanation
Indices: 242008--242040 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
241998 GTTACTTTAG
242008 GCATGAAGTTTTCAA
1 GCATGAAGTTTTCAA
*
242023 GCATGGAGTTTTCAA
1 GCATGAAGTTTTCAA
242038 GCA
1 GCA
242041 AAGAAGAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (15 bp):
GCATGAAGTTTTCAA
Found at i:245219 original size:23 final size:23
Alignment explanation
Indices: 245184--245251 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
245174 AACCTTATAT
*
245184 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
245207 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
245230 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
245252 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:250980 original size:21 final size:20
Alignment explanation
Indices: 250937--250981 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
250927 ACAATATTTT
* *
250937 TAAATTATTAAAACCATTAA
1 TAAATTAATAAAACCAATAA
*
250957 TAAATTAATAAAGACGAATAA
1 TAAATTAATAAA-ACCAATAA
250978 TAAA
1 TAAA
250982 ATTTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAATTAATAAAACCAATAA
Found at i:264036 original size:20 final size:20
Alignment explanation
Indices: 264011--264056 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
264001 AATGCTGGCT
264011 TGGTTGGTGAAGCGGAGATG
1 TGGTTGGTGAAGCGGAGATG
264031 TGGTTGGTGAAGCGGAGATG
1 TGGTTGGTGAAGCGGAGATG
264051 TGGTTG
1 TGGTTG
264057 AAGAGAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.50, T:0.28
Consensus pattern (20 bp):
TGGTTGGTGAAGCGGAGATG
Found at i:269470 original size:21 final size:21
Alignment explanation
Indices: 269444--269504 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
269434 TCGTAGAATT
269444 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
*
269465 TGTCCCGAAGGACCAC-TATA
1 TGTCCCGAAGGACCACGTAGA
* *
269485 T-CCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
269505 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.34
20 7 0.20
21 16 0.46
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTAGA
Found at i:269632 original size:15 final size:13
Alignment explanation
Indices: 269586--269632 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
269576 CATTACACAT
269586 TCACAT-GTTCATA
1 TCACATAGTTC-TA
*
269599 TCACATAGTTCTT
1 TCACATAGTTCTA
269612 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
269627 TCACAT
1 TCACAT
269633 TTCATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 15 0.52
14 5 0.17
15 9 0.31
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Found at i:272934 original size:28 final size:28
Alignment explanation
Indices: 272883--272936 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
272873 TTGTTGCTTT
* *
272883 CAAGCACTGACTCGGCGACCTAATGTTC
1 CAAGCACTGACTCGACGACATAATGTTC
* *
272911 CAAGCATTGACTCGATGACATAATGT
1 CAAGCACTGACTCGACGACATAATGT
272937 AAAAGGAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (28 bp):
CAAGCACTGACTCGACGACATAATGTTC
Found at i:273218 original size:58 final size:57
Alignment explanation
Indices: 273075--273218 Score: 168
Period size: 59 Copynumber: 2.5 Consensus size: 57
273065 GAATATATGA
*
273075 ATAGTTGGATGATTATTTTATACTTTTAATAGTCGGAGACTCAATAAAATAATATTCT
1 ATAGTT-GATGATTATTTTATACTTTTAATAATCGGAGACTCAATAAAATAATATTCT
* * * *
273133 ATAGTCGATGGTCATTTTATAACTTTTAATAATCAGGGGACTCAATAAAATAATA-TCTT
1 ATAGTTGATGATTATTTTAT-ACTTTTAATAATC-GGAGACTCAATAAAATAATATTC-T
273192 ATAGTTG-TAGATTATTTATATA-TTTTA
1 ATAGTTGAT-GATTATTT-TATACTTTTA
273219 CCCTAAATTG
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
57 12 0.16
58 25 0.34
59 33 0.45
60 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (57 bp):
ATAGTTGATGATTATTTTATACTTTTAATAATCGGAGACTCAATAAAATAATATTCT
Found at i:275819 original size:64 final size:64
Alignment explanation
Indices: 275715--275838 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
275705 CAGAGTGTTT
* * * * *
275715 AGCCAAATTGAGCAAAGACGACAATGCTTCTGCACGAATTAGAAAAAGATAAGGACTCAACGGG
1 AGCCAAATTAAGCAAAAACGACAATCCTCCTGCACAAATTAGAAAAAGATAAGGACTCAACGGG
275779 AGCCAAATTAAGCAAAAACGACAATCCTCCTGCACAAATTAGAAAAAGATAAGGACTCAA
1 AGCCAAATTAAGCAAAAACGACAATCCTCCTGCACAAATTAGAAAAAGATAAGGACTCAA
275839 AGGGTCCCCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (64 bp):
AGCCAAATTAAGCAAAAACGACAATCCTCCTGCACAAATTAGAAAAAGATAAGGACTCAACGGG
Found at i:293479 original size:27 final size:28
Alignment explanation
Indices: 293429--293488 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
293419 ATCATGTATC
*
293429 TTAAACTATAAACTTTAAACCCTA-ACTT
1 TTAAACTATAAACTCTAAACCCTATA-TT
* *
293457 TTAAACT-TATACTCTAAATCCTATATT
1 TTAAACTATAAACTCTAAACCCTATATT
293484 TTAAA
1 TTAAA
293489 TAAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAAACTATAAACTCTAAACCCTATATT
Found at i:294824 original size:60 final size:58
Alignment explanation
Indices: 294752--294863 Score: 179
Period size: 60 Copynumber: 1.9 Consensus size: 58
294742 TAATAGTCGG
* * *
294752 TGACCATTTTGTAACTTTTAATAGTCAAGGGACTTAACAAAGTAATGACCTATAAACAGA
1 TGACCATTTTGTAACTTTTAATAGTC--GGGACTCAACAAAGTAACGACATATAAACAGA
294812 TGACCATTTTGTAACTTTTAATAGTCGGGACTCAACAAAGTAACGACATATA
1 TGACCATTTTGTAACTTTTAATAGTCGGGACTCAACAAAGTAACGACATATA
294864 GTCATGGGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 23 0.47
60 26 0.53
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (58 bp):
TGACCATTTTGTAACTTTTAATAGTCGGGACTCAACAAAGTAACGACATATAAACAGA
Found at i:295473 original size:22 final size:22
Alignment explanation
Indices: 295437--295485 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
295427 TCATTAAACT
*
295437 ATTAATTTTATCAAACATATCA
1 ATTAATTTTATCAAAAATATCA
*
295459 TTTAATTATTA-CAAAAATATCA
1 ATTAATT-TTATCAAAAATATCA
295481 ATTAA
1 ATTAA
295486 ACCATATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATTTTATCAAAAATATCA
Found at i:298888 original size:60 final size:60
Alignment explanation
Indices: 298795--298932 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
298785 GATTTAGGGT
* * *
298795 AAAG-TACACAAATGGTCATTCTATTATAAGATATTACTTTATTGAATCTCTAAACTACTA
1 AAAGTTACA-AAATGGTCATTCAATTATAAGATATTACTTTATAGAATCCCTAAACTACTA
* * * * * *
298855 AAAGTTACAAAATGGTCATTCAATTATAGGATATTATTTTGTAGAGTCCCTCAACTATTA
1 AAAGTTACAAAATGGTCATTCAATTATAAGATATTACTTTATAGAATCCCTAAACTACTA
298915 AAAGTTACAAAATGGTCA
1 AAAGTTACAAAATGGTCA
298933 CCCAACTAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 64 0.94
61 4 0.06
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCATTCAATTATAAGATATTACTTTATAGAATCCCTAAACTACTA
Found at i:307241 original size:3 final size:3
Alignment explanation
Indices: 307233--307258 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
307223 TAATTAACAA
307233 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
307259 AAGGGGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:314838 original size:17 final size:17
Alignment explanation
Indices: 314816--314853 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
314806 TTATTAATAA
314816 AAAATACATAAAAATTT
1 AAAATACATAAAAATTT
* *
314833 AAAATATATAAGAATTT
1 AAAATACATAAAAATTT
314850 AAAA
1 AAAA
314854 ATTTTAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATACATAAAAATTT
Found at i:316431 original size:17 final size:18
Alignment explanation
Indices: 316409--316453 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
316399 TATGGAATTG
*
316409 GATTCTAATTCC-TGACA
1 GATTCTAATTCCTTCACA
316426 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
*
316444 AATTCTAATT
1 GATTCTAATT
316454 AACTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:318529 original size:138 final size:138
Alignment explanation
Indices: 318276--318551 Score: 498
Period size: 138 Copynumber: 2.0 Consensus size: 138
318266 TCAATAGCTA
* *
318276 CACTGATACAATTGTTTTAATCTGCAATGGTGAGTAATACAATGAGCTTCAGAAAGCTCAGTAAC
1 CACTAATACAATTCTTTTAATCTGCAATGGTGAGTAATACAATGAGCTTCAGAAAGCTCAGTAAC
318341 ACAGAACTACCAGATGATGCTGAAAAACGTGCAGATACATATAAACAAATATTTCCTTATTTGTT
66 ACAGAACTACCAGATGATGCTGAAAAACGTGCAGATACATATAAACAAATATTTCCTTATTTGTT
318406 CAGATATT
131 CAGATATT
* *
318414 CACTAATACAATTCTTTTAATCTGCAATGGTGAGTAATACAATGAGCTTCAGAAATCTCAGTAAT
1 CACTAATACAATTCTTTTAATCTGCAATGGTGAGTAATACAATGAGCTTCAGAAAGCTCAGTAAC
* *
318479 ACAGAATTACCAGATGATGTTGAAAAACGTGCAGATACATATAAACAAATATTTCCTTATTTGTT
66 ACAGAACTACCAGATGATGCTGAAAAACGTGCAGATACATATAAACAAATATTTCCTTATTTGTT
318544 CAGATATT
131 CAGATATT
318552 TACAGATTTT
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (138 bp):
CACTAATACAATTCTTTTAATCTGCAATGGTGAGTAATACAATGAGCTTCAGAAAGCTCAGTAAC
ACAGAACTACCAGATGATGCTGAAAAACGTGCAGATACATATAAACAAATATTTCCTTATTTGTT
CAGATATT
Found at i:319118 original size:24 final size:24
Alignment explanation
Indices: 319060--319192 Score: 133
Period size: 24 Copynumber: 5.5 Consensus size: 24
319050 AAACGGAGAT
* *
319060 ATCAGAAATCAAAACGGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * * *
319084 ATTA-AATATCATAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAA
* *
319108 ATCAGAAATCAGAACATAATTCAT
1 ATCAGAAATCAGAACAGAATTCAA
* *
319132 ATCAGAAATTAGAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
*
319156 ATCGGAAATCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* *
319180 ATCGGAATTCAGA
1 ATCAGAAATCAGA
319193 TAAAACATTC
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.02
24 87 0.96
25 2 0.02
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:319120 original size:12 final size:12
Alignment explanation
Indices: 319098--319193 Score: 59
Period size: 12 Copynumber: 8.0 Consensus size: 12
319088 AATATCATAA
*
319098 CAGAATCCAGAT
1 CAGAATTCAGAT
* *
319110 CAGAAATCAGAA
1 CAGAATTCAGAT
* *
319122 CATAATTCATAT
1 CAGAATTCAGAT
*
319134 CAGAAATT-AGAA
1 CAG-AATTCAGAT
* *
319146 CATAATTCAAAT
1 CAGAATTCAGAT
* * *
319158 CGGAAATCAGAA
1 CAGAATTCAGAT
*
319170 CAGAATTCAAAT
1 CAGAATTCAGAT
*
319182 CGGAATTCAGAT
1 CAGAATTCAGAT
319194 AAAACATTCA
Statistics
Matches: 58, Mismatches: 24, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
11 4 0.07
12 50 0.86
13 4 0.07
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (12 bp):
CAGAATTCAGAT
Found at i:321378 original size:22 final size:20
Alignment explanation
Indices: 321342--321392 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
321332 GTTAAACGCC
*
321342 CGGTCAACACCGGTCAAAGTT
1 CGGTCAACAACGGTCAAAG-T
* *
321363 CTGGTCAACAATGGTCAACGT
1 C-GGTCAACAACGGTCAAAGT
321384 CGGTCAACA
1 CGGTCAACA
321393 GTCGACCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (20 bp):
CGGTCAACAACGGTCAAAGT
Found at i:326352 original size:2 final size:2
Alignment explanation
Indices: 326345--326373 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
326335 AAGATAGTTG
326345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326374 TGATTTCACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:326940 original size:2 final size:2
Alignment explanation
Indices: 326933--326966 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
326923 ATCTACGAGG
326933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
326967 TCTCTTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:331555 original size:2 final size:2
Alignment explanation
Indices: 331548--331581 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
331538 TAGATTATCA
331548 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
331582 GAATGTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332997 original size:23 final size:20
Alignment explanation
Indices: 332961--333001 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
332951 ATATTTTTTT
332961 TATTTTTAAATGATGATGTGA
1 TATTTTTAAATGAT-ATGTGA
332982 TATTATTTATAATGATATGT
1 TATT-TTTA-AATGATATGT
333002 CAACATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
TATTTTTAAATGATATGTGA
Found at i:341158 original size:22 final size:22
Alignment explanation
Indices: 341110--341151 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
341100 TCTTAATACT
* *
341110 TGAATGAAATATATTGAATTTG
1 TGAATGAAATAAATTAAATTTG
341132 TGAATGAAATAAATTAAATT
1 TGAATGAAATAAATTAAATT
341152 GTGGAATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
TGAATGAAATAAATTAAATTTG
Found at i:342153 original size:7 final size:7
Alignment explanation
Indices: 342141--342165 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
342131 AATCCTTTAT
342141 AATTTGG
1 AATTTGG
342148 AATTTGG
1 AATTTGG
342155 AATTTGG
1 AATTTGG
342162 AATT
1 AATT
342166 CGGATTCTGT
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (7 bp):
AATTTGG
Found at i:346226 original size:25 final size:25
Alignment explanation
Indices: 346183--346231 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
346173 ATAACTATAT
* * *
346183 TTTTTATGTATATTTAATAATTAAC
1 TTTTTATGTAAAATAAATAATTAAC
*
346208 TTTTTATGTAAAATAAATATTTAA
1 TTTTTATGTAAAATAAATAATTAA
346232 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTTATGTAAAATAAATAATTAAC
Found at i:351064 original size:9 final size:9
Alignment explanation
Indices: 351050--351127 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
351040 GCTGCTGGAA
351050 ACCGGTTTG
1 ACCGGTTTG
351059 ACCGGTTTG
1 ACCGGTTTG
* *
351068 ATCGGTTTCA
1 ACCGGTTT-G
*
351078 ACCGGTTCG
1 ACCGGTTTG
*
351087 AACTGGTTTG
1 -ACCGGTTTG
*
351097 ACCGGTCTG
1 ACCGGTTTG
* *
351106 AACCGGTCTA
1 -ACCGGTTTG
*
351116 ACCGGTCTG
1 ACCGGTTTG
351125 ACC
1 ACC
351128 CGACCGTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
9 34 0.62
10 21 0.38
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:351108 original size:19 final size:18
Alignment explanation
Indices: 351052--351125 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
351042 TGCTGGAAAC
* * *
351052 CGGTTTGACCGGTTTGAT
1 CGGTTTAACCGGTCTGAA
351070 CGGTTTCAACCGGT-TCGAA
1 CGGTTT-AACCGGTCT-GAA
*
351089 CTGGTTTGACCGGTCTGAA
1 C-GGTTTAACCGGTCTGAA
*
351108 CCGGTCTAACCGGTCTGA
1 -CGGTTTAACCGGTCTGA
351126 CCCGACCGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.15
19 32 0.70
20 7 0.15
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (18 bp):
CGGTTTAACCGGTCTGAA
Found at i:351140 original size:12 final size:12
Alignment explanation
Indices: 351123--351161 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
351113 CTAACCGGTC
351123 TGACCCGACCGT
1 TGACCCGACCGT
351135 TGACCCGACC--
1 TGACCCGACCGT
*
351145 CGACCCGACCGT
1 TGACCCGACCGT
351157 TGACC
1 TGACC
351162 ATTGACCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:358316 original size:9 final size:9
Alignment explanation
Indices: 358302--358370 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
358292 GCTGCTGGAA
358302 ACCGGTTTG
1 ACCGGTTTG
358311 ACCGGTTTG
1 ACCGGTTTG
* *
358320 ATCGGTTTCA
1 ACCGGTTT-G
*
358330 ACCGGTTCG
1 ACCGGTTTG
358339 AACCGGTTTG
1 -ACCGGTTTG
*
358349 ACCGGTCTG
1 ACCGGTTTG
*
358358 AACCGGTCTG
1 -ACCGGTTTG
358368 ACC
1 ACC
358371 CGACCGTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:358347 original size:29 final size:28
Alignment explanation
Indices: 358301--358364 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
358291 GGCTGCTGGA
* * *
358301 AACCGGTTTGACCGGTTTGATCGGTTTC
1 AACCGGTTCGACCGGTTTGACCGGTCTC
*
358329 AACCGGTTCGAACCGGTTTGACCGGTCTG
1 AACCGGTTCG-ACCGGTTTGACCGGTCTC
358358 AACCGGT
1 AACCGGT
358365 CTGACCCGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (28 bp):
AACCGGTTCGACCGGTTTGACCGGTCTC
Found at i:358352 original size:19 final size:19
Alignment explanation
Indices: 358301--358370 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
358291 GGCTGCTGGA
*
358301 AACCGGTTTGACCGGTTTG
1 AACCGGTTTGACCGGTTCG
* *
358320 -ATCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
358339 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
358358 AACCGGTCTGACC
1 AACCGGTTTGACC
358371 CGACCGTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.21
19 26 0.62
20 7 0.17
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:358404 original size:22 final size:22
Alignment explanation
Indices: 358379--358421 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
358369 CCCGACCGTT
358379 GACCCGACCCGACCGTTGACCA
1 GACCCGACCCGACCGTTGACCA
358401 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
358422 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:0.21, C:0.47, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCA
Found at i:358421 original size:17 final size:17
Alignment explanation
Indices: 358367--358409 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
358357 GAACCGGTCT
*
358367 GACCCGACCGTTGACCC
1 GACCCGACCGTTGACCA
358384 GACCCGACCGTTGACCA
1 GACCCGACCGTTGACCA
358401 GACCCGACC
1 GACCCGACC
358410 CGACCGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.47, G:0.23, T:0.09
Consensus pattern (17 bp):
GACCCGACCGTTGACCA
Found at i:367168 original size:17 final size:18
Alignment explanation
Indices: 367127--367165 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
367117 ATTATATAAG
367127 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
367144 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
367162 TAAA
1 TAAA
367166 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:370338 original size:24 final size:24
Alignment explanation
Indices: 370306--370367 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
370296 CCATCTCCTG
*
370306 CTCCTTCGCCATCAGAAACACCAT
1 CTCCATCGCCATCAGAAACACCAT
*
370330 CTCCATCGCCATCAGAATCACCAT
1 CTCCATCGCCATCAGAAACACCAT
* *
370354 CGCCATCGTCATCA
1 CTCCATCGCCATCA
370368 ATTCCCGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.42, G:0.10, T:0.21
Consensus pattern (24 bp):
CTCCATCGCCATCAGAAACACCAT
Found at i:372453 original size:3 final size:3
Alignment explanation
Indices: 372445--372509 Score: 80
Period size: 3 Copynumber: 22.3 Consensus size: 3
372435 TCTACCAAAA
**
372445 TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
372491 TAT TTT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
372510 TACATTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:374171 original size:30 final size:30
Alignment explanation
Indices: 374135--374201 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
374125 CCCGAAGGAC
* *
374135 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
374165 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
374195 CTGTCCA
1 CTATCCA
374202 TATGTTCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:374231 original size:31 final size:31
Alignment explanation
Indices: 374193--374317 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
374183 GATCCTCGGC
*
374193 AACTGTCCATATGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
** *
374224 AACTGTCCATATGTTCCTTAGAACATAGGTT
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
374255 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
374286 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
374318 TACCCTCAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.04
31 49 0.63
32 23 0.29
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:374309 original size:63 final size:62
Alignment explanation
Indices: 374194--374316 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
374184 ATCCTCGGCA
* *
374194 ACTGTCCATATGTTCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTTT
1 ACTGTCCATATGTTCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTTT
*
374256 ACTGTCCATATG-TCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGT
1 ACTGTCCATATGTTC-CGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGT
374317 ATACCCTCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
61 3 0.05
62 25 0.45
63 27 0.49
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (62 bp):
ACTGTCCATATGTTCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTTT
Found at i:376739 original size:61 final size:61
Alignment explanation
Indices: 376674--376803 Score: 143
Period size: 61 Copynumber: 2.1 Consensus size: 61
376664 GTCCTTCCAG
* * *
376674 TTTCTATTAATACTAATTTAATCCCTAAACTTTTTATTTTTTGCTATTTTAGTCCTTTAAC
1 TTTCTATTAATACTAATTTAATCCCTAAACTTTCTATTTTTTACTATTTTAATCCTTTAAC
** * * * * * * * *
376735 TTTCTATTTTTCCTATTTTAGTCCTTTAACTTTCTGTTTTTTATTATTTTAATCCTTTAAG
1 TTTCTATTAATACTAATTTAATCCCTAAACTTTCTATTTTTTACTATTTTAATCCTTTAAC
376796 TTTCTATT
1 TTTCTATT
376804 TTTGTTGTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.22, C:0.15, G:0.04, T:0.59
Consensus pattern (61 bp):
TTTCTATTAATACTAATTTAATCCCTAAACTTTCTATTTTTTACTATTTTAATCCTTTAAC
Found at i:376743 original size:31 final size:31
Alignment explanation
Indices: 376701--376853 Score: 159
Period size: 30 Copynumber: 5.0 Consensus size: 31
376691 TTAATCCCTA
*
376701 AACTTTTTATTTTTTGCTATTTTAGTCCTTT
1 AACTTTCTATTTTTTGCTATTTTAGTCCTTT
*
376732 AACTTTCTA-TTTTTCCTATTTTAGTCCTTT
1 AACTTTCTATTTTTTGCTATTTTAGTCCTTT
* ** *
376762 AACTTTCTGTTTTTTATTATTTTAATCCTTT
1 AACTTTCTATTTTTTGCTATTTTAGTCCTTT
* * * * *
376793 AAGTTTCTA-TTTTTGTTGTTTTAATCCTGT
1 AACTTTCTATTTTTTGCTATTTTAGTCCTTT
* * *
376823 AAATTTCTGTTTTTTTCTA-TTTAGTCCTTT
1 AACTTTCTATTTTTTGCTATTTTAGTCCTTT
376853 A
1 A
376854 TTTTACTAAG
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
30 63 0.62
31 39 0.38
ACGTcount: A:0.18, C:0.14, G:0.07, T:0.62
Consensus pattern (31 bp):
AACTTTCTATTTTTTGCTATTTTAGTCCTTT
Found at i:376804 original size:61 final size:61
Alignment explanation
Indices: 376710--376853 Score: 184
Period size: 61 Copynumber: 2.4 Consensus size: 61
376700 AAACTTTTTA
* * * *
376710 TTTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTTCCTATTTTAGTCCTTTAACTTTCTG
1 TTTTTTTCTATTTTAGTCCTTTAACTTTCTATTTTTCCTATTTTAATCCTGTAAATTTCTG
* * ** *
376771 TTTTTTAT-TATTTTAATCCTTTAAGTTTCTATTTTTGTTGTTTTAATCCTGTAAATTTCTG
1 TTTTTT-TCTATTTTAGTCCTTTAACTTTCTATTTTTCCTATTTTAATCCTGTAAATTTCTG
376832 TTTTTTTCTA-TTTAGTCCTTTA
1 TTTTTTTCTATTTTAGTCCTTTA
376854 TTTTACTAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
60 12 0.17
61 59 0.83
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (61 bp):
TTTTTTTCTATTTTAGTCCTTTAACTTTCTATTTTTCCTATTTTAATCCTGTAAATTTCTG
Found at i:377916 original size:66 final size:66
Alignment explanation
Indices: 377839--377974 Score: 263
Period size: 66 Copynumber: 2.1 Consensus size: 66
377829 TTATAGGATC
377839 TCTACTAAAAGATCTCTTGTTATATTGTTGGAGTTCAATATGTACATTAACTTTTATTTTGAATA
1 TCTACTAAAAGATCTCTTGTTATATTGTTGGAGTTCAATATGTACATTAACTTTTATTTTGAATA
377904 G
66 G
*
377905 TCTACTAAAAGATCTCTTGTTATATTGTTGGAGTTCAATATGTACGTTAACTTTTATTTTGAATA
1 TCTACTAAAAGATCTCTTGTTATATTGTTGGAGTTCAATATGTACATTAACTTTTATTTTGAATA
377970 G
66 G
377971 TCTA
1 TCTA
377975 AGAGTGATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (66 bp):
TCTACTAAAAGATCTCTTGTTATATTGTTGGAGTTCAATATGTACATTAACTTTTATTTTGAATA
G
Found at i:379002 original size:6 final size:6
Alignment explanation
Indices: 378993--379031 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
378983 CCATCTCCTG
* *
378993 CACCAC CACCAC CACCAT CACCAT CACCAT CACCAT CAC
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CAC
379032 ATCCAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.56, G:0.00, T:0.10
Consensus pattern (6 bp):
CACCAT
Found at i:384459 original size:26 final size:25
Alignment explanation
Indices: 384442--384489 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
384432 TAATTTAGAT
* *
384442 TAATTGTTTAACAAATTAAATATTGA
1 TAATTGTTAAAAAAATT-AATATTGA
384468 TAATTGTTAAAAAAATT-ATATT
1 TAATTGTTAAAAAAATTAATATT
384490 ATTCAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
26 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
TAATTGTTAAAAAAATTAATATTGA
Found at i:385274 original size:3 final size:3
Alignment explanation
Indices: 385266--385290 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
385256 TGAAGATAAC
385266 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
385291 AATTATGAAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:387317 original size:60 final size:60
Alignment explanation
Indices: 387218--387338 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
387208 AGAACCCACG
* *
387218 CAAGGCATCGTCACCTAATTTTTCAATGTTCTAAAGTCTACCCCAGTTTCTGGTTCTCCT
1 CAAGGCATCGTCACCTAATTTTTCAATGTGCCAAAGTCTACCCCAGTTTCTGGTTCTCCT
*
387278 CAAGGCATCGTCACCTAATTTTTCAATGTGCCAATGTCTACCCCAGTTTCTGGTTCTCCT
1 CAAGGCATCGTCACCTAATTTTTCAATGTGCCAAAGTCTACCCCAGTTTCTGGTTCTCCT
387338 C
1 C
387339 TATTCATCTC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.36
Consensus pattern (60 bp):
CAAGGCATCGTCACCTAATTTTTCAATGTGCCAAAGTCTACCCCAGTTTCTGGTTCTCCT
Found at i:387566 original size:20 final size:20
Alignment explanation
Indices: 387541--387580 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
387531 TTTGATTCAC
387541 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
387561 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAGTG
387581 AATAGGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:400808 original size:19 final size:17
Alignment explanation
Indices: 400773--400811 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
400763 ATTTGATTTC
400773 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
400790 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
400809 TCT
1 TCT
400812 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:401136 original size:8 final size:9
Alignment explanation
Indices: 401125--401200 Score: 57
Period size: 9 Copynumber: 8.4 Consensus size: 9
401115 ATTTGGATTG
401125 TAAT-TTTA
1 TAATATTTA
401133 TAATATTTA
1 TAATATTTA
*
401142 -ATGTATTTAA
1 TA-ATATTT-A
* *
401152 TAATAATAA
1 TAATATTTA
* *
401161 TAATAATAA
1 TAATATTTA
401170 TAATATTTA
1 TAATATTTA
*
401179 TAATAATTA
1 TAATATTTA
*
401188 TAATAATTA
1 TAATATTTA
401197 TAAT
1 TAAT
401201 TAAATAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
8 5 0.09
9 47 0.82
10 4 0.07
11 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
TAATATTTA
Found at i:401157 original size:3 final size:3
Alignment explanation
Indices: 401149--401224 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
401139 TTAATGTATT
* * * *
401149 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
401197 TAA TTA -AA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
401225 TGGGTAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:401816 original size:113 final size:113
Alignment explanation
Indices: 401587--402266 Score: 1037
Period size: 113 Copynumber: 6.0 Consensus size: 113
401577 TAGAATTATG
* ** *
401587 CAAAAAGTTGAACAAGCTCTTCTTATTATGAAC---TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * * * *
401648 TCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAA
63 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
401699 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
401764 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
* * * *
401812 CAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * * * * *
401877 TCATTATGAACTCTCTTTGGCAATGTTAATCCATCAAATGATGAATTTAAA
63 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
401928 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
401993 TTATGAACTTTCTCTAGAAAAGCTGATCCATCAAATGATGGATTTAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
402041 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
402106 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
402154 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
402219 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
402267 TCTTTGCTAA
Statistics
Matches: 520, Mismatches: 40, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
112 31 0.06
113 373 0.72
115 5 0.01
116 111 0.21
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
Found at i:401914 original size:229 final size:226
Alignment explanation
Indices: 401589--402266 Score: 1109
Period size: 229 Copynumber: 3.0 Consensus size: 226
401579 GAATTATGCA
** *
401589 AAAAGTTGAACAAGCTCTTCTTATTATGAA--CTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 AAAAGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
*
401652 TATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAAT
66 TATGAACTCT-CTTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAAT
401716 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
401781 AAAAGCTGATCCATCAAATGATGGATTTGAGC
195 AAAAGCTGATCCATCAAATGATGGATTTAAAC
401813 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
1 AAAAG-TTGAACAAATTCTTCTCATTATGAA-TTCTTCTTC-TTCTTCAGATGACGAGTTCTTCT
401878 CATTATGAACTCTCTTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
63 CATTATGAACTCTCTTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
401943 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
128 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
402008 AGAAAAGCTGATCCATCAAATGATGGATTTAAAC
193 GGAAAAGCTGATCCATCAAATGATGGATTTAAAC
*
402042 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTCT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAA-TTCTTCTT-CTTCTTCAGATGACGAGTTCTTCT
* * * * * *
402104 CATTATGAACT-TTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAGGTTGAACA
63 CATTATGAACTCTCTT-TGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
402168 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
127 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
402233 TGGAAAAGCTGATCCATCAAATGATGGATTTAAA
192 TGGAAAAGCTGATCCATCAAATGATGGATTTAAA
402267 TCTTTGCTAA
Statistics
Matches: 429, Mismatches: 16, Indels: 16
0.93 0.03 0.03
Matches are distributed among these distances:
224 5 0.01
225 25 0.06
226 162 0.38
228 8 0.02
229 227 0.53
230 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (226 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
TATGAACTCTCTTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAATGATGGATTTAAAC
Found at i:402032 original size:342 final size:336
Alignment explanation
Indices: 401587--402266 Score: 1031
Period size: 342 Copynumber: 2.0 Consensus size: 336
401577 TAGAATTATG
* *
401587 CAAAAAGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCAT
* * * *
401652 TATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATT
64 TATGAACTCTACCTAGAAAAGCTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATT
401717 CTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
129 CTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* * *
401782 AAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAATTCTTCTCATTATGAATTT
194 AAAGCTGATCCATCAAATGATGGATTTAAACAAAAGATTGAACAAATTCTTCTCATTATGAACTT
* * * * * *
401847 CTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTCTTTGGCAATGTTAATCCATC
259 ATTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTAATCCATC
401912 AAATGATGAATTTAAA
321 AAATGATGAATTTAAA
* *
401928 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT-GAGTTCTTCTC
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAAC---TTCTT-CTTCTTCAGATAGAGTTCTTCTC
* * *
401992 ATTATGAACT-TTCTCTAGAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAA
62 ATTATGAACTCTAC-CTAGAAAAGCTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
*
402056 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCT
126 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
402121 GGAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
191 GGAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAGATTGAACAAATTCTTCTCATTATGAA
* *
402186 CTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
256 CTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTAATCCATC
*
402251 AAATGATGGATTTAAA
321 AAATGATGAATTTAAA
402267 TCTTTGCTAA
Statistics
Matches: 309, Mismatches: 25, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
339 53 0.17
341 31 0.10
342 209 0.68
344 5 0.02
345 11 0.04
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (336 bp):
CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATAGAGTTCTTCTCATTA
TGAACTCTACCTAGAAAAGCTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
AGCTGATCCATCAAATGATGGATTTAAACAAAAGATTGAACAAATTCTTCTCATTATGAACTTAT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTAATCCATCAAATG
ATGAATTTAAA
Found at i:403002 original size:83 final size:82
Alignment explanation
Indices: 402863--403393 Score: 905
Period size: 83 Copynumber: 6.5 Consensus size: 82
402853 CCTACTGAAT
* *
402863 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCAT-TTCCAAATTCAA
402928 TGATTGGTTTTACCAAAC
65 TGATTGGTTTTACCAAAC
* *
402946 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTC-A
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCAT-TTCCAAATTCAA
403010 TGATTGGTTTTACCAAAC
65 TGATTGGTTTTACCAAAC
403028 CAGATCAGATAACTCAAAGAACACTTCCA-AAGATGCTATGAGCATATTCA-TTCCAAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCC-AAATTCAA
403091 TGA-TGGTTTTACCAAAC
65 TGATTGGTTTTACCAAAC
* *
403108 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCAT-TTCCAAATTCAA
403173 TGATTGGTTTTACCAAAC
65 TGATTGGTTTTACCAAAC
403191 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTT-CCAAATTCAA
403256 TGATTGGTTTTACCAAAC
65 TGATTGGTTTTACCAAAC
403274 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA-ATTCATTTCCAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCCAAATTCAAT
403338 GATTGG-TTT-CCAAAC
66 GATTGGTTTTACCAAAC
*
403353 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
403394 GGTCTCCTTA
Statistics
Matches: 434, Mismatches: 7, Indels: 18
0.95 0.02 0.04
Matches are distributed among these distances:
79 49 0.11
80 51 0.12
81 63 0.15
82 68 0.16
83 203 0.47
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCCAAATTCAAT
GATTGGTTTTACCAAAC
Found at i:403133 original size:162 final size:165
Alignment explanation
Indices: 402863--403393 Score: 934
Period size: 162 Copynumber: 3.2 Consensus size: 165
402853 CCTACTGAAT
* *
402863 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCAT-TTCCAAATTCAA
402928 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
65 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
402993 TTCATCTTTCAACTTC-ATGATTGGTTTTACCAAAC
130 TTCATCTTTCAACTTCAATGATTGGTTTTACCAAAC
403028 CAGATCAGATAACTCAAAGAACACTTCCA-AAGATGCTATGAGCATATTCA-TTCCAAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCC-AAATTCAA
403091 TGA-TGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
65 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
403155 TTCATCTTTCAACTTCAATGATTGGTTTTACCAAAC
130 TTCATCTTTCAACTTCAATGATTGGTTTTACCAAAC
403191 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTT-CCAAATTCAA
403256 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA-A
65 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
* *
403320 TTCAT-TTCCAAATTCAATGATTGG-TTT-CCAAAC
130 TTCATCTTTCAACTTCAATGATTGGTTTTACCAAAC
*
403353 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
403394 GGTCTCCTTA
Statistics
Matches: 355, Mismatches: 5, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
162 126 0.35
163 61 0.17
164 59 0.17
165 48 0.14
166 61 0.17
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (165 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTCCAAATTCAAT
GATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATAT
TCATCTTTCAACTTCAATGATTGGTTTTACCAAAC
Found at i:403353 original size:245 final size:245
Alignment explanation
Indices: 402863--403393 Score: 955
Period size: 245 Copynumber: 2.2 Consensus size: 245
402853 CCTACTGAAT
402863 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
402928 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
66 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
* *
402993 TTCATCTTTCAACTTCATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAA
131 TTCATCTTCCAAATTCATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAA
403058 AGATGCTATGAGCATATTCATTCCAAAATTCAATGATGGTTTTACCAAAC
196 AGATGCTATGAGCATATTCATTCCAAAATTCAATGATGGTTTTACCAAAC
403108 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
403173 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
66 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
403238 TTCAT-TTCCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCC
131 TTCATCTT-CCAAATTC-ATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCC
403302 AGAAGATGCTATGAGCA-ATTCATTTCC-AAATTCAATGATTGG-TTT-CCAAAC
194 A-AAGATGCTATGAGCATATTCA-TTCCAAAATTCAATGA-TGGTTTTACCAAAC
*
403353 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
403394 GGTCTCCTTA
Statistics
Matches: 278, Mismatches: 3, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
244 2 0.01
245 187 0.67
246 67 0.24
247 22 0.08
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (245 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAACTTCAA
TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATA
TTCATCTTCCAAATTCATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAA
AGATGCTATGAGCATATTCATTCCAAAATTCAATGATGGTTTTACCAAAC
Found at i:404582 original size:8 final size:8
Alignment explanation
Indices: 404564--404619 Score: 78
Period size: 8 Copynumber: 6.9 Consensus size: 8
404554 TTGACCCCCC
404564 CTTTTTCTT
1 CTTTTT-TT
404573 CTTTTTTT
1 CTTTTTTT
404581 CTTTTTTTT
1 C-TTTTTTT
404590 CTTTTTTT
1 CTTTTTTT
*
404598 -TTTCTTT
1 CTTTTTTT
404605 CTTTTTTT
1 CTTTTTTT
404613 CTTTTTT
1 CTTTTTT
404620 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
7 6 0.14
8 23 0.53
9 14 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
CTTTTTTT
Done.