Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014852.1 Kokia drynarioides strain JFW-HI SEQ_129895, 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: 730378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 125 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:12183 original size:30 final size:30
Alignment explanation
Indices: 12125--12183 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
12115 TTAATATAAT
* * *
12125 ATTTGGTATTTGAACTTGACATTTTTTTTA
1 ATTTGGTACTTAAACTTGACATTCTTTTTA
12155 ATTTGGTACTTAAACTTGAC-TCTCTTTTT
1 ATTTGGTACTTAAACTTGACAT-TCTTTTT
12184 TAAGTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTGACATTCTTTTTA
Found at i:12512 original size:58 final size:57
Alignment explanation
Indices: 12424--12569 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 57
12414 ATCGAATCTA
* *
12424 AAAAATAGTTTAGGTGCCAAATTATAAAAAA-TACCAAGTTTA-AGTGTCAAATTGGGTCC
1 AAAAA-AGTTTAGGTACCAAATTA-AAAAAAGTACCAAGTTTAGA-TGCCAAATTGGGT-C
* ****
12483 AAAAAAGTTTAGGTATCAAATTAAGAAAAAGTGTTGAGTTTAGATGCCAAATTGGGTC
1 AAAAAAGTTTAGGTACCAAATTAA-AAAAAGTACCAAGTTTAGATGCCAAATTGGGTC
* *
12541 AAAAAAATTTAGGTACCAAATAAAAAAAA
1 AAAAAAGTTTAGGTACCAAATTAAAAAAA
12570 AATCAAATTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
57 6 0.08
58 43 0.58
59 24 0.32
60 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (57 bp):
AAAAAAGTTTAGGTACCAAATTAAAAAAAGTACCAAGTTTAGATGCCAAATTGGGTC
Found at i:20642 original size:21 final size:21
Alignment explanation
Indices: 20617--20660 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20607 AAGCATTTTC
20617 ATTTAAGTA-TATATATATAAT
1 ATTTAAGTATTATATAT-TAAT
**
20638 ATTTATTTATTATATATTAAT
1 ATTTAAGTATTATATATTAAT
20659 AT
1 AT
20661 ACTTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTAAGTATTATATATTAAT
Found at i:20672 original size:23 final size:22
Alignment explanation
Indices: 20626--20672 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
20616 CATTTAAGTA
*
20626 TATATATATAATATTTATTTAT
1 TATATATATAATATTTATTAAT
20648 TATATAT-TAATATACTTATTAAT
1 TATATATATAATAT--TTATTAAT
20671 TA
1 TA
20673 CTGTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATATATAATATTTATTAAT
Found at i:21674 original size:30 final size:30
Alignment explanation
Indices: 21628--21938 Score: 296
Period size: 29 Copynumber: 10.5 Consensus size: 30
21618 GTTTTCTTTG
*
21628 AAAATTATATTTTTAACCCCTAAACTTTTCT
1 AAAATTACA-TTTTAACCCCTAAACTTTTCT
*
21659 AAAATTGCATTTTAACCCC-AAACTTCTT-T
1 AAAATTACATTTTAACCCCTAAACTT-TTCT
* *
21688 AAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* *
21718 AAACTTACATTTTAA-CCCTAAAGCTTCTCT
1 AAAATTACATTTTAACCCCTAAA-CTTTTCT
* *
21748 AAAATTACATTTTAACCTC-AAACTTCTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* * *
21777 AAAATCACATTTTAACCCCTAAACCTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* * *
21807 AAAATCACATTTTAACCCTTAAAC-CTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* * * *
21836 CAAAATCACATTTTGACCTC-AAACTTGTCT
1 -AAAATTACATTTTAACCCCTAAACTTTTCT
* * * *
21866 AAAATCATATTTTAA-CCCTAAACTTTCCC
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* * *
21895 AAAATTACGTTTTTACCCC-AAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCT
*
21924 AAAATTACGTTTTAA
1 AAAATTACATTTTAA
21939 TATCGAATTC
Statistics
Matches: 234, Mismatches: 36, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.01
29 118 0.50
30 105 0.45
31 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCT
Found at i:21789 original size:89 final size:87
Alignment explanation
Indices: 21628--21938 Score: 363
Period size: 89 Copynumber: 3.5 Consensus size: 87
21618 GTTTTCTTTG
* * * * *
21628 AAAATTATATTTTTAACCCCTAAACTTTTCTAAAATTGCATTTTAACCCCAAACTTCTTTAAAAT
1 AAAATTACA-TTTTAA-CCCTAAACTTCTCTAAAATTACATTTTAACCTCAAACTTCTCTAAAAT
*
21693 TACATTTTGACCCCTAAACTTTTCC
64 CACATTTT-ACCCCTAAACTTTTCC
*
21718 AAACTTACATTTTAACCCTAAAGCTTCTCTAAAATTACATTTTAACCTCAAACTTCTCTAAAATC
1 AAAATTACATTTTAACCCTAAA-CTTCTCTAAAATTACATTTTAACCTCAAACTTCTCTAAAATC
*
21783 ACATTTTAACCCCTAAACCTTTCC
65 ACATTTT-ACCCCTAAACTTTTCC
* * * *
21807 AAAATCACATTTTAACCCTTAAACCTTCTC-AAAATCACATTTTGACCTCAAACTTGTCTAAAAT
1 AAAATTACATTTTAACCC-TAAA-CTTCTCTAAAATTACATTTTAACCTCAAACTTCTCTAAAAT
* * *
21871 CATATTTTAACCCTAAACTTTCCC
64 CACATTTTACCCCTAAACTTTTCC
* * * * * *
21895 AAAATTACGTTTTTACCCCAAACTTTTCCAAAATTACGTTTTAA
1 AAAATTACATTTTAACCCTAAACTTCTCTAAAATTACATTTTAA
21939 TATCGAATTC
Statistics
Matches: 191, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
86 5 0.03
87 15 0.08
88 35 0.18
89 119 0.62
90 17 0.09
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (87 bp):
AAAATTACATTTTAACCCTAAACTTCTCTAAAATTACATTTTAACCTCAAACTTCTCTAAAATCA
CATTTTACCCCTAAACTTTTCC
Found at i:23303 original size:31 final size:28
Alignment explanation
Indices: 23249--23305 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
23239 GTTTATTTGA
*
23249 AAATTAAAAAAATTTGGATAAAAAAATT
1 AAATTAAAAAAATTTAGATAAAAAAATT
23277 AAATTAAAAAATAAGTTTAGATAAAAAAA
1 AAATT-AAAAA-AA-TTTAGATAAAAAAA
23306 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 5 0.20
30 2 0.08
31 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (28 bp):
AAATTAAAAAAATTTAGATAAAAAAATT
Found at i:23318 original size:17 final size:17
Alignment explanation
Indices: 23280--23319 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
23270 AAAAATTAAA
*
23280 TTAAAAAATAAGTTTAG
1 TTAAAAAAAAAGTTTAG
* *
23297 ATAAAAAAAAAGTTTAT
1 TTAAAAAAAAAGTTTAG
23314 TTAAAA
1 TTAAAA
23320 TATGAATCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
TTAAAAAAAAAGTTTAG
Found at i:25099 original size:8 final size:9
Alignment explanation
Indices: 25069--25098 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25059 CTATAATGGC
*
25069 AAAAGAACA
1 AAAAGTACA
25078 AAAAGTACA
1 AAAAGTACA
25087 AAAAGTACA
1 AAAAGTACA
25096 AAA
1 AAA
25099 GATGGAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (9 bp):
AAAAGTACA
Found at i:28336 original size:24 final size:24
Alignment explanation
Indices: 28307--28362 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
28297 TAGACTAACA
*
28307 AGAGTTTGACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
28331 AGAGTTTAATTGAAACAAGTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
28355 AGAGTTTA
1 AGAGTTTA
28363 TCTAAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:34636 original size:40 final size:40
Alignment explanation
Indices: 34591--34686 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
34581 TTCATAGGTT
* *
34591 CATAAGTCTTCCTTTTAATCACTCTTATGCTTTACCGAGC
1 CATAAGTCTTCCTTTTAATCACTCTTATGCTCTACCAAGC
*
34631 CATAAGTCTTTCTTTTAATCACTCTTATGCTCTACCAAGC
1 CATAAGTCTTCCTTTTAATCACTCTTATGCTCTACCAAGC
34671 CATAAGTCTTCCTTTT
1 CATAAGTCTTCCTTTT
34687 TTAAAAAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (40 bp):
CATAAGTCTTCCTTTTAATCACTCTTATGCTCTACCAAGC
Found at i:34759 original size:41 final size:41
Alignment explanation
Indices: 34714--34807 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
34704 AAGCTCATTT
34714 TGAGACATGAGTATTCCTTTAATATAATCTCATTCGCATCC
1 TGAGACATGAGTATTCCTTTAATATAATCTCATTCGCATCC
* *
34755 TGAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCC
1 TGAGACATGAGTATTCCTTTAATATAATCTCATTCGCATCC
*
34796 CGAGACATGAGT
1 TGAGACATGAGT
34808 TTGCCATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (41 bp):
TGAGACATGAGTATTCCTTTAATATAATCTCATTCGCATCC
Found at i:41015 original size:21 final size:21
Alignment explanation
Indices: 40937--41015 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
40927 AATAGTGCAG
* * *
40937 ACTTCTACCAATACTTGTGAT
1 ACTTCTACCGATACTAGTTAT
* *
40958 AGTTCTACCGATACAAGTGTA-
1 ACTTCTACCGATACTAGT-TAT
* * *
40979 ACATCTACTGAAACTAGTTAT
1 ACTTCTACCGATACTAGTTAT
41000 ACTTCTACCGATACTA
1 ACTTCTACCGATACTA
41016 AAAACTCCAG
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (21 bp):
ACTTCTACCGATACTAGTTAT
Found at i:41720 original size:40 final size:40
Alignment explanation
Indices: 41676--41811 Score: 193
Period size: 40 Copynumber: 3.4 Consensus size: 40
41666 CTTCATAGGT
* *
41676 TCATAAGTCTCCCTTTTAATCACTCTTATGTTCTATCGAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATGTTCTACCGAG
* *
41716 TCATAAGTCTTCCTTCTAATCACTCTTATGCTT-TACCAAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATG-TTCTACCGAG
* *
41756 CCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATGTTCTACCGAG
*
41796 TCATAAATCTTCCTTT
1 TCATAAGTCTTCCTTT
41812 AAAAAAAACA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 81 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (40 bp):
TCATAAGTCTTCCTTTTAATCACTCTTATGTTCTACCGAG
Found at i:41900 original size:41 final size:41
Alignment explanation
Indices: 41839--41942 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
41829 CGCTTATTTT
** *
41839 GAGACATGAGTCTTATTTTAATATAATATCATTCTCATCTC
1 GAGACATGAGTCTTCCTTTAATATAATATCATTCTCATCCC
*
41880 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
1 GAGACATGAGTCTTCCTTTAATATAATATCATTCTCATCCC
*
41921 GAGACATGAGTCGTCCATTTAA
1 GAGACATGAGTCTTCC-TTTAA
41943 ATATTGAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 52 0.91
42 5 0.09
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (41 bp):
GAGACATGAGTCTTCCTTTAATATAATATCATTCTCATCCC
Found at i:48353 original size:6 final size:6
Alignment explanation
Indices: 48342--48395 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
48332 TGAGAAAAGG
* **
48342 AAATAA ATATAA TTATAA AAATAA AAATAA AAA-AA TAAA-AA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA -AAATAA AAATAA
48389 AAA-AA AA
1 AAATAA AA
48396 TAATTGGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
5 9 0.21
6 33 0.79
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:48365 original size:12 final size:12
Alignment explanation
Indices: 48343--48399 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
48333 GAGAAAAGGA
*
48343 AATAAATATAAT
1 AATAAAAATAAT
* *
48355 TATAAAAATAAA
1 AATAAAAATAAT
48367 AATAAAAA-AAT
1 AATAAAAATAAT
*
48378 AAAAAAAATAA-
1 AATAAAAATAAT
48389 AA-AAAAATAAT
1 AATAAAAATAAT
48400 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
10 8 0.22
11 11 0.30
12 18 0.49
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:48375 original size:14 final size:14
Alignment explanation
Indices: 48358--48398 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
48348 ATATAATTAT
48358 AAAAATAAAAATAA
1 AAAAATAAAAATAA
48372 AAAAATAAAAA-AA
1 AAAAATAAAAATAA
48385 ATAAAA-AAAAATAA
1 A-AAAATAAAAATAA
48399 TTGGGTTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:48377 original size:8 final size:8
Alignment explanation
Indices: 48364--48393 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
48354 TTATAAAAAT
48364 AAAAATAA
1 AAAAATAA
48372 AAAAATAAA
1 AAAAAT-AA
48381 AAAAATAA
1 AAAAATAA
48389 AAAAA
1 AAAAA
48394 AATAATTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:48382 original size:9 final size:9
Alignment explanation
Indices: 48364--48394 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
48354 TTATAAAAAT
48364 AAAAAT-AA
1 AAAAATAAA
48372 AAAAATAAA
1 AAAAATAAA
48381 AAAAATAAA
1 AAAAATAAA
48390 AAAAA
1 AAAAA
48395 ATAATTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:51967 original size:19 final size:19
Alignment explanation
Indices: 51943--51985 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
51933 AAACGTAGAC
51943 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
51962 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
51981 TAAAT
1 TAAAT
51986 CCGAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:65469 original size:14 final size:15
Alignment explanation
Indices: 65450--65482 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
65440 ATGCATTTCT
65450 TTATTT-ACTTTCAG
1 TTATTTCACTTTCAG
*
65464 TTATTTCACTTTTAG
1 TTATTTCACTTTCAG
65479 TTAT
1 TTAT
65483 GTTGTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (15 bp):
TTATTTCACTTTCAG
Found at i:78686 original size:15 final size:14
Alignment explanation
Indices: 78662--78700 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
78652 CATTTTTACA
*
78662 TTTTCTTTTATTTG
1 TTTTCTTTTACTTG
78676 TTTTACTTTTACTTG
1 TTTT-CTTTTACTTG
*
78691 TTTTGTTTTA
1 TTTTCTTTTA
78701 TATTCTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTACTTG
Found at i:81031 original size:51 final size:51
Alignment explanation
Indices: 80972--81203 Score: 265
Period size: 51 Copynumber: 4.5 Consensus size: 51
80962 AAACGAAAGG
* * *
80972 GTCCGATGACTATGTGTCATCATGAGTAAATGAATCCTTTACAGATCAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAA
* *
81023 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATACTTTACGGATTAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAA
* * * ** *
81074 GTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGATGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAA
* * *
81125 GTCCGATGACTCAGTGTCATCGTGAGT--ATGAATTCCTATAC-GAAATAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACAG-ATTAAAA
*
81175 GATCTGATGACTATA-TGTCATCGTGAGTA
1 G-TCCGATGACTA-AGTGTCATCGTGAGTA
81204 TTAAATGAAA
Statistics
Matches: 155, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
49 6 0.04
50 10 0.06
51 138 0.89
52 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAA
Found at i:87320 original size:21 final size:22
Alignment explanation
Indices: 87296--87340 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
87286 GTAAATATAG
*
87296 AATGATT-AATAAGGTTAACAA
1 AATGATTAAATAAAGTTAACAA
* *
87317 AATGGTTAAATAAAGTTAATAA
1 AATGATTAAATAAAGTTAACAA
87339 AA
1 AA
87341 GACATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (22 bp):
AATGATTAAATAAAGTTAACAA
Found at i:88287 original size:54 final size:53
Alignment explanation
Indices: 88206--88384 Score: 251
Period size: 51 Copynumber: 3.5 Consensus size: 53
88196 GAAAGGGTTT
*
88206 GATGACTAAGTG-CATCGTGAGTAAATGAATCCTTTACGAATTAAAAGTCTAAC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAAGTCT-AC
*
88259 GATGACTAAGTGTCATAGTGAGTAAATGAATCCTTTACGGATTAAAAGTCTA-
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAAGTCTAC
* * * *
88311 -ATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTC--C
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAAGTCTAC
*
88361 GATGACTCAGTGTCATCGTGAGTA
1 GATGACTAAGTGTCATCGTGAGTA
88385 TGAATTCCTA
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
51 66 0.57
53 13 0.11
54 36 0.31
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (53 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAAGTCTAC
Found at i:88415 original size:51 final size:48
Alignment explanation
Indices: 88311--88436 Score: 119
Period size: 51 Copynumber: 2.5 Consensus size: 48
88301 TAAAAGTCTA
* **
88311 ATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCG
1 ATGACT-AGTGTCATCGTGAGT--ATGAATCCATGATGAAACAAAGGTCCG
*
88362 ATGACTCAGTGTCATCGTGAGTATGAATTCCTAT-ATGAAACAAGAGGTTCG
1 ATGACT-AGTGTCATCGTGAGTATGAA-TCC-ATGATGAAACAA-AGGTCCG
* *
88413 ATGACTATATTTCATCGTGAGTAT
1 ATGACTA-GTGTCATCGTGAGTAT
88437 TAAATGAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
49 5 0.08
50 10 0.16
51 49 0.77
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (48 bp):
ATGACTAGTGTCATCGTGAGTATGAATCCATGATGAAACAAAGGTCCG
Found at i:88417 original size:102 final size:102
Alignment explanation
Indices: 88192--88435 Score: 228
Period size: 102 Copynumber: 2.4 Consensus size: 102
88182 TTCAAGCTAT
* * *
88192 AAACGAAAGGGTTTGATGACTAAGTG-CATCGTGAGTAAATGAATCCTTTACGAATTAAAAGTCT
1 AAAC-AAA-GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAAGTC-
*
88256 AACGATGACTAAGTGTCATAGTGAGTAAATGAATCCTTTACG
63 -ACGATGACTAAGTGTCATAGTGAGT-AATGAATCCTATACG
* ** * * * * *
88298 GATTAAAAG-TCTAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTC-C
1 AAACAAAGGTTC-GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAAGTCAC
* * *
88361 GATGACTCAGTGTCATCGTGAGT-ATGAATTCCTATATG
65 GATGACTAAGTGTCATAGTGAGTAATGAA-TCCTATACG
*
88399 AAACAAGAGGTTCGATGACTATA-TTTCATCGTGAGTA
1 AAACAA-AGGTTCGATGACTA-AGTGTCATCGTGAGTA
88436 TTAAATGAAA
Statistics
Matches: 111, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
100 5 0.05
101 10 0.09
102 44 0.40
103 4 0.04
104 12 0.11
105 35 0.32
106 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (102 bp):
AAACAAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAAGTCACG
ATGACTAAGTGTCATAGTGAGTAATGAATCCTATACG
Found at i:96938 original size:25 final size:25
Alignment explanation
Indices: 96901--96950 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
96891 GCAATACAAA
96901 TTTTTCTTCTTTTCTTTTCTCTTTC
1 TTTTTCTTCTTTTCTTTTCTCTTTC
* *
96926 TTTTTC-TCATTTTTTTTTCTTTTTC
1 TTTTTCTTC-TTTTCTTTTCTCTTTC
96951 AAGTGACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCTTCTTTTCTTTTCTCTTTC
Found at i:96944 original size:13 final size:12
Alignment explanation
Indices: 96901--96949 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
96891 GCAATACAAA
96901 TTTTTCTTCTTTT
1 TTTTTC-TCTTTT
* *
96914 CTTTTCTCTTTC
1 TTTTTCTCTTTT
96926 TTTTTCTCATTTT
1 TTTTTCTC-TTTT
96939 TTTTTCT-TTTT
1 TTTTTCTCTTTT
96950 CAAGTGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 4 0.13
12 12 0.39
13 15 0.48
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:96944 original size:19 final size:19
Alignment explanation
Indices: 96901--96950 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
96891 GCAATACAAA
96901 TTTTTCTTCTTT-TCTTTTC
1 TTTTTCTT-TTTCTCTTTTC
*
96920 TCTTTCTTTTTCTCATTTT-
1 TTTTTCTTTTTCTC-TTTTC
96939 TTTTTCTTTTTC
1 TTTTTCTTTTTC
96951 AAGTGACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.74
20 4 0.15
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTTCTCTTTTC
Found at i:98046 original size:15 final size:15
Alignment explanation
Indices: 98026--98055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
98016 CATTCTCTTC
*
98026 TTCTTTTTCTTCCTT
1 TTCTTTGTCTTCCTT
98041 TTCTTTGTCTTCCTT
1 TTCTTTGTCTTCCTT
98056 CTCATTCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (15 bp):
TTCTTTGTCTTCCTT
Found at i:115030 original size:24 final size:24
Alignment explanation
Indices: 114996--115042 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
114986 ATTAATCTTT
*
114996 TATTAATTTGCTCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
115019 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
115043 TACTCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:122448 original size:21 final size:19
Alignment explanation
Indices: 122422--122470 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
122412 GTTAGTTGCA
*
122422 TGCATTTCTTTTAATTGTCAT
1 TGCATTT-TTTT-ATTGCCAT
*
122443 TGCATTATTTTTATTGCCTT
1 TGCATT-TTTTTATTGCCAT
122463 TGCATTTT
1 TGCATTTT
122471 ATTTGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 10 0.40
22 1 0.04
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.59
Consensus pattern (19 bp):
TGCATTTTTTTATTGCCAT
Found at i:143937 original size:18 final size:19
Alignment explanation
Indices: 143914--143952 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
143904 ATTAATTTTG
143914 ATCAAATAAATT-AAATTA
1 ATCAAATAAATTAAAATTA
*
143932 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
143951 AT
1 AT
143953 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:144052 original size:20 final size:18
Alignment explanation
Indices: 144028--144076 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
144018 AATAGTGTTT
144028 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
144046 GTAATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
144066 T-TTAATTTAAT
1 TATTAATTTAAT
144077 GTTTATCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 4 0.15
20 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:146660 original size:27 final size:27
Alignment explanation
Indices: 146622--146754 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 27
146612 TGGCAAACAT
*
146622 AGAATAATACTCTTTCGAGCCAGATAC
1 AGAATAACACTCTTTCGAGCCAGATAC
146649 AGAATAACACTCTTTCGAGCCAGATAC
1 AGAATAACACTCTTTCGAGCCAGATAC
* * ** * * *
146676 AAAATAGCGTTCTTTCGAGTCAAATAT
1 AGAATAACACTCTTTCGAGCCAGATAC
*
146703 AGAATAACACTCTTTCAAGCCAGATAC
1 AGAATAACACTCTTTCGAGCCAGATAC
* ***
146730 AAAATATTGCTCTTTCGAGCCAGAT
1 AGAATAACACTCTTTCGAGCCAGAT
146755 CTCAAAGTGT
Statistics
Matches: 85, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (27 bp):
AGAATAACACTCTTTCGAGCCAGATAC
Found at i:146690 original size:54 final size:54
Alignment explanation
Indices: 146631--146754 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
146621 TAGAATAATA
*
146631 CTCTTTCGAGCCAGATACAGAATAACACTCTTTCGAGCCAGATACAAAATAGCG
1 CTCTTTCGAGCCAGATACAGAATAACACTCTTTCAAGCCAGATACAAAATAGCG
* * * * **
146685 TTCTTTCGAGTCAAATATAGAATAACACTCTTTCAAGCCAGATACAAAATATTG
1 CTCTTTCGAGCCAGATACAGAATAACACTCTTTCAAGCCAGATACAAAATAGCG
146739 CTCTTTCGAGCCAGAT
1 CTCTTTCGAGCCAGAT
146755 CTCAAAGTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (54 bp):
CTCTTTCGAGCCAGATACAGAATAACACTCTTTCAAGCCAGATACAAAATAGCG
Found at i:152640 original size:4 final size:4
Alignment explanation
Indices: 152598--152631 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
152588 CACATATACA
*
152598 TATG TATG TATG TATG TATG TATG AATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
152632 AATGTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:152855 original size:18 final size:18
Alignment explanation
Indices: 152818--152861 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
152808 ATGAGGATTT
152818 TAAATAAATTAATATGATA
1 TAAAT-AATTAATATGATA
152837 TAAATAATTATATAT-ATA
1 TAAATAATTA-ATATGATA
*
152855 TATATAA
1 TAAATAA
152862 GTGTGAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAATAATTAATATGATA
Found at i:179373 original size:27 final size:28
Alignment explanation
Indices: 179324--179376 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
179314 AACTAATAAT
**
179324 TATAACTATAATTATAATTATTTTTAAA
1 TATAACTATAATTATAACAATTTTTAAA
*
179352 TATAA-TATAATTATCACAATTTTTA
1 TATAACTATAATTATAACAATTTTTA
179377 TTAAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAACTATAATTATAACAATTTTTAAA
Found at i:180212 original size:17 final size:17
Alignment explanation
Indices: 180190--180243 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
180180 TCACGTTAGC
*
180190 AATTAATTAATTTTAAA
1 AATTAAATAATTTTAAA
* *
180207 AATTAAAAAAATTGTAAA
1 AATT-AAATAATTTTAAA
180225 AATTAAAT-ATTATTAAA
1 AATTAAATAATT-TTAAA
180242 AA
1 AA
180244 CTACAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 14 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTAAATAATTTTAAA
Found at i:187212 original size:14 final size:14
Alignment explanation
Indices: 187193--187295 Score: 109
Period size: 14 Copynumber: 7.3 Consensus size: 14
187183 TATATCACTA
*
187193 AACTATTGTATACG
1 AACTATTGTATGCG
*
187207 AACTATTATATGCG
1 AACTATTGTATGCG
* *
187221 AACTATTTTATGTG
1 AACTATTGTATGCG
*
187235 AACTATTGTATGTG
1 AACTATTGTATGCG
*
187249 AACCATTGTATGCG
1 AACTATTGTATGCG
**
187263 AA-TCATTGTATATG
1 AACT-ATTGTATGCG
187277 AACTAATTGTATGCG
1 AACT-ATTGTATGCG
187292 AACT
1 AACT
187296 GGTTATGTGC
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
14 61 0.82
15 13 0.18
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (14 bp):
AACTATTGTATGCG
Found at i:187261 original size:42 final size:42
Alignment explanation
Indices: 187193--187294 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
187183 TATATCACTA
* * * *
187193 AACTATTGTATACGAACTATTATATGCGAA-CTATTTTATGTG
1 AACTATTGTATGCGAACCATTATATGCGAATC-ATTGTATATG
* *
187235 AACTATTGTATGTGAACCATTGTATGCGAATCATTGTATATG
1 AACTATTGTATGCGAACCATTATATGCGAATCATTGTATATG
187277 AACTAATTGTATGCGAAC
1 AACT-ATTGTATGCGAAC
187295 TGGTTATGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 38 0.75
43 13 0.25
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (42 bp):
AACTATTGTATGCGAACCATTATATGCGAATCATTGTATATG
Found at i:187881 original size:15 final size:16
Alignment explanation
Indices: 187850--187881 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
187840 GTTTATGGAT
187850 GGTGTGAATGATGGTA
1 GGTGTGAATGATGGTA
187866 GGTGTGAATG-TGGTA
1 GGTGTGAATGATGGTA
187881 G
1 G
187882 TTTCTAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (16 bp):
GGTGTGAATGATGGTA
Found at i:209185 original size:62 final size:59
Alignment explanation
Indices: 209110--209224 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 59
209100 TTATTATCTT
* * * *
209110 AATATTAAATTTAATTTAATGTTTATCTTGTACATAAATATTTTATTATTTTAATAAGATTC
1 AATATTAAATTTAATATAATATTTATCTTG---ATAAATATTATATTAATTTAATAAGATTC
209172 AATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATA
1 AATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATA
209225 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.43
62 28 0.57
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
AATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATAAGATTC
Found at i:212729 original size:28 final size:28
Alignment explanation
Indices: 212685--212759 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
212675 TTTATTGAAA
212685 GGAAGCCTTTGTGGCTATTCTGATATGT
1 GGAAGCCTTTGTGGCTATTCTGATATGT
* *
212713 GGAAGGCTTTGTAGCTATTCTGATATGT
1 GGAAGCCTTTGTGGCTATTCTGATATGT
**
212741 GGAAGTATTTGTGGCTATT
1 GGAAGCCTTTGTGGCTATT
212760 TTCGTTACCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.40
Consensus pattern (28 bp):
GGAAGCCTTTGTGGCTATTCTGATATGT
Found at i:224959 original size:39 final size:39
Alignment explanation
Indices: 224916--224995 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
224906 GAAAAATCTA
*
224916 ATTTATCATTCTTCTATTGTAAAGAGATAGGGATGACAT
1 ATTTATCATTCTTCTATTGTAAAGAGATAAGGATGACAT
224955 ATTTATCATTCTTCTATTGTAAAGAGATAAGGATGACAT
1 ATTTATCATTCTTCTATTGTAAAGAGATAAGGATGACAT
224994 AT
1 AT
224996 AATCACAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (39 bp):
ATTTATCATTCTTCTATTGTAAAGAGATAAGGATGACAT
Found at i:233964 original size:24 final size:24
Alignment explanation
Indices: 233937--233984 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
233927 AGTTTTCTCA
233937 CCTGTTGGGGTAAAAATGAAAATT
1 CCTGTTGGGGTAAAAATGAAAATT
233961 CCTGTTGGGGTAAAAATGAAAATT
1 CCTGTTGGGGTAAAAATGAAAATT
233985 ATTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (24 bp):
CCTGTTGGGGTAAAAATGAAAATT
Found at i:237305 original size:28 final size:29
Alignment explanation
Indices: 237255--237336 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
237245 AATTTTTTTT
* * **
237255 TTCAATTTTTAAAGAGTCCAAAAAA-ATG
1 TTCAACTTTTAAAGGGTTTAAAAAATATG
* *
237283 TTCAACTTTTAAAGGGTTTAAAAAATTTT
1 TTCAACTTTTAAAGGGTTTAAAAAATATG
*
237312 TTACCAACTTTTAAGGGGTTTAAAA
1 TT--CAACTTTTAAAGGGTTTAAAA
237337 TTTTTTTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 21 0.48
29 3 0.07
31 20 0.45
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (29 bp):
TTCAACTTTTAAAGGGTTTAAAAAATATG
Found at i:237323 original size:31 final size:30
Alignment explanation
Indices: 237285--237370 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 30
237275 AAAAAATGTT
237285 CAACTTTTAAAGGGTTTAAAAAATTTTTTAC
1 CAACTTTTAAAGGGTTT-AAAAATTTTTTAC
* * *
237316 CAACTTTTAAGGGGTTTAAAATTTTTTTTC
1 CAACTTTTAAAGGGTTTAAAAATTTTTTAC
* * *
237346 CAA-TTTTTAAGGATTTCAAAATTTT
1 CAACTTTTAAAGGGTTTAAAAATTTT
237371 AATTTATTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.36
30 14 0.30
31 16 0.34
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
CAACTTTTAAAGGGTTTAAAAATTTTTTAC
Found at i:237342 original size:30 final size:30
Alignment explanation
Indices: 237285--237370 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
237275 AAAAAATGTT
*
237285 CAACTTTTAAAGGGTTTAAAAAATTTTTTAC
1 CAACTTTT-AAGGGTTTAAAAATTTTTTTAC
*
237316 CAACTTTTAAGGGGTTT-AAAATTTTTTTTC
1 CAACTTTTAA-GGGTTTAAAAATTTTTTTAC
* * *
237346 CAATTTTTAAGGATTTCAAAATTTT
1 CAACTTTTAAGGGTTTAAAAATTTT
237371 AATTTATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.10
30 30 0.61
31 14 0.29
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
CAACTTTTAAGGGTTTAAAAATTTTTTTAC
Found at i:239489 original size:3 final size:3
Alignment explanation
Indices: 239441--239469 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
239431 GTGTCGATAA
239441 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
239470 ATTTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:240220 original size:90 final size:89
Alignment explanation
Indices: 240093--240255 Score: 218
Period size: 90 Copynumber: 1.8 Consensus size: 89
240083 ATTGCCTTTT
* *** * *
240093 TTTTTTTGAAAATTTTTAGGGTTTTTTTGATACATTTTGAAAATTCAAGTATCCAATTGAATGCA
1 TTTTTTTGAAAATTTTAAGAACTTTTTTGATACATTTTGAAAATTCAAATATCCAAGTGAATGCA
240158 AAATAAAAGCAAGGGTGTAATTGA
66 AAATAAAAGCAAGGGTGTAATTGA
** ** *
240182 TTTTTTTGAAAAATTTTAAGAACTTTTTTGATGTATTTTGAAAATTCAAATATTTAAGTGAGTGC
1 TTTTTTTG-AAAATTTTAAGAACTTTTTTGATACATTTTGAAAATTCAAATATCCAAGTGAATGC
240247 AAAATAAAA
65 AAAATAAAA
240256 AAACAAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 8 0.13
90 54 0.87
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (89 bp):
TTTTTTTGAAAATTTTAAGAACTTTTTTGATACATTTTGAAAATTCAAATATCCAAGTGAATGCA
AAATAAAAGCAAGGGTGTAATTGA
Found at i:241840 original size:17 final size:16
Alignment explanation
Indices: 241818--241856 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
241808 TTTTTTTTAG
241818 TTAAAAGTGTAATTAA
1 TTAAAAGTGTAATTAA
* *
241834 TTTAAAATTTTAATTAA
1 -TTAAAAGTGTAATTAA
241851 TTAAAA
1 TTAAAA
241857 TCTTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
TTAAAAGTGTAATTAA
Found at i:244490 original size:125 final size:123
Alignment explanation
Indices: 244263--244492 Score: 336
Period size: 125 Copynumber: 1.9 Consensus size: 123
244253 AAAAAAAAAT
* * * *
244263 TTGCGTGTATAATATATTTATATATACTTAATTTTTGCTTAGCTAATAATATAAATTATTTTGAG
1 TTGCGTGTATAATATATTTATATATACTTAATTTTTGCTTAGCGAATAATATAAATTATATTAAA
* * * * *
244328 CTTTTATCTGGTGAAGTAAACCGAATTGGTTGTCCTCATCTAGTGGCGGTAAAATAGG
66 ATTTTATCTAGTGAAGTAAACCCAAGTGATTGTCCTCATCTAGTGGCGGTAAAATAGG
*
244386 TTGCGTGTATAATATATTTATATATACACTTAATTTTTGCTTAGCGAATAGTATAAATTATATTA
1 TTGCGTGTATAATATATTTATATAT--ACTTAATTTTTGCTTAGCGAATAATATAAATTATATTA
244451 AAATTTTATCTAGTGAAGTAAACCCAAGTGATTCG-CCTCATC
64 AAATTTTATCTAGTGAAGTAAACCCAAGTGATT-GTCCTCATC
244493 AATCGAGAGA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
123 25 0.27
125 68 0.72
126 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (123 bp):
TTGCGTGTATAATATATTTATATATACTTAATTTTTGCTTAGCGAATAATATAAATTATATTAAA
ATTTTATCTAGTGAAGTAAACCCAAGTGATTGTCCTCATCTAGTGGCGGTAAAATAGG
Found at i:246805 original size:59 final size:59
Alignment explanation
Indices: 246690--246829 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 59
246680 ATTTTATGGT
* * * *
246690 AAAATGGTAATTTTTGGAAAGTTTCGGGTGAAAAATAAAATTTTTGGACACCCGGGGAT-
1 AAAATGGTAATTTTTAGAAAG-TTCGGGTCAAAAAGAAAATCTTTGGACACCCGGGGATG
* * **
246749 AACATGGTAATTTTTAGAAAGTTCGAGGTCAAAAAGGAAATCTTTGGA-AGTTCGGGGATG
1 AAAATGGTAATTTTTAGAAAGTTCG-GGTCAAAAAGAAAATCTTTGGACA-CCCGGGGATG
*
246809 AAAAT-GTAA-TTTTAGGAAGTT
1 AAAATGGTAATTTTTAGAAAGTT
246830 TGGGGGAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 16 0.24
59 48 0.71
60 4 0.06
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAAGTTCGGGTCAAAAAGAAAATCTTTGGACACCCGGGGATG
Found at i:246858 original size:28 final size:27
Alignment explanation
Indices: 246791--246934 Score: 164
Period size: 27 Copynumber: 5.1 Consensus size: 27
246781 AAAGGAAATC
*
246791 TTTGGAAGTTCGGGGATGAAAATGTAATT
1 TTTGGAAGTTTGGGG--GAAAATGTAATT
*
246820 TTAGGAAGTTTGGGGGAAAATGTAATT
1 TTTGGAAGTTTGGGGGAAAATGTAATT
*
246847 TTTGTGAAGTTTAGGGGTCAAAATGTAATT
1 TTTG-GAAGTTT-GGGG-GAAAATGTAATT
*
246877 TTTGGAAGTTTAGGAGG-AAATGTAATTT
1 TTTGGAAGTTT-GGGGGAAAATGTAA-TT
* *
246905 TTTGGAAGTTTAGGGGAAAATATAATT
1 TTTGGAAGTTTGGGGGAAAATGTAATT
246932 TTT
1 TTT
246935 CTGAAGTTCG
Statistics
Matches: 101, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
27 31 0.31
28 27 0.27
29 28 0.28
30 15 0.15
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.38
Consensus pattern (27 bp):
TTTGGAAGTTTGGGGGAAAATGTAATT
Found at i:246870 original size:57 final size:55
Alignment explanation
Indices: 246808--246933 Score: 175
Period size: 57 Copynumber: 2.3 Consensus size: 55
246798 GTTCGGGGAT
*
246808 GAAAATGTAATTTTAGGAAGTTT-GGGGGAAAATGTAA-TTTTTGTGAAGTTTAGGG
1 GAAAATGTAATTTTAGGAAGTTTAGGAGG-AAATGTAATTTTTTG-GAAGTTTAGGG
*
246863 GTCAAAATGTAATTTTTGGAAGTTTAGGAGGAAATGTAATTTTTTGGAAGTTTAGGG
1 G--AAAATGTAATTTTAGGAAGTTTAGGAGGAAATGTAATTTTTTGGAAGTTTAGGG
*
246920 GAAAATATAATTTT
1 GAAAATGTAATTTT
246934 TCTGAAGTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
55 13 0.20
57 41 0.64
58 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38
Consensus pattern (55 bp):
GAAAATGTAATTTTAGGAAGTTTAGGAGGAAATGTAATTTTTTGGAAGTTTAGGG
Found at i:246933 original size:85 final size:85
Alignment explanation
Indices: 246810--246974 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 85
246800 TCGGGGATGA
* * *
246810 AAATGTAATTTTAGGAAGTTTGGGGGAAAATGTAATTTTTGTGAAGTTTAG-GGGTCAAAATGTA
1 AAATGTAATTTTAGGAAGTTTAGGGGAAAATATAATTTTTCTGAAG-TTAGAGGGTCAAAATGTA
*
246874 ATTTTT-GGAAGTTTAGGAGG
65 ATTTTTAGAAAGTTTAGGAGG
* * * *
246894 AAATGTAATTTTTTGGAAGTTTAGGGGAAAATATAATTTTTCTGAAGTTCGAGGGTTAAAGTGTA
1 AAATGTAA-TTTTAGGAAGTTTAGGGGAAAATATAATTTTTCTGAAGTTAGAGGGTCAAAATGTA
246959 ATTTTTAGAAAGTTTA
65 ATTTTTAGAAAGTTTA
246975 AGGGTTAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 11 0.16
85 51 0.73
86 8 0.11
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (85 bp):
AAATGTAATTTTAGGAAGTTTAGGGGAAAATATAATTTTTCTGAAGTTAGAGGGTCAAAATGTAA
TTTTTAGAAAGTTTAGGAGG
Found at i:246940 original size:28 final size:27
Alignment explanation
Indices: 246808--246995 Score: 171
Period size: 30 Copynumber: 6.6 Consensus size: 27
246798 GTTCGGGGAT
** *
246808 GAAAATGTAATTTTAGGAAGTTTGGGG
1 GAAAATGTAATTTTTTGAAGTTTAGGG
246835 GAAAATGTAATTTTTGTGAAGTTTAGGG
1 GAAAATGTAATTTTT-TGAAGTTTAGGG
*
246863 GTCAAAATGTAATTTTTGGAAGTTTAGGAG
1 G--AAAATGTAATTTTTTGAAGTTTAGG-G
246893 G-AAATGTAATTTTTTGGAAGTTTAGGG
1 GAAAATGTAATTTTTT-GAAGTTTAGGG
* *
246920 GAAAATATAATTTTTCTGAAGTTCGAGGG
1 GAAAATGTAATTTTT-TGAAGTT-TAGGG
* * *
246949 TTAAAGTGTAATTTTTAGAAAGTTTAAGGG
1 -GAAAATGTAATTTTTTG-AAGTTT-AGGG
* *
246979 TTAAAATATAATTTTTT
1 -GAAAATGTAATTTTTT
246996 AAAATACGAT
Statistics
Matches: 135, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
27 29 0.21
28 39 0.29
29 16 0.12
30 51 0.38
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (27 bp):
GAAAATGTAATTTTTTGAAGTTTAGGG
Found at i:246964 original size:57 final size:54
Alignment explanation
Indices: 246808--246994 Score: 164
Period size: 57 Copynumber: 3.3 Consensus size: 54
246798 GTTCGGGGAT
* *
246808 GAAAATGTAATTTTAGGAAGTTTG-GG-GGAAAATGTAATTTTTGTGAAGTTTAGGG
1 GAAAATATAATTTTTGGAAG-TTGAGGAGG-AAATGTAATTTTTG-GAAGTTTAGGG
* *
246863 GTCAAAATGTAATTTTTGGAAGTTTAGGAGGAAATGTAATTTTTTGGAAGTTTAGGG
1 G--AAAATATAATTTTTGGAAGTTGAGGAGGAAATGTAA-TTTTTGGAAGTTTAGGG
* * *
246920 GAAAATATAATTTTTCTGAAGTTCGAGG-GTTAAAGTGTAATTTTTAGAAAGTTTAAGGG
1 GAAAATATAATTTTT-GGAAGTT-GAGGAG-GAAA-TGTAATTTTT-GGAAGTTT-AGGG
*
246979 TTAAAATATAATTTTT
1 -GAAAATATAATTTTT
246995 TAAAATACGA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
55 14 0.12
56 9 0.08
57 51 0.46
58 20 0.18
59 4 0.04
60 14 0.12
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (54 bp):
GAAAATATAATTTTTGGAAGTTGAGGAGGAAATGTAATTTTTGGAAGTTTAGGG
Found at i:248041 original size:3 final size:3
Alignment explanation
Indices: 248035--248062 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
248025 ATTTTTTTAA
248035 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
248063 AGGCTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:248785 original size:37 final size:36
Alignment explanation
Indices: 248727--248810 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
248717 GGAATTGGGT
248727 CATTTGAAATTGGACCCAATTGGG-TTGTAATTTTGGA
1 CATTTGAAATTGGACCCAATTGGGCTTGT-A-TTTGGA
* * *
248764 CATTTGTAATTGGGCCTAATTGGGCTTGTATTTGGA
1 CATTTGAAATTGGACCCAATTGGGCTTGTATTTGGA
*
248800 CATTTTAAATT
1 CATTTGAAATT
248811 TAATTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 15 0.37
37 22 0.54
38 4 0.10
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.42
Consensus pattern (36 bp):
CATTTGAAATTGGACCCAATTGGGCTTGTATTTGGA
Found at i:248823 original size:17 final size:17
Alignment explanation
Indices: 248803--248951 Score: 102
Period size: 17 Copynumber: 8.4 Consensus size: 17
248793 ATTTGGACAT
** *
248803 TTTAAATTTAATTTAAT
1 TTTAAATTTAAAATAAA
* ** *
248820 TTTAAGTTTAAAACCAT
1 TTTAAATTTAAAATAAA
*
248837 TTTAAATTT-AACTAAA
1 TTTAAATTTAAAATAAA
*
248853 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
248870 TTTAAATTTAAAAATAAATTTAAA
1 TTTAAATTT----A-AAA--TAAA
248894 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
248911 TTTAAATTCAAAAATCAA
1 TTTAAATT-TAAAATAAA
* *
248929 TTTAAACTTAATATAAA
1 TTTAAATTTAAAATAAA
248946 TTTAAA
1 TTTAAA
248952 ATCAAAAGTT
Statistics
Matches: 104, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
16 12 0.12
17 58 0.56
18 14 0.13
19 3 0.03
20 1 0.01
21 1 0.01
22 3 0.03
24 12 0.12
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:248846 original size:6 final size:6
Alignment explanation
Indices: 248837--248951 Score: 87
Period size: 6 Copynumber: 20.0 Consensus size: 6
248827 TTAAAACCAT
* **
248837 TTTAAA TTT-AA -CTAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * ** *
248882 AATAAA TTTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTCAAA AATCAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
248929 TTTAAA CTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
248952 ATCAAAAGTT
Statistics
Matches: 80, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
4 1 0.01
5 14 0.17
6 65 0.81
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:248875 original size:23 final size:23
Alignment explanation
Indices: 248849--248918 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
248839 TAAATTTAAC
*
248849 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAATAAATT
248872 TAAATTT--A---AAAATAAATT
1 TAAATTTAAATTTAAAATAAATT
248890 TAAATTTAAATTTAAAATAAATT
1 TAAATTTAAATTTAAAATAAATT
248913 TAAATT
1 TAAATT
248919 CAAAAATCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
18 16 0.39
20 1 0.02
21 1 0.02
23 23 0.56
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATT
Found at i:248905 original size:41 final size:41
Alignment explanation
Indices: 248849--248939 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
248839 TAAATTTAAC
*
248849 TAAATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATT
1 TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
* *
248890 TAAATTTAAATTTAAAATAAATTTAAATTCAAAAATCAATT
1 TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
*
248931 TAAACTTAA
1 TAAATTTAA
248940 TATAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (41 bp):
TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
Found at i:248911 original size:35 final size:34
Alignment explanation
Indices: 248849--248952 Score: 93
Period size: 35 Copynumber: 3.0 Consensus size: 34
248839 TAAATTTAAC
** *
248849 TAAATTTAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAATTAAA-ATAAATTTAAAAA
*
248884 TAAATTTAAATTTAAATTTAAAATAAATTT-AAAT
1 TAAATTTAAATTTAAA-TTAAAATAAATTTAAAAA
** * *
248918 TCAAAAATCAATTTAAACTTAATATAAATTTAAAA
1 T-AAATTTAAATTTAAA-TTAAAATAAATTTAAAA
248953 TCAAAAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
34 4 0.07
35 47 0.82
36 6 0.11
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAATTTAAATTTAAATTAAAATAAATTTAAAAA
Found at i:248957 original size:35 final size:35
Alignment explanation
Indices: 248892--248958 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
248882 AATAAATTTA
* *
248892 AATTTAAATTTAAAATAAATTTAAATTCAAAAATC
1 AATTTAAACTTAAAATAAATTTAAAATCAAAAATC
*
248927 AATTTAAACTTAATATAAATTTAAAATCAAAA
1 AATTTAAACTTAAAATAAATTTAAAATCAAAA
248959 GTTTGATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (35 bp):
AATTTAAACTTAAAATAAATTTAAAATCAAAAATC
Found at i:249149 original size:53 final size:53
Alignment explanation
Indices: 249064--249177 Score: 183
Period size: 53 Copynumber: 2.2 Consensus size: 53
249054 GGATGCCCAA
* * * *
249064 TTTGTCAGGTCTCATCTCTTTAATGCTGTTCCTTCAATTGGCCTGCCTTTCGT
1 TTTGTCAGGTCTCATCTCTTTAATGCTCTTCCTTCAACTGACCCGCCTTTCGT
*
249117 TTTGTCAGGTCTCATCTCTTTGATGCTCTTCCTTCAACTGACCCGCCTTTCGT
1 TTTGTCAGGTCTCATCTCTTTAATGCTCTTCCTTCAACTGACCCGCCTTTCGT
249170 TTTGTCAG
1 TTTGTCAG
249178 TTGTCCAATC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.44
Consensus pattern (53 bp):
TTTGTCAGGTCTCATCTCTTTAATGCTCTTCCTTCAACTGACCCGCCTTTCGT
Found at i:249787 original size:195 final size:198
Alignment explanation
Indices: 249447--250251 Score: 1050
Period size: 209 Copynumber: 4.0 Consensus size: 198
249437 TAACCATTTT
* *
249447 ATTG-CTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTG
1 ATTGCCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTG
* *
249511 AGCTTGGCTTTATTGATTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGT
66 AGCTTGGCTTCATTGATTTGACCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGT
* * *
249576 TTCAATCCGCTTCTCTGTATCTAATCAGAAAGGCGAATTTGGTTCACTTCTCAGTATCTCATTAG
131 TTCAATCCGCTTCTCTGTATCTCATCAGAAAGGCGAATTTGGTCCACTTCTTAGTATCTCATTAG
249641 -G-
196 AGC
*
249642 A-TGCCTTCGACCTGCTTCTCAGTATCTCATC-AGAAAGTTGGGGTTCGAAGATTTGCTCACTTT
1 ATTGCCTTCGACCTGCTTCTCAGTATCTCATCAAG-AAGCTGGGGTTCGAAGATTTGCTCACTTT
* *
249705 GAGCTTGGCTTCATTGATTTGACCTTCTTCTCAGTATCTCATCAGGTAGATGACCGTATCACTTG
65 GAGCTTGGCTTCATTGATTTGACCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
*
249770 TTTCAATCCGTTTCTCTGTATCTCATCA-AGAAGGCGAATTTGGTCCACTTCTTAGTATCTCATT
130 TTTCAATCCGCTTCTCTGTATCTCATCAGA-AAGGCGAATTTGGTCCACTTCTTAGTATCTCATT
249834 AGAAAGCTAACC
194 AG--AG-----C
* *
249846 ATTTTATTG-CTTCGACCTGCTTCTTAGTATCTCATCAAGAAGCTGGGGTTTGAAGATTTGCTCA
1 -----ATTGCCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCA
* * *
249910 CTTTGAGCTTAGATTCATTGATTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
61 CTTTGAGCTTGGCTTCATTGATTTGACCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
* * *
249975 CTTGTTTCAATCCGCTTCTTTGTATCTCATCAGGAAGGTGAATTTGGTCCACTTCTTAGTATCTC
126 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGAAAGGCGAATTTGGTCCACTTCTTAGTATCTC
250040 ATTAGGAAGCTAACC
191 ATTA-G-AG-----C
* * * *
250055 ATTTTCTTGCTTCGACCTGCTTCTCAGTATCTTAACAAGAAGCTAGGGTTCGAAGATTTGCTCAC
1 A-TTGC---CTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
* * * *
250120 TTTGGGCTTGGCTTCATTAATTTGGA-CTTCTTCTTAGTATCTCATCAGGAAGATGACCTCATCA
62 TTTGAGCTTGGCTTCATTGATTT-GACCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
* * *
250184 CTTATTTCAATCCGCTTCTTTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTTAGTATCTC
126 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGAAAGGCGAATTTGGTCCACTTCTTAGTATCTC
250249 ATT
191 ATT
250252 CGGAAGATGA
Statistics
Matches: 545, Mismatches: 38, Indels: 40
0.87 0.06 0.06
Matches are distributed among these distances:
194 4 0.01
195 176 0.32
198 1 0.00
204 1 0.00
205 2 0.00
209 355 0.65
210 6 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (198 bp):
ATTGCCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTG
AGCTTGGCTTCATTGATTTGACCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGT
TTCAATCCGCTTCTCTGTATCTCATCAGAAAGGCGAATTTGGTCCACTTCTTAGTATCTCATTAG
AGC
Found at i:262443 original size:59 final size:59
Alignment explanation
Indices: 262380--262511 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
262370 GTAAAACGGT
* * * * *
262380 AATTTTTAGACATTTGGGTGCAAAATGGTGA-TTTTTGGAAGATTCGAGGTAAAAAATGA
1 AATTTTTGGACATCTGGGGGCAAAATGGTAATTTTTTGAAAGATTCGA-GTAAAAAATGA
* ** * *
262439 AATTTTTGGATATCTGGGGGTGAAATGGTAATTTTTTGAAAGTTTCGAGTCAAAAATGA
1 AATTTTTGGACATCTGGGGGCAAAATGGTAATTTTTTGAAAGATTCGAGTAAAAAATGA
*
262498 AATATTTGGACATC
1 AATTTTTGGACATC
262512 CGAGATAACA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 46 0.77
60 14 0.23
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (59 bp):
AATTTTTGGACATCTGGGGGCAAAATGGTAATTTTTTGAAAGATTCGAGTAAAAAATGA
Found at i:262538 original size:58 final size:60
Alignment explanation
Indices: 262402--262540 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 60
262392 TTTGGGTGCA
* * * * * * *
262402 AAATGGTGATTTTTGG-AAGATTCGAGGTAAAAAATGAAATTTTTGGATATCTGGGGGTG
1 AAATGGTAATTTTTGGAAAGTTTCGAGGTAAAAAATGAAATATTTGGACATCTCGAGATG
* *
262461 AAATGGTAATTTTTTGAAAGTTTCGA-GTCAAAAATGAAATATTTGGACATC-CGAGAT-
1 AAATGGTAATTTTTGGAAAGTTTCGAGGTAAAAAATGAAATATTTGGACATCTCGAGATG
262518 AACATGGTAATTTTTGGAAAGTT
1 AA-ATGGTAATTTTTGGAAAGTT
262541 CGGCTTAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 2 0.03
58 22 0.32
59 36 0.53
60 8 0.12
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (60 bp):
AAATGGTAATTTTTGGAAAGTTTCGAGGTAAAAAATGAAATATTTGGACATCTCGAGATG
Found at i:262703 original size:87 final size:85
Alignment explanation
Indices: 262559--262733 Score: 221
Period size: 87 Copynumber: 2.0 Consensus size: 85
262549 AAAGGGAATC
* *
262559 TTTGGAAGTTCGGGGATGAATGTAATTTTTAAAGTTCAAGGGTAAAAATGTAATTTTTATGAAGT
1 TTTGGAAGTTCGGGGAGGAATGTAATTTTTAAAGTTCAAGGGCAAAAATGTAATTTTTATGAAGT
*
262624 TT-GAGGGTCAAAATGTAGTT
66 TTAG-GGGTCAAAATGTAATT
* * *
262644 TTTGGAAGTTCGAGGG-GGAATGTAATTTTTTTGGAA-TTTAAGGGCAAAAATGTAATTTTTGTG
1 TTTGGAAGTTCG-GGGAGGAATGTAA--TTTTT-AAAGTTCAAGGGCAAAAATGTAATTTTTATG
*
262707 AAGTTTAGGGGTCAAAGTGTAATT
62 AAGTTTAGGGGTCAAAATGTAATT
262731 TTT
1 TTT
262734 AGAAAGTTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
85 20 0.26
86 3 0.04
87 52 0.67
88 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (85 bp):
TTTGGAAGTTCGGGGAGGAATGTAATTTTTAAAGTTCAAGGGCAAAAATGTAATTTTTATGAAGT
TTAGGGGTCAAAATGTAATT
Found at i:262794 original size:30 final size:30
Alignment explanation
Indices: 262577--262831 Score: 199
Period size: 30 Copynumber: 8.7 Consensus size: 30
262567 TTCGGGGATG
* *
262577 AATGTAATTTTT--AAAGTTCAAGGGTAAA
1 AATGTAATTTTTGGAAAGTTTAAGGGTCAA
* *
262605 AATGTAATTTTTATG-AAGTTTGAGGGTCAA
1 AATGTAATTTTT-GGAAAGTTTAAGGGTCAA
* ** **
262635 AATGTAGTTTTTGG-AAGTTCGAGGG--GG
1 AATGTAATTTTTGGAAAGTTTAAGGGTCAA
262662 AATGTAATTTTTTTGG-AA-TTTAAGGG-CAAA
1 AATGTAA--TTTTTGGAAAGTTTAAGGGTC-AA
*
262692 AATGTAATTTTTGTG-AAGTTTAGGGGTCAA
1 AATGTAATTTTTG-GAAAGTTTAAGGGTCAA
* * *
262722 AGTGTAATTTTTAGAAAGTTT-AGTGGTTAA
1 AATGTAATTTTTGGAAAGTTTAAG-GGTCAA
262752 AATGTAATTTTTGGAAAGTTTAAGGGTCAA
1 AATGTAATTTTTGGAAAGTTTAAGGGTCAA
* * * *
262782 AATGTACTTTTTGGAAAATTTAGGGGTTAA
1 AATGTAATTTTTGGAAAGTTTAAGGGTCAA
* * *
262812 AATATGATTTTTGGATAGTT
1 AATGTAATTTTTGGAAAGTT
262832 CAGGGACCTT
Statistics
Matches: 184, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
27 6 0.03
28 24 0.13
29 25 0.14
30 126 0.68
31 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (30 bp):
AATGTAATTTTTGGAAAGTTTAAGGGTCAA
Found at i:263914 original size:3 final size:3
Alignment explanation
Indices: 263908--263950 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
263898 TTTTTTTTTA
** * *
263908 ATT ATT ATT ATT AAA AAT ATT ATT ATT ATT TTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
263951 AGGCTGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:264648 original size:36 final size:36
Alignment explanation
Indices: 264602--264690 Score: 108
Period size: 36 Copynumber: 2.4 Consensus size: 36
264592 TTAATTGGAA
*
264602 TTGGATCATTTGAAATTGGACCCAATTGG-GTTGTATT
1 TTGGA-CATTTGAAATTGGACCCAATTGGACTTGTA-T
* * *
264639 TTGTACATTTGTAATTGGGCCCAATTGGACTTGTAT
1 TTGGACATTTGAAATTGGACCCAATTGGACTTGTAT
*
264675 TTGGACATTTTAAATT
1 TTGGACATTTGAAATT
264691 TAATTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 35 0.80
37 9 0.20
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (36 bp):
TTGGACATTTGAAATTGGACCCAATTGGACTTGTAT
Found at i:264699 original size:11 final size:11
Alignment explanation
Indices: 264683--264727 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
264673 ATTTGGACAT
*
264683 TTTAAATTTAA
1 TTTAAAATTAA
*
264694 TTTAAAATAAA
1 TTTAAAATTAA
*
264705 TTTAAAATCAA
1 TTTAAAATTAA
*
264716 TTTAAACTTAA
1 TTTAAAATTAA
264727 T
1 T
264728 ATGAATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAATTAA
Found at i:265549 original size:33 final size:32
Alignment explanation
Indices: 265504--265572 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
265494 AATATTTGGT
*
265504 ACTTAAATTTTTTTTACGCAATTTGATACCTGA
1 ACTTAAATTTTTTTT-CGCAATTTGATACCTAA
**
265537 ACTTGAAA-TTTTTTTCTTAATTTGATACCTAA
1 ACTT-AAATTTTTTTTCGCAATTTGATACCTAA
265569 ACTT
1 ACTT
265573 TTTTTTTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 18 0.56
33 11 0.34
34 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (32 bp):
ACTTAAATTTTTTTTCGCAATTTGATACCTAA
Found at i:265910 original size:31 final size:30
Alignment explanation
Indices: 265859--265948 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 30
265849 CCCAAAGGTT
*
265859 TAAGTACCAACTTAAAAAAAAGTGTCAAGTA
1 TAAGTACCAAATT-AAAAAAAGTGTCAAGTA
* * *
265890 TAAGTACTAAATTAATAAAAAGTATCAAGTT
1 TAAGTACCAAATTAA-AAAAAGTGTCAAGTA
265921 TGAA-TACCAAATTAAAAAAA-TGTCAAGT
1 T-AAGTACCAAATTAAAAAAAGTGTCAAGT
265949 TTAAATAGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
29 7 0.14
30 7 0.14
31 35 0.69
32 2 0.04
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (30 bp):
TAAGTACCAAATTAAAAAAAGTGTCAAGTA
Found at i:265961 original size:29 final size:30
Alignment explanation
Indices: 265873--265961 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
265863 TACCAACTTA
* *
265873 AAAAAAAGTGTCAAGTATAAGTACTAAATT
1 AAAAAAAGTGTCAAGTTTAAATACTAAATT
* * *
265903 AATAAAAAGTATCAAGTTTGAATACCAAATT
1 AA-AAAAAGTGTCAAGTTTAAATACTAAATT
*
265934 AAAAAAA-TGTCAAGTTTAAATAGTAAAT
1 AAAAAAAGTGTCAAGTTTAAATACTAAAT
265962 GTTATATTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.35
30 7 0.14
31 25 0.51
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (30 bp):
AAAAAAAGTGTCAAGTTTAAATACTAAATT
Found at i:266887 original size:100 final size:102
Alignment explanation
Indices: 266763--266946 Score: 275
Period size: 100 Copynumber: 1.8 Consensus size: 102
266753 ATTTATCTAG
**
266763 AAAAAATCAATTTTTTTTGGTGTTGGCCATTGCATGGTTGACACCCTC-TTTTTGTCAGAT-AAT
1 AAAAAATCAATTTTTTTTGGTGTTGGCCATTGCATGGCCGACACCC-CATTTTTGTCAGATAAAT
* *
266826 TTTTTTTTGTGTTGGCCATGCCCTTATTTATTTGATAA
65 TTTTTTTGGTGCTGGCCATGCCCTTATTTATTTGATAA
* *
266864 AAAAAATCAATTTTTTTT-GTGTTGGTCGTTGCATGGCCGACACCCCATTTTTGTCAGATAAAAT
1 AAAAAATCAATTTTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTTGTCAGAT-AAAT
266928 TTTTTTTGGTGCTGGCCAT
65 TTTTTTTGGTGCTGGCCAT
266947 TGCATGGTCG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
99 1 0.01
100 35 0.47
101 18 0.24
102 20 0.27
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (102 bp):
AAAAAATCAATTTTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTTGTCAGATAAATT
TTTTTTGGTGCTGGCCATGCCCTTATTTATTTGATAA
Found at i:266950 original size:54 final size:53
Alignment explanation
Indices: 266872--266980 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 53
266862 AAAAAAAATC
* * * *
266872 AATTTTTTTTGTGTTGGTCGTTGCATGGCCGACACC-CCATTTTTGTCAGATAA
1 AATTTTTTTTGTGCTGGCCATTGCATGGCCGACACCACC-TTTTTATCAGATAA
* *
266925 AATTTTTTTTGGTGCTGGCCATTGCATGGTCGACACCACCTTTTTATCTGATAA
1 AATTTTTTTT-GTGCTGGCCATTGCATGGCCGACACCACCTTTTTATCAGATAA
266979 AA
1 AA
266981 AAATCAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 10 0.21
54 36 0.75
55 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (53 bp):
AATTTTTTTTGTGCTGGCCATTGCATGGCCGACACCACCTTTTTATCAGATAA
Found at i:267004 original size:60 final size:57
Alignment explanation
Indices: 266930--267086 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 57
266920 GATAAAATTT
* *
266930 TTTTTGGTGCTGGCCATTGCA-TGGTCGACACCACCTTT-TTATCTGATAAAAAAATCAAA
1 TTTTTGGTGTTGGCCA-TGCATTGGTCGACACCA-CTTTATTATCAGATAAAAAAA-C-AA
* *
266989 TTTATTGGTGTTGGCCATGCATTGGCCGACACCACTATTAGTTGTCAGATAAAAAAACAA
1 TTT-TTGGTGTTGGCCATGCATTGGTCGACACCACT-TTA-TTATCAGATAAAAAAACAA
* *
267049 TTTTTTGTGTTGGCCATGCATTGGTCAACACCAACTTT
1 TTTTTGGTGTTGGCCATGCATTGGTCGACACC-ACTTT
267087 CCTTCCTTTC
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
59 37 0.44
60 33 0.39
61 1 0.01
62 14 0.16
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (57 bp):
TTTTTGGTGTTGGCCATGCATTGGTCGACACCACTTTATTATCAGATAAAAAAACAA
Found at i:272510 original size:18 final size:20
Alignment explanation
Indices: 272487--272523 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
272477 TTTGAATTTC
272487 TTAAAAGTT-AAAA-TAGAG
1 TTAAAAGTTGAAAACTAGAG
272505 TTAAAAGTTGAAAACTAGA
1 TTAAAAGTTGAAAACTAGA
272524 TTACTTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.27
Consensus pattern (20 bp):
TTAAAAGTTGAAAACTAGAG
Found at i:277728 original size:18 final size:20
Alignment explanation
Indices: 277705--277743 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
277695 TTTGAATTTC
277705 TTAAAAGTT-AAAA-TAGAT
1 TTAAAAGTTGAAAACTAGAT
277723 TTAAAAGTTGAAAACTAGAT
1 TTAAAAGTTGAAAACTAGAT
277743 T
1 T
277744 ACTTCTACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (20 bp):
TTAAAAGTTGAAAACTAGAT
Found at i:285626 original size:16 final size:16
Alignment explanation
Indices: 285605--285646 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
285595 ATACATATAT
285605 TTTTTCTTATTTTCCC
1 TTTTTCTTATTTTCCC
*
285621 TTTTTCTCT-TTTTCTC
1 TTTTTCT-TATTTTCCC
*
285637 TTTTTTTTAT
1 TTTTTCTTAT
285647 GTGACTGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTATTTTCCC
Found at i:286697 original size:15 final size:15
Alignment explanation
Indices: 286674--286707 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
286664 ACTTCTGTTC
*
286674 CTTCCTTTCTTTCTT
1 CTTCCTTTCCTTCTT
*
286689 CTTCTTTTCCTTCTT
1 CTTCCTTTCCTTCTT
286704 CTTC
1 CTTC
286708 ATCCACTTCT
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTCCTTTCCTTCTT
Found at i:290523 original size:24 final size:24
Alignment explanation
Indices: 290491--290538 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
290481 TACTTTCGCT
290491 CTATCCACTTCAATGCCTTGACTA
1 CTATCCACTTCAATGCCTTGACTA
290515 CTATCCACTTCAATGCCTTGACTA
1 CTATCCACTTCAATGCCTTGACTA
290539 GAAATGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.08, T:0.33
Consensus pattern (24 bp):
CTATCCACTTCAATGCCTTGACTA
Found at i:302847 original size:18 final size:18
Alignment explanation
Indices: 302818--302868 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
302808 GTGGCTCTAT
* *
302818 TTCTTCAAGATCTTCTTC
1 TTCTTCAGGATCTTCCTC
*
302836 TTCTTTAGGATCTTCCTC
1 TTCTTCAGGATCTTCCTC
*
302854 TTCTTCATGATCTTC
1 TTCTTCAGGATCTTC
302869 ACTTGAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.27, G:0.08, T:0.51
Consensus pattern (18 bp):
TTCTTCAGGATCTTCCTC
Found at i:303805 original size:26 final size:26
Alignment explanation
Indices: 303755--303806 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
303745 GTATAAAATA
*
303755 TTAACAATTTAAAATAAATTAAAAAG
1 TTAACAATTTAAAACAAATTAAAAAG
303781 TTAACAATTT-AAACAAATTAGAAAAG
1 TTAACAATTTAAAACAAATTA-AAAAG
303807 AATTTCCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (26 bp):
TTAACAATTTAAAACAAATTAAAAAG
Found at i:320885 original size:62 final size:61
Alignment explanation
Indices: 320779--320901 Score: 228
Period size: 62 Copynumber: 2.0 Consensus size: 61
320769 AAGCCATAAT
*
320779 CGGATCCTCTCTTGTTAATTTTTTTTTGTATATTTTGATCCTTGAAATTTGGTGCATGTAA
1 CGGATCCTCTCTTGTTAATTTTTTTTTGTATATTTTGATCCTTGAAATTTCGTGCATGTAA
320840 CGGATCCTCTCTTGTTAATTTTTTTTTTGTATATTTTGATCCTTGAAATTTCGTGCATGTAA
1 CGGATCCTCTCTTGTTAA-TTTTTTTTTGTATATTTTGATCCTTGAAATTTCGTGCATGTAA
320902 TCTAGTAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 18 0.30
62 42 0.70
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (61 bp):
CGGATCCTCTCTTGTTAATTTTTTTTTGTATATTTTGATCCTTGAAATTTCGTGCATGTAA
Found at i:321586 original size:20 final size:20
Alignment explanation
Indices: 321561--321649 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
321551 ACCTAAGTAT
**
321561 TCAGGCTTTATGCCGGTAAA
1 TCAGGCTTTATGCCGGTGTA
* *
321581 TCAGGCTTTGTGCCGATGTA
1 TCAGGCTTTATGCCGGTGTA
321601 TCAGGCTTTATGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
* *
321621 TCAAGCTTTGTGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
321641 ACAGGCTTT
1 TCAGGCTTT
321650 GTGCGGGATA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (20 bp):
TCAGGCTTTATGCCGGTGTA
Found at i:321606 original size:40 final size:40
Alignment explanation
Indices: 321561--321649 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
321551 ACCTAAGTAT
*
321561 TCAGGCTTTATGCCGGTAAATCAGGCTTTGTGCCGATGTA
1 TCAGGCTTTATGCCGGTAAATCAAGCTTTGTGCCGATGTA
** *
321601 TCAGGCTTTATGCCGGTGTATCAAGCTTTGTGCCGGTGTA
1 TCAGGCTTTATGCCGGTAAATCAAGCTTTGTGCCGATGTA
*
321641 ACAGGCTTT
1 TCAGGCTTT
321650 GTGCGGGATA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (40 bp):
TCAGGCTTTATGCCGGTAAATCAAGCTTTGTGCCGATGTA
Found at i:322542 original size:20 final size:21
Alignment explanation
Indices: 322495--322547 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
322485 CTAAAATGCA
* *
322495 TTCAGGGGCACAAGTGTGATG
1 TTCAGGGGCACAAGAGTGACG
*
322516 TTC-GGGGCACTAGAGT-ACG
1 TTCAGGGGCACAAGAGTGACG
*
322535 TTCAGGGGTACAA
1 TTCAGGGGCACAA
322548 ATGTGCAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.23
Consensus pattern (21 bp):
TTCAGGGGCACAAGAGTGACG
Found at i:342826 original size:17 final size:18
Alignment explanation
Indices: 342796--342836 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
342786 TTGAAAGCAT
*
342796 AAAATA-AAATATAATAG
1 AAAATAGAAATATAAAAG
342813 AAAATAGAAA-ATAAAAG
1 AAAATAGAAATATAAAAG
*
342830 CAAATAG
1 AAAATAG
342837 TTGAGATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAATAGAAATATAAAAG
Found at i:353613 original size:22 final size:23
Alignment explanation
Indices: 353586--353632 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
353576 ATTTTTCGAA
*
353586 CATCAACACTACATATTCAC-AT
1 CATCAACACAACATATTCACTAT
*
353608 CATCAACACAATATATTCACTAT
1 CATCAACACAACATATTCACTAT
353631 CA
1 CA
353633 CATGGCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.28
Consensus pattern (23 bp):
CATCAACACAACATATTCACTAT
Found at i:355240 original size:29 final size:29
Alignment explanation
Indices: 355171--355246 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
355161 TGGGATATTA
*
355171 CACAAGGTA-TCACATATAATAGGTTCTGC
1 CACAAGG-ACTCACATATAACAGGTTCTGC
*
355200 CACAATGACTCACATATAACAGGTTCTGC
1 CACAAGGACTCACATATAACAGGTTCTGC
* *
355229 CACAAGGGCTCACTTATA
1 CACAAGGACTCACATATA
355247 GCAAAACAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (29 bp):
CACAAGGACTCACATATAACAGGTTCTGC
Found at i:355304 original size:30 final size:29
Alignment explanation
Indices: 355248--355332 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
355238 TCACTTATAG
* *
355248 CAAAACAACAACAAAAGGCTCACACATGTAA
1 CAAAACAACCAC-AAAGGCTTACACAT-TAA
* * * *
355279 CAGAACAGCCACAAAGGCTTTCACA-TAT
1 CAAAACAACCACAAAGGCTTACACATTAA
*
355307 CAAAACAACCACAAAGGCTTCCACAT
1 CAAAACAACCACAAAGGCTTACACAT
355333 ATCGGTAACT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
28 24 0.55
30 11 0.25
31 9 0.20
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.13
Consensus pattern (29 bp):
CAAAACAACCACAAAGGCTTACACATTAA
Found at i:355322 original size:28 final size:28
Alignment explanation
Indices: 355282--355335 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
355272 CATGTAACAG
* *
355282 AACAGCCACAAAGGCTTTCACATATCAA
1 AACAACCACAAAGGCTTCCACATATCAA
355310 AACAACCACAAAGGCTTCCACATATC
1 AACAACCACAAAGGCTTCCACATATC
355336 GGTAACTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (28 bp):
AACAACCACAAAGGCTTCCACATATCAA
Found at i:359684 original size:21 final size:22
Alignment explanation
Indices: 359651--359704 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
359641 TAAAATTAAT
** *
359651 ATAATAATTTAATA-CTTAAAA
1 ATAATAAAATAATAGCTCAAAA
359672 ATAATAAAATAATAGTCTCAAAA
1 ATAATAAAATAATAG-CTCAAAA
359695 ATCAATAAAA
1 AT-AATAAAA
359705 ATATCTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAATAAAATAATAGCTCAAAA
Found at i:361497 original size:25 final size:25
Alignment explanation
Indices: 361460--361511 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
361450 CGAAGTACTT
*
361460 AACAGAAGTGCATAAGTGCTGGGGA
1 AACAGAAGCGCATAAGTGCTGGGGA
361485 AACAGAAGCGCATAAGTGCTGGGGA
1 AACAGAAGCGCATAAGTGCTGGGGA
361510 AA
1 AA
361512 TAGTAGGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.35, T:0.13
Consensus pattern (25 bp):
AACAGAAGCGCATAAGTGCTGGGGA
Found at i:361546 original size:22 final size:23
Alignment explanation
Indices: 361513--361566 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
361503 CTGGGGAAAT
*
361513 AGTAGGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTGAAC
361536 AG-AAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTGAAC
361558 AGTAAGCAC
1 AGTAAGCAC
361567 GCTAGCGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCTGAAC
Found at i:366384 original size:22 final size:22
Alignment explanation
Indices: 366358--366481 Score: 212
Period size: 22 Copynumber: 5.6 Consensus size: 22
366348 GAAACAGTAG
366358 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
366380 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
*
366402 GCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCTGAACAGAA
*
366424 GCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCTGAACAGAA
*
366446 GCACACACAATGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
*
366468 GCACACATAGTGCT
1 GCACACACAGTGCT
366482 AAACTGCTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 97 1.00
ACGTcount: A:0.42, C:0.27, G:0.20, T:0.10
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAGAA
Found at i:366407 original size:44 final size:44
Alignment explanation
Indices: 366358--366522 Score: 213
Period size: 44 Copynumber: 3.5 Consensus size: 44
366348 GAAACAGTAG
366358 GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAGAA
* *
366402 GCACACACAGTGCTGAACAAAAGCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAGAA
* *
366446 GCACACACAATGCTGAACAGAAGCACACATAGTGCTAAACTGCTAAACAGAA
1 GCACACACAGTGCTGAACAGAAGCACACACAGTG-----CTG---AACAGAA
366498 GCACACACAGTGCTGAACAGTAAGC
1 GCACACACAGTGCTGAACAG-AAGC
366523 GTGCTAGCGT
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
44 73 0.70
49 3 0.03
52 25 0.24
53 4 0.04
ACGTcount: A:0.42, C:0.27, G:0.20, T:0.11
Consensus pattern (44 bp):
GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAGAA
Found at i:371219 original size:2 final size:2
Alignment explanation
Indices: 371212--371256 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
371202 AATAATATAA
* * *
371212 AC AC AC AC AT AC AC AC AT AC AC AC AC AC AT AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
371254 AC A
1 AC A
371257 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (2 bp):
AC
Found at i:376750 original size:18 final size:18
Alignment explanation
Indices: 376724--376798 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
376714 AAAGGATTAA
*
376724 CATATTGGCTCATTTGAG
1 CATATTGGCTCATTAGAG
*
376742 CATACTGGCTCATTAGAG
1 CATATTGGCTCATTAGAG
* *
376760 CATATTGGCTCGTTGGAG
1 CATATTGGCTCATTAGAG
* * * *
376778 CACATTGACTCGTAAGAG
1 CATATTGGCTCATTAGAG
376796 CAT
1 CAT
376799 TACTGGATCG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (18 bp):
CATATTGGCTCATTAGAG
Found at i:376796 original size:36 final size:36
Alignment explanation
Indices: 376724--376798 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
376714 AAAGGATTAA
* * * *
376724 CATATTGGCTCATTTGAGCATACTGGCTCATTAGAG
1 CATATTGGCTCATTGGAGCACACTGACTCATAAGAG
* * *
376760 CATATTGGCTCGTTGGAGCACATTGACTCGTAAGAG
1 CATATTGGCTCATTGGAGCACACTGACTCATAAGAG
376796 CAT
1 CAT
376799 TACTGGATCG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (36 bp):
CATATTGGCTCATTGGAGCACACTGACTCATAAGAG
Found at i:382070 original size:52 final size:52
Alignment explanation
Indices: 382001--382291 Score: 370
Period size: 52 Copynumber: 5.6 Consensus size: 52
381991 GTTTCATTTA
* * * *
382001 TTACTAACAATGACACATAGTCATTGGACCT-ATTAATTCGTAAAGAAATCAT
1 TTACTCACAATGACACATAGTCATCGGACCTCA-TAATTCGTAAAGGATTCAT
* * * * *
382053 ATACACACAATGCCACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
*
382105 TTACTCACAATGACACATAGTCATCGGACATCATAATTCGTAAAGGATTCAT
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
* * * * *
382157 TTACTCACGATGACACATAGTCATCGAACCTTATAATCCATAAAGGATTCAT
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
*
382209 TTACTCACGATGACACATAGTCATCGGACCTCATAA-TCTGTAAAGGATTCAT
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTC-GTAAAGGATTCAT
* * * *
382261 TTACACACGATGATACATAGTCATCGAACCT
1 TTACTCACAATGACACATAGTCATCGGACCT
382292 TTTTTCATTT
Statistics
Matches: 209, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
51 1 0.00
52 207 0.99
53 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (52 bp):
TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
Found at i:382292 original size:104 final size:104
Alignment explanation
Indices: 382001--382292 Score: 419
Period size: 104 Copynumber: 2.8 Consensus size: 104
381991 GTTTCATTTA
* * * * * *
382001 TTACTAACAATGACACATAGTCATTGGACCT-ATTAATTCGTAAAGAAATCATATACACACAATG
1 TTACTCACAATGACACATAGTCATCGGACCTCA-TAATTCGTAAAGGATTCATTTACACACGATG
* * *
382065 CCACATAGTCATC-AGACCTCATAATCCGTAAAGGATTCAT
65 ACACATAGTCATCGA-ACCTTATAATCCATAAAGGATTCAT
* *
382105 TTACTCACAATGACACATAGTCATCGGACATCATAATTCGTAAAGGATTCATTTACTCACGATGA
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATTTACACACGATGA
382170 CACATAGTCATCGAACCTTATAATCCATAAAGGATTCAT
66 CACATAGTCATCGAACCTTATAATCCATAAAGGATTCAT
*
382209 TTACTCACGATGACACATAGTCATCGGACCTCATAA-TCTGTAAAGGATTCATTTACACACGATG
1 TTACTCACAATGACACATAGTCATCGGACCTCATAATTC-GTAAAGGATTCATTTACACACGATG
*
382273 ATACATAGTCATCGAACCTT
65 ACACATAGTCATCGAACCTT
382293 TTTTCATTTA
Statistics
Matches: 170, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
103 2 0.01
104 166 0.98
105 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (104 bp):
TTACTCACAATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATTTACACACGATGA
CACATAGTCATCGAACCTTATAATCCATAAAGGATTCAT
Found at i:383990 original size:7 final size:7
Alignment explanation
Indices: 383968--384000 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
383958 ACTAAATTTT
383968 AATTCAAA
1 AATTC-AA
383976 AATT-AA
1 AATTCAA
383982 AATTCAA
1 AATTCAA
383989 AATTCAA
1 AATTCAA
383996 AATTC
1 AATTC
384001 TATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTCAA
Found at i:390481 original size:5 final size:5
Alignment explanation
Indices: 390471--390543 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
390461 GGGTAGGACT
* * *
390471 TGATA TGATA TGATA T-ACTG TGAT- TCGATA TGATA TGATT TGTTA TGATA
1 TGATA TGATA TGATA TGA-TA TGATA T-GATA TGATA TGATA TGATA TGATA
* * *
390521 CGTTAA TGATA TGATA AGATA TG
1 TGAT-A TGATA TGATA TGATA TG
390544 CTCTGATTTG
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
4 2 0.04
5 45 0.87
6 5 0.10
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (5 bp):
TGATA
Found at i:390519 original size:25 final size:25
Alignment explanation
Indices: 390472--390536 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
390462 GGTAGGACTT
* *
390472 GATATGATATGATATACTGTGATTC
1 GATATGATATGATATACTATGATAC
* **
390497 GATATGATATGATTTGTTATGATAC
1 GATATGATATGATATACTATGATAC
*
390522 GTTAATGATATGATA
1 GAT-ATGATATGATA
390537 AGATATGCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.42
Consensus pattern (25 bp):
GATATGATATGATATACTATGATAC
Found at i:404694 original size:16 final size:17
Alignment explanation
Indices: 404673--404704 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
404663 AGTTAGCATT
404673 CTTGCA-TTTTATTGTG
1 CTTGCATTTTTATTGTG
404689 CTTGCATTTTTATTGT
1 CTTGCATTTTTATTGT
404705 CACTGCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (17 bp):
CTTGCATTTTTATTGTG
Found at i:409691 original size:5 final size:5
Alignment explanation
Indices: 409675--409725 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
409665 GGGGAAGGAC
* * * *
409675 ATGAT ATAAT ATGAT ATGAT ATGTT ATGTT ATGAT A-CATT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGA-T ATGAT ATGAT
409725 A
1 A
409726 AGACATGCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
4 1 0.03
5 36 0.95
6 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (5 bp):
ATGAT
Found at i:409695 original size:15 final size:15
Alignment explanation
Indices: 409675--409725 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
409665 GGGGAAGGAC
*
409675 ATGATATAATATGAT
1 ATGATATATTATGAT
* *
409690 ATGATATGTTATGTT
1 ATGATATATTATGAT
*
409705 ATGATACATTATGAT
1 ATGATATATTATGAT
409720 ATGATA
1 ATGATA
409726 AGACATGCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (15 bp):
ATGATATATTATGAT
Found at i:412960 original size:18 final size:20
Alignment explanation
Indices: 412923--412960 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
412913 GTTTAAATTT
412923 TATTTTACTCATAATTTAATC
1 TATTTTACTCAT-ATTTAATC
412944 TATTTT-CTCAT-TTTAAT
1 TATTTTACTCATATTTAAT
412961 ATCATACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTACTCATATTTAATC
Found at i:421441 original size:7 final size:7
Alignment explanation
Indices: 421429--421454 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
421419 CCATTCCTAA
421429 TCATCCC
1 TCATCCC
421436 TCATCCC
1 TCATCCC
421443 TCATCCC
1 TCATCCC
421450 TCATC
1 TCATC
421455 TTTCTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:429281 original size:29 final size:29
Alignment explanation
Indices: 429239--429296 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
429229 TTTTAGGACC
429239 CTTAGAAAACAATAGGACTTAAAAATCTT
1 CTTAGAAAACAATAGGACTTAAAAATCTT
*
429268 CTTAGAAAATAATAGGACTTAAAAATCTT
1 CTTAGAAAACAATAGGACTTAAAAATCTT
429297 ATTTTTGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (29 bp):
CTTAGAAAACAATAGGACTTAAAAATCTT
Done.