Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008363.1 Hibiscus syriacus cultivar Beakdansim tig00111102_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: 118867
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3911 original size:23 final size:23
Alignment explanation
Indices: 3863--3952 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
3853 CACCACAGCT
* * *
3863 CGTATAAATGCA-CGAAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCG
* *
3885 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGTAGTGCCG
*
3908 CGTAGAAATGCACTGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
3931 CGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
3953 ATATAAGGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 10 0.18
23 47 0.82
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCG
Found at i:3935 original size:46 final size:45
Alignment explanation
Indices: 3863--3951 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 45
3853 CACCACAGCT
* * *
3863 CGTATAAATGCACGAAGTGCCACGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACGAAGTGCCACGTAGAAATGCACCGAAGTGCTG
* *
3908 CGTAGAAATGCACTGTAGTGCCGCGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCAC-GAAGTGCCACGTAGAAATGCACCGAAGTGC
3952 CATATAAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
45 12 0.32
46 26 0.68
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (45 bp):
CGTAGAAATGCACGAAGTGCCACGTAGAAATGCACCGAAGTGCTG
Found at i:4347 original size:2 final size:2
Alignment explanation
Indices: 4340--4372 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4330 TGTCTTATCC
4340 TA TA 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 TA TA T
4373 CACATATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5540 original size:24 final size:20
Alignment explanation
Indices: 5483--5560 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
5473 TTTCCCTTGA
*
5483 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
5503 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
5526 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
5547 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
5561 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:9949 original size:27 final size:27
Alignment explanation
Indices: 9919--9972 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
9909 GGTCACTGAA
*
9919 TGTGGAATGTTGTTGTTGTACATGGTG
1 TGTGGAATGTTATTGTTGTACATGGTG
*
9946 TGTGGAATGTTATTGTTGTGCATGGTG
1 TGTGGAATGTTATTGTTGTACATGGTG
9973 CATGGTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.37, T:0.44
Consensus pattern (27 bp):
TGTGGAATGTTATTGTTGTACATGGTG
Found at i:13174 original size:153 final size:154
Alignment explanation
Indices: 12909--13202 Score: 500
Period size: 153 Copynumber: 1.9 Consensus size: 154
12899 TCGTAAACCG
*
12909 TATAAATATAACTATTCGAACTTTTATCCTCTAATGAGAACAATAATTCTTATTATCATTAAGGT
1 TATAAATATAACTATTCGAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGT
*
12974 AACTCAAAAAATATTAGAATGCATTAGTTAAATATGTTCTTATATACCAAAACGATTAATTATAA
66 AACTCAAAAAATATTAGAATGCAATAGTTAAATATGTTCTTATATACCAAAACGATTAATTATAA
13039 AAAAT-ATCACTATTCATACACCA
131 AAAATGATCACTATTCATACACCA
* * *
13062 TATAAATATAACTATTCTAACTTTTATTCTCTAACGAGAACAATGATTCTTATTATCATTAAGGT
1 TATAAATATAACTATTCGAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGT
* * * *
13127 AACTCAATAAATATTAGAATGGAATAGTTAAATATGTTGTTATATACCTAAACGATTAATTATAA
66 AACTCAAAAAATATTAGAATGCAATAGTTAAATATGTTCTTATATACCAAAACGATTAATTATAA
13192 AAAATGATCAC
131 AAAATGATCAC
13203 GTTAGCGTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
153 126 0.96
154 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (154 bp):
TATAAATATAACTATTCGAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGT
AACTCAAAAAATATTAGAATGCAATAGTTAAATATGTTCTTATATACCAAAACGATTAATTATAA
AAAATGATCACTATTCATACACCA
Found at i:15921 original size:36 final size:36
Alignment explanation
Indices: 15871--15946 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
15861 GTTATAGCAA
*
15871 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
15907 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
15943 AAAA
1 AAAA
15947 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:20437 original size:15 final size:15
Alignment explanation
Indices: 20419--20448 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20409 CCACGGTGCT
20419 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
20434 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
20449 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:20921 original size:36 final size:36
Alignment explanation
Indices: 20871--20946 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
20861 GTTATAGCAA
*
20871 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
20907 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
20943 AAAA
1 AAAA
20947 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:22132 original size:27 final size:26
Alignment explanation
Indices: 22077--22132 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
22067 ATATAACAAA
*
22077 TAAGTACCTAAAGTATCTTTTCTATT
1 TAAGTACCTAAAGTATCTTTTCTAGT
*
22103 TAAGTACTTAAAGTTATCTTTTTCT-GT
1 TAAGTACCTAAAG-TATC-TTTTCTAGT
22130 TAA
1 TAA
22133 AATAGGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 12 0.46
27 8 0.31
28 6 0.23
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (26 bp):
TAAGTACCTAAAGTATCTTTTCTAGT
Found at i:22155 original size:29 final size:29
Alignment explanation
Indices: 22121--22180 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
22111 TAAAGTTATC
* *
22121 TTTTTCTGTTAAAATAGGTATCTAAAATA
1 TTTTTCGGTCAAAATAGGTATCTAAAATA
*
22150 TTTTTCGGTCAAAATAGGTATCTAAAGTA
1 TTTTTCGGTCAAAATAGGTATCTAAAATA
22179 TT
1 TT
22181 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTTCGGTCAAAATAGGTATCTAAAATA
Found at i:22301 original size:28 final size:28
Alignment explanation
Indices: 22265--22343 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
22255 AAAAAGTTTG
* * *
22265 AATAGTTTAGGTACCTATTTTGACATAA
1 AATACTTTAAGTACATATTTTGACATAA
*
22293 AATACTTTATGTACATATTTTGACATAA
1 AATACTTTAAGTACATATTTTGACATAA
22321 AATACTTTAAGTACATATTTTGA
1 AATACTTTAAGTACATATTTTGA
22344 TTTATTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (28 bp):
AATACTTTAAGTACATATTTTGACATAA
Found at i:22629 original size:21 final size:21
Alignment explanation
Indices: 22605--22656 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
22595 TAAGGGTTCG
22605 TACAAATTGTGGTGTACGGAT
1 TACAAATTGTGGTGTACGGAT
*
22626 TACAAATTGCGGTGTACGGAT
1 TACAAATTGTGGTGTACGGAT
22647 TACAAATTGT
1 TACAAATTGT
22657 CCATATCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (21 bp):
TACAAATTGTGGTGTACGGAT
Found at i:23110 original size:44 final size:45
Alignment explanation
Indices: 23046--23159 Score: 176
Period size: 44 Copynumber: 2.6 Consensus size: 45
23036 TTCTATCCAA
* * *
23046 AATTATATGGATTTTGAATTTAAAATAAATAAAAAATTA-GATAT
1 AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
**
23090 AATTATATGAATTTAAAATTTAAAATAAATAAAAAAATAGGATAC
1 AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
23135 AATTATATGAATTTTGAATTTAAAA
1 AATTATATGAATTTTGAATTTAAAA
23160 GAGATAATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 35 0.56
45 27 0.44
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (45 bp):
AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
Found at i:23173 original size:45 final size:43
Alignment explanation
Indices: 23046--23159 Score: 165
Period size: 45 Copynumber: 2.6 Consensus size: 43
23036 TTCTATCCAA
* *
23046 AATTATATGGATTTTGAATTTAAAATAAATAAAAAATTAGATAT
1 AATTATATGAATTTTGAATTTAAAATAAATAAAAAA-TAGATAC
**
23090 AATTATATGAATTTAAAATTTAAAATAAATAAAAAAATAGGATAC
1 AATTATATGAATTTTGAATTTAAAATAAAT-AAAAAATA-GATAC
23135 AATTATATGAATTTTGAATTTAAAA
1 AATTATATGAATTTTGAATTTAAAA
23160 GAGATAATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
44 29 0.47
45 33 0.53
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (43 bp):
AATTATATGAATTTTGAATTTAAAATAAATAAAAAATAGATAC
Found at i:23694 original size:28 final size:31
Alignment explanation
Indices: 23641--23720 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 31
23631 AATTCTCAAA
*
23641 ATAAAATGATATTTATAATTTGATG-ACTAAT
1 ATAAAAT-ATATTTATAATTTGATGAACCAAT
*
23672 ATAAAATATTTTTA-AATTT-ATGAACCAAT
1 ATAAAATATATTTATAATTTGATGAACCAAT
* * *
23701 TTAAAATAAAGTTATAATTT
1 ATAAAATATATTTATAATTT
23721 AGACATTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 3 0.07
29 20 0.49
30 11 0.27
31 7 0.17
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (31 bp):
ATAAAATATATTTATAATTTGATGAACCAAT
Found at i:30626 original size:19 final size:19
Alignment explanation
Indices: 30602--30641 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
30592 ACACTTCTCT
30602 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
30621 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
30640 CA
1 CA
30642 CACTTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:32495 original size:9 final size:9
Alignment explanation
Indices: 32483--32514 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
32473 GAAAAACAAA
32483 AAAAAAATT
1 AAAAAAATT
32492 AAAAAAATT
1 AAAAAAATT
32501 AAAAAAATT
1 AAAAAAATT
*
32510 TAAAA
1 AAAAA
32515 TTTTCAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAAAATT
Found at i:32495 original size:10 final size:10
Alignment explanation
Indices: 32482--32514 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
32472 TGAAAAACAA
32482 AAAAAAAATT
1 AAAAAAAATT
32492 -AAAAAAATT
1 AAAAAAAATT
*
32501 AAAAAAATTT
1 AAAAAAAATT
32511 AAAA
1 AAAA
32515 TTTTCAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:36572 original size:21 final size:20
Alignment explanation
Indices: 36530--36573 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
36520 TCAAAAGAAG
*
36530 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
36550 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
36571 TTT
1 TTT
36574 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:40697 original size:22 final size:21
Alignment explanation
Indices: 40669--40732 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
40659 GTCGAGGGTT
*
40669 TCATAGGTCATTCGGGGACAAC
1 TCATAGGTCCTTC-GGGACAAC
*
40691 TCATAGGTCCTTCGGGACATAT
1 TCATAGGTCCTTCGGGACA-AC
*
40713 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
40733 AATTTCATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.18
22 31 0.82
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:41348 original size:22 final size:21
Alignment explanation
Indices: 41277--41332 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
41267 CCGAAATTAT
*
41277 TGTAGCAAGGGTATCGGTACAC
1 TGTAGC-AGGGTATCAGTACAC
41299 TGTAGCAGGGTATCAGTACAC
1 TGTAGCAGGGTATCAGTACAC
41320 TGTAGCAGGGTAT
1 TGTAGCAGGGTAT
41333 TGATACCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (21 bp):
TGTAGCAGGGTATCAGTACAC
Found at i:41427 original size:19 final size:19
Alignment explanation
Indices: 41405--41445 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41395 ACTGTTCACG
*
41405 ATATTGT-TCAGTACTGTTC
1 ATATTGTAT-AGTACTATTC
41424 ATATTGTATAGTACTATTC
1 ATATTGTATAGTACTATTC
41443 ATA
1 ATA
41446 AAACATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (19 bp):
ATATTGTATAGTACTATTC
Found at i:44680 original size:19 final size:19
Alignment explanation
Indices: 44653--44690 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44643 TGTTTAAAAC
*
44653 TATCGATACTTATATAAAG
1 TATCAATACTTATATAAAG
44672 TATCAATACTTATATAAAG
1 TATCAATACTTATATAAAG
44691 CATCGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (19 bp):
TATCAATACTTATATAAAG
Found at i:44701 original size:19 final size:19
Alignment explanation
Indices: 44654--44701 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44644 GTTTAAAACT
* *
44654 ATCGATACTTATATAAAGT
1 ATCGAAACTTATATAAAGC
44673 ATC-AATACTTATATAAAGC
1 ATCGAA-ACTTATATAAAGC
44692 ATCGAAACTT
1 ATCGAAACTT
44702 TTGCAGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.88
20 2 0.08
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (19 bp):
ATCGAAACTTATATAAAGC
Found at i:45857 original size:48 final size:48
Alignment explanation
Indices: 45793--45885 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
45783 AAGTGACTAG
*
45793 GTTGCCTCCTTTAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
1 GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
* *
45841 GTTGTCTCCTTCAGCTGTTTTAACACCCCTCACATCAGTGTTTAA
1 GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAA
45886 AAAGGCGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.39
Consensus pattern (48 bp):
GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
Found at i:50402 original size:15 final size:15
Alignment explanation
Indices: 50382--50434 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
50372 TCAGCATTTG
50382 AATCATTCATCGCTT
1 AATCATTCATCGCTT
50397 AATCATTCAGT-GCTT
1 AATCATTCA-TCGCTT
*
50412 AATCATTCAGCGCTT
1 AATCATTCATCGCTT
50427 AATCATTC
1 AATCATTC
50435 TGAAGTAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 34 0.97
16 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (15 bp):
AATCATTCATCGCTT
Found at i:56359 original size:92 final size:93
Alignment explanation
Indices: 56209--56385 Score: 250
Period size: 92 Copynumber: 1.9 Consensus size: 93
56199 ATCAATCACA
* * **
56209 ACATGGTTTAAAGTTAAAAGCAATATGAGCATGAAAACTTAAAAGACACGAAAATCTACATGAAC
1 ACATGGTTTAAAGTTAAAAGCAAAAAGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAAC
*
56274 AGGCTTTGGAAGATGTATGACAATCATT
66 AGACTTTGGAAGATGTATGACAATCATT
** * *
56302 ACATGGTTTAAAGTT-AAAG-AAAAGAGAGCATGAAAACTTACGAGGCACGAAAATCTACGCCAA
1 ACATGGTTTAAAGTTAAAAGCAAAA-AGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAA
56365 CAGACTTTGGAAGATGTATGA
65 CAGACTTTGGAAGATGTATGA
56386 AACTGCGAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
91 3 0.04
92 56 0.76
93 15 0.20
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.23
Consensus pattern (93 bp):
ACATGGTTTAAAGTTAAAAGCAAAAAGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAAC
AGACTTTGGAAGATGTATGACAATCATT
Found at i:62402 original size:46 final size:46
Alignment explanation
Indices: 62346--62434 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
62336 CAGTACTAGT
62346 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
1 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
62392 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCA
1 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCA
62435 CTTGAACGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (46 bp):
GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
Found at i:64813 original size:33 final size:33
Alignment explanation
Indices: 64771--64837 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
64761 TGTGAAGGGT
64771 TGAACTTTAATTTTCACCATTTAACTATTTTTA
1 TGAACTTTAATTTTCACCATTTAACTATTTTTA
64804 TGAACTTTAATTTTCACCATTTAACTATTTTTA
1 TGAACTTTAATTTTCACCATTTAACTATTTTTA
64837 T
1 T
64838 TTTATGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (33 bp):
TGAACTTTAATTTTCACCATTTAACTATTTTTA
Found at i:65252 original size:2 final size:2
Alignment explanation
Indices: 65245--65269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65235 ATTTTGAAAT
65245 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 T
65270 TAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65253 original size:22 final size:22
Alignment explanation
Indices: 65210--65257 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
65200 ATATAAATAA
*
65210 ATATTCTTGAATTTATTCATAT
1 ATATTCTTGAAATTATTCATAT
65232 GATATT-TTGAAATTATAT-ATAT
1 -ATATTCTTGAAATTAT-TCATAT
65254 ATAT
1 ATAT
65258 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (22 bp):
ATATTCTTGAAATTATTCATAT
Found at i:67773 original size:29 final size:29
Alignment explanation
Indices: 67741--67822 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
67731 GCACCCATTT
67741 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
67770 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
67799 CGAATTAATTCCCAGAATAGCACC
1 CGAATTAATTCCCAGAATAGCACC
67823 GGTCAACGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (29 bp):
CGAATTAATTCCCAGAATAGCACCAAAAC
Found at i:67855 original size:20 final size:19
Alignment explanation
Indices: 67830--67925 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 19
67820 ACCGGTCAAC
67830 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
67850 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
67870 GGTCAACGGT--CGGGTCG
1 GGTCAACGGTAACGGGTCG
*
67887 GGTAAACTGGT--CGGGTCG
1 GGTCAAC-GGTAACGGGTCG
*
67905 GGTAAACGGGTAAACGGGTCG
1 GGTCAAC-GGT-AACGGGTCG
67926 TGACCGGTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
17 13 0.19
18 20 0.29
20 30 0.43
21 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.17
Consensus pattern (19 bp):
GGTCAACGGTAACGGGTCG
Found at i:67880 original size:7 final size:7
Alignment explanation
Indices: 67822--67865 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
67812 AGAATAGCAC
67822 CGGTCAA
1 CGGTCAA
67829 CGGTCAA
1 CGGTCAA
67836 CGGTCAA
1 CGGTCAA
67843 CGGGTC--
1 C-GGTCAA
*
67849 GGGTCAA
1 CGGTCAA
67856 CGGTCAA
1 CGGTCAA
67863 CGG
1 CGG
67866 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
7 24 0.75
8 4 0.12
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:67882 original size:12 final size:13
Alignment explanation
Indices: 67857--67885 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
67847 TCGGGTCAAC
67857 GGTCAACGGGTCG
1 GGTCAACGGGTCG
67870 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
67882 GGTC
1 GGTC
67886 GGGTAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:67900 original size:18 final size:17
Alignment explanation
Indices: 67843--67913 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
67833 CAACGGTCAA
*
67843 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
*
67860 CAACGGGTCGGGTCAACGGT
1 ---CGGGTCGGGTAAACGGT
67880 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
67898 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
67914 GTAAACGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:67958 original size:11 final size:10
Alignment explanation
Indices: 67928--67979 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
67918 ACGGGTCGTG
67928 ACCGGTC-AA
1 ACCGGTCAAA
67937 ACCGGTCAAA
1 ACCGGTCAAA
67947 ACCGGTTCAAA
1 ACCGG-TCAAA
*
67958 ACCGGT-TAA
1 ACCGGTCAAA
67967 ACCGGTCAAA
1 ACCGGTCAAA
67977 ACC
1 ACC
67980 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:75115 original size:29 final size:29
Alignment explanation
Indices: 75097--75178 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
75087 GCACCCATTT
75097 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
75126 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
75155 CGAATTAATTCCCAGAATAGCACC
1 CGAATTAATTCCCAGAATAGCACC
75179 GGTCAACGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (29 bp):
CGAATTAATTCCCAGAATAGCACCAAAAC
Found at i:75211 original size:20 final size:19
Alignment explanation
Indices: 75186--75281 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 19
75176 ACCGGTCAAC
75186 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
75206 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGT-AACGGGTCG
75226 GGTCAACGGT--CGGGTCG
1 GGTCAACGGTAACGGGTCG
*
75243 GGTAAACTGGT--CGGGTCG
1 GGTCAAC-GGTAACGGGTCG
*
75261 GGTAAACGGGTAAACGGGTCG
1 GGTCAAC-GGT-AACGGGTCG
75282 TGACCGGTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
17 13 0.19
18 20 0.29
20 30 0.43
21 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.17
Consensus pattern (19 bp):
GGTCAACGGTAACGGGTCG
Found at i:75236 original size:7 final size:7
Alignment explanation
Indices: 75178--75221 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
75168 AGAATAGCAC
75178 CGGTCAA
1 CGGTCAA
75185 CGGTCAA
1 CGGTCAA
75192 CGGTCAA
1 CGGTCAA
75199 CGGGTC--
1 C-GGTCAA
*
75205 GGGTCAA
1 CGGTCAA
75212 CGGTCAA
1 CGGTCAA
75219 CGG
1 CGG
75222 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
7 24 0.75
8 4 0.12
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:75238 original size:12 final size:13
Alignment explanation
Indices: 75213--75241 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
75203 TCGGGTCAAC
75213 GGTCAACGGGTCG
1 GGTCAACGGGTCG
75226 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
75238 GGTC
1 GGTC
75242 GGGTAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:75256 original size:18 final size:17
Alignment explanation
Indices: 75199--75269 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
75189 CAACGGTCAA
*
75199 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
*
75216 CAACGGGTCGGGTCAACGGT
1 ---CGGGTCGGGTAAACGGT
75236 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
75254 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
75270 GTAAACGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:75298 original size:9 final size:9
Alignment explanation
Indices: 75284--75331 Score: 69
Period size: 9 Copynumber: 5.1 Consensus size: 9
75274 ACGGGTCGTG
75284 ACCGGTCAA
1 ACCGGTCAA
75293 ACCGGTCAA
1 ACCGGTCAA
75302 ACCGGTTCAAA
1 ACCGG-TC-AA
*
75313 ACCGGTTAA
1 ACCGGTCAA
75322 ACCGGTCAA
1 ACCGGTCAA
75331 A
1 A
75332 ACCAGTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 25 0.71
10 3 0.09
11 7 0.20
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:75316 original size:20 final size:19
Alignment explanation
Indices: 75284--75334 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
75274 ACGGGTCGTG
75284 ACCGGTC-AAACCGGTCAA
1 ACCGGTCAAAACCGGTCAA
*
75302 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTCAA
75322 ACCGGTCAAAACC
1 ACCGGTCAAAACC
75335 AGTTTCCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 15 0.50
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTCAA
Found at i:85330 original size:18 final size:17
Alignment explanation
Indices: 85307--85341 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
85297 AAACCTGTCA
85307 GACTGGATGTATGGTTAG
1 GACTGG-TGTATGGTTAG
*
85325 GACTGGTTTATGGTTAG
1 GACTGGTGTATGGTTAG
85342 TGTTACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (17 bp):
GACTGGTGTATGGTTAG
Found at i:86829 original size:35 final size:36
Alignment explanation
Indices: 86778--86849 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
86768 GATGGAGAAA
* *
86778 GTTTCGTTCTTTTCTTTC-TGTCTAGTTTGTGTGTG
1 GTTTCGTTCTTCTCTTTCTTGTCTAATTTGTGTGTG
*
86813 GTTTTGTTCTTCTCTTTCTTTGTCTAATTTGTGTGTG
1 GTTTCGTTCTTCTCTTTC-TTGTCTAATTTGTGTGTG
86850 CTTTATCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 16 0.50
37 16 0.50
ACGTcount: A:0.04, C:0.14, G:0.21, T:0.61
Consensus pattern (36 bp):
GTTTCGTTCTTCTCTTTCTTGTCTAATTTGTGTGTG
Found at i:89699 original size:31 final size:32
Alignment explanation
Indices: 89658--89718 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
89648 AAGTATAAAT
89658 TATGTGTTTAATATATAAATTATTAGTTTTGG
1 TATGTGTTTAATATATAAATTATTAGTTTTGG
* * *
89690 TATGT-TTTAATATCTAAATTTTTATTTTT
1 TATGTGTTTAATATATAAATTATTAGTTTT
89719 TTTAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.59
Consensus pattern (32 bp):
TATGTGTTTAATATATAAATTATTAGTTTTGG
Found at i:90446 original size:21 final size:21
Alignment explanation
Indices: 90429--90488 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
90419 ATATTTAGGA
*
90429 TTTAGAGTTTGTGGTTTAGAG
1 TTTAGAGTTTATGGTTTAGAG
* * *
90450 TTTGGAGTTTATGGTTTATAA
1 TTTAGAGTTTATGGTTTAGAG
* *
90471 TTTATAGTTTATGTTTTA
1 TTTAGAGTTTATGGTTTA
90489 AGGGTGTAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTAGAGTTTATGGTTTAGAG
Found at i:98005 original size:29 final size:29
Alignment explanation
Indices: 97959--98039 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
97949 ACCGTTAACC
*
97959 GGTGCTATTATGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
97988 GGTGCTATTCTGGCAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
98017 GGTGCTATTCTGGTAATTAATTC
1 GGTGCTATTCTGGTAAATAATTC
98040 AAAATGGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:98072 original size:29 final size:29
Alignment explanation
Indices: 98017--98084 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
98007 ATTCGGTTTT
* * *
98017 GGTGCTATTCTGGTAATTAATTCAAAATG
1 GGTGCTATTTTGGTAAATAATTCAAAAAG
* *
98046 GGTGCTATTTTGGTAAATATTTTAAAAAG
1 GGTGCTATTTTGGTAAATAATTCAAAAAG
*
98075 GGTACTATTT
1 GGTGCTATTT
98085 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGTAAATAATTCAAAAAG
Found at i:101212 original size:19 final size:16
Alignment explanation
Indices: 101175--101206 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
101165 TTCAAGAGTC
101175 AAGCAAATTGATATTT
1 AAGCAAATTGATATTT
101191 AAGCAAATTGATATTT
1 AAGCAAATTGATATTT
101207 TTTAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AAGCAAATTGATATTT
Found at i:110285 original size:20 final size:20
Alignment explanation
Indices: 110260--110628 Score: 476
Period size: 20 Copynumber: 18.4 Consensus size: 20
110250 GATTTTCCAT
* ** *
110260 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
110280 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
110300 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
110320 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
110340 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
110360 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
110380 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
110400 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
110420 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
110440 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
110460 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
110480 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
110500 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
110520 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
110540 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
110560 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
110580 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
110600 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
110620 AATCACAAC
1 AATCGCAAC
110629 ACTGAAATTT
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.01
20 303 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:111339 original size:24 final size:24
Alignment explanation
Indices: 111300--111346 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
111290 AAATTTGGTC
111300 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
111324 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
111347 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:111538 original size:12 final size:12
Alignment explanation
Indices: 111521--111545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111511 ATATAATCCT
111521 GAAGAAGAAAAA
1 GAAGAAGAAAAA
111533 GAAGAAGAAAAA
1 GAAGAAGAAAAA
111545 G
1 G
111546 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:113861 original size:19 final size:19
Alignment explanation
Indices: 113839--114142 Score: 331
Period size: 19 Copynumber: 17.4 Consensus size: 19
113829 CGGAAAATAC
*
113839 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113858 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
113872 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
113892 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
113906 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
113925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113944 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
113958 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
113976 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
* *
113994 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
114008 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
114027 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
114046 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
114065 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
114084 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
114098 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
114117 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
114135 AATCGCAA
1 AATCGCAA
114143 CGAGATAATC
Statistics
Matches: 244, Mismatches: 13, Indels: 57
0.78 0.04 0.18
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 18 0.07
17 18 0.07
18 30 0.12
19 116 0.48
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:113954 original size:52 final size:53
Alignment explanation
Indices: 113867--114142 Score: 331
Period size: 52 Copynumber: 5.2 Consensus size: 53
113857 AAATCCCAAC
*
113867 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
113920 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
113972 ATG-AAATCGCAATGCG-AATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
114022 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
114079 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
114131 ATG-AAATCGCAA
1 ATGAAAATCGCAA
114143 CGAGATAATC
Statistics
Matches: 207, Mismatches: 8, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
49 2 0.01
50 31 0.15
51 34 0.16
52 86 0.42
53 18 0.09
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:114012 original size:32 final size:36
Alignment explanation
Indices: 113833--114164 Score: 262
Period size: 33 Copynumber: 9.6 Consensus size: 36
113823 GCAACACGGA
* * * *
113833 AAATACAATCGCAACGCGAAATGAAAATCCCAACATG
1 AAATA-AATCGCAATGCGAAATGAAAATCGCAATACG
113870 --A-AAATCGCAATGCGGAAATGAAAATCGC-A-ACG
1 AAATAAATCGCAATGC-GAAATGAAAATCGCAATACG
* * *
113902 AGA-GAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AAATAAATCGCAATGCGAAATGAAAATCGCAATACG
* *
113937 AAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATACG
*
113970 AAATGAAATCGCAATGCG-AATGAAAATCG-AA-CCG
1 AAAT-AAATCGCAATGCGAAATGAAAATCGCAATACG
* *
114004 ACAT-AATCGCAATGCGAAATTAAAATCGCAATACG
1 AAATAAATCGCAATGCGAAATGAAAATCGCAATACG
*
114039 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATACG
*
114077 AAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATACG
114110 AAATGAAAATCGCAATGCGAAATG-AAATCGC-A-ACG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATACG
*
114145 AGAT-AATCGCAATGCGAAAT
1 AAATAAATCGCAATGCGAAAT
114165 TATAAACGCA
Statistics
Matches: 254, Mismatches: 19, Indels: 49
0.79 0.06 0.15
Matches are distributed among these distances:
32 39 0.15
33 80 0.31
34 37 0.15
35 24 0.09
36 16 0.06
37 6 0.02
38 52 0.20
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (36 bp):
AAATAAATCGCAATGCGAAATGAAAATCGCAATACG
Found at i:114012 original size:102 final size:108
Alignment explanation
Indices: 113867--114091 Score: 329
Period size: 102 Copynumber: 2.1 Consensus size: 108
113857 AAATCCCAAC
*
113867 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCA
* *
113932 ATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
66 ATACGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
* *
113972 ATG-AAATCGCAATGC-G-AATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGC
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGACAGAATCGCAATGCGAAATGAAAATCGC
114033 AATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
65 AATACGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
114079 ATGAAAATCGCAA
1 ATGAAAATCGCAA
114092 CGAAAGAATC
Statistics
Matches: 108, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
101 2 0.02
102 59 0.55
103 1 0.01
104 14 0.13
105 3 0.03
106 1 0.01
107 19 0.18
108 9 0.08
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (108 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCA
ATACGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:114100 original size:140 final size:137
Alignment explanation
Indices: 113839--114174 Score: 470
Period size: 140 Copynumber: 2.4 Consensus size: 137
113829 CGGAAAATAC
* * *
113839 AATCGCAACGCGAAATGAAAATCCCAACATGA-A-AATCGCAATGCGGAAATGAAAATCGC-AAC
1 AATCGCAATGCGAAATG-AAATCGCAAC--GACATAATCGCAATGC-GAAATTAAAATCGCAAAC
* *
113901 GAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
62 GAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
113966 TGCGAAATG-A
127 TGCGAAATGAA
113976 AATCGCAATGCG-AATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATG-AAATCGCAA-CGACATAATCGCAATGCGAAATTAAAATCGCAA-ACG
114039 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGC
63 --A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGC
114104 AATGCGAAATGAA
125 AATGCGAAATGAA
*
114117 AATCGCAATGCGAAATGAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAATCGCAACGACATAATCGCAATGCGAAATTA-AAATCGCA
114175 TTGCGATTTT
Statistics
Matches: 181, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
134 2 0.01
135 16 0.09
136 23 0.13
137 14 0.08
139 1 0.01
140 70 0.39
141 46 0.25
142 9 0.05
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAATCGCAACGACATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:114180 original size:51 final size:52
Alignment explanation
Indices: 113906--114164 Score: 245
Period size: 51 Copynumber: 4.9 Consensus size: 52
113896 GCAACGAGAG
*
113906 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
* **
113958 AATCGCAATGCGAAATG-AAATCGCAATGCGAATGAA----AAT-CGAACCGACA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAGAATCGCAATGCGAAATGA-A
*
114007 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGC-A-ACGAAA-G--AATCGCAATGCGAAATGAA
114065 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
114117 AATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
114165 TATAAACGCA
Statistics
Matches: 180, Mismatches: 10, Indels: 35
0.80 0.04 0.16
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
48 4 0.02
50 17 0.09
51 55 0.31
52 55 0.31
53 1 0.01
54 3 0.02
55 6 0.03
56 1 0.01
57 24 0.13
58 4 0.02
59 6 0.03
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:114280 original size:19 final size:19
Alignment explanation
Indices: 114171--114272 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
114161 AAATTATAAA
114171 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
114190 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
114210 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
114226 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
114243 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
114262 CGCATTGCGAT
1 CGCATTGCGAT
114273 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:114398 original size:14 final size:14
Alignment explanation
Indices: 114379--114415 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
114369 CATCAATTAC
114379 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
114393 ACAAATCATCTTTT
1 ACAAATCAACTTTT
114407 ACAAATCAA
1 ACAAATCAA
114416 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:114443 original size:37 final size:36
Alignment explanation
Indices: 114396--114465 Score: 122
Period size: 37 Copynumber: 1.9 Consensus size: 36
114386 AACTTTTACA
*
114396 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATT-AACAATCAAAATTG
114433 AATCAACTTTTACAAATCAATTAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAACAATCAAAA
114466 AACAATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 11 0.34
37 21 0.66
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (36 bp):
AATCAACTTTTACAAATCAATTAACAATCAAAATTG
Found at i:114473 original size:36 final size:37
Alignment explanation
Indices: 114396--114474 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
114386 AACTTTTACA
* ***
114396 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
114433 AATCAACTTTTACAAATCAATT-AACAATCAAAAAAC
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
114469 AATCAA
1 AATCAA
114475 TTAAACTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
36 17 0.45
37 21 0.55
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
Found at i:116350 original size:14 final size:14
Alignment explanation
Indices: 116331--116387 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
116321 GCGAAATGAA
*
116331 AATCGCAACGACAG
1 AATCGCAACGAAAG
116345 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
116362 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
116378 AATCGCAACG
1 AATCGCAACG
116388 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:116358 original size:33 final size:33
Alignment explanation
Indices: 116312--116403 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
116302 GCGAAACCAA
*
116312 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
116345 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
116378 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
116404 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:116369 original size:19 final size:19
Alignment explanation
Indices: 116275--116408 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
116265 TAGTTTACTT
* *
116275 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
116295 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
116314 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
116333 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
116347 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
116366 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
116380 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
116398 TCGCAATGCGA
1 TCGCAACGCGA
116409 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:116426 original size:19 final size:19
Alignment explanation
Indices: 116404--116532 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
116394 GAAATCGCAA
116404 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
116423 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
116437 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
116456 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
116470 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
116489 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
116508 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
116528 TGCGA
1 TGCGA
116533 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:116446 original size:33 final size:33
Alignment explanation
Indices: 116404--116495 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
116394 GAAATCGCAA
116404 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
116437 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
116470 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
116496 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:116890 original size:186 final size:183
Alignment explanation
Indices: 116576--116953 Score: 713
Period size: 186 Copynumber: 2.0 Consensus size: 183
116566 TTGAATGGAT
116576 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116641 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
116706 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAC
131 AC--TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGC-AACCGAAC
116762 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116826 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 -GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
116891 TACTTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TACTTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
116945 AAATTTACT
1 AAATTTACT
116954 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
183 17 0.09
184 43 0.23
185 25 0.13
186 106 0.55
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (183 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:116892 original size:92 final size:93
Alignment explanation
Indices: 116576--116953 Score: 719
Period size: 92 Copynumber: 4.1 Consensus size: 93
116566 TTGAATGGAT
116576 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116641 -GTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
116668 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116733 AGTTTAGCAGAATTGGCAGCAAACCGAAC
66 AGTTTAGCAGAATTGGCAGC-AACCGAAC
116762 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116826 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
116854 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC--TTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
116917 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
116945 AAATTTACT
1 AAATTTACT
116954 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
91 60 0.21
92 112 0.40
93 64 0.23
94 47 0.17
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:118664 original size:13 final size:13
Alignment explanation
Indices: 118646--118670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
118636 TTGAAATGAA
118646 AATCGCAACGCGG
1 AATCGCAACGCGG
118659 AATCGCAACGCG
1 AATCGCAACGCG
118671 AGATGACAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (13 bp):
AATCGCAACGCGG
Found at i:118682 original size:32 final size:32
Alignment explanation
Indices: 118638--118750 Score: 165
Period size: 32 Copynumber: 3.5 Consensus size: 32
118628 TCTTTTGGTT
*
118638 GAAATGAAAATCGCAACGCGGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGGAATCGCAACGC
* * *
118670 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGA-GGAATCGCAACGC
118703 GAAATGAAAATCGCAACGAGAGAATCGC-ACGC
1 GAAATGAAAATCGCAACGAG-GAATCGCAACGC
118735 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
118751 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 36 0.50
33 36 0.50
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (32 bp):
GAAATGAAAATCGCAACGAGGAATCGCAACGC
Found at i:118683 original size:19 final size:19
Alignment explanation
Indices: 118659--118755 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
118649 CGCAACGCGG
*
118659 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAGATGAA
*
118678 AATCGCAA--C--GAT-AG
1 AATCGCAACGCGAGATGAA
*
118692 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATGAA
118711 AATCGCAA--CGAGA-G--
1 AATCGCAACGCGAGATGAA
*
118725 AATCGC-ACGCGAAATGAA
1 AATCGCAACGCGAGATGAA
*
118743 AATCGCAATGCGA
1 AATCGCAACGCGA
118756 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
13 1 0.02
14 15 0.25
15 7 0.11
16 3 0.05
17 5 0.08
18 8 0.13
19 22 0.36
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAGATGAA
Found at i:118700 original size:33 final size:33
Alignment explanation
Indices: 118638--118750 Score: 167
Period size: 33 Copynumber: 3.5 Consensus size: 33
118628 TCTTTTGGTT
*
118638 GAAATGAAAATCGCAACG-CGGAATCGCAACGC
1 GAAATGAAAATCGCAACGACAGAATCGCAACGC
* * *
118670 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGACAGAATCGCAACGC
*
118703 GAAATGAAAATCGCAACGAGAGAATCGC-ACGC
1 GAAATGAAAATCGCAACGACAGAATCGCAACGC
118735 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
118751 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 36 0.49
33 37 0.51
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGACAGAATCGCAACGC
Found at i:118851 original size:19 final size:18
Alignment explanation
Indices: 118775--118858 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 18
118765 CGCGTTGCGA
118775 TTCTCGTTGCGATTTCCAT
1 TTCTCGTTGCGATTT-CAT
*
118794 TTCGCGTTGCGA-TTC--
1 TTCTCGTTGCGATTTCAT
**
118809 -TCTCGTTGCGACAGTCAT
1 TTCTCGTTGCGA-TTTCAT
118827 TCTCTCGTTGCGATTTCAT
1 T-TCTCGTTGCGATTTCAT
118846 TATCTCGTTGCGA
1 T-TCTCGTTGCGA
118859 CTCTTCTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.19
16 2 0.04
17 1 0.02
18 2 0.04
19 27 0.51
20 11 0.21
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (18 bp):
TTCTCGTTGCGATTTCAT
Done.