Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001421.1 Hibiscus syriacus cultivar Beakdansim tig00002759_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: 159969
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:400 original size:40 final size:41
Alignment explanation
Indices: 347--484 Score: 109
Period size: 42 Copynumber: 3.3 Consensus size: 41
337 ATTATTATAA
* * * *
347 AAACGCCGCAATAGAGTATAATTTTGTGGCATTT-TAGCC-C
1 AAACGCCGTAATAGAGTATAAATTAGCGGCATTTATA-CCAC
* *
387 AAATGCCGTAATAGAGTGGTAAATTAGCGGCATTTATACCAC
1 AAACGCCGTAATAGAGT-ATAAATTAGCGGCATTTATACCAC
* * *** * *
429 AAACGCCGTAATTGAGTATACATATAGCGATGTTTATTCCTC
1 AAACGCCGTAATAGAGTATAAAT-TAGCGGCATTTATACCAC
*
471 AAACGCCGCAATAG
1 AAACGCCGTAATAG
485 TGTTAATCAA
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
40 15 0.19
41 19 0.25
42 43 0.56
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
AAACGCCGTAATAGAGTATAAATTAGCGGCATTTATACCAC
Found at i:590 original size:41 final size:41
Alignment explanation
Indices: 470--590 Score: 179
Period size: 41 Copynumber: 3.0 Consensus size: 41
460 GTTTATTCCT
* * * *
470 CAAACGCCGCAATAGTGTTAATCAATGGTGGCATTTTTAGA
1 CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTTGA
* **
511 CAAACGTCTTAATAGTGTTAATCAATAGTGGCGTTTTTTGA
1 CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTTGA
552 CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTT
1 CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTT
591 TGTATAAACG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (41 bp):
CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTTGA
Found at i:3920 original size:42 final size:42
Alignment explanation
Indices: 3874--4071 Score: 261
Period size: 42 Copynumber: 4.7 Consensus size: 42
3864 AGAGTTGTAA
* * *
3874 TTTAGTGGTGTTTTTGAAATAAACGCTGCAATTGCTTTCTCC
1 TTTAGTGGTGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
** *
3916 TTTAGTGGCATTTTTGAAATAAACGCCGCAATTGTTTTCTCC
1 TTTAGTGGTGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
*
3958 TTTAGTGGCGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
1 TTTAGTGGTGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
* * * * *
4000 GTTAGTGGTATTTTCGTAATAAATGCCGCAATTGTTTTATCC
1 TTTAGTGGTGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
* * *
4042 GTTAGTGGTGTTTTCGTAATAAATGCCGCA
1 TTTAGTGGTGTTTTTGTAATAAACGCCGCA
4072 GTAGTTTATC
Statistics
Matches: 143, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 143 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (42 bp):
TTTAGTGGTGTTTTTGTAATAAACGCCGCAATTGTTTTCTCC
Found at i:4123 original size:126 final size:125
Alignment explanation
Indices: 3875--4123 Score: 270
Period size: 126 Copynumber: 2.0 Consensus size: 125
3865 GAGTTGTAAT
* * * * * *
3875 TTAGTGGTGTTTTTGAAATAAACGCTGCAATTGCTTTCTCCTTTAGTGGCATTTTTGAAATAAAC
1 TTAGTGGTATTTTCGAAATAAACGCCGCAATTGCTTTATCCGTTAGTGGCATTTTCGAAATAAAC
* * *
3940 GCCGCAATTGTTTTCTCCTTTAGTGGCGTTTTTGTAATAAACGCCGCAATTGTTTTCTCCG
66 GCCGCAATAGTTTTCTCCATTAGTGGCG-TTTTGTAATAAACGCCACAATTGTTTTCTCCG
* * * ** * *
4001 TTAGTGGTATTTTCGTAATAAATGCCGCAATTGTTTTATCCGTTAGTGGTGTTTTCGTAATAAAT
1 TTAGTGGTATTTTCGAAATAAACGCCGCAATTGCTTTATCCGTTAGTGGCATTTTCGAAATAAAC
* *
4066 GCCGCAGTAGTTTATC-CCATT-GTGGCG-TTTGTAATATAAACGCCACCATTGTCTTTCT
66 GCCGCAATAGTTT-TCTCCATTAGTGGCGTTTTGT-A-ATAAACGCCACAATTGT-TTTCT
4124 TTTATCAAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
123 5 0.05
124 1 0.01
125 21 0.21
126 72 0.71
127 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (125 bp):
TTAGTGGTATTTTCGAAATAAACGCCGCAATTGCTTTATCCGTTAGTGGCATTTTCGAAATAAAC
GCCGCAATAGTTTTCTCCATTAGTGGCGTTTTGTAATAAACGCCACAATTGTTTTCTCCG
Found at i:10062 original size:44 final size:44
Alignment explanation
Indices: 9932--10077 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 44
9922 TTATGTGTTA
* * * *
9932 TTTAGCGGCGTTTGTAACA-AAAAATGCCACAATATATCATACA
1 TTTAGCGGCGTTTGTAGCATAAAAATGCCACTATATATCAGACC
* * **
9975 TTTAGCGGCGTTT-TAGGATACAAGCGCCACTATATA-CTAGACC
1 TTTAGCGGCGTTTGTAGCATAAAAATGCCACTATATATC-AGACC
* * *
10018 TTTAGCGTCGTTTGTAGCATAAAAATGCCGCTATATATCGGACC
1 TTTAGCGGCGTTTGTAGCATAAAAATGCCACTATATATCAGACC
* *
10062 TTTCGCGACGTTTGTA
1 TTTAGCGGCGTTTGTA
10078 TCCAAAAACG
Statistics
Matches: 82, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
42 4 0.05
43 41 0.50
44 36 0.44
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTAGCATAAAAATGCCACTATATATCAGACC
Found at i:10210 original size:43 final size:42
Alignment explanation
Indices: 10163--10266 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 42
10153 GCAGCATTTT
*
10163 TGAGAAAAACGCCTCTAATTCTCAACACTTATAGTGGCGTTTG
1 TGAGAAAAACGCCTCTAA-TCTCAACACTTATAGCGGCGTTTG
* *
10206 TGAGAAAAATG-CTGCTGAATCTCAACACTTATTGCGGCGTTTG
1 TGAGAAAAACGCCT-CT-AATCTCAACACTTATAGCGGCGTTTG
* *
10249 TGGGAAAAACGCCGCTAA
1 TGAGAAAAACGCCTCTAA
10267 ACACCACCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 4 0.08
43 45 0.87
44 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
TGAGAAAAACGCCTCTAATCTCAACACTTATAGCGGCGTTTG
Found at i:11578 original size:116 final size:116
Alignment explanation
Indices: 11374--11607 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 116
11364 TTAAATTTCC
11374 TAGATGACATGTATACGAATAAGAAATGTCTAAGATATATTATTAGGGTTATAAATATGAATCGA
1 TAGATGACATGTATACGAATAAGAAATGTCTAAGATATATTATTAGGGTTATAAATATGAATCGA
11439 AGTTTTATATTTTAGATAAAAATTATATTTTACGAGAACAAAGAAATATTT
66 AGTTTTATATTTTAGATAAAAATTATATTTTACGAGAACAAAGAAATATTT
*
11490 TAGATGACATGTATATGAATAAGAAATGTCTAAGATATATTATTAGGGTTATAAATATGAATCGA
1 TAGATGACATGTATACGAATAAGAAATGTCTAAGATATATTATTAGGGTTATAAATATGAATCGA
11555 AGTTTTATATTTTAGATAAAAATTATATTTTACGAGAACAAAGAAATATTT
66 AGTTTTATATTTTAGATAAAAATTATATTTTACGAGAACAAAGAAATATTT
11606 TA
1 TA
11608 AAATTAGGCA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (116 bp):
TAGATGACATGTATACGAATAAGAAATGTCTAAGATATATTATTAGGGTTATAAATATGAATCGA
AGTTTTATATTTTAGATAAAAATTATATTTTACGAGAACAAAGAAATATTT
Found at i:12960 original size:2 final size:2
Alignment explanation
Indices: 12953--12987 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12943 TTAAAAATAC
*
12953 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12988 ATTTGATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19207 original size:22 final size:22
Alignment explanation
Indices: 19182--19283 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 22
19172 TGATAAAATA
*
19182 AAAATTAGTAAAAAAGAAAAAG
1 AAAATTAATAAAAAAGAAAAAG
* * *
19204 AAAA-TAATATAATAA-CAAAAT
1 AAAATTAATA-AAAAAGAAAAAG
* * *
19225 AAAATAAATGACAAAAATAAACA-
1 AAAATTAAT-A-AAAAAGAAAAAG
* *
19248 AAAGTTAGTAAAAAAGAAAAAG
1 AAAATTAATAAAAAAGAAAAAG
19270 AAAA-TAATAAAAAA
1 AAAATTAATAAAAAA
19284 TAAGAAGGTT
Statistics
Matches: 59, Mismatches: 16, Indels: 11
0.69 0.19 0.13
Matches are distributed among these distances:
21 30 0.51
22 15 0.25
23 11 0.19
24 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAATTAATAAAAAAGAAAAAG
Found at i:19240 original size:17 final size:17
Alignment explanation
Indices: 19204--19245 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19194 AAAGAAAAAG
*
19204 AAAATAATATAATAAC-
1 AAAATAAAATAATAACA
*
19220 AAAATAAAATAAATGACA
1 AAAATAAAAT-AATAACA
19238 AAAATAAA
1 AAAATAAA
19246 CAAAAGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAATAACA
Found at i:19286 original size:42 final size:41
Alignment explanation
Indices: 19220--19325 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 41
19210 ATATAATAAC
*
19220 AAAATAAAATAAATGACAAAAATAAACAAAAGTTAG-TAAAAAAG
1 AAAAGAAAATAAAT-A-AAAAAT-AA-AAAAGTTAGTTAAAAAAG
* *
19264 AAAAAGAAAAT-AATAAAAAATAAGAAGGTTAGTTTAAAAAAG
1 -AAAAGAAAATAAATAAAAAATAAAAAAGTTAG-TTAAAAAAG
*
19306 AAAATAAAATAAATAAAAAA
1 AAAAGAAAATAAATAAAAAA
19326 GGAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
40 7 0.13
41 11 0.20
42 23 0.43
43 1 0.02
44 3 0.06
45 9 0.17
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (41 bp):
AAAAGAAAATAAATAAAAAATAAAAAAGTTAGTTAAAAAAG
Found at i:19346 original size:21 final size:21
Alignment explanation
Indices: 19298--19339 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19288 AAGGTTAGTT
*
19298 TAAAAAAGAAAATAAAATAAA
1 TAAAAAAGAAAATAAAACAAA
*
19319 TAAAAAAGGAAATAAAACAAA
1 TAAAAAAGAAAATAAAACAAA
19340 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (21 bp):
TAAAAAAGAAAATAAAACAAA
Found at i:20510 original size:3 final size:3
Alignment explanation
Indices: 20504--20541 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20494 GATGATGATG
20504 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20542 TTAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20641 original size:41 final size:39
Alignment explanation
Indices: 20550--20652 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 39
20540 ATTTAAAAAG
** *
20550 AATTTTTTTAAAAAAAATATATAATATACATTTTTAAAGC
1 AATTTTTTTAAAAACTATATATAATATAAATTTTTAAA-C
*
20590 TATTTCTTTTAAAAACTATATATTATATATAAATTTTTAAA-
1 AATTT-TTTTAAAAACTATATA-TA-ATATAAATTTTTAAAC
20631 AATGTTTTTTAAAAACTATATA
1 AAT-TTTTTTAAAAACTATATA
20653 ATTTTTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
40 4 0.07
41 32 0.59
42 4 0.07
43 14 0.26
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (39 bp):
AATTTTTTTAAAAACTATATATAATATAAATTTTTAAAC
Found at i:20672 original size:30 final size:30
Alignment explanation
Indices: 20615--20775 Score: 189
Period size: 30 Copynumber: 5.2 Consensus size: 30
20605 CTATATATTA
*
20615 TATATAAATTTTTAAAAATGTTTTTTAAAAAC
1 TATAT-AATTTTCAAAAATG-TTTTTAAAAAC
*
20647 TATATAATTTTTAAAAATGTTTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
*
20677 TATATAATTTTCAAAAATGTTTTAAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
*
20707 TATATAATTTTCAAAAAT-TGTTTTAAAAATTA
1 TATATAATTTTCAAAAATGT-TTTTAAAAA--C
* * *
20739 TATATAAGTTTTAAAAAATATTTTCAAAAAC
1 TATATAA-TTTTCAAAAATGTTTTTAAAAAC
*
20770 CATATA
1 TATATA
20776 CTATATAAGT
Statistics
Matches: 116, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.01
30 65 0.56
31 19 0.16
32 12 0.10
33 18 0.16
34 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAC
Found at i:20814 original size:39 final size:37
Alignment explanation
Indices: 20707--20931 Score: 218
Period size: 37 Copynumber: 6.2 Consensus size: 37
20697 TTTAAAAAAC
*
20707 TATATAA-TTTTCAAAAATTGTTTT-AAAA--AT-TA-
1 TATATAAGTTTT-AAAAAATGTTTTAAAAACTATATAT
* * *
20739 TATATAAGTTTTAAAAAATATTTTCAAAAACCATATAC
1 TATATAAGTTTTAAAAAATGTTTT-AAAAACTATATAT
20777 TATATAAGTTTTAAAAAATGTTTTCAAAAAGCTATATAT
1 TATATAAGTTTTAAAAAATGTTTT-AAAAA-CTATATAT
** *
20816 TATATATA-TTTTCTAAAATGTTTTAAAGACTATATAT
1 TATATA-AGTTTTAAAAAATGTTTTAAAAACTATATAT
* *
20853 TATAT-AGTTTTCAAAAGTGTTTTAAAAACTATATAT
1 TATATAAGTTTTAAAAAATGTTTTAAAAACTATATAT
* *
20889 TATATACA-TTTTCAAAATAT-TTTTAGAAACTATATAT
1 TATATA-AGTTTT-AAAAAATGTTTTAAAAACTATATAT
20926 TATATA
1 TATATA
20932 CGTATTTTCA
Statistics
Matches: 165, Mismatches: 15, Indels: 21
0.82 0.07 0.10
Matches are distributed among these distances:
32 17 0.10
33 4 0.02
34 4 0.02
35 1 0.01
36 33 0.20
37 41 0.25
38 38 0.23
39 26 0.16
40 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (37 bp):
TATATAAGTTTTAAAAAATGTTTTAAAAACTATATAT
Found at i:20900 original size:73 final size:70
Alignment explanation
Indices: 20707--20945 Score: 234
Period size: 73 Copynumber: 3.2 Consensus size: 70
20697 TTTAAAAAAC
* * *
20707 TATATAATTTTCAAAAATTGTTTTAAAAA-T-TATA-TATA-AGTTTTAAAAAATATTTTCAAAA
1 TATATAGTTTTCAAAAA-TGTTTTAAAAACTATATATTATATAATTTT-CAAAATATTTT--AAA
* *
20768 ACCATATAC
62 ACTATATAT
* *
20777 TATATAAGTTTTAAAAAATGTTTTCAAAAAGCTATATATTATATATATTTTCTAAAATGTTTTAA
1 TATAT-AGTTTTCAAAAATGTTTT-AAAAA-CTATATATTATATA-ATTTTC-AAAATATTTTAA
20842 AGACTATATAT
61 A-ACTATATAT
*
20853 TATATAGTTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTTTCAAAATATTTTTAGAAA
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATATA-ATTTTCAAAATA-TTTTA-AAA
20918 CTATATAT
63 CTATATAT
20926 TATATACGTATTTTCAAAAA
1 TATATA-G--TTTTCAAAAA
20946 CCGTTTGAAA
Statistics
Matches: 142, Mismatches: 12, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
70 11 0.08
71 15 0.11
72 5 0.04
73 41 0.29
74 12 0.08
75 23 0.16
76 22 0.15
77 13 0.09
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (70 bp):
TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAATATTTTAAAACTA
TATAT
Found at i:20938 original size:112 final size:110
Alignment explanation
Indices: 20707--20945 Score: 276
Period size: 112 Copynumber: 2.2 Consensus size: 110
20697 TTTAAAAAAC
20707 TATATA-ATTTTCAAAAATTGTTTTAAAAATTATATATAAGTTTTAAAAAATATTTTCAAAAACC
1 TATATATATTTTCAAAAATTGTTTTAAAAATTATATATAAGTTTTAAAAAATATTTTCAAAAACC
20771 ATATACTATATAAGTTTTAAAAAATGTTTTCAAAAAGCTATATAT
66 ATATACTATATAAGTTTTAAAAAATGTTTTCAAAAAGCTATATAT
* * * * *
20816 TATATATATTTTCTAAAA-TGTTTTAAAGACTATATATTATATAGTTTTCAAAAGTGTTTT-AAA
1 TATATATATTTTCAAAAATTGTTTTAAA-AAT-TATA-TATA-AGTTTTAAAAAATATTTTCAAA
* * * *
20879 AACTATATATTATATACA-TTTTCAAAATAT-TTTT-AGAAA-CTATATAT
62 AACCATATACTATATA-AGTTTT-AAAAAATGTTTTCAAAAAGCTATATAT
20926 TATATACGTATTTTCAAAAA
1 TATATA--TATTTTCAAAAA
20946 CCGTTTGAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
109 15 0.14
110 26 0.23
111 8 0.07
112 40 0.36
113 22 0.20
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (110 bp):
TATATATATTTTCAAAAATTGTTTTAAAAATTATATATAAGTTTTAAAAAATATTTTCAAAAACC
ATATACTATATAAGTTTTAAAAAATGTTTTCAAAAAGCTATATAT
Found at i:21224 original size:21 final size:21
Alignment explanation
Indices: 21198--21238 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21188 CGATATTGTT
*
21198 TAAAT-ATATATTATTTTTTAG
1 TAAATAAT-TATTATTATTTAG
21219 TAAATAATTATTATTATTTA
1 TAAATAATTATTATTATTTA
21239 ATTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAAATAATTATTATTATTTAG
Found at i:32393 original size:18 final size:18
Alignment explanation
Indices: 32370--32412 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
32360 CTTTAGATTA
*
32370 TTTATTTAAATATTTTCT
1 TTTATTTAAATATTATCT
* *
32388 TTTATTTAATTCTTATCT
1 TTTATTTAAATATTATCT
32406 TTTATTT
1 TTTATTT
32413 TAAAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAAATATTATCT
Found at i:39695 original size:7 final size:7
Alignment explanation
Indices: 39685--39754 Score: 52
Period size: 7 Copynumber: 9.1 Consensus size: 7
39675 AAAAATTACC
39685 TCTTTCT
1 TCTTTCT
39692 TCTTTCT
1 TCTTTCT
39699 TCTTTCTT
1 TCTTTC-T
*
39707 TCTCTCT
1 TCTTTCT
*
39714 TCCCTTCT
1 T-CTTTCT
39722 TCTATTTTCT
1 TC---TTTCT
39732 TCTTTTCT
1 TC-TTTCT
39740 T-TTCTCT
1 TCTT-TCT
39747 TCTTTCT
1 TCTTTCT
39754 T
1 T
39755 ATTTTCCCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 2 0.04
7 24 0.46
8 20 0.38
10 6 0.12
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (7 bp):
TCTTTCT
Found at i:39714 original size:15 final size:15
Alignment explanation
Indices: 39685--39754 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
39675 AAAAATTACC
*
39685 TCTTTC-TTCTTTCT
1 TCTTTCTTTCTCTCT
39699 TCTTTCTTTCTCTCT
1 TCTTTCTTTCTCTCT
* * *
39714 TCCCTTCTTCTATTTTCT
1 T-CTTTCTT-T-CTCTCT
39732 TCTTTTCTTT-TCTCT
1 TC-TTTCTTTCTCTCT
39747 TCTTTCTT
1 TCTTTCTT
39755 ATTTTCCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 12 0.27
15 14 0.31
16 6 0.13
17 3 0.07
18 10 0.22
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTTCTTTCTCTCT
Found at i:39758 original size:30 final size:30
Alignment explanation
Indices: 39685--39760 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 30
39675 AAAAATTACC
*
39685 TCTTTCTT-CTTTCTTCTTTCTTTCTCTCT
1 TCTTTCTTATTTTCTTCTTTCTTTCTCTCT
*
39714 TCCCTTCTTCTATTTTCTTCTTTTCTTT-TCTCT
1 T-CTTTC-T-TATTTTCTTC-TTTCTTTCTCTCT
39747 TCTTTCTTATTTTC
1 TCTTTCTTATTTTC
39761 CCATTTGTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 1 0.03
30 11 0.28
31 2 0.05
32 5 0.13
33 13 0.33
34 7 0.18
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (30 bp):
TCTTTCTTATTTTCTTCTTTCTTTCTCTCT
Found at i:43545 original size:44 final size:44
Alignment explanation
Indices: 43461--43653 Score: 157
Period size: 44 Copynumber: 4.4 Consensus size: 44
43451 TAAAAGTAAA
* * ** *
43461 AAAAAGT-ATGATTGAAAAAAAATTATGGACCTTGACTATAAAGGT
1 AAAAAGTGA-GATTG-AAAAAAATTAGGGAACTAAATTATAAAGGT
**
43506 -AAAAGTGAGATTG-AAAAAATTAGGGGTCTAAATTATATAA-GT
1 AAAAAGTGAGATTGAAAAAAATTAGGGAACTAAATTATA-AAGGT
* *
43548 AAAAAATTG-GATTGAAAAAAATTA-GGAACCTCAATTATAAAGGT
1 -AAAAAGTGAGATTGAAAAAAATTAGGGAA-CTAAATTATAAAGGT
* * * * *
43592 AAAAAGTAAGATAGAAAAAAATCA-AGAACTTAATTATAAAGGT
1 AAAAAGTGAGATTGAAAAAAATTAGGGAACTAAATTATAAAGGT
*
43635 ACAAAGTGAGATTGAAAAA
1 AAAAAGTGAGATTGAAAAA
43654 CTTAGGATTA
Statistics
Matches: 121, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
42 20 0.17
43 47 0.39
44 53 0.44
45 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (44 bp):
AAAAAGTGAGATTGAAAAAAATTAGGGAACTAAATTATAAAGGT
Found at i:43596 original size:43 final size:43
Alignment explanation
Indices: 43470--43762 Score: 134
Period size: 43 Copynumber: 6.7 Consensus size: 43
43460 AAAAAAGTAT
** * *
43470 GATTGAAAAAAAATTATGG-ACCTTGACTATAAAGGT-AAAAGTG
1 GATTG-AAAAAAATTA-GGAACCTCAATTATAAAGGTAAAAATTG
*** *
43513 AGATTG-AAAAAATTAGGGGTCTAAATTATATAA-GTAAAAAATTG
1 -GATTGAAAAAAATTAGGAACCTCAATTATA-AAGGT-AAAAATTG
**
43557 GATTGAAAAAAATTAGGAACCTCAATTATAAAGGTAAAAAGTAA
1 GATTGAAAAAAATTAGGAACCTCAATTATAAAGGTAAAAA-TTG
* * * * * *
43601 GATAGAAAAAAATCAAGAA-CTTAATTATAAAGGTACAAAGTG
1 GATTGAAAAAAATTAGGAACCTCAATTATAAAGGTAAAAATTG
* *** ** *
43643 AGATTG-AAAAACTTAGGATTATCAATTATAAATATAAAAAAAAATGG
1 -GATTGAAAAAAATTAGGAACCTCAATTATAAAGGT----AAAAATTG
* * ** * * *
43690 GATTGAAAAAAACTAAGTGCCTTAATTATAAAGATAAAAAGTAG
1 GATTGAAAAAAATTAGGAACCTCAATTATAAAGGTAAAAA-TTG
*
43734 GATT-ACAAAAATTA-GAGACCTCAATTATA
1 GATTGAAAAAAATTAGGA-ACCTCAATTATA
43763 CAAATAGAAA
Statistics
Matches: 186, Mismatches: 47, Indels: 33
0.70 0.18 0.12
Matches are distributed among these distances:
41 2 0.01
42 28 0.15
43 70 0.38
44 56 0.30
46 5 0.03
47 25 0.13
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (43 bp):
GATTGAAAAAAATTAGGAACCTCAATTATAAAGGTAAAAATTG
Found at i:47199 original size:30 final size:28
Alignment explanation
Indices: 47136--47212 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
47126 CCTGTTCTAA
*
47136 AATATTAATATTAATATAG---TTTTAT
1 AATAGTAATATTAATATAGTTTTTTTAT
*
47161 ATTAGTAATATTAATATAGTTTTTTTATGT
1 AATAGTAATATTAATATAGTTTTTTTA--T
47191 AATAGTAATATTAATATAGTTT
1 AATAGTAATATTAATATAGTTT
47213 AAATATACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
25 17 0.39
28 5 0.11
30 22 0.50
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (28 bp):
AATAGTAATATTAATATAGTTTTTTTAT
Found at i:51833 original size:31 final size:31
Alignment explanation
Indices: 51798--51868 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
51788 TCAAAACACA
*
51798 TAAGTTTTGGTCAGTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
*
51829 TAAGTTTTGGTCACTTATGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
51860 TAAGTTTTG
1 TAAGTTTTG
51869 ATTACTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCGTTTTAT
Found at i:58111 original size:34 final size:33
Alignment explanation
Indices: 58073--58139 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
58063 GTAATAAACA
58073 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
58107 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
58140 CATATTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:58931 original size:85 final size:85
Alignment explanation
Indices: 58788--58958 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
58778 AGACGGTGGC
58788 TGTTGTGCAGGTCCTGCTGGTACAGTTGATGATGAACCAGAAGCACCTGCTCTCCGTCCACGAGT
1 TGTTGTGCAGGTCCTGCTGGTACAGTTGATGATGAACCAGAAGCACCTGCTCTCCGTCCACGAGT
58853 CGGGGGATGATGGTGTTGTG
66 CGGGGGATGATGGTGTTGTG
58873 TGTTGTGCAGGTCCTGCTGGTACAGTTGATGATGAACCAGAAGCACCTGCTCTCCGTCCACGAGT
1 TGTTGTGCAGGTCCTGCTGGTACAGTTGATGATGAACCAGAAGCACCTGCTCTCCGTCCACGAGT
58938 CGGGGGATGATGGTGTTGTG
66 CGGGGGATGATGGTGTTGTG
58958 T
1 T
58959 TGGAGAACGT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.18, C:0.21, G:0.34, T:0.27
Consensus pattern (85 bp):
TGTTGTGCAGGTCCTGCTGGTACAGTTGATGATGAACCAGAAGCACCTGCTCTCCGTCCACGAGT
CGGGGGATGATGGTGTTGTG
Found at i:59156 original size:128 final size:128
Alignment explanation
Indices: 58928--59183 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 128
58918 CCTGCTCTCC
58928 GTCCACGAGTCGGGGGATGATGGTGTTGTGTTGGAGAACGTCTCTGTCGACCTCATGGAAAGGTC
1 GTCCACGAGTCGGGGGATGATGGTGTTGTGTTGGAGAACGTCTCTGTCGACCTCATGGAAAGGTC
58993 CGCCCTCATGCATCATCGGGAAGCAGAAACAATTTCCCGTTTCTGTTGAACCACTCAAAATAA
66 CGCCCTCATGCATCATCGGGAAGCAGAAACAATTTCCCGTTTCTGTTGAACCACTCAAAATAA
59056 GTCCACGAGTCGGGGGATGATGGTGTTGTGTTGGAGAACGTCTCTGTCGACCTCATGGAAAGGTC
1 GTCCACGAGTCGGGGGATGATGGTGTTGTGTTGGAGAACGTCTCTGTCGACCTCATGGAAAGGTC
*
59121 CGCCCTCATGCATCATCGGGAAGCAGAAACAATTTCCCGTTTCTGTTGAACCACTCATAATAA
66 CGCCCTCATGCATCATCGGGAAGCAGAAACAATTTCCCGTTTCTGTTGAACCACTCAAAATAA
59184 TCATCACCAC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (128 bp):
GTCCACGAGTCGGGGGATGATGGTGTTGTGTTGGAGAACGTCTCTGTCGACCTCATGGAAAGGTC
CGCCCTCATGCATCATCGGGAAGCAGAAACAATTTCCCGTTTCTGTTGAACCACTCAAAATAA
Found at i:60620 original size:21 final size:21
Alignment explanation
Indices: 60591--60653 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
60581 ATATGCAAAA
*
60591 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
60612 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
60635 -AA-AAA-TATAATAAAATATT
1 AAATAAATTA-AATAAAATATT
60654 CCTTAGACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 8 0.21
20 2 0.05
21 18 0.47
22 2 0.05
23 8 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:65680 original size:43 final size:43
Alignment explanation
Indices: 65632--65713 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
65622 TGTAAAAGTT
*
65632 TGTAGGGCTTTATAGCGGATAACCAATATTAGTATGAATTTCA
1 TGTAGGGCTTTATAGAGGATAACCAATATTAGTATGAATTTCA
*
65675 TGTAGGGTTTTATAGAGGATAACCAATATTAGTATGAAT
1 TGTAGGGCTTTATAGAGGATAACCAATATTAGTATGAAT
65714 GCCAATGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (43 bp):
TGTAGGGCTTTATAGAGGATAACCAATATTAGTATGAATTTCA
Found at i:68256 original size:14 final size:16
Alignment explanation
Indices: 68234--68265 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
68224 TAAATTCAAG
68234 TTTAGGAA-TTATCTT
1 TTTAGGAATTTATCTT
68249 TTTA-GAATTTATCTT
1 TTTAGGAATTTATCTT
68264 TT
1 TT
68266 GTATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTAGGAATTTATCTT
Found at i:69757 original size:13 final size:13
Alignment explanation
Indices: 69739--69766 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
69729 CCTTTAACAT
69739 TATTCAAAAGATC
1 TATTCAAAAGATC
69752 TATTCAAAAGATC
1 TATTCAAAAGATC
69765 TA
1 TA
69767 ATATGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (13 bp):
TATTCAAAAGATC
Found at i:71890 original size:3 final size:3
Alignment explanation
Indices: 71882--71922 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
71872 TTTTTATCCA
71882 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
71923 ATTTATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:72437 original size:19 final size:19
Alignment explanation
Indices: 72398--72438 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
72388 AAAAACGGAG
* *
72398 AGAAACAGAAAGAAGAGAC
1 AGAAACAGAAAAAAAAGAC
*
72417 AGAAACAGAAAAAAAATAC
1 AGAAACAGAAAAAAAAGAC
72436 AGA
1 AGA
72439 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.10, G:0.20, T:0.02
Consensus pattern (19 bp):
AGAAACAGAAAAAAAAGAC
Found at i:73381 original size:24 final size:22
Alignment explanation
Indices: 73333--73381 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
73323 GTTTTAATAG
* *
73333 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
73355 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
73379 TAT
1 TAT
73382 ATAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:85087 original size:19 final size:19
Alignment explanation
Indices: 85059--85095 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
85049 GTTCAACTTA
*
85059 TTGGAGATTCAATTTATTT
1 TTGGAAATTCAATTTATTT
85078 TTGGAAATTCAATTTATT
1 TTGGAAATTCAATTTATT
85096 CTTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGGAAATTCAATTTATTT
Found at i:86021 original size:52 final size:52
Alignment explanation
Indices: 85958--86307 Score: 544
Period size: 52 Copynumber: 6.7 Consensus size: 52
85948 TGAATGTGCT
85958 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
*
86010 CATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
86062 CATAACATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
86114 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
* *
86166 CATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGGACAAAAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC-AGAA
* *
86219 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAAAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
86271 TCA-ACCATAACATCTGGAAGTGTTCTTTGAGTTATCT
1 -CATAGCAT--CTTCTGGAAGTGTTCTTTGAGTTATCT
86308 TTTACTAGAA
Statistics
Matches: 279, Mismatches: 12, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.01
52 196 0.70
53 55 0.20
54 26 0.09
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:87187 original size:110 final size:111
Alignment explanation
Indices: 86885--87626 Score: 978
Period size: 116 Copynumber: 6.6 Consensus size: 111
86875 CATCATCTGG
** *
86885 TGGATCATCTTTT-CCAGTTAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGA
1 TGGATCAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
* ** *
86949 AGTTCATAATGAGAAGAACTTGTTCAATCTTTAGCTCAAATCCATCACTTGA
62 AGTTCATAATGAGAAGAACTTGTTCAATCTTT--TTTGAATTCATCACTTGA
*
87001 TGGATCAGCTTTT-CCAGTTAG-A-GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
1 TGGATCA-TTTTTGCCAG--AGAAGGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAA
* *
87063 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTGAATTCATCACTTGA
60 GAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTTGAATTCATCACTTGA
87115 TGGAT-ATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
*
87179 CATAATGAGAAGAACTTGTTCAATCTTTTTTAAATTCATCACTTGA
66 CATAATGAGAAGAACTTGTTCAATCTTTTTTGAATTCATCACTTGA
*
87225 TGGATTA-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
87289 CATAATGAGAAGAACTTGTTCAATCTTTTTTTGAATTCATCACTTGA
66 CATAATGAGAAGAACTTGTTCAATC-TTTTTTGAATTCATCACTTGA
* *
87336 TGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTT
1 TGGATCATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
87401 CATAATAAGAAGAACTTGCTCAATCTTTTGCTTGAATTCATCATTTGA
66 CATAATGAGAAGAACTTGTTCAATCTTTT--TTGAATTCATCACTTGA
** * *
87449 TGGATCAACTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGA
1 TGGATCATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
*
87513 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGA
62 AGTTCATAATGAGAAGAACTTGTTCAATCTTTT--TTGAATTCATCACTTGA
** ** * *
87565 TGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 TGGATCATTTTTGCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
87627 TTTATTCAAT
Statistics
Matches: 576, Mismatches: 33, Indels: 37
0.89 0.05 0.06
Matches are distributed among these distances:
110 155 0.27
111 35 0.06
112 87 0.15
113 76 0.13
114 33 0.06
115 2 0.00
116 168 0.29
117 18 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (111 bp):
TGGATCATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAATCTTTTTTGAATTCATCACTTGA
Found at i:87770 original size:3 final size:3
Alignment explanation
Indices: 87762--87823 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
87752 TTTTTATCCA
87762 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
87810 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
87824 ATTTATATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:88339 original size:19 final size:19
Alignment explanation
Indices: 88286--88340 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
88276 CCCACCTGAA
*
88286 AAAAAAAACGGAGAGAACAG
1 AAAAAAAACAGAGA-AACAG
* * * *
88306 AAAGAAGAGACAGAAACAG
1 AAAAAAAACAGAGAAACAG
88325 AAAAAAAACAGAGAAA
1 AAAAAAAACAGAGAAA
88341 AAAAAAGACA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.69, C:0.09, G:0.22, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAGAGAAACAG
Found at i:95260 original size:17 final size:17
Alignment explanation
Indices: 95198--95260 Score: 108
Period size: 17 Copynumber: 3.7 Consensus size: 17
95188 ATGGGAGTTG
*
95198 AGGGGTGCCCCCATTTA
1 AGGGGTCCCCCCATTTA
*
95215 AGGGGTGCCCCCATTTA
1 AGGGGTCCCCCCATTTA
95232 AGGGGTCCCCCCATTTA
1 AGGGGTCCCCCCATTTA
95249 AGGGGTCCCCCC
1 AGGGGTCCCCCC
95261 CTTGTTTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.21
Consensus pattern (17 bp):
AGGGGTCCCCCCATTTA
Found at i:95992 original size:114 final size:118
Alignment explanation
Indices: 95796--96014 Score: 320
Period size: 117 Copynumber: 1.9 Consensus size: 118
95786 AAAACATGAA
* *
95796 TAAATTTTGATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGTCAAAAACTAAAT
1 TAAATTTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGT-AAAAACTAAAA
* *
95861 ATTTTATGAAATTAT-AAAATTTAGGGCCCTAATTATAAATATAAAAAATTGTT
65 ATTTTATGAAATTATAAAAATTAAGGACCCTAATTATAAATATAAAAAATTGTT
* * * *
95914 TAAA-TTTAATTCAAAATTGGATGAATTAATAATATAAAT-GAAAAAGAGGGT-AAAACTAAAAA
1 TAAATTTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGTAAAAACTAAAAA
*
95976 TTTTATGAAATTATAAAAATTAAGGACCCTAATTGTAAA
66 TTTTATGAAATTATAAAAATTAAGGACCCTAATTATAAA
96015 AAAAAATTAA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
114 24 0.26
115 21 0.23
116 12 0.13
117 30 0.33
118 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (118 bp):
TAAATTTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGTAAAAACTAAAAA
TTTTATGAAATTATAAAAATTAAGGACCCTAATTATAAATATAAAAAATTGTT
Found at i:96014 original size:22 final size:22
Alignment explanation
Indices: 95984--96040 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 22
95974 AATTTTATGA
95984 AATTATAAAAATTAAGGACCCT
1 AATTATAAAAATTAAGGACCCT
*
96006 AATTGTAAAAAAAAATTAAGGACCCT
1 AA-T-T--ATAAAAATTAAGGACCCT
96032 AATTATAAA
1 AATTATAAA
96041 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 6 0.21
23 1 0.03
24 2 0.07
25 1 0.03
26 19 0.66
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (22 bp):
AATTATAAAAATTAAGGACCCT
Found at i:96019 original size:26 final size:27
Alignment explanation
Indices: 95990--96047 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
95980 ATGAAATTAT
*
95990 AAAAATTAAGGACCCTAATTGTAAA-A
1 AAAAATTAAGGACCCTAATTATAAATA
96016 AAAAATTAAGGACCCTAATTATAAATA
1 AAAAATTAAGGACCCTAATTATAAATA
96043 AAAAA
1 AAAAA
96048 ATTGGGGTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (27 bp):
AAAAATTAAGGACCCTAATTATAAATA
Found at i:96527 original size:2 final size:2
Alignment explanation
Indices: 96520--96587 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
96510 AATATAAAAG
96520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96562 AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
96588 GAATTAGTAG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:97378 original size:39 final size:39
Alignment explanation
Indices: 97307--97392 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
97297 TTTTTAAAAA
* * *
97307 AAGAAACAAAATGGCCAAGCAACCTAAGCAACAAGAATAC
1 AAGAAA-AAAAAGGCCAAGCAACCGAAACAACAAGAATAC
* *
97347 AAGAAAAAAAAGGTCAAGCGACCGAAACAACAAGAATAC
1 AAGAAAAAAAAGGCCAAGCAACCGAAACAACAAGAATAC
97386 AA-AAAAA
1 AAGAAAAA
97393 GAATGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 5 0.12
39 30 0.73
40 6 0.15
ACGTcount: A:0.60, C:0.19, G:0.15, T:0.06
Consensus pattern (39 bp):
AAGAAAAAAAAGGCCAAGCAACCGAAACAACAAGAATAC
Found at i:99169 original size:38 final size:37
Alignment explanation
Indices: 99104--99213 Score: 91
Period size: 38 Copynumber: 2.9 Consensus size: 37
99094 TTTTTTTTAG
* * *
99104 AGAAAATATCACAAGTGATATACAATTTTTATTTCTAA-
1 AGAAACTATCTCAAGTGAAATA-AATTTTTATTTC-AAT
* *
99142 AGAAACTATCTCAAGTGAGATGAAA--TTTGTTTCAAT
1 AGAAACTATCTCAAGTGAAAT-AAATTTTTATTTCAAT
* *
99178 AGAAAGCTATCTCAAGCGAAACAAAATTTTTATTTC
1 AGAAA-CTATCTCAAGTGAAA-TAAATTTTTATTTC
99214 GAGACAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
35 2 0.03
36 12 0.21
37 16 0.28
38 20 0.34
39 8 0.14
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (37 bp):
AGAAACTATCTCAAGTGAAATAAATTTTTATTTCAAT
Found at i:99439 original size:58 final size:62
Alignment explanation
Indices: 99370--99490 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 62
99360 TGTCATCGAT
*
99370 AAAGAGGAAAATAGTCTTGAAAAAGACAA-ATTT-TTTT-A-TTTTTTAATGAAA-CCTCAA
1 AAAGAGGAAAATAGTCTTGAAAAAGACAAGATTTGTTTTAAGTTTTTTAATAAAATCCTCAA
*
99427 AAAGAGGGAAAATGGTCTTGAAAAAGACAAGATTTGTTTTGAAGTTTTTTAATAAAATCCTCAA
1 AAAGA-GGAAAATAGTCTTGAAAAAGACAAGATTTGTTTT-AAGTTTTTTAATAAAATCCTCAA
99491 GAGAAGGGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
57 5 0.09
58 23 0.42
59 4 0.07
60 4 0.07
62 1 0.02
63 12 0.22
64 6 0.11
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (62 bp):
AAAGAGGAAAATAGTCTTGAAAAAGACAAGATTTGTTTTAAGTTTTTTAATAAAATCCTCAA
Found at i:103762 original size:25 final size:24
Alignment explanation
Indices: 103733--103782 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
103723 AATTATGATT
103733 TAAATTTAAAATTTGA-TTTGATTAA
1 TAAA-TTAAAATTT-ATTTTGATTAA
*
103758 TAAATTATAATTTATTTTGATTAA
1 TAAATTAAAATTTATTTTGATTAA
103782 T
1 T
103783 TATAAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 18 0.78
25 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAAATTAAAATTTATTTTGATTAA
Found at i:105553 original size:19 final size:19
Alignment explanation
Indices: 105527--105621 Score: 100
Period size: 19 Copynumber: 5.0 Consensus size: 19
105517 TATGCATTGG
105527 GCTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
*
105546 GTTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
* * * *
105565 GCTATGAATTTCACAGTAG
1 GCTATGAATTTGAAAATAA
* *
105584 GCTATGAGTATGAAAATAA
1 GCTATGAATTTGAAAATAA
* * *
105603 GTTATGAATATGGAAATAA
1 GCTATGAATTTGAAAATAA
105622 TTTCTGATTC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
GCTATGAATTTGAAAATAA
Found at i:106168 original size:17 final size:17
Alignment explanation
Indices: 106148--106191 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
106138 AATCGAAGTT
106148 TTATATTTTAGATAAAA
1 TTATATTTTAGATAAAA
106165 TTATATTTTAGATAAAA
1 TTATATTTTAGATAAAA
106182 TTATATTTTA
1 TTATATTTTA
106192 CGAGAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TTATATTTTAGATAAAA
Found at i:106483 original size:15 final size:16
Alignment explanation
Indices: 106463--106499 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
106453 GGTGTTACAC
*
106463 AATATTAAT-TTTAAT
1 AATATTAATGTTAAAT
106478 AATATTAATGTTAAAT
1 AATATTAATGTTAAAT
106494 AATATT
1 AATATT
106500 TATATCCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AATATTAATGTTAAAT
Found at i:116166 original size:2 final size:2
Alignment explanation
Indices: 116159--116192 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116149 TGCCGAAATA
116159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116193 GTTTACAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120378 original size:150 final size:150
Alignment explanation
Indices: 120107--120405 Score: 508
Period size: 150 Copynumber: 2.0 Consensus size: 150
120097 CCATGCCTAC
120107 CCCTAAGGGTGAAGTGCTCGACATAAATCCTCAAAAGAAACAAAGAACACAAATTGTCCATAAAC
1 CCCTAAGGGTGAAGTGCTCGACATAAATCCTCAAAAGAAACAAAGAACACAAATTGTCCATAAAC
* * * *
120172 ATCAATGCCCTCTCTGGATCCTTCCTCAAGCTACTCAGCTGGGACTGTGAGGTAATTATGAATCG
66 ATCAATCCCCTCTCTGGATCCTTCCTCAAGCTACTCAGCTAGGAATGTGAGGTAATTATGAATCA
*
120237 TATGGAACACATTCTAGCTA
131 CATGGAACACATTCTAGCTA
* *
120257 CCCTAAGGGTGAAGTGCTCGGCATGAATCCTCAAAAGAAACAAAGAACACAAATTGTCCATAAAC
1 CCCTAAGGGTGAAGTGCTCGACATAAATCCTCAAAAGAAACAAAGAACACAAATTGTCCATAAAC
*
120322 ATCAATCCCCTCTTTGGATCCTTCCTCAAGCTACTCAGCTAGGAATGTGAGGTAATTATGAATCA
66 ATCAATCCCCTCTCTGGATCCTTCCTCAAGCTACTCAGCTAGGAATGTGAGGTAATTATGAATCA
* *
120387 CATGTAACCCATTCTAGCT
131 CATGGAACACATTCTAGCT
120406 GGCTCAAACT
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 139 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (150 bp):
CCCTAAGGGTGAAGTGCTCGACATAAATCCTCAAAAGAAACAAAGAACACAAATTGTCCATAAAC
ATCAATCCCCTCTCTGGATCCTTCCTCAAGCTACTCAGCTAGGAATGTGAGGTAATTATGAATCA
CATGGAACACATTCTAGCTA
Found at i:121834 original size:28 final size:28
Alignment explanation
Indices: 121794--121916 Score: 128
Period size: 28 Copynumber: 4.5 Consensus size: 28
121784 GACGATTGAG
121794 CACCTCTGTGCTTCAATCTAGGATCTGA
1 CACCTCTGTGCTTCAATCTAGGATCTGA
* ** *
121822 CACCTATGTGCTT---TGGGATGAT-TGA
1 CACCTCTGTGCTTCAAT-CTAGGATCTGA
* * *
121847 GCACATATGTGCTTCAATCTAGGATTTGA
1 -CACCTCTGTGCTTCAATCTAGGATCTGA
*
121876 CACCTCTGTGCTTCAATCTAGGATCTGT
1 CACCTCTGTGCTTCAATCTAGGATCTGA
121904 CACCTCTGTGCTT
1 CACCTCTGTGCTT
121917 TTAGGGATGA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.05
26 16 0.21
28 53 0.69
29 4 0.05
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (28 bp):
CACCTCTGTGCTTCAATCTAGGATCTGA
Found at i:121836 original size:54 final size:54
Alignment explanation
Indices: 121768--121888 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
121758 CTAGCACAGG
* *
121768 CACCTCTGTGCTTTGAGACGATTGAGCACCTCTGTGCTTCAATCTAGGATCTGA
1 CACCTCTGTGCTTTGAGACGATTGAGCACATATGTGCTTCAATCTAGGATCTGA
* * * *
121822 CACCTATGTGCTTTGGGATGATTGAGCACATATGTGCTTCAATCTAGGATTTGA
1 CACCTCTGTGCTTTGAGACGATTGAGCACATATGTGCTTCAATCTAGGATCTGA
121876 CACCTCTGTGCTT
1 CACCTCTGTGCTT
121889 CAATCTAGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (54 bp):
CACCTCTGTGCTTTGAGACGATTGAGCACATATGTGCTTCAATCTAGGATCTGA
Found at i:122041 original size:73 final size:73
Alignment explanation
Indices: 121922--122063 Score: 230
Period size: 73 Copynumber: 1.9 Consensus size: 73
121912 TGCTTTTAGG
* * * *
121922 GATGATTGAGCACCTTTGTGCTTCAATATAAAATATGGCACCTCTGTGCAGTAAAGAAACGATTG
1 GATGATTGAACACCTCTGTACTTCAATATAAAATATGACACCTCTGTGCAGTAAAGAAACGATTG
121987 AGCATAGA
66 AGCATAGA
* *
121995 GATGATTGAACACCTCTGTACTTCAATATAAAATCTGATACCTCTGTGCAGTAAAGAAACGATTG
1 GATGATTGAACACCTCTGTACTTCAATATAAAATATGACACCTCTGTGCAGTAAAGAAACGATTG
122060 AGCA
66 AGCA
122064 CCTCTGTGCG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (73 bp):
GATGATTGAACACCTCTGTACTTCAATATAAAATATGACACCTCTGTGCAGTAAAGAAACGATTG
AGCATAGA
Found at i:122122 original size:28 final size:29
Alignment explanation
Indices: 122062--122128 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 29
122052 AACGATTGAG
122062 CACCTCTGTGCGTCAATCATTAAAATGGA
1 CACCTCTGTGCGTCAATCATTAAAATGGA
* *
122091 -ACCTATGTGCGTCAATCATTGAAAT-GA
1 CACCTCTGTGCGTCAATCATTAAAATGGA
122118 CACCTCTGTGC
1 CACCTCTGTGC
122129 ATTAAGAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (29 bp):
CACCTCTGTGCGTCAATCATTAAAATGGA
Found at i:122176 original size:28 final size:28
Alignment explanation
Indices: 122056--122185 Score: 93
Period size: 28 Copynumber: 4.6 Consensus size: 28
122046 TAAAGAAACG
*
122056 ATTGAGCACCTCTGTGCGTCAATCATTAA
1 ATTG-GCACCTCTGTGCATCAATCATTAA
* * * *
122085 AATGGAACCTATGTGCGTCAATCATTGAA
1 ATTGGCACCTCTGTGCATCAATCATT-AA
* * * * **
122114 A-TGACACCTCTGTGCATTAA-GAATCG
1 ATTGGCACCTCTGTGCATCAATCATTAA
*
122140 ATTGAGCACCTCTGTGCATCAATCTTTAA
1 ATTG-GCACCTCTGTGCATCAATCATTAA
* *
122169 ATTGGCACTTCTATGCA
1 ATTGGCACCTCTGTGCA
122186 ATTACCATAC
Statistics
Matches: 76, Mismatches: 21, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
26 1 0.01
27 4 0.05
28 60 0.79
29 11 0.14
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (28 bp):
ATTGGCACCTCTGTGCATCAATCATTAA
Found at i:124859 original size:10 final size:9
Alignment explanation
Indices: 124822--124851 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
124812 AATTATAAAT
124822 TTAAAATAAA
1 TTAAAA-AAA
124832 TTAAAAAAA
1 TTAAAAAAA
124841 TTAAAAAAA
1 TTAAAAAAA
124850 TT
1 TT
124852 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:125401 original size:30 final size:30
Alignment explanation
Indices: 125367--125432 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
125357 ATTTGCGGAA
125367 AGTGGTTTTAATGAACCATTTATATAGTTG
1 AGTGGTTTTAATGAACCATTTATATAGTTG
125397 AGTGGTTTTAATGAACCATTTATATAGTTG
1 AGTGGTTTTAATGAACCATTTATATAGTTG
125427 AGTGGT
1 AGTGGT
125433 ATGTTTGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (30 bp):
AGTGGTTTTAATGAACCATTTATATAGTTG
Found at i:127329 original size:16 final size:16
Alignment explanation
Indices: 127310--127340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
127300 CATCCATTAA
*
127310 AATTTTATAAGTTTAT
1 AATTTTATAACTTTAT
127326 AATTTTATAACTTTA
1 AATTTTATAACTTTA
127341 CCGTCGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTTATAACTTTAT
Found at i:132670 original size:21 final size:22
Alignment explanation
Indices: 132644--132687 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
132634 ATGAAATGGC
132644 TTAATCATTTCAT-AAAAGAAT
1 TTAATCATTTCATGAAAAGAAT
* *
132665 TTAATCTTTTCATGAAGAGAAT
1 TTAATCATTTCATGAAAAGAAT
132687 T
1 T
132688 GTTGAATAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TTAATCATTTCATGAAAAGAAT
Found at i:138922 original size:17 final size:17
Alignment explanation
Indices: 138900--138932 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
138890 CAAACTTGCT
138900 AACTAAACTAACCAGCG
1 AACTAAACTAACCAGCG
138917 AACTAAACTAACCAGC
1 AACTAAACTAACCAGC
138933 TAACAACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.30, G:0.09, T:0.12
Consensus pattern (17 bp):
AACTAAACTAACCAGCG
Found at i:140182 original size:20 final size:23
Alignment explanation
Indices: 140137--140192 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 23
140127 GCATGGGTAG
140137 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
140161 TGCATCGATGCAC-TG-T-AGAA
1 TGCATCGATGCACATGTTAAGAA
*
140181 TGCATCAATGCA
1 TGCATCGATGCA
140193 TTTAAAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 2 0.06
24 13 0.42
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:141255 original size:23 final size:23
Alignment explanation
Indices: 141187--141247 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
141177 ACATTTTATA
*
141187 TGGCACTTCGGTGAAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
141210 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
141233 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
141248 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:145880 original size:23 final size:23
Alignment explanation
Indices: 145812--145870 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
145802 ACATTTTATA
145812 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
*
145835 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
145858 TGGCACTTCGGTG
1 TGGCACTTCGGTG
145871 CATTTATACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGTAATTCTACG
Found at i:147094 original size:37 final size:37
Alignment explanation
Indices: 147044--147122 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
147034 TTAATTTTTC
147044 ATGAAGGACATTGGATTCATGAAACTAAGCTAAAAAG
1 ATGAAGGACATTGGATTCATGAAACTAAGCTAAAAAG
147081 ATGAAGGACATTGGATTCATGAAACTAAGCTAAAAAG
1 ATGAAGGACATTGGATTCATGAAACTAAGCTAAAAAG
147118 ATGAA
1 ATGAA
147123 ATTCTGTAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (37 bp):
ATGAAGGACATTGGATTCATGAAACTAAGCTAAAAAG
Found at i:149341 original size:19 final size:19
Alignment explanation
Indices: 149317--149356 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
149307 AAAGAAAAGA
149317 AATAACTTTATAAAACTAG
1 AATAACTTTATAAAACTAG
149336 AATAACTTTATAAAACTAG
1 AATAACTTTATAAAACTAG
149355 AA
1 AA
149357 AGAAGAATAA
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:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (19 bp):
AATAACTTTATAAAACTAG
Found at i:154538 original size:42 final size:41
Alignment explanation
Indices: 154454--154539 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 41
154444 TAATATTATT
* * *
154454 AACATGTCTATATTAAATAAATTCGATCTTGCGGAGTAAAA
1 AACATGTCTAAATTAAATAAATTCGATCTTGAGGAGCAAAA
* *
154495 AACATGTCTCAAATTGAATAAATTCGATCTTGATGAGCCAAAA
1 AACATGTCT-AAATTAAATAAATTCGATCTTGAGGAG-CAAAA
154538 AA
1 AA
154540 AACATGCCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 9 0.24
42 23 0.61
43 6 0.16
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (41 bp):
AACATGTCTAAATTAAATAAATTCGATCTTGAGGAGCAAAA
Done.