Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003578.1 Hibiscus syriacus cultivar Beakdansim tig00007551_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: 105866
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3683 original size:25 final size:25
Alignment explanation
Indices: 3655--3717 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
3645 TTTTAAACAA
*
3655 CACTTTTAAAAGTTTTTTTCTACCG
1 CACTTTTAAAAGTTCTTTTCTACCG
3680 CACTTTTAAAAGTTCTTTTCTACCG
1 CACTTTTAAAAGTTCTTTTCTACCG
*
3705 CATTTTTAAAAGT
1 CACTTTTAAAAGT
3718 CAATTTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (25 bp):
CACTTTTAAAAGTTCTTTTCTACCG
Found at i:4045 original size:28 final size:28
Alignment explanation
Indices: 4013--4077 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
4003 AATTTTCGAT
*
4013 TGCCTTTCCTTTTAAATTTGTATCAGTA
1 TGCCTTTCCTTTTAAACTTGTATCAGTA
*
4041 TGCCTTTCCTTTTAAACTTGTATTAGTA
1 TGCCTTTCCTTTTAAACTTGTATCAGTA
4069 TG-CTTTCCT
1 TGCCTTTCCT
4078 AGACATTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 7 0.20
28 28 0.80
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (28 bp):
TGCCTTTCCTTTTAAACTTGTATCAGTA
Found at i:7800 original size:16 final size:17
Alignment explanation
Indices: 7779--7811 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7769 ACACACTAAA
*
7779 TCGGTT-TCGGTTTTTT
1 TCGGTTATCGATTTTTT
7795 TCGGTTATCGATTTTTT
1 TCGGTTATCGATTTTTT
7812 GGATCGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGATTTTTT
Found at i:15685 original size:37 final size:36
Alignment explanation
Indices: 15643--15717 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 36
15633 CATTAAACCG
15643 TTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATAAA
1 TTTTATAATTTT-AATTTTGTAAAAAAAA-TATATAAA
* *
15680 TTTTATGAATTTTAATTTTTTAAAGAAAATATATAAA
1 TTTTAT-AATTTTAATTTTGTAAAAAAAATATATAAA
15717 T
1 T
15718 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 15 0.44
38 14 0.41
39 5 0.15
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTTATAATTTTAATTTTGTAAAAAAAATATATAAA
Found at i:16337 original size:29 final size:29
Alignment explanation
Indices: 16295--16359 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
16285 GGAAGAGAGA
* * *
16295 GAAAGAAACGTTAGGCACCAAACTATAAC
1 GAAATAAACGTTAGACACCAAACTAGAAC
* *
16324 GAAATAAACGTTAGACGCCAAACTGGAAC
1 GAAATAAACGTTAGACACCAAACTAGAAC
16353 GAAATAA
1 GAAATAA
16360 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (29 bp):
GAAATAAACGTTAGACACCAAACTAGAAC
Found at i:16404 original size:21 final size:20
Alignment explanation
Indices: 16353--16406 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
16343 AAACTGGAAC
*
16353 GAAATAATTTTTTATTTTCA
1 GAAATCATTTTTTATTTTCA
16373 GAAATCATTTTTTATTTTCA
1 GAAATCATTTTTTATTTTCA
16393 GAAATCATTTTTTA
1 GAAATCATTTTTTA
16407 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (20 bp):
GAAATCATTTTTTATTTTCA
Found at i:16418 original size:21 final size:20
Alignment explanation
Indices: 16354--16418 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
16344 AACTGGAACG
* * * *
16354 AAATAATTTTTTATTTTCAG
1 AAATCATTTTTTATATTAAA
* * *
16374 AAATCATTTTTTATTTTCAG
1 AAATCATTTTTTATATTAAA
16394 AAATCATTTTTTAATATTAAA
1 AAATCATTTTTT-ATATTAAA
16415 AAAT
1 AAAT
16419 ATGTCAGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 31 0.77
21 9 0.22
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (20 bp):
AAATCATTTTTTATATTAAA
Found at i:17052 original size:37 final size:35
Alignment explanation
Indices: 17014--17435 Score: 436
Period size: 37 Copynumber: 11.6 Consensus size: 35
17004 AGTCATATTG
*
17014 AAATTATACAATATATAGTCTTTTAAAAAACATTTTG-
1 AAATTATATAATATATAG--TTTT-AAAAACATTTTGA
* * *
17051 AAAGTATATAATATATGGTTTTTAAAACATTTTGA
1 AAATTATATAATATATAGTTTTAAAAACATTTTGA
* * *
17086 AAACTTATATAATGTATAGTTTTGAAATCATTTTGA
1 AAA-TTATATAATATATAGTTTTAAAAACATTTTGA
* *
17122 AAATATATATAATATATAGTTTTTAAAACTTTTTTGA
1 AAAT-TATATAATATATAGTTTTAAAAAC-ATTTTGA
* *
17159 AAACTTATATAATATATAGTTTTGAAATCATTTTGA
1 AAA-TTATATAATATATAGTTTTAAAAACATTTTGA
* *
17195 AAATATATATAATATTATTGTTTTTAAAACATTTTTGA
1 AAAT-TATATAATA-TATAGTTTTAAAAACA-TTTTGA
* *
17233 AAACTTATATAATATATAGCTTTAAAAAAAATTTTGAA
1 AAA-TTATATAATATATAG-TTTTAAAAACATTTTG-A
17271 AAATTATATAATATATAGTTTTAAAAACATTTTTGAA
1 AAATTATATAATATATAGTTTTAAAAACA-TTTTG-A
*
17308 AAATTATATAATATATAGTTTTAAAATCATTTTGA
1 AAATTATATAATATATAGTTTTAAAAACATTTTGA
* * * *
17343 AAACTTATACAATATATAGTTTTGAAAACTTTTTTA
1 AAA-TTATATAATATATAGTTTTAAAAACATTTTGA
* * *
17379 AAA-AATATAATATATAGTTTAAAAAAATATTTTTG-
1 AAATTATATAATATATAGTTT-TAAAAACA-TTTTGA
*
17414 AAATATATATAATTTATAGTTT
1 AAAT-TATATAATATATAGTTT
17436 ATATTATTTT
Statistics
Matches: 328, Mismatches: 40, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
34 26 0.08
35 20 0.06
36 117 0.36
37 133 0.41
38 31 0.09
39 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
AAATTATATAATATATAGTTTTAAAAACATTTTGA
Found at i:17164 original size:73 final size:73
Alignment explanation
Indices: 17017--17435 Score: 498
Period size: 73 Copynumber: 5.7 Consensus size: 73
17007 CATATTGAAA
* * * *
17017 TTATACAATATATAGTCTTTTAAAAAACATTTTG-AAA-GTATATAATATATGGTTTTTAAAACA
1 TTATATAATATATAG--TTTT-AAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAACA
17080 -TTTTGAAAAC
63 TTTTTGAAAAC
* * *
17090 TTATATAATGTATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAACTTTT
1 TTATATAATATATAGTTTTAAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
17155 TTGAAAAC
66 TTGAAAAC
* *
17163 TTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATTATTGTTTTTAAAACATT
1 TTATATAATATATAGTTTTAAAATCATTTTGAAAATATATATAATA-TATAGTTTTTAAAACATT
17228 TTTGAAAAC
65 TTTGAAAAC
* ** *
17237 TTATATAATATATAGCTTTAAAAAAAATTTTGAAAA-ATTATATAATATATAGTTTTAAAAACAT
1 TTATATAATATATAG-TTTTAAAATCATTTTGAAAATA-TATATAATATATAGTTTTTAAAACAT
*
17301 TTTTGAAAAA
64 TTTTGAAAAC
* *
17311 TTATATAATATATAGTTTTAAAATCATTTTGAAAACT-TATACAATATATAGTTTTGAAAAC-TT
1 TTATATAATATATAGTTTTAAAATCATTTTGAAAA-TATATATAATATATAGTTTTTAAAACATT
*
17374 TTTTAAAA-
65 TTTGAAAAC
* * *
17382 -AATATAATATATAGTTTAAAAAAAT-ATTTTTG-AAATATATATAATTTATAGTTT
1 TTATATAATATATAGTTT--TAAAATCA-TTTTGAAAATATATATAATATATAGTTT
17436 ATATTATTTT
Statistics
Matches: 307, Mismatches: 27, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
70 27 0.09
71 26 0.08
72 42 0.14
73 107 0.35
74 80 0.26
75 25 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (73 bp):
TTATATAATATATAGTTTTAAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
TTGAAAAC
Found at i:17463 original size:21 final size:21
Alignment explanation
Indices: 17430--17487 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
17420 ATATAATTTA
*
17430 TAGTTTATATTATTTTATTAT
1 TAGTTTATTTTATTTTATTAT
* *
17451 TAGTATATTTTATTTTTTTAT
1 TAGTTTATTTTATTTTATTAT
17472 TCA-TTTATTTTATTTT
1 T-AGTTTATTTTATTTT
17488 GTTTTGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
TAGTTTATTTTATTTTATTAT
Found at i:18496 original size:18 final size:17
Alignment explanation
Indices: 18456--18500 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
18446 ATTTTTCAGT
*
18456 ATTTAATTTTTTATTTCA
1 ATTT-ATTTTTTATTCCA
*
18474 TTTTATTTTTTATTCCAA
1 ATTTATTTTTTATTCC-A
18492 ATTTATTTT
1 ATTTATTTT
18501 GGTTTGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATTTTTTATTCCA
Found at i:18571 original size:18 final size:18
Alignment explanation
Indices: 18522--18577 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
18512 TCATATTTTC
18522 ATTATTATTTTTTATCTA-T
1 ATTA-TATTTTTTAT-TATT
18541 ATT-TATTTATTTTATTATT
1 ATTATA-TT-TTTTATTATT
*
18560 ATTATATTTTTTAATATT
1 ATTATATTTTTTATTATT
18578 GTTTCTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 2 0.06
18 13 0.41
19 15 0.47
20 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTATATTTTTTATTATT
Found at i:21255 original size:28 final size:28
Alignment explanation
Indices: 21223--21289 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
21213 TTTTAAGAGT
*
21223 GATGCACCGATGCACCAATCCATGCATC
1 GATGCACCGATACACCAATCCATGCATC
21251 GATGCACCGATACACCAATCCATGCATC
1 GATGCACCGATACACCAATCCATGCATC
21279 GATGCACCGAT
1 GATGCACCGAT
21290 TAATTTTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (28 bp):
GATGCACCGATACACCAATCCATGCATC
Found at i:21358 original size:45 final size:46
Alignment explanation
Indices: 21309--21399 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
21299 AAATATCGAA
* * *
21309 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
*
21354 TGCATTTGATGCATCGATGCACAAGATCATGAATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
21400 CCTTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
Found at i:26956 original size:23 final size:23
Alignment explanation
Indices: 26881--26961 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
26871 ACACTTAACA
*
26881 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
26903 GTGCATCGATTCAC-CAC--GAAG
1 GTGCATCGATGCACAC-CTTGAAT
* *
26924 GTGTACCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
26947 GTGCATCGATGCACA
1 GTGCATCGATGCACA
26962 AGGCCATGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
21 15 0.33
22 14 0.30
23 17 0.37
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:28816 original size:45 final size:45
Alignment explanation
Indices: 28766--28864 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
28756 CAAACATCGA
*
28766 ATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 ATGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
* *
28810 AGTGCATTTGATGCATCGATGCACAAGATCATGCATCGATGCACTC
1 A-TGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
*
28856 ATGCTTTTT
1 ATGCATTTT
28865 CAAAACATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 1 0.02
45 27 0.56
46 20 0.42
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (45 bp):
ATGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:30832 original size:95 final size:95
Alignment explanation
Indices: 30723--30915 Score: 314
Period size: 95 Copynumber: 2.0 Consensus size: 95
30713 ATATTATATG
30723 TATACAATAAAGCTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
30788 ATTCAGCTAGCCTGATAAAGGCGATTATAA
66 ATTCAGCTAGCCTGATAAAGGCGATTATAA
** * * *
30818 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
* * *
30883 ATTCAGCTAGCCTGATAAATGTGCTTATAA
66 ATTCAGCTAGCCTGATAAAGGCGATTATAA
30913 TAT
1 TAT
30916 TAAGTTGTCC
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
ATTCAGCTAGCCTGATAAAGGCGATTATAA
Found at i:32221 original size:84 final size:84
Alignment explanation
Indices: 32075--33614 Score: 1621
Period size: 84 Copynumber: 18.5 Consensus size: 84
32065 AAAAAAAACT
* * * * *
32075 ATTTGCAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAA-CAAAGTCCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
32139 CTCAGCTCAAAGGCACATC
66 CTCAGCTCAAAGGCACATC
* * * * * * *
32158 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
*
32223 CTCAGCTCAAGGGCACATC
66 CTCAGCTCAAAGGCACATC
* * * *
32242 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTCCA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* *
32306 CTCAACTCAAAGGTACATC
66 CTCAGCTCAAAGGCACATC
* * ** * *
32325 ATTTGCAGCATAGCTTAATTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* * *
32390 CTCAG-TGTAAGGGCACAAC
66 CTCAGCT-CAAAGGCACATC
* * * * * * *
32409 ATTTGCATCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGATTTTGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
** *
32474 CTCAGCTCTGAGGCATATC
66 CTCAGCTCAAAGGCACATC
* * * * *
32493 ATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTTGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
**
32557 CTCAGCTCAAACACACATC
66 CTCAGCTCAAAGGCACATC
* *
32576 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* *
32641 CTCAGCTCAAAGACATATC
66 CTCAGCTCAAAGGCACATC
* * *
32660 ATTTCCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
*
32725 CTCAGCTCCAAGGCACATC
66 CTCAGCTCAAAGGCACATC
* * * * * *
32744 ATTTGTAGCACAACTCAAGGCTAGAAGGGCTATCTGCC-ACTAAAAAACCTTCGAGATCGACTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTAC
* *
32808 GCTCAGCTCAAAGGCATATC
65 ACTCAGCTCAAAGGCACATC
* **
32828 ATTTCCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* *
32893 CTCAGCTCCAAGGTACATC
66 CTCAGCTCAAAGGCACATC
* * *
32912 ATTTGCAGTATAACTCAAGGCTAGAAGGGCTATTTGCC-ACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
* * * *
32976 GCTCAACTCCAAGGCATATC
65 ACTCAGCTCAAAGGCACATC
* * **
32996 ATTTGAAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* * *
33061 CTCAGCTCCAAGGCATATT
66 CTCAGCTCAAAGGCACATC
* * * * * * *
33080 ATTTGTAGAATAGCTCAAGGCTATAAGGGTTATCTACC-ACCAAAAGACCTTTGAGTTCGGCTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
* *
33144 GCTCAGCTCCAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
* * * * * * * * * *
33164 ATTTGCAACATAGCTCAAAGCAAAAAGGGTTATTTTCTAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* * *
33229 CTCAGCTTCGAGGGCACACC
66 CTCAGC-TCAAAGGCACATC
* * * * * * *
33249 ATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAA-CAAAAACCTTTGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
*
33313 CTCAGCTCAACGGCACATC
66 CTCAGCTCAAAGGCACATC
* * * * * * *
33332 ATTTGTAGTATAGCTCAAGGCTAGAAGGGCTATCTG-C-A--AAAGACCCTCAAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* * *
33393 CTCATCTACGAGGGCACATC
66 CTCAGCT-CAAAGGCACATC
* * * * * *
33413 ATTTACAACATAACCCAAGGCTAGAAGGGTTATAT----ATCAAAGACCTTCGAGTTCGACTCCA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
33474 CTCAGCTCAAAGGCACCATC
66 CTCAGCTCAAAGGCA-CATC
* * *
33494 ATTTGCAGCATAGA-TCAAGG-TAAGAATGGTTATCTG----CCAAAGACCTTCGAGTTCGATTC
1 ATTTGCAGCATA-ACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
33553 CACTCAGCTTAAAGGCACCATA
64 CACTCAGCTCAAAGGCA-CATC
* * * *
33575 ATTTACAGCATAGCTCAAGGCAATAAGGGTTATCTGCCAA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
33615 AAAAGTTATC
Statistics
Matches: 1227, Mismatches: 205, Indels: 48
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.00
80 32 0.03
81 163 0.13
82 2 0.00
83 223 0.18
84 759 0.62
85 47 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
CTCAGCTCAAAGGCACATC
Found at i:34291 original size:36 final size:36
Alignment explanation
Indices: 34202--34629 Score: 457
Period size: 36 Copynumber: 11.8 Consensus size: 36
34192 AGTTAGAAGT
34202 CATTTTG-AAA-TTATATAATATATAGTCTTTTAAAAATA
1 CATTTTGAAAACTTATATAATATATAGT-TTTT--AAA-A
*
34240 CATTTTG-AAA-GTATATAATATAT-GATTTTTAAAA
1 CATTTTGAAAACTTATATAATATATAG-TTTTTAAAA
* * *
34274 CATTTTGAAAACTTATATAATGTATAGTTTTGAAAT
1 CATTTTGAAAACTTATATAATATATAGTTTTTAAAA
*
34310 CATTTTGAAAA-TATATATAATATATAATTTTTAAAA
1 CATTTTGAAAACT-TATATAATATATAGTTTTTAAAA
* *
34346 CATTTTTGAAAACTTATATAATATATAGTTTTGAAAT
1 CA-TTTTGAAAACTTATATAATATATAGTTTTTAAAA
34383 CATTTTGAAAACTTATATAATATATAGTTTTTAAAA
1 CATTTTGAAAACTTATATAATATATAGTTTTTAAAA
*
34419 CATTTTTGAAAACTTATATAATATATAGTTTTAAAAAA
1 CA-TTTTGAAAACTTATATAATATATAGTTTT-TAAAA
* *
34457 CATTTTTGAAAAATTATATAATATATAG-TTTAAAAA
1 CA-TTTTGAAAACTTATATAATATATAGTTTTTAAAA
* *
34493 CATTTTTGAAAAATTATATAGTATATAG-TTTTAAAA
1 CA-TTTTGAAAACTTATATAATATATAGTTTTTAAAA
* *
34529 TCATTTTGAAAACGTATATAATATATAGTTTTGAAAA
1 -CATTTTGAAAACTTATATAATATATAGTTTTTAAAA
* * *
34566 CTTTTTTTAAAA---ATATAATATATAGTTTTAAAAA
1 C-ATTTTGAAAACTTATATAATATATAGTTTTTAAAA
* * * *
34600 TATTTTTAATA-TATATATAATTTATAGTTT
1 CATTTTGAAAACT-TATATAATATATAGTTT
34630 ATTTTATTTT
Statistics
Matches: 346, Mismatches: 29, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
33 8 0.02
34 29 0.08
35 7 0.02
36 161 0.47
37 86 0.25
38 55 0.16
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
CATTTTGAAAACTTATATAATATATAGTTTTTAAAA
Found at i:34367 original size:147 final size:145
Alignment explanation
Indices: 34204--34630 Score: 545
Period size: 147 Copynumber: 3.0 Consensus size: 145
34194 TTAGAAGTCA
34204 TTTTG-AAATTATATAATATATAGTCTTTTAAAAATACATTTTG-AAA-GTATATAATATAT-GA
1 TTTTGAAAATTATATAATATATAG--TTTT-AAAAT-CATTTTGAAAACGTATATAATATATAG-
* *
34265 TTTTTAAAACATTTTGAAAACTTATATAATGTATAGTTTT-GAAATCATTTTGAAAATATATATA
61 TTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATA
* *
34329 ATATATAATTTTTAAAACAT
126 ATATATAAGTTTAAAAACAT
* *
34349 TTTTGAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAACTTATATAATATATAGTTTT
1 TTTTGAAAA-TTATATAATATATAGTTTTAAAATCATTTTGAAAACGTATATAATATATAGTTTT
*
34414 TAAAACATTTTTGAAAACTTATATAATATATAGTTTTAAAAAACATTTTTGAAAA-ATTATATAA
65 TAAAACA-TTTTGAAAACTTATATAATATATAGTTTTAAAAATCA-TTTTGAAAATA-TATATAA
34478 TATAT-AGTTTAAAAACAT
127 TATATAAGTTTAAAAACAT
*
34496 TTTTGAAAAATTATATAGTATATAGTTTTAAAATCATTTTGAAAACGTATATAATATATAGTTTT
1 TTTTG-AAAATTATATAATATATAGTTTTAAAATCATTTTGAAAACGTATATAATATATAGTTTT
* * * * * *
34561 GAAAACTTTTTTTAAAA---ATATAATATATAGTTTTAAAAAT-ATTTTTAATATATATATAATT
65 TAAAAC-ATTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATA
34622 TAT-AGTTTA
129 TATAAGTTTA
34631 TTTTATTTTA
Statistics
Matches: 253, Mismatches: 17, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
142 24 0.09
143 9 0.04
144 29 0.11
145 32 0.13
146 32 0.13
147 102 0.40
148 25 0.10
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (145 bp):
TTTTGAAAATTATATAATATATAGTTTTAAAATCATTTTGAAAACGTATATAATATATAGTTTTT
AAAACATTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATATA
TAAGTTTAAAAACAT
Found at i:34377 original size:73 final size:74
Alignment explanation
Indices: 34204--34625 Score: 505
Period size: 73 Copynumber: 5.8 Consensus size: 74
34194 TTAGAAGTCA
* *
34204 TTTTG-AAA-TTATATAATATATAGTCTTTTAAAAATACATTTTG-AAA-GTATATAATATATGA
1 TTTTGAAAACTTATATAATATATAG--TTTTAAAAAT-CATTTTGAAAATATATATAATATATAA
34265 TTTTTAAAACA-
63 TTTTTAAAACAT
* *
34276 TTTTGAAAACTTATATAATGTATAGTTTT-GAAATCATTTTGAAAATATATATAATATATAATTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATATATAATTT
34340 TTAAAACAT
66 TTAAAACAT
* *
34349 TTTTGAAAACTTATATAATATATAGTTTT-GAAATCATTTTGAAAACT-TATATAATATATAGTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAA-TATATATAATATATAATT
34412 TTTAAAACAT
65 TTTAAAACAT
* *
34422 TTTTGAAAACTTATATAATATATAGTTTTAAAAAACATTTTTGAAAA-ATTATATAATATAT-AG
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCA-TTTTGAAAATA-TATATAATATATAAT
*
34485 TTTAAAAACAT
64 TTTTAAAACAT
* * ** *
34496 TTTTGAAAAATTATATAGTATATAGTTTT-AAAATCATTTTGAAAACGTATATAATATATAGTTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATATATAATTT
* *
34560 TGAAAACTT
66 TTAAAACAT
* * * *
34569 TTTTTAAAA---ATATAATATATAGTTTTAAAAAT-ATTTTTAATATATATATAATTTATA
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATATATA
34626 GTTTATTTTA
Statistics
Matches: 311, Mismatches: 26, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
70 43 0.14
71 12 0.04
72 54 0.17
73 124 0.40
74 57 0.18
75 21 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (74 bp):
TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATATATATAATATATAATTT
TTAAAACAT
Found at i:35796 original size:5 final size:5
Alignment explanation
Indices: 35778--35889 Score: 52
Period size: 5 Copynumber: 21.2 Consensus size: 5
35768 GTATTTAATT
* * * *
35778 TTTTA TTTCA TTTTA TTTT- TTATTCCAA TTTTA TTTTG GTTTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA TT-TT---A TTTTA TTTTA TTTTA TTTTA
* *
35826 TTGTA TTTTTA TTATTA TTATT- TTTTA TCTCTA -TTTA -TTTA TTTTA
1 TTTTA -TTTTA TT-TTA TT-TTA TTTTA T-TTTA TTTTA TTTTA TTTTA
35872 TTATTTA TTTTA TTTTA T
1 -T-TTTA TTTTA TTTTA T
35890 ATTTTTCCTT
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
4 11 0.13
5 49 0.58
6 17 0.20
7 4 0.05
8 2 0.02
9 2 0.02
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:35814 original size:17 final size:17
Alignment explanation
Indices: 35770--35814 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
35760 ATTTTTCAGT
* *
35770 ATTTAATTTTTTATTTC
1 ATTTTATTTTTTATTCC
35787 ATTTTATTTTTTATTCC
1 ATTTTATTTTTTATTCC
35804 AATTTTATTTT
1 -ATTTTATTTT
35815 GGTTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTATTTTTTATTCC
Found at i:35852 original size:16 final size:15
Alignment explanation
Indices: 35821--35895 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 15
35811 TTTTGGTTTG
*
35821 TTTTATTGTATTTTTA
1 TTTTATTAT-TTTTTA
35837 TTATTATTATTTTTTA
1 TT-TTATTATTTTTTA
* *
35853 TCTCTA-T-TTATTTA
1 T-TTTATTATTTTTTA
35867 TTTTATTATTTATTTTA
1 TTTTATTA-TT-TTTTA
35884 TTTTA-TATTTTT
1 TTTTATTATTTTT
35896 CCTTTTTGAC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 3 0.06
14 11 0.23
15 3 0.06
16 15 0.31
17 16 0.33
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTTTTA
Found at i:35877 original size:12 final size:12
Alignment explanation
Indices: 35837--35894 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
35827 TGTATTTTTA
*
35837 TTATTATTATTTT
1 TTATT-TTATTAT
*
35850 TTATCTCTATTTAT
1 TTAT-TTTA-TTAT
35864 TTATTTTATTAT
1 TTATTTTATTAT
35876 TTATTTTATT-T
1 TTATTTTATTAT
35887 TATATTTT
1 T-TATTTT
35895 TCCTTTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.05
12 20 0.51
13 9 0.23
14 8 0.21
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:36063 original size:139 final size:137
Alignment explanation
Indices: 35808--36063 Score: 288
Period size: 139 Copynumber: 1.9 Consensus size: 137
35798 TATTCCAATT
* * * *
35808 TTATTTTGGTTTGTTTTATTGTATTTTTATTATTATTATTTTTTATCTCTATTTATTTATTTTAT
1 TTATTTTGGTTTGTTTTATTGTATTTCTATTATTATTATTTTTTATCTCGATGTATTTAATTTAT
* * * ***
35873 TATTTATTTTATTTTATATTTTTCCTTTTTGACTTTTTTATTTTCTCTTTTTTCTCTTTCCTTTT
66 TATTTATTTTATTTTATATTTTACATTTTCGACTTTTTTATTTTAGATTTTTTCTCTTTCCTTTT
35938 TGATTTA
131 TGATTTA
* * * *
35945 TTATTTTGGTATTTTATTTATT-TATTTACTATTATTATTATTTTTCTTTTTGGATGTATTTAAT
1 TTATTTTGGT-TTGT-TTTATTGTATTT-CTATTATTATTATTTTT-TATCTCGATGTATTTAAT
36009 TT-TTATTTATTGTTATTATTAT-TTTTGACATTTTCGAC-TTTTT-TTTTAGATTTTT
62 TTATTATTTATT-TTATT-TTATATTTT-ACATTTTCGACTTTTTTATTTTAGATTTTT
36064 AACCAATCAA
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
137 10 0.10
138 8 0.08
139 40 0.41
140 28 0.29
141 12 0.12
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (137 bp):
TTATTTTGGTTTGTTTTATTGTATTTCTATTATTATTATTTTTTATCTCGATGTATTTAATTTAT
TATTTATTTTATTTTATATTTTACATTTTCGACTTTTTTATTTTAGATTTTTTCTCTTTCCTTTT
TGATTTA
Found at i:37143 original size:2 final size:2
Alignment explanation
Indices: 37136--37173 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37126 TAAATTTTTG
37136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37174 ATTTATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38236 original size:24 final size:25
Alignment explanation
Indices: 38184--38236 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
38174 AATTATGGTG
* *
38184 TTTTCTTAAAAAAAGAATTTTTAAG
1 TTTTCTTAAAAAAAGAATTTTGAAA
* *
38209 TTTTTTTAAATAAA-AATTTTGAAA
1 TTTTCTTAAAAAAAGAATTTTGAAA
38233 TTTT
1 TTTT
38237 ATAAATGTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTCTTAAAAAAAGAATTTTGAAA
Found at i:44828 original size:29 final size:29
Alignment explanation
Indices: 44786--44882 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
44776 TTAATAGAAC
*
44786 CATTCAACGCTGAATGTTGAACTGTTTAT
1 CATTCAGCGCTGAATGTTGAACTGTTTAT
*
44815 CATTCAGCGTTGAATGTTGAACTGTTTAT
1 CATTCAGCGCTGAATGTTGAACTGTTTAT
*
44844 CATTCAGTGCTGAATGTTGAACTGTTTAT
1 CATTCAGCGCTGAATGTTGAACTGTTTAT
44873 CATTCAGCGC
1 CATTCAGCGC
44883 CTTTGTTTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (29 bp):
CATTCAGCGCTGAATGTTGAACTGTTTAT
Found at i:45083 original size:2 final size:2
Alignment explanation
Indices: 45076--45104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45066 GGGTCAGCTA
45076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45105 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52851 original size:22 final size:22
Alignment explanation
Indices: 52825--52885 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
52815 ATAGGGCAGA
52825 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
52847 GGGAACCGATTCCCACTTTGAAG
1 GGGAATCGATACCC-CCTTGAAG
52870 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
52886 CACGGGTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:54947 original size:2 final size:2
Alignment explanation
Indices: 54940--55007 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
54930 CCAACTTAAG
54940 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
54982 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
55008 CAATTGGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62097 original size:10 final size:10
Alignment explanation
Indices: 62081--62116 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
62071 ATGTTAAGAT
*
62081 AAAATATATT
1 AAAATATATA
*
62091 TAAATATATA
1 AAAATATATA
62101 AAAATATATA
1 AAAATATATA
62111 AAAATA
1 AAAATA
62117 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATATA
Found at i:62106 original size:20 final size:20
Alignment explanation
Indices: 62081--62137 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
62071 ATGTTAAGAT
62081 AAAATATATTTAAATATATA
1 AAAATATATTTAAATATATA
*
62101 AAAATATA--TAAAAATA-A
1 AAAATATATTTAAATATATA
62118 AAAATATATTTTAAATATAT
1 AAAATATA-TTTAAATATAT
62138 GGATTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
20 15 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATATTTAAATATATA
Found at i:62133 original size:18 final size:19
Alignment explanation
Indices: 62081--62136 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 19
62071 ATGTTAAGAT
62081 AAAATATATTTAAATATATA
1 AAAATATATTTAAA-ATATA
*
62101 AAAATATA-TAAAAATA-A
1 AAAATATATTTAAAATATA
*
62118 AAAATATATTTTAAATATA
1 AAAATATATTTAAAATATA
62137 TGGATTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 5 0.16
20 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATATTTAAAATATA
Found at i:62471 original size:19 final size:19
Alignment explanation
Indices: 62447--62493 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
62437 TAATTGATAG
*
62447 AAAATAAAT-ATATTAAATT
1 AAAATAAATCA-ATTAAAAT
62466 AAAATAAATCAATTAAAAT
1 AAAATAAATCAATTAAAAT
*
62485 AGAATAAAT
1 AAAATAAAT
62494 TTAATCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAAATCAATTAAAAT
Found at i:70683 original size:11 final size:11
Alignment explanation
Indices: 70664--70693 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
70654 TAGAGAACAC
*
70664 AAATGAATACT
1 AAATAAATACT
70675 AAATAAATACT
1 AAATAAATACT
70686 AAATAAAT
1 AAATAAAT
70694 CAAAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (11 bp):
AAATAAATACT
Found at i:70709 original size:11 final size:12
Alignment explanation
Indices: 70700--70782 Score: 55
Period size: 14 Copynumber: 6.7 Consensus size: 12
70690 AAATCAAAAG
70700 AAATAAAAAATA
1 AAATAAAAAATA
70712 AAATAAAACAACTA
1 AAATAAAA-AA-TA
*
70726 AAAAAATAAAATA
1 AAATAA-AAAATA
*
70739 ACAT--AAAAT-
1 AAATAAAAAATA
*
70748 AAATAACAAATA
1 AAATAAAAAATA
*
70760 AAAAAACCAAAATA
1 AAATAA--AAAATA
70774 ACAATAAAA
1 A-AATAAAA
70783 TACAAGAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
9 3 0.06
10 5 0.09
11 4 0.07
12 13 0.24
13 8 0.15
14 15 0.28
15 6 0.11
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.14
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:70719 original size:21 final size:22
Alignment explanation
Indices: 70686--70739 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
70676 AATAAATACT
*
70686 AAAT-AAATCAAAAGAAAT-AAA
1 AAATAAAAT-AAAACAAATAAAA
*
70707 AAATAAAATAAAACAACTAAAA
1 AAATAAAATAAAACAAATAAAA
70729 AAATAAAATAA
1 AAATAAAATAA
70740 CATAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.15
Consensus pattern (22 bp):
AAATAAAATAAAACAAATAAAA
Found at i:70733 original size:17 final size:17
Alignment explanation
Indices: 70711--70765 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
70701 AATAAAAAAT
70711 AAAATAAAACAACTAAA
1 AAAATAAAACAACTAAA
*
70728 AAAATAAAATAACATAAA
1 AAAATAAAACAAC-TAAA
*
70746 ATAAAT--AACAAATAAA
1 A-AAATAAAACAACTAAA
70762 AAAA
1 AAAA
70766 CCAAAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 5 0.15
17 16 0.48
18 5 0.15
19 4 0.12
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAACAACTAAA
Found at i:70763 original size:27 final size:26
Alignment explanation
Indices: 70686--70763 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
70676 AATAAATACT
* *
70686 AAATAAATCAAA-AGAAATAAAAAATA
1 AAATAAAACAAATAAAAAT-AAAAATA
* *
70712 AAATAAAACAACTAAAAAAATAAAATA
1 AAATAAAACAAATAAAAATA-AAAATA
* *
70739 ACATAAAATAAATAACAAATAAAAA
1 AAATAAAACAAATAA-AAATAAAAA
70764 AACCAAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
26 11 0.27
27 26 0.63
28 4 0.10
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (26 bp):
AAATAAAACAAATAAAAATAAAAATA
Found at i:70779 original size:6 final size:5
Alignment explanation
Indices: 70706--70784 Score: 54
Period size: 5 Copynumber: 15.2 Consensus size: 5
70696 AAAGAAATAA
* * *
70706 AAAAT AAAAT AAAAC AACTAAA AAAAT AAAAT AACAT AAAAT -AAAT AACAAAT
1 AAAAT AAAAT AAAAT AA--AAT AAAAT AAAAT AAAAT AAAAT AAAAT -A-AAAT
**
70759 AAAA- AAACC AAAAT AACAAT AAAAT A
1 AAAAT AAAAT AAAAT AA-AAT AAAAT A
70785 CAAGAATACG
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
4 7 0.12
5 38 0.64
6 6 0.10
7 8 0.14
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:70997 original size:23 final size:23
Alignment explanation
Indices: 70953--70997 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
70943 TAAAAAGGAC
*
70953 TAAAATAATGATTAAACCAAATG
1 TAAAATAATGATTAAAACAAATG
* *
70976 TAAAATAGTGATTAAAATAAAT
1 TAAAATAATGATTAAAACAAAT
70998 TTTACATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (23 bp):
TAAAATAATGATTAAAACAAATG
Found at i:72260 original size:18 final size:18
Alignment explanation
Indices: 72237--72275 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
72227 CCATAAAACA
*
72237 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
72255 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
72273 GAA
1 GAA
72276 AGGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:72286 original size:27 final size:27
Alignment explanation
Indices: 72237--72288 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
72227 CCATAAAACA
**
72237 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAGGAAATGAATAAAGT
72264 GAATAAAATGAAAGGAAAT-AATAAA
1 GAAT-AAATGAAAGGAAATGAATAAA
72289 AATACTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAGGAAATGAATAAAGT
Found at i:72390 original size:68 final size:68
Alignment explanation
Indices: 72308--72541 Score: 181
Period size: 72 Copynumber: 3.4 Consensus size: 68
72298 AATAATATAG
* *
72308 ACTATATAATATATATATCTCAAAAAATATTTTTTAAACTATATATTATATTTAAAAATGTTTTC
1 ACTATATAATATATATATTTCAAAAAATATTTTTTAAACTATATATTATATTTCAAAATGTTTTC
72373 AAA
66 AAA
** * * * *
72376 ACTATATACCATATAGT-TTTC-AAAAATGA-TTTTAAAAATATTATATGAGT-TTTCCAAAATA
1 ACTATATAATATATA-TATTTCAAAAAAT-ATTTTTTAAACTA-TATATTA-TATTT-CAAAATG
*
72437 TTTTTAAA
61 TTTTCAAA
* * * * * *
72445 ACTATATATTATATAAAATTTTCAAAAATGTTTTTTTTAAACTATACATTATATTTTCAAAATGA
1 ACTATATAATATAT-ATA-TTTCAAAAA-ATATTTTTTAAACTATATATTATA-TTTCAAAATGT
72510 TTTCAAA
62 TTTCAAA
* **
72517 AATATATGTTATATA-ATTTTCAAAA
1 ACTATATAATATATATA-TTTCAAAA
72542 TGTTTTAAAA
Statistics
Matches: 130, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
67 15 0.12
68 26 0.20
69 26 0.20
70 11 0.08
71 6 0.05
72 33 0.25
73 13 0.10
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (68 bp):
ACTATATAATATATATATTTCAAAAAATATTTTTTAAACTATATATTATATTTCAAAATGTTTTC
AAA
Found at i:72429 original size:33 final size:31
Alignment explanation
Indices: 72386--72453 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
72376 ACTATATACC
72386 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
72418 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
72450 ATAT
1 ATAT
72454 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:72536 original size:35 final size:35
Alignment explanation
Indices: 72497--72615 Score: 98
Period size: 39 Copynumber: 3.2 Consensus size: 35
72487 TATACATTAT
72497 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
72532 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
* * * *
72569 AGTTTTCAAAAACGTTTAAAAAAAACTATATTATATATA
1 A-TTTTC-AAAATGTTT-CAAAATA-TATATTGTATATA
72608 TATTTTCA
1 -ATTTTCA
72616 GAAACCATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
34 7 0.10
35 12 0.17
37 12 0.17
38 9 0.13
39 25 0.36
40 5 0.07
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:72541 original size:107 final size:108
Alignment explanation
Indices: 72387--72585 Score: 257
Period size: 107 Copynumber: 1.9 Consensus size: 108
72377 CTATATACCA
* * *
72387 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAAC-TATA
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAAT-GTTTTAAAACTTATA
*
72451 TATTATATA-AAATTTTCAAAAATGTTTTTTTTAAACTATACAT
65 TATTATATATAAATTTTCAAAAACGTTTTTTTTAAACTATACAT
72494 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAATGTTTTAAAACTT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATGTTTTAAAACTT
* *
72555 ATATATTGTATATAAGTTTTCAAAAACGTTT
62 ATATATTATATATAAATTTTCAAAAACGTTT
72586 AAAAAAAACT
Statistics
Matches: 80, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
105 10 0.12
106 18 0.22
107 25 0.31
108 21 0.26
109 6 0.08
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (108 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATGTTTTAAAACTTATAT
ATTATATATAAATTTTCAAAAACGTTTTTTTTAAACTATACAT
Found at i:73489 original size:84 final size:82
Alignment explanation
Indices: 73369--74435 Score: 868
Period size: 84 Copynumber: 12.9 Consensus size: 82
73359 GGGACTTTGG
* * *
73369 CAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* * *
73434 CTCGAAGGTTTTTTGGTCA
65 CTCAAAGGGTCTTTGGT-A
* * ** ** * *
73453 CAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCCCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
**
73518 ACTC-GGGGGTCTTTGG--
64 ACTCAAAGGGTCTTTGGTA
* * * *
73534 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
73599 CTCAAA-GGTCTTTTGGTCA
65 CTCAAAGGGTC-TTTGGT-A
* * * * * *
73618 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
**
73683 ACTC-GGGGGTCTTTGG--
64 ACTCAAAGGGTCTTTGGTA
* * * * *
73699 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
*
73764 CTCAAA-GGTCTTTGGTTGG
65 CTCAAAGGGTCTTTGG-T-A
* * *
73783 CAGACAACCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTT-AAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGA
*
73847 ACTCAAA-GATCTTTTGGTCA
64 ACTCAAAGGGTC-TTTGGT-A
* * * *
73867 CAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* *
73932 CTC-AATGGTCTTTGCTGA
65 CTCAAAGGGTCTTTGGT-A
* * * * * * *
73950 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
*
74015 ACT-TAAGGGTCTTTGG--
64 ACTCAAAGGGTCTTTGGTA
* * * * * * *
74031 CATATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
74096 CTCAAA-GGTCTTTGCCG-A
65 CTCAAAGGGTCTTTG--GTA
* * * * * * * *
74114 CAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
*
74179 ACT-TAAGGGTCTTTGG--
64 ACTCAAAGGGTCTTTGGTA
* * * * * * *
74195 CATATAGCTCTTATCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
*
74260 CTCAAA-GGTCTTTGCTGA
65 CTCAAAGGGTCTTTGGT-A
* * * * * * * *
74278 CAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
*
74343 ACT-TAAGGGTCTTTGG--
64 ACTCAAAGGGTCTTTGGTA
* * * * * *
74359 CATATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
*
74424 CTCGAA-GGTCTT
65 CTCAAAGGGTCTT
74436 GGTGGCAGGT
Statistics
Matches: 788, Mismatches: 152, Indels: 90
0.77 0.15 0.09
Matches are distributed among these distances:
80 138 0.18
81 180 0.23
82 2 0.00
83 121 0.15
84 296 0.38
85 51 0.06
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (82 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAC
TCAAAGGGTCTTTGGTA
Found at i:74100 original size:164 final size:164
Alignment explanation
Indices: 73286--74435 Score: 1552
Period size: 164 Copynumber: 7.0 Consensus size: 164
73276 GTCTTCGGTC
* ** * * ** * * *
73286 GACAAATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCAAGCTAAGAGTAATT
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
* * * *
73351 GAACTCGAGGGACTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTA
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
* * *
73416 GAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGT
131 GAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGCT
* * * **
73451 CACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCCCGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
**
73516 GAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TT
*
73581 -GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGT
130 GGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCT
* * *
73616 CACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
**
73681 GAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TT
* *
73746 -GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTT
130 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCT
* * * * * * * * *
73781 GGCAGACAACCCTTCTAG-ATTCAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGT
1 GACAGATAACCCTTCTAGCCTT-GAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
* * * * * * * * * *
73844 CGAACTCAAAGATCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
65 CGAACTCAAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
73909 CCTTGGAGCTGAGCGTAGTCGAACTCAATGGTCTTTGCT
126 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
*
73948 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
* * *
74013 GAACTTAAGGGTCTTTGGCATATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
* *
74078 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGCC
131 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
* *
74112 GACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
* * * *
74177 GAACTTAAGGGTCTTTGGCATATAGCTCTTATCGACTTAAGCTATACTGCAAATGATGTGCCTTG
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
74242 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
131 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
* *
74276 GACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
* * *
74341 GAACTTAAGGGTCTTTGGCATATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
66 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
*
74406 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 GAGCTGAGCGTAGTCGAACTCAAAGGTCTT
74436 GGTGGCAGGT
Statistics
Matches: 896, Mismatches: 78, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
164 418 0.47
165 339 0.38
166 2 0.00
167 43 0.05
168 94 0.10
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATC
GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
Found at i:77840 original size:19 final size:20
Alignment explanation
Indices: 77816--77862 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
77806 AGTTAATGTG
*
77816 AATGCAAAGAAAAT-AACAA
1 AATGCAAAGAAAATAAAAAA
77835 AATGCAAAGAAAATAAAAAA
1 AATGCAAAGAAAATAAAAAA
77855 AATGCAAA
1 AATGCAAA
77863 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.70, C:0.09, G:0.11, T:0.11
Consensus pattern (20 bp):
AATGCAAAGAAAATAAAAAA
Found at i:79647 original size:11 final size:11
Alignment explanation
Indices: 79628--79657 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
79618 TAGAGAACAC
*
79628 AAATGAATACT
1 AAATAAATACT
79639 AAATAAATACT
1 AAATAAATACT
79650 AAATAAAT
1 AAATAAAT
79658 CAAAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (11 bp):
AAATAAATACT
Found at i:79673 original size:11 final size:12
Alignment explanation
Indices: 79664--79747 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 12
79654 AAATCAAAAG
79664 AAATAAAAAATA
1 AAATAAAAAATA
79676 AAATAAAACAACT-
1 AAATAAAA-AA-TA
79689 -AA-AAAAAATA
1 AAATAAAAAATA
79699 AAATAACATAAA-A
1 AAATAA-A-AAATA
*
79712 TAAATAACAAATA
1 -AAATAAAAAATA
*
79725 AAAAAACCAAAATA
1 AAATAA--AAAATA
79739 ACAATAAAA
1 A-AATAAAA
79748 TACAAGAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
9 1 0.02
10 2 0.04
11 6 0.11
12 20 0.36
13 7 0.12
14 16 0.29
15 4 0.07
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.14
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:79698 original size:18 final size:18
Alignment explanation
Indices: 79670--79730 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
79660 AAAGAAATAA
79670 AAAATAAAATAAAACAACT
1 AAAA-AAAATAAAACAACT
*
79689 AAAAAAAATAAAATAACAT
1 AAAAAAAATAAAACAAC-T
* *
79708 AAAATAAAT--AACAAAT
1 AAAAAAAATAAAACAACT
79724 AAAAAAA
1 AAAAAAA
79731 CCAAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 12 0.33
19 13 0.36
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAAATAAAACAACT
Found at i:79721 original size:35 final size:35
Alignment explanation
Indices: 79672--79749 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
79662 AGAAATAAAA
* *
79672 AATAAAAT-AAAACAACTAAAAAAAATAAAATAAC
1 AATAAAATAAAAACAAATAAAAAAAACAAAATAAC
*
79706 -ATAAAATAAATAACAAATAAAAAAACCAAAATAAC
1 AATAAAATAAA-AACAAATAAAAAAAACAAAATAAC
79741 AATAAAATA
1 AATAAAATA
79750 CAAGAATACG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 7 0.18
34 2 0.05
35 21 0.55
36 8 0.21
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (35 bp):
AATAAAATAAAAACAAATAAAAAAAACAAAATAAC
Found at i:79729 original size:28 final size:27
Alignment explanation
Indices: 79650--79729 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
79640 AATAAATACT
* *
79650 AAATAAATCAAA-AGAAATAAAAAATA
1 AAATAAAACAAATAAAAATAAAAAATA
* *
79676 AAATAAAACAACTAAAAAAAATAAAATA
1 AAATAAAACAAATAAAAATAA-AAAATA
* *
79704 ACATAAAATAAATAACAAATAAAAAA
1 AAATAAAACAAATAA-AAATAAAAAA
79730 ACCAAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 10 0.23
27 6 0.14
28 22 0.51
29 5 0.12
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.15
Consensus pattern (27 bp):
AAATAAAACAAATAAAAATAAAAAATA
Found at i:79744 original size:6 final size:5
Alignment explanation
Indices: 79670--79749 Score: 60
Period size: 5 Copynumber: 16.2 Consensus size: 5
79660 AAAGAAATAA
* * *
79670 AAAAT AAAAT AAAA- CAACT AAAA- AAAAT AAAAT AACAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
**
79717 AACAAAT AAAA- AAACC AAAAT AACAAT AAAAT A
1 -A-AAAT AAAAT AAAAT AAAAT AA-AAT AAAAT A
79750 CAAGAATACG
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 13 0.22
5 36 0.61
6 6 0.10
7 4 0.07
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:79960 original size:23 final size:23
Alignment explanation
Indices: 79916--79960 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
79906 TAAAAAGGAC
*
79916 TAAAATAATGATTAAACCAAATG
1 TAAAATAATGATTAAAACAAATG
* *
79939 TAAAATAGTGATTAAAATAAAT
1 TAAAATAATGATTAAAACAAAT
79961 TTTACATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (23 bp):
TAAAATAATGATTAAAACAAATG
Found at i:81223 original size:18 final size:18
Alignment explanation
Indices: 81200--81238 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
81190 CCATAAAACA
*
81200 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
81218 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
81236 GAA
1 GAA
81239 AGGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:81249 original size:27 final size:27
Alignment explanation
Indices: 81200--81251 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
81190 CCATAAAACA
**
81200 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAGGAAATGAATAAAGT
81227 GAATAAAATGAAAGGAAAT-AATAAA
1 GAAT-AAATGAAAGGAAATGAATAAA
81252 AATACTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAGGAAATGAATAAAGT
Found at i:81521 original size:35 final size:37
Alignment explanation
Indices: 81460--81542 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 37
81450 TATACATTAT
81460 ATTTTCAAAATGATTCCAAAAATATAT-GT-TATATA
1 ATTTTCAAAATGATTCCAAAAATATATAGTGTATATA
** * *
81495 ATTTTCAAAATG-TTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGATTCCAAAA-ATATATAGTGTATATA
81532 AGTTTTCAAAA
1 A-TTTTCAAAA
81543 ACGTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 6 0.15
35 17 0.43
36 1 0.03
37 7 0.17
38 9 0.22
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (37 bp):
ATTTTCAAAATGATTCCAAAAATATATAGTGTATATA
Found at i:87138 original size:5 final size:5
Alignment explanation
Indices: 87125--87168 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
87115 TTATAAAATA
*
87125 ATTAT -TTAT ATTAT A-TAT -TTAT ATTAT ATTAT ATTTT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
87169 AAACCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 10 0.29
5 24 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATTAT
Found at i:87145 original size:13 final size:13
Alignment explanation
Indices: 87127--87169 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
87117 ATAAAATAAT
87127 TATTTATATTATA
1 TATTTATATTATA
87140 TATTTATATTATA
1 TATTTATATTATA
*
87153 TTATATTTTATTATA
1 -TAT-TTATATTATA
87168 TA
1 TA
87170 AACCATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.48
14 5 0.19
15 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTATATTATA
Found at i:87153 original size:18 final size:16
Alignment explanation
Indices: 87126--87168 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
87116 TATAAAATAA
87126 TTATTTATATTATATAT
1 TTATTTATATTATAT-T
87143 TTATATTATATTATATT
1 TTAT-TTATATTATATT
87160 TTA-TTATAT
1 TTATTTATAT
87169 AAACCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTATATTATATT
Found at i:93628 original size:13 final size:13
Alignment explanation
Indices: 93610--93634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93600 TCGAATATAC
93610 TTAGAAAATCTTT
1 TTAGAAAATCTTT
93623 TTAGAAAATCTT
1 TTAGAAAATCTT
93635 AAAATTCATT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:95890 original size:21 final size:21
Alignment explanation
Indices: 95865--95944 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
95855 CAGAACCCCA
95865 GGGGGTATCGATTCCCCT-AT
1 GGGGGTATCGATTCCCCTCAT
* * *
95885 GGGGGGAGTCGGTTCCCCTTCAAA
1 GGGGGTA-TCGATTCCCC-TC-AT
* *
95909 GGGGGAATCGGTT-CCCTCAT
1 GGGGGTATCGATTCCCCTCAT
95929 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
95945 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 18 0.38
21 13 0.27
22 4 0.08
23 6 0.12
24 7 0.15
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTCAT
Found at i:99780 original size:22 final size:21
Alignment explanation
Indices: 99737--99777 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
99727 TGAGTTTATT
*
99737 ATCATTTTTCAATTTTGAAAC
1 ATCATTTTTCAATTTTAAAAC
99758 ATCATTTTT-ATATTTTAAAA
1 ATCATTTTTCA-ATTTTAAAA
99778 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
ATCATTTTTCAATTTTAAAAC
Done.