Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:4221 original size:9 final size:9
Alignment explanation
Indices: 4207--4240 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
4197 TTTTTTCAAA
4207 AAAAAAAAC
1 AAAAAAAAC
4216 AAAAAAAAGC
1 AAAAAAAA-C
4226 AAAAAAAAC
1 AAAAAAAAC
4235 AAAAAA
1 AAAAAA
4241 GCTAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:4221 original size:10 final size:10
Alignment explanation
Indices: 4206--4240 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4196 TTTTTTTCAA
4206 AAAAAAAAAC
1 AAAAAAAAAC
*
4216 AAAAAAAAGC
1 AAAAAAAAAC
4226 -AAAAAAAAC
1 AAAAAAAAAC
4235 AAAAAA
1 AAAAAA
4241 GCTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:4231 original size:17 final size:18
Alignment explanation
Indices: 4207--4247 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
4197 TTTTTTCAAA
4207 AAAAAAAACAAAAAAAAGC-
1 AAAAAAAAC--AAAAAAGCT
4226 AAAAAAAACAAAAAAGCT
1 AAAAAAAACAAAAAAGCT
4244 AAAA
1 AAAA
4248 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.83, C:0.10, G:0.05, T:0.02
Consensus pattern (18 bp):
AAAAAAAACAAAAAAGCT
Found at i:13694 original size:14 final size:14
Alignment explanation
Indices: 13674--13709 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13664 AGTGCTTCAA
13674 CTTCTTTTCTTTCTT
1 CTTCTTTTCTTT-TT
13689 -TTCTTTTCTTTTT
1 CTTCTTTTCTTTTT
13702 CTTCTTTT
1 CTTCTTTT
13710 GAGTGCTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
CTTCTTTTCTTTTT
Found at i:18931 original size:23 final size:23
Alignment explanation
Indices: 18904--18957 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
18894 AAAAATCAGA
* *
18904 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
18927 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
18951 -AAGAAAA
1 AAAGAAAA
18958 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:36231 original size:23 final size:24
Alignment explanation
Indices: 36182--36234 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
36172 TTCTTTGCTT
* *
36182 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
36205 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
36228 TTTCTTT
1 TTTCTTT
36235 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:38846 original size:24 final size:24
Alignment explanation
Indices: 38819--38864 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38809 TGGCTTTTGG
38819 AGAACTAAA-AGGTGTGACTTTTAA
1 AGAAC-AAATAGGTGTGACTTTTAA
* *
38843 AGAACAAATAGTTGTTACTTTT
1 AGAACAAATAGGTGTGACTTTT
38865 GGTGATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (24 bp):
AGAACAAATAGGTGTGACTTTTAA
Found at i:44452 original size:23 final size:23
Alignment explanation
Indices: 44420--44466 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44410 TTTTTCTTCC
*
44420 TTTTTGAGTGCTTTCAATTTCTT
1 TTTTTCAGTGCTTTCAATTTCTT
* * *
44443 TTTTTCAGTGTTTTGATTTTCTT
1 TTTTTCAGTGCTTTCAATTTCTT
44466 T
1 T
44467 GCTGGATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.66
Consensus pattern (23 bp):
TTTTTCAGTGCTTTCAATTTCTT
Found at i:73845 original size:273 final size:273
Alignment explanation
Indices: 73358--73887 Score: 943
Period size: 273 Copynumber: 1.9 Consensus size: 273
73348 AACTCTCACA
* * *
73358 AATATTTGAATAAACAAAGTAAATTGGTTTTTACAAATGAAATTGAAATCTATATTTATAGGCCT
1 AATATTTGAATAAACAAAGTAAATTGGTTTTTACAAATGAAATGGAAAGCTATATTTATAGGCAT
* *
73423 AACAACGTATGGTGTGAATACAAAACATTCATTGAGTGAACCTTAAAGGATGAATGTTCATCCTT
66 AACAACGCATGGTGTGAATACAAAACATTCAATGAGTGAACCTTAAAGGATGAATGTTCATCCTT
*
73488 AAGTAGATACAATGTTCGACCCCTATGCAAGTTTATGGACTAATTAAATAAATGAATGTTCATCA
131 AAGTAGATACAATGTACGACCCCTATGCAAGTTTATGGACTAATTAAATAAATGAATGTTCATCA
73553 ATTTAATTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGGTGTGAACATGTTGGTTCACTT
196 ATTTAATTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGGTGTGAACATGTTGGTTCACTT
73618 AAGAACTAAAGAG
261 AAGAACTAAAGAG
* *
73631 AATATTTGATTAAACAAAGTTAATTGGTTTTTACAAATGAAATGGAAAGCTATATTTATAGGCAT
1 AATATTTGAATAAACAAAGTAAATTGGTTTTTACAAATGAAATGGAAAGCTATATTTATAGGCAT
** * *
73696 AACAGTGCATGGTGTGAATACAAAATATTCAATGAGTGAACCTTGAAGGATGAATGTTCATCCTT
66 AACAACGCATGGTGTGAATACAAAACATTCAATGAGTGAACCTTAAAGGATGAATGTTCATCCTT
*
73761 AAGTAGATACAATGTACGACCCCTATGCAAGTTTATGGACTAATTAAATAAATGAATGTTCATCC
131 AAGTAGATACAATGTACGACCCCTATGCAAGTTTATGGACTAATTAAATAAATGAATGTTCATCA
73826 ATTTAATTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGGTGTGAACATGTTGGTTCA
196 ATTTAATTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGGTGTGAACATGTTGGTTCA
73888 TATCCTTGCA
Statistics
Matches: 244, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
273 244 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (273 bp):
AATATTTGAATAAACAAAGTAAATTGGTTTTTACAAATGAAATGGAAAGCTATATTTATAGGCAT
AACAACGCATGGTGTGAATACAAAACATTCAATGAGTGAACCTTAAAGGATGAATGTTCATCCTT
AAGTAGATACAATGTACGACCCCTATGCAAGTTTATGGACTAATTAAATAAATGAATGTTCATCA
ATTTAATTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGGTGTGAACATGTTGGTTCACTT
AAGAACTAAAGAG
Found at i:82702 original size:11 final size:11
Alignment explanation
Indices: 82688--82743 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
82678 CTCTTTTGAA
82688 TTTCTTTTTCT
1 TTTCTTTTTCT
82699 TTTCTTTTTTTCT
1 TTTC--TTTTTCT
*
82712 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
82724 TATCTTTTTCT
1 TTTCTTTTTCT
82735 TTTCTTTTT
1 TTTCTTTTT
82744 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.08
11 17 0.47
12 3 0.08
13 10 0.28
14 3 0.08
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:84319 original size:15 final size:16
Alignment explanation
Indices: 84299--84341 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
84289 AGTTATCATC
84299 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
84314 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
84330 AAAATAACTATA
1 ATAATAACTATA
84342 TTAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:97474 original size:17 final size:17
Alignment explanation
Indices: 97449--97492 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
97439 TGTTCTCCTC
*
97449 CAAGTTAGCTTGAGTGT
1 CAAGCTAGCTTGAGTGT
97466 CAAGCTAGCTTGAGTGT
1 CAAGCTAGCTTGAGTGT
**
97483 GGAGCTAGCT
1 CAAGCTAGCT
97493 ATCAAGCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.30
Consensus pattern (17 bp):
CAAGCTAGCTTGAGTGT
Found at i:99908 original size:24 final size:24
Alignment explanation
Indices: 99858--99910 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
99848 GGTGCAGCCT
* * * *
99858 TGTGCTTGGAATGATGGATGGTGA
1 TGTGCATGGAATGACGGATAGTCA
*
99882 TGTGCATGGAATGACGGCTAGTCA
1 TGTGCATGGAATGACGGATAGTCA
99906 TGTGC
1 TGTGC
99911 TCCATCTTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.38, T:0.30
Consensus pattern (24 bp):
TGTGCATGGAATGACGGATAGTCA
Found at i:111103 original size:20 final size:22
Alignment explanation
Indices: 111065--111104 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
111055 CATGCTTAAT
*
111065 CATTCATTTGTTAGTTCATATG
1 CATTCATTTGTTAGCTCATATG
111087 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
111105 GGTCTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:122508 original size:14 final size:14
Alignment explanation
Indices: 122488--122523 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
122478 AGTGCTTCAA
122488 CTTCTTTTCTTTCTT
1 CTTCTTTTCTTT-TT
122503 -TTCTTTTCTTTTT
1 CTTCTTTTCTTTTT
122516 CTTCTTTT
1 CTTCTTTT
122524 GAGTGCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
CTTCTTTTCTTTTT
Found at i:124812 original size:22 final size:22
Alignment explanation
Indices: 124787--124830 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
124777 CCATTCACGC
* *
124787 CCATATCATCATCCTTCCATTA
1 CCATATCATCATCATTCAATTA
* *
124809 CCATCTCTTCATCATTCAATTA
1 CCATATCATCATCATTCAATTA
124831 TCCTTCATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (22 bp):
CCATATCATCATCATTCAATTA
Found at i:130329 original size:24 final size:25
Alignment explanation
Indices: 130294--130348 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
130284 ACTTGGAGCC
*
130294 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
130318 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
130342 TCAAGTG
1 TCAAGTG
130349 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:134482 original size:23 final size:23
Alignment explanation
Indices: 134451--134510 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
134441 ACAAAGTGCT
* *
134451 ACAACAAAAAAA-AAAGCAACAAG
1 ACAAAAAAAAAAGAAAACAA-AAG
134474 ACAAAAAAAAAAGAAAACAAAAG
1 ACAAAAAAAAAAGAAAACAAAAG
* *
134497 AGAAAAGAAAAAGA
1 ACAAAAAAAAAAGA
134511 CTCCTACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.78, C:0.10, G:0.12, T:0.00
Consensus pattern (23 bp):
ACAAAAAAAAAAGAAAACAAAAG
Found at i:134566 original size:14 final size:15
Alignment explanation
Indices: 134532--134578 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
134522 AATTTGGAGT
134532 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
134547 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
134561 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
134578 G
1 G
134579 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:136847 original size:18 final size:18
Alignment explanation
Indices: 136824--136860 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
136814 GACAAGTTGC
136824 ATACTTTAGTGAAAAGTT
1 ATACTTTAGTGAAAAGTT
136842 ATACTTTAGTGAAAAGTT
1 ATACTTTAGTGAAAAGTT
136860 A
1 A
136861 AGTGGTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (18 bp):
ATACTTTAGTGAAAAGTT
Found at i:142064 original size:22 final size:22
Alignment explanation
Indices: 142036--142079 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
142026 AAGTGGACTA
*
142036 GAAGTAGCTTGGAGAGTAGCTG
1 GAAGTAGCTGGGAGAGTAGCTG
142058 GAAGTAGCTGGGAGAGTAGCTG
1 GAAGTAGCTGGGAGAGTAGCTG
142080 AGGAGCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.43, T:0.20
Consensus pattern (22 bp):
GAAGTAGCTGGGAGAGTAGCTG
Found at i:142079 original size:12 final size:12
Alignment explanation
Indices: 142038--142084 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
142028 GTGGACTAGA
*
142038 AGTAGCTTGGAG
1 AGTAGCTGGGAG
142050 AGTAGCT-GGA-
1 AGTAGCTGGGAG
142060 AGTAGCTGGGAG
1 AGTAGCTGGGAG
142072 AGTAGCTGAGGAG
1 AGTAGCTG-GGAG
142085 CTGGGAAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.22
11 6 0.19
12 15 0.47
13 4 0.12
ACGTcount: A:0.28, C:0.09, G:0.45, T:0.19
Consensus pattern (12 bp):
AGTAGCTGGGAG
Found at i:171916 original size:13 final size:13
Alignment explanation
Indices: 171898--171955 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
171888 CTACCTATAA
171898 CATCACCATCTTC
1 CATCACCATCTTC
*
171911 CATCACCAT-TTT
1 CATCACCATCTTC
* * **
171923 CA-CGCC-TATAA
1 CATCACCATCTTC
171934 CATCACCATCTTC
1 CATCACCATCTTC
171947 CATCACCAT
1 CATCACCAT
171956 TGCACGCCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 7 0.21
13 20 0.59
ACGTcount: A:0.28, C:0.41, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:171938 original size:36 final size:35
Alignment explanation
Indices: 171891--171967 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
171881 TAAGAAACTA
*
171891 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTGCACG
171927 CCTATAACATCACCATCTTCCATCACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTGCACG
171962 CCTATA
1 CCTATA
171968 TTATCATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 12 0.30
36 28 0.70
ACGTcount: A:0.29, C:0.39, G:0.04, T:0.29
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTGCACG
Found at i:171987 original size:35 final size:35
Alignment explanation
Indices: 171891--171991 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
171881 TAAGAAACTA
* *
171891 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCAACTTCCATCACCA-TTGCACG
*
171927 CCTATAACATCACCATCTTCCATCACCATTGCACG
1 CCTATAACATCACCAACTTCCATCACCATTGCACG
** * **
171962 CCTATATTATCATCAACTTTTATCACCATT
1 CCTATAACATCACCAACTTCCATCACCATT
171992 TCATGTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 30 0.52
36 28 0.48
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCAACTTCCATCACCATTGCACG
Found at i:185328 original size:19 final size:20
Alignment explanation
Indices: 185287--185337 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
185277 TGAAACCCTT
*
185287 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
185307 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
185326 TGAAGATACATG
1 TGAAAATACATG
185338 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:188726 original size:16 final size:16
Alignment explanation
Indices: 188695--188744 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
188685 TTGGCTTTGC
*
188695 TTTCTTTTTGAATTCTT
1 TTTCTTTTTG-TTTCTT
188712 TTTCTTTTCT-TTTCTT
1 TTTCTTTT-TGTTTCTT
*
188728 CTTCTTTTTGTTTCTT
1 TTTCTTTTTGTTTCTT
188744 T
1 T
188745 CTTTTTGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 18 0.64
17 8 0.29
18 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTCTTTTTGTTTCTT
Found at i:189511 original size:19 final size:20
Alignment explanation
Indices: 189470--189520 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
189460 GAAACCCCTT
*
189470 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
189490 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
189509 TGAAGATACATG
1 TGAAAATACATG
189521 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:193989 original size:13 final size:13
Alignment explanation
Indices: 193971--194041 Score: 76
Period size: 13 Copynumber: 5.7 Consensus size: 13
193961 CTACCTATAA
193971 CATCACCATCTTC
1 CATCACCATCTTC
193984 CATCACCATCTTC
1 CATCACCATCTTC
*
193997 CATCACCAT-TTT
1 CATCACCATCTTC
* * **
194009 CA-CTCC-TATAA
1 CATCACCATCTTC
194020 CATCACCATCTTC
1 CATCACCATCTTC
194033 CATCACCAT
1 CATCACCAT
194042 TGCACGCCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.13
12 7 0.15
13 33 0.70
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:194130 original size:11 final size:11
Alignment explanation
Indices: 194114--194140 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
194104 TACCATCTAT
194114 TCATCCTTCAA
1 TCATCCTTCAA
194125 TCATCCTTCAA
1 TCATCCTTCAA
194136 TCATC
1 TCATC
194141 ATCAAGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (11 bp):
TCATCCTTCAA
Found at i:194249 original size:15 final size:15
Alignment explanation
Indices: 194225--194260 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
194215 TCTTTAATAA
*
194225 CATTTCTTTCCATTT
1 CATTTATTTCCATTT
194240 CATTTATTTCCATTT
1 CATTTATTTCCATTT
194255 CTATTT
1 C-ATTT
194261 CCTTTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (15 bp):
CATTTATTTCCATTT
Found at i:197796 original size:22 final size:20
Alignment explanation
Indices: 197771--197810 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
197761 ATGTTTGTTT
197771 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
197793 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
197811 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:198442 original size:16 final size:16
Alignment explanation
Indices: 198421--198457 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
198411 TAATTTGGGC
198421 ATATCTTGATCTCCCA
1 ATATCTTGATCTCCCA
198437 ATATCTTGATCTCCCA
1 ATATCTTGATCTCCCA
198453 ATATC
1 ATATC
198458 GGATTGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATATCTTGATCTCCCA
Found at i:205341 original size:24 final size:24
Alignment explanation
Indices: 205314--205360 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
205304 TTCTGATTTC
205314 TTTA-TTATCTTATTTTATATTTTG
1 TTTATTTATCTT-TTTTATATTTTG
*
205338 TTTATTTATCTTTTTTTTATTTT
1 TTTATTTATCTTTTTTATATTTT
205361 ATTCTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTATTTATCTTTTTTATATTTTG
Found at i:205342 original size:16 final size:16
Alignment explanation
Indices: 205323--205362 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
205313 CTTTATTATC
205323 TTATTTTATATTTTGT
1 TTATTTTATATTTTGT
* *
205339 TTA-TTTATCTTTTTT
1 TTATTTTATATTTTGT
205354 TTATTTTAT
1 TTATTTTAT
205363 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTATTTTATATTTTGT
Found at i:212628 original size:28 final size:28
Alignment explanation
Indices: 212575--212628 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
212565 ATAAAATGAA
**
212575 TGATAATCATGCTGCCTTGATGTATATG
1 TGATAATCATGCTGAATTGATGTATATG
*
212603 TGATAATCATGCTTAATATGAT-TATA
1 TGATAATCATGCTGAAT-TGATGTATA
212629 AGACTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (28 bp):
TGATAATCATGCTGAATTGATGTATATG
Found at i:213764 original size:50 final size:50
Alignment explanation
Indices: 213681--213776 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
213671 TATAAAGACC
* *
213681 TTGGTGCCAAGATGAACCAACACATTATCATTCGGCCAAGGAAGATAACT
1 TTGGTGCCAAGATGAACCAACACATCATCATTCGACCAAGGAAGATAACT
* *
213731 TTGGTGCCAAGATGAA-CAAGCATATCA-CAATTCGACCAAGGGAGAT
1 TTGGTGCCAAGATGAACCAA-CACATCATC-ATTCGACCAAGGAAGAT
213777 GTATCTTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 4 0.10
50 36 0.90
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (50 bp):
TTGGTGCCAAGATGAACCAACACATCATCATTCGACCAAGGAAGATAACT
Found at i:215559 original size:35 final size:35
Alignment explanation
Indices: 215513--215591 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
215503 ATTATTAAGG
*
215513 GATGGTGATGATATAGGCGTGAAATAGTGATGGAA
1 GATGGTGATGATATAGGCATGAAATAGTGATGGAA
*
215548 GATGGTGATGATATAGGCATGAAATGGTGATGGAA
1 GATGGTGATGATATAGGCATGAAATAGTGATGGAA
*
215583 GATGTTGAT
1 GATGGTGAT
215592 AGACATATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.03, G:0.37, T:0.28
Consensus pattern (35 bp):
GATGGTGATGATATAGGCATGAAATAGTGATGGAA
Found at i:218047 original size:124 final size:124
Alignment explanation
Indices: 217827--218075 Score: 417
Period size: 124 Copynumber: 2.0 Consensus size: 124
217817 TAAATACTTA
* *
217827 TGATGCAAGCACGTTTTCATTAATAAAAGGAGTACTCTTGAAAACTTTTATATTGAAATTACTAT
1 TGATGCAAGCACGTTTTCATCAATAAAAGGAGTACTCTTGAAAACCTTTATATTGAAATTACTAT
* * *
217892 ATATTAGTTATATACTACATATTTTTATAATACAATCCGTGATAAGAATTCTTGTTATG
66 ATATTAGTTATATACGACATACTTTTATAATACAATCCATGATAAGAATTCTTGTTATG
* *
217951 TGATGCAAGCACGTTTTCATCAATAAAGGGAGTACTCTTGAACACCTTTATATTGAAATTACTAT
1 TGATGCAAGCACGTTTTCATCAATAAAAGGAGTACTCTTGAAAACCTTTATATTGAAATTACTAT
* *
218016 ATATTAGTTATATACGACATACTTTTATAATATAATTCATGATAAGAATTCTTGTTATG
66 ATATTAGTTATATACGACATACTTTTATAATACAATCCATGATAAGAATTCTTGTTATG
218075 T
1 T
218076 AGTTAAAGAA
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 116 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (124 bp):
TGATGCAAGCACGTTTTCATCAATAAAAGGAGTACTCTTGAAAACCTTTATATTGAAATTACTAT
ATATTAGTTATATACGACATACTTTTATAATACAATCCATGATAAGAATTCTTGTTATG
Found at i:227759 original size:11 final size:13
Alignment explanation
Indices: 227727--227756 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
227717 TGGCCAAAGA
227727 TGAAAAGGTATGT
1 TGAAAAGGTATGT
227740 TGAAAAGGTATG-
1 TGAAAAGGTATGT
227752 TGAAA
1 TGAAA
227757 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:239555 original size:18 final size:18
Alignment explanation
Indices: 239532--239577 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
239522 ATTCATGCCT
239532 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
239550 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
239568 TTATTTCATT
1 TTAGTTCATT
239578 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:241116 original size:10 final size:9
Alignment explanation
Indices: 241095--241131 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
241085 CGGGTTAGTT
241095 AAAAAATTA
1 AAAAAATTA
241104 AAAAAATTA
1 AAAAAATTA
241113 AAAAAA--A
1 AAAAAATTA
241120 GAAAAAATTA
1 -AAAAAATTA
241130 AA
1 AA
241132 GAGGGGGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 1 0.04
8 6 0.24
9 17 0.68
10 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (9 bp):
AAAAAATTA
Found at i:244712 original size:18 final size:18
Alignment explanation
Indices: 244670--244715 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
244660 TATTTTGATT
*
244670 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
244688 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
244706 AATGAACTAA
1 AATGAACTAA
244716 AGGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:245797 original size:18 final size:18
Alignment explanation
Indices: 245771--245814 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
245761 GTGAAGTATG
*
245771 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
245789 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
245807 AGTGTTGT
1 AATGTTGT
245815 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:249016 original size:19 final size:19
Alignment explanation
Indices: 248989--249031 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
248979 GTGCTGCAAC
248989 AAAAACAAAAAGA-AATAAG
1 AAAAACAAAAAGAGAA-AAG
*
249008 AAAACCAAAAAGAGAAAAG
1 AAAAACAAAAAGAGAAAAG
249027 AAAAA
1 AAAAA
249032 GACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAAGAGAAAAG
Found at i:253710 original size:15 final size:16
Alignment explanation
Indices: 253683--253719 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
253673 CTTTATTATC
253683 TTATTTCATCTTTCAT
1 TTATTTCATCTTTCAT
253699 TTATTT-ATCTTTCAT
1 TTATTTCATCTTTCAT
253714 TTATTT
1 TTATTT
253720 TATTCTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATCTTTCAT
Found at i:254072 original size:8 final size:8
Alignment explanation
Indices: 254059--254108 Score: 66
Period size: 8 Copynumber: 6.0 Consensus size: 8
254049 CTATTTTTTT
254059 CAAAAAAA
1 CAAAAAAA
254067 CAAAAAAA
1 CAAAAAAA
254075 C-AAAAAA
1 CAAAAAAA
254082 CAAAAAAA
1 CAAAAAAA
254090 GGCAAAAAAAA
1 --C-AAAAAAA
254101 CAAAAAAA
1 CAAAAAAA
254109 GAGCCAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.18
8 22 0.58
9 1 0.03
10 1 0.03
11 7 0.18
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:254100 original size:19 final size:19
Alignment explanation
Indices: 254060--254119 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
254050 TATTTTTTTC
254060 AAAAAAACAAAAAAA--C-
1 AAAAAAACAAAAAAAGGCA
254076 -AAAAAACAAAAAAAGGCA
1 AAAAAAACAAAAAAAGGCA
254094 AAAAAAACAAAAAAAGAGCCA
1 AAAAAAACAAAAAAAG-G-CA
254115 AAAAA
1 AAAAA
254120 CCCAAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.37
17 1 0.03
19 15 0.39
20 1 0.03
21 7 0.18
ACGTcount: A:0.82, C:0.12, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAGGCA
Found at i:258977 original size:2 final size:2
Alignment explanation
Indices: 258972--258996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
258962 ATTTATTTTC
258972 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 A
258997 GTTATTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:262388 original size:14 final size:13
Alignment explanation
Indices: 262371--262401 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
262361 ATAAAAAGTT
*
262371 AAAAAATCAAAAG
1 AAAAAAACAAAAG
262384 AAAAAAACAAAAG
1 AAAAAAACAAAAG
262397 AAAAA
1 AAAAA
262402 GGTTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAG
Found at i:262560 original size:15 final size:15
Alignment explanation
Indices: 262540--262574 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
262530 AGATCCATCA
262540 AGTTCAATCTAAGGG
1 AGTTCAATCTAAGGG
262555 AGTTCAATCTAAGGG
1 AGTTCAATCTAAGGG
262570 AGTTC
1 AGTTC
262575 TACCTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (15 bp):
AGTTCAATCTAAGGG
Found at i:268536 original size:14 final size:15
Alignment explanation
Indices: 268517--268545 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
268507 GGAATGTTTG
268517 GTGAGGTT-TTTTTT
1 GTGAGGTTATTTTTT
268531 GTGAGGTTATTTTTT
1 GTGAGGTTATTTTTT
268546 ATTACTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (15 bp):
GTGAGGTTATTTTTT
Found at i:269550 original size:22 final size:21
Alignment explanation
Indices: 269524--269564 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
269514 GGTTATGGAA
269524 TTGATGGTCTTGATGGATGACG
1 TTGATGGTCTTGAT-GATGACG
*
269546 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
269565 AATAGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.05, G:0.37, T:0.39
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGACG
Found at i:270780 original size:15 final size:17
Alignment explanation
Indices: 270762--270814 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 17
270752 AGTTATTATC
270762 ATAATA-AT-TATAGAT
1 ATAATATATATATAGAT
*
270777 ATAATATATATATATAT
1 ATAATATATATATAGAT
*
270794 ATATATATATATATATAT
1 ATA-ATATATATATAGAT
270812 ATA
1 ATA
270815 TGATAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 6 0.18
16 2 0.06
17 9 0.26
18 17 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAATATATATATAGAT
Found at i:270787 original size:2 final size:2
Alignment explanation
Indices: 270770--270815 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
270760 TCATAATAAT
*
270770 TA TA GA TA TA -A 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 TA TA
270811 TA TA T
1 TA TA T
270816 GATAATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:275364 original size:2 final size:2
Alignment explanation
Indices: 275352--275390 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
275342 TCATAATAAC
*
275352 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
275391 GATAATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:285714 original size:10 final size:10
Alignment explanation
Indices: 285695--285725 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
285685 TGGTTTTATG
285695 CTTCATTCTT
1 CTTCATTCTT
*
285705 CTTTATTCTT
1 CTTCATTCTT
285715 CTTCATTCTT
1 CTTCATTCTT
285725 C
1 C
285726 ATTGGTGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.29, G:0.00, T:0.61
Consensus pattern (10 bp):
CTTCATTCTT
Found at i:287842 original size:26 final size:27
Alignment explanation
Indices: 287807--287857 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
287797 TCTTTCTTTC
*
287807 TTTTCTTCTTTTTCT-AAGTGCTTCTT
1 TTTTCTTCTTCTTCTGAAGTGCTTCTT
*
287833 TTTTCTTCTTCTTCTGGAGTGCTTC
1 TTTTCTTCTTCTTCTGAAGTGCTTC
287858 AATTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.06, C:0.22, G:0.12, T:0.61
Consensus pattern (27 bp):
TTTTCTTCTTCTTCTGAAGTGCTTCTT
Found at i:287863 original size:26 final size:26
Alignment explanation
Indices: 287808--287865 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
287798 CTTTCTTTCT
* **
287808 TTTCTTCTTTTTCTAAGTGCTTCTTT
1 TTTCTTCTTCTTCTAAGTGCTTCTAA
*
287834 TTTCTTCTTCTTCTGGAGTGCTTC-AA
1 TTTCTTCTTCTTCT-AAGTGCTTCTAA
287860 TTTCTT
1 TTTCTT
287866 TTGCTGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.09, C:0.21, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTCTTCTAAGTGCTTCTAA
Found at i:300225 original size:16 final size:17
Alignment explanation
Indices: 300185--300286 Score: 74
Period size: 16 Copynumber: 6.2 Consensus size: 17
300175 TAAACATGTG
* *
300185 GATATATTATAT-GCAT
1 GATATATCATATAACAT
300201 GA-ATATCATATAACAT
1 GATATATCATATAACAT
300217 GATAT-TCATAATAA-AT
1 GATATATCAT-ATAACAT
* ** *
300233 GATAAATGTTATATGCAT
1 GATATATCATATA-ACAT
300251 GA-ATATCATATAACAT
1 GATATATCATATAACAT
300267 GATAT-TCATAATAA-AT
1 GATATATCAT-ATAACAT
300283 GATA
1 GATA
300287 AATGGAAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
15 8 0.12
16 35 0.51
17 21 0.31
18 4 0.06
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (17 bp):
GATATATCATATAACAT
Found at i:300246 original size:50 final size:50
Alignment explanation
Indices: 300191--300290 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
300181 TGTGGATATA
300191 TTATATGCATGAATATCATATAACATGATATTCATAATAAATGATAAATG
1 TTATATGCATGAATATCATATAACATGATATTCATAATAAATGATAAATG
300241 TTATATGCATGAATATCATATAACATGATATTCATAATAAATGATAAATG
1 TTATATGCATGAATATCATATAACATGATATTCATAATAAATGATAAATG
300291 GAAACATGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (50 bp):
TTATATGCATGAATATCATATAACATGATATTCATAATAAATGATAAATG
Found at i:311877 original size:24 final size:25
Alignment explanation
Indices: 311849--311910 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
311839 TTGTGAATCA
311849 CCAAAAGTCATGA-CTATTAGTTTT
1 CCAAAAGTCATGATCTATTAGTTTT
* * *
311873 TCAAAAGTCA-CATCTTTTAGTTTT
1 CCAAAAGTCATGATCTATTAGTTTT
*
311897 CCAAAAGCCATGAT
1 CCAAAAGTCATGAT
311911 TTTTTAATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 27 0.90
25 2 0.07
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (25 bp):
CCAAAAGTCATGATCTATTAGTTTT
Found at i:315582 original size:19 final size:20
Alignment explanation
Indices: 315541--315591 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
315531 GAAACCCCTT
* *
315541 TGAAATTACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
315561 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
315580 TGAAGATACATG
1 TGAAAATACATG
315592 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:319772 original size:19 final size:20
Alignment explanation
Indices: 319731--319781 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
319721 GAAACCCCTT
* *
319731 TGAAATTACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
319751 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
319770 TGAAGATACATG
1 TGAAAATACATG
319782 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:324894 original size:22 final size:21
Alignment explanation
Indices: 324857--324897 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
324847 CCATCTCTAT
324857 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
324878 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
324898 ATTCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:325248 original size:22 final size:21
Alignment explanation
Indices: 325215--325263 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 21
325205 AGAAAAGATA
325215 AAAAGAAGAAAAATTCAGAAAAG
1 AAAAGAAGAAAAA-TCA-AAAAG
325238 AAAAGAA-AAAAATCAAAAAG
1 AAAAGAAGAAAAATCAAAAAG
325258 AGAAAG
1 A-AAAG
325264 CAAGCCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.24
21 7 0.28
22 5 0.20
23 7 0.28
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (21 bp):
AAAAGAAGAAAAATCAAAAAG
Found at i:331583 original size:15 final size:16
Alignment explanation
Indices: 331563--331616 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 16
331553 CTTAAATTAT
331563 TATTATTATTATA-AA
1 TATTATTATTATATAA
*
331578 TATTATTATTATATTA
1 TATTATTATTATATAA
*
331594 TATATATTATTAAATAA
1 TAT-TATTATTATATAA
331611 TTATTA
1 -TATTA
331617 CAAGCCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 13 0.39
16 4 0.12
17 13 0.39
18 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTATTATATAA
Found at i:331614 original size:20 final size:20
Alignment explanation
Indices: 331555--331606 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
331545 TCATTTTACT
331555 TAAATTATTATT-AT-TATTA
1 TAAA-TATTATTAATATATTA
*
331574 TAAATATTATTATTATATTA
1 TAAATATTATTAATATATTA
*
331594 TATATATTATTAA
1 TAAATATTATTAA
331607 ATAATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 5 0.18
20 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATATTATTAATATATTA
Found at i:331616 original size:3 final size:3
Alignment explanation
Indices: 331558--331605 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
331548 TTTTACTTAA
* *
331558 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT A-T ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
331602 ATT A
1 ATT A
331606 AATAATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:333115 original size:33 final size:34
Alignment explanation
Indices: 333078--333146 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
333068 TTTTAAATAA
333078 TTAAACATTA-TAAAA-ATTATAATTTAGTTTTAT
1 TTAAA-ATTATTAAAATATTATAATTTAGTTTTAT
* * *
333111 TT-AAATTATTAAAATTTTATTATTTATTTTTAT
1 TTAAAATTATTAAAATATTATAATTTAGTTTTAT
333144 TTA
1 TTA
333147 TTAATATCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
31 4 0.13
32 7 0.23
33 19 0.63
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (34 bp):
TTAAAATTATTAAAATATTATAATTTAGTTTTAT
Found at i:333890 original size:16 final size:15
Alignment explanation
Indices: 333869--333911 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
333859 TCTTTCAAAT
333869 TTTTTATTACTTATTA
1 TTTTTATTA-TTATTA
333885 TTTTTATATATTATTA
1 TTTTTAT-TATTATTA
*
333901 TTATTATTATT
1 TTTTTATTATT
333912 TATTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 19 0.76
17 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATTATTATTA
Found at i:333899 original size:3 final size:3
Alignment explanation
Indices: 333872--333911 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
333862 TTCAAATTTT
*
333872 TTA TTA CTTA TTA TTT TTA TATA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
333912 TATTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:333914 original size:16 final size:15
Alignment explanation
Indices: 333867--333936 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 15
333857 TTTCTTTCAA
*
333867 ATTTT-TTATTACTT
1 ATTTTATTATTATTT
*
333881 ATTATTTTTA-TATATT
1 ATT-TTATTATTAT-TT
333897 ATTATTATTATTATTT
1 ATT-TTATTATTATTT
333913 A-TTTATTTATTTATTT
1 ATTTTA-TTA-TTATTT
333929 ATTTTATT
1 ATTTTATT
333937 CAAGTATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.13
15 8 0.17
16 26 0.55
17 7 0.15
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:333916 original size:4 final size:4
Alignment explanation
Indices: 333907--333932 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
333897 ATTATTATTA
333907 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
333933 TATTCAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:336272 original size:21 final size:22
Alignment explanation
Indices: 336247--336296 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
336237 AGTAAACACC
336247 TTTTCATATATGCA-TTTTCAT
1 TTTTCATATATGCATTTTTCAT
* *
336268 TTTTCATCTTTGCATTTTTCAT
1 TTTTCATATATGCATTTTTCAT
336290 TTTTCAT
1 TTTTCAT
336297 TCATACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTCATATATGCATTTTTCAT
Found at i:336273 original size:7 final size:7
Alignment explanation
Indices: 336261--336297 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
336251 CATATATGCA
336261 TTTTCAT
1 TTTTCAT
336268 TTTTCAT
1 TTTTCAT
*
336275 CTTTGCAT
1 -TTTTCAT
336283 TTTTCAT
1 TTTTCAT
336290 TTTTCAT
1 TTTTCAT
336297 T
1 T
336298 CATACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.14, C:0.16, G:0.03, T:0.68
Consensus pattern (7 bp):
TTTTCAT
Found at i:343190 original size:22 final size:22
Alignment explanation
Indices: 343164--343240 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
343154 ATCTACACTC
343164 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
343186 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
343208 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
343230 TTCAAAGATGA
1 TTCAAAGATGA
343241 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:344069 original size:166 final size:167
Alignment explanation
Indices: 343757--344083 Score: 559
Period size: 166 Copynumber: 2.0 Consensus size: 167
343747 AAAATTAGCA
343757 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAATAGAATGAGAAAAC
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAATA-AATGAGAAAAC
**
343822 GATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
65 GATTTTCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
* *
343887 TCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
**
343925 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAAAT-AATGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAATAAATGAGAAAACG
*
343988 ATTTTCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
66 ATTTTCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
344053 CCTTAGTTTTTTTACTTAATAAACTATTTCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCC
344084 CACATCTGTA
Statistics
Matches: 151, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
165 40 0.26
166 62 0.41
167 6 0.04
168 43 0.28
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (167 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAATAAATGAGAAAACG
ATTTTCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
Found at i:344185 original size:76 final size:76
Alignment explanation
Indices: 344086--344723 Score: 1150
Period size: 76 Copynumber: 8.4 Consensus size: 76
344076 CTATTTCCCA
*
344086 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
344151 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
344162 CATCTTTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
344227 AGCCTTAGGGT
66 AGCCTTAGGGT
*
344238 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
344303 AGCCTTAGGGT
66 AGCCTTAGGGT
*
344314 CATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
344379 AGCCTTACGGA
66 AGCCTTAGGGT
* *
344390 CATCTGTAAGTCCTACAGTGCATGATGTTTACAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
344455 AGCCTTAGGGT
66 AGCCTTAGGGT
*
344466 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGATTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
344531 AGCCTTAGGGT
66 AGCCTTAGGGT
344542 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
344607 AACCTTAGGGT
66 AGCCTTAGGGT
344618 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
344683 AACCTTAGGGT
66 AGCCTTAGGGT
* *
344694 CATCTGTAAGTCCTTCAGTACATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
344724 TTAAGACCTC
Statistics
Matches: 540, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 540 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:344900 original size:12 final size:12
Alignment explanation
Indices: 344885--344932 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 12
344875 AAATTATTAT
344885 TATTATTATAAA
1 TATTATTATAAA
*
344897 TATTATTATATTA
1 TATTATTATA-AA
344910 TATATATTATTAAA
1 TAT-TATTA-TAAA
344924 TAATTATTA
1 T-ATTATTA
344933 CAAGCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.33
13 4 0.13
14 12 0.40
15 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTATAAA
Found at i:346225 original size:31 final size:33
Alignment explanation
Indices: 346190--346252 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
346180 ATAATTAAAC
346190 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
346221 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
346253 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:347047 original size:13 final size:13
Alignment explanation
Indices: 347029--347063 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
347019 TCATCCTATG
347029 CACAAGGCTGCAC
1 CACAAGGCTGCAC
*
347042 CACAAGGTTGCAC
1 CACAAGGCTGCAC
347055 CACAAGGCT
1 CACAAGGCT
347064 CTCTAGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.11
Consensus pattern (13 bp):
CACAAGGCTGCAC
Found at i:347595 original size:23 final size:23
Alignment explanation
Indices: 347569--347613 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
347559 TCAATGGAAG
**
347569 ATGGATGATGGTTTTGAAGTTGA
1 ATGGATGATGGTGATGAAGTTGA
347592 ATGGATGATGGTGATGAAGTTG
1 ATGGATGATGGTGATGAAGTTG
347614 TGTCTGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.36
Consensus pattern (23 bp):
ATGGATGATGGTGATGAAGTTGA
Found at i:350145 original size:19 final size:19
Alignment explanation
Indices: 350094--350134 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
350084 CATTTCTAAT
*
350094 TAGAACCATTGTGTTTTGG
1 TAGAAGCATTGTGTTTTGG
350113 TAGAAGCATTGTGTTTTGG
1 TAGAAGCATTGTGTTTTGG
350132 TAG
1 TAG
350135 GGACATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.41
Consensus pattern (19 bp):
TAGAAGCATTGTGTTTTGG
Found at i:353257 original size:15 final size:14
Alignment explanation
Indices: 353237--353267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
353227 ATCATCATAC
353237 ATATAGATGTAATAT
1 ATATAGATG-AATAT
353252 ATATAGATGAATAT
1 ATATAGATGAATAT
353266 AT
1 AT
353268 TTATGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (14 bp):
ATATAGATGAATAT
Found at i:355093 original size:216 final size:216
Alignment explanation
Indices: 354719--355155 Score: 739
Period size: 216 Copynumber: 2.0 Consensus size: 216
354709 AGATTGAGTG
*
354719 ACATTAAAGTTTCTTTGGAGTAACTTGCGAGACCTTGTGAGAACATTTTTGGTAAGGTCATTCAA
1 ACATTAAAGTTTCTTTGGAGTAACTTGCGAGACCCTGTGAGAACATTTTTGGTAAGGTCATTCAA
* * *
354784 CACATTTCTTTCTATTATTATCACTAACTTGTCTCCTTTATATAGCATCTTTGTTGTCAAAAGAA
66 CACATTTCTTTCTATTATTATCACTAACATGTCACCTTTATATAACATCTTTGTTGTCAAAAGAA
354849 AACTAAGCATTCAAAGCCAAGAAGATGAACAAAGGGAAAATAGCTTCTATACCAAATGTCATGCG
131 AACTAAGCATTCAAAGCCAAGAAGATGAACAAAGGGAAAATAGCTTCTATACCAAATGTCATGCG
* *
354914 GGAGATGAAGTCTACATATGA
196 GGAGATAAAATCTACATATGA
* * * *
354935 ACATTAAAGTTTCTTTGGAGTAACTTGCGAGGCCCTGTGAGAGCATTTTTTGTAAGGTCCTTCAA
1 ACATTAAAGTTTCTTTGGAGTAACTTGCGAGACCCTGTGAGAACATTTTTGGTAAGGTCATTCAA
*
355000 CATATTTCTTTCTATTATTATCACTAACATGTCACCTTTATATAACATCTTTGTTGTCAAAAGAA
66 CACATTTCTTTCTATTATTATCACTAACATGTCACCTTTATATAACATCTTTGTTGTCAAAAGAA
* * *
355065 CACTAAGTATTCAAAGCCAAGAAGATGAACAAAGGGAGAATAGCTTCTATACCAAATGTCATGCG
131 AACTAAGCATTCAAAGCCAAGAAGATGAACAAAGGGAAAATAGCTTCTATACCAAATGTCATGCG
355130 GGAGATAAAATCTACATATGA
196 GGAGATAAAATCTACATATGA
*
355151 TCATT
1 ACATT
355156 GATGGAGGAA
Statistics
Matches: 206, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 206 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (216 bp):
ACATTAAAGTTTCTTTGGAGTAACTTGCGAGACCCTGTGAGAACATTTTTGGTAAGGTCATTCAA
CACATTTCTTTCTATTATTATCACTAACATGTCACCTTTATATAACATCTTTGTTGTCAAAAGAA
AACTAAGCATTCAAAGCCAAGAAGATGAACAAAGGGAAAATAGCTTCTATACCAAATGTCATGCG
GGAGATAAAATCTACATATGA
Found at i:359458 original size:21 final size:21
Alignment explanation
Indices: 359420--359459 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
359410 ACTGCATGAT
* *
359420 GTTTTTTATTGATTTATATTA
1 GTTTTTCATTGATATATATTA
*
359441 GTTTTTCATTTATATATAT
1 GTTTTTCATTGATATATAT
359460 AGGTTTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (21 bp):
GTTTTTCATTGATATATATTA
Found at i:369227 original size:23 final size:23
Alignment explanation
Indices: 369201--369253 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
369191 TGAGAAGACC
369201 AAAGCTAACTTGCTTGAGTTCAT
1 AAAGCTAACTTGCTTGAGTTCAT
369224 AAAGCTAACTTGCTTGAGTTCAT
1 AAAGCTAACTTGCTTGAGTTCAT
*
369247 CAAGCTA
1 AAAGCTA
369254 TAGCTCACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (23 bp):
AAAGCTAACTTGCTTGAGTTCAT
Found at i:371811 original size:18 final size:18
Alignment explanation
Indices: 371780--371817 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
371770 TGCCTATTTC
371780 ATATTCTATAACATAGTT
1 ATATTCTATAACATAGTT
*
371798 ATATT-TATATACATATTT
1 ATATTCTATA-ACATAGTT
371816 AT
1 AT
371818 CTTATACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTCTATAACATAGTT
Found at i:372411 original size:50 final size:49
Alignment explanation
Indices: 372356--372450 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
372346 TGAGAGATTG
*
372356 GGCACCAAAATGAACCAACACAT-CATCATTCGACCAAGGGAGATGTCTTT
1 GGCACCAAAAT-AACCAA-ACATGCACCATTCGACCAAGGGAGATGTCTTT
* * *
372406 GGCACCAAGATAACCAAGCATGTACCATTCGACCAAGGGAGATGT
1 GGCACCAAAATAACCAAACATGCACCATTCGACCAAGGGAGATGT
372451 ATCATCATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 3 0.08
49 27 0.68
50 10 0.25
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (49 bp):
GGCACCAAAATAACCAAACATGCACCATTCGACCAAGGGAGATGTCTTT
Found at i:384484 original size:14 final size:14
Alignment explanation
Indices: 384467--384494 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
384457 ATATGCGTGA
384467 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
384481 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
384495 GTAGTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:396271 original size:17 final size:17
Alignment explanation
Indices: 396246--396290 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
396236 GTATGTTGTT
*
396246 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
396263 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
*
396280 CATTTATGCAT
1 CATTTAAGCAT
396291 CTAGTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:396347 original size:18 final size:18
Alignment explanation
Indices: 396324--396371 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
396314 ATTCATGCAT
*
396324 TTAGTTCATTGAATAAAG
1 TTAGTTCATTAAATAAAG
*
396342 TTAGTTCATTAAATAATG
1 TTAGTTCATTAAATAAAG
*
396360 TTATTTCATTAA
1 TTAGTTCATTAA
396372 TCAAACTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTAAATAAAG
Found at i:400022 original size:18 final size:18
Alignment explanation
Indices: 399999--400046 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
399989 ATTCATGCAT
399999 TTAGTTCATTAAATAAAG
1 TTAGTTCATTAAATAAAG
* *
400017 TTAGTTCATTGAATAATG
1 TTAGTTCATTAAATAAAG
*
400035 TTATTTCATTAA
1 TTAGTTCATTAA
400047 TCAAACTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTAAATAAAG
Found at i:404109 original size:244 final size:243
Alignment explanation
Indices: 403630--405050 Score: 1834
Period size: 244 Copynumber: 5.8 Consensus size: 243
403620 TAACATATTA
* * * * * * * *
403630 ACAT-AAAAAAGTACATCAAAAACACGTAACAACATAAAATAAAGAAAGGTTTAGATTACATGAT
1 ACATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGAT
* **
403694 TAAATTATGTCAAATTAAAGTGTGGGGACTAGAGCTTAAATTTTAGTGTAACAGAGGGACTAATA
66 TAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAATA
* * *
403759 TCATAATTATATTAATAAAAAATAATATCATAATTGTAGCTAAAATTGCATGTAGTAGAAGAAAA
131 TCATAATTATATTAATAAAAAATAATATCATAATTATAACTAAAATTGCATGAAGTAGAAGAAAA
* *
403824 TAAAGAATTAAAACTAGACATGGTGTTAATACTTTTGAAGTTCATAAT
196 TAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
* *
403872 CACATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAA-GGTTTAGATTACAGGG
1 -ACATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGA
** * * * *
403936 TTAAATTATACCAAATTAAAATGTGGGGACTAAAGCTTAAATTTCAACATAACAGATGGACTAAT
65 TTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAAT
* * * * *
404001 ATCATAATTATGTTAATAAAAAAATAATGTTATAATTATAACTAATATTGCATGAAGTAGAATAA
130 ATCATAATTATATTAAT-AAAAAATAATATCATAATTATAACTAAAATTGCATGAAGTAGAAGAA
*
404066 AATAAAGAATTAAAACTAGAAATGGTATTAATACTTCTGAAGTTCATAAT
194 AATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
* * *
404116 AACATTAAAAGAGTACTTCGAAAATACATAACAAACA-AAAATAAAGAAGGGTTTAGACTACAAG
1 -ACATCAAAAGAGTACTTCGAAAATACATAACAAA-AGAAAATAAAGAAGGGTTTAGATTACATG
* * * * *
404180 ATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTAAATTTCAGTATAGCA-ATGGGACAA
64 ATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGA-GGGACTA
* *
404244 ATATCATAATTATATTAATTAAAAATTAATATCATAATTAT-ACGTAAAATT-CATTGAAGTACA
128 ATATCATAATTATATTAA-TAAAAAATAATATCATAATTATAAC-TAAAATTGCA-TGAAGTAGA
* * * * *
404307 AGAAAATAAAGAATCAAAGCTATACATTGTATTAATACTTATGAAGTTCATAAT
190 AGAAAATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
* ** * *
404361 AGCAACAAAAGAGTACTTTAAAAATACATAACAAAAGAAAATAAAGAATGGTTTAGATTACATCA
1 A-CATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGA
* *
404426 TTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCGTAACAGAGGGACTATT
65 TTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAAT
* *
404491 ATCATAATTATATTAATAAAAAATAATATCATAATTATATCTAAAATTGCATGATGCT-GAAGAA
130 ATCATAATTATATTAATAAAAAATAATATCATAATTATAACTAAAATTGCATGAAG-TAGAAGAA
* * * * *
404555 TATAAAGAATTAAAACTAGGCATGGAATTAAAACTTCTGAAGTTCGTAAT
194 AATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
* * * *
404605 AGCATCAAAAGAGTACTTCGAAAAGT-CATAATAAAAGAAAATAAAAAAGGGTTTAAATTACAAG
1 A-CATCAAAAGAGTACTTCGAAAA-TACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATG
* *
404669 ATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCTTAATAGAGGGACTAA
64 ATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAA
* * * * * **
404734 TGTCATAATTATATTAATAAAAAATAATATCTTAATTTTACCTAAAATTGCATGAAATATTAGAA
129 TATCATAATTATATTAATAAAAAATAATATCATAATTATAACTAAAATTGCATGAAGTAGAAGAA
* * * *
404799 AATAAAGAATTAAAACTAGACGTCGTATTAATACTTCTGATGTTCGTAAT
194 AATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
* * * *
404849 -CTAATCAAAAAAGTACCTCGAAAATACATAACCAAAGAAAATAAAGAAGAGTTTAGATTACATG
1 AC--ATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATG
* * * * *
404913 ATTAAATTATGTCAAATTAAACTATGGGGACCAAACCTTAAATTTTAGCATAATAGAGGGACTAA
64 ATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAA
* ** * *
404978 TATCATAATTATATTAATAAAAAATAATTTCATAACCATACCTAAAATTGCATGAGGTAGAAGAA
129 TATCATAATTATATTAATAAAAAATAATATCATAATTATAACTAAAATTGCATGAAGTAGAAGAA
405043 AATGAAAG
194 AAT-AAAG
405051 TATGGGGACT
Statistics
Matches: 1025, Mismatches: 133, Indels: 38
0.86 0.11 0.03
Matches are distributed among these distances:
242 1 0.00
243 92 0.09
244 632 0.62
245 298 0.29
246 2 0.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (243 bp):
ACATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGAT
TAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCATAACAGAGGGACTAATA
TCATAATTATATTAATAAAAAATAATATCATAATTATAACTAAAATTGCATGAAGTAGAAGAAAA
TAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAAGTTCATAAT
Found at i:404758 original size:733 final size:718
Alignment explanation
Indices: 403133--405050 Score: 2432
Period size: 733 Copynumber: 2.7 Consensus size: 718
403123 CATTTATGAT
* **
403133 ATTAATACTTATGAAGTTCATAATAGTATCAAAAGAGTACTTTTAAAATACATAACAAAAG---A
1 ATTAATACTTATGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAA
* * * *
403195 -AAAAAAGGG-TTAAGATTA-TAGTATTAAATTATGTCAAATTAAACTATGGGGACTAATGCTTA
66 TAAAAAAGGGTTTAA-ATTACAAG-ATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTA
* *
403257 AATTTCAGCATAATAGAGGGACTAA-GTTCATAATTATATTAATAAAAAAATAACATCATAATTA
129 AATTTCAGCATAATAGAGGGACTAATG-TCATAATTATATTAATAAAAAAATAATATTATAATTA
* * * *
403321 TACCTAAAATTGCATGATGTAGAAGAAAATAAAGAATAAAAACAAGACATGGTATTAATACTTTT
193 TACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAAAACTAGACATGGTATTAATACTTCT
* * * * * *
403386 GAAGTTCATATTTGCATCAAAAGAGTACTTCGAATATGCACAACAAAAGAAAATAAAGTAGGGTT
258 GAAGTTCATAATTACATCAAAAGAGTACTTCGAAAATACATAACAAAA-AAAATAAAGAAGGGTT
* * * *
403451 TAGATTACATGATTAAATTATGTAAAATTAAAGTTTGGGAACTAAAGCTTAAATTTAAGCATAAC
322 TAGATTACATGATTAAATTATGTCAAATTAAAATATGGGGACTAAAGCTTAAATTTAAGCATAAC
* * * * *
403516 AGTGGGACTAATATAATAACTATATTATTTAAAAATAATATCACAATTATACCTAAAATTGCATG
387 AATGGGACTAATATCATAATTATATTAATTAAAAATAATATCATAATTATACCTAAAATTGCATG
* * * *
403581 AAGTAAAAGAACATAACGAATTAAAACTAGATATGGTAATAACATATTAACATAAAAAAGTACAT
452 AAGTAAAAGAAAATAAAGAATCAAAACTAGACATGGTAATAACATATTAACATAAAAAAGTACAT
* * * *
403646 CAAAAACACGTAACAACATAAAATAAAGAAAGGTTTAGATTACATGATTAAATTATGTCAAATTA
517 CAAAAACACATAACAAAAGAAAATAAAGAAAGGTTTAGATTACATCATTAAATTATGTCAAATTA
* *
403711 AAGTGTGGGGACTAGAGCTTAAATTTTAGTGTAACAGAGGGACTAATATCATAATTATATTAATA
582 AAGTGTGGGGACTAAAGCTTAAATTTTAGCGTAACAGAGGGACTAATATCATAATTATATTAATA
*
403776 AAAAATAATATCATAATTGTAGCTAAAATTGCATGTAGTAGAAGAAAATAAAGAATTAAAACTAG
647 AAAAATAATATCATAATTATAGCTAAAATTGCATGTAGTAGAAGAAAATAAAGAATTAAAACTAG
*
403841 ACATGGT
712 ACATGGA
* *
403848 GTTAATACTTTTGAAGTTCATAATCA-CATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAA
1 ATTAATACTTATGAAGTTCATAAT-AGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAA
* * * * **
403912 ATAAAGAA-GGTTTAGATTACAGGGTTAAATTATACCAAATTAAAATGTGGGGACTAAAGCTTAA
65 ATAAAAAAGGGTTTAAATTACAAGATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTAA
* * * * * *
403976 ATTTCAACATAACAGATGGACTAATATCATAATTATGTTAATAAAAAAATAATGTTATAATTATA
130 ATTTCAGCATAATAGAGGGACTAATGTCATAATTATATTAATAAAAAAATAATATTATAATTATA
* * * *
404041 ACTAATATTGCATGAAGTAGAATAAAATAAAGAATTAAAACTAGAAATGGTATTAATACTTCTGA
195 CCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGA
* *
404106 AGTTCATAATAACATTAAAAGAGTACTTCGAAAATACATAACAAACAAAAATAAAGAAGGGTTTA
260 AGTTCATAATTACATCAAAAGAGTACTTCGAAAATACATAACAAA-AAAAATAAAGAAGGGTTTA
* * * * * *
404171 GACTACAAGATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTAAATTTCAGTATAGCAA
324 GATTACATGATTAAATTATGTCAAATTAAAATATGGGGACTAAAGCTTAAATTTAAGCATAACAA
* *
404236 TGGGACAAATATCATAATTATATTAATTAAAAATTAATATCATAATTATACGTAAAATT-CATTG
389 TGGGACTAATATCATAATTATATTAATTAAAAA-TAATATCATAATTATACCTAAAATTGCA-TG
* * * * *
404300 AAGTACAAGAAAATAAAGAATCAAAGCTATACATTGTATTAATACTTATGAAGTTCATA-ATAGC
452 AAGTAAAAGAAAATAAAGAATCAAAACTAGACATGGTAAT-A-AC--AT--A-TT-A-ACAT---
* * * *
404364 AACAAAAGAGTACTTTAAAAATACATAACAAAAGAAAATAAAGAATGGTTTAGATTACATCATTA
505 -A-AAAA-AGTACATCAAAAACACATAACAAAAGAAAATAAAGAAAGGTTTAGATTACATCATTA
*
404429 AATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCGTAACAGAGGGACTATTATC
567 AATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCGTAACAGAGGGACTAATATC
* *
404494 ATAATTATATTAATAAAAAATAATATCATAATTATATCTAAAATTGCATG-ATGCT-GAAGAATA
632 ATAATTATATTAATAAAAAATAATATCATAATTATAGCTAAAATTGCATGTA-G-TAGAAGAAAA
*
404557 TAAAGAATTAAAACTAGGCATGGA
695 TAAAGAATTAAAACTAGACATGGA
* * * *
404581 ATTAAAACTTCTGAAGTTCGTAATAGCATCAAAAGAGTACTTCGAAAAGT-CATAATAAAAGAAA
1 ATTAATACTTATGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAA-TACATAACAAAAGAAA
*
404645 ATAAAAAAGGGTTTAAATTACAAGATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAA
65 ATAAAAAAGGGTTTAAATTACAAGATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTAA
* * *
404710 ATTTTAGCTTAATAGAGGGACTAATGTCATAATTATATTAAT-AAAAAATAATATCT-TAATTTT
130 ATTTCAGCATAATAGAGGGACTAATGTCATAATTATATTAATAAAAAAATAATAT-TATAATTAT
* ** * *
404773 ACCTAAAATTGCATGAAATATTAGAAAATAAAGAATTAAAACTAGACGTCGTATTAATACTTCTG
194 ACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAAAACTAGACATGGTATTAATACTTCTG
* * * * * *
404838 ATGTTCGTAATCTA-ATCAAAAAAGTACCTCGAAAATACATAACCAAAGAAAATAAAGAAGAGTT
259 AAGTTCATAAT-TACATCAAAAGAGTACTTCGAAAATACATAA-CAAAAAAAATAAAGAAGGGTT
* * * * *
404902 TAGATTACATGATTAAATTATGTCAAATTAAACTATGGGGACCAAACCTTAAATTTTAGCATAAT
322 TAGATTACATGATTAAATTATGTCAAATTAAAATATGGGGACTAAAGCTTAAATTTAAGCATAAC
* * **
404967 AGA-GGGACTAATATCATAATTATATTAATAAAAAATAATTTCATAACCATACCTAAAATTGCAT
387 A-ATGGGACTAATATCATAATTATATTAATTAAAAATAATATCATAATTATACCTAAAATTGCAT
* *
405031 GAGGTAGAAGAAAATGAAAG
451 GAAGTAAAAGAAAAT-AAAG
405051 TATGGGGACT
Statistics
Matches: 1030, Mismatches: 136, Indels: 56
0.84 0.11 0.05
Matches are distributed among these distances:
715 54 0.05
716 1 0.00
718 296 0.29
719 66 0.06
720 1 0.00
721 2 0.00
723 2 0.00
725 1 0.00
726 2 0.00
727 3 0.00
728 1 0.00
731 1 0.00
732 41 0.04
733 465 0.45
734 94 0.09
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (718 bp):
ATTAATACTTATGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAA
TAAAAAAGGGTTTAAATTACAAGATTAAATTATGTCAAATTAAAATGTGGGGACTAAAGCTTAAA
TTTCAGCATAATAGAGGGACTAATGTCATAATTATATTAATAAAAAAATAATATTATAATTATAC
CTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAAAACTAGACATGGTATTAATACTTCTGAA
GTTCATAATTACATCAAAAGAGTACTTCGAAAATACATAACAAAAAAAATAAAGAAGGGTTTAGA
TTACATGATTAAATTATGTCAAATTAAAATATGGGGACTAAAGCTTAAATTTAAGCATAACAATG
GGACTAATATCATAATTATATTAATTAAAAATAATATCATAATTATACCTAAAATTGCATGAAGT
AAAAGAAAATAAAGAATCAAAACTAGACATGGTAATAACATATTAACATAAAAAAGTACATCAAA
AACACATAACAAAAGAAAATAAAGAAAGGTTTAGATTACATCATTAAATTATGTCAAATTAAAGT
GTGGGGACTAAAGCTTAAATTTTAGCGTAACAGAGGGACTAATATCATAATTATATTAATAAAAA
ATAATATCATAATTATAGCTAAAATTGCATGTAGTAGAAGAAAATAAAGAATTAAAACTAGACAT
GGA
Found at i:405119 original size:116 final size:115
Alignment explanation
Indices: 404930--405165 Score: 337
Period size: 116 Copynumber: 2.0 Consensus size: 115
404920 TATGTCAAAT
* *
404930 TAAACTATGGGGACCAAACCTTAAATTTTAGCATAATAGAGGGACTAATATCATAATTATATTAA
1 TAAAGTATGGGGACCAAACCTTAAATTTTAGCATAATAGAGGGACTAATATCATAATTATAATAA
* * **
404995 TAAAAAATAATTTCATAACCATACCTAAAATTGCATGAGGTAGAAGAAAA
66 TAAAAAATAATATCATAACCACACCTAAAATTGCATGAAATAGAAGAAAA
* * *
405045 TGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATAATA
1 T-AAAGTATGGGGACCAAACCTTAAATTTTAGCATAATAGAGGGACTAATATCATAATTATAATA
* * ** *
405110 TTAATAAATAATATCATAATTACACCTAAAATTGCATTAAATAGAAGAAAA
65 ATAAAAAATAATATCATAACCACACCTAAAATTGCATGAAATAGAAGAAAA
405161 TAAAG
1 TAAAG
405166 AATTAAAACT
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
115 5 0.05
116 101 0.95
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (115 bp):
TAAAGTATGGGGACCAAACCTTAAATTTTAGCATAATAGAGGGACTAATATCATAATTATAATAA
TAAAAAATAATATCATAACCACACCTAAAATTGCATGAAATAGAAGAAAA
Found at i:405354 original size:360 final size:360
Alignment explanation
Indices: 404682--405408 Score: 1130
Period size: 360 Copynumber: 2.0 Consensus size: 360
404672 AAATTATGTC
* * * *
404682 AAATTAAAGTGTGGGGACTAAAGCTTAAATTTTAGCTTAATAGAGGGACTAATGTCATAATTATA
1 AAATGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATA
* * ** **
404747 TTAATAAAAAATAATATCTTAATTTTACCTAAAATTGCATGAAATATTAGAAAATAAAGAATTAA
66 ATAATAAAAAATAATATCATAATTACACCTAAAATTGCATGAAATAGAAGAAAATAAAGAATTAA
* *
404812 AACTAGACGTCGTATTAATACTTCTGATGTTCGTAATCTAATCAAAAAAGTACCTCGAAAATACA
131 AACTAGACGTCGTATTAATACTTCTGAAGTTCATAATCTAATCAAAAAAGTACCTCGAAAATACA
* *
404877 TAACCAAAGAAAATAAAGAAGAGTTTAGATTACATGATTAAATTATGTCAAATTAAACTATGGGG
196 TAACAAAAGAAAATAAAGAAGAGTTTAGATTACATGATTAAATTATGTCAAATTAAACTATAGGG
* * * *
404942 ACCAAACCTTAAATTTTAGCATAATAGAGGGACTAATATCATAATTATATTAATAAAAAATAATT
261 ACAAAACCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATGATATTAATAAAAAATAATT
405007 TCATAACCATACCTAAAATTGCATGAGGTAGAAGA
326 TCATAACCATACCTAAAATTGCATGAGGTAGAAGA
405042 AAATGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATA
1 AAATGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATA
* * *
405107 ATATTAATAAATAATATCATAATTACACCTAAAATTGCATTAAATAGAAGAAAATAAAGAATTAA
66 ATAATAAAAAATAATATCATAATTACACCTAAAATTGCATGAAATAGAAGAAAATAAAGAATTAA
* * * * * * * *
405172 AACTATACGTTGTATTGATACTTCTGAAGTTCATAATCTAATTAAAAGAGTACTTTGAAATTACA
131 AACTAGACGTCGTATTAATACTTCTGAAGTTCATAATCTAATCAAAAAAGTACCTCGAAAATACA
* * *
405237 TAACAAAAGAAAATAAAGAAGGGTTTAGATTGCATGATTAAATTATGTTAAATTAAACTATAGGG
196 TAACAAAAGAAAATAAAGAAGAGTTTAGATTACATGATTAAATTATGTCAAATTAAACTATAGGG
* *
405302 ACAAAAGCTTAAATTTCAGTATAACAGAGGGACTAATATCATAATGATATTAATAAAAAATAATT
261 ACAAAACCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATGATATTAATAAAAAATAATT
* *
405367 TCTTAATCATACCTAAAATTGCATGAGGTAGAAGA
326 TCATAACCATACCTAAAATTGCATGAGGTAGAAGA
405402 AAATGAA
1 AAATGAA
405409 GAATCAAAAC
Statistics
Matches: 331, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
360 331 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (360 bp):
AAATGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATA
ATAATAAAAAATAATATCATAATTACACCTAAAATTGCATGAAATAGAAGAAAATAAAGAATTAA
AACTAGACGTCGTATTAATACTTCTGAAGTTCATAATCTAATCAAAAAAGTACCTCGAAAATACA
TAACAAAAGAAAATAAAGAAGAGTTTAGATTACATGATTAAATTATGTCAAATTAAACTATAGGG
ACAAAACCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATGATATTAATAAAAAATAATT
TCATAACCATACCTAAAATTGCATGAGGTAGAAGA
Found at i:405490 original size:244 final size:244
Alignment explanation
Indices: 405042--406315 Score: 1576
Period size: 244 Copynumber: 5.2 Consensus size: 244
405032 AGGTAGAAGA
* * * * * *
405042 AAATGAAAGTATGGGGACTAAAGCTTAAATTTTAGCGTAATAGAGGGACTAATATCATAATTATA
1 AAATTAAAGTGTGGGGACAAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTATA
* * * * * *
405107 ATATTAATAAATAATATCATAATTACACCTAAAATTGCATTAAATAGAAGAAAATAAAGAATTAA
66 TTAATAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
* * * * *** * * *
405172 AACTATACGTTGTATTGATACTTCTGAAGTTCATAATCTAATTAAAAGAGTACTTTGAAATTACA
131 AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACA
* *
405237 TAACAAAAGAAAATAAAGAAGGGTTTAGATTGCATGATTAAATTATGTT
196 TAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTC
* * * * *
405286 AAATTAAACTATAGGGACAAAAGCTTAAATTTCAGTATAACAGAGGGACTAATATCATAATGATA
1 AAATTAAAGTGTGGGGACAAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTATA
* * * * * *
405351 TTAATAAAAAATAATTTCTTAATCATACCTAAAATTGCATGAGGTAGAAGAAAATGAAGAATCAA
66 TTAATAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
*
405416 AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACG
131 AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACA
* * * * *
405481 CAACAAAAGAAAATAAAGATGGATTTAGATTA-TTGGATTAAATATTATGTG
196 TAACAAAAGAAAATAAAGAAGGGTTTAGATTACAT-GATT-AA-ATTATGTC
* * * * * *
405532 AAATTAAAGTGTGGGGACTAAATCTTAAATTTCAACATAACTGATGGACTAATATCATAATTATT
1 AAATTAAAGTGTGGGGACAAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTATA
* *
405597 TTAATAAAAAATAATATCATAATTAGACCTAAAATTGCATGAAGTATAAGAAAATAAAGAATTAA
66 TTAATAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
* * * * *
405662 AACTAGACATGGTATTAATACTTCTGAAGTTCATATTTGCATCAAAAGAGTTCTTCAAAAATACG
131 AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACA
* * *
405727 TAACAAAAGAAAATAAAGAAGGGTTTAGAATACATTATTAAATTATGTT
196 TAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTC
* * * *
405776 AAATTAAAGTTTGGGGACTAAAA-CTTAAACTTCAGCATAACAAAGAGACTAATATCATAATTAT
1 AAATTAAAGTGTGGGGAC-AAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTAT
* * * * * *
405840 AATAATTAAAAAATAATATGACAGTTATACCTAAAATTGCATGAAGTATAAGAAAATAAAAAATT
65 ATTAA-TAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATT
* * * * * * *
405905 ACAAA-TAGACCTGATTTTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGCATTTCAAAAAC
129 A-AAACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAAT
* *
405969 ACATAACAAAATAAAATAAAGAAGGGTTTAGATTACATGATTGAATTATGTC
193 ACATAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTC
* * * * * *
406021 AAATTAAAGTGTCGGGACAAAAGCTTAAATTTCA-CATTAGATAAGGACTAATATCATAATTTTA
1 AAATTAAAGTGTGGGGACAAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTATA
* * *
406085 TTAAT-AAAAATAACATCATAATTATACCTAAAACTGCATGAAGTAGAAGAAAATAAAAAATTAA
66 TTAATAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
* * * *
406149 AACTAGACATGGTAATAATACTTCTGAAGTTCAT-AGACCATTAAAAGAGTACTTCGAAAATACA
131 AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACA
* * *
406213 TACCAAAAGAATATAAA-AAGGGTTTAGATTACACGATTAAATTATGTC
196 TAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTC
*
406261 AAATTAAAGTGTGGGGA-ATAAAGATTAAATTTCAGCATAATC-GAGGGACTAATAT
1 AAATTAAAGTGTGGGGACA-AAAGCTTAAATTTCAGCATAA-CAGAGGGACTAATAT
406316 GTTACACGCC
Statistics
Matches: 882, Mismatches: 136, Indels: 27
0.84 0.13 0.03
Matches are distributed among these distances:
239 1 0.00
240 59 0.07
241 55 0.06
242 79 0.09
243 2 0.00
244 288 0.33
245 184 0.21
246 213 0.24
247 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (244 bp):
AAATTAAAGTGTGGGGACAAAAGCTTAAATTTCAGCATAACAGAGGGACTAATATCATAATTATA
TTAATAAAAAATAATATCATAATTATACCTAAAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
AACTAGACATGGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACA
TAACAAAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTC
Found at i:406572 original size:554 final size:558
Alignment explanation
Indices: 405778--406871 Score: 1600
Period size: 554 Copynumber: 2.0 Consensus size: 558
405768 ATTATGTTAA
*
405778 ATTAAAGTTTGGGGACTAAAACTTAAACTTCAGCATAACAAAGAGACTAATATCATAATTATAAT
1 ATTAAAGTTTGGGGACTAAAACTTAAACTTAAGCATAACAAAGAGACTAATATCATAATTATAAT
* * *
405843 AATTAAAAAATAATATGACAGTTATACCTAAAATTGCATGAAGTATAAGAAAATAAAAAATTACA
66 AATTAAAAAATAATATCACAATTATACCTAAAATTACATGAAGTATAAGAAAATAAAAAATTACA
* * *
405908 AATAGACCTGATTTTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGCATTTCAAAAACACAT
131 AATAGACCTGATTTTAATACTTCTCAAATTCATAATAGCATCAAAAGAGCACTTCAAAAACACAT
* *
405973 AACAAAATAAAATAAAGAAGGGTTTAGATTACATGATTGAATTATGTCAAATTAAAGTGTCGGGA
196 AACAAAATAAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAAATTAAAGTGT-GGGA
* * * *
406038 CAAAAGCTTAAATTTCACATTAGATA-A-GGACTAATATCATAATTTTATTAAT-AAAAATAACA
260 CAAAAGCTTAAATTTCAAAATA-ACAGAGGGACTAATATCATAATTATATTAATAAAAAATAACA
406100 TCATAATTATACCTAAAACTGCATGAAGTAGAAGAAAATAAAAAATTAAAACTAGACATGGTAAT
324 TCATAATTATACCTAAAACTGCATGAAGTAGAAGAAAATAAAAAATTAAAACTAGACATGGTAAT
* * * *
406165 AATACTTCTGAAGTTCATAG-ACCATTAAAAGAGTACT-TCGAAAATACATACCAAAAGAATATA
389 AATACTTCTGAAGTTCATAGTAACATCAAAAGAGTACTAT-GAAAATACATAACAAAAGAAAATA
406228 AA-AAGGGTTTAGATTACACGATTAAATTATGTCAAATTAAAGTGTGGGGAATAAAGA-TTAAAT
453 AAGAAGGGTTTAGATTACACGATTAAATTATGTCAAATTAAAGTGTGGGGAATAAA-ACTTAAAT
* * *
406291 TTCAGCATAATCGAGGGACTAATATGTTACACGCCAATTTTT
517 TTCAGCATAACCGAGAGACGAATATGTTACACGCCAATTTTT
* * * * *
406333 ATTAAA-TTGTGGGGACTAAAGCTTAAATTTAAGCATAATAAAGAGTCTAATATCATAATTATAT
1 ATTAAAGTT-TGGGGACTAAAACTTAAACTTAAGCATAACAAAGAGACTAATATCATAATTATAA
* * *
406397 TAATT-AAAAATAATATCACAATTATACTTAAAATTACATGAAGT-TGAAGAAAATTAAGAATTA
65 TAATTAAAAAATAATATCACAATTATACCTAAAATTACATGAAGTAT-AAGAAAATAAAAAATTA
* * * * *
406460 -AAACTCGACCTTG-TTTTAATACTTCTCAAATTCATAATAGCATGAAAAGAGTACTTCAGAAAT
129 CAAA-TAGACC-TGATTTTAATACTTCTCAAATTCATAATAGCATCAAAAGAGCACTTCAAAAAC
* * * *
406523 TCATAACATAATGAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCGAATTAAAGTGTG
192 ACATAACAAAATAAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAAATTAAAGTGTG
***
406588 GGGTTAAAGCTTAAATTTCAAAATAACAGAGGGACTAATATCATAATTATATTAATAAAAAATAA
257 GGACAAAAGCTTAAATTTCAAAATAACAGAGGGACTAATATCATAATTATATTAATAAAAAATAA
* * * *
406653 TATCATAATTATACCTTAAATTGCATGAAGTAGAAGAAAATAAAGAATTAAAACTAGACATGGTA
322 CATCATAATTATACCTAAAACTGCATGAAGTAGAAGAAAATAAAAAATTAAAACTAGACATGGTA
* * *
406718 ATAATACTTTTGAAGTTCATAGTAACATCAAAGGTGTACTATGAAAATACATAACAAAAGAAAAT
387 ATAATACTTCTGAAGTTCATAGTAACATCAAAAGAGTACTATGAAAATACATAACAAAAGAAAAT
*
406783 AAAGAAGGGTTTAGATTACATGATTAAATTATGTCAAATTAAAGTGTGGGGAATAAAACTTAAAT
452 AAAGAAGGGTTTAGATTACACGATTAAATTATGTCAAATTAAAGTGTGGGGAATAAAACTTAAAT
406848 TTCAGCATAACCGAGAGACGAATA
517 TTCAGCATAACCGAGAGACGAATA
406872 GGTCAAACCC
Statistics
Matches: 480, Mismatches: 48, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
552 2 0.00
553 26 0.05
554 182 0.38
555 152 0.32
556 38 0.08
557 80 0.17
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (558 bp):
ATTAAAGTTTGGGGACTAAAACTTAAACTTAAGCATAACAAAGAGACTAATATCATAATTATAAT
AATTAAAAAATAATATCACAATTATACCTAAAATTACATGAAGTATAAGAAAATAAAAAATTACA
AATAGACCTGATTTTAATACTTCTCAAATTCATAATAGCATCAAAAGAGCACTTCAAAAACACAT
AACAAAATAAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAAATTAAAGTGTGGGAC
AAAAGCTTAAATTTCAAAATAACAGAGGGACTAATATCATAATTATATTAATAAAAAATAACATC
ATAATTATACCTAAAACTGCATGAAGTAGAAGAAAATAAAAAATTAAAACTAGACATGGTAATAA
TACTTCTGAAGTTCATAGTAACATCAAAAGAGTACTATGAAAATACATAACAAAAGAAAATAAAG
AAGGGTTTAGATTACACGATTAAATTATGTCAAATTAAAGTGTGGGGAATAAAACTTAAATTTCA
GCATAACCGAGAGACGAATATGTTACACGCCAATTTTT
Found at i:406789 original size:243 final size:245
Alignment explanation
Indices: 406333--406851 Score: 681
Period size: 243 Copynumber: 2.1 Consensus size: 245
406323 GCCAATTTTT
* * * * *
406333 ATTAAATTGTGGGGACTAAAGCTTAAATTT-AAGCATAATAAAGAGTCTAATATCATAATTATAT
1 ATTAAAGTGTGGGGAATAAAGCTTAAATTTCAAGAATAACAAAGAGACTAATATCATAATTATAT
* * *
406397 TAATTAAAAATAATATCACAATTATACTTAAAATTACATGAAGTTGAAGAAAATTAAGAATTAAA
66 TAATAAAAAATAATATCACAATTATACTTAAAATTACATGAAGTAGAAGAAAATAAAGAATTAAA
* * * ** * * *
406462 ACTCGACCTTGTTTTAATACTTCTCAAATTCATAATAGCATGAAAAGAGTACTTCAGAAATTCAT
131 ACTAGACATGGTAATAATACTTCTCAAATTCATAATAACATCAAAAGAGTACTTCAGAAATACAT
* *
406527 AACATAATGAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCGA
196 AACATAAAGAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAA
* * *
406577 ATTAAAGTGTGGGG-TTAAAGCTTAAATTTCAA-AATAACAGAGGGACTAATATCATAATTATAT
1 ATTAAAGTGTGGGGAATAAAGCTTAAATTTCAAGAATAACAAAGAGACTAATATCATAATTATAT
* *
406640 TAATAAAAAATAATATCATAATTATACCTT-AAATTGCATGAAGTAGAAGAAAATAAAGAATTAA
66 TAATAAAAAATAATATCACAATTATA-CTTAAAATTACATGAAGTAGAAGAAAATAAAGAATTAA
* * * * * * *
406704 AACTAGACATGGTAATAATACTTTTGAAGTTCATAGTAACATCAAAGGTGTACTATGA-AAATAC
130 AACTAGACATGGTAATAATACTTCTCAAATTCATAATAACATCAAAAGAGTACT-TCAGAAATAC
*
406768 ATAACA-AAAGAAAATAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAA
194 ATAACATAAAG-AAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAA
*
406820 ATTAAAGTGTGGGGAATAAAACTTAAATTTCA
1 ATTAAAGTGTGGGGAATAAAGCTTAAATTTCA
406852 GCATAACCGA
Statistics
Matches: 238, Mismatches: 32, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
242 3 0.01
243 200 0.84
244 35 0.15
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.31
Consensus pattern (245 bp):
ATTAAAGTGTGGGGAATAAAGCTTAAATTTCAAGAATAACAAAGAGACTAATATCATAATTATAT
TAATAAAAAATAATATCACAATTATACTTAAAATTACATGAAGTAGAAGAAAATAAAGAATTAAA
ACTAGACATGGTAATAATACTTCTCAAATTCATAATAACATCAAAAGAGTACTTCAGAAATACAT
AACATAAAGAAACAAAGAAGGGTTTAGATTACATGATTAAATTATGTCAA
Found at i:408029 original size:30 final size:30
Alignment explanation
Indices: 407988--408065 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
407978 TGACTTTGAC
407988 TGACAGTTGACTTTGACCAAAGTT-AATCGT
1 TGACAGTTGACTTTGACCAAAGTTAAAT-GT
* *
408018 TGACTGTTGACTTTGACCAGAGTTAAATGT
1 TGACAGTTGACTTTGACCAAAGTTAAATGT
*
408048 TGGCAGTTGACTTTGACC
1 TGACAGTTGACTTTGACC
408066 CAAAAAGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 40 0.93
31 3 0.07
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (30 bp):
TGACAGTTGACTTTGACCAAAGTTAAATGT
Found at i:411497 original size:240 final size:239
Alignment explanation
Indices: 410854--411713 Score: 975
Period size: 240 Copynumber: 3.6 Consensus size: 239
410844 AAATCCCAAC
* * * *
410854 AAATATCGTAATTATACATAAAATTGCATCAAGTATAAGAAAATAAAGAATTAAAACTATACATG
1 AAATATCATAATTATACCTAAAATTGCATGAAGTAT---AAAATAAAGAATTAAAACTAGACATG
* * * * *
410919 GTATTAATATTTCT-AAATTCACAATAGCATCAAAAGAGTA-TTCGAAAATACATAAAAAAAGTA
63 GTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAA
* * * *
410982 AATAAAGAAGCATTTAGATTACAAGATTAAATTATGTTAAATTAAAGTGTAGAGAATAAACCTTA
128 AATAAAGAATCATTTAGATTACAAGATTAAATTATGTCAAATTAAAGTGT-GAGACTAAAGCTTA
** * *
411047 AATTTCTGCATAAC-ATAGGGAATAATATCATATTTATATTAATAAAAA
192 AATTTCAACATAACAAT-GGGACTAATATCATAATTATATTAATAAAAA
* * * *
411095 ATAATATCATAATTACACCTAAAATTGCTTGAAGTAGAAGAAAATAAAGAATTAAAACTATACAT
1 A-AATATCATAATTATACCTAAAATTGCATGAAGT---ATAAAATAAAGAATTAAAACTAGACAT
* * * * *
411160 GGTATTAATACTTCTGAAGTTAATAATAGCATTAAAAGAGTACTTCAAAAATATATAACAAAATA
62 GGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGA
* * * * * * * *
411225 ACATAACGAAAT-GTTTAGATTACAATATTAAATTAAGTCGAATTAAAGTGTGTTGACTAAAGAT
127 AAATAAAG-AATCATTTAGATTACAAGATTAAATTATGTCAAATTAAAGTGTG-AGACTAAAGCT
411289 TAAATTTCAACATAACAATGGGACTAATATCATAATTATATTAATAAGAAA
190 TAAATTTCAACATAACAATGGGACTAATATCATAATTATATTAATAA-AAA
*
411340 AGAATATCATAATTATACCTAAAATTGCATGAAGTAT-AAA-AAAGAATTAAATA-TAGACATTG
1 A-AATATCATAATTATACCTAAAATTGCATGAAGTATAAAATAAAGAATTAAA-ACTAGACATGG
* * * *
411402 TATTAATACTTATGAAGTTCATAATAGAATCAAAAGGGTACTTCGAAAGTACATAACAAAAGAAA
64 TATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAA
* * * *
411467 ATAAAGAATCTTTTAGATTATAGGATTAAATTATGTCAAATTAAAGTGTGGGGACTAAAGCTTAA
129 ATAAAGAATCATTTAGATTACAAGATTAAATTATGTCAAATTAAAGTGT-GAGACTAAAGCTTAA
* * *
411532 ATTTCATCATAACAGA-GGGACTAATACCATAATTATATTATTAAAAA
193 ATTTCAACATAACA-ATGGGACTAATATCATAATTATATTAATAAAAA
* * *
411579 AAATATTATAATTATTCCTAAGA-TGTCATGAAGTATAAGAAAATAAAGAATTAAAACTAGACAT
1 AAATATCATAATTATACCTAAAATTG-CATGAAGTAT---AAAATAAAGAATTAAAACTAGACAT
* * * * *
411643 GATATTAATACTTTTTAAGTTCATAATAGCATCAAAAGAGTGCTTCGAAACA-ACACAACAAAAG
62 GGTATTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAA-ATACATAACAAAAG
411707 AAAATAA
126 AAAATAA
411714 TTATAACACC
Statistics
Matches: 525, Mismatches: 72, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
237 2 0.00
238 29 0.06
239 7 0.01
240 162 0.31
241 7 0.01
242 72 0.14
243 102 0.19
244 104 0.20
245 40 0.08
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (239 bp):
AAATATCATAATTATACCTAAAATTGCATGAAGTATAAAATAAAGAATTAAAACTAGACATGGTA
TTAATACTTCTGAAGTTCATAATAGCATCAAAAGAGTACTTCGAAAATACATAACAAAAGAAAAT
AAAGAATCATTTAGATTACAAGATTAAATTATGTCAAATTAAAGTGTGAGACTAAAGCTTAAATT
TCAACATAACAATGGGACTAATATCATAATTATATTAATAAAAA
Found at i:412345 original size:15 final size:13
Alignment explanation
Indices: 412320--412353 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
412310 AAAAATAAAA
412320 TTTTAAAATATAT
1 TTTTAAAATATAT
412333 TTTTAAAATATAT
1 TTTTAAAATATAT
412346 TTTTAAAA
1 TTTTAAAA
412354 ACATAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:414929 original size:14 final size:14
Alignment explanation
Indices: 414880--414916 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
414870 AAGTCAATGG
414880 GTTGACTCGAACGA
1 GTTGACTCGAACGA
*
414894 GTTGACTCGGACGA
1 GTTGACTCGAACGA
414908 GTTGACTCG
1 GTTGACTCG
414917 TATGGGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (14 bp):
GTTGACTCGAACGA
Found at i:423445 original size:23 final size:23
Alignment explanation
Indices: 423419--423466 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
423409 ATAAAGTACA
*
423419 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
423442 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
423465 AT
1 AT
423467 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:423710 original size:30 final size:29
Alignment explanation
Indices: 423670--423736 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
423660 TCATTTGCAC
* * *
423670 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
423700 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
423729 AATAATAT
1 AA-AATAT
423737 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:423918 original size:23 final size:23
Alignment explanation
Indices: 423892--423954 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
423882 ATATAACCAC
423892 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
423915 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
423938 TACCTATTACATCATAT
1 TACCTATTACATTATAT
423955 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:424416 original size:34 final size:34
Alignment explanation
Indices: 424376--424441 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
424366 AAGTTGTAGA
* *
424376 TTTTGATTTCCTTTTGCTTGGCATCATATGAGAT
1 TTTTGATTTCCTTTTGCTTAGCACCATATGAGAT
424410 TTTTGATTTCCTTTTGCTTAGCACCATATGAG
1 TTTTGATTTCCTTTTGCTTAGCACCATATGAG
424442 CTTTAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (34 bp):
TTTTGATTTCCTTTTGCTTAGCACCATATGAGAT
Found at i:424735 original size:18 final size:18
Alignment explanation
Indices: 424712--424748 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
424702 GCCGAAATAT
424712 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
424730 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
424748 A
1 A
424749 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:425212 original size:23 final size:23
Alignment explanation
Indices: 425186--425248 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
425176 ATATAACCAC
425186 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
425209 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
425232 TACCTATTACATCATAT
1 TACCTATTACATTATAT
425249 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:425491 original size:25 final size:25
Alignment explanation
Indices: 425434--425499 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
425424 CACTCAAAAG
*
425434 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
425459 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
425484 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
425500 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:428280 original size:183 final size:183
Alignment explanation
Indices: 427965--428638 Score: 1190
Period size: 183 Copynumber: 3.7 Consensus size: 183
427955 TTAAAATTAC
*
427965 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* * *
428029 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* *
428094 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* * *
428148 CGATACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
428212 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACTGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
*
428277 TATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
428331 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
428396 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
428461 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
428514 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
*
428579 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAAACCGGTATATTTATA
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGC-ATAAAACCGGTATATTTATA
428639 ATATGTTGAA
Statistics
Matches: 473, Mismatches: 16, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
183 451 0.95
184 22 0.05
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:430105 original size:3 final size:3
Alignment explanation
Indices: 430097--430177 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
430087 ACTTGTTTGG
* * * **
430097 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
430145 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
430178 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:430114 original size:12 final size:12
Alignment explanation
Indices: 430101--430189 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
430091 GTTTGGATCA
* *
430101 TCATCTTCATCA
1 TCATCGTCATCT
* *
430113 TCATCATCATCA
1 TCATCGTCATCT
* *
430125 TCGTCATCATCT
1 TCATCGTCATCT
* *
430137 TCATCGCCAGCT
1 TCATCGTCATCT
*
430149 TCATCGTCATCA
1 TCATCGTCATCT
430161 TCATCGTCATCT
1 TCATCGTCATCT
*
430173 TCATCGTCAGCT
1 TCATCGTCATCT
430185 TCATC
1 TCATC
430190 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:430120 original size:18 final size:18
Alignment explanation
Indices: 430101--430192 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
430091 GTTTGGATCA
* *
430101 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
430119 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
430137 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
430155 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
430173 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
430191 TC
1 TC
430193 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:430153 original size:36 final size:36
Alignment explanation
Indices: 430113--430189 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
430103 ATCTTCATCA
*
430113 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
430149 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
430185 TCATC
1 TCATC
430190 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:430192 original size:6 final size:6
Alignment explanation
Indices: 430101--430192 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
430091 GTTTGGATCA
* * * * * * * *
430101 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
430149 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
430193 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:432040 original size:198 final size:199
Alignment explanation
Indices: 431645--433194 Score: 2774
Period size: 198 Copynumber: 7.8 Consensus size: 199
431635 TTTAAATTAG
* * *
431645 TATCGACACAAACTATATTAGTGGCGACACATGATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
431710 CTTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
431774 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
431839 AAAA
196 AAAA
* *
431843 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
431908 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGTAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
431973 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGCTTTCCATTCATTATGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
432038 AAAA
196 AAAA
*
432042 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
432107 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
432172 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
432236 AAAA
196 AAAA
*
432240 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
432305 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGTAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
432370 CAACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
432435 AAAA
196 AAAA
*
432439 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAA-CGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
432503 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
432567 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
432631 AAAA
196 AAAA
*
432635 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
432700 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGAGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
432765 CGACACTTTTTATATATGGATCGACACTTTATGGGTTCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
432830 AAAA
196 AAAA
432834 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
432899 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTCGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
432964 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTAATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
433028 AAAA
196 AAAA
* * * *
433032 TAGCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
* * *
433097 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
433162 TTGACAC-TTTT-TATATGGATCGACACTTTATGG
130 TCGACACTTTTTATATATGGATCGACACTTTATGG
433195 TAAATTTGCC
Statistics
Matches: 1310, Mismatches: 36, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
196 64 0.05
197 129 0.10
198 580 0.44
199 537 0.41
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:432378 original size:397 final size:398
Alignment explanation
Indices: 431645--433194 Score: 2785
Period size: 397 Copynumber: 3.9 Consensus size: 398
431635 TTTAAATTAG
* * *
431645 TATCGACACAAACTATATTAGTGGCGACACATGATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
431710 CTTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
431774 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
* *
431839 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
431904 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
431969 GTATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGCTTTCCATTCATTATGG
326 GTATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGG
432034 AAAAAAAA
391 AAAAAAAA
*
432042 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
432107 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
432172 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
432236 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
432301 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
432366 GTATCAACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGG
326 GTATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGG
432431 AAAAAAAA
391 AAAAAAAA
*
432439 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAA-CGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
432503 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
432567 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
432631 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
432696 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* *
432761 AG-ATCGACACTTTTTATATATGGATCGACACTTTATGGGTTCACCCTGTTTTCCATTCATTCTG
326 -GTATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATG
432825 GAAAAAAAA
390 GAAAAAAAA
432834 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
432899 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTCGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
432964 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTAATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
* * *
433028 AAAATAGCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
* * * *
433093 TAGACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTT
* *
433158 GGGATTGACAC-TTTT-TATATGGATCGACACTTTATGG
325 GGTATCGACACTTTTTATATATGGATCGACACTTTATGG
433195 TAAATTTGCC
Statistics
Matches: 1120, Mismatches: 26, Indels: 15
0.96 0.02 0.01
Matches are distributed among these distances:
395 326 0.29
396 201 0.18
397 455 0.41
398 138 0.12
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GTATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGG
AAAAAAAA
Done.