Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007495.1 Hibiscus syriacus cultivar Beakdansim tig00020730_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: 426237
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:9761 original size:26 final size:26
Alignment explanation
Indices: 9730--9792 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
9720 CTTGGCTTGC
9730 TTTTCTCTTTTTC-GAAATCTTT-TTCT
1 TTTTCTCTTTTTCTG-AAT-TTTCTTCT
9756 TTTTCT-TATTTTCTGAATTTTCTTCT
1 TTTTCTCT-TTTTCTGAATTTTCTTCT
*
9782 TTTTGTCTTTT
1 TTTTCTCTTTT
9793 CTTTCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.12
26 26 0.81
27 2 0.06
ACGTcount: A:0.10, C:0.16, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTTCTGAATTTTCTTCT
Found at i:10999 original size:32 final size:32
Alignment explanation
Indices: 10962--11098 Score: 91
Period size: 35 Copynumber: 4.1 Consensus size: 32
10952 GTTGATGAAT
*
10962 GAAGGATGAT-TTATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTATGGCG-TGAAATGGTAATG
* *
10994 GAAGGATGATGTTATGGCGTGATATGGTGATG
1 GAAGGATGATGTTATGGCGTGAAATGGTAATG
* *
11026 GAATATGG-TGATGATATAGGCGTGATAATGGTGATG
1 G-A-A-GGATGATGTTAT-GGCGTGA-AATGGTAATG
* * *
11062 GACTATGG-TGATGATATAGCATGATAATGGTAATG
1 GA--A-GGATGATGTTATGGCGTGA-AATGGTAATG
11097 GA
1 GA
11099 CAGATTGTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
32 22 0.24
33 8 0.09
34 9 0.10
35 27 0.30
36 24 0.27
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (32 bp):
GAAGGATGATGTTATGGCGTGAAATGGTAATG
Found at i:11031 original size:13 final size:12
Alignment explanation
Indices: 11014--11078 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
11004 GTTATGGCGT
11014 GATATGGTGATG
1 GATATGGTGATG
11026 GAATATGGTGAT-
1 G-ATATGGTGATG
*
11038 GATATAGGCG-T-
1 GATAT-GGTGATG
11049 GATAATGGTGATG
1 GAT-ATGGTGATG
11062 GACTATGGTGAT-
1 GA-TATGGTGATG
11074 GATAT
1 GATAT
11079 AGCATGATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:11061 original size:36 final size:36
Alignment explanation
Indices: 11000--11098 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
10990 AATGGAAGGA
*
11000 TGATGTTAT-GGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
11034 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
11070 TGATGATATA-GCATGATAATGGTAATGGA
1 TGATGATATAGGCGTGATAATGGTGATGGA
11099 CAGATTGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
34 8 0.14
35 25 0.42
36 26 0.44
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:26947 original size:23 final size:24
Alignment explanation
Indices: 26904--26952 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
26894 AGAGGTTAAG
*
26904 AAAGATGATAAGGTAATGAAAAGA
1 AAAGATGATAAGATAATGAAAAGA
*
26928 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAAAGA
26951 AA
1 AA
26953 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAAAGA
Found at i:27193 original size:17 final size:17
Alignment explanation
Indices: 27171--27203 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27161 GTAGGAGTCT
27171 TTTTCTT-TTCTCTTTTG
1 TTTTCTTCTT-TCTTTTG
27188 TTTTCTTCTTTCTTTT
1 TTTTCTTCTTTCTTTT
27204 TGCTTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTG
Found at i:27596 original size:33 final size:33
Alignment explanation
Indices: 27546--27622 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
27536 TATGCCTTGT
*
27546 TGGTGAAT-GAAGGATGAT-TTAATGGTGATGAAA
1 TGGT-AATGGAAGGATGATGTTAATGGCG-TGAAA
* *
27579 TGGTAATGGAAGGATGATGTTATTGGCGTGATA
1 TGGTAATGGAAGGATGATGTTAATGGCGTGAAA
*
27612 TGGTGATGGAA
1 TGGTAATGGAA
27623 TATGGTGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
33 28 0.74
34 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.31
Consensus pattern (33 bp):
TGGTAATGGAAGGATGATGTTAATGGCGTGAAA
Found at i:27627 original size:13 final size:12
Alignment explanation
Indices: 27608--27693 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
27598 TTATTGGCGT
27608 GATATGGTGATG
1 GATATGGTGATG
27620 GAATATGGTGAT-
1 G-ATATGGTGATG
*
27632 GATATAGGCG-T-
1 GATAT-GGTGATG
27643 GATAATGGTGATG
1 GAT-ATGGTGATG
27656 GACTATGGTGAT-
1 GA-TATGGTGATG
*
27668 GATATAGGCG-T-
1 GATAT-GGTGATG
27679 GATAATGGTGATG
1 GAT-ATGGTGATG
27692 GA
1 GA
27694 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:27663 original size:36 final size:36
Alignment explanation
Indices: 27593--27694 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
27583 AATGGAAGGA
* * *
27593 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
27628 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
27664 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
27695 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:36554 original size:22 final size:22
Alignment explanation
Indices: 36526--36568 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
36516 AGTTGGCGCA
36526 AATTTGGATGGAAGATGATGCC
1 AATTTGGATGGAAGATGATGCC
36548 AATTTGGATGGAAGATGATGC
1 AATTTGGATGGAAGATGATGC
36569 TTGGCCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (22 bp):
AATTTGGATGGAAGATGATGCC
Found at i:39878 original size:33 final size:33
Alignment explanation
Indices: 39799--39902 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
39789 ATACAATCTG
* *
39799 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
39835 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
39868 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
39901 TC
1 TC
39903 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:47628 original size:19 final size:19
Alignment explanation
Indices: 47604--47648 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
47594 AGCTCACAAA
47604 CAGCTCACAAGGAACATGG
1 CAGCTCACAAGGAACATGG
47623 CAGCTCACAAGGAACATGG
1 CAGCTCACAAGGAACATGG
47642 CAGCTCA
1 CAGCTCA
47649 TAGAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.29, G:0.24, T:0.11
Consensus pattern (19 bp):
CAGCTCACAAGGAACATGG
Found at i:57660 original size:36 final size:36
Alignment explanation
Indices: 57613--57690 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
57603 ACAATCTGTC
57613 CATCACCATTATCACGCCTATATCATCACCATAGTA
1 CATCACCATTATCACGCCTATATCATCACCATAGTA
* * *
57649 CATCACCATTATCACGTCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTA
57685 CATCAC
1 CATCAC
57691 TTTCACGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTA
Found at i:58190 original size:14 final size:15
Alignment explanation
Indices: 58156--58202 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
58146 ATTTTGGAGT
58156 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
58171 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
58185 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
58202 G
1 G
58203 TGAGGCAAGT
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:61788 original size:36 final size:36
Alignment explanation
Indices: 61739--61819 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
61729 GATATAATCT
61739 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
61775 GTCCATCATCATTATCATGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
61811 TTCCATCAC
1 GTCCATCAC
61820 TTTCACGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.32
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:63473 original size:35 final size:35
Alignment explanation
Indices: 63434--63511 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
63424 ACTATCTATT
* *
63434 CATCACCACCTTCCATCACCATTTCACGCCTATAA
1 CATCACCACATTCCATCACCATATCACGCCTATAA
** * * *
63469 CATCACCTTATTCCATTACTATATCACGCCTATAT
1 CATCACCACATTCCATCACCATATCACGCCTATAA
*
63504 TATCACCA
1 CATCACCA
63512 ACATATAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.31
Consensus pattern (35 bp):
CATCACCACATTCCATCACCATATCACGCCTATAA
Found at i:67850 original size:36 final size:35
Alignment explanation
Indices: 67810--67886 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
67800 TATCTATTCG
* *
67810 TCACCACCTTCCATTACCATTTTCACGCCTATAACA
1 TCACCACATTCCATTACCA-TATCACGCCTATAACA
* * **
67846 TCACCATATTCCATTACTATATCACGCCTATATTA
1 TCACCACATTCCATTACCATATCACGCCTATAACA
67881 TCACCA
1 TCACCA
67887 ACTTATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (35 bp):
TCACCACATTCCATTACCATATCACGCCTATAACA
Found at i:67884 original size:35 final size:36
Alignment explanation
Indices: 67818--67886 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
67808 CGTCACCACC
*
67818 TTCCATTACCATTTTCACGCCTATAACATCACCATA
1 TTCCATTACCATTATCACGCCTATAACATCACCATA
* **
67854 TTCCATTACTA-TATCACGCCTATATTATCACCA
1 TTCCATTACCATTATCACGCCTATAACATCACCA
67887 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.30, C:0.32, G:0.03, T:0.35
Consensus pattern (36 bp):
TTCCATTACCATTATCACGCCTATAACATCACCATA
Found at i:69393 original size:41 final size:41
Alignment explanation
Indices: 69336--69421 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
69326 ATGTTATGGC
*
69336 AGCTCATTTCATCATTTAAGGAGTTTCAACTTAGCTAGAGG
1 AGCTCATTTCATCATTTAAGGAGTTTCAACTTAGCTAAAGG
69377 AGCTCATTTCATCATTTAAGGAGTTTCAACTTAGCTAAAGG
1 AGCTCATTTCATCATTTAAGGAGTTTCAACTTAGCTAAAGG
69418 AGCT
1 AGCT
69422 AGCATGTAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (41 bp):
AGCTCATTTCATCATTTAAGGAGTTTCAACTTAGCTAAAGG
Found at i:74683 original size:11 final size:13
Alignment explanation
Indices: 74651--74680 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
74641 TGGCCAAAGA
74651 TGAAAAGGTATGT
1 TGAAAAGGTATGT
74664 TGAAAAGGTATG-
1 TGAAAAGGTATGT
74676 TGAAA
1 TGAAA
74681 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:80654 original size:90 final size:89
Alignment explanation
Indices: 80501--80675 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 89
80491 CATAAGACAC
* * *
80501 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAGTTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
80566 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* * *
80591 CCTTTTATATCCGAGTTACCCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
80656 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
80676 ATATTTGGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:84925 original size:19 final size:21
Alignment explanation
Indices: 84875--84926 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
84865 GAAACCCCTT
84875 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
84896 TAAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
84915 TGAAGATACATG
1 TGAAAATACATG
84927 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:87156 original size:19 final size:21
Alignment explanation
Indices: 87109--87160 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
87099 GAAACCCCTT
*
87109 TGAAAATACATGATTTTTAAA
1 TGAAGATACATGATTTTTAAA
*
87130 TAAAGATACATGA-TTTT-AA
1 TGAAGATACATGATTTTTAAA
87149 TGAAGATACATG
1 TGAAGATACATG
87161 CTATTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAGATACATGATTTTTAAA
Found at i:90285 original size:18 final size:16
Alignment explanation
Indices: 90264--90343 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 16
90254 CCTTGGCTTG
90264 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG--TTTTT
90282 CTTT-TTCTTT-TCTTTT
1 CTTTCTT-TTTGT-TTTT
90298 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TG-TTTTT
90315 CTCTTCTTTTGTGTTTTT
1 CT-TTCTTTT-TGTTTTT
90333 CTTTCTTTTTG
1 CTTTCTTTTTG
90344 CACTCCAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
15 5 0.09
16 10 0.19
17 14 0.26
18 15 0.28
19 9 0.17
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (16 bp):
CTTTCTTTTTGTTTTT
Found at i:90302 original size:13 final size:12
Alignment explanation
Indices: 90278--90324 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
90268 CTTTTTGAAT
90278 TTTTC-TTTTTC
1 TTTTCTTTTTTC
90289 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
90302 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
*
90316 TCTTCTTTT
1 TTTTCTTTT
90325 GTGTTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
13 9 0.29
14 8 0.26
15 3 0.10
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:90314 original size:17 final size:17
Alignment explanation
Indices: 90284--90341 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
90274 GAATTTTTCT
*
90284 TTTTCTTTTCTTTTCTTC
1 TTTTCTGTT-TTTTCTTC
90302 TTTTCTGATTTTTCTCTTC
1 TTTTCTG-TTTTT-TCTTC
*
90321 TTTTGTG-TTTTTCTTTC
1 TTTTCTGTTTTTTC-TTC
90338 TTTT
1 TTTT
90342 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
18 9 0.26
19 13 0.37
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTCTGTTTTTTCTTC
Found at i:91099 original size:19 final size:21
Alignment explanation
Indices: 91052--91103 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
91042 GAAACCCCTT
*
91052 TGAAAATACATGATTTTTAAA
1 TGAAGATACATGATTTTTAAA
*
91073 TAAAGATACATGA-TTTT-AA
1 TGAAGATACATGATTTTTAAA
91092 TGAAGATACATG
1 TGAAGATACATG
91104 CTATTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAGATACATGATTTTTAAA
Found at i:94688 original size:19 final size:21
Alignment explanation
Indices: 94645--94696 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
94635 GAAACCCCTT
94645 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
94666 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
94685 TGAAGATACATG
1 TGAAAATACATG
94697 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:107632 original size:36 final size:35
Alignment explanation
Indices: 107559--107663 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
107549 ATTTATAAGT
* * *
107559 TGGTGATAATATAGACGTGATATGGT-AGTGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGA-TGGACTA
107594 TGGTGATGATATAGGCGTGATGATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
107630 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
107664 ATATTGTATC
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 19 0.30
36 44 0.69
37 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:108050 original size:19 final size:20
Alignment explanation
Indices: 108003--108053 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
107993 GAAATCCCTT
**
108003 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
108023 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
108042 TGAAGATACATG
1 TGAAAATACATG
108054 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:111823 original size:36 final size:35
Alignment explanation
Indices: 111750--111854 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
111740 ATTTATAAGT
* * *
111750 TGGTGATAATATAGGCGTGATATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
111785 TGGTGATGATATAGGCGTGATGATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
111821 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
111855 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:112241 original size:19 final size:20
Alignment explanation
Indices: 112194--112244 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
112184 GAAATCCCTT
**
112194 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
112214 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
112233 TGAAGATACATG
1 TGAAAATACATG
112245 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:113950 original size:20 final size:21
Alignment explanation
Indices: 113910--113951 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
113900 TGAAACCCCT
113910 TTGAAAATACATGACTTTTAA
1 TTGAAAATACATGACTTTTAA
113931 TTGAAAATACATGA-TTTTAA
1 TTGAAAATACATGACTTTTAA
113951 T
1 T
113952 GAAGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TTGAAAATACATGACTTTTAA
Found at i:114648 original size:30 final size:31
Alignment explanation
Indices: 114609--114668 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
114599 ACATGCTGCC
**
114609 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
114640 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
114669 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:119805 original size:22 final size:23
Alignment explanation
Indices: 119763--119806 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
119753 CTTTTTGAAT
* *
119763 TTTTCTTATCTTTTCTTTTCTTA
1 TTTTCTGATCTTTTCTCTTCTTA
119786 TTTTCTGAT-TTTTCTCTTCTT
1 TTTTCTGATCTTTTCTCTTCTT
119807 TTGTCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTCTGATCTTTTCTCTTCTTA
Found at i:127067 original size:36 final size:35
Alignment explanation
Indices: 126994--127098 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
126984 ATTTATAAGT
* * *
126994 TGGTGATAATATAGGCGTGATATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
127029 TGGTGATGATATAGGCGTGATGATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
127065 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
127099 ATATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:127885 original size:18 final size:18
Alignment explanation
Indices: 127862--127901 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
127852 TGAAAAGGCA
127862 CTTCTCAGAATGGCAACT
1 CTTCTCAGAATGGCAACT
*
127880 CTTCTCGGAATGGCAACT
1 CTTCTCAGAATGGCAACT
127898 CTTC
1 CTTC
127902 GCGGAATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (18 bp):
CTTCTCAGAATGGCAACT
Found at i:127906 original size:18 final size:18
Alignment explanation
Indices: 127869--127910 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
127859 GCACTTCTCA
*
127869 GAATGGCAACTCTTCTCG
1 GAATGGCAACTCTTCGCG
127887 GAATGGCAACTCTTCGCG
1 GAATGGCAACTCTTCGCG
127905 GAATGG
1 GAATGG
127911 TACAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (18 bp):
GAATGGCAACTCTTCGCG
Found at i:131127 original size:15 final size:14
Alignment explanation
Indices: 131091--131130 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
131081 GAGTCTTTTC
*
131091 TTTCTCTTTTTGTT
1 TTTCTCTTTTTCTT
*
131105 TTTTTCTTCTTTCTT
1 TTTCTCTT-TTTCTT
131120 TTTCTCTTTTT
1 TTTCTCTTTTT
131131 GTTGCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTCTCTTTTTCTT
Found at i:131594 original size:36 final size:35
Alignment explanation
Indices: 131521--131625 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 35
131511 ATTTATAAGC
* *
131521 TGGTGATAATATAGGCGTGATATGGT-AGTGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGA-TGGACTA
131556 TGGTGATGATATAGGCGTGATGATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
131592 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
131626 AGATTGTATC
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 20 0.31
36 44 0.68
37 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:144895 original size:35 final size:37
Alignment explanation
Indices: 144856--144926 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 37
144846 TTAGAAGTTG
144856 GTGATAATATAGGCGTGA-AATGGTGATGGA-ATATA
1 GTGATAATATAGGCGTGATAATGGTGATGGACATATA
*
144891 GTGATGATATAGGCGTGATAATGGTGATGGACATAT
1 GTGATAATATAGGCGTGATAATGGTGATGGACATAT
144927 TGTATCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 17 0.52
36 12 0.36
37 4 0.12
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (37 bp):
GTGATAATATAGGCGTGATAATGGTGATGGACATATA
Found at i:148602 original size:6 final size:6
Alignment explanation
Indices: 148591--148634 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
148581 GATGCAGGAG
*
148591 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
148635 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:152898 original size:19 final size:20
Alignment explanation
Indices: 152835--152906 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
152825 GAAACCCCTT
152835 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
*
152856 TGAAAATACTTGATTTTAAA
1 TGAAAATACATGATTTTAAA
152876 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
152895 TGAAGATACATG
1 TGAAAATACATG
152907 CTCTTGGCCG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 13 0.27
20 23 0.48
21 12 0.25
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:153836 original size:30 final size:31
Alignment explanation
Indices: 153795--153854 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
153785 ACATGTTGCC
**
153795 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
153826 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
153855 TAAAGCTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:159982 original size:17 final size:17
Alignment explanation
Indices: 159951--159999 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
159941 TTGGTGTGCA
*
159951 AAAAGAAAGAAAAAAAAT
1 AAAAG-AAGAGAAAAAAT
*
159969 AAAAGAAGAGAAAAATT
1 AAAAGAAGAGAAAAAAT
*
159986 AAAAGAAAAGAAAA
1 AAAAGAAGAGAAAA
160000 GAAAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAGAAGAGAAAAAAT
Found at i:159994 original size:5 final size:5
Alignment explanation
Indices: 159951--160008 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
159941 TTGGTGTGCA
* * *
159951 AAAAG -AAAG AAAA- AAAAT AAAAG AAGAG AAAAATT AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAA-G AAAAG AAAAG AAAAG
160001 AAAAG AAA
1 AAAAG AAA
160009 TTCAAAAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 8 0.18
5 29 0.66
6 7 0.16
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:167320 original size:20 final size:21
Alignment explanation
Indices: 167283--167321 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
167273 GATGGTCTTG
*
167283 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
167304 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
167322 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:167700 original size:19 final size:20
Alignment explanation
Indices: 167659--167709 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
167649 GAAACCCCTT
*
167659 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
167679 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
167698 TGAAGATACATG
1 TGAAAATACATG
167710 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:168659 original size:30 final size:31
Alignment explanation
Indices: 168619--168678 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
168609 ACATGCTTCC
**
168619 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
168650 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
168679 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:171029 original size:19 final size:21
Alignment explanation
Indices: 170986--171037 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
170976 GAAACCCCTT
170986 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
171007 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
171026 TGAAGATACATG
1 TGAAAATACATG
171038 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:174421 original size:11 final size:11
Alignment explanation
Indices: 174407--174462 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
174397 TCTTTTTGAA
174407 TTCTTTTTCTT
1 TTCTTTTTCTT
174418 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
174431 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
174444 TGTCTTTTTC-T
1 T-TCTTTTTCTT
174455 TTCTTTTT
1 TTCTTTTT
174463 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:174431 original size:19 final size:18
Alignment explanation
Indices: 174407--174462 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
174397 TCTTTTTGAA
174407 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
174425 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
174444 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
174462 T
1 T
174463 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:175232 original size:19 final size:21
Alignment explanation
Indices: 175189--175240 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
175179 GAAACCCCTT
175189 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
175210 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
175229 TGAAGATACATG
1 TGAAAATACATG
175241 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:177211 original size:17 final size:17
Alignment explanation
Indices: 177191--177288 Score: 75
Period size: 17 Copynumber: 5.9 Consensus size: 17
177181 CTTTTTGAAA
177191 TTCTTCTTTTTTTTCTT
1 TTCTTCTTTTTTTTCTT
* *
177208 TTCTTCTATTCTTAT-TT
1 TTCTTCT-TTTTTTTCTT
177225 TT-TTC-TTTTTTTCTT
1 TTCTTCTTTTTTTTCTT
177240 TTCTTTCTTTTTTTGAT-TT
1 TTC-TTCTTTTTTT--TCTT
*
177259 TTC-TCTTCTTTTGTC-T
1 TTCTTCTT-TTTTTTCTT
177275 TT-TTCTTTTTTTTC
1 TTCTTCTTTTTTTTC
177289 ACTCCAATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
14 5 0.08
15 10 0.15
16 11 0.17
17 18 0.28
18 15 0.23
19 5 0.08
20 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (17 bp):
TTCTTCTTTTTTTTCTT
Found at i:177214 original size:8 final size:8
Alignment explanation
Indices: 177191--177250 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
177181 CTTTTTGAAA
177191 TTCTTCTTT
1 TTCTTC-TT
*
177200 TTTTTCTT
1 TTCTTCTT
*
177208 TTCTTCTA
1 TTCTTCTT
*
177216 TTCTTATT
1 TTCTTCTT
*
177224 TTTTTCTT
1 TTCTTCTT
*
177232 TTTTTCTT
1 TTCTTCTT
177240 TTCTTTCTT
1 TTC-TTCTT
177249 TT
1 TT
177251 TTTGATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
8 30 0.71
9 12 0.29
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTCTTCTT
Found at i:177214 original size:32 final size:30
Alignment explanation
Indices: 177173--177251 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
177163 CTTTCCTTGG
*
177173 CTTTGCTTCTTTTTGAAATTCTTCTTTTTTTT
1 CTTTTCTTCTTTTT-AAATTCTTC-TTTTTTT
** *
177205 CTTTTCTTCTATTCTTATTTTTTTCTTTTTTT
1 CTTTTCTTCT-TT-TTAAATTCTTCTTTTTTT
177237 CTTTTCTTTCTTTTT
1 CTTTTC-TTCTTTTT
177252 TTGATTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 2 0.05
32 24 0.60
33 12 0.30
34 2 0.05
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (30 bp):
CTTTTCTTCTTTTTAAATTCTTCTTTTTTT
Found at i:177225 original size:25 final size:23
Alignment explanation
Indices: 177190--177285 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 23
177180 TCTTTTTGAA
177190 ATTCTTCTTTTTTTTCTTTTCTTCT
1 ATTCTT-TTTTTTTTCTTTT-TTCT
*
177215 ATTCTTATTTTTTTCTTTTTTTCT
1 ATTCTTTTTTTTTTC-TTTTTTCT
* **
177239 TTTCTTTCTTTTTTTGATTTTTCT
1 ATTCTTT-TTTTTTTCTTTTTTCT
*
177263 CTTCTTTTGTCTTTTTCTTTTTT
1 ATTCTTTT-T-TTTTTCTTTTTT
177286 TTCACTCCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 31 0.53
25 27 0.46
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (23 bp):
ATTCTTTTTTTTTTCTTTTTTCT
Found at i:177284 original size:24 final size:25
Alignment explanation
Indices: 177224--177284 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
177214 TATTCTTATT
* * *
177224 TTTTTCTTTTTTTCTTTTCTTTCTT
1 TTTTTCTTTTTCTCTTCTCTTTCTC
* *
177249 TTTTTGATTTTTCTCTTCT-TTTGTC
1 TTTTT-CTTTTTCTCTTCTCTTTCTC
177274 TTTTTCTTTTT
1 TTTTTCTTTTT
177285 TTTCACTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 5 0.17
25 14 0.48
26 10 0.34
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (25 bp):
TTTTTCTTTTTCTCTTCTCTTTCTC
Found at i:177285 original size:8 final size:8
Alignment explanation
Indices: 177198--177286 Score: 79
Period size: 8 Copynumber: 10.9 Consensus size: 8
177188 AAATTCTTCT
177198 TTTTTTTC
1 TTTTTTTC
*
177206 TTTTCTTC
1 TTTTTTTC
* * *
177214 TATTCTTA
1 TTTTTTTC
177222 TTTTTTTC
1 TTTTTTTC
177230 TTTTTTTC
1 TTTTTTTC
177238 TTTTCTTTC
1 TTTT-TTTC
*
177247 TTTTTTTGA
1 TTTTTTT-C
*
177256 TTTTTCTC
1 TTTTTTTC
* *
177264 TTCTTTTG
1 TTTTTTTC
*
177272 TCTTTTTC
1 TTTTTTTC
177280 TTTTTTT
1 TTTTTTT
177287 TCACTCCAAT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
8 49 0.78
9 14 0.22
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:177654 original size:20 final size:21
Alignment explanation
Indices: 177617--177655 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
177607 GATGGTCTTG
*
177617 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
177638 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
177656 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:178035 original size:19 final size:20
Alignment explanation
Indices: 177994--178044 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
177984 GAAACCCCTT
*
177994 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
178014 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
178033 TGAAGATACATG
1 TGAAAATACATG
178045 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:179388 original size:17 final size:17
Alignment explanation
Indices: 179348--179400 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
179338 AATTTCTTTT
*
179348 TTTTTCTTCTTTTCTGAATT
1 TTTTTCTTCTTTT-TG--TC
179368 TTTTTCTTCTTTTTGTC
1 TTTTTCTTCTTTTTGTC
179385 -TTTTCTTTCTTTTTGT
1 TTTTTC-TTCTTTTTGT
179401 ACTCCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
19 2 0.06
20 13 0.42
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTCTTCTTTTTGTC
Found at i:179390 original size:16 final size:17
Alignment explanation
Indices: 179369--179400 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
179359 TTCTGAATTT
179369 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
179385 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
179401 ACTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:179977 original size:18 final size:18
Alignment explanation
Indices: 179934--179971 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
179924 GTGAAGTATG
*
179934 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
179952 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
179970 AA
1 AA
179972 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:191128 original size:11 final size:11
Alignment explanation
Indices: 191114--191153 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
191104 TTTTTTTCCA
191114 AAAAAAAAAAC
1 AAAAAAAAAAC
*
191125 AAAAAAAAGAC
1 AAAAAAAAAAC
191136 AAAAAAACAAA-
1 AAAAAAA-AAAC
191147 AAAAAAA
1 AAAAAAA
191154 GCCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:191130 original size:9 final size:9
Alignment explanation
Indices: 191116--191151 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
191106 TTTTTCCAAA
191116 AAAAAAAAC
1 AAAAAAAAC
*
191125 AAAAAAAAG
1 AAAAAAAAC
191134 ACAAAAAAAC
1 A-AAAAAAAC
191144 AAAAAAAA
1 AAAAAAAA
191152 AAGCCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:191140 original size:21 final size:21
Alignment explanation
Indices: 191114--191159 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
191104 TTTTTTTCCA
*
191114 AAAAAAAAAACAAAAAAAAGAC
1 AAAAAAACAA-AAAAAAAAGAC
*
191136 AAAAAAACAAAAAAAAAAGCC
1 AAAAAAACAAAAAAAAAAGAC
191157 AAA
1 AAA
191160 TTTTCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAAAGAC
Found at i:192639 original size:239 final size:239
Alignment explanation
Indices: 192200--192676 Score: 922
Period size: 239 Copynumber: 2.0 Consensus size: 239
192190 TCTTTCAAAG
192200 GACAACGATCCAGACAAGTACATCGGATGGGAAGGAAAAGTTGATCTCATGTTCGCATACCATGA
1 GACAACGATCCAGACAAGTACATCGGATGGGAAGGAAAAGTTGATCTCATGTTCGCATACCATGA
192265 CTGCCCCCAAGATAAACAAGTTCACCTCATCACCATACATTTGAAGGATATGCTCGAACTTGGTG
66 CTGCCCCCAAGATAAACAAGTTCACCTCATCACCATACATTTGAAGGATATGCTCGAACTTGGTG
192330 GATGCAAACAAGGAAAAAGATCCAGAACTTCCAAATTCCAACAATCACTTCTTGGACCGACCTCA
131 GATGCAAACAAGGAAAAAGATCCAGAACTTCCAAATTCCAACAATCACTTCTTGGACCGACCTCA
192395 ACAAACCATGAGGAACCGATTCCTACCGACACATTATACACGAA
196 ACAAACCATGAGGAACCGATTCCTACCGACACATTATACACGAA
192439 GACAACGATCCAGACAAGTACATCGGATGGGAAGGAAAAGTTGATCTCATGTTCGCATACCATGA
1 GACAACGATCCAGACAAGTACATCGGATGGGAAGGAAAAGTTGATCTCATGTTCGCATACCATGA
192504 CTGCCCCCAAGATAAACAAGTTCACCTCATCACCATACAATTTGAAGGATATGCTCGAACTTGGT
66 CTGCCCCCAAGATAAACAAGTTCACCTCATCACCATAC-ATTTGAAGGATATGCTCGAACTTGGT
192569 GGATGCAAACAAGGAAAAAGATCCAGAACTTCCAAATT-CAACAATCA-TTCTTGGACCGACCTC
130 GGATGCAAACAAGGAAAAAGATCCAGAACTTCCAAATTCCAACAATCACTTCTTGGACCGACCTC
192632 AAACAAACCATGAGGAACCGATTCCTACCGACACATTATACACGA
195 -AACAAACCATGAGGAACCGATTCCTACCGACACATTATACACGA
192677 GAAGTTAAAC
Statistics
Matches: 236, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
238 16 0.07
239 156 0.66
240 64 0.27
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (239 bp):
GACAACGATCCAGACAAGTACATCGGATGGGAAGGAAAAGTTGATCTCATGTTCGCATACCATGA
CTGCCCCCAAGATAAACAAGTTCACCTCATCACCATACATTTGAAGGATATGCTCGAACTTGGTG
GATGCAAACAAGGAAAAAGATCCAGAACTTCCAAATTCCAACAATCACTTCTTGGACCGACCTCA
ACAAACCATGAGGAACCGATTCCTACCGACACATTATACACGAA
Found at i:198378 original size:19 final size:21
Alignment explanation
Indices: 198328--198379 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
198318 GAAACCCCTT
198328 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
198349 TAAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
198368 TGAAGATACATG
1 TGAAAATACATG
198380 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:201758 original size:29 final size:28
Alignment explanation
Indices: 201726--201796 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
201716 CTTGGCTTGC
* *
201726 TTTCTCTTTTTTTTTTCTTGTTTTCTTCT
1 TTTCTCTTTTTTTTTTCTTCTTTT-GTCT
** *
201755 TTTCTGATTTTTTTCTCTTCTTTTGTCT
1 TTTCTCTTTTTTTTTTCTTCTTTTGTCT
*
201783 TTT-TCTTTCTTTTT
1 TTTCTCTTTTTTTTT
201797 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
27 7 0.21
28 6 0.18
29 20 0.61
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.77
Consensus pattern (28 bp):
TTTCTCTTTTTTTTTTCTTCTTTTGTCT
Found at i:201796 original size:18 final size:19
Alignment explanation
Indices: 201746--201797 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
201736 TTTTTTCTTG
*
201746 TTTTC-TTCTTTTCTGATTT
1 TTTTCTTTCTTTT-TGATCT
201765 TTTTCTCTTC-TTTTG-TCT
1 TTTTCT-TTCTTTTTGATCT
201783 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
201798 CACTCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 13 0.45
19 7 0.24
20 3 0.10
21 3 0.10
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTCTTTCTTTTTGATCT
Found at i:206211 original size:22 final size:25
Alignment explanation
Indices: 206186--206238 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
206176 AAAATCAGCA
206186 AAGAAATTG-AAGCACTC-AAAA-G
1 AAGAAATTGAAAGCACTCAAAAAGG
206208 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAATTGAAAGCACTCAAAAAGG
206233 AAGAAA
1 AAGAAA
206239 AAGAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.32
23 8 0.29
24 4 0.14
25 7 0.25
ACGTcount: A:0.58, C:0.11, G:0.19, T:0.11
Consensus pattern (25 bp):
AAGAAATTGAAAGCACTCAAAAAGG
Found at i:206244 original size:25 final size:23
Alignment explanation
Indices: 206195--206244 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
206185 AAAGAAATTG
**
206195 AAGCACTCAAAAGAAGAAATTGA
1 AAGCACTCAAAAGAAGAAAAAGA
206218 AAGCACTCAAAAAGGAAGAAAAAGA
1 AAGCACTC-AAAA-GAAGAAAAAGA
206243 AA
1 AA
206245 AGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 4 0.17
25 11 0.48
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGCACTCAAAAGAAGAAAAAGA
Found at i:208501 original size:22 final size:22
Alignment explanation
Indices: 208476--208526 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
208466 CATTCATCCA
208476 TGAATGTTCAATCATTAAATCT
1 TGAATGTTCAATCATTAAATCT
208498 TGAATGTTCAATCATTAAATCT
1 TGAATGTTCAATCATTAAATCT
*
208520 TGTATGT
1 TGAATGT
208527 GCATCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (22 bp):
TGAATGTTCAATCATTAAATCT
Found at i:212171 original size:2 final size:2
Alignment explanation
Indices: 212164--212244 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
212154 TGACAGCGGA
212164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
212206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
212245 AGTTGGTGAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:212811 original size:21 final size:21
Alignment explanation
Indices: 212772--212811 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
212762 AAGGAAGATT
*
212772 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
212793 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
212812 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:212883 original size:23 final size:22
Alignment explanation
Indices: 212835--212889 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
212825 TTGCGGAATT
* *
212835 GATGGTCTTGATGGATGATGAT
1 GATGGTGTTGATGGATGATGAA
212857 GATGGTGTTGAT-GATGAAATGAA
1 GATGGTGTTGATGGATG--ATGAA
212880 GATGGTGTTG
1 GATGGTGTTG
212890 TTGTTGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 11 0.38
23 14 0.48
ACGTcount: A:0.25, C:0.02, G:0.38, T:0.35
Consensus pattern (22 bp):
GATGGTGTTGATGGATGATGAA
Found at i:214942 original size:33 final size:33
Alignment explanation
Indices: 214900--214968 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
214890 GTTGATGAAT
*
214900 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
214933 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
214966 GAA
1 GAA
214969 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:219409 original size:33 final size:33
Alignment explanation
Indices: 219367--219435 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
219357 GTTGATGAAT
*
219367 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
219400 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
219433 GAA
1 GAA
219436 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:223879 original size:33 final size:33
Alignment explanation
Indices: 223837--223905 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
223827 GTTGATGAAT
*
223837 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
223870 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
223903 GAA
1 GAA
223906 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:228458 original size:2 final size:2
Alignment explanation
Indices: 228451--228483 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
228441 TGACGGCGGA
228451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
228484 AGTTGGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229050 original size:21 final size:21
Alignment explanation
Indices: 229011--229050 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
229001 AAGGAAGATT
*
229011 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
229032 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
229051 AAGGATAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:229810 original size:33 final size:33
Alignment explanation
Indices: 229768--229836 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
229758 GATACAATCT
*
229768 TTCCATTACCATATC-ACGCCAATAACATCATCC
1 TTCCATTACCATATCAACACCAATAA-ATCATCC
* *
229801 TTCCATTACCATTTCAACACCATTAAATCATCC
1 TTCCATTACCATATCAACACCAATAAATCATCC
229834 TTC
1 TTC
229837 ATTTATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.35, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATTACCATATCAACACCAATAAATCATCC
Found at i:230205 original size:12 final size:12
Alignment explanation
Indices: 230179--230220 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
230169 TGTTACAACA
230179 AAAAGA-AACAAG
1 AAAAGAGAA-AAG
230191 -AAAGAAGAAAAG
1 AAAAG-AGAAAAG
230203 AAAAGAGAAAAG
1 AAAAGAGAAAAG
230215 AAAAGA
1 AAAAGA
230221 CTCCTACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.15
12 17 0.63
13 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAAAG
Found at i:235447 original size:33 final size:33
Alignment explanation
Indices: 235405--235473 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
235395 GATACAATCT
*
235405 TTCCATTACCATATC-ACGCCAATAACATCATCC
1 TTCCATTACCATATCAACACCAATAA-ATCATCC
* *
235438 TTCCATTACCATTTCAACACCATTAAATCATCC
1 TTCCATTACCATATCAACACCAATAAATCATCC
235471 TTC
1 TTC
235474 ATTTATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.35, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATTACCATATCAACACCAATAAATCATCC
Found at i:241389 original size:31 final size:31
Alignment explanation
Indices: 241354--241431 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
241344 ATGTGATAAT
*
241354 CATGCTTCATATGATTATAAGAATATTCTAA
1 CATGCTTAATATGATTATAAGAATATTCTAA
*
241385 CATGCTTAATATGATTATAAGACTATTCTAA
1 CATGCTTAATATGATTATAAGAATATTCTAA
241416 CATGCTTAATAT-ATTA
1 CATGCTTAATATGATTA
241432 AATAACAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (31 bp):
CATGCTTAATATGATTATAAGAATATTCTAA
Found at i:242658 original size:19 final size:20
Alignment explanation
Indices: 242634--242682 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
242624 TATCCTTTAT
242634 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
242653 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
242673 -TATTATTATT
1 TTATT-TTATT
242683 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:251247 original size:13 final size:11
Alignment explanation
Indices: 251206--251290 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
251196 TACAATCTTC
251206 CATCACCATTAT
1 CATCACCA-TAT
*
251218 CA-CGCCTATAT
1 CATCACC-ATAT
251229 CATCACCATAGT
1 CATCACCATA-T
251241 CCATCACCATTAT
1 -CATCACCA-TAT
*
251254 CA-CGCCTATAT
1 CATCACC-ATAT
251265 CATCACCATATT
1 CATCACCATA-T
251277 CCATCACCATAT
1 -CATCACCATAT
251289 CA
1 CA
251291 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:251251 original size:36 final size:36
Alignment explanation
Indices: 251204--251307 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
251194 GATACAATCT
251204 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
251240 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
251276 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
251308 ACTTCTAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:254622 original size:19 final size:21
Alignment explanation
Indices: 254598--254649 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
254588 CAGCCAAGAG
*
254598 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
254617 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
254638 CATGTATTTTCA
1 CATGTATTTTCA
254650 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:255104 original size:19 final size:17
Alignment explanation
Indices: 255061--255104 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
255051 TATCCTTTAT
*
255061 TTATTTTTATTTCATTC
1 TTATATTTATTTCATTC
255078 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
255098 TTATATT
1 TTATATT
255105 ATTATTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 5 0.22
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:264630 original size:16 final size:17
Alignment explanation
Indices: 264609--264643 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
264599 GGAGTGCAAA
264609 AAGAAAAG-ACAAAAAG
1 AAGAAAAGAACAAAAAG
*
264625 AAGAAAAGAAGAAAAAG
1 AAGAAAAGAACAAAAAG
264642 AA
1 AA
264644 AAAGATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAACAAAAAG
Found at i:265581 original size:19 final size:20
Alignment explanation
Indices: 265533--265584 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
265523 GAAACCCCTT
265533 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTT-AA
265554 TGAAAATACATGATTTTT-A
1 TGAAAATACATGATTTTTAA
*
265573 TGAAGATACATG
1 TGAAAATACATG
265585 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
21 18 0.60
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:273095 original size:11 final size:11
Alignment explanation
Indices: 273074--273115 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
273064 GTGCTGGAAT
273074 CAAGATAAAAA
1 CAAGATAAAAA
* *
273085 TAAGATTAAAA
1 CAAGATAAAAA
273096 CAAGATAAAGAA
1 CAAGATAAA-AA
273108 -AAGATAAA
1 CAAGATAAA
273116 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:275228 original size:33 final size:33
Alignment explanation
Indices: 275186--275254 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
275176 GTTGATGAAT
*
275186 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
275219 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
275252 GAA
1 GAA
275255 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:279690 original size:33 final size:33
Alignment explanation
Indices: 279648--279716 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
279638 GTTGATGAAT
*
279648 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
279681 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
279714 GAA
1 GAA
279717 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:283659 original size:11 final size:11
Alignment explanation
Indices: 283638--283679 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
283628 GTGCTGGAAT
283638 CAAGATAAAAA
1 CAAGATAAAAA
* *
283649 TAAGATTAAAA
1 CAAGATAAAAA
283660 CAAGATAAAGAA
1 CAAGATAAA-AA
283672 -AAGATAAA
1 CAAGATAAA
283680 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:289414 original size:6 final size:6
Alignment explanation
Indices: 289403--289447 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
289393 TCTTTTTGAA
*
289403 TCTTTT TCTTTT TC--TT T-TTTT TCTTTT TCTTTT TGTCTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCT-TTT TCTTT
289448 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
4 3 0.09
5 3 0.09
6 22 0.67
7 5 0.15
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:289423 original size:15 final size:15
Alignment explanation
Indices: 289405--289453 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
289395 TTTTTGAATC
289405 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
289420 TTTTTCTTTTTC-TT
1 TTTTTCTTTTTCTTT
*
289434 TTTGTC-TTTTCTTT
1 TTTTTCTTTTTCTTT
289448 CTTTTT
1 -TTTTT
289454 GCACTCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 5 0.17
14 9 0.30
15 16 0.53
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:289441 original size:23 final size:22
Alignment explanation
Indices: 289404--289453 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
289394 CTTTTTGAAT
*
289404 CTTTTTCTTTTTCT-TTTTTTT
1 CTTTTTCTTTTTCTCTTTTTTC
* *
289425 CTTTTTCTTTTTGTCTTTTCTTT
1 CTTTTTCTTTTTCTCTTTT-TTC
289448 CTTTTT
1 CTTTTT
289454 GCACTCCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.50
22 4 0.15
23 9 0.35
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (22 bp):
CTTTTTCTTTTTCTCTTTTTTC
Found at i:292050 original size:21 final size:21
Alignment explanation
Indices: 292010--292060 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
292000 GCTACGGAAT
*
292010 TGATGGTCTTGATGGATGAAGA
1 TGATGGTGTTGATGGATGAA-A
*
292032 TGATGGTGTTTAT-GATGAAA
1 TGATGGTGTTGATGGATGAAA
292052 TAGATGGTG
1 T-GATGGTG
292061 GTGTGTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 11 0.42
ACGTcount: A:0.27, C:0.02, G:0.35, T:0.35
Consensus pattern (21 bp):
TGATGGTGTTGATGGATGAAA
Found at i:295164 original size:22 final size:22
Alignment explanation
Indices: 295138--295191 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
295128 AGGATGCTTA
295138 AATGGTGATGAAATGATAAGGG
1 AATGGTGATGAAATGATAAGGG
*
295160 AATGGTGATGAAATGATAAGGT
1 AATGGTGATGAAATGATAAGGG
*
295182 AACGGTGATG
1 AATGGTGATG
295192 GTATAGGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.35, T:0.24
Consensus pattern (22 bp):
AATGGTGATGAAATGATAAGGG
Found at i:295384 original size:19 final size:17
Alignment explanation
Indices: 295362--295413 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
295352 TTTCTTATGT
295362 TATACTATAGTTATTATCA
1 TATA-TATAGTTATTAT-A
*
295381 TATATAT-GTAATATATA
1 TATATATAGTTAT-TATA
295398 TATATATAGTTATTAT
1 TATATATAGTTATTAT
295414 GATAATAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 15 0.52
18 10 0.34
19 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATATAGTTATTATA
Found at i:300090 original size:47 final size:47
Alignment explanation
Indices: 300037--300130 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
300027 AATATAAGAT
*
300037 AGGGTAAGAAAGAACTCCCTTAGAATAAGCAATGAAAAACATCCATG
1 AGGGTAAGAAAGAACTACCTTAGAATAAGCAATGAAAAACATCCATG
*
300084 AGGGTAAGAAAGAACTACCTTAGAATCAGCAATGAAAAACATCCATG
1 AGGGTAAGAAAGAACTACCTTAGAATAAGCAATGAAAAACATCCATG
300131 TTGTGATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (47 bp):
AGGGTAAGAAAGAACTACCTTAGAATAAGCAATGAAAAACATCCATG
Found at i:302036 original size:2 final size:2
Alignment explanation
Indices: 302029--302077 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
302019 AGTTATTATC
302029 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
302069 AT AT AT AT A
1 AT AT AT AT A
302078 GTTATTTGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:303665 original size:9 final size:9
Alignment explanation
Indices: 303620--303681 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
303610 TAGAGTACAT
303620 AAAGAAAAGA
1 AAAGAAAA-A
*
303630 AAATACAAAA
1 AAAGA-AAAA
303640 AGAAGAAAAA
1 A-AAGAAAAA
**
303650 TTCAGAAAAA
1 -AAAGAAAAA
303660 AAAGAAAAA
1 AAAGAAAAA
*
303669 AAAGAAGAA
1 AAAGAAAAA
303678 AAAG
1 AAAG
303682 TCAAATATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.45
10 17 0.40
11 6 0.14
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:306597 original size:24 final size:23
Alignment explanation
Indices: 306555--306601 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
306545 ACTTTGCTTA
*
306555 TTTCATATGTTATACTATAGTTAT
1 TTTCATATATTATACTATA-TTAT
306579 TTTCATATATATATA-TATATTAT
1 TTTCATATAT-TATACTATATTAT
306602 ATATATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTCATATATTATACTATATTAT
Found at i:308154 original size:18 final size:18
Alignment explanation
Indices: 308131--308182 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
308121 AAAATTAGAG
308131 TACAAAAAGAAAAGAAAA
1 TACAAAAAGAAAAGAAAA
*
308149 TACAAAAAGAAGA-AAAA
1 TACAAAAAGAAAAGAAAA
*
308166 TTCAAAAA-AAAAGAAAA
1 TACAAAAAGAAAAGAAAA
308183 GAAATAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 15 0.50
18 12 0.40
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.08
Consensus pattern (18 bp):
TACAAAAAGAAAAGAAAA
Found at i:308165 original size:17 final size:17
Alignment explanation
Indices: 308131--308200 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 17
308121 AAAATTAGAG
*
308131 TACAAAAAGAAAAGAAAA
1 TACAAAAAGAAGA-AAAA
308149 TACAAAAAGAAGAAAAA
1 TACAAAAAGAAGAAAAA
* *
308166 TTCAAAAAAAAAGAAAAGA
1 TAC-AAAAAGAAGAAAA-A
308185 -A-ATAAAAGAAGAAAAA
1 TACA-AAAAGAAGAAAAA
308201 GTCAAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 2 0.05
17 17 0.39
18 24 0.55
19 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.11, T:0.07
Consensus pattern (17 bp):
TACAAAAAGAAGAAAAA
Found at i:308172 original size:35 final size:35
Alignment explanation
Indices: 308133--308208 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
308123 AATTAGAGTA
* * *
308133 CAAAAAGAAAAGAAAATACA-AAAAGAAGAAAAATT
1 CAAAAA-AAAAGAAAAGAAATAAAAGAAGAAAAAGT
308168 CAAAAAAAAAGAAAAGAAATAAAAGAAGAAAAAGT
1 CAAAAAAAAAGAAAAGAAATAAAAGAAGAAAAAGT
308203 CAAAAA
1 CAAAAA
308209 TAGAAAGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 11 0.30
35 26 0.70
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (35 bp):
CAAAAAAAAAGAAAAGAAATAAAAGAAGAAAAAGT
Found at i:308208 original size:17 final size:17
Alignment explanation
Indices: 308133--308208 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
308123 AATTAGAGTA
*
308133 CAAAAAGAA-AAGAAAAT
1 CAAAAAGAAGAA-AAAGT
*
308150 ACAAAAAGAAGAAAAATT
1 -CAAAAAGAAGAAAAAGT
* *
308168 CAAAAA-AAAAGAAAAGA
1 CAAAAAGAAGA-AAAAGT
*
308185 AATAAAAGAAGAAAAAGT
1 CA-AAAAGAAGAAAAAGT
308203 CAAAAA
1 CAAAAA
308209 TAGAAAGCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
16 3 0.07
17 15 0.33
18 23 0.50
19 5 0.11
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (17 bp):
CAAAAAGAAGAAAAAGT
Found at i:311119 original size:24 final size:23
Alignment explanation
Indices: 311074--311119 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
311064 CTAACTTTGC
*
311074 TTATTTCATATGTTATACTATAG
1 TTATTTCATATATTATACTATAG
311097 TTATTATCATATATATATA-TATA
1 TTATT-TCATATAT-TATACTATA
311120 TATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (23 bp):
TTATTTCATATATTATACTATAG
Found at i:311207 original size:19 final size:18
Alignment explanation
Indices: 311173--311219 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
311163 GATATAAGTT
311173 ATTATTATATACTATAGTCAC
1 ATTATTATA-ACTATA--CAC
311194 ATTATTATAA-TATACAC
1 ATTATTATAACTATACAC
311211 ATT-TTATAA
1 ATTATTATAA
311220 GTTTATATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.23
17 6 0.23
19 4 0.15
20 1 0.04
21 9 0.35
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTATTATAACTATACAC
Found at i:311552 original size:15 final size:15
Alignment explanation
Indices: 311532--311562 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
311522 AGCGAATAGT
311532 TGCCACCTCAGGAGG
1 TGCCACCTCAGGAGG
311547 TGCCACCTCAGGAGG
1 TGCCACCTCAGGAGG
311562 T
1 T
311563 ACCTTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (15 bp):
TGCCACCTCAGGAGG
Found at i:312779 original size:18 final size:18
Alignment explanation
Indices: 312753--312815 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
312743 AAAATTAGAG
*
312753 TACATAAAGAAAAGAAAA
1 TACAAAAAGAAAAGAAAA
*
312771 TACAAAAAGAAGA-AAAA
1 TACAAAAAGAAAAGAAAA
* *
312788 TTCAGAAA-AAAAGAAAA
1 TACAAAAAGAAAAGAAAA
* *
312805 GAAAAAAAGAA
1 TACAAAAAGAA
312816 GAAAAAGTCA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 3 0.09
17 18 0.53
18 13 0.38
ACGTcount: A:0.75, C:0.05, G:0.13, T:0.08
Consensus pattern (18 bp):
TACAAAAAGAAAAGAAAA
Found at i:312807 original size:13 final size:13
Alignment explanation
Indices: 312791--312815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312781 AGAAAAATTC
312791 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
312804 AGAAAAAAAGAA
1 AGAAAAAAAGAA
312816 GAAAAAGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:312812 original size:34 final size:33
Alignment explanation
Indices: 312762--312829 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
312752 GTACATAAAG
* * *
312762 AAAAGAAAATACAAAAAGAAGAAAAATTCAGAAA
1 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCA-AAA
312796 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
1 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
312829 A
1 A
312830 TAGAAAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.06
Consensus pattern (33 bp):
AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
Found at i:315743 original size:24 final size:23
Alignment explanation
Indices: 315698--315743 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
315688 CTAACTTTGC
*
315698 TTATTTCATATGTTATACTATAG
1 TTATTTCATATATTATACTATAG
315721 TTATTATCATATATATATA-TATA
1 TTATT-TCATATAT-TATACTATA
315744 TATATATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (23 bp):
TTATTTCATATATTATACTATAG
Found at i:320700 original size:24 final size:24
Alignment explanation
Indices: 320645--320693 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
320635 AGTGCAAAAG
* *
320645 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
320669 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
320692 AA
1 AA
320694 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:325822 original size:21 final size:22
Alignment explanation
Indices: 325782--325831 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
325772 ACAATCTGTC
325782 CATCACCATTATCACGCCTATAT
1 CATCA-CATTATCACGCCTATAT
*
325805 CATCACATT-TCACTCCTATAT
1 CATCACATTATCACGCCTATAT
*
325826 TATCAC
1 CATCAC
325832 CAACTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.30, C:0.34, G:0.02, T:0.34
Consensus pattern (22 bp):
CATCACATTATCACGCCTATAT
Done.