Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008439.1 Hibiscus syriacus cultivar Beakdansim tig00111238_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: 2703160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:1299 original size:80 final size:80
Alignment explanation
Indices: 1166--1325 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
1156 AAAGATATTT
1166 TGTAGCTTTCATTGAATTCTGGGCGAGACAAGCTAATCTAAAATCAGTGGGGAGTTTATTTTTTG
1 TGTAGCTTTCATTGAATTCTGGGCGAGACAAGCTAATCTAAAATCAGTGGGGAGTTTATTTTTTG
1231 GATGAAAAATCTGCC
66 GATGAAAAATCTGCC
1246 TGTAGCTTTCATTGAATTCTGGGCGAGACAAGCTAATCTAAAATCAGTGGGGAGTTTATTTTTTG
1 TGTAGCTTTCATTGAATTCTGGGCGAGACAAGCTAATCTAAAATCAGTGGGGAGTTTATTTTTTG
1311 GATGAAAAATCTGCC
66 GATGAAAAATCTGCC
1326 CACCTGCTCG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (80 bp):
TGTAGCTTTCATTGAATTCTGGGCGAGACAAGCTAATCTAAAATCAGTGGGGAGTTTATTTTTTG
GATGAAAAATCTGCC
Found at i:6600 original size:21 final size:21
Alignment explanation
Indices: 6574--6614 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6564 GTTTGTTAAA
6574 ATGATTTAAAAAATAAATAAT
1 ATGATTTAAAAAATAAATAAT
* *
6595 ATGATTTTAAGAATAAATAA
1 ATGATTTAAAAAATAAATAA
6615 ATTAGTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
ATGATTTAAAAAATAAATAAT
Found at i:11025 original size:13 final size:13
Alignment explanation
Indices: 11007--11033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10997 TTTAGTCTTA
11007 TTCGAATATTATT
1 TTCGAATATTATT
11020 TTCGAATATTATT
1 TTCGAATATTATT
11033 T
1 T
11034 AATCAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TTCGAATATTATT
Found at i:12866 original size:21 final size:22
Alignment explanation
Indices: 12842--12894 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
12832 GCGTATTCAG
12842 TTATATATTTATTCTA-TTTAT
1 TTATATATTTATTCTATTTTAT
* *
12863 TTATATATGTATTGTATTTTAT
1 TTATATATTTATTCTATTTTAT
*
12885 TT-TATTTTTA
1 TTATATATTTA
12895 ATTTTCTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (22 bp):
TTATATATTTATTCTATTTTAT
Found at i:13351 original size:39 final size:39
Alignment explanation
Indices: 13308--13388 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
13298 TTTTACAATC
13308 ATTTTATACATAATTAAATTCCTTTCAATATCTTTTATT
1 ATTTTATACATAATTAAATTCCTTTCAATATCTTTTATT
* * * * *
13347 ATTTTATACATCATTAAATTTCTTTTAATGTTTTTTATT
1 ATTTTATACATAATTAAATTCCTTTCAATATCTTTTATT
13386 ATT
1 ATT
13389 CTGTCAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.58
Consensus pattern (39 bp):
ATTTTATACATAATTAAATTCCTTTCAATATCTTTTATT
Found at i:19204 original size:2 final size:2
Alignment explanation
Indices: 19197--19226 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19187 ACTCAATTTC
19197 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19227 CTCACCGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:36433 original size:28 final size:30
Alignment explanation
Indices: 36402--36457 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
36392 CAAAAATAAC
*
36402 ATACAGAAGA-AA-ACACACTCCTACAAAA
1 ATACAGAAGACAAGAAACACTCCTACAAAA
**
36430 ATACTTAAGACAAGAAACACTCCTACAA
1 ATACAGAAGACAAGAAACACTCCTACAA
36458 TACCTCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 2 0.09
30 13 0.57
ACGTcount: A:0.54, C:0.25, G:0.07, T:0.14
Consensus pattern (30 bp):
ATACAGAAGACAAGAAACACTCCTACAAAA
Found at i:47028 original size:32 final size:31
Alignment explanation
Indices: 46960--47079 Score: 154
Period size: 30 Copynumber: 3.9 Consensus size: 31
46950 GAATGACCTA
* *
46960 TCCATATGTTTCGAATAACATAGGTAA-CTG
1 TCCATATGTCTCGAATGACATAGGTAATCTG
*
46990 TCCATATGTCTCGAAGGACATAGGTAATCCTG
1 TCCATATGTCTCGAATGACATAGGTAAT-CTG
* *
47022 TCCATATGTCCCGAATGACATAGGTAAAT-TA
1 TCCATATGTCTCGAATGACATAGGT-AATCTG
*
47053 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCTCGAATGACATAGGTAA
47080 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.33
31 24 0.30
32 26 0.33
33 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (31 bp):
TCCATATGTCTCGAATGACATAGGTAATCTG
Found at i:47077 original size:63 final size:62
Alignment explanation
Indices: 46960--47079 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
46950 GAATGACCTA
** * *
46960 TCCATATGTTTCGAATAACATAGGTAACTGTCCATATGTCTCGAAGGACATAGGTAATCCTG
1 TCCATATGTCCCGAATAACATAGGTAACTATCCATATGTCTCGAAAGACATAGGTAATCCTG
* *
47022 TCCATATGTCCCGAATGACATAGGTAAATTATCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCCCGAATAACATAGGT-AACTATCCATATGTCTCGAAAGACATAGGTAA
47080 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 22 0.43
63 29 0.57
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (62 bp):
TCCATATGTCCCGAATAACATAGGTAACTATCCATATGTCTCGAAAGACATAGGTAATCCTG
Found at i:50240 original size:13 final size:13
Alignment explanation
Indices: 50222--50246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50212 GCCTTTTCCA
50222 AAACCCTAAAAAG
1 AAACCCTAAAAAG
50235 AAACCCTAAAAA
1 AAACCCTAAAAA
50247 TAATAATCGC
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:0.64, C:0.24, G:0.04, T:0.08
Consensus pattern (13 bp):
AAACCCTAAAAAG
Found at i:51447 original size:19 final size:21
Alignment explanation
Indices: 51420--51458 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
51410 CCCTACTTGC
*
51420 AATTTTTTCT-AT-TTTGTTT
1 AATTATTTCTCATGTTTGTTT
51439 AATTATTTCTCATGTTTGTT
1 AATTATTTCTCATGTTTGTT
51459 ATTCTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (21 bp):
AATTATTTCTCATGTTTGTTT
Found at i:51798 original size:18 final size:18
Alignment explanation
Indices: 51736--51806 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
51726 TGAGGATGAT
*
51736 GACGATGATGATTCTGAG
1 GACGAAGATGATTCTGAG
* * *
51754 GATGAA-AGTGGTTCTGAC
1 GACGAAGA-TGATTCTGAG
**
51772 GACTCAGATGATTCTGAG
1 GACGAAGATGATTCTGAG
*
51790 GACGAAGATGAATCTGA
1 GACGAAGATGATTCTGA
51807 TGAGGTTTCT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
17 1 0.03
18 37 0.95
19 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (18 bp):
GACGAAGATGATTCTGAG
Found at i:55472 original size:48 final size:48
Alignment explanation
Indices: 55395--55486 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
55385 AAGAAAAGAA
* * *
55395 CAATGTTTTTCAGTTTCTGTGATCCCAAAAGAGCCTACTTTTCCTGAT
1 CAATGTTGTTCAGTTTCTGGGATCACAAAAGAGCCTACTTTTCCTGAT
*
55443 CAATGTTGTTCGGTTTCTGGGATCACAAAAGAGCCTACTTTTCC
1 CAATGTTGTTCAGTTTCTGGGATCACAAAAGAGCCTACTTTTCC
55487 AACTAGACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (48 bp):
CAATGTTGTTCAGTTTCTGGGATCACAAAAGAGCCTACTTTTCCTGAT
Found at i:57798 original size:15 final size:15
Alignment explanation
Indices: 57778--57808 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57768 AGCTTCAAGG
57778 TAATATTCTACACTT
1 TAATATTCTACACTT
57793 TAATATTCTACACTT
1 TAATATTCTACACTT
57808 T
1 T
57809 TATTTGTATC
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:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATTCTACACTT
Found at i:59078 original size:2 final size:2
Alignment explanation
Indices: 59071--59095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59061 TTAGAAGCAA
59071 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
59096 AAACACCAAT
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:62052 original size:33 final size:33
Alignment explanation
Indices: 62015--62078 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
62005 TAATGCTTAA
*
62015 AAAATTAAAATGATATATATTAAATGTTTTTAT
1 AAAATTAAAATGACATATATTAAATGTTTTTAT
*
62048 AAAATTAAAATGACATGTATTAAATGTTTTT
1 AAAATTAAAATGACATATATTAAATGTTTTT
62079 TATAGTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (33 bp):
AAAATTAAAATGACATATATTAAATGTTTTTAT
Found at i:63548 original size:17 final size:17
Alignment explanation
Indices: 63526--63576 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
63516 TATTTCTAAG
63526 ATTAATCATATTAAAAA
1 ATTAATCATATTAAAAA
* ** *
63543 ATTAATC-TTTTCTAAG
1 ATTAATCATATTAAAAA
63559 ATTAATCATATTAAAAA
1 ATTAATCATATTAAAAA
63576 A
1 A
63577 ATTTAATCTT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTAATCATATTAAAAA
Found at i:63555 original size:33 final size:35
Alignment explanation
Indices: 63518--63588 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 35
63508 AAGAAAAATA
63518 TTTCTAAGATTAATCATATT-AAAAAA-TTAATCT
1 TTTCTAAGATTAATCATATTAAAAAAATTTAATCT
63551 TTTCTAAGATTAATCATATTAAAAAAATTTAATCT
1 TTTCTAAGATTAATCATATTAAAAAAATTTAATCT
63586 TTT
1 TTT
63589 AATAATTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 20 0.56
34 6 0.17
35 10 0.28
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTCTAAGATTAATCATATTAAAAAAATTTAATCT
Found at i:63564 original size:16 final size:17
Alignment explanation
Indices: 63518--63567 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
63508 AAGAAAAATA
63518 TTTCTAAGATTAATCAT
1 TTTCTAAGATTAATCAT
* ** *
63535 ATTAAAAAATTAATC-T
1 TTTCTAAGATTAATCAT
63551 TTTCTAAGATTAATCAT
1 TTTCTAAGATTAATCAT
63568 ATTAAAAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTCTAAGATTAATCAT
Found at i:64491 original size:15 final size:15
Alignment explanation
Indices: 64454--64482 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64444 TAATATCTAT
64454 AAATTTTATTAAATA
1 AAATTTTATTAAATA
64469 AAATTTTATTAAAT
1 AAATTTTATTAAAT
64483 TAAGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATTAAATA
Found at i:64715 original size:11 final size:10
Alignment explanation
Indices: 64690--64714 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
64680 TAAAAAATCT
64690 AAAAATTTAA
1 AAAAATTTAA
64700 AAAAATTTAA
1 AAAAATTTAA
64710 AAAAA
1 AAAAA
64715 AATCCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:67433 original size:15 final size:14
Alignment explanation
Indices: 67407--67457 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
67397 TTTAATATCT
67407 ATAAAATTTATTAA
1 ATAAAATTTATTAA
67421 ATAAAAGTTTATTAA
1 ATAAAA-TTTATTAA
* *
67436 ATTAAGATTTAATAA
1 A-TAAAATTTATTAA
*
67451 AAAAAAT
1 ATAAAAT
67458 AAAATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.32
15 17 0.55
16 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
ATAAAATTTATTAA
Found at i:72865 original size:29 final size:29
Alignment explanation
Indices: 72823--72879 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
72813 AGTGTTGGCC
* * *
72823 GTAGGTCGTCATGCATTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGACGACCTT
72852 GTAGGTCGCCATGCACTCCGGACGACCT
1 GTAGGTCGCCATGCACTCCGGACGACCT
72880 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGACGACCTT
Found at i:73056 original size:33 final size:33
Alignment explanation
Indices: 73015--73089 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
73005 GCGACCTACC
* *
73015 CTCGCTCGGCTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGCTACCCTCGGATGCCCTCGCATAG
73048 CTCGCTCGGCTACCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGCTACCCTCGGATGCCCTCGCATAG
*
73081 CTCGTTCGG
1 CTCGCTCGG
73090 ATGGCCTCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.09, C:0.41, G:0.25, T:0.24
Consensus pattern (33 bp):
CTCGCTCGGCTACCCTCGGATGCCCTCGCATAG
Found at i:73113 original size:20 final size:21
Alignment explanation
Indices: 73086--73137 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
73076 CATAGCTCGT
73086 TCGGATGGCCTCA-GATGCTC
1 TCGGATGGCCTCATGATGCTC
*
73106 TTGGATGGCCT-ATGATGCTC
1 TCGGATGGCCTCATGATGCTC
*
73126 TCGGATAGCCTC
1 TCGGATGGCCTC
73138 GGTCAGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (21 bp):
TCGGATGGCCTCATGATGCTC
Found at i:73233 original size:29 final size:29
Alignment explanation
Indices: 73196--73253 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
73186 GCTATCTCTT
**
73196 GTAGCTCGCGGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
73225 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
73254 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.38, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:76124 original size:34 final size:33
Alignment explanation
Indices: 76086--76161 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 33
76076 AACACGCTGG
* *
76086 GCATCCGAGGCCATCCGACCGAGGCTATCCGATA
1 GCATCCGAGGCCATCCGAACGA-GCTATCCGAGA
* * *
76120 GCATCAGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGAACGAGCTATCCGAGA
76153 GCATCCGAG
1 GCATCCGAG
76162 CGAGATATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.44
34 20 0.56
ACGTcount: A:0.25, C:0.32, G:0.30, T:0.13
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGAACGAGCTATCCGAGA
Found at i:76157 original size:23 final size:23
Alignment explanation
Indices: 76126--76183 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
76116 GATAGCATCA
* *
76126 GAGGCCATCCGAACGAGCTATGC
1 GAGGGCATCCGAACGAGATATGC
*
76149 GAGGGCATCCGAGCGAGATATGC
1 GAGGGCATCCGAACGAGATATGC
*
76172 GAGGGAATCCGA
1 GAGGGCATCCGA
76184 GAGCAGCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.24, G:0.36, T:0.12
Consensus pattern (23 bp):
GAGGGCATCCGAACGAGATATGC
Found at i:76361 original size:29 final size:29
Alignment explanation
Indices: 76315--76371 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
76305 GAGTGTATGT
*
76315 AGGTCGCCCGGAGTGCATGGTGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
76344 AGGTCGCCCGGAAG-GCATGGCGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
76372 GGACAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:79213 original size:18 final size:19
Alignment explanation
Indices: 79179--79216 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
79169 TCATAAATGA
*
79179 ATAATTATATTTTAATATT
1 ATAATTATATGTTAATATT
79198 ATAATT-TATGTTAATATT
1 ATAATTATATGTTAATATT
79216 A
1 A
79217 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATAATTATATGTTAATATT
Found at i:83202 original size:30 final size:30
Alignment explanation
Indices: 83162--83223 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
83152 AATGTATTTA
83162 AAAAGTAAA-TTAATAAGATT-TTTAAATATT
1 AAAAGTAAATTTAATAA-ATTATTT-AATATT
* *
83192 AAAATTAAATTTTATAAATTATTTAATATT
1 AAAAGTAAATTTAATAAATTATTTAATATT
83222 AA
1 AA
83224 GATAATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
AAAAGTAAATTTAATAAATTATTTAATATT
Found at i:84944 original size:45 final size:45
Alignment explanation
Indices: 84880--84968 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
84870 AACATGCACT
* * *
84880 AATGTTTGAAACAAGCCAAACATATTTCTTGTTTTTTCTTTTTCC
1 AATGTCTGAAACAAGCCAAACATATTCCTTGTTTTTCCTTTTTCC
*
84925 AATGTCTGAAACAAGCCAAACATGTTCCTTGTTTTTCCTTTTTC
1 AATGTCTGAAACAAGCCAAACATATTCCTTGTTTTTCCTTTTTC
84969 TAACAGAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (45 bp):
AATGTCTGAAACAAGCCAAACATATTCCTTGTTTTTCCTTTTTCC
Found at i:97696 original size:36 final size:36
Alignment explanation
Indices: 97650--97720 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
97640 TATATGTGAA
97650 AAAAAAAATTCAAACACCCTACAT-GAGCGAGGAAGG
1 AAAAAAAATTCAAACACCCTACATGGA-CGAGGAAGG
* *
97686 AAAAAAAATTCCAACGCCCTACATGGACGAGGAAG
1 AAAAAAAATTCAAACACCCTACATGGACGAGGAAG
97721 CCAATATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (36 bp):
AAAAAAAATTCAAACACCCTACATGGACGAGGAAGG
Found at i:97783 original size:19 final size:20
Alignment explanation
Indices: 97753--97798 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
97743 TAACAAAAAT
97753 GTTAAAAAATTA-CATGAAA
1 GTTAAAAAATTATCATGAAA
*
97772 -TTAAAAATATTATGATGAAA
1 GTTAAAAA-ATTATCATGAAA
97792 GTTAAAA
1 GTTAAAA
97799 GTGATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 4 0.17
20 6 0.26
21 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (20 bp):
GTTAAAAAATTATCATGAAA
Found at i:103939 original size:21 final size:21
Alignment explanation
Indices: 103915--103967 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
103905 TTTAGCTTTG
*
103915 TATTATATTTTTATTGAATTT
1 TATTATATTTTTATTCAATTT
* *
103936 TATTCAT-TTTTAATTCATTTT
1 TATT-ATATTTTTATTCAATTT
103957 TATT-TATTTTT
1 TATTATATTTTT
103968 TAAAAATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 4 0.15
21 19 0.73
22 2 0.08
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTATATTTTTATTCAATTT
Found at i:103951 original size:11 final size:10
Alignment explanation
Indices: 103921--103967 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
103911 TTTGTATTAT
*
103921 ATTTTTATTG
1 ATTTTTATTC
*
103931 AATTTTATTC
1 ATTTTTATTC
103941 ATTTTTAATTC
1 ATTTTT-ATTC
*
103952 ATTTTTATTT
1 ATTTTTATTC
103962 ATTTTT
1 ATTTTT
103968 TAAAAATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 22 0.69
11 10 0.31
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:105452 original size:20 final size:20
Alignment explanation
Indices: 105429--105475 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
105419 GTTTACAGAT
*
105429 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
105449 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
105469 TTGCAAC
1 TCGCAAC
105476 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:106323 original size:24 final size:24
Alignment explanation
Indices: 106296--106349 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
106286 GTATTCGAAA
106296 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
106320 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
106344 TTTGAT
1 TTTGAT
106350 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:108812 original size:20 final size:20
Alignment explanation
Indices: 108787--108863 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
108777 TTACACATTC
*
108787 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
108807 ATTTGACTATCACAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
108827 ATTTGATTATTGCAATGGGA
1 ATTTGACTATCGCAACGCGA
108847 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
108864 AGAAAATCAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:108849 original size:40 final size:40
Alignment explanation
Indices: 108787--108863 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
108777 TTACACATTC
108787 ATTTGAATATCGCAACGCGAATTTGACTATCACAACGTGA
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACGTGA
* * * * *
108827 ATTTGATTATTGCAATGGGAATTTGACTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACG
108864 AGAAAATCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCACAACGTGA
Found at i:108931 original size:20 final size:21
Alignment explanation
Indices: 108906--108959 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
108896 CGCGAATTCA
108906 CTTTCGCGTTGCGATTTTG-G
1 CTTTCGCGTTGCGATTTTGAG
*
108926 CTTTCGCATTGCGATTTTGAG
1 CTTTCGCGTTGCGATTTTGAG
*
108947 -TTTAGCGTTGCGA
1 CTTTCGCGTTGCGA
108960 AAGTGTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (21 bp):
CTTTCGCGTTGCGATTTTGAG
Found at i:110532 original size:21 final size:21
Alignment explanation
Indices: 110508--110590 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
110498 GAATGGTGGG
*
110508 AGGGACCTCTTCAACGATGAT
1 AGGGACCTCTTGAACGATGAT
* * **
110529 AGGGGCCTCTTGAACGGTGGG
1 AGGGACCTCTTGAACGATGAT
* **
110550 AGGGGA-CTCTTTAGGGATGAT
1 A-GGGACCTCTTGAACGATGAT
*
110571 AGGGGCCTCTTGAACGATGA
1 AGGGACCTCTTGAACGATGA
110591 CAGGTGAGTC
Statistics
Matches: 44, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
AGGGACCTCTTGAACGATGAT
Found at i:110552 original size:42 final size:42
Alignment explanation
Indices: 110493--110586 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
110483 GTGAATCGGG
*
110493 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGATAGGGGC
* **
110535 CTCTTGAACGGTGGGAGGGGACTCTTTAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGATAGGGGC
110577 CTCTTGAACG
1 CTCTTGAACG
110587 ATGACAGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGATAGGGGC
Found at i:111094 original size:20 final size:20
Alignment explanation
Indices: 111069--111106 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
111059 AATAGTTTAT
111069 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
111089 GAAACTTAAAATTGCAAC
1 GAAACTTAAAATCGCAAC
111107 GTGAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:111112 original size:20 final size:20
Alignment explanation
Indices: 111067--111112 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
111057 AGAATAGTTT
111067 ATGAAACTTAAAATCGCAAC
1 ATGAAACTTAAAATCGCAAC
* *
111087 ACGAAACTTAAAATTGCAAC
1 ATGAAACTTAAAATCGCAAC
*
111107 GTGAAA
1 ATGAAA
111113 ATGACTATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (20 bp):
ATGAAACTTAAAATCGCAAC
Found at i:114813 original size:31 final size:32
Alignment explanation
Indices: 114773--114868 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 32
114763 GAGTCGAGGG
114773 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
114805 TTTA-CTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
114835 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
114867 TT
1 TT
114869 ACCGAGGATC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
30 7 0.13
31 37 0.70
32 9 0.17
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:114894 original size:62 final size:60
Alignment explanation
Indices: 114774--114901 Score: 152
Period size: 62 Copynumber: 2.1 Consensus size: 60
114764 AGTCGAGGGT
* * *
114774 TTACCTATGTTCTACGGAACATATGGACAGTTTTACTATGTCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAGTTTTACGAGGTCTTTC-AGACATATGGACAG
* *
114835 TATACCTATGTTCTAAGGAACATATGGACAG-TTTACCGAGGATCTTT-ATGACCTCTGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAGTTTTA-CGAGG-TCTTTCA-GACATATGGACAG
114897 TTACC
1 TTACC
114902 GAGGATCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
61 10 0.17
62 43 0.74
63 5 0.09
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (60 bp):
TTACCTATGTTCTAAGGAACATATGGACAGTTTTACGAGGTCTTTCAGACATATGGACAG
Found at i:114903 original size:30 final size:30
Alignment explanation
Indices: 114859--114932 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
114849 AAGGAACATA
114859 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
114890 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
114920 TGGATAGTTACCG
1 TGGACAGTTACCG
114933 GGGTCTGTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:114951 original size:27 final size:29
Alignment explanation
Indices: 114867--114953 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 29
114857 TATGGACAGT
*
114867 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATC-TTATGACCTCTGGATAG
114897 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATC-TTATGACCTCTGGATAG
* *
114927 TTACCG-GGGTC-TGTGACCTCTGGATAG
1 TTACCGAGGATCTTATGACCTCTGGATAG
114954 GTCCTCGGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 15 0.28
29 4 0.07
30 35 0.65
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (29 bp):
TTACCGAGGATCTTATGACCTCTGGATAG
Found at i:115958 original size:16 final size:16
Alignment explanation
Indices: 115937--115973 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
115927 TGAAGTAATG
115937 CAATTCATTCAAGTTT
1 CAATTCATTCAAGTTT
115953 CAATTCATTCAAGTTT
1 CAATTCATTCAAGTTT
115969 CAATT
1 CAATT
115974 TGCAGAAGAA
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:0.32, C:0.19, G:0.05, T:0.43
Consensus pattern (16 bp):
CAATTCATTCAAGTTT
Found at i:116025 original size:20 final size:20
Alignment explanation
Indices: 116002--116057 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
115992 TCTGAAACTT
116002 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
116022 AAAATCACAATACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
116042 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
116058 TTTGATTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:116102 original size:19 final size:19
Alignment explanation
Indices: 116078--116121 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
116068 GCAACGAGAT
*
116078 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGAGAAACT-AA
116097 AATCGCAACGAGAAACTAA
1 AATCGCAACGAGAAACTAA
116116 AATCGC
1 AATCGC
116122 GTTGCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGAGAAACTAA
Found at i:116107 original size:33 final size:34
Alignment explanation
Indices: 116045--116109 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
116035 GAAAATGACT
* **
116045 ATCGCAACGCGAATTTGATTATCGCAACGAGATA
1 ATCGCAACGCGAATATGAAAATCGCAACGAGATA
116079 ATCGCAACGCGAA-ATGAAAATCGCAACGAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGAGA
116110 AACTAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGAGATA
Found at i:124181 original size:16 final size:17
Alignment explanation
Indices: 124150--124182 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
124140 TTTACCTAAA
*
124150 AAACATCATCATTCCAC
1 AAACATCATCAGTCCAC
124167 AAACA-CATCAGTCCAC
1 AAACATCATCAGTCCAC
124183 CAGCGGACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.36, G:0.03, T:0.18
Consensus pattern (17 bp):
AAACATCATCAGTCCAC
Found at i:138545 original size:235 final size:237
Alignment explanation
Indices: 138137--138599 Score: 670
Period size: 239 Copynumber: 1.9 Consensus size: 237
138127 GTCAGGTCAG
* *
138137 GTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA
1 GTCGGTTTTTTTAAGTGTGATATTCGGGTC--GTCGAGTTAGGGTTTAGGGTGAAAAAAACCCGA
* * * *
138202 CCCGAAAATATATATAATTTTATCTTGTATATTTAGGAATAATTACAATAATACCCCTTTTTATA
64 CCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC-TTCTATA
* *
138267 TATATATATATTTTCAATTAAGTTACTGTTTTTATTGAATAAAAATA-TTTTTTATTATTTTGGG
128 TATATATATATTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATATTTTTTTATTATTTTGGG
* *
138331 TTGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGA
193 TCGGGTCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGA
138376 GTCGAGTTTTTTTAAGTGTGATATTCGGGTC-T-G-GTTAGGGTTTAGGGTGAAAAAAACCGGAC
1 GTCG-GTTTTTTTAAGTGTGATATTCGGGTCGTCGAGTTAGGGTTTAGGGTGAAAAAAA-C---C
138438 CGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC-TCTA
61 CGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTTCTA
*
138502 TATATA-AT-TTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATATTTTTTTTATTATTTT
126 TATATATATATATTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATA-TTTTTTTATTATTTT
* * *
138565 GTGTCGTGTCGGGTCAGTTTTCTAATTCATATATT
190 GGGTCGGGTCGGGTCAGATTTCTAATTCATATATT
138600 GAATAAAAAT
Statistics
Matches: 203, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
235 57 0.28
236 4 0.02
237 54 0.27
239 62 0.31
240 26 0.13
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (237 bp):
GTCGGTTTTTTTAAGTGTGATATTCGGGTCGTCGAGTTAGGGTTTAGGGTGAAAAAAACCCGACC
CGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTTCTATATAT
ATATATATTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATATTTTTTTATTATTTTGGGTCG
GGTCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGA
Found at i:138762 original size:12 final size:12
Alignment explanation
Indices: 138745--138770 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
138735 TAAGCATGAT
138745 TTTTATAATTTA
1 TTTTATAATTTA
138757 TTTTATAATTTA
1 TTTTATAATTTA
138769 TT
1 TT
138771 GAAATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATAATTTA
Found at i:138971 original size:17 final size:18
Alignment explanation
Indices: 138949--138995 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
138939 TATGAAATTG
*
138949 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
138966 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
138984 GATTCCAATTCC
1 GATTCCAATTCC
138996 CTCATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:141064 original size:68 final size:68
Alignment explanation
Indices: 140955--141097 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 68
140945 TTATCACCTA
* *
140955 TTCATAACTGCTTTGTGATAGTTATTCTTGGGAAAACGTGGTAATTCTTTTGGTTTGTGATTCTG
1 TTCATAACTGCTTTGTGATAGTTATTCTTGGGAAAACGTGGTAATTCTTCTAGTTTGTGATTCTG
141020 CTC
66 CTC
* * *
141023 TTCATAACTGCTTTGTGATTGTTATTCTT-GGAAACATGTGGTAATTCTTCTAGTTTGTGATTTT
1 TTCATAACTGCTTTGTGATAGTTATTCTTGGGAAA-ACGTGGTAATTCTTCTAGTTTGTGATTCT
*
141087 GTTC
65 GCTC
141091 TTCATAA
1 TTCATAA
141098 ATGTCTGCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 5 0.07
68 63 0.93
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.48
Consensus pattern (68 bp):
TTCATAACTGCTTTGTGATAGTTATTCTTGGGAAAACGTGGTAATTCTTCTAGTTTGTGATTCTG
CTC
Found at i:141834 original size:189 final size:190
Alignment explanation
Indices: 141513--141892 Score: 753
Period size: 189 Copynumber: 2.0 Consensus size: 190
141503 TGCTGTAATA
141513 ATGTACGATTAGAACTACTCTTTTAGAAATTATATCTTGAGAATATAGCCTTGATAAAATTTCAA
1 ATGTACGATTAGAACTACTCTTTTAGAAATTATATCTTGAGAATATAGCCTTGATAAAATTTCAA
141578 TGTCTTGATAGTCTCTGAACCTGATTAGTGTGAATTCTCCACTAGATTTTATTTGTTGTACCTGT
66 TGTCTTGATAGTCTCTGAACCTGATTAGTGTGAATTCTCCACTAGATTTTATTTGTTGTACCTGT
141643 ATTTTCTACTTTTTGGAAATTACCAATCTGATCTCAAAGTAATAGGCTATTGGATGATGT
131 ATTTTCTACTTTTTGGAAATTACCAATCTGATCTCAAAGTAATAGGCTATTGGATGATGT
141703 ATGTACGATTAGAACTACTCTTTTAGAAATTATATCTTGAGAATATAG-CTTGATAAAATTTCAA
1 ATGTACGATTAGAACTACTCTTTTAGAAATTATATCTTGAGAATATAGCCTTGATAAAATTTCAA
141767 TGTCTTGATAGTCTCTGAACCTGATTAGTGTGAATTCTCCACTAGATTTTATTTGTTGTACCTGT
66 TGTCTTGATAGTCTCTGAACCTGATTAGTGTGAATTCTCCACTAGATTTTATTTGTTGTACCTGT
141832 ATTTTCTACTTTTTGGAAATTACCAATCTGATCTCAAAGTAATAGGCTATTGGATGATGT
131 ATTTTCTACTTTTTGGAAATTACCAATCTGATCTCAAAGTAATAGGCTATTGGATGATGT
141892 A
1 A
141893 GTTGTCTTAT
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 142 0.75
190 48 0.25
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (190 bp):
ATGTACGATTAGAACTACTCTTTTAGAAATTATATCTTGAGAATATAGCCTTGATAAAATTTCAA
TGTCTTGATAGTCTCTGAACCTGATTAGTGTGAATTCTCCACTAGATTTTATTTGTTGTACCTGT
ATTTTCTACTTTTTGGAAATTACCAATCTGATCTCAAAGTAATAGGCTATTGGATGATGT
Found at i:142247 original size:12 final size:12
Alignment explanation
Indices: 142230--142254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
142220 TGGATCTCAT
142230 GAAAATTCAGAA
1 GAAAATTCAGAA
142242 GAAAATTCAGAA
1 GAAAATTCAGAA
142254 G
1 G
142255 TGGATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (12 bp):
GAAAATTCAGAA
Found at i:147006 original size:18 final size:18
Alignment explanation
Indices: 146985--147023 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
146975 AATAGATTAT
146985 AAATAAAAAATATAAAAG
1 AAATAAAAAATATAAAAG
**
147003 AAATTTAAAATATAAAAG
1 AAATAAAAAATATAAAAG
147021 AAA
1 AAA
147024 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATATAAAAG
Found at i:147037 original size:20 final size:18
Alignment explanation
Indices: 146991--147039 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
146981 TTATAAATAA
*
146991 AAAATATAAAAGAAATTT
1 AAAATATAAAAGAAAATT
147009 AAAATATAAAAGAAAATT
1 AAAATATAAAAGAAAATT
147027 AAATTATATAAAA
1 AAA--ATATAAAA
147040 TAGTGCTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 20 0.71
20 8 0.29
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (18 bp):
AAAATATAAAAGAAAATT
Found at i:147393 original size:35 final size:35
Alignment explanation
Indices: 147347--147418 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
147337 GCAGGCTGCC
147347 CCATAGGCTGAATATACCAAAAATTAACTGTGCAA
1 CCATAGGCTGAATATACCAAAAATTAACTGTGCAA
147382 CCATAGGCTGAATATACCAAAAATTAACTGTGCAA
1 CCATAGGCTGAATATACCAAAAATTAACTGTGCAA
147417 CC
1 CC
147419 CCCCCAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (35 bp):
CCATAGGCTGAATATACCAAAAATTAACTGTGCAA
Found at i:157791 original size:22 final size:22
Alignment explanation
Indices: 157702--157794 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
157692 GTTCAGTATT
*
157702 CGTCCCGAATGACCACT--AT-
1 CGTCCCGAAGGACCACTGGATA
* *
157721 -GTCCTGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
* *
157742 CGTCCTGAAGGACCATTGGATA
1 CGTCCCGAAGGACCACTGGATA
157764 CGTCCCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
157786 CGTCCCGAA
1 CGTCCCGAA
157795 TGACTAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
18 14 0.22
20 2 0.03
22 48 0.75
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:161238 original size:64 final size:65
Alignment explanation
Indices: 161147--161309 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 65
161137 TCCCTTGACG
* * * * * * * *
161147 GGTGAATCGATGCACTACC-CATACATCGGTGCATAAATCATATTCGATGTT-TA-TATTTTAAG
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCACATTAGATGTTCAATTAATTTAA-
161209 CA-
64 -AT
* **
161211 GGTGCATCGATGCACTCCTTATGCATCGATGCATAACTGGCATTAGATGTTCAATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCACATTAGATGTTCAATTAATTTAAAT
161276 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
161310 CCTTCAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.02
64 40 0.48
65 2 0.02
66 39 0.47
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCACATTAGATGTTCAATTAATTTAAAT
Found at i:164616 original size:18 final size:18
Alignment explanation
Indices: 164593--164627 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
164583 GTTCAGTATT
*
164593 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
164611 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
164628 GGATACATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:164664 original size:22 final size:22
Alignment explanation
Indices: 164593--164667 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
164583 GTTCAGTATT
164593 TGTCCCGAATGACCAC----TA
1 TGTCCCGAATGACCACTGGATA
*
164611 TGTCCCGAAGGACCACTGGATA
1 TGTCCCGAATGACCACTGGATA
**
164633 CATCCCGAATGACCACTGGATA
1 TGTCCCGAATGACCACTGGATA
164655 TGTCCCGAATGAC
1 TGTCCCGAATGAC
164668 TAATATACCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.32
22 32 0.68
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (22 bp):
TGTCCCGAATGACCACTGGATA
Found at i:165376 original size:2 final size:2
Alignment explanation
Indices: 165369--165425 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
165359 TACAAATTCC
165369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
165411 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
165426 CTAACTCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166153 original size:64 final size:63
Alignment explanation
Indices: 166044--166206 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 63
166034 TCCCTTGACG
* * * * *
166044 GGTGCATCGATGCATTACC-CATGCATCGGTGCATAAATCATATTCGATGTT-TGTATTTTAAGC
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCACATTCGATGTTAT-TAATTTAA--
166107 A-
62 AT
* **
166108 GGTGCATCGATGCACTCCTTATGCATCGATGCATAACTGGCATTCGATGTTCAATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCACATTCGATGTT--ATTAATTTAAAT
166173 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
166207 CCTTCAACAA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.49
65 1 0.01
66 39 0.46
67 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCACATTCGATGTTATTAATTTAAAT
Found at i:170550 original size:2 final size:2
Alignment explanation
Indices: 170545--170597 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
170535 AAAAAAAATC
170545 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
170587 AT AT AT -T AT AT
1 AT AT AT AT AT AT
170598 TTGTCGATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:170948 original size:15 final size:16
Alignment explanation
Indices: 170928--170961 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
170918 TAGAGATTAT
*
170928 AGATTTTA-GTATTTA
1 AGATTTTAGGGATTTA
170943 AGATTTTAGGGATTTA
1 AGATTTTAGGGATTTA
170959 AGA
1 AGA
170962 ATTTGTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (16 bp):
AGATTTTAGGGATTTA
Found at i:173752 original size:14 final size:14
Alignment explanation
Indices: 173735--173765 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
173725 TTACATGTTA
*
173735 TTTATTAAATATAT
1 TTTAATAAATATAT
173749 TTTAATAAATATAT
1 TTTAATAAATATAT
173763 TTT
1 TTT
173766 TATGTGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAATAAATATAT
Found at i:181145 original size:2 final size:2
Alignment explanation
Indices: 181138--181176 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
181128 CCACTGAGGC
181138 TA TA TA 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
181177 CTAATTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:182960 original size:19 final size:19
Alignment explanation
Indices: 182936--182992 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
182926 CTTAAAATAA
182936 TTTGAGCTGAGCCGAGCCG
1 TTTGAGCTGAGCCGAGCCG
182955 TTTGAGCTGAGCCGAGCCG
1 TTTGAGCTGAGCCGAGCCG
182974 TTTGAGCTGAGCCGAGCCG
1 TTTGAGCTGAGCCGAGCCG
182993 AGCCGCCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (19 bp):
TTTGAGCTGAGCCGAGCCG
Found at i:184463 original size:132 final size:130
Alignment explanation
Indices: 184243--184505 Score: 508
Period size: 132 Copynumber: 2.0 Consensus size: 130
184233 CAGGAATGAT
184243 TGAATATCCTCGAGCTCTGAAATGAATGGAATAAAACTGAACATCAAATTACCAAATACCTTATG
1 TGAATATCCTCGAGCTCTGAAATGAATGGAATAAAACTGAACATCAAATTACCAAATACCTTATG
184308 GCCTAAATTAAGTAAATGTCTTGGATTAATTAAGGAATCCAAGTAAGCATAGGTATTGGACTACC
66 GCCTAAATTAAGTAAATGTCTTGGATTAATTAAGGAATCCAAGTAAGCATAGGTATTGGACTACC
184373 TGAATATCCTCGAGCTCTGAAATGAATGGAATAAAAACTGAACATCAAATTACCAAATACCCTTA
1 TGAATATCCTCGAGCTCTGAAATGAATGGAAT-AAAACTGAACATCAAATTACCAAATA-CCTTA
184438 TGGCCTAAATTAAGTAAATGTCTTGGATTAATTAAGGAATCCAAGTAAGCATAGGTATTGGACTA
64 TGGCCTAAATTAAGTAAATGTCTTGGATTAATTAAGGAATCCAAGTAAGCATAGGTATTGGACTA
184503 CC
129 CC
184505 T
1 T
184506 TTAAAGGTAA
Statistics
Matches: 131, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
130 32 0.24
131 26 0.20
132 73 0.56
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (130 bp):
TGAATATCCTCGAGCTCTGAAATGAATGGAATAAAACTGAACATCAAATTACCAAATACCTTATG
GCCTAAATTAAGTAAATGTCTTGGATTAATTAAGGAATCCAAGTAAGCATAGGTATTGGACTACC
Found at i:187463 original size:14 final size:14
Alignment explanation
Indices: 187417--187464 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
187407 GAAGCCTGAG
187417 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
*
187431 GAGTCGTTTGAGCC
1 GAGCCGTTTGAGCC
* *
187445 AAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
187459 GAGCCG
1 GAGCCG
187465 AGCCGCCTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:189586 original size:35 final size:35
Alignment explanation
Indices: 189540--189611 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
189530 AAATAAAGAC
*
189540 CATTAGAATATTTGCTTGTCTCCTTAAGATCTATT
1 CATTAGAATATTTGCTTGTCTCCTTAAGATATATT
189575 CATTAGAATATTTGCTTGTCTCCTTAAGATATATT
1 CATTAGAATATTTGCTTGTCTCCTTAAGATATATT
189610 CA
1 CA
189612 GTGATGACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (35 bp):
CATTAGAATATTTGCTTGTCTCCTTAAGATATATT
Found at i:190113 original size:24 final size:24
Alignment explanation
Indices: 190014--190113 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
190004 ATATTTTATC
* *
190014 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
190038 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * *
190062 TGAT-TCCT-AACTTGGATTCTGTTA
1 TGATAT-CTGATC-TGAATTCTGTTT
*
190086 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
190110 TGAT
1 TGAT
190114 TTTTGATATC
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 52 0.90
25 3 0.05
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:190271 original size:16 final size:16
Alignment explanation
Indices: 190250--190281 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
190240 GGAACCTACA
190250 CATTATGTTGTGTTGG
1 CATTATGTTGTGTTGG
190266 CATTATGTTGTGTTGG
1 CATTATGTTGTGTTGG
190282 GATGTGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
CATTATGTTGTGTTGG
Found at i:198831 original size:38 final size:38
Alignment explanation
Indices: 198787--198864 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
198777 TTACTTTAAT
198787 AAATGATTGACTTGGTGAAATGAAGGAGATGAATAAAA
1 AAATGATTGACTTGGTGAAATGAAGGAGATGAATAAAA
198825 AAATGATTGACTTGGTGAAATGAAGGAGATGAATAAAA
1 AAATGATTGACTTGGTGAAATGAAGGAGATGAATAAAA
198863 AA
1 AA
198865 TTTGAAGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (38 bp):
AAATGATTGACTTGGTGAAATGAAGGAGATGAATAAAA
Found at i:204314 original size:16 final size:16
Alignment explanation
Indices: 204288--204326 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
204278 GAACATTGTC
204288 TCTTAGGATTCAAGGAA
1 TCTT-GGATTCAAGGAA
204305 TCTTGGATTCAAGGAA
1 TCTTGGATTCAAGGAA
204321 TCTTGG
1 TCTTGG
204327 CCTTGTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (16 bp):
TCTTGGATTCAAGGAA
Found at i:210020 original size:32 final size:30
Alignment explanation
Indices: 209959--210034 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
209949 TAGTAAATTT
* *
209959 AAAT-TAAATAATTATTTTATTTATATTTTA
1 AAATATAAATATTTA-TATATTTATATTTTA
*
209989 AAATATTAATATTTATATATTTATATTTTTTA
1 AAATATAAATATTTATATATTTATA--TTTTA
*
210021 AATTATAAATATTT
1 AAATATAAATATTT
210035 TATTAAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 13 0.34
31 8 0.21
32 17 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AAATATAAATATTTATATATTTATATTTTA
Found at i:213431 original size:149 final size:149
Alignment explanation
Indices: 213161--213465 Score: 565
Period size: 149 Copynumber: 2.0 Consensus size: 149
213151 CATTTTCTCA
* *
213161 TATGAAACATTACAAATCACATAATTAATGTATTTTTACAGTACTGTACTGCTTTGTTAGGTAAG
1 TATGAAACATAACAAATCACATAATTAATGTACTTTTACAGTACTGTACTGCTTTGTTAGGTAAG
*
213226 ATAAAGAAATATCAACTAGATGTTTGAAGATAAATTTCTTTTAGCAGTGGTGACTTTCAACCTAA
66 AAAAAGAAATATCAACTAGATGTTTGAAGATAAATTTCTTTTAGCAGTGGTGACTTTCAACCTAA
213291 TGGATCATGCCTTCTCAAT
131 TGGATCATGCCTTCTCAAT
*
213310 TATGAAACATAACAAATCACATAATTAATGTACTTTTAGAGTACTGTACTGCTTTGTTAGGTAAG
1 TATGAAACATAACAAATCACATAATTAATGTACTTTTACAGTACTGTACTGCTTTGTTAGGTAAG
*
213375 AAAAAGAAATATCAACTAGATGTTTGAAGATAAATTTGTTTTAGCAGTGGTGACTTTCAACCTAA
66 AAAAAGAAATATCAACTAGATGTTTGAAGATAAATTTCTTTTAGCAGTGGTGACTTTCAACCTAA
213440 TGGATCATGCCTTCTCAAT
131 TGGATCATGCCTTCTCAAT
213459 TATGAAA
1 TATGAAA
213466 ACCTTGCATC
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (149 bp):
TATGAAACATAACAAATCACATAATTAATGTACTTTTACAGTACTGTACTGCTTTGTTAGGTAAG
AAAAAGAAATATCAACTAGATGTTTGAAGATAAATTTCTTTTAGCAGTGGTGACTTTCAACCTAA
TGGATCATGCCTTCTCAAT
Found at i:214943 original size:16 final size:16
Alignment explanation
Indices: 214922--214973 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
214912 GATAGAATTT
214922 ATATAAAAAATTATAA
1 ATATAAAAAATTATAA
**
214938 ATATAATTAATTATTAA
1 ATATAAAAAATTA-TAA
* * *
214955 ATATATAATATTTTAA
1 ATATAAAAAATTATAA
214971 ATA
1 ATA
214974 AAATATTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAAAATTATAA
Found at i:216068 original size:15 final size:15
Alignment explanation
Indices: 216048--216084 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
216038 GATAATGATA
216048 AAGAAGA-GGAGCAAG
1 AAGAAGAGGGAG-AAG
216063 AAGAAGAGGGAGAAG
1 AAGAAGAGGGAGAAG
216078 AAGAAGA
1 AAGAAGA
216085 TAATCATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.57, C:0.03, G:0.41, T:0.00
Consensus pattern (15 bp):
AAGAAGAGGGAGAAG
Found at i:220625 original size:28 final size:28
Alignment explanation
Indices: 220594--220774 Score: 186
Period size: 29 Copynumber: 6.4 Consensus size: 28
220584 CATTTTACAG
* *
220594 AAATAACACACTTTTTAAAATAATTAC-A
1 AAATAACAC-CATTTTAAATTAATTACTA
*
220622 AAATAACA-CATTTTTGAATTAATTACTA
1 AAATAACACCA-TTTTAAATTAATTACTA
* * *
220650 AAGTAGCACCTATTTTGAATTAATTACTA
1 AAATAACACC-ATTTTAAATTAATTACTA
* *
220679 AAATAGCACCATTTTGAATTAATTACTA
1 AAATAACACCATTTTAAATTAATTACTA
* *
220707 AAATAACACCCATTTCAAATTAATTACTG
1 AAATAACA-CCATTTTAAATTAATTACTA
* *
220736 AAATAGCACTCATTTCAAATTAATTACTA
1 AAATAACAC-CATTTTAAATTAATTACTA
*
220765 AAATAGCACC
1 AAATAACACC
220775 CGATCAACGG
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.01
27 13 0.10
28 42 0.31
29 78 0.58
30 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATAACACCATTTTAAATTAATTACTA
Found at i:220668 original size:29 final size:29
Alignment explanation
Indices: 220614--220774 Score: 195
Period size: 29 Copynumber: 5.7 Consensus size: 29
220604 CTTTTTAAAA
* *
220614 TAATTAC-AAAATAACACAT-TTTTGAAT
1 TAATTACTAAAATAGCACCTATTTTGAAT
*
220641 TAATTACTAAAGTAGCACCTATTTTGAAT
1 TAATTACTAAAATAGCACCTATTTTGAAT
220670 TAATTACTAAAATAGCACC-ATTTTGAAT
1 TAATTACTAAAATAGCACCTATTTTGAAT
* * **
220698 TAATTACTAAAATAACACCCATTTCAAAT
1 TAATTACTAAAATAGCACCTATTTTGAAT
* **
220727 TAATTACTGAAATAGCA-CTCATTTCAAAT
1 TAATTACTAAAATAGCACCT-ATTTTGAAT
220756 TAATTACTAAAATAGCACC
1 TAATTACTAAAATAGCACC
220775 CGATCAACGG
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
27 7 0.06
28 37 0.31
29 73 0.62
30 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (29 bp):
TAATTACTAAAATAGCACCTATTTTGAAT
Found at i:220698 original size:57 final size:57
Alignment explanation
Indices: 220614--220775 Score: 211
Period size: 57 Copynumber: 2.8 Consensus size: 57
220604 CTTTTTAAAA
* * * **
220614 TAATTAC-AAAATAACA-CATTTTTGAATTAATTACTAAAGTAGCACCTATTTTGAAT
1 TAATTACTAAAATAGCACCA-TTTTGAATTAATTACTAAAATAGCACCCATTTCAAAT
*
220670 TAATTACTAAAATAGCACCATTTTGAATTAATTACTAAAATAACACCCATTTCAAAT
1 TAATTACTAAAATAGCACCATTTTGAATTAATTACTAAAATAGCACCCATTTCAAAT
* **
220727 TAATTACTGAAATAGCACTCATTTCAAATTAATTACTAAAATAGCACCC
1 TAATTACTAAAATAGCAC-CATTTTGAATTAATTACTAAAATAGCACCC
220776 GATCAACGGT
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 7 0.08
57 57 0.61
58 29 0.31
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (57 bp):
TAATTACTAAAATAGCACCATTTTGAATTAATTACTAAAATAGCACCCATTTCAAAT
Found at i:220743 original size:86 final size:84
Alignment explanation
Indices: 220614--220774 Score: 220
Period size: 86 Copynumber: 1.9 Consensus size: 84
220604 CTTTTTAAAA
** **
220614 TAATTACAAAATAACACATTTTTGAATTAATTACTAAAGTAGCAC-CTATTTTGAATTAATTACT
1 TAATTACAAAATAACACATTTTCAAATTAATTACTAAAGTAGCACTC-ATTTCAAATTAATTACT
220678 AAAATAGCACCATTTTGAAT
65 AAAATAGCACCATTTTGAAT
220698 TAATTACTAAAATAACACCCA-TTTCAAATTAATTACTGAAA-TAGCACTCATTTCAAATTAATT
1 TAATTAC-AAAATAACA--CATTTTCAAATTAATTACT-AAAGTAGCACTCATTTCAAATTAATT
220761 ACTAAAATAGCACC
62 ACTAAAATAGCACC
220775 CGATCAACGG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
84 7 0.10
85 9 0.13
86 46 0.68
87 6 0.09
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (84 bp):
TAATTACAAAATAACACATTTTCAAATTAATTACTAAAGTAGCACTCATTTCAAATTAATTACTA
AAATAGCACCATTTTGAAT
Found at i:222284 original size:121 final size:121
Alignment explanation
Indices: 222070--222313 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 121
222060 ATCTGCGTAT
*
222070 GATTTCTGCCTATCAAATGCATCTCCTAAGCGATCACGGATCAGTTTGACAATATCTTCAATCTC
1 GATTTCTGCCTATCAAATGCATCTCCTAAGCGATCACGGATCAGTTTGACAATATCTTCAATATC
* *
222135 TCAAACCAAGTTTGGACCCAAAGTTTTTCTATCATGCAACTCTGTCCAACAAATAG
66 TCAAACCAAGTCTAGACCCAAAGTTTTTCTATCATGCAACTCTGTCCAACAAATAG
* * *
222191 GATTTTTGCCTATCAAATGCATCTCCTAAGCGATCACGGATCAGTTTGACAGTATCTTCAGTATC
1 GATTTCTGCCTATCAAATGCATCTCCTAAGCGATCACGGATCAGTTTGACAATATCTTCAATATC
222256 TCAAACCAAGTCTAGACCCAAAGTTTTTCTATCATGCAACTCTGTCCAACAAATAG
66 TCAAACCAAGTCTAGACCCAAAGTTTTTCTATCATGCAACTCTGTCCAACAAATAG
222312 GA
1 GA
222314 GCACGACATC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (121 bp):
GATTTCTGCCTATCAAATGCATCTCCTAAGCGATCACGGATCAGTTTGACAATATCTTCAATATC
TCAAACCAAGTCTAGACCCAAAGTTTTTCTATCATGCAACTCTGTCCAACAAATAG
Found at i:228078 original size:57 final size:57
Alignment explanation
Indices: 228015--228196 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 57
228005 CATTTTATAG
*
228015 AAATAGCACCATTTTTAAAATAATTACAAGAATAGCACCTTTTCGAATTAATTACTA
1 AAATAGCACCATTTTTAAATTAATTACAAGAATAGCACCTTTTCGAATTAATTACTA
* * *
228072 AAATAGCA-CATATTTTGAATTAATTACTAA-AATAACACCATTTCGAATTAATTACTA
1 AAATAGCACCAT-TTTTAAATTAATTAC-AAGAATAGCACCTTTTCGAATTAATTACTA
* * * *
228129 AAATATCACCCA-TTTCAAATTAATTAC-TGAAATAGTATCCATTTT-GAATTAATTACTA
1 AAATAGCA-CCATTTTTAAATTAATTACAAG-AATAGCA-CC-TTTTCGAATTAATTACTA
*
228187 AAATAACACC
1 AAATAGCACC
228197 CGGTCAACGG
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
56 3 0.03
57 73 0.70
58 24 0.23
59 5 0.05
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (57 bp):
AAATAGCACCATTTTTAAATTAATTACAAGAATAGCACCTTTTCGAATTAATTACTA
Found at i:228097 original size:29 final size:28
Alignment explanation
Indices: 228015--228196 Score: 195
Period size: 29 Copynumber: 6.4 Consensus size: 28
228005 CATTTTATAG
** *
228015 AAATAGCACCATTTTTAAAATAATTAC-A
1 AAATAGCACCA-TTTCGAATTAATTACTA
*
228043 AGAATAGCACCTTTTCGAATTAATTACTA
1 A-AATAGCACCATTTCGAATTAATTACTA
* *
228072 AAATAGCACATATTTTGAATTAATTACTA
1 AAATAGCAC-CATTTCGAATTAATTACTA
*
228101 AAATAACACCATTTCGAATTAATTACTA
1 AAATAGCACCATTTCGAATTAATTACTA
* * *
228129 AAATATCACCCATTTCAAATTAATTACTG
1 AAATAGCA-CCATTTCGAATTAATTACTA
* *
228158 AAATAGTATCCATTTTGAATTAATTACTA
1 AAATAGCA-CCATTTCGAATTAATTACTA
*
228187 AAATAACACC
1 AAATAGCACC
228197 CGGTCAACGG
Statistics
Matches: 129, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
28 47 0.36
29 82 0.64
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATAGCACCATTTCGAATTAATTACTA
Found at i:229834 original size:30 final size:30
Alignment explanation
Indices: 229785--229841 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
229775 AACATCCTGA
* *
229785 TCTTCTTCTTCTTCCACCTCCTCTTCTATT
1 TCTTCCTCTTCTTCCACCTCCACTTCTATT
* *
229815 TCTTCCTCTTGTTCTACCTCCACTTCT
1 TCTTCCTCTTCTTCCACCTCCACTTCT
229842 TCATACTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.07, C:0.40, G:0.02, T:0.51
Consensus pattern (30 bp):
TCTTCCTCTTCTTCCACCTCCACTTCTATT
Found at i:231601 original size:29 final size:29
Alignment explanation
Indices: 231565--231622 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
231555 TGCTAGGATA
231565 AGTTTATAGTTACTGATATTAGAGATAGC
1 AGTTTATAGTTACTGATATTAGAGATAGC
231594 AGTTTATAGTTACTGATATTAGAGATAGC
1 AGTTTATAGTTACTGATATTAGAGATAGC
231623 TTCACGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
AGTTTATAGTTACTGATATTAGAGATAGC
Found at i:240593 original size:15 final size:15
Alignment explanation
Indices: 240573--240607 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
240563 ATAAAATATA
240573 AAATTTAAATTACTG
1 AAATTTAAATTACTG
*
240588 AAATTTAGATTACTG
1 AAATTTAAATTACTG
240603 AAATT
1 AAATT
240608 AAGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (15 bp):
AAATTTAAATTACTG
Found at i:240668 original size:26 final size:25
Alignment explanation
Indices: 240617--240672 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
240607 TAAGACTAAA
*
240617 TTAAATAAAAATTAAAGTTTACATT
1 TTAAATAAAAATTAAAGTTTAAATT
*
240642 TTAAACTAAAAATT-AATTTCTAAATT
1 TTAAA-TAAAAATTAAAGTT-TAAATT
240668 TTAAA
1 TTAAA
240673 AGTGGGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAAATAAAAATTAAAGTTTAAATT
Found at i:243554 original size:20 final size:20
Alignment explanation
Indices: 243518--243555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
243508 ATCCTATTCC
**
243518 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
243538 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
243556 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:261480 original size:24 final size:24
Alignment explanation
Indices: 261448--261504 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
261438 GGATTGCAAC
261448 ATTCCCAACCCCTGGTAATCCTTT
1 ATTCCCAACCCCTGGTAATCCTTT
*
261472 ATTCCCAACCCCTGGTAATCTTTT
1 ATTCCCAACCCCTGGTAATCCTTT
261496 ATTCCCAAC
1 ATTCCCAAC
261505 AGTGGTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.37, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTCCCAACCCCTGGTAATCCTTT
Found at i:267716 original size:2 final size:2
Alignment explanation
Indices: 267709--267744 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
267699 ACTTTTAAAA
267709 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
267745 TATTTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267943 original size:255 final size:255
Alignment explanation
Indices: 267492--267973 Score: 860
Period size: 255 Copynumber: 1.9 Consensus size: 255
267482 GTATCTATCT
* * *
267492 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTGGTTAATA
1 TTTTTATAAAACTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGTTAATA
*
267557 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTGT
66 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATTTTGTGTGT
267622 AAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
131 AAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
*
267687 ATAAATTACATAACTTTTAAAAATA-TATATATATATATATATATATATATATATATATTA
196 ATAAATTACATAAC-TTTAAAAAAAGTATATATATATATATATATATATATATATATATTA
*
267747 TTTTTATAAAACTGTCCGTACTTATTTCACTGTGGAAAACATATTTATTATTATATTTGGTTAAT
1 TTTTTATAAAACTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATTATATTTGGTTAAT
*
267812 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAA-AATAAAATAATTTTTTGTG
65 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATTTTGTGTG
*
267876 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA
130 TAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA
267941 CATAAATTACATAACTTTAAAAAAAGTATATAT
195 CATAAATTACATAACTTTAAAAAAAGTATATAT
267974 CATTTTTATA
Statistics
Matches: 217, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
254 9 0.04
255 134 0.62
256 74 0.34
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (255 bp):
TTTTTATAAAACTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGTTAATA
TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATTTTGTGTGT
AAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
ATAAATTACATAACTTTAAAAAAAGTATATATATATATATATATATATATATATATATTA
Found at i:268364 original size:181 final size:182
Alignment explanation
Indices: 268065--268538 Score: 688
Period size: 181 Copynumber: 2.6 Consensus size: 182
268055 TCGATCCAAA
* * * * *
268065 TAAAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACTGGTATA-GAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGT-TACAAAATG
* * * *
268129 ATAAAACCGGTAAAGCGCTACCGGATACATT-AAAGTGTCGGTACTTTAATATAAGGATCGACAC
65 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
*
268193 TTCGTGAATTTAAAAGAGAAGT-AGTTTTAAATCCTATAAAGTGTCGATACTTT
130 TTCGTGAATTTAAAAGAGAA-TCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
*
268246 TAAAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTTACAAAATGA
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
*
268311 TAAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACT
66 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* ** * *
268375 TTGTGAATTTAAAAGAGAATCAGTTTTAGCGCTTATAATGTGTCGATACTTT
131 TCGTGAATTTAAAAGAGAATCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
* * * *
268427 CAAAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGG-TATCAAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTA-CAAAATG
*
268491 ATAAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
268539 CGTAAGTACG
Statistics
Matches: 266, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
180 5 0.02
181 246 0.92
182 15 0.06
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
TCGTGAATTTAAAAGAGAATCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
Found at i:268507 original size:17 final size:19
Alignment explanation
Indices: 268468--268510 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
268458 ATGTAAAAAT
268468 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
268488 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
268505 ATGATA
1 ATGATA
268511 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:270740 original size:21 final size:21
Alignment explanation
Indices: 270716--270759 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
270706 AAGACAATCA
270716 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
270737 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
270758 AG
1 AG
270760 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:272678 original size:19 final size:19
Alignment explanation
Indices: 272654--272702 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
272644 AATGTAGGGT
272654 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
272673 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
272692 TATTTTTGTAT
1 TAATTTTGTAT
272703 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:273683 original size:198 final size:198
Alignment explanation
Indices: 272821--274188 Score: 2547
Period size: 199 Copynumber: 6.9 Consensus size: 198
272811 CAATATGGCC
* *
272821 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCTAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
272886 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
272951 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
273016 TGGAA
194 TGGAA
273021 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
273086 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
273151 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
273216 GGAA
195 GGAA
273220 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
273285 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
273350 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCTAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
273415 GGAA
195 GGAA
* *
273419 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATATAGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
273484 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
273549 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
273614 GAA
196 GAA
273617 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
273682 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
273747 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
273812 GAA
196 GAA
273815 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCGAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAAACATCGAAC
* *
273880 CCAAAAGTATAGTGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
273945 GAATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCAAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
274010 GGAA
195 GGAA
* *
274014 AACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
274079 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
274144 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
274189 CTAATTTAAA
Statistics
Matches: 1146, Mismatches: 21, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
198 406 0.35
199 680 0.59
200 60 0.05
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:273857 original size:397 final size:397
Alignment explanation
Indices: 272821--274188 Score: 2560
Period size: 397 Copynumber: 3.4 Consensus size: 397
272811 CAATATGGCC
* *
272821 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCTAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
272886 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
272951 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
273016 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
195 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
273081 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
*
273146 GAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAA
273211 TGAATGGAA
389 TGAATGGAA
273220 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
273285 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
273350 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCTAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
* *
273415 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATATAG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
*
273480 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAAGTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
273545 AGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
326 AGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
273610 AATGGAA
391 AATGGAA
273617 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
273682 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
273747 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
273811 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATC
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAAACATC
* *
273876 GAACCCAAAAGTATAGTGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
* *
273941 GAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCAAGAAT
325 GAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAAT
274006 GAATGGAA
390 GAATGGAA
* *
274014 AACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
274079 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
274144 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
274189 CTAATTTAAA
Statistics
Matches: 949, Mismatches: 19, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
396 74 0.08
397 526 0.55
398 289 0.30
399 60 0.06
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (397 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
AATGGAA
Found at i:275608 original size:16 final size:16
Alignment explanation
Indices: 275576--275609 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
275566 TATCTACAAC
* *
275576 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
275592 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
275608 AA
1 AA
275610 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:294024 original size:15 final size:15
Alignment explanation
Indices: 294004--294039 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
293994 AATATTCTGA
294004 ATCAGTGGAATTTTC
1 ATCAGTGGAATTTTC
294019 ATCAGTGGAATTTTC
1 ATCAGTGGAATTTTC
*
294034 AGCAGT
1 ATCAGT
294040 AGACAGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (15 bp):
ATCAGTGGAATTTTC
Found at i:298012 original size:11 final size:11
Alignment explanation
Indices: 297996--298020 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
297986 GTCTCCCAAT
297996 ATATAAAAAAA
1 ATATAAAAAAA
298007 ATATAAAAAAA
1 ATATAAAAAAA
298018 ATA
1 ATA
298021 GGATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATATAAAAAAA
Found at i:300203 original size:169 final size:171
Alignment explanation
Indices: 299924--300238 Score: 616
Period size: 169 Copynumber: 1.9 Consensus size: 171
299914 TTCAAGGAAT
299924 ATATTCTTATTTATTATTGTTAATCTTAATCGTTTATTTTCGTTCATTTAATGATCTTAAATCTA
1 ATATTCTTATTTATTATTGTTAATCTTAATCGTTTATTTTCGTTCATTTAATGATCTTAAATCTA
299989 TATAAAACTAAAAGAGTTTTAATTAATTAATCAGTGATCATGATATTGCTATTGAATGACAATGT
66 TATAAAACTAAAAGAGTTTTAATTAATTAATCAGTGATCATGATATTGCTATTGAATGACAATGT
300054 CA-TTAATC-TAATTTAATTAGATACGATCAATTGGTATAC
131 CACTTAATCTTAATTTAATTAGATACGATCAATTGGTATAC
300093 ATATTCTTATTTATTATTGTTAATCTTAATCGTTTATTTTCGTTCATTTAATGATCTTAAATCTA
1 ATATTCTTATTTATTATTGTTAATCTTAATCGTTTATTTTCGTTCATTTAATGATCTTAAATCTA
300158 TATAAAACTAAAAGAGTTTTAATTAATTAATCAGTGATCATGATATTGCTATTGAATGACAATGT
66 TATAAAACTAAAAGAGTTTTAATTAATTAATCAGTGATCATGATATTGCTATTGAATGACAATGT
300223 CACTTAATCTTAATTT
131 CACTTAATCTTAATTT
300239 TTACGATCAT
Statistics
Matches: 144, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
169 132 0.92
170 6 0.04
171 6 0.04
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (171 bp):
ATATTCTTATTTATTATTGTTAATCTTAATCGTTTATTTTCGTTCATTTAATGATCTTAAATCTA
TATAAAACTAAAAGAGTTTTAATTAATTAATCAGTGATCATGATATTGCTATTGAATGACAATGT
CACTTAATCTTAATTTAATTAGATACGATCAATTGGTATAC
Found at i:302483 original size:3 final size:3
Alignment explanation
Indices: 302475--302503 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
302465 AATTTATTTG
302475 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
302504 TTTTTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:303851 original size:21 final size:21
Alignment explanation
Indices: 303814--303857 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
303804 CATTCAATAA
*
303814 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
303834 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
303856 TT
1 TT
303858 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:304150 original size:19 final size:19
Alignment explanation
Indices: 304105--304152 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
304095 TTTTCATTGC
*
304105 TTTATATTTTATTTTATTA
1 TTTATATTTTATTTTATCA
* *
304124 TGTGTATTTT-TTTTATCCA
1 TTTATATTTTATTTTAT-CA
304143 TTTATATTTT
1 TTTATATTTT
304153 GTTATATTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATATTTTATTTTATCA
Found at i:308104 original size:89 final size:89
Alignment explanation
Indices: 307954--308131 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
307944 CCTGAGTTTG
307954 AGAAGTTCGACGGGAACAGTTGCCCTCAGCCCATATCACTATGTTCTGTCGAAAGATGACAGGAT
1 AGAAGTTCGACGGGAACAGTTGCCCTCAGCCCATATCACTATGTTCTGTCGAAAGATGACAGGAT
308019 ATGGAGGGAA-GATCAACTCCTGA
66 ATGGAGGGAATGATCAACTCCTGA
308042 AGAAGTTCGACGGGAACAGTTGCCCTTCAGCCCATATCACTATGTTCTGTCGAAAGATGACAGGA
1 AGAAGTTCGACGGGAACAGTTGCCC-TCAGCCCATATCACTATGTTCTGTCGAAAGATGACAGGA
308107 TATGGAGGGAATGATCAACTCCTGA
65 TATGGAGGGAATGATCAACTCCTGA
308132 TCCATTGTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
88 25 0.28
89 50 0.57
90 13 0.15
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (89 bp):
AGAAGTTCGACGGGAACAGTTGCCCTCAGCCCATATCACTATGTTCTGTCGAAAGATGACAGGAT
ATGGAGGGAATGATCAACTCCTGA
Found at i:315469 original size:105 final size:105
Alignment explanation
Indices: 315287--315846 Score: 902
Period size: 105 Copynumber: 5.4 Consensus size: 105
315277 CAGGTTTTAC
315287 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
315352 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
315392 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
315457 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
315497 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
315562 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* *
315602 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* * * * *
315667 GACGAAGGGACCGTTGCTTGTCAAC-AACGACTTCCCAATC
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* *
315707 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
315772 GACCGAAGGGACCGCTGCTTGTCAACAAA-A-TT-TC-A-T
66 GA-CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
** * *
315808 TC--ATTCAATTTCAACTTCACAACGAAGGACATCGGACTC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
315847 GAAACAACAC
Statistics
Matches: 435, Mismatches: 17, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
99 33 0.08
101 2 0.00
102 1 0.00
103 1 0.00
104 5 0.01
105 369 0.85
106 22 0.05
107 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:316179 original size:17 final size:17
Alignment explanation
Indices: 316121--316183 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
316111 CTTACATAAA
316121 ATTATTA-TATATATATAT
1 ATTATTATTAT-TATAT-T
* *
316139 ATAATATATAATTAT-TT
1 ATTAT-TATTATTATATT
*
316156 GTT-TTATTATTATATT
1 ATTATTATTATTATATT
316172 ATTATTATTATT
1 ATTATTATTATT
316184 TTTTTTTTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
15 8 0.23
16 5 0.14
17 10 0.29
18 5 0.14
19 5 0.14
20 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTATTATTATTATATT
Found at i:317242 original size:21 final size:21
Alignment explanation
Indices: 317205--317249 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
317195 CATTCAATAA
*
317205 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
317225 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
317247 TTA
1 TTA
317250 CTATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:317277 original size:24 final size:23
Alignment explanation
Indices: 317240--317293 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
317230 TATTTCCCCT
317240 TTTACTTTTACTATT-TATTATTTA
1 TTTA-TTTTACTATTATATTA-TTA
317264 TTTATTTTAGCTATTATATTATTA
1 TTTATTTTA-CTATTATATTATTA
317288 TTTATT
1 TTTATT
317294 ATTATATACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.18
24 18 0.64
25 5 0.18
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTTACTATTATATTATTA
Found at i:318295 original size:2 final size:2
Alignment explanation
Indices: 318288--318325 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
318278 TAATTTATGA
318288 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
318326 CTTTATATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:319092 original size:15 final size:15
Alignment explanation
Indices: 319072--319101 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
319062 TGTTGATAAA
319072 GATATGAGTCTTAAT
1 GATATGAGTCTTAAT
319087 GATATGAGTCTTAAT
1 GATATGAGTCTTAAT
319102 TAATGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
GATATGAGTCTTAAT
Done.