Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011687.1 Kokia drynarioides strain JFW-HI SEQ_126680, 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: 338835
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 133 characters in sequence are not A, C, G, or T
Found at i:560 original size:52 final size:52
Alignment explanation
Indices: 428--663 Score: 307
Period size: 52 Copynumber: 4.6 Consensus size: 52
418 TTTTCATTTA
* * *
428 ATACTCACGATG--ACATAGTCATCGGACCTCACAATCCGTAAAGGGTTCAG
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
478 AT-CTCACGATGACACATAGTAATCAGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
529 ATACTCATGATGACACATAATCATCGGACCTCATAATCTGTAAAGTATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * **
581 ATACTCATGATGACACGTAGTCATCGAACCTCATGCTCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
633 ATACTCACGATGACACGTAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
664 TTTACATTTA
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 9 0.06
50 2 0.01
51 34 0.21
52 116 0.72
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:14289 original size:26 final size:26
Alignment explanation
Indices: 14268--14533 Score: 256
Period size: 26 Copynumber: 10.2 Consensus size: 26
14258 CCGATTACAT
* *
14268 GTTTACGCTCGTAAGCATGATTATGC
1 GTTTACGCTCGTCAGCATGATTATAC
* * *
14294 GTTTACGCTTG-CTACCATGAATATAC
1 GTTTACGCTCGTC-AGCATGATTATAC
14320 GTTTACGCTCGTCAGCATGGA-TATAC
1 GTTTACGCTCGTCAGCAT-GATTATAC
* *
14346 GTTTACACTCGTTAGCATGATTATAC
1 GTTTACGCTCGTCAGCATGATTATAC
* *
14372 ATTTACGCTCGTTAGCATGGA-TATAC
1 GTTTACGCTCGTCAGCAT-GATTATAC
* * * *
14398 GTTT-CTACTCATAAGCATGGA-TATAT
1 GTTTAC-GCTCGTCAGCAT-GATTATAC
*
14424 GCTTACGCTCGTCAGCATGGA-TATAC
1 GTTTACGCTCGTCAGCAT-GATTATAC
* *
14450 GTTTATGCTCATCAGCATGATTATAC
1 GTTTACGCTCGTCAGCATGATTATAC
*
14476 ATTTACGCTCGTCAGCATGATTATAC
1 GTTTACGCTCGTCAGCATGATTATAC
* * *
14502 GTTTACGCTCGCCAGCATGGTTATGC
1 GTTTACGCTCGTCAGCATGATTATAC
14528 GTTTAC
1 GTTTAC
14534 ACTACTAAAT
Statistics
Matches: 201, Mismatches: 31, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.02
26 190 0.95
27 6 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (26 bp):
GTTTACGCTCGTCAGCATGATTATAC
Found at i:18290 original size:15 final size:15
Alignment explanation
Indices: 18228--18291 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 15
18218 ATTATTGAAA
* *
18228 ATATTCAATATTAAT
1 ATATTAAATATAAAT
18243 ATATT-AATAATAAAT
1 ATATTAAAT-ATAAAT
18258 ATTTATTACAATTATAAAT
1 A--TATTA-AA-TATAAAT
18277 ATATTAAATATAAAT
1 ATATTAAATATAAAT
18292 CTTTGTAGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
14 3 0.07
15 18 0.43
16 2 0.05
17 9 0.21
19 9 0.21
20 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTAAATATAAAT
Found at i:18571 original size:2 final size:2
Alignment explanation
Indices: 18558--18588 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18548 ACAATGTAAA
*
18558 AT AT AA 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 A
18589 ATAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22203 original size:18 final size:18
Alignment explanation
Indices: 22180--22215 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22170 TTTTTTTTTT
22180 TGTGGAAAACACTTACAA
1 TGTGGAAAACACTTACAA
22198 TGTGGAAAACACTTACAA
1 TGTGGAAAACACTTACAA
22216 ACTAAGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
TGTGGAAAACACTTACAA
Found at i:35910 original size:58 final size:57
Alignment explanation
Indices: 35799--35917 Score: 159
Period size: 58 Copynumber: 2.1 Consensus size: 57
35789 ACTCATCAAC
** * * *
35799 AAACTAAATTCAAATATTTTTAAATCCAAATATAATTTCGTTCTTCAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACT-AT
*
35857 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAA-AACACTAT
35914 AAAC
1 AAAC
35918 AACTCCTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
57 9 0.17
58 45 0.83
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (57 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACTAT
Found at i:36714 original size:58 final size:58
Alignment explanation
Indices: 36649--36768 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
36639 ACTCATCAAC
** * * *
36649 AAACTAAATTCAAATATTTTTAAACCCAAATATAATTTTGTTCTTCAAA-AACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTCAT
*
36707 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
36765 AAAC
1 AAAC
36769 AACTCCTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 3 0.05
58 52 0.95
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
Found at i:38986 original size:2 final size:2
Alignment explanation
Indices: 38979--39008 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38969 TGATCATCGA
38979 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
39009 TGGTATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45033 original size:22 final size:22
Alignment explanation
Indices: 45008--45056 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
44998 AACATTAGTG
*
45008 TTTATTTTGTAAATTTATTATT
1 TTTATTTTATAAATTTATTATT
45030 TTTATTTTATAAATTTATTATT
1 TTTATTTTATAAATTTATTATT
45052 TTTAT
1 TTTAT
45057 GATATCGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTTTATAAATTTATTATT
Found at i:47524 original size:16 final size:16
Alignment explanation
Indices: 47489--47535 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
47479 TTTTTGTATA
*
47489 TATTAAAATATT-TTAT
1 TATTAAAAT-TTATTAC
*
47505 TATTTAAATTTATTAC
1 TATTAAAATTTATTAC
47521 TATTAAAATTTATTA
1 TATTAAAATTTATTA
47536 TCAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAAAATTTATTAC
Found at i:47578 original size:34 final size:34
Alignment explanation
Indices: 47527--47595 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 34
47517 TTACTATTAA
47527 AATTTATTATCAAAATAAA-ATTGAAAT-ATTAAAT
1 AATTTATTATCAAAATAAATA-T-AAATAATTAAAT
*
47561 AATTTATTAT-ATGAATAAATATAAATAATTAAAT
1 AATTTATTATCA-AAATAAATATAAATAATTAAAT
47595 A
1 A
47596 TATATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
33 5 0.16
34 25 0.81
35 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (34 bp):
AATTTATTATCAAAATAAATATAAATAATTAAAT
Found at i:47642 original size:15 final size:16
Alignment explanation
Indices: 47624--47656 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
47614 AAAAAAATTA
47624 ATATTTT-ATATTTTT
1 ATATTTTAATATTTTT
47639 ATATTTTAAATATTTTT
1 ATATTTT-AATATTTTT
47656 A
1 A
47657 AATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATTTTAATATTTTT
Found at i:53167 original size:21 final size:21
Alignment explanation
Indices: 53116--53179 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
53106 TTTTAGTTTA
*
53116 ATTTTTTATAGAATTTA-TAAT
1 ATTTTTAATA-AATTTAGTAAT
53137 ATTTTATAATAAATTTAGTAAT
1 ATTTT-TAATAAATTTAGTAAT
*
53159 ATTTTTAATTTAATTTAGTAA
1 ATTTTTAA-TAAATTTAGTAA
53180 ATTAATATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 14 0.37
22 24 0.63
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTTTAATAAATTTAGTAAT
Found at i:55794 original size:17 final size:16
Alignment explanation
Indices: 55764--55803 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
55754 ATGAAGAAGA
55764 AAGAGAGTAAAGAAC-
1 AAGAGAGTAAAGAACG
55779 AAGAGATGTAAAAGAACG
1 AAGAGA-GT-AAAGAACG
55797 AAGAGAG
1 AAGAGAG
55804 CAATATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 2 0.09
17 8 0.36
18 6 0.27
ACGTcount: A:0.57, C:0.05, G:0.30, T:0.07
Consensus pattern (16 bp):
AAGAGAGTAAAGAACG
Found at i:60342 original size:13 final size:13
Alignment explanation
Indices: 60326--60368 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
60316 TTTTATTAAT
60326 TTTAATATTAAAA
1 TTTAATATTAAAA
*
60339 TTTAAGTA--AAAT
1 TTTAA-TATTAAAA
60351 TTTAATATTAAAA
1 TTTAATATTAAAA
60364 TTTAA
1 TTTAA
60369 GTAATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.08
12 8 0.32
13 13 0.52
14 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TTTAATATTAAAA
Found at i:60364 original size:14 final size:14
Alignment explanation
Indices: 60323--60366 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
60313 CATTTTTATT
60323 AATTTTAATATTAA
1 AATTTTAATATTAA
*
60337 AA-TTT-A-AGTAA
1 AATTTTAATATTAA
60348 AATTTTAATATTAA
1 AATTTTAATATTAA
60362 AATTT
1 AATTT
60367 AAGTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AATTTTAATATTAA
Found at i:60382 original size:31 final size:25
Alignment explanation
Indices: 60323--60372 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
60313 CATTTTTATT
60323 AATTTTAATATTAAAATTTAAGTAA
1 AATTTTAATATTAAAATTTAAGTAA
60348 AATTTTAATATTAAAATTTAAGTAA
1 AATTTTAATATTAAAATTTAAGTAA
60373 TTATAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AATTTTAATATTAAAATTTAAGTAA
Found at i:61350 original size:26 final size:26
Alignment explanation
Indices: 61321--61408 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
61311 ATAACTATAG
*
61321 AGGCATCCAAATTGAGATAGTCATAT
1 AGGCATCCAAATTGAGATAGCCATAT
* *
61347 AGGCATCC-AATAAGAAATAGCCATAT
1 AGGCATCCAAAT-TGAGATAGCCATAT
* *
61373 AGGC-TTCTAATTAGAGATAGCCATAT
1 AGGCATCCAAATT-GAGATAGCCATAT
61399 AGGCATCCAA
1 AGGCATCCAA
61409 TATCTACGCC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
25 5 0.10
26 42 0.84
27 3 0.06
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (26 bp):
AGGCATCCAAATTGAGATAGCCATAT
Found at i:61541 original size:29 final size:29
Alignment explanation
Indices: 61509--61590 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
61499 AGCCATAAAG
*
61509 GCTCGCATATAACAGAATCAACCACAAAA
1 GCTCACATATAACAGAATCAACCACAAAA
* ** *
61538 GCTCACATATAATAGAATCAGTCACAAAG
1 GCTCACATATAACAGAATCAACCACAAAA
*
61567 GCTCTCATATAACAGAATCAACCA
1 GCTCACATATAACAGAATCAACCA
61591 TAAATGGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (29 bp):
GCTCACATATAACAGAATCAACCACAAAA
Found at i:71261 original size:13 final size:13
Alignment explanation
Indices: 71228--71252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71218 ATTTAATTTC
71228 CAATTTCAAGGAT
1 CAATTTCAAGGAT
71241 CAATTTCAAGGA
1 CAATTTCAAGGA
71253 CTATATTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
CAATTTCAAGGAT
Found at i:72234 original size:23 final size:23
Alignment explanation
Indices: 72207--72252 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
72197 AGAAAAATCC
72207 TTTTCTATTTTTGAAAATTGAAA
1 TTTTCTATTTTTGAAAATTGAAA
72230 TTTTCTATTTTTGAAAATTGAAA
1 TTTTCTATTTTTGAAAATTGAAA
72253 CTGTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTTCTATTTTTGAAAATTGAAA
Found at i:75302 original size:19 final size:20
Alignment explanation
Indices: 75278--75315 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
75268 AAGGAAGTGT
75278 CTAATATAGAC-TTATGTGC
1 CTAATATAGACTTTATGTGC
*
75297 CTAATATAGGCTTTATGTG
1 CTAATATAGACTTTATGTG
75316 GGAAGGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (20 bp):
CTAATATAGACTTTATGTGC
Found at i:76011 original size:29 final size:30
Alignment explanation
Indices: 75977--76036 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
75967 AAAACCATCC
* *
75977 TACAACTACTTGGAAATGTGGG-GGTGTCT
1 TACAACCACTTGAAAATGTGGGAGGTGTCT
*
76006 TACAACCATTTGAAAATGTGGGAGGTGTCT
1 TACAACCACTTGAAAATGTGGGAGGTGTCT
76036 T
1 T
76037 GCTAAATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (30 bp):
TACAACCACTTGAAAATGTGGGAGGTGTCT
Found at i:83873 original size:32 final size:32
Alignment explanation
Indices: 83810--83874 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
83800 CATTATAAAC
* * * *
83810 TGATAAATTGATTACTTGAATTTAATTACTCA
1 TGATAAATTAATTAATTGAATTCAATAACTCA
*
83842 TGATAAATTAATTAATTTAATTCAATAACTCA
1 TGATAAATTAATTAATTGAATTCAATAACTCA
83874 T
1 T
83875 ATTGATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (32 bp):
TGATAAATTAATTAATTGAATTCAATAACTCA
Found at i:84415 original size:16 final size:15
Alignment explanation
Indices: 84367--84417 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
84357 ATAATTGGTA
84367 ATAATAATAAT-TGAT
1 ATAATAATAATAT-AT
84382 ATAATAGAT-ATATTAT
1 ATAATA-ATAATA-TAT
84398 ATAATGAATAATATAT
1 ATAAT-AATAATATAT
84414 ATAA
1 ATAA
84418 CCATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 8 0.26
16 18 0.58
17 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:84543 original size:17 final size:17
Alignment explanation
Indices: 84521--84554 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
84511 CAATACATAA
84521 AATATTATTAA-AAAATT
1 AATATT-TTAATAAAATT
84538 AATATTTTAATAAAATT
1 AATATTTTAATAAAATT
84555 TTTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTTTAATAAAATT
Found at i:96322 original size:13 final size:13
Alignment explanation
Indices: 96302--96335 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
96292 TCACTGGTAA
96302 GAAATTTCGAGGC
1 GAAATTTCGAGGC
*
96315 GGAATTTCGAGGC
1 GAAATTTCGAGGC
96328 GAAATTTC
1 GAAATTTC
96336 CCTAAGAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (13 bp):
GAAATTTCGAGGC
Found at i:97760 original size:36 final size:36
Alignment explanation
Indices: 97708--97807 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
97698 TAGTAATAAG
*
97708 CATGACCTTTG-GGTCAACAAGGAGTAAAGT-GAGCAA
1 CATGACC-TTGAGGTCAACAGGGAGTAAA-TAGAGCAA
*
97744 CATGATCTTCGA-GTCAACAGGGAGTAAATAGAGCAA
1 CATGACCTT-GAGGTCAACAGGGAGTAAATAGAGCAA
*
97780 CATGACCTTTAGGTCAACAGGGAGTAAA
1 CATGACCTTGAGGTCAACAGGGAGTAAA
97808 ACAAATAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
35 4 0.07
36 52 0.93
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (36 bp):
CATGACCTTGAGGTCAACAGGGAGTAAATAGAGCAA
Found at i:98406 original size:21 final size:24
Alignment explanation
Indices: 98354--98412 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
98344 TTTTTACTTG
*
98354 GGTTGTATCGGTAGTTCTGTGTAT
1 GGTTGTATCGGTAGTTCAGTGTAT
*
98378 GCTTGTATCGGTAGTT-AG-G-AT
1 GGTTGTATCGGTAGTTCAGTGTAT
*
98399 GGTTGTATTGGTAG
1 GGTTGTATCGGTAG
98413 AAGTTACAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 14 0.45
22 1 0.03
23 1 0.03
24 15 0.48
ACGTcount: A:0.15, C:0.07, G:0.36, T:0.42
Consensus pattern (24 bp):
GGTTGTATCGGTAGTTCAGTGTAT
Found at i:112933 original size:180 final size:182
Alignment explanation
Indices: 112628--112991 Score: 624
Period size: 180 Copynumber: 2.0 Consensus size: 182
112618 GGCCAGGACT
* * *
112628 CTTTCCTAATTTGCACATGAAACAATTCTTAGGTAACATACATTACTTTCAGCAGTTTCTATCAC
1 CTTTCCTAATTTGCACACGAAACAATTCTTAGGTAACATACATCACTTTCAGCAGTTTCTATCAA
* * *
112693 TATACCAACACCTAATTCCAAGTAGGAGAGAATACATGGTCAAATTTAAAAAGGAAGCCTCGCCG
66 TATACCAACACCTAATGCCAAGTAGGAGAGAATACATGGTCAAATCTAAAAAGGAAGCCTCACCG
*
112758 TCAATCAGACAAGTATCTCAGCAAAGGAAGTTGATTTCTA-AAACAAATTAC
131 TAAATCAGACAAGTATCTCAGCAAAGGAAGTTGATTTCTACAAACAAATTAC
* *
112809 CTTTCCTAATTTGCGCACGAAACAATTCTTAGGTAACATACATCACTTTTAGCAGTTTCTATCAA
1 CTTTCCTAATTTGCACACGAAACAATTCTTAGGTAACATACATCACTTTCAGCAGTTTCTATCAA
*
112874 TATA-CAACACCTAATGCCAAGTAGGAGAGCATACATGGTCAAATCTAAAAAGGAAGCCTCACCG
66 TATACCAACACCTAATGCCAAGTAGGAGAGAATACATGGTCAAATCTAAAAAGGAAGCCTCACCG
112938 TAAATCAGACAAGTATCTCAGCAAAGGAAGTTGATTTCTACAAACAAATTAC
131 TAAATCAGACAAGTATCTCAGCAAAGGAAGTTGATTTCTACAAACAAATTAC
112990 CT
1 CT
112992 CCGTTCTCCA
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
180 95 0.55
181 77 0.45
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (182 bp):
CTTTCCTAATTTGCACACGAAACAATTCTTAGGTAACATACATCACTTTCAGCAGTTTCTATCAA
TATACCAACACCTAATGCCAAGTAGGAGAGAATACATGGTCAAATCTAAAAAGGAAGCCTCACCG
TAAATCAGACAAGTATCTCAGCAAAGGAAGTTGATTTCTACAAACAAATTAC
Found at i:117725 original size:20 final size:20
Alignment explanation
Indices: 117694--117745 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
117684 ATTTGAAGTG
*
117694 TTAAAATGATTTTGACTTGA
1 TTAAAATCATTTTGACTTGA
* *
117714 TTGAAATCATTTTGACTTGT
1 TTAAAATCATTTTGACTTGA
117734 TTAAAATCATTT
1 TTAAAATCATTT
117746 AAAATTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTGACTTGA
Found at i:130342 original size:14 final size:14
Alignment explanation
Indices: 130323--130350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
130313 ACAAAGTGAC
130323 CAGTCTCCAAATGT
1 CAGTCTCCAAATGT
130337 CAGTCTCCAAATGT
1 CAGTCTCCAAATGT
130351 TACAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
CAGTCTCCAAATGT
Found at i:136138 original size:21 final size:21
Alignment explanation
Indices: 136114--136156 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
136104 TTGAGGGCTT
*
136114 GGCGCAAGATAGAGCAAGTTA
1 GGCGCAAGATAGAGCAAATTA
136135 GGCGCAAGATAGAGCAAATTA
1 GGCGCAAGATAGAGCAAATTA
136156 G
1 G
136157 TCGAAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.33, T:0.14
Consensus pattern (21 bp):
GGCGCAAGATAGAGCAAATTA
Found at i:136651 original size:17 final size:17
Alignment explanation
Indices: 136625--136669 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
136615 GTAGTATAAT
*
136625 TGTCCCTGCATTATTAA
1 TGTCACTGCATTATTAA
* * *
136642 TGTCATTGCATTTTTAT
1 TGTCACTGCATTATTAA
136659 TGTCACTGCAT
1 TGTCACTGCAT
136670 CTACATTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (17 bp):
TGTCACTGCATTATTAA
Found at i:140080 original size:15 final size:15
Alignment explanation
Indices: 140062--140105 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
140052 CTAAAGTATT
*
140062 CTAAATTAAATTAAA
1 CTAAACTAAATTAAA
* *
140077 CTAAACTAAGTTAAG
1 CTAAACTAAATTAAA
140092 CTAAGACTAAATTA
1 CTAA-ACTAAATTA
140106 TATTCCTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (15 bp):
CTAAACTAAATTAAA
Found at i:140794 original size:12 final size:12
Alignment explanation
Indices: 140779--140804 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
140769 AATTAAAGAA
140779 ATAATAGCATTC
1 ATAATAGCATTC
140791 ATAATAGCATTC
1 ATAATAGCATTC
140803 AT
1 AT
140805 CATGACAACA
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:148566 original size:17 final size:17
Alignment explanation
Indices: 148495--148566 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
148485 TGTTAGTAAG
*
148495 CATTGTCATCACATTCT
1 CATTGTCATTACATTCT
*
148512 CATTGTCATTACATTTT
1 CATTGTCATTACATTCT
* * *
148529 AATTGTCACTGCATT-T
1 CATTGTCATTACATTCT
* *
148545 GCATTGTCATTGCATTCC
1 -CATTGTCATTACATTCT
148563 CATT
1 CATT
148567 TTTCATTGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.02
17 44 0.98
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (17 bp):
CATTGTCATTACATTCT
Found at i:154546 original size:19 final size:20
Alignment explanation
Indices: 154522--154571 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
154512 TTTAAACTTT
154522 TTATAATAATTAATATA-AA
1 TTATAATAATTAATATATAA
*
154541 TTATAA-AATTGAATTTATAA
1 TTATAATAATT-AATATATAA
154561 TT-TAAT-ATTAA
1 TTATAATAATTAA
154572 GAATTATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.22
19 17 0.63
20 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATAATAATTAATATATAA
Found at i:158262 original size:34 final size:34
Alignment explanation
Indices: 158219--158288 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
158209 TGATAAATGG
158219 AAATGCAATGA-TAACGCAAATGTAGTGACAATTA
1 AAATGCAATGACTAA-GCAAATGTAGTGACAATTA
* *
158253 AAATGCAATGACTAAGGAAATGTGGTGACAATTA
1 AAATGCAATGACTAAGCAAATGTAGTGACAATTA
158287 AA
1 AA
158289 TTACAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 30 0.91
35 3 0.09
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (34 bp):
AAATGCAATGACTAAGCAAATGTAGTGACAATTA
Found at i:180307 original size:18 final size:17
Alignment explanation
Indices: 180275--180313 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
180265 CAATCTCGTT
180275 TAAAAAAAACTAAAAA-
1 TAAAAAAAACTAAAAAC
180291 TAAAAATAAAGCTAAAAAC
1 TAAAAA-AAA-CTAAAAAC
180310 TAAA
1 TAAA
180314 GTCTAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 7 0.35
19 4 0.20
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (17 bp):
TAAAAAAAACTAAAAAC
Found at i:193045 original size:8 final size:8
Alignment explanation
Indices: 193026--193072 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
193016 ATCATAATTT
193026 TTTTTTCA
1 TTTTTTCA
193034 -TTTTTCA
1 TTTTTTCA
193041 TTTTTTCA
1 TTTTTTCA
*
193049 TTTTCTTCC
1 TTTT-TTCA
193058 TTTTTCCTCA
1 TTTTT--TCA
193068 TTTTT
1 TTTTT
193073 CTTTCTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.36
9 7 0.21
10 7 0.21
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTTCA
Found at i:202615 original size:28 final size:28
Alignment explanation
Indices: 202583--202639 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
202573 CGGCCTTAAT
**
202583 GACAAATAAAATGACATTTTAACACTTA
1 GACAAATAAAACAACATTTTAACACTTA
202611 GACAAATAAAACAACATTTTAACACTTA
1 GACAAATAAAACAACATTTTAACACTTA
202639 G
1 G
202640 GTTACACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (28 bp):
GACAAATAAAACAACATTTTAACACTTA
Found at i:221275 original size:24 final size:24
Alignment explanation
Indices: 221170--221266 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
221160 TTTGGTCTCA
*
221170 TAAGAGCTAATCATTCTGGGCTCG
1 TAAGAGCTAATCATTCTGAGCTCG
221194 TAAGAGCTAATCATTCTGAGCTCG
1 TAAGAGCTAATCATTCTGAGCTCG
* * *
221218 TAAGAGCTAACCATTCT-AGGCCCA
1 TAAGAGCTAATCATTCTGA-GCTCG
221242 TAAGAGCTAATCATTCTGAGCTCG
1 TAAGAGCTAATCATTCTGAGCTCG
221266 T
1 T
221267 GTGGGCTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAGAGCTAATCATTCTGAGCTCG
Found at i:221275 original size:48 final size:48
Alignment explanation
Indices: 221170--221266 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
221160 TTTGGTCTCA
* * * *
221170 TAAGAGCTAATCATTCTGGGCTCGTAAGAGCTAATCATTCTGAGCTCG
1 TAAGAGCTAACCATTCTAGGCCCATAAGAGCTAATCATTCTGAGCTCG
221218 TAAGAGCTAACCATTCTAGGCCCATAAGAGCTAATCATTCTGAGCTCG
1 TAAGAGCTAACCATTCTAGGCCCATAAGAGCTAATCATTCTGAGCTCG
221266 T
1 T
221267 GTGGGCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (48 bp):
TAAGAGCTAACCATTCTAGGCCCATAAGAGCTAATCATTCTGAGCTCG
Found at i:221433 original size:9 final size:9
Alignment explanation
Indices: 221416--221448 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
221406 TAATCGTGAA
221416 CTTACTAAG
1 CTTACTAAG
*
221425 CTTAATAAG
1 CTTACTAAG
221434 CTTACTAAG
1 CTTACTAAG
221443 CTTACT
1 CTTACT
221449 CGTGAATCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (9 bp):
CTTACTAAG
Found at i:225617 original size:21 final size:18
Alignment explanation
Indices: 225582--225622 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
225572 TGGCAATATA
225582 TTTCTTTTCTTTTTTTCT
1 TTTCTTTTCTTTTTTTCT
225600 TTTCTTCTTCTTTCTTTTTCT
1 TTTCTT-TTC-TT-TTTTTCT
225621 TT
1 TT
225623 ATTTTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 2 0.10
21 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTTCT
Found at i:225618 original size:16 final size:13
Alignment explanation
Indices: 225582--225627 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 13
225572 TGGCAATATA
225582 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
225595 TTTCTTTTCTTCTT
1 TTTCTTTTCTT-TT
225609 CTTTCTTTTTCTTTAT
1 -TTTC-TTTTCTTT-T
225625 TTT
1 TTT
225628 TATGAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
15 8 0.28
16 8 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:226403 original size:21 final size:21
Alignment explanation
Indices: 226377--226417 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
226367 CTCGCCTTCT
226377 TCTTTGCGC-TTCTTCTTCTTA
1 TCTTTGCGCATTC-TCTTCTTA
*
226398 TCTTTGTGCATTCTCTTCTT
1 TCTTTGCGCATTCTCTTCTT
226418 GTCCTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.05, C:0.27, G:0.10, T:0.59
Consensus pattern (21 bp):
TCTTTGCGCATTCTCTTCTTA
Found at i:226756 original size:17 final size:16
Alignment explanation
Indices: 226721--226760 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
226711 CTGAAGTTCA
* *
226721 TCTTCCTCTCCTTCCT
1 TCTTCTTCTCCTGCCT
226737 TCTTCTTCTCCTCGCCT
1 TCTTCTTCTCCT-GCCT
226754 TCTTCTT
1 TCTTCTT
226761 GTTGTGCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (16 bp):
TCTTCTTCTCCTGCCT
Found at i:234107 original size:16 final size:16
Alignment explanation
Indices: 234086--234117 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
234076 TCATTACAAA
*
234086 TTTAGTCGTTTAACAT
1 TTTAGTCCTTTAACAT
234102 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
234118 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:237972 original size:35 final size:35
Alignment explanation
Indices: 237926--237995 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
237916 GAGTCATCAG
237926 TGGTACCTAATTATTCTGCAAAAGACAAACGAGAA
1 TGGTACCTAATTATTCTGCAAAAGACAAACGAGAA
237961 TGGTACCTAATTATTCTGCAAAAGACAAACGAGAA
1 TGGTACCTAATTATTCTGCAAAAGACAAACGAGAA
237996 GTTAACCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (35 bp):
TGGTACCTAATTATTCTGCAAAAGACAAACGAGAA
Found at i:241600 original size:20 final size:21
Alignment explanation
Indices: 241575--241613 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
241565 GCAAGGAAAT
241575 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
241595 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
241614 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:246914 original size:14 final size:14
Alignment explanation
Indices: 246895--246921 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
246885 CATGCAATCA
246895 AAGTTAAATGTCAG
1 AAGTTAAATGTCAG
246909 AAGTTAAATGTCA
1 AAGTTAAATGTCA
246922 ATGTACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (14 bp):
AAGTTAAATGTCAG
Found at i:250679 original size:19 final size:19
Alignment explanation
Indices: 250652--250688 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
250642 TATACCAGAT
*
250652 TGGACAGCTCACACATTTC
1 TGGACAGCTAACACATTTC
*
250671 TGGATAGCTAACACATTT
1 TGGACAGCTAACACATTT
250689 ATGTTCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (19 bp):
TGGACAGCTAACACATTTC
Found at i:265655 original size:43 final size:42
Alignment explanation
Indices: 265607--265720 Score: 99
Period size: 43 Copynumber: 2.7 Consensus size: 42
265597 AAAATTATAG
265607 AAAAATTTAAAAATAAAAATAATTCAAACAAAT-TTTAAAAAAT
1 AAAAATTTAAAAATAAAAATAATT-AAA-AAATATTTAAAAAAT
* * * * * *
265650 AAAAATATATAAAGAAAATAAAATTACAAAATATTTAAAAATT
1 AAAAATTTAAAAATAAAA-ATAATTAAAAAATATTTAAAAAAT
* * *
265693 ACAAATTAAAAAATGAAAAT-A-TAAAAAA
1 AAAAATTTAAAAATAAAAATAATTAAAAAA
265721 CTAAAAATAT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
40 6 0.11
41 1 0.02
42 5 0.09
43 38 0.69
44 5 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (42 bp):
AAAAATTTAAAAATAAAAATAATTAAAAAATATTTAAAAAAT
Found at i:265668 original size:29 final size:29
Alignment explanation
Indices: 265605--265668 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
265595 CAAAAATTAT
*
265605 AGAAAAATTTAAAAATAAAAATAATTCAA
1 AGAAAATTTTAAAAATAAAAATAATTCAA
*
265634 A-CAAATTTTAAAAAATAAAAAT-ATAT-AA
1 AGAAAATTTT-AAAAATAAAAATAAT-TCAA
265662 AGAAAAT
1 AGAAAAT
265669 AAAATTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (29 bp):
AGAAAATTTTAAAAATAAAAATAATTCAA
Found at i:265706 original size:15 final size:15
Alignment explanation
Indices: 265686--265739 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
265676 CAAAATATTT
265686 AAAAATTACAAAT-TA
1 AAAAATTA-AAATATA
*
265701 AAAAATGAAAATATA
1 AAAAATTAAAATATA
*
265716 AAAAACTAAAAATATA
1 AAAAA-TTAAAATATA
265732 TAAAAATT
1 -AAAAATT
265740 TAAGAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 10 0.30
17 5 0.15
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAATATA
Found at i:265719 original size:16 final size:16
Alignment explanation
Indices: 265700--265738 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
265690 ATTACAAATT
*
265700 AAAAAATGAAAATATA
1 AAAAAATAAAAATATA
*
265716 AAAAACTAAAAATATA
1 AAAAAATAAAAATATA
*
265732 TAAAAAT
1 AAAAAAT
265739 TTAAGAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAAATATA
Found at i:265819 original size:7 final size:8
Alignment explanation
Indices: 265795--265821 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
265785 AGTTGAAAAC
265795 AAATTAAA
1 AAATTAAA
265803 AAATTAAA
1 AAATTAAA
265811 AAATTAAA
1 AAATTAAA
265819 AAA
1 AAA
265822 AAGCTATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATTAAA
Found at i:266064 original size:31 final size:30
Alignment explanation
Indices: 266037--266093 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
266027 CTTTTAACTA
*
266037 TTTTT-ATTTTTA-AATTATATATATTTAAT
1 TTTTTAATTTTTATAA-CATATATATTTAAT
266066 TTTTTGAATTTTTATAACATATATATTT
1 TTTTT-AATTTTTATAACATATATATTT
266094 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
31 17 0.71
32 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTTAATTTTTATAACATATATATTTAAT
Found at i:269233 original size:86 final size:86
Alignment explanation
Indices: 269088--269260 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
269078 TGAAAGCTCT
269088 TTAGCATACTTGCATATGCTGTTAGGAAAACTAATGAAAAGATATGCTTTTGAGATTTTATTGCT
1 TTAGCATACTTGCATATGCTGTTAGGAAAACTAATGAAAAGATATGCTTTTGAGATTTTATTGCT
269153 TTAACCAATCAAATCTCATCC
66 TTAACCAATCAAATCTCATCC
269174 TTAGCATACTTGCATATGCTGTTAGGAAAACTAATGAAAAGATATGCTTTTGAGATTTTATTGCT
1 TTAGCATACTTGCATATGCTGTTAGGAAAACTAATGAAAAGATATGCTTTTGAGATTTTATTGCT
269239 TTAACCAATCAAATCTCATCC
66 TTAACCAATCAAATCTCATCC
269260 T
1 T
269261 CTTTTTTTTG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (86 bp):
TTAGCATACTTGCATATGCTGTTAGGAAAACTAATGAAAAGATATGCTTTTGAGATTTTATTGCT
TTAACCAATCAAATCTCATCC
Found at i:278938 original size:12 final size:12
Alignment explanation
Indices: 278921--278946 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
278911 CTTTTACTGA
278921 TTATTAATTCTT
1 TTATTAATTCTT
278933 TTATTAATTCTT
1 TTATTAATTCTT
278945 TT
1 TT
278947 CAATTTTCTT
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTAATTCTT
Found at i:286431 original size:15 final size:15
Alignment explanation
Indices: 286411--286447 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
286401 ATTAGAGCCA
286411 ATGAAGAAGCACGAG
1 ATGAAGAAGCACGAG
*
286426 ATGAAGGAGCACGAG
1 ATGAAGAAGCACGAG
*
286441 AAGAAGA
1 ATGAAGA
286448 GAAAGAGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.35, T:0.05
Consensus pattern (15 bp):
ATGAAGAAGCACGAG
Found at i:286903 original size:17 final size:17
Alignment explanation
Indices: 286877--286921 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
286867 ACATGCATTT
286877 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
286894 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
*
286911 ATTTTATTTGT
1 ATTTTAATTGT
286922 TTTAGCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:291413 original size:21 final size:21
Alignment explanation
Indices: 291388--291443 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
291378 AATAGTGCAG
*
291388 ACTTCTACCGATACAAGTGTCT
1 ACTTCTACCGATACAAGTCT-T
* *
291410 -CTTCTATCGAAACAAGTCTT
1 ACTTCTACCGATACAAGTCTT
*
291430 ACTTCTACTGATAC
1 ACTTCTACCGATAC
291444 TAAAAATTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCTT
Found at i:295003 original size:58 final size:58
Alignment explanation
Indices: 294926--295342 Score: 395
Period size: 60 Copynumber: 7.1 Consensus size: 58
294916 AAACATCTAG
* *
294926 GGGTAAAATGGTAATTTTGG-AAAATTG-GGTCAAAAATGGAATTTTAGGAAGTTCGGG
1 GGGTAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTC-GA
* *
294983 GGGTAAAATGGTAACTTTTGGAAAGAATCGAGGTTAAAAATGGAATTCATAGG-AGTTCGA
1 GGGTAAAATGGTAA-TTTTGGAAA-AATCGAGGTCAAAAATGGAATT-TTAGGAAGTTCGA
* * * * * *
295043 GGGTAAAATAGTATTTTTTGGAAAAAATCGAGGTTAAAAATGGGATTTTTGAAAGTTCGA
1 GGGTAAAATGGTA-ATTTTGG-AAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGA
** * * * *
295103 GGGTAAAATAATAATTTTTAGGAAAATTAG-GGTTAATAATGGAATTTTAGGAAGTTCGA
1 GGGTAAAATGGTAA-TTTT-GGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGA
* * * * *
295162 GGTTAAAATGGTAACATTTGGAAAAATCGAGGTC-AAAATGGAATTTTTGAAAATTCG-
1 GGGTAAAATGGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGA
* *
295219 GGGTAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGGATTTCT-GAAAGTTC-A
1 GGGTAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTT-TAGGAAGTTCGA
* * * * *
295276 GGGTAAAATGATAATTTTGGGAAAAAATTG-GTTCAAAAATTG-ATTTTTGGAAAGTTCGA
1 GGGTAAAATGGTAATTTT-GG-AAAAATCGAGGTCAAAAATGGAATTTTAGG-AAGTTCGA
295335 GGGTAAAA
1 GGGTAAAA
295343 ATATAATTTT
Statistics
Matches: 302, Mismatches: 39, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
56 19 0.06
57 67 0.22
58 52 0.17
59 62 0.21
60 73 0.24
61 25 0.08
62 4 0.01
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGA
Found at i:295066 original size:60 final size:58
Alignment explanation
Indices: 294864--295301 Score: 342
Period size: 60 Copynumber: 7.5 Consensus size: 58
294854 TTTAGACATC
* * * * * * **
294864 CGAGGGTATAATGGAAATTTTTGG-AAAGTACGAGGTTTAAAATGGAATTTTTA-AACAT
1 CGAGGGTAAAATGGTAACTTTTGGAAAAAT-CGAGGTTAAAAATGGAA-TTTTAGGAGTT
* * *
294922 CTAGGGGTAAAATGGTAA-TTTTGG-AAAATTG-GGTCAAAAATGGAATTTTAGGAAGTT
1 CGA-GGGTAAAATGGTAACTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAGG-AGTT
* *
294979 CGGGGGGTAAAATGGTAACTTTTGGAAAGAATCGAGGTTAAAAATGGAATTCATAGGAGTT
1 C-GAGGGTAAAATGGTAACTTTTGGAAA-AATCGAGGTTAAAAATGGAATT-TTAGGAGTT
* ** * * *
295040 CGAGGGTAAAATAGTATTTTTTGGAAAAAATCGAGGTTAAAAATGGGATTTTTGAAAGTT
1 CGAGGGTAAAATGGTAACTTTTGG-AAAAATCGAGGTTAAAAATGGAATTTTAG-GAGTT
** * * * *
295100 CGAGGGTAAAATAATAATTTTTAGGAAAATTAG-GGTTAATAATGGAATTTTAGGAAGTT
1 CGAGGGTAAAATGGTAACTTTT-GGAAAAATCGAGGTTAAAAATGGAATTTTAGG-AGTT
* * * * * *
295159 CGAGGTTAAAATGGTAACATTTGGAAAAATCGAGG-TCAAAATGGAATTTTTGAAAATT
1 CGAGGGTAAAATGGTAACTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAG-GAGTT
* * *
295217 CG-GGGTAAAATGGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGGATTTCT-GAAAGTT
1 CGAGGGTAAAATGGTAACTTTTGGAAAAATCGAGGTTAAAAATGGAATTT-TAG-GAGTT
*
295274 C-AGGGTAAAATGATAA-TTTTGGGAAAAA
1 CGAGGGTAAAATGGTAACTTTT-GGAAAAA
295302 ATTGGTTCAA
Statistics
Matches: 311, Mismatches: 50, Indels: 38
0.78 0.13 0.10
Matches are distributed among these distances:
55 5 0.02
56 28 0.09
57 66 0.21
58 53 0.17
59 56 0.18
60 74 0.24
61 25 0.08
62 4 0.01
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (58 bp):
CGAGGGTAAAATGGTAACTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAGGAGTT
Found at i:295074 original size:31 final size:31
Alignment explanation
Indices: 295039--295128 Score: 78
Period size: 31 Copynumber: 2.9 Consensus size: 31
295029 TCATAGGAGT
295039 TCGAGGGTAAAATAGTATTTTTTGGAAAAAA
1 TCGAGGGTAAAATAGTATTTTTTGGAAAAAA
* * * **
295070 TCGAGGTTAAAAATGGGA-TTTTT-G-AAAGT
1 TCGAGGGT-AAAATAGTATTTTTTGGAAAAAA
* *
295099 TCGAGGGTAAAATAATAATTTTTAGGAAAA
1 TCGAGGGTAAAATAGT-ATTTTTTGGAAAA
295129 TTAGGGTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
28 5 0.11
29 11 0.25
30 5 0.11
31 13 0.30
32 10 0.23
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.32
Consensus pattern (31 bp):
TCGAGGGTAAAATAGTATTTTTTGGAAAAAA
Found at i:295110 original size:29 final size:29
Alignment explanation
Indices: 294864--295283 Score: 151
Period size: 28 Copynumber: 14.4 Consensus size: 29
294854 TTTAGACATC
* * *
294864 CGAGGGT-ATAATGGAAATTTTTGGAAAGTA
1 CGAGGGTAAAAATGG-AATTTTT-GAAAATT
* *
294894 CGAGGTTTAAAATGGAATTTTT-AAACA-T
1 CGAGGGTAAAAATGGAATTTTTGAAA-ATT
* *
294922 CTAGGGGT-AAAATGGTAATTTTGGAAAATT
1 CGA-GGGTAAAAATGG-AATTTTTGAAAATT
* * *
294952 ---GGGTCAAAAATGGAATTTTAGGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGAAAATT
* * *
294979 CGGGGGGT-AAAATGGTAACTTTTGGAAAGAAT
1 C-GAGGGTAAAAATGG-AA-TTTTTGAAA-ATT
* ** * *
295011 CGAGGTTAAAAATGGAATTCAT-AGGAGTT
1 CGAGGGTAAAAATGGAATTTTTGA-AAATT
* * *
295040 CGAGGGT-AAAATAGTATTTTTTGGAAAAAAT
1 CGAGGGTAAAAAT-GGAATTTTT-G-AAAATT
* * *
295071 CGAGGTTAAAAATGGGATTTTTGAAAGTT
1 CGAGGGTAAAAATGGAATTTTTGAAAATT
295100 CGAGGGTAAAATAAT--AATTTTTAGGAAAATT
1 CGAGGGT-AAA-AATGGAATTTTT--GAAAATT
* * * *
295131 --AGGGTTAATAATGGAATTTTAGGAAGTT
1 CGAGGG-TAAAAATGGAATTTTTGAAAATT
* * * *
295159 CGA-GGTTAAAATGGTAACATTTGGAAAAAT
1 CGAGGGTAAAAATGG-AA-TTTTTGAAAATT
*
295189 CGA-GGTCAAAATGGAATTTTTGAAAATT
1 CGAGGGTAAAAATGGAATTTTTGAAAATT
* *
295217 CG-GGGT-AAAATGGTAATTTTGGAAAAAT
1 CGAGGGTAAAAATGG-AATTTTTGAAAATT
* * *
295245 CGA-GGTCAAAAATGGGATTTCTGAAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGAAAATT
295274 C-AGGGTAAAA
1 CGAGGGTAAAA
295284 TGATAATTTT
Statistics
Matches: 290, Mismatches: 61, Indels: 80
0.67 0.14 0.19
Matches are distributed among these distances:
26 4 0.01
27 18 0.06
28 75 0.26
29 71 0.24
30 61 0.21
31 46 0.16
32 15 0.05
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (29 bp):
CGAGGGTAAAAATGGAATTTTTGAAAATT
Found at i:295158 original size:59 final size:58
Alignment explanation
Indices: 294864--295342 Score: 392
Period size: 57 Copynumber: 8.2 Consensus size: 58
294854 TTTAGACATC
* * * * **
294864 CGAGGGTATAATGGAAATTTTTGG-AAAGTACGAGGTTTAAAATGGAATTTTTA--AACAT
1 CGAGGGTAAAATGGTAA-TTTTGGAAAAAT-CGAGGTTAAAAATGGAA-TTTTAGGAAGTT
* * *
294922 CTAGGGGTAAAATGGTAATTTTGG-AAAATTG-GGTCAAAAATGGAATTTTAGGAAGTT
1 CGA-GGGTAAAATGGTAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT
* *
294979 CGGGGGGTAAAATGGTAACTTTTGGAAAGAATCGAGGTTAAAAATGGAATTCATAGG-AGTT
1 C-GAGGGTAAAATGGTAA-TTTTGGAAA-AATCGAGGTTAAAAATGGAATT-TTAGGAAGTT
* * * * *
295040 CGAGGGTAAAATAGTATTTTTTGGAAAAAATCGAGGTTAAAAATGGGATTTTTGAAAGTT
1 CGAGGGTAAAATGGTA-ATTTTGG-AAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT
** * * *
295100 CGAGGGTAAAATAATAATTTTTAGGAAAATTAG-GGTTAATAATGGAATTTTAGGAAGTT
1 CGAGGGTAAAATGGTAA-TTTT-GGAAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT
* * * * * *
295159 CGAGGTTAAAATGGTAACATTTGGAAAAATCGAGG-TCAAAATGGAATTTTTGAAAATT
1 CGAGGGTAAAATGGTAA-TTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT
* * *
295217 CG-GGGTAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGGATTTCT-GAAAGTT
1 CGAGGGTAAAATGGTAATTTTGGAAAAATCGAGGTTAAAAATGGAATTT-TAGGAAGTT
* * * *
295274 C-AGGGTAAAATGATAATTTTGGGAAAAAAT--TGGTTCAAAAATTG-ATTTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTT-GG-AAAAATCGAGGTT-AAAAATGGAATTTTAGG-AAGTT
295332 CGAGGGTAAAA
1 CGAGGGTAAAA
295343 ATATAATTTT
Statistics
Matches: 345, Mismatches: 52, Indels: 47
0.78 0.12 0.11
Matches are distributed among these distances:
55 5 0.01
56 29 0.08
57 75 0.22
58 62 0.18
59 72 0.21
60 73 0.21
61 25 0.07
62 4 0.01
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.31
Consensus pattern (58 bp):
CGAGGGTAAAATGGTAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT
Found at i:295234 original size:28 final size:27
Alignment explanation
Indices: 294901--295285 Score: 130
Period size: 29 Copynumber: 13.3 Consensus size: 27
294891 GTACGAGGTT
*
294901 TAAAATGGAATTTTT-AAACATCTAGGGG
1 TAAAATGGAATTTTTGAAA-AT-TCGGGG
*
294929 TAAAATGGTAATTTTGGAAAATT--GGG
1 TAAAATGG-AATTTTTGAAAATTCGGGG
* * *
294955 TCAAAAATGGAATTTTAGGAAGTTCGGGGGG
1 T--AAAATGGAATTTTTGAAAATTC--GGGG
* * *
294986 TAAAATGGTAACTTTTGGAAAGAATCGAGGT
1 TAAAATGG-AA-TTTTTGAAA-ATTCG-GGG
** * *
295017 TAAAAATGGAATTCAT-AGGAGTTCGAGGG
1 T-AAAATGGAATTTTTGA-AAATTCG-GGG
* * * *
295046 TAAAATAGTATTTTTTGGAAAAAATCGAGGT
1 TAAAAT-GGAATTTTT-G-AAAATTCG-GGG
* *
295077 TAAAAATGGGATTTTTGAAAGTTCGAGGG
1 T-AAAATGGAATTTTTGAAAATTCG-GGG
** * *
295106 TAAAATAATAATTTTTAGGAAAATTAGGGT
1 TAAAAT-GGAATTTTT--GAAAATTCGGGG
* * * *
295136 TAATAATGGAATTTTAGGAAGTTCGAGGT
1 TAA-AATGGAATTTTTGAAAATTCG-GGG
* * * *
295165 TAAAATGGTAACATTTGGAAAAATCGAGG
1 TAAAATGG-AA-TTTTTGAAAATTCGGGG
295194 TCAAAATGGAATTTTTGAAAATTCGGGG
1 T-AAAATGGAATTTTTGAAAATTCGGGG
* * *
295222 TAAAATGGTAATTTTGGAAAAATCGAGG
1 TAAAATGG-AATTTTTGAAAATTCGGGG
* * * *
295250 TCAAAAATGGGATTTCTGAAAGTTCAGGG
1 T--AAAATGGAATTTTTGAAAATTCGGGG
295279 TAAAATG
1 TAAAATG
295286 ATAATTTTGG
Statistics
Matches: 264, Mismatches: 63, Indels: 61
0.68 0.16 0.16
Matches are distributed among these distances:
26 4 0.02
27 24 0.09
28 68 0.26
29 69 0.26
30 44 0.17
31 40 0.15
32 15 0.06
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (27 bp):
TAAAATGGAATTTTTGAAAATTCGGGG
Found at i:295259 original size:30 final size:29
Alignment explanation
Indices: 294930--295388 Score: 162
Period size: 28 Copynumber: 15.8 Consensus size: 29
294920 ATCTAGGGGT
294930 AAAATGGTAATTTTGGAAAATT-G-GGTCA
1 AAAATGGTAATTTTGGAAAATTCGAGGT-A
* *
294958 AAAATGG-AATTTTAGG-AAGTTCGGGGGGT-
1 AAAATGGTAATTTT-GGAAAATTC--GAGGTA
*
294987 AAAATGGTAACTTTTGGAAAGAATCGAGGTTA
1 AAAATGGTAA-TTTTGGAAA-ATTCGAGG-TA
* *
295019 AAAATGG-AATTCATAGG--AGTTCGAGGGT-
1 AAAATGGTAATT--TTGGAAAATTCGA-GGTA
* * *
295047 AAAATAGTATTTTTTGGAAAAAATCGAGGTTA
1 AAAATGGTA-ATTTTGG-AAAATTCGAGG-TA
* * *
295079 AAAATGG-GATTTTTGAAAGTTCGAGGGT-
1 AAAATGGTAATTTTGGAAAATTCGA-GGTA
** *
295107 AAAATAATAATTTTTAGGAAAATTAG-GGTTA
1 AAAATGGTAA-TTTT-GGAAAATTCGAGG-TA
* * *
295138 ATAATGG-AATTTTAGG-AAGTTCGAGGTT
1 AAAATGGTAATTTT-GGAAAATTCGAGGTA
* * *
295166 AAAATGGTAACATTTGGAAAAATCGAGGTC
1 AAAATGGTAA-TTTTGGAAAATTCGAGGTA
* *
295196 AAAATGG-AATTTTTGAAAATTCGGGGT-
1 AAAATGGTAATTTTGGAAAATTCGAGGTA
*
295223 AAAATGGTAATTTTGGAAAAATCGAGGTCA
1 AAAATGGTAATTTTGGAAAATTCGAGGT-A
* *
295253 AAAATGG-GATTTCT-GAAAGTTC-AGGGT-
1 AAAATGGTAATTT-TGGAAAATTCGA-GGTA
* *
295280 AAAATGATAATTTTGGGAAAAAATT-G-GTTCA
1 AAAATGGTAATTTT-GG--AAAATTCGAGGT-A
* * *
295311 AAAATTG-ATTTTTGGAAAGTTCGAGGGTA
1 AAAATGGTAATTTTGGAAAATTCGA-GGTA
* * * *
295340 AAAAT-ATAATTTTGTAAAGTT-TAGGGT-
1 AAAATGGTAATTTTGGAAAATTCGA-GGTA
*
295367 CAAATGG-AATTTTGGAAAATTC
1 AAAATGGTAATTTTGGAAAATTC
295389 AAGGGTCAAA
Statistics
Matches: 319, Mismatches: 62, Indels: 100
0.66 0.13 0.21
Matches are distributed among these distances:
27 45 0.14
28 77 0.24
29 75 0.24
30 65 0.20
31 39 0.12
32 18 0.06
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAATTCGAGGTA
Found at i:295342 original size:29 final size:30
Alignment explanation
Indices: 295310--295412 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 30
295300 AAATTGGTTC
* *
295310 AAAAAT-TGATTTTTGGAAAGTTCGAGGGT
1 AAAAATATGAATTTTGGAAAGTTCAAGGGT
* *
295339 AAAAATAT-AATTTTGTAAAGTT-TAGGGT
1 AAAAATATGAATTTTGGAAAGTTCAAGGGT
* * *
295367 -CAAAT-GGAATTTTGGAAAATTCAAGGGT
1 AAAAATATGAATTTTGGAAAGTTCAAGGGT
* *
295395 CAAAATATGATTTTTGGA
1 AAAAATATGAATTTTGGA
295413 TAGCTTAGGG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 16 0.28
28 10 0.17
29 22 0.38
30 10 0.17
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAAATATGAATTTTGGAAAGTTCAAGGGT
Found at i:296533 original size:3 final size:3
Alignment explanation
Indices: 296525--296609 Score: 62
Period size: 3 Copynumber: 27.7 Consensus size: 3
296515 TTTTATTCAT
* ** * * *
296525 TTA TTA TTA ATA TTA AAA TTA TTA TTA CTA TTA TTA ATG TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
** * *
296571 TTA CCA TTA TTTA TTA TTA ATA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
296610 GTTAATTTAT
Statistics
Matches: 60, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
3 54 0.90
4 6 0.10
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:296635 original size:47 final size:47
Alignment explanation
Indices: 296544--296635 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
296534 ATATTAAAAT
* *
296544 TATTATTACTATTATTAATGTTATTTATTACCATTATTTATTATTAA
1 TATTATTACTATCATTAATGTTATTTATGACCATTATTTATTATTAA
* *
296591 TATTATTATTATCATTATTGTTAATTTATGACC-TTATTTATTATT
1 TATTATTACTATCATTAATGTT-ATTTATGACCATTATTTATTATT
296636 GATTAACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.77
48 9 0.22
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.59
Consensus pattern (47 bp):
TATTATTACTATCATTAATGTTATTTATGACCATTATTTATTATTAA
Found at i:296651 original size:47 final size:47
Alignment explanation
Indices: 296548--296652 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 47
296538 TAAAATTATT
* * * *
296548 ATTACTATTATTAATGTTATTTATTACCATTATTTATTATTAATATT
1 ATTAGTATCATTAATGTTATTTATGACCATTATTTATTATTAATATA
* * *
296595 ATTATTATCATTATTGTTAATTTATGACC-TTATTTATTATTGAT-TA
1 ATTAGTATCATTAATGTT-ATTTATGACCATTATTTATTATTAATATA
296641 ACTTAGTATCAT
1 A-TTAGTATCAT
296653 ACATTTAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
46 2 0.04
47 38 0.78
48 9 0.18
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (47 bp):
ATTAGTATCATTAATGTTATTTATGACCATTATTTATTATTAATATA
Found at i:297340 original size:17 final size:17
Alignment explanation
Indices: 297311--297410 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
297301 TTTCAAAGTT
297311 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
* *
297327 TAAATTTAAATTTACAT
1 TAAATTTAAATTTAAAA
** * *
297344 TAAATCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
297361 TAAAGTTTAAATTTAAAG
1 TAAA-TTTAAATTTAAAA
* *
297379 TGAATTCAAATTT-AAA
1 TAAATTTAAATTTAAAA
* *
297395 TAAATATAGATTTAAA
1 TAAATTTAAATTTAAA
297411 TTTTAAAAAA
Statistics
Matches: 61, Mismatches: 20, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
16 18 0.30
17 32 0.52
18 11 0.18
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:307094 original size:99 final size:99
Alignment explanation
Indices: 306971--307558 Score: 662
Period size: 99 Copynumber: 5.9 Consensus size: 99
306961 ATGAACCTAG
* * * * * *
306971 TACCTTAAAAGATGTGATGAGAAGGATCGAGGCCGTAACGGTGGATCTGGTACCATGAAGGTATG
1 TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
* *
307036 AAGGGAATGGTTGAGGCCGTAACGGCGAACCTGA
66 AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
* * * **
307070 TACTTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGCAAATCTGGTACCATGAAGATATG
1 TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
* *
307135 AAGGGAAAGGTTGAGGCCGTAACAGCGAACCCGG
66 AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
* * * *
307169 TACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGGATCTGGTACCATGAAGATATA
1 TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
* * *
307234 AAGGGAAAGGTTGAGGCCGTAATGGCAAACCAGA
66 AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
* * *
307268 TACCTTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATG
1 TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
* * ** *
307333 AAGGGAAAGGTTGAGGCTGCAACGATGAACCCGG
66 AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
* * * ** *
307367 TACCTTAGAAGACATGTTGGGAAAGATCGAGGCCGCAATAGCGGATTTGGTACCATGAAGATATG
1 TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
* * * *
307432 AAGGGAAATGTTGAGGCCGCAACGGTGAA-CCTA
66 AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
* * ** ** *
307465 GTACCTTAGAAGATGTGATGGGAAGGATTGAGGTTGCAACGATGAATCTGG-ATCCATGAAGATC
1 -TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTA-CCATGAAGAT-
* * * *
307529 GTG--GAGAAAGATTGAGGCCGTAATGGCGAA
63 ATGAAGGGAAAGGTTGAGGCCGTAACGGCGAA
307559 TCTGGAACCA
Statistics
Matches: 408, Mismatches: 78, Indels: 7
0.83 0.16 0.01
Matches are distributed among these distances:
98 24 0.06
99 382 0.94
100 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.19
Consensus pattern (99 bp):
TACCTTAGAAGATATGATGGGAAGGATCGAGGCCGCAACGGCGGATCTGGTACCATGAAGATATG
AAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGA
Found at i:307103 original size:50 final size:50
Alignment explanation
Indices: 306963--307497 Score: 346
Period size: 49 Copynumber: 10.8 Consensus size: 50
306953 TCACAACGAT
* * * * * *
306963 GAACCTAGTACCTTAAAAGATGTGAT-GAGAAGGATCGAGGCCGTAACGGT
1 GAACCTGGTACCTTAGAAGATATGATAG-GAAGGATTGAGGCCGCAACGGC
* * * * *
307013 GGATCTGGTACCAT-GAAGGTATGA-AGGGAATGG-TTGAGGCCGTAACGGC
1 GAACCTGGTACCTTAGAAGATATGATA-GGAA-GGATTGAGGCCGCAACGGC
* *
307062 GAACCTGATACTTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
1 GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
* * * * *
307112 AAATCTGGTACCAT-GAAGATATGA-AGGGAAAGG-TTGAGGCCGTAACAGC
1 GAACCTGGTACCTTAGAAGATATGATA-GG-AAGGATTGAGGCCGCAACGGC
* * * * * *
307161 GAACCCGGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGAC
1 GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
* * * * * *
307211 GGATCTGGTACCAT-GAAGATAT-AAAGGGAAAGG-TTGAGGCCGTAATGGC
1 GAACCTGGTACCTTAGAAGATATGATA-GG-AAGGATTGAGGCCGCAACGGC
* * * * *
307260 AAACCAGATACCTTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGGT
1 GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
* * * **
307310 GAATCTGGTACCAT-GAAGATATGA-AGGGAAAGG-TTGAGGCTGCAACGAT
1 GAACCTGGTACCTTAGAAGATATGATA-GG-AAGGATTGAGGCCGCAACGGC
* * * * * * **
307359 GAACCCGGTACCTTAGAAGACATGTTGGGAAAGATCGAGGCCGCAATAGC
1 GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
* ** * * *
307409 GGATTTGGTACCAT-GAAGATATGA-AGGGAAATG-TTGAGGCCGCAACGGT
1 GAACCTGGTACCTTAGAAGATATGATA-GG-AAGGATTGAGGCCGCAACGGC
* * *
307458 GAACCTAGTACCTTAGAAGATGTGATGGGAAGGATTGAGG
1 GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGG
307498 TTGCAACGAT
Statistics
Matches: 361, Mismatches: 98, Indels: 52
0.71 0.19 0.10
Matches are distributed among these distances:
48 2 0.01
49 182 0.50
50 175 0.48
51 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (50 bp):
GAACCTGGTACCTTAGAAGATATGATAGGAAGGATTGAGGCCGCAACGGC
Found at i:307439 original size:297 final size:297
Alignment explanation
Indices: 306971--307527 Score: 747
Period size: 297 Copynumber: 1.9 Consensus size: 297
306961 ATGAACCTAG
* * * *
306971 TACCTTAAAAGATGTGATGAGAAGGATCGAGGCCGTAACGGTGGATCTGGTACCATGAAGGTATG
1 TACCTTAAAAGATATGATGAGAAGGATCGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATG
* * * * * * * *
307036 AAGGGAATGGTTGAGGCCGTAACGGCGAACCTGATACTTTAGAAGATATGATAGGAAGGATTGAG
66 AAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGACATGATAGGAAAGATCGAG
* *
307101 GCCGCAACGGCAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACAGCGAACC
131 GCCGCAACAGCAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACC
* *
307166 CGGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGGATCTGG-TACCATGAAGA
196 CAGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGAATCTGGAT-CCATGAAGA
307230 TATAAAGGGAAAGGTTGAGGCCGTAATGGCAAACCAGA
260 TATAAAGGGAAAGGTTGAGGCCGTAATGGCAAACCAGA
* * *
307268 TACCTTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATG
1 TACCTTAAAAGATATGATGAGAAGGATCGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATG
* * * * *
307333 AAGGGAAAGGTTGAGGCTGCAACGATGAACCCGGTACCTTAGAAGACATGTTGGGAAAGATCGAG
66 AAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGACATGATAGGAAAGATCGAG
* ** * * * *
307398 GCCGCAATAGCGGATTTGGTACCATGAAGATATGAAGGGAAATGTTGAGGCCGCAACGGTGAACC
131 GCCGCAACAGCAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACC
* ** * * ** *
307463 TAGTACCTTAGAAGATGTGATGGGAAGGATTGAGGTTGCAACGATGAATCTGGATCCATGAAGAT
196 CAGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGAATCTGGATCCATGAAGAT
307528 CGTGGAGAAA
Statistics
Matches: 220, Mismatches: 39, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
297 219 1.00
298 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.20
Consensus pattern (297 bp):
TACCTTAAAAGATATGATGAGAAGGATCGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATG
AAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGACATGATAGGAAAGATCGAG
GCCGCAACAGCAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACC
CAGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGAATCTGGATCCATGAAGAT
ATAAAGGGAAAGGTTGAGGCCGTAATGGCAAACCAGA
Found at i:307513 original size:198 final size:198
Alignment explanation
Indices: 306891--307527 Score: 797
Period size: 198 Copynumber: 3.2 Consensus size: 198
306881 AGGTTTGAAA
* * * * *
306891 GGGAA-GATTGAGGTCGCAACGGTGAATCTGATACCCTGGAA-ATACGGAGGGAAAGGTTGAGG-
1 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCAT-GAAGATATGAAGGGAAAGGTTGAGGC
* ** * ** * * * *
306953 TCACAACGATGAACCTAGTACCTTAAAAGATGTGATGAGAAGGATCGAGGCCGTAACGGTGGATC
65 T-GCAACGATGAACCCGGTACCTTAGAAGACATGATGGGAAGGATCGAGGCCGCAA-AGCGGATC
* *
307018 TGGTACCATGAAGGTATGAAGGG-AATGGTTGAGGCCGTAACGGCGAACCT-GATACTTTAGAAG
128 TGGTACCATGAAGATATGAAGGGAAAT-GTTGAGGCCGTAACGGCGAACCTAGATACCTTAGAAG
307081 ATATGAT
192 ATATGAT
* ** *
307088 AGGAAGGATTGAGGCCGCAACGGCAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
1 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCT
* * * *
307153 GTAAC-AGCGAACCCGGTACCTTAGAAGACATAATGGGAAGGATCGAGGCCGCAACGACGGATCT
66 GCAACGA-TGAACCCGGTACCTTAGAAGACATGATGGGAAGGATCGAGGCCGCAAAG-CGGATCT
* * * *
307217 GGTACCATGAAGATATAAAGGGAAAGGTTGAGGCCGTAATGGCAAACC-AGATACCTTAGAAGAT
129 GGTACCATGAAGATATGAAGGGAAATGTTGAGGCCGTAACGGCGAACCTAGATACCTTAGAAGAT
307281 ATGAT
194 ATGAT
307286 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCT
1 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCT
* * *
307351 GCAACGATGAACCCGGTACCTTAGAAGACATGTTGGGAAAGATCGAGGCCGCAATAGCGGATTTG
66 GCAACGATGAACCCGGTACCTTAGAAGACATGATGGGAAGGATCGAGGCCGCAA-AGCGGATCTG
* * *
307416 GTACCATGAAGATATGAAGGGAAATGTTGAGGCCGCAACGGTGAACCTAG-TACCTTAGAAGATG
130 GTACCATGAAGATATGAAGGGAAATGTTGAGGCCGTAACGGCGAACCTAGATACCTTAGAAGATA
307480 TGAT
195 TGAT
** *
307484 GGGAAGGATTGAGGTTGCAACGATGAATCTGG-ATCCATGAAGAT
1 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTA-CCATGAAGAT
307528 CGTGGAGAAA
Statistics
Matches: 380, Mismatches: 49, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
197 10 0.03
198 364 0.96
199 6 0.02
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (198 bp):
GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCT
GCAACGATGAACCCGGTACCTTAGAAGACATGATGGGAAGGATCGAGGCCGCAAAGCGGATCTGG
TACCATGAAGATATGAAGGGAAATGTTGAGGCCGTAACGGCGAACCTAGATACCTTAGAAGATAT
GAT
Found at i:318511 original size:62 final size:62
Alignment explanation
Indices: 318414--318539 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
318404 GACATGATGT
* *
318414 CACAATAACAACAGTCTCAACACAATCTCATGATATTATATCAGAGTATGAAATTCAGTGCA
1 CACAATAACAACAGTCTCAAAACAATCTCATGATATTATATCAGAGTATGAAATTCAATGCA
*
318476 CACAATAACAACAGTCTCAAAACAATCTCGTGATATTATATCAGAGTATGAAATTCAATGCA
1 CACAATAACAACAGTCTCAAAACAATCTCATGATATTATATCAGAGTATGAAATTCAATGCA
318538 CA
1 CA
318540 TTATACTCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (62 bp):
CACAATAACAACAGTCTCAAAACAATCTCATGATATTATATCAGAGTATGAAATTCAATGCA
Found at i:321194 original size:2 final size:2
Alignment explanation
Indices: 321187--321211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
321177 TCGATTTCAG
321187 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
321212 ATTTTATTGT
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:322464 original size:5 final size:5
Alignment explanation
Indices: 322454--322485 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
322444 CAACACTATG
322454 TGTGT TGTGT TGTGT TGTGT TGTGT TGTGT TG
1 TGTGT TGTGT TGTGT TGTGT TGTGT TGTGT TG
322486 CAACTCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (5 bp):
TGTGT
Found at i:325745 original size:34 final size:34
Alignment explanation
Indices: 325682--325761 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
325672 TGTTACAGTG
* * ** *
325682 ATTTGGTGTGTTGGAAGGACTAGGTCTTACGAGC
1 ATTTGGTGTGTTGGAAGAACAAGCACTTACAAGC
* *
325716 ATTTGGTGTGTTGGATGAACAAGCACTTACAAGT
1 ATTTGGTGTGTTGGAAGAACAAGCACTTACAAGC
325750 ATTTGGTGTGTT
1 ATTTGGTGTGTT
325762 AATTGGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (34 bp):
ATTTGGTGTGTTGGAAGAACAAGCACTTACAAGC
Found at i:328252 original size:33 final size:33
Alignment explanation
Indices: 328176--328252 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
328166 CCTATTTACT
* * * ** *
328176 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
328209 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
328241 TAAAATAAACAA
1 TAAAATAAACAA
328253 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:333306 original size:33 final size:33
Alignment explanation
Indices: 333230--333306 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
333220 CCTATTTACT
* * * ** *
333230 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
333263 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
333295 TAAAATAAACAA
1 TAAAATAAACAA
333307 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:336255 original size:7 final size:8
Alignment explanation
Indices: 336233--336270 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
336223 TTTAATTTTT
336233 TAAAATTA
1 TAAAATTA
336241 TAAAATTA
1 TAAAATTA
336249 T-AAATTA
1 TAAAATTA
336256 TTAAAATT-
1 -TAAAATTA
336264 TAAAATT
1 TAAAATT
336271 TAATTTCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 13 0.46
8 10 0.36
9 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TAAAATTA
Found at i:336255 original size:15 final size:15
Alignment explanation
Indices: 336235--336267 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
336225 TAATTTTTTA
336235 AAATTA-TAAAATTAT
1 AAATTATTAAAATT-T
336250 AAATTATTAAAATTT
1 AAATTATTAAAATTT
336265 AAA
1 AAA
336268 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTATTAAAATTT
Found at i:336271 original size:7 final size:7
Alignment explanation
Indices: 336231--336273 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
336221 GATTTAATTT
336231 TTTAAAA
1 TTTAAAA
336238 TTATAAAA
1 TT-TAAAA
*
336246 TTATAAAT
1 TT-TAAAA
336254 TATTAAAA
1 T-TTAAAA
336262 TTTAAAA
1 TTTAAAA
336269 TTTAA
1 TTTAA
336274 TTTCGACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.41
8 18 0.56
9 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Done.