Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 180 of 259
Found at i:58365545 original size:28 final size:28
Alignment explanation
Indices: 58365514--58365568 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
58365504 GGGATTGGGA
58365514 AGATAGTTAAGGGATTTAGTGTACCATG
1 AGATAGTTAAGGGATTTAGTGTACCATG
58365542 AGATAGTTAAGGGATTTAGTGTACCAT
1 AGATAGTTAAGGGATTTAGTGTACCAT
58365569 TAGTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (28 bp):
AGATAGTTAAGGGATTTAGTGTACCATG
Found at i:58379293 original size:19 final size:19
Alignment explanation
Indices: 58379256--58379304 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
58379246 ATTATCATCA
*
58379256 TCATTTTTT-TACTTTATT
1 TCATTTTTTATACTTAATT
58379274 T-ATTTTTTATATCTTAATT
1 TCATTTTTTATA-CTTAATT
58379293 TCATTTTCTTAT
1 TCATTTT-TTAT
58379305 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 7 0.27
20 5 0.19
21 4 0.15
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
TCATTTTTTATACTTAATT
Found at i:58381755 original size:28 final size:29
Alignment explanation
Indices: 58381709--58381774 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
58381699 CTTTATGTAC
*
58381709 TTAATTTTTCCAATAAATTTTTAATTTT-A
1 TTAA-TTTTCCAATAAATTTCTAATTTTAA
* *
58381738 TTGAATTTTCCACT-AATTTCTATTTTTAA
1 TT-AATTTTCCAATAAATTTCTAATTTTAA
58381767 TTAATTTT
1 TTAATTTT
58381775 AACTATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 17 0.53
29 13 0.41
30 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (29 bp):
TTAATTTTCCAATAAATTTCTAATTTTAA
Found at i:58385015 original size:30 final size:30
Alignment explanation
Indices: 58384960--58385023 Score: 71
Period size: 30 Copynumber: 2.1 Consensus size: 30
58384950 TATTAACTTA
58384960 ATTTAATTAATTATATTATAGATATAGT-TT
1 ATTTAATTAATTATATTATAGATATA-TCTT
*
58384990 ATTTAATTTAATTATCA-TAT-TATATATCTT
1 ATTTAA-TTAATTAT-ATTATAGATATATCTT
58385020 ATTT
1 ATTT
58385024 TTAATCGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 1 0.03
30 17 0.57
31 11 0.37
32 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (30 bp):
ATTTAATTAATTATATTATAGATATATCTT
Found at i:58387729 original size:17 final size:18
Alignment explanation
Indices: 58387696--58387729 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58387686 TTGAATAAAT
*
58387696 TATTTTTAAAAATAAAAA
1 TATTTTTAAAAAGAAAAA
58387714 TATTTTT-AAAAGAAAA
1 TATTTTTAAAAAGAAAA
58387730 TGAAACTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TATTTTTAAAAAGAAAAA
Found at i:58387887 original size:20 final size:21
Alignment explanation
Indices: 58387862--58387901 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
58387852 GTGAGTTGCA
58387862 ACTGAT-TATACAATGATAGC
1 ACTGATATATACAATGATAGC
*
58387882 ACTGATAATATTCAATGATA
1 ACTGAT-ATATACAATGATA
58387902 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
ACTGATATATACAATGATAGC
Found at i:58390356 original size:28 final size:28
Alignment explanation
Indices: 58390316--58390374 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
58390306 TTATAAAAAC
*
58390316 TTTATCTATTTTTGAAAATTTTATCTAT
1 TTTATCTAATTTTGAAAATTTTATCTAT
* * * * *
58390344 TTTATTTAATTTTTAGATTTTTATGTAT
1 TTTATCTAATTTTGAAAATTTTATCTAT
58390372 TTT
1 TTT
58390375 TAAAAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.66
Consensus pattern (28 bp):
TTTATCTAATTTTGAAAATTTTATCTAT
Found at i:58391602 original size:22 final size:22
Alignment explanation
Indices: 58391577--58391632 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
58391567 AAAAAACTTC
58391577 AATATATAATTAATCATGAGTG
1 AATATATAATTAATCATGAGTG
58391599 AATATATAATTAATCATGAGTG
1 AATATATAATTAATCATGAGTG
*
58391621 AACATAATAATT
1 AATAT-ATAATT
58391633 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
AATATATAATTAATCATGAGTG
Found at i:58392173 original size:46 final size:46
Alignment explanation
Indices: 58392123--58392215 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
58392113 TTATTTATTT
* * *
58392123 TATTTATTATTA-TTAATTTTTAAATTTTTGAAATATATA-TTTAAAA
1 TATTTATTAATACATAATTTTTAAA-TATT-AAATATATATTTTAAAA
* *
58392169 TATTTTTTAATACATATTTTTTAAATATTAAATATATATTTTAAAA
1 TATTTATTAATACATAATTTTTAAATATTAAATATATATTTTAAAA
58392215 T
1 T
58392216 TACATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 9 0.22
46 21 0.52
47 10 0.25
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (46 bp):
TATTTATTAATACATAATTTTTAAATATTAAATATATATTTTAAAA
Found at i:58392211 original size:34 final size:35
Alignment explanation
Indices: 58392163--58392273 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 35
58392153 AAATATATAT
*
58392163 TTAAA-ATATTTTTTAATACA-TA-TTTTTTAAATA
1 TTAAATATATTTTTTAATA-ATTACATTTTTAAATA
* *
58392196 TTAAATATATATTTTAA-AATTACATTTTTAAATT
1 TTAAATATATTTTTTAATAATTACATTTTTAAATA
* * *
58392230 TTAAATATTATTTTTTAATATTTAAATATTTTAAACTT
1 TTAAATA-TATTTTTTAATAATTACAT-TTTTAAA-TA
58392268 TTAAAT
1 TTAAAT
58392274 TTGTTATTAG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
32 1 0.02
33 8 0.12
34 26 0.40
35 9 0.14
36 6 0.09
37 7 0.11
38 8 0.12
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (35 bp):
TTAAATATATTTTTTAATAATTACATTTTTAAATA
Found at i:58392230 original size:21 final size:22
Alignment explanation
Indices: 58392187--58392259 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
58392177 AATACATATT
* *
58392187 TTTTAAATATTAA-ATAT-ATA
1 TTTTAAATATTAATTTTTAATA
58392207 TTTTAAA-ATTACATTTTTAA-A
1 TTTTAAATATTA-ATTTTTAATA
*
58392228 TTTTAAATATTATTTTTTAATA
1 TTTTAAATATTAATTTTTAATA
58392250 -TTTAAATATT
1 TTTTAAATATT
58392260 TTAAACTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.09
20 8 0.18
21 27 0.60
22 6 0.13
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAAATATTAATTTTTAATA
Found at i:58392342 original size:14 final size:15
Alignment explanation
Indices: 58392317--58392349 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
58392307 TTAATTTGTT
58392317 TTATAATATTTTAAA
1 TTATAATATTTTAAA
58392332 TTATAAT-TTTTAAA
1 TTATAATATTTTAAA
58392346 TTAT
1 TTAT
58392350 TTTTAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAATATTTTAAA
Found at i:58392668 original size:15 final size:15
Alignment explanation
Indices: 58392627--58392668 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
58392617 AATTAAAAAA
*
58392627 TAAAAAAT-ATTTGT
1 TAAAAAATAATTTAT
58392641 TAAAAAATGAATTTAT
1 TAAAAAAT-AATTTAT
*
58392657 TTAAAAATAATT
1 TAAAAAATAATT
58392669 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TAAAAAATAATTTAT
Found at i:58398937 original size:42 final size:42
Alignment explanation
Indices: 58398878--58398962 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
58398868 GAAGAAGTAA
58398878 GAGGATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGT
1 GAGGATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGT
58398920 GAGGATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGT
1 GAGGATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGT
58398962 G
1 G
58398963 TTTCTTGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (42 bp):
GAGGATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGT
Found at i:58401671 original size:29 final size:28
Alignment explanation
Indices: 58401629--58401720 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
58401619 ACATGGCTTG
* *
58401629 GAAT-TGATTCGGGCCGGATGGGCCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
58401657 GAATGTGATTTGGGCCTAATGGACCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
58401686 GAATGTGATTTGGGCCTAGTGGGCCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
58401715 GCATGT
1 GAATGT
58401721 ATGTAAACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 4 0.07
29 52 0.93
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (28 bp):
GAATGTGATTTGGGCCAATGGGCCATAT
Found at i:58403019 original size:16 final size:17
Alignment explanation
Indices: 58402987--58403019 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
58402977 TTTAAAGAAG
58402987 GGTTTTCAATGAAAACAA
1 GGTTTTCAA-GAAAACAA
58403005 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
58403020 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAA
Found at i:58407980 original size:22 final size:22
Alignment explanation
Indices: 58407950--58408001 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
58407940 TAGGATTTTC
*
58407950 TTTG-TATTTTGGG-CTTGTATT
1 TTTGTTATTTTGGGTC-TGTAAT
58407971 TTTGTTA-TTTGGGTCTGTAAT
1 TTTGTTATTTTGGGTCTGTAAT
58407992 TTTGTTATTT
1 TTTGTTATTT
58408002 ATTAAGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.12, C:0.04, G:0.21, T:0.63
Consensus pattern (22 bp):
TTTGTTATTTTGGGTCTGTAAT
Found at i:58408220 original size:45 final size:45
Alignment explanation
Indices: 58408156--58408287 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 45
58408146 GCAACCATGT
* * *
58408156 TCTTCAATCTGCCCTACTGCAACTTTAGGGAGATAAGATTTGTTA
1 TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGTCA
58408201 TCTTCAATCTGCTCTACTGCAA-TTTCAAGGAGATAAGATTTG-CA
1 TCTTCAATCTGCTCTACTGCAACTTT-AAGGAGATAAGATTTGTCA
* * * * * *
58408245 TATTCAATTTTCTCCACTGCAACTTCAAGGAGATAAGGTTTGT
1 TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGT
58408288 GGCTTCAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 37 0.49
45 38 0.51
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (45 bp):
TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGTCA
Found at i:58408295 original size:44 final size:44
Alignment explanation
Indices: 58408171--58408330 Score: 160
Period size: 44 Copynumber: 3.6 Consensus size: 44
58408161 AATCTGCCCT
* * * * *
58408171 ACTGCAACTTTAGGGAGATAAGATTTGTTATCTTCAATCTGCTCT
1 ACTGCAACTTCAAGGAGATAAGATTTG-TATCTTCAATATACTCC
* * * * *
58408216 ACTGCAATTTCAAGGAGATAAGATTTGCATATTCAATTTTCTCC
1 ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
* **
58408260 ACTGCAACTTCAAGGAGATAAGGTTTGTGGCTTCAATATACTCC
1 ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
* *
58408304 ACTGCAACTAC-AGAGAAATAAGATTTG
1 ACTGCAACTTCAAG-GAGATAAGATTTG
58408331 CCATGGTAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.02
44 69 0.73
45 24 0.25
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (44 bp):
ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
Found at i:58408343 original size:89 final size:89
Alignment explanation
Indices: 58408171--58408381 Score: 194
Period size: 88 Copynumber: 2.3 Consensus size: 89
58408161 AATCTGCCCT
* * * * * * * * *
58408171 ACTGCAACTTTAGGGAGATAAGATTTGTTATCTTCAATCTGCTCTACTGCAATTTCAAGGAGATA
1 ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAGGAAATA
* *
58408236 AGATTTGCATATTCAATTTTCTCC
66 AGATTTGCATAGTAAATTTTCTCC
* *
58408260 ACTGCAACTTCAAGGAGATAAGGTTTG-TGGCTTCAATATACTCCACTGCAACTAC-AGAGAAAT
1 ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAG-GAAAT
*
58408323 AAGATTTGCCATGGTAAATTTGATCTAACC
65 AAGATTTG-CATAGTAAATTT--TCT--CC
*
58408353 TACTGCAACTTCAGAGG-TATAAGATTTGT
1 -ACTGCAACTTCA-AGGAGATAAGATTTGT
58408382 AACTTGTAGC
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
87 2 0.02
88 33 0.34
89 33 0.34
91 3 0.03
93 2 0.02
94 21 0.22
95 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (89 bp):
ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAGGAAATA
AGATTTGCATAGTAAATTTTCTCC
Found at i:58409379 original size:30 final size:30
Alignment explanation
Indices: 58409339--58409400 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
58409329 ACTTCTAGAG
58409339 GACCCTTTTGGACTTGATATGAATTTCGGA
1 GACCCTTTTGGACTTGATATGAATTTCGGA
*
58409369 GACCTTTTTGGACTTGATATGAATTTCGGA
1 GACCCTTTTGGACTTGATATGAATTTCGGA
58409399 GA
1 GA
58409401 TTTAGAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (30 bp):
GACCCTTTTGGACTTGATATGAATTTCGGA
Found at i:58414372 original size:3 final size:3
Alignment explanation
Indices: 58414364--58414504 Score: 94
Period size: 3 Copynumber: 47.3 Consensus size: 3
58414354 ATAAAAGACC
** *
58414364 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA CCT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * * *
58414411 ATG ATA CTA ATA ATA GTA ATA ATA AGA A-A ATTA ATA TTA GTA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
* * *
58414456 ATA ATA ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA GTA ATA ATA
1 ATA ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58414501 ATA A
1 ATA A
58414505 ACGTGAAATT
Statistics
Matches: 107, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
2 9 0.08
3 93 0.87
4 3 0.03
5 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58414692 original size:12 final size:12
Alignment explanation
Indices: 58414675--58414700 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58414665 TATGTACATA
58414675 ATATATATATGT
1 ATATATATATGT
58414687 ATATATATATGT
1 ATATATATATGT
58414699 AT
1 AT
58414701 TAGAAAATGT
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:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:58415120 original size:81 final size:81
Alignment explanation
Indices: 58415012--58415175 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
58415002 AGAAAAGAGT
*
58415012 AAAAAAAAGGACGAAATTGGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
1 AAAAAAAAGGACGAAATTGGGTTGAAAACGAAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
58415077 GGAGGGGACTGATTTG
66 GGAGGGGACTGATTTG
58415093 AAAAAAAAGGACGAAATTGGGTTGAAAACGAAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
1 AAAAAAAAGGACGAAATTGGGTTGAAAACGAAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
58415158 GGAGGGGACTGATTTG
66 GGAGGGGACTGATTTG
58415174 AA
1 AA
58415176 CACACGAGCA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.22
Consensus pattern (81 bp):
AAAAAAAAGGACGAAATTGGGTTGAAAACGAAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
GGAGGGGACTGATTTG
Found at i:58415693 original size:17 final size:17
Alignment explanation
Indices: 58415668--58415710 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
58415658 TTTTTCTCTC
* *
58415668 ATTTTTTTAATTTATGT
1 ATTTATTTAATATATGT
58415685 ATTTATTTAATATATGT
1 ATTTATTTAATATATGT
58415702 ATGTTATTT
1 AT-TTATTT
58415711 TTAATAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (17 bp):
ATTTATTTAATATATGT
Found at i:58416685 original size:43 final size:43
Alignment explanation
Indices: 58416638--58416921 Score: 183
Period size: 43 Copynumber: 6.5 Consensus size: 43
58416628 CGATCTATTT
*
58416638 CCCTACTACTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* * * * *
58416681 CCCTACTGCTTAGGGGTTTAAG----GCCCATGCATCGTTGATCAA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGC-CTG-T-TA
* ** * * *
58416723 CTCCACTACTGCTTAGGGAG-ATAAGATCT-ATAATCTTCAACCTGCTG
1 --CC-CTACTGCTTAGGG-GTTTAAGATCTGCCAA--TTCAGCCTGTTA
* **
58416770 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* *
58416813 CCCTACTGCTTAGGGGTTTAAGGCCCATC-GCC--TTC-GATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-G---ATCTGCCAATTCAG-CCTGTTA
* * **
58416857 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
58416900 CCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGTTTAAG
58416922 GCCCATCGTC
Statistics
Matches: 183, Mismatches: 34, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
39 8 0.04
40 4 0.02
41 2 0.01
42 1 0.01
43 82 0.45
44 53 0.29
45 21 0.11
46 2 0.01
47 3 0.02
48 1 0.01
49 2 0.01
50 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
Found at i:58417008 original size:43 final size:42
Alignment explanation
Indices: 58416728--58417001 Score: 172
Period size: 44 Copynumber: 6.3 Consensus size: 42
58416718 ATCAACTCCA
* * * * *
58416728 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTGCTGCC
1 CTACTGCTTAGGG-GTTAAGATCTATAAAC-TCAGCCTGTTACC
* *
58416772 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTA-GGGGTTAAGATCTATAAACTCAGCCTGTTACC
** * *** * *
58416815 CTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGATCTATAAAC-TCAG-CCTGTTACC
* * *
58416859 CTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACC
1 CTACTGCTTA-GGGGTTAAGATCTATAAACTCAGCCTGTTACC
** * *** ** * *
58416902 CTACTGCTTAGGGGTTTAAGGCCCATCGTCTTTGATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGATCTATAAACTCAG-CCTGTTACC
* * *
58416946 CTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACC
1 CTACTGCTTAGGG-GTTAAGATCTATAAACTCAGCCTGTTACC
58416989 CTACTGCTTAGGG
1 CTACTGCTTAGGG
58417002 AGATAAGGCT
Statistics
Matches: 166, Mismatches: 55, Indels: 19
0.69 0.23 0.08
Matches are distributed among these distances:
42 8 0.05
43 74 0.45
44 76 0.46
45 8 0.05
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (42 bp):
CTACTGCTTAGGGGTTAAGATCTATAAACTCAGCCTGTTACC
Found at i:58417010 original size:87 final size:87
Alignment explanation
Indices: 58416770--58417001 Score: 401
Period size: 87 Copynumber: 2.7 Consensus size: 87
58416760 CAACCTGCTG
58416770 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
58416835 GCCCATCGCCTTCGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
*
58416857 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
58416922 GCCCATCGTCTTTGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
* * * *
58416944 CCCTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACCCTACTGCTTAGGG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
58417002 AGATAAGGCT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 137 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GCCCATCGCCTTCGATCTGTTT
Found at i:58424147 original size:9 final size:9
Alignment explanation
Indices: 58424135--58424195 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
58424125 GCTTTTTTTT
58424135 GTTAATTCG
1 GTTAATTCG
*
58424144 GTTAATTCA
1 GTTAATTCG
*
58424153 GTTAAATCG
1 GTTAATTCG
* * *
58424162 TTTAAATAG
1 GTTAATTCG
*
58424171 GTTAAATCG
1 GTTAATTCG
58424180 GTTAATTCG
1 GTTAATTCG
58424189 GTTAATT
1 GTTAATT
58424196 TTTATACTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (9 bp):
GTTAATTCG
Found at i:58424367 original size:12 final size:12
Alignment explanation
Indices: 58424350--58424374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58424340 TGCTATTTCG
58424350 GGTCGGTTAACC
1 GGTCGGTTAACC
58424362 GGTCGGTTAACC
1 GGTCGGTTAACC
58424374 G
1 G
58424375 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:58428251 original size:93 final size:93
Alignment explanation
Indices: 58428122--58428293 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
58428112 CGCCCATAAG
* * *
58428122 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58428187 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
58428215 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58428280 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
58428294 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:58428290 original size:46 final size:46
Alignment explanation
Indices: 58428115--58428290 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
58428105 TGTAACCCGC
* * * *
58428115 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
58428161 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
58428211 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
58428254 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
58428291 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:58428309 original size:46 final size:46
Alignment explanation
Indices: 58428164--58428302 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
58428154 TTCGCATCCA
58428164 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
58428212 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
58428257 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
58428303 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:58447759 original size:3 final size:3
Alignment explanation
Indices: 58447751--58447894 Score: 100
Period size: 3 Copynumber: 48.3 Consensus size: 3
58447741 ATAAAAGACC
**
58447751 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
58447798 CCT- ATG ATA CTA ATA ATA GTA ATA ATA AGA A-A ATTA ATA TTA GTA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * *
58447843 TTA ATA ATA ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA GTA ATA
1 ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58447888 ATA ATA A
1 ATA ATA A
58447895 ACGTGAAATT
Statistics
Matches: 110, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
2 9 0.08
3 96 0.87
4 3 0.03
5 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58448079 original size:12 final size:12
Alignment explanation
Indices: 58448062--58448087 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58448052 TATGTACATA
58448062 ATATATATATGT
1 ATATATATATGT
58448074 ATATATATATGT
1 ATATATATATGT
58448086 AT
1 AT
58448088 TAGAAAATGT
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:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:58448500 original size:79 final size:79
Alignment explanation
Indices: 58448396--58448555 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 79
58448386 AGAAAAGAGT
*
58448396 AAAAAAAAGGACGAAATGGGTTGAAAACGGAATTTAGAGGCGAA-TTTAGAATAAATAAAGGAGG
1 AAAAAAAAGGACGAAATGGGTTGAAAACGAAATTTAGAGGCGAATTTTAGAATAAATAAAGGAGG
58448460 AGGGGACTGATTTG
66 AGGGGACTGATTTG
58448474 AAAAAAAAGGACGAAATTGGGTTGAAAACGAAATTTAGAGGCGAATTTTAGAATAAATAAAGGAG
1 AAAAAAAAGGACGAAA-TGGGTTGAAAACGAAATTTAGAGGCGAATTTTAGAATAAATAAAGGAG
58448539 GAGGGGACTGATTTG
65 GAGGGGACTGATTTG
58448554 AA
1 AA
58448556 CACACGAGCA
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
78 16 0.20
79 27 0.34
80 36 0.46
ACGTcount: A:0.46, C:0.05, G:0.29, T:0.20
Consensus pattern (79 bp):
AAAAAAAAGGACGAAATGGGTTGAAAACGAAATTTAGAGGCGAATTTTAGAATAAATAAAGGAGG
AGGGGACTGATTTG
Found at i:58449067 original size:17 final size:17
Alignment explanation
Indices: 58449041--58449087 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
58449031 TTTTTCTCTC
*
58449041 ATTT-TTTAATTTATGT
1 ATTTATTTAATATATGT
58449057 ATTTATTTAATATATGT
1 ATTTATTTAATATATGT
58449074 ATGTTATTTTAATA
1 AT-TTA-TTTAATA
58449088 AGACAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 13 0.48
18 3 0.11
19 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTTATTTAATATATGT
Found at i:58450050 original size:43 final size:43
Alignment explanation
Indices: 58450003--58450286 Score: 183
Period size: 43 Copynumber: 6.5 Consensus size: 43
58449993 TCGATCTATT
*
58450003 CCCTACTACTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* * * * *
58450046 CCCTACTGCTTAGGGGTTTAAG----GCCCATGCATCGTTGATCAA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGC-CTG-T-TA
* ** * * *
58450088 CTCCACTACTGCTTAGGGAG-ATAAGATCT-ATAATCTTCAACCTGCTG
1 --CC-CTACTGCTTAGGG-GTTTAAGATCTGCCAA--TTCAGCCTGTTA
* **
58450135 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* *
58450178 CCCTACTGCTTAGGGGTTTAAGGCCCATC-GCC--TTC-GATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-G---ATCTGCCAATTCAG-CCTGTTA
* * **
58450222 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
58450265 CCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGTTTAAG
58450287 GCCCATCGTC
Statistics
Matches: 183, Mismatches: 34, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
39 8 0.04
40 4 0.02
41 2 0.01
42 1 0.01
43 82 0.45
44 53 0.29
45 21 0.11
46 2 0.01
47 3 0.02
48 1 0.01
49 2 0.01
50 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
Found at i:58450156 original size:89 final size:86
Alignment explanation
Indices: 58449953--58450156 Score: 218
Period size: 86 Copynumber: 2.3 Consensus size: 86
58449943 TAATTTCCAG
* * *
58449953 CCTGTTACCCTACTGCTT-GAGGGGTTAAGGCCCATCATCTTCGATCTATTCCCTACTACTTAGG
1 CCTGCTACCCTACTGCTTAG-GGGGTTAAGGCCCATCATCTTCGATCAACTCCCTACTACTTAGG
* * *
58450017 GGTTTAAGATCTGCCAATTCAG
65 GGTATAAGATCTGACAATTCAA
* * *
58450039 CCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATGCATCGTT-GATCAACTCCACTACTGCTTA
1 CCTGCTACCCTACTGCTTAGGGGGTTAAGGCCCAT-CATC-TTCGATCAACTCC-CTACTACTTA
*
58450103 GGGAG-ATAAGATCT-ATAATCTTCAA
63 GGG-GTATAAGATCTGACAA--TTCAA
*
58450128 CCTGCTGCCCTACTGCTTAGGGGGTTAAG
1 CCTGCTACCCTACTGCTTAGGGGGTTAAG
58450157 ATCTGTAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
86 32 0.32
87 15 0.15
88 22 0.22
89 31 0.31
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (86 bp):
CCTGCTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCAACTCCCTACTACTTAGGG
GTATAAGATCTGACAATTCAA
Found at i:58450373 original size:43 final size:42
Alignment explanation
Indices: 58450093--58450366 Score: 172
Period size: 44 Copynumber: 6.3 Consensus size: 42
58450083 ATCAACTCCA
* * * * *
58450093 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTGCTGCC
1 CTACTGCTTAGGG-GTTAAGATCTATAAAC-TCAGCCTGTTACC
* *
58450137 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTA-GGGGTTAAGATCTATAAACTCAGCCTGTTACC
** * *** * *
58450180 CTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGATCTATAAAC-TCAG-CCTGTTACC
* * *
58450224 CTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACC
1 CTACTGCTTA-GGGGTTAAGATCTATAAACTCAGCCTGTTACC
** * *** ** * *
58450267 CTACTGCTTAGGGGTTTAAGGCCCATCGTCTTTGATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGATCTATAAACTCAG-CCTGTTACC
* * *
58450311 CTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACC
1 CTACTGCTTAGGG-GTTAAGATCTATAAACTCAGCCTGTTACC
58450354 CTACTGCTTAGGG
1 CTACTGCTTAGGG
58450367 AGATAAGGCT
Statistics
Matches: 166, Mismatches: 55, Indels: 19
0.69 0.23 0.08
Matches are distributed among these distances:
42 8 0.05
43 74 0.45
44 76 0.46
45 8 0.05
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (42 bp):
CTACTGCTTAGGGGTTAAGATCTATAAACTCAGCCTGTTACC
Found at i:58450375 original size:87 final size:87
Alignment explanation
Indices: 58450135--58450366 Score: 401
Period size: 87 Copynumber: 2.7 Consensus size: 87
58450125 CAACCTGCTG
58450135 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
58450200 GCCCATCGCCTTCGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
*
58450222 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
58450287 GCCCATCGTCTTTGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
* * * *
58450309 CCCTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACCCTACTGCTTAGGG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
58450367 AGATAAGGCT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 137 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GCCCATCGCCTTCGATCTGTTT
Found at i:58457517 original size:9 final size:9
Alignment explanation
Indices: 58457505--58457565 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
58457495 CTTTTTTTTT
58457505 GTTAATTCG
1 GTTAATTCG
*
58457514 GTTAATTCA
1 GTTAATTCG
*
58457523 GTTAAATCG
1 GTTAATTCG
* * *
58457532 TTTAAATAG
1 GTTAATTCG
*
58457541 GTTAAATCG
1 GTTAATTCG
58457550 GTTAATTCG
1 GTTAATTCG
58457559 GTTAATT
1 GTTAATT
58457566 TTTATACTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (9 bp):
GTTAATTCG
Found at i:58457738 original size:12 final size:12
Alignment explanation
Indices: 58457721--58457745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58457711 TGCTATTTCG
58457721 GGTCGGTTAACC
1 GGTCGGTTAACC
58457733 GGTCGGTTAACC
1 GGTCGGTTAACC
58457745 G
1 G
58457746 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:58461631 original size:93 final size:93
Alignment explanation
Indices: 58461502--58461673 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
58461492 CGCCCATAAG
* * *
58461502 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58461567 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
58461595 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58461660 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
58461674 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:58461670 original size:46 final size:46
Alignment explanation
Indices: 58461495--58461670 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
58461485 TGTAACCCGC
* * * *
58461495 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
58461541 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
58461591 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
58461634 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
58461671 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:58461689 original size:46 final size:46
Alignment explanation
Indices: 58461544--58461682 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
58461534 TTCGCATCCA
58461544 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
58461592 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
58461637 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
58461683 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:58469618 original size:4 final size:4
Alignment explanation
Indices: 58469609--58469641 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
58469599 TGAAATAAGC
58469609 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
58469642 TAAAACATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:58469747 original size:3 final size:3
Alignment explanation
Indices: 58469739--58469870 Score: 67
Period size: 3 Copynumber: 44.3 Consensus size: 3
58469729 ATAAAAGACC
** * *
58469739 ATA ATA ATA ATA ATA ACG ATA ATA ATA AT- ATA ATA CCT- ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* * ** * * *
58469783 CTA ATA ATA GTA ATA ATA GGA A-A ATTA ATA TTA GTA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * *
58469828 ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA GTA ATA ATA ATA A
1 AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58469871 ACGTGAAATT
Statistics
Matches: 96, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 9 0.09
3 82 0.85
4 3 0.03
5 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58469747 original size:18 final size:20
Alignment explanation
Indices: 58469724--58469773 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
58469714 TGATAAAAGG
*
58469724 ATAATATAA-AA-GACCATA
1 ATAATATAATAACGACAATA
*
58469742 ATAATAATAATAACGATAATA
1 ATAAT-ATAATAACGACAATA
58469763 ATAATATAATA
1 ATAATATAATA
58469774 CCTATGATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 8 0.30
21 10 0.37
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAATATAATAACGACAATA
Found at i:58470340 original size:25 final size:22
Alignment explanation
Indices: 58470311--58470355 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 22
58470301 GTAACAGTAA
58470311 TAAAATATAATATTATGAATAATAT
1 TAAAAT-TAA-ATTA-GAATAATAT
58470336 TAAAATTAAATTAGAATAAT
1 TAAAATTAAATTAGAATAAT
58470356 GAGAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 3 0.15
25 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAAATTAAATTAGAATAATAT
Found at i:58479931 original size:21 final size:21
Alignment explanation
Indices: 58479881--58479933 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
58479871 CTAGGGTTTT
* *
58479881 CTTTG-TATTTTGGGCTTGTAT
1 CTTTGTTA-TTTGGGCTTATAA
* *
58479902 TTTTATTATTTGGGCTTATAA
1 CTTTGTTATTTGGGCTTATAA
58479923 CTTTGTTATTT
1 CTTTGTTATTT
58479934 ATTAAGGCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60
Consensus pattern (21 bp):
CTTTGTTATTTGGGCTTATAA
Found at i:58481886 original size:63 final size:63
Alignment explanation
Indices: 58481791--58481916 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 63
58481781 TCGGATTTGA
* * * *
58481791 GTGTGAGTGTCGCCTATAGATATATGGAGTTGATACATCTATGTTCTTTTTGCTTATTTGAGT
1 GTGTGAGTGTCGCCTATAGATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
* *
58481854 GTGTGCGTGTCGCCTATAGGTATAAAT-G-GTTGATACATTTATGTTCTCTTCGCGTATTTGAGT
1 GTGTGAGTGTCGCCTATA-G-ATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
58481917 CTAAGTGTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 48 0.87
64 2 0.04
65 5 0.09
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.43
Consensus pattern (63 bp):
GTGTGAGTGTCGCCTATAGATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
Found at i:58482459 original size:235 final size:232
Alignment explanation
Indices: 58481980--58482683 Score: 868
Period size: 235 Copynumber: 2.9 Consensus size: 232
58481970 ATGTGGAAGG
*
58481980 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGTATAAGGGTACTTAAAAAGAAAAAAAATG
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGAT-AGGGTACTTAAAAAG---AAAAATG
* * * *
58482045 AATAGTCCGAACAACATAGGAAAAATATTTATATCTTCTCATTTATTTGATTGTGAAAGTTAATG
62 AATAGT-CGAACAACATAGGAAAAA-ATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGG
* * * * *
58482110 AACAATAGGATATGATCTGTTAAGGCGTTGAAGTTACTGAATGTCTTTCTGGATATTTGATGTTT
125 AACAATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAAT-TCTTTCTGAATATTT-ATGTCT
** * *
58482175 GGTAATAATTTTTTTATTTATTTATGATCTACCGATAGGTGCCCT
188 GGTAATAAGCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
* *
58482220 TTGTTAGAGGATCTTATCTCCTTTGGAAATGTGTTGGATAGGGATACTTAAAAAGAAAAATGAAT
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGG-TACTTAAAAAGAAAAATGAAT
* *
58482285 AGTCGAAACAACAGAGGAAAAAAGTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACA
65 AGTCG-AACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACA
* *
58482350 ATGGGATATGATCTATTAAGGTGTTGAAGTTATTGAATTCTTTCTGAATATTTAATGGCTGGTAA
129 ATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAATTCTTTCTGAATATTT-ATGTCTGGTAA
* *
58482415 TAAGCTATTCATTTATTTATGATCTACCGGTAGGTGCTCT
193 TAAGCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
* *
58482455 TTGTTAGAGGATCATATCTCCTTCGAAAATGTGTTGGATAGGGTTACTTAAAAAGAAAAACGAAT
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGG-TACTTAAAAAGAAAAATGAAT
*
58482520 AGTCGGAAGAACATAGGAAAAAAATTTACATCTTTCCCATTTATTTGATTGTGAAAGTGAATGAA
65 AGTC-GAACAACATAGG-AAAAAATTTACATC-TTCCCATTTATTTGATTGTGAAAGT--A--AA
** * * * * * * * *
58482585 GTTGAACAATGAAATATAATATTTTGAGGTGTTCAAGTTACTGAACGTCTTTCTGCATATTTTTG
123 G--GAACAATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAA-TTCTTTCTGAATATTTATG
** *
58482650 TCTGGTAATAAGCTATTGGTTTATTTCTGATCTA
185 TCTGGTAATAAGCTATTCATTTATTTATGATCTA
58482684 TCAATTGGTG
Statistics
Matches: 406, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
235 130 0.32
236 88 0.22
237 53 0.13
239 5 0.01
240 47 0.12
241 3 0.01
243 66 0.16
244 14 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (232 bp):
TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGGTACTTAAAAAGAAAAATGAATA
GTCGAACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACAAT
GGGATATGATCTATTAAGGTGTTGAAGTTACTGAATTCTTTCTGAATATTTATGTCTGGTAATAA
GCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
Found at i:58484331 original size:96 final size:96
Alignment explanation
Indices: 58484128--58484379 Score: 305
Period size: 96 Copynumber: 2.6 Consensus size: 96
58484118 GTCGTTCCCG
* * *
58484128 TAGTTCTGTGAACAATACTGGGAATCCTCCTGCATCCCTACCAAACAGCGAACTGAACTCCTTTG
1 TAGTTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCTTTG
* ***
58484193 CCAGTTTTAACAGCCTGAGTGCAATCTCTTC
66 CCAGTTTTAACAGCCTCAACCCAATCTCTTC
* * *
58484224 TAATTCTGTGAACAATTCTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTAAACTCCTCTT
1 TAGTTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCT-TT
*
58484289 -CCAGTTTTAACAGCC-CAACCCAGT-TCAGTAT-
65 GCCAGTTTTAACAGCCTCAACCCAATCTC--T-TC
* * * *
58484320 TAGTTCCGTGAACAATAGTGGGAACTCTCCTGCATCCCTACCGAACAACCAACTGAACTC
1 TAGTTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTC
58484380 TACTGCTTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
94 2 0.01
95 4 0.03
96 125 0.93
97 3 0.02
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (96 bp):
TAGTTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCTTTG
CCAGTTTTAACAGCCTCAACCCAATCTCTTC
Found at i:58486111 original size:29 final size:29
Alignment explanation
Indices: 58486069--58486129 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
58486059 ATATTTCACG
*
58486069 AATTAAATAAATAACTCGATCCGTAAACA
1 AATTAAACAAATAACTCGATCCGTAAACA
58486098 AATTAAACAAATAACTCGATCCGTAAACA
1 AATTAAACAAATAACTCGATCCGTAAACA
58486127 AAT
1 AAT
58486130 CTACATTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (29 bp):
AATTAAACAAATAACTCGATCCGTAAACA
Found at i:58487952 original size:31 final size:31
Alignment explanation
Indices: 58487914--58487974 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
58487904 AACAGTTCAA
*
58487914 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTCGAATAATTTAG
*
58487945 TGACTTAAATGAAAACTTTCGAATAATTTA
1 TGACTTAAATAAAAACTTTCGAATAATTTA
58487975 ATGATCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAATTTAG
Found at i:58491382 original size:29 final size:29
Alignment explanation
Indices: 58491309--58491367 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
58491299 TTTGACTCAA
* *
58491309 TGTATAATGTCATACATAAATTTTAATTT
1 TGTATAATTTTATACATAAATTTTAATTT
*
58491338 TGTATGATTTTATACATAAAATTTTAATTT
1 TGTATAATTTTATACAT-AAATTTTAATTT
58491368 GATTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (29 bp):
TGTATAATTTTATACATAAATTTTAATTT
Found at i:58498679 original size:9 final size:9
Alignment explanation
Indices: 58498665--58498690 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
58498655 CAACTCTGTG
58498665 AAAATAAAA
1 AAAATAAAA
58498674 AAAATAAAA
1 AAAATAAAA
58498683 AAAATAAA
1 AAAATAAA
58498691 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:58503943 original size:15 final size:15
Alignment explanation
Indices: 58503923--58503954 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58503913 GTGGCTATGC
58503923 GTAGTTCTAAGTATT
1 GTAGTTCTAAGTATT
58503938 GTAGTTCTAAGTATT
1 GTAGTTCTAAGTATT
58503953 GT
1 GT
58503955 GTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (15 bp):
GTAGTTCTAAGTATT
Found at i:58504997 original size:14 final size:14
Alignment explanation
Indices: 58504978--58505004 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58504968 ATAATTTTAA
58504978 TAAATTAAAAATAT
1 TAAATTAAAAATAT
58504992 TAAATTAAAAATA
1 TAAATTAAAAATA
58505005 ATATAACAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:58506082 original size:16 final size:17
Alignment explanation
Indices: 58506061--58506096 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
58506051 ATTTATAAAA
58506061 ATAAAAAT-AACTTAAT
1 ATAAAAATAAACTTAAT
*
58506077 ATAAAAATAAATTTAAT
1 ATAAAAATAAACTTAAT
58506094 ATA
1 ATA
58506097 TTTTACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAATAAACTTAAT
Found at i:58507054 original size:20 final size:21
Alignment explanation
Indices: 58507015--58507054 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
58507005 AACATGCAAG
*
58507015 AAATTATTAATAATATTATTT
1 AAATTATTAATAATAATATTT
*
58507036 AAATTA-TAATAGTAATATT
1 AAATTATTAATAATAATATT
58507055 CAAACCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTATTAATAATAATATTT
Found at i:58507462 original size:23 final size:23
Alignment explanation
Indices: 58507436--58507501 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
58507426 ATTATTACAC
58507436 ATTAAGATATTTTTATGTAACAA
1 ATTAAGATATTTTTATGTAACAA
*
58507459 ATTAA-A-A-TTTCAT-T-ACAA
1 ATTAAGATATTTTTATGTAACAA
58507477 ATTAAGATATTTTTATG-ATACAA
1 ATTAAGATATTTTTATGTA-ACAA
58507500 AT
1 AT
58507502 ACATACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 6 0.17
21 6 0.17
22 1 0.03
23 11 0.31
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAGATATTTTTATGTAACAA
Found at i:58520431 original size:6 final size:6
Alignment explanation
Indices: 58520420--58520451 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
58520410 TAATTATTAG
*
58520420 TTTTAT TTTTAT TTTGAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
58520452 CTCTCTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:58526220 original size:38 final size:38
Alignment explanation
Indices: 58526164--58526255 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 38
58526154 TTATCAATTG
* * * * *
58526164 CATGTTCAGCATGCCTACTGTTACTGTTGAACTGATTA
1 CATGTTAAGCATGTCTACTGCTACTATTGAACTGAATA
*
58526202 CATGTTAAGCATGTCTACTGCTACTATTGAATTGAATA
1 CATGTTAAGCATGTCTACTGCTACTATTGAACTGAATA
58526240 CAT-TTAAGCATGTCTA
1 CATGTTAAGCATGTCTA
58526256 TTATTTTTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 13 0.27
38 35 0.73
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACTGCTACTATTGAACTGAATA
Found at i:58529907 original size:13 final size:13
Alignment explanation
Indices: 58529891--58529918 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58529881 CCGGTAAATT
58529891 TACTTTTAATTTA
1 TACTTTTAATTTA
58529904 TACTTTTAATTTA
1 TACTTTTAATTTA
58529917 TA
1 TA
58529919 GGCACAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (13 bp):
TACTTTTAATTTA
Found at i:58537782 original size:15 final size:15
Alignment explanation
Indices: 58537764--58537793 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58537754 TATTTTTTCC
58537764 TTTACCTTTTTATAT
1 TTTACCTTTTTATAT
58537779 TTTACCTTTTTATAT
1 TTTACCTTTTTATAT
58537794 ATTATATGAA
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:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTACCTTTTTATAT
Found at i:58539099 original size:14 final size:15
Alignment explanation
Indices: 58539058--58539103 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
58539048 AAAAAATATT
*
58539058 TTTTTACAATTTTGTA
1 TTTTTATAATTTT-TA
58539074 TTTTTAATAATTTTTA
1 TTTTT-ATAATTTTTA
58539090 -TTTTATAATTTTTA
1 TTTTTATAATTTTTA
58539104 AAAAAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
16 7 0.25
17 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTTTA
Found at i:58539571 original size:24 final size:24
Alignment explanation
Indices: 58539524--58539571 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
58539514 TTAGTATGAC
*
58539524 AAAATAAAATCTAAATAATTATAA
1 AAAATAAAATCTAAATAATCATAA
*
58539548 AAAATTAAAATC-AAATTATCATAA
1 AAAA-TAAAATCTAAATAATCATAA
58539572 CTATATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATAAAATCTAAATAATCATAA
Found at i:58540243 original size:44 final size:43
Alignment explanation
Indices: 58540184--58540285 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 43
58540174 CTTTGATAAC
*
58540184 ATTTCTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
1 ATTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
*
58540227 ATTTTTTTATAAATAATATAACTTTTTCATAATTTTATAAAGTT
1 A-TTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
58540271 ATTTTTTATAAATAA
1 ATTTTTTATAAATAA
58540286 GTTATGATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
43 15 0.27
44 41 0.73
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (43 bp):
ATTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
Found at i:58540438 original size:13 final size:13
Alignment explanation
Indices: 58540420--58540448 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
58540410 AATATATTAT
58540420 AATACTTATAATA
1 AATACTTATAATA
58540433 AATACTTATAATA
1 AATACTTATAATA
58540446 AAT
1 AAT
58540449 TTTTTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
AATACTTATAATA
Found at i:58540510 original size:24 final size:23
Alignment explanation
Indices: 58540483--58540557 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
58540473 TTTAGGATTC
58540483 AAATAATATTTTTATTACTTTATA
1 AAATAATATTTTTATTA-TTTATA
* * *
58540507 AAATACACA-ATTTATTTTTTATA
1 AAATA-ATATTTTTATTATTTATA
* *
58540530 ATATAAT-TTTTTAGTATTTATA
1 AAATAATATTTTTATTATTTATA
*
58540552 ATATAA
1 AAATAA
58540558 GAAGTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 18 0.44
23 10 0.24
24 11 0.27
25 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
AAATAATATTTTTATTATTTATA
Found at i:58542892 original size:14 final size:14
Alignment explanation
Indices: 58542873--58542901 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58542863 TGAAAGATAA
58542873 ATTTTATTAAAACT
1 ATTTTATTAAAACT
58542887 ATTTTATTAAAACT
1 ATTTTATTAAAACT
58542901 A
1 A
58542902 AGTAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTATTAAAACT
Found at i:58543619 original size:13 final size:15
Alignment explanation
Indices: 58543591--58543622 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
58543581 TATTAAATAT
58543591 TTTTTTATTATGTAA
1 TTTTTTATTATGTAA
58543606 TTTTTT-TTAT-TAA
1 TTTTTTATTATGTAA
58543619 TTTT
1 TTTT
58543623 GCATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTATTATGTAA
Found at i:58547947 original size:11 final size:12
Alignment explanation
Indices: 58547923--58547949 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58547913 TATGATCAGT
58547923 AATTTTTATAAA
1 AATTTTTATAAA
58547935 AATTTTTATAAA
1 AATTTTTATAAA
58547947 AAT
1 AAT
58547950 CTGCACCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTTTTATAAA
Found at i:58555381 original size:21 final size:21
Alignment explanation
Indices: 58555355--58555408 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
58555345 AGACATAAAT
58555355 TAAATTTTTTTTAAAAA-AGTA
1 TAAATTTTTTTTAAAAAGA-TA
** *
58555376 TAAATTAATATTAAAAAGATA
1 TAAATTTTTTTTAAAAAGATA
58555397 TAACATTTTTTT
1 TAA-ATTTTTTT
58555409 GGAGAAGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAATTTTTTTTAAAAAGATA
Found at i:58555582 original size:23 final size:24
Alignment explanation
Indices: 58555556--58555600 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
58555546 CACAAAAATA
58555556 CAAACTAATAT-TATTTTAATATC
1 CAAACTAATATATATTTTAATATC
* * *
58555579 CAAATTTATCTATATTTTAATA
1 CAAACTAATATATATTTTAATA
58555601 AAATATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (24 bp):
CAAACTAATATATATTTTAATATC
Found at i:58555613 original size:24 final size:23
Alignment explanation
Indices: 58555582--58555627 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
58555572 TAATATCCAA
58555582 ATTTATCTATAT-TTTAATAAAAT
1 ATTTATCTATATATTTAA-AAAAT
*
58555605 ATTTAATCTTTATATTTAAAAAA
1 ATTT-ATCTATATATTTAAAAAA
58555628 GTTAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATCTATATATTTAAAAAAT
Found at i:58561608 original size:19 final size:19
Alignment explanation
Indices: 58561579--58561643 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
58561569 TAATAAACTA
58561579 TTAAT-ATAAATTATTATT
1 TTAATAATAAATTATTATT
58561597 TTAATAATAAATTATTATT
1 TTAATAATAAATTATTATT
** *
58561616 AAAATAAT-AA-T-TTATA
1 TTAATAATAAATTATTATT
58561632 TTAATAATAAAT
1 TTAATAATAAAT
58561644 ATTTTGTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 10 0.26
17 3 0.08
18 7 0.18
19 19 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAATAAATTATTATT
Found at i:58561647 original size:19 final size:18
Alignment explanation
Indices: 58561577--58561643 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
58561567 TATAATAAAC
58561577 TATTAAT-ATAAATTATTA
1 TATTAATAATAAATT-TTA
* *
58561595 TTTTAATAATAAATTAT-
1 TATTAATAATAAATTTTA
*
58561612 TATTAA-AATAATAATTTA
1 TATTAATAATAA-ATTTTA
58561630 TATTAATAATAAAT
1 TATTAATAATAAAT
58561644 ATTTTGTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.13
17 8 0.21
18 14 0.36
19 12 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATAATAAATTTTA
Found at i:58566302 original size:22 final size:22
Alignment explanation
Indices: 58566272--58566327 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
58566262 AATTATTCTG
58566272 TAATATTTAAATTTAGAA-AAATT
1 TAAT-TTTAAATTTA-AATAAATT
*
58566295 TAATTTTAATTTTAAATAAATT
1 TAATTTTAAATTTAAATAAATT
* *
58566317 AAATTTAAAAT
1 TAATTTTAAAT
58566328 GATACGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAATTTTAAATTTAAATAAATT
Found at i:58570975 original size:22 final size:22
Alignment explanation
Indices: 58570950--58570991 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
58570940 ATAAGCTCAT
*
58570950 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
58570972 TTACATTCAATCAATAAATG
1 TTACATTCAATCAATAAATG
58570992 AGAAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:58571435 original size:11 final size:11
Alignment explanation
Indices: 58571419--58571443 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58571409 TGTTGAACTT
58571419 CTAAATTATCA
1 CTAAATTATCA
58571430 CTAAATTATCA
1 CTAAATTATCA
58571441 CTA
1 CTA
58571444 GAATGAATTT
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:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
CTAAATTATCA
Found at i:58574735 original size:24 final size:24
Alignment explanation
Indices: 58574703--58574758 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
58574693 TAATTAGATA
58574703 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
58574728 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
58574752 ATTATAT
1 AATATAT
58574759 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:58574753 original size:11 final size:11
Alignment explanation
Indices: 58574705--58574756 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
58574695 ATTAGATAAA
58574705 TATTATTTTAT
1 TATTATTTTAT
*
58574716 TAATATTTTAAT
1 TATTATTTT-AT
*
58574728 AATATATTTTAT
1 TAT-TATTTTAT
58574740 TATTATTTTAT
1 TATTATTTTAT
58574751 TATTAT
1 TATTAT
58574757 ATAAAGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 22 0.63
12 7 0.20
13 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:58576932 original size:46 final size:46
Alignment explanation
Indices: 58576880--58577107 Score: 277
Period size: 46 Copynumber: 5.0 Consensus size: 46
58576870 AGTGTGCTCT
*
58576880 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATATAAGACCATGGTTGAAAGATACCATGGCAAC
58576926 CTGATATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAAT-ATATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
58576972 GTGATATGAAATGA-ATAAGACCATGGTTGAAAAATACCATGGCAAC
1 CTGATATGAAAT-ATATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
58577018 GTGACATGAAA-ATAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATAT-ATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
58577064 ATGACA-GAAA-ATGAGTAAGACAATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATAT-A-TAAGACCATGGTTGAAAGATACCATGGCA
58577108 TTATGTCAAA
Statistics
Matches: 167, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.01
45 7 0.04
46 158 0.95
47 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATATATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:58577038 original size:92 final size:92
Alignment explanation
Indices: 58576881--58577095 Score: 310
Period size: 92 Copynumber: 2.3 Consensus size: 92
58576871 GTGTGCTCTC
* *
58576881 TGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAG
1 TGATATGAAATGA-GTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAG
*
58576945 ACCATGGTTGAAAGATACCATGGCAACG
65 ACCATGGTTGAAAGATACCATGGCAACA
* *
58576973 TGATATGAAATGAATAAGACCATGGTTGAAAAATACCATGGCAACGTGACATGAAAAT-AATAAG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATG-AAATGAATAAG
58577037 ACCATGGTTGAAAGATACCATGGCAACA
65 ACCATGGTTGAAAGATACCATGGCAACA
* * *
58577065 TGACA-GAAAATGAGTAAGACAATAGTTGAAA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAA
58577096 GACACTATGG
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
91 1 0.01
92 105 0.95
93 5 0.05
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (92 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAGA
CCATGGTTGAAAGATACCATGGCAACA
Found at i:58578513 original size:13 final size:13
Alignment explanation
Indices: 58578495--58578522 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58578485 TAAATGTATG
58578495 AATTATGTATGTT
1 AATTATGTATGTT
58578508 AATTATGTATGTT
1 AATTATGTATGTT
58578521 AA
1 AA
58578523 ATGATGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTATGTATGTT
Found at i:58580713 original size:53 final size:53
Alignment explanation
Indices: 58580517--58580720 Score: 135
Period size: 53 Copynumber: 3.8 Consensus size: 53
58580507 AGGGTTTAAG
* * * * * * * * *
58580517 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAG
1 GATACCATGTAAGACTATTCCAAGACATGACAATGGTAAG-TTCATAAGGCAAA
* * * * * * * *
58580571 GAAATCATGTAAGACTATGT-CAAAACATGGCATTGATAAACTACGATAAGGCAAA
1 GATACCATGTAAGACTAT-TCCAAGACATGACAATGGT-AAGTTC-ATAAGGCAAA
* * * *
58580626 GATCCCATGTAAGACTATTCCAAGGCATGACAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACTATTCCAAGACATGACAATGGTAAGTTCATAAGGCAAA
*
58580679 GATACCATGTAAGAGC-ATGT-CAAGACATGTCAATGGTAAGTT
1 GATACCATGTAAGA-CTAT-TCCAAGACATGACAATGGTAAGTT
58580721 TAAAAAGGAT
Statistics
Matches: 115, Mismatches: 29, Indels: 13
0.73 0.18 0.08
Matches are distributed among these distances:
53 43 0.37
54 35 0.30
55 37 0.32
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (53 bp):
GATACCATGTAAGACTATTCCAAGACATGACAATGGTAAGTTCATAAGGCAAA
Found at i:58587814 original size:87 final size:88
Alignment explanation
Indices: 58587665--58587867 Score: 237
Period size: 87 Copynumber: 2.3 Consensus size: 88
58587655 AATTTGATCT
* * * * *
58587665 CAACTTATCGGTACAGTGGTTTACCGCATTGTACCACTTGTACGTCAGCTTTGTTGCATACTATT
1 CAACTTATCGGTACAGTAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATT
* * *
58587730 ATCTGATCTGGTAGTTT-AACTG
66 ATCTAATCTAGCAGTTTAAACTG
* * * * * * *
58587752 TAACTTATAGGTACAGCAGTTTACCGCACTATACCGCATGTATGTCAGTTTTGCTGCGTACTATT
1 CAACTTATCGGTACAGTAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATT
58587817 ATCTAATCTAGCAGTTTAAACTG
66 ATCTAATCTAGCAGTTTAAACTG
* * *
58587840 CAACATATCTGTGCAGTAGTTTACCGCA
1 CAACTTATCGGTACAGTAGTTTACCGCA
58587868 ATGCACTGTA
Statistics
Matches: 94, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
87 67 0.71
88 27 0.29
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (88 bp):
CAACTTATCGGTACAGTAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATT
ATCTAATCTAGCAGTTTAAACTG
Found at i:58589569 original size:25 final size:25
Alignment explanation
Indices: 58589541--58589589 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
58589531 ATTTTATAAT
58589541 CAGAATAACATTTCATTATCAGAAC
1 CAGAATAACATTTCATTATCAGAAC
* * *
58589566 CAGAATGACATTTGATTATTAGAA
1 CAGAATAACATTTCATTATCAGAA
58589590 TTGAAGTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (25 bp):
CAGAATAACATTTCATTATCAGAAC
Found at i:58596558 original size:17 final size:17
Alignment explanation
Indices: 58596538--58596570 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58596528 GATATCAGGA
*
58596538 TAAAATTTTAATATTAT
1 TAAAATTTAAATATTAT
58596555 TAAAATTTAAATATTA
1 TAAAATTTAAATATTA
58596571 AAAACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTTAAATATTAT
Found at i:58599833 original size:3 final size:3
Alignment explanation
Indices: 58599825--58599851 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
58599815 TTATCATATT
58599825 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
58599852 AGAATTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58600276 original size:3 final size:3
Alignment explanation
Indices: 58600268--58600299 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58600258 CAGGTATTAA
58600268 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
58600300 TTTTATCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:58603201 original size:51 final size:51
Alignment explanation
Indices: 58603141--58603245 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
58603131 ACCAAGGTTA
*
58603141 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCGAT
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
58603192 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
58603243 GTT
1 GTT
58603246 AAGGGTATCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.40
Consensus pattern (51 bp):
GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
Found at i:58608520 original size:39 final size:39
Alignment explanation
Indices: 58608463--58608589 Score: 200
Period size: 39 Copynumber: 3.2 Consensus size: 39
58608453 GGACTGTAGC
* * * *
58608463 CCGGACATATTTCTAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
58608502 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
*
58608541 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTTAAGC
1 CCGGATATAATTCCAGCACATAGCCTGCGGACC-TTAAGT
58608581 CCGGATATA
1 CCGGATATA
58608590 CGTCAAATAT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 68 0.83
40 14 0.17
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:58617361 original size:3 final size:3
Alignment explanation
Indices: 58617345--58617382 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
58617335 CAGGTATTAA
* *
58617345 TTC TTC ATC ATC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
58617383 TTTATCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:58624113 original size:2 final size:2
Alignment explanation
Indices: 58624108--58624134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58624098 TATACATATA
58624108 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
58624135 TGGATTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:58625146 original size:13 final size:13
Alignment explanation
Indices: 58625128--58625159 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
58625118 ATTTAGTCCA
58625128 TATACTAAATCCC
1 TATACTAAATCCC
58625141 TATACTAAATCCC
1 TATACTAAATCCC
58625154 TATACT
1 TATACT
58625160 TTAAAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (13 bp):
TATACTAAATCCC
Found at i:58629181 original size:24 final size:24
Alignment explanation
Indices: 58629154--58629205 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
58629144 ACTAATCCGG
58629154 CTCCCACCGGCCCTACCACGACTC
1 CTCCCACCGGCCCTACCACGACTC
* * *
58629178 CTCCGACTGGCCCTACCATGACTC
1 CTCCCACCGGCCCTACCACGACTC
58629202 CTCC
1 CTCC
58629206 GACTGGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.15, C:0.54, G:0.13, T:0.17
Consensus pattern (24 bp):
CTCCCACCGGCCCTACCACGACTC
Found at i:58629206 original size:24 final size:24
Alignment explanation
Indices: 58629162--58629253 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
58629152 GGCTCCCACC
58629162 GGCCCTACCACGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
*
58629186 GGCCCTACCATGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
** * * *
58629210 GGGACAACCACAACTCCTCCAACT
1 GGCCCTACCACGACTCCTCCGACT
** * *
58629234 GGGACAACCACAACTCCTCC
1 GGCCCTACCACGACTCCTCC
58629254 AACAGGGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.24, C:0.46, G:0.15, T:0.15
Consensus pattern (24 bp):
GGCCCTACCACGACTCCTCCGACT
Found at i:58629254 original size:24 final size:24
Alignment explanation
Indices: 58629198--58629292 Score: 163
Period size: 24 Copynumber: 4.0 Consensus size: 24
58629188 CCCTACCATG
* *
58629198 ACTCCTCCGACTGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
*
58629222 ACTCCTCCAACTGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
58629246 ACTCCTCCAACAGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
58629270 ACTCCTCCAACAGGGACAACCAC
1 ACTCCTCCAACAGGGACAACCAC
58629293 GAGTCCAGGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.34, C:0.42, G:0.14, T:0.11
Consensus pattern (24 bp):
ACTCCTCCAACAGGGACAACCACA
Found at i:58632491 original size:22 final size:21
Alignment explanation
Indices: 58632449--58632491 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
58632439 CACAAAATAT
* *
58632449 ATGAAAAAATCTTTTTAAAAA
1 ATGAAAAAATCATGTTAAAAA
*
58632470 ATGAAAATAATCATGTTGAAAA
1 ATGAAAA-AATCATGTTAAAAA
58632492 CATTCCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (21 bp):
ATGAAAAAATCATGTTAAAAA
Found at i:58634770 original size:20 final size:20
Alignment explanation
Indices: 58634713--58634775 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
58634703 TTTATTCATA
*
58634713 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT-TT
*
58634733 TAATATAA--ATTTATTATTT
1 TAATA-AATTATTTAATATTT
58634752 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
58634772 TAAT
1 TAAT
58634776 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.19
20 25 0.69
21 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:58634795 original size:13 final size:15
Alignment explanation
Indices: 58634779--58634821 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
58634769 TTTTAATTTT
58634779 ATTTT-AATAATA-A
1 ATTTTAAATAATATA
58634792 ATTTTAAATAATAATA
1 ATTTTAAATAAT-ATA
58634808 ATTTTAAATAATAT
1 ATTTTAAATAATAT
58634822 TCTTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 3 0.11
16 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTTAAATAATATA
Found at i:58634812 original size:16 final size:17
Alignment explanation
Indices: 58634783--58634820 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
58634773 AATTTTATTT
58634783 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
58634800 TAATAAT-AATTTTAAA
1 TAATAATAAATTTTAAA
58634816 TAATA
1 TAATA
58634821 TTCTTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:58636869 original size:29 final size:31
Alignment explanation
Indices: 58636821--58636884 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
58636811 TTTATAGTTA
*
58636821 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
58636852 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
58636881 TTTA
1 TTTA
58636885 TTATTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:58636873 original size:8 final size:8
Alignment explanation
Indices: 58636862--58636894 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
58636852 TTTAATAAGA
58636862 TATTTTAT
1 TATTTTAT
58636870 TATTTTAT
1 TATTTTAT
58636878 TATTTTAT
1 TATTTTAT
58636886 TATTTTAT
1 TATTTTAT
58636894 T
1 T
58636895 TAGTCTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:58642957 original size:8 final size:8
Alignment explanation
Indices: 58642930--58642960 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
58642920 ACAAAATGCT
58642930 GGCTTTTC
1 GGCTTTTC
*
58642938 GGCATTTC
1 GGCTTTTC
58642946 GGCTTTTC
1 GGCTTTTC
58642954 GGCTTTT
1 GGCTTTT
58642961 GCCGATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GGCTTTTC
Found at i:58644834 original size:19 final size:18
Alignment explanation
Indices: 58644797--58644840 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
58644787 ATACATGCAG
58644797 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
58644814 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
58644833 TACTAATT
1 TAATAATT
58644841 AATATATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:58646668 original size:28 final size:27
Alignment explanation
Indices: 58646570--58646668 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
58646560 GTGTTAACTA
* *
58646570 GGCCTTAGCCCATATCAATATTAATCTG
1 GGCC-TAGCCCATATCAGTATCAATCTG
* *
58646598 GGCCATAGCCCCT-TACAGTATCAGAGTATATTG
1 GGCC-TAGCCCATAT-CAGTATC--A--AT-CTG
58646631 GGCCTAGCCCATATCAGTATCAATCTG
1 GGCCTAGCCCATATCAGTATCAATCTG
58646658 GGCCGTAGCCC
1 GGCC-TAGCCC
58646669 TATTACAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 24 0.43
30 2 0.04
32 16 0.29
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (27 bp):
GGCCTAGCCCATATCAGTATCAATCTG
Found at i:58646701 original size:60 final size:59
Alignment explanation
Indices: 58646570--58646704 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
58646560 GTGTTAACTA
* * *
58646570 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATATTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATACTG
* *
58646631 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATACTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATACTG
* *
58646691 GGTCTTGCCCATAT
1 GGCCTAGCCCATAT
58646705 TAACATAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.06
60 51 0.80
61 9 0.14
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATACTG
Found at i:58648328 original size:19 final size:18
Alignment explanation
Indices: 58648291--58648334 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
58648281 ATACATGCAG
58648291 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
58648308 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
58648327 TACTAATT
1 TAATAATT
58648335 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:58652547 original size:28 final size:28
Alignment explanation
Indices: 58652515--58652578 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
58652505 TTTTCAGTGT
58652515 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATTTATCAGTTTCATTTAGTAA
58652543 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATTTATCAGTTTCATTTAGTAA
58652571 CATTCAAT
1 CATTCAAT
58652579 CATTCAGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (28 bp):
CATTCAATTTATCAGTTTCATTTAGTAA
Found at i:58652585 original size:28 final size:28
Alignment explanation
Indices: 58652515--58652586 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
58652505 TTTTCAGTGT
*
58652515 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATATATCAGTTTCATTTAGTAA
*
58652543 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATATATCAGTTTCATTTAGTAA
58652571 CATTCAATCAT-TCAGT
1 CATTCAAT-ATATCAGT
58652587 AGCAATTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (28 bp):
CATTCAATATATCAGTTTCATTTAGTAA
Found at i:58652595 original size:28 final size:28
Alignment explanation
Indices: 58652515--58652596 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
58652505 TTTTCAGTGT
* ** *
58652515 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATATATCAGTAGCAATTAGTAA
* ** *
58652543 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATATATCAGTAGCAATTAGTAA
58652571 CATTCAATCAT-TCAGTAGCAATTAGT
1 CATTCAAT-ATATCAGTAGCAATTAGT
58652597 TGTTCAGCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 48 0.98
29 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (28 bp):
CATTCAATATATCAGTAGCAATTAGTAA
Found at i:58652662 original size:18 final size:18
Alignment explanation
Indices: 58652566--58652656 Score: 83
Period size: 18 Copynumber: 5.1 Consensus size: 18
58652556 AGTTTCATTT
* *
58652566 AGTAACATTCAATCATTC
1 AGTAACAATCAATTATTC
* * * *
58652584 AGTAGCAATTAGTTGTTC
1 AGTAACAATCAATTATTC
* * *
58652602 AGCAACAATCATTTACTC
1 AGTAACAATCAATTATTC
* *
58652620 AGTAGCAATCAGTTATTC
1 AGTAACAATCAATTATTC
58652638 AGTAACAATCAATTATTC
1 AGTAACAATCAATTATTC
58652656 A
1 A
58652657 AGAACAGCCA
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (18 bp):
AGTAACAATCAATTATTC
Found at i:58654055 original size:19 final size:18
Alignment explanation
Indices: 58654033--58654079 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
58654023 TATTCTGTTA
58654033 CTTTGTTTCTTTTCTATTT
1 CTTTGTTTCTTTT-TATTT
*
58654052 CTTTATTTCTTTTTATTT
1 CTTTGTTTCTTTTTATTT
58654070 CATTTGTTTC
1 C-TTTGTTTC
58654080 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTGTTTCTTTTTATTT
Found at i:58654123 original size:21 final size:21
Alignment explanation
Indices: 58654093--58654133 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58654083 TATTTTATAA
*
58654093 TAATATTATAATAATATAATT
1 TAATAATATAATAATATAATT
* *
58654114 TAATAATATACTTATATAAT
1 TAATAATATAATAATATAAT
58654134 AAATATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAATATAATAATATAATT
Found at i:58654132 original size:13 final size:13
Alignment explanation
Indices: 58654089--58654134 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
58654079 CATTTATTTT
58654089 ATAATAATATTATA
1 ATAAT-ATATTATA
58654103 ATAATATAATT-TA
1 ATAATAT-ATTATA
58654116 ATAATATACTTAT-
1 ATAATATA-TTATA
58654129 ATAATA
1 ATAATA
58654135 AATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 19 0.66
14 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATTATA
Done.