Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 35
Found at i:3455456 original size:40 final size:40
Alignment explanation
Indices: 3455412--3455533 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
3455402 AGATTGACAG
* *
3455412 ATAACCCAAAGGATTTACAAATTACCCGAAGGCTTTACAA
1 ATAACCCAGAGGTTTTACAAATTACCCGAAGGCTTTACAA
* * * * *
3455452 ATAACCCAGTGGTTTTACAAATAACTCGGAGGTTTTACAA
1 ATAACCCAGAGGTTTTACAAATTACCCGAAGGCTTTACAA
* * *
3455492 ATAACCCGGAGGTTTTACAAATTACCCAAATGCTTTACAA
1 ATAACCCAGAGGTTTTACAAATTACCCGAAGGCTTTACAA
3455532 AT
1 AT
3455534 CCTTGGGAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (40 bp):
ATAACCCAGAGGTTTTACAAATTACCCGAAGGCTTTACAA
Found at i:3471600 original size:27 final size:27
Alignment explanation
Indices: 3471562--3471631 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
3471552 ATATTCCATA
*
3471562 ATCATAATTAAACAAATAACATAATAT
1 ATCATAATTAAACAAATAACACAATAT
3471589 ATCATAATTAAACAAATAACACAATAT
1 ATCATAATTAAACAAATAACACAATAT
3471616 ATCATAATT-AACAAAT
1 ATCATAATTAAACAAAT
3471632 GCAACACTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 35 0.83
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.29
Consensus pattern (27 bp):
ATCATAATTAAACAAATAACACAATAT
Found at i:3479909 original size:18 final size:17
Alignment explanation
Indices: 3479880--3479913 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3479870 AGTCATCGAT
3479880 GAAAGTATGAAGTAATG
1 GAAAGTATGAAGTAATG
3479897 GAAAGTAATGAAGTAAT
1 GAAAGT-ATGAAGTAAT
3479914 AGAATCCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (17 bp):
GAAAGTATGAAGTAATG
Found at i:3484034 original size:37 final size:38
Alignment explanation
Indices: 3483940--3484044 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 38
3483930 CATTTTCATC
3483940 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
** *
3483978 -TGTTAGGATTCAAACTCCTAAAAATAGGAT-AGATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
* * * *
3484014 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3484045 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 5 0.09
37 52 0.91
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (38 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:3484441 original size:18 final size:17
Alignment explanation
Indices: 3484402--3484444 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3484392 ATTATATGGA
3484402 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
3484418 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
3484436 TATTATTAT
1 TATTATTAT
3484445 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:3484611 original size:22 final size:22
Alignment explanation
Indices: 3484569--3484611 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
3484559 AATTATTACT
* *
3484569 TTACTATTTTTTTTTTCTTATC
1 TTACTATTTATTTTATCTTATC
3484591 TTACTTATTTATTTTAT-TTAT
1 TTAC-TATTTATTTTATCTTAT
3484612 TTTATTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (22 bp):
TTACTATTTATTTTATCTTATC
Found at i:3484657 original size:27 final size:27
Alignment explanation
Indices: 3484586--3484658 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
3484576 TTTTTTTTTC
*
3484586 TTATCTTA-CTTATTTATTTTATTTATT
1 TTAT-TTACCTTATTTATCTTATTTATT
* * *
3484613 TTATTTTCCTCT-TGTATCTTATTTGTT
1 TTATTTACCT-TATTTATCTTATTTATT
*
3484640 TTCTTTACCTTATTTATCT
1 TTATTTACCTTATTTATCT
3484659 AACACATTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
26 3 0.08
27 32 0.89
28 1 0.03
ACGTcount: A:0.16, C:0.14, G:0.03, T:0.67
Consensus pattern (27 bp):
TTATTTACCTTATTTATCTTATTTATT
Found at i:3488797 original size:183 final size:183
Alignment explanation
Indices: 3488489--3489025 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
3488479 ATTAAATCCG
3488489 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
3488554 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
3488619 TTGTCAGGCCAAAGACCTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCCC
* * *
3488672 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGAAAACTCAAAAGCCCTGGATTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
3488737 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
3488802 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCCC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCCC
* *
3488855 TAAAGCTGACCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
3488920 ATAGATTACATTCAAA-TCATGACATTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
3488984 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
3489026 TAAACCTGAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 337 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCCC
Found at i:3490257 original size:72 final size:75
Alignment explanation
Indices: 3490166--3490341 Score: 209
Period size: 72 Copynumber: 2.4 Consensus size: 75
3490156 CTGCAAATGA
* * ** *
3490166 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGATTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
3490228 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
3490238 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
3490303 AAGAAGGCAT
66 AAGAAGGCAT
** *
3490313 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
3490342 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 49 0.55
73 11 0.12
74 1 0.01
75 4 0.04
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:3490295 original size:36 final size:36
Alignment explanation
Indices: 3490181--3490288 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
3490171 TCACTCAAAT
*
3490181 TTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGA
1 TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGA
** * * * **
3490217 TTGTTTTTCTCGAAAGAAGATTTATTTCACTCAAGA
1 TTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGA
*
3490253 TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA
1 TTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGA
3490289 CCGTTTTCAC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
35 1 0.02
36 54 0.98
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGA
Found at i:3490400 original size:39 final size:39
Alignment explanation
Indices: 3490357--3490509 Score: 119
Period size: 39 Copynumber: 3.6 Consensus size: 39
3490347 TTTTATCTTG
*
3490357 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
3490396 CTTGAGACAGTTTCTCTTGAAAACATTTCCCATGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG--AA-A-----CA-G-AA--AATTTTGTCTC-C
*
3490448 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
3490486 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
3490510 TAAACATTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
38 2 0.02
39 45 0.51
41 4 0.04
42 2 0.02
43 2 0.02
47 2 0.02
48 2 0.02
49 4 0.04
51 24 0.27
52 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:3490578 original size:105 final size:104
Alignment explanation
Indices: 3490412--3490730 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
3490402 ACAGTTTCTC
* * *
3490412 TTGAAAACATTTCCCATGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
3490477 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
3490516 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
3490581 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
3490621 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
3490683 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
3490722 TTGAAAACA
1 TTGAAAACA
3490731 ATTTAACGAA
Statistics
Matches: 203, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 52 0.26
105 102 0.50
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:3490677 original size:36 final size:36
Alignment explanation
Indices: 3490630--3490705 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3490620 ATTGAAAACA
* * *
3490630 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
3490666 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
3490702 TTTC
1 TTTC
3490706 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:3491105 original size:105 final size:105
Alignment explanation
Indices: 3490872--3491535 Score: 951
Period size: 105 Copynumber: 6.3 Consensus size: 105
3490862 CAAACATCCA
* * * * * * *
3490872 CAATTTCAACTCCACGACGGAGGATATCGTGACAATCGAGACAACACAAGTTCAACTTCACAACG
1 CAATTTCAACTTCACAACGAAGGATATTG-GAC--TCCAGACAACGCAAGTTCAACTTCACGACG
* *
3490937 AAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGC
63 AAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGC
*
3490981 CAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3491046 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
*
3491086 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
3491151 GGACCGCTGCTTGTCAAAAACAACTTCCCAATCTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
*
3491191 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAAGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3491256 GGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* *
3491296 CAATTTCAACTTCACAATGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
3491361 GGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGT
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* * * * *
3491396 CAATTTCAACTTCATAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * ** *
3491461 GGACGGCTGGTTGTCAACAAACAATTTCTCGGTTCCAGAGC
66 GGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGC
* *
3491502 CAATTTCAACTTCACGACGGAGGATATTGGACTC
1 CAATTTCAACTTCACAACGAAGGATATTGGACTC
3491536 GGAACAATAC
Statistics
Matches: 509, Mismatches: 40, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 306 0.60
106 82 0.16
108 3 0.01
109 24 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
Found at i:3492132 original size:37 final size:37
Alignment explanation
Indices: 3492078--3492182 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
3492068 CATTTTCATC
*
3492078 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* ** * *
3492115 TTGTTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * *
3492152 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
3492183 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
Found at i:3492579 original size:18 final size:17
Alignment explanation
Indices: 3492540--3492582 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3492530 ATTATATGGA
3492540 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
3492556 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
3492574 TATTATTAT
1 TATTATTAT
3492583 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:3495758 original size:5 final size:5
Alignment explanation
Indices: 3495750--3495781 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
3495740 CAAGTTAAAC
*
3495750 TTAAT TTAAT TTAAT TTAAT TTAAT TAAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
3495782 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:3495770 original size:15 final size:15
Alignment explanation
Indices: 3495744--3495781 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3495734 TTCATTCAAG
*
3495744 TTAAACTTAATTTAA
1 TTAAATTTAATTTAA
*
3495759 TTTAATTTAATTTAA
1 TTAAATTTAATTTAA
3495774 TTAAATTT
1 TTAAATTT
3495782 TAAAAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATTTAATTTAA
Found at i:3507017 original size:21 final size:21
Alignment explanation
Indices: 3506992--3507046 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3506982 AATAGTGAAT
*
3506992 AGATCGATCCTTTATTGAAAG
1 AGATCGATCCTTTATCGAAAG
* * * **
3507013 GGATCAATCTTTTATCGCGAG
1 AGATCGATCCTTTATCGAAAG
3507034 AGATCGATCCTTT
1 AGATCGATCCTTT
3507047 TTTTAAGAAC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (21 bp):
AGATCGATCCTTTATCGAAAG
Found at i:3509948 original size:23 final size:23
Alignment explanation
Indices: 3509922--3509973 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
3509912 ATAAGAAAAC
* * *
3509922 TCTCAATTATACAGGCAATTGAA
1 TCTCAAGTATAAAGGCAATTCAA
*
3509945 TCTCAAGTATAAATGCAATTCAA
1 TCTCAAGTATAAAGGCAATTCAA
3509968 TCTCAA
1 TCTCAA
3509974 AAGGAGTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (23 bp):
TCTCAAGTATAAAGGCAATTCAA
Found at i:3511558 original size:28 final size:28
Alignment explanation
Indices: 3511521--3511589 Score: 120
Period size: 28 Copynumber: 2.4 Consensus size: 28
3511511 CATTGGACAA
*
3511521 ACGGACTCCATACAACTCCCATTTGCTT
1 ACGGACTCCATACAACTCACATTTGCTT
3511549 ACGGACTCCATACAACTCACATTTGCTT
1 ACGGACTCCATACAACTCACATTTGCTT
3511577 ACGGACTCACATA
1 ACGGACTC-CATA
3511590 GATCCAAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (28 bp):
ACGGACTCCATACAACTCACATTTGCTT
Found at i:3512064 original size:2 final size:2
Alignment explanation
Indices: 3512057--3512083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3512047 AATTAACCAA
3512057 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3512084 ATACAATGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3521671 original size:46 final size:45
Alignment explanation
Indices: 3521613--3521703 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
3521603 TTGAAAAAGC
* *
3521613 CTGAGTGAATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGAATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
* * *
3521659 CTGAGTGCATCGATGCATGGTATGTGTATTGATGCATAAAATGCA
1 CTGAGTGAATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
3521704 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 20 0.50
46 20 0.50
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
CTGAGTGAATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
Found at i:3521751 original size:20 final size:20
Alignment explanation
Indices: 3521723--3521761 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3521713 CAAGAAATTA
3521723 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
3521743 ATTGGTGCATCGATGCATG
1 ATTGATGCATCGATGCATG
3521762 CCCTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:3522847 original size:21 final size:21
Alignment explanation
Indices: 3522823--3522866 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3522813 GAGACGGACG
*
3522823 AGGAGAAGCACGAGAGGAGCT
1 AGGAGAAGCACGAGAGGAACT
* * *
3522844 AGGAGCAGCCCGTGAGGAACT
1 AGGAGAAGCACGAGAGGAACT
3522865 AG
1 AG
3522867 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.41, T:0.07
Consensus pattern (21 bp):
AGGAGAAGCACGAGAGGAACT
Found at i:3526050 original size:19 final size:19
Alignment explanation
Indices: 3526027--3526092 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
3526017 TTGGACTCTT
* *
3526027 AGTGCAACGGTGCACTAAT
1 AGTGCATCGGTGCACTAAG
3526046 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
3526065 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
3526084 AGTGCATCG
1 AGTGCATCG
3526093 ATGTATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:3526178 original size:46 final size:45
Alignment explanation
Indices: 3526119--3526216 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
3526109 CGATGTTTTG
* * *
3526119 AAAAAGCA-TGAGTGTATCGATACATGATCTTGTGCATCGATGCAT
1 AAAATGCACTGAGTGCATCGATACATGAT-ATGTGCATCGATGCAT
* * *
3526164 CAAATGCACTGAGTGCATCGATGCATGGTATGTGCATCGATGCAT
1 AAAATGCACTGAGTGCATCGATACATGATATGTGCATCGATGCAT
3526209 AAAATGCA
1 AAAATGCA
3526217 TTCGATGTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 28 0.62
46 17 0.38
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (45 bp):
AAAATGCACTGAGTGCATCGATACATGATATGTGCATCGATGCAT
Found at i:3526264 original size:20 final size:20
Alignment explanation
Indices: 3526236--3526273 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3526226 CAATAAATTA
3526236 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
3526256 ATTGGTGCATCGATGCAT
1 ATTGATGCATCGATGCAT
3526274 CCTCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:3537257 original size:23 final size:23
Alignment explanation
Indices: 3537227--3537272 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3537217 AGAGATTGAT
3537227 TACTTCAAGAATGTTGATAAAAG
1 TACTTCAAGAATGTTGATAAAAG
3537250 TACTTCAAGAATGTTGATAAAAG
1 TACTTCAAGAATGTTGATAAAAG
3537273 AAAAGAACTT
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:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (23 bp):
TACTTCAAGAATGTTGATAAAAG
Found at i:3542552 original size:24 final size:26
Alignment explanation
Indices: 3542520--3542574 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
3542510 ATATTATGAT
* *
3542520 TAAAGAAGAA-AAGAAAAATAA-AAA
1 TAAAAAAGAATAAGAAAAAAAATAAA
*
3542544 TAAAAAAGAATATGAAAAAAAATAAA
1 TAAAAAAGAATAAGAAAAAAAATAAA
3542570 TAAAA
1 TAAAA
3542575 TAAAAGGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 9 0.35
26 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (26 bp):
TAAAAAAGAATAAGAAAAAAAATAAA
Found at i:3543217 original size:19 final size:18
Alignment explanation
Indices: 3543195--3543285 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 18
3543185 ATTGTTGTTG
3543195 AAAGAGAAGAAAAAATGAA
1 AAAGAGAAGAAAAAA-GAA
3543214 AAAG-GAA-ATGAAAAAGAA
1 AAAGAGAAGA--AAAAAGAA
* *
3543232 GAAAGAGAAAGAATAAGGAA
1 -AAAGAG-AAGAAAAAAGAA
* * *
3543252 AAGGAAAAGGAAAAAGAA
1 AAAGAGAAGAAAAAAGAA
*
3543270 AAAGAAAAAGAAAAAA
1 AAAG-AGAAGAAAAAA
3543286 AACCCAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.02
18 18 0.32
19 27 0.48
20 7 0.12
21 2 0.04
22 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAAGAGAAGAAAAAAGAA
Found at i:3543253 original size:38 final size:38
Alignment explanation
Indices: 3543194--3543284 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 38
3543184 GATTGTTGTT
* *
3543194 GAAAGAG-AAGAAAAAATGAAAAAGG-AAATGAAAAAGAA
1 GAAAGAGAAAG-AAAAA-GGAAAAGGAAAAGGAAAAAGAA
*
3543232 GAAAGAGAAAGAATAAGGAAAAGGAAAAGGAAAAAGAA
1 GAAAGAGAAAGAAAAAGGAAAAGGAAAAGGAAAAAGAA
*
3543270 -AAAGAAAAAGAAAAA
1 GAAAGAGAAAGAAAAA
3543285 AAACCCAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 20 0.43
38 23 0.50
39 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (38 bp):
GAAAGAGAAAGAAAAAGGAAAAGGAAAAGGAAAAAGAA
Found at i:3543260 original size:18 final size:18
Alignment explanation
Indices: 3543205--3543284 Score: 79
Period size: 19 Copynumber: 4.3 Consensus size: 18
3543195 AAAGAGAAGA
* *
3543205 AAAAATGAAAAAGGAAATG
1 AAAAA-GAAAAAGAAAAAG
*
3543224 AAAAAGAAGAAAGAGAAAG
1 AAAAAGAA-AAAGAAAAAG
* * *
3543243 AATAAGGAAAAGGAAAAGG
1 AA-AAAGAAAAAGAAAAAG
3543262 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAG
3543280 AAAAA
1 AAAAA
3543285 AAACCCAAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
18 21 0.43
19 23 0.47
20 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:3543284 original size:25 final size:25
Alignment explanation
Indices: 3543223--3543312 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 25
3543213 AAAAGGAAAT
* *
3543223 GAAAAAGAAGAAAGAGAAAGAATAAG
1 GAAAAAGAA-AAAGAAAAAGAAAAAG
* *
3543249 GAAAAGGAAAAGGAAAAAGAAAAA-
1 GAAAAAGAAAAAGAAAAAGAAAAAG
3543273 GAAAAAGAAAAA-AAACCCAAG-AAAAG
1 GAAAAAGAAAAAGAAA---AAGAAAAAG
3543299 G--AAAGAAAAAGAAA
1 GAAAAAGAAAAAGAAA
3543313 GAAAAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
23 3 0.06
24 19 0.36
25 19 0.36
26 12 0.23
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.01
Consensus pattern (25 bp):
GAAAAAGAAAAAGAAAAAGAAAAAG
Found at i:3543302 original size:6 final size:6
Alignment explanation
Indices: 3543205--3543284 Score: 79
Period size: 6 Copynumber: 12.8 Consensus size: 6
3543195 AAAGAGAAGA
* * * * *
3543205 AAAAATG AAAAAG GAAATG AAAAAG AAGAAAG AGAAAG AATAAGG AAAAGG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AA-AAAG AAAAAG
*
3543256 AAAAGG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
3543285 AAACCCAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
6 48 0.76
7 15 0.24
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:3543968 original size:43 final size:43
Alignment explanation
Indices: 3543897--3544006 Score: 134
Period size: 43 Copynumber: 2.5 Consensus size: 43
3543887 CTTATTTTGC
* * *
3543897 TCGATTCTATCACT-GAAGGAGGTAGATCAACA-TCGACATTTTGT
1 TCGATTCT-TCA-TAGAAGGAGTTGGATCAACAGT-GACATTCTGT
* *
3543941 TTGATTCTTCATAGAAGGAGTTGGATCAACAGTGTCATTCTGT
1 TCGATTCTTCATAGAAGGAGTTGGATCAACAGTGACATTCTGT
3543984 TCGATTCTTCATAGAAGGAGTTG
1 TCGATTCTTCATAGAAGGAGTTG
3544007 AATTATTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.02
43 49 0.84
44 8 0.14
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (43 bp):
TCGATTCTTCATAGAAGGAGTTGGATCAACAGTGACATTCTGT
Found at i:3550524 original size:26 final size:25
Alignment explanation
Indices: 3550494--3550555 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3550484 CCTACAATAA
3550494 ATTAATCAAACTTATTTTCTTTAATT
1 ATTAATCAAACTTATTTT-TTTAATT
* ** *
3550520 GTTAATTGAATTTATTTTTTTAATT
1 ATTAATCAAACTTATTTTTTTAATT
*
3550545 ATTAACCAAAC
1 ATTAATCAAAC
3550556 CAAATAAAGC
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (25 bp):
ATTAATCAAACTTATTTTTTTAATT
Found at i:3550692 original size:19 final size:17
Alignment explanation
Indices: 3550662--3550696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
3550652 TTTATTTGGG
3550662 TTAAAATTTAATTGGTTC
1 TTAAAATTTAA-TGGTTC
3550680 TTAAAATTTTAATGGTT
1 TTAAAA-TTTAATGGTT
3550697 ACAGTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (17 bp):
TTAAAATTTAATGGTTC
Found at i:3551111 original size:2 final size:2
Alignment explanation
Indices: 3551104--3551129 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3551094 GTGTTTGTTC
3551104 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
3551130 GAATATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3551948 original size:32 final size:32
Alignment explanation
Indices: 3551907--3551972 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3551897 CTCTATCTAA
3551907 TAAGATCATGTTTAATCAAAACTAATCAAATT
1 TAAGATCATGTTTAATCAAAACTAATCAAATT
3551939 TAAGATCATGTTTAATCAAAACTAATCAAATT
1 TAAGATCATGTTTAATCAAAACTAATCAAATT
3551971 TA
1 TA
3551973 GATATCGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (32 bp):
TAAGATCATGTTTAATCAAAACTAATCAAATT
Found at i:3553347 original size:2 final size:2
Alignment explanation
Indices: 3553340--3553377 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3553330 ATTTGATTAA
3553340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3553378 GGGAAGCCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3554009 original size:31 final size:32
Alignment explanation
Indices: 3553953--3554012 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3553943 TTTTGATCTC
*
3553953 GTTTCTTCATTTTCTATTATTAATTATATATT
1 GTTTCTTCATTTTCTATAATTAATTATATATT
3553985 GTTTC-TCTATTTT-TATAATTAATTATAT
1 GTTTCTTC-ATTTTCTATAATTAATTATAT
3554013 TTTATCCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (32 bp):
GTTTCTTCATTTTCTATAATTAATTATATATT
Found at i:3556735 original size:20 final size:20
Alignment explanation
Indices: 3556706--3556757 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3556696 GAGATAAATA
*
3556706 GTATCTATACCATCCT-TGTG
1 GTATCGATACCATCCTCT-TG
3556726 GTATCGATACTC-TCCTCTTG
1 GTATCGATAC-CATCCTCTTG
3556746 GTATCGATACCA
1 GTATCGATACCA
3556758 ATTGAATCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 25 0.89
21 2 0.07
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (20 bp):
GTATCGATACCATCCTCTTG
Found at i:3563099 original size:49 final size:45
Alignment explanation
Indices: 3562995--3563112 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 45
3562985 TTCATTTGGG
* * *
3562995 CATCCTTTCATACCCATTATGTATTGTTTACGTTTTCCTTTATGA
1 CATCCTTTCATACCAATTATGCATTGTTTACGTTTTCCTATATGA
* * *
3563040 CATCCATTCATACCAATTATGCATTGTTGTACCTTTTATATCTATATGA
1 CATCCTTTCATACCAATTATGCATTGTT-TA-CGTTT-T-CCTATATGA
*
3563089 CATCCTTTCATACCACTTATGCAT
1 CATCCTTTCATACCAATTATGCAT
3563113 CTTTTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 25 0.41
46 2 0.03
47 4 0.07
48 1 0.02
49 29 0.48
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.44
Consensus pattern (45 bp):
CATCCTTTCATACCAATTATGCATTGTTTACGTTTTCCTATATGA
Found at i:3563249 original size:81 final size:82
Alignment explanation
Indices: 3563141--3563310 Score: 211
Period size: 81 Copynumber: 2.1 Consensus size: 82
3563131 TTATAATTCC
* * * **
3563141 TTTAGTCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATGATTGACATTTTTCTACCA
1 TTTAGTCTTTTACCCAAAGGCATTTAACCATTCATCTAACTGGCATAATTGACACATTTCTACCA
* *
3563206 AATGTACAACTATGCCA
66 AATGCACAACTAGGCCA
* * *
3563223 TTTA-TCTTTTACTCAACGGTC-TTTAACCATTCATCTAACTGGCATAATTGACACATTTCTGCC
1 TTTAGTCTTTTACCCAAAGG-CATTTAACCATTCATCTAACTGGCATAATTGACACATTTCTACC
*
3563286 AAATGCACAGCTAGGCCA
65 AAATGCACAACTAGGCCA
3563304 -TTAGTCT
1 TTTAGTCT
3563311 GTAGTTTTGC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
80 3 0.04
81 67 0.89
82 5 0.07
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (82 bp):
TTTAGTCTTTTACCCAAAGGCATTTAACCATTCATCTAACTGGCATAATTGACACATTTCTACCA
AATGCACAACTAGGCCA
Found at i:3567070 original size:23 final size:23
Alignment explanation
Indices: 3566997--3567076 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
3566987 CACAGCAGAG
**
3566997 TGCATCGATGCACATTCAAGTAA
1 TGCATCGATGCACATTCAAGGGA
* * *
3567020 TGCATC-AGTTCACCTTC-ATGG-
1 TGCATCGA-TGCACATTCAAGGGA
*
3567041 TGAATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAAGGGA
*
3567064 TGCATCGGTGCAC
1 TGCATCGATGCAC
3567077 TATCTAGTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
21 12 0.29
22 6 0.14
23 24 0.57
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:3570932 original size:21 final size:20
Alignment explanation
Indices: 3570906--3570956 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3570896 GAGATTATTT
*
3570906 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTT-AAAAA
**
3570927 TCATTTTTGTATTTTAAAAA
1 TCATTTTTCAATTTTAAAAA
*
3570947 TAATTTTTCA
1 TCATTTTTCA
3570957 TAATCCGAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (20 bp):
TCATTTTTCAATTTTAAAAA
Found at i:3577444 original size:20 final size:21
Alignment explanation
Indices: 3577398--3577458 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3577388 TTCCCCTGTG
3577398 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
3577421 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
3577441 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
3577459 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:3603700 original size:21 final size:21
Alignment explanation
Indices: 3603631--3603714 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
3603621 TTAGTATAGA
3603631 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-TGAAG
* * *
3603653 GGGAACCGATTCCTCCTTTGAAG
1 GGGAATCGATACC-CC-CTGAAG
* *
3603676 GGGAATCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGAAG
3603697 GGGAATCGATACCCCCTG
1 GGGAATCGATACCCCCTG
3603715 GGGTTCTGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
21 21 0.40
22 13 0.25
23 19 0.36
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:3605306 original size:18 final size:17
Alignment explanation
Indices: 3605278--3605325 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 17
3605268 ATGAACCAAA
3605278 ACAGCACGAGGAACAAGC
1 ACAGCA-GAGGAACAAGC
3605296 ACGAGCAGAGGAACAAGC
1 AC-AGCAGAGGAACAAGC
3605314 ACAGCCAGAGGA
1 ACAG-CAGAGGA
3605326 TCAAATGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (17 bp):
ACAGCAGAGGAACAAGC
Found at i:3609740 original size:7 final size:7
Alignment explanation
Indices: 3609725--3609813 Score: 90
Period size: 7 Copynumber: 12.7 Consensus size: 7
3609715 GTTAGAGTAC
3609725 ACCCTAA
1 ACCCTAA
*
3609732 ACTCTAA
1 ACCCTAA
*
3609739 ACTCTAA
1 ACCCTAA
**
3609746 ACTATAA
1 ACCCTAA
3609753 ACCCTAA
1 ACCCTAA
3609760 ACCCTAA
1 ACCCTAA
3609767 A-CCTCAA
1 ACCCT-AA
3609774 ACCCTAA
1 ACCCTAA
3609781 ACCCTAA
1 ACCCTAA
*
3609788 ACCTTAA
1 ACCCTAA
*
3609795 GCCCTAA
1 ACCCTAA
* *
3609802 GCACTAA
1 ACCCTAA
3609809 ACCCT
1 ACCCT
3609814 TAATCCAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
6 3 0.04
7 64 0.91
8 3 0.04
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:3609932 original size:21 final size:21
Alignment explanation
Indices: 3609908--3609954 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3609898 CTATATACTA
* *
3609908 TAAACCCTAAACCTTAAGCCT
1 TAAACCCTAAACCTTAAACCC
*
3609929 TAAACCCTAAGCCTTAAACCC
1 TAAACCCTAAACCTTAAACCC
3609950 TAAAC
1 TAAAC
3609955 TCTTAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.34, G:0.04, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAACCTTAAACCC
Found at i:3609934 original size:14 final size:14
Alignment explanation
Indices: 3609915--3609952 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3609905 CTATAAACCC
*
3609915 TAAACCTTAAGCCT
1 TAAACCCTAAGCCT
3609929 TAAACCCTAAGCCT
1 TAAACCCTAAGCCT
3609943 TAAACCCTAA
1 TAAACCCTAA
3609953 ACTCTTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAGCCT
Found at i:3611374 original size:23 final size:23
Alignment explanation
Indices: 3611344--3611410 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
3611334 ATCAAGCTTG
*
3611344 AATCGAGCTTGAATCAAGTTCAA
1 AATCGAGCTTGAATCGAGTTCAA
* * *
3611367 AATTGAGCTTGAATTGAGCTCAA
1 AATCGAGCTTGAATCGAGTTCAA
3611390 AATCGAGCTTGAATCGAGTTC
1 AATCGAGCTTGAATCGAGTTC
3611411 GAATTTTGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGTTCAA
Found at i:3611414 original size:11 final size:11
Alignment explanation
Indices: 3611333--3611407 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
3611323 TCAAGCTCAA
*
3611333 AATCAAGCTTG
1 AATCGAGCTTG
3611344 AATCGAGCTTG
1 AATCGAGCTTG
* *
3611355 AATCAAG-TTCAA
1 AATCGAGCTT--G
*
3611367 AATTGAGCTTG
1 AATCGAGCTTG
* **
3611378 AATTGAGCTCAA
1 AATCGAGCT-TG
3611390 AATCGAGCTTG
1 AATCGAGCTTG
3611401 AATCGAG
1 AATCGAG
3611408 TTCGAATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 2 0.04
11 32 0.65
12 13 0.27
13 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (11 bp):
AATCGAGCTTG
Found at i:3613273 original size:24 final size:23
Alignment explanation
Indices: 3613246--3613290 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3613236 TTAAAAGCTT
3613246 GATGATGAAGAAAACAAAACAAAA
1 GATGATGAAG-AAACAAAACAAAA
*
3613270 GATGATGAAGAAATAAAACAA
1 GATGATGAAGAAACAAAACAA
3613291 TAAAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.64, C:0.07, G:0.18, T:0.11
Consensus pattern (23 bp):
GATGATGAAGAAACAAAACAAAA
Found at i:3613976 original size:18 final size:18
Alignment explanation
Indices: 3613953--3613991 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3613943 CCGGTTAACT
*
3613953 GGTTCAACCGATCGAATC
1 GGTTCAACCGATCGAACC
*
3613971 GGTTCAACCGGTCGAACC
1 GGTTCAACCGATCGAACC
3613989 GGT
1 GGT
3613992 CCTACCGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.21
Consensus pattern (18 bp):
GGTTCAACCGATCGAACC
Found at i:3614757 original size:10 final size:10
Alignment explanation
Indices: 3614744--3614783 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3614734 AAAACAAAAA
3614744 TCCCGGTTTT
1 TCCCGGTTTT
3614754 TCCCGGTTTT
1 TCCCGGTTTT
* *
3614764 TTCTGGTTTT
1 TCCCGGTTTT
*
3614774 TTCCGGTTTT
1 TCCCGGTTTT
3614784 CAGTCGGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.20, T:0.57
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:3620265 original size:21 final size:21
Alignment explanation
Indices: 3620239--3620429 Score: 155
Period size: 21 Copynumber: 9.2 Consensus size: 21
3620229 AATTCGTAAC
*
3620239 GCGAACTTCGACTACCGCAAT
1 GCGAACTTCGACTATCGCAAT
3620260 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
* *
3620281 GTGAA-TAT-GTA-AATCGCAAT
1 GCGAACT-TCG-ACTATCGCAAT
*
3620301 GCGATA-GTCGACTATCGCAAT
1 GCGA-ACTTCGACTATCGCAAT
* * *
3620322 ACGAACTTGGACTATCGCAAC
1 GCGAACTTCGACTATCGCAAT
*
3620343 GCGAACTTCAACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
* *
3620364 GTGAA-TAT-GTA-AATCGCAAT
1 GCGAACT-TCG-ACTATCGCAAT
*
3620384 GCGATAGTT-GACTATCGCAAT
1 GCGA-ACTTCGACTATCGCAAT
* *
3620405 GCGAACTTGGACTATCGCATT
1 GCGAACTTCGACTATCGCAAT
3620426 GCGA
1 GCGA
3620430 TTTACATATT
Statistics
Matches: 137, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
20 32 0.23
21 104 0.76
22 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:3620312 original size:41 final size:41
Alignment explanation
Indices: 3620254--3620405 Score: 166
Period size: 41 Copynumber: 3.7 Consensus size: 41
3620244 CTTCGACTAC
*
3620254 CGCAATGCGAACTTCGACTATCGCAATGTGAATATGTAAAT
1 CGCAATGCGAACGTCGACTATCGCAATGTGAATATGTAAAT
** * *
3620295 CGCAATGCGATA-GTCGACTATCGCAATACGAACT-TGGACTAT
1 CGCAATGCGA-ACGTCGACTATCGCAATGTGAA-TATGTA-AAT
* * *
3620337 CGCAACGCGAACTTCAACTATCGCAATGTGAATATGTAAAT
1 CGCAATGCGAACGTCGACTATCGCAATGTGAATATGTAAAT
*
3620378 CGCAATGCGATA-GTTGACTATCGCAATG
1 CGCAATGCGA-ACGTCGACTATCGCAATG
3620406 CGAACTTGGA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 56 0.63
42 33 0.37
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (41 bp):
CGCAATGCGAACGTCGACTATCGCAATGTGAATATGTAAAT
Found at i:3620341 original size:83 final size:83
Alignment explanation
Indices: 3620240--3620429 Score: 317
Period size: 83 Copynumber: 2.3 Consensus size: 83
3620230 ATTCGTAACG
* * *
3620240 CGAACTTCGACTACCGCAATGCGAACTTCGACTATCGCAATGTGAATATGTAAATCGCAATGCGA
1 CGAACTTGGACTATCGCAATGCGAACTTCAACTATCGCAATGTGAATATGTAAATCGCAATGCGA
3620305 TAGTCGACTATCGCAATA
66 TAGTCGACTATCGCAATA
*
3620323 CGAACTTGGACTATCGCAACGCGAACTTCAACTATCGCAATGTGAATATGTAAATCGCAATGCGA
1 CGAACTTGGACTATCGCAATGCGAACTTCAACTATCGCAATGTGAATATGTAAATCGCAATGCGA
* *
3620388 TAGTTGACTATCGCAATG
66 TAGTCGACTATCGCAATA
*
3620406 CGAACTTGGACTATCGCATTGCGA
1 CGAACTTGGACTATCGCAATGCGA
3620430 TTTACATATT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (83 bp):
CGAACTTGGACTATCGCAATGCGAACTTCAACTATCGCAATGTGAATATGTAAATCGCAATGCGA
TAGTCGACTATCGCAATA
Found at i:3620443 original size:41 final size:41
Alignment explanation
Indices: 3620414--3620495 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
3620404 TGCGAACTTG
*
3620414 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTC
* *
3620455 GACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTC
3620496 CAAGTTCGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTC
Found at i:3620444 original size:20 final size:20
Alignment explanation
Indices: 3620419--3620488 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
3620409 ACTTGGACTA
3620419 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
3620439 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
3620460 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
3620480 TCGCATTGC
1 TCGCATTGC
3620489 AATAGTCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.05
20 24 0.56
21 15 0.35
22 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:3620465 original size:21 final size:21
Alignment explanation
Indices: 3620376--3620581 Score: 119
Period size: 21 Copynumber: 9.9 Consensus size: 21
3620366 GAATATGTAA
* *
3620376 ATCGCAATGCGATAGTTGACT
1 ATCGCATTGCGATAGTCGACT
* * *
3620397 ATCGCAATGCGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
*
3620418 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
3620437 ATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACT
*
3620459 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* * *
3620478 ATTCGCATTGCAATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
* *
3620501 -TCGCATTGTGATAGTCGAAGT
1 ATCGCATTGCGATAGTCG-ACT
*
3620522 -TCGCATTGCGATAGTCGAAGT
1 ATCGCATTGCGATAGTCG-ACT
* *
3620543 -TCGTATTGCGATAGTCGAAGT
1 ATCGCATTGCGATAGTCG-ACT
3620564 -TCGCATTGCGATAGTCGA
1 ATCGCATTGCGATAGTCGA
3620582 AGTTCGCGTT
Statistics
Matches: 156, Mismatches: 15, Indels: 29
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.03
19 6 0.04
20 26 0.17
21 112 0.72
22 4 0.03
23 3 0.02
24 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:3620582 original size:21 final size:21
Alignment explanation
Indices: 3620438--3620595 Score: 198
Period size: 21 Copynumber: 7.6 Consensus size: 21
3620428 GATTTACATA
*
3620438 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
3620458 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
* *
3620479 TTCGCATTGCAATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
3620500 TTCGCATTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
3620521 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
3620542 TTCGTATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
3620563 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
3620584 TTCGCGTTGCGA
1 TTCGCATTGCGA
3620596 ATCTGGAAAC
Statistics
Matches: 121, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.12
21 105 0.87
22 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:3620956 original size:38 final size:38
Alignment explanation
Indices: 3620905--3620981 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
3620895 TATTTATTAA
*
3620905 TATGTACATTAAAAAAATCGTTTAACAGACAGTTCTTT
1 TATGTACATTAAAAAAATCGTTTAACAGACAATTCTTT
3620943 TATGTACATTAAAAAAATCGTTTAACAGACAATTCTTT
1 TATGTACATTAAAAAAATCGTTTAACAGACAATTCTTT
3620981 T
1 T
3620982 CTTAATTAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (38 bp):
TATGTACATTAAAAAAATCGTTTAACAGACAATTCTTT
Found at i:3630231 original size:21 final size:21
Alignment explanation
Indices: 3630205--3630264 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
3630195 ATTTACCATG
3630205 ATTGCGGCCGTCGCGGGTGCT
1 ATTGCGGCCGTCGCGGGTGCT
* **
3630226 ATTGCGGCCGTCACGGACGCT
1 ATTGCGGCCGTCGCGGGTGCT
3630247 ATTGCGGCCGTCGCGGGT
1 ATTGCGGCCGTCGCGGGT
3630265 AACTCAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.08, C:0.30, G:0.40, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGTGCT
Found at i:3630620 original size:31 final size:31
Alignment explanation
Indices: 3630507--3630626 Score: 109
Period size: 32 Copynumber: 3.8 Consensus size: 31
3630497 GTTTGGGTCA
* * *
3630507 GGTCAA-ATCGGTTCGGTTAGTTTTCGGGTCG
1 GGTCAATATCGGATCGGTT-GGTTTCGAGTCG
* * * *
3630538 TGTCAAAATAGGATCGGTTGGTGTTCGGGTCG
1 GGTCAATATCGGATCGGTTGGT-TTCGAGTCG
* * *
3630570 GGTTAATCTCGGATTGGTTGGTTTCGAGT-G
1 GGTCAATATCGGATCGGTTGGTTTCGAGTCG
3630600 GGATCAATATCGGATCGGTTGGTTTCG
1 GG-TCAATATCGGATCGGTTGGTTTCG
3630627 GTTGGGTAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
30 3 0.04
31 34 0.47
32 35 0.49
ACGTcount: A:0.16, C:0.13, G:0.36, T:0.35
Consensus pattern (31 bp):
GGTCAATATCGGATCGGTTGGTTTCGAGTCG
Found at i:3630694 original size:46 final size:46
Alignment explanation
Indices: 3630616--3630755 Score: 144
Period size: 46 Copynumber: 3.1 Consensus size: 46
3630606 ATATCGGATC
* * * * *
3630616 GGTTGGTTTCGGTT-GGGTAAAGCTTTAGATTTTTGGGTCAATTCA
1 GGTTGGTTTTGGTTCGGATAAACCTTTAAATTTTTGGGTCAATTCG
* *
3630661 GGTTGGTTTTGGTTCGGATCAACCTTTAAATTTTCGGGTCAATTCG
1 GGTTGGTTTTGGTTCGGATAAACCTTTAAATTTTTGGGTCAATTCG
* * * *
3630707 GGTTGGTTTTAGTTC--A-GAACCTTTAGATTTTTTGGGTTAATTCG
1 GGTTGGTTTTGGTTCGGATAAACCTTTA-AATTTTTGGGTCAATTCG
3630751 GGTTG
1 GGTTG
3630756 TTTCTGTTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
43 8 0.10
44 21 0.26
45 13 0.16
46 39 0.48
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.44
Consensus pattern (46 bp):
GGTTGGTTTTGGTTCGGATAAACCTTTAAATTTTTGGGTCAATTCG
Found at i:3631082 original size:4 final size:4
Alignment explanation
Indices: 3631073--3631109 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3631063 TTATAATAAT
3631073 AATA AATA AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA A
3631110 TTTGTTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3631243 original size:16 final size:16
Alignment explanation
Indices: 3631222--3631330 Score: 60
Period size: 16 Copynumber: 6.8 Consensus size: 16
3631212 CCAATTCAGA
*
3631222 TTGATTTCGGTTTGGG
1 TTGATTTCGGTTCGGG
*
3631238 TTGATTTTTGGTTCGGG
1 TTGA-TTTCGGTTCGGG
* * **
3631255 TTGCTTTCGATTC-AA
1 TTGATTTCGGTTCGGG
*
3631270 TT-ACTTTCGGCTCGGG
1 TTGA-TTTCGGTTCGGG
** * *
3631286 TTCTTTTCGCTTCGAG
1 TTGATTTCGGTTCGGG
* *
3631302 TTATATTTCGGTTTGGG
1 TT-GATTTCGGTTCGGG
3631319 TTGATTTCGGTT
1 TTGATTTCGGTT
3631331 AAACTATAAT
Statistics
Matches: 66, Mismatches: 22, Indels: 10
0.67 0.22 0.10
Matches are distributed among these distances:
15 9 0.14
16 33 0.50
17 24 0.36
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.50
Consensus pattern (16 bp):
TTGATTTCGGTTCGGG
Found at i:3631842 original size:15 final size:15
Alignment explanation
Indices: 3631819--3631857 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3631809 TCAAAAACTC
3631819 CTCCCAAATTCTAAA
1 CTCCCAAATTCTAAA
*
3631834 CTCCTAAATTCTAAA
1 CTCCCAAATTCTAAA
3631849 CTCCCAAAT
1 CTCCCAAAT
3631858 AAAAATGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (15 bp):
CTCCCAAATTCTAAA
Found at i:3632796 original size:90 final size:89
Alignment explanation
Indices: 3632644--3632806 Score: 299
Period size: 90 Copynumber: 1.8 Consensus size: 89
3632634 ACACACCCTT
3632644 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
3632709 ATTAATTGGAGTTTAATAATCCTC
66 ATTAATTGGAGTTTAATAATCCTC
* *
3632733 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
3632798 AATTAATTG
65 AATTAATTG
3632807 ATATTAAATA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 30 0.42
90 41 0.58
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGGAGTTTAATAATCCTC
Found at i:3639592 original size:90 final size:89
Alignment explanation
Indices: 3639440--3639612 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
3639430 ACACACCCTT
*
3639440 TTATAGCCAAGTTACCCTAATAATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTGACCCTAATAATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
3639505 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* * *
3639529 TTATATCCAAGTGACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTGACCCTAATAATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
3639594 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
3639613 TTCGGTATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 28 0.36
90 49 0.64
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (89 bp):
TTATAGCCAAGTGACCCTAATAATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:3643311 original size:18 final size:18
Alignment explanation
Indices: 3643268--3643311 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
3643258 TAATTGAATT
*
3643268 TTAAATTCAATTATATTA
1 TTAAATTTAATTATATTA
3643286 TTAAATTTAATTATATTA
1 TTAAATTTAATTATATTA
3643304 TTAAATTT
1 TTAAATTT
3643312 CCATGTGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTTAATTATATTA
Found at i:3645674 original size:18 final size:18
Alignment explanation
Indices: 3645610--3645676 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
3645600 AATTATAAAT
*
3645610 TTTTGCAATTATCAGAT-
1 TTTTACAATTATCAGATG
* *
3645627 TATTTTCGATTATCAGATAG
1 T-TTTACAATTATCAGAT-G
*
3645647 --TTACAGTTATCAGATG
1 TTTTACAATTATCAGATG
3645663 TTTTACAATTATCA
1 TTTTACAATTATCA
3645677 TACGTAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.33
18 25 0.64
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTACAATTATCAGATG
Found at i:3652464 original size:18 final size:17
Alignment explanation
Indices: 3652441--3652496 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
3652431 AAGTTTACAA
3652441 TTATCAGATGATTTTCAG
1 TTATCAGAT-ATTTTCAG
* *
3652459 TTATCATATATTTACAG
1 TTATCAGATATTTTCAG
*
3652476 TTATCAGATTATTTTAAG
1 TTATCAGA-TATTTTCAG
3652494 TTA
1 TTA
3652497 ACATATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (17 bp):
TTATCAGATATTTTCAG
Found at i:3652476 original size:17 final size:17
Alignment explanation
Indices: 3652434--3652489 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
3652424 ATTCTAAAAG
*
3652434 TTTACAATTATCAGATGA
1 TTTACAGTTATCAGAT-A
* *
3652452 TTTTCAGTTATCATATA
1 TTTACAGTTATCAGATA
3652469 TTTACAGTTATCAGATTA
1 TTTACAGTTATCAGA-TA
3652487 TTT
1 TTT
3652490 TAAGTTAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:3652514 original size:35 final size:35
Alignment explanation
Indices: 3652434--3652531 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
3652424 ATTCTAAAAG
* * *
3652434 TTTACAATTATCAGATGATTTTCAGTTATCATATA
1 TTTACAGTTATCAGATGATTTTAAGTTAACATATA
* *
3652469 TTTACAGTTATCAGATTATTTTAAGTTAACATATG
1 TTTACAGTTATCAGATGATTTTAAGTTAACATATA
** *
3652504 TTTATTGTTATCAAATG-TTTTACAGTTA
1 TTTACAGTTATCAGATGATTTTA-AGTTA
3652532 CCAGACGTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 5 0.09
35 48 0.91
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (35 bp):
TTTACAGTTATCAGATGATTTTAAGTTAACATATA
Found at i:3652531 original size:18 final size:18
Alignment explanation
Indices: 3652434--3652531 Score: 60
Period size: 18 Copynumber: 5.6 Consensus size: 18
3652424 ATTCTAAAAG
* *
3652434 TTTACAATTATCAGATGAT
1 TTTACAGTTATCAAATG-T
* *
3652453 TTT-CAGTTATCATAT-A
1 TTTACAGTTATCAAATGT
* *
3652469 TTTACAGTTATCAGATTAT
1 TTTACAGTTATCA-AATGT
* *
3652488 TTTA-AGTTAACATATG-
1 TTTACAGTTATCAAATGT
**
3652504 TTTATTGTTATCAAATGT
1 TTTACAGTTATCAAATGT
3652522 TTTACAGTTA
1 TTTACAGTTA
3652532 CCAGACGTAG
Statistics
Matches: 59, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
16 7 0.12
17 19 0.32
18 26 0.44
19 7 0.12
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (18 bp):
TTTACAGTTATCAAATGT
Found at i:3652645 original size:7 final size:7
Alignment explanation
Indices: 3652633--3652662 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3652623 AAGTGAGTGT
3652633 TTATCAG
1 TTATCAG
*
3652640 TTATCAA
1 TTATCAG
3652647 TTATCAG
1 TTATCAG
3652654 TTATCAG
1 TTATCAG
3652661 TT
1 TT
3652663 TAGGTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (7 bp):
TTATCAG
Found at i:3672237 original size:24 final size:25
Alignment explanation
Indices: 3672210--3672261 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3672200 TAGAACCATT
*
3672210 AAAGCT-AAATCCACCCAAAAGAAA
1 AAAGCTCAAATCAACCCAAAAGAAA
* *
3672234 AAAGTTCATATCAACCCAAAAGAAA
1 AAAGCTCAAATCAACCCAAAAGAAA
3672259 AAA
1 AAA
3672262 AATTACTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.12
Consensus pattern (25 bp):
AAAGCTCAAATCAACCCAAAAGAAA
Found at i:3672822 original size:22 final size:23
Alignment explanation
Indices: 3672797--3672840 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3672787 CTTTAACTCA
*
3672797 TGGA-ACTTTGAAACGACTAAAC
1 TGGACACTTTGAAACCACTAAAC
* *
3672819 TGGACGCTTTGATACCACTAAA
1 TGGACACTTTGAAACCACTAAA
3672841 TATAACACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (23 bp):
TGGACACTTTGAAACCACTAAAC
Found at i:3674072 original size:65 final size:65
Alignment explanation
Indices: 3673968--3674110 Score: 232
Period size: 65 Copynumber: 2.2 Consensus size: 65
3673958 TATTCCCCCA
**
3673968 TGAGTATCGATACCAAATTTGGATTTAATGTTTTCAAAAATATGTCAATATCAATACTTACCCTC
1 TGAGTATCGATACCAAATTTGGATTTAATGTTTTCAAAAATACATCAATATCAATACTTACCCTC
* * * *
3674033 TGAGTATCGATACCAACTTTGGCTTTAATGTTTTCAAAAATACATCGATATCAATACTTACTCTC
1 TGAGTATCGATACCAAATTTGGATTTAATGTTTTCAAAAATACATCAATATCAATACTTACCCTC
3674098 TGAGTATCGATAC
1 TGAGTATCGATAC
3674111 TGGACCCCGA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (65 bp):
TGAGTATCGATACCAAATTTGGATTTAATGTTTTCAAAAATACATCAATATCAATACTTACCCTC
Found at i:3683398 original size:46 final size:46
Alignment explanation
Indices: 3683273--3683547 Score: 347
Period size: 46 Copynumber: 6.0 Consensus size: 46
3683263 ATTACAGTAT
* * * * *
3683273 TGGCATCCTTTCATGCCTTAATGAATCCTTTTATG-ATTTTAGTTA
1 TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
* *
3683318 TGGCAAT-CGTTCATGTCTTAATGCATCATTTTTATGCATTTTAATTA
1 TGGC-ATCCGTTCATGCCTTAATGCATCA-TTTCATGCATTTTAATTA
* * * * *
3683365 TGGCATCCATCCATGCCTTAATGCATCATTTTATACATTTTACTTA
1 TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
*
3683411 TGGAATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
1 TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
* * *
3683457 TGGCATTCGTTCATGCCTTAATGCATCCTTTCATGCATTTTACTTA
1 TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
* * *
3683503 TGGCATTCGTTCATGCCTAAATGCATCCTTTCATGCATTTTAATT
1 TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATT
3683548 TTGGTATTCT
Statistics
Matches: 204, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
45 21 0.10
46 152 0.75
47 31 0.15
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (46 bp):
TGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAATTA
Found at i:3683469 original size:26 final size:26
Alignment explanation
Indices: 3683440--3683518 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
3683430 AATGCATCAT
3683440 TTCATGCATTTTAATTATGGCATTCG
1 TTCATGCATTTTAATTATGGCATTCG
* * *
3683466 TTCATGC--CTT-A--AT-GCATCCT
1 TTCATGCATTTTAATTATGGCATTCG
*
3683486 TTCATGCATTTTACTTATGGCATTCG
1 TTCATGCATTTTAATTATGGCATTCG
3683512 TTCATGC
1 TTCATGC
3683519 CTAAATGCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 12 0.30
21 2 0.05
22 2 0.05
23 1 0.03
24 2 0.05
25 2 0.05
26 19 0.47
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (26 bp):
TTCATGCATTTTAATTATGGCATTCG
Found at i:3683489 original size:20 final size:20
Alignment explanation
Indices: 3683415--3683538 Score: 59
Period size: 20 Copynumber: 5.6 Consensus size: 20
3683405 TACTTATGGA
3683415 ATCCGTTCATGCCTTAATGC
1 ATCCGTTCATGCCTTAATGC
** *
3683435 ATCATTTCATGCATTTTAATTATGGC
1 ATCCGTTCATGC--CTT-A--AT-GC
*
3683461 ATTCGTTCATGCCTTAATGC
1 ATCCGTTCATGCCTTAATGC
* *
3683481 ATCCTTTCATGCATTTTACTTATGGC
1 ATCCGTTCATGC--CTTA---AT-GC
* *
3683507 ATTCGTTCATGCCTAAATGC
1 ATCCGTTCATGCCTTAATGC
*
3683527 ATCCTTTCATGC
1 ATCCGTTCATGC
3683539 ATTTTAATTT
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
20 34 0.45
21 4 0.05
22 5 0.07
23 2 0.03
24 4 0.05
25 4 0.05
26 23 0.30
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (20 bp):
ATCCGTTCATGCCTTAATGC
Found at i:3693073 original size:90 final size:89
Alignment explanation
Indices: 3692921--3693086 Score: 305
Period size: 90 Copynumber: 1.9 Consensus size: 89
3692911 ATTTTTTAGC
3692921 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
* *
3692986 GGAATTTAATAATCCTCTTATATT
66 GAAATTAAATAATCCTCTTATATT
3693010 CAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 CAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
3693075 TGAAATTAAATA
65 TGAAATTAAATA
3693087 TTCAGGGTTA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 24 0.32
90 50 0.68
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
GAAATTAAATAATCCTCTTATATT
Found at i:3699789 original size:90 final size:89
Alignment explanation
Indices: 3699637--3699809 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
3699627 ACACACCATT
*
3699637 TTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATATCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
3699702 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
3699726 TTATATTCAAGTTACCCTAATCATATTAGTGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATATCCAAGTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTATATTT
3699791 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
3699810 TTTAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 28 0.35
90 51 0.65
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (89 bp):
TTATATCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:3699810 original size:22 final size:21
Alignment explanation
Indices: 3699771--3699840 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
3699761 TATTATTTCA
**
3699771 AATTAATT-AAATCTATATTT
1 AATTAATTAAAATAAATATTT
*
3699791 AATTAATTGAAATTAAATATTT
1 AATTAATT-AAAATAAATATTT
*
3699813 AGGATT-ATTAAAATATATATTT
1 A--ATTAATTAAAATAAATATTT
3699835 AATTAA
1 AATTAA
3699841 CTCTAGATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 11 0.28
21 1 0.03
22 22 0.55
23 3 0.08
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (21 bp):
AATTAATTAAAATAAATATTT
Found at i:3703646 original size:20 final size:21
Alignment explanation
Indices: 3703603--3703654 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
3703593 AAATACATTG
*
3703603 GTATCGATA-TTGACCCTTTGA
1 GTATCGATACTAGACCC-TTGA
3703624 GTATCGATACTAGACCC-TGA
1 GTATCGATACTAGACCCTTGA
3703644 GTATCGATACT
1 GTATCGATACT
3703655 TTTATAGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.48
21 9 0.31
22 6 0.21
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
GTATCGATACTAGACCCTTGA
Found at i:3704980 original size:30 final size:29
Alignment explanation
Indices: 3704929--3704996 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
3704919 ATTTTCTTGA
* *
3704929 GGTACA-TTTTTTATGATACATCCCTGGT
1 GGTACATTTTTTTATGAGACATCCCTAGT
3704957 GGTACATTTTTTTCATGAGACATCCCTAGT
1 GGTACATTTTTTT-ATGAGACATCCCTAGT
3704987 GGTTACATTT
1 GG-TACATTT
3704997 ATGGGGGTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 6 0.17
29 6 0.17
30 16 0.46
31 7 0.20
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
GGTACATTTTTTTATGAGACATCCCTAGT
Found at i:3706239 original size:24 final size:25
Alignment explanation
Indices: 3706212--3706263 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3706202 TATAACCATT
* *
3706212 AAAGCT-AAATCCACTCAAAAGAAC
1 AAAGCTCAAATCAACCCAAAAGAAC
* *
3706236 AAAGTTCATATCAACCCAAAAGAAC
1 AAAGCTCAAATCAACCCAAAAGAAC
3706261 AAA
1 AAA
3706264 ATTACTTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.56, C:0.23, G:0.08, T:0.13
Consensus pattern (25 bp):
AAAGCTCAAATCAACCCAAAAGAAC
Found at i:3708810 original size:3 final size:3
Alignment explanation
Indices: 3708794--3708889 Score: 75
Period size: 3 Copynumber: 31.3 Consensus size: 3
3708784 GTCGAAAATA
* * *
3708794 TAT TAT TAAA TAT TAT TAT TAT TAG TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * * * *
3708840 TAT TGT CGT TGT TGT TGT TAA TAT TAG TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
3708886 TAT T
1 TAT T
3708890 TAAAACCTAC
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
3 72 0.94
4 5 0.06
ACGTcount: A:0.30, C:0.01, G:0.08, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3709871 original size:30 final size:29
Alignment explanation
Indices: 3709802--3709876 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
3709792 TTTTAGTCAC
3709802 TTAAGTTTCTGATTTTGCTATTTATGTCCT
1 TTAAGTTTCTG-TTTTGCTATTTATGTCCT
*
3709832 TTAAATTTCTGTTTTAGCTATTT-TAG-CCT
1 TTAAGTTTCTGTTTT-GCTATTTAT-GTCCT
*
3709861 TGTAAGTTTCTATTTT
1 T-TAAGTTTCTGTTTT
3709877 TACCATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (29 bp):
TTAAGTTTCTGTTTTGCTATTTATGTCCT
Found at i:3709885 original size:30 final size:30
Alignment explanation
Indices: 3709851--3709907 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3709841 TGTTTTAGCT
3709851 ATTTT-AGCCTTGTAAGTTTC-TATTTTTACC
1 ATTTTAAGCCTT-TAAG-TTCATATTTTTACC
*
3709881 ATTTTAATCCTTTAAGTTCATATTTTT
1 ATTTTAAGCCTTTAAGTTCATATTTTT
3709908 GCTAGATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.12
30 16 0.67
31 5 0.21
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (30 bp):
ATTTTAAGCCTTTAAGTTCATATTTTTACC
Found at i:3715094 original size:43 final size:43
Alignment explanation
Indices: 3715045--3715173 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 43
3715035 ACGAAGGGGC
* * *
3715045 CATCCACGATTTCAACTCCATGACGGAGGATATTGTACCCACG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * *
3715088 GATCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* ** * *
3715131 CATCCACGTTTTCAACTTTACGACGAAGGGA-ATCGTACACACA
1 CATCCACGATTTCAACTCCACGACGGA-GGATATCGTACCCACA
3715174 AGCAGCATCC
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 68 0.96
44 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:3715407 original size:335 final size:338
Alignment explanation
Indices: 3714788--3715501 Score: 1026
Period size: 335 Copynumber: 2.1 Consensus size: 338
3714778 ACGAAGGGGT
* * *
3714788 CATCCACGGTTTCAAATTCACGACGAAGAGAATCGTACACACAAGCAACATCCATCTCTAGATTG
1 CATCCACGATTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAACATCCATCTCTA-ATT-
* * * * *
3714853 GATTTTTGGATTTCAAGTTCACGATGAAGGATATCCAACACAAATAAGGAGTGTTTGTCAATAAA
64 GA--TTTGGATTTCAACTTCACGACGAAGGATATCCAACACAAAGAAAGAGTGTATGTCAATAAA
* *
3714918 CTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCGAAGGATATTGGACTCGAAACATACAATAC
127 CTTTCCAGTTTCAGAGCCAATTTCAACTTCAT-GCGAAGGATATTGGACTCGAAACACACAAGAC
* * * * *
3714983 TTGGATTTCAACTTCACGACAAAGGATTTTCAAGTCAAGGCTCAATTTTATGACGAAGGGGCCAT
191 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCAT
* * * * *
3715048 CCACGATTTCAACTCCATGACGGAGGATATTGTACCCACGGATCCACGATTTCAACTCCACGATG
256 CCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACGATTTAAACTCAACGACG
*
3715113 GAGGATATCGTGCCCACA
321 AAGGATATCGTGCCCACA
* * *
3715131 CATCCACGTTTTCAACTTTACGACGAAGGGAATCGTACACACAAGCAGCATCCATCTCT-A-T-A
1 CATCCACGATTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAACATCCATCTCTAATTGA
* *
3715193 -TTGGATTTCAACTTCACGACGAAGGATATTCAACTCAAAGAAAGAGTGTATGTCAATAAACTTT
66 TTTGGATTTCAACTTCACGACGAAGGATATCCAACACAAAGAAAGAGTGTATGTCAATAAACTTT
* * *
3715257 CCAGTTTTAGAGCCAATTTCAGCTTTACAT-CGAAGGATATTGGACTCGAAATAGCACAAGA-TT
131 CCAGTTTCAGAGCCAATTTCAAC-TT-CATGCGAAGGATATTGGACTCGAAACA-CACAAGACTT
* *
3715320 GGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGTCATCC
193 GGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCATCC
3715385 ACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACGATTTAAACTCAACGACGAA
258 ACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACGATTTAAACTCAACGACGAA
3715450 GGATATCGTGCCCACA
323 GGATATCGTGCCCACA
*
3715466 CAACCACGATTTCAACTTCACGACGAAGGGAATCGT
1 CATCCACGATTTCAACTTCACGACGAAGGGAATCGT
3715502 GTGCACCCAC
Statistics
Matches: 335, Mismatches: 33, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
335 268 0.80
336 7 0.02
337 3 0.01
338 1 0.00
340 1 0.00
341 1 0.00
343 54 0.16
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (338 bp):
CATCCACGATTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAACATCCATCTCTAATTGA
TTTGGATTTCAACTTCACGACGAAGGATATCCAACACAAAGAAAGAGTGTATGTCAATAAACTTT
CCAGTTTCAGAGCCAATTTCAACTTCATGCGAAGGATATTGGACTCGAAACACACAAGACTTGGA
TTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCATCCACG
ATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACGATTTAAACTCAACGACGAAGGA
TATCGTGCCCACA
Found at i:3715429 original size:43 final size:43
Alignment explanation
Indices: 3715380--3715494 Score: 151
Period size: 43 Copynumber: 2.7 Consensus size: 43
3715370 ACGAAGGGGT
* *
3715380 CATCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGA
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCAC-A
* * *
3715424 -ATCCACGATTTAAACTCAACGACGAAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACA
* *
3715466 CAACCACGATTTCAACTTCACGACGAAGG
1 CATCCACGATTTCAACTCCACGACGAAGG
3715495 GAATCGTGTG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.19
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACA
Found at i:3715672 original size:206 final size:210
Alignment explanation
Indices: 3715317--3715810 Score: 723
Period size: 206 Copynumber: 2.4 Consensus size: 210
3715307 ATAGCACAAG
*
3715317 ATTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCA
*
3715382 TCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACGATTTAAACTCAACGAC
66 TCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACAATTTAAACTCAACGAC
* *
3715447 GAAGGATATCGTGCCCACACAACCACGATTTCAACTTCACGACGAAGGGA-ATCGTGTGCACCCA
131 GAAGGATATCGTGCCCACACAACCACGATTTCAACTTCACGAC-AAAGGATATCGTGTCCA-CCA
3715511 -CAACA-T-A-CAAT-A
194 GCAACATTCATCAATAA
* * * *
3715523 CTTGGATTTCAACTTCATGACGAAGGATATTCAAGTCAAGGATGAACTTCACGACGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCA
* * * *
3715588 TCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGGATCCACAATTTCAACTCCACGAT
66 TCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACAATTTAAACTCAACGAC
* * *
3715653 GAAGGATATCGTGCCCACACATCCACGATTTTAACTTCACGACAAAGGATATCGTGTCCATCAGC
131 GAAGGATATCGTGCCCACACAACCACGATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGC
* **
3715718 AATATTCATCTTTAA
196 AACATTCATCAATAA
* * *
3715733 ATTGGATTTCAACTTCACGACGAAGGATATCCAA-TCCGAGGCTCAACTTCACGACGAAGGGGCC
1 ATTGGATTTCAACTTCACGACGAAGGATATTCAAGT-CAAGGCTAAACTTCACGACGAAGGGGCC
3715797 ATCCACGATTTCAA
65 ATCCACGATTTCAA
3715811 ATTTTATCTC
Statistics
Matches: 257, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
205 7 0.03
206 174 0.68
207 1 0.00
208 1 0.00
209 3 0.01
210 71 0.28
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (210 bp):
ATTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTAAACTTCACGACGAAGGGGCCA
TCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACGAATCCACAATTTAAACTCAACGAC
GAAGGATATCGTGCCCACACAACCACGATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGC
AACATTCATCAATAA
Found at i:3715708 original size:43 final size:43
Alignment explanation
Indices: 3715586--3715708 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 43
3715576 ACGAAGGGGC
* * * *
3715586 CATCCACGATTTCAACTCCACGACGGAGGATATTGTACCCACG
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACA
* * *
3715629 GATCCACAATTTCAACTCCACGATGAAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACA
* * *
3715672 CATCCACGATTTTAACTTCACGACAAAGGATATCGTG
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTG
3715709 TCCATCAGCA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACA
Found at i:3715863 original size:37 final size:37
Alignment explanation
Indices: 3715809--3715880 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3715799 CCACGATTTC
*
3715809 AAATTTTATCTCTCTTGAGACAG-TTTCTCTTGAAACA
1 AAATTTTATCTCACTTGAGACAGTTTTC-CTTGAAACA
* *
3715846 AAATTTTGTCTCACTTGAGACGGTTTTCCTTGAAA
1 AAATTTTATCTCACTTGAGACAGTTTTCCTTGAAA
3715881 TATAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 27 0.87
38 4 0.13
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (37 bp):
AAATTTTATCTCACTTGAGACAGTTTTCCTTGAAACA
Found at i:3716139 original size:46 final size:44
Alignment explanation
Indices: 3716083--3716411 Score: 177
Period size: 46 Copynumber: 7.6 Consensus size: 44
3716073 CAGATAACCA
*
3716083 ACCGTTCTCATCACGTAGGAACCGTGTTATCATCCTTAGATGGCCT
1 ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGAT--CCT
* * *
3716129 ACCGTCCTCATCACGTAGGAACCGTGTCAT-AACC-CA-A-CCT
1 ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGATCCT
* * * * * ** *
3716169 GATC-TACTCATCATGTAGGAGCCGTCTTA--A-CCCCAGATAACCA
1 -ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGAT--CCT
* * **
3716212 ACCGTCCTCATCACGTAAGAATCGTGTTATCATCCTTAGATGGTTT
1 ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGAT--CCT
* * *
3716258 ACCGTCCTCATCACGTAGGAACCGTGTCATCA-CC-CA-A-CTT
1 ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGATCCT
* * * * * *
3716298 GATC-TCCTCATCACGTAGGAGCTGTGTTAACCTCATATA-AT-C-
1 -ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCT-TAGATCCT
* *
3716340 AGCCGTCCTTATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCT
1 A-CCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGAT--CCT
* *
3716387 GCCGTCCTCATCATGTAGGAACCGT
1 ACCGTCCTCATCACGTAGGAACCGT
3716412 ATCATCACCC
Statistics
Matches: 211, Mismatches: 50, Indels: 44
0.69 0.16 0.14
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 49 0.23
41 6 0.03
42 5 0.02
43 52 0.25
44 2 0.01
45 6 0.03
46 86 0.41
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (44 bp):
ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAGATCCT
Found at i:3716210 original size:129 final size:129
Alignment explanation
Indices: 3715998--3716543 Score: 673
Period size: 129 Copynumber: 4.2 Consensus size: 129
3715988 AAAGATGACA
* * * * *
3715998 TACCGTCCTCATCACGTAGGAACCGTGTCGTC-CTACCGACCAGATCTCTTTATCACATAGGAGC
1 TACCGTCCTCATCACGTAGGAACCGTGTCATCAC--CCAACCTGATCTCTTCATCACGTAGGAGC
* * *
3716062 CATGTTAACCCCAGATAACCAACCGTTCTCATCACGTAGGAACCGTGTTATCATCCTTAGATGGC
64 CGTGTTAACCCCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGC
3716127 C
129 C
* *
3716128 TACCGTCCTCATCACGTAGGAACCGTGTCATAACCCAACCTGATCTAC-TCATCATGTAGGAGCC
1 TACCGTCCTCATCACGTAGGAACCGTGTCATCACCCAACCTGATCT-CTTCATCACGTAGGAGCC
* * * * **
3716192 GTCTTAACCCCAGATAACCAACCGTCCTCATCACGTAAGAATCGTGTTATCATCCTTAGATGGTT
65 GTGTTAACCCCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC
* * *
3716257 TACCGTCCTCATCACGTAGGAACCGTGTCATCACCCAACTTGATCTCCTCATCACGTAGGAGCTG
1 TACCGTCCTCATCACGTAGGAACCGTGTCATCACCCAACCTGATCTCTTCATCACGTAGGAGCCG
* * * * *
3716322 TGTTAACCTCATATAATCAGCCGTCCTTATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC
66 TGTTAACCCCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC
* * * * * * *
3716386 TGCCGTCCTCATCATGTAGGAACCGTATCATCACCCGACCTAATCTCTTCATCACGTAAGAGTCG
1 TACCGTCCTCATCACGTAGGAACCGTGTCATCACCCAACCTGATCTCTTCATCACGTAGGAGCCG
* * * * * * *
3716451 TGTCAACCTCAGATAACCAGCCTTCCTCATCAAGTAGGAACTGTGTTATCACCCTTAGATGGCA
66 TGTTAACCCCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC
** * *
3716515 TGTCGTCCTCATCACATAGGAATCGTGTC
1 TACCGTCCTCATCACGTAGGAACCGTGTC
3716544 GTATAAGTCG
Statistics
Matches: 361, Mismatches: 52, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
128 1 0.00
129 328 0.91
130 31 0.09
131 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (129 bp):
TACCGTCCTCATCACGTAGGAACCGTGTCATCACCCAACCTGATCTCTTCATCACGTAGGAGCCG
TGTTAACCCCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC
Found at i:3716706 original size:3 final size:3
Alignment explanation
Indices: 3716700--3716831 Score: 147
Period size: 3 Copynumber: 43.3 Consensus size: 3
3716690 TCGAAAAAAA
* * * * *
3716700 TAT TAT TAAA TAT TAT TTT TAT TTT TAT TTT TAT TAT TAT TAG TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3716746 TAG TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
3716794 TGT TGT TAA TAT TAG TAT TATT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
3716832 TAAAACCTAC
Statistics
Matches: 107, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
3 102 0.95
4 5 0.05
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3717766 original size:30 final size:29
Alignment explanation
Indices: 3717693--3717766 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 29
3717683 TTTAGTCAGT
* * *
3717693 TAAGTTTATGCTTTTGCTATTTATGTCTTT
1 TAAGTTTCTG-TTTTGCTATTTATGCCTTG
* *
3717723 TAAATTTCCGTTTTAGCTATTT-TAGCCTTG
1 TAAGTTTCTGTTTT-GCTATTTAT-GCCTTG
3717753 TAAGTTTCTGTTTT
1 TAAGTTTCTGTTTT
3717767 TACCATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.57
Consensus pattern (29 bp):
TAAGTTTCTGTTTTGCTATTTATGCCTTG
Found at i:3721366 original size:22 final size:21
Alignment explanation
Indices: 3721324--3721363 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3721314 AAGACTGTTT
3721324 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
3721345 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
3721364 ATAGAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3732039 original size:20 final size:20
Alignment explanation
Indices: 3732014--3732063 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3732004 TTAGACGAGG
3732014 GTATCGATACTCACCCTTGC
1 GTATCGATACTCACCCTTGC
3732034 GTATCGATACTCACCCTTGC
1 GTATCGATACTCACCCTTGC
*
3732054 ATATCGATAC
1 GTATCGATAC
3732064 ATGATGTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACTCACCCTTGC
Found at i:3737747 original size:17 final size:17
Alignment explanation
Indices: 3737710--3737748 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3737700 GGTTAGTTAG
*
3737710 ATTAATGAACTAGTTTA
1 ATTAATGAACTACTTTA
3737727 ATTAATGAACTAACTTT-
1 ATTAATGAACT-ACTTTA
3737744 ATTAA
1 ATTAA
3737749 ATAAACTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTAATGAACTACTTTA
Found at i:3742156 original size:21 final size:20
Alignment explanation
Indices: 3742112--3742157 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3742102 TTTTAAATGT
* *
3742112 TTTTCAAACTTAGTCAAACC
1 TTTTCAAACATAGTCAAACA
*
3742132 TTTTCAAAACATAGTCAATCA
1 TTTTC-AAACATAGTCAAACA
3742153 TTTTC
1 TTTTC
3742158 GCACTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (20 bp):
TTTTCAAACATAGTCAAACA
Found at i:3744435 original size:21 final size:21
Alignment explanation
Indices: 3744387--3744469 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
3744377 TCTTTGGCTC
*
3744387 AAAGGATCGATCCCTTAG-CA
1 AAAGGATCGATCCCTTTGACA
*
3744407 AAAGGATCGATCCCTTTGACC
1 AAAGGATCGATCCCTTTGACA
* * *
3744428 AGAGGATCAATCCCCTTGA-A
1 AAAGGATCGATCCCTTTGACA
*
3744448 AAAGAATCGA-CCCTTTGGACA
1 AAAGGATCGATCCCTTT-GACA
3744469 A
1 A
3744470 CAGTGAGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.10
20 26 0.52
21 19 0.38
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTGACA
Found at i:3747577 original size:35 final size:35
Alignment explanation
Indices: 3747538--3747609 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3747528 ATAACATTAT
*
3747538 GGGAGCGTTTGGTTCGT-GAAAAAGATCATTACTAA
1 GGGAGCATTTGGTTCGTAGAAAAA-ATCATTACTAA
*
3747573 GGGAGCATTTGGTTCGTAGAAAAAATTATTACTAA
1 GGGAGCATTTGGTTCGTAGAAAAAATCATTACTAA
3747608 GG
1 GG
3747610 AGAATGATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 28 0.82
36 6 0.18
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (35 bp):
GGGAGCATTTGGTTCGTAGAAAAAATCATTACTAA
Found at i:3765405 original size:9 final size:9
Alignment explanation
Indices: 3765391--3765425 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3765381 GTTTGACCCA
3765391 ACCCGACTG
1 ACCCGACTG
*
3765400 ACCCGACCCG
1 ACCCGA-CTG
3765410 ACCCGACTG
1 ACCCGACTG
3765419 ACCCGAC
1 ACCCGAC
3765426 CCGACTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.23, C:0.51, G:0.20, T:0.06
Consensus pattern (9 bp):
ACCCGACTG
Found at i:3765407 original size:5 final size:5
Alignment explanation
Indices: 3765385--3765430 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
3765375 TAACCGGTTT
* * *
3765385 GACCC AACCC GA-CT GACCC GACCC GACCC GA-CT GACCC GACCC GAC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GAC
3765431 TGTTGATCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:3765413 original size:19 final size:19
Alignment explanation
Indices: 3765385--3765430 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3765375 TAACCGGTTT
*
3765385 GACCCAACCCGACTGACCC
1 GACCCGACCCGACTGACCC
3765404 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
3765423 GACCCGAC
1 GACCCGAC
3765431 TGTTGATCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:3765421 original size:14 final size:14
Alignment explanation
Indices: 3765404--3765432 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3765394 CGACTGACCC
3765404 GACCCGACCCGACT
1 GACCCGACCCGACT
3765418 GACCCGACCCGACT
1 GACCCGACCCGACT
3765432 G
1 G
3765433 TTGATCGTTG
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:0.21, C:0.48, G:0.24, T:0.07
Consensus pattern (14 bp):
GACCCGACCCGACT
Found at i:3768635 original size:15 final size:15
Alignment explanation
Indices: 3768614--3768655 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
3768604 GAAATAGAAT
3768614 AAAGAAAGGAAAT-G
1 AAAGAAAGGAAATGG
3768628 ATAAGAAAGGAAATGG
1 A-AAGAAAGGAAATGG
3768644 AAATGAAAGGAA
1 AAA-GAAAGGAA
3768656 TTGAATGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 14 0.56
16 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.10
Consensus pattern (15 bp):
AAAGAAAGGAAATGG
Found at i:3773596 original size:19 final size:20
Alignment explanation
Indices: 3773559--3773598 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3773549 GGATAATAAT
3773559 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
3773579 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
3773598 A
1 A
3773599 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:3774054 original size:19 final size:21
Alignment explanation
Indices: 3774011--3774062 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
3774001 GAAACCCCTT
*
3774011 TGAAGATACATCATTTTTAAA
1 TGAAGATACATGATTTTTAAA
*
3774032 TGAAAATACATGA-TTTT-AA
1 TGAAGATACATGATTTTTAAA
3774051 TGAAGATACATG
1 TGAAGATACATG
3774063 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAGATACATGATTTTTAAA
Found at i:3777998 original size:19 final size:21
Alignment explanation
Indices: 3777955--3778006 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3777945 GAAACCCCTT
3777955 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
3777976 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
3777995 TGAAGATACATG
1 TGAAAATACATG
3778007 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Done.