Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005296.1 Hibiscus syriacus cultivar Beakdansim tig00011988_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: 182134
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:6476 original size:22 final size:20
Alignment explanation
Indices: 6422--6459 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
6412 TTCCCATTGA
6422 AGTGCATCG-TGCATTCTTC
1 AGTGCATCGATGCATTCTTC
6441 AGTGCATCGATGCATTCTT
1 AGTGCATCGATGCATTCTT
6460 TAACATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:6567 original size:19 final size:20
Alignment explanation
Indices: 6525--6568 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6515 ATTTTAAGGG
*
6525 GATGCATCGATGCACTCCTC
1 GATGCATCGATGCACTCCAC
*
6545 -ATGCATCGATGCA-TGCAC
1 GATGCATCGATGCACTCCAC
6563 GATGCA
1 GATGCA
6569 ACTGTACTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (20 bp):
GATGCATCGATGCACTCCAC
Found at i:13927 original size:127 final size:127
Alignment explanation
Indices: 13699--14075 Score: 623
Period size: 127 Copynumber: 3.0 Consensus size: 127
13689 ATAAATTAGG
* * * *
13699 TTTATAAATTTCACAAATTAATATGTGATCTAATTATAATTAAAATATGATTATAAAACCTAATT
1 TTTATAAATTTCACATATT-A-ATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATA
*
13764 TTATATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTAACAT
64 TTGTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTAACAT
*
13828 TTTATAAATTTCTCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
1 TTTATAAATTTCACATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
*
13893 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
66 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTAACAT
* *
13955 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAAATTAATAT
1 TTTATAAATTTCACATATTAATGTGATCTAATTATAATTAAAATAAGATTAT-AAAAACTAATAT
*
14020 CGTATAAATA-T-TATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTT
65 TGTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTT
14076 TACGTGATCT
Statistics
Matches: 237, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
126 45 0.19
127 154 0.65
128 21 0.09
129 17 0.07
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (127 bp):
TTTATAAATTTCACATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTAACAT
Found at i:26054 original size:23 final size:23
Alignment explanation
Indices: 25990--26054 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
25980 CAGCTCGTAT
*
25990 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCATGTAG
* * *
26013 AATTGCACCGTATTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
26036 AAATGCACCGAAGTGCCAT
1 AAATGCACCGAAGTGCCAT
26055 ATAATAATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:26063 original size:23 final size:23
Alignment explanation
Indices: 25991--26063 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
25981 AGCTCGTATA
*
25991 AATGCACCGAAGTGCCACGTAGAAT
1 AATGCACCGAAGTGCCA--TATAAT
* * *
26016 --TGCACCGTATTGCCATGTAGA-
1 AATGCACCGAAGTGCCATATA-AT
26037 AATGCACCGAAGTGCCATATAAT
1 AATGCACCGAAGTGCCATATAAT
26060 AATG
1 AATG
26064 TCCATAAGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 33 0.89
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
AATGCACCGAAGTGCCATATAAT
Found at i:27067 original size:2 final size:2
Alignment explanation
Indices: 27056--27087 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27046 TAATACATAC
27056 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27088 CACATATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27494 original size:21 final size:21
Alignment explanation
Indices: 27470--27514 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27460 TTTTGTTCGT
* *
27470 TTGAATGGGTATCGGTTCCCC
1 TTGAATGGGTACCGATTCCCC
*
27491 TTGAATGTGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
27512 TTG
1 TTG
27515 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:28445 original size:16 final size:16
Alignment explanation
Indices: 28406--28448 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
28396 ATCATCAGTT
*
28406 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
28422 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
28439 CTTATCAATC
1 CTTATCAATC
28449 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:31119 original size:23 final size:23
Alignment explanation
Indices: 31086--31145 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
31076 TTGTATAAAA
*
31086 GCACCGAAGTGCCACGTAGAATT
1 GCACCGAAGTGCCACGTAGAAAT
* * *
31109 GTACCGTAGTGCCGCGTAGAAAT
1 GCACCGAAGTGCCACGTAGAAAT
31132 GCACCGAAGTGCCA
1 GCACCGAAGTGCCA
31146 TATAATAATG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (23 bp):
GCACCGAAGTGCCACGTAGAAAT
Found at i:34234 original size:23 final size:24
Alignment explanation
Indices: 34198--34265 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
34188 TTATGTTATG
*
34198 ATACCTGACCTGGATTCTGATCTA
1 ATACATGACCTGGATTCTGATCTA
* * *
34222 ATA-TTGACATGGATTCTGATCTG
1 ATACATGACCTGGATTCTGATCTA
34245 ATACATGACCTGGATTCTGAT
1 ATACATGACCTGGATTCTGAT
34266 ATGATACTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (24 bp):
ATACATGACCTGGATTCTGATCTA
Found at i:34258 original size:24 final size:24
Alignment explanation
Indices: 34196--34277 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
34186 AATTATGTTA
*
34196 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
34220 TAATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
34243 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
34267 TGATACTTGAC
1 TGATACTTGAC
34278 TTGAATTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:34429 original size:35 final size:35
Alignment explanation
Indices: 34355--34421 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
34345 TGGAGGAAGA
*
34355 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGACC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGACC
*
34390 TTACTTGCAGGCTCTTCGGCTTTGTGCTCAGG
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGG
34422 GTCTTACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.10, C:0.27, G:0.28, T:0.34
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGACC
Found at i:36200 original size:2 final size:2
Alignment explanation
Indices: 36193--36256 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
36183 TAATTCTAAA
36193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36235 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
36257 TTGTGATTAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44671 original size:2 final size:2
Alignment explanation
Indices: 44664--44707 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
44654 ACATTTGCTT
44664 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
44706 GA
1 GA
44708 CCTTATGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:49432 original size:12 final size:12
Alignment explanation
Indices: 49415--49457 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
49405 GTGATCACAC
*
49415 GCCACCGTCGTT
1 GCCACCATCGTT
49427 GCCACCATCGTT
1 GCCACCATCGTT
*
49439 GCCACCATCGTC
1 GCCACCATCGTT
49451 GCCACCA
1 GCCACCA
49458 CCTTTGTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (12 bp):
GCCACCATCGTT
Found at i:51854 original size:5 final size:6
Alignment explanation
Indices: 51840--51864 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51830 TAACATTACC
51840 TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT T
51865 GCTCATCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:53351 original size:23 final size:23
Alignment explanation
Indices: 53325--53369 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53315 GTTTGAAAAA
*
53325 AAAATTA-ATAATTATTTTAAATT
1 AAAATTATATAA-TATATTAAATT
53348 AAAATTATATAATATATTAAAT
1 AAAATTATATAATATATTAAAT
53370 ATATCCGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATATAATATATTAAATT
Found at i:53668 original size:54 final size:54
Alignment explanation
Indices: 53595--53731 Score: 231
Period size: 54 Copynumber: 2.5 Consensus size: 54
53585 AATATTTTAC
*
53595 TAAATATGC-AAATTTTCCTTATTTACATGCCCATCCAAATCTCATTATTTGAGT
1 TAAATACGCTAAA-TTTCCTTATTTACATGCCCATCCAAATCTCATTATTTGAGT
*
53649 TAAATACGGTAAATTTCCTTATTTACATGCCCATCCAAATCTCATTATTTGAGT
1 TAAATACGCTAAATTTCCTTATTTACATGCCCATCCAAATCTCATTATTTGAGT
*
53703 TAAATATGCTAAATTTCCTTATTTACATG
1 TAAATACGCTAAATTTCCTTATTTACATG
53732 TCCTATGGTG
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 75 0.96
55 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (54 bp):
TAAATACGCTAAATTTCCTTATTTACATGCCCATCCAAATCTCATTATTTGAGT
Found at i:56311 original size:21 final size:21
Alignment explanation
Indices: 56281--56374 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
56271 CGTTTAAATG
* *
56281 GCGTTACGAATTTTGACTATC
1 GCGTTGCGAATTTCGACTATC
*
56302 GCGTTGCGAATTTCGACTTTC
1 GCGTTGCGAATTTCGACTATC
* *
56323 GCATTGCGAATTTCGACTTTC
1 GCGTTGCGAATTTCGACTATC
*
56344 GCGTTG-GAATTT-GA-GATC
1 GCGTTGCGAATTTCGACTATC
56362 GCGTTGCGAATTT
1 GCGTTGCGAATTT
56375 GTTGGTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.12
19 8 0.12
20 6 0.09
21 43 0.66
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
GCGTTGCGAATTTCGACTATC
Found at i:61739 original size:2 final size:2
Alignment explanation
Indices: 61732--61758 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61722 ATTGAAAAAC
61732 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
61759 CACACACACA
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:65988 original size:18 final size:19
Alignment explanation
Indices: 65941--65990 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
65931 GTCGCGAATA
*
65941 TCTCTGTCGC-GTCTGCGT
1 TCTCTGTCGCGGTCTGCGG
65959 TCTCTGTCGCGGTC-GCGG
1 TCTCTGTCGCGGTCTGCGG
65977 TCTCTGTCGCGGTC
1 TCTCTGTCGCGGTC
65991 CCTCTCTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.00, C:0.34, G:0.32, T:0.34
Consensus pattern (19 bp):
TCTCTGTCGCGGTCTGCGG
Found at i:81549 original size:19 final size:19
Alignment explanation
Indices: 81525--81571 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
81515 CAACACTCTC
81525 ATGTTTCTTTCATTCTTTT
1 ATGTTTCTTTCATTCTTTT
81544 ATGTTTCTTTCATTCTTTT
1 ATGTTTCTTTCATTCTTTT
81563 ATGTTTCTT
1 ATGTTTCTT
81572 ATGCTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.11, C:0.15, G:0.06, T:0.68
Consensus pattern (19 bp):
ATGTTTCTTTCATTCTTTT
Found at i:86793 original size:59 final size:60
Alignment explanation
Indices: 86670--86802 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
86660 GTCGGGTGAT
* * ** *
86670 CATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAGAAACAACCTATAGTCAGGGGAT
1 CATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGAAACAACCTATAGTCAACGGAC
* * * ** *
86730 CATTTTATAATTTTTAATAGT-TAGGGACTCAACAAAGCATTATCCTATAGTCAACGGAC
1 CATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGAAACAACCTATAGTCAACGGAC
86789 CATTTT-TATACTTT
1 CATTTTATA-ACTTT
86803 ACCCTATTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
58 2 0.03
59 39 0.65
60 19 0.32
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGAAACAACCTATAGTCAACGGAC
Found at i:87419 original size:17 final size:17
Alignment explanation
Indices: 87397--87435 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
87387 TGTGGAGATG
87397 CGAGTAGACTTTGTAAC
1 CGAGTAGACTTTGTAAC
87414 CGAGTAGACTTTGTAAC
1 CGAGTAGACTTTGTAAC
87431 CGAGT
1 CGAGT
87436 TTATGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (17 bp):
CGAGTAGACTTTGTAAC
Found at i:87723 original size:25 final size:24
Alignment explanation
Indices: 87695--87746 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
87685 ATTCGAGTGT
* * *
87695 TATTTATAATTTTTTTTTATAAAAA
1 TATTTAAAAATTTCTTTT-TAAAAA
87720 TA-TTAAAAATTTCTTTTTAAAAA
1 TATTTAAAAATTTCTTTTTAAAAA
87743 TATT
1 TATT
87747 AACTTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 8 0.35
24 13 0.57
25 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTAAAAATTTCTTTTTAAAAA
Found at i:88856 original size:103 final size:103
Alignment explanation
Indices: 88661--88877 Score: 409
Period size: 102 Copynumber: 2.1 Consensus size: 103
88651 GTCAAATCGA
* *
88661 ATCGAAGTTTTTAATATTAAATTGAATTAAAAAAATTAATTTTTTAAAGTAGAGCTAAGTTTTAT
1 ATCGATGTTTTCAATATTAAATTGAATTAAAAAAATTAATTTTTTAAAGTAGAGCTAAGTTTTAT
88726 TTACCCTAACTGAACCCATAAGCTTTTTTGCTCTTTTC
66 TTACCCTAACTGAACCCATAAGCTTTTTTGCTCTTTTC
88764 ATCGATGTTTTCAATATTAAATTGAATTAAAAAAATTAA-TTTTTAAAGTAGAGCTAAGTTTTAT
1 ATCGATGTTTTCAATATTAAATTGAATTAAAAAAATTAATTTTTTAAAGTAGAGCTAAGTTTTAT
88828 TTACCCTAACTGAACCCATAAGCTTTTTTGCTCTTTTC
66 TTACCCTAACTGAACCCATAAGCTTTTTTGCTCTTTTC
88866 ATCGATGTTTTC
1 ATCGATGTTTTC
88878 CCAATATGAT
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 75 0.67
103 37 0.33
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (103 bp):
ATCGATGTTTTCAATATTAAATTGAATTAAAAAAATTAATTTTTTAAAGTAGAGCTAAGTTTTAT
TTACCCTAACTGAACCCATAAGCTTTTTTGCTCTTTTC
Found at i:92273 original size:2 final size:2
Alignment explanation
Indices: 92266--92292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92256 ACCTAATTTA
92266 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
92293 AGAAAGTCCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96719 original size:15 final size:15
Alignment explanation
Indices: 96699--96742 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
96689 TTTTAACTAC
96699 AAATTTACTATTTTT
1 AAATTTACTATTTTT
96714 AAATTTACTATTTTT
1 AAATTTACTATTTTT
*
96729 AAATTTAGTATTTT
1 AAATTTACTATTTT
96743 AGTTTTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (15 bp):
AAATTTACTATTTTT
Found at i:96964 original size:2 final size:2
Alignment explanation
Indices: 96957--96984 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96947 GAATATGACG
96957 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
96985 GATTAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102532 original size:18 final size:20
Alignment explanation
Indices: 102509--102546 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
102499 CATTTAAAAA
102509 TTTAAA-ATTA-TTATATAT
1 TTTAAATATTATTTATATAT
102527 TTTAAATATTATTTATATAT
1 TTTAAATATTATTTATATAT
102547 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAAATATTATTTATATAT
Found at i:103810 original size:60 final size:60
Alignment explanation
Indices: 103729--103841 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
103719 TATGACTATT
*
103729 ACTCTAAACTAGTTCTCAAACTTTTGAATA-TTTC-AATTTCATCTCCAAATTATTACCTTA
1 ACTCTAAACTAGTTCCCAAACTTTTGAA-ACTTTCTAATTTCATC-CCAAATTATTACCTTA
* * * *
103789 ACTCTAAATTGGTTCCCAAACTTTTTAAACTTTCTAATTTTATCCCAAATTAT
1 ACTCTAAACTAGTTCCCAAACTTTTGAAACTTTCTAATTTCATCCCAAATTAT
103842 ACATATACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 37 0.80
61 8 0.17
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
ACTCTAAACTAGTTCCCAAACTTTTGAAACTTTCTAATTTCATCCCAAATTATTACCTTA
Found at i:104081 original size:60 final size:61
Alignment explanation
Indices: 103970--104147 Score: 170
Period size: 60 Copynumber: 3.0 Consensus size: 61
103960 GAATTTGGGG
* * **
103970 ATGAAATTGGAATATTC-AAAAGTTTGAGAACCAATCGAGAAA-GAG-GCTCATAGTTTAGAG-
1 ATGAAATTGTAATA-TCAAAAAGTTTAAGAACCAATTTA-AAATGAGAG-TCATAGTTTAGAGA
* * * * * *
104030 ATGAAATTAG-AATGTTAAAAATTTTAAGAACTAATTTAGAATGAGAGTCATAGTTT-GGGA
1 ATGAAATT-GTAATATCAAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAGAGA
* *
104090 ATGAAATTGTAATATCCAAAAGTTTAAGAACCAATTTAAAATGAGAGTTATAGTTTAG
1 ATGAAATTGTAATATCAAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAG
104148 GAACATATGA
Statistics
Matches: 95, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
59 6 0.06
60 86 0.91
61 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (61 bp):
ATGAAATTGTAATATCAAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAGAGA
Found at i:105567 original size:44 final size:43
Alignment explanation
Indices: 105517--105632 Score: 169
Period size: 44 Copynumber: 2.7 Consensus size: 43
105507 TTATGTGTTA
*
105517 TTTAGCGGCGTTTGTATCTTAAAAACGCTGCTATATACTAGACC
1 TTTAGCGGCGTTTGTATCCTAAAAACGC-GCTATATACTAGACC
* * *
105561 TTTAGCGGCATTTGTATCCTAAAAACAACGCTATATACTATACC
1 TTTAGCGGCGTTTGTATCCTAAAAAC-GCGCTATATACTAGACC
*
105605 TTTAGCGGCGTTTATATCCTAAAAACGC
1 TTTAGCGGCGTTTGTATCCTAAAAACGC
105633 CACTACCATA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 62 0.97
45 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTATCCTAAAAACGCGCTATATACTAGACC
Found at i:105810 original size:42 final size:43
Alignment explanation
Indices: 105748--105882 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 43
105738 TGGGAAAAAT
*** * * *
105748 GCCGCTAAATATCAAAACCTATTGCAGTGTTTG-TCTTACAAA-
1 GCCGCTAAATATCGTTACCTATTACAGCGTTTGTTC-AACAAAC
*
105790 GCCGCTAAATATCGTTACCTATTACGGCGTTTGTTCAACAAAC
1 GCCGCTAAATATCGTTACCTATTACAGCGTTTGTTCAACAAAC
* *
105833 GTCGCTATATATCGTTACCTATTAC-GTCGTTTTTTGTT-AACAAAC
1 GCCGCTAAATATCGTTACCTATTACAG-CG---TTTGTTCAACAAAC
105878 GCCGC
1 GCCGC
105883 GAACTTTAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
42 33 0.43
43 27 0.35
45 11 0.14
46 6 0.08
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (43 bp):
GCCGCTAAATATCGTTACCTATTACAGCGTTTGTTCAACAAAC
Found at i:106213 original size:20 final size:20
Alignment explanation
Indices: 106188--106225 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
106178 CTACACTTTT
106188 TCTTTAT-AATAAAATAATTA
1 TCTTTATAAAT-AAATAATTA
106208 TCTTTATAAATAAATAAT
1 TCTTTATAAATAAATAAT
106226 AGAGATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TCTTTATAAATAAATAATTA
Found at i:106396 original size:20 final size:20
Alignment explanation
Indices: 106371--106408 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
106361 CTACACTTTT
106371 TCTTTAT-AATAAAATAATTA
1 TCTTTATAAAT-AAATAATTA
106391 TCTTTATAAATAAATAAT
1 TCTTTATAAATAAATAAT
106409 AGAGATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TCTTTATAAATAAATAATTA
Found at i:108468 original size:24 final size:24
Alignment explanation
Indices: 108441--108506 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
108431 AAATATAAAT
*
108441 GAATGAACATAAACGAACATAATC
1 GAATGAACATAAACGAACATAACC
*
108465 GAATGAACATAAACAAACATAACC
1 GAATGAACATAAACGAACATAACC
* *
108489 GAACGAACATAATCGAAC
1 GAATGAACATAAACGAAC
108507 GTTCACGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (24 bp):
GAATGAACATAAACGAACATAACC
Found at i:108506 original size:14 final size:14
Alignment explanation
Indices: 108452--108507 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
108442 AATGAACATA
108452 AACGAACATAATCG
1 AACGAACATAATCG
*
108466 AATGAACAT-A---
1 AACGAACATAATCG
* *
108476 AACAAACATAACCG
1 AACGAACATAATCG
108490 AACGAACATAATCG
1 AACGAACATAATCG
108504 AACG
1 AACG
108508 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 7 0.21
11 1 0.03
13 1 0.03
14 24 0.73
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.12
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:112010 original size:2 final size:2
Alignment explanation
Indices: 112003--112029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
111993 CTTGGTAGCA
112003 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
112030 ACATCTCTGA
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:113692 original size:23 final size:22
Alignment explanation
Indices: 113665--113714 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
113655 AAGTGATGAC
* *
113665 GTGATCCATGTCACATGTTTAAA
1 GTGAT-CACGTCACATATTTAAA
* *
113688 GTGATGACGTGACATATTTAAA
1 GTGATCACGTCACATATTTAAA
113710 GTGAT
1 GTGAT
113715 AATGTGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (22 bp):
GTGATCACGTCACATATTTAAA
Found at i:113721 original size:22 final size:22
Alignment explanation
Indices: 113672--113726 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
113662 GACGTGATCC
* * *
113672 ATGTCACATGTTTAAAGTGATG
1 ATGTGACATATTTAAAGTGATA
*
113694 ACGTGACATATTTAAAGTGATA
1 ATGTGACATATTTAAAGTGATA
*
113716 ATGTGAAATAT
1 ATGTGACATAT
113727 GTTATATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (22 bp):
ATGTGACATATTTAAAGTGATA
Found at i:122391 original size:64 final size:64
Alignment explanation
Indices: 122322--122478 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
122312 TAATGAAGGT
* **
122322 ATGCATCGATGCACTACTTGTGCATCGGTG-AATAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCAAT-AAATGCATTCGATCGTTTTATT-TTAAAAG
122385 A
64 A
* * * * *
122386 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCAATAAATGCATTCGATCGTTTTATTTTAAAAGA
* *
122450 GTGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
122479 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 66 0.86
65 10 0.13
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCAATAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:128653 original size:15 final size:15
Alignment explanation
Indices: 128629--128662 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
128619 CCATAGGGCC
128629 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
128644 ACTACGTCCCGAATG
1 ACTACATCCCGAAGG
128659 ACTA
1 ACTA
128663 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:129263 original size:64 final size:64
Alignment explanation
Indices: 129192--129312 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
129182 TGAAGGTATG
* *
129192 CATCGATGCAT-TACTTGTGCATCGATGTA-TAAAATGCATTCGAT-GTTTTATTATTAATGAAA
1 CATCGATGCATGT-CTTATGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAATGAAA
129254 TT
63 TT
* *
129256 CATCGATGCATGTCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAA
1 CATCGATGCATGTCTTATGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAA
129313 AAGAGTGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
64 41 0.82
65 9 0.18
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (64 bp):
CATCGATGCATGTCTTATGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAATGAAATT
Found at i:129324 original size:64 final size:63
Alignment explanation
Indices: 129189--129345 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 63
129179 TAATGAAGGT
* *
129189 ATGCATCGATGCATTACTTGTGCATCGATGTATAAAATGCATTCGATGTTTTATTATTAATGAA
1 ATGCATCGATGCATTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAA-GAA
* * *
129253 ATTCATCGATGCATGT-CTTATGCATCGATGCACT-AATTGCATTCGATCTTTTTATT-TTAA-A
1 ATGCATCGATGCAT-TACTTATGCATCGATGCA-TAAAATGCATTCGAT-GTTTTATTATTAAGA
129314 A
63 A
* * * *
129315 GAGTGCATCGATGTACTACCTGTGCATCGAT
1 -A-TGCATCGATGCATTACTTATGCATCGAT
129346 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 64 0.83
65 9 0.12
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (63 bp):
ATGCATCGATGCATTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAGAA
Found at i:130488 original size:69 final size:69
Alignment explanation
Indices: 130380--130516 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
130370 ATGTTACTTT
130380 TATGTTGTCAAAGAAAACCCATCACAATCATTGTTTGTTACATCCTTACCACCATAGTTAGATGA
1 TATGTTGTCAAAGAAAACCCATCACAATCATTGTTTGTTACATCCTTACCACCATAGTTAGATGA
130445 ATTA
66 ATTA
* *
130449 TATGTTGTCAAAGAAAACCCATCACAATCATTGTTTGTTACATCTTTACTACCATAGTTAGATGA
1 TATGTTGTCAAAGAAAACCCATCACAATCATTGTTTGTTACATCCTTACCACCATAGTTAGATGA
130514 ATT
66 ATT
130517 GTCAACACGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (69 bp):
TATGTTGTCAAAGAAAACCCATCACAATCATTGTTTGTTACATCCTTACCACCATAGTTAGATGA
ATTA
Found at i:131178 original size:20 final size:20
Alignment explanation
Indices: 131155--131201 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
131145 AATTTGTAAA
131155 TCGCAACACAGA-AGTCAAAT
1 TCGCAACAC-GATAGTCAAAT
**
131175 TCGCAATGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
131195 TCGCAAC
1 TCGCAAC
131202 GCGAATCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:131199 original size:40 final size:40
Alignment explanation
Indices: 131150--131340 Score: 159
Period size: 40 Copynumber: 4.8 Consensus size: 40
131140 ACGTAAATTT
131150 GTAAATCGCAACACAGAAGTCAAATTCGCAATGCG-AT-A
1 GTAAATCGCAACACAGAAGTCAAATTCGCAATGCGAATCA
* *
131188 GTCAAATTCGCAACGC-GAA-TCTGTAAA-TCGCAATGCGAATCT
1 GT-AAA-TCGCAACACAGAAGTC---AAATTCGCAATGCGAATCA
* * *
131230 GTAAATCGTAACGC-GAA-TCTGTAAA-TCGCAATGCGAATCT
1 GTAAATCGCAACACAGAAGTC---AAATTCGCAATGCGAATCA
*
131270 GTAAATCGCAACACAGAAGTCAAATTCGCAACGCG-AT-A
1 GTAAATCGCAACACAGAAGTCAAATTCGCAATGCGAATCA
*
131308 GTCAAATTCGCAACACAAAAGTCAAATTCGCAA
1 GT-AAA-TCGCAACACAGAAGTCAAATTCGCAA
131341 CTGAATTTCA
Statistics
Matches: 133, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
38 6 0.05
39 14 0.11
40 98 0.74
41 11 0.08
42 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
GTAAATCGCAACACAGAAGTCAAATTCGCAATGCGAATCA
Found at i:131202 original size:60 final size:60
Alignment explanation
Indices: 131149--131321 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
131139 AACGTAAATT
*
131149 TGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATAGTCAAATTCGCAACGCGAATC
1 TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATC
** * * *
131209 TGTAAATCGCAATGC-GAA-TCTGTAAA-TCGTAACGCGAATCTGT-AAA-TCGCAATGCGAATC
1 TGTAAATCGCAACACAGAAGTC---AAATTCGCAACGCG-AT-AGTCAAATTCGCAACGCGAATC
131269 TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
1 TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
131322 ACAAAAGTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
58 4 0.04
59 11 0.12
60 62 0.67
61 11 0.12
62 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (60 bp):
TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATC
Found at i:131205 original size:20 final size:22
Alignment explanation
Indices: 131167--131341 Score: 123
Period size: 20 Copynumber: 8.7 Consensus size: 22
131157 GCAACACAGA
*
131167 AGTCAAATTCGCAATGCG-AT-
1 AGTCAAATTCGCAACGCGAATC
131187 AGTCAAATTCGCAACGCGAATC
1 AGTCAAATTCGCAACGCGAATC
* *
131209 TGT-AAA-TCGCAATGCGAATC
1 AGTCAAATTCGCAACGCGAATC
* *
131229 TGT-AAA-TCGTAACGCGAATC
1 AGTCAAATTCGCAACGCGAATC
* *
131249 TGT-AAA-TCGCAATGCGAATC
1 AGTCAAATTCGCAACGCGAATC
* *
131269 TGT-AAA-TCGCAACAC-AGA--
1 AGTCAAATTCGCAACGCGA-ATC
131287 AGTCAAATTCGCAACGCG-AT-
1 AGTCAAATTCGCAACGCGAATC
* *
131307 AGTCAAATTCGCAACAC-AA-A
1 AGTCAAATTCGCAACGCGAATC
131327 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
131342 TGAATTTCAA
Statistics
Matches: 134, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.01
19 5 0.04
20 120 0.90
21 5 0.04
22 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (22 bp):
AGTCAAATTCGCAACGCGAATC
Found at i:131380 original size:38 final size:40
Alignment explanation
Indices: 131309--131418 Score: 118
Period size: 39 Copynumber: 2.8 Consensus size: 40
131299 AACGCGATAG
* * **
131309 TCAAATTCGCAACACAAAAGTCAAATTCGCAACT-GAATT
1 TCAAATTCACAACACGAATTTCAAATTCGCAACTAGAATT
* *
131348 TCAAATTCACAAC-TGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCACAACACGAATTTCAAATTCGCAACTAGAATT
* * *
131387 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCACAACACGAATTTCAAATTCGCAAC
131419 AGGTTTTAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 16 0.27
39 37 0.63
40 6 0.10
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (40 bp):
TCAAATTCACAACACGAATTTCAAATTCGCAACTAGAATT
Found at i:131393 original size:20 final size:19
Alignment explanation
Indices: 131329--131418 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
131319 AACACAAAAG
131329 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
131348 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
*
131367 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
131387 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
131407 T-AATTTCGCAAC
1 TCAAATTCGCAAC
131419 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 40 0.66
20 21 0.34
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:131419 original size:19 final size:19
Alignment explanation
Indices: 131392--131438 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
131382 GATTTTCGAA
131392 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
131411 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
131429 TTCGCAACAC
1 TTCGCAACAC
131439 AAATATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:132214 original size:12 final size:12
Alignment explanation
Indices: 132193--132226 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
132183 ACCACATTTC
*
132193 CAATACCAAACA
1 CAATATCAAACA
132205 CAATATCAAACA
1 CAATATCAAACA
*
132217 CAATCTCAAA
1 CAATATCAAA
132227 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:132387 original size:24 final size:24
Alignment explanation
Indices: 132352--132405 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
132342 GTATTCAAAA
* *
132352 TTTGATCTTGGTTAATACCCAGAC
1 TTTGATCCTGGTCAATACCCAGAC
* *
132376 TTTGATCCTGGTCAATACTCAGAT
1 TTTGATCCTGGTCAATACCCAGAC
132400 TTTGAT
1 TTTGAT
132406 GATGTGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCCTGGTCAATACCCAGAC
Found at i:134673 original size:18 final size:18
Alignment explanation
Indices: 134650--134685 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
134640 AAGCAAAAGG
134650 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
134668 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
134686 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:135026 original size:14 final size:14
Alignment explanation
Indices: 134988--135026 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
134978 AAAGTCAAAT
134988 TCGCAACGCG-AAA
1 TCGCAACGCGAAAA
135001 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
135015 TCGCAACGCGAA
1 TCGCAACGCGAA
135027 TTTTACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:136673 original size:21 final size:21
Alignment explanation
Indices: 136600--136697 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
136590 GTGAATCGGG
* * *
136600 CTCTTGAACGATGACAGAGGC
1 CTCTTGAATGATGAGAGGGGC
* *
136621 CTCTTGAA-CAGTGGGAGGGGC
1 CTCTTGAATGA-TGAGAGGGGC
136642 CTCTTTG-ATGATGAGAGGGGC
1 CTC-TTGAATGATGAGAGGGGC
* *
136663 CTCTTGAATGAT-AGGAGGCGT
1 CTCTTGAATGATGA-GAGGGGC
136684 CTCTTGAATGATGA
1 CTCTTGAATGATGA
136698 TAAGTGCATC
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.08
21 53 0.84
22 5 0.08
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (21 bp):
CTCTTGAATGATGAGAGGGGC
Found at i:138918 original size:19 final size:20
Alignment explanation
Indices: 138874--138920 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
138864 TCGTAACACC
138874 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*
138894 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
138913 AAAATCGC
1 AAAATCGC
138921 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:139310 original size:20 final size:21
Alignment explanation
Indices: 139287--139351 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
139277 TCTGAGAGAT
139287 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
139307 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
139329 GAAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
139351 G
1 G
139352 TAGAGAGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 6 0.16
22 32 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:139321 original size:22 final size:22
Alignment explanation
Indices: 139294--139351 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
139284 GATGGAGATA
*
139294 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
139316 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
139338 GACGGATGTCGCCG
1 GACGGATTTCGCCG
139352 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:139479 original size:20 final size:20
Alignment explanation
Indices: 139454--139656 Score: 253
Period size: 20 Copynumber: 10.1 Consensus size: 20
139444 TAATATTGTG
139454 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
139474 TTTCGCTTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
139494 TTTTGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
139514 TATCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
139534 TTTTGTGTTGCGAATTTGAA
1 TTTCGCGTTGCGAATTTGAC
* *
139554 ATTCAGTGTTGCGAATTTGAC
1 TTTC-GCGTTGCGAATTTGAC
*
139575 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
139595 TTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
139615 TTTTGTGTTGCGGATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
139635 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
139655 TT
1 TT
139657 CTGTGTTGCG
Statistics
Matches: 156, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
20 139 0.89
21 17 0.11
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:139677 original size:121 final size:120
Alignment explanation
Indices: 139456--139687 Score: 360
Period size: 121 Copynumber: 1.9 Consensus size: 120
139446 ATATTGTGTT
139456 TCGCGTTGCGAATTTGACTTTCGCTTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTATCGCA
1 TCGCGTTGCGAATTTGACTTTCGCTTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTATCGCA
* * *
139521 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTA
66 TTGCGAATTTGACTTCTGTGTTGCGAATTTCAAATTC-GCGTTGCGAATTTGACTA
* * *
139577 TCGCGTTGCGAATTTGACTTTTG-TGTTGCGAATTTGACTTTTGTGTTGCGGATTTGACTATCGC
1 TCGCGTTGCGAATTTGACTTTCGCT-TTGCGAATTTGACTTTTGCGTTGCGAATTTGACTATCGC
*
139641 GTTGCGAATTTGACTTCTGTGTTGCG-ATTTACAAATTCGCGTTGCGA
65 ATTGCGAATTTGACTTCTGTGTTGCGAATTT-CAAATTCGCGTTGCGA
139688 TTTACAGATT
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
120 13 0.13
121 89 0.87
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (120 bp):
TCGCGTTGCGAATTTGACTTTCGCTTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTATCGCA
TTGCGAATTTGACTTCTGTGTTGCGAATTTCAAATTCGCGTTGCGAATTTGACTA
Found at i:139681 original size:40 final size:41
Alignment explanation
Indices: 139460--139687 Score: 254
Period size: 40 Copynumber: 5.7 Consensus size: 41
139450 TGTGTTTCGC
* * *
139460 GTTGCGAATTTGAC-TTTCGCTTTGCGAATTTGACTTTTGC
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTTTGT
* *
139500 GTTGCGAATTTGACTA-TCGCATTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTTTGT
* * * *
139540 GTTGCGAATTTGA-AATTCAGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACAATTC-GCGTTGCGAATTTGACTTTTGT
* * *
139581 GTTGCGAATTTGAC-TTTTGTGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTTTGT
* * *
139621 GTTGCGGATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTTTGT
139661 GTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 GTTGCGAATTTGAC-AATTCGCGTTGCGA
139688 TTTACAGATT
Statistics
Matches: 161, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 6 0.04
40 121 0.75
41 32 0.20
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (41 bp):
GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTTTGT
Found at i:139684 original size:20 final size:20
Alignment explanation
Indices: 139661--139708 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
139651 TGACTTCTGT
139661 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
139681 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
139701 GTTGCGAT
1 GTTGCGAT
139709 ATTGGAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:139685 original size:60 final size:60
Alignment explanation
Indices: 139456--139687 Score: 308
Period size: 60 Copynumber: 3.9 Consensus size: 60
139446 ATATTGTGTT
* * *
139456 TCGCGTTGCGAATTTGACTTTCGCT-TTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTG-TGTTGCGAATTTGACATTCGCGTTGCGAATTTGACTA
* * *
139516 TCGCATTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACATTC-GCGTTGCGAATTTGACTA
* * * *
139577 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACATTCGCGTTGCGAATTTGACTA
*
139637 TCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC--ATTCGCGTTGCGA
139688 TTTACAGATT
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
58 2 0.01
59 5 0.03
60 90 0.59
61 55 0.36
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACATTCGCGTTGCGAATTTGACTA
Found at i:150648 original size:7 final size:7
Alignment explanation
Indices: 150636--150745 Score: 220
Period size: 7 Copynumber: 15.7 Consensus size: 7
150626 TTACTTAACT
150636 TTTTCCC
1 TTTTCCC
150643 TTTTCCC
1 TTTTCCC
150650 TTTTCCC
1 TTTTCCC
150657 TTTTCCC
1 TTTTCCC
150664 TTTTCCC
1 TTTTCCC
150671 TTTTCCC
1 TTTTCCC
150678 TTTTCCC
1 TTTTCCC
150685 TTTTCCC
1 TTTTCCC
150692 TTTTCCC
1 TTTTCCC
150699 TTTTCCC
1 TTTTCCC
150706 TTTTCCC
1 TTTTCCC
150713 TTTTCCC
1 TTTTCCC
150720 TTTTCCC
1 TTTTCCC
150727 TTTTCCC
1 TTTTCCC
150734 TTTTCCC
1 TTTTCCC
150741 TTTTC
1 TTTTC
150746 GGTAATTGAG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 103 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTCCC
Found at i:154896 original size:30 final size:30
Alignment explanation
Indices: 154851--154914 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
154841 TCGGTCCATA
*
154851 TAAGATTTAATGGTTCATATCAAATGTTGT
1 TAAGATTTAATGGTTCATAACAAATGTTGT
* *
154881 TAAGGTTTTATGGTTCATAACAAATGTTGT
1 TAAGATTTAATGGTTCATAACAAATGTTGT
154911 TAAG
1 TAAG
154915 TTATTCTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (30 bp):
TAAGATTTAATGGTTCATAACAAATGTTGT
Found at i:155516 original size:17 final size:16
Alignment explanation
Indices: 155494--155550 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
155484 ATAAATAAAT
155494 ATATTAAAATTTATATA
1 ATATTAAAATTTAT-TA
155511 ATATT--AA-TTATTA
1 ATATTAAAATTTATTA
*
155524 ATATCAAAATTTATGTA
1 ATATTAAAATTTAT-TA
155541 A-ATATAAAAT
1 ATAT-TAAAAT
155551 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 4 0.12
16 6 0.18
17 13 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATTAAAATTTATTA
Found at i:158182 original size:18 final size:18
Alignment explanation
Indices: 158161--158196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
158151 AAGAGAATAT
* *
158161 GCTCTTCGAATCGAATCG
1 GCTCTTCAAATCAAATCG
158179 GCTCTTCAAATCAAATCG
1 GCTCTTCAAATCAAATCG
158197 AATTTAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
GCTCTTCAAATCAAATCG
Found at i:164012 original size:28 final size:27
Alignment explanation
Indices: 163973--164031 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
163963 TATTCATATA
*
163973 CATTTTTTTTGCTTAATGTCGGAGTTG
1 CATTTTTTTTGCTTAATATCGGAGTTG
*
164000 CATTTTCTTTTGCTTAATATTGGAGTTG
1 CATTTT-TTTTGCTTAATATCGGAGTTG
164028 CATT
1 CATT
164032 AAGTGTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.53
Consensus pattern (27 bp):
CATTTTTTTTGCTTAATATCGGAGTTG
Found at i:170874 original size:26 final size:26
Alignment explanation
Indices: 170845--170901 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
170835 CTCTAAAATG
*
170845 AAATATTATGGGCTAAAATACTTCAA
1 AAATATTATGGGCCAAAATACTTCAA
**
170871 AAATA-TATGGGCCAAAATGTTTCAA
1 AAATATTATGGGCCAAAATACTTCAA
170896 AAATAT
1 AAATAT
170902 GAGTCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (26 bp):
AAATATTATGGGCCAAAATACTTCAA
Found at i:171423 original size:22 final size:21
Alignment explanation
Indices: 171389--171430 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
171379 TAAATTGTTT
171389 TTATTAAATAATTA-TTTAAA
1 TTATTAAATAATTACTTTAAA
171409 TTATTATATATAATTACTTTAA
1 TTATTA-A-ATAATTACTTTAA
171431 GTTTCGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 7 0.37
23 5 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTAAATAATTACTTTAAA
Found at i:173229 original size:15 final size:15
Alignment explanation
Indices: 173209--173372 Score: 186
Period size: 15 Copynumber: 10.5 Consensus size: 15
173199 TAATAAGGTT
173209 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
173224 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
* *
173239 ATTTAGTATAAAATA
1 ATTTATTTTAAAATA
*
173254 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
173269 ATTTATTTTAAAAATA
1 ATTTATTTT-AAAATA
*
173285 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
173300 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
173315 AATTATTATAAAATATTGA
1 ATTTATT-TTAAA-A-T-A
173334 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
173352 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
173366 ATTTATT
1 ATTTATT
173373 AGTATGTATT
Statistics
Matches: 131, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.09
15 85 0.65
16 18 0.14
17 1 0.01
18 2 0.02
19 2 0.02
20 1 0.01
21 4 0.03
22 6 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:173251 original size:30 final size:30
Alignment explanation
Indices: 173209--173372 Score: 213
Period size: 30 Copynumber: 5.2 Consensus size: 30
173199 TAATAAGGTT
173209 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
173239 ATTTAGTATAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
173269 ATTTATTTTAAAAATAATTTATTATAAAATA
1 ATTTATTTT-AAAATAATTTATTATAAAATA
*
173300 ATTTATTTTAAAATAAATTATTATAAAATATTGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-A-T-A
*
173334 TTGATTTATTTTAAAATAATTTATT-TTAAATA
1 ---ATTTATTTTAAAATAATTTATTATAAAATA
173366 ATTTATT
1 ATTTATT
173373 AGTATGTATT
Statistics
Matches: 119, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.06
30 49 0.41
31 33 0.28
32 2 0.02
33 2 0.02
34 2 0.02
35 2 0.02
36 1 0.01
37 21 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:173291 original size:61 final size:60
Alignment explanation
Indices: 173209--173370 Score: 209
Period size: 61 Copynumber: 2.6 Consensus size: 60
173199 TAATAAGGTT
*
173209 ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTATAAAATA
* *
173269 ATTTATTTTAAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATTGA
1 ATTTATTTT-AAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTAT-AAA-A-T-A
*
173334 TTGATTTATTTTAAAATAATTTATT-TTAAATAATTTA
1 ---ATTTATTTTAAAATAATTTATTATAAAATAATTTA
173371 TTAGTATGTA
Statistics
Matches: 90, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
60 9 0.10
61 42 0.47
62 3 0.03
63 1 0.01
64 1 0.01
65 1 0.01
66 11 0.12
67 13 0.14
68 9 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (60 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTATAAAATA
Found at i:173348 original size:22 final size:22
Alignment explanation
Indices: 173317--173412 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
173307 TTAAAATAAA
*
173317 TTATTATAAAATATTGATTGAT
1 TTATTTTAAAATATTGATTGAT
* * *
173339 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATTGA-TTGAT
* * * *
173363 ATAATTTATTAGTA-TGTATTGAT
1 TTATTTTA-AAATATTG-ATTGAT
*
173386 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATTGATTGAT
173408 TTATT
1 TTATT
173413 ATTGTAGTTG
Statistics
Matches: 53, Mismatches: 16, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
22 25 0.47
23 15 0.28
24 11 0.21
25 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (22 bp):
TTATTTTAAAATATTGATTGAT
Found at i:173480 original size:22 final size:21
Alignment explanation
Indices: 173455--173499 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
173445 AATTTATTAG
173455 TATGGATTGATTTACTTTAGAA
1 TATGGATTGATTTACTTTA-AA
*
173477 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTACTTTAAA
173498 TA
1 TA
173500 ATTTATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (21 bp):
TATGGATTGATTTACTTTAAA
Found at i:173495 original size:54 final size:54
Alignment explanation
Indices: 173423--173792 Score: 463
Period size: 54 Copynumber: 6.9 Consensus size: 54
173413 ATTGTAGTTG
* * *
173423 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAGAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
173477 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
173531 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * ***
173584 TA---ATTTATTTA---TAGATTGATTTATTTTAAAATAGGATTGATTATTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TTAGTAT-GGATTGA-T-TTATTTTA-AAA
*
173639 TATGGATTGA-TTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
173692 TATGGATTGATTTA-TTTAAATAATTTATTAGTATAGATTGATTTA-TTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
173744 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
173793 AAATAATTTA
Statistics
Matches: 274, Mismatches: 25, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
47 2 0.01
48 7 0.03
50 13 0.05
51 6 0.02
52 22 0.08
53 82 0.30
54 111 0.41
55 3 0.01
56 7 0.03
57 8 0.03
58 4 0.01
59 7 0.03
60 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:173534 original size:22 final size:22
Alignment explanation
Indices: 173509--173551 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
173499 AATTTATTAG
173509 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
173531 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
173552 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:173673 original size:31 final size:31
Alignment explanation
Indices: 173638--173825 Score: 184
Period size: 31 Copynumber: 6.7 Consensus size: 31
173628 TATTGTAGTT
173638 GTATGGATTGA-TTATTTTAAATAATTTATTA
1 GTATGGATTGATTTA-TTTAAATAATTTATTA
*
173669 GTATGGATTGATTTACTT---TAA---A--A
1 GTATGGATTGATTTATTTAAATAATTTATTA
173692 -TATGGATTGATTTATTTAAATAATTTATTA
1 GTATGGATTGATTTATTTAAATAATTTATTA
*
173722 GTATAGATTGATTTA-TT---TAA---A--A
1 GTATGGATTGATTTATTTAAATAATTTATTA
173744 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTA-TTTAAATAATTTATTA
*
173775 GTATAGATTGATTTATTTAAATAATTTATT-
1 GTATGGATTGATTTATTTAAATAATTTATTA
173805 GTATGGATTGATTTATTTAAA
1 GTATGGATTGATTTATTTAAA
173826 ACATGGATTG
Statistics
Matches: 130, Mismatches: 6, Indels: 43
0.73 0.03 0.24
Matches are distributed among these distances:
21 13 0.10
22 17 0.13
23 3 0.02
24 1 0.01
25 4 0.03
26 3 0.02
27 3 0.02
28 4 0.03
29 1 0.01
30 23 0.18
31 42 0.32
32 16 0.12
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.51
Consensus pattern (31 bp):
GTATGGATTGATTTATTTAAATAATTTATTA
Found at i:173695 original size:22 final size:21
Alignment explanation
Indices: 173670--173711 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
173660 AATTTATTAG
173670 TATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTA-TTTAAAA
173692 TATGGATTGATTTATTTAAA
1 TATGGATTGATTTATTTAAA
173712 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:173700 original size:53 final size:52
Alignment explanation
Indices: 173639--173795 Score: 271
Period size: 53 Copynumber: 3.0 Consensus size: 52
173629 ATTGTAGTTG
*
173639 TATGGATTGATTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAA
1 TATGGATTGATTATTTTAAATAATTTATTAGTATAGATTGATTTA-TTTAAAA
173692 TATGGATTGATT-TATTTAAATAATTTATTAGTATAGATTGATTTATTTAAAA
1 TATGGATTGATTAT-TTTAAATAATTTATTAGTATAGATTGATTTATTTAAAA
173744 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAA
1 TATGGATTGA-TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAA
173796 TAATTTATTG
Statistics
Matches: 100, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
52 18 0.18
53 81 0.81
54 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (52 bp):
TATGGATTGATTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAAA
Found at i:173753 original size:21 final size:21
Alignment explanation
Indices: 173727--173766 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
173717 TATTAGTATA
173727 GATTGATTTATTTAAAATATG
1 GATTGATTTATTTAAAATATG
*
173748 GATTGATTTATTTTAAATA
1 GATTGATTTATTTAAAATA
173767 ATTTATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
GATTGATTTATTTAAAATATG
Found at i:173814 original size:30 final size:31
Alignment explanation
Indices: 173744--173825 Score: 139
Period size: 30 Copynumber: 2.6 Consensus size: 31
173734 TTATTTAAAA
173744 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTA-TTTAAATAATTTATTAG
*
173776 TATAGATTGATTTATTTAAATAATTTATT-G
1 TATGGATTGATTTATTTAAATAATTTATTAG
173806 TATGGATTGATTTATTTAAA
1 TATGGATTGATTTATTTAAA
173826 ACATGGATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 20 0.42
31 15 0.31
32 13 0.27
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (31 bp):
TATGGATTGATTTATTTAAATAATTTATTAG
Found at i:173822 original size:21 final size:21
Alignment explanation
Indices: 173798--173848 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
173788 TATTTAAATA
173798 ATTTATTGTATGGATTGATTT
1 ATTTATTGTATGGATTGATTT
****
173819 ATTTAAAACATGGATTGATTT
1 ATTTATTGTATGGATTGATTT
173840 A-TTATTGTA
1 ATTTATTGTA
173849 GTTGTATGGA
Statistics
Matches: 22, Mismatches: 8, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (21 bp):
ATTTATTGTATGGATTGATTT
Found at i:173884 original size:108 final size:107
Alignment explanation
Indices: 173352--173950 Score: 592
Period size: 108 Copynumber: 5.5 Consensus size: 107
173342 TTTTAAAATA
* *
173352 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTACTTTAAATAATTTATT--TATGGATTGATTTA-TTTAAAA-ATGGATTGATTTATTATTG
*
173417 TAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
62 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTG
* * * * * **
173464 ATTTACTTTAGAATATGGATTGATTTAT--TTTAAATAATTTATTAGTATGGATTGATTTA-T-T
1 ATTTACTTTA-AATA---ATTTATTTATGGATTGATTTATTTA--AAAATGGATTGATTTATTAT
***
173525 T-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
60 TGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTG
* * *
173572 ATTTATTTTAAATAATTTATTTATAGATTGATTTATTTTAAAATAGGATTGA-TTATTATTGTAG
1 ATTTACTTTAAATAATTTATTTATGGATTGATTTATTTAAAAAT-GGATTGATTTATTATTGTAG
173636 TTGTATGGATTGA-TTATTTTAAATAATTTATTAGTATGGATTG
65 TTGTATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTG
** **
173679 ATTTACTTT--A-AA---A--TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATT-
1 ATTTACTTTAAATAATTTATTTATGGATTGATTTATTTAAA-AATGGATT-G-ATTTATT-ATTG
* *
173735 TATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTG
62 TAGTT---GTATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTG
173785 ATTTA-TTTAAATAATTTATTGTATGGATTGATTTATTTAAAACATGGATTGATTTATTATTGTA
1 ATTTACTTTAAATAATTTATT-TATGGATTGATTTATTTAAAA-ATGGATTGATTTATTATTGTA
173849 GTTGTATGGATTGA-TTATTTTAAATAATTTATTAGTATGTATTG
64 GTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTG
*
173893 ATTT--TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAGGATTGATTTATT
1 ATTTACTTTAAATAATTTATT--TATGGATTGATTTATTTAAAAAT-GGATTGATTTATT
173951 TTAAATAATT
Statistics
Matches: 408, Mismatches: 41, Indels: 80
0.77 0.08 0.15
Matches are distributed among these distances:
99 21 0.05
100 4 0.01
101 2 0.00
102 7 0.02
103 3 0.01
104 17 0.04
105 22 0.05
106 44 0.11
107 62 0.15
108 126 0.31
109 12 0.03
110 2 0.00
111 9 0.02
112 36 0.09
113 7 0.02
114 28 0.07
116 6 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (107 bp):
ATTTACTTTAAATAATTTATTTATGGATTGATTTATTTAAAAATGGATTGATTTATTATTGTAGT
TGTATGGATTGATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:173902 original size:30 final size:30
Alignment explanation
Indices: 173852--174007 Score: 145
Period size: 28 Copynumber: 5.5 Consensus size: 30
173842 TATTGTAGTT
173852 GTATGGATTGATTATTTTAAATAATTTATTA
1 GTATGGATTGATT-TTTTAAATAATTTATTA
*
173883 GTATGTATTGATTTTTTAAATAATTTATTA
1 GTATGGATTGATTTTTTAAATAATTTATTA
*
173913 GTATGGATTGATTTATTT---TAA---AATA
1 GTATGGATTGATTT-TTTAAATAATTTATTA
* * *
173938 GGATTGATT--TATTTTAAATAATTTATTA
1 GTATGGATTGATTTTTTAAATAATTTATTA
* *
173966 GTATAGATTGATTTATTT---TAATTTATTT
1 GTATGGATTGATTT-TTTAAATAATTTATTA
173994 GTATGGATTGATTT
1 GTATGGATTGATTT
174008 ATTTTAAAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
22 3 0.03
23 2 0.02
25 13 0.13
28 35 0.34
30 32 0.31
31 18 0.17
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (30 bp):
GTATGGATTGATTTTTTAAATAATTTATTA
Found at i:173921 original size:26 final size:28
Alignment explanation
Indices: 173860--173926 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
173850 TTGTATGGAT
173860 TGATTATTTTAAATAATTTATTAGTATG
1 TGATTATTTTAAATAATTTATTAGTATG
173888 T-ATTGATTTTTTAAATAATTTATTAGTATG
1 TGATT-A--TTTTAAATAATTTATTAGTATG
173918 -GATTGATTT
1 TGATT-ATTT
173927 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 3 0.09
28 5 0.14
30 27 0.77
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (28 bp):
TGATTATTTTAAATAATTTATTAGTATG
Found at i:173927 original size:191 final size:187
Alignment explanation
Indices: 173692--174086 Score: 638
Period size: 191 Copynumber: 2.1 Consensus size: 187
173682 TACTTTAAAA
173692 TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATTTA-TTTAAAATATGGATTGATT
1 TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATA-GGATTGATT
173756 TATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAATAATTTA-TTGTATGGATTGATTTA
65 TATTTTAAATAATTTATTAGTATAGATTGATTTATTT---TAATTTATTTGTATGGATTGATTTA
*
173820 -TTTAAAACATGGATTGATTTATTATTGTAGTTGTATGGATTGA-TTATTTTAAATAATTTATTA
127 TTTTAAAACAT-GATT-A-TTATTATTG--GTTGTATGGATTGATTTATTCTAAATAATTTATTA
173883 G
187 G
* *
173884 TATGTATTGATTT-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAGGATTGATTT
1 TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAGGATTGATTT
173948 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAATTTATTTGTATGGATTGATTTATTTT
66 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAATTTATTTGTATGGATTGATTTATTTT
*
174013 AAAATATGATTATTATTATTGGTTGTATGGATTGATTTATTCTAAATAATTTATTAG
131 AAAACATGATTATTATTATTGGTTGTATGGATTGATTTATTCTAAATAATTTATTAG
174070 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
174087 TAAAATATGG
Statistics
Matches: 193, Mismatches: 5, Indels: 15
0.91 0.02 0.07
Matches are distributed among these distances:
185 14 0.07
186 32 0.17
187 12 0.06
188 8 0.04
189 21 0.11
190 9 0.05
191 76 0.39
192 21 0.11
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (187 bp):
TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAGGATTGATTT
ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAATTTATTTGTATGGATTGATTTATTTT
AAAACATGATTATTATTATTGGTTGTATGGATTGATTTATTCTAAATAATTTATTAG
Found at i:173977 original size:32 final size:32
Alignment explanation
Indices: 173939--174015 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 32
173929 TTTAAAATAG
173939 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
173971 GATTGATTTA-TTT---TAATTTATTTGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
173999 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
174016 ATATGATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 23 0.59
29 3 0.08
31 3 0.08
32 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:174048 original size:103 final size:94
Alignment explanation
Indices: 173938--174144 Score: 274
Period size: 103 Copynumber: 2.1 Consensus size: 94
173928 TTTTAAAATA
* *
173938 GGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAATTTATTTGTATGGATT
1 GGATTGATTTATTCTAAATAATTTATTAGTATAGATTGATTTATTTTAA---A---ATATGGATT
*
174003 GATTTATTTTAAA-ATATGATTATTATTATTGGTTGTAT
60 GATTTATTTTAAATA-AT--TTATTATT-TTAGTTGTAT
*
174041 GGATTGATTTATTCTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA
1 GGATTGATTTATTCTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTA
174106 TTTTAAATAATTTATTATTTTAGTTGTAT
66 TTTTAAATAATTTATTATTTTAGTTGTAT
174135 GGATT-ATTTA
1 GGATTGATTTA
174145 AATTTCAGTA
Statistics
Matches: 99, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
93 5 0.05
94 14 0.14
95 8 0.08
97 23 0.23
98 1 0.01
100 1 0.01
103 47 0.47
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (94 bp):
GGATTGATTTATTCTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTA
TTTTAAATAATTTATTATTTTAGTTGTAT
Found at i:174125 original size:21 final size:22
Alignment explanation
Indices: 174070--174112 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
174060 AATTTATTAG
174070 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
174092 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
174113 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:174185 original size:30 final size:31
Alignment explanation
Indices: 174137--174194 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
174127 AGTTGTATGG
* *
174137 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
174168 ATTATTT-AATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
174195 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:174899 original size:24 final size:24
Alignment explanation
Indices: 174881--174927 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
174871 AGTCAGTATT
174881 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
174905 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
174928 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:174939 original size:24 final size:24
Alignment explanation
Indices: 174886--174932 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
174876 GTATTCGAAA
*
174886 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
174910 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
174933 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:177298 original size:2 final size:2
Alignment explanation
Indices: 177291--177323 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
177281 TATTGGGTGT
177291 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
177324 TATATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:177579 original size:21 final size:20
Alignment explanation
Indices: 177555--177619 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
177545 GCCGATTCTA
177555 CACCTCGACACTGAGATCCAT
1 CACCTCGACAC-GAGATCCAT
* * *
177576 CACCTCTAGC-CGA-CTCTA-
1 CACCTCGA-CACGAGATCCAT
177594 CACCTCGACACCGAGATCCAT
1 CACCTCGACA-CGAGATCCAT
177615 CACCT
1 CACCT
177620 ATTCCATCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 6 0.18
20 5 0.15
21 13 0.39
22 1 0.03
ACGTcount: A:0.26, C:0.43, G:0.12, T:0.18
Consensus pattern (20 bp):
CACCTCGACACGAGATCCAT
Found at i:177598 original size:39 final size:41
Alignment explanation
Indices: 177520--177619 Score: 159
Period size: 39 Copynumber: 2.5 Consensus size: 41
177510 TTCTCCACTT
*
177520 ACACCGAGATCCATCACCTCATCGAGCCGATTCTACACCTCG
1 ACACCGAGATCCATCACCTCATC-AGCCGACTCTACACCTCG
*
177562 ACACTGAGATCCATCACCTC-T-AGCCGACTCTACACCTCG
1 ACACCGAGATCCATCACCTCATCAGCCGACTCTACACCTCG
177601 ACACCGAGATCCATCACCT
1 ACACCGAGATCCATCACCT
177620 ATTCCATCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.64
41 1 0.02
42 19 0.35
ACGTcount: A:0.27, C:0.41, G:0.13, T:0.19
Consensus pattern (41 bp):
ACACCGAGATCCATCACCTCATCAGCCGACTCTACACCTCG
Found at i:179039 original size:22 final size:22
Alignment explanation
Indices: 179009--179058 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
178999 GGGGGATTGC
* *
179009 CGGAAATGGGGACGGATGTCGT
1 CGGAGATGGGGACAGATGTCGT
179031 CGGAGATGGGGACAGATGTCGT
1 CGGAGATGGGGACAGATGTCGT
179053 CGGAGA
1 CGGAGA
179059 GAATGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.46, T:0.16
Consensus pattern (22 bp):
CGGAGATGGGGACAGATGTCGT
Found at i:179222 original size:60 final size:60
Alignment explanation
Indices: 179158--179291 Score: 207
Period size: 60 Copynumber: 2.2 Consensus size: 60
179148 TAAAAGCTGA
* * * * * *
179158 GTTGCGAAATTTAAATTCGCGTTGCGAATTCGAAAATCGAGTTGCGAAAATGAAATTCGT
1 GTTGCGAAATTTAAACTCACGTTGCGAATTAGAAAATCAAGTTGCGAAAACGAAACTCGT
179218 GTTGCGAAATTTAAACTCACGTTGCGAATTAGAAAATCAAGTTGCGAAAACGAAACTCGT
1 GTTGCGAAATTTAAACTCACGTTGCGAATTAGAAAATCAAGTTGCGAAAACGAAACTCGT
179278 GTTGCG-AATTTAAA
1 GTTGCGAAATTTAAA
179292 AATCGAGTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 8 0.12
60 60 0.88
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (60 bp):
GTTGCGAAATTTAAACTCACGTTGCGAATTAGAAAATCAAGTTGCGAAAACGAAACTCGT
Found at i:179242 original size:40 final size:39
Alignment explanation
Indices: 179136--179245 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 39
179126 CAAAACATTA
* * *
179136 GTGTTGCGAAATTAAAAGCTGAGTTGCGAAATTTAAATTC
1 GTGTTGCGAAATTAAAA-CTCAGTTGCGAAAATGAAATTC
*
179176 GCGTTGCG-AATTCGAAAA-TCGAGTTGCGAAAATGAAATTC
1 GTGTTGCGAAATT--AAAACTC-AGTTGCGAAAATGAAATTC
*
179216 GTGTTGCGAAATTTAAACTCACGTTGCGAA
1 GTGTTGCGAAATTAAAACTCA-GTTGCGAA
179246 TTAGAAAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
39 9 0.16
40 41 0.71
41 8 0.14
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (39 bp):
GTGTTGCGAAATTAAAACTCAGTTGCGAAAATGAAATTC
Found at i:179370 original size:20 final size:19
Alignment explanation
Indices: 179156--179369 Score: 90
Period size: 20 Copynumber: 10.6 Consensus size: 19
179146 ATTAAAAGCT
*
179156 GAGTTGCGAAATTTAAATTC
1 GAGTTGCG-AATTGAAATTC
* *
179176 GCGTTGCGAATTCGAAAATC
1 GAGTTGCGAATT-GAAATTC
*
179196 GAGTTGCGAAAATGAAATTC
1 GAGTTGCG-AATTGAAATTC
* * *
179216 GTGTTGCGAAATTTAAACTC
1 GAGTTGCG-AATTGAAATTC
*
179236 -ACGTTGCGAATTAGAAAATC
1 GA-GTTGCGAATT-GAAATTC
* ** *
179256 AAGTTGCGAAAACGAAACTC
1 GAGTTGCG-AATTGAAATTC
* * *
179276 GTGTTGCGAATTTAAAAATC
1 GAGTTGCGAA-TTGAAATTC
* * *
179296 GAGTTACAAAAATGTCAAATTC
1 GAGTTGC--GAAT-TGAAATTC
* *
179318 GAGTTGTGAATT-ATACTTC
1 GAGTTGCGAATTGA-AATTC
* *
179337 TGTGTTGCGAATTCCAAATTC
1 -GAGTTGCGAATT-GAAATTC
179358 GAGTTGCGAATT
1 GAGTTGCGAATT
179370 CAGAAACTGT
Statistics
Matches: 145, Mismatches: 35, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 104 0.72
21 11 0.08
22 14 0.10
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (19 bp):
GAGTTGCGAATTGAAATTC
Found at i:179383 original size:20 final size:19
Alignment explanation
Indices: 179336--179384 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
179326 AATTATACTT
179336 CTGTGTTGCGAATTCCAAA
1 CTGTGTTGCGAATTCCAAA
* * *
179355 TTCGAGTTGCGAATTCAGAAA
1 CT-GTGTTGCGAATTC-CAAA
179376 CTGTGTTGC
1 CTGTGTTGC
179385 AAAATTAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (19 bp):
CTGTGTTGCGAATTCCAAA
Found at i:180095 original size:3 final size:3
Alignment explanation
Indices: 180076--180114 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
180066 ATCTCTAGAT
180076 TAA TAA -AA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
180115 AACATTGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:181170 original size:22 final size:22
Alignment explanation
Indices: 181144--181188 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
181134 TATAAGAGGT
*
181144 TGGTGACTATTTATATAGTTTA
1 TGGTGACTATTTATATAGGTTA
181166 TGGTGACTATTTATATAGGTTA
1 TGGTGACTATTTATATAGGTTA
181188 T
1 T
181189 TCTTTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (22 bp):
TGGTGACTATTTATATAGGTTA
Done.