Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 35 of 39
Found at i:5036182 original size:30 final size:30
Alignment explanation
Indices: 5036132--5036219 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
5036122 TATTAATTTT
*
5036132 TATTAAAAATTTATCTAAATATAAATTAAAG
1 TATTAAAAA-TTATTTAAATATAAATTAAAG
* *
5036163 -ATTATAAAATTATTTAAATACAAATAAAAAG
1 TATTA-AAAATTATTTAAATATAAAT-TAAAG
*
5036194 TATTAAAATTTATTTAAATATAAATT
1 TATTAAAAATTATTTAAATATAAATT
5036220 TTAAATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
30 18 0.38
31 26 0.54
32 4 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTAAAAATTATTTAAATATAAATTAAAG
Found at i:5036210 original size:31 final size:30
Alignment explanation
Indices: 5036137--5036252 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 30
5036127 ATTTTTATTA
* * *
5036137 AAAATTTATCTAAATATAAAT-TAAAGATT
1 AAAATTTATTTAAATACAAATAAAAAGATT
*
5036166 ATAAAATTATTTAAATACAAATAAAAAGTATT
1 A-AAATTTATTTAAATACAAATAAAAAG-ATT
* ***
5036198 AAAATTTATTTAAATATAAATTTTAA-ATT
1 AAAATTTATTTAAATACAAATAAAAAGATT
*
5036227 AATATTTTATTTAAATAC-AATAAAAA
1 AA-AATTTATTTAAATACAAATAAAAA
5036253 TAAAAAAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
29 11 0.16
30 30 0.43
31 24 0.35
32 4 0.06
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTTATTTAAATACAAATAAAAAGATT
Found at i:5036214 original size:61 final size:61
Alignment explanation
Indices: 5036132--5036279 Score: 166
Period size: 61 Copynumber: 2.5 Consensus size: 61
5036122 TATTAATTTT
5036132 TATTAAAAATTTATCTAAATATAAA-TTAAAGATT-ATAAAATTATTTAAATACAAATAAAAAG
1 TATTAAAAATTTATCTAAATATAAATTTAAA-ATTAAT-AAATTATTTAAATAC-AATAAAAAG
* * **
5036194 TATT-AAAATTTATTTAAATATAAATTTTAAATTAATATTTTATTTAAATACAATAAAAA-
1 TATTAAAAATTTATCTAAATATAAATTTAAAATTAATAAATTATTTAAATACAATAAAAAG
* *
5036253 TA--AAAAAATTATCTAAGTA-AAATTTAA
1 TATTAAAAATTTATCTAAATATAAATTTAA
5036280 TATTTTTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
57 7 0.09
58 13 0.17
59 2 0.03
60 8 0.11
61 35 0.47
62 10 0.13
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (61 bp):
TATTAAAAATTTATCTAAATATAAATTTAAAATTAATAAATTATTTAAATACAATAAAAAG
Found at i:5036638 original size:22 final size:24
Alignment explanation
Indices: 5036596--5036642 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
5036586 TTCGATTTAA
*
5036596 AATTAATTTTATTTAAAAAATTAT
1 AATTAATTTTATTAAAAAAATTAT
5036620 AATT-ATTTT-TTAAAAAAATTAT
1 AATTAATTTTATTAAAAAAATTAT
5036642 A
1 A
5036643 TTTCTGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 5 0.23
24 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAATTTTATTAAAAAAATTAT
Found at i:5037348 original size:16 final size:18
Alignment explanation
Indices: 5037322--5037377 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 18
5037312 TTTATATTTT
*
5037322 TATTAAATATTTA-TTAA
1 TATTTAATATTTATTTAA
5037339 -ATTTAATATTTATTTAA
1 TATTTAATATTTATTTAA
*
5037356 TATTTAAAATTATATTTTAA
1 TATTTAATATT-TA-TTTAA
5037376 TA
1 TA
5037378 AAATTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 11 0.33
17 4 0.12
18 9 0.27
19 2 0.06
20 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAATATTTATTTAA
Found at i:5039880 original size:20 final size:19
Alignment explanation
Indices: 5039841--5039883 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5039831 TAATATTTTA
* *
5039841 AAATTTTTTTAAATATATT
1 AAATTTTTTTAAAAAAATT
5039860 AAATTTTTTTAAAAAAAATT
1 AAATTTTTTT-AAAAAAATT
5039880 AAAT
1 AAAT
5039884 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTTTTTAAAAAAATT
Found at i:5048111 original size:20 final size:20
Alignment explanation
Indices: 5048086--5048123 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5048076 GGTATAGATT
*
5048086 TATATTTTTAAATTTTTTTA
1 TATATTTTAAAATTTTTTTA
5048106 TATATTTTAAAATTTTTT
1 TATATTTTAAAATTTTTT
5048124 ATGCGAGAGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATATTTTAAAATTTTTTTA
Found at i:5048115 original size:19 final size:18
Alignment explanation
Indices: 5048084--5048125 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
5048074 CCGGTATAGA
*
5048084 TTTATATTTTTAAATTTT
1 TTTATATTTTTAAAATTT
5048102 TTTATATATTTTAAAATTT
1 TTTATAT-TTTTAAAATTT
5048121 TTTAT
1 TTTAT
5048126 GCGAGAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATATTTTTAAAATTT
Found at i:5064865 original size:12 final size:12
Alignment explanation
Indices: 5064850--5064874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5064840 TGAAGAAGAA
5064850 GCAGAAGCAGAT
1 GCAGAAGCAGAT
5064862 GCAGAAGCAGAT
1 GCAGAAGCAGAT
5064874 G
1 G
5064875 TGGTTAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.36, T:0.08
Consensus pattern (12 bp):
GCAGAAGCAGAT
Found at i:5064892 original size:15 final size:15
Alignment explanation
Indices: 5064869--5064898 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5064859 GATGCAGAAG
*
5064869 CAGATGTGGTTAAAT
1 CAGAAGTGGTTAAAT
5064884 CAGAAGTGGTTAAAT
1 CAGAAGTGGTTAAAT
5064899 TCGGACCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (15 bp):
CAGAAGTGGTTAAAT
Found at i:5066150 original size:2 final size:2
Alignment explanation
Indices: 5066143--5066200 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
5066133 TGCCTTTAGA
* *
5066143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5066185 AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5066201 TAGTGTCGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5073893 original size:49 final size:48
Alignment explanation
Indices: 5073827--5073929 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
5073817 TAATATAAAT
* * * *
5073827 ATATAAATTATCAAGTATCATTCATTATTCTTTTTATATATCTTTTTGA
1 ATATTAATTATCAAGTATCATGCACTAAT-TTTTTATATATCTTTTTGA
* * * *
5073876 ATATTAATTGTCAAGTATCATGGACTAATTTTTTATCTGTCTTTTTGA
1 ATATTAATTATCAAGTATCATGCACTAATTTTTTATATATCTTTTTGA
5073924 ATATTA
1 ATATTA
5073930 GAGAGAGACT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
48 23 0.50
49 23 0.50
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (48 bp):
ATATTAATTATCAAGTATCATGCACTAATTTTTTATATATCTTTTTGA
Found at i:5074075 original size:2 final size:2
Alignment explanation
Indices: 5074063--5074093 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5074053 TAATTTGTTC
5074063 AT AT A- 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
5074094 GCAGTTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5077473 original size:2 final size:2
Alignment explanation
Indices: 5077466--5077494 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5077456 TTGATTTAAC
5077466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5077495 GTTGCAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5078029 original size:11 final size:10
Alignment explanation
Indices: 5077991--5078041 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
5077981 ATATAAAATG
*
5077991 ATATATTTAA
1 ATATATTTAT
*
5078001 ATATAATTAAT
1 ATAT-ATTTAT
5078012 ATAATATTTAT
1 AT-ATATTTAT
5078023 ATGATATTTAT
1 AT-ATATTTAT
5078034 ATATATTT
1 ATATATTT
5078042 TTTAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 10 0.29
11 23 0.66
12 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATATATTTAT
Found at i:5078746 original size:2 final size:2
Alignment explanation
Indices: 5078739--5078799 Score: 51
Period size: 2 Copynumber: 32.0 Consensus size: 2
5078729 TAAATATAAC
* *
5078739 AT AT AT AT AT AT AT -T CACT -T A- AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT
5078780 AT AT AT AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5078800 TGATTAACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
1 5 0.10
2 42 0.88
4 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5081008 original size:3 final size:3
Alignment explanation
Indices: 5080964--5080990 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5080954 TCTTGAGGTC
5080964 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
5080991 ACAATTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5084959 original size:26 final size:27
Alignment explanation
Indices: 5084892--5084962 Score: 72
Period size: 33 Copynumber: 2.4 Consensus size: 27
5084882 TATAATTATA
5084892 TTTAAAATATTTTATATCTACATAAAT
1 TTTAAAATATTTTATATCTACATAAAT
*
5084919 TTTAATACGTTAATATTTTATAT-TATATAAAT
1 TTT-A-A----AATATTTTATATCTACATAAAT
5084951 TTTAAAATATTT
1 TTTAAAATATTT
5084963 ATTCGTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
26 7 0.19
27 3 0.08
28 1 0.03
29 1 0.03
30 1 0.03
31 1 0.03
32 11 0.30
33 12 0.32
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (27 bp):
TTTAAAATATTTTATATCTACATAAAT
Found at i:5088765 original size:16 final size:17
Alignment explanation
Indices: 5088746--5088786 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
5088736 ATTTTGAAAT
5088746 TTATATTTATATTTT-A
1 TTATATTTATATTTTAA
5088762 TTATA-TTATATTTTAA
1 TTATATTTATATTTTAA
5088778 TTAT-TTTAT
1 TTATATTTAT
5088787 TTATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTATATTTTAA
Found at i:5089415 original size:28 final size:28
Alignment explanation
Indices: 5089384--5089441 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5089374 AATTTAATTA
5089384 ATTTACATAATT-AT-TTTTAAAATATAAT
1 ATTTA-ATAATTAATATTTT-AAATATAAT
* *
5089412 ATTTAATATTTAATATTTTAATTATAAT
1 ATTTAATAATTAATATTTTAAATATAAT
5089440 AT
1 AT
5089442 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 17 0.65
29 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTAATAATTAATATTTTAAATATAAT
Found at i:5089416 original size:14 final size:14
Alignment explanation
Indices: 5089399--5089441 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5089389 CATAATTATT
5089399 TTTAAAATATAATA
1 TTTAAAATATAATA
* *
5089413 TTTAATATTTAATA
1 TTTAAAATATAATA
* *
5089427 TTTTAATTATAATA
1 TTTAAAATATAATA
5089441 T
1 T
5089442 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAATATAATA
Found at i:5090698 original size:21 final size:22
Alignment explanation
Indices: 5090658--5090698 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5090648 CTGCTAGGGA
*
5090658 TTTTCTTTCTTTTTTATTTTAC
1 TTTTCTTTCTTTTGTATTTTAC
*
5090680 TTTT-TTTCTTTTGTGTTTT
1 TTTTCTTTCTTTTGTATTTT
5090699 TGCCCATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (22 bp):
TTTTCTTTCTTTTGTATTTTAC
Found at i:5090931 original size:2 final size:2
Alignment explanation
Indices: 5090924--5090953 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5090914 AGCTTATTTG
5090924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5090954 CACAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5091444 original size:18 final size:17
Alignment explanation
Indices: 5091402--5091450 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
5091392 ATATCTCTTT
5091402 TATAGTATTTAAAAAAA
1 TATAGTATTTAAAAAAA
*
5091419 TA-ATTATTTACAGAAAAA
1 TATAGTATTTA-A-AAAAA
5091437 TATA-TATTTAAAAA
1 TATAGTATTTAAAAA
5091451 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 10 0.36
17 4 0.14
18 13 0.46
19 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
TATAGTATTTAAAAAAA
Found at i:5096069 original size:2 final size:2
Alignment explanation
Indices: 5096062--5096090 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5096052 AATCAGGCAA
5096062 AT 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 AT A
5096091 ACTTGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5096170 original size:6 final size:6
Alignment explanation
Indices: 5096143--5096191 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
5096133 TATTAAATTT
* * *
5096143 TATAAA AATAAA TTTATAA TATATA TATAAA TATAAA TATAAA TATAAA
1 TATAAA TATAAA TATA-AA TATAAA TATAAA TATAAA TATAAA TATAAA
5096192 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:5096177 original size:12 final size:12
Alignment explanation
Indices: 5096131--5096189 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
5096121 TTTCCCTATT
5096131 TATAT-TAAAT-
1 TATATATAAATA
* *
5096141 TTTATAAAAATA
1 TATATATAAATA
* *
5096153 AATTTAT-AATA
1 TATATATAAATA
5096164 TATATATAAATA
1 TATATATAAATA
*
5096176 TAAATATAAATA
1 TATATATAAATA
5096188 TA
1 TA
5096190 AAATTTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
10 4 0.11
11 13 0.35
12 20 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATAAATA
Found at i:5101592 original size:10 final size:10
Alignment explanation
Indices: 5101577--5101601 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5101567 GATATCAAAT
5101577 TTTATTTATA
1 TTTATTTATA
5101587 TTTATTTATA
1 TTTATTTATA
5101597 TTTAT
1 TTTAT
5101602 AAATAGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTTATA
Found at i:5101689 original size:34 final size:35
Alignment explanation
Indices: 5101630--5101695 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
5101620 TATATTTTTT
*
5101630 TAATTTAATTTTTTATTAAATTTTAAA-ATATAAA
1 TAATTTAATTGTTTATTAAATTTTAAATATATAAA
5101664 TAATTTAATGTGTTT-TT-AATATTTAAATATAT
1 TAATTTAAT-TGTTTATTAAAT-TTTAAATATAT
5101696 TTATATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 3 0.11
34 17 0.61
35 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATTTAATTGTTTATTAAATTTTAAATATATAAA
Found at i:5102035 original size:21 final size:23
Alignment explanation
Indices: 5101987--5102035 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
5101977 AATAATGTAT
**
5101987 AATAATTTTATATTTATATGTTA
1 AATAATTTTATATTTATATAATA
*
5102010 TATAATTTT-TA-TTATATAATA
1 AATAATTTTATATTTATATAATA
5102031 AATAA
1 AATAA
5102036 AATATAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATAATTTTATATTTATATAATA
Found at i:5102364 original size:17 final size:17
Alignment explanation
Indices: 5102337--5102387 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
5102327 TTTAGAGTTA
5102337 AAATCAAACTTATTTTTT
1 AAAT-AAACTTATTTTTT
5102355 AAATAAAC-T-TTTTTT
1 AAATAAACTTATTTTTT
* *
5102370 AATCTAAATTTATTTTTT
1 AA-ATAAACTTATTTTTT
5102388 TGAAACTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 5 0.18
18 10 0.36
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATAAACTTATTTTTT
Found at i:5102995 original size:21 final size:22
Alignment explanation
Indices: 5102943--5103002 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
5102933 AAATTTTTAT
*
5102943 TTAATAATAAAATTATTTAAATA
1 TTAAT-ATAAAATTATATAAATA
*
5102966 TT--TAAAAAATT-TATAAATA
1 TTAATATAAAATTATATAAATA
*
5102985 TTAATATAAAAATATATA
1 TTAATATAAAATTATATA
5103003 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 9 0.30
20 7 0.23
21 8 0.27
22 4 0.13
23 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATAAAATTATATAAATA
Found at i:5104810 original size:3 final size:3
Alignment explanation
Indices: 5104802--5104831 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5104792 AATAGGATGA
5104802 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
5104832 TTAGCTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:5106984 original size:9 final size:9
Alignment explanation
Indices: 5106935--5107009 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 9
5106925 AAAAATAATA
5106935 TTTATATAT
1 TTTATATAT
5106944 TTTATCATAT
1 TTTAT-ATAT
5106954 TATATATATAT
1 T-T-TATATAT
* *
5106965 TTAAAATAT
1 TTTATATAT
*
5106974 TTTATA-AA
1 TTTATATAT
5106982 TTTA-A-AT
1 TTTATATAT
5106989 TTTA-ATAT
1 TTTATATAT
*
5106997 ATTA-ATAT
1 TTTATATAT
5107005 TTTAT
1 TTTAT
5107010 GTTATATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 7 0.13
8 17 0.32
9 14 0.26
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTATATAT
Found at i:5107065 original size:28 final size:29
Alignment explanation
Indices: 5106997--5107066 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
5106987 ATTTTAATAT
* *
5106997 ATTAATATTTTATGTTATATAAATTTTTA
1 ATTAATTTTTTATGTCATATAAATTTTTA
*
5107026 AAT-ATTTATTTAT-TCATAT-AATATTTTA
1 ATTAATTT-TTTATGTCATATAAAT-TTTTA
5107054 ATTAATTTTTTAT
1 ATTAATTTTTTAT
5107067 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 3 0.09
28 20 0.59
29 11 0.32
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
ATTAATTTTTTATGTCATATAAATTTTTA
Found at i:5107127 original size:17 final size:16
Alignment explanation
Indices: 5107095--5107136 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
5107085 GTTTAATATT
5107095 ATAAAATTTAAATTTAA
1 ATAAAA-TTAAATTTAA
*
5107112 ATTAAATTAAATTTTAA
1 ATAAAATTAAA-TTTAA
5107129 ATAAAATT
1 ATAAAATT
5107137 TTTTATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAATTAAATTTAA
Found at i:5107948 original size:63 final size:61
Alignment explanation
Indices: 5107851--5108029 Score: 275
Period size: 63 Copynumber: 3.0 Consensus size: 61
5107841 AGATATAGTC
*
5107851 ATATTTTAATCAAATCTATTAAAAATCATAAAAAAAATCAATTATTATATTTAATATAAAATT
1 ATATTTTAATCAAATCTATTAAAAATCAT-TAAAAAATCAATTATTATATTTAATAT-AAATT
5107914 ATATTTTAATCAAATCTATTAAAAATCATTAAAAAATCAATTATTATATTTAATATAAA-T
1 ATATTTTAATCAAATCTATTAAAAATCATTAAAAAATCAATTATTATATTTAATATAAATT
5107974 ATA-TTTAATC-AATCTA-T--AAATCATT-AAAAATCAATTATTATA-TTAATATAAATT
1 ATATTTTAATCAAATCTATTAAAAATCATTAAAAAATCAATTATTATATTTAATATAAATT
5108028 AT
1 AT
5108030 CTATAATAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 11
0.90 0.01 0.09
Matches are distributed among these distances:
53 10 0.09
54 20 0.18
55 8 0.07
57 1 0.01
58 6 0.05
59 7 0.06
60 4 0.04
61 3 0.03
62 26 0.23
63 29 0.25
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (61 bp):
ATATTTTAATCAAATCTATTAAAAATCATTAAAAAATCAATTATTATATTTAATATAAATT
Found at i:5108615 original size:2 final size:2
Alignment explanation
Indices: 5108608--5108635 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5108598 AACTGAATCC
5108608 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
5108636 TTGTATATCA
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:5108832 original size:3 final size:3
Alignment explanation
Indices: 5108818--5108859 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
5108808 ATTTCTGAAT
5108818 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T
5108860 TTAATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5109123 original size:2 final size:2
Alignment explanation
Indices: 5109116--5109147 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5109106 CATGCCATGC
*
5109116 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5109148 CTCAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5112351 original size:20 final size:20
Alignment explanation
Indices: 5112311--5112384 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
5112301 GTATTTAAGA
* * *
5112311 TAATATAGTTATATAAATTT
1 TAATATATTTATATTATTTT
5112331 TAATATATTTATATTATTTT
1 TAATATATTTATATTATTTT
5112351 T-ATATTATTT-T-TTATTTT
1 TAATA-TATTTATATTATTTT
*
5112369 ATATTATATTTTATAT
1 -TAATATA-TTTATAT
5112385 CATATATACG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.16
19 7 0.16
20 28 0.64
21 1 0.02
22 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TAATATATTTATATTATTTT
Found at i:5112354 original size:11 final size:11
Alignment explanation
Indices: 5112338--5112366 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5112328 TTTTAATATA
5112338 TTTATATTATT
1 TTTATATTATT
5112349 TTTATATTATT
1 TTTATATTATT
5112360 TTT-TATT
1 TTTATATT
5112367 TTATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATATTATT
Found at i:5112356 original size:17 final size:17
Alignment explanation
Indices: 5112334--5112384 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
5112324 TAAATTTTAA
5112334 TATATTTATATTATTTT
1 TATATTTATATTATTTT
5112351 TATA--T-TA-T-TTTT
1 TATATTTATATTATTTT
5112363 TAT-TTTATATTATATTT
1 TATATTTATATTAT-TTT
5112380 TATAT
1 TATAT
5112385 CATATATACG
Statistics
Matches: 27, Mismatches: 0, Indels: 13
0.68 0.00 0.32
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 4 0.15
15 2 0.07
16 1 0.04
17 10 0.37
18 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTATATTATTTT
Found at i:5112378 original size:12 final size:12
Alignment explanation
Indices: 5112333--5112384 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
5112323 ATAAATTTTA
5112333 ATATATTTATATT
1 ATAT-TTTATATT
5112346 AT-TTTTATATT
1 ATATTTTATATT
* *
5112357 ATTTTTTATTTT
1 ATATTTTATATT
* *
5112369 ATATTATATTTT
1 ATATTTTATATT
5112381 ATAT
1 ATAT
5112385 CATATATACG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.29
12 23 0.66
13 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:5116996 original size:64 final size:64
Alignment explanation
Indices: 5116890--5117015 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
5116880 GCAATGAATC
* *
5116890 TCAAATGTAAACTGTCAAAACTGCTATCAGAAACTAGATAAACTAGTTGCAGACAACCTCTATT
1 TCAAATGTAAACTGTCAAAACTGCTATCAGAAACCAGATAAACAAGTTGCAGACAACCTCTATT
*
5116954 TCAAATGTAAACTGTCAAAACTGCTATCAGAAACCAGGTAAACAAGTTGCAGACAACCTCTA
1 TCAAATGTAAACTGTCAAAACTGCTATCAGAAACCAGATAAACAAGTTGCAGACAACCTCTA
5117016 AACTATAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (64 bp):
TCAAATGTAAACTGTCAAAACTGCTATCAGAAACCAGATAAACAAGTTGCAGACAACCTCTATT
Found at i:5118786 original size:6 final size:6
Alignment explanation
Indices: 5118769--5118806 Score: 51
Period size: 7 Copynumber: 6.2 Consensus size: 6
5118759 TTTACGTTGG
5118769 AAATTT -AATTT AAATTT AAATTTT AAATTTT AAATTT A
1 AAATTT AAATTT AAATTT AAA-TTT AAA-TTT AAATTT A
5118807 TTTTGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 12 0.40
7 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:5118824 original size:23 final size:21
Alignment explanation
Indices: 5118798--5118839 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
5118788 ATTTTAAATT
5118798 TTAAATTTATTTTGAAATAAAAA
1 TTAAATTTA-TTT-AAATAAAAA
5118821 TTAAATTTATTTAAATAAA
1 TTAAATTTATTTAAATAAA
5118840 TTTATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAATTTATTTAAATAAAAA
Found at i:5118955 original size:12 final size:12
Alignment explanation
Indices: 5118938--5118978 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
5118928 GAGTCAATTA
5118938 TTAAATTATAAT
1 TTAAATTATAAT
*
5118950 TTAAATAATAA-
1 TTAAATTATAAT
*
5118961 TTAATTTA-AAT
1 TTAAATTATAAT
5118972 TTAAATT
1 TTAAATT
5118979 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
10 2 0.08
11 12 0.50
12 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAAATTATAAT
Found at i:5123644 original size:28 final size:28
Alignment explanation
Indices: 5123613--5123684 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
5123603 ATATAATAAT
* *
5123613 TAATTATAAATATATAATATTTTAAATA
1 TAATTATAAATATATAATAATATAAATA
* * *
5123641 TAATT-TTAATATAAAAATAATATGAATA
1 TAATTATAAATAT-ATAATAATATAAATA
*
5123669 TAA-TATAATTATATAA
1 TAATTATAAATATATAA
5123685 CATGTATAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TAATTATAAATATATAATAATATAAATA
Found at i:5123681 original size:11 final size:11
Alignment explanation
Indices: 5123608--5123681 Score: 54
Period size: 11 Copynumber: 7.3 Consensus size: 11
5123598 AATTTATATA
5123608 ATAAT-TAATT
1 ATAATATAATT
5123618 ATAA-AT-A-T
1 ATAATATAATT
*
5123626 ATAATAT-TTT
1 ATAATATAATT
5123636 A-AATATAATT
1 ATAATATAATT
* **
5123646 TTAATATAAAA
1 ATAATATAATT
5123657 ATAATATGAA-T
1 ATAATAT-AATT
5123668 ATAATATAATT
1 ATAATATAATT
5123679 ATA
1 ATA
5123682 TAACATGTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.10
9 8 0.16
10 11 0.22
11 24 0.48
12 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
ATAATATAATT
Found at i:5124171 original size:19 final size:19
Alignment explanation
Indices: 5124146--5124189 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5124136 AAAAATCATA
5124146 ATTTTTAAATTAAAT-TTT
1 ATTTTTAAATTAAATATTT
*
5124164 ATTATTT-AATTAATTATTT
1 ATT-TTTAAATTAAATATTT
5124183 ATTTTTA
1 ATTTTTA
5124190 TAATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTAAATTAAATATTT
Found at i:5124504 original size:2 final size:2
Alignment explanation
Indices: 5124497--5124564 Score: 82
Period size: 2 Copynumber: 33.5 Consensus size: 2
5124487 ACTACAAAGA
* * * * *
5124497 AT AT AT AT AT AG AT AT AT AT AT AC AT AC ACC AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
5124540 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5124565 CATACACCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:5135081 original size:28 final size:28
Alignment explanation
Indices: 5135048--5135129 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
5135038 TAATAATTTT
*
5135048 ATATTTATTTATTTATATATATTTTAAA
1 ATATTTATATATTTATATATATTTTAAA
* *
5135076 ATATTTATATATTCATAT-TCATTTTATA
1 ATATTTATATATTTATATAT-ATTTTAAA
* *
5135104 TTATTT-TGTATATTATATCATATTTT
1 ATATTTATATAT-TTATAT-ATATTTT
5135130 TATTATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 5 0.11
28 33 0.75
29 5 0.11
30 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (28 bp):
ATATTTATATATTTATATATATTTTAAA
Found at i:5135304 original size:21 final size:22
Alignment explanation
Indices: 5135264--5135305 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5135254 GATTGTTTAA
*
5135264 ATAATTTTTTTAATTTAGTATAT
1 ATAATTTTTTT-ATTCAGTATAT
5135287 ATAATTTTTTT-TTCAGTAT
1 ATAATTTTTTTATTCAGTAT
5135306 GTGTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (22 bp):
ATAATTTTTTTATTCAGTATAT
Found at i:5137581 original size:15 final size:15
Alignment explanation
Indices: 5137558--5137591 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5137548 ACAATTTATG
*
5137558 TTCTTTTTTT-CTTT
1 TTCTTTTTTTCCATT
5137572 TTCTTTTTTTCCATT
1 TTCTTTTTTTCCATT
5137587 TTCTT
1 TTCTT
5137592 CTTAAGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTTTTTCCATT
Found at i:5145757 original size:14 final size:13
Alignment explanation
Indices: 5145732--5145761 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5145722 AAAATTTTAT
5145732 AAATAAATTAATA
1 AAATAAATTAATA
5145745 AAATAATATTAATA
1 AAATAA-ATTAATA
5145759 AAA
1 AAA
5145762 ATTTTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTAATA
Found at i:5146880 original size:2 final size:2
Alignment explanation
Indices: 5146873--5146898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5146863 GTTGTACTAT
5146873 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5146899 CTTATTAAAT
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):
TA
Found at i:5147195 original size:21 final size:21
Alignment explanation
Indices: 5147162--5147203 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5147152 ATTGATGTGT
*
5147162 TTTTTTAAGAATAATATATTA
1 TTTTATAAGAATAATATATTA
* *
5147183 TTTTATAATAATATTATATTA
1 TTTTATAAGAATAATATATTA
5147204 AATATTATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTATAAGAATAATATATTA
Found at i:5147741 original size:27 final size:26
Alignment explanation
Indices: 5147694--5147769 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
5147684 TATAATTATT
*
5147694 TTTAAAATATTTATAATTTATATAAA
1 TTTAAAATATTAATAATTTATATAAA
5147720 TTTAAATATATTAAT-ATATTATATAAA
1 TTTAAA-ATATTAATAAT-TTATATAAA
5147747 TTTTAAAAT-TT-ATACATTTATAT
1 -TTTAAAATATTAATA-ATTTATAT
5147770 CATATTACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
25 2 0.05
26 16 0.36
27 20 0.45
28 6 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAAAATATTAATAATTTATATAAA
Found at i:5148230 original size:2 final size:2
Alignment explanation
Indices: 5148223--5148251 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5148213 AATCAAACTC
5148223 AT 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 AT A
5148252 AAATTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5148279 original size:54 final size:54
Alignment explanation
Indices: 5148197--5148305 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
5148187 ATAAGAAAAG
*
5148197 AAAATTTTTCCTGTCCAATCAAACTCATATATATATATATATATATATATATAT
1 AAAATTTTTCCTGTACAATCAAACTCATATATATATATATATATATATATATAT
*
5148251 AAAATTTTTCCTGTACAATCAACCTCATATATATATATATATATATATATATAT
1 AAAATTTTTCCTGTACAATCAAACTCATATATATATATATATATATATATATAT
5148305 A
1 A
5148306 TATATGGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.42
Consensus pattern (54 bp):
AAAATTTTTCCTGTACAATCAAACTCATATATATATATATATATATATATATAT
Found at i:5148284 original size:2 final size:2
Alignment explanation
Indices: 5148277--5148310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5148267 AATCAACCTC
5148277 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
5148311 GGATTTACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5151797 original size:18 final size:18
Alignment explanation
Indices: 5151774--5151820 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5151764 ATCGTGTGAA
5151774 TATAAATATAATAAAAAT
1 TATAAATATAATAAAAAT
*
5151792 TATAAA-ATATATTAAAAT
1 TATAAATATA-ATAAAAAT
*
5151810 TTTAAATATAA
1 TATAAATATAA
5151821 ATATAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAATATAATAAAAAT
Found at i:5153646 original size:12 final size:12
Alignment explanation
Indices: 5153629--5153653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5153619 TCTACATTAC
5153629 ACACACACACAT
1 ACACACACACAT
5153641 ACACACACACAT
1 ACACACACACAT
5153653 A
1 A
5153654 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:5154227 original size:2 final size:2
Alignment explanation
Indices: 5154220--5154255 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5154210 AAGCAAATGT
5154220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5154256 CATGTTCCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5161829 original size:220 final size:219
Alignment explanation
Indices: 5161427--5161856 Score: 646
Period size: 220 Copynumber: 2.0 Consensus size: 219
5161417 CAAAGGATAC
* * *
5161427 AAAAAAAAGAAGGCAAATAAACTCCTCGTTGCTTTTCCCCTCAAGCCCCAATTTCTATTCCATTT
1 AAAAAAAAAAAGGCAAATAAACTCCTCGTTACTCTTCCCCTCAAGCCCCAATTTCTATTCCATTT
* * *
5161492 GCAATGAAGAAACTTCAAGGTTTTAATTTCCTAAACTTGGGTTAGGATGCAGTTAACAATAAATG
66 GCAATGAAGAAACTTCAAGGTTTGAATTGCCTAAACTTGGGTTAGGATGCAGTTAACAACAAATG
*
5161557 ATCCAGGCATCTATATCTCAGATGCAGCATGTTTCTTTATCCTTTATGAGAATCAAGATATTAAT
131 ATCCAGGCATCTATAACTCAGATGCAGCATGTTTCTTTATCCTTTATGAGAATCAAGATATTAAT
5161622 ATTCAAGAT-TTCAACCGAACAAAA
196 ATTCAA-ATATTCAACCGAACAAAA
* *
5161646 AAAAAAGAAAAAGGCAAATAAACTCCTCTTTACTCTTCCCCTCAAGCCCCAATTTCTTTTCCATT
1 AAAAAA-AAAAAGGCAAATAAACTCCTCGTTACTCTTCCCCTCAAGCCCCAATTTCTATTCCATT
* **
5161711 TGCAATGAAGAAACTTCAAGGTTTGAATTGCCTTAACTTGGGTTAGGATGCAGTTATTAACAAAT
65 TGCAATGAAGAAACTTCAAGGTTTGAATTGCCTAAACTTGGGTTAGGATGCAGTTAACAACAAAT
* ** * * * * * *
5161776 GATCCAGGCATCTTTAACTCATTTGCGGCGTGTTTCTTTATTCTTTGTGAGAATCAAGTTATTAG
130 GATCCAGGCATCTATAACTCAGATGCAGCATGTTTCTTTATCCTTTATGAGAATCAAGATATTAA
5161841 TATTCAAATATTCAAC
195 TATTCAAATATTCAAC
5161857 TGATTTTGAA
Statistics
Matches: 188, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
219 8 0.04
220 180 0.96
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (219 bp):
AAAAAAAAAAAGGCAAATAAACTCCTCGTTACTCTTCCCCTCAAGCCCCAATTTCTATTCCATTT
GCAATGAAGAAACTTCAAGGTTTGAATTGCCTAAACTTGGGTTAGGATGCAGTTAACAACAAATG
ATCCAGGCATCTATAACTCAGATGCAGCATGTTTCTTTATCCTTTATGAGAATCAAGATATTAAT
ATTCAAATATTCAACCGAACAAAA
Found at i:5164187 original size:2 final size:2
Alignment explanation
Indices: 5164182--5164208 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5164172 ACACTTAACT
5164182 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5164209 AACGCTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5164648 original size:22 final size:22
Alignment explanation
Indices: 5164623--5164664 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5164613 AACTTATGAT
*
5164623 TAAAGCTTAAAAAAATAAATTA
1 TAAAACTTAAAAAAATAAATTA
* *
5164645 TAAAACTTAATATAATAAAT
1 TAAAACTTAAAAAAATAAAT
5164665 ATATTTGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAACTTAAAAAAATAAATTA
Found at i:5164695 original size:16 final size:17
Alignment explanation
Indices: 5164674--5164715 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5164664 TATATTTGTA
*
5164674 TTATATTTAT-ATATTT
1 TTATATTTATAAAATTT
5164690 TTATATATTATAAAATTT
1 TTATAT-TTATAAAATTT
*
5164708 ATATATTT
1 TTATATTT
5164716 TTAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 6 0.27
18 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTATAAAATTT
Found at i:5164707 original size:26 final size:26
Alignment explanation
Indices: 5164678--5164737 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
5164668 TTTGTATTAT
5164678 ATTTATATATTTTT-ATATATTATAAA
1 ATTTATATATTTTTAATATATTA-AAA
*
5164704 ATTTATATATTTTTAATATATTAATA
1 ATTTATATATTTTTAATATATTAAAA
5164730 ATTTATAT
1 ATTTATAT
5164738 TATATAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTATATATTTTTAATATATTAAAA
Found at i:5164724 original size:45 final size:42
Alignment explanation
Indices: 5164663--5164745 Score: 103
Period size: 45 Copynumber: 1.9 Consensus size: 42
5164653 AATATAATAA
* * *
5164663 ATATATTTGTATTATATTTATATATTTTTATATATTATAAAATTT
1 ATATATTTGTAATATATTAATA-ATTTATAT-TA-TATAAAATTT
*
5164708 ATATATTTTTAATATATTAATAATTTATATTATATAAA
1 ATATATTTGTAATATATTAATAATTTATATTATATAAA
5164746 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 6 0.18
43 2 0.06
44 7 0.21
45 19 0.56
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (42 bp):
ATATATTTGTAATATATTAATAATTTATATTATATAAAATTT
Found at i:5165467 original size:13 final size:13
Alignment explanation
Indices: 5165449--5165473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5165439 AATGTGCCAT
5165449 AAATAAAATTAAA
1 AAATAAAATTAAA
5165462 AAATAAAATTAA
1 AAATAAAATTAA
5165474 TCTCGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATTAAA
Found at i:5165605 original size:11 final size:11
Alignment explanation
Indices: 5165495--5165612 Score: 52
Period size: 11 Copynumber: 11.0 Consensus size: 11
5165485 TTTATTTTTT
*
5165495 ATTTAAATTAA
1 ATTTAATTTAA
* *
5165506 AATTAAGTTAA
1 ATTTAATTTAA
*
5165517 ATTTAAAATTTAT
1 ATTT--AATTTAA
5165530 A-TT-ATTTAA
1 ATTTAATTTAA
* *
5165539 ATATATATTAAA
1 ATTTA-ATTTAA
* *
5165551 AATTAATATATA
1 ATTTAATTTA-A
5165563 A-TTAATTT-A
1 ATTTAATTTAA
5165572 A-TTAATTTAA
1 ATTTAATTTAA
* *
5165582 A-TTGA-TAAA
1 ATTTAATTTAA
*
5165591 ATTTTATTTAA
1 ATTTAATTTAA
5165602 ATTTAATTTAA
1 ATTTAATTTAA
5165613 TATCGTTTCA
Statistics
Matches: 80, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
9 19 0.24
10 9 0.11
11 34 0.43
12 12 0.15
13 6 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:5167900 original size:16 final size:16
Alignment explanation
Indices: 5167847--5167903 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5167837 AATATGTATA
*
5167847 AATATAAATATTAAAT
1 AATATAAATTTTAAAT
*
5167863 -AT-TAATATTTTAAAAA
1 AATATAA-ATTTT-AAAT
5167879 AATATAAATTTTAAAT
1 AATATAAATTTTAAAT
5167895 AATATAAAT
1 AATATAAAT
5167904 GGTGTTACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 15 0.44
17 7 0.21
18 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAATTTTAAAT
Found at i:5169071 original size:20 final size:21
Alignment explanation
Indices: 5169034--5169073 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
5169024 CGCGCCACTC
*
5169034 TGTTTGTAATTTCCTTTTTTT
1 TGTTTGTAATTTACTTTTTTT
5169055 TGTTT-TAATTTA-TTTTTTT
1 TGTTTGTAATTTACTTTTTTT
5169074 ATTTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (21 bp):
TGTTTGTAATTTACTTTTTTT
Found at i:5169619 original size:3 final size:3
Alignment explanation
Indices: 5169611--5169641 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5169601 TGAAGCTAAG
5169611 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5169642 GTCCATCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5173969 original size:22 final size:21
Alignment explanation
Indices: 5173927--5173970 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5173917 TCCGCTTCAG
*
5173927 TTTCCTCGCTTTCTTTATTGT
1 TTTCCTCCCTTTCTTTATTGT
* *
5173948 TTTCCTCTCCTTTGTTTTTTGT
1 TTTCCTC-CCTTTCTTTATTGT
5173970 T
1 T
5173971 CGTGGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.02, C:0.23, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTCCTCCCTTTCTTTATTGT
Found at i:5174119 original size:15 final size:14
Alignment explanation
Indices: 5174095--5174128 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5174085 TTTTATAAAT
5174095 ATTAAAATAAAAAA
1 ATTAAAATAAAAAA
*
5174109 ATTATAAATAATAAA
1 ATTA-AAATAAAAAA
5174124 ATTAA
1 ATTAA
5174129 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAATAAAAAA
Found at i:5174388 original size:13 final size:13
Alignment explanation
Indices: 5174370--5174394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5174360 GCATTGATTT
5174370 TTAATTTTAATGA
1 TTAATTTTAATGA
5174383 TTAATTTTAATG
1 TTAATTTTAATG
5174395 TAACTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTAATTTTAATGA
Found at i:5174552 original size:30 final size:29
Alignment explanation
Indices: 5174522--5174604 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 29
5174512 ATTTATTTAT
5174522 TTTTAAAATTTATAATATTTAAATTATTA
1 TTTTAAAATTTATAATATTTAAATTATTA
* *
5174551 -TTTAAAA-ATATAATA-TTAAAATATTA
1 TTTTAAAATTTATAATATTTAAATTATTA
*
5174577 TTTTAATATTTATATATATTTATAATTA
1 TTTTAAAATTTATA-ATATTTA-AATTA
5174605 AATTTAAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 10 0.23
27 13 0.30
28 11 0.25
29 3 0.07
30 3 0.07
31 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTTAAAATTTATAATATTTAAATTATTA
Found at i:5174582 original size:13 final size:13
Alignment explanation
Indices: 5174539--5174582 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
5174529 ATTTATAATA
*
5174539 TTTAAATTATTAT
1 TTTAAAATATTAT
* *
5174552 TTAAAAATATAAT
1 TTTAAAATATTAT
*
5174565 ATTAAAATATTAT
1 TTTAAAATATTAT
5174578 TTTAA
1 TTTAA
5174583 TATTTATATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAATATTAT
Found at i:5174593 original size:19 final size:19
Alignment explanation
Indices: 5174559--5174602 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5174549 TATTTAAAAA
5174559 TATAATATTAAAATATTATT
1 TATAATATTAAAATA-TATT
* *
5174579 T-TAATATTTATATATATT
1 TATAATATTAAAATATATT
5174597 TATAAT
1 TATAAT
5174603 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATATTAAAATATATT
Found at i:5176918 original size:26 final size:26
Alignment explanation
Indices: 5176859--5176919 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
5176849 GGATTCACTA
* *
5176859 AGCTTTTGATTTTAATGGAGGCTGAT
1 AGCTTTTTAATTTAATGGAGGCTGAT
5176885 AGCTTTTTAATTTAATGGAGGCTGAT
1 AGCTTTTTAATTTAATGGAGGCTGAT
5176911 AGCTTTTTA
1 AGCTTTTTA
5176920 TTGTTGGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (26 bp):
AGCTTTTTAATTTAATGGAGGCTGAT
Found at i:5178908 original size:23 final size:23
Alignment explanation
Indices: 5178876--5178929 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5178866 TACGATTTAA
* *
5178876 TAATATATAAAATTAT-ATATTAT
1 TAATAAATAAAATCATGATATT-T
5178899 TAATAAATAAAATCATGATATTT
1 TAATAAATAAAATCATGATATTT
*
5178922 TATTAAAT
1 TAATAAAT
5178930 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAAATAAAATCATGATATTT
Found at i:5179795 original size:2 final size:2
Alignment explanation
Indices: 5179790--5179825 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5179780 AAACACACAC
*
5179790 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5179826 GTCTGTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5185058 original size:7 final size:7
Alignment explanation
Indices: 5185046--5185073 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5185036 ATTTAGATTT
5185046 AATTTAA
1 AATTTAA
5185053 AATTTAA
1 AATTTAA
5185060 AATTTAA
1 AATTTAA
5185067 AATTTAA
1 AATTTAA
5185074 TTTAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTTAA
Found at i:5185239 original size:13 final size:13
Alignment explanation
Indices: 5185205--5185241 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
5185195 ATTATATTTG
5185205 AATATAAATAATTA
1 AATATAAA-AATTA
5185219 AAT-T-AAAATTA
1 AATATAAAAATTA
5185230 AATATAAAAATT
1 AATATAAAAATT
5185242 TTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.38
12 3 0.14
13 7 0.33
14 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATAAAAATTA
Found at i:5185277 original size:14 final size:13
Alignment explanation
Indices: 5185254--5185286 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
5185244 ATTTTATTTT
5185254 ATTTAATAAATAA
1 ATTTAATAAATAA
5185267 ATTTAATTAAATAA
1 ATTTAA-TAAATAA
5185281 ATTTAA
1 ATTTAA
5185287 ATTATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAATAAATAA
Found at i:5185301 original size:51 final size:51
Alignment explanation
Indices: 5185208--5185305 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
5185198 ATATTTGAAT
*
5185208 ATAAATAATTAAATTAAAATTAAATATAAAAATTTTATTTTATTTTATTTA
1 ATAAATAATTAAATTAAAATTAAATATAAAAATTTAATTTTATTTTATTTA
* * *
5185259 ATAAATAAATTTAATT-AAA-TAAATTTAAATTATTTAATTTTATTTTA
1 ATAAAT-AATTAAATTAAAATTAAATATAAA-AATTTAATTTTATTTTA
5185306 AATGAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 9 0.22
51 24 0.59
52 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (51 bp):
ATAAATAATTAAATTAAAATTAAATATAAAAATTTAATTTTATTTTATTTA
Found at i:5190186 original size:22 final size:24
Alignment explanation
Indices: 5190155--5190217 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
5190145 ATTAACATTA
5190155 AATATTTAAAAATTATACTAT-TT
1 AATATTTAAAAATTATACTATATT
* *
5190178 ATTA-TTAAAAATTA-ATTATATT
1 AATATTTAAAAATTATACTATATT
5190200 AATATTTAAAATATTATA
1 AATATTTAAAA-ATTATA
5190218 ATAATCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
23 9 0.27
24 4 0.12
25 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTAAAAATTATACTATATT
Found at i:5190278 original size:19 final size:19
Alignment explanation
Indices: 5190263--5190322 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 19
5190253 TATTATTTTA
5190263 TTAATATAATAATATTTAAT
1 TTAA-ATAATAATATTTAAT
* *
5190283 TTAAATAATATTAAATTTTTAT
1 TTAAATAATA--ATA-TTTAAT
*
5190305 TTAAAAAATAATATTTAA
1 TTAAATAATAATATTTAA
5190323 ATCTCTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 10 0.31
20 6 0.19
21 2 0.06
22 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAATAATAATATTTAAT
Found at i:5190284 original size:24 final size:21
Alignment explanation
Indices: 5190239--5190314 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
5190229 AATTTTTAAA
5190239 AAATAAATATAAAATATTATTT
1 AAAT-AATATAAAATATTATTT
* *
5190261 TATTAATATAATAATATTTAATTT
1 AAATAATATAA-AATA-TT-ATTT
* *
5190285 AAATAATATTAAATTTTTATTT
1 AAATAATA-TAAAATATTATTT
*
5190307 AAAAAATA
1 AAATAATA
5190315 ATATTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 7 0.16
22 17 0.40
23 4 0.09
24 12 0.28
25 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAATATAAAATATTATTT
Found at i:5190291 original size:16 final size:16
Alignment explanation
Indices: 5190270--5190300 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5190260 TTATTAATAT
*
5190270 AATAATATTTAATTTA
1 AATAATATTAAATTTA
5190286 AATAATATTAAATTT
1 AATAATATTAAATTT
5190301 TTATTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAATATTAAATTTA
Found at i:5192406 original size:85 final size:85
Alignment explanation
Indices: 5192262--5192419 Score: 280
Period size: 85 Copynumber: 1.9 Consensus size: 85
5192252 CCACATACAA
* *
5192262 ACTGAACCAAATTAACCCAAGCCTTCATATAAGATTTGCAAGACAAACATCTTCTTAACAGAAAG
1 ACTGAACCAAATTAACCCAAGCCTTCATATAAGATTTGCAAGACAAACACCTTCCTAACAGAAAG
5192327 TGCAGATCAGTGTGTATTAC
66 TGCAGATCAGTGTGTATTAC
* *
5192347 ACTGAACCAAATTAACCCAAGCTTTCATATTAGATTTGCAAGACAAACACCTTCCTAACAGAAAG
1 ACTGAACCAAATTAACCCAAGCCTTCATATAAGATTTGCAAGACAAACACCTTCCTAACAGAAAG
5192412 TGCAGATC
66 TGCAGATC
5192420 CATGTATTGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (85 bp):
ACTGAACCAAATTAACCCAAGCCTTCATATAAGATTTGCAAGACAAACACCTTCCTAACAGAAAG
TGCAGATCAGTGTGTATTAC
Found at i:5193439 original size:15 final size:15
Alignment explanation
Indices: 5193390--5193502 Score: 95
Period size: 15 Copynumber: 7.3 Consensus size: 15
5193380 AAATCAGATT
*
5193390 AATTTTAATT-ATTAA
1 AATTTAAATTAATT-A
*
5193405 AATTTAAAATAATTTTA
1 AATTTAAATTAA--TTA
5193422 AATTTAAATTAATTA
1 AATTTAAATTAATTA
* *
5193437 AATTTAAATTATTTT
1 AATTTAAATTAATTA
*
5193452 AATTTAAAATTATTTTA
1 AATTT-AAATTA-ATTA
5193469 AATTTAAATTAATTA
1 AATTTAAATTAATTA
* **
5193484 ATTTTTTATT-ATTA
1 AATTTAAATTAATTA
5193498 AATTT
1 AATTT
5193503 TTTGATGAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 39 0.48
16 13 0.16
17 20 0.24
18 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTAAATTAATTA
Found at i:5193441 original size:47 final size:47
Alignment explanation
Indices: 5193390--5193499 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 47
5193380 AAATCAGATT
5193390 AATTTTAATTATTAAAATTTAAAATAATTTTAAATTTAAATTAATTA
1 AATTTTAATTATTAAAATTTAAAATAATTTTAAATTTAAATTAATTA
* ** *
5193437 AATTTAAATTATTTTAATTTAAAATTATTTTAAATTTAAATTAATTA
1 AATTTTAATTATTAAAATTTAAAATAATTTTAAATTTAAATTAATTA
* *
5193484 ATTTTTTATTATTAAA
1 AATTTTAATTATTAAA
5193500 TTTTTTGATG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (47 bp):
AATTTTAATTATTAAAATTTAAAATAATTTTAAATTTAAATTAATTA
Found at i:5193461 original size:16 final size:17
Alignment explanation
Indices: 5193404--5193476 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 17
5193394 TTAATTATTA
*
5193404 AAATTTAAAATAATTTT
1 AAATTTAAAATTATTTT
*
5193421 AAATTT-AAATTA-ATT
1 AAATTTAAAATTATTTT
5193436 AAATTT-AAATTATTTT
1 AAATTTAAAATTATTTT
5193452 -AATTTAAAATTATTTT
1 AAATTTAAAATTATTTT
5193468 AAATTTAAA
1 AAATTTAAA
5193477 TTAATTAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
15 19 0.38
16 17 0.34
17 14 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTAAAATTATTTT
Found at i:5193477 original size:16 final size:16
Alignment explanation
Indices: 5193390--5193479 Score: 105
Period size: 16 Copynumber: 5.7 Consensus size: 16
5193380 AAATCAGATT
* *
5193390 AATTTTAATTA-TTAA
1 AATTTAAATTATTTTA
*
5193405 AATTTAAAATAATTTTA
1 AATTT-AAATTATTTTA
*
5193422 AATTTAAATTA-ATTA
1 AATTTAAATTATTTTA
5193437 AATTTAAATTATTTT-
1 AATTTAAATTATTTTA
5193452 AATTTAAAATTATTTTA
1 AATTT-AAATTATTTTA
5193469 AATTTAAATTA
1 AATTTAAATTA
5193480 ATTAATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
15 24 0.38
16 27 0.42
17 13 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:5193485 original size:31 final size:29
Alignment explanation
Indices: 5193387--5193571 Score: 104
Period size: 32 Copynumber: 6.0 Consensus size: 29
5193377 ATCAAATCAG
* * *
5193387 ATTAATTTTAATTATTAAAATTTAAAATA
1 ATTAATTTAAATTATTTAAATTTAAATTA
*
5193416 ATTTTAAATTTAAATTAATTAAATTTAAATTA
1 A--TT-AATTTAAATTATTTAAATTTAAATTA
*
5193448 TTTTAATTTAAAATTATTTTAAATTTAAATTA
1 -ATTAATTT-AAATTA-TTTAAATTTAAATTA
** ** *
5193480 ATTAATTTTTTATTA-TTAAATTTTTTGATGAA
1 ATTAA-TTTAAATTATTTAAA--TTTAAAT-TA
* * * * *
5193512 ATCAAATTAAATTAGATTAAAATTTAAGTGA
1 ATTAATTTAAATT--ATTTAAATTTAAATTA
*
5193543 ATTAATTAAAATT-TTTAAATTTAAATTA
1 ATTAATTTAAATTATTTAAATTTAAATTA
5193571 A
1 A
5193572 AATTGTTAGA
Statistics
Matches: 116, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
28 13 0.11
29 6 0.05
30 5 0.04
31 39 0.34
32 48 0.41
33 1 0.01
34 4 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (29 bp):
ATTAATTTAAATTATTTAAATTTAAATTA
Found at i:5193587 original size:20 final size:20
Alignment explanation
Indices: 5193546--5193588 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5193536 TAAGTGAATT
* *
5193546 AATTAAAATTTTTAAATTTA
1 AATTAAAATTGTTAAATATA
*
5193566 AATTAAAATTGTTAGATATA
1 AATTAAAATTGTTAAATATA
5193586 AAT
1 AAT
5193589 AAGGGTAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTAAAATTGTTAAATATA
Found at i:5194106 original size:4 final size:4
Alignment explanation
Indices: 5194092--5194126 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
5194082 TTTTTAAATT
5194092 TTAA TTTAA TTAA TTAA TTAA TGTAA TTAA TTAA T
1 TTAA -TTAA TTAA TTAA TTAA T-TAA TTAA TTAA T
5194127 ATTTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:5194106 original size:9 final size:9
Alignment explanation
Indices: 5194092--5194141 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
5194082 TTTTTAAATT
5194092 TTAATTTAA
1 TTAATTTAA
5194101 TTAA-TTAA
1 TTAATTTAA
*
5194109 TTAATGTAA
1 TTAATTTAA
5194118 TTAA-TTAA
1 TTAATTTAA
5194126 -T-ATTTAA
1 TTAATTTAA
*
5194133 TAAATTTAA
1 TTAATTTAA
5194142 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 11 0.32
9 17 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TTAATTTAA
Found at i:5194118 original size:17 final size:17
Alignment explanation
Indices: 5194092--5194126 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5194082 TTTTTAAATT
*
5194092 TTAATTTAATTAATTAA
1 TTAATGTAATTAATTAA
5194109 TTAATGTAATTAATTAA
1 TTAATGTAATTAATTAA
5194126 T
1 T
5194127 ATTTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTAATGTAATTAATTAA
Found at i:5194124 original size:13 final size:12
Alignment explanation
Indices: 5194092--5194126 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5194082 TTTTTAAATT
5194092 TTAATTTAATTAA
1 TTAA-TTAATTAA
5194105 TTAATTAATGTAA
1 TTAATTAAT-TAA
5194118 TTAATTAAT
1 TTAATTAAT
5194127 ATTTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
TTAATTAATTAA
Found at i:5194153 original size:28 final size:27
Alignment explanation
Indices: 5194084--5194159 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
5194074 GATAGTAATT
* *
5194084 TTTAAATTTTAATTTAATTAATTAATTAA
1 TTTAAA-TTTAATTTAA-TATTTAATAAA
*
5194113 TGT-AA-TTAA-TTAATATTTAATAAA
1 TTTAAATTTAATTTAATATTTAATAAA
5194137 TTTAAATTTAAATTTAATATTTA
1 TTTAAATTT-AATTTAATATTTA
5194160 TAATAAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 11 0.28
25 6 0.15
26 6 0.15
27 2 0.05
28 12 0.31
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TTTAAATTTAATTTAATATTTAATAAA
Found at i:5194217 original size:20 final size:19
Alignment explanation
Indices: 5194189--5194229 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5194179 ATGTAATTTT
5194189 AAAATTAATAAAATAATAA
1 AAAATTAATAAAATAATAA
**
5194208 AAAATATAATAATGTAATAA
1 AAAAT-TAATAAAATAATAA
5194228 AA
1 AA
5194230 TTTTAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATTAATAAAATAATAA
Found at i:5198565 original size:50 final size:50
Alignment explanation
Indices: 5198439--5198671 Score: 342
Period size: 50 Copynumber: 4.6 Consensus size: 50
5198429 ATGGCCACAT
** *
5198439 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGACCACCTCTCTCTA
*
5198489 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTAT-AGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGA-CCACCTCTCTCTA
* *
5198540 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGACCATCTCTTTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGACCACCTCTCTCTA
* * *
5198590 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGATCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGACCACCTCTCTCTA
* *
5198640 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
5198672 GGCAACAACT
Statistics
Matches: 166, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
50 120 0.72
51 46 0.28
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGACCACCTCTCTCTA
Found at i:5203234 original size:50 final size:50
Alignment explanation
Indices: 5203083--5203301 Score: 294
Period size: 50 Copynumber: 4.4 Consensus size: 50
5203073 ATGGCCACAT
* *
5203083 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCATCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCTA
* * * * * *
5203133 TTTGTCAAAAGTTGGTGAAGAATTGTTAACAATTATGGCCAACTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCTA
* *
5203184 TTGTCAAAGGTTGGTGAAGAATCGTCAATAATAATGGTCACCTCTTTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCTA
* * *
5203234 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGATCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCTA
* *
5203284 TTGTTAAAGGTTGTTGAA
1 TTGTCAAAGGTTGGTGAA
5203302 AGATAGTCTA
Statistics
Matches: 146, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 103 0.71
51 43 0.29
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCTA
Found at i:5205314 original size:2 final size:2
Alignment explanation
Indices: 5205302--5205364 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
5205292 CAACCTCAAC
* * * * *
5205302 TA TA AA TA TA TA TA TA CA TA TA TA TA TA TA TA CA TA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5205344 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5205365 GTAATCAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5210633 original size:19 final size:17
Alignment explanation
Indices: 5210611--5210664 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
5210601 TAAAAAAATT
5210611 TAAATATTATAAATTAA
1 TAAATATTATAAATTAA
* *
5210628 TGTAAAGATTAAAAATTAA
1 --TAAATATTATAAATTAA
*
5210647 TAAATTATTATTAATTAA
1 TAAA-TATTATAAATTAA
5210665 ATTCAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 15 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATATTATAAATTAA
Found at i:5212257 original size:17 final size:17
Alignment explanation
Indices: 5212235--5212267 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5212225 ATTAGAAACG
5212235 AAATAAATAAAATATAA
1 AAATAAATAAAATATAA
*
5212252 AAATAATTAAAATATA
1 AAATAAATAAAATATA
5212268 TTATAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAATAAAATATAA
Found at i:5212276 original size:27 final size:26
Alignment explanation
Indices: 5212244--5212302 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
5212234 GAAATAAATA
5212244 AAATATAAAAATAAT-TAAAATATATT
1 AAATATAAAAATAATATAAAATAT-TT
*
5212270 ATAATATAAAGATAATATAAAATATTT
1 A-AATATAAAAATAATATAAAATATTT
5212297 AAATAT
1 AAATAT
5212303 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 6 0.20
27 16 0.53
28 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATATAAAAATAATATAAAATATTT
Found at i:5212301 original size:45 final size:45
Alignment explanation
Indices: 5212237--5212323 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
5212227 TAGAAACGAA
5212237 ATAAATAAAATATAAAAATA-ATTAAAATATAT-TATAATATAAAG
1 ATAAATAAAATATAAAAATATATTAAAATATATATA-AATATAAAG
** * *
5212281 ATAATATAAAATATTTAAATATTTTAAAATTTATATAAATATA
1 ATAA-ATAAAATATAAAAATATATTAAAATATATATAAATATA
5212324 TAATATCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 4 0.11
45 14 0.39
46 16 0.44
47 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (45 bp):
ATAAATAAAATATAAAAATATATTAAAATATATATAAATATAAAG
Found at i:5212465 original size:17 final size:16
Alignment explanation
Indices: 5212436--5212472 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5212426 TTTTGTTCAA
*
5212436 TTTAAAATAATATTTT
1 TTTAAAATAATATATT
5212452 TTTAAAAGTAATATATT
1 TTTAAAA-TAATATATT
5212469 TTTA
1 TTTA
5212473 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAAATAATATATT
Found at i:5213403 original size:30 final size:31
Alignment explanation
Indices: 5213367--5213445 Score: 81
Period size: 34 Copynumber: 2.5 Consensus size: 31
5213357 GAATAATATT
*
5213367 TTTAATTAAAATAATAT-ATTTTTATTTAAA
1 TTTAATTAAAATAATATAATTTTTATATAAA
* **
5213397 TTTAATTATAAAATAAAAATAATTTTTATATACT
1 TTTAA-T-TAAAAT-AATATAATTTTTATATAAA
5213431 TTTAA-TAAAATAATA
1 TTTAATTAAAATAATA
5213446 GTGATTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
30 8 0.20
31 7 0.17
32 6 0.15
33 4 0.10
34 15 0.38
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTAATTAAAATAATATAATTTTTATATAAA
Found at i:5213735 original size:2 final size:2
Alignment explanation
Indices: 5213728--5213760 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5213718 AGACTCCAAT
5213728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5213761 TCTAGAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5215953 original size:25 final size:26
Alignment explanation
Indices: 5215902--5215953 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
5215892 TTGATTTAAA
*
5215902 TTAATATTTAATAATAAAAATTTTAT
1 TTAATATTTAATAATAAAAATTATAT
*
5215928 TTAA-ATTTAATTAT-AAAATATATAT
1 TTAATATTTAATAATAAAAAT-TATAT
5215953 T
1 T
5215954 AACAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 14 0.61
26 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATATTTAATAATAAAAATTATAT
Found at i:5216812 original size:17 final size:17
Alignment explanation
Indices: 5216769--5216806 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5216759 GTGGAAAGGC
* *
5216769 CAAAACTTATCTACATT
1 CAAAACTTTTCTACAAT
5216786 CAAAACTTTTCTACAAT
1 CAAAACTTTTCTACAAT
5216803 CAAA
1 CAAA
5216807 CATTTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (17 bp):
CAAAACTTTTCTACAAT
Found at i:5218059 original size:5 final size:5
Alignment explanation
Indices: 5218051--5218123 Score: 55
Period size: 5 Copynumber: 14.8 Consensus size: 5
5218041 TATCGACATG
* * *
5218051 AATAT AATAT AATA- AAAAT AATA- AAAAT AAATAT AATAT AAAATT AATATT
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATA-T AATA-T
*
5218102 AATAT AA-AT TAT-T AATAT AATA
1 AATAT AATAT AATAT AATAT AATA
5218124 ATATTTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 12 0.22
5 28 0.52
6 14 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:5218091 original size:17 final size:17
Alignment explanation
Indices: 5218071--5218123 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
5218061 AATAAAAATA
*
5218071 ATAAAAATAAATATAAT
1 ATAAAAATTAATATAAT
5218088 AT-AAAATTAATATTAAT
1 ATAAAAATTAATA-TAAT
*
5218105 ATAAATTATTAATATAAT
1 ATAAA-AATTAATATAAT
5218123 A
1 A
5218124 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 7 0.23
19 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATTAATATAAT
Done.