Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 158 of 168
Found at i:47219912 original size:21 final size:23
Alignment explanation
Indices: 47219888--47219931 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
47219878 AAATACTTTT
*
47219888 TAAATTTTT-TTATTT-TTAAAA
1 TAAATTTTTGGTATTTATTAAAA
47219909 TAAATTTTTGGTATTTATTAAAA
1 TAAATTTTTGGTATTTATTAAAA
47219932 AATGGGCCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TAAATTTTTGGTATTTATTAAAA
Found at i:47219917 original size:22 final size:22
Alignment explanation
Indices: 47219888--47219931 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
47219878 AAATACTTTT
**
47219888 TAAATTTTTTTATTT-TTAAAA
1 TAAATTTTGGTATTTATTAAAA
47219909 TAAATTTTTGGTATTTATTAAAA
1 TAAA-TTTTGGTATTTATTAAAA
47219932 AATGGGCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TAAATTTTGGTATTTATTAAAA
Found at i:47221494 original size:5 final size:5
Alignment explanation
Indices: 47221484--47221509 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47221474 TGAGCATTCG
47221484 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
47221510 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:47225415 original size:18 final size:18
Alignment explanation
Indices: 47225388--47225423 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47225378 ATCAAAGTTT
* *
47225388 TATTTTAATGTTTTTATA
1 TATTTCAATGTTGTTATA
47225406 TATTTCAATGTTGTTATA
1 TATTTCAATGTTGTTATA
47225424 CATATTGTTT
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:0.03, G:0.08, T:0.61
Consensus pattern (18 bp):
TATTTCAATGTTGTTATA
Found at i:47232060 original size:3 final size:3
Alignment explanation
Indices: 47232052--47232089 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47232042 AAGTAGGTGC
47232052 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47232090 GCATATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47232223 original size:32 final size:32
Alignment explanation
Indices: 47232163--47232225 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
47232153 ATTAATCAGT
* *
47232163 ATGAATTATAAAATTAAATTAATTAATTTATC
1 ATGAATTATAAAATTAAAGTAATCAATTTATC
* * *
47232195 ATGAGTTATTAAATTCAAGTAATCAATTTAT
1 ATGAATTATAAAATTAAAGTAATCAATTTAT
47232226 AAATTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (32 bp):
ATGAATTATAAAATTAAAGTAATCAATTTATC
Found at i:47233090 original size:102 final size:101
Alignment explanation
Indices: 47232952--47233148 Score: 288
Period size: 102 Copynumber: 1.9 Consensus size: 101
47232942 AAAATTAATG
* *
47232952 AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAGTTTTAATAATATGGATAAT
1 AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAATTGTAATAATATGGATAAT
* *
47233017 TTATATTTCATTAGTTATTAAAATTAAATTTTAAAA
66 TGATATTTCATTAATTATTAAAATTAAATTTTAAAA
* * * *
47233053 AAAAATATTATTGAATAATAGAGTTTTATTTGA-ATTTTGTATTCAAATTGTAATAATATTGATA
1 AAAAATATTATTGAA-AATAGAATCTTATTT-ATATTTTATATTCAAATTGTAATAATATGGATA
*
47233117 ATTGATATTTCGTTAATTATTAAAATTAAATT
64 ATTGATATTTCATTAATTATTAAAATTAAATT
47233149 CATATTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 15 0.18
102 69 0.81
103 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (101 bp):
AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAATTGTAATAATATGGATAAT
TGATATTTCATTAATTATTAAAATTAAATTTTAAAA
Found at i:47233707 original size:12 final size:11
Alignment explanation
Indices: 47233676--47233763 Score: 62
Period size: 11 Copynumber: 8.4 Consensus size: 11
47233666 ATTTTTTTAA
47233676 TTTTAAAATAC
1 TTTTAAAATAC
47233687 TTTTAAAATAC
1 TTTTAAAATAC
*
47233698 TTTTTTAAAT--
1 -TTTTAAAATAC
*
47233708 TTTT----TAA
1 TTTTAAAATAC
*
47233715 TTTTAAAATAT
1 TTTTAAAATAC
47233726 TTTTAAAATAC
1 TTTTAAAATAC
**
47233737 TTTGTAAAATTT
1 TTT-TAAAATAC
*
47233749 TTTTAAAATAA
1 TTTTAAAATAC
47233760 TTTT
1 TTTT
47233764 TTTTAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
5 1 0.02
7 4 0.06
9 4 0.06
11 36 0.58
12 17 0.27
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:47233713 original size:39 final size:39
Alignment explanation
Indices: 47233659--47233751 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
47233649 AATATTTTAT
* *
47233659 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAAATTTTTTAATTTTAAAATACTTTTAAAATAC
*
47233698 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTTTAATTTTAAAATACTTTTAAAATAC
* *
47233737 TTTGTAAAATTTTTT
1 TTTTTTAAATTTTTT
47233752 TAAAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (39 bp):
TTTTTTAAATTTTTTAATTTTAAAATACTTTTAAAATAC
Found at i:47233785 original size:11 final size:11
Alignment explanation
Indices: 47233712--47233785 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
47233702 TTAAATTTTT
47233712 TAATTTTAAAA
1 TAATTTTAAAA
*
47233723 TATTTTTAAAA
1 TAATTTTAAAA
*
47233734 TACTTTGTAAAA
1 TAATTT-TAAAA
**
47233746 TTTTTTTAAAA
1 TAATTTTAAAA
***
47233757 TAATTTT-TTT
1 TAATTTTAAAA
47233767 TAATTTTTAAAA
1 TAA-TTTTAAAA
47233779 TAATTTT
1 TAATTTT
47233786 TGGTATTTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
10 3 0.06
11 33 0.69
12 12 0.25
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:47233798 original size:23 final size:22
Alignment explanation
Indices: 47233747--47233801 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
47233737 TTTGTAAAAT
**
47233747 TTTTTTAAAATAATTTTTTTTA
1 TTTTTTAAAATAATTTTTGGTA
*
47233769 ATTTTTAAAATAATTTTTGGTA
1 TTTTTTAAAATAATTTTTGGTA
47233791 TTTATTTAAAA
1 TTT-TTTAAAA
47233802 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTTTAAAATAATTTTTGGTA
Found at i:47235484 original size:16 final size:16
Alignment explanation
Indices: 47235463--47235495 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47235453 TTATATTATT
*
47235463 TTATTTAATTTTAAAA
1 TTATTTAATATTAAAA
47235479 TTATTTAATATTAAAA
1 TTATTTAATATTAAAA
47235495 T
1 T
47235496 AATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAATATTAAAA
Found at i:47243053 original size:17 final size:17
Alignment explanation
Indices: 47243031--47243064 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47243021 AAAAAGTATT
* *
47243031 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
47243048 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
47243065 AGTATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:47243076 original size:41 final size:41
Alignment explanation
Indices: 47242994--47243137 Score: 195
Period size: 40 Copynumber: 3.5 Consensus size: 41
47242984 AATAAAAATT
47242994 TATTTTAAAAATTAAAATAAAATTTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAATTT-AAAAAAGTATTTTAAAAA
47243038 TATTTTAAAATTAAAAAAAATTT-AAAAAGTATTTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTTAAAAAAGTA-TTTTAAAAA
* * *
47243079 -AATTTAAAATT-TAAAAAATTTAATAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTTAA-AAAAGTATTTTAAAAA
47243119 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
47243138 TAAAAAATAA
Statistics
Matches: 90, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
39 9 0.10
40 27 0.30
41 26 0.29
42 12 0.13
43 10 0.11
44 6 0.07
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAAGTATTTTAAAAA
Found at i:47245179 original size:2 final size:2
Alignment explanation
Indices: 47245172--47245207 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
47245162 GGTGGGCTGC
*
47245172 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47245208 ACTAGTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47252274 original size:20 final size:20
Alignment explanation
Indices: 47252249--47252287 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47252239 TAGTACAAAA
47252249 TTTTAATATTTTAAATTAAT
1 TTTTAATATTTTAAATTAAT
* *
47252269 TTTTAATTTTTTATATTAA
1 TTTTAATATTTTAAATTAA
47252288 AAACTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATATTTTAAATTAAT
Found at i:47261398 original size:158 final size:156
Alignment explanation
Indices: 47261105--47261403 Score: 411
Period size: 158 Copynumber: 1.9 Consensus size: 156
47261095 CAACCGTGGC
* * *
47261105 ACTCTAGCAGAACTAGAAAAACGAGCCCGTACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
1 ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
* *
47261170 CAATGGAGACCGAGTACGAGACTGCCTTGTTGACCCTCTCTGCATAAGCAAAGAATAATGTTACA
66 CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCATAAGCAAAGAATAA--TTACA
47261235 GGAGGAACTTAAATTCTAAAGGAAAGGG
129 GGAGGAACTTAAATTCTAAAGGAAAGGG
* * *
47261263 ACTCCAGCAGAAGTAGGAGAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
1 ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
* * * * **
47261328 CACTGAAGACTGAGTACGGGATTGCCGTGTTGGGCCTCTCTGCATTAGAAGCAAAGAATAA-TAC
66 CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCA-T--AAGCAAAGAATAATTAC
*
47261392 ATGAGGAACTTA
128 AGGAGGAACTTA
47261404 TACAAATTCA
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
158 109 0.89
159 1 0.01
161 13 0.11
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (156 bp):
ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCATAAGCAAAGAATAATTACAGG
AGGAACTTAAATTCTAAAGGAAAGGG
Found at i:47266041 original size:13 final size:13
Alignment explanation
Indices: 47266023--47266048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47266013 TCACCCATGT
47266023 GACGTTTATTATA
1 GACGTTTATTATA
47266036 GACGTTTATTATA
1 GACGTTTATTATA
47266049 AACTGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GACGTTTATTATA
Found at i:47293919 original size:15 final size:15
Alignment explanation
Indices: 47293899--47293932 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47293889 CATGTTTATT
47293899 TTTTTTAA-ATATTTA
1 TTTTTTAATAT-TTTA
47293914 TTTTTTAATATTTTA
1 TTTTTTAATATTTTA
47293929 TTTT
1 TTTT
47293933 ACCCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAATATTTTA
Found at i:47293923 original size:14 final size:14
Alignment explanation
Indices: 47293895--47293932 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
47293885 TTGTCATGTT
47293895 TATTT-TTTTTAAA
1 TATTTATTTTTAAA
*
47293908 TATTTATTTTTTAA
1 TATTTATTTTTAAA
47293922 TATTTTATTTT
1 TA-TTTATTTT
47293933 ACCCTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTATTTTTAAA
Found at i:47295148 original size:20 final size:20
Alignment explanation
Indices: 47295102--47295141 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
47295092 TGTTTTTGAA
*
47295102 TTTTTATGAACTTTTTAATT
1 TTTTTTTGAACTTTTTAATT
47295122 TTTTTTTGAA-TTTTT-ATT
1 TTTTTTTGAACTTTTTAATT
47295140 TT
1 TT
47295142 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 9 0.47
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTGAACTTTTTAATT
Found at i:47295149 original size:12 final size:12
Alignment explanation
Indices: 47295114--47295149 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
47295104 TTTATGAACT
47295114 TTTTAATTTTT-
1 TTTTAATTTTTA
47295125 TTTTGAATTTTTA
1 TTTT-AATTTTTA
47295138 TTTTAATTTTTA
1 TTTTAATTTTTA
47295150 AAATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 15 0.65
13 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:47299996 original size:25 final size:25
Alignment explanation
Indices: 47299947--47299996 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
47299937 TTGGCTATAA
* *
47299947 TGTCCAATTTGGTACTTGAATTTTG
1 TGTCCAATTTGGTACCTGAAGTTTG
47299972 TGTCTCAATTTGGTACCTG-AGTTTG
1 TGTC-CAATTTGGTACCTGAAGTTTG
47299997 GATTCATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (25 bp):
TGTCCAATTTGGTACCTGAAGTTTG
Found at i:47307698 original size:58 final size:58
Alignment explanation
Indices: 47307605--47307797 Score: 235
Period size: 58 Copynumber: 3.2 Consensus size: 58
47307595 ACTTCTGATC
* * * * *
47307605 AGTGACAAGTGATAAGTGGTAGTTTTAGTTGCACTTATCTGATCAGTGACAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
*
47307663 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACAAGTGGCAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTG---A----CAAGTGACA
* *
47307728 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATATGATCAGTGACAAGAGATA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
*
47307785 AATGATAAGTGAT
1 AGTGATAAGTGAT
47307798 TCCATGTAAG
Statistics
Matches: 119, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
57 19 0.16
58 43 0.36
61 2 0.02
64 23 0.19
65 32 0.27
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (58 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
Found at i:47307722 original size:7 final size:7
Alignment explanation
Indices: 47307707--47307745 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
47307697 TTATTTGATC
47307707 AGTGACA
1 AGTGACA
*
47307714 AGTGGCA
1 AGTGACA
47307721 AGTGACA
1 AGTGACA
*
47307728 AGTGATA
1 AGTGACA
*
47307735 AGTGATA
1 AGTGACA
47307742 AGTG
1 AGTG
47307746 GTAGCTTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (7 bp):
AGTGACA
Found at i:47307730 original size:65 final size:64
Alignment explanation
Indices: 47307649--47307797 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
47307639 TTATCTGATC
*
47307649 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATATGATCAGTGACA
*
47307714 AGTGGCAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
* * * *
47307778 AGAGATAAATGATAAGTGAT
1 AGTGACAAGTGACAAGTGAT
47307798 TCCATGTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 41 0.53
65 36 0.47
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (64 bp):
AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
Found at i:47310341 original size:3 final size:3
Alignment explanation
Indices: 47310329--47310365 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
47310319 AGTCCCTCTA
47310329 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47310366 GTTAATTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47313883 original size:14 final size:14
Alignment explanation
Indices: 47313866--47313900 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
47313856 ATAAAATATA
*
47313866 AATTTATATTTAAT
1 AATTCATATTTAAT
*
47313880 AATTCATTTTTAAT
1 AATTCATATTTAAT
47313894 AATTCAT
1 AATTCAT
47313901 TAATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTCATATTTAAT
Found at i:47313901 original size:14 final size:14
Alignment explanation
Indices: 47313874--47313901 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47313864 TAAATTTATA
47313874 TTTAATAATTCATT
1 TTTAATAATTCATT
47313888 TTTAATAATTCATT
1 TTTAATAATTCATT
47313902 AATTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:47319478 original size:41 final size:39
Alignment explanation
Indices: 47319426--47319517 Score: 139
Period size: 41 Copynumber: 2.3 Consensus size: 39
47319416 ATATTTTTTA
47319426 TTTTTTTATTTTTTAAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTATTTTTTAAATTTTAAAATACTTTTAAAATAC
* *
47319465 TTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTT--ATTTTTTAAATTTTAAAATACTTTTAAAATAC
*
47319506 TTTTTTAATTTT
1 TTTTTTTATTTT
47319518 AAAATACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
39 12 0.25
41 36 0.75
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTTATTTTTTAAATTTTAAAATACTTTTAAAATAC
Found at i:47319488 original size:30 final size:30
Alignment explanation
Indices: 47319454--47319557 Score: 122
Period size: 30 Copynumber: 3.3 Consensus size: 30
47319444 TTTAAAATAC
47319454 TTTTAAAATACTTTTTTTAAATTTTTTTAA
1 TTTTAAAATACTTTTTTTAAATTTTTTTAA
*
47319484 TTTTAAAATA--TTTTTAAAATACTTTTTTAA
1 TTTTAAAATACTTTTTTTAAAT--TTTTTTAA
*
47319514 TTTTAAAATACTTTTTTTTAATTTTTGTTTTAA
1 TTTTAAAATAC-TTTTTTTAA-ATTT-TTTTAA
47319547 TTTTTAAAATA
1 -TTTTAAAATA
47319558 AATTTTTGGT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
28 9 0.14
30 28 0.44
32 2 0.03
33 13 0.21
34 11 0.17
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTAAAATACTTTTTTTAAATTTTTTTAA
Found at i:47319492 original size:17 final size:17
Alignment explanation
Indices: 47319467--47319500 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47319457 TAAAATACTT
* *
47319467 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
47319484 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
47319501 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:47319496 original size:19 final size:20
Alignment explanation
Indices: 47319495--47319538 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
47319485 TTTAAAATAT
47319495 TTTTAAAATA-CTTTTTTAA
1 TTTTAAAATACCTTTTTTAA
*
47319514 TTTTAAAATACTTTTTTTTAA
1 TTTTAAAATAC-CTTTTTTAA
47319535 TTTT
1 TTTT
47319539 TGTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATACCTTTTTTAA
Found at i:47319528 original size:11 final size:11
Alignment explanation
Indices: 47319443--47319468 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47319433 ATTTTTTAAA
47319443 TTTTAAAATAC
1 TTTTAAAATAC
47319454 TTTTAAAATAC
1 TTTTAAAATAC
47319465 TTTT
1 TTTT
47319469 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:47320249 original size:6 final size:6
Alignment explanation
Indices: 47320238--47320270 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
47320228 TTAAGGATAT
47320238 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
47320271 GGTTGATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:47323411 original size:21 final size:21
Alignment explanation
Indices: 47323385--47323425 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47323375 TAGCAAGATT
47323385 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCAAGTTAACTA
* *
47323406 GCTGATGTTGCCAGTTAACT
1 GCTGATGTGGCAAGTTAACT
47323426 TGCCACATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTA
Found at i:47324386 original size:49 final size:49
Alignment explanation
Indices: 47324333--47324426 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
47324323 CCTAATTGAT
*
47324333 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAGGGGAAATTGAAATTG
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
*
47324382 ATTTCCTCCATGAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
47324427 GTTTAATAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (49 bp):
ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
Found at i:47333983 original size:23 final size:23
Alignment explanation
Indices: 47333956--47334006 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
47333946 GGTTAATTAT
* *
47333956 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
47333979 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
47334002 AGTAA
1 TGTAA
47334007 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:47337317 original size:22 final size:22
Alignment explanation
Indices: 47337289--47337366 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
47337279 ATATGTGAAA
47337289 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
47337311 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
47337333 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
47337355 CATGAGAGCTTA
1 CATGAGAGCTTA
47337367 TATTTATATC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:47339471 original size:18 final size:18
Alignment explanation
Indices: 47339426--47339472 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
47339416 CCATGTGGAC
* *
47339426 CGCCCGTCTAGGGGCACA
1 CGCCCGTATGGGGGCACA
47339444 CGCCCGTATGGGGGCACA
1 CGCCCGTATGGGGGCACA
*
47339462 TGCCCGTATGG
1 CGCCCGTATGG
47339473 TCACGAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.34, G:0.36, T:0.15
Consensus pattern (18 bp):
CGCCCGTATGGGGGCACA
Found at i:47340969 original size:21 final size:21
Alignment explanation
Indices: 47340943--47341092 Score: 104
Period size: 21 Copynumber: 7.1 Consensus size: 21
47340933 CCGAAGGCTG
*
47340943 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
47340964 AACAGAAACCCGTAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
47340985 AACGGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
47341006 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
47341027 AACAGAAGCTCAAAATAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
47341048 AACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
47341069 AACAGAAGCTCATGAA-AGCTA
1 AACAGAAGCTCAT-AAGAGCTA
47341090 AAC
1 AAC
47341093 GAAAAGTAAA
Statistics
Matches: 91, Mismatches: 37, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
21 90 0.99
22 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:47340994 original size:42 final size:42
Alignment explanation
Indices: 47340943--47341096 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
47340933 CCGAAGGCTG
* *
47340943 AACAGAAGCTCATGAGAGCTAAACAGAAACCCGTAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
* * *
47340985 AACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
* * * * * * *
47341027 AACAGAAGCTCAAAATAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
47341069 AACAGAAGCTCATGAA-AGCTAAAC-GAAA
1 AACAGAAGCTCAT-AAGAGCTAAACAGAAA
47341097 AGTAAACACG
Statistics
Matches: 96, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 4 0.04
42 90 0.94
43 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
Found at i:47344899 original size:56 final size:56
Alignment explanation
Indices: 47344832--47344944 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
47344822 AGGAATTGAG
* * *
47344832 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTTTGGATTAGGGTTTGGTAAGCT
1 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
47344888 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
1 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
47344944 C
1 C
47344945 ACCTTATTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (56 bp):
CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
Found at i:47352372 original size:25 final size:25
Alignment explanation
Indices: 47352344--47352417 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
47352334 CGAGCATGTA
47352344 AACGGGAAGCTCTTTCGAGCCATAT
1 AACGGGAAGCTCTTTCGAGCCATAT
** * *
47352369 AACGAAAAGCTCATGT-GAGCTATAT
1 AACGGGAAGCTC-TTTCGAGCCATAT
* *
47352394 AACGGGAAGCTCATGCGAGCCATA
1 AACGGGAAGCTCTTTCGAGCCATA
47352418 AATTAGGAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCTTTCGAGCCATAT
Found at i:47358243 original size:7 final size:7
Alignment explanation
Indices: 47358231--47358264 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
47358221 ATAATAAAAA
47358231 TATATTT
1 TATATTT
47358238 TATA-TT
1 TATATTT
*
47358244 GATATTT
1 TATATTT
47358251 TATATTT
1 TATATTT
47358258 TATATTT
1 TATATTT
47358265 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:47358265 original size:13 final size:14
Alignment explanation
Indices: 47358231--47358264 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
47358221 ATAATAAAAA
47358231 TATATTTTATA-TT
1 TATATTTTATATTT
*
47358244 GATATTTTATATTT
1 TATATTTTATATTT
47358258 TATATTT
1 TATATTT
47358265 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATATTTTATATTT
Found at i:47360914 original size:22 final size:22
Alignment explanation
Indices: 47360883--47360949 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
47360873 TAAAATTAAC
*
47360883 AATAATAAATAGTAATAATAGT
1 AATAATAAATAGTAATAATAAT
* **
47360905 AATAAAAAATAACAATAATAAT
1 AATAATAAATAGTAATAATAAT
*
47360927 AATAATAAAT-GTAATGATAAT
1 AATAATAAATAGTAATAATAAT
47360948 AA
1 AA
47360950 CATTCAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 10 0.27
22 27 0.73
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (22 bp):
AATAATAAATAGTAATAATAAT
Found at i:47360921 original size:19 final size:19
Alignment explanation
Indices: 47360883--47360928 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
47360873 TAAAATTAAC
* * *
47360883 AATAATAAATAGTAATAAT
1 AATAATAAAAAATAACAAT
*
47360902 AGTAATAAAAAATAACAAT
1 AATAATAAAAAATAACAAT
47360921 AATAATAA
1 AATAATAA
47360929 TAATAAATGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AATAATAAAAAATAACAAT
Found at i:47360949 original size:3 final size:3
Alignment explanation
Indices: 47360883--47360934 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
47360873 TAAAATTAAC
* * *
47360883 AAT AAT AAAT AGT AAT AAT AGT AAT AA- AA- AAT AAC AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47360927 AAT AAT AA
1 AAT AAT AA
47360935 ATGTAATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:47362632 original size:44 final size:44
Alignment explanation
Indices: 47362561--47363111 Score: 373
Period size: 44 Copynumber: 12.7 Consensus size: 44
47362551 AACTAATACG
* * * * *
47362561 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTTTTACTTCA
** * **
47362605 ATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTA-CTTCA
* * * * *
47362649 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-C-CTGA-TACG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTACTTCA
* * * * * *
47362690 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTTTTACTTCA
** * **
47362734 ATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTA-CTTCA
* * * * *
47362778 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-C-CTGA-TACG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTACTTCA
* * * * * *
47362819 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTTTTACTTCA
* * * *
47362863 ATCCGCTCCACTGTAATCTCAGGAAGATAGGAT-TTCTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTA-CTTCA
* **
47362907 ATCTGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTA-CTTCA
* * * *
47362951 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTACTTCA
* * * * * *
47362992 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTTTTACTTCA
* * * *
47363036 ATCCGCTCCACTGTAATCTCAGGAAGATAGGAT-TTCTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTA-CTTCA
47363080 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA
47363112 CCTGATGCGA
Statistics
Matches: 391, Mismatches: 93, Indels: 46
0.74 0.18 0.09
Matches are distributed among these distances:
40 3 0.01
41 85 0.22
42 3 0.01
43 20 0.05
44 276 0.71
45 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTTACTTCA
Found at i:47362695 original size:129 final size:129
Alignment explanation
Indices: 47362540--47362935 Score: 720
Period size: 129 Copynumber: 3.1 Consensus size: 129
47362530 ACTACTGCTT
* * *
47362540 AGGGAGATAAGAACTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
47362605 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
66 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
47362669 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
47362734 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
66 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
*
47362798 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
* * * *
47362863 ATCCGCTCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAATCTC
66 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
47362927 AGGGAGATA
1 AGGGAGATA
47362936 GGATTACTAG
Statistics
Matches: 259, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 259 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (129 bp):
AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
Found at i:47362878 original size:173 final size:173
Alignment explanation
Indices: 47362739--47363108 Score: 722
Period size: 173 Copynumber: 2.1 Consensus size: 173
47362729 TTTTAATCCA
*
47362739 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
47362804 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
66 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
47362869 TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
131 TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
47362912 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
*
47362977 ATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
66 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
47363042 TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
131 TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
47363085 CTCCACTGTAATCTCAGGGAGATA
1 CTCCACTGTAATCTCAGGGAGATA
47363109 AGACCTGATG
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 195 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (173 bp):
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
Found at i:47363005 original size:129 final size:128
Alignment explanation
Indices: 47362540--47363132 Score: 549
Period size: 129 Copynumber: 4.6 Consensus size: 128
47362530 ACTACTGCTT
* * * * * * **
47362540 AGGGAGATAAGAACTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTA
1 AGGGAGATAAGACCTGATACAATCTACTCCACTGTAACTTCAGAGAGATAAGATC-CTGATTGCA
* *
47362605 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
65 ATCCACTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTC
* * * * **
47362669 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
1 AGGGAGATAAGACCTGATACAATCTACTCCACTGTAACTTCAGAGAGATAAGATC-CTGATTGCA
* *
47362734 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
65 ATCCACTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTC
* * * **
47362798 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 AGGGAGATAAGACCTGATACAATCTACTCCACTGTAACTTCAGAGAGATAAGATCC-TGATTGCA
* *
47362863 ATCCGCTCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAATCTC
65 ATCCACTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTC
* * * * * *
47362927 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA-TCTCAGGGAGATAAGA-CCTGA-T
1 AGGGAGATAAGA--CCT-GATACAATCTACTCCACTGTAACT-TCAGAGAGATAAGATCCTGATT
* * * * * * * *
47362989 GCGATCTACTCTACTGTAA-CTTCA-GAGAGATAAGATCCT-TTA-TTTTAATCCGCTCCACTGT
62 GCAATCCACTCCACTGTAATC-TCAGGA-AGATAGGAT--TACTAGCTTCAATCTGCTCCACTGT
47363050 AATCTC
123 AATCTC
* * * * * * *
47363056 AGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAA-TCTCAGGGAGATAAGA-CCTGA-T
1 AGGGAGATAAGA--CCT-GATACAATCTACTCCACTGTAACT-TCAGAGAGATAAGATCCTGATT
* *
47363118 GCGATCTACTCCACT
62 GCAATCCACTCCACT
47363133 ACTGCTTAGG
Statistics
Matches: 424, Mismatches: 31, Indels: 18
0.90 0.07 0.04
Matches are distributed among these distances:
128 3 0.01
129 381 0.90
130 4 0.01
131 6 0.01
132 30 0.07
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (128 bp):
AGGGAGATAAGACCTGATACAATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGATTGCAA
TCCACTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTC
Found at i:47363146 original size:40 final size:43
Alignment explanation
Indices: 47363100--47363328 Score: 135
Period size: 44 Copynumber: 5.3 Consensus size: 43
47363090 CTGTAATCTC
*
47363100 AGGGAGATAAGA-C-CTG-ATGCGATCTACTCCACTACTGCTT
1 AGGGAGATAAGATCGCCGTATGCGATCTACTCCACTACTGCTT
* * *
47363140 AGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-TCGCCGTATGCGATCTACTCCACTACTGCTT
* ** * * * * * *
47363184 AGGGAGATAGGATCTAACATCTTCGACCTGCTCCGCTACTGCTT
1 AGGGAGATAAGATC-GCCGTATGCGATCTACTCCACTACTGCTT
* * ** ** * *
47363228 AGGGAGATAGGACTGGTGGCT-T-AAATCTGCTTCACTACTGCTT
1 AGGGAGATAAGA-TCGCCG-TATGCGATCTACTCCACTACTGCTT
* ** * * *
47363271 AGGAAGATGGGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-TCGCCGTATGCGATCTACTCCACTACTGCTT
47363315 AGGGAGATAAGATC
1 AGGGAGATAAGATC
47363329 TGATACGATC
Statistics
Matches: 148, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
40 12 0.08
42 2 0.01
43 36 0.24
44 96 0.65
45 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (43 bp):
AGGGAGATAAGATCGCCGTATGCGATCTACTCCACTACTGCTT
Found at i:47363173 original size:129 final size:129
Alignment explanation
Indices: 47362902--47363176 Score: 394
Period size: 129 Copynumber: 2.1 Consensus size: 129
47362892 GGATTTCTAG
*
47362902 CTTCAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA
1 CTTCAATCTGCTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA
* * **
47362967 TCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
66 TCTCAGGGAGATAAGACCTGATGCGATCTACTCCACTCTAACTTCAGAGAGATAAGATCCCGTA
* * * *
47363031 TTTTAATCCGCTCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAA
1 CTTCAATCTGCTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA
* *
47363096 TCTCAGGGAGATAAGACCTGATGCGATCTACTCCACTACT-GCTT-AGGGAGATAAGATTCGCCG
66 TCTCAGGGAGATAAGACCTGATGCGATCTACTCCACT-CTAACTTCAGAGAGATAAGA-TC-CCG
47363159 T-
128 TA
*
47363160 CTTCGATCTGCTCCACT
1 CTTCAATCTGCTCCACT
47363177 ACTGCTTAGG
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
128 11 0.09
129 114 0.89
130 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (129 bp):
CTTCAATCTGCTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA
TCTCAGGGAGATAAGACCTGATGCGATCTACTCCACTCTAACTTCAGAGAGATAAGATCCCGTA
Found at i:47363175 original size:44 final size:44
Alignment explanation
Indices: 47363119--47363323 Score: 243
Period size: 44 Copynumber: 4.7 Consensus size: 44
47363109 AGACCTGATG
* *
47363119 CGATCTACTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATTCGCCGTCTT
** *
47363163 CGATCTGCTCCACTACTGCTTAGGGAGATAGGA-TCTAACATCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATTC-GCCGTCTT
* * * ** *
47363207 CGACCTGCTCCGCTACTGCTTAGGGAGATAGGACT-GGTGGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATTCGCCGTCTT
** * * *
47363250 AAATCTGCTTCACTACTGCTTAGGAAGATGGGATTCGCCGTCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATTCGCCGTCTT
47363294 CGATCTGCTCCACTACTGCTTAGGGAGATA
1 CGATCTGCTCCACTACTGCTTAGGGAGATA
47363324 AGATCTGATA
Statistics
Matches: 130, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
43 32 0.25
44 97 0.75
45 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (44 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAGGATTCGCCGTCTT
Found at i:47363175 original size:302 final size:302
Alignment explanation
Indices: 47362610--47363176 Score: 924
Period size: 302 Copynumber: 1.9 Consensus size: 302
47362600 TTTTAATCCA
*
47362610 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
47362675 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCAC
66 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCAC
* *
47362740 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
131 TCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
* * ** * *
47362805 TAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCT
196 TAAGACCTGATACGATCTACTCCACTCTAACTTCAGAGAGATAAGATCCCGTACTTCAATCCGCT
47362870 CCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
261 CCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
47362912 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
* * *
47362977 ATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
66 ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCAC
*
47363042 TCCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
131 TCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
* * * * *
47363107 TAAGACCTGATGCGATCTACTCCACTACT-GCTT-AGGGAGATAAGATTCGCCGT-CTTCGATCT
196 TAAGACCTGATACGATCTACTCCACT-CTAACTTCAGAGAGATAAGA-TC-CCGTACTTCAATCC
47363169 GCTCCACT
258 GCTCCACT
47363177 ACTGCTTAGG
Statistics
Matches: 244, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
301 11 0.05
302 230 0.94
303 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (302 bp):
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCAC
TCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
TAAGACCTGATACGATCTACTCCACTCTAACTTCAGAGAGATAAGATCCCGTACTTCAATCCGCT
CCACTGTAATCTCAGGAAGATAGGATTTCTAGCTTCAATCTG
Found at i:47363215 original size:129 final size:128
Alignment explanation
Indices: 47362927--47363323 Score: 378
Period size: 129 Copynumber: 3.1 Consensus size: 128
47362917 CTGTAATCTC
47362927 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
1 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
* * * * ** * ** * *
47362992 ATCTACTCTACT-GTAACTTCAGAGAGATAAGA-TC-CTTTATTTTAATCCGCTCCACTGTAAT-
66 ATCTACTCCACTACT-GCTT-AGGGAGATAAGATTCGCCGT-CTTCGATCTGCTCCAC--TACTG
*
47363053 CTC
126 CTT
* *
47363056 AGGAAGATAGGATTTCTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
1 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
47363121 ATCTACTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
66 ATCTACTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
* * * * * * * *
47363184 AGGGAGATAGGATCTAAC-ATCTTCGACCTGCTCCGC--TACTGCTTAGGGAGATAGGA-CTGGT
1 AGGGAGATAGGAT-T-ACTAGCTTCAATCTGCTCCACTGTAAT-CTCAGGGAGATAAGACCTGAT
* * * * **
47363245 GGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGGGATTCGCCGTCTTCGATCTGCTCCACTAC
63 -GC---GATCTACTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
47363310 TGCTT
124 TGCTT
47363315 AGGGAGATA
1 AGGGAGATA
47363324 AGATCTGATA
Statistics
Matches: 227, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
127 10 0.04
128 40 0.18
129 106 0.47
130 4 0.02
131 67 0.30
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (128 bp):
AGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
ATCTACTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
Found at i:47363270 original size:87 final size:87
Alignment explanation
Indices: 47363126--47363323 Score: 236
Period size: 87 Copynumber: 2.3 Consensus size: 87
47363116 ATGCGATCTA
* * ** * ** *
47363126 CTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAGGACT-GGTGGCTTAAATCTGCTCCACTACTGCTTAGGAAGA
47363191 TAGGA-TCTAACATCTTCGACCTG
65 TAGGATTC-AACATCTTCGACCTG
* *
47363214 CTCCGCTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGAT
1 CTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAAGAT
* ** * *
47363279 GGGATTCGCCGTCTTCGATCTG
66 AGGATTCAACATCTTCGACCTG
47363301 CTCCACTACTGCTTAGGGAGATA
1 CTCCACTACTGCTTAGGGAGATA
47363324 AGATCTGATA
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 66 0.71
88 27 0.29
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (87 bp):
CTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAAGAT
AGGATTCAACATCTTCGACCTG
Found at i:47363430 original size:86 final size:86
Alignment explanation
Indices: 47363337--47363767 Score: 512
Period size: 88 Copynumber: 5.0 Consensus size: 86
47363327 TCTGATACGA
* *
47363337 TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTGTTTCCGACCTGCTTCGCTGTTAG
1 TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTGTTT-CGATCTGCTTCGCTGTTAA
47363402 CGCAAGAAGGCAAGATCTGCT-
65 CGCAAGAAGGCAAGATCTGCTG
* * **
47363423 TCTTTAACCAGCTCCACTGCAATCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTG-TTTCGATCTGCTTCGCTGTTAA
*
47363488 CGCAGGAAGGCAAGATCTGCTG
65 CGCAAGAAGGCAAGATCTGCTG
* * * * * *
47363510 TCTTCAACCAGCTCCACTATAACC-AAGAGAGGCAATGTTTGTGTCTTCGATCTGCTTCGCTATC
1 TCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGTTT-TGT-TTCGATCTGCTTCGCTGTT
* * *
47363574 AAGGCAGGAAGGCAAGATCTGTTG
63 AACGCAAGAAGGCAAGATCTGCTG
* *
47363598 TCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTC
1 TCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGTTT-TGT-TTCGATCTGCTTCGCTGTT
* *
47363662 AATGCAAGAAGGCAAGATCTGAT-
63 AACGCAAGAAGGCAAGATCTGCTG
* * * * *
47363685 TCTTTAACCAGCTTCACTGCAACCGATGAAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAA
1 TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTG-TTTCGATCTGCTTCGCTGTTAA
47363750 C-CAAGGAAGGCAAGATCT
65 CGCAA-GAAGGCAAGATCT
47363768 ACAACTTCAT
Statistics
Matches: 303, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
85 3 0.01
86 111 0.37
87 67 0.22
88 121 0.40
89 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (86 bp):
TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTGTTTCGATCTGCTTCGCTGTTAAC
GCAAGAAGGCAAGATCTGCTG
Found at i:47363557 original size:43 final size:42
Alignment explanation
Indices: 47363508--47363645 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 42
47363498 CAAGATCTGC
47363508 TGTCTTCAACCAGCTCCACTATAACCAAGAGAGGCAATGTTTG
1 TGTCTTCAACCAGCTCCACTATAACCAAGAGAGGCAA-GTTTG
* * * * * * * *
47363551 TGTCTTCGATCTGCTTCGCTATCAAGGCAGGA-AGGCAAGATCTG
1 TGTCTTCAACCAGCTCCACTAT-AA-CCAAGAGAGGCAAG-TTTG
* *
47363595 TTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
1 -TGTCTTCAACCAGCTCCACTATAACCAAGAGAGGCAA-GTTTG
47363639 TGTCTTC
1 TGTCTTC
47363646 GATCTGCTTC
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 28 0.39
44 22 0.31
45 21 0.30
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (42 bp):
TGTCTTCAACCAGCTCCACTATAACCAAGAGAGGCAAGTTTG
Found at i:47363587 original size:44 final size:42
Alignment explanation
Indices: 47363467--47363677 Score: 122
Period size: 44 Copynumber: 4.8 Consensus size: 42
47363457 AGACTTTGTT
* * *
47363467 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTGTC
1 TTCGATCTGCTTCGCTATCAA-GCAGGAAGGCAAG-TTTG-TGTC
* * * * * * *
47363512 TTCAACCAGCTCCACTAT-AACCAAGAGAGGCAATGTTTGTGTC
1 TTCGATCTGCTTCGCTATCAAGCAGGA-AGGCAA-GTTTGTGTC
*
47363555 TTCGATCTGCTTCGCTATCAAGGCAGGAAGGCAAGATCTGTTGTC
1 TTCGATCTGCTTCGCTATCAA-GCAGGAAGGCAAG-TTTG-TGTC
* * * * * *
47363600 TTCAACCAGCTCCACTA-CAA-CCGAGAGAGGCAAGGTTTGTGTC
1 TTCGATCTGCTTCGCTATCAAGCAG-GA-AGGCAA-GTTTGTGTC
* *
47363643 TTCGATCTGCTTCGCTGTCAATGCAAGAAGGCAAG
1 TTCGATCTGCTTCGCTATCAA-GCAGGAAGGCAAG
47363678 ATCTGATTCT
Statistics
Matches: 122, Mismatches: 32, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
42 2 0.02
43 40 0.33
44 43 0.35
45 36 0.30
46 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (42 bp):
TTCGATCTGCTTCGCTATCAAGCAGGAAGGCAAGTTTGTGTC
Found at i:47365018 original size:6 final size:7
Alignment explanation
Indices: 47364996--47365028 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
47364986 AATTTTACTA
47364996 TTTCATT
1 TTTCATT
47365003 TTTCATT
1 TTTCATT
47365010 TTTCA-T
1 TTTCATT
*
47365016 TTTCTTT
1 TTTCATT
47365023 TTTCAT
1 TTTCAT
47365029 CTCTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCATT
Found at i:47365451 original size:15 final size:14
Alignment explanation
Indices: 47365405--47365452 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
47365395 TTTTCTTTTT
47365405 CTTTTTTGTTTTGA
1 CTTTTTTGTTTTGA
* * *
47365419 CTTTGATTGATTTCA
1 CTTT-TTTGTTTTGA
47365434 CTTTTTTGCTTTTGA
1 CTTTTTTG-TTTTGA
47365449 CTTT
1 CTTT
47365453 GCTTTTGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (14 bp):
CTTTTTTGTTTTGA
Found at i:47365469 original size:30 final size:27
Alignment explanation
Indices: 47365401--47365470 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
47365391 CTCCTTTTCT
47365401 TTTTCTTTTTTGTTTTGACTTTGATTGA
1 TTTT-TTTTTTGTTTTGACTTTGATTGA
* *
47365429 TTTCACTTTTTTGCTTTTGACTTTGCTTTTGA
1 TTT--TTTTTTTG-TTTTGACTTTG--ATTGA
47365461 TTTTTTTTTT
1 TTTTTTTTTT
47365471 TGAATGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 3 0.09
29 7 0.21
30 17 0.50
32 7 0.21
ACGTcount: A:0.09, C:0.10, G:0.11, T:0.70
Consensus pattern (27 bp):
TTTTTTTTTTGTTTTGACTTTGATTGA
Found at i:47381949 original size:17 final size:17
Alignment explanation
Indices: 47381927--47381959 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47381917 AAGCATATAA
*
47381927 TAAAATTTTAAAAAATT
1 TAAAATATTAAAAAATT
47381944 TAAAATATTAAAAAAT
1 TAAAATATTAAAAAAT
47381960 ATTTTCATGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATTAAAAAATT
Found at i:47382582 original size:17 final size:19
Alignment explanation
Indices: 47382541--47382589 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
47382531 TTGCTACTGC
*
47382541 TTTGTTGTTATTGTATAAC
1 TTTGTTGTTATTGTATAAA
47382560 TCTTGTT-TTATTGT-TAAA
1 T-TTGTTGTTATTGTATAAA
*
47382578 TTTGTTGCTATT
1 TTTGTTGTTATT
47382590 TTAGAGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 8 0.31
19 8 0.31
20 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.14, T:0.61
Consensus pattern (19 bp):
TTTGTTGTTATTGTATAAA
Found at i:47384444 original size:26 final size:26
Alignment explanation
Indices: 47384415--47384492 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
47384405 CAAATACAAT
47384415 AAATGAAAGAGAATAACATATATGTA
1 AAATGAAAGAGAATAACATATATGTA
** *
47384441 AAAT--AA-A-AA-CCCAAATATG-A
1 AAATGAAAGAGAATAACATATATGTA
* *
47384461 GGAAGGAAAGAGAATAACATATATGTA
1 -AAATGAAAGAGAATAACATATATGTA
47384488 AAATG
1 AAATG
47384493 GAGATATTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 14
0.59 0.17 0.24
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 2 0.06
23 3 0.09
24 3 0.09
25 2 0.06
26 14 0.40
27 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (26 bp):
AAATGAAAGAGAATAACATATATGTA
Found at i:47385635 original size:27 final size:27
Alignment explanation
Indices: 47385601--47385660 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
47385591 AAAATAACCT
*
47385601 AAATATTATAACTTTTTTTATTTACCA
1 AAATATTATAAATTTTTTTATTTACCA
47385628 AAATATTATAAATTTTTTTATTTACCA
1 AAATATTATAAATTTTTTTATTTACCA
47385655 AAATAT
1 AAATAT
47385661 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATATTATAAATTTTTTTATTTACCA
Found at i:47386324 original size:19 final size:19
Alignment explanation
Indices: 47386300--47386358 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
47386290 TCTAATTAAG
*
47386300 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
47386319 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
47386337 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
47386356 TAA
1 TAA
47386359 AATATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:47394439 original size:19 final size:20
Alignment explanation
Indices: 47394417--47394457 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
47394407 AATTTGATAT
*
47394417 AAACTTATAAAAATTA-TAA
1 AAACTGATAAAAATTATTAA
*
47394436 AAACTGATAAATATTATTAA
1 AAACTGATAAAAATTATTAA
47394456 AA
1 AA
47394458 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
AAACTGATAAAAATTATTAA
Found at i:47394476 original size:8 final size:8
Alignment explanation
Indices: 47394458--47394507 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
47394448 ATTATTAAAA
47394458 TATATATTT
1 TATA-ATTT
47394467 TATAATTT
1 TATAATTT
*
47394475 TATAAGTT
1 TATAATTT
47394483 TAT-ATTT
1 TATAATTT
47394490 TAATAATATT
1 T-ATAAT-TT
47394500 TAT-ATTT
1 TATAATTT
47394507 T
1 T
47394508 TTTACAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 7 0.19
8 18 0.50
9 8 0.22
10 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATAATTT
Found at i:47394495 original size:16 final size:16
Alignment explanation
Indices: 47394465--47394507 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
47394455 AAATATATAT
*
47394465 TTTATAATTTTATAA-G
1 TTTAT-ATTTTATAATA
47394481 TTTATATTTTAATAATA
1 TTTATATTTT-ATAATA
47394498 TTTATATTTT
1 TTTATATTTT
47394508 TTTACAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTATATTTTATAATA
Found at i:47394602 original size:22 final size:22
Alignment explanation
Indices: 47394560--47394602 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
47394550 CACCCCAAAT
**
47394560 TTTGGGGTTAGAAGTTTTGAGC
1 TTTGGGGTTAGAAGTAGTGAGC
47394582 TTTGGGGTTA-AAGTCAGTGAG
1 TTTGGGGTTAGAAGT-AGTGAG
47394603 TAGGTTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (22 bp):
TTTGGGGTTAGAAGTAGTGAGC
Found at i:47394825 original size:21 final size:21
Alignment explanation
Indices: 47394801--47394854 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
47394791 TTTTTTATTA
*
47394801 TTTATTTTTCTTAATGTTTAT
1 TTTATTTTTCTTAATGGTTAT
**
47394822 TTTATTTTT-TATTTTGGTTAT
1 TTTATTTTTCT-TAATGGTTAT
47394843 TTTATTTTTCTT
1 TTTATTTTTCTT
47394855 CCTTGTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTATTTTTCTTAATGGTTAT
Found at i:47395492 original size:19 final size:20
Alignment explanation
Indices: 47395468--47395507 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
47395458 TTTAAATAAA
47395468 TTTTATTAA-ATTTAT-AGTT
1 TTTTA-TAATATTTATAAGTT
47395487 TTTTATAATATTTATAAGTT
1 TTTTATAATATTTATAAGTT
47395507 T
1 T
47395508 ATATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 11 0.58
20 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATAATATTTATAAGTT
Found at i:47395519 original size:19 final size:17
Alignment explanation
Indices: 47395468--47395519 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
47395458 TTTAAATAAA
*
47395468 TTTTATTAAATTTATAG
1 TTTTATTAATTTTATAG
*
47395485 TTTTTTATAATATTTATAAG
1 TTTTAT-TAAT-TTTAT-AG
47395505 TTTATATTAATTTTA
1 TTT-TATTAATTTTA
47395520 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.18
18 3 0.11
19 9 0.32
20 9 0.32
21 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTATTAATTTTATAG
Found at i:47399302 original size:40 final size:40
Alignment explanation
Indices: 47399247--47399329 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
47399237 TTTAAAAGAA
* * *
47399247 TTTTCAAGTTATCATTTAGATTTAATAATGTGATTTTCGT
1 TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
* *
47399287 TTTTCAAGGTATCATTTGGATTTAATAAAGTTATTTTCAT
1 TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
47399327 TTT
1 TTT
47399330 CTCTTTCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (40 bp):
TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
Found at i:47408133 original size:44 final size:44
Alignment explanation
Indices: 47408082--47408169 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
47408072 TAGTTCAGTG
47408082 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
1 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
47408126 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
1 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
47408170 TACCCATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (44 bp):
ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
Found at i:47417364 original size:16 final size:16
Alignment explanation
Indices: 47417343--47417376 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47417333 CAAAATTTCA
* *
47417343 TCAATCTTTCCAATTT
1 TCAATCCTTCAAATTT
47417359 TCAATCCTTCAAATTT
1 TCAATCCTTCAAATTT
47417375 TC
1 TC
47417377 TTTAGACCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (16 bp):
TCAATCCTTCAAATTT
Found at i:47418257 original size:3 final size:3
Alignment explanation
Indices: 47418251--47418288 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47418241 ATCATCATCA
47418251 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
47418289 CCCAACGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:47434579 original size:15 final size:15
Alignment explanation
Indices: 47434530--47434580 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
47434520 TTTCCTCATA
*
47434530 TTACATTTTAGTCAC
1 TTACGTTTTAGTCAC
* *
47434545 TTATGTTTGAGAT-A-
1 TTACGTTTTAG-TCAC
47434559 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
47434574 TTACGTT
1 TTACGTT
47434581 ATCGTGTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:47437130 original size:7 final size:7
Alignment explanation
Indices: 47437114--47437143 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
47437104 TAACAATACC
47437114 TTTC-TT
1 TTTCTTT
47437120 TTTCTTT
1 TTTCTTT
47437127 TTTCTTT
1 TTTCTTT
47437134 TTTCTTT
1 TTTCTTT
47437141 TTT
1 TTT
47437144 TTTAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTCTTT
Found at i:47447094 original size:24 final size:24
Alignment explanation
Indices: 47447027--47447094 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
47447017 TTTAAAAAAT
*
47447027 AATTATA-TTAA-AAATATTATTA
1 AATTATATTTAATAATTATTATTA
* ** * *
47447049 AATTATATATGGTTATTTTTATTA
1 AATTATATTTAATAATTATTATTA
47447073 AATTATATTTAATAATTATTAT
1 AATTATATTTAATAATTATTAT
47447095 ATTAAAAGAT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 7 0.21
23 1 0.03
24 25 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTATATTTAATAATTATTATTA
Found at i:47447094 original size:62 final size:60
Alignment explanation
Indices: 47447024--47447160 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
47447014 AATTTTAAAA
* * * *
47447024 AATAATTATATTAAAAATATTATTAAATTATATATGGTTATTT-TTATTAAATTATATTTAAT
1 AATAATTATATTAAAAAGATGACT-AATT-TAT-TGATTATTTATTATTAAATTATATTTAAT
* * *
47447086 AATTATTATATT-AAAAGATGACTAATTTATTTATTATTTATTATTAAATTATTTTTAAT
1 AATAATTATATTAAAAAGATGACTAATTTATTGATTATTTATTATTAAATTATATTTAAT
47447145 AATAATCT-TATTAAAA
1 AATAAT-TATATTAAAA
47447161 TTTAATAACA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
58 7 0.11
59 30 0.47
60 8 0.12
61 8 0.12
62 11 0.17
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (60 bp):
AATAATTATATTAAAAAGATGACTAATTTATTGATTATTTATTATTAAATTATATTTAAT
Found at i:47447543 original size:7 final size:7
Alignment explanation
Indices: 47447531--47447561 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
47447521 CATAAGAGAG
47447531 CTTGAGC
1 CTTGAGC
47447538 CTTGAGC
1 CTTGAGC
47447545 CTTGAGC
1 CTTGAGC
47447552 CTTGAGC
1 CTTGAGC
47447559 CTT
1 CTT
47447562 AAGCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.26, T:0.32
Consensus pattern (7 bp):
CTTGAGC
Found at i:47448517 original size:25 final size:25
Alignment explanation
Indices: 47448472--47448521 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
47448462 GGGTAGAGTG
47448472 GAAAAGTGAAAGAATAGAAAGAAAA
1 GAAAAGTGAAAGAATAGAAAGAAAA
47448497 GAAAAGTAGAAA-AAT-GAAAAGAAAA
1 GAAAAGT-GAAAGAATAG-AAAGAAAA
47448522 TTAATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 18 0.78
26 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (25 bp):
GAAAAGTGAAAGAATAGAAAGAAAA
Found at i:47448700 original size:7 final size:7
Alignment explanation
Indices: 47448688--47448712 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47448678 TTATATTTTT
47448688 TTTTAAA
1 TTTTAAA
47448695 TTTTAAA
1 TTTTAAA
47448702 TTTTAAA
1 TTTTAAA
47448709 TTTT
1 TTTT
47448713 TTCTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:47449131 original size:16 final size:16
Alignment explanation
Indices: 47449110--47449143 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
47449100 TTCCAACTTC
47449110 TTTTTGTTTATTAGGT
1 TTTTTGTTTATTAGGT
47449126 TTTTTGTTTATTAGGT
1 TTTTTGTTTATTAGGT
47449142 TT
1 TT
47449144 GATTGAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (16 bp):
TTTTTGTTTATTAGGT
Found at i:47451414 original size:36 final size:36
Alignment explanation
Indices: 47451367--47451438 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
47451357 TCTTTTTATC
47451367 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
1 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
47451403 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
1 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
47451439 AACTCAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (36 bp):
TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
Found at i:47482267 original size:25 final size:25
Alignment explanation
Indices: 47482235--47482283 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
47482225 TAGACAAATG
47482235 AAAAAAAT-ATATACAATATAATACT
1 AAAAAAATAATAT-CAATATAATACT
*
47482260 AAAAAAATAATATGAATATAATAC
1 AAAAAAATAATATCAATATAATAC
47482284 AACTAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAAATAATATCAATATAATACT
Found at i:47493391 original size:2 final size:2
Alignment explanation
Indices: 47493386--47493412 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47493376 GTGTGTGTGT
47493386 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
47493413 GAAGTGTATG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47495368 original size:36 final size:36
Alignment explanation
Indices: 47495321--47495392 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
47495311 TGAAATTGAG
47495321 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
1 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
47495357 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
1 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
47495393 CATTCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (36 bp):
TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
Found at i:47497521 original size:27 final size:27
Alignment explanation
Indices: 47497491--47497544 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
47497481 ATTTTTTCAT
47497491 GTTTATCATTTAAATTTAATTTAAATA
1 GTTTATCATTTAAATTTAATTTAAATA
47497518 GTTTATCATTTAAATTTAATTTAAATA
1 GTTTATCATTTAAATTTAATTTAAATA
47497545 CATATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
GTTTATCATTTAAATTTAATTTAAATA
Found at i:47499566 original size:50 final size:50
Alignment explanation
Indices: 47499484--47499583 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
47499474 TTAAACCCCT
*
47499484 CTTTTTTTTACACTCAATCGAGCACTTGAACTTTCAAAATGCATCAAAAA
1 CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
* * *
47499534 CTTTTTTTTTCACTCAATTGAGTACTTAAACTTTCAAAATGCATCAAAAA
1 CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
47499584 TACCCTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (50 bp):
CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
Found at i:47499939 original size:25 final size:24
Alignment explanation
Indices: 47499905--47499959 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
47499895 GTACGATAGT
*
47499905 TTTTATAAAAAAAATTTTTACAAA
1 TTTTATAAAAAAAAATTTTACAAA
47499929 TTTTATAAAAAAAAATTTTACAAA
1 TTTTATAAAAAAAAATTTTACAAA
*
47499953 ATTTATA
1 TTTTATA
47499960 CTTCTTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTTATAAAAAAAAATTTTACAAA
Found at i:47500005 original size:29 final size:29
Alignment explanation
Indices: 47499972--47500044 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
47499962 TCTTTACATT
47499972 TTTTATAATTTTCTTACGA-ATTTATAAAA
1 TTTTATAATTTT-TTACGATATTTATAAAA
*
47500001 TTTTATAATTTTTTACGATTTTTATAAAA
1 TTTTATAATTTTTTACGATATTTATAAAA
* *
47500030 TTTTACAATATTTTA
1 TTTTATAATTTTTTA
47500045 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTATAATTTTTTACGATATTTATAAAA
Found at i:47500025 original size:19 final size:19
Alignment explanation
Indices: 47500001--47500070 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
47499991 ATTTATAAAA
*
47500001 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACAAT
**
47500020 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
*
47500039 ATTTTA-ATTTTTTTTACAAT
1 -TTTTATA-ATTTTTTACAAT
47500059 TTTTAT-ATTTTT
1 TTTTATAATTTTT
47500071 CTAATTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 5 0.12
19 22 0.54
20 14 0.34
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:47500053 original size:20 final size:20
Alignment explanation
Indices: 47500030--47500070 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
47500020 TTTTATAAAA
47500030 TTTTACAATATTTTA-ATTTT
1 TTTTACAAT-TTTTATATTTT
47500050 TTTTACAATTTTTATATTTT
1 TTTTACAATTTTTATATTTT
47500070 T
1 T
47500071 CTAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTACAATTTTTATATTTT
Found at i:47500100 original size:19 final size:19
Alignment explanation
Indices: 47500072--47500121 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
47500062 TATATTTTTC
47500072 TAAT-TTTTAATAAATTAT
1 TAATATTTTAATAAATTAT
**
47500090 TAATATTTTAATATTTTAT
1 TAATATTTTAATAAATTAT
*
47500109 TAA-AATTTAATAA
1 TAATATTTTAATAA
47500122 TATTTATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTTTAATAAATTAT
Found at i:47500138 original size:29 final size:28
Alignment explanation
Indices: 47499992--47500138 Score: 106
Period size: 29 Copynumber: 5.2 Consensus size: 28
47499982 TTCTTACGAA
* *
47499992 TTTA-TAAAATTTTATAATTTTTTACGATT
1 TTTATTAAAATTTAATAATATTTTA--ATT
* *
47500021 TTTA-TAAAATTTTACAATATTTTAATT
1 TTTATTAAAATTTAATAATATTTTAATT
* * * *
47500048 TTTTTTACAATTT-TTATATTTTTCTAATT
1 TTTATTAAAATTTAATA-ATATTT-TAATT
* *
47500077 TTTAAT-AAA-TTATTAATATTTTAATAT
1 TTTATTAAAATTTAATAATATTTTAAT-T
*
47500104 TTTATTAAAATTTAATAATATTTATAGTT
1 TTTATTAAAATTTAATAATATTT-TAATT
47500133 TTTATT
1 TTTATT
47500139 GATTTTAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.04
27 20 0.21
28 20 0.21
29 49 0.51
30 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTATTAAAATTTAATAATATTTTAATT
Found at i:47500279 original size:91 final size:91
Alignment explanation
Indices: 47500182--47500359 Score: 218
Period size: 91 Copynumber: 2.0 Consensus size: 91
47500172 GTAAAAGCAT
* * *
47500182 GAGCTTAATTGCATTT-TTTTAAAAAGTTTGAGCATCTTTTTGAT-TCATTTTGAAAGTTCAAGT
1 GAGCTTAATTGC-TTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGT-ATTTTAAAAGTTCAAGT
* * *
47500245 AC-CTAATTGAGTGTAAAAGAAAAAGTAG
64 ACTC-AAATGAGTGGAAAAAAAAAAGTAG
* * * *
47500273 GAGCTTAATTGCTTTCTTTGAAAAGGTTTGAGGACCTTTTTGATGTATTTTAAAATTTTAAGTAC
1 GAGCTTAATTGCTTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGTATTTTAAAAGTTCAAGTAC
47500338 TCAAATGAGTGGAAAAAAAAAA
66 TCAAATGAGTGGAAAAAAAAAA
47500360 CTTAAATACT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
90 3 0.04
91 69 0.93
92 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (91 bp):
GAGCTTAATTGCTTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGTATTTTAAAAGTTCAAGTAC
TCAAATGAGTGGAAAAAAAAAAGTAG
Found at i:47501624 original size:40 final size:40
Alignment explanation
Indices: 47501569--47501682 Score: 219
Period size: 40 Copynumber: 2.9 Consensus size: 40
47501559 GAGAATTGAT
*
47501569 TGTATGAAACAGAGGCACCGTGCTATCTTGTATCAAGGAC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
47501609 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
47501649 TGTATGAAACAGAGGCACTGTGCTATCTTGTATC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATC
47501683 TCTTTCCAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (40 bp):
TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
Found at i:47501898 original size:7 final size:7
Alignment explanation
Indices: 47501886--47501928 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
47501876 TTTCAAGTTT
47501886 ATGATTC
1 ATGATTC
47501893 ATGATTC
1 ATGATTC
47501900 ATGATTC
1 ATGATTC
47501907 ATGATTC
1 ATGATTC
*
47501914 AAGATTC
1 ATGATTC
*
47501921 AAGATTC
1 ATGATTC
47501928 A
1 A
47501929 AGGTTCAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (7 bp):
ATGATTC
Found at i:47501929 original size:7 final size:7
Alignment explanation
Indices: 47501869--47501935 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
47501859 ATAGTTCGAG
47501869 TTCAAGA
1 TTCAAGA
47501876 TTTCAAG-
1 -TTCAAGA
* *
47501883 TTTATGA
1 TTCAAGA
*
47501890 TTCATGA
1 TTCAAGA
*
47501897 TTCATGA
1 TTCAAGA
*
47501904 TTCATGA
1 TTCAAGA
47501911 TTCAAGA
1 TTCAAGA
47501918 TTCAAGA
1 TTCAAGA
*
47501925 TTCAAGG
1 TTCAAGA
47501932 TTCA
1 TTCA
47501936 GGGTAAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (7 bp):
TTCAAGA
Found at i:47501935 original size:21 final size:21
Alignment explanation
Indices: 47501869--47501928 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
47501859 ATAGTTCGAG
*
47501869 TTCAAGATTTCAAG-TTTATGA
1 TTCAAGA-TTCAAGATTCATGA
* *
47501890 TTCATGATTCATGATTCATGA
1 TTCAAGATTCAAGATTCATGA
47501911 TTCAAGATTCAAGATTCA
1 TTCAAGATTCAAGATTCA
47501929 AGGTTCAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
TTCAAGATTCAAGATTCATGA
Found at i:47502917 original size:14 final size:13
Alignment explanation
Indices: 47502883--47502920 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
47502873 CGGTTCAAAT
47502883 AATATAA-TTTTA
1 AATATAATTTTTA
47502895 AAT-TAATTTTTA
1 AATATAATTTTTA
47502907 AATTATAATTTTTA
1 AA-TATAATTTTTA
47502921 TTTTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 10 0.43
13 1 0.04
14 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATAATTTTTA
Found at i:47508498 original size:26 final size:26
Alignment explanation
Indices: 47508466--47508534 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
47508456 ATCAGGAAGC
47508466 TCCCGA-TATATGGCTCTTTGTGAGCT
1 TCCCGATTA-ATGGCTCTTTGTGAGCT
*
47508492 TCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCCGATTAATGGCTCTTTGTGAGCT
*
47508518 TCCTGATTAATGGCTCT
1 TCCCGATTAATGGCTCT
47508535 CCGAAGCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
TCCCGATTAATGGCTCTTTGTGAGCT
Found at i:47508548 original size:25 final size:24
Alignment explanation
Indices: 47508461--47508607 Score: 84
Period size: 26 Copynumber: 5.9 Consensus size: 24
47508451 CATATATCAG
* *
47508461 GAAGC-TCCCGATATATGGCTCTTT
1 GAAGCTTCCTGATA-ATGGCTCTCT
* * * *
47508485 GTGAGCTTCCCGATTAAAGGCTCTTT
1 G-AAGCTTCCTGA-TAATGGCTCTCT
* *
47508511 GTGAGCTTCCTGATTAATGGCTCTCC
1 G-AAGCTTCCTGA-TAATGGCTCTCT
* *
47508537 GAAGCTTCCTGAT-ATGACTCGCTT
1 GAAGCTTCCTGATAATGGCTCTC-T
* *
47508561 GAA-CTTCCCGATATATGGCTATCT
1 GAAGCTTCCTGATA-ATGGCTCTCT
*
47508585 GAAGCTTCTTGATTAATGGCTCT
1 GAAGCTTCCTGA-TAATGGCTCT
47508608 TTAGAGCTAC
Statistics
Matches: 98, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
23 15 0.15
24 9 0.09
25 32 0.33
26 40 0.41
27 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (24 bp):
GAAGCTTCCTGATAATGGCTCTCT
Found at i:47515374 original size:2 final size:2
Alignment explanation
Indices: 47515327--47515363 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47515317 CTTCCTTATT
47515327 TC TC TC TC TC 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 TC TC TC TC TC T
47515364 TGTTTTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:47516758 original size:17 final size:17
Alignment explanation
Indices: 47516736--47516774 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
47516726 AGAAAAGTCC
47516736 CTTTTATGAGGTGAGGA
1 CTTTTATGAGGTGAGGA
47516753 CTTTTATGAGGTGAGGA
1 CTTTTATGAGGTGAGGA
47516770 CTTTT
1 CTTTT
47516775 GGTGTGTAGG
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:0.21, C:0.08, G:0.31, T:0.41
Consensus pattern (17 bp):
CTTTTATGAGGTGAGGA
Found at i:47522813 original size:33 final size:33
Alignment explanation
Indices: 47522767--47522850 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
47522757 CCCAGATTCT
**
47522767 CCTCCACCACCACCACCTTTGCCACCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* * * * * *
47522800 CCTCCGCCCCCACCTCCATCATCTCCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* *
47522833 CCTCCTCCTCCACCACCT
1 CCTCCACCACCACCACCT
47522851 CTACCAACAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.61, G:0.02, T:0.20
Consensus pattern (33 bp):
CCTCCACCACCACCACCTTCACCACCTTCACCA
Found at i:47522846 original size:15 final size:15
Alignment explanation
Indices: 47522822--47522851 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47522812 CCTCCATCAT
*
47522822 CTCCTTCACCACCTC
1 CTCCTCCACCACCTC
47522837 CTCCTCCACCACCTC
1 CTCCTCCACCACCTC
47522852 TACCAACACT
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:0.13, C:0.63, G:0.00, T:0.23
Consensus pattern (15 bp):
CTCCTCCACCACCTC
Found at i:47537487 original size:37 final size:37
Alignment explanation
Indices: 47537426--47537575 Score: 252
Period size: 37 Copynumber: 4.1 Consensus size: 37
47537416 TACGTATGAT
* *
47537426 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
47537461 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
47537498 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
47537535 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG-
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
47537571 CACTT
1 CACTT
47537576 TGTCTCTTGA
Statistics
Matches: 109, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.08
36 8 0.07
37 92 0.84
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:47537584 original size:29 final size:29
Alignment explanation
Indices: 47537542--47537600 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
47537532 AGCCACTTAT
*
47537542 CACTTTGTTTCTTGATCAGATAAGTGTAG
1 CACTTTGTCTCTTGATCAGATAAGTGTAG
47537571 CACTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTTGTCTCTTGATCAGATAAGTGTAG
47537600 C
1 C
47537601 TAAAGCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (29 bp):
CACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:47537638 original size:46 final size:46
Alignment explanation
Indices: 47537571--47537878 Score: 373
Period size: 46 Copynumber: 6.4 Consensus size: 46
47537561 ATAAGTGTAG
* * * *
47537571 CACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTAT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* *
47537617 CACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* * *
47537663 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
*
47537715 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* *
47537761 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* * *
47537807 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
47537859 CACTTTGTCACTTGATCAGA
1 CACTTTGTCACTTGATCAGA
47537879 AGTACTCAAA
Statistics
Matches: 231, Mismatches: 19, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
46 147 0.64
48 1 0.00
49 2 0.01
50 1 0.00
52 80 0.35
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
Found at i:47537694 original size:98 final size:98
Alignment explanation
Indices: 47537575--47537872 Score: 392
Period size: 98 Copynumber: 3.0 Consensus size: 98
47537565 GTGTAGCACT
* *
47537575 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCACTTGATCAGATAA
47537640 GTATAGCCGAAGCTATCACTTATCACTTTTCAC
66 GTATAGCCGAAGCTATCACTTATCACTTTTCAC
**
47537673 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCACTTGATCAGATAA
47537738 GTATAGCCGAAGCTATCACTTATCAC---T---
66 GTATAGCCGAAGCTATCACTTATCACTTTTCAC
* **
47537765 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCAC--T----TTGTCACTTGATC
* ** *
47537830 AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
60 AGATAAGTATAGCCGAAGCTATCACTTATCACTTT-TCAC
47537870 TTG
1 TTG
47537873 ATCAGAAGTA
Statistics
Matches: 174, Mismatches: 13, Indels: 19
0.84 0.06 0.09
Matches are distributed among these distances:
92 40 0.23
94 1 0.01
95 1 0.01
98 128 0.74
102 1 0.01
105 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (98 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTTCAC
Found at i:47537759 original size:144 final size:144
Alignment explanation
Indices: 47537571--47537878 Score: 544
Period size: 144 Copynumber: 2.1 Consensus size: 144
47537561 ATAAGTGTAG
* * * * *
47537571 CACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTTGATCAG
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
*
47537636 ATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTA
66 ATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTA
47537701 AAGCTACCACTTAT
131 AAGCTACCACTTAT
*
47537715 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAG
1 CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
*
47537780 ATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTA
66 ATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTA
47537845 AAGCTACCACTTAT
131 AAGCTACCACTTAT
47537859 CACTTTGTCACTTGATCAGA
1 CACTTTGTCACTTGATCAGA
47537879 AGTACTCAAA
Statistics
Matches: 156, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 156 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
ATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTA
AAGCTACCACTTAT
Found at i:47549896 original size:20 final size:21
Alignment explanation
Indices: 47549854--47549899 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
47549844 ATAACAGCTT
* *
47549854 TTAAAATAATTATCTTTTAAA
1 TTAAAAAAATTATCTTATAAA
47549875 TTAAAAAAATTATC-TATAAA
1 TTAAAAAAATTATCTTATAAA
47549895 TTAAA
1 TTAAA
47549900 TTCTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAAATTATCTTATAAA
Found at i:47568176 original size:10 final size:9
Alignment explanation
Indices: 47568160--47568225 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
47568150 AATTATACAA
47568160 ATAAAAATT
1 ATAAAAATT
47568169 ACTAAAAATT
1 A-TAAAAATT
**
47568179 ATTAAATTTT
1 A-TAAAAATT
47568189 AATAAAAATT
1 -ATAAAAATT
47568199 ATAAAAATCGT
1 ATAAAAAT--T
*
47568210 AAAAAAAATT
1 -ATAAAAATT
47568220 ATAAAA
1 ATAAAA
47568226 CATAATATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 14 0.31
10 22 0.49
11 2 0.04
12 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Done.