Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 133 of 150
Found at i:40009813 original size:33 final size:33
Alignment explanation
Indices: 40009776--40010086 Score: 166
Period size: 33 Copynumber: 8.8 Consensus size: 33
40009766 TCCCCCAAGG
*
40009776 GGTTGCTAAGTGATGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
40009809 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
40009851 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
40009884 GGTTGCTAAGTGCTGATTCCAACGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
40009926 GGTTGCTAAGTGCTGATTCTCC---TGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
40009953 GGTTGCTAAGTGCTGATTCCCCAAATAATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
40009986 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
* *
40010028 GGTTGCTAAGTGTTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
40010061 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
40010087 AACGGATAAC
Statistics
Matches: 217, Mismatches: 27, Indels: 67
0.70 0.09 0.22
Matches are distributed among these distances:
27 21 0.10
28 2 0.01
30 2 0.01
32 2 0.01
33 78 0.36
34 12 0.06
35 4 0.02
36 4 0.02
37 8 0.04
38 9 0.04
39 5 0.02
40 2 0.01
41 7 0.03
42 61 0.28
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:40009868 original size:42 final size:41
Alignment explanation
Indices: 40009809--40009944 Score: 171
Period size: 42 Copynumber: 3.5 Consensus size: 41
40009799 ATTCATTGGT
40009809 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* *
40009851 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
*
40009884 GGTTGCTAAGTGCTGATTCCAACGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
40009926 GGTTGCTAAGTGCTGATTC
1 GGTTGCTAAGTGCTGATTC
40009945 TCCTGAGGGG
Statistics
Matches: 80, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 21 0.26
34 2 0.03
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 40 0.50
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:40009895 original size:75 final size:75
Alignment explanation
Indices: 40009772--40009944 Score: 310
Period size: 75 Copynumber: 2.3 Consensus size: 75
40009762 TGATTCCCCC
* * *
40009772 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATC
40009837 TTAAATGTGA
66 TTAAATGTGA
40009847 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATC
40009912 TTAAATGTGA
66 TTAAATGTGA
*
40009922 AGGGGGTTGCTAAGTGCTGATTC
1 AAGGGGTTGCTAAGTGCTGATTC
40009945 TCCTGAGGGG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATC
TTAAATGTGA
Found at i:40009954 original size:102 final size:102
Alignment explanation
Indices: 40009848--40010046 Score: 335
Period size: 102 Copynumber: 2.0 Consensus size: 102
40009838 TAAATGTGAA
* * * *
40009848 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCAAATAATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCT
*
40009913 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCTCCTG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCTCCTG
*
40009950 AGGGGTTGCTAAGTGCTGATTCCCCAAATAATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCAAATAATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCT
*
40010015 TAAATGTGAAAGGGGTTGCTAAGTGTTGATTC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTC
40010047 CCCGACTCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCAAATAATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCTCCTG
Found at i:40010047 original size:177 final size:177
Alignment explanation
Indices: 40009746--40010081 Score: 573
Period size: 177 Copynumber: 1.9 Consensus size: 177
40009736 TGAATATAAC
* * * *
40009746 GGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGG
1 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGATGATTCCCCAAATAATTGGTGG
*
40009811 TTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAC
66 TTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAC
*
40009876 TCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATCTTAAATGTGAA
131 TCATTGGTGGTTGCTAAGTGCTGAATCCAACGTATCTTAAATGTGAA
* ** *
40009923 GGGGGTTGCTAAGTGCTGATTCTCCTGAGGGGTTGCTAAGTGCTGATTCCCCAAATAATTGGTGG
1 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGATGATTCCCCAAATAATTGGTGG
*
40009988 TTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCGAC
66 TTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAC
40010053 TCATTGGTGGTTGCTAAGTGCTGAATCCA
131 TCATTGGTGGTTGCTAAGTGCTGAATCCA
40010082 CCGATAACGG
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
177 148 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (177 bp):
GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGATGATTCCCCAAATAATTGGTGG
TTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAC
TCATTGGTGGTTGCTAAGTGCTGAATCCAACGTATCTTAAATGTGAA
Found at i:40010751 original size:20 final size:20
Alignment explanation
Indices: 40010726--40010765 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40010716 GGGGAAAATT
40010726 TACGGAACTTAATTTGGAGC
1 TACGGAACTTAATTTGGAGC
40010746 TACGGAACTTAATTTGGAGC
1 TACGGAACTTAATTTGGAGC
40010766 CCTGTAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TACGGAACTTAATTTGGAGC
Found at i:40015200 original size:43 final size:42
Alignment explanation
Indices: 40015098--40015218 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
40015088 GATTTCGTGG
* * * * *
40015098 AAGACCATGTCTGGGACATTAGCATCGATATGAGATTACGTGT
1 AAGACCATGTCTGGGATA-TGGCATCGATATGTGATAACATGT
* *
40015141 AAGACCCTATCTGGGATAGTGGCATCGATATGTGATAACATGT
1 AAGACCATGTCTGGGATA-TGGCATCGATATGTGATAACATGT
*
40015184 AAGACCATGTCTGGGATATGGCATTG-TATGTGATA
1 AAGACCATGTCTGGGATATGGCATCGATATGTGATA
40015219 TATGTGTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 9 0.13
42 7 0.10
43 51 0.76
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
AAGACCATGTCTGGGATATGGCATCGATATGTGATAACATGT
Found at i:40015771 original size:15 final size:15
Alignment explanation
Indices: 40015751--40015787 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
40015741 TTTTGGGAAG
*
40015751 TATGTTTCATGGTTA
1 TATGTTTCATGGCTA
40015766 TATGTTTCATGGCTA
1 TATGTTTCATGGCTA
40015781 TATGTTT
1 TATGTTT
40015788 TGGTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (15 bp):
TATGTTTCATGGCTA
Found at i:40017545 original size:50 final size:50
Alignment explanation
Indices: 40017470--40017711 Score: 367
Period size: 50 Copynumber: 4.8 Consensus size: 50
40017460 GATCATAACA
* ** *
40017470 TGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
40017520 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTTTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40017570 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAGCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
40017620 TGCCAATGCCATGTCCCAGGCATGATCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
40017670 TGCCAATGCCATGCCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40017712 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 175 1.00
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40017827 original size:13 final size:13
Alignment explanation
Indices: 40017806--40017835 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40017796 GCTTGGGTCA
40017806 TCATCAAATAAAT
1 TCATCAAATAAAT
*
40017819 TCATGAAATAAAT
1 TCATCAAATAAAT
40017832 TCAT
1 TCAT
40017836 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:40025866 original size:30 final size:33
Alignment explanation
Indices: 40025830--40025908 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
40025820 ATGTGGAGGG
*
40025830 TTTAA-TTGATTTTTTTG-T-ATTATTTTATGA
1 TTTAATTTAATTTTTTTGTTAATTATTTTATGA
*
40025860 TTTAATTTAATTTTTTTGTTAATTATTTTAGGAAA
1 TTTAATTTAATTTTTTTGTTAATTATTTTATG--A
*
40025895 CTTAATTTAATTTT
1 TTTAATTTAATTTT
40025909 AGATATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.12
31 11 0.27
32 1 0.02
33 10 0.24
35 14 0.34
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (33 bp):
TTTAATTTAATTTTTTTGTTAATTATTTTATGA
Found at i:40025943 original size:10 final size:9
Alignment explanation
Indices: 40025917--40026050 Score: 81
Period size: 10 Copynumber: 13.9 Consensus size: 9
40025907 TTAGATATTA
40025917 TATAAAAAT
1 TATAAAAAT
* *
40025926 TCTCAAAATT
1 TAT-AAAAAT
40025936 TATAAAAAT
1 TATAAAAAT
40025945 TATTAAAATAT
1 TA-TAAAA-AT
*
40025956 TA-AAATAT
1 TATAAAAAT
* *
40025964 TTTAGAAAT
1 TATAAAAAT
40025973 TATAGAAAAT
1 TATA-AAAAT
40025983 TATATAAGAAT
1 TATA-AA-AAT
* *
40025994 AATTAAAAT
1 TATAAAAAT
*
40026003 GATAAAAAT
1 TATAAAAAT
40026012 TAATAAAAAAGT
1 T-AT-AAAAA-T
40026024 TATAAAAATT
1 TATAAAAA-T
* *
40026034 TATTAAAAG
1 TATAAAAAT
40026043 TATAAAAA
1 TATAAAAA
40026051 GATGTAAAAA
Statistics
Matches: 96, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
8 3 0.03
9 36 0.38
10 39 0.41
11 16 0.17
12 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (9 bp):
TATAAAAAT
Found at i:40025952 original size:19 final size:19
Alignment explanation
Indices: 40025917--40026041 Score: 69
Period size: 19 Copynumber: 6.4 Consensus size: 19
40025907 TTAGATATTA
* *
40025917 TATAAAAATTCTCAAAATT
1 TATAAAAATTATTAAAATT
40025936 TATAAAAATTATTAAAATAT
1 TATAAAAATTATTAAAAT-T
*
40025956 TA-AAATATT-TTAGAAA-T
1 TATAAAAATTATTA-AAATT
40025973 TATAGAAAATTATATAAGAA-T
1 TATA-AAAATTAT-TAA-AATT
* * * *
40025994 AATTAAAATGATAAAAATT
1 TATAAAAATTATTAAAATT
* *
40026013 AATAAAAAAGTTATAAAAATT
1 TAT-AAAAA-TTATTAAAATT
40026034 TATTAAAA
1 TA-TAAAA
40026042 GTATAAAAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.04
18 6 0.07
19 36 0.43
20 16 0.19
21 22 0.26
22 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TATAAAAATTATTAAAATT
Found at i:40026030 original size:21 final size:19
Alignment explanation
Indices: 40026004--40026050 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
40025994 AATTAAAATG
40026004 ATAAAAATTAATAAAAAAGTT
1 ATAAAAATTAAT-AAAAAG-T
* *
40026025 ATAAAAATTTATTAAAAGT
1 ATAAAAATTAATAAAAAGT
40026044 ATAAAAA
1 ATAAAAA
40026051 GATGTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
ATAAAAATTAATAAAAAGT
Found at i:40026435 original size:20 final size:18
Alignment explanation
Indices: 40026388--40026434 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
40026378 TTTTAGAAAA
40026388 TTATAAAAAGTATATAAG
1 TTATAAAAAGTATATAAG
40026406 TTATTAAAAAGTAT-TAAATG
1 TTA-TAAAAAGTATAT-AA-G
40026426 TTATAAAAA
1 TTATAAAAA
40026435 ATTTAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATAAAAAGTATATAAG
Found at i:40026522 original size:30 final size:30
Alignment explanation
Indices: 40026488--40026559 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
40026478 TATAATCCCT
* ** *
40026488 AAATCAATTAAGCCCTTTTAAAATAATTAA
1 AAATCAATTAAGCCATCATAAAATAATAAA
40026518 AAATCAATTTAAGCCATCATAAAATAATAAA
1 AAATCAA-TTAAGCCATCATAAAATAATAAA
40026549 AAAT-AATTAAG
1 AAATCAATTAAG
40026560 TCCTCCACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 5 0.14
30 9 0.24
31 23 0.62
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATCAATTAAGCCATCATAAAATAATAAA
Found at i:40029290 original size:14 final size:16
Alignment explanation
Indices: 40029266--40029297 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40029256 AATTAGTTGC
40029266 AAAAAAGAAA-GGGTG
1 AAAAAAGAAAGGGGTG
40029281 AAAAAA-AAAGGGGTG
1 AAAAAAGAAAGGGGTG
40029296 AA
1 AA
40029298 GATATACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAGGGGTG
Found at i:40032935 original size:13 final size:13
Alignment explanation
Indices: 40032896--40032924 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40032886 AAATTGTGAT
40032896 AATTA-TAATTAA
1 AATTATTAATTAA
40032908 AATTATTAATTAA
1 AATTATTAATTAA
40032921 AATT
1 AATT
40032925 TTTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTAATTAA
Found at i:40033248 original size:25 final size:24
Alignment explanation
Indices: 40033220--40033267 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40033210 CGTTTTGAGC
40033220 AATTTAATTCTTTTATGTTCTTTTA
1 AATTTAATTCTTTT-TGTTCTTTTA
** *
40033245 AATTTCTTTCTTTTTTTTCTTTT
1 AATTTAATTCTTTTTGTTCTTTT
40033268 TTTTCCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (24 bp):
AATTTAATTCTTTTTGTTCTTTTA
Found at i:40033546 original size:23 final size:24
Alignment explanation
Indices: 40033520--40033566 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
40033510 ATAGGAAAGT
40033520 TTAAAGAACATAAAA-GAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
** *
40033543 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
40033567 ATATGAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (24 bp):
TTAAAGAACATAAAACGAAAAAAA
Found at i:40034493 original size:18 final size:18
Alignment explanation
Indices: 40034472--40034518 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
40034462 TATTAAAAAC
*
40034472 AAATAAAAACATCAT-TAA
1 AAATAAAAAAAT-ATATAA
40034490 AAATAATAAAAATATATAA
1 AAATAA-AAAAATATATAA
40034509 AAATTAAAAA
1 AAA-TAAAAA
40034519 TTATGACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.32
19 14 0.56
20 3 0.12
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAAAAATATATAA
Found at i:40034512 original size:10 final size:10
Alignment explanation
Indices: 40034453--40034512 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
40034443 ATTTATATTA
*
40034453 ATATTAAAAT
1 ATATAAAAAT
*
40034463 AT-TAAAAAC
1 ATATAAAAAT
* *
40034472 AAATAAAAAC
1 ATATAAAAAT
40034482 ATCATTAAAAAT
1 AT-A-TAAAAAT
40034494 A-ATAAAAAT
1 ATATAAAAAT
40034503 ATATAAAAAT
1 ATATAAAAAT
40034513 TAAAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 14 0.34
10 19 0.46
11 1 0.02
12 7 0.17
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:40034914 original size:3 final size:3
Alignment explanation
Indices: 40034906--40034970 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
40034896 TATCAAGCGG
40034906 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40034954 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
40034971 AGGACACATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40035581 original size:14 final size:14
Alignment explanation
Indices: 40035562--40035588 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40035552 AAAAAGAGTT
40035562 GAAATTCAAAATTC
1 GAAATTCAAAATTC
40035576 GAAATTCAAAATT
1 GAAATTCAAAATT
40035589 ACATCCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
GAAATTCAAAATTC
Found at i:40037561 original size:17 final size:18
Alignment explanation
Indices: 40037529--40037562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40037519 ATAAAAACAA
*
40037529 ATAATTTTTGTTTAATTC
1 ATAATTGTTGTTTAATTC
40037547 ATAATTGTT-TTTAATT
1 ATAATTGTTGTTTAATT
40037563 TTTATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (18 bp):
ATAATTGTTGTTTAATTC
Found at i:40040912 original size:20 final size:20
Alignment explanation
Indices: 40040867--40040904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40040857 GAATTGAATT
*
40040867 TATTAGTAATAAACTATTAC
1 TATTACTAATAAACTATTAC
40040887 TATTACTAATAAA-TATTA
1 TATTACTAATAAACTATTA
40040905 ACTTTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTACTAATAAACTATTAC
Found at i:40050960 original size:3 final size:3
Alignment explanation
Indices: 40050954--40050978 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40050944 AAAAAGCAAA
40050954 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
40050979 GAGAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40052628 original size:7 final size:6
Alignment explanation
Indices: 40052577--40052710 Score: 51
Period size: 6 Copynumber: 22.5 Consensus size: 6
40052567 AATATTTACT
* * * ** *
40052577 AAATTA AAATTA ATA-TA ACATCA AAATTA AAACCCA AAGTTA AAACTTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAA-TTA AAATTA AAA-TTA
* * * * * *
40052626 AAATTA AAA--A AAATTA ACATCA CAGTTA AAATTCA AATTTA AAATCA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATT-A AAATTA AAATTA
** * * * *
40052673 AAATT- ATCTTA AATTTA AAATAA AAAATA AAAATA AAA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAA
40052711 CATATGAAAT
Statistics
Matches: 90, Mismatches: 31, Indels: 14
0.67 0.23 0.10
Matches are distributed among these distances:
4 4 0.04
5 7 0.08
6 65 0.72
7 14 0.16
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:40052655 original size:48 final size:48
Alignment explanation
Indices: 40052577--40052678 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
40052567 AATATTTACT
** *
40052577 AAATTAAAATTAATATAACATCAAAATTAAAACCCAAAGTTAAAACTTA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAA-TCA
* * ** *
40052626 AAATTAAAAAAAAT-TAACATCACAGTTAAAATTCAAATTTAAAATCA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAATCA
40052673 AAATTA
1 AAATTA
40052679 TCTTAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
47 8 0.18
48 25 0.56
49 12 0.27
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (48 bp):
AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAATCA
Found at i:40061560 original size:21 final size:21
Alignment explanation
Indices: 40061536--40061587 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
40061526 AACGGAGGAA
40061536 GTTGAGCAGTTTA-TCTACACC
1 GTTGAGCAGTTTATTC-ACACC
**
40061557 GTTGAGTGGTTTATTCACACC
1 GTTGAGCAGTTTATTCACACC
40061578 GTTTGAGCAG
1 G-TTGAGCAG
40061588 CTTTTATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
GTTGAGCAGTTTATTCACACC
Found at i:40068164 original size:111 final size:111
Alignment explanation
Indices: 40067987--40068199 Score: 275
Period size: 111 Copynumber: 1.9 Consensus size: 111
40067977 TACATAATTC
* * *
40067987 ATATTATAAACATAAAAATAGGTTGAGCTTAAGCTTTGGATATTAATCTCGCACCCAATTTGTAT
1 ATATTATAAACATAAAAATAGGTTAAGCTTAAACTTTGGATATTAATCTCGCACCCAATTTATAT
*
40068052 TTTAAACAAGATTAAATTTTTGTTCAAGTCACTTCTCGAGCTTTAT
66 TTTAAACAAGATTAAATTTTTATTCAAGTCACTTCTCGAGCTTTAT
* * * * **
40068098 ATATTATAAACTTAAAAATAGTTTAAGCTTAAACTTTGGATATTAGA-CTCGTATCTGATTTATA
1 ATATTATAAACATAAAAATAGGTTAAGCTTAAACTTTGGATATTA-ATCTCGCACCCAATTTATA
* * * * *
40068162 TTTTAAACGAGTTTAATTTTTTATTTAAGTTACTTCTC
65 TTTTAAACAAGATTAAATTTTTATTCAAGTCACTTCTC
40068200 AAGTTTTTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 85 0.99
112 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (111 bp):
ATATTATAAACATAAAAATAGGTTAAGCTTAAACTTTGGATATTAATCTCGCACCCAATTTATAT
TTTAAACAAGATTAAATTTTTATTCAAGTCACTTCTCGAGCTTTAT
Found at i:40068856 original size:7 final size:7
Alignment explanation
Indices: 40068844--40068868 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40068834 AAACAGTAGA
40068844 TTTTGCT
1 TTTTGCT
40068851 TTTTGCT
1 TTTTGCT
40068858 TTTTGCT
1 TTTTGCT
40068865 TTTT
1 TTTT
40068869 ATTCCATAAA
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:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGCT
Found at i:40072229 original size:5 final size:5
Alignment explanation
Indices: 40072219--40072244 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40072209 TTCTCATGTC
40072219 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
40072245 GTCTAAATTA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40072381 original size:158 final size:160
Alignment explanation
Indices: 40072102--40072393 Score: 421
Period size: 158 Copynumber: 1.8 Consensus size: 160
40072092 AAGTATATAG
* *
40072102 ATTAAATCTCAAATTTGAGCCAAATAAAGGGATCATAAATAAAATTTAACCAATCTCATATAATC
1 ATTAAATCTCAAATTTGAGCCAAATAAAGGGATCATAAATAAAATTTAACCAATCTCACACAATC
* * * * * *
40072167 TTTAAAAGGTAGATGGATTAGAACTGAAATTTTGCCATTATTTTCTCATGTCAAAAGAAAAGAAA
66 TTAAAAAGATAGATGGATTAGAACTGAAATTTAGCAATTAATTTCTCATGCCAAAAGAAAAGAAA
40072232 AGAAAAGAAAAGAGTCTAAATTATGTCAAA
131 AGAAAAGAAAAGAGTCTAAATTATGTCAAA
** * * *
40072262 ATTAAATCTCAAATTTGAGTGAAATATA-GGATCA-AAACTAAAATTTAACCATTCTTACACAAT
1 ATTAAATCTCAAATTTGAGCCAAATAAAGGGATCATAAA-TAAAATTTAACCAATCTCACACAAT
40072325 CTTAAAAAGATAGA-GGATTAGAACTGAAATTTAGCAATTACATTT-TCATGCCAAAAGAAAAGA
65 CTTAAAAAGATAGATGGATTAGAACTGAAATTTAGCAATTA-ATTTCTCATGCCAAAAGAAAAGA
40072388 AAAGAA
129 AAAGAA
40072394 TGAATAGGTT
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
158 50 0.43
159 42 0.36
160 25 0.21
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (160 bp):
ATTAAATCTCAAATTTGAGCCAAATAAAGGGATCATAAATAAAATTTAACCAATCTCACACAATC
TTAAAAAGATAGATGGATTAGAACTGAAATTTAGCAATTAATTTCTCATGCCAAAAGAAAAGAAA
AGAAAAGAAAAGAGTCTAAATTATGTCAAA
Found at i:40073142 original size:22 final size:23
Alignment explanation
Indices: 40073114--40073168 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
40073104 ATTTAGTGAT
*
40073114 TTTTAAATATTATTTAATAAA-A
1 TTTTAAAAATTATTTAATAAATA
* *
40073136 TTTTAAAAATTGTTTCATAAATA
1 TTTTAAAAATTATTTAATAAATA
40073159 TTTCTAAAAA
1 TTT-TAAAAA
40073169 AAATCTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.64
23 4 0.14
24 6 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTAAAAATTATTTAATAAATA
Found at i:40075272 original size:16 final size:17
Alignment explanation
Indices: 40075239--40075273 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40075229 ACCGTTATTA
40075239 AACCTTTAAATAGAAGG
1 AACCTTTAAATAGAAGG
*
40075256 AACCTTT-AATAGGAGG
1 AACCTTTAAATAGAAGG
40075272 AA
1 AA
40075274 TCTTATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (17 bp):
AACCTTTAAATAGAAGG
Found at i:40077776 original size:17 final size:17
Alignment explanation
Indices: 40077754--40077794 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
40077744 GGTACTTTAA
*
40077754 AATTGAATTATATTCAT
1 AATTGAATTAAATTCAT
40077771 AATTGAATTAAATTCAT
1 AATTGAATTAAATTCAT
*
40077788 AAGTGAA
1 AATTGAA
40077795 ATGAAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (17 bp):
AATTGAATTAAATTCAT
Found at i:40078288 original size:37 final size:36
Alignment explanation
Indices: 40078241--40078315 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
40078231 TATGTGATTG
* * *
40078241 ATATTGAAATGACAAAGATGATAAATGAATATGAGAT
1 ATATTGAAATGAAAAAGATGAGAAATG-AGATGAGAT
*
40078278 ATATTGAAATGAAAAATATGAGAAATGAGATGAGAT
1 ATATTGAAATGAAAAAGATGAGAAATGAGATGAGAT
40078314 AT
1 AT
40078316 GATATATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 10 0.29
37 24 0.71
ACGTcount: A:0.52, C:0.01, G:0.20, T:0.27
Consensus pattern (36 bp):
ATATTGAAATGAAAAAGATGAGAAATGAGATGAGAT
Found at i:40078871 original size:23 final size:25
Alignment explanation
Indices: 40078831--40078884 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
40078821 TCAGGTTATG
40078831 TTGGTATGCTAGCCTAGTTT-ATATT
1 TTGGTATGCTAGCCTAGTTTCATA-T
*
40078856 TTGGTATG-T-GCTTAGTTTCATAT
1 TTGGTATGCTAGCCTAGTTTCATAT
40078879 TTGGTA
1 TTGGTA
40078885 ACTTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 15 0.56
24 4 0.15
25 8 0.30
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (25 bp):
TTGGTATGCTAGCCTAGTTTCATAT
Found at i:40079399 original size:52 final size:51
Alignment explanation
Indices: 40079326--40079433 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 51
40079316 TATTTTTTAG
* *
40079326 ACTATTTTTAGGGTCTCGTAGACTTGTAATA-AGGGCTGTAAGAGTAAATTTT
1 ACTATTTTTAGGGTATCGTAGACTAGTAATAGA-GG-TGTAAGAGTAAATTTT
40079378 ACTATTTTTAGGGTATCGTAGACTAGTAATAGAGGTGTAAGAGTAAATTTT
1 ACTATTTTTAGGGTATCGTAGACTAGTAATAGAGGTGTAAGAGTAAATTTT
40079429 ACTAT
1 ACTAT
40079434 GAATTAGGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
51 21 0.40
52 31 0.58
53 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.38
Consensus pattern (51 bp):
ACTATTTTTAGGGTATCGTAGACTAGTAATAGAGGTGTAAGAGTAAATTTT
Found at i:40081231 original size:28 final size:27
Alignment explanation
Indices: 40081183--40081268 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
40081173 GAATCCTACT
*
40081183 TATAAGATAGTCCTGACGGACTTCCACA
1 TATAAAATAGTCCTG-CGGACTTCCACA
* * * *
40081211 TATAAAATCGTCTTGATGGACTTCAACA
1 TATAAAATAGTCCTG-CGGACTTCCACA
*
40081239 TATAAAATAGTCCTGCGAACTTCCACA
1 TATAAAATAGTCCTGCGGACTTCCACA
40081266 TAT
1 TAT
40081269 TTTTTCATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 12 0.25
28 36 0.75
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (27 bp):
TATAAAATAGTCCTGCGGACTTCCACA
Found at i:40088216 original size:19 final size:18
Alignment explanation
Indices: 40088180--40088220 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
40088170 AGATTAAATT
*
40088180 TTAATTAATTATGATTAA
1 TTAATTAATTAGGATTAA
*
40088198 GTTAATTAATTAGGTTTAA
1 -TTAATTAATTAGGATTAA
40088217 TTAA
1 TTAA
40088221 AATTAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
TTAATTAATTAGGATTAA
Found at i:40090172 original size:28 final size:28
Alignment explanation
Indices: 40090132--40090187 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
40090122 AAAAACATGT
* *
40090132 TATAAAATTAAAAGAAATATAGAATGGA
1 TATAAAACTAAAAGAAATATAAAATGGA
40090160 TATAAAACTAAAAGAAATATAAAATGGA
1 TATAAAACTAAAAGAAATATAAAATGGA
40090188 CAAAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.23
Consensus pattern (28 bp):
TATAAAACTAAAAGAAATATAAAATGGA
Found at i:40096921 original size:19 final size:20
Alignment explanation
Indices: 40096897--40096945 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
40096887 TGAGTTAGTA
*
40096897 ATTTATTTTATGTATTTTG-
1 ATTTATTTTATGTATATTGT
*
40096916 ATTTA-TTTATTTATATTGT
1 ATTTATTTTATGTATATTGT
40096935 ATTTATTTTAT
1 ATTTATTTTAT
40096946 TTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (20 bp):
ATTTATTTTATGTATATTGT
Found at i:40096926 original size:14 final size:13
Alignment explanation
Indices: 40096898--40096951 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 13
40096888 GAGTTAGTAA
*
40096898 TTTATTTTATGTAT
1 TTTA-TTTATTTAT
40096912 TTTGATTTATTTAT
1 TTT-ATTTATTTAT
40096926 TTATATTGTATTTAT
1 TT-TATT-TATTTAT
40096941 TTTATTT-TTTA
1 TTTATTTATTTA
40096952 ATGTTCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 20 0.56
15 11 0.31
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:40096942 original size:23 final size:25
Alignment explanation
Indices: 40096897--40096955 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
40096887 TGAGTTAGTA
40096897 ATTTATTT-TATGTATTTTGA-TTT
1 ATTTATTTATATGTATTTTGATTTT
40096920 ATTTATTTATATTGTA-TTT-ATTTT
1 ATTTATTTATA-TGTATTTTGATTTT
40096944 ATTT-TTTA-ATGT
1 ATTTATTTATATGT
40096956 TCATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 13 0.39
24 12 0.36
25 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (25 bp):
ATTTATTTATATGTATTTTGATTTT
Found at i:40099031 original size:20 final size:20
Alignment explanation
Indices: 40099006--40099056 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40098996 AAAATGTATA
* *
40099006 TGATTGCAGTTCAACACCCC
1 TGATTGCACTCCAACACCCC
**
40099026 TGATTGCACTCCAATGCCCC
1 TGATTGCACTCCAACACCCC
40099046 TGATTGCACTC
1 TGATTGCACTC
40099057 TAGTGCCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (20 bp):
TGATTGCACTCCAACACCCC
Found at i:40099075 original size:21 final size:20
Alignment explanation
Indices: 40099022--40099085 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
40099012 CAGTTCAACA
* *
40099022 CCCCTGATTGCACTCCAATG
1 CCCCTGATTGCACTCTAGTG
40099042 CCCCTGATTGCACTCTAGTG
1 CCCCTGATTGCACTCTAGTG
* *
40099062 CCTCTGATTTGCACTCTTGTG
1 CCCCTGA-TTGCACTCTAGTG
40099083 CCC
1 CCC
40099086 TTGTATGTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.14, C:0.38, G:0.17, T:0.31
Consensus pattern (20 bp):
CCCCTGATTGCACTCTAGTG
Found at i:40103823 original size:29 final size:29
Alignment explanation
Indices: 40103786--40103844 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
40103776 TACTAACAAT
* *
40103786 TTGAGCTAATTAATAACATTATAAAAATA
1 TTGAACTAATTAAGAACATTATAAAAATA
40103815 TTGAACTAATTAAGAACATTATAAAAATA
1 TTGAACTAATTAAGAACATTATAAAAATA
40103844 T
1 T
40103845 AGAGACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (29 bp):
TTGAACTAATTAAGAACATTATAAAAATA
Found at i:40105256 original size:30 final size:30
Alignment explanation
Indices: 40105181--40105270 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
40105171 GTACGGGTAA
*
40105181 CCTAATATAAACTT-AGCTTGTGTGATCAAT
1 CCTAATATAAA-TTCAGCTTGTGTGATCAAC
* *
40105211 CTTAATATAAATTCAGCTTGTGTGAGCAAC
1 CCTAATATAAATTCAGCTTGTGTGATCAAC
* * * * *
40105241 CCTGATGTAATTTCAGGTTATGTGATCAAC
1 CCTAATATAAATTCAGCTTGTGTGATCAAC
40105271 ATAGTTCACC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
29 2 0.04
30 47 0.96
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (30 bp):
CCTAATATAAATTCAGCTTGTGTGATCAAC
Found at i:40106515 original size:12 final size:12
Alignment explanation
Indices: 40106498--40106522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40106488 GGTGTTCATT
40106498 CGGTTAACCGAC
1 CGGTTAACCGAC
40106510 CGGTTAACCGAC
1 CGGTTAACCGAC
40106522 C
1 C
40106523 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:40106702 original size:9 final size:9
Alignment explanation
Indices: 40106683--40106768 Score: 127
Period size: 9 Copynumber: 9.6 Consensus size: 9
40106673 TTTGGTTAAA
*
40106683 AATTAACCG
1 AATTACCCG
*
40106692 AATTACTCG
1 AATTACCCG
40106701 AATTACCCG
1 AATTACCCG
*
40106710 AATTAACCG
1 AATTACCCG
40106719 AATTACCCG
1 AATTACCCG
40106728 AATTACCCG
1 AATTACCCG
*
40106737 AATTAACCG
1 AATTACCCG
40106746 AATTACCCG
1 AATTACCCG
*
40106755 AATTAACCG
1 AATTACCCG
40106764 AATTA
1 AATTA
40106769 ATCAAATTGA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:40106776 original size:27 final size:27
Alignment explanation
Indices: 40106683--40106769 Score: 156
Period size: 27 Copynumber: 3.2 Consensus size: 27
40106673 TTTGGTTAAA
*
40106683 AATTAACCGAATTACTCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
40106710 AATTAACCGAATTACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
*
40106737 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTACCCG
40106764 AATTAA
1 AATTAA
40106770 TCAAATTGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTACCCG
Found at i:40108007 original size:45 final size:45
Alignment explanation
Indices: 40107893--40108112 Score: 212
Period size: 45 Copynumber: 4.9 Consensus size: 45
40107883 AACCGTTACA
* * * *
40107893 CGGTGG-ATCAGCACATAGC-ACTACCCTTATAATTAATTATATT-
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGAT-TTC
* * * ** *
40107936 CGGTAGAATTAGCATATAGCAACCACCTTTATTTTTAATGATTTC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATTTC
* * **
40107981 CGGTGGAGTCAGCACATAGCAGCCACCTTTATTTTCAATGATTTC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATTTC
* * * * * **
40108026 TGATGGAGTCAACACATAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATTTC
*
40108071 CGATGGAATCAGCACATAGCAACCACCTTTATAATCAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGAT
40108113 ACTCAATACA
Statistics
Matches: 147, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.03
44 13 0.09
45 129 0.88
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATTTC
Found at i:40108188 original size:51 final size:53
Alignment explanation
Indices: 40108125--40108225 Score: 125
Period size: 55 Copynumber: 1.9 Consensus size: 53
40108115 TCAATACACG
*
40108125 TAGTAGCCTGCACATAGTAC-T-ACACATGTGAGCATTACTATCACTTTCACA
1 TAGTAGCCTGCACACAGTACGTCACACATGTGAGCATTACTATCACTTTCACA
* * * *
40108176 TAGTGGCCTGCACACAGTCCGTGCCACACATGTGATCATTACTGTCACTT
1 TAGTAGCCTGCACACAGTACGT--CACACATGTGAGCATTACTATCACTT
40108226 CATTCGTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 17 0.41
52 1 0.02
55 23 0.56
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (53 bp):
TAGTAGCCTGCACACAGTACGTCACACATGTGAGCATTACTATCACTTTCACA
Found at i:40111309 original size:30 final size:30
Alignment explanation
Indices: 40111253--40111325 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
40111243 AATTTTCAAA
* * *
40111253 AAAAATTAAAAGGTACAATGAGAATTTTC-
1 AAAAATTTAAAGGTACAATAAAAATTTTCT
*
40111282 AAAAATTTAAAGGTTCTAATAAAAATTTTCT
1 AAAAATTTAAAGGTAC-AATAAAAATTTTCT
* *
40111313 GAAAATTTCAAGG
1 AAAAATTTAAAGG
40111326 GAGAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 11 0.31
31 11 0.31
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAAATTTAAAGGTACAATAAAAATTTTCT
Found at i:40113119 original size:3 final size:3
Alignment explanation
Indices: 40113111--40113160 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
40113101 TTTCTTTTAT
* *
40113111 TTA TTA TTA -TA TTA TTA TTA TTTA TTA TTA TTA TTA TCA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
40113156 TTA TT
1 TTA TT
40113161 GTTCCTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:40113132 original size:21 final size:22
Alignment explanation
Indices: 40113107--40113160 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
40113097 TAATTTTCTT
*
40113107 TTATTTATTATTA-TATTATTA
1 TTATTTATTATTATTATTATCA
40113128 TTATTTATTATTATTATTATCA
1 TTATTTATTATTATTATTATCA
*
40113150 TTA-CTATTATT
1 TTATTTATTATT
40113161 GTTCCTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTATTATTATTATTATCA
Found at i:40113273 original size:25 final size:26
Alignment explanation
Indices: 40113208--40113278 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
40113198 TATATATATG
40113208 TATTTTTAT-GTATAGTATATACGCA
1 TATTTTTATAGTATAGTATATACGCA
* * * *
40113233 TAGTTTTTTTAATATA-TATATAGGTA
1 TA-TTTTTATAGTATAGTATATACGCA
40113259 TATTTTTATAGTATACGTAT
1 TATTTTTATAGTATA-GTAT
40113279 GTTATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
25 13 0.36
26 16 0.44
27 7 0.19
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.52
Consensus pattern (26 bp):
TATTTTTATAGTATAGTATATACGCA
Found at i:40114738 original size:19 final size:19
Alignment explanation
Indices: 40114716--40114752 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40114706 TTTAAAATAC
40114716 TTTTAAAATAATTTTTTAT
1 TTTTAAAATAATTTTTTAT
40114735 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
40114753 ATGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:40114759 original size:20 final size:19
Alignment explanation
Indices: 40114717--40114759 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
40114707 TTAAAATACT
*
40114717 TTTAAAATAATTTTTTATT
1 TTTAAAATAATTTTTTATG
40114736 TTTAAAATAATTTTTTAATG
1 TTTAAAATAATTTTTT-ATG
40114756 TTTA
1 TTTA
40114760 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAAATAATTTTTTATG
Found at i:40117317 original size:9 final size:9
Alignment explanation
Indices: 40117270--40117319 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
40117260 TGATGAAAAG
*
40117270 AATTTTAAG
1 AATTTTAAA
40117279 AATTTTAAA
1 AATTTTAAA
*
40117288 AATATATAAA
1 AAT-TTTAAA
*
40117298 AAGTTTCAAA
1 AA-TTTTAAA
40117308 AATTTTAAA
1 AATTTTAAA
40117317 AAT
1 AAT
40117320 ATCTTACGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 20 0.59
10 13 0.38
11 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (9 bp):
AATTTTAAA
Found at i:40118950 original size:2 final size:2
Alignment explanation
Indices: 40118943--40118970 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40118933 CTAAAATTTA
40118943 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
40118971 TTCCAATATC
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:40120352 original size:7 final size:7
Alignment explanation
Indices: 40120340--40120371 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40120330 TTTGGCAAAA
40120340 ACATAAT
1 ACATAAT
40120347 ACATAAT
1 ACATAAT
40120354 ACATAAT
1 ACATAAT
40120361 ACATAAT
1 ACATAAT
40120368 ACAT
1 ACAT
40120372 TAAATTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATAAT
Found at i:40128103 original size:9 final size:9
Alignment explanation
Indices: 40128085--40128142 Score: 98
Period size: 9 Copynumber: 6.4 Consensus size: 9
40128075 TTTGGTTAAA
40128085 AATTAACCG
1 AATTAACCG
*
40128094 AATTACCCG
1 AATTAACCG
40128103 AATTAACCG
1 AATTAACCG
40128112 AATTAACCG
1 AATTAACCG
*
40128121 AATTACCCG
1 AATTAACCG
40128130 AATTAACCG
1 AATTAACCG
40128139 AATT
1 AATT
40128143 GAATCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:40128117 original size:27 final size:27
Alignment explanation
Indices: 40128085--40128142 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
40128075 TTTGGTTAAA
40128085 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
40128112 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
40128139 AATT
1 AATT
40128143 GAATCACTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:40128193 original size:6 final size:6
Alignment explanation
Indices: 40128182--40128210 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40128172 ACTTTTAGAC
40128182 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
40128211 AATTTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:40128291 original size:18 final size:18
Alignment explanation
Indices: 40128251--40128294 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40128241 AATTTTTATG
*
40128251 ATTGGGTTGGGTTAGGTA
1 ATTGGGTTGGGTTAGATA
40128269 ATTGGGTTGGGTT-GAATA
1 ATTGGGTTGGGTTAG-ATA
*
40128287 CTTGGGTT
1 ATTGGGTT
40128295 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTAGATA
Found at i:40128627 original size:27 final size:27
Alignment explanation
Indices: 40128597--40128999 Score: 421
Period size: 27 Copynumber: 14.9 Consensus size: 27
40128587 GTAAATAACC
*
40128597 GAAATACCCTTGAAGGGTAAAATGACT
1 GAAATACCCTCGAAGGGTAAAATGACT
** *
40128624 GAAATACCCTCGAAGGACAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* *
40128651 GAAATAGCCTCGAAGGGTAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* * * * * *
40128678 AAAATACCCCCTAAAGATAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* * * *
40128705 GAAATACCCTAGAAAGGTAAAATAACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* * *
40128732 AAAATACCCCCGAAGGGTAAAATGAGT
1 GAAATACCCTCGAAGGGTAAAATGACT
* *
40128759 GAAATACCCTCAAAAGGTAAAATGACT
1 GAAATACCCTCGAAGGGTAAAATGACT
* * * *
40128786 AAAATACCCTTGAATGGTAAAATAACT
1 GAAATACCCTCGAAGGGTAAAATGACT
*
40128813 GAAATACCCTCGAAGGGTAAAATAACT
1 GAAATACCCTCGAAGGGTAAAATGACT
* * *
40128840 GAAATACTCGCGAAGGGTAAAATGACA
1 GAAATACCCTCGAAGGGTAAAATGACT
* *
40128867 AAAATACCCTCGAAGGGTAAAATGATT
1 GAAATACCCTCGAAGGGTAAAATGACT
** *
40128894 GAAATACCCTTAAAGGGTAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* * * *
40128921 GAAATGCCCCCGAAGGGCAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACT
* *
40128948 GAAATACCCCCGAAGGGTAAAATAACT
1 GAAATACCCTCGAAGGGTAAAATGACT
*
40128975 GAAATACCC-CCATAGGGTAAAATGA
1 GAAATACCCTCGA-AGGGTAAAATGA
40129000 TTTTTATACC
Statistics
Matches: 311, Mismatches: 64, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 2 0.01
27 309 0.99
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATGACT
Found at i:40129416 original size:28 final size:28
Alignment explanation
Indices: 40129371--40129473 Score: 145
Period size: 28 Copynumber: 3.7 Consensus size: 28
40129361 ACTGTAATGT
*
40129371 TACTATATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
40129399 TATTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
40129427 TGCTGTATTGGGCTAAGGCCCACACT-A
1 TACTGTATTGGGCTAAGGCCCACACTGA
* *
40129454 CTACTGAATTGGGATAAGGC
1 -TACTGTATTGGGCTAAGGC
40129474 ATTCATTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 1 0.01
28 66 0.99
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGA
Found at i:40130948 original size:21 final size:21
Alignment explanation
Indices: 40130909--40130949 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40130899 CAAAATATAT
**
40130909 TCTGTAACACCCCTTACTCGG
1 TCTGTAACACCCCGAACTCGG
*
40130930 TCTGTAACCCCCCGAACTCG
1 TCTGTAACACCCCGAACTCG
40130950 TGTCCGTCGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.41, G:0.15, T:0.24
Consensus pattern (21 bp):
TCTGTAACACCCCGAACTCGG
Found at i:40131153 original size:2 final size:2
Alignment explanation
Indices: 40131146--40131217 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
40131136 AAGTCATCTC
40131146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40131187 AT 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 AT A
40131218 CTAATTAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40131508 original size:23 final size:23
Alignment explanation
Indices: 40131474--40131711 Score: 206
Period size: 23 Copynumber: 10.2 Consensus size: 23
40131464 TGGACAACTC
* * *
40131474 TTATACATCAAATCGGTCAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
40131497 TTATACACCAAAATTTGACGGCAT
1 TTATACACC-AAATTGGACAGCAT
* * * *
40131521 ATATATACAAAATTGGATAGCAT
1 TTATACACCAAATTGGACAGCAT
* **
40131544 TTATACACGAAATTGGGTAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
40131567 ATATATACCAATTTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
40131590 TTATACACGAAATTGGGCAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
40131613 ATATATACCAATTTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
40131636 TTATACACCAAAATTTGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
* * *
40131660 ATATATACAAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
40131683 TTACACACCAAAATTTGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
*
40131707 ATATA
1 TTATA
40131712 TATAAAATTG
Statistics
Matches: 166, Mismatches: 46, Indels: 5
0.76 0.21 0.02
Matches are distributed among these distances:
23 116 0.70
24 50 0.30
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (23 bp):
TTATACACCAAATTGGACAGCAT
Found at i:40131546 original size:47 final size:47
Alignment explanation
Indices: 40131491--40131721 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 47
40131481 TCAAATCGGT
*
40131491 CAGCATTTATACACCAAAATTTGACGGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
* * * ** * *
40131538 TAGCATTTATACA-CGAAATTGGGTAGCATATATATACCAATTTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
* * * * *
40131584 CAGCATTTATACA-CGAAATTGGGCAGCATATATATACCAATTTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
40131630 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
* *
40131677 CAGCATTTACACACCAAAATTTGACAGCATATATATATAAAATTG
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTG
40131722 ATCTAGATAA
Statistics
Matches: 166, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 83 0.50
47 83 0.50
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.29
Consensus pattern (47 bp):
CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
Found at i:40131763 original size:2 final size:2
Alignment explanation
Indices: 40131756--40131797 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
40131746 TCATAATTTC
* * *
40131756 AT AT AT AT AA AT AT AT AT GT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40131798 CCAAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40131780 original size:16 final size:16
Alignment explanation
Indices: 40131756--40131796 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
40131746 TCATAATTTC
40131756 ATATATATAAATATAT
1 ATATATATAAATATAT
*
40131772 ATGTATATAAATATAT
1 ATATATATAAATATAT
40131788 ATATATATA
1 ATATATATA
40131797 TCCAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATATATAAATATAT
Found at i:40132380 original size:311 final size:311
Alignment explanation
Indices: 40131817--40132445 Score: 1204
Period size: 311 Copynumber: 2.0 Consensus size: 311
40131807 AATTTCATAT
40131817 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
1 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
40131882 TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
66 TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
40131947 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCAACTTACC
131 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCAACTTACC
* *
40132012 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATTTGATTTTTTATACTCGATCT
196 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTTATACTCGATCT
*
40132077 TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
261 TAATTTATTACAACCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
40132128 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
1 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
40132193 TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
66 TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
*
40132258 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
131 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCAACTTACC
*
40132323 ATATTTTTATAACTCGAATAAATATATACCTGAGCCTTTCTAATCTGAATTTTTATACTCGATCT
196 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTTATACTCGATCT
*
40132388 TAATTTATTACAACCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAT
261 TAATTTATTACAACCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
40132439 ATCAAAC
1 ATCAAAC
40132446 GTTTCGTATA
Statistics
Matches: 312, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
311 312 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (311 bp):
ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCAACTTACC
ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTTATACTCGATCT
TAATTTATTACAACCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
Found at i:40132522 original size:43 final size:44
Alignment explanation
Indices: 40132456--40132572 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
40132446 GTTTCGTATA
* * *
40132456 ATGCCATCGTCCCAAACGTGGTCTTACATGT-AATAACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAATAACAAATCG
* * *
40132499 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACAAATCT
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAAATAACAAATCG
*
40132543 ATGCCAACGTCTCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG
40132573 ACAACACATA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
42 1 0.02
43 25 0.41
44 33 0.54
45 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAATAACAAATCG
Found at i:40132903 original size:15 final size:15
Alignment explanation
Indices: 40132883--40132911 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40132873 GTTATTGATC
40132883 TAAACACATTCAAAT
1 TAAACACATTCAAAT
40132898 TAAACACATTCAAA
1 TAAACACATTCAAA
40132912 CGTAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAACACATTCAAAT
Found at i:40139620 original size:8 final size:9
Alignment explanation
Indices: 40139596--40139620 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40139586 ATAAAAAATT
40139596 TTTAAAAAC
1 TTTAAAAAC
40139605 TTTAAAAAC
1 TTTAAAAAC
40139614 TTTAAAA
1 TTTAAAA
40139621 TTAACTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (9 bp):
TTTAAAAAC
Found at i:40140100 original size:10 final size:10
Alignment explanation
Indices: 40140060--40140133 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 10
40140050 ATAAATACCA
40140060 AAAATTATTTT
1 AAAA-TATTTT
*
40140071 AAAAT-TTTA
1 AAAATATTTT
40140080 AAAAGTATTTT
1 AAAA-TATTTT
40140091 AAAATATTTT
1 AAAATATTTT
40140101 -AAA-A--TT
1 AAAATATTTT
*
40140107 AAAAAATTTT
1 AAAATATTTT
40140117 AAAAAGTATTTT
1 -AAAA-TATTTT
40140129 AAAAT
1 AAAAT
40140134 TAAAAATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 2 0.04
9 10 0.19
10 11 0.21
11 19 0.37
12 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:40140110 original size:16 final size:16
Alignment explanation
Indices: 40140089--40140120 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40140079 AAAAAGTATT
*
40140089 TTAAAATATTTTAAAA
1 TTAAAAAATTTTAAAA
40140105 TTAAAAAATTTTAAAA
1 TTAAAAAATTTTAAAA
40140121 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:40140148 original size:28 final size:28
Alignment explanation
Indices: 40140059--40140160 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
40140049 AATAAATACC
*
40140059 AAAAATTATTTTAAAATTTTAAAAAGTATTT
1 AAAAAGTATTTTAAAA--TTAAAAA-TATTT
*
40140090 TAAAA-TATTTTAAAATTAAAAA-ATTTT
1 AAAAAGTATTTTAAAATTAAAAATA-TTT
* *
40140117 AAAAAGTATTTTAAAATTAAAAATAATA
1 AAAAAGTATTTTAAAATTAAAAATATTT
40140145 AAAAAGTATTTTAAAA
1 AAAAAGTATTTTAAAA
40140161 ATATTTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 7 0.11
28 41 0.64
29 1 0.02
30 10 0.16
31 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAAAGTATTTTAAAATTAAAAATATTT
Found at i:40140149 original size:38 final size:38
Alignment explanation
Indices: 40140071--40140178 Score: 132
Period size: 38 Copynumber: 2.8 Consensus size: 38
40140061 AAATTATTTT
*** *
40140071 AAAATTTTAAAAAGTATTTTAAAATATTTTAA-AATTAA
1 AAAATTTTAAAAAGTATTTTAAAAT-TAAAAATAATAAA
40140109 AAAATTTTAAAAAGTATTTTAAAATTAAAAATAATAAA
1 AAAATTTTAAAAAGTATTTTAAAATTAAAAATAATAAA
40140147 AAAGTATTTTAAAAA-TATTTT-AAATTAAAAAT
1 AAA--ATTTTAAAAAGTATTTTAAAATTAAAAAT
40140179 TAAAAATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
37 3 0.05
38 44 0.70
39 6 0.10
40 10 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAATTTTAAAAAGTATTTTAAAATTAAAAATAATAAA
Found at i:40164872 original size:3 final size:3
Alignment explanation
Indices: 40164864--40164894 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
40164854 TGACTCTGTT
40164864 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
40164895 ATGAGGAAGG
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:40178774 original size:2 final size:2
Alignment explanation
Indices: 40178767--40178795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40178757 AACATAAAAC
40178767 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
40178796 AAGTGAATTA
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:40180908 original size:29 final size:30
Alignment explanation
Indices: 40180852--40180909 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
40180842 CAGAGATAAT
* * * *
40180852 CATTTAATTATAAAAAATTTTCAGTTTAAG
1 CATTTAATAATAAAAAAATTACAATTTAAG
40180882 CATTTAA-AATAAAAAAATTACAATTTAA
1 CATTTAATAATAAAAAAATTACAATTTAA
40180910 ACACTCATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (30 bp):
CATTTAATAATAAAAAAATTACAATTTAAG
Found at i:40181692 original size:5 final size:6
Alignment explanation
Indices: 40181672--40181708 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
40181662 GAGGGGGAAA
* *
40181672 GGGGCG GGGATG GGGGTG GGGGTG GGGGTG GGGGTG G
1 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG G
40181709 TGGGAGGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.03, G:0.81, T:0.14
Consensus pattern (6 bp):
GGGGTG
Found at i:40181717 original size:18 final size:18
Alignment explanation
Indices: 40181677--40181718 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40181667 GGAAAGGGGC
*
40181677 GGGGATGGGGGTGGGGGTG
1 GGGG-TGGGGGTGGGGGTA
40181696 GGGGTGGGGGTGGTGGG-A
1 GGGGTGGGGGTGG-GGGTA
40181714 GGGGT
1 GGGGT
40181719 ATGAGGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.05, C:0.00, G:0.79, T:0.17
Consensus pattern (18 bp):
GGGGTGGGGGTGGGGGTA
Found at i:40181858 original size:21 final size:23
Alignment explanation
Indices: 40181806--40181858 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
40181796 TAATATAAAA
* *
40181806 TTTAAATTTATTATTATATATTT
1 TTTAAATATATTATGATATATTT
40181829 TTTGAAA-ATATTTATGATATA-TT
1 TTT-AAATATA-TTATGATATATTT
40181852 TTTAAAT
1 TTTAAAT
40181859 TTATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 10 0.40
24 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTAAATATATTATGATATATTT
Found at i:40184130 original size:42 final size:42
Alignment explanation
Indices: 40184051--40184158 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
40184041 ATGAATTTTC
* *
40184051 GTTCAACCCTAATGGGTTTCTATTCAGCTCTATTGAGCTTCA
1 GTTCAACCCTTATGGGTTTCTGTTCAGCTCTATTGAGCTTCA
* * * *
40184093 GTTTAACCTTTATGGGTTTCTGTTCAGCTGT-TATGAGCTTCC
1 GTTCAACCCTTATGGGTTTCTGTTCAGCTCTAT-TGAGCTTCA
* *
40184135 GTTCAACCCTTACGAGTTTCTGTT
1 GTTCAACCCTTATGGGTTTCTGTT
40184159 TAACACTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 54 0.98
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (42 bp):
GTTCAACCCTTATGGGTTTCTGTTCAGCTCTATTGAGCTTCA
Found at i:40191289 original size:25 final size:24
Alignment explanation
Indices: 40191257--40191313 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
40191247 TCTTAGATAT
* * *
40191257 AAATATATATATTTATTATATTTTA
1 AAATATATAAATATATTA-AATTTA
40191282 AAATATATAAATATATTAAATTTA
1 AAATATATAAATATATTAAATTTA
*
40191306 AATTATAT
1 AAATATAT
40191314 TCAAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATATATAAATATATTAAATTTA
Found at i:40191314 original size:16 final size:16
Alignment explanation
Indices: 40191289--40191327 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40191279 TTAAAATATA
40191289 TAAATATATT-AAATT
1 TAAATATATTCAAATT
40191304 TAAATTATATTCAAATT
1 TAAA-TATATTCAAATT
*
40191321 TATATAT
1 TAAATAT
40191328 GAAATGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 8 0.38
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATATTCAAATT
Found at i:40191406 original size:20 final size:19
Alignment explanation
Indices: 40191378--40191417 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
40191368 TAAAATTTAC
40191378 TTTTAATATATAAA-TTATA
1 TTTTAATAT-TAAAGTTATA
40191397 TTTTAGATATTAAAGTTATA
1 TTTTA-ATATTAAAGTTATA
40191417 T
1 T
40191418 AGAAACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTAATATTAAAGTTATA
Found at i:40192677 original size:30 final size:30
Alignment explanation
Indices: 40192643--40192701 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
40192633 CTTATTTTAT
40192643 TGTTAATTTTGTTATTATTTTAAAGGTATC
1 TGTTAATTTTGTTATTATTTTAAAGGTATC
*
40192673 TGTTAATTTTGTTATTATTTTAGAGGTAT
1 TGTTAATTTTGTTATTATTTTAAAGGTAT
40192702 TTGCTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TGTTAATTTTGTTATTATTTTAAAGGTATC
Found at i:40192842 original size:11 final size:11
Alignment explanation
Indices: 40192826--40192856 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40192816 TATATATATT
40192826 TAAAAATTATA
1 TAAAAATTATA
*
40192837 TAAAAATAATA
1 TAAAAATTATA
40192848 TAAAAATTA
1 TAAAAATTA
40192857 ATATGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:40192853 original size:12 final size:11
Alignment explanation
Indices: 40192826--40192860 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
40192816 TATATATATT
*
40192826 TAAAAATTATA
1 TAAAAATAATA
40192837 TAAAAATAATA
1 TAAAAATAATA
40192848 TAAAAATTAATA
1 TAAAAA-TAATA
40192860 T
1 T
40192861 GGGCGGGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:40200471 original size:20 final size:20
Alignment explanation
Indices: 40200446--40200496 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
40200436 AATTAATAAG
*
40200446 CCTTAATTAATTAA-ACTAAA
1 CCTTAATTAACTAATACT-AA
40200466 CCTTAATTAACTAATACTAA
1 CCTTAATTAACTAATACTAA
*
40200486 GCTTAATTAAC
1 CCTTAATTAAC
40200497 AAAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (20 bp):
CCTTAATTAACTAATACTAA
Found at i:40203305 original size:18 final size:18
Alignment explanation
Indices: 40203275--40203322 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
40203265 ATTTAATTAT
40203275 TTTGTTGTTATTGTATAAC
1 TTTGTTGTTATTGT-TAAC
*
40203294 TTTGTT-TTATTGTTAAT
1 TTTGTTGTTATTGTTAAC
*
40203311 TTTGTTGCTATT
1 TTTGTTGTTATT
40203323 TTAGAGGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.65
Consensus pattern (18 bp):
TTTGTTGTTATTGTTAAC
Found at i:40205339 original size:20 final size:20
Alignment explanation
Indices: 40205314--40205351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40205304 CGTAAAATGA
*
40205314 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
40205334 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
40205352 TAGAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40205343 original size:34 final size:34
Alignment explanation
Indices: 40205299--40205364 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
40205289 CAGTAAAATA
* * *
40205299 TTTTCCGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTATAGAAAATATTTTAC
*
40205333 TTTTCTGTAAAATGATTTATAGAAAATATTTT
1 TTTTCCGTAAAATGATTTATAGAAAATATTTT
40205365 CTAGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTATAGAAAATATTTTAC
Found at i:40205984 original size:2 final size:2
Alignment explanation
Indices: 40205969--40206016 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
40205959 CCAGTAAATA
40205969 AT AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40206009 AT AT AT AT
1 AT AT AT AT
40206017 GGTCCTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40206179 original size:21 final size:21
Alignment explanation
Indices: 40206155--40206198 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40206145 TCCATCCATC
40206155 CAATTCCGGGCTCAACTACAA
1 CAATTCCGGGCTCAACTACAA
40206176 CAATTCCGGGCTCAACTACAA
1 CAATTCCGGGCTCAACTACAA
40206197 CA
1 CA
40206199 TCCATGTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
CAATTCCGGGCTCAACTACAA
Found at i:40209715 original size:7 final size:7
Alignment explanation
Indices: 40209705--40209746 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
40209695 CATTATTTTA
40209705 CATTTCC
1 CATTTCC
40209712 CATTTCC
1 CATTTCC
*
40209719 C-CTTCC
1 CATTTCC
40209725 CATTTCC
1 CATTTCC
40209732 CATTTCC
1 CATTTCC
40209739 CATTTCC
1 CATTTCC
40209746 C
1 C
40209747 CGACCCCGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.12, C:0.48, G:0.00, T:0.40
Consensus pattern (7 bp):
CATTTCC
Found at i:40209726 original size:13 final size:13
Alignment explanation
Indices: 40209708--40209747 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
40209698 TATTTTACAT
40209708 TTCCCATTTCCCC
1 TTCCCATTTCCCC
*
40209721 TTCCCATTTCCCAT
1 TTCCCATTTCCC-C
40209735 TTCCCATTTCCCC
1 TTCCCATTTCCCC
40209748 GACCCCGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.10, C:0.50, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCCCATTTCCCC
Found at i:40213999 original size:24 final size:24
Alignment explanation
Indices: 40213954--40214000 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
40213944 TTAACTAAGT
* ** *
40213954 TTTTCTGAAAAATTAAACTAAAAG
1 TTTTATGAAAAACAAAAATAAAAG
40213978 TTTTATGAAAAACAAAAATAAAA
1 TTTTATGAAAAACAAAAATAAAA
40214001 TAAAGGACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
TTTTATGAAAAACAAAAATAAAAG
Found at i:40215587 original size:17 final size:16
Alignment explanation
Indices: 40215552--40215590 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40215542 GATAAAAATG
40215552 AATTTTATTTTTATTA
1 AATTTTATTTTTATTA
40215568 AATTTATATGTTTT-TTA
1 AATTT-TAT-TTTTATTA
40215585 AATTTT
1 AATTTT
40215591 TATAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
AATTTTATTTTTATTA
Found at i:40229925 original size:40 final size:39
Alignment explanation
Indices: 40229881--40230014 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
40229871 ACCAACTTGG
* *
40229881 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTAA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGA
* * *
40229921 CACCCAGTGTCTCATCGGCTAA-CCGAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
* **
40229957 CACCCAGTGCCCCATCAAATATATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATA-ATCCGAAGTAAT-AATTGA
*
40229998 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
40230015 ACTTGAAGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
36 18 0.24
37 3 0.04
38 8 0.11
39 7 0.09
40 20 0.27
41 19 0.25
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
Found at i:40230978 original size:22 final size:22
Alignment explanation
Indices: 40230941--40231004 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
40230931 TTTTCTTTTC
40230941 TTTA-TTTATT-TCATTTACTTA
1 TTTATTTTATTAT-ATTTACTTA
40230962 TTTATTTTATTATATTTACTT-
1 TTTATTTTATTATATTTACTTA
*
40230983 TATTATATTA-TATATTTACTTA
1 T-TTATTTTATTATATTTACTTA
40231005 AATATTAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 16 0.42
22 21 0.55
23 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTTTATTATATTTACTTA
Found at i:40230979 original size:14 final size:14
Alignment explanation
Indices: 40230940--40230991 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
40230930 TTTTTCTTTT
40230940 CTTTATT-TATTT-
1 CTTTATTATATTTA
*
40230952 CATTTACT-TATTTA
1 C-TTTATTATATTTA
*
40230966 TTTTATTATATTTA
1 CTTTATTATATTTA
40230980 CTTTATTATATT
1 CTTTATTATATT
40230992 ATATATTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 1 0.03
13 15 0.45
14 17 0.52
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTATTATATTTA
Found at i:40230992 original size:5 final size:4
Alignment explanation
Indices: 40230941--40231000 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
40230931 TTTTCTTTTC
*
40230941 TTTA TTTA TTTCA TTTA CTTA TTTA TTTTA TTATA TTTA CTTTA -TTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TT-TA TTTA -TTTA TTTA
*
40230988 TATTA TATA TTTA
1 T-TTA TTTA TTTA
40231001 CTTAAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
3 3 0.07
4 23 0.50
5 20 0.43
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:40231009 original size:19 final size:21
Alignment explanation
Indices: 40230972--40231011 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40230962 TTTATTTTAT
*
40230972 TATATTTACTTTATTATATTA
1 TATATTTACTTTATAATATTA
40230993 TATATTTAC-TTA-AATATTA
1 TATATTTACTTTATAATATTA
40231012 AGTAATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTTACTTTATAATATTA
Found at i:40234318 original size:27 final size:27
Alignment explanation
Indices: 40234266--40234318 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
40234256 CTGAATCAAT
* * **
40234266 AAAATTAAACTCCAACACAATTTTTAA
1 AAAATTAAAATCCAAAACAAAATTTAA
40234293 AAAATTAAAATCCAAAACAAAATTTA
1 AAAATTAAAATCCAAAACAAAATTTA
40234319 CAGAGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAATTAAAATCCAAAACAAAATTTAA
Found at i:40234625 original size:16 final size:16
Alignment explanation
Indices: 40234588--40234637 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
40234578 GGCGCAAATG
**
40234588 AATAAAATAATAATAAT
1 AATAAAAT-ATAATTTT
40234605 AATAATAATA-AATTTT
1 AATAA-AATATAATTTT
40234621 AATAAAATATAATTTT
1 AATAAAATATAATTTT
40234637 A
1 A
40234638 GATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 16 0.55
17 6 0.21
18 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAATATAATTTT
Found at i:40235019 original size:20 final size:20
Alignment explanation
Indices: 40234994--40235176 Score: 90
Period size: 22 Copynumber: 8.8 Consensus size: 20
40234984 TTTAGATTAG
*
40234994 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
40235014 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
40235036 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
* *
40235055 AATGTTGTATGAATATTGTA
1 AATTTTGTATGAATATTATA
* * *
40235075 ATTATTTTATAATTAA-ATT-TG
1 A--ATTTTGT-ATGAATATTATA
* * *
40235096 TATTTATAGTTTTG--GATTAGTA
1 AATTT-T-G-TATGAATATTA-TA
* *
40235118 ATTTTTTGTATGAATATTGT-
1 A-ATTTTGTATGAATATTATA
40235138 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTATA
40235158 AATTTTTTGTATGAATATT
1 AA--TTTTGTATGAATATT
40235177 GTAATATTAT
Statistics
Matches: 122, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
19 36 0.30
20 28 0.23
21 4 0.03
22 47 0.39
23 7 0.06
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:40235183 original size:49 final size:49
Alignment explanation
Indices: 40235130--40235430 Score: 471
Period size: 49 Copynumber: 6.2 Consensus size: 49
40235120 TTTTTGTATG
*
40235130 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * **
40235179 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * *
40235228 AATTTTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* *
40235277 AATATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* *
40235326 AATTTTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
40235375 AATATTGTAATTTTGTATGAATATTATAA-TTTTTT-TATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
40235422 AATGTTGTA
1 AATATTGTA
40235431 TGAATATTGT
Statistics
Matches: 230, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
47 20 0.09
48 6 0.03
49 204 0.89
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
Found at i:40235198 original size:27 final size:25
Alignment explanation
Indices: 40235130--40235518 Score: 334
Period size: 27 Copynumber: 16.1 Consensus size: 25
40235120 TTTTTGTATG
*
40235130 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
40235157 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
40235179 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
*
40235205 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
40235228 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
* *
40235253 -ATATTTTTTTTGAATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
40235277 AATATTATAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
40235304 -A-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
40235326 AATTTTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
40235353 -A-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
40235375 AATATTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
*
40235400 -ATAATT-TTTT-TATGAATATTG-
1 AATATTTATTTTGTATGAATATTGT
*
40235421 --TA---ATGTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
40235441 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
40235467 CA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
40235489 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
40235516 AAT
1 AAT
40235519 GTGGGGATAT
Statistics
Matches: 302, Mismatches: 17, Indels: 86
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.01
19 11 0.04
20 10 0.03
21 21 0.07
22 83 0.27
23 9 0.03
24 23 0.08
25 22 0.07
26 8 0.03
27 112 0.37
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:40235473 original size:19 final size:19
Alignment explanation
Indices: 40234994--40235443 Score: 187
Period size: 19 Copynumber: 25.2 Consensus size: 19
40234984 TTTAGATTAG
*
40234994 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
40235013 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
40235035 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
40235055 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
40235074 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
40235097 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
40235117 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
40235138 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
40235157 AAATTTT-T-TG--TA-TG-
1 -AATTTTGTATGAATATTGT
* *
40235171 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
40235187 AGTTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
40235206 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
40235220 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
*
40235236 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
* *
40235255 -ATTTTTTTTG-A-A-TG-
1 AATTTTGTATGAATATTGT
* *
40235269 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
40235285 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
40235304 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
40235318 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
40235334 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
40235353 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
*
40235367 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
*
40235383 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
40235402 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
40235422 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
40235441 AAT
1 AAT
40235444 ATTATAATTT
Statistics
Matches: 323, Mismatches: 50, Indels: 115
0.66 0.10 0.24
Matches are distributed among these distances:
13 11 0.03
14 22 0.07
15 20 0.06
16 38 0.12
17 1 0.00
18 24 0.07
19 107 0.33
20 57 0.18
21 10 0.03
22 22 0.07
23 7 0.02
24 3 0.01
25 1 0.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:40235487 original size:48 final size:46
Alignment explanation
Indices: 40235338--40235547 Score: 179
Period size: 48 Copynumber: 4.6 Consensus size: 46
40235328 TTTTGTAATT
* *
40235338 TTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATA
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATG
* * *
40235379 TTG--T-AATTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATG
1 TTGTATGAATATTG--T-AATATTATAA-TTTTGTATGAATATTGCAATG
*
40235426 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTT
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAA--TG
* **
40235474 TTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTATAATG
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATG
** *
40235520 -TG-GGGATATATTGTAATATTGTAATTTT
1 TTGTATGA-ATATTGTAATATTATAATTTT
40235548 TTATATGAAT
Statistics
Matches: 141, Mismatches: 13, Indels: 26
0.78 0.07 0.14
Matches are distributed among these distances:
38 6 0.04
39 1 0.01
40 1 0.01
41 3 0.02
42 1 0.01
43 3 0.02
44 3 0.02
45 23 0.16
46 18 0.13
47 32 0.23
48 43 0.30
49 1 0.01
50 6 0.04
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.52
Consensus pattern (46 bp):
TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATG
Found at i:40235559 original size:21 final size:22
Alignment explanation
Indices: 40235534--40235574 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40235524 GATATATTGT
*
40235534 AATATTGTAATT-TTTTATATG
1 AATATTATAATTATTTTATATG
40235555 AATATTATAATTATTTTATA
1 AATATTATAATTATTTTATA
40235575 ATTAATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
AATATTATAATTATTTTATATG
Done.