Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 22 of 37
Found at i:3846756 original size:38 final size:37
Alignment explanation
Indices: 3846682--3846757 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 37
3846672 ATATGGCATA
3846682 GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC
1 GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC
*
3846719 GGTTCAGAATAAAAATCACTATTCTT-ATCCGGTGGCAC
1 GGTT-AGAATAAAAATCACTATT-TTAATCCGATGGCAC
3846757 G
1 G
3846758 ACAAAACCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 4 0.11
38 30 0.83
39 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (37 bp):
GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC
Found at i:3846808 original size:31 final size:31
Alignment explanation
Indices: 3846729--3846837 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
3846719 GGTTCAGAAT
*
3846729 AAAAATCACTATTCTTATCCGGTGGCACGAC
1 AAAAACCACTATTCTTATCCGGTGGCACGAC
* * *
3846760 -AAAACCATTATTATTATCTGGTGGCACGAC
1 AAAAACCACTATTCTTATCCGGTGGCACGAC
**
3846790 AAAAACCACTATTCTTATCCGGTGGCACGGT
1 AAAAACCACTATTCTTATCCGGTGGCACGAC
*
3846821 AAAAATCACTATTCTTA
1 AAAAACCACTATTCTTA
3846838 ACTGATAGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
30 26 0.39
31 41 0.61
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (31 bp):
AAAAACCACTATTCTTATCCGGTGGCACGAC
Found at i:3849930 original size:21 final size:20
Alignment explanation
Indices: 3849906--3849972 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 20
3849896 AAAAAATACA
3849906 TATAAATTTTTTAAAATTTT
1 TATAAATTTTTTAAAATTTT
* *
3849926 GTATAAATTATTTATAATTTT
1 -TATAAATTTTTTAAAATTTT
*
3849947 T-TTAATTTTTT--AATTTT
1 TATAAATTTTTTAAAATTTT
*
3849964 TATATATTT
1 TATAAATTT
3849973 AAATAAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 7 0.18
18 5 0.13
19 8 0.21
20 1 0.03
21 18 0.46
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TATAAATTTTTTAAAATTTT
Found at i:3849941 original size:11 final size:10
Alignment explanation
Indices: 3849906--3849972 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
3849896 AAAAAATACA
3849906 TATAAATTTT
1 TATAAATTTT
3849916 T-TAAAATTTT
1 TAT-AAATTTT
3849926 GTATAAATTATT
1 -TATAAATT-TT
3849938 TAT-AATTTT
1 TATAAATTTT
*
3849947 T-TTAATTTT
1 TATAAATTTT
3849956 T-T-AATTTT
1 TATAAATTTT
*
3849964 TATATATTT
1 TATAAATTT
3849973 AAATAAAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
8 8 0.16
9 13 0.27
10 16 0.33
11 9 0.18
12 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (10 bp):
TATAAATTTT
Found at i:3850855 original size:14 final size:14
Alignment explanation
Indices: 3850826--3850867 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3850816 TCACCCATTT
*
3850826 TTTATTTTTAAT-A
1 TTTAATTTTAATAA
*
3850839 TTTCATTTTAATAA
1 TTTAATTTTAATAA
*
3850853 TTTAATATTAATAA
1 TTTAATTTTAATAA
3850867 T
1 T
3850868 CCTTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAATTTTAATAA
Found at i:3853316 original size:20 final size:20
Alignment explanation
Indices: 3853291--3853344 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3853281 GTTTGAAGCA
* *
3853291 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTACC
*
3853311 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
3853331 ATGTATCGATACAA
1 ATGTATCGATACAA
3853345 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3853417 original size:19 final size:20
Alignment explanation
Indices: 3853373--3853424 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3853363 CTGCCAGTTT
**
3853373 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
3853393 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
3853412 CATGTATCGATAC
1 CATGTATCGATAC
3853425 CAAGCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3853438 original size:20 final size:20
Alignment explanation
Indices: 3853394--3853444 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3853384 ACAATTGTCC
*
3853394 ATGTATCGATA-CAATGAAC
1 ATGTATCGATACCAATGAAA
3853413 ATGTATCGATACCAA-GCAAA
1 ATGTATCGATACCAATG-AAA
*
3853433 ATGTATCAATAC
1 ATGTATCGATAC
3853445 ATCTGGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (20 bp):
ATGTATCGATACCAATGAAA
Found at i:3855804 original size:22 final size:21
Alignment explanation
Indices: 3855769--3855818 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3855759 TTTGTTGATG
*
3855769 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
3855789 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
3855810 AATTTGAAG
1 ATTTTGAAG
3855819 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:3855815 original size:21 final size:22
Alignment explanation
Indices: 3855776--3855818 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3855766 ATGATTTTGA
* *
3855776 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
3855798 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
3855819 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:3862228 original size:20 final size:20
Alignment explanation
Indices: 3862203--3862260 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
3862193 CTGCTAGTTT
*
3862203 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
* *
3862223 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGTA
*
3862242 CATGTATCGTTAC-ATTGTA
1 CATGTATCGATACAATTGTA
3862261 TCAATAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.52
20 14 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:3863767 original size:59 final size:58
Alignment explanation
Indices: 3863684--3863828 Score: 168
Period size: 59 Copynumber: 2.5 Consensus size: 58
3863674 CTCGATTTAT
* * * ** * *
3863684 GACCATTTTAATAATTTTCGATGATTTAAGGGTTATTATG-TAATTTCAATGTATTTTAAA
1 GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCT-ATTTC-ATGCATTGT-AA
*
3863744 GA-CATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAG
1 GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAA
3863801 GACCATTTTAGTCATTTTCTCATGATTT
1 GACCATTTTAGTCATTTTC-CATGATTT
3863829 TATGATTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
57 3 0.04
58 23 0.31
59 45 0.61
60 3 0.04
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (58 bp):
GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAA
Found at i:3864097 original size:18 final size:18
Alignment explanation
Indices: 3864074--3864109 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3864064 ATGTTGCCTT
3864074 AAAATCAAGTCCTTAGGA
1 AAAATCAAGTCCTTAGGA
*
3864092 AAAATCGAGTCCTTAGGA
1 AAAATCAAGTCCTTAGGA
3864110 TCATGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (18 bp):
AAAATCAAGTCCTTAGGA
Found at i:3864311 original size:76 final size:76
Alignment explanation
Indices: 3864092--3864399 Score: 242
Period size: 75 Copynumber: 4.1 Consensus size: 76
3864082 GTCCTTAGGA
** *
3864092 AAAATCGAGTCCTTAGGATCATGTGA-AACTTTTGTGTCAAAACATGTCTC-TTAAA-GTAATTT
1 AAAATCGAGT-C-TAGGATCATGTGAGAACTTTCATGTCAAAACATGTC-CATTAAATGTATTTT
*
3864154 AGGTTATAGTACCCTT
63 A-GTAATAGTA-CCTT
* * * * * * ** *
3864170 AAAAT-GA-TTTTGGAATCATGTGGGAACATTCGTGTCGAAACATGT-CATT-AGGGTCATTTCA
1 AAAATCGAGTCTAGG-ATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGT-ATTTTA
*
3864231 GTAATAATACCTT
64 GTAATAGTACCTT
* *
3864244 AAAATCGAGTCTAGGATAATGTGAGAACTTTCATGTCAAAACATATCCATTAAATGTATTTTAGT
1 AAAATCGAGTCTAGGATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGTATTTTAGT
3864309 AATAGTACCTT
66 AATAGTACCTT
* * * * *
3864320 AAAATTGATTCTAGAAGCATGTG-GAAACGTT-AGTGTC-AAACATGTCCATTAGAAT-TATTTT
1 AAAATCGAGTCTAGGATCATGTGAG-AACTTTCA-TGTCAAAACATGTCCATTA-AATGTATTTT
* *
3864381 GGTAATAGTACCTC
63 AGTAATAGTACCTT
3864395 AAAAT
1 AAAAT
3864400 GGAAGCCCTA
Statistics
Matches: 186, Mismatches: 32, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
74 14 0.08
75 84 0.45
76 78 0.42
77 5 0.03
78 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (76 bp):
AAAATCGAGTCTAGGATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGTATTTTAGT
AATAGTACCTT
Found at i:3864314 original size:151 final size:152
Alignment explanation
Indices: 3864092--3864371 Score: 365
Period size: 151 Copynumber: 1.8 Consensus size: 152
3864082 GTCCTTAGGA
* ** *
3864092 AAAATCGAGTCCTTAGGATCATGTGAAACTTTTGTGTCAAAACATGTCTCTTAAAGTAATTTAGG
1 AAAATCGAGTCCTTAGGATAATGTGAAACTTTCATGTCAAAACATATCTCTTAAAGTAATTTAGG
* * * * * *
3864157 TTATAGTACCCTTAAAA-TGATTTTGGAATCATGTGGGAACATTCGTGTCGAAACATGT-CATTA
66 TAATAGTA-CCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTC-AAACATGTCCATTA
3864220 GGGTCATTTCAGTAATAATACCTT
129 GGGTCATTTCAGTAATAATACCTT
*
3864244 AAAATCGAGT-C-TAGGATAATGTGAGAACTTTCATGTCAAAACATATC-CATTAAATGTATTTT
1 AAAATCGAGTCCTTAGGATAATGTGA-AACTTTCATGTCAAAACATATCTC-TTAAA-GTAATTT
*
3864306 A-GTAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACGTTAGTGTCAAACATGTCCATT
63 AGGTAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTCAAACATGTCCATT
3864370 AG
128 AG
3864372 AATTATTTTG
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
150 29 0.26
151 65 0.59
152 17 0.15
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (152 bp):
AAAATCGAGTCCTTAGGATAATGTGAAACTTTCATGTCAAAACATATCTCTTAAAGTAATTTAGG
TAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTCAAACATGTCCATTAGG
GTCATTTCAGTAATAATACCTT
Found at i:3866095 original size:79 final size:78
Alignment explanation
Indices: 3866012--3866291 Score: 325
Period size: 79 Copynumber: 3.6 Consensus size: 78
3866002 ACCCTCGATA
* *
3866012 ATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGCAT-TCTGTCGGAAATAAAGGGGT
1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCT-TCGGAAATAAAGGGGT
3866076 TGAAGTATCCCCAAG
65 TGAAGTATCCCC-AG
* * * * * *
3866091 ATGAAAAATTTAATATTTTTGAAAATAAAAACGGGATTGGAGTATCCCTTTGAAAATAATGGGGC
1 ATGAAAAATTTAATA-TTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGT
*
3866156 TGGAGTA-CCCTCA-
65 TGAAGTATCCC-CAG
* * * *
3866169 A-GAAAAATTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCTCTTCAGAAATAACGGGGTT
1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGTT
*
3866233 GAAATATCCCCGAG
66 GAAGTATCCCC-AG
* ** *
3866247 ATGAAAATTTTAATATTTTGAAAATAAAAGTGGGGTTAGAGTATC
1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATC
3866292 CCCAAAGATG
Statistics
Matches: 170, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
76 46 0.27
77 17 0.10
78 2 0.01
79 58 0.34
80 45 0.26
81 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (78 bp):
ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGTT
GAAGTATCCCCAG
Found at i:3866948 original size:228 final size:228
Alignment explanation
Indices: 3866540--3866993 Score: 872
Period size: 228 Copynumber: 2.0 Consensus size: 228
3866530 AGGGGGTAAA
3866540 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA
1 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA
3866605 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG
66 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG
*
3866670 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCTGATCGAGTTGCTAAAACCTCT
131 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT
3866735 ATACTTGAGTATGTTAATGTTCCCATGTCTAGG
196 ATACTTGAGTATGTTAATGTTCCCATGTCTAGG
* *
3866768 CAAGGTACTGTTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA
1 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA
*
3866833 ATCACTTTCTAGGCAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG
66 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG
3866898 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT
131 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT
3866963 ATACTTGAGTATGTTAATGTTCCCATGTCTA
196 ATACTTGAGTATGTTAATGTTCCCATGTCTA
3866994 TGCTCAGTCA
Statistics
Matches: 222, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 222 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (228 bp):
CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA
ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG
GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT
ATACTTGAGTATGTTAATGTTCCCATGTCTAGG
Found at i:3868873 original size:11 final size:11
Alignment explanation
Indices: 3868859--3868893 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3868849 AACCAAAAAT
3868859 AAAAAAAATG-
1 AAAAAAAATGA
3868869 AAAAAAAATGA
1 AAAAAAAATGA
*
3868880 AAAAAAAAAGA
1 AAAAAAAATGA
3868891 AAA
1 AAA
3868894 TTGATTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:3868893 original size:9 final size:10
Alignment explanation
Indices: 3868853--3868886 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
3868843 ATGTTAAACC
3868853 AAAAAT-AAA
1 AAAAATGAAA
3868862 AAAAATGAAA
1 AAAAATGAAA
3868872 AAAAATGAAA
1 AAAAATGAAA
3868882 AAAAA
1 AAAAA
3868887 AAGAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:3873353 original size:45 final size:45
Alignment explanation
Indices: 3873289--3873431 Score: 189
Period size: 45 Copynumber: 3.1 Consensus size: 45
3873279 CCTTTTTACA
*
3873289 AAACAATATTAAAAGTAAAACCCATGATCCTAATCTCCAAAAGAC
1 AAACAATATTAAAAATAAAACCCATGATCCTAATCTCCAAAAGAC
* *
3873334 AAACAATATTAAAAATAAAATAAAATCCACGATCCTAATCTCCAAAAGAC
1 AAACAATATT----A-AAAATAAAACCCATGATCCTAATCTCCAAAAGAC
*
3873384 AAACAATATTAAAAATAAAGCCCATGATCCTAATC-CTCAAAAGAC
1 AAACAATATTAAAAATAAAACCCATGATCCTAATCTC-CAAAAGAC
3873429 AAA
1 AAA
3873432 AAAAAAAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
44 1 0.01
45 42 0.49
46 1 0.01
49 1 0.01
50 41 0.48
ACGTcount: A:0.54, C:0.21, G:0.06, T:0.20
Consensus pattern (45 bp):
AAACAATATTAAAAATAAAACCCATGATCCTAATCTCCAAAAGAC
Found at i:3873377 original size:50 final size:51
Alignment explanation
Indices: 3873298--3873402 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 51
3873288 AAAACAATAT
*
3873298 TAAAAGTAAAACCCATGATCCTAATCTCCAAAAGACAAACAATATTAAAAA
1 TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA
*
3873349 TAAAA-TAAAATCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA
1 TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA
3873399 TAAA
1 TAAA
3873403 GCCCATGATC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 47 0.90
51 5 0.10
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.20
Consensus pattern (51 bp):
TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA
Found at i:3877318 original size:20 final size:20
Alignment explanation
Indices: 3877293--3877346 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3877283 GTTACAAGCA
*
3877293 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
3877313 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
3877333 ATGTATTGATACAA
1 ATGTATCGATACAA
3877347 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3877404 original size:20 final size:20
Alignment explanation
Indices: 3877375--3877468 Score: 129
Period size: 19 Copynumber: 4.8 Consensus size: 20
3877365 CTGCCAGTTT
**
3877375 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
3877395 CATATATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
**
3877414 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
3877434 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
3877453 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3877469 GTATCGATAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 33 0.52
20 31 0.48
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3877424 original size:39 final size:39
Alignment explanation
Indices: 3877375--3877468 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
3877365 CTGCCAGTTT
3877375 CATGTATCGATACAATTGTCCATATATCGATACAATGAA
1 CATGTATCGATACAATTGTCCATATATCGATACAATGAA
*
3877414 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTCCATATATCGATACAATGAA
3877453 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3877469 GTATCGATAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (39 bp):
CATGTATCGATACAATTGTCCATATATCGATACAATGAA
Found at i:3877472 original size:13 final size:13
Alignment explanation
Indices: 3877454--3877480 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3877444 TACAATGAAC
3877454 ATGTATCGATACA
1 ATGTATCGATACA
3877467 ATGTATCGATACA
1 ATGTATCGATACA
3877480 A
1 A
3877481 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3878106 original size:25 final size:25
Alignment explanation
Indices: 3878078--3878136 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
3878068 TTTCCCTTAA
3878078 TCAAAGCAAAAATTTATTTTATTTT
1 TCAAAGCAAAAATTTATTTTATTTT
3878103 TCAAAGCAAAAATTTATTTTATTTT
1 TCAAAGCAAAAATTTATTTTATTTT
3878128 TCAAAGCAA
1 TCAAAGCAA
3878137 TATATATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (25 bp):
TCAAAGCAAAAATTTATTTTATTTT
Found at i:3886176 original size:20 final size:20
Alignment explanation
Indices: 3886151--3886190 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3886141 GTTACAAGCA
*
3886151 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATGCATC
3886171 ATGTATCGATACAATGCATC
1 ATGTATCGATACAATGCATC
3886191 GATACAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGCATC
Found at i:3886192 original size:33 final size:33
Alignment explanation
Indices: 3886149--3886214 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3886139 TTGTTACAAG
* * *
3886149 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGCATCGATACAATGCACCATGTATCGATA
3886182 CAATGCATCGATACAATGCACCATGTATCGATA
1 CAATGCATCGATACAATGCACCATGTATCGATA
3886215 TAAATAGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (33 bp):
CAATGCATCGATACAATGCACCATGTATCGATA
Found at i:3886193 original size:13 final size:13
Alignment explanation
Indices: 3886175--3886201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3886165 TTCATCATGT
3886175 ATCGATACAATGC
1 ATCGATACAATGC
3886188 ATCGATACAATGC
1 ATCGATACAATGC
3886201 A
1 A
3886202 CCATGTATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ATCGATACAATGC
Found at i:3886213 original size:20 final size:19
Alignment explanation
Indices: 3886143--3886214 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 19
3886133 TTATAGTTGT
3886143 TACAA-GCA-ATGTATCGA
1 TACAATGCACATGTATCGA
*
3886160 TACAATTCATCATGTATCGA
1 TACAATGCA-CATGTATCGA
3886180 TACAATG--C----ATCGA
1 TACAATGCACATGTATCGA
3886193 TACAATGCACCATGTATCGA
1 TACAATGCA-CATGTATCGA
3886213 TA
1 TA
3886215 TAAATAGTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 17
0.69 0.03 0.27
Matches are distributed among these distances:
13 12 0.28
16 1 0.02
17 6 0.14
18 2 0.05
20 22 0.51
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (19 bp):
TACAATGCACATGTATCGA
Found at i:3886271 original size:20 final size:20
Alignment explanation
Indices: 3886246--3886321 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
3886236 CTACCAGTTT
3886246 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
3886266 CATGTATCGATACAATTGTCC
1 CATGTATCGATACAATTGT-C
**
3886287 CATGTATCGATGA-AA-TGAA
1 CATGTATCGAT-ACAATTGTC
3886306 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3886322 ATATCAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.02
19 13 0.26
20 21 0.42
21 14 0.28
22 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:3886416 original size:71 final size:71
Alignment explanation
Indices: 3886333--3886494 Score: 297
Period size: 71 Copynumber: 2.3 Consensus size: 71
3886323 TATCAATACA
* *
3886333 AAGCATAATGTATCGATACATTTGGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC
1 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC
3886398 TAAGTC
66 TAAGTC
3886404 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC
1 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC
3886469 TAAGTC
66 TAAGTC
*
3886475 AACCATAATGTATCGATACA
1 AAGCATAATGTATCGATACA
3886495 AATTTTGTTG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (71 bp):
AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC
TAAGTC
Found at i:3902909 original size:11 final size:11
Alignment explanation
Indices: 3902889--3902962 Score: 89
Period size: 11 Copynumber: 6.6 Consensus size: 11
3902879 AGCGTCCTCC
3902889 ACAAAAAAAAA
1 ACAAAAAAAAA
3902900 ACAAATAAAAAA
1 ACAAA-AAAAAA
*
3902912 AC-AAAAACAA
1 ACAAAAAAAAA
3902922 ACAAAAAAAAA
1 ACAAAAAAAAA
3902933 ACAAAAAATAAA
1 ACAAAAAA-AAA
*
3902945 A-AAAAACAACA
1 ACAAAAA-AAAA
3902956 ACAAAAA
1 ACAAAAA
3902963 GGGTCCGGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
10 7 0.13
11 30 0.55
12 18 0.33
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:3902911 original size:17 final size:17
Alignment explanation
Indices: 3902891--3902956 Score: 87
Period size: 18 Copynumber: 3.8 Consensus size: 17
3902881 CGTCCTCCAC
3902891 AAAAAAAAAACAAATAA
1 AAAAAAAAAACAAATAA
*
3902908 AAAAACAAAAACAAACAA
1 AAAAA-AAAAACAAATAA
*
3902926 AAAAAAAACAAAAAATAA
1 AAAAAAAA-AACAAATAA
*
3902944 AAAAAAACAACAA
1 AAAAAAAAAACAA
3902957 CAAAAAGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 12 0.29
18 30 0.71
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAACAAATAA
Found at i:3902917 original size:22 final size:21
Alignment explanation
Indices: 3902892--3902962 Score: 90
Period size: 20 Copynumber: 3.4 Consensus size: 21
3902882 GTCCTCCACA
3902892 AAAAAAAAACAAATAAAAAAAC
1 AAAAAAAAACAAA-AAAAAAAC
*
3902914 AAAAACAAACAAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAAC
* *
3902935 AAAAAATAA-AAAAAAACAAC
1 AAAAAAAAACAAAAAAAAAAC
*
3902955 AACAAAAA
1 AAAAAAAA
3902963 GGGTCCGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.37
21 15 0.35
22 12 0.28
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAAAC
Found at i:3902928 original size:32 final size:31
Alignment explanation
Indices: 3902889--3902962 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 31
3902879 AGCGTCCTCC
3902889 ACAAAAAAAAAACAAATAAA-AAAACAAAAACAA
1 ACAAAAAAAAAACAAA-AAATAAAA-AAAAAC-A
3902922 ACAAAAAAAAAACAAAAAATAAAAAAAAACA
1 ACAAAAAAAAAACAAAAAATAAAAAAAAACA
*
3902953 ACAACAAAAA
1 ACAAAAAAAA
3902963 GGGTCCGGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 10 0.26
32 9 0.23
33 20 0.51
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (31 bp):
ACAAAAAAAAAACAAAAAATAAAAAAAAACA
Found at i:3902948 original size:38 final size:35
Alignment explanation
Indices: 3902891--3902962 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
3902881 CGTCCTCCAC
*
3902891 AAAAAAAAAACAAATAAAAAAACAAAAACAAACAA
1 AAAAAAAAAAAAAATAAAAAAACAAAAACAAACAA
*
3902926 AAAAAAAACAAAAAATAAAAAAA-AACAAC-AACAA
1 AAAAAAAA-AAAAAATAAAAAAACAAAAACAAACAA
3902960 AAA
1 AAA
3902963 GGGTCCGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 8 0.24
35 13 0.38
36 13 0.38
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (35 bp):
AAAAAAAAAAAAAATAAAAAAACAAAAACAAACAA
Found at i:3902962 original size:1 final size:1
Alignment explanation
Indices: 3902891--3902950 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
3902881 CGTCCTCCAC
* * * * * * *
3902891 AAAAAAAAAACAAATAAAAAAACAAAAACAAACAAAAAAAAAACAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3902951 CAACAACAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:3904491 original size:28 final size:28
Alignment explanation
Indices: 3904392--3904555 Score: 184
Period size: 28 Copynumber: 5.8 Consensus size: 28
3904382 CTTACCTCCC
***
3904392 AAAGCCCACAAGTCAGTGGCATGTTTTTCA
1 AAAGCCCACAAGTCAGTGGCA--ACCTTCA
* * * * **
3904422 AAAGGCCACAGGTCAGTGGCATCTTTTTT
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
3904451 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
3904479 AAAGCCCATAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
3904507 AAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
3904535 AAAGCCCACAAGTCAATGGCA
1 AAAGCCCACAAGTCAGTGGCA
3904556 CATTTTTCCT
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
28 75 0.64
29 23 0.20
30 19 0.16
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.21
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:3904577 original size:33 final size:33
Alignment explanation
Indices: 3904551--3904860 Score: 304
Period size: 33 Copynumber: 9.3 Consensus size: 33
3904541 CACAAGTCAA
* * *
3904551 TGGCACATTTTTCCTTTCAAGTCCACAACTCTG
1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG
* *
3904584 TGGCATCTTTTTCCTTTTAAGTCCACAACTCCA
1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG
* * *
3904617 CGGCACCTTGTTCCTTTTAAGTCCACAACTTCG
1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG
*
3904650 TGGCACCTTTTT-CTTTTCAAAGTCCACAACTCTG
1 TGGCACCTTTTTCCTTTT--AAGTCCACAACTCCG
*
3904684 TGGCA-CTTTGTTCCTTTTAAATCCACAACTCCG
1 TGGCACCTTT-TTCCTTTTAAGTCCACAACTCCG
* * * **
3904717 TGGCACCTTTTTCTTTTTAAAGCCCACAGCTTTG
1 TGGCACCTTTTTCCTTTT-AAGTCCACAACTCCG
* * * * *
3904751 TGGCA-CATTTTCTTTTTAAGTCTACGACTCCA
1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG
* * * *
3904783 TGGTACCCTTTTCTCTTTTAAGCCCACAACTCCA
1 TGGCACCTTTTTC-CTTTTAAGTCCACAACTCCG
*
3904817 TGGCATCCCTTTTTCC-TATAAGTCCACAACTCCG
1 TGGCA--CCTTTTTCCTTTTAAGTCCACAACTCCG
3904851 TGGCACCTTT
1 TGGCACCTTT
3904861 AAGATCAATG
Statistics
Matches: 226, Mismatches: 41, Indels: 21
0.78 0.14 0.07
Matches are distributed among these distances:
32 22 0.10
33 112 0.50
34 79 0.35
35 6 0.03
36 7 0.03
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (33 bp):
TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG
Found at i:3904712 original size:100 final size:99
Alignment explanation
Indices: 3904551--3904860 Score: 347
Period size: 100 Copynumber: 3.1 Consensus size: 99
3904541 CACAAGTCAA
* * *
3904551 TGGCACATTTTTCCTTTCAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCC
1 TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* *
3904616 ACGGCACCTTGTTCCTTTTAAGTCCACAACTTCG
66 ATGGCACCTTTTTCCTTTTAAGTCCACAACTTCG
*
3904650 TGGCACCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA-CTTTGTTCCTTTTAAATCCACAACT
1 TGGCACCTTTTTCTTTTC-AAGTCCACAACTCTGTGGCACCTTT-TTCCTTTTAAGTCCACAACT
* * * * *
3904714 CCGTGGCACCTTTTTCTTTTTAAAGCCCACAGCTTTG
64 CCATGGCACCTTTTTCCTTTT-AAGTCCACAACTTCG
* * * * ** * * *
3904751 TGGCA-CATTTTCTTTTTAAGTCTACGACTCCATGGTACCCTTTTCTCTTTTAAGCCCACAACTC
1 TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTC-CTTTTAAGTCCACAACTC
* *
3904815 CATGGCATCCCTTTTTCC-TATAAGTCCACAACTCCG
65 CATGGCA--CCTTTTTCCTTTTAAGTCCACAACTTCG
3904851 TGGCACCTTT
1 TGGCACCTTT
3904861 AAGATCAATG
Statistics
Matches: 175, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
99 38 0.22
100 107 0.61
101 22 0.13
102 8 0.05
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (99 bp):
TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
ATGGCACCTTTTTCCTTTTAAGTCCACAACTTCG
Found at i:3904921 original size:43 final size:43
Alignment explanation
Indices: 3904851--3905262 Score: 302
Period size: 43 Copynumber: 9.2 Consensus size: 43
3904841 CACAACTCCG
* *
3904851 TGGCACCTTTAAGAT-CAATGTCGCTAGCCTTGAATCAGCACAT
1 TGGCACCTTTAAG-TCCAATATCGCTAGCCTTGAATCAGCATAT
* *
3904894 TGGCACCTTTAAGTCCACTATCACTAGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
* * *
3904937 TGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACAT
1 TGGCA-C-----CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
* * *
3904986 TAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
*
3905029 TGGCACCTTTACCATATTGAGTCCAATATCGCTAGCCTTGAATCAACATAT
1 TGGCACC-TT----TA---AGTCCAATATCGCTAGCCTTGAATCAGCATAT
* * * * *
3905080 TGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACAT
1 TGGCACC---T-T-TAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
* *
3905128 TGGCA----TAAGCCCAATATCGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
* * * * *
3905167 TGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACAT
1 TGGCACC-----TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
* * *
3905215 TGGCA-C---AAGCCCAATATTGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
3905254 TGGCACCTT
1 TGGCACCTT
3905263 CATCTTTAAG
Statistics
Matches: 301, Mismatches: 38, Indels: 61
0.75 0.09 0.15
Matches are distributed among these distances:
39 70 0.23
40 1 0.00
42 1 0.00
43 80 0.27
44 3 0.01
47 1 0.00
48 69 0.23
49 36 0.12
51 38 0.13
53 1 0.00
54 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (43 bp):
TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
Found at i:3904972 original size:49 final size:49
Alignment explanation
Indices: 3904857--3905643 Score: 568
Period size: 49 Copynumber: 16.9 Consensus size: 49
3904847 TCCGTGGCAC
* * *
3904857 CTTTAAGATCAATGTCGCTAGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * *
3904900 CTTTAAGTCCACTATCACTAGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3904949 CTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTAGCA----C--
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
3904992 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * *
3905041 CATATTGAGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-GT
1 C-T-TTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3905091 CTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3905133 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3905178 ATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3905220 C---AAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * ** * *
3905266 CTTTAAGACCGATGTCATTGGCCTTGAATCAACACATTAGCACCTTAACCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT
* * * * *
3905318 CTTTAAGTCCAATGTCG-TCAGCCTTGAATCAGTACATTGGCATCTTCAT
1 CTTTAAGACCAATATCGCT-GGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
3905367 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTAGCACCGTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
3905416 CTTTAAGACCAATGTCGCTAGCCCTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * **
3905458 ---TGAG-CCTAATATCGCTAGCCTTGAATTAGCATGTTGGCACCTTCAT
1 CTTTAAGACC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
3905504 CTTTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACGTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
3905553 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
3905602 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCA
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
3905644 TCTGTAACAT
Statistics
Matches: 586, Mismatches: 105, Indels: 100
0.74 0.13 0.13
Matches are distributed among these distances:
38 2 0.00
39 94 0.16
43 74 0.13
45 4 0.01
46 1 0.00
48 63 0.11
49 263 0.45
50 5 0.01
51 41 0.07
52 39 0.07
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:3905153 original size:39 final size:39
Alignment explanation
Indices: 3905094--3905258 Score: 159
Period size: 39 Copynumber: 4.0 Consensus size: 39
3905084 ACCTTGTCTC
* *
3905094 TAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
3905133 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG---C----A
* *
3905179 TTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
1 --TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * *
3905220 CAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
3905259 CCTTCATCTT
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
39 68 0.65
41 1 0.01
42 1 0.01
45 1 0.01
46 1 0.01
48 33 0.31
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:3905173 original size:138 final size:140
Alignment explanation
Indices: 3904905--3905175 Score: 411
Period size: 138 Copynumber: 1.9 Consensus size: 140
3904895 GGCACCTTTA
* * * *
3904905 AGTCCACTATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAG
1 AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG
* *
3904970 CCTTGAATCAGCACATTAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCAC
66 CCTTGAATCAGCACATTAGCA-C--TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
3905035 CTTTACCATATTG
128 CTTTACCATATTG
* * *
3905048 AGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACC-TTGTCTCTAAGACCAATGTCACTGG
1 AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG
*
3905112 CCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
66 CCTTGAATCAGCACATTAGCACTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
3905176 GTATTTAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
138 41 0.35
142 41 0.35
143 36 0.31
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (140 bp):
AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG
CCTTGAATCAGCACATTAGCACTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
TACCATATTG
Found at i:3905199 original size:87 final size:87
Alignment explanation
Indices: 3905051--3905308 Score: 390
Period size: 87 Copynumber: 3.0 Consensus size: 87
3905041 CATATTGAGT
* * *
3905051 CCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
*
3905116 GAATCAGCACATTGGCATAAGC
66 GAATCAGCACATTGGCACAAGC
* **
3905138 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
3905203 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* * * *
3905225 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCATTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCACTGGCCT
* *
3905290 TGAATCAACACATTAGCAC
65 TGAATCAGCACATTGGCAC
3905309 CTTAACCATC
Statistics
Matches: 154, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 117 0.76
88 37 0.24
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:3905506 original size:238 final size:229
Alignment explanation
Indices: 3904857--3905643 Score: 910
Period size: 238 Copynumber: 3.4 Consensus size: 229
3904847 TCCGTGGCAC
*
3904857 CTTTAAGAT-CAATGTCGCTAGCCTTGAATCAGCACATTGGCAC-CTTTAAGTCC-ACTATCACT
1 CTTTAAG-TCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGA-TATCGCT
*
3904919 AGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCAC
64 GGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCAC
* * * * *
3904984 ATTAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATATTGA
128 ATTGGCA----TAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-T-TTAA
* * * * * *
3905049 GTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-GT
187 GACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCAT
* * * * * *
3905091 CTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG--CA---TAAGCCCAATATCGCTGG
1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGATATCGCTGG
* * * *
3905151 CCTTGAATCAGCATATTGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATT
66 CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATT
* * * *
3905216 GGCACAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGT
131 GGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGT
* *
3905281 CATTGGCCTTGAATCAACACATTAGCACCTTAACCAT
196 CGTTGGCCTTGAATCAACACATTGGCACCTT---CAT
*
3905318 CTTTAAGTCCAATGTCG-TCAGCCTTGAATCAGTACATTGGCATCTTCATCTTTAAGTCCGATAT
1 CTTTAAGTCCAATGTCGCT-AGCCTTGAATCAGCACATTGGCA----CA-CTTTAAGTCCGATAT
* * *
3905382 CGCTGGCCTTGAATCAGCATATTAGCACCGTCATCTTTAAGACCAATGTCGCTAGCCCTGAATCA
60 CGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCTAGCCTTGAATCA
* * * *
3905447 GCACATTGGCATGAGCCTAATATCGCTAGCCTTGAATTAGCATGTTGGCACCTTCATCTTTAAGA
124 GCACATTGGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA
*
3905512 CCAATGTCGTTGGCCTTGAATCAACACATTGGCACGTTCAT
189 CCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCAT
* * *
3905553 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATC
1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA----CA-CTTTAAGTCCGATATC
*
3905618 GTTGGCCTTGAATCAGCATATTGGCA
61 GCTGGCCTTGAATCAGCATATTGGCA
3905644 TCTGTAACAT
Statistics
Matches: 473, Mismatches: 60, Indels: 39
0.83 0.10 0.07
Matches are distributed among these distances:
223 35 0.07
224 1 0.00
225 41 0.09
226 1 0.00
227 34 0.07
229 41 0.09
230 36 0.08
231 1 0.00
232 1 0.00
233 2 0.00
234 35 0.07
235 85 0.18
236 1 0.00
237 38 0.08
238 121 0.26
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (229 bp):
CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGATATCGCTGG
CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATT
GGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGT
CGTTGGCCTTGAATCAACACATTGGCACCTTCAT
Found at i:3911070 original size:20 final size:20
Alignment explanation
Indices: 3911045--3911098 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3911035 TGCCAATCTT
**
3911045 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAATTGAAC
*
3911065 ATGTATCGATAC-AGTGAAC
1 ATGTATCGATACAATTGAAC
3911084 ATGTATCGATACAAT
1 ATGTATCGATACAAT
3911099 GTATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:3911102 original size:13 final size:13
Alignment explanation
Indices: 3911084--3911109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3911074 TACAGTGAAC
3911084 ATGTATCGATACA
1 ATGTATCGATACA
3911097 ATGTATCGATACA
1 ATGTATCGATACA
3911110 TCTGGGTGTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3912733 original size:45 final size:43
Alignment explanation
Indices: 3912614--3912733 Score: 105
Period size: 45 Copynumber: 2.7 Consensus size: 43
3912604 TAGATGTATT
** * * *
3912614 GAGTTTGACCAAGGCTAAACCTTTTGTCCAATGAAATAAAAAG
1 GAGTTTGACCAAGGCTAAACCTCATGTCAAAAGAAATAAAAAA
* * * ** *
3912657 GAGTTTGACTAGGGCTAAGCCGTCACATCAAACAGAGATAAAAAA
1 GAGTTTGACCAAGGCTAAACC-TCATGTCAAA-AGAAATAAAAAA
*
3912702 GAGTTTGACCAAGACTAAACCATCATGTCAAA
1 GAGTTTGACCAAGGCTAAACC-TCATGTCAAA
3912734 TGAAGTATGA
Statistics
Matches: 57, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
43 18 0.32
44 5 0.09
45 34 0.60
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (43 bp):
GAGTTTGACCAAGGCTAAACCTCATGTCAAAAGAAATAAAAAA
Found at i:3912751 original size:45 final size:45
Alignment explanation
Indices: 3912702--3912867 Score: 149
Period size: 45 Copynumber: 3.7 Consensus size: 45
3912692 AGATAAAAAA
* *
3912702 GAGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATGAAAG
1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG
* ** * * *
3912747 GAGTTTGACTAGGGTTGAACCATTACGTCAAACGAAGGTGA-GAAA-
1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAA-GT-ATGAAAG
* * * *
3912792 -AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAATAAAAG
1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG
** * *
3912836 GAGTTTGACCAGGGTTGAACTATCACGTCAAA
1 GAGTTTGACCAGGACTAAACCATCACGTCAAA
3912868 CAAGGGTGAT
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.01
43 4 0.04
44 29 0.31
45 54 0.57
46 6 0.06
47 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (45 bp):
GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG
Found at i:3912812 original size:89 final size:89
Alignment explanation
Indices: 3912703--3912893 Score: 267
Period size: 89 Copynumber: 2.1 Consensus size: 89
3912693 GATAAAAAAG
* * * *
3912703 AGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATGAAAGGAGTTTGACTAGGGTTGAACC
1 AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC
*
3912768 ATTACGTCAAACGAA-GGTGAGAAA
66 ATCACGTCAAAC-AAGGGTGAGAAA
* * * *
3912792 AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAATAAAAGGAGTTTGACCAGGGTTGAACT
1 AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC
* *
3912857 ATCACGTCAAACAAGGGTGATAAG
66 ATCACGTCAAACAAGGGTGAGAAA
3912881 AGTTTGACCAAGA
1 AGTTTGACCAAGA
3912894 TTAACGCCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
88 2 0.02
89 86 0.98
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (89 bp):
AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC
ATCACGTCAAACAAGGGTGAGAAA
Found at i:3912890 original size:44 final size:44
Alignment explanation
Indices: 3912698--3912934 Score: 142
Period size: 45 Copynumber: 5.3 Consensus size: 44
3912688 ACAGAGATAA
* ** * * * **
3912698 AAAAGAGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATG
1 AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAA-CAAGGGTG
* * *
3912743 AAAGGAGTTTGACTAGGGTTGAACCATTACGTCAAACGAA-GGTG
1 AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAAC-AAGGGTG
* ** * ** *
3912787 AGAAA-AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAAT-
1 A-AAAGAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGG-GTG
*
3912831 AAAAGGAGTTTGACCAGGGTTGAACTATCACGTCAAACAAGGGTG
1 AAAA-GAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGGGTG
* * * * *
3912876 ATAAGAGTTTGACCAAGATT-AACGCCAATTTA-GTCAAACAATGGTG
1 AAAAGAGTTTGACCAGGGTTGAA--CC-A-TCACGTCAAACAAGGGTG
3912922 AAAAGAGTTTGAC
1 AAAAGAGTTTGAC
3912935 TAAGACTAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
43 6 0.04
44 47 0.32
45 66 0.45
46 26 0.18
47 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (44 bp):
AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGGGTG
Found at i:3913138 original size:47 final size:47
Alignment explanation
Indices: 3912862--3913496 Score: 386
Period size: 47 Copynumber: 13.6 Consensus size: 47
3912852 GAACTATCAC
* * * * * **
3912862 GTCAAACAAGGGTGATAAGAGTTTGACCAAGAT-TAACGCCAATTTA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * * *
3912908 GTCAAACAATGGTGAAAAGAGTTTGACTAAG-ACTAATGCCAATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * ** *
3912954 GTCAAACAAAGGTAAAAAAAGGTTTAACTAGGCCCTTACGCCAATACA
1 GTCAAACAAGGGTAAAAAGA-GTTTGACTAGGTTCTAACGCCAATACA
* ** ** * * * * * * *
3913002 ATCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAACACTAATATA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * * *
3913049 GTCAAACGAGGATAAAAA-AGTTTAACTAGGTCCTAATGCCAATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * *
3913095 GGT-AAACAAGGGAAAAAAGAGTTTGACGAGGTTCTAACACCAATATA
1 -GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * *
3913142 GTCAAACAAGTGTAAAAAGAGTTTGACCAGG-TCTTAACGTCAATAAA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTC-TAACGCCAATACA
* ** * *
3913189 ATCAAATGAGGGTAAAAAGAGTTTGACTAGGTCCTAATGCCAATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
*
3913236 GTCAAACAAGGGTAAAAAGAGTTTGACTAGG-TCATAATGCCAATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTC-TAACGCCAATACA
* ** ** * * * * *
3913283 GTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* ** * * * * **
3913330 ATCAAATGA-GGTATGAAAAGAGTTTGACCAAG-ACTAATGCCAATATT
1 GTCAAACAAGGGTA--AAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * * * *
3913377 GTCAAACAAGGGTAAAAAGAGTATGACCAAGTCCTAATGCCAATACA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
* * ** * * * * *
3913424 GTCAAACGAGAGTGGAAAGAGTTTGACCAGGTCCTAATGCTAATATA
1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
** * *
3913471 GTCAAATGATGGTGAAAAGAGTTTGA
1 GTCAAACAAGGGTAAAAAGAGTTTGA
3913497 GCATGTTTTA
Statistics
Matches: 464, Mismatches: 111, Indels: 27
0.77 0.18 0.04
Matches are distributed among these distances:
46 112 0.24
47 308 0.66
48 44 0.09
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (47 bp):
GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA
Found at i:3913461 original size:94 final size:93
Alignment explanation
Indices: 3912907--3913496 Score: 443
Period size: 94 Copynumber: 6.3 Consensus size: 93
3912897 ACGCCAATTT
* * * * * *
3912907 AGTCAAACAATGGTGAAAAGAGTTTGACTAAG-ACTAATGCCAATACAGTCAAACAAAGGTAAAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAAC-GAGGTAAAA
* * * * * *
3912971 AAAGGTTTAACTAGGCCCTTACGCCAATACA
65 AGA-GTTTGACCAGGTCCTAATGCCAATA-A
** ** * * ** * *
3913002 A-TCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAACACTAATATAGTCAAACGAGGATAAAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGG-TAAAA
* *
3913066 A-AGTTTAACTAGGTCCTAATGCCAATACA
65 AGAGTTTGACCAGGTCCTAATGCCAATA-A
* * * * ** * *
3913095 GGT-AAACAAGGGAAAAAAGAGTTTGACGAGGTTCTAACACCAATATAGTCAAACAAGTGTAAAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAG-GTAAAA
* * *
3913159 AGAGTTTGACCAGGTCTTAACGTCAATAA
65 AGAGTTTGACCAGGTCCTAATGCCAATAA
* ** * *
3913188 AATCAAATGAGGGTAAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGA-GGTAAAA
* * *
3913253 AGAGTTTGACTAGGTCATAATGCCAATAC
65 AGAGTTTGACCAGGTCCTAATGCCAATAA
* ** ** * * * * * *
3913282 AGTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACAATCAAATGAGGTATGAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGGTA--AA
* * *
3913347 AAGAGTTTGACCAAG-ACTAATGCCAATAT
64 AAGAGTTTGACCAGGTCCTAATGCCAATAA
* * * **
3913376 TGTCAAACAAGGGTAAAAAGAGTATGACCAAGTCCTAATGCCAATACAGTCAAACGAGAGTGGAA
1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAG-GTAAAA
* *
3913441 AGAGTTTGACCAGGTCCTAATGCTAATAT
65 AGAGTTTGACCAGGTCCTAATGCCAATAA
** * *
3913470 AGTCAAATGATGGTGAAAAGAGTTTGA
1 AGTCAAACAAGGGTAAAAAGAGTTTGA
3913497 GCATGTTTTA
Statistics
Matches: 397, Mismatches: 87, Indels: 23
0.78 0.17 0.05
Matches are distributed among these distances:
93 94 0.24
94 261 0.66
95 42 0.11
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (93 bp):
AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGGTAAAAA
GAGTTTGACCAGGTCCTAATGCCAATAA
Found at i:3913523 original size:141 final size:141
Alignment explanation
Indices: 3912920--3913496 Score: 565
Period size: 141 Copynumber: 4.1 Consensus size: 141
3912910 CAAACAATGG
* * * * * *
3912920 TGAAAAGAGTTTGACTAAG-ACTAATGCCAATACAGTCAAACAAAGGTAAAAAAAGGTTTAACTA
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGA-GTTTGACCA
* * * * * * ** * * *
3912984 GGCCCTTACGCCAATACAATCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAAC-ACTAATAT
65 GGTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTC-AATAT
* *
3913048 AGTCAAACGAGGA
129 AATCAAATGAGGA
* * * *
3913061 T-AAAAAAGTTTAACTAGGTCCTAATGCCAATACAGGT-AAACAAGGGAAAAAAGAGTTTGACGA
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACA-GTCAAACAAGGGTAAAAAGAGTTTGACCA
* ** * * * *
3913124 GGTTCTAACACCAATATAGTCAAACAAGTGTAAAAAGAGTTTGACCAGGTCTTAACGTCAATAAA
65 GGTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATA
*
3913189 ATCAAATGAGGG
130 ATCAAATGAGGA
* *
3913201 TAAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACTAG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG
* * * * * * * * *
3913266 GTCATAATGCCAATACAGTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACAA
66 GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATAA
3913331 TCAAATGAGGTA
131 TCAAATGAGG-A
* * * ** * *
3913343 TGAAAAGAGTTTGACCAAG-ACTAATGCCAATATTGTCAAACAAGGGTAAAAAGAGTATGACCAA
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG
* ** *
3913407 GTCCTAATGCCAATACAGTCAAACGAGAGTGGAAAGAGTTTGACCAGGTCCTAATG-CTAATATA
66 GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTC-AATATA
*
3913471 GTCAAATGATGG-
130 ATCAAATGA-GGA
3913483 TGAAAAGAGTTTGA
1 TGAAAAGAGTTTGA
3913497 GCATGTTTTA
Statistics
Matches: 359, Mismatches: 69, Indels: 17
0.81 0.16 0.04
Matches are distributed among these distances:
140 95 0.26
141 244 0.68
142 20 0.06
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (141 bp):
TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG
GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATAA
TCAAATGAGGA
Found at i:3914647 original size:17 final size:16
Alignment explanation
Indices: 3914627--3914694 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
3914617 TCTCTCTCTC
* *
3914627 TTTTGTTTTTTTTCTT
1 TTTTTTTTTTTTTGTT
*
3914643 TTTTTTTGGTTTTTGTT
1 TTTTTTT-TTTTTTGTT
* *
3914660 CTTCTTTCTTTTTTGTT
1 -TTTTTTTTTTTTTGTT
3914677 TTTTTTGTTTTTTTGTT
1 TTTTTT-TTTTTTTGTT
3914694 T
1 T
3914695 GCCCCCTCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
16 11 0.27
17 25 0.61
18 5 0.12
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTTTTGTT
Found at i:3914656 original size:43 final size:43
Alignment explanation
Indices: 3914610--3914690 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
3914600 TATTATCTAT
* *
3914610 TTTTTTTTC-TCTCTCTCTTTTGTTTTTTTTCTTTTTTTTTGG
1 TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTTTTGG
* *
3914652 TTTTTGTTCTTCTTTCTTTTTTGTTTTTTTTGTTTTTTT
1 TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTT
3914691 GTTTGCCCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 8 0.24
43 26 0.76
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (43 bp):
TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTTTTGG
Found at i:3915674 original size:13 final size:13
Alignment explanation
Indices: 3915656--3915681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3915646 TACACCAAGT
3915656 ATGTATCGATACA
1 ATGTATCGATACA
3915669 ATGTATCGATACA
1 ATGTATCGATACA
3915682 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3915679 original size:32 final size:33
Alignment explanation
Indices: 3915638--3915701 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3915628 TAGCCAAACT
* **
3915638 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3915670 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3915702 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3921944 original size:73 final size:75
Alignment explanation
Indices: 3921854--3922004 Score: 198
Period size: 73 Copynumber: 2.0 Consensus size: 75
3921844 ACCCTAGAGA
* * *
3921854 ACTCAAAAAGGATAAAAACCAACCTATTTC-AATTCCTACCTGCGACATGGAAGTAGACCGA-TA
1 ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA
*
3921917 GTTTTATAGG
66 GTTTTATAAG
* * * * *
3921927 ACTCAGAAAGGATAAAAACCAACCAATTCCTAATTCTTACCTTCGGCATAGAAGTAGACCTAGTA
1 ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA
*
3921992 TTTTTATAAG
66 GTTTTATAAG
3922002 ACT
1 ACT
3922005 AGGTTTCAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
73 27 0.41
74 26 0.39
75 13 0.20
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (75 bp):
ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA
GTTTTATAAG
Found at i:3922654 original size:141 final size:142
Alignment explanation
Indices: 3922365--3923301 Score: 1107
Period size: 141 Copynumber: 6.6 Consensus size: 142
3922355 AGGGGATATG
* * * *
3922365 AAAAA-TTTTGAAAATTTCTGTACTCCTACGAAAAACCATAAG-A-ATTAGAAATCTTGAAAAAT
1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT
* ** * ** * * *
3922427 TAAGACAATAATTTTTAATTAAAATTTTTTTATTTCCAA-AAATATTTATTTCATACATAAATGG
66 TAAGATAATAATTTTT-ATT-TGA-TTTTTAATTTTTAAGAAA-ATTCATTTCATACCTTAATGG
*
3922491 AGAAACGAAAAGATAC
127 AGAACCGAAAAGATAC
* * *
3922507 AAAAAGTTTTGAAGATTTCTATACCTCTACGGAAAACCATAAGAATATTAGAAATCCTAAAAAAT
1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT
* *
3922572 TAAGATAATAA-TTTTATTTGATTTTTCATTTTTAAGAAAATTCATTTCGTACCTTAATGGAGAA
66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA
3922636 CCGAAAAGATAC
131 CCGAAAAGATAC
* * * *
3922648 AAAAAGTTTTGAAGATTTTTATACCCCCACAAGAAAACCATAAGAATATTAGAAATCTTAAAAAA
1 AAAAAGTTTTGAAGATTTCTATACCCCTAC-GGAAAACCATAAGAATATTAGAAATCTTGAAAAA
* * *
3922713 TTAAAATAATAATTTTTGTTTGATTTGTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGA
65 TTAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGA
3922778 ACCGAAAAGATAC
130 ACCGAAAAGATAC
* * * * * * * *
3922791 GAAAAGTTTTGAAAAGATTTCTATACCCCTATGAAAAACTATAGGAGTATTACAAATTTTGAAAA
1 AAAAAGTTTTG--AAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAA
* * * * *
3922856 CTTAAGAAAATAATTTTTATTTGATTTTTAATTTTTAAAAAAATTTATTTCGTACCTTAATGGAG
64 ATTAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAG
* * *
3922921 AATCGAAAATATAT
129 AACCGAAAAGATAC
* * *
3922935 GAAAAGTTTTGAAGATTTTTATACCCCTACGGAAAACCATAGGAATATTAGAAATCTTGAAAAAT
1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT
* **
3923000 TAAAATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCCGACCTTAATGGAGAA
66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA
* * * *
3923065 TCAAAAAGACAT
131 CCGAAAAGATAC
* * ** * * *
3923077 AAAAA-TTTTGAAGATTTCTATACTCATACAAAAAACCATAGGAATAATAAAAATCTTGAAAAAT
1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT
* * * *
3923141 TAAGATAATAACTTTTATTTGATTTTTAATTTTTAAAAAAATTCATTTCACACCTCAATGGAGAA
66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA
* *
3923206 CC-AAAAAATAT
131 CCGAAAAGATAC
* * * *
3923217 GAAAAGTTTTGAAGATTTTTATACCCCTACGGAAAACTATAAGAATATTA-ATAATTTTGAAAAA
1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGA-AATCTTGAAAAA
* *
3923281 TTAAGAAAATAAGTTTTATTT
65 TTAAGATAATAATTTTTATTT
3923302 TGGGATAAAA
Statistics
Matches: 688, Mismatches: 97, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
140 12 0.02
141 248 0.36
142 170 0.25
143 106 0.15
144 109 0.16
145 43 0.06
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (142 bp):
AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT
TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA
CCGAAAAGATAC
Found at i:3924606 original size:19 final size:18
Alignment explanation
Indices: 3924560--3924645 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
3924550 TTCAACTAAT
*
3924560 TTGTATCGATACAAACTG
1 TTGTATCGATACAAAGTG
3924578 TAACTGTATCGATACATAAGTG
1 T---TGTATCGATACA-AAGTG
3924600 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
* *
3924614 -TATATCGATACATAAGTT
1 TTGTATCGATACA-AAGTG
3924632 TTGTATCGATACAA
1 TTGTATCGATACAA
3924646 TGTATCACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 20
0.71 0.04 0.26
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
18 2 0.04
19 22 0.40
21 12 0.22
22 5 0.09
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:3924625 original size:32 final size:32
Alignment explanation
Indices: 3924584--3924651 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
3924574 ACTGTAACTG
3924584 TATCGATACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
* *
3924616 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATA
3924648 TATC
1 TATC
3924652 ACTACGAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:3924715 original size:13 final size:13
Alignment explanation
Indices: 3924697--3924724 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3924687 ATTACTCAAA
3924697 TGTATCGATACAT
1 TGTATCGATACAT
3924710 TGTATCGATACAT
1 TGTATCGATACAT
3924723 TG
1 TG
3924725 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3928488 original size:167 final size:161
Alignment explanation
Indices: 3928258--3928845 Score: 547
Period size: 167 Copynumber: 3.5 Consensus size: 161
3928248 AAATTTCATG
* * * *
3928258 AAATAAATTGAATTTTCTAAAACTGATATACTATGAGTGTAATGAA-AATATTAGATGAATTTTA
1 AAATAAATT-AATTTT-TGAAACTGAT-TA-TATGAAT-TAAT-AATGATATTTGATGAATTTTA
* * *
3928322 AAAATTTTAAACCGAGAAAAATCCCCCCGAAAACATTTATTGAATAAAAAATTTGATTTTTCGAA
60 AAAATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATTT-ATTTTTCGAA
* *
3928387 AACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCATGA
124 AATAGAGAAATTTCAAGGAAAA-AATGAAAAACTTATGA
*
3928426 AAATAAATTAATTTTTCGAAATTGACTTACTATGAATTGAATAATGATATTTGATGAATTTTAAA
1 AAATAAATTAATTTTT-GAAACTGA-TTA-TATGAATT-AATAATGATATTTGATGAATTTTAAA
** * * * *
3928491 AATTATAAACTGAGAAAAATCCTCCCGAAAACTTTTATAGAGTAGAAAATTCTATTTTTC-AACA
62 AATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATT-TATTTTTCGAA-A
* * * *
3928555 ATAG-GAAAATTTCTAGGAAAAAATTAAAATCTTAGGA
125 ATAGAG-AAATTTCAAGGAAAAAATGAAAAACTTATGA
* * * * *
3928592 ATATAAATTAATTTTTGAAAACAGATTTATTATAAATTAATGATGATATTTGATGAATTTTGAAA
1 AAATAAATTAATTTTTG-AAACTGA-TTA-TATGAATTAATAATGATATTTGATGAATTTTAAAA
* * * * *
3928657 ATTATAAATCAAGAAAAATTCTCTCGAAAACATTTA-TGAAGTAGAAAATTTCATATTTTAG-AA
63 ATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAA-TAGAAAATTT-AT-TTTTCGAAA
* *
3928720 ATAGAGAAATTTCAAGAAAAAAATGAAAAATTTATGA
125 ATAGAGAAATTTCAAGGAAAAAATGAAAAACTTATGA
* * * * * *
3928757 AAATAAATAAATTTTTTAAAGCTGATTAAATGGTGATTAGATAATAATATTTGATGAAATTTTGA
1 AAATAAATTAATTTTTGAAA-CTGATTATAT-G-AATTA-ATAATGATATTTGATG-AATTTTAA
* *
3928822 AAATTTTAAACAAAGAAAAATCCC
61 AAATTATAAACCAAGAAAAATCCC
3928846 TATAAAATCA
Statistics
Matches: 347, Mismatches: 55, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
163 2 0.01
164 9 0.03
165 118 0.34
166 69 0.20
167 138 0.40
168 11 0.03
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (161 bp):
AAATAAATTAATTTTTGAAACTGATTATATGAATTAATAATGATATTTGATGAATTTTAAAAATT
ATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATTTATTTTTCGAAAATAGAG
AAATTTCAAGGAAAAAATGAAAAACTTATGA
Found at i:3928687 original size:165 final size:165
Alignment explanation
Indices: 3928305--3928772 Score: 495
Period size: 165 Copynumber: 2.8 Consensus size: 165
3928295 TGTAATGAAA
* * * * *
3928305 ATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAATCCCCCCGAAAACATTTATTGAATAAA
1 ATATTTGATGAATTTTAAAAATTATAAA-CGAGAAAAATCCTCCCGAAAACATTTA-TGAGTAGA
*
3928370 AAATT-TGATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCATGAAAATAAAT
64 AAATTCT-ATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAAT
** *
3928434 TAATTTTTCGAAATTGACTTACTATGAATTGAATAATG
128 TAATTTTTCGAAACAGACTTACTATAAATTGAATAATG
*
3928472 ATATTTGATGAATTTTAAAAATTATAAACTGAGAAAAATCCTCCCGAAAACTTTTATAGAGTAGA
1 ATATTTGATGAATTTTAAAAATTATAAAC-GAGAAAAATCCTCCCGAAAACATTTAT-GAGTAGA
* * * * * *
3928537 AAATTCTATTTTTC-AACAATAG-GAAAATTTCTAGGAAAA-AATTAAAATCTTAGGAATATAAA
64 AAATTCTATTTTTCGAA-AACAGAG-AAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAA
* * *
3928599 TTAATTTTT-GAAAACAGATTTATTATAAATT-AATGATG
127 TTAATTTTTCG-AAACAGACTTACTATAAATTGAATAATG
* * * *
3928637 ATATTTGATGAATTTTGAAAATTATAAATCAAGAAAAATTCTCTCGAAAACATTTATGAAGTAGA
1 ATATTTGATGAATTTTAAAAATTATAAA-CGAGAAAAATCCTCCCGAAAACATTTATG-AGTAGA
* * * * * *
3928702 AAATT-TCATATTTTAG-AAATAGAGAAATTTCAA-GAAAAAAATGAAAAATTTATGAAAATAAA
64 AAATTCT-AT-TTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAA
*
3928764 TAAATTTTT
127 TTAATTTTT
3928773 TAAAGCTGAT
Statistics
Matches: 256, Mismatches: 32, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
164 7 0.03
165 109 0.43
166 54 0.21
167 85 0.33
168 1 0.00
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (165 bp):
ATATTTGATGAATTTTAAAAATTATAAACGAGAAAAATCCTCCCGAAAACATTTATGAGTAGAAA
ATTCTATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAATTAA
TTTTTCGAAACAGACTTACTATAAATTGAATAATG
Found at i:3938294 original size:24 final size:24
Alignment explanation
Indices: 3938267--3938313 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3938257 AAATGCATGG
* **
3938267 GAAATAAAAATGGCATGGAAAAAT
1 GAAAAAAAAATGAAATGGAAAAAT
3938291 GAAAAAAAAATGAAATGGAAAAA
1 GAAAAAAAAATGAAATGGAAAAA
3938314 AAATGGCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.19, T:0.13
Consensus pattern (24 bp):
GAAAAAAAAATGAAATGGAAAAAT
Found at i:3938312 original size:16 final size:16
Alignment explanation
Indices: 3938287--3938318 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3938277 TGGCATGGAA
3938287 AAATGAAAAAAAAATG
1 AAATGAAAAAAAAATG
*
3938303 AAATGGAAAAAAAATG
1 AAATGAAAAAAAAATG
3938319 GCCATTTAGC
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
AAATGAAAAAAAAATG
Found at i:3939563 original size:141 final size:141
Alignment explanation
Indices: 3939354--3939619 Score: 331
Period size: 141 Copynumber: 1.9 Consensus size: 141
3939344 TAATAATAAA
* * * *
3939354 TTTTCAAGATTTTTAGTATTCCTATGGTTTTTCGTAGGAGTATAGAAATCTTCAAAAATTTTCAT
1 TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGTAGGAGTACAGAAATCTTCAAAAATTTTCAT
* * *
3939419 ATCTTTT-TTACTCTCCATTAAGGTAAAAAATGA-ATTTTTAAAAAATTAAAAATTAAATAAAAA
66 ATCTTTTATT--TCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATAAAAA
3939482 TTATTATCTTAAT
129 TTATTATCTTAAT
* * * **
3939495 TTTTCAATATTTCTAATATTCTTATAGTTTTTCGTAAGG-GTACAGAAATCTTCAAAACTTTTTG
1 TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGT-AGGAGTACAGAAATCTTCAAAAATTTTCA
** **
3939559 TATCTTTTCATTTCTCCATTAAAGTATGAAATGAGATTTTCAAAACTTTAAAAATAAAATA
65 TATCTTTT-ATTTCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATA
3939620 TTACATTATT
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
141 78 0.74
142 25 0.24
143 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (141 bp):
TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGTAGGAGTACAGAAATCTTCAAAAATTTTCAT
ATCTTTTATTTCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATAAAAATT
ATTATCTTAAT
Found at i:3941417 original size:13 final size:13
Alignment explanation
Indices: 3941399--3941429 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3941389 ACAATTCATC
3941399 ATGTATCGATACA
1 ATGTATCGATACA
3941412 ATGTATCGATACA
1 ATGTATCGATACA
*
3941425 TTGTA
1 ATGTA
3941430 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3941417 original size:33 final size:33
Alignment explanation
Indices: 3941378--3941442 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3941368 CGTTACAAGT
*
3941378 AATGTATCGATACAATT-CATCATGTATCGATAC
1 AATGTATCGATAC-ATTGCACCATGTATCGATAC
*
3941411 AATGTATCGATACATTGTACCATGTATCGATA
1 AATGTATCGATACATTGCACCATGTATCGATA
3941443 TAAACAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACATTGCACCATGTATCGATAC
Found at i:3941532 original size:13 final size:13
Alignment explanation
Indices: 3941514--3941572 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
3941504 TACAATGAAC
3941514 ATGTATCGATACA
1 ATGTATCGATACA
3941527 ATGTATCGATACA
1 ATGTATCGATACA
*
3941540 A---AGC-AT--A
1 ATGTATCGATACA
3941547 ATGTATCGATACA
1 ATGTATCGATACA
3941560 ATGTATCGATACA
1 ATGTATCGATACA
3941573 TTATCTGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
9 2 0.05
10 4 0.11
11 2 0.05
13 28 0.74
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3941556 original size:33 final size:32
Alignment explanation
Indices: 3941495--3941572 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 32
3941485 ATAATTGTCC
*
3941495 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
3941527 ATGTATCGATACAAAGCATA-ATGTATCGATACA
1 ATGTATCGATACAAAG-A-ACATGTATCGATACA
3941560 ATGTATCGATACA
1 ATGTATCGATACA
3941573 TTATCTGGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
32 15 0.35
33 27 0.63
34 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:3942127 original size:22 final size:22
Alignment explanation
Indices: 3942100--3942179 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
3942090 AGTTTTCATT
3942100 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAGAA
*
3942122 TTTCTCCCCCTTAATTAAAAAAAA
1 TTTCTCCCCCTTAATT--AAAGAA
* * *
3942146 ATTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATTAAAGAA
*
3942168 TTTCTCTCCCTT
1 TTTCTCCCCCTT
3942180 TGTCAAATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
22 30 0.61
24 19 0.39
ACGTcount: A:0.30, C:0.31, G:0.03, T:0.36
Consensus pattern (22 bp):
TTTCTCCCCCTTAATTAAAGAA
Found at i:3942155 original size:24 final size:22
Alignment explanation
Indices: 3942101--3942160 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
3942091 GTTTTCATTT
* *
3942101 TTCTCCCCCTTAATTAAAGAAT
1 TTCTCCCCCTTAATTAAAAAAA
3942123 TTCTCCCCCTTAATTAAAAAAAAA
1 TTCTCCCCCTTAATT--AAAAAAA
3942147 TTCTCCCCCTTAAT
1 TTCTCCCCCTTAAT
3942161 CAAAGCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 15 0.44
24 19 0.56
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (22 bp):
TTCTCCCCCTTAATTAAAAAAA
Found at i:3948721 original size:13 final size:13
Alignment explanation
Indices: 3948703--3948727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3948693 CATAAAGTGT
3948703 TGTATCGATACAA
1 TGTATCGATACAA
3948716 TGTATCGATACA
1 TGTATCGATACA
3948728 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3948725 original size:33 final size:33
Alignment explanation
Indices: 3948683--3948749 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3948673 TTCAACGATT
3948683 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
3948716 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3948749 T
1 T
3948750 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3948808 original size:13 final size:13
Alignment explanation
Indices: 3948790--3948814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3948780 ATCACTTAAA
3948790 TGTATCGATACAT
1 TGTATCGATACAT
3948803 TGTATCGATACA
1 TGTATCGATACA
3948815 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3948867 original size:52 final size:51
Alignment explanation
Indices: 3948803--3948951 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
3948793 ATCGATACAT
**
3948803 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
3948855 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
3948907 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
3948952 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:3956607 original size:13 final size:13
Alignment explanation
Indices: 3956589--3956613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3956579 AAAACTCAGA
3956589 TGTATCGATACAG
1 TGTATCGATACAG
3956602 TGTATCGATACA
1 TGTATCGATACA
3956614 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3959023 original size:13 final size:13
Alignment explanation
Indices: 3959005--3959029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3958995 ATAATGCACA
3959005 GTATCGATACATT
1 GTATCGATACATT
3959018 GTATCGATACAT
1 GTATCGATACAT
3959030 GACCACTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3959139 original size:32 final size:33
Alignment explanation
Indices: 3959098--3959161 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
3959088 CCTTAACTGT
3959098 TTGTATCGATACAT-A-CAAGATGTATCGATACC
1 TTGTATCGATACATGACCAA-ATGTATCGATACC
3959130 TTGTATCGATACATGACCAAATGTATCGATAC
1 TTGTATCGATACATGACCAAATGTATCGATAC
3959162 ATTGGCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 13 0.43
34 3 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACC
Found at i:3962603 original size:21 final size:21
Alignment explanation
Indices: 3962559--3962604 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3962549 TTTTTGCCAA
* *
3962559 AATGTGTCGATACATGCCCTT
1 AATGTATCGATACAGGCCCTT
3962580 AATGTATCGATACAAGGCCC-T
1 AATGTATCGATAC-AGGCCCTT
3962601 AATG
1 AATG
3962605 GTCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (21 bp):
AATGTATCGATACAGGCCCTT
Found at i:3965000 original size:51 final size:51
Alignment explanation
Indices: 3964920--3965088 Score: 162
Period size: 51 Copynumber: 3.3 Consensus size: 51
3964910 ATTTTTCATC
**
3964920 TCGGGGATACTCCAA-TCCCGATTCCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTTCTTAA
* * * * *** **
3964971 TCGGGGATATTCCAACTCCGATTTTATTTCTAAAGCATTAATTAACCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA
* * *
3965022 TCGGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAA-TTTTCTATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCT-TAA
**
3965073 TTAGGGATACTCCAAC
1 TCGGGGATACTCCAAC
3965089 CCTGTTATTT
Statistics
Matches: 90, Mismatches: 26, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
50 2 0.02
51 87 0.97
52 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA
Found at i:3965158 original size:79 final size:79
Alignment explanation
Indices: 3965024--3965244 Score: 318
Period size: 79 Copynumber: 2.8 Consensus size: 79
3965014 AACCGCAATC
* * * *
3965024 GGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
3965089 CCTGTTATTTCCGA
66 CCTGTTATTTCCGA
* *
3965103 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATCAGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
**
3965168 CCTGTTATTTTTGA
66 CCTGTTATTTCCGA
* * * *
3965182 GTGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTT-TCATAAACGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCT-ATAATCAGGGATACTCCA
3965245 GCCCCGTTGT
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.01
79 127 0.99
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
CCTGTTATTTCCGA
Found at i:3967693 original size:19 final size:19
Alignment explanation
Indices: 3967647--3967701 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3967637 TGCCAATTTT
**
3967647 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
*
3967667 ACGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
3967686 ATGTATCGATACAATG
1 ATGTATCGATACAATG
3967702 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:3967704 original size:13 final size:13
Alignment explanation
Indices: 3967686--3967712 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3967676 TACAATGAAC
3967686 ATGTATCGATACA
1 ATGTATCGATACA
3967699 ATGTATCGATACA
1 ATGTATCGATACA
3967712 A
1 A
3967713 GGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3969401 original size:20 final size:19
Alignment explanation
Indices: 3969376--3969466 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 19
3969366 ACCCTAGAAA
3969376 GTATCGATACATATCCAGAT
1 GTATCGATACATATCCA-AT
* **
3969396 GTATCGATACATTATGCTTT
1 GTATCGATACA-TATCCAAT
* * *
3969416 GTATCGATACATGTTCATT
1 GTATCGATACATATCCAAT
3969435 GTATCGATACATA-CTCAATT
1 GTATCGATACATATC-CAA-T
3969455 GTATCGATACAT
1 GTATCGATACAT
3969467 GAAACTGGCA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 19 0.32
20 36 0.61
21 4 0.07
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATCCAAT
Found at i:3969445 original size:39 final size:40
Alignment explanation
Indices: 3969376--3969467 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 40
3969366 ACCCTAGAAA
* *
3969376 GTATCGATACATATCCAGATGTATCGATACATTA-TGC-TTT
1 GTATCGATACATGTCCAGATGTATCGATACA-TACT-CAATT
* *
3969416 GTATCGATACATGTTCA-TTGTATCGATACATACTCAATT
1 GTATCGATACATGTCCAGATGTATCGATACATACTCAATT
3969455 GTATCGATACATG
1 GTATCGATACATG
3969468 AAACTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.07
39 28 0.61
40 15 0.33
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (40 bp):
GTATCGATACATGTCCAGATGTATCGATACATACTCAATT
Found at i:3970563 original size:33 final size:33
Alignment explanation
Indices: 3970519--3970587 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3970509 CTACCACTGT
*
3970519 TTGTATCGATACAT-AGGACATTGTATCGTTACA
1 TTGTATCGATACATGAGGA-ATTGTATCGATACA
* *
3970552 TTGTATTGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAATTGTATCGATACA
3970585 TTG
1 TTG
3970588 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAATTGTATCGATACA
Found at i:3976714 original size:21 final size:19
Alignment explanation
Indices: 3976690--3976737 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
3976680 TAAATCCTTT
*
3976690 TCAAAATTCATCATTTTCACA
1 TCAAAATACAT-ATTTT-ACA
*
3976711 TCAAAACTACATATTTTTCA
1 TCAAAA-TACATATTTTACA
3976731 TCAAAAT
1 TCAAAAT
3976738 CTTCATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 11 0.46
22 4 0.17
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAAAATACATATTTTACA
Found at i:3978165 original size:15 final size:15
Alignment explanation
Indices: 3978145--3978175 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3978135 TTACTTTTCC
*
3978145 TCTAGTGATGATGAG
1 TCTAGTGACGATGAG
3978160 TCTAGTGACGATGAG
1 TCTAGTGACGATGAG
3978175 T
1 T
3978176 AATAGGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32
Consensus pattern (15 bp):
TCTAGTGACGATGAG
Found at i:3979139 original size:13 final size:13
Alignment explanation
Indices: 3979121--3979180 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
3979111 ACATTATGCT
3979121 TTGTATCGATACA
1 TTGTATCGATACA
*
3979134 TTGTATCAATACA
1 TTGTATCGATACA
*
3979147 -TG---GGA--CA
1 TTGTATCGATACA
3979154 TTGTATCGATACA
1 TTGTATCGATACA
*
3979167 TTGTATAGATACA
1 TTGTATCGATACA
3979180 T
1 T
3979181 GGTAAAAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
11 2 0.06
12 2 0.06
13 27 0.75
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3979146 original size:33 final size:34
Alignment explanation
Indices: 3979102--3979180 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
3979092 CATATCTAGA
* * *
3979102 TGTATCGATACATTATG-CTTTGTATCGATACAT
1 TGTATCAATACATTAGGACATTGTATCGATACAT
*
3979135 TGTATCAATACA-TGGGACATTGTATCGATACAT
1 TGTATCAATACATTAGGACATTGTATCGATACAT
3979168 TGTAT-AGATACAT
1 TGTATCA-ATACAT
3979181 GGTAAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 3 0.08
33 36 0.92
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (34 bp):
TGTATCAATACATTAGGACATTGTATCGATACAT
Found at i:3979181 original size:33 final size:33
Alignment explanation
Indices: 3979121--3979201 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
3979111 ACATTATGCT
*
3979121 TTGTATCGATACATTGTATCAATACATGGGACA
1 TTGTATCGATACATTGTATCAATACATGGGAAA
*
3979154 TTGTATCGATACATTGTAT-AGATACATGGTAAA
1 TTGTATCGATACATTGTATCA-ATACATGGGAAA
**
3979187 AAGTATCGATACATT
1 TTGTATCGATACATT
3979202 ATGCCCAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATTGTATCAATACATGGGAAA
Found at i:3984930 original size:50 final size:51
Alignment explanation
Indices: 3984816--3984930 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 51
3984806 TACATTGAAG
* *
3984816 AATGTATCGATACATTTGGATCAAAAACCTAGAATGTGTCAATATAATAAGA
1 AATGTATCGATACATTTGGATC-AAAACCTAGAATGTATCAATATAATAAAA
* *
3984868 AATGTATTGATACATTTGGATC-AAACCTAGAATGTATCGATATAATGAAAA
1 AATGTATCGATACATTTGGATCAAAACCTAGAATGTATCAATATAAT-AAAA
3984919 AAT-TATCGATAC
1 AATGTATCGATAC
3984931 CTTTTCTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
50 30 0.53
51 6 0.11
52 21 0.37
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (51 bp):
AATGTATCGATACATTTGGATCAAAACCTAGAATGTATCAATATAATAAAA
Found at i:3985522 original size:20 final size:20
Alignment explanation
Indices: 3985497--3985535 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3985487 GCACTTTGAA
3985497 AAGTAAATGTATCAATATAT
1 AAGTAAATGTATCAATATAT
*
3985517 AAGTAAATGTATCGATATA
1 AAGTAAATGTATCAATATA
3985536 CTTACTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (20 bp):
AAGTAAATGTATCAATATAT
Found at i:3989196 original size:12 final size:12
Alignment explanation
Indices: 3989166--3989210 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
3989156 GCAAAAGCGT
*
3989166 AAAAGGAAAATG
1 AAAAGAAAAATG
3989178 -AAA-AAAAATG
1 AAAAGAAAAATG
3989188 AAAAGAAAAA-G
1 AAAAGAAAAATG
3989199 AAAAAGAAAAAT
1 -AAAAGAAAAAT
3989211 AAAGTGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.21
11 7 0.25
12 15 0.54
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (12 bp):
AAAAGAAAAATG
Found at i:3991935 original size:155 final size:153
Alignment explanation
Indices: 3991639--3992017 Score: 413
Period size: 155 Copynumber: 2.4 Consensus size: 153
3991629 CTAAGTTCAA
* * ** * **
3991639 GAAAAATTACGAAAATGCTCTTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAAA
1 GAAAAATTATGAAAATGC-CCTAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA
* * * * *
3991704 CTTAAAAAAGATAATAGATGAGATGAACCTATCATTAATATCTACCTTCGGCATAAAAGCAGACC
64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC
*
3991769 CAATGATAACCTAGGACGT-AATTCT
129 CAATGACAACCTAGGAC-TCAATTCT
* *
3991794 GAAAAATTATGAAATTGCCCATAAGGGACATTTTCGACGTAAAAGTACCCGATATCCCTAAAGGA
1 GAAAAATTATGAAAATGCCC-TAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA
* * * *
3991859 CTTAAAAAGGATAACATATGAGATGAGCCTATCCTAAATATCTACCTCCGACATAAAAGCAAACC
64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC
** * *
3991924 CGGTGACAACCTAGGACTCGATTTT
129 CAATGACAACCTAGGACTCAATTCT
* * * *
3991949 AAAAAATTATGAAAATGACCCT-AGAGG-ATTACTTCAATGTAAAAGTACCCAATACCCCTAAAG
1 GAAAAATTATGAAAATG-CCCTAAG-GGAATT--TTCGACGTAAAAGTACCCGATACCCCTAAAG
3992012 GACTTA
62 GACTTA
3992018 GGATAATGCT
Statistics
Matches: 188, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 178 0.95
156 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (153 bp):
GAAAAATTATGAAAATGCCCTAAGGGAATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGACT
TAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACCCA
ATGACAACCTAGGACTCAATTCT
Found at i:3993480 original size:13 final size:13
Alignment explanation
Indices: 3993462--3993487 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3993452 CAATTTTTTG
3993462 TGTATCGATACAT
1 TGTATCGATACAT
3993475 TGTATCGATACAT
1 TGTATCGATACAT
3993488 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3993572 original size:20 final size:20
Alignment explanation
Indices: 3993547--3993619 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3993537 CAACTTTTTT
3993547 ATGTATCGATACATTACAAC
1 ATGTATCGATACATTACAAC
****
3993567 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TACAAC
*
3993588 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTACAAC
3993608 ATGTATCGATAC
1 ATGTATCGATAC
3993620 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTACAAC
Found at i:3993585 original size:41 final size:41
Alignment explanation
Indices: 3993526--3993619 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
3993516 CTGCCAAGAA
*
3993526 ATGTATCGATACAACTTTTTTATGTATCGATACATTACAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
* *
3993567 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
3993608 ATGTATCGATAC
1 ATGTATCGATAC
3993620 TTTGAATTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
Found at i:3993601 original size:21 final size:21
Alignment explanation
Indices: 3993526--3993601 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3993516 CTGCCAAGAA
* *
3993526 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3993547 ATGTATCGATACAT-TACAAC
1 ATGTATCGATACATCTTTTTC
3993567 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3993588 ATGTATCGATACAT
1 ATGTATCGATACAT
3993602 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3994353 original size:100 final size:100
Alignment explanation
Indices: 3994180--3994381 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
3994170 TACGAATTCG
3994180 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA
1 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA
3994245 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
66 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
3994280 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA
1 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA
3994345 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
66 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
3994380 TA
1 TA
3994382 TTTTCACTTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.28, C:0.29, G:0.06, T:0.37
Consensus pattern (100 bp):
TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA
ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
Found at i:3996180 original size:13 final size:13
Alignment explanation
Indices: 3996162--3996200 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3996152 ATAATCACCC
*
3996162 TGTATCGATACAG
1 TGTATCGATACAA
3996175 TGTATCGATACAA
1 TGTATCGATACAA
3996188 TGTATCGATACAA
1 TGTATCGATACAA
3996201 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3996211 original size:20 final size:20
Alignment explanation
Indices: 3996186--3996264 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
3996176 GTATCGATAC
3996186 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3996206 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
3996231 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
3996251 CATGTATCGATACA
1 AATGTATCGATACA
3996265 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3998297 original size:15 final size:15
Alignment explanation
Indices: 3998277--3998307 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3998267 ATTTCGTTTG
*
3998277 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3998292 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3998307 G
1 G
3998308 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4000140 original size:21 final size:21
Alignment explanation
Indices: 4000111--4000155 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4000101 AAGTTTTCAT
*
4000111 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4000131 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4000153 TTT
1 TTT
4000156 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4002373 original size:13 final size:13
Alignment explanation
Indices: 4002355--4002380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4002345 CAATTTTTTG
4002355 TGTATCGATACAT
1 TGTATCGATACAT
4002368 TGTATCGATACAT
1 TGTATCGATACAT
4002381 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4002466 original size:20 final size:20
Alignment explanation
Indices: 4002441--4002513 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4002431 AACTTTTTTT
4002441 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4002461 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4002482 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4002502 ATGTATCGATAC
1 ATGTATCGATAC
4002514 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4002492 original size:41 final size:42
Alignment explanation
Indices: 4002419--4002513 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
4002409 CTGCCAAGAA
*
4002419 ATGTATCGATACAACTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
*
4002461 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
4002502 ATGTATCGATAC
1 ATGTATCGATAC
4002514 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 37 0.73
42 14 0.27
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (42 bp):
ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
Found at i:4004487 original size:168 final size:166
Alignment explanation
Indices: 4004094--4004547 Score: 546
Period size: 168 Copynumber: 2.7 Consensus size: 166
4004084 ATATACAAAA
* * * * ** * *
4004094 AAAATTAATG-AAATAAATTAAAATTTTCAAAACTGA-ATTAATGAGAGTTTAATTACAATATTA
1 AAAACTAATGAAAATAAATT-AATTTTTCAAAACT-ATTTTAATGAGAATTCCATGACATTATTA
* * * * * ** * *
4004157 GATGCATTTTAAAAGTTTTAGACCAAAGAAAATCCCTTCGGAAATATTTATCGAATAGAAAACTT
64 GATACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCCAAAAATATTTATGGATTAGAAAACTT
* * * *
4004222 TGTTTGTCGAGAAAAAGGGGATTGTAAAGAAAAAATTT
129 TGTTTGTCGAGAAAAAAGAGATTGTAAAGAAAAAAATC
4004260 AAAACTAATGAAAATAAATTAATTTTTCAAAACCT-TTTTAATG-GAAATTCCATGACATTATTA
1 AAAACTAATGAAAATAAATTAATTTTTCAAAA-CTATTTTAATGAG-AATTCCATGACATTATTA
4004323 GATACATTTTAAAAATTTTAAATCAAAGAAAATCACC-CCAAAAATATTTATGGATTAGAAAAC-
64 GATACATTTTAAAAATTTTAAATCAAAGAAAATC-CCTCCAAAAATATTTATGGATTAGAAAACT
* *
4004386 TTGATTTTTCGGGAAAAAAAGAGATT-TCAAAGAAAAAAAATC
128 TTG-TTTGTCGAG-AAAAAAGAGATTGT-AAAG-AAAAAAATC
*
4004428 AAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA
1 AAAACTAATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA
4004493 TACATTTTAAAAATTTTAAATCAAAGAAAA-CCCTCCTAAAAATATTTATGGATTA
66 TACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCC-AAAAATATTTATGGATTA
4004548 AAGAACTCGA
Statistics
Matches: 251, Mismatches: 24, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
165 4 0.02
166 100 0.40
167 32 0.13
168 114 0.45
169 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (166 bp):
AAAACTAATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA
TACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCCAAAAATATTTATGGATTAGAAAACTTTG
TTTGTCGAGAAAAAAGAGATTGTAAAGAAAAAAATC
Found at i:4004643 original size:131 final size:132
Alignment explanation
Indices: 4004425--4004689 Score: 423
Period size: 131 Copynumber: 2.0 Consensus size: 132
4004415 AAGAAAAAAA
* *
4004425 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATT
1 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT
*
4004490 AGATACATTTTAAAAATTTT-AAATCAAAGAAAA-C-CCTCCTAAAAATATTTATGGATTA-AAG
66 AGATACATTTTAAAAATTTTAAAAT-AAAGAAAATCACC-CC-AAAAATAGTTATGGATTAGAA-
4004551 AACTCG
127 AACTCG
*
4004557 ATCAAAACTCATGAAAATAAATTAATTTTTTAAAACTATTTTAAT-AAAATTCCACGACATTATT
1 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT
4004621 AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT
66 AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT
4004686 CG
131 CG
4004688 AT
1 AT
4004690 TTTTTGGGGG
Statistics
Matches: 125, Mismatches: 4, Indels: 9
0.91 0.03 0.07
Matches are distributed among these distances:
131 70 0.56
132 53 0.42
133 2 0.02
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (132 bp):
ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT
AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT
CG
Found at i:4005156 original size:165 final size:167
Alignment explanation
Indices: 4004718--4005175 Score: 466
Period size: 165 Copynumber: 2.8 Consensus size: 167
4004708 ATTCCAAAGA
* * * * * * * ***
4004718 AAAAAAATT-AAAAGCTCATGAAAATGAAAGAATTTCTCAAAACTGATTCAATCCAAAATAAATA
1 AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA
* * *
4004782 ATAATATTTG-TGGAATTTAAAAAAATTTTACACCCATGAAAATCT-TCCCAAAAAAATTTACGG
66 ATAATATTTGAT-GAA-TTATAAAAATTTTAAACCCATGAAAATCTCT-CCAAAAAAATTTACGA
* ** *
4004845 AGTAAAAAATTTTATATTTCAAAAACAATGAAATTTTAAG
128 AGTAAAAAACTGCATATTTCAAAAACAATGAAATTTCAAG
* * *
4004885 GAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGGAATAAATA
1 AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA
* * * * * * *
4004950 GTAATATTTGATGAATTTTAAAAA-TTAAAAACTAAGAAAATCTCTCCAAAAAAA-TTATGAAGT
66 ATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAATCTCTCCAAAAAAATTTACGAAGT
* * *
4005013 AGAAAACTGCGTATTTCGAAAACAGA-GAAATTTCAAG
131 AAAAAACTGCATATTTCAAAAACA-ATGAAATTTCAAG
* * * *
4005050 AAAAAAATAT-AGAAACTCATGAAAATGAAT-AATTTTTTAAAAACTAATTTACTATGAAATAAG
1 AAAAAAAT-TCAAAAACCCATGAAAATGAATGAA-TTTTTAAAAACTAATTTAATATGAAATAAA
* *
4005113 TAATAATATTTGATGAA-TATAAAAATTTTAAACCCATGAAAATCCTCCCCAAAAAATTTTACG
64 TAATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAAT-CTCTCCAAAAAAATTTACG
4005176 GTGAAAAAAA
Statistics
Matches: 237, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
164 9 0.04
165 115 0.49
166 36 0.15
167 20 0.08
168 56 0.24
169 1 0.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29
Consensus pattern (167 bp):
AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA
ATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAATCTCTCCAAAAAAATTTACGAAGT
AAAAAACTGCATATTTCAAAAACAATGAAATTTCAAG
Found at i:4006773 original size:33 final size:33
Alignment explanation
Indices: 4006736--4006805 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
4006726 TTCAACGATT
4006736 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
4006769 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
4006802 TGTA
1 TGTA
4006806 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:4006774 original size:13 final size:13
Alignment explanation
Indices: 4006756--4006780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4006746 CATAAAATGT
4006756 TGTATCGATACAA
1 TGTATCGATACAA
4006769 TGTATCGATACA
1 TGTATCGATACA
4006781 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4006863 original size:13 final size:13
Alignment explanation
Indices: 4006845--4006869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4006835 ATTACTCACA
4006845 TGTATCGATACAT
1 TGTATCGATACAT
4006858 TGTATCGATACA
1 TGTATCGATACA
4006870 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4006934 original size:52 final size:52
Alignment explanation
Indices: 4006878--4007006 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
4006868 CACTGATCTT
*
4006878 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA
*
4006929 CTGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 -TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA
* *
4006982 TGTATCGATACATGCAAATAAATTT
1 TGTATCGATACATGCAGACAAATTT
4007007 TCATATTTCG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 67 0.94
53 4 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:4010162 original size:60 final size:59
Alignment explanation
Indices: 4010081--4010195 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
4010071 CACCTATATT
* * *
4010081 GAGAGTAAAGTCCAATATAGCTAGC-CCTATGGCAAGCCTAGTGAAGTTGCCCTATATAAA
1 GAGAGTAAAGCCCAATATAGCTA-CTAC-ATGGCAAGCCTAGTGAAATTGCCCTATATAAA
* * *
4010141 GAGAGTCAAGCCCAATGTAGCTACTACATGGTAAGCCTAGTGAAATTGCCCTATA
1 GAGAGTAAAGCCCAATATAGCTACTACATGGCAAGCCTAGTGAAATTGCCCTATA
4010196 CCAAGAGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 27 0.56
60 21 0.44
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (59 bp):
GAGAGTAAAGCCCAATATAGCTACTACATGGCAAGCCTAGTGAAATTGCCCTATATAAA
Done.