Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 6 of 276
Found at i:1839643 original size:25 final size:26
Alignment explanation
Indices: 1839602--1839652 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1839592 AGTTGTAGAG
1839602 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
* *
1839628 AGAAAATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
1839653 GATTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTT
Found at i:1840646 original size:35 final size:35
Alignment explanation
Indices: 1840600--1840667 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1840590 ACTGGCCTAG
1840600 ACTATGCTTATATGTTTTTCTTGAATGAATCGTAA
1 ACTATGCTTATATGTTTTTCTTGAATGAATCGTAA
1840635 ACTATGCTTATATGTTTTTCTTGAATGAATCGT
1 ACTATGCTTATATGTTTTTCTTGAATGAATCGT
1840668 TGGCGGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (35 bp):
ACTATGCTTATATGTTTTTCTTGAATGAATCGTAA
Found at i:1841163 original size:58 final size:58
Alignment explanation
Indices: 1841023--1841208 Score: 200
Period size: 58 Copynumber: 3.2 Consensus size: 58
1841013 GTAAGATAAA
* * * * * *
1841023 CCTTAGTGGACTTCCCAACACTAGATAGTCTTAACGGACATCC-CTTCATTTGATAAT
1 CCTTAGCGTACTTCCCAAAACTAGATAGTCCTAACAGACATCCTCTTCATTTGATAGT
* *
1841080 CCTT-G-GTTGACTTCCCAACAA-TAGATAGTCCTAACAGACATCCTCCTCATTCGATAGT
1 CCTTAGCG-T-ACTTCCCAA-AACTAGATAGTCCTAACAGACATCCTCTTCATTTGATAGT
* * *
1841138 CCTTAGCGTACTTCTCAAAACTAGATAGTCCTAATAGACATCCTCTTCATTTGTTAGT
1 CCTTAGCGTACTTCCCAAAACTAGATAGTCCTAACAGACATCCTCTTCATTTGATAGT
* *
1841196 CCCTAGCGAACTT
1 CCTTAGCGTACTT
1841209 TATAGAATAG
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.01
56 1 0.01
57 35 0.32
58 68 0.63
59 2 0.02
60 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.32
Consensus pattern (58 bp):
CCTTAGCGTACTTCCCAAAACTAGATAGTCCTAACAGACATCCTCTTCATTTGATAGT
Found at i:1858771 original size:17 final size:17
Alignment explanation
Indices: 1858749--1858819 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
1858739 TAAATAAAAG
*
1858749 AATATTATAACAATAAT
1 AATATTATAATAATAAT
*
1858766 AATATTATTATAATAAT
1 AATATTATAATAATAAT
* *
1858783 CATATTAATATTAATAAT
1 AATATT-ATAATAATAAT
* *
1858801 CATATTATAGTAATAAT
1 AATATTATAATAATAAT
1858818 AA
1 AA
1858820 ATATATGAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
17 31 0.67
18 15 0.33
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
AATATTATAATAATAAT
Found at i:1858841 original size:47 final size:47
Alignment explanation
Indices: 1858787--1858893 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 47
1858777 AATAATCATA
*
1858787 TTAATATTAATAATCATATTATAGTAATAATAAATATATGAAGCAAT
1 TTAATATTAATAATCATATTATAGTAATAATAAATAAATGAAGCAAT
1858834 TTAATATTAATAATCATATTATAGTAATAATAAATAAATGAAGCAAT
1 TTAATATTAATAATCATATTATAGTAATAATAAATAAATGAAGCAAT
* *
1858881 TTAAAATAAATAA
1 TTAATATTAATAA
1858894 AAAATGGAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (47 bp):
TTAATATTAATAATCATATTATAGTAATAATAAATAAATGAAGCAAT
Found at i:1864231 original size:28 final size:30
Alignment explanation
Indices: 1864166--1864235 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1864156 CATGATGACC
* *
1864166 CCCGAGTGTCACACACGGCCTAGACACATG
1 CCCGTGTGTCACACACGGCCTAGACACACG
*
1864196 CCCGTGTGTCACACACTGCCTAGACACACG
1 CCCGTGTGTCACACACGGCCTAGACACACG
*
1864226 CCTGTGTGTC
1 CCCGTGTGTC
1864236 TACCCGTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (30 bp):
CCCGTGTGTCACACACGGCCTAGACACACG
Found at i:1864993 original size:45 final size:43
Alignment explanation
Indices: 1864918--1865041 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 43
1864908 ACAAGTTACA
* * *
1864918 AATCTTATCTCCCCAATGTTGCAGTTGAGCAGATTAAAGATAACG
1 AATCTTATCTCCCTAA-GTTGTAGTGGAGCAGATTAAAGAT-ACG
* * * * *
1864963 AATCTTATTTCCCTAAGGTTGTAGTGGAGCATATTGAAGCTACT
1 AATCTTATCTCCCTAA-GTTGTAGTGGAGCAGATTAAAGATACG
1865007 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATT
1 AATCTTATCTCCCT-AAGTTGTAGTGGAGCAGATT
1865042 GAAGCGACAA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
44 32 0.48
45 35 0.52
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (43 bp):
AATCTTATCTCCCTAAGTTGTAGTGGAGCAGATTAAAGATACG
Found at i:1865020 original size:44 final size:44
Alignment explanation
Indices: 1864918--1865046 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 44
1864908 ACAAGTTACA
* * * * *
1864918 AATCTTATCTCCCCAATGTTGCAGTTGAGCAGATTAAAGATAACG
1 AATCTTATCTCCCTAA-GTTGTAGTGGAGCAGATTGAAGCTAACG
* * *
1864963 AATCTTATTTCCCTAAGGTTGTAGTGGAGCATATTGAAGCT-ACT
1 AATCTTATCTCCCTAA-GTTGTAGTGGAGCAGATTGAAGCTAACG
1865007 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGC
1 AATCTTATCTCCCT-AAGTTGTAGTGGAGCAGATTGAAGC
1865047 GACAATTTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 37 0.51
45 35 0.49
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (44 bp):
AATCTTATCTCCCTAAGTTGTAGTGGAGCAGATTGAAGCTAACG
Found at i:1865065 original size:44 final size:44
Alignment explanation
Indices: 1864918--1865077 Score: 139
Period size: 44 Copynumber: 3.6 Consensus size: 44
1864908 ACAAGTTACA
* * * * ** *
1864918 AATCTTATCTCCC-CAATGTTGCAGTTGAGCAGATTAAAGATAACG
1 AATCTTATCTCCCTGAA-GTTGTAGTGGAGCAGATTGAAG-CGACT
* * *
1864963 AATCTTATTTCCCT-AAGGTTGTAGTGGAGCATATTGAAGCTACT
1 AATCTTATCTCCCTGAA-GTTGTAGTGGAGCAGATTGAAGCGACT
1865007 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCGAC-
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCGACT
* *
1865050 AATTTCTATAC-CCCTGAAGTTGCAGTGG
1 AATCT-TAT-CTCCCTGAAGTTGTAGTGG
1865078 GTTAGAATGA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
43 4 0.04
44 58 0.60
45 35 0.36
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCGACT
Found at i:1870917 original size:35 final size:35
Alignment explanation
Indices: 1870878--1871004 Score: 89
Period size: 36 Copynumber: 3.6 Consensus size: 35
1870868 ACTCTTTGTT
*
1870878 TTGGT-TATTTAGGTTGGACTAGCTCTTCG-GAGCCA
1 TTGGTGTATTTAGGATGGACTAGCTCTT-GTGAG-CA
* * *
1870913 TTGGTGTGTTTCGGATGGATTAGCTCTTGTGAGCA
1 TTGGTGTATTTAGGATGGACTAGCTCTTGTGAGCA
* * * * *
1870948 TTGGTGTGTCTT-GGGTCGACCAGCTCTTATGAGCA
1 TTGGTGTAT-TTAGGATGGACTAGCTCTTGTGAGCA
* * *
1870983 TTTGGTGTGTTTGGGTTGGACT
1 -TTGGTGTATTTAGGATGGACT
1871005 GCCGATGTAC
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
35 37 0.49
36 38 0.51
ACGTcount: A:0.13, C:0.14, G:0.33, T:0.39
Consensus pattern (35 bp):
TTGGTGTATTTAGGATGGACTAGCTCTTGTGAGCA
Found at i:1871966 original size:25 final size:25
Alignment explanation
Indices: 1871932--1871984 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1871922 CTCAAGAGTT
* *
1871932 ACACAGCCTGGCACACGGGCGTGTG
1 ACACAGCCTGCCACACGAGCGTGTG
*
1871957 ACACGGCCTGCCACACGAGCGTGTG
1 ACACAGCCTGCCACACGAGCGTGTG
1871982 ACA
1 ACA
1871985 TGGCTGTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.23, C:0.34, G:0.32, T:0.11
Consensus pattern (25 bp):
ACACAGCCTGCCACACGAGCGTGTG
Found at i:1879069 original size:12 final size:13
Alignment explanation
Indices: 1879047--1879075 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1879037 TAATTAAATG
1879047 AATTAAAAAGCCA
1 AATTAAAAAGCCA
1879060 AATT-AAAAGCCA
1 AATTAAAAAGCCA
1879072 AATT
1 AATT
1879076 TTTGTCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAAAAAGCCA
Found at i:1879905 original size:42 final size:42
Alignment explanation
Indices: 1879833--1879943 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
1879823 GATATTTACG
* * * *
1879833 TGTAAGACCATATCTGGGATATGGCATCGATACGGGACTTCG
1 TGTAAGACCATAGCTAGGATATGGCATCGATACGAGACTTCA
* *
1879875 T-TAAGACCATAGCTAGGCTATTGGCATCGATACGAGATTTCA
1 TGTAAGACCATAGCTAGGATA-TGGCATCGATACGAGACTTCA
* *
1879917 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATAGCTAGGATATGGCAT
1879944 TGGTATGGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
41 16 0.28
42 26 0.45
43 16 0.28
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATAGCTAGGATATGGCATCGATACGAGACTTCA
Found at i:1882086 original size:385 final size:385
Alignment explanation
Indices: 1881376--1882534 Score: 2228
Period size: 385 Copynumber: 3.0 Consensus size: 385
1881366 GGACGTGTGA
1881376 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
1 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
*
1881441 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACGGGTTCG
66 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
* * * *
1881506 CGACACGGGTTTGTGTGACCACACGGCCTGCCCACACAGGCGTGTCCTAGGCCACACGGGCGTGT
131 AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGCCACACGGGCGTGT
**
1881571 GACCCCTGTTTAGGCAAAAATCTTCTGAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
196 GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
*
1881636 GAATCACTTCCAAAGCACATTTTGGGTCTCGTCGGCTCGAATTAGGGACTTTATGCTTGATTTCA
261 GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
*
1881701 AAAATTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
326 AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
1881761 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
1 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
1881826 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
66 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
*
1881891 AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGTCACACGGGCGTGT
131 AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGCCACACGGGCGTGT
1881956 GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
196 GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
1882021 GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
261 GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
1882086 AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
326 AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
1882146 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
1 TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
1882211 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
66 CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
1882276 AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGCCACACGGGCGTGT
131 AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGCCACACGGGCGTGT
1882341 GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
196 GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
1882406 GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
261 GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
1882471 AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
326 AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
1882531 TCCG
1 TCCG
1882535 GTAATGCCTC
Statistics
Matches: 763, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
385 763 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (385 bp):
TCCGATTGTGTGTCCCCTGCACCTAAATTGTTGCAAAACAGAATGCTCAGTATCGAGCACACGGG
CGTGTGACTTGGCTATGTGACTTCAATTTGTTCTTGGGTGACAAAAAGAGAGTTACACAGGTTCG
AGACACGGGTGTGTGTGACCACACGGCCTGCCCACACAGGCATGTCCCAGGCCACACGGGCGTGT
GACCCCTGTTTAGGCAAAAATCTTCCAAGTGTTGTAAAATTTTCTAAAGTTCTCGATTTAGTCCC
GAATCACTTCCAAAGCACATTTTGGGTCTCGTAGGCTCGAATTAGGGACTTTATGCTTGATTTCA
AAAAGTTTTAATTTGGACGAAAATTTATGACTCGGAAATGCATGTTTGCTTGTGTTTAAG
Found at i:1885646 original size:14 final size:14
Alignment explanation
Indices: 1885627--1885656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1885617 ATTTTATTCC
1885627 AAAATTTCGAAAAT
1 AAAATTTCGAAAAT
*
1885641 AAAATTTCTAAAAT
1 AAAATTTCGAAAAT
1885655 AA
1 AA
1885657 TTATTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAATTTCGAAAAT
Found at i:1885757 original size:18 final size:18
Alignment explanation
Indices: 1885730--1885767 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1885720 TTTGAAATTA
*
1885730 TTTATTAATTTAT-TATTT
1 TTTATGAATTT-TCTATTT
1885748 TTTATGAATTTTCTATTT
1 TTTATGAATTTTCTATTT
1885766 TT
1 TT
1885768 ATAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATGAATTTTCTATTT
Found at i:1885933 original size:16 final size:16
Alignment explanation
Indices: 1885883--1885936 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1885873 GTTTGGTTCA
*
1885883 CTGTAATGAAATAGAG
1 CTGTAATGGAATAGAG
* *
1885899 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
1885915 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
1885931 CTGTAA
1 CTGTAA
1885937 CCAGTAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:1886005 original size:44 final size:46
Alignment explanation
Indices: 1885919--1886012 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
1885909 ATAGAGCTGT
1885919 AATGGAATAGAGCTGTAACCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAACCAGTAATTCAATTGTTTGGTTGAATGG
* *
1885965 AATGGAATAGAGCTGTAA-TAG-AATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAACCAGTAATTCAAT-TGTTTGGTTGAATGG
1886009 AATG
1 AATG
1886013 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 24 0.53
45 2 0.04
46 18 0.40
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAACCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:1886116 original size:25 final size:26
Alignment explanation
Indices: 1886083--1886133 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1886073 GTTGGTAGAT
*
1886083 GATTATTGTT-ATTAAATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
*
1886108 GATTATTGTTAAATATATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
1886134 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
GATTATTGTTAAATAAATTTTAATAA
Found at i:1886223 original size:12 final size:12
Alignment explanation
Indices: 1886197--1886295 Score: 84
Period size: 12 Copynumber: 8.4 Consensus size: 12
1886187 TTTAATAAAA
1886197 TAATATATATT-T
1 TAATA-ATATTAT
*
1886209 TAATAACATTAT
1 TAATAATATTAT
1886221 TAAT-ATAATTAT
1 TAATAAT-ATTAT
1886233 TAATAATATTTAT
1 TAATAATA-TTAT
* *
1886246 TAATAATTTTAA
1 TAATAATATTAT
*
1886258 T-ATAAAATTAT
1 TAATAATATTAT
1886269 TAATAATA-T-T
1 TAATAATATTAT
1886279 TAATAATAATT-T
1 TAATAAT-ATTAT
1886291 TAATA
1 TAATA
1886296 TAAAATTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
10 8 0.11
11 15 0.21
12 36 0.50
13 13 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:1886235 original size:24 final size:22
Alignment explanation
Indices: 1886173--1886298 Score: 72
Period size: 23 Copynumber: 5.6 Consensus size: 22
1886163 TAACATAATT
*
1886173 ATTATTAA-ATACAATTTAATAA
1 ATTATTAATATA-ATTTTAATAA
1886195 A--A-TAATATATATTTTAATAA
1 ATTATTAATATA-ATTTTAATAA
1886215 CATTATTAATATAATTATTAATAA
1 -ATTATTAATATAATT-TTAATAA
1886239 TATTTATT-A-ATAATTTTAATATAAA
1 -A-TTATTAATATAATTTT-A-AT-AA
1886264 ATTATT-A-ATAATATTTAATAATA
1 ATTATTAATATAAT-TTTAAT-A-A
1886287 ATT-TTAATATAA
1 ATTATTAATATAA
1886299 AATTATTATT
Statistics
Matches: 87, Mismatches: 3, Indels: 26
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.03
20 13 0.15
21 1 0.01
22 9 0.10
23 28 0.32
24 26 0.30
25 7 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATTAATATAATTTTAATAA
Found at i:1886267 original size:36 final size:36
Alignment explanation
Indices: 1886227--1886306 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
1886217 TTATTAATAT
*
1886227 AATTATTAATAATATTTATTAATAATTTTAATATAA
1 AATTATTAATAATATTTAATAATAATTTTAATATAA
1886263 AATTATTAATAATATTTAATAATAATTTTAATATAA
1 AATTATTAATAATATTTAATAATAATTTTAATATAA
1886299 AATTATTA
1 AATTATTA
1886307 TTAAGAACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AATTATTAATAATATTTAATAATAATTTTAATATAA
Found at i:1886302 original size:13 final size:13
Alignment explanation
Indices: 1886250--1886302 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
1886240 ATTTATTAAT
1886250 AATTTTAATATAA
1 AATTTTAATATAA
1886263 AATTATT-A-ATAA
1 AATT-TTAATATAA
* *
1886275 TA-TTTAATA-AT
1 AATTTTAATATAA
1886286 AATTTTAATATAA
1 AATTTTAATATAA
1886299 AATT
1 AATT
1886303 ATTATTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
10 2 0.06
11 4 0.13
12 13 0.42
13 10 0.32
14 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTAATATAA
Found at i:1894824 original size:16 final size:16
Alignment explanation
Indices: 1894793--1894822 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1894783 TTGATATCTC
1894793 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
1894809 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
1894823 TACTATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:1904692 original size:27 final size:28
Alignment explanation
Indices: 1904661--1904721 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1904651 TAAGATGATT
1904661 ATATAAAAATTT-TC-AATATATAAAAAA
1 ATATAAAAATTTATCAAATAT-TAAAAAA
* * *
1904688 ATATATAAATTTATTAAATATTAAAATA
1 ATATAAAAATTTATCAAATATTAAAAAA
1904716 ATATAA
1 ATATAA
1904722 TATAAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 11 0.39
28 12 0.43
29 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAAAAATTTATCAAATATTAAAAAA
Found at i:1912611 original size:43 final size:42
Alignment explanation
Indices: 1912534--1912694 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 42
1912524 TACCATACCA
* *
1912534 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
1912576 ATGTCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATG-CCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
1912619 ACGCCATATCCCAAATAAGGTCTTACACGAAATCTCATA-CG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
1912660 ATGCCATATTCCAGATATGGTCTTACACGTAATCT
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCT
1912695 TGTAACCCTA
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
41 32 0.31
42 34 0.33
43 36 0.35
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:1915219 original size:61 final size:61
Alignment explanation
Indices: 1915123--1915313 Score: 337
Period size: 61 Copynumber: 3.1 Consensus size: 61
1915113 TGAACTTATG
*
1915123 TAATTTATATAAAAAAATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1 TAATTTATAT-AAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1915185 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
* * *
1915246 TACTTTATATAAAAAATTTATATTAAAAAGTTTATTCCAATTTTTAATTTTGTAATGTATT
1 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1915307 TAATTTA
1 TAATTTA
1915314 AATTACAAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
61 114 0.92
62 10 0.08
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (61 bp):
TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
Found at i:1915332 original size:48 final size:49
Alignment explanation
Indices: 1915260--1915363 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 49
1915250 TTATATAAAA
* *
1915260 AATTTATATTAAAAAGTTTATTCCAATT-TTTAATTTTGTAATGTATTT
1 AATTTAAATTAAAAAGTTTATTCCAATTAATTAATTTTGTAATGTATTT
*
1915308 AATTTAAATTACAAAA-TTTGTTCCAATTAGATTAATTTTGTAATGTATTT
1 AATTTAAATTA-AAAAGTTTATTCCAATTA-ATTAATTTTGTAATGTATTT
1915358 AATTTA
1 AATTTA
1915364 TATAACAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
48 21 0.42
49 4 0.08
50 25 0.50
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (49 bp):
AATTTAAATTAAAAAGTTTATTCCAATTAATTAATTTTGTAATGTATTT
Found at i:1919794 original size:44 final size:44
Alignment explanation
Indices: 1919744--1919831 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
1919734 CACATGCATC
* *
1919744 GCATCCATAATGAACTCGGACCAACTCAACGAGCTTAGATGCTT
1 GCATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTT
* * *
1919788 GCATCCATAATTAACTCAGACCAACTCAATGAGCTCGGATGCTT
1 GCATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTT
1919832 CACATATATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (44 bp):
GCATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTT
Found at i:1919880 original size:45 final size:45
Alignment explanation
Indices: 1919831--1919921 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
1919821 CTCGGATGCT
* * * *
1919831 TCACATATATCACGAACTTGGACCACCTCAACAAGTTTGGATTTC
1 TCACATATATCACGAACTCGGACCAACTCAACAAGTTCGAATTTC
*
1919876 TCACATATATCACGAACTCGGACCAACTCAACGAGTTCGAATTTC
1 TCACATATATCACGAACTCGGACCAACTCAACAAGTTCGAATTTC
1919921 T
1 T
1919922 AAATTCCTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.27
Consensus pattern (45 bp):
TCACATATATCACGAACTCGGACCAACTCAACAAGTTCGAATTTC
Found at i:1920857 original size:28 final size:28
Alignment explanation
Indices: 1920817--1920876 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1920807 TGGAAGCTTG
1920817 AACATAAACCCTACCCATGGCTTCCTCT
1 AACATAAACCCTACCCATGGCTTCCTCT
**
1920845 AACATAAACCCTACCTGTGGCTTCCTCT
1 AACATAAACCCTACCCATGGCTTCCTCT
1920873 AACA
1 AACA
1920877 GTCGGCTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.37, G:0.08, T:0.25
Consensus pattern (28 bp):
AACATAAACCCTACCCATGGCTTCCTCT
Found at i:1926212 original size:13 final size:13
Alignment explanation
Indices: 1926194--1926222 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1926184 TTTAGTTTAA
1926194 TTAGTTAATTAGT
1 TTAGTTAATTAGT
1926207 TTAGTTAATTAGT
1 TTAGTTAATTAGT
1926220 TTA
1 TTA
1926223 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:1931745 original size:17 final size:17
Alignment explanation
Indices: 1931723--1931763 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1931713 CCTCCTATCT
* **
1931723 TTTTATTTTTATTTTTA
1 TTTTATTTTGATTTCAA
1931740 TTTTATTTTGATTTCAA
1 TTTTATTTTGATTTCAA
1931757 TTTTATT
1 TTTTATT
1931764 ATTTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTTTGATTTCAA
Found at i:1934700 original size:13 final size:13
Alignment explanation
Indices: 1934682--1934709 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1934672 TTAGTTTAAC
1934682 TAGTTAATTAGTT
1 TAGTTAATTAGTT
1934695 TAGTTAATTAGTT
1 TAGTTAATTAGTT
1934708 TA
1 TA
1934710 ATAAACAACC
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:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TAGTTAATTAGTT
Found at i:1938755 original size:16 final size:15
Alignment explanation
Indices: 1938734--1938765 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1938724 TTAACCGAAG
1938734 CTATATCGGTATCGCA
1 CTATATCGGTAT-GCA
1938750 CTATATCGGTATGCA
1 CTATATCGGTATGCA
1938765 C
1 C
1938766 ACTTAGTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (15 bp):
CTATATCGGTATGCA
Found at i:1940960 original size:30 final size:30
Alignment explanation
Indices: 1940926--1940986 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1940916 TTCCCGAGCC
1940926 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
1940956 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1940986 T
1 T
1940987 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:1950106 original size:47 final size:47
Alignment explanation
Indices: 1949999--1950380 Score: 566
Period size: 47 Copynumber: 8.1 Consensus size: 47
1949989 GAAATGATAG
1949999 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
1950048 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
1950095 TAAGGCCTAATGGCCGATGAGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
1950142 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
1950189 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
1950236 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1950283 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
1950330 CAAGGCCGAGTGGCCAACGTAATGGATGTGGAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1950377 TAAG
1 TAAG
1950381 TCCCGAAAGG
Statistics
Matches: 308, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 273 0.89
49 35 0.11
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:1950555 original size:37 final size:37
Alignment explanation
Indices: 1950499--1950577 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1950489 CCGAGCTCTA
* * *
1950499 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
1950536 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
1950573 AAGAC
1 AAGAC
1950578 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:1954197 original size:39 final size:39
Alignment explanation
Indices: 1954154--1954236 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
1954144 ATCATTTAAC
*
1954154 ATCATAAAACTCATGAATTCATCAATGGCATCTCATCAA
1 ATCATAAAACTCATGAATTCATCAATGACATCTCATCAA
* **
1954193 ATCATAAAACTCTTGAATTCATCAATGATGTCTCATCAA
1 ATCATAAAACTCATGAATTCATCAATGACATCTCATCAA
1954232 ATCAT
1 ATCAT
1954237 CAACAATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (39 bp):
ATCATAAAACTCATGAATTCATCAATGACATCTCATCAA
Found at i:1959843 original size:17 final size:17
Alignment explanation
Indices: 1959821--1959853 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1959811 AAAACATAAA
1959821 ATAAAAT-TTAAGAAAAC
1 ATAAAATCTTAA-AAAAC
1959838 ATAAAATCTTAAAAAA
1 ATAAAATCTTAAAAAA
1959854 TTAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAATCTTAAAAAAC
Found at i:1960279 original size:23 final size:23
Alignment explanation
Indices: 1960253--1960298 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1960243 TAACATTAAT
1960253 CCATTAATTTATAACAAAAATAA
1 CCATTAATTTATAACAAAAATAA
*
1960276 CCATTAATTTTTAACAAAAATAA
1 CCATTAATTTATAACAAAAATAA
1960299 TTAACCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (23 bp):
CCATTAATTTATAACAAAAATAA
Found at i:1960353 original size:17 final size:15
Alignment explanation
Indices: 1960322--1960356 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
1960312 TTCTATTTTT
1960322 TTCTTCTCTTTCTCC
1 TTCTTCTCTTTCTCC
1960337 TTCTCTCTCTGTTCTCC
1 TTCT-TCTCT-TTCTCC
1960354 TTC
1 TTC
1960357 ACTTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (15 bp):
TTCTTCTCTTTCTCC
Found at i:1961116 original size:33 final size:33
Alignment explanation
Indices: 1961079--1961149 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
1961069 GAAGTCCAAG
*
1961079 GAGCTTGCTTTTGAAGCCTCCAAGAAA-GCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAA-AAAGGCCGAT
*
1961112 GAGCTTGCTCTTGAAGCTTCCAAAAAGGCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
1961145 GAGCT
1 GAGCT
1961150 CAGAGTCGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 32 0.91
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (33 bp):
GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
Found at i:1962594 original size:6 final size:6
Alignment explanation
Indices: 1962583--1962618 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1962573 ATTATTCAGT
1962583 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1962619 GAGTTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:1964957 original size:36 final size:36
Alignment explanation
Indices: 1964910--1964987 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
1964900 CCACACACTC
** *
1964910 GTGTGGGTCACATGGCCGTGTGGAATGGTTCAGTCG
1 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
*
1964946 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCT
1 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
1964982 GTGTGG
1 GTGTGG
1964988 CTCCTGCAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.18, G:0.41, T:0.27
Consensus pattern (36 bp):
GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
Found at i:1968448 original size:48 final size:48
Alignment explanation
Indices: 1968393--1968513 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 48
1968383 ATATATTTGT
*
1968393 GCCGATGCCATGTCCCAGACATGGTCTTATACTAGCAAACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
* * * * *
1968441 GCTGATGCCATGTCTCAGACATGGTCTTACACTGGCACACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
1968489 GCCGATGCCATGTCCCAGACATGGT
1 GCCGATGCCATGTCCCAGACATGGT
1968514 TTTTGTGACA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
Found at i:1970226 original size:41 final size:41
Alignment explanation
Indices: 1970166--1970315 Score: 185
Period size: 41 Copynumber: 3.7 Consensus size: 41
1970156 TCGGGGTTTA
*
1970166 AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
1970207 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCTAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
1970248 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* *
1970288 AGTCCGAGCTTGGTCTTGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1970316 TGAGTCAGCG
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 30 0.34
41 59 0.66
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:1981956 original size:41 final size:38
Alignment explanation
Indices: 1981910--1982130 Score: 174
Period size: 38 Copynumber: 5.7 Consensus size: 38
1981900 ACAGCGGCAT
* *
1981910 AAAGCCTGCTAGGCATAAAGCCTGATATAATACACCAGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGA-AT-AT-CACCAGCAC
* * * *
1981951 GAAGCCTACTAGGCACAGAGCCCGAATATCACCGGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
** * **
1981989 AAAGCCTGCTAGGCACATTGTCTAAATATCACCAGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
* * * * * * *
1982027 AAAGCCTGGTAGGTACAGAGCCCAAATATTACGAGCTC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
* * * * ** *
1982065 AAAACCTTCTAGGCA-ATAAGCCTGATTATCACTGGCCC
1 AAAGCCTGCTAGGCACA-AAGCCCGAATATCACCAGCAC
1982103 AAAGCCTGCTAGGCACAAAGCCCGAATA
1 AAAGCCTGCTAGGCACAAAGCCCGAATA
1982131 ATGTTACGTT
Statistics
Matches: 139, Mismatches: 39, Indels: 7
0.75 0.21 0.04
Matches are distributed among these distances:
37 1 0.01
38 113 0.81
39 3 0.02
40 2 0.01
41 20 0.14
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (38 bp):
AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
Found at i:1982095 original size:76 final size:76
Alignment explanation
Indices: 1981904--1982130 Score: 208
Period size: 76 Copynumber: 2.9 Consensus size: 76
1981894 TATAACACAG
* * * *
1981904 CGGCATAAAGCCTGCTAGGC-ATAAAGCCTGATATAATACACCAGCACGAAGCCTACTAGGCACA
1 CGGCACAAAACCTGCTAGGCAAT-AAGCCTGAT-T-AT-CACCAGCACAAAGCCTGCTAGGCACA
1981968 GAGCCCGAATATCAC
62 GAGCCCGAATATCAC
* * * * * * *
1981983 CGGCACAAAGCCTGCTAGGCACAT-TGTCTAAATATCACCAGCACAAAGCCTGGTAGGTACAGAG
1 CGGCACAAAACCTGCTAGGCA-ATAAGCCTGATTATCACCAGCACAAAGCCTGCTAGGCACAGAG
* *
1982047 CCCAAATATTA-
65 CCCGAATATCAC
* * ** * *
1982058 CGAGCTCAAAACCTTCTAGGCAATAAGCCTGATTATCACTGGCCCAAAGCCTGCTAGGCACAAAG
1 CG-GCACAAAACCTGCTAGGCAATAAGCCTGATTATCACCAGCACAAAGCCTGCTAGGCACAGAG
1982123 CCCGAATA
65 CCCGAATA
1982131 ATGTTACGTT
Statistics
Matches: 119, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
75 4 0.03
76 87 0.73
77 2 0.02
78 1 0.01
79 23 0.19
81 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (76 bp):
CGGCACAAAACCTGCTAGGCAATAAGCCTGATTATCACCAGCACAAAGCCTGCTAGGCACAGAGC
CCGAATATCAC
Found at i:1983721 original size:36 final size:35
Alignment explanation
Indices: 1983677--1983751 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 35
1983667 TGTTATTATC
1983677 ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
1 ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
*
1983712 ATAAGATTTGCTTGAAAACGAAATCTCCACCACTAT
1 ATAA-ATTTGCTTGAAAACCAAATCTCCACCACTAT
1983748 ATAA
1 ATAA
1983752 TGAGATGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (35 bp):
ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
Found at i:1985031 original size:15 final size:15
Alignment explanation
Indices: 1985011--1985040 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1985001 TATAAGTCCG
*
1985011 ACAAATAGAATAAAA
1 ACAAATAAAATAAAA
1985026 ACAAATAAAATAAAA
1 ACAAATAAAATAAAA
1985041 GATAGTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (15 bp):
ACAAATAAAATAAAA
Found at i:1989289 original size:39 final size:40
Alignment explanation
Indices: 1989194--1989455 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
1989184 TTGAATGATG
*
1989194 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1989232 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1989273 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1989312 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1989351 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
1989390 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
1989429 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1989456 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:2023757 original size:16 final size:16
Alignment explanation
Indices: 2023725--2023754 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2023715 AGAAACTTAA
2023725 TAATTCAAATATAAAT
1 TAATTCAAATATAAAT
2023741 TAATTC-AATATAAA
1 TAATTCAAATATAAA
2023755 ATTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTCAAATATAAAT
Found at i:2023889 original size:67 final size:68
Alignment explanation
Indices: 2023777--2023904 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 68
2023767 AGTTATTAAA
*
2023777 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAGCATGATAAATGATA
1 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAACATGATAAATGATA
2023842 ATT
66 ATT
* * * ** *
2023845 AAATTTATTTAACCAAA-TATTTTAGTAAAATTA-AATCTTTTATTTATAAATATGATAAAT
1 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAAT-TCCTATTTATAAACATGATAAAT
2023905 TTTATAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 3 0.06
67 33 0.63
68 16 0.31
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (68 bp):
AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAACATGATAAATGATA
ATT
Found at i:2023922 original size:18 final size:19
Alignment explanation
Indices: 2023885--2023930 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2023875 TTAAATCTTT
*
2023885 TATTTATAAATATGATAAA
1 TATTTATAAATATGAAAAA
2023904 T-TTTATAAATAAT-AAAAA
1 TATTTATAAAT-ATGAAAAA
2023922 TATTTATAA
1 TATTTATAA
2023931 TGGTAGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTTATAAATATGAAAAA
Found at i:2024376 original size:15 final size:15
Alignment explanation
Indices: 2024356--2024386 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2024346 GGGTCAAATA
2024356 TGTTAGATAATCTAG
1 TGTTAGATAATCTAG
2024371 TGTTAGATAATCTAG
1 TGTTAGATAATCTAG
2024386 T
1 T
2024387 AACTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TGTTAGATAATCTAG
Found at i:2029961 original size:47 final size:46
Alignment explanation
Indices: 2029907--2030037 Score: 185
Period size: 46 Copynumber: 2.8 Consensus size: 46
2029897 GGAAATTGAG
2029907 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCACTTATGGATG-CAAGC
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGTCAA-C
* *
2029954 ATCCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGTGAAC
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAC
* *
2030000 ACCCGAGCTCGTTGAGTTGCGTTCCGAGGTT-ATTATGG
1 ATCCGAACTCGTTGAGTTGCGTTCCGA-GTTCATTATGG
2030038 GTGAAATTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
46 41 0.53
47 36 0.47
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAC
Found at i:2034855 original size:30 final size:29
Alignment explanation
Indices: 2034821--2034879 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2034811 ACATTTCGAG
*
2034821 TACACACATGGTATCGATTTCGATGCAAAA
1 TACACACATGGCATCGATTT-GATGCAAAA
* *
2034851 TACACATATGGCATCGATTTGATTCAAAA
1 TACACACATGGCATCGATTTGATGCAAAA
2034880 CCACTCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (29 bp):
TACACACATGGCATCGATTTGATGCAAAA
Found at i:2037610 original size:20 final size:20
Alignment explanation
Indices: 2037572--2037637 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
2037562 TAATTAATTT
*
2037572 TTAAATTTA-AAAAATAAGTA
1 TTAAAATTATAAAAA-AAGTA
*
2037592 TTAAAATTATTAAAAAAGTA
1 TTAAAATTATAAAAAAAGTA
* *
2037612 TAAAAATTATAAAAGAAAATA
1 TTAAAATTATAAAA-AAAGTA
2037633 TTAAA
1 TTAAA
2037638 TGTAACATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAAAATTATAAAAAAAGTA
Found at i:2040913 original size:30 final size:30
Alignment explanation
Indices: 2040877--2040936 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2040867 TTATTTTTAA
*
2040877 TTAAATTTGACCCTAAACTTTTTAAAAAAG
1 TTAAATTTGACCATAAACTTTTTAAAAAAG
* *
2040907 TTAAATTTGACCATCAATTTTTTAAAAAAG
1 TTAAATTTGACCATAAACTTTTTAAAAAAG
2040937 AGTTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAAATTTGACCATAAACTTTTTAAAAAAG
Found at i:2042686 original size:14 final size:15
Alignment explanation
Indices: 2042634--2042687 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 15
2042624 AGTTTTGACA
2042634 ATTTTATTTAAGTTT
1 ATTTTATTTAAGTTT
2042649 AATTTT-TTTAA-TTT
1 -ATTTTATTTAAGTTT
*
2042663 TTTTTATTTAAGTTT
1 ATTTTATTTAAGTTT
2042678 ATTTT-TTTAA
1 ATTTTATTTAA
2042688 TCAATTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 4 0.12
14 13 0.38
15 12 0.35
16 5 0.15
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
ATTTTATTTAAGTTT
Found at i:2048494 original size:59 final size:59
Alignment explanation
Indices: 2048399--2048516 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
2048389 TCAATTTTCC
* *
2048399 TGCTGATTTCATGCCCTTTCCGTCCAGCCCAAATAAATTTTGGGTCTAATT-TCCTTTTA
1 TGCTGATTTCATGCCCTTGCCGTCCAGCCCAAATAAATTTTAGGTCTAATTGT-CTTTTA
* *
2048458 NTGCTGATTTCATGCCC-TGCCGTCCAGTCCAAATAAATTTTAGTTCTAATTGTCTTTTA
1 -TGCTGATTTCATGCCCTTGCCGTCCAGCCCAAATAAATTTTAGGTCTAATTGTCTTTTA
2048517 AATCCTTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 36 0.68
60 17 0.32
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (59 bp):
TGCTGATTTCATGCCCTTGCCGTCCAGCCCAAATAAATTTTAGGTCTAATTGTCTTTTA
Found at i:2055540 original size:40 final size:39
Alignment explanation
Indices: 2055486--2055667 Score: 240
Period size: 40 Copynumber: 4.6 Consensus size: 39
2055476 TATTCGAATG
* *
2055486 ATATCCGGGTTAAGTCCCGAAGGCATTTATGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAT
*
2055525 AATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 -ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-T
* *
2055566 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-T
* * *
2055606 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGAT
*
2055646 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
2055668 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
39 14 0.11
40 111 0.87
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAT
Found at i:2058885 original size:50 final size:50
Alignment explanation
Indices: 2058806--2058904 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
2058796 TTATAACTTC
*
2058806 AGATACGGAACTCCAAATTAATATCCGTTAATTTTATCTGAAAATAGACA
1 AGATACGGAACTCCAAATTAAGATCCGTTAATTTTATCTGAAAATAGACA
* *
2058856 AGATACGGAAGTCCAAATTAAGATTCGTTAATTTTATCTGAAAATAGAC
1 AGATACGGAACTCCAAATTAAGATCCGTTAATTTTATCTGAAAATAGAC
2058905 TCATATATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (50 bp):
AGATACGGAACTCCAAATTAAGATCCGTTAATTTTATCTGAAAATAGACA
Found at i:2059958 original size:58 final size:58
Alignment explanation
Indices: 2059888--2060004 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
2059878 TAGTCCTAGT
*
2059888 TTTATTTAGTTAATTTTGCAATATTCCAATTTTGCCCTTAATTTATCAATTTTCCTGC
1 TTTATTTAGTTAATTTTGCAATATTCCAATTTTACCCTTAATTTATCAATTTTCCTGC
*
2059946 TTTATTTAGTTAATTTTGCAATATTCCAATTTTACCCTTAATTTATCAATTTTTCTGC
1 TTTATTTAGTTAATTTTGCAATATTCCAATTTTACCCTTAATTTATCAATTTTCCTGC
2060004 T
1 T
2060005 GATTTTCATG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (58 bp):
TTTATTTAGTTAATTTTGCAATATTCCAATTTTACCCTTAATTTATCAATTTTCCTGC
Found at i:2059995 original size:28 final size:28
Alignment explanation
Indices: 2059897--2059989 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
2059887 TTTTATTTAG
*
2059897 TTAATTTTGCAATATTCCAATTTTGCCC
1 TTAATTTTGCAATATTCCAATTTTACCC
* ** ****
2059925 TTAATTTAT-CAATTTTCCTGCTTTATTTAG
1 TTAATTT-TGCAATATTCC-AATTT-TACCC
2059955 TTAATTTTGCAATATTCCAATTTTACCC
1 TTAATTTTGCAATATTCCAATTTTACCC
2059983 TTAATTT
1 TTAATTT
2059990 ATCAATTTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 23 0.49
29 8 0.17
30 16 0.34
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (28 bp):
TTAATTTTGCAATATTCCAATTTTACCC
Found at i:2063877 original size:209 final size:209
Alignment explanation
Indices: 2063507--2063912 Score: 620
Period size: 209 Copynumber: 1.9 Consensus size: 209
2063497 AGCAGGGAAC
* * * *
2063507 CCAGAAACCGTTCTGGCCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTGTCCATATGAT
1 CCAGAAACCGTTCTGGCCCTGTCCCACAAAAACCTGAATATCTCTTAACATACTGCCCATATGAT
* * *
2063572 CGTTTCGTTACTTCTATATGAAAATAGACTCATCGAGCTTCGATTACATAATTTATTCACTATTT
66 CGTTTCGTTACTTCTACATGAAAACAGACTCATCGAGCTTCGATTACATAATTTATTCACTAATT
* *
2063637 AATTCCATTCCTACTAATTTTTGTAATTTTTCAATCCCACGTCACTGCTGCTGCCAGCATCTGTT
131 AATTCCACTCCTACTAATTTTTGTAATTTTTCAATCCCACGACACTGCTGCTGCCAGCATCTGTT
2063702 ACTGAAGCAAGAAT
196 ACTGAAGCAAGAAT
* * *
2063716 CCAGAAACCGTTCTGGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATACTGCCCATATGAT
1 CCAGAAACCGTTCTGGCCCTGTCCCACAAAAACCTGAATATCTCTTAACATACTGCCCATATGAT
*
2063781 CTTTTCGTTACTTCCT-CATGAAAACAGACTCATCGAGCTTCGATTACATAATTTATTCA-TCAA
66 CGTTTCGTTACTT-CTACATGAAAACAGACTCATCGAGCTTCGATTACATAATTTATTCACT-AA
* * *
2063844 TTAATTCCACTCCTACT-ATTTTTAGTGATTTTTCAATCTCATGACACTGCTGCTGCCAGCATCT
129 TTAATTCCACTCCTACTAATTTTT-GTAATTTTTCAATCCCACGACACTGCTGCTGCCAGCATCT
2063908 GTTAC
193 GTTAC
2063913 GAAAGTAACT
Statistics
Matches: 178, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
208 7 0.04
209 169 0.95
210 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (209 bp):
CCAGAAACCGTTCTGGCCCTGTCCCACAAAAACCTGAATATCTCTTAACATACTGCCCATATGAT
CGTTTCGTTACTTCTACATGAAAACAGACTCATCGAGCTTCGATTACATAATTTATTCACTAATT
AATTCCACTCCTACTAATTTTTGTAATTTTTCAATCCCACGACACTGCTGCTGCCAGCATCTGTT
ACTGAAGCAAGAAT
Found at i:2064052 original size:60 final size:59
Alignment explanation
Indices: 2063977--2064095 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 59
2063967 CGTGCCATTT
* * * * *
2063977 TCGCATGGCTTAAAGTTTACATGCCAAAATTCAAACACAACGTAATAGCTTATACATGCC
1 TCGCATGGCTAAAAGTTTACATACCAAAATTC-AACAAAACATAATAGCCTATACATGCC
* *
2064037 TCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATATTAGCCTATACATGCC
1 TCGCATGGCTAAAAGTTTACATACCAAAATTCAACAAAACATAATAGCCTATACATGCC
2064096 GAAATGTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
59 23 0.44
60 29 0.56
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.27
Consensus pattern (59 bp):
TCGCATGGCTAAAAGTTTACATACCAAAATTCAACAAAACATAATAGCCTATACATGCC
Found at i:2064386 original size:146 final size:146
Alignment explanation
Indices: 2064128--2064408 Score: 445
Period size: 146 Copynumber: 1.9 Consensus size: 146
2064118 AAAAAGAAGA
* *
2064128 TACCAAAAGTTGCTAGCCGGTGTGATGACTCCGATGACAGCCCGATCACGCAAAAAGAGACGAGT
1 TACCAAAACTTGCTAGCCGGTGTGATGACTCCGATGACAGCCCGACCACGCAAAAAGAGACGAGT
2064193 CCAAGAAACCTAAAATAGGTGACAAGGAAACACCGAGTGAGTATATAACTCAGTAAGTCATAAGC
66 CCAAGAAACCTAAAATAGGTGACAAGGAAACACCGAGTGAGTATATAACTCAGTAAGTCATAAGC
2064258 AATGCTAAGAAGAAAG
131 AATGCTAAGAAGAAAG
* * * * * * *
2064274 TACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCTGACCCCGCAAAAATAGATGAGT
1 TACCAAAACTTGCTAGCCGGTGTGATGACTCCGATGACAGCCCGACCACGCAAAAAGAGACGAGT
* * * *
2064339 CCAAGCAACCTATAATGGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAAGC
66 CCAAGAAACCTAAAATAGGTGACAAGGAAACACCGAGTGAGTATATAACTCAGTAAGTCATAAGC
2064404 AATGC
131 AATGC
2064409 ACTACCATCC
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
146 122 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (146 bp):
TACCAAAACTTGCTAGCCGGTGTGATGACTCCGATGACAGCCCGACCACGCAAAAAGAGACGAGT
CCAAGAAACCTAAAATAGGTGACAAGGAAACACCGAGTGAGTATATAACTCAGTAAGTCATAAGC
AATGCTAAGAAGAAAG
Found at i:2064738 original size:65 final size:66
Alignment explanation
Indices: 2064634--2064756 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 66
2064624 CACCCATCCT
* *
2064634 ACGATAAATTTTATGTACGTGACTTCAAGTATAGTTGTCACATAGGTTC-AACTTACCGATATTC
1 ACGATAAATCTTATGTACGTGACTTCAAGTATAATTGTCACATAGGTTCAAACTTACCGATATTC
2064698 C
66 C
*
2064699 ACGATAAATCTTATGTACGTGACTTCAATTATAATTGTCACATAGGTTCAAACTTACC
1 ACGATAAATCTTATGTACGTGACTTCAAGTATAATTGTCACATAGGTTCAAACTTACC
2064757 AAGCTCAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
65 46 0.85
66 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (66 bp):
ACGATAAATCTTATGTACGTGACTTCAAGTATAATTGTCACATAGGTTCAAACTTACCGATATTC
C
Found at i:2064954 original size:28 final size:28
Alignment explanation
Indices: 2064891--2064988 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
2064881 ATATTAAGTC
*
2064891 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
2064918 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
2064946 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
2064974 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2064989 GTTCGCACAC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.32
28 46 0.68
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:2065014 original size:46 final size:45
Alignment explanation
Indices: 2064945--2065033 Score: 160
Period size: 46 Copynumber: 2.0 Consensus size: 45
2064935 ATAATCAAAC
2064945 TCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTGT
1 TCGCACACTTAGTGCTACATAATCAAA-TCGCACACTTAGTGCTGT
*
2064991 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCT
2065034 ACATAGTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 16 0.38
46 26 0.62
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (45 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTGT
Found at i:2065022 original size:101 final size:100
Alignment explanation
Indices: 2064891--2065087 Score: 286
Period size: 101 Copynumber: 2.0 Consensus size: 100
2064881 ATATTAAGTC
* * *
2064891 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
*
2064956 GTGCTACATAATCAAACTCGCACACTTAGTGCTGTT
66 GTGCCACATAATC-AACTCGCACACTTAGTGCTGTT
* * *
2064992 CGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
* ** *
2065057 GTGCCGCATGGTCAATTCGCACACTTAGTGC
66 GTGCCACATAATCAACTCGCACACTTAGTGC
2065088 ATCATATTCA
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 17 0.20
101 68 0.80
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (100 bp):
CGCACACTCAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCCACATAATCAACTCGCACACTTAGTGCTGTT
Found at i:2065029 original size:27 final size:27
Alignment explanation
Indices: 2064991--2065143 Score: 182
Period size: 27 Copynumber: 5.6 Consensus size: 27
2064981 TTAGTGCTGT
* *
2064991 TCGCACACTTAGTGCTACGTAATCAAA
1 TCGCACACTTAGTGCTACATAGTCAAA
2065018 TCGCACACTTAGTGCTACATAGTCAAA
1 TCGCACACTTAGTGCTACATAGTCAAA
** * *
2065045 CTCGCACACTTAGTGCCGCATGGTCAAT
1 -TCGCACACTTAGTGCTACATAGTCAAA
* **
2065073 TCGCACACTTAGTGC-ATCATATTCATT
1 TCGCACACTTAGTGCTA-CATAGTCAAA
* *
2065100 TCGCACACTTAGTGCAACATAGTCATA
1 TCGCACACTTAGTGCTACATAGTCAAA
2065127 TCGCACACTTAGTGCTA
1 TCGCACACTTAGTGCTA
2065144 TACAATTTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
27 86 0.78
28 24 0.22
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (27 bp):
TCGCACACTTAGTGCTACATAGTCAAA
Found at i:2065044 original size:73 final size:75
Alignment explanation
Indices: 2064917--2065142 Score: 271
Period size: 82 Copynumber: 2.9 Consensus size: 75
2064907 TATAATCAAC
* *
2064917 TCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACT
1 TCGCACACTTAGTGCTACATAATCAAA-TCGCACACTTAGTGCTACATAGTCAAACTCGCACACT
2064982 TAGTGCT-G-T
65 TAGTGCTGGAT
*
2064991 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
2065056 AGTGCCGCATGGTCAAT
66 AGT---GC-TGG---AT
* ** * *
2065073 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATA-TCGCACACT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACT
2065136 TAGTGCT
65 TAGTGCT
2065143 ATACAATTTA
Statistics
Matches: 133, Mismatches: 9, Indels: 17
0.84 0.06 0.11
Matches are distributed among these distances:
73 40 0.30
74 25 0.19
76 2 0.02
77 2 0.02
78 3 0.02
81 14 0.11
82 47 0.35
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (75 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
AGTGCTGGAT
Found at i:2067587 original size:64 final size:64
Alignment explanation
Indices: 2067486--2067610 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
2067476 GGCTGCCTTT
*
2067486 AGACTTTCACGGATTACCCTTACTTTCTGTTCGGCATCTTTAATCAAATCGACTCCGAAAACTC
1 AGACTTTCACGAATTACCCTTACTTTCTGTTCGGCATCTTTAATCAAATCGACTCCGAAAACTC
***
2067550 AGACTTTCACGAATTATTTTTACTTTCTGTTCGGCATCTTTAATCAAATCGACTCCGAAAA
1 AGACTTTCACGAATTACCCTTACTTTCTGTTCGGCATCTTTAATCAAATCGACTCCGAAAA
2067611 TTTTACTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (64 bp):
AGACTTTCACGAATTACCCTTACTTTCTGTTCGGCATCTTTAATCAAATCGACTCCGAAAACTC
Found at i:2074381 original size:28 final size:28
Alignment explanation
Indices: 2074318--2075255 Score: 1842
Period size: 28 Copynumber: 33.5 Consensus size: 28
2074308 ATATTAAGTC
* *
2074318 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
2074345 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074373 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074401 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074429 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074457 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074485 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074513 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074541 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074569 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074597 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074625 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074653 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074681 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074709 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074737 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074765 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074793 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074821 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074849 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074877 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074905 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074933 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074961 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2074989 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075017 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075045 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075073 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075101 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075129 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075157 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075185 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075213 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
2075241 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2075256 GTACAATTTA
Statistics
Matches: 908, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
27 22 0.02
28 886 0.98
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:2087833 original size:68 final size:68
Alignment explanation
Indices: 2087760--2087901 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 68
2087750 TTTCTATGGT
** ** * **
2087760 TGAAGGCTTGGTGGTAGAGAGATGCAAACAGCAGTGGTGCACAATGAAAAGAGAGCGGTGAATGG
1 TGAAGGCTTGGCAGTAGAGAGACACAAACAGCAGTGATGCACAATGAAAAGAGAGCGACGAATGG
2087825 TGG
66 TGG
* * ** * * *
2087828 TGAAGGCTTGGCAGTGGAGGGACACAAACAGTGGTGATGCACAGTGAAAAGGGAGCGACGAATTG
1 TGAAGGCTTGGCAGTAGAGAGACACAAACAGCAGTGATGCACAATGAAAAGAGAGCGACGAATGG
2087893 TGG
66 TGG
2087896 TGAAGG
1 TGAAGG
2087902 TTTGACAATG
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.32, C:0.11, G:0.40, T:0.17
Consensus pattern (68 bp):
TGAAGGCTTGGCAGTAGAGAGACACAAACAGCAGTGATGCACAATGAAAAGAGAGCGACGAATGG
TGG
Found at i:2088121 original size:26 final size:27
Alignment explanation
Indices: 2088083--2088133 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
2088073 GGTGAAGAAG
2088083 AAAAAGAAGAGGGAAAAAAAAGAAAAT
1 AAAAAGAAGAGGGAAAAAAAAGAAAAT
*
2088110 AAAAAGAA-AGGGAAAGAAAAGAAA
1 AAAAAGAAGAGGGAAAAAAAAGAAA
2088134 TAAGGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (27 bp):
AAAAAGAAGAGGGAAAAAAAAGAAAAT
Found at i:2093224 original size:19 final size:18
Alignment explanation
Indices: 2093184--2093229 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
2093174 AATGGCAAAT
* *
2093184 ATGAGAAATGATTATGAG
1 ATGAGAAATGAATATGAA
2093202 ATGAGAAATGAAATATGAA
1 ATGAGAAATG-AATATGAA
*
2093221 ATGATAAAT
1 ATGAGAAAT
2093230 TGAGATGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (18 bp):
ATGAGAAATGAATATGAA
Found at i:2093507 original size:43 final size:43
Alignment explanation
Indices: 2093444--2093646 Score: 280
Period size: 43 Copynumber: 4.7 Consensus size: 43
2093434 TGAAAAACCT
* * * * *
2093444 CCGCTATAGAACGTGACCTTTAGTGGCGCTTTTCTCATAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
* * *
2093487 TCGCTATAGAACGTGGCCTTTAGCGGTGCTTGTCCCATAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
** *
2093530 TTGCTATAGAACGTGGCCTTTAGAGGCGCTTGTCCCACAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
* *
2093573 CCGCTATAAAACGTGGCCTTTAGCGGCACTTGTCCCACAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
*
2093616 CCGCTATAGAAAGTGGCCTTTAGCGGCGCTT
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTT
2093647 TCACCAAAAA
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 142 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (43 bp):
CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
Found at i:2093934 original size:68 final size:68
Alignment explanation
Indices: 2093821--2093952 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
2093811 ATGTTAAAGG
2093821 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACGTCTAGGATGGCAGATTCTGCGGCTGC
1 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACGTCTAGGATGGCAGATTCTGCGGCTGC
2093886 TGA
66 TGA
* *
2093889 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAATGTTTAGGATGGCAGATTCTGCGGCTG
1 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACGTCTAGGATGGCAGATTCTGCGGCTG
2093953 TTGAAACTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (68 bp):
TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACGTCTAGGATGGCAGATTCTGCGGCTGC
TGA
Found at i:2094051 original size:21 final size:20
Alignment explanation
Indices: 2094009--2094063 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2093999 CTGCTTTGCG
*
2094009 CTGCTTCCCTCGCTATTACCT
1 CTGCTTCCCTCG-TACTACCT
*
2094030 CTGCTTCCCTCGTAGCTGCCT
1 CTGCTTCCCTCGTA-CTACCT
*
2094051 CTACTTCCCTCGT
1 CTGCTTCCCTCGT
2094064 TGTTACCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.07, C:0.44, G:0.13, T:0.36
Consensus pattern (20 bp):
CTGCTTCCCTCGTACTACCT
Found at i:2099647 original size:9 final size:9
Alignment explanation
Indices: 2099635--2099706 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
2099625 GGGTGTAAAC
2099635 TATGTAAGT
1 TATGTAAGT
2099644 TATGTAAGT
1 TATGTAAGT
*
2099653 TATGCAAGT
1 TATGTAAGT
* *
2099662 TATGATATGA
1 TATG-TAAGT
* *
2099672 TATAT-ATT
1 TATGTAAGT
*
2099680 TATGTACGT
1 TATGTAAGT
*
2099689 TATGTAAAT
1 TATGTAAGT
2099698 TATGTAAGT
1 TATGTAAGT
2099707 CCATAGATAT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
8 4 0.09
9 38 0.81
10 5 0.11
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:2099701 original size:45 final size:46
Alignment explanation
Indices: 2099635--2099746 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 46
2099625 GGGTGTAAAC
*
2099635 TATGTAAGTTATGTAAGTTATGCAAGT-TAT-GATATGATATATATT
1 TATGT-AGTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
* *
2099680 TATGTACGTTATGTAAATTATGTAAGTCCATAGATATGATATATATT
1 TATGTA-GTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
2099727 TATGTA-TTATGTAAGTTATG
1 TATGTAGTTATGTAAGTTATG
2099747 ATCTAATGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
44 1 0.02
45 36 0.60
46 2 0.03
47 21 0.35
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.45
Consensus pattern (46 bp):
TATGTAGTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
Found at i:2100454 original size:41 final size:41
Alignment explanation
Indices: 2100408--2100508 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
2100398 CCATAGTAGA
* * *
2100408 GAAAATAATAAAATAAATGATAAATATAATAGTATAATAGC
1 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
*
2100449 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGT
1 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
2100490 GAAAATAATAAAATAAATG
1 GAAAATAATAAAATAAATG
2100509 TAAGAATTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (41 bp):
GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
Found at i:2102650 original size:41 final size:41
Alignment explanation
Indices: 2102601--2102702 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
2102591 AAAGAAACAT
* * *
2102601 CACTATTGCTCAACCTTTTGCGGCATTTCGACCAAAAACTC
1 CACTATTGCTCAACCTTTTGCAGCATTTCGACAAAAAACGC
* * *
2102642 CACTATTGCTCAA-CTTTTAGCAGCGTTTTGATAAAAAACGC
1 CACTATTGCTCAACCTTTT-GCAGCATTTCGACAAAAAACGC
*
2102683 CACTATTGCTCAACTTTTTG
1 CACTATTGCTCAACCTTTTG
2102703 TGGCGCTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.10
41 43 0.83
42 4 0.08
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.33
Consensus pattern (41 bp):
CACTATTGCTCAACCTTTTGCAGCATTTCGACAAAAAACGC
Found at i:2108305 original size:43 final size:43
Alignment explanation
Indices: 2108250--2108479 Score: 286
Period size: 43 Copynumber: 5.3 Consensus size: 43
2108240 CGTTTTTTAA
* * * *
2108250 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGTGCTTTTTT
1 AAAAAACGCCGCTATAGACCAGTACTTTTAGCGGCGCTTTTTT
* * *
2108293 AAAAAGCGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTGTA
1 AAAAAACGCCGCTATAGACCAGTACTTTTAGCGGCGCTTTT-TT
* * *
2108337 AAAAAACGCCGCTATAGACCAAGAAC-TTCAGCGGCGCTTTTAT
1 AAAAAACGCCGCTATAGACC-AGTACTTTTAGCGGCGCTTTTTT
* *
2108380 AAAAAACGCCGCTATAGACCTA-TACTTTTAGCGGCACTTTTAT
1 AAAAAACGCCGCTATAGACC-AGTACTTTTAGCGGCGCTTTTTT
*
2108423 AAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG-TTTTTT
1 AAAAAACGCCGCTATAGACCAGTACTTTTAGCGGCGCTTTTTT
2108465 AAAAAAGCGCCGCTA
1 AAAAAA-CGCCGCTA
2108480 ATTTGCCCAG
Statistics
Matches: 162, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
42 13 0.08
43 112 0.69
44 34 0.21
45 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (43 bp):
AAAAAACGCCGCTATAGACCAGTACTTTTAGCGGCGCTTTTTT
Found at i:2108356 original size:87 final size:87
Alignment explanation
Indices: 2108244--2108479 Score: 325
Period size: 87 Copynumber: 2.7 Consensus size: 87
2108234 TCGTGGCGTT
* *
2108244 TTTTA-AAAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGTGCTTTTTTAAAAAGCGCCGCTAT
1 TTTTATAAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAGCGCCGCTAT
* *
2108308 AGACCTGTACTTTTAGCGGCGC
66 AGACCTATACTTTTAGCGGCAC
* * * * * *
2108330 TTTTGTAAAAAAACGCCGCTATAGACCAAGAACTTCAGCGGCGCTTTTATAAAAAACGCCGCTAT
1 TTTTATAAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAGCGCCGCTAT
2108395 AGACCTATACTTTTAGCGGCAC
66 AGACCTATACTTTTAGCGGCAC
* * *
2108417 TTTTAT-AAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG-TTTTTTAAAAAAGCGCCGCTA
1 TTTTATAAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTTT-AAAAAGCGCCGCTA
2108480 ATTTGCCCAG
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
85 5 0.04
86 47 0.36
87 77 0.60
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (87 bp):
TTTTATAAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAGCGCCGCTAT
AGACCTATACTTTTAGCGGCAC
Found at i:2108390 original size:130 final size:129
Alignment explanation
Indices: 2108244--2108479 Score: 357
Period size: 130 Copynumber: 1.8 Consensus size: 129
2108234 TCGTGGCGTT
** * *
2108244 TTTTAAAAAAAACGCCGCTAAAGACC-AGGACCTTTAGCGGTGCTTTTTTAAAAAGCGCCGCTAT
1 TTTTAAAAAAAACGCCGCTAAAGACCTA-GACCTTTAGCGGCACTTTTATAAAAAACGCCGCTAT
2108308 AGACCTGTACTTTTAGCGGCGCTTTTGTAAAAAAACGCCGCTATAGACCAAGAACTTCAGCGGCG
65 AGACCTGTACTTTTAGCGGCG-TTTTGTAAAAAAACGCCGCTATAGACCAAGAACTTCAGCGGCG
2108373 C
129 C
* * * *
2108374 TTTTATAAAAAACGCCGCTATAGACCTATACTTTTAGCGGCACTTTTATAAAAAACGCCGCTATA
1 TTTTAAAAAAAACGCCGCTAAAGACCTAGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATA
* *
2108439 GACCTGTACTTTTAGCGGCGTTTTTTAAAAAAGCGCCGCTA
66 GACCTGTACTTTTAGCGGCGTTTTGTAAAAAAACGCCGCTA
2108480 ATTTGCCCAG
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
129 19 0.20
130 75 0.79
131 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (129 bp):
TTTTAAAAAAAACGCCGCTAAAGACCTAGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATA
GACCTGTACTTTTAGCGGCGTTTTGTAAAAAAACGCCGCTATAGACCAAGAACTTCAGCGGCGC
Found at i:2108802 original size:21 final size:21
Alignment explanation
Indices: 2108776--2108816 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2108766 TCCTGTTCTG
* *
2108776 CTCCGCCTCCTTTGCTGCTGT
1 CTCCGCCTCCCTCGCTGCTGT
2108797 CTCCGCCTCCCTCGCTGCTG
1 CTCCGCCTCCCTCGCTGCTG
2108817 CCTTCGCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.49, G:0.20, T:0.32
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGT
Found at i:2109411 original size:18 final size:18
Alignment explanation
Indices: 2109379--2109416 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2109369 TACAATATAG
2109379 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
2109398 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
2109415 TA
1 TA
2109417 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:2114721 original size:21 final size:21
Alignment explanation
Indices: 2114697--2114736 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2114687 AAATTAATTC
*
2114697 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
2114718 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
2114737 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:2116793 original size:19 final size:20
Alignment explanation
Indices: 2116769--2116808 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2116759 GACTTCAGTC
2116769 TGCAGAACAAAG-AATCATA
1 TGCAGAACAAAGCAATCATA
*
2116788 TGCAGACCAAAGCAATCATA
1 TGCAGAACAAAGCAATCATA
2116808 T
1 T
2116809 TCTACCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (20 bp):
TGCAGAACAAAGCAATCATA
Found at i:2118760 original size:18 final size:19
Alignment explanation
Indices: 2118723--2118761 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2118713 AAATCATATT
2118723 TATTATTTTCATATAAAAA
1 TATTATTTTCATATAAAAA
*
2118742 TATTATTTTGATA-AAAAA
1 TATTATTTTCATATAAAAA
2118760 TA
1 TA
2118762 AAAAAGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTATTTTCATATAAAAA
Found at i:2119823 original size:41 final size:42
Alignment explanation
Indices: 2119778--2120036 Score: 291
Period size: 41 Copynumber: 6.3 Consensus size: 42
2119768 TTATATAACT
* * *
2119778 TTTAGTGGCGTTTTAGCAAAAGCG-CAGTTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
* *
2119819 TTTAGCGGCGTTTTACCAAAAGCGTC-GCTAATGCTCAGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
* *
2119860 TTTAGCGGCGTTTTACCAAAAGCGCC-GCTAATGCTCTAGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
*
2119901 TTTAGCGGCGTTTTACCAAAAGCGCCA-CTAGTGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
* * *
2119942 TTTAGCGGCGTTTTACCAACAGCGCCA-CTAGTGCTCT-GTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
* * * * * *
2119982 TTTAGTGGCGTTTTAACAAAAAACGCC-GCTATTGCTC-AGTT
1 TTTAGCGGCGTTTT-ACCAAAAGCGCCAGCTAATGCTCTGGTC
*
2120023 TTTAGCGGCATTTT
1 TTTAGCGGCGTTTT
2120037 TGTTAAAACG
Statistics
Matches: 193, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
40 15 0.08
41 177 0.92
42 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCAGCTAATGCTCTGGTC
Found at i:2119921 original size:123 final size:122
Alignment explanation
Indices: 2119777--2120036 Score: 344
Period size: 123 Copynumber: 2.1 Consensus size: 122
2119767 GTTATATAAC
* * *
2119777 TTTTAGTGGCGTTTTAGCAAAAGCG-CAGTTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCA-CTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAG
* * * *
2119841 CGTCGCTAATGCTCAGGTCTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTAGT
65 CGCCACTAATGCTC-GGTCTTTAGCGGCGTTTTAACAAAAAACGCCGCTAATGCTC-AGT
* *
2119900 TTTTAGCGGCGTTTTACCAAAAGCGCCACTAGTGCTCTGGTCTTTAGCGGCGTTTTACCAACAGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
* * * * *
2119965 GCCACTAGTGCTCTGTTTTTAGTGGCGTTTTAACAAAAAACGCCGCTATTGCTCAGT
66 GCCACTAATGCTCGGTCTTTAGCGGCGTTTTAACAAAAAACGCCGCTAATGCTCAGT
*
2120022 TTTTAGCGGCATTTT
1 TTTTAGCGGCGTTTT
2120037 TGTTAAAACG
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
122 32 0.27
123 86 0.72
124 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (122 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
GCCACTAATGCTCGGTCTTTAGCGGCGTTTTAACAAAAAACGCCGCTAATGCTCAGT
Found at i:2120108 original size:12 final size:12
Alignment explanation
Indices: 2120091--2120116 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2120081 GTTTATTGAT
2120091 AAAACGCCGCTA
1 AAAACGCCGCTA
2120103 AAAACGCCGCTA
1 AAAACGCCGCTA
2120115 AA
1 AA
2120117 GCCTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:2127881 original size:26 final size:25
Alignment explanation
Indices: 2127839--2127894 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
2127829 AAACAAATAC
2127839 TCATA-TTTATATAATTAAAACAT-
1 TCATATTTTATATAATTAAAACATG
*
2127862 TCATATTTTATACTAGATTAAAATATG
1 TCATATTTTATA-TA-ATTAAAACATG
2127889 TCATAT
1 TCATAT
2127895 GTCCCTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 2 0.07
26 9 0.32
27 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (25 bp):
TCATATTTTATATAATTAAAACATG
Found at i:2128120 original size:20 final size:20
Alignment explanation
Indices: 2128095--2128136 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2128085 TTTATTTAAA
*
2128095 AATTACACATCAACCAAATT
1 AATTACACATCAACAAAATT
2128115 AATTACACATCAACAAAATT
1 AATTACACATCAACAAAATT
2128135 AA
1 AA
2128137 CAATGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (20 bp):
AATTACACATCAACAAAATT
Found at i:2129203 original size:9 final size:10
Alignment explanation
Indices: 2129186--2129292 Score: 54
Period size: 9 Copynumber: 11.4 Consensus size: 10
2129176 ACTTATTAAA
*
2129186 ATTAAAAAAT
1 ATTATAAAAT
2129196 A-TATAAAA-
1 ATTATAAAAT
2129204 ACTTAT-AAAT
1 A-TTATAAAAT
2129214 ATTAT-AAA-
1 ATTATAAAAT
2129222 ATTATAAAA-
1 ATTATAAAAT
*
2129231 ATTATAAAAA
1 ATTATAAAAT
*
2129241 ATTATGAAAT
1 ATTATAAAAT
*
2129251 -TAATAAAACTT
1 ATTATAAAA--T
*
2129262 ATT-TGAAAT
1 ATTATAAAAT
2129271 ATT-TAAAAT
1 ATTATAAAAT
* *
2129280 -TAAAAAAAT
1 ATTATAAAAT
2129289 ATTA
1 ATTA
2129293 GAATTCTTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
8 7 0.09
9 48 0.63
10 15 0.20
11 5 0.07
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:2129205 original size:28 final size:27
Alignment explanation
Indices: 2129174--2129264 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
2129164 ATATTGATAT
2129174 AAACTTATTAAAATTAAAAAATATATAA
1 AAACTTATTAAAATTAAAAAAT-TATAA
*
2129202 AAACTTA-TAAATATTATAAAATTATAA
1 AAACTTATTAAA-ATTAAAAAATTATAA
* **
2129229 AAA-TTATAAAAAATTATGAAATTA-ATA
1 AAACTTAT-TAAAATTAAAAAATTATA-A
2129256 AAACTTATT
1 AAACTTATT
2129265 TGAAATATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
26 4 0.07
27 27 0.50
28 23 0.43
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
AAACTTATTAAAATTAAAAAATTATAA
Found at i:2129211 original size:36 final size:34
Alignment explanation
Indices: 2129171--2129263 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 34
2129161 TTAATATTGA
*
2129171 TATAAACTTATTAAAATTA-AAAAATATATAAAAACT
1 TATAAA-TTA-TAAAATTATAAAAAT-TATAAAAAAT
2129207 TATAAATATTATAAAATTATAAAAATTATAAAAAAT
1 TAT-AA-ATTATAAAATTATAAAAATTATAAAAAAT
2129243 TATGAAATTAATAAAACTTAT
1 TAT-AAATT-ATAAAA-TTAT
2129264 TTGAAATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
35 3 0.06
36 31 0.62
37 15 0.30
38 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (34 bp):
TATAAATTATAAAATTATAAAAATTATAAAAAAT
Found at i:2129228 original size:17 final size:17
Alignment explanation
Indices: 2129171--2129263 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 17
2129161 TTAATATTGA
* *
2129171 TATAAACTTATTAAAAT
1 TATAAAATTATAAAAAT
*
2129188 TAAAAAATATATAAAAACT
1 TATAAAAT-TATAAAAA-T
2129207 TATAAATATTAT-AAAAT
1 TATAAA-ATTATAAAAAT
2129224 TATAAAAATTATAAAAAAT
1 TAT-AAAATTAT-AAAAAT
* *
2129243 TATGAAATTAATAAAACT
1 TATAAAATT-ATAAAAAT
2129261 TAT
1 TAT
2129264 TTGAAATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.24
18 27 0.43
19 19 0.30
20 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (17 bp):
TATAAAATTATAAAAAT
Found at i:2129306 original size:19 final size:19
Alignment explanation
Indices: 2129282--2129444 Score: 326
Period size: 19 Copynumber: 8.6 Consensus size: 19
2129272 TTTAAAATTA
2129282 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129301 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129320 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129339 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129358 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129377 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129396 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129415 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
2129434 AAAAAATATTA
1 AAAAAATATTA
2129445 AAATATTAAA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 144 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAAATATTAGAATTCTT
Found at i:2129912 original size:19 final size:19
Alignment explanation
Indices: 2129888--2129962 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
2129878 CATGTTGAAG
2129888 TTTTTATGATTTTTTATAA
1 TTTTTATGATTTTTTATAA
* * *
2129907 TTTTTATAAATTTATATGAA
1 TTTTTATGATTTTTTAT-AA
* *
2129927 -TTTTA--ATATTTTATCA
1 TTTTTATGATTTTTTATAA
2129943 TTTTTATGATTTTTATATAA
1 TTTTTATGATTTTT-TATAA
2129963 CTGTAATATG
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
16 1 0.02
17 11 0.26
19 24 0.57
20 6 0.14
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATGATTTTTTATAA
Found at i:2129970 original size:36 final size:36
Alignment explanation
Indices: 2129899--2129971 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
2129889 TTTTATGATT
* *
2129899 TTTTATAATTTTTATAAATTTATATGAATTTTAATA
1 TTTTATAATTTTTATAAATTTATATGAACTGTAATA
* **
2129935 TTTTATCATTTTTATGATTTTTATAT-AACTGTAATA
1 TTTTATAATTTTTAT-AAATTTATATGAACTGTAATA
2129971 T
1 T
2129972 GTTTTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 23 0.74
37 8 0.26
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (36 bp):
TTTTATAATTTTTATAAATTTATATGAACTGTAATA
Found at i:2130013 original size:19 final size:18
Alignment explanation
Indices: 2129991--2130053 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
2129981 AAAAATAAAT
2129991 ATTTTTATAATTTATTAGA
1 ATTTTTATAATTTATTA-A
*
2130010 ATTTTTAT-ATTCTTTTATA
1 ATTTTTATAATT-TATTA-A
*
2130029 ATTTTTTTAAGTTTATATAA
1 ATTTTTATAA-TTTAT-TAA
2130049 ATTTT
1 ATTTT
2130054 CATATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 3 0.08
19 20 0.56
20 9 0.25
21 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTTATAATTTATTAA
Found at i:2130035 original size:10 final size:10
Alignment explanation
Indices: 2129992--2130064 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
2129982 AAAATAAATA
2129992 TTTTTATAAT
1 TTTTTATAAT
* *
2130002 TTATTAGAA-
1 TTTTTATAAT
2130011 TTTTTAT-AT
1 TTTTTATAAT
2130020 TCTTTTATAAT
1 T-TTTTATAAT
*
2130031 TTTTT-TAAG
1 TTTTTATAAT
* *
2130040 TTTATATAAA
1 TTTTTATAAT
*
2130050 TTTTCAT-AT
1 TTTTTATAAT
2130059 TTTTTA
1 TTTTTA
2130065 ATATTTAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
8 1 0.02
9 19 0.40
10 25 0.52
11 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:2131156 original size:35 final size:35
Alignment explanation
Indices: 2131110--2131179 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2131100 GTGAGTAAAC
2131110 GAAAACATGTTTGAGATTCATAGTAGTATTCAGAT
1 GAAAACATGTTTGAGATTCATAGTAGTATTCAGAT
2131145 GAAAACATGTTTGAGATTCATAGTAGTATTCAGAT
1 GAAAACATGTTTGAGATTCATAGTAGTATTCAGAT
2131180 TCCCCCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (35 bp):
GAAAACATGTTTGAGATTCATAGTAGTATTCAGAT
Found at i:2131181 original size:18 final size:18
Alignment explanation
Indices: 2131123--2131181 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
2131113 AACATGTTTG
2131123 AGATTCATAGTAGTATTC
1 AGATTCATAGTAGTATTC
* * ** *
2131141 AGA-TGAAAACATGT-TTG
1 AGATTCATAGTA-GTATTC
2131158 AGATTCATAGTAGTATTC
1 AGATTCATAGTAGTATTC
2131176 AGATTC
1 AGATTC
2131182 CCCCTTTTTT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (18 bp):
AGATTCATAGTAGTATTC
Found at i:2131553 original size:30 final size:30
Alignment explanation
Indices: 2131518--2131577 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2131508 AACCACTTTA
2131518 TTATATGTTTCCAATGTATTTTGATAGCTT
1 TTATATGTTTCCAATGTATTTTGATAGCTT
*
2131548 TTATATGTTTCCAATGTATTTTGGTAGCTT
1 TTATATGTTTCCAATGTATTTTGATAGCTT
2131578 AGAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (30 bp):
TTATATGTTTCCAATGTATTTTGATAGCTT
Found at i:2133961 original size:14 final size:14
Alignment explanation
Indices: 2133942--2133969 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2133932 CAAATATACA
2133942 AATGACACGTAAAG
1 AATGACACGTAAAG
2133956 AATGACACGTAAAG
1 AATGACACGTAAAG
2133970 TTTAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
AATGACACGTAAAG
Found at i:2137393 original size:22 final size:23
Alignment explanation
Indices: 2137368--2137414 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2137358 TTGAAATAAT
*
2137368 TAATATAAAATAAA-AAATCCAG
1 TAATATAAAACAAATAAATCCAG
* *
2137390 TAATATACAACAAATAAATCGAG
1 TAATATAAAACAAATAAATCCAG
2137413 TA
1 TA
2137415 TGTTATCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (23 bp):
TAATATAAAACAAATAAATCCAG
Found at i:2146117 original size:21 final size:21
Alignment explanation
Indices: 2146093--2146133 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2146083 TTGCCTAGGA
*
2146093 TATGAATTAAATTAAATTGAG
1 TATGAAATAAATTAAATTGAG
**
2146114 TATGAAATGGATTAAATTGA
1 TATGAAATAAATTAAATTGA
2146134 CATTAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
TATGAAATAAATTAAATTGAG
Found at i:2164301 original size:10 final size:9
Alignment explanation
Indices: 2164263--2164297 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2164253 AATAATGTGG
2164263 TTTT-ATAT
1 TTTTAATAT
2164271 ATTTTAATAT
1 -TTTTAATAT
2164281 TTTTAATAT
1 TTTTAATAT
2164290 TTTTAATA
1 TTTTAATA
2164298 ATTTCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 21 0.84
10 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTAATAT
Found at i:2165945 original size:13 final size:14
Alignment explanation
Indices: 2165910--2165955 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
2165900 TAATACGTGA
*
2165910 AAAATATTA-TTTA
1 AAAATATTATTTTT
2165923 AAAATATTATTTTT
1 AAAATATTATTTTT
*
2165937 AAAAT-TTATTATT
1 AAAATATTATTTTT
2165950 AAAATA
1 AAAATA
2165956 AAATTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTATTTTT
Found at i:2165946 original size:16 final size:16
Alignment explanation
Indices: 2165914--2165953 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
2165904 ACGTGAAAAA
2165914 TATTATTTAAAAATAT
1 TATTATTTAAAAATAT
2165930 TATT-TTT-AAAAT-T
1 TATTATTTAAAAATAT
2165943 TATTA-TTAAAA
1 TATTATTTAAAA
2165954 TAAAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTTAAAAATAT
Found at i:2166013 original size:25 final size:26
Alignment explanation
Indices: 2165985--2166034 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2165975 ATTTTAATAA
* *
2165985 ATTATATTAATT-ATATTAATAATTT
1 ATTATATGAATTAATATAAATAATTT
*
2166010 ATTATATGACTTAATATAAATAATT
1 ATTATATGAATTAATATAAATAATT
2166035 AAATACGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTATATGAATTAATATAAATAATTT
Found at i:2177027 original size:17 final size:17
Alignment explanation
Indices: 2177005--2177038 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2176995 TATATATTTC
2177005 TTAATAACAGGGAAAAG
1 TTAATAACAGGGAAAAG
2177022 TTAATAACAGGGAAAAG
1 TTAATAACAGGGAAAAG
2177039 GAAGGACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (17 bp):
TTAATAACAGGGAAAAG
Done.