Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 8 of 144
Found at i:1856791 original size:21 final size:22
Alignment explanation
Indices: 1856744--1856804 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1856734 CCTAACCTTA
*
1856744 AAACCTAAAA-TCTCAAAACTAT
1 AAACCTAAAACTCT-AAATCTAT
1856766 AAACCTAAAACTCTAAATCT-T
1 AAACCTAAAACTCTAAATCTAT
*
1856787 AAACCCT-AAACCCTAAAT
1 AAA-CCTAAAACTCTAAAT
1856805 TCGAAACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.40
22 18 0.51
23 3 0.09
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCTAAAACTCTAAATCTAT
Found at i:1856801 original size:29 final size:29
Alignment explanation
Indices: 1856731--1856803 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
1856721 AATAACCCCC
*
1856731 AACCCT-AACCTTAAAACCTAAAATCTCA
1 AACCCTAAACCCTAAAACCTAAAATCTCA
* * *
1856759 AA-ACTATAAACCTAAAACTCT-AAATCTTA
1 AACCCTA-AACCCTAAAAC-CTAAAATCTCA
1856788 AACCCTAAACCCTAAA
1 AACCCTAAACCCTAAA
1856804 TTCGAAACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.06
28 2 0.06
29 26 0.74
30 5 0.14
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (29 bp):
AACCCTAAACCCTAAAACCTAAAATCTCA
Found at i:1856879 original size:7 final size:7
Alignment explanation
Indices: 1856867--1856892 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1856857 ACATTGACAC
1856867 CTAAATT
1 CTAAATT
1856874 CTAAATT
1 CTAAATT
1856881 CTAAATT
1 CTAAATT
1856888 CTAAA
1 CTAAA
1856893 CCCTAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (7 bp):
CTAAATT
Found at i:1856898 original size:14 final size:14
Alignment explanation
Indices: 1856866--1856899 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1856856 AACATTGACA
*
1856866 CCTAAATTCTAAAT
1 CCTAAATTCTAAAC
*
1856880 TCTAAATTCTAAAC
1 CCTAAATTCTAAAC
1856894 CCTAAA
1 CCTAAA
1856900 CCTTGAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
CCTAAATTCTAAAC
Found at i:1857052 original size:27 final size:27
Alignment explanation
Indices: 1856994--1857077 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
1856984 ACTAACCCCC
1856994 AAACCATAACATCCAAACCTAAATCAT
1 AAACCATAACATCCAAACCTAAATCAT
* * * *
1857021 GAACCCTAAC-TCTAAACCTAAAGTCTT
1 AAACCATAACATCCAAACCTAAA-TCAT
* * * *
1857048 AAACCTTAAAACCCAAACCTTAAATAAT
1 AAACCATAACATCCAAACC-TAAATCAT
1857076 AA
1 AA
1857078 TCCCTAAGCC
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
26 11 0.26
27 18 0.42
28 10 0.23
29 4 0.09
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.21
Consensus pattern (27 bp):
AAACCATAACATCCAAACCTAAATCAT
Found at i:1858249 original size:42 final size:42
Alignment explanation
Indices: 1858199--1858315 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
1858189 AACAAAAACG
*
1858199 CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCA
1 CCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCA
* * **
1858241 CCTCTAAAGAACATGTTCTTTAGCGGTGTTTTTTTCTAAGTG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCA
* *
1858283 CCGCTAAAGAACATGTTCGTTAGCGGCGCTTTT
1 CCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
1858316 ATATAAAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (42 bp):
CCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCA
Found at i:1858662 original size:21 final size:21
Alignment explanation
Indices: 1858633--1858682 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1858623 TTTTGCTCTG
*
1858633 CTCTACTTCTCTCGCTACAGC
1 CTCTACTTCCCTCGCTACAGC
* * *
1858654 CTCTGCTTCCCTCGCTGCCGC
1 CTCTACTTCCCTCGCTACAGC
1858675 CTCTACTT
1 CTCTACTT
1858683 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.46, G:0.12, T:0.34
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTACAGC
Found at i:1860196 original size:115 final size:111
Alignment explanation
Indices: 1859948--1860331 Score: 362
Period size: 114 Copynumber: 3.4 Consensus size: 111
1859938 AACTTTGTCC
* * * * *
1859948 AAAGCCCTAAGCATTAGCGGCGCTTCACTAAAAA-ACCACTAAATCCCCAAAAAGCTAATAAAAC
1 AAAGCCCGAA-CATTAGCGGCGCTTTACTAAAAACGCCACTAAAGCCCC--AAAGCTCATAAAAC
* ** *
1860012 GGCATCGTCGGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCT
63 GGCGTCGT-GGGCTTAGGTTTCTTTGCGGCGCTTTACCGAAAACGCCGCT
* * *
1860062 AAAGCCCTAAGCATTAGCGGCGCTTTACTAAAAACGCCACTAAAGACCCAAAGGCTCAGAAAACG
1 AAAGCCCGAA-CATTAGCGGCGCTTTACTAAAAACGCCACTAAAGCCCCAAA-GCTCATAAAACG
* * *
1860127 GCGTCAGTGGGCTTAGGTTTTCTTTGCGGCGCTTTACTGAAAACACCGCA
64 GCGTC-GTGGGCTTAGG-TTTCTTTGCGGCGCTTTACCGAAAACGCCGCT
* * * * * * *
1860177 AAAGCCCGGAACATCAGCGGCAC-TTACTTACAAACGCCGCGAAAGCCCCGAAGCTCATTAAACG
1 AAAGCCC-GAACATTAGCGGCGCTTTAC-TAAAAACGCCACTAAAGCCCCAAAGCTCATAAAACG
* * *
1860241 GCGTCGTTGGGATTAGGTTT-TTTGTGGCG-TTTTCGCGAAAACGCCGCT
64 GCGTCG-TGGGCTTAGGTTTCTTTGCGGCGCTTTAC-CGAAAACGCCGCT
* * * *
1860289 AAAGCCCTGATCATTAGCGGCGCTTTATTAAAATCGCCGCTAA
1 AAAGCCC-GAACATTAGCGGCGCTTTACTAAAAACGCCACTAA
1860332 TGCTTATTTT
Statistics
Matches: 224, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
111 4 0.02
112 49 0.22
113 10 0.04
114 84 0.38
115 75 0.33
116 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (111 bp):
AAAGCCCGAACATTAGCGGCGCTTTACTAAAAACGCCACTAAAGCCCCAAAGCTCATAAAACGGC
GTCGTGGGCTTAGGTTTCTTTGCGGCGCTTTACCGAAAACGCCGCT
Found at i:1862874 original size:3 final size:3
Alignment explanation
Indices: 1862866--1862898 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1862856 TTTGATTCAC
1862866 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1862899 TACTTTCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1865070 original size:18 final size:18
Alignment explanation
Indices: 1865030--1865071 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1865020 TTTCAAAAAG
1865030 GTTTAAACATCTTCATTTT
1 GTTT-AACATCTTCATTTT
* *
1865049 -TTTAACATTTTCGTTTT
1 GTTTAACATCTTCATTTT
1865066 GTTTAA
1 GTTTAA
1865072 TTTTAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (18 bp):
GTTTAACATCTTCATTTT
Found at i:1868696 original size:15 final size:15
Alignment explanation
Indices: 1868676--1868706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1868666 ACAATAACAA
1868676 TGGCCCAAACTACAG
1 TGGCCCAAACTACAG
*
1868691 TGGCCCAAATTACAG
1 TGGCCCAAACTACAG
1868706 T
1 T
1868707 CAGAAACCCT
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:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (15 bp):
TGGCCCAAACTACAG
Found at i:1869387 original size:12 final size:12
Alignment explanation
Indices: 1869370--1869400 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1869360 AAGGGGAGAG
1869370 TTTTTTTGAAGT
1 TTTTTTTGAAGT
1869382 TTTTTTTGAAGT
1 TTTTTTTGAAGT
1869394 TTTTTTT
1 TTTTTTT
1869401 AAAAGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (12 bp):
TTTTTTTGAAGT
Found at i:1869951 original size:107 final size:107
Alignment explanation
Indices: 1869781--1869994 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
1869771 AATGAGAAAG
* *
1869781 TCTTAATAAATAATTTAATTAAGGATTACATTTTTTTTAACTCTTGACTTTAAGACATTAATTAA
1 TCTTAATAAATAATTTAATTAAGGATCACATTTTTTTTAACTCTCGACTTTAAGACATTAATTAA
*
1869846 TCAATTTGGTTCCAATTTTTTGGGCGTTACGAGGGTGCTAATC
66 TCAATTTGGTACCAA-TTTTTGGGCGTTACGAGGGTGCTAATC
1869889 TCTTAATAAATAATTTAATTAAGGATCACA-TTTTTTTAACTCTCGACTTTAAGACATTAATTAA
1 TCTTAATAAATAATTTAATTAAGGATCACATTTTTTTTAACTCTCGACTTTAAGACATTAATTAA
1869953 TCAATTTGGTACCAATTTTTGGGCGTTACGAGGGTGCTAATC
66 TCAATTTGGTACCAATTTTTGGGCGTTACGAGGGTGCTAATC
1869995 GTTCCTCGTA
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 27 0.26
107 47 0.46
108 29 0.28
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (107 bp):
TCTTAATAAATAATTTAATTAAGGATCACATTTTTTTTAACTCTCGACTTTAAGACATTAATTAA
TCAATTTGGTACCAATTTTTGGGCGTTACGAGGGTGCTAATC
Found at i:1870237 original size:193 final size:193
Alignment explanation
Indices: 1869996--1870357 Score: 652
Period size: 193 Copynumber: 1.9 Consensus size: 193
1869986 GTGCTAATCG
* * * *
1869996 TTCCTCGTATGTAGCTGACTCCCGAATCTGTTTTTCTAAAACTCGTAGACCAAAGCTATTTTTTA
1 TTCCTCGTACGTAACTGACTCCCGAATCCGTTTTTCTAAAAATCGTAGACCAAAGCTATTTTTTA
1870061 GGTGATCCAATCACACCTCAATAAAAGATTAGTGGCGACTCCCAATTTTTAAAGTCGACAACTAA
66 GGTGATCCAATCACACCTCAATAAAAGATTAGTGGCGACTCCCAATTTTTAAAGTCGACAACTAA
1870126 TTTTTGTTTTTTTCCAAAATAAAAAGTTGGTTTCGACAGCTTGGCGACTCCACTGGGGACTTT
131 TTTTTGTTTTTTTCCAAAATAAAAAGTTGGTTTCGACAGCTTGGCGACTCCACTGGGGACTTT
1870189 TTCCTCGTACGTAACTGACTCCCGAATCCGTTTTTCTAAAAATCGTAGACCAAAGCTATTTTTTA
1 TTCCTCGTACGTAACTGACTCCCGAATCCGTTTTTCTAAAAATCGTAGACCAAAGCTATTTTTTA
*
1870254 GGTGATCCAATCACACCTCAATAAAAGATTGGTGGCGACTCCCAATTTTTAAAGTCGACAACTAA
66 GGTGATCCAATCACACCTCAATAAAAGATTAGTGGCGACTCCCAATTTTTAAAGTCGACAACTAA
* **
1870319 TTTTTGTTTTTTTCCAAGATAAAAAGTTTTTTTCGACAG
131 TTTTTGTTTTTTTCCAAAATAAAAAGTTGGTTTCGACAG
1870358 ACACCTCCTT
Statistics
Matches: 161, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
193 161 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (193 bp):
TTCCTCGTACGTAACTGACTCCCGAATCCGTTTTTCTAAAAATCGTAGACCAAAGCTATTTTTTA
GGTGATCCAATCACACCTCAATAAAAGATTAGTGGCGACTCCCAATTTTTAAAGTCGACAACTAA
TTTTTGTTTTTTTCCAAAATAAAAAGTTGGTTTCGACAGCTTGGCGACTCCACTGGGGACTTT
Found at i:1881667 original size:39 final size:39
Alignment explanation
Indices: 1881613--1881691 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
1881603 AAAACACTCT
* *
1881613 GCATTCATGCAAACATTATTCATACACGTCTAGTTAGGA
1 GCATTCATGCAAACATCAGTCATACACGTCTAGTTAGGA
*
1881652 GCATTCATGCAAACATCAGTCATACATGTCTAGTTAGGA
1 GCATTCATGCAAACATCAGTCATACACGTCTAGTTAGGA
1881691 G
1 G
1881692 TATTTGATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (39 bp):
GCATTCATGCAAACATCAGTCATACACGTCTAGTTAGGA
Found at i:1881950 original size:44 final size:45
Alignment explanation
Indices: 1881881--1882626 Score: 234
Period size: 44 Copynumber: 17.0 Consensus size: 45
1881871 TAGGTTGAAA
* *
1881881 ATAGTAGATCTTGTC-TTCATGTATTGGT-GTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * *
1881925 ATAGCAGGTCCTGTCTTTCTATATTGGTAG-GAAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTTCTATATTGGTGGTGAAGTAGATCGAAG
* * * * * * * *
1881969 GT-GCAGCTCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTTCTATATTGGTGGTGAAGTAGATCGAAG
* * * * *
1882013 AAAGCAGATCTTATC-TTCATGTATTAG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * *
1882057 ATAGTAGATCCTGT-TTTCCTATATTGGTAG-G-A--AG-T-G--G
1 ATAGCAGATCTTGTCTTT-CTATATTGGTGGTGAAGTAGATCGAAG
* * * * * *
1882094 AT-TCAAGATCTTGTCTTCCCATATTAGTGGCGAAGTAGATCAAAG
1 ATAGC-AGATCTTGTCTTTCTATATTGGTGGTGAAGTAGATCGAAG
* * * * * * *
1882139 AAAGCAGATCTTATC-TTCATGTATTAG-CGTCAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * * * * * *
1882183 AAAGCAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATTGAAG
1 ATAGCAGATCTTGTCTTTCTATATTGGTGGTGAAGTAGATCGAAG
* * * * *
1882228 ATAGTAGATCTTGTCTTCCCATACTGGTGGGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTCTATATTGGT-GGTGAAGTAGATCGAAG
* * * ** *
1882274 AAAGCAGATCTTGTC-TTCATGTATCGG-CATGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * *
1882318 GTAGAAGATCTTGTC-TTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
** * * * ** *
1882362 A-AAAAGAATCTTAT-TTTCATGTATCGG-CATGAAGTAGATCAAAG
1 ATAGCAG-ATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * *
1882406 GTAGAAGATCTTGTC-TTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
** * * * ** *
1882450 A-AAAAGAATCTTAT-TTTCATGTATCGG-CATGAAGTAGATCAAAG
1 ATAGCAG-ATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * *
1882494 GTAGAAGATCTTGTC-TTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
** * * * ** *
1882538 A-AAAAGAATCTTAT-TTTCATGTATCGG-CATGAAGTAGATCAAAG
1 ATAGCAG-ATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
* * * *
1882582 GTAGAAGATCTTGTC-TTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTTC-TATATTGGTGGTGAAGTAGATCGAAG
1882626 A
1 A
1882627 AAAAGAATCT
Statistics
Matches: 539, Mismatches: 127, Indels: 72
0.73 0.17 0.10
Matches are distributed among these distances:
37 20 0.04
38 3 0.01
39 2 0.00
40 1 0.00
41 4 0.01
42 1 0.00
43 33 0.06
44 356 0.66
45 87 0.16
46 32 0.06
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTTCTATATTGGTGGTGAAGTAGATCGAAG
Found at i:1882030 original size:132 final size:129
Alignment explanation
Indices: 1881877--1882334 Score: 541
Period size: 126 Copynumber: 3.5 Consensus size: 129
1881867 GGAGTAGGTT
* * * * * *
1881877 GAAAATAGTAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTT
1 GAAAAAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTT
*
1881942 TCTATATTGGTAGGAAGTGGATCGAAGGTGCAGCTCTTATCTTCCCATACTGGTGGCGAAGTAGA
66 TCTATATTGGTAGGAAGTGGATCGAA-GTG-AG-TCTTGTCTTCCCATACTGGTGGCGAAGTAGA
1882007 TC
128 TC
*
1882009 GAAAAAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGTAGATCCTGT-TT
1 GAAAAAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTT
* *
1882073 TCCTATATTGGTAGGAAGTGGATTC-AA--GA-TCTTGTCTTCCCATATTAGTGGCGAAGTAGAT
66 T-CTATATTGGTAGGAAGTGGA-TCGAAGTGAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
1882134 C
129 C
* * * *
1882135 -AAAGAAAGCAGATCTTATCTTCATGTATTAGCGTCAAGTAGATCGAAAAAAGCAAATCCTGTCT
1 GAAA-AAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCT
* *
1882199 TCCTATATTGGTAGCGAAGTGGATTGAAGATAGTAGATCTTGTCTTCCCATACTGGTGGGCGAAG
65 TTCTATATTGGTAG-GAAGTGGATCGAAG-T-G-AG-TCTTGTCTTCCCATACTGGT-GGCGAAG
1882264 TAGATC
124 TAGATC
* * ** * * * * *
1882270 GAAGAAAGCAGATCTTGTCTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAGATCTTGTCTT
1 GAAAAAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTT
1882335 CATGTATTGG
Statistics
Matches: 279, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
125 3 0.01
126 96 0.34
127 12 0.04
128 1 0.00
129 1 0.00
131 4 0.01
132 78 0.28
133 2 0.01
134 18 0.06
135 62 0.22
136 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (129 bp):
GAAAAAAGCAGATCTTATCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTT
TCTATATTGGTAGGAAGTGGATCGAAGTGAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
Found at i:1882373 original size:88 final size:88
Alignment explanation
Indices: 1882260--1882714 Score: 831
Period size: 88 Copynumber: 5.2 Consensus size: 88
1882250 ACTGGTGGGC
* * *
1882260 GAAGTAGATCGAAGAAAGCAG-ATCTTGTCTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAA
1 GAAGTAGATCGAAGAAA-AAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAA
1882324 GATCTTGTCTTCATGTATTGGCGT
65 GATCTTGTCTTCATGTATTGGCGT
1882348 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1882413 ATCTTGTCTTCATGTATTGGCGT
66 ATCTTGTCTTCATGTATTGGCGT
1882436 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1882501 ATCTTGTCTTCATGTATTGGCGT
66 ATCTTGTCTTCATGTATTGGCGT
1882524 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
1882589 ATCTTGTCTTCATGTATTGGCGT
66 ATCTTGTCTTCATGTATTGGCGT
*
1882612 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAGGGTAGAAG
1 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
* * *
1882677 ATCTTGTCTTAATGTATCGGCAT
66 ATCTTGTCTTCATGTATTGGCGT
1882700 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
1882715 TATAAATCTT
Statistics
Matches: 359, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
87 2 0.01
88 357 0.99
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (88 bp):
GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCATGAAGTAGATCAAAGGTAGAAG
ATCTTGTCTTCATGTATTGGCGT
Found at i:1882637 original size:44 final size:43
Alignment explanation
Indices: 1882125--1882714 Score: 493
Period size: 44 Copynumber: 13.3 Consensus size: 43
1882115 TATTAGTGGC
* * * *
1882125 GAAGTAGATCAAAGAAAGCAGATCTTATCTTCATGTATTAGCGT
1 GAAGTAGATCGAAGAAA-AAGATCTTGTCTTCATGTATTGGCGT
* * * * * * *
1882169 CAAGTAGATCGAA-AAAAGCAAATCCTGTCTTCCTATATTGGTAGC
1 GAAGTAGATCGAAGAAAA--AGATCTTGTCTTCATGTATTGG-CGT
* * ** * ** *
1882214 GAAGTGGATTGAAGATAGTAGATCTTGTCTTCCCATACTGGTGG-GC
1 GAAGTAGATCGAAGA-AAAAGATCTTGTCTT--CAT-GTATTGGCGT
* * *
1882260 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATCGGCAT
1 GAAGTAGATCGAAGAAA-AAGATCTTGTCTTCATGTATTGGCGT
* * *
1882304 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAA-GAAAAAGATCTTGTCTTCATGTATTGGCGT
* * * *
1882348 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCAT
1 GAAGTAGATCGAAGAAAAAG-ATCTTGTCTTCATGTATTGGCGT
* * *
1882392 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAA-GAAAAAGATCTTGTCTTCATGTATTGGCGT
* * * *
1882436 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCAT
1 GAAGTAGATCGAAGAAAAAG-ATCTTGTCTTCATGTATTGGCGT
* * *
1882480 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAA-GAAAAAGATCTTGTCTTCATGTATTGGCGT
* * * *
1882524 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCAT
1 GAAGTAGATCGAAGAAAAAG-ATCTTGTCTTCATGTATTGGCGT
* * *
1882568 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAA-GAAAAAGATCTTGTCTTCATGTATTGGCGT
* * * *
1882612 GAAGTAGATCGAAGAAAAAGAATCTTATTTTCATGTATCGGCAT
1 GAAGTAGATCGAAGAAAAAG-ATCTTGTCTTCATGTATTGGCGT
* * * * *
1882656 GAAGTAGATC-AAGGGTAGAAGATCTTGTCTTAATGTATCGGCAT
1 GAAGTAGATCGAA--GAAAAAGATCTTGTCTTCATGTATTGGCGT
1882700 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
1882715 TATAAATCTT
Statistics
Matches: 432, Mismatches: 93, Indels: 43
0.76 0.16 0.08
Matches are distributed among these distances:
43 29 0.07
44 322 0.75
45 46 0.11
46 28 0.06
47 3 0.01
48 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (43 bp):
GAAGTAGATCGAAGAAAAAGATCTTGTCTTCATGTATTGGCGT
Found at i:1882782 original size:44 final size:45
Alignment explanation
Indices: 1882715--1882840 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 45
1882705 AGATCGAAGA
1882715 TATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 TATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * **
1882760 TATAATTC-TATC-CCCTTGAAGTTGCAGTGGAGCGGATTAAA-AT
1 TATAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * * *
1882803 TATAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGAT
1 TATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1882841 CGCAACGAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 9 0.13
44 49 0.73
45 9 0.13
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (45 bp):
TATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
Found at i:1883603 original size:13 final size:12
Alignment explanation
Indices: 1883571--1883603 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
1883561 CTATTCTATA
1883571 TTTTCTTTTATT
1 TTTTCTTTTATT
1883583 TTTTCTTTTATT
1 TTTTCTTTTATT
1883595 TTTTACTTT
1 TTTT-CTTT
1883604 GCTAAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTATT
Found at i:1885825 original size:16 final size:16
Alignment explanation
Indices: 1885801--1885834 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1885791 ATTTTAAATC
*
1885801 AAGTTAAAATGATTTT
1 AAGTAAAAATGATTTT
*
1885817 AAGTAAAAATTATTTT
1 AAGTAAAAATGATTTT
1885833 AA
1 AA
1885835 CTTGTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (16 bp):
AAGTAAAAATGATTTT
Found at i:1889303 original size:121 final size:121
Alignment explanation
Indices: 1889089--1889335 Score: 467
Period size: 121 Copynumber: 2.0 Consensus size: 121
1889079 AAGACTCTGG
* *
1889089 CATATGCATCTCGTTAGCTCAAGTCGAATGAAAAGAACCACTCAACACATGACTTGGAACTAGTA
1 CATATGCATCTCGTTAGCTCAAGTCAAATGAAAAGAACCACTCAACACACGACTTGGAACTAGTA
1889154 GTTGTAGTGTTAGCACTAAAAATATGAAAACATTATCTCTATGGGGAAAAGTGTCA
66 GTTGTAGTGTTAGCACTAAAAATATGAAAACATTATCTCTATGGGGAAAAGTGTCA
1889210 CATATGCATCTCGTTAGCTCAAGTCAAATGAAAAGAACCACTCAACACACGACTTGGAACTAGTA
1 CATATGCATCTCGTTAGCTCAAGTCAAATGAAAAGAACCACTCAACACACGACTTGGAACTAGTA
*
1889275 GTTGTAGTGTTAGCACTAAAAATCTGAAAACATTATCTCTATGGGGAAAAGTGTCA
66 GTTGTAGTGTTAGCACTAAAAATATGAAAACATTATCTCTATGGGGAAAAGTGTCA
1889331 CATAT
1 CATAT
1889336 TCTCAGACCA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 123 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (121 bp):
CATATGCATCTCGTTAGCTCAAGTCAAATGAAAAGAACCACTCAACACACGACTTGGAACTAGTA
GTTGTAGTGTTAGCACTAAAAATATGAAAACATTATCTCTATGGGGAAAAGTGTCA
Found at i:1896230 original size:123 final size:124
Alignment explanation
Indices: 1895906--1896255 Score: 612
Period size: 125 Copynumber: 2.8 Consensus size: 124
1895896 TTATTTCGAG
1895906 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
1895971 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTAATGTAAGAAATA-TATTTTT
* * *
1896031 TTGATGTTTCTAAGAAAATAGTATAAAATCGCTTCTACCAGTATGCTATTTGAGAAGAAATTGTG
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
1896096 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTAATGTAAGAAATA-ATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTAATGTAAGAAATATATTTTT
*
1896154 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1896219 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
1896256 CAAGTTTGGG
Statistics
Matches: 212, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 101 0.48
125 111 0.52
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTAATGTAAGAAATATATTTTT
Found at i:1900181 original size:19 final size:19
Alignment explanation
Indices: 1900153--1900197 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1900143 GCGAGAGACA
*
1900153 TATTTTCGTTTGGCGGCGC
1 TATTTCCGTTTGGCGGCGC
*
1900172 TATTTCCGTTTGGTGGCGC
1 TATTTCCGTTTGGCGGCGC
1900191 TATTTCC
1 TATTTCC
1900198 AAAGCGAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.07, C:0.22, G:0.27, T:0.44
Consensus pattern (19 bp):
TATTTCCGTTTGGCGGCGC
Found at i:1900998 original size:55 final size:55
Alignment explanation
Indices: 1900913--1901749 Score: 1644
Period size: 55 Copynumber: 15.3 Consensus size: 55
1900903 ACATTATGTA
*
1900913 AAATTATGTAAAA---TTAAGTCCAAAATTTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1900965 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901020 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901075 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901130 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901185 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901240 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901295 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901350 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901405 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901460 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901515 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901570 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901625 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901680 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1901735 AAATTATGTAAAATT
1 AAATTATGTAAAATT
1901750 AGGTTAGGGT
Statistics
Matches: 781, Mismatches: 1, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
52 13 0.02
55 768 0.98
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (55 bp):
AAATTATGTAAAATTCTTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:1901779 original size:29 final size:29
Alignment explanation
Indices: 1901745--1901978 Score: 383
Period size: 29 Copynumber: 8.3 Consensus size: 29
1901735 AAATTATGTA
1901745 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1901774 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
1901804 AAATTAGGTTAAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1901833 -AA--A--TTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
1901856 AAATTAGGTTAGGGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1901885 AAATTAGGTTAGGGTTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1901913 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
1901942 AATTTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1901971 AAATTAGG
1 AAATTAGG
1901979 ATTTTTATTA
Statistics
Matches: 192, Mismatches: 5, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
23 17 0.09
24 5 0.03
26 2 0.01
28 33 0.17
29 107 0.56
30 28 0.15
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:1901858 original size:52 final size:52
Alignment explanation
Indices: 1901745--1901957 Score: 291
Period size: 52 Copynumber: 3.9 Consensus size: 52
1901735 AAATTATGTA
1901745 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--A--TTA-GG-TTAGGGTTTTTAATT
*
1901804 AAATTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
*
1901856 AAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-T----TTTTAATT
*
1901913 AAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1901958 AGGGTTTTTA
Statistics
Matches: 144, Mismatches: 5, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
52 57 0.40
53 3 0.02
54 3 0.02
56 2 0.01
57 49 0.34
58 2 0.01
59 28 0.19
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (52 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
Found at i:1901897 original size:57 final size:58
Alignment explanation
Indices: 1901745--1901978 Score: 383
Period size: 57 Copynumber: 4.1 Consensus size: 58
1901735 AAATTATGTA
1901745 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
1901804 AAATTAGGTTAAGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
*
1901856 AAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
*
1901913 AAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1901971 AAATTAGG
1 AAATTAGG
1901979 ATTTTTATTA
Statistics
Matches: 163, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
52 42 0.26
53 4 0.02
54 3 0.02
55 1 0.01
56 1 0.01
57 58 0.36
58 26 0.16
59 28 0.17
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (58 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:1901955 original size:23 final size:23
Alignment explanation
Indices: 1901815--1901957 Score: 106
Period size: 23 Copynumber: 5.5 Consensus size: 23
1901805 AATTAGGTTA
*
1901815 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAATTT
1901838 AGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGTTAGGGTTTTTAATT-AA-T---TT
* *
1901866 AGGGTTAAGGTTTTTAATTAAATT
1 A-GGTTAGGGTTTTTAATTAATTT
1901890 AGGTTAGGGTTAGGGTTTTAATTAAATTAGGTT
1 AGGTTAGGG-T----TTTTAATT-AA-T---TT
1901923 AGGGTTAGGGTTTTTAATTAATTT
1 A-GGTTAGGGTTTTTAATTAATTT
1901947 AGGTTAGGGTT
1 AGGTTAGGGTT
1901958 AGGGTTTTTA
Statistics
Matches: 98, Mismatches: 5, Indels: 34
0.72 0.04 0.25
Matches are distributed among these distances:
23 35 0.36
24 9 0.09
27 1 0.01
28 15 0.15
29 26 0.27
33 4 0.04
34 8 0.08
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAATTT
Found at i:1902090 original size:25 final size:25
Alignment explanation
Indices: 1902056--1902166 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
1902046 TTTCTATGCC
*
1902056 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
1902081 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
1902102 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
1902127 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
1902152 TATTACATCAAATAA
1 TATTACATCAAATAA
1902167 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:1902091 original size:71 final size:71
Alignment explanation
Indices: 1901984--1902168 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
1901974 TTAGGATTTT
* *
1901984 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTTAAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
1902049 CTATGCC
65 CTATGCC
* *
1902056 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTC
*
1902121 TATGCG
66 TATGCC
1902127 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1902169 AATTTAAATA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTC
TATGCC
Found at i:1902597 original size:18 final size:18
Alignment explanation
Indices: 1902570--1902604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1902560 CGGAAAAGGA
* *
1902570 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
1902588 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
1902605 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:1903266 original size:7 final size:7
Alignment explanation
Indices: 1903256--1903280 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1903246 TTATATACAT
1903256 AATACTA
1 AATACTA
1903263 AATACTA
1 AATACTA
1903270 AATACTA
1 AATACTA
1903277 AATA
1 AATA
1903281 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1904715 original size:29 final size:26
Alignment explanation
Indices: 1904674--1904732 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
1904664 GATGTCCTGG
*
1904674 AAAATGGACCATTCCGGTAAATAATTAA
1 AAAATGGACCATTCCGATAAAT--TTAA
* *
1904702 AAAATCGGCCCATTTCGATAAATTTAA
1 AAAAT-GGACCATTCCGATAAATTTAA
1904729 AAAA
1 AAAA
1904733 AAATGACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (26 bp):
AAAATGGACCATTCCGATAAATTTAA
Found at i:1905648 original size:20 final size:20
Alignment explanation
Indices: 1905619--1905656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1905609 ATGACTTAAA
*
1905619 TGTTAGGATTTAAGATTTGG
1 TGTTAAGATTTAAGATTTGG
*
1905639 TGTTAAGATTTAGGATTT
1 TGTTAAGATTTAAGATTT
1905657 AAGATTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
TGTTAAGATTTAAGATTTGG
Found at i:1905660 original size:14 final size:14
Alignment explanation
Indices: 1905621--1905665 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1905611 GACTTAAATG
1905621 TTAGGATTTAAGAT
1 TTAGGATTTAAGAT
1905635 TT-GG-TGTTAAGAT
1 TTAGGAT-TTAAGAT
1905648 TTAGGATTTAAGAT
1 TTAGGATTTAAGAT
1905662 TTAG
1 TTAG
1905666 AGTTAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 11 0.39
14 15 0.54
15 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TTAGGATTTAAGAT
Found at i:1905927 original size:32 final size:32
Alignment explanation
Indices: 1905891--1905953 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1905881 TAAACAGTTA
*
1905891 AATTTTGAAAATTTTATGAAAAGAGAAATAAC
1 AATTTTGAAAATTTGATGAAAAGAGAAATAAC
* * *
1905923 AATTTTTAAAATTTGATGAAATGATAAATAA
1 AATTTTGAAAATTTGATGAAAAGAGAAATAA
1905954 TATTTTATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (32 bp):
AATTTTGAAAATTTGATGAAAAGAGAAATAAC
Found at i:1905977 original size:132 final size:128
Alignment explanation
Indices: 1905841--1906117 Score: 326
Period size: 132 Copynumber: 2.1 Consensus size: 128
1905831 ATCATTTCAT
*
1905841 AAACAGTTAAAATTAAAACTATCAAAATAT-TTAAAATATTTAAACAGTT-AAATTTTGAAAATT
1 AAACAGTAAAAATTAAAA-TAT-AAAATATCTT--AATATTTAAACAGTTAAAATTTT--AAATT
* *
1905904 TTATGAAAAGAGAAATAACAA-TTTTTAAAATTTGATGAAATGATAAATAATATTTTATCCTTCA
60 TTATGAAAAGAGAAAT-ACAATTTTTTAAAATTTGATGAAAGGATAAATAATATTTTATCCTTAA
1905968 AATTA
124 AATTA
* **
1905973 AAACAGTCAAAATATTTAAAATATTATTTATCCTTAATATTTAAACAGTTAAAATTTTAAATTTT
1 AAACAGT-AAAA-A-TTAAAATATAAAATAT-CTTAATATTTAAACAGTTAAAATTTTAAATTTT
* * * * *
1906038 ATGAAAGGATAAATGCAATTTTTTAAAATTTGATGAAAGGATGAATGATATTTTATCCTTAAAAT
62 ATGAAAAGAGAAATACAATTTTTTAAAATTTGATGAAAGGATAAATAATATTTTATCCTTAAAAT
1906103 TA
127 TA
*
1906105 AAACAGTCAAAAT
1 AAACAGTAAAAAT
1906118 ATTTAATTTA
Statistics
Matches: 126, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
129 1 0.01
130 1 0.01
131 6 0.05
132 77 0.61
133 22 0.17
134 11 0.09
135 8 0.06
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (128 bp):
AAACAGTAAAAATTAAAATATAAAATATCTTAATATTTAAACAGTTAAAATTTTAAATTTTATGA
AAAGAGAAATACAATTTTTTAAAATTTGATGAAAGGATAAATAATATTTTATCCTTAAAATTA
Found at i:1906003 original size:42 final size:42
Alignment explanation
Indices: 1905948--1906033 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 42
1905938 ATGAAATGAT
1905948 AAATAATATTTTATCCTTCAA-ATTAAAACAGTCAAAATATTTA
1 AAATAATATTTTATCCTT-AATATTAAAACAGTCAAAAT-TTTA
* * *
1905991 AAATATTA-TTTATCCTTAATATTTAAACAGTTAAAATTTTA
1 AAATAATATTTTATCCTTAATATTAAAACAGTCAAAATTTTA
1906032 AA
1 AA
1906034 TTTTATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
41 8 0.21
42 24 0.62
43 7 0.18
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (42 bp):
AAATAATATTTTATCCTTAATATTAAAACAGTCAAAATTTTA
Found at i:1906156 original size:132 final size:132
Alignment explanation
Indices: 1905878--1906141 Score: 336
Period size: 132 Copynumber: 2.0 Consensus size: 132
1905868 TATTTAAAAT
1905878 ATTTAAACAGTT-AAATTTTGAAAATTTTATGAAAAGAGAAATAACAATTTTTAAAATTTGATGA
1 ATTT-AACAGTTAAAATTTT-AAAATTTTATGAAAAGAGAAATAACAATTTTTAAAATTTGATGA
* * ** * *
1905942 AATGATAAATAATATTTTATCCTTCAAATTAAAACAGTCAAAATATTTAAAATATTATTTATCCT
64 AAGGATAAATAATATTTTATCCTTAAAATTAAAACAGTCAAAATATTTAAAATAAAATTAAACCT
* *
1906007 TAAT
129 AAAG
* * *
1906011 ATTTAAACAGTTAAAATTTT-AAATTTTATGAAAGGATAAAT-GCAATTTTTTAAAATTTGATGA
1 ATTT-AACAGTTAAAATTTTAAAATTTTATGAAAAGAGAAATAACAA-TTTTTAAAATTTGATGA
* * **
1906074 AAGGATGAATGATATTTTATCCTTAAAATTAAAACAGTCAAAATATTTAATTTAAAATTAAACCT
64 AAGGATAAATAATATTTTATCCTTAAAATTAAAACAGTCAAAATATTTAAAATAAAATTAAACCT
1906139 AAA
129 AAA
1906142 AGACTTTTTA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
131 3 0.03
132 93 0.81
133 12 0.10
134 7 0.06
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.38
Consensus pattern (132 bp):
ATTTAACAGTTAAAATTTTAAAATTTTATGAAAAGAGAAATAACAATTTTTAAAATTTGATGAAA
GGATAAATAATATTTTATCCTTAAAATTAAAACAGTCAAAATATTTAAAATAAAATTAAACCTAA
AG
Found at i:1906725 original size:39 final size:40
Alignment explanation
Indices: 1906648--1906743 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 40
1906638 GCGTTTGGAT
*
1906648 GAAAAACGCCACTAAAATCGAGCATTAGCGGCACTTTTTA
1 GAAAAACGCCGCTAAAATCGAGCATTAGCGGCACTTTTTA
* ***
1906688 -AAAAACGCCGCTAAAGAT-GAGCATTAGTGGTGTTTTTTA
1 GAAAAACGCCGCTAAA-ATCGAGCATTAGCGGCACTTTTTA
* *
1906727 GAAAAGCGCCGCAAAAA
1 GAAAAACGCCGCTAAAA
1906744 ACCTAATCCC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 32 0.68
40 15 0.32
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.22
Consensus pattern (40 bp):
GAAAAACGCCGCTAAAATCGAGCATTAGCGGCACTTTTTA
Found at i:1906838 original size:41 final size:41
Alignment explanation
Indices: 1906781--1906932 Score: 216
Period size: 41 Copynumber: 3.7 Consensus size: 41
1906771 ACCTTTCGGG
* *
1906781 GCTTTAGCAGCGTTTTTGAAAAAGCACCGCTAATGTTCAGA
1 GCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* *
1906822 GCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGA
1 GCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* *
1906863 GCTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAATGCTC-GG
1 GCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* * *
1906903 GATTTAGCGGCGTTTTTGAAAAATCGCCGC
1 GCTTTAGCAGCGTTTTTGAAAAAGCGCCGC
1906933 AAAAACATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 27 0.27
41 72 0.73
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (41 bp):
GCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
Found at i:1906964 original size:20 final size:19
Alignment explanation
Indices: 1906939--1906980 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1906929 CCGCAAAAAC
1906939 ATTTTATATGTCTATTTACT
1 ATTTTATATGTCTATTTA-T
* *
1906959 ATTTTATTTGTTTATTTAT
1 ATTTTATATGTCTATTTAT
1906978 ATT
1 ATT
1906981 AATTAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTATATGTCTATTTAT
Found at i:1907140 original size:14 final size:14
Alignment explanation
Indices: 1907115--1907151 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1907105 GGGTTTAATA
1907115 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
1907129 TATATGGTTTAGTG
1 TATATGGTTTAGGG
*
1907143 TTTATGGTT
1 TATATGGTT
1907152 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:1907226 original size:14 final size:15
Alignment explanation
Indices: 1907199--1907232 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1907189 TAAGGTTTAT
1907199 AGATTATGGGATTAG
1 AGATTATGGGATTAG
1907214 AGATTAT-GGATTAG
1 AGATTATGGGATTAG
*
1907228 GGATT
1 AGATT
1907233 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (15 bp):
AGATTATGGGATTAG
Found at i:1907437 original size:21 final size:21
Alignment explanation
Indices: 1907379--1907437 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1907369 TAAATAATGT
* *
1907379 TTAGGGTTTAGAGGTTAGGGG
1 TTAGGGGTTAGAGGTTAGGGA
* *
1907400 TTGGGGGCTAGTA-GTTAGGGA
1 TTAGGGGTTAG-AGGTTAGGGA
1907421 TTAGGGGTTAGAGGTTA
1 TTAGGGGTTAGAGGTTA
1907438 AGAGTTAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.46, T:0.32
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAGGGA
Found at i:1907562 original size:7 final size:7
Alignment explanation
Indices: 1907550--1907589 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
1907540 ATTGTAAAAG
1907550 AGGGGTT
1 AGGGGTT
1907557 AGGGGTT
1 AGGGGTT
*
1907564 AGAGGTT
1 AGGGGTT
1907571 AGGGGTT
1 AGGGGTT
1907578 AGGGGTTT
1 AGGGG-TT
1907586 AGGG
1 AGGG
1907590 CTTATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.17, C:0.00, G:0.55, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:1908706 original size:11 final size:11
Alignment explanation
Indices: 1908690--1908715 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1908680 TTTTCTTCAT
1908690 TTTTCTTTTTG
1 TTTTCTTTTTG
1908701 TTTTCTTTTTG
1 TTTTCTTTTTG
1908712 TTTT
1 TTTT
1908716 ACAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:1910297 original size:13 final size:13
Alignment explanation
Indices: 1910279--1910321 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1910269 TTTTATTTTG
*
1910279 ATTTAAAATTAGA
1 ATTTAAAATTAAA
*
1910292 ATTTAAAAATAAA
1 ATTTAAAATTAAA
* *
1910305 ATTCAAAATTACA
1 ATTTAAAATTAAA
1910318 ATTT
1 ATTT
1910322 TGCATTGAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:1912738 original size:43 final size:43
Alignment explanation
Indices: 1912642--1912793 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 43
1912632 TTATGTTTTT
* * *
1912642 AGCGGCGTTTGTGA-AAAAGCGTCGCTAAAGGTCAT--TCTTC
1 AGCGGCGTTTGTGAGAAAAGCGCCACAAAAGGTCATGATCTTC
* * ** * *
1912682 ATAGTGGCATTTGTG-GTTGAAGCGCCACAAAAGGTCATGATTTTT
1 --AGCGGCGTTTGTGAG-AAAAGCGCCACAAAAGGTCATGATCTTC
* *
1912727 AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTC
1 AGCGGCGTTTGTGAGAAAAGCGCCACAAAAGGTCATGATCTTC
* * *
1912770 AGCGGCGATTGTAACAAAAGCGCC
1 AGCGGCGTTTGTGAGAAAAGCGCC
1912794 GCTAAAGATC
Statistics
Matches: 85, Mismatches: 20, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
42 11 0.13
43 70 0.82
44 1 0.01
45 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (43 bp):
AGCGGCGTTTGTGAGAAAAGCGCCACAAAAGGTCATGATCTTC
Found at i:1912791 original size:86 final size:86
Alignment explanation
Indices: 1912637--1912846 Score: 205
Period size: 86 Copynumber: 2.5 Consensus size: 86
1912627 TAAAGTTATG
* * *****
1912637 TTTTTAGCGGCGTTTGTGA-AAAAGCGTCGCTAAAGGTCATTCTTCATAGTGGCATTTGTGGTTG
1 TTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATTCTTCA-AGCGGCATTTGTAACAA
*
1912701 AAGCGCCACAAAAGGTCAT-GA
65 AAGCGCCACAAAAGATCATGGA
1912722 TTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTC-AGCGGCGA-TTGTAAC
1 TTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCAT--TCTTCAAGCGGC-ATTTGTAAC
* * * *
1912785 AAAAGCGCCGCTAAAGATCTTGGC
63 AAAAGCGCCACAAAAGATCATGGA
* * * *
1912809 CTTTT-GTGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTC
1 TTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTC
1912847 CTTGCCTTGA
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
85 19 0.18
86 74 0.71
87 6 0.06
88 5 0.05
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (86 bp):
TTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATTCTTCAAGCGGCATTTGTAACAAA
AGCGCCACAAAAGATCATGGA
Found at i:1912794 original size:43 final size:43
Alignment explanation
Indices: 1912701--1912800 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
1912691 TTTGTGGTTG
* * * * * * *
1912701 AAGCGCCACAAAAGGTCATGATTTTTAGCGGCGTTTGTGAGAA
1 AAGCGCCGCTAAAGGTCATGATCTTCAGCGGCGATTGTAACAA
1912744 AAGCGCCGCTAAAGGTCATGATCTTCAGCGGCGATTGTAACAA
1 AAGCGCCGCTAAAGGTCATGATCTTCAGCGGCGATTGTAACAA
1912787 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
1912801 ATCTTGGCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGATCTTCAGCGGCGATTGTAACAA
Found at i:1912866 original size:43 final size:42
Alignment explanation
Indices: 1912727--1912867 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 42
1912717 CATGATTTTT
* *
1912727 AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTC
1 AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTG-CCTTC
* * * * *
1912770 AGCGGCGATTGTAACAAAAGCGCCGCTAAAGATCTTGGCCTTT
1 AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTT-GCCTTC
* * * * *
1912813 TGTGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTTGCCTTG
1 AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGT-CTTGCCTTC
1912856 AGCGGCGTTTGT
1 AGCGGCGTTTGT
1912868 TTCTAAAAAT
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 73 0.95
44 4 0.05
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (42 bp):
AGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGCCTTC
Found at i:1913463 original size:96 final size:97
Alignment explanation
Indices: 1913293--1913480 Score: 297
Period size: 96 Copynumber: 1.9 Consensus size: 97
1913283 GATTCAGCTC
* * * *
1913293 CCATATCATATTCTACCATTAAACCATGATCCCCTGATATTTACCAGCTGGGAGAGTTGGTGATC
1 CCATATCATATTCTACCATTAAACCATGATCCCCTGATACTCACCAGCTGGGAGAGTCGGGGATC
1913358 ATGTTGATAGCGATCACCATGGAGTTTATGTA
66 ATGTTGATAGCGATCACCATGGAGTTTATGTA
* *
1913390 CCATCTCATATTCTACCATTAAACCATGATCCCTTGAT-CTCACCAGCTGGGAGAGTCGGGGATC
1 CCATATCATATTCTACCATTAAACCATGATCCCCTGATACTCACCAGCTGGGAGAGTCGGGGATC
* *
1913454 ATGTTGATAGTGATGACCATGGAGTTT
66 ATGTTGATAGCGATCACCATGGAGTTT
1913481 GTAAACCAGC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 47 0.57
97 36 0.43
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (97 bp):
CCATATCATATTCTACCATTAAACCATGATCCCCTGATACTCACCAGCTGGGAGAGTCGGGGATC
ATGTTGATAGCGATCACCATGGAGTTTATGTA
Found at i:1915314 original size:114 final size:113
Alignment explanation
Indices: 1915173--1915836 Score: 736
Period size: 114 Copynumber: 5.9 Consensus size: 113
1915163 TGATTTCCAA
1915173 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTTTCGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTT-CCGAGCTTTCGGGGATTTAGCGGCG
* *
1915237 TTTTCAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
65 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
* * * ** * * * *
1915286 AAAACGCTGCAAAAAAACCTAAGCCCAACAACGTTGTTTTCTGAGCATTCGGGGATTTAGCAGTG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTCCGAGCTTTCGGGGATTTAGCGGCG
* *
1915351 TTTTTAATAAAGCGCCGCTAATGCTCAGGGATTTAGCGGTGTTTTTGAG
65 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
** * * *
1915400 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGATCATTCGGGGATTTAGCGACG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTCCGAGCTTTCGGGGATTTAGCGGCG
* * * * ** * * *
1915465 TTTTTAATAAAGCACTGCTAATTCTCAGGTCTTTTGGCGGCATTTTTTAG
65 TTTTTAAGAAAGCGCCGCTAATGCTCAGG-GATTTAGCGGCGTTTTTGAG
* *
1915515 AAAGCGCTGCAAAAAAACCTAAGCCCAACGA---CG---CCGAGCTTTTCGGGGATTTAGTGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCCGAGC-TTTCGGGGATTTAGCGGCG
* * *
1915574 TTTTTAGGAAAGCGCCGCTAATGCTCATGGATTTAGCGACGTTTTTGAG
65 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
** ** *
1915623 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTTAATATTTCAGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTC-CGAGCTTTCGGGGATTTAGCGGCG
* * *
1915688 TTTTTAA-AGAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGGG
65 TTTTTAAGA-AAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
* * * * * * *
1915737 AAAACGCGGCAAGAAAAA-CTAAGCCCAAC-AGCGCCATTTTCTATGCTTTCAGAGATTTAGCGG
1 AAAGCGCCGCAA-AAAAACCTAAGCCCAACGA-CGCCGTTTCCGA-GCTTTCGGGGATTTAGCGG
*
1915800 CGTTTTAAAGAAAGCGCCGCTAATGCTCAGGGATTTA
63 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTA
1915837 AAATAATTTA
Statistics
Matches: 460, Mismatches: 75, Indels: 31
0.81 0.13 0.05
Matches are distributed among these distances:
108 47 0.10
109 39 0.08
111 2 0.00
112 2 0.00
113 11 0.02
114 305 0.66
115 54 0.12
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (113 bp):
AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCCGAGCTTTCGGGGATTTAGCGGCGT
TTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
Found at i:1915608 original size:223 final size:222
Alignment explanation
Indices: 1915173--1915836 Score: 771
Period size: 223 Copynumber: 2.9 Consensus size: 222
1915163 TGATTTCCAA
** * *
1915173 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTTTCGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTATTGATCATTCGGGGATTTAGCGGCG
*
1915237 TTTTCAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAACGCTGCAAAAAA
66 TTTTTAA-AAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAACGCTGCAAAAAA
* * *
1915302 ACCTAAGCCCAACAACGTTGTTTTCTGAGCATTCGGGGATTTAGCAGTGTTTTTAATAAAGCGCC
130 ACCTAAGCCCAACAAC--TG---TCCGAGCATTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCC
**
1915367 GCTAATGCTCAGGGATTTAGCGGTGTTTTTGAG
190 GCTAATGCTCAGGGATTTAGCGACGTTTTTGAG
* *
1915400 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGATCATTCGGGGATTTAGCGACG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTATTGATCATTCGGGGATTTAGCGGCG
* * * * * * * *
1915465 TTTTTAATAAAGCACTGCTAATTCTCAGGTCTTTTGGCGGCATTTTTTAGAAAGCGCTGCAAAAA
66 TTTTTAA-AAAGCGCCGCTAATGCTCAGGGC-TTTAGCGGCGTTTTTGAGAAAACGCTGCAAAAA
* * ** *
1915530 AACCTAAGCCCAACGAC-G-CCGAGCTTTTCGGGGATTTAGTGGCGTTTTTAGGAAAGCGCCGCT
129 AACCTAAGCCCAACAACTGTCCGAGC-ATTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCT
*
1915593 AATGCTCATGGATTTAGCGACGTTTTTGAG
193 AATGCTCAGGGATTTAGCGACGTTTTTGAG
* * *
1915623 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTCTTAAT-ATTTCAGGGATTTAGCGGC
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTATTGATCA-TTCGGGGATTTAGCGGC
* * *
1915687 GTTTTTAAAGAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGGGAAAACGCGGCAAGAA
65 GTTTTTAAA-AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAACGCTGCAA-AA
* * * * * * * * *
1915752 AAA-CTAAGCCCAACAGCGCCATTTTCTATGCTTTCAGAGATTTAGCGGCGTTTTAAAGAAAGCG
128 AAACCTAAGCCCAACA---AC-TGTCCGA-GCATTCGGGGATTTAGCAGCGTTTTTAAGAAAGCG
1915816 CCGCTAATGCTCAGGGATTTA
188 CCGCTAATGCTCAGGGATTTA
1915837 AAATAATTTA
Statistics
Matches: 371, Mismatches: 53, Indels: 25
0.83 0.12 0.06
Matches are distributed among these distances:
222 41 0.11
223 148 0.40
225 1 0.00
226 1 0.00
227 10 0.03
228 123 0.33
229 47 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (222 bp):
AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTATTGATCATTCGGGGATTTAGCGGCG
TTTTTAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAACGCTGCAAAAAAA
CCTAAGCCCAACAACTGTCCGAGCATTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAAT
GCTCAGGGATTTAGCGACGTTTTTGAG
Found at i:1916116 original size:38 final size:37
Alignment explanation
Indices: 1916072--1916159 Score: 133
Period size: 38 Copynumber: 2.4 Consensus size: 37
1916062 GGATTTAAGG
*
1916072 TTTAAGGGTTA-GGTGTTATGCTTTAGGGGTTAGGGGGA
1 TTTAAGGGTTATGG-GTTATGCTTTAAGGGTTA-GGGGA
1916110 TTTAAGGGTTATGGGTTATGCTTTAAGGGTTAGGGGA
1 TTTAAGGGTTATGGGTTATGCTTTAAGGGTTAGGGGA
*
1916147 TTTATGGGTTATG
1 TTTAAGGGTTATG
1916160 AATTTGGGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 17 0.36
38 28 0.60
39 2 0.04
ACGTcount: A:0.19, C:0.02, G:0.39, T:0.40
Consensus pattern (37 bp):
TTTAAGGGTTATGGGTTATGCTTTAAGGGTTAGGGGA
Found at i:1916170 original size:30 final size:31
Alignment explanation
Indices: 1916118--1916175 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1916108 GATTTAAGGG
*
1916118 TTATGGGTTATGCTTTAAGGG-TTAGGGGAT
1 TTATGGGTTATGATTTAAGGGTTTAGGGGAT
*
1916148 TTATGGGTTATGAATTT-GGGGTTTAGGG
1 TTATGGGTTATG-ATTTAAGGGTTTAGGG
1916176 TTTCAACGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.19, C:0.02, G:0.38, T:0.41
Consensus pattern (31 bp):
TTATGGGTTATGATTTAAGGGTTTAGGGGAT
Found at i:1916474 original size:21 final size:21
Alignment explanation
Indices: 1916450--1916494 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1916440 AATAAAATTT
*
1916450 TTAGGGGTTATGCTTTAGGGG
1 TTAGGGGTTATGCTTTAAGGG
*
1916471 TTAGGGTTTATGCTTTAAGGG
1 TTAGGGGTTATGCTTTAAGGG
1916492 TTA
1 TTA
1916495 AGGAGGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.42
Consensus pattern (21 bp):
TTAGGGGTTATGCTTTAAGGG
Found at i:1918691 original size:9 final size:9
Alignment explanation
Indices: 1918677--1918836 Score: 90
Period size: 9 Copynumber: 18.4 Consensus size: 9
1918667 ATTTCACATA
1918677 ATAACTTAC
1 ATAACTTAC
1918686 ATAACTTAC
1 ATAACTTAC
1918695 ATAACTTA-
1 ATAACTTAC
* *
1918703 ACAACTCAC
1 ATAACTTAC
*
1918712 ATAATTTAC
1 ATAACTTAC
1918721 ATAA--TAC
1 ATAACTTAC
1918728 ATATA-TATATGTC
1 ATA-ACT-TA---C
*
1918741 ATAACGTA-
1 ATAACTTAC
*
1918749 ACAACTTA-
1 ATAACTTAC
* *
1918757 ACAACTCAC
1 ATAACTTAC
*
1918766 ATAATTTAC
1 ATAACTTAC
*
1918775 ATAATTTAC
1 ATAACTTAC
1918784 ATAA--TAC
1 ATAACTTAC
1918791 ATAACTTA-
1 ATAACTTAC
1918799 ATAACTTA-
1 ATAACTTAC
* *
1918807 ACAACTCAC
1 ATAACTTAC
*
1918816 ATAATTTAC
1 ATAACTTAC
1918825 ATAACTTA-
1 ATAACTTAC
1918833 ATAA
1 ATAA
1918837 TTTTAAAATA
Statistics
Matches: 121, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
7 13 0.11
8 38 0.31
9 61 0.50
10 2 0.02
12 3 0.02
13 4 0.03
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1918696 original size:21 final size:21
Alignment explanation
Indices: 1918654--1918698 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1918644 ATGTCCAACT
* *
1918654 TAATAACTTATATATTTCACA
1 TAATAACTTACATACTTCACA
1918675 TAATAACTTACATAACTT-ACA
1 TAATAACTTACAT-ACTTCACA
1918696 TAA
1 TAA
1918699 CTTAACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAACTTACATACTTCACA
Found at i:1918713 original size:17 final size:18
Alignment explanation
Indices: 1918677--1918721 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1918667 ATTTCACATA
* *
1918677 ATAACTTACATAACTTAC
1 ATAACTTACACAACTCAC
1918695 ATAACTTA-ACAACTCAC
1 ATAACTTACACAACTCAC
*
1918712 ATAATTTACA
1 ATAACTTACA
1918722 TAATACATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAACTTACACAACTCAC
Found at i:1918815 original size:50 final size:49
Alignment explanation
Indices: 1918683--1918837 Score: 202
Period size: 50 Copynumber: 3.0 Consensus size: 49
1918673 CATAATAACT
*
1918683 TACATAACTTACATAACTTAACAACTCACATAATTTACATAATACATATATATA
1 TACATAACTTA-ATAACTTAACAACTCACATAATTTACATAAT--TTA-ATA-A
* * *
1918737 TGTCATAACGTAACAACTTAACAACTCACATAATTTACATAATTTACATAA
1 T-ACATAACTTAATAACTTAACAACTCACATAATTTACATAATTTA-ATAA
*
1918788 TACATAACTTAATAACTTAACAACTCACATAATTTACATAACTTAATAA
1 TACATAACTTAATAACTTAACAACTCACATAATTTACATAATTTAATAA
1918837 T
1 T
1918838 TTTAAAATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
49 5 0.05
50 40 0.44
51 2 0.02
52 5 0.05
54 31 0.34
55 8 0.09
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (49 bp):
TACATAACTTAATAACTTAACAACTCACATAATTTACATAATTTAATAA
Found at i:1918954 original size:17 final size:17
Alignment explanation
Indices: 1918932--1919003 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
1918922 ATAACTCACA
1918932 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
1918949 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
1918966 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
1918982 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
1919000 TAAT
1 TAAT
1919004 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:1918976 original size:25 final size:26
Alignment explanation
Indices: 1918940--1919003 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
1918930 CATAATAACT
*
1918940 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
1918965 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
1918991 TACATAACTTAAT
1 TACATAACTTAAT
1919004 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:1928121 original size:27 final size:27
Alignment explanation
Indices: 1928091--1928142 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1928081 AAAGATTGTT
*
1928091 AAAACTCTTCTAAAAG-AAAACTCAAGA
1 AAAACTCTT-GAAAAGAAAAACTCAAGA
*
1928118 AAAATTCTTGAAAAGAAAAACTCAA
1 AAAACTCTTGAAAAGAAAAACTCAA
1928143 AGAGAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (27 bp):
AAAACTCTTGAAAAGAAAAACTCAAGA
Found at i:1929200 original size:115 final size:115
Alignment explanation
Indices: 1928913--1929296 Score: 372
Period size: 114 Copynumber: 3.4 Consensus size: 115
1928903 AAAATAAGCA
* * * * * *
1928913 TTAGCGGCGATTTTAATAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCGTTTTCGCG-AAAACG
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTT-GAGTAAAGCG
* * * *
1928977 CCAC-AA-AAAACCTAATCCCAACGACGCCGTTTAATGAG-CTTCGGGGCT
65 CCGCAAAGAAAACCTAAGCCCAACGACGCCGTTTTATGAGCCTTTGGGGCT
* * * * * * * *
1929025 TTCGCGGCGTTTGTAAGT-AAGTGCCGCTGATG-TTCCGGGCTTTTGCGGTGTTTTCAGTAAAGC
1 TTAGCGGCGTTT-TTAGTAAAGCGCCGCTAATGCTT-AGGGCTTTAGCGGCGTTTTGAGTAAAGC
* *
1929088 GCCGCAAAGAAAACCTAAGCCC-ACTGACGCCGTTTTCTGAGCCTTTGGGTCT
64 GCCGCAAAGAAAACCTAAGCCCAAC-GACGCCGTTTTATGAGCCTTTGGGGCT
* *
1929140 TTAGTGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGGGTAAAGCGC
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGAGTAAAGCGC
** * * * * *
1929205 CGCAAAG-GGACCTAAGCCCGACGATGCCGTTTTATTAGCTTTTTGGGGAT
66 CGCAAAGAAAACCTAAGCCCAACGACGCCGTTTTATGAGC-CTTTGGGGCT
* * *
1929255 TTAGTGG-TTTTTTAGTGAAGCGCCGCTAATGCTTAGGGCTTT
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTT
1929297 GGACAAAGTT
Statistics
Matches: 222, Mismatches: 39, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
111 2 0.01
112 46 0.21
113 7 0.03
114 87 0.39
115 78 0.35
116 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (115 bp):
TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGAGTAAAGCGC
CGCAAAGAAAACCTAAGCCCAACGACGCCGTTTTATGAGCCTTTGGGGCT
Found at i:1930592 original size:21 final size:21
Alignment explanation
Indices: 1930566--1930611 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1930556 AACTTAAAGT
*
1930566 AGAGGCGGCAGCGAGGGAAGC
1 AGAGGCGGCAGCGAGAGAAGC
* * *
1930587 AGAGGCTGTAGCGAGAGAAGT
1 AGAGGCGGCAGCGAGAGAAGC
1930608 AGAG
1 AGAG
1930612 CAGAGCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.48, T:0.07
Consensus pattern (21 bp):
AGAGGCGGCAGCGAGAGAAGC
Found at i:1930995 original size:42 final size:42
Alignment explanation
Indices: 1930929--1931090 Score: 234
Period size: 42 Copynumber: 3.8 Consensus size: 42
1930919 GTTTTTATAT
* * *
1930929 AAAAGCGCCGCTAACGAACATGTTCTTTAGCGGCACTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * *
1930971 AAAAACACCGCTAAAGAACATGTTCTTTAGAGGTGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* *
1931013 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGTCGCTTAGAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AA
*
1931056 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
1931091 TTTTTGTTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 71 0.66
43 36 0.34
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:1932132 original size:44 final size:42
Alignment explanation
Indices: 1932055--1932304 Score: 202
Period size: 43 Copynumber: 5.8 Consensus size: 42
1932045 AAATCCTAAA
* * ** *
1932055 ATTAGTGGCGTTT-TGAGAAAAAGCACCTTTAAAGATCACAAAAC
1 ATTAGCGGCGTTTGTGAG-AAAAGCGCCGCTAAAGA--ACATAAC
* *
1932099 AATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATGAC
1 ATTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATAAC
*
1932141 ATTTAGCGGCGTTTGTGA-AAAATGCGCCGCTAAAGAACATTACC
1 A-TTAGCGGCGTTTGTGAGAAAA-GCGCCGCTAAAGAACA-TAAC
* * * * *
1932185 TTTAGCGGCGCTTGTGAAAAAACCGCCGCTAAAGAACATTACC
1 ATTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACA-TAAC
* * * *
1932228 TTTCGCGGCGTTTATGA-ATAAAGCGCCGCTAAAGAACATTACC
1 ATTAGCGGCGTTTGTGAGA-AAAGCGCCGCTAAAGAACA-TAAC
* * *
1932271 TTTAGCGGCGCTTGTG-GATAAAGCGCCGCAAAAG
1 ATTAGCGGCGTTTGTGAGA-AAAGCGCCGCTAAAG
1932305 TTAGCGGCGT
Statistics
Matches: 178, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
42 11 0.06
43 132 0.74
44 31 0.17
45 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (42 bp):
ATTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATAAC
Found at i:1932155 original size:43 final size:42
Alignment explanation
Indices: 1932101--1932304 Score: 282
Period size: 43 Copynumber: 4.7 Consensus size: 42
1932091 CACAAAACAA
* *
1932101 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATGACATT
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGAACATTACCTT
1932144 TAGCGGCGTTTGTGAAAAATGCGCCGCTAAAGAACATTACCTT
1 TAGCGGCGTTTGTGAAAAA-GCGCCGCTAAAGAACATTACCTT
* *
1932187 TAGCGGCGCTTGTGAAAAAACCGCCGCTAAAGAACATTACCTT
1 TAGCGGCGTTTGTG-AAAAAGCGCCGCTAAAGAACATTACCTT
* *
1932230 TCGCGGCGTTTATGAATAAAGCGCCGCTAAAGAACATTACCTT
1 TAGCGGCGTTTGTGAA-AAAGCGCCGCTAAAGAACATTACCTT
* * *
1932273 TAGCGGCGCTTGTGGATAAAGCGCCGCAAAAG
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAG
1932305 TTAGCGGCGT
Statistics
Matches: 144, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
42 6 0.04
43 131 0.91
44 7 0.05
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGAACATTACCTT
Found at i:1932711 original size:22 final size:23
Alignment explanation
Indices: 1932679--1932721 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1932669 TAGTGTTAAA
*
1932679 TTTTTATAAATTATAA-ATAATT
1 TTTTTAAAAATTATAATATAATT
*
1932701 TTTTTAAAAATTTTAATATAA
1 TTTTTAAAAATTATAATATAA
1932722 AAATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTTAAAAATTATAATATAATT
Found at i:1935359 original size:34 final size:32
Alignment explanation
Indices: 1935319--1935405 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
1935309 TCCAATGCTT
1935319 AAATCAATTCGGCAATATATATGTATAC-ATATGC
1 AAATCAATTCGGCAATATATA--TAT-CTATATGC
* * **
1935353 AAATCAATTCGACAATGTATATATCTATATTT
1 AAATCAATTCGGCAATATATATATCTATATGC
*
1935385 AAATCAATTTGGCAATATATA
1 AAATCAATTCGGCAATATATA
1935406 AAACATATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
31 1 0.02
32 25 0.56
34 19 0.42
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (32 bp):
AAATCAATTCGGCAATATATATATCTATATGC
Found at i:1940267 original size:23 final size:23
Alignment explanation
Indices: 1940236--1940347 Score: 92
Period size: 23 Copynumber: 5.1 Consensus size: 23
1940226 GGCTTTGCCG
* *
1940236 ATCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
*
1940259 ATCAGGCACTTTATGTGTCGTA-
1 ATCAGGCACCTTATGTGTCGTAT
***
1940281 ATTCAGGCACCCCGTGTGTCGTAT
1 A-TCAGGCACCTTATGTGTCGTAT
**
1940305 -T-AGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
1940325 -TCAGGCA-CTTATGTGACGTAT
1 ATCAGGCACCTTATGTGTCGTAT
1940346 AT
1 AT
1940348 TGATCAGGTA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.15
21 23 0.31
22 3 0.04
23 38 0.51
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:1940320 original size:44 final size:44
Alignment explanation
Indices: 1940249--1940332 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
1940239 AAGCACTTTA
* *
1940249 TGTGTCGTATATCAGGCACTTTATGTGTCGTAATTCAGGCACCCCG
1 TGTGTCGTATATCAGGCACCTCATGTGTCGT--TTCAGGCACCCCG
*
1940295 TGTGTCGTAT-T-AGGCACCTCGTGTGTCGTTTCAGGCAC
1 TGTGTCGTATATCAGGCACCTCATGTGTCGTTTCAGGCAC
1940333 TTATGTGACG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 9 0.26
44 15 0.43
45 1 0.03
46 10 0.29
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (44 bp):
TGTGTCGTATATCAGGCACCTCATGTGTCGTTTCAGGCACCCCG
Found at i:1943835 original size:51 final size:51
Alignment explanation
Indices: 1943759--1943861 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
1943749 TTTTATTAAA
*
1943759 GTTGATGCTGTGATATTCATGCAAGAGGTGAAACTAATCGAACGTCTATGG
1 GTTGATGCTGTGATATTCATGCAAGAGGTGAAACCAATCGAACGTCTATGG
*
1943810 GTTGATGCTGTGATATTCATGCAAGAGGTGAAACCAATTGAACGTCTATGG
1 GTTGATGCTGTGATATTCATGCAAGAGGTGAAACCAATCGAACGTCTATGG
1943861 G
1 G
1943862 CCAGTTTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (51 bp):
GTTGATGCTGTGATATTCATGCAAGAGGTGAAACCAATCGAACGTCTATGG
Found at i:1944109 original size:41 final size:41
Alignment explanation
Indices: 1944052--1944135 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
1944042 TATCTAATGT
1944052 CTTCTCTTGTCCGCTAATATAGGTTTTGTATACAAAATTGA
1 CTTCTCTTGTCCGCTAATATAGGTTTTGTATACAAAATTGA
*
1944093 CTTCTCTTGTCTGCTAATATAGGTTTTGTATACAAAATTGA
1 CTTCTCTTGTCCGCTAATATAGGTTTTGTATACAAAATTGA
1944134 CT
1 CT
1944136 AATTTGACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (41 bp):
CTTCTCTTGTCCGCTAATATAGGTTTTGTATACAAAATTGA
Found at i:1951703 original size:22 final size:22
Alignment explanation
Indices: 1951676--1951725 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1951666 ACTGAAACTA
1951676 CATGAATTTGAGTTAAAAAGGG
1 CATGAATTTGAGTTAAAAAGGG
* *
1951698 CATGAATTTTAGTTAAAAATGG
1 CATGAATTTGAGTTAAAAAGGG
1951720 CATGAA
1 CATGAA
1951726 AAAGTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (22 bp):
CATGAATTTGAGTTAAAAAGGG
Found at i:1953842 original size:16 final size:15
Alignment explanation
Indices: 1953811--1953844 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1953801 GTTTAAAAGC
1953811 AAATAAATTATTAAA
1 AAATAAATTATTAAA
1953826 AAATAAAATT-TTAAA
1 AAAT-AAATTATTAAA
1953841 AAAT
1 AAAT
1953845 TGGTTCAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAATTATTAAA
Found at i:1958746 original size:22 final size:20
Alignment explanation
Indices: 1958694--1958746 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1958684 AATGTATTAT
*
1958694 TATAAAATTTTATATATGAA
1 TATAAAATTTTATATATAAA
** *
1958714 TATAACGTTTTTTATATAAA
1 TATAAAATTTTATATATAAA
1958734 TAATTAAAATTTT
1 T-A-TAAAATTTT
1958747 CTGTTTCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TATAAAATTTTATATATAAA
Found at i:1958988 original size:17 final size:18
Alignment explanation
Indices: 1958947--1959011 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 18
1958937 TCTTATAAAT
1958947 AATAATAAATATATATAA
1 AATAATAAATATATATAA
1958965 AATAATAAA-ATCAT-TAA
1 AATAATAAATAT-ATATAA
* * *
1958982 TATAATAAACA-ATAAAA
1 AATAATAAATATATATAA
*
1958999 AAT-ATAGATATAT
1 AATAATAAATATAT
1959012 GAGGTAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 7 0.18
17 19 0.50
18 12 0.32
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAATAAATATATATAA
Found at i:1959566 original size:13 final size:12
Alignment explanation
Indices: 1959548--1959578 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1959538 TTTCCTGGTC
*
1959548 AAAAAAAGGAAA
1 AAAAAAAAGAAA
1959560 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1959572 AAAAAAA
1 AAAAAAA
1959579 CTTCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1963935 original size:14 final size:14
Alignment explanation
Indices: 1963916--1963950 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1963906 ATAATAAATA
*
1963916 TATTTTTTTATTTT
1 TATTTTTTAATTTT
1963930 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
1963944 TAATTTT
1 TATTTTT
1963951 AAAATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:1964006 original size:26 final size:24
Alignment explanation
Indices: 1963958--1964008 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1963948 TTTAAAATAC
* *
1963958 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
1963982 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
1964008 T
1 T
1964009 AAAAAATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:1964321 original size:26 final size:25
Alignment explanation
Indices: 1964292--1964344 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
1964282 CATCAGTGGC
1964292 ATCGCAGCAAAGCTGCCAGCAGTAGT
1 ATCGCAGCAAAGCTGCCAGCA-TAGT
* *
1964318 ATCGCAGCAAAGTTGCCAGTATAGT
1 ATCGCAGCAAAGCTGCCAGCATAGT
1964343 AT
1 AT
1964345 ATGTGGCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (25 bp):
ATCGCAGCAAAGCTGCCAGCATAGT
Found at i:1964364 original size:26 final size:25
Alignment explanation
Indices: 1964333--1964396 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 25
1964323 AGCAAAGTTG
*
1964333 CCAGTATAGTATATGTGGCCA-AGCCA
1 CCAGTACAGTAT-TGTGG-CAGAGCCA
1964359 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGT-ACAGT-ATTGTGGCAGAGCCA
1964386 CCAGTACAGTA
1 CCAGTACAGTA
1964397 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
25 1 0.03
26 12 0.35
27 19 0.56
28 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (25 bp):
CCAGTACAGTATTGTGGCAGAGCCA
Found at i:1964585 original size:27 final size:27
Alignment explanation
Indices: 1964551--1964893 Score: 341
Period size: 27 Copynumber: 12.8 Consensus size: 27
1964541 TTGACCTCGA
*
1964551 GGGTATTACGGTTATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * *
1964578 GGGCATTACGGTCATTTTATCTTACAA
1 GGGTATTACGGTCATTTTACCCTACAG
*
1964605 GGGTATTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
1964632 GGGCATTACGGTTATTTTACCCTACCG
1 GGGTATTACGGTCATTTTACCCTACAG
*
1964659 GGGTATTATGGTCATTTTACCCTA-AG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
1964685 GGGCATTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
1964712 GGGCATTACGGTCATTTTACCTTATAG
1 GGGTATTACGGTCATTTTACCCTACAG
*
1964739 GGGTATTACGGTTATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * * *
1964766 GGGTATTACTGTTATTTTACCATATAA
1 GGGTATTACGGTCATTTTACCCTACAG
* * **
1964793 GGGTATTTCGGT-ATTCTACCCTATGG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
1964819 GGGTATTTCGGTCATTTTACCCTATAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * * *
1964846 GGGCATTTCAGTTATTTTACCC-ATAG
1 GGGTATTACGGTCATTTTACCCTACAG
** *
1964872 AGGGTATTTTGTTCATTTTACC
1 -GGGTATTACGGTCATTTTACC
1964894 TTTCGAAGGT
Statistics
Matches: 265, Mismatches: 48, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 48 0.18
27 217 0.82
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTACCCTACAG
Found at i:1964702 original size:107 final size:107
Alignment explanation
Indices: 1964551--1964893 Score: 388
Period size: 107 Copynumber: 3.2 Consensus size: 107
1964541 TTGACCTCGA
* * * * * *
1964551 GGGTATTACGGTTATTTTACCCTACAGGGGCATTACGGTCATTTTATCTTACAAGGGTATTACGA
1 GGGTATTATGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGG
*
1964616 TCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACCG
66 TCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCTA-CG
* *
1964659 GGGTATTATGGTCATTTTACCCTA-AGGGGCATTACGATCATTTTACCCTACAGGGGCATTACGG
1 GGGTATTATGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGG
* *
1964723 TCATTTTACCTTATAGGGGTATTACGGTTATTTTACCCTACAG
66 TCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCTAC-G
* * * * * * * ** *
1964766 GGGTATTACT-GTTATTTTACCATATAAGGGTATTTCGGT-ATTCTACCCTATGGGGGTATTTCG
1 GGGTATTA-TGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACG
* *
1964829 GTCATTTTACCCTATAGGGGCATTTCAGTTATTTTACCCATA-G
65 GTCATTTTACCCTATAGGGGCATTACGGTTATTTTACCC-TACG
* *
1964872 AGGGTATTTTGTTCATTTTACC
1 -GGGTATTATGGTCATTTTACC
1964894 TTTCGAAGGT
Statistics
Matches: 200, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
106 3 0.01
107 162 0.81
108 35 0.17
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (107 bp):
GGGTATTATGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGG
TCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCTACG
Found at i:1964797 original size:134 final size:134
Alignment explanation
Indices: 1964555--1964893 Score: 405
Period size: 134 Copynumber: 2.5 Consensus size: 134
1964545 CCTCGAGGGT
* * * *
1964555 ATTACGGTTATTTTACCCTACAGGGGCATTACGGTCATTTTATCTTACAAGGGTATTACGATCAT
1 ATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTATAGGGGTATTACGATCAT
* ** *
1964620 TTTACCCTACAGGGGCATTACGGTTATTTTACCCTACCGGGGTATTAT-GGTCATTTTACCCTA-
66 TTTACCCTACAGGGGCATTACGGTTATTTTACCATACAAGGGTATT-TCGGT-ATTCTACCCTAT
1964683 AGGGGC
129 AGGGGC
* * *
1964689 ATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTATAGGGGTATTACGGTTAT
1 ATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTATAGGGGTATTACGATCAT
* * * *
1964754 TTTACCCTACAGGGGTATTACTGTTATTTTACCATATAAGGGTATTTCGGTATTCTACCCTATGG
66 TTTACCCTACAGGGGCATTACGGTTATTTTACCATACAAGGGTATTTCGGTATTCTACCCTATAG
*
1964819 GGGT
131 GGGC
* * * * * * ** *
1964823 ATTTCGGTCATTTTACCCTATAGGGGCATTTCAGTTATTTTACC-CATAGAGGGTATTTTGTTCA
1 ATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTATAG-GGGTATTACGATCA
1964887 TTTTACC
65 TTTTACC
1964894 TTTCGAAGGT
Statistics
Matches: 175, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
133 15 0.09
134 160 0.91
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (134 bp):
ATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTATAGGGGTATTACGATCAT
TTTACCCTACAGGGGCATTACGGTTATTTTACCATACAAGGGTATTTCGGTATTCTACCCTATAG
GGGC
Found at i:1964880 original size:80 final size:78
Alignment explanation
Indices: 1964555--1964867 Score: 313
Period size: 80 Copynumber: 3.9 Consensus size: 78
1964545 CCTCGAGGGT
* * * * * * * *
1964555 ATTACGGTTATTTTACCCTACAGGGGCATTACGGTCATTTTATCTTACAAGGGTATTACGATCAT
1 ATTACGG-TATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA-AGGGGCATTACG-TTAT
1964620 TTTACCCTACAGGGGC
63 TTTACCCTACAGGGGC
** *
1964636 ATTACGGTTATTTTACCCTACCGGGGTATTAT-GGTCATTTTACCCTAAGGGGCATTACGATCAT
1 ATTACGG-TATTTTACCCTATAGGGGTATT-TCGGTCATTTTACCCTAAGGGGCATTACG-TTAT
1964700 TTTACCCTACAGGGGC
63 TTTACCCTACAGGGGC
* * * *
1964716 ATTACGGTCATTTTACCTTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACTGTTAT
1 ATTACGGT-ATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA-AGGGGCATTAC-GTTAT
* * * *
1964781 TTTACCATATAAGGGT
63 TTTACCCTACAGGGGC
* * * *
1964797 ATTTCGGTATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGCATTTCAGTTATT
1 ATTACGGTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA-AGGGGCATTAC-GTTATT
1964862 TTACCC
64 TTACCC
1964868 ATAGAGGGTA
Statistics
Matches: 198, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
79 1 0.01
80 123 0.62
81 73 0.37
82 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (78 bp):
ATTACGGTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAAGGGGCATTACGTTATTTT
ACCCTACAGGGGC
Found at i:1966373 original size:10 final size:10
Alignment explanation
Indices: 1966360--1966389 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1966350 ACAATGGCAA
*
1966360 GAAGAAGGCT
1 GAAGATGGCT
1966370 GAAGATGGCT
1 GAAGATGGCT
1966380 GAAGATGGCT
1 GAAGATGGCT
1966390 CCCACAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.40, T:0.17
Consensus pattern (10 bp):
GAAGATGGCT
Found at i:1966623 original size:24 final size:23
Alignment explanation
Indices: 1966604--1966653 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1966594 GAAAATGAGC
*
1966604 TTTAAA-TAATTAGTATAAATTGA
1 TTTAAAGTAAATAGTATAAA-TGA
1966627 TTTAAAGTAAATAGTATATAATGA
1 TTTAAAGTAAATAGTATA-AATGA
1966651 TTT
1 TTT
1966654 TAAAAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 16 0.67
25 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
TTTAAAGTAAATAGTATAAATGA
Found at i:1967230 original size:75 final size:75
Alignment explanation
Indices: 1967098--1967240 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 75
1967088 GCTTTCTCTG
* * * * *
1967098 CTAGGGTTCCAAATTTTAACTGTCGCTGTCACTCCAAACACCGATTTTGGCCTGGCCTCCAATTG
1 CTAGGGTTCCAAATTTTAACTGCCGCCGCCACTCCAAACACCGATTTCGGCCCGGCCTCCAATTG
1967163 CGACTCCCTA
66 CGACTCCCTA
* * * *
1967173 CTAGGGTTCCAAATTTTAGCTGCCGCCGCCGCTCCAAACCCCGATTTCGGCCCGGCCTCCGATTG
1 CTAGGGTTCCAAATTTTAACTGCCGCCGCCACTCCAAACACCGATTTCGGCCCGGCCTCCAATTG
1967238 CGA
66 CGA
1967241 TAGAGGAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.26
Consensus pattern (75 bp):
CTAGGGTTCCAAATTTTAACTGCCGCCGCCACTCCAAACACCGATTTCGGCCCGGCCTCCAATTG
CGACTCCCTA
Found at i:1967439 original size:14 final size:14
Alignment explanation
Indices: 1967420--1967447 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1967410 ATTCGTCCTC
1967420 TTTACACTGATTTT
1 TTTACACTGATTTT
1967434 TTTACACTGATTTT
1 TTTACACTGATTTT
1967448 CCCCCTCCTT
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:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTACACTGATTTT
Found at i:1974047 original size:52 final size:52
Alignment explanation
Indices: 1973969--1974074 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
1973959 TTATATATTA
*
1973969 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAATTGCT
1 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
*
1974021 TATTGGCAATGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
1 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
1974073 TA
1 TA
1974075 CTTTGTGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (52 bp):
TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
Found at i:1975063 original size:53 final size:53
Alignment explanation
Indices: 1974983--1975095 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 53
1974973 TGTGACTTGG
* * * *
1974983 CCGTGTAACCAAGTTAGAGAGTTACACGGGCATGGACATGGGCTAGGACATGA
1 CCGTGTGACCAAGTCAGAGAGTTACACGGGCACGGACATGGGCTAGGACACGA
* *
1975036 CCGTGTGACCAAGTCAGAGAGTTACACGGGCACGGACATGGGTTAGGACACGG
1 CCGTGTGACCAAGTCAGAGAGTTACACGGGCACGGACATGGGCTAGGACACGA
1975089 CCGTGTG
1 CCGTGTG
1975096 TCCTCATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.27, C:0.21, G:0.35, T:0.18
Consensus pattern (53 bp):
CCGTGTGACCAAGTCAGAGAGTTACACGGGCACGGACATGGGCTAGGACACGA
Found at i:1977107 original size:22 final size:24
Alignment explanation
Indices: 1977082--1977127 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1977072 TGGATTGGTC
1977082 AACTCTAAATG-AAGC-TATTGTA
1 AACTCTAAATGAAAGCTTATTGTA
* *
1977104 AACTGTAGATGAAAGCTTATTGTA
1 AACTCTAAATGAAAGCTTATTGTA
1977128 TTGAAATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (24 bp):
AACTCTAAATGAAAGCTTATTGTA
Found at i:1983460 original size:45 final size:44
Alignment explanation
Indices: 1983408--1983856 Score: 246
Period size: 44 Copynumber: 10.1 Consensus size: 44
1983398 AGTTGCAAAC
* * * *
1983408 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACCAATT
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTA-CAATT
* * * * * *
1983453 CTTATCTCCTTAAAATTGCAGCGGAGTAGATCGAAGCTACAAAT
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTACAATT
* * * * * * *
1983497 CTCT-TCTCCCTAAAATTACATTAGAGCAGATCAAAACCACAATC
1 CT-TATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTACAATT
* * * * * **
1983541 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAATTACCAATT
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTA-CAATT
* * ** * *
1983586 CTTATCTCCTTAAAGTTGCAGAAGAGTAGATCGAAGCTACAAAT
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTACAATT
* * * * *
1983630 C-T-CCTCCTTGAAA-TTACATTGGAGCAGATCGAAGCCACAATC
1 CTTATCTCCCT-AAAGTTACAGTGGAGCAGATCGAAGCTACAATT
* ** ** *
1983672 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGATAAAAAATACAAAAGT
1 CTTATCTCCCTAAAGTTACAGTGGAGCA-GATCGAAGCTAC--AATT
* * * *
1983719 CTTATCTCCCTAAAGTTACAGTGGAGAAGGTTGAAGTTACCAATT
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTA-CAATT
*** * * * *
1983764 CTTATCTTATTGAAGTTGA-AGCGGAGTAGATCGAAGCTACAAGT
1 CTTATCTCCCTAAAGTT-ACAGTGGAGCAGATCGAAGCTACAATT
* * * *
1983808 CTCT-TCTCCTTGAAGTTACATTGGAGCAGATCGAAAC-ACCAATT
1 CT-TATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTA-CAATT
1983852 CTTAT
1 CTTAT
1983857 ACCCCTGAAG
Statistics
Matches: 303, Mismatches: 85, Indels: 33
0.72 0.20 0.08
Matches are distributed among these distances:
42 28 0.09
43 12 0.04
44 122 0.40
45 105 0.35
46 7 0.02
47 29 0.10
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTACAGTGGAGCAGATCGAAGCTACAATT
Found at i:1983727 original size:133 final size:132
Alignment explanation
Indices: 1983407--1983701 Score: 466
Period size: 133 Copynumber: 2.2 Consensus size: 132
1983397 AAGTTGCAAA
* * *
1983407 CCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTAAAATTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
**
1983472 AGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACATTAGAGCAGATCAAAACCAC
66 AGAAGAGTAGATCGAAGCTACAAATCTC-TCTCCCTAAAATTACATTAGAGCAGATCAAAACCAC
1983537 AAT
130 AAT
*
1983540 CCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
* * * * *
1983605 AGAAGAGTAGATCGAAGCTACAAATCTC-CTCCTTGAAATTACATTGGAGCAGATCGAAGCCACA
66 AGAAGAGTAGATCGAAGCTACAAATCTCTCTCCCTAAAATTACATTAGAGCAGATCAAAACCACA
1983669 AT
131 AT
*
1983671 CCTTATCTCCCTAAAGTTGCAGTGGAGCAGG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGG
1983702 ATAAAAAATA
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 62 0.42
133 87 0.58
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (132 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
AGAAGAGTAGATCGAAGCTACAAATCTCTCTCCCTAAAATTACATTAGAGCAGATCAAAACCACA
AT
Found at i:1988531 original size:5 final size:5
Alignment explanation
Indices: 1988509--1988546 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1988499 ATCCTGTTAT
1988509 ATAT- ATAT- ATAT- ATATG ATATG ATATG ATATG ATATG A
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG A
1988547 AGCAATGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:1990052 original size:31 final size:32
Alignment explanation
Indices: 1989989--1990053 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1989979 GGCAAATTAC
*
1989989 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTATTTA
1990021 AAGAGTAATTGAATCCTAAT-AAAACTATTTA
1 AAGAGTAATTGAATCCTAATAAAAACTATTTA
1990052 AA
1 AA
1990054 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTATTTA
Found at i:1997536 original size:36 final size:36
Alignment explanation
Indices: 1997490--1997680 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
1997480 GGTAGCTTTA
*
1997490 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
1997526 GCTATACTTATCTGATCAAGTGAAAAAGTGATACGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
1997562 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA--G-T
1997601 AGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -G-C-TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
1997644 GTTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1997680 G
1 G
1997681 GTAGCCTAGC
Statistics
Matches: 138, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 97 0.70
38 2 0.01
39 1 0.01
40 3 0.02
41 1 0.01
42 3 0.02
43 1 0.01
44 2 0.01
46 28 0.20
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:1997609 original size:118 final size:118
Alignment explanation
Indices: 1997454--1997676 Score: 392
Period size: 118 Copynumber: 1.9 Consensus size: 118
1997444 TTTGCGTACT
* *
1997454 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1997519 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATACGTGCTATACTTA
66 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATACGTGCTATACTTA
* *
1997572 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
1997637 GATAAGTGTTATACTTATCTGATCAAGTGACAAAGTGATA
66 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATA
1997677 AGTGGTAGCC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (118 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATACGTGCTATACTTA
Found at i:1997617 original size:82 final size:81
Alignment explanation
Indices: 1997526--1997706 Score: 317
Period size: 82 Copynumber: 2.2 Consensus size: 81
1997516 AGTGATAAGT
* *
1997526 GCTATACTTATCTGATCAAGTGAAAAAGTGATACGTGCTATACTTATCTGATCAAGTGACAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGT
*
1997591 GATAAGTGTTAGCCTTA
66 GATAAGTGGTAGCC-TA
*
1997608 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGACAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGT
1997673 GATAAGTGGTAGCCTA
66 GATAAGTGGTAGCCTA
1997689 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
1997707 GGGACAAGTG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 20 0.21
82 75 0.79
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (81 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGT
GATAAGTGGTAGCCTA
Found at i:1998864 original size:21 final size:20
Alignment explanation
Indices: 1998837--1998883 Score: 85
Period size: 21 Copynumber: 2.3 Consensus size: 20
1998827 GTAGGCAACT
1998837 TTTTTTTTTGCGCTTTTTGC
1 TTTTTTTTTGCGCTTTTTGC
1998857 TTCTTTTTTTGCGCTTTTTGC
1 TT-TTTTTTTGCGCTTTTTGC
1998878 TTTTTT
1 TTTTTT
1998884 CTGTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.00, C:0.15, G:0.13, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGCGCTTTTTGC
Found at i:1999468 original size:31 final size:31
Alignment explanation
Indices: 1999430--1999493 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1999420 GGCAAATTAC
1999430 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1999461 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1999492 AA
1 AA
1999494 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:2010985 original size:41 final size:40
Alignment explanation
Indices: 2010928--2011008 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 40
2010918 CACCTACGGC
*
2010928 ATTCCTGTCCAAAACTACGTTGAATAGATTTAATTTTAAG
1 ATTCCTGCCCAAAACTACGTTGAATAGATTTAATTTTAAG
2010968 NATTCCTGCCCAAAACTACGTTGAATAGATTTAATTTTAAG
1 -ATTCCTGCCCAAAACTACGTTGAATAGATTTAATTTTAAG
2011009 CTAGTAGGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (40 bp):
ATTCCTGCCCAAAACTACGTTGAATAGATTTAATTTTAAG
Found at i:2016432 original size:34 final size:34
Alignment explanation
Indices: 2016379--2016473 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 34
2016369 CAGTATAAAT
* * * *
2016379 CATTTGGTATGGTGAATGGATTTGCTCTTACGAG
1 CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
*
2016413 CATTTGGTGTGCTGGATGGATTGGCTCTTGCGAG
1 CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
* *
2016447 CATTTGGTGTGCTGGTTGGAATGGCTC
1 CATTTGGTGTGCTGGATGGATTGGCTC
2016474 ACTTGAGCAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.37
Consensus pattern (34 bp):
CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
Found at i:2016482 original size:34 final size:33
Alignment explanation
Indices: 2016379--2016499 Score: 109
Period size: 34 Copynumber: 3.6 Consensus size: 33
2016369 CAGTATAAAT
* * * * *
2016379 CATTTGGTATGGTGAATGGATTTGCTCTTACGAG
1 CATTTGGTGTGCTGGATGGAATGGCTCTT-CGAG
*
2016413 CATTTGGTGTGCTGGATGGATTGGCTCTTGCGAG
1 CATTTGGTGTGCTGGATGGAATGGCTCTT-CGAG
*
2016447 CATTTGGTGTGCTGGTTGGAATGGCTCACTT-GAG
1 CATTTGGTGTGCTGGATGGAATGGCT--CTTCGAG
***
2016481 CATACAGTGTGCTGGATGG
1 CATTTGGTGTGCTGGATGG
2016500 TTAAATGACA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
34 71 0.96
36 3 0.04
ACGTcount: A:0.17, C:0.14, G:0.35, T:0.35
Consensus pattern (33 bp):
CATTTGGTGTGCTGGATGGAATGGCTCTTCGAG
Found at i:2020809 original size:2 final size:2
Alignment explanation
Indices: 2020804--2020835 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2020794 AAATTGGCAG
2020804 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2020836 TGTAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2025374 original size:20 final size:20
Alignment explanation
Indices: 2025351--2025407 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
2025341 AATTTATTAA
2025351 ATTTTATTAAAATTAAATAT
1 ATTTTATTAAAATTAAATAT
* *
2025371 ATTTTATT-AAATGAAATTT
1 ATTTTATTAAAATTAAATAT
*
2025390 AGTTT-TTAAATATTAAAT
1 ATTTTATTAAA-ATTAAAT
2025408 TTTTGATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.06
19 15 0.48
20 14 0.45
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTATTAAAATTAAATAT
Found at i:2026498 original size:30 final size:30
Alignment explanation
Indices: 2026464--2026527 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
2026454 TTGGATTTAT
* * *
2026464 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGATTCTATTTAATAATAGAGGGACTAAA
*
2026494 TTGA-TCTATTTAATAATAGAGGGACTAAT
1 TTGATTCTATTTAATAATAGAGGGACTAAA
2026523 TTGAT
1 TTGAT
2026528 ACACTCTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
TTGATTCTATTTAATAATAGAGGGACTAAA
Found at i:2039337 original size:3 final size:3
Alignment explanation
Indices: 2039331--2039367 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2039321 TATTATTTCT
*
2039331 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2039368 GAAAGATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2044367 original size:97 final size:101
Alignment explanation
Indices: 2044110--2044459 Score: 288
Period size: 103 Copynumber: 3.5 Consensus size: 101
2044100 GATGGTACCG
* * * * * * * * *
2044110 TTCTTACCCTTGGCTCAAACACACTCCTTTGTAAATCAAATCAAGTGCTCATAATGGTGGATTCG
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATC-AATGAAATCCTCGTAATGGTGGATTCA
* ** *
2044175 TAATGGGGTCCACCATTTGATAATGAAACCAATCGGTAA-TA
65 TAATGGAGTCCA-CA-TTGGCAATG-AACCAA--GGCAACTA
* * * * * *
2044216 TTATTACCTTTGGCTC-CA-ACACCCCTTTCTGAATCAATGAAATGCTCGTTATGGTGGATTTGA
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGA-TTCA
* *
2044279 -AATGGAGTCCACATAT-TCAATGAA-C-A-G-TACTA
65 TAATGGAGTCCACAT-TGGCAATGAACCAAGGCAACTA
* *
2044311 TTCTTGCCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTTGTAATGGTGGATTCAT
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGATTCAT
*
2044376 AATGGAGTTCACATTGGCAATGAACCGAATGGCAACTA
66 AATGGAGTCCACATTGGCAATGAACC-AA-GGCAACTA
* * *
2044414 TTCTTACCTTTGG-TCCAATCACACCCCTTTATGAATCTATGGAATC
1 TTCTTACCTTTGGCT-CAAACACACCCCTTTATGAATCAATGAAATC
2044460 TGTTTTAAAC
Statistics
Matches: 199, Mismatches: 31, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
94 1 0.01
95 17 0.09
96 5 0.03
97 56 0.28
98 2 0.01
99 1 0.01
100 3 0.02
101 5 0.03
102 5 0.03
103 73 0.37
104 16 0.08
105 1 0.01
106 14 0.07
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (101 bp):
TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGATTCAT
AATGGAGTCCACATTGGCAATGAACCAAGGCAACTA
Found at i:2049025 original size:13 final size:13
Alignment explanation
Indices: 2049009--2049033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2048999 TTTTTTTTAA
2049009 TTTTTAATTAATC
1 TTTTTAATTAATC
2049022 TTTTTAATTAAT
1 TTTTTAATTAAT
2049034 AACTCTTTTA
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:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:2050427 original size:17 final size:17
Alignment explanation
Indices: 2050405--2050437 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2050395 AAATTTTAAA
2050405 ATTTTTATAT-ATTTTTT
1 ATTTTTA-ATCATTTTTT
2050422 ATTTTTAATCATTTTT
1 ATTTTTAATCATTTTT
2050438 ATGAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTAATCATTTTTT
Found at i:2050796 original size:20 final size:20
Alignment explanation
Indices: 2050768--2050811 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2050758 GGTCTGCCGC
*
2050768 CGCCGCCGCCAAC-GTCACGT
1 CGCCACCGCC-ACGGTCACGT
*
2050788 CGCCACCGCCCCGGTCACGT
1 CGCCACCGCCACGGTCACGT
2050808 CGCC
1 CGCC
2050812 GCCCCACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.11, C:0.55, G:0.25, T:0.09
Consensus pattern (20 bp):
CGCCACCGCCACGGTCACGT
Found at i:2054660 original size:17 final size:18
Alignment explanation
Indices: 2054629--2054675 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2054619 CCCAAATTTT
2054629 TTTTATGCTTCTTTCTT-C
1 TTTT-TGCTTCTTTCTTGC
*
2054647 TTTTTGCTTGTTTCTTGC
1 TTTTTGCTTCTTTCTTGC
*
2054665 TTCTTGCTTCT
1 TTTTTGCTTCT
2054676 CCTCCTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.02, C:0.21, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTTGCTTCTTTCTTGC
Found at i:2056305 original size:49 final size:47
Alignment explanation
Indices: 2056228--2056382 Score: 142
Period size: 49 Copynumber: 3.3 Consensus size: 47
2056218 ACTTGTATTG
*
2056228 AATTGCATAAATTATGGTATTATGCTTAGATGCTTATATTAAACATTT
1 AATTGCATCAATTATGGTATTATGCTTAGATGCTTATATT-AACATTT
* * * * **
2056276 AAATTGCATCAATTATGTTTTTTTACTTAGA----TATGGTAAC--TT
1 -AATTGCATCAATTATGGTATTATGCTTAGATGCTTATATTAACATTT
* * *
2056318 ATTTGCATCGATTATGGTATTATGCTTAGATGCTTGTATTGAACATTT
1 AATTGCATCAATTATGGTATTATGCTTAGATGCTTATATT-AACATTT
2056366 GAATTGCATCAATTATG
1 -AATTGCATCAATTATG
2056383 TTTTTTTTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
41 24 0.30
42 2 0.03
44 3 0.04
45 7 0.09
46 3 0.04
48 2 0.03
49 39 0.49
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (47 bp):
AATTGCATCAATTATGGTATTATGCTTAGATGCTTATATTAACATTT
Done.