Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 49 of 230
Found at i:13260772 original size:22 final size:22
Alignment explanation
Indices: 13260746--13260790 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
13260736 TAAGAATGAG
13260746 AAAGAATGCTGCAAAGCTACGA
1 AAAGAATGCTGCAAAGCTACGA
13260768 AAAGAATGCTGCAAAGCTACGA
1 AAAGAATGCTGCAAAGCTACGA
13260790 A
1 A
13260791 TTTCTACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (22 bp):
AAAGAATGCTGCAAAGCTACGA
Found at i:13269725 original size:32 final size:32
Alignment explanation
Indices: 13269687--13269753 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
13269677 AAAAAATAGG
*
13269687 GATTAGAGGGCTTTGTTTAGGGTTTAAAAAAA
1 GATTAGAGGGCTTTGTTTAAGGTTTAAAAAAA
*
13269719 GATTAGAGGGTTTTGTTTAAGGTTTAAAAAAA
1 GATTAGAGGGCTTTGTTTAAGGTTTAAAAAAA
13269751 GAT
1 GAT
13269754 CAAAAAGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (32 bp):
GATTAGAGGGCTTTGTTTAAGGTTTAAAAAAA
Found at i:13269777 original size:34 final size:34
Alignment explanation
Indices: 13269702--13269795 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 34
13269692 GAGGGCTTTG
* * * **
13269702 TTTAGGGTTTAAAAAAAGAT--TAGAGGGTTTTG
1 TTTAGGGTTTAAAAAAAGATCAAAAAGGATTTCA
*
13269734 TTTAAGGTTTAAAAAAAGATCAAAAAGGATTTCA
1 TTTAGGGTTTAAAAAAAGATCAAAAAGGATTTCA
13269768 TTTAGGGTTTTAACAGAAAAGATCAAAA
1 TTTAGGG-TTTAA-A-AAAAGATCAAAA
13269796 GAGGTAACTT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 19 0.38
34 13 0.26
35 5 0.10
36 1 0.02
37 12 0.24
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (34 bp):
TTTAGGGTTTAAAAAAAGATCAAAAAGGATTTCA
Found at i:13270214 original size:14 final size:13
Alignment explanation
Indices: 13270192--13270241 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
13270182 AACTGTTTAG
*
13270192 TATTTTTGTAATGA
1 TATTATTGTAAT-A
*
13270206 TATTATTGTACTA
1 TATTATTGTAATA
13270219 TATTTATTGTAATA
1 TA-TTATTGTAATA
13270233 T-TTATTGTA
1 TATTATTGTA
13270242 TTACATTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 21 0.66
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (13 bp):
TATTATTGTAATA
Found at i:13270235 original size:12 final size:12
Alignment explanation
Indices: 13270192--13270241 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
13270182 AACTGTTTAG
13270192 TATTT-TTGTAA
1 TATTTATTGTAA
13270203 TGATATTATTGTACTA
1 T-AT-TTATTGTA--A
13270219 TATTTATTGTAA
1 TATTTATTGTAA
13270231 TATTTATTGTA
1 TATTTATTGTA
13270242 TTACATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.03
12 14 0.41
13 2 0.06
14 13 0.38
15 2 0.06
16 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (12 bp):
TATTTATTGTAA
Found at i:13270240 original size:26 final size:28
Alignment explanation
Indices: 13270192--13270250 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
13270182 AACTGTTTAG
13270192 TATTT-TTGTAATGATATTATTGTACTA
1 TATTTATTGTAATGATATTATTGTACTA
*
13270219 TATTTATTGTAAT-AT-TTATTGTATTA
1 TATTTATTGTAATGATATTATTGTACTA
*
13270245 CATTTA
1 TATTTA
13270251 GGTGTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.52
27 7 0.24
28 7 0.24
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTATTGTAATGATATTATTGTACTA
Found at i:13272722 original size:33 final size:34
Alignment explanation
Indices: 13272680--13272755 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
13272670 ATGCAAAAAT
13272680 AACAAACTTTG-AAATTTAAATGAGATGTATTGG
1 AACAAACTTTGTAAATTTAAATGAGATGTATTGG
* *
13272713 AACAAACTTTGTAATTTTAAATGAGATGTGTTGG
1 AACAAACTTTGTAAATTTAAATGAGATGTATTGG
13272747 AACAAACTT
1 AACAAACTT
13272756 GGAACAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 11 0.28
34 29 0.73
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (34 bp):
AACAAACTTTGTAAATTTAAATGAGATGTATTGG
Found at i:13272774 original size:45 final size:45
Alignment explanation
Indices: 13272709--13272810 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
13272699 ATGAGATGTA
**
13272709 TTGGAACAAACTTTGTAATTTTAAATGAGATGTGTTGGAACAAAC
1 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
13272754 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
1 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
13272799 TTGGAACAAACT
1 TTGGAACAAACT
13272811 ATGTAATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (45 bp):
TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
Found at i:13287111 original size:44 final size:43
Alignment explanation
Indices: 13287046--13287174 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 43
13287036 ATATATGATA
* *
13287046 TCGTGTAAGACCTTGTTTGGGACGCTGGCATCGATTTGAGATT
1 TCGTGTAAGACCATGTCTGGGACGCTGGCATCGATTTGAGATT
* * *
13287089 TACGTGTAAGACCATGTCTGGGACATCT-GCATCG-TATAAGATT
1 T-CGTGTAAGACCATGTCTGGGAC-GCTGGCATCGATTTGAGATT
* * *
13287132 TCGTGTAAGACCCTATCTGGGATAG-TGGCATCGATATTG-GATT
1 TCGTGTAAGACCATGTCTGGGA-CGCTGGCATCGAT-TTGAGATT
13287175 ACATGTTGGA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 25 0.36
43 14 0.20
44 27 0.39
45 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACGCTGGCATCGATTTGAGATT
Found at i:13288157 original size:27 final size:27
Alignment explanation
Indices: 13288116--13288339 Score: 243
Period size: 27 Copynumber: 8.3 Consensus size: 27
13288106 GTAATGAGCC
* *
13288116 TAAAATGACAGAAATGCCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
13288143 TAAAGTGACCAAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
13288170 TAAAATGGCCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
13288197 TAAAATGACTGAGATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
13288224 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*** *
13288251 TAAAATGATTAAAATACCC-CTGAAAGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
* *
13288278 TAAAATGACTGAAATACCTTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
13288305 TAAAATGATCGAAATACCCCCGTAGGA
1 TAAAATGACCGAAATACCCTCGAAGGG
13288332 TAAAATGA
1 TAAAATGA
13288340 TTGTTATACC
Statistics
Matches: 165, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
27 164 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.20
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:13288336 original size:81 final size:81
Alignment explanation
Indices: 13288116--13288341 Score: 276
Period size: 81 Copynumber: 2.8 Consensus size: 81
13288106 GTAATGAGCC
* * * * * * ****
13288116 TAAAATGACAGAAATGCCCTCGAAGGGTAAAGTGACCAAAATACCCTTGAAGGGTAAAATGGCCG
1 TAAAATGACTGAAATACCTTCGAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGATTA
*
13288181 AAATACCCTCGAAGGG
66 AAATACCCTCGAAAGG
*
13288197 TAAAATGACTGAGATACCCTT-GAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGATT
1 TAAAATGACTGAAATA-CCTTCGAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGATT
13288261 AAAATACCC-CTGAAAGG
65 AAAATACCCTC-GAAAGG
** * *
13288278 TAAAATGACTGAAATACCTTCGAAGGGTAAAATGATCGAAATACCCCCGTAGGATAAAATGATT
1 TAAAATGACTGAAATACCTTCGAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGATT
13288342 GTTATACCCT
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
80 5 0.04
81 117 0.94
82 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (81 bp):
TAAAATGACTGAAATACCTTCGAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGATTA
AAATACCCTCGAAAGG
Found at i:13288546 original size:25 final size:26
Alignment explanation
Indices: 13288515--13288588 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 26
13288505 TTGCCACATA
* *
13288515 TACTGTTAGTAGCAGCTTTGCTGC-T
1 TACTGTTACTGGCAGCTTTGCTGCAT
13288540 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
* *
13288566 CACTATTACTGGCAGCTTTGCTG
1 TACTGTTACTGGCAGCTTTGCTG
13288589 AGATATTGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 22 0.50
26 22 0.50
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCAT
Found at i:13288581 original size:26 final size:25
Alignment explanation
Indices: 13288526--13288588 Score: 99
Period size: 26 Copynumber: 2.5 Consensus size: 25
13288516 ACTGTTAGTA
* *
13288526 GCAGCTTTGCTGCTTACTGTTACTG
1 GCAGCTTTGCTGCTCACTATTACTG
13288551 GCAGCTTTGCTGCATCACTATTACTG
1 GCAGCTTTGCTGC-TCACTATTACTG
13288577 GCAGCTTTGCTG
1 GCAGCTTTGCTG
13288589 AGATATTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.37
Consensus pattern (25 bp):
GCAGCTTTGCTGCTCACTATTACTG
Found at i:13293155 original size:35 final size:35
Alignment explanation
Indices: 13293112--13293178 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
13293102 ACTGTGATAA
* *
13293112 TTTATAACAGTATATTAAAATAGTATATTACAAAT
1 TTTATAACAATATATTAAAACAGTATATTACAAAT
*
13293147 TTTATAACAATATATTAAACCAGTATATTACA
1 TTTATAACAATATATTAAAACAGTATATTACA
13293179 TTAATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (35 bp):
TTTATAACAATATATTAAAACAGTATATTACAAAT
Found at i:13295796 original size:84 final size:84
Alignment explanation
Indices: 13295646--13295801 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
13295636 GGCTCGTACA
* *
13295646 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAAACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAAACAGGGT
13295711 CTTACACAAATCAAATACG
66 CTTACACAAATCAAATACG
* *
13295730 ATGCCAATGTCCCAGACATGGTCTTACACGT-ATACACA-ATTCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAT-CACATA-TCGATGCC-ACTGTCCCAAACAG
13295791 TGGTCTTACAC
63 -GGTCTTACAC
13295802 TAAAATACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
83 4 0.06
84 58 0.91
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAAACAGGGT
CTTACACAAATCAAATACG
Found at i:13295801 original size:43 final size:43
Alignment explanation
Indices: 13295646--13295801 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 43
13295636 GGCTCGTACA
*
13295646 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCAC-ATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATA-CACAAT-TCG
* ** *
13295689 ATGCC-ACTGTCCCAAACAG-GGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATACACAATTCG
* *
13295730 ATGCCAATGTCCCAGACATGGTCTTACACGTATACACAATTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
13295773 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
13295802 TAAAATACAT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 27 0.29
42 9 0.10
43 55 0.60
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
Found at i:13297104 original size:13 final size:13
Alignment explanation
Indices: 13297072--13297175 Score: 127
Period size: 13 Copynumber: 7.8 Consensus size: 13
13297062 TCACAATAAT
*
13297072 AGTATATTTATAAC
1 AGTATA-TTAAAAC
13297086 AGTATATTAAAAC
1 AGTATATTAAAAC
*
13297099 ATTATATTAAAAC
1 AGTATATTAAAAC
*
13297112 AGTATATTTATAAC
1 AGTATA-TTAAAAC
*
13297126 AGTATACTAAAAC
1 AGTATATTAAAAC
13297139 AGTATATTAAAAC
1 AGTATATTAAAAC
*
13297152 AATATATTAAAAC
1 AGTATATTAAAAC
* *
13297165 AATATAATAAA
1 AGTATATTAAA
13297176 CTAGTTATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
13 62 0.77
14 18 0.22
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.34
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:13297127 original size:40 final size:40
Alignment explanation
Indices: 13297072--13297159 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
13297062 TCACAATAAT
* *
13297072 AGTATATTTATAACAGTATATTAAAACATTATATTAAAAC
1 AGTATATTTATAACAGTATACTAAAACAGTATATTAAAAC
13297112 AGTATATTTATAACAGTATACTAAAACAGTATATTAAAAC
1 AGTATATTTATAACAGTATACTAAAACAGTATATTAAAAC
*
13297152 AATATATT
1 AGTATATT
13297160 AAAACAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (40 bp):
AGTATATTTATAACAGTATACTAAAACAGTATATTAAAAC
Found at i:13299749 original size:139 final size:139
Alignment explanation
Indices: 13299500--13299825 Score: 424
Period size: 139 Copynumber: 2.3 Consensus size: 139
13299490 GTGAATCAAG
* * * * *
13299500 GAGTATTTATTCCATATAACGCC-AAATTGGGAGTGAAGTCAAGAAAATAGTTAACGTAAAATAA
1 GAGTATTTGTTCCATATAACGCCGAAATCGGGAGTGAAGTCGAGAAAGTAGTTAACGTAAAACAA
* * * * * * *
13299564 TAACCCTTCTTCTTCATTCATCACTGCTGAACCTAGTGGGGTTGTTTTCAAACAAACAAGCGAAA
66 TAACCCTTCTTCTTCATCCACCACTGCTGAACCCAGCGAGGTTGTTTTCAAACAAACAAACAAAA
13299629 GATTTACAC
131 GATTTACAC
* * *
13299638 GAGTATTTGTTCCA-ATTAACGCCGGAATCGGGAATGAAGTCGAGAAAGTAGTTAGCAG-AAAAC
1 GAGTATTTGTTCCATA-TAACGCCGAAATCGGGAGTGAAGTCGAGAAAGTAGTTAAC-GTAAAAC
* * *
13299701 AATAACCCTTCTTCTTCATCCACCACTGTTGAACCCAGCGAGGTTGTTTTGAGACAAACAAACAA
64 AATAACCCTTCTTCTTCATCCACCACTGCTGAACCCAGCGAGGTTGTTTTCAAACAAACAAACAA
*
13299766 AATATTTACAC
129 AAGATTTACAC
*
13299777 GAGTATTTGTTCCATATAACGTCGAAATCGGGGAGTGAAGTCGAGAAAG
1 GAGTATTTGTTCCATATAACGCCGAAATC-GGGAGTGAAGTCGAGAAAG
13299826 GAGTATTTGT
Statistics
Matches: 161, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
137 1 0.01
138 20 0.12
139 120 0.75
140 20 0.12
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (139 bp):
GAGTATTTGTTCCATATAACGCCGAAATCGGGAGTGAAGTCGAGAAAGTAGTTAACGTAAAACAA
TAACCCTTCTTCTTCATCCACCACTGCTGAACCCAGCGAGGTTGTTTTCAAACAAACAAACAAAA
GATTTACAC
Found at i:13302688 original size:20 final size:20
Alignment explanation
Indices: 13302660--13302698 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13302650 AATATGCGTA
*
13302660 ACAGCGGCACCAAA-GTGTAG
1 ACAGAGGCA-CAAATGTGTAG
13302680 ACAGAGGCACAAATGTGTA
1 ACAGAGGCACAAATGTGTA
13302699 CTCAGAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.13
Consensus pattern (20 bp):
ACAGAGGCACAAATGTGTAG
Found at i:13302724 original size:20 final size:20
Alignment explanation
Indices: 13302701--13302739 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13302691 AATGTGTACT
13302701 CAGAGGAACTGAAGTGCAAA
1 CAGAGGAACTGAAGTGCAAA
*
13302721 CAGAGGCACTGAAGTGCAA
1 CAGAGGAACTGAAGTGCAA
13302740 TCTCGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.31, T:0.10
Consensus pattern (20 bp):
CAGAGGAACTGAAGTGCAAA
Found at i:13308000 original size:91 final size:91
Alignment explanation
Indices: 13307862--13308069 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
13307852 TTGATTTTAG
* *
13307862 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
13307927 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
13307954 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
13308019 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
13308045 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
13308070 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:13308038 original size:26 final size:28
Alignment explanation
Indices: 13307984--13308044 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
13307974 TATTATCAAG
* *
13307984 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
13308012 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
13308038 AATTATA
1 AATTATA
13308045 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:13308044 original size:44 final size:43
Alignment explanation
Indices: 13307902--13308044 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
13307892 GAATTTTATG
* *
13307902 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
13307946 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
13307993 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
13308037 AAATTATA
1 AAATTATA
13308045 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:13308193 original size:66 final size:64
Alignment explanation
Indices: 13308123--13308321 Score: 177
Period size: 66 Copynumber: 3.2 Consensus size: 64
13308113 AAATATATTT
*
13308123 AATATTAATTATTTCAAATTATCTTTTATAGTAGCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
13308188 G
64 G
* * * * * **
13308189 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
13308243 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
13308308 G
64 G
*
13308309 AATATTGATTATT
1 AATATTAATTATT
13308322 AAGAATTTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 29
0.68 0.13 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 9 0.09
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:13308209 original size:120 final size:120
Alignment explanation
Indices: 13308085--13308382 Score: 508
Period size: 120 Copynumber: 2.5 Consensus size: 120
13308075 AATTATTTTA
* * *
13308085 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
13308149 TATAGTAGCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTAGCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
13308205 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
13308270 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTAGCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
13308325 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
13308383 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTAGCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:13308225 original size:61 final size:61
Alignment explanation
Indices: 13308158--13308345 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
13308148 TTATAGTAGC
13308158 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
13308219 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
13308277 C
61 T
*
13308278 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
13308339 ATATATT
1 ATATATT
13308346 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:13308245 original size:15 final size:15
Alignment explanation
Indices: 13308210--13308261 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13308200 TTAAGAATTT
*
13308210 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13308224 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13308238 TATTTAATAATAAT-
1 TATTTAATTATAATA
13308252 TATGTTAATT
1 TAT-TTAATT
13308262 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:13308354 original size:18 final size:17
Alignment explanation
Indices: 13308326--13308360 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13308316 ATTATTAAGA
*
13308326 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13308343 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13308361 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13308590 original size:44 final size:45
Alignment explanation
Indices: 13308521--13308610 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
13308511 TTACACCTCT
* *
13308521 ATTCCATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCC
***
13308565 ATTCCATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCC
1 ATTCCATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCC
13308610 A
1 A
13308611 ATACACCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 23 0.57
45 17 0.43
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (45 bp):
ATTCCATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCC
Found at i:13308617 original size:16 final size:16
Alignment explanation
Indices: 13308596--13308664 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
13308586 GATTAGCTAT
13308596 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13308612 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
13308629 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13308645 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13308661 TACA
1 TACA
13308665 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:13308638 original size:33 final size:32
Alignment explanation
Indices: 13308596--13308664 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
13308586 GATTAGCTAT
13308596 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
13308629 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
13308661 TACA
1 TACA
13308665 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:13315397 original size:15 final size:14
Alignment explanation
Indices: 13315369--13315411 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
13315359 AATCAAAGTT
13315369 AAAATAAAGTACATAA
1 AAAATAAA--ACATAA
*
13315385 AAACTTAAAACATAA
1 AAA-ATAAAACATAA
13315400 AAAATAAAACAT
1 AAAATAAAACAT
13315412 CATCTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 9 0.38
16 3 0.12
17 4 0.17
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAATAAAACATAA
Found at i:13326093 original size:13 final size:13
Alignment explanation
Indices: 13326064--13326129 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
13326054 CTTAAACCAA
**
13326064 ACTTTTCAAAAAT
1 ACTTTTCAAAAGC
*
13326077 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
13326090 ACTTTTTCACAA-C
1 AC-TTTTCAAAAGC
* *
13326103 ACTTTTTAAAAAC
1 ACTTTTCAAAAGC
13326116 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
13326129 A
1 A
13326130 TTGCTAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
12 7 0.17
13 28 0.67
14 7 0.17
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:13327583 original size:40 final size:40
Alignment explanation
Indices: 13327539--13327778 Score: 381
Period size: 40 Copynumber: 6.0 Consensus size: 40
13327529 AATGTCTGAG
13327539 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
* *
13327579 TGCACATTCGTGCCTCTGTTTGTACTTTGGTACCCTTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
13327619 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
* * *
13327659 TGCACATTCGTGCCCCTATTTGTACTACGGTACCCCTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
* * *
13327699 TGCACATTCATGCCCCCGTTTGTACTTCGGTACCCCTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
* * *
13327739 TGCACATTCATGCCCCTGTTAGTACTTCGGTACTCTTGAA
1 TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
13327779 GGCATATACA
Statistics
Matches: 185, Mismatches: 15, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 185 1.00
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.34
Consensus pattern (40 bp):
TGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCTTGAA
Found at i:13327714 original size:20 final size:20
Alignment explanation
Indices: 13327691--13327756 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
13327681 TACTACGGTA
13327691 CCCCTGAATGCACATTCATG
1 CCCCTGAATGCACATTCATG
* ** * * *
13327711 CCCCCGTTTGTAC-TTCGGTA
1 CCCCTGAATGCACATTC-ATG
13327731 CCCCTGAATGCACATTCATG
1 CCCCTGAATGCACATTCATG
13327751 CCCCTG
1 CCCCTG
13327757 TTAGTACTTC
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.18, C:0.38, G:0.17, T:0.27
Consensus pattern (20 bp):
CCCCTGAATGCACATTCATG
Found at i:13341292 original size:18 final size:17
Alignment explanation
Indices: 13341271--13341318 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
13341261 TATTATTTTT
* *
13341271 ATTATTATTATATTACTC
1 ATTATTTTTATATCA-TC
13341289 ATTATTTTTATCATCATC
1 ATTATTTTTAT-ATCATC
13341307 ATTATTTTTATA
1 ATTATTTTTATA
13341319 CACTTACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 23 0.85
19 3 0.11
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTTTATATCATC
Found at i:13341449 original size:46 final size:45
Alignment explanation
Indices: 13341381--13341469 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
13341371 ATGTGCATCT
* * *
13341381 TACATATATATATATGCATTATTATTTTATTTT-CATATTTTTTA
1 TACATATATATATATACATTATTAATATATTTTACATATTTTTTA
* *
13341425 TACATATATATACTCATACTTTATTAATATATTTTACTTATTTTT
1 TACATATATATA-T-ATACATTATTAATATATTTTACATATTTTT
13341470 ATTTATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 12 0.32
45 1 0.03
46 16 0.43
47 8 0.22
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (45 bp):
TACATATATATATATACATTATTAATATATTTTACATATTTTTTA
Found at i:13342636 original size:18 final size:18
Alignment explanation
Indices: 13342613--13342652 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13342603 TTAAACCATT
*
13342613 TATAAATATTTT-TAATAA
1 TATAAA-ATTTTAAAATAA
13342631 TATAAAATTTTAAAATAA
1 TATAAAATTTTAAAATAA
13342649 TATA
1 TATA
13342653 TTAAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATTTTAAAATAA
Found at i:13343972 original size:14 final size:14
Alignment explanation
Indices: 13343953--13343992 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13343943 TTGATTGCTA
13343953 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
13343967 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
13343981 GGAAAATGTTTT
1 GTAAAATGTTTT
13343993 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:13344145 original size:20 final size:19
Alignment explanation
Indices: 13344120--13344166 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
13344110 ACATATATTA
13344120 ATATATATTAATAAATTTTT
1 ATATATATTAAT-AATTTTT
* *
13344140 ATATAT-TAAATTATTTTT
1 ATATATATTAATAATTTTT
*
13344158 ACATATATT
1 ATATATATT
13344167 GCAATGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATATTAATAATTTTT
Found at i:13350495 original size:22 final size:22
Alignment explanation
Indices: 13350467--13350518 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
13350457 CCGTGCTCTT
13350467 TGATTAGCTCTTATGTCCTATC
1 TGATTAGCTCTTATGTCCTATC
* *
13350489 TGATTAGCTCTTATGTGCTATT
1 TGATTAGCTCTTATGTCCTATC
*
13350511 TGTTTAGC
1 TGATTAGC
13350519 ACTTTGATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TGATTAGCTCTTATGTCCTATC
Found at i:13350542 original size:20 final size:20
Alignment explanation
Indices: 13350517--13350573 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
13350507 TATTTGTTTA
*
13350517 GCACTTTGATGCCTTTGATT
1 GCACTTTGATGCCTCTGATT
* *
13350537 GCACTTTGGTGCCTCTGTTT
1 GCACTTTGATGCCTCTGATT
* *
13350557 GCACTTCGTTGCCTCTG
1 GCACTTTGATGCCTCTG
13350574 GTTACACTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (20 bp):
GCACTTTGATGCCTCTGATT
Found at i:13350581 original size:20 final size:20
Alignment explanation
Indices: 13350546--13350583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13350536 TGCACTTTGG
* *
13350546 TGCCTCTGTTTGCACTTCGT
1 TGCCTCTGGTTACACTTCGT
13350566 TGCCTCTGGTTACACTTC
1 TGCCTCTGGTTACACTTC
13350584 AATAGCTTTG
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:0.08, C:0.32, G:0.18, T:0.42
Consensus pattern (20 bp):
TGCCTCTGGTTACACTTCGT
Found at i:13357373 original size:27 final size:26
Alignment explanation
Indices: 13357317--13357376 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
13357307 CTAATAGATG
*
13357317 AAAATGACTGAAATATCCCATAGGGT
1 AAAATGACTGAAATACCCCATAGGGT
13357343 AAAATGA-TCGAAATACCCTCATAGGGT
1 AAAATGACT-GAAATACCC-CATAGGGT
13357370 AAAATGA
1 AAAATGA
13357377 ATGTTATACC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 15 0.48
27 15 0.48
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (26 bp):
AAAATGACTGAAATACCCCATAGGGT
Found at i:13357387 original size:27 final size:27
Alignment explanation
Indices: 13357317--13357376 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
13357307 CTAATAGATG
*
13357317 AAAATGA-CTGAAATATCC-CATAGGGT
1 AAAATGATC-GAAATACCCTCATAGGGT
13357343 AAAATGATCGAAATACCCTCATAGGGT
1 AAAATGATCGAAATACCCTCATAGGGT
13357370 AAAATGA
1 AAAATGA
13357377 ATGTTATACC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (27 bp):
AAAATGATCGAAATACCCTCATAGGGT
Found at i:13357642 original size:26 final size:25
Alignment explanation
Indices: 13357611--13357691 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 25
13357601 TTTGCCATAT
*
13357611 ATACTGTTACTGGCAACTTTGCTGCG
1 ATACTGTTACTGG-AGCTTTGCTGCG
* *
13357637 ATACTGATACTGGTAGCTCTGCTGCG
1 ATACTGTTACTGG-AGCTTTGCTGCG
* *
13357663 ATGCTATTACTTGGAGCTTTGCTGCG
1 ATACTGTTAC-TGGAGCTTTGCTGCG
13357689 ATA
1 ATA
13357692 TTGGTGTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 42 0.93
27 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (25 bp):
ATACTGTTACTGGAGCTTTGCTGCG
Found at i:13357783 original size:58 final size:58
Alignment explanation
Indices: 13357693--13357823 Score: 199
Period size: 58 Copynumber: 2.3 Consensus size: 58
13357683 GCTGCGATAT
* * *
13357693 TGGTGTGTTGGCTAGGTGGGTCAATTTTATCCCTACATGGTGTGTTGGTGGTACATAG
1 TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
** **
13357751 TGGTGTGTTGGCTGGGTGGGTTGATTTTATCCCCACATGGTGTGTTGGTGGTATGGAG
1 TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
13357809 TGGTGTGTTGGCTGG
1 TGGTGTGTTGGCTGG
13357824 ATTGTGATGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (58 bp):
TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
Found at i:13357891 original size:28 final size:28
Alignment explanation
Indices: 13357851--13358057 Score: 312
Period size: 28 Copynumber: 7.4 Consensus size: 28
13357841 TATTGCACTG
13357851 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
*
13357879 CACTGTTACTGTATTGAGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
13357907 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
*
13357935 CACTGATT-CTGTATTGGACTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
13357963 CACTATTACTGTATTGGGCTAAGGGCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* **
13357991 CACTGTGACTGTATTGGGCTAAGGATCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
13358019 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
13358047 CACTG-TACTGT
1 CACTGTTACTGT
13358058 CTTTGAATAG
Statistics
Matches: 164, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.05
28 154 0.94
29 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:13362119 original size:40 final size:40
Alignment explanation
Indices: 13362021--13362190 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
13362011 TCCTCGTTCA
* * * *
13362021 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
13362060 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
13362100 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * * *
13362140 AACGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
13362180 AAGGCCTTCGG
1 AATGCCTTCGG
13362191 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 34 0.29
40 84 0.71
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:13362176 original size:80 final size:79
Alignment explanation
Indices: 13362019--13362243 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 79
13362009 GCTCCTCGTT
* * * * * *
13362019 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCACAAAGCCTTCGGGACTTAACCCGGA
13362084 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * *
13362098 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAACGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCAC-AAAGCCTTCGGGACTTAACCCGG
** *
13362163 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
* * * * * * *
13362178 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAATAAC-TCGCACAAAGCCTTCGGGACTTAACCCG
13362242 GA
64 GA
13362244 CAACATTCAA
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 38 0.31
80 79 0.65
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCACAAAGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:13362203 original size:40 final size:40
Alignment explanation
Indices: 13362024--13362243 Score: 212
Period size: 40 Copynumber: 5.5 Consensus size: 40
13362014 TCGTTCAAAT
* * * * * *
13362024 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
* * *
13362063 GCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
13362103 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
* * * *
13362143 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
** * * * * *
13362183 GCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AAA
1 GCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAAC
*
13362223 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
13362244 CAACATTCAA
Statistics
Matches: 156, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 34 0.22
40 114 0.73
41 8 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAAC
Found at i:13362252 original size:41 final size:41
Alignment explanation
Indices: 13362175--13362252 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
13362165 TTAGTATCTC
* * *
13362175 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGAAACATTCACTTA
13362216 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAACATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGA-AACATTCA
13362253 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGAAACATTCACTTA
Found at i:13370525 original size:32 final size:32
Alignment explanation
Indices: 13370484--13370547 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
13370474 CATTCTAAGA
13370484 AAGGATGCCTTAAAATGAACCCCTGAAACTAT
1 AAGGATGCCTTAAAATGAACCCCTGAAACTAT
* *
13370516 AAGGATGCCTTCAAATGAATCCCTGAAACTAT
1 AAGGATGCCTTAAAATGAACCCCTGAAACTAT
13370548 TTTAGATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (32 bp):
AAGGATGCCTTAAAATGAACCCCTGAAACTAT
Found at i:13375445 original size:74 final size:74
Alignment explanation
Indices: 13375356--13375506 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 74
13375346 CTAAATTGGG
*
13375356 AAAAATGTCATTTCATGGCAATAGAAGGCATTGTGTTAGGCCATCATATCTCTCTTCAAGGAATT
1 AAAAATGTCATTTCATGGCAATAGAAGGCATTGTGTTAGGCCATCATATCTCTCGTCAAGGAATT
*
13375421 GAAGTCAAC
66 GAAATCAAC
13375430 AAAAATGTCATTTCATGGCAATAGAAGGCATTGTGTTAGGCCATCATATCTCTCGTCAAGGAATT
1 AAAAATGTCATTTCATGGCAATAGAAGGCATTGTGTTAGGCCATCATATCTCTCGTCAAGGAATT
13375495 GAAATCAAC
66 GAAATCAAC
13375504 AAA
1 AAA
13375507 GCTAAAGTGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (74 bp):
AAAAATGTCATTTCATGGCAATAGAAGGCATTGTGTTAGGCCATCATATCTCTCGTCAAGGAATT
GAAATCAAC
Found at i:13379762 original size:17 final size:16
Alignment explanation
Indices: 13379740--13379774 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
13379730 GTTAGTGAAC
*
13379740 ATTGTCATTGCATTGTT
1 ATTGTCATCGCATT-TT
13379757 ATTGTCATCGCATTTT
1 ATTGTCATCGCATTTT
13379773 AT
1 AT
13379775 GCATGATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (16 bp):
ATTGTCATCGCATTTT
Found at i:13383383 original size:48 final size:48
Alignment explanation
Indices: 13383309--13383401 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 48
13383299 AGAGATTTGG
* * * *
13383309 AAAGAGTAAGTTAATATGACTTTGTAT-CTGATATATGTTATGTATTGA
1 AAAGAGTAAATTAACATGACTGTGTATGC-GATAAATGTTATGTATTGA
*
13383357 AAAGAGTAAATTAACATGA-TAGTGTATGCGTTAAATGTTATGTAT
1 AAAGAGTAAATTAACATGACT-GTGTATGCGATAAATGTTATGTAT
13383402 AATTGCTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
47 1 0.03
48 36 0.95
49 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (48 bp):
AAAGAGTAAATTAACATGACTGTGTATGCGATAAATGTTATGTATTGA
Found at i:13383667 original size:26 final size:26
Alignment explanation
Indices: 13383637--13383693 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
13383627 CTCTTTGGTG
* * *
13383637 TAAAGATGAAAGTATTCGCCCAATGT
1 TAAAGAAGAAAGTATACGCCCAATAT
*
13383663 TAAAGAAGAAAGTATACGCCCGATAT
1 TAAAGAAGAAAGTATACGCCCAATAT
13383689 TAAAG
1 TAAAG
13383694 TTCACCCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (26 bp):
TAAAGAAGAAAGTATACGCCCAATAT
Found at i:13390786 original size:23 final size:23
Alignment explanation
Indices: 13390760--13390805 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
13390750 GGAAATAAAA
13390760 GGAGAAGTATGGAATGCTATGCT
1 GGAGAAGTATGGAATGCTATGCT
13390783 GGAGAAGTATGGAATGCTATGCT
1 GGAGAAGTATGGAATGCTATGCT
13390806 ACTGCTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (23 bp):
GGAGAAGTATGGAATGCTATGCT
Found at i:13392153 original size:19 final size:19
Alignment explanation
Indices: 13392126--13392200 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
13392116 AATCTTCAAG
* *
13392126 GATAAGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
*
13392145 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
13392164 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
13392185 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
13392201 AGATATGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 32 0.64
21 18 0.36
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13392822 original size:36 final size:36
Alignment explanation
Indices: 13392747--13392822 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
13392737 CATACATGCA
*
13392747 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
13392784 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
13392820 TTT
1 TTT
13392823 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:13392943 original size:23 final size:22
Alignment explanation
Indices: 13392917--13392960 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
13392907 ATAATTCACA
*
13392917 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
13392940 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
13392961 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:13394165 original size:3 final size:3
Alignment explanation
Indices: 13394157--13394195 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13394147 TATGTTACCT
13394157 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13394196 AGCTATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13395574 original size:31 final size:30
Alignment explanation
Indices: 13395539--13395652 Score: 77
Period size: 31 Copynumber: 3.7 Consensus size: 30
13395529 TACTCACGTT
*
13395539 AATATTAAATTAATAAAATACTATCAAGATC
1 AATATTAAATTAATAAAATA-TATCAAGATA
* * ** * * *
13395570 AATATTTAATCAAATTTAATATCTCACG-TT
1 AATATTAAAT-TAATAAAATATATCAAGATA
* * *
13395600 AATATTAAATTCATAAATTAATATCAATATA
1 AATATTAAATTAATAAAAT-ATATCAAGATA
*
13395631 AATATTAAATTAAATTAAATAT
1 AATATTAAATT-AATAAAATAT
13395653 TAAATTTATT
Statistics
Matches: 59, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
29 4 0.07
30 15 0.25
31 28 0.47
32 12 0.20
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (30 bp):
AATATTAAATTAATAAAATATATCAAGATA
Found at i:13395616 original size:61 final size:61
Alignment explanation
Indices: 13395531--13395652 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
13395521 ATTGAAATTA
* * * *
13395531 CTCACGTTAATATTAAATTAATAAAATACTATCAAGATCAATATTTAATCAAATTTAATAT
1 CTCACGTTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAATCAAATTAAATAT
* * * *
13395592 CTCACGTTAATATTAAATTCATAAATTAATATCAATATAAATATTAAATTAAATTAAATAT
1 CTCACGTTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAATCAAATTAAATAT
13395653 TAAATTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (61 bp):
CTCACGTTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAATCAAATTAAATAT
Found at i:13395622 original size:32 final size:32
Alignment explanation
Indices: 13395531--13395624 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 32
13395521 ATTGAAATTA
* * *
13395531 CTCACGTTAATATTAAATTAATAAAATACTA-
1 CTCACGTTAATATTAAATTCATAAATTAATAT
* * * *
13395562 -TCAAGATCAATATTTAA-TCA-AATTTAATAT
1 CTCACG-TTAATATTAAATTCATAAATTAATAT
13395592 CTCACGTTAATATTAAATTCATAAATTAATAT
1 CTCACGTTAATATTAAATTCATAAATTAATAT
13395624 C
1 C
13395625 AATATAAATA
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
29 6 0.13
30 15 0.32
31 16 0.34
32 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (32 bp):
CTCACGTTAATATTAAATTCATAAATTAATAT
Found at i:13399158 original size:43 final size:43
Alignment explanation
Indices: 13399083--13399215 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 43
13399073 AAACACATAT
* * * * *
13399083 ATCACATA-CAATGCC-ATATCCCAGATATGGTCTTACATGTT
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
* *
13399124 ATCACATATCGATGTCACA-GTCCCAGACAGGGTCTTACACGTA
1 ATCACATATCGATGCCA-ATGTCCCAGACATGGTCTTACACGTA
* * **
13399167 ATCTCATATCGATGCCAATGACCCAGACATGGTCTTACACAAA
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
13399210 ATCACA
1 ATCACA
13399216 CCTCAGGAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 8 0.11
42 6 0.08
43 59 0.80
44 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
Found at i:13411928 original size:21 final size:21
Alignment explanation
Indices: 13411904--13411943 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13411894 TAATGATCAG
* *
13411904 CACATTTTGGTGGTATATCCA
1 CACATTCTGGTAGTATATCCA
13411925 CACATTCTGGTAGTATATC
1 CACATTCTGGTAGTATATC
13411944 AGCGATTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (21 bp):
CACATTCTGGTAGTATATCCA
Found at i:13422398 original size:24 final size:21
Alignment explanation
Indices: 13422363--13422405 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
13422353 GATCGATTAA
13422363 AAAATAAGATGTGTGGTATTGAG
1 AAAATAAGATGT-T-GTATTGAG
*
13422386 AAAATACATATGTTGTATTG
1 AAAATA-AGATGTTGTATTG
13422406 TTCTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 7 0.39
24 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (21 bp):
AAAATAAGATGTTGTATTGAG
Found at i:13423930 original size:17 final size:18
Alignment explanation
Indices: 13423892--13423930 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13423882 CCCTCGTCTT
* *
13423892 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
13423910 CTAAGGGAAAGAAGAAA-
1 CTAAGGGAAAGAAGAAAG
13423927 CTAA
1 CTAA
13423931 CTAAGTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.51, C:0.10, G:0.31, T:0.08
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:13427033 original size:17 final size:18
Alignment explanation
Indices: 13427013--13427073 Score: 74
Period size: 17 Copynumber: 3.4 Consensus size: 18
13427003 ATTTTAATAG
13427013 ATTTAATATT-AAGTTTA
1 ATTTAATATTAAAGTTTA
13427030 ATTTAATATTAAAGTGATT-
1 ATTTAATATTAAAGT--TTA
13427049 ATCTTAATATTAAAG-TTA
1 AT-TTAATATTAAAGTTTA
13427067 ATTTAAT
1 ATTTAAT
13427074 GTTTATCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 17 0.44
18 6 0.15
19 2 0.05
20 14 0.36
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
ATTTAATATTAAAGTTTA
Found at i:13436068 original size:15 final size:15
Alignment explanation
Indices: 13436048--13436079 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13436038 TATTTTTTAA
13436048 AATTTATAATTATAT
1 AATTTATAATTATAT
*
13436063 AATTTATAATTTTAT
1 AATTTATAATTATAT
13436078 AA
1 AA
13436080 AAATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTATAATTATAT
Found at i:13436444 original size:15 final size:15
Alignment explanation
Indices: 13436424--13436452 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13436414 TATTTTATTG
13436424 TAAATTTTATTTTTA
1 TAAATTTTATTTTTA
13436439 TAAATTTTATTTTT
1 TAAATTTTATTTTT
13436453 TTTAGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TAAATTTTATTTTTA
Found at i:13436461 original size:16 final size:16
Alignment explanation
Indices: 13436409--13436464 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
13436399 ATTTATTTTC
* *
13436409 AATTATATTTTATTGTA
1 AATTTTATTTT-TTATA
13436426 AATTTTA-TTTTTATA
1 AATTTTATTTTTTATA
*
13436441 AATTTTATTTTTTTTA
1 AATTTTATTTTTTATA
*
13436457 GATTTTAT
1 AATTTTAT
13436465 ATATATTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.32
16 17 0.50
17 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (16 bp):
AATTTTATTTTTTATA
Found at i:13441352 original size:4 final size:4
Alignment explanation
Indices: 13441343--13441368 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
13441333 TTCCTAAAAT
13441343 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
13441369 CCAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:13447113 original size:42 final size:42
Alignment explanation
Indices: 13447049--13447183 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 42
13447039 CAGGTTTATA
* * *
13447049 CTTCGGTTTAGCCAATGATGCACTTATGTGCTAGTATATTTG
1 CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
* * *
13447091 CTTCAGTTTATCCGATGATGCACTTACGTTCCAGTATATTTG
1 CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
** *
13447133 CTTCAGTTTATCCAATGATGTGC-TATGCTTGCCAGTATAATTG
1 CTTCAGTTTATCCAATGATGCACTTATG--TGCCAGTATATTTG
13447176 CTTCAGTT
1 CTTCAGTT
13447184 CGTTTGATGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 3 0.04
42 56 0.71
43 20 0.25
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (42 bp):
CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
Found at i:13447278 original size:43 final size:43
Alignment explanation
Indices: 13447231--13447329 Score: 171
Period size: 43 Copynumber: 2.3 Consensus size: 43
13447221 TCGGCTTGCT
*
13447231 CGATGATGCACTATGTGTGTCAGTATCTTTTTTTTAATATATC
1 CGATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATC
*
13447274 CGATGTTGCACTATGTGTGTCAGTATCTTTTCTTTAATATATC
1 CGATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATC
*
13447317 TGATGATGCACTA
1 CGATGATGCACTA
13447330 CAGTGCCAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (43 bp):
CGATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATC
Found at i:13449231 original size:16 final size:16
Alignment explanation
Indices: 13449207--13449244 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
13449197 TTTGGTTCGC
* *
13449207 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
13449223 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
13449239 TGTAAT
1 TGTAAT
13449245 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:13449287 original size:45 final size:44
Alignment explanation
Indices: 13449223--13449317 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
13449213 GGATTAGAGG
13449223 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
13449268 TGTAATGGAATAGAGGTGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
13449312 TGTAAT
1 TGTAAT
13449318 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.48
45 24 0.52
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:13449499 original size:18 final size:17
Alignment explanation
Indices: 13449478--13449512 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13449468 TTATTATTAA
*
13449478 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
13449496 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13449513 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:13449642 original size:16 final size:16
Alignment explanation
Indices: 13449605--13449672 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
13449595 TTAATCATAT
*
13449605 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
13449621 TT-AAATATATTATAA
1 TTAAAATATATTATAA
*
13449636 TTAAAATATATAATTTAA
1 TTAAAATATAT--TATAA
13449654 -TAAAAT-TATTAATAA
1 TTAAAATATATT-ATAA
13449669 TTAA
1 TTAA
13449673 TATTCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 13 0.30
16 16 0.37
17 6 0.14
18 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:13449646 original size:18 final size:18
Alignment explanation
Indices: 13449625--13449672 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
13449615 TTATTATTAA
13449625 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
13449643 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
13449660 -TAT-TAATAATTAA
1 ATATATTATAATTAA
13449673 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:13449653 original size:14 final size:15
Alignment explanation
Indices: 13449614--13449655 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13449604 TTTAAACATA
*
13449614 ATTATTATTAAATAT
1 ATTATAATTAAATAT
13449629 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
13449643 A-TATAATTTAATA
1 ATTATAATTAAATA
13449656 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:13449666 original size:147 final size:147
Alignment explanation
Indices: 13449399--13449671 Score: 503
Period size: 147 Copynumber: 1.9 Consensus size: 147
13449389 ATGATTATTG
*
13449399 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
* *
13449464 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
66 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAGCAG
13449529 AAATTTGTTTTGGTAAA
131 AAATTTGTTTTGGTAAA
13449546 TTATT-TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA
1 TTATTGTTA-TTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA
13449610 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTA
65 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTA
13449672 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
146 3 0.02
147 119 0.98
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:13449744 original size:120 final size:121
Alignment explanation
Indices: 13449603--13449900 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
13449593 ATTTAATCAT
* *
13449603 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTTGAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
13449668 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATA-AA
13449725 A-TT-AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTTGAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
13449788 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATAAA
66 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATAAA
* *
13449844 ATTTGAA-ATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
13449901 TAAAATAATT
Statistics
Matches: 168, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
119 3 0.02
120 157 0.93
121 7 0.04
122 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATAAA
Found at i:13449764 original size:16 final size:16
Alignment explanation
Indices: 13449743--13449792 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
13449733 AATAATTATT
13449743 AAATATATTATAATTA
1 AAATATATTATAATTA
*
13449759 AAATATATAATTTAA-TA
1 AAATATAT--TATAATTA
13449776 AAAT-TATTAATAATTA
1 AAATATATT-ATAATTA
13449792 A
1 A
13449793 TATTCTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.11
16 14 0.50
17 6 0.21
18 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATATTATAATTA
Found at i:13449838 original size:61 final size:61
Alignment explanation
Indices: 13449653--13449840 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
13449643 ATATAATTTA
*
13449653 ATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACT
1 ATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * * *
13449714 GTAAAA-TATAAATTAACATAATAATTATTAAAT--ATATTA-T--AATTAAAATATATAAT-TT
1 ATAAAATTATTAA-TAA-TTAAT-ATTCTTATATGAAT-TTACTCAAATCATAATATATGATACT
13449772 AATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
13449834 ATAAAAT
1 ATAAAAT
13449841 AAAATTTGAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 8 0.08
58 8 0.08
59 23 0.24
60 10 0.10
61 31 0.32
62 8 0.08
63 8 0.08
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:13449913 original size:28 final size:27
Alignment explanation
Indices: 13449837--13449913 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
13449827 TGATACTATA
*
13449837 AAATAAAATTTGAAATAATTA-ATATT
1 AAATAAAATTTAAAATAATTATATATT
* *
13449863 AAATATATTTTAATTAA-AA-TATATGATT
1 AAATAAAATTTAA--AATAATTATAT-ATT
*
13449891 TAATAAAATTTAAAATAATTATA
1 AAATAAAATTTAAAATAATTATA
13449914 ACTAATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
26 14 0.36
27 6 0.15
28 19 0.49
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AAATAAAATTTAAAATAATTATATATT
Found at i:13450025 original size:90 final size:91
Alignment explanation
Indices: 13449916--13450122 Score: 283
Period size: 90 Copynumber: 2.3 Consensus size: 91
13449906 TAATTATAAC
* * * *
13449916 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
13449980 TAATATATAATTTCAT-AAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
* * *
13450006 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
13450071 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
**
13450097 TAATAAAATGGTATTATATGAATTTA
1 TAAT-AAATTATATTATATGAATTTA
13450123 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
90 68 0.67
91 16 0.16
92 18 0.18
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:13450082 original size:44 final size:43
Alignment explanation
Indices: 13449941--13450082 Score: 103
Period size: 44 Copynumber: 3.2 Consensus size: 43
13449931 TATGAATTTG
* *
13449941 TATAATTTAAAATAA-TAATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAA-TATTAAATATAATTTAAT-ATGATA
** * * *
13449985 TATAATTTCATAAATTCTTGATAATAAAT-T--TTCTTATATGAATTTA
1 TATAATTT-A-AAATAATTAATATTAAATATAATT-TAATATG-A--TA
*
13450031 TACAATTTAAAATAATTAATATTAAATATAATTTAATAGTGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATA-TGATA
13450075 TATAATTT
1 TATAATTT
13450083 CATAAAATTC
Statistics
Matches: 73, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
43 4 0.05
44 35 0.48
45 4 0.05
46 24 0.33
47 6 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATATGATA
Found at i:13451548 original size:15 final size:15
Alignment explanation
Indices: 13451528--13451558 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13451518 ATATTATGTA
*
13451528 TAATTGACGTAAAAT
1 TAATTGACCTAAAAT
13451543 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
13451558 T
1 T
13451559 TGAAGGTTGA
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:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:13462313 original size:18 final size:17
Alignment explanation
Indices: 13462290--13462323 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13462280 TGAATAGAAA
13462290 ATGTGTATGATATAATGT
1 ATGTGTATGAT-TAATGT
*
13462308 ATGTGTTTGATTAATG
1 ATGTGTATGATTAATG
13462324 AATTGATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
ATGTGTATGATTAATGT
Found at i:13474159 original size:18 final size:18
Alignment explanation
Indices: 13474138--13474177 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13474128 GAAATATTTA
*
13474138 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
13474156 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
13474174 TTTT
1 TTTT
13474178 TAAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:13474702 original size:16 final size:16
Alignment explanation
Indices: 13474681--13474717 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13474671 CTTGAATTTT
*
13474681 AAAATTTTAAAATAAA
1 AAAATTATAAAATAAA
*
13474697 AAAATTATGAAATAAA
1 AAAATTATAAAATAAA
13474713 AAAAT
1 AAAAT
13474718 GAATTAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATTATAAAATAAA
Found at i:13482997 original size:17 final size:17
Alignment explanation
Indices: 13482975--13483012 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
13482965 CAATTAAGTT
* *
13482975 AATTTTAAAGTTTTTAA
1 AATTTTAAAATATTTAA
13482992 AATTTTAAAATATTTAA
1 AATTTTAAAATATTTAA
13483009 AATT
1 AATT
13483013 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTTAAAATATTTAA
Found at i:13484150 original size:24 final size:24
Alignment explanation
Indices: 13484123--13484172 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
13484113 GACGAATACA
*
13484123 AAGACGATGGTGGAA-ATGAAGATG
1 AAGACGATGGT-CAAGATGAAGATG
13484147 AAGACGATGGTCAAGATGAAGATG
1 AAGACGATGGTCAAGATGAAGATG
13484171 AA
1 AA
13484173 TATGGGGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.44, C:0.06, G:0.34, T:0.16
Consensus pattern (24 bp):
AAGACGATGGTCAAGATGAAGATG
Found at i:13489716 original size:38 final size:39
Alignment explanation
Indices: 13489616--13489732 Score: 200
Period size: 39 Copynumber: 3.0 Consensus size: 39
13489606 ACCCAACCCA
* *
13489616 ACCCAATTACCCAACGCAATAAAACTAAAAATAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
13489655 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
*
13489694 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
13489732 A
1 A
13489733 ACTCTTAAGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
38 29 0.39
39 46 0.61
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:13489952 original size:18 final size:18
Alignment explanation
Indices: 13489929--13489978 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
13489919 GTAGTGATTC
*
13489929 AATTCGGGTAATTTAGG-T
1 AATTCGGTTAATTT-GGTT
13489947 AATTCGGTTAATTTGGTT
1 AATTCGGTTAATTTGGTT
13489965 AATTCGGTTAATTT
1 AATTCGGTTAATTT
13489979 TTAACCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (18 bp):
AATTCGGTTAATTTGGTT
Found at i:13489958 original size:9 final size:9
Alignment explanation
Indices: 13489946--13489977 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
13489936 GTAATTTAGG
13489946 TAATTCGGT
1 TAATTCGGT
*
13489955 TAATTTGGT
1 TAATTCGGT
13489964 TAATTCGGT
1 TAATTCGGT
13489973 TAATT
1 TAATT
13489978 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (9 bp):
TAATTCGGT
Found at i:13492447 original size:33 final size:33
Alignment explanation
Indices: 13492385--13492463 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
13492375 GGACTTTATC
* **
13492385 TGTTCTGTGTTTATTGTCCCAGTGAACTATCTA
1 TGTTCTGTGTTTATTGTCCAACAGAACTATCTA
* *
13492418 TGTTCTGTGTTTATTGTCCTAACAG-ACTATTTC
1 TGTTCTGTGTTTATTGTCC-AACAGAACTATCTA
*
13492451 TGTTATGTGTTTA
1 TGTTCTGTGTTTA
13492464 CTATCCAGCG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.49
Consensus pattern (33 bp):
TGTTCTGTGTTTATTGTCCAACAGAACTATCTA
Found at i:13493805 original size:38 final size:37
Alignment explanation
Indices: 13493763--13493836 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 37
13493753 ATATAATTAC
*
13493763 TTTAATATTAAATTAATA-AAATACTATTAAGATAAATA
1 TTTAAT-TTAAATTAATATAAATA-TATTAAAATAAATA
*
13493801 TTTAATTTAATTTAATATTAAATATATTAAAATAAA
1 TTTAATTTAAATTAATA-TAAATATATTAAAATAAA
13493837 ATTATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 10 0.31
38 17 0.53
39 5 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (37 bp):
TTTAATTTAAATTAATATAAATATATTAAAATAAATA
Found at i:13498793 original size:43 final size:43
Alignment explanation
Indices: 13498700--13498794 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
13498690 ACATAGTTAG
** * * *
13498700 CCCATTGATGAATACTATACACAAGTAAACTTTGTACAATTCG
1 CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
**
13498743 CCCATTGGCGAATACTATACACAAGCAGTCTTTATACAATTCA
1 CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
13498786 CCCATTGGC
1 CCCATTGGC
13498795 AAAATACCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (43 bp):
CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
Found at i:13500015 original size:20 final size:20
Alignment explanation
Indices: 13499991--13500090 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
13499981 AAGTACTTGT
*
13499991 AGTTTATCTGCAATACTGGT
1 AGTTTATCTGCAATACTGGC
* * *** *
13500011 GGTTTGTCCATAATACTAGC
1 AGTTTATCTGCAATACTGGC
* * *
13500031 ATTTTATCTGTAATACTGGT
1 AGTTTATCTGCAATACTGGC
* * * **
13500051 GGCTTGTCCACAATACTGGC
1 AGTTTATCTGCAATACTGGC
13500071 AGTTTATCTGCAATACTGGC
1 AGTTTATCTGCAATACTGGC
13500091 GACTTGTCCA
Statistics
Matches: 53, Mismatches: 27, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
AGTTTATCTGCAATACTGGC
Found at i:13500048 original size:40 final size:40
Alignment explanation
Indices: 13499991--13500121 Score: 174
Period size: 40 Copynumber: 3.3 Consensus size: 40
13499981 AAGTACTTGT
*
13499991 AGTTTATCTGCAATACTGGTGGTTTGTCCATAATACTAGC
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
* * * *
13500031 ATTTTATCTGTAATACTGGTGGCTTGTCCACAATACTGGC
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
* * *
13500071 AGTTTATCTGCAATACTGGCGACTTGTCCATAATACT-GAT
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAG-C
13500111 AGTTTATCTGC
1 AGTTTATCTGC
13500122 GATTACCAGG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 78 0.99
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (40 bp):
AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
Found at i:13505966 original size:7 final size:7
Alignment explanation
Indices: 13505956--13506009 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
13505946 ACCCTAAAGT
13505956 TTGAACC
1 TTGAACC
13505963 TTGAACC
1 TTGAACC
**
13505970 -CAAACC
1 TTGAACC
*
13505976 -CGAACC
1 TTGAACC
13505982 -TGAACC
1 TTGAACC
*
13505988 TTGAATC
1 TTGAACC
13505995 TTGAACC
1 TTGAACC
13506002 TTGAACC
1 TTGAACC
13506009 T
1 T
13506010 AGGGTTCGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
6 14 0.35
7 26 0.65
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (7 bp):
TTGAACC
Found at i:13516574 original size:24 final size:24
Alignment explanation
Indices: 13516540--13516591 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13516530 TTTTTAGAAG
* * *
13516540 ATTTAGTATTTATGAGTATAATGT
1 ATTTAGCATTTATGAGCATAATAT
*
13516564 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
13516588 ATTT
1 ATTT
13516592 GACTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:13521273 original size:18 final size:20
Alignment explanation
Indices: 13521250--13521292 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
13521240 AATCTAGCAG
13521250 ACCCAAAC-AACACCCAA-A
1 ACCCAAACAAACACCCAATA
*
13521268 ACCCAAACAAAGACCCAATA
1 ACCCAAACAAACACCCAATA
13521288 ACCCA
1 ACCCA
13521293 GCCCAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.53, C:0.42, G:0.02, T:0.02
Consensus pattern (20 bp):
ACCCAAACAAACACCCAATA
Found at i:13521317 original size:12 final size:13
Alignment explanation
Indices: 13521281--13521317 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
13521271 CAAACAAAGA
*
13521281 CCCAATAACCCAG
1 CCCAATAACCTAG
13521294 CCCAATAACCTAG
1 CCCAATAACCTAG
13521307 CCCAA-AACCTA
1 CCCAATAACCTA
13521318 AAATGGCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.41, C:0.43, G:0.05, T:0.11
Consensus pattern (13 bp):
CCCAATAACCTAG
Found at i:13522470 original size:3 final size:3
Alignment explanation
Indices: 13522460--13522514 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
13522450 AAAATAATAA
* * * *
13522460 ATT A-T ATT ATT ATT AGT ATT ATT ATT AAT ATT AAT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
13522507 ATT GTT AT
1 ATT ATT AT
13522515 ATTTTCATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:13522619 original size:20 final size:21
Alignment explanation
Indices: 13522594--13522635 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13522584 TTGTTATATG
13522594 TATATACATACATACAT-TTT
1 TATATACATACATACATATTT
* *
13522614 TATATATATACGTACATATTT
1 TATATACATACATACATATTT
13522635 T
1 T
13522636 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATACATACATACATATTT
Found at i:13523730 original size:173 final size:173
Alignment explanation
Indices: 13523478--13523830 Score: 645
Period size: 173 Copynumber: 2.0 Consensus size: 173
13523468 ATTCTTCAAA
13523478 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
*
13523543 GGTGTTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
66 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
*
13523608 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAATAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
* *
13523651 GTTTTCAATTTTCGACATCAAGATATTAGCTAATTAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
*
13523716 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTGTGGACCAAAA
66 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
*
13523781 TTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
13523824 -TTTTCAA
1 GTTTTCAA
13523831 GGTGATATGA
Statistics
Matches: 174, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
172 7 0.04
173 167 0.96
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (173 bp):
GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
Found at i:13533240 original size:18 final size:18
Alignment explanation
Indices: 13533196--13533240 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
13533186 TTGAACAAAA
13533196 TGACAAGATATCGTATTGG
1 TGACAAGATATCG-ATTGG
13533215 TGACAAGATATC-ATTGAG
1 TGACAAGATATCGATTG-G
*
13533233 TGATAAGA
1 TGACAAGA
13533241 AGAGAAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
19 12 0.50
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (18 bp):
TGACAAGATATCGATTGG
Found at i:13533624 original size:49 final size:49
Alignment explanation
Indices: 13533571--13534032 Score: 255
Period size: 50 Copynumber: 9.3 Consensus size: 49
13533561 AGCTACATCG
*
13533571 GCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
1 GCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
** * ** * * * * *
13533620 GCGAATCTTATTTCCCTTG-CGGTGCAGTGGAATAGATTGAAGCTACAAC-
1 GCGAATCTTGCTTCCC-CGACATTGCAAT-TAAAAGATTGAGGCCACAACA
* *
13533669 GACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATCGAGGCCACAA-T
1 G-CGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
* * * ** * * * * * *
13533718 GACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAACA
1 G-CGAATCTTGCTTCCCCGACATTGCAAT-TAAAAGATTGAGGCCACAACA
** * *
13533769 GCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATCAAGGCCCCAACG
1 GCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
* ** * * ** * * * * *
13533818 GCGAATCTTACTTTTCTGGCGGTGCAGTGGAACAGATTGAAGCCACAACT
1 GCGAATCTTGCTTCCCCGACATTGCAAT-TAAAAGATTGAGGCCACAACA
* * *
13533868 GCAAATCTTGCTTCCTCGACATTGCAATTAAAAGATTGGGGCCACAACA
1 GCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
** ** * **** * * * * * *
13533917 GCGAATCTTAATTTTCTGGTGGTGCAATGGAACAGATTGAAGCTACAGCG
1 GCGAATCTTGCTTCCCCGACATTGCAAT-TAAAAGATTGAGGCCACAACA
* * * *
13533967 GTGAATCTTGCTTCCCTGACATTGCAATTAAATAGATTGAAGCTACAACA
1 GCGAATCTTGCTTCCCCGACATTGCAATTAAA-AGATTGAGGCCACAACA
* *
13534017 ACGAATCTTACTTCCC
1 GCGAATCTTGCTTCCC
13534033 TGGTGAATAG
Statistics
Matches: 289, Mismatches: 114, Indels: 19
0.68 0.27 0.05
Matches are distributed among these distances:
49 125 0.43
50 163 0.56
51 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (49 bp):
GCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
Found at i:13533727 original size:99 final size:98
Alignment explanation
Indices: 13533556--13534035 Score: 590
Period size: 99 Copynumber: 4.8 Consensus size: 98
13533546 ATAAAACCTT
* * *
13533556 ATTGAAGCTACATCGGCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACAG
1 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA-
* *
13533621 CGAATCTTATTTCCCTTGCGGTGCAGTGGAATAG
65 CGAATCTTATTTCCCTGGCGGTGCAGTGGAACAG
* *
13533655 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATCGAGGCCACAATGA
1 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAA-CA
* *
13533720 CGAATCTTACTTCCCTGGCGGTGTAGTGGAACAG
65 CGAATCTTATTTCCCTGGCGGTGCAGTGGAACAG
** *
13533754 ATTGAAGCTACAAC-AGCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATCAAGGCCCCAACG
1 ATTGAAGCTACAACGA-CGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAAC-
* *
13533818 GCGAATCTTACTTT-TCTGGCGGTGCAGTGGAACAG
64 ACGAATCTTA-TTTCCCTGGCGGTGCAGTGGAACAG
* * * *
13533853 ATTGAAGCCACAACTG-CAAATCTTGCTTCCTCGACATTGCAATTAAAAGATTGGGGCCACAACA
1 ATTGAAGCTACAAC-GACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACA
* * *
13533917 GCGAATCTTAATTT-TCTGGTGGTGCAATGGAACAG
65 -CGAATCTT-ATTTCCCTGGCGGTGCAGTGGAACAG
* ** * * *
13533952 ATTGAAGCTACAGCGGTGAATCTTGCTTCCCTGACATTGCAATTAAATAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAA-AGATTGAGGCCACAAC-
*
13534017 ACGAATCTTACTTCCCTGG
64 ACGAATCTTATTTCCCTGG
13534036 TGAATAGATT
Statistics
Matches: 332, Mismatches: 37, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
98 2 0.01
99 300 0.90
100 29 0.09
101 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (98 bp):
ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACAC
GAATCTTATTTCCCTGGCGGTGCAGTGGAACAG
Found at i:13535722 original size:3 final size:3
Alignment explanation
Indices: 13535708--13535810 Score: 81
Period size: 3 Copynumber: 35.7 Consensus size: 3
13535698 TTGTATTTTG
* ** *
13535708 ATT ATT -TT ATT ATT AAT ATT -TT GATT ATT -TT ATT ATT AAA AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
* * * *
13535751 AAT A-A ATT A-T ATT ATT ATT AGT ATT ATT ATT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
13535797 GTT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
13535811 ATTTTCATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
2 9 0.11
3 70 0.86
4 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:13535731 original size:23 final size:23
Alignment explanation
Indices: 13535701--13535746 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
13535691 CCTCTGCTTG
13535701 TATTTTGATTATTTTATTATTAA
1 TATTTTGATTATTTTATTATTAA
13535724 TATTTTGATTATTTTATTATTAA
1 TATTTTGATTATTTTATTATTAA
13535747 AAATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTGATTATTTTATTATTAA
Found at i:13535915 original size:20 final size:21
Alignment explanation
Indices: 13535890--13535931 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13535880 TTGTTATATG
13535890 TATATACATACATACAT-TTT
1 TATATACATACATACATATTT
* *
13535910 TATATATATACGTACATATTT
1 TATATACATACATACATATTT
13535931 T
1 T
13535932 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATACATACATACATATTT
Found at i:13537028 original size:173 final size:173
Alignment explanation
Indices: 13536776--13537128 Score: 636
Period size: 173 Copynumber: 2.0 Consensus size: 173
13536766 ATTCTTCAAA
13536776 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
* *
13536841 GGTGTTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
66 AGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
*
13536906 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAATAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
* *
13536949 GTTTTCAATTTTCGACATCAAGATATTAGCTAATTAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
*
13537014 AGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTGTGGACCAAAA
66 AGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
*
13537079 TTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
13537122 -TTTTCAA
1 GTTTTCAA
13537129 GGTGATATGA
Statistics
Matches: 173, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
172 7 0.04
173 166 0.96
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (173 bp):
GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
AGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCGTTTTCTGAATTTTATGGACCAAAA
TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
Found at i:13537597 original size:15 final size:15
Alignment explanation
Indices: 13537577--13537606 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13537567 GGTAAAAAAA
*
13537577 GGGGTGGGGGTGGGT
1 GGGGTGGGGGGGGGT
13537592 GGGGTGGGGGGGGGT
1 GGGGTGGGGGGGGGT
13537607 AATGGGTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.83, T:0.17
Consensus pattern (15 bp):
GGGGTGGGGGGGGGT
Found at i:13539710 original size:24 final size:24
Alignment explanation
Indices: 13539659--13539710 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13539649 AATTGAGTTT
* * *
13539659 CTTTTCCTAGTTAAACTCTACTAT
1 CTTTTCCTAGTCAAACTCTAATAA
13539683 CTTTTCCTAGTCAAACTCTAATAA
1 CTTTTCCTAGTCAAACTCTAATAA
13539707 CTTT
1 CTTT
13539711 AGGGATATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44
Consensus pattern (24 bp):
CTTTTCCTAGTCAAACTCTAATAA
Done.