Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 60 of 163
Found at i:19770614 original size:35 final size:35
Alignment explanation
Indices: 19770570--19770711 Score: 169
Period size: 35 Copynumber: 4.1 Consensus size: 35
19770560 TTCACTTGTC
* * *
19770570 TTTTATTGCAGGGAATCTCTCCTGTTCACGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* *
19770605 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* * *
19770640 -TTTCTTGCAGGGAATCTCTCCTGTCCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* * * *
19770674 TGTTGTTGCAGGGAATCTCTCCAGTTCATGTATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
19770709 TTT
1 TTT
19770712 CTTTTTGGAC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
34 29 0.33
35 59 0.67
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
Found at i:19770653 original size:34 final size:34
Alignment explanation
Indices: 19770575--19770701 Score: 173
Period size: 35 Copynumber: 3.7 Consensus size: 34
19770565 TTGTCTTTTA
*
19770575 TTGCAGGGAATCTCTCCTGTTCACGTATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* * * *
19770610 TTGCAGGGAATCTCTCCTATTCACACATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
*
19770644 TTGCAGGGAATCTCTCCTGTCCACGCATTATGTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTAT-TTG
*
19770679 TTGCAGGGAATCTCTCCAGTTCA
1 TTGCAGGGAATCTCTCCTGTTCA
19770702 TGTATCATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 30 0.38
35 49 0.62
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
Found at i:19778654 original size:29 final size:29
Alignment explanation
Indices: 19778622--19778891 Score: 283
Period size: 29 Copynumber: 9.3 Consensus size: 29
19778612 TGGATAGTTT
*
19778622 CGACCATCGACTATGAAAAGGGATGGTAA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
19778651 CGACCATCAACAATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
19778680 TGACCATCAACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * * **
19778709 CGACCATCAAATATGAAAAGGGATAGTTT
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
19778738 CGACTATCAACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * **
19778767 CGATCATCGAATATGAAAAGGGA-GAGTTT
1 CGACCATCGACTATGAAAAGGGATG-GTGA
*
19778796 CGACTATCGACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * *
19778825 TGACCATTGATTATGAAAAGGGATGGTTG-
1 CGACCATCGACTATGAAAAGGGATGG-TGA
* * * *
19778854 TGACCATCGAATATTAAAAGGGATGGTTA
1 CGACCATCGACTATGAAAAGGGATGGTGA
*
19778883 TGACCATCG
1 CGACCATCG
19778892 TTTAGCACAC
Statistics
Matches: 203, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 198 0.98
30 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (29 bp):
CGACCATCGACTATGAAAAGGGATGGTGA
Found at i:19778754 original size:87 final size:87
Alignment explanation
Indices: 19778607--19778891 Score: 326
Period size: 87 Copynumber: 3.3 Consensus size: 87
19778597 ATTAATTAAA
* * * * *
19778607 GAAAATGGATAGTTTCGACCATCGACTATGAAAAGGGATGGTAACGACCATCAACAATGAAAAGG
1 GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
19778672 GATGGTGATGACCATC-AACTAT
66 GATGGTGATGACCATCGAA-TAT
* * * * * *
19778694 GAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGG
1 GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
* *
19778759 GATGGTGACGATCATCGAATAT
66 GATGGTGATGACCATCGAATAT
* * ** *
19778781 GAAAAGGGA-GAGTTTCGACTATCGACTATGAAAAGGGATGGTGAT-GACCATTGATTATGAAAA
1 GAAAAGGGATG-GTTACGACCATCGACTATGAAAAGGGATGGT-ATCGACCATCAACTATGAAAA
19778844 GGGATGGTTG-TGACCATCGAATAT
64 GGGATGG-TGATGACCATCGAATAT
* *
19778868 TAAAAGGGATGGTTATGACCATCG
1 GAAAAGGGATGGTTACGACCATCG
19778892 TTTAGCACAC
Statistics
Matches: 163, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
86 1 0.01
87 156 0.96
88 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (87 bp):
GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
GATGGTGATGACCATCGAATAT
Found at i:19779030 original size:20 final size:20
Alignment explanation
Indices: 19779005--19779043 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
19778995 TTATGAAAGG
19779005 AACGATTTAAGTGATGTTAA
1 AACGATTTAAGTGATGTTAA
19779025 AACGATTTAAGTGATGTTA
1 AACGATTTAAGTGATGTTA
19779044 TGTTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
AACGATTTAAGTGATGTTAA
Found at i:19782593 original size:20 final size:20
Alignment explanation
Indices: 19782568--19782614 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
19782558 AGCTCGTTTC
*
19782568 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
19782588 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
19782608 CAGCTCA
1 CAGCTCA
19782615 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:19789564 original size:30 final size:30
Alignment explanation
Indices: 19789525--19789699 Score: 124
Period size: 30 Copynumber: 5.9 Consensus size: 30
19789515 GGATCACATC
*
19789525 ACCATCCCTTTTCATAGTTCAATAGTCG-A
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * * * *
19789554 AGCTATCCCTTATCATAATTCGATGGTCGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTCGTA
* * * *
19789585 ACCATCCCTTTTCATTGTT-TATGGTCGTC
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * * *
19789614 ACCATCCTTTTTCATTGTT-GATGGTCGTT
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * *
19789643 ACCATCCCTTTTCACAATTCGATAGCCG-A
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * *
19789672 AGCTATCCCTTTTCGTATTTCGATAGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTC
19789700 AAAGCTATCC
Statistics
Matches: 116, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
29 52 0.45
30 63 0.54
31 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (30 bp):
ACCATCCCTTTTCATAGTTCGATAGTCGTA
Found at i:19789611 original size:29 final size:29
Alignment explanation
Indices: 19789575--19789656 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
19789565 ATCATAATTC
19789575 GATGGTCGTCACCATCCCTTTTCATTGTT
1 GATGGTCGTCACCATCCCTTTTCATTGTT
* *
19789604 TATGGTCGTCACCATCCTTTTTCATTGTT
1 GATGGTCGTCACCATCCCTTTTCATTGTT
*
19789633 GATGGTCGTTACCATCCCTTTTCA
1 GATGGTCGTCACCATCCCTTTTCA
19789657 CAATTCGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.43
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATTGTT
Found at i:19789705 original size:30 final size:30
Alignment explanation
Indices: 19789646--19789717 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
19789636 GGTCGTTACC
** *
19789646 ATCCCTTTTCACAATTCGATAGCCGAAGCT
1 ATCCCTTTTCGTAATTCGATAGCCAAAGCT
* *
19789676 ATCCCTTTTCGTATTTCGATAGTCAAAGCT
1 ATCCCTTTTCGTAATTCGATAGCCAAAGCT
19789706 ATCCCTTTTCGT
1 ATCCCTTTTCGT
19789718 TGGTCGACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCGTAATTCGATAGCCAAAGCT
Found at i:19803642 original size:18 final size:18
Alignment explanation
Indices: 19803619--19803653 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19803609 CAAGAATAGT
19803619 AAGCATAAAAATAGTTTC
1 AAGCATAAAAATAGTTTC
*
19803637 AAGCATGAAAATAGTTT
1 AAGCATAAAAATAGTTT
19803654 GGCACATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATAAAAATAGTTTC
Found at i:19818524 original size:63 final size:63
Alignment explanation
Indices: 19818403--19818560 Score: 226
Period size: 63 Copynumber: 2.5 Consensus size: 63
19818393 TGTCTCTGTG
* * ** *
19818403 GATGCCATGGAGTCTTTCATCAATGGTCTTACAATGATCTGCCACCTTAGCGTACTATCATAT
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
* * * * *
19818466 GATGTCATGCAGTCTTTCATCCATGGTCTTACAATAATCCACCATCTTGGCGTGCTATCATAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
19818529 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
19818561 TCATTATACC
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (63 bp):
GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
Found at i:19821179 original size:27 final size:27
Alignment explanation
Indices: 19821149--19821264 Score: 121
Period size: 26 Copynumber: 4.4 Consensus size: 27
19821139 GTGGATGATT
19821149 GAAATACCCCCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
** *
19821176 GAAATA-CCCTAAAGGGTAAAATAACC
1 GAAATACCCCCGAAGGGTAAAATGACC
* *
19821202 AAAATACCCTCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
* * *
19821229 AAAATACCCTCGTAA-GG-AAAATGACT
1 GAAATACCCCCG-AAGGGTAAAATGACC
*
19821255 GATATACCCC
1 GAAATACCCC
19821265 TAGGAGTCGG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
26 37 0.49
27 36 0.48
28 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (27 bp):
GAAATACCCCCGAAGGGTAAAATGACC
Found at i:19821262 original size:53 final size:53
Alignment explanation
Indices: 19821143--19821264 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 53
19821133 TTGTGGGTGG
* *
19821143 ATGATTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTAAAGGGTAAA
1 ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCTAAAGGGTAAA
* ** * *
19821196 ATAACCAAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCGTAA-GG-AAA
1 ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCT--AAAGGGTAAA
*
19821249 ATGACTGATATACCCC
1 ATGACTGAAATACCCC
19821265 TAGGAGTCGG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
53 51 0.93
54 2 0.04
55 2 0.04
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (53 bp):
ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCTAAAGGGTAAA
Found at i:19821263 original size:26 final size:27
Alignment explanation
Indices: 19821150--19821253 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
19821140 TGGATGATTG
* *
19821150 AAATACCCCCGAAGGGTAAAATGACCG
1 AAATACCCTCGAAGGGTAAAATGACCA
* *
19821177 AAATACCCT-AAAGGGTAAAATAACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
19821203 AAATACCCTCGAAGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
19821230 AAATACCCTCGTAA-GG-AAAATGAC
1 AAATACCCTCG-AAGGGTAAAATGAC
19821254 TGATATACCC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 31 0.45
27 36 0.52
28 2 0.03
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.14
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCA
Found at i:19822406 original size:17 final size:18
Alignment explanation
Indices: 19822379--19822419 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19822369 AACTCTTAAA
*
19822379 GTAGAGAAAACT-GATACT
1 GTAG-GAAAACTAGAAACT
19822397 GTAGGAAAACTAGAAACT
1 GTAGGAAAACTAGAAACT
19822415 GTAGG
1 GTAGG
19822420 GAGACTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.20
Consensus pattern (18 bp):
GTAGGAAAACTAGAAACT
Found at i:19829686 original size:18 final size:18
Alignment explanation
Indices: 19829663--19829702 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
19829653 AAAGGTAGAT
19829663 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
19829681 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
19829699 AGAA
1 AGAA
19829703 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:19831494 original size:33 final size:34
Alignment explanation
Indices: 19831457--19831528 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
19831447 GAGTTAGTTT
*
19831457 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
* * *
19831490 ATTAATTTTAGTTCAACTTAAATAAGTGTTGGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
19831524 ATTAA
1 ATTAA
19831529 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:19832629 original size:12 final size:12
Alignment explanation
Indices: 19832612--19832636 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19832602 CCTTATACAC
19832612 ATTACACATTGA
1 ATTACACATTGA
19832624 ATTACACATTGA
1 ATTACACATTGA
19832636 A
1 A
19832637 ATCAGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:19834773 original size:27 final size:27
Alignment explanation
Indices: 19834636--19834789 Score: 150
Period size: 27 Copynumber: 5.7 Consensus size: 27
19834626 TCGTGGGCGG
*
19834636 ATGACTGAAATACCCTCGAAA-GGTAAA
1 ATGACTGAAATACCC-CTAAAGGGTAAA
* ** * * *
19834663 ATAACCAAAATACCCTTGAAGCGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
* *
19834690 ATAACTAAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
*
19834717 ATGACTTAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
**
19834744 ATGA-TCGAAATACCCCTGTAGGGTAAA
1 ATGACT-GAAATACCCCTAAAGGGTAAA
* *
19834771 ATGACTGATATACACCTAA
1 ATGACTGAAATACCCCTAA
19834790 GAGTCGGAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.03
27 100 0.96
28 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (27 bp):
ATGACTGAAATACCCCTAAAGGGTAAA
Found at i:19834789 original size:81 final size:81
Alignment explanation
Indices: 19834636--19834789 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
19834626 TCGTGGGCGG
*
19834636 ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCTTGAAGCGTAAAATAACTAAAAT
1 ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAAT
*
19834701 ACCCCTAAAGGGTAAA
66 ACACCTAAAGGGTAAA
* * * * * * * * * *
19834717 ATGACTTAAATACCC-CTAAAGGGTAAAATGATCGAAATACCCCTGTAGGGTAAAATGACTGATA
1 ATGACTGAAATACCCTCGAAA-GGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAA
19834781 TACACCTAA
65 TACACCTAA
19834790 GAGTCGGAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 4 0.07
81 56 0.93
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (81 bp):
ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAAT
ACACCTAAAGGGTAAA
Found at i:19838015 original size:27 final size:27
Alignment explanation
Indices: 19837784--19838036 Score: 273
Period size: 27 Copynumber: 9.4 Consensus size: 27
19837774 CTAATAGATG
* *
19837784 AAAATGACTGAAATACACCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
19837811 AAAATGACTGAAATACCCCTATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
19837838 AAAATGACT-AAAGTACCCTCATAGGGT
1 AAAATGACTGAAA-TACCCCCATAGGGT
**
19837865 AAAATGACTGAAATACCCAAATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
19837892 AAAATAACTGAAATACCCTCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
19837919 AAAATGATTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
19837946 AACATGA-TCGAAATACCCCCATAAGAT
1 AAAATGACT-GAAATACCCCCATAGGGT
*
19837973 AAAATGA-TCAAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* **
19838000 AAAATGATTGTTATA-CCCC-TAGGAGAT
1 AAAATGACTGAAATACCCCCATAGG-G-T
19838027 AAAATGACTG
1 AAAATGACTG
19838037 TTATGGCCTT
Statistics
Matches: 196, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
25 4 0.02
26 9 0.05
27 179 0.91
28 4 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:19838277 original size:26 final size:26
Alignment explanation
Indices: 19838241--19838321 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
19838231 TTTGCCACAT
*
19838241 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
19838267 ATACTGATACTGACAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
19838293 ATGCT-ATTACTGGCAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
19838319 ATA
1 ATA
19838322 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:19838472 original size:28 final size:28
Alignment explanation
Indices: 19838423--19838573 Score: 182
Period size: 28 Copynumber: 5.4 Consensus size: 28
19838413 TATTGCACTG
*
19838423 CACTGTTATTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* * *
19838451 CAGTGATT-CTGTATTGGACTAAGCCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
** * *
19838479 TGCTGTTACTGTATTAGACTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
19838507 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
*
19838535 CACTGTTACTGTATTGGGCTAAGGACCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
19838563 CACTG-TACTGT
1 CACTGTTACTGT
19838574 CACTGAATAG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.10
28 91 0.87
29 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:19838514 original size:56 final size:56
Alignment explanation
Indices: 19838423--19838567 Score: 209
Period size: 56 Copynumber: 2.6 Consensus size: 56
19838413 TATTGCACTG
* *
19838423 CACTGTTATTGTATTGGGCTAAGGCCCACAGTGATTCTGTATTGGACTAAGCCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
** * * * *
19838479 TGCTGTTACTGTATTAGACTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
*
19838535 CACTGTTACTGTATTGGGCTAAGGACCACACTG
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTG
19838568 TACTGTCACT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 76 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
Found at i:19838605 original size:61 final size:56
Alignment explanation
Indices: 19838423--19838605 Score: 150
Period size: 56 Copynumber: 3.2 Consensus size: 56
19838413 TATTGCACTG
* * * * * * * * *
19838423 CACTGTTATTGTATTGGGCTAAGGCCCACAGTGATTCTGTATTGGACTAAGCCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
** * * *
19838479 TGCTGTTACTGTATTAGACTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
* * *
19838535 CACTGTTACTGTATTGGGCTAAGGACCACACTGTACTGTCACTGAATAGGGCTTAGGCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTG-A-T-T--CTGAATAGGGCTAAGGCCCA
**
19838596 GTCTGTTACT
1 CACTGTTACT
19838606 ACATGTTGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
56 76 0.73
57 1 0.01
58 1 0.01
59 1 0.01
61 25 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
Found at i:19845235 original size:16 final size:16
Alignment explanation
Indices: 19845214--19845270 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
19845204 TCCTATAGTA
19845214 TCACAATTTATAGTTT
1 TCACAATTTATAGTTT
*
19845230 TCACAATTCTATTG-TT
1 TCACAATT-TATAGTTT
*
19845246 TCA-AAGTCTATAGTTT
1 TCACAA-TTTATAGTTT
19845262 TCAC-ATTTA
1 TCACAATTTA
19845271 AACAACACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 9 0.27
16 20 0.61
17 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (16 bp):
TCACAATTTATAGTTT
Found at i:19845261 original size:15 final size:16
Alignment explanation
Indices: 19845206--19845266 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
19845196 CTATAGTCTC
*
19845206 CTATAGTATCACAA-T
1 CTATAGTTTCACAAGT
* *
19845221 TTATAGTTTTCACAATT
1 CTATAG-TTTCACAAGT
*
19845238 CTATTGTTTCA-AAGT
1 CTATAGTTTCACAAGT
19845253 CTATAGTTTTCACA
1 CTATAG-TTTCACA
19845267 TTTAAACAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 13 0.36
16 17 0.47
17 6 0.17
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.44
Consensus pattern (16 bp):
CTATAGTTTCACAAGT
Found at i:19846732 original size:20 final size:20
Alignment explanation
Indices: 19846709--19846750 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
19846699 CATAAATTAA
* *
19846709 TTAATTAAATAAAATTTTAT
1 TTAAGTAAATAAAATTATAT
19846729 TTAAGTAAATAAAATTATAT
1 TTAAGTAAATAAAATTATAT
19846749 TT
1 TT
19846751 CACTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGTAAATAAAATTATAT
Found at i:19854999 original size:17 final size:16
Alignment explanation
Indices: 19854973--19855004 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19854963 TGATAGATCT
19854973 CCGACGAGCTTCCAAA
1 CCGACGAGCTTCCAAA
19854989 CCGATCGAGCTTCCAA
1 CCGA-CGAGCTTCCAA
19855005 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (16 bp):
CCGACGAGCTTCCAAA
Found at i:19863017 original size:43 final size:43
Alignment explanation
Indices: 19862967--19863053 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
19862957 CCATAAGTTA
*
19862967 ACCTATACATGTCATTATAACCTTGATTACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
19863010 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
19863053 A
1 A
19863054 AAAATATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (43 bp):
ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
Found at i:19864401 original size:138 final size:138
Alignment explanation
Indices: 19864150--19864408 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 138
19864140 AGGCCTACTC
* *
19864150 ACACAAGCTGACGGTTAAAATGTAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTG
1 ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTA
** * **
19864215 ACTAAAGCCGAACTGCAGCCATCAGTAGGACATTCAGGACCAGTACCCGAAACATGGTAACTTGG
66 ACTAAAGAAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACTTGG
19864280 GTCTGCTT
131 GTCTGCTT
* * * * *
19864288 ACACAAGCTGACGGTTAGAATGAAAGTTACATGATGCTGCTCATACAAGCTGATGAGTAT-TCGT
1 ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCT-GT
* * *
19864352 AAC-AAATGTAAGACCT-CAGCCATCGGTAGAACATTCAGGACCAAAACCCGCAACATG
65 AACTAAA-G-AAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATG
19864409 AAAGCCCTAA
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 4 0.04
138 95 0.92
139 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (138 bp):
ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTA
ACTAAAGAAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACTTGG
GTCTGCTT
Found at i:19865629 original size:20 final size:20
Alignment explanation
Indices: 19865604--19865648 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
19865594 TAAATACACA
19865604 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
19865624 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
19865644 TAATT
1 TAATT
19865649 CGGTTAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:19865654 original size:20 final size:19
Alignment explanation
Indices: 19865614--19865658 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
19865604 TAATTAAAAC
19865614 TAGACACAATTAATTAAGT
1 TAGACACAATTAATTAAGT
**
19865633 TAAGACACAATTAATTCGGT
1 T-AGACACAATTAATTAAGT
19865653 TAGACA
1 TAGACA
19865659 AGACATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (19 bp):
TAGACACAATTAATTAAGT
Found at i:19870093 original size:19 final size:19
Alignment explanation
Indices: 19870071--19870173 Score: 66
Period size: 19 Copynumber: 5.3 Consensus size: 19
19870061 CACTTACATG
*
19870071 CCCCTGTCGTACTTCGGTA
1 CCCCTGTCGTACTTCAGTA
* * *
19870090 CCCCTGATTGCACTT-ACGTG
1 CCCCTG-TCGTACTTCA-GTA
* *
19870110 CTCCTATCGTACTTCAGTA
1 CCCCTGTCGTACTTCAGTA
* *
19870129 CCCCTGATCGCACTT-ACGTG
1 CCCCTG-TCGTACTTCA-GTA
* *
19870149 TCCCTGTCGTACTTTAGTA
1 CCCCTGTCGTACTTCAGTA
19870168 CCCCTG
1 CCCCTG
19870174 GTTGCGCTTA
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
19 33 0.54
20 28 0.46
ACGTcount: A:0.15, C:0.36, G:0.17, T:0.32
Consensus pattern (19 bp):
CCCCTGTCGTACTTCAGTA
Found at i:19870120 original size:39 final size:39
Alignment explanation
Indices: 19870053--19870188 Score: 175
Period size: 39 Copynumber: 3.5 Consensus size: 39
19870043 TAATTATACT
* * *
19870053 CCTGATCGCACTTACATGCCCCTGTCGTACTTCGGTACC
1 CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
* *
19870092 CCTGATTGCACTTACGTGCTCCTATCGTACTTCAGTACC
1 CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
*
19870131 CCTGATCGCACTTACGTG-TCCCTGTCGTACTTTAGTACC
1 CCTGATCGCACTTACGTGCT-CCTGTCGTACTTCAGTACC
* * *
19870170 CCTGGTTGCGCTTACGTGC
1 CCTGATCGCACTTACGTGC
19870189 CCCAGTTGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.01
39 83 0.99
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.32
Consensus pattern (39 bp):
CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
Found at i:19870220 original size:78 final size:77
Alignment explanation
Indices: 19870048--19870228 Score: 211
Period size: 78 Copynumber: 2.3 Consensus size: 77
19870038 TTATATAATT
* *
19870048 ATACTCCTGATCGCACTTACATGCCCCTGTCGTACTTCGGTACCCCTGATTGCACTTACGTGCTC
1 ATACTCCTGATCGCACTTACGTGCCCCTGTCGTACTTCAGTACCCCTGATTGCACTTACGTGCTC
* *
19870113 CTATCGTACTTC
66 CCATCGTACCTC
* * * * *
19870125 AGTACCCCTGATCGCACTTACGTGTCCCTGTCGTACTTTAGTACCCCTGGTTGCGCTTACGTGC-
1 A-TACTCCTGATCGCACTTACGTGCCCCTGTCGTACTTCAGTACCCCTGATTGCACTTACGTGCT
*
19870189 CCCAGTTGTACCTC
65 CCCA-TCGTACCTC
* * *
19870203 GATACTCTTGATGGCACTTTCGTGCC
1 -ATACTCCTGATCGCACTTACGTGCC
19870229 GTGGTCACAC
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
77 4 0.05
78 81 0.94
79 1 0.01
ACGTcount: A:0.15, C:0.34, G:0.19, T:0.32
Consensus pattern (77 bp):
ATACTCCTGATCGCACTTACGTGCCCCTGTCGTACTTCAGTACCCCTGATTGCACTTACGTGCTC
CCATCGTACCTC
Found at i:19874125 original size:20 final size:20
Alignment explanation
Indices: 19874082--19874138 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
19874072 GATGCATAAC
*
19874082 AGGGGCACCAAAGTGCAAAC
1 AGGGGCACCAAAGTGCAAAA
** *
19874102 AGGGGCACTGAAGTTCAAAA
1 AGGGGCACCAAAGTGCAAAA
*
19874122 AGGGTCA-CAAACGTGCA
1 AGGGGCACCAAA-GTGCA
19874139 TTCAAGGGTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.39, C:0.21, G:0.30, T:0.11
Consensus pattern (20 bp):
AGGGGCACCAAAGTGCAAAA
Found at i:19881763 original size:14 final size:14
Alignment explanation
Indices: 19881744--19881790 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
19881734 AAATGCAAAG
19881744 TATGAAGTGAAATA
1 TATGAAGTGAAATA
* * *
19881758 TATGAAATG-AGTT
1 TATGAAGTGAAATA
*
19881771 TATGAAGTGAAATG
1 TATGAAGTGAAATA
19881785 TATGAA
1 TATGAA
19881791 ATGAGTTTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (14 bp):
TATGAAGTGAAATA
Found at i:19881775 original size:27 final size:27
Alignment explanation
Indices: 19881744--19881799 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
19881734 AAATGCAAAG
19881744 TATGAAGTGAAATATATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
*
19881771 TATGAAGTGAAATGTATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
19881798 TA
1 TA
19881800 GCAACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (27 bp):
TATGAAGTGAAATATATGAAATGAGTT
Found at i:19883306 original size:20 final size:20
Alignment explanation
Indices: 19883281--19883332 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19883271 AATCAAGTGC
*
19883281 AAATGATTTTAACCATGTCA
1 AAATGATTTTAACCAAGTCA
* *
19883301 AAATGATTTCAATCAAGTCA
1 AAATGATTTTAACCAAGTCA
*
19883321 AAATCATTTTAA
1 AAATGATTTTAA
19883333 AATAATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:19886391 original size:54 final size:53
Alignment explanation
Indices: 19886309--19886448 Score: 156
Period size: 54 Copynumber: 2.6 Consensus size: 53
19886299 AAATATTGTT
* * * **
19886309 AAATGACTGAATTACCCCCAGAGGGTAAAATGATCGAATTACCCCCGA-AGGGTA
1 AAATGACCGAAATA-CCCCAAAGGGTAAAATGATAAAATT-CCCCCGATAGGGTA
* *
19886363 AAATGACCGAAATACCCCTAAAGGGTAAAATGATAAAATTGCCCCTATAGGGTA
1 AAATGACCGAAATACCCC-AAAGGGTAAAATGATAAAATTCCCCCGATAGGGTA
* *
19886417 AAATGACCGTAATAACCCCATAGGGTAAAATG
1 AAATGACCGAAAT-ACCCCAAAGGGTAAAATG
19886449 TCTGAAATAC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 9 0.12
54 60 0.81
55 5 0.07
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (53 bp):
AAATGACCGAAATACCCCAAAGGGTAAAATGATAAAATTCCCCCGATAGGGTA
Found at i:19886457 original size:27 final size:28
Alignment explanation
Indices: 19886309--19886457 Score: 121
Period size: 27 Copynumber: 5.5 Consensus size: 28
19886299 AAATATTGTT
* * *
19886309 AAATGACTG-AATTACCCCCAGAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* * *
19886336 AAATGA-TCGAATTACCCCCGA-AGGGTA
1 AAATGACT-GAAATAACCCCTATAGGGTA
* *
19886363 AAATGACCGAAAT-ACCCCTAAAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* **
19886390 AAATGA-TAAAATTGCCCCTATAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* *
19886417 AAATGACCGTAATAACCCC-ATAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
*
19886444 AAATGTCTGAAATA
1 AAATGACTGAAATA
19886458 CATGTGTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
26 10 0.10
27 72 0.75
28 14 0.15
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (28 bp):
AAATGACTGAAATAACCCCTATAGGGTA
Found at i:19886531 original size:24 final size:23
Alignment explanation
Indices: 19886498--19886580 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 23
19886488 CTCGTGGGTA
* * *
19886498 AATGATTGATTTGTCCGTGATGT
1 AATGACTGATTTGTCTGTGATTT
*
19886521 ATATGACTGATTTGTCTTTGATTT
1 A-ATGACTGATTTGTCTGTGATTT
19886545 AAATGACTGATTTGTCTGTGATTT
1 -AATGACTGATTTGTCTGTGATTT
19886569 GAATGACTGATT
1 -AATGACTGATT
19886581 CTGAGCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGATTT
Found at i:19886766 original size:32 final size:32
Alignment explanation
Indices: 19886725--19886927 Score: 291
Period size: 32 Copynumber: 6.4 Consensus size: 32
19886715 CCTTCGATGC
19886725 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
19886757 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
19886789 TACTGATGGCTTTGTGCCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* **
19886821 TATTGATGGCTTTGTGCAAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * *
19886853 TACTGATGGCTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
19886885 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
19886916 TACTTATGGCTT
1 TACTGATGGCTT
19886928 GTAGCCATTC
Statistics
Matches: 153, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 11 0.07
32 142 0.93
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:19886973 original size:29 final size:29
Alignment explanation
Indices: 19886918--19886973 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
19886908 TATTACTGTA
* * *
19886918 CTTATGGCTTGTAGCCATTCTGCTTATAG
1 CTTATAGCTTATAGCCATCCTGCTTATAG
* *
19886947 CTTATAGCTTATAGCTATCCTGTTTAT
1 CTTATAGCTTATAGCCATCCTGCTTAT
19886974 GGCTCTTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
CTTATAGCTTATAGCCATCCTGCTTATAG
Found at i:19887640 original size:16 final size:17
Alignment explanation
Indices: 19887608--19887640 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19887598 TTTCAAGAAG
19887608 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
19887626 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
19887641 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:19891502 original size:25 final size:27
Alignment explanation
Indices: 19891474--19891553 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
19891464 ACAATCATAC
*
19891474 ATAACATA-GAGCAT-GCAGTCATTTT
1 ATAACATAGGAGCATAACAGTCATTTT
*
19891499 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAGGAGCATAACAGTCATTTT
*
19891526 ACT-ACGTGAGG-GCATAACAGTCATTTT
1 A-TAACAT-AGGAGCATAACAGTCATTTT
19891553 A
1 A
19891554 CATCAGTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.17
26 5 0.10
27 31 0.65
28 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (27 bp):
ATAACATAGGAGCATAACAGTCATTTT
Found at i:19891524 original size:27 final size:27
Alignment explanation
Indices: 19891489--19891554 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
19891479 ATAGAGCATG
19891489 CAGTCATTTTA-TAACAT-AGGGGCATAA
1 CAGTCATTTTACT-ACATGA-GGGCATAA
*
19891516 CAGTCATTTTACTACGTGAGGGCATAA
1 CAGTCATTTTACTACATGAGGGCATAA
19891543 CAGTCATTTTAC
1 CAGTCATTTTAC
19891555 ATCAGTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (27 bp):
CAGTCATTTTACTACATGAGGGCATAA
Found at i:19895254 original size:20 final size:19
Alignment explanation
Indices: 19895226--19895276 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
19895216 AATCAAGTGC
*
19895226 AAATGATTTTAACCATGTCA
1 AAATAATTTTAACCA-GTCA
* *
19895246 AAATAATTTCAATCAGTCA
1 AAATAATTTTAACCAGTCA
*
19895265 AAATCATTTTAA
1 AAATAATTTTAA
19895277 AATGATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (19 bp):
AAATAATTTTAACCAGTCA
Found at i:19896586 original size:14 final size:15
Alignment explanation
Indices: 19896550--19896588 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
19896540 TCAATCTTTG
*
19896550 CACATAATCATGCAT
1 CACAAAATCATGCAT
19896565 CAACAAAATCATGC-T
1 C-ACAAAATCATGCAT
19896580 CACAAAATC
1 CACAAAATC
19896589 TTTTTATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (15 bp):
CACAAAATCATGCAT
Found at i:19901488 original size:42 final size:42
Alignment explanation
Indices: 19901420--19901532 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
19901410 ACAGCCGTGG
* * * *
19901420 CACACGCCCGTGTGCCAGGCCGTGTAACTCTCGAAA-CTGGCC
1 CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATC-AGCC
*
19901462 CACATGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
1 CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
*
19901504 CACACGCCCGTGTGCTAGGCTATGTAACT
1 CACACGCCCGTGTGCTAGGCCATGTAACT
19901533 AACTGACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
Found at i:19904078 original size:24 final size:25
Alignment explanation
Indices: 19904036--19904082 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
19904026 CAAAATTTCT
19904036 TAACGAAACTTTAATACAACCTTAC
1 TAACGAAACTTTAATACAACCTTAC
19904061 TAACGAAAC-TTAATACAACCTT
1 TAACGAAACTTTAATACAACCTT
19904083 CATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (25 bp):
TAACGAAACTTTAATACAACCTTAC
Found at i:19912975 original size:61 final size:61
Alignment explanation
Indices: 19912887--19913004 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
19912877 ACATACGGCC
* *
19912887 TGGCGACATAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGTGTTACGGGT
1 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTACGGGT
19912948 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTAC
1 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTAC
19913005 ATGTCCCTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (61 bp):
TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTACGGGT
Found at i:19921223 original size:24 final size:24
Alignment explanation
Indices: 19921191--19921238 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19921181 CTAGATGATT
19921191 TGTTTGACCAATTGAAGGGAACCA
1 TGTTTGACCAATTGAAGGGAACCA
19921215 TGTTTGACCAATTGAAGGGAACCA
1 TGTTTGACCAATTGAAGGGAACCA
19921239 CTGTGTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
TGTTTGACCAATTGAAGGGAACCA
Found at i:19923166 original size:41 final size:42
Alignment explanation
Indices: 19923145--19923282 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 42
19923135 ATCCAATATA
19923145 CATTT-CAATACCACAATAATTC-ATTTAATTCAAATCATAG
1 CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
*
19923185 CATTTGCAATACCACAATAATTCATTTAATTCATTTAATTCAAATCATAT
1 CATTTGCAATACCACAATAATTC-----A---ATTTAATTCAAATCATAG
* *
19923235 CTTTTGCAATACCACAATAATTC-ATTTAATTCAAATCATAT
1 CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
19923276 CATTTGC
1 CATTTGC
19923283 TAATTCACGT
Statistics
Matches: 85, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
40 5 0.06
41 41 0.48
50 39 0.46
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (42 bp):
CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
Found at i:19923170 original size:21 final size:21
Alignment explanation
Indices: 19923145--19923211 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
19923135 ATCCAATATA
19923145 CATTTCAATACCACAATAATT
1 CATTTCAATACCACAATAATT
* * *
19923166 CATTT-AAT-TCA-AATCATAG
1 CATTTCAATACCACAATAAT-T
19923185 CATTTGCAATACCACAATAATT
1 CATTT-CAATACCACAATAATT
19923207 CATTT
1 CATTT
19923212 AATTCATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 3 0.09
21 8 0.23
22 7 0.20
23 5 0.14
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (21 bp):
CATTTCAATACCACAATAATT
Found at i:19923215 original size:50 final size:50
Alignment explanation
Indices: 19923161--19923267 Score: 196
Period size: 50 Copynumber: 2.1 Consensus size: 50
19923151 AATACCACAA
19923161 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
1 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
* *
19923211 TAATTCATTTAATTCAAATCATATCTTTTGCAATACCACAATAATTCATT
1 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
19923261 TAATTCA
1 TAATTCA
19923268 AATCATATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (50 bp):
TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
Found at i:19923216 original size:9 final size:9
Alignment explanation
Indices: 19923202--19923226 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19923192 AATACCACAA
19923202 TAATTCATT
1 TAATTCATT
19923211 TAATTCATT
1 TAATTCATT
19923220 TAATTCA
1 TAATTCA
19923227 AATCATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATTCATT
Found at i:19923288 original size:22 final size:22
Alignment explanation
Indices: 19923220--19923289 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
19923210 TTAATTCATT
*
19923220 TAATTCAAATCATATCTTTTGC
1 TAATTCAAATCATATCATTTGC
* *
19923242 -AATACCACAATAAT-TCA-TT--
1 TAAT-TCA-AATCATATCATTTGC
19923261 TAATTCAAATCATATCATTTGC
1 TAATTCAAATCATATCATTTGC
19923283 TAATTCA
1 TAATTCA
19923290 CGTACAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
18 5 0.14
19 5 0.14
20 5 0.14
21 5 0.14
22 11 0.31
23 5 0.14
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.40
Consensus pattern (22 bp):
TAATTCAAATCATATCATTTGC
Found at i:19924831 original size:45 final size:45
Alignment explanation
Indices: 19924767--19924855 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
19924757 AACAGATACT
* * *
19924767 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
* *
19924812 CGGTGGAATCAACACATAGCAACCACTTTGCTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
19924856 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:19924973 original size:51 final size:50
Alignment explanation
Indices: 19924862--19925053 Score: 233
Period size: 51 Copynumber: 3.8 Consensus size: 50
19924852 ATGTTCAGTT
* * * **
19924862 CACATAGTAGCCTGCACATAGGTTCTACACATGTGACCATTACCATTCAATA
1 CACATAGTAGCCTGCACATA-GTACTACACATGTGACCA-TACTATCCGGTA
* * *
19924914 CACGTAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATACTATCCGGTA
* * *
19924965 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATA-TTTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATACTATCCGGTA
*
19925015 CACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
19925054 CACTTTCACT
Statistics
Matches: 121, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
49 2 0.02
50 43 0.36
51 55 0.45
52 21 0.17
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATACTATCCGGTA
Found at i:19925031 original size:101 final size:102
Alignment explanation
Indices: 19924864--19925049 Score: 279
Period size: 101 Copynumber: 1.8 Consensus size: 102
19924854 GTTCAGTTCA
* *
19924864 CATAGTAGCCTGCACATAGGTTCTACACATGTGACCATTACCATTCAATACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGGTACTACACATGCGACCATTA-CATTCAATACACGTAGTAGCCTGC
19924929 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
65 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
* **
19924967 CATAGTAGCCTGCACATA-GTACTACACATGCGACC-TATA-TTTCCGGTACACGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGGTACTACACATGCGACCAT-TACATT-CAATACACGTAGTAGCCTG
19925029 CACATAGTACTACACATGTGA
64 CACATAGTACTACACATGTGA
19925050 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
100 2 0.03
101 39 0.51
102 17 0.22
103 18 0.24
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGGTACTACACATGCGACCATTACATTCAATACACGTAGTAGCCTGCA
CATAGTACTACACATGTGATCGAAACTATCCGGTACG
Found at i:19929001 original size:50 final size:50
Alignment explanation
Indices: 19928894--19929047 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 50
19928884 GGGGACGAGA
* **
19928894 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGATGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG---TACCGA-G--ATGAGAGG
19928950 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
* * * *
19929000 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGA
19929048 ACTCCCATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
50 52 0.57
52 1 0.01
53 4 0.04
56 34 0.37
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
Found at i:19929071 original size:50 final size:50
Alignment explanation
Indices: 19928950--19929078 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
19928940 TTATGAGAGG
* * * * **
19928950 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
19929000 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
19929050 TCCCATGTACGAACATATCTGGGATATGG
1 TCCCACGTAAGAACATATCTGGGACATGG
19929079 TATTTGCAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:19929361 original size:20 final size:20
Alignment explanation
Indices: 19929336--19929374 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19929326 TGAGTTATTT
19929336 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
19929356 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
19929375 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:19932636 original size:18 final size:18
Alignment explanation
Indices: 19932613--19932652 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
19932603 AAAGGAAGAC
19932613 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
19932631 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
19932649 AGAA
1 AGAA
19932653 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:19934456 original size:33 final size:34
Alignment explanation
Indices: 19934419--19934490 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
19934409 GAGTTAGTTT
*
19934419 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
* *
19934452 ATTAATTTTAGTTCAGCTTAAATAAGTGTCAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
19934486 ATTAA
1 ATTAA
19934491 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
Found at i:19948882 original size:18 final size:18
Alignment explanation
Indices: 19948855--19948906 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
19948845 CTATCGAATC
19948855 AAAA-TTGTAATTACAAA
1 AAAACTTGTAATTACAAA
19948872 AAAACTTGTAATTAATACAAA
1 AAAACTTGTAA-T--TACAAA
*
19948893 GAAACTTGTAATTA
1 AAAACTTGTAATTA
19948907 ATATATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 1 0.03
20 1 0.03
21 16 0.53
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (18 bp):
AAAACTTGTAATTACAAA
Found at i:19948892 original size:21 final size:21
Alignment explanation
Indices: 19948866--19948909 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19948856 AAATTGTAAT
19948866 TACAAAAAAACTTGTAATTAA
1 TACAAAAAAACTTGTAATTAA
*
19948887 TACAAAGAAACTTGTAATTAA
1 TACAAAAAAACTTGTAATTAA
19948908 TA
1 TA
19948910 TATATTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.30
Consensus pattern (21 bp):
TACAAAAAAACTTGTAATTAA
Found at i:19949215 original size:13 final size:13
Alignment explanation
Indices: 19949197--19949223 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19949187 CATAAAAAGT
19949197 AAACTTTTACAAA
1 AAACTTTTACAAA
19949210 AAACTTTTACAAA
1 AAACTTTTACAAA
19949223 A
1 A
19949224 GTTTTTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AAACTTTTACAAA
Found at i:19950493 original size:28 final size:28
Alignment explanation
Indices: 19950432--19950498 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
19950422 CCTATTCCGT
*
19950432 AACAGT-ACAGTGTGGGCCTTAGCCCAA
1 AACAGTAACAATGTGGGCCTTAGCCCAA
*
19950459 TACAGTAACAATGTGGGCCTTAGCCCAA
1 AACAGTAACAATGTGGGCCTTAGCCCAA
* *
19950487 AATAGTATCAAT
1 AACAGTAACAAT
19950499 ATCGTGCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (28 bp):
AACAGTAACAATGTGGGCCTTAGCCCAA
Found at i:19950623 original size:23 final size:24
Alignment explanation
Indices: 19950597--19950647 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
19950587 GCCAACACAC
19950597 AATATCGTAGCAAAGCTGCCAGTA
1 AATATCGTAGCAAAGCTGCCAGTA
*
19950621 ATAGTATTGTAGCAAAGCTGCCAGTA
1 A-A-TATCGTAGCAAAGCTGCCAGTA
19950647 A
1 A
19950648 TAGTAAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 1 0.04
26 22 0.92
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (24 bp):
AATATCGTAGCAAAGCTGCCAGTA
Found at i:19950632 original size:26 final size:26
Alignment explanation
Indices: 19950603--19950652 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
19950593 ACACAATATC
19950603 GTAGCAAAGCTGCCAGTAATAGTATT
1 GTAGCAAAGCTGCCAGTAATAGTATT
19950629 GTAGCAAAGCTGCCAGTAATAGTA
1 GTAGCAAAGCTGCCAGTAATAGTA
19950653 AATGCGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (26 bp):
GTAGCAAAGCTGCCAGTAATAGTATT
Found at i:19950857 original size:27 final size:27
Alignment explanation
Indices: 19950827--19950887 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
19950817 TCATCTCTTA
*
19950827 AGGGTATAATAGTTATTTTACCCTATG
1 AGGGTATAATAGTCATTTTACCCTATG
** * *
19950854 AGGGTATTTTGGTCATTTTACCTTATG
1 AGGGTATAATAGTCATTTTACCCTATG
19950881 AGGGTAT
1 AGGGTAT
19950888 TTCGATCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.43
Consensus pattern (27 bp):
AGGGTATAATAGTCATTTTACCCTATG
Found at i:19950888 original size:27 final size:27
Alignment explanation
Indices: 19950841--19950957 Score: 128
Period size: 27 Copynumber: 4.1 Consensus size: 27
19950831 TATAATAGTT
*
19950841 ATTTTACCCTATGAGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTC
* *
19950868 ATTTTACCTTATGAGGGTATTTCGATC
1 ATTTTACCCTATGAGGGTATTTCGGTC
*
19950895 ATTTCACCCTATG-GAGGTATTTCGGTC
1 ATTTTACCCTATGAG-GGTATTTCGGTC
*
19950922 ATTTTACCTTATACTATGAGGGTATTTCGATC
1 ATTTTACC-----CTATGAGGGTATTTCGGTC
19950954 ATTT
1 ATTT
19950958 ATTGACCTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.71
32 20 0.27
33 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTATTTCGGTC
Found at i:19950904 original size:54 final size:56
Alignment explanation
Indices: 19950841--19950957 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 56
19950831 TATAATAGTT
* *
19950841 ATTTTACCCTAT-GAGGGTATTTTGGTCATTTTACC-T-TATGAGGGTATTTCGATC
1 ATTTCACCCTATGGA-GGTATTTCGGTCATTTTACCTTATATGAGGGTATTTCGATC
19950895 ATTTCACCCTATGGAGGTATTTCGGTCATTTTACCTTATACTATGAGGGTATTTCGATC
1 ATTTCACCCTATGGAGGTATTTCGGTCATTTTACC-T-TA-TATGAGGGTATTTCGATC
19950954 ATTT
1 ATTT
19950958 ATTGACCTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
54 30 0.55
55 2 0.04
57 1 0.02
59 22 0.40
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (56 bp):
ATTTCACCCTATGGAGGTATTTCGGTCATTTTACCTTATATGAGGGTATTTCGATC
Found at i:19963005 original size:6 final size:6
Alignment explanation
Indices: 19962991--19963029 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
19962981 TGGGAAAAAT
*
19962991 AAATGA AAATTA AAA-TA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
19963030 GATCCCCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:19963520 original size:30 final size:31
Alignment explanation
Indices: 19963486--19963543 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
19963476 AACAGTTCGA
*
19963486 TGACTTAAAT-AAAACTTTTGAATAGTTTAG
1 TGACTTAAATGAAAACTTTTAAATAGTTTAG
19963516 TGACTTAAATGAAAACTTTTAAATAGTT
1 TGACTTAAATGAAAACTTTTAAATAGTT
19963544 CAACTATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTAAATAGTTTAG
Found at i:19963981 original size:41 final size:39
Alignment explanation
Indices: 19963934--19964035 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 39
19963924 TATTAAATTT
*
19963934 ATATTAGAAAAATTATTTATTTGATAAATTAGTGAATAT-A
1 ATATTAGAAAAATTATTTATTTGATAAA--AGTAAATATCA
*
19963974 AGTATTAGATATAATTATATTATTTGATAAAAGTAAATATCA
1 A-TATTAGA-AAAATTAT-TTATTTGATAAAAGTAAATATCA
*
19964016 ATTTTA-AAAAA-TATTTATTT
1 ATATTAGAAAAATTATTTATTT
19964036 TTTAAATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
37 6 0.11
38 3 0.06
39 3 0.06
40 2 0.04
41 19 0.35
42 9 0.17
43 12 0.22
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATTAGAAAAATTATTTATTTGATAAAAGTAAATATCA
Found at i:19965190 original size:21 final size:21
Alignment explanation
Indices: 19965155--19965204 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
19965145 CATTGTTTCT
*
19965155 AATCTCACCACTACAATATCC
1 AATCTCACCACTACAATAACC
** * *
19965176 AATCTCACCTTTACAGTAACT
1 AATCTCACCACTACAATAACC
19965197 AATCTCAC
1 AATCTCAC
19965205 TGTCACCGCT
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:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:19968402 original size:19 final size:19
Alignment explanation
Indices: 19968380--19968416 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19968370 TATAAAAAAT
19968380 AAAAAATAATAAATTTTAG
1 AAAAAATAATAAATTTTAG
* *
19968399 AAAAATTATTAAATTTTA
1 AAAAAATAATAAATTTTA
19968417 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAAATAATAAATTTTAG
Found at i:19968722 original size:16 final size:16
Alignment explanation
Indices: 19968703--19968733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19968693 ATTTATTCTA
*
19968703 TTTTTAATATTTAATT
1 TTTTTAAAATTTAATT
19968719 TTTTTAAAATTTAAT
1 TTTTTAAAATTTAAT
19968734 AATATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTAATT
Found at i:19968991 original size:90 final size:91
Alignment explanation
Indices: 19968820--19969010 Score: 233
Period size: 90 Copynumber: 2.1 Consensus size: 91
19968810 TTTTTTTTTT
* * *
19968820 AAGTTTGAAGGT-CTTTTTTATACATTTTGAAAGTTCAAGTACCCAATTGAATGCCAAAAAAAAG
1 AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
* * *
19968884 TAGGGGGTTAATTGCTTTTTCTGAAA
66 TAAGGGGTTAATTGCTTTTCCTAAAA
* * * * ** *
19968910 AGGTTTTAAGGTATTTTTTTATGCATTTTGAAAGTTTAAGTATTCAAATGATTG-AAAAAAAAAG
1 AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
* *
19968974 TAATGGTTTAATTGCTTTTCCTAAAA
66 TAAGGGGTTAATTGCTTTTCCTAAAA
19969000 AAGTTTGAAGG
1 AAGTTTGAAGG
19969011 CTTTTTGTAC
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
90 49 0.59
91 34 0.41
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (91 bp):
AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
TAAGGGGTTAATTGCTTTTCCTAAAA
Found at i:19969218 original size:21 final size:21
Alignment explanation
Indices: 19969171--19969219 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
19969161 TGATAATCTA
*
19969171 AAAAATATATTAAAAATTAAT
1 AAAAATATATTAAAAAATAAT
*
19969192 AAAAATATTTTAAAAAATAA-
1 AAAAATATATTAAAAAATAAT
19969212 AACAAATA
1 AA-AAATA
19969220 CAAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATATTAAAAAATAAT
Found at i:19976073 original size:25 final size:27
Alignment explanation
Indices: 19976045--19976151 Score: 98
Period size: 27 Copynumber: 4.0 Consensus size: 27
19976035 ACAGTCATAC
*
19976045 ATAACATTAA-GCAT-ACAGTTATTTT
1 ATAACATTAAGGCATAACAGTCATTTT
*
19976070 ATAACA-TAAGGGCATAATAGTCATTTT
1 ATAACATTAA-GGCATAACAGTCATTTT
* *
19976097 ATAACA-TAGGGGCATAATAGTCATTTT
1 ATAACATTA-AGGCATAACAGTCATTTT
* *
19976124 ATAACA-TAGGGGCATAATAGTCATTTT
1 ATAACATTA-AGGCATAACAGTCATTTT
19976151 A
1 A
19976152 GTCATTTTAG
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.04
25 6 0.08
26 4 0.05
27 62 0.83
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (27 bp):
ATAACATTAAGGCATAACAGTCATTTT
Found at i:19976098 original size:27 final size:27
Alignment explanation
Indices: 19976065--19976255 Score: 172
Period size: 27 Copynumber: 7.4 Consensus size: 27
19976055 GCATACAGTT
*
19976065 ATTTTATAACATAAGGGCATAATAGTC
1 ATTTTATAACATAGGGGCATAATAGTC
19976092 ATTTTATAACATAGGGGCATAATAGTC
1 ATTTTATAACATAGGGGCATAATAGTC
19976119 ATTTTATAACATAGGGGCATAATAGTC
1 ATTTTATAACATAGGGGCATAATAGTC
*
19976146 ATTTTAGT--CAT-------T-TTAGTC
1 ATTTTA-TAACATAGGGGCATAATAGTC
* * * *
19976164 ATTTTATAGCATATGGGCATAACCA-TT
1 ATTTTATAACATAGGGGCATAA-TAGTC
*
19976191 ATTTTATAACATAGGGGTATAATAGTC
1 ATTTTATAACATAGGGGCATAATAGTC
** * *
19976218 ATTTTACCACGT-GAGGGCATAACAGTC
1 ATTTTATAACATAG-GGGCATAATAGTC
19976245 ATTTTATAACA
1 ATTTTATAACA
19976256 GTTTGGGGGT
Statistics
Matches: 132, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 11 0.08
19 4 0.03
26 6 0.05
27 108 0.82
28 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (27 bp):
ATTTTATAACATAGGGGCATAATAGTC
Found at i:19976155 original size:9 final size:9
Alignment explanation
Indices: 19976141--19976169 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
19976131 AGGGGCATAA
19976141 TAGTCATTT
1 TAGTCATTT
19976150 TAGTCATTT
1 TAGTCATTT
19976159 TAGTCATTT
1 TAGTCATTT
19976168 TA
1 TA
19976170 TAGCATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.55
Consensus pattern (9 bp):
TAGTCATTT
Found at i:19976183 original size:72 final size:72
Alignment explanation
Indices: 19976087--19976223 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
19976077 AAGGGCATAA
*
19976087 TAGTCATTTTATAACATAGGGGCATAA-TAGTCATTTTATAACATAGGGGCATAATAGTCATTTT
1 TAGTCATTTTATAACATAGGGGCATAACCA-TCATTTTATAACATAGGGGCATAATAGTCATTTT
19976151 AGTCATTT
65 AGTCATTT
* * * *
19976159 TAGTCATTTTATAGCATATGGGCATAACCATTATTTTATAACATAGGGGTATAATAGTCATTTTA
1 TAGTCATTTTATAACATAGGGGCATAACCATCATTTTATAACATAGGGGCATAATAGTCATTTTA
19976224 CCACGTGAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 58 0.98
73 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (72 bp):
TAGTCATTTTATAACATAGGGGCATAACCATCATTTTATAACATAGGGGCATAATAGTCATTTTA
GTCATTT
Found at i:19976236 original size:99 final size:99
Alignment explanation
Indices: 19976065--19976250 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 99
19976055 GCATACAGTT
* *
19976065 ATTTTATAACATAAGGGCATAATAGTCATTTTATAACATAGGGGCATAATAGTCATTTTATAACA
1 ATTTTATAACATAAGGGCATAACAGTCATTTTATAACATAGGGGCATAATAGTCATTTTACAACA
*
19976130 TAGGGGCATAATAGTCATTTTAGTCATTTTAGTC
66 TAGGGGCATAACAGTCATTTTAGTCATTTTAGTC
* * * * *
19976164 ATTTTATAGCATATGGGCATAACCA-TTATTTTATAACATAGGGGTATAATAGTCATTTTACCAC
1 ATTTTATAACATAAGGGCATAA-CAGTCATTTTATAACATAGGGGCATAATAGTCATTTTACAAC
*
19976228 GT-GAGGGCATAACAGTCATTTTA
65 ATAG-GGGCATAACAGTCATTTTA
19976251 TAACAGTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 1 0.01
99 74 0.97
100 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (99 bp):
ATTTTATAACATAAGGGCATAACAGTCATTTTATAACATAGGGGCATAATAGTCATTTTACAACA
TAGGGGCATAACAGTCATTTTAGTCATTTTAGTC
Found at i:19987685 original size:33 final size:33
Alignment explanation
Indices: 19987637--19987709 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
19987627 ATACAACATG
* *
19987637 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGT-ACAGTCTGGGCCTGAGCCCAATACAGTAA
* *
19987671 CAGTACAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
*
19987704 TAGTAC
1 CAGTAC
19987710 GTGCAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (33 bp):
CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
Found at i:19987835 original size:26 final size:26
Alignment explanation
Indices: 19987805--19987885 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
19987795 AACACACTAA
*
19987805 TATCGCAGCAAACCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
19987831 TATCGTAGCGAAGCTGCCAGT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
*
19987857 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
19987883 TAT
1 TAT
19987886 ATGTGGCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.04
26 44 0.94
27 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:19987910 original size:52 final size:52
Alignment explanation
Indices: 19987805--19987911 Score: 135
Period size: 52 Copynumber: 2.1 Consensus size: 52
19987795 AACACACTAA
* * **
19987805 TATCGCAGCAAACCTGCCAGTAATAGTATCGTAGCGAAGCTGCCAGTATCAG
1 TATCGCAGCAAACCTGCCAGTAACAGTATCGTAGCAAAGCCACCAGTATCAG
* * *
19987857 TATCGCAGCAAAGCTGCCAGTAACAGTATATGTGGCAAAGCCACCAGTA-CAG
1 TATCGCAGCAAACCTGCCAGTAACAGTAT-CGTAGCAAAGCCACCAGTATCAG
19987909 TAT
1 TAT
19987912 ATTTCCTCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 33 0.70
53 14 0.30
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (52 bp):
TATCGCAGCAAACCTGCCAGTAACAGTATCGTAGCAAAGCCACCAGTATCAG
Found at i:19989052 original size:21 final size:21
Alignment explanation
Indices: 19989026--19989081 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
19989016 AACAGCGGTG
*
19989026 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
19989047 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
19989068 GCCGTGAGATTAGA
1 GCGGTGAGATTAGA
19989082 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:19989190 original size:36 final size:37
Alignment explanation
Indices: 19989150--19989223 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
19989140 AAAAATGACT
*
19989150 ATTAAGGACATCAGATTAGAATTGATATAT-AATAGA
1 ATTAAGGACATCAGATTAGAAATGATATATAAATAGA
* *
19989186 ATTAAGGACATTAGATTAGAAATGGTATATAAATAGA
1 ATTAAGGACATCAGATTAGAAATGATATATAAATAGA
19989223 A
1 A
19989224 AGTTTTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.30
Consensus pattern (37 bp):
ATTAAGGACATCAGATTAGAAATGATATATAAATAGA
Found at i:19990466 original size:14 final size:15
Alignment explanation
Indices: 19990421--19990476 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
19990411 ATTAATAAGA
19990421 TTAAATTTTTAA-AC
1 TTAAATTTTTAACAC
* ** *
19990435 AATAAAAATTTAATAC
1 -TTAAATTTTTAACAC
19990451 TT-AATTTTTAACAC
1 TTAAATTTTTAACAC
19990465 TTAAATTTTTAA
1 TTAAATTTTTAA
19990477 TTTATGAAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 11 0.34
15 19 0.59
16 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTTTTAACAC
Found at i:19992739 original size:4 final size:4
Alignment explanation
Indices: 19992727--19992761 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
19992717 TAAAATTAGT
19992727 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
19992762 AAGGATAGNN
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:20001352 original size:50 final size:49
Alignment explanation
Indices: 20001247--20001361 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 49
20001237 GCAAACACAC
* * * *
20001247 CATAGCTCATATGAGCTTACTAATTTCAGCTCGTGAGAGCTTACCGATT
1 CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
* * *
20001296 CCTAGCTCGTATGAGCTTACCGATTTATAGCTCGTGAGAGCATACCAATT
1 CATAGCTCGTATGAGCTTACCAATTT-CAGCTCGTGAGAGCATACCAATT
20001346 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
20001362 ATACATGTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 22 0.39
50 35 0.61
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (49 bp):
CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
Found at i:20001365 original size:25 final size:25
Alignment explanation
Indices: 20001247--20001361 Score: 112
Period size: 25 Copynumber: 4.6 Consensus size: 25
20001237 GCAAACACAC
* *
20001247 CATAGCTCATATGAGCTTACTAATT
1 CATAGCTCGTATGAGCTTACCAATT
*
20001272 --TCAGCTCGTGA-GAGCTTACCGATT
1 CAT-AGCTCGT-ATGAGCTTACCAATT
* *
20001296 CCTAGCTCGTATGAGCTTACCGATT
1 CATAGCTCGTATGAGCTTACCAATT
* *
20001321 TATAGCTCGTGA-GAGCATACCAATT
1 CATAGCTCGT-ATGAGCTTACCAATT
20001346 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
20001362 ATACATGTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
23 1 0.01
24 19 0.25
25 53 0.71
26 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (25 bp):
CATAGCTCGTATGAGCTTACCAATT
Found at i:20002950 original size:21 final size:21
Alignment explanation
Indices: 20002926--20002967 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20002916 TTAAAAGGAG
20002926 AGAGTGAGTTTTCGAAACTCA
1 AGAGTGAGTTTTCGAAACTCA
20002947 AGAGTGAGTTTTCGAAACTCA
1 AGAGTGAGTTTTCGAAACTCA
20002968 GTGCGTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
AGAGTGAGTTTTCGAAACTCA
Found at i:20003070 original size:33 final size:32
Alignment explanation
Indices: 20003016--20003107 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 32
20003006 TGTAACAGTC
* * *
20003016 TGGGCCTGAGCCCTATTCAGTAAT-AGTATAGTG
1 TGGGCCTTAGCCC-ATACAGTAATCAGTAT-GAG
20003049 TGGGCCTTAGCCCAGTACAGT-ATCA--ATGAG
1 TGGGCCTTAGCCCA-TACAGTAATCAGTATGAG
20003079 TGGGCCTTAGCCCATTACAGTAATCAGTA
1 TGGGCCTTAGCCCA-TACAGTAATCAGTA
20003108 CAATGCAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
30 22 0.44
31 6 0.12
32 3 0.06
33 19 0.38
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (32 bp):
TGGGCCTTAGCCCATACAGTAATCAGTATGAG
Found at i:20003266 original size:26 final size:26
Alignment explanation
Indices: 20003217--20003286 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
20003207 AACATCGCAG
* * * * *
20003217 CAAAGCTGTCAGTAATAATGACACAT
1 CAAAGCTGCCAGTAACAGTAACACAA
*
20003243 TAAAGCTGCCAGTAACAGTAACACAA
1 CAAAGCTGCCAGTAACAGTAACACAA
20003269 CAAAGCTGCCAGTAACAG
1 CAAAGCTGCCAGTAACAG
20003287 AAAAGAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (26 bp):
CAAAGCTGCCAGTAACAGTAACACAA
Found at i:20006709 original size:87 final size:87
Alignment explanation
Indices: 20006587--20006917 Score: 493
Period size: 87 Copynumber: 3.8 Consensus size: 87
20006577 TCTAGTGCTG
*
20006587 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGGTGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
20006652 CGATCTGCTTTGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
20006674 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGGTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
20006739 CGATCTGCTTCACTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * * * * **
20006761 AGGAAGGGAAGATCTGTTATCTTTAACTAGCTCCACTACAACCAATGGAGGTGAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
20006826 CGATCTGCTTCGTTGTTAACTC
66 CGATCTGCTTCGCTGTTAACGC
* * * *
20006848 AAGAACGCAAGATCTGCT-CCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
20006912 CGATCT
66 CGATCT
20006918 ACTGATCTGT
Statistics
Matches: 218, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
86 45 0.21
87 173 0.79
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:20032552 original size:22 final size:22
Alignment explanation
Indices: 20032522--20032564 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20032512 TACGTGCAAC
20032522 AAAATAAAACAA-TACAAAAAG
1 AAAATAAAACAAGTACAAAAAG
*
20032543 AAAATCAAAACAAGTAGAAAAA
1 AAAAT-AAAACAAGTACAAAAA
20032565 TACTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAATAAAACAAGTACAAAAAG
Found at i:20034407 original size:24 final size:24
Alignment explanation
Indices: 20034375--20034421 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20034365 CTAAATTTAT
*
20034375 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
20034399 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
20034422 ATTTACCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:20036528 original size:49 final size:49
Alignment explanation
Indices: 20036443--20036543 Score: 114
Period size: 49 Copynumber: 2.1 Consensus size: 49
20036433 CTCGTTTTCT
** * * * *
20036443 CGATGCCATAGTTCAACTATGGTCTTACATGTAATCACCTATCA-TATAC
1 CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACT-TAC
* *
20036492 CGATGCCATAGCCCAGCTATGGTCCTATAAGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACTTAC
20036541 CGA
1 CGA
20036544 AAGTACTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACTTAC
Found at i:20037468 original size:27 final size:28
Alignment explanation
Indices: 20037428--20037480 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
20037418 CAATGATTCC
*
20037428 GGGAATCAACACTTAGTAA-CCCCTTGG
1 GGGAATCAACACTTAGCAATCCCCTTGG
**
20037455 GGGAATCAGTACTTAGCAATCCCCTT
1 GGGAATCAACACTTAGCAATCCCCTT
20037481 TATATTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGAATCAACACTTAGCAATCCCCTTGG
Found at i:20037581 original size:51 final size:51
Alignment explanation
Indices: 20037495--20037797 Score: 339
Period size: 51 Copynumber: 6.0 Consensus size: 51
20037485 TTCAAAGATA
* * *
20037495 CTGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * * *
20037546 CTGATACACGTAGTAGCCTGCACATAGTAGTACACACGTGATCGA--AGCTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTAT
* * * *
20037597 TTGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * * *
20037648 CCGATACACGTAGTAGCCTGCACATAGTACTACGCATGTGATCGA--AGCTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTAT
* * * *
20037699 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTAT
*
20037749 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
20037798 TTCACTTTTA
Statistics
Matches: 208, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.02
50 45 0.22
51 153 0.74
52 5 0.02
53 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
Found at i:20037689 original size:102 final size:101
Alignment explanation
Indices: 20037503--20037789 Score: 459
Period size: 102 Copynumber: 2.8 Consensus size: 101
20037493 TACTGGTTCA
*
20037503 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TATCTGATACACGTAGTAGCCTGCA
* **
20037568 CATAGTAGTACACACGTGATCGAAGCTATTTGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
*
20037605 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TATCTGATACACGTAGTAGCCTGCA
* *
20037670 CATAGTACTACGCATGTGATCGAAGCTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* *
20037707 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT-TCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCATATCTGATACACGTAGTAGCCTGCA
20037771 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
20037790 CCATCACTTT
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 38 0.22
102 129 0.75
103 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATCATATCTGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:20038063 original size:31 final size:29
Alignment explanation
Indices: 20038023--20038081 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
20038013 AAAATCACAC
20038023 TTTGAAAAATT-TACATTTTTGCCCCTAGAG
1 TTTGAAAAATTAT-CA-TTTTGCCCCTAGAG
*
20038053 TTTGACAAAATTATGATTTTGCCCCTAGA
1 TTTGA-AAAATTATCATTTTGCCCCTAGA
20038082 CTCGTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.69
31 7 0.27
32 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTGAAAAATTATCATTTTGCCCCTAGAG
Found at i:20039967 original size:24 final size:24
Alignment explanation
Indices: 20039935--20039981 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20039925 CTAAATTTAT
*
20039935 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
20039959 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
20039982 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:20043860 original size:61 final size:61
Alignment explanation
Indices: 20043764--20043992 Score: 278
Period size: 61 Copynumber: 3.8 Consensus size: 61
20043754 TTGACAGAAA
* * * *
20043764 TCACCACAAAGGCTTACCTTTCAAGAGTTTTGCCACAAAGGCTATCCTTTACATCCAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * *
20043825 TCTCTACAATGGCTTTCCTGTCCAGAGTTTAGCCACAAAGGTTGTCCTTTACATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * * *
20043886 TCACCACAAAGGCTTTTCTGTCCAGAGTGTTGCCACAAATGTTGTACTTTATATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * *
20043947 TCGCCACAAAGGCTTTCCTATCAAAAGTTTTGCCACAAAGGTTATC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATC
20043993 TTTCTCCTGG
Statistics
Matches: 140, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 140 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (61 bp):
TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
Found at i:20044246 original size:18 final size:19
Alignment explanation
Indices: 20044211--20044246 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20044201 TGGGACATTG
*
20044211 ATTTTGGATTTTACTTTGT
1 ATTTTGGATTTGACTTTGT
20044230 ATTTTGG-TTTGACTTTG
1 ATTTTGGATTTGACTTTG
20044247 CATGATTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.06, G:0.19, T:0.61
Consensus pattern (19 bp):
ATTTTGGATTTGACTTTGT
Found at i:20045134 original size:20 final size:20
Alignment explanation
Indices: 20045063--20045135 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
20045053 CCAATTTGGG
* * *
20045063 GACAAGCCACCAGTATTGCA
1 GACAAGCTACCAGTAATGTA
* * * *
20045083 GATAAACTGCCAGTAATGTG
1 GACAAGCTACCAGTAATGTA
20045103 GACAAG-TCACCAGTAATGTA
1 GACAAGCT-ACCAGTAATGTA
20045123 GACAAGCTACCAG
1 GACAAGCTACCAG
20045136 ATTTGTGGAC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
GACAAGCTACCAGTAATGTA
Found at i:20049379 original size:22 final size:22
Alignment explanation
Indices: 20049345--20049387 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20049335 TACACCAAAA
* *
20049345 TAGGCTTTTAGCGGCATTTTTT
1 TAGGCCTTCAGCGGCATTTTTT
*
20049367 TAGGCCTTCAGCGGCGTTTTT
1 TAGGCCTTCAGCGGCATTTTT
20049388 AAGCGCCACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
TAGGCCTTCAGCGGCATTTTTT
Found at i:20049522 original size:43 final size:43
Alignment explanation
Indices: 20049473--20049715 Score: 312
Period size: 43 Copynumber: 5.7 Consensus size: 43
20049463 AAAAATGCCA
* *
20049473 CTAAAGATCATGGCCTTTAGCGACGCTTTTATCACAAACGTCG
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
* *
20049516 CTAAAGATCATGACCTTTAGCGACGCTTTTACCACAAACGCCA
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
*
20049559 CTAAAGATCATGACCTTTAGC-AGCTCTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCGA-CGCTTTTATCACAAACGCCG
* * * * * *
20049602 CTAAAGGTCATGATCTTCAGCAACGCTTTTGTCACAAATGCCG
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
*
20049645 CTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCGACGC-TTTTATCACAAACGCCG
* *
20049689 CTATAA-AACA-AACCTTTAGCGACGCTT
1 CTA-AAGATCATGACCTTTAGCGACGCTT
20049716 CTCACAAAAA
Statistics
Matches: 175, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
42 3 0.02
43 147 0.84
44 23 0.13
45 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
Found at i:20049714 original size:86 final size:87
Alignment explanation
Indices: 20049465--20049740 Score: 321
Period size: 86 Copynumber: 3.2 Consensus size: 87
20049455 TTATGTGAAA
* * *
20049465 AAATGCCACTAAAGATCATGGCCTTTAGCGACGC-TTTTATCACAAACGTCGCTAAAGATCATGA
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTAAAGATCATGA
*
20049529 CCTTTAGCGACGCTTTTACCAC
66 CCTTTAGCGACGCTTTTAACAC
* * *
20049551 AAACGCCACTAAAGATCATGACCTTTAGC-A-GCTCTTTTATCACAAACGCCGCTAAAGGTCATG
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCT-TTTTATCACAAACGCCGCTAAAGATCATG
* * * **
20049614 ATCTTCAGCAACGCTTTTGTCAC
65 ACCTTTAGCGACGCTTTTAACAC
* * *
20049637 AAATGCCGCTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTATAA-AACA-A
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTA-AAGATCATG
* * *
20049700 ACCTTTAGCGACGCTTCTCACAA
65 ACCTTTAGCGACGCTTTTAACAC
*
20049723 AAATGCCGCTAAA-AACAT
1 AAATGCCACTAAAGAACAT
20049741 AACATTTAAA
Statistics
Matches: 163, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
84 2 0.01
85 6 0.04
86 127 0.78
87 23 0.14
88 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (87 bp):
AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTAAAGATCATGA
CCTTTAGCGACGCTTTTAACAC
Found at i:20049731 original size:129 final size:129
Alignment explanation
Indices: 20049463--20049735 Score: 320
Period size: 129 Copynumber: 2.1 Consensus size: 129
20049453 GTTTATGTGA
* * * * * *
20049463 AAAAATGCCACTAAAGATCATGGCCTTTAGCGACGCTTTTATCACAAACGTCGCTAAAGATCATG
1 AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
* * * *
20049528 ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGATCATGACCTTTAGCAGCTCTTTTATC
66 ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGAACATAACCTTTAGCAGCTCTCTCATC
* * * * * *
20049592 ACAAACGCCGCTAAAGGTCATGATCTTCAGCAACGCTTTTGTCACAAATGCCGCTAAAGAACATG
1 AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
* *
20049657 ACCTTTAGCGACGCTTTTTATCACAAACGCCGCTATAA-AACA-AACCTTTAGCGACGCT-TCTC
66 ACCTTTAGCGACGC-TTTTACCACAAACGCCACTA-AAGAACATAACCTTTAGC-A-GCTCTCTC
20049719 A-C
127 ATC
20049721 AAAAATGCCGCTAAA
1 AAAAATGCCGCTAAA
20049736 AACATAACAT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
129 90 0.75
130 25 0.21
131 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (129 bp):
AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGAACATAACCTTTAGCAGCTCTCTCATC
Found at i:20050808 original size:16 final size:16
Alignment explanation
Indices: 20050787--20050817 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20050777 AGTCCCAAAC
20050787 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
20050803 TATTGTAAACATCAG
1 TATTGTAAACATCAG
20050818 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:20052578 original size:39 final size:39
Alignment explanation
Indices: 20052524--20052600 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
20052514 TGAACAAAGA
20052524 AAGTTACCAAAATTCACATGCTTCAAGTGCCACCTCATG
1 AAGTTACCAAAATTCACATGCTTCAAGTGCCACCTCATG
20052563 AAGTTACCAAAATTCACATGCTTCAAGTGCCACCTCAT
1 AAGTTACCAAAATTCACATGCTTCAAGTGCCACCTCAT
20052601 CATCAGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.26
Consensus pattern (39 bp):
AAGTTACCAAAATTCACATGCTTCAAGTGCCACCTCATG
Found at i:20054030 original size:41 final size:42
Alignment explanation
Indices: 20054001--20054286 Score: 279
Period size: 41 Copynumber: 7.0 Consensus size: 42
20053991 GCCACTATCG
20054001 CCCTGAACATTAGCGGCGCTTTTTC-AAAAACGCCGCTAAAGA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA-A
* * *
20054043 CCC--AATCATTAGTGACGCTTTCT-AAAAAACGCCGCTAAAA
1 CCCTGAA-CATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * * * *
20054083 CCATGAGCATTAGCGGCGC-TTCTCCAAAAACACCGCTAAAGA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA-A
* * **
20054125 CCC-GATCATTAGCGGCGCTTTTT-AAAAAACACCATTAAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * *
20054165 CCCT-AAGCATTAGCGGCGCCTATTC-AAAAACGCCGCTAAAT
1 CCCTGAA-CATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* *
20054206 CCCTGAGCATTAGCGGCGC-TTTACAAAAAACGCCGCTAAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * *
20054247 CCCTGAGCATTAGCGGTGCTTTTT-AAAAAACGCCACTAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA
20054287 GCCCCAAAAA
Statistics
Matches: 202, Mismatches: 29, Indels: 27
0.78 0.11 0.10
Matches are distributed among these distances:
40 17 0.08
41 171 0.85
42 14 0.07
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
Done.