Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 91 of 253
Found at i:28244733 original size:51 final size:51
Alignment explanation
Indices: 28244653--28244800 Score: 226
Period size: 51 Copynumber: 2.9 Consensus size: 51
28244643 GAGGAAGTGC
*
28244653 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTT-TGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATCG
* *
28244705 AAAAGGGCTTTGCCCCAGTTCATCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTTGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATCG
* * *
28244756 AAAAGGACTTTGCCCCAGTTTACCGAAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTTGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTT
28244801 ATTAAAAGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 9 0.10
51 70 0.79
52 10 0.11
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTTGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATCG
Found at i:28246877 original size:25 final size:25
Alignment explanation
Indices: 28246849--28246916 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
28246839 GAACTAGAAT
*
28246849 CAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
* *
28246874 CAGAATTAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
*
28246899 CAAAATCA-ATATCAGAAT
1 CAGAATCAGA-ATCAGAAT
28246917 GTGAATGCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:28246885 original size:6 final size:6
Alignment explanation
Indices: 28246844--28246869 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28246834 TATTAGAACT
28246844 AGAATC AGAATC AGAATC AGAATC AG
1 AGAATC AGAATC AGAATC AGAATC AG
28246870 GTGACAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGAATC
Found at i:28247181 original size:27 final size:26
Alignment explanation
Indices: 28247133--28247184 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28247123 GCGAGGCTGC
*
28247133 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
28247159 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
28247185 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28247451 original size:27 final size:27
Alignment explanation
Indices: 28247421--28247696 Score: 313
Period size: 27 Copynumber: 10.2 Consensus size: 27
28247411 AACACCCTAG
* *
28247421 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
28247448 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
28247475 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * * * *
28247502 GGGTAAAACAATAATTCTATCAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
28247529 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
28247556 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
28247583 GGGTAAAACT-GTAATTCTGTAAATCGA
1 GGGTAAAA-TAGTAATTTTGTAAATCGA
* * * *
28247610 GGGTAAAATAATAATTCTATAAATCAA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * **
28247637 GGGTAAAA-CGATAATTTTATAAATTAA
1 GGGTAAAATAG-TAATTTTGTAAATCGA
* * * *
28247664 GGGTCAAACAGTAATTTTTTTAATTCGA
1 GGGTAAAATAGTAA-TTTTGTAAATCGA
28247692 GGGTA
1 GGGTA
28247697 CTTTGATAAT
Statistics
Matches: 215, Mismatches: 29, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.00
27 199 0.93
28 15 0.07
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (27 bp):
GGGTAAAATAGTAATTTTGTAAATCGA
Found at i:28247556 original size:81 final size:81
Alignment explanation
Indices: 28247421--28247679 Score: 349
Period size: 81 Copynumber: 3.2 Consensus size: 81
28247411 AACACCCTAG
** * *
28247421 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATAG
28247486 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* * *
28247502 GGGTAAAACAATAATTCTATCAATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATAG
28247567 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* * * * * *
28247583 GGGTAAAACTGTAATTCTGTAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAA-CG
1 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATAG
* **
28247647 ATAATTTTATAAATTAA
66 -TAATTTTGTAAATCGA
*
28247664 GGGTCAAACAGTAATT
1 GGGTAAAACAGTAATT
28247680 TTTTTAATTC
Statistics
Matches: 156, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
80 1 0.01
81 155 0.99
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (81 bp):
GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATAG
TAATTTTGTAAATCGA
Found at i:28247718 original size:27 final size:25
Alignment explanation
Indices: 28247681--28247765 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 25
28247671 ACAGTAATTT
*
28247681 TTTTAATTCGAGGGTACTTTGA-TAA
1 TTTTAATTCGAGGGTA-TTTCAGTAA
28247706 TTTTACATGTCGAGGGTATTTCAGTAA
1 TTTTA-AT-TCGAGGGTATTTCAGTAA
* *
28247733 TTTTGCAA-ACTGAGGGTATTTCGGTAA
1 TTTT--AATTC-GAGGGTATTTCAGTAA
28247760 TTTTAA
1 TTTTAA
28247766 AAATTGAGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
25 7 0.14
26 7 0.14
27 35 0.69
28 1 0.02
29 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (25 bp):
TTTTAATTCGAGGGTATTTCAGTAA
Found at i:28247773 original size:27 final size:27
Alignment explanation
Indices: 28247717--28247843 Score: 116
Period size: 27 Copynumber: 4.7 Consensus size: 27
28247707 TTTACATGTC
* **
28247717 GAGGGTATTTCAGTAATTTTGCAAACT
1 GAGGGTATTTCGGTAATTTTAAAAACT
*
28247744 GAGGGTATTTCGGTAATTTTAAAAATT
1 GAGGGTATTTCGGTAATTTTAAAAACT
* * * *
28247771 GAGGATATTTGGGTAATTTTATAAATT
1 GAGGGTATTTCGGTAATTTTAAAAACT
*
28247798 G-GAGGTACTTT-GGTAATTTT-ACAACT
1 GAG-GGTA-TTTCGGTAATTTTAAAAACT
* *
28247824 GGGGGTATTTCAGTAATTTT
1 GAGGGTATTTCGGTAATTTT
28247844 GTAAACTAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.04
26 17 0.20
27 61 0.73
28 3 0.04
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (27 bp):
GAGGGTATTTCGGTAATTTTAAAAACT
Found at i:28247780 original size:54 final size:53
Alignment explanation
Indices: 28247693--28247850 Score: 149
Period size: 54 Copynumber: 2.9 Consensus size: 53
28247683 TTAATTCGAG
* * ** *
28247693 GGTACTTTGATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAACT-GA
1 GGTACTTTGGTAATTTTAAAACT-GAGGGTATTTCAGTAATTTTGTAAACTGGA
* * ** * *
28247746 GGGTA-TTTCGGTAATTTTAAAAATTGAGGATATTTGGGTAATTTTATAAATTGGA
1 -GGTACTTT-GGTAATTTT-AAAACTGAGGGTATTTCAGTAATTTTGTAAACTGGA
* *
28247801 GGTACTTTGGTAATTTTACAACTGGGGGTATTTCAGTAATTTTGTAAACT
1 GGTACTTTGGTAATTTTAAAACTGAGGGTATTTCAGTAATTTTGTAAACT
28247851 AAAGTATTCT
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
53 28 0.34
54 46 0.56
55 8 0.10
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (53 bp):
GGTACTTTGGTAATTTTAAAACTGAGGGTATTTCAGTAATTTTGTAAACTGGA
Found at i:28250046 original size:27 final size:26
Alignment explanation
Indices: 28249999--28250057 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
28249989 CGAGGCTACT
*
28249999 AGATATTGTGACAAAGTCACCAGATAC
1 AGATATTGTGACAAAGCCACCAGA-AC
* *
28250026 AGATATTGTGGCTAAGCCACCAGAAC
1 AGATATTGTGACAAAGCCACCAGAAC
28250052 AGATAT
1 AGATAT
28250058 ATATATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (26 bp):
AGATATTGTGACAAAGCCACCAGAAC
Found at i:28250070 original size:33 final size:32
Alignment explanation
Indices: 28250019--28250082 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
28250009 ACAAAGTCAC
*
28250019 CAGATACAGATATTGTGGCTAAGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
28250051 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
28250083 TTGCAGCGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:28250146 original size:27 final size:26
Alignment explanation
Indices: 28250098--28250149 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28250088 GCGAGGCTGC
*
28250098 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
28250124 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
28250150 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28250416 original size:27 final size:27
Alignment explanation
Indices: 28250386--28250635 Score: 249
Period size: 27 Copynumber: 9.2 Consensus size: 27
28250376 TAACACCCTA
* *
28250386 AGGGTAAAATCGTAATTTTATAAATTG
1 AGGGTAAAATCGTAATTCTGTAAATTG
* *
28250413 AGGGTAAAATGGTAATTCTATAAATTG
1 AGGGTAAAATCGTAATTCTGTAAATTG
* *
28250440 AGGGTAAAATAGTAATTTTGTAAATTG
1 AGGGTAAAATCGTAATTCTGTAAATTG
* **
28250467 AGGGTAAAA-CAGTAATTCTGTCAATCA
1 AGGGTAAAATC-GTAATTCTGTAAATTG
28250494 AGGGTAAAA-CGGTAATTCTGTAAATTG
1 AGGGTAAAATC-GTAATTCTGTAAATTG
* * *
28250521 AGGGTAAAATAGTAATTTTGTAAATCG
1 AGGGTAAAATCGTAATTCTGTAAATTG
* * **
28250548 AGGGTAAAATAGTAATTCTGTCAATCA
1 AGGGTAAAATCGTAATTCTGTAAATTG
*
28250575 AGGGTAAAA-CGATAATTCTGTAAATCG
1 AGGGTAAAATCG-TAATTCTGTAAATTG
*
28250602 AGGGTAAAA-CAGTAATT-TTTATAATTCG
1 AGGGTAAAATC-GTAATTCTGTA-AATT-G
28250630 AGGGTA
1 AGGGTA
28250636 CTTTGATAAT
Statistics
Matches: 192, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.02
27 180 0.94
28 8 0.04
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (27 bp):
AGGGTAAAATCGTAATTCTGTAAATTG
Found at i:28250468 original size:54 final size:54
Alignment explanation
Indices: 28250386--28250635 Score: 297
Period size: 54 Copynumber: 4.6 Consensus size: 54
28250376 TAACACCCTA
* * ** * *
28250386 AGGGTAAAATCGTAATTTTATAAATTGAGGGTAAAATGGTAATTCTATAAATTG
1 AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTCTGTAAATCG
* *
28250440 AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTCTGTCAATCA
1 AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTCTGTAAATCG
** * * *
28250494 AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTCTGTAAATCG
* * **
28250548 AGGGTAAAATAGTAATTCTGTCAATCAAGGGTAAAAC-GATAATTCTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAG-TAATTCTGTAAATCG
*
28250602 AGGGTAAAACAGTAATTTT-TATAATTCGAGGGTA
1 AGGGTAAAATAGTAATTTTGTA-AATT-GAGGGTA
28250636 CTTTGATAAT
Statistics
Matches: 166, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
53 2 0.01
54 158 0.95
55 6 0.04
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (54 bp):
AGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTCTGTAAATCG
Found at i:28250521 original size:81 final size:81
Alignment explanation
Indices: 28250413--28250635 Score: 358
Period size: 81 Copynumber: 2.7 Consensus size: 81
28250403 TTATAAATTG
* *
28250413 AGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACA
1 AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACA
28250478 GTAATTCTGTCAATCA
66 GTAATTCTGTCAATCA
* *
28250494 AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATA
1 AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACA
28250559 GTAATTCTGTCAATCA
66 GTAATTCTGTCAATCA
* * *
28250575 AGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGTAATTTT-TATAATTCGAGGGTA
1 AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTA-AATT-GAGGGTA
28250636 CTTTGATAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
80 2 0.02
81 123 0.93
82 7 0.05
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (81 bp):
AGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAACA
GTAATTCTGTCAATCA
Found at i:28250685 original size:26 final size:26
Alignment explanation
Indices: 28250656--28250780 Score: 110
Period size: 27 Copynumber: 4.7 Consensus size: 26
28250646 TTTACATGTC
*
28250656 GAGGGTATTTAGTAATTTTGCAAACT
1 GAGGGTATTTAGTAATTTTACAAACT
* *
28250682 GAGGGTATTTCGATAATTTTA-AAAAT
1 GAGGGTATTTAG-TAATTTTACAAACT
* * *
28250708 CGAGGATATTTGGGTAATTTTATAAACT
1 -GAGGGTATTT-AGTAATTTTACAAACT
* *
28250736 GGGGGTACTTTGGTAATTTTAC-AACT
1 GAGGGTA-TTTAGTAATTTTACAAACT
*
28250762 GGGGGTATTTCAGTAATTT
1 GAGGGTATTT-AGTAATTT
28250781 GGTAAACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
25 3 0.04
26 33 0.40
27 39 0.47
28 8 0.10
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (26 bp):
GAGGGTATTTAGTAATTTTACAAACT
Found at i:28250701 original size:53 final size:54
Alignment explanation
Indices: 28250629--28250780 Score: 166
Period size: 53 Copynumber: 2.9 Consensus size: 54
28250619 TTTATAATTC
** *
28250629 GAGGGTACTTTGATAATTTTACATGTCGAGGGTATTT-AGTAATTTTGCAAACT
1 GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACT
* * ** *
28250682 GAGGGTA-TTTCGATAATTTTAAAAATCGAGGATATTTGGGTAATTTTATAAACT
1 GAGGGTACTTT-GATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACT
* * * *
28250736 GGGGGTACTTTGGTAATTTTACAACT-GGGGGTATTTCAGTAATTT
1 GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTT
28250781 GGTAAACTAA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
52 3 0.04
53 44 0.54
54 31 0.38
55 3 0.04
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (54 bp):
GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACT
Found at i:28250712 original size:27 final size:26
Alignment explanation
Indices: 28250618--28250759 Score: 101
Period size: 27 Copynumber: 5.3 Consensus size: 26
28250608 AAACAGTAAT
* *
28250618 TTTTATAATTCGAGGGTACTTTGATAA
1 TTTTACAAATCGAGGGTA-TTTGATAA
**
28250645 TTTTACATGTCGAGGGTATTT-AGTAA
1 TTTTACAAATCGAGGGTATTTGA-TAA
*
28250671 TTTTGCAAA-CTGAGGGTATTTCGATAA
1 TTTTACAAATC-GAGGGTATTT-GATAA
* * *
28250698 TTTTAAAAATCGAGGATATTTGGGTAA
1 TTTTACAAATCGAGGGTATTT-GATAA
* * *
28250725 TTTTATAAA-CTGGGGGTACTTTGGTAA
1 TTTTACAAATC-GAGGGTA-TTTGATAA
28250752 TTTTACAA
1 TTTTACAA
28250760 CTGGGGGTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
25 2 0.02
26 23 0.25
27 63 0.68
28 5 0.05
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (26 bp):
TTTTACAAATCGAGGGTATTTGATAA
Found at i:28250788 original size:27 final size:25
Alignment explanation
Indices: 28250721--28250780 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
28250711 GGATATTTGG
*
28250721 GTAATTTTATAAACTGGGGGTACTTTG
1 GTAA-TTT-TAAACTGGGGGTACTTTA
28250748 GTAATTTTACAACTGGGGGTA-TTTCA
1 GTAATTTTA-AACTGGGGGTACTTT-A
28250774 GTAATTT
1 GTAATTT
28250781 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 21 0.70
27 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
GTAATTTTAAACTGGGGGTACTTTA
Found at i:28255294 original size:23 final size:22
Alignment explanation
Indices: 28255242--28255294 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28255232 TCCACGTCTT
*
28255242 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28255264 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28255287 TTTCTTTT
1 TTTCTTTT
28255295 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:28257647 original size:12 final size:13
Alignment explanation
Indices: 28257630--28257658 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28257620 TTAAACTAAG
28257630 TAAATAAAT-AAA
1 TAAATAAATAAAA
28257642 TAAATAAATAAAA
1 TAAATAAATAAAA
28257655 TAAA
1 TAAA
28257659 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:28260417 original size:28 final size:28
Alignment explanation
Indices: 28260377--28260448 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
28260367 TTTAAATTGC
28260377 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
*
28260405 ATAGCACTAAGTGTGCGAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
* *
28260433 GTAACACTAAGTGTGC
1 ATAGCACTAAGTGTGC
28260449 GGACTTACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCAAGTTTGATTAT
Found at i:28260449 original size:28 final size:28
Alignment explanation
Indices: 28260352--28260449 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 28
28260342 ATGAGATTGG
* * ** *
28260352 CACTAAGTGTGCGGGTTTAAATTGCATAG
1 CACTAAGTGTGCGAGTTT-GATTATATAA
* *
28260381 CACTAAGTGTGCAAGTTTGATTATATAG
1 CACTAAGTGTGCGAGTTTGATTATATAA
*
28260409 CACTAAGTGTGCGAGTTTGATTATGTAA
1 CACTAAGTGTGCGAGTTTGATTATATAA
28260437 CACTAAGTGTGCG
1 CACTAAGTGTGCG
28260450 GACTTACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
28 45 0.74
29 16 0.26
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATATAA
Found at i:28265141 original size:46 final size:46
Alignment explanation
Indices: 28265074--28265244 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
28265064 CGCCCCTAAG
* *
28265074 TGAACTCGGACTCAACTCAACGAGCTCAGG-TGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTC-GGATGTTAGCATCCATAAA
* * * **
28265120 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGATG-TTAGCATCCAT-AAA
* ** * *
28265167 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCATAAA
* *
28265213 TGAACTCAGACTCAACTCAACGAGTTCAGATG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATG
28265245 CTCAACCATC
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
45 2 0.02
46 61 0.62
47 36 0.36
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCATAAA
Found at i:28265234 original size:93 final size:93
Alignment explanation
Indices: 28265075--28265245 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
28265065 GCCCCTAAGT
** *
28265075 GAACTCGGACTCAACTCAACGAGCTCAGGTGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAATGAACTCAGACTCAACTCAA
*
28265140 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* * *
28265168 GAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAATGAACTCAGACTCAACTCA
28265232 ACGAGTTCAGATGC
65 ACGAGTTCAGATGC
28265246 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAATGAACTCAGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:28266201 original size:22 final size:22
Alignment explanation
Indices: 28266162--28266220 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
28266152 GTTTTAAGAA
*
28266162 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
28266183 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
28266205 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
28266221 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:28266237 original size:26 final size:24
Alignment explanation
Indices: 28266191--28266250 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
28266181 ATTTGTTTTA
*
28266191 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
28266215 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
28266241 TTTTTTATTT
1 ATATTTATTT
28266251 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:28274906 original size:44 final size:43
Alignment explanation
Indices: 28274821--28274908 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
28274811 ATGTGTTATC
* *
28274821 GTGTAAGACCACATCTGGGACTTTGGCATCGAATTCTATTTTGT
1 GTGTAAGACCACATCTAGGACATTGGCATCG-ATTCTATTTTGT
*
28274865 GTGTAAGACCATATCTAGGACATTGGCATCG-TGTCTAATTTTGT
1 GTGTAAGACCACATCTAGGACATTGGCATCGAT-TCT-ATTTTGT
28274909 ATAGGACTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 3 0.08
44 35 0.90
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (43 bp):
GTGTAAGACCACATCTAGGACATTGGCATCGATTCTATTTTGT
Found at i:28276453 original size:29 final size:29
Alignment explanation
Indices: 28276418--28276491 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
28276408 GTTGTGAGAT
* *
28276418 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
28276447 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
28276476 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28276492 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:28282888 original size:27 final size:27
Alignment explanation
Indices: 28282805--28283091 Score: 233
Period size: 27 Copynumber: 10.7 Consensus size: 27
28282795 CTCCTGTAGG
* * *
28282805 GTAAAATTACTGAAATACCCTTGGTTT
1 GTAAAATTACCGAAATACCCTCGATTT
** * *
28282832 ACAAAATTACTG-AATACCCT-GGTTT
1 GTAAAATTACCGAAATACCCTCGATTT
*
28282857 GTAAAATTACCGAAATACCCTCAATTT
1 GTAAAATTACCGAAATACCCTCGATTT
* *
28282884 GTAAAATTACCAAAATACCC-CTAATTT
1 GTAAAATTACCGAAATACCCTC-GATTT
* * * * **
28282911 GTGAAATTATCAAAACACCCTCGACCT
1 GTAAAATTACCGAAATACCCTCGATTT
* * * *
28282938 GTAAAATTATCGAAATACCCCCAACTT
1 GTAAAATTACCGAAATACCCTCGATTT
*
28282965 ATAAAATTACCGAAATACCCTCGATTT
1 GTAAAATTACCGAAATACCCTCGATTT
* * *
28282992 GTAAAGTTACCAAAATACCC-CTTATTT
1 GTAAAATTACCGAAATACCCTC-GATTT
* *
28283019 GGAAAATTACCGAAATACCCTAGATTT
1 GTAAAATTACCGAAATACCCTCGATTT
* *
28283046 GGAAAATTACAGAAATACCC-CTGATTT
1 GTAAAATTACCGAAATACCCTC-GATTT
** *
28283073 ACAAAATTACAGAAATACC
1 GTAAAATTACCGAAATACC
28283092 ATTGACTTTC
Statistics
Matches: 215, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
25 14 0.07
26 18 0.08
27 182 0.85
28 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTCGATTT
Found at i:28283153 original size:27 final size:27
Alignment explanation
Indices: 28282805--28283176 Score: 156
Period size: 27 Copynumber: 13.8 Consensus size: 27
28282795 CTCCTGTAGG
** *
28282805 GTAAAATTACTGAAATACCCTTGGTTT
1 GTAAAATTACCAAAATACCCTTAGTTT
** ** *
28282832 ACAAAATTA-CTGAATACCC-TGGTTT
1 GTAAAATTACCAAAATACCCTTAGTTT
* * *
28282857 GTAAAATTACCGAAATACCCTCAATTT
1 GTAAAATTACCAAAATACCCTTAGTTT
* *
28282884 GTAAAATTACCAAAATACCCCTAATTT
1 GTAAAATTACCAAAATACCCTTAGTTT
* * * * **
28282911 GTGAAATTATCAAAACACCC-TCGACCT
1 GTAAAATTACCAAAATACCCTTAG-TTT
* * ** **
28282938 GTAAAATTATCGAAATACCCCCAACTT
1 GTAAAATTACCAAAATACCCTTAGTTT
* * *
28282965 ATAAAATTACCGAAATACCC-TCGATTT
1 GTAAAATTACCAAAATACCCTTAG-TTT
*
28282992 GTAAAGTTACCAAAATACCCCTTA-TTT
1 GTAAAATTACCAAAATA-CCCTTAGTTT
* *
28283019 GGAAAATTACCGAAATACCC-TAGATTT
1 GTAAAATTACCAAAATACCCTTAG-TTT
* *
28283046 GGAAAATTA-CAGAAATACCCCT-GATTT
1 GTAAAATTACCA-AAATACCCTTAG-TTT
** * *
28283073 ACAAAATTA-CAGAAATACCATTGACTTT
1 GTAAAATTACCA-AAATACCCTT-AGTTT
* * * *
28283101 -CAAATTTTA-TAGAAATACCAC-CAGTTT
1 GTAAA-ATTACCA-AAATACC-CTTAGTTT
*
28283128 GTAAAATTACTAAAATACCCTTAGTTT
1 GTAAAATTACCAAAATACCCTTAGTTT
* * *
28283155 GTAGATTTACCAAAATGCCCTT
1 GTAAAATTACCAAAATACCCTT
28283177 GTAGGGTGAA
Statistics
Matches: 267, Mismatches: 60, Indels: 36
0.74 0.17 0.10
Matches are distributed among these distances:
25 15 0.06
26 21 0.08
27 206 0.77
28 24 0.09
29 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
GTAAAATTACCAAAATACCCTTAGTTT
Found at i:28283238 original size:27 final size:27
Alignment explanation
Indices: 28283176--28283299 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 27
28283166 AAAATGCCCT
* * *
28283176 TGTAGGGTGAAATGACTAAAATACCCC
1 TGTAGGGTAAAATGACCATAATACCCC
* * * *
28283203 TAATA-GGTAAAAAGACCGTAATGCCCC
1 T-GTAGGGTAAAATGACCATAATACCCC
*
28283230 TGTAGGGTAAAATGACCATAAAACCCC
1 TGTAGGGTAAAATGACCATAATACCCC
*
28283257 TGTAGGGTAAAGTGACCATAATACCCC
1 TGTAGGGTAAAATGACCATAATACCCC
*
28283284 TGTATGGTAAAATGAC
1 TGTAGGGTAAAATGAC
28283300 AATTATGCCC
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.03
27 75 0.95
28 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCATAATACCCC
Found at i:28291014 original size:37 final size:37
Alignment explanation
Indices: 28290903--28291038 Score: 130
Period size: 37 Copynumber: 3.7 Consensus size: 37
28290893 TGAGTACGTA
* * *
28290903 TAAGACCATAGCTGGGCTATCGCATCGTAATACCGTG
1 TAAGACCATAGCTGGGCTATGGCATCGTAATCCCATG
* * * * **
28290940 TAAGACCATAACTAGGCTATGACATCATAATGACATG
1 TAAGACCATAGCTGGGCTATGGCATCGTAATCCCATG
* * *
28290977 TAAGACCATAGTTGGGCTATGGCATTGTTATCCCATG
1 TAAGACCATAGCTGGGCTATGGCATCGTAATCCCATG
* *
28291014 TAAGATCAT-GTCTGGGATATGGCAT
1 TAAGACCATAG-CTGGGCTATGGCAT
28291039 TGGTATCAAT
Statistics
Matches: 78, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
36 1 0.01
37 77 0.99
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (37 bp):
TAAGACCATAGCTGGGCTATGGCATCGTAATCCCATG
Found at i:28291062 original size:48 final size:48
Alignment explanation
Indices: 28291006--28291101 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
28290996 TGGCATTGTT
* *
28291006 ATCCCATGTAAGATC-ATGTCTGGGATATGGCATTGGTATCAATATGTG
1 ATCCCATGTAAGA-CAATGTCTGGGACATGGCATTGGCATCAATATGTG
28291054 ATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCAATATGTG
1 ATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCAATATGTG
28291102 GCACCCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (48 bp):
ATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCAATATGTG
Found at i:28292470 original size:53 final size:54
Alignment explanation
Indices: 28292403--28292593 Score: 195
Period size: 55 Copynumber: 3.5 Consensus size: 54
28292393 TTACCATTTT
* * * *
28292403 CATGTCTTGACATGGTCTTACTTGGTATCCTTGCCTTAT-GAACTCACCATTGC
1 CATGTCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGC
* * * ** *
28292456 CATGACTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAATGC
1 CATGTCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAG-AACTTACCAATGC
* * * * * *
28292511 CATGTCTTGGCATGGTCTTACATGATTTTCTGGCCTTATAAAACTTACCAATGT
1 CATGTCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGC
* *
28292565 CATGCCTTGGCATGGTCTTTACTTGGTAT
1 CATGTCTTGGCATGGTC-TTACATGGTAT
28292594 TCTTAAACGC
Statistics
Matches: 109, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
53 34 0.31
54 26 0.24
55 49 0.45
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (54 bp):
CATGTCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGC
Found at i:28296215 original size:174 final size:174
Alignment explanation
Indices: 28295925--28296273 Score: 698
Period size: 174 Copynumber: 2.0 Consensus size: 174
28295915 TTCACCTGAG
28295925 ACTATATGTCCAAGAAAACCAACTTCTCGTAACCAGAACTCACTTTTGCTAAACTTGGCATAAAG
1 ACTATATGTCCAAGAAAACCAACTTCTCGTAACCAGAACTCACTTTTGCTAAACTTGGCATAAAG
28295990 CTAATTATCTCTCAAAGTCTGTAAAACTGTTCTCAAATGCTCTGAATGCTCAGTCTTATCATGAG
66 CTAATTATCTCTCAAAGTCTGTAAAACTGTTCTCAAATGCTCTGAATGCTCAGTCTTATCATGAG
28296055 AATAAATCAAGATATCATCAATGAACACAACTACAAATTTATCC
131 AATAAATCAAGATATCATCAATGAACACAACTACAAATTTATCC
28296099 ACTATATGTCCAAGAAAACCAACTTCTCGTAACCAGAACTCACTTTTGCTAAACTTGGCATAAAG
1 ACTATATGTCCAAGAAAACCAACTTCTCGTAACCAGAACTCACTTTTGCTAAACTTGGCATAAAG
28296164 CTAATTATCTCTCAAAGTCTGTAAAACTGTTCTCAAATGCTCTGAATGCTCAGTCTTATCATGAG
66 CTAATTATCTCTCAAAGTCTGTAAAACTGTTCTCAAATGCTCTGAATGCTCAGTCTTATCATGAG
28296229 AATAAATCAAGATATCATCAATGAACACAACTACAAATTTATCC
131 AATAAATCAAGATATCATCAATGAACACAACTACAAATTTATCC
28296273 A
1 A
28296274 AGTAAGGTCT
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 175 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (174 bp):
ACTATATGTCCAAGAAAACCAACTTCTCGTAACCAGAACTCACTTTTGCTAAACTTGGCATAAAG
CTAATTATCTCTCAAAGTCTGTAAAACTGTTCTCAAATGCTCTGAATGCTCAGTCTTATCATGAG
AATAAATCAAGATATCATCAATGAACACAACTACAAATTTATCC
Found at i:28300159 original size:55 final size:54
Alignment explanation
Indices: 28300004--28300210 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
28299994 TTCCTTTTTA
* * * *
28300004 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTACCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
28300057 AACTCACCATTGCCATGCCTTGGCATAGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
28300111 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
28300166 AACTTACCAATTCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28300211 AAACCCTAAT
Statistics
Matches: 122, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 44 0.36
54 37 0.30
55 41 0.34
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:28300561 original size:30 final size:30
Alignment explanation
Indices: 28300527--28300583 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28300517 CCTTAACTCT
*
28300527 AACTTTGGAAAATTTATGATTTTTCCCCTA
1 AACTTTGGAAAATTTATAATTTTTCCCCTA
* * *
28300557 AACTTTTGCATATTTATAATTTTTCCC
1 AACTTTGGAAAATTTATAATTTTTCCC
28300584 AAAGGCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (30 bp):
AACTTTGGAAAATTTATAATTTTTCCCCTA
Found at i:28304042 original size:26 final size:26
Alignment explanation
Indices: 28304006--28304057 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28303996 TGTTCCTGAA
28304006 AGAGTAATTTAGAAATCTGACACTAT
1 AGAGTAATTTAGAAATCTGACACTAT
28304032 AGAGTAATTTAGAAATCTGACACTAT
1 AGAGTAATTTAGAAATCTGACACTAT
28304058 GTCCTAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (26 bp):
AGAGTAATTTAGAAATCTGACACTAT
Found at i:28306282 original size:29 final size:29
Alignment explanation
Indices: 28306250--28306308 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28306240 AGTCAATGTT
28306250 AGGTGAAAATTTGGTGGCTAAATTGACTA
1 AGGTGAAAATTTGGTGGCTAAATTGACTA
28306279 AGGTGAAAATTTGGTGGCTAAATTGACTA
1 AGGTGAAAATTTGGTGGCTAAATTGACTA
28306308 A
1 A
28306309 AAAGAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (29 bp):
AGGTGAAAATTTGGTGGCTAAATTGACTA
Found at i:28306315 original size:29 final size:29
Alignment explanation
Indices: 28306254--28306315 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
28306244 AATGTTAGGT
***
28306254 GAAAATTTGGTGGCTAAATTGACTAAGGT
1 GAAAATTTGGTGGCTAAATTGACTAAAAA
28306283 GAAAATTTGGTGGCTAAATTGACTAAAAA
1 GAAAATTTGGTGGCTAAATTGACTAAAAA
28306312 GAAA
1 GAAA
28306316 TAAAATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (29 bp):
GAAAATTTGGTGGCTAAATTGACTAAAAA
Found at i:28307301 original size:46 final size:47
Alignment explanation
Indices: 28307121--28307480 Score: 193
Period size: 47 Copynumber: 7.7 Consensus size: 47
28307111 TCTGTGTGCT
* * * **
28307121 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTA-CAAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGTAGAGCC
* * *
28307167 AGTGTAGGACCATGTCTGGGACATGGCATC--CT-CATTAAGACG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACA-T--GATGTAGAGCC
* **
28307215 AGTGTAAGACATGTCTGGGATATGCATCGGCCTTGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACATGATGTAGAGCC
* *
28307261 TGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGT--A-TC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGTAGAGCC
* * * *
28307305 AGTATAAGACCATGCCTGGGACATGGCATCGGC-ACGGAT-ACGTGAGAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC--ATGATGT-AGAGCC
* *
28307355 AGT-TAAGACCATGTCTGGGACATGGCATCGACTTA-ACG-TG-AGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACATGATGTAGAGCC
* * * *
28307401 AGTGTAAGACCATGTCTGCGACATGGCGTCGACTTAGC--G-TG-AAAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TA-CATGATGTAGAGCC
28307448 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
28307481 ATTATACCAT
Statistics
Matches: 257, Mismatches: 31, Indels: 51
0.76 0.09 0.15
Matches are distributed among these distances:
44 8 0.03
45 21 0.08
46 73 0.28
47 97 0.38
48 21 0.08
49 30 0.12
50 6 0.02
51 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGTAGAGCC
Found at i:28307424 original size:47 final size:47
Alignment explanation
Indices: 28307161--28307478 Score: 280
Period size: 47 Copynumber: 6.8 Consensus size: 47
28307151 CCACATTACA
* ** *
28307161 AGAGCCAGTGTAGGACCATGTCTGGGACATGGCATCCTCATTAA-GACG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTAACG-TG
* * * *
28307209 AGAGCTAGTGTAAGA-CATGTCTGGGATAT-GCATCGGCCTTGA-GATG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTAACG-TG
* * *
28307255 TA-AGCCTGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-ACATG
1 -AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAACGTG
* * * **
28307298 ATGTA-TCAGTATAAGACCATGCCTGGGACATGGCATCGGCACGGATACGTG
1 A-G-AGCCAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTA-ACGTG
*
28307349 AGAGTCAGT-TAAGACCATGTCTGGGACATGGCATCGACTTAACGTG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAACGTG
* * *
28307395 AGAGCCAGTGTAAGACCATGTCTGCGACATGGCGTCGACTTAGCGTG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAACGTG
*
28307442 AAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
28307479 GCATTATACC
Statistics
Matches: 226, Mismatches: 29, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 9 0.04
45 16 0.07
46 58 0.26
47 87 0.38
48 15 0.07
49 26 0.12
50 6 0.03
51 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (47 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAACGTG
Found at i:28322068 original size:48 final size:45
Alignment explanation
Indices: 28321876--28322101 Score: 238
Period size: 45 Copynumber: 4.9 Consensus size: 45
28321866 TTTGGGTGAC
* * * *
28321876 ATGTGAGCCAATGTATGACCATGTTGGACATGGCATCGGCGTTGA
1 ATGTGAGCTAGTGTAAGACCATGTTGGACATGGCATCGGCCTTGA
* * * * *
28321921 TTGTGAGCCAGTGTAAAACCATGTTGGACATGGAATTGGCCTTGA
1 ATGTGAGCTAGTGTAAGACCATGTTGGACATGGCATCGGCCTTGA
* * *
28321966 TTGTGAGCTAGTGTAAGACCATGTTGGACATGGCTTTGGCAC-TGA
1 ATGTGAGCTAGTGTAAGACCATGTTGGACATGGCATCGGC-CTTGA
* *
28322011 GATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
1 -ATGTGAGCTAGTGTAAGACCATG-TT-GGACATGGCATCGGCCTTGA
* *
28322059 CATGTGAGCTAGTGCAAGACCACGTTTGGGACATGGCATCGGC
1 -ATGTGAGCTAGTGTAAGACCATG-TT-GGACATGGCATCGGC
28322102 AATTCACCCT
Statistics
Matches: 156, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
45 77 0.49
46 22 0.14
47 3 0.02
48 54 0.35
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (45 bp):
ATGTGAGCTAGTGTAAGACCATGTTGGACATGGCATCGGCCTTGA
Found at i:28332598 original size:26 final size:25
Alignment explanation
Indices: 28332569--28332619 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
28332559 ATTAATAAAG
28332569 ATTTAAAAAAATGAGATAATGAGTAT
1 ATTTAAAAAAATGAGAT-ATGAGTAT
* * *
28332595 ATTTGAATAAATGTGATATGAGTAT
1 ATTTAAAAAAATGAGATATGAGTAT
28332620 CGAACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (25 bp):
ATTTAAAAAAATGAGATATGAGTAT
Found at i:28334346 original size:23 final size:23
Alignment explanation
Indices: 28334320--28334367 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28334310 ATGCATTTCT
*
28334320 ATGATAT-TTCATGCCAATAATAA
1 ATGATATCATCATG-CAATAATAA
*
28334343 ATGATATCATCATGCATTAATAA
1 ATGATATCATCATGCAATAATAA
28334366 AT
1 AT
28334368 CATACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (23 bp):
ATGATATCATCATGCAATAATAA
Found at i:28337718 original size:22 final size:22
Alignment explanation
Indices: 28337690--28337732 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28337680 CCCTTTTGTC
**
28337690 TAAATATCTTGGGAAATAAAAT
1 TAAATATCTTGAAAAATAAAAT
28337712 TAAATATCTTGAAAAATAAAA
1 TAAATATCTTGAAAAATAAAA
28337733 GGAAAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
TAAATATCTTGAAAAATAAAAT
Found at i:28340881 original size:120 final size:120
Alignment explanation
Indices: 28340668--28340908 Score: 437
Period size: 120 Copynumber: 2.0 Consensus size: 120
28340658 ACAAAGAATC
*
28340668 CACCTACCTCAGCTTTTATCTTAAAACAGTATGGAGAAACAAATAAAGACGCATGTTAGTACACC
1 CACCTACCTCAGCTATTATCTTAAAACAGTATGGAGAAACAAATAAAGACGCATGTTAGTACACC
*
28340733 TATAGCTCTAACAGCAACGATGAAGTCACAATCTCATAGTGTCCAAGCTGGAACA
66 TATAGCTCTAACAGCAAAGATGAAGTCACAATCTCATAGTGTCCAAGCTGGAACA
* *
28340788 CACCTACCTCAGCTATTATCTTAAAAGAGTATGGAGAAACAAATAAAGACGTATGTTAGTACACC
1 CACCTACCTCAGCTATTATCTTAAAACAGTATGGAGAAACAAATAAAGACGCATGTTAGTACACC
*
28340853 TATAGCTCTAACAGCAAAGATGAAGTCACAATCTCATAGTGTCCAAGCTGGGACA
66 TATAGCTCTAACAGCAAAGATGAAGTCACAATCTCATAGTGTCCAAGCTGGAACA
28340908 C
1 C
28340909 CCACTAAACA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (120 bp):
CACCTACCTCAGCTATTATCTTAAAACAGTATGGAGAAACAAATAAAGACGCATGTTAGTACACC
TATAGCTCTAACAGCAAAGATGAAGTCACAATCTCATAGTGTCCAAGCTGGAACA
Found at i:28346749 original size:96 final size:96
Alignment explanation
Indices: 28346577--28346752 Score: 246
Period size: 96 Copynumber: 1.8 Consensus size: 96
28346567 CTCACACACT
* * * * *
28346577 AAGTGCCAATATCATGGCCTGAAGCCAACTCAATATATCTTGCACTCGAAGTGCTAATATCAGGG
1 AAGTGCCAATATCATGGCCTAAAGCCAAATCAATATAACTTGCACCCGAAGTGCCAATATCAGGG
** *
28346642 CCCGTATCCAAATCAGTGAAGCTCGTTCCCG
66 CCCAAAGCCAAATCAGTGAAGCTCGTTCCCG
* *
28346673 AAGTGCCAATATCATGGCCTAAATCCAAATCAA-AGTAACTTGCACCCGAAGTGCCAATATCATG
1 AAGTGCCAATATCATGGCCTAAAGCCAAATCAATA-TAACTTGCACCCGAAGTGCCAATATCAGG
28346737 GCCCAAAGCCAAATCA
65 GCCCAAAGCCAAATCA
28346753 ATGTATACCC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 68 0.99
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (96 bp):
AAGTGCCAATATCATGGCCTAAAGCCAAATCAATATAACTTGCACCCGAAGTGCCAATATCAGGG
CCCAAAGCCAAATCAGTGAAGCTCGTTCCCG
Found at i:28346753 original size:48 final size:48
Alignment explanation
Indices: 28346577--28346753 Score: 171
Period size: 48 Copynumber: 3.7 Consensus size: 48
28346567 CTCACACACT
** * * *
28346577 AAGTGCCAATATCATGGCCTGAAGCCAACTCAATA-TATCTTGCACTCG
1 AAGTGCCAATATCATGGCCCAAAGCCAAATCAA-AGTAACTTGCACCCG
* * ** * * **
28346625 AAGTGCTAATATCAGGGCCCGTATCCAAATC--AGTGAAGCTCGTTCCCG
1 AAGTGCCAATATCATGGCCCAAAGCCAAATCAAAGT-AA-CTTGCACCCG
* *
28346673 AAGTGCCAATATCATGGCCTAAATCCAAATCAAAGTAACTTGCACCCG
1 AAGTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTTGCACCCG
28346721 AAGTGCCAATATCATGGCCCAAAGCCAAATCAA
1 AAGTGCCAATATCATGGCCCAAAGCCAAATCAA
28346754 TGTATACCCT
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 1 0.01
47 1 0.01
48 95 0.92
49 2 0.02
50 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (48 bp):
AAGTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTTGCACCCG
Found at i:28349886 original size:37 final size:37
Alignment explanation
Indices: 28349827--28349935 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
28349817 AGCTCAGACG
* *
28349827 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
28349864 AAATCTCCACACGTAGTCATCGGGTGTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28349901 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28349936 ATATATTTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:28350197 original size:98 final size:98
Alignment explanation
Indices: 28350081--28350362 Score: 507
Period size: 98 Copynumber: 2.9 Consensus size: 98
28350071 GCACATCGCC
*
28350081 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
28350146 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTTTACCACATATGCATATCTCA
28350179 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
28350244 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTTTACCACATATGCATATCTCA
* *
28350277 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATAGACATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
28350340 -AGCCATTCGGCTTTACCACATAT
66 GA-CCATTCGGCTTTACCACATAT
28350363 ATGCATGTTC
Statistics
Matches: 180, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
95 1 0.01
96 35 0.19
98 144 0.80
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (98 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
GACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:28350205 original size:48 final size:48
Alignment explanation
Indices: 28350081--28350363 Score: 435
Period size: 48 Copynumber: 5.8 Consensus size: 48
28350071 GCACATCGCC
*
28350081 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
28350131 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
28350179 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
28350229 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
28350277 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
28350325 TAGACATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
28350364 TGCATGTTCA
Statistics
Matches: 216, Mismatches: 11, Indels: 14
0.90 0.05 0.06
Matches are distributed among these distances:
48 126 0.58
49 4 0.02
50 86 0.40
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:28350407 original size:47 final size:47
Alignment explanation
Indices: 28350333--28350620 Score: 468
Period size: 47 Copynumber: 6.1 Consensus size: 47
28350323 CATAGACATT
* * * *
28350333 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
28350380 CCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
28350427 TCACATTGGCCATTCGGCCTTATCATATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
28350474 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
28350521 TCACATTGGCCATTTGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
28350568 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
28350615 TCACAT
1 TCACAT
28350621 AAAATCCTAA
Statistics
Matches: 225, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 225 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:28350548 original size:22 final size:22
Alignment explanation
Indices: 28350473--28350548 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
28350463 GTTCACATTC
*
28350473 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTTGGCCTT
* ** *
28350495 ATCACATATATG-CATGTTCACATT
1 ATCACAT-T-GGCCAT-TTGGCCTT
28350519 CATCACATTGGCCATTTGGCCTT
1 -ATCACATTGGCCATTTGGCCTT
28350542 ATCACAT
1 ATCACAT
28350549 ATATGCATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 14 0.35
23 10 0.25
24 9 0.22
25 7 0.17
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTTGGCCTT
Found at i:28360749 original size:31 final size:31
Alignment explanation
Indices: 28360627--28360740 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
28360617 TTAGTCTTGA
* *
28360627 CATAT-ACTGGGCCAAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28360657 CATATCACTGGGCTGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28360688 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28360719 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
28360741 ACTGTAAATG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 18 0.23
31 61 0.77
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:28360811 original size:42 final size:42
Alignment explanation
Indices: 28360764--28360855 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
28360754 TGGCCCTTAG
* *
28360764 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGGAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
28360806 GCCCATTTTAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
28360848 GCCCATTT
1 GCCCATTT
28360856 GGGGAGACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:28361031 original size:25 final size:25
Alignment explanation
Indices: 28361003--28361072 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
28360993 CTCTTTTAAT
*
28361003 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCAG-TA
28361028 AACTGGGGCAAAGCCCTTTTCAGTA
1 AACTGGGGCAAAGCCCTTTTCAGTA
*
28361053 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28361073 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 37 0.88
26 5 0.12
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCAGTA
Found at i:28361552 original size:20 final size:22
Alignment explanation
Indices: 28361527--28361568 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28361517 TGGGCCCAAA
*
28361527 AGCCCATT-TGGCCCAA-TTAC
1 AGCCCATTGAGGCCCAACTTAC
28361547 AGCCCATTGAGGCCCAACTTAC
1 AGCCCATTGAGGCCCAACTTAC
28361569 CATCGTGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (22 bp):
AGCCCATTGAGGCCCAACTTAC
Found at i:28361947 original size:27 final size:27
Alignment explanation
Indices: 28361888--28361962 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
28361878 CATATTCGTC
28361888 ATTTTACCATATAGGGGTATTACGGTA
1 ATTTTACCATATAGGGGTATTACGGTA
* * *
28361915 ACTTTACCCTATAGGGGCT-TTACGGTC
1 ATTTTACCATATAGGGG-TATTACGGTA
* *
28361942 TTTTTACC-TATTAAGGGTATT
1 ATTTTACCATA-TAGGGGTATT
28361963 TTAGTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 35 0.90
28 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (27 bp):
ATTTTACCATATAGGGGTATTACGGTA
Found at i:28362098 original size:56 final size:55
Alignment explanation
Indices: 28361980--28362191 Score: 168
Period size: 54 Copynumber: 3.9 Consensus size: 55
28361970 TTTCATCCTA
* * * * *
28361980 CAAGGGTGTTTTGGTAAATCTAC-AAACCAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAATCAAGGGTATTTCAGTAATTTTGTAAAC
* *
28362034 CAATGGTATTTTTA-TAATTTTTA-AAAAGTCAAGGGTATTTCTA-TAATTTTGTAAAT
1 CAAGGGTA-TTTTAGTAA-TTTTACAAAA-TCAAGGGTATTTC-AGTAATTTTGTAAAC
* ** ***
28362090 CAGGGGTATTTTAGTAATTTTACAAAAT-AAGGGTATTTTGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAATCAAGGGTATTTCAGTAATTTTGTAAAC
* * * **
28362144 C-AGTGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTT
1 CAAG-GGTATTTTAGTAATTTTACAAAATCAAGGGTATTTCAGTAATTTT
28362192 ACCCTATAGG
Statistics
Matches: 129, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
53 1 0.01
54 69 0.53
55 21 0.16
56 37 0.29
57 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (55 bp):
CAAGGGTATTTTAGTAATTTTACAAAATCAAGGGTATTTCAGTAATTTTGTAAAC
Found at i:28362123 original size:27 final size:27
Alignment explanation
Indices: 28361981--28362222 Score: 125
Period size: 27 Copynumber: 8.9 Consensus size: 27
28361971 TTCATCCTAC
* * * * **
28361981 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTAGTAATTTTACAAAAT
* ** **
28362008 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTACAAAAT
*
28362035 AATGGTATTTTTA-TAATTTTTA-AAAAGT
1 AAGGGTA-TTTTAGTAA-TTTTACAAAA-T
**
28362063 CAAGGGTATTTCTA-TAATTTT-GTAAAT
1 -AAGGGTATTT-TAGTAATTTTACAAAAT
*
28362090 CAGGGGTATTTTAGTAATTTTACAAAAT
1 -AAGGGTATTTTAGTAATTTTACAAAAT
* * *
28362118 AAGGGTATTTTGGTAATTTCAC-AAAC
1 AAGGGTATTTTAGTAATTTTACAAAAT
* * *
28362144 CAGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTAGTAATTTTACAAAAT
* * ***
28362172 AGGGGTATTTTGGTAATTTTACCCTAT
1 AAGGGTATTTTAGTAATTTTACAAAAT
* * *
28362199 AGGGGTATTTCAGTAATTTCACAA
1 AAGGGTATTTTAGTAATTTTACAA
28362223 TCAAGGGTAA
Statistics
Matches: 169, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.04
27 126 0.75
28 25 0.15
29 11 0.07
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTACAAAAT
Found at i:28362259 original size:27 final size:27
Alignment explanation
Indices: 28362226--28362312 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
28362216 TTCACAATCA
* *
28362226 AGGGTAAAACGGTAATTTTGTAAATTG
1 AGGGTAAAACAGTAATTCTGTAAATTG
* **
28362253 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAACAGTAATTCTGTAAATTG
* * *
28362280 AGGGTGAAACAGTGATTCTATAAATCT-
1 AGGGTAAAACAGTAATTCTGTAAAT-TG
28362307 AGGGTA
1 AGGGTA
28362313 CTTTGGTAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
AGGGTAAAACAGTAATTCTGTAAATTG
Found at i:28365807 original size:79 final size:81
Alignment explanation
Indices: 28365674--28365853 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 81
28365664 AATGATGTCC
* *
28365674 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGATTAAGATCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGATTAAGATCCGAAGGCATTTGT
*
28365738 GCGAGATACTA-ATTCT
66 GCGAGATACTATA-ACT
* * * *
28365754 GGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGATTAAGAT-CCGAAGGCATTTG
*
28365816 TGCGAGTTACTATAACT
65 TGCGAGATACTATAACT
*
28365833 GGGCTATGTCCCGAAGGCATT
1 GGGCTAAGTCCCGAAGGCATT
28365854 TGAACGAGGA
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 59 0.68
80 27 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (81 bp):
GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGATTAAGATCCGAAGGCATTTGT
GCGAGATACTATAACT
Found at i:28365819 original size:40 final size:40
Alignment explanation
Indices: 28365671--28365855 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
28365661 TTGAATGATG
* * * *
28365671 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
28365711 TCCGGATTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28365751 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28365790 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28365831 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28365856 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 33 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28365877 original size:79 final size:77
Alignment explanation
Indices: 28365701--28365888 Score: 200
Period size: 79 Copynumber: 2.4 Consensus size: 77
28365691 CTTTGTGCTA
* *
28365701 AGTGACCATATCCGGATTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAGCCCG
1 AGTGACTATATCCGG-TTAAG-TCCGAAGGCATTTGTGCGAGATACTAATACTGGGCTAAGCCCG
**
28365766 AAGGCATTGGTGCG
64 AAGGCATTGGAACG
* * * *
28365780 AGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACTGGGCTATGTCC
1 AGTGACTATATCC-GGTTAAGT-CCGAAGGCATTTGTGCGAGATACTAAT-ACTGGGCTAAG-CC
*
28365844 CGAAGGCATTTGAACG
62 CGAAGGCATTGGAACG
*
28365860 AG-GAGCTATATCCGGTTAAATTCCGAAGG
1 AGTGA-CTATATCCGGTT-AAGTCCGAAGG
28365889 TACGTGATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
78 3 0.03
79 59 0.65
80 29 0.32
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (77 bp):
AGTGACTATATCCGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAATACTGGGCTAAGCCCGAA
GGCATTGGAACG
Found at i:28370472 original size:4 final size:4
Alignment explanation
Indices: 28370463--28370491 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28370453 ATGTCTATAC
28370463 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
28370492 GAGAACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:28377123 original size:16 final size:16
Alignment explanation
Indices: 28377076--28377123 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
28377066 CGTTGTAGTT
* *
28377076 AACCATGCATGAATCC
1 AACCATGCATGCACCC
28377092 -ACCTATGCATTGCACCC
1 AACC-ATGCA-TGCACCC
28377109 AACCATGCATGCACC
1 AACCATGCATGCACC
28377124 TTGCATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 10 0.37
18 3 0.11
ACGTcount: A:0.31, C:0.38, G:0.12, T:0.19
Consensus pattern (16 bp):
AACCATGCATGCACCC
Found at i:28377453 original size:20 final size:20
Alignment explanation
Indices: 28377428--28377465 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28377418 AGATAAAATG
*
28377428 AAGCTGAAATGAGCTCAAAC
1 AAGCTGAAATAAGCTCAAAC
28377448 AAGCTGAAATAAGCTCAA
1 AAGCTGAAATAAGCTCAA
28377466 GTAAGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (20 bp):
AAGCTGAAATAAGCTCAAAC
Found at i:28382712 original size:24 final size:24
Alignment explanation
Indices: 28382646--28382720 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
28382636 TATCCGGTGC
* **
28382646 TTCCTGATAAAAACTCTTCGGAGT
1 TTCCTGATTAAAACTCTTATGAGT
* *
28382670 TACCTG-TT-AAGCTC-TATGAGT
1 TTCCTGATTAAAACTCTTATGAGT
28382691 TTCCTGATTAAAACTCTTATGAGT
1 TTCCTGATTAAAACTCTTATGAGT
28382715 TTCCTG
1 TTCCTG
28382721 TTTAGCCCAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 10 0.24
22 7 0.17
23 6 0.15
24 18 0.44
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (24 bp):
TTCCTGATTAAAACTCTTATGAGT
Found at i:28387058 original size:51 final size:50
Alignment explanation
Indices: 28386935--28387051 Score: 143
Period size: 49 Copynumber: 2.4 Consensus size: 50
28386925 TGTCACTAGT
* * *
28386935 AAGTG-TGGTACTATGTGAAGGCCACTGTGAGAAGAGTTAGCTTGGTCAC
1 AAGTGATGGTACTATGTGAAGGCCACTGTGAGAAAAGGTAGCTTGGACAC
*
28386984 AAGTGA-GGTACTATGTGAAGGCCACTTTGTGA-AAAAGGTAGCTTTGACTAC
1 AAGTGATGGTACTATGTGAAGGCCAC--TGTGAGAAAAGGTAGCTTGGAC-AC
28387035 AAG-GATGGTACTATGTG
1 AAGTGATGGTACTATGTG
28387052 CGGGCCATCG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
49 24 0.41
50 14 0.24
51 21 0.36
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (50 bp):
AAGTGATGGTACTATGTGAAGGCCACTGTGAGAAAAGGTAGCTTGGACAC
Found at i:28390293 original size:16 final size:16
Alignment explanation
Indices: 28390272--28390302 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28390262 TTCACTATTA
28390272 TGTCTTTTATATTTTC
1 TGTCTTTTATATTTTC
28390288 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
28390303 GCATGCATAG
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:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:28392324 original size:48 final size:47
Alignment explanation
Indices: 28392187--28392368 Score: 189
Period size: 48 Copynumber: 3.9 Consensus size: 47
28392177 ACATAGTAAG
*
28392187 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACAGATC
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* * * *
28392234 --G--AA-GCCGATAGCCCA-ACTATGGTCTTACACGATG-TCTCATATC
1 ATGCCAATGCC-ATATCCCAGA-TATGGTCTTACATG-GGATCACATATC
* *
28392277 AATGCCAATGCCATATCCCAGATATGGTCTTACGTGGGATCAAATATC
1 -ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* *
28392325 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
1 -ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACA
28392369 CATAACCCTA
Statistics
Matches: 108, Mismatches: 16, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
42 4 0.04
43 29 0.27
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 67 0.62
49 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (47 bp):
ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
Found at i:28394494 original size:212 final size:212
Alignment explanation
Indices: 28394127--28394551 Score: 805
Period size: 212 Copynumber: 2.0 Consensus size: 212
28394117 TAGAAACAAC
28394127 TTTTGTGAAAGGTGATAGCATGAAAACACCTAAAGAGACCATTTTACATAAGTTGTAAAATAGAT
1 TTTTGTGAAAGGTGATAGCATGAAAACACCTAAAGAGACCATTTTACATAAGTTGTAAAATAGAT
*
28394192 GAAAAATGTGTGAAATAGTAGGATTTTGGAGTTTCTATAAGATTAAAAAGGGTTTGGTTTGCTTA
66 GAAAAATGTGTGAAATAGTAGGATTTTGGAGTTTCTATAAGATTAAAAAGGGTTTGGCTTGCTTA
28394257 AGATGCGAAGAAATTCGATAAAAATCGATTTTCAAGCCTAGGGGTAAAATGGTCATTTTGTCAAA
131 AGATGCGAAGAAATTCGATAAAAATCGATTTTCAAGCCTAGGGGTAAAATGGTCATTTTGTCAAA
*
28394322 GTATATGGGCAAAATGG
196 GTATAGGGGCAAAATGG
*
28394339 TTTTGTGAAAGGTGATAGCATGAAAACACCTAAAGAGACCATTTTGCATAAGTTGTAAAATAGAT
1 TTTTGTGAAAGGTGATAGCATGAAAACACCTAAAGAGACCATTTTACATAAGTTGTAAAATAGAT
* *
28394404 GAAAAATGTGTGAGATAGTAGGATTTTGGAGTTTTTATAAGATTAAAAAGGGTTTGGCTTGCTTA
66 GAAAAATGTGTGAAATAGTAGGATTTTGGAGTTTCTATAAGATTAAAAAGGGTTTGGCTTGCTTA
28394469 AGATGCGAAGAAATTCGATAAAAATCGATTTTCAAGCCTAGGGGTAAAATGGTCATTTTGTCAAA
131 AGATGCGAAGAAATTCGATAAAAATCGATTTTCAAGCCTAGGGGTAAAATGGTCATTTTGTCAAA
28394534 GTATAGGGGCAAAATGG
196 GTATAGGGGCAAAATGG
28394551 T
1 T
28394552 CATTTTACAA
Statistics
Matches: 208, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
212 208 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (212 bp):
TTTTGTGAAAGGTGATAGCATGAAAACACCTAAAGAGACCATTTTACATAAGTTGTAAAATAGAT
GAAAAATGTGTGAAATAGTAGGATTTTGGAGTTTCTATAAGATTAAAAAGGGTTTGGCTTGCTTA
AGATGCGAAGAAATTCGATAAAAATCGATTTTCAAGCCTAGGGGTAAAATGGTCATTTTGTCAAA
GTATAGGGGCAAAATGG
Found at i:28394960 original size:46 final size:46
Alignment explanation
Indices: 28394902--28395122 Score: 158
Period size: 46 Copynumber: 4.7 Consensus size: 46
28394892 TCACATGTGT
* * *
28394902 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGG
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
* * * ** * **
28394948 GAGCCAGTGTAAGACCATGTCTGGGATATGGCAT-TGACATTGAGACAA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CAATATGA
* * * * *
28394996 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAACACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATG-A
* * * * *
28395043 -AGCCAATGTAAGACATGTTTGGGACATGCGTCGGCTACAAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
* * *
28395088 TAGTCAGTATAAGACCATGTCTGGGACATGGCATC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
28395123 AGCACCTTAC
Statistics
Matches: 132, Mismatches: 35, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
45 1 0.01
46 65 0.49
47 45 0.34
48 21 0.16
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
Found at i:28398200 original size:28 final size:28
Alignment explanation
Indices: 28398168--28398237 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
28398158 AATGAGATTG
28398168 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
28398196 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
28398224 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28398238 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:28406479 original size:40 final size:40
Alignment explanation
Indices: 28406395--28406618 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
28406385 TTGAATGATG
* * * *
28406395 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28406435 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28406475 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28406513 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28406553 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28406594 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28406619 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28406613 original size:80 final size:80
Alignment explanation
Indices: 28406395--28406618 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
28406385 TTGAATGATG
* * * * *
28406395 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
28406458 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
28406475 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
28406537 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
28406553 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
28406618 G
66 G
28406619 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:28414244 original size:40 final size:40
Alignment explanation
Indices: 28414160--28414384 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
28414150 TTGAATGATG
* * * *
28414160 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28414200 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28414240 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28414279 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28414319 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28414360 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28414385 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28414406 original size:119 final size:119
Alignment explanation
Indices: 28414160--28414417 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
28414150 TTGAATGATG
* *
28414160 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
28414225 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
28414279 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
28414342 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
28414399 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28414418 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:28421282 original size:68 final size:67
Alignment explanation
Indices: 28421169--28421305 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 67
28421159 TCCAAATCCT
28421169 ATGTCTGATAATTTTCTCATGTAGCTTCAACTGGCTCGAGGCATAAGCTATCACCTTGCCTTCTT
1 ATGTCTGATAATTTTCTCATGTAGCTTCAACTGGCTCGAGGCATAAGCTATCACCTTGCCTTCTT
28421234 GC
66 GC
* * *
28421236 ATGTTTGATAATTTTTCTCATGTGGCTTCAACTTGCTCGAGGCATAAGCTATCACCTTGCCTTCT
1 ATGTCTGATAA-TTTTCTCATGTAGCTTCAACTGGCTCGAGGCATAAGCTATCACCTTGCCTTCT
28421301 TGC
65 TGC
28421304 AT
1 AT
28421306 AAGTACACAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 10 0.15
68 56 0.85
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (67 bp):
ATGTCTGATAATTTTCTCATGTAGCTTCAACTGGCTCGAGGCATAAGCTATCACCTTGCCTTCTT
GC
Found at i:28432645 original size:40 final size:40
Alignment explanation
Indices: 28432590--28432767 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
28432580 CAGATGATAA
* *
28432590 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
28432630 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28432670 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
28432710 CCGAGCTAAGTCCCAAAGGCATTTGAGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28432750 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28432768 TACTTGGTTG
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.12
40 107 0.87
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28447231 original size:42 final size:43
Alignment explanation
Indices: 28447131--28447269 Score: 147
Period size: 42 Copynumber: 3.2 Consensus size: 43
28447121 TGAGATATCA
* * * **
28447131 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATATCTGATTT-CG
*
28447175 TGTAAGACCATGTCTGGGACATAGGCATC-ATATCTGATTTCG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATATCTGATTTCG
* * * * *
28447217 TGTAAGACCCTGTCTGGGATAGAGGCATCGATA-CTGAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGATATCTG-ATTTCG
28447260 TGTAAGACCA
1 TGTAAGACCA
28447270 CGTTCGGGAC
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.38
43 24 0.30
44 26 0.32
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATATCTGATTTCG
Found at i:28449214 original size:38 final size:38
Alignment explanation
Indices: 28449145--28449289 Score: 155
Period size: 38 Copynumber: 3.6 Consensus size: 38
28449135 ATTGATTCAT
* *
28449145 TAACGTGGAGCTAAGTGGATTTACCACGGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* * *
28449183 TAATGTGGTGCTAAGTGGATATGCCAAGGTTACATACATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG
*
28449224 ATTCATTAACGTGGTGCTAAGTGGATATACCACGATTAAACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
28449268 TAACGTGGTGCTAAGTGGATAT
1 TAACGTGGTGCTAAGTGGATAT
28449290 GTCATGGTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
38 49 0.55
39 1 0.01
40 3 0.03
41 2 0.02
44 2 0.02
45 3 0.03
46 1 0.01
47 28 0.31
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
Found at i:28449225 original size:85 final size:85
Alignment explanation
Indices: 28449098--28449299 Score: 297
Period size: 85 Copynumber: 2.4 Consensus size: 85
28449088 CATATTGATG
*
28449098 CATGTAACGTGGTGCT-A---GATATGCCACA-GTTACATATATTGATTCATTAACGTGGAGCTA
1 CATGTAACGTGGTGCTAAGTGGATATGCCA-AGGTTACATACATTGATTCATTAACGTGGAGCTA
* *
28449158 AGTGGATTTACCACGGTTAAA
65 AGTGGATATACCACGATTAAA
* *
28449179 CATGTAATGTGGTGCTAAGTGGATATGCCAAGGTTACATACATTGATTCATTAACGTGGTGCTAA
1 CATGTAACGTGGTGCTAAGTGGATATGCCAAGGTTACATACATTGATTCATTAACGTGGAGCTAA
28449244 GTGGATATACCACGATTAAA
66 GTGGATATACCACGATTAAA
* *
28449264 CATGTAACGTGGTGCTAAGTGGATATGTCATGGTTA
1 CATGTAACGTGGTGCTAAGTGGATATGCCAAGGTTA
28449300 TACATGTTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
81 15 0.14
82 1 0.01
84 1 0.01
85 91 0.84
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (85 bp):
CATGTAACGTGGTGCTAAGTGGATATGCCAAGGTTACATACATTGATTCATTAACGTGGAGCTAA
GTGGATATACCACGATTAAA
Found at i:28452162 original size:48 final size:48
Alignment explanation
Indices: 28451939--28452168 Score: 242
Period size: 48 Copynumber: 4.9 Consensus size: 48
28451929 CACATAGTAA
* * * *
28451939 GATGCCAATGCTATATCCTAGATATGGTCTTACATGGGATCACAGATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * * * * *
28451987 GAAGCC---G--ATAGCCCAG-CTATGGTATTACACGATG-TCTCATATC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACATG-GGATCACATATC
* * *
28452030 GATGCCAATGTCATATCCCAGATATGGTCTTACATGGGATCAAAT-TC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
*
28452077 GATGCCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* *
28452125 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACA
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACA
28452169 CATAACCTTA
Statistics
Matches: 148, Mismatches: 24, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
43 30 0.20
44 1 0.01
45 1 0.01
46 1 0.01
47 44 0.30
48 71 0.48
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:28460326 original size:47 final size:47
Alignment explanation
Indices: 28460273--28460740 Score: 722
Period size: 47 Copynumber: 10.0 Consensus size: 47
28460263 TTAGGATTTT
*
28460273 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28460320 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28460367 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28460414 ATGTGATGAATGTGAACATGCATATATGTGATGAA-GCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGAT-AAGGCCGAATGGCCA
* *
28460461 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28460508 ATGTGGTGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28460555 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28460602 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28460649 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
28460696 ATGTGGTGAATATGAAAATGCATATATGCGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
28460741 TAGTGTGAAA
Statistics
Matches: 388, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
46 2 0.01
47 384 0.99
48 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28460608 original size:22 final size:22
Alignment explanation
Indices: 28460580--28460655 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28460570 GCATGCATAT
28460580 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
28460602 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
28460624 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
28460649 ATGTGAT
1 ATGTGAT
28460656 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 16 0.39
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:28460676 original size:23 final size:23
Alignment explanation
Indices: 28460602--28460676 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
28460592 CGAATGGCCA
28460602 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
* * *
28460625 ATGTG-TGATAAG-GCCGAATGGCCA-
1 ATGTGATGA-ATGTG-AGCAT-G-CAT
28460649 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
28460672 ATGTG
1 ATGTG
28460677 TGATAAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 6 0.15
23 16 0.41
24 11 0.28
25 6 0.15
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAGCATGCAT
Found at i:28460953 original size:37 final size:37
Alignment explanation
Indices: 28460903--28461017 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
28460893 GGAAATATAT
*
28460903 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28460940 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * *
28460977 TCCGGGTACGACCCGATAACTTCGTGTGGAGATTACG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28461014 TCCG
1 TCCG
28461018 AGCTAAAGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28471331 original size:20 final size:20
Alignment explanation
Indices: 28471306--28471346 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28471296 CCTCGAACAC
28471306 AAATCTATAGGATGATAGTT
1 AAATCTATAGGATGATAGTT
28471326 AAATCTATAGGATGATAGTT
1 AAATCTATAGGATGATAGTT
28471346 A
1 A
28471347 TCCATATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
AAATCTATAGGATGATAGTT
Found at i:28480750 original size:65 final size:65
Alignment explanation
Indices: 28480646--28480782 Score: 256
Period size: 65 Copynumber: 2.1 Consensus size: 65
28480636 CTCAAGTGTA
28480646 TTCTTGTTTATTTGTGCTTTATTGACAAACATTCTGATCTTGTAAGGATTATTTCTAAGTTTTTT
1 TTCTTGTTTATTTGTGCTTTATTGACAAACATTCTGATCTTGTAAGGATTATTTCTAAGTTTTTT
*
28480711 TTCTTGTTTATTTGTGCTTTATTGACAAACATTCTGATCTTGTAAGGATTATTTCTTAGTTTTTT
1 TTCTTGTTTATTTGTGCTTTATTGACAAACATTCTGATCTTGTAAGGATTATTTCTAAGTTTTTT
*
28480776 TTTTTGT
1 TTCTTGT
28480783 AATTCTTTGA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (65 bp):
TTCTTGTTTATTTGTGCTTTATTGACAAACATTCTGATCTTGTAAGGATTATTTCTAAGTTTTTT
Found at i:28483206 original size:46 final size:46
Alignment explanation
Indices: 28483156--28483330 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28483146 TGGTTGAGCA
28483156 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28483202 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28483247 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28483295 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28483331 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 17 0.15
46 48 0.44
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28483312 original size:93 final size:92
Alignment explanation
Indices: 28483153--28483323 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
28483143 GGATGGTTGA
* *
28483153 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28483218 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
*
28483246 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28483311 TGAGTCGAGTTCG
66 TGAGTCGAGTTCG
28483324 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 8 0.11
93 67 0.89
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:28486427 original size:27 final size:27
Alignment explanation
Indices: 28486390--28486590 Score: 251
Period size: 27 Copynumber: 7.4 Consensus size: 27
28486380 TAAATTGTAC
28486390 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
28486417 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28486444 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28486470 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28486498 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28486526 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28486553 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28486580 AGCACTGAGTG
1 AGCACTAAGTG
28486591 AGCGGACTCA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28494259 original size:46 final size:46
Alignment explanation
Indices: 28494209--28494384 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
28494199 TGGTTGAGCA
28494209 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
28494255 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
28494300 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * **
28494348 CCCGAGCTCGTTGAGTTGAGTCTGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28494385 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 60 0.56
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:28494365 original size:93 final size:93
Alignment explanation
Indices: 28494206--28494375 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
28494196 GGATGGTTGA
*
28494206 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
28494271 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28494299 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
*
28494364 TGAGTCTGAGTT
66 TGAGTCCGAGTT
28494376 TGCTTATGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28499060 original size:28 final size:28
Alignment explanation
Indices: 28499029--28499133 Score: 165
Period size: 28 Copynumber: 3.8 Consensus size: 28
28499019 TACTCGATGC
28499029 CTCGCACACTAAGTGCCATACTCAATAT
1 CTCGCACACTAAGTGCCATACTCAATAT
*
28499057 CTCGCACACTAAGTGCCATTCTCAATAT
1 CTCGCACACTAAGTGCCATACTCAATAT
* * *
28499085 CTCGCACACTAAATGTCATACTCGATAT
1 CTCGCACACTAAGTGCCATACTCAATAT
*
28499113 CTTGCACACTAAGTGCCATAC
1 CTCGCACACTAAGTGCCATAC
28499134 ATAGCCGAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.27
Consensus pattern (28 bp):
CTCGCACACTAAGTGCCATACTCAATAT
Found at i:28499209 original size:39 final size:40
Alignment explanation
Indices: 28499116--28499215 Score: 139
Period size: 40 Copynumber: 2.5 Consensus size: 40
28499106 TCGATATCTT
** * *
28499116 GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAGATC
1 GCACACTAAGTGCCATATTTAGCCGAAGCTATATCAGAAC
*
28499156 GCACACTAAGTGCCAAATTTAGCCGAAGCTATATC-GAAC
1 GCACACTAAGTGCCATATTTAGCCGAAGCTATATCAGAAC
*
28499195 GCACAATAAGTGCCATATTTA
1 GCACACTAAGTGCCATATTTA
28499216 TCCAATATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 22 0.42
40 31 0.58
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (40 bp):
GCACACTAAGTGCCATATTTAGCCGAAGCTATATCAGAAC
Found at i:28501504 original size:12 final size:12
Alignment explanation
Indices: 28501487--28501524 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
28501477 TACATGCCCA
28501487 TGTGCTAGACCG
1 TGTGCTAGACCG
28501499 TGTGCTAGACCG
1 TGTGCTAGACCG
28501511 TGTGCTAGACCG
1 TGTGCTAGACCG
28501523 TG
1 TG
28501525 CCAAACCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.26
Consensus pattern (12 bp):
TGTGCTAGACCG
Found at i:28509575 original size:30 final size:30
Alignment explanation
Indices: 28509539--28509606 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
28509529 TGATCGTTAC
28509539 TTTGAGTACTAGCTAAGCCATACCTTAATT
1 TTTGAGTACTAGCTAAGCCATACCTTAATT
**
28509569 TTTGAGTTTTTAGCTAAGCCATACCTTAATT
1 TTTGAG-TACTAGCTAAGCCATACCTTAATT
28509600 TTTGAGT
1 TTTGAGT
28509607 TTTTTTAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (30 bp):
TTTGAGTACTAGCTAAGCCATACCTTAATT
Found at i:28509585 original size:31 final size:31
Alignment explanation
Indices: 28509548--28509610 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
28509538 CTTTGAGTAC
28509548 TAGCTAAGCCATACCTTAATTTTTGAGTTTT
1 TAGCTAAGCCATACCTTAATTTTTGAGTTTT
28509579 TAGCTAAGCCATACCTTAATTTTTGAGTTTT
1 TAGCTAAGCCATACCTTAATTTTTGAGTTTT
28509610 T
1 T
28509611 TTAGTGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (31 bp):
TAGCTAAGCCATACCTTAATTTTTGAGTTTT
Found at i:28510360 original size:43 final size:42
Alignment explanation
Indices: 28510274--28510422 Score: 113
Period size: 43 Copynumber: 3.5 Consensus size: 42
28510264 AAATTACATA
** * *
28510274 TAAGACCATGTCAGGGACATTGGCATTGTATTGAGATTACGTG
1 TAAGACCATGTTTGGGATATTGGCATCGTATT-AGATTACGTG
*
28510317 TAAGACCATGTTTGGGATATTGGCATCGTTAATT-GATTTCGTG
1 TAAGACCATGTTTGGGATATTGGCATCG-T-ATTAGATTACGTG
* * * * * *
28510360 TAAGACCCTATTTGGGATAGTGGAATCGATATGT-GATAACATG
1 TAAGACCATGTTTGGGATATTGGCATCG-TAT-TAGATTACGTG
* * *
28510403 TAAAACCATATCTGGGATAT
1 TAAGACCATGTTTGGGATAT
28510423 GGTATTGTAC
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 2 0.02
43 80 0.93
44 1 0.01
45 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (42 bp):
TAAGACCATGTTTGGGATATTGGCATCGTATTAGATTACGTG
Found at i:28512354 original size:51 final size:51
Alignment explanation
Indices: 28512274--28512421 Score: 251
Period size: 51 Copynumber: 2.9 Consensus size: 51
28512264 ATGATACACG
*
28512274 GTGGCCTTCACATAGTACCACACTCGTGTCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28512325 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGATATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28512376 GTGGCATTGACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
28512422 CTAAGGTTCA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 90 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:28512489 original size:24 final size:24
Alignment explanation
Indices: 28512457--28512580 Score: 169
Period size: 24 Copynumber: 5.0 Consensus size: 24
28512447 ACTTAGCACC
**
28512457 ATGCCATGGACTTATTTCGTTTAG
1 ATGCCATGGACTTATTTCACTTAG
28512481 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
28512505 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
*
28512529 CACATTGCCATAGACTTATTTCACTTAG
1 ---A-TGCCATGGACTTATTTCACTTAG
28512557 ATGCCATGGTA-TTATTTCACTTAG
1 ATGCCATGG-ACTTATTTCACTTAG
28512581 CACAATGCCG
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
24 66 0.73
25 2 0.02
27 1 0.01
28 22 0.24
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTAG
Found at i:28512583 original size:52 final size:52
Alignment explanation
Indices: 28512457--28512589 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
28512447 ACTTAGCACC
** *
28512457 ATGCCATGGACTTATTTCGTTTAG----ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAGCACAATGCCATAGACTTATTTCACTTAG
*
28512505 ATGCCATGGACTTATTTCACTTAGCACATTGCCATAGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAGCACAATGCCATAGACTTATTTCACTTAG
28512557 ATGCCATGGTA-TTATTTCACTTAGCACAATGCC
1 ATGCCATGG-ACTTATTTCACTTAGCACAATGCC
28512590 GTATCCTAGA
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
48 22 0.29
52 52 0.69
53 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (52 bp):
ATGCCATGGACTTATTTCACTTAGCACAATGCCATAGACTTATTTCACTTAG
Found at i:28515196 original size:47 final size:46
Alignment explanation
Indices: 28515131--28515337 Score: 170
Period size: 47 Copynumber: 4.4 Consensus size: 46
28515121 TTGTGGGCTT
* * *
28515131 GTGTAAGACATGTTTGGGACATGCATCAGCCAC-ATTATGAGACCCA
1 GTGTAAGACATGTCTGGGACATGCATCAGCCACGA-GATGAGAGCCA
** * *
28515177 GTGTAAGACCATGTCTGGGACATGACATCAG-CATCGAGACAAGTGCTA
1 GTGTAAGA-CATGTCTGGGACATG-CATCAGCCA-CGAGATGAGAGCCA
** * * *
28515225 GTGTAAGATGTGTCTGGGACATGCATCAGCTACGAGATGATAGTCA
1 GTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGCCA
* * *
28515271 GTGTAAGACCATGTCTGGGACATGGCATC-GACATGAGAT-ATGAGCTA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACGAGATGA-GAGCCA
*
28515318 GTGTAAGACCGTGTCTGGGA
1 GTGTAAGA-CATGTCTGGGA
28515338 TAAGGCATCG
Statistics
Matches: 128, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
46 31 0.24
47 71 0.55
48 25 0.20
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGCCA
Found at i:28515292 original size:94 final size:93
Alignment explanation
Indices: 28515131--28515337 Score: 256
Period size: 94 Copynumber: 2.2 Consensus size: 93
28515121 TTGTGGGCTT
* * *
28515131 GTGTAAGACATGTTTGGGACATGCATCAGCCACATTATGAGACCCAGTGTAAGACCATGTCTGGG
1 GTGTAAGACGTGTCTGGGACATGCATCAGCCACATGATGAGACCCAGTGTAAGACCATGTCTGGG
*
28515196 ACATGACATC-AGCATCGAGACAAGTGCTA
66 ACATGACATCGA-CAT-GAGACAAGAGCTA
* * * **
28515225 GTGTAAGATGTGTCTGGGACATGCATCAGCTACGA-GATGATAGTCAGTGTAAGACCATGTCTGG
1 GTGTAAGACGTGTCTGGGACATGCATCAGCCAC-ATGATGAGACCCAGTGTAAGACCATGTCTGG
* * *
28515289 GACATGGCATCGACATGAGATATGAGCTA
65 GACATGACATCGACATGAGACAAGAGCTA
28515318 GTGTAAGACCGTGTCTGGGA
1 GTGTAAGA-CGTGTCTGGGA
28515338 TAAGGCATCG
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
93 18 0.19
94 77 0.79
95 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (93 bp):
GTGTAAGACGTGTCTGGGACATGCATCAGCCACATGATGAGACCCAGTGTAAGACCATGTCTGGG
ACATGACATCGACATGAGACAAGAGCTA
Found at i:28520054 original size:12 final size:12
Alignment explanation
Indices: 28520037--28520064 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28520027 TAATGTGTTA
28520037 TTGAAGCTTACT
1 TTGAAGCTTACT
28520049 TTGAAGCTTACT
1 TTGAAGCTTACT
28520061 TTGA
1 TTGA
28520065 TATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (12 bp):
TTGAAGCTTACT
Found at i:28520260 original size:14 final size:14
Alignment explanation
Indices: 28520241--28520272 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28520231 TACAAGGGGC
28520241 ATGTTATGAAAAAT
1 ATGTTATGAAAAAT
*
28520255 ATGTTATGAAAATT
1 ATGTTATGAAAAAT
28520269 ATGT
1 ATGT
28520273 GGTCTGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (14 bp):
ATGTTATGAAAAAT
Found at i:28522066 original size:47 final size:46
Alignment explanation
Indices: 28521994--28522123 Score: 165
Period size: 47 Copynumber: 2.8 Consensus size: 46
28521984 CACTTGTGAA
* *
28521994 AGCCAGTGTAAGACATGTCTAGGACAT-GCATCGGCTACGAGATGAT-
1 AGCCAGTGTAAGACATGTCTGGGACATGGCATCGACT-CGAGAT-ATG
* *
28522040 AGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATG
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGACTCGAGATATG
*
28522087 AGCCAGTGTAAGATCGTGTCTGGGACATGGCATCGAC
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGAC
28522124 ACTTTACCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 14 0.19
47 52 0.70
48 8 0.11
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
AGCCAGTGTAAGACATGTCTGGGACATGGCATCGACTCGAGATATG
Found at i:28532845 original size:46 final size:46
Alignment explanation
Indices: 28532778--28532952 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
28532768 TCACTTGTGA
* *
28532778 AAGCCAATGTAAGACATGTCTGGGACAT-GCATCGACCTTGGGACGT
1 AAGCCAGTGTAAGACATGTCTGGGACATGGCATCGA-CTTGAGACGT
* *
28532824 AAGCCAGTGTAAGACATGTCTGGGACAT-GCGTCGGCTTCGAG--GT
1 AAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACTT-GAGACGT
* * **
28532868 GATAGTCAGTGTAAGACCATGTCTGGGACATGGCTTCGACTTGAGATAT
1 -A-AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGACTTGAGACGT
* * *
28532917 GAGCCAGTGTAAGACTGTGTCTGGGATATGGCATCG
1 AAGCCAGTGTAAGAC-ATGTCTGGGACATGGCATCG
28532953 GGACCTTACC
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
44 2 0.02
45 4 0.04
46 47 0.44
47 46 0.43
48 8 0.07
49 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (46 bp):
AAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACTTGAGACGT
Found at i:28532899 original size:47 final size:44
Alignment explanation
Indices: 28532779--28532952 Score: 170
Period size: 47 Copynumber: 3.8 Consensus size: 44
28532769 CACTTGTGAA
* *
28532779 AGCCAATGTAAGACATGTCTGGGACATGCATCGACCTTGGGACGTA-
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGA-CTT--GAGGTAT
* *
28532825 AGCCAGTGTAAGACATGTCTGGGACATGCGTCGGCTTCGAGGTGAT
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACTT-GAGGT-AT
* * *
28532871 AGTCAGTGTAAGACCATGTCTGGGACATGGCTTCGACTTGAGATAT
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTTGAGGTAT
* *
28532917 GAGCCAGTGTAAGACTGTGTCTGGGATATGGCATCG
1 -AGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCG
28532953 GGACCTTACC
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
44 4 0.04
45 4 0.04
46 46 0.42
47 47 0.43
48 8 0.07
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (44 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGACTTGAGGTAT
Found at i:28536651 original size:41 final size:40
Alignment explanation
Indices: 28536553--28536743 Score: 170
Period size: 43 Copynumber: 4.6 Consensus size: 40
28536543 TTTTATCAAA
* *
28536553 TCACCGGCATTTAGCCTGCTAGGTTTTAAACCTGAATTCA-
1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCTGAA-TCAT
* *** * *
28536593 TCACCAGCACGAAGCCTGCTAGACTTTAAGTCTGAACTCAT
1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCTGAA-TCAT
* *
28536634 TCACCGGCATTTCGCCTGCTAGGCTTGAAGCCTGATATCATT
1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCTGA-ATCA-T
** *
28536676 TCACCGGCATTATAGCCTGCTAGGCCCTAAG-CTCGATATTAT
1 TCACCGGCATT-TAGCCTGCTAGGCTTTAAGCCT-GA-ATCAT
28536718 CTCACCGGCATTATAGCCTGCTAGGC
1 -TCACCGGCATT-TAGCCTGCTAGGC
28536744 CCGAAGCCTG
Statistics
Matches: 123, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 31 0.25
41 30 0.24
42 16 0.13
43 46 0.37
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (40 bp):
TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCTGAATCAT
Found at i:28536758 original size:43 final size:43
Alignment explanation
Indices: 28536634--28536758 Score: 173
Period size: 43 Copynumber: 2.9 Consensus size: 43
28536624 CTGAACTCAT
* ** * *
28536634 TCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCTGATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCTGATATTATC
*
28536676 TCACCGGCATTATAGCCTGCTAGGCCCTAAG-CTCGATATTATC
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCT-GATATTATC
28536719 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCTGATATT
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCTGATATT
28536759 GTTATTCACC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
42 13 0.18
43 58 0.79
44 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCTGATATTATC
Found at i:28546801 original size:21 final size:22
Alignment explanation
Indices: 28546762--28546802 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28546752 GTTGAAATGT
28546762 CACATGAACGTGTTGCCCCTCC
1 CACATGAACGTGTTGCCCCTCC
28546784 CACATG-A-GTGTGTGCCCCT
1 CACATGAACGTGT-TGCCCCT
28546803 GTGTTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.17, C:0.37, G:0.22, T:0.24
Consensus pattern (22 bp):
CACATGAACGTGTTGCCCCTCC
Found at i:28570342 original size:47 final size:47
Alignment explanation
Indices: 28570288--28570831 Score: 971
Period size: 47 Copynumber: 11.6 Consensus size: 47
28570278 TATTTGAATA
*
28570288 AATGTGAAAATGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28570335 AATGTGAAAGTGTATATATGTGATAAGGCCGAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570382 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570429 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570476 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570523 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28570570 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570617 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28570664 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28570711 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
28570758 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28570805 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
28570832 TCCCGAAGGG
Statistics
Matches: 482, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 482 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:28574378 original size:5 final size:6
Alignment explanation
Indices: 28574352--28574376 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28574342 AATGTGAATT
28574352 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
28574377 TAGTATCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:28580481 original size:30 final size:30
Alignment explanation
Indices: 28580447--28580507 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28580437 TCCTTAACTC
28580447 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28580477 AAACTTTTGCATATTTACAGTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28580507 A
1 A
28580508 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:28589114 original size:44 final size:45
Alignment explanation
Indices: 28589046--28589139 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
28589036 AGTACATGTA
* *
28589046 TCGCATCCATAATGAACTTAGACCAACTCAACGAGCTCAGATG-C
1 TCGCATCCATAATAAACTCAGACCAACTCAACGAGCTCAGATGCC
* * *
28589090 TCGCATCCATAATAAACTCGGACCAACTCAATGAGCTCGGATGCC
1 TCGCATCCATAATAAACTCAGACCAACTCAACGAGCTCAGATGCC
28589135 TCGCA
1 TCGCA
28589140 CATGTCACGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 38 0.86
45 6 0.14
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (45 bp):
TCGCATCCATAATAAACTCAGACCAACTCAACGAGCTCAGATGCC
Done.