Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 13 of 203
Found at i:4382323 original size:36 final size:36
Alignment explanation
Indices: 4382272--4382391 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
4382262 GTTAGCCATG
*
4382272 TATACCAGCAGCCATGTATAACAACATAAGCAACAA
1 TATACCAGCAACCATGTATAACAACATAAGCAACAA
* *
4382308 TATACCAGTAACCATGTATAACAACATAAGCAGCAA
1 TATACCAGCAACCATGTATAACAACATAAGCAACAA
** * * * *
4382344 TATATTAGCAACAATATGTAACTACATAAGCAACAA
1 TATACCAGCAACCATGTATAACAACATAAGCAACAA
*
4382380 TATACCAACAAC
1 TATACCAGCAAC
4382392 AATATTACAA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (36 bp):
TATACCAGCAACCATGTATAACAACATAAGCAACAA
Found at i:4382392 original size:36 final size:36
Alignment explanation
Indices: 4382272--4382410 Score: 145
Period size: 36 Copynumber: 3.9 Consensus size: 36
4382262 GTTAGCCATG
* * *
4382272 TATACCAGCAGCCATGTATAACAACATAAGCAACAA
1 TATACCAGCAACAATATATAACAACATAAGCAACAA
* * * *
4382308 TATACCAGTAACCATGTATAACAACATAAGCAGCAA
1 TATACCAGCAACAATATATAACAACATAAGCAACAA
** * *
4382344 TATATTAGCAACAATATGTAACTACATAAGCAACAA
1 TATACCAGCAACAATATATAACAACATAAGCAACAA
* *
4382380 TATACCAACAACAATAT-TACAAAACATAAGC
1 TATACCAGCAACAATATATA-ACAACATAAGC
4382411 CGGTTTTCAG
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 2 0.02
36 84 0.98
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.20
Consensus pattern (36 bp):
TATACCAGCAACAATATATAACAACATAAGCAACAA
Found at i:4382766 original size:3 final size:3
Alignment explanation
Indices: 4382758--4382791 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4382748 CCTCTTCTCA
* *
4382758 TTC TTC TTC TTC TTT TTC TTC TTT TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4382792 CTAACCCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:4383063 original size:27 final size:27
Alignment explanation
Indices: 4383033--4383087 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
4383023 TTGACGGAAT
* *
4383033 AAAAGTTTAAGAACCAACTAGATCCAA
1 AAAAATTTAAGAACCAACTAGATACAA
* * *
4383060 AAAAATTTAGGGACTAACTAGATACAA
1 AAAAATTTAAGAACCAACTAGATACAA
4383087 A
1 A
4383088 TAGAAAAGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.20
Consensus pattern (27 bp):
AAAAATTTAAGAACCAACTAGATACAA
Found at i:4389123 original size:37 final size:37
Alignment explanation
Indices: 4389080--4389154 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
4389070 TCTTTCCTAG
*
4389080 ATTCAAGTTGTGTCAACATTGGTGCCTCTATCAACAT
1 ATTCAAGCTGTGTCAACATTGGTGCCTCTATCAACAT
*
4389117 ATTCAAGCTGTGTCAACATTGGTGCCTCTGTCAACAT
1 ATTCAAGCTGTGTCAACATTGGTGCCTCTATCAACAT
4389154 A
1 A
4389155 ATTTTCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (37 bp):
ATTCAAGCTGTGTCAACATTGGTGCCTCTATCAACAT
Found at i:4389150 original size:18 final size:18
Alignment explanation
Indices: 4389090--4389153 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
4389080 ATTCAAGTTG
4389090 TGTCAACATTGGTGCCTC
1 TGTCAACATTGGTGCCTC
* *** *
4389108 TATCAACATATTCAAG-CTG
1 TGTCAAC--ATTGGTGCCTC
4389127 TGTCAACATTGGTGCCTC
1 TGTCAACATTGGTGCCTC
4389145 TGTCAACAT
1 TGTCAACAT
4389154 AATTTTCAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
17 4 0.12
18 17 0.52
19 8 0.24
20 4 0.12
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (18 bp):
TGTCAACATTGGTGCCTC
Found at i:4392903 original size:43 final size:44
Alignment explanation
Indices: 4392797--4392909 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
4392787 TGTGTTGTCG
* *
4392797 TGTAAGACCACGTCTGGTACGTTGGCATCGACTTGTGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTACA
* * *
4392841 TGTAAAACC-CTGTTTGGGACAG-TGGGATCGA-TATGTGA-TTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTTACA
*
4392884 TGTAAGACCACGTCTGGGACGATGGC
1 TGTAAGACCACGTCTGGGACGTTGGC
4392910 GTTGTACGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
42 1 0.02
43 25 0.45
44 29 0.52
45 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTACA
Found at i:4393739 original size:47 final size:46
Alignment explanation
Indices: 4393685--4393975 Score: 339
Period size: 47 Copynumber: 6.2 Consensus size: 46
4393675 ATTCGATTCA
* * *
4393685 TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGT
1 TGTCCAATTTGGTGTATATATGCTGTCCAA-TTTGGTGTATATATGC
* * *
4393732 TGTCCAATTTGGTATATATATGCTGCCCAATTTGGTGTCTATATGC
1 TGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATATATGC
* * * *
4393778 TGTCCAATTTTGGTGTAAAAATGTTGTCCAATTTGGTATATATATGC
1 TGTCCAA-TTTGGTGTATATATGCTGTCCAATTTGGTGTATATATGC
* * *
4393825 TGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATATATGC
1 TGTCCAA-TTTGGTGTATATATGCTGTCCAATTTGGTGTATATATGC
* *
4393872 TGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTATAAATGC
1 TGTCCAATTTGGTGTATATATGCTGTCCAA-TTTGGTGTATATATGC
* * * *** *
4393919 TATTCAATTTGGTGTTTATATGCTGTCCAAACGGGATGTATAAATGC
1 TGTCCAATTTGGTGTATATATGCTGTCCAATTTGG-TGTATATATGC
4393966 TGTCCAATTT
1 TGTCCAATTT
4393976 TATGTATAAG
Statistics
Matches: 213, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
46 42 0.20
47 171 0.80
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (46 bp):
TGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATATATGC
Found at i:4393820 original size:117 final size:117
Alignment explanation
Indices: 4393685--4393975 Score: 458
Period size: 117 Copynumber: 2.5 Consensus size: 117
4393675 ATTCGATTCA
*
4393685 TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGTTGTCCAATTTGGTATATA
1 TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATA
* *
4393750 TATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGT
66 TATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGC
*
4393802 TGTCCAATTTGGTATATATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATA
1 TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATA
*
4393867 TATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTATAAATGC
66 TATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGC
* * * *** *
4393919 TATTCAATTTGGTGTTTATATGCTGTCCAA-ACGGGATGTATAAATGCTGTCCAATTT
1 TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGG-TGTAAAAATGCTGTCCAATTT
4393976 TATGTATAAG
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
116 2 0.01
117 158 0.99
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (117 bp):
TGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATA
TATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGC
Found at i:4393939 original size:70 final size:71
Alignment explanation
Indices: 4393685--4393984 Score: 349
Period size: 70 Copynumber: 4.3 Consensus size: 71
4393675 ATTCGATTCA
* *
4393685 TGTCCAA-TTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAATGTTGTCCAATTTGGTATAT
1 TGTCCAATTTTGGTGTATAAATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATAT
4393749 ATATGC
66 ATATGC
* * * *
4393755 TGCCCAA-TTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGTTGTCCAATTTGGTATAT
1 TGTCCAATTTTGGTGTATAAATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATAT
4393819 ATATGC
66 ATATGC
* * * * * *
4393825 TGTCCAATTTTGGTGTAAAAATGCTGTCCAA-TTTGGTATATATATGCTGCCCAATTTGGTGTAT
1 TGTCCAATTTTGGTGTATAAATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATAT
4393889 ATATGC
66 ATATGC
* * ** * *** *
4393895 TGTCCAATTTTGGTGTATAAATGCTATTCAA-TTTGGTGTTTATATGCTGTCCAAACGGGATGTA
1 TGTCCAATTTTGGTGTATAAATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGG-TATA
*
4393959 TAAATGC
65 TATATGC
*
4393966 TGTCCAATTTT-ATGTATAA
1 TGTCCAATTTTGGTGTATAA
4393985 GAGCTATCTA
Statistics
Matches: 205, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 164 0.80
71 41 0.20
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (71 bp):
TGTCCAATTTTGGTGTATAAATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATAT
ATATGC
Found at i:4399659 original size:24 final size:24
Alignment explanation
Indices: 4399632--4399678 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4399622 CAATAATAAA
4399632 CTACATGAATTATTAATATATCAT
1 CTACATGAATTATTAATATATCAT
4399656 CTACATGAATTATTAATATATCA
1 CTACATGAATTATTAATATATCA
4399679 AAGATGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (24 bp):
CTACATGAATTATTAATATATCAT
Found at i:4403049 original size:33 final size:33
Alignment explanation
Indices: 4403012--4403079 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
4403002 TCCATAGAGC
*
4403012 AAATGACTGTTTGCTCATGCATTTGACAATACT
1 AAATGACTGTTTGCTCATGCATATGACAATACT
4403045 AAATGACTGTTTGCTCATGCATATGACAATACT
1 AAATGACTGTTTGCTCATGCATATGACAATACT
4403078 AA
1 AA
4403080 GTAATGATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
AAATGACTGTTTGCTCATGCATATGACAATACT
Found at i:4407751 original size:19 final size:19
Alignment explanation
Indices: 4407716--4407758 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4407706 GATAACTAAC
4407716 TATAAAAATTTAATAAATA
1 TATAAAAATTTAATAAATA
*
4407735 TATATAAAA-TTATTAAATA
1 TATA-AAAATTTAATAAATA
4407754 T-TAAA
1 TATAAA
4407759 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 14 0.64
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAAAAATTTAATAAATA
Found at i:4408143 original size:11 final size:11
Alignment explanation
Indices: 4408085--4408151 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
4408075 TCAATTTTGC
4408085 TATTTAT-ATA
1 TATTTATAATA
*
4408095 TTTTTATAATA
1 TATTTATAATA
*
4408106 GTATTTAT-CTA
1 -TATTTATAATA
4408117 TAATTTATAATCTA
1 T-ATTTATAA--TA
4408131 TATTTATAATA
1 TATTTATAATA
4408142 TATTTATAAT
1 TATTTATAAT
4408152 TCTATAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.15
11 23 0.49
12 6 0.13
13 8 0.17
14 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (11 bp):
TATTTATAATA
Found at i:4408425 original size:21 final size:19
Alignment explanation
Indices: 4408401--4408446 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4408391 AAAAAATTCA
4408401 AATTTTTAATTAAATAAATAT
1 AATTTTTAA--AAATAAATAT
*
4408422 AATTTTTAAATATAAATAT
1 AATTTTTAAAAATAAATAT
*
4408441 GATTTT
1 AATTTT
4408447 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
21 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AATTTTTAAAAATAAATAT
Found at i:4408839 original size:6 final size:6
Alignment explanation
Indices: 4408828--4408859 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4408818 ATAATATAAA
4408828 ATAATT ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT ATAATT AT
4408860 TTGTTAGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:4409663 original size:80 final size:81
Alignment explanation
Indices: 4409522--4409697 Score: 221
Period size: 80 Copynumber: 2.2 Consensus size: 81
4409512 CAAAACAATT
* ** * * * *
4409522 TTATCGATACTTTATAAGTTTTGTGAGAAACATAATGTTATTTTTAGTATCGTTTTTAAGAAGGG
1 TTATCGATAC-TTATTAGGGTT-TGAAAAACAAAATGTCATTTTTAGTATCGCTTTTAAGAAGGG
4409587 GTATCAATAATTCAGAAAA
64 GTATCAATAATTCA-AAAA
*
4409606 -TATCGATACTTATTAGGGTTTGAAAAACAAAATGTCA-TTTTGGTATCGCTTTTAAGAAGGGGT
1 TTATCGATACTTATTAGGGTTTGAAAAACAAAATGTCATTTTTAGTATCGCTTTTAAGAAGGGGT
* *
4409669 ATTAATATTTCAAAAA
66 ATCAATAATTCAAAAA
4409685 TTATCGATACTTA
1 TTATCGATACTTA
4409698 ATCAAAAGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 4 0.05
80 46 0.57
81 14 0.17
82 8 0.10
83 9 0.11
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (81 bp):
TTATCGATACTTATTAGGGTTTGAAAAACAAAATGTCATTTTTAGTATCGCTTTTAAGAAGGGGT
ATCAATAATTCAAAAA
Found at i:4409704 original size:21 final size:21
Alignment explanation
Indices: 4409678--4409718 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4409668 TATTAATATT
*
4409678 TCAAAAATTATCGATACTTAA
1 TCAAAAAGTATCGATACTTAA
* *
4409699 TCAAAAGGTATTGATACTTA
1 TCAAAAAGTATCGATACTTA
4409719 TTAGGGTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
TCAAAAAGTATCGATACTTAA
Found at i:4409784 original size:100 final size:100
Alignment explanation
Indices: 4409610--4409796 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 100
4409600 AGAAAATATC
* * *
4409610 GATACTTATTAGGGTTTGAAAAACAAAATGTCATTTTGGTATCGCTTTTAAGAAGGGGTATTAAT
1 GATACTTATTAGGGTTTGAAAAACAAAATGCCACTTTGGTATCGC-TTTAAGAAGGGGTATCAAT
* * *
4409675 ATTTCAAAAATTATCGATACTTAATCAAAAGGTATT
65 AATTCAAAAAATATCAATACTTAATCAAAAGGTATT
* * * * *
4409711 GATACTTATTAGGGTTTGTGAAAATAGAATGCCACTTTGGTATTG-TTTAAG-AGAGGGTATCGA
1 GATACTTATTAGGGTTTG-AAAAACAAAATGCCACTTTGGTATCGCTTTAAGAAG-GGGTATCAA
4409774 TAATTCAAAAAATATCAATACTT
64 TAATTCAAAAAATATCAATACTT
4409797 GGCCAAAAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
99 2 0.03
100 33 0.45
101 18 0.25
102 20 0.27
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (100 bp):
GATACTTATTAGGGTTTGAAAAACAAAATGCCACTTTGGTATCGCTTTAAGAAGGGGTATCAATA
ATTCAAAAAATATCAATACTTAATCAAAAGGTATT
Found at i:4409803 original size:21 final size:22
Alignment explanation
Indices: 4409779--4409819 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4409769 ATCGATAATT
4409779 CAAAAA-ATATCAATACTTGGC
1 CAAAAAGATATCAATACTTGGC
* *
4409800 CAAAAAGGTATCGATACTTG
1 CAAAAAGATATCAATACTTG
4409820 TTGGTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (22 bp):
CAAAAAGATATCAATACTTGGC
Found at i:4409804 original size:100 final size:101
Alignment explanation
Indices: 4409606--4409818 Score: 243
Period size: 101 Copynumber: 2.1 Consensus size: 101
4409596 ATTCAGAAAA
* *
4409606 TATCGATACTTATTAGGGTTTGAAAAACAAAATGTCATTTTGGTATCGCTTTTAAGAAGGGGTAT
1 TATCGATACTTATTAGGGTTTGAAAAACAAAATGCCACTTTGGTATCGC-TTTAAGAAGGGGTAT
* * * * *
4409671 TAATATTTCAAAAATTATCGATACTTAATC-AAAAGG
65 CAATAATTCAAAAAATATCAATACTTAACCAAAAAGG
* * * * *
4409707 TATTGATACTTATTAGGGTTTGTGAAAATAGAATGCCACTTTGGTATTG-TTTAAG-AGAGGGTA
1 TATCGATACTTATTAGGGTTTG-AAAAACAAAATGCCACTTTGGTATCGCTTTAAGAAG-GGGTA
* **
4409770 TCGATAATTCAAAAAATATCAATACTTGGCCAAAAAGG
64 TCAATAATTCAAAAAATATCAATACTTAACCAAAAAGG
4409808 TATCGATACTT
1 TATCGATACTT
4409819 GTTGGTTTAG
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
99 2 0.02
100 34 0.37
101 37 0.40
102 20 0.22
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (101 bp):
TATCGATACTTATTAGGGTTTGAAAAACAAAATGCCACTTTGGTATCGCTTTAAGAAGGGGTATC
AATAATTCAAAAAATATCAATACTTAACCAAAAAGG
Found at i:4412247 original size:8 final size:8
Alignment explanation
Indices: 4412236--4412267 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
4412226 TGAATAACAT
4412236 ATTTATAA
1 ATTTATAA
4412244 ATTTATAA
1 ATTTATAA
4412252 ATTTATAA
1 ATTTATAA
4412260 ATTTATAA
1 ATTTATAA
4412268 GTTCAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTATAA
Found at i:4412748 original size:18 final size:18
Alignment explanation
Indices: 4412714--4412751 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4412704 TTAAAATACA
*
4412714 ATTATTTTTAATAATATT
1 ATTATTTTTAAAAATATT
4412732 ATTA-TTTTAAAAGATATT
1 ATTATTTTTAAAA-ATATT
4412750 AT
1 AT
4412752 CTTTTTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTATTTTTAAAAATATT
Found at i:4412751 original size:15 final size:16
Alignment explanation
Indices: 4412699--4412743 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
4412689 TTATTTATCT
*
4412699 TTATTTTAAAATACAA
1 TTATTTTAAAATACTA
*
4412715 TTATTTTTAATAATATTA
1 TTA-TTTTAA-AATACTA
4412733 TTATTTTAAAA
1 TTATTTTAAAA
4412744 GATATTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 12 0.48
18 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTTTAAAATACTA
Found at i:4417755 original size:29 final size:29
Alignment explanation
Indices: 4417697--4417755 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
4417687 TCCACCTTGA
* * * *
4417697 CACGAATCCTCAATGAATAAGTTTTTCAC
1 CACGAATCCTCAACGAACAAGTTCTCCAC
4417726 CACGAA-CTCTCAACGAACAAGTTCTCCAC
1 CACGAATC-CTCAACGAACAAGTTCTCCAC
4417755 C
1 C
4417756 TCTTCCATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (29 bp):
CACGAATCCTCAACGAACAAGTTCTCCAC
Found at i:4423568 original size:23 final size:22
Alignment explanation
Indices: 4423485--4423575 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
4423475 CATAAAATCT
4423485 ATAAAATAATA-TAT-TACAAAA
1 ATAAAATAATACTATATA-AAAA
* *
4423506 ATAAAATAATAATATATGGAAAAC
1 ATAAAATAATACTATAT--AAAAA
***
4423530 GCCAAATAATACTATATAATAAA
1 ATAAAATAATACTATATAA-AAA
4423553 ATAAAATAA-ACGTATATAAAAA
1 ATAAAATAATAC-TATATAAAAA
4423575 A
1 A
4423576 GGTTAGGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.20
22 11 0.20
23 16 0.29
24 16 0.29
25 1 0.02
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (22 bp):
ATAAAATAATACTATATAAAAA
Found at i:4423627 original size:3 final size:3
Alignment explanation
Indices: 4423621--4423659 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
4423611 ATACTACTAC
*
4423621 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA -AGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
4423660 ACAGAACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4424634 original size:18 final size:19
Alignment explanation
Indices: 4424608--4424653 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4424598 GTGGTCCCTG
*
4424608 GCGGTGGCGTGGC-TCGGC
1 GCGGAGGCGTGGCTTCGGC
* *
4424626 TCGGAGGCGTGGCTTTGGC
1 GCGGAGGCGTGGCTTCGGC
4424645 GCGGAGGCG
1 GCGGAGGCG
4424654 CTACATGTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.04, C:0.24, G:0.54, T:0.17
Consensus pattern (19 bp):
GCGGAGGCGTGGCTTCGGC
Found at i:4424928 original size:13 final size:13
Alignment explanation
Indices: 4424910--4424939 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4424900 ATTATTATTA
*
4424910 TTATTTTTTTGGT
1 TTATTTTGTTGGT
4424923 TTATTTTGTTGGT
1 TTATTTTGTTGGT
4424936 TTAT
1 TTAT
4424940 GGGCCGGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.17, T:0.73
Consensus pattern (13 bp):
TTATTTTGTTGGT
Found at i:4428287 original size:28 final size:28
Alignment explanation
Indices: 4428255--4428401 Score: 138
Period size: 28 Copynumber: 5.2 Consensus size: 28
4428245 AGTTCCTGAG
4428255 GACTCTTGCTTGAAAGATAGTCCATGTA
1 GACTCTTGCTTGAAAGATAGTCCATGTA
** **
4428283 GACTCTTGCTT-AAAGGATAGTTTATGGG
1 GACTCTTGCTTGAAA-GATAGTCCATGTA
* * * *
4428311 GACTCTGGCTGGAATGATAGTCCATGTG
1 GACTCTTGCTTGAAAGATAGTCCATGTA
* * *
4428339 GACTCTTACATG-AAGAATAGTCCATGCA
1 GACTCTTGCTTGAAAG-ATAGTCCATGTA
*
4428367 GACTCTTGCTTGAATGATAGTCCATGT-
1 GACTCTTGCTTGAAAGATAGTCCATGTA
4428394 GAACTCTT
1 G-ACTCTT
4428402 ACATGGAATA
Statistics
Matches: 93, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
27 6 0.06
28 83 0.89
29 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (28 bp):
GACTCTTGCTTGAAAGATAGTCCATGTA
Found at i:4428406 original size:56 final size:56
Alignment explanation
Indices: 4428255--4428425 Score: 186
Period size: 56 Copynumber: 3.1 Consensus size: 56
4428245 AGTTCCTGAG
* * * * * ** **
4428255 GACTCTTGCTTGAAAGATAGTCCATGT-AGACTCTTGCTTAAAGGATAGTTTATGGG
1 GACTCTTGCTTGAATGATAGTCCATGTGA-ACTCTTACATGAAGAATAGTCCATGCA
* * *
4428311 GACTCTGGCTGGAATGATAGTCCATGTGGACTCTTACATGAAGAATAGTCCATGCA
1 GACTCTTGCTTGAATGATAGTCCATGTGAACTCTTACATGAAGAATAGTCCATGCA
* *
4428367 GACTCTTGCTTGAATGATAGTCCATGTGAACTCTTACATG--GAATAGTCCTTGTA
1 GACTCTTGCTTGAATGATAGTCCATGTGAACTCTTACATGAAGAATAGTCCATGCA
4428421 GACTC
1 GACTC
4428426 ATACCTAAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
54 17 0.18
56 80 0.82
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (56 bp):
GACTCTTGCTTGAATGATAGTCCATGTGAACTCTTACATGAAGAATAGTCCATGCA
Found at i:4430503 original size:5 final size:5
Alignment explanation
Indices: 4430493--4430521 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4430483 TTGAATACTT
4430493 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
4430522 TTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:4433384 original size:7 final size:7
Alignment explanation
Indices: 4433365--4433399 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
4433355 ACGTGGGGAA
4433365 TATTTAT
1 TATTTAT
4433372 TA-TTAT
1 TATTTAT
4433378 TATTTAT
1 TATTTAT
4433385 TATTTAT
1 TATTTAT
4433392 TATTTAT
1 TATTTAT
4433399 T
1 T
4433400 CTTTTGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTTAT
Found at i:4440796 original size:40 final size:40
Alignment explanation
Indices: 4440752--4440838 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
4440742 GTAAAAATTA
*
4440752 GACTTAAA-TGTGCATGTTTGAAATGATGTCCGATAAGCAT
1 GACTTAAATTGT-CATGTATGAAATGATGTCCGATAAGCAT
* * ***
4440792 GACTTAAGTTGTTATGTATGGTCTGATGTCCGATAAGCAT
1 GACTTAAATTGTCATGTATGAAATGATGTCCGATAAGCAT
4440832 GACTTAA
1 GACTTAA
4440839 GTTTGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (40 bp):
GACTTAAATTGTCATGTATGAAATGATGTCCGATAAGCAT
Found at i:4444157 original size:20 final size:21
Alignment explanation
Indices: 4444134--4444172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4444124 ATTTCCTCCC
4444134 CTTTCTTTTC-TTTTCTTTTT
1 CTTTCTTTTCTTTTTCTTTTT
*
4444154 CTTTGTTTTCTTTTTCTTT
1 CTTTCTTTTCTTTTTCTTT
4444173 ATTGACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (21 bp):
CTTTCTTTTCTTTTTCTTTTT
Found at i:4444162 original size:15 final size:15
Alignment explanation
Indices: 4444144--4444172 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4444134 CTTTCTTTTC
4444144 TTTTCTTTTTCTTTG
1 TTTTCTTTTTCTTTG
4444159 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
4444173 ATTGACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTTTG
Found at i:4445637 original size:28 final size:28
Alignment explanation
Indices: 4445604--4445686 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
4445594 AGTATCAGTG
**
4445604 TGTGGGCCACAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
4445632 TGTGGGCCTTAGCCCAATACAGTAACAT
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
4445660 TGTGGGCCTTAGCCCAATGCAGAAACA
1 TGTGGGCCTTAGCCCAATACAGTAACA
4445687 GTGTCAGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:4445978 original size:32 final size:32
Alignment explanation
Indices: 4445932--4446154 Score: 252
Period size: 32 Copynumber: 7.0 Consensus size: 32
4445922 ATAAGTAAAC
* *
4445932 TAATATGATTGGCACAAAGCCATCAGTAGCAA
1 TAATATGATCGGCACAAAGCCATCAGTAGCAG
* * * * *
4445964 TGATATGACCGGCACACAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAG
4445996 TAATATGATCGGCACAAAGCCATCAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAG
* * * * *
4446028 TGATATGATCGGTACACAA-CCATCAATAACGG
1 TAATATGATCGGCACA-AAGCCATCAGTAGCAG
*
4446060 TAATATGATCGGCACAAAGCCATTAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAG
* * *
4446092 TGATATGATCGGCACACAA-CCATCAGTAACGG
1 TAATATGATCGGCACA-AAGCCATCAGTAGCAG
* *
4446124 TAATATGACCGGCACAAAGCCATTAGTAGCA
1 TAATATGATCGGCACAAAGCCATCAGTAGCA
4446155 TCGTAGCAAA
Statistics
Matches: 155, Mismatches: 32, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
31 4 0.03
32 147 0.95
33 4 0.03
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAGCAG
Found at i:4446010 original size:64 final size:64
Alignment explanation
Indices: 4445932--4446154 Score: 365
Period size: 64 Copynumber: 3.5 Consensus size: 64
4445922 ATAAGTAAAC
* * * *
4445932 TAATATGATTGGCACAAAGCCATCAGTAGCAATGATATGACCGGCACACAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACGG
* *
4445996 TAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGTACACAACCATCAATAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACGG
*
4446060 TAATATGATCGGCACAAAGCCATTAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACGG
* *
4446124 TAATATGACCGGCACAAAGCCATTAGTAGCA
1 TAATATGATCGGCACAAAGCCATCAGTAGCA
4446155 TCGTAGCAAA
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 149 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (64 bp):
TAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACGG
Found at i:4446193 original size:27 final size:27
Alignment explanation
Indices: 4446169--4446232 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
4446159 AGCAAAGCTG
4446169 CTAGTAACAGT-ATATGTGGCCAAGCCA
1 CTAGTAACAGTGAT-TGTGGCCAAGCCA
4446196 CTAGTAACAGTGATTGTGG-CAGAGCCA
1 CTAGTAACAGTGATTGTGGCCA-AGCCA
*
4446223 CCAGT-ACAGT
1 CTAGTAACAGT
4446233 ACTTCCTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CTAGTAACAGTGATTGTGGCCAAGCCA
Found at i:4446342 original size:24 final size:23
Alignment explanation
Indices: 4446296--4446374 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 23
4446286 CCATGCTCAG
*
4446296 AATCAGTTATACAATTCATAGACA
1 AATCAGTTATACAA-TCACAGACA
*
4446320 AATTAGTTATACCAATCACAGACA
1 AATCAGTTATA-CAATCACAGACA
*
4446344 AATCAGTCATTTA-AATCACAGACA
1 AATCAGT--TATACAATCACAGACA
4446368 AATCAGT
1 AATCAGT
4446375 CATTTACATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 42 0.88
25 3 0.06
26 3 0.06
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.27
Consensus pattern (23 bp):
AATCAGTTATACAATCACAGACA
Found at i:4446375 original size:24 final size:24
Alignment explanation
Indices: 4446333--4446429 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
4446323 TAGTTATACC
*
4446333 AATCACAGACAAATCAGTCATTTA
1 AATCACAGACAAATCAATCATTTA
*
4446357 AATCACAGACAAATCAGTCATTTA
1 AATCACAGACAAATCAATCATTTA
* * * *
4446381 CATCTCAGACTAATCAATCACTTA
1 AATCACAGACAAATCAATCATTTA
* *
4446405 CATCACAAACAAATCAATCATTTA
1 AATCACAGACAAATCAATCATTTA
4446429 A
1 A
4446430 CCTCGAGGGG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (24 bp):
AATCACAGACAAATCAATCATTTA
Found at i:4446548 original size:27 final size:26
Alignment explanation
Indices: 4446501--4446615 Score: 144
Period size: 27 Copynumber: 4.3 Consensus size: 26
4446491 AGGTATTATA
4446501 GTCATTTTA-CCTACAGGGGCATTAC
1 GTCATTTTACCCTACAGGGGCATTAC
*
4446526 AGTCATTTTACCCTACAGGGGCATTATG
1 -GTCATTTTACCCTACAGGGGCATTA-C
* *
4446554 GTTATTTTACCCTACAGGGGTATTAC
1 GTCATTTTACCCTACAGGGGCATTAC
*
4446580 GATCATTTTAACCTACA-GGGCATTAC
1 G-TCATTTTACCCTACAGGGGCATTAC
4446606 GATCATTTTA
1 G-TCATTTTA
4446616 TAAATTTTGG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
26 28 0.35
27 51 0.65
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (26 bp):
GTCATTTTACCCTACAGGGGCATTAC
Found at i:4446935 original size:19 final size:17
Alignment explanation
Indices: 4446895--4446937 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
4446885 TTTATCCGTG
4446895 TGGCCCACAAGCCCACT
1 TGGCCCACAAGCCCACT
* *
4446912 GGGCCCACACAGCCCATTT
1 TGGCCCACA-AGCCCA-CT
4446931 TGGCCCA
1 TGGCCCA
4446938 TTGAGGCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.14
Consensus pattern (17 bp):
TGGCCCACAAGCCCACT
Found at i:4448804 original size:23 final size:23
Alignment explanation
Indices: 4448774--4448895 Score: 192
Period size: 23 Copynumber: 5.3 Consensus size: 23
4448764 CATAAATCCA
4448774 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
4448797 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
4448820 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
4448843 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
4448866 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
*
4448889 CATTGAT
1 CACTGAT
4448896 CAATAACACT
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
22 1 0.01
23 89 0.99
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:4448841 original size:46 final size:46
Alignment explanation
Indices: 4448774--4448895 Score: 217
Period size: 46 Copynumber: 2.7 Consensus size: 46
4448764 CATAAATCCA
*
4448774 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
4448820 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
4448866 CACTGAATTGTAGCCGAAGCTACCATTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
4448896 CAATAACACT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:4459408 original size:20 final size:20
Alignment explanation
Indices: 4459383--4459431 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4459373 AGGGGCAATT
*
4459383 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATC
*
4459403 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAAAATC
*
4459423 AAATAAAAT
1 AAATCAAAT
4459432 CAGGATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:4460992 original size:30 final size:30
Alignment explanation
Indices: 4460958--4461017 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4460948 ACAAAATTTT
4460958 AACCCTCAAATTCATGCAACCAAAACCCAA
1 AACCCTCAAATTCATGCAACCAAAACCCAA
4460988 AACCCTCAAATTCATGCAACCAAAACCCAA
1 AACCCTCAAATTCATGCAACCAAAACCCAA
4461018 CTTGGTCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.37, G:0.03, T:0.13
Consensus pattern (30 bp):
AACCCTCAAATTCATGCAACCAAAACCCAA
Found at i:4464209 original size:15 final size:15
Alignment explanation
Indices: 4464189--4464227 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
4464179 ATCGTTAAAA
4464189 TTATTATCATTGTAT
1 TTATTATCATTGTAT
4464204 TTATTA-CTATTGTAT
1 TTATTATC-ATTGTAT
4464219 TTATTATCA
1 TTATTATCA
4464228 CGATATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (15 bp):
TTATTATCATTGTAT
Found at i:4476141 original size:44 final size:44
Alignment explanation
Indices: 4476080--4476777 Score: 259
Period size: 44 Copynumber: 15.7 Consensus size: 44
4476070 GATCGCATCT
4476080 AGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG-AAGCA
* * *
4476124 AGTATTATCCTCCTGAAGTTTCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACTGAAGA-AGCA
* ** * *
4476169 AATCTTAT-CTCCCTGAAGTTATAGTGGAGCAG-TTGCAGAGAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGA-AGCA
*
4476213 GATCGCATCTAGTCTTCTCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 -A--G--TCT--T-ATC-CT-CCTGAAGTTGCAGTGGAGCAGACTGAAG-AAGCA
* * *
4476267 AGTCTTATCCTCTTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACTGAAGA-AGCA
* ** * **
4476312 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCTG-A
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGAAGCA
* * * ** ** * * *
4476355 TAATCCTATCTTTTTGAAGTTGCAGTGGAGTGGA-TTAA-AACCTT
1 -AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGAAGC-A
* * * * * *
4476399 GGATCTTAT-CTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCT
1 AG-TCTTATCCTC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAGCA
*
4476440 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAGCA
* * * *
4476484 AATCTTATCCTCCTGAAGTTACAGTGAAGCAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AGCA
* * * ** * **
4476529 AATCTTAT-CTCCCTGAAGTTGTAGTGGAGTAGGTTAAAGCCG-A
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGAAGCA
* * * * ** * * *
4476572 TAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGA-TTAA-AACCTT
1 -AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGAAGC-A
* * * * * * *
4476616 GGATCTTAT-CTCTCTGAAGTTGCAG-AGAGAAGA-T--CGCATCT
1 AG-TCTTATCCTC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAGCA
*
4476657 AGTCTTAT-CTCCCTAAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG-AAGCA
*
4476701 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACTGAAGA-AGCA
* *
4476746 AATCTTAT-CTCCCTGAAGTTGTAGTGGAGCAG
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAG
4476778 GTTAAAGCCG
Statistics
Matches: 490, Mismatches: 108, Indels: 111
0.69 0.15 0.16
Matches are distributed among these distances:
40 37 0.08
41 20 0.04
42 6 0.01
43 30 0.06
44 213 0.43
45 135 0.28
46 8 0.02
47 1 0.00
49 6 0.01
51 2 0.00
52 1 0.00
53 1 0.00
54 28 0.06
55 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGAAGCA
Found at i:4476314 original size:143 final size:143
Alignment explanation
Indices: 4476056--4476343 Score: 513
Period size: 143 Copynumber: 2.0 Consensus size: 143
4476046 ATCTCTCTGA
4476056 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
*
4476121 GCAAGTATTATCCTCCTGAAGTTTCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTATTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
*
4476186 GTTATAGTGGAGC
131 GTTACAGTGGAGC
*
4476199 AGTTGCAGAGAGCAGATCGCATCTAGTCTTCTCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
* * *
4476264 GCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTATTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
*
4476329 GTTGCAGTGGAGC
131 GTTACAGTGGAGC
4476342 AG
1 AG
4476344 GTTAAAGCTG
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (143 bp):
AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
GCAAGTATTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
GTTACAGTGGAGC
Found at i:4476459 original size:217 final size:217
Alignment explanation
Indices: 4476199--4476904 Score: 1268
Period size: 217 Copynumber: 3.3 Consensus size: 217
4476189 ATAGTGGAGC
*
4476199 AGTTGCAGAGAGCAGATCGCATCTAGTCTTCTCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
* *
4476264 GCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* * *
4476329 GTTGCAGTGGAGCAGGTTAAAGCTGATAATCCTATCTTTTTGAAGTTGCAGTGGAGTGGATTAAA
131 GTTGTAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGATTAAA
4476394 ACCTTGGATCTTATCTCTCTGA
196 ACCTTGGATCTTATCTCTCTGA
*
4476416 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
* * *
4476481 GCAAATCTTATCCTCCTGAAGTTACAGTGAAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
*
4476546 GTTGTAGTGGAGTAGGTTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGATTAAA
131 GTTGTAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGATTAAA
4476611 ACCTTGGATCTTATCTCTCTGA
196 ACCTTGGATCTTATCTCTCTGA
* *
4476633 AGTTGCAGAGAGAAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
4476698 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
*
4476763 GTTGTAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAA
131 GTTGTAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGATTAAA
*
4476828 ACATTGGATCTTATCTCTCTGA
196 ACCTTGGATCTTATCTCTCTGA
*
4476850 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATTTCCCTGAAGTTGCAGTGGAGCA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
4476905 AGTATTATCT
Statistics
Matches: 466, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 466 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (217 bp):
AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
GTTGTAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAGTGGATTAAA
ACCTTGGATCTTATCTCTCTGA
Found at i:4480829 original size:4 final size:4
Alignment explanation
Indices: 4480820--4480845 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4480810 AATATGGAAT
4480820 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
4480846 CCTATCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:4481929 original size:28 final size:29
Alignment explanation
Indices: 4481890--4481948 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
4481880 TTTAAACGAT
4481890 TTTTTATTATTTTACAAGAACTTAATTGA
1 TTTTTATTATTTTACAAGAACTTAATTGA
* **
4481919 TTTTT-TTATTTTACGAGGGCTTAATTGA
1 TTTTTATTATTTTACAAGAACTTAATTGA
4481947 TT
1 TT
4481949 ACTTAAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTTTATTATTTTACAAGAACTTAATTGA
Found at i:4482124 original size:23 final size:23
Alignment explanation
Indices: 4482078--4482125 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4482068 CTATAAATGT
* *
4482078 TTTTAGAAAAATATTATAATATA
1 TTTTAGAAAAATATGATAAAATA
4482101 TTTTAGAAAAATATGGA-AAAATA
1 TTTTAGAAAAATAT-GATAAAATA
4482124 TT
1 TT
4482126 GAAACATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (23 bp):
TTTTAGAAAAATATGATAAAATA
Found at i:4482868 original size:10 final size:10
Alignment explanation
Indices: 4482853--4482903 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
4482843 TTTCTATACC
4482853 TTTTTTTATA
1 TTTTTTTATA
4482863 TTTTTTTATA
1 TTTTTTTATA
4482873 TTTTTTCTATA
1 TTTTTT-TATA
* *
4482884 TTTTTCTAAA
1 TTTTTTTATA
*
4482894 ATTTTTTATA
1 TTTTTTTATA
4482904 ACATTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:4482919 original size:30 final size:31
Alignment explanation
Indices: 4482885--4482962 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 31
4482875 TTTTCTATAT
4482885 TTTTCTAAAATTTTTTATAA-CATTTAAAAA
1 TTTTCTAAAATTTTTTATAATCATTTAAAAA
* * * *
4482915 TTTTCTATAA-TTTCTATAATTATTTATAAA
1 TTTTCTAAAATTTTTTATAATCATTTAAAAA
*
4482945 -TTTCTAATAATATTTTAT
1 TTTTCTAA-AATTTTTTAT
4482963 GAATTTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 14 0.37
30 19 0.50
31 5 0.13
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTCTAAAATTTTTTATAATCATTTAAAAA
Found at i:4482958 original size:73 final size:73
Alignment explanation
Indices: 4482819--4482960 Score: 162
Period size: 73 Copynumber: 1.9 Consensus size: 73
4482809 ATATTATTAT
* * * * * * * * **
4482819 AAATTTTTTATAACATTTAAGATTTTTCTATACCTTTTTTTATATTTTTTTATATTTTTTCTATA
1 AAATTTTTTATAACATTTAAAAATTTTCTATACATTTCTATATATTTTTATAAATTTCTAATATA
4482884 TTTTTCTA
66 TTTTTCTA
4482892 AAATTTTTTATAACATTTAAAAATTTTCTATA-ATTTCTATA-ATTATTTATAAATTTCTAATAA
1 AAATTTTTTATAACATTTAAAAATTTTCTATACATTTCTATATATT-TTTATAAATTTCTAAT-A
4482955 TATTTT
64 TATTTT
4482961 ATGAATTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
71 3 0.05
72 17 0.30
73 37 0.65
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (73 bp):
AAATTTTTTATAACATTTAAAAATTTTCTATACATTTCTATATATTTTTATAAATTTCTAATATA
TTTTTCTA
Found at i:4482961 original size:21 final size:20
Alignment explanation
Indices: 4482886--4482968 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 20
4482876 TTTCTATATT
*
4482886 TTTCTAAAATTTTTTATAACA
1 TTTCTAAAATATTTTATAA-A
*
4482907 -TT-TAAAA-ATTTTCTATAA
1 TTTCTAAAATATTTTATA-AA
*
4482925 TTTCTATAAT-TATTTATAAA
1 TTTCTAAAATAT-TTTATAAA
*
4482945 TTTCTAATAATATTTTATGAA
1 TTTCTAA-AATATTTTATAAA
4482966 TTT
1 TTT
4482969 TATATTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
18 7 0.14
19 8 0.16
20 15 0.31
21 18 0.37
22 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTCTAAAATATTTTATAAA
Found at i:4483948 original size:39 final size:41
Alignment explanation
Indices: 4483859--4483957 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 41
4483849 TTAGATAACG
*
4483859 TTATTGACAATAACAATATCGAAAATTTAAATTAAATAAATA
1 TTATTAACAATAA-AATATCGAAAATTTAAATTAAATAAATA
* *
4483901 TT-TGTAACAATAAAATATC-AAAATTTTATATT-AA-GAATA
1 TTAT-TAACAATAAAATATCGAAAA-TTTAAATTAAATAAATA
4483940 TTATTAACAATAAAATAT
1 TTATTAACAATAAAATAT
4483958 TTATAGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
39 20 0.39
40 7 0.14
41 14 0.27
42 10 0.20
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (41 bp):
TTATTAACAATAAAATATCGAAAATTTAAATTAAATAAATA
Found at i:4492262 original size:6 final size:5
Alignment explanation
Indices: 4492251--4492293 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
4492241 TAAGTCTAAG
4492251 AAAAT AACAAT AAACAT AAAAAT AAAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAA-AT -AAAAT -AAAAT AAAAT AAAAT AAAA
4492294 CAAATGGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 17 0.49
6 15 0.43
7 3 0.09
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4492274 original size:12 final size:11
Alignment explanation
Indices: 4492251--4492293 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
4492241 TAAGTCTAAG
4492251 AAAATAACAATA
1 AAAATAA-AATA
*
4492263 AACATAAAAATA
1 AAAAT-AAAATA
4492275 AAAATAAAAT-
1 AAAATAAAATA
4492285 AAAATAAAA
1 AAAATAAAA
4492294 CAAATGGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
11 5 0.18
12 12 0.43
13 2 0.07
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4492274 original size:18 final size:17
Alignment explanation
Indices: 4492251--4492293 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4492241 TAAGTCTAAG
*
4492251 AAAATAACAATAAACATA
1 AAAATAAAAATAAA-ATA
4492269 AAAATAAAAATAAAAT-
1 AAAATAAAAATAAAATA
4492285 AAAATAAAA
1 AAAATAAAA
4492294 CAAATGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:4495341 original size:2 final size:2
Alignment explanation
Indices: 4495334--4495371 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4495324 GCCACAAATG
4495334 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4495372 TATATACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4500824 original size:47 final size:47
Alignment explanation
Indices: 4500761--4501111 Score: 603
Period size: 47 Copynumber: 7.4 Consensus size: 47
4500751 CCCTTCGGGA
* * * *
4500761 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4500808 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4500855 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4500902 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4500949 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4500996 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
4501043 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4501092 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
4501112 GTACATCAAT
Statistics
Matches: 293, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 250 0.85
49 43 0.15
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4508462 original size:21 final size:19
Alignment explanation
Indices: 4508420--4508463 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
4508410 ACTAATCAAT
*
4508420 ATTTTTTTTCATTTCTCTA
1 ATTTTTTTTCATTTCTCCA
*
4508439 ATTTTTTTTCAATTTGGTCCA
1 ATTTTTTTTC-ATTT-CTCCA
4508460 ATTT
1 ATTT
4508464 CCAATAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 4 0.19
21 7 0.33
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTTTTCATTTCTCCA
Found at i:4509851 original size:21 final size:19
Alignment explanation
Indices: 4509809--4509852 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
4509799 ACTAATCAAT
*
4509809 ATTTTTTTTCATTTCTCTA
1 ATTTTTTTTCATTTCTCCA
*
4509828 ATTTTTTTTCAATTTGGTCCA
1 ATTTTTTTTC-ATTT-CTCCA
4509849 ATTT
1 ATTT
4509853 CCAATAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 4 0.19
21 7 0.33
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTTTTCATTTCTCCA
Found at i:4515662 original size:18 final size:18
Alignment explanation
Indices: 4515622--4515681 Score: 97
Period size: 17 Copynumber: 3.4 Consensus size: 18
4515612 CTTCTCAAAT
*
4515622 TCTTTTTCGATTTCTTT-
1 TCTTTTTCAATTTCTTTC
4515639 TCTTTTTCAATTT-TTTC
1 TCTTTTTCAATTTCTTTC
4515656 TCTTTTTCAATTTCTTTC
1 TCTTTTTCAATTTCTTTC
4515674 TCTTTTTC
1 TCTTTTTC
4515682 TTCTTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
16 3 0.08
17 25 0.62
18 12 0.30
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTCTTTC
Found at i:4519335 original size:18 final size:18
Alignment explanation
Indices: 4519312--4519346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4519302 GACAATGGTG
*
4519312 CTCCAAGGGCGGCAACAC
1 CTCCAAGGGAGGCAACAC
*
4519330 CTCCAATGGAGGCAACA
1 CTCCAAGGGAGGCAACA
4519347 AAAGGATCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.26, T:0.09
Consensus pattern (18 bp):
CTCCAAGGGAGGCAACAC
Found at i:4522019 original size:19 final size:19
Alignment explanation
Indices: 4521997--4522034 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4521987 TCAATCATCC
4521997 CTCATCACATCA-TCTCTCA
1 CTCAT-ACATCATTCTCTCA
*
4522016 CTCATTCATCATTCTCTCA
1 CTCATACATCATTCTCTCA
4522035 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATACATCATTCTCTCA
Found at i:4535394 original size:157 final size:157
Alignment explanation
Indices: 4535104--4535423 Score: 577
Period size: 157 Copynumber: 2.0 Consensus size: 157
4535094 AATTATTCTT
4535104 GGAAGACCTTTTCTTGCTACAGACAGGACTTTAATTGATGTGCAGAAAGGTGAACTGACCATGAG
1 GGAAGACCTTTTCTTGCTACAGACAGGACTTTAATTGATGTGCAGAAAGGTGAACTGACCATGAG
* * *
4535169 GATGAATGATCAGCATGTCACATTCAATGTTTTTAATGCGCTAATGATAATGACGAATGTTGTGC
66 GATGAATGATCAGCATGTCACATTCAATGTTTTTAATGCGCTAATGATAATGAAGAATGTCGTAC
4535234 CATTGACTTGAGAGGAGTAGCAGTGGA
131 CATTGACTTGAGAGGAGTAGCAGTGGA
* * *
4535261 GGAAGACCTTTTCTTGCTACAGATAGGAGTTTAATTGATGTGCAGAAAGGTGAACTGACTATGAG
1 GGAAGACCTTTTCTTGCTACAGACAGGACTTTAATTGATGTGCAGAAAGGTGAACTGACCATGAG
4535326 GATGAATGATCAGCATGTCACATTCAATGTTTTTAATGCGCTAATGATAATGAAGAATGTCGTAC
66 GATGAATGATCAGCATGTCACATTCAATGTTTTTAATGCGCTAATGATAATGAAGAATGTCGTAC
*
4535391 CATTGACTTGATAGGAGTAGCAGTGGA
131 CATTGACTTGAGAGGAGTAGCAGTGGA
4535418 GGAAGA
1 GGAAGA
4535424 GTTCACGAGA
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (157 bp):
GGAAGACCTTTTCTTGCTACAGACAGGACTTTAATTGATGTGCAGAAAGGTGAACTGACCATGAG
GATGAATGATCAGCATGTCACATTCAATGTTTTTAATGCGCTAATGATAATGAAGAATGTCGTAC
CATTGACTTGAGAGGAGTAGCAGTGGA
Found at i:4541767 original size:40 final size:40
Alignment explanation
Indices: 4541490--4541753 Score: 349
Period size: 40 Copynumber: 6.6 Consensus size: 40
4541480 CGAATGATGT
* * * *
4541490 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
4541530 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
4541570 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
4541608 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
4541649 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
4541689 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
4541729 CCGGGCTATGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
4541754 AACGAGTAGC
Statistics
Matches: 201, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 33 0.16
40 158 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:4541784 original size:159 final size:159
Alignment explanation
Indices: 4541490--4541786 Score: 379
Period size: 159 Copynumber: 1.9 Consensus size: 159
4541480 CGAATGATGT
*
4541490 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
* * ** *
4541555 TGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGAGTTAAGT
66 TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
4541620 CCCGAAGGCATTTGTGCGAGTTACTATAA
131 CCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
4541649 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATT
* * * *
4541712 TGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGCTATATCCG-GT
64 TGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAAATCCGAGT
*
4541774 TAAATTCCGAAGG
126 TAAATCCCGAAGG
4541787 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
158 3 0.03
159 84 0.71
160 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (159 bp):
CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
CCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:4549994 original size:18 final size:17
Alignment explanation
Indices: 4549971--4550006 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
4549961 AATAAACATG
*
4549971 ATTTAAGCTTAGATATCC
1 ATTTAAACTTAGAT-TCC
4549989 ATTTAAACTTAGATTCC
1 ATTTAAACTTAGATTCC
4550006 A
1 A
4550007 ACTCAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (17 bp):
ATTTAAACTTAGATTCC
Found at i:4551411 original size:19 final size:18
Alignment explanation
Indices: 4551373--4551408 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4551363 CGATAAGATT
4551373 TTTTTATAAAATAATTAA
1 TTTTTATAAAATAATTAA
4551391 TTTTTATAAAATAATTAA
1 TTTTTATAAAATAATTAA
4551409 ATTGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTATAAAATAATTAA
Found at i:4551419 original size:19 final size:18
Alignment explanation
Indices: 4551377--4551420 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4551367 AAGATTTTTT
* *
4551377 TATAAAATAATTAATTTT
1 TATAAAATAATTAAATTG
4551395 TATAAAATAATTAAATTG
1 TATAAAATAATTAAATTG
4551413 TATTAAAA
1 TA-TAAAA
4551421 ATTTGAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TATAAAATAATTAAATTG
Found at i:4553110 original size:419 final size:419
Alignment explanation
Indices: 4552332--4553169 Score: 1541
Period size: 419 Copynumber: 2.0 Consensus size: 419
4552322 ATTTAATCAG
4552332 TTTAGCTTGAATTTAATTTGTGTTGGGTTGATTGCATTCCATCCTCTTGATTTGTTAAATTTATG
1 TTTAGCTTGAATTTAATTTGTGTTGGGTTGATTGCATTCCATCCTCTTGATTTGTTAAATTTATG
* *
4552397 TTTATGCTGTTATAGGCCTCGGTAAAATGTTTGATTAAGTAAAACCATGATTAAGTTATTTTTTC
66 TTTATGCTGTTATAGGCCTCGGTAAAATGTTTGATTAAGTAAAACCATGATTAAGTTATTATTGC
* **
4552462 ATTACAATTATGAGATAAATAAAGAATTAATTATTTAAATGCATTGAAATTGTAATTAATGGACA
131 ATTACAATTATAAGATAAATAAAGAATTAATTATTTAAACACATTGAAATTGTAATTAATGGACA
*
4552527 CAGTACTTAATCAGTGCATGTTTAATTCTTCAAAGGTAGCTGAAGATTAGATTAGCATTGTATTT
196 CAGTACTTAATCAGTGCATGTTTAATTCTTCAAAGGTAGCTAAAGATTAGATTAGCATTGTATTT
4552592 GGCGATACATATGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTACTTCAAGGTAAGGATA
261 GGCGATACATATGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTACTTCAAGGTAAGGATA
*
4552657 CTTTGTTACCTTACATAGTCTTTTATATGCTTATTAGGTTGAATTAATCGTTTGAATCGACATAG
326 CTTTGTTACCTCACATAGTCTTTTATATGCTTATTAGGTTGAATTAATCGTTTGAATCGACATAG
4552722 GAATATGCGAGAGATTGTTTAATCTAATA
391 GAATATGCGAGAGATTGTTTAATCTAATA
4552751 TTTAGCTTGAATTTAATTTGTGTTGGGTTGATTGCATTCCATCCTCTTGATTTGTTAAATTTATG
1 TTTAGCTTGAATTTAATTTGTGTTGGGTTGATTGCATTCCATCCTCTTGATTTGTTAAATTTATG
4552816 TTTATGCTGTTATAGGCCTCGGTAAAATGTTTGATTAAGTAAAACCATGATTAAGTTATTATTGC
66 TTTATGCTGTTATAGGCCTCGGTAAAATGTTTGATTAAGTAAAACCATGATTAAGTTATTATTGC
* * * * *
4552881 ATTCCAATTGTAAGATAACTAAATAATTAATTATTTAAACATATTGAAATTGTAATTAATGGACA
131 ATTACAATTATAAGATAAATAAAGAATTAATTATTTAAACACATTGAAATTGTAATTAATGGACA
*
4552946 CAGTACTTAATCAGTGCATGTTTAATTCTTCTAAGGTAGCTAAAGATTAGATTAGCATTGTATTT
196 CAGTACTTAATCAGTGCATGTTTAATTCTTCAAAGGTAGCTAAAGATTAGATTAGCATTGTATTT
**
4553011 GGCGATACATATGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTGTTTCAAGGTAAGGATA
261 GGCGATACATATGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTACTTCAAGGTAAGGATA
4553076 CTTTGTTACCTCACATAGTCTTTTATATGCTTATTAGGTTGAATTAATCGTTTGAATCGACATAG
326 CTTTGTTACCTCACATAGTCTTTTATATGCTTATTAGGTTGAATTAATCGTTTGAATCGACATAG
4553141 GAATATGCGAGAGATTGTTTAATCTAATA
391 GAATATGCGAGAGATTGTTTAATCTAATA
4553170 AGTATGTATG
Statistics
Matches: 404, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
419 404 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (419 bp):
TTTAGCTTGAATTTAATTTGTGTTGGGTTGATTGCATTCCATCCTCTTGATTTGTTAAATTTATG
TTTATGCTGTTATAGGCCTCGGTAAAATGTTTGATTAAGTAAAACCATGATTAAGTTATTATTGC
ATTACAATTATAAGATAAATAAAGAATTAATTATTTAAACACATTGAAATTGTAATTAATGGACA
CAGTACTTAATCAGTGCATGTTTAATTCTTCAAAGGTAGCTAAAGATTAGATTAGCATTGTATTT
GGCGATACATATGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTACTTCAAGGTAAGGATA
CTTTGTTACCTCACATAGTCTTTTATATGCTTATTAGGTTGAATTAATCGTTTGAATCGACATAG
GAATATGCGAGAGATTGTTTAATCTAATA
Found at i:4553436 original size:5 final size:5
Alignment explanation
Indices: 4553426--4553472 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
4553416 GCATTAAAAC
4553426 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
4553473 ACTTTGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4561264 original size:51 final size:50
Alignment explanation
Indices: 4561137--4561324 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 50
4561127 CATCTTTTGA
* * * *
4561137 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCTAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCAG
* *
4561187 TTCACGTAGTAGCCTGCACATAGTACTACACACATGACCAAAGCCTTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CCTTCCAG
* * * * * *
4561238 TACACATAGTAGCCTGCACATTGTACTACACATGTGACCATTATCTATCGA-
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AACCT-TCCAG
*
4561289 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
4561325 TTTATAGGCA
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
50 38 0.32
51 75 0.64
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCAG
Found at i:4562457 original size:38 final size:39
Alignment explanation
Indices: 4562402--4562478 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
4562392 AAATAATGGT
*
4562402 CTAATTACCACATAAGGACCCCTAATTTATAATTCCATA
1 CTAATTACCACACAAGGACCCCTAATTTATAATTCCATA
*
4562441 CTAATT-CCACACAAGGATCCCTAATTTATAATTCCATA
1 CTAATTACCACACAAGGACCCCTAATTTATAATTCCATA
4562479 ACAATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 30 0.83
39 6 0.17
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (39 bp):
CTAATTACCACACAAGGACCCCTAATTTATAATTCCATA
Found at i:4562710 original size:88 final size:88
Alignment explanation
Indices: 4562561--4562735 Score: 305
Period size: 88 Copynumber: 2.0 Consensus size: 88
4562551 AGTGCCCAAA
* * **
4562561 CGTCAAAATTTTCGAACGAAATTTTCACGAAATCTTTCCGTGAAATTGTAGACCATAAAAATATA
1 CGTCAAAATTTTCGAACGAAATTTTCACAAAATCTGTCCGCAAAATTGTAGACCATAAAAATATA
4562626 GTAAAAATAAAATTTTCCTCTTT
66 GTAAAAATAAAATTTTCCTCTTT
4562649 CGTCAAAATTTTCGAACGAAATTTTCACAAAATCTGTCCGCAAAATTGTAGACCATAAAAATATA
1 CGTCAAAATTTTCGAACGAAATTTTCACAAAATCTGTCCGCAAAATTGTAGACCATAAAAATATA
*
4562714 GTAAAAATAAATTTTTCCTCTT
66 GTAAAAATAAAATTTTCCTCTT
4562736 CAAATTTGTG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.33
Consensus pattern (88 bp):
CGTCAAAATTTTCGAACGAAATTTTCACAAAATCTGTCCGCAAAATTGTAGACCATAAAAATATA
GTAAAAATAAAATTTTCCTCTTT
Found at i:4566041 original size:24 final size:25
Alignment explanation
Indices: 4566008--4566054 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
4565998 TTTTGAGAAG
*
4566008 AAAGTTGTTT-TGAAGGAATTCTTCA
1 AAAGTTGTTTCTG-AGAAATTCTTCA
4566033 AAAG-TGTTTCTGAGAAATTCTT
1 AAAGTTGTTTCTGAGAAATTCTT
4566055 TCCGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (25 bp):
AAAGTTGTTTCTGAGAAATTCTTCA
Found at i:4566856 original size:14 final size:14
Alignment explanation
Indices: 4566833--4566862 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4566823 CATCCCTCAT
*
4566833 TCACATCTCTTCTC
1 TCACAACTCTTCTC
4566847 TCACAACTCTTCTC
1 TCACAACTCTTCTC
4566861 TC
1 TC
4566863 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:4567833 original size:5 final size:5
Alignment explanation
Indices: 4567823--4567847 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4567813 ATTAGAACTC
4567823 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
4567848 ACTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:4575764 original size:41 final size:41
Alignment explanation
Indices: 4575719--4575874 Score: 118
Period size: 41 Copynumber: 3.8 Consensus size: 41
4575709 CATGGGTACC
*
4575719 GAAGTACAAACAA-AGGCACGTATATGCAATTTAAGGGTTTT
1 GAAGTACAAA-AAGAGGCACATATATGCAATTTAAGGGTTTT
* * ***
4575760 GAAGTACAAAAAGGGGCACATATATGCAATTTAGGGGTACC
1 GAAGTACAAAAAGAGGCACATATATGCAATTTAAGGGTTTT
* * * * * ***
4575801 GAAGTA-AAAATAGGGGCACGTATGTGCAATTCAGGGGTACC
1 GAAGTACAAAA-AGAGGCACATATATGCAATTTAAGGGTTTT
* * * *
4575842 GAACTACAAATAGGGGCACATATGTGCAATTTA
1 GAAGTACAAAAAGAGGCACATATATGCAATTTA
4575875 GGGAATAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.06
41 90 0.91
42 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (41 bp):
GAAGTACAAAAAGAGGCACATATATGCAATTTAAGGGTTTT
Found at i:4575798 original size:82 final size:82
Alignment explanation
Indices: 4575649--4575877 Score: 235
Period size: 82 Copynumber: 2.8 Consensus size: 82
4575639 GAATTGTAAC
* * * ** ** * * *
4575649 AAGGCACGTA-AGTGCTATTCAAGGGTACCGAAGTATAAAAAGGGGCACATAGGTGTTACTCATG
1 AAGGCACGTATA-TGCAATTCAAGGGTACCGAACTACAAAAAGGGGCACATATATGCAATTTAGG
*
4575713 GGTACCGAAGTACAAACA
65 GGTACCGAAGTAAAAACA
* *** *
4575731 AAGGCACGTATATGCAATTTAAGGGTTTTGAAGTACAAAAAGGGGCACATATATGCAATTTAGGG
1 AAGGCACGTATATGCAATTCAAGGGTACCGAACTACAAAAAGGGGCACATATATGCAATTTAGGG
*
4575796 GTACCGAAGTAAAAATA
66 GTACCGAAGTAAAAACA
** * * * *
4575813 GGGGCACGTATGTGCAATTCAGGGGTACCGAACTACAAATAGGGGCACATATGTGCAATTTAGGG
1 AAGGCACGTATATGCAATTCAAGGGTACCGAACTACAAAAAGGGGCACATATATGCAATTTAGGG
4575878 AATAATTAAG
Statistics
Matches: 120, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
82 119 0.99
83 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.22
Consensus pattern (82 bp):
AAGGCACGTATATGCAATTCAAGGGTACCGAACTACAAAAAGGGGCACATATATGCAATTTAGGG
GTACCGAAGTAAAAACA
Found at i:4590824 original size:27 final size:29
Alignment explanation
Indices: 4590793--4590847 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
4590783 TTAGGACTTA
4590793 TCTTTT-AATT-T-CTTGCTGTCAATTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTT
4590820 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
4590848 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 4 0.16
29 11 0.44
30 4 0.16
ACGTcount: A:0.16, C:0.15, G:0.09, T:0.60
Consensus pattern (29 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTT
Found at i:4591842 original size:39 final size:39
Alignment explanation
Indices: 4591754--4591908 Score: 197
Period size: 39 Copynumber: 3.9 Consensus size: 39
4591744 TTAGACAAAC
* *
4591754 ATTAATGATG-TCAGAATGTAAGACACTTAATTAAA-ACACAT
1 ATTAATGATGTTCA-AA-CTAAGACA--TAATTAAAGACATAT
*
4591795 ATTAATGATGTTCAAAATAAGACATAATTAAAGACATAT
1 ATTAATGATGTTCAAACTAAGACATAATTAAAGACATAT
* *
4591834 ATTAATGATGTTTAAACTAAGACATAATTAAATACATAT
1 ATTAATGATGTTCAAACTAAGACATAATTAAAGACATAT
* *
4591873 ATTAATGATGTTTAAACTAAGACATAATTAAGGACA
1 ATTAATGATGTTCAAACTAAGACATAATTAAAGACA
4591909 CAAACTAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
38 8 0.08
39 75 0.71
40 7 0.07
41 12 0.11
42 3 0.03
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (39 bp):
ATTAATGATGTTCAAACTAAGACATAATTAAAGACATAT
Found at i:4597147 original size:42 final size:42
Alignment explanation
Indices: 4597084--4597234 Score: 241
Period size: 42 Copynumber: 3.6 Consensus size: 42
4597074 CCACCACCAA
*
4597084 GCCCACCCGGAATAGTTCCGAACCCGCCGATTATATTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCGCCGATTATATTTCCAG
4597126 GCCCACCCGGAATAGTCCCGAACCCGCCGATTATATTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCGCCGATTATATTTCCAG
* * *
4597168 GCCCACCCGGAATAGTCCCGAACCCACCTAGTA-ATTTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCGCCGATTATA-TTTCCAG
*
4597210 GCCCACCTGGAATAGTCCCGAACCC
1 GCCCACCCGGAATAGTCCCGAACCC
4597235 ACCTAGTATT
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
41 1 0.01
42 102 0.99
ACGTcount: A:0.25, C:0.38, G:0.19, T:0.19
Consensus pattern (42 bp):
GCCCACCCGGAATAGTCCCGAACCCGCCGATTATATTTCCAG
Found at i:4597195 original size:21 final size:21
Alignment explanation
Indices: 4597127--4597237 Score: 59
Period size: 21 Copynumber: 5.3 Consensus size: 21
4597117 TATTTCCAGG
4597127 CCCACCCGGAATAGTCCCGAA
1 CCCACCCGGAATAGTCCCGAA
* * * *
4597148 CCC-GCC-GATTATATTTCC-AGG
1 CCCACCCGGA--ATAGTCCCGA-A
4597169 CCCACCCGGAATAGTCCCGAA
1 CCCACCCGGAATAGTCCCGAA
* * ** * *
4597190 CCCACCTAGTAATTTTCCAG-G
1 CCCACC-CGGAATAGTCCCGAA
*
4597211 CCCACCTGGAATAGTCCCGAA
1 CCCACCCGGAATAGTCCCGAA
4597232 CCCACC
1 CCCACC
4597238 TAGTATTTTT
Statistics
Matches: 62, Mismatches: 20, Indels: 16
0.63 0.20 0.16
Matches are distributed among these distances:
19 2 0.03
20 11 0.18
21 36 0.58
22 11 0.18
23 2 0.03
ACGTcount: A:0.25, C:0.41, G:0.17, T:0.17
Consensus pattern (21 bp):
CCCACCCGGAATAGTCCCGAA
Found at i:4597238 original size:21 final size:21
Alignment explanation
Indices: 4597169--4597238 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
4597159 TATTTCCAGG
*
4597169 CCCACCCGGAATAGTCCCGAA
1 CCCACCTGGAATAGTCCCGAA
* ** * *
4597190 CCCACCTAGTAATTTTCCAG-G
1 CCCACCT-GGAATAGTCCCGAA
4597211 CCCACCTGGAATAGTCCCGAA
1 CCCACCTGGAATAGTCCCGAA
4597232 CCCACCT
1 CCCACCT
4597239 AGTATTTTTC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 8 0.22
21 20 0.56
22 8 0.22
ACGTcount: A:0.26, C:0.41, G:0.16, T:0.17
Consensus pattern (21 bp):
CCCACCTGGAATAGTCCCGAA
Found at i:4597248 original size:42 final size:42
Alignment explanation
Indices: 4597084--4597255 Score: 238
Period size: 42 Copynumber: 4.1 Consensus size: 42
4597074 CCACCACCAA
* * *
4597084 GCCCACCCGGAATAGTTCCGAACCCGCCGATTATATTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCACCGAGTATATTTCCAG
* *
4597126 GCCCACCCGGAATAGTCCCGAACCCGCCGATTATATTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCACCGAGTATATTTCCAG
*
4597168 GCCCACCCGGAATAGTCCCGAACCCACCTAGTA-ATTTTCCAG
1 GCCCACCCGGAATAGTCCCGAACCCACCGAGTATA-TTTCCAG
* * * *
4597210 GCCCACCTGGAATAGTCCCGAACCCACCTAGTATTTTTCCAA
1 GCCCACCCGGAATAGTCCCGAACCCACCGAGTATATTTCCAG
4597252 GCCC
1 GCCC
4597256 TCCACAAGCA
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
41 1 0.01
42 120 0.99
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.20
Consensus pattern (42 bp):
GCCCACCCGGAATAGTCCCGAACCCACCGAGTATATTTCCAG
Found at i:4608096 original size:194 final size:193
Alignment explanation
Indices: 4607767--4608162 Score: 729
Period size: 194 Copynumber: 2.0 Consensus size: 193
4607757 ACACAATAGC
*
4607767 AATAAAAAAGTCAAACTATATTCAAGAAAACAACGTGAAAAAGCGCAAGAAGCCAATGACCAACA
1 AATAAAAAAGTCAAACTAAATTCAAGAAAACAACGTGAAAAAGCGCAAGAAGCCAATGACCAACA
4607832 CTTCACCACAGCAAAAATGAAAATGCACAAATGGTTTTGCAATCAAATTTAATAGTAAAGATCTT
66 CTTCACCACAGCAAAAATGAAAATGCACAAATGGTTTTGCAATCAAATTTAATAGTAAAGATCTT
*
4607897 AATGTAACAGAAGACAGCAATCATTTTTTTTTTTAAATATCAGTACCATATTTTGGCGAACACA
131 AATGTAA-AGAAGACAGCAATCATTTTTTTTTTTAAATATCAGTACCATATTTTGGCAAACACA
*
4607961 AATAAAAAAGTCAAACTAAATTCAAGAAAACAATGTGAAAAAGCGCAAGAAGCCAATGACCAACA
1 AATAAAAAAGTCAAACTAAATTCAAGAAAACAACGTGAAAAAGCGCAAGAAGCCAATGACCAACA
*
4608026 CTTCACCACAGCAAAAATGAAAATGCACAAATGGTTTTGCGATCAAATTTAATAGTAAAGATCTT
66 CTTCACCACAGCAAAAATGAAAATGCACAAATGGTTTTGCAATCAAATTTAATAGTAAAGATCTT
*
4608091 AATGTAAAGAAGATAGCAATCATTTTTTTTTTTAAATATCAGTACCATATTTTGGCAAACACA
131 AATGTAAAGAAGACAGCAATCATTTTTTTTTTTAAATATCAGTACCATATTTTGGCAAACACA
*
4608154 AAGAAAAAA
1 AATAAAAAA
4608163 TTTTAGGTCT
Statistics
Matches: 196, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
193 62 0.32
194 134 0.68
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (193 bp):
AATAAAAAAGTCAAACTAAATTCAAGAAAACAACGTGAAAAAGCGCAAGAAGCCAATGACCAACA
CTTCACCACAGCAAAAATGAAAATGCACAAATGGTTTTGCAATCAAATTTAATAGTAAAGATCTT
AATGTAAAGAAGACAGCAATCATTTTTTTTTTTAAATATCAGTACCATATTTTGGCAAACACA
Found at i:4610576 original size:15 final size:15
Alignment explanation
Indices: 4610556--4610587 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4610546 TTTTATTTTA
4610556 GAGTTCTACCAACAT
1 GAGTTCTACCAACAT
*
4610571 GAGTTCTACCAATAT
1 GAGTTCTACCAACAT
4610586 GA
1 GA
4610588 TTGGATAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (15 bp):
GAGTTCTACCAACAT
Found at i:4611606 original size:22 final size:22
Alignment explanation
Indices: 4611581--4611627 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
4611571 GAGCCGTGGA
4611581 GGAC-CGAAGGTGGATCGGTGCC
1 GGACTCGAA-GTGGATCGGTGCC
*
4611603 GGACTGGAAGTGGATCGGTGCC
1 GGACTCGAAGTGGATCGGTGCC
4611625 GGA
1 GGA
4611628 GTTGAAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.15
Consensus pattern (22 bp):
GGACTCGAAGTGGATCGGTGCC
Found at i:4616561 original size:31 final size:31
Alignment explanation
Indices: 4616520--4616596 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
4616510 ATTTAAAAAA
4616520 TTGTT-ATTTTAGTCAC-T-CATGGTAGATAAG
1 TTGTTAATTTTAGTCACTTCCAT--TAGATAAG
*
4616550 TTGTTAATTTTAGTTACTTCCATTAGATAAG
1 TTGTTAATTTTAGTCACTTCCATTAGATAAG
* *
4616581 TAGTCAATTTTAGTCA
1 TTGTTAATTTTAGTCA
4616597 TTTTACCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.12
31 31 0.77
32 1 0.03
33 3 0.08
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (31 bp):
TTGTTAATTTTAGTCACTTCCATTAGATAAG
Found at i:4617027 original size:30 final size:31
Alignment explanation
Indices: 4616958--4617031 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
4616948 AAAATTTGTT
* ** **
4616958 ATTTTAGTCACTCTTGTTAGATAAGTTGTTA
1 ATTTTAGCCACTCCCGTTAGATAAGTTGACA
*
4616989 ATTTTAGCCACTCCCGTTAGGTAAGTTGACA
1 ATTTTAGCCACTCCCGTTAGATAAGTTGACA
4617020 A-TTTAGCCACTC
1 ATTTTAGCCACTC
4617032 TACCGTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (31 bp):
ATTTTAGCCACTCCCGTTAGATAAGTTGACA
Found at i:4618318 original size:31 final size:31
Alignment explanation
Indices: 4618234--4618309 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
4618224 TTTAAACCAT
* *
4618234 AGAGTGACTAAAATTGACAACTTATTTAACA
1 AGAGTGACTAAAATTGACAATTTATCTAACA
*
4618265 GGAGTGACTAAAATTGACAATTTATCTAACA
1 AGAGTGACTAAAATTGACAATTTATCTAACA
4618296 AGAGTGACTAAAAT
1 AGAGTGACTAAAAT
4618310 AATAAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (31 bp):
AGAGTGACTAAAATTGACAATTTATCTAACA
Found at i:4619210 original size:12 final size:12
Alignment explanation
Indices: 4619193--4619237 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
4619183 ACTAATCTTT
4619193 TCTCAAATTTCC
1 TCTCAAATTTCC
*
4619205 TCTC-AATTTGC
1 TCTCAAATTTCC
4619216 TCTCAAA-TTCC
1 TCTCAAATTTCC
4619227 T-TCCAAATTTC
1 TCT-CAAATTTC
4619238 TCTGAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:4619235 original size:23 final size:21
Alignment explanation
Indices: 4619193--4619245 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
4619183 ACTAATCTTT
4619193 TCTCAAATTTCCTCTCAATTTGC
1 TCTCAAA-TTCCTCTCAATTT-C
4619216 TCTCAAATTCCT-TCCAAATTTC
1 TCTCAAATTCCTCT-C-AATTTC
*
4619238 TCTGAAAT
1 TCTCAAAT
4619246 CCATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (21 bp):
TCTCAAATTCCTCTCAATTTC
Found at i:4619276 original size:11 final size:11
Alignment explanation
Indices: 4619256--4619280 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4619246 CCATATTTAA
4619256 TCTCAATTTGC
1 TCTCAATTTGC
4619267 TCTCAATTTGC
1 TCTCAATTTGC
4619278 TCT
1 TCT
4619281 TAAATTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TCTCAATTTGC
Found at i:4619286 original size:51 final size:50
Alignment explanation
Indices: 4619205--4619304 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
4619195 TCAAATTTCC
4619205 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTT-CAAATTTCTCTGAAATCCATATTTAA
* * *
4619256 TCTCAATTTGCTCTCAATTTGCTCTT-AAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATT-C-CTTCAAATTTCTCTGAAATCCATATTT
4619305 TTAAATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 40 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (50 bp):
TCTCAATTTGCTCTCAAATTCCTTCAAATTTCTCTGAAATCCATATTTAA
Found at i:4619291 original size:11 final size:12
Alignment explanation
Indices: 4619260--4619296 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
4619250 ATTTAATCTC
*
4619260 AATTTGCTC-TC
1 AATTTGCTCTTA
4619271 AATTTGCTCTTA
1 AATTTGCTCTTA
4619283 AATTT-CTCTTA
1 AATTTGCTCTTA
4619294 AAT
1 AAT
4619297 CCCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (12 bp):
AATTTGCTCTTA
Found at i:4619344 original size:12 final size:13
Alignment explanation
Indices: 4619322--4619350 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4619312 ATTTTGAAAA
4619322 AAATTATTTTTTT
1 AAATTATTTTTTT
4619335 AAATTA-TTTTTT
1 AAATTATTTTTTT
4619347 AAAT
1 AAAT
4619351 CGTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AAATTATTTTTTT
Found at i:4620461 original size:7 final size:7
Alignment explanation
Indices: 4620449--4620474 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4620439 TAGTCGATTG
4620449 GTATTTA
1 GTATTTA
4620456 GTATTTA
1 GTATTTA
4620463 GTATTTA
1 GTATTTA
4620470 GTATT
1 GTATT
4620475 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:4621152 original size:18 final size:18
Alignment explanation
Indices: 4621125--4621164 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4621115 CAGGTGCGTT
* *
4621125 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
4621143 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
4621161 TCCT
1 TCCT
4621165 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:4621563 original size:22 final size:22
Alignment explanation
Indices: 4621547--4621825 Score: 331
Period size: 21 Copynumber: 13.0 Consensus size: 22
4621537 TTTAATTGAC
4621547 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
4621569 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
4621590 AAACTCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
**
4621611 AAACCCTAAACTTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
4621633 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
4621655 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* * * *
4621677 AAACCAT-AACCATTGACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
4621698 AAACACTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
****
4621720 AAACCCT-AACCC-TAACCCCT
1 AAACCCTAAACCCTTAACTTAA
* * *
4621740 AAACCCT-AATCCTTAAATAAA
1 AAACCCTAAACCCTTAACTTAA
*
4621761 AAACCCTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
4621783 AAACACT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
4621804 AAACTCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
4621825 A
1 A
4621826 TATAATTTGA
Statistics
Matches: 218, Mismatches: 35, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.07
21 105 0.48
22 98 0.45
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:4621715 original size:43 final size:42
Alignment explanation
Indices: 4621547--4621825 Score: 326
Period size: 43 Copynumber: 6.5 Consensus size: 42
4621537 TTTAATTGAC
4621547 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
* **
4621590 AAACTCTAACCCTTAACTTAAAAACCCTAAACTTTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAA
*
4621633 AAACCCTAAACCCTTAACCTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAA
* * * * *
4621677 AAACCATAACCATTGACTTTAAAACACTAAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAA
**** * * *
4621720 AAACCCTAACCC-TAACCCCTAAACCCTAATCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
* *
4621761 AAACCCTAAACCCTTAACTTTAAAACACTAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
*
4621804 AAACTCTAACCCTTAACTTAAA
1 AAACCCTAACCCTTAACTTAAA
4621826 TATAATTTGA
Statistics
Matches: 198, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
41 18 0.09
42 49 0.25
43 92 0.46
44 39 0.20
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (42 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
Found at i:4621957 original size:114 final size:114
Alignment explanation
Indices: 4621825--4622084 Score: 484
Period size: 114 Copynumber: 2.3 Consensus size: 114
4621815 CTTAACTTAA
*
4621825 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCACTTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
4621890 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
4621939 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
* *
4622004 TGTTAGATTTGAAAATATGTTTTGACTGGTACTAATAATTAATAATTTG
66 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
*
4622053 ATATAATTTGATAATTTTACTAACAATTAATA
1 ATATAATTTGATAATTTTACTAACCATTAATA
4622085 ATTGAAAAAA
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 142 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (114 bp):
ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
Found at i:4621961 original size:37 final size:37
Alignment explanation
Indices: 4621919--4622087 Score: 105
Period size: 37 Copynumber: 4.5 Consensus size: 37
4621909 TTTTGACTGG
4621919 TACTAACAATTAATAATTTGATATAATTTGATAATTT
1 TACTAACAATTAATAATTTGATATAATTTGATAATTT
* * * *
4621956 TACTAACCATTAATACAATT-AT-CAA-TTAATAATTT
1 TACTAACAATTAATA-ATTTGATATAATTTGATAATTT
* * ** ** * **
4621991 TACATTCACATAATGTTAGATTTGA-A-AATATGTTTTGACTGG
1 TAC--TAACA-ATTAATA-ATTTGATATAAT-T-TGAT-AATTT
*
4622033 TACTAATAATTAATAATTTGATATAATTTGATAATTT
1 TACTAACAATTAATAATTTGATATAATTTGATAATTT
4622070 TACTAACAATTAATAATT
1 TACTAACAATTAATAATT
4622088 GAAAAAAATA
Statistics
Matches: 93, Mismatches: 27, Indels: 24
0.65 0.19 0.17
Matches are distributed among these distances:
35 12 0.13
36 2 0.02
37 38 0.41
38 20 0.22
39 7 0.08
40 7 0.08
41 2 0.02
42 5 0.05
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (37 bp):
TACTAACAATTAATAATTTGATATAATTTGATAATTT
Found at i:4625382 original size:127 final size:125
Alignment explanation
Indices: 4625094--4625519 Score: 579
Period size: 124 Copynumber: 3.4 Consensus size: 125
4625084 CCCAAACATG
* *
4625094 CTACTGTAGCAAAAGCACGTCTACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * *
4625159 TAGAAGCGTTTTTGT-ACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
66 TTGAAGCATTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
** *
4625218 CTACTGTAGCAAAAGTGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
4625283 TTGAAGCATTTTTTTAAACTATTTGCACAGAAACGTCAACTCGAAACTATTTCTTCCAGGAC
66 TTGAAGCATTTTTTT-AACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * *
4625345 CTGCTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGTATCCTA
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
* * *
4625409 CTTGGAGCA-TTTTTTATACTCTTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAGGAC
65 CTTGAAGCATTTTTTTA-ACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * *
4625470 CTACTATAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATCCTTCT
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCT
4625520 GATACAGCAT
Statistics
Matches: 267, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
124 72 0.27
125 52 0.19
126 69 0.26
127 72 0.27
128 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGAAGCATTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:4629555 original size:5 final size:5
Alignment explanation
Indices: 4629547--4629572 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4629537 GAGATGGAAT
4629547 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
4629573 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:4629989 original size:30 final size:31
Alignment explanation
Indices: 4629950--4630009 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4629940 AGAGGTGAGA
*
4629950 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
4629981 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
4630010 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:4630319 original size:9 final size:9
Alignment explanation
Indices: 4630302--4630343 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
4630292 TCGAGTTGAT
*
4630302 TCGAATAAC
1 TCGATTAAC
4630311 TCGATTAAC
1 TCGATTAAC
4630320 TCGATTAAC
1 TCGATTAAC
*
4630329 TCGAATAAC
1 TCGATTAAC
4630338 TCGATT
1 TCGATT
4630344 CGTTTAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (9 bp):
TCGATTAAC
Found at i:4631484 original size:42 final size:42
Alignment explanation
Indices: 4631409--4631501 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
4631399 TCAAGTTAGT
* * *
4631409 GAGTTAGACGGCCTAGCACACGGACGCGTGTGGCAATTCAGA
1 GAGTTACACGGCCTAGCACACGGACGCGCGTGGCAACTCAGA
* * * *
4631451 GAGTTACACGGCCTGGCACACAGG-CGTGCGTGGCAGCTCAGT
1 GAGTTACACGGCCTAGCACAC-GGACGCGCGTGGCAACTCAGA
4631493 GAGTTACAC
1 GAGTTACAC
4631502 AGGTGAGGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.17
Consensus pattern (42 bp):
GAGTTACACGGCCTAGCACACGGACGCGCGTGGCAACTCAGA
Found at i:4638373 original size:21 final size:21
Alignment explanation
Indices: 4638347--4638430 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
4638337 TTTGGGTGGA
*
4638347 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
4638368 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
4638389 TCAGCTCTTTCGAGCTTATGT
1 TCAGCTCTTACGAGCTTCTGT
* * *
4638410 TAAGCT-TTATGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
4638430 T
1 T
4638431 GGCGTGTTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 12 0.22
21 42 0.78
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:4638394 original size:42 final size:41
Alignment explanation
Indices: 4638347--4638430 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
4638337 TTTGGGTGGA
* *
4638347 TCAGCTCTCACGAGCTTCTGTTCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTCACGAGCTTATGTTAAGCT-TTATGAGCTTCTGT
** *
4638389 TCAGCTCTTTCGAGCTTATGTTAAGCTTTATGAGCTTTTGT
1 TCAGCTCTCACGAGCTTATGTTAAGCTTTATGAGCTTCTGT
4638430 T
1 T
4638431 GGCGTGTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 14 0.38
42 23 0.62
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (41 bp):
TCAGCTCTCACGAGCTTATGTTAAGCTTTATGAGCTTCTGT
Found at i:4647249 original size:16 final size:16
Alignment explanation
Indices: 4647228--4647258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4647218 TTGTTTTAAT
4647228 ATAAATGAATCTATGC
1 ATAAATGAATCTATGC
*
4647244 ATAAATGTATCTATG
1 ATAAATGAATCTATG
4647259 TTGTGATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (16 bp):
ATAAATGAATCTATGC
Found at i:4655854 original size:48 final size:48
Alignment explanation
Indices: 4655801--4655893 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
4655791 ATTTATAGAG
4655801 ATAATTTTTAGGTTAATTGAATCTTGGATGGGCTATTTCATTTACTCT
1 ATAATTTTTAGGTTAATTGAATCTTGGATGGGCTATTTCATTTACTCT
4655849 ATAATTTTTAGGTTAATTGAATCTTGGATGGGCTATTTCATTTAC
1 ATAATTTTTAGGTTAATTGAATCTTGGATGGGCTATTTCATTTAC
4655894 AAAGTGCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (48 bp):
ATAATTTTTAGGTTAATTGAATCTTGGATGGGCTATTTCATTTACTCT
Found at i:4656069 original size:15 final size:15
Alignment explanation
Indices: 4656049--4656082 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4656039 ATATGTTAAT
4656049 AATAATATAAA-ATAA
1 AATAATA-AAAGATAA
4656064 AATAATAAAAGATAA
1 AATAATAAAAGATAA
4656079 AATA
1 AATA
4656083 TTAGAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATAAAAGATAA
Done.