Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 176 of 318
Found at i:54665785 original size:145 final size:145
Alignment explanation
Indices: 54665515--54665875 Score: 568
Period size: 145 Copynumber: 2.5 Consensus size: 145
54665505 ACACGTTTCG
* * * **
54665515 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
54665580 AT--CTC--ATACATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
66 ATCACACATATACATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
*
54665641 TGTTCACATTCATCA
131 TGTTCACATCCATCA
* *
54665656 CATTGGCCATTCGGCCTTATCACACATACGCATGCTCACATTCATCACATTGGCCATTCGGACTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* *
54665721 ATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
66 ATCACACATATACATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
54665786 TGTTCACATCCATCA
131 TGTTCACATCCATCA
*
54665801 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGTCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
54665866 ATCACACATA
66 ATCACACATA
54665876 CGCATGATCA
Statistics
Matches: 200, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
141 60 0.30
143 2 0.01
145 138 0.69
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (145 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATATACATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
TGTTCACATCCATCA
Found at i:54679975 original size:22 final size:21
Alignment explanation
Indices: 54679924--54679975 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
54679914 CAGCCCGCAG
**
54679924 CACGGGCGTGTCCCAGGGTCA
1 CACGGGCGTGTCCCAGGACCA
* *
54679945 CACGAGCGTGTCCCTTGGACCA
1 CACGGGCGTGTCCC-AGGACCA
54679967 CACGGGCGT
1 CACGGGCGT
54679976 TTGAGCCCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (21 bp):
CACGGGCGTGTCCCAGGACCA
Found at i:54684691 original size:54 final size:54
Alignment explanation
Indices: 54684620--54684724 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
54684610 TGACTTTTAA
* * * *
54684620 ACATGGCCATGGTACACGCCCGTGTGGACTGCCCGTGTTCAATACTAACTTGGG
1 ACATGGCCATGGGACACGCCAGTGTGGACTACCCGTGTCCAATACTAACTTGGG
* * *
54684674 ACATGGCTATGGGACACGCCAGTGTGGCCTACCCGTGTCCTATACTAACTT
1 ACATGGCCATGGGACACGCCAGTGTGGACTACCCGTGTCCAATACTAACTT
54684725 ATAAATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.25
Consensus pattern (54 bp):
ACATGGCCATGGGACACGCCAGTGTGGACTACCCGTGTCCAATACTAACTTGGG
Found at i:54684993 original size:37 final size:37
Alignment explanation
Indices: 54684929--54685004 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
54684919 TTACAAGTCA
54684929 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
54684966 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
54685003 AA
1 AA
54685005 CATCGATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 30 0.86
38 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:54691988 original size:124 final size:124
Alignment explanation
Indices: 54691767--54691990 Score: 306
Period size: 124 Copynumber: 1.8 Consensus size: 124
54691757 GAATTATGTG
** * * * *
54691767 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTCGAATGATACCCGG
1 AAATGAAATATGGATGTCCAATGATTATTGATGTATGTGTGCATGAGAATTCGAATGATACCCGG
* * * *
54691832 GCTAAGTCCCGAAGGCGATTATGCTAGTAATTATAATTGTGTTGGAGCCTTAGTAACGA
66 GCTAAGCCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTGGAGCCTTAGTAACGA
* * *
54691891 AAATGAAATATGTATGTCCAATGATTATTGATGTCTGTGTGCATGAGAAATT-GAATGATATCCG
1 AAATGAAATATGGATGTCCAATGATTATTGATGTATGTGTGCATGAG-AATTCGAATGATACCCG
*
54691955 GGCTAAGCCCCGAAGACAATTATGCTGGAAATTATA
65 GGCTAAGCCCCGAAGACAATTATGCTAGAAATTATA
54691991 TCCGGGTTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
124 82 0.96
125 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (124 bp):
AAATGAAATATGGATGTCCAATGATTATTGATGTATGTGTGCATGAGAATTCGAATGATACCCGG
GCTAAGCCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTGGAGCCTTAGTAACGA
Found at i:54692113 original size:40 final size:40
Alignment explanation
Indices: 54691986--54692115 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
54691976 ATGCTGGAAA
*
54691986 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCTAGTGG
* * * **
54692026 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCTAGTGG
* **
54692066 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCTCTTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCTAGTGG
54692106 TTATATCCGG
1 TTATATCCGG
54692116 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 3 0.04
40 71 0.96
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCTAGTGG
Found at i:54697013 original size:28 final size:27
Alignment explanation
Indices: 54696950--54697019 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
54696940 ATAGTGAGTC
54696950 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54696977 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54697005 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54697020 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54705018 original size:28 final size:27
Alignment explanation
Indices: 54704955--54705024 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
54704945 ATAGTGAGTC
54704955 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54704982 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54705010 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54705025 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54713043 original size:28 final size:27
Alignment explanation
Indices: 54712980--54713049 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
54712970 ATAGTGAGTC
54712980 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54713007 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54713035 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54713050 GTACAAGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54715181 original size:13 final size:13
Alignment explanation
Indices: 54715163--54715189 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54715153 GGCTCACAAC
54715163 CATGGTCGTGTGT
1 CATGGTCGTGTGT
54715176 CATGGTCGTGTGT
1 CATGGTCGTGTGT
54715189 C
1 C
54715190 CCTGTACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.19, G:0.37, T:0.37
Consensus pattern (13 bp):
CATGGTCGTGTGT
Found at i:54718472 original size:22 final size:22
Alignment explanation
Indices: 54718436--54718482 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54718426 AACGCCGTAG
*
54718436 ACAGGATAGCACATAGCCATAA
1 ACAGGACAGCACATAGCCATAA
* * *
54718458 ACAGGACAGCGCATAGTCGTAA
1 ACAGGACAGCACATAGCCATAA
54718480 ACA
1 ACA
54718483 TTATAGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (22 bp):
ACAGGACAGCACATAGCCATAA
Found at i:54718721 original size:22 final size:23
Alignment explanation
Indices: 54718685--54718746 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
54718675 GCAAATACGT
* *
54718685 TTGGAACACAGCCATAAT-TAGG
1 TTGGCACAAAGCCATAATGTAGG
54718707 TTGGCACAGAA-CCAT-ATGTAGG
1 TTGGCACA-AAGCCATAATGTAGG
*
54718729 TTGGCGCAAAGCCATAAT
1 TTGGCACAAAGCCATAAT
54718747 CAGAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 4 0.12
22 26 0.79
23 3 0.09
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (23 bp):
TTGGCACAAAGCCATAATGTAGG
Found at i:54719014 original size:41 final size:41
Alignment explanation
Indices: 54718892--54719014 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
54718882 AAAAGCCACC
* * *
54718892 GGTGGATCCATGGTCATCAAGCAACCATGCGATCCTTC-ATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCC-TCAATT
* *
54718933 GGTGGATCCACGGTTGTCAAGCAACCATACGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
*
54718974 GGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
54719015 TCTTCCTCCG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 2 0.03
41 71 0.97
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
Found at i:54719288 original size:27 final size:27
Alignment explanation
Indices: 54719262--54719542 Score: 148
Period size: 27 Copynumber: 10.4 Consensus size: 27
54719252 ATCTAAAAAC
*
54719262 CAAGGGTATTTCGATAATTTTGTAAAC
1 CAAGGGTATTTCGATAATTTTGTAAAT
*
54719289 CAATGGTATTTCTG-TAATTTT-TGAAAGT
1 CAAGGGTATTTC-GATAATTTTGT-AAA-T
* *
54719317 CAAGGATATTTTTG-TAATTTTGTAAAT
1 CAAGGGTA-TTTCGATAATTTTGTAAAT
* **
54719344 CAGGGGTATTTCTG-TAATTTACTAAAT
1 CAAGGGTATTTC-GATAATTTTGTAAAT
* * *
54719371 CAATGGTATTT-TAGTAATTTTCTAAAT
1 CAAGGGTATTTCGA-TAATTTTGTAAAT
* * * **
54719398 AAAGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTGTAAAT
* * **
54719425 CGAGGGTATTT-TAGTAA-TTTCCAAAT
1 CAAGGGTATTTCGA-TAATTTTGTAAAT
* * * * ** *
54719451 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGATAATTTTGTAAAT
* * * *
54719478 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTCGATAATTTTGTAAAT
*
54719505 CAAGGGTA-TTC-AGTAATTTTGTAAAC
1 CAAGGGTATTTCGA-TAATTTTGTAAAT
54719531 CAAGGGTATTTC
1 CAAGGGTATTTC
54719543 AGTAATTCTA
Statistics
Matches: 202, Mismatches: 38, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
26 46 0.23
27 134 0.66
28 18 0.09
29 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTCGATAATTTTGTAAAT
Found at i:54719397 original size:54 final size:54
Alignment explanation
Indices: 54719262--54719549 Score: 232
Period size: 53 Copynumber: 5.4 Consensus size: 54
54719252 ATCTAAAAAC
* * * * *
54719262 CAAGGGTA-TTTCGATAATTTTGTAAACCAATGGTATTTCTGTAATTT-TTGAAAGT
1 CAAGGGTATTTTAG-TAATTTTCTAAATCAAGGGTATTTCTGTAATTTACT-AAA-T
* * * *
54719317 CAAGGATATTTTTGTAATTTTGTAAATCAGGGGTATTTCTGTAATTTACTAAAT
1 CAAGGGTATTTTAGTAATTTTCTAAATCAAGGGTATTTCTGTAATTTACTAAAT
* *
54719371 CAATGGTATTTTAGTAATTTTCTAAATAAAGGGTATTT-TGGTAATTTTAC-AAAT
1 CAAGGGTATTTTAGTAATTTTCTAAATCAAGGGTATTTCT-GTAA-TTTACTAAAT
* * * * *
54719425 CGAGGGTATTTTAGTAA-TTTCCAAATTAGGGGTATTT-TGGTAATTTTAC-AAAC
1 CAAGGGTATTTTAGTAATTTTCTAAATCAAGGGTATTTCT-GTAA-TTTACTAAAT
* * * * * ** *
54719478 CAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTA-TTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTCTAAATCAAGGGTATTTCTGTAATTTACTAAAT
*
54719531 CAAGGGTATTTCAGTAATT
1 CAAGGGTATTTTAGTAATT
54719550 CTACCCTACA
Statistics
Matches: 194, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
52 3 0.02
53 73 0.38
54 68 0.35
55 45 0.23
56 5 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (54 bp):
CAAGGGTATTTTAGTAATTTTCTAAATCAAGGGTATTTCTGTAATTTACTAAAT
Found at i:54719521 original size:53 final size:54
Alignment explanation
Indices: 54719238--54719549 Score: 263
Period size: 54 Copynumber: 5.8 Consensus size: 54
54719228 CACCCTACAC
* * * * * *
54719238 GGGTGTTTCGGTAAATCTAAAAACCAAGGGTA-TTTCGATAATTTTGTAAACCAA
1 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAG-TAATTTTGTAAATCAA
* * ** * * * *
54719292 TGGTATTTCTGTAATTTTTGAAAGTCAAGGATATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTCGGTAATTTTACAAA-CCAAGGGTATTTTAGTAATTTTGTAAATCAA
* * * * *
54719347 GGGTATTTCTGTAA-TTTACTAAATCAATGGTATTTTAGTAATTTTCTAAATAAA
1 GGGTATTTCGGTAATTTTAC-AAACCAAGGGTATTTTAGTAATTTTGTAAATCAA
* * * ** * *
54719401 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTAGTAA-TTTCCAAATTAG
1 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCAA
* * * *
54719454 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCAA
* ** *
54719508 GGGTA-TTCAGTAATTTTGTAAACCAAGGGTATTTCAGTAATT
1 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGTAATT
54719550 CTACCCTACA
Statistics
Matches: 209, Mismatches: 44, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
53 76 0.36
54 87 0.42
55 42 0.20
56 4 0.02
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (54 bp):
GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCAA
Found at i:54719641 original size:27 final size:27
Alignment explanation
Indices: 54719531--54719641 Score: 152
Period size: 27 Copynumber: 4.1 Consensus size: 27
54719521 TTTTGTAAAC
*
54719531 CAAGGGTATTTCAGTAATTCTACCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
*
54719558 C-AGGAGCATTTCAGTAATTCTATCCTA
1 CAAGG-GCATTTCAGTAATTCTACCCTA
*
54719585 TAAGGGCATTTCAGTAATTCTACCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
* * *
54719612 CAAGGGTATTTCAGTAATACTAGCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
54719639 CAA
1 CAA
54719642 ATATGAGATC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 3 0.04
27 68 0.92
28 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (27 bp):
CAAGGGCATTTCAGTAATTCTACCCTA
Found at i:54720749 original size:24 final size:24
Alignment explanation
Indices: 54720703--54720749 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54720693 ACATGTTTGG
* *
54720703 TTTCATCATGTGAATATATCAAAA
1 TTTCATCATATGAATATAACAAAA
54720727 TTTCATCA-ATGAATATAGACAAA
1 TTTCATCATATGAATATA-ACAAA
54720750 TCGATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (24 bp):
TTTCATCATATGAATATAACAAAA
Found at i:54723812 original size:40 final size:39
Alignment explanation
Indices: 54723763--54723858 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
54723753 CTAACTCGGT
54723763 ATCGCACACTTAGTGCCTCA-TATAGCCAAAGCTATTCCA
1 ATCGCACACTTAGTGCCT-ATTATAGCCAAAGCTATTCCA
* **
54723802 ATTCGCACACTTAGTG-CTATTTATAGCCGAAGCTATTTGA
1 A-TCGCACACTTAGTGCCTA-TTATAGCCAAAGCTATTCCA
54723842 ATCGCACACTTAGTGCC
1 ATCGCACACTTAGTGCC
54723859 GAACATAGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.02
39 17 0.34
40 32 0.64
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (39 bp):
ATCGCACACTTAGTGCCTATTATAGCCAAAGCTATTCCA
Found at i:54728444 original size:20 final size:20
Alignment explanation
Indices: 54728419--54728465 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
54728409 CTAGCACATG
* *
54728419 TTTTCATAAAATTTTAGAAT
1 TTTTCATAAAATTTTACAAC
*
54728439 TTTTCATCAAATTTTACAAC
1 TTTTCATAAAATTTTACAAC
54728459 TTTTCAT
1 TTTTCAT
54728466 TTTACTCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTCATAAAATTTTACAAC
Found at i:54730890 original size:41 final size:40
Alignment explanation
Indices: 54730835--54730946 Score: 111
Period size: 41 Copynumber: 2.8 Consensus size: 40
54730825 ATATTGAGCT
* *
54730835 TTTAGTGGCG-TTTTTTTAAAAACGCCGCTAAAGATTGAG
1 TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAAAGATTGAG
* * * * ** *
54730874 TATTAGCGGCGCTTTTTAAAAAAATGCTGCTATAGATACACC
1 T-TTAGCGGCGCTTTTTTAAAAAACGCCGCTAAAGATTGA-G
54730916 TTTAGCGGCGC-TTTTTAAAAAACGCCGCTAA
1 TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAA
54730947 TACTCGATCT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.02
40 24 0.42
41 31 0.54
42 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (40 bp):
TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAAAGATTGAG
Found at i:54731275 original size:21 final size:22
Alignment explanation
Indices: 54731249--54731290 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54731239 TTTATGGATT
54731249 AGTTTAAGGGTT-GGGGTTTAA
1 AGTTTAAGGGTTAGGGGTTTAA
*
54731270 AGTTTAGGGGTTAGGGGTTTA
1 AGTTTAAGGGTTAGGGGTTTA
54731291 GTGTAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (22 bp):
AGTTTAAGGGTTAGGGGTTTAA
Found at i:54732962 original size:40 final size:40
Alignment explanation
Indices: 54732905--54733086 Score: 161
Period size: 40 Copynumber: 4.5 Consensus size: 40
54732895 GCTCGATTGT
* * * * * *
54732905 CTTCGGGACCTAGCCCGGTTATAGTGATTCGTACGATTGC
1 CTTCGGGTCTTAGCCCGGATATAGTAATTCGCACGAATGC
* * * *
54732945 CTTCGGGTCTTAACCCGGATTTGGTAACTT-GCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTAA-TTCGCACGAATGC
** *
54732985 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTAATTCGCACGAATGC
* * * * *
54733025 CTTCGGGTCTTAGCCCGGATATAATTACTAGCA-TAATTGC
1 CTTCGGGTCTTAGCCCGGATATAGTAATTCGCACGAA-TGC
*
54733065 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
54733087 CATTCCAATG
Statistics
Matches: 117, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.03
40 112 0.96
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.29
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTAATTCGCACGAATGC
Found at i:54732999 original size:80 final size:80
Alignment explanation
Indices: 54732905--54733086 Score: 211
Period size: 80 Copynumber: 2.3 Consensus size: 80
54732895 GCTCGATTGT
* * *** * * * * **
54732905 CTTCGGGACCTAGCCCGGTTATAGTGATTCGTACGATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
*
54732970 AACTTGCACAAATGC
66 AACTAGCACAAATGC
* *
54732985 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
* * *
54733050 TACTAGCATAATTGC
66 AACTAGCACAAATGC
54733065 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
54733087 CATTCCAATG
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.29
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
AACTAGCACAAATGC
Found at i:54738778 original size:10 final size:10
Alignment explanation
Indices: 54738765--54738790 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54738755 TTTTCATGAC
54738765 TTTTATAATA
1 TTTTATAATA
54738775 TTTTATAATA
1 TTTTATAATA
54738785 TTTTAT
1 TTTTAT
54738791 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATAATA
Found at i:54744247 original size:36 final size:36
Alignment explanation
Indices: 54744200--54744271 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
54744190 TCAGCAAAGA
54744200 AACTCCCATGCTAATAAGGGATTTTTAATGTCTTTC
1 AACTCCCATGCTAATAAGGGATTTTTAATGTCTTTC
* *
54744236 AACTCCCATGCTAGTAAGTGATTTTTAATGTCTTTC
1 AACTCCCATGCTAATAAGGGATTTTTAATGTCTTTC
54744272 TTGATGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
AACTCCCATGCTAATAAGGGATTTTTAATGTCTTTC
Found at i:54746577 original size:46 final size:46
Alignment explanation
Indices: 54746510--54746773 Score: 222
Period size: 46 Copynumber: 5.7 Consensus size: 46
54746500 TGTAACCCGC
*
54746510 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGGTGT-TCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGTGTATCGCAT
* * **
54746556 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG-TG--TA-TCGCAT
* * * *
54746606 -C-TCA-CGATCTCGGACTCAACTCAACGAGTTTGAATGT-TCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG-GTGTATCGCAT
* * * **
54746649 CCATAAGTGAACTCGAACTCAACTCAATGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG-TG--TA-TCGCAT
*
54746699 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGG-GTATCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGTGTATCGCAT
* *
54746741 CCATAAGTGAACTCAGACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
54746774 TGGATGCCCA
Statistics
Matches: 170, Mismatches: 31, Indels: 35
0.72 0.13 0.15
Matches are distributed among these distances:
42 4 0.02
43 7 0.04
44 3 0.02
45 30 0.18
46 58 0.34
47 52 0.31
48 6 0.04
49 2 0.01
50 8 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGTGTATCGCAT
Found at i:54746629 original size:47 final size:47
Alignment explanation
Indices: 54746564--54746731 Score: 191
Period size: 47 Copynumber: 3.6 Consensus size: 47
54746554 ATCCATAAGT
*
54746564 GAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * ** * *
54746611 GATCTCGGACTCAACTCAACGAGTTTGAATG--T--TCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
* *
54746657 GAACTCGAACTCAACTCAATGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
54746704 GAACTCGGACTCAACTCAACGAGTTCGG
1 GAACTCGGACTCAACTCAACGAGTTCGG
54746732 GTATCGCATC
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 3 0.03
46 26 0.27
47 53 0.56
48 3 0.03
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54746633 original size:93 final size:91
Alignment explanation
Indices: 54746517--54746781 Score: 397
Period size: 93 Copynumber: 2.9 Consensus size: 91
54746507 CGCCCATAAG
54746517 CGAACTCGGACTCAACTCAACGAGCTCAGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAG-TC-GGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54746582 ACAAGTTCGGATGCCTAGTTACATCTCA
64 ACGAGTTCGGATGCCTAGTTACATCTCA
* * * *
54746610 CGATCTCGGACTCAACTCAACGAGTTTGAATGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAG-TCG-GTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54746675 ATGAGTTCGGATGCCTAGTTACATCTCA
64 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54746703 CGAACTCGGACTCAACTCAACGAGTTCGG-GTATCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAG-TCGGTGT-TCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54746767 ACGAGTTTGGATGCC
64 ACGAGTTCGGATGCC
54746782 CAAATATCCT
Statistics
Matches: 156, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
91 2 0.01
92 44 0.28
93 110 0.71
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGTCGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:54755342 original size:46 final size:46
Alignment explanation
Indices: 54755292--54755510 Score: 273
Period size: 46 Copynumber: 4.7 Consensus size: 46
54755282 TTGGGCATCT
*
54755292 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
54755338 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
* ** * *
54755384 GAACTCGTTGAGTTGAGTCCGAGTT---TGAAAGATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG--TCC
* * * *
54755431 GAGCTCGTTGAGTTGAGCCCGAGTTCACTTATGGATGCGAATGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
* *
54755477 GAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54755511 GCGGGTTACA
Statistics
Matches: 149, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
43 8 0.05
45 2 0.01
46 104 0.70
47 26 0.17
48 2 0.01
50 7 0.05
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
Found at i:54758897 original size:40 final size:40
Alignment explanation
Indices: 54758838--54759045 Score: 200
Period size: 40 Copynumber: 5.2 Consensus size: 40
54758828 CAATTGAATG
* * * *
54758838 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * ** *
54758878 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
54758918 ACATCCGGGCTAAGACCTGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
54758958 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
54758998 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
54759038 ATATCCGG
1 ATATCCGG
54759046 TTGTATTCCG
Statistics
Matches: 138, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:54758981 original size:80 final size:80
Alignment explanation
Indices: 54758839--54759045 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
54758829 AATTGAATGA
* * ** * ** * *
54758839 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAATCCGGGCTAAGACCCGAAGGCAA
*
54758904 TTGTGCTAG-CG-AC
66 TTGTGCAAGTCGTAC
* * *
54758917 TACATCCGGGCTAAGACCTGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAATCCGGGCTAAGACCCGAAGGC
* *
54758982 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
54758999 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAATCCGG
54759046 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
80 102 0.95
81 2 0.02
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:54763312 original size:48 final size:48
Alignment explanation
Indices: 54763157--54763495 Score: 301
Period size: 48 Copynumber: 7.1 Consensus size: 48
54763147 ATTAGGGTTG
54763157 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
* * * * * *
54763205 TATGAGA-CATCGTGTAAGACCATAGT-TGGG-C-T---ATCGGCTTCGA
1 TATGTGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCAA
*
54763248 TATGCATGATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCAA
1 TATG--TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
* *
54763298 AATGTGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCAA
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
* * * * * *
54763346 TATGAGA-CATCGTGTAAGACCATAGT-TGGG-C-T---ATCGGCTTCGA
1 TATGTGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCAA
* *
54763389 TATGCATGATCCCATGTAAGACCATGTCTGGGACATAGCATTGGCATCGA
1 TATG--TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
** * *
54763439 TATGTGATCCCATGTAAGACCATACCTGGGATATAGCATTGGCATTCAA
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-TCAA
54763488 CTATGTGA
1 -TATGTGA
54763496 ATGTGATTTC
Statistics
Matches: 234, Mismatches: 33, Indels: 46
0.75 0.11 0.15
Matches are distributed among these distances:
43 24 0.10
44 4 0.02
45 36 0.15
46 6 0.03
47 6 0.03
48 121 0.52
49 7 0.03
50 30 0.13
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (48 bp):
TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAA
Found at i:54763478 original size:141 final size:141
Alignment explanation
Indices: 54763157--54763492 Score: 573
Period size: 141 Copynumber: 2.4 Consensus size: 141
54763147 ATTAGGGTTG
54763157 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGAGACATCGTGTAA
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGAGACATCGTGTAA
*
54763222 GACCATAGTTGGGCTATCGGCTTCGATATGCATGATCCCATGTAAGACCATGTCTGGGACATGGC
66 GACCATAGTTGGGCTATCGGCTTCGATATGCATGATCCCATGTAAGACCATGTCTGGGACATAGC
54763287 ATTAGCATCAA
131 ATTAGCATCAA
* *
54763298 AATGTGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCGTGTAA
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGAGACATCGTGTAA
54763363 GACCATAGTTGGGCTATCGGCTTCGATATGCATGATCCCATGTAAGACCATGTCTGGGACATAGC
66 GACCATAGTTGGGCTATCGGCTTCGATATGCATGATCCCATGTAAGACCATGTCTGGGACATAGC
* *
54763428 ATTGGCATCGA
131 ATTAGCATCAA
** * *
54763439 TATGTGATCCCATGTAAGACCATACCTGGGATATAGCATTGGCATTCAACTATG
1 TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-TCAA-TATG
54763493 TGAATGTGAT
Statistics
Matches: 182, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
141 174 0.96
142 4 0.02
143 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (141 bp):
TATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGAGACATCGTGTAA
GACCATAGTTGGGCTATCGGCTTCGATATGCATGATCCCATGTAAGACCATGTCTGGGACATAGC
ATTAGCATCAA
Found at i:54767185 original size:40 final size:40
Alignment explanation
Indices: 54767122--54767348 Score: 379
Period size: 40 Copynumber: 5.7 Consensus size: 40
54767112 ACTACTTGCT
54767122 CAAATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
54767161 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
54767201 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
54767241 CAAATGCCTTCGGGACTTAGCCC-GATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
54767280 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
54767320 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
54767349 CATCCGAATA
Statistics
Matches: 179, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
39 51 0.28
40 127 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:54767280 original size:79 final size:79
Alignment explanation
Indices: 54767122--54767343 Score: 376
Period size: 79 Copynumber: 2.8 Consensus size: 79
54767112 ACTACTTGCT
*
54767122 CAAATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-G
*
54767186 TTATAGTAACTCGCA
65 ATATAGTAACTCGCA
54767201 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
54767266 TATAGTAACTCGCA
66 TATAGTAACTCGCA
* *
54767280 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
54767344 GTTATCATCC
Statistics
Matches: 137, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
78 1 0.01
79 86 0.63
80 50 0.36
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
TATAGTAACTCGCA
Found at i:54767321 original size:119 final size:119
Alignment explanation
Indices: 54767122--54767344 Score: 378
Period size: 119 Copynumber: 1.9 Consensus size: 119
54767112 ACTACTTGCT
* *
54767122 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGT
1 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
54767187 TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
66 TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
54767241 CAAATGCCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
54767305 A-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
65 ATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
54767345 TTATCATCCG
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
118 1 0.01
119 86 0.88
120 11 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (119 bp):
CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54775221 original size:40 final size:40
Alignment explanation
Indices: 54775168--54775352 Score: 318
Period size: 40 Copynumber: 4.6 Consensus size: 40
54775158 ACTACTTGCT
*
54775168 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54775208 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
54775248 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54775288 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
54775328 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54775353 TTATCATCCG
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
39 1 0.01
40 138 0.99
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54778562 original size:28 final size:27
Alignment explanation
Indices: 54778519--54778586 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
54778509 CAAAATGATG
*
54778519 TAAAATTTGGTTTTTGATATTATAATA
1 TAAAATTTGGTCTTTGATATTATAATA
54778546 TAAAATATTGGTCTTTGATATTATAAGATA
1 TAAAAT-TTGGTCTTTGATATTAT-A-ATA
*
54778576 CAAAATTTGGT
1 TAAAATTTGGT
54778587 TTTTAGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 6 0.17
28 16 0.44
29 6 0.17
30 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (27 bp):
TAAAATTTGGTCTTTGATATTATAATA
Found at i:54778823 original size:16 final size:17
Alignment explanation
Indices: 54778789--54778833 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
54778779 TTTAATGATT
*
54778789 TTTATAATTATTTACAA
1 TTTATAATTATTTAAAA
*
54778806 TTTATGATT-TTTAAAA
1 TTTATAATTATTTAAAA
54778822 TTT-TAATTATTT
1 TTTATAATTATTT
54778834 TTAATATTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 12 0.50
17 8 0.33
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATAATTATTTAAAA
Found at i:54779704 original size:12 final size:12
Alignment explanation
Indices: 54779659--54779717 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
54779649 AATTTGTGTA
*
54779659 TTGTTTTAATAA
1 TTGTTTTAATAT
*
54779671 TTGTTTTAGTA-
1 TTGTTTTAATAT
*
54779682 TTATTTT--TAT
1 TTGTTTTAATAT
54779692 TTGTTTTAATAT
1 TTGTTTTAATAT
* *
54779704 TTATTTTTATAT
1 TTGTTTTAATAT
54779716 TT
1 TT
54779718 TTAAATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 6 0.15
12 25 0.64
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:54779710 original size:22 final size:22
Alignment explanation
Indices: 54779671--54779729 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
54779661 GTTTTAATAA
*
54779671 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
54779692 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
54779714 AT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
54779730 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:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:54779727 original size:24 final size:25
Alignment explanation
Indices: 54779700--54779759 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
54779690 ATTTGTTTTA
54779700 ATATTTATTT-TTATATTTTTAAAT
1 ATATTTATTTATTATATTTTTAAAT
54779724 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTTATTATATTTTTAAAT
*
54779750 -TTTTTATTTA
1 ATATTTATTTA
54779760 ATGAAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 11 0.33
25 8 0.24
26 14 0.42
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATATTTATTTATTATATTTTTAAAT
Found at i:54785693 original size:16 final size:16
Alignment explanation
Indices: 54785655--54785712 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
54785645 ACGTTTGGTT
54785655 AGCTGTAATAGAATAG
1 AGCTGTAATAGAATAG
* *
54785671 -GATTGTAATTGAATAG
1 AG-CTGTAATAGAATAG
*
54785687 AGCTGTAATGGAATAG
1 AGCTGTAATAGAATAG
54785703 AGCTGTAATA
1 AGCTGTAATA
54785713 AGTAATTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 33 0.94
17 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (16 bp):
AGCTGTAATAGAATAG
Found at i:54785748 original size:46 final size:44
Alignment explanation
Indices: 54785693--54785786 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
54785683 ATAGAGCTGT
* *
54785693 AATGGAATAGAGCTGTAATAAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTC-ATGTGTTTGGTTGAATGA
* *
54785739 AATGGAATAGAATTGTAATAGTATTCCTGTGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGA
54785783 AATG
1 AATG
54785787 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 3 0.07
46 17 0.40
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGA
Found at i:54785914 original size:14 final size:14
Alignment explanation
Indices: 54785878--54785918 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
54785868 GTTATTAAAT
*
54785878 TTTAAT-AAAATTA
1 TTTAATAAAAATAA
*
54785891 -TTATTAAAAATAA
1 TTTAATAAAAATAA
54785904 TTTAATAAAAATAA
1 TTTAATAAAAATAA
54785918 T
1 T
54785919 AAATAGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAAAAATAA
Found at i:54785973 original size:16 final size:16
Alignment explanation
Indices: 54785954--54785985 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54785944 AATTATTATT
54785954 AAATATAATTTAATAA
1 AAATATAATTTAATAA
54785970 AAATATAATTTAATAA
1 AAATATAATTTAATAA
54785986 CATTCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:54785984 original size:26 final size:26
Alignment explanation
Indices: 54785878--54785984 Score: 70
Period size: 26 Copynumber: 3.9 Consensus size: 26
54785868 GTTATTAAAT
* * *
54785878 TTTAATAAAATTATTATTAAAAATAA
1 TTTAATAAAAATATAATTAAATATAA
* *
54785904 TTTAATAAAAATAATAAATAGTTTAACTATAT
1 TTTAATAAAAAT-AT--A-A--TTAAATATAA
* * * *
54785936 TTTAACATAATTATTATTAAATATAA
1 TTTAATAAAAATATAATTAAATATAA
*
54785962 TTTAATAAAAATATAATTTAATA
1 TTTAATAAAAATATAATTAAATA
54785985 ACATTCTTAA
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
26 37 0.63
27 2 0.03
28 1 0.02
30 1 0.02
31 2 0.03
32 16 0.27
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (26 bp):
TTTAATAAAAATATAATTAAATATAA
Found at i:54790250 original size:2 final size:2
Alignment explanation
Indices: 54790196--54790231 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54790186 GATTAACTCT
54790196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54790232 AAGCTACTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54793280 original size:16 final size:16
Alignment explanation
Indices: 54793250--54793311 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
54793240 TAGGTAAAAG
* *
54793250 AATAGAGCTGCAATGA
1 AATAAAGCTGTAATGA
54793266 AAT-AAGACTGTAATGA
1 AATAAAG-CTGTAATGA
*
54793282 AATAAAGCTGTAATGG
1 AATAAAGCTGTAATGA
**
54793298 AATTGAGCTGTAAT
1 AATAAAGCTGTAAT
54793312 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 34 0.87
17 3 0.08
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (16 bp):
AATAAAGCTGTAATGA
Found at i:54793553 original size:35 final size:36
Alignment explanation
Indices: 54793514--54793584 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 36
54793504 AAAATAAAAA
54793514 TAAAT-AATTTAAT-CATACTTTAATATAATTATTAT
1 TAAATAAATTTAATACATAC-TTAATATAATTATTAT
*
54793549 TAAATACAATTTAATAACATTCTTAATATAATTATT
1 TAAATA-AATTTAAT-ACATACTTAATATAATTATT
54793585 TTTATATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 5 0.16
37 8 0.26
38 14 0.45
39 4 0.13
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (36 bp):
TAAATAAATTTAATACATACTTAATATAATTATTAT
Found at i:54797729 original size:22 final size:21
Alignment explanation
Indices: 54797699--54797764 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
54797689 TACAAATTAA
54797699 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
54797721 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
54797742 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
54797761 ATCT
1 ATCT
54797765 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:54797751 original size:19 final size:19
Alignment explanation
Indices: 54797716--54797813 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
54797706 AGATTACAAG
54797716 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
54797737 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54797756 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
54797773 ATCATATCTAAGGTTGCAT
1 ATCATATCTAAGATTGCAT
*
54797792 ATCATATCTAAGATTACAT
1 ATCATATCTAAGATTGCAT
54797811 ATC
1 ATC
54797814 CTTAAAGATT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.22
19 47 0.65
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:54797780 original size:36 final size:37
Alignment explanation
Indices: 54797716--54797806 Score: 139
Period size: 36 Copynumber: 2.4 Consensus size: 37
54797706 AGATTACAAG
54797716 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
*
54797756 ATCATATCTAAGATTG-TATCATATCTAAGGTTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
54797792 ATCATATCTAAGATT
1 ATCATATCTAAGATT
54797807 ACATATCCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 34 0.68
38 7 0.14
39 1 0.02
40 8 0.16
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:54799839 original size:24 final size:24
Alignment explanation
Indices: 54799811--54799863 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
54799801 GTTATAGGTC
* * *
54799811 AAATAAACTATGCTAATTAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54799835 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54799859 AAATA
1 AAATA
54799864 TTCTAGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54802478 original size:79 final size:81
Alignment explanation
Indices: 54802364--54802546 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
54802354 TACTCGTTCA
* *
54802364 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAAACCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAAACCGG
* *
54802427 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
54802444 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAAACCGGA
* *
54802507 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
54802523 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
54802547 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAAACCGGA
TATAGTAACTTAGCAC
Found at i:54802546 original size:40 final size:40
Alignment explanation
Indices: 54802343--54802546 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
54802333 CGGAATTTAA
** *
54802343 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* **
54802383 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAA
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54802423 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54802462 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54802502 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54802542 CCGGA
1 CCGGA
54802547 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54818698 original size:24 final size:24
Alignment explanation
Indices: 54818671--54818733 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
54818661 ATAAACAATG
54818671 CTAATAAATGCTAAATTTATTATA
1 CTAATAAATGCTAAATTTATTATA
54818695 CTAATAAATGCTAAATTTATTATA
1 CTAATAAATGCTAAATTTATTATA
*
54818719 CTAATAAATACTAAA
1 CTAATAAATGCTAAA
54818734 CCTTCTAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCTAAATTTATTATA
Found at i:54820534 original size:2 final size:2
Alignment explanation
Indices: 54820527--54820553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54820517 TAGCTTTGGC
54820527 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
54820554 GGCACTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54820622 original size:41 final size:42
Alignment explanation
Indices: 54820577--54820655 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
54820567 CAAGACTGAG
* *
54820577 ATAGCTTCGGTTATG-AAAGGCACTTAGTGTGCGAGATTATA
1 ATAGCTTCGATTATGCAAAGGCACTTAATGTGCGAGATTATA
** *
54820618 ATAGCTTCGATTATGCTTAGGCACTTAATGTGCTAGAT
1 ATAGCTTCGATTATGCAAAGGCACTTAATGTGCGAGAT
54820656 ATCAAGTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
ATAGCTTCGATTATGCAAAGGCACTTAATGTGCGAGATTATA
Found at i:54822441 original size:39 final size:39
Alignment explanation
Indices: 54822397--54822517 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
54822387 AATTATGTTA
* *
54822397 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACTTTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
54822436 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
54822475 CCAGCACGAAGCCTGCGGGTCTTTAGCTCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
54822514 CCAG
1 CCAG
54822518 TGTCTTGCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:54827001 original size:46 final size:46
Alignment explanation
Indices: 54826940--54827117 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
54826930 GATATTTGGG
*
54826940 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *** * * * *
54826986 TATCCGAACTTGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-A
* *
54827033 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
54827079 CA-CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54827118 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
45 3 0.03
46 67 0.64
47 34 0.33
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:54827097 original size:93 final size:93
Alignment explanation
Indices: 54826938--54827109 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
54826928 AGGATATTTG
* * *
54826938 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTTGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATCCCAACTCGTTGAG
54827003 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
54827031 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACA-CCCAAGCTCGTTGA
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATCCCAA-CTCGTTGA
54827095 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
54827110 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 70 0.95
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATCCCAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:54831945 original size:40 final size:40
Alignment explanation
Indices: 54831890--54832172 Score: 349
Period size: 40 Copynumber: 7.1 Consensus size: 40
54831880 TGAATGATAC
* * * * **
54831890 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * *
54831930 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
54831970 CCGGGCTAA-TCCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
54832009 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
54832049 CCGGGCTAATACCCGAAGGCATTTGCGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
54832089 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
54832129 CCGGGCTAAGACCCGAGGGCATTCGTGC--GTGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-TG-TTATAT
54832169 CCGG
1 CCGG
54832173 TTGTATTCCG
Statistics
Matches: 217, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.01
39 33 0.15
40 182 0.84
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:54834183 original size:40 final size:40
Alignment explanation
Indices: 54834071--54834223 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
54834061 GGATATAGCG
* * * * ***
54834071 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
54834111 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
54834151 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
54834191 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
54834224 CATCATTCGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 78 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:54842266 original size:49 final size:49
Alignment explanation
Indices: 54842206--54842541 Score: 613
Period size: 49 Copynumber: 6.9 Consensus size: 49
54842196 GTATGAGATA
*
54842206 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54842255 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54842304 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54842353 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54842402 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54842451 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54842498 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
54842542 TATATGTGTG
Statistics
Matches: 280, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
47 45 0.16
49 235 0.84
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:54842682 original size:37 final size:37
Alignment explanation
Indices: 54842628--54842718 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
54842618 AACTTGGAAA
* *
54842628 TATGTTCCGGGTGAGACCTGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
54842666 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
54842703 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
54842719 TTCGTAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 47 0.92
38 4 0.08
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:54844594 original size:40 final size:40
Alignment explanation
Indices: 54844539--54844810 Score: 490
Period size: 40 Copynumber: 6.8 Consensus size: 40
54844529 GAGAATTGAG
*
54844539 AGTGATGTATCCGGACTAAGTTCCGAGGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
54844579 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
54844619 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
54844659 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* *
54844699 AGTGATGTATCCGGACTAAGTTTCGAGGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
54844739 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
54844779 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCA
54844811 ATCATGCTGG
Statistics
Matches: 224, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 224 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:54846011 original size:82 final size:82
Alignment explanation
Indices: 54845862--54846031 Score: 315
Period size: 81 Copynumber: 2.1 Consensus size: 82
54845852 GCCCTTTTTG
54845862 CATACATAGCACAAAGTGTGATCATGATTAACCATCCAATGGCTAATCGTTTCAAAACAATTCCA
1 CATACATAGCACAAAGTGTGATCATGATTAACCATCCAATGGCTAATCGTTTCAAAACAATTCCA
54845927 TA-CCCATAATGATCAA
66 TACCCCATAATGATCAA
*
54845943 CATACATAGGACAAAGTGTGATCATGATTAACCATTCCAATGGCTAATCGTTTCAAAACAATTCC
1 CATACATAGCACAAAGTGTGATCATGATTAACCA-TCCAATGGCTAATCGTTTCAAAACAATTCC
54846008 ATACCCCATAATGATCAA
65 ATACCCCATAATGATCAA
54846026 CATACA
1 CATACA
54846032 AACATTATAG
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
81 33 0.38
82 33 0.38
83 20 0.23
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (82 bp):
CATACATAGCACAAAGTGTGATCATGATTAACCATCCAATGGCTAATCGTTTCAAAACAATTCCA
TACCCCATAATGATCAA
Found at i:54846741 original size:39 final size:39
Alignment explanation
Indices: 54846610--54846800 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
54846600 GGATATAACG
* ** **
54846610 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
54846650 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
54846690 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
54846728 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
54846768 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
54846801 CATCATTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:54846745 original size:78 final size:80
Alignment explanation
Indices: 54846650--54846800 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
54846640 GGTTATAGCG
* * * *
54846650 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
54846712 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
54846728 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
54846793 AGCCCGGA
66 AGCCCGGA
54846801 CATCATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:54851921 original size:49 final size:49
Alignment explanation
Indices: 54851861--54852100 Score: 453
Period size: 49 Copynumber: 4.9 Consensus size: 49
54851851 GTATGAGATA
*
54851861 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54851910 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54851959 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54852008 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54852057 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
54852101 TATATGTGTG
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 187 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:54855918 original size:40 final size:40
Alignment explanation
Indices: 54855806--54855958 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
54855796 GGATATAGCG
* * * * ***
54855806 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
54855846 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
54855886 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
54855926 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
54855959 CATCATTCGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 78 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:54856673 original size:2 final size:2
Alignment explanation
Indices: 54856666--54856691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54856656 ATGTGCAAAC
54856666 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54856692 GCTAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54874029 original size:28 final size:27
Alignment explanation
Indices: 54873966--54874035 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54873956 ATAGTGAGTC
*
54873966 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54873993 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54874021 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54874036 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54877103 original size:39 final size:39
Alignment explanation
Indices: 54877049--54877127 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
54877039 ATAGTTCGGG
*
54877049 ACTAAACTAAACTTTAAAATTTTTTGGGAAAACTTAGAA
1 ACTAAACTAAACTTTAAAAATTTTTGGGAAAACTTAGAA
*
54877088 ACTAAACTGAACTTTAAAAATTTTTGGGAAAACTTAGAA
1 ACTAAACTAAACTTTAAAAATTTTTGGGAAAACTTAGAA
54877127 A
1 A
54877128 ATTATCATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (39 bp):
ACTAAACTAAACTTTAAAAATTTTTGGGAAAACTTAGAA
Found at i:54879893 original size:46 final size:44
Alignment explanation
Indices: 54879789--54879896 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
54879779 TGTCTTTGAC
** * * *
54879789 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
54879833 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
54879879 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
54879897 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:54886602 original size:28 final size:28
Alignment explanation
Indices: 54886570--54886624 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
54886560 TGAAAAATGC
*
54886570 ATAAAAACCAAAATAAACACAAATAAAT
1 ATAAAAACAAAAATAAACACAAATAAAT
*
54886598 ATAAAAACAAAAATAAACACACATAAA
1 ATAAAAACAAAAATAAACACAAATAAA
54886625 ACTTATGTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.13
Consensus pattern (28 bp):
ATAAAAACAAAAATAAACACAAATAAAT
Found at i:54889792 original size:2 final size:2
Alignment explanation
Indices: 54889785--54889813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54889775 TTGATAGAAA
54889785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54889814 GTGGTTCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54889882 original size:29 final size:29
Alignment explanation
Indices: 54889843--54889922 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
54889833 CTTAATAATC
*
54889843 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
54889873 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
54889902 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
54889923 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:54897792 original size:29 final size:29
Alignment explanation
Indices: 54897753--54897832 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
54897743 CTTAATAATC
*
54897753 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
54897783 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
54897812 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
54897833 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:54903474 original size:72 final size:72
Alignment explanation
Indices: 54903389--54903537 Score: 280
Period size: 72 Copynumber: 2.1 Consensus size: 72
54903379 ATGTGTTTGT
*
54903389 GGATTAAATTGAATGAATTGGTGATTAAATGGGTTAATTTTGAATACATATAGATCAAGAAAGAG
1 GGATTAAATTGAATGAATTGGTGATTAAATGGGTTAATTTTGAATACATATAGATCAAGAAAGAA
54903454 AGAATTA
66 AGAATTA
*
54903461 GGATTCAATTGAATGAATTGGTGATTAAATGGGTTAATTTTGAATACATATAGATCAAGAAAGAA
1 GGATTAAATTGAATGAATTGGTGATTAAATGGGTTAATTTTGAATACATATAGATCAAGAAAGAA
54903526 AGAATTA
66 AGAATTA
54903533 GGATT
1 GGATT
54903538 TAGAACGAGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.32
Consensus pattern (72 bp):
GGATTAAATTGAATGAATTGGTGATTAAATGGGTTAATTTTGAATACATATAGATCAAGAAAGAA
AGAATTA
Found at i:54903776 original size:40 final size:40
Alignment explanation
Indices: 54903712--54903787 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
54903702 ATGATGTTTG
* *
54903712 GCACTTAGTGTGCATTTGGAAATAGCTTCAGCTATAAATA
1 GCACTTAGTGTGCAATTGGAAATAGCGTCAGCTATAAATA
*
54903752 GCACTTAGTGTGCGAATTGG-AATAGCGTCGGCTATA
1 GCACTTAGTGTGC-AATTGGAAATAGCGTCAGCTATA
54903788 TGAGGCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 27 0.84
41 5 0.16
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (40 bp):
GCACTTAGTGTGCAATTGGAAATAGCGTCAGCTATAAATA
Found at i:54903796 original size:40 final size:40
Alignment explanation
Indices: 54903711--54903796 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
54903701 TATGATGTTT
* *
54903711 GGCACTTAGTGTGCATTTGGAAATAGCTTCAGCTATAAATA
1 GGCACTTAGTGTGCAATTGGAAATAGCGTCAGCTAT-AATA
*
54903752 -GCACTTAGTGTGCGAATTGG-AATAGCGTCGGCTAT-ATGA
1 GGCACTTAGTGTGC-AATTGGAAATAGCGTCAGCTATAAT-A
54903791 GGCACT
1 GGCACT
54903797 AAGTTTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 2 0.05
39 1 0.03
40 31 0.79
41 5 0.13
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (40 bp):
GGCACTTAGTGTGCAATTGGAAATAGCGTCAGCTATAATA
Found at i:54909347 original size:15 final size:16
Alignment explanation
Indices: 54909327--54909364 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
54909317 TAATTAATGA
54909327 TATATAAATAT-AATT
1 TATATAAATATGAATT
54909342 TATAT-AATATGAATT
1 TATATAAATATGAATT
54909357 TATGATAA
1 TAT-ATAA
54909365 TTAAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 12 0.60
16 2 0.10
17 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TATATAAATATGAATT
Found at i:54909373 original size:29 final size:28
Alignment explanation
Indices: 54909307--54909374 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
54909297 TTTATTTGTT
54909307 TTAAATTATATAATTAATGATATATAAA
1 TTAAATTATATAATTAATGATATATAAA
* *
54909335 TATAATTTATATAA-T-ATGAATTTATGATAA
1 T-TAAATTATATAATTAATG-ATATAT-A-AA
54909365 TTAAATTATA
1 TTAAATTATA
54909375 ATGATATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.09
28 7 0.21
29 20 0.61
30 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
TTAAATTATATAATTAATGATATATAAA
Found at i:54914591 original size:93 final size:93
Alignment explanation
Indices: 54914431--54914601 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
54914421 GGGATATTTG
* * *
54914431 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCCGAACTCGTTGAG
54914496 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* * *
54914524 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTTACCTATGGATGCAAACG-CCTGAGCTCGTTTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCC-GAACTCGTTGA
*
54914588 GTTGAGTCTGAGTT
65 GTTGAGTCCGAGTT
54914602 TGCTTATGGG
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:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:54921475 original size:13 final size:13
Alignment explanation
Indices: 54921459--54921483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54921449 AAAGATAATT
54921459 ATTAAATTATATA
1 ATTAAATTATATA
54921472 ATTAAATTATAT
1 ATTAAATTATAT
54921484 GATTTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAAATTATATA
Found at i:54921736 original size:11 final size:11
Alignment explanation
Indices: 54921722--54921747 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54921712 GAAAAACAGA
54921722 GGAAGAAAAGG
1 GGAAGAAAAGG
54921733 GGAAGAAAAGG
1 GGAAGAAAAGG
54921744 GGAA
1 GGAA
54921748 ATTTGAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (11 bp):
GGAAGAAAAGG
Found at i:54922706 original size:24 final size:22
Alignment explanation
Indices: 54922683--54922725 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
54922673 TTTATAATAT
*
54922683 TTCGGGTGTGTTTGGGCTGGATA
1 TTCGAGTGTGTTTGGG-TGGATA
*
54922706 TTCTAGTGTGTTTGGGTGGA
1 TTCGAGTGTGTTTGGGTGGA
54922726 ATCCGTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.09, C:0.07, G:0.42, T:0.42
Consensus pattern (22 bp):
TTCGAGTGTGTTTGGGTGGATA
Found at i:54926291 original size:25 final size:26
Alignment explanation
Indices: 54926247--54926304 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
54926237 TGAAGTTCTC
* *
54926247 AAGAAAATAGAAAAGCAAAGAGAGAA
1 AAGAAAAGAGAAAAGCAAAGAAAGAA
54926273 TAAGAAAAGA-AAAAG-AAAGAAAGAA
1 -AAGAAAAGAGAAAAGCAAAGAAAGAA
54926298 AAGAAAA
1 AAGAAAA
54926305 CTTCCTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.24
25 9 0.31
26 5 0.17
27 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.03
Consensus pattern (26 bp):
AAGAAAAGAGAAAAGCAAAGAAAGAA
Found at i:54929923 original size:130 final size:130
Alignment explanation
Indices: 54929731--54930016 Score: 347
Period size: 130 Copynumber: 2.2 Consensus size: 130
54929721 CCGAGCATTA
* * ** *
54929731 CCTTCGTTTTAAAGGATTTTTAGAAGACCTGAGCGAAGTTTTGAAGGGATATTTGATTATTTTAA
1 CCTTCGTTTTAAA-GA-TTTTAAAAGACATGAGCGAAAATTTGAAGGGATACTTGATTATTTTAA
* * *
54929796 ACAAATGGGAAATTGCAACCCAACACGTTAAGGCACGATTCCACGAATTGCCAAATATCGCATAT
64 ACAAATGCGAAATTGCAACCCAACACGTTAAGGCACGATTCCACGAATTGCCAAATATAGAATAT
*
54929861 TG
129 CG
* * * * *
54929863 CCTTCGTTTTAAAGATTTTAAAAGATATGAGTGAAAATTTGAAGTGATACTTGATTATTTTGAGC
1 CCTTCGTTTTAAAGATTTTAAAAGACATGAGCGAAAATTTGAAGGGATACTTGATTATTTTAAAC
* * * * * *
54929928 AAATGCGAAATTGCAACCCAACACGTTAGGGCGCTATTCCGCGCATTGCCAAATATAGAATCTCG
66 AAATGCGAAATTGCAACCCAACACGTTAAGGCACGATTCCACGAATTGCCAAATATAGAATATCG
*
54929993 TCTTCGTTTTAAAGAATCTTTAAA
1 CCTTCGTTTTAAAG-AT-TTTAAA
54930017 TGAATACTTG
Statistics
Matches: 131, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 108 0.82
131 4 0.03
132 19 0.15
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (130 bp):
CCTTCGTTTTAAAGATTTTAAAAGACATGAGCGAAAATTTGAAGGGATACTTGATTATTTTAAAC
AAATGCGAAATTGCAACCCAACACGTTAAGGCACGATTCCACGAATTGCCAAATATAGAATATCG
Found at i:54930708 original size:2 final size:2
Alignment explanation
Indices: 54930701--54930734 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54930691 AGAACATGCT
54930701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54930735 AAAGATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54931806 original size:18 final size:18
Alignment explanation
Indices: 54931779--54931816 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54931769 AAGAAAATAA
54931779 AAAAAAAAAACT-AAAATG
1 AAAAAAAAAA-TAAAAATG
*
54931797 AAAAATAAAATAAAAATG
1 AAAAAAAAAATAAAAATG
54931815 AA
1 AA
54931817 GAATTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAAAAAATAAAAATG
Found at i:54933623 original size:132 final size:132
Alignment explanation
Indices: 54933447--54933775 Score: 484
Period size: 132 Copynumber: 2.5 Consensus size: 132
54933437 CAACCGTCAG
* *
54933447 CCTACTCCACTACAACTTTAGGGAGCTAGGGTGATAGT--C-CAAATCTGCTTCACTGCAACATC
1 CCTACTCCACTACAACTTTAGGGAGCTA-GGT--TAGTGACTTAAATCTGCTTCACTGCAACTTC
** * * * *
54933509 AGGAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGCAACTTCAGGGAAACGAGATCTAAAAT
63 AGGAAGCAAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAAGGAAACGAAATCTAAAAT
54933574 TTCAA
128 TTCAA
*
54933579 CCTACTCCACTACAACCTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
* * *
54933644 AAGTAAAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAAGGAGACGAAATCTAAAATTTC
66 AAGCAAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAAGGAAACGAAATCTAAAATTTC
*
54933709 AG
131 AA
*
54933711 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTTACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
54933776 GAAACAGGAT
Statistics
Matches: 179, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
129 4 0.02
131 4 0.02
132 171 0.96
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (132 bp):
CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
AAGCAAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAAGGAAACGAAATCTAAAATTTC
AA
Found at i:54946711 original size:67 final size:69
Alignment explanation
Indices: 54946640--54946836 Score: 274
Period size: 71 Copynumber: 2.8 Consensus size: 69
54946630 ACACCCTGTA
* * * *
54946640 GTAGCTAGGTCACATGTGTGATAC-AGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAGA
1 GTAGCTAGGTCGCATGCGTGATACAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
54946702 TAAAT
65 TAAAT
*
54946707 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGA-TACAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
54946772 ATAAAT
64 ATAAAT
*
54946778 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGA-TACAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
54946837 AGACAAATCG
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
67 19 0.16
68 5 0.04
69 2 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (69 bp):
GTAGCTAGGTCGCATGCGTGATACAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGAT
AAAT
Found at i:54946750 original size:41 final size:41
Alignment explanation
Indices: 54946705--54946822 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
54946695 TGAAAGATAA
54946705 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
54946746 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54946776 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54946817 ATGTAG
1 ATGTAG
54946823 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54946761 original size:71 final size:71
Alignment explanation
Indices: 54946673--54946836 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
54946663 CAGATGTATC
54946673 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54946738 AGGACA
66 AGGACA
54946744 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54946809 AGGACA
66 AGGACA
54946815 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54946837 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54954324 original size:41 final size:41
Alignment explanation
Indices: 54954279--54954396 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
54954269 TGAAAGATAA
54954279 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
54954320 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54954350 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54954391 ATGTAG
1 ATGTAG
54954397 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54954335 original size:71 final size:71
Alignment explanation
Indices: 54954247--54954410 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
54954237 GAGATGTATC
54954247 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54954312 AGGACA
66 AGGACA
54954318 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54954383 AGGACA
66 AGGACA
54954389 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54954411 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54955875 original size:27 final size:26
Alignment explanation
Indices: 54955797--54955952 Score: 199
Period size: 27 Copynumber: 5.9 Consensus size: 26
54955787 TTACAATTAC
*
54955797 AAATACCCT-GCTTTGTAAAATTACTA
1 AAATACCCTAG-TTTGTAAAATTACCA
* * *
54955823 AAATACCATTGGTT-TAAAATTACCA
1 AAATACCCTAGTTTGTAAAATTACCA
54955848 AAATACCCCTAGTTTGTAAAATTACCA
1 AAATA-CCCTAGTTTGTAAAATTACCA
*
54955875 AAATACCCTAGTTTGTAAAATTATTCA
1 AAATACCCTAGTTTGTAAAATTA-CCA
54955902 AAATACCCTAGTTTGTAAAATTACCA
1 AAATACCCTAGTTTGTAAAATTACCA
* *
54955928 AAATACCTCTAATTTGTGAAATTAC
1 AAATACC-CTAGTTTGTAAAATTAC
54955953 TGAATACCCT
Statistics
Matches: 115, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.13
26 43 0.37
27 57 0.50
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
AAATACCCTAGTTTGTAAAATTACCA
Found at i:54955917 original size:53 final size:52
Alignment explanation
Indices: 54955797--54955952 Score: 199
Period size: 53 Copynumber: 3.0 Consensus size: 52
54955787 TTACAATTAC
* * * *
54955797 AAATACCCT-GCTTTGTAAAATTACTAAAATACCATTGGTT-TAAAATTACCA
1 AAATACCCTAG-TTTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTACCA
*
54955848 AAATACCCCTAGTTTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTATTCA
1 AAATA-CCCTAGTTTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTA-CCA
* *
54955902 AAATACCCTAGTTTGTAAAATTACCAAAATACCTCTAATTTGTGAAATTAC
1 AAATACCCTAGTTTGTAAAATTACCAAAATACC-CTAGTTTGTAAAATTAC
54955953 TGAATACCCT
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
51 5 0.05
52 29 0.32
53 37 0.40
54 21 0.23
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (52 bp):
AAATACCCTAGTTTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTACCA
Found at i:54955981 original size:25 final size:26
Alignment explanation
Indices: 54955946--54956001 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
54955936 CTAATTTGTG
54955946 AAATTACTG-AATACCCTCGACCTGA
1 AAATTACTGAAATACCCTCGACCTGA
* * *
54955971 AAATTATTGAAATACCCTCGACTTTA
1 AAATTACTGAAATACCCTCGACCTGA
54955997 AAATT
1 AAATT
54956002 GCCAAAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (26 bp):
AAATTACTGAAATACCCTCGACCTGA
Found at i:54956039 original size:27 final size:27
Alignment explanation
Indices: 54956009--54956352 Score: 394
Period size: 27 Copynumber: 12.8 Consensus size: 27
54955999 ATTGCCAAAG
* *
54956009 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
54956036 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54956063 TACCC-CGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
54956089 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
54956116 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54956143 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
54956170 TACCC-CAGATTTACATAATTATCG-TT
1 TACCCTC-GATTTACAGAATTACCGTTT
54956196 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54956223 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
54956250 TACCCTCGATTTATAGAA-TACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54956276 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54956303 TACCCTTGATTTTACAAAATTACTGTTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
54956331 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
54956353 TAAATACCCT
Statistics
Matches: 280, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
26 69 0.25
27 184 0.66
28 27 0.10
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:54956093 original size:80 final size:81
Alignment explanation
Indices: 54956009--54956353 Score: 400
Period size: 80 Copynumber: 4.3 Consensus size: 81
54955999 ATTGCCAAAG
* **
54956009 TACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCC-CGAT
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGAT
* *
54956072 TTATAGAATTACCGTTT
65 TTACAGAATTACCATTT
* * * *
54956089 TACCCTC-AGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-CTAA
1 TACCCTCGA-TTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTC-GA
*
54956152 TTTACATAATTACCATTT
64 TTTACAGAATTACCATTT
* *
54956170 TACCC-CAGATTTACATAATTA-TCG-TTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGA
1 TACCCTC-GATTTACAGAATTACT-GTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGA
54956232 TTTACAGAATTACCATTT
64 TTTACAGAATTACCATTT
* * * *
54956250 TACCCTCGATTTATAGAA-TACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGA-T
* **
54956314 TTACAAAATTACTGTTT
65 TTACAGAATTACCATTT
*
54956331 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
54956354 AAATACCCTT
Statistics
Matches: 229, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
79 4 0.02
80 154 0.67
81 66 0.29
82 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
TACAGAATTACCATTT
Found at i:54956133 original size:107 final size:106
Alignment explanation
Indices: 54956009--54956352 Score: 399
Period size: 107 Copynumber: 3.2 Consensus size: 106
54955999 ATTGCCAAAG
*
54956009 TACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCCGATTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTT-TAAAATTACCGTTTTACCCCGATTT
* * *
54956074 ATAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTATTT
65 ACAAAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTT
* * *
54956116 TACCCTCGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTACCATTTTACCCCAGAT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTTA-A-AATTACCGTTTTACCCC-GAT
* * *
54956180 TTACATAATTATCG-TTTACCCTC-GATTTACAGAATTACCGTTT
63 TTACAAAATTACCGTTTTACCCTCAG-TTTACAGAATTACTGTTT
* * * * *
54956223 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAA-TACTGTTTTACCCTTGATT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTT-TAAAATTACCGTTTTACCC-CGATT
* * * *
54956287 TACAAAATTACTGTTTTACCCTTGATTTTACAAAATTACTGTTT
64 TACAAAATTACCGTTTTACCC-TCAGTTTACAGAATTACTGTTT
* *
54956331 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTATAGAATTAC
54956353 TAAATACCCT
Statistics
Matches: 202, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
105 2 0.01
106 31 0.15
107 111 0.55
108 56 0.28
109 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (106 bp):
TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTTAAAATTACCGTTTTACCCCGATTTA
CAAAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTT
Found at i:54957610 original size:25 final size:25
Alignment explanation
Indices: 54957581--54957628 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54957571 TTATAATATG
* * *
54957581 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54957606 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54957629 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54957697 original size:20 final size:20
Alignment explanation
Indices: 54957672--54957730 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
54957662 TAAATATGGT
54957672 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
54957692 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
54957712 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
54957731 GTAATCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:54957848 original size:23 final size:24
Alignment explanation
Indices: 54957780--54957945 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
54957770 GAGGAAGTGA
54957780 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54957804 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54957828 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54957851 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
54957874 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
54957898 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
54957922 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54957946 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
23 46 0.35
24 76 0.57
25 11 0.08
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:54957856 original size:47 final size:47
Alignment explanation
Indices: 54957780--54957945 Score: 246
Period size: 47 Copynumber: 3.5 Consensus size: 47
54957770 GAGGAAGTGA
54957780 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
54957827 CAAAAGGGCTTATG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
** *
54957874 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
*
54957922 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54957946 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
46 13 0.12
47 62 0.56
48 24 0.22
49 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
Found at i:54958199 original size:30 final size:31
Alignment explanation
Indices: 54958135--54958228 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
54958125 CGTTTACAGT
54958135 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54958166 AAAGGCTTCGGCCCAGTAATATGAAAT-TGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
54958196 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54958227 AA
1 AA
54958229 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 29 0.48
31 32 0.52
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54961109 original size:27 final size:27
Alignment explanation
Indices: 54961025--54961201 Score: 236
Period size: 27 Copynumber: 6.7 Consensus size: 27
54961015 TTTGGTTTAC
54961025 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * * *
54961051 AAAATTACTAAAATA-CCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
54961077 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
54961104 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
54961131 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
54961158 AAAATTACCAAAATACCCCTA-ATTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
54961184 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
54961202 TCGACCTGTA
Statistics
Matches: 136, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
26 54 0.40
27 82 0.60
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:54961212 original size:53 final size:54
Alignment explanation
Indices: 54961048--54961255 Score: 165
Period size: 54 Copynumber: 3.9 Consensus size: 54
54961038 TACCCTGCTT
* * * * * * * **
54961048 TGTAAAATTACTAAAATA-CCTTGGTTTATAAAATTACCAAAATACCCCTAGTT
1 TGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATCAAAATACCCCGAGCC
* * **
54961101 TGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTT
1 TGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATCAAAATACCCCGAGCC
* *
54961155 TGTAAAATTACCAAAATACCCCTA-ATTGTGAAATTA-CTGAAATACCCTCGA-CC
1 TGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATC-AAAATACCC-CGAGCC
*** * * *
54961208 TGTAAAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCC
1 TGTAAAATTACCAAAATACCCCTAGA-TTGTAAAATTATCAAAATACCC
54961256 TCGATTTATA
Statistics
Matches: 131, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
52 5 0.04
53 51 0.39
54 74 0.56
55 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (54 bp):
TGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATCAAAATACCCCGAGCC
Found at i:54961212 original size:80 final size:80
Alignment explanation
Indices: 54961025--54961255 Score: 229
Period size: 80 Copynumber: 2.9 Consensus size: 80
54961015 TTTGGTTTAC
* * * * *
54961025 AAAATTACCAAAATA-CCC-TGCTTTGTAAAATTA-CTAAAATACCTTGGTTTATAAAATTACCA
1 AAAATTACCAAAATACCCCGAGC-CTGTAAAATTATC-AAAATACCCTAGTTTGTAAAATTACCA
*
54961087 AAATACCCCTAGTTTGT
64 AAATACCCCTAGATTGT
* **
54961104 AAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATA-CCCTAGTTTGTAAAATTACCAA
54961169 AATACCCCTA-ATTGT
65 AATACCCCTAGATTGT
* ** ** * *
54961184 GAAATTACTGAAATACCCTCGA-CCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCA
1 AAAATTACCAAAATACCC-CGAGCCTGTAAAATTATCAAAATACCCTAG-TTTGTAAAATTACCA
*
54961248 AAGTACCC
64 AAATACCC
54961256 TCGATTTATA
Statistics
Matches: 129, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
79 20 0.16
80 76 0.59
81 33 0.26
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCTAGTTTGTAAAATTACCAAA
ATACCCCTAGATTGT
Found at i:54961222 original size:27 final size:27
Alignment explanation
Indices: 54961185--54961259 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
54961175 CCTAATTGTG
54961185 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
54961212 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
54961239 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
54961260 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:54961271 original size:54 final size:54
Alignment explanation
Indices: 54961076--54961382 Score: 160
Period size: 54 Copynumber: 5.7 Consensus size: 54
54961066 CCTTGGTTTA
* * * * * * *
54961076 TAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTCGA-CTTG
* * * * * * * *
54961130 TAAAATTATCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAATTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTCGACTTG
* * ** * * **
54961183 TGAAATTACTGAAA-TACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTG
1 TAAAATTAC-CAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
*** *
54961237 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTG
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
**** *** *
54961291 TAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGTT-
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
* ***
54961343 TACAGAATTACTATTTTACCCTCGATTTATAGAATTACCG
1 TA-A-AATTACCAAAGTACCCTCGATTTATAGAATTACCG
54961383 TACCCCTAAT
Statistics
Matches: 215, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
52 2 0.01
53 40 0.19
54 173 0.80
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (54 bp):
TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
Found at i:54961591 original size:27 final size:27
Alignment explanation
Indices: 54961251--54961590 Score: 374
Period size: 27 Copynumber: 12.8 Consensus size: 27
54961241 ATTACCAAAG
*
54961251 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
54961278 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54961305 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
54961332 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
54961359 TACCCTCGATTTATAGAATTACCG---
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54961383 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
54961410 TACCC-CAGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
54961437 TA-CCTCGATTTACA-AATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54961462 TACCCTCGATTTACAGAATTACC-ATT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
54961488 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54961515 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
54961542 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54961569 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
54961591 TAAAATACCC
Statistics
Matches: 275, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.00
24 18 0.07
25 12 0.04
26 46 0.17
27 197 0.72
28 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:54961617 original size:81 final size:80
Alignment explanation
Indices: 54961278--54961603 Score: 249
Period size: 78 Copynumber: 4.1 Consensus size: 80
54961268 ATTACCGTTT
* ** * * *
54961278 TACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGT
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACC-ATTTACCCTCGA-T
* ***
54961342 TTACAGAATTACTATTT
64 TTACAAAATTACTAAAA
* * * * *
54961359 TACCCTCGATTTATAGAATTACCG---TACCC-CTAATTTACATAATTACCATTTTACCC-CAGA
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTC-GATTTACAAAATTACCA-TTTACCCTC-GA
* **
54961419 TTTACATAATTATCGT--TT
63 TTTACAAAATTA-C-TAAAA
* *
54961437 TA-CCTCGATTTAC-AAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTACCCTCGATTT
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTACCCTCGATTT
* * ***
54961500 ATAGAATTACTATTT
66 ACAAAATTACTAAAA
* * **
54961515 TACCCTTGATTTACAAAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTAC-CATTTACCCTCGATT
54961580 TACAAAATTACTAAAA
65 TACAAAATTACTAAAA
54961596 TACCCTTG
1 TACCCTTG
54961604 GTTTGTGAAA
Statistics
Matches: 205, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
76 9 0.04
77 13 0.06
78 63 0.31
79 33 0.16
80 33 0.16
81 54 0.26
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (80 bp):
TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTACCCTCGATTT
ACAAAATTACTAAAA
Found at i:54961627 original size:81 final size:80
Alignment explanation
Indices: 54961278--54961634 Score: 185
Period size: 81 Copynumber: 4.5 Consensus size: 80
54961268 ATTACCGTTT
* ** *** * * *
54961278 TACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACC-ATTTACCCTCGA-T
* ***
54961342 TTACAGAATTACTATTT
64 TTACAAAATTACTAAAA
* * * * *
54961359 TACCCTCGATTTATAGAATTACCG---TACCC-CTAATTTACATAATTACCATTTTACCC-CAGA
1 TACCCTTGATTTACAAAATTACCGCAATACCCTC-GATTTACAAAATTACCA-TTTACCCTC-GA
* **
54961419 TTTACATAATTATCGT--TT
63 TTTACAAAATTA-C-TAAAA
* *** *
54961437 TA-CCTCGATTTAC-AAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTACCCTCGATTT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTACCCTCGATTT
* * ***
54961500 ATAGAATTACTATTT
66 ACAAAATTACTAAAA
* *** * **
54961515 TACCCTTGATTTACAAAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTAC-CATTTACCCTCGATT
54961580 TACAAAATTACTAAAA
65 TACAAAATTACTAAAA
* *** *
54961596 TACCCTTGGTTTGTGAAATTACCGCAATACCCTCAATTT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTT
54961635 GTAAAACTAC
Statistics
Matches: 226, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
76 9 0.04
77 13 0.06
78 63 0.28
79 33 0.15
80 33 0.15
81 75 0.33
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (80 bp):
TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTACCCTCGATTT
ACAAAATTACTAAAA
Found at i:54962852 original size:25 final size:25
Alignment explanation
Indices: 54962823--54962870 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54962813 TTATAATATG
* * *
54962823 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54962848 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54962871 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Done.