Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 18 of 190
Found at i:4970591 original size:36 final size:38
Alignment explanation
Indices: 4970551--4970633 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 38
4970541 GAAAAAAGAA
* *
4970551 AGAAAAAGAAGGAAAGAA-AAG-GAA-AGGAGAAGGAAG
1 AGAAAAAAAAAGAAAGAAGAAGAGAAGAGG-GAAGGAAG
4970587 AGAAAAAAAAAGAAAGAAGAAGAAGAAGAGGGAAGGAAG
1 AGAAAAAAAAAGAAAGAAGAAG-AGAAGAGGGAAGGAAG
4970626 A-AAAAAAA
1 AGAAAAAAA
4970634 GTAATTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 16 0.39
37 3 0.07
38 7 0.17
39 12 0.29
40 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (38 bp):
AGAAAAAAAAAGAAAGAAGAAGAGAAGAGGGAAGGAAG
Found at i:4975909 original size:18 final size:18
Alignment explanation
Indices: 4975882--4975926 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4975872 ATCCCAATGA
*
4975882 TCGCCGCCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
4975900 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
4975918 TCACCACCA
1 TCGCCACCA
4975927 ACCATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.51, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:4976791 original size:3 final size:3
Alignment explanation
Indices: 4976773--4976831 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
4976763 AATAACATCT
* *
4976773 TAA TAC TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4976821 TAA TAC TAA TA
1 TAA TAA TAA TA
4976832 CTAACTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4976966 original size:11 final size:11
Alignment explanation
Indices: 4976950--4976989 Score: 66
Period size: 10 Copynumber: 3.8 Consensus size: 11
4976940 AAAAAATACG
4976950 TTCTTTTTCTC
1 TTCTTTTTCTC
4976961 TTCTTTTTCTC
1 TTCTTTTTCTC
4976972 -TCTTTTTCTC
1 TTCTTTTTCTC
4976982 TT-TTTTTC
1 TTCTTTTTC
4976990 CGCAGCACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTTTTCTC
Found at i:4976976 original size:21 final size:20
Alignment explanation
Indices: 4976951--4976989 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
4976941 AAAAATACGT
4976951 TCTTTTTCTCTTCTTTTTCTC
1 TCTTTTTCTCTT-TTTTTCTC
4976972 TCTTTTTCTCTTTTTTTC
1 TCTTTTTCTCTTTTTTTC
4976990 CGCAGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTTTTTCTCTTTTTTTCTC
Found at i:4977114 original size:27 final size:27
Alignment explanation
Indices: 4977074--4977134 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
4977064 ACGAGTAGTC
* *
4977074 CCGCCAATCAGTATGGCACCATTGGTG
1 CCGCCAAGCAGTATGGCACCATCGGTG
*
4977101 CTGCCAAGCAGTATGGCACCATCGGTG
1 CCGCCAAGCAGTATGGCACCATCGGTG
4977128 CCGCCAA
1 CCGCCAA
4977135 TCAAAATCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (27 bp):
CCGCCAAGCAGTATGGCACCATCGGTG
Found at i:4978649 original size:35 final size:36
Alignment explanation
Indices: 4978566--4978653 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
4978556 TAATTTTTTA
* *
4978566 TTTTAGACTTT-AATATCCTTAGATTTAATTTATGT
1 TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
*
4978601 TTGATATAAATTTTAAATATTCCTTAGATTT-ACTTAT-T
1 TT--T-TAGATTTTAAATA-TCCTTAGATTTAACTTATGT
4978639 TTTTAGATTTTAAAT
1 TTTTAGATTTTAAAT
4978654 TTTTGGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
35 13 0.30
36 1 0.02
37 1 0.02
38 9 0.20
39 9 0.20
40 11 0.25
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (36 bp):
TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
Found at i:4981805 original size:40 final size:38
Alignment explanation
Indices: 4981725--4981807 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 38
4981715 ATGTAGTACG
*
4981725 TATATATTTTATTATCATATTATTTTATTTTTATAGTT
1 TATATATTTTATTATCATATTATTTTATTTTTATAATT
4981763 TATATATTTT-TTAT-ATACATTCATTTT-TTTTTATGATATT
1 TATATATTTTATTATCAT--ATT-ATTTTATTTTTAT-A-ATT
4981803 TATAT
1 TATAT
4981808 TTTCATGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
36 2 0.05
37 4 0.10
38 20 0.51
39 6 0.15
40 7 0.18
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (38 bp):
TATATATTTTATTATCATATTATTTTATTTTTATAATT
Found at i:4985370 original size:26 final size:27
Alignment explanation
Indices: 4985321--4985371 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4985311 ACTTGATTCG
* *
4985321 GTTTTTAATTTTTTATATTAATTTTTT
1 GTTTTAAATTTTTAATATTAATTTTTT
*
4985348 GTTTTAAATTTTTAAT-TTTATTTT
1 GTTTTAAATTTTTAATATTAATTTT
4985372 GACAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (27 bp):
GTTTTAAATTTTTAATATTAATTTTTT
Found at i:4986083 original size:18 final size:18
Alignment explanation
Indices: 4986060--4986104 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
4986050 CTCAAGGGAT
4986060 TTACAAGAT-TTCCTAAGA
1 TTACAAGATCTT-CTAAGA
*
4986078 TTACAAAATCTTCTAAGA
1 TTACAAGATCTTCTAAGA
4986096 TTACAAGAT
1 TTACAAGAT
4986105 ATTGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
TTACAAGATCTTCTAAGA
Found at i:4987281 original size:12 final size:12
Alignment explanation
Indices: 4987248--4987281 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4987238 ATAGATTAAA
4987248 TTAGACTTTGAC
1 TTAGACTTTGAC
*
4987260 TTTGACTTTGAC
1 TTAGACTTTGAC
*
4987272 TTAGATTTTG
1 TTAGACTTTG
4987282 GTTTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (12 bp):
TTAGACTTTGAC
Found at i:4992253 original size:49 final size:49
Alignment explanation
Indices: 4992125--4992259 Score: 144
Period size: 49 Copynumber: 2.8 Consensus size: 49
4992115 ATAATGATTT
* ** * *
4992125 AAAACCATCATTGTCTGGCCAATCAAGATGATAGAATATGCAAAGAGTA
1 AAAACCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAGTA
* ** * *
4992174 AAAACCGTCATTGTCGGGCCACTTGAGATGGTAGAATATGCAAATAGTG
1 AAAACCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAGTA
** * *
4992223 AAAGTCATCATTGTTGGGCCACCCGGGATGGTAGAAT
1 AAAACCATCATTGTCGGGCCACCCGAGATGGTAGAAT
4992260 GTACAAGTTC
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (49 bp):
AAAACCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAGTA
Found at i:4993325 original size:4 final size:4
Alignment explanation
Indices: 4993316--4993355 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
4993306 AGATTAAACT
4993316 TTAA TTAA TT-A -TAA TTAAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA T
4993356 ATTTAACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 2 0.06
4 26 0.79
5 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:4993361 original size:19 final size:21
Alignment explanation
Indices: 4993315--4993367 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
4993305 AAGATTAAAC
4993315 TTTAATTAATTATAATTAAATTA
1 TTTAATTAA-T-TAATTAAATTA
*
4993338 ATTAATTAATTAATT-AA-TA
1 TTTAATTAATTAATTAAATTA
*
4993357 TTTAACTAATT
1 TTTAATTAATT
4993368 TTAACCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 5 0.19
22 1 0.04
23 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATTAATTAATTAAATTA
Found at i:4993366 original size:27 final size:27
Alignment explanation
Indices: 4993316--4993367 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4993306 AGATTAAACT
*
4993316 TTAATTAATTATAATTAAATTAATTAA
1 TTAATTAATTATAATTAAACTAATTAA
*
4993343 TTAATTAATTA-ATATTTAACTAATT
1 TTAATTAATTATA-ATTAAACTAATT
4993368 TTAACCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATTAATTATAATTAAACTAATTAA
Found at i:4993680 original size:10 final size:10
Alignment explanation
Indices: 4993665--4993697 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4993655 ACTAAGATTA
4993665 AATTTTAATT
1 AATTTTAATT
4993675 AATTTTAATT
1 AATTTTAATT
*
4993685 AA-CTTAATT
1 AATTTTAATT
4993694 AATT
1 AATT
4993698 AATAATTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
AATTTTAATT
Found at i:4993693 original size:19 final size:20
Alignment explanation
Indices: 4993669--4993708 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4993659 AGATTAAATT
*
4993669 TTAATTAATT-TTAATTAAC
1 TTAATTAATTAATAATTAAC
4993688 TTAATTAATTAATAATTAAC
1 TTAATTAATTAATAATTAAC
4993708 T
1 T
4993709 AATGTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTAATTAATAATTAAC
Found at i:4994660 original size:49 final size:49
Alignment explanation
Indices: 4994536--4994670 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 49
4994526 ATAATGATTC
* * ** *
4994536 AAAA-CCATCATTGTTAGGCCACTCAAGATGATAGAATATGCAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATGCAAATAGT
* *
4994584 CAAAGCCATCATCGTTGTGCCACTCGGGATGGTAGAATATGCAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATGCAAATAGT
* * * *
4994633 AAAAGTCATCA-CTGTTGGGTCATTCGGGATGGTTGAAT
1 AAAAGCCATCATC-GTTGGGCCACTCGGGATGGTAGAAT
4994671 GTACAAGTTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 4 0.06
49 68 0.94
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (49 bp):
AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATGCAAATAGT
Found at i:4996566 original size:20 final size:20
Alignment explanation
Indices: 4996541--4996578 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4996531 CCTATGTAGC
4996541 AGTCAAGGTGGCCATGCAGG
1 AGTCAAGGTGGCCATGCAGG
4996561 AGTCAAGGTGGCCATGCA
1 AGTCAAGGTGGCCATGCA
4996579 AGGAACGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.37, T:0.16
Consensus pattern (20 bp):
AGTCAAGGTGGCCATGCAGG
Found at i:5001062 original size:20 final size:20
Alignment explanation
Indices: 5001032--5001076 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5001022 GTCAGCTCCT
5001032 ATGCAGCAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
* *
5001052 GTGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
5001072 ATGCA
1 ATGCA
5001077 AGGAACGTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.38, T:0.16
Consensus pattern (20 bp):
ATGCAGCAGTCAAGGTGGCC
Found at i:5007262 original size:33 final size:33
Alignment explanation
Indices: 5007225--5007320 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
5007215 TTTATTTTAT
5007225 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5007258 TTTAGTTTGTTTACTTATATGTTGTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5007291 TTTAGTTTGTTTACTTATGTGTTTTAGTTT
1 TTTAGTTTGTTTACTTATATGTTTTAGTTT
5007321 ACTACTATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.66
Consensus pattern (33 bp):
TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
Found at i:5016899 original size:18 final size:18
Alignment explanation
Indices: 5016858--5016902 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5016848 AAAGTGATCT
*
5016858 AAAAAATATAGAAAAAAA
1 AAAAAATACAGAAAAAAA
* *
5016876 AGAAAATACAAAAAAAAGA
1 AAAAAATACAGAAAAAA-A
5016895 AAAAAATA
1 AAAAAATA
5016903 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (18 bp):
AAAAAATACAGAAAAAAA
Found at i:5024785 original size:2 final size:2
Alignment explanation
Indices: 5024778--5024814 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5024768 TAAAAACAAC
5024778 AT AT AT AT 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 AT AT AT AT A
5024815 CATTAAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5025516 original size:6 final size:6
Alignment explanation
Indices: 5025479--5025521 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
5025469 CCAAACACAC
* *
5025479 CAGTAAA CAGTAAA CAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGT-AA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
5025522 TTCAACACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (6 bp):
CAGTAA
Found at i:5025590 original size:46 final size:46
Alignment explanation
Indices: 5025505--5025657 Score: 200
Period size: 46 Copynumber: 3.2 Consensus size: 46
5025495 GTAACGGTAG
* *
5025505 CAGTAACAGTAACAGTA-TTCAACACACAAAGTGCTGAATCTGTAA
1 CAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCAGTAA
* * *
5025550 CAGTAACGGTAACAGTATTTCGACACACAAAGTGCCGAATCGGTAA
1 CAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCAGTAA
*
5025596 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAACCAGTAA
1 CAGTAACAGTAACAGT---A-T-TTCAACACACAAAGTGCCGAATCAGTAA
5025647 CAGTAACAGTA
1 CAGTAACAGTA
5025658 GTCGGCACAT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
45 16 0.17
46 40 0.43
49 1 0.01
50 1 0.01
51 36 0.38
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (46 bp):
CAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCAGTAA
Found at i:5025603 original size:6 final size:6
Alignment explanation
Indices: 5025592--5025618 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5025582 TGCCGAATCG
5025592 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
5025619 TTCAACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:5025654 original size:51 final size:51
Alignment explanation
Indices: 5025493--5025657 Score: 223
Period size: 51 Copynumber: 3.3 Consensus size: 51
5025483 AAACAGTAAA
* * *
5025493 CAGTAACGGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
* * *
5025544 CTGTAACAGTAACGGTAACAGT---A-T-TTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
* *
5025590 CGGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAC
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
5025641 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
5025658 GTCGGCACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
46 40 0.41
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 54 0.55
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (51 bp):
CAGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:5026318 original size:10 final size:10
Alignment explanation
Indices: 5026303--5026333 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5026293 GATTCACATA
5026303 TTTATTTATT
1 TTTATTTATT
5026313 TTTATTTATT
1 TTTATTTATT
5026323 TATTATTTATT
1 T-TTATTTATT
5026334 CAATTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTATT
Found at i:5026320 original size:14 final size:15
Alignment explanation
Indices: 5026301--5026333 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5026291 AAGATTCACA
5026301 TATTTATTTATT-TT
1 TATTTATTTATTATT
5026315 TATTTATTTATTATT
1 TATTTATTTATTATT
5026330 TATT
1 TATT
5026334 CAATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:5027209 original size:2 final size:2
Alignment explanation
Indices: 5027202--5027229 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5027192 TACTTTATTT
5027202 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
5027230 ATAATGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5027247 original size:8 final size:9
Alignment explanation
Indices: 5027202--5027247 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
5027192 TACTTTATTT
5027202 TATATATATA
1 TATATATA-A
5027212 TATATATATA
1 TATATATA-A
5027222 TATATATAA
1 TATATATAA
5027231 TA-ATGATAA
1 TATAT-ATAA
5027240 TA-ATATAA
1 TATATATAA
5027248 ATTTATTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 6 0.17
9 11 0.31
10 18 0.51
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
TATATATAA
Found at i:5027500 original size:24 final size:24
Alignment explanation
Indices: 5027473--5027540 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
5027463 CCTACATTTG
*
5027473 TTATGTCTTAAT-TAATTAATTAAT
1 TTATGTCATAATATAA-TAATTAAT
*
5027497 TTATTTCATAATATAATAATTAAT
1 TTATGTCATAATATAATAATTAAT
* * * *
5027521 ATATTTTATAATTTAATAAT
1 TTATGTCATAATATAATAAT
5027541 AGATAAAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (24 bp):
TTATGTCATAATATAATAATTAAT
Found at i:5034241 original size:4 final size:4
Alignment explanation
Indices: 5034232--5034366 Score: 261
Period size: 4 Copynumber: 33.8 Consensus size: 4
5034222 ATTTCATTTA
5034232 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5034280 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5034328 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5034367 ATTTGATTTC
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 129 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:5037352 original size:23 final size:23
Alignment explanation
Indices: 5037326--5037420 Score: 154
Period size: 23 Copynumber: 4.1 Consensus size: 23
5037316 TTATTGATCT
**
5037326 GTGGTAGCTTCGGCTACATTTCA
1 GTGGTAGCTTCGGCTACATAACA
*
5037349 GTGGTAGCTTCGGCAACATAACA
1 GTGGTAGCTTCGGCTACATAACA
5037372 GTGGTAGCTTCGGCTACATAACA
1 GTGGTAGCTTCGGCTACATAACA
*
5037395 GTGGTAGCTTCGGCTACATATCA
1 GTGGTAGCTTCGGCTACATAACA
5037418 GTG
1 GTG
5037421 TTGCACTTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (23 bp):
GTGGTAGCTTCGGCTACATAACA
Found at i:5037679 original size:15 final size:16
Alignment explanation
Indices: 5037649--5037681 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5037639 TAGTTATATG
*
5037649 TTAAAAGTGTTAATTA
1 TTAAAAGAGTTAATTA
5037665 TTAAAAGAG-TAATTA
1 TTAAAAGAGTTAATTA
5037680 TT
1 TT
5037682 GTTTACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (16 bp):
TTAAAAGAGTTAATTA
Found at i:5045104 original size:4 final size:4
Alignment explanation
Indices: 5045095--5045133 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
5045085 ATTTCATTTA
5045095 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5045134 ATTTGATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5061216 original size:19 final size:19
Alignment explanation
Indices: 5061194--5061231 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5061184 AACGTAAGGG
5061194 TAAAATAGTAAA-TAAATAA
1 TAAAAT-GTAAATTAAATAA
5061213 TAAAATGTAAATTAAATAA
1 TAAAATGTAAATTAAATAA
5061232 AACTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAATGTAAATTAAATAA
Found at i:5068804 original size:122 final size:122
Alignment explanation
Indices: 5068587--5068953 Score: 540
Period size: 122 Copynumber: 3.0 Consensus size: 122
5068577 AAATATTCAC
* * **
5068587 AATATTAACTCAAAAATCAAGGCT-TGACCACTCTTGGTTCCACCAACCTAATCCTTCTAACCCA
1 AATATTAACTCAAAAATC-AGGCTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACTTA
* * * *
5068651 GTTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
65 ATTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
*
5068709 AATATTAACTCAAAAATCAGGTTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACTTAA
1 AATATTAACTCAAAAATCAGGCTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACTTAA
5068774 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * * * *
5068831 AATAGTAACTTAAAAATCAGGGC-GTGACCGCTCTTAGTTCCACTAACCCAATCCTTCTAACTTG
1 AATATTAACTCAAAAATCA-GGCTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACTTA
* * * *
5068895 ATTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACCT
65 ATTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5068953 A
1 A
5068954 GAGTCAGTTG
Statistics
Matches: 224, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
121 4 0.02
122 218 0.97
123 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGCTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACTTAA
TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5080273 original size:59 final size:59
Alignment explanation
Indices: 5080181--5080299 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
5080171 TGGTTGATAT
*
5080181 TTGGCAACAATCTGGCCTCACCATTTTTCATCAATTGAAACGTGTGATAGATTTGAATA
1 TTGGCAACAAGCTGGCCTCACCATTTTTCATCAATTGAAACGTGTGATAGATTTGAATA
5080240 TTGGCAACAAGCTGGCCTCACCATTTTTCATCAATTGAAACGTGTGATAGATTTGAATA
1 TTGGCAACAAGCTGGCCTCACCATTTTTCATCAATTGAAACGTGTGATAGATTTGAATA
5080299 T
1 T
5080300 AAGCTTGCTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (59 bp):
TTGGCAACAAGCTGGCCTCACCATTTTTCATCAATTGAAACGTGTGATAGATTTGAATA
Found at i:5080607 original size:4 final size:4
Alignment explanation
Indices: 5080598--5080624 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5080588 ATTTCATTTA
5080598 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
5080625 ATTTGATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:5092683 original size:19 final size:19
Alignment explanation
Indices: 5092659--5092696 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5092649 AACGTAAGGG
5092659 TAAAATAGTAAA-TAAATAA
1 TAAAATA-TAAATTAAATAA
5092678 TAAAATATAAATTAAATAA
1 TAAAATATAAATTAAATAA
5092697 AACTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAATATAAATTAAATAA
Found at i:5100164 original size:122 final size:122
Alignment explanation
Indices: 5099997--5100326 Score: 518
Period size: 122 Copynumber: 2.7 Consensus size: 122
5099987 AAGGCTTGAC
* * *
5099997 TTCCACTAACCCGATCCTTCTAACCCAGTTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAG
1 TTCCACTAACCCAATCCTTCTAACCCAATTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAG
5100062 AAAGTTCAATTAATCAACCTAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGG
66 AAAGTTCAATTAATCAACCTAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGG
* *
5100119 TTCCACTAACCCAATCCTTCTAACCCAATTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAG
1 TTCCACTAACCCAATCCTTCTAACCCAATTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAG
* * *
5100184 AAAGTTCAATTTATCAACCTAATATTAACTCAAAAATCAGGGTGTGACCGCTCTTGG
66 AAAGTTCAATTAATCAACCTAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGG
*** * *
5100241 TTCCACTAACCCAATCCTTCTAACTTGATTTTTTGGATGTGATAAT-AGGAGTTTTAATTAGAAA
1 TTCCACTAACCCAATCCTTCTAACCCAATTTTTAGGATGTGACAATAAGGA-TTTTAATTAGAAA
*
5100305 GAAAGTTGAATTAATCAACCTA
65 GAAAGTTCAATTAATCAACCTA
5100327 GAGTCAGTTG
Statistics
Matches: 190, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 2 0.01
122 188 0.99
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (122 bp):
TTCCACTAACCCAATCCTTCTAACCCAATTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAG
AAAGTTCAATTAATCAACCTAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGG
Found at i:5100629 original size:34 final size:34
Alignment explanation
Indices: 5100591--5100655 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
5100581 ATAGATTTTA
* *
5100591 AAATTGAATTAATTAACTAGATGCAAATTAACCG
1 AAATTAAATTAATTAACTAGATGAAAATTAACCG
5100625 AAATTAAATTAATTAACTAGATGAAAATTAA
1 AAATTAAATTAATTAACTAGATGAAAATTAA
5100656 TCAGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (34 bp):
AAATTAAATTAATTAACTAGATGAAAATTAACCG
Found at i:5102012 original size:33 final size:33
Alignment explanation
Indices: 5101969--5102040 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
5101959 TGTGCATGAC
*
5101969 ATATTCGGAGGTTATTAATTTATGCTATGTATT
1 ATATTTGGAGGTTATTAATTTATGCTATGTATT
5102002 ATATTTGGAGGTTATTAATTTATGCTATGTATT
1 ATATTTGGAGGTTATTAATTTATGCTATGTATT
*
5102035 GTATTT
1 ATATTT
5102041 TGTTGTACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.51
Consensus pattern (33 bp):
ATATTTGGAGGTTATTAATTTATGCTATGTATT
Found at i:5103657 original size:122 final size:121
Alignment explanation
Indices: 5103440--5103806 Score: 572
Period size: 122 Copynumber: 3.0 Consensus size: 121
5103430 AAATATTCAC
* * * *
5103440 AATATTAACTCAAAAATCAAGGCTTGACCACTTTTGGTTCCACTAACCCAATCCTTCTAACCCAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAA-CCAA
* * *
5103505 TTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
65 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5103562 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAATCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAA-CCAA
5103627 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
65 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* **
5103684 AATATTAACTCAAAAATCAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACTTGA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAAC-CAA
* * * * *
5103749 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGCTGAATTAATCAACCT
65 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5103806 A
1 A
5103807 GGGTCAGTTG
Statistics
Matches: 228, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
121 1 0.00
122 227 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (121 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCAAT
TTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5107066 original size:122 final size:122
Alignment explanation
Indices: 5106849--5107215 Score: 572
Period size: 122 Copynumber: 3.0 Consensus size: 122
5106839 AAATATTCAC
* * * *
5106849 AATATTAACTCAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCTTTCTAACCCAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * *
5106914 TTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5106971 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
*
5107036 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTTATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * * ***
5107093 AATATTAACTAAAAAATTAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACTTGA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * * *
5107158 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5107215 A
1 A
5107216 GAGTCAGTTG
Statistics
Matches: 226, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 226 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5109815 original size:71 final size:71
Alignment explanation
Indices: 5109719--5109859 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
5109709 AGAGTTTTGG
* *
5109719 TAGAAGTGCAGGGAATGTTGAACTTTTGCTACTGACTTGACTTGTTTC-GATAGAAGTCCTCAAG
1 TAGAAGTGCAGAGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTG-TAGAAGTCCTCAAG
*
5109783 GTATCGA
65 ATATCGA
5109790 TAGAAGTGCA-AGAGATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
1 TAGAAGTGCAGAGA-ATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
5109854 ATATCG
65 ATATCG
5109860 GTAACACTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
70 2 0.03
71 62 0.95
72 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (71 bp):
TAGAAGTGCAGAGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAGA
TATCGA
Found at i:5110328 original size:26 final size:25
Alignment explanation
Indices: 5110298--5110358 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5110288 AATTTTTAGT
*
5110298 GTTAATTTTCAATCTCAATAT-TTTAA
1 GTTAAATTT-AAT-TCAATATATTTAA
**
5110324 GTTAAATTTAATTTTATATATTTAA
1 GTTAAATTTAATTCAATATATTTAA
5110349 GTTAAATTTA
1 GTTAAATTTA
5110359 TTTATTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.16
25 18 0.58
26 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (25 bp):
GTTAAATTTAATTCAATATATTTAA
Found at i:5111944 original size:4 final size:4
Alignment explanation
Indices: 5111935--5111965 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5111925 ATTTCATTTA
5111935 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
5111966 ATTTGATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:5140183 original size:25 final size:24
Alignment explanation
Indices: 5140155--5140247 Score: 107
Period size: 25 Copynumber: 3.8 Consensus size: 24
5140145 ACCTATTATA
*
5140155 TGGCTCTCACGAGCTTCCCAATATT
1 TGGCTCTCATGAGCTTCCCAAT-TT
*
5140180 TGGCTCTCATGAGCTTCCCAATTAA
1 TGGCTCTCATGAGCTTCCCAATT-T
* *
5140205 TGGCTCTCTTGAGCTTCCC-GTTT
1 TGGCTCTCATGAGCTTCCCAATTT
*
5140228 ATGGCTCTTATGAGCTTCCC
1 -TGGCTCTCATGAGCTTCCC
5140248 GATAATTGGC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.34
25 39 0.66
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.35
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCCCAATTT
Found at i:5140247 original size:49 final size:51
Alignment explanation
Indices: 5140149--5140247 Score: 132
Period size: 49 Copynumber: 2.0 Consensus size: 51
5140139 TGAGCAACCT
5140149 ATTATATGGCTCTCACGAGCTTCCCAATATTTGGCTCTCATGAGCTTCCCA
1 ATTATATGGCTCTCACGAGCTTCCCAATATTTGGCTCTCATGAGCTTCCCA
** * *
5140200 ATTA-ATGGCTCTCTTGAGCTTCCC-GT-TTATGGCTCTTATGAGCTTCCC
1 ATTATATGGCTCTCACGAGCTTCCCAATATT-TGGCTCTCATGAGCTTCCC
5140248 GATAATTGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 2 0.05
49 19 0.44
50 18 0.42
51 4 0.09
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (51 bp):
ATTATATGGCTCTCACGAGCTTCCCAATATTTGGCTCTCATGAGCTTCCCA
Found at i:5140267 original size:25 final size:24
Alignment explanation
Indices: 5140215--5140271 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
5140205 TGGCTCTCTT
* * * *
5140215 GAGCTTCCCGTTTATGGCTCTTAT
1 GAGCTTCCCGATAATGGCTCGTAA
5140239 GAGCTTCCCGATAATTGGCTCGTAA
1 GAGCTTCCCGATAA-TGGCTCGTAA
5140264 GAGCTTCC
1 GAGCTTCC
5140272 TGTTATACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATAATGGCTCGTAA
Found at i:5140360 original size:25 final size:25
Alignment explanation
Indices: 5140265--5140351 Score: 129
Period size: 25 Copynumber: 3.5 Consensus size: 25
5140255 GGCTCGTAAG
* * **
5140265 AGCTTCCTGTTATACAGCTCGCACG
1 AGCTTCCCGTTATACAGCTCACATA
*
5140290 AGCTTCCCGTTATACAGCTCACATG
1 AGCTTCCCGTTATACAGCTCACATA
5140315 AGCTTCCCGTTATACAGCTCACATA
1 AGCTTCCCGTTATACAGCTCACATA
5140340 AGCTTCCCGTTA
1 AGCTTCCCGTTA
5140352 CATGACTCAG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (25 bp):
AGCTTCCCGTTATACAGCTCACATA
Found at i:5140368 original size:50 final size:50
Alignment explanation
Indices: 5140262--5140373 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 50
5140252 ATTGGCTCGT
* * *
5140262 AAGAGCTTCCTGTTATACAGCTCGCACGAGCTTCCCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCACACAAGCTTCCCGTTATACAGCTCAC
* * *
5140312 ATGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCG-T-TACATGACTCAG
1 AAGAGCTTCCCGTTATACAGCTCACACAAGCTTCCCGTTATACA-G-CTCAC
5140362 AAGAGCTTCCCG
1 AAGAGCTTCCCG
5140374 ATTACATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.08
49 2 0.04
50 47 0.89
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (50 bp):
AAGAGCTTCCCGTTATACAGCTCACACAAGCTTCCCGTTATACAGCTCAC
Found at i:5145221 original size:35 final size:35
Alignment explanation
Indices: 5145181--5145255 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5145171 CTCTAACAAT
* *
5145181 CATTTCCATGATGCCGCTATGTAGAGCCAGTACAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
* *
5145216 CATTTCCATGATGCCACTCCGTAGAGCCAGTAGAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
5145251 CATTT
1 CATTT
5145256 TCGACCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (35 bp):
CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
Found at i:5149618 original size:31 final size:32
Alignment explanation
Indices: 5149566--5149627 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
5149556 GACAATTGAA
*
5149566 ATATAAATTATTCTATTTATTT-TTTATTTTT
1 ATATAAATTATTCTATTTATTTATCTATTTTT
5149597 ATATAAA-TATT-TATTTATATTTATCTATTTT
1 ATATAAATTATTCTA-TT-TATTTATCTATTTT
5149628 GTTCGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 2 0.07
30 6 0.22
31 12 0.44
32 7 0.26
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (32 bp):
ATATAAATTATTCTATTTATTTATCTATTTTT
Found at i:5149943 original size:86 final size:83
Alignment explanation
Indices: 5149761--5150043 Score: 300
Period size: 87 Copynumber: 3.3 Consensus size: 83
5149751 TCTAAAAGTG
* ** * * *
5149761 AATAAAATATGTTTTGGGATTTATTCCAGCCGTTCAATAGATTTTATTCCAATTTGATTTTATTT
1 AATAAAATCTGTTTCAGGATTTATTCC-GCCGTTCAACAGATTTTATT-CATTTTAATTTTATTT
5149826 CCAAAACGAGAATTTAAATTAA
64 CCAAAACGAGAA-TTAAATT-A
* * * **
5149848 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCTTTTTTCTTTTATTTC
1 AATAAAATCTGTTTCAGGATTTATTC-CGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
5149913 CAAAACGAGAAATTAAAATTA
65 CAAAACGAG-AATT-AAATTA
* *
5149934 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATT-CCGCCG-TTCAAC-AGATTTTATTC-ATTTTAATTTTAT
* **
5149998 TT-CTAAATTAGAATTAAATTA
62 TTCCAAAACGAGAATTAAATTA
*
5150019 AATAAAATCTGTTTCGGGATTTATT
1 AATAAAATCTGTTTCAGGATTTATT
5150044 ATCGTCATTT
Statistics
Matches: 168, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
85 30 0.18
86 61 0.36
87 65 0.39
88 12 0.07
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (83 bp):
AATAAAATCTGTTTCAGGATTTATTCCGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTCC
AAAACGAGAATTAAATTA
Found at i:5150079 original size:85 final size:85
Alignment explanation
Indices: 5149923--5150084 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
5149913 CAAAACGAGA
* * *
5149923 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCCCGCCGATTAACAAGATTCTATTCGATT
1 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTACCGCCGATTAACAAGATTCTATTCAATA
*
5149988 TTAATTTTGTTTCTAAATTAG
66 TCAA-TTTGTTTCTAAATTAG
* * * *
5150009 AATT-AAATTAAATAAAATCTGTTTCGGGATTTATTATCGTC-ATTTAACAAGATTTTATTCAAT
1 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTACCGCCGA-TTAACAAGATTCTATTCAAT
5150072 ATCAATTTGTTTC
65 ATCAATTTGTTTC
5150085 AAAACGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 9 0.13
85 54 0.81
86 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (85 bp):
AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTACCGCCGATTAACAAGATTCTATTCAATA
TCAATTTGTTTCTAAATTAG
Found at i:5150166 original size:58 final size:59
Alignment explanation
Indices: 5150104--5150214 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 59
5150094 ACTTAATCAA
*** * * *
5150104 ATAATTTTGTTTGGGGATTTATTCCCGTC-GTTAACAAAATTTATTTTGATTTAATTAC
1 ATAATTTTGTTTCAAGATTTAGTCCCGCCAGTTAACAAAATTAATTTTGATTTAATTAC
* * *
5150162 ATAATTTTTTTTCAAGATTTAGTCCTGCCATTTAACAAAATTAATTTTGATTT
1 ATAATTTTGTTTCAAGATTTAGTCCCGCCAGTTAACAAAATTAATTTTGATTT
5150215 TGTTTCAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
58 22 0.51
59 21 0.49
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (59 bp):
ATAATTTTGTTTCAAGATTTAGTCCCGCCAGTTAACAAAATTAATTTTGATTTAATTAC
Found at i:5156986 original size:43 final size:42
Alignment explanation
Indices: 5156931--5157087 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 42
5156921 ATATCGAACA
* *
5156931 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TATCACATATCG
* *
5156974 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATCACATATCG
* * * * *
5157015 GTGCCAATGTCCTAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT-ATCACATA-TCG
*
5157058 ATGCCGACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
5157088 AAAACACATA
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
41 26 0.29
42 13 0.14
43 51 0.56
44 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATCACATATCG
Found at i:5175653 original size:27 final size:27
Alignment explanation
Indices: 5175621--5175740 Score: 161
Period size: 27 Copynumber: 4.4 Consensus size: 27
5175611 AGACCCTAAA
5175621 ATAAGGTAAAATGACCAAAATACCCCC
1 ATAAGGTAAAATGACCAAAATACCCCC
* *
5175648 AGAAGGTAAAATGACCGAAATACCCCC
1 ATAAGGTAAAATGACCAAAATACCCCC
* * * *
5175675 ATAGGGTAAAATAATCGAAATACCCCC
1 ATAAGGTAAAATGACCAAAATACCCCC
5175702 AT-AGGATAAAATGACCAAAATACCCCC
1 ATAAGG-TAAAATGACCAAAATACCCCC
*
5175729 ATAGGGTAAAAT
1 ATAAGGTAAAAT
5175741 AACTGTTATA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.03
27 76 0.95
28 2 0.03
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.16
Consensus pattern (27 bp):
ATAAGGTAAAATGACCAAAATACCCCC
Found at i:5178851 original size:39 final size:39
Alignment explanation
Indices: 5178792--5179231 Score: 637
Period size: 39 Copynumber: 11.2 Consensus size: 39
5178782 AAATCTTATA
5178792 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5178831 TAGTATAATCAGTGGGTAATGTTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5178870 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5178909 CAGCATAATCAGTGGATATTGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
** * *
5178948 CAACATAATTAGTGGATATTGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5178987 CAGCATAATCAGTGGATAATGCTTGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5179026 CAGTATAATTAATGGATAATGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5179065 CAGCATAATCAGTGGATAATGCTCATTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTC-GTTTGAGCAAGCATT
*
5179105 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
5179144 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * * * *
5179183 CAATATAATAAGTGGATATTGCTCGTTTGAACAAATCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGC-AAGCATT
5179223 CAGTATAAT
1 CAGTATAAT
5179232 TAGTATTCTA
Statistics
Matches: 366, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 315 0.86
40 51 0.14
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (39 bp):
CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
Found at i:5186128 original size:3 final size:3
Alignment explanation
Indices: 5186096--5186147 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
5186086 TCTTCCTCAT
* *
5186096 TTC TT- TTC TT- TT- TTC TTA TTT TTC -TC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5186140 TTC TTC TT
1 TTC TTC TT
5186148 TATTTTTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:5186813 original size:63 final size:63
Alignment explanation
Indices: 5186712--5186852 Score: 192
Period size: 63 Copynumber: 2.2 Consensus size: 63
5186702 TGGCAGGCCA
* * * * *
5186712 TGTAACTCACTATTTTTGAATTGGAGGCACACGAGCTAGGGGCATGGGCATGTGTCTAGGCTG
1 TGTAACTCACTATTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCCAGGCTG
* * * * *
5186775 TGTAACTCACTGTTTTAGATTTAGAGTCACACGGGCTAGGGACATGGACATGTGTCCAGGTTG
1 TGTAACTCACTATTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCCAGGCTG
5186838 TGTAACTCACTATTT
1 TGTAACTCACTATTT
5186853 CAAGCCACAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (63 bp):
TGTAACTCACTATTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCCAGGCTG
Found at i:5187890 original size:21 final size:21
Alignment explanation
Indices: 5187851--5187892 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5187841 TTAACATCTG
*
5187851 GGCCGGGTATGGGGTGTTACA
1 GGCCGGGTATGGGGGGTTACA
5187872 GGCCGGGT-TGGGGAGGTTACA
1 GGCCGGGTATGGGG-GGTTACA
5187893 AAGGAGCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.50, T:0.21
Consensus pattern (21 bp):
GGCCGGGTATGGGGGGTTACA
Found at i:5190046 original size:17 final size:17
Alignment explanation
Indices: 5190024--5190056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5190014 TTTAATTAAC
5190024 TAAATTAATTTTTCAAT
1 TAAATTAATTTTTCAAT
*
5190041 TAAATTATTTTTTCAA
1 TAAATTAATTTTTCAA
5190057 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTAATTTTTCAAT
Found at i:5194408 original size:25 final size:25
Alignment explanation
Indices: 5194380--5194430 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5194370 GGATGCCATA
5194380 GTCATTTTGTTTTAGTGGTTCCTAT
1 GTCATTTTGTTTTAGTGGTTCCTAT
5194405 GTCATTTTGTTTTAGTGGTTCCTAT
1 GTCATTTTGTTTTAGTGGTTCCTAT
5194430 G
1 G
5194431 ATACTGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (25 bp):
GTCATTTTGTTTTAGTGGTTCCTAT
Found at i:5202704 original size:20 final size:20
Alignment explanation
Indices: 5202679--5202718 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5202669 TGTGGTTAAC
* *
5202679 TTTGATGACGATACGGAAGT
1 TTTGATGAAGATACAGAAGT
5202699 TTTGATGAAGATACAGAAGT
1 TTTGATGAAGATACAGAAGT
5202719 GTTGGAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (20 bp):
TTTGATGAAGATACAGAAGT
Found at i:5212060 original size:22 final size:23
Alignment explanation
Indices: 5212035--5212079 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
5212025 TGGTTAATTC
5212035 ACATGTTAGTTAATTTT-TTTCT
1 ACATGTTAGTTAATTTTCTTTCT
5212057 ACATGTTAGTTAATTTTCTTTCT
1 ACATGTTAGTTAATTTTCTTTCT
5212080 TTCTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (23 bp):
ACATGTTAGTTAATTTTCTTTCT
Found at i:5215098 original size:12 final size:12
Alignment explanation
Indices: 5215081--5215108 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5215071 TTTTAAAATC
5215081 ATATAAAAATTA
1 ATATAAAAATTA
5215093 ATATAAAAATTA
1 ATATAAAAATTA
5215105 ATAT
1 ATAT
5215109 GAGCGGGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:5216905 original size:54 final size:54
Alignment explanation
Indices: 5216823--5216927 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
5216813 ACCTACCAAT
5216823 TTAGCCTATTCATACTTCACTTATACTATTATGCTTTTGTTCATGCTAAACATG
1 TTAGCCTATTCATACTTCACTTATACTATTATGCTTTTGTTCATGCTAAACATG
5216877 TTAGCCTATTCATACTTCACTTATACTATTATGCTTTTGTTCATGCTAAAC
1 TTAGCCTATTCATACTTCACTTATACTATTATGCTTTTGTTCATGCTAAAC
5216928 TGTCATTTGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (54 bp):
TTAGCCTATTCATACTTCACTTATACTATTATGCTTTTGTTCATGCTAAACATG
Found at i:5217649 original size:28 final size:28
Alignment explanation
Indices: 5217598--5217695 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
5217588 CACGTGACCG
* * *
5217598 ATTTGCTCACACAACCTCTAATATTCGA
1 ATTTGCTCACACAAGCTATGATATTCGA
* * * *
5217626 ATTTGCTCACGCAAGTTGTGATATTTGA
1 ATTTGCTCACACAAGCTATGATATTCGA
*
5217654 ATTTGCTCACACAAGCTATGATATTTG-
1 ATTTGCTCACACAAGCTATGATATTCGA
**
5217681 GGTTGCTCACACAAG
1 ATTTGCTCACACAAG
5217696 TGTAGGTTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
27 13 0.22
28 46 0.78
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTATGATATTCGA
Found at i:5219306 original size:21 final size:20
Alignment explanation
Indices: 5219282--5219322 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5219272 AACAGAGAAG
*
5219282 GAAAGAAGGAAAGAAGGAAAA
1 GAAAGAAAGAAA-AAGGAAAA
*
5219303 GAAAGAAAGAAAAGGGAAAA
1 GAAAGAAAGAAAAAGGAAAA
5219323 TTTAGGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAAAGGAAAA
Found at i:5219314 original size:8 final size:8
Alignment explanation
Indices: 5219277--5219313 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
5219267 AATGAAACAG
5219277 AGAAGGAA
1 AGAAGGAA
5219285 AGAAGGAA
1 AGAAGGAA
5219293 AGAAGGAAA
1 AGAAGG-AA
*
5219302 AGAAAGAA
1 AGAAGGAA
5219310 AGAA
1 AGAA
5219314 AAGGGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (8 bp):
AGAAGGAA
Found at i:5219711 original size:20 final size:20
Alignment explanation
Indices: 5219664--5219704 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5219654 GAATATGGAG
*
5219664 TTAGAATGGGAAAATAAAAT
1 TTAGATTGGGAAAATAAAAT
5219684 TTAGATTGGGAAAATAAAAT
1 TTAGATTGGGAAAATAAAAT
5219704 T
1 T
5219705 AGTATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (20 bp):
TTAGATTGGGAAAATAAAAT
Found at i:5220506 original size:23 final size:23
Alignment explanation
Indices: 5220455--5220561 Score: 80
Period size: 23 Copynumber: 4.9 Consensus size: 23
5220445 TCTGCCGATT
* * *
5220455 AGGCACTTTATGTGTCGTGTATC
1 AGGCACCTTATGTGTCGTATTTC
* *
5220478 AAGCACTTTATGTGTCGTATTTC
1 AGGCACCTTATGTGTCGTATTTC
**
5220501 AGGCACCTCGTGTGTCGTA--TC
1 AGGCACCTTATGTGTCGTATTTC
* **
5220522 AGACACCTCGTGTGTCGT-TTT-
1 AGGCACCTTATGTGTCGTATTTC
*
5220543 AGACA-CTTATGTGTCGTAT
1 AGGCACCTTATGTGTCGTAT
5220562 ACTGATCAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.14
21 25 0.35
22 1 0.01
23 35 0.49
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
AGGCACCTTATGTGTCGTATTTC
Found at i:5220546 original size:21 final size:21
Alignment explanation
Indices: 5220488--5220548 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
5220478 AAGCACTTTA
*
5220488 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGT-TTT-AGACACCTCG
* *
5220511 TGTGTCGTATCAGACACCTCG
1 TGTGTCGTTTTAGACACCTCG
5220532 TGTGTCGTTTTAGACAC
1 TGTGTCGTTTTAGACAC
5220549 TTATGTGTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 24 0.73
22 1 0.03
23 8 0.24
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (21 bp):
TGTGTCGTTTTAGACACCTCG
Found at i:5221800 original size:21 final size:20
Alignment explanation
Indices: 5221763--5221801 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5221753 CAAAAATTTT
* *
5221763 ACTTATTCAAAATTCAGTTC
1 ACTTATTAAAAACTCAGTTC
5221783 ACTTATATAAAAACTCAGT
1 ACTTAT-TAAAAACTCAGT
5221802 AAATATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
ACTTATTAAAAACTCAGTTC
Found at i:5229865 original size:21 final size:21
Alignment explanation
Indices: 5229839--5229879 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5229829 TCCTAAAATG
* *
5229839 TGAATTTGATTGAATTGAGTA
1 TGAATTTCATTAAATTGAGTA
5229860 TGAATTTCATTAAATTGAGT
1 TGAATTTCATTAAATTGAGT
5229880 TAAATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (21 bp):
TGAATTTCATTAAATTGAGTA
Found at i:5230446 original size:25 final size:25
Alignment explanation
Indices: 5230392--5230452 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
5230382 GGCTCTTAAT
*
5230392 GAGCTTCCT-A-ATATGGCTCACTT
1 GAGCTTCCTGATATATGGCTCACTG
*
5230415 GAACTTCCTGATATATGGCT-ATCTG
1 GAGCTTCCTGATATATGGCTCA-CTG
5230440 GAGCTTCCTGATA
1 GAGCTTCCTGATA
5230453 ATAGCTCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.25
24 2 0.06
25 22 0.69
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGATATATGGCTCACTG
Found at i:5230566 original size:25 final size:25
Alignment explanation
Indices: 5230532--5230580 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5230522 TATAGCCCGG
*
5230532 ATAAACTTCCTGTTACATGGCTCGC
1 ATAAACTTCCTATTACATGGCTCGC
* *
5230557 ATAAGCTTCCTATTATATGGCTCG
1 ATAAACTTCCTATTACATGGCTCG
5230581 AGAAAGTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (25 bp):
ATAAACTTCCTATTACATGGCTCGC
Found at i:5234579 original size:39 final size:39
Alignment explanation
Indices: 5234550--5234743 Score: 237
Period size: 39 Copynumber: 5.0 Consensus size: 39
5234540 ATCCTATTAC
*
5234550 ACATATAATCACCTAACATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * * * *
5234589 ATATTTAATCTCATAACATTTAAGCACATATCACAACT-T
1 ACATATAATCACATAACATTCAAGCATATATCACAA-TAT
* *
5234628 TCATATAATCACATAATATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * *
5234667 ACATATAATCTCATAAAATTTAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
** * *
5234706 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5234744 ATAAAAAACA
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
38 1 0.01
39 131 0.98
40 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (39 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATAT
Found at i:5234633 original size:78 final size:78
Alignment explanation
Indices: 5234550--5234743 Score: 273
Period size: 78 Copynumber: 2.5 Consensus size: 78
5234540 ATCCTATTAC
* * * *
5234550 ACATATAATCACCTAACATTCAAGCATATATCACAATATATATTTAATCTCATAACATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
5234615 CATATCACAACT-T
66 CATATCACAA-TAT
* *
5234628 TCATATAATCACATAATATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
5234693 TATATCACAATAT
66 CATATCACAATAT
** * *
5234706 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5234744 ATAAAAAACA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 1 0.01
78 101 0.99
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (78 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
CATATCACAATAT
Found at i:5237158 original size:245 final size:242
Alignment explanation
Indices: 5236560--5237199 Score: 984
Period size: 245 Copynumber: 2.6 Consensus size: 242
5236550 ATTTTAAAAA
* *
5236560 AAAAACCATAAAAAA-ATTA-CTGATATACCATGTCGCAAAATTTCGAACACACTAAGGCTAAAA
1 AAAAACCATAAAAAACATTATC-GATATACCATGTCGCAAAA-TTCTAACACTCTAAGGCTAAAA
* *
5236623 TTCTTAAAATA-CCCTAAAACTCCTAGGCCTTATTTT-AGGGTGTTACATACACATTCAAGATTG
64 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGA-GGTGTTACATACACATTCAAGATTG
* * *
5236686 TCTCTTATTAAATATTTTCCCAAGAAACACTCTAAGGTTAAAATTCGTAAAATACCCCTAAAACC
128 TCTCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAATACCCCTAAAACC
* * *
5236751 ATAAAAAACCATAAATCTTTTCCCTAAAACAATCTAAGGCTTAAATTCCT
193 ATAAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
5236801 -AAAAGCATAAAAAACATTATCGATATATCATATCGCAAAATTCTGAACACTCTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTATCGATATACCATGTCGCAAAATTCT-AACACTCTAAGGCTAAAAT
* *
5236865 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTCTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGAGGTGTTACATACACATTCAAGATTGTC
*
5236930 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAGTACCCCTAAAACCAT
130 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAATACCCCTAAAACCAT
* *
5236995 AAAAAAAACCATAAATATTTTCCCTAAAACACTCGAAGGCTAAAATTTCT
195 --AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* *
5237045 AAAAACCATAAAAAACATTATCAATATACCATGTCGCAAAATTCCTAATACTCTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTATCGATATACCATGTCGCAAAATT-CTAACACTCTAAGGCTAAAAT
*
5237110 TCCTAAAATACCCCTAAAACTCTTAGGCCCTATTTTGAGGTGTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGAGGTGTTACATACACATTCAAGATTGTC
*
5237175 TCTTATTAAATATTTTTCCAAGAAA
130 TCTTATTAAATATTTTCCCAAGAAA
5237200 TGATATTTAA
Statistics
Matches: 363, Mismatches: 27, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
240 16 0.04
241 48 0.13
242 112 0.31
244 43 0.12
245 142 0.39
246 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (242 bp):
AAAAACCATAAAAAACATTATCGATATACCATGTCGCAAAATTCTAACACTCTAAGGCTAAAATT
CCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGAGGTGTTACATACACATTCAAGATTGTCT
CTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAATACCCCTAAAACCATA
AAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
Found at i:5238144 original size:21 final size:21
Alignment explanation
Indices: 5238118--5238157 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5238108 CTAAAAGACA
5238118 CATAATATGACGTGTTTATGC
1 CATAATATGACGTGTTTATGC
* *
5238139 CATAATTTGACTTGTTTAT
1 CATAATATGACGTGTTTAT
5238158 TTGTTGTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (21 bp):
CATAATATGACGTGTTTATGC
Found at i:5238694 original size:13 final size:13
Alignment explanation
Indices: 5238676--5238700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5238666 GTAGATGAGG
5238676 TTTTATTTTTATA
1 TTTTATTTTTATA
5238689 TTTTATTTTTAT
1 TTTTATTTTTAT
5238701 TTGGTGTGTG
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTATA
Found at i:5248168 original size:38 final size:38
Alignment explanation
Indices: 5248117--5248192 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5248107 TGTCACGACG
5248117 TCACTTGATCCAGGTCACGCCCTTGAGCACTATTCCAA
1 TCACTTGATCCAGGTCACGCCCTTGAGCACTATTCCAA
5248155 TCACTTGATCCAGGTCACGCCCTTGAGCACTATTCCAA
1 TCACTTGATCCAGGTCACGCCCTTGAGCACTATTCCAA
5248193 CATTTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (38 bp):
TCACTTGATCCAGGTCACGCCCTTGAGCACTATTCCAA
Found at i:5267902 original size:18 final size:18
Alignment explanation
Indices: 5267870--5267938 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
5267860 CTTTTATCTT
*
5267870 CTTTTGTTC-TTCTTTTC
1 CTTTTCTTCTTTCTTTTC
5267887 CTTTTCTTCTTTC-TTTC
1 CTTTTCTTCTTTCTTTTC
* **
5267904 GTCTTTCACCTTTCTTTTC
1 CT-TTTCTTCTTTCTTTTC
*
5267923 TTTTTCTT-TTTCTTTT
1 CTTTTCTTCTTTCTTTT
5267939 TGCTTGCTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 21 0.50
18 16 0.38
19 5 0.12
ACGTcount: A:0.01, C:0.25, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTCTTCTTTCTTTTC
Found at i:5267908 original size:25 final size:26
Alignment explanation
Indices: 5267856--5267909 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
5267846 CTTTAACATT
* *
5267856 TTTTCTTTTATCTTCTTTTGTTCTTC
1 TTTTCCTTTATCTTCTTTTGTTCGTC
5267882 TTTTCCTTT-TCTTCTTTCT-TTCGTC
1 TTTTCCTTTATCTTCTTT-TGTTCGTC
5267907 TTT
1 TTT
5267910 CACCTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTCCTTTATCTTCTTTTGTTCGTC
Found at i:5269888 original size:25 final size:26
Alignment explanation
Indices: 5269827--5269939 Score: 121
Period size: 25 Copynumber: 4.5 Consensus size: 26
5269817 TCGTATTCAA
* *
5269827 GAAGCTCATGCGAGCCAA-T-ATCGA
1 GAAGCTCATGAGAGCCAATTAATCGG
5269851 GAAGCTC-TGGAGAGCC-ATTAATCGG
1 GAAGCTCAT-GAGAGCCAATTAATCGG
*
5269876 GAACCTCATGAGAGCCAATT-ATCGG
1 GAAGCTCATGAGAGCCAATTAATCGG
* *
5269901 GAAGCTCGTGAGAGCCAAATAA-CGG
1 GAAGCTCATGAGAGCCAATTAATCGG
*
5269926 GAAGCTCAAGAGAG
1 GAAGCTCATGAGAG
5269940 TCATATATGC
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
23 2 0.03
24 14 0.19
25 54 0.72
26 5 0.07
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (26 bp):
GAAGCTCATGAGAGCCAATTAATCGG
Found at i:5270224 original size:14 final size:16
Alignment explanation
Indices: 5270201--5270232 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5270191 GTCCGTTTGA
5270201 TTTCCAGTAAAAT-AT
1 TTTCCAGTAAAATGAT
5270216 TTTCC-GTAAAATGAT
1 TTTCCAGTAAAATGAT
5270231 TT
1 TT
5270233 CTGGAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
TTTCCAGTAAAATGAT
Found at i:5277272 original size:21 final size:20
Alignment explanation
Indices: 5277243--5277281 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5277233 GCGTTAAAAG
5277243 AAATGGAGAATGTGAGAAAACA
1 AAATGGAGAA-GT-AGAAAACA
5277265 AAAT-GAGAAGTAGAAAA
1 AAATGGAGAAGTAGAAAA
5277282 GAATGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 5 0.29
22 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.13
Consensus pattern (20 bp):
AAATGGAGAAGTAGAAAACA
Found at i:5277400 original size:18 final size:19
Alignment explanation
Indices: 5277379--5277419 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
5277369 GAATACATAA
5277379 AAAAAATTAT-AAAATTT-T
1 AAAAAA-TATGAAAATTTCT
*
5277397 AAAACATATGAAAATTTCT
1 AAAAAATATGAAAATTTCT
5277416 AAAA
1 AAAA
5277420 TTATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATATGAAAATTTCT
Found at i:5279339 original size:12 final size:12
Alignment explanation
Indices: 5279319--5279411 Score: 55
Period size: 12 Copynumber: 7.5 Consensus size: 12
5279309 CGATACCAAT
5279319 AAATTTATTTTA
1 AAATTTATTTTA
*
5279331 AAATGTATTTT-
1 AAATTTATTTTA
5279342 AAATTTATATTTAA
1 AAATTTAT-TTT-A
5279356 AAATTTTATTTGTA
1 AAA-TTTATTT-TA
**
5279370 CAAA-AAATTTTA
1 -AAATTTATTTTA
* *
5279382 AAATATAATTTA
1 AAATTTATTTTA
* * *
5279394 AACTTAAATTTA
1 AAATTTATTTTA
5279406 AAATTT
1 AAATTT
5279412 TTTGTTATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
11 10 0.16
12 34 0.54
13 4 0.06
14 6 0.10
15 9 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:5279998 original size:11 final size:11
Alignment explanation
Indices: 5279982--5280007 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5279972 TGTAGCACTA
5279982 ATTATATAATT
1 ATTATATAATT
5279993 ATTATATAATT
1 ATTATATAATT
5280004 ATTA
1 ATTA
5280008 ATGCCCGTGA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTATATAATT
Found at i:5281181 original size:16 final size:16
Alignment explanation
Indices: 5281160--5281192 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5281150 ATTTTTTTCC
5281160 TGCAAGTTCTGGTCAA
1 TGCAAGTTCTGGTCAA
5281176 TGCAAGTTCTGGTCAA
1 TGCAAGTTCTGGTCAA
5281192 T
1 T
5281193 CTTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (16 bp):
TGCAAGTTCTGGTCAA
Found at i:5289658 original size:17 final size:17
Alignment explanation
Indices: 5289636--5289670 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5289626 CTTACAAGTT
5289636 AGTCTTTACCATTTGTG
1 AGTCTTTACCATTTGTG
5289653 AGTCTTTACCATTTGTG
1 AGTCTTTACCATTTGTG
5289670 A
1 A
5289671 CCAAGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (17 bp):
AGTCTTTACCATTTGTG
Found at i:5296191 original size:25 final size:25
Alignment explanation
Indices: 5296146--5296243 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 25
5296136 GTCATTAGGG
* *
5296146 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
5296170 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
* * *
5296195 TTACCGTTATTCAGCTCAG-AAGAGC
1 TTACCGATACTCAGCTC-GTATGAGC
*
5296220 TTACCGTTTA-T-AGCTCGTATGAGC
1 TTACCG-ATACTCAGCTCGTATGAGC
5296244 ATACATGTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
23 1 0.02
24 19 0.30
25 40 0.62
26 4 0.06
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:5298738 original size:11 final size:12
Alignment explanation
Indices: 5298722--5298754 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5298712 ATGCAACAGG
5298722 AAACCAGCA-GC
1 AAACCAGCATGC
*
5298733 AAACCAGTATGC
1 AAACCAGCATGC
5298745 AAACCAGCAT
1 AAACCAGCAT
5298755 CCAAGCTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.09
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:5303841 original size:103 final size:103
Alignment explanation
Indices: 5303572--5303941 Score: 573
Period size: 105 Copynumber: 3.6 Consensus size: 103
5303562 TGTATATAAA
** * * *
5303572 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
5303636 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
5303676 AGGGGTTGCAAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
5303741 TTGAAATGAAAAGGGGGGTTGTTATGTGCTGATTCCCCCG
65 TTGAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCG
5303781 AGGGGTTGCTAAGTGCTGATTCCCC-ATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
5303845 TGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
5303883 AGGGGTTGCTAAGTGTTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
5303942 ATAACGGCTA
Statistics
Matches: 247, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
102 50 0.20
103 78 0.32
104 28 0.11
105 90 0.36
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:5306541 original size:49 final size:48
Alignment explanation
Indices: 5306411--5306561 Score: 130
Period size: 49 Copynumber: 3.1 Consensus size: 48
5306401 AAAAATAGTT
* * *
5306411 AATTTATATTTTATGTATCATTATATTAAATTATTTAAACATTTTATG
1 AATTTATATTTTATGTATCATTATATTAAATTATTGAAAAATTTTATA
* *** *
5306459 TATCATTA-ATTTTACAAATAATTTATATT-AATTACTTGAAAAATATTTA-A
1 AAT--TTATATTTTATGTATCA-TTATATTAAATTA-TTGAAAAAT-TTTATA
* * *
5306509 AATTTATATTTTATGTATCATTATATTAAATTATTTAAATATTGTAT-
1 AATTTATATTTTATGTATCATTATATTAAATTATTGAAAAATTTTATA
5306556 AATTTA
1 AATTTA
5306562 ACTAATTTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
47 9 0.11
48 19 0.24
49 28 0.35
50 19 0.24
51 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (48 bp):
AATTTATATTTTATGTATCATTATATTAAATTATTGAAAAATTTTATA
Found at i:5306551 original size:33 final size:31
Alignment explanation
Indices: 5306412--5306545 Score: 105
Period size: 33 Copynumber: 4.2 Consensus size: 31
5306402 AAAATAGTTA
5306412 ATTTATATTTTATGTATCATTATATTAAATT
1 ATTTATATTTTATGTATCATTATATTAAATT
* * *
5306443 ATTTAAACATTTTATGTATCATTAATTTTACAAATA
1 ATTT--ATATTTTATGTATCATT-ATATT--AAATT
** *
5306479 ATTTATATTAATTACT-TGAAAAATAT-TTAAA--
1 ATTTATATT--TTA-TGT-ATCATTATATTAAATT
5306510 ATTTATATTTTATGTATCATTATATTAAATT
1 ATTTATATTTTATGTATCATTATATTAAATT
5306541 ATTTA
1 ATTTA
5306546 AATATTGTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
28 6 0.08
29 9 0.11
31 18 0.22
33 19 0.24
34 8 0.10
35 2 0.03
36 14 0.17
37 4 0.05
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTTATATTTTATGTATCATTATATTAAATT
Found at i:5316024 original size:36 final size:36
Alignment explanation
Indices: 5315968--5316041 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
5315958 TTATTTGTGA
* * * *
5315968 TTGTTTTTTCCAACATTCAAAGGTTGAAACCTGCAT
1 TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
*
5316004 TTGTTCTTTCCGACAATCAAAGGTTCAAACATGCAT
1 TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
5316040 TT
1 TT
5316042 TCTTTGTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
Found at i:5322677 original size:19 final size:19
Alignment explanation
Indices: 5322655--5322708 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
5322645 AATATAAAAT
*
5322655 AATTCAAAATAATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
*
5322674 AATTAAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
5322693 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
5322709 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:5322687 original size:18 final size:19
Alignment explanation
Indices: 5322655--5322693 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5322645 AATATAAAAT
* *
5322655 AATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
5322674 AATTAAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
5322692 AA
1 AA
5322694 ATTCTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:5325159 original size:16 final size:17
Alignment explanation
Indices: 5325130--5325161 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5325120 TATCATGGAG
5325130 TTTGTCCTAATGTGCTT
1 TTTGTCCTAATGTGCTT
5325147 TTTGTCC-AATGTGCT
1 TTTGTCCTAATGTGCT
5325162 CTGTGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (17 bp):
TTTGTCCTAATGTGCTT
Found at i:5326315 original size:30 final size:30
Alignment explanation
Indices: 5326274--5326332 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
5326264 AAAATTATTA
* *
5326274 TAAACAAAAATTATTAAAATTTACTATTTTT
1 TAAACAAAAATTA-GAAAATTTAATATTTTT
5326305 TAAA-AAAAATTAGAAAATTTAATATTTT
1 TAAACAAAAATTAGAAAATTTAATATTTT
5326333 AAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 14 0.54
30 8 0.31
31 4 0.15
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAACAAAAATTAGAAAATTTAATATTTTT
Found at i:5326333 original size:27 final size:29
Alignment explanation
Indices: 5326269--5326337 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
5326259 TTACTAAAAT
* *
5326269 TATTATAAACAAAAATTATTAAAATTTACTA
1 TATTTTAAA-AAAAATTATGAAAATTTAC-A
*
5326300 TTTTTTAAAAAAAATTA-GAAAATTTA-A
1 TATTTTAAAAAAAATTATGAAAATTTACA
5326327 TATTTTAAAAA
1 TATTTTAAAAA
5326338 TTTTATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 11 0.32
29 8 0.24
30 8 0.24
31 7 0.21
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (29 bp):
TATTTTAAAAAAAATTATGAAAATTTACA
Found at i:5347346 original size:9 final size:9
Alignment explanation
Indices: 5347332--5347356 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5347322 TTTCACATTG
5347332 TGTGAACTT
1 TGTGAACTT
5347341 TGTGAACTT
1 TGTGAACTT
5347350 TGTGAAC
1 TGTGAAC
5347357 ATGCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (9 bp):
TGTGAACTT
Found at i:5366067 original size:2 final size:2
Alignment explanation
Indices: 5366056--5366098 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5366046 CTAATAAATC
5366056 TA TA -A 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 TA TA TA
5366097 TA
1 TA
5366099 AAGTCAGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5367892 original size:20 final size:18
Alignment explanation
Indices: 5367842--5367893 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
5367832 CTATAAGATA
5367842 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
5367859 AATATTAAGA-TAATTATTTT
1 AATATTAA-ATTAA-TA-TTT
5367879 AATATTAAATTAATA
1 AATATTAAATTAATA
5367894 AAATACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:5368377 original size:5 final size:5
Alignment explanation
Indices: 5368349--5368429 Score: 103
Period size: 5 Copynumber: 16.4 Consensus size: 5
5368339 AAAATATCAT
* *
5368349 ATTTA TTTTA A-TTA ATTTG A-TTA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* *
5368397 ATTTA ATTTA ATTTA ATTTCA AATTA CTTTA AT
1 ATTTA ATTTA ATTTA ATTT-A ATTTA ATTTA AT
5368430 CAAATTCTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
4 7 0.11
5 54 0.83
6 4 0.06
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:5369713 original size:13 final size:13
Alignment explanation
Indices: 5369695--5369730 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5369685 ATATTAATTT
5369695 ATAATAAAACAAA
1 ATAATAAAACAAA
*
5369708 ATAATAAAATAAA
1 ATAATAAAACAAA
5369721 ATAATTAAAA
1 ATAA-TAAAA
5369731 AGAAACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAACAAA
Found at i:5369772 original size:18 final size:18
Alignment explanation
Indices: 5369729--5369785 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5369719 AAATAATTAA
*
5369729 AAAGAAACAAAGCAAAAACG
1 AAAGAAAGAAAG-AAAAA-G
5369749 -AA-AAAG-AAGAAAAAAG
1 AAAGAAAGAAAG-AAAAAG
5369765 AAAGAAAGAAAGAAAAAG
1 AAAGAAAGAAAGAAAAAG
5369783 AAA
1 AAA
5369786 ATGGAGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 10 0.31
18 16 0.50
19 5 0.16
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAAAG
Found at i:5370467 original size:25 final size:25
Alignment explanation
Indices: 5370342--5370454 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
5370332 GGCTCTCTGA
* * *
5370342 AGCTTCCCGATAT-TGGATCGTATG
1 AGCTTCCCGTTATATGGCTCGAATG
* ***
5370366 AGCTTCCTGTTA-ATGGCTC-TCCG
1 AGCTTCCCGTTATATGGCTCGAATG
**
5370389 AAGCTTCCCGTTATACAGCTC-ACATG
1 -AGCTTCCCGTTATATGGCTCGA-ATG
*
5370415 AGCTTCCCGTTATATGGCTCGAAAG
1 AGCTTCCCGTTATATGGCTCGAATG
5370440 AGCTTCCCGTT-TATG
1 AGCTTCCCGTTATATG
5370455 TGCTTGTGTG
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 2 0.03
24 30 0.43
25 36 0.51
26 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATG
Found at i:5377798 original size:13 final size:14
Alignment explanation
Indices: 5377780--5377809 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5377770 GAAAATATCT
5377780 TATATTT-TAAAAA
1 TATATTTATAAAAA
5377793 TATATTTATAAAAA
1 TATATTTATAAAAA
5377807 TAT
1 TAT
5377810 TTCAATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATTTATAAAAA
Found at i:5380930 original size:18 final size:18
Alignment explanation
Indices: 5380888--5380933 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5380878 TATTTTCAAT
*
5380888 AATTTATAATTAAAACTAT
1 AATTT-TAATTAAAACTAA
* *
5380907 ATTTTTAATTAAAAGTAA
1 AATTTTAATTAAAACTAA
5380925 AATTTTAAT
1 AATTTTAAT
5380934 CAAATAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AATTTTAATTAAAACTAA
Found at i:5381030 original size:9 final size:9
Alignment explanation
Indices: 5381016--5381046 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5381006 GTTAAACGAA
5381016 TCGAGTTAT
1 TCGAGTTAT
*
5381025 TCGAGTTAA
1 TCGAGTTAT
5381034 TCGAGTTAT
1 TCGAGTTAT
5381043 TCGA
1 TCGA
5381047 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5381117 original size:9 final size:9
Alignment explanation
Indices: 5381100--5381136 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5381090 TGAGTTTTCG
5381100 AATTCGAAT
1 AATTCGAAT
*
5381109 AACTCGAAT
1 AATTCGAAT
5381118 AATTCGAAT
1 AATTCGAAT
5381127 AATTCGAAT
1 AATTCGAAT
5381136 A
1 A
5381137 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5388283 original size:125 final size:126
Alignment explanation
Indices: 5387862--5388301 Score: 720
Period size: 126 Copynumber: 3.5 Consensus size: 126
5387852 AAATCAAAGT
* * *
5387862 AGGATGTTTTATCAGAAGAATTTCTGAAATCGCACCCACGTAGACGCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * *
5387927 CTTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTACAAAAACACGCTTCAGGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACGCTTCAAGC
* * *
5387988 ATGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * *
5388053 CCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGTAAATAGTATAAAAAGACGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACGCTTCAAGC
* * *
5388114 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACATGGACCCGCTTTTGCTACAATAGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
*
5388179 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAA-ACGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACGCTTCAAGC
*
5388239 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
5388302 CATGTTTGGG
Statistics
Matches: 290, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
125 70 0.24
126 220 0.76
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (126 bp):
AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACGCTTCAAGC
Done.