Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 178 of 216
Found at i:55605198 original size:13 final size:13
Alignment explanation
Indices: 55605180--55605206 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55605170 GGTTTCAGAC
55605180 GGTTTGGCACATG
1 GGTTTGGCACATG
55605193 GGTTTGGCACATG
1 GGTTTGGCACATG
55605206 G
1 G
55605207 CCTGCGATAC
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:0.15, C:0.15, G:0.41, T:0.30
Consensus pattern (13 bp):
GGTTTGGCACATG
Found at i:55614725 original size:14 final size:14
Alignment explanation
Indices: 55614706--55614732 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55614696 GTTGTTGTTA
55614706 TGAATATTTTATTT
1 TGAATATTTTATTT
55614720 TGAATATTTTATT
1 TGAATATTTTATT
55614733 GAAACCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TGAATATTTTATTT
Found at i:55615282 original size:16 final size:16
Alignment explanation
Indices: 55615261--55615299 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
55615251 GTTTGGTTCG
55615261 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
55615277 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
55615293 CTGTAAT
1 CTGTAAT
55615300 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:55615345 original size:45 final size:44
Alignment explanation
Indices: 55615281--55615373 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
55615271 ATAGAACTGT
*
55615281 AATGGAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
55615326 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
55615370 AATG
1 AATG
55615374 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:55615382 original size:39 final size:41
Alignment explanation
Indices: 55615281--55615385 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
55615271 ATAGAACTGT
55615281 AATGGAATAGA-GCTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
55615321 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
55615365 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
55615386 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 8 0.14
40 9 0.16
41 2 0.04
42 2 0.04
43 3 0.05
44 22 0.39
45 10 0.18
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:55615552 original size:17 final size:17
Alignment explanation
Indices: 55615526--55615560 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55615516 AATTATTATT
55615526 AAATACAATTTAATAAA
1 AAATACAATTTAATAAA
*
55615543 AAATATAATTTAATAAA
1 AAATACAATTTAATAAA
55615560 A
1 A
55615561 TTCTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATACAATTTAATAAA
Found at i:55622668 original size:27 final size:27
Alignment explanation
Indices: 55622618--55622670 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
55622608 TGTCCACTTC
**
55622618 TCCCAGATTGGTACCTATGGTTTTTTG
1 TCCCAGATTGGTACCTATACTTTTTTG
55622645 TCCCAGATTGGTACCTGA-ACTTTTTT
1 TCCCAGATTGGTACCT-ATACTTTTTT
55622671 TCTGTCCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (27 bp):
TCCCAGATTGGTACCTATACTTTTTTG
Found at i:55624651 original size:17 final size:17
Alignment explanation
Indices: 55624629--55624673 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
55624619 CCAAATTTTG
55624629 ATACCCATATCTTTCTA
1 ATACCCATATCTTTCTA
*
55624646 ATACCCATATCTTTCTG
1 ATACCCATATCTTTCTA
55624663 ATACCCATATC
1 ATACCCATATC
55624674 CTTGACTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.02, T:0.38
Consensus pattern (17 bp):
ATACCCATATCTTTCTA
Found at i:55631000 original size:4 final size:4
Alignment explanation
Indices: 55630991--55631019 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55630981 CCTTTGATAA
55630991 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
55631020 TTGAAAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:55632798 original size:55 final size:55
Alignment explanation
Indices: 55632728--55632864 Score: 170
Period size: 54 Copynumber: 2.5 Consensus size: 55
55632718 CAATTTGAAT
* * * * *
55632728 CAATTGCTTAGTTTGA-TCGCTTTAGACTATGGACAACTTATATTACCTACCAATA
1 CAATTGCTTAATTTGATTC-CTTTAGACTATGGACAACATAGACTACCTACCAAGA
* *
55632783 CAATTGCTCAATTTGATTCC-TTAGACTATGGACAACATAGACTACCTACTAAGA
1 CAATTGCTTAATTTGATTCCTTTAGACTATGGACAACATAGACTACCTACCAAGA
* *
55632837 CATTTGGTTAATTTGATTCCTTTAGACT
1 CAATTGCTTAATTTGATTCCTTTAGACT
55632865 CTGTATTATG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
54 46 0.66
55 22 0.31
56 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (55 bp):
CAATTGCTTAATTTGATTCCTTTAGACTATGGACAACATAGACTACCTACCAAGA
Found at i:55644624 original size:9 final size:9
Alignment explanation
Indices: 55644610--55644641 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
55644600 TAAAAGTCAT
55644610 TAAGCAAAA
1 TAAGCAAAA
55644619 TAAGCAAAA
1 TAAGCAAAA
55644628 TTAAGCAAAA
1 -TAAGCAAAA
55644638 TAAG
1 TAAG
55644642 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (9 bp):
TAAGCAAAA
Found at i:55644634 original size:10 final size:10
Alignment explanation
Indices: 55644608--55644638 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
55644598 AATAAAAGTC
55644608 ATTAAGCAAA
1 ATTAAGCAAA
55644618 A-TAAGCAAA
1 ATTAAGCAAA
55644627 ATTAAGCAAA
1 ATTAAGCAAA
55644637 AT
1 AT
55644639 AAGTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (10 bp):
ATTAAGCAAA
Found at i:55647064 original size:12 final size:12
Alignment explanation
Indices: 55647047--55647071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55647037 TCTGCATATT
55647047 ATGACAAAATGA
1 ATGACAAAATGA
55647059 ATGACAAAATGA
1 ATGACAAAATGA
55647071 A
1 A
55647072 CAAAAATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
ATGACAAAATGA
Found at i:55648166 original size:32 final size:32
Alignment explanation
Indices: 55648115--55648310 Score: 232
Period size: 32 Copynumber: 6.2 Consensus size: 32
55648105 GAATGGCTAC
* * *
55648115 AAGCCATAAGTA-CAGTAATATGATTGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
*
55648146 AAGCCATCAGTAGTAGTAATATAATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * *
55648178 CAGCCATCAATAGTAGTAGTATGATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* *
55648210 AAGCCATCAGTAGTAATAATATGATCGGTACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * *
55648242 CAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * * * *
55648274 CAGCCATCAGTAATGGTATTATGATCGGTACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
55648306 AAGCC
1 AAGCC
55648311 TTCAATAGCA
Statistics
Matches: 143, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
31 11 0.08
32 132 0.92
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAGTAGTAATATGATCGGCACA
Found at i:55648208 original size:64 final size:64
Alignment explanation
Indices: 55648128--55648318 Score: 256
Period size: 64 Copynumber: 3.0 Consensus size: 64
55648118 CCATAAGTAC
* * *
55648128 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATAATCGGCACACAGCCATCAATAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
* * * *
55648192 AGTAGTATGATCGGCACAAAGCCATCAGTAGTAATAATATGATCGGTACACAGCCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
* * * * * * *
55648256 GGTAATATGATCGGCACACAGCCATCAGTAATGGTATTATGATCGGTACAAAGCCTTCAATAG
1 AGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAG
55648319 CATCGCAACA
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 109 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (64 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
Found at i:55648247 original size:96 final size:96
Alignment explanation
Indices: 55648130--55648310 Score: 263
Period size: 96 Copynumber: 1.9 Consensus size: 96
55648120 ATAAGTACAG
* * *
55648130 TAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATAATCGGCACACAGCCATCAATAGTAGT
1 TAATATGATCGGCACAAAGCCATCAGTAATAGTAATATAATCGGCACACAGCCATCAATAATAGT
55648195 AGTATGATCGGCACAAAGCCATCAGTAGTAA
66 AGTATGATCGGCACAAAGCCATCAGTAGTAA
* * * * * *
55648226 TAATATGATCGGTACACAGCCATCAGTAATGGTAATATGATCGGCACACAGCCATCAGTAATGGT
1 TAATATGATCGGCACAAAGCCATCAGTAATAGTAATATAATCGGCACACAGCCATCAATAATAGT
* *
55648291 ATTATGATCGGTACAAAGCC
66 AGTATGATCGGCACAAAGCC
55648311 TTCAATAGCA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (96 bp):
TAATATGATCGGCACAAAGCCATCAGTAATAGTAATATAATCGGCACACAGCCATCAATAATAGT
AGTATGATCGGCACAAAGCCATCAGTAGTAA
Found at i:55648372 original size:26 final size:26
Alignment explanation
Indices: 55648320--55648373 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
55648310 CTTCAATAGC
*
55648320 ATCGCAACAAAGCTACTAGCAAAAGT
1 ATCGCAACAAAGCTACCAGCAAAAGT
* * * *
55648346 ATCGCAGCAAAGCTGCCAGTAACAGT
1 ATCGCAACAAAGCTACCAGCAAAAGT
55648372 AT
1 AT
55648374 ATGTGGCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTACCAGCAAAAGT
Found at i:55648547 original size:24 final size:24
Alignment explanation
Indices: 55648489--55648574 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
55648479 CCATGCACGG
** *
55648489 AATCATTCATACAAATCACAAACA
1 AATCATTCATTTAAATCACAGACA
**
55648513 AATCAGCCATTTAAATCACAGACA
1 AATCATTCATTTAAATCACAGACA
* *
55648537 AATCATTCATTTACATCAAAGGA-A
1 AATCATTCATTTAAATCACA-GACA
*
55648561 AATCAATCATTTAA
1 AATCATTCATTTAA
55648575 CCCTGAGGGG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
24 48 0.96
25 2 0.04
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (24 bp):
AATCATTCATTTAAATCACAGACA
Found at i:55648625 original size:53 final size:53
Alignment explanation
Indices: 55648567--55648748 Score: 197
Period size: 53 Copynumber: 3.4 Consensus size: 53
55648557 GGAAAATCAA
* * * * *
55648567 TCATTTAACCCTGAGGGGAAAAATAGTCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTCAGGGGCATAACAGTCATTTTACCCTACAGGGGCATTACGG
* * *
55648620 TCATTTTACCCTACAGGCGCATGACGGTCATTTTACCCTACAGGGGCATTAC-G
1 TCATTTTACCCT-CAGGGGCATAACAGTCATTTTACCCTACAGGGGCATTACGG
* * * *
55648673 TCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAGGGGCGTTACGG
1 TCATTTTACCC-TCAGGGGCATAACAGTCATTTTACCCTACAGGGGCATTACGG
*
55648727 TTC-TTTTACCCTACAGAGGCAT
1 -TCATTTTACCCT-CAGGGGCAT
55648749 TACGACTATG
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
53 57 0.53
54 49 0.45
55 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (53 bp):
TCATTTTACCCTCAGGGGCATAACAGTCATTTTACCCTACAGGGGCATTACGG
Found at i:55648676 original size:80 final size:80
Alignment explanation
Indices: 55648592--55648752 Score: 243
Period size: 80 Copynumber: 2.0 Consensus size: 80
55648582 GGGAAAAATA
* * *
55648592 GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGCGCATGACGG-TCATTTTAC
1 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAGGCGCATGACGGTTC-TTTTAC
*
55648656 CCTACAGGGGCATTAC
65 CCTACAGAGGCATTAC
* * *
55648672 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAGGGGCGTTACGGTTCTTTTACC
1 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAGGCGCATGACGGTTCTTTTACC
55648737 CTACAGAGGCATTAC
66 CTACAGAGGCATTAC
55648752 G
1 G
55648753 ACTATGCAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 71 0.97
81 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (80 bp):
GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAGGCGCATGACGGTTCTTTTACC
CTACAGAGGCATTAC
Found at i:55648751 original size:27 final size:27
Alignment explanation
Indices: 55648592--55648752 Score: 236
Period size: 27 Copynumber: 6.0 Consensus size: 27
55648582 GGGAAAAATA
55648592 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
55648619 GTCATTTTACCCTACAGGCGCATGACG
1 GTCATTTTACCCTACAGGGGCATTACG
55648646 GTCATTTTACCCTACAGGGGCATTAC-
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
55648672 GTCATTTTACCCAACAGCGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
55648699 GTCATTTTACCCTACAGGGGCGTTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
55648726 GTTC-TTTTACCCTACAGAGGCATTACG
1 G-TCATTTTACCCTACAGGGGCATTACG
55648753 ACTATGCAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 24 0.20
27 94 0.78
28 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:55661192 original size:54 final size:54
Alignment explanation
Indices: 55661110--55661249 Score: 169
Period size: 54 Copynumber: 2.6 Consensus size: 54
55661100 GTCGATATAC
* * * *
55661110 GACCGAAATACCCTCATAGGGTAAAATGA-TCGAAATACTCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGATAAAATGACT-AAAATACCCCCATAGGGTAAAAT
55661164 GACCGAAATACCCCCATAGGATAAAATGACTAAAATACCCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGATAAAATGACTAAAATACCCCCATAGGGTAAAAT
* **
55661218 GTCCGTTATA-CCCC-TAGGAGATAAAATGACTA
1 GACCGAAATACCCCCATA-G-GATAAAATGACTA
55661250 TTATGGCCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
52 2 0.03
53 5 0.07
54 68 0.89
55 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (54 bp):
GACCGAAATACCCCCATAGGATAAAATGACTAAAATACCCCCATAGGGTAAAAT
Found at i:55661231 original size:27 final size:27
Alignment explanation
Indices: 55661110--55661218 Score: 164
Period size: 27 Copynumber: 4.0 Consensus size: 27
55661100 GTCGATATAC
*
55661110 GACCGAAATACCCTCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* *
55661137 GATCGAAATACTCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
*
55661164 GACCGAAATACCCCCATAGGATAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
**
55661191 GACTAAAATACCCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
55661218 G
1 G
55661219 TCCGTTATAC
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
GACCGAAATACCCCCATAGGGTAAAAT
Found at i:55661253 original size:27 final size:28
Alignment explanation
Indices: 55661117--55661253 Score: 92
Period size: 27 Copynumber: 5.1 Consensus size: 28
55661107 TACGACCGAA
* * *
55661117 ATACCCTCATAGGG-TAAAATGATCGA-A
1 ATACCCCCATAGGGATAAAATGA-CTATT
* * *
55661144 ATACTCCCATAGGG-TAAAATGACCGA-A
1 ATACCCCCATAGGGATAAAATGA-CTATT
**
55661171 ATACCCCCATA-GGATAAAATGACTAAA
1 ATACCCCCATAGGGATAAAATGACTATT
* **
55661198 ATACCCCCATAGGG-TAAAATGTCCGTT
1 ATACCCCCATAGGGATAAAATGACTATT
55661225 ATA-CCCC-TAGGAGATAAAATGACTATT
1 ATACCCCCATAGG-GATAAAATGACTATT
55661252 AT
1 AT
55661254 GGCCTTATGT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.04
26 9 0.10
27 77 0.84
28 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (28 bp):
ATACCCCCATAGGGATAAAATGACTATT
Found at i:55661693 original size:28 final size:28
Alignment explanation
Indices: 55661617--55661693 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
55661607 ACTGTAATGT
*
55661617 TACTATATTGGGCTAAGGCCCACACTGA
1 TACTATATTGGGCTAAGGCCTACACTGA
* *
55661645 TACTATATTGGGCTAAAGCCTACACTGC
1 TACTATATTGGGCTAAGGCCTACACTGA
55661673 TACTGA-ATTGGGCTAAGGCCT
1 TACT-ATATTGGGCTAAGGCCT
55661694 TCATTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (28 bp):
TACTATATTGGGCTAAGGCCTACACTGA
Found at i:55664212 original size:18 final size:18
Alignment explanation
Indices: 55664200--55664253 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
55664190 CCTTCTTCTC
55664200 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
55664218 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
55664236 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
55664254 GGGTTGCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTTTCCCCTTCCCCTT
Found at i:55664215 original size:6 final size:6
Alignment explanation
Indices: 55664198--55664253 Score: 85
Period size: 6 Copynumber: 9.2 Consensus size: 6
55664188 ACCCTTCTTC
* *
55664198 TCCCCTT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT TCCCTT TCCCCT
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
55664247 TCCCCT T
1 TCCCCT T
55664254 GGGTTGCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 40 0.89
7 5 0.11
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:55668027 original size:19 final size:21
Alignment explanation
Indices: 55667980--55668027 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
55667970 TATATTTATT
* *
55667980 TATAAATAAATCATTGTAATA
1 TATAAAAAAATCATTGTAAAA
*
55668001 TATGAAAAAAT-ATT-TAAAA
1 TATAAAAAAATCATTGTAAAA
55668020 TATAAAAA
1 TATAAAAA
55668028 TTTATTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TATAAAAAAATCATTGTAAAA
Found at i:55668037 original size:16 final size:18
Alignment explanation
Indices: 55668014--55668065 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
55668004 GAAAAAATAT
* *
55668014 TTAAAATATAAAAATTTA
1 TTAATATATATAAATTTA
55668032 TTAATATGTATATAAATTTA
1 TTAATA--TATATAAATTTA
*
55668052 TTAATATATGTAAA
1 TTAATATATATAAA
55668066 AATAACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
20 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAATATATATAAATTTA
Found at i:55668060 original size:22 final size:20
Alignment explanation
Indices: 55668020--55668068 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
55668010 ATATTTAAAA
55668020 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
55668040 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
55668060 TGTAAAAAT
1 TATAAAAAT
55668069 AACTTTTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:55668195 original size:20 final size:20
Alignment explanation
Indices: 55668156--55668196 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
55668146 AAATATTTTC
*
55668156 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTCCCAGAAA
*
55668176 AGTAAATCATTTCCCGGAAA
1 AGTAAATCATTTCCCAGAAA
55668196 A
1 A
55668197 CATTTTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (20 bp):
AGTAAATCATTTCCCAGAAA
Found at i:55668625 original size:21 final size:21
Alignment explanation
Indices: 55668592--55668644 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
55668582 CGCTGTTTCT
* * *
55668592 AATCTTACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
55668613 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
55668634 AATCTCACCGC
1 AATCTCACCGC
55668645 CACCGCAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:55670634 original size:2 final size:2
Alignment explanation
Indices: 55670627--55670664 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
55670617 TAGAACCCAT
55670627 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
55670665 TATATATGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55675574 original size:46 final size:45
Alignment explanation
Indices: 55675507--55675719 Score: 228
Period size: 36 Copynumber: 5.1 Consensus size: 45
55675497 AGTACTTCTA
* *
55675507 ATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTG
55675553 ATCAAGTGAAAAAGTGATAA---GT-G----G-TACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
* * *
55675589 ATCAAGAGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTG
55675635 ATCAAGTGAAAAAGTGATAAGT-GT--C--A--T--ACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
*
55675671 ATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
55675716 ATCA
1 ATCA
55675720 GGGACAAATG
Statistics
Matches: 140, Mismatches: 8, Indels: 39
0.75 0.04 0.21
Matches are distributed among these distances:
36 60 0.43
37 3 0.02
38 1 0.01
39 3 0.02
40 2 0.01
41 1 0.01
42 1 0.01
43 3 0.02
45 16 0.11
46 50 0.36
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (45 bp):
ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
Found at i:55675644 original size:82 final size:81
Alignment explanation
Indices: 55675507--55675719 Score: 356
Period size: 82 Copynumber: 2.6 Consensus size: 81
55675497 AGTACTTCTA
*
55675507 ATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGAGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
55675572 AGTGGT-ACACTTATCTG
65 AGT-GTCACACTTATCTG
55675589 ATCAAGAGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGAGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
*
55675654 AGTGTCATACTTATCTG
65 AGTGTCACACTTATCTG
* *
55675671 ATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCA
1 ATCAAGAGACAAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCA
55675720 GGGACAAATG
Statistics
Matches: 125, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
81 23 0.18
82 102 0.82
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (81 bp):
ATCAAGAGACAAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAA
GTGTCACACTTATCTG
Found at i:55677342 original size:43 final size:42
Alignment explanation
Indices: 55677265--55677420 Score: 188
Period size: 42 Copynumber: 3.7 Consensus size: 42
55677255 AGGCTAAACA
* ** *
55677265 GAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTGAATC
1 GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
*
55677307 GAAACCCATAAGGGGTTAAACTGAAGCTCAAAAGAGCTTAA-C
1 GAAACCCATAA-GGGTTAAACGGAAGCTCAAAAGAGCTTAATC
* * * *
55677349 AGAAACCCATTAGGGTTAAACTGAAGCTAAAAAGAGCTTAATG
1 -GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
* *
55677392 GAAACCCATTAGGGTTAAACGGAAACTCA
1 GAAACCCATAAGGGTTAAACGGAAGCTCA
55677421 TATGACTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
42 66 0.66
43 34 0.34
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
Found at i:55679801 original size:3 final size:3
Alignment explanation
Indices: 55679793--55679829 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
55679783 CTTTGCTTAT
*
55679793 ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
55679830 TAAAAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:55681030 original size:9 final size:9
Alignment explanation
Indices: 55681013--55681049 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55681003 TGAGTTTTCG
55681013 AATTCGAAT
1 AATTCGAAT
*
55681022 AACTCGAAT
1 AATTCGAAT
55681031 AATTCGAAT
1 AATTCGAAT
55681040 AATTCGAAT
1 AATTCGAAT
55681049 A
1 A
55681050 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:55683891 original size:50 final size:50
Alignment explanation
Indices: 55683824--55684121 Score: 301
Period size: 50 Copynumber: 5.8 Consensus size: 50
55683814 TTTCTTGTAC
* * * * * ** *
55683824 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTAGG
* * * * * *
55683874 TGCCCATGCCATGTCCCAGACATGGTCTTAAAGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTAGG
* * * *
55683924 TGCTAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTAGG
55683974 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCA-G
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCT-AGG
* * * *
55684024 TGCCAACGCCATGTACCAGACATGGTCTTACATGTGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC---ATCT--A-GG
* * *
55684080 TGCCAATGCCATGTCTCAAACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
55684122 TTACCCAAAT
Statistics
Matches: 206, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
50 165 0.80
53 4 0.02
54 1 0.00
56 36 0.17
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:55684035 original size:150 final size:152
Alignment explanation
Indices: 55683824--55684122 Score: 361
Period size: 150 Copynumber: 2.0 Consensus size: 152
55683814 TTTCTTGTAC
* * * ** * * *
55683824 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTC
1 TGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTA
* *
55683889 CCAGACATGGTCTTAAAGGGGACCTCTC-ATCT-TGGTGCTAACGCCATGTCCCAAACATGGTCT
66 CCAGACATGGTCTTAAAGGGGACCTCTCAATCTATGATGCCAACGCCATGTCCCAAACATGGTCT
55683952 TACATGGGACCTCTTATCTCGA
131 TACATGGGACCTCTTATCTCGA
* * *
55683974 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCA-GTGCCAACGCCATGT
1 TGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATAT-AGGTGCCAACGCCATGT
* * * * *
55684038 ACCAGACATGGTCTTACATGTGACCTCTCATAATCTCAATGATGCCAATGCCATGTCTCAAACAT
65 ACCAGACATGGTCTTAAAGGGGACCTCTC--AATCT--ATGATGCCAACGCCATGTCCCAAACAT
*
55684103 GGTCTTACATGGGATCTCTT
126 GGTCTTACATGGGACCTCTT
55684123 TACCCAAATG
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
150 77 0.63
151 1 0.01
153 4 0.03
156 41 0.33
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (152 bp):
TGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTA
CCAGACATGGTCTTAAAGGGGACCTCTCAATCTATGATGCCAACGCCATGTCCCAAACATGGTCT
TACATGGGACCTCTTATCTCGA
Found at i:55685830 original size:43 final size:43
Alignment explanation
Indices: 55685782--55686468 Score: 628
Period size: 43 Copynumber: 15.9 Consensus size: 43
55685772 CCGGTACGTA
* *
55685782 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
** * * *
55685825 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAT
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * * *
55685868 AGTGCATCATCAGATGAAA-CTGAAACTACTATATTGGCACACAT
1 AGTGCATCATCGGAT-AAATC-GAAGCAAATATACTGGCACACAC
* * * * * * *
55685912 AGGGCATCATTGGATCAACCGAAGAAAATATATTGGCACATAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
** * *
55685955 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * ** *
55685998 AGTGCATCATCAGATGAAA-CTGAAACTACTATTTTGGCACACAT
1 AGTGCATCATCGGAT-AAATC-GAAGCAAATATACTGGCACACAC
* * * *
55686042 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * * *
55686085 AGTGCATCATCGAATGAAACCGAAGCTACTCTGCTGGCACACAC
1 AGTGCATCATCGGAT-AAATCGAAGCAAATATACTGGCACACAC
* * * *
55686129 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * *
55686172 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * * *
55686215 AGTGCATCATCAGATGAAATCAAAGCTAGTGA-ATTTGCACACAC
1 AGTGCATCATCGGAT-AAATCGAAGCAAAT-ATACTGGCACACAC
* *
55686259 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* *
55686302 AGTGCATCATCGGATATATCGAAGCAAATATACTAG--CACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * *
55686343 AGTGCATCATCAGATATACCAAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * *
55686386 AGTGCTTAATCAGATATACCGAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
* * * * *
55686429 AATGCATGATCGGATATACCGAAGCAAATATACAGGCACA
1 AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACA
55686469 TGTAGTGCAT
Statistics
Matches: 524, Mismatches: 108, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
41 37 0.07
42 1 0.00
43 351 0.67
44 134 0.26
45 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (43 bp):
AGTGCATCATCGGATAAATCGAAGCAAATATACTGGCACACAC
Found at i:55685936 original size:130 final size:128
Alignment explanation
Indices: 55685782--55686468 Score: 675
Period size: 130 Copynumber: 5.3 Consensus size: 128
55685772 CCGGTACGTA
55685782 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGAT-AATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * ** * *
55685847 AGCAAATATACTAGCACACATAGTGCATCATCAGATGAAACTGAAA-CTACTATATTGGCACACA
65 AGCAAATATACTAGCACACACAGTGCATCATCAGAT-AAA-TCAAAGAAAATATACTGGCACACA
*
55685911 T
128 C
* * * *
55685912 AGGGCATCATTGGATCAACCGAAGAAAATATATTGGCACATACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGAT-AATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* ** * **
55685977 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTGAAA-CTACTATTTTGGCACACA
65 AGCAAATATACTAGCACACACAGTGCATCATCAGAT-AAA-TCAAAGAAAATATACTGGCACACA
*
55686041 T
128 C
* * * *
55686042 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACACAGTGCATCATCGAATGAAACCG
1 AGTGCATCATTGGAT-AATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAAT-ATATCG
* * * * * *
55686107 AAGCTACTCTGCTGGCACACACAGTGCATCAT-TGTATAAATCAAAGAAAATATACTGGCACACA
64 AAGCAAATATACTAGCACACACAGTGCATCATCAG-ATAAATCAAAGAAAATATACTGGCACACA
55686171 C
128 C
* * * * * * *
55686172 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACACACAGTGCATCATCAGATGAAATCA
1 AGTGCATCATTGGATA-ATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAAT-ATATCG
* * * * *
55686237 AAGCTAGTGA-ATTTGCACACACAGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACA
64 AAGCAAAT-ATACTAGCACACACAGTGCATCATCAGATAAATCAAAGAAAATATACTGGCACACA
55686301 C
128 C
* * * * * *
55686302 AGTGCATCATCGGATATATCGAAGCAAATATACTAG--CACACAGTGCATCATCAGATATACCAA
1 AGTGCATCATTGGATA-ATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * * * * * *
55686365 AGCAAATATACTGGCACACACAGTGCTTAATCAGATATACCGAAGCAAATATACTGGCACACAC
65 AGCAAATATACTAGCACACACAGTGCATCATCAGATAAATCAAAGAAAATATACTGGCACACAC
* * * * * *
55686429 AATGCATGATCGGATATACCGAAGCAAATATACAGGCACA
1 AGTGCATCATTGGATA-ATCGAAGAAAATATACTGGCACA
55686469 TGTAGTGCAT
Statistics
Matches: 486, Mismatches: 62, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
126 1 0.00
127 87 0.18
128 20 0.04
129 7 0.01
130 337 0.69
131 34 0.07
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (128 bp):
AGTGCATCATTGGATAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGAA
GCAAATATACTAGCACACACAGTGCATCATCAGATAAATCAAAGAAAATATACTGGCACACAC
Found at i:55686035 original size:87 final size:85
Alignment explanation
Indices: 55685782--55686495 Score: 514
Period size: 87 Copynumber: 8.3 Consensus size: 85
55685772 CCGGTACGTA
** * * * *
55685782 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATA-TCG
1 AGTGCATCATCAGATATATCGAAGCAAATATACTGGCACACACAGTGCATCATC-GATAAACT-G
* * *
55685846 AAGCAAATATACTAGCACACAT
64 AAACAAATATACTGGCACACAC
* * * * * * * * * *
55685868 AGTGCATCATCAGATGA-AACTGAAACTACTATATTGGCACACATAGGGCATCATTGGATCAACC
1 AGTGCATCATCAGAT-ATATC-GAAGCAAATATACTGGCACACACAGTGCATCA-TCGATAAACT
* *
55685932 GAAGA-AAATATATTGGCACATAC
63 GAA-ACAAATATACTGGCACACAC
* *
55685955 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTG
1 AGTGCATCATCAGATATATCGAAGCAAATATACTGGCACACACAGTGCATCATC-GAT-AAACTG
* * ** *
55686020 AAACTACTATTTTGGCACACAT
64 AAACAAATATACTGGCACACAC
** * * *
55686042 AGTGCATCATTGGATCA-ACCGAAGAAAATATACTGGCACACACAGTGCATCATCGAATGAAACC
1 AGTGCATCATCAGAT-ATATCGAAGCAAATATACTGGCACACACAGTGCATCATCG-AT-AAACT
* * * * *
55686106 GAAGCTACTCTGCTGGCACACAC
63 GAAACAAATATACTGGCACACAC
* * * * * *
55686129 AGTGCATCAT-TGTATAAATCAAAGAAAATATACTGGCACACACAATGCATCATCGAATATA-TC
1 AGTGCATCATCAG-ATATATCGAAGCAAATATACTGGCACACACAGTGCATCATCG-ATAAACT-
*
55686192 GAAGCAAATATACTGGCACACAC
63 GAAACAAATATACTGGCACACAC
* * * * * *
55686215 AGTGCATCATCAGATGAAATCAAAGCTAGTGA-ATTTGCACACACAGTGCATCATCGGATAAA-T
1 AGTGCATCATCAGAT-ATATCGAAGCAAAT-ATACTGGCACACACAGTGCATCATC-GATAAACT
* *
55686278 CAAAGAAAATATACTGGCACACAC
63 GAAA-CAAATATACTGGCACACAC
* * * *
55686302 AGTGCATCATCGGATATATCGAAGCAAATATACTAG--CACACAGTGCATCATCAGATATAC-CA
1 AGTGCATCATCAGATATATCGAAGCAAATATACTGGCACACACAGTGCATCATC-GATAAACTGA
55686364 AAGCAAATATACTGGCACACAC
65 AA-CAAATATACTGGCACACAC
* * * * * * *
55686386 AGTGCTTAATCAGATATACCGAAGCAAATATACTGGCACACACAATGCATGATCGGATATACCGA
1 AGTGCATCATCAGATATATCGAAGCAAATATACTGGCACACACAGTGCATCATC-GATAAACTGA
* * ***
55686451 AGCAAATATACAGGCACATGT
65 AACAAATATACTGGCACACAC
* * *
55686472 AGTGCATCGTTAGATATACCGAAG
1 AGTGCATCATCAGATATATCGAAG
55686496 TATAACCTGT
Statistics
Matches: 506, Mismatches: 98, Indels: 48
0.78 0.15 0.07
Matches are distributed among these distances:
84 75 0.15
85 2 0.00
86 152 0.30
87 273 0.54
88 4 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (85 bp):
AGTGCATCATCAGATATATCGAAGCAAATATACTGGCACACACAGTGCATCATCGATAAACTGAA
ACAAATATACTGGCACACAC
Found at i:55687408 original size:13 final size:13
Alignment explanation
Indices: 55687390--55687417 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55687380 CTAATTGTAT
55687390 ATAGAAAAATAAC
1 ATAGAAAAATAAC
55687403 ATAGAAAAATAAC
1 ATAGAAAAATAAC
55687416 AT
1 AT
55687418 TGACAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (13 bp):
ATAGAAAAATAAC
Found at i:55696927 original size:12 final size:12
Alignment explanation
Indices: 55696910--55696941 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55696900 ATTCGTAGAT
55696910 GCATGACAGTAA
1 GCATGACAGTAA
*
55696922 GCATGAAAGTAA
1 GCATGACAGTAA
55696934 GCATGACA
1 GCATGACA
55696942 TGATCATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.16
Consensus pattern (12 bp):
GCATGACAGTAA
Found at i:55712571 original size:22 final size:22
Alignment explanation
Indices: 55712540--55712587 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
55712530 TGTCTTAAGG
55712540 CAAAAACTTGCATATCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
* ** *
55712562 CAAAAGCTTGTTTGTCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
55712584 CAAA
1 CAAA
55712588 GTTTACCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
CAAAAACTTGCATATCTCGAGA
Found at i:55724213 original size:12 final size:12
Alignment explanation
Indices: 55724181--55724214 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
55724171 AGTTGTTAAA
55724181 TTGTTAG-TAGT
1 TTGTTAGTTAGT
55724192 TTGGTTAGTTAGT
1 TT-GTTAGTTAGT
55724205 TTGTTAGTTA
1 TTGTTAGTTA
55724215 TTTAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 13 0.62
13 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
TTGTTAGTTAGT
Found at i:55728543 original size:24 final size:24
Alignment explanation
Indices: 55728481--55728543 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 24
55728471 CAAGAACCAT
*
55728481 ATAACGGGAAGCTCGTGAGAGCCAA
1 ATAAC-GGAAGCTCATGAGAGCCAA
* * *
55728506 ATATCAGAATGCTCATGAGAG-CTA
1 ATAACGGAA-GCTCATGAGAGCCAA
55728530 ATAACGGAACGCTC
1 ATAACGGAA-GCTC
55728544 TTTCGAGCTG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
ATAACGGAAGCTCATGAGAGCCAA
Found at i:55732581 original size:46 final size:46
Alignment explanation
Indices: 55732507--55732645 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
55732497 ACAAGGCTAT
*
55732507 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
55732553 AACTCAGTATGGTTTTCTTTACCAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
**
55732599 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTA-TGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACT-TTTCAC
55732645 A
1 A
55732646 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 84 0.99
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:55733916 original size:17 final size:17
Alignment explanation
Indices: 55733872--55733904 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55733862 AAATTCTTTT
*
55733872 TAAATCACAAAATTCAA
1 TAAATCAAAAAATTCAA
55733889 TAAATCAAAAAATTCA
1 TAAATCAAAAAATTCA
55733905 CTAATTTAAA
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:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCAAAAAATTCAA
Found at i:55742691 original size:25 final size:25
Alignment explanation
Indices: 55742663--55742801 Score: 152
Period size: 25 Copynumber: 5.6 Consensus size: 25
55742653 GTAAACTTGA
* *
55742663 GAATTCTCTGGAAAGCCTTTGTGGT
1 GAATTATCTGGAAAGCCTTTGTGGC
* ** *
55742688 GAATTCTCTAAAAAGCTTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* * *
55742713 GTATCATTTGGAAAGCCTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* * *
55742738 GAATTATTTGGAAAGCCCTTGTAGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* *
55742763 GTATTATTTGGAAAGCCTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
55742788 GAATTATCTGGAAA
1 GAATTATCTGGAAA
55742802 TTCATTATGG
Statistics
Matches: 94, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 94 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (25 bp):
GAATTATCTGGAAAGCCTTTGTGGC
Found at i:55742753 original size:50 final size:50
Alignment explanation
Indices: 55742671--55742801 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
55742661 GAGAATTCTC
* * ** ** *
55742671 TGGAAAGCCTTTGTGGTGAATTCTCTAAAAAGCTTTTGTGGCGTATCATT
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTAGCGTATCATT
* *
55742721 TGGAAAGCCTTTGTGGCGAATTATTTGGAAAGCCCTTGTAGCGTATTATT
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTAGCGTATCATT
55742771 TGGAAAGCCTTTGTGGCGAATTATCTGGAAA
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAA
55742802 TTCATTATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (50 bp):
TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTAGCGTATCATT
Found at i:55751202 original size:42 final size:42
Alignment explanation
Indices: 55751155--55751266 Score: 197
Period size: 42 Copynumber: 2.6 Consensus size: 42
55751145 AACTACCTCC
55751155 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
1 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
55751197 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
1 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
* *
55751239 ATTGCATTATAGAAATAAATTTTGACAT
1 ATTGCATCATAG-AATAAATTCTGACAT
55751267 GAAAATTCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 53 0.79
43 14 0.21
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (42 bp):
ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
Found at i:55752943 original size:16 final size:17
Alignment explanation
Indices: 55752892--55752927 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
55752882 GTTTTTTATT
55752892 TTTTGGATTTAGGGTCA
1 TTTTGGATTTAGGGTCA
*
55752909 TTTT-GATTTAGGGTTA
1 TTTTGGATTTAGGGTCA
55752925 TTT
1 TTT
55752928 AGGGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (17 bp):
TTTTGGATTTAGGGTCA
Found at i:55752949 original size:6 final size:6
Alignment explanation
Indices: 55752934--55752968 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
55752924 ATTTAGGGTT
*
55752934 ATTTTG ATTTTA ATTTTG ATTTTG ATTTTGG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT-G ATTT
55752969 AGGGGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (6 bp):
ATTTTG
Found at i:55755146 original size:77 final size:77
Alignment explanation
Indices: 55755060--55755233 Score: 224
Period size: 77 Copynumber: 2.3 Consensus size: 77
55755050 TTAGTGAGTG
* * * *
55755060 TTTTTTAATATGCATGCAGTTTTTTTTAATTTATCTATGTATGATTGTTGGTGGGGTTGGTCGCA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTATGTATGATTGTTGGTGGGGATAGTCACA
55755125 TGC-GATTGACTA
66 TGCTG-TTGACTA
* * * * * *
55755137 TTTTTTAATATACATGTAGTGTTTTTTAATTTGTCTGTGTATGATTGTTGGTGGGGATAGTTATA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTATGTATGATTGTTGGTGGGGATAGTCACA
*
55755202 TGCTGTTGACTC
66 TGCTGTTGACTA
*
55755214 TTTTTTAATATGCATACAGT
1 TTTTTTAATATGCATGCAGT
55755234 AACGTTTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 81 0.99
78 1 0.01
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (77 bp):
TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTATGTATGATTGTTGGTGGGGATAGTCACA
TGCTGTTGACTA
Found at i:55756005 original size:21 final size:21
Alignment explanation
Indices: 55755921--55756011 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
55755911 GTGGTTGCCT
*
55755921 CAACTCAACAACAGGCTACCC
1 CAACTCAACAAGAGGCTACCC
* **
55755942 CAAATCAGTAAGAGAG-TACCC
1 CAACTCAACAAGAG-GCTACCC
* **
55755963 CAACTCAGCAAGAGAATACCC
1 CAACTCAACAAGAGGCTACCC
*
55755984 CAACTCAACAAGAGGCTGCCC
1 CAACTCAACAAGAGGCTACCC
55756005 CAACTCA
1 CAACTCA
55756012 GTTACAAACT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 56 0.98
22 1 0.02
ACGTcount: A:0.40, C:0.35, G:0.14, T:0.11
Consensus pattern (21 bp):
CAACTCAACAAGAGGCTACCC
Found at i:55756830 original size:36 final size:36
Alignment explanation
Indices: 55756790--55756913 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
55756780 CATGTATAAC
55756790 AACATAAGCAACAATATACCAACAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
** * * * * *
55756826 AACATAAGCTGGTTCTCCATGTATACCAACAGCCATGTATA-AC
1 AACATAA----G--CAACA-ATATACCAACAACAATAT-TACAA
*
55756869 AACATAAGCAACAATATACCAGCAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
55756905 AACATAAGC
1 AACATAAGC
55756914 TGGTTAGCCA
Statistics
Matches: 64, Mismatches: 15, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
35 2 0.03
36 30 0.47
37 3 0.05
39 1 0.02
40 1 0.02
42 3 0.05
43 22 0.34
44 2 0.03
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.19
Consensus pattern (36 bp):
AACATAAGCAACAATATACCAACAACAATATTACAA
Found at i:55756863 original size:16 final size:16
Alignment explanation
Indices: 55756842--55756872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55756832 AGCTGGTTCT
*
55756842 CCATGTATACCAACAG
1 CCATGTATAACAACAG
55756858 CCATGTATAACAACA
1 CCATGTATAACAACA
55756873 TAAGCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (16 bp):
CCATGTATAACAACAG
Found at i:55756878 original size:79 final size:79
Alignment explanation
Indices: 55756747--55756993 Score: 431
Period size: 79 Copynumber: 3.1 Consensus size: 79
55756737 TGTAAGCAAC
* *
55756747 AACATAAGCTAGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAA
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
55756812 CAACAATATTACAA
66 CAACAATATTACAA
** *
55756826 AACATAAGCTGGTTCTCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAG
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
55756891 CAACAATATTACAA
66 CAACAATATTACAA
* *
55756905 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAATAACATAAGAAACAATATACCAG
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
55756970 CAACAATATTACAA
66 CAACAATATTACAA
55756984 AACATAAGCT
1 AACATAAGCT
55756994 AGTTTTCAGT
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 158 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.21
Consensus pattern (79 bp):
AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
CAACAATATTACAA
Found at i:55758598 original size:25 final size:25
Alignment explanation
Indices: 55758560--55758648 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
55758550 AATAACGGGT
*
55758560 AGCTCCGAAGAGCC-TTTAATCGAGA
1 AGCTCCGAAGAGCCATAT-ATCGAGA
* *
55758585 AGCTCCGGATAGCCATATATCGAGA
1 AGCTCCGAAGAGCCATATATCGAGA
* *
55758610 AG-TTC-AAGCGAGCCATAT-TAG-GA
1 AGCTCCGAA--GAGCCATATATCGAGA
*
55758633 AGCTCCGGAGAGCCAT
1 AGCTCCGAAGAGCCAT
55758649 TAATGGGAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 12 0.24
24 6 0.12
25 30 0.60
26 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATATATCGAGA
Found at i:55758645 original size:23 final size:25
Alignment explanation
Indices: 55758581--55758648 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
55758571 GCCTTTAATC
* *
55758581 GAGAAGCTCCGGATAGCCATATATC
1 GAGAAGCTCCGGAGAGCCATATATA
* ** *
55758606 GAGAAGTTCAAGCGAGCCATAT-TA
1 GAGAAGCTCCGGAGAGCCATATATA
55758630 G-GAAGCTCCGGAGAGCCAT
1 GAGAAGCTCCGGAGAGCCAT
55758649 TAATGGGAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
23 14 0.42
24 2 0.06
25 17 0.52
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGAAGCTCCGGAGAGCCATATATA
Found at i:55758676 original size:25 final size:26
Alignment explanation
Indices: 55758641--55758699 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
55758631 GAAGCTCCGG
*
55758641 AGAGCCATTAA-TGGGAAGCTCACAA
1 AGAGCCATTAATTGGGAAACTCACAA
* * *
55758666 AGAGCCTTTAATTGGGAAACTTACGA
1 AGAGCCATTAATTGGGAAACTCACAA
55758692 AGAGCCAT
1 AGAGCCAT
55758700 ATAACGGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATTGGGAAACTCACAA
Found at i:55774929 original size:14 final size:15
Alignment explanation
Indices: 55774899--55774935 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
55774889 ATGAGAAGAG
55774899 AGAAAAATAAAAGGGA
1 AGAAAAA-AAAAGGGA
55774915 AGAAAAAAAAA-GGA
1 AGAAAAAAAAAGGGA
55774929 A-AAAAAA
1 AGAAAAAA
55774936 GAACAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 4 0.19
15 4 0.19
16 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAAGGGA
Found at i:55775624 original size:33 final size:35
Alignment explanation
Indices: 55775573--55775645 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 35
55775563 AATATTAAAA
*
55775573 ATTTCAAAATGTAAAATTTATATATGAA-ATATTAT
1 ATTTTAAAATGTAAAATTTATATAT-AATATATTAT
55775608 -TTTTAAAAT-TAAAATTTATATATAATATATTAT
1 ATTTTAAAATGTAAAATTTATATATAATATATTAT
55775641 ATTTT
1 ATTTT
55775646 CATGTGTGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 2 0.06
33 21 0.60
34 12 0.34
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (35 bp):
ATTTTAAAATGTAAAATTTATATATAATATATTAT
Found at i:55777201 original size:34 final size:34
Alignment explanation
Indices: 55777098--55777202 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
55777088 GGTTTGAATT
* * *
55777098 AAAAAAAGATAAAAGGGTTTTGATTAGGGTCTAA
1 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAA
* * ***
55777132 AAAAAGA-ATTAGGGGGTTTTGTTTAAAAT-TAAA
1 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCT-AA
55777165 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAA
1 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAA
55777199 AAAA
1 AAAA
55777203 GGGCTAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
32 1 0.02
33 23 0.42
34 30 0.55
35 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.30
Consensus pattern (34 bp):
AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAA
Found at i:55777747 original size:14 final size:14
Alignment explanation
Indices: 55777730--55777760 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55777720 TGTAATGGTA
55777730 TTATTGTACTATAT
1 TTATTGTACTATAT
*
55777744 TTATTGTATTATAT
1 TTATTGTACTATAT
55777758 TTA
1 TTA
55777761 GGTGATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTGTACTATAT
Found at i:55779617 original size:96 final size:95
Alignment explanation
Indices: 55779517--55779828 Score: 351
Period size: 96 Copynumber: 3.3 Consensus size: 95
55779507 TGGGGTTTTT
* ** * * * * *
55779517 AAAAAATTAAATAAACAAAGGATTAGGGTTTCTTAATTAAATTGATTATAAAATTTTCAAAATTA
1 AAAAAATCAAATAAATTAAGGTTTAGGGTTTCTTGAGTAAATTAATTATAAAATTTTAAAAATTA
* *
55779582 GATTAGGGTTTCGTGTTTATAGTTTTTAAGG
66 GATTAGGGTTTAGTGTTTA-GGTTTTTAAGG
* * *
55779613 AAAAAGTCAATTAAATTAAGGTTTAGGGTTAT-TTGAGTAAATTAATTATAAATTTTTAAGAAAT
1 AAAAAATCAAATAAATTAAGGTTTAGGGTT-TCTTGAGTAAATTAATTATAAAATTTTAA-AAAT
* * *
55779677 CAGATTAGAGTTTAGTGTTAAGGGTTTTTAA-G
64 TAGATTAGGGTTTAGTGTTTA-GGTTTTTAAGG
* *
55779709 AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT-AAATTTTAAAAAAAT
1 AAAAAATCAAATAAATTAAGGTTTAGGGTTTCTTGAGTAAATTAATTATAAAATTTT--AAAAAT
* *
55779773 TAGTTTAGGGTTTAGTGTTTAGGGTTTTAAGG
64 TAGATTAGGGTTTAGTGTTTAGGTTTTTAAGG
* *
55779805 AAAAACTCAAATAAATTAGGGTTT
1 AAAAAATCAAATAAATTAAGGTTT
55779829 GGGATTTAGG
Statistics
Matches: 182, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
95 14 0.08
96 136 0.75
97 32 0.18
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (95 bp):
AAAAAATCAAATAAATTAAGGTTTAGGGTTTCTTGAGTAAATTAATTATAAAATTTTAAAAATTA
GATTAGGGTTTAGTGTTTAGGTTTTTAAGG
Found at i:55780138 original size:126 final size:126
Alignment explanation
Indices: 55779899--55780161 Score: 422
Period size: 126 Copynumber: 2.1 Consensus size: 126
55779889 TTTTTTACTT
*
55779899 CAGTAGTTAC-TGAAAAAATAATTTCGAGAAGACGTTTTTGAGTAAATAGTGGTAAAAACGCTTT
1 CAGTAGTT-CTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGTAAAAACGCTTT
* * *
55779963 AAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACATAGACGCTCTTTTGCTA
65 AAACAGGATACATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACATAGACGCTATTTTGCTA
*
55780025 CAGTGGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGT-GTAAAAAACGCTTT
1 CAGTAGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGT-AAAAACGCTTT
* * *
55780089 AAACAGGATACTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTAGACGTTATTTTGCTA
65 AAACAGGATACATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACATAGACGCTATTTTGCTA
55780151 CAGTAGTTCTT
1 CAGTAGTTCTT
55780162 ATTTGGCTGA
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
125 3 0.02
126 123 0.98
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (126 bp):
CAGTAGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGTAAAAACGCTTTA
AACAGGATACATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACATAGACGCTATTTTGCTA
Found at i:55781655 original size:61 final size:59
Alignment explanation
Indices: 55781465--55781658 Score: 188
Period size: 61 Copynumber: 3.3 Consensus size: 59
55781455 ATATTGTATT
*
55781465 ATTTATATTTT-TTAAAATTAAATAATATAGAAATATTCAAAATATTGTCTTATTTAAAAGA
1 ATTTCTATTTTATT-AAA-TAAATAATATAGAAATATTCAAAATATTGTCTTA-TTAAAAGA
* * * * ** *
55781526 ATTTCTATTTTATT-AA-AAATATTAAAGTAA-ATT-ACAAT-TACT-TTATTCAAAACA
1 ATTTCTATTTTATTAAATAAATAATATAGAAATATTCAAAATATTGTCTTATT-AAAAGA
55781580 ACGTTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATGTAAAAGA
1 A--TTTCTATTTTATTAAAT-AAATAATATAGAAATATTCAAAATATTGTCTTAT-TAAAAGA
55781642 ATTTCTATTTTATTAAA
1 ATTTCTATTTTATTAAA
55781659 AATATAAAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
53 2 0.02
54 9 0.09
55 11 0.10
56 9 0.09
57 3 0.03
58 22 0.21
59 3 0.03
60 9 0.09
61 24 0.23
62 12 0.11
63 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (59 bp):
ATTTCTATTTTATTAAATAAATAATATAGAAATATTCAAAATATTGTCTTATTAAAAGA
Found at i:55782161 original size:18 final size:18
Alignment explanation
Indices: 55782120--55782162 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
55782110 GACTAGAAAA
* * *
55782120 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
55782138 ATGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
55782156 AGGATAC
1 AGGATAC
55782163 GCACCTGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:55782786 original size:7 final size:7
Alignment explanation
Indices: 55782774--55782857 Score: 141
Period size: 7 Copynumber: 11.6 Consensus size: 7
55782764 TATTAGTTAT
55782774 ATACTAA
1 ATACTAA
55782781 ATACTAA
1 ATACTAA
55782788 ATACTAA
1 ATACTAA
55782795 ATACTAAA
1 ATACT-AA
55782803 TACTACTAA
1 -A-TACTAA
55782812 ATACTAA
1 ATACTAA
55782819 ATACTAA
1 ATACTAA
55782826 ATACTAA
1 ATACTAA
55782833 ATACTAA
1 ATACTAA
55782840 ATACTAA
1 ATACTAA
55782847 ATACTAA
1 ATACTAA
55782854 ATAC
1 ATAC
55782858 GAATCGACTA
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
7 64 0.86
8 3 0.04
9 3 0.04
10 4 0.05
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (7 bp):
ATACTAA
Found at i:55784073 original size:13 final size:13
Alignment explanation
Indices: 55784034--55784073 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
55784024 GAAAGGATTT
55784034 GAGATAAATATGA
1 GAGATAAATATGA
*
55784047 GAGA-ATAT-TG-
1 GAGATAAATATGA
55784057 GAGATAAATATGA
1 GAGATAAATATGA
55784070 GAGA
1 GAGA
55784074 ATTTGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.18
11 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (13 bp):
GAGATAAATATGA
Found at i:55784081 original size:21 final size:21
Alignment explanation
Indices: 55784030--55784081 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 21
55784020 ATTTGAAAGG
55784030 ATTTGAGATAAATATGAGAGA
1 ATTTGAGATAAATATGAGAGA
55784051 ATATTGGAGATAAATATGAGAGA
1 AT-TT-GAGATAAATATGAGAGA
55784074 ATTTGAGA
1 ATTTGAGA
55784082 AAAAGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (21 bp):
ATTTGAGATAAATATGAGAGA
Found at i:55785657 original size:5 final size:5
Alignment explanation
Indices: 55785647--55785671 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55785637 AAATCCAAAG
55785647 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
55785672 ATAACTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:55795009 original size:28 final size:28
Alignment explanation
Indices: 55794976--55795032 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
55794966 AACCCGTAAT
* *
55794976 CCCAAATATTTAAACCTTGAACCCAAAC
1 CCCAAACACTTAAACCTTGAACCCAAAC
* * *
55795004 CCCAAACCCTTGAACCTTGAACTCAAAC
1 CCCAAACACTTAAACCTTGAACCCAAAC
55795032 C
1 C
55795033 TTCAACCTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.37, G:0.05, T:0.19
Consensus pattern (28 bp):
CCCAAACACTTAAACCTTGAACCCAAAC
Found at i:55795039 original size:28 final size:27
Alignment explanation
Indices: 55794988--55795055 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
55794978 CAAATATTTA
55794988 AACCTTGAACCCAAACCCCAAACCCTTG
1 AACCTTGAACCCAAACCCCAAA-CCTTG
* *
55795016 AACCTTGAACTCAAACCTTC-AACCTTG
1 AACCTTGAACCCAAACC-CCAAACCTTG
*
55795043 AATCCTTAAACCC
1 AA-CCTTGAACCC
55795056 TCAACCTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 7 0.21
28 26 0.76
29 1 0.03
ACGTcount: A:0.35, C:0.38, G:0.06, T:0.21
Consensus pattern (27 bp):
AACCTTGAACCCAAACCCCAAACCTTG
Found at i:55807962 original size:55 final size:55
Alignment explanation
Indices: 55807878--55807988 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
55807868 ATTAGCCAGG
55807878 TAAGTTTGTATGAACTATGTTATGTATAATGTTGATTAAATTTAATTTTAATATA
1 TAAGTTTGTATGAACTATGTTATGTATAATGTTGATTAAATTTAATTTTAATATA
55807933 TAAGTTTGTATGAACTATGTTATGTATAATGTTGATTAAATTTAATTTTAATATA
1 TAAGTTTGTATGAACTATGTTATGTATAATGTTGATTAAATTTAATTTTAATATA
55807988 T
1 T
55807989 GATTTTATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.50
Consensus pattern (55 bp):
TAAGTTTGTATGAACTATGTTATGTATAATGTTGATTAAATTTAATTTTAATATA
Found at i:55808131 original size:29 final size:29
Alignment explanation
Indices: 55808089--55808347 Score: 159
Period size: 29 Copynumber: 8.9 Consensus size: 29
55808079 ATCGACCAAA
*
55808089 AAAAAGGATAGCTTCGGCTATCAATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
55808118 AAAAGGGATAGCTTCGGCTAT-AGATTATG
1 AAAAGGGATAGCTTCGGCTATCA-ATTATG
* * * * * *
55808147 AAAAGGGATTG-TGGCGACCATCTACTATG
1 AAAAGGGATAGCT-TCGGCTATCAATTATG
* * * * *
55808176 AAAAGGAAT-GGTGACGACCATCGAA-TATG
1 AAAAGGGATAGCT-TCGGCTATC-AATTATG
** * *
55808205 AAAAACGATAGCTTTGGCTATCAATGATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* * *
55808234 AAAAGAGATAGCTTCAGCTATCGATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* ** * * *
55808263 AAAAGGGATGGCAACGACCATCGAA-TACG
1 AAAAGGGATAGCTTCGGCTATC-AATTATG
* * *
55808292 AAAAGGGATATCTTCGGCTAACGATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* * *
55808321 AAAAGGGATAGTTTTGGCTATCGATTA
1 AAAAGGGATAGCTTCGGCTATCAATTA
55808348 AAGAAAATGG
Statistics
Matches: 174, Mismatches: 47, Indels: 18
0.73 0.20 0.08
Matches are distributed among these distances:
28 6 0.03
29 164 0.94
30 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGGCTATCAATTATG
Found at i:55808263 original size:87 final size:86
Alignment explanation
Indices: 55808172--55808383 Score: 217
Period size: 87 Copynumber: 2.4 Consensus size: 86
55808162 GACCATCTAC
* * * *
55808172 TATGAAAAGGAATGGTGACGACCATCGAATATGAAAAACGATAGCTTTGGCTATCAATGATGAAA
1 TATGAAAAGG-ATGGTAACGACCATCGAATAAGAAAAACGATAGCTTCGGCTAACAATGATGAAA
55808237 AGAGATAGCTTCAGCTATCGAT
65 AGAGATAGCTTCAGCTATCGAT
* * ** * * *
55808259 TATGAAAAGGGATGGCAACGACCATCGAATACGAAAAGGGATATCTTCGGCTAACGATTATGAAA
1 TATGAAAA-GGATGGTAACGACCATCGAATAAGAAAAACGATAGCTTCGGCTAACAATGATGAAA
* * **
55808324 AGGGATAGTTTTGGCTATCGAT
65 AGAGATAGCTTCAGCTATCGAT
* ** *
55808346 TAAAGAAAATGGATGGTTTCGACCATCGACTAAGAAAA
1 T-ATGAAAA-GGATGGTAACGACCATCGAATAAGAAAA
55808384 GGGACGGTTA
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
87 71 0.70
88 31 0.30
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (86 bp):
TATGAAAAGGATGGTAACGACCATCGAATAAGAAAAACGATAGCTTCGGCTAACAATGATGAAAA
GAGATAGCTTCAGCTATCGAT
Found at i:55808295 original size:116 final size:116
Alignment explanation
Indices: 55808089--55808297 Score: 301
Period size: 116 Copynumber: 1.8 Consensus size: 116
55808079 ATCGACCAAA
* * * *
55808089 AAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATAGCTTCGGCTATAGATTATGAAAAGGG
1 AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
* *** * * *
55808154 ATTGTGGCGACCATCTACTATGAAAAGGAATGGTGACGACCATCGAATATG
66 ATGGCAACGACCATCGAATACGAAAAGGAATGGTGACGACCATCGAATATG
* *
55808205 AAAAACGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATCGATTATGAAAAGGG
1 AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
55808270 ATGGCAACGACCATCGAATACGAAAAGG
66 ATGGCAACGACCATCGAATACGAAAAGG
55808298 GATATCTTCG
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
116 80 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.22
Consensus pattern (116 bp):
AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
ATGGCAACGACCATCGAATACGAAAAGGAATGGTGACGACCATCGAATATG
Found at i:55808321 original size:116 final size:116
Alignment explanation
Indices: 55808089--55808342 Score: 287
Period size: 116 Copynumber: 2.2 Consensus size: 116
55808079 ATCGACCAAA
* * * *
55808089 AAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATAGCTTCGGCTATAGATTATGAAAAGGG
1 AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
* *** * * * * *
55808154 ATTGTGGCGACCATCTACTATGAAAAGGAATGGTGACGACCATCGAATATG
66 ATGGCAACGACCATCGAATACGAAAAGGAATGCTGACGACCAACGAATATG
* *
55808205 AAAAACGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATCGATTATGAAAAGGG
1 AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
* * * *
55808270 ATGGCAACGACCATCGAATACGAAAAGGGATAT-CT-TCGGCTAACGATTATG
66 ATGGCAACGACCATCGAATACGAAAA-GGA-ATGCTGACGACCAACGAATATG
* *
55808321 AAAAGGGATAGTTTTGGCTATC
1 AAAAAGGATAGCTTTGGCTATC
55808343 GATTAAAGAA
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
116 108 0.95
117 4 0.04
118 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (116 bp):
AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATTATGAAAAGGG
ATGGCAACGACCATCGAATACGAAAAGGAATGCTGACGACCAACGAATATG
Found at i:55813785 original size:21 final size:20
Alignment explanation
Indices: 55813761--55813799 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55813751 GGACTAATTT
55813761 AAAACAAATAAAAAATTTGGG
1 AAAA-AAATAAAAAATTTGGG
**
55813782 AAAAAGTTAAAAAATTTG
1 AAAAAAATAAAAAATTTG
55813800 AAAACAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAAAAATTTGGG
Found at i:55819394 original size:79 final size:79
Alignment explanation
Indices: 55819253--55819417 Score: 213
Period size: 79 Copynumber: 2.1 Consensus size: 79
55819243 TGAAATTGTA
** * * * * * *
55819253 TTCTATTTGTAAATAGAAATCAATTGAACAATTCTATTTTAGGATTTTATTCTTGCTATTCAACA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
* *
55819318 GAATTTGTTTGATT
66 AAATTTATTTGATT
* *
55819332 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTGTTTTAGGATTCTATTCCTACCGTTCAACA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
55819397 AAATTTATTTGATT
66 AAATTTATTTGATT
*
55819411 TTTTATT
1 TTCTATT
55819418 GTTAACGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (79 bp):
TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
AAATTTATTTGATT
Found at i:55838402 original size:43 final size:42
Alignment explanation
Indices: 55838339--55838499 Score: 144
Period size: 43 Copynumber: 3.8 Consensus size: 42
55838329 CGGAAGCTCT
* *
55838339 TACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAA
* * * * * **
55838381 TATCAATGTCACTGTCCCAGACAAGGTCTTACACGAAATCGTA
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAA
* *
55838424 TACGATGCCAATGTCCCAAACATGGTCTTACATGTAAATCTCAAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGT-AA--TCAAA
** * *
55838469 T-CAACACCAATGTCTCAGACGTGGTCTTACA
1 TACAATGCCAATGTCCCAGACATGGTCTTACA
55838500 CAAAATCACA
Statistics
Matches: 91, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 28 0.31
43 35 0.38
44 24 0.26
45 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAA
Found at i:55842076 original size:3 final size:3
Alignment explanation
Indices: 55842068--55842095 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55842058 ATATGTATAG
55842068 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55842096 ATGGGGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55846247 original size:49 final size:48
Alignment explanation
Indices: 55846171--55846555 Score: 332
Period size: 49 Copynumber: 7.9 Consensus size: 48
55846161 AAAATTTAAA
* * *
55846171 AAAAAAAAAATTGGGTGCT-ACCTTGTCAATGGCCGGCACCAGCATACG
1 AAAAAAAAATTTTGGTGCTGGCC-TGTCAATGGCCGGCACCAGCATACG
* *
55846219 AAAAAAAAATTTTAGGTGCTGGACTGTCAATGGCCGGCACCACCAATACG
1 AAAAAAAAATTTT-GGTGCTGGCCTGTCAATGGCCGGCACCAGC-ATACG
* * * *
55846269 -AAAAAAAATTTGTGATGCTGGCCTGTCAATGGTCGGCACAAGCAATATG
1 AAAAAAAAATTT-TGGTGCTGGCCTGTCAATGGCCGGCACCAGC-ATACG
* * *
55846318 AAAAAAAAAATTTGGTGCTGGCCTGTTAATGGCCGGCACCAACAGTACGG
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGCA-TAC-G
****** * * *
55846368 AAATTTTTTTTTTTGGTGTTGGCTTGTCAAT-GCCGGCACCAGTATACG
1 AAA-AAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGCATACG
* *
55846416 AAAAAAAAA-TTT-GTGCTGGCCTGTCAATGGCCTGCACCAGTATAC-
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGCATACG
* * * * *
55846461 AAAAAAATAACTTTTTTGAGTGCTAGCCTGTCAATAGACGGCACTAGAAGTACG
1 AAAAAAA-AA---TTTTG-GTGCTGGCCTGTCAATGGCCGGCACCAGCA-TACG
* *
55846515 AAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCTGGCACCA
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCA
55846556 AATTTATCAA
Statistics
Matches: 268, Mismatches: 51, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
45 21 0.08
46 20 0.07
48 16 0.06
49 119 0.44
50 39 0.15
51 17 0.06
52 24 0.09
53 5 0.02
54 7 0.03
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (48 bp):
AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGCATACG
Found at i:55846528 original size:197 final size:197
Alignment explanation
Indices: 55846192--55846556 Score: 515
Period size: 197 Copynumber: 1.8 Consensus size: 197
55846182 TGGGTGCTAC
55846192 CTTGTCAATGGCCGGCACCAGCATACGAAAAAAAAATTTTAGGTGCTGGACTGTCAATGGCCGGC
1 CTTGTCAATGGCCGGCACCAGCATACGAAAAAAAAATTTTA-GTGCTGGACTGTCAATGGCCGGC
* * * * *
55846257 ACCACCAATACGAAAAAAAATTTGTGATGCTGGCCTGTCAATGGTCGGCACAAGCAATATGAAAA
65 ACCACCAATACAAAAAAAAATTTGTGATGCTAGCCTGTCAATAGACGGCACAAGCAATACGAAAA
*
55846322 AAAAAATTTGGTGCTGGCCTGTTAATGGCCGGCACCAACAGTACGGAAATTTTTTTTTTTGGTGT
130 AAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAACAGTACGGAAATTTTTTTTTTTGGTGT
55846387 TGG
195 TGG
* * *
55846390 CTTGTCAAT-GCCGGCACCAGTATACGAAAAAAAAA-TTT-GTGCTGGCCTGTCAATGGCCTGCA
1 CTTGTCAATGGCCGGCACCAGCATACGAAAAAAAAATTTTAGTGCTGGACTGTCAATGGCCGGCA
** * *
55846452 CCA-GTATACAAAAAAATAACTTTTTTGAGTGCTAGCCTGTCAATAGACGGCACTAG-AAGTACG
66 CCACCAATACAAAAAAA-AA--TTTGTGA-TGCTAGCCTGTCAATAGACGGCACAAGCAA-TACG
*
55846515 AAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCTGGCACCAA
126 AAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAA
55846557 ATTTATCAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
193 10 0.07
194 27 0.18
196 11 0.07
197 91 0.61
198 9 0.06
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (197 bp):
CTTGTCAATGGCCGGCACCAGCATACGAAAAAAAAATTTTAGTGCTGGACTGTCAATGGCCGGCA
CCACCAATACAAAAAAAAATTTGTGATGCTAGCCTGTCAATAGACGGCACAAGCAATACGAAAAA
AAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAACAGTACGGAAATTTTTTTTTTTGGTGTT
GG
Found at i:55863142 original size:28 final size:26
Alignment explanation
Indices: 55863111--55863168 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
55863101 AATTCATACA
* *
55863111 TTTTGCATGCACATTAATTTATTTAGT
1 TTTTG-ATGAACATTAAATTATTTAGT
* *
55863138 GTTTTGATGAACTTTAAATTCTTTAGT
1 -TTTTGATGAACATTAAATTATTTAGT
55863165 TTTT
1 TTTT
55863169 AAGTGTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 17 0.65
28 5 0.19
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (26 bp):
TTTTGATGAACATTAAATTATTTAGT
Found at i:55866585 original size:9 final size:9
Alignment explanation
Indices: 55866561--55866674 Score: 70
Period size: 10 Copynumber: 12.0 Consensus size: 9
55866551 TTATTAGATT
55866561 TTTTTATAAA
1 TTTTTAT-AA
55866571 TTTTTATAA
1 TTTTTATAA
*
55866580 TATTTAATAA
1 T-TTTTATAA
55866590 TCTTTTATAA
1 T-TTTTATAA
*
55866600 CTTTTATAA
1 TTTTTATAA
* *
55866609 GGTTATATCAA
1 -TTTTTAT-AA
*
55866620 TTTTAAT-A
1 TTTTTATAA
* *
55866628 TTTTTTTTA
1 TTTTTATAA
55866637 TTTTTATAA
1 TTTTTATAA
55866646 GTTTTTAATAA
1 -TTTTT-ATAA
*
55866657 -TTTTATATG
1 TTTTTATA-A
55866666 TTTTTATAA
1 TTTTTATAA
55866675 AATTCAAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
8 9 0.11
9 23 0.28
10 43 0.53
11 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:55866660 original size:19 final size:18
Alignment explanation
Indices: 55866562--55866674 Score: 86
Period size: 19 Copynumber: 6.0 Consensus size: 18
55866552 TATTAGATTT
*
55866562 TTTTATAAATTTTTATAA
1 TTTTATAAGTTTTTATAA
55866580 TATTTAATAA-TCTTTTATAA
1 T-TTT-ATAAGT-TTTTATAA
* *
55866600 CTTTTATAAGGTTATATCAA
1 -TTTTATAAGTTTTTAT-AA
* * *
55866620 TTTTA-ATATTTTTTTTAT
1 TTTTATA-AGTTTTTATAA
55866638 TTTTATAAGTTTTTAATAA
1 TTTTATAAGTTTTT-ATAA
*
55866657 TTTTATATGTTTTTATAA
1 TTTTATAAGTTTTTATAA
55866675 AATTCAAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
18 18 0.24
19 39 0.52
20 17 0.23
21 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTATAAGTTTTTATAA
Found at i:55866735 original size:9 final size:9
Alignment explanation
Indices: 55866723--55866807 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 9
55866713 TAATGTTTTC
55866723 TTTATAATT
1 TTTATAATT
55866732 TTTATAAGTT
1 TTTATAA-TT
*
55866742 TATATCAA-T
1 TTTAT-AATT
*
55866751 TTTATTATT
1 TTTATAATT
55866760 TTT-TAAATAT
1 TTTAT-AAT-T
55866770 TTT-TAATT
1 TTTATAATT
55866778 TTTAATAA-T
1 TTT-ATAATT
*
55866787 TTTA-ATTT
1 TTTATAATT
*
55866795 TTTATTATT
1 TTTATAATT
55866804 TTTA
1 TTTA
55866808 AGAGAAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 1 0.02
8 12 0.20
9 31 0.52
10 14 0.23
11 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:55866784 original size:16 final size:17
Alignment explanation
Indices: 55866757--55866808 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
55866747 CAATTTTATT
55866757 ATTTTTTAAATATTTTTA
1 ATTTTTT-AATATTTTTA
*
55866775 A-TTTTTAATAATTTTA
1 ATTTTTTAATATTTTTA
*
55866791 ATTTTTTATTATTTTTA
1 ATTTTTTAATATTTTTA
55866808 A
1 A
55866809 GAGAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.33
17 19 0.63
18 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTAATATTTTTA
Found at i:55871871 original size:16 final size:16
Alignment explanation
Indices: 55871850--55871887 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55871840 ACTGATATAC
*
55871850 GAAAAAAGGAAAAAAA
1 GAAAAAAGCAAAAAAA
*
55871866 GAAAAACGCAAAAAAA
1 GAAAAAAGCAAAAAAA
55871882 -AAAAAA
1 GAAAAAA
55871888 TTTTGATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (16 bp):
GAAAAAAGCAAAAAAA
Found at i:55871989 original size:56 final size:57
Alignment explanation
Indices: 55871928--55872046 Score: 204
Period size: 56 Copynumber: 2.1 Consensus size: 57
55871918 CCAATACAAA
55871928 TTTAAAAAAAATTCTCTTTTTTGTGTCAGAATCAAATATAAATATACG-AAAAAAAT
1 TTTAAAAAAAATTCTCTTTTTTGTGTCAGAATCAAATATAAATATACGAAAAAAAAT
* * *
55871984 TTTAAAAAAAATTCTTTTTTTTGTGTTAGAATCAGATATAAATATACGAAAAAAAAT
1 TTTAAAAAAAATTCTCTTTTTTGTGTCAGAATCAAATATAAATATACGAAAAAAAAT
55872041 TTTAAA
1 TTTAAA
55872047 TTTGTACTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
56 45 0.76
57 14 0.24
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (57 bp):
TTTAAAAAAAATTCTCTTTTTTGTGTCAGAATCAAATATAAATATACGAAAAAAAAT
Found at i:55874630 original size:91 final size:91
Alignment explanation
Indices: 55874515--55874695 Score: 247
Period size: 91 Copynumber: 2.0 Consensus size: 91
55874505 ATTGTATATA
* * *
55874515 TATTAATATTGTTATTGATTGAGTTGGCGTCACAAATTAACTCGACACCAA-TTTAGAATTGATA
1 TATTAATAATGTTATTGATTGAGTTGGCATCACAAATTAACTCGACACCAACTTAAG-ATTGATA
* *
55874579 TATTTATTTAGTCCTCTTAATCTGATG
65 TAGTTATTTAGTACTCTTAATCTGATG
* * * * *
55874606 TATTAATAATGTTATTGATTGAGTTGGTATTACAAATTAACTTGACACCAACTTAAGATTTATGT
1 TATTAATAATGTTATTGATTGAGTTGGCATCACAAATTAACTCGACACCAACTTAAGATTGATAT
*
55874671 AGTTATTTAGTATTCTTAATCTGAT
66 AGTTATTTAGTACTCTTAATCTGAT
55874696 TTAAATTTCG
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 74 0.95
92 4 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (91 bp):
TATTAATAATGTTATTGATTGAGTTGGCATCACAAATTAACTCGACACCAACTTAAGATTGATAT
AGTTATTTAGTACTCTTAATCTGATG
Found at i:55875558 original size:15 final size:16
Alignment explanation
Indices: 55875538--55875575 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55875528 ATAAATATGA
* *
55875538 TAAATTT-GTTCTTAT
1 TAAATTTCGTTATAAT
55875553 TAAATTTCGTTATAAT
1 TAAATTTCGTTATAAT
55875569 TAAATTT
1 TAAATTT
55875576 TATTATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (16 bp):
TAAATTTCGTTATAAT
Found at i:55876313 original size:30 final size:31
Alignment explanation
Indices: 55876245--55876319 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
55876235 AACTACATAA
55876245 TTAGTCAC-CAAACTATTAAGTTCTTTCTGTT
1 TTAGTCACTC-AACTATTAAGTTCTTTCTGTT
* * *
55876276 TTGGTCACTCAACTATTAA-TTTTTTTTGTT
1 TTAGTCACTCAACTATTAAGTTCTTTCTGTT
55876306 TTAGTCACTCAACT
1 TTAGTCACTCAACT
55876320 TTTCAAAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 22 0.56
31 16 0.41
32 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (31 bp):
TTAGTCACTCAACTATTAAGTTCTTTCTGTT
Found at i:55877908 original size:43 final size:43
Alignment explanation
Indices: 55877860--55877945 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
55877850 TATGTTATTG
* * *
55877860 ATATTGAAATGGAAAAGATGATAACTGAATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
* * *
55877903 ATATTGAAATGGCAAATATGAGAAATGATTATGAAATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
55877946 TGAAATATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
Found at i:55877943 original size:18 final size:19
Alignment explanation
Indices: 55877920--55877960 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
55877910 AATGGCAAAT
*
55877920 ATGAGAAATG-ATTATGAA
1 ATGAGAAATGAAATATGAA
55877938 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
55877957 ATGA
1 ATGA
55877961 TGAATTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:55879324 original size:49 final size:49
Alignment explanation
Indices: 55879252--55879348 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
55879242 TCAAGAAGGG
* *
55879252 ATAAATAGTGATAAGAGTGTAGACAATGGAAAACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAAACCAAGTTTAGAAATGT
* * *
55879301 ATAAATAGTGATAAGTGTGTAGACAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAAACCAAGTTTAGAAATG
55879349 CATAGCATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.26
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAATGGAAAACCAAGTTTAGAAATGT
Found at i:55886776 original size:18 final size:19
Alignment explanation
Indices: 55886743--55886778 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
55886733 GAACTGATGC
*
55886743 ATAAAATTTTATAATTTAG
1 ATAAAATTTTAAAATTTAG
55886762 ATAAAA-TTTAAAATTTA
1 ATAAAATTTTAAAATTTA
55886779 CGATGAGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTAAAATTTAG
Found at i:55891121 original size:45 final size:45
Alignment explanation
Indices: 55891057--55891148 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
55891047 TCAAAGTTTA
55891057 TAACTTTGGACTTAGTCAGGCAAGAGGCCGAGTGGTTTAGGAATC
1 TAACTTTGGACTTAGTCAGGCAAGAGGCCGAGTGGTTTAGGAATC
55891102 TAACTTTGGACTTAGTCAGGCAAGAGGCCGAGTGGTTTAGGAATC
1 TAACTTTGGACTTAGTCAGGCAAGAGGCCGAGTGGTTTAGGAATC
55891147 TA
1 TA
55891149 CTTGCAGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (45 bp):
TAACTTTGGACTTAGTCAGGCAAGAGGCCGAGTGGTTTAGGAATC
Found at i:55891644 original size:87 final size:86
Alignment explanation
Indices: 55891542--55891704 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 86
55891532 TGTACATGCA
* *
55891542 TAAGGTTGAGTTCTTACTCTTAATGAATTCATATCCTAGGGTTTGGGTGGTCCT-ATTGAGAC-A
1 TAAGGTTGAGTTCTTACTCTTAATGAATTCATATCCTAGAGTTTGGGTAGTCCTAATT-AGACGA
*
55891605 GACTTTATGAATTCACTGACATG
65 -ACTTGATGAATTCACTGACATG
* *
55891628 TAAGGTTGAGTTTCTTACTTTTAATGAGTTCATATCCTAGAGTTTGGGTAGTCCTAATTAGACGA
1 TAAGGTTGAG-TTCTTACTCTTAATGAATTCATATCCTAGAGTTTGGGTAGTCCTAATTAGACGA
55891693 ACTTGATGAATT
65 ACTTGATGAATT
55891705 TACCAAATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
86 10 0.14
87 55 0.80
88 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (86 bp):
TAAGGTTGAGTTCTTACTCTTAATGAATTCATATCCTAGAGTTTGGGTAGTCCTAATTAGACGAA
CTTGATGAATTCACTGACATG
Found at i:55894157 original size:42 final size:42
Alignment explanation
Indices: 55894093--55894192 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
55894083 CTTTCCATTT
* * *
55894093 AGCTCTCACGAGCTTCTATTTAACTCATATGA-TTTTTCGTTC
1 AGCTCTTACGAGCTTCTATTTAACCCATATGAGTTTCT-GTTC
** * *
55894135 AGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTCTGTTC
1 AGCTCTTACGAGCTTCTATTTAACCCATATGAGTTTCTGTTC
55894177 AGCTCTTACGAGCTTC
1 AGCTCTTACGAGCTTC
55894193 CGTCCAACCC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
42 44 0.92
43 4 0.08
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTATTTAACCCATATGAGTTTCTGTTC
Found at i:55894172 original size:21 final size:21
Alignment explanation
Indices: 55894143--55894217 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
55894133 TCAGCTCTTT
*
55894143 TGAGCTTCTGTTTAACCCTTA
1 TGAGCTTCTGTTCAACCCTTA
* * *
55894164 TGAGTTTCTGTTCAGCTCTTA
1 TGAGCTTCTGTTCAACCCTTA
* * *
55894185 CGAGCTTCCGTCCAACCCTTA
1 TGAGCTTCTGTTCAACCCTTA
* *
55894206 TGGGTTTCTGTT
1 TGAGCTTCTGTT
55894218 TAGCTTACAT
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (21 bp):
TGAGCTTCTGTTCAACCCTTA
Found at i:55894202 original size:42 final size:42
Alignment explanation
Indices: 55894127--55894222 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
55894117 TCATATGATT
** * **
55894127 TTTC-GTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCCGTCCAACCCTTATGAG
*
55894168 TTTCTGTTCAGCTCTTACGAGCTTCCGTCCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTACGAGCTTCCGTCCAACCCTTATGAG
*
55894210 TTTCTGTTTAGCT
1 TTTCTGTTCAGCT
55894223 TACATGAGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTACGAGCTTCCGTCCAACCCTTATGAG
Found at i:55898441 original size:23 final size:23
Alignment explanation
Indices: 55898398--55898441 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
55898388 TTAATTAAAT
* *
55898398 TGTAATTTTTATAATAATAAAAA
1 TGTAATTTTTAAAAGAATAAAAA
*
55898421 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAATAAA
55898442 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAATAAAAA
Found at i:55900384 original size:40 final size:41
Alignment explanation
Indices: 55900296--55900385 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 41
55900286 TTTTTCCACG
* * *
55900296 AAATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAG
1 AAATCGCGTCCACGTCAGCGCGATGTCAGCGTACGTGACAC
* * *
55900337 AACATCGCGTCCACGTCAGTGCGAT-T-TGCTTACGTGGACAC
1 AA-ATCGCGTCCACGTCAGCGCGATGTCAGCGTACGT-GACAC
55900378 AAATCGCG
1 AAATCGCG
55900386 CCTACGAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
40 12 0.29
41 8 0.20
42 21 0.51
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.21
Consensus pattern (41 bp):
AAATCGCGTCCACGTCAGCGCGATGTCAGCGTACGTGACAC
Found at i:55903078 original size:25 final size:25
Alignment explanation
Indices: 55903045--55903096 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
55903035 AAACTCAAAT
55903045 AACTAATCTTTAATAATTGTTTACA
1 AACTAATCTTTAATAATTGTTTACA
*
55903070 AACTCATCTTTAATAATTGTTTACA
1 AACTAATCTTTAATAATTGTTTACA
55903095 AA
1 AA
55903097 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (25 bp):
AACTAATCTTTAATAATTGTTTACA
Found at i:55903106 original size:25 final size:25
Alignment explanation
Indices: 55903053--55903106 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
55903043 ATAACTAATC
* **
55903053 TTTAATAATTGTTTACAAACTCATC
1 TTTAATAATTGTTTACAAAATCAAA
55903078 TTTAATAATTGTTTACAAAATCAAA
1 TTTAATAATTGTTTACAAAATCAAA
55903103 TTTA
1 TTTA
55903107 TTTTTGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAATAATTGTTTACAAAATCAAA
Found at i:55908413 original size:3 final size:3
Alignment explanation
Indices: 55908405--55908444 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
55908395 ACCAGATCTT
*
55908405 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55908445 AAGGTAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55908563 original size:19 final size:19
Alignment explanation
Indices: 55908539--55908576 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55908529 GATAGTTATC
55908539 ATATGGTAT-CTATTATTTG
1 ATATGGTATGC-ATTATTTG
55908558 ATATGGTATGCATTATTTG
1 ATATGGTATGCATTATTTG
55908577 TGGTATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (19 bp):
ATATGGTATGCATTATTTG
Found at i:55911445 original size:28 final size:27
Alignment explanation
Indices: 55911409--55911466 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
55911399 TATATAGTAT
* *
55911409 CAGTACAGTGTGGGCCTTAACCCATTA
1 CAGTACAGTGTAGGCCTTAACCCAATA
*
55911436 CAGTAACAGTGTAGGCCTTAGCCCAATA
1 CAGT-ACAGTGTAGGCCTTAACCCAATA
55911464 CAG
1 CAG
55911467 AAATTAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (27 bp):
CAGTACAGTGTAGGCCTTAACCCAATA
Found at i:55911631 original size:26 final size:26
Alignment explanation
Indices: 55911575--55911632 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
55911565 GCCAACACAC
55911575 CAATATCGCAGAAAAGCCGCCAGTAA
1 CAATATCGCAGAAAAGCCGCCAGTAA
* * * * * *
55911601 TAATATCGTAGTAAAGCTGTCAGTGA
1 CAATATCGCAGAAAAGCCGCCAGTAA
55911627 CAATAT
1 CAATAT
55911633 ATGTGGCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (26 bp):
CAATATCGCAGAAAAGCCGCCAGTAA
Found at i:55911979 original size:81 final size:81
Alignment explanation
Indices: 55911864--55912033 Score: 254
Period size: 81 Copynumber: 2.1 Consensus size: 81
55911854 GTTATTTTGG
* **
55911864 GTAATTTTACCCTTTGAGGGTATTTTGGGAATTTTAACCTTCGAGGATATTTCTG-TAATTTTAC
1 GTAATTTTACCCTTTGAGGGTATTTCGACAATTTTAACCTTCGAGGATATTTC-GATAATTTTAC
*
55911928 CCTTTGAGGGTATTTCA
65 CCTTTGAGGGCATTTCA
* *
55911945 GTAATTTTACTCTTCT-AGGGTATTTCGACAATTTTAACCTTCGAGGGTATTTCGATAATTTTAC
1 GTAATTTTACCCTT-TGAGGGTATTTCGACAATTTTAACCTTCGAGGATATTTCGATAATTTTAC
55912009 CCTTTGAGGGCATTTCA
65 CCTTTGAGGGCATTTCA
55912026 GTAATTTT
1 GTAATTTT
55912034 TTGGCCTAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 1 0.01
81 79 0.98
82 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (81 bp):
GTAATTTTACCCTTTGAGGGTATTTCGACAATTTTAACCTTCGAGGATATTTCGATAATTTTACC
CTTTGAGGGCATTTCA
Found at i:55912024 original size:27 final size:27
Alignment explanation
Indices: 55911827--55912033 Score: 181
Period size: 27 Copynumber: 7.6 Consensus size: 27
55911817 ACCTTACGGA
* *
55911827 GGTATTTCGATCATTTTACCTTTTTG-G
1 GGTATTTCGATAATTTTACC-CTTTGAG
* * *
55911854 GTTATTTTGGGTAATTTTACCCTTTGAG
1 GGTA-TTTCGATAATTTTACCCTTTGAG
* ** * *
55911882 GGTATTTTGGGAATTTTAACCTTCGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
*
55911909 GATATTTCTG-TAATTTTACCCTTTGAG
1 GGTATTTC-GATAATTTTACCCTTTGAG
*
55911936 GGTATTTC-AGTAATTTTACTCTTCT-AG
1 GGTATTTCGA-TAATTTTACCCTT-TGAG
* * *
55911963 GGTATTTCGACAATTTTAACCTTCGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
55911990 GGTATTTCGATAATTTTACCCTTTGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
*
55912017 GGCATTTC-AGTAATTTT
1 GGTATTTCGA-TAATTTT
55912034 TTGGCCTAAG
Statistics
Matches: 146, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.01
27 125 0.86
28 20 0.14
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCCTTTGAG
Found at i:55912399 original size:28 final size:27
Alignment explanation
Indices: 55912340--55912615 Score: 180
Period size: 27 Copynumber: 10.2 Consensus size: 27
55912330 TATAACAGTT
* * * * *
55912340 ATTTTAACCTATAGGGGTATTTCGGTT
1 ATTTTACCCTTTAAGGGTATTTTGGTA
*
55912367 ATTTTACCCTTT-GGGGTTATTTTGGGTA
1 ATTTTACCCTTTAAGGG-TATTTT-GGTA
55912395 ATTTTACCCTTTAAGGGTATTTTGGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* ** ** * *
55912422 ATTTTAACCTTCGAGAATATTTCGATA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * **
55912449 ATTTTACCTTTTGAGGGTATTTCAGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * **
55912476 ATTTTACCCTTTTAGGATATTTCAGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * *
55912503 ATTTTACCCTTCGAA-GGTATTTCGATA
1 ATTTTACCCTT-TAAGGGTATTTTGGTA
** *
55912530 ATTTTACCCTTCGATGGTATTTCT-GTA
1 ATTTTACCCTTTAAGGGTATTT-TGGTA
** * *
55912557 ATTTTACCCTTCGATGGTATTTTTGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
** * *
55912584 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
55912611 ATTTT
1 ATTTT
55912616 CTAGCCCAAT
Statistics
Matches: 207, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.03
27 176 0.85
28 22 0.11
29 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (27 bp):
ATTTTACCCTTTAAGGGTATTTTGGTA
Found at i:55912470 original size:54 final size:54
Alignment explanation
Indices: 55912354--55912615 Score: 269
Period size: 54 Copynumber: 4.8 Consensus size: 54
55912344 TAACCTATAG
* * * * * * **
55912354 GGGTATTTCGGTTATTTTACCCTTTGGGGTTATTTTGGGTAATTTTACCCTTTAA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATA-TTTCGATAATTTTACCCTTCGA
* * * * *
55912409 GGGTATTTTGGTAATTTTAACCTTCGAGAATATTTCGATAATTTTACCTTTTGA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTTACCCTTCGA
* **
55912463 GGGTATTTCAGTAATTTTACCCTTTTAGGATATTTC-AGTAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGA-TAATTTTACCCTTCGA
* *
55912517 AGGTATTTCGATAATTTTACCCTTCGATGG-TATTTCTG-TAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA-GGATATTTC-GATAATTTTACCCTTCGA
* ** *
55912571 TGGTATTTTTGTAATTTTACCCTTCGAGGGTATTTCGATAATTTT
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTT
55912616 CTAGCCCAAT
Statistics
Matches: 173, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
53 4 0.02
54 142 0.82
55 27 0.16
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (54 bp):
GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTTACCCTTCGA
Found at i:55912504 original size:81 final size:80
Alignment explanation
Indices: 55912356--55912615 Score: 299
Period size: 81 Copynumber: 3.2 Consensus size: 80
55912346 ACCTATAGGG
* * ** *
55912356 GTATTTCGGTTATTTTACCCTTTG-GGGTTATTTTGGGTAATTTTACCCTTTAAGGGTATTTTGG
1 GTATTTCGATAATTTTACCCTTTGAGGG-TA-TTTCAGTAATTTTACCCTTTAA-GGTATTTTAG
*
55912420 TAATTTTAACCTTCGAGA
63 TAATTTTACCCTTCGAGA
* * * *
55912438 ATATTTCGATAATTTTACCTTTTGAGGGTATTTCAGTAATTTTACCCTTTTAGGATATTTCAGTA
1 GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTTTAAGG-TATTTTAGTA
55912503 ATTTTACCCTTCGA-A
65 ATTTTACCCTTCGAGA
* * * * * *
55912518 GGTATTTCGATAATTTTACCCTTCGATGGTATTTCTGTAATTTTACCCTTCGATGGTATTTTTGT
1 -GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTT-TAAGGTATTTTAGT
*
55912583 AATTTTACCCTTCGAGG
64 AATTTTACCCTTCGAGA
55912600 GTATTTCGATAATTTT
1 GTATTTCGATAATTTT
55912616 CTAGCCCAAT
Statistics
Matches: 152, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.02
81 122 0.80
82 24 0.16
83 3 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (80 bp):
GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTTTAAGGTATTTTAGTAA
TTTTACCCTTCGAGA
Done.