Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 80 of 325
Found at i:27531214 original size:287 final size:286
Alignment explanation
Indices: 27530638--27531351 Score: 953
Period size: 287 Copynumber: 2.5 Consensus size: 286
27530628 GATTTGTAAC
* * * * ** * * * * * *
27530638 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTCTATCTTCAGTTTGCTCT
1 TTGTAGCTTTAATCTGTTCCACTACAACCTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * *
27530703 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATATGCTCCACTGCAACTTCAAGAAGATA
66 TACAGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCCACTGCAACTTTAGGAAGATA
* * * *
27530768 AGATTCGCCATATTTGTAGTTTTAATTTGTTCCATTGCAACGTCAGGGAAATAAGATTCGCTGTC
131 AGATCCGCCATATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTC
* *
27530833 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGTTCCACTGCAAC
196 TTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCAAC
*
27530898 TTCAAGAAGATAAGATTCGCTATAAT
261 TTCAAGAAGATAAGATCCGCTATAAT
* * *
27530924 TTGTAGCTTTAATCTGTTCCACTATAACGTCAGCAAAATAAGATTCGTTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACCTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * **
27530989 -GCAGCAACTTTAGAGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGTGACTTTAGGAAGATA
66 TACAGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCCACTGCAACTTTAGGAAGATA
* * * *
27531053 AGATCCTCCATAATTTGTAGTTTTAATCTGTTCTACTACGACGTCAGGGAAATAAGATTCGTTGT
131 AGATCCGCCAT-ATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGT
* *
27531118 CTTCAGTCTACTCCTACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
195 CTTCAGTCTACTCC-ACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCA
* * *
27531183 ACTTCGAGAAGATAATATCCTCTATAAT
259 ACTTCAAGAAGATAAGATCCGCTATAAT
* *
27531211 TTGTAGCTTTAATCTGTTCCACTACAACCTCAGCTAAATAAGATTCGCTGTCTTCAGTTTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACCTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * **
27531276 TACTGCAACTTCAGGGAGATAAGGTTGATGGCTTCAATCTATTCCACTGCAACTTTAGGAAGATA
66 TACAGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCCACTGCAACTTTAGGAAGATA
*
27531341 AGATTCGCCAT
131 AGATCCGCCAT
27531352 TTTCGATCTA
Statistics
Matches: 366, Mismatches: 59, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
285 63 0.17
286 111 0.30
287 131 0.36
288 61 0.17
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (286 bp):
TTGTAGCTTTAATCTGTTCCACTACAACCTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
TACAGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCCACTGCAACTTTAGGAAGATA
AGATCCGCCATATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTC
TTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCAAC
TTCAAGAAGATAAGATCCGCTATAAT
Found at i:27531327 original size:44 final size:42
Alignment explanation
Indices: 27531277--27531434 Score: 136
Period size: 44 Copynumber: 3.6 Consensus size: 42
27531267 GTTTGCTCCT
*
27531277 ACTGCAACTTCAGGGAGATAAGGTTGATGGCTTCAATCTATTCC
1 ACTGCAACTTCAGGGAGATAAGATTGAT--CTTCAATCTATTCC
* * * * *
27531321 ACTGCAACTTTAGGAAGATAAGATTCGCCATTTTCGATCTACTCC
1 ACTGCAACTTCAGGGAGATAAGATT-G--ATCTTCAATCTATTCC
* * * *
27531366 ACTGCAACTTCAAGGAGATAAGATCTACAACTTCAATCTGTTCC
1 ACTGCAACTTCAGGGAGATAAGAT-T-GATCTTCAATCTATTCC
** *
27531410 ACCACTACTTCAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
27531435 TGTGGATTCA
Statistics
Matches: 90, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
43 1 0.01
44 53 0.59
45 33 0.37
46 1 0.01
47 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (42 bp):
ACTGCAACTTCAGGGAGATAAGATTGATCTTCAATCTATTCC
Found at i:27535319 original size:15 final size:15
Alignment explanation
Indices: 27535296--27535326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27535286 CGCAAACAGG
*
27535296 AGAAGAAAAAGGGGA
1 AGAAAAAAAAGGGGA
27535311 AGAAAAAAAAGGGGA
1 AGAAAAAAAAGGGGA
27535326 A
1 A
27535327 AAATTGGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAGGGGA
Found at i:27541812 original size:3 final size:3
Alignment explanation
Indices: 27541804--27541982 Score: 109
Period size: 3 Copynumber: 60.0 Consensus size: 3
27541794 AAAGGAAGAC
* *
27541804 AAT AAT AAT AGT AAT AAT AATT AA- ATT AATT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT
* * * * *
27541849 AAGT AAAT AA- ACAC AAA AAG AA- AAT -AT AAT TAT AAT AGT AAT AAT
1 AA-T -AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
27541894 AAT AAA AAT AAT AAC AAT AAT AAT AGT GAT AA- AAT TAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * **
27541941 AGT AAT AAT AAT AAT GAT AGT AAT AAT AGC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27541983 GTTAAATTAA
Statistics
Matches: 135, Mismatches: 30, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
2 10 0.07
3 114 0.84
4 9 0.07
5 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27541856 original size:72 final size:72
Alignment explanation
Indices: 27541768--27541918 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 72
27541758 GTATTTAAAG
* * *
27541768 AATAATAATAAGTAAATAAATTCA-AAAAAG-GAAGACAATAATAATAGTAATAATAATTAAATT
1 AATAATAATAAGTAAATAAA--CACAAAAAGAAAAGACAATAATAATAGTAATAATAATAAAAAT
*
27541831 AATTAATAAT
64 AA-TAACAAT
* * *
27541841 AA-AATAATAAGTAAATAAACACAAAAAGAAAATATAATTATAATAGTAATAATAATAAAAATAA
1 AATAATAATAAGTAAATAAACACAAAAAGAAAAGACAATAATAATAGTAATAATAATAAAAATAA
27541905 TAACAAT
66 TAACAAT
27541912 AATAATA
1 AATAATA
27541919 GTGATAAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
70 2 0.03
71 14 0.21
72 50 0.74
73 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.26
Consensus pattern (72 bp):
AATAATAATAAGTAAATAAACACAAAAAGAAAAGACAATAATAATAGTAATAATAATAAAAATAA
TAACAAT
Found at i:27543381 original size:21 final size:20
Alignment explanation
Indices: 27543357--27543396 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27543347 AATTAAATAA
*
27543357 TTTTGTTAGTAAGATTTTAAC
1 TTTT-TTAGTAAAATTTTAAC
*
27543378 TTTTTTGGTAAAATTTTAA
1 TTTTTTAGTAAAATTTTAA
27543397 ACTCTTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTTTTAGTAAAATTTTAAC
Found at i:27548679 original size:24 final size:24
Alignment explanation
Indices: 27548613--27548686 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
27548603 TAAGTCATAT
* *
27548613 ATTAGATATTAGTAATATAATAACA
1 ATTA-ATATTAATAAGATAATAACA
* **
27548638 ATTACTATTAATTTGATAATAACA
1 ATTAATATTAATAAGATAATAACA
27548662 ATTAATATTACA-AAGATAAT-ACA
1 ATTAATATTA-ATAAGATAATAACA
27548685 AT
1 AT
27548687 ATAGTGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 5 0.12
24 30 0.75
25 5 0.12
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (24 bp):
ATTAATATTAATAAGATAATAACA
Found at i:27550228 original size:32 final size:32
Alignment explanation
Indices: 27550186--27550253 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
27550176 AAACAAAAGT
27550186 GAAC-AAAGTAAGCAAACATACAACCATTGTC
1 GAACAAAAGTAAGCAAACATACAACCATTGTC
27550217 GAACAAAAGTAAGCAAACATACAACCATTGTC
1 GAACAAAAGTAAGCAAACATACAACCATTGTC
*
27550249 AAACA
1 GAACA
27550254 TCATGAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (32 bp):
GAACAAAAGTAAGCAAACATACAACCATTGTC
Found at i:27550578 original size:17 final size:16
Alignment explanation
Indices: 27550544--27550575 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27550534 TATCAAGCAC
27550544 TTTGATAGTTTTTGAA
1 TTTGATAGTTTTTGAA
27550560 TTTGATAGTTTTTGAA
1 TTTGATAGTTTTTGAA
27550576 ATTCCATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (16 bp):
TTTGATAGTTTTTGAA
Found at i:27551900 original size:20 final size:20
Alignment explanation
Indices: 27551847--27551902 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
27551837 TGGTGAGCTC
27551847 CAAGCTCACACCAAAA-TTT
1 CAAGCTCACACCAAAATTTT
* ** *
27551866 CTAAGAT-TTAGCAAAATTTT
1 C-AAGCTCACACCAAAATTTT
27551886 CAAGCTCACACCAAAAT
1 CAAGCTCACACCAAAAT
27551903 ATCTAACTTC
Statistics
Matches: 26, Mismatches: 8, Indels: 5
0.67 0.21 0.13
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (20 bp):
CAAGCTCACACCAAAATTTT
Found at i:27552675 original size:13 final size:13
Alignment explanation
Indices: 27552657--27552683 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27552647 ATTAAACTTT
27552657 TATCACAATTTCC
1 TATCACAATTTCC
27552670 TATCACAATTTCC
1 TATCACAATTTCC
27552683 T
1 T
27552684 TATTCAGATA
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:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (13 bp):
TATCACAATTTCC
Found at i:27553038 original size:32 final size:32
Alignment explanation
Indices: 27553002--27553073 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
27552992 AAATTTTATG
27553002 AAATATTTT-CAGGAAATT-TTCCAAACAATAGA
1 AAATATTTTACA-GAAATTATT-CAAACAATAGA
* *
27553034 AAATATTTTACATAAATTCATTCAAACACTAGA
1 AAATATTTTACAGAAATT-ATTCAAACAATAGA
27553067 AAATATT
1 AAATATT
27553074 AGCTTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 14 0.40
33 19 0.54
34 2 0.06
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (32 bp):
AAATATTTTACAGAAATTATTCAAACAATAGA
Found at i:27555762 original size:32 final size:33
Alignment explanation
Indices: 27555662--27555776 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 33
27555652 GGTGTACACT
* * **
27555662 CCTTTCCAAGTGGTACACACAAAGTATACCTTTT
1 CCTTTCCAAGTTGTACACACAAAGTATA-CATAA
* * * * *
27555696 TCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTTGTACACACAAAGTATACATAA
*
27555729 CCTTTCCAAG-TGTACACACAAAGTGTACATAA
1 CCTTTCCAAGTTGTACACACAAAGTATACATAA
*
27555761 CCTTTTCAAGTTGTAC
1 CCTTTCCAAGTTGTAC
27555777 CATTTGGGTA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
32 28 0.43
33 13 0.20
34 23 0.35
35 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.33
Consensus pattern (33 bp):
CCTTTCCAAGTTGTACACACAAAGTATACATAA
Found at i:27560525 original size:4 final size:4
Alignment explanation
Indices: 27560511--27560565 Score: 62
Period size: 4 Copynumber: 14.0 Consensus size: 4
27560501 TCAGAGGTAT
*
27560511 TGAA GTGAA TGAA TGAA T--A TGAA TGAA TGAA TGAA TGAA T-AT TGATA
1 TGAA -TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGA-A
27560558 TGAA TGAA
1 TGAA TGAA
27560566 ATATGCATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 2 0.05
4 33 0.75
5 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (4 bp):
TGAA
Found at i:27560539 original size:18 final size:19
Alignment explanation
Indices: 27560511--27560546 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
27560501 TCAGAGGTAT
27560511 TGAAGTGAATGAATGAATA
1 TGAAGTGAATGAATGAATA
27560530 TGAA-TGAATGAATGAAT
1 TGAAGTGAATGAATGAAT
27560547 GAATATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (19 bp):
TGAAGTGAATGAATGAATA
Found at i:27560541 original size:22 final size:24
Alignment explanation
Indices: 27560511--27560565 Score: 87
Period size: 22 Copynumber: 2.3 Consensus size: 24
27560501 TCAGAGGTAT
27560511 TGAAGTGAATGAATGAATA-TGA-A
1 TGAA-TGAATGAATGAATATTGATA
27560534 TGAATGAATGAATGAATATTGATA
1 TGAATGAATGAATGAATATTGATA
27560558 TGAATGAA
1 TGAATGAA
27560566 ATATGCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.47
23 7 0.23
24 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (24 bp):
TGAATGAATGAATGAATATTGATA
Found at i:27560778 original size:20 final size:20
Alignment explanation
Indices: 27560753--27560796 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
27560743 GGCCTAGCCC
27560753 CACGGCCATATCCCAGGCCA
1 CACGGCCATATCCCAGGCCA
*
27560773 CACGGCCATGTCCCAGGCCA
1 CACGGCCATATCCCAGGCCA
27560793 CACG
1 CACG
27560797 AACGTTGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.09
Consensus pattern (20 bp):
CACGGCCATATCCCAGGCCA
Found at i:27565526 original size:32 final size:32
Alignment explanation
Indices: 27565490--27565590 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 32
27565480 CTTGAGGTGC
27565490 ACATTCCTTTCCAAATGGTACACACAAAGTAT
1 ACATTCCTTTCCAAATGGTACACACAAAGTAT
** * *
27565522 ACATTTCCTTTTTATATGGTATACACAAAGTAT
1 ACA-TTCCTTTCCAAATGGTACACACAAAGTAT
* * * * *
27565555 ACCTAACCTTTCCAAGT-GTACATACAAAGTGT
1 ACAT-TCCTTTCCAAATGGTACACACAAAGTAT
27565587 ACAT
1 ACAT
27565591 AACCTTTTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
32 19 0.36
33 34 0.64
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (32 bp):
ACATTCCTTTCCAAATGGTACACACAAAGTAT
Found at i:27565594 original size:32 final size:33
Alignment explanation
Indices: 27565546--27565608 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
27565536 TATGGTATAC
*
27565546 ACAAAGTATACCTAACCTTTCCAAG-TGTACAT
1 ACAAAGTATACATAACCTTTCCAAGTTGTACAT
* *
27565578 ACAAAGTGTACATAACCTTTTCAAGTTGTAC
1 ACAAAGTATACATAACCTTTCCAAGTTGTAC
27565609 CATTTGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (33 bp):
ACAAAGTATACATAACCTTTCCAAGTTGTACAT
Found at i:27570840 original size:22 final size:22
Alignment explanation
Indices: 27570815--27570858 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27570805 AAACCATATG
27570815 TAAATGATTTTTCCTCTTTTGA
1 TAAATGATTTTTCCTCTTTTGA
27570837 TAAATGATTTTTCCTCTTTTGA
1 TAAATGATTTTTCCTCTTTTGA
27570859 ACAAAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (22 bp):
TAAATGATTTTTCCTCTTTTGA
Found at i:27577155 original size:13 final size:13
Alignment explanation
Indices: 27577125--27577164 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
27577115 AAAATAATTT
27577125 AAAT-TTAATTATA
1 AAATATTAA-TATA
27577138 AAATATTAATATA
1 AAATATTAATATA
27577151 AAATATTTAATATA
1 AAATA-TTAATATA
27577165 TATATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATTAATATA
Found at i:27577160 original size:14 final size:14
Alignment explanation
Indices: 27577127--27577164 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
27577117 AATAATTTAA
27577127 ATTTAATTATAAAAT
1 ATTTAA-TATAAAAT
27577142 A-TTAATATAAAAT
1 ATTTAATATAAAAT
27577155 ATTTAATATA
1 ATTTAATATA
27577165 TATATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 12 0.55
15 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAATATAAAAT
Found at i:27581323 original size:25 final size:23
Alignment explanation
Indices: 27581295--27581344 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
27581285 GTATAGAACT
*
27581295 TTTTTATAAATTTTTATAAATATAA
1 TTTTTAT-AATATTT-TAAATATAA
*
27581320 TTTTTATAGTATTTTAAATATAA
1 TTTTTATAATATTTTAAATATAA
27581343 TT
1 TT
27581345 ATAGTTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 5 0.22
25 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTATAATATTTTAAATATAA
Found at i:27587289 original size:31 final size:30
Alignment explanation
Indices: 27587249--27587327 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
27587239 GATTGAATCA
*
27587249 AAATTAAAGTTTCATGTATA-AATTTAAACC
1 AAATCAAAGTTTCATGTATATAA-TTAAACC
* **
27587279 ACAATCAAAGTTTCATATATATAATTGCACC
1 A-AATCAAAGTTTCATGTATATAATTAAACC
27587310 AAATCAAAGTTT-ATGTAT
1 AAATCAAAGTTTCATGTAT
27587328 CGAATTGCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 12 0.29
31 23 0.55
32 2 0.05
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTTCATGTATATAATTAAACC
Found at i:27595242 original size:19 final size:19
Alignment explanation
Indices: 27595218--27595261 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
27595208 AAGTGCTTTT
27595218 AGAAAAAAGAAAGAAAGAA
1 AGAAAAAAGAAAGAAAGAA
** *
27595237 AGAAAAATTAAAGAGAGAA
1 AGAAAAAAGAAAGAAAGAA
27595256 A-AAAAA
1 AGAAAAA
27595262 GGAGTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (19 bp):
AGAAAAAAGAAAGAAAGAA
Found at i:27598893 original size:21 final size:21
Alignment explanation
Indices: 27598867--27598907 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27598857 AGACGAGCAA
* *
27598867 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
27598888 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
27598908 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:27602450 original size:54 final size:54
Alignment explanation
Indices: 27602331--27602440 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 54
27602321 GGAATTGGGT
*
27602331 TTGGAATAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
1 TTGGAACAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
* * * *
27602385 TTGGAACAGAATAATGGGATGGAGA-CTCAAATTTCGGAGGGTATTGAAGTGGGC
1 TTGGAACAGAATAATGGGATGGAAATC-CAAATTTCAGAGGGTAATGAAGTAGGC
27602439 TT
1 TT
27602441 TAATGAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (54 bp):
TTGGAACAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
Found at i:27610532 original size:43 final size:43
Alignment explanation
Indices: 27610484--27610650 Score: 153
Period size: 43 Copynumber: 3.9 Consensus size: 43
27610474 ATCAAGATGT
*
27610484 GATTACATGTAAGACCATGTTTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
* * * * * *
27610527 GATTACGTGTAATACCATGTCTGAGACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TATTGA
* * * * *
27610570 GATTTCATGTAAGACCCTGTCTAGGACAGTGGCATTG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGA
* *
27610613 G-TTAACATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 GATT-ACATGTAAGACCATGTCTGGGACATTGGCATTGTA
27610651 CGAGCTTATG
Statistics
Matches: 97, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.01
42 11 0.11
43 82 0.85
44 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
Found at i:27616264 original size:2 final size:2
Alignment explanation
Indices: 27616251--27616298 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
27616241 GGTTGCTGTA
*
27616251 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27616293 -G AG AG A
1 AG AG AG A
27616299 CCAGACAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27620880 original size:208 final size:211
Alignment explanation
Indices: 27620507--27621009 Score: 522
Period size: 208 Copynumber: 2.4 Consensus size: 211
27620497 TTGGGTATCT
* * * * **
27620507 TTTTTTAAAATATATATATTTTAATATTTTACTATA-CTCT--A-TACACTTGTTAACTCCCTAA
1 TTTTTAAAAACATATATATTTTTATATTTTACTATATCT-TAGAGGACACTTGACAAC-CCCTAA
* * * *
27620568 CTTTACTTATGGAGTTTAAAAACTCTATTGACAATATATCAAATATTATTCTTATGTTTTATTAT
64 CTTTACTTATAGAGTCTAAAAACTCTACTGACAATATATCAAATATTA-T-TTATATTTTATTAT
* * * *
27620633 TTTTAAACAATAAAATATATTAAACTCAATCATCTCAAAGATGAATAATATAAACTCAATCACAG
127 TTTTAAACAATAAAATAAATTAAACTCAATCAGCTCAAAGATAAAAAATATAAACTCAATCACAG
* * *
27620698 CCTAAAACAGTTTGGGTCTCT
192 CCTAAAACAATTT-GGTCCCC
* **
27620719 TTTTTTAAAACAT-T-TA-TTTTATGATTTTACTATATCTTATTGGATC-CTTGACAACCCCTAA
1 TTTTTAAAAACATATATATTTTTAT-ATTTTACTATATCTTAGAGGA-CACTTGACAACCCCTAA
* * *
27620780 CTTTATTTATAGAGTCTAAAAACTC-ACTGACCATATATTAAATATTA-TTATATTTTATTATTT
64 CTTTACTTATAGAGTCTAAAAACTCTACTGACAATATATCAAATATTATTTATATTTTATTATTT
**** * * * * *
27620843 TTAAACAATAAAATAAATTGTGGTCAATGAGCTCAAAGCTAAAAAATATAAATTCAATCATAGCT
129 TTAAACAATAAAATAAATTAAACTCAATCAGCTCAAAGATAAAAAATATAAACTCAATCACAGCC
*
27620908 TAAAACAATTTGTTCCCC
194 TAAAACAATTTGGTCCCC
* * * *
27620926 TTTTTAAAAATATATATATTTTTTATATTTTACTATATCTTAGAGGACATTTGCCAACCCCTAAT
1 TTTTTAAAAACATATATA-TTTTTATATTTTACTATATCTTAGAGGACACTTGACAACCCCTAAC
*
27620991 TTTACTTATAGAATCTAAA
65 TTTACTTATAGAGTCTAAA
27621010 TATTTAATTG
Statistics
Matches: 241, Mismatches: 39, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
207 15 0.06
208 78 0.32
209 8 0.03
210 63 0.26
211 28 0.12
212 40 0.17
213 8 0.03
214 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (211 bp):
TTTTTAAAAACATATATATTTTTATATTTTACTATATCTTAGAGGACACTTGACAACCCCTAACT
TTACTTATAGAGTCTAAAAACTCTACTGACAATATATCAAATATTATTTATATTTTATTATTTTT
AAACAATAAAATAAATTAAACTCAATCAGCTCAAAGATAAAAAATATAAACTCAATCACAGCCTA
AAACAATTTGGTCCCC
Found at i:27626038 original size:19 final size:19
Alignment explanation
Indices: 27626002--27626038 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27625992 TAATTAGGCT
* *
27626002 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
27626021 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
27626039 GAAAAAGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:27626637 original size:12 final size:12
Alignment explanation
Indices: 27626620--27626647 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27626610 TAAAAGATAT
27626620 TTATTATAATTA
1 TTATTATAATTA
27626632 TTATTATAATTA
1 TTATTATAATTA
27626644 TTAT
1 TTAT
27626648 CATTATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTATAATTA
Found at i:27626782 original size:17 final size:18
Alignment explanation
Indices: 27626750--27626786 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
27626740 ATTGGAAAAC
*
27626750 AAGAAGAAAGAAAAGGGA
1 AAGAAGAAAAAAAAGGGA
27626768 AAGAA-AAAAAAAAGGGA
1 AAGAAGAAAAAAAAGGGA
27626785 AA
1 AA
27626787 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAAAAAAGGGA
Found at i:27627165 original size:17 final size:18
Alignment explanation
Indices: 27627143--27627176 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27627133 TAAATGAGTT
27627143 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
27627160 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
27627177 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:27627670 original size:13 final size:14
Alignment explanation
Indices: 27627649--27627688 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
27627639 ATTTGATTGG
27627649 AAAATGAATTAAA-
1 AAAATGAATTAAAT
*
27627662 AATATGAATTAAAT
1 AAAATGAATTAAAT
27627676 AAAAGTGAATTAA
1 AAAA-TGAATTAA
27627689 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAT
Found at i:27628077 original size:23 final size:22
Alignment explanation
Indices: 27628051--27628112 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
27628041 TAAGCACTTT
27628051 ATGTGTCGTATATCAGGCACCTC
1 ATGTGTCGT-TATCAGGCACCTC
27628074 ATGTGTCG-TATCAGGCACCTC
1 ATGTGTCGTTATCAGGCACCTC
*
27628095 GTGTGTCGTT-TCAGGCAC
1 ATGTGTCGTTATCAGGCAC
27628113 TTATTTGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 28 0.76
22 1 0.03
23 8 0.22
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (22 bp):
ATGTGTCGTTATCAGGCACCTC
Found at i:27630911 original size:15 final size:16
Alignment explanation
Indices: 27630893--27631034 Score: 64
Period size: 17 Copynumber: 8.7 Consensus size: 16
27630883 ATCACATTAT
27630893 TATTAAATTAAA-AAA
1 TATTAAATTAAATAAA
*
27630908 TATT--ATCAAGATAAA
1 TATTAAATTAA-ATAAA
27630923 TATTAAATTAAATTAAA
1 TATTAAATTAAA-TAAA
* * * *
27630940 TA-TATCATATATATTAG
1 TATTA-AAT-TAAATAAA
27630957 TATTAAATT-AATAAA
1 TATTAAATTAAATAAA
* *
27630972 -A-TACTATCTAGATAAA
1 TATTA-AAT-TAAATAAA
*
27630988 TATTAAATTAATATTAA
1 TATTAAATTAA-ATAAA
*
27631005 TATTAATATTAATATTAA
1 TATTAA-ATTAA-ATAAA
27631023 TATTAATATTAA
1 TATTAA-ATTAA
27631035 TACTAATTGT
Statistics
Matches: 97, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
13 6 0.06
14 4 0.04
15 15 0.15
16 11 0.11
17 31 0.32
18 30 0.31
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (16 bp):
TATTAAATTAAATAAA
Found at i:27630995 original size:31 final size:30
Alignment explanation
Indices: 27630893--27631000 Score: 119
Period size: 31 Copynumber: 3.4 Consensus size: 30
27630883 ATCACATTAT
*
27630893 TATTAAATTAA-AAAATATTATCAAGATAAA
1 TATTAAATTAATAAAATA-TATCTAGATAAA
* * *
27630923 TATTAAATTAAATTAAATATATCATATATATTAG
1 TATTAAATT-AATAAAATATATC-TAGATA--AA
27630957 TATTAAATTAATAAAATACTATCTAGATAAA
1 TATTAAATTAATAAAATA-TATCTAGATAAA
27630988 TATTAAATTAATA
1 TATTAAATTAATA
27631001 TTAATATTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
30 9 0.14
31 20 0.31
32 9 0.14
33 13 0.20
34 14 0.22
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (30 bp):
TATTAAATTAATAAAATATATCTAGATAAA
Found at i:27631005 original size:6 final size:6
Alignment explanation
Indices: 27630986--27631041 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
27630976 TATCTAGATA
27630986 AATATT AA-ATT AATATT AATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
*
27631033 AATACT AAT
1 AATATT AAT
27631042 TGTTTCTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:27631526 original size:52 final size:50
Alignment explanation
Indices: 27631451--27631557 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 50
27631441 AAAAGCTAAA
* *
27631451 TAAATAAAAATGAAATTCTATTAGATTAATTATCTTTTTGAAATTAAAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTAT-TTTTT-AAATTAAAAATC
* *
27631503 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTTAACTTATAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTTAAATTAAAAATC
27631553 TAAAT
1 TAAAT
27631558 TTGACTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 15 0.29
51 5 0.10
52 31 0.61
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (50 bp):
TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTTAAATTAAAAATC
Found at i:27641031 original size:19 final size:19
Alignment explanation
Indices: 27641009--27641052 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27640999 TTATTAAAAT
27641009 ATTATAATAAAAT-TAGAAA
1 ATTATAA-AAAATATAGAAA
*
27641028 ATTATAAAAATTATAGAAA
1 ATTATAAAAAATATAGAAA
*
27641047 AATATA
1 ATTATA
27641053 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATAAAAAATATAGAAA
Found at i:27641159 original size:26 final size:24
Alignment explanation
Indices: 27641113--27641167 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
27641103 ATTGTGAAAA
27641113 AAAATGAAAAAACATAGAAATTAT
1 AAAATGAAAAAACATAGAAATTAT
*
27641137 ATAAATTAAAAAA-ATAGAAAAATTAT
1 A-AAATGAAAAAACATAG--AAATTAT
27641163 AAAAT
1 AAAAT
27641168 ATTGTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.19
25 14 0.52
26 8 0.30
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (24 bp):
AAAATGAAAAAACATAGAAATTAT
Found at i:27641163 original size:24 final size:25
Alignment explanation
Indices: 27641114--27641165 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
27641104 TTGTGAAAAA
*
27641114 AAATGAAAAAACATAGAAATTATAT
1 AAATGAAAAAACATAGAAAATATAT
*
27641139 AAATTAAAAAA-ATAGAAAA-ATTAT
1 AAATGAAAAAACATAGAAAATA-TAT
27641163 AAA
1 AAA
27641166 ATATTGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.54
25 10 0.42
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (25 bp):
AAATGAAAAAACATAGAAAATATAT
Found at i:27643986 original size:21 final size:22
Alignment explanation
Indices: 27643962--27644004 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
27643952 GTATTGCTAT
27643962 AATAATT-ATAATTA-TAATCAA
1 AATAATTAAT-ATTATTAATCAA
27643983 AATAATTAATATTATTAATCAA
1 AATAATTAATATTATTAATCAA
27644005 CAATCTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAATATTATTAATCAA
Found at i:27648968 original size:16 final size:16
Alignment explanation
Indices: 27648947--27648982 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
27648937 ATTTAAATCA
27648947 AATTTAAATTCGAA-AT
1 AATTTAAATTC-AATAT
27648963 AATTTAAATTCAATAT
1 AATTTAAATTCAATAT
27648979 AATT
1 AATT
27648983 AAAACCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTAAATTCAATAT
Found at i:27650238 original size:14 final size:14
Alignment explanation
Indices: 27650215--27650249 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27650205 TACAATATTC
*
27650215 AAATAATAACAACA
1 AAATAGTAACAACA
27650229 AAATAGTAACAACA
1 AAATAGTAACAACA
*
27650243 TAATAGT
1 AAATAGT
27650250 GAAATGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:27650579 original size:18 final size:18
Alignment explanation
Indices: 27650556--27650595 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
27650546 TAGTGGTCGA
27650556 GGGTTCAATCCTCGCCTT
1 GGGTTCAATCCTCGCCTT
*
27650574 GGGTTCAATCTTCGCCTT
1 GGGTTCAATCCTCGCCTT
27650592 GGGT
1 GGGT
27650596 ATGAAGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.28, G:0.28, T:0.35
Consensus pattern (18 bp):
GGGTTCAATCCTCGCCTT
Found at i:27650907 original size:23 final size:23
Alignment explanation
Indices: 27650856--27650907 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27650846 TCATTTAAAC
*
27650856 AAATACTCATATTTATATAATTA
1 AAATATTCATATTTATATAATTA
*
27650879 AAATATTCATATTT-TATACTATA
1 AAATATTCATATTTATATAAT-TA
27650902 AAATAT
1 AAATAT
27650908 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATATTCATATTTATATAATTA
Found at i:27651048 original size:17 final size:18
Alignment explanation
Indices: 27651011--27651048 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
27651001 TTATTATTGT
*
27651011 TAAAATTTACTATTAAAA
1 TAAAATTTACAATTAAAA
*
27651029 TAAAATTTA-AATTTAAA
1 TAAAATTTACAATTAAAA
27651046 TAA
1 TAA
27651049 TTTATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTACAATTAAAA
Found at i:27654546 original size:11 final size:10
Alignment explanation
Indices: 27654511--27654574 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
27654501 TGTACTCTAT
*
27654511 TTTTTTTAAA
1 TTTTTATAAA
*
27654521 TTTTTATGAAC
1 TTTTTAT-AAA
27654532 TTTTTATAAGA
1 TTTTTATAA-A
*
27654543 -TTTT-TAAT
1 TTTTTATAAA
*
27654551 TTTTTTTAAA
1 TTTTTATAAA
27654561 TATTTTATAAA
1 T-TTTTATAAA
27654572 TTT
1 TTT
27654575 AAAATTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 7 0.16
10 18 0.42
11 18 0.42
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:27655676 original size:26 final size:26
Alignment explanation
Indices: 27655638--27655697 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
27655628 TGTCGTCATC
* * * *
27655638 TTCTATTCGTTTCTTTCTTTTTGTTG
1 TTCTTTTCGTTTCCTTCATTTTCTTG
*
27655664 TTCTTTTCTTTTCCTTCATTTTCTTG
1 TTCTTTTCGTTTCCTTCATTTTCTTG
27655690 TCTCTTTT
1 T-TCTTTT
27655698 TGATTCTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.03, C:0.20, G:0.07, T:0.70
Consensus pattern (26 bp):
TTCTTTTCGTTTCCTTCATTTTCTTG
Found at i:27668771 original size:87 final size:87
Alignment explanation
Indices: 27668680--27669045 Score: 318
Period size: 87 Copynumber: 4.2 Consensus size: 87
27668670 GGATGCCAAA
*
27668680 TCATCTTGGATTTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTC
1 TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTC
*
27668745 GAATATGGAGACGTCAAATCTG
66 GAATATGGAGACGCCAAATCTG
* *
27668767 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTACTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGT
* * *
27668831 CGAA-ATAGAGATGCCAGATCTG
65 CGAATATGGAGACGCCAAATCTG
* * ** * * * * * *
27668853 TTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTG-T
1 TCATCTTGGATCTACTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATG---T-G-TCTGCT
* ** *** *
27668917 -TCCTTATAA-ACACAAGAATGCCAAA----
59 CTCCGTCGAATA-TGGAG-ACGCCAAATCTG
* *
27668942 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTC
1 TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTC
* *
27669007 GAATATGGAGAAGCCAGATCTG
66 GAATATGGAGACGCCAAATCTG
*
27669029 TTATCTTGGATCTACTT
1 TCATCTTGGATCTACTT
27669046 TGATGTGAAA
Statistics
Matches: 216, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
82 3 0.01
83 7 0.03
84 9 0.04
85 1 0.00
86 35 0.16
87 98 0.45
88 22 0.10
89 20 0.09
91 8 0.04
92 3 0.01
93 10 0.05
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (87 bp):
TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTC
GAATATGGAGACGCCAAATCTG
Found at i:27668962 original size:175 final size:177
Alignment explanation
Indices: 27668767--27669091 Score: 521
Period size: 175 Copynumber: 1.8 Consensus size: 177
27668757 GTCAAATCTG
* * *
27668767 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTACTTCAGTATAAA-CACCTGAAGGTTAGATCTGCTATGTATCTGCCCTCCGT
* * * *
27668831 CGAA-ATAGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTG-AGAACATCCGAAAGTCA
65 CGAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCA
27668894 AATCTGCTATGTCTTCGATTTGTTCCTTATAAACACAAGAATGCCAAA
130 AATCTGCTATGTCTTCGATTTGTTCCTTATAAACACAAGAATGCCAAA
*
27668942 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTC
1 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTATCTGCCCTCCGTC
* * *
27669007 GAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCTGGAAGTCAA
66 GAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
27669072 ATCTGCTATGTCTTCGATTT
131 ATCTGCTATGTCTTCGATTT
27669092 ACTCCTCGTC
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
175 60 0.44
176 41 0.30
177 35 0.26
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (177 bp):
TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTATCTGCCCTCCGTC
GAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
ATCTGCTATGTCTTCGATTTGTTCCTTATAAACACAAGAATGCCAAA
Found at i:27669171 original size:183 final size:177
Alignment explanation
Indices: 27668741--27669174 Score: 500
Period size: 175 Copynumber: 2.4 Consensus size: 177
27668731 GTCTGCTCTC
* * * * *
27668741 CGTCGAATATGGAGACGTCAAATCTGTCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTTA
1 CGTCGAACATAGAGAAGCCAAATCTGT-ATCTTGGATCTGCTTCAGTTAAA-CA-CTGAAGGTTA
* * *
27668806 GATCTGCTATGTATCTGCTCTCCGTCGAAATAGAGATGCCAGATCTGTTATCTTGGATCTGCTTT
63 GATCTGCTATGTATCTGCCCTCCGTCGAAATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTT
* * **
27668871 GGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCT
128 GATGTGAAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
** * * *
27668921 TAT-AAACACA-AGAATGCCAAATC---ATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTA
1 CGTCGAACATAGAGAA-GCCAAATCTGTATCTTGGATCTGCTTCAGT-TAAACA-CTGAAGGTTA
* *
27668981 GATCTGCTATGTGTCTGCCCTCCGTCGAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTT
63 GATCTGCTATGTATCTGCCCTCCGTCGAA-ATAGAGAAGCCAGATCTGTTATCTTGGATCTACTT
* *
27669046 TGATGTGAAAAACATCTGGAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
127 TGATGTG-AAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
* * **
27669098 CGTCGAAGATAGAGAAGCCAAATCTTGTTATCTTGGATCTGCTTTAGTGTAAACACGTGAAGGCC
1 CGTCGAACATAGAGAAGCCAAATC-TG-TATCTTGGATCTGCTTCAGT-TAAACAC-TGAAGGTT
27669163 AGATCTGCTATG
62 AGATCTGCTATG
27669175 CTTTGGTCTG
Statistics
Matches: 210, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
175 57 0.27
176 41 0.20
177 40 0.19
178 15 0.07
179 14 0.07
180 1 0.00
182 1 0.00
183 41 0.20
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (177 bp):
CGTCGAACATAGAGAAGCCAAATCTGTATCTTGGATCTGCTTCAGTTAAACACTGAAGGTTAGAT
CTGCTATGTATCTGCCCTCCGTCGAAATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGAT
GTGAAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
Found at i:27680269 original size:21 final size:21
Alignment explanation
Indices: 27680245--27680298 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
27680235 AACTTCTTGA
*
27680245 TGAGTTGGGGTAGTAGGTATC
1 TGAGTTGGGGTAGTAGGTAAC
*
27680266 TGAGTTGGGGCAGTAGGTAAC
1 TGAGTTGGGGTAGTAGGTAAC
27680287 TGAGTTGGGGTA
1 TGAGTTGGGGTA
27680299 CCTTCTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.06, G:0.44, T:0.30
Consensus pattern (21 bp):
TGAGTTGGGGTAGTAGGTAAC
Found at i:27680913 original size:16 final size:17
Alignment explanation
Indices: 27680882--27680914 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27680872 AACATAAGCA
*
27680882 TATATCACTCATTTCAT
1 TATATCAATCATTTCAT
27680899 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
27680915 GCTCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:27681378 original size:46 final size:46
Alignment explanation
Indices: 27681197--27681378 Score: 238
Period size: 46 Copynumber: 4.0 Consensus size: 46
27681187 TTTGACATGA
* * * * ** * *
27681197 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *** *
27681243 TACCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
27681289 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
27681335 TGCCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
27681379 AGAGCACACT
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 120 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:27684626 original size:42 final size:43
Alignment explanation
Indices: 27684456--27684633 Score: 247
Period size: 43 Copynumber: 4.2 Consensus size: 43
27684446 AAAAAAAAAC
* *
27684456 TCATTGCATGCATATTAAAAAATAGGCAACA-C--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
27684496 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
27684539 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* * * *
27684582 TCATTGCATACAGATTAAAAGA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
27684624 TCACTGCATG
1 TCATTGCATG
27684634 TAATCAGCAA
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 30 0.24
41 1 0.01
42 25 0.20
43 67 0.54
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:27686012 original size:30 final size:31
Alignment explanation
Indices: 27685988--27686046 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
27685978 GTAAATACTC
*
27685988 AAAATTTGAGAGG-TTAA-AGTGTAAATATGA
1 AAAATTTGA-AGGATCAATAGTGTAAATATGA
27686018 AAAATTTGAAGGATCAATAGTGTAAATAT
1 AAAATTTGAAGGATCAATAGTGTAAATAT
27686047 TTTAAGGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 12 0.46
31 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGATCAATAGTGTAAATATGA
Found at i:27686299 original size:11 final size:11
Alignment explanation
Indices: 27686285--27686340 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
27686275 AGATAAATAT
27686285 TATTTTATTAA
1 TATTTTATTAA
*
27686296 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
27686309 TATTTTATTAT
1 TATTTTATTAA
*
27686320 TATTTTATTAT
1 TATTTTATTAA
27686331 TATTTTATTA
1 TATTTTATTA
27686341 GTATATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 27 0.68
12 6 0.15
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:27688525 original size:46 final size:46
Alignment explanation
Indices: 27688456--27688714 Score: 323
Period size: 46 Copynumber: 5.7 Consensus size: 46
27688446 AGTGTGCTCT
* *
27688456 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
27688502 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
27688548 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGC-A-
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
27688592 ---ATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
27688635 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
27688681 ATGACA-GAAAAGGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGA
27688715 CAATATGGCA
Statistics
Matches: 192, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.19
42 1 0.01
45 2 0.01
46 153 0.80
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:27688654 original size:87 final size:87
Alignment explanation
Indices: 27688475--27688684 Score: 276
Period size: 87 Copynumber: 2.4 Consensus size: 87
27688465 AATGTGTAAA
**
27688475 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGC-A----ATATGAAATGAATAAGACCATGGTTGAAAGATACC
* * **
27688540 ATGACAACCTGATATGAAATGTGTAAG
61 ATGACAACCTGACATGAAAAGAATAAG
* * *
27688567 ACCATAGTTGAAAGATACCATGGCAATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGC
1 ACCATGGTTGAAAGATACCATGGCAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGAC
*
27688632 AACGTGACATGAAAAGAATAAG
66 AACCTGACATGAAAAGAATAAG
*
27688654 ACCATGGTTGAAAGATACCATGGCAACATGA
1 ACCATGGTTGAAAGATACCATGGCAATATGA
27688685 CAGAAAAGGA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
87 82 0.77
91 1 0.01
92 23 0.22
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (87 bp):
ACCATGGTTGAAAGATACCATGGCAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGAC
AACCTGACATGAAAAGAATAAG
Found at i:27688699 original size:133 final size:133
Alignment explanation
Indices: 27688459--27688714 Score: 370
Period size: 133 Copynumber: 1.9 Consensus size: 133
27688449 GTGCTCTCTG
** * * **
27688459 ATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACC
1 ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
* * * *
27688524 ATGGTTGAAAGATACCATGACAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATG
66 ATGGTTGAAAGATACCATGACAACATGACATGAAAGGAGTAAGACCATAGTTGAAAGATACCATG
27688589 GCA
131 GCA
* * *
27688592 ATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACC
1 ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
*
27688657 ATGGTTGAAAGATACCATGGCAACATGACA-GAAAAGGAGTAAGACCATAGTTGAAAGA
66 ATGGTTGAAAGATACCATGACAACATGACATG-AAAGGAGTAAGACCATAGTTGAAAGA
27688715 CAATATGGCA
Statistics
Matches: 108, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
132 1 0.01
133 107 0.99
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (133 bp):
ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
ATGGTTGAAAGATACCATGACAACATGACATGAAAGGAGTAAGACCATAGTTGAAAGATACCATG
GCA
Found at i:27690013 original size:15 final size:15
Alignment explanation
Indices: 27689993--27690022 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27689983 ATGCATCACT
27689993 ATCACTACCAGACAC
1 ATCACTACCAGACAC
27690008 ATCACTACCAGACAC
1 ATCACTACCAGACAC
27690023 GTTTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:27690377 original size:62 final size:62
Alignment explanation
Indices: 27690306--27690540 Score: 335
Period size: 62 Copynumber: 3.8 Consensus size: 62
27690296 TAGGAGCTTG
* *
27690306 GATACAAACAATGACAGATATAGACAATAAACATCAGTTTAATAATGTATAATTTAATCGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
* * *
27690368 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATTGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
* * * * ** *
27690430 GATACAAACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATG-TA-TAATTTAATCGCA
*
27690494 GATACAAACAATGACAGATATACACAATAAACATCAATTTGATAATG
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATG
27690541 ACATTCATAC
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
62 104 0.65
63 1 0.01
64 55 0.34
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (62 bp):
GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
Found at i:27690551 original size:34 final size:34
Alignment explanation
Indices: 27690449--27690551 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 34
27690439 AATGGCAGAT
27690449 ATACACAATAAACATCAATTTGATAATGACATTC
1 ATACACAATAAACATCAATTTGATAATGACATTC
** * * *
27690483 AT--ACAATGGCAGATACAA----ACAATGACAGAT-
1 ATACACAAT-AAACAT-CAATTTGATAATGACA-TTC
27690513 ATACACAATAAACATCAATTTGATAATGACATTC
1 ATACACAATAAACATCAATTTGATAATGACATTC
27690547 ATACA
1 ATACA
27690552 ATGGCAGATA
Statistics
Matches: 49, Mismatches: 10, Indels: 20
0.62 0.13 0.25
Matches are distributed among these distances:
30 13 0.27
31 4 0.08
32 10 0.20
33 4 0.08
34 18 0.37
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (34 bp):
ATACACAATAAACATCAATTTGATAATGACATTC
Found at i:27690566 original size:112 final size:112
Alignment explanation
Indices: 27690437--27690690 Score: 418
Period size: 112 Copynumber: 2.3 Consensus size: 112
27690427 GCAGATACAA
*
27690437 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGGCAGATACAAA
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGACAGATACAAA
27690502 CAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
66 CAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* * *
27690549 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAATGACAGATACAAA
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGACAGATACAAA
* * * *
27690614 CAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCAT
66 CAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* *
27690661 ACAATGGCAGATACAAACAATAAACATCAA
1 ACAATGGCAGATATACACAATAAACATCAA
27690691 AATCAAAATC
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
112 130 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (112 bp):
ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGACAGATACAAA
CAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:27690617 original size:48 final size:48
Alignment explanation
Indices: 27690501--27690609 Score: 182
Period size: 48 Copynumber: 2.3 Consensus size: 48
27690491 GCAGATACAA
27690501 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
1 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* * *
27690549 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCAT
1 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
*
27690597 ATAATGACAGATA
1 ACAATGACAGATA
27690610 CAAACAATGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (48 bp):
ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:27690617 original size:64 final size:64
Alignment explanation
Indices: 27690549--27690681 Score: 239
Period size: 64 Copynumber: 2.1 Consensus size: 64
27690539 TGACATTCAT
*
27690549 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAATGACAGATACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
* *
27690613 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGGCAGATACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
27690677 ACAAT
1 ACAAT
27690682 AAACATCAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (64 bp):
ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
Found at i:27690846 original size:18 final size:18
Alignment explanation
Indices: 27690823--27690905 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 18
27690813 AAATAACCCT
27690823 AAATCAAAATCTAAATCG
1 AAATCAAAATCTAAATCG
27690841 AAATCAAAATC-AAAT--
1 AAATCAAAATCTAAATCG
* *
27690856 ---TC-TAATCCTAAATTG
1 AAATCAAAAT-CTAAATCG
* * *
27690871 AGATCAAAATCGAAATTG
1 AAATCAAAATCTAAATCG
27690889 AAATCAAAATCTAAATC
1 AAATCAAAATCTAAATC
27690906 AGAATCAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 4 0.08
17 4 0.08
18 34 0.67
19 3 0.06
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (18 bp):
AAATCAAAATCTAAATCG
Found at i:27690911 original size:12 final size:12
Alignment explanation
Indices: 27690821--27690860 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
27690811 CGAAATAACC
27690821 CTAAATCAAAAT
1 CTAAATCAAAAT
*
27690833 CTAAATCGAAAT
1 CTAAATCAAAAT
* *
27690845 CAAAATCAAATT
1 CTAAATCAAAAT
27690857 CTAA
1 CTAA
27690861 TCCTAAATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (12 bp):
CTAAATCAAAAT
Found at i:27690964 original size:12 final size:12
Alignment explanation
Indices: 27690922--27690970 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
27690912 AGTGAGTGTT
* *
27690922 TCAAAATTGTAA
1 TCAAAATCGAAA
27690934 TCAAAATCGAAA
1 TCAAAATCGAAA
27690946 T-AGAAATCGAAA
1 TCA-AAATCGAAA
*
27690958 TCAAAATCAAAA
1 TCAAAATCGAAA
27690970 T
1 T
27690971 TAAATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.22
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:27690970 original size:18 final size:18
Alignment explanation
Indices: 27690922--27690964 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
27690912 AGTGAGTGTT
* *
27690922 TCAAAATTGTAATCAAAA
1 TCAAAATAGAAATCAAAA
* *
27690940 TCGAAATAGAAATCGAAA
1 TCAAAATAGAAATCAAAA
27690958 TCAAAAT
1 TCAAAAT
27690965 CAAAATTAAA
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:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (18 bp):
TCAAAATAGAAATCAAAA
Found at i:27691501 original size:31 final size:29
Alignment explanation
Indices: 27691462--27691534 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
27691452 GGTAACTGTT
*
27691462 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
*
27691492 ACGTTAGTGA-TCGTTTTGTTACTTTTTGAA
1 A-GTTAGTGACT-GTTTTGTCACTTTTTGAA
27691522 AGTTAAGTGACTG
1 AGTT-AGTGACTG
27691535 AAATGAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 24 0.65
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:27692862 original size:11 final size:10
Alignment explanation
Indices: 27692826--27692892 Score: 66
Period size: 10 Copynumber: 6.7 Consensus size: 10
27692816 ATTATTATTC
27692826 TAGAATTTTT
1 TAGAATTTTT
27692836 T--AATTTTT
1 TAGAATTTTT
*
27692844 TAAAATTTTT
1 TAGAATTTTT
*
27692854 TATGTATTTTT
1 TA-GAATTTTT
27692865 TAGAATTTTTT
1 TAGAA-TTTTT
*
27692876 TATAATTTTT
1 TAGAATTTTT
*
27692886 TAAAATT
1 TAGAATT
27692893 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
8 8 0.17
10 23 0.48
11 17 0.35
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (10 bp):
TAGAATTTTT
Found at i:27692864 original size:21 final size:20
Alignment explanation
Indices: 27692831--27692892 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
27692821 TATTCTAGAA
27692831 TTTTT-TAATTTTTTAAAAT
1 TTTTTATAATTTTTTAAAAT
* *
27692850 TTTTTATGTATTTTTTAGAATT
1 TTTTTAT-AATTTTTTA-AAAT
27692872 TTTTTATAATTTTTTAAAAT
1 TTTTTATAATTTTTTAAAAT
27692892 T
1 T
27692893 ATAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 16 0.44
22 10 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTATAATTTTTTAAAAT
Found at i:27702747 original size:51 final size:49
Alignment explanation
Indices: 27702692--27702900 Score: 171
Period size: 44 Copynumber: 4.5 Consensus size: 49
27702682 AATCTTCTTC
27702692 ACTGCAACTTCAGGAAGATAAGATTTGTGGTTTGTATCTTTAATCTGCT-CT
1 ACTGCAACTTCAGGAAGATAAGATTTGTGG--T-TATCTTTAATCTGCTCCT
27702743 ACTGCAACTTCA-GATAGATAAGA-TT-T-GTTATCTTTAATCTGCTCCT
1 ACTGCAACTTCAGGA-AGATAAGATTTGTGGTTATCTTTAATCTGCTCCT
* * *
27702789 -CTACAACTTCAGGGAGATAAGATTTGTGG----CTTTAATCTGCTTC-
1 ACTGCAACTTCAGGAAGATAAGATTTGTGGTTATCTTTAATCTGCTCCT
* * * * **
27702832 GCTGCAAATTTAGGGAGATAAGATTAATGGTT-TC---AATCTGCT-CT
1 ACTGCAACTTCAGGAAGATAAGATTTGTGGTTATCTTTAATCTGCTCCT
* *
27702876 ACTACAACTTCAGGAAAATAAGATT
1 ACTGCAACTTCAGGAAGATAAGATT
27702901 CGTCATGATA
Statistics
Matches: 133, Mismatches: 14, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
43 1 0.01
44 64 0.48
45 33 0.25
46 6 0.05
47 2 0.02
48 2 0.02
49 1 0.01
50 4 0.03
51 20 0.15
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (49 bp):
ACTGCAACTTCAGGAAGATAAGATTTGTGGTTATCTTTAATCTGCTCCT
Found at i:27703030 original size:44 final size:44
Alignment explanation
Indices: 27702974--27703217 Score: 213
Period size: 44 Copynumber: 5.5 Consensus size: 44
27702964 ATTAACTTGT
* *
27702974 TCCACTGTAACTTCAGGGAGATAAGACTTGTAACATCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGC
* * * ** * * *
27703018 TCTACTGCAACTTCAGGGAGATAAG-GTTCATGGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAACCTGC
* *
27703062 TCCACTGCATCTTCAGGGAGATAAGACTAT-TAACTTTAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACT-TGTAACTTCAACCTGC
* * ** * * * *
27703106 CCCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTCGATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCAACCTGC
* * *
27703151 TCCACTGCAACTCCAGGGAGATAAAACTCGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGC
* * *
27703195 CCCACTACAACTTCAGGGGGATA
1 TCCACTGCAACTTCAGGGAGATA
27703218 GGATTTATGG
Statistics
Matches: 153, Mismatches: 42, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
43 3 0.02
44 116 0.76
45 33 0.22
46 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGC
Found at i:27703120 original size:88 final size:88
Alignment explanation
Indices: 27702971--27703264 Score: 335
Period size: 88 Copynumber: 3.3 Consensus size: 88
27702961 AGCATTAACT
* * * *
27702971 TGTTCCACTGTAACTTCAGGGAGATAAGACTTGTAACATCAACCTGCTCTACTGCAACTTCAGGG
1 TGTTCCACTGCAACTTCAGGGAGATAAGACTT-TAACTTCAACCTGCCCCACTGCAACTTCAGGG
*
27703036 AGATAAGG-TTCATGGCTTTAATC
65 GGATAAGGATTCATGGCTTTAATC
* *
27703059 TGTTCCACTGCATCTTCAGGGAGATAAGACTATTAACTTTAACCTGCCCCACTGCAACTTCAGGG
1 TGTTCCACTGCAACTTCAGGGAGATAAGACT-TTAACTTCAACCTGCCCCACTGCAACTTCAGGG
* **
27703124 GGATAAGGTTTGCTAT--CTTCGATC
65 GGATAAGGATT-C-ATGGCTTTAATC
** * * * *
27703148 TACTCCACTGCAACTCCAGGGAGATAAAACTCGTAACTTCAACCTGCCCCACTACAACTTCAGGG
1 TGTTCCACTGCAACTTCAGGGAGATAAGACT-TTAACTTCAACCTGCCCCACTGCAACTTCAGGG
*
27703213 GGAT-AGGATTTATGGCTTTAATC
65 GGATAAGGATTCATGGCTTTAATC
* * *
27703236 TGTTCCACTGCATCTTTAAGGAGATAAGA
1 TGTTCCACTGCAACTTCAGGGAGATAAGA
27703265 TTCGCCATAA
Statistics
Matches: 171, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
86 2 0.01
88 97 0.57
89 69 0.40
90 1 0.01
91 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (88 bp):
TGTTCCACTGCAACTTCAGGGAGATAAGACTTTAACTTCAACCTGCCCCACTGCAACTTCAGGGG
GATAAGGATTCATGGCTTTAATC
Found at i:27707235 original size:19 final size:20
Alignment explanation
Indices: 27707221--27707264 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
27707211 TGTGAAATTT
*
27707221 AATGCATATG-ATGAAATGC
1 AATGCAGATGCATGAAATGC
27707240 AATGCAGATGCATGAAATG-
1 AATGCAGATGCATGAAATGC
27707259 AATGCA
1 AATGCA
27707265 AAAAGAGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
AATGCAGATGCATGAAATGC
Found at i:27709323 original size:3 final size:3
Alignment explanation
Indices: 27709315--27709343 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27709305 TAAGTAGATA
27709315 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27709344 AAAAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27709369 original size:27 final size:26
Alignment explanation
Indices: 27709330--27709396 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
27709320 TAATAATAAT
*
27709330 AATAATAATAATAAAAAAGATAAAACAA
1 AATAA-AAGAATAAAAAAGATAAAA-AA
* * *
27709358 AATAAAAGAATATAAAATATATAAAA
1 AATAAAAGAATAAAAAAGATAAAAAA
*
27709384 AATGAATAGAATA
1 AAT-AAAAGAATA
27709397 CATAATAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 5 0.15
27 23 0.70
28 5 0.15
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (26 bp):
AATAAAAGAATAAAAAAGATAAAAAA
Found at i:27709521 original size:18 final size:17
Alignment explanation
Indices: 27709500--27709540 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
27709490 AAAAAATAAT
27709500 AATAAAATAAATCAAACA
1 AATAAAATAAAT-AAACA
* *
27709518 AATAACATAAATAAATA
1 AATAAAATAAATAAACA
27709535 AATAAA
1 AATAAA
27709541 TAAGACGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAATAAATAAACA
Found at i:27709531 original size:4 final size:4
Alignment explanation
Indices: 27709504--27709543 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
27709494 AATAATAATA
*
27709504 AAAT AAAT CAAAC AAAT AACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA
27709544 GACGAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 25 0.78
5 7 0.22
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:27713145 original size:26 final size:26
Alignment explanation
Indices: 27713116--27713173 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
27713106 CATGAAATTC
27713116 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
27713142 TTATCATGGAACATTTATCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
27713168 TTATCA
1 TTATCA
27713174 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:27716343 original size:12 final size:12
Alignment explanation
Indices: 27716326--27716359 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
27716316 CGGCCTGGCC
27716326 ATATTAATTTTT
1 ATATTAATTTTT
*
27716338 ATATTATTTTTT
1 ATATTAATTTTT
27716350 ATA-TAATTTT
1 ATATTAATTTT
27716360 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:27721605 original size:15 final size:16
Alignment explanation
Indices: 27721584--27721644 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 16
27721574 TATATAAAGG
27721584 GTAATAAATAATAAAA
1 GTAATAAATAATAAAA
27721600 -TAATAATAGATAATAAAA
1 GTAAT-A-A-ATAATAAAA
27721618 TTGTAAT-AATAATAAAA
1 --GTAATAAATAATAAAA
27721635 GT-ATAAATAA
1 GTAATAAATAA
27721645 AATAAATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 1 0.03
17 10 0.26
18 10 0.26
21 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
GTAATAAATAATAAAA
Found at i:27721624 original size:21 final size:17
Alignment explanation
Indices: 27721585--27721634 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
27721575 ATATAAAGGG
27721585 TAATAAATAATAAAATAA
1 TAAT-AATAATAAAATAA
**
27721603 TAATAGATAATAAAATTG
1 TAATA-ATAATAAAATAA
27721621 TAATAATAATAAAA
1 TAATAATAATAAAA
27721635 GTATAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATAATAATAAAATAA
Found at i:27721643 original size:18 final size:17
Alignment explanation
Indices: 27721590--27721650 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
27721580 AAGGGTAATA
27721590 AATAATAAAATA-ATAAT
1 AATAATAAAATATA-AAT
*
27721607 AGATAATAAAAT-TGTAAT
1 A-ATAATAAAATAT-AAAT
27721625 AATAATAAAAGTATAAAT
1 AATAATAAAA-TATAAAT
27721643 AA-AATAAA
1 AATAATAAA
27721651 TAACAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 16 0.43
18 20 0.54
19 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAATAAAATATAAAT
Found at i:27721822 original size:20 final size:20
Alignment explanation
Indices: 27721750--27721825 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 20
27721740 TATATTAATA
* *
27721750 AATAAATGAACAAACGAAT-
1 AATAAATAAACAAATGAATG
27721769 AAGTAAAATAAA-AGAAT-AATG
1 AA-T-AAATAAACA-AATGAATG
27721790 AATATATATAAACAAATGAATG
1 AATA-A-ATAAACAAATGAATG
27721812 AATAAATAAACAAA
1 AATAAATAAACAAA
27721826 CTAAAAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
19 3 0.06
20 16 0.34
21 19 0.40
22 9 0.19
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (20 bp):
AATAAATAAACAAATGAATG
Found at i:27730407 original size:26 final size:26
Alignment explanation
Indices: 27730370--27730427 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
27730360 TGATACAAAT
27730370 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
27730396 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
27730422 TGATAA
1 TGATAA
27730428 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:27737353 original size:19 final size:19
Alignment explanation
Indices: 27737329--27737366 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27737319 TCAGACTATC
*
27737329 ACCCTTTTCTCGTTGTGTT
1 ACCCTTATCTCGTTGTGTT
27737348 ACCCTTATCTCGTTGTGTT
1 ACCCTTATCTCGTTGTGTT
27737367 TACTCGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.16, T:0.50
Consensus pattern (19 bp):
ACCCTTATCTCGTTGTGTT
Found at i:27738857 original size:32 final size:33
Alignment explanation
Indices: 27738783--27738875 Score: 102
Period size: 32 Copynumber: 2.8 Consensus size: 33
27738773 AAAGGGTGAT
**
27738783 ACTTGAAAAGGACTTATGTAC-CCAAGTG-GTACA
1 ACTTGAAAAGG--TTATGTACACCTTGTGTGTACA
27738816 ACTTGAAAAGGTTATGTACACCTTGTGTGTAC-
1 ACTTGAAAAGGTTATGTACACCTTGTGTGTACA
* * *
27738848 ACTTGAAAAGGTTAGGTATACTTTGTGT
1 ACTTGAAAAGGTTATGTACACCTTGTGT
27738876 ATACCATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.15
32 30 0.57
33 15 0.28
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (33 bp):
ACTTGAAAAGGTTATGTACACCTTGTGTGTACA
Found at i:27738924 original size:33 final size:33
Alignment explanation
Indices: 27738811--27738926 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 33
27738801 TACCCAAGTG
* ** * * *
27738811 GTACAACTTGAAAAGGTTATGTACACCTTGTGT
1 GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
**
27738844 GTA-CACTTGAAAAGGTTAGGTATACTTTGTGT
1 GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
* *
27738876 ATACCA-TATAAAAAGGAAAGGTATACTTTGTGT
1 GTACCACT-TGAAAAGGAAAGGTATACTTTGTGT
*
27738909 GTACCACTTGGAAAGGAA
1 GTACCACTTGAAAAGGAA
27738927 TGTAGACCTC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
32 28 0.41
33 40 0.58
34 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (33 bp):
GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
Found at i:27739681 original size:15 final size:13
Alignment explanation
Indices: 27739645--27739699 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
27739635 CAATTCAATG
*
27739645 ATAATA-ATAACA
1 ATAATATATAATA
27739657 ATAAT-TATAATA
1 ATAATATATAATA
27739669 ATAACTATCATAATA
1 ATAA-TAT-ATAATA
*
27739684 TTAATATA-AATA
1 ATAATATATAATA
27739696 ATAA
1 ATAA
27739700 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 21 0.58
13 2 0.06
14 4 0.11
15 9 0.25
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATATATAATA
Found at i:27739846 original size:14 final size:17
Alignment explanation
Indices: 27739796--27739840 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
27739786 TAGATGAATA
**
27739796 AATAATAAAATAATAAT
1 AATAATAAAATGTTAAT
27739813 AGATAATAAAATGTTAAT
1 A-ATAATAAAATGTTAAT
27739831 AATAATAAAA
1 AATAATAAAA
27739841 GTATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AATAATAAAATGTTAAT
Found at i:27739849 original size:18 final size:18
Alignment explanation
Indices: 27739796--27739856 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
27739786 TAGATGAATA
27739796 AATAATAAAA-TA-ATAAT
1 AATAATAAAAGTATA-AAT
27739813 AGATAATAAAATGT-T-AAT
1 A-ATAATAAAA-GTATAAAT
27739831 AATAATAAAAGTATAAAT
1 AATAATAAAAGTATAAAT
27739849 AA-AATAAA
1 AATAATAAA
27739857 TAACGAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.05
17 17 0.45
18 18 0.47
20 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AATAATAAAAGTATAAAT
Found at i:27747639 original size:15 final size:16
Alignment explanation
Indices: 27747621--27747650 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27747611 AATTATCCAA
27747621 AAAAAAAAGT-AAAAG
1 AAAAAAAAGTGAAAAG
27747636 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
27747651 TTAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAAAAAGTGAAAAG
Found at i:27754327 original size:30 final size:31
Alignment explanation
Indices: 27754293--27754357 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
27754283 ATACATAAAT
* *
27754293 ATTTTCTA-AAAAATATAATAATAAATTTTA
1 ATTTTATATAAAAATATAATAATAAATTTAA
* * *
27754323 ATTTTATATTAATATATATTAATAAATTTAA
1 ATTTTATATAAAAATATAATAATAAATTTAA
27754354 ATTT
1 ATTT
27754358 CATTATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTTTATATAAAAATATAATAATAAATTTAA
Found at i:27754335 original size:21 final size:21
Alignment explanation
Indices: 27754306--27754345 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27754296 TTCTAAAAAA
*
27754306 TATAATAATAAATTTTAATTT
1 TATAATAATAAATATTAATTT
* *
27754327 TATATTAATATATATTAAT
1 TATAATAATAAATATTAAT
27754346 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATAATAATAAATATTAATTT
Found at i:27754346 original size:31 final size:32
Alignment explanation
Indices: 27754305--27754366 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
27754295 TTTCTAAAAA
* *
27754305 ATATAATAATAAATTTTAATTTTA-TATTAAT
1 ATATAATAATAAATTTAAATTTCATTATTAAT
*
27754336 ATATATTAATAAATTTAAATTTCATTATTAA
1 ATATAATAATAAATTTAAATTTCATTATTAA
27754367 ATAGCATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
ATATAATAATAAATTTAAATTTCATTATTAAT
Found at i:27758610 original size:93 final size:93
Alignment explanation
Indices: 27758480--27758651 Score: 335
Period size: 93 Copynumber: 1.8 Consensus size: 93
27758470 AGCCATTTAA
*
27758480 TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
1 TTTTAATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
27758545 TTTTTTTATATTTTCATTATATATATTC
66 TTTTTTTATATTTTCATTATATATATTC
27758573 TTTTAATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
1 TTTTAATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
27758638 TTTTTTTATATTTT
66 TTTTTTTATATTTT
27758652 TATTTGAAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.20, C:0.19, G:0.00, T:0.62
Consensus pattern (93 bp):
TTTTAATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
TTTTTTTATATTTTCATTATATATATTC
Found at i:27764897 original size:26 final size:24
Alignment explanation
Indices: 27764867--27764916 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
27764857 AAATAAAAAA
27764867 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAATATAA-AAA-CAAATAT
27764893 ATTTAAAAATATAAAAACAAATAT
1 ATTTAAAAATATAAAAACAAATAT
27764917 TAAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTTAAAAATATAAAAACAAATAT
Found at i:27764914 original size:12 final size:12
Alignment explanation
Indices: 27764899--27764931 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27764889 ATATATTTAA
27764899 AAATATAAAAAC
1 AAATATAAAAAC
*
27764911 AAATATTAAAAC
1 AAATATAAAAAC
27764923 AAATA-AAAA
1 AAATATAAAA
27764932 TGATACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATATAAAAAC
Found at i:27764926 original size:24 final size:25
Alignment explanation
Indices: 27764871--27764932 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
27764861 AAAAAAATTT
**
27764871 AAAAATATAATAAATCAAATATATTT
1 AAAAATATAA-AAATCAAATATATAA
27764897 AAAAATATAAAAA-CAAATAT-TAA
1 AAAAATATAAAAATCAAATATATAA
*
27764920 AACAA-ATAAAAAT
1 AAAAATATAAAAAT
27764933 GATACTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 7 0.22
23 5 0.16
24 7 0.22
25 3 0.09
26 10 0.31
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAATATAAAAATCAAATATATAA
Found at i:27768868 original size:37 final size:38
Alignment explanation
Indices: 27768805--27768974 Score: 127
Period size: 38 Copynumber: 4.4 Consensus size: 38
27768795 ATAGTATTAT
*
27768805 ATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATTCATATAAGAATATTTA
*** *
27768842 ATATTAAGAATTTTATTAAATT-ATATATTTTTATAATT-
1 ATATTAAGAATTTTATTAAATTCATATA--AGAATATTTA
* * * *
27768880 ATATTTAATAATAATTATTTTAAATT-ATATTA-TATAGTATTA
1 ATA-TTAAGAAT--TT-TATTAAATTCATATAAGAATA-T-TTA
*
27768922 TATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATTCATATAAGAATATTTA
27768960 ATATTAAGAATTTTA
1 ATATTAAGAATTTTA
27768975 AATTATATAT
Statistics
Matches: 103, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
37 19 0.18
38 33 0.32
39 24 0.23
40 3 0.03
41 6 0.06
42 15 0.15
43 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (38 bp):
ATATTAAGAATTTTATTAAATTCATATAAGAATATTTA
Found at i:27768900 original size:45 final size:47
Alignment explanation
Indices: 27768835--27768934 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 47
27768825 TCATATAAGA
* * *
27768835 ATATTTAATATTAAGAATTTT-ATTAAATTATATATTTTTATA-ATT
1 ATATTTAATAATAAGAATTTTAATTAAATTATATAGTATTATATATT
** *
27768880 ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATT
1 ATATTTAATAATAAGAATTTT-AATTAAATTATATAGTATTATATATT
27768928 ATGATTT
1 AT-ATTT
27768935 TATTAAATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 18 0.40
47 18 0.40
48 5 0.11
49 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (47 bp):
ATATTTAATAATAAGAATTTTAATTAAATTATATAGTATTATATATT
Found at i:27768979 original size:14 final size:16
Alignment explanation
Indices: 27768948--27768979 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27768938 TAAATTCATA
27768948 TAAGAATATTTAATAT
1 TAAGAATATTTAATAT
27768964 TAAGAAT-TTTAA-AT
1 TAAGAATATTTAATAT
27768978 TA
1 TA
27768980 TATATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 5 0.31
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TAAGAATATTTAATAT
Found at i:27769061 original size:117 final size:117
Alignment explanation
Indices: 27768787--27769083 Score: 517
Period size: 117 Copynumber: 2.5 Consensus size: 117
27768777 ATTATTAATC
27768787 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
*
27768852 TTTTATTAAATTATATATTTTTATAATTATATTTAATAATAATTATTTTAAAT
66 -TTTATTAAATTATATATTTTTATAATTATATTTAATAATAATTATGTTAAAT
27768905 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
27768970 -TT-TTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTATTAAATTATATATTTTTA-T-AATTATATTTAATAATAATTATGTTAAAT
* **
27769022 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAA
27769084 TTTTTTTCTA
Statistics
Matches: 173, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
115 18 0.10
116 3 0.02
117 87 0.50
118 65 0.38
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (117 bp):
TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
TTTATTAAATTATATATTTTTATAATTATATTTAATAATAATTATGTTAAAT
Found at i:27769358 original size:16 final size:16
Alignment explanation
Indices: 27769337--27769378 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27769327 TTATTAAATT
*
27769337 ATATATTTTAATTATA
1 ATATATTTTAATAATA
27769353 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
27769368 AT-TATGTTTAA
1 ATATAT-TTTAA
27769379 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:27769363 original size:15 final size:15
Alignment explanation
Indices: 27769328--27769369 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27769318 TTAAGAATTT
*
27769328 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27769342 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27769356 TATTTAATAATAAT
1 TATTTAATTATAAT
27769370 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27769514 original size:16 final size:16
Alignment explanation
Indices: 27769493--27769534 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27769483 TTATTAAATT
*
27769493 ATATATTTTAATTATA
1 ATATATTTTAATAATA
27769509 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
27769524 AT-TATGTTTAA
1 ATATAT-TTTAA
27769535 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:27769519 original size:15 final size:15
Alignment explanation
Indices: 27769484--27769525 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27769474 TTAAGAATTT
*
27769484 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27769498 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27769512 TATTTAATAATAAT
1 TATTTAATTATAAT
27769526 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27769665 original size:18 final size:17
Alignment explanation
Indices: 27769637--27769671 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27769627 ATTATTAAGA
*
27769637 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27769654 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27769672 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27769726 original size:157 final size:157
Alignment explanation
Indices: 27769314--27769784 Score: 881
Period size: 157 Copynumber: 3.0 Consensus size: 157
27769304 AAGAATATTG
27769314 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
27769379 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAAC-ATA
66 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
27769443 ATAATTTACCAAAACAAATTTCTGCTA
131 ATAATTTACCAAAACAAATTTCTGCTA
27769470 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
27769535 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
27769600 ATAATTTACCAAAACAAATTTCTGCTA
131 ATAATTTACCAAAACAAATTTCTGCTA
*
27769627 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
* *
27769692 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
* * *
27769757 ATCATTTACTAAAACAAATTTATGCTA
131 ATAATTTACCAAAACAAATTTCTGCTA
27769784 A
1 A
27769785 GGGTATTCTA
Statistics
Matches: 308, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
156 126 0.41
157 182 0.59
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTCTGCTA
Found at i:27769928 original size:16 final size:16
Alignment explanation
Indices: 27769907--27769974 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
27769897 GATTTGCTAT
27769907 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
27769923 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
27769939 TACACCTCCAATCCAA
1 TACACCTCTAATCCAA
27769955 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
27769971 TACA
1 TACA
27769975 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:27777487 original size:16 final size:16
Alignment explanation
Indices: 27777466--27777496 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27777456 GATATTTTAA
27777466 TATATTATATTAATAT
1 TATATTATATTAATAT
*
27777482 TATATTATGTTAATA
1 TATATTATATTAATA
27777497 AAATAATAAA
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:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:27777593 original size:12 final size:12
Alignment explanation
Indices: 27777576--27777606 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27777566 GAAGCAGGGG
27777576 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
27777588 AGAAAAAGGGAA
1 AGAAAAAGAGAA
27777600 AGAAAAA
1 AGAAAAA
27777607 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:27781107 original size:4 final size:4
Alignment explanation
Indices: 27781098--27781122 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27781088 CCCTTTTCTA
27781098 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
27781123 CACGTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:27782447 original size:17 final size:18
Alignment explanation
Indices: 27782416--27782450 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27782406 GAAAATACTA
27782416 ATAAAAAGTAAAATTTAG
1 ATAAAAAGTAAAATTTAG
*
27782434 ATAAAAA-TAGAATTTAG
1 ATAAAAAGTAAAATTTAG
27782451 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
ATAAAAAGTAAAATTTAG
Done.