Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, whole genome shotgun sequence
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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 12 of 12
Found at i:6708688 original size:41 final size:41
Alignment explanation
Indices: 6708643--6708733 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
6708633 GTAATAATTA
* * *
6708643 ATAATTTAATCATTACAAATTAGCATATTAATATTTTATTT
1 ATAATTTAATCATTAAAAATTAGAATAGTAATATTTTATTT
*
6708684 ATAATTTAATCATTAAAAATTAGAATAGTATTATTTTATTT
1 ATAATTTAATCATTAAAAATTAGAATAGTAATATTTTATTT
6708725 ATAATTTAA
1 ATAATTTAA
6708734 ATATTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (41 bp):
ATAATTTAATCATTAAAAATTAGAATAGTAATATTTTATTT
Found at i:6708815 original size:29 final size:29
Alignment explanation
Indices: 6708780--6708837 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
6708770 ATTTTTAAAT
*
6708780 TTAAAATATTA-ATTTTTTATAATATATAA
1 TTAAAATATTAGACTTTTTATAATA-ATAA
* *
6708809 TTAAAATTTTAGACTTTTTATTATAATAA
1 TTAAAATATTAGACTTTTTATAATAATAA
6708838 GATTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAAAATATTAGACTTTTTATAATAATAA
Found at i:6709061 original size:14 final size:13
Alignment explanation
Indices: 6709019--6709068 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
6709009 AATATTAGTG
6709019 TATTTTTCTATTTT
1 TATTTTT-TATTTT
6709033 TATCTGTTTTTATTTT
1 TA--T-TTTTTATTTT
6709049 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
6709063 TATTTT
1 TATTTT
6709069 AAGATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.16
14 14 0.44
16 9 0.28
17 4 0.12
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:6709099 original size:17 final size:16
Alignment explanation
Indices: 6709074--6709133 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
6709064 ATTTTAAGAT
6709074 ATTATTTATAATTTAAA
1 ATTA-TTATAATTTAAA
*
6709091 CATTATTATTA-TTAAA
1 -ATTATTATAATTTAAA
6709107 A-TATTAATAATTTTAAA
1 ATTATT-ATAA-TTTAAA
*
6709124 ATTTTTATAA
1 ATTATTATAA
6709134 AAAGATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 5 0.14
17 15 0.43
18 7 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTATAATTTAAA
Found at i:6718678 original size:25 final size:25
Alignment explanation
Indices: 6718644--6718693 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6718634 AAATTTTATA
*
6718644 GCATGTTGTTAATGTTACCGACTTG
1 GCATGGTGTTAATGTTACCGACTTG
*
6718669 GCATGGTGTTAATGTTACGGACTTG
1 GCATGGTGTTAATGTTACCGACTTG
6718694 AAACTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (25 bp):
GCATGGTGTTAATGTTACCGACTTG
Found at i:6719010 original size:73 final size:73
Alignment explanation
Indices: 6718868--6719012 Score: 173
Period size: 73 Copynumber: 2.0 Consensus size: 73
6718858 GAATATTGCG
* * * * * *
6718868 GAGACTAAGCAAACTTATCTATTTCATAATGATATTGAATATTATGGATATTAAGCAAACCTATT
1 GAGACCAAGCAAACCTATCTATTTCATAATGATACTAAATATTATGGATACTAAGCAAACCTATC
6718933 TTGTAATT
66 TTGTAATT
* ** * * **
6718941 GAGACCAAGCAAGCCTATCTATTTTGTAATGATACTAAATATTGTGGATACTAAGCTAGTCTATC
1 GAGACCAAGCAAACCTATCTATTTCATAATGATACTAAATATTATGGATACTAAGCAAACCTATC
6719006 TTGTAAT
66 TTGTAAT
6719013 AATCTATCTC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (73 bp):
GAGACCAAGCAAACCTATCTATTTCATAATGATACTAAATATTATGGATACTAAGCAAACCTATC
TTGTAATT
Found at i:6720212 original size:8 final size:8
Alignment explanation
Indices: 6720172--6720227 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
6720162 AAAATAATGT
*
6720172 AATATTTT
1 AATATTTA
6720180 AATA-TTA
1 AATATTTA
*
6720187 ATTATTTA
1 AATATTTA
6720195 AATATTTA
1 AATATTTA
*
6720203 AATATATA
1 AATATTTA
6720211 AA-ATTATTA
1 AATA-T-TTA
6720220 AATATTTA
1 AATATTTA
6720228 GTTTTAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.15
8 27 0.69
9 5 0.13
10 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATATTTA
Found at i:6728030 original size:29 final size:28
Alignment explanation
Indices: 6727986--6728143 Score: 133
Period size: 28 Copynumber: 5.4 Consensus size: 28
6727976 CTTTAACATA
*
6727986 TTTGTCCTAATTTAGACAAAAAAACATAT
1 TTTGTCTTAATTTAGACAAAAAAA-ATAT
* *
6728015 TTTATCTTAATTTAGAC-AAGAAAATAT
1 TTTGTCTTAATTTAGACAAAAAAAATAT
* *
6728042 GTTTGTCTTAATTTAAAACAAGAAAAATATTT
1 -TTTGTCTTAATTT-AGACAA-AAAAA-ATAT
* * *
6728074 TTTATCTTAATCTAGAC-AAGAAAATAT
1 TTTGTCTTAATTTAGACAAAAAAAATAT
*
6728101 ATTTGT-TTCAATTTAGACAAGATAAAATAT
1 -TTTGTCTT-AATTTAGACAA-AAAAAATAT
6728131 ATTTGTCTTAATT
1 -TTTGTCTTAATT
6728144 AAAGACAAGA
Statistics
Matches: 104, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
27 9 0.09
28 33 0.32
29 20 0.19
30 22 0.21
31 17 0.16
32 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAAAAAAATAT
Found at i:6728090 original size:59 final size:58
Alignment explanation
Indices: 6727983--6728142 Score: 209
Period size: 59 Copynumber: 2.8 Consensus size: 58
6727973 CAGCTTTAAC
* * *
6727983 ATATTTGTCCTAATTTAGACAA-AAAAACATATTTTATCTTAATTTAGACAAGAAAAT
1 ATATTTGTCTTAATTTAGACAAGAAAAATATATTTTATCTTAATCTAGACAAGAAAAT
* * *
6728040 ATGTTTGTCTTAATTTAAAACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAAAAT
1 ATATTTGTCTTAATTT-AGACAAGAAAAATATATTTTATCTTAATCTAGACAAGAAAAT
*
6728099 ATATTTGT-TTCAATTTAGACAAGATAAAATATA-TTTGTCTTAAT
1 ATATTTGTCTT-AATTTAGACAAGA-AAAATATATTTTATCTTAAT
6728143 TAAAGACAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
57 14 0.16
58 24 0.27
59 51 0.57
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (58 bp):
ATATTTGTCTTAATTTAGACAAGAAAAATATATTTTATCTTAATCTAGACAAGAAAAT
Found at i:6728122 original size:28 final size:28
Alignment explanation
Indices: 6727983--6728154 Score: 175
Period size: 29 Copynumber: 5.9 Consensus size: 28
6727973 CAGCTTTAAC
* * *
6727983 ATATTTGTCCTAATTTAGACAAAAAAAC
1 ATATTTGTCTTAATTTAGACAAGAAAAT
*
6728011 ATATTTTATCTTAATTTAGACAAGAAAAT
1 ATA-TTTGTCTTAATTTAGACAAGAAAAT
* *
6728040 ATGTTTGTCTTAATTTAAAACAAGAAAAAT
1 ATATTTGTCTTAATTT-AGACAAG-AAAAT
* * *
6728070 ATTTTTTATCTTAATCTAGACAAGAAAAT
1 A-TATTTGTCTTAATTTAGACAAGAAAAT
6728099 ATATTTGT-TTCAATTTAGACAAGATAAAAT
1 ATATTTGTCTT-AATTTAGACAAG--AAAAT
*
6728129 ATATTTGTCTTAATTAAAGACAAGAA
1 ATATTTGTCTTAATT-TAGACAAGAA
6728155 TTGTCTTAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.02
28 31 0.26
29 37 0.31
30 29 0.24
31 21 0.17
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (28 bp):
ATATTTGTCTTAATTTAGACAAGAAAAT
Found at i:6729279 original size:28 final size:27
Alignment explanation
Indices: 6729228--6729307 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
6729218 TGCACTCGAG
* * **
6729228 AACGTCACTTATACGTTATGCACTTAA
1 AACGTCACTTGTGCGTTACACACTTAA
**
6729255 AAGCGTCACTTGTGCGTTACACACTTGG
1 AA-CGTCACTTGTGCGTTACACACTTAA
* * *
6729283 AACATCACTTGTGCATTGCACACTT
1 AACGTCACTTGTGCGTTACACACTT
6729308 GAAATGTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (27 bp):
AACGTCACTTGTGCGTTACACACTTAA
Found at i:6730146 original size:58 final size:59
Alignment explanation
Indices: 6730016--6730158 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 59
6730006 TCCAACAAGT
* **
6730016 CCAATAAAGCTATTGCTACTACACAAAAGAAAAAAGACCACTACCAATATGAAGTGAGC
1 CCAATAAAGCTATTACTACTACACAAAAGAAAAAAGACCACTACCAATATGAAACGAGC
* * * * * * *
6730075 CTAGTAAAACTATTACTACTACATAAAAGAAGAAA-ACCATTGCCAATATGAAACGAGC
1 CCAATAAAGCTATTACTACTACACAAAAGAAAAAAGACCACTACCAATATGAAACGAGC
* *
6730133 CCAATAAAGCTATTATTGCTACACAA
1 CCAATAAAGCTATTACTACTACACAA
6730159 GAAGTAGCAA
Statistics
Matches: 68, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
58 39 0.57
59 29 0.43
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.20
Consensus pattern (59 bp):
CCAATAAAGCTATTACTACTACACAAAAGAAAAAAGACCACTACCAATATGAAACGAGC
Found at i:6744676 original size:2 final size:2
Alignment explanation
Indices: 6744669--6744712 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
6744659 AATTTATGTC
6744669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
6744711 TA
1 TA
6744713 ATTTTACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6756271 original size:2 final size:2
Alignment explanation
Indices: 6756264--6756297 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6756254 ATAATCTTCA
6756264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6756298 GATAAATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6773765 original size:21 final size:21
Alignment explanation
Indices: 6773736--6773775 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6773726 TTCGTTTTTT
6773736 TAATAATTTTTAATCTACGTA
1 TAATAATTTTTAATCTACGTA
*
6773757 TAATTATTTTTAATCTACG
1 TAATAATTTTTAATCTACG
6773776 CATAGGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TAATAATTTTTAATCTACGTA
Found at i:6782519 original size:12 final size:12
Alignment explanation
Indices: 6782502--6782527 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6782492 ATCAGTTCAG
6782502 AGTATTTTTTAA
1 AGTATTTTTTAA
6782514 AGTATTTTTTAA
1 AGTATTTTTTAA
6782526 AG
1 AG
6782528 CCCTTTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (12 bp):
AGTATTTTTTAA
Found at i:6783281 original size:45 final size:46
Alignment explanation
Indices: 6783205--6783293 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
6783195 CTTGCGGGTG
*
6783205 AGAGATTATAGGATCGTCAACTTTGTGAAGCTTGAGGGTGAGAGTA
1 AGAGATTATAGGATCATCAACTTTGTGAAGCTTGAGGGTGAGAGTA
*
6783251 AGAGATTATAGGA-CATCGACTTTGTGAAGCTTGAGGGTGAGAG
1 AGAGATTATAGGATCATCAACTTTGTGAAGCTTGAGGGTGAGAG
6783294 ATTAGAGGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 28 0.68
46 13 0.32
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (46 bp):
AGAGATTATAGGATCATCAACTTTGTGAAGCTTGAGGGTGAGAGTA
Found at i:6785254 original size:19 final size:18
Alignment explanation
Indices: 6785223--6785267 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
6785213 CCTCAAGTGA
*
6785223 ATTTT-TTTTTCTTTTTG
1 ATTTTATTTTTCTTTTGG
6785240 ATTTTATTTTATCTTTTGG
1 ATTTTATTTT-TCTTTTGG
*
6785259 ATTTAATTT
1 ATTTTATTT
6785268 ATTGTTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 15 0.62
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (18 bp):
ATTTTATTTTTCTTTTGG
Found at i:6785268 original size:18 final size:19
Alignment explanation
Indices: 6785232--6785269 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6785222 AATTTTTTTT
* *
6785232 TCTTTTTGATTTTATTTTA
1 TCTTTTGGATTTTAATTTA
6785251 TCTTTTGGA-TTTAATTTA
1 TCTTTTGGATTTTAATTTA
6785269 T
1 T
6785270 TGTTTCTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.68
Consensus pattern (19 bp):
TCTTTTGGATTTTAATTTA
Found at i:6787847 original size:19 final size:20
Alignment explanation
Indices: 6787811--6787848 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6787801 AAATAAAAAT
*
6787811 AAAAGAATTTGATGAATTTG
1 AAAAGAATTTAATGAATTTG
*
6787831 AAAA-AATTTAATTAATTT
1 AAAAGAATTTAATGAATTT
6787849 ATTTACTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAAGAATTTAATGAATTTG
Found at i:6788035 original size:135 final size:136
Alignment explanation
Indices: 6787762--6788028 Score: 342
Period size: 135 Copynumber: 2.0 Consensus size: 136
6787752 TCTTGAAAAT
* * * *
6787762 ATGGATTAAATCATTCAAGTTAATATTAGATTATCACACAAATAAAAATAAAAGAATTTGATGAA
1 ATGGATTAAACCATTCAAGTTAATATTAGATTATCACACAAACAAAAATAAAAAAAATTGATGAA
* * * *
6787827 TTTGAAAAAATTTAATTAATTTATTTACTTACATGATTTTAGATAAGCAACATAAAAATCAAACC
66 TTTGAAAAAATTTAACTAATTTATTTACTTACATGAGTTCAGATAAACAACATAAAAATCAAACC
6787892 AATATG
131 AATATG
* * *
6787898 ATGGATTAAACCGTTCAAGTTAAT-TTAGATTAAT-GCACAAACAAATATAAAAAAAATTGATGA
1 ATGGATTAAACCATTCAAGTTAATATTAGATT-ATCACACAAACAAAAATAAAAAAAATTGATGA
* * * * * *
6787961 CTTTGAATAAATTTAACTAATTTATTTACTTATATGAGTTCACG-TAAATAATATAAAAATTAAA
65 ATTTGAAAAAATTTAACTAATTTATTTACTTACATGAGTTCA-GATAAACAACATAAAAATCAAA
6788025 CCAA
129 CCAA
6788029 CTTGATGATG
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
135 87 0.78
136 25 0.22
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (136 bp):
ATGGATTAAACCATTCAAGTTAATATTAGATTATCACACAAACAAAAATAAAAAAAATTGATGAA
TTTGAAAAAATTTAACTAATTTATTTACTTACATGAGTTCAGATAAACAACATAAAAATCAAACC
AATATG
Found at i:6793961 original size:24 final size:24
Alignment explanation
Indices: 6793934--6793981 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6793924 CTGCTATTTA
6793934 ACTTGTTGCTCAAGCAAGAAAAAG
1 ACTTGTTGCTCAAGCAAGAAAAAG
6793958 ACTTGTTGCTCAAGCAAGAAAAAG
1 ACTTGTTGCTCAAGCAAGAAAAAG
6793982 CTCTGATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (24 bp):
ACTTGTTGCTCAAGCAAGAAAAAG
Found at i:6803686 original size:2 final size:2
Alignment explanation
Indices: 6803679--6803733 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
6803669 ATTGATTGTT
6803679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6803721 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
6803734 GATGTTTCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6804828 original size:4 final size:4
Alignment explanation
Indices: 6804819--6804843 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6804809 AAGATGCTGC
6804819 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
6804844 GTGATAGCGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:6809636 original size:45 final size:44
Alignment explanation
Indices: 6809573--6809657 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
6809563 TTACCTTTAA
* * *
6809573 TTTATTTTTATTTATAATATTTTTTAATTTAAAATTATTTCTTT
1 TTTATTTTTATTCATAATATTATATAATTTAAAATTATTTCTTT
6809617 TTTATTTTTTATTCATAATATTATATAATTTAAAATTATTT
1 TTTA-TTTTTATTCATAATATTATATAATTTAAAATTATTT
6809658 TTAATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (44 bp):
TTTATTTTTATTCATAATATTATATAATTTAAAATTATTTCTTT
Found at i:6812175 original size:2 final size:2
Alignment explanation
Indices: 6812168--6812202 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6812158 TCCCAACCAA
6812168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6812203 GTTCAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6814200 original size:98 final size:98
Alignment explanation
Indices: 6814018--6814213 Score: 297
Period size: 98 Copynumber: 2.0 Consensus size: 98
6814008 AAGCAAAAAT
* * *
6814018 AACTAATCTTGAAGAAATTAAGAAAATTTTAGAAAAAAATAATTATATTATTCTCAAAAAAACAA
1 AACTAAACTTGAAGAAATTAAGAAAAATTTAGAAAAAAATAATTATATTATTCCCAAAAAAACAA
*
6814083 ACATAGCCTAAATTATTGAATGCTTGAAAATGA
66 ACATAGCCTAAATTATTGAACGCTTGAAAATGA
*
6814116 AACTAAACTTGAAGAAATTAA-AAAAATTTA-AAAAAAATAATTATTTTATTCCCAAAGAAAACA
1 AACTAAACTTGAAGAAATTAAGAAAAATTTAGAAAAAAATAATTATATTATTCCCAAA-AAAACA
* *
6814179 AACATAGCCTTAATTACTTGAACGCTTGAATATGA
65 AACATAGCCTAAATTA-TTGAACGCTTGAAAATGA
6814214 GTGCAATTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
96 24 0.27
97 29 0.33
98 36 0.40
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (98 bp):
AACTAAACTTGAAGAAATTAAGAAAAATTTAGAAAAAAATAATTATATTATTCCCAAAAAAACAA
ACATAGCCTAAATTATTGAACGCTTGAAAATGA
Found at i:6816777 original size:34 final size:35
Alignment explanation
Indices: 6816739--6816816 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
6816729 TTGTAATGTC
* * *
6816739 ATTTAAATTGTTATTTG-GATATTTG-TTTTTAGTT
1 ATTTAAATTGATATTTGAAATATTTGATTTTGA-TT
*
6816773 ATTTAAGTTGATATTTGAAATATTTGATTTTGATT
1 ATTTAAATTGATATTTGAAATATTTGATTTTGATT
6816808 ATTTAAATT
1 ATTTAAATT
6816817 TAAATTTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 15 0.41
35 17 0.46
36 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (35 bp):
ATTTAAATTGATATTTGAAATATTTGATTTTGATT
Found at i:6817813 original size:17 final size:16
Alignment explanation
Indices: 6817788--6817845 Score: 77
Period size: 17 Copynumber: 3.7 Consensus size: 16
6817778 TTTGTTTAGA
6817788 TTTAAAAATAAGATAT
1 TTTAAAAATAAGATAT
6817804 TTTGAAAAAT-A-AT-T
1 TTT-AAAAATAAGATAT
6817818 TTTAAAAATAAGATATT
1 TTTAAAAATAAGATA-T
6817835 TTTAAAAATAA
1 TTTAAAAATAA
6817846 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.16
14 5 0.14
15 4 0.11
16 4 0.11
17 18 0.49
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TTTAAAAATAAGATAT
Found at i:6817822 original size:30 final size:30
Alignment explanation
Indices: 6817788--6817854 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
6817778 TTTGTTTAGA
6817788 TTTAAAAATAAGATATTTTGAAAAATAATT
1 TTTAAAAATAAGATATTTTGAAAAATAATT
*
6817818 TTTAAAAATAAGATATTTTTAAAAATAATT
1 TTTAAAAATAAGATATTTTGAAAAATAATT
6817848 TTTAAAA
1 TTTAAAA
6817855 TAATTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTAAAAATAAGATATTTTGAAAAATAATT
Found at i:6817854 original size:12 final size:13
Alignment explanation
Indices: 6817788--6817861 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 13
6817778 TTTGTTTAGA
6817788 TTTAAAAATAAGATAT
1 TTTAAAAAT-A-AT-T
6817804 TTTGAAAAATAATT
1 TTT-AAAAATAATT
6817818 TTTAAAAATAAGATATT
1 TTTAAAAAT---A-ATT
6817835 TTTAAAAATAATT
1 TTTAAAAATAATT
6817848 TTT-AAAATAATT
1 TTTAAAAATAATT
6817860 TT
1 TT
6817862 AATTATTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.21
13 12 0.23
14 5 0.09
15 2 0.04
16 5 0.09
17 18 0.34
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (13 bp):
TTTAAAAATAATT
Found at i:6818097 original size:75 final size:76
Alignment explanation
Indices: 6817957--6818099 Score: 218
Period size: 75 Copynumber: 1.9 Consensus size: 76
6817947 TACACTATGG
* * * *
6817957 TTAGATTGTTACATGTCATGTTAAAAAAAAATACTATTGTTATATATTATGAACAAAAACGTGTT
1 TTAGATTGTTACACGTCATGTTAAAAAAAAATACTATTGTTACATACTATGAACAAAAACATGTT
6818022 ACATGCCATAA
66 ACATGCCATAA
*
6818033 TTAGATTGTTACACGTCATGTT-AAAAAAAATACTATTGTTACATGCTAT-ATACAAAAACATGT
1 TTAGATTGTTACACGTCATGTTAAAAAAAAATACTATTGTTACATACTATGA-ACAAAAACATGT
6818096 TACA
65 TACA
6818100 CACTATAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
74 1 0.02
75 39 0.64
76 21 0.34
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (76 bp):
TTAGATTGTTACACGTCATGTTAAAAAAAAATACTATTGTTACATACTATGAACAAAAACATGTT
ACATGCCATAA
Found at i:6820985 original size:14 final size:15
Alignment explanation
Indices: 6820966--6820998 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6820956 AAGTAGTATT
6820966 TTAATTAATGA-TAA
1 TTAATTAATGATTAA
*
6820980 TTAATTAATTATTAA
1 TTAATTAATGATTAA
6820995 TTAA
1 TTAA
6820999 ATTTATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTAATTAATGATTAA
Found at i:6823115 original size:2 final size:2
Alignment explanation
Indices: 6823108--6823154 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
6823098 GCAGTATTGA
*
6823108 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6823150 -T AT AT
1 AT AT AT
6823155 TTCCGAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6828803 original size:15 final size:15
Alignment explanation
Indices: 6828763--6828806 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
6828753 TCCTACAATG
6828763 TAATGTGATTGTTG-
1 TAATGTGATTGTTGA
**
6828777 TAATGCAATTGTTGA
1 TAATGTGATTGTTGA
*
6828792 TAATGTGGTTGTTGA
1 TAATGTGATTGTTGA
6828807 GAAAATAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.45
Consensus pattern (15 bp):
TAATGTGATTGTTGA
Found at i:6828946 original size:27 final size:26
Alignment explanation
Indices: 6828915--6828965 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
6828905 TTTTTATAAC
*
6828915 TAAATTAGCTAATTAAATTAATTAATT
1 TAAATCAGCTAATT-AATTAATTAATT
*
6828942 TAAATCAGCTAATTGATTAATTAA
1 TAAATCAGCTAATTAATTAATTAA
6828966 ATGAGATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (26 bp):
TAAATCAGCTAATTAATTAATTAATT
Found at i:6839152 original size:16 final size:17
Alignment explanation
Indices: 6839131--6839162 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6839121 TTTCATGGAC
6839131 ATATAGT-AAATTAATT
1 ATATAGTAAAATTAATT
6839147 ATATAGTAAAATTAAT
1 ATATAGTAAAATTAAT
6839163 CAGGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATAGTAAAATTAATT
Found at i:6844230 original size:2 final size:2
Alignment explanation
Indices: 6844223--6844251 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6844213 TTACTACTTT
6844223 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6844252 AAAGTCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6864285 original size:27 final size:27
Alignment explanation
Indices: 6864255--6864310 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6864245 AGATCATGAA
*
6864255 AATTTATTAATTAAT-TAATAAATTAAT
1 AATTTATAAATTAATAT-ATAAATTAAT
* *
6864282 AATTTATAAATTTATATATCAATTAAT
1 AATTTATAAATTAATATATAAATTAAT
6864309 AA
1 AA
6864311 AAAATTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
AATTTATAAATTAATATATAAATTAAT
Found at i:6864290 original size:15 final size:16
Alignment explanation
Indices: 6864260--6864293 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6864250 ATGAAAATTT
6864260 ATTAATTAATTAATAA
1 ATTAATTAATTAATAA
*
6864276 ATTAA-TAATTTATAA
1 ATTAATTAATTAATAA
6864291 ATT
1 ATT
6864294 TATATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTAATTAATAA
Found at i:6864705 original size:14 final size:16
Alignment explanation
Indices: 6864667--6864709 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
6864657 GGACCGACTA
*
6864667 AAAATATTATTTAATC
1 AAAATATTAATTAATC
6864683 AAAATTATTAATT-ATC
1 AAAA-TATTAATTAATC
6864699 -AAATATTAATT
1 AAAATATTAATT
6864710 TATAGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 7 0.28
17 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATATTAATTAATC
Found at i:6865560 original size:53 final size:53
Alignment explanation
Indices: 6865482--6865602 Score: 154
Period size: 53 Copynumber: 2.3 Consensus size: 53
6865472 AAAAAATACT
* * * * *
6865482 ATATCAACATTTGTTATTATGTTTTTATAAAAAATATATATA-TATTTCTTATC
1 ATATCAACATTTCTTATTATATTTTTATAAAAAATA-AAAAACCATTTCTTATC
*
6865535 ATATCAACATTTCTTATTATATTTTTATCAAAAATAAAAAACCATTTCTTATC
1 ATATCAACATTTCTTATTATATTTTTATAAAAAATAAAAAACCATTTCTTATC
* *
6865588 GTGTCAACATTTCTT
1 ATATCAACATTTCTT
6865603 GTCACATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
52 3 0.05
53 56 0.95
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (53 bp):
ATATCAACATTTCTTATTATATTTTTATAAAAAATAAAAAACCATTTCTTATC
Found at i:6882269 original size:22 final size:23
Alignment explanation
Indices: 6882218--6882279 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
6882208 TTTTTTAAAT
*
6882218 TAAAAATTAAAAATTATAATTTA
1 TAAAAATTAAAAATTATAATTAA
**
6882241 TATAAAATTAAATTTTA-AATTAA
1 TA-AAAATTAAAAATTATAATTAA
*
6882264 TAAAAAGT-AAAATTAT
1 TAAAAATTAAAAATTAT
6882280 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 5 0.16
22 5 0.16
23 9 0.29
24 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAATTAAAAATTATAATTAA
Found at i:6882396 original size:16 final size:18
Alignment explanation
Indices: 6882375--6882415 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
6882365 CTTTTAAAGT
6882375 AAATTATCAATTT-TA-A
1 AAATTATCAATTTGTATA
*
6882391 AAATTAATGAATTTGTATA
1 AAATT-ATCAATTTGTATA
6882410 AAATTA
1 AAATTA
6882416 CGATTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 3 0.14
19 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
AAATTATCAATTTGTATA
Found at i:6889544 original size:9 final size:9
Alignment explanation
Indices: 6889532--6889570 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
6889522 ATTAACCGAC
6889532 TAATTCGAT
1 TAATTCGAT
6889541 TAATTC-AGT
1 TAATTCGA-T
6889550 TAATTCGAT
1 TAATTCGAT
*
6889559 TAAATCGAT
1 TAATTCGAT
6889568 TAA
1 TAA
6889571 AAAATTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.93
10 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (9 bp):
TAATTCGAT
Found at i:6889702 original size:2 final size:2
Alignment explanation
Indices: 6889697--6889743 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
6889687 TCACACAGAT
6889697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6889739 TA TA T
1 TA TA T
6889744 GAATGAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6890216 original size:32 final size:28
Alignment explanation
Indices: 6890144--6890223 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
6890134 TAAACTATAA
6890144 TAATATAGTATAACTTATATTAATAATT
1 TAATATAGTATAACTTATATTAATAATT
*
6890172 TAATATAG--TAACTTATTAATATATTAATGT
1 TAATATAGTATAACTTA-T-AT-TAATAAT-T
* *
6890202 TATTATAGTATAACTTAAATTA
1 TAATATAGTATAACTTATATTA
6890224 CTAAAGTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 7 0.16
27 1 0.02
28 10 0.23
29 8 0.19
30 10 0.23
32 7 0.16
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (28 bp):
TAATATAGTATAACTTATATTAATAATT
Found at i:6890452 original size:19 final size:21
Alignment explanation
Indices: 6890428--6890466 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
6890418 GTATATTTAT
6890428 AAACTATATA-AGT-ATATAC
1 AAACTATATATAGTAATATAC
6890447 AAACTATATATAGTAATATA
1 AAACTATATATAGTAATATA
6890467 TTAATACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (21 bp):
AAACTATATATAGTAATATAC
Found at i:6890496 original size:26 final size:26
Alignment explanation
Indices: 6890456--6890523 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
6890446 CAAACTATAT
*
6890456 ATAGTA-ATATATTAATACA-CTGTAC
1 ATAGTATATATATTAATACATC-ATAC
*
6890481 ATAGTATATATCTTAATACATCATAC
1 ATAGTATATATATTAATACATCATAC
*
6890507 ATAGTATATTTATTAAT
1 ATAGTATATATATTAAT
6890524 GCACTAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.16
26 30 0.81
27 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (26 bp):
ATAGTATATATATTAATACATCATAC
Found at i:6892944 original size:30 final size:29
Alignment explanation
Indices: 6892905--6892961 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
6892895 TAATTAGAAA
6892905 AAAATTTATTTGA-TTCAAAATAAAAGTTT
1 AAAATTTATTTGACTT-AAAATAAAAGTTT
6892934 AAAATCTTATTTGACTTAAAATAAAAGT
1 AAAAT-TTATTTGACTTAAAATAAAAGT
6892962 ATAACTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 5 0.19
30 19 0.73
31 2 0.08
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (29 bp):
AAAATTTATTTGACTTAAAATAAAAGTTT
Found at i:6893884 original size:14 final size:15
Alignment explanation
Indices: 6893865--6894016 Score: 61
Period size: 14 Copynumber: 10.1 Consensus size: 15
6893855 TAGTGTTATA
6893865 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
6893879 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
* *
6893894 A-TAATATAAGAATCAAAA
1 ATTAAAATAA-AAT---AT
*
6893912 ATTAAAATAAAATAA
1 ATTAAAATAAAATAT
* * *
6893927 AAT-AATTAAAATTT
1 ATTAAAATAAAATAT
* *
6893941 ATATAATATAGGTAAAAGAA
1 AT-TAA-A-A--TAAAATAT
6893961 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
6893976 A-TAATATAAAA-A-
1 ATTAAAATAAAATAT
* *
6893988 ATTATATTAAAA-AT
1 ATTAAAATAAAATAT
6894002 A--AAAATAAAATAT
1 ATTAAAATAAAATAT
6894015 AT
1 AT
6894017 AAGATTATAA
Statistics
Matches: 102, Mismatches: 20, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
12 8 0.08
13 12 0.12
14 38 0.37
15 18 0.18
16 1 0.01
17 2 0.02
18 6 0.06
19 10 0.10
20 7 0.07
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:6893917 original size:33 final size:32
Alignment explanation
Indices: 6893861--6893938 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
6893851 TTTGTAGTGT
6893861 TATAATTAAAATAAAAATATTAAAATAAAATA
1 TATAATTAAAATAAAAATATTAAAATAAAATA
*
6893893 TATAATATAAGAATCAAAA-ATTAAAATAAAATAA
1 TATAAT-TAA-AATAAAAATATTAAAATAAAAT-A
*
6893927 AATAATTAAAAT
1 TATAATTAAAAT
6893939 TTATATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 9 0.22
33 19 0.46
34 13 0.32
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (32 bp):
TATAATTAAAATAAAAATATTAAAATAAAATA
Found at i:6893986 original size:49 final size:46
Alignment explanation
Indices: 6893864--6893986 Score: 135
Period size: 49 Copynumber: 2.6 Consensus size: 46
6893854 GTAGTGTTAT
*
6893864 AATTAAAATAAAA-ATATTAAAATAAAATATATAATATAAGAATCAAA
1 AATTAAAATAAAATATA-TAATATAAAATATATAATATAAGAA-CAAA
* *
6893911 AATTAAAATAAAATAAAATAAT-TAAAATTTATATAATATAGGTAA-AAGA
1 AATTAAAATAAAAT-ATATAATATAAAA--TATATAATATAAG-AACAA-A
6893960 AATTAAAATAAAATATATAATATAAAA
1 AATTAAAATAAAATATATAATATAAAA
6893987 AATTATATTA
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
47 18 0.28
48 11 0.17
49 34 0.52
50 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (46 bp):
AATTAAAATAAAATATATAATATAAAATATATAATATAAGAACAAA
Found at i:6894006 original size:6 final size:6
Alignment explanation
Indices: 6893995--6894044 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
6893985 AAAATTATAT
* * *
6893995 TAAAAA TAAAAA TAAAATA TATAAGA TTATAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAA-A TA-AAAA TAAAAA TAAAAA TAAAAA TAAAAA
6894045 ATATATATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 29 0.81
7 5 0.14
8 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (6 bp):
TAAAAA
Found at i:6894014 original size:32 final size:32
Alignment explanation
Indices: 6893964--6894065 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 32
6893954 AAAAGAAATT
*
6893964 AAAATAAAATATATAATATAAAAAATTATATTA
1 AAAATAAAA-ATAAAATATAAAAAATTATATTA
* * *
6893997 AAAATAAAAATAAAATATATAAGATTATAATA
1 AAAATAAAAATAAAATATAAAAAATTATATTA
* * * *
6894029 AAAATAAAAATAAAAAAT-ATATATGATATTA
1 AAAATAAAAATAAAATATAAAAAATTATATTA
6894060 AAAATA
1 AAAATA
6894066 TATTTAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.24
32 36 0.61
33 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATTATATTA
Found at i:6894075 original size:18 final size:18
Alignment explanation
Indices: 6894041--6894075 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6894031 AATAAAAATA
*
6894041 AAAAATATATATGATATT
1 AAAAATATATATAATATT
*
6894059 AAAAATATATTTAATAT
1 AAAAATATATATAATAT
6894076 ATGATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAAATATATATAATATT
Found at i:6897768 original size:16 final size:16
Alignment explanation
Indices: 6897743--6897773 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6897733 GCAGATTTTA
6897743 GAAATGATTTTTCTTT
1 GAAATGATTTTTCTTT
*
6897759 GAAATTATTTTTCTT
1 GAAATGATTTTTCTT
6897774 ACTATACATA
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:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (16 bp):
GAAATGATTTTTCTTT
Found at i:6906394 original size:29 final size:29
Alignment explanation
Indices: 6906359--6906421 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
6906349 TTCTCTATAC
*
6906359 TCTTTTCAGAAGAGTAACATATTCTAATA
1 TCTTTTCAGAAGAGCAACATATTCTAATA
6906388 TCTTTTCAGAAGAGCAACATATTCTAATA
1 TCTTTTCAGAAGAGCAACATATTCTAATA
6906417 TCTTT
1 TCTTT
6906422 GGTTTGGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (29 bp):
TCTTTTCAGAAGAGCAACATATTCTAATA
Found at i:6907726 original size:2 final size:2
Alignment explanation
Indices: 6907719--6907743 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6907709 AATAGATTTG
6907719 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6907744 AAGAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6911758 original size:36 final size:36
Alignment explanation
Indices: 6911706--6911777 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
6911696 CCACTATCTG
* *
6911706 CAATCTGTAATCTTCTGATAACTCATCAGTGATTTT
1 CAATCTGTAACCTTCTGATAACTCACCAGTGATTTT
*
6911742 CAATGTGTAACCTTCTGATAACTCACCAGTGATTTT
1 CAATCTGTAACCTTCTGATAACTCACCAGTGATTTT
6911778 AACTTGTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (36 bp):
CAATCTGTAACCTTCTGATAACTCACCAGTGATTTT
Found at i:6913720 original size:22 final size:22
Alignment explanation
Indices: 6913669--6913770 Score: 86
Period size: 22 Copynumber: 4.5 Consensus size: 22
6913659 TAGATTTTTT
6913669 AAATATTAATAATTTAGAATTTAATTA
1 AAATATTAATAA-TT--AA-TT-ATTA
6913696 AAATATTAATAATTAATTATTA
1 AAATATTAATAATTAATTATTA
6913718 AAATATTAAT-ATT--TTATTTA
1 AAATATTAATAATTAATTA-TTA
* * *
6913738 TAAT-TTAGTCATTAATATATTA
1 AAATATTAATAATTAAT-TATTA
6913760 AAATATTAATA
1 AAATATTAATA
6913771 TTTTATTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
19 7 0.11
20 9 0.14
21 3 0.05
22 21 0.33
23 8 0.12
24 2 0.03
26 2 0.03
27 12 0.19
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATATTAATAATTAATTATTA
Found at i:6913862 original size:16 final size:16
Alignment explanation
Indices: 6913841--6913898 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
6913831 TTAATAATTA
6913841 ATTAATTATTTAAAAT
1 ATTAATTATTTAAAAT
*
6913857 ATTAATAATTT--AAT
1 ATTAATTATTTAAAAT
6913871 CATTAATCT-TTTAAAAT
1 -ATTAAT-TATTTAAAAT
6913888 ATTAA-TATTTA
1 ATTAATTATTTA
6913899 TTTAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 4 0.11
15 13 0.37
16 15 0.43
17 3 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTATTTAAAAT
Found at i:6913884 original size:31 final size:28
Alignment explanation
Indices: 6913820--6913906 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 28
6913810 ATTTTATTTT
6913820 ATTTTT-AAATATTAATAA-TT-AATTA
1 ATTTTTAAAATATTAATAATTTAAATTA
6913845 ATTATTTAAAATATTAATAATTTAATCATTA
1 ATT-TTTAAAATATTAATAATTTAA--ATTA
*
6913876 ATCTTTTAAAATATTAAT-ATTT-ATTTA
1 AT-TTTTAAAATATTAATAATTTAAATTA
6913903 ATTT
1 ATTT
6913907 AAATATTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
25 3 0.06
26 5 0.09
27 17 0.31
28 2 0.04
29 2 0.04
30 4 0.07
31 20 0.37
32 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTTTAAAATATTAATAATTTAAATTA
Found at i:6913886 original size:124 final size:128
Alignment explanation
Indices: 6913732--6913996 Score: 362
Period size: 130 Copynumber: 2.1 Consensus size: 128
6913722 ATTAATATTT
* * *
6913732 TATTTATAATTTAGTCATTAATATATTAAAATATTAATATTTTATTTAATTTAAATATTGTTATG
1 TATTAATAATTTAATCATTAATATATTAAAATATTAATA-TTTATTTAATTTAAATATTATTATG
* *
6913797 A-TAA-ATTA-TT-TTT-ATTTTATTTTATTTTTAAATATTAATAATTAATTAA-TTATTTAAAA
65 ATTAATATTATTTATTTCATTTTATTTTATTTTTAAATATTAACAATT-AGTAATTTATTTAAAA
* *
6913856 TATTAATAATTTAATCATTAATCTTTTAAAATATTAATATTTATTTAATTTAAATATTATTATGA
1 TATTAATAATTTAATCATTAATATATTAAAATATTAATATTTATTTAATTTAAATATTATTATGA
* * *
6913921 TTAATTTTTATTTTATTTCTTTTTATTTTATTTTTAAATATTAACAATTGGTAATTTATTTAAAA
66 TTAA-TATTA-TTTATTTCATTTTATTTTATTTTTAAATATTAACAATTAGTAATTTATTTAAAA
6913986 TATTAATAATT
1 TATTAATAATT
6913997 GATGATTTAA
Statistics
Matches: 123, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
123 25 0.20
124 38 0.31
126 3 0.02
128 2 0.02
129 6 0.05
130 49 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (128 bp):
TATTAATAATTTAATCATTAATATATTAAAATATTAATATTTATTTAATTTAAATATTATTATGA
TTAATATTATTTATTTCATTTTATTTTATTTTTAAATATTAACAATTAGTAATTTATTTAAAA
Found at i:6913945 original size:15 final size:15
Alignment explanation
Indices: 6913925--6913953 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6913915 TTATGATTAA
6913925 TTTTTATTTTATTTC
1 TTTTTATTTTATTTC
6913940 TTTTTATTTTATTT
1 TTTTTATTTTATTT
6913954 TTAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTATTTC
Found at i:6914004 original size:27 final size:28
Alignment explanation
Indices: 6913947--6914005 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
6913937 TTCTTTTTAT
* *
6913947 TTTATTTTTAAATATTAACAATTGGTAA
1 TTTATTTTAAAATATTAACAATTGATAA
* *
6913975 TTTA-TTTAAAATATTAATAATTGATGA
1 TTTATTTTAAAATATTAACAATTGATAA
6914002 TTTA
1 TTTA
6914006 ATTATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTATTTTAAAATATTAACAATTGATAA
Found at i:6914133 original size:26 final size:26
Alignment explanation
Indices: 6914103--6914155 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
6914093 TTTATTAATA
6914103 ATTTATAATTTAAATATTAATATTTT
1 ATTTATAATTTAAATATTAATATTTT
* * *
6914129 ATTTATAATTTAATTTTTATTATTTT
1 ATTTATAATTTAAATATTAATATTTT
6914155 A
1 A
6914156 AACTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATAATTTAAATATTAATATTTT
Found at i:6914156 original size:41 final size:41
Alignment explanation
Indices: 6914111--6914210 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
6914101 TAATTTATAA
* *
6914111 TTTAAATATTAATATTTTATTTATAATTTAATTTTTATTAT-
1 TTTAAATATTAATATTTTATTTATAATTTAA-TATTAATATG
6914152 TTTAAACTATTAATATTTTATTTATAATTTAATATTAATATG
1 TTTAAA-TATTAATATTTTATTTATAATTTAATATTAATATG
* *
6914194 CTAAAATATTAATATTT
1 TTTAAATATTAATATTT
6914211 ATTAAAAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 24 0.45
42 29 0.55
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (41 bp):
TTTAAATATTAATATTTTATTTATAATTTAATATTAATATG
Found at i:6914183 original size:19 final size:20
Alignment explanation
Indices: 6914095--6914210 Score: 87
Period size: 19 Copynumber: 5.5 Consensus size: 20
6914085 TAAGTTATTT
6914095 TATTAATAATTTATAATTTA-AA
1 TATTAAT-ATTT-T-ATTTATAA
6914117 TATTAATATTTTATTTATAA
1 TATTAATATTTTATTTATAA
*
6914137 T-TTAAT-TTTTATTATTTTAAA
1 TATTAATATTTTA-T-TTAT-AA
6914158 CTATTAATATTTTATTTATAA
1 -TATTAATATTTTATTTATAA
* * *
6914179 T-TTAATATTAATATGCTAAAA
1 TATTAATATT-TTAT-TTATAA
6914200 TATTAATATTT
1 TATTAATATTT
6914211 ATTAAAAGTT
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
18 5 0.06
19 19 0.24
20 11 0.14
21 13 0.17
22 19 0.24
23 6 0.08
24 5 0.06
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (20 bp):
TATTAATATTTTATTTATAA
Found at i:6914761 original size:15 final size:15
Alignment explanation
Indices: 6914737--6914850 Score: 68
Period size: 15 Copynumber: 8.1 Consensus size: 15
6914727 ATATTTAACT
6914737 TTTA-AATTAAAATA
1 TTTATAATTAAAATA
6914751 TTTATAATTAAAATA
1 TTTATAATTAAAATA
** *
6914766 --T-TAATTTCATTA
1 TTTATAATTAAAATA
**
6914778 TTTATTTTTAAAATA
1 TTTATAATTAAAATA
* *
6914793 -TTAAAATATAAAAAA
1 TTTATAAT-TAAAATA
6914808 TTTATAATT-AAA-A
1 TTTATAATTAAAATA
*
6914821 TTT-TAATT-TAATA
1 TTTATAATTAAAATA
6914834 TTTA-AATTTAAAATA
1 TTTATAA-TTAAAATA
6914849 TT
1 TT
6914851 AACTTTTTAT
Statistics
Matches: 75, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
12 15 0.20
13 11 0.15
14 14 0.19
15 29 0.39
16 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATAATTAAAATA
Found at i:6914811 original size:57 final size:55
Alignment explanation
Indices: 6914740--6914852 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 55
6914730 TTTAACTTTT
* * **
6914740 AAATTAAAATATTTATAATTAAAATATTAATTTCATTATTTATTTTTAAAATATTA
1 AAATTAAAAAATTTATAATTAAAATATTAATTT-AATATTTAAATTTAAAATATTA
*
6914796 AAATATAAAAAATTTATAATTAAAATTTTAATTTAATATTTAAATTTAAAATATTA
1 AAAT-TAAAAAATTTATAATTAAAATATTAATTTAATATTTAAATTTAAAATATTA
6914852 A
1 A
6914853 CTTTTTATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 24 0.47
57 27 0.53
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (55 bp):
AAATTAAAAAATTTATAATTAAAATATTAATTTAATATTTAAATTTAAAATATTA
Found at i:6914822 original size:13 final size:14
Alignment explanation
Indices: 6914804--6914847 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
6914794 TAAAATATAA
6914804 AAAATTTATAA-TT
1 AAAATTTATAATTT
6914817 AAAATTT-TAATTT
1 AAAATTTATAATTT
*
6914830 AATATTTA-AATTT
1 AAAATTTATAATTT
6914843 AAAAT
1 AAAAT
6914848 ATTAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 24 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATTTATAATTT
Found at i:6914943 original size:23 final size:22
Alignment explanation
Indices: 6914900--6914943 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
6914890 TTTTAAATTC
*
6914900 ATTTTAATTTTTTTATTTTTAT
1 ATTTTAATTTTTTTATCTTTAT
6914922 ATTTTCAATTTATTTTA-CTTTA
1 ATTTT-AATTT-TTTTATCTTTA
6914944 GGAAGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTAATTTTTTTATCTTTAT
Found at i:6916206 original size:34 final size:33
Alignment explanation
Indices: 6916134--6916211 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
6916124 ATGTTTTAAA
6916134 ATTTTTTTAATTTATTTAGAAAAATTTAAATAT
1 ATTTTTTTAATTTATTTAGAAAAATTTAAATAT
* * ** **
6916167 TTTTTTTTTATTATATTTAGTTAAATTTTTATAT
1 ATTTTTTTAATT-TATTTAGAAAAATTTAAATAT
6916201 A-TTTTTTAATT
1 ATTTTTTTAATT
6916212 AAATAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (33 bp):
ATTTTTTTAATTTATTTAGAAAAATTTAAATAT
Found at i:6916211 original size:18 final size:20
Alignment explanation
Indices: 6916171--6916209 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6916161 AAATATTTTT
6916171 TTTTTATTATATTTAGTTAAA
1 TTTTTATTATATTTA-TTAAA
*
6916192 TTTTTA-TATATTTTTTAA
1 TTTTTATTATATTTATTAA
6916210 TTAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTATTATATTTATTAAA
Found at i:6919803 original size:21 final size:21
Alignment explanation
Indices: 6919780--6919821 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6919770 AAACAAAAGT
6919780 AAATAGTAAAAAATAATTAATA
1 AAATAG-AAAAAATAATTAATA
**
6919802 AAATAGAAGTAATAATTAAT
1 AAATAGAAAAAATAATTAAT
6919822 GGAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAATAGAAAAAATAATTAATA
Found at i:6930559 original size:2 final size:2
Alignment explanation
Indices: 6930552--6930583 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6930542 GCCCCTACAA
6930552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6930584 TTACTACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6949209 original size:3 final size:3
Alignment explanation
Indices: 6949191--6949228 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
6949181 ATTTACAGCA
6949191 TTC TT- TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TT
6949229 TTTTTTACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6979066 original size:15 final size:14
Alignment explanation
Indices: 6979031--6979071 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
6979021 TTGTTTAATA
*
6979031 TTTTAAATTATATT
1 TTTTAAATTAAATT
6979045 TTTTAAATTAAATT
1 TTTTAAATTAAATT
6979059 TTTCTAAATTAAA
1 TTT-TAAATTAAA
6979072 GACTACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATTAAATT
Found at i:6980020 original size:17 final size:16
Alignment explanation
Indices: 6980000--6980063 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
6979990 AAGATAAAAA
6980000 TTAAATTGAAATAATTT
1 TTAAATT-AAATAATTT
*
6980017 TTAAAATTAAA-AA--A
1 TT-AAATTAAATAATTT
6980031 TTAAATTAAAATAATTT
1 TTAAATT-AAATAATTT
*
6980048 TTAAAATTAAAAAATT
1 TT-AAATTAAATAATT
6980064 AAATTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
13 5 0.13
14 5 0.13
15 2 0.05
16 2 0.05
17 14 0.37
18 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TTAAATTAAATAATTT
Found at i:6980033 original size:31 final size:31
Alignment explanation
Indices: 6979995--6980079 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
6979985 CATTAAAGAT
*
6979995 AAAAATTAAATTGAAATAATTTTTAAAATTA
1 AAAAATTAAATTAAAATAATTTTTAAAATTA
6980026 AAAAATTAAATTAAAATAATTTTTAAAATTA
1 AAAAATTAAATTAAAATAATTTTTAAAATTA
**
6980057 AAAAATTAAATTATTATAATTTT
1 AAAAATTAAATTAAAATAATTTT
6980080 GAATAGATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAAATTAAATTAAAATAATTTTTAAAATTA
Found at i:6980038 original size:13 final size:13
Alignment explanation
Indices: 6980020--6980069 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
6980010 ATAATTTTTA
6980020 AAATTAAAAAATT
1 AAATTAAAAAATT
6980033 AAATTAAAATAATTTTT
1 AAATTAAAA-AA---TT
6980050 AAAATTAAAAAATT
1 -AAATTAAAAAATT
6980064 AAATTA
1 AAATTA
6980070 TTATAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 15 0.47
14 4 0.12
17 4 0.12
18 9 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:6980056 original size:18 final size:17
Alignment explanation
Indices: 6980002--6980063 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 17
6979992 GATAAAAATT
*
6980002 AAATTGAAATAATTTTTA
1 AAATT-AAAAAATTTTTA
6980020 AAATTAAAAAA---TT-
1 AAATTAAAAAATTTTTA
6980033 AAATTAAAATAATTTTTA
1 AAATTAAAA-AATTTTTA
6980051 AAATTAAAAAATT
1 AAATTAAAAAATT
6980064 AAATTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
17 11 0.29
18 14 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTAAAAAATTTTTA
Found at i:6980724 original size:18 final size:20
Alignment explanation
Indices: 6980701--6980740 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
6980691 CACATCACTT
*
6980701 TTTCAAGAAATT-TT-TTTA
1 TTTCAAAAAATTCTTATTTA
6980719 TTTCAAAAAATTCTTATTTA
1 TTTCAAAAAATTCTTATTTA
6980739 TT
1 TT
6980741 AAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTCAAAAAATTCTTATTTA
Found at i:6980840 original size:17 final size:17
Alignment explanation
Indices: 6980764--6980860 Score: 65
Period size: 18 Copynumber: 5.4 Consensus size: 17
6980754 ATATTATTGG
*
6980764 TTTTTATTT-TTATATAA
1 TTTTTATTTATTAAAT-A
*
6980781 TTTATTATTAATTATAA-A
1 TTT-TTATTTATTA-AATA
*
6980799 TTTTATATTATATAAAAATA
1 TTTT-TATT-TAT-TAAATA
*
6980819 TTTTTCATATTTTTAAA-A
1 TTTTT-AT-TTATTAAATA
6980837 TTTTTATTTATTAAATA
1 TTTTTATTTATTAAATA
6980854 TTTTTAT
1 TTTTTAT
6980861 AATAATTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
16 7 0.11
17 14 0.22
18 19 0.30
19 11 0.17
20 11 0.17
21 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATTTATTAAATA
Found at i:6980857 original size:16 final size:15
Alignment explanation
Indices: 6980826--6980860 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
6980816 ATATTTTTCA
6980826 TATTTTTAAAATTTT
1 TATTTTTAAAATTTT
6980841 TATTTATTAAATATTTT
1 TATTT-TTAAA-ATTTT
6980858 TAT
1 TAT
6980861 AATAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTTAAAATTTT
Done.