Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 21 of 133
Found at i:5220875 original size:20 final size:19
Alignment explanation
Indices: 5220824--5220863 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5220814 ATAATTCATG
5220824 AATATGATTTTTTAAATTA
1 AATATGATTTTTTAAATTA
5220843 AATATGATTTTTTAAATTA
1 AATATGATTTTTTAAATTA
5220862 AA
1 AA
5220864 ACCTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AATATGATTTTTTAAATTA
Found at i:5220930 original size:22 final size:23
Alignment explanation
Indices: 5220871--5220936 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
5220861 AAAACCTTAT
* *
5220871 TTTTTTAAAAAAAATAAAGAAATA
1 TTTTTT-AAAAAATTAAAAAAATA
5220895 TTTTATTAAAAAATTAAAAAAATA
1 TTTT-TTAAAAAATTAAAAAAATA
*
5220919 -TTTTTAAAAAATTTAAAA
1 TTTTTTAAAAAATTAAAAA
5220937 TATTAGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
24 19 0.50
25 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TTTTTTAAAAAATTAAAAAAATA
Found at i:5221061 original size:23 final size:21
Alignment explanation
Indices: 5221020--5221061 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5221010 TTTTTATCAA
*
5221020 TTTTTAATTTTTCAAACATAC
1 TTTTTAAATTTTCAAACATAC
5221041 TTTTTGAAATTTTCAAGACAT
1 TTTTT-AAATTTTCAA-ACAT
5221062 TTTAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTTAAATTTTCAAACATAC
Found at i:5227475 original size:19 final size:19
Alignment explanation
Indices: 5227451--5227487 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5227441 CTCTTATTAA
*
5227451 TTTAAACAGATTTGAATAT
1 TTTAAACAAATTTGAATAT
*
5227470 TTTAAATAAATTTGAATA
1 TTTAAACAAATTTGAATA
5227488 ATACTAAATA
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:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (19 bp):
TTTAAACAAATTTGAATAT
Found at i:5228437 original size:2 final size:2
Alignment explanation
Indices: 5228430--5228476 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5228420 GAAGATAGAT
5228430 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5228472 GA GA G
1 GA GA G
5228477 TACATCATGT
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5228895 original size:26 final size:25
Alignment explanation
Indices: 5228866--5228914 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5228856 GACATTTTTT
5228866 GATTAAATCAAATTAAATTAAATTCA
1 GATTAAATCAAATTAAA-TAAATTCA
** *
5228892 GATTCGATCAAATTGAATAAATT
1 GATTAAATCAAATTAAATAAATT
5228915 TTTCGAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (25 bp):
GATTAAATCAAATTAAATAAATTCA
Found at i:5229857 original size:15 final size:16
Alignment explanation
Indices: 5229837--5229870 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5229827 TTAGTTTGAA
*
5229837 AATATAAAA-ATTTAT
1 AATATAAAATAATTAT
5229852 AATATAAAATAATTAT
1 AATATAAAATAATTAT
5229868 AAT
1 AAT
5229871 CTTAAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:5231008 original size:19 final size:19
Alignment explanation
Indices: 5230962--5231012 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
5230952 ATGGTCTTAT
*
5230962 TAATTTAAACAAATTTGAA
1 TAATTTAAATAAATTTGAA
*
5230981 TATTTTAAATAAATTTGAA
1 TAATTTAAATAAATTTGAA
*
5231000 TAATCTAAATAAA
1 TAATTTAAATAAA
5231013 GTAAATAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (19 bp):
TAATTTAAATAAATTTGAA
Found at i:5233225 original size:21 final size:21
Alignment explanation
Indices: 5233201--5233246 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
5233191 GGTTCAAAGA
*
5233201 GTTTAGGGTTTTGTTTTTAGG
1 GTTTAAGGTTTTGTTTTTAGG
5233222 GTTTAAGGTTTTGTTTTTAGG
1 GTTTAAGGTTTTGTTTTTAGG
5233243 GTTT
1 GTTT
5233247 TAGATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (21 bp):
GTTTAAGGTTTTGTTTTTAGG
Found at i:5233254 original size:21 final size:21
Alignment explanation
Indices: 5233209--5233254 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5233199 GAGTTTAGGG
*
5233209 TTTTGTTTTTAGGGTTTAAGG
1 TTTTGTTTTTAGGGTTTAAGA
*
5233230 TTTTGTTTTTAGGGTTTTAGA
1 TTTTGTTTTTAGGGTTTAAGA
5233251 TTTT
1 TTTT
5233255 AGGGTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.63
Consensus pattern (21 bp):
TTTTGTTTTTAGGGTTTAAGA
Found at i:5233256 original size:15 final size:14
Alignment explanation
Indices: 5233223--5233269 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
5233213 GTTTTTAGGG
* *
5233223 TTTAAGGTTTTGTT
1 TTTAGGGTTTTGAT
5233237 TTTAGGGTTTTAGAT
1 TTTAGGGTTTT-GAT
5233252 TTTAGGGTTTATGAT
1 TTTAGGGTTT-TGAT
5233267 TTT
1 TTT
5233270 GATTTTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.34
15 18 0.62
16 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:5233261 original size:36 final size:36
Alignment explanation
Indices: 5233202--5233276 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
5233192 GTTCAAAGAG
* *
5233202 TTTAGGGTTTTGTTTTTAGGGTTTAAGGTTTTG-TT
1 TTTAGGGTTTTGATTTTAGGGTTTAAGATTTTGATT
*
5233237 TTTAGGGTTTTAGATTTTAGGGTTTATGATTTTGATT
1 TTTAGGGTTTT-GATTTTAGGGTTTAAGATTTTGATT
5233274 TTT
1 TTT
5233277 GGAATTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 11 0.31
36 19 0.54
37 5 0.14
ACGTcount: A:0.15, C:0.00, G:0.25, T:0.60
Consensus pattern (36 bp):
TTTAGGGTTTTGATTTTAGGGTTTAAGATTTTGATT
Found at i:5233856 original size:14 final size:15
Alignment explanation
Indices: 5233832--5233860 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5233822 ACTATATATA
5233832 AAAAATCAAAAAAAT
1 AAAAATCAAAAAAAT
5233847 AAAAAT-AAAAAAAT
1 AAAAATCAAAAAAAT
5233861 TACTTGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATCAAAAAAAT
Found at i:5234991 original size:17 final size:14
Alignment explanation
Indices: 5234956--5234983 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5234946 ATATTAAACA
5234956 ATTATTAATATTTT
1 ATTATTAATATTTT
5234970 ATTATTAATATTTT
1 ATTATTAATATTTT
5234984 TCTATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTAATATTTT
Found at i:5236256 original size:12 final size:13
Alignment explanation
Indices: 5236222--5236259 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
5236212 AATTTAATCA
*
5236222 TTATAAATGCACTT
1 TTATAAATG-ATTT
5236236 TTATAAATGATTT
1 TTATAAATGATTT
5236249 TTAT-AATGATT
1 TTATAAATGATT
5236260 ACCCTGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (13 bp):
TTATAAATGATTT
Found at i:5237553 original size:15 final size:14
Alignment explanation
Indices: 5237532--5237572 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5237522 GCATTAATAT
*
5237532 TAATAAATAATTTA
1 TAATAAAAAATTTA
*
5237546 TAAATAAAAAATATA
1 T-AATAAAAAATTTA
5237561 TAATAAAAAATT
1 TAATAAAAAATT
5237573 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAAAAAATTTA
Found at i:5242996 original size:43 final size:43
Alignment explanation
Indices: 5242867--5242997 Score: 199
Period size: 43 Copynumber: 3.0 Consensus size: 43
5242857 TGTCCCATTC
* *
5242867 CAAGTACGAAGTCGGCAGGATAAAAGCCAAGAATACAACATCA
1 CAAGTACTAAGCCGGCAGGATAAAAGCCAAGAATACAACATCA
* *
5242910 AAAGTACTAAGCCGGCAGGATAAAAGCTAAGAATACAACATCA
1 CAAGTACTAAGCCGGCAGGATAAAAGCCAAGAATACAACATCA
* * *
5242953 CAAGTACTAAGCCGGAAGAATAAAAGCCAAGAATAAAACATCA
1 CAAGTACTAAGCCGGCAGGATAAAAGCCAAGAATACAACATCA
5242996 CA
1 CA
5242998 GAGTCGGCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (43 bp):
CAAGTACTAAGCCGGCAGGATAAAAGCCAAGAATACAACATCA
Found at i:5243127 original size:90 final size:90
Alignment explanation
Indices: 5242974--5243152 Score: 331
Period size: 90 Copynumber: 2.0 Consensus size: 90
5242964 CCGGAAGAAT
*
5242974 AAAAGCCAAGAATAAAACATCACAGAGTCGGCAACTGAACGTCAAAACCAATAATAAAGCTTATA
1 AAAAGCCAAGAATAAAACATCACAGAGTCCGCAACTGAACGTCAAAACCAATAATAAAGCTTATA
*
5243039 ACATCTTAAAGTTTGATATTTACTA
66 ACAGCTTAAAGTTTGATATTTACTA
*
5243064 AAAAGCCAAGAATAACACATCACAGAGTCCGCAACTGAACGTCAAAACCAATAATAAAGCTTATA
1 AAAAGCCAAGAATAAAACATCACAGAGTCCGCAACTGAACGTCAAAACCAATAATAAAGCTTATA
5243129 ACAGCTTAAAGTTTGATATTTACT
66 ACAGCTTAAAGTTTGATATTTACT
5243153 GCTACTTTTA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (90 bp):
AAAAGCCAAGAATAAAACATCACAGAGTCCGCAACTGAACGTCAAAACCAATAATAAAGCTTATA
ACAGCTTAAAGTTTGATATTTACTA
Found at i:5245390 original size:175 final size:172
Alignment explanation
Indices: 5245119--5245443 Score: 490
Period size: 175 Copynumber: 1.9 Consensus size: 172
5245109 TATACTAGTA
* *
5245119 CCATGCTCCATGATAGGCTCAATGAACAAGCACAAAATGACTTTTCCCTTCTTCGTTTGTTGCCC
1 CCATGCTCCATGACAGGCTCAATGAACAAGCACAAAATGACTTTTCCCTTCTTCATTTGTTGCCC
5245184 TTCCTACCATTTCTTTCCTTTGATCTAGTTTATGTGCTATAAAAATCTTATTTGGCCATACCAAG
66 TTCCTACCATTTCTTTCCTTTGATCTAGTTTATGT--TATAAAAATCTTATTTGGCCATACCAAG
5245249 TCATTTCACACAATCACATTCATAACTTATACCAGCACCATGCT
129 TCATTTCACACAATCACATTCATAACTTATACCAGCACCATGCT
* * * * *
5245293 CCATGCTCCATGACATGTTCAATGGACAAGCACAAAATGACTTTTTTCCTTC-TCTATTTGTTGT
1 CCATGCTCCATGACAGGCTCAATGAACAAGCACAAAATGAC-TTTTCCCTTCTTC-ATTTGTTGC
* ** *
5245357 CCTTCCTACCATTTCTTTCCTTTGATCTAGTTTATGTTATAAAAATCTTATTTGGTCATATTAGG
64 CCTTCCTACCATTTCTTTCCTTTGATCTAGTTTATGTTATAAAAATCTTATTTGGCCATACCAAG
* *
5245422 TCATTTCACATAGTCACATTCA
129 TCATTTCACACAATCACATTCA
5245444 GGTTCCATAC
Statistics
Matches: 136, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
173 44 0.32
174 39 0.29
175 53 0.39
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (172 bp):
CCATGCTCCATGACAGGCTCAATGAACAAGCACAAAATGACTTTTCCCTTCTTCATTTGTTGCCC
TTCCTACCATTTCTTTCCTTTGATCTAGTTTATGTTATAAAAATCTTATTTGGCCATACCAAGTC
ATTTCACACAATCACATTCATAACTTATACCAGCACCATGCT
Found at i:5251639 original size:52 final size:52
Alignment explanation
Indices: 5251546--5251649 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
5251536 ATGACAATAA
* * *
5251546 GACTTGCAGAAAAAGAATTCTAAGAGAAAAATAATTTTTAATAAGCAAGTTT
1 GACTTGCAAAAAAAAAATTCTAAGAGAAAAATAATTCTTAATAAGCAAGTTT
* *
5251598 GACTTGCAAAAAAAAAATTCTAAGAGGAAAGA-AATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAAAAAAATTCTAAGA-GAAAAATAATTCTTAATAAGCAAGTTT
5251650 ATATGCTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 41 0.89
53 5 0.11
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (52 bp):
GACTTGCAAAAAAAAAATTCTAAGAGAAAAATAATTCTTAATAAGCAAGTTT
Found at i:5251886 original size:35 final size:35
Alignment explanation
Indices: 5251836--5251905 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
5251826 ATAATGAATT
* * *
5251836 GGTACATATGAATATGTGTTTATTTATATTGAAAA
1 GGTACATATGAATATGTATTTATTTAAATTAAAAA
* *
5251871 GGTACATATGGATATGTATTTGTTTAAATTAAAAA
1 GGTACATATGAATATGTATTTATTTAAATTAAAAA
5251906 TATTTCATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (35 bp):
GGTACATATGAATATGTATTTATTTAAATTAAAAA
Found at i:5252123 original size:23 final size:21
Alignment explanation
Indices: 5252085--5252127 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
5252075 TAATTAATTA
*
5252085 TTTAATTTTATTTTTATTGAC
1 TTTAATTTTATATTTATTGAC
5252106 TTTAATATTTCATATTTATTGA
1 TTTAAT-TTT-ATATTTATTGA
5252128 ATCGAGGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTAATTTTATATTTATTGAC
Found at i:5257898 original size:12 final size:12
Alignment explanation
Indices: 5257872--5257905 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5257862 CCCCCCCCCC
5257872 CAAAAA-AAAAA
1 CAAAAACAAAAA
5257883 -AAAAACAAAAA
1 CAAAAACAAAAA
5257894 CAAAAACAAAAA
1 CAAAAACAAAAA
5257906 AAAGGCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 5 0.24
12 11 0.52
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAACAAAAA
Found at i:5258041 original size:6 final size:6
Alignment explanation
Indices: 5258032--5258132 Score: 60
Period size: 6 Copynumber: 16.3 Consensus size: 6
5258022 AAGAAAAAGC
* * * *
5258032 TGCTGT TGCTGT TGATGT TGCTTT TGTTGT TGTTGT TGCTGT TG-TAGT
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCT-GT
* ** * * * *
5258080 GGAAACTGT AACTGT GGTTGC TGCTGT TGCTGT TGCTGT TGCTGT TCCTGT
1 TG---CTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
5258131 TG
1 TG
5258133 TTGGGGTTGA
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 68 0.94
9 2 0.03
10 1 0.01
ACGTcount: A:0.07, C:0.13, G:0.32, T:0.49
Consensus pattern (6 bp):
TGCTGT
Found at i:5259430 original size:16 final size:16
Alignment explanation
Indices: 5259409--5259440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5259399 CACATTTGGA
*
5259409 TTTATTTTTTGTTTTT
1 TTTATTTTTTATTTTT
5259425 TTTATTTTTTATTTTT
1 TTTATTTTTTATTTTT
5259441 AAAAATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTATTTTTTATTTTT
Found at i:5259533 original size:22 final size:22
Alignment explanation
Indices: 5259499--5259579 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
5259489 GCCAACCCAA
5259499 CTTTTTTCTTTTT-TATTTTTTT
1 CTTTTTTCTTTTTCT-TTTTTTT
5259521 CTTTTTGTC-TTTTCTTTTTTTT
1 CTTTTT-TCTTTTTCTTTTTTTT
** **
5259543 CCTTATTTTAAGTTTT-TTTCCTTT
1 -CTT-TTTT-CTTTTTCTTTTTTTT
5259567 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
5259580 ATATTTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
21 4 0.08
22 21 0.44
23 10 0.21
24 9 0.19
25 4 0.08
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (22 bp):
CTTTTTTCTTTTTCTTTTTTTT
Found at i:5259540 original size:15 final size:13
Alignment explanation
Indices: 5259500--5259542 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5259490 CCAACCCAAC
5259500 TTTTTTCTTTTTTAT
1 TTTTTTC-TTTTT-T
*
5259515 TTTTTTCTTTTTG
1 TTTTTTCTTTTTT
*
5259528 TCTTTTCTTTTTT
1 TTTTTTCTTTTTT
5259541 TT
1 TT
5259543 CCTTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 12 0.50
14 5 0.21
15 7 0.29
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:5265651 original size:17 final size:16
Alignment explanation
Indices: 5265614--5265657 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
5265604 CTTTTTTTGC
5265614 TTTTT-TTTTTTCACT
1 TTTTTGTTTTTTCACT
5265629 TTTTTGCTTTTTTCAAC-
1 TTTTTG-TTTTTTC-ACT
5265646 TTTTTGTTTTTT
1 TTTTTGTTTTTT
5265658 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 6 0.23
17 13 0.50
18 2 0.08
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTTGTTTTTTCACT
Found at i:5268102 original size:16 final size:16
Alignment explanation
Indices: 5268072--5268111 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
5268062 AAATTAAGAG
*
5268072 ATATAT-ATGCTTTAT
1 ATATATGATACTTTAT
5268087 ATATATGATACTTTAT
1 ATATATGATACTTTAT
5268103 ATATATGAT
1 ATATATGAT
5268112 CAGATGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (16 bp):
ATATATGATACTTTAT
Found at i:5275915 original size:26 final size:25
Alignment explanation
Indices: 5275886--5275950 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
5275876 TATTATTTTT
5275886 TATTTTAATTTAAAATATATTTAAAA
1 TATTTTAATTTAAAATAT-TTTAAAA
** *
5275912 TATTAAAATTTAATAATATTTTAATA
1 TATTTTAATTTAA-AATATTTTAAAA
5275938 -ATTTT--TTTAAAAT
1 TATTTTAATTTAAAAT
5275951 TTTGAACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 3 0.09
23 5 0.15
25 3 0.09
26 17 0.52
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTTAATTTAAAATATTTTAAAA
Found at i:5277567 original size:3 final size:3
Alignment explanation
Indices: 5277559--5277605 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5277549 ATTTTGATTC
5277559 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5277606 TTGTTATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5278540 original size:20 final size:20
Alignment explanation
Indices: 5278517--5278564 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
5278507 CCTTATTTTT
*
5278517 TATTTAAGGGTCTTAATTGA
1 TATTTAACGGTCTTAATTGA
5278537 TATTTAACGGTCTTAATTGA
1 TATTTAACGGTCTTAATTGA
5278557 TATTTAAC
1 TATTTAAC
5278565 CTTAATTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (20 bp):
TATTTAACGGTCTTAATTGA
Found at i:5279763 original size:22 final size:22
Alignment explanation
Indices: 5279738--5279812 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 22
5279728 TAAGACATTG
5279738 CATTTCATGCATATGCGTTACA
1 CATTTCATGCATATGCGTTACA
* * *
5279760 CATTT--TGTAT-TGTACGTATGCTG
1 CATTTCATGCATATG--CGT-TAC-A
*
5279783 CATTTCATGCATATGCATTACA
1 CATTTCATGCATATGCGTTACA
5279805 CATTTCAT
1 CATTTCAT
5279813 ATAAAGTTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 3 0.08
22 15 0.38
23 7 0.18
24 2 0.05
25 4 0.10
26 2 0.05
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (22 bp):
CATTTCATGCATATGCGTTACA
Found at i:5284977 original size:15 final size:15
Alignment explanation
Indices: 5284957--5284986 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5284947 GAGCAAGATT
5284957 CATAAGTCTTTTAAA
1 CATAAGTCTTTTAAA
*
5284972 CATAAGTTTTTTAAA
1 CATAAGTCTTTTAAA
5284987 TTTTCAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
CATAAGTCTTTTAAA
Found at i:5285134 original size:126 final size:125
Alignment explanation
Indices: 5284853--5285137 Score: 295
Period size: 126 Copynumber: 2.3 Consensus size: 125
5284843 TGAATAAAAG
* * * **
5284853 TTTTTTAATTTTTAAAGTTTCAAGCCTCTTTTTAGAAGAGTATTCAAAGATGTTGAGATTTATAA
1 TTTTTTAATTTTTAAAGTTTCAAGCCT-TTTTTAGAAAAGCATTCAAAGATATCAAGATTTATAA
* * * * *
5284918 GACCTCCAAGCCTAGTCTCTAAGTATTTCGAGCAAGATTCATAAGTCTTTTAAACATAAGT
65 GACATCCAAGCCTAGTCTCTAAGTATTTCGAGCAAAATTCATAAATCCTCTAAACATAAGT
* * * * *
5284979 TTTTTAAATTTTCAAAGTTTCAAAACCTTTTTTAGAAAAGCATTTAAAGATATCAAGATTTGTAA
1 TTTTTTAATTTTTAAAGTTTC-AAGCCTTTTTTAGAAAAGCATTCAAAGATATCAAGATTTATAA
* * * * *** *
5285044 GACATCCAGGCCTAGTCTCTAAAGTCCTTT-GGGCAAAATTCGTAAATCCTCTAGGTATAATT
65 GACATCCAAGCCTAGTCTCT-AAGT-ATTTCGAGCAAAATTCATAAATCCTCTAAACATAAGT
*
5285106 TTTTTTAATTTTTAAA-TTTTAAGGCCTTTTTT
1 TTTTTTAATTTTTAAAGTTTCAA-GCCTTTTTT
5285138 TTAAAGGAGT
Statistics
Matches: 128, Mismatches: 27, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
125 2 0.02
126 78 0.61
127 45 0.35
128 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (125 bp):
TTTTTTAATTTTTAAAGTTTCAAGCCTTTTTTAGAAAAGCATTCAAAGATATCAAGATTTATAAG
ACATCCAAGCCTAGTCTCTAAGTATTTCGAGCAAAATTCATAAATCCTCTAAACATAAGT
Found at i:5287831 original size:14 final size:14
Alignment explanation
Indices: 5287812--5287853 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
5287802 TTTATTTTTT
*
5287812 AAATAAAATAATAA
1 AAATAAAATAAGAA
5287826 AAATAAAATAAGAA
1 AAATAAAATAAGAA
5287840 ACAAT-AAATAAGAA
1 A-AATAAAATAAGAA
5287854 GAATGATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 23 0.88
15 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (14 bp):
AAATAAAATAAGAA
Found at i:5294003 original size:39 final size:39
Alignment explanation
Indices: 5293952--5294059 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
5293942 GATTGGATAG
5293952 GGTGGGGA-GGATTGGGTGTGGTGGGGTGTTGGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAA
* *
5293990 GGTGGGGAGGGATTGGATGTGGTGGGATGTTGGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAA
* * *
5294029 GGAGGAGAGGGATTGGGTGTGGTAGGGTGTT
1 GGTGGGGAGGGATTGGGTGTGGTGGGGTGTT
5294060 TGGAGGGTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 8 0.13
39 54 0.87
ACGTcount: A:0.14, C:0.00, G:0.62, T:0.24
Consensus pattern (39 bp):
GGTGGGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAA
Found at i:5294571 original size:26 final size:26
Alignment explanation
Indices: 5294543--5294591 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5294533 TAAAAAATAA
*
5294543 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
5294568 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
5294592 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:5295914 original size:32 final size:32
Alignment explanation
Indices: 5295860--5295924 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
5295850 AATGGGTGAA
*
5295860 TCAGTATCAAAATTTTTGATATATGATCGACT
1 TCAGTATAAAAATTTTTGATATATGATCGACT
5295892 TCAGTATAAAAAATTTTT-ATATATGATCGACT
1 TCAGTAT-AAAAATTTTTGATATATGATCGACT
5295924 T
1 T
5295925 TCTTTTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 22 0.71
33 9 0.29
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (32 bp):
TCAGTATAAAAATTTTTGATATATGATCGACT
Found at i:5298062 original size:18 final size:18
Alignment explanation
Indices: 5298035--5298070 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5298025 GTTTAAGTCC
*
5298035 AGATGATGATGGTGATGG
1 AGATGATGATAGTGATGG
*
5298053 AGATGGTGATAGTGATGG
1 AGATGATGATAGTGATGG
5298071 TGCGAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (18 bp):
AGATGATGATAGTGATGG
Found at i:5298439 original size:18 final size:18
Alignment explanation
Indices: 5298416--5298507 Score: 71
Period size: 18 Copynumber: 4.9 Consensus size: 18
5298406 ATGGTTATTA
5298416 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
5298434 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
* *
5298455 TCCACCTTAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
5298474 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
5298491 TCCACCAT-AAATGTATC
1 TCCACC-TCAAATGTATC
5298508 ATCCTCAATC
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 37 0.66
19 1 0.02
21 17 0.30
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:5298446 original size:21 final size:21
Alignment explanation
Indices: 5298420--5298461 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5298410 TTATTATCCA
*
5298420 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
5298441 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
5298462 TAAATGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.43, G:0.02, T:0.29
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:5315124 original size:5 final size:5
Alignment explanation
Indices: 5315114--5315156 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
5315104 TTATCTATAA
*
5315114 TTTAT TTTAT TTTAT TTTAT TACTTAT TTTAT CTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT T--TTAT TTTAT TTTAT TTTAT TT
5315157 GTTGTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 25 0.76
7 5 0.15
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:5315126 original size:38 final size:36
Alignment explanation
Indices: 5315084--5315156 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
5315074 CTAATTATCA
5315084 ATTTTATGTTT-TTACTT-TGTTTATCTATAATTTATTTT
1 ATTTTAT-TTTATTACTTAT-TTTATCT-T-ATTTATTTT
5315122 ATTTTATTTTATTACTTATTTTATCTTATTTATTT
1 ATTTTATTTTATTACTTATTTTATCTTATTTATTT
5315157 GTTGTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 8 0.24
37 4 0.12
38 20 0.61
39 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (36 bp):
ATTTTATTTTATTACTTATTTTATCTTATTTATTTT
Found at i:5321507 original size:10 final size:10
Alignment explanation
Indices: 5321492--5321517 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5321482 ATGTTAAAAG
5321492 ATAAAGAAAC
1 ATAAAGAAAC
5321502 ATAAAGAAAC
1 ATAAAGAAAC
5321512 ATAAAG
1 ATAAAG
5321518 TTTTAGGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAC
Found at i:5324980 original size:14 final size:14
Alignment explanation
Indices: 5324961--5325007 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5324951 TATCACTTTA
5324961 TATTTT-AAGTTTTT
1 TATTTTCAA-TTTTT
5324975 TATTTTCAATTTTT
1 TATTTTCAATTTTT
* *
5324989 TATTATCAATTTAT
1 TATTTTCAATTTTT
5325003 TATTT
1 TATTT
5325008 CATTGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 27 0.93
15 2 0.07
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (14 bp):
TATTTTCAATTTTT
Found at i:5331057 original size:176 final size:175
Alignment explanation
Indices: 5330700--5331088 Score: 399
Period size: 176 Copynumber: 2.2 Consensus size: 175
5330690 CCTAGTAGTT
* * * * * *
5330700 TTATTTTTTAAACTTATGACTCAGTC-CTGGTTATTCAATCTTGGCTCAGCCCAAATCATTTACT
1 TTATTTTTTAGACTTGTGACTCAATCTC-GGTCATTCAATCTTCGCTCAACCCAAATCATTTACT
* * *
5330764 TGACTCATAGTTTTATTTCGATCATTCATTTTTAACCTCGACTCGATCTTGGTCGTTTTATCTTT
65 TGACTCATAGTTTCATTTCGATCATTCATCTTTAACCTCGACTCGATCTTGATCGTTTTATCTTT
* *
5330829 TAGACTCATAGTTTCGTATCGATCATCCGATCTCGACTTAATCCAGA
130 TAGACTCATAGTTTC-TATCGATCATCCGATCTCGACTCAATCCAAA
* * * * **
5330876 TTATTTTTCAGACTTGTGACTCAATCTCGGTCATTCAATCTTCTCTCAATCCATATCATTTTTTT
1 TTATTTTTTAGACTTGTGACTCAATCTCGGTCATTCAATCTTCGCTCAACCCAAATCATTTACTT
* * *
5330941 GACTCACTA-TTTCATTTGGATCATTCATCTTTGATCTCGACTCGAT-TCTGATCGTTTTATCTT
66 GACTCA-TAGTTTCATTTCGATCATTCATCTTTAACCTCGACTCGATCT-TGATCGTTTTATCTT
* * ** * * * *
5331004 TTAGACTCGTGGTTT-TATCCTGATTGTTCGATTTCGGCTCAATCTAAA
129 TTAGACTCATAGTTTCTAT-C-GATCATCCGATCTCGACTCAATCCAAA
* * * * *
5331052 TTATTTTTTTGACTTGCGATTCAATCTTGATCATTCA
1 TTATTTTTTAGACTTGTGACTCAATCTCGGTCATTCA
5331089 TTTTTAACCA
Statistics
Matches: 174, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
174 3 0.02
175 2 0.01
176 166 0.95
177 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.44
Consensus pattern (175 bp):
TTATTTTTTAGACTTGTGACTCAATCTCGGTCATTCAATCTTCGCTCAACCCAAATCATTTACTT
GACTCATAGTTTCATTTCGATCATTCATCTTTAACCTCGACTCGATCTTGATCGTTTTATCTTTT
AGACTCATAGTTTCTATCGATCATCCGATCTCGACTCAATCCAAA
Found at i:5331688 original size:121 final size:120
Alignment explanation
Indices: 5331292--5331689 Score: 372
Period size: 121 Copynumber: 3.3 Consensus size: 120
5331282 TCTTGATCAT
* * * * * ** * *
5331292 TTTATCTTTTAGACTCATGATTTTATCTTGGTTATTTAATCTAGACTCAGTCTAGATCATTTTCT
1 TTTATCTTTTAGACTCATGATTTCATCTTGATCATTTGATCTCGGTTCAGTCCAGATCATTTTTT
* * * * * *
5331357 TGATTTGTGG-TTCAATTTTGGTCATTCATATTTGACATCGATTCGGTCCTAGTCAC
66 TGACTTGTGGTTTC-ATTTCGGTCATTCAT-TTTAACCTCGACTCGGTCCTAGTCGC
* * * * * *
5331413 TTTATTTTTTAGACTTATGA-CTCAGTCCCTG-TCATTCGATCTCGGTTCAG-CCTAGGTCATTT
1 TTTATCTTTTAGACTCATGATTTCA-T-CTTGATCATTTGATCTCGGTTCAGTCC-AGATCATTT
* * * * * * *
5331475 TTCTGACTCGTGATTTCATTTCGGTCATTCATTTTTTACCTCAACTTGATCCTAGTCGC
63 TTTTGACTTGTGGTTTCATTTCGGTCATTCA-TTTTAACCTCGACTCGGTCCTAGTCGC
* * ** * *
5331534 TTTATTTTTTAGACTTATGATTTTGTCTCGATCATTTGATCTCGGTTCAGTCCAGATTATTTTTT
1 TTTATCTTTTAGACTCATGATTTCATCTTGATCATTTGATCTCGGTTCAGTCCAGATCATTTTTT
* * *
5331599 TGACTTGTGGTTTCATTTCGATCATTTATTTTCAACCTCGACTCGGTCCTAGTTGC
66 TGACTTGTGGTTTCATTTCGGTCATTCATTTT-AACCTCGACTCGGTCCTAGTCGC
5331655 TTTATCTTTTAGACTCATGATTTCATCTTGATCAT
1 TTTATCTTTTAGACTCATGATTTCATCTTGATCAT
5331690 CCAATCTCGA
Statistics
Matches: 219, Mismatches: 49, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
120 9 0.04
121 200 0.91
122 10 0.05
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (120 bp):
TTTATCTTTTAGACTCATGATTTCATCTTGATCATTTGATCTCGGTTCAGTCCAGATCATTTTTT
TGACTTGTGGTTTCATTTCGGTCATTCATTTTAACCTCGACTCGGTCCTAGTCGC
Found at i:5335232 original size:12 final size:12
Alignment explanation
Indices: 5335179--5335238 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
5335169 GTGTTTTTAC
5335179 TTTA-TTTATCTA
1 TTTATTTTAT-TA
* *
5335191 TATATTTTTTTA
1 TTTATTTTATTA
5335203 TTTATCCTTT-TTA
1 TTTAT--TTTATTA
5335216 TTTTATTTTATTA
1 -TTTATTTTATTA
5335229 TTTATTTTAT
1 TTTATTTTAT
5335239 CTTACTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 22 0.55
13 10 0.25
14 8 0.20
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:5335234 original size:17 final size:18
Alignment explanation
Indices: 5335212--5335249 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5335202 ATTTATCCTT
*
5335212 TTTATTTTATTTTA-TTA
1 TTTATTTTATCTTACTTA
5335229 TTTATTTTATCTTACTTA
1 TTTATTTTATCTTACTTA
5335247 TTT
1 TTT
5335250 GTTATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTATCTTACTTA
Found at i:5335301 original size:19 final size:19
Alignment explanation
Indices: 5335279--5335317 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5335269 ATTTTCTTAT
*
5335279 ATTTATCTAATTTTTTAAA
1 ATTTATCTAATTATTTAAA
*
5335298 ATTTATCTAGTTATTTAAA
1 ATTTATCTAATTATTTAAA
5335317 A
1 A
5335318 AAAAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTATCTAATTATTTAAA
Found at i:5335785 original size:18 final size:18
Alignment explanation
Indices: 5335764--5335813 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5335754 ATTTTTTTTC
*
5335764 TTTATTTTATTAGTT-CTA
1 TTTATTTAATTA-TTACTA
*
5335782 TTTATTTAATTATTATTA
1 TTTATTTAATTATTACTA
*
5335800 TTTATTTATTTATT
1 TTTATTTAATTATT
5335814 TGTGATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTACTA
Found at i:5337139 original size:26 final size:26
Alignment explanation
Indices: 5337110--5337165 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
5337100 ATGTCTAATT
*
5337110 ATAAATTTACGGATCTATATATCATG
1 ATAAATATACGGATCTATATATCATG
* * *
5337136 ATAAATATATGGATCTATATGTTATG
1 ATAAATATACGGATCTATATATCATG
5337162 ATAA
1 ATAA
5337166 TGTTCACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (26 bp):
ATAAATATACGGATCTATATATCATG
Found at i:5340178 original size:34 final size:32
Alignment explanation
Indices: 5340116--5340178 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
5340106 TTTTTATAAA
* * *
5340116 ATATAATATAGATATATAAATTTTAATATTTT
1 ATATAACATAAATATATAAATTTAAATATTTT
5340148 ATATAACATAAATATATAAATGATTAAATAT
1 ATATAACATAAATATATAAAT--TTAAATAT
5340179 AATATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
34 7 0.27
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (32 bp):
ATATAACATAAATATATAAATTTAAATATTTT
Found at i:5340575 original size:19 final size:17
Alignment explanation
Indices: 5340551--5340585 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
5340541 GAACTGAATT
5340551 TTAAATTTTAATATTTAAA
1 TTAAA-TTTAA-ATTTAAA
5340570 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAA
5340586 TACTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:5341896 original size:17 final size:16
Alignment explanation
Indices: 5341862--5341920 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
5341852 CATTAATGAT
* *
5341862 TAATTAAGTTCATGAA
1 TAATTAAATTCATAAA
5341878 TAATATAAATTCATAAA
1 TAAT-TAAATTCATAAA
*
5341895 TAATTAAATTTATAAA
1 TAATTAAATTCATAAA
*
5341911 TAATTGAATT
1 TAATTAAATT
5341921 TGTGCAACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 24 0.63
17 14 0.37
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
TAATTAAATTCATAAA
Found at i:5342557 original size:17 final size:18
Alignment explanation
Indices: 5342530--5342563 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5342520 AAAATTACCA
5342530 AAAAAATTAAAAATTGAG
1 AAAAAATTAAAAATTGAG
*
5342548 AAAAAA-TAAAACTTGA
1 AAAAAATTAAAAATTGA
5342564 TATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (18 bp):
AAAAAATTAAAAATTGAG
Found at i:5345982 original size:15 final size:15
Alignment explanation
Indices: 5345964--5345998 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5345954 TTATTTAAAT
5345964 TTTATTTGATTA-TTA
1 TTTATTT-ATTATTTA
5345979 TTTATTTATTATTTA
1 TTTATTTATTATTTA
5345994 TTTAT
1 TTTAT
5345999 AATAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:5346031 original size:17 final size:17
Alignment explanation
Indices: 5346011--5346043 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5346001 TAATATTAAA
*
5346011 ATTTTATTTTTATTTTT
1 ATTTTAATTTTATTTTT
5346028 ATTTTAATTTTATTTT
1 ATTTTAATTTTATTTT
5346044 AAAATTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTAATTTTATTTTT
Found at i:5346043 original size:11 final size:11
Alignment explanation
Indices: 5346010--5346045 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5346000 ATAATATTAA
5346010 AATTTTATTTTT
1 AATTTTA-TTTT
*
5346022 ATTTTTATTTT
1 AATTTTATTTT
5346033 AATTTTATTTT
1 AATTTTATTTT
5346044 AA
1 AA
5346046 AATTCGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:5346133 original size:14 final size:14
Alignment explanation
Indices: 5346068--5346156 Score: 52
Period size: 14 Copynumber: 6.9 Consensus size: 14
5346058 TTTATTTTGT
* *
5346068 TTTATTTATTTAAA
1 TTTATTTATATATA
*
5346082 TTTTTTTATCATA-A
1 TTTATTTAT-ATATA
5346096 TTTA-TT-TAT-TA
1 TTTATTTATATATA
*
5346107 TTTA--TAAATATA
1 TTTATTTATATATA
5346119 TTTATTTATATATA
1 TTTATTTATATATA
* *
5346133 TTT-GTGA-ATATA
1 TTTATTTATATATA
5346145 TTTATTTA-ATAT
1 TTTATTTATATAT
5346157 TTATGAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 1 0.02
11 9 0.15
12 15 0.25
13 10 0.17
14 22 0.37
15 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTATTTATATATA
Found at i:5346174 original size:22 final size:23
Alignment explanation
Indices: 5346095--5346176 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
5346085 TTTTATCATA
* *
5346095 ATTTATTTATTATTTATAAATAT
1 ATTTATTTAATATTTATGAATAT
*
5346118 ATTTATTTATATATATTTGTGAATAT
1 ATTTA-TT-TA-ATATTTATGAATAT
5346144 ATTTATTTAATATTTATGAATA-
1 ATTTATTTAATATTTATGAATAT
*
5346166 ATTTTTTTAAT
1 ATTTATTTAAT
5346177 TTAATTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.20
23 17 0.33
24 4 0.08
25 4 0.08
26 16 0.31
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTTATTTAATATTTATGAATAT
Found at i:5346174 original size:26 final size:26
Alignment explanation
Indices: 5346095--5346181 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
5346085 TTTTATCATA
* *
5346095 ATTTATTTATTATTTATAAATATATTT
1 ATTTATTTAATATTTATGAATA-ATTT
* *
5346122 ATTTATAT-ATATTTGTGAAT-A--T
1 ATTTATTTAATATTTATGAATAATTT
5346144 ATTTATTTAATATTTATGAATAATTT
1 ATTTATTTAATATTTATGAATAATTT
*
5346170 TTTTAATTTAAT
1 ATTT-ATTTAAT
5346182 TAAATTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
22 8 0.17
23 11 0.23
24 2 0.04
26 13 0.27
27 14 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTTATTTAATATTTATGAATAATTT
Found at i:5346623 original size:12 final size:12
Alignment explanation
Indices: 5346598--5346659 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 12
5346588 ATATTTTATA
5346598 AATTT-ATA-GT
1 AATTTAATATGT
5346608 AATTTAATATGT
1 AATTTAATATGT
5346620 AA-TTAA-ATGT
1 AATTTAATATGT
* *
5346630 TATGT-A-AT-T
1 AATTTAATATGT
5346639 AATTTAATATGT
1 AATTTAATATGT
5346651 AATTTAATA
1 AATTTAATA
5346660 AAAATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.10
10 14 0.33
11 10 0.24
12 14 0.33
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AATTTAATATGT
Found at i:5355474 original size:7 final size:7
Alignment explanation
Indices: 5355464--5355488 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5355454 AAAAATAGAA
5355464 AAAAGAC
1 AAAAGAC
5355471 AAAAGAC
1 AAAAGAC
5355478 AAAAGAC
1 AAAAGAC
5355485 AAAA
1 AAAA
5355489 AAAAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAC
Found at i:5355495 original size:14 final size:14
Alignment explanation
Indices: 5355462--5355495 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5355452 ATAAAAATAG
*
5355462 AAAAAAGACAAAAG
1 AAAAAAGACAAAAA
*
5355476 ACAAAAGACAAAAA
1 AAAAAAGACAAAAA
5355490 AAAAAA
1 AAAAAA
5355496 ACCAAGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAGACAAAAA
Found at i:5355567 original size:17 final size:16
Alignment explanation
Indices: 5355545--5355586 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5355535 AAGATATTAA
5355545 ATAATAATTTAGTAAAT
1 ATAATAATTTA-TAAAT
*
5355562 ATAATACATATATAAAT
1 ATAATA-ATTTATAAAT
5355579 ATAA-AATT
1 ATAATAATT
5355587 AAAATGGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 1 0.05
17 15 0.68
18 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAATAATTTATAAAT
Found at i:5356214 original size:28 final size:28
Alignment explanation
Indices: 5356173--5356229 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
5356163 GATGTAATTT
*
5356173 AAAAAAAAGAAAAGAAGA-GAGAAAGAAA
1 AAAAAAAACAAAAGAAGATGA-AAAGAAA
*
5356201 AAAAAAAACTAAAGAAGATGAAAAGAAA
1 AAAAAAAACAAAAGAAGATGAAAAGAAA
5356229 A
1 A
5356230 TAAGTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (28 bp):
AAAAAAAACAAAAGAAGATGAAAAGAAA
Found at i:5356385 original size:15 final size:15
Alignment explanation
Indices: 5356365--5356394 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5356355 TTTAAATTAT
5356365 AAAATAAAATAATAA
1 AAAATAAAATAATAA
*
5356380 AAAATATAATAATAA
1 AAAATAAAATAATAA
5356395 TGATAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAAAATAATAA
Found at i:5356696 original size:10 final size:11
Alignment explanation
Indices: 5356677--5356735 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
5356667 CAAAAAAGTT
*
5356677 AAAATAAAAAA
1 AAAAGAAAAAA
5356688 AAAAGAAAACAA
1 AAAAGAAAA-AA
* *
5356700 AAAATATAAAA
1 AAAAGAAAAAA
5356711 AAAAGTAAAAAA
1 AAAAG-AAAAAA
5356723 GAAAAGCAAAAAA
1 -AAAAG-AAAAAA
5356736 CCCATCCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 14 0.36
12 14 0.36
13 11 0.28
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:5356734 original size:24 final size:22
Alignment explanation
Indices: 5356683--5356735 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
5356673 AGTTAAAATA
*
5356683 AAAAAAAAAGAAAACAAAAAAT
1 AAAAAAAAAGAAAACAAAAAAC
5356705 ATAAAAAAAAGTAAAA-AAGAAAAGC
1 A-AAAAAAAAG-AAAACAA-AAAA-C
5356730 AAAAAA
1 AAAAAA
5356736 CCCATCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 11 0.42
24 13 0.50
25 1 0.04
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.06
Consensus pattern (22 bp):
AAAAAAAAAGAAAACAAAAAAC
Found at i:5357526 original size:22 final size:23
Alignment explanation
Indices: 5357498--5357540 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5357488 TAAATTTTTA
5357498 GTAAAAAG-GAAATACAAAAAGG
1 GTAAAAAGAGAAATACAAAAAGG
*
5357520 GTAAAAAGAGAAATAGAAAAA
1 GTAAAAAGAGAAATACAAAAA
5357541 AAATGGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.09
Consensus pattern (23 bp):
GTAAAAAGAGAAATACAAAAAGG
Found at i:5357665 original size:20 final size:21
Alignment explanation
Indices: 5357642--5357682 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5357632 ATTGAAATAG
5357642 AAAAGTA-AAAAAAAAAACCA
1 AAAAGTAGAAAAAAAAAACCA
*
5357662 AAAAGTATGAAAAAGAAAACC
1 AAAAGTA-GAAAAAAAAAACC
5357683 TAACGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAGTAGAAAAAAAAAACCA
Found at i:5357890 original size:2 final size:2
Alignment explanation
Indices: 5357883--5357912 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5357873 ATCCATACCT
*
5357883 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5357913 CATTCAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5368521 original size:90 final size:90
Alignment explanation
Indices: 5368409--5368592 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 90
5368399 AGTTAAAAGA
* *
5368409 TAAATCTAGTCAAACCTAGTAAACTGGAAATTCTACTCATCAACAAATTAGGTT-CCCAGAATTA
1 TAAATCTAGTCAAACCTAGTAAACTGGAAATACTACTCATCAACAAATCAGGTTCCCCAGAATTA
5368473 AGACATGTTAGATTTAAGTTTAAAAC
66 AGACATGTTAGATTTAAGTTT-AAAC
* * *
5368499 TAAATCTAGTCAAGCCTAGTAAACTGGAAATAGTATTCATCAACAAATCAGGTTCCCCAGAATTA
1 TAAATCTAGTCAAACCTAGTAAACTGGAAATACTACTCATCAACAAATCAGGTTCCCCAGAATTA
5368564 AGACATGTTAGATTTAAGTTTAAAC
66 AGACATGTTAGATTTAAGTTTAAAC
5368589 TAAA
1 TAAA
5368593 CTTTAACATG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 57 0.65
91 31 0.35
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.29
Consensus pattern (90 bp):
TAAATCTAGTCAAACCTAGTAAACTGGAAATACTACTCATCAACAAATCAGGTTCCCCAGAATTA
AGACATGTTAGATTTAAGTTTAAAC
Found at i:5378405 original size:22 final size:22
Alignment explanation
Indices: 5378378--5378422 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5378368 AATTTTTGTC
*
5378378 TTTAATTCT-AGAGATATAAATA
1 TTTAATTCTAAG-GATACAAATA
5378400 TTTAATTCTAAGGATACAAATA
1 TTTAATTCTAAGGATACAAATA
5378422 T
1 T
5378423 AAATATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTAATTCTAAGGATACAAATA
Found at i:5386709 original size:26 final size:27
Alignment explanation
Indices: 5386675--5386725 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
5386665 GAAGGTAGAA
5386675 CTGATAAAATGTGATGGCAA-AATTTGG
1 CTGATAAAATG-GATGGCAAGAATTTGG
*
5386702 CTGA-AAAATGGCTGGCAAGAATTT
1 CTGATAAAATGGATGGCAAGAATTT
5386726 TCAAATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (27 bp):
CTGATAAAATGGATGGCAAGAATTTGG
Found at i:5389507 original size:15 final size:15
Alignment explanation
Indices: 5389455--5389507 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5389445 TTTTTAAATT
*
5389455 AATAAATTTATCTTTA
1 AATAAATTTA-ATTTA
*
5389471 AATATA-TTAATTTA
1 AATAAATTTAATTTA
*
5389485 ATTAAATTTAATTTA
1 AATAAATTTAATTTA
*
5389500 AATCAATT
1 AATAAATT
5389508 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.27
15 17 0.57
16 5 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAAATTTAATTTA
Found at i:5389508 original size:29 final size:29
Alignment explanation
Indices: 5389448--5389519 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
5389438 TTATAAATTT
*
5389448 TTAAATTAATAAATTTATCTTTAAATATA
1 TTAAATTAATAAATTTATATTTAAATATA
*
5389477 TTAATTTAATTAAATTTA-ATTTAAATCA-A
1 TTAAATTAA-TAAATTTATATTTAAAT-ATA
5389506 TTAAAATTAA-AAAT
1 TT-AAATTAATAAAT
5389520 AGAGTTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.11
29 18 0.49
30 15 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAATTAATAAATTTATATTTAAATATA
Found at i:5389559 original size:14 final size:14
Alignment explanation
Indices: 5389540--5389566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5389530 TAAAATTAAA
5389540 TTTAATTTTAAAAT
1 TTTAATTTTAAAAT
5389554 TTTAATTTTAAAA
1 TTTAATTTTAAAA
5389567 GAATTAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTTAAAAT
Found at i:5390527 original size:17 final size:17
Alignment explanation
Indices: 5390507--5390542 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5390497 TATTTAATTT
5390507 TTCTCAATTGTATTAAA
1 TTCTCAATTGTATTAAA
5390524 TTCTCAATTGTATTAAA
1 TTCTCAATTGTATTAAA
5390541 TT
1 TT
5390543 TATTTGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTCAATTGTATTAAA
Found at i:5391839 original size:105 final size:105
Alignment explanation
Indices: 5391712--5391922 Score: 404
Period size: 105 Copynumber: 2.0 Consensus size: 105
5391702 AGATTAAGGG
*
5391712 AAAAAAGTTTAAATAAAAAACTTTTAAATTGTTATGGAAGATAAATAACTAATGTTTGATTTTGA
1 AAAAAAGTTTAAATAAAAAACTTTTAAATTGTTATAGAAGATAAATAACTAATGTTTGATTTTGA
*
5391777 TCGGGTTATTATTTCAATTCATTTTTGGTTATGTTCACTC
66 TCGGATTATTATTTCAATTCATTTTTGGTTATGTTCACTC
5391817 AAAAAAGTTTAAATAAAAAACTTTTAAATTGTTATAGAAGATAAATAACTAATGTTTGATTTTGA
1 AAAAAAGTTTAAATAAAAAACTTTTAAATTGTTATAGAAGATAAATAACTAATGTTTGATTTTGA
5391882 TCGGATTATTATTTCAATTCATTTTTGGTTATGTTCACTC
66 TCGGATTATTATTTCAATTCATTTTTGGTTATGTTCACTC
5391922 A
1 A
5391923 TTTTGGGTTT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (105 bp):
AAAAAAGTTTAAATAAAAAACTTTTAAATTGTTATAGAAGATAAATAACTAATGTTTGATTTTGA
TCGGATTATTATTTCAATTCATTTTTGGTTATGTTCACTC
Found at i:5393410 original size:22 final size:22
Alignment explanation
Indices: 5393380--5393515 Score: 96
Period size: 22 Copynumber: 6.2 Consensus size: 22
5393370 GTAATCATTT
* *
5393380 ATAATTTAATAGTAAATTAATG
1 ATAACTTAATAGTAAATTAATA
5393402 ATAACTTAATAGTAAATTAATA
1 ATAACTTAATAGTAAATTAATA
* ** * *
5393424 ACAGTTTAGTAGTAAA-TAATTG
1 ATAACTTAATAGTAAATTAA-TA
** *
5393446 ATAACTTTTTAGTAAATTAGTA
1 ATAACTTAATAGTAAATTAATA
* *
5393468 ATAA-TATAATAATATATTAATA
1 ATAACT-TAATAGTAAATTAATA
* * * *
5393490 ATACCTTAATGGTAAATAAATT
1 ATAACTTAATAGTAAATTAATA
5393512 ATAA
1 ATAA
5393516 TATAGTTATG
Statistics
Matches: 84, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
21 4 0.05
22 77 0.92
23 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATA
Found at i:5393421 original size:11 final size:11
Alignment explanation
Indices: 5393385--5393423 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5393375 CATTTATAAT
5393385 TTAATAGTAAA
1 TTAATAGTAAA
*
5393396 TTAAT-GATAAC
1 TTAATAG-TAAA
5393407 TTAATAGTAAA
1 TTAATAGTAAA
5393418 TTAATA
1 TTAATA
5393424 ACAGTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (11 bp):
TTAATAGTAAA
Found at i:5393464 original size:66 final size:65
Alignment explanation
Indices: 5393364--5393490 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 65
5393354 TCAGTATAAC
* * * *
5393364 TTAGTAGTAATCATTTATAATTTAATAGTAAATTAATGATAACT-TAATAGTAAATTAATAACAG
1 TTAGTAGTAATAATTGATAATTTAATAGTAAATTAATAATAA-TATAATAATAAATTAATAACAG
5393428 T
65 T
* * *
5393429 TTAGTAGTAAATAATTGATAACTTT-TTAGTAAATTAGTAATAATATAATAATATATTAATAA
1 TTAGTAGT-AATAATTGATAA-TTTAATAGTAAATTAATAATAATATAATAATAAATTAATAA
5393491 TACCTTAATG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
65 9 0.17
66 40 0.77
67 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (65 bp):
TTAGTAGTAATAATTGATAATTTAATAGTAAATTAATAATAATATAATAATAAATTAATAACAGT
Found at i:5393615 original size:11 final size:11
Alignment explanation
Indices: 5393600--5393638 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5393590 AATTAATTAT
5393600 TAATAACTTAGA
1 TAATAACTTA-A
*
5393612 -AATAAATTAA
1 TAATAACTTAA
5393622 TAATAACTTAA
1 TAATAACTTAA
5393633 TAATAA
1 TAATAA
5393639 ATTAGTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (11 bp):
TAATAACTTAA
Found at i:5393619 original size:22 final size:22
Alignment explanation
Indices: 5393589--5393662 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
5393579 TAAAATTTAT
* *
5393589 TAATTAATTATTAATAACTTAGA
1 TAATAAATTAATAATAACTTA-A
5393612 -AATAAATTAATAATAACTTAA
1 TAATAAATTAATAATAACTTAA
* * *
5393633 TAATAAATTAGTATTAATTTAA
1 TAATAAATTAATAATAACTTAA
*
5393655 TAGTAAAT
1 TAATAAAT
5393663 CAGTTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.02
22 43 0.98
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (22 bp):
TAATAAATTAATAATAACTTAA
Found at i:5393802 original size:22 final size:22
Alignment explanation
Indices: 5393614--5393830 Score: 76
Period size: 22 Copynumber: 10.2 Consensus size: 22
5393604 AACTTAGAAA
* * *
5393614 TAAATTAATAATAACTTAATAA
1 TAAATTAGTGATAACTTAATAG
*
5393636 TAAATTAGT-ATTAATTTAATAG
1 TAAATTAGTGA-TAACTTAATAG
* ** *
5393658 TAAATCAGTTTTAATTTAATA-
1 TAAATTAGTGATAACTTAATAG
* * * *
5393679 TTAATTAAT--TGA--TAGTAG
1 TAAATTAGTGATAACTTAATAG
* * * *
5393697 TAAATAATTGATAATTTAGTAG
1 TAAATTAGTGATAACTTAATAG
* * * * *
5393719 TTAATCATTGA-AACTTAAAAA
1 TAAATTAGTGATAACTTAATAG
*
5393740 TAAATTAGT-ATAACTTAGTAG
1 TAAATTAGTGATAACTTAATAG
* * *
5393761 TAAATTATTAATAACATAATAG
1 TAAATTAGTGATAACTTAATAG
* * *
5393783 TTAATTAGTGATAATTTAATAA
1 TAAATTAGTGATAACTTAATAG
* *
5393805 TAAATCA-TGCATAATTTAATA-
1 TAAATTAGTG-ATAACTTAATAG
5393826 TAAAT
1 TAAAT
5393831 CCATAATAAA
Statistics
Matches: 148, Mismatches: 37, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
17 4 0.03
18 6 0.04
19 2 0.01
20 3 0.02
21 41 0.28
22 92 0.62
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (22 bp):
TAAATTAGTGATAACTTAATAG
Found at i:5393842 original size:22 final size:21
Alignment explanation
Indices: 5393793--5393846 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
5393783 TTAATTAGTG
*
5393793 ATAATTTAATAATAAATCATGC
1 ATAATTTAAT-ATAAATCATGA
5393815 ATAATTTAATATAAATCCAT-A
1 ATAATTTAATATAAAT-CATGA
*
5393836 ATAAATTAATA
1 ATAATTTAATA
5393847 ATAACCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATTTAATATAAATCATGA
Found at i:5393847 original size:11 final size:11
Alignment explanation
Indices: 5393733--5393887 Score: 75
Period size: 11 Copynumber: 14.3 Consensus size: 11
5393723 TCATTGAAAC
*
5393733 TTAAAAATAAA
1 TTAATAATAAA
* *
5393744 TTAGT-ATAAC
1 TTAATAATAAA
* *
5393754 TTAGTAGTAAA
1 TTAATAATAAA
*
5393765 TTATTAATAACA
1 TTAATAATAA-A
* *
5393777 -TAATAGTTAA
1 TTAATAATAAA
* * *
5393787 TTAGTGATAAT
1 TTAATAATAAA
5393798 TTAATAATAAA
1 TTAATAATAAA
* * *
5393809 -TCATGCATAAT
1 TTAAT-AATAAA
5393820 TTAAT-ATAAA
1 TTAATAATAAA
**
5393830 TCCATAATAAA
1 TTAATAATAAA
*
5393841 TTAATAATAAC
1 TTAATAATAAA
*
5393852 CTAATAATAAA
1 TTAATAATAAA
* *
5393863 TTAGTAATAAT
1 TTAATAATAAA
*
5393874 TTAATAGTAAA
1 TTAATAATAAA
5393885 TTA
1 TTA
5393888 GTTTTAATTT
Statistics
Matches: 102, Mismatches: 36, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
10 20 0.20
11 78 0.76
12 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (11 bp):
TTAATAATAAA
Found at i:5394006 original size:43 final size:44
Alignment explanation
Indices: 5393952--5394055 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 44
5393942 CAAATCAATA
* * *
5393952 ATAAATTAGTAGTTAATAATTGAAAACTTAAAAATAAATTAG-T
1 ATAATTTAGTAGTAAATAATTGAAAACATAAAAATAAATTAGTT
* * * * *
5393995 ATAATTTAGTAGTAAATTATTGATAACATAATAGTTAATTAGTT
1 ATAATTTAGTAGTAAATAATTGAAAACATAAAAATAAATTAGTT
* *
5394039 ATAATTTAATAATAAAT
1 ATAATTTAGTAGTAAAT
5394056 CATGCATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 34 0.68
44 16 0.32
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (44 bp):
ATAATTTAGTAGTAAATAATTGAAAACATAAAAATAAATTAGTT
Found at i:5394231 original size:19 final size:19
Alignment explanation
Indices: 5394209--5394313 Score: 77
Period size: 19 Copynumber: 5.2 Consensus size: 19
5394199 ATAATAAATC
5394209 ATTAATAATTTAATAGTAA
1 ATTAATAATTTAATAGTAA
* **
5394228 ATTAATAACTTAGCAGTAA
1 ATTAATAATTTAATAGTAA
* * *
5394247 ATCATTAATGTAATAGTAA
1 ATTAATAATTTAATAGTAA
*
5394266 ATTACTAATAATTTGATTA-TAA
1 A-T--TAATAATTT-AATAGTAA
5394288 ATTAGTAATAATTTAATAGTAA
1 A-T--TAATAATTTAATAGTAA
5394310 ATTA
1 ATTA
5394314 GTTAATTATT
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
19 32 0.48
20 1 0.02
21 4 0.06
22 26 0.39
23 3 0.05
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.40
Consensus pattern (19 bp):
ATTAATAATTTAATAGTAA
Found at i:5394315 original size:22 final size:21
Alignment explanation
Indices: 5393837--5394313 Score: 145
Period size: 22 Copynumber: 22.3 Consensus size: 21
5393827 AAATCCATAA
** *
5393837 TAAATTAATAATAACCTAATAA
1 TAAATT-ATAATAATTTAATAG
5393859 TAAATTAGTAATAATTTAATAG
1 TAAATTA-TAATAATTTAATAG
**
5393881 TAAATTAGTTTTAATTTAATA-
1 TAAATTA-TAATAATTTAATAG
* * * *
5393902 TTAATTA-ATTGA--TAGTAG
1 TAAATTATAATAATTTAATAG
* *
5393920 TAAATCATAAATAATTTAGTAG
1 TAAATTAT-AATAATTTAATAG
* * * *
5393942 CAAATCAATAATAAATTAGTAG
1 TAAAT-TATAATAATTTAATAG
* * * * *
5393964 TTAATAATTGAA-AACTTAAAAA
1 TAAATTA-T-AATAATTTAATAG
*
5393986 TAAATTAGT-ATAATTTAGTAG
1 TAAATTA-TAATAATTTAATAG
* **
5394007 TAAATTATTGATAACATAATAG
1 TAAATTA-TAATAATTTAATAG
* * *
5394029 TTAATTAGTTATAATTTAATAA
1 TAAATTA-TAATAATTTAATAG
* *
5394051 TAAATCATGCATAATTTAATA-
1 TAAATTAT-AATAATTTAATAG
* * *
5394072 TAAATCTATAATAACTTGATCG
1 TAAAT-TATAATAATTTAATAG
* ** *
5394094 TAAATCATAGATAATTTGGTAA
1 TAAATTATA-ATAATTTAATAG
* * **
5394116 TAAATCAAAGATAATTTTGTAG
1 TAAATTATA-ATAATTTAATAG
** * *
5394138 TAAAAAATAAAAAATTTAGTA-
1 TAAATTAT-AATAATTTAATAG
* * **
5394159 TAAA-AATGATAACATAATAG
1 TAAATTATAATAATTTAATAG
* *
5394179 TAAATATATAAATAAATATAATAA
1 TAAAT-TAT-AAT-AATTTAATAG
*
5394203 TAAATCATTAATAATTTAATAG
1 TAAATTA-TAATAATTTAATAG
* **
5394225 TAAA-T-TAATAACTTAGCAG
1 TAAATTATAATAATTTAATAG
* *
5394244 TAAATCAT--TAATGTAATAG
1 TAAATTATAATAATTTAATAG
*
5394263 TAAATTACTAATAATTTGATTA-
1 TAAATTA-TAATAATTT-AATAG
5394285 TAAATTAGTAATAATTTAATAG
1 TAAATTA-TAATAATTTAATAG
5394307 TAAATTA
1 TAAATTA
5394314 GTTAATTATT
Statistics
Matches: 340, Mismatches: 86, Indels: 58
0.70 0.18 0.12
Matches are distributed among these distances:
17 4 0.01
18 5 0.01
19 38 0.11
20 12 0.04
21 48 0.14
22 205 0.60
23 14 0.04
24 14 0.04
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (21 bp):
TAAATTATAATAATTTAATAG
Found at i:5394451 original size:65 final size:66
Alignment explanation
Indices: 5394382--5394508 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 66
5394372 TCTTTATAAT
* * * *
5394382 AATCATTAGTAACTTAGTGGTAAATCATCAATAATTTAACA-AAAATCATTCATAACTTAATGAT
1 AATCATTAGTAAATTAGTAGCAAATAATCAATAATTTAACAGAAAATCATTCATAACTTAATGAT
5394446 A
66 A
* * * * * *
5394447 AATCATTTGTAAATTAGTAGCAAATAATTAATAATTTAATAGTAAATTATTGATAACTTAAT
1 AATCATTAGTAAATTAGTAGCAAATAATCAATAATTTAACAGAAAATCATTCATAACTTAAT
5394509 ACAAATAACT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
65 34 0.67
66 17 0.33
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (66 bp):
AATCATTAGTAAATTAGTAGCAAATAATCAATAATTTAACAGAAAATCATTCATAACTTAATGAT
A
Found at i:5394452 original size:22 final size:22
Alignment explanation
Indices: 5394382--5394453 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
5394372 TCTTTATAAT
* *
5394382 AATCATT-AGTAACTTAGTGGTA
1 AATCATTCA-TAACTTAATGATA
* * *
5394404 AATCA-TCAATAATTTAA-CAAA
1 AATCATTC-ATAACTTAATGATA
5394425 AATCATTCATAACTTAATGATA
1 AATCATTCATAACTTAATGATA
5394447 AATCATT
1 AATCATT
5394454 TGTAAATTAG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 15 0.39
22 22 0.58
23 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (22 bp):
AATCATTCATAACTTAATGATA
Found at i:5394502 original size:22 final size:22
Alignment explanation
Indices: 5394424--5394529 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 22
5394414 AATTTAACAA
* *
5394424 AAATCATTCATAACTTAAT-GAT
1 AAATAATTAATAACTTAATAG-T
* ** * * *
5394446 AAATCATTTGTAAATTAGTAGC
1 AAATAATTAATAACTTAATAGT
*
5394468 AAATAATTAATAATTTAATAGT
1 AAATAATTAATAACTTAATAGT
* * *
5394490 AAATTATTGATAACTTAATA-C
1 AAATAATTAATAACTTAATAGT
*
5394511 AAATAACTAATAACTTAAT
1 AAATAATTAATAACTTAAT
5394530 TGTTGATCAT
Statistics
Matches: 65, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
21 16 0.25
22 48 0.74
23 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (22 bp):
AAATAATTAATAACTTAATAGT
Found at i:5394870 original size:22 final size:22
Alignment explanation
Indices: 5394774--5394952 Score: 105
Period size: 22 Copynumber: 8.1 Consensus size: 22
5394764 AACAACATAT
* **
5394774 TAATAAATCAATGATAGGTTAA
1 TAATAAATTAATGATAATTTAA
* *
5394796 TAA-AAAATAAGTGATAACTTAA
1 TAATAAATTAA-TGATAATTTAA
* * *
5394818 TAACAAATCAATGATAACTTAA
1 TAATAAATTAATGATAATTTAA
*** *
5394840 TAGCGAATTAGTGATAATTTAA
1 TAATAAATTAATGATAATTTAA
** *
5394862 TAATAAATTAATTTTAATTTAG
1 TAATAAATTAATGATAATTTAA
*
5394884 TAAT-TATTAATTGATAAATTTAA
1 TAATAAATTAA-TGAT-AATTTAA
* *
5394907 TAGTAAATCATAA--ATAATTTAG
1 TAATAAAT--TAATGATAATTTAA
* *
5394929 TAGTAAATTAATAATAATTTAA
1 TAATAAATTAATGATAATTTAA
5394951 TA
1 TA
5394953 CTTAATGTCA
Statistics
Matches: 122, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.02
21 10 0.08
22 88 0.72
23 16 0.13
24 2 0.02
26 3 0.02
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
TAATAAATTAATGATAATTTAA
Found at i:5395562 original size:16 final size:17
Alignment explanation
Indices: 5395541--5395578 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
5395531 AATTCATGAA
5395541 TTTATTTTG-AAATATT
1 TTTATTTTGAAAATATT
5395557 TTTA-TTTGAAAATATT
1 TTTATTTTGAAAATATT
5395573 TTTATT
1 TTTATT
5395579 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 15 0.75
17 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTATTTTGAAAATATT
Found at i:5395706 original size:16 final size:15
Alignment explanation
Indices: 5395679--5395730 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 15
5395669 ATTTAATATT
* *
5395679 AAAAAATGA-AAACA
1 AAAAAATAATAAAAA
*
5395693 AAAAAATTATAAAAA
1 AAAAAATAATAAAAA
*
5395708 TAAAAAATAATAAGAA
1 -AAAAAATAATAAAAA
5395724 AAAAAAT
1 AAAAAAT
5395731 GAAATCTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 13 0.41
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAAAATAATAAAAA
Found at i:5396121 original size:13 final size:13
Alignment explanation
Indices: 5396102--5396134 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5396092 AACCTCATTG
5396102 AAAAATTCCAC-A
1 AAAAATTCCACTA
5396114 AGAAAATTCCACTA
1 A-AAAATTCCACTA
5396128 AAAAATT
1 AAAAATT
5396135 AAAGTATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 16 0.84
14 2 0.11
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAAATTCCACTA
Found at i:5396172 original size:10 final size:10
Alignment explanation
Indices: 5396157--5396200 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
5396147 CCAAACTCAG
*
5396157 AAAAAACCCA
1 AAAAAATCCA
*
5396167 AAAAAAT-CT
1 AAAAAATCCA
*
5396176 AAAAAATCTA
1 AAAAAATCCA
5396186 AAAAAATCCA
1 AAAAAATCCA
5396196 AAAAA
1 AAAAA
5396201 TCCTTAAACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATCCA
Found at i:5396179 original size:9 final size:9
Alignment explanation
Indices: 5396167--5396202 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
5396157 AAAAAACCCA
5396167 AAAAAATCT
1 AAAAAATCT
5396176 AAAAAATCT
1 AAAAAATCT
*
5396185 AAAAAAATCC
1 -AAAAAATCT
5396195 AAAAAATC
1 AAAAAATC
5396203 CTTAAACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAATCT
Found at i:5396181 original size:19 final size:19
Alignment explanation
Indices: 5396157--5396200 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5396147 CCAAACTCAG
*
5396157 AAAAAACCCAAAAAAATCT
1 AAAAAACCCAAAAAAATCC
* *
5396176 AAAAAATCTAAAAAAATCC
1 AAAAAACCCAAAAAAATCC
5396195 AAAAAA
1 AAAAAA
5396201 TCCTTAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAACCCAAAAAAATCC
Found at i:5396201 original size:19 final size:19
Alignment explanation
Indices: 5396166--5396202 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5396156 GAAAAAACCC
*
5396166 AAAAAAATCTAAAAAATCT
1 AAAAAAATCCAAAAAATCT
5396185 AAAAAAATCCAAAAAATC
1 AAAAAAATCCAAAAAATC
5396203 CTTAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAATCCAAAAAATCT
Found at i:5396588 original size:51 final size:51
Alignment explanation
Indices: 5396483--5396632 Score: 165
Period size: 51 Copynumber: 2.9 Consensus size: 51
5396473 TATTTGATTT
* * * * * ***
5396483 TCATTTTAATGAGAATTGATTTTGAAATCAAATCCCAAAAATTTCTCTTTA
1 TCATTTTAATGTGAATTGATTATGGAATTAAATCCCAAAAATCTCTCCACA
* *
5396534 TCATTTTAATGTGAATTGATTATGGAATTAAATCCCGATAATCTCTCCACA
1 TCATTTTAATGTGAATTGATTATGGAATTAAATCCCAAAAATCTCTCCACA
* * * *
5396585 TCATTTTTAATGTCAATTGATTCTAGAATTAAATCCAAAAAATCTCTC
1 TCA-TTTTAATGTGAATTGATTATGGAATTAAATCCCAAAAATCTCTC
5396633 AATCATGGTT
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
51 44 0.54
52 38 0.46
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (51 bp):
TCATTTTAATGTGAATTGATTATGGAATTAAATCCCAAAAATCTCTCCACA
Found at i:5396763 original size:22 final size:21
Alignment explanation
Indices: 5396735--5396823 Score: 64
Period size: 22 Copynumber: 4.4 Consensus size: 21
5396725 AACTTAGTAG
5396735 TAGTTAATTATCGATAACTTAA
1 TAGTTAATTAT-GATAACTTAA
5396757 TAGTT-A--A--ATAACTTAA
1 TAGTTAATTATGATAACTTAA
* *
5396773 TAGTAAATTATGGATAATTTAA
1 TAGTTAATTAT-GATAACTTAA
* *
5396795 TA-TAAATTAGTGATAACTTGA
1 TAGTTAATTA-TGATAACTTAA
*
5396816 TAATTAAT
1 TAGTTAAT
5396824 AATGGTTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
16 13 0.24
17 1 0.02
19 2 0.04
21 18 0.33
22 20 0.37
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.40
Consensus pattern (21 bp):
TAGTTAATTATGATAACTTAA
Found at i:5396769 original size:16 final size:15
Alignment explanation
Indices: 5396748--5396780 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5396738 TTAATTATCG
5396748 ATAACTTAATAGTTAA
1 ATAACTTAATAG-TAA
5396764 ATAACTTAATAGTAA
1 ATAACTTAATAGTAA
5396779 AT
1 AT
5396781 TATGGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAACTTAATAGTAA
Found at i:5396802 original size:21 final size:22
Alignment explanation
Indices: 5396764--5396845 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
5396754 TAATAGTTAA
*
5396764 ATAACTTAATAGTAAATTATGG
1 ATAACTTAATAATAAATTATGG
*
5396786 ATAATTTAAT-ATAAATTA-GTG
1 ATAACTTAATAATAAATTATG-G
* * *
5396807 ATAACTTGATAATTAATAATGG
1 ATAACTTAATAATAAATTATGG
* *
5396829 TTAATTTAATAATAAAT
1 ATAACTTAATAATAAAT
5396846 CTGTGATGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 16 0.34
22 29 0.62
23 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (22 bp):
ATAACTTAATAATAAATTATGG
Found at i:5396869 original size:44 final size:43
Alignment explanation
Indices: 5396764--5396870 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
5396754 TAATAGTTAA
* *
5396764 ATAACTTAATAGTAAATTATGGATAATTTAATATAAATTAGTG
1 ATAACTTGATAGTAAATAATGGATAATTTAATATAAATTAGTG
* * *
5396807 ATAACTTGATAATTAATAATGGTTAATTTAATAATAAATCT-GTG
1 ATAACTTGATAGTAAATAATGGATAATTTAAT-ATAAAT-TAGTG
* * *
5396851 ATGATTTTATAGTAAATAAT
1 ATAACTTGATAGTAAATAAT
5396871 CGAAAATTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 27 0.52
44 24 0.46
45 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (43 bp):
ATAACTTGATAGTAAATAATGGATAATTTAATATAAATTAGTG
Found at i:5396932 original size:44 final size:44
Alignment explanation
Indices: 5396884--5396999 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
5396874 AAATTAAGTA
* * * * *
5396884 GTAAATCAATTATAATGTAATAGTAAATCATTGATAATTTAAAT
1 GTAAATCAATTATAATTTAGTAGTAAATCACTAATAACTTAAAT
** * **
5396928 GTAAA-CTTTTGATAGTTTAGTAGTAAATCACTAATAACTTAGTT
1 GTAAATCAATT-ATAATTTAGTAGTAAATCACTAATAACTTAAAT
*
5396972 GTAAATCAATAATAATTTAGTAGTAAAT
1 GTAAATCAATTATAATTTAGTAGTAAAT
5397000 TAGTTAACCA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
43 3 0.05
44 51 0.91
45 2 0.04
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (44 bp):
GTAAATCAATTATAATTTAGTAGTAAATCACTAATAACTTAAAT
Found at i:5396969 original size:22 final size:22
Alignment explanation
Indices: 5396944--5396999 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
5396934 TTTTGATAGT
*
5396944 TTAGTAGTAAATCACTAATAAC
1 TTAGTAGTAAATCAATAATAAC
* *
5396966 TTAGTTGTAAATCAATAATAAT
1 TTAGTAGTAAATCAATAATAAC
5396988 TTAGTAGTAAAT
1 TTAGTAGTAAAT
5397000 TAGTTAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (22 bp):
TTAGTAGTAAATCAATAATAAC
Found at i:5397116 original size:22 final size:22
Alignment explanation
Indices: 5397062--5397251 Score: 118
Period size: 22 Copynumber: 8.7 Consensus size: 22
5397052 ACTTTATAAC
* *
5397062 AAATCATTAGTAACTTAGTA-T
1 AAATCATTAATAATTTAGTAGT
* *
5397083 -AATCATCAATAATTTAATAGT
1 AAATCATTAATAATTTAGTAGT
* *
5397104 AAATCATTTATAAATTAGTAGT
1 AAATCATTAATAATTTAGTAGT
5397126 AAATCTATGT--TAATTTAGTAGT
1 AAATC-AT-TAATAATTTAGTAGT
** * *
5397148 AAATTGTTGATAATTTAGAAGT
1 AAATCATTAATAATTTAGTAGT
* ** *
5397170 ATATCATTAATAGCTTAGTATT
1 AAATCATTAATAATTTAGTAGT
* * ** *
5397192 AAATTATTGATAAAATAATAGT
1 AAATCATTAATAATTTAGTAGT
* * * *
5397214 AAATTAATGATAACTTAGTAGT
1 AAATCATTAATAATTTAGTAGT
*
5397236 CAATCATTAATAATTT
1 AAATCATTAATAATTT
5397252 TCTTTTATAC
Statistics
Matches: 126, Mismatches: 37, Indels: 11
0.72 0.21 0.06
Matches are distributed among these distances:
20 16 0.13
21 2 0.02
22 105 0.83
23 2 0.02
24 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATCATTAATAATTTAGTAGT
Found at i:5397188 original size:66 final size:65
Alignment explanation
Indices: 5397091--5397248 Score: 149
Period size: 66 Copynumber: 2.4 Consensus size: 65
5397081 ATAATCATCA
* * ** * *
5397091 ATAATTTA-ATAGTAAATCATTTATAAATTAGTAGTAAATCTA-TGTTAATTTAGTAGTAAATTG
1 ATAATTTAGA-AGT-AATCATTAATAAATTAGTAGTAAAT-TATTGATAAAATAATAGTAAATTA
*
5397154 TTG
63 ATG
** *
5397157 ATAATTTAGAAGTATATCATTAATAGCTTAGTATTAAATTATTGATAAAATAATAGTAAATTAAT
1 ATAATTTAGAAGTA-ATCATTAATAAATTAGTAGTAAATTATTGATAAAATAATAGTAAATTAAT
5397222 G
65 G
* *
5397223 ATAACTTAGTAGTCAATCATTAATAA
1 ATAATTTAGAAGT-AATCATTAATAA
5397249 TTTTCTTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
65 3 0.04
66 70 0.93
67 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (65 bp):
ATAATTTAGAAGTAATCATTAATAAATTAGTAGTAAATTATTGATAAAATAATAGTAAATTAATG
Found at i:5397561 original size:21 final size:21
Alignment explanation
Indices: 5397535--5397607 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
5397525 CTAAAAGGTT
*
5397535 AATTATTAAAATTATATAAAA
1 AATTATCAAAATTATATAAAA
* * *
5397556 AATTATCAAAATTTTATCAAT
1 AATTATCAAAATTATATAAAA
* * *
5397577 AGTTATCAAAATTATTTAATA
1 AATTATCAAAATTATATAAAA
5397598 AATTATCAAA
1 AATTATCAAA
5397608 CTAATATTGG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (21 bp):
AATTATCAAAATTATATAAAA
Found at i:5397642 original size:21 final size:22
Alignment explanation
Indices: 5397618--5397674 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
5397608 CTAATATTGG
*
5397618 ATGTTACCAAAATTATATCA-A
1 ATGTTATCAAAATTATATCACA
* *
5397639 ATGTTATTAAAATTTTATCACA
1 ATGTTATCAAAATTATATCACA
5397661 A-GTTATCAAAATTA
1 ATGTTATCAAAATTA
5397675 AAATTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.39
Consensus pattern (22 bp):
ATGTTATCAAAATTATATCACA
Found at i:5397693 original size:27 final size:27
Alignment explanation
Indices: 5397644--5397697 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5397634 ATCAAATGTT
* * * *
5397644 ATTAAAATTTTATCACAAGTTATCAAA
1 ATTAAAATTATATAAAAAATTATCAAA
5397671 ATTAAAATTATATAAAAAATTATCAAA
1 ATTAAAATTATATAAAAAATTATCAAA
5397698 TCTTACTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTAAAATTATATAAAAAATTATCAAA
Found at i:5397771 original size:21 final size:20
Alignment explanation
Indices: 5397747--5397792 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
5397737 ATATTTATTA
*
5397747 TTATTATCATAATATAAAATT
1 TTATTATCATAAAAT-AAATT
*
5397768 TTATT-TTATAAAATAAATT
1 TTATTATCATAAAATAAATT
5397787 TT-TTAT
1 TTATTAT
5397793 AAATAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 8 0.36
20 7 0.32
21 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTATCATAAAATAAATT
Found at i:5398390 original size:38 final size:38
Alignment explanation
Indices: 5398339--5398416 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5398329 AAAAACTACT
5398339 TTACTTTTTCTTCCTTTTCGTTTTCTTGATCATTTAAC
1 TTACTTTTTCTTCCTTTTCGTTTTCTTGATCATTTAAC
5398377 TTACTTTTTCTTCCTTTTCGTTTTCTTGATCATTTAAC
1 TTACTTTTTCTTCCTTTTCGTTTTCTTGATCATTTAAC
5398415 TT
1 TT
5398417 CTCATCTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.13, C:0.21, G:0.05, T:0.62
Consensus pattern (38 bp):
TTACTTTTTCTTCCTTTTCGTTTTCTTGATCATTTAAC
Found at i:5401961 original size:21 final size:21
Alignment explanation
Indices: 5401937--5402065 Score: 113
Period size: 21 Copynumber: 6.2 Consensus size: 21
5401927 TATATTTTAG
5401937 TAACCTTTAATAAAATTTTGA
1 TAACCTTTAATAAAATTTTGA
*
5401958 TAACCTTCAATAAAATTTTGA
1 TAACCTTTAATAAAATTTTGA
* *
5401979 TAACCTTTGATATTAA-TTTGA
1 TAACCTTTAATA-AAATTTTGA
**
5402000 TAA-CTTATAATATTATTTTG-
1 TAACCTT-TAATAAAATTTTGA
* *
5402020 TAA-TTATTAATACAATTTTGA
1 TAACCT-TTAATAAAATTTTGA
** *
5402041 TAATTTTTTATAAAATTTTGA
1 TAACCTTTAATAAAATTTTGA
5402062 TAAC
1 TAAC
5402066 ATCTTGATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
20 20 0.22
21 66 0.73
22 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (21 bp):
TAACCTTTAATAAAATTTTGA
Found at i:5402423 original size:44 final size:43
Alignment explanation
Indices: 5402374--5402467 Score: 116
Period size: 44 Copynumber: 2.2 Consensus size: 43
5402364 ATTAAAAAAT
* * * *
5402374 TATCAATGATTGACAATTAAGTTATCATTGATTTACTACTATGC
1 TATCAATGATTGACAATTAAGCTATAAATGATTTACTA-TAAGC
* * *
5402418 TATCAATGATTTACTATTATGCTATAAATGATTTACTATAAGC
1 TATCAATGATTGACAATTAAGCTATAAATGATTTACTATAAGC
5402461 TATCAAT
1 TATCAAT
5402468 ATTTTATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 11 0.26
44 32 0.74
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (43 bp):
TATCAATGATTGACAATTAAGCTATAAATGATTTACTATAAGC
Done.