Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 68 of 171
Found at i:25001607 original size:3 final size:3
Alignment explanation
Indices: 25001601--25001673 Score: 67
Period size: 3 Copynumber: 23.3 Consensus size: 3
25001591 AATAATGTTA
* *
25001601 ATT ATT AAT ATTT ATT ATT ATT ATT ATT AATT ACT ACTT -TT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT -ATT ATT A-TT ATT ATT ATT
* *
25001648 ATT ATT ATT AATT ATC ATT TTT ATT A
1 ATT ATT ATT -ATT ATT ATT ATT ATT A
25001674 CTACTGATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 2 0.04
3 46 0.81
4 9 0.16
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:25001620 original size:16 final size:15
Alignment explanation
Indices: 25001580--25001628 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
25001570 GATTTTCTTT
25001580 TTTATATTATTAATAA
1 TTTATATTATTAAT-A
25001596 TGTTA-ATTATTAATA
1 T-TTATATTATTAATA
*
25001611 TTTATTATTATTATTA
1 TTTA-TATTATTAATA
25001627 TT
1 TT
25001629 AATTACTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 3 0.10
15 2 0.07
16 21 0.72
17 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTATATTATTAATA
Found at i:25001671 original size:16 final size:16
Alignment explanation
Indices: 25001604--25001673 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
25001594 AATGTTAATT
* * *
25001604 ATTAATATTTATTATT
1 ATTATTATTAATTATC
25001620 ATTATTATTAATTA-C
1 ATTATTATTAATTATC
*
25001635 --TACTT-TT-ATTATT
1 ATTA-TTATTAATTATC
25001648 ATTATTATTAATTATC
1 ATTATTATTAATTATC
*
25001664 ATTTTTATTA
1 ATTATTATTA
25001674 CTACTGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.10
13 4 0.10
14 4 0.10
15 4 0.10
16 26 0.62
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATTAATTATC
Found at i:25001994 original size:27 final size:27
Alignment explanation
Indices: 25001955--25002006 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
25001945 AGTCTCTGTT
*
25001955 TGGCTATAAAGCCAAGATTTTCAATCC
1 TGGCTATAAAGCCAAGATTTACAATCC
* * *
25001982 TGGCTTTATAGCCAATATTTACAAT
1 TGGCTATAAAGCCAAGATTTACAAT
25002007 GATTTTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
TGGCTATAAAGCCAAGATTTACAATCC
Found at i:25002481 original size:24 final size:24
Alignment explanation
Indices: 25002454--25002504 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
25002444 AATTTAAAAC
* *
25002454 AAATTTAAATTTAAAAATGAATTT
1 AAATTTAAATTTAAAAATAAATCT
*
25002478 AAATTTAAATTTAGAAATAAATCT
1 AAATTTAAATTTAAAAATAAATCT
25002502 AAA
1 AAA
25002505 ACTAATCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATTTAAATTTAAAAATAAATCT
Found at i:25002499 original size:18 final size:17
Alignment explanation
Indices: 25002438--25002486 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
25002428 GTTTAAAATT
25002438 ATTTCAAATTTAAAACAA
1 ATTT-AAATTTAAAACAA
25002456 ATTTAAATTTAAAA-ATGA
1 ATTTAAATTTAAAACA--A
25002474 ATTTAAATTTAAA
1 ATTTAAATTTAAA
25002487 TTTAGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 18 0.62
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:25003041 original size:49 final size:49
Alignment explanation
Indices: 25002974--25003261 Score: 196
Period size: 49 Copynumber: 5.8 Consensus size: 49
25002964 TTCATGTTTC
* * *
25002974 TGAGGTA-TAAGGTTCGCCATTGAGACTTAAACCTTTCCCCTT-GTGGCTT
1 TGAGGTACT-AGGTCCGCCATTGCGACTTAAACCTTT-CCCTTCATGGCTT
* * * ** *
25003023 TGCGGTACT-GGATCCGCCATTGCGGCTTAGATATTTCCCTTCATGTCTTT
1 TGAGGTACTAGG-TCCGCCATTGCGACTTAAACCTTTCCCTTCATGGC-TT
** *
25003073 TGAGGTACTAGGTTTGCCATTGCGACTTAAACCTTTCCCCTT-GTGGCTT
1 TGAGGTACTAGGTCCGCCATTGCGACTTAAACCTTT-CCCTTCATGGCTT
* * * * *
25003122 CGCGTTACT-GGATCCGCCATTGC-AGCTTAGATCTTTCCCTTCATGGCTT
1 TGAGGTACTAGG-TCCGCCATTGCGA-CTTAAACCTTTCCCTTCATGGCTT
* * * **
25003171 CTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTACCTTTATATC-T
1 -TGAGGTACTAGGTCCGCCATTGCGACTTAAACCTTTCCCTTCATGGCTT
* * * *
25003220 TCATGGTACT-GGATCCGCCGTTGCGACTTAGATCTTTCCCTT
1 TGA-GGTACTAGG-TCCGCCATTGCGACTTAAACCTTTCCCTT
25003262 GTGTTTTCAT
Statistics
Matches: 183, Mismatches: 42, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
48 19 0.10
49 90 0.49
50 64 0.35
51 10 0.05
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (49 bp):
TGAGGTACTAGGTCCGCCATTGCGACTTAAACCTTTCCCTTCATGGCTT
Found at i:25003150 original size:99 final size:98
Alignment explanation
Indices: 25002958--25003401 Score: 424
Period size: 99 Copynumber: 4.5 Consensus size: 98
25002948 TGCCATTGCT
* *
25002958 TTTCCTTTCATGT-TTCTGAGGTA-TAAGGTTCGCCATTGAGACTTAAACCTTTCCCCTTGTGGC
1 TTTCCCTTCATGTCTTCTGAGGTACT-AGGTTCGCCATTGCGACTTAAACCTTTCCCCTTGTGGC
* *
25003021 TTTGCGGTACTGGATCCGCCATTGCGGCTTAGATA
65 TTCGCGGTACTGGATCCGCCATTGC-GCTTAGATC
* *
25003056 TTTCCCTTCATGTCTTTTGAGGTACTAGGTTTGCCATTGCGACTTAAACCTTTCCCCTTGTGGCT
1 TTTCCCTTCATGTCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCCTTGTGGCT
*
25003121 TCGCGTTACTGGATCCGCCATTGCAGCTTAGATC
66 TCGCGGTACTGGATCCGCCATTGC-GCTTAGATC
* * * * **
25003155 TTTCCCTTCATGGCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTACCTTTATATCT
1 TTTCCCTTCATGTCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCCTTGTGGCT
** *
25003220 TCATGGTACTGGATCCGCCGTTGCGACTTAGATC
66 TCGCGGTACTGGATCCGCCATTGCG-CTTAGATC
* * * * ** * * *
25003254 TTTCCCTT-GTGT-TT-TCATGGTA-TTGGATCCGCTGTTGC-AGCTTAGA-TTTTTCCCTTGTG
1 TTTCCCTTCATGTCTTCTGA-GGTACTAGG-TTCGCCATTGCGA-CTTAAACCTTTCCCCTTGTG
* ** **
25003313 TCTTCATGGTACTGGATCCGCTGTTGCAGCTTAGATC
63 GCTTCGCGGTACTGGATCCGCCATTGC-GCTTAGATC
** *
25003350 TTTCCCTT-GGGTCTTC-GTAGGTA-TAGGGTTCGCCGTTGCGACTTAAACCTTT
1 TTTCCCTTCATGTCTTCTG-AGGTACTA-GGTTCGCCATTGCGACTTAAACCTTT
25003402 TCCTTTTATT
Statistics
Matches: 292, Mismatches: 41, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
96 59 0.20
97 41 0.14
98 22 0.08
99 169 0.58
100 1 0.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (98 bp):
TTTCCCTTCATGTCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCCTTGTGGCT
TCGCGGTACTGGATCCGCCATTGCGCTTAGATC
Found at i:25003281 original size:48 final size:48
Alignment explanation
Indices: 25003026--25003365 Score: 244
Period size: 48 Copynumber: 7.0 Consensus size: 48
25003016 GTGGCTTTGC
* * * * *
25003026 GGTACTGGATCCGCCATTGCGGCTTAGATATTTCCCTTCATGTCTT-TT
1 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTT-GTGTCTTCAT
** * * * * **
25003074 GAGGTACTAGG-TTTGCCATTGC-GACTTAAACCTTTCCCCTTGTGGCTTCGC
1 --GGTACT-GGATCCGCCGTTGCAG-CTTAGATCTTT-CCCTTGTGTCTTCAT
* * * *
25003125 GTTACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTTCATGGCTTC-T
1 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTT-GTGTCTTCAT
* * * * * * *
25003173 GAGGTACTAGG-TTCGCCATTGC-GACTTAAACCTTTACCTTTATATCTTCAT
1 --GGTACT-GGATCCGCCGTTGCAG-CTTAGATCTTT-CCCTTGTGTCTTCAT
*
25003224 GGTACTGGATCCGCCGTTGC-GACTTAGATCTTTCCCTTGTGTTTTCAT
1 GGTACTGGATCCGCCGTTGCAG-CTTAGATCTTTCCCTTGTGTCTTCAT
* * *
25003272 GGTATTGGATCCGCTGTTGCAGCTTAGATTTTTCCCTTGTGTCTTCAT
1 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTGTGTCTTCAT
* *
25003320 GGTACTGGATCCGCTGTTGCAGCTTAGATCTTTCCCTTGGGTCTTC
1 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTGTGTCTTC
25003366 GTAGGTATAG
Statistics
Matches: 237, Mismatches: 38, Indels: 32
0.77 0.12 0.10
Matches are distributed among these distances:
48 105 0.44
49 59 0.25
50 59 0.25
51 14 0.06
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.38
Consensus pattern (48 bp):
GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTGTGTCTTCAT
Found at i:25003424 original size:195 final size:196
Alignment explanation
Indices: 25003127--25003506 Score: 450
Period size: 195 Copynumber: 1.9 Consensus size: 196
25003117 GGCTTCGCGT
*
25003127 TACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTTCATGGCTTCTGAGGTACTAGGTTCGCCAT
1 TACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTT-AGGGCTTCTGAGGTACTAGGTTCGCCAT
* * *
25003192 TGCGACTTAAACCTTTACCTTTATATCTTCATGGTACTGGATCCGCCGTTGCGACTTAGAT-CTT
65 TGCGACTTAAACCTTTACCTTTATATCTTCATGGTACTAGATCCACCGTTGCGACTTAAATACTT
* * * * *
25003256 TCC-CTTGTGT-TTTCATGGTATTGGATCCGCTGTTGCAGCTTAGATTTTTCCCTTGTGTCTTCA
130 TCCTCTTGTATCTTT-ATGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTGTGTCTTCA
25003319 TGG
194 TGG
**
25003322 TACTGGATCCGCTGTTGCAGCTTAGATCTTTCCCTT-GGGTCTTC-GTAGGTA-TAGGGTTCGCC
1 TACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTTAGGG-CTTCTG-AGGTACTA-GGTTCGCC
* * * ** * *
25003384 GTTGCGACTTAAACCTTTTCCTTT-TATTTTGTTGTGGTACTAGATTCACCGTTGCGGCTTAAAT
63 ATTGCGACTTAAACCTTTACCTTTATA-TCT-TCATGGTACTAGATCCACCGTTGCGACTTAAAT
* * * *
25003448 ATTTTCCTCTTGTATCTTTGTGGTACTGGATCTACCGTTGCGGCTTAGATCTTTCCCTT
126 ACTTTCCTCTTGTATCTTTATGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTT
25003507 CATACTTCGT
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
193 7 0.05
194 41 0.26
195 60 0.39
196 5 0.03
197 39 0.25
198 3 0.02
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (196 bp):
TACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTTAGGGCTTCTGAGGTACTAGGTTCGCCATT
GCGACTTAAACCTTTACCTTTATATCTTCATGGTACTAGATCCACCGTTGCGACTTAAATACTTT
CCTCTTGTATCTTTATGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTGTGTCTTCATG
G
Found at i:25003436 original size:50 final size:50
Alignment explanation
Indices: 25003382--25003494 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 50
25003372 ATAGGGTTCG
* * *
25003382 CCGTTGCGACTTAAACCTTTTCCT-TT-TATTTTGTTGTGGTACTAGAT-TCA
1 CCGTTGCGGCTTAAACATTTTCCTCTTGTA-TCT-TTGTGGTACTAGATCT-A
* *
25003432 CCGTTGCGGCTTAAATATTTTCCTCTTGTATCTTTGTGGTACTGGATCTA
1 CCGTTGCGGCTTAAACATTTTCCTCTTGTATCTTTGTGGTACTAGATCTA
25003482 CCGTTGCGGCTTA
1 CCGTTGCGGCTTA
25003495 GATCTTTCCC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
50 48 0.87
51 5 0.09
52 2 0.04
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.43
Consensus pattern (50 bp):
CCGTTGCGGCTTAAACATTTTCCTCTTGTATCTTTGTGGTACTAGATCTA
Found at i:25005287 original size:16 final size:16
Alignment explanation
Indices: 25005266--25005297 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25005256 CCTTCATGTA
25005266 CTTCTTCTAGGATTTT
1 CTTCTTCTAGGATTTT
25005282 CTTCTTCTAGGATTTT
1 CTTCTTCTAGGATTTT
25005298 TTTAGCCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (16 bp):
CTTCTTCTAGGATTTT
Found at i:25006978 original size:11 final size:11
Alignment explanation
Indices: 25006952--25006985 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
25006942 AATAAATATT
*
25006952 AATATTAA-AT
1 AATATTAATAA
25006962 AATATTAATAA
1 AATATTAATAA
25006973 AATATTAATAA
1 AATATTAATAA
25006984 AA
1 AA
25006986 AATAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATTAATAA
Found at i:25006987 original size:13 final size:13
Alignment explanation
Indices: 25006940--25006989 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 13
25006930 GATAACAGTT
*
25006940 ATAATAAATATTA
1 ATAAAAAATATTA
25006953 ATATTAAATAATATTA
1 ATA--AAA-AATATTA
25006969 AT--AAAATATTA
1 ATAAAAAATATTA
25006980 ATAAAAAATA
1 ATAAAAAATA
25006990 GTAAAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 9 0.29
15 2 0.06
16 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAAAAATATTA
Found at i:25008109 original size:29 final size:29
Alignment explanation
Indices: 25008039--25008245 Score: 144
Period size: 29 Copynumber: 7.1 Consensus size: 29
25008029 CTCTGGAGGT
** *
25008039 CCCTAAACTATC-CAAAAATTGTATTTTGAG
1 CCCTAAACT-TCTCAAAAATTACATTTT-AC
* * *
25008069 CCCTGAACTTCTCCAAAATTACA-TTTAA
1 CCCTAAACTTCTCAAAAATTACATTTTAC
*
25008097 CCCTAAAACTTCTCCAAAATTACATTTTGAC
1 CCCT-AAACTTCTCAAAAATTACATTTT-AC
*
25008128 CCCTAAACTT-ACAAAAATTACATTTTAC
1 CCCTAAACTTCTCAAAAATTACATTTTAC
**
25008156 CCCTAAACTTC-CAAAAATTTTATTTTTGAC
1 CCCTAAACTTCTCAAAAATTACA-TTTT-AC
* *
25008186 CCC-GAACTTC-CAAAAATTCCATTTTTTAC
1 CCCTAAACTTCTCAAAAATTACA--TTTTAC
*
25008215 CCC-AGAAC-TCTC-GAAATTATCATTTTAC
1 CCCTA-AACTTCTCAAAAATTA-CATTTTAC
25008243 CCC
1 CCC
25008246 CGTATGTCCA
Statistics
Matches: 149, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
28 35 0.23
29 68 0.46
30 41 0.28
31 5 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCTCAAAAATTACATTTTAC
Found at i:25008157 original size:28 final size:29
Alignment explanation
Indices: 25008039--25008210 Score: 163
Period size: 29 Copynumber: 5.9 Consensus size: 29
25008029 CTCTGGAGGT
** *
25008039 CCCTAAACTATCCAAAAATTGTATTTTGAG
1 CCCTAAACT-TCCAAAAATTACATTTTGAC
* * *
25008069 CCCTGAACTTCTCCAAAATTACA-TTT-AA
1 CCCTAAACTTC-CAAAAATTACATTTTGAC
*
25008097 CCCTAAAACTTCTCCAAAATTACATTTTGAC
1 CCCT-AAACTTC-CAAAAATTACATTTTGAC
*
25008128 CCCTAAACTTACAAAAATTACATTTT-AC
1 CCCTAAACTTCCAAAAATTACATTTTGAC
**
25008156 CCCTAAACTTCCAAAAATTTTATTTTTGAC
1 CCCTAAACTTCCAAAAATTACA-TTTTGAC
* *
25008186 CCC-GAACTTCCAAAAATTCCATTTT
1 CCCTAAACTTCCAAAAATTACATTTT
25008211 TTACCCCAGA
Statistics
Matches: 121, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 30 0.25
29 56 0.46
30 30 0.25
31 5 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTGAC
Found at i:25008316 original size:117 final size:116
Alignment explanation
Indices: 25008185--25008473 Score: 298
Period size: 116 Copynumber: 2.5 Consensus size: 116
25008175 TTATTTTTGA
* * * * *
25008185 CCCCGAACTTCCAAAAAT-TCCATTTTTTACCCCAGAACTCT-CGAAATTATCATTTTACCCCC-
1 CCCCGAACGTCC-AAAATGT-CATTTTTAACCCCAAAACTCTCCAAAATTACCATTTTACCCCCA
* * *
25008247 GTATGTCC-AAAATTCCATTTTTTTATCCTGATTTTTTCAAAAATTACTATTTTAC
64 G-ATGTCCAAAAATTCCA-TTTTTGATCCCGA-TTTTTCAAAAATTACCATTTTAC
* * *
25008302 CCCCGAACGTCCAAAATGTCATTTTTAACCTCAAAATTTTCCAAAATTACCATTTTACCCCCAGA
1 CCCCGAACGTCCAAAATGTCATTTTTAACCCCAAAACTCTCCAAAATTACCATTTTACCCCCAGA
* *
25008367 TGTCCAAAAATTCTATTTTTGATCCCGATTTTTCCAAAATTACCATTTTAC
66 TGTCCAAAAATTCCATTTTTGATCCCGATTTTTCAAAAATTACCATTTTAC
*** * * * ** * *
25008418 CTTGGAACGTCTAAAATGTCATTTTTAACTCTAAATTTTTCCAAACTTACCATTTT
1 CCCCGAACGTCCAAAATGTCATTTTTAACCCCAAAACTCTCCAAAATTACCATTTT
25008474 GCTCCCAAGA
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
116 89 0.61
117 48 0.33
118 9 0.06
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.38
Consensus pattern (116 bp):
CCCCGAACGTCCAAAATGTCATTTTTAACCCCAAAACTCTCCAAAATTACCATTTTACCCCCAGA
TGTCCAAAAATTCCATTTTTGATCCCGATTTTTCAAAAATTACCATTTTAC
Found at i:25008357 original size:58 final size:57
Alignment explanation
Indices: 25008228--25008473 Score: 214
Period size: 58 Copynumber: 4.2 Consensus size: 57
25008218 AGAACTCTCG
* * * * * * *
25008228 AAATTATCATTTTACCCCCGTATGTCCAAAATTCCATTTTTTTATCCT-GATTTTTTCAA
1 AAATTACCATTTTACCCCCGAACGTCCAAAATT-CA--TTTTTAACCTCAAATTTTTCCA
* *
25008287 AAATTACTATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACCTCAAAATTTTCCA
1 AAATTACCATTTTACCCCCGAACGTCCAAAAT-TCATTTTTAACCTCAAATTTTTCCA
* * *
25008345 AAATTACCATTTTACCCCC-AGATGTCCAAAAATTCTATTTTTGATCC-C-GATTTTTCCA
1 AAATTACCATTTTACCCCCGA-ACGTCC-AAAATTC-ATTTTT-AACCTCAAATTTTTCCA
*** *
25008403 AAATTACCATTTTACCTTGGAACGTCTAAAATGTCATTTTTAA-CTCTAAATTTTTCCA
1 AAATTACCATTTTACCCCCGAACGTCCAAAAT-TCATTTTTAACCTC-AAATTTTTCCA
*
25008461 AACTTACCATTTT
1 AAATTACCATTTT
25008474 GCTCCCAAGA
Statistics
Matches: 154, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
55 1 0.01
56 2 0.01
57 21 0.14
58 83 0.54
59 43 0.28
60 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (57 bp):
AAATTACCATTTTACCCCCGAACGTCCAAAATTCATTTTTAACCTCAAATTTTTCCA
Found at i:25008415 original size:29 final size:28
Alignment explanation
Indices: 25008338--25008418 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
25008328 AACCTCAAAA
25008338 TTTTCCAAAATTACCATTTTACCCCCAG
1 TTTTCCAAAATTACCATTTTACCCCCAG
* * * * * *
25008366 ATGTCCAAAAATT-CTATTTTTGATCCCGAT
1 TTTTCC-AAAATTACCA-TTTT-ACCCCCAG
25008396 TTTTCCAAAATTACCATTTTACC
1 TTTTCCAAAATTACCATTTTACC
25008419 TTGGAACGTC
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
28 8 0.21
29 20 0.51
30 11 0.28
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTTCCAAAATTACCATTTTACCCCCAG
Found at i:25008434 original size:116 final size:117
Alignment explanation
Indices: 25008228--25008473 Score: 329
Period size: 116 Copynumber: 2.1 Consensus size: 117
25008218 AGAACTCTCG
* * *
25008228 AAATTATCATTTTACCCCCGTATGTCCAAAATTCCATTTTTTTATCCTGATTTTTTCAAAAATTA
1 AAATTACCATTTTACCCCCGTATGTCCAAAATTCCATTTTTTGATCCCGATTTTTTCAAAAATTA
*
25008293 CTATTTTACCCCCGAACGTCCAAAATGTCATTTTTAAC-CTCAAAATTTTCCA
66 CCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACTCT-AAAATTTTCCA
* *
25008345 AAATTACCATTTTACCCCCAG-ATGTCCAAAAATTCTA-TTTTTGATCCCGA-TTTTTCCAAAAT
1 AAATTACCATTTTACCCCC-GTATGTCC-AAAATTCCATTTTTTGATCCCGATTTTTTCAAAAAT
*** * *
25008407 TACCATTTTACCTTGGAACGTCTAAAATGTCATTTTTAACTCTAAATTTTTCCA
64 TACCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACTCTAAAATTTTCCA
*
25008461 AACTTACCATTTT
1 AAATTACCATTTT
25008474 GCTCCCAAGA
Statistics
Matches: 114, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
116 68 0.60
117 37 0.32
118 9 0.08
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (117 bp):
AAATTACCATTTTACCCCCGTATGTCCAAAATTCCATTTTTTGATCCCGATTTTTTCAAAAATTA
CCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACTCTAAAATTTTCCA
Found at i:25008493 original size:116 final size:117
Alignment explanation
Indices: 25008228--25008502 Score: 326
Period size: 116 Copynumber: 2.3 Consensus size: 117
25008218 AGAACTCTCG
* * * *
25008228 AAATTATCATTTTACCCC-CGTATGTCCAAAATTCCATTTTTTTATCCTGATTTTTTCAAAAATT
1 AAATTACCATTTTACCCCAAG-ATGTCCAAAATTCCATTTTTTGATCCCGATTTTTTCAAAAATT
*
25008292 ACTATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACCTCAAAATTTTCCA
65 ACCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACCTCAAAATTTTCCA
* * *
25008345 AAATTACCATTTTACCCCCAGATGTCCAAAAATTCTA-TTTTTGATCCCGA-TTTTTCCAAAATT
1 AAATTACCATTTTACCCCAAGATGTCC-AAAATTCCATTTTTTGATCCCGATTTTTTCAAAAATT
*** * *
25008408 ACCATTTTACCTTGGAACGTCTAAAATGTCATTTTTAA-CTCTAAATTTTTCCA
65 ACCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACCTC-AAAATTTTCCA
* *
25008461 AACTTACCATTTTGCTCCCAAGA-GTCTCAAAATTACCATTTT
1 AAATTACCATTTTAC-CCCAAGATGTC-CAAAATT-CCATTTT
25008503 GCCCCCGAGT
Statistics
Matches: 135, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
115 3 0.02
116 77 0.57
117 43 0.32
118 12 0.09
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (117 bp):
AAATTACCATTTTACCCCAAGATGTCCAAAATTCCATTTTTTGATCCCGATTTTTTCAAAAATTA
CCATTTTACCCCCGAACGTCCAAAATGTCATTTTTAACCTCAAAATTTTCCA
Found at i:25016755 original size:58 final size:57
Alignment explanation
Indices: 25016491--25016829 Score: 224
Period size: 58 Copynumber: 5.8 Consensus size: 57
25016481 ATCGGAGTTG
* * ** * *
25016491 AAAATGAGATTTTTGG--GTATTCGAGGGTAAAATGGTAATTTTAGGAAGTTAGAGATTA
1 AAAATGA-ATTTTTGGAAGT-TT-GAGGGTAAAATGGTAATTTTTGAAAAATCGAGATCA
* * ** * *
25016549 AAAATGAAATTTTAGGCA-TCCGGGGGTAAAATGATAATTTTTGGAAAGAATCGAGATCA
1 AAAATG-AATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAA-AATCGAGATCA
* ** * * * * *
25016608 AAAATGATTTTTTTTAAGTTTTAGGGTAAAATAGTAATTTTGGGAAGAATCGATG-TTA
1 AAAATGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTT-TGAAAAATCGA-GATCA
* * * * **
25016666 AAAATGAAATTTTGAGAGGATTGGGGGTAAAATGGTAATTTTTGAAAAAAAGAGATCA
1 AAAATGAATTTTTG-GAAGTTTGAGGGTAAAATGGTAATTTTTGAAAAATCGAGATCA
* * * *
25016724 AAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTACTTTTTGGAAAAATCGGGGTC-
1 AAAAT-GAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAAATCGAGATCA
*
25016782 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGAAAA
1 AAAAT-GAATTTTTGG-AAGTTTGAGGGT-AAAATGGTAATTTTTGAAAA
25016830 GTTCAAGGTC
Statistics
Matches: 215, Mismatches: 52, Indels: 29
0.73 0.18 0.10
Matches are distributed among these distances:
57 30 0.14
58 105 0.49
59 80 0.37
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (57 bp):
AAAATGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAAATCGAGATCA
Found at i:25016755 original size:117 final size:117
Alignment explanation
Indices: 25016514--25016776 Score: 311
Period size: 117 Copynumber: 2.3 Consensus size: 117
25016504 TGGGTATTCG
* *
25016514 AGGGTAAAATGGTAATTTTAGGAAG-TTAGAGATTAAAAATGAAATTTTAGGCATCCGGGGGTAA
1 AGGGTAAAATGGTAATTTTAGGAAGAATCGAGATTAAAAATGAAATTTTAGGCATCCGGGGGTAA
** * ** *
25016578 AATGATAATTTTTGGAAAGAATCGAGATCAAAAATGATTTTTTTTAAGTTTT
66 AATGATAATTTTTGGAAAGAAAAGAGATCAAAAATGAATTTTTGGAAGTTTA
* * * *
25016630 AGGGTAAAATAGTAATTTTGGGAAGAATCGATG-TTAAAAATGAAATTTTGAGAGGAT-TGGGGG
1 AGGGTAAAATGGTAATTTTAGGAAGAATCGA-GATTAAAAATGAAATTTT-AG-GCATCCGGGGG
*
25016693 TAAAATGGTAATTTTT-GAAA-AAAAGAGATCAAAAATGGAATTTTTGGAAGTTTA
63 TAAAATGATAATTTTTGGAAAGAAAAGAGATCAAAAAT-GAATTTTTGGAAGTTTA
* * *
25016747 AGGGTAAAATGGTACTTTTTGGAAAAATCG
1 AGGGTAAAATGGTAATTTTAGGAAGAATCG
25016777 GGGTCAAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
116 37 0.30
117 62 0.50
118 23 0.18
119 3 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.32
Consensus pattern (117 bp):
AGGGTAAAATGGTAATTTTAGGAAGAATCGAGATTAAAAATGAAATTTTAGGCATCCGGGGGTAA
AATGATAATTTTTGGAAAGAAAAGAGATCAAAAATGAATTTTTGGAAGTTTA
Found at i:25016828 original size:29 final size:29
Alignment explanation
Indices: 25016723--25016853 Score: 97
Period size: 29 Copynumber: 4.5 Consensus size: 29
25016713 AAAAGAGATC
* * **
25016723 AAAAATGGAATTTTTGGAAGTTTAAGGGT
1 AAAAATGTAATTTTTGAAAGTTCGAGGGT
* **
25016752 -AAAATGGTACTTTTTGGAAAAATCG-GGGT
1 AAAAAT-GTAATTTTT-GAAAGTTCGAGGGT
* * *
25016781 CAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAAATGTAATTTTTGAAAGTTCGAGGGT
*
25016810 AAAAATGTAATTTTTGAAAAGTTC-AAGGT
1 AAAAATGTAATTTTTG-AAAGTTCGAGGGT
*
25016839 CAAAAATATAATTTT
1 -AAAAATGTAATTTT
25016854 AAAGAAGTTT
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
28 12 0.15
29 38 0.48
30 29 0.37
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAAATGTAATTTTTGAAAGTTCGAGGGT
Found at i:25016831 original size:30 final size:30
Alignment explanation
Indices: 25016723--25016853 Score: 94
Period size: 30 Copynumber: 4.5 Consensus size: 30
25016713 AAAAGAGATC
* * **
25016723 AAAAATGGAATTTTTG-GAAGTTTAAGGGT
1 AAAAATGTAATTTTTGAAAAGTTCGAGGGT
* *
25016752 -AAAATGGTACTTTTTGGAAAA-ATCG-GGGT
1 AAAAAT-GTAATTTTT-GAAAAGTTCGAGGGT
* * *
25016781 CAAAATGGAA-TTTTGGAAAGTTCGAGGGT
1 AAAAATGTAATTTTTGAAAAGTTCGAGGGT
*
25016810 AAAAATGTAATTTTTGAAAAGTTC-AAGGT
1 AAAAATGTAATTTTTGAAAAGTTCGAGGGT
*
25016839 CAAAAATATAATTTT
1 -AAAAATGTAATTTT
25016854 AAAGAAGTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.05
28 12 0.15
29 29 0.37
30 32 0.41
31 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAAAAGTTCGAGGGT
Found at i:25017913 original size:3 final size:3
Alignment explanation
Indices: 25017907--25017987 Score: 101
Period size: 3 Copynumber: 26.3 Consensus size: 3
25017897 AATAATGTTA
* * *
25017907 ATT ATT AAT ATTT ATT ATT ATT ACTA ATT ACT ACTT -TT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT ATT ATT
25017954 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25017988 CTACTACTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.03
3 61 0.90
4 5 0.07
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:25017915 original size:13 final size:13
Alignment explanation
Indices: 25017889--25017987 Score: 64
Period size: 12 Copynumber: 8.0 Consensus size: 13
25017879 GATTTTTTTT
*
25017889 ATATT-ATTAATA
1 ATATTAATTATTA
*
25017901 ATGTTAATTATTA
1 ATATTAATTATTA
*
25017914 ATATTTATTATTA
1 ATATTAATTATTA
* * *
25017927 TTACTAATTACTA
1 ATATTAATTATTA
* *
25017940 CT-TTTATTATTA
1 ATATTAATTATTA
*
25017952 TTATT-ATTATTA
1 ATATTAATTATTA
*
25017964 TTATT-ATTATTA
1 ATATTAATTATTA
*
25017976 TTATT-ATTATTA
1 ATATTAATTATTA
25017988 CTACTACTGA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
12 43 0.60
13 29 0.40
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (13 bp):
ATATTAATTATTA
Found at i:25018824 original size:18 final size:18
Alignment explanation
Indices: 25018803--25018868 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
25018793 GTTTAAAATT
25018803 ATTTCAAATTT-AAACTAA
1 ATTT-AAATTTAAAACTAA
*
25018821 ATTTGAATTTAAAAC-AA
1 ATTTAAATTTAAAACTAA
* *
25018838 ATTTAAATTTAAAAATGA
1 ATTTAAATTTAAAACTAA
25018856 ATTTAAATTTAAA
1 ATTTAAATTTAAA
25018869 TTTAGAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 20 0.48
18 22 0.52
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (18 bp):
ATTTAAATTTAAAACTAA
Found at i:25018845 original size:6 final size:6
Alignment explanation
Indices: 25018803--25018872 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
25018793 GTTTAAAATT
* * **
25018803 ATTTCAA ATTTAA A-CTAA ATTTGA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** *
25018850 AAATGA ATTTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTA
25018873 GAAATAAATC
Statistics
Matches: 47, Mismatches: 14, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:25018858 original size:29 final size:28
Alignment explanation
Indices: 25018807--25018862 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
25018797 AAAATTATTT
**
25018807 CAAATTTAAACTAAATTTGAATTTAAAA
1 CAAATTTAAACTAAAAATGAATTTAAAA
*
25018835 CAAATTTAAATTTAAAAATGAATTTAAA
1 CAAATTTAAA-CTAAAAATGAATTTAAA
25018863 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (28 bp):
CAAATTTAAACTAAAAATGAATTTAAAA
Found at i:25018866 original size:24 final size:24
Alignment explanation
Indices: 25018836--25018886 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
25018826 AATTTAAAAC
* *
25018836 AAATTTAAATTTAAAAATGAATTT
1 AAATTTAAATTTAAAAATAAATCT
*
25018860 AAATTTAAATTTAGAAATAAATCT
1 AAATTTAAATTTAAAAATAAATCT
25018884 AAA
1 AAA
25018887 ACTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATTTAAATTTAAAAATAAATCT
Found at i:25018881 original size:18 final size:17
Alignment explanation
Indices: 25018788--25018868 Score: 83
Period size: 17 Copynumber: 4.7 Consensus size: 17
25018778 GAATTTAATT
* *
25018788 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
25018804 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
* *
25018822 TTTGAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
25018839 TTTAAATTTAAAAATGAA
1 TTTAAATTT-AAAATAAA
25018857 TTTAAATTTAAA
1 TTTAAATTTAAA
25018869 TTTAGAAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
16 3 0.06
17 31 0.58
18 19 0.36
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:25021752 original size:9 final size:9
Alignment explanation
Indices: 25021737--25021785 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
25021727 TATTAAAAAA
25021737 TATA-TTTT
1 TATACTTTT
*
25021745 TATAATTTT
1 TATACTTTT
25021754 TATACTTATT
1 TATACTT-TT
25021764 TAATACTTTT
1 T-ATACTTTT
*
25021774 GATACTTTT
1 TATACTTTT
25021783 TAT
1 TAT
25021786 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 4 0.11
9 20 0.57
10 5 0.14
11 6 0.17
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (9 bp):
TATACTTTT
Found at i:25022233 original size:29 final size:32
Alignment explanation
Indices: 25022180--25022247 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
25022170 TTTAAATCAC
*
25022180 TAATTAATAATAATAATAATAATATCTA-TATT
1 TAATT-ATAATAATAATAAAAATATCTATTATT
*
25022212 TAATTATAA-AAT-ATAAAAATATTTATTATT
1 TAATTATAATAATAATAAAAATATCTATTATT
25022242 T-ATTAT
1 TAATTAT
25022248 CTTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 16 0.48
30 8 0.24
31 4 0.12
32 5 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TAATTATAATAATAATAAAAATATCTATTATT
Found at i:25025769 original size:30 final size:28
Alignment explanation
Indices: 25025720--25025888 Score: 114
Period size: 30 Copynumber: 5.8 Consensus size: 28
25025710 TTTGGATACC
*
25025720 CGAGGG-AAAAATGATAATTTTGGTGAAAT
1 CGAGGGTAAAAATG-GAATTTT-GTGAAAT
* *
25025749 CGAGGTTAAAAAATGGAATTTTG-AAAAGTT
1 CGAGGGT-AAAAATGGAATTTTGTGAAA--T
*
25025779 CGAGGGT-AAAATGGTAATTTTTTATGAAAT
1 CGAGGGTAAAAATGG-AA--TTTTGTGAAAT
* *
25025809 CGAGGCTAAAAATGAAATTTTG-GAAAGTT
1 CGAGGGTAAAAATGGAATTTTGTGAAA--T
*
25025838 CGAGGGT-AAAATGGTAATTTTTGGTGAAAC
1 CGAGGGTAAAAATGG-AA-TTTT-GTGAAAT
*
25025868 CGAGGTTAAAAATGGAATTTT
1 CGAGGGTAAAAATGGAATTTT
25025889 AGAAGGTTCG
Statistics
Matches: 111, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
27 4 0.04
28 20 0.18
29 21 0.19
30 34 0.31
31 25 0.23
32 7 0.06
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (28 bp):
CGAGGGTAAAAATGGAATTTTGTGAAAT
Found at i:25025797 original size:59 final size:59
Alignment explanation
Indices: 25025720--25025920 Score: 280
Period size: 59 Copynumber: 3.4 Consensus size: 59
25025710 TTTGGATACC
* *
25025720 CGAGGGAAAAATGATAA-TTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGAAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAAATGGAATTTTGAAAAGTT
** * * *
25025779 CGAGGGTAAAATGGTAATTTTTTATGAAATCGAGGCTAAAAATGAAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTT
* *
25025838 CGAGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTT-AGAAGGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTT
*
25025897 CGAGGGTAAAATGGCAATTTTTGG
1 CGAGGGTAAAATGGTAATTTTTGG
25025921 AAGTTTTAGG
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 109 0.87
60 16 0.13
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTT
Found at i:25026746 original size:19 final size:19
Alignment explanation
Indices: 25026722--25026758 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25026712 TTTCTAAATC
* *
25026722 GAACCCAGATCTGGAAAAG
1 GAACCCAAATATGGAAAAG
25026741 GAACCCAAATATGGAAAA
1 GAACCCAAATATGGAAAA
25026759 TTTTCAAACA
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:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (19 bp):
GAACCCAAATATGGAAAAG
Found at i:25026960 original size:7 final size:7
Alignment explanation
Indices: 25026948--25026991 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
25026938 TTATAAAAAT
25026948 ATTATTA
1 ATTATTA
25026955 ATTATTA
1 ATTATTA
**
25026962 TAACATTA
1 -ATTATTA
25026970 ATTATT-
1 ATTATTA
25026976 ATTATTA
1 ATTATTA
25026983 ATTATTA
1 ATTATTA
25026990 AT
1 AT
25026992 AAATATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 6 0.19
7 20 0.65
8 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:25026962 original size:10 final size:10
Alignment explanation
Indices: 25026947--25027008 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
25026937 ATTATAAAAA
25026947 TATTATTAAT
1 TATTATTAAT
25026957 TATTA-TAA-
1 TATTATTAAT
*
25026965 CATTAATT-AT
1 TATT-ATTAAT
25026975 TATTATTAAT
1 TATTATTAAT
* *
25026985 TATTAATAAA
1 TATTATTAAT
*
25026995 TATTAAT-AT
1 TATTATTAAT
25027004 TATTA
1 TATTA
25027009 AAACAGTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 3 0.07
9 14 0.33
10 26 0.60
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTATTAAT
Found at i:25026971 original size:15 final size:13
Alignment explanation
Indices: 25026951--25026989 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
25026941 TAAAAATATT
25026951 ATTAATTATTATAAC
1 ATTAATTATTAT--C
*
25026966 ATTAATTATTATT
1 ATTAATTATTATC
25026979 ATTAATTATTA
1 ATTAATTATTA
25026990 ATAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATTATTATC
Found at i:25026978 original size:47 final size:47
Alignment explanation
Indices: 25026921--25027023 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 47
25026911 ATTTTCTTTT
** * * * *
25026921 TTATTATTATTTCTTTATTATAAAAATATTATTAATTATTATAACATTAA
1 TTATTATTA-TTAATTATTA-ATAAATATTAAT-ATTATTAAAACAGTAA
*
25026971 TTATTATTATTAATTATTAATAAATATTAATATTATTAAAACAGTCA
1 TTATTATTATTAATTATTAATAAATATTAATATTATTAAAACAGTAA
25027018 TTATTA
1 TTATTA
25027024 ATGTTTTCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 19 0.41
48 10 0.22
49 8 0.17
50 9 0.20
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (47 bp):
TTATTATTATTAATTATTAATAAATATTAATATTATTAAAACAGTAA
Found at i:25027755 original size:6 final size:6
Alignment explanation
Indices: 25027735--25027775 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
25027725 TCAAATTTGT
*
25027735 TTTAATA TTTTAA TTTAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25027776 ATCAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.13
6 22 0.73
7 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:25029186 original size:7 final size:7
Alignment explanation
Indices: 25029174--25029214 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
25029164 AGTGAAGAGC
25029174 AAGAAGT
1 AAGAAGT
25029181 AAGAAGT
1 AAGAAGT
25029188 AAGAAGT
1 AAGAAGT
25029195 AAGAAGT
1 AAGAAGT
25029202 AAGAAGT
1 AAGAAGT
25029209 AAGAAG
1 AAGAAG
25029215 AGAAGAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (7 bp):
AAGAAGT
Found at i:25029187 original size:21 final size:20
Alignment explanation
Indices: 25029163--25029221 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
25029153 GAGAAAGGAA
25029163 AAGTGAAGAGCAAGAAGTAAG
1 AAGTGAAGAG-AAGAAGTAAG
25029184 AAGT-AAGAAGTAAGAAGTAAG
1 AAGTGAAG-AG-AAGAAGTAAG
25029205 AAGTAAGAAGAGAAGAA
1 AAGT--GAAGAGAAGAA
25029222 ATCATCTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 20 0.61
22 5 0.15
23 2 0.06
24 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.31, T:0.10
Consensus pattern (20 bp):
AAGTGAAGAGAAGAAGTAAG
Found at i:25030301 original size:23 final size:23
Alignment explanation
Indices: 25030274--25030417 Score: 157
Period size: 23 Copynumber: 6.2 Consensus size: 23
25030264 ACACTAGCGC
* *
25030274 GCTCTCTGTTTAGCACTATATGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
25030297 GCTCTCTGTTCAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
25030320 GCTCTCTGTTCAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
25030343 GCTCTCTATTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
25030366 GCTCTTTGTTATTAGCACT-TCGTGT
1 GCTCTCTG-T-TTAGCACTGT-GTGT
* *
25030391 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
25030414 GCTC
1 GCTC
25030418 AGTACTTTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.03
23 81 0.78
24 2 0.02
25 17 0.16
26 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:25034053 original size:16 final size:17
Alignment explanation
Indices: 25034018--25034055 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
25034008 ATAAATAATG
* *
25034018 AAAAATAAAAAGCCCTA
1 AAAAATAAAAAGCACAA
25034035 AAAAATAAAAAG-ACAA
1 AAAAATAAAAAGCACAA
25034051 AAAAA
1 AAAAA
25034056 CCTTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.76, C:0.11, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAAGCACAA
Found at i:25037175 original size:7 final size:7
Alignment explanation
Indices: 25037163--25037188 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25037153 CCCTACGTTT
25037163 TCTCTTC
1 TCTCTTC
25037170 TCTCTTC
1 TCTCTTC
25037177 TCTCTTC
1 TCTCTTC
25037184 TCTCT
1 TCTCT
25037189 AATTTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTCTTC
Found at i:25043031 original size:16 final size:16
Alignment explanation
Indices: 25043010--25043049 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
25043000 CGTTTGGTTT
*
25043010 GCTGTAATAGAATATG
1 GCTGTAATAGAATAGG
*
25043026 GCTGTAATGGAATAGG
1 GCTGTAATAGAATAGG
25043042 GCTGTAAT
1 GCTGTAAT
25043050 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (16 bp):
GCTGTAATAGAATAGG
Found at i:25043274 original size:58 final size:58
Alignment explanation
Indices: 25043212--25043370 Score: 207
Period size: 58 Copynumber: 2.7 Consensus size: 58
25043202 ATTATTAAAA
* *
25043212 TTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-T
1 TTTAATATA-ATTATTATTAAATATAATTTAAT-AAAATAATAAATAATTTAATAACATT
* ** *
25043270 TTTAACATAATTATTATTAAATGCAATTTAATAAAATAATATATAATTTAATAACATT
1 TTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACATT
25043328 TTTAATATAATTATTATTAAAATATGAA-TTAATAAAATAATAA
1 TTTAATATAATTATTATT-AAATAT-AATTTAATAAAATAATAA
25043371 TATATAATAT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
57 21 0.24
58 45 0.52
59 19 0.22
60 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (58 bp):
TTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACATT
Found at i:25047845 original size:17 final size:17
Alignment explanation
Indices: 25047823--25047861 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
25047813 AGATGGAGAA
* *
25047823 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
25047840 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
25047857 CTTGT
1 CTTGT
25047862 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:25061821 original size:6 final size:6
Alignment explanation
Indices: 25061815--25061858 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
25061805 ACCGCCACCT
* * *
25061815 CCTCCT CCTCCA CCTCCA CCTCCA CCTCCA CCTCTA CCGCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
25061859 ACTTCCGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.14, C:0.66, G:0.02, T:0.18
Consensus pattern (6 bp):
CCTCCA
Found at i:25061826 original size:21 final size:21
Alignment explanation
Indices: 25061802--25061843 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25061792 CTGAACCATG
*
25061802 TCCACCGCCACCTCCTCCTCC
1 TCCACCGCCACCTCCACCTCC
*
25061823 TCCACCTCCACCTCCACCTCC
1 TCCACCGCCACCTCCACCTCC
25061844 ACCTCTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.67, G:0.02, T:0.19
Consensus pattern (21 bp):
TCCACCGCCACCTCCACCTCC
Found at i:25061829 original size:15 final size:15
Alignment explanation
Indices: 25061809--25061848 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
25061799 ATGTCCACCG
*
25061809 CCACCTCCTCCTCCT
1 CCACCTCCACCTCCT
25061824 CCACCTCCA---CCT
1 CCACCTCCACCTCCT
25061836 CCACCTCCACCTC
1 CCACCTCCACCTC
25061849 TACCGCCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 12 0.57
15 9 0.43
ACGTcount: A:0.12, C:0.68, G:0.00, T:0.20
Consensus pattern (15 bp):
CCACCTCCACCTCCT
Found at i:25061934 original size:18 final size:18
Alignment explanation
Indices: 25061908--25061942 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25061898 GCCATGTCCA
*
25061908 CCTCCACCACCTCCTCCT
1 CCTCCACCACCGCCTCCT
*
25061926 CCTCTACCACCGCCTCC
1 CCTCCACCACCGCCTCC
25061943 ACCACCTCCT
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:0.11, C:0.66, G:0.03, T:0.20
Consensus pattern (18 bp):
CCTCCACCACCGCCTCCT
Found at i:25061950 original size:21 final size:21
Alignment explanation
Indices: 25061911--25061958 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25061901 ATGTCCACCT
* *
25061911 CCACCACCTCCTCCTCCTCTA
1 CCACCACCTCCACCACCTCTA
*
25061932 CCACCGCCTCCACCACCTCCTA
1 CCACCACCTCCACCACCT-CTA
25061954 -CACCA
1 CCACCA
25061959 TTTCCATACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.62, G:0.02, T:0.17
Consensus pattern (21 bp):
CCACCACCTCCACCACCTCTA
Found at i:25061992 original size:12 final size:12
Alignment explanation
Indices: 25061962--25062002 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
25061952 TACACCATTT
*
25061962 CCATACCCAGAC
1 CCATATCCAGAC
* *
25061974 CCGTATCCGGAC
1 CCATATCCAGAC
25061986 CCATATCCAGAC
1 CCATATCCAGAC
25061998 CCATA
1 CCATA
25062003 CCCTTGGCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.44, G:0.12, T:0.15
Consensus pattern (12 bp):
CCATATCCAGAC
Found at i:25062044 original size:3 final size:3
Alignment explanation
Indices: 25062038--25062068 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25062028 CCTCCTCCTT
25062038 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
25062069 TCCTCCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:25063231 original size:31 final size:29
Alignment explanation
Indices: 25063196--25063264 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
25063186 GTTAATAATT
**
25063196 TATAAGAATTAAATTAAATAAAAGATTCATA
1 TATAA-AATTAAACAAAATAAAA-ATTCATA
* *
25063227 TATAAAATTACACAAAATCAAAATTCATA
1 TATAAAATTAAACAAAATAAAAATTCATA
25063256 TATAAAATT
1 TATAAAATT
25063265 TCATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 13 0.38
31 5 0.15
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (29 bp):
TATAAAATTAAACAAAATAAAAATTCATA
Found at i:25064101 original size:32 final size:29
Alignment explanation
Indices: 25064043--25064108 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
25064033 TCAAGTTTTT
* *
25064043 TTACCAAATAATATAAAAATAATAATTAA
1 TTACAAAAAAATATAAAAATAATAATTAA
25064072 TTACAAAAAAATATGAAAAAT-AT-ATTAA
1 TTACAAAAAAATAT-AAAAATAATAATTAA
*
25064100 TTACGAAAA
1 TTACAAAAA
25064109 TAGATATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 13 0.39
29 14 0.42
30 6 0.18
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (29 bp):
TTACAAAAAAATATAAAAATAATAATTAA
Found at i:25064446 original size:22 final size:21
Alignment explanation
Indices: 25064416--25064472 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
25064406 ATTTTATATG
*
25064416 AAATTTAAAAAA-TTACTATTTT
1 AAATATAAAAAATTTA-T-TTTT
*
25064438 AAATATAAAATATTTATTTTT
1 AAATATAAAAAATTTATTTTT
25064459 AAATTATAAAAAAT
1 AAA-TATAAAAAAT
25064473 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 20 0.67
23 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATAAAAAATTTATTTTT
Found at i:25064492 original size:20 final size:20
Alignment explanation
Indices: 25064458--25064501 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
25064448 TATTTATTTT
*
25064458 TAAATTATAAAAAAT-AAAA
1 TAAAATATAAAAAATAAAAA
25064477 TAAAATATAAATAAATAAAAA
1 TAAAATATAAA-AAATAAAAA
25064498 TAAA
1 TAAA
25064502 TTCTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 4 0.18
21 8 0.36
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAATATAAAAAATAAAAA
Found at i:25064502 original size:20 final size:18
Alignment explanation
Indices: 25064458--25064502 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
25064448 TATTTATTTT
25064458 TAAATTATAAAAAATAAAA
1 TAAA-TATAAAAAATAAAA
25064477 TAAAATATAAATAAATAAAAA
1 T-AAATATAAA-AAAT-AAAA
25064498 TAAAT
1 TAAAT
25064503 TCTATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATATAAAAAATAAAA
Found at i:25065286 original size:2 final size:2
Alignment explanation
Indices: 25065279--25065304 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25065269 TCATCAAATA
25065279 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
25065305 CATTACATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25067729 original size:41 final size:41
Alignment explanation
Indices: 25067679--25067757 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
25067669 TAATTTTTTT
* * * *
25067679 ATTATATAATCTCAAATTTTTCATGCTAAATTGAAAGTTTG
1 ATTACATAATCTCAAATCTTTCATACTAAATTAAAAGTTTG
**
25067720 ATTACATAATCTTGAATCTTTCATACTAAATTAAAAGT
1 ATTACATAATCTCAAATCTTTCATACTAAATTAAAAGT
25067758 AAAGGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (41 bp):
ATTACATAATCTCAAATCTTTCATACTAAATTAAAAGTTTG
Found at i:25068479 original size:11 final size:10
Alignment explanation
Indices: 25068445--25068584 Score: 86
Period size: 9 Copynumber: 14.7 Consensus size: 10
25068435 TTTTATGATT
25068445 TTTTATATAA
1 TTTTATATAA
25068455 TTTT-TATAA
1 TTTTATATAA
*
25068464 GTTTATATGAA
1 TTTTATAT-AA
*
25068475 TTTTA-ATAT
1 TTTTATATAA
*
25068484 TTTTTTAT-A
1 TTTTATATAA
*
25068493 TTTT-TATGA
1 TTTTATATAA
* *
25068502 TTTTTTAGAA
1 TTTTATATAA
25068512 TTTTA-ATATA
1 TTTTATATA-A
25068522 TTTTATA-AA
1 TTTTATATAA
*
25068531 ATTT-TA-AA
1 TTTTATATAA
*
25068539 TGTTATATTAA
1 TTTTATA-TAA
25068550 TTTTATA-AA
1 TTTTATATAA
25068559 TTTT-TAT-A
1 TTTTATATAA
*
25068567 TTTTATTATAT
1 TTTTA-TATAA
25068578 TTTTATA
1 TTTTATA
25068585 ACGTCATATC
Statistics
Matches: 102, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
8 16 0.16
9 36 0.35
10 30 0.29
11 20 0.20
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
TTTTATATAA
Found at i:25068500 original size:28 final size:26
Alignment explanation
Indices: 25068473--25068585 Score: 93
Period size: 28 Copynumber: 4.0 Consensus size: 26
25068463 AGTTTATATG
*
25068473 AATTTTAATATTTTTTTATATTTTTATGA
1 AATTTTAA-ATTTTATTATA-TTTTAT-A
** *
25068502 TTTTTTAGAATTTTAATATATTTTATAA
1 AATTTTA-AATTTTATTATATTTTAT-A
25068530 AATTTTAAATGTTATATTA-ATTTTATA
1 AATTTTAAAT-TT-TATTATATTTTATA
*
25068557 AATTTTTATATTTTATTATATTTTTATA
1 AA-TTTTAAATTTTATTATA-TTTTATA
25068585 A
1 A
25068586 CGTCATATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.07
27 9 0.13
28 36 0.52
29 18 0.26
30 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
AATTTTAAATTTTATTATATTTTATA
Found at i:25068514 original size:29 final size:28
Alignment explanation
Indices: 25068435--25068583 Score: 81
Period size: 28 Copynumber: 5.2 Consensus size: 28
25068425 TCCTATTAAC
* *
25068435 TTTTATGATTTTTTATATAATTTTTATAAGT
1 TTTTATGATTTTTTAAAT-TTTTTTAT-A-T
* *
25068466 TTATATGA-ATTTTAATATTTTTTTATAT
1 TTTTATGATTTTTTAA-ATTTTTTTATAT
**
25068494 TTTTATGATTTTTTAGAATTTTAATATA-
1 TTTTATGATTTTTTA-AATTTTTTTATAT
* ** *
25068522 TTTTATAAAATTTTAAATGTTATATTA-A-
1 TTTTATGATTTTTTAAAT-TT-TTTTATAT
* * * *
25068550 TTTTATAAATTTTTATATTTTATTATAT
1 TTTTATGATTTTTTAAATTTTTTTATAT
25068578 TTTTAT
1 TTTTAT
25068584 AACGTCATAT
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.05
27 6 0.06
28 45 0.46
29 19 0.20
30 13 0.13
31 9 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATGATTTTTTAAATTTTTTTATAT
Found at i:25068661 original size:19 final size:18
Alignment explanation
Indices: 25068617--25068673 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
25068607 TTTTAATATT
* *
25068617 TGATATTTATATTTTTGA
1 TGATTTTTATATTTTTTA
* *
25068635 TAAATTTTATATTTTTTTA
1 TGATTTTTATA-TTTTTTA
25068654 TGATTTTTATAATTTTTTA
1 TGATTTTTAT-ATTTTTTA
25068673 T
1 T
25068674 AAGAAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 8 0.26
19 22 0.71
20 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TGATTTTTATATTTTTTA
Found at i:25068848 original size:25 final size:25
Alignment explanation
Indices: 25068820--25068871 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
25068810 GTAAATTTAC
*
25068820 TACAAAATTTTAATTGA-TTTTTTTT
1 TACAAAATTTTAA-AGACTTTTTTTT
**
25068845 TACAATTTTTTAAAGACTTTTTTTT
1 TACAAAATTTTAAAGACTTTTTTTT
25068870 TA
1 TA
25068872 TATACAAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (25 bp):
TACAAAATTTTAAAGACTTTTTTTT
Found at i:25079032 original size:25 final size:24
Alignment explanation
Indices: 25078995--25079143 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
25078985 ACACTAGCGC
25078995 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
25079018 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
25079043 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
25079066 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
25079089 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
25079112 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
25079135 GCTCTCTGT
1 GCTCTCTGT
25079144 TAGTACTTCG
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:25079095 original size:46 final size:46
Alignment explanation
Indices: 25079016--25079151 Score: 211
Period size: 46 Copynumber: 2.9 Consensus size: 46
25079006 AGCACGTCTC
*
25079016 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
*
25079064 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
* *
25079110 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTAGTACTT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTT
25079152 CGGTACTCTC
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
45 9 0.11
46 64 0.77
48 10 0.12
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
Found at i:25079134 original size:69 final size:69
Alignment explanation
Indices: 25079016--25079164 Score: 194
Period size: 69 Copynumber: 2.2 Consensus size: 69
25079006 AGCACGTCTC
* *
25079016 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCA
1 GTGCTCTCTG-TATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTAGCA
25079081 CTTTGT
64 CTTTGT
* * * *
25079087 GTGCTCTCTG-ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTAGTACT
1 GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTAGCACT
*
25079151 TCG-
66 TTGT
*
25079154 GTACTCTCTGT
1 GTGCTCTCTGT
25079165 TTGTTCCGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
67 9 0.13
68 9 0.13
69 41 0.59
71 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (69 bp):
GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTAGCACT
TTGT
Found at i:25086394 original size:25 final size:24
Alignment explanation
Indices: 25086357--25086505 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
25086347 ACACTAGCGC
25086357 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
25086380 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
25086405 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
25086428 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
25086451 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
25086474 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
25086497 GCTCTCTGT
1 GCTCTCTGT
25086506 TAGTACTTCG
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:25086457 original size:46 final size:46
Alignment explanation
Indices: 25086378--25086513 Score: 211
Period size: 46 Copynumber: 2.9 Consensus size: 46
25086368 AGCACGTCTC
*
25086378 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
*
25086426 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
* *
25086472 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTAGTACTT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTT
25086514 CGGTACTCTC
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
45 9 0.11
46 64 0.77
48 10 0.12
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
Found at i:25086496 original size:69 final size:69
Alignment explanation
Indices: 25086378--25086526 Score: 194
Period size: 69 Copynumber: 2.2 Consensus size: 69
25086368 AGCACGTCTC
* *
25086378 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCA
1 GTGCTCTCTG-TATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTAGCA
25086443 CTTTGT
64 CTTTGT
* * * *
25086449 GTGCTCTCTG-ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTAGTACT
1 GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTAGCACT
*
25086513 TCG-
66 TTGT
*
25086516 GTACTCTCTGT
1 GTGCTCTCTGT
25086527 TTGTTCCGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
67 9 0.13
68 9 0.13
69 41 0.59
71 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (69 bp):
GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTAGCACT
TTGT
Found at i:25093992 original size:39 final size:39
Alignment explanation
Indices: 25093938--25094016 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
25093928 GATAACTCCA
*
25093938 AAACAAAAGAAATTAATTTAACCTTAATCATGCATATTC
1 AAACAAAAGAAATTAATTTAACCTTAATCATGCACATTC
25093977 AAACAAAAGAAATTAATTTAACCTTAATCATGCACATTC
1 AAACAAAAGAAATTAATTTAACCTTAATCATGCACATTC
25094016 A
1 A
25094017 CGTTAGGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.29
Consensus pattern (39 bp):
AAACAAAAGAAATTAATTTAACCTTAATCATGCACATTC
Found at i:25094290 original size:96 final size:97
Alignment explanation
Indices: 25094120--25094431 Score: 387
Period size: 96 Copynumber: 3.2 Consensus size: 97
25094110 AAAGCAGGAG
* * *
25094120 GGGAAAGATTTAAG-CTGCAACGGTAAATCCAGTGCCACGAAGATGTCAAAGGAAAGGTTTAAGC
1 GGGAAAGATTTAAGTC-GCAACGGAAAATCCAGTACCACGAAGATGTCAAGGGAAAGGTTTAAGC
* *
25094184 CGTAACGGCGAACCTTGTACCTCAGAAAATGAA
65 CGCAATGGCGAACCTTGTACCTCAGAAAATGAA
*
25094217 -GGAAAGATTTAAGTCGCAACGGAAAATCCAGTACCACGAAGATGTCAAGGGAAAGGTTTGAGCC
1 GGGAAAGATTTAAGTCGCAACGGAAAATCCAGTACCACGAAGATGTCAAGGGAAAGGTTTAAGCC
* *
25094281 ACAATGGCGAACCTTGTACCTTAGAAAATGAA
66 GCAATGGCGAACCTTGTACCTCAGAAAATGAA
* ** * * ** * *
25094313 GGGAAAGATTTAAGTCGCAAAGGCGAATTCAATACCGTGAAGACAATG-AAAGGTAAAGGTTTAA
1 GGGAAAGATTTAAGTCGCAACGGAAAATCCAGTACCACGAAG---ATGTCAAGGGAAAGGTTTAA
* *
25094377 GTCGCAATGGCGAACCTTGTACCTCAGAAAATAAA
63 GCCGCAATGGCGAACCTTGTACCTCAGAAAATGAA
*
25094412 GGGAAAGATTTAAGCCGCAA
1 GGGAAAGATTTAAGTCGCAA
25094432 TGACGAACCT
Statistics
Matches: 187, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
96 86 0.46
97 35 0.19
99 63 0.34
100 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (97 bp):
GGGAAAGATTTAAGTCGCAACGGAAAATCCAGTACCACGAAGATGTCAAGGGAAAGGTTTAAGCC
GCAATGGCGAACCTTGTACCTCAGAAAATGAA
Found at i:25094338 original size:48 final size:48
Alignment explanation
Indices: 25094170--25094482 Score: 285
Period size: 48 Copynumber: 6.4 Consensus size: 48
25094160 AGATGTCAAA
* * *
25094170 GGAAAGGTTTAAGCCGTAACGGCGAACCTTGTACCTCAGAAAATGAA-
1 GGAAAGATTTAAGCCGCAATGGCGAACCTTGTACCTCAGAAAATGAAG
* * ** * * *
25094217 GGAAAGATTTAAGTCGCAACGGAAAATCC-AGTACCAC-GAAGATGTCAAG
1 GGAAAGATTTAAGCCGCAATGGCGAA-CCTTGTACCTCAGAAAATG--AAG
* * * *
25094266 GGAAAGGTTTGAGCCACAATGGCGAACCTTGTACCTTAGAAAATGAAG
1 GGAAAGATTTAAGCCGCAATGGCGAACCTTGTACCTCAGAAAATGAAG
* * * * *
25094314 GGAAAGATTTAAGTCGCAAAGGCGAA--TTCAATACCGTGAAGACAATGAAAG
1 GGAAAGATTTAAGCCGCAATGGCGAACCTT--GTACC-T-CAGAAAATG-AAG
* * * *
25094365 GTAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAAATAAAG
1 GGAAAGATTTAAGCCGCAATGGCGAACCTTGTACCTCAGAAAATGAAG
* *
25094413 GGAAAGATTTAAGCCGCAATGACGAACCTTGTACCTCAGAAGCATGAAG
1 GGAAAGATTTAAGCCGCAATGGCGAACCTTGTACCTCAGAA-AATGAAG
25094462 GGAAAGATTTAAGCCGCAATG
1 GGAAAGATTTAAGCCGCAATG
25094483 ATAAATTCAA
Statistics
Matches: 212, Mismatches: 40, Indels: 26
0.76 0.14 0.09
Matches are distributed among these distances:
46 8 0.04
47 27 0.13
48 74 0.35
49 57 0.27
50 14 0.07
51 30 0.14
53 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (48 bp):
GGAAAGATTTAAGCCGCAATGGCGAACCTTGTACCTCAGAAAATGAAG
Found at i:25094550 original size:50 final size:50
Alignment explanation
Indices: 25094307--25094579 Score: 209
Period size: 50 Copynumber: 5.5 Consensus size: 50
25094297 TACCTTAGAA
* * * * * * *
25094307 AATGAAGGGAAAGATTTAAGTCGCAAAGGCGAATTCAATACCGTGAAGAC
1 AATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCGAGACGAC
* * * * * *
25094357 AATGAAAGGTAAAGGTTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGA--A-
1 AATG-AAGGGAAAGATTTAAGCCGCAATGACGAATCC-AGTACC-GAGACGAC
* * * *
25094406 AATAAAGGGAAAGATTTAAGCCGCAATGACGAA-CCTTGTACCTCAGAAG-C
1 AATGAAGGGAAAGATTTAAGCCGCAATGACGAATCC-AGTACC-GAGACGAC
** * * *
25094456 -ATGAAGGGAAAGATTTAAGCCGCAATGATAAATTCAATATCGAGACGAC
1 AATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCGAGACGAC
* *
25094505 AATGAAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCGAGACGAC
1 AATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCGAGACGAC
* *
25094555 AATGAAAGGAAAAGGTTTAAGCCGC
1 AATG-AAGGGAAAGATTTAAGCCGC
25094580 CACGGCTAAC
Statistics
Matches: 181, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
48 43 0.24
49 36 0.20
50 53 0.29
51 47 0.26
52 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (50 bp):
AATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCGAGACGAC
Found at i:25102992 original size:31 final size:29
Alignment explanation
Indices: 25102912--25102992 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
25102902 AAATTGAATC
25102912 AAATCAAAATTTCATGTATAAAATCACACA
1 AAATCAAAA-TTCATGTATAAAATCACACA
* * * *
25102942 AAACCAAAGTTCATGTATAACATTACACA
1 AAATCAAAATTCATGTATAAAATCACACA
*
25102971 TTAAATCAAAATTCATATATAA
1 --AAATCAAAATTCATGTATAA
25102993 TTTTGATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.43
30 7 0.17
31 17 0.40
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (29 bp):
AAATCAAAATTCATGTATAAAATCACACA
Found at i:25103801 original size:25 final size:25
Alignment explanation
Indices: 25103752--25103802 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
25103742 ACTTTTTTTC
*
25103752 TTGAAACAAAATAAAATACTACAAT
1 TTGAAACAAAATAAAATAATACAAT
* *
25103777 TTGAAACGAAATAAAATAATGCAAT
1 TTGAAACAAAATAAAATAATACAAT
25103802 T
1 T
25103803 CAAATAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (25 bp):
TTGAAACAAAATAAAATAATACAAT
Found at i:25106143 original size:21 final size:22
Alignment explanation
Indices: 25106117--25106175 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
25106107 CACGGTCTAG
*
25106117 CACATGGTC-GTGTGCCCGGCT
1 CACATGGACTGTGTGCCCGGCT
25106138 CACAT-GACTGTGTGCCCGGCT
1 CACATGGACTGTGTGCCCGGCT
25106159 CACAT-GACTGTGTGCCC
1 CACATGGACTGTGTGCCC
25106176 ATCCTGTGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.24
Consensus pattern (22 bp):
CACATGGACTGTGTGCCCGGCT
Found at i:25107500 original size:22 final size:24
Alignment explanation
Indices: 25107460--25107503 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
25107450 TTAGGATACC
*
25107460 AAATTATATATTAACTATTTTTAT
1 AAATTATATATTAAATATTTTTAT
25107484 AAATTA-AT-TTAAATATTTTT
1 AAATTATATATTAAATATTTTT
25107504 TTAGTGCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATTATATATTAAATATTTTTAT
Found at i:25108375 original size:21 final size:22
Alignment explanation
Indices: 25108329--25108373 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
25108319 ATTGATCAAA
25108329 TTGTTTTTGAACAAGCATAACCAAC
1 TTGTTTTTGAACAAGCAT-A--AAC
25108354 TTGTTTTTGAACAAGCATAA
1 TTGTTTTTGAACAAGCATAA
25108374 CTATCATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
24 1 0.05
25 18 0.90
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TTGTTTTTGAACAAGCATAAAC
Found at i:25116654 original size:16 final size:17
Alignment explanation
Indices: 25116635--25116676 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
25116625 CCATCTATCA
*
25116635 AATTTTCTATCCCTT-C
1 AATTTTCTATCCATTCC
*
25116651 AATTTTCCA-CCATTCC
1 AATTTTCTATCCATTCC
25116667 AATTTTCTAT
1 AATTTTCTAT
25116677 ACACTCTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTCTATCCATTCC
Found at i:25121057 original size:18 final size:19
Alignment explanation
Indices: 25121009--25121057 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
25120999 TATACAATCG
*
25121009 ATAAAAATAATAAAACATGT
1 ATAAAAA-AATAAAACATAT
* *
25121029 GTAATAAAATAAAA-ATAT
1 ATAAAAAAATAAAACATAT
25121047 ATAAAAAAATA
1 ATAAAAAAATA
25121058 TCAAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 12 0.50
19 7 0.29
20 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
ATAAAAAAATAAAACATAT
Found at i:25121201 original size:18 final size:18
Alignment explanation
Indices: 25121160--25121201 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25121150 TTTTCTTAAA
*
25121160 TTAAAATCTAAATTATCT
1 TTAAAATATAAATTATCT
* *
25121178 TCAAAATATAAATTATTT
1 TTAAAATATAAATTATCT
25121196 TTAAAA
1 TTAAAA
25121202 AGAAAGATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATATAAATTATCT
Found at i:25140208 original size:18 final size:18
Alignment explanation
Indices: 25140185--25140222 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25140175 CGGAATAAAA
25140185 TTTAAATAAAAATATATT
1 TTTAAATAAAAATATATT
**
25140203 TTTAAATTTAAATATATT
1 TTTAAATAAAAATATATT
25140221 TT
1 TT
25140223 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAAAAATATATT
Found at i:25142343 original size:3 final size:3
Alignment explanation
Indices: 25142337--25142369 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25142327 GATGATGATG
25142337 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25142370 TTACTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25146228 original size:14 final size:15
Alignment explanation
Indices: 25146209--25146238 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25146199 TTGCGGATGA
25146209 TGGTGGTGGT-GTTG
1 TGGTGGTGGTGGTTG
25146223 TGGTGGTGGTGGTTG
1 TGGTGGTGGTGGTTG
25146238 T
1 T
25146239 CGTCGACGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (15 bp):
TGGTGGTGGTGGTTG
Found at i:25148563 original size:113 final size:112
Alignment explanation
Indices: 25148433--25148654 Score: 392
Period size: 113 Copynumber: 2.0 Consensus size: 112
25148423 TGAAAGAAGA
25148433 AAGTGCATATAAAAATCCCATTTCTTGCACAAATTGATAGCCAAAGATACTGCATTAAGCTATTA
1 AAGTGCATATAAAAATCCCATTTCTTGCACAAATTGATAGCCAAAGATACTGCATTAAGCTATTA
*
25148498 AAGAAATACAGAAAAACAAATAACCCAATT-TTATTTTTATTTTTGCTG
66 AAGAAATACAGAAAAACAAAAAACCCAATTCTT-TTTTT-TTTTTGCTG
* *
25148546 AAGTGCATATAAAAATCCCATTTCTTGGATAAATTGATAGCCAAAGATACTGCATTAAGCTATTA
1 AAGTGCATATAAAAATCCCATTTCTTGCACAAATTGATAGCCAAAGATACTGCATTAAGCTATTA
25148611 AAGAAATACAGAAAAACAAAAAACCCAATTCTTTTTTTTTTTTG
66 AAGAAATACAGAAAAACAAAAAACCCAATTCTTTTTTTTTTTTG
25148655 GCTCAGCAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
112 6 0.06
113 97 0.92
114 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (112 bp):
AAGTGCATATAAAAATCCCATTTCTTGCACAAATTGATAGCCAAAGATACTGCATTAAGCTATTA
AAGAAATACAGAAAAACAAAAAACCCAATTCTTTTTTTTTTTTGCTG
Found at i:25153449 original size:11 final size:11
Alignment explanation
Indices: 25153430--25153463 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
25153420 GATAAAATTA
25153430 GATACTGTAAC
1 GATACTGTAAC
*
25153441 GATATTGTAAC
1 GATACTGTAAC
25153452 GATACTGTAAC
1 GATACTGTAAC
25153463 G
1 G
25153464 TGAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (11 bp):
GATACTGTAAC
Found at i:25154837 original size:18 final size:19
Alignment explanation
Indices: 25154796--25154843 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
25154786 GATAATTACG
*
25154796 TTTATTTTTTGAATTAAGA
1 TTTATTTTTTAAATTAAGA
* *
25154815 GTTATTTTTTAAATTTA-A
1 TTTATTTTTTAAATTAAGA
25154833 TTTATTATTTT
1 TTTATT-TTTT
25154844 CCACATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTATTTTTTAAATTAAGA
Found at i:25159222 original size:2 final size:2
Alignment explanation
Indices: 25159215--25159247 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25159205 CTCTAACTAA
25159215 TC TC 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 TC TC T
25159248 TCACATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25167460 original size:156 final size:156
Alignment explanation
Indices: 25167173--25167626 Score: 687
Period size: 156 Copynumber: 2.9 Consensus size: 156
25167163 CATGGGCCAT
*
25167173 TCTTTTGTGAAAACGGCAACGTTTTACATTATTTTCATAA-AGTGTTCATTTAGTGCAATAAACC
1 TCTTTTGTGAAAACGGCAACGTTTTACATTATTTT-A-AATAGAG-T-ATTTAGTGCAATAAACC
*
25167237 AACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGAC
62 AATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGAC
**
25167302 CTGCATGGGCCATTGTTACAATTTCCTTTG
127 CTGCATGGGCCATTAATACAATTTCCTTTG
*
25167332 TCTTTTGTGAAAACGGCAACGTTTTACATTACTTTT-AATAGAGTATTTGGTGCAATAAACCAAT
1 TCTTTTGTGAAAACGGCAACGTTTTACATTA-TTTTAAATAGAGTATTTAGTGCAATAAACCAAT
25167396 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
65 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* * *
25167461 CATGGGCCATTAATGCAATTTCTTTTT
130 CATGGGCCATTAATACAATTTCCTTTG
* *
25167488 TCTTTTGTGGAAACTGCAACGTTTTACATTATTTTAAATAGAGTATTTAGTGCAATAAACCAATG
1 TCTTTTGTGAAAACGGCAACGTTTTACATTATTTTAAATAGAGTATTTAGTGCAATAAACCAATG
* * * * * *
25167553 GCCCATTAGCTCAGCCGTTTAGAGCGTCGTGCTAATATCGCGAAGGGCGTAGGTTCGAGACCTGC
66 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
* *
25167618 CTAGGCCAT
131 ATGGGCCAT
25167627 ATTTTTGTCA
Statistics
Matches: 273, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
155 4 0.01
156 228 0.84
157 3 0.01
158 3 0.01
159 31 0.11
160 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (156 bp):
TCTTTTGTGAAAACGGCAACGTTTTACATTATTTTAAATAGAGTATTTAGTGCAATAAACCAATG
GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
ATGGGCCATTAATACAATTTCCTTTG
Found at i:25181954 original size:17 final size:17
Alignment explanation
Indices: 25181931--25181971 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25181921 TTGGTTAAAT
*
25181931 ATATATTTGCACTTGTA
1 ATATATTTGCACGTGTA
* *
25181948 TTATATTTGTACGTGTA
1 ATATATTTGCACGTGTA
25181965 ATATATT
1 ATATATT
25181972 AATTTATACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (17 bp):
ATATATTTGCACGTGTA
Found at i:25182676 original size:23 final size:22
Alignment explanation
Indices: 25182637--25182686 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
25182627 AACAACTTTT
* *
25182637 AATAAAATTAAAAAATATTAAA
1 AATAAAAATAAAAAATAATAAA
* *
25182659 AATAAAACATAAATAATAATAAT
1 AATAAAA-ATAAAAAATAATAAA
25182682 AATAA
1 AATAA
25182687 TATTTATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAAAATAAAAAATAATAAA
Found at i:25183218 original size:23 final size:23
Alignment explanation
Indices: 25183192--25183236 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
25183182 AATCGTTTAA
*
25183192 TTTAATCTTTCTTTTCTCTATTT
1 TTTAAGCTTTCTTTTCTCTATTT
*
25183215 TTTAAGGTTTCTTTTCTCTATT
1 TTTAAGCTTTCTTTTCTCTATT
25183237 AATTAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTAAGCTTTCTTTTCTCTATTT
Found at i:25183242 original size:23 final size:23
Alignment explanation
Indices: 25183199--25183242 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25183189 TAATTTAATC
**
25183199 TTTCTTTTCTCTATTTTTTAAGG
1 TTTCTTTTCTCTATTAATTAAGG
25183222 TTTCTTTTCTCTATTAATTAA
1 TTTCTTTTCTCTATTAATTAA
25183243 AGTAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTCTTTTCTCTATTAATTAAGG
Found at i:25183579 original size:119 final size:123
Alignment explanation
Indices: 25183345--25183584 Score: 330
Period size: 119 Copynumber: 2.0 Consensus size: 123
25183335 AGCCTTCCAC
* * *
25183345 AATGGACACCTGTCCATTGTTTTTTCTTCTCTTTTTACATGAGAATACAACGGTAAATTTTAATT
1 AATGGACACCTGTCCATTGTTTTTTCTTCTCTTTTCACATGAGAACACAACGGTAAATTTCAATT
* * *
25183410 CCAATCCCTTCATTTTTGTTTAAATTATAAGAATGGTTAAATTTCTATTTGATCTTTAT
66 CCAATCCCTT-ATATCTGTTTAAATTATAAGAATGGTTAAATTTCAATTTGATCTTTAT
* * *
25183469 AATGGACACCTGTCTA-T-TTTTTTCTT-T-TTTTCACATGAGAACATAATGGGTAAATTTCAAT
1 AATGGACACCTGTCCATTGTTTTTTCTTCTCTTTTCACATGAGAACACAA-CGGTAAATTTCAAT
25183530 TCCAATCCCTT-TATCT-TTTAAGATTATAAGAATGGTTAAATTTCAATTTGATCTT
65 TCCAATCCCTTATATCTGTTTAA-ATTATAAGAATGGTTAAATTTCAATTTGATCTT
25183585 ATATTTCACT
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
118 5 0.05
119 35 0.33
120 16 0.15
121 24 0.23
122 9 0.09
123 1 0.01
124 15 0.14
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (123 bp):
AATGGACACCTGTCCATTGTTTTTTCTTCTCTTTTCACATGAGAACACAACGGTAAATTTCAATT
CCAATCCCTTATATCTGTTTAAATTATAAGAATGGTTAAATTTCAATTTGATCTTTAT
Found at i:25189364 original size:29 final size:29
Alignment explanation
Indices: 25189263--25189607 Score: 299
Period size: 29 Copynumber: 11.9 Consensus size: 29
25189253 CTAAACTTCA
* *
25189263 CAAAAATTACATTTTTACTCC-CAAACTTTT
1 CAAAAATCACATTTTTAC-CCTCGAAC-TTT
* * ** * *
25189293 TAAAAATTACA-TTTCGCCCCCGAACTTC
1 CAAAAATCACATTTTTACCCTCGAACTTT
*
25189321 CAAAAATCACATTTTTTCCCTCGAACTTT
1 CAAAAATCACATTTTTACCCTCGAACTTT
* * *
25189350 TAAAAATCACATTTTTACCCTCGATCTTC
1 CAAAAATCACATTTTTACCCTCGAACTTT
* * *
25189379 CAAAAATTACATTTTTACCCTTGAACTTC
1 CAAAAATCACATTTTTACCCTCGAACTTT
*
25189408 CAAAAATCACATTTTTTCCCTCGAACTTT
1 CAAAAATCACATTTTTACCCTCGAACTTT
* * * *
25189437 TAAAAATAACATTTTTACCCTCGATCTTC
1 CAAAAATCACATTTTTACCCTCGAACTTT
* **
25189466 CAAAAATTACATTTTTACCCTTAAACTTT
1 CAAAAATCACATTTTTACCCTCGAACTTT
*
25189495 CAAAAATCACATTTTT-CCCTAG-ACTTCT
1 CAAAAATCACATTTTTACCCTCGAACTT-T
* *
25189523 CAAAAATCACATATTTACCCT-GAACTCTC
1 CAAAAATCACATTTTTACCCTCGAACT-TT
* * *
25189552 CTAAAATAACATTTTTACCC-CTAAAGCTTT
1 CAAAAATCACATTTTTACCCTC-GAA-CTTT
* * *
25189582 CCAAAATTACATTTTAACCC-CGAACT
1 CAAAAATCACATTTTTACCCTCGAACT
25189608 CTCTAAAACT
Statistics
Matches: 258, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
27 4 0.02
28 36 0.14
29 184 0.71
30 32 0.12
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
CAAAAATCACATTTTTACCCTCGAACTTT
Found at i:25189595 original size:87 final size:88
Alignment explanation
Indices: 25189318--25189596 Score: 399
Period size: 87 Copynumber: 3.2 Consensus size: 88
25189308 GCCCCCGAAC
25189318 TTCCAAAAATCACATTTTTTCCCTCGAACTTTTAAAAATCACATTTTTACCCTCGATCTTCCAAA
1 TTCCAAAAATCACATTTTTTCCCTCGAACTTTTAAAAATCACATTTTTACCCTCGATCTTCCAAA
*
25189383 AATTACATTTTTACCCTTGAAC-
66 AATTACATTTTTACCCTTAAACT
*
25189405 TTCCAAAAATCACATTTTTTCCCTCGAACTTTTAAAAATAACATTTTTACCCTCGATCTTCCAAA
1 TTCCAAAAATCACATTTTTTCCCTCGAACTTTTAAAAATCACATTTTTACCCTCGATCTTCCAAA
25189470 AATTACATTTTTACCCTTAAACT
66 AATTACATTTTTACCCTTAAACT
* * * * *
25189493 TT-CAAAAATCACA-TTTTTCCCTAG-ACTTCTCAAAAATCACATATTTACCCT-GAACTCTCCT
1 TTCCAAAAATCACATTTTTTCCCTCGAACTT-TTAAAAATCACATTTTTACCCTCGATCT-TCCA
* *
25189554 AAAATAACATTTTTACCCCTAAAGCT
64 AAAATTACATTTTTACCCTTAAA-CT
*
25189580 TTCC-AAAATTACATTTT
1 TTCCAAAAATCACATTTT
25189597 AACCCCGAAC
Statistics
Matches: 175, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
85 8 0.05
86 53 0.30
87 108 0.62
88 6 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (88 bp):
TTCCAAAAATCACATTTTTTCCCTCGAACTTTTAAAAATCACATTTTTACCCTCGATCTTCCAAA
AATTACATTTTTACCCTTAAACT
Found at i:25190922 original size:18 final size:17
Alignment explanation
Indices: 25190893--25190947 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
25190883 CTTAATAATC
* *
25190893 AAATTTAGAATAATTTT
1 AAATTTAAAATAAATTT
25190910 AAATTTATAAATAAATTT
1 AAATTTA-AAATAAATTT
25190928 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATTT
25190945 AAA
1 AAA
25190948 AAATGGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:25191189 original size:3 final size:3
Alignment explanation
Indices: 25191181--25191229 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
25191171 ATCAACATTA
25191181 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25191229 A
1 A
25191230 CTATAATCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25193568 original size:19 final size:19
Alignment explanation
Indices: 25193529--25193569 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
25193519 CTTCATGCAA
* *
25193529 AATTCATGTACGTTGATTG
1 AATTCATGTACGTCGAATG
*
25193548 AATTCATGTGCGTCGAATG
1 AATTCATGTACGTCGAATG
25193567 AAT
1 AAT
25193570 GCAAGAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (19 bp):
AATTCATGTACGTCGAATG
Found at i:25196147 original size:18 final size:16
Alignment explanation
Indices: 25196115--25196150 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
25196105 ATGGAATGAG
25196115 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
25196131 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
25196149 AA
1 AA
25196151 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:25201475 original size:24 final size:24
Alignment explanation
Indices: 25201448--25201516 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
25201438 GAGCGAAGCT
*
25201448 AAATTTTTTTATATAATTTATATA
1 AAATATTTTTATATAATTTATATA
* *
25201472 AAATAATTTTAT-TAAATATATATA
1 AAATATTTTTATAT-AATTTATATA
*
25201496 ATTTATATTTTTATATAATTT
1 A--AATATTTTTATATAATTT
25201517 TTAGAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.03
24 20 0.57
26 13 0.37
27 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATATTTTTATATAATTTATATA
Found at i:25202151 original size:19 final size:19
Alignment explanation
Indices: 25202105--25202163 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
25202095 AAGTCCTTTT
*
25202105 AAAAAT-TAAAAATTAT-T
1 AAAAATATAAAAATTATAA
*
25202122 AACAATCATAAAAATTATAA
1 AAAAAT-ATAAAAATTATAA
25202142 AAAAATATAAAATATTA-AA
1 AAAAATATAAAA-ATTATAA
25202161 AAA
1 AAA
25202164 CAACAATACC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 5 0.14
19 21 0.60
20 9 0.26
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATATAAAAATTATAA
Found at i:25208317 original size:12 final size:14
Alignment explanation
Indices: 25208292--25208321 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25208282 TATAAATATT
25208292 ATATATAAAGAAAA
1 ATATATAAAGAAAA
*
25208306 ATATATAAAAAAAA
1 ATATATAAAGAAAA
25208320 AT
1 AT
25208322 TAGTTGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
ATATATAAAGAAAA
Found at i:25219625 original size:6 final size:6
Alignment explanation
Indices: 25219607--25219689 Score: 68
Period size: 6 Copynumber: 14.0 Consensus size: 6
25219597 TTAAATTGAT
*
25219607 TTTAAA TTT--A TTTGAA TTTAAA TTT--A TCTTAAA TTTAATTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA--A TTTAAA
* *
25219654 TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
25219690 ACAAATTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
4 6 0.10
5 5 0.08
6 40 0.63
7 6 0.10
8 6 0.10
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:25219689 original size:25 final size:23
Alignment explanation
Indices: 25219616--25219681 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 23
25219606 TTTTAAATTT
*
25219616 ATTTGAATTTAAATTT-ATCTTAA
1 ATTTAAATTTAAATTTAAT-TTAA
**
25219639 ATTTAATTATTTAAATTTACCTTAA
1 ATTTAA--ATTTAAATTTAATTTAA
25219664 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAA
25219682 ATTATAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.44
25 20 0.56
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:25231561 original size:76 final size:75
Alignment explanation
Indices: 25231434--25231841 Score: 483
Period size: 76 Copynumber: 5.5 Consensus size: 75
25231424 TTGAGGTAGA
* *
25231434 GTCTTTATCTCTGAAATTGAAGTAAGAGC-AG-CGTCATTTCCTATCCACTTGAAATTGAAGTAA
1 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAC--CATTTCCTATCCTCTTGAAATTGAAGTAG
* *
25231497 AGTTGGATATCAA
64 AG-TGGATAACAC
* *
25231510 ATCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCTTTTCCTATCCTCTTGAAATTGAAGTAGAG
1 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAATTGAAGTAGAG
*
25231575 TCGGATAGCAC
66 T-GGATAACAC
* * * *
25231586 GTTTTTATCTCCGAAATTGAAGTAAGGGC-A-A-C--GT-C-ATCCTCTTGAAATTGAAGTAGAG
1 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAATTGAAGTAGAG
25231644 TGGATAACAC
66 TGGATAACAC
* * *
25231654 ATCTTTATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG
1 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAATTGAAGTAGAG
25231719 TGGATAACAC
66 TGGATAACAC
* * * *
25231729 GTCTTTATCTCTGGAATTGAAATAAGAGCAAGATCATTTTCCTATCCTCTTGAAATTGAAGTAAA
1 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCA-TTTCCTATCCTCTTGAAATTGAAGTAGA
* *
25231794 GCTGGATATCAA
65 G-TGGATAACAC
* *
25231806 GTCTTTATCTCTCTGAAATTGAAGCAAGAGCTAGAC
1 GTCTTTA--TCTCTGAAATTGAAGTAAGAGCAAGAC
25231842 GAAGCATCAA
Statistics
Matches: 288, Mismatches: 30, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
68 32 0.11
69 25 0.09
70 2 0.01
71 2 0.01
73 2 0.01
74 2 0.01
75 67 0.23
76 116 0.40
77 17 0.06
78 1 0.00
79 22 0.08
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (75 bp):
GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAATTGAAGTAGAG
TGGATAACAC
Found at i:25231563 original size:38 final size:37
Alignment explanation
Indices: 25231521--25231792 Score: 121
Period size: 38 Copynumber: 7.4 Consensus size: 37
25231511 TCTTTATCTC
25231521 TGAAATTGAAGTAAGAGCAAGACCTTTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGACCTTTT-CTATCCTCT
*
25231559 TGAAATTGAAGT-AGAGTCGGATAGCACGTTTT-TAT-CTC-
1 TGAAATTGAAGTAAGAG-C--A-AG-ACCTTTTCTATCCTCT
* * *
25231597 CGAAATTGAAGTAAGGGC-A-A-C--GTC-ATCCTCT
1 TGAAATTGAAGTAAGAGCAAGACCTTTTCTATCCTCT
* * *
25231628 TGAAATTGAAGTAGAGTGGATA-ACACATCTT-TAT-CTC-
1 TGAAATTGAAGTA-AGAGCA-AGAC-C-TTTTCTATCCTCT
* * *
25231665 TGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGA-CCTTTTCTATCCTCT
* * *
25231703 TGAAATTGAAGTAGAGTGGATA-ACACGTCTT-TAT-CTC-
1 TGAAATTGAAGTA-AGAGCA-AGAC-C-TTTTCTATCCTCT
* * *
25231740 TGGAATTGAAATAAGAGCAAGATCATTTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGA-CCTTTT-CTATCCTCT
25231779 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
25231793 AGCTGGATAT
Statistics
Matches: 172, Mismatches: 29, Indels: 65
0.65 0.11 0.24
Matches are distributed among these distances:
29 3 0.02
30 3 0.02
31 12 0.07
32 4 0.02
34 3 0.02
35 7 0.04
36 13 0.08
37 36 0.21
38 48 0.28
39 28 0.16
40 7 0.04
41 2 0.01
42 6 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (37 bp):
TGAAATTGAAGTAAGAGCAAGACCTTTTCTATCCTCT
Found at i:25231675 original size:144 final size:149
Alignment explanation
Indices: 25231434--25231841 Score: 490
Period size: 144 Copynumber: 2.7 Consensus size: 149
25231424 TTGAGGTAGA
* * * * *
25231434 GTCTTTATCTCTGAAATTGAAGTAAGAGC-AGCGTCATTTCCTATCCACTTGAAATTGAAGTAAA
1 GTCTTTATCTCCGAAATTGAAATAAGAGCAAG-ATC-TGTCCTATCCTCTTGAAATTGAAGTAAA
* *
25231498 GTTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCTTTTCCTATCCTCTTGAA
64 GCTGGATATC-AATCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAA
*
25231563 ATTGAAGTAGAGTCGGATAGCAC
128 ATTGAAGTAGAGT-GGATAACAC
* * * *
25231586 GTTTTTATCTCCGAAATTGAAGTAAGGGC-A-A-C-GT-C-ATCCTCTTGAAATTGAAGTAGAG-
1 GTCTTTATCTCCGAAATTGAAATAAGAGCAAGATCTGTCCTATCCTCTTGAAATTGAAGTAAAGC
* * *
25231644 TGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAAT
66 TGGATATCA-ATCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAAT
25231709 TGAAGTAGAGTGGATAACAC
130 TGAAGTAGAGTGGATAACAC
* * *
25231729 GTCTTTATCTCTGGAATTGAAATAAGAGCAAGATCATTTTCCTATCCTCTTGAAATTGAAGTAAA
1 GTCTTTATCTCCGAAATTGAAATAAGAGCAAGATC--TGTCCTATCCTCTTGAAATTGAAGTAAA
* *
25231794 GCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGCAAGAGCTAGAC
64 GCTGGATATCAA-TCTTTA--TCTCTGAAATTGAAGTAAGAGCAAGAC
25231842 GAAGCATCAA
Statistics
Matches: 219, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
143 33 0.15
144 71 0.32
145 22 0.10
146 2 0.01
147 1 0.00
149 2 0.01
150 1 0.00
151 23 0.11
152 41 0.19
154 23 0.11
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (149 bp):
GTCTTTATCTCCGAAATTGAAATAAGAGCAAGATCTGTCCTATCCTCTTGAAATTGAAGTAAAGC
TGGATATCAATCTTTATCTCTGAAATTGAAGTAAGAGCAAGACCATTTCCTATCCTCTTGAAATT
GAAGTAGAGTGGATAACAC
Found at i:25232229 original size:6 final size:6
Alignment explanation
Indices: 25232208--25232274 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 6
25232198 TTAAATTGAT
* *
25232208 TTTAAA TTT--A TCTTAAA TTTAATTA TTTAAA TTT-AC CTTAAA TTTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA
25232256 TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TT-TAAA
25232275 ACAAATTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 5 0.10
6 31 0.62
7 6 0.12
8 6 0.12
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:25232239 original size:25 final size:23
Alignment explanation
Indices: 25232208--25232265 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 23
25232198 TTAAATTGAT
*
25232208 TTTAAATTTATCTTAAATTTAATTA
1 TTTAAATTTACCTTAAATTTAA--A
25232233 TTTAAATTTACCTTAAATTTAAA
1 TTTAAATTTACCTTAAATTTAAA
25232256 TTTAAATTTA
1 TTTAAATTTA
25232266 AATTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 11 0.34
25 21 0.66
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATTTACCTTAAATTTAAA
Found at i:25235990 original size:19 final size:19
Alignment explanation
Indices: 25235957--25236001 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
25235947 AAAATTTAAA
*
25235957 ATAATTTTATTTTATTTTT
1 ATAAATTTATTTTATTTTT
25235976 A-AAATTTATTATTATTTTT
1 ATAAATTTATT-TTATTTTT
25235995 ATAAATT
1 ATAAATT
25236002 AAATAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAAATTTATTTTATTTTT
Found at i:25238621 original size:23 final size:23
Alignment explanation
Indices: 25238591--25238636 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
25238581 AAAATAAATC
25238591 AATTTAAATTAAAA-TCTAAATTT
1 AATTTAAA-TAAAAGTCTAAATTT
25238614 AATTTAAATAAAATGTCTAAATT
1 AATTTAAATAAAA-GTCTAAATT
25238637 ACAAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
AATTTAAATAAAAGTCTAAATTT
Found at i:25238683 original size:22 final size:22
Alignment explanation
Indices: 25238658--25238703 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
25238648 ACCCACATAT
*
25238658 ACAAGCCTAAATCACAAAACCC
1 ACAAGCCCAAATCACAAAACCC
*
25238680 ACAAGCCCAAATCATAAAACCC
1 ACAAGCCCAAATCACAAAACCC
25238702 AC
1 AC
25238704 TAAACATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.37, G:0.04, T:0.09
Consensus pattern (22 bp):
ACAAGCCCAAATCACAAAACCC
Found at i:25238765 original size:16 final size:16
Alignment explanation
Indices: 25238744--25238800 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
25238734 ACCATCACTA
*
25238744 CCACGTCAGCACCTGT
1 CCACGTCAGCACATGT
25238760 CCACGTCAGCACATGT
1 CCACGTCAGCACATGT
* * *
25238776 TCACGTCAACA-ATCT
1 CCACGTCAGCACATGT
25238791 CCACGTCAGC
1 CCACGTCAGC
25238801 GCCATGTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
15 11 0.31
16 24 0.69
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (16 bp):
CCACGTCAGCACATGT
Done.