Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_pilon, 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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 21
Found at i:1985690 original size:130 final size:130
Alignment explanation
Indices: 1985486--1985733 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1985476 AATTTTCTTC
* *
1985486 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATATGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
** *
1985551 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
1985616 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTTAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
1985681 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1985734 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1986180 original size:35 final size:35
Alignment explanation
Indices: 1986130--1986205 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1986120 AATTGAATTT
* *
1986130 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1986165 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1986200 AATTGA
1 AATTGA
1986206 GGACTGCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1991772 original size:64 final size:63
Alignment explanation
Indices: 1991640--1991800 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
1991630 AATTGTTCAG
* * * * *
1991640 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATT
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
* * **
1991703 GGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGCATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATT
** * *
1991767 TGTGCATCGATGCACGGGTACTGCATCGATGCAC
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCAC
1991801 ATGCTAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 29 0.35
64 53 0.65
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (63 bp):
TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
Found at i:1991834 original size:20 final size:20
Alignment explanation
Indices: 1991769--1991865 Score: 115
Period size: 20 Copynumber: 4.7 Consensus size: 20
1991759 AGGTGATTTG
* * *
1991769 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
1991788 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
1991812 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
1991832 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
1991852 TGCATCGATGCACT
1 TGCATCGATGCACT
1991866 TCAAGGGAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.19
20 38 0.56
22 1 0.01
23 2 0.03
24 14 0.21
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:1992348 original size:2 final size:2
Alignment explanation
Indices: 1992341--1992403 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1992331 CATGTTACAG
1992341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1992383 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1992404 GAGTTGTGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1992992 original size:31 final size:30
Alignment explanation
Indices: 1992957--1993035 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
1992947 GTCTTTCGAG
*
1992957 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGT-TACCTAGGTTCTAAGGA
* ** *
1992988 ACATATGGATAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAG-TTACCTAGGTTCTAAGGA
*
1993019 ACCTATGGACAGTTACC
1 ACATATGGACAGTTACC
1993036 GAGGATCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.12
31 34 0.85
32 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
ACATATGGACAGTTACCTAGGTTCTAAGGA
Found at i:1993052 original size:30 final size:30
Alignment explanation
Indices: 1993018--1993120 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
1993008 GGTTCTTCGG
* *
1993018 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1993048 GACCTCTGGATAGTTACCGAGAATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1993078 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1993108 GACCTCTGGATAG
1 GACCTCTGGATAG
1993121 GTCCTTCGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1994820 original size:17 final size:17
Alignment explanation
Indices: 1994784--1994831 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1994774 GTTACAAAAT
*
1994784 AATATAATATTATAACA
1 AATATAAAATTATAACA
* *
1994801 AATATAAAATTTTAATA
1 AATATAAAATTATAACA
*
1994818 AATTTAACAATTAT
1 AATATAA-AATTAT
1994832 TTTATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATTATAACA
Found at i:1994838 original size:31 final size:31
Alignment explanation
Indices: 1994803--1994887 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
1994793 TTATAACAAA
1994803 TATAA-AATTTTAAT-AAATTTAACAATTATTT
1 TATAATAA-TTTAATAAAATTTAA-AATTATTT
1994834 TATAATAATTTAATAAAATTTAAAATTATTT
1 TATAATAATTTAATAAAATTTAAAATTATTT
* * **
1994865 TAAAATTATTTGGTAAAATTTAA
1 TATAATAATTTAATAAAATTTAA
1994888 TTACTATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 38 0.79
32 10 0.21
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
TATAATAATTTAATAAAATTTAAAATTATTT
Found at i:1994851 original size:42 final size:41
Alignment explanation
Indices: 1994804--1994888 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
1994794 TATAACAAAT
* *
1994804 ATAAAATTT-TAATAAATTTAACAATTATTTTATAATAATTTA
1 ATAAAATTTAAAATAAATTTAA-AATTATTTGATAA-AATTTA
* * *
1994846 ATAAAATTTAAAATTATTTTAAAATTATTTGGTAAAATTTA
1 ATAAAATTTAAAATAAATTTAAAATTATTTGATAAAATTTA
1994887 AT
1 AT
1994889 TACTATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 8 0.22
42 20 0.54
43 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (41 bp):
ATAAAATTTAAAATAAATTTAAAATTATTTGATAAAATTTA
Found at i:1994956 original size:27 final size:30
Alignment explanation
Indices: 1994925--1994986 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 30
1994915 ATGATTTTTT
* *
1994925 AAATAGTTTTTTAAA-A-ATTT-ATAATTA
1 AAATAATTATTTAAATAGATTTAATAATTA
1994952 AAATAATTATTTAAATATGATTTAATAATTA
1 AAATAATTATTTAAATA-GATTTAATAATTA
1994983 AAAT
1 AAAT
1994987 GATATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.45
28 1 0.03
30 4 0.14
31 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATAATTATTTAAATAGATTTAATAATTA
Found at i:1995014 original size:20 final size:21
Alignment explanation
Indices: 1994955--1995023 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
1994945 ATAATTAAAA
1994955 TAAT-TATTTAAAT-ATGA-TT
1 TAATATATTTAAATGAT-ATTT
*
1994974 TAATA-ATTAAAATGATATTT
1 TAATATATTTAAATGATATTT
*
1994994 TAGTATATTTAAATGAT-TTT
1 TAATATATTTAAATGATATTT
1995014 TAATATATTT
1 TAATATATTT
1995024 TTATCCAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 12 0.29
20 20 0.48
21 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATATATTTAAATGATATTT
Found at i:2012036 original size:60 final size:60
Alignment explanation
Indices: 2011951--2012122 Score: 170
Period size: 60 Copynumber: 2.9 Consensus size: 60
2011941 AGTATGATTC
* * * ** * * * *
2011951 TCATTTTAAATTAGTCTTTAAACTTTTAAATGTTTCAATTTCGTCTCTAAACTATGA-CT
1 TCATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCT
* *
2012010 ATCATTATAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCCCAAACCATTACCT
1 -TCATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCT
* * *
2012071 TCATTCTAAATTGGTCCCCAAACTTTTTAAACA-TTCTAATTTCAT-CCCAAAC
1 TCATTATAAATTAGTCCTCAAAC-TTTTAAACATTTC-AATTTCATCCCCAAAC
2012123 TATACGTATA
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
60 76 0.81
61 18 0.19
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
TCATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCT
Found at i:2013824 original size:19 final size:20
Alignment explanation
Indices: 2013796--2013834 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2013786 TTTGGGAAAA
*
2013796 ATCGG-TTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
2013815 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
2013835 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:2016239 original size:21 final size:21
Alignment explanation
Indices: 2016215--2016254 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2016205 TTTATTTTAT
2016215 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2016236 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2016255 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2016300 original size:33 final size:33
Alignment explanation
Indices: 2016249--2016347 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
2016239 TTTGTTTCAA
2016249 TTATCGAAC-TTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
2016281 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
* * * * *
2016314 TCATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
2016347 T
1 T
2016348 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 9 0.15
33 52 0.85
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
Found at i:2016312 original size:17 final size:17
Alignment explanation
Indices: 2016258--2016312 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
2016248 ATTATCGAAC
2016258 TTGAAGTTTTTAAGTAT
1 TTGAAGTTTTTAAGTAT
* * *
2016275 TTGAA-TTTAT-CGAACT
1 TTGAAGTTTTTAAGTA-T
2016291 TTGAAGTTTTTAAGTAT
1 TTGAAGTTTTTAAGTAT
2016308 TTGAA
1 TTGAA
2016313 TTCATCAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 15 0.52
18 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (17 bp):
TTGAAGTTTTTAAGTAT
Found at i:2016376 original size:13 final size:13
Alignment explanation
Indices: 2016333--2016387 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2016323 TTGGAAGTAT
2016333 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2016346 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2016360 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2016373 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2016386 TT
1 TT
2016388 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2016608 original size:21 final size:21
Alignment explanation
Indices: 2016582--2016639 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2016572 TTGGAGCATG
*
2016582 AGGGAATCGGTACCCTCTCAT
1 AGGGAATCGGTTCCCTCTCAT
* *
2016603 AGGGAATCGGTTTCATCTCAT
1 AGGGAATCGGTTCCCTCTCAT
2016624 AGGGAATCGGTTCCCT
1 AGGGAATCGGTTCCCT
2016640 AAGTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
AGGGAATCGGTTCCCTCTCAT
Found at i:2016829 original size:15 final size:15
Alignment explanation
Indices: 2016804--2016859 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2016794 ATCTGGAATA
*
2016804 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2016819 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
2016834 TAGAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
2016851 TTAAAACCG
1 TTAAAACCG
2016860 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2016976 original size:15 final size:17
Alignment explanation
Indices: 2016950--2016981 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2016940 TTCTATGGGG
2016950 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
2016966 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
2016982 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:2022714 original size:26 final size:26
Alignment explanation
Indices: 2022678--2022730 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2022668 GATTGGAAAA
2022678 GTTGTCAATTTTCTCCACTCCCTCAT
1 GTTGTCAATTTTCTCCACTCCCTCAT
2022704 GTTGTCAATTTTCTCCACTCCCTCAT
1 GTTGTCAATTTTCTCCACTCCCTCAT
2022730 G
1 G
2022731 AGACGACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.09, T:0.42
Consensus pattern (26 bp):
GTTGTCAATTTTCTCCACTCCCTCAT
Found at i:2028397 original size:19 final size:19
Alignment explanation
Indices: 2028373--2028409 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2028363 ATGACCAACA
*
2028373 AAATCGCAATGTGATCTCT
1 AAATCGCAACGTGATCTCT
2028392 AAATCGCAACGTGATCTC
1 AAATCGCAACGTGATCTC
2028410 CAGTATCGCA
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:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGCAACGTGATCTCT
Found at i:2028515 original size:21 final size:21
Alignment explanation
Indices: 2028491--2028566 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
2028481 TGAATATGTA
2028491 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
* **
2028512 AATCGTAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
2028533 -ATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
*
2028553 AAGCGCAACGCGAT
1 AATCGCAACGCGAT
2028567 TCTAACTATC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:2028537 original size:41 final size:41
Alignment explanation
Indices: 2028492--2028626 Score: 193
Period size: 41 Copynumber: 3.3 Consensus size: 41
2028482 GAATATGTAA
*
2028492 ATCGCAACGCGATAATACATAATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* *
2028533 ATCGCAACGCGATAATACATAAGCGCAACGCGATTCTAACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
**
2028574 ATCGCAACGCGATTCTGAC-T-ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAAT-ACATAATCGCAACGCGATTCTGACT
*
2028614 GTCGCAACGCGAT
1 ATCGCAACGCGAT
2028627 TCTGACTGTC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 30 0.35
41 53 0.62
42 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
Found at i:2028541 original size:20 final size:20
Alignment explanation
Indices: 2028513--2028643 Score: 174
Period size: 20 Copynumber: 6.5 Consensus size: 20
2028503 ATAATACATA
*
2028513 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
2028533 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
2028553 AAGCGCAACGCGATTCTAACT
1 -ATCGCAACGCGATTCTGACT
2028574 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2028594 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2028614 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2028634 GTCGCAACGC
1 ATCGCAACGC
2028644 TGAATTTCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.82
21 14 0.14
22 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2029496 original size:24 final size:24
Alignment explanation
Indices: 2029464--2029517 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2029454 GTATTTGAAA
2029464 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2029488 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2029512 TTTGAT
1 TTTGAT
2029518 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2029725 original size:15 final size:15
Alignment explanation
Indices: 2029707--2029743 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2029697 AGAAAAAGAA
2029707 GAAGAAAAAATCCCC
1 GAAGAAAAAATCCCC
*
2029722 GAAG-AAAAGTCCCC
1 GAAGAAAAAATCCCC
2029736 GAAGAAAA
1 GAAGAAAA
2029744 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAATCCCC
Found at i:2031789 original size:12 final size:12
Alignment explanation
Indices: 2031774--2031804 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2031764 CAAGAAAAAG
2031774 GCAATCAAAATC
1 GCAATCAAAATC
2031786 GCAATCAAAATC
1 GCAATCAAAATC
2031798 GCAATCA
1 GCAATCA
2031805 CAACCGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:2032114 original size:140 final size:140
Alignment explanation
Indices: 2031862--2032144 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
2031852 GCAAACGTTG
*
2031862 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTATGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
2031927 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
2031992 CGAATTTGAC
131 CGAATTTGAC
*
2032002 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAAGTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
2032067 TTGAACATTGCTATGATATGTTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
2032132 TGAATTTGAC
131 CGAATTTGAC
2032142 TAT
1 TAT
2032145 CGCAACTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:2032182 original size:20 final size:20
Alignment explanation
Indices: 2032157--2032279 Score: 125
Period size: 20 Copynumber: 6.5 Consensus size: 20
2032147 CAACTCAAAA
*
2032157 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
2032177 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATTTGACT
* *
2032197 ATCGCAATGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
2032211 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* * *
2032231 ATCGCAATGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
2032251 ATCGCAACAG-GAATTTGACT
1 ATCGCAAC-GCGAATTTGACT
2032271 ATCGCAACG
1 ATCGCAACG
2032280 AGAAAAACGC
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
14 9 0.11
15 3 0.04
19 4 0.05
20 68 0.80
21 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:2032197 original size:54 final size:55
Alignment explanation
Indices: 2032115--2032258 Score: 220
Period size: 54 Copynumber: 2.7 Consensus size: 55
2032105 TTACACATTC
*
2032115 ATTTGAATATCGCAATGTGAATTTGACTATCGCAACT-CAAAAATCGCAACGCAA
1 ATTTGACTATCGCAATGTGAATTTGACTATCGCAACTGCAAAAATCGCAACGCAA
* * * *
2032169 ATTTGACTATCGCAACGCGAATATGACTATCGCAA-TGCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAATGTGAATTTGACTATCGCAACTGCAAAAATCGCAACGCAA
*
2032223 ATTTGACTATCGCAATGTGAATTTGATTATCGCAAC
1 ATTTGACTATCGCAATGTGAATTTGACTATCGCAAC
2032259 AGGAATTTGA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 78 0.99
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (55 bp):
ATTTGACTATCGCAATGTGAATTTGACTATCGCAACTGCAAAAATCGCAACGCAA
Found at i:2032235 original size:74 final size:74
Alignment explanation
Indices: 2032157--2032328 Score: 206
Period size: 74 Copynumber: 2.3 Consensus size: 74
2032147 CAACTCAAAA
* * * * *
2032157 ATCGCAACGCAAATTTGACTATCGCAAC-GCGAATATGACTATCGCAATGCA-AAAATCGCAACG
1 ATCGCAATGCGAATTTGACTATCGCAACAG-GAATATGACTATCGCAACG-AGAAAAACGCAAAG
*
2032220 CGAATTTGACT
64 CGAATTAGACT
* * *
2032231 ATCGCAATGTGAATTTGATTATCGCAACAGGAATTTGACTATCGCAACGAGAAAAACGCAAAGCG
1 ATCGCAATGCGAATTTGACTATCGCAACAGGAATATGACTATCGCAACGAGAAAAACGCAAAGCG
*
2032296 TATTAGACT
66 AATTAGACT
*
2032305 ATCGCAATGCGAA-TTGACTTTCGC
1 ATCGCAATGCGAATTTGACTATCGC
2032329 GTTGCGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
73 10 0.12
74 72 0.87
75 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (74 bp):
ATCGCAATGCGAATTTGACTATCGCAACAGGAATATGACTATCGCAACGAGAAAAACGCAAAGCG
AATTAGACT
Found at i:2032367 original size:40 final size:40
Alignment explanation
Indices: 2032301--2032414 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
2032291 AAGCGTATTA
* * *
2032301 GACTATCGCAATGCGA-ATTGACTTTCGCGTTGCGATTTT
1 GACTTTCGCATTGCGATTTTGACTTTCGCGTTGCGATTTT
* * *
2032340 GGCTTTCGCATTGCGATTTTGACTTTCGCATTGTGATTTT
1 GACTTTCGCATTGCGATTTTGACTTTCGCGTTGCGATTTT
* *
2032380 GACTTTCGCATTGCGATTTTGAGTTTAGCGTTGCG
1 GACTTTCGCATTGCGATTTTGACTTTCGCGTTGCG
2032415 GAAGTGTATC
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 13 0.21
40 50 0.79
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (40 bp):
GACTTTCGCATTGCGATTTTGACTTTCGCGTTGCGATTTT
Found at i:2032414 original size:20 final size:20
Alignment explanation
Indices: 2032318--2032401 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
2032308 GCAATGCGAA
*
2032318 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2032338 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2032358 TTGACTTTCGCATTGTGATT
1 TTGACTTTCGCATTGCGATT
2032378 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
2032398 TTGA
1 TTGA
2032402 GTTTAGCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:2034006 original size:42 final size:42
Alignment explanation
Indices: 2033947--2034039 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
2033937 ATGAATCGGG
*
2033947 CTCTTGAATAGTGGGA-GGGACCTCTTCAACG-ATGACAGGGGC
1 CTCTTGAACAGTGGGAGGGGA-CTCTT-AACGAATGACAGGGGC
* * *
2033989 CTCTTGAACAGTGGGAGGGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACAGTGGGAGGGGACTCTTAACGAATGACAGGGGC
2034031 CTCTTGAAC
1 CTCTTGAAC
2034040 GATGTCAGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 2 0.04
42 39 0.87
43 4 0.09
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACAGTGGGAGGGGACTCTTAACGAATGACAGGGGC
Found at i:2034007 original size:21 final size:21
Alignment explanation
Indices: 2033947--2034039 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
2033937 ATGAATCGGG
* * *
2033947 CTCTTGAATAGTGGGAGGGAC
1 CTCTTGAACAGTGAGAGGGGC
* *
2033968 CTCTTCAAC-GATGACAGGGGC
1 CTCTTGAACAG-TGAGAGGGGC
* *
2033989 CTCTTGAACAGTGGGAGGGGA
1 CTCTTGAACAGTGAGAGGGGC
** * *
2034010 CTCTTGAGGAATGATAGGGGC
1 CTCTTGAACAGTGAGAGGGGC
2034031 CTCTTGAAC
1 CTCTTGAAC
2034040 GATGTCAGGT
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACAGTGAGAGGGGC
Found at i:2034564 original size:19 final size:20
Alignment explanation
Indices: 2034522--2034564 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2034512 AATAGTTTCT
*
2034522 GAAACTTAAAACCGCAACAT
1 GAAACTTAAAACCGCAACAC
* *
2034542 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAACCGCAACAC
2034561 GAAA
1 GAAA
2034565 ATAACTATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAACCGCAACAC
Found at i:2034576 original size:20 final size:20
Alignment explanation
Indices: 2034551--2034619 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
2034541 TGAAACTTAA
*
2034551 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
*
2034571 ATCGCAATGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
**
2034591 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2034611 ATCGCAACG
1 ATCGCAACG
2034620 GGATAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2034648 original size:19 final size:20
Alignment explanation
Indices: 2034624--2034662 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2034614 GCAACGGGAT
*
2034624 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
2034643 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
2034663 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:2034692 original size:20 final size:20
Alignment explanation
Indices: 2034663--2034700 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2034653 CGAAACTAAA
*
2034663 TTCGCGTTGCGATATTCATT
1 TTCGCATTGCGATATTCATT
*
2034683 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATATTCA
2034701 CGTTGTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (20 bp):
TTCGCATTGCGATATTCATT
Found at i:2034765 original size:20 final size:20
Alignment explanation
Indices: 2034740--2034778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2034730 ATCCCATTGC
2034740 GATAGTCAAATTCGCGTTGT
1 GATAGTCAAATTCGCGTTGT
**
2034760 GATAGTCATTTTCGCGTTG
1 GATAGTCAAATTCGCGTTG
2034779 CGATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (20 bp):
GATAGTCAAATTCGCGTTGT
Found at i:2034958 original size:22 final size:21
Alignment explanation
Indices: 2034916--2034959 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2034906 CAGTATTGGC
* *
2034916 AGCAATCGAATGAATTTACTA
1 AGCAATCGAATGAAATAACTA
*
2034937 AGCAATCTAAGTGAAATAACTA
1 AGCAATCGAA-TGAAATAACTA
2034959 A
1 A
2034960 TCTAAGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.25
Consensus pattern (21 bp):
AGCAATCGAATGAAATAACTA
Found at i:2036722 original size:20 final size:20
Alignment explanation
Indices: 2036699--2036770 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2036689 GAAACTTAAA
2036699 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
2036719 ATCGCAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
* *
2036738 ATCTCAACACAAAAATGACT
1 ATCGCAACACGAAAATGACT
* *
2036758 ATCACAACGCGAA
1 ATCGCAACACGAA
2036771 TTAAACTATC
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2036753 original size:39 final size:39
Alignment explanation
Indices: 2036696--2036770 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
2036686 TTTGAAACTT
* *
2036696 AAAATCGCAACACGAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACACAAAAATGACTATCACAACGCGAAATG
*
2036735 AAAATCTCAACACAAAAATGACTATCACAACGCGAA
1 AAAATCGCAACACAAAAATGACTATCACAACGCGAA
2036771 TTAAACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.13
Consensus pattern (39 bp):
AAAATCGCAACACAAAAATGACTATCACAACGCGAAATG
Found at i:2037165 original size:22 final size:22
Alignment explanation
Indices: 2037140--2037187 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2037130 GGAGATAGAT
*
2037140 GGATTTCGCCGGAGTTGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
2037162 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
2037184 GGAT
1 GGAT
2037188 GTCACCGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.46, T:0.23
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:2037378 original size:20 final size:20
Alignment explanation
Indices: 2037353--2037588 Score: 275
Period size: 20 Copynumber: 11.6 Consensus size: 20
2037343 ATTTTGTATT
2037353 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
2037373 ATCGCGTTGCGATTATGT-ATA
1 ATCGCGTTGCGA-TA-GTCAGA
2037394 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
2037414 ATCGCGTTGCGATTATGT-ATA
1 ATCGCGTTGCGA-TA-GTCAGA
2037435 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
2037455 ATCGCGTTGCGATTATGT-ATA
1 ATCGCGTTGCGA-TA-GTCAGA
2037476 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
2037496 ATCGCGTTGCGATTATGT-ATA
1 ATCGCGTTGCGA-TA-GTCAGA
2037517 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
2037537 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
2037557 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
2037577 ATCGCGTTGCGA
1 ATCGCGTTGCGA
2037589 ATCTGGAAAC
Statistics
Matches: 186, Mismatches: 16, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
19 9 0.05
20 104 0.56
21 65 0.35
22 8 0.04
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:2037392 original size:41 final size:41
Alignment explanation
Indices: 2037331--2037588 Score: 437
Period size: 41 Copynumber: 6.3 Consensus size: 41
2037321 GCGCTTTGAA
* * *
2037331 AATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
2037372 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
2037413 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
2037454 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
2037495 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
** * * *
2037536 AATCGCGTTGCGATT-TACATATTCGCATTGCGATAGTCAA
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
2037576 AATCGCGTTGCGA
1 AATCGCGTTGCGA
2037589 ATCTGGAAAC
Statistics
Matches: 209, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
40 33 0.16
41 176 0.84
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAG
Found at i:2037638 original size:19 final size:19
Alignment explanation
Indices: 2037614--2037650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2037604 TGCGATATTG
*
2037614 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGTGATTTA
2037633 GAGATCGCATTGTGATTT
1 GAGATCGCATTGTGATTT
2037651 TATTGGTTAT
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:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (19 bp):
GAGATCGCATTGTGATTTA
Found at i:2043270 original size:27 final size:28
Alignment explanation
Indices: 2043217--2043270 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
2043207 AGTTTTTTTT
* * *
2043217 TTTTTCTCATTATTTTCTCTTTTTGAAG
1 TTTTTCTCATGATTTTCACTTTCTGAAG
*
2043245 TTTTTCTCATGGTTTTCAC-TTCTGAA
1 TTTTTCTCATGATTTTCACTTTCTGAA
2043271 TCTATGTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (28 bp):
TTTTTCTCATGATTTTCACTTTCTGAAG
Found at i:2064507 original size:29 final size:28
Alignment explanation
Indices: 2064459--2064528 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2064449 GGTCGTACTC
* *
2064459 CTTTTATATTTATATCTAGGACTTCATT
1 CTTTTATCTTTATATCTAGGACTTCACT
* *
2064487 CTTTTAATCTTTATGAT-TAGGATTTTACT
1 CTTTT-ATCTTTAT-ATCTAGGACTTCACT
2064516 CTTTTGATCTTTA
1 CTTTT-ATCTTTA
2064529 CAGCTATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.14
29 28 0.80
30 2 0.06
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.56
Consensus pattern (28 bp):
CTTTTATCTTTATATCTAGGACTTCACT
Found at i:2067369 original size:15 final size:15
Alignment explanation
Indices: 2067349--2067380 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2067339 CTAATCTTTT
2067349 CAAGCTTCAAAATCC
1 CAAGCTTCAAAATCC
2067364 CAAGCTTCAAAATCC
1 CAAGCTTCAAAATCC
2067379 CA
1 CA
2067381 TCTTCCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.34, G:0.06, T:0.19
Consensus pattern (15 bp):
CAAGCTTCAAAATCC
Found at i:2071238 original size:16 final size:17
Alignment explanation
Indices: 2071207--2071242 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2071197 CGTATCGCCG
*
2071207 ACAAAAGTTTACTATTC
1 ACAAAAGTTCACTATTC
2071224 ACAAAA-TTCACTATTC
1 ACAAAAGTTCACTATTC
2071240 ACA
1 ACA
2071243 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (17 bp):
ACAAAAGTTCACTATTC
Found at i:2073718 original size:20 final size:20
Alignment explanation
Indices: 2073643--2073833 Score: 244
Period size: 20 Copynumber: 9.6 Consensus size: 20
2073633 GCGAATATGA
* *
2073643 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2073663 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2073683 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
2073703 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2073723 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2073743 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2073763 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2073783 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2073803 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
2073823 AAATCGCAACG
1 AAATCGCAACG
2073834 AGAATCTATA
Statistics
Matches: 152, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 149 0.98
21 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2073847 original size:20 final size:20
Alignment explanation
Indices: 2073624--2073839 Score: 236
Period size: 20 Copynumber: 10.8 Consensus size: 20
2073614 GATTTTCCAG
* ** *
2073624 AATCACAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
2073644 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
*
2073664 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2073684 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
2073704 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2073724 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2073744 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
2073764 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2073784 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
**
2073804 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
*
2073824 AATCGCAACGAGAATC
1 AATCGCAACGCGAATC
2073840 TATAAATCAC
Statistics
Matches: 173, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 172 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:2074584 original size:24 final size:24
Alignment explanation
Indices: 2074545--2074591 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2074535 AAATTTGGTC
2074545 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2074569 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2074592 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2077125 original size:33 final size:33
Alignment explanation
Indices: 2077074--2077324 Score: 238
Period size: 33 Copynumber: 7.2 Consensus size: 33
2077064 CGGAAATTAC
* *
2077074 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
2077107 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
2077141 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AA-GAAAATCGCAATGCGAAATGAA
* *
2077179 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * * *
2077213 AATCTCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
*
2077252 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAAGAAAATCGCAATGCGAAATGAA
* *
2077284 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
2077317 AATCGCAA
1 AATCGCAA
2077325 TGCGAAATGA
Statistics
Matches: 180, Mismatches: 20, Indels: 36
0.76 0.08 0.15
Matches are distributed among these distances:
31 1 0.01
32 8 0.04
33 80 0.44
34 32 0.18
36 3 0.02
38 22 0.12
39 33 0.18
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:2077157 original size:19 final size:19
Alignment explanation
Indices: 2077088--2077348 Score: 310
Period size: 19 Copynumber: 14.7 Consensus size: 19
2077078 GCAACGAGAG
2077088 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2077107 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
2077121 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2077141 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2077160 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2077179 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2077193 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2077213 AATCTCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2077232 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2077246 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2077265 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2077284 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2077298 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2077317 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2077336 AATCGCATTGCGA
1 AATCGCAATGCGA
2077349 TTCTCTCGTT
Statistics
Matches: 209, Mismatches: 11, Indels: 44
0.79 0.04 0.17
Matches are distributed among these distances:
14 40 0.19
15 5 0.02
16 6 0.03
17 8 0.04
18 2 0.01
19 122 0.58
20 26 0.12
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2077181 original size:72 final size:72
Alignment explanation
Indices: 2077088--2077320 Score: 293
Period size: 72 Copynumber: 3.3 Consensus size: 72
2077078 GCAACGAGAG
2077088 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2077153 AAATGAA
66 AAATGAA
* * * *
2077160 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCTCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2077225 AAATGAA
66 AAATGAA
* * * * * *
2077232 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
2077292 CG--A-GAG
64 CGAAATGAA
2077298 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
2077321 GCAATGCGAA
Statistics
Matches: 139, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
64 1 0.01
65 6 0.04
66 13 0.09
67 1 0.01
69 2 0.01
71 15 0.11
72 92 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:2077202 original size:105 final size:102
Alignment explanation
Indices: 2077074--2077342 Score: 391
Period size: 105 Copynumber: 2.6 Consensus size: 102
2077064 CGGAAATTAC
2077074 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-AA-GAAAATCGCAATGCGGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAAATGAAAATCGCAA--C-G--
2077136 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2077179 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCTCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA-GC-AAATGAAAATCGCAACGAG
*
2077244 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2077284 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-GC-AAATGAAAATCGCA
2077343 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 3, Indels: 13
0.91 0.02 0.08
Matches are distributed among these distances:
104 33 0.21
105 90 0.58
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (102 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAAATGAAAATCGCAACGAGAAA
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2077362 original size:52 final size:52
Alignment explanation
Indices: 2077074--2077342 Score: 413
Period size: 52 Copynumber: 5.1 Consensus size: 52
2077064 CGGAAATTAC
*
2077074 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2077121 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2077179 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCTCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2077232 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2077284 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2077336 AATCGCA
1 AATCGCA
2077343 TTGCGATTCT
Statistics
Matches: 205, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 99 0.48
53 80 0.39
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2077396 original size:53 final size:52
Alignment explanation
Indices: 2077338--2077444 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 52
2077328 GAAATGAAAA
2077338 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
2077391 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
2077443 TC
1 TC
2077445 AACATAATGC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 20 0.37
53 34 0.63
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:2077397 original size:19 final size:19
Alignment explanation
Indices: 2077357--2077444 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
2077347 GATTCTCTCG
2077357 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2077377 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2077396 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2077410 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2077429 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2077445 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2077554 original size:14 final size:14
Alignment explanation
Indices: 2077535--2077585 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
2077525 CATCAATTAC
2077535 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2077549 ACAAATCATCTTTT
1 ACAAATCAACTTTT
*
2077563 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2077577 ACAAATCAA
1 ACAAATCAA
2077586 TTAAACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2079549 original size:19 final size:19
Alignment explanation
Indices: 2079507--2079660 Score: 103
Period size: 19 Copynumber: 8.6 Consensus size: 19
2079497 TAGTTTACTT
* *
2079507 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
2079527 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
2079546 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
2079565 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2079584 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2079598 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2079617 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
2079631 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
2079650 TTGCAATGCGA
1 TCGCAACGCGA
2079661 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 6 0.06
17 7 0.07
18 1 0.01
19 63 0.59
20 12 0.11
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2079644 original size:33 final size:33
Alignment explanation
Indices: 2079525--2079655 Score: 145
Period size: 33 Copynumber: 3.8 Consensus size: 33
2079515 CGAAACTTAA
* *
2079525 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAG-----AG
** *
2079563 AATCGCAACGCGAAACCAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
2079596 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
2079629 AATCACAACGCGAAATGAAAATTGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2079656 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
33 54 0.67
38 27 0.33
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2079678 original size:19 final size:18
Alignment explanation
Indices: 2079656--2079714 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
2079646 AAAATTGCAA
2079656 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2079675 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2079689 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2079708 TGCGATT
1 TGCGATT
2079715 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:2079691 original size:14 final size:14
Alignment explanation
Indices: 2079672--2079728 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2079662 TTTGGTTTCG
*
2079672 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2079686 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2079705 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2079719 CGTTGCGATT
1 CGTTGCGATT
2079729 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2079704 original size:33 final size:33
Alignment explanation
Indices: 2079656--2079730 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
2079646 AAAATTGCAA
** *
2079656 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2079689 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2079722 TGCGATTTT
1 TGCGATTTT
2079731 AAGTTTCGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.08, C:0.20, G:0.25, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2080005 original size:93 final size:93
Alignment explanation
Indices: 2079846--2080252 Score: 778
Period size: 93 Copynumber: 4.4 Consensus size: 93
2079836 AGGGTATTAG
2079846 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
2079911 CTATTTCACAGTGTTAAAGAATACACAA
66 CTATTTCACAGTGTTAAAGAATACACAA
2079939 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
2080004 CTATTTCACAGTGTTAAAGAATACACAA
66 CTATTTCACAGTGTTAAAGAATACACAA
2080032 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
2080097 CTATTTCACAGTGTTAAAGAATACACAG
66 CTATTTCACAGTGTTAAAGAATACACAA
*
2080125 TTTAGCAGAATTGGCAGCAACCAAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
2080190 CTATTTCACAGTGTTAAAGAATACACAG
66 CTATTTCACAGTGTTAAAGAATACACAA
*
2080218 TTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2080253 AAGCAATCTA
Statistics
Matches: 310, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 310 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAA
Found at i:2081968 original size:20 final size:20
Alignment explanation
Indices: 2081937--2082033 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
2081927 TTTTGGTTGA
2081937 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2081957 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2081977 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
2081996 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
2082011 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2082031 AAT
1 AAT
2082034 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2081989 original size:21 final size:21
Alignment explanation
Indices: 2081935--2081999 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2081925 TCTTTTGGTT
2081935 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2081956 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2081976 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2081997 GAA
1 GAA
2082000 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2082003 original size:14 final size:14
Alignment explanation
Indices: 2081984--2082040 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2081974 GAGAAATGAA
2081984 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2081998 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2082017 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2082031 AATCGCAACG
1 AATCGCAACG
2082041 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2082016 original size:33 final size:33
Alignment explanation
Indices: 2081935--2082057 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2081925 TCTTTTGGTT
*
2081935 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
2081976 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2082009 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2082042 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2082058 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2082074 original size:19 final size:19
Alignment explanation
Indices: 2082058--2082151 Score: 98
Period size: 19 Copynumber: 4.7 Consensus size: 19
2082048 AAAATCGCAA
**
2082058 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
2082077 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2082096 TGCGATTTTCATTTTTCTCGT
1 TGCGATTTTCA--TTTCGCGT
** *
2082117 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
2082138 TGCGATTTTCATTT
1 TGCGATTTTCATTT
2082152 ATCTCGTTGC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 31 0.48
20 6 0.09
21 21 0.33
22 6 0.09
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2082117 original size:21 final size:20
Alignment explanation
Indices: 2082069--2082163 Score: 111
Period size: 21 Copynumber: 4.7 Consensus size: 20
2082059 GCGATTTTGG
2082069 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
2082088 TTTCGCGTTGCGATTTTCATT
1 TTTCGCGTTGCGATTTTCA-T
* **
2082109 TTTCTCGTTGCAGATAGTCAT
1 TTTCGCGTTGC-GATTTTCAT
*
2082130 TTTCACGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
2082150 TTATCTCGTTGCGA
1 TT-TCGCGTTGCGA
2082164 CTCTTCTGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 19 0.29
20 9 0.14
21 31 0.48
22 6 0.09
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:2082285 original size:33 final size:33
Alignment explanation
Indices: 2082243--2082313 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2082233 AATACTAACT
2082243 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
2082276 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
2082309 TGAAA
1 TGAAA
2082314 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:2082721 original size:20 final size:20
Alignment explanation
Indices: 2082696--2082885 Score: 240
Period size: 20 Copynumber: 9.4 Consensus size: 20
2082686 TAAAAATCGT
2082696 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2082716 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
2082737 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2082757 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2082777 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2082797 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2082817 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2082837 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2082857 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2082877 GTTGCGATT
1 GTTGCGATT
2082886 CTGGAAAATC
Statistics
Matches: 149, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 131 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2094329 original size:31 final size:31
Alignment explanation
Indices: 2094291--2094350 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2094281 AGGGTCGAGG
*
2094291 GTTTACCTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
2094322 GTTTACCTATGTTCTTCGGGACATATGGA
1 GTTTACCTATGTTCTTCGGGACATATGGA
2094351 CTAATTACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:2094367 original size:31 final size:31
Alignment explanation
Indices: 2094293--2094371 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
2094283 GGTCGAGGGT
* * * **
2094293 TTACCTATGTTCTTCGGGATATATGGATTGT
1 TTACCTAGGTTCTTCGGGACATATGGACTAA
*
2094324 TTACCTATGTTCTTCGGGACATATGGACTAA
1 TTACCTAGGTTCTTCGGGACATATGGACTAA
*
2094355 TTACTTAGGTTCTTCGG
1 TTACCTAGGTTCTTCGG
2094372 AATCTATGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (31 bp):
TTACCTAGGTTCTTCGGGACATATGGACTAA
Found at i:2098237 original size:23 final size:22
Alignment explanation
Indices: 2098189--2098267 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 22
2098179 TCGAAATGGA
2098189 GTGCATGGATGCAC--C-GCATG
1 GTGCATGGATGCACTGCAGCA-G
* *
2098209 GTGCATCGATGCACTAGTAGCAG
1 GTGCATGGATGCACT-GCAGCAG
* *
2098232 GTGCATGGATGTACTGCAGGA-
1 GTGCATGGATGCACTGCAGCAG
2098253 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2098268 TTGACACCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
20 13 0.27
21 14 0.29
22 4 0.08
23 14 0.29
24 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (22 bp):
GTGCATGGATGCACTGCAGCAG
Found at i:2098655 original size:18 final size:18
Alignment explanation
Indices: 2098628--2098668 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2098618 ACATTCTCAA
* *
2098628 TAATCTTATTCCCGCCGG
1 TAATCCTATTCCCACCGG
*
2098646 TAATCCTATTCCCACTGG
1 TAATCCTATTCCCACCGG
2098664 TAATC
1 TAATC
2098669 TTACATTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (18 bp):
TAATCCTATTCCCACCGG
Found at i:2103608 original size:16 final size:17
Alignment explanation
Indices: 2103577--2103611 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2103567 CGTATCACCG
*
2103577 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
2103594 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
2103610 AC
1 AC
2103612 GTAAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:2104299 original size:30 final size:31
Alignment explanation
Indices: 2104265--2104326 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
2104255 AATAATATAG
2104265 TATGTATA-ACATTATTTAAAATGATGATAT
1 TATGTATACACATTATTTAAAATGATGATAT
*
2104295 TATGTATATCACATTATTTAAAGTGATGATAT
1 TATGTATA-CACATTATTTAAAATGATGATAT
2104327 GACATGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 8 0.28
32 21 0.72
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (31 bp):
TATGTATACACATTATTTAAAATGATGATAT
Found at i:2106048 original size:29 final size:29
Alignment explanation
Indices: 2106015--2106081 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
2106005 ATTAGTTAGA
* ** * *
2106015 TTACAAATGTATTATCTGGTTTCAAAAAG
1 TTACAAATGTATCATCTAATTTAAAAAAC
2106044 TTACAAATGTATCATCTAATTTAAAAAAC
1 TTACAAATGTATCATCTAATTTAAAAAAC
2106073 TTACAAATG
1 TTACAAATG
2106082 AATTGATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (29 bp):
TTACAAATGTATCATCTAATTTAAAAAAC
Found at i:2108086 original size:18 final size:18
Alignment explanation
Indices: 2108056--2108116 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
2108046 ATAAAGAGAA
**
2108056 ATAAATAGG-TAAAGTAT
1 ATAAATAGGATAAACCAT
2108073 ATAAATAGGATAAACCAT
1 ATAAATAGGATAAACCAT
* *
2108091 ACAAATAGGATAAAACAT
1 ATAAATAGGATAAACCAT
*
2108109 ACAAATAG
1 ATAAATAG
2108117 TACCTAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 9 0.23
18 30 0.77
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.21
Consensus pattern (18 bp):
ATAAATAGGATAAACCAT
Found at i:2118045 original size:2 final size:2
Alignment explanation
Indices: 2118038--2118067 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2118028 CTTGTTAATC
2118038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2118068 TACATACCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2129090 original size:30 final size:30
Alignment explanation
Indices: 2129054--2129116 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2129044 TATATAGTGG
* *
2129054 AGATTAAAGAGGAAATAAATTGAAATGTTA
1 AGATTAAAGAGGAAAAAAATTGAAAGGTTA
2129084 AGATTAAAGAGGAAAAAAATTGAAAGGTTA
1 AGATTAAAGAGGAAAAAAATTGAAAGGTTA
2129114 AGA
1 AGA
2129117 CCATTTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (30 bp):
AGATTAAAGAGGAAAAAAATTGAAAGGTTA
Found at i:2129375 original size:20 final size:21
Alignment explanation
Indices: 2129344--2129382 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2129334 ATAATAAGAG
*
2129344 ACATCTTAATTTTATATATTA
1 ACATCTTAATTTAATATATTA
2129365 ACATC-TAATTTAATATAT
1 ACATCTTAATTTAATATAT
2129383 AATATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
ACATCTTAATTTAATATATTA
Found at i:2137197 original size:38 final size:38
Alignment explanation
Indices: 2137155--2137241 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
2137145 TCTCATAGAA
* * * *
2137155 GATAACATCTCATGCGGATGATGA-TTTTCGTCGTGGAG
1 GATAACATCTCATGCGAAGGATGACTTCTC-TCGTGAAG
2137193 GATAACATCTCATGCGAAGGATGACTTCTCTCGTGAAG
1 GATAACATCTCATGCGAAGGATGACTTCTCTCGTGAAG
2137231 GA-AACATCTCA
1 GATAACATCTCA
2137242 CGCAGAGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 9 0.20
38 31 0.70
39 4 0.09
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (38 bp):
GATAACATCTCATGCGAAGGATGACTTCTCTCGTGAAG
Found at i:2137251 original size:37 final size:37
Alignment explanation
Indices: 2137155--2137251 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
2137145 TCTCATAGAA
* * *
2137155 GATAACATCTCATGCGGATGATGATTTTCGTCGTGGAG
1 GATAACATCTCATGC-GAGGATGATTCTCGTCGTGAAG
2137193 GATAACATCTCATGCGAAGGATGACTTCTC-TCGTGAAG
1 GATAACATCTCATGCG-AGGATGA-TTCTCGTCGTGAAG
*
2137231 GA-AACATCTCACGCAGAGGAT
1 GATAACATCTCATGC-GAGGAT
2137252 AACGGGGAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
37 17 0.33
38 31 0.60
39 4 0.08
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (37 bp):
GATAACATCTCATGCGAGGATGATTCTCGTCGTGAAG
Found at i:2141619 original size:21 final size:21
Alignment explanation
Indices: 2141593--2141636 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2141583 ATTCTGGGCT
* *
2141593 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2141614 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2141635 AG
1 AG
2141637 CGAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2141708 original size:23 final size:22
Alignment explanation
Indices: 2141664--2141708 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2141654 AATGTCATGG
*
2141664 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
2141686 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
2141709 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:2143328 original size:23 final size:23
Alignment explanation
Indices: 2143301--2143352 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2143291 ATTATTATAT
*
2143301 GGCACTATGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
2143324 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2143347 GGCACT
1 GGCACT
2143353 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2143359 original size:23 final size:23
Alignment explanation
Indices: 2143301--2143360 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2143291 ATTATTATAT
**
2143301 GGCACTATGGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* *
2143324 GGCACTACGGTGCAATTCTACGT
1 GGCACTACAGTGCAATTCTACGC
*
2143347 GGCACTTCAGTGCA
1 GGCACTACAGTGCA
2143361 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:2147029 original size:45 final size:45
Alignment explanation
Indices: 2146957--2147046 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
2146947 ACAAGTTTGG
*
2146957 AACATAATGAATAGTCAAATGACCATTTTATAACTTTCAATAGTC
1 AACATAATGAATAGACAAATGACCATTTTATAACTTTCAATAGTC
* * *
2147002 AACATAATGAATAGACAAGTGATCATTTTGTAACTTTCAATAGTC
1 AACATAATGAATAGACAAATGACCATTTTATAACTTTCAATAGTC
2147047 GAGTAACTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (45 bp):
AACATAATGAATAGACAAATGACCATTTTATAACTTTCAATAGTC
Found at i:2152503 original size:61 final size:61
Alignment explanation
Indices: 2152456--2152587 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 61
2152446 GCGAATTGGG
* * * *
2152456 AAAATCGCAATGCA-ATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACG-AGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
2152517 AAAATCGCAACGAGATACTGACTTTCGCAACGTGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
2152578 ATAATCGCAA
1 AAAATCGCAA
2152588 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 1 0.02
61 60 0.98
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2152509 original size:20 final size:20
Alignment explanation
Indices: 2152459--2152593 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
2152449 AATTGGGAAA
*
2152459 ATCGCAATGCAATACTGACT
1 ATCGCAATGCGATACTGACT
*
2152479 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2152499 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2152520 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
2152540 TTCGCAACGTGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
2152560 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2152580 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2152594 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2152789 original size:22 final size:22
Alignment explanation
Indices: 2152761--2152804 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2152751 CACTCTCTCA
2152761 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2152783 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2152805 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2153121 original size:20 final size:20
Alignment explanation
Indices: 2153067--2153125 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2153057 GCGATTCTCT
**
2153067 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2153087 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2153107 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2153126 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2154465 original size:18 final size:18
Alignment explanation
Indices: 2154444--2154488 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2154434 TCCACTTCGG
2154444 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2154462 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2154480 GAGCCATCA
1 GAGCCATCA
2154489 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2154995 original size:20 final size:20
Alignment explanation
Indices: 2154970--2155015 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2154960 TAGTTTACTT
*
2154970 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
2154990 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2155010 TCGCAA
1 TCGCAA
2155016 TGTGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2155031 original size:19 final size:19
Alignment explanation
Indices: 2155009--2155105 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
2154999 GGAAATGGCT
*
2155009 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2155028 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2155042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2155061 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2155075 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2155094 GTCGCAATGCGA
1 ATCGCAATGCGA
2155106 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 3 0.05
18 2 0.03
19 31 0.50
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2155044 original size:14 final size:14
Alignment explanation
Indices: 2155025--2155081 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2155015 ATGTGAAATG
2155025 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2155039 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2155058 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2155072 AAAATCGCAA
1 AAAATCGCAA
2155082 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2155056 original size:33 final size:33
Alignment explanation
Indices: 2155009--2155100 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2154999 GGAAATGGCT
*
2155009 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2155042 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2155075 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2155101 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2155136 original size:14 final size:14
Alignment explanation
Indices: 2155117--2155206 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
2155107 TTGTGTTTCG
2155117 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2155131 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2155147 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
2155163 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2155180 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2155196 CGTTGCGATTT
1 CGTTGCGATTT
2155207 GCATTTCGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2155181 original size:33 final size:33
Alignment explanation
Indices: 2155112--2155223 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
2155102 GCGATTTGTG
*
2155112 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2155144 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
2155177 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2155210 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2155224 AGCTATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2155189 original size:19 final size:18
Alignment explanation
Indices: 2155133--2155223 Score: 90
Period size: 14 Copynumber: 5.4 Consensus size: 18
2155123 GATTTTGTCG
2155133 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
2155151 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
2155165 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
2155184 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
2155198 TTGCGATTTGCATTTCGCA
1 TTGCGATTT-CATTTCGCA
2155217 TTGCGAT
1 TTGCGAT
2155224 AGCTATTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 8 0.14
17 8 0.14
18 12 0.20
19 13 0.22
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:2155242 original size:20 final size:19
Alignment explanation
Indices: 2155196--2155263 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
2155186 GCGATTTTGT
*
2155196 CGTTGCGATTTGC-ATTTCG
1 CGTTGCGA-TAGCTATTTCG
*
2155215 CATTGCGATAGCTATTTCCG
1 CGTTGCGATAGCTATTT-CG
2155235 CGTTGCGATAG-TCATTTTCG
1 CGTTGCGATAGCT-A-TTTCG
*
2155255 CGTTACGAT
1 CGTTGCGAT
2155264 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.07
19 12 0.29
20 23 0.56
21 3 0.07
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGCTATTTCG
Found at i:2155726 original size:41 final size:41
Alignment explanation
Indices: 2155630--2155717 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
2155620 GACTCACCTG
* * *
2155630 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
2155672 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
2155713 TCATC
1 TCATC
2155718 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:2157161 original size:14 final size:14
Alignment explanation
Indices: 2157127--2157165 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2157117 TTGATTGTTT
2157127 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2157141 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2157155 TGTTGATTTGT
1 AATTGATTTGT
2157166 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2157291 original size:20 final size:20
Alignment explanation
Indices: 2157262--2157299 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2157252 TGTTGAAGGC
2157262 AAAACAGACTATCGCAACAT
1 AAAACAGACTATCGCAACAT
*
2157282 AAAACTGACTATCGCAAC
1 AAAACAGACTATCGCAAC
2157300 GAGAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (20 bp):
AAAACAGACTATCGCAACAT
Found at i:2157311 original size:14 final size:14
Alignment explanation
Indices: 2157292--2157345 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2157282 AAAACTGACT
2157292 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2157306 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG--A-GAAA
2157325 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2157339 ATCGCAA
1 ATCGCAA
2157346 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.46
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 9 0.26
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:2157394 original size:20 final size:20
Alignment explanation
Indices: 2157369--2157464 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
2157359 TCGCATTGCG
*
2157369 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
2157389 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
* *
2157410 A-TTTCGAATTGTGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
2157429 ATTTTCGTGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
2157449 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
2157465 TTCCCCGTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:2157980 original size:12 final size:12
Alignment explanation
Indices: 2157961--2157994 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2157951 CTCTCCGGCG
2157961 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2157973 ATATCCGTTCCT
1 ACATCCGTTCCT
2157985 ACATCC-TTCC
1 ACATCCGTTCC
2157995 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2158600 original size:24 final size:24
Alignment explanation
Indices: 2158549--2158602 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2158539 GTATTCGAAA
* *
2158549 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
2158573 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
2158597 TTTGAT
1 TTTGAT
2158603 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:2158794 original size:12 final size:12
Alignment explanation
Indices: 2158777--2158813 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2158767 ATATAATCCT
2158777 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2158789 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2158801 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2158813 G
1 G
2158814 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2161127 original size:19 final size:19
Alignment explanation
Indices: 2161105--2161235 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2161095 GGAAATTACT
*
2161105 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2161124 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2161138 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2161157 ATCGCAACGC-AAAT----
1 ATCGCAATGCGAAATGAAA
*
2161171 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2161190 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2161204 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2161223 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2161236 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 27 0.32
15 6 0.07
16 4 0.05
17 3 0.04
18 6 0.07
19 39 0.46
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2161142 original size:33 final size:33
Alignment explanation
Indices: 2161105--2161231 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
2161095 GGAAATTACT
*
2161105 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2161138 ATCGCAATGCGAAATGAAAATCGCAACGCA-A-A
1 ATCGCAATGCGAAATGAAAATCGCAACG-AGAGA
* *
2161170 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2161204 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2161232 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
32 2 0.02
33 82 0.95
34 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2161212 original size:66 final size:66
Alignment explanation
Indices: 2161106--2161238 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
2161096 GAAATTACTA
*
2161106 TCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
2161171 T
66 T
* *
2161172 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
2161237 T
66 T
2161238 T
1 T
2161239 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
T
Done.