Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 24
Found at i:2000630 original size:30 final size:30
Alignment explanation
Indices: 2000588--2000649 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2000578 ATAAATTAAG
2000588 ATAAATATTTGATGATGTTAGTTTTACAAC
1 ATAAATATTTGATGATGTTAGTTTTACAAC
2000618 ATAAATCA-TTGATGATGTTAGTTTTACAAC
1 ATAAAT-ATTTGATGATGTTAGTTTTACAAC
2000648 AT
1 AT
2000650 CCTGCACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (30 bp):
ATAAATATTTGATGATGTTAGTTTTACAAC
Found at i:2003541 original size:15 final size:16
Alignment explanation
Indices: 2003521--2003551 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2003511 ATGGACACTG
2003521 AACATGTA-TCATATA
1 AACATGTATTCATATA
2003536 AACATGTATTCATATA
1 AACATGTATTCATATA
2003552 TATTATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
AACATGTATTCATATA
Found at i:2003922 original size:20 final size:22
Alignment explanation
Indices: 2003897--2003954 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2003887 TTCCCCTTGA
2003897 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
2003917 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2003940 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2003955 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2006723 original size:98 final size:98
Alignment explanation
Indices: 2006554--2006751 Score: 378
Period size: 98 Copynumber: 2.0 Consensus size: 98
2006544 TTATAATACA
* *
2006554 AGGACCGAGTCTCCGTTTGCACCTCCTCTTTTAATTACAAGGGGATTCCCCTTGGTTTTCATGTT
1 AGGACCGAGTCTCCGTTTGCACCTCCTCTTTTAATTACAAGAGGATTCCCCTAGGTTTTCATGTT
2006619 GCATCACAAACTGAGAATATTGAATTACGTTTT
66 GCATCACAAACTGAGAATATTGAATTACGTTTT
2006652 AGGACCGAGTCTCCGTTTGCACCTCCTCTTTTAATTACAAGAGGATTCCCCTAGGTTTTCATGTT
1 AGGACCGAGTCTCCGTTTGCACCTCCTCTTTTAATTACAAGAGGATTCCCCTAGGTTTTCATGTT
2006717 GCATCACAAACTGAGAATATTGAATTACGTTTT
66 GCATCACAAACTGAGAATATTGAATTACGTTTT
2006750 AG
1 AG
2006752 AGGTCTTAGA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (98 bp):
AGGACCGAGTCTCCGTTTGCACCTCCTCTTTTAATTACAAGAGGATTCCCCTAGGTTTTCATGTT
GCATCACAAACTGAGAATATTGAATTACGTTTT
Found at i:2017061 original size:17 final size:18
Alignment explanation
Indices: 2017029--2017063 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2017019 ATAAAATTTA
2017029 AAAATGATTATTAAAAAT
1 AAAATGATTATTAAAAAT
*
2017047 AAAAT-ATTTTTAAAAAT
1 AAAATGATTATTAAAAAT
2017064 CGGATGATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAATGATTATTAAAAAT
Found at i:2018212 original size:23 final size:23
Alignment explanation
Indices: 2018168--2018232 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
2018158 TCTAAAAACT
*
2018168 GAGTCAACTCGAATTGAGTTGACC
1 GAGTCAACTC-AAATGAGTTGACC
2018192 GAGTCAACTCAAATGAGTTGACC
1 GAGTCAACTCAAATGAGTTGACC
2018215 GAGTCAACTCAAATGAGT
1 GAGTCAACTCAAATGAGT
2018233 CAGTCGAGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 30 0.75
24 10 0.25
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (23 bp):
GAGTCAACTCAAATGAGTTGACC
Found at i:2020036 original size:23 final size:23
Alignment explanation
Indices: 2020010--2020078 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2020000 CACCACAGCT
*
2020010 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
2020033 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2020056 CGTAGAATTACACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2020079 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2020349 original size:24 final size:24
Alignment explanation
Indices: 2020321--2020373 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2020311 TGTAGTTCTT
*
2020321 TCACATAGCTCATCAT-CATATAAA
1 TCACATAGCCCAT-ATACATATAAA
*
2020345 TCACATATCCCATATACATATAAA
1 TCACATAGCCCATATACATATAAA
2020369 -CACAT
1 TCACAT
2020374 GGTTCACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.28
Consensus pattern (24 bp):
TCACATAGCCCATATACATATAAA
Found at i:2025733 original size:22 final size:22
Alignment explanation
Indices: 2025708--2025767 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
2025698 TTTCCTTTAG
2025708 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCCTCCTGT
2025730 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCCTCCTGT
2025752 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
2025768 CTATGAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.10, C:0.27, G:0.38, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCCTGT
Found at i:2029391 original size:21 final size:21
Alignment explanation
Indices: 2029367--2029407 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2029357 TAATGGAATC
* *
2029367 ATTCATCATTTAGCGTGTTTA
1 ATTCAGCATTAAGCGTGTTTA
2029388 ATTCAGCATTAAGCGTGTTT
1 ATTCAGCATTAAGCGTGTTT
2029408 GAATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (21 bp):
ATTCAGCATTAAGCGTGTTTA
Found at i:2034838 original size:19 final size:19
Alignment explanation
Indices: 2034814--2034852 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2034804 TTGAGTAGAA
* * *
2034814 ACAACACCAGCATATTAAG
1 ACAACAACACCATATAAAG
2034833 ACAACAACACCATATAAAG
1 ACAACAACACCATATAAAG
2034852 A
1 A
2034853 TTGCAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.26, G:0.08, T:0.13
Consensus pattern (19 bp):
ACAACAACACCATATAAAG
Found at i:2043105 original size:3 final size:3
Alignment explanation
Indices: 2043093--2043138 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
2043083 AATTATTTTT
2043093 TAA T-A TAA TAA T-A TATA TAA TAA TATA TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TA-A TAA TAA
2043139 ATAAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 4 0.11
3 25 0.66
4 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2043118 original size:10 final size:10
Alignment explanation
Indices: 2043093--2043142 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
2043083 AATTATTTTT
2043093 TAATATAATAA
1 TAATAT-ATAA
2043104 T-ATATATAA
1 TAATATATAA
2043113 TAATATATAA
1 TAATATATAA
2043123 TAATA-ATATA
1 TAATATATA-A
*
2043133 TAATAAATAA
1 TAATATATAA
2043143 ATAAAATGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.22
10 24 0.67
11 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATATATAA
Found at i:2043118 original size:20 final size:21
Alignment explanation
Indices: 2043093--2043142 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2043083 AATTATTTTT
2043093 TAATATAATAAT-ATATATAA
1 TAATATAATAATAATATATAA
2043113 TAATATATAATAATAATATATAA
1 T-A-ATATAATAATAATATATAA
2043136 TAA-ATAA
1 TAATATAA
2043143 ATAAAATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 11 0.41
23 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATAATAATAATATATAA
Found at i:2043127 original size:13 final size:13
Alignment explanation
Indices: 2043097--2043138 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2043087 ATTTTTTAAT
2043097 ATAATAATATAT-
1 ATAATAATATATA
2043109 ATAATAATATATA
1 ATAATAATATATA
2043122 ATAATAATATATA
1 ATAATAATATATA
2043135 ATAA
1 ATAA
2043139 ATAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:2043438 original size:17 final size:17
Alignment explanation
Indices: 2043381--2043439 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2043371 TTGAACAAGC
2043381 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
* *
2043398 TCTTATTC-TTCAGATG-AGT
1 TCTT-CTCATT--G-TGAACT
2043417 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
2043434 TCTTCT
1 TCTTCT
2043440 GGAAATGCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 4 0.12
19 9 0.28
20 2 0.06
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:2043858 original size:114 final size:113
Alignment explanation
Indices: 2043483--2043916 Score: 595
Period size: 114 Copynumber: 3.8 Consensus size: 113
2043473 ATAGAGTCAT
* ** *
2043483 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
2043548 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* * *
2043596 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCATATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* ** * *
2043660 CATTATGAACTCTTTCACTGGGGATGCTGATCCATCAAATGATGAATTCAA
65 CATTATGAA--CTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* * *
2043711 ACAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
2043776 ATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAAC-TTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
*
2043825 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2043890 A-TATGAACTTTTTCTGGAAAAGC-GATC
66 ATTATGAACTTTCTCTGGAAAAGCTGATC
2043917 GATGAGTTCT
Statistics
Matches: 286, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
111 4 0.01
112 15 0.05
113 71 0.25
114 103 0.36
115 93 0.33
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
Found at i:2043926 original size:41 final size:42
Alignment explanation
Indices: 2043876--2043958 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
2043866 TCCTTCTTCA
2043876 GATGAGTTCTTCTCA-TATGAACTTTTTCTGGAAAAGC-GATC
1 GATGAGTTCTTCTCATTATGAAC-TTTTCTGGAAAAGCTGATC
2043917 GATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGCTGATC
1 GATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGCTGATC
2043959 CATCAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 29 0.73
42 11 0.28
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (42 bp):
GATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGCTGATC
Found at i:2044960 original size:35 final size:36
Alignment explanation
Indices: 2044921--2044991 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2044911 TTTCAGCTCA
*
2044921 GATGTAAAA-TTTGACAACACATTCATCCTTTTCTG
1 GATGTAAAACATTGACAACACATTCATCCTTTTCTG
2044956 GATGTAAAACATTGACAACACATTCATCCTTTTCTG
1 GATGTAAAACATTGACAACACATTCATCCTTTTCTG
2044992 TGGCTTCTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.26
36 25 0.74
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (36 bp):
GATGTAAAACATTGACAACACATTCATCCTTTTCTG
Found at i:2047071 original size:115 final size:115
Alignment explanation
Indices: 2046905--2047361 Score: 700
Period size: 115 Copynumber: 4.0 Consensus size: 115
2046895 GATCATGCAG
* * * * * *
2046905 TTCATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * * *
2046969 AACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
2047019 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
2047084 AACACTTCTAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* * * *
2047134 TTCATCTTTTAAATCTAATGATTAGTTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * * *
2047199 AACACTTCTAGAAGATGCTATCGGGTCTTCTTATTTCTAATATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
2047249 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
2047314 AACACTTCCAAAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
2047362 TATGGCACTT
Statistics
Matches: 313, Mismatches: 29, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
114 22 0.07
115 291 0.93
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:2053546 original size:20 final size:20
Alignment explanation
Indices: 2053521--2053573 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2053511 TTTCTTTGAT
2053521 ATTAAAAAAATAAATAAATA
1 ATTAAAAAAATAAATAAATA
* * *
2053541 ATTAAAATAATTAATATATA
1 ATTAAAAAAATAAATAAATA
* *
2053561 ATTTATAAAATAA
1 ATTAAAAAAATAA
2053574 GATATTTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAAAAATAAATAAATA
Found at i:2053636 original size:121 final size:116
Alignment explanation
Indices: 2053429--2053667 Score: 282
Period size: 121 Copynumber: 2.0 Consensus size: 116
2053419 AAATATATAT
* * * *
2053429 TAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGG
1 TAATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
* * * *
2053494 TGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAAATAAATAAATAATTAAAA
66 TACCTTAAGACAGCTCCTTTC-TTAATATT-AAAAAAGAAATAAAT-ATTAAAA
*
2053548 TAATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCC
1 TAATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCC
* ** * **
2053613 AGTTATTTTAAGACTGC-CCTTTCTTAATATTGGAAAAGAAATAAATATTAAAA
63 AGGTACCTTAAGACAGCTCCTTTCTTAATATTAAAAAAGAAATAAATATTAAAA
2053666 TA
1 TA
2053668 GGATTAAAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
118 9 0.09
119 23 0.23
120 13 0.13
121 39 0.38
122 18 0.18
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (116 bp):
TAATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
TACCTTAAGACAGCTCCTTTCTTAATATTAAAAAAGAAATAAATATTAAAA
Found at i:2055146 original size:3 final size:3
Alignment explanation
Indices: 2055138--2055194 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
2055128 AATTATTTTT
2055138 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA
2055183 TAA TAA TAA TAA
1 TAA TAA TAA TAA
2055195 ATAAAATGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2056925 original size:24 final size:24
Alignment explanation
Indices: 2056869--2056930 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
2056859 CAGTGGATTG
* * *
2056869 ATCTGCATCCTCTTTTGGAGCGTC
1 ATCTGCAACCTCTTTCGGAGCATC
*
2056893 GTCTGCAACCTCTTTCGGAGCATC
1 ATCTGCAACCTCTTTCGGAGCATC
*
2056917 ATCTTCAACCTCTT
1 ATCTGCAACCTCTT
2056931 GTAATATTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (24 bp):
ATCTGCAACCTCTTTCGGAGCATC
Found at i:2062146 original size:15 final size:15
Alignment explanation
Indices: 2062108--2062146 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2062098 TCCTTCTCTA
*
2062108 CCTCCTCCTCCGCAT
1 CCTCCTCCTCCACAT
**
2062123 CCTTGTCCTCCACAT
1 CCTCCTCCTCCACAT
2062138 CCTCCTCCT
1 CCTCCTCCT
2062147 TTTTCGCTTC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.56, G:0.05, T:0.31
Consensus pattern (15 bp):
CCTCCTCCTCCACAT
Found at i:2064016 original size:20 final size:20
Alignment explanation
Indices: 2063954--2064016 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
2063944 AAGACAGAGT
2063954 TATAAAAAATAAATGAAACAA
1 TATAAAAAATAAATGAAA-AA
**
2063975 -ATAAAAAATAAA-GATATGA
1 TATAAAAAATAAATGA-AAAA
2063994 TATAAAAAATAAATGAAAAA
1 TATAAAAAATAAATGAAAAA
2064014 TAT
1 TAT
2064017 TAACAACGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.09
20 30 0.86
21 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (20 bp):
TATAAAAAATAAATGAAAAA
Found at i:2066996 original size:21 final size:22
Alignment explanation
Indices: 2066966--2067007 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2066956 TATTTTTAAT
*
2066966 TTTTTTAATTTACTC-ATTGAA
1 TTTTTAAATTTACTCAATTGAA
*
2066987 TTTTTAAATTTCCTCAATTGA
1 TTTTTAAATTTACTCAATTGA
2067008 TCTAGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTTAAATTTACTCAATTGAA
Found at i:2073480 original size:12 final size:12
Alignment explanation
Indices: 2073463--2073527 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
2073453 AAAAAAATTA
2073463 ATTAAATAAAAT
1 ATTAAATAAAAT
*
2073475 ATTAAAGCAATTAAAT
1 ATT--A--AATAAAAT
2073491 AATTAAATAAAAT
1 -ATTAAATAAAAT
*
2073504 ACT-AATAAAAT
1 ATTAAATAAAAT
*
2073515 ATTAAATATAAT
1 ATTAAATAAAAT
2073527 A
1 A
2073528 AAATATACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 10 0.24
12 13 0.31
13 7 0.17
14 1 0.02
15 1 0.02
16 7 0.17
17 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:2073528 original size:17 final size:18
Alignment explanation
Indices: 2073500--2073533 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2073490 TAATTAAATA
2073500 AAATACTAATAAAATATT
1 AAATACTAATAAAATATT
2073518 AAATA-TAATAAAATAT
1 AAATACTAATAAAATAT
2073534 ACCTTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATACTAATAAAATATT
Found at i:2073883 original size:19 final size:19
Alignment explanation
Indices: 2073859--2073895 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2073849 CTATTTTTTT
*
2073859 TTCATCTGATATGGTATTG
1 TTCATCTGATATGATATTG
2073878 TTCATCTGATATGATATT
1 TTCATCTGATATGATATT
2073896 TACTTTGATA
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:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (19 bp):
TTCATCTGATATGATATTG
Found at i:2076858 original size:22 final size:22
Alignment explanation
Indices: 2076810--2076859 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2076800 GACTGCTACG
* *
2076810 AAAGGGATTTTTCAATTCCACC
1 AAAGTGATTTTTCAATTCCAAC
2076832 AAAGTGATTTTTCAATTCCAAC
1 AAAGTGATTTTTCAATTCCAAC
2076854 AAAGTG
1 AAAGTG
2076860 TAAAAAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
AAAGTGATTTTTCAATTCCAAC
Found at i:2077779 original size:31 final size:31
Alignment explanation
Indices: 2077741--2077821 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
2077731 AAATTTTTTT
*
2077741 TTGTTCATGTTCTTTCATTAAGGAATATAGC
1 TTGTTCATGTTCGTTCATTAAGGAATATAGC
*
2077772 TTGTTCATGTTCGTTCATTAAGGAATATAGT
1 TTGTTCATGTTCGTTCATTAAGGAATATAGC
* *
2077803 TTGTTCATATTTGTTCATT
1 TTGTTCATGTTCGTTCATT
2077822 TAAATAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (31 bp):
TTGTTCATGTTCGTTCATTAAGGAATATAGC
Found at i:2077874 original size:13 final size:12
Alignment explanation
Indices: 2077827--2077899 Score: 55
Period size: 13 Copynumber: 6.1 Consensus size: 12
2077817 TCATTTAAAT
2077827 AATAAACGAAAACA
1 AATAAACG--AACA
*
2077841 AATGAACGAAC-
1 AATAAACGAACA
2077852 -ATAAACGAACA
1 AATAAACGAACA
*
2077863 TAATAAATGAAC-
1 -AATAAACGAACA
2077875 -ATAAACGAACA
1 AATAAACGAACA
*
2077886 CAATAAATGAACA
1 -AATAAACGAACA
2077899 A
1 A
2077900 CACAAACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
10 18 0.38
12 4 0.08
13 19 0.40
14 7 0.15
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (12 bp):
AATAAACGAACA
Found at i:2077878 original size:23 final size:23
Alignment explanation
Indices: 2077828--2077898 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
2077818 CATTTAAATA
* * *
2077828 ATAAACGAAAACAAATGAACGAAC
1 ATAAACGAACAC-AATAAATGAAC
*
2077852 ATAAACGAACATAATAAATGAAC
1 ATAAACGAACACAATAAATGAAC
2077875 ATAAACGAACACAATAAATGAAC
1 ATAAACGAACACAATAAATGAAC
2077898 A
1 A
2077899 ACACAAACAC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 32 0.76
24 10 0.24
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.13
Consensus pattern (23 bp):
ATAAACGAACACAATAAATGAAC
Found at i:2078180 original size:14 final size:16
Alignment explanation
Indices: 2078161--2078192 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2078151 GCTATATGTT
2078161 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
2078175 CGAACATATAATCGAA
1 CGAACATATAATCGAA
2078191 CG
1 CG
2078193 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:2080557 original size:157 final size:153
Alignment explanation
Indices: 2080271--2080557 Score: 448
Period size: 157 Copynumber: 1.8 Consensus size: 153
2080261 GAAAGATGGT
* *
2080271 GTTGAGTCAAAACAGAAGGAGCATGTGACAAGGCTGAAGGCTAAAGAGATTTTTGGGGTCGTGGA
1 GTTGAGTCAAAACAGAAGGAGCATGTGACAAGGCTGAAGGCTAAAGAGATTTTTAGGGTCATGGA
* * * * *
2080336 TGGTGGTGATTTTGGGGAGATATGTATAATTTTGAAAATCACAAAGTTTAAAGGAATTAGAGTCA
66 TGGTGGTGATCTTAGAGAGATATGTATAATTTTAAAAATCACAAAGTTTAAAGGAATTAAAGTCA
2080401 TATTTAATGAAAGATAGTGTTAA
131 TATTTAATGAAAGATAGTGTTAA
*
2080424 GTTGAGTCAAAACAGAAGGAGCATGTGACAAGGCTGAAGGCTAAAGTGATTTTTAATTAGGGTCA
1 GTTGAGTCAAAACAGAAGGAGCATGTGACAAGGCTGAAGGCTAAAGAGA--TTT--TTAGGGTCA
* *
2080489 TGGATGGTGGTGATCTTAGAGAGATATGTATAATTTTAAAAATCACACAGTTTAAGGGAATTAAA
62 TGGATGGTGGTGATCTTAGAGAGATATGTATAATTTTAAAAATCACAAAGTTTAAAGGAATTAAA
2080554 GTCA
127 GTCA
2080558 GCTTAGGCAG
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
153 48 0.40
155 3 0.03
157 69 0.57
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.29
Consensus pattern (153 bp):
GTTGAGTCAAAACAGAAGGAGCATGTGACAAGGCTGAAGGCTAAAGAGATTTTTAGGGTCATGGA
TGGTGGTGATCTTAGAGAGATATGTATAATTTTAAAAATCACAAAGTTTAAAGGAATTAAAGTCA
TATTTAATGAAAGATAGTGTTAA
Found at i:2081694 original size:5 final size:5
Alignment explanation
Indices: 2081686--2081733 Score: 80
Period size: 5 Copynumber: 9.6 Consensus size: 5
2081676 TCGTCTCGTC
2081686 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC-GG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
2081734 TGGTAATACG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.10
5 32 0.78
6 5 0.12
ACGTcount: A:0.00, C:0.21, G:0.56, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:2081853 original size:22 final size:22
Alignment explanation
Indices: 2081825--2081894 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
2081815 TTTGGAAAAA
2081825 CGCAACGACAACTGTAGACTAT
1 CGCAACGACAACTGTAGACTAT
* * **
2081847 CGCAACG--AA-TTTGGAAAAT
1 CGCAACGACAACTGTAGACTAT
2081866 CGCAACGACAACTGTAGACTAT
1 CGCAACGACAACTGTAGACTAT
2081888 CGCAACG
1 CGCAACG
2081895 CGATTTTCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 13 0.35
20 2 0.05
21 2 0.05
22 20 0.54
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (22 bp):
CGCAACGACAACTGTAGACTAT
Found at i:2081857 original size:41 final size:41
Alignment explanation
Indices: 2081812--2081894 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2081802 ATCTTTTTAA
2081812 GAATTTGGAAAAACGCAACGACAACTGTAGACTATCGCAAC
1 GAATTTGGAAAAACGCAACGACAACTGTAGACTATCGCAAC
*
2081853 GAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC
1 GAATTTGGAAAAACGCAACGACAACTGTAGACTATCGCAAC
2081894 G
1 G
2081895 CGATTTTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
GAATTTGGAAAAACGCAACGACAACTGTAGACTATCGCAAC
Found at i:2081909 original size:21 final size:21
Alignment explanation
Indices: 2081883--2081926 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2081873 ACAACTGTAG
2081883 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
2081904 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
2081925 AC
1 AC
2081927 GCGAATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:2082362 original size:31 final size:31
Alignment explanation
Indices: 2082315--2082382 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
2082305 GTTGAATATT
*
2082315 TTATAATTTTAGATATTTATAAATTAAATTAA
1 TTAT-ATTATAGATATTTATAAATTAAATTAA
2082347 TTATATTATAGATATTTATAAATTAAATTAA
1 TTATATTATAGATATTTATAAATTAAATTAA
2082378 TTATA
1 TTATA
2082383 CTCATCGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATATTATAGATATTTATAAATTAAATTAA
Found at i:2083743 original size:2 final size:2
Alignment explanation
Indices: 2083736--2083760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2083726 TTTGGTTTCT
2083736 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 T
2083761 GTTTGATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2091888 original size:20 final size:20
Alignment explanation
Indices: 2091859--2091896 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2091849 TTTCAAAGGG
2091859 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
2091879 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
2091897 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2091934 original size:45 final size:45
Alignment explanation
Indices: 2091879--2092072 Score: 241
Period size: 45 Copynumber: 4.3 Consensus size: 45
2091869 GCACCAATCC
* * *
2091879 ATGCATCGATGCAC-CAATGAATAAATT-GAACATCGAATGCAGTTT
1 ATGCATCGATGCACTC-A-GATTAAATTAAAACATCGAATGCATTTT
* *
2091924 ATGCATCGATGCACTCAGGATTTAA-TGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCA-GATTAAATTAAAACATCGAATGCATTTT
* **
2091969 ATGCATCGATGCACTCAGGTTATTTTAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGATTAAATTAAAACATCGAATGCATTTT
* **
2092014 ATGCATCGATGCACTCAGGTTATTTTAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGATTAAATTAAAACATCGAATGCATTTT
2092059 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2092073 ACTTAGTGCA
Statistics
Matches: 136, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
44 4 0.03
45 131 0.96
46 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGATTAAATTAAAACATCGAATGCATTTT
Found at i:2092032 original size:90 final size:89
Alignment explanation
Indices: 2091907--2092072 Score: 280
Period size: 90 Copynumber: 1.8 Consensus size: 89
2091897 GAATAAATTG
*
2091907 AACATCGAATGCAGTTTATGCATCGATGCACTCAGG-ATTTAATGAAACATCGAATGCATTTTAT
1 AACATCGAATGCAGTTTATGCATCGATGCACTCAGGTATTT--TAAAACATCGAATGCATTTTAT
2091971 GCATCGATGCACTCAGGTTATTTTAA
64 GCATCGATGCACTCAGGTTATTTTAA
*
2091997 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTATTTTAAAACATCGAATGCATTTTATG
1 AACATCGAATGCAGTTTATGCATCGATGCACTCAGG-TATTTTAAAACATCGAATGCATTTTATG
2092062 CATCGATGCAC
65 CATCGATGCAC
2092073 ACTTAGTGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
90 68 0.94
92 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (89 bp):
AACATCGAATGCAGTTTATGCATCGATGCACTCAGGTATTTTAAAACATCGAATGCATTTTATGC
ATCGATGCACTCAGGTTATTTTAA
Found at i:2098262 original size:64 final size:62
Alignment explanation
Indices: 2098059--2098266 Score: 226
Period size: 64 Copynumber: 3.3 Consensus size: 62
2098049 TGAACCAATC
* * * * * *
2098059 CATGCATCGATGCAC-CAATGAATAAATTGAACATCGAATGCAGTTTATGCATCAATGCACTCT
1 CATGCATCGATGCACTC-AGGATTTAA-TGAACATCGAATGCATTTTATGCATCGATGCACACT
2098122 CCATGCATCGATGCACTCAGGATTTAATGAAACATCGAATGCATTTTATGCATCGATGCACAAGC
1 -CATGCATCGATGCACTCAGGATTTAATG-AACATCGAATGCATTTTATGCATCGATGCAC-A-C
2098187 -
62 T
2098187 CATGCATCGATGCACTCAGGCTATTTTAA-G-ACATCGAATGCATTTTATGCATCGATGCACACT
1 CATGCATCGATGCACTCAGG--A-TTTAATGAACATCGAATGCATTTTATGCATCGATGCACACT
* *
2098250 TAGTGCACCGATGCACT
1 CA-TGCATCGATGCACT
2098267 AAGTGTTCCA
Statistics
Matches: 127, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 113 0.89
65 1 0.01
66 3 0.02
67 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (62 bp):
CATGCATCGATGCACTCAGGATTTAATGAACATCGAATGCATTTTATGCATCGATGCACACT
Found at i:2100456 original size:21 final size:22
Alignment explanation
Indices: 2100431--2100488 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
2100421 TATATCTAAT
*
2100431 ATAATTTTAAAAATAAAAAT-A
1 ATAATTTTAATAATAAAAATGA
* *
2100452 ATAATTTTGATAA-AAATATGA
1 ATAATTTTAATAATAAAAATGA
2100473 ATAATTTTAATAATAA
1 ATAATTTTAATAATAA
2100489 TAGTAATAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 5 0.16
21 24 0.77
22 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
ATAATTTTAATAATAAAAATGA
Found at i:2100490 original size:21 final size:20
Alignment explanation
Indices: 2100431--2100496 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
2100421 TATATCTAAT
* *
2100431 ATAATTTTAAAAATAAAAATA
1 ATAATTTTAATAAT-AATATA
* *
2100452 ATAATTTTGATAAAAATATGA
1 ATAATTTTAATAATAATAT-A
2100473 ATAATTTTAATAATAATAGTA
1 ATAATTTTAATAATAATA-TA
2100494 ATA
1 ATA
2100497 GGTTTAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 32 0.86
22 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAATTTTAATAATAATATA
Found at i:2100548 original size:21 final size:21
Alignment explanation
Indices: 2100427--2100556 Score: 63
Period size: 21 Copynumber: 6.2 Consensus size: 21
2100417 TGTCTATATC
* *
2100427 TAAT-ATAATTTTAAAAATAA
1 TAATAATAATTTGAATAATAA
* *
2100447 AAATAATAATTTTG-ATAAAAA
1 TAATAATAA-TTTGAATAATAA
*
2100468 T-ATGAATAATTTTAATAATAA
1 TAAT-AATAATTTGAATAATAA
* * * *
2100489 TAGTAATAGGTTT-AACAATAT
1 TAATAATA-ATTTGAATAATAA
** **
2100510 TTTTAATAACGGTG-ATAATAA
1 TAATAATAA-TTTGAATAATAA
*
2100531 TAATAATAATTTGAATAACAA
1 TAATAATAATTTGAATAATAA
2100552 TAATA
1 TAATA
2100557 TTAAAAATTA
Statistics
Matches: 78, Mismatches: 23, Indels: 17
0.66 0.19 0.14
Matches are distributed among these distances:
20 10 0.13
21 61 0.78
22 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (21 bp):
TAATAATAATTTGAATAATAA
Found at i:2100709 original size:31 final size:32
Alignment explanation
Indices: 2100665--2100725 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
2100655 TCTCGAATTT
2100665 AAAATTATTAAGTTCAACTTAAGTTGAAAATAA
1 AAAATTA-TAAGTTCAACTTAAGTTGAAAATAA
* * *
2100698 AAAATTA-AAGTTTAACTTGAGTTTAAAA
1 AAAATTATAAGTTCAACTTAAGTTGAAAA
2100726 AAGATTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
33 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (32 bp):
AAAATTATAAGTTCAACTTAAGTTGAAAATAA
Found at i:2101688 original size:2 final size:2
Alignment explanation
Indices: 2101681--2101710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2101671 TGCGTAATTT
2101681 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2101711 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2122677 original size:16 final size:16
Alignment explanation
Indices: 2122656--2122702 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2122646 ACTCATGTAA
2122656 TTTTAAAAATTTTATT
1 TTTTAAAAATTTTATT
* * *
2122672 TTTTAAAAAATATAGAT
1 TTTTAAAAATTTTA-TT
2122689 TTTT-AAAATTTTAT
1 TTTTAAAAATTTTAT
2122703 AAAGGTGACA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAAAAATTTTATT
Found at i:2124877 original size:30 final size:31
Alignment explanation
Indices: 2124841--2124916 Score: 109
Period size: 30 Copynumber: 2.4 Consensus size: 31
2124831 TTCCGCAAAA
2124841 ATTAATATTTCTTATTGTCAA-TTCTCATCG
1 ATTAATATTTCTTATTGTCAATTTCTCATCG
*
2124871 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCTTATTGTCAA--T-TTCTCATCG
2124905 ATTAATATTTCT
1 ATTAATATTTCT
2124917 GTTATATGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 20 0.50
34 20 0.50
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.51
Consensus pattern (31 bp):
ATTAATATTTCTTATTGTCAATTTCTCATCG
Found at i:2125182 original size:36 final size:36
Alignment explanation
Indices: 2125129--2125214 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
2125119 AATTACATCC
* *
2125129 ACTTTAGC-TTAGGTAAAAGCTTAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
2125164 ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
2125200 ACTTTAGCTTTAGGT
1 ACTTTAGCTTTAGGT
2125215 TAACTAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 8 0.17
36 40 0.83
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
Found at i:2126478 original size:15 final size:15
Alignment explanation
Indices: 2126460--2126488 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2126450 TTCATTTCAA
2126460 AATTTTATAAAATAC
1 AATTTTATAAAATAC
2126475 AATTTTATAAAATA
1 AATTTTATAAAATA
2126489 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:2129855 original size:17 final size:17
Alignment explanation
Indices: 2129833--2129867 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2129823 ACGAGACGGT
2129833 CTGTTGATGACTTGTCA
1 CTGTTGATGACTTGTCA
*
2129850 CTGTTGATGATTTGTCA
1 CTGTTGATGACTTGTCA
2129867 C
1 C
2129868 CTCAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (17 bp):
CTGTTGATGACTTGTCA
Found at i:2130213 original size:32 final size:32
Alignment explanation
Indices: 2130078--2130213 Score: 100
Period size: 32 Copynumber: 4.2 Consensus size: 32
2130068 TAACATAAAC
*
2130078 ATTTTACTTGTTA-CCGAAACATACAAATGCAG
1 ATTTTACTTGTTATCC-AAACATACAAGTGCAG
* **
2130110 ATTTTACTTTGATTATCCAAA-GTA-AAGTGACCTTT
1 ATTTTAC-TTG-TTATCCAAACATACAAGTG--C-AG
* * * * *
2130145 AATTTA-TTATTATCCAAAGAAACAAGTGCAC
1 ATTTTACTTGTTATCCAAACATACAAGTGCAG
*
2130176 CTTTTACTTGTTATCCAAACATACAAGTGCAG
1 ATTTTACTTGTTATCCAAACATACAAGTGCAG
2130208 ATTTTA
1 ATTTTA
2130214 TTTAACATAA
Statistics
Matches: 78, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
31 4 0.05
32 47 0.60
33 8 0.10
34 12 0.15
35 7 0.09
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTTTACTTGTTATCCAAACATACAAGTGCAG
Found at i:2132068 original size:23 final size:22
Alignment explanation
Indices: 2132017--2132087 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
2132007 TATATTTATG
**
2132017 AACATTAAACATGCACATTACA
1 AACATTAAACAAACACATTACA
* *
2132039 AAAATTAAACAAACATATTAACA
1 AACATTAAACAAACACATT-ACA
** *
2132062 AACATTAAATGAACA-AATACA
1 AACATTAAACAAACACATTACA
2132083 AACAT
1 AACAT
2132088 ATAGTTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.20
22 17 0.43
23 15 0.38
ACGTcount: A:0.59, C:0.17, G:0.03, T:0.21
Consensus pattern (22 bp):
AACATTAAACAAACACATTACA
Found at i:2143605 original size:20 final size:20
Alignment explanation
Indices: 2143580--2143625 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2143570 TTTCTGGAAA
2143580 GGAGCTGATCAAAAAGCTCT
1 GGAGCTGATCAAAAAGCTCT
2143600 GGAGCTGATCAAAAAGCTCT
1 GGAGCTGATCAAAAAGCTCT
2143620 GGAGCT
1 GGAGCT
2143626 AGAGTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (20 bp):
GGAGCTGATCAAAAAGCTCT
Found at i:2144476 original size:16 final size:17
Alignment explanation
Indices: 2144450--2144484 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2144440 GGGATATATG
2144450 TGATCTTTGATTTTCTT
1 TGATCTTTGATTTTCTT
2144467 TGAT-TTTGATTTTCTT
1 TGATCTTTGATTTTCTT
2144483 TG
1 TG
2144485 TAAGTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.11, C:0.09, G:0.14, T:0.66
Consensus pattern (17 bp):
TGATCTTTGATTTTCTT
Found at i:2146167 original size:15 final size:15
Alignment explanation
Indices: 2146144--2146173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2146134 TGTTTAAATC
*
2146144 AATTTATTAATTTTA
1 AATTAATTAATTTTA
2146159 AATTAATTAATTTTA
1 AATTAATTAATTTTA
2146174 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTAATTAATTTTA
Found at i:2148631 original size:23 final size:22
Alignment explanation
Indices: 2148599--2148648 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
2148589 TAAAATTGTA
*
2148599 TTAAAAAT-AAATCAAATTAATG
1 TTAAAAATAAAAT-AAAATAATG
2148621 TTAAACAATAAAATAAAATAATG
1 TTAAA-AATAAAATAAAATAATG
2148644 TTAAA
1 TTAAA
2148649 TAAATGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 16 0.64
24 4 0.16
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
TTAAAAATAAAATAAAATAATG
Found at i:2152023 original size:103 final size:103
Alignment explanation
Indices: 2151916--2152219 Score: 500
Period size: 101 Copynumber: 3.0 Consensus size: 103
2151906 TACATGGTTA
*
2151916 CCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCT
1 CCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCT
2151981 TGGCATATGTATATGATTCTTAAGGAATGATATGTGGT
66 TGGCATATGTATATGATTCTTAAGGAATGATATGTGGT
*
2152019 CCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAG--ATATACTTGATCCT
1 CCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCT
2152082 TGGCATATGTATATGATTCTTAAGGAATGATATGT-GT
66 TGGCATATGTATATGATTCTTAAGGAATGATATGTGGT
*
2152119 CCTTCGGGACATATATGTATTC-TTGGAACATGTGTGAAGTCTGGTGAGACACATAC-T--TCCC
1 CCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCT
* *
2152180 TAGTATATGTATATGATTCTTAAGGAATG--ATGTGGT
66 TGGCATATGTATATGATTCTTAAGGAATGATATGTGGT
2152216 CCTT
1 CCTT
2152220 ATGGACATTA
Statistics
Matches: 192, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
96 4 0.02
97 6 0.03
98 30 0.16
99 26 0.14
100 25 0.13
101 53 0.28
103 48 0.25
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
CCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCT
TGGCATATGTATATGATTCTTAAGGAATGATATGTGGT
Found at i:2152281 original size:23 final size:22
Alignment explanation
Indices: 2152233--2152292 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
2152223 GACATTATTG
*
2152233 GCACTACGGTGCATTCTACGCG
1 GCACTACGGTGCATTCTACGCA
* *
2152255 GCACTACGGTGCAATTCTATGTA
1 GCACTACGGTGC-ATTCTACGCA
**
2152278 GCACTTTGGTGCATT
1 GCACTACGGTGCATT
2152293 TATATGAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
GCACTACGGTGCATTCTACGCA
Found at i:2157018 original size:100 final size:101
Alignment explanation
Indices: 2156845--2157152 Score: 483
Period size: 100 Copynumber: 3.1 Consensus size: 101
2156835 GTCGAGGGTC
*
2156845 TATGTGGTCTTTCGGGACATATAT-TA-TCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGA-ACATAC
2156908 TTGATCCTTGGCATATGTATAGATTCTTAAGGAATGA
65 TTGATCCTTGGCATATGTATAGATTCTTAAGGAATGA
2156945 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAG-ACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGAACATACT
2157009 TGATCCTTGGCATATGTATATGA-TCTTAAGGAATGA
66 TGATCCTTGGCATATGTATA-GATTCTTAAGGAATGA
2157045 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGA-ACATAC
* * *
2157110 TTGATCC-TAG--TACGTATA-TTTCTTAAGGAATG-
65 TTGATCCTTGGCATATGTATAGATTCTTAAGGAATGA
2157142 -ATGTGGTCCTT
1 TATGTGGTCCTT
2157153 ATGGACATTA
Statistics
Matches: 198, Mismatches: 4, Indels: 16
0.91 0.02 0.07
Matches are distributed among these distances:
96 11 0.06
98 12 0.06
99 7 0.04
100 120 0.61
101 6 0.03
102 42 0.21
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGAACATACT
TGATCCTTGGCATATGTATAGATTCTTAAGGAATGA
Found at i:2158190 original size:20 final size:19
Alignment explanation
Indices: 2158165--2158229 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2158155 CTACATTATA
2158165 TTTTCAAAAACTATAATATG
1 TTTTCAAAAA-TATAATATG
2158185 TTTTC-AAAA-AT--TATG
1 TTTTCAAAAATATAATATG
* *
2158200 TTTTTAAAAATATAATATA
1 TTTTCAAAAATATAATATG
*
2158219 TTTTTAAAAAT
1 TTTTCAAAAAT
2158230 TATATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 8 0.21
16 4 0.10
17 4 0.10
19 18 0.46
20 5 0.13
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (19 bp):
TTTTCAAAAATATAATATG
Found at i:2158201 original size:15 final size:15
Alignment explanation
Indices: 2158181--2158210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2158171 AAAACTATAA
2158181 TATGTTTTCAAAAAT
1 TATGTTTTCAAAAAT
*
2158196 TATGTTTTTAAAAAT
1 TATGTTTTCAAAAAT
2158211 ATAATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TATGTTTTCAAAAAT
Found at i:2158228 original size:34 final size:35
Alignment explanation
Indices: 2158159--2158234 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
2158149 AGTAACCTAC
*
2158159 ATTATATTTTCAAAAACTATAATATGTTTTCAAAA
1 ATTATATTTTCAAAAACTATAATATATTTTCAAAA
* * *
2158194 ATTATGTTTTTAAAAA-TATAATATATTTTTAAAA
1 ATTATATTTTCAAAAACTATAATATATTTTCAAAA
2158228 ATTATAT
1 ATTATAT
2158235 ATATTAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (35 bp):
ATTATATTTTCAAAAACTATAATATATTTTCAAAA
Found at i:2158312 original size:18 final size:18
Alignment explanation
Indices: 2158285--2158325 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2158275 CCATACATAT
* *
2158285 TATATGTTTTCAAAACTA
1 TATATATTTTCAAAACCA
2158303 TATATATTTTCAAAACCA
1 TATATATTTTCAAAACCA
2158321 TATAT
1 TATAT
2158326 TATATACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATTTTCAAAACCA
Found at i:2161454 original size:14 final size:14
Alignment explanation
Indices: 2161435--2161463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2161425 ACGGCCAACG
2161435 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
2161449 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
2161463 G
1 G
2161464 ACCGGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:2161486 original size:10 final size:9
Alignment explanation
Indices: 2161458--2161518 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
2161448 AGTCGGGTCG
*
2161458 GGTCAGACC
1 GGTCAAACC
2161467 GGTCAAACC
1 GGTCAAACC
2161476 GGTCGAAACC
1 GGTC-AAACC
2161486 GGTCAGAACC
1 GGTCA-AACC
* *
2161496 GGTTGAAAACT
1 GG-T-CAAACC
2161507 GGTCAAACC
1 GGTCAAACC
2161516 GGT
1 GGT
2161519 TTCCAGCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 20 0.47
10 16 0.37
11 6 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2161519 original size:20 final size:19
Alignment explanation
Indices: 2161464--2161519 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
2161454 GTCGGGTCAG
*
2161464 ACCGGTCAAACCGGTCGAA
1 ACCGGTCAAACCGGTTGAA
2161483 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTTG-AA
*
2161504 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
2161520 TCCAGCCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 8 0.24
20 16 0.48
21 9 0.27
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTGAA
Found at i:2168644 original size:10 final size:10
Alignment explanation
Indices: 2168614--2168647 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2168604 TCAGTCGGGT
2168614 CGGTTCAGAC
1 CGGTTCAGAC
*
2168624 CGG-TCAAAC
1 CGGTTCAGAC
2168633 CGGTTCAGAC
1 CGGTTCAGAC
2168643 CGGTT
1 CGGTT
2168648 TGAACCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (10 bp):
CGGTTCAGAC
Found at i:2172036 original size:14 final size:14
Alignment explanation
Indices: 2172012--2172045 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2172002 AATCTGATTG
2172012 AAAATTTAAATTTAT
1 AAAA-TTAAATTTAT
*
2172027 TAAATTAAATTTAT
1 AAAATTAAATTTAT
2172041 AAAAT
1 AAAAT
2172046 ATGTAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTAAATTTAT
Found at i:2172380 original size:19 final size:20
Alignment explanation
Indices: 2172356--2172406 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2172346 AATGACCAAT
2172356 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2172375 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2172395 AAAATCGCAACG
1 AAAATCGCAACG
2172407 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2172400 original size:20 final size:20
Alignment explanation
Indices: 2172356--2172620 Score: 122
Period size: 20 Copynumber: 12.9 Consensus size: 20
2172346 AATGACCAAT
* *
2172356 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2172375 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2172395 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2172415 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
2172435 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2172456 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2172479 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
2172499 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2172519 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2172539 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2172559 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
2172579 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* *
2172602 AGAATCGCAATGCGATTTA
1 AAAATCGCAACGCGATTTA
2172621 TAGAATTTTC
Statistics
Matches: 195, Mismatches: 39, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
19 17 0.09
20 134 0.69
21 15 0.08
22 1 0.01
23 28 0.14
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2172625 original size:20 final size:20
Alignment explanation
Indices: 2172481--2172626 Score: 193
Period size: 20 Copynumber: 7.2 Consensus size: 20
2172471 TTTAGAAGAA
2172481 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
2172501 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
2172521 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
*
2172541 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* * *
2172561 AGTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-ATAG
* *
2172584 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAG
*
2172604 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
2172624 AAT
1 AAT
2172627 TTTCTCTAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
20 92 0.82
21 3 0.03
22 2 0.02
23 15 0.13
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:2173392 original size:6 final size:6
Alignment explanation
Indices: 2173381--2173431 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
2173371 TCTCGTCTCG
2173381 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2173429 GGT
1 GGT
2173432 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2173535 original size:20 final size:20
Alignment explanation
Indices: 2173510--2173553 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2173500 TTTTTAACTA
*
2173510 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2173530 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2173550 TTCT
1 TTCT
2173554 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2173563 original size:20 final size:20
Alignment explanation
Indices: 2173540--2173837 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
2173530 TTCTTTTTAA
2173540 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2173560 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
** * *
2173580 CAATGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2173600 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2173620 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
2173640 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
2173663 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2173683 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2173703 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** **
2173726 CGTTGCGAACTTGGACGCTCG
1 CGTTGCGATTTTCTA-AATCG
* *
2173747 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2173765 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2173787 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2173807 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2173826 CGTTGCGATTTT
1 CGTTGCGATTTT
2173838 ATTGGTCATT
Statistics
Matches: 222, Mismatches: 45, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 155 0.70
21 15 0.07
22 5 0.02
23 28 0.13
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2173587 original size:40 final size:40
Alignment explanation
Indices: 2173542--2173733 Score: 222
Period size: 40 Copynumber: 4.7 Consensus size: 40
2173532 CTTTTTAACG
* *
2173542 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
2173582 ATGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
2173622 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGATTCTC-TC--AATCGCA
* * *
2173665 TTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
*
2173705 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCATTGCGA
2173734 ACTTGGACGC
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 74 0.58
41 2 0.02
42 4 0.03
43 48 0.38
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:2173686 original size:63 final size:62
Alignment explanation
Indices: 2173540--2173733 Score: 266
Period size: 63 Copynumber: 3.1 Consensus size: 62
2173530 TTCTTTTTAA
* * * * *
2173540 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCAATGCGA-TTC-TATAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTCTTCTAAATCG
* * *
2173600 CATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATT-TCTTCTAAATCG
* *
2173663 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGA-TTTCTTCTAAATCG
2173726 CGTTGCGA
1 CGTTGCGA
2173734 ACTTGGACGC
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
60 41 0.35
61 1 0.01
62 2 0.02
63 71 0.61
64 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (62 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTCTTCTAAATCG
Found at i:2173827 original size:19 final size:20
Alignment explanation
Indices: 2173787--2173837 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2173777 TTCTTTTTAA
*
2173787 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2173807 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2173826 CGTTGCGATTTT
1 CGTTGCGATTTT
2173838 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2175960 original size:19 final size:19
Alignment explanation
Indices: 2175936--2175973 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2175926 AACTAGTCCA
2175936 AAATCAACATTTTAATATT
1 AAATCAACATTTTAATATT
* *
2175955 AAATCAATATTTTACTATT
1 AAATCAACATTTTAATATT
2175974 TGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATCAACATTTTAATATT
Found at i:2178817 original size:18 final size:18
Alignment explanation
Indices: 2178796--2178855 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
2178786 CTGCGCTATT
2178796 CTTTTTCTTGTATCGTTC
1 CTTTTTCTTGTATCGTTC
** *
2178814 CTTTCAC-TGTA-C-TATT
1 CTTTTTCTTGTATCGT-TC
*
2178830 CTTTTTCCTGTATCGTTC
1 CTTTTTCTTGTATCGTTC
2178848 CTTTTTCT
1 CTTTTTCT
2178856 ATGATGATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
15 1 0.03
16 7 0.23
17 8 0.26
18 14 0.45
19 1 0.03
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (18 bp):
CTTTTTCTTGTATCGTTC
Found at i:2178820 original size:34 final size:34
Alignment explanation
Indices: 2178781--2178851 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2178771 TACTAATTTT
* *
2178781 TTTCACTGCGCTATTCTTTTTCTTGTATCGTTCC
1 TTTCACTGCACTATTCTTTTTCCTGTATCGTTCC
*
2178815 TTTCACTGTACTATTCTTTTTCCTGTATCGTTCC
1 TTTCACTGCACTATTCTTTTTCCTGTATCGTTCC
2178849 TTT
1 TTT
2178852 TTCTATGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.10, C:0.25, G:0.10, T:0.55
Consensus pattern (34 bp):
TTTCACTGCACTATTCTTTTTCCTGTATCGTTCC
Found at i:2178852 original size:17 final size:17
Alignment explanation
Indices: 2178798--2178852 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2178788 GCGCTATTCT
*
2178798 TTTTCTTGTATCGTTCC
1 TTTTCCTGTATCGTTCC
* *
2178815 -TTTCACTGTA-CTATTCT
1 TTTTC-CTGTATC-GTTCC
2178832 TTTTCCTGTATCGTTCC
1 TTTTCCTGTATCGTTCC
2178849 TTTT
1 TTTT
2178853 TCTATGATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 5 0.17
17 19 0.66
18 5 0.17
ACGTcount: A:0.09, C:0.24, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTTCCTGTATCGTTCC
Found at i:2180279 original size:19 final size:19
Alignment explanation
Indices: 2180255--2180292 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2180245 AACTAGTCCA
2180255 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
2180274 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
2180293 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:2180781 original size:31 final size:30
Alignment explanation
Indices: 2180746--2180803 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2180736 TTAAGTCTCT
* *
2180746 ACTTTTTCATAATATACAATTTAGTCCACAA
1 ACTTTATCA-AATATACAAATTAGTCCACAA
* *
2180777 ACTTTATCAAATTTCCAAATTAGTCCA
1 ACTTTATCAAATATACAAATTAGTCCA
2180804 ATTTCACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
ACTTTATCAAATATACAAATTAGTCCACAA
Found at i:2180988 original size:20 final size:20
Alignment explanation
Indices: 2180950--2180988 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2180940 AAATTAGTCC
* * *
2180950 AATTTTACATTTTATCATCG
1 AATTTAACATTCTAACATCG
2180970 AATTTAACATTCTAACATC
1 AATTTAACATTCTAACATC
2180989 TAAAGATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTTAACATTCTAACATCG
Found at i:2191209 original size:19 final size:21
Alignment explanation
Indices: 2191154--2191210 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
2191144 ATAAGGCAGA
2191154 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTT-AAG
* * *
2191176 GGGAACCAATTCCCCC-T-AG
1 GGGAATCGATACCCCCTTAAG
2191195 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
2191211 CTGGGGTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.52
21 1 0.03
22 13 0.45
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTAAG
Found at i:2195557 original size:60 final size:60
Alignment explanation
Indices: 2195473--2195587 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
2195463 GGTCCCTCGA
*
2195473 CTATAGGGTGTTACTTTGTGGAGTCTCTCAACTATCAAAAGTTACAAAATGATCATTTTT
1 CTATAGGATGTTACTTTGTGGAGTCTCTCAACTATCAAAAGTTACAAAATGATCATTTTT
** * * * *
2195533 CTATAGGATGTTGTTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATTATCA
1 CTATAGGATGTTACTTTGTGGAGTCTCTCAACTATCAAAAGTTACAAAATGATCA
2195588 CCCAATTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (60 bp):
CTATAGGATGTTACTTTGTGGAGTCTCTCAACTATCAAAAGTTACAAAATGATCATTTTT
Found at i:2215445 original size:30 final size:30
Alignment explanation
Indices: 2215409--2215469 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2215399 CAAATTTGAG
2215409 TGAGGTTCCAACCCTTCCAACACTTCTTCA
1 TGAGGTTCCAACCCTTCCAACACTTCTTCA
*
2215439 TGAGGTTTCAACCCTTCCAACACTTCTTCA
1 TGAGGTTCCAACCCTTCCAACACTTCTTCA
2215469 T
1 T
2215470 CCTTACGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.34, G:0.10, T:0.33
Consensus pattern (30 bp):
TGAGGTTCCAACCCTTCCAACACTTCTTCA
Found at i:2219607 original size:20 final size:20
Alignment explanation
Indices: 2219584--2219635 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2219574 AACGCGATCC
2219584 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2219604 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2219624 CCAAAATCGCAA
1 CCAGAATCGCAA
2219636 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2219716 original size:20 final size:20
Alignment explanation
Indices: 2219691--2219884 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2219681 GATTTTCCAT
* *
2219691 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2219711 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2219731 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2219751 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2219771 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2219791 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2219811 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2219831 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2219852 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2219872 AATCGCAACGCGA
1 AATCGCAACGCGA
2219885 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2219736 original size:40 final size:39
Alignment explanation
Indices: 2219687--2219884 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
2219677 TTGCGATTTT
* ** *
2219687 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
2219725 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
2219766 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
2219806 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
2219845 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2219885 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:2219774 original size:60 final size:60
Alignment explanation
Indices: 2219691--2219883 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2219681 GATTTTCCAT
* ** * *
2219691 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2219751 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2219811 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2219872 AATCGCAACGCG
1 AATCGCAACGCG
2219884 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2220055 original size:21 final size:22
Alignment explanation
Indices: 2220029--2220082 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2220019 CTCTCTACGG
2220029 CGAAGAAATCCGT-CCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
2220050 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
2220072 CGGCGAAATCC
1 CGAAGAAATCC
2220083 CTCACAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:2220301 original size:33 final size:33
Alignment explanation
Indices: 2220262--2220332 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2220252 TTCACTTAGA
*
2220262 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2220295 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2220328 TTTCA
1 TTTCA
2220333 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2220471 original size:14 final size:14
Alignment explanation
Indices: 2220452--2220506 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2220442 AGAATGACTG
2220452 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2220466 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2220485 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2220499 TCGCAACG
1 TCGCAACG
2220507 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2220489 original size:33 final size:33
Alignment explanation
Indices: 2220452--2220522 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2220442 AGAATGACTG
**
2220452 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2220485 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2220518 TCGCA
1 TCGCA
2220523 TTGCGATTTT
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:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2220540 original size:19 final size:19
Alignment explanation
Indices: 2220518--2220615 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2220508 GAAACCAAAA
*
2220518 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2220537 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2220551 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2220570 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2220584 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2220603 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2220616 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2220559 original size:14 final size:14
Alignment explanation
Indices: 2220540--2220629 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2220530 TTTCATTTCG
2220540 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2220554 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2220573 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2220587 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2220604 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2220620 CGTTGCGATT
1 CGTTGCGATT
2220630 TCATTTCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2220565 original size:33 final size:33
Alignment explanation
Indices: 2220523--2220636 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2220513 CAAAATCGCA
2220523 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2220556 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2220589 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2220622 TTGCGA-TTTCATTTC
1 TTGCGATTTTCATTTC
2220637 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 7 0.09
33 70 0.91
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2222562 original size:185 final size:186
Alignment explanation
Indices: 2222332--2223082 Score: 1479
Period size: 185 Copynumber: 4.0 Consensus size: 186
2222322 TAGATTGCTT
*
2222332 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222397 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2222462 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222517 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222582 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2222647 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222703 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222767 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2222832 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222953 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2223018 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2223074 AGTAAATTT
1 AGTAAATTT
2223083 ATCCATTCAA
Statistics
Matches: 563, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.60
186 224 0.40
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2222646 original size:93 final size:93
Alignment explanation
Indices: 2222332--2223082 Score: 1479
Period size: 93 Copynumber: 8.1 Consensus size: 93
2222322 TAGATTGCTT
*
2222332 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222397 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222425 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222489 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222517 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222582 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222610 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222675 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222703 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222767 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222795 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222860 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222953 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2222981 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2223046 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2223074 AGTAAATTT
1 AGTAAATTT
2223083 ATCCATTCAA
Statistics
Matches: 655, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.28
93 471 0.72
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2222829 original size:278 final size:278
Alignment explanation
Indices: 2222332--2223082 Score: 1484
Period size: 278 Copynumber: 2.7 Consensus size: 278
2222322 TAGATTGCTT
*
2222332 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222397 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2222462 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
2222527 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
2222592 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
2222610 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222675 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2222740 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
2222805 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
2222870 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
2222888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2222953 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2223018 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
2223083 ATCCATTCAA
Statistics
Matches: 471, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
278 432 0.92
279 39 0.08
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:2223166 original size:19 final size:19
Alignment explanation
Indices: 2223126--2223254 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2223116 TAGTTTACTT
* *
2223126 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2223146 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2223165 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2223184 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2223198 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2223217 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2223231 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2223250 TCGCA
1 TCGCA
2223255 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2223205 original size:33 final size:32
Alignment explanation
Indices: 2223162--2223254 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2223152 CGCGAAACCA
**
2223162 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2223194 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2223227 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2223255 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2223252 original size:52 final size:52
Alignment explanation
Indices: 2223126--2223254 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2223116 TAGTTTACTT
**
2223126 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2223178 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2223231 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2223255 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2223272 original size:19 final size:19
Alignment explanation
Indices: 2223250--2223314 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
2223240 GAAACCAAAA
2223250 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2223269 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
2223285 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2223302 TCGCATTGCGATT
1 TCGCATTGCGATT
2223315 CTGTCGTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 6 0.15
16 8 0.20
17 8 0.20
19 18 0.45
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2223291 original size:14 final size:14
Alignment explanation
Indices: 2223272--2223328 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2223262 TTTCATTTCG
2223272 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2223286 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2223303 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2223319 CGTTGCGATT
1 CGTTGCGATT
2223329 TTGGTTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2223297 original size:33 final size:33
Alignment explanation
Indices: 2223255--2223347 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2223245 CAAAATCGCA
*
2223255 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2223288 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
2223321 TTGCGATTTTGGTTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2223348 TTAAGTTTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2223343 original size:19 final size:20
Alignment explanation
Indices: 2223319--2223365 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2223309 GCGATTCTGT
*
2223319 CGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTTTAAGTTTCG
2223338 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAAGTTTCG
*
2223358 TGTTGCGA
1 CGTTGCGA
2223366 AAGTAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTAAGTTTCG
Found at i:2225306 original size:14 final size:14
Alignment explanation
Indices: 2225287--2225322 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2225277 ATTGTTTAAT
2225287 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2225301 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2225315 TGATTTGT
1 TGATTTGT
2225323 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2225445 original size:19 final size:19
Alignment explanation
Indices: 2225429--2225530 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2225419 AAAAATGACT
2225429 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2225448 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2225467 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2225481 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2225500 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2225520 ATCGCAATGCG
1 ATCGCAATGCG
2225531 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2225583 original size:19 final size:19
Alignment explanation
Indices: 2225559--2225846 Score: 338
Period size: 19 Copynumber: 16.4 Consensus size: 19
2225549 GATTATCTCG
2225559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2225578 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2225597 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2225611 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2225630 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2225649 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2225668 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
2225682 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2225701 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2225720 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2225734 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2225753 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2225772 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2225786 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2225806 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2225820 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2225839 TTGCGATT
1 TTGCGATT
2225847 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 10, Indels: 52
0.79 0.03 0.18
Matches are distributed among these distances:
14 35 0.15
16 31 0.13
17 27 0.12
18 3 0.01
19 125 0.54
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2225599 original size:52 final size:49
Alignment explanation
Indices: 2225537--2225846 Score: 298
Period size: 52 Copynumber: 5.9 Consensus size: 49
2225527 TGCGTTTATA
*
2225537 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
*
2225589 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-T-TTTCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
** * *
2225641 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATTTC-G-CGTTGCGATTTTC
* * * *
2225693 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * * *
2225745 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
*
2225797 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTC--GTTGCGA-TTTCATTTCGCGTTGCGATT
2225847 GTATTTTCCG
Statistics
Matches: 234, Mismatches: 12, Indels: 23
0.87 0.04 0.09
Matches are distributed among these distances:
50 13 0.06
51 4 0.02
52 174 0.74
53 30 0.13
54 7 0.03
55 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTCATTTCGCGTTGCGATTTTC
Found at i:2225634 original size:71 final size:71
Alignment explanation
Indices: 2225559--2225846 Score: 366
Period size: 71 Copynumber: 4.1 Consensus size: 71
2225549 GATTATCTCG
2225559 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2225624 TTCGCA
66 TTCGCA
* *
2225630 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2225695 TTCGCA
66 TTCGCA
*
2225701 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
2225761 TTCATTTCGCA
61 TTCATTTCGCA
* *
2225772 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTC--GTTGCGATTTT
*
2225830 CATTTCGCG
63 CATTTCGCA
2225839 TTGCGATT
1 TTGCGATT
2225847 GTATTTTCCG
Statistics
Matches: 193, Mismatches: 9, Indels: 32
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.06
67 27 0.14
68 14 0.07
69 13 0.07
70 2 0.01
71 119 0.62
72 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:2225685 original size:123 final size:124
Alignment explanation
Indices: 2225521--2225779 Score: 468
Period size: 123 Copynumber: 2.1 Consensus size: 124
2225511 GAAATGAAAA
*
2225521 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
2225585 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
2225644 TCGCATTGCGATTT-TAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
2225708 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
2225767 TCGCATTGCGATT
1 TCGCATTGCGATT
2225780 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
123 128 0.98
124 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (124 bp):
TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Done.