Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 39
Found at i:184647 original size:33 final size:33
Alignment explanation
Indices: 184602--184681 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
184592 AAAAAAGACT
* *
184602 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
184635 ATTGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
184668 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
184682 CCAAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:184730 original size:20 final size:20
Alignment explanation
Indices: 184705--184800 Score: 99
Period size: 19 Copynumber: 4.9 Consensus size: 20
184695 CGCGATTATA
*
184705 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
*
184725 GTTTCGCGTTGCGA-ATTTC
1 GTTTCGCGTTGCGATTTTTC
* *
184744 ATTTCGCATTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
*
184763 GTTTCGCGTTGCGCTTTTT-
1 GTTTCGCGTTGCGATTTTTC
* *
184782 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
184801 CATTTCAACC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 32 0.51
20 31 0.49
ACGTcount: A:0.08, C:0.20, G:0.23, T:0.49
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:184767 original size:58 final size:58
Alignment explanation
Indices: 184696--184806 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
184686 AAATTGCAAC
*
184696 GCGATTATAGTTTCGCGTTGCGATTTTTGGTT-TCGCGTTGCGAATTTCATTTCGCATT
1 GCGATTATAGTTTCGCGTTGCGATTTTT-ATTCTCGCGTTGCGAATTTCATTTCGCATT
* * * * *
184754 GCGATTTTCGTTTCGCGTTGCGCTTTTTATTCTCTCGTTGCGATTTTCATTTC
1 GCGATTATAGTTTCGCGTTGCGATTTTTATTCTCGCGTTGCGAATTTCATTTC
184807 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.04
58 44 0.96
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.48
Consensus pattern (58 bp):
GCGATTATAGTTTCGCGTTGCGATTTTTATTCTCGCGTTGCGAATTTCATTTCGCATT
Found at i:184795 original size:39 final size:38
Alignment explanation
Indices: 184706--184806 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 38
184696 GCGATTATAG
*
184706 TTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGAATTTCA
1 TTTCGCGTTGCGA-TTTTCGTTTCGCGTTGCGAATTTCA
* ** *
184745 TTTCGCATTGCGATTTTCGTTTCGCGTTGCGCTTTTTA
1 TTTCGCGTTGCGATTTTCGTTTCGCGTTGCGAATTTCA
* *
184783 TTCTCTCGTTGCGATTTTCATTTC
1 TT-TCGCGTTGCGATTTTCGTTTC
184807 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 23 0.43
39 30 0.57
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (38 bp):
TTTCGCGTTGCGATTTTCGTTTCGCGTTGCGAATTTCA
Found at i:185009 original size:94 final size:94
Alignment explanation
Indices: 184895--185270 Score: 568
Period size: 94 Copynumber: 4.1 Consensus size: 94
184885 ATAGATTGCA
* * *
184895 TTAC-TTCAACCAAAATACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAGT
*
184959 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
184988 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAGT
185053 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
185082 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAGT
* *
185147 TTAGCAGAATGGGGCAGCAACCGAATAAAT
66 TTAGCAGAAT-TGGCAGCAACCGAACAAAT
* * *
185177 TTAC-TTC-ACCAAAAGATAAAACAAAAGACAAATACTAACTTCATAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAG
* *
185236 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
185266 TTACT
1 TTACT
185271 AAGCAATCTA
Statistics
Matches: 265, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
89 22 0.08
90 17 0.06
93 18 0.07
94 187 0.71
95 21 0.08
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:185714 original size:20 final size:18
Alignment explanation
Indices: 185674--185714 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
185664 CGGGTCGATC
*
185674 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGAGTG
185692 AGGTGATGGCTCTCGAAGTG
1 AGGTGATGGCTCT-G-AGTG
185712 AGG
1 AGG
185715 AAGTGGAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 1 0.05
20 6 0.30
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.24
Consensus pattern (18 bp):
AGGTGATGGCTCTGAGTG
Found at i:186945 original size:20 final size:19
Alignment explanation
Indices: 186892--186967 Score: 91
Period size: 19 Copynumber: 3.9 Consensus size: 19
186882 TCTTTTGGTT
* *
186892 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
186911 GAGAATG-AAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
186930 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
186950 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
186968 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 33 0.69
20 15 0.31
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:187021 original size:19 final size:19
Alignment explanation
Indices: 186989--187048 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
186979 ATGCGTTTGG
186989 TTTCGCGTTTGCGATTTTCA
1 TTTCGCG-TTGCGATTTTCA
**
187009 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
187028 TTCCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
187047 TT
1 TT
187049 CTCAAAACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:187607 original size:20 final size:20
Alignment explanation
Indices: 187584--187923 Score: 270
Period size: 20 Copynumber: 16.9 Consensus size: 20
187574 CGATAGTCAG
187584 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
187604 ATTCGTATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
187624 AATTCGCATTGTGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
187645 AATCGCGTTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * *
187665 ATTCGCATTGTGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* ** *
187686 AATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* * * * *
187705 AAATCGCAATGCGAATTAGGAA
1 -ATTCGCATTGCGATTTACG-T
* * * *
187727 AATCGCAATGCGA-ATACAT
1 ATTCGCATTGCGATTTACGT
*
187746 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
187766 ATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
187786 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
187807 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
187827 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
187847 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
187867 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
187887 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
187907 ATTTGCGTTGCGATTTA
1 ATTCGCATTGCGATTTA
187924 GGAAAATCGC
Statistics
Matches: 261, Mismatches: 52, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.05
20 191 0.73
21 58 0.22
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:187677 original size:40 final size:40
Alignment explanation
Indices: 187584--187923 Score: 306
Period size: 40 Copynumber: 8.4 Consensus size: 40
187574 CGATAGTCAG
* * * *
187584 ATTCGCATTGCGATTTACGTATTCGTATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* * * *
187624 AATTCGCATTGTGATTTACTTAATCGCGTTACGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* * * * ** *
187665 ATTCGCATTGTGAATTATGAAAATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGATTTACG-TAATCGCATTGCGATTTACGT
* * * * * * * *
187705 AAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACAT
1 -ATTCGCATTGCGATTTACG-TAATCGCATTGCGATTTACGT
* * * * *
187746 AATCGCATTGCGATTTACGTATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
*
187786 AATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* *
187827 ATTCGCGTTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* *
187867 ATTCGCGTTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* *
187907 ATTTGCGTTGCGATTTA
1 ATTCGCATTGCGATTTA
187924 GGAAAATCGC
Statistics
Matches: 254, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
39 10 0.04
40 135 0.53
41 109 0.43
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
Found at i:187700 original size:21 final size:21
Alignment explanation
Indices: 187667--187764 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
187657 ATTTACGTAT
* * *
187667 TCGCATTGTGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
187688 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
187708 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
187729 TCGCAATGCGAA-TAC-ATAA
1 TCGCAATGCGAATTACGAAAA
* *
187748 TCGCATTGCGATTTACG
1 TCGCAATGCGAATTACG
187765 TATTCACATT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 13 0.21
20 22 0.35
21 27 0.44
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:187793 original size:101 final size:100
Alignment explanation
Indices: 187644--187882 Score: 230
Period size: 101 Copynumber: 2.4 Consensus size: 100
187634 GTGATTTACT
* * * *
187644 TAATCGCGTTACGATTTACGTATTCGCATTGTGAATTATGAAAATCGCAACGCGA-ATACGTAAA
1 TAATCGCGTTGCGATTTACGTATTCGCATTGCG-ATTTTCAAAATCGCAACGCGATATACGT-AA
*
187708 TCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACA
64 TCGCAATGCGAATTACG-AAATCGCAATGCGATATACA
* * * * ** *
187745 TAATCGCATTGCGATTTACGTATTCACATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAAT
1 TAATCGCGTTGCGATTTACGTATTCGCATTGCGATTTT-CAAAATCGCAACGCGATATACGTAAT
** * * * ** * *
187810 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTACG
65 CGCAATGCGAATTACGAAATCGCAATGCGATATACA
*
187846 TAATCGCGTTGCGATTTACGTATTCGCGTTGCGATTT
1 TAATCGCGTTGCGATTTACGTATTCGCATTGCGATTT
187883 ACGTAATCGC
Statistics
Matches: 111, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
100 14 0.13
101 92 0.83
102 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (100 bp):
TAATCGCGTTGCGATTTACGTATTCGCATTGCGATTTTCAAAATCGCAACGCGATATACGTAATC
GCAATGCGAATTACGAAATCGCAATGCGATATACA
Found at i:189021 original size:2 final size:2
Alignment explanation
Indices: 189014--189058 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
189004 ATTTCACCCC
189014 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
189056 TA T
1 TA T
189059 TATTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:193890 original size:15 final size:15
Alignment explanation
Indices: 193852--193890 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
193842 AACCGAATTT
*
193852 TAAAAAATAAAATAA
1 TAAAAAATAAAAAAA
* *
193867 CAAATAATAAAAAAA
1 TAAAAAATAAAAAAA
193882 TAAAAAATA
1 TAAAAAATA
193891 TAGAATAAAA
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:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:193897 original size:22 final size:23
Alignment explanation
Indices: 193853--193901 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
193843 ACCGAATTTT
*
193853 AAAAAATAAAATAACAAATAATA
1 AAAAAATAAAATAACAAAGAATA
* *
193876 AAAAAATAAAA-AATATAGAATA
1 AAAAAATAAAATAACAAAGAATA
193898 AAAA
1 AAAA
193902 TGTAATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAATAAAATAACAAAGAATA
Found at i:198192 original size:23 final size:23
Alignment explanation
Indices: 198142--198192 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
198132 GGAAATAATT
198142 TTAAA-TAAGGACTAAAATAAAA
1 TTAAATTAAGGACTAAAATAAAA
* * * *
198164 TAAAATTATGGACTAAATTATAA
1 TTAAATTAAGGACTAAAATAAAA
198187 TTAAAT
1 TTAAAT
198193 AAATCAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAAATTAAGGACTAAAATAAAA
Found at i:198221 original size:18 final size:18
Alignment explanation
Indices: 198159--198224 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
198149 AGGACTAAAA
*
198159 TAAAATAAAATTATGGAC
1 TAAATTAAAATTATGGAC
* * *
198177 TAAATTATAATTAAAT-AAA
1 TAAATTAAAATT--ATGGAC
*
198196 TCAATTAAAATTATGGAC
1 TAAATTAAAATTATGGAC
198214 TAAATTAAAAT
1 TAAATTAAAAT
198225 GTATAGAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 21 0.58
19 11 0.31
20 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (18 bp):
TAAATTAAAATTATGGAC
Found at i:202552 original size:21 final size:21
Alignment explanation
Indices: 202523--202601 Score: 140
Period size: 21 Copynumber: 3.8 Consensus size: 21
202513 CACTAGTGCA
202523 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
202544 GGTGTATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
202565 GGTGTATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
202586 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
202602 TTGACACCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:205365 original size:30 final size:31
Alignment explanation
Indices: 205296--205365 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
205286 ATGATAATAC
* *
205296 TTTATTTTTATTACCCTTTTAACTTCTGTTAT
1 TTTA-TTTTATTACCCTTTAAACTTATGTTAT
* *
205328 TTAATTTTA-TACACCTTTAAATTTATGTT-T
1 TTTATTTTATTAC-CCTTTAAACTTATGTTAT
205358 TTTATTTT
1 TTTATTTT
205366 TCTTTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 11 0.34
31 18 0.56
32 3 0.09
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTATTTTATTACCCTTTAAACTTATGTTAT
Found at i:205836 original size:117 final size:117
Alignment explanation
Indices: 205624--205868 Score: 334
Period size: 117 Copynumber: 2.1 Consensus size: 117
205614 CTCTATGATG
* * * * *
205624 GAAATATTGATCCACCTCTCTTTGTGATGGAATCGAGCCAAGGTTGAACCGATTTTTCTCATTAT
1 GAAATGTTGATCCACCTCTCTTTGTGATGGAATCAAACCAAGGTTGAACAGATTCTTCTCATTAT
* * * *
205689 GAACTTCTTCTTCCTCGTCGAATGAATTCTTCTCGTTATGAACTTTCCACTA
66 GAACTTCTTCTCCCTCATCGAATGAATTCTTCTCATTATGAACTCTCCACTA
205741 GAAATGTTGATCCACCTC-CTTCTGTGATGGAATCAAACCAAGGTTGAACA-AGTTCTTCTCATT
1 GAAATGTTGATCCACCTCTCTT-TGTGATGGAATCAAACCAAGGTTGAACAGA-TTCTTCTCATT
* * *
205804 ATGAACTTCTTCTCCCTCATC-AGATGAGTTCTTCTCATTATGAACTCTCCGCTG
64 ATGAACTTCTTCTCCCTCATCGA-ATGAATTCTTCTCATTATGAACTCTCCACTA
205858 GAAATGTTGAT
1 GAAATGTTGAT
205869 TGGTTTATCC
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
116 5 0.04
117 108 0.96
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (117 bp):
GAAATGTTGATCCACCTCTCTTTGTGATGGAATCAAACCAAGGTTGAACAGATTCTTCTCATTAT
GAACTTCTTCTCCCTCATCGAATGAATTCTTCTCATTATGAACTCTCCACTA
Found at i:207433 original size:54 final size:54
Alignment explanation
Indices: 207301--207595 Score: 284
Period size: 54 Copynumber: 5.5 Consensus size: 54
207291 TAGGCTTATA
* * * * * *
207301 TTCTTTAAAAAATGATTTGAAAACAACAATAAACCCCCGAAAATCAGGCTTAGC
1 TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCTTAGC
* * * *
207355 TTCTTTAAAAATTTATTAGAAAACATCAAGAAACCCCTGAAAACCAGGCTTAGC
1 TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCTTAGC
** * *
207409 TTCTTTTGAAATCCATTTGTAAACATCAAGAAA-CCC----AATCAAG-TATAGC
1 TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCT-TAGC
*
207458 TCCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCTTAGC
1 TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCTTAGC
* * ** * *
207512 TTCTTTCAAAATTCATTTGAAGTAATCATCAAG-AACCCCTAAAAATTTTA-TTTAGT
1 TTCTTTAAAAATTCATTTGAA--AA-CATCAAGAAACCCCTGAAAA-TCAAGCTTAGC
207568 TTC-TTAAAAATTTCATTTGAAAACATCA
1 TTCTTTAAAAA-TTCATTTGAAAACATCA
207596 TATTGTTTGG
Statistics
Matches: 201, Mismatches: 28, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
48 1 0.00
49 37 0.18
50 3 0.01
53 8 0.04
54 106 0.53
55 7 0.03
56 30 0.15
57 9 0.04
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (54 bp):
TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAAGCTTAGC
Found at i:208912 original size:20 final size:20
Alignment explanation
Indices: 208884--208922 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
208874 TTTCAGGTTG
*
208884 GCTTCTTTAGTTAAGGTCTA
1 GCTTCTTTAATTAAGGTCTA
* *
208904 GCTTTTTTAATTATGGTCT
1 GCTTCTTTAATTAAGGTCT
208923 TTATTGTTCT
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:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
GCTTCTTTAATTAAGGTCTA
Found at i:210385 original size:19 final size:19
Alignment explanation
Indices: 210361--210423 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
210351 CAACCTAACT
210361 CGACCTGTTGACTTTGACC
1 CGACCTGTTGACTTTGACC
* * *
210380 CGACCTATTCACTTTTACC
1 CGACCTGTTGACTTTGACC
* * *
210399 CAACCCGTTGACTTTGACT
1 CGACCTGTTGACTTTGACC
210418 CGACCT
1 CGACCT
210424 AAATCTAAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (19 bp):
CGACCTGTTGACTTTGACC
Found at i:230622 original size:47 final size:47
Alignment explanation
Indices: 230568--230664 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
230558 TCCGGGGATC
230568 CGTTACACTTTCACATCATTCAGATTGAGAGTGACGGGGGCTCCAAT
1 CGTTACACTTTCACATCATTCAGATTGAGAGTGACGGGGGCTCCAAT
230615 CGTTACACTTTCACATCATTCAGATTGAGAGTGACGGGGGCTCCAAT
1 CGTTACACTTTCACATCATTCAGATTGAGAGTGACGGGGGCTCCAAT
230662 CGT
1 CGT
230665 CGGTGAGAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (47 bp):
CGTTACACTTTCACATCATTCAGATTGAGAGTGACGGGGGCTCCAAT
Found at i:230765 original size:13 final size:13
Alignment explanation
Indices: 230747--230771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230737 GTTCGAAAGG
230747 AAATAAAAAATAA
1 AAATAAAAAATAA
230760 AAATAAAAAATA
1 AAATAAAAAATA
230772 TAATTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:238784 original size:21 final size:21
Alignment explanation
Indices: 238760--238799 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
238750 TAACAAAGGT
*
238760 AGTATTGATACTCC-CTATAGG
1 AGTATCGATAC-CCTCTATAGG
238781 AGTATCGATACCCTCTATA
1 AGTATCGATACCCTCTATA
238800 ATGTGCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (21 bp):
AGTATCGATACCCTCTATAGG
Found at i:242486 original size:21 final size:20
Alignment explanation
Indices: 242462--242501 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
242452 CCATTGATCA
*
242462 TTGATTGCTGACTGTTGACCT
1 TTGATCGCTGACT-TTGACCT
*
242483 TTGATCGTTGACTTTGACC
1 TTGATCGCTGACTTTGACC
242502 AAAACGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGATCGCTGACTTTGACCT
Found at i:243389 original size:39 final size:39
Alignment explanation
Indices: 243279--243449 Score: 157
Period size: 39 Copynumber: 4.4 Consensus size: 39
243269 TTTTTCAGGT
* * *
243279 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACCGTAGGT
1 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGAAGGC
* * *
243318 TCTTCGGCTTTGTGCTAAGGGTAAGTCCTTACTGAAGGC
1 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGAAGGC
* *
243357 TCCTCGACATTGTGCTCAGAGTAAGTCCTTACT-ATAGGC
1 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGA-AGGC
** * * * * * *
243396 TCCTCTCCTTTATGCACATGATAAGACCTTACTGCAGGC
1 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGAAGGC
*
243435 TCTTCTG-CTTTGTGC
1 TCCTC-GACTTTGTGC
243450 ATAGCCCTTA
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 104 0.99
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (39 bp):
TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGAAGGC
Found at i:243448 original size:78 final size:78
Alignment explanation
Indices: 243279--243449 Score: 184
Period size: 78 Copynumber: 2.2 Consensus size: 78
243269 TTTTTCAGGT
* * * * * * * *
243279 TCCTCGACTTTGTGCTCAGGGTAAGTCCTTACCGTAGGTTCTTCGGCTTTGTGCTAAGGGTAAGT
1 TCCTCGACTTTGTGCTCAGAGTAAGTCCTTACCATAGGCTCCTCGCCTTTATGCTAAGGATAAGA
243344 CCTTACTGAAGGC
66 CCTTACTGAAGGC
* * * *
243357 TCCTCGACATTGTGCTCAGAGTAAGTCCTTACTATAGGCTCCTCTCCTTTATGC-ACATGATAAG
1 TCCTCGACTTTGTGCTCAGAGTAAGTCCTTACCATAGGCTCCTCGCCTTTATGCTA-AGGATAAG
*
243421 ACCTTACTGCAGGC
65 ACCTTACTGAAGGC
*
243435 TCTTCTG-CTTTGTGC
1 TCCTC-GACTTTGTGC
243450 ATAGCCCTTA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
77 1 0.01
78 74 0.97
79 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (78 bp):
TCCTCGACTTTGTGCTCAGAGTAAGTCCTTACCATAGGCTCCTCGCCTTTATGCTAAGGATAAGA
CCTTACTGAAGGC
Found at i:243478 original size:12 final size:12
Alignment explanation
Indices: 243461--243492 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
243451 TAGCCCTTAC
243461 TGGGTGTACAGG
1 TGGGTGTACAGG
243473 TGGGTGTACAGG
1 TGGGTGTACAGG
243485 TGGGTGTA
1 TGGGTGTA
243493 TAGTTCTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.50, T:0.28
Consensus pattern (12 bp):
TGGGTGTACAGG
Found at i:250450 original size:39 final size:39
Alignment explanation
Indices: 250325--250440 Score: 178
Period size: 39 Copynumber: 3.0 Consensus size: 39
250315 CGCTTTTCGC
* *
250325 AGGCTCCTCGGCTTTGTGTTCAGGGTAAGTCCTTACCGT
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGT
* * *
250364 AGGTTCCTCGGCTTTGTGCTCAGGGTAAGTCTTTATTGT
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGT
*
250403 AGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTG
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTG
250441 CAAACTCCTC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (39 bp):
AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGT
Found at i:250478 original size:39 final size:39
Alignment explanation
Indices: 250435--250509 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
250425 GGGTAAGTCC
* *
250435 TTACTGCAAACTCCTCTGCTTTATGCATAGGATAAGAGT
1 TTACTACAAACTCCTCTGCTTTATGCACAGGATAAGAGT
** * *
250474 TTACTACAGGCTCCTCTGCTTTTTGCACAGGGTAAG
1 TTACTACAAACTCCTCTGCTTTATGCACAGGATAAG
250510 CCCTTATTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (39 bp):
TTACTACAAACTCCTCTGCTTTATGCACAGGATAAGAGT
Found at i:250485 original size:78 final size:77
Alignment explanation
Indices: 250324--250515 Score: 188
Period size: 78 Copynumber: 2.5 Consensus size: 77
250314 CCGCTTTTCG
* * *** * *
250324 CAGGCTCCTCGGCTTTGTGTTCAGGGTAAGTCCTTACCGTAGGTTCCTCGGCTTTGTGCTCAGGG
1 CAGGCTCCTC-GCTTTGTGCTCAGGGTAAGTCCTTACCGCAAACTCCTCGGCTTTATGCTCAGGA
* * *
250389 TAAGTCTTTATTG
65 TAAGACTTTACTA
* * *
250402 TAGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGCAAACTCCTCTGCTTTATGCAT-AGG
1 CAGGCTCCTCG-CTTTGTGCTCAGGGTAAGTCCTTACCGCAAACTCCTCGGCTTTATGC-TCAGG
*
250466 ATAAGAGTTTACTA
64 ATAAGACTTTACTA
* * *
250480 CAGGCTCCTCTGCTTTTTGCACAGGGTAAGCCCTTA
1 CAGGCTCCTC-GCTTTGTGCTCAGGGTAAGTCCTTA
250516 TTGGGTTTAC
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
77 1 0.01
78 90 0.97
79 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (77 bp):
CAGGCTCCTCGCTTTGTGCTCAGGGTAAGTCCTTACCGCAAACTCCTCGGCTTTATGCTCAGGAT
AAGACTTTACTA
Found at i:251481 original size:20 final size:20
Alignment explanation
Indices: 251456--251494 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
251446 AGATTGCTAG
*
251456 GAGGGTACTGATACCCCCAA
1 GAGGGTACCGATACCCCCAA
251476 GAGGGTACCGATACCCCCA
1 GAGGGTACCGATACCCCCA
251495 TCTTATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGTACCGATACCCCCAA
Found at i:253172 original size:21 final size:21
Alignment explanation
Indices: 253147--253186 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
253137 AAGACTTTAT
253147 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
253168 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
253187 AAATAGCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:257012 original size:23 final size:24
Alignment explanation
Indices: 256981--257039 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
256971 TAGTGCAGGA
*
256981 GGTATCGATACCCCC-CTTGAAG-G
1 GGTACCGATACCCCCTCTTG-AGTG
*
257004 GGTACCGAT-CCCCCTTTTGAGTG
1 GGTACCGATACCCCCTCTTGAGTG
257027 GGTACCGATACCC
1 GGTACCGATACCC
257040 TCCACGGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 21 0.68
24 3 0.10
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (24 bp):
GGTACCGATACCCCCTCTTGAGTG
Found at i:257469 original size:20 final size:20
Alignment explanation
Indices: 257446--257488 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
257436 AAAAAAATTG
257446 TTTTGATTCTAAAT-TGTTGT
1 TTTTGATT-TAAATATGTTGT
*
257466 TTTTGATTTAATTATGTTGT
1 TTTTGATTTAAATATGTTGT
257486 TTT
1 TTT
257489 CATGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.65
Consensus pattern (20 bp):
TTTTGATTTAAATATGTTGT
Found at i:264613 original size:2 final size:2
Alignment explanation
Indices: 264606--264638 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
264596 TTATTATTAT
264606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
264639 TACTAAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:271198 original size:24 final size:24
Alignment explanation
Indices: 271166--271214 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
271156 AGTCTTCCTA
271166 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
271190 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
271214 A
1 A
271215 ATGCATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:272515 original size:30 final size:31
Alignment explanation
Indices: 272481--272539 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
272471 TTGATCCTTG
* * * *
272481 AACTTTTCAAAGT-TTATACTTTGGTCACCA
1 AACTTTACAAAATCTTATAATTTAGTCACCA
272511 AACTTTACAAAATCTTATAATTTAGTCAC
1 AACTTTACAAAATCTTATAATTTAGTCAC
272540 TCACTAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (31 bp):
AACTTTACAAAATCTTATAATTTAGTCACCA
Found at i:274124 original size:8 final size:8
Alignment explanation
Indices: 274108--274222 Score: 121
Period size: 8 Copynumber: 14.1 Consensus size: 8
274098 ACATCTCTCA
274108 TCTTTTTT
1 TCTTTTTT
274116 T-TATTTTT
1 TCT-TTTTT
274124 T-TTTTTT
1 TCTTTTTT
274131 T-TTTTTT
1 TCTTTTTT
274138 TCTTTTTTT
1 TC-TTTTTT
*
274147 TTTTTTTT
1 TCTTTTTT
*
274155 TTTTTTTT
1 TCTTTTTT
274163 TCTTTTTT
1 TCTTTTTT
274171 TCTTTTTCT
1 TCTTTTT-T
274180 TCTTTTTT
1 TCTTTTTT
274188 TC-TTTTT
1 TCTTTTTT
274195 TCTTCTTTT
1 TCTT-TTTT
*
274204 TCTTCTTCT
1 TCTT-TTTT
274213 TCTTGTTTT
1 TCTT-TTTT
274222 T
1 T
274223 TTAGCTCTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
7 21 0.22
8 40 0.42
9 35 0.36
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.87
Consensus pattern (8 bp):
TCTTTTTT
Found at i:274132 original size:17 final size:17
Alignment explanation
Indices: 274110--274224 Score: 126
Period size: 17 Copynumber: 6.7 Consensus size: 17
274100 ATCTCTCATC
*
274110 TTTTTTTTATTTT-TTT
1 TTTTTTTTTTTTTCTTT
274126 TTTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTCTTT
274143 TTTTTTTTTTTTT-TTT
1 TTTTTTTTTTTTTCTTT
*
274159 TTTTTCTTTTTTTCTTT
1 TTTTTTTTTTTTTCTTT
* *
274176 TTCTTCTTTTTTTCTTT
1 TTTTTTTTTTTTTCTTT
*
274193 TTTCTTCTTTTTCTTCTTCT
1 TTT-TT-TTTTTTTTCTT-T
* *
274213 TCTTGTTTTTTT
1 TTTTTTTTTTTT
274225 AGCTCTTATG
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
16 27 0.32
17 37 0.44
18 8 0.09
19 10 0.12
20 3 0.04
ACGTcount: A:0.01, C:0.10, G:0.01, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTCTTT
Found at i:274147 original size:33 final size:32
Alignment explanation
Indices: 274110--274207 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 32
274100 ATCTCTCATC
*
274110 TTTTTTTTATTTTTTTTTTTTTTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTT
274142 TTTTTTTTTTTTTTTTTTTTTTCTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTT-TTTTTTTCTT
* * * *
274175 TTTCTTCTTTTTTTCTTTTTTCTTCTTTTTCTT
1 TTT-TTTTTTTTTTTTTTTTTTTTTTTTTTCTT
274208 CTTCTTCTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
32 21 0.36
33 22 0.37
34 16 0.27
ACGTcount: A:0.01, C:0.09, G:0.00, T:0.90
Consensus pattern (32 bp):
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTT
Found at i:274204 original size:1 final size:1
Alignment explanation
Indices: 274110--274195 Score: 109
Period size: 1 Copynumber: 86.0 Consensus size: 1
274100 ATCTCTCATC
* * * *
274110 TTTTTTTTATTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
274175 TTTCTTCTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
274196 CTTCTTTTTC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.01, C:0.07, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:274213 original size:33 final size:31
Alignment explanation
Indices: 274123--274224 Score: 131
Period size: 33 Copynumber: 3.3 Consensus size: 31
274113 TTTTTATTTT
*
274123 TTTTTTTTTTTTTTTTCTTTTT-TTTT-TT-
1 TTTTTTTTTTTTTCTTCTTTTTCTTTTCTTC
274151 TTTTTTTTTTTTTCTT-TTTTTCTTTTTCTTC
1 TTTTTTTTTTTTTCTTCTTTTTC-TTTTCTTC
274182 TTTTTTTCTTTTTTCTTCTTTTTCTTCTTCTTC
1 TTTTTTT-TTTTTTCTTCTTTTTCTT-TTCTTC
*
274215 TTGTTTTTTT
1 TTTTTTTTTT
274225 AGCTCTTATG
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.08
28 15 0.23
29 4 0.06
30 2 0.03
31 7 0.11
32 14 0.22
33 18 0.28
ACGTcount: A:0.00, C:0.12, G:0.01, T:0.87
Consensus pattern (31 bp):
TTTTTTTTTTTTTCTTCTTTTTCTTTTCTTC
Found at i:276919 original size:23 final size:23
Alignment explanation
Indices: 276878--276934 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
276868 ATAATATAAA
*
276878 ATTTCTTACCA-ATATACTTGTC
1 ATTTATTACCATATATACTTGTC
276900 ATTTATTACCATATATACTTGTC
1 ATTTATTACCATATATACTTGTC
276923 ATTTATT-CCATA
1 ATTTATTACCATA
276935 AGCTCGTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTATTACCATATATACTTGTC
Found at i:280646 original size:2 final size:2
Alignment explanation
Indices: 280639--280677 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
280629 GTACACTAAG
280639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
280678 AGAGATTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:283832 original size:25 final size:25
Alignment explanation
Indices: 283804--283861 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
283794 CGATCCTTCG
*
283804 GGACAAATTTCTACGTGGTTATTCA
1 GGACAAATTTCTACGTGGTCATTCA
* * *
283829 GGACAAATTTCTGCGTGGTCCTTCG
1 GGACAAATTTCTACGTGGTCATTCA
283854 GGACAAAT
1 GGACAAAT
283862 CTATGTGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
GGACAAATTTCTACGTGGTCATTCA
Found at i:288634 original size:39 final size:39
Alignment explanation
Indices: 288588--288678 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
288578 AAGGACCAGT
* *
288588 AGTAAGGACTTACCATGAGCACAAAGCAGATGACCATGC
1 AGTAAGGACTTACCACGAGCACAAAGCAGAAGACCATGC
* * * *
288627 GGTAAGGACTTACCACGTGCACAAAGTAGAAGAGCATGC
1 AGTAAGGACTTACCACGAGCACAAAGCAGAAGACCATGC
*
288666 AGTAAGGTCTTAC
1 AGTAAGGACTTAC
288679 AAGTCCTAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (39 bp):
AGTAAGGACTTACCACGAGCACAAAGCAGAAGACCATGC
Found at i:290505 original size:22 final size:23
Alignment explanation
Indices: 290475--290521 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
290465 AAAATATATT
290475 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* * *
290498 TATT-ATATTTTTGATATTATAA
1 TATTAATATTTCTAATAATATAA
290520 TA
1 TA
290522 AAATAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:290528 original size:30 final size:33
Alignment explanation
Indices: 290469--290548 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
290459 ATATTTAAAA
* *
290469 TATATTTATTAATATTTCTAATAATATAAT-AT
1 TATATTTATTAATATTTATAATAAAATAATAAT
*
290501 TATATTT-TTGATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT-AAT
*
290533 TATATTCTAATAATAT
1 TATATT-TATTAATAT
290549 AAGATATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 13 0.34
31 5 0.13
32 15 0.39
33 1 0.03
34 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (33 bp):
TATATTTATTAATATTTATAATAAAATAATAAT
Found at i:290662 original size:19 final size:18
Alignment explanation
Indices: 290638--290706 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
290628 ATATTATTAA
290638 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
290657 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
290675 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
290697 ATT-TTAATAA
1 ATTATTAATAA
290707 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:290721 original size:23 final size:23
Alignment explanation
Indices: 290701--290745 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
290691 AATAATATTT
290701 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
290724 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
290746 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:290863 original size:17 final size:19
Alignment explanation
Indices: 290843--290878 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
290833 AAAATTATAA
290843 AAATAA-TA-TTTAATATT
1 AAATAATTATTTTAATATT
290860 AAATAATTATTTTAATATT
1 AAATAATTATTTTAATATT
290879 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATAATTATTTTAATATT
Found at i:291607 original size:161 final size:162
Alignment explanation
Indices: 291405--291728 Score: 641
Period size: 161 Copynumber: 2.0 Consensus size: 162
291395 TAAAGTTAAC
291405 TTTAGGTGCCTAAAGAATTTTTTCGTTAAAAAAATGTCTAACGTTTCTAACGTTACACTTTAGGT
1 TTTAGGTGCCTAAAGAATTTTTTCGTTAAAAAAATGTCTAACGTTTCTAACGTTACACTTTAGGT
291470 GCTTGAACCATTAATACAATTAAATTCGACCGTTAAGTGACACGTGTTAGGCATATAAAATTTC-
66 GCTTGAACCATTAATACAATTAAATTCGACCGTTAAGTGACACGTGTTAGGCATATAAAATTTCA
291534 AAAAAAATTAAATTTTATAGGCCTAACACTTA
131 AAAAAAATTAAATTTTATAGGCCTAACACTTA
291566 TTTAGGTGCCTAAAGAATTTTTTCGTTAAAAAAATGTCTAACGTTTCTAACGTTACACTTTAGGT
1 TTTAGGTGCCTAAAGAATTTTTTCGTTAAAAAAATGTCTAACGTTTCTAACGTTACACTTTAGGT
291631 GCTTGAACCATTAATACAATTAAATTCGACCGTTAAGTGACACGTGTTAGGCATATAAAATTTCA
66 GCTTGAACCATTAATACAATTAAATTCGACCGTTAAGTGACACGTGTTAGGCATATAAAATTTCA
291696 AAAAAAATTAAATTTTATAGGCCTAACACTTA
131 AAAAAAATTAAATTTTATAGGCCTAACACTTA
291728 T
1 T
291729 CACTTAACGA
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 129 0.80
162 33 0.20
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (162 bp):
TTTAGGTGCCTAAAGAATTTTTTCGTTAAAAAAATGTCTAACGTTTCTAACGTTACACTTTAGGT
GCTTGAACCATTAATACAATTAAATTCGACCGTTAAGTGACACGTGTTAGGCATATAAAATTTCA
AAAAAAATTAAATTTTATAGGCCTAACACTTA
Found at i:293314 original size:21 final size:22
Alignment explanation
Indices: 293275--293320 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
293265 ATATTTATTC
293275 AATATAGATTGATTTATTTTAA
1 AATATAGATTGATTTATTTTAA
*
293297 AATATGGATTGA-TTATTTTAA
1 AATATAGATTGATTTATTTTAA
293318 AAT
1 AAT
293321 TATTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
AATATAGATTGATTTATTTTAA
Found at i:296890 original size:29 final size:29
Alignment explanation
Indices: 296846--296920 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
296836 CGTGCATGGC
* *
296846 CGTGCATGGCGACCTATAAGGACGTCGGG
1 CGTGCATGGCGACCTATAAAGACGCCGGG
*
296875 CTTGCATGGCGACCTATAAAGACGCCGGG
1 CGTGCATGGCGACCTATAAAGACGCCGGG
296904 CGTGCATGGCGACCTAT
1 CGTGCATGGCGACCTAT
296921 GGTGGTTCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (29 bp):
CGTGCATGGCGACCTATAAAGACGCCGGG
Found at i:302400 original size:32 final size:32
Alignment explanation
Indices: 302359--302455 Score: 194
Period size: 32 Copynumber: 3.0 Consensus size: 32
302349 AGAAGATTCG
302359 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
1 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
302391 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
1 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
302423 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
1 AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
302455 A
1 A
302456 CTTCCAATTG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (32 bp):
AAGCCTTTGTGGAACCTCAAGTTTCCAAACTA
Found at i:304077 original size:18 final size:19
Alignment explanation
Indices: 304056--304096 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
304046 CTACAAGATA
304056 ACAAACTATTCTAGAACT-
1 ACAAACTATTCTAGAACTC
304074 ACAAACTATTCTAGAACTC
1 ACAAACTATTCTAGAACTC
304093 ACAA
1 ACAA
304097 CATATCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (19 bp):
ACAAACTATTCTAGAACTC
Found at i:306452 original size:15 final size:15
Alignment explanation
Indices: 306434--306467 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
306424 CTTGCACAGA
*
306434 TGGAGTATGTACTGG
1 TGGAGTATGAACTGG
306449 TGGAGTATGAACTGG
1 TGGAGTATGAACTGG
306464 TGGA
1 TGGA
306468 CCACACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.41, T:0.29
Consensus pattern (15 bp):
TGGAGTATGAACTGG
Found at i:306671 original size:15 final size:15
Alignment explanation
Indices: 306653--306704 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
306643 CACACATTGA
306653 TGGAGCAGATGCTGG
1 TGGAGCAGATGCTGG
* * * *
306668 TGGAGCACACGTTGA
1 TGGAGCAGATGCTGG
306683 TGGAGCAGATGCTGG
1 TGGAGCAGATGCTGG
306698 TGGAGCA
1 TGGAGCA
306705 TGTGTTGTCT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.19
Consensus pattern (15 bp):
TGGAGCAGATGCTGG
Found at i:306702 original size:30 final size:30
Alignment explanation
Indices: 306633--306704 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
306623 CATAGACAAA
*
306633 GCTGGTGGAACACACATTGATGGAGCAGAT
1 GCTGGTGGAGCACACATTGATGGAGCAGAT
*
306663 GCTGGTGGAGCACACGTTGATGGAGCAGAT
1 GCTGGTGGAGCACACATTGATGGAGCAGAT
306693 GCTGGTGGAGCA
1 GCTGGTGGAGCA
306705 TGTGTTGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.39, T:0.19
Consensus pattern (30 bp):
GCTGGTGGAGCACACATTGATGGAGCAGAT
Found at i:310294 original size:28 final size:27
Alignment explanation
Indices: 310241--310294 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
310231 TAAATATCTT
*
310241 GAAGAGGAAAAAAAAAGTGAAGAATGA
1 GAAGAGGAAAAAAAAAGGGAAGAATGA
*
310268 GAAGTAGGAAAATGAAAAGGGAA-AATG
1 GAAG-AGGAAAA-AAAAAGGGAAGAATG
310295 TCTTCATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 11 0.48
29 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.09
Consensus pattern (27 bp):
GAAGAGGAAAAAAAAAGGGAAGAATGA
Found at i:320284 original size:2 final size:2
Alignment explanation
Indices: 320277--320380 Score: 140
Period size: 2 Copynumber: 51.5 Consensus size: 2
320267 AATATTTTTA
320277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
320319 AT AT AT AT AT AT AT AT AT AT AT AT AT CACT AT -T AT AT TT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT
* *
320361 AGT AT GT AC AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT A
320381 CCTTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.02
2 85 0.93
3 3 0.03
4 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321660 original size:9 final size:9
Alignment explanation
Indices: 321643--321672 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
321633 TTTCGTGTTT
*
321643 ATTTTCATC
1 ATTTGCATC
321652 ATTTGCATC
1 ATTTGCATC
321661 ATTTGCATC
1 ATTTGCATC
321670 ATT
1 ATT
321673 CAAAAGAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (9 bp):
ATTTGCATC
Found at i:324584 original size:91 final size:92
Alignment explanation
Indices: 324479--324655 Score: 257
Period size: 92 Copynumber: 1.9 Consensus size: 92
324469 TAATATTATA
** * * *
324479 TATATACAATAAAGCTTG-GTTGTCCCTCTAGAGTAATTGGTTAAACGCCCCGGCCTTATGGATA
1 TATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACCTTATGGATA
* *
324543 ATATTCGGCTAACCTGATAAAGGTGAT
66 AGATTCAGCTAACCTGATAAAGGTGAT
** *
324570 TATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAATTCCCCGACTTTATGGATA
1 TATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACCTTATGGATA
324635 AGATTCAGCTAACCTGATAAA
66 AGATTCAGCTAACCTGATAAA
324656 AGTGTTTACG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 18 0.24
92 57 0.76
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (92 bp):
TATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACCTTATGGATA
AGATTCAGCTAACCTGATAAAGGTGAT
Found at i:326223 original size:110 final size:110
Alignment explanation
Indices: 326025--326282 Score: 294
Period size: 110 Copynumber: 2.4 Consensus size: 110
326015 GCTTCCCAAT
*
326025 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGTACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGTACTCAAGACAACACAAGCTCAACTTCA
* * *
326090 CAATGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * * *
326135 TTCAGAGTCAATTTCAACTTTACAACGAAGGATATTAG-ACTCGAGATAGCACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATT-GTACTCAAGACAACACAAGCTCAACTTC
* * * * *
326199 ACAGCGAAGGGGCGGCTGGCTGTCAATAAACAA-TTTCCCAG-TTC-
65 ACAACGAAGGGGCGACTGACTGTCAACAAACAACTTT-TCAGTTTCA
* ** *
326243 --CAGAACCAATTTCAACTTCACGGCGAAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGTACTC
326283 GGAACAACAC
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
105 1 0.01
106 33 0.26
109 6 0.05
110 85 0.67
111 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGTACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:326909 original size:35 final size:35
Alignment explanation
Indices: 326803--326931 Score: 163
Period size: 37 Copynumber: 3.6 Consensus size: 35
326793 ACAAGGGGTC
*
326803 GTCTCTCTTAAGACTAATTTACTCA--AAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CT-ATTAAACAAA-TTTT
* *
326840 GTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTT
1 GTCTCTCTTGAGACAATTTCTATTA-AAC-AAATTTT
326877 GTCTCTCTTGAGACAATTTCTATTAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTATTAAACAAATTTT
326912 GTCTCTCTTGAGACAATTTC
1 GTCTCTCTTGAGACAATTTC
326932 CCTTGAAACA
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
35 29 0.35
36 8 0.10
37 43 0.52
38 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.42
Consensus pattern (35 bp):
GTCTCTCTTGAGACAATTTCTATTAAACAAATTTT
Found at i:326980 original size:65 final size:65
Alignment explanation
Indices: 326899--327261 Score: 311
Period size: 65 Copynumber: 5.4 Consensus size: 65
326889 ACAATTTCTA
*
326899 TTAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
* * **
326964 TTAAACAAATTTTGTCTCTCTTGAGACAGTTT--CTTTAGAACTAAAT-TTTGTCTCTTGAGACA
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA-AACAAAATCTTTGAAT-TT--G---
*
327026 TTTTCTCG
59 TTTTC-CT
* *
327034 TAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
* * * * ***
327099 TTAAACAAATTTTGTCTCTCTTGAGACAGTTT-CTTTTAGAACTAAATTTTATCTCTCTTGAGAC
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA-AACAAAATCTT-TGAAT-TT--G--
*
327163 ATTTTCTCG
59 -TTTTC-CT
* * * ** * *
327172 TAAAACAAATTTTGTCTCTATTGAGACAGTTTCTCTTGAAACAAAATCTCCGAATCTGGTTTCCT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
* * *
327237 TGAAACAAATTTCGTCTCCCTTGAG
1 TTAAACAAATTTTGTCTCTCTTGAG
327262 GCAATTTCTT
Statistics
Matches: 235, Mismatches: 42, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
63 9 0.04
64 13 0.06
65 94 0.40
66 12 0.05
67 1 0.00
69 8 0.03
70 32 0.14
71 9 0.04
72 15 0.06
73 39 0.17
74 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (65 bp):
TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
Found at i:327206 original size:36 final size:36
Alignment explanation
Indices: 326827--327216 Score: 320
Period size: 36 Copynumber: 11.2 Consensus size: 36
326817 TAATTTACTC
*
326827 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
326864 AGAACTAAATTTTGTCTCTCTTGAGACAATTTCTATT
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
326901 -AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * **
326936 GAAACAAA------ATCT-TTGA-ATTTGTTT-TCCTT
1 AAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCT-CTT
*
326965 TAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-TT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
327000 AGAACTAAATTTTG--TCTCTTGAGACATTTTCTCGT
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
327035 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
327071 GAAACAAA------ATCT-TTGA-ATCTGTTT-TCCTT
1 AAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCT-CTT
* *
327100 TAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * * *
327136 AGAACTAAATTTTATCTCTCTTGAGACATTTTCTCGT
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
327173 AAAACAAATTTTGTCTCTATTGAGACAGTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
327209 GAAACAAA
1 AAAACAAA
327217 ATCTCCGAAT
Statistics
Matches: 281, Mismatches: 43, Indels: 59
0.73 0.11 0.15
Matches are distributed among these distances:
28 2 0.01
29 36 0.13
30 6 0.02
34 25 0.09
35 45 0.16
36 99 0.35
37 65 0.23
38 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:327317 original size:102 final size:102
Alignment explanation
Indices: 327177--327376 Score: 276
Period size: 102 Copynumber: 2.0 Consensus size: 102
327167 TCTCGTAAAA
* * *
327177 CAAATTTTGTCTCTATTGAGACAGTTTCTCTTGAAACAAAATCTCCGAATCTGGTTTCC-TTGAA
1 CAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAACCTCCGAATATGGTTTCCATT-AA
* * * *
327241 ACAAATTTCGTCTCCCTTGAGGCAATTTCTTTTGGAAC
65 ACAAATTTCGCCTCACTCGAGACAATTTCTTTTGGAAC
* * ** *
327279 CAAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAAAACCTTTGAATATGTTTTCCATTAAA
1 CAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAACCTCCGAATATGGTTTCCATTAAA
327344 CAAATTTCGCCTCACTCGAGACAATTTCTTTTG
66 CAAATTTCGCCTCACTCGAGACAATTTCTTTTG
327377 AGACAGTTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 83 0.98
103 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (102 bp):
CAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAACCTCCGAATATGGTTTCCATTAAA
CAAATTTCGCCTCACTCGAGACAATTTCTTTTGGAAC
Found at i:327318 original size:138 final size:138
Alignment explanation
Indices: 326828--327306 Score: 759
Period size: 138 Copynumber: 3.5 Consensus size: 138
326818 AATTTACTCA
*
326828 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
* * * *
326893 TTTCT-ATTAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATTTG
65 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG
326957 TTTTCCTTT
130 TTTTCCTTT
326966 AAACAAATTTTGTCTCTCTTGAGACAGTTTC-TTTAGAACTAAATTTTG--TCTCTTGAGACATT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATT
327028 TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
66 TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
327093 TTTCCTTT
131 TTTCCTTT
*
327101 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTATCTCTCTTGAGACATT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATT
* * ** *
327166 TTCTCGTAAAACAAATTTTGTCTCTATTGAGACAGTTTCTCTTGAAACAAAATCTCCGAATCTGG
66 TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
*
327231 TTTCCTTG
131 TTTCCTTT
* * * * * *
327239 AAACAAATTTCGTCTCCCTTGAGGCAATTTCTTTTGGAACCAAATTTTGTCTCTCTTGAGACATT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATT
327304 TTC
66 TTC
327307 CCTTGAAACA
Statistics
Matches: 318, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
134 17 0.05
135 95 0.30
136 33 0.10
137 24 0.08
138 149 0.47
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (138 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATT
TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
TTTCCTTT
Found at i:329186 original size:2 final size:2
Alignment explanation
Indices: 329179--329203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
329169 TATTTTAATT
329179 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
329204 CACTATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:329456 original size:29 final size:27
Alignment explanation
Indices: 329422--329480 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
329412 TCATTTGTTA
329422 TTTTATGTT-TTTTTTATTCCTATTTCTAT
1 TTTTATGTTATTTTTTA-TCCT-TTT-TAT
*
329451 TTTTATTTTATTTTTTATCCTTTTTAT
1 TTTTATGTTATTTTTTATCCTTTTTAT
329478 TTT
1 TTT
329481 CTTTCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.21
28 3 0.11
29 12 0.43
30 7 0.25
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTATGTTATTTTTTATCCTTTTTAT
Found at i:329457 original size:12 final size:11
Alignment explanation
Indices: 329409--329465 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
329399 AATTGTTACC
*
329409 ATTTCATTTGTT
1 ATTTTATTT-TT
329421 ATTTTATGTTTT
1 ATTTTAT-TTTT
**
329433 -TTTTATTCCT
1 ATTTTATTTTT
329443 ATTTCTATTTTT
1 ATTT-TATTTTT
329455 ATTTTATTTTT
1 ATTTTATTTTT
329466 TATCCTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.05
11 16 0.43
12 17 0.46
13 2 0.05
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:330129 original size:60 final size:58
Alignment explanation
Indices: 330004--330130 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 58
329994 TTTTATACTT
* * *
330004 AAACTATGACTAGCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCC
1 AAACTATGACTA-CATTATAAATTAGTCCCCAAACTTTTGAACATTCCAATTTCATCCC
** * *
330063 CCACTATGACCT-CATTATAAATTGGTCCCCAAAATTTTTGGAACATTCCAATTTCATCCC
1 AAACTATGA-CTACATTATAAATTAGTCCCC-AAACTTTT-GAACATTCCAATTTCATCCC
330123 AAACTATG
1 AAACTATG
330131 TGTATCTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
58 15 0.27
59 14 0.25
60 27 0.48
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (58 bp):
AAACTATGACTACATTATAAATTAGTCCCCAAACTTTTGAACATTCCAATTTCATCCC
Found at i:330385 original size:60 final size:59
Alignment explanation
Indices: 330249--330437 Score: 168
Period size: 60 Copynumber: 3.1 Consensus size: 59
330239 TATTTGGATA
* *
330249 AATTTGGGGATAAAATTGGAAAATTCAAAAGTTTGGGGACCAATTTAGAAAGAGGGTCAT
1 AATTT-GGGATAAAATTGGAAAATTCAAAAGTTTGAGGACCAATTTAGAAAGAGAGTCAT
* ** * *
330309 AATTTAGGGATGAAATTGGAATGTTCAAAAGTTTGAGGACTAATTTAGAATA-AGAGTTAT
1 AATTT-GGGATAAAATTGGAAAATTCAAAAGTTTGAGGACCAATTTAGAA-AGAGAGTCAT
* * * * * * *
330369 AGTTTGTGGATAAAATT-AAAATATTAAAAAATTT-AGGGACCGATTTAAAAATGAGAATCAT
1 AATTTG-GGATAAAATTGGAAA-ATTCAAAAGTTTGA-GGACCAATTTAGAAA-GAGAGTCAT
330430 AATTTGGG
1 AATTTGGG
330438 GACAGATGCA
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
59 5 0.05
60 85 0.83
61 12 0.12
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.31
Consensus pattern (59 bp):
AATTTGGGATAAAATTGGAAAATTCAAAAGTTTGAGGACCAATTTAGAAAGAGAGTCAT
Found at i:333887 original size:14 final size:15
Alignment explanation
Indices: 333868--333902 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
333858 TTATGTTCGG
333868 ATTATAAATATTA-T
1 ATTATAAATATTACT
*
333882 ATTATAATTATTACT
1 ATTATAAATATTACT
333897 ATTATA
1 ATTATA
333903 TTTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATAAATATTACT
Found at i:333899 original size:6 final size:5
Alignment explanation
Indices: 333875--333979 Score: 52
Period size: 5 Copynumber: 19.8 Consensus size: 5
333865 CGGATTATAA
* *
333875 ATATT ATATT ATAAT -TATT ACTATT ATATT TTATT ATTATT ATTATT
1 ATATT ATATT ATATT ATATT A-TATT ATATT ATATT A-TATT A-TATT
* * * * * *
333922 GTAATA ATTATT AAATA AAATT ATAAT A-ATT ATTATT AGTATT ATATT
1 AT-ATT A-TATT ATATT ATATT ATATT ATATT A-TATT A-TATT ATATT
333970 AATATT ATAT
1 -ATATT ATAT
333980 ATGTTTTTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
4 6 0.08
5 36 0.47
6 34 0.44
7 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (5 bp):
ATATT
Found at i:333911 original size:3 final size:3
Alignment explanation
Indices: 333876--333977 Score: 59
Period size: 3 Copynumber: 35.0 Consensus size: 3
333866 GGATTATAAA
* *
333876 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
333921 TGT AAT AAT TAT TAAA TAA AAT TAT AAT AAT TAT TAT TAG TAT TA-
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
333966 TAT TAA TAT TAT
1 TAT TAT TAT TAT
333978 ATATGTTTTT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
2 8 0.11
3 66 0.87
4 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:336172 original size:30 final size:30
Alignment explanation
Indices: 336105--336221 Score: 191
Period size: 30 Copynumber: 3.9 Consensus size: 30
336095 TATGGATAGT
336105 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
336135 TTTACCGAGGATCTTTATGACCTCTGGACAG
1 -TTACCGAGGATCTTTATGACCTCTGGACAG
336166 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
* **
336196 TTACCG-GGGTCTTGGTGACCTCTGGA
1 TTACCGAGGATCTTTATGACCTCTGGA
336222 TAGGTCCTTC
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
29 17 0.20
30 36 0.43
31 30 0.36
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGACAG
Found at i:336173 original size:61 final size:59
Alignment explanation
Indices: 336105--336221 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 59
336095 TATGGATAGT
*
336105 TTACCGAGGATCTTTATGACCTCTGGACAGTTTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG-TTACCG-GGATCTTGATGACCTCTGGACAG
* *
336166 TTACCGAGGATCTTTATGACCTCTGGACAGTTACCGGGGTCTTGGTGACCTCTGGA
1 TTACCGAGGATCTTTATGACCTCTGGACAGTTACCGGGATCTTGATGACCTCTGGA
336222 TAGGTCCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
59 17 0.32
60 6 0.11
61 30 0.57
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (59 bp):
TTACCGAGGATCTTTATGACCTCTGGACAGTTACCGGGATCTTGATGACCTCTGGACAG
Found at i:339435 original size:21 final size:21
Alignment explanation
Indices: 339402--339442 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
339392 TTCTGGGCAA
* *
339402 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
339423 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
339443 CGAACAACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:339513 original size:23 final size:22
Alignment explanation
Indices: 339469--339513 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
339459 AATGCCAGAG
*
339469 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
339491 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
339514 AAATGCGAAT
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:340760 original size:30 final size:30
Alignment explanation
Indices: 340722--340842 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
340712 TCGAGACATA
340722 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
340753 T-GACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
340783 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
**
340813 TGGACAGTTACCG-GG-TCTTGGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
340841 TG
1 TG
340843 ATAGGTCCTT
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
28 13 0.15
29 2 0.02
30 66 0.76
31 6 0.07
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:343124 original size:21 final size:23
Alignment explanation
Indices: 343098--343144 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
343088 CACACGAATA
*
343098 TTTTACCATT-TTCTT-TTATTT
1 TTTTACCATTATTATTATTATTT
343119 TTTTACCATTATTATTATTATTT
1 TTTTACCATTATTATTATTATTT
343142 TTT
1 TTT
343145 CAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.43
22 4 0.17
23 9 0.39
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTACCATTATTATTATTATTT
Found at i:343170 original size:20 final size:20
Alignment explanation
Indices: 343114--343164 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
343104 CATTTTCTTT
* * * *
343114 TATTTTTTTACCATTATTAT
1 TATTATTTTATCAATATTAA
*
343134 TATTATTTTTTCAATATTAA
1 TATTATTTTATCAATATTAA
343154 TATTATTTTAT
1 TATTATTTTAT
343165 GTATATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTTTATCAATATTAA
Found at i:343370 original size:12 final size:12
Alignment explanation
Indices: 343353--343385 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
343343 GTCTTCGCCG
343353 TGTTTTTATTCT
1 TGTTTTTATTCT
*
343365 TG-TTTTGTTCT
1 TGTTTTTATTCT
343376 TGTTTTTATT
1 TGTTTTTATT
343386 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (12 bp):
TGTTTTTATTCT
Found at i:353925 original size:13 final size:13
Alignment explanation
Indices: 353909--353954 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
353899 GGGAAAAAAG
353909 AACAAAAAAACAA
1 AACAAAAAAACAA
*
353922 AACAAAAGAACAA
1 AACAAAAAAACAA
353935 AA-AAAAATAA-AA
1 AACAAAAA-AACAA
353947 AACAAAAA
1 AACAAAAA
353955 GAGAAAAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (13 bp):
AACAAAAAAACAA
Found at i:353940 original size:17 final size:17
Alignment explanation
Indices: 353914--353954 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
353904 AAAAGAACAA
*
353914 AAAAACAAAACAAAAGAAC
1 AAAAA-AAAATAAAA-AAC
353933 AAAAAAAAATAAAAAAC
1 AAAAAAAAATAAAAAAC
353950 AAAAA
1 AAAAA
353955 GAGAAAAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAC
Found at i:353961 original size:14 final size:13
Alignment explanation
Indices: 353904--353963 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
353894 AAGTTGGGAA
353904 AAAAGAACAAAAA-
1 AAAA-AACAAAAAG
353917 AACAAAAC-AAAAG
1 AA-AAAACAAAAAG
*
353930 AACAAAA-AAAAAT
1 AA-AAAACAAAAAG
353943 AAAAAACAAAAAG
1 AAAAAACAAAAAG
353956 AGAAAAAC
1 A-AAAAAC
353964 GTTTAGGGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 8 0.20
13 24 0.60
14 8 0.20
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAAAG
Found at i:354034 original size:8 final size:9
Alignment explanation
Indices: 354000--354033 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
353990 CCCTAAATTG
354000 AAAAA-AGA
1 AAAAAGAGA
354008 AAAAAGAGA
1 AAAAAGAGA
354017 AAAAAGAGA
1 AAAAAGAGA
354026 ACAAAAGA
1 A-AAAAGA
354034 AGAGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.21
9 13 0.54
10 6 0.25
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:354848 original size:43 final size:43
Alignment explanation
Indices: 354800--355057 Score: 113
Period size: 43 Copynumber: 5.4 Consensus size: 43
354790 CAGAGTCAAT
354800 TTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAG
* * ** * * *
354843 TTCAACTTCA-AGACGAAGGGACCGCTGGTTGTCAATAAACAATCCCAGAGTCAAT
1 TTCAACTTCACA-ACGAA-GGA-TGTTGG-ACTC--CAGACAA---C---G-CAAG
* *
354898 TTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAG
* * * ** * * *
354941 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCAGAGCCAAT
1 TTCAACTTCACAACGAA-GGA-TGTTGG-ACTC--CAGACAA---C---G-CAAG
*
354996 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAG
*
355039 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
355058 GACCGCTGGT
Statistics
Matches: 153, Mismatches: 36, Indels: 52
0.63 0.15 0.22
Matches are distributed among these distances:
42 1 0.01
43 55 0.36
44 7 0.05
45 7 0.05
46 4 0.03
47 2 0.01
48 10 0.07
50 10 0.07
51 2 0.01
52 4 0.03
53 6 0.04
54 7 0.05
55 37 0.24
56 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAG
Found at i:355523 original size:98 final size:98
Alignment explanation
Indices: 354790--355515 Score: 1317
Period size: 98 Copynumber: 7.4 Consensus size: 98
354780 AGGTTTTACC
* * *
354790 CAGAGTCAATTTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCAAG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
354855 ACGAAGGGACCGCTGGTTGTCAATAAACAATCC
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* *
354888 CAGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
354953 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
354986 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
355051 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
355084 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
355149 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* *
355182 CAGGGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
355247 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
355280 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
355345 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* *
355378 CAGGGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
355443 ACTAAGGGACCGCTGGTTGTCAGTAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
355476 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
355516 GAAACAACAC
Statistics
Matches: 607, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 607 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (98 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:357164 original size:2 final size:2
Alignment explanation
Indices: 357157--357192 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
357147 CTTTATTTTC
357157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357193 GTATTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:358988 original size:17 final size:17
Alignment explanation
Indices: 358945--358996 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
358935 TGTACAGTAG
*
358945 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
358962 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
358977 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
358994 AAA
1 AAA
358997 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:359676 original size:13 final size:13
Alignment explanation
Indices: 359637--359680 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
359627 CAAATTTTAT
359637 TTTATTTTTATATA
1 TTTA-TTTTATATA
* *
359651 TTTATATAATATA
1 TTTATTTTATATA
*
359664 TTTATTTTCTATA
1 TTTATTTTATATA
359677 TTTA
1 TTTA
359681 CATTTTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATTTTATATA
Found at i:360686 original size:2 final size:2
Alignment explanation
Indices: 360675--360703 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
360665 TTGAAATTAA
360675 AT AT -T 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
360704 TAAAATGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:361565 original size:60 final size:60
Alignment explanation
Indices: 361436--361566 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 60
361426 TTATGGCCCT
* * * * *
361436 CATTCTAAATTGGTCATTAAACTTTTAACCATTCCAATTTCATCTCCAAATTATATCTCT
1 CATTCTAAATTGATCATCAAACTTTTAACCATTCCAACTTCATCTCCAAACTATATCTCA
* * * *
361496 CATTTTAAATTGAT-ACTCAAACTTTTGAGCATTCTAACTTCAT-TCTCAAACTATGATC-CA
1 CATTCTAAATTGATCA-TCAAACTTTTAACCATTCCAACTTCATCTC-CAAACTAT-ATCTCA
361556 CATTCTAAATT
1 CATTCTAAATT
361567 AGTCCCTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 3 0.05
60 52 0.90
61 3 0.05
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (60 bp):
CATTCTAAATTGATCATCAAACTTTTAACCATTCCAACTTCATCTCCAAACTATATCTCA
Found at i:366029 original size:18 final size:18
Alignment explanation
Indices: 366006--366058 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
365996 ACTGAATATT
366006 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
366024 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
366042 TGTCCCGAAGAACCACT
1 TGTCCCGAAGGACCACT
366059 GATAATTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:368238 original size:18 final size:18
Alignment explanation
Indices: 368215--368273 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
368205 AATATTTATT
368215 CCGAAGGACCACTATGTC
1 CCGAAGGACCACTATGTC
368233 CCGAAGGACCACTATGTC
1 CCGAAGGACCACTATGTC
* * *
368251 ACAAAAGACCACTATGTC
1 CCGAAGGACCACTATGTC
368269 CCGAA
1 CCGAA
368274 AAACCACTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (18 bp):
CCGAAGGACCACTATGTC
Found at i:368279 original size:18 final size:18
Alignment explanation
Indices: 368222--368281 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
368212 ATTCCGAAGG
**
368222 ACCACTATGTCCCGAAGG
1 ACCACTATGTCCCGAAAA
*
368240 ACCACTATGTCAC-AAAA
1 ACCACTATGTCCCGAAAA
368257 GACCACTATGTCCCGAAAA
1 -ACCACTATGTCCCGAAAA
368276 ACCACT
1 ACCACT
368282 GATAATTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.83
19 4 0.11
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (18 bp):
ACCACTATGTCCCGAAAA
Found at i:369020 original size:64 final size:66
Alignment explanation
Indices: 368907--369054 Score: 162
Period size: 64 Copynumber: 2.3 Consensus size: 66
368897 ATACCTTGTC
*
368907 TAGGGTATAGATACCCTAATGACATTCTGAAATTTTCATGTTAAGA-GGGGTATCGATAC-CCTT
1 TAGGGTATAGATACCCTAATGACATTCTGAAATTTTCA-GTTAAAAGGGGGTATCGATACACCTT
368970 -A
65 CA
* ** *
368971 TAGGGTATCAG-TACCCTACTGACATTCTGTATTTTTTC-GTTCAAAAGGGGGTATCGATACACT
1 TAGGGTAT-AGATACCCTAATGACATTCTG-AAATTTTCAGTT-AAAAGGGGGTATCGATACACC
369034 TTCA
63 TTCA
**
369038 TAGGGTACCGATACCCT
1 TAGGGTATAGATACCCT
369055 TTGCCCAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
63 3 0.04
64 28 0.40
65 21 0.30
66 4 0.06
67 14 0.20
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (66 bp):
TAGGGTATAGATACCCTAATGACATTCTGAAATTTTCAGTTAAAAGGGGGTATCGATACACCTTC
A
Found at i:371030 original size:65 final size:64
Alignment explanation
Indices: 370960--371117 Score: 149
Period size: 65 Copynumber: 2.4 Consensus size: 64
370950 CGAGGTATAT
* **
370960 ATACCCTGTCTAGGGTATATATACCCTA-ATGACATTCT-AAAATTTTCATGTTAAGGGGGGTAT
1 ATACCCT-TCTAGGGTATAGATACCCTACA-GACATTCTGAAAATTTTCAT-TTAAAAGGGGTAT
371023 CG
63 CG
* * * * * *
371025 ATACCCCCTATAGGGTATCGGTACCCTACAGACATTCTGTAATTTTTCATTTAAAAGGGGTATCG
1 ATA-CCCTTCTAGGGTATAGATACCCTACAGACATTCTGAAAATTTTCATTTAAAAGGGGTATCG
**
371090 ATACACCTTCATAGGGTACCGATACCCT
1 ATAC-CCTTC-TAGGGTATAGATACCCT
371118 CTGCCCAGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
64 1 0.01
65 46 0.61
66 28 0.37
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
ATACCCTTCTAGGGTATAGATACCCTACAGACATTCTGAAAATTTTCATTTAAAAGGGGTATCG
Found at i:371242 original size:11 final size:11
Alignment explanation
Indices: 371221--371253 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
371211 TCATACTTGA
371221 ACTCA-TCAAT
1 ACTCATTCAAT
371231 ACTCATTCAAT
1 ACTCATTCAAT
371242 ACTCATTCAAT
1 ACTCATTCAAT
371253 A
1 A
371254 TATCTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (11 bp):
ACTCATTCAAT
Found at i:381254 original size:20 final size:21
Alignment explanation
Indices: 381229--381268 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
381219 TCTACATATT
381229 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
381249 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
381269 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:386867 original size:16 final size:16
Alignment explanation
Indices: 386846--386881 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
386836 TATTAGTGAT
386846 GATTTATTATAATGAC
1 GATTTATTATAATGAC
386862 GATTTATTATAATGAC
1 GATTTATTATAATGAC
386878 GATT
1 GATT
386882 CAATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (16 bp):
GATTTATTATAATGAC
Found at i:389669 original size:104 final size:104
Alignment explanation
Indices: 389472--389698 Score: 334
Period size: 104 Copynumber: 2.2 Consensus size: 104
389462 TACTCGTCAT
* * *
389472 ACATATAATATCA-TGCTTTGGGGATTCTTTTTGTCGTTGAGACTTGACACTGCTAATCAGTTTT
1 ACATATAATA-CATTG-ATTGGGGATTCTTTTTGTCGATGAGACTCGACACTGCTAATCAGTTTT
**
389536 ATATAGATATGAAGACTAGGGGCATTGCACCTGATGTTGTG
64 ATATAGATATGAAGACTAGGGGCATTGCACCTGATACTGTG
*
389577 ACATATAATACATTGATTGGGGATTTTTTTTGTCGATGAGACTCGACACTGCTAATC-GATTTTA
1 ACATATAATACATTGATTGGGGATTCTTTTTGTCGATGAGACTCGACACTGCTAATCAG-TTTTA
389641 TGA-AGATATGAAGACTAGGGGCATTGCACCTGATACTGTG
65 T-ATAGATATGAAGACTAGGGGCATTGCACCTGATACTGTG
*
389681 ACGTATAATACATTGATT
1 ACATATAATACATTGATT
389699 AATGGATATA
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
103 1 0.01
104 98 0.88
105 13 0.12
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (104 bp):
ACATATAATACATTGATTGGGGATTCTTTTTGTCGATGAGACTCGACACTGCTAATCAGTTTTAT
ATAGATATGAAGACTAGGGGCATTGCACCTGATACTGTG
Found at i:393203 original size:3 final size:3
Alignment explanation
Indices: 393197--393238 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
393187 TGATGACAAC
*
393197 GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
393239 AAGAGTGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:393527 original size:21 final size:22
Alignment explanation
Indices: 393488--393536 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
393478 TTCTTGTTTA
393488 TTAA-TTATTTACCTTTTATGAC
1 TTAATTTATTTA-CTTTTATGAC
*
393510 TTAATTTATTTA-TTTTATTAC
1 TTAATTTATTTACTTTTATGAC
393531 TTAATT
1 TTAATT
393537 GAAGCGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 14 0.56
22 4 0.16
23 7 0.28
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAATTTATTTACTTTTATGAC
Found at i:393596 original size:38 final size:38
Alignment explanation
Indices: 393515--393597 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
393505 ATGACTTAAT
* * *
393515 TTATTTATTTTATTACTTAATTGAAGCGAATGATTTTA
1 TTATTTATTTTATCACTTAATTGAAGCGAATAAGTTTA
* *
393553 GTATTT-TGTTTATCACTTAATTGAAGTGAATAAGTTTA
1 TTATTTAT-TTTATCACTTAATTGAAGCGAATAAGTTTA
393591 TTATTTA
1 TTATTTA
393598 CTGAATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (38 bp):
TTATTTATTTTATCACTTAATTGAAGCGAATAAGTTTA
Found at i:395820 original size:17 final size:17
Alignment explanation
Indices: 395800--395838 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
395790 TCCCATTATG
395800 CCATTAAATTCATTACA
1 CCATTAAATTCATTACA
395817 CCATTAAATTCATTACA
1 CCATTAAATTCATTACA
395834 -CATTA
1 CCATTA
395839 CTATAGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (17 bp):
CCATTAAATTCATTACA
Found at i:398614 original size:51 final size:51
Alignment explanation
Indices: 398538--398642 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
398528 ATATGTGGAA
* *
398538 TTCCGTTTCAAGTAGTGCTAAATGCAAATCGACAATAACTCATCAAATGGT
1 TTCCGTTTCAAGTAGTGATAAATGCAAATCAACAATAACTCATCAAATGGT
*
398589 TTCCGTTTCAAGTAGTGATAAATGCAAATTAACAATAACTCATCAAATGGT
1 TTCCGTTTCAAGTAGTGATAAATGCAAATCAACAATAACTCATCAAATGGT
398640 TTC
1 TTC
398643 ATAGTTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (51 bp):
TTCCGTTTCAAGTAGTGATAAATGCAAATCAACAATAACTCATCAAATGGT
Found at i:400303 original size:29 final size:29
Alignment explanation
Indices: 400268--400329 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
400258 TTTATGAGAT
400268 CAAATCAGTTAATAAAGTATTTTAAAATG
1 CAAATCAGTTAATAAAGTATTTTAAAATG
400297 CAAATCAGTTAATAAAGTATTTTAAAATG
1 CAAATCAGTTAATAAAGTATTTTAAAATG
400326 -AAAT
1 CAAAT
400330 ATTAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (29 bp):
CAAATCAGTTAATAAAGTATTTTAAAATG
Found at i:400340 original size:29 final size:29
Alignment explanation
Indices: 400269--400341 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
400259 TTATGAGATC
* *
400269 AAATCAGTTAATAAAGTATTTTAAAATGC
1 AAATCAATTAATAAAGTATTTTAAAATGA
*
400298 AAATCAGTTAATAAAGTATTTTAAAATGA
1 AAATCAATTAATAAAGTATTTTAAAATGA
*
400327 AATATTAATT-ATAAA
1 AA-ATCAATTAATAAA
400342 ACTTAAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 35 0.88
30 5 0.12
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (29 bp):
AAATCAATTAATAAAGTATTTTAAAATGA
Found at i:400738 original size:3 final size:3
Alignment explanation
Indices: 400730--400820 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
400720 TAATAAACAA
400730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
400778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
400821 TAACTCACTT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:402962 original size:2 final size:2
Alignment explanation
Indices: 402957--402999 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
402947 TATATATATA
402957 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
402999 T
1 T
403000 ATTTATCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:405867 original size:23 final size:23
Alignment explanation
Indices: 405841--405964 Score: 108
Period size: 23 Copynumber: 5.4 Consensus size: 23
405831 GTTCTACGCA
405841 GTCCTTCGGGACAATTCTATGTG
1 GTCCTTCGGGACAATTCTATGTG
* * *
405864 GTCCTTTGGGACAATTCTACGCG
1 GTCCTTCGGGACAATTCTATGTG
* * * * * *
405887 GTCTTTTGGAAAAAATGTATGTG
1 GTCCTTCGGGACAATTCTATGTG
*
405910 GTCCTTCGGGACAATTCTACGTG
1 GTCCTTCGGGACAATTCTATGTG
* *
405933 G-CATTTCGGGACAAATCTATGTG
1 GTC-CTTCGGGACAATTCTATGTG
405956 G-CACTTCGG
1 GTC-CTTCGG
405965 TGCATATTCT
Statistics
Matches: 79, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
22 1 0.01
23 78 0.99
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
GTCCTTCGGGACAATTCTATGTG
Found at i:405954 original size:46 final size:46
Alignment explanation
Indices: 405845--405988 Score: 159
Period size: 46 Copynumber: 3.1 Consensus size: 46
405835 TACGCAGTCC
* * *
405845 TTCGGGACAATTCTATGTGGTCCTTTGGGACAATTCTACGCGGTC-T
1 TTCGGGACAAATCTATGTGGTCCTTCGGGACAATTCTACGTGG-CAT
* * * *
405891 TTTGGAAAAAATGTATGTGGTCCTTCGGGACAATTCTACGTGGCAT
1 TTCGGGACAAATCTATGTGGTCCTTCGGGACAATTCTACGTGGCAT
*
405937 TTCGGGACAAATCTATGTGG-CACTTCGGTG-CATATTCTACGTGGCAC
1 TTCGGGACAAATCTATGTGGTC-CTTCGG-GACA-ATTCTACGTGGCAT
405984 TTCGG
1 TTCGG
405989 TGCAAATTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
45 2 0.02
46 61 0.74
47 19 0.23
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (46 bp):
TTCGGGACAAATCTATGTGGTCCTTCGGGACAATTCTACGTGGCAT
Found at i:405980 original size:24 final size:23
Alignment explanation
Indices: 405913--405993 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
405903 GTATGTGGTC
405913 CTTCGG-GACAATTCTACGTGGCA
1 CTTCGGTG-CAATTCTACGTGGCA
* * *
405936 TTTCGG-GACAAATCTATGTGGCA
1 CTTCGGTG-CAATTCTACGTGGCA
405959 CTTCGGTGCATATTCTACGTGGCA
1 CTTCGGTGCA-ATTCTACGTGGCA
405983 CTTCGGTGCAA
1 CTTCGGTGCAA
405994 ATTTTAAGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
23 28 0.56
24 22 0.44
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
CTTCGGTGCAATTCTACGTGGCA
Done.