Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 102 of 105
Found at i:18673468 original size:39 final size:40
Alignment explanation
Indices: 18673383--18673475 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 40
18673373 AACCGAGAAT
* * ***
18673383 AGACTGAAAGAGGCTTGTGAAAAAGAAGCAATTGACAAAG
1 AGACTCAAAGAAGCTTGTGAAAAAGAAGCAACACACAAAG
* *
18673423 -GGCTCAAAGAAGCTTGTGAAAAAGAAG-AGCACACAAAG
1 AGACTCAAAGAAGCTTGTGAAAAAGAAGCAACACACAAAG
18673461 AGACTCAAAGAAGCT
1 AGACTCAAAGAAGCT
18673476 CGTCACAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 7 0.16
39 37 0.84
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.13
Consensus pattern (40 bp):
AGACTCAAAGAAGCTTGTGAAAAAGAAGCAACACACAAAG
Found at i:18678177 original size:29 final size:29
Alignment explanation
Indices: 18678126--18678206 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
18678116 TTTACTCCTC
*
18678126 TAATAAATAATATAT-AATATAAA-TATAA
1 TAATAAAT-ATATATGAATTTAAATTATAA
18678154 -AATATGAATATGATATG-ATTTAAAATTATAA
1 TAATA--AATAT-ATATGAATTT-AAATTATAA
18678185 TAATAAATATATATGAATTTAA
1 TAATAAATATATATGAATTTAA
18678207 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
27 4 0.09
28 2 0.05
29 17 0.39
30 12 0.27
31 5 0.11
32 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
TAATAAATATATATGAATTTAAATTATAA
Found at i:18679425 original size:4 final size:4
Alignment explanation
Indices: 18679416--18679448 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
18679406 ATATGGAGCT
*
18679416 TTTA TTTA TTTA CTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
18679449 ATATACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:18686256 original size:137 final size:138
Alignment explanation
Indices: 18686000--18686426 Score: 352
Period size: 137 Copynumber: 3.2 Consensus size: 138
18685990 AGAGTTATAA
* *
18686000 AAATTTTTCATACCAAAAAATCAAAAAGAAAAAGGTTACAGAGCAAGAGAAAAAAAATCAAAGAG
1 AAATTCTTCATACCAAAAAATCAAAAAGAAAAAGGTTAAAGAGCAAGAGAAAAAAAATCAAAGAG
* * ** * * *
18686065 TGAGTAACAGTCGTCATTGTTACAATAAAATGTGAAAATTTTTTTCCTATAAGTAAGCATGTAGT
66 TAAGTAACAGTCGCCATTACTACAATAAAAAGTGAAAAATTTTTGCCTATAAGTAAGCATGTAGT
18686130 AGTTGTAG
131 AGTTGTAG
* * * **
18686138 AAATTCTTCATACTAAAAAATTAAAAAG-AAAA-GTTAAAGAGCGAGAGAGAAAAAAATTTAAGA
1 AAATTCTTCATACCAAAAAATCAAAAAGAAAAAGGTTAAAGAGCAAGAGA-AAAAAAATCAAAGA
* * * * * *
18686201 GTAAGTACCAGTTGCCGTTACTACAGTAAAAAGTGAAAAATTTTTGCTTATAAGTAGGCA--T--
65 GTAAGTAACAGTCGCCATTACTACAATAAAAAGTGAAAAATTTTTGCCTATAAGTAAGCATGTAG
18686262 TA---G-A-
130 TAGTTGTAG
* * * *
18686266 AAATT-TTCATACCAAAAAATCAAGAA-AAAAA-GCTAGAGAGCAAAAGAGAAAAAAAATTAAAG
1 AAATTCTTCATACCAAAAAATCAAAAAGAAAAAGGTTAAAGAGC--AAGAGAAAAAAAATCAAAG
* * ** * * * ** *
18686328 AGTGAGTAATAGTCATCGTTACTACAGTGAAACA-TGAAAAATTTTTAACTATAAAT-AGACATG
64 AGTAAGTAACAGTCGCCATTACTACAAT-AAAAAGTGAAAAATTTTTGCCTATAAGTAAG-CATG
18686391 --G-AGTTGTAG
127 TAGTAGTTGTAG
**
18686400 AAATTCTTCATATAAAAAAATCAAAAA
1 AAATTCTTCATACCAAAAAATCAAAAA
18686427 CCAAAGTTAG
Statistics
Matches: 232, Mismatches: 42, Indels: 33
0.76 0.14 0.11
Matches are distributed among these distances:
127 31 0.13
128 59 0.25
129 11 0.05
130 1 0.00
132 1 0.00
133 3 0.01
134 5 0.02
135 19 0.08
136 14 0.06
137 63 0.27
138 25 0.11
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (138 bp):
AAATTCTTCATACCAAAAAATCAAAAAGAAAAAGGTTAAAGAGCAAGAGAAAAAAAATCAAAGAG
TAAGTAACAGTCGCCATTACTACAATAAAAAGTGAAAAATTTTTGCCTATAAGTAAGCATGTAGT
AGTTGTAG
Found at i:18686275 original size:127 final size:129
Alignment explanation
Indices: 18686138--18686373 Score: 300
Period size: 128 Copynumber: 1.8 Consensus size: 129
18686128 GTAGTTGTAG
* * * * * *
18686138 AAATTCTTCATACTAAAAAATTAA-AAAGAAAAGTTAAAGAGCGAGAGAG-AAAAAAATTTAAGA
1 AAATTCTTCATACCAAAAAATCAAGAAA-AAAAGCTAAAGAGCAAAAGAGAAAAAAAATTAAAGA
* **
18686201 GTAAGTACCAGTTGCCGTTACTACAGT-AAAAAGTGAAAAATTTTTGCTTATAAGTAGGCATTAG
65 GTAAGTAACAGTCACCGTTACTACAGTGAAAAA-TGAAAAATTTTTGCTTATAAGTAGGCATTAG
18686265 A
129 A
*
18686266 AAATT-TTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGCAAAAGAGAAAAAAAATTAAAGAG
1 AAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAAAGAGCAAAAGAGAAAAAAAATTAAAGAG
* * * *
18686330 TGAGTAATAGTCATCGTTACTACAGTGAAACATGAAAAATTTTT
66 TAAGTAACAGTCACCGTTACTACAGTGAAAAATGAAAAATTTTT
18686374 AACTATAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
127 33 0.36
128 54 0.59
129 4 0.04
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (129 bp):
AAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAAAGAGCAAAAGAGAAAAAAAATTAAAGAG
TAAGTAACAGTCACCGTTACTACAGTGAAAAATGAAAAATTTTTGCTTATAAGTAGGCATTAGA
Found at i:18687129 original size:133 final size:133
Alignment explanation
Indices: 18686885--18687130 Score: 330
Period size: 133 Copynumber: 1.8 Consensus size: 133
18686875 AGTGAGAGTC
* * * *
18686885 ATCATTACTATAGTGAAACATGAAATATTTTTGCCTATAAGTAGGCATAAAGTTGTCGAAATTCT
1 ATCATTACTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGCATAAAGTTGTCGAAACTCT
* * *
18686950 TCATACCAAAATATCAAGAAGAAAAGCAAAAAAGCAGGAGATAAAAAATTAAAGAATGAGTGACA
66 TCATACCAAAAAATCAAGAAGAAAAGCAAAAAAGCAAGAGAGAAAAAATTAAAGAATGAGTGACA
18687015 ATT
131 ATT
* ** * **
18687018 ATCATTATTATAGTGATTCATGAAAAAATTTTACCTATAAGTAGGTATGGAGTTGTCGAAACTCT
1 ATCATTACTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGCATAAAGTTGTCGAAACTCT
*** * *
18687083 TCATACCAAAAAATCAAGAAGAAAATTTAGAGAGCAAGAGAGAAAAAA
66 TCATACCAAAAAATCAAGAAGAAAAGCAAAAAAGCAAGAGAGAAAAAA
18687131 AAATCAAAGA
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
133 95 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (133 bp):
ATCATTACTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGCATAAAGTTGTCGAAACTCT
TCATACCAAAAAATCAAGAAGAAAAGCAAAAAAGCAAGAGAGAAAAAATTAAAGAATGAGTGACA
ATT
Found at i:18687189 original size:161 final size:159
Alignment explanation
Indices: 18687006--18687311 Score: 396
Period size: 161 Copynumber: 1.9 Consensus size: 159
18686996 AATTAAAGAA
* **
18687006 TGAGTGACAATTATCATTATTATAGTGATTCATGAAAAAATTTTACCTATAAGTAGGTATGGAGT
1 TGAGTGACAATCATCATTATTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGTATGGAGT
* ** * ** *
18687071 TGTCGAAACTCTTCATACCAAAAAATCAAGAAGAAAATTTAGAGAGCAAGAGAGAAAAAAAAATC
66 AGTAAAAACTCTTCACACCAAAAAATCAAGAAGAAAAGCTAGAAAGCAAG-G-GAAAAAAAAATC
*
18687136 AAAGAGTGAATGACAGTAATGAATCAAAAAG
129 AAAAAGTGAATGACAGTAATGAATCAAAAAG
** * * * * *
18687167 TGAGTGACAATCATTGTTATTATTGTGAAACGTGAAAAATTTTTGCCTATAAGTTGGTATGGAGT
1 TGAGTGACAATCATCATTATTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGTATGGAGT
* * *
18687232 AGTAAAAATTCTTTACACCAAAAAATCAAGAAGAAAAGCTAGAAAGCAAGGGAGAAAAAAATCAA
66 AGTAAAAACTCTTCACACCAAAAAATCAAGAAGAAAAGCTAGAAAGCAAGGGAAAAAAAAATCAA
*
18687297 AAAGTGAGTGACAGT
131 AAAGTGAATGACAGT
18687312 TGTCATTACT
Statistics
Matches: 123, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
159 26 0.21
160 1 0.01
161 96 0.78
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (159 bp):
TGAGTGACAATCATCATTATTATAGTGAAACATGAAAAAATTTTACCTATAAGTAGGTATGGAGT
AGTAAAAACTCTTCACACCAAAAAATCAAGAAGAAAAGCTAGAAAGCAAGGGAAAAAAAAATCAA
AAAGTGAATGACAGTAATGAATCAAAAAG
Found at i:18687570 original size:9 final size:9
Alignment explanation
Indices: 18687556--18687628 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
18687546 CGAGTATACG
18687556 TTTAATATA
1 TTTAATATA
18687565 TTTAATATA
1 TTTAATATA
18687574 TTTAATATA
1 TTTAATATA
* **
18687583 TTTAACACG
1 TTTAATATA
*
18687592 TTTAACATA
1 TTTAATATA
**
18687601 TTTTTTATA
1 TTTAATATA
* *
18687610 TTTATTTTAA
1 TTTAATAT-A
18687620 TTTAATATA
1 TTTAATATA
18687629 AATATATAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
9 44 0.86
10 7 0.14
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (9 bp):
TTTAATATA
Found at i:18688050 original size:29 final size:29
Alignment explanation
Indices: 18688018--18688091 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
18688008 TCGTGTTTTA
18688018 ATATATATTCATATTAATCGTATCTATTC
1 ATATATATTCATATTAATCGTATCTATTC
* *
18688047 ATATATA-TCAATATTAATCTTGTCTATTC
1 ATATATATTC-ATATTAATCGTATCTATTC
18688076 ATATATATTCATATTA
1 ATATATATTCATATTA
18688092 TTCATATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 37 0.90
30 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (29 bp):
ATATATATTCATATTAATCGTATCTATTC
Found at i:18688086 original size:10 final size:10
Alignment explanation
Indices: 18688018--18688108 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
18688008 TCGTGTTTTA
18688018 ATATATATTC
1 ATATATATTC
*
18688028 ATAT-TAATC
1 ATATATATTC
* *
18688037 GTATCTATTC
1 ATATATATTC
18688047 ATATATA-TC
1 ATATATATTC
*
18688056 A-ATATTAATC
1 ATATA-TATTC
* * *
18688066 TTGTCTATTC
1 ATATATATTC
18688076 ATATATATTC
1 ATATATATTC
18688086 ATAT-TATTC
1 ATATATATTC
* *
18688095 ATATTTATAC
1 ATATATATTC
18688105 ATAT
1 ATAT
18688109 CGTGTTTAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 3 0.05
9 21 0.33
10 38 0.60
11 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.49
Consensus pattern (10 bp):
ATATATATTC
Found at i:18688093 original size:19 final size:19
Alignment explanation
Indices: 18688018--18688108 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 19
18688008 TCGTGTTTTA
*
18688018 ATATATATTCATATTAATC
1 ATATATATTCATATTATTC
* *
18688037 GTATCTATTCATA-TATATC
1 ATATATATTCATATTAT-TC
* * *
18688056 A-ATATTAATCTTGTCTATTC
1 ATATA-TATTCATAT-TATTC
18688076 ATATATATTCATATTATTC
1 ATATATATTCATATTATTC
* *
18688095 ATATTTATACATAT
1 ATATATATTCATAT
18688109 CGTGTTTAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
18 4 0.07
19 35 0.65
20 9 0.17
21 6 0.11
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATATTCATATTATTC
Found at i:18688544 original size:134 final size:135
Alignment explanation
Indices: 18688269--18688752 Score: 705
Period size: 134 Copynumber: 3.6 Consensus size: 135
18688259 TACCTACCTA
18688269 ATAAGTAGGCATGGAGTTGTAGAAACTT-TTCATACCAAAAAATCAAGAAAAAAAGCTAGAGA--
1 ATAAGTAGGCATGGAGTTGTAGAAA-TTCTTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGC
* * * * *
18688331 AAAAGAGAGAAAAATTCAAAGAGTGAGTGATAGTCGTCGTTACTACAATAAAACGTGAAAAATAT
65 AAAAGAGAAAAAAAATCAAAGAGTGAGTGACAGTCGTCGTTACTACAATGAAACGTGAAAAATTT
*
18688396 TTGCTT
130 TTGCCT
* *
18688402 ATAAGTAGGCATGGAGTTGTAGAAATTCTTCATACCAAAAAATCAAGAAAAAAATCTAGAGAGGA
1 ATAAGTAGGCATGGAGTTGTAGAAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGCA
* * *
18688467 AAAGAG-AAAAAAATCAAATAGTGAGTGACAGTCGTCGTTACTATAATGAAACATGAAAAATTTT
66 AAAGAGAAAAAAAATCAAAGAGTGAGTGACAGTCGTCGTTACTACAATGAAACGTGAAAAATTTT
18688531 TGCCT
131 TGCCT
* *
18688536 ATAAGTAGGCATAGAGTTGTAGAAATTCTTCGTACCAAAAAATCAAGAAAAAAAGCTAGAGAGCA
1 ATAAGTAGGCATGGAGTTGTAGAAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGCA
* * * * *
18688601 AGAGAGAAAAAAAATCAAAGAATGAGCGACAGTTGTCG-TACTACAGTG-AACGTGAAAAATTTT
66 AAAGAGAAAAAAAATCAAAGAGTGAGTGACAGTCGTCGTTACTACAATGAAACGTGAAAAATTTT
*
18688664 TGTCT
131 TGCCT
* * *
18688669 ATAAGTAGGCATGGAGCTATAGAAATTCTTCATACCAAAAAATC-A-AAGAAAAGCTAGAGAGCA
1 ATAAGTAGGCATGGAGTTGTAGAAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGCA
18688732 AAAGAGAAAAAAAATCAAAGA
66 AAAGAGAAAAAAAATCAAAGA
18688753 ATGAATGAGC
Statistics
Matches: 318, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
131 37 0.12
132 3 0.01
133 116 0.36
134 128 0.40
135 34 0.11
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (135 bp):
ATAAGTAGGCATGGAGTTGTAGAAATTCTTCATACCAAAAAATCAAGAAAAAAAGCTAGAGAGCA
AAAGAGAAAAAAAATCAAAGAGTGAGTGACAGTCGTCGTTACTACAATGAAACGTGAAAAATTTT
TGCCT
Found at i:18690743 original size:27 final size:27
Alignment explanation
Indices: 18690653--18690745 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
18690643 AATTTCGAAA
**
18690653 AAAAATTGATACTTTCAACTTTTCCTC
1 AAAAATTGATACTTTCAACTTTTTTTC
* ** * *
18690680 AAAAATTCATTTTTTGAAAACTTATTTTTTAAG
1 AAAAATTGATACTTT--CAAC-T-TTTTTT--C
18690713 AAAAATTGATACTTTCAACTTTTTTTC
1 AAAAATTGATACTTTCAACTTTTTTTC
18690740 AAAAAT
1 AAAAAT
18690746 ATATATTTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
27 18 0.38
29 9 0.19
30 2 0.04
31 7 0.15
33 12 0.25
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.44
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTTTTC
Found at i:18690875 original size:58 final size:58
Alignment explanation
Indices: 18690595--18690875 Score: 325
Period size: 58 Copynumber: 4.7 Consensus size: 58
18690585 TTTGTACAGA
* * ** *
18690595 AAAATTTGATACTTTTAACTTTTTCTCAAAAATA-TTTTTTGAAACTTTAATTTCGAAAA
1 AAAA-TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTT-ATTTTTAAAG
* * *
18690654 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TCATTTTTTGAAAACTTATTTTTTAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATAT--TTTTTTGAAAATTTATTTTTAAAG
* * *
18690713 AAAAATTGATACTTTCAACTTTTTTTCAAAAATATATATTTTTTTTGAAAACTTTAATTTTAAGG
1 -AAAATTGATACTTTCAACTTTTTCTC--AAA-A-ATA-TTTTTTTGAAAA-TTTATTTTTAAAG
18690778 AAAATTGATACTTTCAAC-TTTTCTTCAAAAATATTTTTTTGAAAATTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTTGAAAATTTATTTTTAAAG
*
18690836 AAAATTGATACCTTCAACTTTTTCTCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTT
18690876 TTACAGTTCC
Statistics
Matches: 191, Mismatches: 18, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
58 70 0.37
59 27 0.14
60 39 0.20
61 1 0.01
62 6 0.03
63 5 0.03
64 33 0.17
65 9 0.05
66 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTTAAAG
Found at i:18691220 original size:33 final size:33
Alignment explanation
Indices: 18691183--18691248 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
18691173 TGGTCGTCTG
18691183 AGGTCCAAAGCTTAATGCACTTGAAGCAACCTT
1 AGGTCCAAAGCTTAATGCACTTGAAGCAACCTT
18691216 AGGTCCAAAGCTTAATGCACTTGAAGCAACCTT
1 AGGTCCAAAGCTTAATGCACTTGAAGCAACCTT
18691249 CAAAAGATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (33 bp):
AGGTCCAAAGCTTAATGCACTTGAAGCAACCTT
Found at i:18693578 original size:20 final size:19
Alignment explanation
Indices: 18693540--18693607 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 19
18693530 AAAAGAAAGA
18693540 AAAAGAAAATAAATCATAAAAT
1 AAAA-AAAA-AAAT-ATAAAAT
*
18693562 AAAAATAAAAATGATAAATAT
1 AAAAAAAAAAAT-ATAAA-AT
*
18693583 GAAATAAAAAAAATCTAAAAT
1 -AAA-AAAAAAAATATAAAAT
18693604 AAAA
1 AAAA
18693608 TGAATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.03
20 12 0.31
21 7 0.18
22 11 0.28
23 8 0.21
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAAAAAAAAATATAAAAT
Found at i:18697482 original size:19 final size:19
Alignment explanation
Indices: 18697458--18697495 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18697448 AATCGAATAA
* *
18697458 AAAATAATATTTTAATATT
1 AAAATAAAATGTTAATATT
18697477 AAAATAAAATGTTAATATT
1 AAAATAAAATGTTAATATT
18697496 TTAATATATA
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATAAAATGTTAATATT
Found at i:18698039 original size:16 final size:16
Alignment explanation
Indices: 18698018--18698078 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 16
18698008 AATAATTCTT
18698018 ATAAATTTTTAAATTA
1 ATAAATTTTTAAATTA
18698034 ATAAATTTATCTTTAAA-TA
1 ATAAA--T-T-TTTAAATTA
*
18698053 TATATATTTTTTAAATTA
1 -ATA-AATTTTTAAATTA
18698071 ATAAATTT
1 ATAAATTT
18698079 ATCTTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 9 0.25
17 9 0.25
18 4 0.11
19 4 0.11
20 9 0.25
21 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAAATTTTTAAATTA
Found at i:18698050 original size:20 final size:20
Alignment explanation
Indices: 18698025--18698088 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
18698015 CTTATAAATT
18698025 TTTAAATTAATAAATTTATC
1 TTTAAATTAATAAATTTATC
*
18698045 TTTAAA-T-ATATATATT-T-
1 TTTAAATTAATAAAT-TTATC
18698062 TTTAAATTAATAAATTTATC
1 TTTAAATTAATAAATTTATC
18698082 TTTAAAT
1 TTTAAAT
18698089 ATATTAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.16
18 9 0.24
19 9 0.24
20 13 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATTAATAAATTTATC
Found at i:18698171 original size:14 final size:14
Alignment explanation
Indices: 18698152--18698181 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18698142 AAATTAAACT
*
18698152 AATTTTAATTTTAA
1 AATTTTAATTTCAA
18698166 AATTTTAATTTCAA
1 AATTTTAATTTCAA
18698180 AA
1 AA
18698182 ATGTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTAATTTCAA
Found at i:18699500 original size:17 final size:17
Alignment explanation
Indices: 18699453--18699500 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18699443 TATGTATTTT
*
18699453 AATTTTTTATATAATAA
1 AATTTTTTAAATAATAA
* * **
18699470 AAATTTATGCATAATAA
1 AATTTTTTAAATAATAA
18699487 AATTTTTTAAATAA
1 AATTTTTTAAATAA
18699501 AAGACAATTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
AATTTTTTAAATAATAA
Found at i:18701148 original size:26 final size:26
Alignment explanation
Indices: 18701119--18701171 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18701109 ATGATAAGGT
* * *
18701119 AATTATTGTGAATTTAATTTTTTTAA
1 AATTATTGTCAACTTAATTTTTATAA
*
18701145 AATTATTGTCTACTTAATTTTTATAA
1 AATTATTGTCAACTTAATTTTTATAA
18701171 A
1 A
18701172 TTTTATTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.55
Consensus pattern (26 bp):
AATTATTGTCAACTTAATTTTTATAA
Found at i:18703509 original size:21 final size:21
Alignment explanation
Indices: 18703475--18703515 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18703465 GTAGTAGCTA
* *
18703475 ATTAATAACATAAATTTAATC
1 ATTAAAAACATAAATGTAATC
*
18703496 ATTAAAAACTTAAATGTAAT
1 ATTAAAAACATAAATGTAAT
18703516 TAATATAACT
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:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
ATTAAAAACATAAATGTAATC
Found at i:18703589 original size:22 final size:22
Alignment explanation
Indices: 18703540--18703590 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
18703530 AGTAATTATC
* *
18703540 GATAACTTAATACTAAATTAAA
1 GATAATTTAATACTAAATGAAA
* * *
18703562 GTTAATTTAATAGTAAATGAAT
1 GATAATTTAATACTAAATGAAA
18703584 GATAATT
1 GATAATT
18703591 CACTACTCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (22 bp):
GATAATTTAATACTAAATGAAA
Found at i:18703885 original size:22 final size:22
Alignment explanation
Indices: 18703841--18703904 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
18703831 AATTAATTGA
** *
18703841 TAATAATAAATAATAAATCAAT
1 TAATAATAAATAATTGATAAAT
**
18703863 TGGTAATAAATCAATT-ATAAAT
1 TAATAATAAAT-AATTGATAAAT
18703885 TAATAATAAATAATTGATAA
1 TAATAATAAATAATTGATAA
18703905 TTTAGTGGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.12
22 27 0.79
23 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (22 bp):
TAATAATAAATAATTGATAAAT
Found at i:18704048 original size:10 final size:9
Alignment explanation
Indices: 18704011--18704061 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
18704001 GCACAATCCA
18704011 TTAATAATTT
1 TTAA-AATTT
18704021 TTAAAATTT
1 TTAAAATTT
**
18704030 TTATCATTT
1 TTAAAATTT
*
18704039 TTAGGAATTT
1 TTA-AAATTT
18704049 TTAAAATTT
1 TTAAAATTT
18704058 TTAA
1 TTAA
18704062 CTATCTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 24 0.69
10 11 0.31
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (9 bp):
TTAAAATTT
Found at i:18704057 original size:19 final size:18
Alignment explanation
Indices: 18704011--18704061 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
18704001 GCACAATCCA
18704011 TTAATAATTTTTAAAATTT
1 TTAA-AATTTTTAAAATTT
** *
18704030 TTATCATTTTTAGGAATTT
1 TTAAAATTTTTA-AAATTT
18704049 TTAAAATTTTTAA
1 TTAAAATTTTTAA
18704062 CTATCTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TTAAAATTTTTAAAATTT
Found at i:18704875 original size:19 final size:19
Alignment explanation
Indices: 18704851--18704894 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
18704841 AATTTAATAT
*
18704851 TAAATTGATAAGTTAGTAG
1 TAAATTGATAAGTTAGTAA
*
18704870 TAAATTGATAATTTAGTAA
1 TAAATTGATAAGTTAGTAA
18704889 TAAATT
1 TAAATT
18704895 ATCAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
TAAATTGATAAGTTAGTAA
Found at i:18704936 original size:22 final size:21
Alignment explanation
Indices: 18704877--18704961 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 21
18704867 TAGTAAATTG
*
18704877 ATAATTTAGTAATAAATTATCA
1 ATAATTTAGTTATAAATTAT-A
* **
18704899 ATAATATA-ACAGTAAATTACTA
1 ATAATTTAGTTA-TAAATTA-TA
*
18704921 ATAATTTAGTTATAAATTAATG
1 ATAATTTAGTTATAAATT-ATA
* *
18704943 ATAATTTTGTTGTAAATTA
1 ATAATTTAGTTATAAATTA
18704962 ATTAATCATT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 45 0.90
23 3 0.06
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (21 bp):
ATAATTTAGTTATAAATTATA
Found at i:18704962 original size:22 final size:22
Alignment explanation
Indices: 18704910--18704963 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
18704900 TAATATAACA
*
18704910 GTAAATTACTAATAATTTAGTT
1 GTAAATTAATAATAATTTAGTT
* * *
18704932 ATAAATTAATGATAATTTTGTT
1 GTAAATTAATAATAATTTAGTT
18704954 GTAAATTAAT
1 GTAAATTAAT
18704964 TAATCATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (22 bp):
GTAAATTAATAATAATTTAGTT
Found at i:18705098 original size:22 final size:22
Alignment explanation
Indices: 18705017--18705164 Score: 84
Period size: 22 Copynumber: 6.7 Consensus size: 22
18705007 TAAATTAGTT
* *
18705017 ATAATTTTATAATAAATTATTA
1 ATAATTTAATAATAAATCATTA
* ** **
18705039 AT-ATCGTAATGGTAAATCACCA
1 ATAAT-TTAATAATAAATCATTA
* ** *
18705061 ACAATTTAATGGTAAATCATTC
1 ATAATTTAATAATAAATCATTA
*
18705083 ATAATTTAATAATAAATTATTTA
1 ATAATTTAATAATAAATCA-TTA
* * * *
18705106 AGAA-TTAGTAGTAAATCATTG
1 ATAATTTAATAATAAATCATTA
* * *
18705127 ATAATTTTACAATAAATTATTA
1 ATAATTTAATAATAAATCATTA
*
18705149 ATAATTTAGTAATAAA
1 ATAATTTAATAATAAA
18705165 AATAACTACT
Statistics
Matches: 90, Mismatches: 32, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
21 7 0.08
22 76 0.84
23 7 0.08
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAATTTAATAATAAATCATTA
Found at i:18705120 original size:44 final size:44
Alignment explanation
Indices: 18705063--18705164 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
18705053 AATCACCAAC
* * *
18705063 AATTTAATGGTAAATCATTCATAATTTAATAATAAATTATTTAAG
1 AATTTAGTAGTAAATCATTCATAATTTAACAATAAATTA-TTAAG
* * *
18705108 AA-TTAGTAGTAAATCATTGATAATTTTACAATAAATTATTAAT
1 AATTTAGTAGTAAATCATTCATAATTTAACAATAAATTATTAAG
*
18705151 AATTTAGTAATAAA
1 AATTTAGTAGTAAA
18705165 AATAACTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 6 0.12
44 41 0.84
45 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (44 bp):
AATTTAGTAGTAAATCATTCATAATTTAACAATAAATTATTAAG
Found at i:18705461 original size:22 final size:22
Alignment explanation
Indices: 18705435--18705540 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
18705425 AACATATTAG
* *
18705435 TAAATTAATTATAAGTTAATAA
1 TAAATTAATGATAACTTAATAA
* * *
18705457 -AAAATAAGTGATAATTTAGTAA
1 TAAATTAA-TGATAACTTAATAA
* *
18705479 TTAA-TAATTAATAACTTAATAA
1 TAAATTAA-TGATAACTTAATAA
*
18705501 TAAATCAATGATAACTTAATAA
1 TAAATTAATGATAACTTAATAA
* *
18705523 TAAATTAGTGACAACTTA
1 TAAATTAATGATAACTTA
18705541 GAAGTAAATC
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.09
22 56 0.85
23 4 0.06
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.36
Consensus pattern (22 bp):
TAAATTAATGATAACTTAATAA
Found at i:18705500 original size:44 final size:43
Alignment explanation
Indices: 18705440--18705523 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
18705430 ATTAGTAAAT
* * *
18705440 TAATTATAAGTTAATAAAAAAT-AAGTGATAATTTAGTAATTAA
1 TAATTATAACTTAATAAAAAATCAA-TGATAACTTAATAATTAA
*
18705483 TAATTAATAACTTAATAATAAATCAATGATAACTTAATAAT
1 TAATT-ATAACTTAATAAAAAATCAATGATAACTTAATAAT
18705524 AAATTAGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.14
44 28 0.80
45 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (43 bp):
TAATTATAACTTAATAAAAAATCAATGATAACTTAATAATTAA
Found at i:18705501 original size:11 final size:11
Alignment explanation
Indices: 18705487--18705525 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18705477 AATTAATAAT
18705487 TAATAACTTAA
1 TAATAACTTAA
* *
18705498 TAATAAATCAA
1 TAATAACTTAA
*
18705509 TGATAACTTAA
1 TAATAACTTAA
18705520 TAATAA
1 TAATAA
18705526 ATTAGTGACA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (11 bp):
TAATAACTTAA
Found at i:18705705 original size:22 final size:21
Alignment explanation
Indices: 18705674--18705732 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
18705664 TATAACTTAG
*
18705674 TAATATTTAATCATCGAGAACT
1 TAATAGTTAATCAT-GAGAACT
* *
18705696 TAATAGTTAAGTAATGATAACT
1 TAATAGTTAA-TCATGAGAACT
* *
18705718 TAATTGTAAATCATG
1 TAATAGTTAATCATG
18705733 GATAATTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.13
22 23 0.77
23 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (21 bp):
TAATAGTTAATCATGAGAACT
Found at i:18705736 original size:22 final size:21
Alignment explanation
Indices: 18705711--18705751 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18705701 GTTAAGTAAT
*
18705711 GATAACTTAATTGTAAATCATG
1 GATAA-TTAATTATAAATCATG
*
18705733 GATAATTTATTATAAATCA
1 GATAATTAATTATAAATCA
18705752 GTAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (21 bp):
GATAATTAATTATAAATCATG
Found at i:18705805 original size:22 final size:22
Alignment explanation
Indices: 18705724--18705800 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
18705714 AACTTAATTG
*
18705724 TAAATCATGGA-TAATTT-ATTA
1 TAAATCAT-GATTAATTTAATAA
* *
18705745 TAAATCA-GTAATAATTTGATAA
1 TAAATCATG-ATTAATTTAATAA
*
18705767 TGAATCATGATTAATTTAATAA
1 TAAATCATGATTAATTTAATAA
18705789 TAAATCTATGAT
1 TAAATC-ATGAT
18705801 GATTTCATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 13 0.28
22 25 0.54
23 6 0.13
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (22 bp):
TAAATCATGATTAATTTAATAA
Found at i:18705833 original size:22 final size:22
Alignment explanation
Indices: 18705808--18705886 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
18705798 GATGATTTCA
18705808 TAGTAAATAATCAAAAACTAAG
1 TAGTAAATAATCAAAAACTAAG
* *
18705830 TAGTAAATTAAT-ATAACATAGTAGTAA
1 TAGTAAA-TAATCA-AA-A-ACTA--AG
*
18705857 TAGTAAATAATCGAAAACTAAG
1 TAGTAAATAATCAAAAACTAAG
18705879 TAGTAAAT
1 TAGTAAAT
18705887 TAATATAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
22 17 0.38
23 6 0.13
24 4 0.09
25 4 0.09
26 6 0.13
27 8 0.18
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.28
Consensus pattern (22 bp):
TAGTAAATAATCAAAAACTAAG
Found at i:18705854 original size:21 final size:21
Alignment explanation
Indices: 18705828--18705907 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 21
18705818 TCAAAAACTA
18705828 AGTAGTAAATTAATATAACAT
1 AGTAGTAAATTAATATAACAT
* *
18705849 AGTAGTAATAGTAAATAATCGAAAACT
1 AGTAGTAA-A-TTAAT-AT--AACA-T
18705876 AAGTAGTAAATTAATATAACAT
1 -AGTAGTAAATTAATATAACAT
18705898 AGTAGTAAAT
1 AGTAGTAAAT
18705908 GTAGAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
21 18 0.38
22 2 0.04
23 7 0.15
24 2 0.04
25 2 0.04
26 7 0.15
27 2 0.04
28 8 0.17
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTAGTAAATTAATATAACAT
Found at i:18705860 original size:49 final size:49
Alignment explanation
Indices: 18705807--18705905 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
18705797 TGATGATTTC
18705807 ATAGTAAATAATCAAAAACTAAGTAGTAAATTAATATAACATAGTAGTA
1 ATAGTAAATAATCAAAAACTAAGTAGTAAATTAATATAACATAGTAGTA
*
18705856 ATAGTAAATAATCGAAAACTAAGTAGTAAATTAATATAACATAGTAGTA
1 ATAGTAAATAATCAAAAACTAAGTAGTAAATTAATATAACATAGTAGTA
18705905 A
1 A
18705906 ATGTAGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (49 bp):
ATAGTAAATAATCAAAAACTAAGTAGTAAATTAATATAACATAGTAGTA
Found at i:18705947 original size:21 final size:22
Alignment explanation
Indices: 18705923--18705963 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18705913 AAATATAATA
*
18705923 GTAAATCATTGA-AATTTAGAT
1 GTAAATCAATGACAATTTAGAT
*
18705944 GTAAATTAATGACAATTTAG
1 GTAAATCAATGACAATTTAG
18705964 CAGCAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (22 bp):
GTAAATCAATGACAATTTAGAT
Found at i:18706062 original size:44 final size:44
Alignment explanation
Indices: 18706014--18706148 Score: 152
Period size: 44 Copynumber: 3.1 Consensus size: 44
18706004 TTAATTATTG
*
18706014 ATAACTTTATAGTAAATCATCAGTAAATTAATAATAAATCAATT-
1 ATAACTTTATAGTAAATCAT-AGTAACTTAATAATAAATCAATTA
* *
18706058 ATAACTTTATAATAAATACTTAGTAACTTAATAATAAATC-ATTA
1 ATAACTTTATAGTAAAT-CATAGTAACTTAATAATAAATCAATTA
* * *
18706102 ATAA-TTTAGTAGCAAATCAATAATAACTTAATAGTAAATC-ATTA
1 ATAACTTTA-TAGTAAATC-ATAGTAACTTAATAATAAATCAATTA
18706146 ATA
1 ATA
18706149 TATTAGTAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
43 8 0.10
44 69 0.87
45 2 0.03
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.36
Consensus pattern (44 bp):
ATAACTTTATAGTAAATCATAGTAACTTAATAATAAATCAATTA
Found at i:18706097 original size:66 final size:66
Alignment explanation
Indices: 18706015--18706140 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
18706005 TAATTATTGA
* * * * * *
18706015 TAACTTTATAGTAAATCATCAGTAAATTAATAATAAATCAATTATAACTTTATAATAAATACTTA
1 TAACTTAATAATAAATCATCAATAAATTAATAACAAATCAATAATAACTTAATAATAAATACTTA
18706080 G
66 G
* * * * *
18706081 TAACTTAATAATAAATCATTAATAATTTAGTAGCAAATCAATAATAACTTAATAGTAAAT
1 TAACTTAATAATAAATCATCAATAAATTAATAACAAATCAATAATAACTTAATAATAAAT
18706141 CATTAATATA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.37
Consensus pattern (66 bp):
TAACTTAATAATAAATCATCAATAAATTAATAACAAATCAATAATAACTTAATAATAAATACTTA
G
Found at i:18706147 original size:22 final size:22
Alignment explanation
Indices: 18706014--18706265 Score: 125
Period size: 22 Copynumber: 11.5 Consensus size: 22
18706004 TTAATTATTG
* *
18706014 ATAACTTTATAGTAAATCATCA
1 ATAACTTAATAGTAAATCATTA
* * *
18706036 GTAAATTAATAATAAATCAATT-
1 ATAACTTAATAGTAAATC-ATTA
* *
18706058 ATAACTTTATAATAAAT-ACTTA
1 ATAACTTAATAGTAAATCA-TTA
* *
18706080 GTAACTTAATAATAAATCATTA
1 ATAACTTAATAGTAAATCATTA
* * * *
18706102 ATAATTTAGTAGCAAATCAATA
1 ATAACTTAATAGTAAATCATTA
18706124 ATAACTTAATAGTAAATCATTA
1 ATAACTTAATAGTAAATCATTA
* * * * *
18706146 ATATA-TTAGTAGTGAGTCAATG
1 ATA-ACTTAATAGTAAATCATTA
* * * * * * *
18706168 TTAATTTAGTTGTCAATTATTG
1 ATAACTTAATAGTAAATCATTA
* * *
18706190 GTAATTTAATAGTATATCA-TA
1 ATAACTTAATAGTAAATCATTA
* * * *
18706211 GATAGCTTAATAATAAATCGTTG
1 -ATAACTTAATAGTAAATCATTA
* * *
18706234 ATAACATAATAGTAAATTAATA
1 ATAACTTAATAGTAAATCATTA
18706256 ATAACTTAAT
1 ATAACTTAAT
18706266 TGTTGATCAT
Statistics
Matches: 169, Mismatches: 53, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.01
21 4 0.02
22 159 0.94
23 5 0.03
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCATTA
Found at i:18706616 original size:22 final size:21
Alignment explanation
Indices: 18706584--18706640 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
18706574 CATCAAGAGT
* *
18706584 TTATTAAAATTTTATAAAAAA
1 TTATCAAAATTATATAAAAAA
* *
18706605 TTATCAATAATTATATCAATAA
1 TTATCAA-AATTATATAAAAAA
18706627 TTATCAAAATTATA
1 TTATCAAAATTATA
18706641 CCATAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTATATAAAAAA
Found at i:18706621 original size:12 final size:12
Alignment explanation
Indices: 18706606--18706630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18706596 TATAAAAAAT
18706606 TATCAATAATTA
1 TATCAATAATTA
18706618 TATCAATAATTA
1 TATCAATAATTA
18706630 T
1 T
18706631 CAAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATCAATAATTA
Found at i:18706639 original size:21 final size:21
Alignment explanation
Indices: 18706584--18706658 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
18706574 CATCAAGAGT
* * * *
18706584 TTATTAAAATTTTATAAAAAA
1 TTATCAAAATTATATCAATAA
18706605 TTATCAATAATTATATCAATAA
1 TTATCAA-AATTATATCAATAA
*
18706627 TTATCAAAATTATA-CCATAA
1 TTATCAAAATTATATCAATAA
*
18706647 GTTATTAAAATT
1 -TTATCAAAATT
18706659 GTGTCAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.11
21 23 0.50
22 18 0.39
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (21 bp):
TTATCAAAATTATATCAATAA
Found at i:18712863 original size:30 final size:28
Alignment explanation
Indices: 18712812--18712878 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
18712802 AAAATATTTT
* **
18712812 TTATTTATTAAAATTTTTATTTATATATA
1 TTATTTAATAAAATTAATATTTA-ATATA
*
18712841 TTATATTAATAAAATTAATATTTAATATT
1 TTAT-TTAATAAAATTAATATTTAATATA
18712870 TTCATTTAA
1 TT-ATTTAA
18712879 AATTAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATTTAATAAAATTAATATTTAATATA
Found at i:18712936 original size:57 final size:56
Alignment explanation
Indices: 18712838--18712981 Score: 143
Period size: 57 Copynumber: 2.5 Consensus size: 56
18712828 TTATTTATAT
* *
18712838 ATATTATA-TTAATAAAATTAATATTTAATATTTTCATTTAAAATTAATTTAATAAAA
1 ATATTATATTTAATAAAATTAATATTTAATATTATCATTTAAAAAT-ATTTAAT-AAA
* *
18712895 ATATTATATTTATATATAATTAA-ATTTTAAT-TTAT-ATTTAAAAATATTTTATAAA
1 ATATTATATTTA-ATAAAATTAATA-TTTAATATTATCATTTAAAAATATTTAATAAA
* * *
18712950 ATGTTATATTAAATTAAATTAATTATATTAAT
1 ATATTATATTTAATAAAATTAA-TAT-TTAAT
18712982 TTAAATCGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
54 8 0.11
55 14 0.19
56 12 0.16
57 17 0.23
58 7 0.10
59 15 0.21
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (56 bp):
ATATTATATTTAATAAAATTAATATTTAATATTATCATTTAAAAATATTTAATAAA
Found at i:18712943 original size:22 final size:22
Alignment explanation
Indices: 18712889--18712945 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
18712879 AATTAATTTA
*
18712889 ATAAAAATATTAT-ATTTATAT
1 ATAAAAATATTTTAATTTATAT
*
18712910 ATAATTAA-ATTTTAATTTATAT
1 ATAA-AAATATTTTAATTTATAT
*
18712932 TTAAAAATATTTTA
1 ATAAAAATATTTTA
18712946 TAAAATGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAAATATTTTAATTTATAT
Found at i:18713047 original size:19 final size:19
Alignment explanation
Indices: 18713025--18713062 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18713015 GAATAAAATA
*
18713025 AAAATAATATTTTAATATT
1 AAAATAATATATTAATATT
*
18713044 AAAATTATATATTAATATT
1 AAAATAATATATTAATATT
18713063 CAAGAGTCAG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATAATATATTAATATT
Found at i:18713613 original size:2 final size:2
Alignment explanation
Indices: 18713606--18713630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18713596 ATAAAAGGTG
18713606 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 A
18713631 GATGTATTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18714447 original size:58 final size:57
Alignment explanation
Indices: 18714361--18714689 Score: 405
Period size: 58 Copynumber: 5.7 Consensus size: 57
18714351 TTATGTAGAG
** * *
18714361 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAA-TTTGATTTTAAAGA
*
18714420 AAAATTGATAC-TTCAACTTTTCCTCAAAAACCT-TTTTTTGAAATTTTATTTTAAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAATTTGATTTTAAAGA
* * * *
18714477 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTTGATTTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAA-TTTGA-TTTTAAAGA
* * *
18714537 AAAATTGATACTTTTAACTTTTCTTCAAAAACCT-TTTTTTGAAATTTTATTTTAAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAATTTGATTTTAAAGA
** *
18714595 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTT-ATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTGATTTTAAAGA
*
18714651 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
18714690 TTATTTTTAT
Statistics
Matches: 236, Mismatches: 24, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
56 46 0.19
57 42 0.18
58 76 0.32
59 26 0.11
60 38 0.16
61 7 0.03
62 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.47
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTGATTTTAAAGA
Found at i:18714607 original size:118 final size:117
Alignment explanation
Indices: 18714361--18714690 Score: 494
Period size: 118 Copynumber: 2.8 Consensus size: 117
18714351 TTATGTAGAG
18714361 AAAATTGATACTTTCAACTTTTT-TTCAAAAATATTTTTTGAAAACTTTGA-TTTTCAAGGAAAA
1 AAAATTGATACTTTCAACTTTTTCTT-AAAAATATTTTTTGAAAA-TTTGATTTTTCAAGGAAAA
*
18714424 TTGATAC-TTCAACTTTTCCTCAAAAACCTTTTTTTGAAATTTTATTTTAAAGA
64 TTGATACTTTCAACTTTTCTTCAAAAACCTTTTTTTGAAATTTTATTTTAAAGA
18714477 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTTGATTTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAA-TTTGATTTTTCAAGGAAAAT
*
18714542 TGATACTTTTAACTTTTCTTCAAAAACCTTTTTTTGAAATTTTATTTTAAAGA
65 TGATACTTTCAACTTTTCTTCAAAAACCTTTTTTTGAAATTTTATTTTAAAGA
* * ** *
18714595 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTG-AAATTT-ATTTTT-AAGAAAAATT
1 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTGATTTTTCAAGGAAAATT
**
18714657 GATACTTTCAACTTTT-TCTCAAAAATATTTTTTT
66 GATACTTTCAACTTTTCT-TCAAAAACCTTTTTTT
18714691 TATTTTTATT
Statistics
Matches: 199, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
113 1 0.01
114 38 0.19
115 6 0.03
116 49 0.25
117 25 0.13
118 80 0.40
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.47
Consensus pattern (117 bp):
AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTGATTTTTCAAGGAAAATT
GATACTTTCAACTTTTCTTCAAAAACCTTTTTTTGAAATTTTATTTTAAAGA
Found at i:18714750 original size:6 final size:6
Alignment explanation
Indices: 18714722--18714799 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
18714712 ATAATAAAAC
* * * *
18714722 AAAATA AAAGTG AAAAT- -AAATA AAAATA AAAA-A ATAAAGA AAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA
* *
18714767 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
18714800 GAATATTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 4 0.07
5 10 0.18
6 40 0.71
7 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:18714757 original size:18 final size:18
Alignment explanation
Indices: 18714734--18714787 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
18714724 AATAAAAGTG
18714734 AAAATAAATAAAAATAAA
1 AAAATAAATAAAAATAAA
* *
18714752 AAAATAAAGAAAAGTAAA
1 AAAATAAATAAAAATAAA
*
18714770 ACAA-AAATAAAAATAAA
1 AAAATAAATAAAAATAAA
18714787 A
1 A
18714788 TAAAGATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAATAAATAAAAATAAA
Found at i:18714796 original size:17 final size:16
Alignment explanation
Indices: 18714704--18714799 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 16
18714694 TTTTATTTAA
18714704 AAAATAGAATAATAAAAC
1 AAAATA-AA-AATAAAAC
*
18714722 AAAATAAAAGTGAAAA-
1 AAAATAAAAAT-AAAAC
*
18714738 TAAATAAAAATAAAA-
1 AAAATAAAAATAAAAC
*
18714753 AAATAAAGAAAAGTAAAAC
1 AAA-ATA-AAAA-TAAAAC
*
18714772 AAAAATAAAAATAAAAT
1 -AAAATAAAAATAAAAC
18714789 AAAGATAAAAA
1 AAA-ATAAAAA
18714800 GAATATTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
15 6 0.09
16 16 0.25
17 22 0.34
18 15 0.23
19 2 0.03
20 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:18714798 original size:22 final size:21
Alignment explanation
Indices: 18714714--18714813 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 21
18714704 AAAATAGAAT
* *
18714714 AATAAAACAAAATAAAAGTGAA
1 AATAAAATAAAATAAAAAT-AA
*
18714736 AAT-AAATAAAAATAAAAAAATA
1 AATAAAAT-AAAATAAAAATA-A
* *
18714758 AAGAAAAGTAAAACAAAAATAAA
1 AATAAAA-TAAAATAAAAAT-AA
*
18714781 AATAAAATAAAGATAAAAAGAA
1 AATAAAATAAA-ATAAAAATAA
* *
18714803 TATTAAATAAA
1 AATAAAATAAA
18714814 CCTAATCTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
21 4 0.07
22 30 0.49
23 25 0.41
24 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
AATAAAATAAAATAAAAATAA
Found at i:18714800 original size:35 final size:32
Alignment explanation
Indices: 18714702--18714800 Score: 92
Period size: 35 Copynumber: 2.9 Consensus size: 32
18714692 ATTTTTATTT
*
18714702 AAAAAATAGAATAATAAAACAAAAT-AAAAGTGAA
1 AAAAAATA-AA-AATAAAA-AAAATAAAAAGTAAA
* *
18714736 AATAAATAAAAATAAAAAAATAAAGAAAAGTAAA
1 AAAAAATAAAAATAAAAAAA-ATA-AAAAGTAAA
18714770 ACAAAAATAAAAATAAAATAAAGATAAAAAG
1 A-AAAAATAAAAATAAAA-AAA-ATAAAAAG
18714801 AATATTAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 3 0.06
32 8 0.15
33 2 0.04
34 16 0.30
35 20 0.37
36 5 0.09
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (32 bp):
AAAAAATAAAAATAAAAAAAATAAAAAGTAAA
Found at i:18715742 original size:45 final size:43
Alignment explanation
Indices: 18715656--18715781 Score: 105
Period size: 44 Copynumber: 2.9 Consensus size: 43
18715646 AATTTCCAGC
* * *
18715656 CAGATAAATCAAAAAAA-TAAAAGAAAAATCAAACGAAAATAAA
1 CAGATAAATAAAAAAAATTAACAGAAAAATCAAAAGAAAAT-AA
* * **
18715699 TCAGATAAATAAAAAAAATTAACAGATAAATTAAAATTAAATAA
1 -CAGATAAATAAAAAAAATTAACAGAAAAATCAAAAGAAAATAA
* * * *
18715743 CAGATAATTACATAAATATTAACAGGAAAA--AAAAGAAAA
1 CAGATAAATA-AAAAAAATTAACAGAAAAATCAAAAGAAAA
18715782 AGAGAAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 7 0.11
43 9 0.14
44 33 0.50
45 17 0.26
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.18
Consensus pattern (43 bp):
CAGATAAATAAAAAAAATTAACAGAAAAATCAAAAGAAAATAA
Found at i:18715910 original size:7 final size:6
Alignment explanation
Indices: 18715872--18715929 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
18715862 TATATAAAAT
* *
18715872 AATAAT AATAAA AAT-AA AATAAA AATGTAAA ATACAAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AA--TAAA A-A-TAAA AATAAA AATAAA
18715923 AATAAA A
1 AATAAA A
18715930 TGAAGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 1 0.02
8 9 0.20
9 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:18715943 original size:39 final size:39
Alignment explanation
Indices: 18715867--18715944 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
18715857 ATACATATAT
* *
18715867 AAAATAATAATAATAAAAATAAAATAAAAATGTAAAATAC
1 AAAATAATAAAAATAAAAATAAAATAAAAA-GAAAAATAC
18715907 AAAA-AATAAAAATAAAAATAAAATGAAGAAA-AAAAATA
1 AAAATAATAAAAATAAAAATAAAAT-AA-AAAGAAAAATA
18715945 TATAGACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 25 0.74
40 6 0.18
41 3 0.09
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (39 bp):
AAAATAATAAAAATAAAAATAAAATAAAAAGAAAAATAC
Found at i:18716514 original size:125 final size:125
Alignment explanation
Indices: 18716141--18716630 Score: 723
Period size: 125 Copynumber: 3.9 Consensus size: 125
18716131 TCCTCTAGGT
* * * * * * * * *
18716141 AGAGGCTCAATGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTAAAAA
1 AGAGGCACCATGACTTTGAGAAA-GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT--AGA
* * *
18716206 AAATAAATTGCTCCTCTAAATAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAAC
63 AAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
* * *
18716269 AGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGAACCATGACTTT-GAAAG
1 AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTAGAAAG
*
18716332 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAAC
66 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
18716392 AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTAGAAAG
1 AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTAGAAAG
* * *
18716457 TAAATTGCTCCTCTAAATAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAAT
66 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
* *
18716517 AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCCAAACAGAGGCACCACGACTTTGGAAAA
1 AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTAG-AAA
* *
18716582 GTAAATTACTCCTCTAAACAGAGGCACCACGACTTTAAGAAAGTAAATT
65 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
18716631 ACTTTTTAAC
Statistics
Matches: 333, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
123 80 0.24
124 37 0.11
125 120 0.36
126 77 0.23
127 3 0.01
128 16 0.05
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (125 bp):
AGAGGCACCATGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTAGAAAG
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
Found at i:18716633 original size:42 final size:42
Alignment explanation
Indices: 18716152--18716630 Score: 698
Period size: 42 Copynumber: 11.5 Consensus size: 42
18716142 GAGGCTCAAT
* * * * *
18716152 GACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAAC
1 GACTTTGAGAAA-GTAAATTGCTCCTCTAAACAGAGGCACCAC
* * * * *
18716195 AACTTTAAAAAAAATAAATTGCTCCTCTAAATAGAGGCACCAC
1 GACTTT-GAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
18716238 GACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
18716280 GACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGAACCAT
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
18716321 GACTTT--GAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
18716361 GACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
18716403 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
18716445 GACTTT-AGAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* * *
18716486 GACTTTTAGAAAGTAAATTGCTCCTCTAAATAGAGGCACCAT
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
18716528 GACTTTGAGAAAGTAAATTGCTCCTCCAAACAGAGGCACCAC
1 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
18716570 GACTTTG-GAAAAGTAAATTACTCCTCTAAACAGAGGCACCAC
1 GACTTTGAG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
18716612 GACTTTAAGAAAGTAAATT
1 GACTTTGAGAAAGTAAATT
18716631 ACTTTTTAAC
Statistics
Matches: 398, Mismatches: 31, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
40 37 0.09
41 78 0.20
42 243 0.61
43 36 0.09
44 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
Found at i:18717916 original size:14 final size:14
Alignment explanation
Indices: 18717878--18717941 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
18717868 CAGGTTTTTT
18717878 TTCTTTTTTT-TCA
1 TTCTTTTTTTCTCA
18717891 TT-TTCTCATTTTCTCA
1 TTCTT-T--TTTTCTCA
18717907 TTCTTTTTTTCT--
1 TTCTTTTTTTCTCA
18717919 TT-TTTTTTTCATCA
1 TTCTTTTTTTC-TCA
18717933 -TCTTTTTTT
1 TTCTTTTTTT
18717942 TTCTTTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 17
0.71 0.00 0.29
Matches are distributed among these distances:
11 8 0.19
12 5 0.12
13 4 0.10
14 13 0.31
15 4 0.10
16 6 0.14
17 2 0.05
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (14 bp):
TTCTTTTTTTCTCA
Found at i:18717927 original size:25 final size:24
Alignment explanation
Indices: 18717899--18717960 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
18717889 CATTTTCTCA
*
18717899 TTTTCTCATTCTTTTTTTCTTTTTT
1 TTTTCTCATTCTTTTTTT-TTTCTT
18717924 TTTTCATCA-TC-TTTTTTTTTCTT
1 TTTTC-TCATTCTTTTTTTTTTCTT
18717947 TTTTCTCATT-TTTT
1 TTTTCTCATTCTTTT
18717961 AACCATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 3 0.09
23 14 0.42
24 6 0.18
25 7 0.21
26 3 0.09
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTCATTCTTTTTTTTTTCTT
Found at i:18717933 original size:26 final size:26
Alignment explanation
Indices: 18717899--18717950 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
18717889 CATTTTCTCA
18717899 TTTTCTCAT-TCTTTTTTTCTTTTTT
1 TTTTCTCATCTCTTTTTTTCTTTTTT
*
18717924 TTTTCATCATCTTTTTTTTTCTTTTTT
1 TTTTC-TCATCTCTTTTTTTCTTTTTT
18717951 CTCATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 15 0.62
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTCTCATCTCTTTTTTTCTTTTTT
Found at i:18718308 original size:15 final size:15
Alignment explanation
Indices: 18718285--18718317 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
18718275 ATGTGTGGCA
18718285 TTTATTTTTATTTTAT
1 TTTATTTTTA-TTTAT
18718301 TTTA-TTTTATTTAT
1 TTTATTTTTATTTAT
18718315 TTT
1 TTT
18718318 TGAGACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:18718315 original size:4 final size:5
Alignment explanation
Indices: 18718285--18718317 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
18718275 ATGTGTGGCA
18718285 TTTATT TTTAT TTTAT TTTAT TTTA- TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
18718318 TGAGACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:18721908 original size:59 final size:57
Alignment explanation
Indices: 18721843--18722237 Score: 470
Period size: 59 Copynumber: 6.7 Consensus size: 57
18721833 TTTATGCAGA
* * *
18721843 AAAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAA-TTTGATTTTAAAG
* *
18721902 AAAAATTGATACTTTCAAATTTTCCTCAAAAATATTTTTTGGAAATTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAA-TTTGATTTTAAAG
* * *
18721961 AAAAATTGATACTTTCAATTTTTCCTCAAAAATCTTTTTTTGAAATTTTATTTTAAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAATTTGATTTTAAAG
** *
18722019 AAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTT-ATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTGATTTTAAAG
* * * * * *
18722075 GAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTTTTTAAATTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA-----TATTTTTTGAAATTTGATTTTAAAG
*
18722137 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGGAAACTTTGATTTTAAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT-GAAA-TTTGATTTTAAAG
*
18722198 GAAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTT
18722238 TTTATTTTTA
Statistics
Matches: 299, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
56 38 0.13
57 14 0.05
58 42 0.14
59 101 0.34
60 11 0.04
61 53 0.18
62 40 0.13
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTGATTTTAAAG
Found at i:18722295 original size:16 final size:15
Alignment explanation
Indices: 18722251--18722411 Score: 69
Period size: 16 Copynumber: 9.9 Consensus size: 15
18722241 ATTTTTATTT
18722251 TAAAA-AAATAGAATAA
1 TAAAATAAATA-AA-AA
* *
18722267 TAAAACAAAATAAAAG
1 TAAAA-TAAATAAAAA
18722283 TGAAAATAAATAAAAA
1 T-AAAATAAATAAAAA
*
18722299 TAAAATAAAAAAGAAAA
1 TAAAAT-AAATA-AAAA
*
18722316 GTAAAACAAAAATAAAAA
1 -T-AAA-ATAAATAAAAA
18722334 TAAAATAAAGATAAAAA
1 TAAAAT-AA-ATAAAAA
* *
18722351 GAATATTAAATAAACCTAA
1 TAA-AATAAATAAA---AA
**
18722370 TCTAATAAAT-AAAA
1 TAAAATAAATAAAAA
18722384 -AAAATAAATAAACAA
1 TAAAATAAATAAA-AA
18722399 -ATAAATAAATAAA
1 TA-AAATAAATAAA
18722412 TTCAAAAAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
13 7 0.06
14 4 0.04
15 9 0.08
16 41 0.36
17 24 0.21
18 18 0.16
19 9 0.08
20 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
TAAAATAAATAAAAA
Found at i:18722301 original size:6 final size:6
Alignment explanation
Indices: 18722273--18722350 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
18722263 ATAATAAAAC
* *
18722273 AAAATA AAAGTG AAAAT- -AAATA AAAAT- AAAATA AAAA-A GAAAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA -AAAA-TA
* *
18722318 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
18722351 GAATATTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.07
5 11 0.19
6 42 0.74
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:18722305 original size:5 final size:5
Alignment explanation
Indices: 18722265--18722349 Score: 59
Period size: 5 Copynumber: 16.4 Consensus size: 5
18722255 AAAATAGAAT
*
18722265 AATAA AACAA AATAA AAGTGAA AAT-A AATAAA AATAA AATAA AA-AA
1 AATAA AATAA AATAA AA-T-AA AATAA AAT-AA AATAA AATAA AATAA
* * *
18722311 GA-AA AGTAA AACAAA AATAAA AATAA AATAA AGATAA AA
1 AATAA AATAA AA-TAA AAT-AA AATAA AATAA A-ATAA AA
18722350 AGAATATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 9 0.14
5 31 0.48
6 20 0.31
7 4 0.06
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:18722306 original size:11 final size:11
Alignment explanation
Indices: 18722255--18722349 Score: 79
Period size: 11 Copynumber: 8.4 Consensus size: 11
18722245 TTATTTTAAA
18722255 AAAATAGAATAAT
1 AAAATA-AA-AAT
*
18722268 AAAA-CAAAAT
1 AAAATAAAAAT
*
18722278 AAAAGTGAAAAT
1 AAAA-TAAAAAT
18722290 -AAATAAAAAT
1 AAAATAAAAAT
*
18722300 AAAATAAAAAAG
1 AAAAT-AAAAAT
18722312 AAAAGTAAAACA-
1 AAAA-TAAAA-AT
18722324 AAAATAAAAAT
1 AAAATAAAAAT
*
18722335 AAAATAAAGAT
1 AAAATAAAAAT
18722346 AAAA
1 AAAA
18722350 AGAATATTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
10 14 0.20
11 28 0.40
12 22 0.31
13 6 0.09
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:18722310 original size:22 final size:22
Alignment explanation
Indices: 18722255--18722407 Score: 77
Period size: 22 Copynumber: 6.9 Consensus size: 22
18722245 TTATTTTAAA
*
18722255 AAAATAGAATAATAAA-ACAAAAT
1 AAAATA-AAAAATAAATA-AAAAT
*
18722278 AAAAGT-GAAAATAAATAAAAAT
1 AAAA-TAAAAAATAAATAAAAAT
*
18722300 AAAATAAAAAAGAAAAGTAAAACA-
1 AAAATAAAAAA-TAAA-TAAAA-AT
*
18722324 AAAAT-AAAAATAAAATAAAGAT
1 AAAATAAAAAAT-AAATAAAAAT
* * **
18722346 AAAA-AGAATATTAAATAAACCT
1 AAAATA-AAAAATAAATAAAAAT
** *
18722368 AATCTAATAAATAAA-AAAAAT
1 AAAATAAAAAATAAATAAAAAT
18722389 -AAATAAACAAATAAATAAA
1 AAAATAAA-AAATAAATAAA
18722408 TAAATTCAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
20 4 0.04
21 13 0.13
22 47 0.48
23 21 0.22
24 11 0.11
25 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.18
Consensus pattern (22 bp):
AAAATAAAAAATAAATAAAAAT
Found at i:18722321 original size:40 final size:38
Alignment explanation
Indices: 18722252--18722350 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 38
18722242 TTTTTATTTT
* **
18722252 AAAAAAATAGAATAATAAAACAAAATAAAAGTGAAAATAA
1 AAAAAAATAAAATAA-AAAACAAAATAAAA-CAAAAATAA
* *
18722292 ATAAAAATAAAATAAAAAAGAAAAGTAAAACAAAAATAA
1 AAAAAAATAAAATAAAAAACAAAA-TAAAACAAAAATAA
18722331 AAATAAAATAAAGATAAAAA
1 AAA-AAAATAAA-ATAAAAA
18722351 GAATATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
39 17 0.34
40 26 0.52
41 7 0.14
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (38 bp):
AAAAAAATAAAATAAAAAACAAAATAAAACAAAAATAA
Found at i:18722351 original size:35 final size:33
Alignment explanation
Indices: 18722252--18722351 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 33
18722242 TTTTTATTTT
* *
18722252 AAAAAAATAGAATAATAAAACAAAAT-AAAAGTGA
1 AAAAAAATA-AA-AATAAAATAAAATAAAAAGTAA
* *
18722286 AAATAAATAAAAATAAAATAAAAAAGAAAAGTAA
1 AAAAAAATAAAAATAAAATAAAATA-AAAAGTAA
18722320 AACAAAAATAAAAATAAAATAAAGATAAAAAG
1 AA-AAAAATAAAAATAAAATAAA-ATAAAAAG
18722352 AATATTAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
32 11 0.20
33 2 0.04
34 17 0.30
35 24 0.43
36 2 0.04
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (33 bp):
AAAAAAATAAAAATAAAATAAAATAAAAAGTAA
Found at i:18722380 original size:4 final size:4
Alignment explanation
Indices: 18722373--18722412 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
18722363 AACCTAATCT
* *
18722373 AATA AATAA AAAA AATA AATA AACA AATA AATA AATA AAT
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AAT
18722413 TCAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:18723484 original size:27 final size:26
Alignment explanation
Indices: 18723438--18723517 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 26
18723428 ATACACATAT
*
18723438 AAAATAATAAT-AATAAAAATAAAATA
1 AAAATAA-AATGAAGAAAAATAAAATA
18723464 AAAATGTAAAAT-ACA-AAAAATAAAAATA
1 AAAA--TAAAATGA-AGAAAAAT-AAAATA
18723492 AAAATAAAATGAAGAAAAATAAAATA
1 AAAATAAAATGAAGAAAAATAAAATA
18723518 TAGATTTACC
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
26 17 0.35
27 17 0.35
28 14 0.29
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (26 bp):
AAAATAAAATGAAGAAAAATAAAATA
Found at i:18723495 original size:21 final size:20
Alignment explanation
Indices: 18723438--18723515 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
18723428 ATACACATAT
* *
18723438 AAAATAATAATAATAAA-AAT
1 AAAATAAAAATAA-AAATAAA
*
18723458 AAAATAAAAATGTAAAATACAA
1 AAAATAAAAAT-AAAAATA-AA
18723480 AAAATAAAAATAAAAATAAA
1 AAAATAAAAATAAAAATAAA
* *
18723500 ATGAAGAAAAATAAAA
1 A-AAATAAAAATAAAA
18723516 TATAGATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 16 0.33
21 20 0.42
22 12 0.25
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATAAAAATAAA
Found at i:18723515 original size:6 final size:6
Alignment explanation
Indices: 18723443--18723500 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
18723433 CATATAAAAT
* *
18723443 AATAAT AATAAA AAT-AA AATAAA AATGTAAA ATACAAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AA--TAAA A-A-TAAA AATAAA AATAAA
18723494 AATAAA A
1 AATAAA A
18723501 TGAAGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 1 0.02
8 9 0.20
9 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:18723516 original size:20 final size:19
Alignment explanation
Indices: 18723436--18723517 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 19
18723426 ATATACACAT
*
18723436 ATAAAATAATAATAATAAAA
1 ATAAAATAA-AATAAGAAAA
* *
18723456 ATAAAATAAAA-ATGTAAA
1 ATAAAATAAAATAAGAAAA
* *
18723474 ATACAA-AAAATAA-AAAT
1 ATAAAATAAAATAAGAAAA
18723491 A-AAAATAAAATGAAGAAAA
1 ATAAAATAAAAT-AAGAAAA
18723510 ATAAAATA
1 ATAAAATA
18723518 TAGATTTACC
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
16 3 0.06
17 12 0.25
18 12 0.25
19 6 0.12
20 15 0.31
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.20
Consensus pattern (19 bp):
ATAAAATAAAATAAGAAAA
Found at i:18725947 original size:19 final size:19
Alignment explanation
Indices: 18725923--18725959 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
18725913 GTAAGGTTAG
18725923 GATTTCTTTTATGTAATAA
1 GATTTCTTTTATGTAATAA
18725942 GATTTCTTTTATGTAATA
1 GATTTCTTTTATGTAATA
18725960 GGATAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (19 bp):
GATTTCTTTTATGTAATAA
Found at i:18726835 original size:18 final size:20
Alignment explanation
Indices: 18726804--18726849 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
18726794 AAAAAAAGTG
*
18726804 GAAAAAAAAGAGAAAAT-AT
1 GAAAATAAAGAGAAAATAAT
18726823 GAAAATAAA-AGAAAATAAT
1 GAAAATAAAGAGAAAATAAT
*
18726842 GATAATAA
1 GAAAATAA
18726850 TGAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (20 bp):
GAAAATAAAGAGAAAATAAT
Found at i:18726837 original size:28 final size:27
Alignment explanation
Indices: 18726805--18726864 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
18726795 AAAAAAGTGG
*
18726805 AAAAAAAAGAGAAAAT-ATGAAAATAA
1 AAAAAAAAAAGAAAATAATGAAAATAA
* * *
18726831 AAGAAAATAATGATAATAATGAAAATAA
1 AA-AAAAAAAAGAAAATAATGAAAATAA
18726859 AAAAAA
1 AAAAAA
18726865 TATAAAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (27 bp):
AAAAAAAAAAGAAAATAATGAAAATAA
Found at i:18726850 original size:9 final size:9
Alignment explanation
Indices: 18726815--18726858 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
18726805 AAAAAAAAGA
18726815 GAAAAT-AT
1 GAAAATAAT
*
18726823 GAAAATAAAA
1 GAAAAT-AAT
18726833 GAAAATAAT
1 GAAAATAAT
*
18726842 GATAATAAT
1 GAAAATAAT
18726851 GAAAATAA
1 GAAAATAA
18726859 AAAAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 6 0.20
9 17 0.57
10 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (9 bp):
GAAAATAAT
Found at i:18726854 original size:18 final size:19
Alignment explanation
Indices: 18726804--18726858 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
18726794 AAAAAAAGTG
*
18726804 GAAAAAAAAGAGAAAAT-AT
1 GAAAATAAA-AGAAAATAAT
18726823 GAAAATAAAAGAAAATAAT
1 GAAAATAAAAGAAAATAAT
* *
18726842 GATAAT-AATGAAAATAA
1 GAAAATAAAAGAAAATAA
18726859 AAAAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (19 bp):
GAAAATAAAAGAAAATAAT
Found at i:18727625 original size:63 final size:63
Alignment explanation
Indices: 18727470--18727628 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 63
18727460 TTAATGGATA
* ** * *
18727470 AAATTTGTTTTAAAATGATTAGTGCTAAGAAACCTATAAGTGGTGACCCAATGATGGAAGACG
1 AAATTTGTTCTAAAATGGCTAGTGCTAAGAAGCCTATAAGTGGTGACCCAATGATGAAAGACG
** * * *
18727533 AAATTTGTTCTGGAATAGCTAATGCTAAGAAGCCTATGAGTGGTGA-CCAAGTGAT-AAATGAC-
1 AAATTTGTTCTAAAATGGCTAGTGCTAAGAAGCCTATAAGTGGTGACCCAA-TGATGAAA-GACG
* *
18727595 AGAATTTATTCTAAAATGGCTAGTGTTAAGAAGC
1 A-AATTTGTTCTAAAATGGCTAGTGCTAAGAAGC
18727629 TTAAAATGGT
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
62 7 0.09
63 70 0.91
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (63 bp):
AAATTTGTTCTAAAATGGCTAGTGCTAAGAAGCCTATAAGTGGTGACCCAATGATGAAAGACG
Found at i:18727980 original size:22 final size:22
Alignment explanation
Indices: 18727952--18727997 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
18727942 GTCCTAAATC
* *
18727952 TTCAAATGAGAATATTTGAGTT
1 TTCAAATAAGAATATTTGAATT
18727974 TTCAAATAAGAATATTTGAATT
1 TTCAAATAAGAATATTTGAATT
18727996 TT
1 TT
18727998 TGAGTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (22 bp):
TTCAAATAAGAATATTTGAATT
Found at i:18728000 original size:30 final size:30
Alignment explanation
Indices: 18727961--18728027 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
18727951 CTTCAAATGA
*
18727961 GAATATTTGAGTTTTCAAAT-AAGAATATTT
1 GAATTTTTGAGTTTTCAAATGAA-AATATTT
* *
18727991 GAATTTTTGAGTTTTCAAATGAAAGTTTTT
1 GAATTTTTGAGTTTTCAAATGAAAATATTT
18728021 GAATTTT
1 GAATTTT
18728028 AAATGAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (30 bp):
GAATTTTTGAGTTTTCAAATGAAAATATTT
Found at i:18728040 original size:21 final size:22
Alignment explanation
Indices: 18727991--18728041 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
18727981 AAGAATATTT
*
18727991 GAATTTTTGAGTTTTCAAATGA
1 GAATTTTTGAATTTTCAAATGA
18728013 -AAGTTTTTGAATTTT-AAATGA
1 GAA-TTTTTGAATTTTCAAATGA
18728034 GAATTTTT
1 GAATTTTT
18728042 AAGAAGAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
GAATTTTTGAATTTTCAAATGA
Found at i:18728630 original size:42 final size:41
Alignment explanation
Indices: 18728513--18728671 Score: 194
Period size: 41 Copynumber: 3.9 Consensus size: 41
18728503 TATGATTATT
* * * *
18728513 GAGGAACATTTATTTTTT-AAAGTTGTGGTGCCTCTATTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGATACCTCTATTTA
* * *
18728553 TAGGAGCATTTATTTTTTCAAAGTTATGGTACCTCTGTTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGATACCTCTATTTA
* *
18728594 GAGGAGCATTTATTTTTTTAAAAGTTATGATGCCTCTATTTA
1 GAGGAGCATTTA-TTTTTTCAAAGTTATGATACCTCTATTTA
* * *
18728636 GAGAAGTATTTATTTTTTCAAAGTTATTATACCTCT
1 GAGGAGCATTTATTTTTTCAAAGTTATGATACCTCT
18728672 GATTAGAAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 16 0.16
41 51 0.50
42 35 0.34
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (41 bp):
GAGGAGCATTTATTTTTTCAAAGTTATGATACCTCTATTTA
Found at i:18728650 original size:83 final size:81
Alignment explanation
Indices: 18728513--18728678 Score: 233
Period size: 83 Copynumber: 2.0 Consensus size: 81
18728503 TATGATTATT
* * * *
18728513 GAGGAACATTTATTTTTTAAAGTTGTGGTGCCTCTATTTATAGGAGCATTTATTTTTTCAAAGTT
1 GAGGAACATTTATTTTTTAAAGTTATGATGCCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTT
* *
18728578 ATGGTACCTCTGTTTA
66 ATGATACCTCTGATTA
* *
18728594 GAGGAGCATTTATTTTTTTAAAAGTTATGATGCCTCTATTTAGAGAAGTATTTATTTTTTCAAAG
1 GAGGAACATTTA-TTTTTT-AAAGTTATGATGCCTCTATTTAGAGAAGCATTTATTTTTTCAAAG
*
18728659 TTATTATACCTCTGATTA
64 TTATGATACCTCTGATTA
18728677 GA
1 GA
18728679 AAAACTTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 11 0.15
82 6 0.08
83 57 0.77
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (81 bp):
GAGGAACATTTATTTTTTAAAGTTATGATGCCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTT
ATGATACCTCTGATTA
Found at i:18728690 original size:42 final size:42
Alignment explanation
Indices: 18728560--18728693 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
18728550 TTATAGGAGC
* * * *
18728560 ATTTATTTTTTCAAAGTTATGGTACCTCTGTTTAGAGGAGC-
1 ATTTATTTTTTCAAAGTTATGATACCTCTGATTAGAAGAACT
* * *
18728601 ATTTATTTTTTTAAAAGTTATGATGCCTCT-ATTTAG-AGAAGT
1 ATTTA-TTTTTTCAAAGTTATGATACCTCTGA-TTAGAAGAACT
* *
18728643 ATTTATTTTTTCAAAGTTATTATACCTCTGATTAGAAAAACT
1 ATTTATTTTTTCAAAGTTATGATACCTCTGATTAGAAGAACT
*
18728685 TTTTATTTT
1 ATTTATTTT
18728694 GCTAGGTTGT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
41 32 0.43
42 43 0.57
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.49
Consensus pattern (42 bp):
ATTTATTTTTTCAAAGTTATGATACCTCTGATTAGAAGAACT
Found at i:18730049 original size:194 final size:195
Alignment explanation
Indices: 18729641--18730049 Score: 540
Period size: 194 Copynumber: 2.1 Consensus size: 195
18729631 TTGCATGACT
* * * *
18729641 AAAATTAAAAAA-AAAATAAA-AAAATAAATTTTGAGAATAAATATTAATGATCCAATGATGGAA
1 AAAATAAAAAAATAAAAAAAATAAAATAAATTTTGAGAACAAATATTAATGATCCAATGATGAAA
* * * * *
18729704 TTGTTAGAATTTTCAAATGGTAAATTTTTACAAAATTTTTAGGTGAAAAATTTTGTGTAAATTTG
66 TTGTTAGAATTTTCAAATGGTAAATTTCTACAAAATTCTTAGATGAAAAATTTTGTCTAAATTTA
* *
18729769 TCTCAAATGGTAGAATAATTAAGATAAAATTTTAATAACAATAATTAATATTTATTTTCAAACAT
131 TCCCAAATGGTAGAATAATTAAGATAAAATTTTAATAACAATAATTAATATTTATTTTCAAACAA
* * * *
18729834 AAAATAAAAAAATACAAAAAATAAAAT-ATTTTTTAGAACAAATATTAATTATCCAATGATGAAA
1 AAAATAAAAAAATAAAAAAAATAAAATAAATTTTGAGAACAAATATTAATGATCCAATGATGAAA
* * * *
18729898 TTTTTAAGAATTTT-AAATGGTAAATTTCTATAAAATTCTTAGATGAGAAATTTTTTCTAAATTT
66 TTGTT-AGAATTTTCAAATGGTAAATTTCTACAAAATTCTTAGATGAAAAATTTTGTCTAAATTT
* * * * *
18729962 ATCCCAAATTGT-GAAATAATTTAGATAAAGTTTTAATAATAATAATTAATATTTATTTTCAAAT
130 ATCCCAAATGGTAG-AATAATTAAGATAAAATTTTAATAACAATAATTAATATTTATTTTCAAAC
18730026 AA
194 AA
*
18730028 AAAATAAAAAGATAAAAAAAAT
1 AAAATAAAAAAATAAAAAAAAT
18730050 TTGGTTGAAA
Statistics
Matches: 186, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
193 12 0.06
194 161 0.87
195 13 0.07
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (195 bp):
AAAATAAAAAAATAAAAAAAATAAAATAAATTTTGAGAACAAATATTAATGATCCAATGATGAAA
TTGTTAGAATTTTCAAATGGTAAATTTCTACAAAATTCTTAGATGAAAAATTTTGTCTAAATTTA
TCCCAAATGGTAGAATAATTAAGATAAAATTTTAATAACAATAATTAATATTTATTTTCAAACAA
Found at i:18733919 original size:40 final size:46
Alignment explanation
Indices: 18733845--18733959 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 46
18733835 ATTATATATA
* * *
18733845 TTATATT-AATAATATTATTATTTAATATTTTAATTTAAGATTAAT
1 TTATATTAAAAAATATTATTATTTAATATTATAATTAAAGATTAAT
**
18733890 TTA-A-T-AAAAATATTA-TATTT-ATA-TATAATTAAATTTTAAT
1 TTATATTAAAAAATATTATTATTTAATATTATAATTAAAGATTAAT
*
18733930 TTATATTAAAAAATATT-TTA-TAAATATTAT
1 TTATATTAAAAAATATTATTATTTAATATTAT
18733960 GTTAAATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
40 16 0.28
41 4 0.07
42 7 0.12
43 24 0.41
44 4 0.07
45 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (46 bp):
TTATATTAAAAAATATTATTATTTAATATTATAATTAAAGATTAAT
Found at i:18733947 original size:22 final size:23
Alignment explanation
Indices: 18733895--18733949 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
18733885 TTAATTTAAT
*
18733895 AAAAATATTAT-ATTTATATATA
1 AAAAATATTTTAATTTATATATA
**
18733917 ATTAA-ATTTTAATTTATAT-TA
1 AAAAATATTTTAATTTATATATA
18733938 AAAAATATTTTA
1 AAAAATATTTTA
18733950 TAAATATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAAATATTTTAATTTATATATA
Found at i:18735931 original size:31 final size:31
Alignment explanation
Indices: 18735893--18735953 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
18735883 CCACCACTTT
18735893 GATAAGTTCAGATACCACGAACAAAGTGTTC
1 GATAAGTTCAGATACCACGAACAAAGTGTTC
18735924 GATAAGTTCAGATACCACGAACAAAGTGTT
1 GATAAGTTCAGATACCACGAACAAAGTGTT
18735954 TGGTCCTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (31 bp):
GATAAGTTCAGATACCACGAACAAAGTGTTC
Found at i:18736660 original size:14 final size:15
Alignment explanation
Indices: 18736596--18736660 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 15
18736586 TTAATTTTAT
* *
18736596 TTATTAATTAATATA
1 TTATTAATTAAAAAA
*
18736611 TT-TTAAATCTATAAAA
1 TTATT-AAT-TAAAAAA
18736627 TTATTAATT-AAAAA
1 TTATTAATTAAAAAA
18736641 TTATTATTATTAAAAAA
1 TTATTA--ATTAAAAAA
18736658 TTA
1 TTA
18736661 AAAAATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.30
15 6 0.15
16 12 0.30
17 10 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTAATTAAAAAA
Found at i:18736660 original size:17 final size:14
Alignment explanation
Indices: 18736596--18736656 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 14
18736586 TTAATTTTAT
*
18736596 TTATTAATTAATATA
1 TTATTAATTAA-AAA
18736611 TT-TTAAATCTATAAAA
1 TTATT-AAT-TA-AAAA
18736627 TTATTAATTAAAAA
1 TTATTAATTAAAAA
18736641 TTATTATTATTAAAAA
1 TTATTA--ATTAAAAA
18736657 ATTAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 12 0.31
15 7 0.18
16 17 0.44
17 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATTAATTAAAAA
Found at i:18736664 original size:24 final size:21
Alignment explanation
Indices: 18736632--18736676 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
18736622 TAAAATTATT
18736632 AATTAAAAATTATTATTATTAAAA
1 AATTAAAAA--ATTA-TATTAAAA
18736656 AATTAAAAAATTATATTAAAA
1 AATTAAAAAATTATATTAAAA
18736677 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 4 0.19
24 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAAAAAATTATATTAAAA
Found at i:18739388 original size:14 final size:15
Alignment explanation
Indices: 18739369--18739402 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
18739359 AGATAATTTA
18739369 ATATTTTTTA-AAAT
1 ATATTTTTTATAAAT
18739383 ATATTTTTTATAAAT
1 ATATTTTTTATAAAT
18739398 A-ATTT
1 ATATTT
18739403 AAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTTTATAAAT
Found at i:18739532 original size:15 final size:16
Alignment explanation
Indices: 18739507--18739552 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
18739497 TAATAAATAT
18739507 TATATGATAAT-TATGTA
1 TATATG-TAATATA-GTA
18739524 TAT-TGTAATATAGTA
1 TATATGTAATATAGTA
18739539 TATATGTAAATATA
1 TATATGT-AATATA
18739553 TGATTAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.38
16 7 0.27
17 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
TATATGTAATATAGTA
Found at i:18739550 original size:17 final size:17
Alignment explanation
Indices: 18739507--18739552 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
18739497 TAATAAATAT
*
18739507 TATATGATAATTAT-GTA
1 TATATG-TAAATATAGTA
18739524 TAT-TGT-AATATAGTA
1 TATATGTAAATATAGTA
18739539 TATATGTAAATATA
1 TATATGTAAATATA
18739553 TGATTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 5 0.20
17 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TATATGTAAATATAGTA
Found at i:18740441 original size:17 final size:16
Alignment explanation
Indices: 18740414--18740446 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
18740404 TTCAGTTTTC
18740414 TTTTACAAGATTATTT
1 TTTTACAAGATTATTT
18740430 TTTTATCAAGATTATTT
1 TTTTA-CAAGATTATTT
18740447 AATCTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTACAAGATTATTT
Found at i:18743324 original size:20 final size:21
Alignment explanation
Indices: 18743287--18743339 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
18743277 ACCCGAAATT
18743287 AATA-AAAATATTATTTTTTA
1 AATATAAAATATTATTTTTTA
18743307 AATATAAAATATTATTTTTTA
1 AATATAAAATATTATTTTTTA
18743328 AATAT-AAATATT
1 AATATAAAATATT
18743340 TAAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATAAAATATTATTTTTTA
Found at i:18743348 original size:30 final size:31
Alignment explanation
Indices: 18743312--18743370 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
18743302 TTTTAAATAT
* *
18743312 AAAATATTATTTTTTAAAT-ATAAATATTTA
1 AAAATATTATTATATAAATAATAAATATTTA
18743342 AAAATATTATTATATAAATAAATAAATAT
1 AAAATATTATTATATAAAT-AATAAATAT
18743371 AAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.68
32 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATATTATTATATAAATAATAAATATTTA
Found at i:18743370 original size:14 final size:14
Alignment explanation
Indices: 18743353--18743380 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18743343 AAATATTATT
18743353 ATATAAATAAATAA
1 ATATAAATAAATAA
18743367 ATATAAATAAATAA
1 ATATAAATAAATAA
18743381 TTAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATATAAATAAATAA
Found at i:18743403 original size:15 final size:16
Alignment explanation
Indices: 18743356--18743397 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
18743346 TATTATTATA
*
18743356 TAAATAAATAAAT-A-
1 TAAATAAATAATTAAT
18743370 TAAATAAATAATTAAT
1 TAAATAAATAATTAAT
18743386 TAAA-AAATAATT
1 TAAATAAATAATT
18743398 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATAAATAATTAAT
Found at i:18744209 original size:17 final size:16
Alignment explanation
Indices: 18744182--18744213 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
18744172 CCAATTTTTT
18744182 TTTACAAAATTGTTTC
1 TTTACAAAATTGTTTC
18744198 TTTACTAAAATTGTTT
1 TTTAC-AAAATTGTTT
18744214 AATCTTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTACAAAATTGTTTC
Found at i:18746467 original size:15 final size:16
Alignment explanation
Indices: 18746447--18746477 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
18746437 TATATAAAAA
18746447 TTAATTTT-TATTTAT
1 TTAATTTTATATTTAT
18746462 TTAATTTTATATTTAT
1 TTAATTTTATATTTAT
18746478 ATATAATATA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAATTTTATATTTAT
Found at i:18746503 original size:26 final size:25
Alignment explanation
Indices: 18746481--18746533 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
18746471 TATTTATATA
18746481 TAATATATTAA-TAAAATTATTATT
1 TAATATATTAATTAAAATTATTATT
*
18746505 TAATATTTTAATTTAAAATTA--ATT
1 TAATATATTAA-TTAAAATTATTATT
18746529 TAATA
1 TAATA
18746534 CAAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 18 0.69
26 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATATATTAATTAAAATTATTATT
Found at i:18747238 original size:2 final size:2
Alignment explanation
Indices: 18747231--18747256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18747221 AAGGTAAAAG
18747231 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
18747257 TGGGCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18749381 original size:6 final size:6
Alignment explanation
Indices: 18749358--18749400 Score: 50
Period size: 6 Copynumber: 6.5 Consensus size: 6
18749348 TGATGAGATC
18749358 TTTTAA TTTATCAA TTTTAA TTTTTAA TTTTAA TTTTTAA TTT
1 TTTTAA TTT-T-AA TTTTAA -TTTTAA TTTTAA -TTTTAA TTT
18749401 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 14 0.42
7 14 0.42
8 5 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:18749384 original size:7 final size:7
Alignment explanation
Indices: 18749358--18749413 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
18749348 TGATGAGATC
18749358 TTTTAAT
1 TTTTAAT
*
18749365 TTATCAA-
1 TT-TTAAT
18749372 TTTTAAT
1 TTTTAAT
18749379 TTTTAA-
1 TTTTAAT
18749385 TTTTAAT
1 TTTTAAT
18749392 TTTTAAT
1 TTTTAAT
*
18749399 TTATTTAT
1 TT-TTAAT
18749407 TTTTAAT
1 TTTTAAT
18749414 AAAAAATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 9 0.22
7 23 0.56
8 9 0.22
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAT
Found at i:18749388 original size:13 final size:13
Alignment explanation
Indices: 18749358--18749400 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
18749348 TGATGAGATC
*
18749358 TTTTAATTTATCAA
1 TTTTAATTT-TTAA
18749372 TTTTAATTTTTAA
1 TTTTAATTTTTAA
18749385 TTTTAATTTTTAA
1 TTTTAATTTTTAA
18749398 TTT
1 TTT
18749401 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:18749865 original size:27 final size:27
Alignment explanation
Indices: 18749826--18749882 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
18749816 TTAATTAATA
*
18749826 ATTTTTTTAAAAAATTAATTTTTATAT
1 ATTTTTTTAAAAAATTAATATTTATAT
*
18749853 ATTTATTTT-AAAAATTAATATTTATTT
1 ATTT-TTTTAAAAAATTAATATTTATAT
18749880 ATT
1 ATT
18749883 AATAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTTTTTAAAAAATTAATATTTATAT
Found at i:18750379 original size:11 final size:11
Alignment explanation
Indices: 18750363--18750424 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
18750353 TAATTTTAAA
18750363 TTATGTTATTT
1 TTATGTTATTT
18750374 TTATGTCTTATTT
1 TTATG--TTATTT
* *
18750387 TTATATTATAT
1 TTATGTTATTT
*
18750398 TTATGTCGTATTA
1 TTATGT--TATTT
*
18750411 TTATGTTATAT
1 TTATGTTATTT
18750422 TTA
1 TTA
18750425 AAATTATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 21 0.52
13 19 0.47
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (11 bp):
TTATGTTATTT
Found at i:18750390 original size:24 final size:24
Alignment explanation
Indices: 18750362--18750424 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
18750352 ATAATTTTAA
* *
18750362 ATTATGTTATTTTTATGTCTTATT
1 ATTATGTTATATTTATGTCGTATT
* *
18750386 TTTATATTATATTTATGTCGTATT
1 ATTATGTTATATTTATGTCGTATT
18750410 ATTATGTTATATTTA
1 ATTATGTTATATTTA
18750425 AAATTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.63
Consensus pattern (24 bp):
ATTATGTTATATTTATGTCGTATT
Done.