Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 24
Found at i:4384273 original size:18 final size:18
Alignment explanation
Indices: 4384203--4384274 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 18
4384193 CAAATATAAG
*
4384203 CAGTATTGATACTCTACACT
1 CAGTATTGATACTC-AC-TT
*
4384223 CAGTACTGATACTTCACTT
1 CAGTATTGATAC-TCACTT
*
4384242 CTATGGTATCGATACTCACTT
1 C-A--GTATTGATACTCACTT
4384263 CAGTATTGATAC
1 CAGTATTGATAC
4384275 CCTTTTGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
18 9 0.21
19 2 0.05
20 15 0.35
21 9 0.21
22 8 0.19
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (18 bp):
CAGTATTGATACTCACTT
Found at i:4395499 original size:2 final size:2
Alignment explanation
Indices: 4395492--4395540 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4395482 ATACACCATG
*
4395492 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4395534 GA GA GA G
1 GA GA GA G
4395541 TATTAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4395793 original size:33 final size:33
Alignment explanation
Indices: 4395755--4395862 Score: 207
Period size: 33 Copynumber: 3.3 Consensus size: 33
4395745 TGCAAAAGCT
4395755 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
1 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
4395788 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
1 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
4395821 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
1 TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
*
4395854 TTTACTGAA
1 TTTGCTGAA
4395863 CTGAAATGGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (33 bp):
TTTGCTGAAATGGTTGGTTCCCAGAAGTGTTAA
Found at i:4397616 original size:102 final size:103
Alignment explanation
Indices: 4397493--4397706 Score: 349
Period size: 105 Copynumber: 2.1 Consensus size: 103
4397483 CCGAAAAACG
* * * *
4397493 TTGAATATCACTACTGGGTTGAAAAATCAAGAAATCAAGAAC-AACAAAAACCCAGATTTGCAAT
1 TTGAATACCACTACAGAGTTGAAAAATCAAGAAATCAAGAACAAAAAAAAACCCAGATTTGCAAT
4397557 CACTAAAATCAAATAATACCAAGAAAAACATAATTACT
66 CACTAAAATCAAATAATACCAAGAAAAACATAATTACT
*
4397595 TTGAATACCACTACAGAGTTGAAAAATTAAGAAATCAAGAACAAGAAAAAAAACCCAGATTTGCA
1 TTGAATACCACTACAGAGTTGAAAAATCAAGAAATCAAGAAC-A-AAAAAAAACCCAGATTTGCA
*
4397660 ATCACTAAAATCAAATAATACCAAGAAACACATAATTACT
64 ATCACTAAAATCAAATAATACCAAGAAAAACATAATTACT
4397700 TTGAATA
1 TTGAATA
4397707 TACAAAGTTG
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
102 38 0.37
105 65 0.63
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (103 bp):
TTGAATACCACTACAGAGTTGAAAAATCAAGAAATCAAGAACAAAAAAAAACCCAGATTTGCAAT
CACTAAAATCAAATAATACCAAGAAAAACATAATTACT
Found at i:4399830 original size:20 final size:20
Alignment explanation
Indices: 4399805--4399857 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4399795 AAACTAAGGT
* *
4399805 AGTATCAATACTGACTCATC
1 AGTATCAATACCGACTCAGC
*
4399825 AGTATCAATACCGACTCAGG
1 AGTATCAATACCGACTCAGC
4399845 AGTATCGAATACC
1 AGTATC-AATACC
4399858 CCTATCAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
AGTATCAATACCGACTCAGC
Found at i:4403233 original size:219 final size:215
Alignment explanation
Indices: 4402547--4403253 Score: 1175
Period size: 217 Copynumber: 3.3 Consensus size: 215
4402537 ATTTAAGAAT
4402547 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
4402612 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAAT-AAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
* * *
4402676 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCACTTTTACA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGG-TCAATTTCAAA
4402741 TGCAAATAAAATTTGGA-GATC
195 TGCAAATAAAATTTGGAGGA-C
* * *
4402762 TAATTTGAAAAAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGACGA
1 TAAATTG-AACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGA
* * *
4402827 GGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGAAATTAATACAAAAAAGTACTAAATTATA
65 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATA
* *
4402892 CCCATTTAAAAAGTTATGTGCCAATTAAAAAACTAGAAATAAGTAATAAGTATGGGTCTATTTCA
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAA-TAGAAATAAGTAATAAGTAT-GGTCAATTTCA
4402957 AATGCAAATAAAATTTGGAGGAC
193 AATGCAAATAAAATTTGGAGGAC
*
4402980 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACAAACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
4403045 GGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAAAAAAAAAGTACTAAATTATC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAAT-AAAAAAAAGTACTAAATTATA
*
4403110 CCTCATTTAAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAATAATAAGTATAGGTCAATTTC
130 CC-CATTT-AAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTAT-GGTCAATTTC
4403175 AAATGCAAATAAAATTTGGAGGAC
192 AAATGCAAATAAAATTTGGAGGAC
*
4403199 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
4403254 AAGAGATCAA
Statistics
Matches: 458, Mismatches: 26, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
215 6 0.01
216 97 0.21
217 145 0.32
218 72 0.16
219 114 0.25
220 24 0.05
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.28
Consensus pattern (215 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGTCAATTTCAAAT
GCAAATAAAATTTGGAGGAC
Found at i:4403339 original size:2 final size:2
Alignment explanation
Indices: 4403334--4403568 Score: 278
Period size: 2 Copynumber: 115.0 Consensus size: 2
4403324 AAAACAACTA
4403334 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
4403376 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
4403418 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
* * * * * *
4403460 AA ACT AG AT AGT TT AT AT AT AA AGT AT AT GT AT AT AT AT AA ACT
1 AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* * * *
4403504 AT AT AGT TT AT AT AT -T AT GT AT AT AT AT AT CAT GT AT AA ACT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T
*
4403546 AT A- AT AT -T AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT
4403569 GAACTATTGT
Statistics
Matches: 200, Mismatches: 22, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
1 3 0.01
2 188 0.94
3 9 0.05
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4403678 original size:29 final size:30
Alignment explanation
Indices: 4403646--4403714 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
4403636 AAACTATTTT
4403646 ATATAAATAGTATAAAATATAG-TT-TATAA
1 ATATAAATA-TATAAAATATAGTTTATATAA
** *
4403675 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAGTTTATATAA
4403704 ATATAAATATA
1 ATATAAATATA
4403715 AACCCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
28 2 0.06
29 21 0.62
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (30 bp):
ATATAAATATATAAAATATAGTTTATATAA
Found at i:4403681 original size:20 final size:20
Alignment explanation
Indices: 4403619--4403688 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
4403609 TAGTTCATAT
*
4403619 ATATAGTATATAAATATAAA
1 ATATAGTTTATAAATATAAA
* *
4403639 CTAT-TTTATATAAATAGTATAAA
1 ATATAGTT-TAT-AA-A-TATAAA
4403662 ATATAGTTTATAAATATAAA
1 ATATAGTTTATAAATATAAA
*
4403682 TTATAGT
1 ATATAGT
4403689 ATGTAGTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.03
20 18 0.46
21 3 0.08
22 3 0.08
23 12 0.31
24 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (20 bp):
ATATAGTTTATAAATATAAA
Found at i:4403759 original size:2 final size:2
Alignment explanation
Indices: 4403726--4403750 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4403716 ACCCTAAACC
4403726 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
4403751 AACTATATAG
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:4403766 original size:18 final size:18
Alignment explanation
Indices: 4403745--4403887 Score: 68
Period size: 20 Copynumber: 7.7 Consensus size: 18
4403735 TATATATATA
4403745 TATATAAACTATATAGTT
1 TATATAAACTATATAGTT
**
4403763 TATATTAATGTATATAGTT
1 TATA-TAAACTATATAGTT
* *
4403782 TACTTATGAACTATATA-TA
1 TA--TATAAACTATATAGTT
* *
4403801 TA-ATATA-TTTGATA-TT
1 TATATAAACTAT-ATAGTT
4403817 TATATATGAAC--TATAGTT
1 TATATA--AACTATATAGTT
4403835 TACATATAAACTATATAGTT
1 T--ATATAAACTATATAGTT
4403855 TATATAGTAAC--TATAGTT
1 TATATA--AACTATATAGTT
4403873 TACATATAAACTATA
1 T--ATATAAACTATA
4403888 GTTGATATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 36
0.67 0.08 0.25
Matches are distributed among these distances:
15 2 0.02
16 9 0.09
17 6 0.06
18 27 0.28
19 18 0.19
20 31 0.33
21 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (18 bp):
TATATAAACTATATAGTT
Found at i:4403867 original size:38 final size:38
Alignment explanation
Indices: 4403815--4403887 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
4403805 ATATTTGATA
4403815 TTTATATATGAACTATAGTTTACATATAAACTATATAG
1 TTTATATATGAACTATAGTTTACATATAAACTATATAG
4403853 TTTATATA-GTAACTATAGTTTACATATAAACTATA
1 TTTATATATG-AACTATAGTTTACATATAAACTATA
4403888 GTTGATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (38 bp):
TTTATATATGAACTATAGTTTACATATAAACTATATAG
Found at i:4404015 original size:27 final size:26
Alignment explanation
Indices: 4403985--4404055 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
4403975 ATTTATATAA
4403985 TATATACTATATATATAAACTATAGTT
1 TATAT-CTATATATATAAACTATAGTT
* *
4404012 TATATTTATATA-ATACATACTCTAGTT
1 TATATCTATATATATA-A-ACTATAGTT
*
4404039 TATATTTATATACTATA
1 TATATCTATATA-TATA
4404056 TATTATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 3 0.08
26 7 0.18
27 25 0.66
29 3 0.08
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (26 bp):
TATATCTATATATATAAACTATAGTT
Found at i:4404064 original size:9 final size:9
Alignment explanation
Indices: 4404045--4404086 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
4404035 AGTTTATATT
4404045 TATATACTA
1 TATATACTA
4404054 TATATTA-TA
1 TATA-TACTA
4404063 TATATAAACTA
1 TATAT--ACTA
4404074 TATATACTA
1 TATATACTA
4404083 TATA
1 TATA
4404087 GTATAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 18 0.62
10 3 0.10
11 7 0.24
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATACTA
Found at i:4404108 original size:34 final size:36
Alignment explanation
Indices: 4404045--4404113 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
4404035 AGTTTATATT
*
4404045 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
4404081 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
4404114 AAAACCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:4404270 original size:51 final size:51
Alignment explanation
Indices: 4404176--4404459 Score: 290
Period size: 51 Copynumber: 5.4 Consensus size: 51
4404166 ATTTATACTA
*
4404176 TAGTATATATAAACTATATAATATATATAAAAACTATATATTATATAGTTTAT
1 TAGTATATATAAACTATATAGTATATAT--AAACTATATATTATATAGTTTAT
* *
4404229 TAGTATATATAAA-TATACAGTATATATATAACTATACATTATATAGTTTAT
1 TAGTATATATAAACTATATAGTATATATA-AACTATATATTATATAGTTTAT
* * * * *
4404280 TAGTATATATAAACTATATAATATATATAAACTATGGTATATATAAACTATACAT
1 TAGTATATATAAACTATATAGTATATATAAACTAT-ATAT-TATATAGT-T-TAT
** *
4404335 TA-TATATAT-TTC-AT-TAGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTTAT
* *
4404382 TAGTATATATAACCTATATAGTATATGGTATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAG--TA---TATAT--AAACTATATATTATATAGTTTAT
4404440 TAGTATATATAAACTATATA
1 TAGTATATATAAACTATATA
4404460 TTGAAAAGTT
Statistics
Matches: 195, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
47 5 0.03
48 8 0.04
49 7 0.04
50 6 0.03
51 59 0.30
52 29 0.15
53 22 0.11
54 8 0.04
55 4 0.02
56 5 0.03
58 42 0.22
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (51 bp):
TAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTTAT
Found at i:4404305 original size:16 final size:17
Alignment explanation
Indices: 4403726--4404375 Score: 117
Period size: 18 Copynumber: 37.5 Consensus size: 17
4403716 ACCCTAAACC
*
4403726 ATATATATATA-TATAT
1 ATATATATAAACTATAT
4403742 ATATATATAAACTATAT
1 ATATATATAAACTATAT
* **
4403759 AGTTTATATTAATGTATAT
1 A-TATATA-TAAACTATAT
* *
4403778 AGTTTACTTATGAACTATAT
1 A-TATA--TATAAACTATAT
**
4403798 ATATA-ATATATTTGATAT
1 ATATATATA-AACT-ATAT
* *
4403816 TTATATATGAACTATAGT
1 ATATATATAAACTATA-T
* *
4403834 TTACATATAAACTATAT
1 ATATATATAAACTATAT
*
4403851 AGTTTATATAGTAACTATAGT
1 A-TATATATA--AACTATA-T
* *
4403872 TTACATATAAACTATAGT
1 ATATATATAAACTATA-T
* *
4403890 -TGATATTTACA-TATGAACT
1 AT-ATATATAAACTAT--A-T
4403909 ATATATATAAACTGTATAGT
1 ATATATATAAAC--TATA-T
* * * *
4403929 TTACATATGACCTATAT
1 ATATATATAAACTATAT
*
4403946 ATATAGT-T-TA-T-TAGT
1 ATATA-TATAAACTATA-T
*
4403961 GAAATATATAAACTAT-T
1 -ATATATATAAACTATAT
*
4403978 -TATATA-ATA-TATACT
1 ATATATATAAACTATA-T
4403993 ATATATATAAACTATAGT
1 ATATATATAAACTATA-T
* * *
4404011 TTATATTTATA-TA-AT
1 ATATATATAAACTATAT
* * ***
4404026 ACATACTCTAGTTTATAT
1 ATATA-TATAAACTATAT
* *
4404044 TTATATACTATA-TAT-T
1 ATATATA-TAAACTATAT
4404060 ATATATATAAACTATAT
1 ATATATATAAACTATAT
*
4404077 ATACTATAT--AGTATAAT
1 ATA-TATATAAACTAT-AT
* * *
4404094 TTACATATGAAC--TAT
1 ATATATATAAACTATAT
*
4404109 ATATA-A-AAACCATAT
1 ATATATATAAACTATAT
*
4404124 A-A-ACTATATACTATAGTT
1 ATATA-TATAAACTATA--T
* *
4404142 GATATTTATATACTATAT
1 -ATATATATAAACTATAT
* * *
4404160 AAAATAATTTATACTATA-
1 -ATAT-ATATAAACTATAT
*
4404178 GTATATATAAACTATAT
1 ATATATATAAACTATAT
4404195 AATATATATAAAAACTATAT
1 -ATATATAT--AAACTATAT
***
4404215 AT-TATATAGTTTAT-T
1 ATATATATAAACTATAT
*
4404230 AGTATATATAAA-TATAC
1 A-TATATATAAACTATAT
*
4404247 AGTATATATATAACTATAC
1 A-TATATATA-AACTATAT
***
4404266 AT-TATATAGTTTAT-T
1 ATATATATAAACTATAT
4404281 AGTATATATAAACTATAT
1 A-TATATATAAACTATAT
*
4404299 AATATATATAAACTAT-G
1 -ATATATATAAACTATAT
* *
4404316 GTATATATAAACTATAC
1 ATATATATAAACTATAT
* *
4404333 AT-TATATATA-TTTCATT
1 ATATATATAAACTAT-A-T
4404350 AGTATATATAAACTATAT
1 A-TATATATAAACTATAT
4404368 AT-TATATA
1 ATATATATA
4404376 GTTCATTAGT
Statistics
Matches: 462, Mismatches: 100, Indels: 144
0.65 0.14 0.20
Matches are distributed among these distances:
13 7 0.02
14 6 0.01
15 31 0.07
16 102 0.22
17 77 0.17
18 121 0.26
19 57 0.12
20 55 0.12
21 3 0.01
22 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (17 bp):
ATATATATAAACTATAT
Found at i:4404305 original size:33 final size:33
Alignment explanation
Indices: 4404247--4404496 Score: 250
Period size: 33 Copynumber: 7.7 Consensus size: 33
4404237 ATAAATATAC
* *
4404247 AGTATATATATAACTATACATTATATAGTTTATT
1 AGTATATATA-AACTATATATTATATAGTTCATT
* **
4404281 AGTATATATAAACTATATAATATATA-TAAACTAT
1 AGTATATATAAACTATATATTATATAGTTCA-T-T
* * *
4404315 GGTATATATAAACTATACATTATATATATTTCATT
1 AGTATATATAAACTATATA-T-TATATAGTTCATT
4404350 AGTATATATAAACTATATATTATATAGTTCATT
1 AGTATATATAAACTATATATTATATAGTTCATT
* *
4404383 AGTATATATAACCTATATAGTATAT-G------
1 AGTATATATAAACTATATATTATATAGTTCATT
*
4404409 -GTATATACAAACTATATATTATATAGTTCATT
1 AGTATATATAAACTATATATTATATAGTTCATT
*
4404441 AGTATATATAAACTATATATTGA-AAAGTTCATT
1 AGTATATATAAACTATATATT-ATATAGTTCATT
*
4404474 AGTATATTATAACCTATATATTA
1 AGTATA-TATAAACTATATATTA
4404497 ATTTATTAAT
Statistics
Matches: 181, Mismatches: 20, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
25 21 0.12
26 1 0.01
32 3 0.02
33 85 0.47
34 44 0.24
35 18 0.10
36 7 0.04
37 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (33 bp):
AGTATATATAAACTATATATTATATAGTTCATT
Found at i:4404353 original size:69 final size:68
Alignment explanation
Indices: 4404248--4404375 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 68
4404238 TAAATATACA
*
4404248 GTATATATATAACTATACATTATATAGTTTATTAGTATATATAAACTATATAATATATATAAACT
1 GTATATATATAACTATACATTATATAATTTATTAGTATATATAAACTATATAATATATATAAACT
4404313 ATG
66 ATG
*
4404316 GTATATATA-AACTATACATTATATATATTTCATTAGTATATATAAACTATATATTATATA
1 GTATATATATAACTATACATTATATA-ATTT-ATTAGTATATATAAACTATATAATATATA
4404376 GTTCATTAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
67 16 0.29
68 12 0.21
69 28 0.50
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (68 bp):
GTATATATATAACTATACATTATATAATTTATTAGTATATATAAACTATATAATATATATAAACT
ATG
Found at i:4404392 original size:2 final size:2
Alignment explanation
Indices: 4403964--4404375 Score: 77
Period size: 2 Copynumber: 197.5 Consensus size: 2
4403954 TATTAGTGAA
* * *
4403964 AT AT AT AA ACT AT TT AT AT A- AT AT AT ACT AT AT AT AT AA ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * * * *
4404006 AT AGT TT AT AT TT AT AT A- AT AC AT ACT CT AGT TT AT AT TT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT
*
4404048 AT ACT AT AT AT -T AT AT AT AT AA ACT AT AT AT ACT AT AT AGT AT
1 AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT
* * * * * *
4404091 A- AT TT AC AT AT GA- ACT AT AT AT AA AA ACC AT AT AA ACT AT AT
1 AT AT AT AT AT AT -AT A-T AT AT AT AT AT A-T AT AT AT A-T AT AT
* * *
4404133 ACT AT AGT -T GAT AT TT AT AT ACT AT AT A- AA AT A- AT TT AT ACT
1 A-T AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
* * *
4404175 AT AGT AT AT AT AA ACT AT AT A- AT AT AT AT AA AA ACT AT AT AT
1 AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
4404217 -T AT AT AGT TT AT -T AGT AT AT AT AA AT AT AC AGT AT AT AT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
4404258 A- ACT AT AC AT -T AT AT AGT TT AT -T AGT AT AT AT AA ACT AT AT
1 AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT
* * * *
4404299 A- AT AT AT AT AA ACT AT GGT AT AT AT AA ACT AT AC AT -T AT AT
1 AT AT AT AT AT AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT AT
* *
4404340 AT AT TT CAT -T AGT AT AT AT AA ACT AT AT AT -T AT AT A
1 AT AT AT -AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT A
4404376 GTTCATTAGT
Statistics
Matches: 295, Mismatches: 62, Indels: 106
0.64 0.13 0.23
Matches are distributed among these distances:
1 18 0.06
2 231 0.78
3 46 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4404423 original size:25 final size:25
Alignment explanation
Indices: 4404384--4404432 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4404374 TAGTTCATTA
* *
4404384 GTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATAGTATATG
*
4404409 GTATATACAAACTATATATTATAT
1 GTATATACAAACTATATAGTATAT
4404433 AGTTCATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (25 bp):
GTATATACAAACTATATAGTATATG
Found at i:4404450 original size:91 final size:94
Alignment explanation
Indices: 4404312--4404493 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 94
4404302 ATATATAAAC
* * *
4404312 TATGGTATATATAAACTATACATTATATATATTTCATTAGTATATATAAACTATATATT-ATATA
1 TATGGTATATACAAACTATACATTATATATAGTTCATTAGTATATATAAACTATATATTGA-AAA
4404376 GTTCATTAGTATA-TATAACCTATATAGTA
65 GTTCATTAGTATATTATAACCTATATAGTA
*
4404405 TATGGTATATACAAACTATATA-T-TATATAGTTCATTAGTATATATAAACTATATATTGAAAAG
1 TATGGTATATACAAACTATACATTATATATAGTTCATTAGTATATATAAACTATATATTGAAAAG
4404468 TTCATTAGTATATTATAACCTATATA
66 TTCATTAGTATATTATAACCTATATA
4404494 TTAATTTATT
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
91 48 0.58
92 15 0.18
93 20 0.24
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (94 bp):
TATGGTATATACAAACTATACATTATATATAGTTCATTAGTATATATAAACTATATATTGAAAAG
TTCATTAGTATATTATAACCTATATAGTA
Found at i:4404634 original size:61 final size:61
Alignment explanation
Indices: 4404553--4404682 Score: 181
Period size: 61 Copynumber: 2.1 Consensus size: 61
4404543 TATAAGGATC
* * * *
4404553 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAACTGTAAT-ATTAAATTTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAACTG-AATCATTAAATCTGGACT
* * *
4404614 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTGCATCATTAAATCTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAACTGAATCATTAAATCTGGACT
4404675 AAATTGAA
1 AAATTGAA
4404683 CAAATTCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 2 0.03
61 59 0.97
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.34
Consensus pattern (61 bp):
AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAACTGAATCATTAAATCTGGACT
Found at i:4405104 original size:112 final size:110
Alignment explanation
Indices: 4404896--4405249 Score: 388
Period size: 122 Copynumber: 3.1 Consensus size: 110
4404886 AAAATCAACT
* * * * * *
4404896 ATGTTCTTTATTTGTTCATCCTTGTTCCTCCCCAAAACCCTCGTTTGATATTCAAAAACTCCAAA
1 ATGTTCTTCATTTGTTCATCC-AGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AA
* *
4404961 ACCAAAACATTTTCATTTTTTTTCGATCAAACACCCAAATATTCATCC
64 ACCAAACCA-TTTCATGTTTTTTCGATCAAACACCCAAATATTCATCC
* * *
4405009 GTGTTCTTCATTTGTTCATCCAAGTTCTTACCTAAAA-CCTCCTTTGATCTTCAAAAACACCTAA
1 ATGTTCTTCATTTGTTCATCC-AGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AA
*
4405073 ACACAAACCATTTCATGTTTTTTCGATCAAACACCCAAATTTTCTTCGGTGTTAATCC
64 AC-CAAACCATTTCATGTTTTTTCGATCAAACACCCAAA---TATTC-------ATCC
*
4405131 ATGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGAACTTCAAAAACACCAAAC
1 ATGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAA-
*
4405196 CCAAACCATTTCGTGTTTTTTTCGATCAAACACCC-AATAATTCATCC
65 CCAAACCATTTCATG-TTTTTTCGATCAAACACCCAAAT-ATTCATCC
4405243 ATTGTTC
1 A-TGTTC
4405250 ATCTGTGTTG
Statistics
Matches: 205, Mismatches: 20, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
112 58 0.28
113 41 0.20
115 4 0.02
118 1 0.00
119 3 0.01
121 31 0.15
122 67 0.33
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (110 bp):
ATGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAAC
CAAACCATTTCATGTTTTTTCGATCAAACACCCAAATATTCATCC
Found at i:4405421 original size:30 final size:30
Alignment explanation
Indices: 4405387--4405451 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
4405377 CCCAAACCTT
* *
4405387 AACCCAGACCTTAACTTTAAATTAAACCCA
1 AACCCAAACCCTAACTTTAAATTAAACCCA
*
4405417 AACCCAAACCCTAACTTTAACTTAAACCCA
1 AACCCAAACCCTAACTTTAAATTAAACCCA
4405447 AACCC
1 AACCC
4405452 GAACTCGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (30 bp):
AACCCAAACCCTAACTTTAAATTAAACCCA
Found at i:4405468 original size:24 final size:24
Alignment explanation
Indices: 4405411--4405469 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
4405401 CTTTAAATTA
* * **
4405411 AACCCAAACCCAAACCCTAACTTT
1 AACCTAAACCCAAACCCGAACTCG
*
4405435 AACTTAAACCCAAACCCGAACTCG
1 AACCTAAACCCAAACCCGAACTCG
*
4405459 AACCTGAACCC
1 AACCTAAACCC
4405470 GAACTATTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.41, G:0.05, T:0.14
Consensus pattern (24 bp):
AACCTAAACCCAAACCCGAACTCG
Found at i:4405698 original size:2 final size:2
Alignment explanation
Indices: 4405691--4405720 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4405681 TATATGCTTG
4405691 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
4405721 GGTTTATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4405758 original size:31 final size:31
Alignment explanation
Indices: 4405720--4406148 Score: 566
Period size: 31 Copynumber: 14.3 Consensus size: 31
4405710 TATATATATA
* *
4405720 TGGTTTATTGTTGTTGATGTAAACGATGTAT
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4405751 TGGTTTA---TTG-T--TGT---CGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
4405773 TGATTTATTATTGTTGATGTAAATG-T--AC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
4405801 TAGTTTATTGCTT-TTGATG---GTGATGTAC
1 TGGTTTATTG-TTGTTGATGTAAATGATGTAC
* *
4405829 TGGTTTATTGATATTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4405860 TGATTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4405891 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4405922 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4405953 TGGTTTATTGTTGTTGATGTAAATGATGTAT
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
4405984 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
4406015 TGGTTTATTGTTGTTGATGTAAATGATATAT
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
4406046 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
4406077 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
** *
4406108 TGGTTTATTACTGTTGATGTAAATGATATAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
4406139 TGGTTTATTG
1 TGGTTTATTG
4406149 CTGTAATGTA
Statistics
Matches: 355, Mismatches: 26, Indels: 34
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.04
25 8 0.02
26 2 0.01
27 2 0.01
28 38 0.11
29 2 0.01
30 1 0.00
31 289 0.81
ACGTcount: A:0.23, C:0.04, G:0.24, T:0.48
Consensus pattern (31 bp):
TGGTTTATTGTTGTTGATGTAAATGATGTAC
Found at i:4405769 original size:22 final size:22
Alignment explanation
Indices: 4405743--4405793 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4405733 TTGATGTAAA
* * *
4405743 CGATGTATTGGTTTATTGTTGT
1 CGATGTACTGATTTATTATTGT
4405765 CGATGTACTGATTTATTATTGT
1 CGATGTACTGATTTATTATTGT
*
4405787 TGATGTA
1 CGATGTA
4405794 AATGTACTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.51
Consensus pattern (22 bp):
CGATGTACTGATTTATTATTGT
Found at i:4407158 original size:34 final size:34
Alignment explanation
Indices: 4407115--4407183 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
4407105 ACTTTGTGCA
4407115 TTTGAATTAGCTGTTAAAGACTGTGATACTTCTT
1 TTTGAATTAGCTGTTAAAGACTGTGATACTTCTT
*
4407149 TTTGAATTAGCTGTTAAAGACTGTGATAGTTCTT
1 TTTGAATTAGCTGTTAAAGACTGTGATACTTCTT
4407183 T
1 T
4407184 CTCTGGTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (34 bp):
TTTGAATTAGCTGTTAAAGACTGTGATACTTCTT
Found at i:4408567 original size:20 final size:20
Alignment explanation
Indices: 4408528--4408588 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
4408518 TGCTTGATTA
* * *
4408528 TGCTTGATTATGTTTTATAT
1 TGCTTGCTTCTGTTTGATAT
*
4408548 TGTTTGCTTCTGTTTGATAT
1 TGCTTGCTTCTGTTTGATAT
4408568 TGCTTGCTTCTAG-TTGATAT
1 TGCTTGCTTCT-GTTTGATAT
4408588 T
1 T
4408589 TGTAAGGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.57
Consensus pattern (20 bp):
TGCTTGCTTCTGTTTGATAT
Found at i:4409497 original size:17 final size:17
Alignment explanation
Indices: 4409475--4409515 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
4409465 TCAAAAAGTA
4409475 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
4409492 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
4409509 ATCATAA
1 ATCATAA
4409516 GTTTATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:4412451 original size:15 final size:15
Alignment explanation
Indices: 4412404--4412452 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
4412394 GGTAAAACAC
4412404 CCAATAATAACAAAA
1 CCAATAATAACAAAA
** *
4412419 CCGGTAA-AAC--AC
1 CCAATAATAACAAAA
4412431 CCAATAATAACAAAA
1 CCAATAATAACAAAA
4412446 CCAATAA
1 CCAATAA
4412453 AAATAATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
12 6 0.24
13 3 0.12
14 3 0.12
15 13 0.52
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (15 bp):
CCAATAATAACAAAA
Found at i:4412454 original size:27 final size:27
Alignment explanation
Indices: 4412384--4412447 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
4412374 TCGGATATGT
4412384 TAACAAAACCGGTAAAACACCCAATAA
1 TAACAAAACCGGTAAAACACCCAATAA
4412411 TAACAAAACCGGTAAAACACCCAATAA
1 TAACAAAACCGGTAAAACACCCAATAA
4412438 TAACAAAACC
1 TAACAAAACC
4412448 AATAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.56, C:0.27, G:0.06, T:0.11
Consensus pattern (27 bp):
TAACAAAACCGGTAAAACACCCAATAA
Found at i:4414056 original size:70 final size:68
Alignment explanation
Indices: 4413971--4414158 Score: 202
Period size: 70 Copynumber: 2.7 Consensus size: 68
4413961 TTTTTGAAAA
*
4413971 TATATAATATTTTTAAAATCATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTTGA
1 TATATAATATTTTTAAAAT-ATTTTGAAAATATATATAATATATAGTTTTG-AAA-ATTTTTTAA
*
4414036 -AATCT
63 GAATAT
* * *
4414041 TATATAATATTTTTAAATTATTTTTGAAAA-CTATATAATATATAGTTTTGTAAATTTTTTAAGA
1 TATATAATATTTTTAAAATA-TTTTGAAAATATATATAATATATAGTTTTGAAAATTTTTTAAGA
4414105 ATAT
65 ATAT
* * * **
4414109 AATAT-ATAGTTTTAAAAAAATATTTTTAAAATATATATGTTATATAGTTT
1 TATATAATA-TTTT--TAAAATATTTTGAAAATATATATAATATATAGTTT
4414159 ATATTATATT
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
67 11 0.11
68 14 0.14
69 28 0.28
70 47 0.47
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (68 bp):
TATATAATATTTTTAAAATATTTTGAAAATATATATAATATATAGTTTTGAAAATTTTTTAAGAA
TAT
Found at i:4414110 original size:32 final size:31
Alignment explanation
Indices: 4414004--4414121 Score: 96
Period size: 32 Copynumber: 3.5 Consensus size: 31
4413994 TTGAAAATAT
* *
4414004 ATATAATATATAGTTTTGAAAACATTTTTTGAA
1 ATATAATATATAGTTTTG-TAA-ATTTTTTAAA
* *
4414037 ATCTTATATAATA-TTTT-TAAATTATTTTTGAAAA
1 ATATAATAT-ATAGTTTTGTAAA-T-TTTTT--AAA
4414071 CTATATAATATATAGTTTTGTAAATTTTTTAAGA
1 --ATATAATATATAGTTTTGTAAATTTTTTAA-A
4414105 ATATAATATATAGTTTT
1 ATATAATATATAGTTTT
4414122 AAAAAAATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
30 1 0.01
31 3 0.04
32 22 0.32
33 13 0.19
34 6 0.09
35 8 0.12
36 12 0.17
37 4 0.06
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (31 bp):
ATATAATATATAGTTTTGTAAATTTTTTAAA
Found at i:4414142 original size:34 final size:31
Alignment explanation
Indices: 4414004--4414143 Score: 109
Period size: 34 Copynumber: 4.2 Consensus size: 31
4413994 TTGAAAATAT
*
4414004 ATATAATATATAGTTTTGAAAACATTTTTTGAA
1 ATATAATATATAGTTTT-AAAA-ATTTTTTAAA
* * * * *
4414037 ATCTTATATAATATTTTTAAATTATTTTTGAAAA
1 ATATAATAT-ATAGTTTTAAA-AATTTTT-TAAA
**
4414071 CTATATAATATATAGTTTTGTAAATTTTTTAAGA
1 --ATATAATATATAGTTTTAAAAATTTTTTAA-A
4414105 ATATAATATATAGTTTTAAAAAAATATTTTTAAA
1 ATATAATATATAGTTTT--AAAAAT-TTTTTAAA
4414139 ATATA
1 ATATA
4414144 TATGTTATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
32 17 0.20
33 18 0.22
34 26 0.31
35 15 0.18
36 7 0.08
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATAATATATAGTTTTAAAAATTTTTTAAA
Found at i:4415418 original size:17 final size:17
Alignment explanation
Indices: 4415398--4415450 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
4415388 ATTTTTCCCT
4415398 TTATTTCTATTTTTTTA
1 TTATTTCTATTTTTTTA
* * *
4415415 TTATCTCTATATTTATA
1 TTATTTCTATTTTTTTA
4415432 TTATTTCT-TTATTTTTA
1 TTATTTCTATT-TTTTTA
4415449 TT
1 TT
4415451 TTTACTCTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 1 0.03
17 28 0.97
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTCTATTTTTTTA
Found at i:4420517 original size:84 final size:84
Alignment explanation
Indices: 4420326--4421121 Score: 827
Period size: 84 Copynumber: 9.6 Consensus size: 84
4420316 TAAACAAACT
* * * * *
4420326 ATTTGCAGCATAGCTTAAGCCGAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
4420387 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCAACGGCACATC
* * *
4420407 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4420472 CTCAGCTCAACGGCACATC
66 CTCAGCTCAACGGCACATC
* * * * *
4420491 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
4420552 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCAACGGCACATC
** ** * *
4420572 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCTGCCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
4420637 CTCAGCTTCGAGGGCATATC
66 CTCAGC-TCAACGGCACATC
* * * * * * *
4420657 ATCTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4420721 CTCAGCTCCAA-GGCATATC
66 CTCAGCT-CAACGGCACATC
* * * * *
4420740 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4420805 CTCAGCTCAACGGCACATC
66 CTCAGCTCAACGGCACATC
* * * *
4420824 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCAACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
4420889 CTCAGCTCCA-GGACATATC
66 CTCAGCTCAACGG-CACATC
* * * * * *
4420908 ATTTGCAGCACAACTTAAATCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4420973 CTCAGCTCAACGACACATC
66 CTCAGCTCAACGGCACATC
* * *
4420992 ATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAA-C---GA-CTCCCGAGTTCGATTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCT-TCGAGTTCGACTAC
* * *
4421052 ACTCAGCTCCGAGGGCACATC
65 GCTCAGCT-CAACGGCACATC
* * * * * *
4421073 ATTTACAGCATAACTCAAGGCTAGAAGAGTTATCTGTCAA-CAAA-ACCTT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
4421122 TGAGATTGTT
Statistics
Matches: 602, Mismatches: 93, Indels: 38
0.82 0.13 0.05
Matches are distributed among these distances:
79 2 0.00
80 48 0.08
81 120 0.20
83 45 0.07
84 285 0.47
85 102 0.17
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCAACGGCACATC
Found at i:4420598 original size:165 final size:165
Alignment explanation
Indices: 4420326--4421125 Score: 1007
Period size: 168 Copynumber: 4.8 Consensus size: 165
4420316 TAAACAAACT
*
4420326 ATTTGCAGCATAGCTTAAGCCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCA
* * *
4420391 GCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACC
4420456 TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
*
4420491 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCA
* **
4420556 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCTGCCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACC
*** * * * * *
4420621 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
131 TTTGAGTTCGACTACGCTCAGC-TCAACGGCACATC
* * * * * * * *
4420657 ATCTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCTTCGAGTTCGATTACAC
* * * * * *
4420722 TCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAG
63 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAG
4420786 ACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
128 ACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* * * *
4420824 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCAACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGATTACA
* * * * * * *
4420889 CTCAGC-TCCAGGACATATCATTTGCAGCACAACTTAAATCTAGAAGGGTTGTCTGCCAACAAAA
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAA
*
4420953 GACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATC
127 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* * * * *
4420992 ATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACGA-CTCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCT-TCGAGTTCGATTACACTC
* * * * * *
4421056 AGCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGAGTTATCTGTCAA-CAAA-AC
65 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGAC
4421119 CTTTGAG
130 CTTTGAG
4421126 ATTGTTTTCC
Statistics
Matches: 552, Mismatches: 76, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
163 11 0.02
164 26 0.05
165 182 0.33
166 39 0.07
167 39 0.07
168 226 0.41
169 29 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
Found at i:4421175 original size:36 final size:36
Alignment explanation
Indices: 4421129--4421287 Score: 205
Period size: 36 Copynumber: 4.4 Consensus size: 36
4421119 CTTTGAGATT
*
4421129 GTTTTCCTTGAAACAAAATTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACA
* *
4421165 GTTTCTCTTGAAAC-AAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAAATTT-GTCTCTCTTGAGACA
*
4421201 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACA
* * *
4421237 GTTTCCCTTGAAACAAATTTTGCCTC-CATGGAGACA
1 GTTTCCCTTGAAACAAAATTTGTCTCTC-TTGAGACA
* *
4421273 GTTTCTCTGGAAACA
1 GTTTCCCTTGAAACA
4421288 CAAAAAACCT
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.06
36 98 0.89
37 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACA
Found at i:4421238 original size:72 final size:72
Alignment explanation
Indices: 4421129--4421287 Score: 237
Period size: 72 Copynumber: 2.2 Consensus size: 72
4421119 CTTTGAGATT
* * * *
4421129 GTTTTCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCT
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGCCTCCAT
*
4421194 TGAGACA
66 GGAGACA
* *
4421201 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGCCTCCAT
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGCCTCCAT
4421266 GGAGACA
66 GGAGACA
* *
4421273 GTTTCTCTGGAAACA
1 GTTTCCCTTGAAACA
4421288 CAAAAAACCT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGCCTCCAT
GGAGACA
Found at i:4421313 original size:33 final size:33
Alignment explanation
Indices: 4421274--4421386 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
4421264 ATGGAGACAG
*
4421274 TTTCTCTGGAAACACAAAAAACCTTTGAAATTA
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
* *
4421307 TTTCTCTTGAAACACAAAAAACCTTTGAACTCA
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
* * *
4421340 TTTCTCTTGAAACAAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
4421373 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
4421387 AAGACCTTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (33 bp):
TTTCTCTTGAAACACAAAAAACCTTTGAAATTA
Found at i:4421546 original size:85 final size:84
Alignment explanation
Indices: 4421383--4421563 Score: 202
Period size: 85 Copynumber: 2.1 Consensus size: 84
4421373 TTTCTCTTGA
* * * **
4421383 AACAAAGACCTTAGAGTTTGATTCCACTCAGCTCAAAGGTATTATCATTTGCAACATAGCTCAAG
1 AACAAAGACCTTAGACTTCGATTCCACTCAGCTCAAAGGCACCATCATTTGCAACATAGCTCAAG
* * **
4421448 GCATTAAGGGCTATCTGCC
66 CCATGAAAAGCTATCTGCC
* * * *
4421467 AACACAAGACCTTCGACTTCGATTGCACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTTAA
1 AACA-AAGACCTTAGACTTCGATTCCACTCAGCTCAAAGGCACCATCATTTGCAACATAGCTCAA
*
4421532 GCCGA-GAAAAGCTATCTGTC
65 GCC-ATGAAAAGCTATCTGCC
*
4421552 AACGAAGACCTT
1 AACAAAGACCTT
4421564 TCGAGTTTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
84 12 0.15
85 67 0.84
86 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
AACAAAGACCTTAGACTTCGATTCCACTCAGCTCAAAGGCACCATCATTTGCAACATAGCTCAAG
CCATGAAAAGCTATCTGCC
Found at i:4421988 original size:36 final size:36
Alignment explanation
Indices: 4421948--4422121 Score: 209
Period size: 36 Copynumber: 4.9 Consensus size: 36
4421938 TAAAATATAT
* *
4421948 ATATATATATTATATAGTTTCGAAAACATTTCGAAA
1 ATATATATATTATATAGTTTTGAAAACATTTTGAAA
4421984 ATATATATATTATATAGTTTTTGAAAA-ATTTTGAAA
1 ATATATATATTATATAG-TTTTGAAAACATTTTGAAA
* * *
4422020 ACATATATAATGTATA-ATTTTTGAAAATACTTTTGAAA
1 ATATATAT-AT-TATATAGTTTTGAAAACA-TTTTGAAA
4422058 ATATATA-A-TATATAGTTTT-AAAATCATTTTGAAA
1 ATATATATATTATATAGTTTTGAAAA-CATTTTGAAA
4422092 ATATATATA--ATATAGTTTTGAAAACATTTT
1 ATATATATATTATATAGTTTTGAAAACATTTT
4422122 TTGAAATCTT
Statistics
Matches: 122, Mismatches: 7, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
34 39 0.32
35 11 0.09
36 42 0.34
37 12 0.10
38 18 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTGAAAACATTTTGAAA
Found at i:4422124 original size:36 final size:35
Alignment explanation
Indices: 4421950--4422239 Score: 195
Period size: 34 Copynumber: 8.5 Consensus size: 35
4421940 AAATATATAT
* * *
4421950 ATATATATTATATAGTTTCGAAAACA-TTTCGAAA
1 ATATATATAATATAGTTTTGAAAACATTTTTGAAA
4421984 ATATATATATTATATAGTTTTTGAAAA-A-TTTTGAAA
1 ATATATATA--ATATAG-TTTTGAAAACATTTTTGAAA
* * * *
4422020 ACATATATAATGTATAATTTTTGAAAATACTTTTGAAA
1 ATATATATAA--TAT-AGTTTTGAAAACATTTTTGAAA
4422058 ATATATA-ATATATAGTTTT-AAAATCA-TTTTGAAA
1 ATATATATA-ATATAGTTTTGAAAA-CATTTTTGAAA
4422092 ATATATATAATATAGTTTTGAAAACATTTTTTG-AA
1 ATATATATAATATAGTTTTGAAAACA-TTTTTGAAA
* * **
4422127 ATCT-TAT-ATATA-TTTTTAAATTATTTTTGAAA
1 ATATATATAATATAGTTTTGAAAACATTTTTGAAA
* *
4422159 A-CTATATAATATAGTTTTG-TAA-ATTTTT---A
1 ATATATATAATATAGTTTTGAAAACATTTTTGAAA
* * *
4422188 AGA-ATAT-ATATAGTTTT-AAAAAATATTTTTAAA
1 ATATATATAATATAGTTTTGAAAACAT-TTTTGAAA
4422221 ATATATATATTATATAGTT
1 ATATATATA--ATATAGTT
4422240 ATATTATATT
Statistics
Matches: 209, Mismatches: 18, Indels: 55
0.74 0.06 0.20
Matches are distributed among these distances:
28 12 0.06
29 8 0.04
30 4 0.02
31 8 0.04
32 20 0.10
33 14 0.07
34 51 0.24
35 16 0.08
36 42 0.20
37 19 0.09
38 15 0.07
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATATAATATAGTTTTGAAAACATTTTTGAAA
Found at i:4423379 original size:2 final size:2
Alignment explanation
Indices: 4423319--4423360 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4423309 TCACTTATGC
4423319 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT -T 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
4423359 AT
1 AT
4423361 TATTCTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4425478 original size:1 final size:1
Alignment explanation
Indices: 4425472--4425496 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4425462 AGAAGGGAAA
4425472 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
4425497 AGCTGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4425592 original size:2 final size:2
Alignment explanation
Indices: 4425585--4425615 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4425575 AATATCACCA
*
4425585 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4425616 AAATAACGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4425858 original size:38 final size:38
Alignment explanation
Indices: 4425811--4425914 Score: 145
Period size: 40 Copynumber: 2.7 Consensus size: 38
4425801 TAACTTTTTC
*
4425811 TAACATTTTTTGTTCAACTAAAAATATTACGAATAATG
1 TAACATTTTTTGTTCAACCAAAAATATTACGAATAATG
* * *
4425849 TAACATTTTTTGTTTTCAACCGAAAATGTTATGAATAATG
1 TAACATTTTTTG--TTCAACCAAAAATATTACGAATAATG
*
4425889 TAATATTTTTTGTTCAACCAAAAATA
1 TAACATTTTTTGTTCAACCAAAAATA
4425915 CTAATAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 24 0.42
40 33 0.58
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (38 bp):
TAACATTTTTTGTTCAACCAAAAATATTACGAATAATG
Found at i:4425935 original size:38 final size:38
Alignment explanation
Indices: 4425811--4425935 Score: 119
Period size: 38 Copynumber: 3.2 Consensus size: 38
4425801 TAACTTTTTC
* * **
4425811 TAACATTTTTTGTTCAACTAAAAATATTACGAATAATG
1 TAACATTTTTTGTTCAACCAAAAATACTAATAATAATG
* * *
4425849 TAACATTTTTTGTTTTCAACCGAAAAT-GTTATGAATAATG
1 TAACATTTTTTG--TTCAACCAAAAATACTAAT-AATAATG
* *
4425889 TAATATTTTTTGTTCAACCAAAAATACTAATAAAAACT-
1 TAACATTTTTTGTTCAACCAAAAATACTAATAATAA-TG
4425927 TAACATTTT
1 TAACATTTT
4425936 AGGTTGCTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
38 36 0.51
39 5 0.07
40 29 0.41
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (38 bp):
TAACATTTTTTGTTCAACCAAAAATACTAATAATAATG
Found at i:4426505 original size:17 final size:17
Alignment explanation
Indices: 4426483--4426516 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4426473 CCAATGTCGA
* *
4426483 TTTTTTGGTTTTAAAAT
1 TTTTTTGATTTGAAAAT
4426500 TTTTTTGATTTGAAAAT
1 TTTTTTGATTTGAAAAT
4426517 AAGCCCATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTTTTGATTTGAAAAT
Found at i:4426763 original size:23 final size:21
Alignment explanation
Indices: 4426729--4426775 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 21
4426719 CTAAAAATCA
4426729 TAAAAACAAAGAAAAGATAATTCC
1 TAAAAACAAAG---AGATAATTCC
4426753 TAAAAAC-AAGAGATAATTCC
1 TAAAAACAAAGAGATAATTCC
4426773 TAA
1 TAA
4426776 GGATAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.57
23 3 0.13
24 7 0.30
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.19
Consensus pattern (21 bp):
TAAAAACAAAGAGATAATTCC
Found at i:4426941 original size:12 final size:12
Alignment explanation
Indices: 4426924--4426957 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4426914 CGTCAGATGC
4426924 GTCATGCCCAAA
1 GTCATGCCCAAA
4426936 GTCATGCCCAAA
1 GTCATGCCCAAA
4426948 GTCATGCCCA
1 GTCATGCCCA
4426958 CTAATCTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (12 bp):
GTCATGCCCAAA
Found at i:4429055 original size:8 final size:8
Alignment explanation
Indices: 4428997--4429070 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
4428987 AAATTAAATA
4428997 AATATAAT
1 AATATAAT
4429005 AATAT--T
1 AATATAAT
4429011 AA-ATAATT
1 AATATAA-T
4429019 AATATAAT
1 AATATAAT
4429027 AA-ATAAT
1 AATATAAT
4429034 AA-ATAATT
1 AATATAA-T
4429042 AAAATATAAT
1 --AATATAAT
4429052 AATAT-AT
1 AATATAAT
*
4429059 AAATATAGT
1 -AATATAAT
4429068 AAT
1 AAT
4429071 TAAAATAGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
5 2 0.04
6 3 0.05
7 13 0.24
8 25 0.45
9 5 0.09
10 3 0.05
11 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (8 bp):
AATATAAT
Found at i:4429064 original size:16 final size:16
Alignment explanation
Indices: 4428994--4429070 Score: 81
Period size: 16 Copynumber: 4.9 Consensus size: 16
4428984 TAGAAATTAA
4428994 ATAAATATAATAATAT
1 ATAAATATAATAATAT
*
4429010 -TAAATA-ATTAATAT
1 ATAAATATAATAATAT
4429024 AATAAATAATAAATAAT-T
1 -ATAAAT-AT-AATAATAT
4429042 A-AAATATAATAATAT
1 ATAAATATAATAATAT
*
4429057 ATAAATATAGTAAT
1 ATAAATATAATAAT
4429071 TAAAATAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
14 13 0.25
15 10 0.20
16 20 0.39
17 2 0.04
18 1 0.02
19 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
ATAAATATAATAATAT
Found at i:4429096 original size:26 final size:23
Alignment explanation
Indices: 4429067--4429114 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
4429057 ATAAATATAG
4429067 TAATTAAAATAGATATTTTATAAAAC
1 TAATTAAAAT--ATATTTT-TAAAAC
*
4429093 TAATTATAATATATTTTTAAAA
1 TAATTAAAATATATTTTTAAAA
4429115 TTTTGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 7 0.33
26 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATTAAAATATATTTTTAAAAC
Found at i:4446102 original size:24 final size:23
Alignment explanation
Indices: 4446069--4446117 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
4446059 TTTATTAGTT
*
4446069 TAATTTAATATATAAAATTATTAA
1 TAATTGAATATATAAAATTA-TAA
* *
4446093 TAATTGAATATGTAATATTATAA
1 TAATTGAATATATAAAATTATAA
4446116 TA
1 TA
4446118 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TAATTGAATATATAAAATTATAA
Found at i:4457260 original size:18 final size:18
Alignment explanation
Indices: 4457234--4457276 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
4457224 CCCTTAGTTT
*
4457234 AACACTTCTCCCATTTAA
1 AACATTTCTCCCATTTAA
4457252 AACATTTCTCCCATTTAA
1 AACATTTCTCCCATTTAA
4457270 AACATTT
1 AACATTT
4457277 AACATTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (18 bp):
AACATTTCTCCCATTTAA
Found at i:4465601 original size:29 final size:30
Alignment explanation
Indices: 4465568--4465624 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
4465558 CAAATTTTGG
* *
4465568 TTAGTGACCATAATATAAA-TTTTGAAAGT
1 TTAGTGACCAAAATATAAAGTTTAGAAAGT
*
4465597 TTAGTGGCCAAAATATAAAGTTTAGAAA
1 TTAGTGACCAAAATATAAAGTTTAGAAA
4465625 ATTTTATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (30 bp):
TTAGTGACCAAAATATAAAGTTTAGAAAGT
Found at i:4465671 original size:30 final size:30
Alignment explanation
Indices: 4465622--4465688 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
4465612 TAAAGTTTAG
*
4465622 AAAATTTTATGGGCTAAAAG-GTAATTTCCT
1 AAAAGTTTATGGGCTAAAAGTGTAATTT-CT
* *
4465652 AAAAGTTTA-GGGACTAAAAGTGTACTTTTT
1 AAAAGTTTATGGG-CTAAAAGTGTAATTTCT
4465682 AAAAGTT
1 AAAAGTT
4465689 AGGTGTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 23 0.72
31 6 0.19
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (30 bp):
AAAAGTTTATGGGCTAAAAGTGTAATTTCT
Found at i:4468274 original size:18 final size:18
Alignment explanation
Indices: 4468218--4468278 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
4468208 TGCATTGGGC
*
4468218 TATGAACTTGAAAATAA-T
1 TATGAATTTG-AAATAAGT
* *
4468236 CTATGAATCTGGAATTAAGT
1 -TATGAAT-TTGAAATAAGT
4468256 TATGAATTTGAAATAAGT
1 TATGAATTTGAAATAAGT
4468274 TATGA
1 TATGA
4468279 GTATGGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 14 0.40
19 18 0.51
20 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (18 bp):
TATGAATTTGAAATAAGT
Found at i:4474430 original size:64 final size:64
Alignment explanation
Indices: 4474361--4474578 Score: 203
Period size: 64 Copynumber: 3.4 Consensus size: 64
4474351 AATGTGCACT
* **
4474361 GATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTC-ATGCA
1 GATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAA-TCGATGCA
4474423 TC
63 TC
* * * *
4474425 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCGGTGCATC
1 GATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGATGCATC
* ** * * * * ** *
4474489 GATGCATAAGG-AGTGCATCGATGCATCTCAGCAATAATACAACATCAAATACATTTTATGCACC
1 GATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGATGCATC
4474553 GATGCATCA-GTAGTGCATCGATGCAT
1 GATGCAT-AGGTAGTGCATCGATGCAT
4474579 ACCTTCATTA
Statistics
Matches: 127, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
63 3 0.02
64 119 0.94
65 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
GATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGATGCATC
Found at i:4475273 original size:31 final size:31
Alignment explanation
Indices: 4475235--4475331 Score: 185
Period size: 31 Copynumber: 3.1 Consensus size: 31
4475225 AGGGTCGAGA
*
4475235 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4475266 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4475297 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4475328 GTTT
1 GTTT
4475332 CTATGGACTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4478218 original size:21 final size:21
Alignment explanation
Indices: 4478194--4478257 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
4478184 GCAAATTCGC
*
4478194 GTTGCATTTCGCGTTGCAATA
1 GTTGCATTTCGCGTTGCGATA
* **
4478215 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
4478235 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
4478256 GT
1 GT
4478258 CTACAGTTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:4478291 original size:19 final size:19
Alignment explanation
Indices: 4478267--4478310 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
4478257 TCTACAGTTG
4478267 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
4478286 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
4478305 TCGTTG
1 TCGTTG
4478311 TGATAGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:4478387 original size:64 final size:60
Alignment explanation
Indices: 4478246--4478418 Score: 249
Period size: 64 Copynumber: 2.8 Consensus size: 60
4478236 TTCCATTTCG
* * *
4478246 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATTTTTCAAATT
1 CGTTGCTATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCGTTGCGATTTTACAAATT
*
4478306 CGTTG-TGATAGTCTACAGTTGTTGTTGCGATAGTTTACAAATTCGTTGCGATAGTTTACAAATT
1 CGTTGCT-ATAGTCTACAGTTGTCGTTGCGAT--TTTACAAATTCGTTGCGAT--TTTACAAATT
*
4478370 CGTTGCTATAGTCTACAGTTGTCGTTGCGATTTTTCAAATTCGTTGCGA
1 CGTTGCTATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCGTTGCGA
4478419 AAATTCGTTG
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
60 28 0.28
62 35 0.35
64 37 0.37
65 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (60 bp):
CGTTGCTATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCGTTGCGATTTTACAAATT
Found at i:4478415 original size:19 final size:20
Alignment explanation
Indices: 4478267--4478418 Score: 121
Period size: 21 Copynumber: 7.5 Consensus size: 20
4478257 TCTACAGTTG
*
4478267 TCGTTGCGAT-TTTCCAAAT
1 TCGTTGCGATATTTACAAAT
*
4478286 TCGTTGCGAT-TTTTCAAAT
1 TCGTTGCGATATTTACAAAT
* * **
4478305 TCGTTGTGATAGTCTACAGTT
1 TCGTTGCGATA-TTTACAAAT
*
4478326 GTTGTTGCGATAGTTTACAAAT
1 -TCGTTGCGATA-TTTACAAAT
4478348 TCGTTGCGATAGTTTACAAAT
1 TCGTTGCGATA-TTTACAAAT
* * **
4478369 TCGTTGCTATAGTCTACAGTT
1 TCGTTGCGATA-TTTACAAAT
*
4478390 GTCGTTGCGAT-TTTTCAAAT
1 -TCGTTGCGATATTTACAAAT
4478410 TCGTTGCGA
1 TCGTTGCGA
4478419 AAATTCGTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 36 0.33
20 5 0.05
21 42 0.39
22 25 0.23
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (20 bp):
TCGTTGCGATATTTACAAAT
Found at i:4478522 original size:6 final size:6
Alignment explanation
Indices: 4478511--4478544 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4478501 AGACACGTAT
4478511 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
4478545 CGAGACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:4479183 original size:22 final size:22
Alignment explanation
Indices: 4479158--4479247 Score: 96
Period size: 22 Copynumber: 4.2 Consensus size: 22
4479148 TGGAAAATCA
4479158 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* *
4479180 CAACAACAACTGTAGACTATTG
1 CAACGACAACTGTAGACTATCG
* * **
4479202 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
*
4479221 CAACGACAACTATAGACTATCG
1 CAACGACAACTGTAGACTATCG
4479243 CAACG
1 CAACG
4479248 CGAAATGGAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 12 0.23
20 2 0.04
21 2 0.04
22 37 0.70
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Found at i:4479221 original size:41 final size:41
Alignment explanation
Indices: 4479176--4479266 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
4479166 ACTGTAGACT
* * *
4479176 ATCGCAACAACAACTGTAGACTATTGCAA-CGAATTTGGAAA
1 ATCGCAACAACAACTATAGACTATCGCAACCGAA-ATGGAAA
*
4479217 ATCGCAACGACAACTATAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACAACAACTATAGACTATCGCAAC-CGAAATGGAAA
4479259 ATCGCAAC
1 ATCGCAAC
4479267 GCGAAATGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 26 0.59
42 14 0.32
43 4 0.09
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACAACAACTATAGACTATCGCAACCGAAATGGAAA
Found at i:4479264 original size:20 final size:20
Alignment explanation
Indices: 4479239--4479290 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
4479229 ACTATAGACT
4479239 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
4479259 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
4479279 ATCGCAACGCGA
1 ATCGCAACGCGA
4479291 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:4479317 original size:21 final size:21
Alignment explanation
Indices: 4479239--4479319 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 21
4479229 ACTATAGACT
*
4479239 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
*
4479259 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
** * *
4479279 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
* *
4479300 ATCGTAACGCGAAATTCAAC
1 ATCGCAACGCGAAATGCAAC
4479320 GCGAATTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 35 0.67
21 17 0.33
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACA
Found at i:4480117 original size:91 final size:90
Alignment explanation
Indices: 4479945--4480118 Score: 203
Period size: 91 Copynumber: 1.9 Consensus size: 90
4479935 AATAGAGGTA
** * *
4479945 TTTTTATCCTAAAATAAAACATTGAGGGTTAAAATGCTTTGTAAAAAATGATAAGGGCCAAAATA
1 TTTTTATCCTAAAATAAAACATTGAGGGCCAAAATGATTTGTAAAAAATGATAAGAGCCAAAATA
* *
4480010 ACTATTCTATTGAATATTAAGAATC
66 ACTATTCTAATAAATATTAAGAATC
4480035 TTTTTATCCTAAAATAAAAACATT-AGGTGGCCAAAAT-ATTT-TAAAAAAAT-ATTAAGAGCCA
1 TTTTTATCCTAAAAT-AAAACATTGA-G-GGCCAAAATGATTTGT-AAAAAATGA-TAAGAGCCA
* *
4480096 AAATAATTATTTTAATAAATATT
61 AAATAACTATTCTAATAAATATT
4480119 GGGTAGTAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
90 18 0.25
91 46 0.65
92 7 0.10
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.34
Consensus pattern (90 bp):
TTTTTATCCTAAAATAAAACATTGAGGGCCAAAATGATTTGTAAAAAATGATAAGAGCCAAAATA
ACTATTCTAATAAATATTAAGAATC
Found at i:4481796 original size:20 final size:20
Alignment explanation
Indices: 4481758--4481797 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4481748 AAATTAGAAA
*
4481758 AATAAAAATTAATATAAAAT
1 AATAAAAATTAATAGAAAAT
* *
4481778 AATATAAATTAGTAGAAAAT
1 AATAAAAATTAATAGAAAAT
4481798 TTTCATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATAAAAATTAATAGAAAAT
Found at i:4485170 original size:72 final size:71
Alignment explanation
Indices: 4485090--4485387 Score: 427
Period size: 72 Copynumber: 4.1 Consensus size: 71
4485080 CGGTTAAAAT
* *
4485090 AAAATAGGCACTACCTATTACATTAAAATACCTACTAGTTTTTTTAAGGTTGCTAATAATGTAAA
1 AAAATAGGCGCTACCTATTACATTAAAATACCTACT-GTTTTTTTAAGGTTTCTAATAATGTAAA
4485155 CGGTAAA
65 CGGTAAA
4485162 AAAATAGGCGCTACCTATTACATTAAAATACCTACTGTTTTTTTTAAGGTTTCTAATAATGTAAA
1 AAAATAGGCGCTACCTATTACATTAAAATACCTACTG-TTTTTTTAAGGTTTCTAATAATGTAAA
4485227 CGGATAAA
65 CGG-TAAA
*
4485235 AAAATAGGCGCTACCTATTACATTAAAATACCTACTG-TTTTTTAAGGTTTATAATAATGTAAAC
1 AAAATAGGCGCTACCTATTACATTAAAATACCTACTGTTTTTTTAAGGTTTCTAATAATGTAAAC
4485299 GGTAAA
66 GGTAAA
* * * * * * * *
4485305 AAAATAGGTGTTACCTATTATATTAAAATACCTAGCAGTTTTTTAAAGATTACTGATAATGTAAA
1 AAAATAGGCGCTACCTATTACATTAAAATACCTA-CTGTTTTTTTAAGGTTTCTAATAATGTAAA
*
4485370 TGGTAAAA
65 CGGT-AAA
4485378 TAAAATAGGC
1 -AAAATAGGC
4485388 ATTGTAAACG
Statistics
Matches: 206, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
70 35 0.17
71 31 0.15
72 88 0.43
73 44 0.21
74 8 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (71 bp):
AAAATAGGCGCTACCTATTACATTAAAATACCTACTGTTTTTTTAAGGTTTCTAATAATGTAAAC
GGTAAA
Found at i:4485347 original size:143 final size:146
Alignment explanation
Indices: 4485084--4485388 Score: 449
Period size: 143 Copynumber: 2.1 Consensus size: 146
4485074 CTTAACCGGT
*
4485084 TAAAATAAAATAGGCACTACCTATTACATTAAAATACCTACTAGTTTTTTTAAGGTTGCTAATAA
1 TAAAATAAAATAGGCACTACCTATTACATTAAAATACCTACTAGTTTTTTTAAGGTTGATAATAA
* * * *
4485149 TGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACTGTTTTTTTTAAGGTTT
66 TGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACAGTTTTTTTAAAGATTA
4485214 CTAATAATGTAAACGG
131 CTAATAATGTAAACGG
* *
4485230 -ATAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACT-G-TTTTTTAAGGTTTATAATA
1 TA-AAATAAAATAGGCACTACCTATTACATTAAAATACCTACTAGTTTTTTTAAGGTTGATAATA
* * *
4485291 ATGTAAACGGTAAAAAAATAGGTGTTACCTATTATATTAAAATACCTAGCAG-TTTTTTAAAGAT
65 ATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CAGTTTTTTTAAAGAT
* *
4485355 TACTGATAATGTAAATGG
129 TACTAATAATGTAAACGG
4485373 TAAAATAAAATAGGCA
1 TAAAATAAAATAGGCA
4485389 TTGTAAACGG
Statistics
Matches: 142, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
143 90 0.63
144 13 0.09
145 36 0.25
146 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (146 bp):
TAAAATAAAATAGGCACTACCTATTACATTAAAATACCTACTAGTTTTTTTAAGGTTGATAATAA
TGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACAGTTTTTTTAAAGATTA
CTAATAATGTAAACGG
Found at i:4485420 original size:99 final size:97
Alignment explanation
Indices: 4485292--4485486 Score: 259
Period size: 100 Copynumber: 2.0 Consensus size: 97
4485282 TTTATAATAA
* * *
4485292 TGTAAACGGTAAAAAAATAGGTGTTACCTATTATATT-A-AAATACCTAGCAGTTTTTTAAAGAT
1 TGTAAACGGTAAAAAAATAGGTGTTACCTATTACATTAACAAAAAACT-G-AGTTTTTTAAAGAT
* *
4485355 TACTGATAATGTAAATGGTAAAATAAAATAGGCAT
64 TACTAATAATGTAAACGGTAAAA-AAAATAGGCAT
* * *
4485390 TGTAAACGGTAAAAACAATAGGTGTTACCTATTACATTAAACAAAAAACTGATTTTTTTTAAGGT
1 TGTAAACGGTAAAAA-AATAGGTGTTACCTATTACATT-AACAAAAAACTGAGTTTTTTAAAGAT
4485455 TACTAATAATGTAAACGGTAAAAAAAATAGGC
64 TACTAATAATGTAAACGGTAAAAAAAATAGGC
4485487 GCTACCTATT
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
98 15 0.18
99 30 0.35
100 32 0.38
101 2 0.02
102 6 0.07
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (97 bp):
TGTAAACGGTAAAAAAATAGGTGTTACCTATTACATTAACAAAAAACTGAGTTTTTTAAAGATTA
CTAATAATGTAAACGGTAAAAAAAATAGGCAT
Found at i:4485520 original size:74 final size:74
Alignment explanation
Indices: 4485390--4486092 Score: 661
Period size: 74 Copynumber: 9.6 Consensus size: 74
4485380 AAATAGGCAT
* * * * * * *
4485390 TGTAAACGGTAAAAACAATAGGTGTTACCTATTACATTAAACA-AAAAACTGATTTTTTTTAAGG
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA-ATACATACCGGTTTTTTTTAAGG
4485454 TTACTAATAA
65 TTACTAATAA
* * ** * *
4485464 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAAGACCTATTGGTTTTTTTAAAGAT
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGGT
4485529 TACTAATAA
66 TACTAATAA
* * * * *
4485538 TGTAAATGCTAAAATAAAATAAGCGCTACCTATTACATTAAAATACATATC-GATTTTTTTAAGG
1 TGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGG
* *
4485602 TTGCTATTAA
65 TTACTAATAA
* * * *
4485612 TGTAAACGGTAAAAAAAATAGGCG--ACCTATTACATTAAACA-AAAAACCAGTTTTTTTAAAGG
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA-ATACATACCGGTTTTTTTTAAGG
4485674 TTACTAATAA
65 TTACTAATAA
** * * * * * ** ** * *
4485684 TAAAAACTGTAAAAAAAAAAGGTGTTACCTATTACATTAAACA-A-AAAATGGGGTTTTTGAAAG
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA-ATACATACCGGTTTTTTTTAAGG
* *
4485747 ATGCTAATAA
65 TTACTAATAA
* * * * * * *
4485757 TGTAAACGGTAAAAAAAATAGGTGTTATCTATTACATTAAAATACCTATCGG-TTTTTTAAAGAT
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGGT
*
4485821 TATTAATAA
66 TACTAATAA
* * * * *
4485830 TGTAAATGGTAAAATAAAATAGGCGCTAACTATTACATTAAACTACTTACC-GATTTTTTTAAGG
1 TGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGG
* *
4485894 TTGCAAATAA
65 TTACTAATAA
* * ** * * * *
4485904 TGTAAACGGTAAAAAAGATATGCATTAACTATTACTTTAAAATACATACCGATTTTTTTTAAGAT
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGGT
4485969 TACTAATAA
66 TACTAATAA
* * * * *
4485978 TGTAAACGGT-AAAAAAATATGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTGAATGT
1 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGGT
*
4486042 TGCTAATAA
66 TACTAATAA
*
4486051 TGTAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAA
1 TGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAA
4486093 CTACCTCCCA
Statistics
Matches: 516, Mismatches: 100, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
71 19 0.04
72 40 0.08
73 184 0.36
74 215 0.42
75 58 0.11
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (74 bp):
TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACATACCGGTTTTTTTTAAGGT
TACTAATAA
Found at i:4485715 original size:220 final size:219
Alignment explanation
Indices: 4485390--4486093 Score: 801
Period size: 220 Copynumber: 3.2 Consensus size: 219
4485380 AAATAGGCAT
* * *
4485390 TGTAAACGGTAAAA-ACAATAGGTGTTACCTATTACATTAAACAAAAAACTGATTTTTTTTAAGG
1 TGTAAACGGTAAAATAAAATAGGCG-TACCTATTACATTAAACAAAAAACCGA-TTTTTTTAAGG
* * *
4485454 TTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAAGACCTATTGGTTT
64 TTACTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAAA-ACATATCGGTTT
* *
4485519 TTTTAAAGATTACTAATAATGTAAATGCTAAAATAAAATAAGCGCTACCTATTACATTAAAATAC
128 TTTTAAAGATTACTAATAATGTAAACGGTAAAA-AAAATAAGCGCTACCTATTACATTAAAATAC
* *
4485584 ATATCGATTTTTTTAAGGTTGCTATTAA
192 CTATCGATTTTTTTAAGGTTGCTAATAA
4485612 TGTAAACGGTAAAA-AAAATAGGCG-ACCTATTACATTAAACAAAAAACC-AGTTTTTTTAAAGG
1 TGTAAACGGTAAAATAAAATAGGCGTACCTATTACATTAAACAAAAAACCGA-TTTTTTT-AAGG
** * * * * * * *
4485674 TTACTAATAATAAAAACTGTAAAAAAAAAAGGTGTTACCTATTACATTAAACAAAAAATGGGGTT
64 TTACTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAA-AACATATCGGTTT
* * * * * *
4485739 TTTGAAAGA-TGCTAATAATGTAAACGGTAAAAAAAATAGGTGTTATCTATTACATTAAAATACC
128 TTTTAAAGATTACTAATAATGTAAACGGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACC
* * * **
4485803 TATCGGTTTTTTAAAGATTATTAATAA
193 TATCGATTTTTTTAAGGTTGCTAATAA
* * * ***
4485830 TGTAAATGGTAAAATAAAATAGGCGCTAACTATTACATTAAACTACTTACCGATTTTTTTAAGGT
1 TGTAAACGGTAAAATAAAATAGGCG-TACCTATTACATTAAACAAAAAACCGATTTTTTTAAGGT
* * * * * * * * *
4485895 TGCAAATAATGTAAACGGTAAAAAAGATATGCATTAACTATTACTTTAAAATACATACCGATTTT
65 TACTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAAA-ACATATCGGTTTT
* *
4485960 TTTTAAGATTACTAATAATGTAAACGGT-AAAAAAATATGCGCTACCTATTACATTAAAATACCT
129 TTTAAAGATTACTAATAATGTAAACGGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACCT
* *
4486024 A-CCAGTTTTTTTGAATGTTGCTAATAA
194 ATCGA-TTTTTTT-AAGGTTGCTAATAA
*
4486051 TGTAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAAC
1 TGTAAACGGTAAAATAAAATAGGCG-TACCTATTACATTAAAC
4486094 TACCTCCCAT
Statistics
Matches: 403, Mismatches: 69, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
218 61 0.15
219 40 0.10
220 182 0.45
221 97 0.24
222 23 0.06
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (219 bp):
TGTAAACGGTAAAATAAAATAGGCGTACCTATTACATTAAACAAAAAACCGATTTTTTTAAGGTT
ACTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAAAACATATCGGTTTTTT
TAAAGATTACTAATAATGTAAACGGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACCTAT
CGATTTTTTTAAGGTTGCTAATAA
Found at i:4485756 original size:73 final size:73
Alignment explanation
Indices: 4485390--4486093 Score: 573
Period size: 73 Copynumber: 9.6 Consensus size: 73
4485380 AAATAGGCAT
* * * *
4485390 TGTAAACGGTAAAAACAATAGGTGTTACCTATTACATTAAACAAAAAA-CTGATTTTTTTTAAGG
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACAAAAAATC-G-GTTTTTTTAAAG
4485454 TTACTAATAA
64 TTACTAATAA
* *** *
4485464 TGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA-AGACCTATTGGTTTTTTTAAAGA
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACA-AAAAATCGGTTTTTTTAAAG-
4485528 TTACTAATAA
64 TTACTAATAA
* * * * * * * *
4485538 TGTAAATGCTAAAATAAAATAAGCGCTACCTATTACATTAAA-ATACATATCGATTTTTTTAAGG
1 TGTAAACGGTAAAA-AAAATAGGCGTTACCTATTACATTAAACA-AAAAATCGGTTTTTTTAAAG
* *
4485602 TTGCTATTAA
64 TTACTAATAA
* *
4485612 TGTAAACGGTAAAAAAAATAGGCG--ACCTATTACATTAAACAAAAAACCAGTTTTTTTAAAGGT
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACAAAAAATCGGTTTTTTTAAA-GT
4485675 TACTAATAA
65 TACTAATAA
** * * * * * * *
4485684 TAAAAACTGTAAAAAAAAAAGGTGTTACCTATTACATTAAACAAAAAATGGGGTTTTTGAAAGAT
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACAAAAAATCGGTTTTTTTAAAGTT
*
4485749 GCTAATAA
66 ACTAATAA
* * ***
4485757 TGTAAACGGTAAAAAAAATAGGTGTTATCTATTACATTAAA-ATACCTATCGG-TTTTTTAAAGA
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACA-AAAAATCGGTTTTTTTAAAG-
*
4485820 TTATTAATAA
64 TTACTAATAA
* * * * *** * * *
4485830 TGTAAATGGTAAAATAAAATAGGCGCTAACTATTACATTAAACTACTTACCGATTTTTTTAAGGT
1 TGTAAACGGTAAAA-AAAATAGGCGTTACCTATTACATTAAACAAAAAATCGGTTTTTTTAAAGT
* *
4485895 TGCAAATAA
65 TACTAATAA
* * * * * * * * * *
4485904 TGTAAACGGTAAAAAAGATATGCATTAACTATTACTTTAAA-ATACATACCGATTTTTTTTAAGA
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACA-AAAAATCGGTTTTTTTAAAG-
4485968 TTACTAATAA
64 TTACTAATAA
* * *** * * *
4485978 TGTAAACGGT-AAAAAAATATGCGCTACCTATTACATTAAA-ATACCTACCAGTTTTTTTGAATG
1 TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACA-AAAAATCGGTTTTTTT-AAAG
*
4486041 TTGCTAATAA
64 TTACTAATAA
* *
4486051 TGTAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAAC
1 TGTAAACGGTAAAA-AAAATAGGCGTTACCTATTACATTAAAC
4486094 TACCTCCCAT
Statistics
Matches: 519, Mismatches: 92, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
71 28 0.05
72 39 0.08
73 187 0.36
74 187 0.36
75 78 0.15
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (73 bp):
TGTAAACGGTAAAAAAAATAGGCGTTACCTATTACATTAAACAAAAAATCGGTTTTTTTAAAGTT
ACTAATAA
Found at i:4487501 original size:20 final size:20
Alignment explanation
Indices: 4487476--4487522 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
4487466 TAAGTAATTA
*
4487476 ATTATTTTATTT-TAATATTT
1 ATTATTTTATTTATAAT-TTG
4487496 ATTATTTTATTTATAATTTG
1 ATTATTTTATTTATAATTTG
4487516 ATTATTT
1 ATTATTT
4487523 AATTGTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTATTTTATTTATAATTTG
Found at i:4487723 original size:14 final size:14
Alignment explanation
Indices: 4487700--4487730 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4487690 ACTATTTAAA
4487700 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
4487714 TTATTTGAATTTAT
1 TTATTAGAATTTAT
4487728 TTA
1 TTA
4487731 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:4490532 original size:32 final size:32
Alignment explanation
Indices: 4490496--4490558 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4490486 AAGAAAAGTT
*
4490496 TATTTTAGGTGTATATGTATGCTTTTATTTAC
1 TATTTTAAGTGTATATGTATGCTTTTATTTAC
*
4490528 TATTTTAAGTGTATGTGTATGCTTTTATTTA
1 TATTTTAAGTGTATATGTATGCTTTTATTTA
4490559 TCGTTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (32 bp):
TATTTTAAGTGTATATGTATGCTTTTATTTAC
Found at i:4496177 original size:21 final size:21
Alignment explanation
Indices: 4496152--4496196 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
4496142 AAAACACAAT
4496152 ATTTTTCAAAAAATAA-TTAA
1 ATTTTTCAAAAAATAATTTAA
*
4496172 ATTTTTGAAAAAATAATTTAA
1 ATTTTTCAAAAAATAATTTAA
4496193 ATTT
1 ATTT
4496197 AAATTGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTTTCAAAAAATAATTTAA
Found at i:4496217 original size:19 final size:20
Alignment explanation
Indices: 4496193--4496232 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4496183 AATAATTTAA
4496193 ATTTAAAT-TGTTGTTTTTG
1 ATTTAAATATGTTGTTTTTG
*
4496212 ATTTAATTATGTTGTTTTTG
1 ATTTAAATATGTTGTTTTTG
4496232 A
1 A
4496233 AAACTACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTTAAATATGTTGTTTTTG
Found at i:4498001 original size:13 final size:13
Alignment explanation
Indices: 4497972--4498006 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
4497962 GGGGAGTAAT
*
4497972 TTTTCAAAATTGA
1 TTTTCAAAAATGA
4497985 -TTTCAAAAATGA
1 TTTTCAAAAATGA
4497997 TTTTCAAAAA
1 TTTTCAAAAA
4498007 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:4498141 original size:19 final size:19
Alignment explanation
Indices: 4498090--4498146 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
4498080 GATATAACAA
* *
4498090 TTAAAGTAT-TATTGAATT
1 TTAAATTATATATTCAATT
*
4498108 TTAAGATTTTATATTCAATT
1 TTAA-ATTATATATTCAATT
4498128 TTAAATTATATATTCAATT
1 TTAAATTATATATTCAATT
4498147 CAATTATTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.12
19 17 0.52
20 12 0.36
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (19 bp):
TTAAATTATATATTCAATT
Found at i:4499999 original size:20 final size:20
Alignment explanation
Indices: 4499967--4500010 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4499957 TAATACCTTG
4499967 AACC-ATTAAAAAACCCTAA
1 AACCAATTAAAAAACCCTAA
*
4499986 AACCAATTATAAAACCCTAA
1 AACCAATTAAAAAACCCTAA
4500006 AACCA
1 AACCA
4500011 TAAACCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (20 bp):
AACCAATTAAAAAACCCTAA
Found at i:4510165 original size:29 final size:29
Alignment explanation
Indices: 4510123--4510197 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
4510113 TTCCATATGT
4510123 TCATGTA-CTCATGTCATTTTTCTTGTGA
1 TCATGTAGCTCATGTCATTTTTCTTGTGA
*
4510151 TCATGTAGCTCATGTCATTTTTGTTGTGA
1 TCATGTAGCTCATGTCATTTTTCTTGTGA
4510180 TCATGTAGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
4510198 GTTCTCATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTTTCTTGTGA
Found at i:4510219 original size:12 final size:12
Alignment explanation
Indices: 4510202--4510236 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
4510192 TGTCATGTTC
4510202 TCATATCACATA
1 TCATATCACATA
4510214 TCATATCACATA
1 TCATATCACATA
4510226 TCATATCACAT
1 TCATATCACAT
4510237 GTGTATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
TCATATCACATA
Found at i:4511850 original size:76 final size:76
Alignment explanation
Indices: 4511724--4511876 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
4511714 ACATTGTCAG
4511724 TTCTTTAGGAATTGTTATAGGAATAATTATTTTTGGGATGAATACCTTTGTTGCATTCACATTTT
1 TTCTTTAGGAATTGTTATAGGAATAATTATTTTTGGGATGAATACCTTTGTTGCATTCACATTTT
4511789 GGATTTGCATT
66 GGATTTGCATT
4511800 TTCTTTAGGAATTGTTATAGGAATAATTATTTTTGGGATGAATACCTTTGTTGCATTCACATTTT
1 TTCTTTAGGAATTGTTATAGGAATAATTATTTTTGGGATGAATACCTTTGTTGCATTCACATTTT
4511865 GGATTTGCATT
66 GGATTTGCATT
4511876 T
1 T
4511877 GTATATTTGC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (76 bp):
TTCTTTAGGAATTGTTATAGGAATAATTATTTTTGGGATGAATACCTTTGTTGCATTCACATTTT
GGATTTGCATT
Found at i:4511909 original size:21 final size:21
Alignment explanation
Indices: 4511850--4511924 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
4511840 AATACCTTTG
*
4511850 TTGCATTCACATTTT-GGA-T
1 TTGCATTCACATTTTAGCATT
***
4511869 TTGCATTTGTATATTT-GCATT
1 TTGCATTCACAT-TTTAGCATT
*
4511890 TTTCATTCACATTTTAGCATT
1 TTGCATTCACATTTTAGCATT
*
4511911 TTGCATTCTCATTT
1 TTGCATTCACATTT
4511925 GCATCATTTG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 9 0.21
20 8 0.19
21 26 0.60
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (21 bp):
TTGCATTCACATTTTAGCATT
Found at i:4511977 original size:28 final size:29
Alignment explanation
Indices: 4511944--4512005 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
4511934 GATTTTTGAG
4511944 CATTTAATTTATGCATCTGAACATTCA-T
1 CATTTAATTTATGCATCTGAACATTCATT
*
4511972 CATTTAATTTATGCATTTGAACATTCATT
1 CATTTAATTTATGCATCTGAACATTCATT
4512001 CATTT
1 CATTT
4512006 CATGAAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (29 bp):
CATTTAATTTATGCATCTGAACATTCATT
Found at i:4514327 original size:21 final size:22
Alignment explanation
Indices: 4514294--4514354 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
4514284 CGAAAGACTG
*
4514294 AAGAAAAACAAAGAAAAAAG-AA
1 AAGAAAGA-AAAGAAAAAAGCAA
* *
4514316 AATGAGA-AAAAGAAAATAGCAA
1 AA-GAAAGAAAAGAAAAAAGCAA
4514338 AAGAAAGAAAAGAAAAA
1 AAGAAAGAAAAGAAAAA
4514355 GAGGAGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 13 0.41
22 16 0.50
23 3 0.09
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (22 bp):
AAGAAAGAAAAGAAAAAAGCAA
Found at i:4514339 original size:13 final size:14
Alignment explanation
Indices: 4514308--4514343 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4514298 AAAACAAAGA
4514308 AAAAAGAAAATGAG
1 AAAAAGAAAATGAG
4514322 AAAAAGAAAAT-AG
1 AAAAAGAAAATGAG
*
4514335 CAAAAGAAA
1 AAAAAGAAA
4514344 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAATGAG
Found at i:4515426 original size:21 final size:20
Alignment explanation
Indices: 4515399--4515458 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
4515389 AATGGAATTG
4515399 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTCA
* *
4515419 TTCAATAAGGGAGAA-AA-T-T
1 TTC-ATAA-TGAGAAGAACTCA
*
4515438 TTCCTAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTCA
4515458 T
1 T
4515459 CCGACGAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 4 0.13
20 5 0.17
21 6 0.20
22 5 0.17
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTCA
Found at i:4515749 original size:115 final size:113
Alignment explanation
Indices: 4515537--4515869 Score: 398
Period size: 115 Copynumber: 2.9 Consensus size: 113
4515527 GGTGGAAGAA
* *
4515537 GTTCATAATGAGAAGAACTCATCCAACGAATGAGAAAAAGTTCATAAT-GAATAACTTATTCAGA
1 GTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGTTCATAATAGAAGAACTT-TT-AGA
* * * * *
4515601 ACTCAACAATATCCATCGCACAATGAGGGGGATCAATATTTCTGATGAAGG
64 ACTCGAC-ATATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAGG
* * *
4515652 GTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCCTAATGAGAAGAACATTTTAGA
1 GTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGTTCATAAT-AGAAGAAC-TTTTAGA
* *
4515717 ACTCGACACATCCATCGCACAAGGAGATGGATCAACATTTCTGAGGAAGG
64 ACTCGACATATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAGG
* * * * *
4515767 GTTCGTAATGAGAACAACTCATCCAACGAAGAAAAAAAAGTTCATAATAAGAAGAACTTGTTTAA
1 GTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGTTCATAAT-AGAAGAAC-T-TTTAG
* * * *
4515832 AACACGACATATCCACCACACAAGGAGGTGAATCAACA
63 AACTCGACATATCCATCGCACAAGGAGGTGGATCAACA
4515870 AAGAGTTCAT
Statistics
Matches: 186, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
115 131 0.70
116 45 0.24
117 8 0.04
118 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGTTCATAATAGAAGAACTTTTAGAAC
TCGACATATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAGG
Found at i:4521576 original size:20 final size:20
Alignment explanation
Indices: 4521547--4521585 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4521537 ATTCTACCAC
4521547 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
*
4521567 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
4521586 TATGAGCTCT
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:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:4521588 original size:10 final size:10
Alignment explanation
Indices: 4521553--4521590 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4521543 CCACATGCAA
4521553 CTATATGATC
1 CTATATGATC
*
4521563 CTAAATGCAT-
1 CTATATG-ATC
4521573 CTATATGATC
1 CTATATGATC
4521583 CTATATGA
1 CTATATGA
4521591 GCTCTTAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (10 bp):
CTATATGATC
Found at i:4530667 original size:20 final size:20
Alignment explanation
Indices: 4530638--4530679 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4530628 ATTCCACCAC
*
4530638 ATACAACTATATGCTCCTAA
1 ATACAACTATATGATCCTAA
*
4530658 ATACATCTATATGATCCTAA
1 ATACAACTATATGATCCTAA
4530678 AT
1 AT
4530680 GGGTTCTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (20 bp):
ATACAACTATATGATCCTAA
Found at i:4532215 original size:22 final size:22
Alignment explanation
Indices: 4532187--4532237 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
4532177 TGATCAGATT
4532187 TTATCATATCCCAATAAACAAG
1 TTATCATATCCCAATAAACAAG
4532209 TTATCATATCCCAATAAACAAG
1 TTATCATATCCCAATAAACAAG
4532231 TTATCAT
1 TTATCAT
4532238 CAAACTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (22 bp):
TTATCATATCCCAATAAACAAG
Found at i:4533471 original size:20 final size:21
Alignment explanation
Indices: 4533432--4533472 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4533422 TGATGATCTG
*
4533432 ATTTTATATTTTTTTTAAATTA
1 ATTTTATA-TTTTTTAAAATTA
4533454 ATTTTATA-TTTTTAAAATT
1 ATTTTATATTTTTTAAAATT
4533473 TTAATACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATATTTTTTAAAATTA
Found at i:4534216 original size:51 final size:50
Alignment explanation
Indices: 4534156--4534267 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 50
4534146 TGAATATAAA
* *
4534156 TAAAATTTTAGAAAAAAAGCTGTTAATCAAA-TAAATAATTAATTAAAAAAC
1 TAAAATTTTAGAAAAAAAGC-ATTAAT-AAATTAAATAATTAATAAAAAAAC
* * * *
4534207 TAAAATTTTAAGATAAACATCATTAATAAATTAAATAATTAATAAAAAAAT
1 TAAAATTTT-AGAAAAAAAGCATTAATAAATTAAATAATTAATAAAAAAAC
*
4534258 TCAAATTTTA
1 TAAAATTTTA
4534268 TAATAATCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
50 4 0.08
51 40 0.77
52 8 0.15
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (50 bp):
TAAAATTTTAGAAAAAAAGCATTAATAAATTAAATAATTAATAAAAAAAC
Found at i:4534446 original size:11 final size:11
Alignment explanation
Indices: 4534432--4534462 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4534422 AAAATATAAT
4534432 AAAAAAAAGAA
1 AAAAAAAAGAA
*
4534443 AAAAAGAAGAA
1 AAAAAAAAGAA
4534454 AAAAAAAAG
1 AAAAAAAAG
4534463 GTACTTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:4536202 original size:80 final size:80
Alignment explanation
Indices: 4536117--4536280 Score: 222
Period size: 80 Copynumber: 2.0 Consensus size: 80
4536107 TTTTGAAAAT
** **
4536117 TATATTTATAACCACTTAAATATTGTCTTTTTTTATTATTGGAAAAATATTATAAGTGTTCTATT
1 TATATTTATAACCACTTAAATATTGTCACTTTTTATTA-TAAAAAAATATTATAAGTGTTCTATT
*
4536182 TGGATAATA-ATAAAC
65 TGGATAAAATATAAAC
* * * *
4536197 TATATTTATGATCACTTAATTGTTGTCACTTTTTATTATAAAAAAATATTATAAGTGTTCTATTT
1 TATATTTATAACCACTTAAATATTGTCACTTTTTATTATAAAAAAATATTATAAGTGTTCTATTT
*
4536262 TGATAAAATATAAAC
66 GGATAAAATATAAAC
4536277 TATA
1 TATA
4536281 CATATGATCA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 31 0.42
80 42 0.58
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (80 bp):
TATATTTATAACCACTTAAATATTGTCACTTTTTATTATAAAAAAATATTATAAGTGTTCTATTT
GGATAAAATATAAAC
Found at i:4536287 original size:80 final size:79
Alignment explanation
Indices: 4536146--4536474 Score: 304
Period size: 80 Copynumber: 4.1 Consensus size: 79
4536136 ATATTGTCTT
** * * * *
4536146 TTTTTATTATTGGAAAAATATTATAAGTGTTCTATTTGGATAATAATAAACTATATTTATGATCA
1 TTTTTATTATAAGAAAAATATTATAAGTATTCTATTTTGATAAAAATAAACTATATATATGATCA
4536211 CTTAATTGTTGTCAC
66 CTTAATTGTTGTC-C
* *
4536226 TTTTTATTATAA-AAAAATATTATAAGTGTTCTATTTTGATAAAATATAAACTATACATATGATC
1 TTTTTATTATAAGAAAAATATTATAAGTATTCTATTTTGATAAAA-ATAAACTATATATATGATC
*
4536290 ATTTAATTGTTGTCC
65 ACTTAATTGTTGTCC
* * * * * * * *
4536305 TTTTTCTTTATAAGAAAAAAATTGTAATTATCCTA-GTTGAATAAAAAATAAACTATATGTACGA
1 TTTTT-ATTATAAGAAAAATATTATAAGTATTCTATTTTG-AT-AAAAATAAACTATATATATGA
*
4536369 TCACTTAAGTGTTGTCTC
63 TCACTTAATTGTTGTC-C
* * * * * * ** * *
4536387 TTTTCATTGTAAGAAAGATATTGTAAGTATTTTATTTAGATAGAGGAT-AAGTTTATATATGATC
1 TTTTTATTATAAGAAAAATATTATAAGTATTCTATTTTGATA-AAAATAAACTATATATATGATC
*
4536451 AATTAATTGTTGTTCC
65 ACTTAATTGTTG-TCC
4536467 TTTTTATT
1 TTTTTATT
4536475 TTGACAATCG
Statistics
Matches: 202, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
79 36 0.18
80 80 0.40
81 75 0.37
82 11 0.05
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (79 bp):
TTTTTATTATAAGAAAAATATTATAAGTATTCTATTTTGATAAAAATAAACTATATATATGATCA
CTTAATTGTTGTCC
Found at i:4536371 original size:81 final size:81
Alignment explanation
Indices: 4536129--4536471 Score: 270
Period size: 81 Copynumber: 4.3 Consensus size: 81
4536119 TATTTATAAC
* * * * ** * * * *
4536129 CACTTAAATATTGTCTTTTTTTATTATTGGAAAAATATTATAAGTGTTCTAT-TTGGAT-AATAA
1 CACTTAATTGTTGTCCTTTTTCATTATAAGAAAAATATTGTAAGTATCCTATGTT-GATAAAAAA
*
4536192 TAAACTATATTTATGAT
65 TAAACTATATATATGAT
* * * * *
4536209 CACTTAATTGTTGTCACTTTTT-ATTATAA-AAAAATATTATAAGTGTTCTATTTTGATAAAATA
1 CACTTAATTGTTGTC-CTTTTTCATTATAAGAAAAATATTGTAAGTATCCTATGTTGATAAAAAA
*
4536272 TAAACTATACATATGAT
65 TAAACTATATATATGAT
* * * *
4536289 CATTTAATTGTTGTCCTTTTTCTTTATAAGAAAAAAATTGTAATTATCCTA-GTTGAATAAAAAA
1 CACTTAATTGTTGTCCTTTTTCATTATAAGAAAAATATTGTAAGTATCCTATGTTG-ATAAAAAA
* *
4536353 TAAACTATATGTACGAT
65 TAAACTATATATATGAT
* * * ** * **
4536370 CACTTAAGTGTTGT-CTCTTTTCATTGTAAGAAAGATATTGTAAGTATTTTAT-TTAGATAGAGG
1 CACTTAATTGTTGTCCT-TTTTCATTATAAGAAAAATATTGTAAGTATCCTATGTT-GATAAAAA
* *
4536433 AT-AAGTTTATATATGAT
64 ATAAACTATATATATGAT
*
4536450 CAATTAATTGTTGTTCCTTTTT
1 CACTTAATTGTTG-TCCTTTTT
4536472 ATTTTGACAA
Statistics
Matches: 213, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
79 31 0.15
80 85 0.40
81 94 0.44
82 3 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (81 bp):
CACTTAATTGTTGTCCTTTTTCATTATAAGAAAAATATTGTAAGTATCCTATGTTGATAAAAAAT
AAACTATATATATGAT
Found at i:4537144 original size:22 final size:22
Alignment explanation
Indices: 4537119--4537174 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
4537109 AAAGATAGTA
*
4537119 CATATGATAATACAAAACATAT
1 CATATAATAATACAAAACATAT
*
4537141 CATATAATAATAATACAAAAGATAT
1 C--AT-ATAATAATACAAAACATAT
4537166 CATATAATA
1 CATATAATA
4537175 GTATATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 2 0.07
25 18 0.62
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.29
Consensus pattern (22 bp):
CATATAATAATACAAAACATAT
Found at i:4537153 original size:25 final size:25
Alignment explanation
Indices: 4537125--4537174 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4537115 AGTACATATG
4537125 ATAATACAAAACATATCATATAATA
1 ATAATACAAAACATATCATATAATA
*
4537150 ATAATACAAAAGATATCATATAATA
1 ATAATACAAAACATATCATATAATA
4537175 GTATATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (25 bp):
ATAATACAAAACATATCATATAATA
Found at i:4542884 original size:64 final size:64
Alignment explanation
Indices: 4542783--4542909 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
4542773 CATATACATA
*
4542783 TTAAGGGTGTTATATACTATATAATATATCCTAAAAGTATTGTAGCACCATCAACACATATGTG
1 TTAAGGGTGTTACATACTATATAATATATCCTAAAAGTATTGTAGCACCATCAACACATATGTG
*
4542847 TTAAGGGTGTTACATACTATATAATATATCCTGAAAGTATTGTAGCACCATCAACACATATGT
1 TTAAGGGTGTTACATACTATATAATATATCCTAAAAGTATTGTAGCACCATCAACACATATGT
4542910 ATTATGTAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (64 bp):
TTAAGGGTGTTACATACTATATAATATATCCTAAAAGTATTGTAGCACCATCAACACATATGTG
Found at i:4551189 original size:21 final size:22
Alignment explanation
Indices: 4551160--4551200 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4551150 TATTCAAGTG
* *
4551160 AATTATATATACTTTTTTAAAA
1 AATTATATACAATTTTTTAAAA
4551182 AATT-TATACAATTTTTTAA
1 AATTATATACAATTTTTTAA
4551201 TTTATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATATACAATTTTTTAAAA
Found at i:4551210 original size:21 final size:19
Alignment explanation
Indices: 4551162--4551223 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
4551152 TTCAAGTGAA
* *
4551162 TTATATATACTTTTTTAAA
1 TTATATATACATTTTTAAT
** *
4551181 AAATTTATACAATTTTTTAAT
1 TTATATATAC-A-TTTTTAAT
4551202 TTATATATACATTTTTAAT
1 TTATATATACATTTTTAAT
4551221 TTA
1 TTA
4551224 GAAGATAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 18 0.55
20 1 0.03
21 14 0.42
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATATACATTTTTAAT
Found at i:4552750 original size:2 final size:2
Alignment explanation
Indices: 4552743--4552772 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4552733 TATAAAGTCA
4552743 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
4552773 GAATTTCACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4553485 original size:22 final size:23
Alignment explanation
Indices: 4553432--4553485 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
4553422 ATTTTTTAAC
* *
4553432 TTATTGATTAAAATATATATTAT
1 TTATTAATAAAAATATATATTAT
* **
4553455 TAAAAAATAAAAATAT-TATTAT
1 TTATTAATAAAAATATATATTAT
4553477 TTATTAATA
1 TTATTAATA
4553486 TCTAAAATCA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTATTAATAAAAATATATATTAT
Found at i:4556143 original size:15 final size:15
Alignment explanation
Indices: 4556119--4556156 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4556109 TGACGGAAAG
*
4556119 AATATTTGATAAAAA
1 AATATATGATAAAAA
4556134 AATATATGATAAAAA
1 AATATATGATAAAAA
*
4556149 TATATATG
1 AATATATG
4556157 TTTTACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (15 bp):
AATATATGATAAAAA
Found at i:4556662 original size:31 final size:31
Alignment explanation
Indices: 4556594--4556716 Score: 140
Period size: 31 Copynumber: 3.8 Consensus size: 31
4556584 ACAGATGTGG
* * *
4556594 TGTAACTTAAAATGTAGTGCAACTATAAATTAAGT
1 TGTAACTTAAAATG-A---CAACAATAAAATAGGT
*
4556629 TGTAATTTAAAATGACAATC-ATAAAATAGGT
1 TGTAACTTAAAATGACAA-CAATAAAATAGGT
* *
4556660 TGTAACTTAAAATGATAACTATAAAATAGGT
1 TGTAACTTAAAATGACAACAATAAAATAGGT
4556691 TGTAACTTAAAATGACAACAATAAAA
1 TGTAACTTAAAATGACAACAATAAAA
4556717 GAGGAGAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.01
31 63 0.80
32 1 0.01
34 1 0.01
35 13 0.16
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (31 bp):
TGTAACTTAAAATGACAACAATAAAATAGGT
Found at i:4556672 original size:17 final size:17
Alignment explanation
Indices: 4556650--4556703 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
4556640 ATGACAATCA
4556650 TAAAATAGGTTGTAACT
1 TAAAATAGGTTGTAACT
*
4556667 TAAAAT--G--ATAACT
1 TAAAATAGGTTGTAACT
4556680 ATAAAATAGGTTGTAACT
1 -TAAAATAGGTTGTAACT
4556698 TAAAAT
1 TAAAAT
4556704 GACAACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 1 0.03
16 1 0.03
17 12 0.40
18 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (17 bp):
TAAAATAGGTTGTAACT
Found at i:4556693 original size:62 final size:65
Alignment explanation
Indices: 4556594--4556716 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 65
4556584 ACAGATGTGG
* *
4556594 TGTAACTTAAAATGTAGTGCAACTATAAATTAAGTTGTAATTTAAAATGACAATC-ATAAAATAG
1 TGTAACTTAAAATGTAGT-CAACTATAAAATAAGTTGTAACTTAAAATGACAA-CAATAAAATAG
4556658 GT
64 GT
*
4556660 TGTAACTTAAAATG-A-T-AACTATAAAATAGGTTGTAACTTAAAATGACAACAATAAAA
1 TGTAACTTAAAATGTAGTCAACTATAAAATAAGTTGTAACTTAAAATGACAACAATAAAA
4556717 GAGGAGAAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 1 0.02
62 36 0.68
64 1 0.02
65 1 0.02
66 14 0.26
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (65 bp):
TGTAACTTAAAATGTAGTCAACTATAAAATAAGTTGTAACTTAAAATGACAACAATAAAATAGGT
Found at i:4556945 original size:16 final size:16
Alignment explanation
Indices: 4556924--4556956 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4556914 GGGTATATGA
4556924 TTCCGGAAAAGATTAT
1 TTCCGGAAAAGATTAT
4556940 TTCCGGAAAAGATTAT
1 TTCCGGAAAAGATTAT
4556956 T
1 T
4556957 CTCCTTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (16 bp):
TTCCGGAAAAGATTAT
Done.