Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 35
Found at i:763066 original size:131 final size:131
Alignment explanation
Indices: 762771--763147 Score: 558
Period size: 131 Copynumber: 2.9 Consensus size: 131
762761 CACTCAAATT
* * * *
762771 AATATTGAATTTTAGGATAAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAATGACTACT
1 AATATTGAATTTTAGGACAAAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCT
* * * * ** * *
762836 TTAAGGCATGAGAAGTCTTTTATTCTCGATT-GAAATAATCATATATTATTTTTTTCTCTCGAAT
66 TTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTATATCGAAT
762900 C
131 C
* * *
762901 AATATTAAATTTTAAGACAAAATAGTAATATCTCTTTATTTCGATTGAAGTAATAAATGACTGCT
1 AATATTGAATTTTAGGACAAAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCT
*
762966 TTAAGGCATGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTATATCGAAT
66 TTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTATATCGAAT
763031 C
131 C
**
763032 AATATTGAATTTTAGGAGGAAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCT
1 AATATTGAATTTTAGGACAAAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCT
* * *
763097 TTAAGGCATGAGAGTTCATTTATTCTCGATTGGAAATAAATAGCTATTATC
66 TTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
763148 ATTTACTCTC
Statistics
Matches: 221, Mismatches: 25, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
130 86 0.39
131 135 0.61
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (131 bp):
AATATTGAATTTTAGGACAAAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCT
TTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTATATCGAAT
C
Found at i:763573 original size:17 final size:17
Alignment explanation
Indices: 763559--763591 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
763549 TGTAAAATTG
763559 TTTTTTAATTAAAATAT
1 TTTTTTAATTAAAATAT
*
763576 TTTTTTTATTAAAATA
1 TTTTTTAATTAAAATA
763592 ACAAATACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTTAATTAAAATAT
Found at i:765098 original size:21 final size:21
Alignment explanation
Indices: 765045--765100 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
765035 ACCACCCCGT
* * *
765045 GAGTATTAAAACTCCTTGAAC
1 GAGTATCAATACTCATTGAAC
765066 GAGTATCAATACTCATTGAAC
1 GAGTATCAATACTCATTGAAC
*
765087 GAGTATCGATACTC
1 GAGTATCAATACTC
765101 CCTTCATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
GAGTATCAATACTCATTGAAC
Found at i:767471 original size:16 final size:16
Alignment explanation
Indices: 767443--767480 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
767433 TAATTCGATC
767443 TAAAAA-TTCAGATAT
1 TAAAAATTTCAGATAT
*
767458 TAAAAATTTTAGATAT
1 TAAAAATTTCAGATAT
767474 TAAAAAT
1 TAAAAAT
767481 AGTGGTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (16 bp):
TAAAAATTTCAGATAT
Found at i:768561 original size:42 final size:42
Alignment explanation
Indices: 768508--768587 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
768498 TATAGCACCC
768508 TTTTTTTTTAAGTTACTTTTCATCCATACGTATCATTTCCCT
1 TTTTTTTTTAAGTTACTTTTCATCCATACGTATCATTTCCCT
768550 TTTTTTTTTAAGTTACTTTTCATCCATACGTATCATTT
1 TTTTTTTTTAAGTTACTTTTCATCCATACGTATCATTT
768588 TCTTTCAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.20, C:0.19, G:0.05, T:0.56
Consensus pattern (42 bp):
TTTTTTTTTAAGTTACTTTTCATCCATACGTATCATTTCCCT
Found at i:772039 original size:24 final size:25
Alignment explanation
Indices: 771987--772104 Score: 75
Period size: 24 Copynumber: 4.6 Consensus size: 25
771977 TATTAAAATA
*
771987 TTAAAAATATATATATTA-A-TATTT
1 TTAATAATATA-ATATTATACTATTT
*
772011 CTAATAATATAATATTATACT-TTT
1 TTAATAATATAATATTATACTATTT
* *
772035 TTAATATTATAATAATATACTCAATTATAT
1 TTAATAATATAATATTATACT--A-T-T-T
*
772065 TGTAATAATATAGGATATTATATTA-TT
1 T-TAATAATATA--ATATTATACTATTT
772092 TTAAT-ATATAATA
1 TTAATAATATAATA
772105 AATTATTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 23
0.71 0.08 0.22
Matches are distributed among these distances:
23 9 0.12
24 31 0.41
25 6 0.08
26 4 0.05
27 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 10 0.13
33 8 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
TTAATAATATAATATTATACTATTT
Found at i:772122 original size:33 final size:34
Alignment explanation
Indices: 772080--772145 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
772070 TAATATAGGA
* *
772080 TATTATATTATTTTAATATATAATAA-ATTATTAT
1 TATTATATTAATTTAATAGA-AATAATATTATTAT
*
772114 TATT-TATTAATTTCATAGAAATAATATTATTA
1 TATTATATTAATTTAATAGAAATAATATTATTA
772146 AATTATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 5 0.18
33 19 0.68
34 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
TATTATATTAATTTAATAGAAATAATATTATTAT
Found at i:772218 original size:23 final size:24
Alignment explanation
Indices: 772180--772241 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
772170 TTTATGTATT
772180 TAATA-TTT-ATATAATA-ATCTAA
1 TAATATTTTAATA-AATATATCTAA
*
772202 TAATATTTTAATAAATATATTTAA
1 TAATATTTTAATAAATATATCTAA
* *
772226 -AATATATTAATTAATA
1 TAATATTTTAATAAATA
772242 CTTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 5 0.15
23 21 0.62
24 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATATTTTAATAAATATATCTAA
Found at i:772268 original size:35 final size:33
Alignment explanation
Indices: 772187--772269 Score: 80
Period size: 35 Copynumber: 2.5 Consensus size: 33
772177 ATTTAATATT
*
772187 TATATAATAAT-CTAATAATATTTTAATAAATA
1 TATATAATAATATTAATAATATTTTAATAAATA
* * *
772219 TATTTAAAATATATTAATTAATACTTTTTA-AAATA
1 TATATAATA-ATATTAA-TAATA-TTTTAATAAATA
772254 TAATATAATAATATTA
1 T-ATATAATAATATTA
772270 TTTTAATAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
32 7 0.17
33 2 0.05
34 3 0.08
35 17 0.43
36 11 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (33 bp):
TATATAATAATATTAATAATATTTTAATAAATA
Found at i:772275 original size:26 final size:24
Alignment explanation
Indices: 772203--772255 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
772193 ATAATCTAAT
* * *
772203 AATATTTTAATAAATA-TATTTAA
1 AATATATTAATTAATACTTTTTAA
772226 AATATATTAATTAATACTTTTTAA
1 AATATATTAATTAATACTTTTTAA
772250 AATATA
1 AATATA
772256 ATATAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATATATTAATTAATACTTTTTAA
Found at i:774983 original size:59 final size:59
Alignment explanation
Indices: 774898--775310 Score: 569
Period size: 59 Copynumber: 7.0 Consensus size: 59
774888 TTTATTTCCC
* * ** *
774898 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTGGCACAC-AAGGTATCCA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAA-GTGCCCT
* * * * ** * * *
774957 ATATGAAAATTCATATATTTAATATGAATTTATTATCATTTTAGTACCCGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
** *
775016 ATACAGAAATTCATACACTTAGTATGAATTCCTTATAATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
* *
775075 ATATGGAAATTCATACACTTAGTATGAATTCATTCTCATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
* *
775134 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCTT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
* *
775193 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACATGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
* *
775252 ATATGGAAATTCATACACTTAGTATGAATTTCTTTAT-ATTTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAA-TTCCTTATCATGTTAGCACACGAAGTGCCCT
775311 TTTTGGTAAT
Statistics
Matches: 315, Mismatches: 37, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
59 307 0.97
60 8 0.03
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (59 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCT
Found at i:778792 original size:15 final size:15
Alignment explanation
Indices: 778772--778807 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
778762 TATATGAATA
778772 AATAATAA-TAATAGT
1 AATAATAATTAA-AGT
778787 AATAATAATTAAAGT
1 AATAATAATTAAAGT
778802 AATAAT
1 AATAAT
778808 TTAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AATAATAATTAAAGT
Found at i:780311 original size:25 final size:23
Alignment explanation
Indices: 780285--780332 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
780275 ATAAGTCTTT
780285 AATATATATTTAATTTGAATTAATTA
1 AATA-ATATTTAATTT--ATTAATTA
*
780311 AATAATATTTTATTTATTAATT
1 AATAATATTTAATTTATTAATT
780333 TGAAATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATAATATTTAATTTATTAATTA
Found at i:780898 original size:2 final size:2
Alignment explanation
Indices: 780891--780927 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
780881 ACATGCATGC
780891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
780928 GTTTGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:791048 original size:10 final size:10
Alignment explanation
Indices: 791033--791062 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
791023 AATAACATGA
791033 AAAAGAAAAT
1 AAAAGAAAAT
791043 AAAAGAAAAT
1 AAAAGAAAAT
791053 AAAAGTAAAA
1 AAAAG-AAAA
791063 CTATACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:797642 original size:17 final size:17
Alignment explanation
Indices: 797620--797688 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
797610 AAAAATTTAA
*
797620 TATATATAATA-TATGTT
1 TATATATAA-ACTATATT
797637 TATATATAAACTATATT
1 TATATATAAACTATATT
797654 TATATTATAAACTATATAAT
1 TATA-TATAAACTATAT--T
*
797674 TAT-TATAAGCTATAT
1 TATATATAAACTATAT
797689 ATAAATTATG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
16 1 0.02
17 18 0.39
18 23 0.50
20 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATATAAACTATATT
Found at i:797643 original size:19 final size:18
Alignment explanation
Indices: 797614--797670 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
797604 TTTTAAAAAA
797614 ATTTAATATATATAA-TAT
1 ATTT-ATATATATAACTAT
797632 ATGTT-TATATATAAACTAT
1 AT-TTATATATAT-AACTAT
797651 ATTTATAT-TATAAACTAT
1 ATTTATATATAT-AACTAT
797669 AT
1 AT
797671 AATTATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.20
18 18 0.51
19 10 0.29
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTTATATATATAACTAT
Found at i:797696 original size:18 final size:18
Alignment explanation
Indices: 797637--797811 Score: 76
Period size: 18 Copynumber: 9.5 Consensus size: 18
797627 AATATATGTT
*
797637 TATA-TATAAACTATATT
1 TATATTATAAACTATATA
797654 TATATTATAAACTATATA
1 TATATTATAAACTATATA
*
797672 -ATTATTATAAGCTATATA
1 TA-TATTATAAACTATATA
* ***
797690 TAAATTAT-GTTTATATGAA
1 TATATTATAAACTATAT--A
797709 CTATATATATAAACTATATA
1 -TATAT-TATAAACTATATA
* * *
797729 TGTAAACTATATATCTATA-A
1 --TATATTATA-AACTATATA
* * *
797749 AATATAAAAAAACTATA-A
1 TATAT-TATAAACTATATA
*
797767 TTTATTATATAA-TATATA
1 TATATTATA-AACTATATA
*
797785 TATATTATATA-TATATA
1 TATATTATAAACTATATA
797802 TATATATATA
1 TATAT-TATA
797812 TTTATGAGTA
Statistics
Matches: 118, Mismatches: 26, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
17 28 0.24
18 59 0.50
19 4 0.03
20 10 0.08
21 12 0.10
22 5 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATTATAAACTATATA
Found at i:797777 original size:2 final size:2
Alignment explanation
Indices: 797772--797834 Score: 85
Period size: 2 Copynumber: 31.5 Consensus size: 2
797762 TATAATTTAT
797772 TA TA TA -A TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
797812 TT TA TGA GTA TA TA TA TA TA TA T
1 TA TA T-A -TA TA TA TA TA TA TA T
797835 TATTCAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 2 0.04
2 50 0.91
3 2 0.04
4 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:797799 original size:45 final size:46
Alignment explanation
Indices: 797736--797837 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 46
797726 ATATGTAAAC
*
797736 TATATATCTATAAAATATAAAAAAACTATA-ATTTATTA-TATAATATA
1 TATATAT-TATAAAATATAAAAAAA-TATATATTTATGAGTAT-ATATA
* * * *
797783 TATATATTAT-ATATATATATATATATATATTTATGAGTATATATA
1 TATATATTATAAAATATAAAAAAATATATATTTATGAGTATATATA
797828 TATATATTAT
1 TATATATTAT
797838 TCAAAATGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 4 0.08
45 31 0.65
46 6 0.12
47 7 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (46 bp):
TATATATTATAAAATATAAAAAAATATATATTTATGAGTATATATA
Found at i:797969 original size:19 final size:20
Alignment explanation
Indices: 797947--797984 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
797937 GAATATAGGG
797947 AAATT-GGAAATTTAGAGGA
1 AAATTGGGAAATTTAGAGGA
797966 AAATTGGGAAATTTAGAGG
1 AAATTGGGAAATTTAGAGG
797985 GAATAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (20 bp):
AAATTGGGAAATTTAGAGGA
Found at i:797974 original size:27 final size:27
Alignment explanation
Indices: 797922--797978 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
797912 TTAGAGAGAG
* *
797922 ATTGAGAAATTTTGAGAATATAGGGAA
1 ATTGAGAAATTTAGAGAAAATAGGGAA
*
797949 ATTG-GAAATTTAGAGGAAAATTGGGAA
1 ATTGAGAAATTTAGA-GAAAATAGGGAA
797976 ATT
1 ATT
797979 TAGAGGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (27 bp):
ATTGAGAAATTTAGAGAAAATAGGGAA
Found at i:798189 original size:2 final size:2
Alignment explanation
Indices: 798182--798322 Score: 66
Period size: 2 Copynumber: 73.0 Consensus size: 2
798172 CTTTTAATTT
* * * * *
798182 TA TA TA TA TA TA TA AA TA TG TG TA TA TG TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
798225 -A AA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA T- TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
798263 GTA TA TA TA TA TA TG TA TA -A CTA -A TA TA AA TA -A TA TA TA GA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
798304 T- TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
798323 GTTAATAGAA
Statistics
Matches: 103, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
1 9 0.09
2 89 0.86
3 5 0.05
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:798529 original size:2 final size:2
Alignment explanation
Indices: 798494--798520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
798484 TAAAACTTTC
798494 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
798521 AACTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:798614 original size:7 final size:7
Alignment explanation
Indices: 798604--798635 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
798594 TAGTTTATAG
798604 AAACCCT
1 AAACCCT
*
798611 AAACCTT
1 AAACCCT
798618 AAACCCT
1 AAACCCT
798625 AAACCCT
1 AAACCCT
798632 AAAC
1 AAAC
798636 TATATATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:798829 original size:53 final size:57
Alignment explanation
Indices: 798772--798903 Score: 164
Period size: 53 Copynumber: 2.4 Consensus size: 57
798762 TGTATACATG
* * * *
798772 TAAACTATCTATGTAACTTATAATATATGTATGTATA-AA-CTGTGTATA-G-TATA
1 TAAACTATATATGTAACCTATAATATATGTATATATACAATCTATGTATATGTTATA
* * *
798825 TAAACTATATATATAACCTATAGTATATGTATATATACAATCTATTTATATGTTATA
1 TAAACTATATATGTAACCTATAATATATGTATATATACAATCTATGTATATGTTATA
*
798882 TAAACTATATATGTAACGTATA
1 TAAACTATATATGTAACCTATA
798904 GTTTATAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 32 0.48
54 2 0.03
55 7 0.11
56 1 0.02
57 24 0.36
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (57 bp):
TAAACTATATATGTAACCTATAATATATGTATATATACAATCTATGTATATGTTATA
Found at i:798839 original size:13 final size:14
Alignment explanation
Indices: 798816--798852 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
798806 ATAAACTGTG
798816 TATAGTATATAAAC
1 TATAGTATATAAAC
*
798830 TATA-TATATAACC
1 TATAGTATATAAAC
798843 TATAGTATAT
1 TATAGTATAT
798853 GTATATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (14 bp):
TATAGTATATAAAC
Found at i:798889 original size:20 final size:22
Alignment explanation
Indices: 798832--798890 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
798822 ATATAAACTA
*
798832 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
798854 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
798877 T-TATATAAACTATA
1 TATATATAAACTATA
798891 TATGTAACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:799075 original size:21 final size:21
Alignment explanation
Indices: 798935--799075 Score: 81
Period size: 21 Copynumber: 6.6 Consensus size: 21
798925 TTAGTGTACT
* *
798935 ATATAGTTTATACTTTATAAC
1 ATATAGTTTATAATTTATAAA
* *
798956 CTATAGTATATAATTTAT-AA
1 ATATAGTTTATAATTTATAAA
* **
798976 ATATAGTTTAT-ATTAATGTTA
1 ATATAGTTTATAATTTAT-AAA
* *
798997 AT-TATCTTAACTATAATTTATATTA
1 ATATA-GTT---TATAATTTATA-AA
* *
799022 ATATAGTATATAGTTTATAAA
1 ATATAGTTTATAATTTATAAA
* * *
799043 CTATACTATATAATTTATAAA
1 ATATAGTTTATAATTTATAAA
799064 ATATAGTTTATA
1 ATATAGTTTATA
799076 TTAATATTAA
Statistics
Matches: 90, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
19 5 0.06
20 12 0.13
21 48 0.53
22 10 0.11
24 3 0.03
25 10 0.11
26 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
ATATAGTTTATAATTTATAAA
Found at i:799084 original size:6 final size:6
Alignment explanation
Indices: 799073--799196 Score: 66
Period size: 6 Copynumber: 20.8 Consensus size: 6
799063 AATATAGTTT
* * * *
799073 ATATTA ATATTA ATTTTA TATACT- ATATTTT ATATT- A-ATTA ATATAA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA ATATTA
* *
799120 ACTATATT ATATTA ATA-TA A-GTTA ATATTA ATATTA AT-TATA ATATATA
1 A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA ATAT-TA
*
799169 AT-TT- ATATTA ATATTA ATTATAA ATATT
1 ATATTA ATATTA ATATTA A-TATTA ATATT
799197 TTACTAATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
4 5 0.05
5 15 0.16
6 48 0.52
7 23 0.25
8 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:799105 original size:88 final size:87
Alignment explanation
Indices: 798935--799111 Score: 259
Period size: 88 Copynumber: 2.0 Consensus size: 87
798925 TTAGTGTACT
* * * *
798935 ATATAGTTTATACTTTATAACCTATAGTATATAATTTATAAATATAGTTTATATTAATGTTAATT
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAATATAGTTTATATTAATATTAATT
799000 ATCTTAACTATAATTTATATTA
66 ATCTTAACTATAATTTATATTA
*
799022 ATATAGTATATAGTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACTATATAATTTAT-AAATATAGTTTATATTAATATTAAT
*
799087 T-T-TATATACTATATTTTATATTA
65 TATCT-TA-ACTATAATTTATATTA
799110 AT
1 AT
799112 TAATATAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
86 1 0.01
87 38 0.47
88 42 0.52
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.50
Consensus pattern (87 bp):
ATATAGTATATACTTTATAAACTATACTATATAATTTATAAATATAGTTTATATTAATATTAATT
ATCTTAACTATAATTTATATTA
Found at i:799159 original size:10 final size:11
Alignment explanation
Indices: 799071--799188 Score: 70
Period size: 10 Copynumber: 10.7 Consensus size: 11
799061 AAAATATAGT
799071 TTATATTAATA
1 TTATATTAATA
*
799082 TTAATTTTATATA
1 TT-ATATTA-ATA
* *
799095 CTATATTTTATA
1 TTATA-TTAATA
799107 TTA-ATTAATA
1 TTATATTAATA
* *
799117 -TAAACT-ATA
1 TTATATTAATA
799126 TTATATTAATA
1 TTATATTAATA
799137 -TA-AGTTAATA
1 TTATA-TTAATA
799147 TTAATATTAATTA
1 TT-ATATTAA-TA
*
799160 TAATATATAAT-
1 TTATAT-TAATA
799171 TTATATTAATA
1 TTATATTAATA
799182 TTA-ATTA
1 TTATATTA
799189 TAAATATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
9 6 0.07
10 27 0.33
11 15 0.18
12 22 0.27
13 13 0.16
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (11 bp):
TTATATTAATA
Found at i:799186 original size:71 final size:69
Alignment explanation
Indices: 799063--799208 Score: 183
Period size: 71 Copynumber: 2.1 Consensus size: 69
799053 TAATTTATAA
* * *
799063 AATAT-AGTTTATATTAATATTAATTTTATATACTATATTTTATATTAATTAA-TATAAACTATA
1 AATATAAGTTAATATTAATATTAATTATATATACTATAATTTATATTAATTAATTATAAA-TAT-
*
799126 TTATATT
64 TT-TACT
799133 AATATAAGTTAATATTAATATTAATTATA-ATA-TATAATTTATATTAATATTAATTATAAATAT
1 AATATAAGTTAATATTAATATTAATTATATATACTATAATTTATATT-A-ATTAATTATAAATAT
799196 TTTACT
64 TTTACT
799202 AATATAA
1 AATATAA
799209 ATTATATAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
69 22 0.32
70 11 0.16
71 29 0.43
72 6 0.09
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (69 bp):
AATATAAGTTAATATTAATATTAATTATATATACTATAATTTATATTAATTAATTATAAATATTT
TACT
Found at i:799215 original size:39 final size:42
Alignment explanation
Indices: 799125--799215 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 42
799115 TATAAACTAT
799125 ATTATATTAATATAAGTTAATATTAATATTAATTATAATATATA
1 ATTATATTAATATAAGTTAATA-TAATATT-ATTATAATATATA
799169 ATTTATATTAATATTAA-TT-ATA-AATATT-TTACTAATATA-A
1 A-TTATATTAATA-TAAGTTAATATAATATTATTA-TAATATATA
799209 ATTATAT
1 ATTATAT
799216 AGGGATGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
39 6 0.14
40 5 0.11
41 7 0.16
42 6 0.14
44 4 0.09
45 13 0.30
46 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (42 bp):
ATTATATTAATATAAGTTAATATAATATTATTATAATATATA
Found at i:799262 original size:6 final size:6
Alignment explanation
Indices: 799251--799318 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
799241 ATATAAAGAA
*
799251 TAATAT TAATAT T-A-AT T-ATAT TAATAT TAATTAT AAATAAT T--TAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAA-TAT TAAT-AT TAATAT
*
799296 TAATAT TAATAGT TTATAT TAAT
1 TAATAT TAATA-T TAATAT TAAT
799319 GACCTCATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 27 0.53
7 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
TAATAT
Found at i:799273 original size:15 final size:15
Alignment explanation
Indices: 799253--799318 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
799243 ATAAAGAATA
799253 ATATTAATATTAATT
1 ATATTAATATTAATT
799268 ATATTAATATTAATT
1 ATATTAATATTAATT
*
799283 ATA--AATAATTTATT
1 ATATTAAT-ATTAATT
*
799297 AATATTAATAGT--TT
1 -ATATTAATATTAATT
799311 ATATTAAT
1 ATATTAAT
799319 GACCTCATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 11 0.24
14 8 0.18
15 21 0.47
16 2 0.04
17 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTAATATTAATT
Found at i:799276 original size:21 final size:21
Alignment explanation
Indices: 799251--799318 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 21
799241 ATATAAAGAA
799251 TAATATTAATATTAATTATAT
1 TAATATTAATATTAATTATAT
799272 TAATATTAATTATAAATAATT-TAT
1 TAATATTAA-TAT---TAATTATAT
*
799296 TAATATTAATAGT--TTATAT
1 TAATATTAATATTAATTATAT
799315 TAAT
1 TAAT
799319 GACCTCATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 1 0.02
21 9 0.22
22 3 0.07
23 2 0.05
24 12 0.29
25 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TAATATTAATATTAATTATAT
Found at i:799298 original size:18 final size:17
Alignment explanation
Indices: 799229--799312 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 17
799219 GATGAAATTG
*
799229 AAATAATTTA-AAATAT
1 AAATAATTTATTAATAT
* *
799245 AAAGAATAATATTAATATT
1 AAATAAT-TTATTAATA-T
*
799264 AATTATATTAATATTAATTAT
1 AAATA-ATT--TATTAA-TAT
799285 AAATAATTTATTAATAT
1 AAATAATTTATTAATAT
* *
799302 TAATAGTTTAT
1 AAATAATTTAT
799313 ATTAATGACC
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.12
17 14 0.27
18 10 0.19
19 4 0.08
20 5 0.10
21 11 0.21
22 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATAATTTATTAATAT
Found at i:799843 original size:25 final size:25
Alignment explanation
Indices: 799830--799899 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
799820 CTAATGTAAT
*
799830 ATGAATTAATAACATGCAATGCAAC
1 ATGAATTAATAACATCCAATGCAAC
** * *
799855 ATGAATTAATAACATGGAATACCAC
1 ATGAATTAATAACATCCAATGCAAC
*
799880 ATGAATTAATAACATGCAAT
1 ATGAATTAATAACATCCAAT
799900 TATTATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (25 bp):
ATGAATTAATAACATCCAATGCAAC
Found at i:799870 original size:13 final size:13
Alignment explanation
Indices: 799830--799901 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
799820 CTAATGTAAT
799830 ATGAATTAATAAC
1 ATGAATTAATAAC
**
799843 ATGCAA-T-GCAAC
1 ATG-AATTAATAAC
799855 ATGAATTAATAAC
1 ATGAATTAATAAC
**
799868 ATGGAA-T-ACCAC
1 AT-GAATTAATAAC
799880 ATGAATTAATAAC
1 ATGAATTAATAAC
799893 ATGCAATTA
1 ATG-AATTA
799902 TTATTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
11 5 0.11
12 13 0.30
13 16 0.36
14 10 0.23
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (13 bp):
ATGAATTAATAAC
Found at i:800769 original size:23 final size:23
Alignment explanation
Indices: 800743--800792 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
800733 TTTTTTCTTC
*
800743 ACATAAATTTAACTATA-TAATTT
1 ACATAAA-TTAAATATATTAATTT
*
800766 ACATAAATTAAATTTATTAATTT
1 ACATAAATTAAATATATTAATTT
800789 ACAT
1 ACAT
800793 TTAATCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
ACATAAATTAAATATATTAATTT
Found at i:800856 original size:22 final size:23
Alignment explanation
Indices: 800831--800884 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
800821 ATTAATCATG
800831 TTTTATATAATTAT-TTAAATAA
1 TTTTATATAATTATATTAAATAA
*
800853 TTTTAT-TAATTTTATTAAATAA
1 TTTTATATAATTATATTAAATAA
800875 -TTTATATAAT
1 TTTTATATAAT
800885 ATGTCTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATATAATTATATTAAATAA
Found at i:809279 original size:20 final size:21
Alignment explanation
Indices: 809245--809285 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
809235 AGAGTTATGT
*
809245 TTGGTGGTATCAATACTATTC
1 TTGGTGGTATCAATACCATTC
*
809266 TTGG-GGTATTAATACCATTC
1 TTGGTGGTATCAATACCATTC
809286 CTAGGGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (21 bp):
TTGGTGGTATCAATACCATTC
Found at i:809300 original size:21 final size:20
Alignment explanation
Indices: 809252--809301 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
809242 TGTTTGGTGG
* * *
809252 TATCAATACTATTCTTGGGG
1 TATCAATACCATTCTAGGGC
*
809272 TATTAATACCATTCCTAGGGC
1 TATCAATACCATT-CTAGGGC
809293 TATCAATAC
1 TATCAATAC
809302 TTTGGGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (20 bp):
TATCAATACCATTCTAGGGC
Found at i:817157 original size:15 final size:15
Alignment explanation
Indices: 817128--817164 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
817118 CTAAATGCAC
817128 AATGCAACATAACCTA
1 AATGC-ACATAACCTA
*
817144 AATGCACATGACCTA
1 AATGCACATAACCTA
817159 AATGCA
1 AATGCA
817165 ATATTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (15 bp):
AATGCACATAACCTA
Found at i:820458 original size:44 final size:44
Alignment explanation
Indices: 820374--820502 Score: 118
Period size: 44 Copynumber: 3.0 Consensus size: 44
820364 TATGTGAAAT
* * * * *
820374 TGAACTAGGTGAATACATGAAAATATGATATAAGCCATATGATA
1 TGAACTACGTGAATACATGAATATGTGATATATGTCATATGATA
* * *
820418 TGAACTACGTGATTACATGCATATGTGATATATGTTATATGATA
1 TGAACTACGTGAATACATGAATATGTGATATATGTCATATGATA
* * * **
820462 -GACCTATGTGACTATGTGAATATGTGAATATATGTC-TATGA
1 TGAACTACGTGAATACATGAATATGTG-ATATATGTCATATGA
820503 GAAGGCATAG
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
43 25 0.36
44 44 0.64
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (44 bp):
TGAACTACGTGAATACATGAATATGTGATATATGTCATATGATA
Found at i:820931 original size:2 final size:2
Alignment explanation
Indices: 820924--820953 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
820914 TAAAGCAATA
820924 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
820954 GTGATATGTG
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:832438 original size:18 final size:18
Alignment explanation
Indices: 832415--832462 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
832405 GAGTCATAGG
832415 ATGCTCCACAACATTCGA
1 ATGCTCCACAACATTCGA
* * *
832433 ATGCTCCATAGCATTGGA
1 ATGCTCCACAACATTCGA
832451 AT--TCCACAACAT
1 ATGCTCCACAACAT
832463 AATCAACAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 8 0.32
18 17 0.68
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25
Consensus pattern (18 bp):
ATGCTCCACAACATTCGA
Found at i:836565 original size:14 final size:16
Alignment explanation
Indices: 836533--836570 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
836523 AAATGAAAAC
836533 AAATATAAATATACAAA
1 AAATA-AAATATACAAA
836550 AAATAAAATA-AC-AA
1 AAATAAAATATACAAA
836564 AAATAAA
1 AAATAAA
836571 GAAAACCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 5 0.24
17 5 0.24
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATATACAAA
Found at i:838181 original size:17 final size:17
Alignment explanation
Indices: 838159--838194 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
838149 TAAATTACCT
838159 TTAGTAAGAAAACAAGG
1 TTAGTAAGAAAACAAGG
838176 TTAGTAAGAAAACAAGG
1 TTAGTAAGAAAACAAGG
838193 TT
1 TT
838195 TGAGTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (17 bp):
TTAGTAAGAAAACAAGG
Found at i:849462 original size:30 final size:30
Alignment explanation
Indices: 849428--849494 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
849418 CAAAATACCT
*
849428 AACTTTTGAAAATTACAC-TTTTGGTCCCTA
1 AACTTTTGAAAATTAC-CTTTTTGGTCCATA
*
849458 AACTTTTGAAAATTACCTTTTTGGTCCATT
1 AACTTTTGAAAATTACCTTTTTGGTCCATA
849488 AACTTTT
1 AACTTTT
849495 CCAAAACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (30 bp):
AACTTTTGAAAATTACCTTTTTGGTCCATA
Found at i:851617 original size:23 final size:23
Alignment explanation
Indices: 851591--851636 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
851581 CACCACAGCT
*
851591 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
851614 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
851637 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:857025 original size:210 final size:210
Alignment explanation
Indices: 856647--857157 Score: 783
Period size: 210 Copynumber: 2.4 Consensus size: 210
856637 GAAAAATACA
*
856647 AATTT-AATAATTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACA
1 AATTTGAAGAATTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAAC-A-A
*
856711 CACATTGATGAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAAA
64 CACA---A--AGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAAA
*
856776 TACTAAATTATACCCATTTAAACAGTTATGGGCCAATT-AAAAATATAAATAAGTAATAAGTATG
124 TACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATG
856840 GGTCAATTTCAGATGCAAATAT
189 GGTCAATTTCAGATGCAAATAT
* * * * *
856862 AATTTGGAGGATTAAATTAAACAAATATTAAATTACAAATAAAAAATTTAAATAAATTAAACAAC
1 AATTTGAAGAATTAAATTGAACAAATATGAAATTACAAAT-TAAAATTTAAATAAATTAAACAAC
* * * *
856927 ACAAAGGGTTCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATATAAAACAAATACTAA
65 ACAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAAATACTAA
* *
856992 ATTTTACCCATTTAAAAAGTTATGGGTCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAA
130 ATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAA
*
857057 TTTCAGATGTAAATAT
195 TTTCAGATGCAAATAT
* *
857073 AATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACA
1 AATTTGAAGAATTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACA
857138 CAAAGGGATCAAATCGAAAT
66 CAAAGGGATCAAATCGAAAT
857158 GATTGCAAAA
Statistics
Matches: 270, Mismatches: 23, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
210 128 0.47
211 81 0.30
212 1 0.00
215 10 0.04
216 30 0.11
217 20 0.07
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.30
Consensus pattern (210 bp):
AATTTGAAGAATTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACA
CAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAAATACTAAA
TTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAAT
TTCAGATGCAAATAT
Found at i:857243 original size:2 final size:2
Alignment explanation
Indices: 857236--857365 Score: 123
Period size: 2 Copynumber: 67.5 Consensus size: 2
857226 AACAACTACA
*
857236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
857277 AT AT -T AT -T AT AT AT -T AT AT AA ACT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
857316 AT A- AT AT GT AT AA ACT AT AT -T AT AT AT AT AT -T AT GT AT AA
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
857356 ACT AT AT AT A
1 A-T AT AT AT A
857366 CCATGTATAA
Statistics
Matches: 106, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
1 8 0.08
2 95 0.90
3 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:857350 original size:27 final size:28
Alignment explanation
Indices: 857243--857362 Score: 129
Period size: 29 Copynumber: 4.2 Consensus size: 28
857233 ACAATATATA
* *
857243 TATA-TATATATATATATATATATATA-
1 TATATTATATATATATATATGTATAAAC
* *
857269 TATATTTTATATTATTATATATTATATAAAC
1 TATATTATATA-TA-TATATA-TGTATAAAC
857300 TATATATTATATATATATAATATGTATAAAC
1 --TATATTATATATATAT-ATATGTATAAAC
857331 TATATTATATATATAT-TATGTATAAAC
1 TATATTATATATATATATATGTATAAAC
857358 TATAT
1 TATAT
857363 ATACCATGTA
Statistics
Matches: 82, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.05
27 21 0.26
28 2 0.02
29 22 0.27
30 7 0.09
31 11 0.13
32 5 0.06
33 10 0.12
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (28 bp):
TATATTATATATATATATATGTATAAAC
Found at i:857371 original size:20 final size:20
Alignment explanation
Indices: 857338--857385 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
857328 AACTATATTA
**
857338 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
857358 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
857378 TATA-ATAC
1 TATATATAC
857386 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:857463 original size:2 final size:2
Alignment explanation
Indices: 857456--857569 Score: 55
Period size: 2 Copynumber: 59.5 Consensus size: 2
857446 TTAAATAGTT
* * * * *
857456 TA TA TA TA AA TA -A TA TA TA AA CTA TA CA -A TT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
857497 TA T- TA TG TA TA -A T- TA TA AA TA -A TA TA TA T- TG TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
857534 T- TA TA TA GTT TA TA TA TA TA TA TA TA TA GTA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA T
857570 GGTTATGGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
1 8 0.10
2 71 0.86
3 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:857470 original size:18 final size:19
Alignment explanation
Indices: 857378--857470 Score: 55
Period size: 22 Copynumber: 4.6 Consensus size: 19
857368 ATGTATAAAC
857378 TATAATACTATATAGTTTATA
1 TATAA-ACTA-ATAGTTTATA
* * **
857399 TATGAACT-ATTGAACTATA
1 TATAAACTAATAG-TTTATA
*
857418 TAAAAACTACATAGTTTATTAA
1 TATAAACTA-ATAGTTTA-T-A
*
857440 TATAAATTAAATAGTTTATA
1 TATAAACT-AATAGTTTATA
857460 TATAAA-TAATA
1 TATAAACTAATA
857471 TATAAACTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
18 7 0.13
19 11 0.20
20 12 0.22
21 9 0.16
22 15 0.27
23 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TATAAACTAATAGTTTATA
Found at i:857691 original size:11 final size:11
Alignment explanation
Indices: 857642--857695 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
857632 TAGTAGTATT
857642 TAAACTATATA
1 TAAACTATATA
857653 TAAAC-A-ATA
1 TAAACTATATA
857662 TAAACTA-ACT-
1 TAAACTATA-TA
* *
857672 TATACTATATG
1 TAAACTATATA
857683 TAAACTATATA
1 TAAACTATATA
857694 TA
1 TA
857696 CTATATAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 18 0.50
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (11 bp):
TAAACTATATA
Found at i:857739 original size:22 final size:21
Alignment explanation
Indices: 857675--857743 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
857665 ACTAACTTAT
*
857675 ACTATATG-TAAACTATATAT
1 ACTATATGTTAAACTATATAA
* *
857695 ACTATATAGTT-TAC-ATATGA
1 ACTATAT-GTTAAACTATATAA
857715 ACTATATGTATAAACTATATAA
1 ACTATATGT-TAAACTATATAA
857737 ACTATAT
1 ACTATAT
857744 ATATAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.05
20 19 0.49
21 5 0.13
22 13 0.33
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (21 bp):
ACTATATGTTAAACTATATAA
Found at i:857748 original size:22 final size:22
Alignment explanation
Indices: 857677--857766 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 22
857667 TAACTTATAC
* *
857677 TATATGTAAACTATATATACTA
1 TATATATAAACTATATAAACTA
* *
857699 TATAGT-T-TAC-ATATGAACTA
1 TATA-TATAAACTATATAAACTA
*
857719 TATGTATAAACTATATAAACTA
1 TATATATAAACTATATAAACTA
* * *
857741 TATATATAAATTATGTAAATTA
1 TATATATAAACTATATAAACTA
857763 TATA
1 TATA
857767 GTTTACATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 12 0.22
21 4 0.07
22 36 0.67
23 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (22 bp):
TATATATAAACTATATAAACTA
Found at i:857807 original size:24 final size:24
Alignment explanation
Indices: 857761--857841 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
857751 TTATGTAAAT
* *
857761 TATATAGTTTACATA-TGACCTATA
1 TATATAGTTTA-TTAGTGAACTATA
857785 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTATTAGTGAACTATA
* *
857809 TAAACTA-TTTATATAGTCTATACTATA
1 TATA-TAGTTTAT-TAGT-GA-ACTATA
857836 TATATA
1 TATATA
857842 AATTATAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 6 0.13
26 3 0.06
27 9 0.19
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATAGTTTATTAGTGAACTATA
Found at i:857837 original size:2 final size:2
Alignment explanation
Indices: 857827--858106 Score: 59
Period size: 2 Copynumber: 138.5 Consensus size: 2
857817 TTATATAGTC
* * * *
857827 TA TA CTA TA TA TA TA AA T- TA TA GTT TA TA TT TA TA TA CTA CA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
857869 TA T- TA TA GTT TA TA TT TA TA TA CTA CA TA CTA TA T- TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * *
857910 TT TA TA TA CTA TA TA TA TT TA TA TA CTA TA T- TT TA TA CTA TT
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * * * *
857952 TA TA TA AA CTA TA -A AA GTA TA TA GTT TA TA -A AA TA TA -A TT
1 TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* *
857992 TA TA T- TA -A TA T- TA -A TA TA GTA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
858031 TA TA AA CTA TA TA TG TA TA AA CTA TA TA AA CTA TA TA GTT TA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA
* *
858075 AA T- TA TA -A TT TA TA T- TA -A TA TA GTA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T
858107 GTATGTATAA
Statistics
Matches: 197, Mismatches: 48, Indels: 66
0.63 0.15 0.21
Matches are distributed among these distances:
1 15 0.08
2 155 0.79
3 27 0.14
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:857873 original size:27 final size:27
Alignment explanation
Indices: 857843--857925 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
857833 ATATATATAA
857843 ATTATAGTTTATATTTATATACTACAT
1 ATTATAGTTTATATTTATATACTACAT
857870 ATTATAGTTTATATTTATATACTACAT
1 ATTATAGTTTATATTTATATACTACAT
* * *
857897 ACTATATTTTATATTTATATACTATAT
1 ATTATAGTTTATATTTATATACTACAT
857924 AT
1 AT
857926 ATTTATATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTATAGTTTATATTTATATACTACAT
Found at i:857928 original size:17 final size:17
Alignment explanation
Indices: 857906--857940 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
857896 TACTATATTT
857906 TATATTTATATACTATA
1 TATATTTATATACTATA
857923 TATATTTATATACTATA
1 TATATTTATATACTATA
857940 T
1 T
857941 TTTATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTTATATACTATA
Found at i:858049 original size:15 final size:15
Alignment explanation
Indices: 858025--858058 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
858015 TATATGTATG
858025 TATATATATAAACTA
1 TATATATATAAACTA
*
858040 TATATGTATAAACTA
1 TATATATATAAACTA
858055 TATA
1 TATA
858059 AACTATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:858049 original size:77 final size:81
Alignment explanation
Indices: 857952--858115 Score: 192
Period size: 87 Copynumber: 2.0 Consensus size: 81
857942 TTATACTATT
* * *
857952 TATATAAACTATAAAAGTATATAGTTTATAAA-ATATA-AT-TTAT-ATTAATATTAATATAGTA
1 TATATAAACTATAAAAGTATAAACTATATAAACATATATATATTATAATTAATATTAATATAGTA
858013 TATATATGTATGTATA
66 TATATATGTATGTATA
* * *
858029 TATATAAACTATATATGTATAAACTATATAAACTATATAGTTTATAAATTATAATTTATATTAAT
1 TATATAAACTATAAAAGTATAAACTATATAAAC-ATATA---TAT--ATTATAATTAATATTAAT
858094 ATAGTATATATATGTATGTATA
60 ATAGTATATATATGTATGTATA
858116 ACTAATATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
77 27 0.38
79 5 0.07
83 2 0.03
86 4 0.06
87 33 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (81 bp):
TATATAAACTATAAAAGTATAAACTATATAAACATATATATATTATAATTAATATTAATATAGTA
TATATATGTATGTATA
Found at i:858061 original size:24 final size:25
Alignment explanation
Indices: 858029--858081 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
858019 TGTATGTATA
858029 TATATAAACTATATA-TGTATAAAC
1 TATATAAACTATATAGTGTATAAAC
* *
858053 TATATAAACTATATAGTTTATAAAT
1 TATATAAACTATATAGTGTATAAAC
858078 TATA
1 TATA
858082 ATTTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (25 bp):
TATATAAACTATATAGTGTATAAAC
Found at i:858343 original size:13 final size:13
Alignment explanation
Indices: 858325--858373 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
858315 CTATGCATAG
*
858325 TATATACAAACTA
1 TATATATAAACTA
858338 TATATATATAACCTA
1 TATATATA-AA-CTA
*
858353 TATATATAACCTA
1 TATATATAAACTA
858366 TAGTATAT
1 TA-TATAT
858374 GTATATATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 12 0.39
14 8 0.26
15 11 0.35
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:858345 original size:15 final size:15
Alignment explanation
Indices: 858325--858360 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
858315 CTATGCATAG
858325 TATATACAAACTATA
1 TATATACAAACTATA
* *
858340 TATATATAACCTATA
1 TATATACAAACTATA
858355 TATATA
1 TATATA
858361 ACCTATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (15 bp):
TATATACAAACTATA
Found at i:858483 original size:21 final size:21
Alignment explanation
Indices: 858457--858509 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
858447 TAGTGTGTTG
* *
858457 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
858478 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
858499 TATAGTTTATA
1 TATAGTTTATA
858510 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:858619 original size:21 final size:21
Alignment explanation
Indices: 858457--858619 Score: 77
Period size: 21 Copynumber: 7.5 Consensus size: 21
858447 TAGTGTGTTG
* * *
858457 TATAGTTTATACTTTATAACC
1 TATAGTATATAATTTATAAAC
858478 TATAGTATATAATTTATAAAC
1 TATAGTATATAATTTATAAAC
* * **
858499 TATAGTTTAT-ATTAATGTAC
1 TATAGTATATAATTTATAAAC
* *
858519 TATATAGTTTATATTAATGTTAATTATC
1 --TATAG--TATA-TAAT-TT-ATAAAC
858547 T-TA--ACTATAATTTATATTAA-
1 TATAGTA-TATAATTTATA--AAC
*
858567 TATAGTATATAGTTTATAAAC
1 TATAGTATATAATTTATAAAC
*
858588 TATACTATATAATTTAT-AAC
1 TATAGTATATAATTTATAAAC
*
858608 TTATAGTTTATA
1 -TATAGTATATA
858620 TTAATATTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
19 2 0.02
20 15 0.14
21 59 0.55
22 17 0.16
23 1 0.01
24 3 0.03
25 3 0.03
26 3 0.03
27 1 0.01
28 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (21 bp):
TATAGTATATAATTTATAAAC
Found at i:858630 original size:88 final size:89
Alignment explanation
Indices: 858478--858689 Score: 249
Period size: 88 Copynumber: 2.4 Consensus size: 89
858468 CTTTATAACC
* * * *
858478 TATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAAT
1 TATAGTATATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAAT
858543 TATCT-TA-ACTATAATTTATATTAA
66 T-T-TATAGACTATAATTTATATTAA
* *
858567 TATAGTATATAGTTTATAAACTATACTATATAATTTAT-AACT-TATAGTTTATATTAATATTAA
1 TATAGTATATAATTTATAAACTATACTATAT-ATTAATGAACTATATAGTTTATATTAATATTAA
*
858630 TTTTATAGACTATATTTTATATTAA
65 TTTTATAGACTATAATTTATATTAA
* * *
858655 TATTAAT-TACAAATTATAAACTATA-T-TATATTAAT
1 TA-TAGTATATAATTTATAAACTATACTATATATTAAT
858690 ATAAGTGTAT
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
85 5 0.05
86 4 0.04
87 4 0.04
88 55 0.51
89 34 0.32
90 5 0.05
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (89 bp):
TATAGTATATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAAT
TTTATAGACTATAATTTATATTAA
Found at i:858649 original size:31 final size:31
Alignment explanation
Indices: 858600--858662 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
858590 TACTATATAA
858600 TTTATAACTTATAGTTTATATTAATATTAAT
1 TTTATAACTTATAGTTTATATTAATATTAAT
*
858631 TTTATAGAC-TATATTTTATATTAATATTAAT
1 TTTATA-ACTTATAGTTTATATTAATATTAAT
858662 T
1 T
858663 ACAAATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTATAACTTATAGTTTATATTAATATTAAT
Found at i:858672 original size:110 final size:109
Alignment explanation
Indices: 858457--858672 Score: 240
Period size: 110 Copynumber: 2.0 Consensus size: 109
858447 TAGTGTGTTG
* * *
858457 TATAGTTTATACTTTATAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTAT
1 TATAGTATATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATGTACTAT
** * * *
858522 ATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAA
66 ATAGACTATATTAATATTAATTA-CTTAACTACAAATTATATTAA
* * *
858567 TATAGTATATAGTTTATAAACTATACTATATAATTTAT-AACTTATAGTTTATATTAATATTAAT
1 TATAGTATATACTTTATAAACTATACTATATAATTTATAAAC-TATAGTTTATATTAAT-GT-AC
* * *
858631 TTTATAGACTATATTTTATATTAA-TA-TTAATTACAAATTATA
63 TATATAGACTATA-TTAATATTAATTACTTAACTACAAATTATA
858673 AACTATATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
109 3 0.03
110 63 0.72
111 1 0.01
112 13 0.15
113 8 0.09
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (109 bp):
TATAGTATATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATGTACTAT
ATAGACTATATTAATATTAATTACTTAACTACAAATTATATTAA
Found at i:858678 original size:36 final size:30
Alignment explanation
Indices: 858600--858725 Score: 89
Period size: 31 Copynumber: 4.0 Consensus size: 30
858590 TACTATATAA
858600 TTTAT-AACTTATAGTTTATATTAATATTAAT
1 TTTATAAAC-TATA-TTTATATTAATATTAAT
*
858631 TTTATAGACTATATTTTATATTAATATTAAT
1 TTTATAAACTATA-TTTATATTAATATTAAT
*
858662 TACAAATTATAAACTATA-TTATATTAATA-TAAG
1 T-----TTATAAACTATATTTATATTAATATTAAT
* * * *
858695 TGTATATTA-TATAATTATTTTAATATTAAT
1 TTTATA-AACTATATTTATATTAATATTAAT
858725 T
1 T
858726 AAATAATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
28 8 0.10
29 11 0.14
30 4 0.05
31 27 0.35
32 2 0.03
33 4 0.05
34 11 0.14
36 11 0.14
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (30 bp):
TTTATAAACTATATTTATATTAATATTAAT
Found at i:861755 original size:2 final size:2
Alignment explanation
Indices: 861748--861786 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
861738 TTTCGTCCCA
861748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
861787 TTATTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:861799 original size:12 final size:13
Alignment explanation
Indices: 861755--861848 Score: 61
Period size: 14 Copynumber: 7.4 Consensus size: 13
861745 CCAATATATA
* *
861755 TATATATATATAT
1 TATATTTATTTAT
* *
861768 ATATATATATATAT
1 -TATATTTATTTAT
861782 TATATTTATTTAT
1 TATATTTATTTAT
*
861795 T-TATTTATTTAC
1 TATATTTATTTAT
**
861807 TATATTCCTTT-T
1 TATATTTATTTAT
*
861819 TCTATTTA--TAT
1 TATATTTATTTAT
*
861830 TATATTATTTTTAT
1 TATATT-TATTTAT
861844 TATAT
1 TATAT
861849 ATATCTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
10 1 0.02
11 6 0.09
12 17 0.27
13 19 0.30
14 21 0.33
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:861803 original size:21 final size:21
Alignment explanation
Indices: 861748--861875 Score: 74
Period size: 21 Copynumber: 6.3 Consensus size: 21
861738 TTTCGTCCCA
861748 ATATATATATATA-TATATAT
1 ATATATATATATATTATATAT
*
861768 ATATATATATATATTATATTT
1 ATATATATATATATTATATAT
* * *
861789 ATTTATTTATTTATT-TACTAT
1 ATATATATATATATTATA-TAT
* * * *
861810 AT-TCCTTTTTCTATT-TATAT
1 ATAT-ATATATATATTATATAT
*
861830 -TATAT-TAT-TTTTAT-TAT
1 ATATATATATATATTATATAT
*
861847 ATATATCTTATATCATTATATAT
1 ATATAT-ATATAT-ATTATATAT
861870 ATATAT
1 ATATAT
861876 TAATTTTTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 19
0.73 0.10 0.16
Matches are distributed among these distances:
17 6 0.07
18 8 0.09
19 2 0.02
20 23 0.27
21 33 0.39
22 4 0.05
23 9 0.11
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATATATATATTATATAT
Found at i:861838 original size:14 final size:15
Alignment explanation
Indices: 861821--861877 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
861811 TTCCTTTTTC
861821 TATTTATATTATAT-
1 TATTTATATTATATA
*
861835 TATTTTTATTATATA
1 TATTTATATTATATA
*
861850 TATCTTATATCATTATA
1 TAT-TTATATTA-TATA
*
861867 TATATATATTA
1 TATTTATATTA
861878 ATTTTTCTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.37
15 3 0.09
16 12 0.34
17 7 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:861975 original size:37 final size:40
Alignment explanation
Indices: 861898--861988 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
861888 ATTTACTATG
861898 TATATATATATATTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
861939 TATATATATAT-TTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATATATTTTCTTAATATTATATTTTATAGTTTT
* *
861976 TATTTATTTATAT
1 TATATATATATAT
861989 CTATTATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
37 14 0.30
38 1 0.02
39 1 0.02
40 19 0.41
41 11 0.24
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (40 bp):
TATATATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:862252 original size:15 final size:15
Alignment explanation
Indices: 862228--862257 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
862218 CATTTTATTC
862228 ATTTTGTTTATTTTT
1 ATTTTGTTTATTTTT
*
862243 ATTTTTTTTATTTTT
1 ATTTTGTTTATTTTT
862258 TACGTGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
ATTTTGTTTATTTTT
Found at i:865621 original size:69 final size:69
Alignment explanation
Indices: 865487--865621 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
865477 TCAAACTATA
* **
865487 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCATCA
1 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAAAATCA
865552 AATG
66 AATG
* *
865556 AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAAAATCA
1 AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAAAATCA
865621 A
66 A
865622 GAGAAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (69 bp):
AGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAAAATCA
AATG
Found at i:867211 original size:36 final size:35
Alignment explanation
Indices: 867164--867248 Score: 116
Period size: 35 Copynumber: 2.4 Consensus size: 35
867154 ATTTAAAATA
** * *
867164 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAC-AAAATTGTCTCCCTTGAGACAG
867200 TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
*
867235 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
867249 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 31 0.70
36 13 0.30
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
Found at i:867256 original size:100 final size:102
Alignment explanation
Indices: 867078--867450 Score: 411
Period size: 100 Copynumber: 3.7 Consensus size: 102
867068 TAAAAAAAAG
* *
867078 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCT-CCTTGAGACAGTTTCTCT
1 ATTTCATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
* *
867142 TGAAACATAAACATTTAAAATATTTCCCTTGAAACGA
66 TGAAACATAAACATTTAAAATATTTCCATTGAAACAA
**
867179 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAA-ATTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
* * *
867242 TGAAACATAAACATTGAAAACATTTCCATTGAAATAA
66 TGAAACATAAACATTTAAAATATTTCCATTGAAACAA
* * * * * *
867279 ATGTCGTCTCTCTTGAGA-CGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
** * **
867342 TGAAACA-AATTATTT-GAATATGTTTTATTTGAAACAA
66 TGAAACATAAACATTTAAAATAT-TTCCA-TTGAAACAA
* * * * * * * *
867379 ATTTCATCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 ATTTCATCTCTCTTGAGATAGTTTCCCTTGA-AACAAAATATTGTCTCCCTTGAGACAGTTTCTC
867443 TTGAAACA
65 TTGAAACA
867451 AATTTCGTCT
Statistics
Matches: 236, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
98 4 0.02
99 32 0.14
100 126 0.53
101 39 0.17
102 35 0.15
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (102 bp):
ATTTCATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTTAAAATATTTCCATTGAAACAA
Found at i:867345 original size:36 final size:36
Alignment explanation
Indices: 867264--867488 Score: 209
Period size: 36 Copynumber: 6.4 Consensus size: 36
867254 ATTGAAAACA
* * *
867264 TTTCCATTGAAATAAATGTCGTCTCTCTTGAGAC-G
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
867299 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
867335 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
867364 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
867400 TTT-CTTTTAGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGA-AAC-AAATTTCGTCTCTCTTGAGACAG
*
867437 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
867473 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
867489 ATCTTTGAAT
Statistics
Matches: 153, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
30 2 0.01
31 1 0.01
34 1 0.01
35 35 0.23
36 64 0.42
37 27 0.18
38 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:867584 original size:67 final size:65
Alignment explanation
Indices: 867437--867603 Score: 208
Period size: 65 Copynumber: 2.5 Consensus size: 65
867427 CTTGAGACAG
* * * * * **
867437 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTA
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAATCTTCAAATTTA
* *
867502 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAATACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTG-AA-ACAAAATCTTCAAATT
867567 TA
64 TA
* *
867569 TTTCCCTTAAAACAAAATTTTGTTTCCATTGAGAC
1 TTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGAC
867604 CGTTTTCATG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 38 0.44
66 2 0.02
67 28 0.32
68 19 0.22
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAATCTTCAAATTTA
Found at i:867616 original size:67 final size:67
Alignment explanation
Indices: 867446--867616 Score: 188
Period size: 67 Copynumber: 2.6 Consensus size: 67
867436 GTTTCTCTTG
* * * * **
867446 AAACAAATTTCGTCTCTC-TTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTTGTCTC-CATTGAGACAATTTCTCATGAAATACAAAATCTTCAAATTTATTTCCC
867508 CTA
65 CTA
* * *
867511 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAATACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCATTGAGACAATTTCTCATGAAATACAAAATCTTCAAATTTATTTCCCC
867576 TA
66 TA
* **
867578 AAACAAAATTTTGTTTCCATTGAGACCGTTT-TCATGAAA
1 AAAC-AAATTTTGTCTCCATTGAGACAATTTCTCATGAAA
867617 CAACAGATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 1 0.01
65 31 0.34
66 2 0.02
67 35 0.38
68 22 0.24
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCATTGAGACAATTTCTCATGAAATACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:869861 original size:14 final size:14
Alignment explanation
Indices: 869842--869881 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
869832 ATTCCTTTTT
869842 TTATTTATATTATA
1 TTATTTATATTATA
*
869856 TTATTTTTATTATA
1 TTATTTATATTATA
869870 TATATCTTATAT
1 T-TAT-TTATAT
869882 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:869959 original size:17 final size:18
Alignment explanation
Indices: 869932--870015 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 18
869922 ATGTATATAT
869932 ATATATATATTTTTCTTA
1 ATATATATATTTTTCTTA
*
869950 ATAT-TATATTTTATACGTTT
1 ATATATATATTTT-T-C-TTA
*
869970 TTATATATATTTTTTCTTA
1 ATATATATA-TTTTTCTTA
* * *
869989 ATAT-TCTATTTTTATTT
1 ATATATATATTTTTCTTA
*
870006 ATTTATATAT
1 ATATATATAT
870016 ATTATATTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
17 18 0.35
18 12 0.24
19 6 0.12
20 6 0.12
21 5 0.10
22 4 0.08
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (18 bp):
ATATATATATTTTTCTTA
Found at i:870011 original size:38 final size:39
Alignment explanation
Indices: 869931--870018 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
869921 TATGTATATA
869931 TATATATATATTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATAT-TTTTTCTTAATATTATATTTTATACGTTTT
* *
869971 TATATATATTTTTTCTTAATATTCTATTTT-TA-TTTATT
1 TATATATATTTTTTCTTAATATTATATTTTATACGTT-TT
870009 TATATATATT
1 TATATATATT
870019 ATATTTTTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 2 0.04
38 14 0.31
39 20 0.44
40 9 0.20
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.65
Consensus pattern (39 bp):
TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
Found at i:870204 original size:16 final size:16
Alignment explanation
Indices: 870170--870224 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
870160 TATTTTTACT
870170 CCTTTTTAATTTCTTTTA
1 CCTTTTTAA-TT-TTTTA
870188 CCTTTTTAATTTTTTA
1 CCTTTTTAATTTTTTA
* * * *
870204 CCCTATTAATATTTTC
1 CCTTTTTAATTTTTTA
870220 CCTTT
1 CCTTT
870225 ATCTGTGTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 20 0.65
17 2 0.06
18 9 0.29
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (16 bp):
CCTTTTTAATTTTTTA
Found at i:871321 original size:23 final size:23
Alignment explanation
Indices: 871273--871321 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
871263 CTTAATGCAG
* *
871273 GATGCTTGCTGAATTGATGCAAT
1 GATGCGTGCTGAATTGATACAAT
*
871296 GATGCGTGCTGAATTGATACATT
1 GATGCGTGCTGAATTGATACAAT
871319 GAT
1 GAT
871322 ACTTGCCGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (23 bp):
GATGCGTGCTGAATTGATACAAT
Found at i:872153 original size:16 final size:16
Alignment explanation
Indices: 872134--872172 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
872124 TGAGTCAATT
* *
872134 ACAGGTCAGGTTCATA
1 ACAGGTCAGATTCAAA
*
872150 ACAGGTCAGATTGAAA
1 ACAGGTCAGATTCAAA
872166 ACAGGTC
1 ACAGGTC
872173 GGGTAATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGATTCAAA
Found at i:874029 original size:20 final size:20
Alignment explanation
Indices: 874006--874119 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
873996 GAATATGTAA
* *
874006 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
874026 ATCGCAACGCTATTCTAACT
1 ATCGCAACGCGATTCTGACT
* *
874046 ATCACAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
874066 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
874086 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
874106 ATCGCAATGCGATT
1 ATCGCAACGCGATT
874120 TTCAAAGTGC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:874320 original size:22 final size:22
Alignment explanation
Indices: 874295--874337 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
874285 GGCAACATCC
874295 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
874317 GTCCCCATCTTCGATGAAATC
1 GTCCCCATCTCCGACGAAATC
874338 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:874796 original size:20 final size:20
Alignment explanation
Indices: 874733--874796 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
874723 GCAATTTTAG
* **
874733 TTTCGAGTTGCGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
874752 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* * *
874772 ATTCGCGTTGTGATAGTCAT
1 TTTCGCGTTGCGATAGTCAA
874792 TTTCG
1 TTTCG
874797 TGTTTCGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:876739 original size:20 final size:20
Alignment explanation
Indices: 876714--876758 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
876704 TTTACTTTCA
876714 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
**
876734 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
876754 CAACG
1 CAACG
876759 AAAGAATCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:876849 original size:20 final size:20
Alignment explanation
Indices: 876824--876871 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
876814 AAATTCGCAT
876824 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
876844 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
876864 TCGCAACG
1 TCGCAACG
876872 AAAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:876912 original size:113 final size:113
Alignment explanation
Indices: 876714--876931 Score: 373
Period size: 113 Copynumber: 1.9 Consensus size: 113
876704 TTTACTTTCA
**
876714 CAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCAAAAT
1 CAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCAAAAT
* *
876779 GAAAATTGCATTGTGATTCTCTCGTTGCGATAGTCAAATTCGCATTCG
66 GAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTCG
* *
876827 CAACGCGAAAATGACTATCGCAACGTGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAAT
1 CAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCAAAAT
*
876892 GAAAATCGCATTGCGATTCTCTCGTTGTGATAGTCAAATT
66 GAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATT
876932 TGCGTTGCAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 98 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (113 bp):
CAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCAAAAT
GAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTCG
Found at i:876968 original size:20 final size:19
Alignment explanation
Indices: 876914--876969 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
876904 GCGATTCTCT
* *
876914 CGTTGTGATAGTCAAATTTG
1 CGTTGCGATAGTC-ATTTTG
*
876934 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCATTTT-G
876954 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
876970 CGTGTTGCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTTG
Found at i:876976 original size:18 final size:19
Alignment explanation
Indices: 876914--876980 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
876904 GCGATTCTCT
*
876914 CGTTGTGATAGTCAAATTT-G
1 CGTTGCGATAGTC--ATTTCG
*
876934 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
876954 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
876972 TGTTGCGAT
1 CGTTGCGAT
876981 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.32
19 3 0.07
20 25 0.61
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:878983 original size:13 final size:14
Alignment explanation
Indices: 878956--878991 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
878946 TTGCTTGTTT
878956 AATT-ATTTATAAA
1 AATTGATTTATAAA
878969 AATTGATTTATAAA
1 AATTGATTTATAAA
*
878983 AGTTGATTT
1 AATTGATTT
878992 GTTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (14 bp):
AATTGATTTATAAA
Found at i:879168 original size:20 final size:20
Alignment explanation
Indices: 879130--879168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
879120 ACGCTAAACT
*
879130 CAAAATCGCAATACGAAAGC
1 CAAAATCGCAACACGAAAGC
* *
879150 CAAAATCGTAACACTAAAG
1 CAAAATCGCAACACGAAAG
879169 TCAATTCGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (20 bp):
CAAAATCGCAACACGAAAGC
Found at i:879204 original size:20 final size:20
Alignment explanation
Indices: 879167--879511 Score: 375
Period size: 20 Copynumber: 17.4 Consensus size: 20
879157 GTAACACTAA
879167 AGTC-AATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
879186 AGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879206 --T----TTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
879220 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
879240 AGTCAAATACCCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879260 AATCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879280 AGTCAAATTCGCGTTGGGAT
1 AGTCAAATTCGCGTTGCGAT
879300 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
879320 AGTCAAATACTCATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879340 AATCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879360 AGTCAAATTCGCGTTACGAT
1 AGTCAAATTCGCGTTGCGAT
879380 AGAT-AAATTCGCGTTGCGAT
1 AG-TCAAATTCGCGTTGCGAT
* * *
879400 AGTTATATTCGTGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
879420 AGTCAAATTCGTGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
879440 AATCAAATTCGTGTTGTGAT
1 AGTCAAATTCGCGTTGCGAT
*
879460 AGTCAAATTCG-TTTGCGATATT
1 AGTCAAATTCGCGTTGCG--A-T
879482 CAAGTCAAATTCGCGTTGCGAT
1 --AGTCAAATTCGCGTTGCGAT
*
879504 ATTCAAAT
1 AGTCAAAT
879512 GAATGTGTAC
Statistics
Matches: 276, Mismatches: 35, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
14 10 0.04
16 1 0.00
18 1 0.00
19 9 0.03
20 234 0.85
21 2 0.01
22 2 0.01
23 1 0.00
24 11 0.04
25 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:879492 original size:24 final size:25
Alignment explanation
Indices: 879460--879509 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
879450 GTGTTGTGAT
*
879460 AGTCAAATTCG-TTTGCGATATTCA
1 AGTCAAATTCGCGTTGCGATATTCA
879484 AGTCAAATTCGCGTTGCGATATTCA
1 AGTCAAATTCGCGTTGCGATATTCA
879509 A
1 A
879510 ATGAATGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (25 bp):
AGTCAAATTCGCGTTGCGATATTCA
Found at i:879736 original size:140 final size:140
Alignment explanation
Indices: 879484--879751 Score: 491
Period size: 140 Copynumber: 1.9 Consensus size: 140
879474 GCGATATTCA
* *
879484 AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTACTAAGTGATAACAACTGAACATATCATA
1 AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
*
879549 CCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAA
66 CCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAA
879614 TACACATAAT
131 TACACATAAT
879624 AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
1 AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
* *
879689 GCAATGCTCAAACTCAAGTTACTAATACATTCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 CCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
879752 TACAACGTTT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (140 bp):
AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
CCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAA
TACACATAAT
Found at i:881900 original size:14 final size:14
Alignment explanation
Indices: 881881--881917 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
881871 TCCCGTGACA
881881 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
881895 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
881909 TTCTTCTTC
1 TT-TTCTTC
881918 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:882141 original size:24 final size:24
Alignment explanation
Indices: 882107--882160 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
882097 CTGAAACATC
882107 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
882131 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
882155 ATCAAA
1 ATCAAA
882161 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:883014 original size:20 final size:20
Alignment explanation
Indices: 882989--883076 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
882979 GTGTTGTGAC
*
882989 AGTCAGCATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
*
883009 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCATTGCGAT
*
883029 AGTCATAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
* * *
883049 -TTACATATTCGCATTGCGAT
1 AGT-CAGAATCGCATTGCGAT
883069 AGTCAGAA
1 AGTCAGAA
883077 AATCGCAACG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 55 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTCAGAATCGCATTGCGAT
Found at i:883089 original size:22 final size:22
Alignment explanation
Indices: 883064--883119 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
883054 TATTCGCATT
883064 GCGATAGTCAGAAAATCGCAAC
1 GCGATAGTCAGAAAATCGCAAC
* ** * *
883086 GCGA-ATTTTGGAAATCGCAAT
1 GCGATAGTCAGAAAATCGCAAC
883107 GCGATAGTCAGAA
1 GCGATAGTCAGAA
883120 TTGCGTTGCA
Statistics
Matches: 24, Mismatches: 9, Indels: 2
0.69 0.26 0.06
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (22 bp):
GCGATAGTCAGAAAATCGCAAC
Found at i:885263 original size:21 final size:23
Alignment explanation
Indices: 885216--885263 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
885206 ACGTATAATT
885216 ATAAATTAGTTGAAAATTAAAGG
1 ATAAATTAGTTGAAAATTAAAGG
*
885239 -TAAATTA-TTTAAAA-TAAAGG
1 ATAAATTAGTTGAAAATTAAAGG
885259 ATAAA
1 ATAAA
885264 AGGATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 10 0.43
22 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (23 bp):
ATAAATTAGTTGAAAATTAAAGG
Found at i:891666 original size:29 final size:29
Alignment explanation
Indices: 891634--891693 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
891624 GGCACCTGGA
891634 TGAGTAAAA-AAATAGTTTAGGCACCTATT
1 TGAG-AAAAGAAATAGTTTAGGCACCTATT
** *
891663 TGAGAAAATGGTATAGTTTAGGCACTTATT
1 TGAGAAAA-GAAATAGTTTAGGCACCTATT
891693 T
1 T
891694 TGATATTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 4 0.15
30 18 0.69
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (29 bp):
TGAGAAAAGAAATAGTTTAGGCACCTATT
Found at i:893309 original size:29 final size:31
Alignment explanation
Indices: 893276--893346 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
893266 AAAATTTTGC
*
893276 TAGTGACCAAAATAT-AATTTTTG-AAAGTT
1 TAGTGACCAAAATATAAATTTTGGAAAAGTT
* * *
893305 TAGTGGCTAAATTATAAATTTTGGAAAAGTT
1 TAGTGACCAAAATATAAATTTTGGAAAAGTT
*
893336 TAGGGACCAAA
1 TAGTGACCAAA
893347 GTGTAGCTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 12 0.36
30 7 0.21
31 14 0.42
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (31 bp):
TAGTGACCAAAATATAAATTTTGGAAAAGTT
Found at i:897059 original size:45 final size:46
Alignment explanation
Indices: 897010--897100 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
897000 GAACATCGAA
* * *
897010 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGTACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
897055 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
897101 GTTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:905690 original size:20 final size:20
Alignment explanation
Indices: 905665--905703 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
905655 TTTTCAAGGG
905665 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
905685 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
905704 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:905774 original size:45 final size:46
Alignment explanation
Indices: 905725--905813 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
905715 ACATCGAATG
* *
905725 CATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTA
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTA
* *
905770 CATTTGATGCATCGATGCACAAGACTATGCATCGATGCATTCAG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
905814 GCTTTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 19 0.49
46 20 0.51
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTA
Found at i:912691 original size:26 final size:26
Alignment explanation
Indices: 912650--912739 Score: 103
Period size: 25 Copynumber: 3.5 Consensus size: 26
912640 CTTGTATATT
912650 TATGTGGC-CTTTCGAGTACGAGTGA
1 TATGTGGCACTTTCGAGTACGAGTGA
* *
912675 TATGTGGCACTTTCGAGTGCGAGTTA
1 TATGTGGCACTTTCGAGTACGAGTGA
** * *
912701 TATGTATCACTTT-TAGTACAAGTGA
1 TATGTGGCACTTTCGAGTACGAGTGA
*
912726 TATATGGCACTTTC
1 TATGTGGCACTTTC
912740 AAGTGCAATA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
25 26 0.50
26 26 0.50
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (26 bp):
TATGTGGCACTTTCGAGTACGAGTGA
Found at i:914976 original size:17 final size:17
Alignment explanation
Indices: 914956--915000 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
914946 TTTTTCTTAT
914956 TGTTCCTTTTATTGTAC
1 TGTTCCTTTTATTGTAC
*
914973 TGTTCTTTTTATTGTAC
1 TGTTCCTTTTATTGTAC
* *
914990 TTTTTCTTTTA
1 TGTTCCTTTTA
915001 CTATACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (17 bp):
TGTTCCTTTTATTGTAC
Found at i:915081 original size:17 final size:16
Alignment explanation
Indices: 914961--915082 Score: 52
Period size: 17 Copynumber: 7.3 Consensus size: 16
914951 CTTATTGTTC
* *
914961 CTTTTATTGTACTGTT
1 CTTTTACTGTACTATT
* *
914977 CTTTTTATTGTACTTTTT
1 C-TTTTACTGTAC-TATT
*
914995 CTTTTACTATACTATTT
1 CTTTTACTGTACTA-TT
*
915012 CTTTTAATGTTA-TATAT
1 CTTTTACTG-TACTAT-T
**
915029 CTTTTGTTGTACTATGT
1 CTTTTACTGTACTAT-T
** *
915046 C--TTACTGTTTTGTT
1 CTTTTACTGTACTATT
915060 ACTTTTACTGTACTATCT
1 -CTTTTACTGTACTAT-T
915078 CTTTT
1 CTTTT
915083 TAGTTTCATT
Statistics
Matches: 79, Mismatches: 17, Indels: 19
0.69 0.15 0.17
Matches are distributed among these distances:
14 1 0.01
15 8 0.10
16 5 0.06
17 58 0.73
18 7 0.09
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.61
Consensus pattern (16 bp):
CTTTTACTGTACTATT
Done.