Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 25
Found at i:3643667 original size:31 final size:31
Alignment explanation
Indices: 3643632--3643690 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3643622 AAATTTAAAA
* *
3643632 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
3643663 AGTTTTATAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
3643691 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:3643743 original size:22 final size:22
Alignment explanation
Indices: 3643713--3644449 Score: 639
Period size: 22 Copynumber: 33.5 Consensus size: 22
3643703 AATAATATTT
*
3643713 TTTTTAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATTTATA
*
3643735 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTTATA
**
3643757 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
*
3643779 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCAATTT--ATA
*
3643801 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTTATA
**
3643823 TTTTAAAATAAAT-TTTTTCATA
1 TTTTAAAATAAATCAATTT-ATA
**
3643845 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
*
3643867 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATTTATA
*
3643889 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCAATTT--ATA
**
3643911 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
*
3643933 TTTTAAAATAAA--ATTTTTCATA
1 TTTTAAAATAAATCA-ATTT-ATA
**
3643955 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
*
3643977 TTTTAAAATAAA--ATTTTTCATA
1 TTTTAAAATAAATCA-ATTT-ATA
*
3643999 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTTATA
3644021 TTTTAAAATAAA--AATTTCCATA
1 TTTTAAAATAAATCAATTT--ATA
* **
3644043 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATTTATA
**
3644065 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
**
3644087 TTTTTAAAATAAAT-TTTTTATA
1 -TTTTAAAATAAATCAATTTATA
**
3644109 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
*
3644131 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTTATA
*
3644153 TTTTAAAATAAAT--TTTTCCATA
1 TTTTAAAATAAATCAATTT--ATA
**
3644175 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
* **
3644197 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATTTATA
**
3644219 TTTTAAAATAAAT-TTTTTCATA
1 TTTTAAAATAAATCAATTT-ATA
*
3644241 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTTATA
*
3644263 TTTTAAAATAAA--ATTTTTCATA
1 TTTTAAAATAAATCA-ATTT-ATA
**
3644285 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
* *
3644307 TTTTAAAACAAAT--TTTTCCATA
1 TTTTAAAATAAATCAATTT--ATA
* **
3644329 TTTTAAATTAAATCAATCCATA
1 TTTTAAAATAAATCAATTTATA
* ***
3644351 TTTTAAAATAATTTTTTTTCATA
1 TTTTAAAATAAATCAATTT-ATA
***
3644374 TTTTAAAATAAATCAATCCGTA
1 TTTTAAAATAAATCAATTTATA
** *
3644396 TTTTAAAATAAATCAATCCATG
1 TTTTAAAATAAATCAATTTATA
* *
3644418 TTTTAAAATTAATCAATATATA
1 TTTTAAAATAAATCAATTTATA
3644440 TTTTAAAATA
1 TTTTAAAATA
3644450 GATTTAAATG
Statistics
Matches: 581, Mismatches: 95, Indels: 78
0.77 0.13 0.10
Matches are distributed among these distances:
20 15 0.03
21 20 0.03
22 497 0.86
23 36 0.06
24 13 0.02
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTTATA
Found at i:3643768 original size:44 final size:44
Alignment explanation
Indices: 3643713--3644449 Score: 794
Period size: 44 Copynumber: 16.7 Consensus size: 44
3643703 AATAATATTT
* **
3643713 TTTTTAAATAAATCAATTTATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
** *
3643757 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCTATA
* ** *
3643801 TTTTAAAATAAATCAATTCATATTTTAAAATAAAT-TTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATA
*
3643845 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
** *
3643889 TTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCTATA
** * *
3643933 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCTATA
** *
3643977 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAAT-TCATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCT-ATA
* *
3644021 TTTTAAAATAAA--AATTTCCATATTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAA--TCCATATTTTAAAATAAATCAATCTATA
** *
3644065 TTTTAAAATAAATCAATCCATATTTTTAAAATAAAT-TTTTTATA
1 TTTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATA
3644109 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
*** *
3644153 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
* ** *
3644197 TTTTAAAATAAACCAATCCATATTTTAAAATAAAT-TTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATA
* ***
3644241 TTTTAAAATAAATCAATTCATATTTTAAAATAAAATTTTTC-ATA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCTATA
* *** *
3644285 TTTTAAAATAAATCAATCCATATTTTAAAACAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
* * *** *
3644329 TTTTAAATTAAATCAATCCATATTTTAAAATAATTTTTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATA
* * *
3644374 TTTTAAAATAAATCAATCCGTATTTTAAAATAAATCAATCCATG
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
* **
3644418 TTTTAAAATTAATCAATATATATTTTAAAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATA
3644450 GATTTAAATG
Statistics
Matches: 610, Mismatches: 66, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
43 33 0.05
44 509 0.83
45 63 0.10
46 5 0.01
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
Found at i:3643802 original size:66 final size:66
Alignment explanation
Indices: 3643713--3644449 Score: 869
Period size: 66 Copynumber: 11.2 Consensus size: 66
3643703 AATAATATTT
* ** **
3643713 TTTTTAAATAAATCAATTTATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCTTTCCAT
3643778 A
66 A
** * *
3643779 TTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATCAAT-TCATATTTTAAAATAAATTTTTTC
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCT-ATATTTTAAAATAAATCTTTCC
3643842 ATA
64 ATA
*
3643845 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTTTAAAATAAAAT-TTTCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAAT-AAATCTTTCCA
3643909 TA
65 TA
*** **
3643911 TTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTTC-ATATTTTAAAATAAATCAATCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCTATATTTTAAAATAAATCTTTCCA
3643975 TA
65 TA
** * **
3643977 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAAT-TCATATTTTAAAATAAAAATTTCC
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCT-ATATTTTAAAATAAATCTTTCC
3644040 ATA
64 ATA
* * **
3644043 TTTTAAAATAAATAAATCCATATTTTAAAATAAATCAATCCATATTTTTAAAATAAAT-TTTTTA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA-TTTTAAAATAAATCTTTCCA
3644107 TA
65 TA
*
3644109 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTTCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCTTTCCAT
3644174 A
66 A
* * * *
3644175 TTTTAAAATAAATCAATCCATATTTTAAAATAAACCAATCCATATTTTAAAATAAATTTTTTCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCTTTCCAT
3644240 A
66 A
* *** **
3644241 TTTTAAAATAAATCAATTCATATTTTAAAATAAAATTTTTC-ATATTTTAAAATAAATCAATCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCTATATTTTAAAATAAATCTTTCCA
3644305 TA
65 TA
* *** * * * * *
3644307 TTTTAAAACAAATTTTTCCATATTTTAAATTAAATCAATCCATATTTTAAAATAATTTTTTTTCA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAA-ATCTTTCCA
3644372 TA
65 TA
* * * * ** **
3644374 TTTTAAAATAAATCAATCCGTATTTTAAAATAAATCAATCCATGTTTTAAAATTAATCAATATAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCTTTCCAT
3644439 A
66 A
3644440 TTTTAAAATA
1 TTTTAAAATA
3644450 GATTTAAATG
Statistics
Matches: 575, Mismatches: 79, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
65 37 0.06
66 450 0.78
67 88 0.15
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (66 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCTTTCCAT
A
Found at i:3661781 original size:13 final size:13
Alignment explanation
Indices: 3661765--3661799 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
3661755 AGATTTTCTT
3661765 TTTTTGAAAATCA
1 TTTTTGAAAATCA
3661778 TTTTTG-AAATCA
1 TTTTTGAAAATCA
3661790 TTTTTGAAAA
1 TTTTTGAAAA
3661800 ATTACTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:3664136 original size:21 final size:21
Alignment explanation
Indices: 3664087--3664142 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3664077 GTACCTCTCG
*
3664087 AGGGGTATCGATACACATTCA
1 AGGGGTATCGATACACATGCA
* *
3664108 AGGTGTATCGATACATA-GCA
1 AGGGGTATCGATACACATGCA
3664128 AGGGGGTATCGATAC
1 A-GGGGTATCGATAC
3664143 CTTGTGCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (21 bp):
AGGGGTATCGATACACATGCA
Found at i:3666158 original size:12 final size:12
Alignment explanation
Indices: 3666141--3666165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3666131 ATGATAGTTC
3666141 TCCAACGTCATG
1 TCCAACGTCATG
3666153 TCCAACGTCATG
1 TCCAACGTCATG
3666165 T
1 T
3666166 GTTTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:3669618 original size:14 final size:14
Alignment explanation
Indices: 3669599--3669628 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3669589 TCTTGAAAGC
3669599 AAAAATGAATATTG
1 AAAAATGAATATTG
3669613 AAAAATGAATATTG
1 AAAAATGAATATTG
3669627 AA
1 AA
3669629 TGAAAATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (14 bp):
AAAAATGAATATTG
Found at i:3673229 original size:19 final size:21
Alignment explanation
Indices: 3673180--3673231 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3673170 CTCTTTCAAG
* *
3673180 AGTATCGAAACTTTGAGTTAT
1 AGTATCGAAACTCTCAGTTAT
*
3673201 AGTTTCGAAACTCTCAG-TA-
1 AGTATCGAAACTCTCAGTTAT
3673220 AGTATCGAAACT
1 AGTATCGAAACT
3673232 AGACAGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 14 0.52
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTATCGAAACTCTCAGTTAT
Found at i:3673272 original size:20 final size:20
Alignment explanation
Indices: 3673247--3673297 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
3673237 GAACAGAATG
**
3673247 TATAAAAGTATCGGTACTTA
1 TATAAAAGTATCGAAACTTA
*
3673267 TAT-AAAGTATCGAAACTTT
1 TATAAAAGTATCGAAACTTA
*
3673286 TACAAAAGTATC
1 TATAAAAGTATC
3673298 AATACTCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TATAAAAGTATCGAAACTTA
Found at i:3674990 original size:20 final size:20
Alignment explanation
Indices: 3674967--3675016 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3674957 TGTGGATTAT
3674967 TTTTATTTTTTGAC-TTTTTC
1 TTTTATTTTTT-ACTTTTTTC
*
3674987 TTTTATTTTTTTCTTTTTTC
1 TTTTATTTTTTACTTTTTTC
3675007 TTTTATTTTT
1 TTTTATTTTT
3675017 CATGAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTATTTTTTACTTTTTTC
Found at i:3675065 original size:10 final size:11
Alignment explanation
Indices: 3675041--3675073 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
3675031 AACTAATAAG
3675041 AATAAATTGAA
1 AATAAATTGAA
3675052 AATAAATT-AA
1 AATAAATTGAA
3675062 AAT-AATTGAA
1 AATAAATTGAA
3675072 AA
1 AA
3675074 AGAACCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 9 0.43
11 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (11 bp):
AATAAATTGAA
Found at i:3675414 original size:19 final size:19
Alignment explanation
Indices: 3675379--3675416 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3675369 GAAAATAAAG
* *
3675379 ATAAAACAAATATAATGAA
1 ATAAAACAAAGACAATGAA
3675398 ATAAAACAAAGACAATGAA
1 ATAAAACAAAGACAATGAA
3675417 TGTAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (19 bp):
ATAAAACAAAGACAATGAA
Found at i:3675794 original size:15 final size:17
Alignment explanation
Indices: 3675769--3675802 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3675759 TAAAAGTCCT
3675769 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
3675785 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
3675801 AA
1 AA
3675803 CATGTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:3677463 original size:3 final size:3
Alignment explanation
Indices: 3677455--3677508 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
3677445 GGAAAAGTTT
3677455 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA -GGA
*
3677501 GGG GGA GG
1 GGA GGA GG
3677509 GAGGGAGAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3688547 original size:2 final size:2
Alignment explanation
Indices: 3688540--3688573 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3688530 TTCTTTGTGC
3688540 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
3688574 TCGTGTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3690556 original size:56 final size:56
Alignment explanation
Indices: 3690467--3690579 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
3690457 GCAATTAATT
3690467 CTTCTGCTGCATCAACACCAACTGGGAGCCATGCAACCCCTGCACTGAATTTTCCA
1 CTTCTGCTGCATCAACACCAACTGGGAGCCATGCAACCCCTGCACTGAATTTTCCA
*
3690523 CTTCTGCTGCATCAACACCAACTGGGAGTCATGCAACCCCTGCACTGAATTTTCCA
1 CTTCTGCTGCATCAACACCAACTGGGAGCCATGCAACCCCTGCACTGAATTTTCCA
3690579 C
1 C
3690580 CTCAGGGTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (56 bp):
CTTCTGCTGCATCAACACCAACTGGGAGCCATGCAACCCCTGCACTGAATTTTCCA
Found at i:3694801 original size:20 final size:20
Alignment explanation
Indices: 3694776--3694815 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3694766 AGCAACAGAA
*
3694776 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
3694796 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
3694816 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:3694858 original size:20 final size:21
Alignment explanation
Indices: 3694829--3694868 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3694819 TAATAGAATA
*
3694829 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
*
3694850 AAAAA-TGATCCTATTTAAT
1 AAAAACTGATCCTATCTAAT
3694869 AACTAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:3694907 original size:20 final size:20
Alignment explanation
Indices: 3694882--3694920 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3694872 TAATAGAATA
*
3694882 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
3694902 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
3694921 ATTTAATTTA
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:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:3694911 original size:52 final size:52
Alignment explanation
Indices: 3694772--3694921 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
3694762 AATTAGCAAC
3694772 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
3694823 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATTTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
3694876 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
3694922 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.47
53 45 0.48
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:3699511 original size:20 final size:20
Alignment explanation
Indices: 3699486--3699525 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3699476 AGCAACAGAA
3699486 TAAAAATGATTC-TATCTAAT
1 TAAAAATGA-TCATATCTAAT
3699506 TAAAAATGATCATATCTAAT
1 TAAAAATGATCATATCTAAT
3699526 AATTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:3699554 original size:53 final size:52
Alignment explanation
Indices: 3699482--3699637 Score: 260
Period size: 52 Copynumber: 3.0 Consensus size: 52
3699472 AATTAGCAAC
*
3699482 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCATATCTAATAATTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAATTAAT
*
3699533 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAATTAAT
* *
3699586 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATATTTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAATTAAT
3699638 TTAGATATTC
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
51 5 0.05
52 49 0.50
53 44 0.45
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAATTAAT
Found at i:3699568 original size:20 final size:21
Alignment explanation
Indices: 3699539--3699578 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3699529 TAATAGAATA
*
3699539 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
3699560 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
3699579 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:3699617 original size:20 final size:20
Alignment explanation
Indices: 3699592--3699630 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3699582 TAATAGAATA
*
3699592 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
3699612 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
3699631 ATTTAATTTA
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:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:3701451 original size:18 final size:19
Alignment explanation
Indices: 3701428--3701463 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3701418 TAAAAAGATG
*
3701428 ATAAAATTAAA-GTTTAAT
1 ATAAAAATAAATGTTTAAT
3701446 ATAAAAATAAATGTTTAA
1 ATAAAAATAAATGTTTAA
3701464 ATTATATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATAAAAATAAATGTTTAAT
Found at i:3701642 original size:13 final size:13
Alignment explanation
Indices: 3701624--3701667 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3701614 TAGAATTTTA
3701624 AATTTTTAAAAAT
1 AATTTTTAAAAAT
*
3701637 AATTTTAAAAAAT
1 AATTTTTAAAAAT
*
3701650 ATTTCTTTAAAAAT
1 AATT-TTTAAAAAT
3701664 AATT
1 AATT
3701668 ATTTTTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:3702004 original size:2 final size:2
Alignment explanation
Indices: 3701997--3702031 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3701987 TTTGTCCGTT
3701997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3702032 ATTTGAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3702107 original size:24 final size:23
Alignment explanation
Indices: 3702078--3702159 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
3702068 TTTTTTAAAT
* *
3702078 ATTTTGAAAATATATAATATATA
1 ATTTTGAAAACATATATTATATA
3702101 ATTTTTGAAAACATATATTATATA
1 A-TTTTGAAAACATATATTATATA
* *
3702125 GTTTTGAAAACATATATTGTATA
1 ATTTTGAAAACATATATTATATA
3702148 ATTTTGAAAACA
1 ATTTTGAAAACA
3702160 ATTTTTAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
23 33 0.62
24 20 0.38
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTTTGAAAACATATATTATATA
Found at i:3702198 original size:39 final size:39
Alignment explanation
Indices: 3702136--3702329 Score: 164
Period size: 39 Copynumber: 5.1 Consensus size: 39
3702126 TTTTGAAAAC
* * *
3702136 ATATATTGTATAATTTT-GAAAACAATTTTT-AAAATAT
1 ATATATTATATAGTTTTAAAAAACAATTTTTAAAAATAT
* *
3702173 ATATAATATATAGTTTTTAAAAAAC-ATTTTTGAAAAACAT
1 ATATATTATATAG-TTTTAAAAAACAATTTTT-AAAAATAT
* * ** *
3702213 ATGTATTACATAGTTTTAAAAATTAGTTTTTAAAAATAT
1 ATATATTATATAGTTTTAAAAAACAATTTTTAAAAATAT
* ** *
3702252 ATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATAT
1 ATATATTATATAGTTTTAAAAAACAATTTTTAAAAATAT
* ** * *
3702291 ATAT-TT-TATAGTTTTGAAAATTAGTTTTTAAATATAT
1 ATATATTATATAGTTTTAAAAAACAATTTTTAAAAATAT
3702328 AT
1 AT
3702330 TATAGAGTTT
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
37 42 0.31
38 12 0.09
39 61 0.45
40 21 0.15
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (39 bp):
ATATATTATATAGTTTTAAAAAACAATTTTTAAAAATAT
Found at i:3702365 original size:72 final size:73
Alignment explanation
Indices: 3702126--3702413 Score: 217
Period size: 72 Copynumber: 3.9 Consensus size: 73
3702116 TATTATATAG
* * * * * * * *
3702126 TTTTGAAAACATATATTGTATAATTTTGAAAA-CAATTTTTAAAATATATATAATATATAGTTTT
1 TTTTAAAAAAATATATTATATAGTTTTGAAAATTAGTTTTT-AAATATATATATTATAGAGTTTT
* ** *
3702190 TAAAAAACAT
65 GAAATTA-GT
* * * *
3702200 TTTTGAAAAACATATGTATTACATAGTTTTAAAAATTAGTTTTTAAAAATATATATATTATATAG
1 TTTT-AAAAA-A-ATATATTATATAGTTTTGAAAATTAGTTTTT--AAATATATATATTATAGAG
3702265 TTTTGAAAATTAGT
61 TTTTG-AAATTAGT
* *
3702279 TTTTAAAAATATATATTTTATAGTTTTGAAAATTAGTTTTT-AA-ATATATATTATAGAGTTTTG
1 TTTTAAAAAAATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATAGAGTTTTG
**
3702342 -AATTTTT
66 AAATTAGT
* * * * *
3702349 TTTTAAAAAAAAATATATTATATGGTTTTGAAAATTACTTTTTTAAA-ACATATATTGTATAGTT
1 TTTT--AAAAAAATATATTATATAGTTTTGAAAATTA-GTTTTTAAATATATATATTATAGAGTT
3702413 T
63 T
3702414 AAAAAAATGT
Statistics
Matches: 175, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
70 9 0.05
72 47 0.27
73 7 0.04
74 21 0.12
75 4 0.02
76 27 0.15
77 17 0.10
78 11 0.06
79 28 0.16
80 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (73 bp):
TTTTAAAAAAATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATAGAGTTTTG
AAATTAGT
Found at i:3702391 original size:39 final size:38
Alignment explanation
Indices: 3702131--3702413 Score: 251
Period size: 37 Copynumber: 7.6 Consensus size: 38
3702121 TATAGTTTTG
* * * * *
3702131 AAAACATATATTGTATAATTTTGAAAA-CAATTTTTAA
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAA
* * * * *
3702168 AATATATATAATATATAGTTTTTAAAA-AACATTTTTGAA
1 AAAATATATATTATATAGTTTTGAAAATTA-GTTTTT-AA
* * *
3702207 AAACATATGTATTACATAGTTTTAAAAATTAGTTTTTAA
1 AAA-ATATATATTATATAGTTTTGAAAATTAGTTTTTAA
3702246 AAATATATATATTATATAGTTTTGAAAATTAGTTTTT-A
1 AAA-ATATATATTATATAGTTTTGAAAATTAGTTTTTAA
*
3702284 AAAATATATATTTTATAGTTTTGAAAATTAGTTTTT--
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAA
* **
3702320 -AAATATATATTATAGAGTTTTG--AATTTTTTTTTAAA
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTT-AA
* * * *
3702356 AAAAAATATATTATATGGTTTTGAAAATTACTTTTT-T
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAA
* *
3702393 AAAACATATATTGTATAGTTT
1 AAAATATATATTATATAGTTT
3702414 AAAAAAATGT
Statistics
Matches: 204, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
33 9 0.04
35 20 0.10
37 91 0.45
38 10 0.05
39 48 0.24
40 25 0.12
41 1 0.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (38 bp):
AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAA
Found at i:3702469 original size:16 final size:17
Alignment explanation
Indices: 3702427--3702466 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3702417 AAAATGTGTT
3702427 TTTATTTATCTATTTTA
1 TTTATTTATCTATTTTA
3702444 TTTCATTTATC-A-TTTA
1 TTT-ATTTATCTATTTTA
3702460 TTTATTT
1 TTTATTT
3702467 TATTTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 4 0.18
18 7 0.32
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATCTATTTTA
Found at i:3703704 original size:25 final size:24
Alignment explanation
Indices: 3703676--3703723 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3703666 TTATCTAACC
*
3703676 TTTTATTATTATTTTTATTATTTTA
1 TTTTATTAATA-TTTTATTATTTTA
*
3703701 TTTTATTAATATTTTGTTATTTT
1 TTTTATTAATATTTTATTATTTT
3703724 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTAATATTTTATTATTTTA
Found at i:3703713 original size:19 final size:18
Alignment explanation
Indices: 3703676--3703723 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
3703666 TTATCTAACC
**
3703676 TTTTATTATTATTTTTATT
1 TTTTATT-TTATTAATATT
3703695 ATTTTATTTTATTAATATT
1 -TTTTATTTTATTAATATT
3703714 TTGTTATTTT
1 TT-TTATTTT
3703724 CTATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTATTTTATTAATATT
Found at i:3709915 original size:29 final size:29
Alignment explanation
Indices: 3709873--3709931 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3709863 ATTTTCACCT
3709873 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
3709902 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
3709931 A
1 A
3709932 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:3716045 original size:12 final size:11
Alignment explanation
Indices: 3716015--3716052 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
3716005 GAAATGACTT
*
3716015 TTAAAATAT-A
1 TTAAATTATAA
3716025 TTAAATTATAA
1 TTAAATTATAA
3716036 TTATAATTATAA
1 TTA-AATTATAA
3716048 TTAAA
1 TTAAA
3716053 AATTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 8 0.32
11 6 0.24
12 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTATAA
Found at i:3716062 original size:13 final size:13
Alignment explanation
Indices: 3716027--3716071 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3716017 AAAATATATT
3716027 AAATTATAATT-A
1 AAATTATAATTAA
*
3716039 TAATTATAATTAA
1 AAATTATAATTAA
*
3716052 AAATTAAAATTAA
1 AAATTATAATTAA
*
3716065 GAATTAT
1 AAATTAT
3716072 TTATTCCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AAATTATAATTAA
Found at i:3727299 original size:175 final size:175
Alignment explanation
Indices: 3727008--3727359 Score: 704
Period size: 175 Copynumber: 2.0 Consensus size: 175
3726998 CATCTTCCAA
3727008 CATGGGTATGGGGATATGACACTCGTAGGATTTTCCCAAATGCATAGAAAAGAAAAAATTGGACA
1 CATGGGTATGGGGATATGACACTCGTAGGATTTTCCCAAATGCATAGAAAAGAAAAAATTGGACA
3727073 TGCCCATGTCAGACACGTACCTGTATCCTAGGGTCACATCTTATTCCAAGTAGCATAGGTCTACT
66 TGCCCATGTCAGACACGTACCTGTATCCTAGGGTCACATCTTATTCCAAGTAGCATAGGTCTACT
3727138 TTACTTCCTTACTCTTTAACTATTTGACCTTTGTGTGGAACTTTG
131 TTACTTCCTTACTCTTTAACTATTTGACCTTTGTGTGGAACTTTG
3727183 CATGGGTATGGGGATATGACACTCGTAGGATTTTCCCAAATGCATAGAAAAGAAAAAATTGGACA
1 CATGGGTATGGGGATATGACACTCGTAGGATTTTCCCAAATGCATAGAAAAGAAAAAATTGGACA
3727248 TGCCCATGTCAGACACGTACCTGTATCCTAGGGTCACATCTTATTCCAAGTAGCATAGGTCTACT
66 TGCCCATGTCAGACACGTACCTGTATCCTAGGGTCACATCTTATTCCAAGTAGCATAGGTCTACT
3727313 TTACTTCCTTACTCTTTAACTATTTGACCTTTGTGTGGAACTTTG
131 TTACTTCCTTACTCTTTAACTATTTGACCTTTGTGTGGAACTTTG
3727358 CA
1 CA
3727360 GGGGGATAGC
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 177 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (175 bp):
CATGGGTATGGGGATATGACACTCGTAGGATTTTCCCAAATGCATAGAAAAGAAAAAATTGGACA
TGCCCATGTCAGACACGTACCTGTATCCTAGGGTCACATCTTATTCCAAGTAGCATAGGTCTACT
TTACTTCCTTACTCTTTAACTATTTGACCTTTGTGTGGAACTTTG
Found at i:3730259 original size:52 final size:52
Alignment explanation
Indices: 3730181--3730339 Score: 230
Period size: 52 Copynumber: 3.1 Consensus size: 52
3730171 ATATCAGCCA
3730181 TTTGCCCTGAGTTAACCCGGTATATTCCATGGTAAATGGTCTTGTCTTGTGC
1 TTTGCCCTGAGTTAACCCGGTATATTCCATGGTAAATGGTCTTGTCTTGTGC
* * *
3730233 TTTGCCCTCAGTTAACCCTGTATATTCCATTGTAAATGGTCTTGTCTTGTGC
1 TTTGCCCTGAGTTAACCCGGTATATTCCATGGTAAATGGTCTTGTCTTGTGC
* ** ** *
3730285 TTTG-CCTGGGTTAGTCCGGTATATTCCATGGGGACTGGTCTTGTCTTGTGC
1 TTTGCCCTGAGTTAACCCGGTATATTCCATGGTAAATGGTCTTGTCTTGTGC
3730336 TTTG
1 TTTG
3730340 TGCTCTGTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 42 0.44
52 53 0.56
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (52 bp):
TTTGCCCTGAGTTAACCCGGTATATTCCATGGTAAATGGTCTTGTCTTGTGC
Found at i:3730648 original size:28 final size:27
Alignment explanation
Indices: 3730600--3730657 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3730590 AGGGGTGTAC
* *
3730600 AAAAAATCTGAATATCCGATTTTGTGAA
1 AAAAAATCCGAATATCCGA-TTTGGGAA
*
3730628 AAAAATATCCGAA-ATCGGATTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTGGGAA
3730655 AAA
1 AAA
3730658 CCGATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.38
28 10 0.38
29 6 0.23
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (27 bp):
AAAAAATCCGAATATCCGATTTGGGAA
Found at i:3733053 original size:21 final size:21
Alignment explanation
Indices: 3733029--3733068 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3733019 TTTATTTTAT
3733029 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3733050 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3733069 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3733116 original size:33 final size:33
Alignment explanation
Indices: 3733063--3733161 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3733053 TTTGTTTCAA
3733063 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3733095 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3733128 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3733161 T
1 T
3733162 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3733190 original size:13 final size:13
Alignment explanation
Indices: 3733147--3733201 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3733137 TTGGAAGTAT
3733147 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
3733160 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
3733174 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
3733187 TTAAGTATTTGAA
1 TTAAGTATTTCAA
3733200 TT
1 TT
3733202 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:3733420 original size:21 final size:21
Alignment explanation
Indices: 3733394--3733450 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3733384 TGGAGCGTGG
*
3733394 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
3733415 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
3733436 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
3733451 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:3733667 original size:18 final size:17
Alignment explanation
Indices: 3733634--3733684 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
3733624 GTTTTTTTAT
3733634 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
3733651 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
*
3733668 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTAAAAA
3733685 CCGAAACCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (17 bp):
AACCGGTTTTTTAAAAA
Found at i:3733685 original size:15 final size:15
Alignment explanation
Indices: 3733615--3733687 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 15
3733605 ATCTGGAATA
*
3733615 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
3733630 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
3733645 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
*
3733662 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
3733679 TTAAAACCG
1 TTAAAACCG
3733688 AAACCGGTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
15 21 0.41
17 30 0.59
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:3741673 original size:17 final size:17
Alignment explanation
Indices: 3741651--3741685 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3741641 GCTCAGGTGT
*
3741651 TGTCTGATACGAGTATG
1 TGTCTGACACGAGTATG
*
3741668 TGTCTGACACGGGTATG
1 TGTCTGACACGAGTATG
3741685 T
1 T
3741686 TCCAAATCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.34
Consensus pattern (17 bp):
TGTCTGACACGAGTATG
Found at i:3747363 original size:23 final size:22
Alignment explanation
Indices: 3747319--3747363 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3747309 AATGCCAGAG
*
3747319 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
3747341 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
3747364 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:3748227 original size:32 final size:31
Alignment explanation
Indices: 3748186--3748281 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 31
3748176 GAGTCGAGGG
3748186 TTTACCTATGTTCTACGCAACATATGGACAGT
1 TTTACCTATGTTCTACG-AACATATGGACAGT
*
3748218 TTTACCTATG-TCTTTCGAGACATATGGACAG-
1 TTTACCTATGTTC-TACGA-ACATATGGACAGT
* *
3748249 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCT-ACGAACATATGGACAGT
3748281 T
1 T
3748282 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTCTACGAACATATGGACAGT
Found at i:3748309 original size:30 final size:30
Alignment explanation
Indices: 3748273--3748425 Score: 263
Period size: 30 Copynumber: 5.1 Consensus size: 30
3748263 AAGGAACATA
3748273 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3748303 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3748333 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3748363 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
3748393 TGGATAGTTATCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3748422 TGGA
1 TGGA
3748426 TAGGTCCTTC
Statistics
Matches: 119, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.15
30 101 0.85
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3748708 original size:2 final size:2
Alignment explanation
Indices: 3748698--3748729 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3748688 GTATGTGTGG
*
3748698 AT AT GT 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
3748730 GAAAGGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3751557 original size:21 final size:21
Alignment explanation
Indices: 3751513--3751557 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3751503 GATTTCTGGG
* * *
3751513 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
3751534 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
3751555 CAA
1 CAA
3751558 ACGAATATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:3751630 original size:23 final size:22
Alignment explanation
Indices: 3751586--3751630 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3751576 AATGCCAGAG
*
3751586 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
3751608 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
3751631 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:3752492 original size:32 final size:31
Alignment explanation
Indices: 3752451--3752546 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 31
3752441 GAGTCGAGGG
3752451 TTTACCTATGTTCTACGCAACATATGGACAGT
1 TTTACCTATGTTCTACG-AACATATGGACAGT
*
3752483 TTTACCTATG-TCTTTCGAGACATATGGACAG-
1 TTTACCTATGTTC-TACGA-ACATATGGACAGT
* *
3752514 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCT-ACGAACATATGGACAGT
3752546 T
1 T
3752547 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTCTACGAACATATGGACAGT
Found at i:3752574 original size:30 final size:30
Alignment explanation
Indices: 3752538--3752720 Score: 332
Period size: 30 Copynumber: 6.1 Consensus size: 30
3752528 AAGGAACATA
3752538 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3752568 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3752598 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3752628 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3752658 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
3752688 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3752717 TGGA
1 TGGA
3752721 TAGGTCATTC
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
29 18 0.12
30 132 0.88
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3753003 original size:2 final size:2
Alignment explanation
Indices: 3752993--3753024 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3752983 GTATGTGTGG
*
3752993 AT AT GT 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
3753025 GTGAAAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3757884 original size:21 final size:21
Alignment explanation
Indices: 3757860--3757899 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3757850 TTCCTACACA
3757860 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
3757881 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
3757900 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:3758339 original size:21 final size:18
Alignment explanation
Indices: 3758293--3758366 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
3758283 ACTGTATATT
*
3758293 TGTCCCGAAGGACTACTA
1 TGTCCCGAAGGACCACTA
*
3758311 TATCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
3758330 TTTGTCCCGAAGGACCACTA
1 --TGTCCCGAAGGACCACTA
3758350 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3758367 CCTTAAGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 32 0.64
19 1 0.02
20 1 0.02
21 16 0.32
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3758339 original size:39 final size:39
Alignment explanation
Indices: 3758290--3758366 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
3758280 GGCACTGTAT
*
3758290 ATTTGTCCCGAAGGACTACTATATCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACTG
*
3758329 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
1 ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACT
3758367 CCTTAAGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (39 bp):
ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACTG
Found at i:3763135 original size:21 final size:21
Alignment explanation
Indices: 3763111--3763150 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3763101 TTCCTACACA
3763111 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
3763132 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
3763151 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:3763588 original size:21 final size:21
Alignment explanation
Indices: 3763541--3763620 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
3763531 GGCATTGTAT
*
3763541 ATTTGTCCCGAAGGTCCACT-
1 ATTTGTCCCGAAGGACCACTG
3763561 A--TGTCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTG
3763580 ATTTGTCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTG
*
3763601 ATTTGTCCCGAATGACCACT
1 ATTTGTCCCGAAGGACCACT
3763621 CCTTAAGAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
18 16 0.29
19 1 0.02
20 1 0.02
21 37 0.67
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (21 bp):
ATTTGTCCCGAAGGACCACTG
Found at i:3763599 original size:39 final size:41
Alignment explanation
Indices: 3763541--3763620 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 41
3763531 GGCATTGTAT
*
3763541 ATTTGTCCCGAAGGTCCACT-A-TGTCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTGATTGTCCCGAAGGACCACTG
*
3763580 ATTTGTCCCGAAGGACCACTGATTTGTCCCGAATGACCACT
1 ATTTGTCCCGAAGGACCACTGA-TTGTCCCGAAGGACCACT
3763621 CCTTAAGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 19 0.53
40 1 0.03
42 16 0.44
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (41 bp):
ATTTGTCCCGAAGGACCACTGATTGTCCCGAAGGACCACTG
Found at i:3772634 original size:26 final size:26
Alignment explanation
Indices: 3772598--3772649 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3772588 TATTGATAAG
3772598 CATAAGCATTCATCCTTGTTTATCTC
1 CATAAGCATTCATCCTTGTTTATCTC
3772624 CATAAGCATTCATCCTTGTTTATCTC
1 CATAAGCATTCATCCTTGTTTATCTC
3772650 TGTAATCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (26 bp):
CATAAGCATTCATCCTTGTTTATCTC
Found at i:3772896 original size:17 final size:19
Alignment explanation
Indices: 3772861--3772898 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
3772851 AATATGTATC
3772861 TTTAAATCTATTAGAAGTG
1 TTTAAATCTATTAGAAGTG
3772880 TTTAAATC-ATT-GAAGTG
1 TTTAAATCTATTAGAAGTG
3772897 TT
1 TT
3772899 AATACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (19 bp):
TTTAAATCTATTAGAAGTG
Found at i:3777425 original size:14 final size:14
Alignment explanation
Indices: 3777389--3777415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3777379 TTATTAAAAA
3777389 AAATAAATTTTATT
1 AAATAAATTTTATT
3777403 AAATAAATTTTAT
1 AAATAAATTTTAT
3777416 AATTTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATAAATTTTATT
Found at i:3788550 original size:2 final size:2
Alignment explanation
Indices: 3788543--3788604 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3788533 ACTTCAAGTT
3788543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3788585 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3788605 GTTTATTTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3789381 original size:23 final size:23
Alignment explanation
Indices: 3789354--3789429 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 23
3789344 TTTTTTATTG
3789354 AATTAATATTTAAATAATTTATA
1 AATTAATATTTAAATAATTTATA
* *
3789377 AATTAA-GTTT-AATAA-ATATA
1 AATTAATATTTAAATAATTTATA
*
3789397 ATATT-ATATTTTAAAAGAATTTATTA
1 A-ATTAATA-TTT-AAATAATTTA-TA
3789423 AATTAAT
1 AATTAAT
3789430 TAAAACGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
20 6 0.15
21 8 0.20
22 6 0.15
23 6 0.15
24 4 0.10
25 5 0.12
26 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
AATTAATATTTAAATAATTTATA
Found at i:3803118 original size:19 final size:19
Alignment explanation
Indices: 3803094--3803133 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3803084 AATAAATTTA
3803094 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
3803113 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
3803132 AT
1 AT
3803134 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:3803180 original size:12 final size:12
Alignment explanation
Indices: 3803156--3803201 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
3803146 CGATTCCCAG
3803156 CCCAATA-CCGA
1 CCCAATACCCGA
3803167 CCCAATACCCGA
1 CCCAATACCCGA
* *
3803179 CCCAATACCTGG
1 CCCAATACCCGA
3803191 CCCAATACCCG
1 CCCAATACCCG
3803202 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:3803183 original size:23 final size:24
Alignment explanation
Indices: 3803156--3803201 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3803146 CGATTCCCAG
3803156 CCCAATACC-GACCCAATACCCGA
1 CCCAATACCTGACCCAATACCCGA
*
3803179 CCCAATACCTGGCCCAATACCCG
1 CCCAATACCTGACCCAATACCCG
3803202 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (24 bp):
CCCAATACCTGACCCAATACCCGA
Found at i:3804248 original size:20 final size:20
Alignment explanation
Indices: 3804223--3804261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3804213 TTGGTTCACA
*
3804223 GAATGTAAGATTATCAGTGG
1 GAATGTAAGATTACCAGTGG
3804243 GAATGTAAGATTACCAGTG
1 GAATGTAAGATTACCAGTG
3804262 TAACACCCCA
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:0.08, G:0.28, T:0.28
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGG
Found at i:3805091 original size:23 final size:23
Alignment explanation
Indices: 3805025--3805110 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
3805015 TCATATAAAT
*
3805025 TTGCACCGAAGTACCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
3805048 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
3805073 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
3805095 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
3805111 TATAATATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.04
23 30 0.58
24 18 0.35
25 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:3806256 original size:22 final size:22
Alignment explanation
Indices: 3806239--3806302 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
3806229 CTCGTATAAA
3806239 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3806261 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3806283 TGCACCGAAGTGCCCGTAGA
1 TGCACCGAAGTGCCCGTAGA
3806303 TTTGTCCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3808024 original size:21 final size:21
Alignment explanation
Indices: 3808000--3808044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3807990 TCTTGTTCGT
* *
3808000 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3808021 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3808042 TTG
1 TTG
3808045 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3811220 original size:22 final size:22
Alignment explanation
Indices: 3811203--3811266 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
3811193 CTCGTATAAA
3811203 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3811225 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3811247 TGCACCGAAGTGCCCGTAGA
1 TGCACCGAAGTGCCCGTAGA
3811267 TTTGTCCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3812986 original size:21 final size:21
Alignment explanation
Indices: 3812962--3813006 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3812952 TCTTGTTCGT
* *
3812962 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3812983 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3813004 TTG
1 TTG
3813007 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3814914 original size:37 final size:37
Alignment explanation
Indices: 3814841--3814915 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
3814831 GTTGAAAAAT
*
3814841 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
3814878 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
3814915 A
1 A
3814916 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:3819770 original size:18 final size:18
Alignment explanation
Indices: 3819730--3819776 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3819720 AGTTAAAACC
*
3819730 CAAATCTAATATGCAACA
1 CAAATCTAATATACAACA
*
3819748 CAAATTTAATATACAATCA
1 CAAATCTAATATACAA-CA
*
3819767 -AAATCCAATA
1 CAAATCTAATA
3819777 CTCTTAACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (18 bp):
CAAATCTAATATACAACA
Found at i:3820178 original size:21 final size:21
Alignment explanation
Indices: 3820154--3820196 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3820144 TATTTAAATT
*
3820154 AATTAATATATACCAAACATA
1 AATTAATAAATACCAAACATA
* * *
3820175 AATTTATAAATATCAAATATA
1 AATTAATAAATACCAAACATA
3820196 A
1 A
3820197 TATCAAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAATAAATACCAAACATA
Found at i:3820364 original size:22 final size:25
Alignment explanation
Indices: 3820313--3820367 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
3820303 AAATCAAATT
*
3820313 TATATTTTATAACATTAATTAATAAA
1 TATATTTTATAAAATTAA-TAATAAA
3820339 TATATTTTA-AAAATTAA-AAT-AA
1 TATATTTTATAAAATTAATAATAAA
3820361 TATATTT
1 TATATTT
3820368 GAAGCAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
25 7 0.25
26 9 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATTTTATAAAATTAATAATAAA
Found at i:3821385 original size:21 final size:21
Alignment explanation
Indices: 3821359--3821520 Score: 216
Period size: 21 Copynumber: 7.7 Consensus size: 21
3821349 GCCATATAAA
3821359 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
*
3821380 ATGTCCCGAAGGACCACATAA
1 ATGTCCCGAAGGACCACATAT
* * *
3821401 ATGTCCTGAATGACCAAATAT
1 ATGTCCCGAAGGACCACATAT
*
3821422 ATGTCCCGAAGGACCGCATAT
1 ATGTCCCGAAGGACCACATAT
* *
3821443 ATGTTCCAAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
* *
3821464 ATGTCCAGAAGGACCGCATAT
1 ATGTCCCGAAGGACCACATAT
* *
3821485 ATGTTCCAAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
*
3821506 ATGTCCAGAAGGACC
1 ATGTCCCGAAGGACC
3821521 GCGTAGAACC
Statistics
Matches: 118, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 118 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:3831076 original size:5 final size:5
Alignment explanation
Indices: 3831066--3831220 Score: 310
Period size: 5 Copynumber: 31.0 Consensus size: 5
3831056 ATTTATCTTA
3831066 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
3831116 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
3831166 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
3831216 AATAT
1 AATAT
3831221 TATACCCGCT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 150 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3836393 original size:27 final size:27
Alignment explanation
Indices: 3836359--3836445 Score: 86
Period size: 33 Copynumber: 3.0 Consensus size: 27
3836349 GTAGTGTTAG
*
3836359 GGTAGCAGGGCATGGTTCGAA-CAACTT
1 GGTAGCAGGACATGGTTC-AAGCAACTT
3836386 GGTAGCAGGACATGGTTCAAGCAACTTAAT
1 GGTAGCAGGACATGGTTCAAGCAAC-T--T
*
3836416 CAAGGTAGCAGGGCATGGTTCAAGCAACTT
1 ---GGTAGCAGGACATGGTTCAAGCAACTT
3836446 AATTAAGGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 2 0.04
27 21 0.41
28 1 0.02
30 2 0.04
32 1 0.02
33 24 0.47
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (27 bp):
GGTAGCAGGACATGGTTCAAGCAACTT
Found at i:3836433 original size:33 final size:33
Alignment explanation
Indices: 3836386--3836479 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
3836376 CGAACAACTT
*
3836386 GGTAGCAGGACATGGTTCAAGCAACTTAATCAA
1 GGTAGCAGGGCATGGTTCAAGCAACTTAATCAA
*
3836419 GGTAGCAGGGCATGGTTCAAGCAACTTAATTAA
1 GGTAGCAGGGCATGGTTCAAGCAACTTAATCAA
* *
3836452 GGTAACAGAGCATGGTTCGAA-CAACTTA
1 GGTAGCAGGGCATGGTTC-AAGCAACTTA
3836480 TAGTGTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (33 bp):
GGTAGCAGGGCATGGTTCAAGCAACTTAATCAA
Found at i:3836982 original size:20 final size:21
Alignment explanation
Indices: 3836943--3836985 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3836933 GTCCGTTTAA
3836943 AAAAATAATTTTAAAAATTAT
1 AAAAATAATTTTAAAAATTAT
*
3836964 AAAAATAATTTT-AATATTAT
1 AAAAATAATTTTAAAAATTAT
3836984 AA
1 AA
3836986 CTGAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATAATTTTAAAAATTAT
Found at i:3842133 original size:12 final size:12
Alignment explanation
Indices: 3842112--3842158 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
3842102 GAGGTAGAGA
*
3842112 TGGTGGTGATGG
1 TGGTGATGATGG
3842124 TGGTGATGATGG
1 TGGTGATGATGG
*
3842136 AGGTGGA-GATGG
1 TGGT-GATGATGG
*
3842148 TGATGATGATG
1 TGGTGATGATG
3842159 AAGTAATGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (12 bp):
TGGTGATGATGG
Found at i:3847366 original size:2 final size:2
Alignment explanation
Indices: 3847359--3847412 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3847349 ATTACATAAG
3847359 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
3847401 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3847413 TCATATGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3847798 original size:23 final size:23
Alignment explanation
Indices: 3847772--3847832 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3847762 AATGAAACTT
*
3847772 CGGTACATTTCTACGCGGCACTA
1 CGGTGCATTTCTACGCGGCACTA
* * *
3847795 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCATTTCTACGCGGCACTA
*
3847818 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
3847833 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTA
Found at i:3852192 original size:2 final size:2
Alignment explanation
Indices: 3852185--3852214 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3852175 TGATTGCATA
3852185 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
3852215 TCATATGATT
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:3852602 original size:23 final size:23
Alignment explanation
Indices: 3852569--3852636 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
3852559 CATATTATAT
3852569 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3852592 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
3852615 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3852637 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3856902 original size:14 final size:14
Alignment explanation
Indices: 3856883--3856909 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3856873 GAACTTCTCA
3856883 GAATTCAGATATAC
1 GAATTCAGATATAC
3856897 GAATTCAGATATA
1 GAATTCAGATATA
3856910 TGTCAGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (14 bp):
GAATTCAGATATAC
Found at i:3863289 original size:20 final size:20
Alignment explanation
Indices: 3863264--3863301 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3863254 ATCCTATTCT
*
3863264 CTGGTAATTTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
3863284 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3863302 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:3868289 original size:3 final size:3
Alignment explanation
Indices: 3868281--3868309 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3868271 GATATCTCTC
3868281 TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3868310 CCCTTGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:3868820 original size:10 final size:11
Alignment explanation
Indices: 3868798--3868836 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3868788 TCATTCACTT
3868798 AAAC-GAAGAA
1 AAACAGAAGAA
3868808 AAACAGAAGAA
1 AAACAGAAGAA
*
3868819 AAACAGAGGAA
1 AAACAGAAGAA
3868830 AAACAGA
1 AAACAGA
3868837 GCAAAGGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (11 bp):
AAACAGAAGAA
Found at i:3873065 original size:25 final size:25
Alignment explanation
Indices: 3873037--3873084 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3873027 TTTAAGTTCT
* *
3873037 ATTTTATAACTTGAATTAAATTTTA
1 ATTTTATAAATTGAATCAAATTTTA
*
3873062 ATTTTTTAAATTGAATCAAATTT
1 ATTTTATAAATTGAATCAAATTT
3873085 ATGAAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTTTATAAATTGAATCAAATTTTA
Found at i:3884981 original size:22 final size:21
Alignment explanation
Indices: 3884939--3884978 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3884929 GAGTTTATTT
*
3884939 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3884960 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3884979 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3889156 original size:37 final size:37
Alignment explanation
Indices: 3889113--3889227 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
3889103 GTTCGGGTCA
*
3889113 GGTCGGGTTTTTTAAGTGTGATTTTTGGGTCGAGTCG
1 GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCG
3889150 GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCG
1 GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCG
* * *
3889187 GGTTGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCG
1 GGTCGGG-TTTTTTAAGTGTGATATTTGGGTCGAGTCG
3889225 GGT
1 GGT
3889228 TCGAGTTTAG
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
37 42 0.58
38 31 0.42
ACGTcount: A:0.11, C:0.08, G:0.39, T:0.42
Consensus pattern (37 bp):
GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCG
Found at i:3889650 original size:18 final size:17
Alignment explanation
Indices: 3889607--3889652 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3889597 ATGGAATTGA
*
3889607 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAG
**
3889624 ATTTTAATTCCTTCACAG
1 ATTCCAATTCC-TCACAG
3889642 ATTCCAATTCC
1 ATTCCAATTCC
3889653 CTCAGAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCCTCACAG
Found at i:3899389 original size:36 final size:38
Alignment explanation
Indices: 3899324--3899399 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
3899314 AAATATAATA
*
3899324 TATATATATATATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACCAAAGTATTAATAAAATAGAA-AAGC
3899362 TATATATATATACCAAA-TACTT-A-AAAATAGAAAAGC
1 TATATATATATACCAAAGTA-TTAATAAAATAGAAAAGC
3899398 TA
1 TA
3899400 CCCTCCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 12 0.34
37 5 0.14
38 18 0.51
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (38 bp):
TATATATATATACCAAAGTATTAATAAAATAGAAAAGC
Found at i:3899809 original size:47 final size:53
Alignment explanation
Indices: 3899730--3899840 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 53
3899720 GATAATTACA
* * ** * *
3899730 ATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAA-G-AAAT-A-T
1 ATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAATGAAAATAATT
3899779 ATATATATATAATAATAATA-AAATAT-AGTAAAAAAATAAATGAAAATAATT
1 ATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAATGAAAATAATT
3899830 ATATATATATA
1 ATATATATATA
3899841 TATATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
47 12 0.23
48 5 0.10
49 22 0.42
50 1 0.02
51 12 0.23
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (53 bp):
ATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAATGAAAATAATT
Found at i:3899836 original size:2 final size:2
Alignment explanation
Indices: 3899829--3899870 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3899819 TGAAAATAAT
*
3899829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3899871 ATAATAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3899901 original size:17 final size:18
Alignment explanation
Indices: 3899868--3899903 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3899858 ATATATACAT
*
3899868 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
3899886 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
3899903 A
1 A
3899904 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:3900377 original size:34 final size:35
Alignment explanation
Indices: 3900300--3900397 Score: 153
Period size: 34 Copynumber: 2.8 Consensus size: 35
3900290 ATAGTAGAAC
3900300 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
*
3900337 TTTATCCTATTTTTAGGAGTTTGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
*
3900371 TCTATCCTATTTTTAGGAGTTTCAATC
1 TCTATCCTATTTTTAGGAGTTTGAATC
3900398 ATAGTAGGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
34 30 0.52
37 28 0.48
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:3901375 original size:107 final size:106
Alignment explanation
Indices: 3900950--3901507 Score: 788
Period size: 107 Copynumber: 5.3 Consensus size: 106
3900940 CATTGTTCCA
* * * **
3900950 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
3901015 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
3901056 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAAA-T-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
3901115 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
3901156 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
3901220 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3901261 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTGTTGACAA
3901326 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3901368 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
3901433 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3901474 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
3901508 CGCGGATGGC
Statistics
Matches: 409, Mismatches: 32, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
100 84 0.21
101 2 0.00
102 5 0.01
104 4 0.01
105 97 0.24
106 97 0.24
107 98 0.24
109 22 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3901389 original size:212 final size:206
Alignment explanation
Indices: 3900950--3901507 Score: 821
Period size: 212 Copynumber: 2.7 Consensus size: 206
3900940 CATTGTTCCA
* * **
3900950 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
3901015 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
* *
3901080 TTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 TTGAAATTGAATCTGAATGAAATTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
3901145 GCGTTGTCTGG
196 GCGTTGTCTGG
* * *
3901156 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
* * ** *
3901220 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
**
3901285 TTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 TTGAAATTGAATCTG-AA-T--G-AAA-T-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
3901350 TGAACTTGCGTTGTCTGG
189 TGAACTTGCGTTGTCTGG
* * *
3901368 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
* *
3901433 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CCA--ATATCCTTCGTTGTG
*
3901498 GAGTTGAAAT
128 AAGTTGAAAT
3901508 CGCGGATGGC
Statistics
Matches: 311, Mismatches: 30, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
205 83 0.27
206 49 0.16
207 1 0.00
209 1 0.00
210 3 0.01
211 1 0.00
212 99 0.32
213 49 0.16
214 3 0.01
216 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGAATCTGAATGAAATTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGG
Found at i:3902284 original size:65 final size:67
Alignment explanation
Indices: 3902098--3902504 Score: 233
Period size: 65 Copynumber: 5.9 Consensus size: 67
3902088 GGAAACGATC
* * * * *
3902098 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAA
3902163 TAAAT
63 TAAAT
** * * *
3902168 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
3902233 AT
66 AT
* * * *
3902235 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-T
*
3902297 --GT
64 AAAT
** * * * * * * *
3902299 CTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAA
1 -TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAG
* * *
3902363 GAAAACATAT
58 GGAAATAAAT
* * * *
3902373 TCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA---
3902436 TCTCAAGA-
63 --T-AA-AT
* ** *
3902444 T-AGACGAAATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCA-AAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
3902505 CTGTCTCAAG
Statistics
Matches: 265, Mismatches: 49, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
64 1 0.00
65 83 0.31
66 10 0.04
67 24 0.09
68 34 0.13
69 3 0.01
70 8 0.03
71 5 0.02
72 56 0.21
73 40 0.15
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:3902295 original size:36 final size:35
Alignment explanation
Indices: 3902244--3902524 Score: 281
Period size: 36 Copynumber: 8.0 Consensus size: 35
3902234 TTCAAAGATT
* *
3902244 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
3902280 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
3902315 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
3902353 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
3902382 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
3902417 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
3902454 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
3902489 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
3902525 CTCTTCTAGT
Statistics
Matches: 205, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.65
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:3902353 original size:138 final size:137
Alignment explanation
Indices: 3902192--3902505 Score: 450
Period size: 138 Copynumber: 2.3 Consensus size: 137
3902182 TTTCAAGAGT
* * *
3902192 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
3902257 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
3902321 TCCAAAAGA
129 TCCAAAAGA
* * * * *
3902330 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
3902395 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
3902460 CAAGAGA
131 CAAAAGA
*
3902467 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
3902506 TGTCTCAAGA
Statistics
Matches: 155, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 50 0.32
138 105 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:3902546 original size:35 final size:36
Alignment explanation
Indices: 3902386--3902558 Score: 163
Period size: 36 Copynumber: 4.8 Consensus size: 36
3902376 AATATTTTGT
* * **
3902386 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
3902422 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
3902458 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
3902494 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * **
3902528 TTCTAGTGAAAACGGTCTCAATCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
3902559 TCTTATTTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
34 5 0.04
35 22 0.18
36 92 0.77
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:3903442 original size:22 final size:22
Alignment explanation
Indices: 3903417--3903467 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3903407 TTGTGTTTGG
*
3903417 TCAAGGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
3903439 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3903461 TCAAAGG
1 TCAAAGG
3903468 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3904146 original size:15 final size:15
Alignment explanation
Indices: 3904122--3904188 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 15
3904112 TGATTTTTGC
*
3904122 TCTTTTTTTCTTTTGT
1 TCTTTGTTTCTTTT-T
3904138 TC-TTGTTTCTCTTTT
1 TCTTTGTTTCT-TTTT
3904153 TCTTTGTTT-TTTTT
1 TCTTTGTTTCTTTTT
3904167 TGCTTT-TTTGCTTCTTT
1 T-CTTTGTTT-CTT-TTT
3904184 TCTTT
1 TCTTT
3904189 TTTGTTCTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 8 0.18
15 15 0.34
16 17 0.39
17 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (15 bp):
TCTTTGTTTCTTTTT
Found at i:3904174 original size:22 final size:22
Alignment explanation
Indices: 3904125--3904192 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
3904115 TTTTTGCTCT
* *
3904125 TTTTTTCTTTTGTTCTTGTTT-C
1 TTTTTTC-TTTGTTTTTTTTTGC
3904147 TCTTTTTCTTTGTTTTTTTTTGC
1 T-TTTTTCTTTGTTTTTTTTTGC
3904170 TTTTTTGCTTCT-TTTCTTTTTTG
1 TTTTTT-CTT-TGTTT-TTTTTTG
3904193 TTCTTGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.44
23 14 0.36
24 8 0.21
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTTTCTTTGTTTTTTTTTGC
Found at i:3904175 original size:23 final size:23
Alignment explanation
Indices: 3904123--3904192 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
3904113 GATTTTTGCT
* *
3904123 CTTTTTTTCTTTTGTTCTTGTTT-
1 CTTTTTTTC-TTTGTTTTTTTTTG
*
3904146 CTCTTTTTCTTTGTTTTTTTTTG
1 CTTTTTTTCTTTGTTTTTTTTTG
*
3904169 CTTTTTTGCTTCT-TTTCTTTTTTG
1 CTTTTTTTCTT-TGTTT-TTTTTTG
3904193 TTCTTGATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.28
23 20 0.51
24 8 0.21
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (23 bp):
CTTTTTTTCTTTGTTTTTTTTTG
Found at i:3907821 original size:18 final size:17
Alignment explanation
Indices: 3907800--3907842 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3907790 ATATATATAT
3907800 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
3907818 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3907835 ATAA-AATA
1 ATAATAATA
3907843 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3908278 original size:37 final size:36
Alignment explanation
Indices: 3908235--3908336 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
3908225 ATAGTAGAAC
3908235 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
3908272 TTTATCCTATTTTTAAGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
3908306 TCTATCCTATTTTTAGGAGTTTCAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
3908337 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 31 0.53
37 27 0.47
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:3926537 original size:2 final size:2
Alignment explanation
Indices: 3926530--3926561 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3926520 AGAGAAATCT
*
3926530 TA TA TA TA TA CA 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
3926562 ATAGAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3930929 original size:2 final size:2
Alignment explanation
Indices: 3930922--3930954 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3930912 CCAGCCAAGC
3930922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3930955 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3934075 original size:60 final size:59
Alignment explanation
Indices: 3933984--3934107 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
3933974 GTCGAGTGAT
* * *
3933984 CATTTTGTAATTTTTAATAGTCGAAGAACTTAACAAAGCAACATTCTATAGTTAAAGGAC
1 CATTTTGTAACTTTTAATAGTCGAAGAACTTAACAAAACAACATCCTATAG-TAAAGGAC
* * ** *
3934044 CATTTTGTAACTTTTAATAGTC-AAGGGACTTAATAAAACAGTATCCTATAGTCAAGGAC
1 CATTTTGTAACTTTTAATAGTCGAA-GAACTTAACAAAACAACATCCTATAGTAAAGGAC
3934103 CATTT
1 CATTT
3934108 GCGTTCTTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 14 0.25
60 41 0.75
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTCGAAGAACTTAACAAAACAACATCCTATAGTAAAGGAC
Found at i:3934296 original size:26 final size:26
Alignment explanation
Indices: 3934252--3934311 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
3934242 AAATTTTTTA
*
3934252 ATAAAA-ATATAATATAATTTGAGAT
1 ATAAAATATATAATAAAATTTGAGAT
3934277 ATAAAATATATAATAAAATTTGAGAT
1 ATAAAATATATAATAAAATTTGAGAT
*
3934303 ATCAAATAT
1 ATAAAATAT
3934312 GGATTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (26 bp):
ATAAAATATATAATAAAATTTGAGAT
Done.