Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 26
Found at i:2888603 original size:2 final size:2
Alignment explanation
Indices: 2888598--2888627 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2888588 ATTTTTTTAT
2888598 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
2888628 CTTTTTTTAA
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):
TA
Found at i:2888902 original size:2 final size:2
Alignment explanation
Indices: 2888895--2888943 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2888885 TTTACTCATT
2888895 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
2888937 TA TA TA T
1 TA TA TA T
2888944 TTCATATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2888978 original size:12 final size:11
Alignment explanation
Indices: 2888950--2889011 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 11
2888940 ATATTTCATA
2888950 TTTTATTTATTT
1 TTTTATTT-TTT
*
2888962 ATTTATTTTTCT
1 TTTTATTTTT-T
2888974 TTTTATTTTTT
1 TTTTATTTTTT
2888985 TTACTTATTTTTAT
1 TT--TTATTTTT-T
*
2888999 TCTTCATTTTTT
1 T-TTTATTTTTT
2889011 T
1 T
2889012 CATTTATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 5 0.12
12 19 0.45
13 15 0.36
14 2 0.05
15 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:2888978 original size:16 final size:16
Alignment explanation
Indices: 2888959--2889009 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2888949 ATTTTATTTA
2888959 TTTATTTATTTTTCTT
1 TTTATTTATTTTTCTT
2888975 TTTATTT-TTTTTACTT
1 TTTATTTATTTTT-CTT
* *
2888991 ATT-TTTATTCTTCATT
1 TTTATTTATTTTTC-TT
2889007 TTT
1 TTT
2889010 TTCATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTCTT
Found at i:2888993 original size:25 final size:25
Alignment explanation
Indices: 2888950--2889011 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
2888940 ATATTTCATA
* * *
2888950 TTTTA-TTTATTTATTTATTTTTCT
1 TTTTATTTTTTTTACTTATTTTTAT
2888974 TTTTATTTTTTTTACTTATTTTTAT
1 TTTTATTTTTTTTACTTATTTTTAT
*
2888999 TCTTCATTTTTTT
1 T-TTTATTTTTTT
2889012 CATTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 5 0.16
25 17 0.53
26 10 0.31
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTATTTTTTTTACTTATTTTTAT
Found at i:2892184 original size:2 final size:2
Alignment explanation
Indices: 2892177--2892226 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2892167 TGCTTATCCA
* *
2892177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2892219 A- AT AT AT A
1 AT AT AT AT A
2892227 ATTTTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2894007 original size:2 final size:2
Alignment explanation
Indices: 2894000--2894085 Score: 101
Period size: 2 Copynumber: 45.5 Consensus size: 2
2893990 CCGCCCTGAT
*
2894000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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
* * *
2894042 TA TA TA TA -A TA T- TT TA TA T- TT TA TA TA AA T- 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
2894080 TA -A TA T
1 TA TA TA T
2894086 TTTATATTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
1 5 0.07
2 68 0.93
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2894106 original size:33 final size:32
Alignment explanation
Indices: 2894059--2894121 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
2894049 AATATTTTAT
2894059 ATTTTATATAAATTATATATATAATATTTTAT
1 ATTTTATATAAATTATATATATAATATTTTAT
* *
2894091 ATTTTTATATTAATTATATATAAAATATTTT
1 A-TTTTATATAAATTATATATATAATATTTT
2894122 CGGGTTCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTTATATAAATTATATATATAATATTTTAT
Found at i:2896667 original size:28 final size:28
Alignment explanation
Indices: 2896634--2896696 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
2896624 TGCACGTGAA
2896634 GCGGCAAGGAAGCATATTCTCGAGCATT
1 GCGGCAAGGAAGCATATTCTCGAGCATT
2896662 GCGGCAAGGAAGCATATTCTCGAGCATT
1 GCGGCAAGGAAGCATATTCTCGAGCATT
2896690 GC-GCAAG
1 GCGGCAAG
2896697 TGTTCGTCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.14
28 30 0.86
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (28 bp):
GCGGCAAGGAAGCATATTCTCGAGCATT
Found at i:2899504 original size:16 final size:17
Alignment explanation
Indices: 2899473--2899506 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2899463 GAATATTATT
*
2899473 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
2899490 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
2899506 T
1 T
2899507 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:2903254 original size:55 final size:54
Alignment explanation
Indices: 2903188--2903330 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 54
2903178 GACATTCAAG
* *
2903188 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAAAT-TGAACCTGATTGAAGAA
1 TGATTCATGAAGAAGGACATCCGATGAATGAAG-AAATCTGAAACTGATTAAAG-A
* *
2903243 TGATTCATGAAGATGGACATCCAATGAATGAAGAAATCTGAAACTGATTAAAGA
1 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGA
* *
2903297 TCGATCCATGAAGAAAGACATCCGATGAATGAAG
1 T-GATTCATGAAGAAGGACATCCGATGAATGAAG
2903331 TTTGAAGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 6 0.08
55 72 0.92
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (54 bp):
TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGA
Found at i:2905489 original size:19 final size:17
Alignment explanation
Indices: 2905467--2905502 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2905457 ACTTTTGTAC
2905467 TTGCATTTAGCATTTGCAT
1 TTGCATTTA-CA-TTGCAT
2905486 TTGCATTTACATTGCAT
1 TTGCATTTACATTGCAT
2905503 GTATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (17 bp):
TTGCATTTACATTGCAT
Found at i:2907617 original size:2 final size:2
Alignment explanation
Indices: 2907610--2907637 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2907600 ATACCCAACA
2907610 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
2907638 GGGTATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2910050 original size:37 final size:37
Alignment explanation
Indices: 2910003--2910575 Score: 287
Period size: 37 Copynumber: 14.9 Consensus size: 37
2909993 GGGCAAGTCA
* *
2910003 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
*
2910040 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * *** * **
2910077 ATCAGTAAGCCTTCCGAGCATGATGATTAAGT-CCTCCAGGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAATCC
* * *
2910119 ATCTTAAGCCTTCACCAAAGAGTAGGGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* **
2910156 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * ***
2910193 ATCAGTAAGCCTT--CCG-AGCA-TGATGATTAAGTCCTCTGGGCC
1 ATC-TTAAGCCTTCACCGAAG-AGT-A-G-TGAAG-CAAAT---CC
* *
2910235 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * **
2910272 ATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * * *** ****
2910309 ATCAGTAAACCTTCTGAGCATGATGATTAAGT-CCTCCGGGCC
1 ATC-TTAAGCCTTC--A-C-CGAAGAGT-AGTGAAGCAAATCC
* *
2910351 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * **
2910388 ATTTTAAGCCTTCACTGAAGAATAGTGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * *** ** *
2910425 ATCAATAAGCCTTCCGAGCATGATGATTAAGT-CCTCCGAGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAATCC
*
2910467 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * *
2910504 ATTTTAAGCCTTCACCGAAGAGTAGTGGAGCAAATCT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
2910541 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
2910576 TGAACTCGAG
Statistics
Matches: 397, Mismatches: 105, Indels: 68
0.70 0.18 0.12
Matches are distributed among these distances:
35 3 0.01
36 12 0.03
37 238 0.60
38 39 0.10
39 7 0.02
40 7 0.02
41 39 0.10
42 37 0.09
43 12 0.03
44 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
Found at i:2910207 original size:116 final size:116
Alignment explanation
Indices: 2910003--2910553 Score: 888
Period size: 116 Copynumber: 4.8 Consensus size: 116
2909993 GGGCAAGTCA
*
2910003 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
** *
2910068 AGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCAGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
2910119 ATCTTAAGCCTTCACCAAAGAGTAGGGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
*
2910184 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCTGGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
2910235 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAATGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2910300 AGCAAATTTATCAGTAAACCTTCTGAGCATGATGATTAAGTCCTCCGGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* * *
2910351 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATTTTAAGCCTTCACTGAAGAATAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2910416 AGCAAATTTATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGAGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* * * * *
2910467 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCGAAGAGTAGTGG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2910532 AGCAAATCTATC-TTAAGCCTTC
66 AGCAAATTTATCAGTAAGCCTTC
2910554 ACCGAAGAGT
Statistics
Matches: 408, Mismatches: 27, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
115 9 0.02
116 399 0.98
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (116 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
Found at i:2914588 original size:55 final size:54
Alignment explanation
Indices: 2914522--2914664 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 54
2914512 GACATTCAAG
* *
2914522 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAAAT-TGAACCTGATTGAAGAA
1 TGATTCATGAAGAAGGACATCCGATGAATGAAG-AAATCTGAAACTGATTAAAG-A
* *
2914577 TGATTCATGAAGATGGACATCCAATGAATGAAGAAATCTGAAACTGATTAAAGA
1 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGA
* *
2914631 TCGATCCATGAAGAAAGACATCCGATGAATGAAG
1 T-GATTCATGAAGAAGGACATCCGATGAATGAAG
2914665 TTTGAAGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 6 0.08
55 72 0.92
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (54 bp):
TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGA
Found at i:2916823 original size:19 final size:17
Alignment explanation
Indices: 2916801--2916836 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2916791 ACTTTTGTAC
2916801 TTGCATTTAGCATTTGCAT
1 TTGCATTTA-CA-TTGCAT
2916820 TTGCATTTACATTGCAT
1 TTGCATTTACATTGCAT
2916837 GTATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (17 bp):
TTGCATTTACATTGCAT
Found at i:2918950 original size:2 final size:2
Alignment explanation
Indices: 2918943--2919003 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2918933 ATACCCAACA
2918943 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
2918985 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2919004 GGGTATACAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2921412 original size:37 final size:37
Alignment explanation
Indices: 2921365--2921937 Score: 287
Period size: 37 Copynumber: 14.9 Consensus size: 37
2921355 GGGCAAGTCA
* *
2921365 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
*
2921402 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * *** * **
2921439 ATCAGTAAGCCTTCCGAGCATGATGATTAAGT-CCTCCAGGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAATCC
* * *
2921481 ATCTTAAGCCTTCACCAAAGAGTAGGGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* **
2921518 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * ***
2921555 ATCAGTAAGCCTT--CCG-AGCA-TGATGATTAAGTCCTCTGGGCC
1 ATC-TTAAGCCTTCACCGAAG-AGT-A-G-TGAAG-CAAAT---CC
* *
2921597 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * **
2921634 ATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * * *** ****
2921671 ATCAGTAAACCTTCTGAGCATGATGATTAAGT-CCTCCGGGCC
1 ATC-TTAAGCCTTC--A-C-CGAAGAGT-AGTGAAGCAAATCC
* *
2921713 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * **
2921750 ATTTTAAGCCTTCACTGAAGAATAGTGAAGCAAATTT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * * * *** ** *
2921787 ATCAATAAGCCTTCCGAGCATGATGATTAAGT-CCTCCGAGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAATCC
*
2921829 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * *
2921866 ATTTTAAGCCTTCACCGAAGAGTAGTGGAGCAAATCT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
2921903 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
2921938 TGAACTCGAG
Statistics
Matches: 397, Mismatches: 105, Indels: 68
0.70 0.18 0.12
Matches are distributed among these distances:
35 3 0.01
36 12 0.03
37 238 0.60
38 39 0.10
39 7 0.02
40 7 0.02
41 39 0.10
42 37 0.09
43 12 0.03
44 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
Found at i:2921569 original size:116 final size:116
Alignment explanation
Indices: 2921365--2921915 Score: 888
Period size: 116 Copynumber: 4.8 Consensus size: 116
2921355 GGGCAAGTCA
*
2921365 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
** *
2921430 AGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCAGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
2921481 ATCTTAAGCCTTCACCAAAGAGTAGGGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
*
2921546 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCTGGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
2921597 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAATGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2921662 AGCAAATTTATCAGTAAACCTTCTGAGCATGATGATTAAGTCCTCCGGGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* * *
2921713 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATTTTAAGCCTTCACTGAAGAATAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2921778 AGCAAATTTATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGAGCC
66 AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* * * * *
2921829 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCGAAGAGTAGTGG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
2921894 AGCAAATCTATC-TTAAGCCTTC
66 AGCAAATTTATCAGTAAGCCTTC
2921916 ACCGAAGAGT
Statistics
Matches: 408, Mismatches: 27, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
115 9 0.02
116 399 0.98
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (116 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
AGCAAATTTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
Found at i:2924128 original size:3 final size:3
Alignment explanation
Indices: 2924120--2924145 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2924110 GAATTGGGTT
2924120 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2924146 TCCGCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2927342 original size:61 final size:61
Alignment explanation
Indices: 2927247--2927368 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
2927237 TATTTTGCCT
2927247 GAAGACCCCGAAATTTCTTGGAATCTTTAGCATTGTATTGTAGAAAACACCTTAGATGGAA
1 GAAGACCCCGAAATTTCTTGGAATCTTTAGCATTGTATTGTAGAAAACACCTTAGATGGAA
*
2927308 GAAGACCCCGAAATTTCTTGGAATCTTTAGCATTGTATTGTAGAAAACACCTTATATGGAA
1 GAAGACCCCGAAATTTCTTGGAATCTTTAGCATTGTATTGTAGAAAACACCTTAGATGGAA
2927369 AAATAACGTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (61 bp):
GAAGACCCCGAAATTTCTTGGAATCTTTAGCATTGTATTGTAGAAAACACCTTAGATGGAA
Found at i:2935184 original size:19 final size:20
Alignment explanation
Indices: 2935147--2935184 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2935137 TACTAAAGTG
2935147 TAAAATTATGTTTTTAAACT
1 TAAAATTATGTTTTTAAACT
2935167 TAAAA-TAT-TTTTTGAAAC
1 TAAAATTATGTTTTT-AAAC
2935185 AATTTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TAAAATTATGTTTTTAAACT
Found at i:2935409 original size:65 final size:64
Alignment explanation
Indices: 2935283--2935418 Score: 186
Period size: 65 Copynumber: 2.1 Consensus size: 64
2935273 ACACCCTAAT
* * *
2935283 TCGAATGCATTTTGTGTACCGATGCACAATCATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
* *
2935347 TCTAATGCATTTTATGTACCGATGCACAGACCATGCATCGATAG-ACTCCTGGCTCTT-TTGAAA
1 TCGAATGCATTTTATGTACCGATGCACA-ACCATGCATCGAT-GCACTCCT-GATCTTATTGAAA
2935410 CA
63 CA
2935412 TCGAATG
1 TCGAATG
2935419 TAATTAGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
64 26 0.41
65 32 0.51
66 5 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
Found at i:2936878 original size:12 final size:12
Alignment explanation
Indices: 2936861--2936887 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2936851 AAAAGGGACG
2936861 AGACAAAGAAGA
1 AGACAAAGAAGA
2936873 AGACAAAGAAGA
1 AGACAAAGAAGA
2936885 AGA
1 AGA
2936888 AGAATGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.26, T:0.00
Consensus pattern (12 bp):
AGACAAAGAAGA
Found at i:2937083 original size:41 final size:41
Alignment explanation
Indices: 2937026--2937109 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
2937016 TTCAAAAGAA
2937026 ATGAAGGCTTCAAAACTAAATCAAAGGAGAATGACCCCATC
1 ATGAAGGCTTCAAAACTAAATCAAAGGAGAATGACCCCATC
2937067 ATGAAGGCTTCAAAACTAAATCAAAGGAGAATGACCCCATC
1 ATGAAGGCTTCAAAACTAAATCAAAGGAGAATGACCCCATC
2937108 AT
1 AT
2937110 ATGCACAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (41 bp):
ATGAAGGCTTCAAAACTAAATCAAAGGAGAATGACCCCATC
Found at i:2941203 original size:44 final size:44
Alignment explanation
Indices: 2941129--2941231 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
2941119 GTGCACAGTG
* * *
2941129 CATCGATACACTATGAAAGTGTATGGATGCATTCCTTGAATGTA
1 CATCGATACACTATGAAAGTGCATGAATGCATGCCTTGAATGTA
* *
2941173 CATCGATACACTATGAAGGTGCACT-AATGCATGCCTTGAATGTG
1 CATCGATACACTATGAAAGTGCA-TGAATGCATGCCTTGAATGTA
*
2941217 TATCGATACACTATG
1 CATCGATACACTATG
2941232 CAGTGTACCG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 51 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
CATCGATACACTATGAAAGTGCATGAATGCATGCCTTGAATGTA
Found at i:2943949 original size:64 final size:65
Alignment explanation
Indices: 2943867--2944022 Score: 203
Period size: 65 Copynumber: 2.4 Consensus size: 65
2943857 ACACCCTAAT
* * * *
2943867 TCGAATACATTTTGTGTACCGATGCACA-A-CTATGCATCGATGCACTCCTGA-TTTTATTGAAA
1 TCGAATGCATTTTATGTACCGATGCACAGATC-ATGCATCGATACACTCCTGACTCTT-TTGAAA
2943929 CA
64 CA
2943931 TCGAATGCATTTTATGTACCGATGCACAGATCATGCATCGATACACTCCTGACTCTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGATCATGCATCGATACACTCCTGACTCTTTTGAAACA
* *
2943996 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
2944023 CCCAAGTGTA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
64 29 0.35
65 49 0.60
66 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAGATCATGCATCGATACACTCCTGACTCTTTTGAAACA
Found at i:2944036 original size:65 final size:65
Alignment explanation
Indices: 2943867--2944042 Score: 182
Period size: 65 Copynumber: 2.7 Consensus size: 65
2943857 ACACCCTAAT
* * * * *
2943867 TCGAATACAT-TTTGTGTACCGATGCACAACTATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATATTAGTGTACCGATGCACCACAATGCATCGATGCACTCCTGATCTTATTGAAACA
* * *
2943931 TCGAATGCATTTTA-TGTACCGATGCA-CAGATCATGCATCGATACACTCCTGACTCTT-TTGAA
1 TCGAATGCATATTAGTGTACCGATGCACCACA--ATGCATCGATGCACTCCTGA-TCTTATTGAA
2943993 ACA
63 ACA
* * *
2943996 TCGAATGTA-ATTAGTGTACCGATGCACCCCAAGTGTATCGATGCACT
1 TCGAATGCATATTAGTGTACCGATGCACCACAA-TGCATCGATGCACT
2944043 AGGTCAACTA
Statistics
Matches: 92, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
63 1 0.01
64 25 0.27
65 61 0.66
66 5 0.05
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (65 bp):
TCGAATGCATATTAGTGTACCGATGCACCACAATGCATCGATGCACTCCTGATCTTATTGAAACA
Found at i:2946883 original size:39 final size:39
Alignment explanation
Indices: 2946829--2946910 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
2946819 AAAGGAGTAA
*
2946829 GACATATTCCTGGCCTCAAAAGAAATTTGATTTCTGTAG
1 GACATATTCCTGGCCTCAAAAGAAATTTAATTTCTGTAG
2946868 GACATATTCCTGGCCTCAAAAGAAATTTAATTTCTGTAG
1 GACATATTCCTGGCCTCAAAAGAAATTTAATTTCTGTAG
2946907 GACA
1 GACA
2946911 GCTTGATGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (39 bp):
GACATATTCCTGGCCTCAAAAGAAATTTAATTTCTGTAG
Found at i:2948781 original size:26 final size:26
Alignment explanation
Indices: 2948751--2948803 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2948741 ATAACCATGC
2948751 ATATTAACCTATAATGTACAAATGTG
1 ATATTAACCTATAATGTACAAATGTG
2948777 ATATTAACCTATAATGTACAAATGTG
1 ATATTAACCTATAATGTACAAATGTG
2948803 A
1 A
2948804 CTCAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (26 bp):
ATATTAACCTATAATGTACAAATGTG
Found at i:2948946 original size:19 final size:18
Alignment explanation
Indices: 2948888--2948946 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 18
2948878 AAAAGTAGTA
2948888 ACTAAAAATTTAAACAT--
1 ACTAAAAA-TTAAACATAG
2948905 ACGT-AAAATTAAACATGATG
1 AC-TAAAAATTAAACAT-A-G
2948925 ACTAAAAATTAAAACATAG
1 ACTAAAAATT-AAACATAG
2948944 ACT
1 ACT
2948947 TAAATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 8 0.23
17 6 0.17
18 1 0.03
19 5 0.14
20 9 0.26
21 6 0.17
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (18 bp):
ACTAAAAATTAAACATAG
Found at i:2950261 original size:3 final size:3
Alignment explanation
Indices: 2950248--2950330 Score: 53
Period size: 3 Copynumber: 28.3 Consensus size: 3
2950238 AAACATAAGC
* * ** * * *
2950248 AAT ATT AAT AAT AAT TAT AAT TTT AAT TAT TAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
2950296 AGT TAT AAT -AT AAT ATT AAT AAT TAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2950331 TTTATAACCC
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2950569 original size:53 final size:53
Alignment explanation
Indices: 2950504--2950614 Score: 179
Period size: 53 Copynumber: 2.1 Consensus size: 53
2950494 TTCGATCAGT
2950504 GGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATATTCTGCCTAC
1 GGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATATTCTGCCTAC
* * *
2950557 GGGTTT-CTTCCCTCTTGCTTTAGGGAGTAGAACTCGAACAATCTTCTGCCTGC
1 GGGTTTGC-TCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATATTCTGCCTAC
2950610 GGGTT
1 GGGTT
2950615 CGATTCACTA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 1 0.02
53 53 0.98
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (53 bp):
GGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATATTCTGCCTAC
Found at i:2951401 original size:20 final size:20
Alignment explanation
Indices: 2951361--2951406 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2951351 ATGCTCGAAA
* **
2951361 GACTTACTGATGGTCTGAAG
1 GACTTACTGATGGCCCAAAG
2951381 GACTTACTGATGGCCCAAAG
1 GACTTACTGATGGCCCAAAG
2951401 GACTTA
1 GACTTA
2951407 AATTGTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
GACTTACTGATGGCCCAAAG
Found at i:2953058 original size:19 final size:20
Alignment explanation
Indices: 2953034--2953080 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
2953024 GATTCGCAAT
2953034 GTAAATCGCAACGCG-ATAC
1 GTAAATCGCAACGCGAATAC
2953053 GTAAATCGCAACGCGAATAC
1 GTAAATCGCAACGCGAATAC
2953073 GTAAATCG
1 GTAAATCG
2953081 GTTTGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
GTAAATCGCAACGCGAATAC
Found at i:2954052 original size:20 final size:20
Alignment explanation
Indices: 2954027--2954074 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2954017 TTTTCCTGAT
* *
2954027 TCGCAATGCAAATATGTAAA
1 TCGCAACGCAAATACGTAAA
*
2954047 TCGCAACGCGAATACGTAAA
1 TCGCAACGCAAATACGTAAA
2954067 TCGCAACG
1 TCGCAACG
2954075 AGATTCTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCAAATACGTAAA
Found at i:2954962 original size:24 final size:24
Alignment explanation
Indices: 2954935--2954988 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2954925 GTATTAGAAA
*
2954935 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGCTCAATACCCGGAC
* *
2954959 TTTGATCTTGCTCAATACTCGGAT
1 TTTGATCTTGCTCAATACCCGGAC
2954983 TTTGAT
1 TTTGAT
2954989 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGCTCAATACCCGGAC
Found at i:2957453 original size:20 final size:20
Alignment explanation
Indices: 2957430--2957503 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
2957420 TAACGCGAAT
2957430 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACACGGAA
**
2957450 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACACGGAA
*
2957470 TTGACTATCGCAACACGGAA
1 ATGACTATCGCAACACGGAA
2957490 ATGACTATCGCAAC
1 ATGACTATCGCAAC
2957504 GAGAGAATCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ATGACTATCGCAACACGGAA
Found at i:2957486 original size:40 final size:41
Alignment explanation
Indices: 2957426--2957502 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
2957416 ATCGTAACGC
2957426 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
2957467 GAAT-TGACTATCGCAACACGGAAATGACTATCGCAA
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAA
2957503 CGAGAGAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (41 bp):
GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
Found at i:2957533 original size:19 final size:19
Alignment explanation
Indices: 2957509--2957632 Score: 186
Period size: 19 Copynumber: 6.7 Consensus size: 19
2957499 GCAACGAGAG
2957509 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2957528 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2957547 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2957566 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2957585 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2957599 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2957619 AATCGCAACGCGAA
1 AATCGCAATGCGAA
2957633 TTCGCATTGC
Statistics
Matches: 96, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 2 0.02
18 3 0.03
19 67 0.70
20 11 0.11
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2957638 original size:33 final size:32
Alignment explanation
Indices: 2957530--2957644 Score: 115
Period size: 38 Copynumber: 3.3 Consensus size: 32
2957520 GAAATGAAAA
*
2957530 TCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGCG-AAT
*
2957563 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGTGAA-
1 -----TCGCAATGCGAAATGAAAATCGCAAC--GCGAAT
2957601 TCGCAATGCGAAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCG-AAATGAAAATCGCAACGCGAAT
*
2957634 TCGCATTGCGA
1 TCGCAATGCGA
2957645 TTCTCTCGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
32 5 0.07
33 19 0.28
34 16 0.23
38 25 0.36
39 2 0.03
40 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAAT
Found at i:2957800 original size:14 final size:14
Alignment explanation
Indices: 2957781--2957817 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2957771 CATCAATTAA
2957781 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2957795 ACAAATCATCTTTT
1 ACAAATCAACATTT
2957809 ACAAATCAA
1 ACAAATCAA
2957818 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2959185 original size:41 final size:42
Alignment explanation
Indices: 2959088--2959185 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 42
2959078 GTTGGAGGGA
* * *
2959088 CCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGTGGCCTCTTGAACGATGGGAGAGG
* ** *
2959130 ACTCTTGAGGGATGATAG-GGCCTCTTGAACGATAGGG-GAGG
1 CCTCTTGAACGATGACAGTGGCCTCTTGAACGAT-GGGAGAGG
2959171 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
2959186 AGGTGAGTCG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGTGGCCTCTTGAACGATGGGAGAGG
Found at i:2959541 original size:20 final size:20
Alignment explanation
Indices: 2959516--2959572 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2959506 TTAGTGCTGA
2959516 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
2959536 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
**
2959556 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
2959573 CGAGAGAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
GAAAATGACTATCGCAATGC
Found at i:2959636 original size:34 final size:37
Alignment explanation
Indices: 2959589--2959754 Score: 136
Period size: 40 Copynumber: 4.5 Consensus size: 37
2959579 AATCGCAATT
*
2959589 TCATTTT-GCATTGCGAT-TC-TTT-CGTTGCGATAG
1 TCATTTTCGCATTGCGATATCTTTTGCATTGCGATAG
2959622 TCATTTTCGCATTGCGATAGTCATTTTTGCATTGCGATAG
1 TCATTTTCGCATTGCGATA-TC--TTTTGCATTGCGATAG
*
2959662 TCATTTTCGCATTGCGATAGTCATTTTCGTATTGCGAT--
1 TCATTTTCGCATTGCGATA-TC-TTTT-GCATTGCGATAG
* *
2959700 TC--TCTCG--TTGCGATAGTCATTTTCGCGTTGCGATAG
1 TCATTTTCGCATTGCGATA-TC-TTTT-GCATTGCGATAG
*
2959736 TCATTTTTGCATTGCGATA
1 TCATTTTCGCATTGCGATA
2959755 GTAAACTATT
Statistics
Matches: 111, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.06
34 35 0.32
36 8 0.07
38 5 0.05
39 7 0.06
40 49 0.44
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.43
Consensus pattern (37 bp):
TCATTTTCGCATTGCGATATCTTTTGCATTGCGATAG
Found at i:2959638 original size:20 final size:20
Alignment explanation
Indices: 2959613--2959756 Score: 201
Period size: 20 Copynumber: 7.5 Consensus size: 20
2959603 GATTCTTTCG
2959613 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2959633 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
2959653 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2959673 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
2959693 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
2959707 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
2959727 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
2959747 TTGCGATAGT
1 TTGCGATAGT
2959757 AAACTATTCT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
18 6 0.05
20 92 0.83
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2961537 original size:20 final size:20
Alignment explanation
Indices: 2961514--2961553 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2961504 CTGAAACTTT
2961514 AAATTGCAACACGAAAATGA
1 AAATTGCAACACGAAAATGA
2961534 AAATTGCAACACGAAAATGA
1 AAATTGCAACACGAAAATGA
2961554 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATTGCAACACGAAAATGA
Found at i:2961562 original size:20 final size:20
Alignment explanation
Indices: 2961519--2961583 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
2961509 ACTTTAAATT
** *
2961519 GCAACACGAAAATGAAAATT
1 GCAACACGAAAATGACTATC
2961539 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* **
2961559 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTATC
2961579 GCAAC
1 GCAAC
2961584 GGAAGAATCG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:2961672 original size:20 final size:20
Alignment explanation
Indices: 2961627--2961675 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2961617 GCGATTCTCT
2961627 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
2961647 CATTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCAAATTCG
2961667 CGTTGCGAT
1 CGTTGCGAT
2961676 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2962272 original size:20 final size:20
Alignment explanation
Indices: 2962247--2962298 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2962237 GCTATGTAAA
2962247 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
2962267 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
2962287 TCGCATTGCGAT
1 TCGCATTGCGAT
2962299 TTACGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:2962308 original size:20 final size:20
Alignment explanation
Indices: 2962285--2962394 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
2962275 CGATAGTCAG
2962285 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2962305 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2962325 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
* * *
2962345 AATCGTATTACGATTTTACGT
1 ATTCGCATTGCGA-TTTACGT
2962366 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2962386 AATCGCATT
1 ATTCGCATT
2962395 ACGAATTAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 64 0.80
21 16 0.20
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2962309 original size:40 final size:40
Alignment explanation
Indices: 2962285--2962583 Score: 178
Period size: 41 Copynumber: 7.3 Consensus size: 40
2962275 CGATAGTCAG
*
2962285 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* * *
2962325 ATTCGCATTGCGATTTATGTAATCGTATTACGATTTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACGT
* * * *
2962366 ATTCGCATTGCGATTTACGTAATCGCATTACGAATTAGGAA
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACG-T
* ** ** * * *
2962407 AATCGCAACGCGAATTTGGGAAATCGCAATGCGATAGT-CAG-
1 ATTCGCATTGCG-ATTTACGTAATCGCATTGCGAT-TTAC-GT
* * * * * * **
2962448 AATCGCGTTGCGA-AT-CTGAAATTCAGTATTGCGATAGT-CAA
1 ATTCGCATTGCGATTTAC-GTAA-TC-GCATTGCGAT-TTACGT
* * * *
2962489 AATCTCGTTGCGATTTACAG-ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTAC-GTAATCGCATTGCGATTTACGT
* *
2962529 ATTCGCGCGTTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 ATT--CGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
2962571 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2962584 ATCAGGAAAA
Statistics
Matches: 203, Mismatches: 41, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
39 6 0.03
40 57 0.28
41 83 0.41
42 53 0.26
43 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
Found at i:2962413 original size:41 final size:40
Alignment explanation
Indices: 2962285--2962398 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
2962275 CGATAGTCAG
* *
2962285 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACGT
* *
2962325 ATTCGCATTGCGATTTATGTAATCGTATTACGATTTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTACGA-TTTACGT
2962366 ATTCGCATTGCGATTTACGTAATCGCATTACGA
1 ATTCGCATTGCGATTTACGTAATCGCATTACGA
2962399 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 29 0.43
41 38 0.57
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACGT
Found at i:2962420 original size:21 final size:21
Alignment explanation
Indices: 2962396--2962440 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2962386 AATCGCATTA
2962396 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
2962417 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
2962438 CGA
1 CGA
2962441 TAGTCAGAAT
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:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:2962519 original size:20 final size:20
Alignment explanation
Indices: 2962496--2962583 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
2962486 CAAAATCTCG
2962496 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
2962516 TTGCGATTTACGTATTCGCGCG
1 TTGCGATTTACGTATT--CGCA
* *
2962538 TTGCGATTTACGTAATCGCG
1 TTGCGATTTACGTATTCGCA
2962558 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2962578 TTGCGA
1 TTGCGA
2962584 ATCAGGAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.69
22 18 0.30
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2962562 original size:42 final size:42
Alignment explanation
Indices: 2962494--2962576 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
2962484 GTCAAAATCT
*
2962494 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCG
1 CGTTGCGATTTACAGAATCGCATTGCGATTTACGTATTCGCG
*
2962536 CGTTGCGATTTAC-GTAATCGCGTTGCGATTTACGTATTCGC
1 CGTTGCGATTTACAG-AATCGCATTGCGATTTACGTATTCGC
2962577 ATTGCGAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (42 bp):
CGTTGCGATTTACAGAATCGCATTGCGATTTACGTATTCGCG
Found at i:2962593 original size:185 final size:182
Alignment explanation
Indices: 2962307--2962708 Score: 524
Period size: 185 Copynumber: 2.2 Consensus size: 182
2962297 ATTTACGTAT
* * * *
2962307 TCGCATTGCGATTTACGTATTCGCATTGCGATTTATGTAATCGTATTACGATTTTACGTATTCGC
1 TCGCGTTGCGATTTACG-ATTCGCATTGCGATTTACGTAATCGCATTACGATTTTACGTAATCGC
* *
2962372 ATTGCGATTTACGTAATCGCATTACGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAAT
65 ATTGCGATTTACGTAATCGCATTACGAATCAGGAAAATCGCAACGCAAATTTGGGAAATCGCAAT
* * * *
2962437 GCGATAGTCAGAATCGCGTTGCGAATCT-GAAATTCAGTATTGCGATAGTCA-AAA
130 GCGATAGTCAAAATCGCGTTACGAATCTGGAAACTCA-T-TTGCGATA-CCAGAAA
* * * *
2962491 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCGCGTTGCGA-TTTACGTAATC
1 TCGCGTTGCGATTTAC-GATTCGCATTGCGATTTACGTAAT--CGCATTACGATTTTACGTAATC
* * *
2962555 GCGTTGCGATTTACGTATTCGCATTGCGAATCAGGAAAATCGCAACGCAAATTTGGGAAATCGCA
63 GCATTGCGATTTACGTAATCGCATTACGAATCAGGAAAATCGCAACGCAAATTTGGGAAATCGCA
* *
2962620 ATGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTGATTTGCGATACCAGAGA
128 ATGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTCATTTGCGATACCAGAAA
*
2962675 TCGCGTTGCGAATTATCGA-TCGCATTGCGATTTA
1 TCGCGTTGCGATTTA-CGATTCGCATTGCGATTTA
2962709 GTTGGTCATT
Statistics
Matches: 191, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
183 17 0.09
184 60 0.31
185 101 0.53
186 13 0.07
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (182 bp):
TCGCGTTGCGATTTACGATTCGCATTGCGATTTACGTAATCGCATTACGATTTTACGTAATCGCA
TTGCGATTTACGTAATCGCATTACGAATCAGGAAAATCGCAACGCAAATTTGGGAAATCGCAATG
CGATAGTCAAAATCGCGTTACGAATCTGGAAACTCATTTGCGATACCAGAAA
Found at i:2969782 original size:26 final size:26
Alignment explanation
Indices: 2969752--2969804 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2969742 ATAACCATGC
2969752 ATATTAACCTATAATGTACAAATGTG
1 ATATTAACCTATAATGTACAAATGTG
*
2969778 ATATTAACTTATAATGTACAAATGTG
1 ATATTAACCTATAATGTACAAATGTG
2969804 A
1 A
2969805 CTCAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (26 bp):
ATATTAACCTATAATGTACAAATGTG
Found at i:2971265 original size:3 final size:3
Alignment explanation
Indices: 2971252--2971351 Score: 71
Period size: 3 Copynumber: 34.3 Consensus size: 3
2971242 AAACATAAGC
* * * ** * *
2971252 AAT ATT AAT AAT AAT ATT AAT AAT AAT TAT AAT TTT AAT TAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
2971300 AAT AAC AAT AAT AGT TAT AAT -AT AAT -AT AAT ATT AAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2971346 -AT AAT A
1 AAT AAT A
2971352 TTTATAACCC
Statistics
Matches: 72, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
2 6 0.08
3 66 0.92
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2971325 original size:5 final size:5
Alignment explanation
Indices: 2971315--2971352 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2971305 CAATAATAGT
*
2971315 TATAA TATAA TATAA TATTAA TA-AT TATAA TATAA TAT
1 TATAA TATAA TATAA TA-TAA TATAA TATAA TATAA TAT
2971353 TTATAACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 21 0.72
6 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:2971326 original size:14 final size:13
Alignment explanation
Indices: 2971307--2971358 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
2971297 AATAATAACA
2971307 ATAATAGTTATAAT
1 ATAATA-TTATAAT
*
2971321 ATAATATAAT-AT
1 ATAATATTATAAT
2971333 -TAATAATTATAAT
1 ATAAT-ATTATAAT
2971346 ATAATATTTATAA
1 ATAATA-TTATAA
2971359 CCCGGACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 6 0.19
13 6 0.19
14 16 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
ATAATATTATAAT
Found at i:2971336 original size:25 final size:25
Alignment explanation
Indices: 2971287--2971352 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
2971277 ATTATAATTT
2971287 TAATTAT--TATAATAATAACAATAA
1 TAATTATAATATAAT-ATAACAATAA
* * *
2971311 TAGTTATAATATAATATAATATTAA
1 TAATTATAATATAATATAACAATAA
2971336 TAATTATAATATAATAT
1 TAATTATAATATAATAT
2971353 TTATAACCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 6 0.17
25 24 0.67
26 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TAATTATAATATAATATAACAATAA
Found at i:2972151 original size:22 final size:21
Alignment explanation
Indices: 2972121--2972163 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2972111 ATTCAAGTAG
2972121 AATAAATTGCAAGA-TAGATAAA
1 AATAAATTG-AA-ATTAGATAAA
*
2972143 AATACATTGAAATTAGATAAA
1 AATAAATTGAAATTAGATAAA
2972164 TAAACATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.26
Consensus pattern (21 bp):
AATAAATTGAAATTAGATAAA
Found at i:2972199 original size:19 final size:19
Alignment explanation
Indices: 2972177--2972220 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2972167 ACATACTATT
2972177 TTTTTTTAAATTTTTATGA
1 TTTTTTTAAATTTTTATGA
* **
2972196 TTTTTGTATTTTTTTATGA
1 TTTTTTTAAATTTTTATGA
2972215 TTTTTT
1 TTTTTT
2972221 AATTCAAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTTTAAATTTTTATGA
Found at i:2972270 original size:111 final size:112
Alignment explanation
Indices: 2972084--2972311 Score: 340
Period size: 111 Copynumber: 2.0 Consensus size: 112
2972074 TCTTTTTTTT
2972084 TTTTTGTTATTTTTTTGATTTTTTTAAATTCAAGTAGAATAAATTGCAAGATAGATAAAAATACA
1 TTTTTGTTATTTTTTTGATTTTTTTAAATTCAAGTAGAATAAATTGCAAGATAGATAAAAATACA
*
2972149 TTGAAATTAGATAA-ATAAACATACTATTTTTTTT-TAAATTTTTATGA
66 TTGAAATTAGATAAGATAAA-AAACTATTTTTTTTGT-AATTTTTATGA
*
2972196 TTTTTG-TATTTTTTT-ATGATTTTTT-AATTCAAGTAGATTAAATTGCAAGATAGATAAAAATA
1 TTTTTGTTATTTTTTTGAT--TTTTTTAAATTCAAGTAGAATAAATTGCAAGATAGATAAAAATA
* * *
2972258 CATTGGAATTAGATAAGTTAAAAAACTATTTTTTTTGTAATTTTTCTGA
64 CATTGAAATTAGATAAGATAAAAAACTATTTTTTTTGTAATTTTTATGA
2972307 TTTTT
1 TTTTT
2972312 TTTAAATTCA
Statistics
Matches: 107, Mismatches: 5, Indels: 9
0.88 0.04 0.07
Matches are distributed among these distances:
110 2 0.02
111 88 0.82
112 17 0.16
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (112 bp):
TTTTTGTTATTTTTTTGATTTTTTTAAATTCAAGTAGAATAAATTGCAAGATAGATAAAAATACA
TTGAAATTAGATAAGATAAAAAACTATTTTTTTTGTAATTTTTATGA
Found at i:2972386 original size:95 final size:94
Alignment explanation
Indices: 2972215--2972387 Score: 276
Period size: 95 Copynumber: 1.8 Consensus size: 94
2972205 TTTTTTATGA
* *
2972215 TTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGGAATTAGATAAGTTAAA
1 TTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAGATAAA
*
2972280 AAACTATTTTTTTTGTAATTTTTCTGATT
66 AAACTAATTTTTTTGTAATTTTTCTGATT
*
2972309 TTTTTTAAATTCAAGTATATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAA-ATAA
1 TTTTTT-AATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAGATAA
*
2972373 ACATACTAATTTTTT
65 A-AAACTAATTTTTT
2972388 GAAACATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
94 10 0.14
95 62 0.86
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (94 bp):
TTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAGATAAA
AAACTAATTTTTTTGTAATTTTTCTGATT
Found at i:2982682 original size:9 final size:9
Alignment explanation
Indices: 2982668--2982692 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2982658 ATAAAATAAT
2982668 ATTTATTTA
1 ATTTATTTA
2982677 ATTTATTTA
1 ATTTATTTA
2982686 ATTTATT
1 ATTTATT
2982693 AATAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTATTTA
Found at i:2983938 original size:18 final size:18
Alignment explanation
Indices: 2983912--2983964 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
2983902 GCTGAATATT
2983912 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
2983930 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2983948 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2983965 GTAAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2985214 original size:2 final size:2
Alignment explanation
Indices: 2985207--2985249 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2985197 CCACGTGTAG
2985207 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
2985249 T
1 T
2985250 CCTTTAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2989760 original size:21 final size:21
Alignment explanation
Indices: 2989734--2989808 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
2989724 GAGCGTGGGA
2989734 TGCATCGATGCAAAGACAAGG
1 TGCATCGATGCAAAGACAAGG
2989755 TGCATCGATGCAAAGACAAGG
1 TGCATCGATGCAAAGACAAGG
2989776 TGCATCGATGCAAAGACAAGG
1 TGCATCGATGCAAAGACAAGG
*
2989797 TGCATCGGTGCA
1 TGCATCGATGCA
2989809 TCAAGTGTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (21 bp):
TGCATCGATGCAAAGACAAGG
Found at i:2989943 original size:64 final size:65
Alignment explanation
Indices: 2989871--2990008 Score: 158
Period size: 64 Copynumber: 2.1 Consensus size: 65
2989861 CACTGGGGTA
* *
2989871 TGCATCGGTGCACAAATAT-ACTTCGATGATTCAA-AATAGC-CGGGGTGCATCGATGCATTGCT
1 TGCATCGGTGCACAAA-ATCAATTCGATGATTCAATAATA-CACGGAGTGCATCGATGCA-TGCT
2989933 -TG
63 ATG
* * * * *
2989935 TGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTATG
1 TGCATCGGTGCACAAAATCAATTCGATGATTCAATAATACACGGAGTGCATCGATGCATGCTATG
2990000 TGCATCGGT
1 TGCATCGGT
2990009 ACATAAAAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 2 0.03
64 31 0.49
65 30 0.48
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCACAAAATCAATTCGATGATTCAATAATACACGGAGTGCATCGATGCATGCTATG
Found at i:2990747 original size:15 final size:17
Alignment explanation
Indices: 2990710--2990747 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
2990700 CCAAAACATA
2990710 AATCCAAACATATAAAC
1 AATCCAAACATATAAAC
2990727 -ATCCAAA-ATA-AAAC
1 AATCCAAACATATAAAC
2990741 AATCCAA
1 AATCCAA
2990748 TAACATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.16
Consensus pattern (17 bp):
AATCCAAACATATAAAC
Found at i:2992503 original size:19 final size:19
Alignment explanation
Indices: 2992476--2992522 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2992466 ATGTTGTTTT
2992476 GCACGATTTAATGATTGAA
1 GCACGATTTAATGATTGAA
*
2992495 GCTCGATTTAATGATTGAA
1 GCACGATTTAATGATTGAA
2992514 GCACGATTT
1 GCACGATTT
2992523 GTAGTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (19 bp):
GCACGATTTAATGATTGAA
Found at i:2992604 original size:18 final size:18
Alignment explanation
Indices: 2992581--2992616 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2992571 GCAGTTTTGA
*
2992581 GAGTGGTGAGAGAGAGAG
1 GAGTGGCGAGAGAGAGAG
*
2992599 GAGTGGCGATAGAGAGAG
1 GAGTGGCGAGAGAGAGAG
2992617 TTTTAGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.53, T:0.11
Consensus pattern (18 bp):
GAGTGGCGAGAGAGAGAG
Found at i:2992705 original size:20 final size:20
Alignment explanation
Indices: 2992680--2992731 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2992670 ACCCGACGTA
2992680 TGTATCGATGCAAGGCAGTG
1 TGTATCGATGCAAGGCAGTG
*
2992700 TGTATCGACGCAAGGCAGTG
1 TGTATCGATGCAAGGCAGTG
* *
2992720 TGCATCAATGCA
1 TGTATCGATGCA
2992732 CATTCAAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (20 bp):
TGTATCGATGCAAGGCAGTG
Found at i:2992812 original size:44 final size:43
Alignment explanation
Indices: 2992723--2992819 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 43
2992713 GGCAGTGTGC
*
2992723 ATCAATGCACATTCAAGGAGTGCATCGGTGCATATTCATTATGT
1 ATCAATGCACATTCAAGGAGTGCATCGATGCATATT-ATTATGT
*
2992767 ATCGATGCACATTCAAAGG-GATGCATCGATGCACTA-T-TTAGTGT
1 ATCAATGCACATTC-AAGGAG-TGCATCGATGCA-TATTATTA-TGT
2992811 ATCAATGCA
1 ATCAATGCA
2992820 TTATGCACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
43 3 0.07
44 25 0.54
45 16 0.35
46 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
ATCAATGCACATTCAAGGAGTGCATCGATGCATATTATTATGT
Found at i:2998562 original size:64 final size:64
Alignment explanation
Indices: 2998471--2998594 Score: 146
Period size: 64 Copynumber: 1.9 Consensus size: 64
2998461 TGCACTGGGG
* *
2998471 TGTGCATCAGTGCACAAATATACTTCGATGATTCAA-AATAGC-CGGGGTGCATCGATGCATTGC
1 TGTGCATCAGTGCACAAATATAATTCGATG-TTCAATAATA-CACGGAGTGCATCGATGCATTGC
2998534 T
64 T
* * * *
2998535 TGTGCATCGGTGCATAAA-ATCAATTCGATGTTTAATAATACATGGAGTGCATCGATGCAT
1 TGTGCATCAGTGCACAAATAT-AATTCGATGTTCAATAATACACGGAGTGCATCGATGCAT
2998595 GGTATGTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 7 0.14
64 44 0.86
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
TGTGCATCAGTGCACAAATATAATTCGATGTTCAATAATACACGGAGTGCATCGATGCATTGCT
Found at i:2998676 original size:64 final size:63
Alignment explanation
Indices: 2998515--2998676 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 63
2998505 AAAATAGCCG
* * * * *
2998515 GGGTGCATCGATGCATTGCTTGTGCATCGGTGCATAAAATCAATTCGATGTTTAATAATACAT
1 GGGTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTTCAATAATACAT
* * * * *
2998578 GGAGTGCATCGATGCATGGTATGTGAATCAGTACATAAAAGCCATTCAATGTTCAATTAAATA-A
1 GG-GTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTTCAA-T-AATACA
2998642 -
63 T
*
2998642 GGGTGCATCGATGCATTGATTTATGCATCGGTACA
1 GGGTGCATCGATGCATTG-TTTGTGCATCGGTACA
2998677 CTTACCTGAA
Statistics
Matches: 80, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
63 17 0.21
64 57 0.71
65 2 0.03
66 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (63 bp):
GGGTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTTCAATAATACAT
Found at i:3000547 original size:18 final size:18
Alignment explanation
Indices: 3000521--3000627 Score: 187
Period size: 18 Copynumber: 5.9 Consensus size: 18
3000511 ACTGAATATT
*
3000521 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
3000539 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3000557 TGTCCCGAAGGACCTCTA
1 TGTCCCGAAGGACCACTA
3000575 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3000593 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3000611 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3000628 GTAAATCCCT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 84 1.00
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3001812 original size:2 final size:2
Alignment explanation
Indices: 3001805--3001838 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3001795 CGTGTAGCTA
3001805 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
3001839 CTCCTTTAAT
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:3008562 original size:29 final size:30
Alignment explanation
Indices: 3008523--3008592 Score: 115
Period size: 29 Copynumber: 2.3 Consensus size: 30
3008513 GTTGACCATA
3008523 TCTATTTTTCACAATAGTATTTGTTT-TATT
1 TCTA-TTTTCACAATAGTATTTGTTTATATT
*
3008553 TTTATTTTCACAATAGTATTTGTTTATATT
1 TCTATTTTCACAATAGTATTTGTTTATATT
3008583 TCTATTTTCA
1 TCTATTTTCA
3008593 AGTTGTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (30 bp):
TCTATTTTCACAATAGTATTTGTTTATATT
Found at i:3011374 original size:16 final size:16
Alignment explanation
Indices: 3011353--3011383 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3011343 TTTTAATATA
3011353 TTTTTAATATTTAATC
1 TTTTTAATATTTAATC
*
3011369 TTTTTAATCTTTAAT
1 TTTTTAATATTTAAT
3011384 ATTTCAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAATATTTAATC
Found at i:3015034 original size:18 final size:18
Alignment explanation
Indices: 3014995--3015035 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3014985 ATATAATAAA
* * *
3014995 TAAATAATATGTATATAT
1 TAAAAAATATGTATACAG
3015013 TAAAAAATATGTATACAG
1 TAAAAAATATGTATACAG
3015031 TAAAA
1 TAAAA
3015036 TGTAAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (18 bp):
TAAAAAATATGTATACAG
Found at i:3016741 original size:105 final size:105
Alignment explanation
Indices: 3016465--3017238 Score: 1442
Period size: 105 Copynumber: 7.4 Consensus size: 105
3016455 GTGTTGTTTC
3016465 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
3016530 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* ** *
3016570 GAGTCC-ATATCCCTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
3016634 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
3016674 GAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
3016739 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
3016779 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
3016844 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
3016884 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
3016949 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
3016989 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGATAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
3017054 CAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
3017094 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
3017159 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
3017199 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
3017239 GGTAAAACCT
Statistics
Matches: 650, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
104 100 0.15
105 550 0.85
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:3018051 original size:48 final size:49
Alignment explanation
Indices: 3017983--3018076 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 49
3017973 CTTTTTCCTC
* * * *
3017983 TTTTTCTTTTTTTAATTTAGGGCGCCCTT-TCGGGTTTTCACCCTAAACG
1 TTTTTCTTTTTTCAACTTAGGAC-ACCTTCTCGGGTTTTCACCCTAAACG
*
3018032 TTTTT-TTTTTTCAACTTAGGACACCTTCTCGGGTTTTCATCCTAA
1 TTTTTCTTTTTTCAACTTAGGACACCTTCTCGGGTTTTCACCCTAA
3018077 GCGAAGTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 4 0.10
48 30 0.77
49 5 0.13
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (49 bp):
TTTTTCTTTTTTCAACTTAGGACACCTTCTCGGGTTTTCACCCTAAACG
Found at i:3027478 original size:16 final size:16
Alignment explanation
Indices: 3027457--3027490 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3027447 AACGGTTAGT
*
3027457 AAAATAAAAATAAATA
1 AAAATAAAAAGAAATA
*
3027473 AAAATAACAAGAAATA
1 AAAATAAAAAGAAATA
3027489 AA
1 AA
3027491 TGGCAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAGAAATA
Found at i:3030757 original size:29 final size:30
Alignment explanation
Indices: 3030701--3030759 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3030691 ATCTAGATTC
*
3030701 TTTAATATTATAATAAATATAATATATTAA
1 TTTAATATTATAATAAAAATAATATATTAA
* * *
3030731 TTTAA-ATTATGATAAAAATATTTTATTAA
1 TTTAATATTATAATAAAAATAATATATTAA
3030760 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTAATATTATAATAAAAATAATATATTAA
Found at i:3030768 original size:21 final size:22
Alignment explanation
Indices: 3030744--3030784 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3030734 AAATTATGAT
3030744 AAAAATA-TTTTATTAAAAATA
1 AAAAATATTTTTATTAAAAATA
3030765 AAAAATATTTTTATTAAAAA
1 AAAAATATTTTTATTAAAAA
3030785 AACTTGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATTTTTATTAAAAATA
Found at i:3033366 original size:26 final size:26
Alignment explanation
Indices: 3033333--3033386 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3033323 TTTGAGATAG
*
3033333 TTACAAAGTAGTGTATGTTTATAAGT
1 TTACAAAGTAGTATATGTTTATAAGT
3033359 TTACAAAGTAGTATATGTTTATAAGT
1 TTACAAAGTAGTATATGTTTATAAGT
3033385 TT
1 TT
3033387 TTTTAATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (26 bp):
TTACAAAGTAGTATATGTTTATAAGT
Found at i:3037142 original size:26 final size:24
Alignment explanation
Indices: 3037089--3037142 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
3037079 CAAAGTATTA
3037089 ATTATTAAAATATTTAAAATATAT
1 ATTATTAAAATATTTAAAATATAT
*
3037113 -TTATTAATAT-TTCTAATAATATAAT
1 ATTATTAAAATATT-TAA-AATAT-AT
3037138 ATTAT
1 ATTAT
3037143 ATTTTTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.08
23 12 0.48
24 5 0.20
25 2 0.08
26 4 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTAAAATATTTAAAATATAT
Found at i:3037144 original size:22 final size:23
Alignment explanation
Indices: 3037114--3037160 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3037104 AAAATATATT
3037114 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* **
3037137 TATT-ATATTTTTAATGTTATAA
1 TATTAATATTTCTAATAATATAA
3037159 TA
1 TA
3037161 AAATAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3037167 original size:30 final size:33
Alignment explanation
Indices: 3037108--3037186 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 33
3037098 ATATTTAAAA
* * *
3037108 TATATTTATTAATATTTCTAATAATATAAT-AT
1 TATATTTATTAATAGTTATAATAAAATAATAAT
3037140 TATATTT-TTAAT-GTTATAATAAAATAATCAAT
1 TATATTTATTAATAGTTATAATAAAATAAT-AAT
*
3037172 TATATTATAATAATA
1 TATATT-TATTAATA
3037187 TAATATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 13 0.34
31 5 0.13
32 15 0.39
33 1 0.03
34 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
TATATTTATTAATAGTTATAATAAAATAATAAT
Found at i:3037191 original size:26 final size:26
Alignment explanation
Indices: 3037155--3037225 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
3037145 TTTTAATGTT
* *
3037155 ATAATAAAATAATCAATTATATTATA
1 ATAATATAATAATAAATTATATTATA
* * * *
3037181 ATAATATAATATTATATTTTATTTTA
1 ATAATATAATAATAAATTATATTATA
3037207 ATAATAT-ATAATAAATTAT
1 ATAATATAATAATAAATTAT
3037226 TAATAAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATATAATAATAAATTATATTATA
Found at i:3037202 original size:23 final size:22
Alignment explanation
Indices: 3037153--3037198 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
3037143 ATTTTTAATG
3037153 TTATAATAAAATAATCAATTATA
1 TTATAATAAAATAAT-AATTATA
*
3037176 TTATAATAATATAAT-ATTATA
1 TTATAATAAAATAATAATTATA
3037197 TT
1 TT
3037199 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATAATAAAATAATAATTATA
Found at i:3037225 original size:23 final size:24
Alignment explanation
Indices: 3037153--3037239 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 24
3037143 ATTTTTAATG
*
3037153 TTATAATAA-A-ATAATCAATTAT
1 TTATAATAATATATAATAAATTAT
**
3037175 ATTATAATAATATAATATTATATTTTAT
1 -TTATAATAATAT-ATA--ATAAATTAT
3037203 TT-TAATAATATATAATAAATTAT
1 TTATAATAATATATAATAAATTAT
* *
3037226 TAATAA-AATTTATA
1 TTATAATAATATATA
3037240 TTATTTATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
23 24 0.47
24 4 0.08
25 3 0.06
26 12 0.24
27 2 0.04
28 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATAATAATATATAATAAATTAT
Found at i:3037380 original size:21 final size:22
Alignment explanation
Indices: 3037340--3037381 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3037330 AATAAAAATA
*
3037340 TTTAAAATATACTACTTAATATT
1 TTTAAAATATAATAC-TAATATT
3037363 TTTAAAATATAATA-TAATA
1 TTTAAAATATAATACTAATA
3037382 CTATTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAATATAATACTAATATT
Found at i:3037458 original size:14 final size:14
Alignment explanation
Indices: 3037413--3037489 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
3037403 TATATAATTT
*
3037413 ATAATATTTTTATTA
1 ATAATA-TTTTAATA
* * *
3037428 ATAAAATTATAAAA
1 ATAATATTTTAATA
3037442 ATAATATTTTAATA
1 ATAATATTTTAATA
* *
3037456 ATAAATATCTT-ATT
1 AT-AATATTTTAATA
* *
3037470 TTAATATTTTAAAA
1 ATAATATTTTAATA
3037484 ATAATA
1 ATAATA
3037490 GTATTAAATT
Statistics
Matches: 46, Mismatches: 14, Indels: 5
0.71 0.22 0.08
Matches are distributed among these distances:
13 7 0.15
14 27 0.59
15 12 0.26
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATATTTTAATA
Found at i:3041304 original size:2 final size:2
Alignment explanation
Indices: 3041297--3041330 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3041287 CCGTTATTCC
3041297 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
3041331 GTATGAGATT
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:3041786 original size:2 final size:2
Alignment explanation
Indices: 3041771--3041813 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3041761 AAATTAACAA
* *
3041771 AT AT AT TT AC 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
3041813 A
1 A
3041814 GTTTTATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3042243 original size:19 final size:20
Alignment explanation
Indices: 3042207--3042254 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
3042197 ATTTTTAATG
*
3042207 TTTTAAATATTATGATTTT-
1 TTTTAAATATTATAATTTTA
*
3042226 TTTTAAATATTTTAATTTTA
1 TTTTAAATATTATAATTTTA
3042246 TCTTTAAAT
1 T-TTTAAAT
3042255 TATGACTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 1 0.04
21 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAATATTATAATTTTA
Found at i:3042256 original size:87 final size:88
Alignment explanation
Indices: 3042136--3042297 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 88
3042126 TTAATTTTAA
* * * * *
3042136 TTTTTTTGAACATTTTTATTTTATTTCTGAATTATGATTATCATTTTAAATTAATC-CCAAAATT
1 TTTTTTTAAACATTTTAATTTTATTTCTAAATTATGACTATCATTCTAAATTAATCTCCAAAATT
*
3042200 TTTAATGTTTTAAATATTATGAT
66 TTGAATGTTTTAAATATTATGAT
* * *
3042223 TTTTTTTAAATATTTTAATTTTATCTT-TAAATTATGACTATCATTCTAAATTAGTCTCCAAACT
1 TTTTTTTAAACATTTTAATTTTAT-TTCTAAATTATGACTATCATTCTAAATTAATCTCCAAAAT
3042287 TTTGAATGTTT
65 TTTGAATGTTT
3042298 CAGTTCCGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
87 46 0.72
88 18 0.28
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (88 bp):
TTTTTTTAAACATTTTAATTTTATTTCTAAATTATGACTATCATTCTAAATTAATCTCCAAAATT
TTGAATGTTTTAAATATTATGAT
Found at i:3042537 original size:7 final size:7
Alignment explanation
Indices: 3042524--3042555 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3042514 TAGAAAATAT
3042524 GGTTTAG
1 GGTTTAG
*
3042531 AGTTTAG
1 GGTTTAG
3042538 GGTTTAG
1 GGTTTAG
3042545 GGTTTAG
1 GGTTTAG
3042552 GGTT
1 GGTT
3042556 ATCGATTTAG
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:0.16, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:3042541 original size:14 final size:14
Alignment explanation
Indices: 3042524--3042570 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3042514 TAGAAAATAT
3042524 GGTTTAGAGTTTAG
1 GGTTTAGAGTTTAG
*
3042538 GGTTTAGGGTTTAG
1 GGTTTAGAGTTTAG
*
3042552 GGTTATCGA-TTTAG
1 GGTT-TAGAGTTTAG
3042566 GGTTT
1 GGTTT
3042571 TAAGTTAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.45
Consensus pattern (14 bp):
GGTTTAGAGTTTAG
Found at i:3043726 original size:60 final size:60
Alignment explanation
Indices: 3043662--3043869 Score: 183
Period size: 60 Copynumber: 3.5 Consensus size: 60
3043652 TTGAAGACTG
* *
3043662 ATTTAGAATTAGAGTCATAGTTTGAAGATGGAATTGGAACATTCAAAAGTTTGGGGATCA
1 ATTTAGAATTAGAGTCATAGTTTGAAGATGAAATTGGAATATTCAAAAGTTTGGGGATCA
* * * * * * *
3043722 ATTTAGAATGAGAGTCACAGTTT-AAGGATGAAAATAGAATGTTCAAAAGTTTGTGGACCA
1 ATTTAGAATTAGAGTCATAGTTTGAA-GATGAAATTGGAATATTCAAAAGTTTGGGGATCA
* * * * * * *
3043782 ATTTAGCA-TA-ATTCATAGTTTG-AGAATGAAATTGAAATTTTCAAAAATTTAAGGAAT-A
1 ATTTAGAATTAGAGTCATAGTTTGAAG-ATGAAATTGGAATATTCAAAAGTTT-GGGGATCA
* * *
3043840 ATTTAGAATAAGATTCATAGTTTGAGGATG
1 ATTTAGAATTAGAGTCATAGTTTGAAGATG
3043870 TATAATGTAA
Statistics
Matches: 116, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
57 1 0.01
58 38 0.33
59 6 0.05
60 70 0.60
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (60 bp):
ATTTAGAATTAGAGTCATAGTTTGAAGATGAAATTGGAATATTCAAAAGTTTGGGGATCA
Found at i:3045694 original size:60 final size:60
Alignment explanation
Indices: 3045586--3045711 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
3045576 TTTATTTTTG
* * **
3045586 AATTATGACTATCATTTTAAATTAATCTTTAAACTTTTAAATATTTCAATTTCATCCTTA
1 AATTATGACCATCATTCTAAATTAATCTCCAAACTTTTAAATATTTCAATTTCATCCTTA
* * * *
3045646 AATTTTGACCATCATTCTAAATTGATCTCCAAACTTTTGAATGA-TTCAATTTCATTCTTA
1 AATTATGACCATCATTCTAAATTAATCTCCAAACTTTTAAAT-ATTTCAATTTCATCCTTA
*
3045706 AGTTAT
1 AATTAT
3045712 TGATATATGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (60 bp):
AATTATGACCATCATTCTAAATTAATCTCCAAACTTTTAAATATTTCAATTTCATCCTTA
Found at i:3046099 original size:32 final size:32
Alignment explanation
Indices: 3046044--3046110 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3046034 GTTTAATTGT
** *
3046044 TGACATGTCACATGTCATGTCATCACCTTATG
1 TGACATGTCACATACCATATCATCACCTTATG
* * *
3046076 TGACATGTTACATACCATATCATCACTTTGTG
1 TGACATGTCACATACCATATCATCACCTTATG
3046108 TGA
1 TGA
3046111 TGTGACACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (32 bp):
TGACATGTCACATACCATATCATCACCTTATG
Found at i:3046784 original size:60 final size:58
Alignment explanation
Indices: 3046659--3046870 Score: 214
Period size: 60 Copynumber: 3.6 Consensus size: 58
3046649 ATGTAATTAA
* * * *
3046659 AATGTTCAAAAGTGTGAGGACTAATTTAGAATTA-GTCATAGTTTGAAGATGGAATTGG
1 AATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGGTCATAGTTTGAAGAT-AAAATGG
* * *
3046717 AACGTTCAAACA-TTTAAGGACTAATTTAGAATGAGGGTTATAGTTTGAAGATAAAAGTGG
1 AATGTTCAAA-AGTTTGAGGACTAATTTAGAATGA-GGTCATAGTTTGAAGATAAAA-TGG
* * * * *
3046777 AATGTTCAAAAGTTTGGGGACCT-ATTTAAAATGAGAGTCATAATTTAAAGATGAAAATGA
1 AATGTTCAAAAGTTTGAGGA-CTAATTTAGAATGAG-GTCATAGTTTGAAGAT-AAAATGG
* *
3046837 AATGTTCAAAAGTTTGTGGACCAATTTAGAATGA
1 AATGTTCAAAAGTTTGAGGACTAATTTAGAATGA
3046871 AATGTTCAGT
Statistics
Matches: 127, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
58 28 0.22
59 6 0.05
60 87 0.69
61 6 0.05
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (58 bp):
AATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGGTCATAGTTTGAAGATAAAATGG
Found at i:3054068 original size:22 final size:22
Alignment explanation
Indices: 3054015--3054060 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3054005 TCACTCTCTA
*
3054015 CGACAACATCCGTCCTCATCTC
1 CGACAAAATCCGTCCTCATCTC
3054037 CGACAAAATCCGTCC-CTATCTC
1 CGACAAAATCCGTCCTC-ATCTC
3054059 CG
1 CG
3054061 GCGAAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.24, C:0.43, G:0.11, T:0.22
Consensus pattern (22 bp):
CGACAAAATCCGTCCTCATCTC
Found at i:3054456 original size:19 final size:20
Alignment explanation
Indices: 3054434--3054486 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3054424 AAATCGCAAC
3054434 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
3054453 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
3054472 GTGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
3054487 AAAAACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:3055404 original size:21 final size:21
Alignment explanation
Indices: 3055380--3055428 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3055370 TATTTCCGAG
3055380 GACCTAATATTATTGGTAGAT
1 GACCTAATATTATTGGTAGAT
3055401 GACCTAATATTATTGGTAGAT
1 GACCTAATATTATTGGTAGAT
3055422 GACCTAA
1 GACCTAA
3055429 ATGCATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (21 bp):
GACCTAATATTATTGGTAGAT
Found at i:3056630 original size:21 final size:20
Alignment explanation
Indices: 3056604--3056720 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 20
3056594 TTCACCTGTC
3056604 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCC-CTCCT
**
3056625 ATCGTTCAAGAGGCCCTTAT
1 ATCGTTCAAGAGGCCCTCCT
* *
3056645 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGG-CCCTCCT
* *
3056667 ACCGTTCAAGAGGTCCCT-GT
1 ATCGTTCAAGAGG-CCCTCCT
*
3056687 CATCGTTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGG-CCCTCCT
*
3056709 ACCGTTCAAGAG
1 ATCGTTCAAGAG
3056721 CCCGATTCAC
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.04
21 70 0.91
22 4 0.05
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTCCT
Found at i:3056654 original size:42 final size:41
Alignment explanation
Indices: 3056602--3056720 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 41
3056592 GATTCACCTG
* *
3056602 TCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGG-CCCTTA
1 TCATCGTTCAAGAGGCC-CTCCCACCGTTCAAGAGGTCCC-TA
* *
3056644 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGTCCCTG
1 TCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAGGTCCCTA
3056686 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
3056721 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 64 0.93
43 5 0.07
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.24
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGTCCCTA
Found at i:3057164 original size:19 final size:19
Alignment explanation
Indices: 3057123--3057171 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3057113 TGGAAATTGA
* *
3057123 GTTGCGGAATTGGAGTTCAC
1 GTTGC-GAATTCGAGATCAC
*
3057143 GTTGCGAATTCGAGATCGC
1 GTTGCGAATTCGAGATCAC
3057162 GTTGCGAATT
1 GTTGCGAATT
3057172 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (19 bp):
GTTGCGAATTCGAGATCAC
Found at i:3058319 original size:22 final size:22
Alignment explanation
Indices: 3058291--3058649 Score: 545
Period size: 22 Copynumber: 16.6 Consensus size: 22
3058281 AATTATTTAA
3058291 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3058313 ATTTA-TTT---ATA--GATTG
1 ATTTATTTTAAAATATGGATTG
3058329 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3058351 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3058373 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3058395 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
***
3058417 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
3058439 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3058461 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3058483 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* **
3058505 ATTTATTTTAAAATATAGA-AA
1 ATTTATTTTAAAATATGGATTG
*
3058526 AGTTTATTTTAAAATATAGATTG
1 A-TTTATTTTAAAATATGGATTG
3058549 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3058571 ATTTATTTTAAATTATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
3058593 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
3058614 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
3058637 ATTTATTTTAAAA
1 ATTTATTTTAAAA
3058650 AATTTATTAT
Statistics
Matches: 307, Mismatches: 20, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.03
17 3 0.01
18 3 0.01
20 3 0.01
21 5 0.02
22 281 0.92
23 2 0.01
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:3060740 original size:8 final size:8
Alignment explanation
Indices: 3060718--3060749 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
3060708 CATAGGCACT
3060718 TATTATCA
1 TATTATCA
3060726 TTATTATCA
1 -TATTATCA
3060735 TATTATCA
1 TATTATCA
3060743 TATTATC
1 TATTATC
3060750 CTAAACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTATCA
Found at i:3060740 original size:17 final size:16
Alignment explanation
Indices: 3060718--3060749 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3060708 CATAGGCACT
3060718 TATTATCATTATTATCA
1 TATTATCA-TATTATCA
3060735 TATTATCATATTATC
1 TATTATCATATTATC
3060750 CTAAACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATCATATTATCA
Found at i:3061021 original size:28 final size:28
Alignment explanation
Indices: 3060946--3061024 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
3060936 CGTAGAAATT
* * *
3060946 TGTCCCAAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
*
3060974 TGTCCCGAAGGATCACGTAGAACACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
*
3061002 TGTCCCGAAGGACCATGTAGAAC
1 TGTCCCGAAGGACCACGTAGAAC
3061025 CCTCGGCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (28 bp):
TGTCCCGAAGGACCACGTAGAACACATA
Found at i:3065045 original size:28 final size:28
Alignment explanation
Indices: 3065002--3065075 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
3064992 CACTATGTCT
* * *
3065002 CGAAGGACCGCATAGAGCACATATATCC
1 CGAAGGACCACGTAGAACACATATATCC
*
3065030 CGAAGGACCACGTAGAACACATATGTCC
1 CGAAGGACCACGTAGAACACATATATCC
*
3065058 CGAATGACCACGTAGAAC
1 CGAAGGACCACGTAGAAC
3065076 CCTCAAATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.14
Consensus pattern (28 bp):
CGAAGGACCACGTAGAACACATATATCC
Found at i:3072720 original size:20 final size:20
Alignment explanation
Indices: 3072695--3072741 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3072685 CACGGAATGT
3072695 AAGATTACCAGTGAAAATAA
1 AAGATTACCAGTGAAAATAA
*
3072715 AAGATTACCAGTGATAATAA
1 AAGATTACCAGTGAAAATAA
*
3072735 AATATTA
1 AAGATTA
3072742 TTAGGGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.26
Consensus pattern (20 bp):
AAGATTACCAGTGAAAATAA
Done.