Multiple sequence alignment - TraesCS4A01G081800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G081800 chr4A 100.000 5176 0 0 1 5176 84935404 84940579 0.000000e+00 9559.0
1 TraesCS4A01G081800 chr4A 100.000 148 0 0 5554 5701 84940957 84941104 2.020000e-69 274.0
2 TraesCS4A01G081800 chr2A 96.301 4353 137 8 162 4500 712854798 712850456 0.000000e+00 7125.0
3 TraesCS4A01G081800 chr2A 97.298 2887 65 1 1627 4500 2357461 2360347 0.000000e+00 4887.0
4 TraesCS4A01G081800 chr2A 96.151 1481 45 6 163 1635 2356026 2357502 0.000000e+00 2409.0
5 TraesCS4A01G081800 chr2A 92.194 948 37 15 4230 5176 2360128 2361039 0.000000e+00 1306.0
6 TraesCS4A01G081800 chr2A 93.251 726 15 11 4230 4954 712850681 712849989 0.000000e+00 1038.0
7 TraesCS4A01G081800 chr2A 93.392 227 6 2 159 377 2362930 2362705 1.530000e-85 327.0
8 TraesCS4A01G081800 chr2A 97.973 148 3 0 5554 5701 712849366 712849219 2.040000e-64 257.0
9 TraesCS4A01G081800 chr2A 95.172 145 6 1 5557 5701 712849855 712849712 1.600000e-55 228.0
10 TraesCS4A01G081800 chr5A 94.762 4353 164 15 163 4500 273998645 273994342 0.000000e+00 6717.0
11 TraesCS4A01G081800 chr5A 96.106 2748 86 9 163 2901 274007326 274004591 0.000000e+00 4462.0
12 TraesCS4A01G081800 chr5A 95.524 2346 70 14 163 2500 35044706 35047024 0.000000e+00 3718.0
13 TraesCS4A01G081800 chr5A 95.815 2222 83 5 2495 4709 35060153 35062371 0.000000e+00 3579.0
14 TraesCS4A01G081800 chr5A 95.442 724 21 5 4230 4952 273994567 273993855 0.000000e+00 1144.0
15 TraesCS4A01G081800 chr5A 97.510 482 12 0 4695 5176 35082672 35083153 0.000000e+00 824.0
16 TraesCS4A01G081800 chr5A 93.907 279 14 3 4900 5176 273993811 273993534 8.830000e-113 418.0
17 TraesCS4A01G081800 chr5A 95.270 148 7 0 5554 5701 273992924 273992777 9.550000e-58 235.0
18 TraesCS4A01G081800 chr5A 95.833 144 5 1 5558 5701 273993718 273993576 1.240000e-56 231.0
19 TraesCS4A01G081800 chr1A 94.637 3263 129 12 1627 4867 582350130 582353368 0.000000e+00 5014.0
20 TraesCS4A01G081800 chr1A 97.070 1024 21 3 163 1178 30798830 30799852 0.000000e+00 1716.0
21 TraesCS4A01G081800 chr7D 96.400 2889 88 8 1627 4500 95099456 95096569 0.000000e+00 4745.0
22 TraesCS4A01G081800 chr7D 96.291 2831 91 10 1627 4455 362368766 362371584 0.000000e+00 4634.0
23 TraesCS4A01G081800 chr7D 95.418 2619 84 7 153 2738 550656662 550659277 0.000000e+00 4139.0
24 TraesCS4A01G081800 chr7D 93.618 1520 49 7 163 1650 95100903 95099400 0.000000e+00 2226.0
25 TraesCS4A01G081800 chr7D 93.224 1520 48 9 163 1650 590592671 590591175 0.000000e+00 2185.0
26 TraesCS4A01G081800 chr7D 93.326 899 36 10 4281 5176 362371365 362372242 0.000000e+00 1306.0
27 TraesCS4A01G081800 chr7D 91.605 953 50 9 4235 5176 590588518 590587585 0.000000e+00 1290.0
28 TraesCS4A01G081800 chr7D 90.579 881 52 10 4230 5099 95096794 95095934 0.000000e+00 1138.0
29 TraesCS4A01G081800 chr7D 94.619 223 3 3 163 377 590576360 590576581 2.540000e-88 337.0
30 TraesCS4A01G081800 chr7D 95.025 201 8 2 4978 5176 95095536 95095336 1.190000e-81 315.0
31 TraesCS4A01G081800 chr7D 95.050 202 6 4 4978 5176 590587688 590587488 1.190000e-81 315.0
32 TraesCS4A01G081800 chr7D 95.000 200 9 1 4978 5176 550680813 550681012 4.290000e-81 313.0
33 TraesCS4A01G081800 chr6D 95.707 2865 95 8 1627 4469 102250885 102248027 0.000000e+00 4584.0
34 TraesCS4A01G081800 chr6D 94.350 1522 44 5 161 1650 102252340 102250829 0.000000e+00 2296.0
35 TraesCS4A01G081800 chr6D 93.054 907 49 9 4281 5176 102248260 102247357 0.000000e+00 1314.0
36 TraesCS4A01G081800 chr6D 95.522 201 7 2 4978 5176 102247412 102247212 2.560000e-83 320.0
37 TraesCS4A01G081800 chr6D 95.050 202 6 4 4978 5176 102247509 102247309 1.190000e-81 315.0
38 TraesCS4A01G081800 chr6D 92.342 222 8 3 161 374 277332850 277333070 2.000000e-79 307.0
39 TraesCS4A01G081800 chr6D 94.483 145 7 1 5557 5701 102247445 102247302 7.430000e-54 222.0
40 TraesCS4A01G081800 chr4D 95.689 2830 105 12 1627 4455 122725175 122722362 0.000000e+00 4534.0
41 TraesCS4A01G081800 chr4D 93.820 1521 51 6 162 1650 122726628 122725119 0.000000e+00 2248.0
42 TraesCS4A01G081800 chr4D 94.098 898 31 8 4281 5176 122722581 122721704 0.000000e+00 1345.0
43 TraesCS4A01G081800 chr4D 95.025 201 8 2 4978 5176 122721807 122721607 1.190000e-81 315.0
44 TraesCS4A01G081800 chr4D 93.827 162 10 0 1 162 379500490 379500329 1.590000e-60 244.0
45 TraesCS4A01G081800 chr4D 95.172 145 6 1 5557 5701 122721646 122721503 1.600000e-55 228.0
46 TraesCS4A01G081800 chr4D 94.483 145 7 1 5557 5701 122721743 122721600 7.430000e-54 222.0
47 TraesCS4A01G081800 chr1D 93.803 2969 119 31 163 3121 80650664 80647751 0.000000e+00 4403.0
48 TraesCS4A01G081800 chr1D 94.847 1863 76 12 163 2014 386773611 386771758 0.000000e+00 2891.0
49 TraesCS4A01G081800 chr1D 93.987 898 28 9 4281 5176 386771502 386770629 0.000000e+00 1336.0
50 TraesCS4A01G081800 chr3D 96.477 2668 69 5 1627 4272 53789836 53792500 0.000000e+00 4383.0
51 TraesCS4A01G081800 chr3D 93.731 1611 74 9 3573 5176 5496771 5498361 0.000000e+00 2390.0
52 TraesCS4A01G081800 chr3D 91.422 851 47 10 4268 5111 53811380 53812211 0.000000e+00 1144.0
53 TraesCS4A01G081800 chr3D 91.860 172 5 3 158 321 53784422 53784592 1.240000e-56 231.0
54 TraesCS4A01G081800 chr3D 93.919 148 8 1 5554 5701 5498839 5498985 7.430000e-54 222.0
55 TraesCS4A01G081800 chr3D 93.919 148 8 1 5554 5701 53812863 53813009 7.430000e-54 222.0
56 TraesCS4A01G081800 chr7A 95.704 931 25 10 164 1085 77598327 77599251 0.000000e+00 1483.0
57 TraesCS4A01G081800 chr7A 95.311 789 27 4 163 943 19961162 19961948 0.000000e+00 1243.0
58 TraesCS4A01G081800 chr7A 78.528 163 27 7 1 162 673013884 673014039 3.630000e-17 100.0
59 TraesCS4A01G081800 chr4B 96.914 162 5 0 1 162 466694893 466694732 7.280000e-69 272.0
60 TraesCS4A01G081800 chr7B 100.000 35 0 0 1 35 649246817 649246851 1.330000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G081800 chr4A 84935404 84941104 5700 False 4916.500000 9559 100.000000 1 5701 2 chr4A.!!$F1 5700
1 TraesCS4A01G081800 chr2A 2356026 2361039 5013 False 2867.333333 4887 95.214333 163 5176 3 chr2A.!!$F1 5013
2 TraesCS4A01G081800 chr2A 712849219 712854798 5579 True 2162.000000 7125 95.674250 162 5701 4 chr2A.!!$R2 5539
3 TraesCS4A01G081800 chr5A 274004591 274007326 2735 True 4462.000000 4462 96.106000 163 2901 1 chr5A.!!$R1 2738
4 TraesCS4A01G081800 chr5A 35044706 35047024 2318 False 3718.000000 3718 95.524000 163 2500 1 chr5A.!!$F1 2337
5 TraesCS4A01G081800 chr5A 35060153 35062371 2218 False 3579.000000 3579 95.815000 2495 4709 1 chr5A.!!$F2 2214
6 TraesCS4A01G081800 chr5A 273992777 273998645 5868 True 1749.000000 6717 95.042800 163 5701 5 chr5A.!!$R2 5538
7 TraesCS4A01G081800 chr1A 582350130 582353368 3238 False 5014.000000 5014 94.637000 1627 4867 1 chr1A.!!$F2 3240
8 TraesCS4A01G081800 chr1A 30798830 30799852 1022 False 1716.000000 1716 97.070000 163 1178 1 chr1A.!!$F1 1015
9 TraesCS4A01G081800 chr7D 550656662 550659277 2615 False 4139.000000 4139 95.418000 153 2738 1 chr7D.!!$F1 2585
10 TraesCS4A01G081800 chr7D 362368766 362372242 3476 False 2970.000000 4634 94.808500 1627 5176 2 chr7D.!!$F4 3549
11 TraesCS4A01G081800 chr7D 95095336 95100903 5567 True 2106.000000 4745 93.905500 163 5176 4 chr7D.!!$R1 5013
12 TraesCS4A01G081800 chr7D 590587488 590592671 5183 True 1263.333333 2185 93.293000 163 5176 3 chr7D.!!$R2 5013
13 TraesCS4A01G081800 chr6D 102247212 102252340 5128 True 1508.500000 4584 94.694333 161 5701 6 chr6D.!!$R1 5540
14 TraesCS4A01G081800 chr4D 122721503 122726628 5125 True 1482.000000 4534 94.714500 162 5701 6 chr4D.!!$R2 5539
15 TraesCS4A01G081800 chr1D 80647751 80650664 2913 True 4403.000000 4403 93.803000 163 3121 1 chr1D.!!$R1 2958
16 TraesCS4A01G081800 chr1D 386770629 386773611 2982 True 2113.500000 2891 94.417000 163 5176 2 chr1D.!!$R2 5013
17 TraesCS4A01G081800 chr3D 53789836 53792500 2664 False 4383.000000 4383 96.477000 1627 4272 1 chr3D.!!$F2 2645
18 TraesCS4A01G081800 chr3D 5496771 5498985 2214 False 1306.000000 2390 93.825000 3573 5701 2 chr3D.!!$F3 2128
19 TraesCS4A01G081800 chr3D 53811380 53813009 1629 False 683.000000 1144 92.670500 4268 5701 2 chr3D.!!$F4 1433
20 TraesCS4A01G081800 chr7A 77598327 77599251 924 False 1483.000000 1483 95.704000 164 1085 1 chr7A.!!$F2 921
21 TraesCS4A01G081800 chr7A 19961162 19961948 786 False 1243.000000 1243 95.311000 163 943 1 chr7A.!!$F1 780

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
747 787 0.929244 CCCCTCCCCAATCACATTCT 59.071 55.000 0.0 0.0 0.00 2.40 F
1928 2074 0.396060 GAGGATGAGCTAGGGCAAGG 59.604 60.000 0.0 0.0 41.70 3.61 F
2287 2433 2.148916 TGTCTACCACAGAAACTGCG 57.851 50.000 0.0 0.0 34.17 5.18 F
3002 3148 2.249139 GACACTAACTCCTGGACCTGT 58.751 52.381 0.0 0.0 0.00 4.00 F
4296 4854 0.399833 TACTGCACCATCACCAGCAA 59.600 50.000 0.0 0.0 36.44 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2423 1.066143 ACCCTATCACCGCAGTTTCTG 60.066 52.381 0.00 0.00 34.12 3.02 R
2951 3097 1.629861 ACAATTCCAAAGGCAATGGGG 59.370 47.619 8.49 0.00 38.54 4.96 R
3256 3448 1.681229 TTCAGGCCCTCTAAACCCAT 58.319 50.000 0.00 0.00 0.00 4.00 R
4298 4856 0.107752 CAGCAGAAGAAGAGGCCCTC 60.108 60.000 1.26 1.26 0.00 4.30 R
5585 8240 1.659098 CGGTTTTGTCGACATCTAGCC 59.341 52.381 20.80 16.87 0.00 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.492007 AAGAATGGATATTGAAGCATAGCG 57.508 37.500 0.00 0.00 0.00 4.26
24 25 5.555017 AGAATGGATATTGAAGCATAGCGT 58.445 37.500 0.00 0.00 0.00 5.07
25 26 6.000219 AGAATGGATATTGAAGCATAGCGTT 59.000 36.000 0.00 0.00 0.00 4.84
26 27 5.618056 ATGGATATTGAAGCATAGCGTTG 57.382 39.130 0.00 0.00 0.00 4.10
27 28 4.702831 TGGATATTGAAGCATAGCGTTGA 58.297 39.130 0.00 0.00 0.00 3.18
28 29 5.122519 TGGATATTGAAGCATAGCGTTGAA 58.877 37.500 0.00 0.00 0.00 2.69
29 30 5.588246 TGGATATTGAAGCATAGCGTTGAAA 59.412 36.000 0.00 0.00 0.00 2.69
30 31 5.909610 GGATATTGAAGCATAGCGTTGAAAC 59.090 40.000 0.00 0.00 0.00 2.78
31 32 6.238484 GGATATTGAAGCATAGCGTTGAAACT 60.238 38.462 0.00 0.00 0.00 2.66
32 33 4.829064 TTGAAGCATAGCGTTGAAACTT 57.171 36.364 0.00 0.00 0.00 2.66
33 34 4.404507 TGAAGCATAGCGTTGAAACTTC 57.595 40.909 0.00 0.00 34.15 3.01
34 35 3.812609 TGAAGCATAGCGTTGAAACTTCA 59.187 39.130 0.00 0.00 39.59 3.02
35 36 4.455533 TGAAGCATAGCGTTGAAACTTCAT 59.544 37.500 0.00 0.00 37.66 2.57
36 37 5.641636 TGAAGCATAGCGTTGAAACTTCATA 59.358 36.000 0.00 0.00 37.66 2.15
37 38 6.316140 TGAAGCATAGCGTTGAAACTTCATAT 59.684 34.615 0.00 0.00 37.66 1.78
38 39 6.683974 AGCATAGCGTTGAAACTTCATATT 57.316 33.333 0.00 0.00 37.00 1.28
39 40 7.088589 AGCATAGCGTTGAAACTTCATATTT 57.911 32.000 0.00 0.00 37.00 1.40
40 41 8.208718 AGCATAGCGTTGAAACTTCATATTTA 57.791 30.769 0.00 0.00 37.00 1.40
41 42 8.840321 AGCATAGCGTTGAAACTTCATATTTAT 58.160 29.630 0.00 0.00 37.00 1.40
42 43 9.107367 GCATAGCGTTGAAACTTCATATTTATC 57.893 33.333 0.00 0.00 37.00 1.75
43 44 9.599322 CATAGCGTTGAAACTTCATATTTATCC 57.401 33.333 0.00 0.00 37.00 2.59
44 45 6.715464 AGCGTTGAAACTTCATATTTATCCG 58.285 36.000 0.00 0.00 37.00 4.18
45 46 5.907391 GCGTTGAAACTTCATATTTATCCGG 59.093 40.000 0.00 0.00 37.00 5.14
46 47 6.238266 GCGTTGAAACTTCATATTTATCCGGA 60.238 38.462 6.61 6.61 37.00 5.14
47 48 7.345192 CGTTGAAACTTCATATTTATCCGGAG 58.655 38.462 11.34 0.00 37.00 4.63
48 49 7.518370 CGTTGAAACTTCATATTTATCCGGAGG 60.518 40.741 11.34 0.00 43.55 4.30
66 67 4.500265 AACGCATGTTCTTGGCCT 57.500 50.000 3.32 0.00 30.83 5.19
67 68 2.732289 AACGCATGTTCTTGGCCTT 58.268 47.368 3.32 0.00 30.83 4.35
68 69 1.904287 AACGCATGTTCTTGGCCTTA 58.096 45.000 3.32 0.00 30.83 2.69
69 70 1.904287 ACGCATGTTCTTGGCCTTAA 58.096 45.000 3.32 0.00 0.00 1.85
70 71 2.446435 ACGCATGTTCTTGGCCTTAAT 58.554 42.857 3.32 0.00 0.00 1.40
71 72 2.164219 ACGCATGTTCTTGGCCTTAATG 59.836 45.455 3.32 0.71 0.00 1.90
72 73 2.164219 CGCATGTTCTTGGCCTTAATGT 59.836 45.455 3.32 0.00 0.00 2.71
73 74 3.514645 GCATGTTCTTGGCCTTAATGTG 58.485 45.455 3.32 0.00 0.00 3.21
74 75 3.676873 GCATGTTCTTGGCCTTAATGTGG 60.677 47.826 3.32 0.00 0.00 4.17
75 76 3.517296 TGTTCTTGGCCTTAATGTGGA 57.483 42.857 3.32 0.00 0.00 4.02
76 77 3.153919 TGTTCTTGGCCTTAATGTGGAC 58.846 45.455 3.32 0.00 0.00 4.02
77 78 3.181434 TGTTCTTGGCCTTAATGTGGACT 60.181 43.478 3.32 0.00 32.71 3.85
78 79 3.806949 TCTTGGCCTTAATGTGGACTT 57.193 42.857 3.32 0.00 32.71 3.01
79 80 3.686016 TCTTGGCCTTAATGTGGACTTC 58.314 45.455 3.32 0.00 32.71 3.01
80 81 2.507407 TGGCCTTAATGTGGACTTCC 57.493 50.000 3.32 0.00 32.71 3.46
81 82 1.707989 TGGCCTTAATGTGGACTTCCA 59.292 47.619 3.32 0.00 45.30 3.53
92 93 1.818060 TGGACTTCCATTTGATTGCGG 59.182 47.619 0.00 0.00 42.01 5.69
93 94 1.818674 GGACTTCCATTTGATTGCGGT 59.181 47.619 0.00 0.00 35.64 5.68
94 95 2.231235 GGACTTCCATTTGATTGCGGTT 59.769 45.455 0.00 0.00 35.64 4.44
95 96 3.501950 GACTTCCATTTGATTGCGGTTC 58.498 45.455 0.00 0.00 0.00 3.62
96 97 2.890311 ACTTCCATTTGATTGCGGTTCA 59.110 40.909 0.00 0.00 0.00 3.18
97 98 3.511146 ACTTCCATTTGATTGCGGTTCAT 59.489 39.130 0.00 0.00 0.00 2.57
98 99 3.781079 TCCATTTGATTGCGGTTCATC 57.219 42.857 0.00 0.00 0.00 2.92
99 100 2.426738 TCCATTTGATTGCGGTTCATCC 59.573 45.455 0.00 0.00 0.00 3.51
112 113 4.616181 GGTTCATCCGGAATGTAACTTG 57.384 45.455 9.01 0.00 37.93 3.16
113 114 4.258543 GGTTCATCCGGAATGTAACTTGA 58.741 43.478 9.01 1.25 37.93 3.02
114 115 4.881850 GGTTCATCCGGAATGTAACTTGAT 59.118 41.667 9.01 0.00 37.93 2.57
115 116 6.053005 GGTTCATCCGGAATGTAACTTGATA 58.947 40.000 9.01 0.00 37.93 2.15
116 117 6.710744 GGTTCATCCGGAATGTAACTTGATAT 59.289 38.462 9.01 0.00 37.93 1.63
117 118 7.228706 GGTTCATCCGGAATGTAACTTGATATT 59.771 37.037 9.01 0.00 37.93 1.28
118 119 8.621286 GTTCATCCGGAATGTAACTTGATATTT 58.379 33.333 9.01 0.00 37.93 1.40
119 120 8.746052 TCATCCGGAATGTAACTTGATATTTT 57.254 30.769 9.01 0.00 36.68 1.82
120 121 9.184523 TCATCCGGAATGTAACTTGATATTTTT 57.815 29.630 9.01 0.00 36.68 1.94
121 122 9.450807 CATCCGGAATGTAACTTGATATTTTTC 57.549 33.333 9.01 0.00 0.00 2.29
122 123 8.568676 TCCGGAATGTAACTTGATATTTTTCA 57.431 30.769 0.00 0.00 0.00 2.69
123 124 8.455682 TCCGGAATGTAACTTGATATTTTTCAC 58.544 33.333 0.00 0.00 0.00 3.18
124 125 8.458843 CCGGAATGTAACTTGATATTTTTCACT 58.541 33.333 0.00 0.00 0.00 3.41
125 126 9.277565 CGGAATGTAACTTGATATTTTTCACTG 57.722 33.333 0.00 0.00 0.00 3.66
128 129 9.912634 AATGTAACTTGATATTTTTCACTGTGG 57.087 29.630 8.11 0.00 0.00 4.17
129 130 7.881142 TGTAACTTGATATTTTTCACTGTGGG 58.119 34.615 8.11 0.00 0.00 4.61
130 131 5.982890 ACTTGATATTTTTCACTGTGGGG 57.017 39.130 8.11 0.00 0.00 4.96
131 132 4.220602 ACTTGATATTTTTCACTGTGGGGC 59.779 41.667 8.11 0.00 0.00 5.80
132 133 2.752354 TGATATTTTTCACTGTGGGGCG 59.248 45.455 8.11 0.00 0.00 6.13
133 134 1.540267 TATTTTTCACTGTGGGGCGG 58.460 50.000 8.11 0.00 0.00 6.13
134 135 1.184970 ATTTTTCACTGTGGGGCGGG 61.185 55.000 8.11 0.00 0.00 6.13
135 136 2.285889 TTTTTCACTGTGGGGCGGGA 62.286 55.000 8.11 0.00 0.00 5.14
136 137 2.075355 TTTTCACTGTGGGGCGGGAT 62.075 55.000 8.11 0.00 0.00 3.85
137 138 1.202099 TTTCACTGTGGGGCGGGATA 61.202 55.000 8.11 0.00 0.00 2.59
138 139 1.906105 TTCACTGTGGGGCGGGATAC 61.906 60.000 8.11 0.00 0.00 2.24
152 153 2.717639 GGATACCACCTTCATGTGCT 57.282 50.000 0.00 0.00 34.85 4.40
153 154 3.838244 GGATACCACCTTCATGTGCTA 57.162 47.619 0.00 0.00 34.85 3.49
154 155 4.357918 GGATACCACCTTCATGTGCTAT 57.642 45.455 0.00 0.00 34.85 2.97
155 156 5.483685 GGATACCACCTTCATGTGCTATA 57.516 43.478 0.00 0.00 34.85 1.31
156 157 5.865085 GGATACCACCTTCATGTGCTATAA 58.135 41.667 0.00 0.00 34.85 0.98
157 158 6.476378 GGATACCACCTTCATGTGCTATAAT 58.524 40.000 0.00 0.00 34.85 1.28
158 159 7.620880 GGATACCACCTTCATGTGCTATAATA 58.379 38.462 0.00 0.00 34.85 0.98
262 265 6.317893 ACACCAACTCTCTCGTAAACAATTTT 59.682 34.615 0.00 0.00 0.00 1.82
461 494 4.308458 CCTGTTCCCGGTCGTGCA 62.308 66.667 0.00 0.00 0.00 4.57
605 645 1.693799 AGAAGAGGAGGAGGAGGACT 58.306 55.000 0.00 0.00 0.00 3.85
645 685 2.125106 GGCGGCCAGATCTTTCGT 60.125 61.111 15.62 0.00 0.00 3.85
747 787 0.929244 CCCCTCCCCAATCACATTCT 59.071 55.000 0.00 0.00 0.00 2.40
859 971 3.408634 TGCTTACAACTAGGGTTTCTGC 58.591 45.455 0.00 0.00 32.73 4.26
899 1011 4.241590 TGTTGCACTCAAATGATGTTCC 57.758 40.909 0.00 0.00 33.37 3.62
1086 1198 0.817654 TGGTAGCACTGATGGAGACG 59.182 55.000 0.00 0.00 0.00 4.18
1198 1311 7.668525 AAGTTAGAGGAAATTTTAGACCACG 57.331 36.000 0.00 0.00 0.00 4.94
1404 1517 1.392853 GAAGCTGAGAGTTGTGATGCG 59.607 52.381 0.00 0.00 0.00 4.73
1474 1587 4.340381 GCAGAATAAATGTGAGCCTGGAAT 59.660 41.667 0.00 0.00 0.00 3.01
1614 1760 6.039829 GGAACAACAAGAAGGAAAGAGTGAAT 59.960 38.462 0.00 0.00 0.00 2.57
1717 1863 9.987726 AGGATAGTGATGATGATGATCTAGTAA 57.012 33.333 0.00 0.00 0.00 2.24
1928 2074 0.396060 GAGGATGAGCTAGGGCAAGG 59.604 60.000 0.00 0.00 41.70 3.61
2023 2169 4.202609 ACATGTTTGAGGAGGACTGGATTT 60.203 41.667 0.00 0.00 0.00 2.17
2081 2227 3.614092 GTGTGGAAGATGATGATGGTGT 58.386 45.455 0.00 0.00 0.00 4.16
2197 2343 4.397103 CAGAGGAGCAATTTGTGAAGCATA 59.603 41.667 0.00 0.00 0.00 3.14
2277 2423 5.355910 TCAAAACAGGAACTTTGTCTACCAC 59.644 40.000 0.00 0.00 34.60 4.16
2287 2433 2.148916 TGTCTACCACAGAAACTGCG 57.851 50.000 0.00 0.00 34.17 5.18
2678 2824 4.525487 AGGTTCAAGATGCATTGTGACAAT 59.475 37.500 4.72 4.72 0.00 2.71
2960 3106 6.710295 GGAACAATAATATTTTCCCCATTGCC 59.290 38.462 5.62 0.00 32.75 4.52
3002 3148 2.249139 GACACTAACTCCTGGACCTGT 58.751 52.381 0.00 0.00 0.00 4.00
3193 3385 4.263112 GGGCCTTTTAAAAGCCATTACCAA 60.263 41.667 27.67 0.00 35.36 3.67
3202 3394 5.869649 AAAGCCATTACCAAAGTGTTTCT 57.130 34.783 0.00 0.00 0.00 2.52
3256 3448 9.739276 ACATATCTACCAGAACTTTCAAAATGA 57.261 29.630 0.00 0.00 0.00 2.57
3291 3483 5.068987 GGGCCTGAATTAAAGCAATACATGA 59.931 40.000 0.84 0.00 0.00 3.07
3418 3610 1.181098 ACTTGGGCCAGACATGCAAC 61.181 55.000 6.23 0.00 0.00 4.17
3419 3611 1.152589 TTGGGCCAGACATGCAACA 60.153 52.632 6.23 0.00 0.00 3.33
3509 3701 4.919774 TGTCAGGGCTAAACCAATTAGA 57.080 40.909 0.00 0.00 43.16 2.10
3564 3756 6.258230 TGGTCAAGTTCAATGCAAATAGAG 57.742 37.500 0.00 0.00 0.00 2.43
3595 3787 9.396022 GATTGAGACTGTAAGATGGGAAATTTA 57.604 33.333 0.00 0.00 37.43 1.40
3757 3949 3.519107 TGCAAGAAGTGGGATATGACAGA 59.481 43.478 0.00 0.00 0.00 3.41
3886 4081 7.619698 CAGTCCCATTATATATCCTGTACCTGA 59.380 40.741 0.00 0.00 0.00 3.86
4005 4200 0.478072 TGAGAAGCCAGCTCCCAAAA 59.522 50.000 0.00 0.00 0.00 2.44
4033 4228 5.656416 CCTCAAAAATGGCCTCAATTACCTA 59.344 40.000 3.32 0.00 0.00 3.08
4157 4352 8.345565 GTCCTAATATTGACTATTTGTTGCTGG 58.654 37.037 0.00 0.00 32.26 4.85
4165 4360 6.446318 TGACTATTTGTTGCTGGTTTGAATC 58.554 36.000 0.00 0.00 0.00 2.52
4291 4849 1.372087 GCTGCTACTGCACCATCACC 61.372 60.000 0.00 0.00 45.31 4.02
4296 4854 0.399833 TACTGCACCATCACCAGCAA 59.600 50.000 0.00 0.00 36.44 3.91
4297 4855 0.892358 ACTGCACCATCACCAGCAAG 60.892 55.000 0.00 0.00 36.44 4.01
4298 4856 1.592400 CTGCACCATCACCAGCAAGG 61.592 60.000 0.00 0.00 45.67 3.61
4299 4857 1.303561 GCACCATCACCAGCAAGGA 60.304 57.895 1.83 0.00 41.22 3.36
4300 4858 1.310933 GCACCATCACCAGCAAGGAG 61.311 60.000 1.83 0.00 41.22 3.69
4301 4859 0.679002 CACCATCACCAGCAAGGAGG 60.679 60.000 1.83 1.70 41.22 4.30
4302 4860 1.077212 CCATCACCAGCAAGGAGGG 60.077 63.158 1.83 0.00 41.22 4.30
4303 4861 1.751927 CATCACCAGCAAGGAGGGC 60.752 63.158 1.83 0.00 41.22 5.19
4304 4862 2.988839 ATCACCAGCAAGGAGGGCC 61.989 63.158 0.00 0.00 41.22 5.80
4306 4864 3.334054 ACCAGCAAGGAGGGCCTC 61.334 66.667 25.80 25.80 46.28 4.70
4307 4865 3.013932 CCAGCAAGGAGGGCCTCT 61.014 66.667 31.39 15.75 46.28 3.69
4308 4866 2.610519 CCAGCAAGGAGGGCCTCTT 61.611 63.158 31.39 23.27 46.28 2.85
4309 4867 1.077858 CAGCAAGGAGGGCCTCTTC 60.078 63.158 31.39 16.97 46.28 2.87
4310 4868 1.229788 AGCAAGGAGGGCCTCTTCT 60.230 57.895 31.39 19.00 46.28 2.85
4311 4869 0.844221 AGCAAGGAGGGCCTCTTCTT 60.844 55.000 31.39 23.39 46.28 2.52
4312 4870 0.393673 GCAAGGAGGGCCTCTTCTTC 60.394 60.000 31.39 15.49 46.28 2.87
4313 4871 1.284313 CAAGGAGGGCCTCTTCTTCT 58.716 55.000 31.39 17.53 46.28 2.85
4314 4872 1.065564 CAAGGAGGGCCTCTTCTTCTG 60.066 57.143 31.39 16.18 46.28 3.02
4315 4873 1.223211 GGAGGGCCTCTTCTTCTGC 59.777 63.158 31.39 9.86 0.00 4.26
4316 4874 1.271127 GGAGGGCCTCTTCTTCTGCT 61.271 60.000 31.39 0.00 0.00 4.24
4317 4875 0.107752 GAGGGCCTCTTCTTCTGCTG 60.108 60.000 26.44 0.00 0.00 4.41
4318 4876 1.077858 GGGCCTCTTCTTCTGCTGG 60.078 63.158 0.84 0.00 0.00 4.85
4319 4877 1.682257 GGCCTCTTCTTCTGCTGGT 59.318 57.895 0.00 0.00 0.00 4.00
4320 4878 0.676151 GGCCTCTTCTTCTGCTGGTG 60.676 60.000 0.00 0.00 0.00 4.17
4321 4879 1.304509 GCCTCTTCTTCTGCTGGTGC 61.305 60.000 0.00 0.00 40.20 5.01
4322 4880 0.324285 CCTCTTCTTCTGCTGGTGCT 59.676 55.000 0.00 0.00 40.48 4.40
4323 4881 1.440708 CTCTTCTTCTGCTGGTGCTG 58.559 55.000 0.00 0.00 40.48 4.41
4324 4882 0.604780 TCTTCTTCTGCTGGTGCTGC 60.605 55.000 0.00 0.00 40.48 5.25
4325 4883 0.605860 CTTCTTCTGCTGGTGCTGCT 60.606 55.000 0.00 0.00 40.48 4.24
4366 4975 3.008330 CACAGAGGGCATCTTCTTCTTG 58.992 50.000 0.00 0.00 35.47 3.02
4387 5041 1.831652 GCTACAGCACCTGGACCAGT 61.832 60.000 20.24 5.80 41.59 4.00
4414 5113 1.077858 GGGCCTCTTCTGCTTCTGG 60.078 63.158 0.84 0.00 0.00 3.86
4422 5121 3.879295 CTCTTCTGCTTCTGGAACAACAA 59.121 43.478 0.00 0.00 38.70 2.83
4524 5229 1.374190 CCACAGAGGACAGCTGCTT 59.626 57.895 15.27 2.70 41.22 3.91
4596 5301 3.767816 CTGCAAAGGGAGCAAGCA 58.232 55.556 0.00 0.00 42.17 3.91
4778 5483 6.478344 TCAAAATACTGTCAATTTGGTTGTGC 59.522 34.615 10.82 0.00 38.95 4.57
5577 8232 5.659440 TCATCAAAGATGCCTAAAAACCC 57.341 39.130 2.19 0.00 0.00 4.11
5578 8233 5.332743 TCATCAAAGATGCCTAAAAACCCT 58.667 37.500 2.19 0.00 0.00 4.34
5579 8234 6.489603 TCATCAAAGATGCCTAAAAACCCTA 58.510 36.000 2.19 0.00 0.00 3.53
5580 8235 6.603201 TCATCAAAGATGCCTAAAAACCCTAG 59.397 38.462 2.19 0.00 0.00 3.02
5581 8236 5.887754 TCAAAGATGCCTAAAAACCCTAGT 58.112 37.500 0.00 0.00 0.00 2.57
5582 8237 5.710099 TCAAAGATGCCTAAAAACCCTAGTG 59.290 40.000 0.00 0.00 0.00 2.74
5583 8238 5.514500 AAGATGCCTAAAAACCCTAGTGA 57.486 39.130 0.00 0.00 0.00 3.41
5584 8239 5.514500 AGATGCCTAAAAACCCTAGTGAA 57.486 39.130 0.00 0.00 0.00 3.18
5585 8240 5.501156 AGATGCCTAAAAACCCTAGTGAAG 58.499 41.667 0.00 0.00 0.00 3.02
5586 8241 4.028993 TGCCTAAAAACCCTAGTGAAGG 57.971 45.455 0.00 0.00 46.09 3.46
5587 8242 2.753452 GCCTAAAAACCCTAGTGAAGGC 59.247 50.000 0.00 0.00 45.03 4.35
5588 8243 3.561528 GCCTAAAAACCCTAGTGAAGGCT 60.562 47.826 2.85 0.00 45.03 4.58
5589 8244 4.324022 GCCTAAAAACCCTAGTGAAGGCTA 60.324 45.833 2.85 0.00 45.03 3.93
5590 8245 5.429130 CCTAAAAACCCTAGTGAAGGCTAG 58.571 45.833 0.00 0.00 45.03 3.42
5591 8246 5.189145 CCTAAAAACCCTAGTGAAGGCTAGA 59.811 44.000 0.00 0.00 45.03 2.43
5592 8247 5.780958 AAAAACCCTAGTGAAGGCTAGAT 57.219 39.130 0.00 0.00 45.03 1.98
5593 8248 4.762289 AAACCCTAGTGAAGGCTAGATG 57.238 45.455 0.00 0.00 45.03 2.90
5594 8249 3.406512 ACCCTAGTGAAGGCTAGATGT 57.593 47.619 0.00 0.00 45.03 3.06
5595 8250 3.301274 ACCCTAGTGAAGGCTAGATGTC 58.699 50.000 0.00 0.00 45.03 3.06
5605 8260 1.659098 GGCTAGATGTCGACAAAACCG 59.341 52.381 24.13 11.14 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.000219 ACGCTATGCTTCAATATCCATTCTT 59.000 36.000 0.00 0.00 0.00 2.52
2 3 5.869753 ACGCTATGCTTCAATATCCATTC 57.130 39.130 0.00 0.00 0.00 2.67
5 6 4.702831 TCAACGCTATGCTTCAATATCCA 58.297 39.130 0.00 0.00 0.00 3.41
6 7 5.673337 TTCAACGCTATGCTTCAATATCC 57.327 39.130 0.00 0.00 0.00 2.59
7 8 6.719365 AGTTTCAACGCTATGCTTCAATATC 58.281 36.000 0.00 0.00 0.00 1.63
8 9 6.683974 AGTTTCAACGCTATGCTTCAATAT 57.316 33.333 0.00 0.00 0.00 1.28
9 10 6.148645 TGAAGTTTCAACGCTATGCTTCAATA 59.851 34.615 0.00 0.00 38.17 1.90
10 11 5.048782 TGAAGTTTCAACGCTATGCTTCAAT 60.049 36.000 0.00 0.00 38.17 2.57
11 12 4.274705 TGAAGTTTCAACGCTATGCTTCAA 59.725 37.500 0.00 0.00 38.17 2.69
12 13 3.812609 TGAAGTTTCAACGCTATGCTTCA 59.187 39.130 0.00 0.00 38.60 3.02
13 14 4.404507 TGAAGTTTCAACGCTATGCTTC 57.595 40.909 0.00 0.00 33.55 3.86
14 15 6.683974 ATATGAAGTTTCAACGCTATGCTT 57.316 33.333 0.00 0.00 41.13 3.91
15 16 6.683974 AATATGAAGTTTCAACGCTATGCT 57.316 33.333 0.00 0.00 41.13 3.79
16 17 9.107367 GATAAATATGAAGTTTCAACGCTATGC 57.893 33.333 0.00 0.00 41.13 3.14
17 18 9.599322 GGATAAATATGAAGTTTCAACGCTATG 57.401 33.333 0.00 0.00 41.13 2.23
18 19 8.495949 CGGATAAATATGAAGTTTCAACGCTAT 58.504 33.333 0.00 0.00 41.13 2.97
19 20 7.042321 CCGGATAAATATGAAGTTTCAACGCTA 60.042 37.037 0.00 0.00 41.13 4.26
20 21 6.238374 CCGGATAAATATGAAGTTTCAACGCT 60.238 38.462 0.00 0.00 41.13 5.07
21 22 5.907391 CCGGATAAATATGAAGTTTCAACGC 59.093 40.000 0.00 0.00 41.13 4.84
22 23 7.241663 TCCGGATAAATATGAAGTTTCAACG 57.758 36.000 0.00 0.00 41.13 4.10
23 24 7.497909 TCCTCCGGATAAATATGAAGTTTCAAC 59.502 37.037 3.57 0.00 41.13 3.18
24 25 7.570132 TCCTCCGGATAAATATGAAGTTTCAA 58.430 34.615 3.57 0.00 41.13 2.69
25 26 7.131907 TCCTCCGGATAAATATGAAGTTTCA 57.868 36.000 3.57 0.00 42.14 2.69
26 27 7.307219 CGTTCCTCCGGATAAATATGAAGTTTC 60.307 40.741 3.57 0.00 0.00 2.78
27 28 6.482308 CGTTCCTCCGGATAAATATGAAGTTT 59.518 38.462 3.57 0.00 0.00 2.66
28 29 5.989777 CGTTCCTCCGGATAAATATGAAGTT 59.010 40.000 3.57 0.00 0.00 2.66
29 30 5.539048 CGTTCCTCCGGATAAATATGAAGT 58.461 41.667 3.57 0.00 0.00 3.01
30 31 4.389077 GCGTTCCTCCGGATAAATATGAAG 59.611 45.833 3.57 0.00 0.00 3.02
31 32 4.202274 TGCGTTCCTCCGGATAAATATGAA 60.202 41.667 3.57 0.00 0.00 2.57
32 33 3.322541 TGCGTTCCTCCGGATAAATATGA 59.677 43.478 3.57 0.00 0.00 2.15
33 34 3.659786 TGCGTTCCTCCGGATAAATATG 58.340 45.455 3.57 0.00 0.00 1.78
34 35 4.253685 CATGCGTTCCTCCGGATAAATAT 58.746 43.478 3.57 0.00 36.73 1.28
35 36 3.070446 ACATGCGTTCCTCCGGATAAATA 59.930 43.478 3.57 0.00 36.73 1.40
36 37 2.158813 ACATGCGTTCCTCCGGATAAAT 60.159 45.455 3.57 0.00 36.73 1.40
37 38 1.208535 ACATGCGTTCCTCCGGATAAA 59.791 47.619 3.57 0.00 36.73 1.40
38 39 0.828022 ACATGCGTTCCTCCGGATAA 59.172 50.000 3.57 0.00 36.73 1.75
39 40 0.828022 AACATGCGTTCCTCCGGATA 59.172 50.000 3.57 0.00 36.73 2.59
40 41 0.462047 GAACATGCGTTCCTCCGGAT 60.462 55.000 3.57 0.00 44.92 4.18
41 42 1.079405 GAACATGCGTTCCTCCGGA 60.079 57.895 2.93 2.93 44.92 5.14
42 43 3.486263 GAACATGCGTTCCTCCGG 58.514 61.111 0.00 0.00 44.92 5.14
49 50 1.904287 TAAGGCCAAGAACATGCGTT 58.096 45.000 5.01 0.00 38.33 4.84
50 51 1.904287 TTAAGGCCAAGAACATGCGT 58.096 45.000 5.01 0.00 0.00 5.24
51 52 2.164219 ACATTAAGGCCAAGAACATGCG 59.836 45.455 5.01 0.00 0.00 4.73
52 53 3.514645 CACATTAAGGCCAAGAACATGC 58.485 45.455 5.01 0.00 0.00 4.06
53 54 3.763360 TCCACATTAAGGCCAAGAACATG 59.237 43.478 5.01 0.44 0.00 3.21
54 55 3.763897 GTCCACATTAAGGCCAAGAACAT 59.236 43.478 5.01 0.00 0.00 2.71
55 56 3.153919 GTCCACATTAAGGCCAAGAACA 58.846 45.455 5.01 0.00 0.00 3.18
56 57 3.421844 AGTCCACATTAAGGCCAAGAAC 58.578 45.455 5.01 0.00 0.00 3.01
57 58 3.806949 AGTCCACATTAAGGCCAAGAA 57.193 42.857 5.01 0.00 0.00 2.52
58 59 3.561313 GGAAGTCCACATTAAGGCCAAGA 60.561 47.826 5.01 0.00 35.64 3.02
59 60 2.755103 GGAAGTCCACATTAAGGCCAAG 59.245 50.000 5.01 0.00 35.64 3.61
60 61 2.109128 TGGAAGTCCACATTAAGGCCAA 59.891 45.455 5.01 0.00 42.01 4.52
61 62 1.707989 TGGAAGTCCACATTAAGGCCA 59.292 47.619 5.01 0.00 42.01 5.36
62 63 2.507407 TGGAAGTCCACATTAAGGCC 57.493 50.000 0.00 0.00 42.01 5.19
73 74 1.818674 ACCGCAATCAAATGGAAGTCC 59.181 47.619 0.00 0.00 0.00 3.85
74 75 3.057596 TGAACCGCAATCAAATGGAAGTC 60.058 43.478 0.00 0.00 0.00 3.01
75 76 2.890311 TGAACCGCAATCAAATGGAAGT 59.110 40.909 0.00 0.00 0.00 3.01
76 77 3.574284 TGAACCGCAATCAAATGGAAG 57.426 42.857 0.00 0.00 0.00 3.46
77 78 3.119173 GGATGAACCGCAATCAAATGGAA 60.119 43.478 0.00 0.00 0.00 3.53
78 79 2.426738 GGATGAACCGCAATCAAATGGA 59.573 45.455 0.00 0.00 0.00 3.41
79 80 2.813061 GGATGAACCGCAATCAAATGG 58.187 47.619 0.00 0.00 0.00 3.16
91 92 4.258543 TCAAGTTACATTCCGGATGAACC 58.741 43.478 4.15 0.00 39.15 3.62
92 93 7.730364 ATATCAAGTTACATTCCGGATGAAC 57.270 36.000 4.15 7.56 39.15 3.18
93 94 8.746052 AAATATCAAGTTACATTCCGGATGAA 57.254 30.769 4.15 0.00 39.15 2.57
94 95 8.746052 AAAATATCAAGTTACATTCCGGATGA 57.254 30.769 4.15 3.31 39.15 2.92
95 96 9.450807 GAAAAATATCAAGTTACATTCCGGATG 57.549 33.333 4.15 8.71 41.71 3.51
96 97 9.184523 TGAAAAATATCAAGTTACATTCCGGAT 57.815 29.630 4.15 0.00 0.00 4.18
97 98 8.455682 GTGAAAAATATCAAGTTACATTCCGGA 58.544 33.333 0.00 0.00 0.00 5.14
98 99 8.458843 AGTGAAAAATATCAAGTTACATTCCGG 58.541 33.333 0.00 0.00 0.00 5.14
99 100 9.277565 CAGTGAAAAATATCAAGTTACATTCCG 57.722 33.333 0.00 0.00 0.00 4.30
102 103 9.912634 CCACAGTGAAAAATATCAAGTTACATT 57.087 29.630 0.62 0.00 0.00 2.71
103 104 8.522830 CCCACAGTGAAAAATATCAAGTTACAT 58.477 33.333 0.62 0.00 0.00 2.29
104 105 7.040062 CCCCACAGTGAAAAATATCAAGTTACA 60.040 37.037 0.62 0.00 0.00 2.41
105 106 7.312899 CCCCACAGTGAAAAATATCAAGTTAC 58.687 38.462 0.62 0.00 0.00 2.50
106 107 6.071616 GCCCCACAGTGAAAAATATCAAGTTA 60.072 38.462 0.62 0.00 0.00 2.24
107 108 5.279456 GCCCCACAGTGAAAAATATCAAGTT 60.279 40.000 0.62 0.00 0.00 2.66
108 109 4.220602 GCCCCACAGTGAAAAATATCAAGT 59.779 41.667 0.62 0.00 0.00 3.16
109 110 4.675146 CGCCCCACAGTGAAAAATATCAAG 60.675 45.833 0.62 0.00 0.00 3.02
110 111 3.192422 CGCCCCACAGTGAAAAATATCAA 59.808 43.478 0.62 0.00 0.00 2.57
111 112 2.752354 CGCCCCACAGTGAAAAATATCA 59.248 45.455 0.62 0.00 0.00 2.15
112 113 2.099098 CCGCCCCACAGTGAAAAATATC 59.901 50.000 0.62 0.00 0.00 1.63
113 114 2.099405 CCGCCCCACAGTGAAAAATAT 58.901 47.619 0.62 0.00 0.00 1.28
114 115 1.540267 CCGCCCCACAGTGAAAAATA 58.460 50.000 0.62 0.00 0.00 1.40
115 116 1.184970 CCCGCCCCACAGTGAAAAAT 61.185 55.000 0.62 0.00 0.00 1.82
116 117 1.830408 CCCGCCCCACAGTGAAAAA 60.830 57.895 0.62 0.00 0.00 1.94
117 118 2.075355 ATCCCGCCCCACAGTGAAAA 62.075 55.000 0.62 0.00 0.00 2.29
118 119 1.202099 TATCCCGCCCCACAGTGAAA 61.202 55.000 0.62 0.00 0.00 2.69
119 120 1.613928 TATCCCGCCCCACAGTGAA 60.614 57.895 0.62 0.00 0.00 3.18
120 121 2.039787 TATCCCGCCCCACAGTGA 59.960 61.111 0.62 0.00 0.00 3.41
121 122 2.189521 GTATCCCGCCCCACAGTG 59.810 66.667 0.00 0.00 0.00 3.66
122 123 3.087906 GGTATCCCGCCCCACAGT 61.088 66.667 0.00 0.00 0.00 3.55
123 124 3.087253 TGGTATCCCGCCCCACAG 61.087 66.667 0.00 0.00 0.00 3.66
124 125 3.404438 GTGGTATCCCGCCCCACA 61.404 66.667 3.28 0.00 46.33 4.17
130 131 0.180406 ACATGAAGGTGGTATCCCGC 59.820 55.000 0.00 0.00 40.75 6.13
131 132 1.953559 CACATGAAGGTGGTATCCCG 58.046 55.000 0.00 0.00 35.13 5.14
132 133 1.212935 AGCACATGAAGGTGGTATCCC 59.787 52.381 0.00 0.00 46.72 3.85
133 134 2.717639 AGCACATGAAGGTGGTATCC 57.282 50.000 0.00 0.00 46.72 2.59
138 139 5.649395 CCCATATTATAGCACATGAAGGTGG 59.351 44.000 0.00 0.00 39.19 4.61
139 140 6.475504 TCCCATATTATAGCACATGAAGGTG 58.524 40.000 0.00 0.00 41.72 4.00
140 141 6.273260 ACTCCCATATTATAGCACATGAAGGT 59.727 38.462 0.00 0.00 0.00 3.50
141 142 6.715280 ACTCCCATATTATAGCACATGAAGG 58.285 40.000 0.00 0.00 0.00 3.46
142 143 9.725019 TTTACTCCCATATTATAGCACATGAAG 57.275 33.333 0.00 0.00 0.00 3.02
146 147 8.960591 GCAATTTACTCCCATATTATAGCACAT 58.039 33.333 0.00 0.00 0.00 3.21
147 148 7.941790 TGCAATTTACTCCCATATTATAGCACA 59.058 33.333 0.00 0.00 0.00 4.57
148 149 8.335532 TGCAATTTACTCCCATATTATAGCAC 57.664 34.615 0.00 0.00 0.00 4.40
149 150 8.382405 TCTGCAATTTACTCCCATATTATAGCA 58.618 33.333 0.00 0.00 0.00 3.49
150 151 8.792830 TCTGCAATTTACTCCCATATTATAGC 57.207 34.615 0.00 0.00 0.00 2.97
154 155 8.691797 GGTTTTCTGCAATTTACTCCCATATTA 58.308 33.333 0.00 0.00 0.00 0.98
155 156 7.180051 TGGTTTTCTGCAATTTACTCCCATATT 59.820 33.333 0.00 0.00 0.00 1.28
156 157 6.667414 TGGTTTTCTGCAATTTACTCCCATAT 59.333 34.615 0.00 0.00 0.00 1.78
157 158 6.013379 TGGTTTTCTGCAATTTACTCCCATA 58.987 36.000 0.00 0.00 0.00 2.74
158 159 4.837860 TGGTTTTCTGCAATTTACTCCCAT 59.162 37.500 0.00 0.00 0.00 4.00
262 265 2.027653 TGTCCGATCAGTGGTATTTGCA 60.028 45.455 0.00 0.00 0.00 4.08
382 405 3.136626 CGGGGGATAAGAGGAAACAGAAT 59.863 47.826 0.00 0.00 0.00 2.40
605 645 3.346315 TGAATTCCACCGAGTACTACGA 58.654 45.455 13.90 0.00 0.00 3.43
608 648 3.028850 CCCTGAATTCCACCGAGTACTA 58.971 50.000 2.27 0.00 0.00 1.82
702 742 2.645802 GACTGGGATCTCACTAGACGT 58.354 52.381 0.00 0.00 33.57 4.34
747 787 2.838202 CCTAACCCTAGCAACAGAAGGA 59.162 50.000 0.00 0.00 31.64 3.36
899 1011 1.518133 GCTAGTGCAGACCAGAGCG 60.518 63.158 0.00 0.00 39.41 5.03
1055 1167 9.283768 CCATCAGTGCTACCAAATTGTAATATA 57.716 33.333 0.00 0.00 0.00 0.86
1198 1311 8.494347 CAATATCTTGTTATTCTGCTCTGCTAC 58.506 37.037 0.00 0.00 0.00 3.58
1404 1517 0.693049 TTGGCTCTTGTTCTCCTCCC 59.307 55.000 0.00 0.00 0.00 4.30
1593 1706 6.484643 TCTCATTCACTCTTTCCTTCTTGTTG 59.515 38.462 0.00 0.00 0.00 3.33
1717 1863 8.386012 AGCCTAGCTAAGATATCACCATATTT 57.614 34.615 5.32 0.00 36.99 1.40
1928 2074 2.552743 GCCCTTCTCTTGTTTGGTACAC 59.447 50.000 0.00 0.00 39.29 2.90
2081 2227 2.737544 ACACATATGCCAATGCCTCAA 58.262 42.857 1.58 0.00 36.33 3.02
2197 2343 7.524717 ACTGGTACACATTTAAGAAGCAAAT 57.475 32.000 0.00 0.00 0.00 2.32
2277 2423 1.066143 ACCCTATCACCGCAGTTTCTG 60.066 52.381 0.00 0.00 34.12 3.02
2287 2433 2.700897 ACTGTGCTATCACCCTATCACC 59.299 50.000 0.00 0.00 42.46 4.02
2678 2824 6.519721 GCTTGGATGCTCCTTCAGATATCTTA 60.520 42.308 1.33 0.00 37.46 2.10
2951 3097 1.629861 ACAATTCCAAAGGCAATGGGG 59.370 47.619 8.49 0.00 38.54 4.96
2960 3106 6.434028 TGTCCTCCTTATCAACAATTCCAAAG 59.566 38.462 0.00 0.00 0.00 2.77
3193 3385 3.909732 TGGGGACAATTGAGAAACACTT 58.090 40.909 13.59 0.00 37.44 3.16
3256 3448 1.681229 TTCAGGCCCTCTAAACCCAT 58.319 50.000 0.00 0.00 0.00 4.00
3418 3610 6.492007 AGTCTGTTTTGCAGTTCATATCTG 57.508 37.500 0.00 0.00 45.23 2.90
3419 3611 7.880195 ACTAAGTCTGTTTTGCAGTTCATATCT 59.120 33.333 0.00 0.00 45.23 1.98
3564 3756 5.065731 CCCATCTTACAGTCTCAATCTTTGC 59.934 44.000 0.00 0.00 0.00 3.68
3595 3787 7.664731 CCTCTAATTTCTCAGCATATGTTGGAT 59.335 37.037 18.16 6.34 0.00 3.41
3886 4081 1.922447 TCCTTGGCCACATATCAGGTT 59.078 47.619 16.75 0.00 0.00 3.50
4005 4200 2.676748 TGAGGCCATTTTTGAGGTGTT 58.323 42.857 5.01 0.00 0.00 3.32
4033 4228 4.503123 GGCCAACCTTTTTGCAATTAGAGT 60.503 41.667 0.00 0.00 0.00 3.24
4157 4352 6.581171 AAGAACAGGAAGATGGATTCAAAC 57.419 37.500 0.00 0.00 0.00 2.93
4165 4360 7.824289 TCAAATAGTGTAAGAACAGGAAGATGG 59.176 37.037 0.00 0.00 35.91 3.51
4291 4849 1.077858 GAAGAGGCCCTCCTTGCTG 60.078 63.158 7.26 0.00 44.46 4.41
4297 4855 1.223211 GCAGAAGAAGAGGCCCTCC 59.777 63.158 7.26 0.00 0.00 4.30
4298 4856 0.107752 CAGCAGAAGAAGAGGCCCTC 60.108 60.000 1.26 1.26 0.00 4.30
4299 4857 1.560866 CCAGCAGAAGAAGAGGCCCT 61.561 60.000 0.00 0.00 0.00 5.19
4300 4858 1.077858 CCAGCAGAAGAAGAGGCCC 60.078 63.158 0.00 0.00 0.00 5.80
4301 4859 0.676151 CACCAGCAGAAGAAGAGGCC 60.676 60.000 0.00 0.00 0.00 5.19
4302 4860 1.304509 GCACCAGCAGAAGAAGAGGC 61.305 60.000 0.00 0.00 41.58 4.70
4303 4861 0.324285 AGCACCAGCAGAAGAAGAGG 59.676 55.000 0.00 0.00 45.49 3.69
4304 4862 1.440708 CAGCACCAGCAGAAGAAGAG 58.559 55.000 0.00 0.00 45.49 2.85
4305 4863 0.604780 GCAGCACCAGCAGAAGAAGA 60.605 55.000 0.00 0.00 45.49 2.87
4306 4864 0.605860 AGCAGCACCAGCAGAAGAAG 60.606 55.000 0.00 0.00 45.49 2.85
4307 4865 0.887836 CAGCAGCACCAGCAGAAGAA 60.888 55.000 0.00 0.00 45.49 2.52
4308 4866 1.302271 CAGCAGCACCAGCAGAAGA 60.302 57.895 0.00 0.00 45.49 2.87
4309 4867 2.979197 GCAGCAGCACCAGCAGAAG 61.979 63.158 0.00 0.00 45.49 2.85
4310 4868 2.115734 TAGCAGCAGCACCAGCAGAA 62.116 55.000 3.17 0.00 45.49 3.02
4311 4869 2.586293 TAGCAGCAGCACCAGCAGA 61.586 57.895 3.17 0.00 45.49 4.26
4312 4870 2.046604 TAGCAGCAGCACCAGCAG 60.047 61.111 3.17 0.00 45.49 4.24
4313 4871 2.359107 GTAGCAGCAGCACCAGCA 60.359 61.111 3.17 0.00 45.49 4.41
4314 4872 2.046507 AGTAGCAGCAGCACCAGC 60.047 61.111 3.17 0.00 45.49 4.85
4315 4873 2.396955 GCAGTAGCAGCAGCACCAG 61.397 63.158 3.17 0.00 45.49 4.00
4316 4874 2.359107 GCAGTAGCAGCAGCACCA 60.359 61.111 3.17 0.00 45.49 4.17
4414 5113 1.757682 TGGTGGTCCAGTTGTTGTTC 58.242 50.000 0.00 0.00 39.03 3.18
4422 5121 1.421646 CCTCTTCTTTGGTGGTCCAGT 59.578 52.381 0.00 0.00 45.22 4.00
4524 5229 3.615224 TGCAGCAGATGATGAACTACA 57.385 42.857 1.56 0.00 32.25 2.74
4595 5300 2.490903 CCTTGGAGGCAAGAAAGATGTG 59.509 50.000 0.00 0.00 34.26 3.21
4596 5301 2.800250 CCTTGGAGGCAAGAAAGATGT 58.200 47.619 0.00 0.00 34.26 3.06
4778 5483 3.996150 AACATCTCAACAGCAGTTTGG 57.004 42.857 0.00 0.00 35.28 3.28
5553 8208 6.441604 AGGGTTTTTAGGCATCTTTGATGATT 59.558 34.615 11.25 1.69 0.00 2.57
5554 8209 5.960202 AGGGTTTTTAGGCATCTTTGATGAT 59.040 36.000 11.25 2.25 0.00 2.45
5555 8210 5.332743 AGGGTTTTTAGGCATCTTTGATGA 58.667 37.500 11.25 0.00 0.00 2.92
5556 8211 5.665916 AGGGTTTTTAGGCATCTTTGATG 57.334 39.130 3.42 3.42 0.00 3.07
5557 8212 6.378280 CACTAGGGTTTTTAGGCATCTTTGAT 59.622 38.462 0.00 0.00 0.00 2.57
5558 8213 5.710099 CACTAGGGTTTTTAGGCATCTTTGA 59.290 40.000 0.00 0.00 0.00 2.69
5559 8214 5.710099 TCACTAGGGTTTTTAGGCATCTTTG 59.290 40.000 0.00 0.00 0.00 2.77
5560 8215 5.887754 TCACTAGGGTTTTTAGGCATCTTT 58.112 37.500 0.00 0.00 0.00 2.52
5561 8216 5.514500 TCACTAGGGTTTTTAGGCATCTT 57.486 39.130 0.00 0.00 0.00 2.40
5562 8217 5.501156 CTTCACTAGGGTTTTTAGGCATCT 58.499 41.667 0.00 0.00 0.00 2.90
5563 8218 4.640647 CCTTCACTAGGGTTTTTAGGCATC 59.359 45.833 0.00 0.00 40.67 3.91
5564 8219 4.600062 CCTTCACTAGGGTTTTTAGGCAT 58.400 43.478 0.00 0.00 40.67 4.40
5565 8220 3.812882 GCCTTCACTAGGGTTTTTAGGCA 60.813 47.826 15.09 0.00 44.80 4.75
5566 8221 2.753452 GCCTTCACTAGGGTTTTTAGGC 59.247 50.000 0.00 0.00 44.91 3.93
5575 8230 2.294791 CGACATCTAGCCTTCACTAGGG 59.705 54.545 0.00 0.00 44.91 3.53
5577 8232 3.628032 TGTCGACATCTAGCCTTCACTAG 59.372 47.826 15.76 0.00 40.92 2.57
5578 8233 3.617284 TGTCGACATCTAGCCTTCACTA 58.383 45.455 15.76 0.00 0.00 2.74
5579 8234 2.447443 TGTCGACATCTAGCCTTCACT 58.553 47.619 15.76 0.00 0.00 3.41
5580 8235 2.941453 TGTCGACATCTAGCCTTCAC 57.059 50.000 15.76 0.00 0.00 3.18
5581 8236 3.953712 TTTGTCGACATCTAGCCTTCA 57.046 42.857 20.80 0.00 0.00 3.02
5582 8237 3.371285 GGTTTTGTCGACATCTAGCCTTC 59.629 47.826 20.80 3.03 0.00 3.46
5583 8238 3.335579 GGTTTTGTCGACATCTAGCCTT 58.664 45.455 20.80 0.00 0.00 4.35
5584 8239 2.674177 CGGTTTTGTCGACATCTAGCCT 60.674 50.000 20.80 0.00 0.00 4.58
5585 8240 1.659098 CGGTTTTGTCGACATCTAGCC 59.341 52.381 20.80 16.87 0.00 3.93
5586 8241 2.334838 ACGGTTTTGTCGACATCTAGC 58.665 47.619 20.80 15.20 0.00 3.42
5605 8260 3.279434 AGGGTATTTTGGCATCTTCGAC 58.721 45.455 0.00 0.00 0.00 4.20


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.