Multiple sequence alignment - TraesCS2A01G391000

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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 TraesCS2A01G391000 chr2A 100.000 6169 0 0 1 6169 640705410 640711578 0.000000e+00 11393.0
1 TraesCS2A01G391000 chr2A 79.207 1640 286 42 3544 5169 640818508 640820106 0.000000e+00 1088.0
2 TraesCS2A01G391000 chr2A 82.432 592 79 18 1147 1726 640816828 640817406 1.540000e-135 494.0
3 TraesCS2A01G391000 chr2A 84.300 293 42 4 1155 1444 640269911 640270202 3.640000e-72 283.0
4 TraesCS2A01G391000 chr2A 78.472 144 27 4 3539 3680 640271185 640271326 2.370000e-14 91.6
5 TraesCS2A01G391000 chr2B 93.683 2913 124 24 2652 5521 579688476 579685581 0.000000e+00 4305.0
6 TraesCS2A01G391000 chr2B 90.189 1162 71 24 1231 2373 579690425 579689288 0.000000e+00 1474.0
7 TraesCS2A01G391000 chr2B 78.755 1638 298 37 3544 5169 579573148 579571549 0.000000e+00 1051.0
8 TraesCS2A01G391000 chr2B 91.337 531 24 11 709 1231 579690654 579691170 0.000000e+00 706.0
9 TraesCS2A01G391000 chr2B 82.877 584 75 17 1152 1726 579574981 579574414 9.230000e-138 501.0
10 TraesCS2A01G391000 chr2B 89.513 267 16 2 5520 5777 579685457 579685194 1.660000e-85 327.0
11 TraesCS2A01G391000 chr2B 88.333 240 18 7 336 567 579691406 579691169 4.710000e-71 279.0
12 TraesCS2A01G391000 chr2B 83.838 297 44 4 1155 1448 581471086 581470791 4.710000e-71 279.0
13 TraesCS2A01G391000 chr2B 83.502 297 26 11 5887 6169 579684053 579683766 7.940000e-64 255.0
14 TraesCS2A01G391000 chr2B 82.906 117 16 4 3566 3680 581469815 581469701 1.090000e-17 102.0
15 TraesCS2A01G391000 chr2B 77.241 145 27 6 3539 3680 42565535 42565676 5.130000e-11 80.5
16 TraesCS2A01G391000 chr2D 95.316 2370 78 16 3069 5421 493079715 493077362 0.000000e+00 3731.0
17 TraesCS2A01G391000 chr2D 91.797 1658 82 27 176 1799 493083069 493081432 0.000000e+00 2259.0
18 TraesCS2A01G391000 chr2D 79.352 1637 289 36 3544 5169 493006019 493004421 0.000000e+00 1105.0
19 TraesCS2A01G391000 chr2D 89.455 825 51 17 1795 2598 493081400 493080591 0.000000e+00 1009.0
20 TraesCS2A01G391000 chr2D 84.583 707 52 26 5414 6086 493076395 493075712 0.000000e+00 649.0
21 TraesCS2A01G391000 chr2D 92.124 419 32 1 2652 3070 493080160 493079743 1.920000e-164 590.0
22 TraesCS2A01G391000 chr2D 82.877 584 75 19 1152 1726 493007876 493007309 9.230000e-138 501.0
23 TraesCS2A01G391000 chr2D 84.122 296 43 4 1155 1447 493177143 493176849 3.640000e-72 283.0
24 TraesCS2A01G391000 chr2D 90.789 152 14 0 2644 2795 133265824 133265673 2.920000e-48 204.0
25 TraesCS2A01G391000 chr2D 94.737 114 4 2 64 175 493084684 493084571 6.360000e-40 176.0
26 TraesCS2A01G391000 chr2D 82.051 117 17 4 3566 3680 493175812 493175698 5.090000e-16 97.1
27 TraesCS2A01G391000 chr2D 97.297 37 0 1 5801 5836 495786051 495786015 1.860000e-05 62.1
28 TraesCS2A01G391000 chr1A 84.454 238 23 7 5327 5562 537448996 537449221 8.050000e-54 222.0
29 TraesCS2A01G391000 chr1A 92.053 151 12 0 2644 2794 208883981 208884131 4.840000e-51 213.0
30 TraesCS2A01G391000 chr1A 92.517 147 11 0 2646 2792 208894032 208893886 1.740000e-50 211.0
31 TraesCS2A01G391000 chr7A 92.568 148 11 0 2645 2792 503428678 503428825 4.840000e-51 213.0
32 TraesCS2A01G391000 chr7A 92.000 150 10 2 2644 2792 86232274 86232126 6.270000e-50 209.0
33 TraesCS2A01G391000 chr7A 73.988 519 107 23 1164 1667 611728110 611728615 1.060000e-42 185.0
34 TraesCS2A01G391000 chr7D 74.759 519 102 24 1164 1667 531439441 531439945 8.110000e-49 206.0
35 TraesCS2A01G391000 chr7D 91.333 150 12 1 2643 2792 428731970 428731822 2.920000e-48 204.0
36 TraesCS2A01G391000 chr6D 91.333 150 13 0 2643 2792 145458834 145458685 8.110000e-49 206.0
37 TraesCS2A01G391000 chr6B 80.843 261 44 5 1169 1426 512234493 512234750 3.770000e-47 200.0
38 TraesCS2A01G391000 chr6B 100.000 33 0 0 5819 5851 71356711 71356743 1.860000e-05 62.1
39 TraesCS2A01G391000 chrUn 95.349 43 1 1 5800 5841 343014670 343014712 3.990000e-07 67.6
40 TraesCS2A01G391000 chrUn 93.478 46 2 1 5800 5844 343024977 343024932 3.990000e-07 67.6
41 TraesCS2A01G391000 chrUn 93.478 46 2 1 5800 5844 374493592 374493547 3.990000e-07 67.6
42 TraesCS2A01G391000 chrUn 95.349 43 1 1 5800 5841 387474634 387474676 3.990000e-07 67.6
43 TraesCS2A01G391000 chr7B 95.349 43 1 1 5800 5841 721442001 721442043 3.990000e-07 67.6
44 TraesCS2A01G391000 chr6A 93.182 44 3 0 5798 5841 21946073 21946116 1.440000e-06 65.8
45 TraesCS2A01G391000 chr5D 92.500 40 2 1 5800 5839 408217891 408217853 8.640000e-04 56.5


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 TraesCS2A01G391000 chr2A 640705410 640711578 6168 False 11393.000000 11393 100.000000 1 6169 1 chr2A.!!$F1 6168
1 TraesCS2A01G391000 chr2A 640816828 640820106 3278 False 791.000000 1088 80.819500 1147 5169 2 chr2A.!!$F3 4022
2 TraesCS2A01G391000 chr2B 579683766 579691406 7640 True 1328.000000 4305 89.044000 336 6169 5 chr2B.!!$R2 5833
3 TraesCS2A01G391000 chr2B 579571549 579574981 3432 True 776.000000 1051 80.816000 1152 5169 2 chr2B.!!$R1 4017
4 TraesCS2A01G391000 chr2B 579690654 579691170 516 False 706.000000 706 91.337000 709 1231 1 chr2B.!!$F2 522
5 TraesCS2A01G391000 chr2D 493075712 493084684 8972 True 1402.333333 3731 91.335333 64 6086 6 chr2D.!!$R4 6022
6 TraesCS2A01G391000 chr2D 493004421 493007876 3455 True 803.000000 1105 81.114500 1152 5169 2 chr2D.!!$R3 4017
7 TraesCS2A01G391000 chr7D 531439441 531439945 504 False 206.000000 206 74.759000 1164 1667 1 chr7D.!!$F1 503

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
28 29 0.179070 GTTGCCTCCTCTCCCGAATC 60.179 60.000 0.00 0.0 0.00 2.52 F
29 30 0.325671 TTGCCTCCTCTCCCGAATCT 60.326 55.000 0.00 0.0 0.00 2.40 F
692 2214 0.620556 GGACAAGAGGCCTTCCATCA 59.379 55.000 15.25 0.0 33.74 3.07 F
2259 4137 0.244721 GGCTGGGCATGTTTCTGAAC 59.755 55.000 0.00 0.0 36.29 3.18 F
2461 4340 0.321122 CAGCAGCGGTTTCTTCTCCT 60.321 55.000 0.00 0.0 0.00 3.69 F
2748 5470 0.457851 CCAACGCAACCAAAAGTCCA 59.542 50.000 0.00 0.0 0.00 4.02 F
3143 5907 1.134367 CTGCAACCCATTGAGAGCATG 59.866 52.381 0.00 0.0 38.15 4.06 F
3145 5909 1.820519 GCAACCCATTGAGAGCATGAA 59.179 47.619 0.00 0.0 38.15 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1126 2894 2.805353 CTCTGGTTCGTCGCCGTG 60.805 66.667 0.00 0.0 35.01 4.94 R
1130 2898 2.811317 CCAGCTCTGGTTCGTCGC 60.811 66.667 7.75 0.0 45.53 5.19 R
2414 4293 0.179048 TGCTCTGGAATGTATGGGCG 60.179 55.000 0.00 0.0 0.00 6.13 R
3525 6598 0.811616 GCTGCCTAACATGAGGACCG 60.812 60.000 0.00 0.0 39.15 4.79 R
3841 6930 1.160137 CGCCAAAAAGGAGAGACAGG 58.840 55.000 0.00 0.0 40.01 4.00 R
4529 7624 1.334869 GCAACCACACCAGAGTCTTTG 59.665 52.381 0.00 0.0 0.00 2.77 R
4922 8017 1.202099 TTGCCATCGGTAGGGGAACA 61.202 55.000 0.00 0.0 31.38 3.18 R
5170 8265 9.557338 CTGTACATAGAGTAGTTTGTTACTGTC 57.443 37.037 0.00 0.0 37.73 3.51 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 2.207580 GAGAGTTGCCTCCTCTCCC 58.792 63.158 11.41 0.00 46.03 4.30
24 25 1.671901 GAGAGTTGCCTCCTCTCCCG 61.672 65.000 11.41 0.00 46.03 5.14
25 26 1.682684 GAGTTGCCTCCTCTCCCGA 60.683 63.158 0.00 0.00 0.00 5.14
26 27 1.229209 AGTTGCCTCCTCTCCCGAA 60.229 57.895 0.00 0.00 0.00 4.30
27 28 0.618968 AGTTGCCTCCTCTCCCGAAT 60.619 55.000 0.00 0.00 0.00 3.34
28 29 0.179070 GTTGCCTCCTCTCCCGAATC 60.179 60.000 0.00 0.00 0.00 2.52
29 30 0.325671 TTGCCTCCTCTCCCGAATCT 60.326 55.000 0.00 0.00 0.00 2.40
30 31 0.757188 TGCCTCCTCTCCCGAATCTC 60.757 60.000 0.00 0.00 0.00 2.75
31 32 0.757188 GCCTCCTCTCCCGAATCTCA 60.757 60.000 0.00 0.00 0.00 3.27
32 33 2.008242 CCTCCTCTCCCGAATCTCAT 57.992 55.000 0.00 0.00 0.00 2.90
33 34 1.892474 CCTCCTCTCCCGAATCTCATC 59.108 57.143 0.00 0.00 0.00 2.92
34 35 1.892474 CTCCTCTCCCGAATCTCATCC 59.108 57.143 0.00 0.00 0.00 3.51
35 36 1.501170 TCCTCTCCCGAATCTCATCCT 59.499 52.381 0.00 0.00 0.00 3.24
36 37 1.892474 CCTCTCCCGAATCTCATCCTC 59.108 57.143 0.00 0.00 0.00 3.71
37 38 1.892474 CTCTCCCGAATCTCATCCTCC 59.108 57.143 0.00 0.00 0.00 4.30
38 39 1.501170 TCTCCCGAATCTCATCCTCCT 59.499 52.381 0.00 0.00 0.00 3.69
39 40 2.716969 TCTCCCGAATCTCATCCTCCTA 59.283 50.000 0.00 0.00 0.00 2.94
40 41 2.823154 CTCCCGAATCTCATCCTCCTAC 59.177 54.545 0.00 0.00 0.00 3.18
41 42 2.447429 TCCCGAATCTCATCCTCCTACT 59.553 50.000 0.00 0.00 0.00 2.57
42 43 2.823154 CCCGAATCTCATCCTCCTACTC 59.177 54.545 0.00 0.00 0.00 2.59
43 44 2.823154 CCGAATCTCATCCTCCTACTCC 59.177 54.545 0.00 0.00 0.00 3.85
44 45 2.823154 CGAATCTCATCCTCCTACTCCC 59.177 54.545 0.00 0.00 0.00 4.30
45 46 3.169908 GAATCTCATCCTCCTACTCCCC 58.830 54.545 0.00 0.00 0.00 4.81
46 47 0.861155 TCTCATCCTCCTACTCCCCC 59.139 60.000 0.00 0.00 0.00 5.40
71 72 6.213677 CGATGAGATTCGGGAGTATTTGTTA 58.786 40.000 0.00 0.00 35.50 2.41
108 109 3.987868 GTCAGTGATCACTAGTTCGCAAA 59.012 43.478 27.44 2.94 40.20 3.68
153 156 2.943449 AGTCCTTTCCGACGAGAATC 57.057 50.000 0.00 0.00 37.85 2.52
156 159 1.146358 CCTTTCCGACGAGAATCCGC 61.146 60.000 0.00 0.00 0.00 5.54
175 178 2.363220 GCGTGATTTGCTGCGTATTAC 58.637 47.619 0.00 0.00 0.00 1.89
176 179 2.030457 GCGTGATTTGCTGCGTATTACT 59.970 45.455 0.00 0.00 0.00 2.24
177 180 3.841372 GCGTGATTTGCTGCGTATTACTC 60.841 47.826 0.00 0.00 0.00 2.59
179 182 2.863740 TGATTTGCTGCGTATTACTCCG 59.136 45.455 0.00 0.00 0.00 4.63
182 185 1.100510 TGCTGCGTATTACTCCGTCT 58.899 50.000 0.00 0.00 0.00 4.18
188 1692 2.098770 GCGTATTACTCCGTCTGTTCCT 59.901 50.000 0.00 0.00 0.00 3.36
226 1730 0.662374 GCTTTTCGAGTCGACGTGGA 60.662 55.000 16.28 6.03 34.89 4.02
336 1840 4.754667 GGGGTCACCGAAGCCGAC 62.755 72.222 0.00 0.00 37.70 4.79
417 1928 1.814169 GCCCGGATCTTCGTTGACC 60.814 63.158 0.73 0.00 0.00 4.02
419 1930 1.153429 CCGGATCTTCGTTGACCCC 60.153 63.158 0.00 0.00 0.00 4.95
421 1932 1.814169 GGATCTTCGTTGACCCCGC 60.814 63.158 0.00 0.00 0.00 6.13
424 1935 1.068741 GATCTTCGTTGACCCCGCTAT 59.931 52.381 0.00 0.00 0.00 2.97
425 1936 0.899720 TCTTCGTTGACCCCGCTATT 59.100 50.000 0.00 0.00 0.00 1.73
506 2018 2.182496 TCGTTCCCGAGCGTTGATA 58.818 52.632 0.89 0.00 38.40 2.15
508 2020 1.135527 TCGTTCCCGAGCGTTGATAAT 59.864 47.619 0.89 0.00 38.40 1.28
509 2021 1.257936 CGTTCCCGAGCGTTGATAATG 59.742 52.381 0.00 0.00 35.63 1.90
569 2081 3.419915 CGTCAGTTTGCTTGTATGCATC 58.580 45.455 0.19 0.00 42.96 3.91
576 2088 3.264998 TGCTTGTATGCATCTGCTACA 57.735 42.857 0.19 0.00 42.66 2.74
652 2174 4.687215 TGCGGTGAGGAGCAGCAC 62.687 66.667 0.00 0.00 45.15 4.40
654 2176 3.006756 GCGGTGAGGAGCAGCACTA 62.007 63.158 0.00 0.00 45.15 2.74
656 2178 1.315981 CGGTGAGGAGCAGCACTAGA 61.316 60.000 0.00 0.00 45.15 2.43
659 2181 1.753649 GTGAGGAGCAGCACTAGATGA 59.246 52.381 0.00 0.00 31.30 2.92
660 2182 2.364970 GTGAGGAGCAGCACTAGATGAT 59.635 50.000 0.00 0.00 31.30 2.45
662 2184 1.693062 AGGAGCAGCACTAGATGATGG 59.307 52.381 0.00 0.00 45.29 3.51
663 2185 1.690893 GGAGCAGCACTAGATGATGGA 59.309 52.381 0.00 0.00 45.29 3.41
664 2186 2.103771 GGAGCAGCACTAGATGATGGAA 59.896 50.000 0.00 0.00 45.29 3.53
685 2207 1.846712 GCCAAGAGGACAAGAGGCCT 61.847 60.000 3.86 3.86 36.17 5.19
686 2208 0.695347 CCAAGAGGACAAGAGGCCTT 59.305 55.000 6.77 0.00 36.89 4.35
687 2209 1.339535 CCAAGAGGACAAGAGGCCTTC 60.340 57.143 6.77 0.00 36.89 3.46
691 2213 0.915364 AGGACAAGAGGCCTTCCATC 59.085 55.000 20.96 10.89 33.74 3.51
692 2214 0.620556 GGACAAGAGGCCTTCCATCA 59.379 55.000 15.25 0.00 33.74 3.07
758 2283 1.953311 GCCCGGCAGGTGAGATTTTTA 60.953 52.381 3.91 0.00 38.26 1.52
759 2284 2.442413 CCCGGCAGGTGAGATTTTTAA 58.558 47.619 1.11 0.00 35.12 1.52
761 2286 3.066760 CCCGGCAGGTGAGATTTTTAATC 59.933 47.826 1.11 0.00 35.12 1.75
775 2302 8.443953 AGATTTTTAATCCATGCTCTCTGTAC 57.556 34.615 0.00 0.00 0.00 2.90
784 2311 1.135228 TGCTCTCTGTACGCGCAATTA 60.135 47.619 5.73 0.00 0.00 1.40
860 2587 2.495270 GGAATCACTCACAGCTCTCTCA 59.505 50.000 0.00 0.00 0.00 3.27
1028 2778 4.154347 GCAGGACAGGCGGAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
1321 3089 2.956964 CGCTCATCGCCTTCGTCC 60.957 66.667 0.00 0.00 36.96 4.79
1792 3569 7.959651 CACAAGCTTAATGATTCTGTAACACTC 59.040 37.037 0.00 0.00 0.00 3.51
1793 3570 7.661437 ACAAGCTTAATGATTCTGTAACACTCA 59.339 33.333 0.00 0.00 0.00 3.41
1869 3703 5.814188 TCACTATCTGTATTGCTCTTGCTTG 59.186 40.000 0.00 0.00 40.48 4.01
2006 3857 2.831685 TTAGGCAAAGCTGACTTCGA 57.168 45.000 0.00 0.00 37.87 3.71
2140 4017 4.588528 TGATATCAGATTGACCGGTGATGA 59.411 41.667 14.63 4.71 32.01 2.92
2142 4019 2.179427 TCAGATTGACCGGTGATGACT 58.821 47.619 14.63 0.00 0.00 3.41
2144 4021 3.007940 TCAGATTGACCGGTGATGACTTT 59.992 43.478 14.63 0.00 0.00 2.66
2145 4022 3.125829 CAGATTGACCGGTGATGACTTTG 59.874 47.826 14.63 0.00 0.00 2.77
2254 4132 0.686789 AAAAGGGCTGGGCATGTTTC 59.313 50.000 0.00 0.00 0.00 2.78
2259 4137 0.244721 GGCTGGGCATGTTTCTGAAC 59.755 55.000 0.00 0.00 36.29 3.18
2262 4140 2.819608 GCTGGGCATGTTTCTGAACTTA 59.180 45.455 0.00 0.00 36.70 2.24
2321 4200 0.524816 CAATTGGATGCGCTGCACTC 60.525 55.000 9.73 0.00 43.04 3.51
2346 4225 3.764972 ACTCTCTGCAGTACCCTAAGAAC 59.235 47.826 14.67 0.00 0.00 3.01
2347 4226 3.097614 TCTCTGCAGTACCCTAAGAACC 58.902 50.000 14.67 0.00 0.00 3.62
2405 4284 2.486982 ACTCATTGTGCTCAAGATGTGC 59.513 45.455 7.35 0.00 36.97 4.57
2414 4293 2.478539 GCTCAAGATGTGCCGATTTTCC 60.479 50.000 0.00 0.00 31.28 3.13
2449 4328 3.611549 CAGAGCATGTATATACAGCAGCG 59.388 47.826 25.65 15.70 39.92 5.18
2452 4331 3.067106 GCATGTATATACAGCAGCGGTT 58.933 45.455 19.80 0.00 39.92 4.44
2461 4340 0.321122 CAGCAGCGGTTTCTTCTCCT 60.321 55.000 0.00 0.00 0.00 3.69
2487 4366 1.386412 GACAATTGCCGCAACATTTCG 59.614 47.619 8.25 0.00 0.00 3.46
2557 4436 2.111999 CTCTCCCGACCAAAGGCACA 62.112 60.000 0.00 0.00 0.00 4.57
2598 4477 9.190317 ACCTTCTGGATCCTGATTTTTAATTAC 57.810 33.333 20.77 0.00 37.04 1.89
2642 5013 2.283298 CCGTCTTGATGGTGGATCTTG 58.717 52.381 0.87 0.00 31.55 3.02
2699 5421 3.244596 ACTTCAACTCAAGACCTTAGGCC 60.245 47.826 0.00 0.00 0.00 5.19
2748 5470 0.457851 CCAACGCAACCAAAAGTCCA 59.542 50.000 0.00 0.00 0.00 4.02
2752 5474 1.546476 ACGCAACCAAAAGTCCAAACA 59.454 42.857 0.00 0.00 0.00 2.83
2757 5479 4.441356 GCAACCAAAAGTCCAAACAGATGA 60.441 41.667 0.00 0.00 0.00 2.92
2763 5485 7.147672 ACCAAAAGTCCAAACAGATGAAAAGAT 60.148 33.333 0.00 0.00 0.00 2.40
2788 5510 8.941995 TCTAGGCAATCTACATATACACTTCT 57.058 34.615 0.00 0.00 0.00 2.85
2806 5528 1.968493 TCTACAACCTCCACCTGTCAC 59.032 52.381 0.00 0.00 0.00 3.67
2949 5671 2.203640 ACGGAGAGTGAGCCACCA 60.204 61.111 2.18 0.00 34.49 4.17
3129 5882 7.076842 TGTTATTCTAATCTTCAGCTGCAAC 57.923 36.000 9.47 0.00 0.00 4.17
3143 5907 1.134367 CTGCAACCCATTGAGAGCATG 59.866 52.381 0.00 0.00 38.15 4.06
3145 5909 1.820519 GCAACCCATTGAGAGCATGAA 59.179 47.619 0.00 0.00 38.15 2.57
3147 5911 3.633525 GCAACCCATTGAGAGCATGAATA 59.366 43.478 0.00 0.00 38.15 1.75
3148 5912 4.098349 GCAACCCATTGAGAGCATGAATAA 59.902 41.667 0.00 0.00 38.15 1.40
3149 5913 5.221382 GCAACCCATTGAGAGCATGAATAAT 60.221 40.000 0.00 0.00 38.15 1.28
3150 5914 6.684613 GCAACCCATTGAGAGCATGAATAATT 60.685 38.462 0.00 0.00 38.15 1.40
3151 5915 7.270047 CAACCCATTGAGAGCATGAATAATTT 58.730 34.615 0.00 0.00 38.15 1.82
3152 5916 7.427989 ACCCATTGAGAGCATGAATAATTTT 57.572 32.000 0.00 0.00 0.00 1.82
3153 5917 7.270047 ACCCATTGAGAGCATGAATAATTTTG 58.730 34.615 0.00 0.00 0.00 2.44
3154 5918 7.124599 ACCCATTGAGAGCATGAATAATTTTGA 59.875 33.333 0.00 0.00 0.00 2.69
3155 5919 7.982919 CCCATTGAGAGCATGAATAATTTTGAA 59.017 33.333 0.00 0.00 0.00 2.69
3156 5920 9.373603 CCATTGAGAGCATGAATAATTTTGAAA 57.626 29.630 0.00 0.00 0.00 2.69
3197 5962 8.725148 CATAGAAGTTTTGAGTTGTCAGCTATT 58.275 33.333 0.00 0.00 32.98 1.73
3199 5964 8.000780 AGAAGTTTTGAGTTGTCAGCTATTTT 57.999 30.769 0.00 0.00 32.98 1.82
3224 5989 6.216662 TCTTTAGTCCTTGGTCATATTTGGGA 59.783 38.462 0.00 0.00 0.00 4.37
3270 6035 5.534654 TCCTTCAAAATGAACTTGATTCCGT 59.465 36.000 0.00 0.00 36.36 4.69
3271 6036 5.630680 CCTTCAAAATGAACTTGATTCCGTG 59.369 40.000 0.00 0.00 36.36 4.94
3319 6123 9.167311 GAACCTCTATAAGTTTGACATCACATT 57.833 33.333 0.00 0.00 0.00 2.71
3496 6313 1.876799 CACATAACACGGGACTTGCAA 59.123 47.619 0.00 0.00 0.00 4.08
3507 6324 3.736433 CGGGACTTGCAAATTCAAACACA 60.736 43.478 0.00 0.00 0.00 3.72
3515 6588 8.767085 ACTTGCAAATTCAAACACAATTATCTG 58.233 29.630 0.00 0.00 0.00 2.90
3841 6930 5.523438 TGATTTGTTCCCACCTTGTTAAC 57.477 39.130 0.00 0.00 0.00 2.01
3984 7073 8.482943 AGGCTACAAGGTTTGTTTCTTTATTTT 58.517 29.630 0.00 0.00 42.22 1.82
4192 7285 8.190122 GGTAAACATTCTGATAAATGCATGACA 58.810 33.333 0.00 0.00 39.72 3.58
4322 7417 2.697751 CAGTCTACCTTCATGGCTAGCT 59.302 50.000 15.72 0.00 40.22 3.32
4362 7457 5.457799 GCATTATCAGTTGCTGCAGTAATTG 59.542 40.000 26.80 26.80 35.95 2.32
4658 7753 3.210232 ACATCTCCCAGATCAATGCTG 57.790 47.619 0.00 0.00 31.32 4.41
5170 8265 3.744530 GCATTTAGGCCTACACACTAGGG 60.745 52.174 13.46 0.00 35.29 3.53
5181 8276 5.011329 CCTACACACTAGGGACAGTAACAAA 59.989 44.000 0.00 0.00 0.00 2.83
5185 8280 5.924825 CACACTAGGGACAGTAACAAACTAC 59.075 44.000 0.00 0.00 35.76 2.73
5247 8343 5.163561 TGCAGTAAATAGGTTTTGCATAGCC 60.164 40.000 1.70 1.70 36.60 3.93
5304 8401 9.665719 TTCTTCTTGTATTGATATGTTGCTGTA 57.334 29.630 0.00 0.00 0.00 2.74
5305 8402 9.836864 TCTTCTTGTATTGATATGTTGCTGTAT 57.163 29.630 0.00 0.00 0.00 2.29
5387 8484 2.378038 GGGCAGCTGATCCAATTGTTA 58.622 47.619 20.43 0.00 0.00 2.41
5411 8508 1.261619 GTCAGTTTCCAGCTGTTGTCG 59.738 52.381 13.81 0.00 35.60 4.35
5481 9552 9.922477 AGATATATGCCAATGAAGAATCATCAT 57.078 29.630 0.00 0.00 45.60 2.45
5549 9749 2.441750 AGAAACCAGCACTTCCCTACAA 59.558 45.455 0.00 0.00 0.00 2.41
5622 9823 3.509442 AGAACCAATTCAAGGCCATTCA 58.491 40.909 5.01 0.00 37.29 2.57
5644 9845 1.479323 CATCTCCAGCCAAAACCATGG 59.521 52.381 11.19 11.19 43.70 3.66
5650 9851 3.323403 TCCAGCCAAAACCATGGTAAAAG 59.677 43.478 20.12 9.14 42.75 2.27
5651 9852 3.070878 CCAGCCAAAACCATGGTAAAAGT 59.929 43.478 20.12 0.00 42.75 2.66
5652 9853 4.282195 CCAGCCAAAACCATGGTAAAAGTA 59.718 41.667 20.12 0.00 42.75 2.24
5653 9854 5.469479 CAGCCAAAACCATGGTAAAAGTAG 58.531 41.667 20.12 4.85 42.75 2.57
5680 9881 5.703130 GCTCACAAGGAAGAACTAACTTCAT 59.297 40.000 0.00 0.00 45.39 2.57
5685 9887 8.190784 CACAAGGAAGAACTAACTTCATGTTTT 58.809 33.333 0.00 0.00 45.39 2.43
5741 9952 3.133464 AACCCACATGCATCGCCG 61.133 61.111 0.00 0.00 0.00 6.46
5766 9977 6.094048 GCTTGATACTGCATCTTTCAGGTTTA 59.906 38.462 0.00 0.00 35.94 2.01
5774 9985 6.013379 TGCATCTTTCAGGTTTACCCATTAA 58.987 36.000 0.00 0.00 36.42 1.40
5802 10023 0.892755 TGAGGAGACGGCGTACAAAT 59.107 50.000 14.74 0.00 0.00 2.32
5807 10028 2.856557 GGAGACGGCGTACAAATTACTC 59.143 50.000 14.74 12.56 0.00 2.59
5809 10030 1.929169 GACGGCGTACAAATTACTCCC 59.071 52.381 14.74 0.00 0.00 4.30
5810 10031 1.551883 ACGGCGTACAAATTACTCCCT 59.448 47.619 12.58 0.00 0.00 4.20
5812 10033 2.558378 GGCGTACAAATTACTCCCTCC 58.442 52.381 0.00 0.00 0.00 4.30
5813 10034 2.199236 GCGTACAAATTACTCCCTCCG 58.801 52.381 0.00 0.00 0.00 4.63
5814 10035 2.417787 GCGTACAAATTACTCCCTCCGT 60.418 50.000 0.00 0.00 0.00 4.69
5816 10037 3.129988 CGTACAAATTACTCCCTCCGTCT 59.870 47.826 0.00 0.00 0.00 4.18
5820 10041 7.255242 CGTACAAATTACTCCCTCCGTCTTATA 60.255 40.741 0.00 0.00 0.00 0.98
5821 10042 7.427989 ACAAATTACTCCCTCCGTCTTATAA 57.572 36.000 0.00 0.00 0.00 0.98
5829 10050 8.578448 ACTCCCTCCGTCTTATAATATAAGAC 57.422 38.462 29.65 29.65 45.92 3.01
5871 11091 2.093106 GTCTGACGCTCCTCCTCTTTA 58.907 52.381 0.00 0.00 0.00 1.85
5876 11096 5.421056 TCTGACGCTCCTCCTCTTTATTTTA 59.579 40.000 0.00 0.00 0.00 1.52
5888 11108 9.898152 CTCCTCTTTATTTTATGAGAAACTCCT 57.102 33.333 0.00 0.00 0.00 3.69
5969 11212 2.199535 CCATGGGCCCCTCATTCC 59.800 66.667 22.27 0.00 0.00 3.01
5971 11214 1.152610 CATGGGCCCCTCATTCCAG 60.153 63.158 22.27 0.00 32.30 3.86
5983 11226 3.523547 CTCATTCCAGAGTCTTCAGCAG 58.476 50.000 0.00 0.00 0.00 4.24
6017 11267 3.027419 AGCCTCCTTGCTTGTGTTC 57.973 52.632 0.00 0.00 38.85 3.18
6018 11268 0.475906 AGCCTCCTTGCTTGTGTTCT 59.524 50.000 0.00 0.00 38.85 3.01
6047 11305 4.336280 ACTAAAAACCTCCTTGCCATCTC 58.664 43.478 0.00 0.00 0.00 2.75
6087 11349 2.729194 ACAGTAGACTTCATCTCGCCT 58.271 47.619 0.00 0.00 39.04 5.52
6090 11352 3.380004 CAGTAGACTTCATCTCGCCTTCT 59.620 47.826 0.00 0.00 39.04 2.85
6091 11353 4.020543 AGTAGACTTCATCTCGCCTTCTT 58.979 43.478 0.00 0.00 39.04 2.52
6094 11356 5.606348 AGACTTCATCTCGCCTTCTTAAT 57.394 39.130 0.00 0.00 28.16 1.40
6095 11357 5.983540 AGACTTCATCTCGCCTTCTTAATT 58.016 37.500 0.00 0.00 28.16 1.40
6096 11358 6.410540 AGACTTCATCTCGCCTTCTTAATTT 58.589 36.000 0.00 0.00 28.16 1.82
6097 11359 6.314896 AGACTTCATCTCGCCTTCTTAATTTG 59.685 38.462 0.00 0.00 28.16 2.32
6098 11360 5.940470 ACTTCATCTCGCCTTCTTAATTTGT 59.060 36.000 0.00 0.00 0.00 2.83
6100 11362 7.278868 ACTTCATCTCGCCTTCTTAATTTGTAG 59.721 37.037 0.00 0.00 0.00 2.74
6101 11363 6.640518 TCATCTCGCCTTCTTAATTTGTAGT 58.359 36.000 0.00 0.00 0.00 2.73
6102 11364 7.778083 TCATCTCGCCTTCTTAATTTGTAGTA 58.222 34.615 0.00 0.00 0.00 1.82
6103 11365 8.421784 TCATCTCGCCTTCTTAATTTGTAGTAT 58.578 33.333 0.00 0.00 0.00 2.12
6104 11366 9.692749 CATCTCGCCTTCTTAATTTGTAGTATA 57.307 33.333 0.00 0.00 0.00 1.47
6105 11367 9.694137 ATCTCGCCTTCTTAATTTGTAGTATAC 57.306 33.333 0.00 0.00 43.42 1.47
6106 11368 8.139989 TCTCGCCTTCTTAATTTGTAGTATACC 58.860 37.037 0.00 0.00 42.12 2.73
6107 11369 7.784037 TCGCCTTCTTAATTTGTAGTATACCA 58.216 34.615 0.00 0.00 42.12 3.25
6108 11370 7.924412 TCGCCTTCTTAATTTGTAGTATACCAG 59.076 37.037 0.00 0.00 42.12 4.00
6111 11373 9.543783 CCTTCTTAATTTGTAGTATACCAGACC 57.456 37.037 0.00 0.00 42.12 3.85
6130 11392 1.405821 CCGTAGACTTCATCTCGCCTT 59.594 52.381 0.00 0.00 39.04 4.35
6131 11393 2.159226 CCGTAGACTTCATCTCGCCTTT 60.159 50.000 0.00 0.00 39.04 3.11
6144 11406 7.748847 TCATCTCGCCTTTTTAATTTGTAGTC 58.251 34.615 0.00 0.00 0.00 2.59
6151 11413 8.879759 CGCCTTTTTAATTTGTAGTCTATCAGA 58.120 33.333 0.00 0.00 0.00 3.27
6160 11422 6.373186 TTGTAGTCTATCAGACCACGTATG 57.627 41.667 2.74 0.00 46.18 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.179070 GATTCGGGAGAGGAGGCAAC 60.179 60.000 0.00 0.00 41.75 4.17
10 11 0.325671 AGATTCGGGAGAGGAGGCAA 60.326 55.000 0.00 0.00 41.75 4.52
11 12 0.757188 GAGATTCGGGAGAGGAGGCA 60.757 60.000 0.00 0.00 41.75 4.75
12 13 0.757188 TGAGATTCGGGAGAGGAGGC 60.757 60.000 0.00 0.00 41.75 4.70
13 14 1.892474 GATGAGATTCGGGAGAGGAGG 59.108 57.143 0.00 0.00 41.75 4.30
14 15 1.892474 GGATGAGATTCGGGAGAGGAG 59.108 57.143 0.00 0.00 41.75 3.69
15 16 1.501170 AGGATGAGATTCGGGAGAGGA 59.499 52.381 0.00 0.00 41.75 3.71
16 17 1.892474 GAGGATGAGATTCGGGAGAGG 59.108 57.143 0.00 0.00 41.75 3.69
17 18 1.892474 GGAGGATGAGATTCGGGAGAG 59.108 57.143 0.00 0.00 41.75 3.20
18 19 1.501170 AGGAGGATGAGATTCGGGAGA 59.499 52.381 0.00 0.00 0.00 3.71
19 20 2.008242 AGGAGGATGAGATTCGGGAG 57.992 55.000 0.00 0.00 0.00 4.30
20 21 2.447429 AGTAGGAGGATGAGATTCGGGA 59.553 50.000 0.00 0.00 0.00 5.14
21 22 2.823154 GAGTAGGAGGATGAGATTCGGG 59.177 54.545 0.00 0.00 0.00 5.14
22 23 2.823154 GGAGTAGGAGGATGAGATTCGG 59.177 54.545 0.00 0.00 0.00 4.30
23 24 2.823154 GGGAGTAGGAGGATGAGATTCG 59.177 54.545 0.00 0.00 0.00 3.34
24 25 3.169908 GGGGAGTAGGAGGATGAGATTC 58.830 54.545 0.00 0.00 0.00 2.52
25 26 2.158081 GGGGGAGTAGGAGGATGAGATT 60.158 54.545 0.00 0.00 0.00 2.40
26 27 1.435168 GGGGGAGTAGGAGGATGAGAT 59.565 57.143 0.00 0.00 0.00 2.75
27 28 0.861155 GGGGGAGTAGGAGGATGAGA 59.139 60.000 0.00 0.00 0.00 3.27
28 29 3.466714 GGGGGAGTAGGAGGATGAG 57.533 63.158 0.00 0.00 0.00 2.90
47 48 4.621991 ACAAATACTCCCGAATCTCATCG 58.378 43.478 0.00 0.00 42.37 3.84
48 49 7.657761 ACATAACAAATACTCCCGAATCTCATC 59.342 37.037 0.00 0.00 0.00 2.92
49 50 7.509546 ACATAACAAATACTCCCGAATCTCAT 58.490 34.615 0.00 0.00 0.00 2.90
50 51 6.884832 ACATAACAAATACTCCCGAATCTCA 58.115 36.000 0.00 0.00 0.00 3.27
51 52 9.141400 GATACATAACAAATACTCCCGAATCTC 57.859 37.037 0.00 0.00 0.00 2.75
52 53 8.871125 AGATACATAACAAATACTCCCGAATCT 58.129 33.333 0.00 0.00 0.00 2.40
53 54 9.490379 AAGATACATAACAAATACTCCCGAATC 57.510 33.333 0.00 0.00 0.00 2.52
54 55 9.273016 CAAGATACATAACAAATACTCCCGAAT 57.727 33.333 0.00 0.00 0.00 3.34
55 56 8.479689 TCAAGATACATAACAAATACTCCCGAA 58.520 33.333 0.00 0.00 0.00 4.30
56 57 8.014070 TCAAGATACATAACAAATACTCCCGA 57.986 34.615 0.00 0.00 0.00 5.14
57 58 8.833231 ATCAAGATACATAACAAATACTCCCG 57.167 34.615 0.00 0.00 0.00 5.14
58 59 9.778741 TGATCAAGATACATAACAAATACTCCC 57.221 33.333 0.00 0.00 0.00 4.30
71 72 6.744175 ATCACTGACCTGATCAAGATACAT 57.256 37.500 0.00 0.00 36.69 2.29
86 87 3.217599 TGCGAACTAGTGATCACTGAC 57.782 47.619 33.76 20.76 42.52 3.51
156 159 3.302480 GGAGTAATACGCAGCAAATCACG 60.302 47.826 0.00 0.00 0.00 4.35
175 178 1.324005 GGGGAGAGGAACAGACGGAG 61.324 65.000 0.00 0.00 0.00 4.63
176 179 1.305046 GGGGAGAGGAACAGACGGA 60.305 63.158 0.00 0.00 0.00 4.69
177 180 2.711922 CGGGGAGAGGAACAGACGG 61.712 68.421 0.00 0.00 0.00 4.79
179 182 1.545706 AAGCGGGGAGAGGAACAGAC 61.546 60.000 0.00 0.00 0.00 3.51
182 185 0.909610 ATGAAGCGGGGAGAGGAACA 60.910 55.000 0.00 0.00 0.00 3.18
188 1692 1.950484 GCAAGAAATGAAGCGGGGAGA 60.950 52.381 0.00 0.00 0.00 3.71
235 1739 3.522731 CACCGCTCGGAGGAGGAG 61.523 72.222 15.95 0.00 40.80 3.69
369 1873 4.398549 TCTACGGTTGCTTGAAAAATCG 57.601 40.909 0.00 0.00 0.00 3.34
434 1945 6.159293 GGGCTGAAATTGGAAAGACTTTTAG 58.841 40.000 1.12 0.00 0.00 1.85
444 1955 1.132881 ACCAAGGGGCTGAAATTGGAA 60.133 47.619 9.65 0.00 44.04 3.53
506 2018 6.586463 ACGCATCGTCGATAAAATATCTCATT 59.414 34.615 7.56 0.00 33.69 2.57
508 2020 5.342259 CACGCATCGTCGATAAAATATCTCA 59.658 40.000 7.56 0.00 38.32 3.27
509 2021 5.718824 GCACGCATCGTCGATAAAATATCTC 60.719 44.000 7.56 0.00 38.32 2.75
576 2088 2.281070 CAACGGTGCAGGAGCTGT 60.281 61.111 0.00 0.00 42.74 4.40
631 2153 4.687215 TGCTCCTCACCGCAGCAC 62.687 66.667 0.00 0.00 38.25 4.40
642 2164 1.693062 CCATCATCTAGTGCTGCTCCT 59.307 52.381 0.00 0.00 0.00 3.69
649 2171 1.141657 TGGCCTTCCATCATCTAGTGC 59.858 52.381 3.32 0.00 37.47 4.40
651 2173 3.387962 TCTTGGCCTTCCATCATCTAGT 58.612 45.455 3.32 0.00 43.05 2.57
652 2174 3.244491 CCTCTTGGCCTTCCATCATCTAG 60.244 52.174 3.32 0.00 43.05 2.43
654 2176 1.493871 CCTCTTGGCCTTCCATCATCT 59.506 52.381 3.32 0.00 43.05 2.90
656 2178 1.213926 GTCCTCTTGGCCTTCCATCAT 59.786 52.381 3.32 0.00 43.05 2.45
659 2181 1.005215 CTTGTCCTCTTGGCCTTCCAT 59.995 52.381 3.32 0.00 43.05 3.41
660 2182 0.401738 CTTGTCCTCTTGGCCTTCCA 59.598 55.000 3.32 0.00 41.55 3.53
662 2184 1.339535 CCTCTTGTCCTCTTGGCCTTC 60.340 57.143 3.32 0.00 0.00 3.46
663 2185 0.695347 CCTCTTGTCCTCTTGGCCTT 59.305 55.000 3.32 0.00 0.00 4.35
664 2186 1.846712 GCCTCTTGTCCTCTTGGCCT 61.847 60.000 3.32 0.00 34.81 5.19
669 2191 0.988063 GGAAGGCCTCTTGTCCTCTT 59.012 55.000 5.23 0.00 32.52 2.85
670 2192 0.178891 TGGAAGGCCTCTTGTCCTCT 60.179 55.000 19.75 0.00 32.52 3.69
671 2193 0.915364 ATGGAAGGCCTCTTGTCCTC 59.085 55.000 19.75 6.31 32.52 3.71
672 2194 0.915364 GATGGAAGGCCTCTTGTCCT 59.085 55.000 19.75 7.59 32.52 3.85
673 2195 0.620556 TGATGGAAGGCCTCTTGTCC 59.379 55.000 5.23 10.49 32.52 4.02
675 2197 3.463048 AAATGATGGAAGGCCTCTTGT 57.537 42.857 5.23 0.00 32.52 3.16
676 2198 4.021916 AGAAAATGATGGAAGGCCTCTTG 58.978 43.478 5.23 0.00 32.52 3.02
677 2199 4.021916 CAGAAAATGATGGAAGGCCTCTT 58.978 43.478 5.23 0.00 35.62 2.85
678 2200 3.267812 TCAGAAAATGATGGAAGGCCTCT 59.732 43.478 5.23 0.00 31.12 3.69
679 2201 3.379688 GTCAGAAAATGATGGAAGGCCTC 59.620 47.826 5.23 0.00 40.92 4.70
680 2202 3.359950 GTCAGAAAATGATGGAAGGCCT 58.640 45.455 0.00 0.00 40.92 5.19
681 2203 2.098117 CGTCAGAAAATGATGGAAGGCC 59.902 50.000 0.00 0.00 40.92 5.19
682 2204 3.411415 CGTCAGAAAATGATGGAAGGC 57.589 47.619 0.00 0.00 40.92 4.35
691 2213 3.051392 GCGCCCCCGTCAGAAAATG 62.051 63.158 0.00 0.00 36.67 2.32
692 2214 2.750237 GCGCCCCCGTCAGAAAAT 60.750 61.111 0.00 0.00 36.67 1.82
758 2283 1.536922 CGCGTACAGAGAGCATGGATT 60.537 52.381 0.00 0.00 0.00 3.01
759 2284 0.031314 CGCGTACAGAGAGCATGGAT 59.969 55.000 0.00 0.00 0.00 3.41
761 2286 2.233654 GCGCGTACAGAGAGCATGG 61.234 63.158 8.43 0.00 0.00 3.66
775 2302 3.664276 CGGTTAGAATGGATAATTGCGCG 60.664 47.826 0.00 0.00 0.00 6.86
784 2311 6.889198 TCTTGATTCTTCGGTTAGAATGGAT 58.111 36.000 11.36 0.00 43.18 3.41
1097 2859 3.999051 CGCGGATCTCCTCGAAAC 58.001 61.111 2.49 0.00 46.30 2.78
1126 2894 2.805353 CTCTGGTTCGTCGCCGTG 60.805 66.667 0.00 0.00 35.01 4.94
1130 2898 2.811317 CCAGCTCTGGTTCGTCGC 60.811 66.667 7.75 0.00 45.53 5.19
1462 3230 2.991190 CACTTGACAAATTGGCAGATGC 59.009 45.455 0.37 0.00 36.33 3.91
1792 3569 4.614535 GCAAGCAACATTTGTAGAGGAGTG 60.615 45.833 0.00 0.00 0.00 3.51
1793 3570 3.503748 GCAAGCAACATTTGTAGAGGAGT 59.496 43.478 0.00 0.00 0.00 3.85
1869 3703 4.051237 GAGCCAACATTTTTCAGTTGTCC 58.949 43.478 0.00 0.00 42.62 4.02
2006 3857 8.092687 ACGTCAAACTACATCACCTAACTAAAT 58.907 33.333 0.00 0.00 0.00 1.40
2066 3941 1.178276 GAGCTCCTCAAGTCGAAGGA 58.822 55.000 0.87 3.61 0.00 3.36
2124 3999 3.244561 ACAAAGTCATCACCGGTCAATCT 60.245 43.478 2.59 0.00 0.00 2.40
2140 4017 4.821805 CACATTCAGTAGGGACAACAAAGT 59.178 41.667 0.00 0.00 0.00 2.66
2142 4019 3.568007 GCACATTCAGTAGGGACAACAAA 59.432 43.478 0.00 0.00 0.00 2.83
2144 4021 2.552155 GGCACATTCAGTAGGGACAACA 60.552 50.000 0.00 0.00 0.00 3.33
2145 4022 2.084546 GGCACATTCAGTAGGGACAAC 58.915 52.381 0.00 0.00 0.00 3.32
2221 4099 7.634869 GCCCAGCCCTTTTATATTTTGTAACAT 60.635 37.037 0.00 0.00 0.00 2.71
2254 4132 4.152402 CCGTTGGAACATGTCTAAGTTCAG 59.848 45.833 0.00 0.00 44.46 3.02
2259 4137 3.328382 TCCCGTTGGAACATGTCTAAG 57.672 47.619 0.00 0.00 39.30 2.18
2262 4140 2.170607 CCTATCCCGTTGGAACATGTCT 59.829 50.000 0.00 0.00 45.98 3.41
2321 4200 1.178276 AGGGTACTGCAGAGAGTTCG 58.822 55.000 23.35 0.00 0.00 3.95
2347 4226 0.827507 CACAAGGTGTTCCCCAAGGG 60.828 60.000 0.00 0.00 46.11 3.95
2375 4254 2.089980 AGCACAATGAGTCAATGAGGC 58.910 47.619 15.15 15.99 0.00 4.70
2405 4284 1.604604 ATGTATGGGCGGAAAATCGG 58.395 50.000 0.00 0.00 0.00 4.18
2414 4293 0.179048 TGCTCTGGAATGTATGGGCG 60.179 55.000 0.00 0.00 0.00 6.13
2449 4328 4.086706 TGTCCTCAAAGGAGAAGAAACC 57.913 45.455 0.00 0.00 46.90 3.27
2461 4340 1.035923 TTGCGGCAATTGTCCTCAAA 58.964 45.000 12.11 7.37 37.11 2.69
2521 4400 1.701847 AGAGCTTCATTCCACACCACT 59.298 47.619 0.00 0.00 0.00 4.00
2557 4436 2.317530 AGGTTGTGTGGGACCTTGT 58.682 52.632 0.00 0.00 43.64 3.16
2598 4477 5.692204 GTGACCGGAACACTATTCATATCTG 59.308 44.000 22.01 0.00 35.66 2.90
2675 5093 4.570930 CCTAAGGTCTTGAGTTGAAGTCC 58.429 47.826 0.00 0.00 32.93 3.85
2678 5096 3.339141 GGCCTAAGGTCTTGAGTTGAAG 58.661 50.000 0.00 0.00 0.00 3.02
2681 5099 1.630878 AGGGCCTAAGGTCTTGAGTTG 59.369 52.381 2.82 0.00 0.00 3.16
2699 5421 5.278169 GCATGAAGCTTAACATGGTATCAGG 60.278 44.000 22.64 7.43 42.53 3.86
2748 5470 7.833183 AGATTGCCTAGATCTTTTCATCTGTTT 59.167 33.333 0.00 0.00 34.75 2.83
2752 5474 8.027524 TGTAGATTGCCTAGATCTTTTCATCT 57.972 34.615 0.00 5.11 35.56 2.90
2763 5485 8.941995 AGAAGTGTATATGTAGATTGCCTAGA 57.058 34.615 0.00 0.00 0.00 2.43
2788 5510 1.053424 GGTGACAGGTGGAGGTTGTA 58.947 55.000 0.00 0.00 0.00 2.41
2806 5528 1.926426 ATCGCCCTCTCCCCTTTTGG 61.926 60.000 0.00 0.00 39.97 3.28
2912 5634 1.278637 CGGCGTGTGGTCTTTGTTC 59.721 57.895 0.00 0.00 0.00 3.18
2949 5671 1.080498 TCCATTGGAGGTGGTAGGAGT 59.920 52.381 0.00 0.00 37.96 3.85
3003 5726 2.828549 ATGGGCGCGGTCAAATCC 60.829 61.111 8.83 0.00 0.00 3.01
3034 5758 0.525455 CGCCGTCAGATCGTGAATCA 60.525 55.000 0.00 0.00 36.74 2.57
3129 5882 7.494211 TCAAAATTATTCATGCTCTCAATGGG 58.506 34.615 0.00 0.00 0.00 4.00
3168 5933 7.715249 AGCTGACAACTCAAAACTTCTATGTAA 59.285 33.333 0.00 0.00 0.00 2.41
3197 5962 7.396055 CCCAAATATGACCAAGGACTAAAGAAA 59.604 37.037 0.00 0.00 0.00 2.52
3199 5964 6.216662 TCCCAAATATGACCAAGGACTAAAGA 59.783 38.462 0.00 0.00 0.00 2.52
3523 6596 0.907704 TGCCTAACATGAGGACCGGT 60.908 55.000 6.92 6.92 39.15 5.28
3525 6598 0.811616 GCTGCCTAACATGAGGACCG 60.812 60.000 0.00 0.00 39.15 4.79
3527 6600 2.012673 CTTGCTGCCTAACATGAGGAC 58.987 52.381 0.00 0.00 39.15 3.85
3528 6601 1.630369 ACTTGCTGCCTAACATGAGGA 59.370 47.619 0.00 0.00 39.15 3.71
3530 6603 5.449588 CCATTTACTTGCTGCCTAACATGAG 60.450 44.000 0.00 0.00 0.00 2.90
3841 6930 1.160137 CGCCAAAAAGGAGAGACAGG 58.840 55.000 0.00 0.00 40.01 4.00
3984 7073 8.904834 ACATGTACACAGTACAATAACCAAAAA 58.095 29.630 13.28 0.00 0.00 1.94
4298 7393 1.834263 AGCCATGAAGGTAGACTGTCC 59.166 52.381 3.76 0.00 40.61 4.02
4313 7408 1.799933 AGCCAGAGTAAGCTAGCCAT 58.200 50.000 12.13 3.15 37.64 4.40
4322 7417 3.328382 AATGCAACGTAGCCAGAGTAA 57.672 42.857 0.00 0.00 0.00 2.24
4529 7624 1.334869 GCAACCACACCAGAGTCTTTG 59.665 52.381 0.00 0.00 0.00 2.77
4658 7753 1.336125 GTGCCAATAGCCTGAGCAATC 59.664 52.381 0.00 0.00 43.56 2.67
4778 7873 2.684001 TCGCCATGTTTCGGTAGATT 57.316 45.000 0.00 0.00 0.00 2.40
4922 8017 1.202099 TTGCCATCGGTAGGGGAACA 61.202 55.000 0.00 0.00 31.38 3.18
5170 8265 9.557338 CTGTACATAGAGTAGTTTGTTACTGTC 57.443 37.037 0.00 0.00 37.73 3.51
5181 8276 9.908747 ATGTCTTCTAACTGTACATAGAGTAGT 57.091 33.333 0.00 0.00 32.19 2.73
5247 8343 1.835483 GCATGCTACAATCTCGCCCG 61.835 60.000 11.37 0.00 0.00 6.13
5304 8401 6.264292 TGTGTGACTTGTTGCCAAAACTATAT 59.736 34.615 0.00 0.00 0.00 0.86
5305 8402 5.590663 TGTGTGACTTGTTGCCAAAACTATA 59.409 36.000 0.00 0.00 0.00 1.31
5387 8484 3.701040 ACAACAGCTGGAAACTGACAATT 59.299 39.130 19.93 0.00 38.55 2.32
5622 9823 2.380064 TGGTTTTGGCTGGAGATGTT 57.620 45.000 0.00 0.00 0.00 2.71
5644 9845 7.376615 TCTTCCTTGTGAGCTACTACTTTTAC 58.623 38.462 0.00 0.00 0.00 2.01
5650 9851 5.394224 AGTTCTTCCTTGTGAGCTACTAC 57.606 43.478 0.00 0.00 0.00 2.73
5651 9852 6.720288 AGTTAGTTCTTCCTTGTGAGCTACTA 59.280 38.462 0.00 0.00 0.00 1.82
5652 9853 5.540719 AGTTAGTTCTTCCTTGTGAGCTACT 59.459 40.000 0.00 0.00 0.00 2.57
5653 9854 5.785243 AGTTAGTTCTTCCTTGTGAGCTAC 58.215 41.667 0.00 0.00 0.00 3.58
5685 9887 2.174639 TGCCTCTCCTTCTGTTGGAAAA 59.825 45.455 0.00 0.00 33.07 2.29
5701 9903 2.684843 CGGCTCAAGCTGTTGCCTC 61.685 63.158 18.00 0.00 42.90 4.70
5741 9952 3.944015 ACCTGAAAGATGCAGTATCAAGC 59.056 43.478 0.91 0.00 38.31 4.01
5774 9985 1.486211 CCGTCTCCTCAACCCTATGT 58.514 55.000 0.00 0.00 0.00 2.29
5832 10053 8.757789 CGTCAGACACTAGTGTATTGTTAAAAA 58.242 33.333 27.98 9.86 45.05 1.94
5833 10054 7.095940 GCGTCAGACACTAGTGTATTGTTAAAA 60.096 37.037 27.98 10.48 45.05 1.52
5834 10055 6.364165 GCGTCAGACACTAGTGTATTGTTAAA 59.636 38.462 27.98 10.80 45.05 1.52
5835 10056 5.860182 GCGTCAGACACTAGTGTATTGTTAA 59.140 40.000 27.98 11.12 45.05 2.01
5836 10057 5.182570 AGCGTCAGACACTAGTGTATTGTTA 59.817 40.000 27.98 11.75 45.05 2.41
5837 10058 4.022242 AGCGTCAGACACTAGTGTATTGTT 60.022 41.667 27.98 12.22 45.05 2.83
5838 10059 3.506455 AGCGTCAGACACTAGTGTATTGT 59.494 43.478 27.98 10.74 45.05 2.71
5839 10060 4.098055 AGCGTCAGACACTAGTGTATTG 57.902 45.455 27.98 25.64 45.05 1.90
5840 10061 3.128938 GGAGCGTCAGACACTAGTGTATT 59.871 47.826 27.98 16.49 45.05 1.89
5841 10062 2.683867 GGAGCGTCAGACACTAGTGTAT 59.316 50.000 27.98 22.69 45.05 2.29
5842 10063 2.082231 GGAGCGTCAGACACTAGTGTA 58.918 52.381 27.98 10.72 45.05 2.90
5844 10065 1.131504 GAGGAGCGTCAGACACTAGTG 59.868 57.143 21.44 21.44 0.00 2.74
5845 10066 1.455248 GAGGAGCGTCAGACACTAGT 58.545 55.000 0.41 0.00 0.00 2.57
5846 10067 0.736053 GGAGGAGCGTCAGACACTAG 59.264 60.000 0.41 0.00 0.00 2.57
5847 10068 0.328592 AGGAGGAGCGTCAGACACTA 59.671 55.000 0.41 0.00 0.00 2.74
5848 10069 0.963355 GAGGAGGAGCGTCAGACACT 60.963 60.000 0.41 0.00 0.00 3.55
5850 10071 0.251386 AAGAGGAGGAGCGTCAGACA 60.251 55.000 0.41 0.00 33.89 3.41
5851 10072 0.892063 AAAGAGGAGGAGCGTCAGAC 59.108 55.000 0.00 0.00 33.89 3.51
5852 10073 2.509166 TAAAGAGGAGGAGCGTCAGA 57.491 50.000 0.00 0.00 33.89 3.27
5853 10074 3.810310 AATAAAGAGGAGGAGCGTCAG 57.190 47.619 0.00 0.00 33.89 3.51
5854 10075 4.553330 AAAATAAAGAGGAGGAGCGTCA 57.447 40.909 0.00 0.00 33.89 4.35
5855 10076 6.281405 TCATAAAATAAAGAGGAGGAGCGTC 58.719 40.000 0.00 0.00 0.00 5.19
5856 10077 6.098409 TCTCATAAAATAAAGAGGAGGAGCGT 59.902 38.462 0.00 0.00 0.00 5.07
5871 11091 6.676189 AGAGGAGGAGGAGTTTCTCATAAAAT 59.324 38.462 0.00 0.00 35.58 1.82
5876 11096 3.774842 AGAGGAGGAGGAGTTTCTCAT 57.225 47.619 0.00 0.00 35.58 2.90
5969 11212 0.458197 CGGAGCTGCTGAAGACTCTG 60.458 60.000 7.01 4.88 32.68 3.35
5971 11214 0.457681 GACGGAGCTGCTGAAGACTC 60.458 60.000 7.01 0.00 0.00 3.36
5983 11226 0.796927 GGCTTTTAGTGTGACGGAGC 59.203 55.000 0.00 0.00 0.00 4.70
6047 11305 3.991773 TGTTACGAGGAAATTGTTCGAGG 59.008 43.478 11.86 0.00 37.73 4.63
6087 11349 8.752187 ACGGTCTGGTATACTACAAATTAAGAA 58.248 33.333 2.25 0.00 0.00 2.52
6090 11352 9.407380 TCTACGGTCTGGTATACTACAAATTAA 57.593 33.333 2.25 0.00 0.00 1.40
6091 11353 8.840321 GTCTACGGTCTGGTATACTACAAATTA 58.160 37.037 2.25 0.00 0.00 1.40
6094 11356 6.418101 AGTCTACGGTCTGGTATACTACAAA 58.582 40.000 2.25 0.00 30.72 2.83
6095 11357 5.994250 AGTCTACGGTCTGGTATACTACAA 58.006 41.667 2.25 0.00 30.72 2.41
6096 11358 5.620738 AGTCTACGGTCTGGTATACTACA 57.379 43.478 2.25 0.00 30.72 2.74
6097 11359 6.051717 TGAAGTCTACGGTCTGGTATACTAC 58.948 44.000 2.25 0.00 31.82 2.73
6098 11360 6.239217 TGAAGTCTACGGTCTGGTATACTA 57.761 41.667 2.25 0.00 31.82 1.82
6100 11362 5.764192 AGATGAAGTCTACGGTCTGGTATAC 59.236 44.000 0.00 0.00 34.69 1.47
6101 11363 5.938279 AGATGAAGTCTACGGTCTGGTATA 58.062 41.667 0.00 0.00 34.69 1.47
6102 11364 4.794334 AGATGAAGTCTACGGTCTGGTAT 58.206 43.478 0.00 0.00 34.69 2.73
6103 11365 4.197750 GAGATGAAGTCTACGGTCTGGTA 58.802 47.826 0.00 0.00 37.29 3.25
6104 11366 3.018149 GAGATGAAGTCTACGGTCTGGT 58.982 50.000 0.00 0.00 37.29 4.00
6105 11367 2.032302 CGAGATGAAGTCTACGGTCTGG 59.968 54.545 0.00 0.00 37.29 3.86
6106 11368 2.539953 GCGAGATGAAGTCTACGGTCTG 60.540 54.545 0.00 0.00 37.29 3.51
6107 11369 1.671845 GCGAGATGAAGTCTACGGTCT 59.328 52.381 0.00 0.00 37.29 3.85
6108 11370 1.268640 GGCGAGATGAAGTCTACGGTC 60.269 57.143 0.00 0.00 37.29 4.79
6111 11373 2.853731 AAGGCGAGATGAAGTCTACG 57.146 50.000 0.00 0.00 37.29 3.51
6144 11406 2.029828 GGCTCCATACGTGGTCTGATAG 60.030 54.545 0.00 0.00 46.16 2.08


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

AutoCloner maintained by Alex Coulton.