Multiple sequence alignment - TraesCS2B01G558000

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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 TraesCS2B01G558000 chr2B 100.000 2625 0 0 998 3622 752477042 752479666 0.000000e+00 4848.0
1 TraesCS2B01G558000 chr2B 84.257 1823 193 49 1014 2809 752406619 752408374 0.000000e+00 1690.0
2 TraesCS2B01G558000 chr2B 100.000 712 0 0 1 712 752476045 752476756 0.000000e+00 1315.0
3 TraesCS2B01G558000 chr2B 86.467 702 63 14 24 709 752405807 752406492 0.000000e+00 741.0
4 TraesCS2B01G558000 chr2B 85.069 288 28 8 3032 3307 752408582 752408866 2.750000e-71 279.0
5 TraesCS2B01G558000 chr2B 92.453 53 4 0 2928 2980 752408502 752408554 3.880000e-10 76.8
6 TraesCS2B01G558000 chrUn 85.989 1927 157 63 998 2883 9575041 9576895 0.000000e+00 1958.0
7 TraesCS2B01G558000 chrUn 92.970 697 35 9 20 709 9574235 9574924 0.000000e+00 1003.0
8 TraesCS2B01G558000 chrUn 83.784 259 20 7 3093 3351 9577077 9577313 3.640000e-55 226.0
9 TraesCS2B01G558000 chrUn 91.724 145 9 2 2885 3026 9576933 9577077 7.930000e-47 198.0
10 TraesCS2B01G558000 chrUn 92.248 129 5 1 3494 3622 9577315 9577438 1.030000e-40 178.0
11 TraesCS2B01G558000 chr2A 84.713 1727 167 55 998 2698 746936501 746938156 0.000000e+00 1637.0
12 TraesCS2B01G558000 chr2A 86.260 968 76 25 1884 2845 746952754 746953670 0.000000e+00 998.0
13 TraesCS2B01G558000 chr2A 85.994 714 63 21 20 709 746935683 746936383 0.000000e+00 730.0
14 TraesCS2B01G558000 chr2A 87.611 226 18 7 3132 3351 746954364 746954585 1.670000e-63 254.0
15 TraesCS2B01G558000 chr2A 87.442 215 16 4 2923 3137 746954104 746954307 1.680000e-58 237.0
16 TraesCS2B01G558000 chr2A 88.525 183 12 6 2234 2407 746963605 746963787 2.830000e-51 213.0
17 TraesCS2B01G558000 chr2A 77.561 410 46 21 2253 2652 746944806 746945179 4.740000e-49 206.0
18 TraesCS2B01G558000 chr2A 85.816 141 14 1 538 678 746944010 746944144 1.050000e-30 145.0
19 TraesCS2B01G558000 chr2A 88.596 114 12 1 3494 3607 746938898 746939010 1.750000e-28 137.0
20 TraesCS2B01G558000 chr2A 78.125 192 33 4 2926 3117 746964573 746964755 2.960000e-21 113.0
21 TraesCS2B01G558000 chr2A 100.000 44 0 0 2843 2886 746953944 746953987 8.340000e-12 82.4
22 TraesCS2B01G558000 chr2A 97.727 44 1 0 2885 2928 746954022 746954065 3.880000e-10 76.8
23 TraesCS2B01G558000 chr2A 100.000 34 0 0 3589 3622 746954647 746954680 3.020000e-06 63.9
24 TraesCS2B01G558000 chr5B 84.223 1686 174 48 1005 2640 61390433 61392076 0.000000e+00 1555.0
25 TraesCS2B01G558000 chr2D 86.845 859 79 26 1012 1850 616939833 616940677 0.000000e+00 929.0
26 TraesCS2B01G558000 chr2D 87.644 696 65 15 1979 2668 616940857 616941537 0.000000e+00 789.0
27 TraesCS2B01G558000 chr2D 84.339 696 67 24 24 712 616938531 616939191 0.000000e+00 643.0
28 TraesCS2B01G558000 chr2D 84.314 153 14 5 2234 2378 616947758 616947908 1.360000e-29 141.0
29 TraesCS2B01G558000 chr6B 87.390 682 82 4 1181 1860 710289728 710289049 0.000000e+00 780.0
30 TraesCS2B01G558000 chr6B 87.652 494 59 2 1181 1673 42368332 42368824 1.130000e-159 573.0
31 TraesCS2B01G558000 chr6B 86.667 150 13 3 3348 3492 16778284 16778137 3.740000e-35 159.0
32 TraesCS2B01G558000 chr6B 87.143 140 13 3 3356 3490 499568711 499568572 1.740000e-33 154.0
33 TraesCS2B01G558000 chr6B 86.765 136 13 1 3360 3490 372775873 372775738 2.910000e-31 147.0
34 TraesCS2B01G558000 chr7B 88.468 607 66 4 1181 1786 532036030 532036633 0.000000e+00 730.0
35 TraesCS2B01G558000 chr7B 80.308 325 58 5 1708 2029 295100945 295100624 1.300000e-59 241.0
36 TraesCS2B01G558000 chr7B 89.542 153 9 4 3347 3492 553132277 553132429 1.720000e-43 187.0
37 TraesCS2B01G558000 chr3B 87.854 494 57 3 1181 1673 773725719 773725228 8.720000e-161 577.0
38 TraesCS2B01G558000 chr4D 82.317 328 47 7 1705 2029 452822818 452823137 1.280000e-69 274.0
39 TraesCS2B01G558000 chr4A 80.000 325 58 6 1708 2029 610736671 610736351 2.170000e-57 233.0
40 TraesCS2B01G558000 chr7D 90.411 146 9 2 3354 3494 365316516 365316661 1.720000e-43 187.0
41 TraesCS2B01G558000 chr6A 89.474 152 10 2 3353 3498 15501121 15501272 1.720000e-43 187.0
42 TraesCS2B01G558000 chr3A 86.842 152 14 3 3353 3498 545898602 545898451 8.050000e-37 165.0
43 TraesCS2B01G558000 chr3D 87.943 141 12 2 3355 3490 586886327 586886467 1.040000e-35 161.0
44 TraesCS2B01G558000 chr5A 82.192 146 20 3 3350 3490 574332976 574333120 1.770000e-23 121.0


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 TraesCS2B01G558000 chr2B 752476045 752479666 3621 False 3081.500000 4848 100.000000 1 3622 2 chr2B.!!$F2 3621
1 TraesCS2B01G558000 chr2B 752405807 752408866 3059 False 696.700000 1690 87.061500 24 3307 4 chr2B.!!$F1 3283
2 TraesCS2B01G558000 chrUn 9574235 9577438 3203 False 712.600000 1958 89.343000 20 3622 5 chrUn.!!$F1 3602
3 TraesCS2B01G558000 chr2A 746935683 746939010 3327 False 834.666667 1637 86.434333 20 3607 3 chr2A.!!$F1 3587
4 TraesCS2B01G558000 chr2A 746952754 746954680 1926 False 285.350000 998 93.173333 1884 3622 6 chr2A.!!$F3 1738
5 TraesCS2B01G558000 chr5B 61390433 61392076 1643 False 1555.000000 1555 84.223000 1005 2640 1 chr5B.!!$F1 1635
6 TraesCS2B01G558000 chr2D 616938531 616941537 3006 False 787.000000 929 86.276000 24 2668 3 chr2D.!!$F2 2644
7 TraesCS2B01G558000 chr6B 710289049 710289728 679 True 780.000000 780 87.390000 1181 1860 1 chr6B.!!$R4 679
8 TraesCS2B01G558000 chr7B 532036030 532036633 603 False 730.000000 730 88.468000 1181 1786 1 chr7B.!!$F1 605

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
379 414 0.618968 ACACCCTGGAGGAGGTCATC 60.619 60.0 0.00 0.0 40.87 2.92 F
531 583 0.679505 TGCCTCTGTTACTCAAGCGT 59.320 50.0 0.00 0.0 0.00 5.07 F
532 584 1.071605 GCCTCTGTTACTCAAGCGTG 58.928 55.0 0.00 0.0 0.00 5.34 F
1703 2158 1.506493 AATCAGCATAGCTACTGCGC 58.494 50.0 17.04 0.0 44.38 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2524 0.036010 GCCAAGCTCTACTGCCTGAA 60.036 55.0 0.0 0.0 0.00 3.02 R
2484 3063 0.829333 TTGATGGCTCAGGCTCTCTC 59.171 55.0 0.0 0.0 38.73 3.20 R
2485 3064 0.831966 CTTGATGGCTCAGGCTCTCT 59.168 55.0 0.0 0.0 38.73 3.10 R
3419 4581 0.038159 AGCATCGTATTAGCCGCTCC 60.038 55.0 0.0 0.0 0.00 4.70 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
22 23 1.548081 TATGGACTTGACCGAACCGA 58.452 50.000 0.00 0.00 0.00 4.69
240 265 4.742201 CGGCCTGGACACGAGGTG 62.742 72.222 0.00 0.00 39.75 4.00
256 281 5.409520 CACGAGGTGATTAATATGGACATGG 59.590 44.000 0.00 0.00 35.23 3.66
379 414 0.618968 ACACCCTGGAGGAGGTCATC 60.619 60.000 0.00 0.00 40.87 2.92
400 435 3.699134 GATCAGGGGGTCGGCCAAC 62.699 68.421 9.07 0.00 36.17 3.77
520 572 3.134804 ACTCTGTGTTACTTTGCCTCTGT 59.865 43.478 0.00 0.00 0.00 3.41
526 578 5.054477 GTGTTACTTTGCCTCTGTTACTCA 58.946 41.667 0.00 0.00 0.00 3.41
527 579 5.526111 GTGTTACTTTGCCTCTGTTACTCAA 59.474 40.000 0.00 0.00 0.00 3.02
529 581 3.142174 ACTTTGCCTCTGTTACTCAAGC 58.858 45.455 0.00 0.00 0.00 4.01
531 583 0.679505 TGCCTCTGTTACTCAAGCGT 59.320 50.000 0.00 0.00 0.00 5.07
532 584 1.071605 GCCTCTGTTACTCAAGCGTG 58.928 55.000 0.00 0.00 0.00 5.34
533 585 1.605712 GCCTCTGTTACTCAAGCGTGT 60.606 52.381 0.00 0.00 0.00 4.49
534 586 2.755650 CCTCTGTTACTCAAGCGTGTT 58.244 47.619 0.00 0.00 0.00 3.32
535 587 3.859627 GCCTCTGTTACTCAAGCGTGTTA 60.860 47.826 0.00 0.00 0.00 2.41
536 588 3.673809 CCTCTGTTACTCAAGCGTGTTAC 59.326 47.826 0.00 0.00 0.00 2.50
565 618 1.761784 TGTGCTTTGAATGGGTTGCTT 59.238 42.857 0.00 0.00 0.00 3.91
1083 1484 2.028045 CGGTGAATTCGTTGAGACATCG 59.972 50.000 0.04 0.00 0.00 3.84
1125 1526 6.499234 TGTTCACAATGGTCAACATCATAG 57.501 37.500 0.00 0.00 39.40 2.23
1146 1567 7.561722 TCATAGGAATAACAGAGCAGTCTTACT 59.438 37.037 0.00 0.00 0.00 2.24
1291 1713 4.971125 GCTCGCCTATCCGCACCC 62.971 72.222 0.00 0.00 0.00 4.61
1393 1815 2.814336 GGTTGGAGAGGCAGTAAAAGTG 59.186 50.000 0.00 0.00 0.00 3.16
1395 1817 2.054799 TGGAGAGGCAGTAAAAGTGGT 58.945 47.619 0.00 0.00 0.00 4.16
1420 1845 6.199937 TGCTTATCATTCTTTGCCTCTTTC 57.800 37.500 0.00 0.00 0.00 2.62
1421 1846 5.163723 TGCTTATCATTCTTTGCCTCTTTCG 60.164 40.000 0.00 0.00 0.00 3.46
1461 1889 7.756722 GCAATTGCAAGTGACAATCTTATACTT 59.243 33.333 29.48 0.00 36.74 2.24
1528 1963 4.113354 GCTATAGAGTTCAACCACTTCCG 58.887 47.826 3.21 0.00 0.00 4.30
1658 2105 5.065218 ACAAGATGTGACAGTCTGAAAACAC 59.935 40.000 6.91 11.02 0.00 3.32
1665 2112 5.294552 GTGACAGTCTGAAAACACTTTAGCT 59.705 40.000 6.91 0.00 0.00 3.32
1669 2116 8.276252 ACAGTCTGAAAACACTTTAGCTTTTA 57.724 30.769 6.91 0.00 0.00 1.52
1701 2156 4.380531 TGGTAAATCAGCATAGCTACTGC 58.619 43.478 15.97 15.97 36.40 4.40
1703 2158 1.506493 AATCAGCATAGCTACTGCGC 58.494 50.000 17.04 0.00 44.38 6.09
1706 2161 1.593750 AGCATAGCTACTGCGCTGC 60.594 57.895 14.80 10.07 45.30 5.25
1745 2201 9.952188 GAAAGCTAATGTAGGGAAACATATTTC 57.048 33.333 0.00 0.00 43.11 2.17
1797 2254 9.606631 AGATTAAGAGACTGATTAAATGGTGAC 57.393 33.333 0.00 0.00 0.00 3.67
1813 2270 3.697045 TGGTGACATTCTTCCAACGTTTT 59.303 39.130 0.00 0.00 33.40 2.43
1827 2286 4.673311 CCAACGTTTTATTTGTGGAGAACG 59.327 41.667 0.00 5.07 43.68 3.95
1829 2288 3.231160 CGTTTTATTTGTGGAGAACGCC 58.769 45.455 0.00 0.00 34.41 5.68
2036 2585 4.736793 GCATTCTGTGAAGTTGTTCAACAG 59.263 41.667 16.31 7.73 44.44 3.16
2050 2599 2.047061 TCAACAGACTTGCCCAGTAGT 58.953 47.619 0.00 0.00 35.01 2.73
2117 2667 4.020573 TCAGAGGTGTGTTTGTATACCCTG 60.021 45.833 0.00 0.00 35.06 4.45
2139 2689 8.306761 CCCTGCTCTATAAATTTCTGTTTGTTT 58.693 33.333 0.00 0.00 0.00 2.83
2185 2738 7.919385 ATATTTGAGGGCAGTTTATTCCATT 57.081 32.000 0.00 0.00 0.00 3.16
2213 2766 8.780846 TTTACTATTTTGCTCGAACTGGATTA 57.219 30.769 0.00 0.00 0.00 1.75
2214 2767 8.780846 TTACTATTTTGCTCGAACTGGATTAA 57.219 30.769 0.00 0.00 0.00 1.40
2216 2769 8.281212 ACTATTTTGCTCGAACTGGATTAAAT 57.719 30.769 0.00 0.00 0.00 1.40
2218 2771 9.573133 CTATTTTGCTCGAACTGGATTAAATTT 57.427 29.630 0.00 0.00 0.00 1.82
2222 2775 6.386654 TGCTCGAACTGGATTAAATTTTTCC 58.613 36.000 11.21 11.21 0.00 3.13
2244 2797 8.616799 TTCCCCCAAAACTATATTTTTGCTAT 57.383 30.769 18.19 0.00 42.68 2.97
2245 2798 8.245195 TCCCCCAAAACTATATTTTTGCTATC 57.755 34.615 18.19 0.00 42.68 2.08
2246 2799 8.065007 TCCCCCAAAACTATATTTTTGCTATCT 58.935 33.333 18.19 0.00 42.68 1.98
2247 2800 8.704668 CCCCCAAAACTATATTTTTGCTATCTT 58.295 33.333 18.19 0.00 42.68 2.40
2248 2801 9.750125 CCCCAAAACTATATTTTTGCTATCTTC 57.250 33.333 18.19 0.00 42.68 2.87
2266 2821 7.012704 GCTATCTTCAATTCTGCATAGTTTCCA 59.987 37.037 0.00 0.00 0.00 3.53
2268 2823 7.325660 TCTTCAATTCTGCATAGTTTCCATC 57.674 36.000 0.00 0.00 0.00 3.51
2280 2835 6.255020 GCATAGTTTCCATCTTTGCTTTGATG 59.745 38.462 0.00 0.00 39.60 3.07
2313 2870 7.254252 CGATTAGTTCACTTGAATCAGGTCATC 60.254 40.741 0.00 0.00 36.33 2.92
2364 2921 3.129109 CACAAGCGAGCTATCATGTGAT 58.871 45.455 17.79 0.68 36.78 3.06
2394 2951 7.222872 CCTTAAGAGATCCATATGCTGTCTTT 58.777 38.462 16.10 5.01 0.00 2.52
2464 3032 3.548268 GCTAATGCACGACAGACTCTAAC 59.452 47.826 0.00 0.00 39.41 2.34
2484 3063 4.516365 ACGGTCACTAAGACTAAGGTTG 57.484 45.455 0.00 0.00 46.72 3.77
2485 3064 4.147321 ACGGTCACTAAGACTAAGGTTGA 58.853 43.478 0.00 0.00 46.72 3.18
2541 3120 1.273759 TGCACTGATGGCTCTTCTCT 58.726 50.000 0.00 0.00 0.00 3.10
2624 3203 6.813649 GTGAAGTTCTGAATGTCATGTAGCTA 59.186 38.462 4.17 0.00 0.00 3.32
2689 3275 6.909550 ATGGCTGTTTATTACCAAAAGACA 57.090 33.333 0.00 0.00 35.41 3.41
2711 3297 6.552008 ACATTCCATTTCTTGAAAGGGTAGA 58.448 36.000 21.20 12.12 35.30 2.59
2764 3350 7.633789 AGTACATGTAGATTGAAGTGGGAATT 58.366 34.615 5.62 0.00 0.00 2.17
2980 3929 1.460743 GGTTACCGCTTCAAACCGTAC 59.539 52.381 0.00 0.00 33.85 3.67
3010 3963 6.260050 TGGTATAGAAATGCTTTGGAATCGAC 59.740 38.462 0.00 0.00 0.00 4.20
3026 3979 1.808390 GACGTACCATGCACCGGTC 60.808 63.158 12.79 0.00 37.99 4.79
3027 3980 2.883730 CGTACCATGCACCGGTCG 60.884 66.667 12.79 12.12 37.99 4.79
3028 3981 2.263540 GTACCATGCACCGGTCGT 59.736 61.111 12.79 0.00 37.99 4.34
3029 3982 1.512230 GTACCATGCACCGGTCGTA 59.488 57.895 12.79 0.00 37.99 3.43
3030 3983 0.103572 GTACCATGCACCGGTCGTAT 59.896 55.000 12.79 2.63 37.99 3.06
3031 3984 0.103390 TACCATGCACCGGTCGTATG 59.897 55.000 20.23 20.23 37.99 2.39
3032 3985 1.142965 CCATGCACCGGTCGTATGA 59.857 57.895 25.25 2.44 0.00 2.15
3033 3986 0.875908 CCATGCACCGGTCGTATGAG 60.876 60.000 25.25 16.30 0.00 2.90
3081 4071 4.035558 TGACTGTCACAGCACTTCATTTTC 59.964 41.667 4.13 0.00 34.37 2.29
3088 4078 5.302568 TCACAGCACTTCATTTTCAAGGATT 59.697 36.000 0.00 0.00 0.00 3.01
3173 4247 6.777580 ACTCAATAGTTGGGATCAGTTTTGTT 59.222 34.615 0.00 0.00 34.45 2.83
3181 4255 2.487762 GGATCAGTTTTGTTCGCCATCA 59.512 45.455 0.00 0.00 0.00 3.07
3245 4404 1.076332 AAGTAGCAAACGCGTCATCC 58.924 50.000 14.44 1.09 0.00 3.51
3313 4473 1.258982 GTCGTTCTTGCACACAGTCAG 59.741 52.381 0.00 0.00 0.00 3.51
3325 4487 2.179427 CACAGTCAGGATGGAGGTGTA 58.821 52.381 0.00 0.00 36.16 2.90
3334 4496 3.456277 AGGATGGAGGTGTACATTTCCTC 59.544 47.826 21.97 20.33 44.78 3.71
3335 4497 3.458189 GATGGAGGTGTACATTTCCTCG 58.542 50.000 21.97 0.00 45.99 4.63
3337 4499 1.066430 GGAGGTGTACATTTCCTCGCA 60.066 52.381 19.44 0.00 45.99 5.10
3358 4520 2.656947 TGGGTGCCATTTATAGAGCC 57.343 50.000 0.00 0.00 0.00 4.70
3359 4521 2.135189 TGGGTGCCATTTATAGAGCCT 58.865 47.619 0.00 0.00 0.00 4.58
3360 4522 2.158623 TGGGTGCCATTTATAGAGCCTG 60.159 50.000 0.00 0.00 0.00 4.85
3361 4523 2.158608 GGGTGCCATTTATAGAGCCTGT 60.159 50.000 0.00 0.00 0.00 4.00
3362 4524 3.555966 GGTGCCATTTATAGAGCCTGTT 58.444 45.455 0.00 0.00 0.00 3.16
3363 4525 3.565902 GGTGCCATTTATAGAGCCTGTTC 59.434 47.826 0.00 0.00 0.00 3.18
3364 4526 3.248602 GTGCCATTTATAGAGCCTGTTCG 59.751 47.826 0.00 0.00 0.00 3.95
3365 4527 3.133901 TGCCATTTATAGAGCCTGTTCGA 59.866 43.478 0.00 0.00 0.00 3.71
3366 4528 4.127171 GCCATTTATAGAGCCTGTTCGAA 58.873 43.478 0.00 0.00 0.00 3.71
3367 4529 4.024809 GCCATTTATAGAGCCTGTTCGAAC 60.025 45.833 21.42 21.42 0.00 3.95
3368 4530 5.360591 CCATTTATAGAGCCTGTTCGAACT 58.639 41.667 27.32 8.68 0.00 3.01
3369 4531 5.463724 CCATTTATAGAGCCTGTTCGAACTC 59.536 44.000 27.32 16.89 0.00 3.01
3370 4532 4.650754 TTATAGAGCCTGTTCGAACTCC 57.349 45.455 27.32 15.59 0.00 3.85
3371 4533 1.183549 TAGAGCCTGTTCGAACTCCC 58.816 55.000 27.32 15.27 0.00 4.30
3372 4534 0.543174 AGAGCCTGTTCGAACTCCCT 60.543 55.000 27.32 19.22 0.00 4.20
3373 4535 0.108567 GAGCCTGTTCGAACTCCCTC 60.109 60.000 27.32 22.52 0.00 4.30
3374 4536 1.079057 GCCTGTTCGAACTCCCTCC 60.079 63.158 27.32 7.79 0.00 4.30
3375 4537 1.215647 CCTGTTCGAACTCCCTCCG 59.784 63.158 27.32 8.24 0.00 4.63
3376 4538 1.215647 CTGTTCGAACTCCCTCCGG 59.784 63.158 27.32 0.00 0.00 5.14
3377 4539 2.125633 GTTCGAACTCCCTCCGGC 60.126 66.667 20.97 0.00 0.00 6.13
3378 4540 2.283676 TTCGAACTCCCTCCGGCT 60.284 61.111 0.00 0.00 0.00 5.52
3379 4541 2.348888 TTCGAACTCCCTCCGGCTC 61.349 63.158 0.00 0.00 0.00 4.70
3380 4542 3.839432 CGAACTCCCTCCGGCTCC 61.839 72.222 0.00 0.00 0.00 4.70
3381 4543 3.839432 GAACTCCCTCCGGCTCCG 61.839 72.222 0.00 0.48 39.44 4.63
3387 4549 4.821589 CCTCCGGCTCCGCAACTC 62.822 72.222 0.00 0.00 38.24 3.01
3388 4550 4.821589 CTCCGGCTCCGCAACTCC 62.822 72.222 0.00 0.00 38.24 3.85
3390 4552 4.473520 CCGGCTCCGCAACTCCAT 62.474 66.667 2.18 0.00 38.24 3.41
3391 4553 2.436646 CGGCTCCGCAACTCCATT 60.437 61.111 0.00 0.00 0.00 3.16
3392 4554 2.464459 CGGCTCCGCAACTCCATTC 61.464 63.158 0.00 0.00 0.00 2.67
3393 4555 2.115291 GGCTCCGCAACTCCATTCC 61.115 63.158 0.00 0.00 0.00 3.01
3394 4556 2.464459 GCTCCGCAACTCCATTCCG 61.464 63.158 0.00 0.00 0.00 4.30
3395 4557 1.815421 CTCCGCAACTCCATTCCGG 60.815 63.158 0.00 0.00 40.25 5.14
3396 4558 2.238847 CTCCGCAACTCCATTCCGGA 62.239 60.000 0.00 0.00 44.85 5.14
3403 4565 2.586245 TCCATTCCGGAGCAGCAG 59.414 61.111 3.34 0.00 39.64 4.24
3404 4566 3.207669 CCATTCCGGAGCAGCAGC 61.208 66.667 3.34 0.00 42.56 5.25
3405 4567 3.207669 CATTCCGGAGCAGCAGCC 61.208 66.667 3.34 0.00 43.56 4.85
3406 4568 3.720601 ATTCCGGAGCAGCAGCCA 61.721 61.111 3.34 0.00 43.56 4.75
3407 4569 3.694058 ATTCCGGAGCAGCAGCCAG 62.694 63.158 3.34 0.00 43.56 4.85
3409 4571 4.711949 CCGGAGCAGCAGCCAGTT 62.712 66.667 0.00 0.00 43.56 3.16
3410 4572 3.429141 CGGAGCAGCAGCCAGTTG 61.429 66.667 0.00 0.00 43.56 3.16
3411 4573 2.282040 GGAGCAGCAGCCAGTTGT 60.282 61.111 0.00 0.00 43.56 3.32
3412 4574 1.003355 GGAGCAGCAGCCAGTTGTA 60.003 57.895 0.00 0.00 43.56 2.41
3413 4575 0.606401 GGAGCAGCAGCCAGTTGTAA 60.606 55.000 0.00 0.00 43.56 2.41
3414 4576 1.457346 GAGCAGCAGCCAGTTGTAAT 58.543 50.000 0.00 0.00 43.56 1.89
3415 4577 1.815003 GAGCAGCAGCCAGTTGTAATT 59.185 47.619 0.00 0.00 43.56 1.40
3416 4578 2.229784 GAGCAGCAGCCAGTTGTAATTT 59.770 45.455 0.00 0.00 43.56 1.82
3417 4579 3.420893 AGCAGCAGCCAGTTGTAATTTA 58.579 40.909 0.00 0.00 43.56 1.40
3418 4580 4.019174 AGCAGCAGCCAGTTGTAATTTAT 58.981 39.130 0.00 0.00 43.56 1.40
3419 4581 4.107622 GCAGCAGCCAGTTGTAATTTATG 58.892 43.478 0.00 0.00 33.58 1.90
3420 4582 4.675510 CAGCAGCCAGTTGTAATTTATGG 58.324 43.478 0.00 0.00 0.00 2.74
3421 4583 4.398988 CAGCAGCCAGTTGTAATTTATGGA 59.601 41.667 0.00 0.00 32.55 3.41
3422 4584 4.641989 AGCAGCCAGTTGTAATTTATGGAG 59.358 41.667 0.00 0.00 32.55 3.86
3423 4585 4.734695 GCAGCCAGTTGTAATTTATGGAGC 60.735 45.833 0.00 0.00 32.55 4.70
3424 4586 3.627577 AGCCAGTTGTAATTTATGGAGCG 59.372 43.478 0.00 0.00 32.55 5.03
3425 4587 3.243068 GCCAGTTGTAATTTATGGAGCGG 60.243 47.826 0.00 0.00 32.55 5.52
3426 4588 3.243068 CCAGTTGTAATTTATGGAGCGGC 60.243 47.826 0.00 0.00 32.55 6.53
3427 4589 3.627577 CAGTTGTAATTTATGGAGCGGCT 59.372 43.478 0.00 0.00 0.00 5.52
3428 4590 4.814234 CAGTTGTAATTTATGGAGCGGCTA 59.186 41.667 0.60 0.00 0.00 3.93
3429 4591 5.295787 CAGTTGTAATTTATGGAGCGGCTAA 59.704 40.000 0.60 0.00 0.00 3.09
3430 4592 6.017109 CAGTTGTAATTTATGGAGCGGCTAAT 60.017 38.462 0.60 2.42 0.00 1.73
3431 4593 7.172532 CAGTTGTAATTTATGGAGCGGCTAATA 59.827 37.037 0.60 1.33 0.00 0.98
3432 4594 7.172703 AGTTGTAATTTATGGAGCGGCTAATAC 59.827 37.037 0.60 0.00 0.00 1.89
3433 4595 5.636121 TGTAATTTATGGAGCGGCTAATACG 59.364 40.000 0.60 0.00 0.00 3.06
3434 4596 4.530710 ATTTATGGAGCGGCTAATACGA 57.469 40.909 0.60 0.00 0.00 3.43
3435 4597 4.530710 TTTATGGAGCGGCTAATACGAT 57.469 40.909 0.60 0.00 0.00 3.73
3436 4598 2.370281 ATGGAGCGGCTAATACGATG 57.630 50.000 0.60 0.00 0.00 3.84
3437 4599 0.319555 TGGAGCGGCTAATACGATGC 60.320 55.000 0.60 0.00 38.55 3.91
3438 4600 0.038159 GGAGCGGCTAATACGATGCT 60.038 55.000 0.60 0.00 35.23 3.79
3439 4601 1.341606 GAGCGGCTAATACGATGCTC 58.658 55.000 0.60 0.00 41.57 4.26
3440 4602 0.038159 AGCGGCTAATACGATGCTCC 60.038 55.000 0.00 0.00 0.00 4.70
3441 4603 1.344942 GCGGCTAATACGATGCTCCG 61.345 60.000 0.00 0.00 38.51 4.63
3442 4604 1.344942 CGGCTAATACGATGCTCCGC 61.345 60.000 0.00 0.00 0.00 5.54
3443 4605 1.014564 GGCTAATACGATGCTCCGCC 61.015 60.000 0.00 0.00 0.00 6.13
3444 4606 1.014564 GCTAATACGATGCTCCGCCC 61.015 60.000 0.00 0.00 0.00 6.13
3445 4607 0.732880 CTAATACGATGCTCCGCCCG 60.733 60.000 0.00 0.00 0.00 6.13
3446 4608 2.758770 TAATACGATGCTCCGCCCGC 62.759 60.000 0.00 0.00 0.00 6.13
3463 4625 4.180946 CTCCGCTCCGTGACCGAG 62.181 72.222 0.00 0.00 35.63 4.63
3466 4628 3.518998 CGCTCCGTGACCGAGGAT 61.519 66.667 3.29 0.00 35.75 3.24
3467 4629 2.893398 GCTCCGTGACCGAGGATT 59.107 61.111 3.29 0.00 35.75 3.01
3468 4630 1.519455 GCTCCGTGACCGAGGATTG 60.519 63.158 3.29 0.00 35.75 2.67
3470 4632 1.304630 TCCGTGACCGAGGATTGGA 60.305 57.895 0.00 0.00 45.05 3.53
3471 4633 1.141881 CCGTGACCGAGGATTGGAG 59.858 63.158 0.00 0.00 45.05 3.86
3472 4634 1.141881 CGTGACCGAGGATTGGAGG 59.858 63.158 0.00 0.00 45.05 4.30
3473 4635 1.522569 GTGACCGAGGATTGGAGGG 59.477 63.158 0.00 0.00 45.05 4.30
3474 4636 1.080354 TGACCGAGGATTGGAGGGT 59.920 57.895 0.00 0.00 45.05 4.34
3475 4637 0.546747 TGACCGAGGATTGGAGGGTT 60.547 55.000 0.00 0.00 45.05 4.11
3476 4638 0.107654 GACCGAGGATTGGAGGGTTG 60.108 60.000 0.00 0.00 45.05 3.77
3477 4639 1.452108 CCGAGGATTGGAGGGTTGC 60.452 63.158 0.00 0.00 45.05 4.17
3478 4640 1.452108 CGAGGATTGGAGGGTTGCC 60.452 63.158 0.00 0.00 0.00 4.52
3479 4641 1.452108 GAGGATTGGAGGGTTGCCG 60.452 63.158 0.00 0.00 0.00 5.69
3480 4642 1.910580 GAGGATTGGAGGGTTGCCGA 61.911 60.000 0.00 0.00 0.00 5.54
3481 4643 1.001393 GGATTGGAGGGTTGCCGAA 60.001 57.895 0.00 0.00 0.00 4.30
3482 4644 1.313091 GGATTGGAGGGTTGCCGAAC 61.313 60.000 0.00 0.00 0.00 3.95
3483 4645 0.608035 GATTGGAGGGTTGCCGAACA 60.608 55.000 0.00 0.00 33.27 3.18
3484 4646 0.893727 ATTGGAGGGTTGCCGAACAC 60.894 55.000 0.00 0.00 35.50 3.32
3485 4647 2.112297 GGAGGGTTGCCGAACACA 59.888 61.111 0.00 0.00 38.03 3.72
3486 4648 1.966451 GGAGGGTTGCCGAACACAG 60.966 63.158 0.00 0.00 38.03 3.66
3487 4649 2.594592 AGGGTTGCCGAACACAGC 60.595 61.111 0.00 0.00 38.03 4.40
3488 4650 3.670377 GGGTTGCCGAACACAGCC 61.670 66.667 0.00 0.00 35.34 4.85
3489 4651 2.594592 GGTTGCCGAACACAGCCT 60.595 61.111 0.00 0.00 35.68 4.58
3490 4652 2.193536 GGTTGCCGAACACAGCCTT 61.194 57.895 0.00 0.00 35.68 4.35
3491 4653 0.887387 GGTTGCCGAACACAGCCTTA 60.887 55.000 0.00 0.00 35.68 2.69
3492 4654 0.948678 GTTGCCGAACACAGCCTTAA 59.051 50.000 0.00 0.00 31.78 1.85
3573 4735 1.278127 CCCACACTAATGTCCCGTTCT 59.722 52.381 0.00 0.00 36.72 3.01
3585 4747 1.515954 CCGTTCTACCGCACATCCT 59.484 57.895 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.607635 CGGTTCGGTCAAGTCCATATTG 59.392 50.000 0.00 0.00 0.00 1.90
1 2 2.498481 TCGGTTCGGTCAAGTCCATATT 59.502 45.455 0.00 0.00 0.00 1.28
2 3 2.100916 CTCGGTTCGGTCAAGTCCATAT 59.899 50.000 0.00 0.00 0.00 1.78
3 4 1.475280 CTCGGTTCGGTCAAGTCCATA 59.525 52.381 0.00 0.00 0.00 2.74
4 5 0.246635 CTCGGTTCGGTCAAGTCCAT 59.753 55.000 0.00 0.00 0.00 3.41
5 6 0.824595 TCTCGGTTCGGTCAAGTCCA 60.825 55.000 0.00 0.00 0.00 4.02
6 7 0.109226 CTCTCGGTTCGGTCAAGTCC 60.109 60.000 0.00 0.00 0.00 3.85
7 8 0.109226 CCTCTCGGTTCGGTCAAGTC 60.109 60.000 0.00 0.00 0.00 3.01
8 9 1.965219 CCTCTCGGTTCGGTCAAGT 59.035 57.895 0.00 0.00 0.00 3.16
9 10 1.446272 GCCTCTCGGTTCGGTCAAG 60.446 63.158 0.00 0.00 0.00 3.02
10 11 2.204461 TGCCTCTCGGTTCGGTCAA 61.204 57.895 0.00 0.00 0.00 3.18
11 12 2.599281 TGCCTCTCGGTTCGGTCA 60.599 61.111 0.00 0.00 0.00 4.02
12 13 2.126031 GTGCCTCTCGGTTCGGTC 60.126 66.667 0.00 0.00 0.00 4.79
13 14 2.600769 AGTGCCTCTCGGTTCGGT 60.601 61.111 0.00 0.00 0.00 4.69
14 15 2.182030 GAGTGCCTCTCGGTTCGG 59.818 66.667 0.00 0.00 33.25 4.30
22 23 2.034376 ACGGAGTCGAGTGCCTCT 59.966 61.111 6.15 0.00 29.74 3.69
90 91 0.106066 TGAATGTGGGATGGATGGGC 60.106 55.000 0.00 0.00 0.00 5.36
240 265 5.106555 CGGTTCAGCCATGTCCATATTAATC 60.107 44.000 0.00 0.00 36.97 1.75
256 281 0.039527 ATTTGGCGTTTCGGTTCAGC 60.040 50.000 0.00 0.00 0.00 4.26
287 312 1.892474 AGTTCTCTGAGTCCAGCAGAC 59.108 52.381 4.32 0.00 46.71 3.51
400 435 1.025812 AGTCCTTGAGCGATCCTACG 58.974 55.000 0.00 0.00 0.00 3.51
442 477 1.543429 GGGAATAATCAGCTCACCGGG 60.543 57.143 6.32 0.00 0.00 5.73
520 572 5.590145 TGTAACAGTAACACGCTTGAGTAA 58.410 37.500 0.00 0.00 0.00 2.24
526 578 4.553938 GCACAATGTAACAGTAACACGCTT 60.554 41.667 0.00 0.00 0.00 4.68
527 579 3.059188 GCACAATGTAACAGTAACACGCT 60.059 43.478 0.00 0.00 0.00 5.07
529 581 4.725556 AGCACAATGTAACAGTAACACG 57.274 40.909 0.00 0.00 0.00 4.49
531 583 6.685527 TCAAAGCACAATGTAACAGTAACA 57.314 33.333 0.00 0.00 0.00 2.41
532 584 7.114811 CCATTCAAAGCACAATGTAACAGTAAC 59.885 37.037 0.00 0.00 0.00 2.50
533 585 7.144661 CCATTCAAAGCACAATGTAACAGTAA 58.855 34.615 0.00 0.00 0.00 2.24
534 586 6.294453 CCCATTCAAAGCACAATGTAACAGTA 60.294 38.462 0.00 0.00 0.00 2.74
535 587 5.509501 CCCATTCAAAGCACAATGTAACAGT 60.510 40.000 0.00 0.00 0.00 3.55
536 588 4.925054 CCCATTCAAAGCACAATGTAACAG 59.075 41.667 0.00 0.00 0.00 3.16
565 618 4.682787 CGAGCTACAACTGAATCCACATA 58.317 43.478 0.00 0.00 0.00 2.29
1010 1063 4.401022 TGGATTTTGCATCTGAAGTGAGT 58.599 39.130 0.00 0.00 0.00 3.41
1044 1445 2.300723 ACCGTAGCAGTTGTCAACCATA 59.699 45.455 12.17 0.59 0.00 2.74
1125 1526 8.950208 ATTAAGTAAGACTGCTCTGTTATTCC 57.050 34.615 0.00 0.00 0.00 3.01
1146 1567 4.505808 CTGTCATGCAAATGCCCAATTAA 58.494 39.130 2.46 0.00 41.18 1.40
1291 1713 0.889186 CAAACTCCACCCCAAGTCCG 60.889 60.000 0.00 0.00 0.00 4.79
1294 1716 1.293683 ACCCAAACTCCACCCCAAGT 61.294 55.000 0.00 0.00 0.00 3.16
1393 1815 5.077134 AGGCAAAGAATGATAAGCAAACC 57.923 39.130 0.00 0.00 0.00 3.27
1395 1817 6.594788 AAGAGGCAAAGAATGATAAGCAAA 57.405 33.333 0.00 0.00 0.00 3.68
1420 1845 4.520078 GCAATTGCATGCATAATTTTCCG 58.480 39.130 25.36 8.30 45.70 4.30
1588 2024 9.817365 CCTAGTGAATTATTGCGAAATATTCTG 57.183 33.333 14.30 0.00 0.00 3.02
1598 2034 6.258727 ACTCATGTTCCTAGTGAATTATTGCG 59.741 38.462 0.00 0.00 34.90 4.85
1602 2038 7.092891 TGGACACTCATGTTCCTAGTGAATTAT 60.093 37.037 16.07 0.00 42.59 1.28
1669 2116 9.101655 GCTATGCTGATTTACCAAAAATCAATT 57.898 29.630 12.68 5.26 43.55 2.32
1673 2127 8.624776 AGTAGCTATGCTGATTTACCAAAAATC 58.375 33.333 0.00 3.98 40.10 2.17
1701 2156 1.559831 TCTGAATATGTGACGCAGCG 58.440 50.000 14.82 14.82 0.00 5.18
1703 2158 3.620374 AGCTTTCTGAATATGTGACGCAG 59.380 43.478 0.00 0.00 0.00 5.18
1706 2161 7.239166 ACATTAGCTTTCTGAATATGTGACG 57.761 36.000 0.00 0.00 0.00 4.35
1774 2230 9.739276 AATGTCACCATTTAATCAGTCTCTTAA 57.261 29.630 0.00 0.00 38.10 1.85
1787 2244 5.067273 ACGTTGGAAGAATGTCACCATTTA 58.933 37.500 0.00 0.00 41.37 1.40
1793 2250 7.434013 ACAAATAAAACGTTGGAAGAATGTCAC 59.566 33.333 0.00 0.00 0.00 3.67
1796 2253 6.699642 CCACAAATAAAACGTTGGAAGAATGT 59.300 34.615 0.00 0.00 0.00 2.71
1797 2254 6.920758 TCCACAAATAAAACGTTGGAAGAATG 59.079 34.615 0.00 0.00 0.00 2.67
1799 2256 6.319152 TCTCCACAAATAAAACGTTGGAAGAA 59.681 34.615 0.00 0.00 0.00 2.52
1808 2265 3.058501 AGGCGTTCTCCACAAATAAAACG 60.059 43.478 0.00 0.00 41.59 3.60
1813 2270 1.948611 GCCAGGCGTTCTCCACAAATA 60.949 52.381 0.00 0.00 0.00 1.40
1827 2286 1.941999 GATGGTTTCTGCAGCCAGGC 61.942 60.000 9.47 1.84 39.61 4.85
1829 2288 2.408271 TAGATGGTTTCTGCAGCCAG 57.592 50.000 9.47 0.00 40.54 4.85
1957 2506 6.323482 TGCCTGAAAGCAAAATAGCCAATATA 59.677 34.615 0.00 0.00 40.56 0.86
1964 2513 3.582714 ACTGCCTGAAAGCAAAATAGC 57.417 42.857 0.00 0.00 43.52 2.97
1965 2514 5.448360 GCTCTACTGCCTGAAAGCAAAATAG 60.448 44.000 0.00 0.00 43.52 1.73
1967 2516 3.192212 GCTCTACTGCCTGAAAGCAAAAT 59.808 43.478 0.00 0.00 43.52 1.82
1972 2521 1.736681 CAAGCTCTACTGCCTGAAAGC 59.263 52.381 0.00 0.00 0.00 3.51
1975 2524 0.036010 GCCAAGCTCTACTGCCTGAA 60.036 55.000 0.00 0.00 0.00 3.02
1976 2525 1.194121 TGCCAAGCTCTACTGCCTGA 61.194 55.000 0.00 0.00 0.00 3.86
2036 2585 3.521947 AACGATACTACTGGGCAAGTC 57.478 47.619 0.00 0.00 40.56 3.01
2050 2599 4.799419 GCGGTTGGCTTAATAAACGATA 57.201 40.909 8.35 0.00 39.20 2.92
2185 2738 8.780846 TCCAGTTCGAGCAAAATAGTAAATAA 57.219 30.769 1.01 0.00 0.00 1.40
2203 2756 6.367374 TGGGGGAAAAATTTAATCCAGTTC 57.633 37.500 19.26 6.62 34.82 3.01
2216 2769 8.221251 AGCAAAAATATAGTTTTGGGGGAAAAA 58.779 29.630 29.37 0.00 44.90 1.94
2218 2771 7.323052 AGCAAAAATATAGTTTTGGGGGAAA 57.677 32.000 29.37 0.00 44.90 3.13
2222 2775 9.750125 GAAGATAGCAAAAATATAGTTTTGGGG 57.250 33.333 29.37 12.92 44.90 4.96
2244 2797 7.114754 AGATGGAAACTATGCAGAATTGAAGA 58.885 34.615 0.00 0.00 30.55 2.87
2245 2798 7.330900 AGATGGAAACTATGCAGAATTGAAG 57.669 36.000 0.00 0.00 30.55 3.02
2246 2799 7.707624 AAGATGGAAACTATGCAGAATTGAA 57.292 32.000 0.00 0.00 30.55 2.69
2247 2800 7.541162 CAAAGATGGAAACTATGCAGAATTGA 58.459 34.615 0.00 0.00 30.55 2.57
2248 2801 6.255020 GCAAAGATGGAAACTATGCAGAATTG 59.745 38.462 0.00 0.00 30.55 2.32
2249 2802 6.154021 AGCAAAGATGGAAACTATGCAGAATT 59.846 34.615 0.00 0.00 34.89 2.17
2250 2803 5.655532 AGCAAAGATGGAAACTATGCAGAAT 59.344 36.000 0.00 0.00 34.89 2.40
2287 2842 5.869344 TGACCTGATTCAAGTGAACTAATCG 59.131 40.000 0.00 0.00 36.80 3.34
2313 2870 1.522668 TGAATGTCCCGTCAGCAAAG 58.477 50.000 0.00 0.00 0.00 2.77
2364 2921 2.212752 ATGGATCTCTTAAGGGCCCA 57.787 50.000 27.56 15.65 0.00 5.36
2394 2951 6.166279 GTCAATTCTCATACTGACCTGACAA 58.834 40.000 0.00 0.00 33.57 3.18
2464 3032 4.458295 TCTCAACCTTAGTCTTAGTGACCG 59.542 45.833 0.00 0.00 46.46 4.79
2484 3063 0.829333 TTGATGGCTCAGGCTCTCTC 59.171 55.000 0.00 0.00 38.73 3.20
2485 3064 0.831966 CTTGATGGCTCAGGCTCTCT 59.168 55.000 0.00 0.00 38.73 3.10
2541 3120 3.689161 CCCTGCATCAATACGTTTCAAGA 59.311 43.478 0.00 0.00 0.00 3.02
2689 3275 6.794534 AGTCTACCCTTTCAAGAAATGGAAT 58.205 36.000 19.39 5.05 38.02 3.01
2744 3330 7.941238 CCTGATAATTCCCACTTCAATCTACAT 59.059 37.037 0.00 0.00 0.00 2.29
2764 3350 9.330063 CAAGCAAACTATGAAGATTACCTGATA 57.670 33.333 0.00 0.00 0.00 2.15
2980 3929 4.339247 CCAAAGCATTTCTATACCACCTGG 59.661 45.833 0.00 0.00 35.03 4.45
3010 3963 2.268988 TACGACCGGTGCATGGTACG 62.269 60.000 14.63 9.53 40.63 3.67
3026 3979 2.247311 GCAGTTGGCAAACTCATACG 57.753 50.000 2.59 0.00 45.07 3.06
3047 4018 5.888161 TGCTGTGACAGTCATCTATCTCTTA 59.112 40.000 14.82 0.00 33.43 2.10
3081 4071 4.549458 CTTGGTACACAAAGCAATCCTTG 58.451 43.478 0.00 0.00 39.29 3.61
3088 4078 2.554344 GGATCCCTTGGTACACAAAGCA 60.554 50.000 0.00 0.00 39.29 3.91
3173 4247 2.659063 CCCACCAGACTGATGGCGA 61.659 63.158 10.81 0.00 44.80 5.54
3181 4255 3.161557 GGAGCAACCCACCAGACT 58.838 61.111 0.00 0.00 0.00 3.24
3191 4267 1.044611 CCTAGCTAGGAGGGAGCAAC 58.955 60.000 32.79 0.00 46.63 4.17
3236 4395 0.872021 GAGGTAAGCAGGATGACGCG 60.872 60.000 3.53 3.53 39.69 6.01
3237 4396 0.461961 AGAGGTAAGCAGGATGACGC 59.538 55.000 0.00 0.00 39.69 5.19
3245 4404 1.021390 CGGTGGCAAGAGGTAAGCAG 61.021 60.000 0.00 0.00 0.00 4.24
3295 4455 0.583438 CCTGACTGTGTGCAAGAACG 59.417 55.000 0.00 0.00 0.00 3.95
3313 4473 3.741388 CGAGGAAATGTACACCTCCATCC 60.741 52.174 21.49 12.63 44.96 3.51
3325 4487 1.176527 CACCCATTGCGAGGAAATGT 58.823 50.000 0.00 0.00 33.93 2.71
3351 4513 1.757699 GGGAGTTCGAACAGGCTCTAT 59.242 52.381 28.78 6.59 0.00 1.98
3352 4514 1.183549 GGGAGTTCGAACAGGCTCTA 58.816 55.000 28.78 0.00 0.00 2.43
3353 4515 0.543174 AGGGAGTTCGAACAGGCTCT 60.543 55.000 28.78 19.23 0.00 4.09
3354 4516 0.108567 GAGGGAGTTCGAACAGGCTC 60.109 60.000 28.78 17.28 0.00 4.70
3355 4517 1.545706 GGAGGGAGTTCGAACAGGCT 61.546 60.000 28.78 9.31 0.00 4.58
3356 4518 1.079057 GGAGGGAGTTCGAACAGGC 60.079 63.158 28.78 17.17 0.00 4.85
3357 4519 1.215647 CGGAGGGAGTTCGAACAGG 59.784 63.158 28.78 6.89 0.00 4.00
3358 4520 4.891566 CGGAGGGAGTTCGAACAG 57.108 61.111 28.78 8.09 0.00 3.16
3377 4539 3.799753 CGGAATGGAGTTGCGGAG 58.200 61.111 0.00 0.00 46.35 4.63
3387 4549 3.207669 GCTGCTGCTCCGGAATGG 61.208 66.667 5.23 0.00 40.09 3.16
3388 4550 3.207669 GGCTGCTGCTCCGGAATG 61.208 66.667 15.64 0.00 39.59 2.67
3389 4551 3.694058 CTGGCTGCTGCTCCGGAAT 62.694 63.158 15.64 0.00 39.59 3.01
3390 4552 4.399395 CTGGCTGCTGCTCCGGAA 62.399 66.667 15.64 0.00 39.59 4.30
3392 4554 4.711949 AACTGGCTGCTGCTCCGG 62.712 66.667 15.64 15.46 39.59 5.14
3393 4555 2.786539 TACAACTGGCTGCTGCTCCG 62.787 60.000 15.64 6.64 39.59 4.63
3394 4556 0.606401 TTACAACTGGCTGCTGCTCC 60.606 55.000 15.64 2.78 39.59 4.70
3395 4557 1.457346 ATTACAACTGGCTGCTGCTC 58.543 50.000 15.64 6.34 39.59 4.26
3396 4558 1.915141 AATTACAACTGGCTGCTGCT 58.085 45.000 15.64 0.00 39.59 4.24
3397 4559 2.730550 AAATTACAACTGGCTGCTGC 57.269 45.000 7.10 7.10 38.76 5.25
3398 4560 4.398988 TCCATAAATTACAACTGGCTGCTG 59.601 41.667 0.00 0.00 0.00 4.41
3399 4561 4.599041 TCCATAAATTACAACTGGCTGCT 58.401 39.130 0.00 0.00 0.00 4.24
3400 4562 4.734695 GCTCCATAAATTACAACTGGCTGC 60.735 45.833 0.00 0.00 0.00 5.25
3401 4563 4.496341 CGCTCCATAAATTACAACTGGCTG 60.496 45.833 0.00 0.00 0.00 4.85
3402 4564 3.627577 CGCTCCATAAATTACAACTGGCT 59.372 43.478 0.00 0.00 0.00 4.75
3403 4565 3.243068 CCGCTCCATAAATTACAACTGGC 60.243 47.826 0.00 0.00 0.00 4.85
3404 4566 3.243068 GCCGCTCCATAAATTACAACTGG 60.243 47.826 0.00 0.00 0.00 4.00
3405 4567 3.627577 AGCCGCTCCATAAATTACAACTG 59.372 43.478 0.00 0.00 0.00 3.16
3406 4568 3.886123 AGCCGCTCCATAAATTACAACT 58.114 40.909 0.00 0.00 0.00 3.16
3407 4569 5.744666 TTAGCCGCTCCATAAATTACAAC 57.255 39.130 0.00 0.00 0.00 3.32
3408 4570 6.146510 CGTATTAGCCGCTCCATAAATTACAA 59.853 38.462 0.00 0.00 0.00 2.41
3409 4571 5.636121 CGTATTAGCCGCTCCATAAATTACA 59.364 40.000 0.00 0.00 0.00 2.41
3410 4572 5.865552 TCGTATTAGCCGCTCCATAAATTAC 59.134 40.000 0.00 0.00 0.00 1.89
3411 4573 6.028146 TCGTATTAGCCGCTCCATAAATTA 57.972 37.500 0.00 0.00 0.00 1.40
3412 4574 4.890088 TCGTATTAGCCGCTCCATAAATT 58.110 39.130 0.00 0.00 0.00 1.82
3413 4575 4.530710 TCGTATTAGCCGCTCCATAAAT 57.469 40.909 0.00 0.00 0.00 1.40
3414 4576 4.242475 CATCGTATTAGCCGCTCCATAAA 58.758 43.478 0.00 0.00 0.00 1.40
3415 4577 3.845178 CATCGTATTAGCCGCTCCATAA 58.155 45.455 0.00 0.00 0.00 1.90
3416 4578 2.416836 GCATCGTATTAGCCGCTCCATA 60.417 50.000 0.00 0.00 0.00 2.74
3417 4579 1.673033 GCATCGTATTAGCCGCTCCAT 60.673 52.381 0.00 0.00 0.00 3.41
3418 4580 0.319555 GCATCGTATTAGCCGCTCCA 60.320 55.000 0.00 0.00 0.00 3.86
3419 4581 0.038159 AGCATCGTATTAGCCGCTCC 60.038 55.000 0.00 0.00 0.00 4.70
3420 4582 1.341606 GAGCATCGTATTAGCCGCTC 58.658 55.000 0.00 0.00 39.10 5.03
3421 4583 0.038159 GGAGCATCGTATTAGCCGCT 60.038 55.000 0.00 0.00 34.37 5.52
3422 4584 1.344942 CGGAGCATCGTATTAGCCGC 61.345 60.000 0.00 0.00 34.37 6.53
3423 4585 2.725644 CGGAGCATCGTATTAGCCG 58.274 57.895 0.00 0.00 34.37 5.52
3450 4612 1.519455 CAATCCTCGGTCACGGAGC 60.519 63.158 6.85 0.00 41.39 4.70
3451 4613 1.141881 CCAATCCTCGGTCACGGAG 59.858 63.158 5.38 5.38 41.39 4.63
3452 4614 1.304630 TCCAATCCTCGGTCACGGA 60.305 57.895 0.00 0.00 41.39 4.69
3453 4615 1.141881 CTCCAATCCTCGGTCACGG 59.858 63.158 0.00 0.00 41.39 4.94
3454 4616 1.141881 CCTCCAATCCTCGGTCACG 59.858 63.158 0.00 0.00 42.74 4.35
3455 4617 1.265454 ACCCTCCAATCCTCGGTCAC 61.265 60.000 0.00 0.00 0.00 3.67
3456 4618 0.546747 AACCCTCCAATCCTCGGTCA 60.547 55.000 0.00 0.00 0.00 4.02
3457 4619 0.107654 CAACCCTCCAATCCTCGGTC 60.108 60.000 0.00 0.00 0.00 4.79
3458 4620 1.991230 CAACCCTCCAATCCTCGGT 59.009 57.895 0.00 0.00 0.00 4.69
3459 4621 1.452108 GCAACCCTCCAATCCTCGG 60.452 63.158 0.00 0.00 0.00 4.63
3460 4622 1.452108 GGCAACCCTCCAATCCTCG 60.452 63.158 0.00 0.00 0.00 4.63
3461 4623 1.452108 CGGCAACCCTCCAATCCTC 60.452 63.158 0.00 0.00 0.00 3.71
3462 4624 1.497309 TTCGGCAACCCTCCAATCCT 61.497 55.000 0.00 0.00 0.00 3.24
3463 4625 1.001393 TTCGGCAACCCTCCAATCC 60.001 57.895 0.00 0.00 0.00 3.01
3464 4626 0.608035 TGTTCGGCAACCCTCCAATC 60.608 55.000 0.00 0.00 0.00 2.67
3465 4627 0.893727 GTGTTCGGCAACCCTCCAAT 60.894 55.000 0.00 0.00 0.00 3.16
3466 4628 1.527380 GTGTTCGGCAACCCTCCAA 60.527 57.895 0.00 0.00 0.00 3.53
3467 4629 2.112297 GTGTTCGGCAACCCTCCA 59.888 61.111 0.00 0.00 0.00 3.86
3468 4630 1.966451 CTGTGTTCGGCAACCCTCC 60.966 63.158 0.00 0.00 0.00 4.30
3469 4631 2.617274 GCTGTGTTCGGCAACCCTC 61.617 63.158 0.00 0.00 44.61 4.30
3470 4632 2.594592 GCTGTGTTCGGCAACCCT 60.595 61.111 0.00 0.00 44.61 4.34
3471 4633 3.670377 GGCTGTGTTCGGCAACCC 61.670 66.667 1.58 0.00 46.81 4.11
3472 4634 0.887387 TAAGGCTGTGTTCGGCAACC 60.887 55.000 0.00 0.00 46.81 3.77
3473 4635 0.948678 TTAAGGCTGTGTTCGGCAAC 59.051 50.000 0.00 0.00 46.81 4.17
3474 4636 1.904287 ATTAAGGCTGTGTTCGGCAA 58.096 45.000 0.00 0.00 46.81 4.52
3475 4637 1.904287 AATTAAGGCTGTGTTCGGCA 58.096 45.000 0.00 0.00 46.81 5.69
3476 4638 2.745281 TGTAATTAAGGCTGTGTTCGGC 59.255 45.455 0.00 0.00 44.51 5.54
3477 4639 5.560966 AATGTAATTAAGGCTGTGTTCGG 57.439 39.130 0.00 0.00 32.46 4.30
3478 4640 8.018520 TGTAAAATGTAATTAAGGCTGTGTTCG 58.981 33.333 0.00 0.00 33.67 3.95
3479 4641 9.685828 TTGTAAAATGTAATTAAGGCTGTGTTC 57.314 29.630 0.00 0.00 33.67 3.18
3480 4642 9.691362 CTTGTAAAATGTAATTAAGGCTGTGTT 57.309 29.630 0.00 0.00 33.67 3.32
3481 4643 8.856103 ACTTGTAAAATGTAATTAAGGCTGTGT 58.144 29.630 0.00 0.00 33.67 3.72
3484 4646 9.485591 CGTACTTGTAAAATGTAATTAAGGCTG 57.514 33.333 0.00 0.00 33.67 4.85
3485 4647 9.223099 ACGTACTTGTAAAATGTAATTAAGGCT 57.777 29.630 0.00 0.00 33.67 4.58
3492 4654 9.480053 ACACACTACGTACTTGTAAAATGTAAT 57.520 29.630 5.05 0.00 0.00 1.89
3513 4675 5.057149 ACCTGATAGTCAAAAGACACACAC 58.943 41.667 0.00 0.00 0.00 3.82
3585 4747 9.366216 CTAACAGTAACATAACTTGAGCATACA 57.634 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.