Multiple sequence alignment - TraesCS6A01G157200

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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 TraesCS6A01G157200 chr6A 100.000 3314 0 0 1 3314 146503385 146500072 0.000000e+00 6120
1 TraesCS6A01G157200 chr7B 88.391 2007 160 26 1276 3218 651454045 651452048 0.000000e+00 2348
2 TraesCS6A01G157200 chr7B 87.683 1916 166 24 1276 3132 651336460 651338364 0.000000e+00 2167
3 TraesCS6A01G157200 chr7B 79.811 1268 222 17 1470 2716 472329424 472328170 0.000000e+00 893
4 TraesCS6A01G157200 chr7B 79.495 1268 223 17 1470 2716 472396292 472395041 0.000000e+00 867
5 TraesCS6A01G157200 chr7B 79.259 1268 229 17 1470 2716 651341190 651339936 0.000000e+00 854
6 TraesCS6A01G157200 chr7B 91.111 630 55 1 1 629 735277957 735277328 0.000000e+00 852
7 TraesCS6A01G157200 chr7B 84.418 661 54 21 730 1380 472397027 472396406 3.660000e-169 604
8 TraesCS6A01G157200 chr7B 84.115 661 55 20 730 1380 472330158 472329538 7.920000e-166 593
9 TraesCS6A01G157200 chr7B 87.397 484 33 10 713 1187 651341893 651341429 6.300000e-147 531
10 TraesCS6A01G157200 chr7B 89.011 273 20 5 782 1045 651454487 651454216 2.470000e-86 329
11 TraesCS6A01G157200 chr7B 93.023 86 5 1 3119 3204 472325904 472325988 1.250000e-24 124
12 TraesCS6A01G157200 chr7B 91.860 86 6 1 3119 3204 472392776 472392860 5.810000e-23 119
13 TraesCS6A01G157200 chr7D 87.124 1561 162 16 1383 2925 583478521 583476982 0.000000e+00 1733
14 TraesCS6A01G157200 chr7D 89.059 1243 89 18 1994 3215 583982285 583983501 0.000000e+00 1498
15 TraesCS6A01G157200 chr7D 89.314 627 65 2 1383 2007 583973501 583974127 0.000000e+00 785
16 TraesCS6A01G157200 chr7D 83.384 662 63 20 730 1380 583479182 583478557 1.330000e-158 569
17 TraesCS6A01G157200 chr7D 83.072 573 72 11 1276 1832 583989146 583988583 6.390000e-137 497
18 TraesCS6A01G157200 chr7D 96.078 153 6 0 809 961 583989661 583989509 1.970000e-62 250
19 TraesCS6A01G157200 chr7D 88.018 217 16 5 741 955 583972789 583972997 7.100000e-62 248
20 TraesCS6A01G157200 chr7D 84.951 206 18 3 3025 3218 583474414 583474210 2.610000e-46 196
21 TraesCS6A01G157200 chr7A 87.013 1463 156 12 1383 2827 675114881 675113435 0.000000e+00 1618
22 TraesCS6A01G157200 chr7A 85.386 609 58 17 781 1380 675115503 675114917 1.320000e-168 603
23 TraesCS6A01G157200 chr7A 84.211 209 18 4 3025 3218 675113141 675112933 4.370000e-44 189
24 TraesCS6A01G157200 chr5B 95.563 631 26 2 1 629 58631108 58630478 0.000000e+00 1009
25 TraesCS6A01G157200 chr3A 94.595 629 34 0 1 629 23185629 23186257 0.000000e+00 974
26 TraesCS6A01G157200 chr1A 94.586 628 34 0 1 628 357440487 357439860 0.000000e+00 972
27 TraesCS6A01G157200 chr4A 93.661 631 39 1 1 630 584873170 584872540 0.000000e+00 942
28 TraesCS6A01G157200 chr4B 93.492 630 39 2 1 629 664952846 664952218 0.000000e+00 935
29 TraesCS6A01G157200 chr4B 93.333 630 41 1 1 629 665066777 665066148 0.000000e+00 929
30 TraesCS6A01G157200 chr3B 93.482 629 41 0 1 629 169358304 169358932 0.000000e+00 935
31 TraesCS6A01G157200 chr5A 93.175 630 42 1 1 629 30115540 30116169 0.000000e+00 924
32 TraesCS6A01G157200 chrUn 93.069 101 7 0 3214 3314 307427600 307427700 7.410000e-32 148
33 TraesCS6A01G157200 chr2A 93.069 101 7 0 3214 3314 690913036 690912936 7.410000e-32 148
34 TraesCS6A01G157200 chr2B 89.623 106 8 3 3211 3314 655213395 655213499 7.460000e-27 132


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 TraesCS6A01G157200 chr6A 146500072 146503385 3313 True 6120.000000 6120 100.000000 1 3314 1 chr6A.!!$R1 3313
1 TraesCS6A01G157200 chr7B 651336460 651338364 1904 False 2167.000000 2167 87.683000 1276 3132 1 chr7B.!!$F3 1856
2 TraesCS6A01G157200 chr7B 651452048 651454487 2439 True 1338.500000 2348 88.701000 782 3218 2 chr7B.!!$R5 2436
3 TraesCS6A01G157200 chr7B 735277328 735277957 629 True 852.000000 852 91.111000 1 629 1 chr7B.!!$R1 628
4 TraesCS6A01G157200 chr7B 472328170 472330158 1988 True 743.000000 893 81.963000 730 2716 2 chr7B.!!$R2 1986
5 TraesCS6A01G157200 chr7B 472395041 472397027 1986 True 735.500000 867 81.956500 730 2716 2 chr7B.!!$R3 1986
6 TraesCS6A01G157200 chr7B 651339936 651341893 1957 True 692.500000 854 83.328000 713 2716 2 chr7B.!!$R4 2003
7 TraesCS6A01G157200 chr7D 583982285 583983501 1216 False 1498.000000 1498 89.059000 1994 3215 1 chr7D.!!$F1 1221
8 TraesCS6A01G157200 chr7D 583474210 583479182 4972 True 832.666667 1733 85.153000 730 3218 3 chr7D.!!$R1 2488
9 TraesCS6A01G157200 chr7D 583972789 583974127 1338 False 516.500000 785 88.666000 741 2007 2 chr7D.!!$F2 1266
10 TraesCS6A01G157200 chr7D 583988583 583989661 1078 True 373.500000 497 89.575000 809 1832 2 chr7D.!!$R2 1023
11 TraesCS6A01G157200 chr7A 675112933 675115503 2570 True 803.333333 1618 85.536667 781 3218 3 chr7A.!!$R1 2437
12 TraesCS6A01G157200 chr5B 58630478 58631108 630 True 1009.000000 1009 95.563000 1 629 1 chr5B.!!$R1 628
13 TraesCS6A01G157200 chr3A 23185629 23186257 628 False 974.000000 974 94.595000 1 629 1 chr3A.!!$F1 628
14 TraesCS6A01G157200 chr1A 357439860 357440487 627 True 972.000000 972 94.586000 1 628 1 chr1A.!!$R1 627
15 TraesCS6A01G157200 chr4A 584872540 584873170 630 True 942.000000 942 93.661000 1 630 1 chr4A.!!$R1 629
16 TraesCS6A01G157200 chr4B 664952218 664952846 628 True 935.000000 935 93.492000 1 629 1 chr4B.!!$R1 628
17 TraesCS6A01G157200 chr4B 665066148 665066777 629 True 929.000000 929 93.333000 1 629 1 chr4B.!!$R2 628
18 TraesCS6A01G157200 chr3B 169358304 169358932 628 False 935.000000 935 93.482000 1 629 1 chr3B.!!$F1 628
19 TraesCS6A01G157200 chr5A 30115540 30116169 629 False 924.000000 924 93.175000 1 629 1 chr5A.!!$F1 628

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
702 703 0.033109 CTCTTTCCCCAATCCCCCAC 60.033 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2741 0.249911 GGCTATTCTGCCCGACGAAT 60.25 55.0 0.0 0.0 46.82 3.34 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
31 32 1.202580 ACTCCATTCGCTACTCATGGC 60.203 52.381 0.00 0.00 37.90 4.40
58 59 5.186992 TGTCACTAGCTACTTGGCTGATTTA 59.813 40.000 0.00 0.00 43.01 1.40
250 251 4.660938 GGGGCCTCGGCAGTTGTT 62.661 66.667 10.51 0.00 44.11 2.83
272 273 2.531771 TCAACAACATAGAGGACCCGA 58.468 47.619 0.00 0.00 0.00 5.14
303 304 3.476485 AGTTCTAGCTACCAGGGAAGT 57.524 47.619 0.00 0.00 0.00 3.01
395 396 1.743772 CGATCAAAGGAGGAACGGCAT 60.744 52.381 0.00 0.00 0.00 4.40
678 679 9.887406 TCGTAAAAGAAATATTTGTCTTTGACC 57.113 29.630 17.34 8.88 41.98 4.02
679 680 9.124807 CGTAAAAGAAATATTTGTCTTTGACCC 57.875 33.333 17.34 7.30 41.98 4.46
682 683 6.272822 AGAAATATTTGTCTTTGACCCTGC 57.727 37.500 5.17 0.00 0.00 4.85
683 684 5.185828 AGAAATATTTGTCTTTGACCCTGCC 59.814 40.000 5.17 0.00 0.00 4.85
684 685 2.683211 ATTTGTCTTTGACCCTGCCT 57.317 45.000 0.00 0.00 0.00 4.75
685 686 1.981256 TTTGTCTTTGACCCTGCCTC 58.019 50.000 0.00 0.00 0.00 4.70
686 687 1.140312 TTGTCTTTGACCCTGCCTCT 58.860 50.000 0.00 0.00 0.00 3.69
687 688 1.140312 TGTCTTTGACCCTGCCTCTT 58.860 50.000 0.00 0.00 0.00 2.85
688 689 1.494721 TGTCTTTGACCCTGCCTCTTT 59.505 47.619 0.00 0.00 0.00 2.52
689 690 2.155279 GTCTTTGACCCTGCCTCTTTC 58.845 52.381 0.00 0.00 0.00 2.62
690 691 1.073923 TCTTTGACCCTGCCTCTTTCC 59.926 52.381 0.00 0.00 0.00 3.13
691 692 0.112412 TTTGACCCTGCCTCTTTCCC 59.888 55.000 0.00 0.00 0.00 3.97
692 693 1.789576 TTGACCCTGCCTCTTTCCCC 61.790 60.000 0.00 0.00 0.00 4.81
693 694 2.121506 ACCCTGCCTCTTTCCCCA 60.122 61.111 0.00 0.00 0.00 4.96
694 695 1.778383 ACCCTGCCTCTTTCCCCAA 60.778 57.895 0.00 0.00 0.00 4.12
695 696 1.149133 ACCCTGCCTCTTTCCCCAAT 61.149 55.000 0.00 0.00 0.00 3.16
696 697 0.396278 CCCTGCCTCTTTCCCCAATC 60.396 60.000 0.00 0.00 0.00 2.67
697 698 0.396278 CCTGCCTCTTTCCCCAATCC 60.396 60.000 0.00 0.00 0.00 3.01
698 699 0.396278 CTGCCTCTTTCCCCAATCCC 60.396 60.000 0.00 0.00 0.00 3.85
699 700 1.075970 GCCTCTTTCCCCAATCCCC 60.076 63.158 0.00 0.00 0.00 4.81
700 701 1.620818 CCTCTTTCCCCAATCCCCC 59.379 63.158 0.00 0.00 0.00 5.40
701 702 1.221213 CCTCTTTCCCCAATCCCCCA 61.221 60.000 0.00 0.00 0.00 4.96
702 703 0.033109 CTCTTTCCCCAATCCCCCAC 60.033 60.000 0.00 0.00 0.00 4.61
703 704 0.778078 TCTTTCCCCAATCCCCCACA 60.778 55.000 0.00 0.00 0.00 4.17
704 705 0.614697 CTTTCCCCAATCCCCCACAC 60.615 60.000 0.00 0.00 0.00 3.82
705 706 1.077298 TTTCCCCAATCCCCCACACT 61.077 55.000 0.00 0.00 0.00 3.55
706 707 1.506028 TTCCCCAATCCCCCACACTC 61.506 60.000 0.00 0.00 0.00 3.51
707 708 2.237965 CCCCAATCCCCCACACTCA 61.238 63.158 0.00 0.00 0.00 3.41
708 709 1.000896 CCCAATCCCCCACACTCAC 60.001 63.158 0.00 0.00 0.00 3.51
709 710 1.000896 CCAATCCCCCACACTCACC 60.001 63.158 0.00 0.00 0.00 4.02
710 711 1.767036 CAATCCCCCACACTCACCA 59.233 57.895 0.00 0.00 0.00 4.17
711 712 0.609131 CAATCCCCCACACTCACCAC 60.609 60.000 0.00 0.00 0.00 4.16
712 713 1.789576 AATCCCCCACACTCACCACC 61.790 60.000 0.00 0.00 0.00 4.61
713 714 3.174987 CCCCCACACTCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
714 715 2.762554 CCCCCACACTCACCACCAA 61.763 63.158 0.00 0.00 0.00 3.67
715 716 1.460255 CCCCACACTCACCACCAAT 59.540 57.895 0.00 0.00 0.00 3.16
716 717 0.609131 CCCCACACTCACCACCAATC 60.609 60.000 0.00 0.00 0.00 2.67
717 718 0.955428 CCCACACTCACCACCAATCG 60.955 60.000 0.00 0.00 0.00 3.34
897 906 0.461870 TTCACGCATCCCCTGATTCG 60.462 55.000 0.00 0.00 42.30 3.34
1067 1131 7.106439 TCCAATTTTTATGAGTTGTGTGTGT 57.894 32.000 0.00 0.00 0.00 3.72
1074 1138 8.719560 TTTTATGAGTTGTGTGTGTAGTGTTA 57.280 30.769 0.00 0.00 0.00 2.41
1142 1211 2.945278 TCGATTTTGCTGGCAATCAAC 58.055 42.857 8.86 1.68 35.70 3.18
1198 1272 4.035091 TGAATCTGTTGGTTTCGTTCTGTG 59.965 41.667 0.00 0.00 0.00 3.66
1227 1322 6.922957 TCTGTTTCTACCAAAAATGTTGATGC 59.077 34.615 0.00 0.00 0.00 3.91
1237 1355 4.914312 AAATGTTGATGCGATTTTGCTG 57.086 36.364 0.00 0.00 35.36 4.41
1238 1356 2.350899 TGTTGATGCGATTTTGCTGG 57.649 45.000 0.00 0.00 35.36 4.85
1239 1357 0.994263 GTTGATGCGATTTTGCTGGC 59.006 50.000 0.00 0.00 35.36 4.85
1240 1358 0.602060 TTGATGCGATTTTGCTGGCA 59.398 45.000 0.00 0.00 40.06 4.92
1241 1359 0.602060 TGATGCGATTTTGCTGGCAA 59.398 45.000 3.72 3.72 39.09 4.52
1243 1361 1.856597 GATGCGATTTTGCTGGCAATC 59.143 47.619 8.86 4.14 39.09 2.67
1244 1362 0.602060 TGCGATTTTGCTGGCAATCA 59.398 45.000 8.86 0.01 35.70 2.57
1245 1363 1.274596 GCGATTTTGCTGGCAATCAG 58.725 50.000 8.86 3.24 46.03 2.90
1286 1435 1.006688 TTAACTCGCGCTGTGCTGA 60.007 52.632 11.82 9.22 43.27 4.26
1293 1443 0.993746 CGCGCTGTGCTGAAAAGTTC 60.994 55.000 11.82 0.00 43.27 3.01
1328 1523 1.556911 AGTGGCTCAGTCAATCCGAAT 59.443 47.619 0.00 0.00 0.00 3.34
1344 1539 4.806330 TCCGAATGATAGTAGAAATCGGC 58.194 43.478 6.44 0.00 45.83 5.54
1410 1640 1.807742 GCATTGTACACGGGCTTGTTA 59.192 47.619 0.00 0.00 0.00 2.41
1435 1673 7.091443 AGCTTCGTTATATACATCTGCTTACC 58.909 38.462 0.00 0.00 0.00 2.85
1530 1769 2.136878 CCTCCCCATCGACCTCCTG 61.137 68.421 0.00 0.00 0.00 3.86
1540 1779 1.169577 CGACCTCCTGATCCGGATAG 58.830 60.000 19.15 11.11 31.43 2.08
1560 1799 1.227497 GCATCTCCTTGAGCTCCCG 60.227 63.158 12.15 1.49 0.00 5.14
1597 1836 2.743718 CTGTCTGCCCGTCTTGGT 59.256 61.111 0.00 0.00 35.15 3.67
1791 2030 2.356667 GTCAGCTTTCCCAGGGGG 59.643 66.667 5.33 0.00 46.11 5.40
1842 2081 3.106054 TGGCTGGTTAATCATGGCAAAT 58.894 40.909 10.53 0.00 0.00 2.32
1915 2154 2.753319 CCCCCAATCACCGGTTTTT 58.247 52.632 2.97 0.00 0.00 1.94
1985 2224 2.945278 TCGTTACGGGTGTTACATGAC 58.055 47.619 4.53 0.00 0.00 3.06
2017 2256 4.314440 GTGTGCAGTCTCCCGGCA 62.314 66.667 0.00 0.00 42.20 5.69
2067 2306 1.529948 TCCTCCGTCCACTTGTCGT 60.530 57.895 0.00 0.00 0.00 4.34
2074 2313 2.279851 CCACTTGTCGTGCCGTCA 60.280 61.111 0.00 0.00 42.42 4.35
2101 2340 2.525629 TCCACCTGGACGGCAAGA 60.526 61.111 0.00 0.00 39.78 3.02
2106 2345 2.359169 CCTGGACGGCAAGAGGCTA 61.359 63.158 0.00 0.00 44.01 3.93
2243 2506 1.073923 GTCATGGGACTTTGGTGGACT 59.926 52.381 0.00 0.00 40.99 3.85
2455 2723 2.588989 CTGAGCTCAGGGAAGGCC 59.411 66.667 32.30 0.00 40.20 5.19
2482 2750 3.940640 CATGCGGCATTCGTCGGG 61.941 66.667 13.81 0.00 41.73 5.14
2521 2789 7.105588 GCATTTTATCAACCAAAGAATTCCCT 58.894 34.615 0.65 0.00 0.00 4.20
2524 2792 6.834168 TTATCAACCAAAGAATTCCCTGAC 57.166 37.500 0.65 0.00 0.00 3.51
2542 2810 6.674861 TCCCTGACCTAAAACCAGATTGTATA 59.325 38.462 0.00 0.00 0.00 1.47
2611 2879 2.091541 CATAACCAATGGAGTGGCGTT 58.908 47.619 6.16 0.00 43.00 4.84
2659 2927 2.358247 GAGGCCGCTTTTCCGTCA 60.358 61.111 0.00 0.00 0.00 4.35
2710 2978 1.671379 GGAAGTCTGGTTCACGCCC 60.671 63.158 0.00 0.00 0.00 6.13
2721 2989 1.272769 GTTCACGCCCAGTCTAGTCTT 59.727 52.381 0.00 0.00 0.00 3.01
2734 3008 4.021544 AGTCTAGTCTTATAGCCATGCTGC 60.022 45.833 0.00 0.00 40.10 5.25
2771 3053 9.914834 TGCTATTTTGGTCCATAATTAAGTAGT 57.085 29.630 12.15 0.00 0.00 2.73
2837 3122 1.075601 TCAGGGTGGAAATCTGCCTT 58.924 50.000 0.00 0.00 0.00 4.35
2852 3137 2.686915 CTGCCTTGAGTTGATGGGAATC 59.313 50.000 0.00 0.00 0.00 2.52
2872 3157 2.038557 TCCCCTTCTTTCCGAAAGTGAG 59.961 50.000 18.32 16.22 39.52 3.51
2886 3171 4.381398 CGAAAGTGAGTCATCTGTCTCCAT 60.381 45.833 0.00 0.00 30.82 3.41
2892 3177 6.554228 AGTGAGTCATCTGTCTCCATGATAAT 59.446 38.462 0.00 0.00 31.71 1.28
2916 3201 7.639113 TTTTCTCTTGTTTCTCTTTTGGCTA 57.361 32.000 0.00 0.00 0.00 3.93
2929 3248 8.402798 TCTCTTTTGGCTATTTTCATGTGTTA 57.597 30.769 0.00 0.00 0.00 2.41
2930 3249 8.514594 TCTCTTTTGGCTATTTTCATGTGTTAG 58.485 33.333 0.00 0.00 0.00 2.34
2931 3250 7.090173 TCTTTTGGCTATTTTCATGTGTTAGC 58.910 34.615 0.00 2.28 35.62 3.09
3037 5813 4.014847 TGTTTCAGAGAAAAGTGTTGCG 57.985 40.909 0.00 0.00 0.00 4.85
3116 5906 0.908198 ATGCTGGAGACCCAAGAGTC 59.092 55.000 0.00 0.00 42.98 3.36
3127 5917 6.936968 AGACCCAAGAGTCTGTACTATTTT 57.063 37.500 0.00 0.00 45.41 1.82
3194 5988 1.112113 GCGACCTGAATAGAGACCCA 58.888 55.000 0.00 0.00 0.00 4.51
3204 5998 3.834489 ATAGAGACCCAGCTCAATGTG 57.166 47.619 0.00 0.00 37.37 3.21
3215 6009 0.679002 CTCAATGTGGGTGCCTCTGG 60.679 60.000 0.00 0.00 0.00 3.86
3218 6012 0.033796 AATGTGGGTGCCTCTGGATG 60.034 55.000 0.00 0.00 0.00 3.51
3219 6013 0.915872 ATGTGGGTGCCTCTGGATGA 60.916 55.000 0.00 0.00 0.00 2.92
3220 6014 1.222936 GTGGGTGCCTCTGGATGAG 59.777 63.158 0.00 0.00 42.30 2.90
3221 6015 1.229625 TGGGTGCCTCTGGATGAGT 60.230 57.895 0.00 0.00 41.11 3.41
3222 6016 1.222936 GGGTGCCTCTGGATGAGTG 59.777 63.158 0.00 0.00 41.11 3.51
3223 6017 1.451028 GGTGCCTCTGGATGAGTGC 60.451 63.158 0.00 0.00 41.11 4.40
3224 6018 1.601171 GTGCCTCTGGATGAGTGCT 59.399 57.895 0.00 0.00 41.11 4.40
3225 6019 0.035630 GTGCCTCTGGATGAGTGCTT 60.036 55.000 0.00 0.00 41.11 3.91
3226 6020 0.035725 TGCCTCTGGATGAGTGCTTG 60.036 55.000 0.00 0.00 41.11 4.01
3227 6021 0.035630 GCCTCTGGATGAGTGCTTGT 60.036 55.000 0.00 0.00 41.11 3.16
3228 6022 1.612726 GCCTCTGGATGAGTGCTTGTT 60.613 52.381 0.00 0.00 41.11 2.83
3229 6023 2.787994 CCTCTGGATGAGTGCTTGTTT 58.212 47.619 0.00 0.00 41.11 2.83
3230 6024 3.869912 GCCTCTGGATGAGTGCTTGTTTA 60.870 47.826 0.00 0.00 41.11 2.01
3231 6025 4.326826 CCTCTGGATGAGTGCTTGTTTAA 58.673 43.478 0.00 0.00 41.11 1.52
3232 6026 4.946157 CCTCTGGATGAGTGCTTGTTTAAT 59.054 41.667 0.00 0.00 41.11 1.40
3233 6027 5.065731 CCTCTGGATGAGTGCTTGTTTAATC 59.934 44.000 0.00 0.00 41.11 1.75
3234 6028 4.943705 TCTGGATGAGTGCTTGTTTAATCC 59.056 41.667 0.00 0.00 34.06 3.01
3235 6029 4.922206 TGGATGAGTGCTTGTTTAATCCT 58.078 39.130 0.00 0.00 34.48 3.24
3236 6030 4.701651 TGGATGAGTGCTTGTTTAATCCTG 59.298 41.667 0.00 0.00 34.48 3.86
3237 6031 4.943705 GGATGAGTGCTTGTTTAATCCTGA 59.056 41.667 0.00 0.00 31.38 3.86
3238 6032 5.065731 GGATGAGTGCTTGTTTAATCCTGAG 59.934 44.000 0.00 0.00 31.38 3.35
3239 6033 5.227569 TGAGTGCTTGTTTAATCCTGAGA 57.772 39.130 0.00 0.00 0.00 3.27
3240 6034 5.620206 TGAGTGCTTGTTTAATCCTGAGAA 58.380 37.500 0.00 0.00 0.00 2.87
3241 6035 5.702670 TGAGTGCTTGTTTAATCCTGAGAAG 59.297 40.000 0.00 0.00 0.00 2.85
3242 6036 5.006386 AGTGCTTGTTTAATCCTGAGAAGG 58.994 41.667 0.00 0.00 0.00 3.46
3243 6037 5.003804 GTGCTTGTTTAATCCTGAGAAGGA 58.996 41.667 0.00 0.00 42.91 3.36
3244 6038 5.123027 GTGCTTGTTTAATCCTGAGAAGGAG 59.877 44.000 0.39 0.00 41.88 3.69
3245 6039 5.013079 TGCTTGTTTAATCCTGAGAAGGAGA 59.987 40.000 0.39 0.00 41.88 3.71
3246 6040 6.118852 GCTTGTTTAATCCTGAGAAGGAGAT 58.881 40.000 0.39 0.00 41.88 2.75
3247 6041 6.038050 GCTTGTTTAATCCTGAGAAGGAGATG 59.962 42.308 0.39 0.00 41.88 2.90
3248 6042 6.627087 TGTTTAATCCTGAGAAGGAGATGT 57.373 37.500 0.39 0.00 41.88 3.06
3249 6043 7.020827 TGTTTAATCCTGAGAAGGAGATGTT 57.979 36.000 0.39 0.00 41.88 2.71
3250 6044 6.881065 TGTTTAATCCTGAGAAGGAGATGTTG 59.119 38.462 0.39 0.00 41.88 3.33
3251 6045 3.557228 ATCCTGAGAAGGAGATGTTGC 57.443 47.619 0.39 0.00 41.88 4.17
3252 6046 2.544721 TCCTGAGAAGGAGATGTTGCT 58.455 47.619 0.00 0.00 33.38 3.91
3253 6047 3.713003 TCCTGAGAAGGAGATGTTGCTA 58.287 45.455 0.00 0.00 33.38 3.49
3254 6048 4.096681 TCCTGAGAAGGAGATGTTGCTAA 58.903 43.478 0.00 0.00 33.38 3.09
3255 6049 4.718774 TCCTGAGAAGGAGATGTTGCTAAT 59.281 41.667 0.00 0.00 33.38 1.73
3256 6050 4.815308 CCTGAGAAGGAGATGTTGCTAATG 59.185 45.833 0.00 0.00 0.00 1.90
3257 6051 5.426504 CTGAGAAGGAGATGTTGCTAATGT 58.573 41.667 0.00 0.00 0.00 2.71
3258 6052 6.407412 CCTGAGAAGGAGATGTTGCTAATGTA 60.407 42.308 0.00 0.00 0.00 2.29
3259 6053 7.129457 TGAGAAGGAGATGTTGCTAATGTAT 57.871 36.000 0.00 0.00 0.00 2.29
3260 6054 6.988580 TGAGAAGGAGATGTTGCTAATGTATG 59.011 38.462 0.00 0.00 0.00 2.39
3261 6055 6.893583 AGAAGGAGATGTTGCTAATGTATGT 58.106 36.000 0.00 0.00 0.00 2.29
3262 6056 7.341805 AGAAGGAGATGTTGCTAATGTATGTT 58.658 34.615 0.00 0.00 0.00 2.71
3263 6057 7.497249 AGAAGGAGATGTTGCTAATGTATGTTC 59.503 37.037 0.00 0.00 0.00 3.18
3264 6058 6.893583 AGGAGATGTTGCTAATGTATGTTCT 58.106 36.000 0.00 0.00 0.00 3.01
3265 6059 6.765036 AGGAGATGTTGCTAATGTATGTTCTG 59.235 38.462 0.00 0.00 0.00 3.02
3266 6060 6.540189 GGAGATGTTGCTAATGTATGTTCTGT 59.460 38.462 0.00 0.00 0.00 3.41
3267 6061 7.066284 GGAGATGTTGCTAATGTATGTTCTGTT 59.934 37.037 0.00 0.00 0.00 3.16
3268 6062 7.755591 AGATGTTGCTAATGTATGTTCTGTTG 58.244 34.615 0.00 0.00 0.00 3.33
3269 6063 6.875948 TGTTGCTAATGTATGTTCTGTTGT 57.124 33.333 0.00 0.00 0.00 3.32
3270 6064 6.667370 TGTTGCTAATGTATGTTCTGTTGTG 58.333 36.000 0.00 0.00 0.00 3.33
3271 6065 6.262049 TGTTGCTAATGTATGTTCTGTTGTGT 59.738 34.615 0.00 0.00 0.00 3.72
3272 6066 6.875948 TGCTAATGTATGTTCTGTTGTGTT 57.124 33.333 0.00 0.00 0.00 3.32
3273 6067 6.898041 TGCTAATGTATGTTCTGTTGTGTTC 58.102 36.000 0.00 0.00 0.00 3.18
3274 6068 6.484977 TGCTAATGTATGTTCTGTTGTGTTCA 59.515 34.615 0.00 0.00 0.00 3.18
3275 6069 7.017645 GCTAATGTATGTTCTGTTGTGTTCAG 58.982 38.462 0.00 0.00 0.00 3.02
3276 6070 5.947228 ATGTATGTTCTGTTGTGTTCAGG 57.053 39.130 0.00 0.00 34.15 3.86
3277 6071 5.029807 TGTATGTTCTGTTGTGTTCAGGA 57.970 39.130 0.00 0.00 34.15 3.86
3278 6072 5.620206 TGTATGTTCTGTTGTGTTCAGGAT 58.380 37.500 0.00 0.00 34.15 3.24
3279 6073 5.469760 TGTATGTTCTGTTGTGTTCAGGATG 59.530 40.000 0.00 0.00 34.15 3.51
3294 6088 5.947228 TCAGGATGACAACTTGTTTGATC 57.053 39.130 0.00 0.00 42.56 2.92
3295 6089 4.761739 TCAGGATGACAACTTGTTTGATCC 59.238 41.667 14.93 14.93 42.56 3.36
3296 6090 4.763793 CAGGATGACAACTTGTTTGATCCT 59.236 41.667 17.56 17.56 39.66 3.24
3297 6091 5.939883 CAGGATGACAACTTGTTTGATCCTA 59.060 40.000 20.39 0.00 38.30 2.94
3298 6092 6.600822 CAGGATGACAACTTGTTTGATCCTAT 59.399 38.462 20.39 7.22 38.30 2.57
3299 6093 7.121759 CAGGATGACAACTTGTTTGATCCTATT 59.878 37.037 20.39 6.76 38.30 1.73
3300 6094 7.121759 AGGATGACAACTTGTTTGATCCTATTG 59.878 37.037 19.87 0.00 38.45 1.90
3301 6095 7.094205 GGATGACAACTTGTTTGATCCTATTGT 60.094 37.037 15.23 0.00 38.73 2.71
3302 6096 6.969366 TGACAACTTGTTTGATCCTATTGTG 58.031 36.000 0.00 0.00 38.73 3.33
3303 6097 6.545666 TGACAACTTGTTTGATCCTATTGTGT 59.454 34.615 0.00 0.00 38.73 3.72
3304 6098 7.068103 TGACAACTTGTTTGATCCTATTGTGTT 59.932 33.333 0.00 0.00 38.73 3.32
3305 6099 7.202526 ACAACTTGTTTGATCCTATTGTGTTG 58.797 34.615 0.00 0.00 38.73 3.33
3306 6100 7.068103 ACAACTTGTTTGATCCTATTGTGTTGA 59.932 33.333 14.67 0.00 38.73 3.18
3307 6101 7.206981 ACTTGTTTGATCCTATTGTGTTGAG 57.793 36.000 0.00 0.00 0.00 3.02
3308 6102 6.207417 ACTTGTTTGATCCTATTGTGTTGAGG 59.793 38.462 0.00 0.00 0.00 3.86
3309 6103 5.875224 TGTTTGATCCTATTGTGTTGAGGA 58.125 37.500 0.00 0.00 43.46 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.681897 CAGCCAAGTAGCTAGTGACAAAG 59.318 47.826 0.73 0.00 42.61 2.77
58 59 6.714810 TGTCAATAGGTTTCTGTATGTGCTTT 59.285 34.615 0.00 0.00 0.00 3.51
114 115 2.430610 GGTGGTGGCTGCCAAACAA 61.431 57.895 25.23 1.92 40.68 2.83
197 198 4.760047 ATCGCGGCAAACGGCTCT 62.760 61.111 6.13 0.00 44.51 4.09
250 251 3.325425 TCGGGTCCTCTATGTTGTTGAAA 59.675 43.478 0.00 0.00 0.00 2.69
272 273 3.778954 AGCTAGAACTTCAAGCACCTT 57.221 42.857 0.00 0.00 38.75 3.50
322 323 5.804692 TGAAAACTTTCTGCTCGTACAAA 57.195 34.783 3.98 0.00 38.02 2.83
395 396 1.206878 ACCACTGCTCCATATGCTGA 58.793 50.000 0.00 0.00 34.27 4.26
652 653 9.887406 GGTCAAAGACAAATATTTCTTTTACGA 57.113 29.630 10.97 5.29 39.54 3.43
653 654 9.124807 GGGTCAAAGACAAATATTTCTTTTACG 57.875 33.333 10.97 3.53 39.54 3.18
656 657 7.657354 GCAGGGTCAAAGACAAATATTTCTTTT 59.343 33.333 10.97 4.55 39.54 2.27
657 658 7.154656 GCAGGGTCAAAGACAAATATTTCTTT 58.845 34.615 8.66 8.66 41.73 2.52
658 659 6.295292 GGCAGGGTCAAAGACAAATATTTCTT 60.295 38.462 0.00 0.00 33.68 2.52
659 660 5.185828 GGCAGGGTCAAAGACAAATATTTCT 59.814 40.000 0.00 0.00 33.68 2.52
660 661 5.185828 AGGCAGGGTCAAAGACAAATATTTC 59.814 40.000 0.00 0.00 33.68 2.17
661 662 5.086621 AGGCAGGGTCAAAGACAAATATTT 58.913 37.500 0.00 0.00 33.68 1.40
662 663 4.677182 AGGCAGGGTCAAAGACAAATATT 58.323 39.130 0.00 0.00 33.68 1.28
663 664 4.018050 AGAGGCAGGGTCAAAGACAAATAT 60.018 41.667 0.00 0.00 33.68 1.28
664 665 3.330701 AGAGGCAGGGTCAAAGACAAATA 59.669 43.478 0.00 0.00 33.68 1.40
665 666 2.108952 AGAGGCAGGGTCAAAGACAAAT 59.891 45.455 0.00 0.00 33.68 2.32
666 667 1.494721 AGAGGCAGGGTCAAAGACAAA 59.505 47.619 0.00 0.00 33.68 2.83
667 668 1.140312 AGAGGCAGGGTCAAAGACAA 58.860 50.000 0.00 0.00 33.68 3.18
668 669 1.140312 AAGAGGCAGGGTCAAAGACA 58.860 50.000 0.00 0.00 33.68 3.41
669 670 2.155279 GAAAGAGGCAGGGTCAAAGAC 58.845 52.381 0.00 0.00 0.00 3.01
670 671 1.073923 GGAAAGAGGCAGGGTCAAAGA 59.926 52.381 0.00 0.00 0.00 2.52
671 672 1.539157 GGAAAGAGGCAGGGTCAAAG 58.461 55.000 0.00 0.00 0.00 2.77
672 673 0.112412 GGGAAAGAGGCAGGGTCAAA 59.888 55.000 0.00 0.00 0.00 2.69
673 674 1.767692 GGGAAAGAGGCAGGGTCAA 59.232 57.895 0.00 0.00 0.00 3.18
674 675 2.231380 GGGGAAAGAGGCAGGGTCA 61.231 63.158 0.00 0.00 0.00 4.02
675 676 1.789576 TTGGGGAAAGAGGCAGGGTC 61.790 60.000 0.00 0.00 0.00 4.46
676 677 1.149133 ATTGGGGAAAGAGGCAGGGT 61.149 55.000 0.00 0.00 0.00 4.34
677 678 0.396278 GATTGGGGAAAGAGGCAGGG 60.396 60.000 0.00 0.00 0.00 4.45
678 679 0.396278 GGATTGGGGAAAGAGGCAGG 60.396 60.000 0.00 0.00 0.00 4.85
679 680 0.396278 GGGATTGGGGAAAGAGGCAG 60.396 60.000 0.00 0.00 0.00 4.85
680 681 1.697297 GGGATTGGGGAAAGAGGCA 59.303 57.895 0.00 0.00 0.00 4.75
681 682 1.075970 GGGGATTGGGGAAAGAGGC 60.076 63.158 0.00 0.00 0.00 4.70
682 683 1.221213 TGGGGGATTGGGGAAAGAGG 61.221 60.000 0.00 0.00 0.00 3.69
683 684 0.033109 GTGGGGGATTGGGGAAAGAG 60.033 60.000 0.00 0.00 0.00 2.85
684 685 0.778078 TGTGGGGGATTGGGGAAAGA 60.778 55.000 0.00 0.00 0.00 2.52
685 686 0.614697 GTGTGGGGGATTGGGGAAAG 60.615 60.000 0.00 0.00 0.00 2.62
686 687 1.077298 AGTGTGGGGGATTGGGGAAA 61.077 55.000 0.00 0.00 0.00 3.13
687 688 1.467190 AGTGTGGGGGATTGGGGAA 60.467 57.895 0.00 0.00 0.00 3.97
688 689 1.928567 GAGTGTGGGGGATTGGGGA 60.929 63.158 0.00 0.00 0.00 4.81
689 690 2.237965 TGAGTGTGGGGGATTGGGG 61.238 63.158 0.00 0.00 0.00 4.96
690 691 1.000896 GTGAGTGTGGGGGATTGGG 60.001 63.158 0.00 0.00 0.00 4.12
691 692 1.000896 GGTGAGTGTGGGGGATTGG 60.001 63.158 0.00 0.00 0.00 3.16
692 693 0.609131 GTGGTGAGTGTGGGGGATTG 60.609 60.000 0.00 0.00 0.00 2.67
693 694 1.767692 GTGGTGAGTGTGGGGGATT 59.232 57.895 0.00 0.00 0.00 3.01
694 695 2.231380 GGTGGTGAGTGTGGGGGAT 61.231 63.158 0.00 0.00 0.00 3.85
695 696 2.852075 GGTGGTGAGTGTGGGGGA 60.852 66.667 0.00 0.00 0.00 4.81
696 697 2.080336 ATTGGTGGTGAGTGTGGGGG 62.080 60.000 0.00 0.00 0.00 5.40
697 698 0.609131 GATTGGTGGTGAGTGTGGGG 60.609 60.000 0.00 0.00 0.00 4.96
698 699 0.955428 CGATTGGTGGTGAGTGTGGG 60.955 60.000 0.00 0.00 0.00 4.61
699 700 0.034756 TCGATTGGTGGTGAGTGTGG 59.965 55.000 0.00 0.00 0.00 4.17
700 701 1.432514 CTCGATTGGTGGTGAGTGTG 58.567 55.000 0.00 0.00 0.00 3.82
701 702 0.320771 GCTCGATTGGTGGTGAGTGT 60.321 55.000 0.00 0.00 0.00 3.55
702 703 1.021390 GGCTCGATTGGTGGTGAGTG 61.021 60.000 0.00 0.00 0.00 3.51
703 704 1.296715 GGCTCGATTGGTGGTGAGT 59.703 57.895 0.00 0.00 0.00 3.41
704 705 0.321564 TTGGCTCGATTGGTGGTGAG 60.322 55.000 0.00 0.00 0.00 3.51
705 706 0.321564 CTTGGCTCGATTGGTGGTGA 60.322 55.000 0.00 0.00 0.00 4.02
706 707 1.308069 CCTTGGCTCGATTGGTGGTG 61.308 60.000 0.00 0.00 0.00 4.17
707 708 1.002134 CCTTGGCTCGATTGGTGGT 60.002 57.895 0.00 0.00 0.00 4.16
708 709 0.322456 TTCCTTGGCTCGATTGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
709 710 0.804989 GTTCCTTGGCTCGATTGGTG 59.195 55.000 0.00 0.00 0.00 4.17
710 711 0.693049 AGTTCCTTGGCTCGATTGGT 59.307 50.000 0.00 0.00 0.00 3.67
711 712 1.089920 CAGTTCCTTGGCTCGATTGG 58.910 55.000 0.00 0.00 0.00 3.16
712 713 1.089920 CCAGTTCCTTGGCTCGATTG 58.910 55.000 0.00 0.00 0.00 2.67
713 714 3.558674 CCAGTTCCTTGGCTCGATT 57.441 52.632 0.00 0.00 0.00 3.34
756 760 3.746889 TTGCTGGATTTGCGGCGG 61.747 61.111 9.78 0.00 0.00 6.13
758 762 2.125952 GGTTGCTGGATTTGCGGC 60.126 61.111 0.00 0.00 0.00 6.53
759 763 2.573340 GGGTTGCTGGATTTGCGG 59.427 61.111 0.00 0.00 0.00 5.69
761 765 2.981302 GGGGGTTGCTGGATTTGC 59.019 61.111 0.00 0.00 0.00 3.68
782 786 3.914713 GGGCATATGGGGTGGGGG 61.915 72.222 4.56 0.00 0.00 5.40
783 787 3.914713 GGGGCATATGGGGTGGGG 61.915 72.222 4.56 0.00 0.00 4.96
784 788 4.284550 CGGGGCATATGGGGTGGG 62.285 72.222 4.56 0.00 0.00 4.61
785 789 4.974721 GCGGGGCATATGGGGTGG 62.975 72.222 4.56 0.00 0.00 4.61
897 906 4.019858 CTGAAAGGAAAGAAAGGGGATCC 58.980 47.826 1.92 1.92 0.00 3.36
1058 1122 5.060506 CCCTCAATAACACTACACACACAA 58.939 41.667 0.00 0.00 0.00 3.33
1122 1191 2.352617 GGTTGATTGCCAGCAAAATCGA 60.353 45.455 9.44 0.60 39.55 3.59
1198 1272 5.831997 ACATTTTTGGTAGAAACAGAGTGC 58.168 37.500 0.00 0.00 0.00 4.40
1238 1356 1.141591 CGGCAAAATCGGCTGATTGC 61.142 55.000 21.35 21.06 44.02 3.56
1239 1357 1.141591 GCGGCAAAATCGGCTGATTG 61.142 55.000 21.35 12.60 44.02 2.67
1240 1358 1.139520 GCGGCAAAATCGGCTGATT 59.860 52.632 15.26 15.26 46.75 2.57
1241 1359 2.800736 GCGGCAAAATCGGCTGAT 59.199 55.556 0.90 0.90 40.08 2.90
1243 1361 4.834892 CCGCGGCAAAATCGGCTG 62.835 66.667 14.67 0.00 40.63 4.85
1248 1366 4.829518 GACGGCCGCGGCAAAATC 62.830 66.667 46.88 32.93 44.11 2.17
1286 1435 6.587608 CACTGAAAGAGCAAAACAGAACTTTT 59.412 34.615 0.00 0.00 37.43 2.27
1293 1443 2.360165 AGCCACTGAAAGAGCAAAACAG 59.640 45.455 0.00 0.00 38.82 3.16
1328 1523 3.133901 TGGCAAGCCGATTTCTACTATCA 59.866 43.478 6.60 0.00 39.42 2.15
1393 1622 1.071071 AGCTAACAAGCCCGTGTACAA 59.929 47.619 0.00 0.00 34.90 2.41
1394 1623 0.682852 AGCTAACAAGCCCGTGTACA 59.317 50.000 0.00 0.00 34.90 2.90
1410 1640 7.039644 AGGTAAGCAGATGTATATAACGAAGCT 60.040 37.037 0.00 0.00 0.00 3.74
1464 1702 3.674753 GTCCTGCCATCGTGAAAATTTTG 59.325 43.478 8.47 0.00 0.00 2.44
1465 1703 3.306019 GGTCCTGCCATCGTGAAAATTTT 60.306 43.478 2.28 2.28 37.17 1.82
1468 1707 1.004745 AGGTCCTGCCATCGTGAAAAT 59.995 47.619 0.00 0.00 40.61 1.82
1476 1715 1.952296 CTTGCATAAGGTCCTGCCATC 59.048 52.381 0.00 0.00 40.61 3.51
1530 1769 2.175202 AGGAGATGCACTATCCGGATC 58.825 52.381 23.08 7.11 38.20 3.36
1540 1779 0.463474 GGGAGCTCAAGGAGATGCAC 60.463 60.000 17.19 0.00 38.12 4.57
1597 1836 2.747460 GGCCGCAGATGCAGAACA 60.747 61.111 5.55 0.00 42.21 3.18
1701 1940 0.462789 GATCCCATAACCCACGACGT 59.537 55.000 0.00 0.00 0.00 4.34
1842 2081 0.816018 GGACGAGATCCGAGAGCTCA 60.816 60.000 17.77 0.00 44.21 4.26
1899 2138 0.955905 ACGAAAAACCGGTGATTGGG 59.044 50.000 8.52 5.20 0.00 4.12
1915 2154 3.822192 CCCCTCGATGCACGACGA 61.822 66.667 0.00 10.97 46.45 4.20
1985 2224 1.401409 GCACACCATGAACATGTTCCG 60.401 52.381 30.66 22.39 38.77 4.30
2017 2256 3.118519 ACAACCTTGTCGTAGAAACACCT 60.119 43.478 0.00 0.00 39.69 4.00
2067 2306 1.591703 GATGACCAGAGTGACGGCA 59.408 57.895 0.00 0.00 0.00 5.69
2101 2340 4.413520 TCCTATCCTTGCAAAAGATAGCCT 59.586 41.667 26.50 7.26 38.66 4.58
2106 2345 5.435291 CTGTCTCCTATCCTTGCAAAAGAT 58.565 41.667 14.24 14.24 0.00 2.40
2243 2506 3.057736 CGTCTTCTTCCTCGGTTTGTCTA 60.058 47.826 0.00 0.00 0.00 2.59
2302 2570 6.071784 TCGAAAGCAAGTACCTAGTGATAACA 60.072 38.462 0.00 0.00 0.00 2.41
2455 2723 2.281761 GCCGCATGTCCCCATAGG 60.282 66.667 0.00 0.00 33.53 2.57
2459 2727 2.440065 GAATGCCGCATGTCCCCA 60.440 61.111 6.63 0.00 0.00 4.96
2473 2741 0.249911 GGCTATTCTGCCCGACGAAT 60.250 55.000 0.00 0.00 46.82 3.34
2482 2750 1.406903 AAATGCCTGGGCTATTCTGC 58.593 50.000 13.05 0.00 42.51 4.26
2542 2810 1.564348 AGGCGGGGAGTTGTGAAATAT 59.436 47.619 0.00 0.00 0.00 1.28
2659 2927 2.127708 GTCCCATAATGACCTCCACCT 58.872 52.381 0.00 0.00 0.00 4.00
2710 2978 5.468592 CAGCATGGCTATAAGACTAGACTG 58.531 45.833 0.00 0.00 36.40 3.51
2721 2989 3.003394 ACAAGTTGCAGCATGGCTATA 57.997 42.857 10.54 0.00 36.40 1.31
2734 3008 6.149633 GGACCAAAATAGCACTTACAAGTTG 58.850 40.000 0.00 0.00 37.08 3.16
2771 3053 4.671831 TCACAGAAAAATCATTAGGGGCA 58.328 39.130 0.00 0.00 0.00 5.36
2772 3054 4.098501 CCTCACAGAAAAATCATTAGGGGC 59.901 45.833 0.00 0.00 0.00 5.80
2773 3055 5.264395 ACCTCACAGAAAAATCATTAGGGG 58.736 41.667 0.00 0.00 0.00 4.79
2852 3137 2.224548 ACTCACTTTCGGAAAGAAGGGG 60.225 50.000 31.26 22.11 40.34 4.79
2855 3140 5.119898 CAGATGACTCACTTTCGGAAAGAAG 59.880 44.000 31.26 26.69 41.02 2.85
2856 3141 4.991056 CAGATGACTCACTTTCGGAAAGAA 59.009 41.667 31.26 19.22 41.02 2.52
2857 3142 4.039245 ACAGATGACTCACTTTCGGAAAGA 59.961 41.667 31.26 13.45 41.02 2.52
2863 3148 3.057245 TGGAGACAGATGACTCACTTTCG 60.057 47.826 12.99 0.00 38.32 3.46
2892 3177 6.530019 AGCCAAAAGAGAAACAAGAGAAAA 57.470 33.333 0.00 0.00 0.00 2.29
2916 3201 4.463539 TCCATGCTGCTAACACATGAAAAT 59.536 37.500 0.00 0.00 43.04 1.82
2929 3248 1.542492 CAACCTTCTTCCATGCTGCT 58.458 50.000 0.00 0.00 0.00 4.24
2930 3249 0.108945 GCAACCTTCTTCCATGCTGC 60.109 55.000 0.00 0.00 34.29 5.25
2931 3250 0.529378 GGCAACCTTCTTCCATGCTG 59.471 55.000 0.00 0.00 37.20 4.41
3037 5813 5.006358 ACAGAACTCACATTTTACACGTCAC 59.994 40.000 0.00 0.00 0.00 3.67
3116 5906 9.924650 AACAACTACTCCTACAAAATAGTACAG 57.075 33.333 0.00 0.00 0.00 2.74
3194 5988 1.001641 GAGGCACCCACATTGAGCT 60.002 57.895 0.00 0.00 0.00 4.09
3215 6009 5.877012 TCTCAGGATTAAACAAGCACTCATC 59.123 40.000 0.00 0.00 0.00 2.92
3218 6012 5.123027 CCTTCTCAGGATTAAACAAGCACTC 59.877 44.000 0.00 0.00 44.19 3.51
3219 6013 5.006386 CCTTCTCAGGATTAAACAAGCACT 58.994 41.667 0.00 0.00 44.19 4.40
3220 6014 5.003804 TCCTTCTCAGGATTAAACAAGCAC 58.996 41.667 0.00 0.00 45.20 4.40
3221 6015 5.241403 TCCTTCTCAGGATTAAACAAGCA 57.759 39.130 0.00 0.00 45.20 3.91
3233 6027 4.478206 TTAGCAACATCTCCTTCTCAGG 57.522 45.455 0.00 0.00 42.50 3.86
3234 6028 5.426504 ACATTAGCAACATCTCCTTCTCAG 58.573 41.667 0.00 0.00 0.00 3.35
3235 6029 5.426689 ACATTAGCAACATCTCCTTCTCA 57.573 39.130 0.00 0.00 0.00 3.27
3236 6030 6.989169 ACATACATTAGCAACATCTCCTTCTC 59.011 38.462 0.00 0.00 0.00 2.87
3237 6031 6.893583 ACATACATTAGCAACATCTCCTTCT 58.106 36.000 0.00 0.00 0.00 2.85
3238 6032 7.497249 AGAACATACATTAGCAACATCTCCTTC 59.503 37.037 0.00 0.00 0.00 3.46
3239 6033 7.281774 CAGAACATACATTAGCAACATCTCCTT 59.718 37.037 0.00 0.00 0.00 3.36
3240 6034 6.765036 CAGAACATACATTAGCAACATCTCCT 59.235 38.462 0.00 0.00 0.00 3.69
3241 6035 6.540189 ACAGAACATACATTAGCAACATCTCC 59.460 38.462 0.00 0.00 0.00 3.71
3242 6036 7.545362 ACAGAACATACATTAGCAACATCTC 57.455 36.000 0.00 0.00 0.00 2.75
3243 6037 7.391554 ACAACAGAACATACATTAGCAACATCT 59.608 33.333 0.00 0.00 0.00 2.90
3244 6038 7.482743 CACAACAGAACATACATTAGCAACATC 59.517 37.037 0.00 0.00 0.00 3.06
3245 6039 7.040478 ACACAACAGAACATACATTAGCAACAT 60.040 33.333 0.00 0.00 0.00 2.71
3246 6040 6.262049 ACACAACAGAACATACATTAGCAACA 59.738 34.615 0.00 0.00 0.00 3.33
3247 6041 6.668323 ACACAACAGAACATACATTAGCAAC 58.332 36.000 0.00 0.00 0.00 4.17
3248 6042 6.875948 ACACAACAGAACATACATTAGCAA 57.124 33.333 0.00 0.00 0.00 3.91
3249 6043 6.484977 TGAACACAACAGAACATACATTAGCA 59.515 34.615 0.00 0.00 0.00 3.49
3250 6044 6.898041 TGAACACAACAGAACATACATTAGC 58.102 36.000 0.00 0.00 0.00 3.09
3251 6045 7.387673 TCCTGAACACAACAGAACATACATTAG 59.612 37.037 0.00 0.00 37.54 1.73
3252 6046 7.220740 TCCTGAACACAACAGAACATACATTA 58.779 34.615 0.00 0.00 37.54 1.90
3253 6047 6.061441 TCCTGAACACAACAGAACATACATT 58.939 36.000 0.00 0.00 37.54 2.71
3254 6048 5.620206 TCCTGAACACAACAGAACATACAT 58.380 37.500 0.00 0.00 37.54 2.29
3255 6049 5.029807 TCCTGAACACAACAGAACATACA 57.970 39.130 0.00 0.00 37.54 2.29
3256 6050 5.700832 TCATCCTGAACACAACAGAACATAC 59.299 40.000 0.00 0.00 37.54 2.39
3257 6051 5.700832 GTCATCCTGAACACAACAGAACATA 59.299 40.000 0.00 0.00 37.54 2.29
3258 6052 4.516698 GTCATCCTGAACACAACAGAACAT 59.483 41.667 0.00 0.00 37.54 2.71
3259 6053 3.876914 GTCATCCTGAACACAACAGAACA 59.123 43.478 0.00 0.00 37.54 3.18
3260 6054 3.876914 TGTCATCCTGAACACAACAGAAC 59.123 43.478 0.00 0.00 37.54 3.01
3261 6055 4.149511 TGTCATCCTGAACACAACAGAA 57.850 40.909 0.00 0.00 37.54 3.02
3262 6056 3.836365 TGTCATCCTGAACACAACAGA 57.164 42.857 0.00 0.00 37.54 3.41
3263 6057 4.214980 GTTGTCATCCTGAACACAACAG 57.785 45.455 14.91 0.00 45.27 3.16
3265 6059 4.096382 ACAAGTTGTCATCCTGAACACAAC 59.904 41.667 1.64 13.10 45.96 3.32
3266 6060 4.269183 ACAAGTTGTCATCCTGAACACAA 58.731 39.130 1.64 0.00 0.00 3.33
3267 6061 3.884895 ACAAGTTGTCATCCTGAACACA 58.115 40.909 1.64 0.00 0.00 3.72
3268 6062 4.900635 AACAAGTTGTCATCCTGAACAC 57.099 40.909 9.40 0.00 0.00 3.32
3269 6063 4.946772 TCAAACAAGTTGTCATCCTGAACA 59.053 37.500 9.40 0.00 38.47 3.18
3270 6064 5.499139 TCAAACAAGTTGTCATCCTGAAC 57.501 39.130 9.40 0.00 38.47 3.18
3271 6065 5.241506 GGATCAAACAAGTTGTCATCCTGAA 59.758 40.000 22.80 3.59 38.47 3.02
3272 6066 4.761739 GGATCAAACAAGTTGTCATCCTGA 59.238 41.667 22.80 15.42 38.47 3.86
3273 6067 4.763793 AGGATCAAACAAGTTGTCATCCTG 59.236 41.667 27.69 14.83 37.79 3.86
3274 6068 4.990526 AGGATCAAACAAGTTGTCATCCT 58.009 39.130 25.13 25.13 38.47 3.24
3275 6069 7.094205 ACAATAGGATCAAACAAGTTGTCATCC 60.094 37.037 22.70 22.70 38.47 3.51
3276 6070 7.752239 CACAATAGGATCAAACAAGTTGTCATC 59.248 37.037 9.40 10.76 38.47 2.92
3277 6071 7.231317 ACACAATAGGATCAAACAAGTTGTCAT 59.769 33.333 9.40 1.92 38.47 3.06
3278 6072 6.545666 ACACAATAGGATCAAACAAGTTGTCA 59.454 34.615 9.40 0.00 38.47 3.58
3279 6073 6.970484 ACACAATAGGATCAAACAAGTTGTC 58.030 36.000 9.40 0.00 38.47 3.18
3280 6074 6.959639 ACACAATAGGATCAAACAAGTTGT 57.040 33.333 1.64 1.64 38.47 3.32
3281 6075 7.424803 TCAACACAATAGGATCAAACAAGTTG 58.575 34.615 0.00 0.00 38.71 3.16
3282 6076 7.255590 CCTCAACACAATAGGATCAAACAAGTT 60.256 37.037 0.00 0.00 31.64 2.66
3283 6077 6.207417 CCTCAACACAATAGGATCAAACAAGT 59.793 38.462 0.00 0.00 31.64 3.16
3284 6078 6.430925 TCCTCAACACAATAGGATCAAACAAG 59.569 38.462 0.00 0.00 34.46 3.16
3285 6079 6.303054 TCCTCAACACAATAGGATCAAACAA 58.697 36.000 0.00 0.00 34.46 2.83
3286 6080 5.875224 TCCTCAACACAATAGGATCAAACA 58.125 37.500 0.00 0.00 34.46 2.83
3287 6081 6.599244 TCATCCTCAACACAATAGGATCAAAC 59.401 38.462 0.00 0.00 45.06 2.93
3288 6082 6.720309 TCATCCTCAACACAATAGGATCAAA 58.280 36.000 0.00 0.00 45.06 2.69
3289 6083 6.312141 TCATCCTCAACACAATAGGATCAA 57.688 37.500 0.00 0.00 45.06 2.57
3290 6084 5.955961 TCATCCTCAACACAATAGGATCA 57.044 39.130 0.00 0.00 45.06 2.92


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

AutoCloner maintained by Alex Coulton.