Multiple sequence alignment - TraesCS5A01G095100

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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 TraesCS5A01G095100 chr5A 100.000 6554 0 0 1 6554 132106737 132100184 0.000000e+00 12104.0
1 TraesCS5A01G095100 chr5B 95.241 4728 169 17 881 5588 134141501 134136810 0.000000e+00 7433.0
2 TraesCS5A01G095100 chr5B 89.908 545 35 11 5845 6387 134136390 134135864 0.000000e+00 684.0
3 TraesCS5A01G095100 chr5D 96.366 3852 116 10 881 4714 121092501 121088656 0.000000e+00 6316.0
4 TraesCS5A01G095100 chr5D 92.047 1031 43 19 4749 5776 121088363 121087369 0.000000e+00 1413.0
5 TraesCS5A01G095100 chr5D 88.710 682 43 15 5842 6521 121087360 121086711 0.000000e+00 802.0
6 TraesCS5A01G095100 chr5D 100.000 28 0 0 5806 5833 522245023 522245050 1.200000e-02 52.8
7 TraesCS5A01G095100 chr4A 94.513 729 34 4 157 881 521916298 521915572 0.000000e+00 1120.0
8 TraesCS5A01G095100 chr4A 98.171 164 3 0 1 164 521916720 521916557 2.990000e-73 287.0
9 TraesCS5A01G095100 chrUn 91.071 728 45 4 157 882 232547052 232546343 0.000000e+00 966.0
10 TraesCS5A01G095100 chrUn 90.659 728 48 4 157 882 369567507 369566798 0.000000e+00 950.0
11 TraesCS5A01G095100 chrUn 90.783 575 33 4 157 729 362421596 362421040 0.000000e+00 750.0
12 TraesCS5A01G095100 chrUn 90.783 575 33 4 157 729 362504234 362504790 0.000000e+00 750.0
13 TraesCS5A01G095100 chrUn 94.545 165 8 1 1 164 232547497 232547333 3.030000e-63 254.0
14 TraesCS5A01G095100 chrUn 94.545 165 8 1 1 164 362422040 362421876 3.030000e-63 254.0
15 TraesCS5A01G095100 chrUn 94.545 165 8 1 1 164 362503792 362503956 3.030000e-63 254.0
16 TraesCS5A01G095100 chr4D 89.271 727 51 13 157 881 483121342 483122043 0.000000e+00 885.0
17 TraesCS5A01G095100 chr4D 95.783 166 5 2 1 164 483120918 483121083 3.900000e-67 267.0
18 TraesCS5A01G095100 chr2D 88.054 745 45 21 157 880 368521129 368521850 0.000000e+00 843.0
19 TraesCS5A01G095100 chr2D 95.181 166 6 2 1 164 368520705 368520870 1.810000e-65 261.0
20 TraesCS5A01G095100 chr1D 87.912 637 51 12 157 791 445781129 445780517 0.000000e+00 726.0
21 TraesCS5A01G095100 chr1D 95.122 164 7 1 1 164 486072695 486072533 2.340000e-64 257.0
22 TraesCS5A01G095100 chr3B 92.529 348 22 2 546 889 86094511 86094164 4.560000e-136 496.0
23 TraesCS5A01G095100 chr3B 90.659 364 24 5 522 880 628757329 628756971 5.950000e-130 475.0
24 TraesCS5A01G095100 chr3B 91.813 342 22 4 157 493 628757751 628757411 7.690000e-129 472.0
25 TraesCS5A01G095100 chr3B 95.732 164 7 0 1 164 86095123 86094960 1.400000e-66 265.0
26 TraesCS5A01G095100 chr2B 90.909 341 26 5 546 881 243697923 243698263 2.790000e-123 453.0
27 TraesCS5A01G095100 chr2B 95.732 164 6 1 1 164 243697314 243697476 5.040000e-66 263.0
28 TraesCS5A01G095100 chr2A 86.318 402 45 7 489 884 770251830 770251433 4.700000e-116 429.0
29 TraesCS5A01G095100 chr6D 83.962 318 30 14 2264 2569 83544409 83544101 1.080000e-72 285.0
30 TraesCS5A01G095100 chr6D 82.759 232 28 7 2340 2569 83103648 83103869 5.180000e-46 196.0
31 TraesCS5A01G095100 chr6D 85.816 141 12 6 2443 2576 84029589 84029450 6.850000e-30 143.0
32 TraesCS5A01G095100 chr6D 78.912 147 14 10 2268 2410 84029724 84029591 4.210000e-12 84.2
33 TraesCS5A01G095100 chr6D 92.105 38 3 0 2262 2299 83114420 83114457 3.000000e-03 54.7
34 TraesCS5A01G095100 chr6B 83.007 306 36 12 2270 2569 159598303 159598008 5.040000e-66 263.0
35 TraesCS5A01G095100 chr6B 85.417 192 26 2 2379 2569 159405813 159405623 1.440000e-46 198.0
36 TraesCS5A01G095100 chr6B 85.052 194 26 3 2382 2573 158146596 158146788 1.860000e-45 195.0
37 TraesCS5A01G095100 chr6B 80.435 92 6 8 2268 2355 159405904 159405821 7.100000e-05 60.2
38 TraesCS5A01G095100 chr7B 89.634 164 17 0 2349 2512 66198316 66198479 6.660000e-50 209.0
39 TraesCS5A01G095100 chr6A 87.963 108 9 1 2382 2489 100182152 100182255 2.480000e-24 124.0


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 TraesCS5A01G095100 chr5A 132100184 132106737 6553 True 12104.000000 12104 100.000000 1 6554 1 chr5A.!!$R1 6553
1 TraesCS5A01G095100 chr5B 134135864 134141501 5637 True 4058.500000 7433 92.574500 881 6387 2 chr5B.!!$R1 5506
2 TraesCS5A01G095100 chr5D 121086711 121092501 5790 True 2843.666667 6316 92.374333 881 6521 3 chr5D.!!$R1 5640
3 TraesCS5A01G095100 chr4A 521915572 521916720 1148 True 703.500000 1120 96.342000 1 881 2 chr4A.!!$R1 880
4 TraesCS5A01G095100 chrUn 369566798 369567507 709 True 950.000000 950 90.659000 157 882 1 chrUn.!!$R1 725
5 TraesCS5A01G095100 chrUn 232546343 232547497 1154 True 610.000000 966 92.808000 1 882 2 chrUn.!!$R2 881
6 TraesCS5A01G095100 chrUn 362421040 362422040 1000 True 502.000000 750 92.664000 1 729 2 chrUn.!!$R3 728
7 TraesCS5A01G095100 chrUn 362503792 362504790 998 False 502.000000 750 92.664000 1 729 2 chrUn.!!$F1 728
8 TraesCS5A01G095100 chr4D 483120918 483122043 1125 False 576.000000 885 92.527000 1 881 2 chr4D.!!$F1 880
9 TraesCS5A01G095100 chr2D 368520705 368521850 1145 False 552.000000 843 91.617500 1 880 2 chr2D.!!$F1 879
10 TraesCS5A01G095100 chr1D 445780517 445781129 612 True 726.000000 726 87.912000 157 791 1 chr1D.!!$R1 634
11 TraesCS5A01G095100 chr3B 628756971 628757751 780 True 473.500000 475 91.236000 157 880 2 chr3B.!!$R2 723
12 TraesCS5A01G095100 chr3B 86094164 86095123 959 True 380.500000 496 94.130500 1 889 2 chr3B.!!$R1 888
13 TraesCS5A01G095100 chr2B 243697314 243698263 949 False 358.000000 453 93.320500 1 881 2 chr2B.!!$F1 880

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
418 739 0.250553 TGATTTTCGCCGGAACCTGT 60.251 50.000 5.05 0.00 0.0 4.00 F
1304 1722 1.073177 GGTGGTAATGTTCGTGTCGG 58.927 55.000 0.00 0.00 0.0 4.79 F
1907 2329 1.294857 GTTTGCCCGCAAATGTTGTT 58.705 45.000 17.16 0.00 45.9 2.83 F
1916 2338 2.032979 CGCAAATGTTGTTTGGCTTTCC 60.033 45.455 3.09 0.00 0.0 3.13 F
2725 3147 2.360801 AGGCACTCGATCTAGAAGCTTC 59.639 50.000 19.11 19.11 0.0 3.86 F
3874 4296 2.205074 CAGTATTGTGCGATGGGTCTC 58.795 52.381 0.00 0.00 0.0 3.36 F
5110 5794 0.036732 AAGCAGTTGGAAGGCATCGA 59.963 50.000 0.00 0.00 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 2329 0.817634 CGACCACACAGGAAAGCCAA 60.818 55.0 0.0 0.0 41.22 4.52 R
2197 2619 0.891904 TTTTAGCTCCCACCGTTGGC 60.892 55.0 0.0 0.0 42.35 4.52 R
3722 4144 0.401395 TTGACAGGGACCCACCTTCT 60.401 55.0 14.6 0.0 39.34 2.85 R
3874 4296 0.609131 AATCCAGTCCAACCAAGCCG 60.609 55.0 0.0 0.0 0.00 5.52 R
4599 5025 0.877743 GGGAGTCAGAAACTGCTTGC 59.122 55.0 0.0 0.0 45.15 4.01 R
5113 5797 0.034670 AATGCCTCCTGACTGCCTTC 60.035 55.0 0.0 0.0 0.00 3.46 R
6379 7286 0.037326 TGCTCAGCTCAACCCTTACG 60.037 55.0 0.0 0.0 0.00 3.18 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
29 30 9.589111 ACAATCGTTTTTGGTTTTTGTTACTAT 57.411 25.926 0.00 0.00 0.00 2.12
142 145 7.040340 TGTTGGAACCGAAGATAATTTTTGCTA 60.040 33.333 0.00 0.00 0.00 3.49
276 595 4.101448 GCAGCGGGGATGGTCACT 62.101 66.667 0.00 0.00 0.00 3.41
287 606 2.171448 GGATGGTCACTATGCTGGAACT 59.829 50.000 0.00 0.00 0.00 3.01
296 616 0.251922 ATGCTGGAACTGGGCAACAT 60.252 50.000 0.00 0.00 39.46 2.71
313 633 1.210234 ACATGGATGCTGGAACGATCA 59.790 47.619 0.00 0.00 0.00 2.92
314 634 2.158711 ACATGGATGCTGGAACGATCAT 60.159 45.455 0.00 0.00 0.00 2.45
409 730 5.837586 TTTTGCTGTAATTGATTTTCGCC 57.162 34.783 0.00 0.00 0.00 5.54
418 739 0.250553 TGATTTTCGCCGGAACCTGT 60.251 50.000 5.05 0.00 0.00 4.00
543 918 2.758736 TTTTGCTGCAACCTTTGTGT 57.241 40.000 15.72 0.00 0.00 3.72
544 919 2.758736 TTTGCTGCAACCTTTGTGTT 57.241 40.000 15.72 0.00 0.00 3.32
745 1149 1.456892 ACCGCGGAGGATATGGTGA 60.457 57.895 35.90 0.00 45.00 4.02
1250 1667 3.791353 CCGTAAATTCCGTAGTCGTTACC 59.209 47.826 0.00 0.00 35.01 2.85
1263 1680 1.481363 TCGTTACCATAATCGGTGGCA 59.519 47.619 0.00 0.00 40.39 4.92
1301 1718 4.643463 TGTATTGGTGGTAATGTTCGTGT 58.357 39.130 0.00 0.00 0.00 4.49
1304 1722 1.073177 GGTGGTAATGTTCGTGTCGG 58.927 55.000 0.00 0.00 0.00 4.79
1512 1930 5.649557 GCAGCATGTACCATTTTTGTATGA 58.350 37.500 0.00 0.00 39.31 2.15
1522 1941 5.123344 ACCATTTTTGTATGACCTTAGCGTC 59.877 40.000 0.00 0.00 0.00 5.19
1639 2058 1.927487 TGGATGCTGCAATTTGAGGT 58.073 45.000 6.36 0.00 0.00 3.85
1659 2079 5.848004 AGGTGGATGATCTAGGCATATAGT 58.152 41.667 0.00 0.00 0.00 2.12
1662 2082 7.563188 AGGTGGATGATCTAGGCATATAGTTAG 59.437 40.741 0.00 0.00 0.00 2.34
1741 2161 3.508402 TCATCTGCAAATGTGATTGTGCT 59.492 39.130 0.00 0.00 37.87 4.40
1761 2182 1.948834 TGTCACTTGTGATTGCTGTGG 59.051 47.619 6.74 0.00 0.00 4.17
1817 2239 8.339714 GTTTATTGCCTATTTATAACTGCGTGA 58.660 33.333 0.00 0.00 0.00 4.35
1824 2246 7.587757 GCCTATTTATAACTGCGTGAGAATTTG 59.412 37.037 0.00 0.00 0.00 2.32
1831 2253 2.221169 TGCGTGAGAATTTGTCTTGCT 58.779 42.857 10.31 0.00 36.41 3.91
1837 2259 5.045872 GTGAGAATTTGTCTTGCTTGCTTT 58.954 37.500 0.00 0.00 36.41 3.51
1849 2271 4.818534 TGCTTGCTTTCTTACAAGTGAG 57.181 40.909 4.83 0.00 44.12 3.51
1864 2286 9.233232 CTTACAAGTGAGTCCAATTTTAAACAC 57.767 33.333 0.00 0.00 27.00 3.32
1865 2287 6.262601 ACAAGTGAGTCCAATTTTAAACACG 58.737 36.000 0.00 0.00 33.18 4.49
1882 2304 9.804758 TTTAAACACGAAACAATTACCTTCAAT 57.195 25.926 0.00 0.00 0.00 2.57
1896 2318 4.565022 ACCTTCAATTATTTGTTTGCCCG 58.435 39.130 0.00 0.00 34.32 6.13
1907 2329 1.294857 GTTTGCCCGCAAATGTTGTT 58.705 45.000 17.16 0.00 45.90 2.83
1916 2338 2.032979 CGCAAATGTTGTTTGGCTTTCC 60.033 45.455 3.09 0.00 0.00 3.13
1937 2359 3.753272 CCTGTGTGGTCGAGAAATTTGAT 59.247 43.478 0.00 0.00 0.00 2.57
1964 2386 7.715249 TGGCTCTTATGAACCATACATTCTAAC 59.285 37.037 0.00 0.00 33.87 2.34
1966 2388 9.277783 GCTCTTATGAACCATACATTCTAACAT 57.722 33.333 0.00 0.00 0.00 2.71
2048 2470 6.579666 AACATGACCATAATCATATGCACC 57.420 37.500 0.00 0.00 37.20 5.01
2049 2471 4.696877 ACATGACCATAATCATATGCACCG 59.303 41.667 0.00 0.00 37.20 4.94
2050 2472 3.073678 TGACCATAATCATATGCACCGC 58.926 45.455 0.00 0.00 38.06 5.68
2055 2477 3.752747 CATAATCATATGCACCGCAAGGA 59.247 43.478 0.00 0.00 46.15 3.36
2074 2496 6.694447 CAAGGAAAAATGATCAAGTCCACAT 58.306 36.000 15.63 0.00 0.00 3.21
2075 2497 6.276832 AGGAAAAATGATCAAGTCCACATG 57.723 37.500 15.63 0.00 0.00 3.21
2086 2508 7.338957 TGATCAAGTCCACATGCATATTTGTTA 59.661 33.333 0.00 0.00 0.00 2.41
2119 2541 2.689983 CACCTTGCTCTGAAAAACCACT 59.310 45.455 0.00 0.00 0.00 4.00
2126 2548 4.278170 TGCTCTGAAAAACCACTACCATTG 59.722 41.667 0.00 0.00 0.00 2.82
2128 2550 5.221244 GCTCTGAAAAACCACTACCATTGTT 60.221 40.000 0.00 0.00 0.00 2.83
2136 2558 5.257082 ACCACTACCATTGTTTGTTGAAC 57.743 39.130 0.00 0.00 38.78 3.18
2146 2568 3.417101 TGTTTGTTGAACCAGTGTCTGT 58.583 40.909 0.00 0.00 37.45 3.41
2181 2603 5.996513 TGCAAAATGGAAATTATGCAAGTGT 59.003 32.000 0.00 0.00 40.47 3.55
2192 2614 8.891671 AAATTATGCAAGTGTTGTTCATTTCT 57.108 26.923 0.00 0.00 0.00 2.52
2197 2619 6.264832 TGCAAGTGTTGTTCATTTCTTACTG 58.735 36.000 0.00 0.00 0.00 2.74
2219 2641 3.349022 CCAACGGTGGGAGCTAAAATTA 58.651 45.455 13.17 0.00 41.77 1.40
2221 2643 4.142469 CCAACGGTGGGAGCTAAAATTAAG 60.142 45.833 13.17 0.00 41.77 1.85
2222 2644 4.296621 ACGGTGGGAGCTAAAATTAAGT 57.703 40.909 0.00 0.00 0.00 2.24
2255 2677 5.927281 ATGCAGCTTTTACTTCATCCAAT 57.073 34.783 0.00 0.00 0.00 3.16
2640 3062 5.942872 ACTGCATAGCTTCAAATGTTGTAC 58.057 37.500 0.00 0.00 0.00 2.90
2645 3067 6.018262 GCATAGCTTCAAATGTTGTACCGATA 60.018 38.462 0.00 0.00 0.00 2.92
2725 3147 2.360801 AGGCACTCGATCTAGAAGCTTC 59.639 50.000 19.11 19.11 0.00 3.86
2729 3151 4.676723 GCACTCGATCTAGAAGCTTCTGTT 60.677 45.833 34.26 20.28 38.19 3.16
2934 3356 7.308408 CGATCAAATATTCAGGTGATGATGCTT 60.308 37.037 5.31 0.00 37.89 3.91
2937 3359 6.630444 AATATTCAGGTGATGATGCTTGTC 57.370 37.500 0.00 0.00 37.89 3.18
3000 3422 2.551721 CCAGATTGTTCTGTGCTGTCCT 60.552 50.000 2.61 0.00 46.71 3.85
3109 3531 5.985530 CCACGATTGCTTGATCTGTCTAATA 59.014 40.000 0.00 0.00 0.00 0.98
3323 3745 5.246203 TGTCTCTTGAGTTACCAAGTATGCT 59.754 40.000 11.34 0.00 42.95 3.79
3344 3766 7.661536 TGCTTAGTTGTATGGTAGAATCTCT 57.338 36.000 0.00 0.00 0.00 3.10
3599 4021 3.669536 TGTTGTCAATCAATACCGAGCA 58.330 40.909 0.00 0.00 38.38 4.26
3638 4060 3.393089 TCTGGAAGTGAAGAGAACAGC 57.607 47.619 0.00 0.00 33.76 4.40
3722 4144 9.853555 CTTCAAGTTATGTTGCCAAATATAACA 57.146 29.630 19.53 3.38 45.60 2.41
3874 4296 2.205074 CAGTATTGTGCGATGGGTCTC 58.795 52.381 0.00 0.00 0.00 3.36
4066 4488 6.325596 GGTTGAGAATTTTCAGGTAAGCATC 58.674 40.000 0.00 0.00 0.00 3.91
4493 4918 6.151480 TGAGTATACAAGTTGACATGTCCGTA 59.849 38.462 22.85 15.16 0.00 4.02
4494 4919 7.108841 AGTATACAAGTTGACATGTCCGTAT 57.891 36.000 22.85 19.80 0.00 3.06
4495 4920 7.553334 AGTATACAAGTTGACATGTCCGTATT 58.447 34.615 22.85 9.70 0.00 1.89
4497 4922 5.607119 ACAAGTTGACATGTCCGTATTTC 57.393 39.130 22.85 5.79 0.00 2.17
4498 4923 5.060506 ACAAGTTGACATGTCCGTATTTCA 58.939 37.500 22.85 0.00 0.00 2.69
4499 4924 5.705441 ACAAGTTGACATGTCCGTATTTCAT 59.295 36.000 22.85 0.00 0.00 2.57
4599 5025 2.040278 TCAGGAGGTGGTGAAAGGATTG 59.960 50.000 0.00 0.00 0.00 2.67
4755 5439 2.984435 GGGGGAAAAGTTTACCTCCA 57.016 50.000 5.03 0.00 41.15 3.86
4758 5442 3.181426 GGGGGAAAAGTTTACCTCCAGAA 60.181 47.826 5.03 0.00 41.15 3.02
4859 5543 8.219546 TGACTCAGAGAAGTCTCATATGTAAG 57.780 38.462 3.79 0.00 44.90 2.34
4863 5547 8.581253 TCAGAGAAGTCTCATATGTAAGTTCA 57.419 34.615 20.08 6.17 45.21 3.18
4933 5617 1.988406 GCTACCCCAACGGAGGAGT 60.988 63.158 0.00 0.00 34.64 3.85
4994 5678 4.284746 AGCCAACTACCTATAAGATCAGGC 59.715 45.833 0.00 0.00 35.14 4.85
5022 5706 2.703416 TCAGCAGCATTGATCGAAAGT 58.297 42.857 0.00 0.00 0.00 2.66
5073 5757 3.679917 CGGAGGCATAGAAAGAAAGCAGA 60.680 47.826 0.00 0.00 0.00 4.26
5103 5787 3.032017 TCGAGAGAAAGCAGTTGGAAG 57.968 47.619 0.00 0.00 37.03 3.46
5104 5788 2.072298 CGAGAGAAAGCAGTTGGAAGG 58.928 52.381 0.00 0.00 0.00 3.46
5105 5789 1.809547 GAGAGAAAGCAGTTGGAAGGC 59.190 52.381 0.00 0.00 0.00 4.35
5106 5790 1.143684 AGAGAAAGCAGTTGGAAGGCA 59.856 47.619 0.00 0.00 0.00 4.75
5107 5791 2.165998 GAGAAAGCAGTTGGAAGGCAT 58.834 47.619 0.00 0.00 0.00 4.40
5108 5792 2.163211 GAGAAAGCAGTTGGAAGGCATC 59.837 50.000 0.00 0.00 0.00 3.91
5109 5793 0.883833 AAAGCAGTTGGAAGGCATCG 59.116 50.000 0.00 0.00 0.00 3.84
5110 5794 0.036732 AAGCAGTTGGAAGGCATCGA 59.963 50.000 0.00 0.00 0.00 3.59
5111 5795 0.392193 AGCAGTTGGAAGGCATCGAG 60.392 55.000 0.00 0.00 0.00 4.04
5112 5796 0.391661 GCAGTTGGAAGGCATCGAGA 60.392 55.000 0.00 0.00 0.00 4.04
5113 5797 1.649664 CAGTTGGAAGGCATCGAGAG 58.350 55.000 0.00 0.00 0.00 3.20
5201 5885 1.272480 GGACTTGTAACCAATGGCCCT 60.272 52.381 0.00 0.00 0.00 5.19
5325 6009 5.694910 TGGAATCTGTCGAAGTTCTTGTTAC 59.305 40.000 0.56 0.00 0.00 2.50
5334 6018 2.132762 AGTTCTTGTTACGTTGAGCCG 58.867 47.619 0.00 0.00 0.00 5.52
5508 6192 2.996621 GGAGATTGTTTCGGACTGACAG 59.003 50.000 0.00 0.00 0.00 3.51
5614 6305 0.941542 TTTGTTTCTGAACGGAGGCG 59.058 50.000 0.00 0.00 38.65 5.52
5619 6310 0.320421 TTCTGAACGGAGGCGAAAGG 60.320 55.000 0.00 0.00 0.00 3.11
5656 6544 7.094463 CCATTCATTAAGCAGAAGAGAGTTGTT 60.094 37.037 0.00 0.00 0.00 2.83
5689 6578 6.519679 AACGAAAAAGGGACTAAAACTGTT 57.480 33.333 0.00 0.00 38.49 3.16
5711 6600 1.472082 CAAACAGTTGAGTGCCACACA 59.528 47.619 0.00 0.00 36.83 3.72
5776 6681 1.374125 CCACTGCGTCATCGGTCAA 60.374 57.895 0.00 0.00 37.56 3.18
5777 6682 0.740868 CCACTGCGTCATCGGTCAAT 60.741 55.000 0.00 0.00 37.56 2.57
5778 6683 0.371301 CACTGCGTCATCGGTCAATG 59.629 55.000 0.00 0.00 37.56 2.82
5779 6684 0.037326 ACTGCGTCATCGGTCAATGT 60.037 50.000 0.00 0.00 37.56 2.71
5780 6685 0.371301 CTGCGTCATCGGTCAATGTG 59.629 55.000 0.00 0.00 37.56 3.21
5782 6687 1.634757 GCGTCATCGGTCAATGTGCA 61.635 55.000 0.00 0.00 37.56 4.57
5785 6690 0.036022 TCATCGGTCAATGTGCACCA 59.964 50.000 15.69 2.61 32.33 4.17
5786 6691 0.168788 CATCGGTCAATGTGCACCAC 59.831 55.000 15.69 5.60 32.33 4.16
5787 6692 0.036732 ATCGGTCAATGTGCACCACT 59.963 50.000 15.69 0.00 35.11 4.00
5788 6693 0.884259 TCGGTCAATGTGCACCACTG 60.884 55.000 15.69 10.67 35.11 3.66
5789 6694 1.286880 GGTCAATGTGCACCACTGC 59.713 57.895 15.69 1.75 44.52 4.40
5797 6702 3.434319 GCACCACTGCGTCATGGG 61.434 66.667 0.00 1.98 40.59 4.00
5798 6703 2.032528 CACCACTGCGTCATGGGT 59.967 61.111 0.00 2.50 40.59 4.51
5799 6704 2.034879 CACCACTGCGTCATGGGTC 61.035 63.158 0.00 0.00 40.59 4.46
5800 6705 2.347114 CCACTGCGTCATGGGTCA 59.653 61.111 0.00 0.00 31.83 4.02
5801 6706 1.078214 CCACTGCGTCATGGGTCAT 60.078 57.895 0.00 0.00 31.83 3.06
5802 6707 0.677731 CCACTGCGTCATGGGTCATT 60.678 55.000 0.00 0.00 31.83 2.57
5803 6708 0.448990 CACTGCGTCATGGGTCATTG 59.551 55.000 0.00 0.00 0.00 2.82
5804 6709 0.036732 ACTGCGTCATGGGTCATTGT 59.963 50.000 0.00 0.00 0.00 2.71
5805 6710 0.729116 CTGCGTCATGGGTCATTGTC 59.271 55.000 0.00 0.00 0.00 3.18
5806 6711 0.676466 TGCGTCATGGGTCATTGTCC 60.676 55.000 0.00 0.00 0.00 4.02
5807 6712 0.392998 GCGTCATGGGTCATTGTCCT 60.393 55.000 0.00 0.00 0.00 3.85
5808 6713 1.950484 GCGTCATGGGTCATTGTCCTT 60.950 52.381 0.00 0.00 0.00 3.36
5809 6714 2.009774 CGTCATGGGTCATTGTCCTTC 58.990 52.381 0.00 0.00 0.00 3.46
5810 6715 2.369394 GTCATGGGTCATTGTCCTTCC 58.631 52.381 0.00 0.00 0.00 3.46
5811 6716 2.025887 GTCATGGGTCATTGTCCTTCCT 60.026 50.000 0.00 0.00 0.00 3.36
5812 6717 3.199946 GTCATGGGTCATTGTCCTTCCTA 59.800 47.826 0.00 0.00 0.00 2.94
5813 6718 3.849574 TCATGGGTCATTGTCCTTCCTAA 59.150 43.478 0.00 0.00 0.00 2.69
5814 6719 4.290985 TCATGGGTCATTGTCCTTCCTAAA 59.709 41.667 0.00 0.00 0.00 1.85
5815 6720 4.028993 TGGGTCATTGTCCTTCCTAAAC 57.971 45.455 0.00 0.00 0.00 2.01
5816 6721 3.655777 TGGGTCATTGTCCTTCCTAAACT 59.344 43.478 0.00 0.00 0.00 2.66
5817 6722 4.262617 GGGTCATTGTCCTTCCTAAACTC 58.737 47.826 0.00 0.00 0.00 3.01
5818 6723 4.019231 GGGTCATTGTCCTTCCTAAACTCT 60.019 45.833 0.00 0.00 0.00 3.24
5819 6724 4.938226 GGTCATTGTCCTTCCTAAACTCTG 59.062 45.833 0.00 0.00 0.00 3.35
5820 6725 5.280011 GGTCATTGTCCTTCCTAAACTCTGA 60.280 44.000 0.00 0.00 0.00 3.27
5821 6726 5.872070 GTCATTGTCCTTCCTAAACTCTGAG 59.128 44.000 2.45 2.45 0.00 3.35
5822 6727 3.963428 TGTCCTTCCTAAACTCTGAGC 57.037 47.619 4.19 0.00 0.00 4.26
5823 6728 3.239449 TGTCCTTCCTAAACTCTGAGCA 58.761 45.455 4.19 0.00 0.00 4.26
5824 6729 3.646162 TGTCCTTCCTAAACTCTGAGCAA 59.354 43.478 4.19 0.00 0.00 3.91
5825 6730 4.249661 GTCCTTCCTAAACTCTGAGCAAG 58.750 47.826 4.19 0.00 0.00 4.01
5826 6731 3.006247 CCTTCCTAAACTCTGAGCAAGC 58.994 50.000 4.19 0.00 0.00 4.01
5827 6732 2.370281 TCCTAAACTCTGAGCAAGCG 57.630 50.000 4.19 0.00 0.00 4.68
5828 6733 1.893137 TCCTAAACTCTGAGCAAGCGA 59.107 47.619 4.19 0.00 0.00 4.93
5829 6734 1.996191 CCTAAACTCTGAGCAAGCGAC 59.004 52.381 4.19 0.00 0.00 5.19
5830 6735 2.353208 CCTAAACTCTGAGCAAGCGACT 60.353 50.000 4.19 0.00 0.00 4.18
5831 6736 1.789506 AAACTCTGAGCAAGCGACTC 58.210 50.000 4.19 0.00 34.62 3.36
5832 6737 0.037790 AACTCTGAGCAAGCGACTCC 60.038 55.000 4.19 0.00 32.98 3.85
5833 6738 1.515952 CTCTGAGCAAGCGACTCCG 60.516 63.158 0.00 0.00 39.16 4.63
5942 6847 1.135689 ACAAACGCAATTCCGCATCTC 60.136 47.619 0.00 0.00 0.00 2.75
6022 6927 6.128715 TGCATACACACAAACAAACAAACAAG 60.129 34.615 0.00 0.00 0.00 3.16
6049 6954 4.148128 AGAATGAGATGGTAGTGCAAGG 57.852 45.455 0.00 0.00 0.00 3.61
6066 6971 0.603975 AGGGAAGAGTGCAAGCGAAC 60.604 55.000 0.00 0.00 0.00 3.95
6071 6976 1.204312 GAGTGCAAGCGAACGGAAC 59.796 57.895 0.00 0.00 0.00 3.62
6090 6995 4.495844 GGAACTCTGTCGGTTTGAAACTTG 60.496 45.833 8.09 1.55 0.00 3.16
6123 7028 1.192146 AAAGTAGAGCAGCCGGTGGA 61.192 55.000 1.90 0.00 0.00 4.02
6131 7036 1.374947 CAGCCGGTGGAGGAAGAAA 59.625 57.895 1.90 0.00 0.00 2.52
6132 7037 0.674895 CAGCCGGTGGAGGAAGAAAG 60.675 60.000 1.90 0.00 0.00 2.62
6136 7041 0.690762 CGGTGGAGGAAGAAAGGGAA 59.309 55.000 0.00 0.00 0.00 3.97
6137 7042 1.339151 CGGTGGAGGAAGAAAGGGAAG 60.339 57.143 0.00 0.00 0.00 3.46
6138 7043 1.004862 GGTGGAGGAAGAAAGGGAAGG 59.995 57.143 0.00 0.00 0.00 3.46
6142 7047 2.270858 GAGGAAGAAAGGGAAGGAGGT 58.729 52.381 0.00 0.00 0.00 3.85
6157 7062 0.737715 GAGGTGCGTGCGAGAAAGAT 60.738 55.000 0.00 0.00 0.00 2.40
6251 7158 3.713858 TGACAAGTTGGCATCAAACAG 57.286 42.857 7.51 0.00 34.28 3.16
6307 7214 2.483014 TGCCTAACATAACGGTGCTT 57.517 45.000 0.00 0.00 0.00 3.91
6324 7231 3.037549 TGCTTTTCCACCACCTGAATTT 58.962 40.909 0.00 0.00 0.00 1.82
6339 7246 4.261741 CCTGAATTTCACTGTTCAACCCTG 60.262 45.833 0.00 0.00 34.26 4.45
6341 7248 2.136298 TTTCACTGTTCAACCCTGCA 57.864 45.000 0.00 0.00 0.00 4.41
6342 7249 1.388547 TTCACTGTTCAACCCTGCAC 58.611 50.000 0.00 0.00 0.00 4.57
6379 7286 0.170116 TTCGTGCGGATTTTGCATCC 59.830 50.000 0.00 0.00 45.34 3.51
6414 7321 6.645700 GCTGAGCATAGCTTAGATGATTAC 57.354 41.667 14.03 0.00 43.59 1.89
6415 7322 6.162079 GCTGAGCATAGCTTAGATGATTACA 58.838 40.000 14.03 0.00 43.59 2.41
6447 7354 2.291282 TGGAACCAACAGACCAGTGTTT 60.291 45.455 0.00 0.00 38.65 2.83
6449 7356 3.564225 GGAACCAACAGACCAGTGTTTAG 59.436 47.826 0.00 0.00 38.65 1.85
6453 7361 3.251004 CCAACAGACCAGTGTTTAGCTTC 59.749 47.826 0.00 0.00 38.65 3.86
6469 7377 7.665559 TGTTTAGCTTCCATACTTGAGATGTTT 59.334 33.333 0.00 0.00 0.00 2.83
6470 7378 7.849804 TTAGCTTCCATACTTGAGATGTTTC 57.150 36.000 0.00 0.00 0.00 2.78
6487 7395 0.537188 TTCCATCGACCAAGAGGCTC 59.463 55.000 6.34 6.34 39.06 4.70
6488 7396 1.144936 CCATCGACCAAGAGGCTCC 59.855 63.158 11.71 0.00 39.06 4.70
6489 7397 1.333636 CCATCGACCAAGAGGCTCCT 61.334 60.000 11.71 0.00 39.06 3.69
6490 7398 1.403814 CATCGACCAAGAGGCTCCTA 58.596 55.000 11.71 0.00 39.06 2.94
6496 7404 2.968574 GACCAAGAGGCTCCTATGATGA 59.031 50.000 11.71 0.00 39.06 2.92
6506 7414 4.433615 GCTCCTATGATGACTTCGTCAAA 58.566 43.478 5.26 0.00 45.96 2.69
6511 7419 9.265901 CTCCTATGATGACTTCGTCAAATTTAT 57.734 33.333 5.26 0.00 45.96 1.40
6521 7429 7.648142 ACTTCGTCAAATTTATGATGTTGTGT 58.352 30.769 0.00 0.00 37.55 3.72
6522 7430 7.803189 ACTTCGTCAAATTTATGATGTTGTGTC 59.197 33.333 0.00 0.00 37.55 3.67
6523 7431 7.195839 TCGTCAAATTTATGATGTTGTGTCA 57.804 32.000 0.00 0.00 37.55 3.58
6524 7432 7.297391 TCGTCAAATTTATGATGTTGTGTCAG 58.703 34.615 0.00 0.00 37.55 3.51
6525 7433 6.032775 CGTCAAATTTATGATGTTGTGTCAGC 59.967 38.462 0.00 0.00 32.75 4.26
6526 7434 7.086376 GTCAAATTTATGATGTTGTGTCAGCT 58.914 34.615 0.00 0.00 0.00 4.24
6527 7435 7.272084 GTCAAATTTATGATGTTGTGTCAGCTC 59.728 37.037 0.00 0.00 0.00 4.09
6528 7436 6.822667 AATTTATGATGTTGTGTCAGCTCA 57.177 33.333 0.00 0.00 0.00 4.26
6529 7437 6.822667 ATTTATGATGTTGTGTCAGCTCAA 57.177 33.333 0.00 0.00 0.00 3.02
6530 7438 6.822667 TTTATGATGTTGTGTCAGCTCAAT 57.177 33.333 0.00 0.00 31.87 2.57
6531 7439 4.696899 ATGATGTTGTGTCAGCTCAATG 57.303 40.909 0.00 0.00 31.87 2.82
6532 7440 3.479489 TGATGTTGTGTCAGCTCAATGT 58.521 40.909 0.00 0.00 31.87 2.71
6533 7441 3.499537 TGATGTTGTGTCAGCTCAATGTC 59.500 43.478 0.00 0.00 31.87 3.06
6534 7442 3.198409 TGTTGTGTCAGCTCAATGTCT 57.802 42.857 0.00 0.00 31.87 3.41
6535 7443 3.133691 TGTTGTGTCAGCTCAATGTCTC 58.866 45.455 0.00 0.00 31.87 3.36
6536 7444 3.133691 GTTGTGTCAGCTCAATGTCTCA 58.866 45.455 0.00 0.00 31.87 3.27
6537 7445 3.036075 TGTGTCAGCTCAATGTCTCAG 57.964 47.619 0.00 0.00 0.00 3.35
6538 7446 2.629617 TGTGTCAGCTCAATGTCTCAGA 59.370 45.455 0.00 0.00 0.00 3.27
6539 7447 3.070015 TGTGTCAGCTCAATGTCTCAGAA 59.930 43.478 0.00 0.00 0.00 3.02
6540 7448 3.679025 GTGTCAGCTCAATGTCTCAGAAG 59.321 47.826 0.00 0.00 0.00 2.85
6541 7449 3.323115 TGTCAGCTCAATGTCTCAGAAGT 59.677 43.478 0.00 0.00 0.00 3.01
6542 7450 3.679025 GTCAGCTCAATGTCTCAGAAGTG 59.321 47.826 0.00 0.00 0.00 3.16
6543 7451 2.415857 CAGCTCAATGTCTCAGAAGTGC 59.584 50.000 0.00 0.00 0.00 4.40
6544 7452 2.302445 AGCTCAATGTCTCAGAAGTGCT 59.698 45.455 0.00 0.00 0.00 4.40
6545 7453 2.672381 GCTCAATGTCTCAGAAGTGCTC 59.328 50.000 0.00 0.00 0.00 4.26
6546 7454 3.863780 GCTCAATGTCTCAGAAGTGCTCA 60.864 47.826 0.00 0.00 0.00 4.26
6547 7455 4.505808 CTCAATGTCTCAGAAGTGCTCAT 58.494 43.478 0.00 0.00 0.00 2.90
6548 7456 5.658468 CTCAATGTCTCAGAAGTGCTCATA 58.342 41.667 0.00 0.00 0.00 2.15
6549 7457 5.658468 TCAATGTCTCAGAAGTGCTCATAG 58.342 41.667 0.00 0.00 0.00 2.23
6550 7458 4.669206 ATGTCTCAGAAGTGCTCATAGG 57.331 45.455 0.00 0.00 0.00 2.57
6551 7459 3.701664 TGTCTCAGAAGTGCTCATAGGA 58.298 45.455 0.00 0.00 0.00 2.94
6552 7460 3.698539 TGTCTCAGAAGTGCTCATAGGAG 59.301 47.826 0.00 0.00 44.33 3.69
6553 7461 3.699038 GTCTCAGAAGTGCTCATAGGAGT 59.301 47.826 6.23 0.00 43.37 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.534298 CACAAATGCACAAAACACCGA 58.466 42.857 0.00 0.00 0.00 4.69
142 145 1.000274 GCAAAAACATGAGCCGGTTCT 60.000 47.619 19.73 0.00 0.00 3.01
199 512 4.518970 AGAAAAATCCGCTTGTAGCAAAGA 59.481 37.500 0.00 0.00 42.58 2.52
276 595 0.403655 TGTTGCCCAGTTCCAGCATA 59.596 50.000 0.00 0.00 36.20 3.14
287 606 1.683025 CCAGCATCCATGTTGCCCA 60.683 57.895 12.75 0.00 41.06 5.36
296 616 2.715749 AATGATCGTTCCAGCATCCA 57.284 45.000 0.00 0.00 0.00 3.41
375 695 2.365582 ACAGCAAAAACACTTCCGTCT 58.634 42.857 0.00 0.00 0.00 4.18
409 730 4.917415 CAGCAAAGAAAAATACAGGTTCCG 59.083 41.667 0.00 0.00 0.00 4.30
418 739 4.588528 AGCCAGTTCCAGCAAAGAAAAATA 59.411 37.500 0.00 0.00 0.00 1.40
732 1136 4.322567 GCTTCAGATTCACCATATCCTCC 58.677 47.826 0.00 0.00 0.00 4.30
745 1149 2.093235 CCCTTCTTCCTCGCTTCAGATT 60.093 50.000 0.00 0.00 0.00 2.40
1250 1667 5.240891 AGATCACTATTGCCACCGATTATG 58.759 41.667 0.00 0.00 0.00 1.90
1263 1680 6.925718 CACCAATACATCACGAGATCACTATT 59.074 38.462 0.00 0.00 30.20 1.73
1483 1901 2.890474 GGTACATGCTGCGACGGG 60.890 66.667 0.00 0.00 0.00 5.28
1484 1902 2.125713 TGGTACATGCTGCGACGG 60.126 61.111 0.00 0.00 0.00 4.79
1512 1930 4.134563 ACAGATGTTTTTGACGCTAAGGT 58.865 39.130 0.00 0.00 0.00 3.50
1566 1985 4.940463 TCGCACAACAGAGTTAGTTAAGT 58.060 39.130 0.00 0.00 0.00 2.24
1583 2002 4.611366 CCTAACTTTGTTCGATTTTCGCAC 59.389 41.667 0.00 0.00 40.21 5.34
1639 2058 9.634021 CTACTAACTATATGCCTAGATCATCCA 57.366 37.037 0.00 0.00 0.00 3.41
1662 2082 9.661187 CTGTTGCAATATCAAAATGAGATCTAC 57.339 33.333 0.59 0.00 26.68 2.59
1669 2089 8.095792 ACATTTCCTGTTGCAATATCAAAATGA 58.904 29.630 26.40 8.00 32.90 2.57
1741 2161 1.948834 CCACAGCAATCACAAGTGACA 59.051 47.619 4.84 0.00 43.11 3.58
1761 2182 7.710475 TGGAAACAAGAAGAAAAATGTGATTCC 59.290 33.333 0.00 0.00 37.44 3.01
1817 2239 5.526506 AGAAAGCAAGCAAGACAAATTCT 57.473 34.783 0.00 0.00 35.32 2.40
1824 2246 4.972440 CACTTGTAAGAAAGCAAGCAAGAC 59.028 41.667 8.77 0.00 44.12 3.01
1831 2253 4.776349 TGGACTCACTTGTAAGAAAGCAA 58.224 39.130 0.00 0.00 0.00 3.91
1837 2259 9.179909 TGTTTAAAATTGGACTCACTTGTAAGA 57.820 29.630 0.00 0.00 0.00 2.10
1849 2271 9.838163 GTAATTGTTTCGTGTTTAAAATTGGAC 57.162 29.630 0.00 0.00 0.00 4.02
1882 2304 3.733337 ACATTTGCGGGCAAACAAATAA 58.267 36.364 19.89 0.00 46.80 1.40
1896 2318 3.002553 CAGGAAAGCCAAACAACATTTGC 59.997 43.478 0.00 0.00 36.29 3.68
1907 2329 0.817634 CGACCACACAGGAAAGCCAA 60.818 55.000 0.00 0.00 41.22 4.52
1916 2338 5.149273 CAATCAAATTTCTCGACCACACAG 58.851 41.667 0.00 0.00 0.00 3.66
2037 2459 2.346766 TTCCTTGCGGTGCATATGAT 57.653 45.000 6.97 0.00 38.76 2.45
2039 2461 2.937469 TTTTCCTTGCGGTGCATATG 57.063 45.000 0.00 0.00 38.76 1.78
2047 2469 4.168760 GACTTGATCATTTTTCCTTGCGG 58.831 43.478 0.00 0.00 0.00 5.69
2048 2470 4.168760 GGACTTGATCATTTTTCCTTGCG 58.831 43.478 0.00 0.00 0.00 4.85
2049 2471 4.925646 GTGGACTTGATCATTTTTCCTTGC 59.074 41.667 0.00 0.00 0.00 4.01
2050 2472 6.088016 TGTGGACTTGATCATTTTTCCTTG 57.912 37.500 0.00 0.00 0.00 3.61
2055 2477 5.471556 TGCATGTGGACTTGATCATTTTT 57.528 34.783 0.00 0.00 0.00 1.94
2064 2486 7.760794 ACATTAACAAATATGCATGTGGACTTG 59.239 33.333 10.16 6.74 0.00 3.16
2065 2487 7.839907 ACATTAACAAATATGCATGTGGACTT 58.160 30.769 10.16 0.00 0.00 3.01
2075 2497 8.702438 GGTGATGCATAACATTAACAAATATGC 58.298 33.333 16.28 13.39 45.60 3.14
2119 2541 4.707448 ACACTGGTTCAACAAACAATGGTA 59.293 37.500 0.00 0.00 39.81 3.25
2126 2548 3.438781 TGACAGACACTGGTTCAACAAAC 59.561 43.478 0.00 0.00 35.51 2.93
2128 2550 3.006940 GTGACAGACACTGGTTCAACAA 58.993 45.455 0.00 0.00 45.13 2.83
2181 2603 4.261405 CCGTTGGCAGTAAGAAATGAACAA 60.261 41.667 0.00 0.00 0.00 2.83
2192 2614 1.373435 CTCCCACCGTTGGCAGTAA 59.627 57.895 0.00 0.00 42.35 2.24
2197 2619 0.891904 TTTTAGCTCCCACCGTTGGC 60.892 55.000 0.00 0.00 42.35 4.52
2219 2641 4.494091 AGCTGCATAAGGACATGTACTT 57.506 40.909 26.19 26.19 37.53 2.24
2221 2643 5.567138 AAAAGCTGCATAAGGACATGTAC 57.433 39.130 0.00 0.00 0.00 2.90
2222 2644 6.414732 AGTAAAAGCTGCATAAGGACATGTA 58.585 36.000 0.00 0.00 0.00 2.29
2238 2660 7.073342 AGTCGTTATTGGATGAAGTAAAAGC 57.927 36.000 0.00 0.00 0.00 3.51
2255 2677 6.183360 TGGCCTGAATCATACATAAGTCGTTA 60.183 38.462 3.32 0.00 0.00 3.18
2334 2756 3.039011 GGGTATCTCCTCTACCTGCAAA 58.961 50.000 0.00 0.00 38.94 3.68
2338 2760 5.896073 AAATTGGGTATCTCCTCTACCTG 57.104 43.478 0.00 0.00 38.94 4.00
2640 3062 6.513393 GCTTGTTGTTAGGGATTCATTATCGG 60.513 42.308 0.00 0.00 33.82 4.18
2645 3067 4.082026 GCAGCTTGTTGTTAGGGATTCATT 60.082 41.667 0.00 0.00 0.00 2.57
2725 3147 7.112984 GGTGCAACTTCGAAATTTTACTAACAG 59.887 37.037 0.00 0.00 36.74 3.16
2729 3151 5.766174 AGGGTGCAACTTCGAAATTTTACTA 59.234 36.000 0.00 0.00 36.74 1.82
2934 3356 4.868171 GGTGCTTGACATAAATAGTCGACA 59.132 41.667 19.50 4.13 38.83 4.35
2937 3359 5.991328 ATGGTGCTTGACATAAATAGTCG 57.009 39.130 0.00 0.00 38.83 4.18
3000 3422 4.021104 ACTTATAGCACTCAACTGCACAGA 60.021 41.667 4.31 0.00 39.86 3.41
3034 3456 9.920946 AAGGAAATACATTTACCACTACATGAT 57.079 29.630 0.00 0.00 30.76 2.45
3109 3531 6.940739 ACTTAGATACAAGTGTGCAGAAGAT 58.059 36.000 0.00 0.00 37.37 2.40
3369 3791 7.986085 AAAGAAGCAGTGTAATGTCATAACT 57.014 32.000 0.00 0.00 0.00 2.24
3396 3818 9.317827 GTATTCTAACCCCTGTTATGACCTATA 57.682 37.037 0.00 0.00 36.40 1.31
3620 4042 1.686587 TCGCTGTTCTCTTCACTTCCA 59.313 47.619 0.00 0.00 0.00 3.53
3638 4060 2.966309 GAAAAGCAGCCCACCGTCG 61.966 63.158 0.00 0.00 0.00 5.12
3722 4144 0.401395 TTGACAGGGACCCACCTTCT 60.401 55.000 14.60 0.00 39.34 2.85
3874 4296 0.609131 AATCCAGTCCAACCAAGCCG 60.609 55.000 0.00 0.00 0.00 5.52
4066 4488 5.005394 GCATGTCCAAACACGTAGTACATAG 59.995 44.000 0.38 0.00 41.61 2.23
4493 4918 4.885907 CACCTGCATCCAAGAGTATGAAAT 59.114 41.667 0.00 0.00 0.00 2.17
4494 4919 4.263462 ACACCTGCATCCAAGAGTATGAAA 60.263 41.667 0.00 0.00 0.00 2.69
4495 4920 3.264193 ACACCTGCATCCAAGAGTATGAA 59.736 43.478 0.00 0.00 0.00 2.57
4497 4922 3.272574 ACACCTGCATCCAAGAGTATG 57.727 47.619 0.00 0.00 0.00 2.39
4498 4923 4.265073 GAAACACCTGCATCCAAGAGTAT 58.735 43.478 0.00 0.00 0.00 2.12
4499 4924 3.674997 GAAACACCTGCATCCAAGAGTA 58.325 45.455 0.00 0.00 0.00 2.59
4599 5025 0.877743 GGGAGTCAGAAACTGCTTGC 59.122 55.000 0.00 0.00 45.15 4.01
4747 5431 8.810990 TGTTTTCTTTACTTTTCTGGAGGTAA 57.189 30.769 0.00 0.00 0.00 2.85
4755 5439 9.301897 AGCATATCCTGTTTTCTTTACTTTTCT 57.698 29.630 0.00 0.00 0.00 2.52
4758 5442 8.635765 TCAGCATATCCTGTTTTCTTTACTTT 57.364 30.769 0.00 0.00 34.47 2.66
4859 5543 4.791411 GCGACCTGAGATGAGATAGTGAAC 60.791 50.000 0.00 0.00 0.00 3.18
4863 5547 2.937519 TGCGACCTGAGATGAGATAGT 58.062 47.619 0.00 0.00 0.00 2.12
4933 5617 1.297689 GGGCACTCTGTGATCAGCA 59.702 57.895 0.00 0.00 41.10 4.41
4994 5678 1.134189 TCAATGCTGCTGATCCCAGAG 60.134 52.381 13.04 0.00 43.02 3.35
5022 5706 0.173481 CTTTCGATGCCTCCTGACGA 59.827 55.000 0.00 0.00 0.00 4.20
5060 5744 2.551938 GCCTCCTGTCTGCTTTCTTTCT 60.552 50.000 0.00 0.00 0.00 2.52
5073 5757 1.480137 CTTTCTCTCGATGCCTCCTGT 59.520 52.381 0.00 0.00 0.00 4.00
5092 5776 0.392193 CTCGATGCCTTCCAACTGCT 60.392 55.000 0.00 0.00 0.00 4.24
5093 5777 0.391661 TCTCGATGCCTTCCAACTGC 60.392 55.000 0.00 0.00 0.00 4.40
5094 5778 1.205655 TCTCTCGATGCCTTCCAACTG 59.794 52.381 0.00 0.00 0.00 3.16
5095 5779 1.561643 TCTCTCGATGCCTTCCAACT 58.438 50.000 0.00 0.00 0.00 3.16
5096 5780 2.275318 CTTCTCTCGATGCCTTCCAAC 58.725 52.381 0.00 0.00 0.00 3.77
5097 5781 1.208052 CCTTCTCTCGATGCCTTCCAA 59.792 52.381 0.00 0.00 0.00 3.53
5098 5782 0.826715 CCTTCTCTCGATGCCTTCCA 59.173 55.000 0.00 0.00 0.00 3.53
5099 5783 0.531753 GCCTTCTCTCGATGCCTTCC 60.532 60.000 0.00 0.00 0.00 3.46
5100 5784 0.176680 TGCCTTCTCTCGATGCCTTC 59.823 55.000 0.00 0.00 0.00 3.46
5101 5785 0.177604 CTGCCTTCTCTCGATGCCTT 59.822 55.000 0.00 0.00 0.00 4.35
5102 5786 0.975040 ACTGCCTTCTCTCGATGCCT 60.975 55.000 0.00 0.00 0.00 4.75
5103 5787 0.529555 GACTGCCTTCTCTCGATGCC 60.530 60.000 0.00 0.00 0.00 4.40
5104 5788 0.174389 TGACTGCCTTCTCTCGATGC 59.826 55.000 0.00 0.00 0.00 3.91
5105 5789 1.202394 CCTGACTGCCTTCTCTCGATG 60.202 57.143 0.00 0.00 0.00 3.84
5106 5790 1.110442 CCTGACTGCCTTCTCTCGAT 58.890 55.000 0.00 0.00 0.00 3.59
5107 5791 0.038310 TCCTGACTGCCTTCTCTCGA 59.962 55.000 0.00 0.00 0.00 4.04
5108 5792 0.455410 CTCCTGACTGCCTTCTCTCG 59.545 60.000 0.00 0.00 0.00 4.04
5109 5793 0.823460 CCTCCTGACTGCCTTCTCTC 59.177 60.000 0.00 0.00 0.00 3.20
5110 5794 1.264045 GCCTCCTGACTGCCTTCTCT 61.264 60.000 0.00 0.00 0.00 3.10
5111 5795 1.220477 GCCTCCTGACTGCCTTCTC 59.780 63.158 0.00 0.00 0.00 2.87
5112 5796 0.913451 ATGCCTCCTGACTGCCTTCT 60.913 55.000 0.00 0.00 0.00 2.85
5113 5797 0.034670 AATGCCTCCTGACTGCCTTC 60.035 55.000 0.00 0.00 0.00 3.46
5114 5798 0.323178 CAATGCCTCCTGACTGCCTT 60.323 55.000 0.00 0.00 0.00 4.35
5115 5799 1.203441 TCAATGCCTCCTGACTGCCT 61.203 55.000 0.00 0.00 0.00 4.75
5201 5885 2.587247 GCTGGTCACCTCTGGCTCA 61.587 63.158 0.00 0.00 0.00 4.26
5334 6018 4.656041 GATGAACATAGTCTTGCAGCAAC 58.344 43.478 2.83 0.00 0.00 4.17
5508 6192 7.284351 GCACTCGCTTCATATTATCAACTTAC 58.716 38.462 0.00 0.00 34.30 2.34
5598 6289 1.194772 CTTTCGCCTCCGTTCAGAAAC 59.805 52.381 0.00 0.00 35.54 2.78
5604 6295 1.462283 GTAAACCTTTCGCCTCCGTTC 59.538 52.381 0.00 0.00 35.54 3.95
5619 6310 7.283127 TCTGCTTAATGAATGGATGAGGTAAAC 59.717 37.037 0.00 0.00 0.00 2.01
5656 6544 7.585579 AGTCCCTTTTTCGTTAATTAACCAA 57.414 32.000 20.08 12.63 32.69 3.67
5689 6578 2.680841 GTGTGGCACTCAACTGTTTGTA 59.319 45.455 19.83 0.00 32.05 2.41
5786 6691 0.729116 GACAATGACCCATGACGCAG 59.271 55.000 0.00 0.00 0.00 5.18
5787 6692 0.676466 GGACAATGACCCATGACGCA 60.676 55.000 0.00 0.00 0.00 5.24
5788 6693 0.392998 AGGACAATGACCCATGACGC 60.393 55.000 0.00 0.00 0.00 5.19
5789 6694 2.009774 GAAGGACAATGACCCATGACG 58.990 52.381 0.00 0.00 0.00 4.35
5790 6695 2.025887 AGGAAGGACAATGACCCATGAC 60.026 50.000 0.00 0.00 0.00 3.06
5791 6696 2.278245 AGGAAGGACAATGACCCATGA 58.722 47.619 0.00 0.00 0.00 3.07
5792 6697 2.814805 AGGAAGGACAATGACCCATG 57.185 50.000 0.00 0.00 0.00 3.66
5793 6698 4.292306 AGTTTAGGAAGGACAATGACCCAT 59.708 41.667 0.00 0.00 0.00 4.00
5794 6699 3.655777 AGTTTAGGAAGGACAATGACCCA 59.344 43.478 0.00 0.00 0.00 4.51
5795 6700 4.019231 AGAGTTTAGGAAGGACAATGACCC 60.019 45.833 0.00 0.00 0.00 4.46
5796 6701 4.938226 CAGAGTTTAGGAAGGACAATGACC 59.062 45.833 0.00 0.00 0.00 4.02
5797 6702 5.794894 TCAGAGTTTAGGAAGGACAATGAC 58.205 41.667 0.00 0.00 0.00 3.06
5798 6703 5.569630 GCTCAGAGTTTAGGAAGGACAATGA 60.570 44.000 0.00 0.00 0.00 2.57
5799 6704 4.633565 GCTCAGAGTTTAGGAAGGACAATG 59.366 45.833 0.00 0.00 0.00 2.82
5800 6705 4.287067 TGCTCAGAGTTTAGGAAGGACAAT 59.713 41.667 0.00 0.00 0.00 2.71
5801 6706 3.646162 TGCTCAGAGTTTAGGAAGGACAA 59.354 43.478 0.00 0.00 0.00 3.18
5802 6707 3.239449 TGCTCAGAGTTTAGGAAGGACA 58.761 45.455 0.00 0.00 0.00 4.02
5803 6708 3.963428 TGCTCAGAGTTTAGGAAGGAC 57.037 47.619 0.00 0.00 0.00 3.85
5804 6709 3.307059 GCTTGCTCAGAGTTTAGGAAGGA 60.307 47.826 0.00 0.00 40.39 3.36
5805 6710 3.006247 GCTTGCTCAGAGTTTAGGAAGG 58.994 50.000 0.00 0.00 40.39 3.46
5806 6711 2.670414 CGCTTGCTCAGAGTTTAGGAAG 59.330 50.000 0.00 0.00 42.25 3.46
5807 6712 2.299013 TCGCTTGCTCAGAGTTTAGGAA 59.701 45.455 0.00 0.00 0.00 3.36
5808 6713 1.893137 TCGCTTGCTCAGAGTTTAGGA 59.107 47.619 0.00 0.00 0.00 2.94
5809 6714 1.996191 GTCGCTTGCTCAGAGTTTAGG 59.004 52.381 0.00 0.00 0.00 2.69
5810 6715 2.920490 GAGTCGCTTGCTCAGAGTTTAG 59.080 50.000 0.00 0.00 33.45 1.85
5811 6716 2.352814 GGAGTCGCTTGCTCAGAGTTTA 60.353 50.000 0.00 0.00 34.83 2.01
5812 6717 1.606737 GGAGTCGCTTGCTCAGAGTTT 60.607 52.381 0.00 0.00 34.83 2.66
5813 6718 0.037790 GGAGTCGCTTGCTCAGAGTT 60.038 55.000 0.00 0.00 34.83 3.01
5814 6719 1.589113 GGAGTCGCTTGCTCAGAGT 59.411 57.895 0.00 0.00 34.83 3.24
5815 6720 1.515952 CGGAGTCGCTTGCTCAGAG 60.516 63.158 0.00 0.00 34.83 3.35
5816 6721 2.568612 CGGAGTCGCTTGCTCAGA 59.431 61.111 0.00 0.00 34.83 3.27
5826 6731 2.649331 TTAGGAAGAAAGCGGAGTCG 57.351 50.000 0.00 0.00 39.81 4.18
5827 6732 3.927758 GAGTTTAGGAAGAAAGCGGAGTC 59.072 47.826 0.00 0.00 0.00 3.36
5828 6733 3.579151 AGAGTTTAGGAAGAAAGCGGAGT 59.421 43.478 0.00 0.00 0.00 3.85
5829 6734 3.929610 CAGAGTTTAGGAAGAAAGCGGAG 59.070 47.826 0.00 0.00 0.00 4.63
5830 6735 3.576982 TCAGAGTTTAGGAAGAAAGCGGA 59.423 43.478 0.00 0.00 0.00 5.54
5831 6736 3.926616 TCAGAGTTTAGGAAGAAAGCGG 58.073 45.455 0.00 0.00 0.00 5.52
5832 6737 3.369451 GCTCAGAGTTTAGGAAGAAAGCG 59.631 47.826 0.00 0.00 0.00 4.68
5833 6738 4.319177 TGCTCAGAGTTTAGGAAGAAAGC 58.681 43.478 0.00 0.00 0.00 3.51
5834 6739 5.106752 GCTTGCTCAGAGTTTAGGAAGAAAG 60.107 44.000 7.64 0.00 42.01 2.62
5835 6740 4.757149 GCTTGCTCAGAGTTTAGGAAGAAA 59.243 41.667 7.64 0.00 42.01 2.52
5836 6741 4.319177 GCTTGCTCAGAGTTTAGGAAGAA 58.681 43.478 7.64 0.00 42.01 2.52
5837 6742 3.615110 CGCTTGCTCAGAGTTTAGGAAGA 60.615 47.826 7.64 0.00 42.01 2.87
5838 6743 2.670414 CGCTTGCTCAGAGTTTAGGAAG 59.330 50.000 0.00 0.00 42.25 3.46
5839 6744 2.299013 TCGCTTGCTCAGAGTTTAGGAA 59.701 45.455 0.00 0.00 0.00 3.36
5840 6745 1.893137 TCGCTTGCTCAGAGTTTAGGA 59.107 47.619 0.00 0.00 0.00 2.94
5841 6746 1.996191 GTCGCTTGCTCAGAGTTTAGG 59.004 52.381 0.00 0.00 0.00 2.69
5842 6747 2.920490 GAGTCGCTTGCTCAGAGTTTAG 59.080 50.000 0.00 0.00 33.45 1.85
5843 6748 2.352814 GGAGTCGCTTGCTCAGAGTTTA 60.353 50.000 0.00 0.00 34.83 2.01
5872 6777 0.179108 GGGTCGATGTTCCTCTTCGG 60.179 60.000 0.00 0.00 41.79 4.30
5964 6869 8.318412 TGTTGAATTCTACTATTCCTGCTTGTA 58.682 33.333 18.63 0.00 34.34 2.41
5965 6870 7.168219 TGTTGAATTCTACTATTCCTGCTTGT 58.832 34.615 18.63 0.00 34.34 3.16
5970 6875 7.066284 CCTGGTTGTTGAATTCTACTATTCCTG 59.934 40.741 18.63 16.30 34.34 3.86
5975 6880 5.648092 GCACCTGGTTGTTGAATTCTACTAT 59.352 40.000 18.63 0.00 0.00 2.12
5981 6886 3.665745 ATGCACCTGGTTGTTGAATTC 57.334 42.857 0.00 0.00 0.00 2.17
6006 6911 7.020914 TCTTTTTGCTTGTTTGTTTGTTTGT 57.979 28.000 0.00 0.00 0.00 2.83
6007 6912 7.905031 TTCTTTTTGCTTGTTTGTTTGTTTG 57.095 28.000 0.00 0.00 0.00 2.93
6008 6913 8.348507 TCATTCTTTTTGCTTGTTTGTTTGTTT 58.651 25.926 0.00 0.00 0.00 2.83
6009 6914 7.869800 TCATTCTTTTTGCTTGTTTGTTTGTT 58.130 26.923 0.00 0.00 0.00 2.83
6022 6927 5.098211 GCACTACCATCTCATTCTTTTTGC 58.902 41.667 0.00 0.00 0.00 3.68
6049 6954 1.493311 CGTTCGCTTGCACTCTTCC 59.507 57.895 0.00 0.00 0.00 3.46
6066 6971 1.860676 TTCAAACCGACAGAGTTCCG 58.139 50.000 0.00 0.00 0.00 4.30
6071 6976 3.202906 TCCAAGTTTCAAACCGACAGAG 58.797 45.455 0.00 0.00 0.00 3.35
6090 6995 7.859875 GCTGCTCTACTTTATTCATTCAATTCC 59.140 37.037 0.00 0.00 0.00 3.01
6123 7028 1.988846 CACCTCCTTCCCTTTCTTCCT 59.011 52.381 0.00 0.00 0.00 3.36
6131 7036 4.021925 GCACGCACCTCCTTCCCT 62.022 66.667 0.00 0.00 0.00 4.20
6136 7041 2.771763 CTTTCTCGCACGCACCTCCT 62.772 60.000 0.00 0.00 0.00 3.69
6137 7042 2.357034 TTTCTCGCACGCACCTCC 60.357 61.111 0.00 0.00 0.00 4.30
6138 7043 0.737715 ATCTTTCTCGCACGCACCTC 60.738 55.000 0.00 0.00 0.00 3.85
6142 7047 1.020861 ATGCATCTTTCTCGCACGCA 61.021 50.000 0.00 0.00 38.73 5.24
6307 7214 3.636300 CAGTGAAATTCAGGTGGTGGAAA 59.364 43.478 0.00 0.00 0.00 3.13
6324 7231 0.813610 CGTGCAGGGTTGAACAGTGA 60.814 55.000 0.00 0.00 31.76 3.41
6355 7262 1.317319 GCAAAATCCGCACGAAATTCG 59.683 47.619 14.35 14.35 46.93 3.34
6379 7286 0.037326 TGCTCAGCTCAACCCTTACG 60.037 55.000 0.00 0.00 0.00 3.18
6380 7287 2.409948 ATGCTCAGCTCAACCCTTAC 57.590 50.000 0.00 0.00 0.00 2.34
6391 7298 6.162079 TGTAATCATCTAAGCTATGCTCAGC 58.838 40.000 0.00 0.00 38.25 4.26
6392 7299 8.774890 AATGTAATCATCTAAGCTATGCTCAG 57.225 34.615 0.00 0.00 33.19 3.35
6424 7331 0.182775 ACTGGTCTGTTGGTTCCACC 59.817 55.000 0.00 0.00 39.22 4.61
6425 7332 1.308998 CACTGGTCTGTTGGTTCCAC 58.691 55.000 0.00 0.00 0.00 4.02
6435 7342 3.126001 TGGAAGCTAAACACTGGTCTG 57.874 47.619 0.00 0.00 0.00 3.51
6447 7354 6.070251 TGGAAACATCTCAAGTATGGAAGCTA 60.070 38.462 0.00 0.00 33.40 3.32
6449 7356 4.943705 TGGAAACATCTCAAGTATGGAAGC 59.056 41.667 0.00 0.00 33.40 3.86
6469 7377 1.330655 GGAGCCTCTTGGTCGATGGA 61.331 60.000 0.00 0.00 42.55 3.41
6470 7378 1.144936 GGAGCCTCTTGGTCGATGG 59.855 63.158 0.00 0.00 42.55 3.51
6506 7414 6.822667 TTGAGCTGACACAACATCATAAAT 57.177 33.333 0.00 0.00 0.00 1.40
6511 7419 3.479489 ACATTGAGCTGACACAACATCA 58.521 40.909 0.00 0.00 0.00 3.07
6521 7429 3.863780 GCACTTCTGAGACATTGAGCTGA 60.864 47.826 0.00 0.00 0.00 4.26
6522 7430 2.415857 GCACTTCTGAGACATTGAGCTG 59.584 50.000 0.00 0.00 0.00 4.24
6523 7431 2.302445 AGCACTTCTGAGACATTGAGCT 59.698 45.455 0.00 0.00 0.00 4.09
6524 7432 2.672381 GAGCACTTCTGAGACATTGAGC 59.328 50.000 0.00 0.00 0.00 4.26
6525 7433 3.922910 TGAGCACTTCTGAGACATTGAG 58.077 45.455 0.00 0.00 0.00 3.02
6526 7434 4.548451 ATGAGCACTTCTGAGACATTGA 57.452 40.909 0.00 0.00 0.00 2.57
6527 7435 4.809958 CCTATGAGCACTTCTGAGACATTG 59.190 45.833 0.00 0.00 0.00 2.82
6528 7436 4.713814 TCCTATGAGCACTTCTGAGACATT 59.286 41.667 0.00 0.00 0.00 2.71
6529 7437 4.285020 TCCTATGAGCACTTCTGAGACAT 58.715 43.478 0.00 0.00 0.00 3.06
6530 7438 3.698539 CTCCTATGAGCACTTCTGAGACA 59.301 47.826 0.00 0.00 0.00 3.41
6531 7439 3.699038 ACTCCTATGAGCACTTCTGAGAC 59.301 47.826 0.00 0.00 42.74 3.36
6532 7440 3.974719 ACTCCTATGAGCACTTCTGAGA 58.025 45.455 0.00 0.00 42.74 3.27


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

AutoCloner maintained by Alex Coulton.