Multiple sequence alignment - TraesCS4D01G354800

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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 TraesCS4D01G354800 chr4D 100.000 4024 0 0 1 4024 504314615 504318638 0.000000e+00 7432.0
1 TraesCS4D01G354800 chr5A 89.208 1844 113 39 1585 3411 688963561 688965335 0.000000e+00 2224.0
2 TraesCS4D01G354800 chr5A 88.081 990 87 19 517 1483 688962564 688963545 0.000000e+00 1146.0
3 TraesCS4D01G354800 chr5A 83.291 395 42 13 1 390 688962035 688962410 3.850000e-90 342.0
4 TraesCS4D01G354800 chr5A 82.963 270 33 9 3739 4005 688965700 688965959 8.700000e-57 231.0
5 TraesCS4D01G354800 chr5A 88.636 132 8 7 3871 3995 688967819 688967950 1.940000e-33 154.0
6 TraesCS4D01G354800 chr5A 95.000 40 2 0 2529 2568 17950274 17950313 3.360000e-06 63.9
7 TraesCS4D01G354800 chr4B 94.184 1410 54 12 1939 3343 650936538 650937924 0.000000e+00 2124.0
8 TraesCS4D01G354800 chr4B 84.675 1664 141 50 1 1613 650934310 650935910 0.000000e+00 1555.0
9 TraesCS4D01G354800 chr4B 94.545 330 16 2 1611 1940 650936049 650936376 3.590000e-140 508.0
10 TraesCS4D01G354800 chr4B 81.707 246 36 9 3768 4006 650938296 650938539 3.170000e-46 196.0
11 TraesCS4D01G354800 chr4B 92.683 41 3 0 2530 2570 63755923 63755883 4.340000e-05 60.2
12 TraesCS4D01G354800 chr4B 94.737 38 2 0 3712 3749 171091082 171091119 4.340000e-05 60.2
13 TraesCS4D01G354800 chr1B 89.567 508 38 7 1066 1561 554152983 554153487 7.340000e-177 630.0
14 TraesCS4D01G354800 chr1B 89.173 508 40 7 1066 1561 625436165 625435661 1.590000e-173 619.0
15 TraesCS4D01G354800 chr2D 89.587 509 34 10 1066 1561 632563526 632563024 2.640000e-176 628.0
16 TraesCS4D01G354800 chr2D 91.304 46 3 1 3712 3757 5239334 5239378 1.210000e-05 62.1
17 TraesCS4D01G354800 chr2D 92.683 41 2 1 2529 2568 432878426 432878386 1.560000e-04 58.4
18 TraesCS4D01G354800 chr7B 89.173 508 40 7 1066 1561 704165055 704165559 1.590000e-173 619.0
19 TraesCS4D01G354800 chr7B 89.066 503 40 9 1066 1555 648223883 648223383 9.560000e-171 610.0
20 TraesCS4D01G354800 chr3B 89.173 508 40 7 1066 1561 33986661 33987165 1.590000e-173 619.0
21 TraesCS4D01G354800 chr2B 89.173 508 40 9 1066 1561 695759599 695760103 1.590000e-173 619.0
22 TraesCS4D01G354800 chr5D 92.105 114 4 3 3866 3974 490026022 490026135 5.380000e-34 156.0
23 TraesCS4D01G354800 chr5D 90.000 110 8 3 3865 3971 546684269 546684160 5.420000e-29 139.0
24 TraesCS4D01G354800 chr5D 92.683 41 2 1 2529 2568 531874424 531874464 1.560000e-04 58.4
25 TraesCS4D01G354800 chr5D 86.275 51 5 2 2530 2578 15663469 15663419 2.000000e-03 54.7
26 TraesCS4D01G354800 chr3D 91.589 107 5 4 3868 3972 604522020 604521916 1.170000e-30 145.0
27 TraesCS4D01G354800 chr4A 92.929 99 6 1 3866 3964 622243455 622243552 4.190000e-30 143.0
28 TraesCS4D01G354800 chr4A 97.143 35 1 0 3715 3749 466924014 466923980 4.340000e-05 60.2
29 TraesCS4D01G354800 chr5B 90.090 111 7 2 3867 3973 604157990 604158100 1.510000e-29 141.0
30 TraesCS4D01G354800 chr5B 92.000 100 5 3 3875 3971 689883666 689883567 1.950000e-28 137.0
31 TraesCS4D01G354800 chr6B 92.683 41 2 1 2529 2568 417353840 417353800 1.560000e-04 58.4
32 TraesCS4D01G354800 chr6A 92.683 41 2 1 2529 2568 332224824 332224864 1.560000e-04 58.4
33 TraesCS4D01G354800 chr1D 92.683 41 2 1 2529 2568 341552914 341552954 1.560000e-04 58.4
34 TraesCS4D01G354800 chr1A 92.683 41 2 1 2529 2568 310311561 310311521 1.560000e-04 58.4


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 TraesCS4D01G354800 chr4D 504314615 504318638 4023 False 7432.00 7432 100.00000 1 4024 1 chr4D.!!$F1 4023
1 TraesCS4D01G354800 chr5A 688962035 688967950 5915 False 819.40 2224 86.43580 1 4005 5 chr5A.!!$F2 4004
2 TraesCS4D01G354800 chr4B 650934310 650938539 4229 False 1095.75 2124 88.77775 1 4006 4 chr4B.!!$F2 4005
3 TraesCS4D01G354800 chr1B 554152983 554153487 504 False 630.00 630 89.56700 1066 1561 1 chr1B.!!$F1 495
4 TraesCS4D01G354800 chr1B 625435661 625436165 504 True 619.00 619 89.17300 1066 1561 1 chr1B.!!$R1 495
5 TraesCS4D01G354800 chr2D 632563024 632563526 502 True 628.00 628 89.58700 1066 1561 1 chr2D.!!$R2 495
6 TraesCS4D01G354800 chr7B 704165055 704165559 504 False 619.00 619 89.17300 1066 1561 1 chr7B.!!$F1 495
7 TraesCS4D01G354800 chr7B 648223383 648223883 500 True 610.00 610 89.06600 1066 1555 1 chr7B.!!$R1 489
8 TraesCS4D01G354800 chr3B 33986661 33987165 504 False 619.00 619 89.17300 1066 1561 1 chr3B.!!$F1 495
9 TraesCS4D01G354800 chr2B 695759599 695760103 504 False 619.00 619 89.17300 1066 1561 1 chr2B.!!$F1 495

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
820 958 0.034283 AGGTACGAGGTCCTCTCCAC 60.034 60.0 17.00 10.78 39.30 4.02 F
1220 1370 0.179040 TCAGGTTGGTTTGGTCGACC 60.179 55.0 28.17 28.17 38.63 4.79 F
1980 3026 0.324091 CCCTGCAGCCTTTCCTCAAT 60.324 55.0 8.66 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 3007 0.324091 ATTGAGGAAAGGCTGCAGGG 60.324 55.0 17.12 0.0 0.0 4.45 R
2895 3946 0.394938 TTTGGAACCTGTAGCGAGCA 59.605 50.0 0.00 0.0 0.0 4.26 R
3650 4898 0.181587 TTCGCAGGAAAAGGGTCACA 59.818 50.0 0.00 0.0 0.0 3.58 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
36 37 3.261897 GTCCCATTTGTTCCTCTCTCTGA 59.738 47.826 0.00 0.00 0.00 3.27
58 59 5.649395 TGACACCTCATTGAAATCTCCAATC 59.351 40.000 0.00 0.00 32.40 2.67
118 119 0.321564 TCGTGTCCCAAATCTGCTGG 60.322 55.000 0.00 0.00 0.00 4.85
128 129 1.345063 AATCTGCTGGCAAAGGCTTT 58.655 45.000 6.68 6.68 40.87 3.51
167 168 5.189180 AGAAGCATGTTAACCTCCATTCTC 58.811 41.667 2.48 0.00 0.00 2.87
174 175 2.367947 AACCTCCATTCTCCCTTCCT 57.632 50.000 0.00 0.00 0.00 3.36
175 176 3.508952 AACCTCCATTCTCCCTTCCTA 57.491 47.619 0.00 0.00 0.00 2.94
176 177 2.765502 ACCTCCATTCTCCCTTCCTAC 58.234 52.381 0.00 0.00 0.00 3.18
177 178 2.319438 ACCTCCATTCTCCCTTCCTACT 59.681 50.000 0.00 0.00 0.00 2.57
179 180 3.389656 CCTCCATTCTCCCTTCCTACTTC 59.610 52.174 0.00 0.00 0.00 3.01
192 196 2.301870 TCCTACTTCTGACAACCGCATT 59.698 45.455 0.00 0.00 0.00 3.56
238 242 5.423704 TGACCCGTAAATTAACTCCATCA 57.576 39.130 0.00 0.00 0.00 3.07
241 245 4.186159 CCCGTAAATTAACTCCATCACGT 58.814 43.478 0.00 0.00 0.00 4.49
244 248 5.349270 CCGTAAATTAACTCCATCACGTCAA 59.651 40.000 0.00 0.00 0.00 3.18
246 250 7.292292 CGTAAATTAACTCCATCACGTCAAAA 58.708 34.615 0.00 0.00 0.00 2.44
259 263 3.065510 CACGTCAAAACACACCAATACCA 59.934 43.478 0.00 0.00 0.00 3.25
260 264 3.886505 ACGTCAAAACACACCAATACCAT 59.113 39.130 0.00 0.00 0.00 3.55
270 275 5.248477 ACACACCAATACCATCACTTCTACT 59.752 40.000 0.00 0.00 0.00 2.57
282 287 2.496470 CACTTCTACTCCCACTACCCAC 59.504 54.545 0.00 0.00 0.00 4.61
299 304 2.094390 CCCACAGCAAAACCATCATCAG 60.094 50.000 0.00 0.00 0.00 2.90
308 313 3.814504 AACCATCATCAGAACCCAACT 57.185 42.857 0.00 0.00 0.00 3.16
322 327 0.600255 CCAACTTCGTCGTCAAGCCT 60.600 55.000 0.00 0.00 0.00 4.58
346 351 5.436175 TCCACTCTCTGTTTTGACAATTGA 58.564 37.500 13.59 0.00 0.00 2.57
402 514 2.357952 CCCCAAATAACTAAGAAGCGGC 59.642 50.000 0.00 0.00 0.00 6.53
418 530 1.084370 CGGCTTTGGACCGTGATCTC 61.084 60.000 0.00 0.00 45.70 2.75
426 538 2.271607 GACCGTGATCTCGCAGCTGA 62.272 60.000 20.43 0.00 0.00 4.26
427 539 1.153765 CCGTGATCTCGCAGCTGAA 60.154 57.895 20.43 3.11 0.00 3.02
452 564 0.321346 TTCTTGAGGCATGACTCGCA 59.679 50.000 23.51 11.82 40.39 5.10
453 565 0.108472 TCTTGAGGCATGACTCGCAG 60.108 55.000 23.51 20.41 40.39 5.18
454 566 1.703438 CTTGAGGCATGACTCGCAGC 61.703 60.000 23.51 0.09 40.39 5.25
455 567 2.176314 TTGAGGCATGACTCGCAGCT 62.176 55.000 23.51 0.00 40.39 4.24
456 568 2.125229 AGGCATGACTCGCAGCTG 60.125 61.111 10.11 10.11 0.00 4.24
457 569 2.125391 GGCATGACTCGCAGCTGA 60.125 61.111 20.43 0.00 0.00 4.26
462 574 2.352651 GCATGACTCGCAGCTGATTTTA 59.647 45.455 20.43 0.00 0.00 1.52
472 584 4.563976 CGCAGCTGATTTTATTTTTGAGGG 59.436 41.667 20.43 0.00 0.00 4.30
474 586 6.165577 GCAGCTGATTTTATTTTTGAGGGAA 58.834 36.000 20.43 0.00 0.00 3.97
475 587 6.091305 GCAGCTGATTTTATTTTTGAGGGAAC 59.909 38.462 20.43 0.00 0.00 3.62
476 588 6.308766 CAGCTGATTTTATTTTTGAGGGAACG 59.691 38.462 8.42 0.00 0.00 3.95
485 597 2.882876 GAGGGAACGTCGCAGCTA 59.117 61.111 0.00 0.00 32.16 3.32
486 598 1.214589 GAGGGAACGTCGCAGCTAA 59.785 57.895 0.00 0.00 32.16 3.09
487 599 0.179108 GAGGGAACGTCGCAGCTAAT 60.179 55.000 0.00 0.00 32.16 1.73
488 600 0.249398 AGGGAACGTCGCAGCTAATT 59.751 50.000 0.00 0.00 0.00 1.40
489 601 1.479323 AGGGAACGTCGCAGCTAATTA 59.521 47.619 0.00 0.00 0.00 1.40
490 602 2.093869 AGGGAACGTCGCAGCTAATTAA 60.094 45.455 0.00 0.00 0.00 1.40
491 603 2.674357 GGGAACGTCGCAGCTAATTAAA 59.326 45.455 0.00 0.00 0.00 1.52
492 604 3.125658 GGGAACGTCGCAGCTAATTAAAA 59.874 43.478 0.00 0.00 0.00 1.52
493 605 4.378666 GGGAACGTCGCAGCTAATTAAAAA 60.379 41.667 0.00 0.00 0.00 1.94
512 624 2.851104 CGTGCTTCGTTCGGGTTC 59.149 61.111 0.00 0.00 34.52 3.62
513 625 2.851104 GTGCTTCGTTCGGGTTCG 59.149 61.111 0.00 0.00 37.82 3.95
514 626 2.356553 TGCTTCGTTCGGGTTCGG 60.357 61.111 0.00 0.00 36.95 4.30
515 627 3.785499 GCTTCGTTCGGGTTCGGC 61.785 66.667 0.00 0.00 36.95 5.54
516 628 3.116531 CTTCGTTCGGGTTCGGCC 61.117 66.667 0.00 0.00 36.95 6.13
521 633 1.284715 GTTCGGGTTCGGCCTTTTG 59.715 57.895 0.00 0.00 37.43 2.44
545 657 1.873591 CCGTGGAAAAACTGTCCAGAG 59.126 52.381 0.40 0.00 45.85 3.35
552 664 0.689623 AAACTGTCCAGAGAGCCCAG 59.310 55.000 0.40 0.00 0.00 4.45
569 682 3.165071 CCCAGATAAACAAACAAGGCCT 58.835 45.455 0.00 0.00 0.00 5.19
593 706 3.731652 TTTTTCTACCCGTGTCTTCGA 57.268 42.857 0.00 0.00 0.00 3.71
669 790 3.458163 CCCGCGAGAACCCTAGCA 61.458 66.667 8.23 0.00 40.46 3.49
680 801 0.846870 ACCCTAGCAAAGAAGCCCCT 60.847 55.000 0.00 0.00 34.23 4.79
681 802 0.106967 CCCTAGCAAAGAAGCCCCTC 60.107 60.000 0.00 0.00 34.23 4.30
683 804 0.915364 CTAGCAAAGAAGCCCCTCCT 59.085 55.000 0.00 0.00 34.23 3.69
820 958 0.034283 AGGTACGAGGTCCTCTCCAC 60.034 60.000 17.00 10.78 39.30 4.02
835 973 2.511452 CCACCCATCTCCTAGCCCG 61.511 68.421 0.00 0.00 0.00 6.13
953 1093 1.021390 CCGCTGATTCGGTTTGCTCT 61.021 55.000 0.00 0.00 44.18 4.09
1029 1169 2.403586 GCGCCCGTTGATGTAAGC 59.596 61.111 0.00 0.00 0.00 3.09
1061 1201 4.046938 TCTCGCAACTTATTAGAGCCAG 57.953 45.455 0.00 0.00 0.00 4.85
1220 1370 0.179040 TCAGGTTGGTTTGGTCGACC 60.179 55.000 28.17 28.17 38.63 4.79
1239 1389 4.054671 GACCTCTTGCCTCTATTGATTCG 58.945 47.826 0.00 0.00 0.00 3.34
1240 1390 3.452627 ACCTCTTGCCTCTATTGATTCGT 59.547 43.478 0.00 0.00 0.00 3.85
1241 1391 4.080863 ACCTCTTGCCTCTATTGATTCGTT 60.081 41.667 0.00 0.00 0.00 3.85
1267 1417 3.696051 CAGCTTAGCAAGGGCAGATTTTA 59.304 43.478 7.07 0.00 44.61 1.52
1275 1430 6.423182 AGCAAGGGCAGATTTTATGTAGTAA 58.577 36.000 0.00 0.00 44.61 2.24
1277 1432 7.561356 AGCAAGGGCAGATTTTATGTAGTAATT 59.439 33.333 0.00 0.00 44.61 1.40
1278 1433 8.846211 GCAAGGGCAGATTTTATGTAGTAATTA 58.154 33.333 0.00 0.00 40.72 1.40
1344 1506 1.345741 CTTCTGGAGAGCTGGTGTTCA 59.654 52.381 0.00 0.00 0.00 3.18
1428 1590 2.249139 AGCGAACACTAGTTTCCCTCT 58.751 47.619 0.00 0.00 38.30 3.69
1468 1632 1.790123 CGCACCATCACGTAAATGTGC 60.790 52.381 17.46 17.46 39.73 4.57
1519 2261 4.920640 TTTCGTCAAATGCCTTTGGTAA 57.079 36.364 13.56 4.41 41.74 2.85
1520 2262 5.461032 TTTCGTCAAATGCCTTTGGTAAT 57.539 34.783 13.56 0.00 41.74 1.89
1534 2276 5.885912 CCTTTGGTAATATAGTGTGGCACTT 59.114 40.000 19.83 9.69 42.59 3.16
1542 2284 9.158233 GTAATATAGTGTGGCACTTCAAAGTTA 57.842 33.333 19.83 7.33 42.59 2.24
1633 2516 8.788325 AGTAAATACAATGGTTTCTCTACACC 57.212 34.615 0.00 0.00 0.00 4.16
1660 2543 5.798125 TTGTCAATCAATTGCCCTTTGTA 57.202 34.783 0.00 0.00 37.68 2.41
1665 2548 5.304101 TCAATCAATTGCCCTTTGTAACAGT 59.696 36.000 0.00 0.00 37.68 3.55
1680 2563 9.268268 CTTTGTAACAGTATTGTCCTCTTTGTA 57.732 33.333 0.00 0.00 36.23 2.41
1703 2586 4.979815 ACTGCAAAGTTAAACGCAATAACC 59.020 37.500 0.00 0.00 34.50 2.85
1710 2593 9.828852 CAAAGTTAAACGCAATAACCTGTAATA 57.171 29.630 2.95 0.00 34.50 0.98
1737 2620 6.588756 GTGAGTAATTAACCATCTCGTTGTCA 59.411 38.462 0.00 0.00 0.00 3.58
1762 2645 5.007430 CAGATTTTAGCTCGCTTGATGTGAT 59.993 40.000 0.00 0.00 34.35 3.06
1782 2665 7.537715 TGTGATTATGATTGCAAGTAAACTGG 58.462 34.615 4.94 0.00 0.00 4.00
1812 2695 9.932207 TTTTCTTCTACTCCGTAACAAATATGA 57.068 29.630 0.00 0.00 0.00 2.15
1924 2807 7.545965 GCTCTCTTAGTACTGCAAAGTTCAATA 59.454 37.037 5.39 0.00 0.00 1.90
1932 2815 5.931532 ACTGCAAAGTTCAATACATCTTCG 58.068 37.500 0.00 0.00 0.00 3.79
1963 3009 9.780186 ATAAATGAGTAAACACTATAGCTTCCC 57.220 33.333 0.00 0.00 0.00 3.97
1980 3026 0.324091 CCCTGCAGCCTTTCCTCAAT 60.324 55.000 8.66 0.00 0.00 2.57
2006 3053 3.265995 CCACCTTTGGTAATAGTGTCCCT 59.734 47.826 0.00 0.00 38.23 4.20
2033 3080 2.753296 TGCTGCAAAGTTAAATGCACC 58.247 42.857 0.00 3.56 46.87 5.01
2040 3087 4.511082 GCAAAGTTAAATGCACCAACACAT 59.489 37.500 8.96 0.00 42.12 3.21
2075 3122 7.759489 TTAGATTTTAGTTTGCCTGATGTGT 57.241 32.000 0.00 0.00 0.00 3.72
2130 3177 6.621316 TTTTTCTACTCGGCAACAAATACA 57.379 33.333 0.00 0.00 0.00 2.29
2133 3180 1.821216 ACTCGGCAACAAATACAGGG 58.179 50.000 0.00 0.00 0.00 4.45
2137 3184 3.223435 TCGGCAACAAATACAGGGAAAA 58.777 40.909 0.00 0.00 0.00 2.29
2143 3190 6.330278 GCAACAAATACAGGGAAAATAGACC 58.670 40.000 0.00 0.00 0.00 3.85
2148 3195 8.487028 ACAAATACAGGGAAAATAGACCTCTAG 58.513 37.037 0.00 0.00 30.66 2.43
2190 3237 9.212641 CTGACCATAGATGAGTAATTAACCATG 57.787 37.037 5.79 0.00 0.00 3.66
2191 3238 7.661437 TGACCATAGATGAGTAATTAACCATGC 59.339 37.037 5.79 0.00 0.00 4.06
2204 3251 1.375013 CCATGCTTTTGGTGCAGCC 60.375 57.895 14.36 5.89 44.04 4.85
2208 3255 0.540923 TGCTTTTGGTGCAGCCTTTT 59.459 45.000 14.36 0.00 38.35 2.27
2210 3257 0.939419 CTTTTGGTGCAGCCTTTTGC 59.061 50.000 14.36 0.00 44.33 3.68
2223 3270 1.403249 CCTTTTGCGAGATGCCTTTGG 60.403 52.381 0.00 0.00 45.60 3.28
2275 3322 8.077991 TGCACCATCGTGTATATAAGTAGTTAC 58.922 37.037 0.00 0.00 42.39 2.50
2324 3371 2.082231 CTCTCATCAGTTGCCCTTGTG 58.918 52.381 0.00 0.00 0.00 3.33
2366 3413 6.889301 TGCTGAGAAGTTGAATTCAGAATT 57.111 33.333 8.20 8.20 39.46 2.17
2439 3486 1.671742 CCCTCTGTAACAGTGCCGT 59.328 57.895 0.00 0.00 32.61 5.68
2460 3508 1.531149 CCTCTTGGTACTGCAACGTTG 59.469 52.381 23.90 23.90 0.00 4.10
2484 3532 6.604396 TGAATGCATCAAGGTGAAATGTATCT 59.396 34.615 0.00 0.00 34.30 1.98
2530 3578 6.256321 CACAGATTTTAGCTTGCTTTGTTTGT 59.744 34.615 0.00 0.00 0.00 2.83
2531 3579 6.476706 ACAGATTTTAGCTTGCTTTGTTTGTC 59.523 34.615 0.00 0.00 0.00 3.18
2533 3581 7.223387 CAGATTTTAGCTTGCTTTGTTTGTCTT 59.777 33.333 0.00 0.00 0.00 3.01
2534 3582 8.413229 AGATTTTAGCTTGCTTTGTTTGTCTTA 58.587 29.630 0.00 0.00 0.00 2.10
2535 3583 7.749539 TTTTAGCTTGCTTTGTTTGTCTTAC 57.250 32.000 0.00 0.00 0.00 2.34
2538 3586 5.906073 AGCTTGCTTTGTTTGTCTTACATT 58.094 33.333 0.00 0.00 0.00 2.71
2539 3587 7.038154 AGCTTGCTTTGTTTGTCTTACATTA 57.962 32.000 0.00 0.00 0.00 1.90
2540 3588 7.661040 AGCTTGCTTTGTTTGTCTTACATTAT 58.339 30.769 0.00 0.00 0.00 1.28
2541 3589 7.596248 AGCTTGCTTTGTTTGTCTTACATTATG 59.404 33.333 0.00 0.00 0.00 1.90
2542 3590 7.148755 GCTTGCTTTGTTTGTCTTACATTATGG 60.149 37.037 0.00 0.00 0.00 2.74
2543 3591 6.686630 TGCTTTGTTTGTCTTACATTATGGG 58.313 36.000 0.00 0.00 0.00 4.00
2544 3592 6.491745 TGCTTTGTTTGTCTTACATTATGGGA 59.508 34.615 0.00 0.00 0.00 4.37
2545 3593 6.806739 GCTTTGTTTGTCTTACATTATGGGAC 59.193 38.462 0.00 3.17 0.00 4.46
2546 3594 6.489127 TTGTTTGTCTTACATTATGGGACG 57.511 37.500 0.00 0.00 0.00 4.79
2547 3595 4.938832 TGTTTGTCTTACATTATGGGACGG 59.061 41.667 0.00 0.00 0.00 4.79
2548 3596 5.180271 GTTTGTCTTACATTATGGGACGGA 58.820 41.667 0.00 0.00 0.00 4.69
2549 3597 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
2550 3598 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
2551 3599 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2552 3600 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2838 3889 1.901464 GCAACAACATCCCACCCGT 60.901 57.895 0.00 0.00 0.00 5.28
2895 3946 2.236146 TGCGTCCACTAACATCCATTCT 59.764 45.455 0.00 0.00 0.00 2.40
3041 4092 1.606350 GAGTTTGACGACTCGGCGTG 61.606 60.000 0.98 7.20 45.72 5.34
3117 4168 2.832129 TGGATCAGGGAGTGTGTAAGAC 59.168 50.000 0.00 0.00 0.00 3.01
3295 4351 7.741216 CAGTTTCAGAATGTTTTGTTTGTGTTG 59.259 33.333 0.00 0.00 37.40 3.33
3412 4497 7.417797 GCATGGTACCTTTTGGATGTCAAATAT 60.418 37.037 14.36 0.00 43.95 1.28
3413 4658 8.477256 CATGGTACCTTTTGGATGTCAAATATT 58.523 33.333 14.36 0.00 43.95 1.28
3427 4672 2.880890 CAAATATTGAGGGCTCCTTCGG 59.119 50.000 0.00 0.00 31.76 4.30
3440 4685 4.127171 GCTCCTTCGGTGCAATAGAATTA 58.873 43.478 0.00 0.00 41.27 1.40
3441 4686 4.757149 GCTCCTTCGGTGCAATAGAATTAT 59.243 41.667 0.00 0.00 41.27 1.28
3447 4692 5.547465 TCGGTGCAATAGAATTATACAGGG 58.453 41.667 0.00 0.00 0.00 4.45
3449 4694 5.408604 CGGTGCAATAGAATTATACAGGGTC 59.591 44.000 0.00 0.00 0.00 4.46
3450 4695 6.296026 GGTGCAATAGAATTATACAGGGTCA 58.704 40.000 0.00 0.00 0.00 4.02
3457 4702 6.936968 AGAATTATACAGGGTCAGTATCCC 57.063 41.667 0.00 0.00 44.90 3.85
3481 4726 7.383843 CCCCGGGAATATTTTCAATTTTAATCG 59.616 37.037 26.32 0.00 33.23 3.34
3494 4739 4.360951 TTTTAATCGTCACCCAGGAGTT 57.639 40.909 0.00 0.00 0.00 3.01
3502 4747 3.356290 GTCACCCAGGAGTTATTTGCAT 58.644 45.455 0.00 0.00 0.00 3.96
3503 4748 4.523083 GTCACCCAGGAGTTATTTGCATA 58.477 43.478 0.00 0.00 0.00 3.14
3504 4749 5.133221 GTCACCCAGGAGTTATTTGCATAT 58.867 41.667 0.00 0.00 0.00 1.78
3505 4750 6.296026 GTCACCCAGGAGTTATTTGCATATA 58.704 40.000 0.00 0.00 0.00 0.86
3506 4751 6.942576 GTCACCCAGGAGTTATTTGCATATAT 59.057 38.462 0.00 0.00 0.00 0.86
3510 4755 8.641541 ACCCAGGAGTTATTTGCATATATTTTG 58.358 33.333 0.00 0.00 0.00 2.44
3511 4756 8.641541 CCCAGGAGTTATTTGCATATATTTTGT 58.358 33.333 0.00 0.00 0.00 2.83
3536 4782 5.302568 TGAAGCATTTTCATCCACTCAAACT 59.697 36.000 0.00 0.00 0.00 2.66
3552 4798 2.038387 AACTGTGGAGTTCGTTTGCT 57.962 45.000 0.00 0.00 38.01 3.91
3553 4799 1.299541 ACTGTGGAGTTCGTTTGCTG 58.700 50.000 0.00 0.00 0.00 4.41
3560 4808 1.846175 GAGTTCGTTTGCTGTTGTTGC 59.154 47.619 0.00 0.00 0.00 4.17
3575 4823 6.449635 TGTTGTTGCTATCAAACACTCTTT 57.550 33.333 0.00 0.00 33.37 2.52
3595 4843 8.416329 ACTCTTTTGCACAAATTTCTCTTACAT 58.584 29.630 0.00 0.00 0.00 2.29
3597 4845 8.412456 TCTTTTGCACAAATTTCTCTTACATGA 58.588 29.630 0.00 0.00 0.00 3.07
3598 4846 9.199982 CTTTTGCACAAATTTCTCTTACATGAT 57.800 29.630 0.00 0.00 0.00 2.45
3628 4876 8.290325 CAGGAGTAATTCTGTGTTTTACCTTTC 58.710 37.037 0.00 0.00 0.00 2.62
3635 4883 9.793259 AATTCTGTGTTTTACCTTTCTCTATGA 57.207 29.630 0.00 0.00 0.00 2.15
3636 4884 9.793259 ATTCTGTGTTTTACCTTTCTCTATGAA 57.207 29.630 0.00 0.00 0.00 2.57
3637 4885 9.793259 TTCTGTGTTTTACCTTTCTCTATGAAT 57.207 29.630 0.00 0.00 34.24 2.57
3648 4896 7.558081 ACCTTTCTCTATGAATAAAAAGAGGGC 59.442 37.037 0.00 0.00 36.85 5.19
3649 4897 7.557719 CCTTTCTCTATGAATAAAAAGAGGGCA 59.442 37.037 0.00 0.00 36.85 5.36
3650 4898 9.129532 CTTTCTCTATGAATAAAAAGAGGGCAT 57.870 33.333 0.00 0.00 36.85 4.40
3651 4899 8.455903 TTCTCTATGAATAAAAAGAGGGCATG 57.544 34.615 0.00 0.00 36.85 4.06
3652 4900 7.577303 TCTCTATGAATAAAAAGAGGGCATGT 58.423 34.615 0.00 0.00 36.85 3.21
3653 4901 7.500227 TCTCTATGAATAAAAAGAGGGCATGTG 59.500 37.037 0.00 0.00 36.85 3.21
3654 4902 7.345691 TCTATGAATAAAAAGAGGGCATGTGA 58.654 34.615 0.00 0.00 0.00 3.58
3655 4903 5.643379 TGAATAAAAAGAGGGCATGTGAC 57.357 39.130 0.00 0.00 0.00 3.67
3656 4904 4.462483 TGAATAAAAAGAGGGCATGTGACC 59.538 41.667 0.00 0.00 46.16 4.02
3663 4911 2.276869 GGGCATGTGACCCTTTTCC 58.723 57.895 0.00 0.00 44.68 3.13
3664 4912 0.251787 GGGCATGTGACCCTTTTCCT 60.252 55.000 0.00 0.00 44.68 3.36
3665 4913 0.890683 GGCATGTGACCCTTTTCCTG 59.109 55.000 0.00 0.00 0.00 3.86
3666 4914 0.244721 GCATGTGACCCTTTTCCTGC 59.755 55.000 0.00 0.00 0.00 4.85
3679 4927 3.348647 TTTCCTGCGAATCAATGAGGA 57.651 42.857 0.00 0.00 0.00 3.71
3686 4934 4.546570 TGCGAATCAATGAGGACGTATAG 58.453 43.478 0.00 0.00 0.00 1.31
3703 4951 8.576936 GACGTATAGTCTAAGGAGGAAAAATG 57.423 38.462 0.00 0.00 46.13 2.32
3704 4952 7.498443 ACGTATAGTCTAAGGAGGAAAAATGG 58.502 38.462 0.00 0.00 0.00 3.16
3708 4956 5.810095 AGTCTAAGGAGGAAAAATGGTCAG 58.190 41.667 0.00 0.00 0.00 3.51
3709 4957 5.310857 AGTCTAAGGAGGAAAAATGGTCAGT 59.689 40.000 0.00 0.00 0.00 3.41
3710 4958 6.500751 AGTCTAAGGAGGAAAAATGGTCAGTA 59.499 38.462 0.00 0.00 0.00 2.74
3711 4959 7.182930 AGTCTAAGGAGGAAAAATGGTCAGTAT 59.817 37.037 0.00 0.00 0.00 2.12
3712 4960 7.829706 GTCTAAGGAGGAAAAATGGTCAGTATT 59.170 37.037 0.00 0.00 0.00 1.89
3713 4961 9.053472 TCTAAGGAGGAAAAATGGTCAGTATTA 57.947 33.333 0.00 0.00 0.00 0.98
3714 4962 9.853177 CTAAGGAGGAAAAATGGTCAGTATTAT 57.147 33.333 0.00 0.00 0.00 1.28
3716 4964 9.547279 AAGGAGGAAAAATGGTCAGTATTATTT 57.453 29.630 0.00 0.00 0.00 1.40
3717 4965 9.547279 AGGAGGAAAAATGGTCAGTATTATTTT 57.453 29.630 0.00 0.00 35.05 1.82
3718 4966 9.803315 GGAGGAAAAATGGTCAGTATTATTTTC 57.197 33.333 0.00 0.00 33.11 2.29
3752 5000 9.624373 ATTATCAAATCTAAGATGCACTTCAGT 57.376 29.630 5.04 0.00 39.72 3.41
3757 5005 4.569943 TCTAAGATGCACTTCAGTTGTCC 58.430 43.478 5.04 0.00 39.72 4.02
3763 5011 4.108699 TGCACTTCAGTTGTCCTTTTTG 57.891 40.909 0.00 0.00 0.00 2.44
3764 5012 3.119173 TGCACTTCAGTTGTCCTTTTTGG 60.119 43.478 0.00 0.00 37.10 3.28
3782 5030 8.947055 CTTTTTGGAGAAAGGAAAAGAAATGA 57.053 30.769 0.00 0.00 40.00 2.57
3783 5031 8.947055 TTTTTGGAGAAAGGAAAAGAAATGAG 57.053 30.769 0.00 0.00 0.00 2.90
3785 5033 4.524328 TGGAGAAAGGAAAAGAAATGAGGC 59.476 41.667 0.00 0.00 0.00 4.70
3787 5035 4.482990 AGAAAGGAAAAGAAATGAGGCCA 58.517 39.130 5.01 0.00 0.00 5.36
3788 5036 5.089434 AGAAAGGAAAAGAAATGAGGCCAT 58.911 37.500 5.01 0.00 33.66 4.40
3789 5037 6.256053 AGAAAGGAAAAGAAATGAGGCCATA 58.744 36.000 5.01 0.00 31.59 2.74
3792 5040 6.535963 AGGAAAAGAAATGAGGCCATAAAG 57.464 37.500 5.01 0.00 31.59 1.85
3800 5049 1.339631 TGAGGCCATAAAGAACGTGGG 60.340 52.381 5.01 0.00 33.58 4.61
3830 5080 2.095110 TGAAGCAGGAAATCAATGCACG 60.095 45.455 11.04 0.00 42.45 5.34
3833 5083 1.202114 GCAGGAAATCAATGCACGGAA 59.798 47.619 0.00 0.00 39.75 4.30
3834 5084 2.352617 GCAGGAAATCAATGCACGGAAA 60.353 45.455 0.00 0.00 39.75 3.13
3836 5087 4.439974 GCAGGAAATCAATGCACGGAAATA 60.440 41.667 0.00 0.00 39.75 1.40
3841 5092 7.041098 AGGAAATCAATGCACGGAAATACTATC 60.041 37.037 0.00 0.00 0.00 2.08
3871 5122 7.920160 TCTGAATACATGCACTAAAACATCA 57.080 32.000 0.00 0.00 0.00 3.07
3953 5204 1.767692 GGTTGGGCCCTTCTCTTCA 59.232 57.895 25.70 0.00 0.00 3.02
3954 5205 0.332972 GGTTGGGCCCTTCTCTTCAT 59.667 55.000 25.70 0.00 0.00 2.57
3955 5206 1.272704 GGTTGGGCCCTTCTCTTCATT 60.273 52.381 25.70 0.00 0.00 2.57
3956 5207 2.025321 GGTTGGGCCCTTCTCTTCATTA 60.025 50.000 25.70 0.00 0.00 1.90
3957 5208 3.563479 GGTTGGGCCCTTCTCTTCATTAA 60.563 47.826 25.70 0.06 0.00 1.40
3958 5209 4.086457 GTTGGGCCCTTCTCTTCATTAAA 58.914 43.478 25.70 0.00 0.00 1.52
3989 5242 3.665173 TTTTTGTGAAATTTGCCACGC 57.335 38.095 0.00 0.00 36.15 5.34
4011 5337 8.566260 CACGCTATTACACCTTAGTTAGTCTAT 58.434 37.037 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.510430 AGAGGAACAAATGGGACCTAATTC 58.490 41.667 0.00 0.00 0.00 2.17
15 16 3.261897 GTCAGAGAGAGGAACAAATGGGA 59.738 47.826 0.00 0.00 0.00 4.37
36 37 4.952335 GGATTGGAGATTTCAATGAGGTGT 59.048 41.667 0.00 0.00 35.26 4.16
58 59 2.489971 TCTACACTTTCGTGGCTTTGG 58.510 47.619 0.00 0.00 45.50 3.28
128 129 2.683742 GCTTCTATGGCAGGGCTAACAA 60.684 50.000 0.00 0.00 0.00 2.83
137 138 4.202441 AGGTTAACATGCTTCTATGGCAG 58.798 43.478 8.10 0.00 43.15 4.85
138 139 4.199310 GAGGTTAACATGCTTCTATGGCA 58.801 43.478 8.10 0.00 44.05 4.92
167 168 2.353803 CGGTTGTCAGAAGTAGGAAGGG 60.354 54.545 0.00 0.00 0.00 3.95
174 175 4.530710 ACTAATGCGGTTGTCAGAAGTA 57.469 40.909 0.00 0.00 0.00 2.24
175 176 3.402628 ACTAATGCGGTTGTCAGAAGT 57.597 42.857 0.00 0.00 0.00 3.01
176 177 4.271049 CCATACTAATGCGGTTGTCAGAAG 59.729 45.833 0.00 0.00 0.00 2.85
177 178 4.188462 CCATACTAATGCGGTTGTCAGAA 58.812 43.478 0.00 0.00 0.00 3.02
179 180 3.531538 ACCATACTAATGCGGTTGTCAG 58.468 45.455 0.00 0.00 0.00 3.51
238 242 3.280295 TGGTATTGGTGTGTTTTGACGT 58.720 40.909 0.00 0.00 0.00 4.34
241 245 5.136828 AGTGATGGTATTGGTGTGTTTTGA 58.863 37.500 0.00 0.00 0.00 2.69
244 248 5.385198 AGAAGTGATGGTATTGGTGTGTTT 58.615 37.500 0.00 0.00 0.00 2.83
246 250 4.640771 AGAAGTGATGGTATTGGTGTGT 57.359 40.909 0.00 0.00 0.00 3.72
259 263 3.012502 TGGGTAGTGGGAGTAGAAGTGAT 59.987 47.826 0.00 0.00 0.00 3.06
260 264 2.380932 TGGGTAGTGGGAGTAGAAGTGA 59.619 50.000 0.00 0.00 0.00 3.41
270 275 0.847373 TTTTGCTGTGGGTAGTGGGA 59.153 50.000 0.00 0.00 0.00 4.37
282 287 3.367703 GGGTTCTGATGATGGTTTTGCTG 60.368 47.826 0.00 0.00 0.00 4.41
308 313 0.599204 GTGGAAGGCTTGACGACGAA 60.599 55.000 3.46 0.00 0.00 3.85
322 327 5.885352 TCAATTGTCAAAACAGAGAGTGGAA 59.115 36.000 5.13 0.00 36.57 3.53
346 351 0.251608 AAAGTATTTGTGGGCCGGCT 60.252 50.000 28.56 6.90 36.60 5.52
377 385 5.395990 CCGCTTCTTAGTTATTTGGGGACTA 60.396 44.000 0.00 0.00 0.00 2.59
383 391 4.965119 AAGCCGCTTCTTAGTTATTTGG 57.035 40.909 0.00 0.00 0.00 3.28
402 514 0.389817 TGCGAGATCACGGTCCAAAG 60.390 55.000 14.41 0.00 0.00 2.77
438 550 2.172372 CAGCTGCGAGTCATGCCTC 61.172 63.158 0.00 0.00 0.00 4.70
439 551 1.969200 ATCAGCTGCGAGTCATGCCT 61.969 55.000 9.47 0.00 0.00 4.75
440 552 1.094073 AATCAGCTGCGAGTCATGCC 61.094 55.000 9.47 0.00 0.00 4.40
442 554 4.808077 ATAAAATCAGCTGCGAGTCATG 57.192 40.909 9.47 0.00 0.00 3.07
443 555 5.824904 AAATAAAATCAGCTGCGAGTCAT 57.175 34.783 9.47 0.00 0.00 3.06
444 556 5.627499 AAAATAAAATCAGCTGCGAGTCA 57.373 34.783 9.47 0.00 0.00 3.41
446 558 6.012658 TCAAAAATAAAATCAGCTGCGAGT 57.987 33.333 9.47 0.00 0.00 4.18
447 559 5.514204 CCTCAAAAATAAAATCAGCTGCGAG 59.486 40.000 9.47 0.45 0.00 5.03
448 560 5.401550 CCTCAAAAATAAAATCAGCTGCGA 58.598 37.500 9.47 0.00 0.00 5.10
449 561 4.563976 CCCTCAAAAATAAAATCAGCTGCG 59.436 41.667 9.47 0.00 0.00 5.18
450 562 5.723295 TCCCTCAAAAATAAAATCAGCTGC 58.277 37.500 9.47 0.00 0.00 5.25
452 564 6.015434 ACGTTCCCTCAAAAATAAAATCAGCT 60.015 34.615 0.00 0.00 0.00 4.24
453 565 6.156519 ACGTTCCCTCAAAAATAAAATCAGC 58.843 36.000 0.00 0.00 0.00 4.26
454 566 6.523201 CGACGTTCCCTCAAAAATAAAATCAG 59.477 38.462 0.00 0.00 0.00 2.90
455 567 6.375377 CGACGTTCCCTCAAAAATAAAATCA 58.625 36.000 0.00 0.00 0.00 2.57
456 568 5.285370 GCGACGTTCCCTCAAAAATAAAATC 59.715 40.000 0.00 0.00 0.00 2.17
457 569 5.158494 GCGACGTTCCCTCAAAAATAAAAT 58.842 37.500 0.00 0.00 0.00 1.82
462 574 1.535462 CTGCGACGTTCCCTCAAAAAT 59.465 47.619 0.00 0.00 0.00 1.82
495 607 2.995450 CGAACCCGAACGAAGCACG 61.995 63.158 0.00 1.99 42.52 5.34
496 608 2.664436 CCGAACCCGAACGAAGCAC 61.664 63.158 0.00 0.00 38.22 4.40
497 609 2.356553 CCGAACCCGAACGAAGCA 60.357 61.111 0.00 0.00 38.22 3.91
498 610 3.785499 GCCGAACCCGAACGAAGC 61.785 66.667 0.00 0.00 38.22 3.86
499 611 3.116531 GGCCGAACCCGAACGAAG 61.117 66.667 0.00 0.00 38.22 3.79
500 612 2.663423 AAAGGCCGAACCCGAACGAA 62.663 55.000 0.00 0.00 40.58 3.85
501 613 2.663423 AAAAGGCCGAACCCGAACGA 62.663 55.000 0.00 0.00 40.58 3.85
502 614 2.255881 AAAAGGCCGAACCCGAACG 61.256 57.895 0.00 0.00 40.58 3.95
503 615 1.284715 CAAAAGGCCGAACCCGAAC 59.715 57.895 0.00 0.00 40.58 3.95
504 616 0.752376 AACAAAAGGCCGAACCCGAA 60.752 50.000 0.00 0.00 40.58 4.30
505 617 1.152922 AACAAAAGGCCGAACCCGA 60.153 52.632 0.00 0.00 40.58 5.14
506 618 1.284715 GAACAAAAGGCCGAACCCG 59.715 57.895 0.00 0.00 40.58 5.28
507 619 1.663739 GGAACAAAAGGCCGAACCC 59.336 57.895 0.00 0.00 40.58 4.11
508 620 1.663739 GGGAACAAAAGGCCGAACC 59.336 57.895 0.00 0.00 39.61 3.62
509 621 1.284715 CGGGAACAAAAGGCCGAAC 59.715 57.895 0.00 0.00 0.00 3.95
510 622 1.152922 ACGGGAACAAAAGGCCGAA 60.153 52.632 0.00 0.00 0.00 4.30
511 623 1.894756 CACGGGAACAAAAGGCCGA 60.895 57.895 0.00 0.00 0.00 5.54
512 624 2.642700 CACGGGAACAAAAGGCCG 59.357 61.111 0.00 0.00 0.00 6.13
513 625 1.110518 TTCCACGGGAACAAAAGGCC 61.111 55.000 0.00 0.00 36.71 5.19
514 626 0.747852 TTTCCACGGGAACAAAAGGC 59.252 50.000 5.02 0.00 41.87 4.35
515 627 3.118920 AGTTTTTCCACGGGAACAAAAGG 60.119 43.478 5.02 0.00 41.87 3.11
516 628 3.862845 CAGTTTTTCCACGGGAACAAAAG 59.137 43.478 5.02 0.00 41.87 2.27
521 633 1.335810 GGACAGTTTTTCCACGGGAAC 59.664 52.381 5.02 0.00 41.87 3.62
545 657 3.367395 GCCTTGTTTGTTTATCTGGGCTC 60.367 47.826 0.00 0.00 34.86 4.70
669 790 0.120172 AGAGGAGGAGGGGCTTCTTT 59.880 55.000 0.00 0.00 0.00 2.52
680 801 0.402504 GCCGGATAGAGAGAGGAGGA 59.597 60.000 5.05 0.00 0.00 3.71
681 802 0.610785 GGCCGGATAGAGAGAGGAGG 60.611 65.000 5.05 0.00 0.00 4.30
683 804 1.073373 CGGCCGGATAGAGAGAGGA 59.927 63.158 20.10 0.00 0.00 3.71
788 926 1.676635 GTACCTGAAAACCCGGGGC 60.677 63.158 27.92 11.77 36.89 5.80
820 958 2.122813 ACCGGGCTAGGAGATGGG 60.123 66.667 6.32 0.00 34.73 4.00
835 973 3.551407 GATGGAGGAGGCGGGACC 61.551 72.222 0.00 0.00 39.61 4.46
1011 1151 2.701006 CTTACATCAACGGGCGCG 59.299 61.111 22.69 22.69 0.00 6.86
1029 1169 0.445436 GTTGCGAGAGTTGCTGGATG 59.555 55.000 0.00 0.00 0.00 3.51
1038 1178 3.447586 TGGCTCTAATAAGTTGCGAGAGT 59.552 43.478 9.95 0.00 36.76 3.24
1220 1370 5.814705 AGAAACGAATCAATAGAGGCAAGAG 59.185 40.000 0.00 0.00 0.00 2.85
1239 1389 1.470494 GCCCTTGCTAAGCTGAGAAAC 59.530 52.381 0.74 0.00 33.53 2.78
1240 1390 1.073763 TGCCCTTGCTAAGCTGAGAAA 59.926 47.619 0.74 0.00 38.71 2.52
1241 1391 0.692476 TGCCCTTGCTAAGCTGAGAA 59.308 50.000 0.74 0.00 38.71 2.87
1275 1430 6.835819 TGCAGACAGACAGTAAGTACTAAT 57.164 37.500 0.00 0.00 34.13 1.73
1277 1432 7.228906 GGATATGCAGACAGACAGTAAGTACTA 59.771 40.741 0.00 0.00 34.13 1.82
1278 1433 6.039941 GGATATGCAGACAGACAGTAAGTACT 59.960 42.308 0.00 0.00 36.90 2.73
1279 1434 6.210078 GGATATGCAGACAGACAGTAAGTAC 58.790 44.000 0.00 0.00 0.00 2.73
1280 1435 5.008712 CGGATATGCAGACAGACAGTAAGTA 59.991 44.000 0.00 0.00 0.00 2.24
1428 1590 4.857871 CGCTTAGCATTGTAGCACTAAA 57.142 40.909 4.70 0.00 36.85 1.85
1457 1621 4.092383 GGTCAATTACTCGCACATTTACGT 59.908 41.667 0.00 0.00 0.00 3.57
1519 2261 8.630054 TTTAACTTTGAAGTGCCACACTATAT 57.370 30.769 0.00 0.00 44.62 0.86
1520 2262 8.511321 CATTTAACTTTGAAGTGCCACACTATA 58.489 33.333 0.00 0.00 44.62 1.31
1617 2500 4.741928 AAAGGGGTGTAGAGAAACCATT 57.258 40.909 0.00 0.00 38.27 3.16
1629 2512 4.743348 GCAATTGATTGACAAAAGGGGTGT 60.743 41.667 10.34 0.00 42.03 4.16
1632 2515 3.337358 GGCAATTGATTGACAAAAGGGG 58.663 45.455 10.34 0.00 45.17 4.79
1660 2543 5.701290 GCAGTACAAAGAGGACAATACTGTT 59.299 40.000 10.07 0.00 40.93 3.16
1680 2563 4.979815 GGTTATTGCGTTTAACTTTGCAGT 59.020 37.500 0.00 0.00 38.75 4.40
1710 2593 7.103641 ACAACGAGATGGTTAATTACTCACAT 58.896 34.615 0.00 0.00 0.00 3.21
1737 2620 4.093998 CACATCAAGCGAGCTAAAATCTGT 59.906 41.667 0.00 0.00 0.00 3.41
1818 2701 4.100189 AGTGCAATCGCCTAGAAATCTAGT 59.900 41.667 14.63 0.00 43.34 2.57
1835 2718 4.297552 GACTAAGGTCAGTGCAAGTGCAA 61.298 47.826 7.71 0.00 45.98 4.08
1940 2823 7.275920 CAGGGAAGCTATAGTGTTTACTCATT 58.724 38.462 0.84 0.00 38.36 2.57
1950 2996 1.542108 GGCTGCAGGGAAGCTATAGTG 60.542 57.143 17.12 0.00 40.64 2.74
1958 3004 0.679321 GAGGAAAGGCTGCAGGGAAG 60.679 60.000 17.12 0.00 0.00 3.46
1961 3007 0.324091 ATTGAGGAAAGGCTGCAGGG 60.324 55.000 17.12 0.00 0.00 4.45
1963 3009 1.830279 TGATTGAGGAAAGGCTGCAG 58.170 50.000 10.11 10.11 0.00 4.41
2006 3053 6.927936 TGCATTTAACTTTGCAGCATTAAGAA 59.072 30.769 12.90 0.00 43.54 2.52
2062 3109 5.981088 ACATCATAAACACATCAGGCAAA 57.019 34.783 0.00 0.00 0.00 3.68
2117 3164 3.651803 TTTTCCCTGTATTTGTTGCCG 57.348 42.857 0.00 0.00 0.00 5.69
2143 3190 1.719600 GCAAGTGCAGTCACCTAGAG 58.280 55.000 0.00 0.00 44.16 2.43
2190 3237 0.939419 CAAAAGGCTGCACCAAAAGC 59.061 50.000 0.50 0.00 43.14 3.51
2191 3238 0.939419 GCAAAAGGCTGCACCAAAAG 59.061 50.000 0.50 0.00 43.14 2.27
2204 3251 1.270550 ACCAAAGGCATCTCGCAAAAG 59.729 47.619 0.00 0.00 45.17 2.27
2208 3255 2.016318 CATTACCAAAGGCATCTCGCA 58.984 47.619 0.00 0.00 45.17 5.10
2210 3257 3.009723 ACACATTACCAAAGGCATCTCG 58.990 45.455 0.00 0.00 0.00 4.04
2275 3322 6.034683 GCACAGAAACTACGGTTCATACTTAG 59.965 42.308 0.00 0.00 34.14 2.18
2287 3334 1.071605 GAGGCTGCACAGAAACTACG 58.928 55.000 0.50 0.00 0.00 3.51
2344 3391 6.581542 CACAATTCTGAATTCAACTTCTCAGC 59.418 38.462 12.50 0.00 36.15 4.26
2386 3433 6.299141 ACAAAAAGGAGCAGAGAAACTATCA 58.701 36.000 0.00 0.00 0.00 2.15
2439 3486 1.045407 ACGTTGCAGTACCAAGAGGA 58.955 50.000 0.00 0.00 38.69 3.71
2460 3508 6.916387 CAGATACATTTCACCTTGATGCATTC 59.084 38.462 0.00 0.00 0.00 2.67
2475 3523 7.669722 ACAAGATGGTTGGTTACAGATACATTT 59.330 33.333 0.00 0.00 0.00 2.32
2530 3578 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2531 3579 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2533 3581 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2534 3582 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2535 3583 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2538 3586 2.852714 TTTACTCCCTCCGTCCCATA 57.147 50.000 0.00 0.00 0.00 2.74
2539 3587 2.172717 CAATTTACTCCCTCCGTCCCAT 59.827 50.000 0.00 0.00 0.00 4.00
2540 3588 1.557832 CAATTTACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
2541 3589 1.746171 GCAATTTACTCCCTCCGTCCC 60.746 57.143 0.00 0.00 0.00 4.46
2542 3590 1.065709 TGCAATTTACTCCCTCCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
2543 3591 2.396590 TGCAATTTACTCCCTCCGTC 57.603 50.000 0.00 0.00 0.00 4.79
2544 3592 2.871096 TTGCAATTTACTCCCTCCGT 57.129 45.000 0.00 0.00 0.00 4.69
2545 3593 5.357032 AGTTTATTGCAATTTACTCCCTCCG 59.643 40.000 18.75 0.00 0.00 4.63
2546 3594 6.405842 CCAGTTTATTGCAATTTACTCCCTCC 60.406 42.308 18.75 0.00 0.00 4.30
2547 3595 6.152831 ACCAGTTTATTGCAATTTACTCCCTC 59.847 38.462 18.75 0.00 0.00 4.30
2548 3596 6.016555 ACCAGTTTATTGCAATTTACTCCCT 58.983 36.000 18.75 1.84 0.00 4.20
2549 3597 6.280855 ACCAGTTTATTGCAATTTACTCCC 57.719 37.500 18.75 0.00 0.00 4.30
2550 3598 8.088365 AGAAACCAGTTTATTGCAATTTACTCC 58.912 33.333 18.75 7.49 32.11 3.85
2551 3599 9.476202 AAGAAACCAGTTTATTGCAATTTACTC 57.524 29.630 18.75 8.90 33.35 2.59
2552 3600 9.830975 AAAGAAACCAGTTTATTGCAATTTACT 57.169 25.926 18.75 17.16 34.64 2.24
2838 3889 3.886505 AGACAAGGAAACGGTGCATTTAA 59.113 39.130 0.00 0.00 0.00 1.52
2895 3946 0.394938 TTTGGAACCTGTAGCGAGCA 59.605 50.000 0.00 0.00 0.00 4.26
3041 4092 3.430556 GCGAAAAGAGACTCTTCTGGTTC 59.569 47.826 17.97 15.51 35.27 3.62
3295 4351 3.559238 ACCGATTCACAAACTCAATGC 57.441 42.857 0.00 0.00 0.00 3.56
3427 4672 6.992715 ACTGACCCTGTATAATTCTATTGCAC 59.007 38.462 0.00 0.00 0.00 4.57
3440 4685 2.011122 CGGGGATACTGACCCTGTAT 57.989 55.000 0.00 0.00 45.91 2.29
3441 4686 3.526211 CGGGGATACTGACCCTGTA 57.474 57.895 0.00 0.00 45.91 2.74
3447 4692 4.635699 AAATATTCCCGGGGATACTGAC 57.364 45.455 24.63 0.00 0.00 3.51
3449 4694 4.980573 TGAAAATATTCCCGGGGATACTG 58.019 43.478 24.63 0.00 34.49 2.74
3450 4695 5.656549 TTGAAAATATTCCCGGGGATACT 57.343 39.130 24.63 10.93 34.49 2.12
3457 4702 8.865590 ACGATTAAAATTGAAAATATTCCCGG 57.134 30.769 0.00 0.00 34.49 5.73
3481 4726 2.790433 TGCAAATAACTCCTGGGTGAC 58.210 47.619 0.00 0.00 0.00 3.67
3503 4748 8.938906 GTGGATGAAAATGCTTCAACAAAATAT 58.061 29.630 0.00 0.00 31.55 1.28
3504 4749 8.149647 AGTGGATGAAAATGCTTCAACAAAATA 58.850 29.630 0.00 0.00 31.55 1.40
3505 4750 6.993902 AGTGGATGAAAATGCTTCAACAAAAT 59.006 30.769 0.00 0.00 31.55 1.82
3506 4751 6.347696 AGTGGATGAAAATGCTTCAACAAAA 58.652 32.000 0.00 0.00 31.55 2.44
3510 4755 5.125100 TGAGTGGATGAAAATGCTTCAAC 57.875 39.130 0.00 0.00 31.55 3.18
3511 4756 5.787953 TTGAGTGGATGAAAATGCTTCAA 57.212 34.783 0.00 0.00 31.55 2.69
3512 4757 5.302568 AGTTTGAGTGGATGAAAATGCTTCA 59.697 36.000 0.00 0.00 0.00 3.02
3536 4782 1.400142 CAACAGCAAACGAACTCCACA 59.600 47.619 0.00 0.00 0.00 4.17
3552 4798 6.449635 AAAGAGTGTTTGATAGCAACAACA 57.550 33.333 0.00 0.00 32.79 3.33
3553 4799 6.291796 GCAAAAGAGTGTTTGATAGCAACAAC 60.292 38.462 0.00 0.00 40.29 3.32
3560 4808 7.935338 ATTTGTGCAAAAGAGTGTTTGATAG 57.065 32.000 1.26 0.00 40.29 2.08
3598 4846 9.880157 GGTAAAACACAGAATTACTCCTGTATA 57.120 33.333 0.00 0.00 41.26 1.47
3628 4876 7.500227 TCACATGCCCTCTTTTTATTCATAGAG 59.500 37.037 0.00 0.00 35.11 2.43
3634 4882 4.142160 GGGTCACATGCCCTCTTTTTATTC 60.142 45.833 0.00 0.00 42.81 1.75
3635 4883 3.769300 GGGTCACATGCCCTCTTTTTATT 59.231 43.478 0.00 0.00 42.81 1.40
3636 4884 3.365472 GGGTCACATGCCCTCTTTTTAT 58.635 45.455 0.00 0.00 42.81 1.40
3637 4885 2.802719 GGGTCACATGCCCTCTTTTTA 58.197 47.619 0.00 0.00 42.81 1.52
3639 4887 3.363787 GGGTCACATGCCCTCTTTT 57.636 52.632 0.00 0.00 42.81 2.27
3645 4893 0.251787 AGGAAAAGGGTCACATGCCC 60.252 55.000 0.00 0.00 46.43 5.36
3646 4894 0.890683 CAGGAAAAGGGTCACATGCC 59.109 55.000 0.00 0.00 0.00 4.40
3647 4895 0.244721 GCAGGAAAAGGGTCACATGC 59.755 55.000 0.00 0.00 0.00 4.06
3648 4896 0.523072 CGCAGGAAAAGGGTCACATG 59.477 55.000 0.00 0.00 0.00 3.21
3649 4897 0.400213 TCGCAGGAAAAGGGTCACAT 59.600 50.000 0.00 0.00 0.00 3.21
3650 4898 0.181587 TTCGCAGGAAAAGGGTCACA 59.818 50.000 0.00 0.00 0.00 3.58
3651 4899 1.468914 GATTCGCAGGAAAAGGGTCAC 59.531 52.381 0.00 0.00 35.40 3.67
3652 4900 1.073125 TGATTCGCAGGAAAAGGGTCA 59.927 47.619 0.00 0.00 35.40 4.02
3653 4901 1.821216 TGATTCGCAGGAAAAGGGTC 58.179 50.000 0.00 0.00 35.40 4.46
3654 4902 2.286365 TTGATTCGCAGGAAAAGGGT 57.714 45.000 0.00 0.00 35.40 4.34
3655 4903 2.754552 TCATTGATTCGCAGGAAAAGGG 59.245 45.455 0.00 0.00 35.40 3.95
3656 4904 3.181493 CCTCATTGATTCGCAGGAAAAGG 60.181 47.826 0.00 0.00 35.40 3.11
3657 4905 3.691118 TCCTCATTGATTCGCAGGAAAAG 59.309 43.478 0.00 0.00 35.40 2.27
3658 4906 3.440173 GTCCTCATTGATTCGCAGGAAAA 59.560 43.478 0.00 0.00 34.98 2.29
3659 4907 3.009723 GTCCTCATTGATTCGCAGGAAA 58.990 45.455 0.00 0.00 34.98 3.13
3660 4908 2.632377 GTCCTCATTGATTCGCAGGAA 58.368 47.619 0.00 0.00 34.98 3.36
3661 4909 1.471501 CGTCCTCATTGATTCGCAGGA 60.472 52.381 0.00 0.00 0.00 3.86
3662 4910 0.933097 CGTCCTCATTGATTCGCAGG 59.067 55.000 0.00 0.00 0.00 4.85
3663 4911 1.645034 ACGTCCTCATTGATTCGCAG 58.355 50.000 0.00 0.00 0.00 5.18
3664 4912 2.951457 TACGTCCTCATTGATTCGCA 57.049 45.000 0.00 0.00 0.00 5.10
3665 4913 4.547532 ACTATACGTCCTCATTGATTCGC 58.452 43.478 0.00 0.00 0.00 4.70
3666 4914 6.003234 AGACTATACGTCCTCATTGATTCG 57.997 41.667 0.00 0.00 43.91 3.34
3679 4927 7.125356 ACCATTTTTCCTCCTTAGACTATACGT 59.875 37.037 0.00 0.00 0.00 3.57
3686 4934 5.561679 ACTGACCATTTTTCCTCCTTAGAC 58.438 41.667 0.00 0.00 0.00 2.59
3733 4981 5.645497 GGACAACTGAAGTGCATCTTAGATT 59.355 40.000 0.00 0.00 36.40 2.40
3745 4993 4.855340 TCTCCAAAAAGGACAACTGAAGT 58.145 39.130 0.00 0.00 43.07 3.01
3746 4994 5.835113 TTCTCCAAAAAGGACAACTGAAG 57.165 39.130 0.00 0.00 43.07 3.02
3757 5005 8.947055 TCATTTCTTTTCCTTTCTCCAAAAAG 57.053 30.769 0.00 0.00 39.13 2.27
3763 5011 4.081972 GGCCTCATTTCTTTTCCTTTCTCC 60.082 45.833 0.00 0.00 0.00 3.71
3764 5012 4.524328 TGGCCTCATTTCTTTTCCTTTCTC 59.476 41.667 3.32 0.00 0.00 2.87
3766 5014 4.871933 TGGCCTCATTTCTTTTCCTTTC 57.128 40.909 3.32 0.00 0.00 2.62
3781 5029 1.379527 CCCACGTTCTTTATGGCCTC 58.620 55.000 3.32 0.00 31.66 4.70
3782 5030 0.679960 GCCCACGTTCTTTATGGCCT 60.680 55.000 3.32 0.00 32.74 5.19
3783 5031 1.807226 GCCCACGTTCTTTATGGCC 59.193 57.895 0.00 0.00 32.74 5.36
3785 5033 1.444836 TTCGCCCACGTTCTTTATGG 58.555 50.000 0.00 0.00 41.18 2.74
3787 5035 5.587043 TCATTATTTCGCCCACGTTCTTTAT 59.413 36.000 0.00 0.00 41.18 1.40
3788 5036 4.936411 TCATTATTTCGCCCACGTTCTTTA 59.064 37.500 0.00 0.00 41.18 1.85
3789 5037 3.754323 TCATTATTTCGCCCACGTTCTTT 59.246 39.130 0.00 0.00 41.18 2.52
3792 5040 3.680789 CTTCATTATTTCGCCCACGTTC 58.319 45.455 0.00 0.00 41.18 3.95
3800 5049 5.581605 TGATTTCCTGCTTCATTATTTCGC 58.418 37.500 0.00 0.00 0.00 4.70
3846 5097 8.510243 TGATGTTTTAGTGCATGTATTCAGAT 57.490 30.769 0.00 0.00 0.00 2.90
3847 5098 7.920160 TGATGTTTTAGTGCATGTATTCAGA 57.080 32.000 0.00 0.00 0.00 3.27
3861 5112 5.888161 AGCTATGGACCCTTTGATGTTTTAG 59.112 40.000 0.00 0.00 0.00 1.85
3863 5114 4.677182 AGCTATGGACCCTTTGATGTTTT 58.323 39.130 0.00 0.00 0.00 2.43
3871 5122 1.561542 CCACTGAGCTATGGACCCTTT 59.438 52.381 5.38 0.00 38.34 3.11
3974 5227 4.557301 GTGTAATAGCGTGGCAAATTTCAC 59.443 41.667 0.00 0.00 32.50 3.18
3976 5229 4.102649 GGTGTAATAGCGTGGCAAATTTC 58.897 43.478 0.00 0.00 0.00 2.17
3979 5232 2.999331 AGGTGTAATAGCGTGGCAAAT 58.001 42.857 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.