Multiple sequence alignment - TraesCS6D01G215900

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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 TraesCS6D01G215900 chr6D 100.000 3086 0 0 1 3086 306026302 306029387 0.000000e+00 5699
1 TraesCS6D01G215900 chr6D 100.000 1237 0 0 3370 4606 306029671 306030907 0.000000e+00 2285
2 TraesCS6D01G215900 chr6D 100.000 486 0 0 4866 5351 306031167 306031652 0.000000e+00 898
3 TraesCS6D01G215900 chr6D 92.135 623 45 4 1705 2326 400087516 400088135 0.000000e+00 876
4 TraesCS6D01G215900 chr6D 87.047 386 48 2 2292 2675 307784142 307784527 8.230000e-118 435
5 TraesCS6D01G215900 chr6D 83.747 363 36 10 2317 2676 1013495 1013837 6.690000e-84 322
6 TraesCS6D01G215900 chr6A 93.562 1227 46 4 3376 4598 440530203 440531400 0.000000e+00 1797
7 TraesCS6D01G215900 chr6A 93.137 408 22 4 1 404 440527623 440528028 1.280000e-165 593
8 TraesCS6D01G215900 chr6A 88.274 452 35 8 1255 1694 440529335 440529780 4.750000e-145 525
9 TraesCS6D01G215900 chr6A 86.792 371 36 7 2665 3033 440529789 440530148 8.350000e-108 401
10 TraesCS6D01G215900 chr6A 97.368 190 5 0 453 642 440528039 440528228 1.860000e-84 324
11 TraesCS6D01G215900 chr6B 91.596 1059 49 15 3544 4598 470801527 470800505 0.000000e+00 1426
12 TraesCS6D01G215900 chr6B 83.695 1153 80 44 640 1699 470803196 470802059 0.000000e+00 989
13 TraesCS6D01G215900 chr6B 93.934 610 29 4 38 642 470803839 470803233 0.000000e+00 915
14 TraesCS6D01G215900 chr6B 87.834 337 30 7 2701 3033 470802029 470801700 8.410000e-103 385
15 TraesCS6D01G215900 chr6B 84.238 387 52 8 2293 2675 181471052 181470671 8.470000e-98 368
16 TraesCS6D01G215900 chrUn 88.355 979 85 14 1695 2670 85480200 85481152 0.000000e+00 1149
17 TraesCS6D01G215900 chrUn 85.677 384 31 11 2296 2676 30575628 30575266 3.020000e-102 383
18 TraesCS6D01G215900 chrUn 85.195 385 34 11 2295 2676 30607428 30607064 1.820000e-99 374
19 TraesCS6D01G215900 chr3A 91.842 711 53 5 1967 2675 31562772 31563479 0.000000e+00 987
20 TraesCS6D01G215900 chr3A 94.904 628 29 3 1704 2331 433996374 433996998 0.000000e+00 979
21 TraesCS6D01G215900 chr3A 93.029 373 25 1 2292 2663 433996914 433997286 1.310000e-150 544
22 TraesCS6D01G215900 chr3D 83.852 997 127 24 1695 2676 433306578 433305601 0.000000e+00 918
23 TraesCS6D01G215900 chr3D 92.563 632 44 3 1700 2331 550912371 550912999 0.000000e+00 904
24 TraesCS6D01G215900 chr3D 91.726 423 24 6 4935 5351 474653816 474653399 1.290000e-160 577
25 TraesCS6D01G215900 chr4D 92.891 633 39 6 1700 2331 381411424 381412051 0.000000e+00 915
26 TraesCS6D01G215900 chr5D 93.581 592 29 7 1734 2320 447098456 447099043 0.000000e+00 874
27 TraesCS6D01G215900 chr5D 88.521 514 25 12 4866 5351 439601810 439601303 4.620000e-165 592
28 TraesCS6D01G215900 chr3B 92.905 592 39 3 1734 2325 508761552 508762140 0.000000e+00 857
29 TraesCS6D01G215900 chr3B 90.679 633 51 7 1701 2331 739337241 739337867 0.000000e+00 835
30 TraesCS6D01G215900 chr3B 92.183 371 28 1 2295 2664 229508764 229509134 1.710000e-144 523
31 TraesCS6D01G215900 chr3B 82.005 389 59 11 2289 2671 829005647 829006030 2.400000e-83 320
32 TraesCS6D01G215900 chr4A 90.342 497 30 9 4866 5351 580292565 580293054 2.100000e-178 636
33 TraesCS6D01G215900 chr4A 87.135 513 32 11 4866 5351 478408172 478407667 7.830000e-153 551
34 TraesCS6D01G215900 chr1D 89.400 500 32 12 4867 5349 475108470 475108965 1.270000e-170 610
35 TraesCS6D01G215900 chr1D 84.439 392 52 9 2293 2679 415524522 415524135 1.410000e-100 377
36 TraesCS6D01G215900 chr7A 86.900 542 53 14 2119 2655 182180044 182180572 4.620000e-165 592
37 TraesCS6D01G215900 chr7A 87.771 507 34 16 4866 5351 200605727 200606226 7.780000e-158 568
38 TraesCS6D01G215900 chr7A 92.819 376 26 1 2295 2669 2976016 2975641 1.310000e-150 544
39 TraesCS6D01G215900 chr7A 86.166 506 41 10 4866 5349 609606479 609605981 2.210000e-143 520
40 TraesCS6D01G215900 chr7A 84.000 525 39 18 4866 5351 129841709 129842227 3.780000e-126 462
41 TraesCS6D01G215900 chr1A 87.819 509 35 11 4869 5351 321280302 321279795 6.010000e-159 571
42 TraesCS6D01G215900 chr2A 90.758 422 32 4 4935 5351 659159563 659159982 1.680000e-154 556
43 TraesCS6D01G215900 chr2A 90.160 437 22 8 4935 5351 767387411 767387846 2.820000e-152 549
44 TraesCS6D01G215900 chr2D 90.090 444 15 12 4935 5351 52040368 52039927 2.820000e-152 549
45 TraesCS6D01G215900 chr2D 90.291 412 36 4 2255 2663 555160874 555160464 2.190000e-148 536
46 TraesCS6D01G215900 chr2D 92.703 370 26 1 2295 2663 355327973 355327604 2.840000e-147 532
47 TraesCS6D01G215900 chr2D 83.562 292 12 14 4866 5127 42739669 42739384 1.930000e-59 241
48 TraesCS6D01G215900 chr1B 92.742 372 22 4 2295 2663 624822695 624822326 2.840000e-147 532
49 TraesCS6D01G215900 chr2B 88.155 439 44 6 4913 5344 653919151 653919588 2.860000e-142 516
50 TraesCS6D01G215900 chr4B 83.824 544 72 14 2120 2657 573500650 573500117 2.220000e-138 503
51 TraesCS6D01G215900 chr7D 82.946 258 28 9 4868 5115 530034342 530034091 9.020000e-53 219


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 TraesCS6D01G215900 chr6D 306026302 306031652 5350 False 2960.666667 5699 100.00000 1 5351 3 chr6D.!!$F4 5350
1 TraesCS6D01G215900 chr6D 400087516 400088135 619 False 876.000000 876 92.13500 1705 2326 1 chr6D.!!$F3 621
2 TraesCS6D01G215900 chr6A 440527623 440531400 3777 False 728.000000 1797 91.82660 1 4598 5 chr6A.!!$F1 4597
3 TraesCS6D01G215900 chr6B 470800505 470803839 3334 True 928.750000 1426 89.26475 38 4598 4 chr6B.!!$R2 4560
4 TraesCS6D01G215900 chrUn 85480200 85481152 952 False 1149.000000 1149 88.35500 1695 2670 1 chrUn.!!$F1 975
5 TraesCS6D01G215900 chr3A 31562772 31563479 707 False 987.000000 987 91.84200 1967 2675 1 chr3A.!!$F1 708
6 TraesCS6D01G215900 chr3A 433996374 433997286 912 False 761.500000 979 93.96650 1704 2663 2 chr3A.!!$F2 959
7 TraesCS6D01G215900 chr3D 433305601 433306578 977 True 918.000000 918 83.85200 1695 2676 1 chr3D.!!$R1 981
8 TraesCS6D01G215900 chr3D 550912371 550912999 628 False 904.000000 904 92.56300 1700 2331 1 chr3D.!!$F1 631
9 TraesCS6D01G215900 chr4D 381411424 381412051 627 False 915.000000 915 92.89100 1700 2331 1 chr4D.!!$F1 631
10 TraesCS6D01G215900 chr5D 447098456 447099043 587 False 874.000000 874 93.58100 1734 2320 1 chr5D.!!$F1 586
11 TraesCS6D01G215900 chr5D 439601303 439601810 507 True 592.000000 592 88.52100 4866 5351 1 chr5D.!!$R1 485
12 TraesCS6D01G215900 chr3B 508761552 508762140 588 False 857.000000 857 92.90500 1734 2325 1 chr3B.!!$F2 591
13 TraesCS6D01G215900 chr3B 739337241 739337867 626 False 835.000000 835 90.67900 1701 2331 1 chr3B.!!$F3 630
14 TraesCS6D01G215900 chr4A 478407667 478408172 505 True 551.000000 551 87.13500 4866 5351 1 chr4A.!!$R1 485
15 TraesCS6D01G215900 chr7A 182180044 182180572 528 False 592.000000 592 86.90000 2119 2655 1 chr7A.!!$F2 536
16 TraesCS6D01G215900 chr7A 129841709 129842227 518 False 462.000000 462 84.00000 4866 5351 1 chr7A.!!$F1 485
17 TraesCS6D01G215900 chr1A 321279795 321280302 507 True 571.000000 571 87.81900 4869 5351 1 chr1A.!!$R1 482
18 TraesCS6D01G215900 chr4B 573500117 573500650 533 True 503.000000 503 83.82400 2120 2657 1 chr4B.!!$R1 537

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
934 1015 0.514255 GAAAGGAACACGTTACCGGC 59.486 55.0 0.00 0.0 38.78 6.13 F
1290 1868 0.251354 GCTCCTGCAATCTGGTGAGA 59.749 55.0 0.00 0.0 39.41 3.27 F
1723 2314 0.745486 AAATACTAACGCCCACCCGC 60.745 55.0 0.00 0.0 0.00 6.13 F
2027 2621 0.829333 TTGCCATGTGTTTTGCAGGT 59.171 45.0 0.00 0.0 34.81 4.00 F
2750 3539 0.948141 GTGCTGTGACTGCCTCTGTC 60.948 60.0 11.94 0.0 33.83 3.51 F
3676 4511 0.385029 TTGCTTTGCACAATGCTCGT 59.615 45.0 18.44 0.0 45.31 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2726 3515 0.109153 AGGCAGTCACAGCACAATCA 59.891 50.000 0.00 0.0 0.00 2.57 R
2942 3732 2.830923 CCCAGACAAATAAACCATGCCA 59.169 45.455 0.00 0.0 0.00 4.92 R
3500 4335 3.084039 GCACTTGTGGGATTCTCATTCA 58.916 45.455 2.81 0.0 0.00 2.57 R
3675 4510 5.460646 TCTTGTGCAAAGCAAGCTATTTAC 58.539 37.500 9.98 0.0 41.47 2.01 R
4238 5074 0.817654 GTGATAAACTGGCCCCTTGC 59.182 55.000 0.00 0.0 40.16 4.01 R
5035 5909 0.905357 ATGTAGAGCTTCAAGGGCGT 59.095 50.000 0.00 0.0 34.52 5.68 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
88 89 7.935338 AGTTTGCACAAAGTATGAAATTCAG 57.065 32.000 1.10 0.00 32.58 3.02
237 241 9.626332 CATTTCAAAATTTTCAAATGCTTTTGC 57.374 25.926 22.07 0.00 41.66 3.68
250 254 1.052287 CTTTTGCGATGCGTTTGGAC 58.948 50.000 0.00 0.00 0.00 4.02
338 342 5.345702 TGAAGCTGCATTTGAATCTATTGC 58.654 37.500 1.02 4.99 0.00 3.56
342 347 4.799949 GCTGCATTTGAATCTATTGCGAAA 59.200 37.500 0.00 0.00 36.11 3.46
449 456 8.691661 AACTCAGCCAGTTTTTAAGAATCTAA 57.308 30.769 0.00 0.00 43.38 2.10
450 457 8.870075 ACTCAGCCAGTTTTTAAGAATCTAAT 57.130 30.769 0.00 0.00 26.56 1.73
451 458 9.301897 ACTCAGCCAGTTTTTAAGAATCTAATT 57.698 29.630 0.00 0.00 26.56 1.40
722 768 9.394767 ACATTGCATGTACTTTGACTATGAATA 57.605 29.630 0.00 0.00 42.78 1.75
804 875 7.914537 AGAAAAATTGAATCGAGTTGTTCAC 57.085 32.000 0.00 0.00 34.34 3.18
823 894 8.072238 TGTTCACGCATGTTAGAATATATGTC 57.928 34.615 0.00 0.00 0.00 3.06
934 1015 0.514255 GAAAGGAACACGTTACCGGC 59.486 55.000 0.00 0.00 38.78 6.13
951 1032 4.596585 CCCGGCCCACCAGTGTTT 62.597 66.667 0.00 0.00 34.57 2.83
952 1033 3.294493 CCGGCCCACCAGTGTTTG 61.294 66.667 0.00 0.00 34.57 2.93
976 1064 0.600255 GCGTGTCTAAGGCGGCATAT 60.600 55.000 13.08 0.00 0.00 1.78
977 1065 1.336517 GCGTGTCTAAGGCGGCATATA 60.337 52.381 13.08 0.00 0.00 0.86
978 1066 2.325761 CGTGTCTAAGGCGGCATATAC 58.674 52.381 13.08 7.30 0.00 1.47
995 1083 3.679824 ATACTAGGATTTGCCGCCTAC 57.320 47.619 0.00 0.00 43.43 3.18
999 1087 2.709475 GATTTGCCGCCTACGCTG 59.291 61.111 0.00 0.00 38.22 5.18
1001 1089 3.976701 ATTTGCCGCCTACGCTGCT 62.977 57.895 0.00 0.00 44.77 4.24
1010 1098 3.057547 CTACGCTGCTGCTCGGTCT 62.058 63.158 14.03 2.16 36.97 3.85
1029 1117 4.845580 CGCAGGCCGCATCCTCTT 62.846 66.667 17.57 0.00 42.60 2.85
1030 1118 2.505982 GCAGGCCGCATCCTCTTA 59.494 61.111 13.61 0.00 41.79 2.10
1031 1119 1.596477 GCAGGCCGCATCCTCTTAG 60.596 63.158 13.61 0.00 41.79 2.18
1139 1262 4.479993 CGAGGCCTCCAAGCAGGG 62.480 72.222 27.20 6.40 38.24 4.45
1260 1838 2.359850 GCAACCCCACATCGCTCA 60.360 61.111 0.00 0.00 0.00 4.26
1286 1864 1.302285 CAGGCTCCTGCAATCTGGT 59.698 57.895 2.59 0.00 41.91 4.00
1287 1865 1.030488 CAGGCTCCTGCAATCTGGTG 61.030 60.000 2.59 0.00 41.91 4.17
1290 1868 0.251354 GCTCCTGCAATCTGGTGAGA 59.749 55.000 0.00 0.00 39.41 3.27
1317 1899 3.847467 GCGCATGCTCATGATGTTCTAAC 60.847 47.826 17.13 0.00 41.20 2.34
1330 1912 6.233434 TGATGTTCTAACAAGTGCTCTCAAT 58.767 36.000 0.00 0.00 43.03 2.57
1345 1927 9.236006 AGTGCTCTCAATTAATTGTACTGATTT 57.764 29.630 23.95 6.38 38.84 2.17
1351 1933 9.421806 CTCAATTAATTGTACTGATTTGCCAAA 57.578 29.630 23.95 0.00 38.84 3.28
1352 1934 9.770097 TCAATTAATTGTACTGATTTGCCAAAA 57.230 25.926 23.95 0.09 38.84 2.44
1427 2009 1.679977 CCCGAGTTCTACGACCCCA 60.680 63.158 0.00 0.00 0.00 4.96
1430 2012 1.246056 CGAGTTCTACGACCCCACCA 61.246 60.000 0.00 0.00 0.00 4.17
1447 2029 3.804325 CCACCATAGACGATGTTGATGAC 59.196 47.826 0.00 0.00 29.54 3.06
1528 2110 2.548480 GTGTTTCACTACCTTGTGCCTC 59.452 50.000 0.00 0.00 37.81 4.70
1563 2145 5.126061 GGTAATCCACTTGATGCTTCACATT 59.874 40.000 1.02 0.00 39.84 2.71
1619 2201 6.533730 TGGACTATAAGATGCCTTTACATGG 58.466 40.000 0.00 0.00 33.94 3.66
1624 2206 8.686334 ACTATAAGATGCCTTTACATGGTTTTG 58.314 33.333 0.00 0.00 33.94 2.44
1633 2224 7.870445 TGCCTTTACATGGTTTTGACTTTTATC 59.130 33.333 0.00 0.00 0.00 1.75
1637 2228 9.703892 TTTACATGGTTTTGACTTTTATCATGG 57.296 29.630 0.00 0.00 36.16 3.66
1684 2275 5.526111 GCAGCGATACTTTTTCCTAATGGTA 59.474 40.000 0.00 0.00 34.23 3.25
1688 2279 7.282450 AGCGATACTTTTTCCTAATGGTAAAGG 59.718 37.037 0.00 6.24 38.79 3.11
1720 2311 2.349590 ACGAAAATACTAACGCCCACC 58.650 47.619 0.00 0.00 0.00 4.61
1723 2314 0.745486 AAATACTAACGCCCACCCGC 60.745 55.000 0.00 0.00 0.00 6.13
1732 2323 3.124921 CCCACCCGCGTGACAATC 61.125 66.667 4.92 0.00 43.14 2.67
1779 2370 3.251245 TCAACGTCCGTTTATGTTTGCAT 59.749 39.130 1.71 0.00 36.00 3.96
2027 2621 0.829333 TTGCCATGTGTTTTGCAGGT 59.171 45.000 0.00 0.00 34.81 4.00
2034 2628 3.090952 TGTGTTTTGCAGGTTACATGC 57.909 42.857 15.40 15.40 44.11 4.06
2257 2932 1.271597 ACTTGACCTGAGATGGCAACC 60.272 52.381 0.00 0.00 0.00 3.77
2349 3134 3.483808 TTGTCAGACATGGCAACTGTA 57.516 42.857 3.45 7.17 45.86 2.74
2355 3140 3.814842 CAGACATGGCAACTGTAGTTCAA 59.185 43.478 0.00 0.00 35.83 2.69
2366 3151 3.565482 ACTGTAGTTCAACAACATGGCAG 59.435 43.478 0.00 0.00 34.60 4.85
2512 3298 2.303600 TCTATTTTGCCCACACGTAGGT 59.696 45.455 5.59 0.00 0.00 3.08
2689 3476 1.884235 AAAGGTGAAGACGGAGCAAG 58.116 50.000 0.00 0.00 0.00 4.01
2698 3485 5.688176 GTGAAGACGGAGCAAGTTATATCTC 59.312 44.000 0.00 0.00 0.00 2.75
2699 3486 5.359860 TGAAGACGGAGCAAGTTATATCTCA 59.640 40.000 0.00 0.00 0.00 3.27
2700 3487 5.854010 AGACGGAGCAAGTTATATCTCAA 57.146 39.130 0.00 0.00 0.00 3.02
2701 3488 6.412362 AGACGGAGCAAGTTATATCTCAAT 57.588 37.500 0.00 0.00 0.00 2.57
2702 3489 7.526142 AGACGGAGCAAGTTATATCTCAATA 57.474 36.000 0.00 0.00 0.00 1.90
2703 3490 8.128322 AGACGGAGCAAGTTATATCTCAATAT 57.872 34.615 0.00 0.00 32.72 1.28
2704 3491 8.247562 AGACGGAGCAAGTTATATCTCAATATC 58.752 37.037 0.00 0.00 30.59 1.63
2705 3492 8.128322 ACGGAGCAAGTTATATCTCAATATCT 57.872 34.615 0.00 0.00 30.59 1.98
2726 3515 9.884814 ATATCTGTTAGAAGTACTATCCCTTGT 57.115 33.333 0.00 0.00 0.00 3.16
2750 3539 0.948141 GTGCTGTGACTGCCTCTGTC 60.948 60.000 11.94 0.00 33.83 3.51
2756 3545 2.158769 TGTGACTGCCTCTGTCAACATT 60.159 45.455 7.87 0.00 42.23 2.71
2768 3557 8.725148 GCCTCTGTCAACATTTATAGGATAATG 58.275 37.037 0.00 0.00 37.67 1.90
2771 3560 7.665559 TCTGTCAACATTTATAGGATAATGGCC 59.334 37.037 0.00 0.00 36.34 5.36
2774 3563 8.299570 GTCAACATTTATAGGATAATGGCCTTG 58.700 37.037 3.32 0.00 36.34 3.61
2775 3564 8.224025 TCAACATTTATAGGATAATGGCCTTGA 58.776 33.333 3.32 0.00 36.34 3.02
2796 3585 9.745880 CCTTGATTTGATAAATTCATGGAGAAG 57.254 33.333 11.67 0.00 40.15 2.85
2842 3631 3.986572 TCATGTTTAGCAAAATTGGCGTG 59.013 39.130 0.00 0.00 36.08 5.34
2853 3643 5.465935 CAAAATTGGCGTGTGTTAATACCT 58.534 37.500 0.00 0.00 0.00 3.08
2855 3645 4.957759 ATTGGCGTGTGTTAATACCTTC 57.042 40.909 0.00 0.00 0.00 3.46
2888 3678 7.617041 ATGTGAGTAAGTATTTTTCAGAGCC 57.383 36.000 0.00 0.00 0.00 4.70
2890 3680 6.874134 TGTGAGTAAGTATTTTTCAGAGCCTC 59.126 38.462 0.00 0.00 0.00 4.70
2919 3709 4.881850 TCTCTGCGTCATACTGATCAAGTA 59.118 41.667 0.00 2.30 45.47 2.24
2961 3751 5.389859 TCTTGGCATGGTTTATTTGTCTG 57.610 39.130 0.00 0.00 0.00 3.51
2968 3758 6.127196 GGCATGGTTTATTTGTCTGGGATAAA 60.127 38.462 0.00 0.00 0.00 1.40
2991 3782 4.566004 TGTGTACAGCTCATTGTTCCTAC 58.434 43.478 0.00 0.00 32.56 3.18
2998 3789 5.182001 ACAGCTCATTGTTCCTACACATTTC 59.818 40.000 0.00 0.00 32.98 2.17
3013 3804 9.927668 CCTACACATTTCATTTCTTAATTTGGT 57.072 29.630 0.00 0.00 0.00 3.67
3045 3853 5.991861 TGTGAGAGGTAACCACTGTTTTAA 58.008 37.500 0.00 0.00 35.87 1.52
3047 3855 6.316890 TGTGAGAGGTAACCACTGTTTTAAAC 59.683 38.462 0.20 0.20 35.87 2.01
3068 3903 6.521527 AACTAGCATGGGGAATCTATCTTT 57.478 37.500 0.00 0.00 0.00 2.52
3069 3904 5.874093 ACTAGCATGGGGAATCTATCTTTG 58.126 41.667 0.00 0.00 0.00 2.77
3070 3905 4.803329 AGCATGGGGAATCTATCTTTGT 57.197 40.909 0.00 0.00 0.00 2.83
3071 3906 5.912149 AGCATGGGGAATCTATCTTTGTA 57.088 39.130 0.00 0.00 0.00 2.41
3072 3907 6.266131 AGCATGGGGAATCTATCTTTGTAA 57.734 37.500 0.00 0.00 0.00 2.41
3073 3908 6.302269 AGCATGGGGAATCTATCTTTGTAAG 58.698 40.000 0.00 0.00 0.00 2.34
3074 3909 5.048434 GCATGGGGAATCTATCTTTGTAAGC 60.048 44.000 0.00 0.00 0.00 3.09
3075 3910 5.975988 TGGGGAATCTATCTTTGTAAGCT 57.024 39.130 0.00 0.00 0.00 3.74
3076 3911 6.327386 TGGGGAATCTATCTTTGTAAGCTT 57.673 37.500 3.48 3.48 0.00 3.74
3077 3912 7.446106 TGGGGAATCTATCTTTGTAAGCTTA 57.554 36.000 0.86 0.86 0.00 3.09
3078 3913 8.045720 TGGGGAATCTATCTTTGTAAGCTTAT 57.954 34.615 9.88 0.00 0.00 1.73
3079 3914 8.502738 TGGGGAATCTATCTTTGTAAGCTTATT 58.497 33.333 9.88 0.00 0.00 1.40
3080 3915 9.004717 GGGGAATCTATCTTTGTAAGCTTATTC 57.995 37.037 9.88 6.13 0.00 1.75
3081 3916 9.785982 GGGAATCTATCTTTGTAAGCTTATTCT 57.214 33.333 9.88 0.00 0.00 2.40
3390 4225 4.530710 ACACCGTAAGCTTATTCTGTGA 57.469 40.909 23.02 0.00 0.00 3.58
3391 4226 5.086104 ACACCGTAAGCTTATTCTGTGAT 57.914 39.130 23.02 11.87 0.00 3.06
3392 4227 4.870426 ACACCGTAAGCTTATTCTGTGATG 59.130 41.667 23.02 12.03 0.00 3.07
3393 4228 5.109210 CACCGTAAGCTTATTCTGTGATGA 58.891 41.667 9.88 0.00 0.00 2.92
3394 4229 5.580691 CACCGTAAGCTTATTCTGTGATGAA 59.419 40.000 9.88 0.00 0.00 2.57
3395 4230 6.092122 CACCGTAAGCTTATTCTGTGATGAAA 59.908 38.462 9.88 0.00 0.00 2.69
3396 4231 6.823689 ACCGTAAGCTTATTCTGTGATGAAAT 59.176 34.615 9.88 0.00 0.00 2.17
3397 4232 7.128331 CCGTAAGCTTATTCTGTGATGAAATG 58.872 38.462 9.88 0.00 0.00 2.32
3398 4233 7.201644 CCGTAAGCTTATTCTGTGATGAAATGT 60.202 37.037 9.88 0.00 0.00 2.71
3402 4237 9.846248 AAGCTTATTCTGTGATGAAATGTTAAC 57.154 29.630 0.00 0.00 0.00 2.01
3428 4263 5.517770 GCATCATTCTTAATTGTGCCTGTTC 59.482 40.000 0.00 0.00 0.00 3.18
3429 4264 6.623486 CATCATTCTTAATTGTGCCTGTTCA 58.377 36.000 0.00 0.00 0.00 3.18
3437 4272 2.655090 TGTGCCTGTTCATTTCCTCA 57.345 45.000 0.00 0.00 0.00 3.86
3438 4273 2.507484 TGTGCCTGTTCATTTCCTCAG 58.493 47.619 0.00 0.00 0.00 3.35
3439 4274 1.200948 GTGCCTGTTCATTTCCTCAGC 59.799 52.381 0.00 0.00 0.00 4.26
3447 4282 6.994496 CCTGTTCATTTCCTCAGCTATGAATA 59.006 38.462 9.85 7.11 38.73 1.75
3458 4293 9.494271 TCCTCAGCTATGAATATGAAAATGTAC 57.506 33.333 0.00 0.00 34.23 2.90
3498 4333 8.744652 TGAACTCTTAATCTGGTTTGTTTGAAA 58.255 29.630 0.00 0.00 0.00 2.69
3520 4355 5.909621 AATGAATGAGAATCCCACAAGTG 57.090 39.130 0.00 0.00 0.00 3.16
3521 4356 3.084039 TGAATGAGAATCCCACAAGTGC 58.916 45.455 0.00 0.00 0.00 4.40
3522 4357 2.885135 ATGAGAATCCCACAAGTGCA 57.115 45.000 0.00 0.00 0.00 4.57
3523 4358 2.655090 TGAGAATCCCACAAGTGCAA 57.345 45.000 0.00 0.00 0.00 4.08
3524 4359 3.159213 TGAGAATCCCACAAGTGCAAT 57.841 42.857 0.00 0.00 0.00 3.56
3525 4360 4.299586 TGAGAATCCCACAAGTGCAATA 57.700 40.909 0.00 0.00 0.00 1.90
3526 4361 4.858850 TGAGAATCCCACAAGTGCAATAT 58.141 39.130 0.00 0.00 0.00 1.28
3527 4362 5.263599 TGAGAATCCCACAAGTGCAATATT 58.736 37.500 0.00 0.00 0.00 1.28
3528 4363 5.357878 TGAGAATCCCACAAGTGCAATATTC 59.642 40.000 0.00 0.00 0.00 1.75
3529 4364 5.513233 AGAATCCCACAAGTGCAATATTCT 58.487 37.500 2.58 2.58 0.00 2.40
3530 4365 5.359009 AGAATCCCACAAGTGCAATATTCTG 59.641 40.000 6.76 0.00 32.68 3.02
3531 4366 3.355378 TCCCACAAGTGCAATATTCTGG 58.645 45.455 0.00 0.00 0.00 3.86
3532 4367 3.010027 TCCCACAAGTGCAATATTCTGGA 59.990 43.478 0.00 0.00 0.00 3.86
3533 4368 3.379372 CCCACAAGTGCAATATTCTGGAG 59.621 47.826 0.00 0.00 0.00 3.86
3534 4369 3.379372 CCACAAGTGCAATATTCTGGAGG 59.621 47.826 0.00 0.00 0.00 4.30
3535 4370 3.019564 ACAAGTGCAATATTCTGGAGGC 58.980 45.455 0.00 0.00 0.00 4.70
3536 4371 2.355010 AGTGCAATATTCTGGAGGCC 57.645 50.000 0.00 0.00 0.00 5.19
3537 4372 1.849039 AGTGCAATATTCTGGAGGCCT 59.151 47.619 3.86 3.86 0.00 5.19
3538 4373 3.048600 AGTGCAATATTCTGGAGGCCTA 58.951 45.455 4.42 0.00 0.00 3.93
3539 4374 3.459598 AGTGCAATATTCTGGAGGCCTAA 59.540 43.478 4.42 0.00 0.00 2.69
3540 4375 4.105377 AGTGCAATATTCTGGAGGCCTAAT 59.895 41.667 4.42 4.14 0.00 1.73
3541 4376 4.829492 GTGCAATATTCTGGAGGCCTAATT 59.171 41.667 4.42 0.00 0.00 1.40
3542 4377 5.302823 GTGCAATATTCTGGAGGCCTAATTT 59.697 40.000 4.42 0.00 0.00 1.82
3543 4378 6.490040 GTGCAATATTCTGGAGGCCTAATTTA 59.510 38.462 4.42 0.00 0.00 1.40
3544 4379 6.716628 TGCAATATTCTGGAGGCCTAATTTAG 59.283 38.462 4.42 0.00 0.00 1.85
3545 4380 6.717084 GCAATATTCTGGAGGCCTAATTTAGT 59.283 38.462 4.42 0.00 0.00 2.24
3586 4421 6.072230 TGTGTTGTGAAGTCTGAAACATGAAA 60.072 34.615 0.00 0.00 33.67 2.69
3675 4510 1.489574 TTTGCTTTGCACAATGCTCG 58.510 45.000 18.44 0.00 45.31 5.03
3676 4511 0.385029 TTGCTTTGCACAATGCTCGT 59.615 45.000 18.44 0.00 45.31 4.18
3726 4561 9.826574 AACACAACTAACCGTGATATATACATT 57.173 29.630 0.00 0.00 36.91 2.71
3831 4666 6.097270 CCATCATGTAATTGTCTGTTTCCCAT 59.903 38.462 0.00 0.00 0.00 4.00
3862 4697 3.572682 CACTTACACTATATCCCCGCAGA 59.427 47.826 0.00 0.00 0.00 4.26
3863 4698 4.038763 CACTTACACTATATCCCCGCAGAA 59.961 45.833 0.00 0.00 0.00 3.02
3907 4743 1.852942 AGTTGTCACTGTACTGCACG 58.147 50.000 0.00 0.00 0.00 5.34
4082 4918 8.934825 CCAATACTAAAATTGTGGATGGTTTTG 58.065 33.333 0.00 0.00 35.48 2.44
4170 5006 5.163602 GGTCAAGACTGATCAGATTCTACGT 60.164 44.000 29.27 4.58 32.42 3.57
4238 5074 4.883083 TCTACTACACCAGAAGTTGCAAG 58.117 43.478 0.00 0.00 0.00 4.01
4598 5438 7.822161 AAACATGAATTGCATATGGTAGCTA 57.178 32.000 4.56 0.00 34.82 3.32
4599 5439 7.822161 AACATGAATTGCATATGGTAGCTAA 57.178 32.000 4.56 0.00 34.82 3.09
4600 5440 7.822161 ACATGAATTGCATATGGTAGCTAAA 57.178 32.000 4.56 0.00 34.82 1.85
4601 5441 7.879070 ACATGAATTGCATATGGTAGCTAAAG 58.121 34.615 4.56 0.00 34.82 1.85
4602 5442 6.317789 TGAATTGCATATGGTAGCTAAAGC 57.682 37.500 4.56 0.00 42.49 3.51
4603 5443 5.827267 TGAATTGCATATGGTAGCTAAAGCA 59.173 36.000 4.56 0.00 45.16 3.91
4604 5444 5.954296 ATTGCATATGGTAGCTAAAGCAG 57.046 39.130 4.56 0.00 45.16 4.24
4895 5735 1.264749 TGTAATGCTCCCCAGTCGCT 61.265 55.000 0.00 0.00 0.00 4.93
5288 6177 3.518998 CCGGACCATCTCGTCGCT 61.519 66.667 0.00 0.00 33.30 4.93
5301 6190 1.018148 CGTCGCTGAGGTAGTCATCT 58.982 55.000 0.00 0.00 33.51 2.90
5311 6200 2.049767 TAGTCATCTCGCGCCCACA 61.050 57.895 0.00 0.00 0.00 4.17
5329 6218 1.452651 ATTAGGGCGTCCTCGTCGA 60.453 57.895 14.54 0.00 43.66 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 241 0.096976 GTCATGGTCCAAACGCATCG 59.903 55.000 0.00 0.00 0.00 3.84
250 254 6.754675 TGTATTACAATAGTGTCGTGTCATGG 59.245 38.462 0.00 0.00 39.30 3.66
457 464 4.344102 TCCATAGTTACTGCTTAAGGCGAT 59.656 41.667 4.29 0.00 45.43 4.58
781 828 6.611464 GCGTGAACAACTCGATTCAATTTTTC 60.611 38.462 0.92 0.00 36.62 2.29
783 830 4.675114 GCGTGAACAACTCGATTCAATTTT 59.325 37.500 0.92 0.00 36.62 1.82
784 831 4.219033 GCGTGAACAACTCGATTCAATTT 58.781 39.130 0.92 0.00 36.62 1.82
785 832 3.249799 TGCGTGAACAACTCGATTCAATT 59.750 39.130 0.92 0.00 36.62 2.32
786 833 2.805671 TGCGTGAACAACTCGATTCAAT 59.194 40.909 0.92 0.00 36.62 2.57
787 834 2.205911 TGCGTGAACAACTCGATTCAA 58.794 42.857 0.92 0.00 36.62 2.69
788 835 1.859383 TGCGTGAACAACTCGATTCA 58.141 45.000 0.00 0.00 37.64 2.57
793 864 2.729360 TCTAACATGCGTGAACAACTCG 59.271 45.455 14.17 0.00 38.32 4.18
934 1015 4.596585 AAACACTGGTGGGCCGGG 62.597 66.667 2.18 0.00 45.50 5.73
947 1028 2.661840 TTAGACACGCCGCCCAAACA 62.662 55.000 0.00 0.00 0.00 2.83
949 1030 1.669760 CTTAGACACGCCGCCCAAA 60.670 57.895 0.00 0.00 0.00 3.28
950 1031 2.047655 CTTAGACACGCCGCCCAA 60.048 61.111 0.00 0.00 0.00 4.12
951 1032 4.077184 CCTTAGACACGCCGCCCA 62.077 66.667 0.00 0.00 0.00 5.36
960 1048 3.762288 CCTAGTATATGCCGCCTTAGACA 59.238 47.826 0.00 0.00 0.00 3.41
976 1064 1.338973 CGTAGGCGGCAAATCCTAGTA 59.661 52.381 13.08 0.00 35.76 1.82
977 1065 0.104304 CGTAGGCGGCAAATCCTAGT 59.896 55.000 13.08 0.00 35.76 2.57
978 1066 1.222115 GCGTAGGCGGCAAATCCTAG 61.222 60.000 13.08 0.00 35.76 3.02
1029 1117 8.561769 TCCTCTTCTCCTTTTCTTCTCTATCTA 58.438 37.037 0.00 0.00 0.00 1.98
1030 1118 7.418378 TCCTCTTCTCCTTTTCTTCTCTATCT 58.582 38.462 0.00 0.00 0.00 1.98
1031 1119 7.654022 TCCTCTTCTCCTTTTCTTCTCTATC 57.346 40.000 0.00 0.00 0.00 2.08
1105 1227 1.072159 CGGGCTCCATGAATCCTCC 59.928 63.158 0.00 0.00 0.00 4.30
1106 1228 0.034616 CTCGGGCTCCATGAATCCTC 59.965 60.000 0.00 0.00 0.00 3.71
1135 1258 4.479993 CGGCTGCTTCTCCCCCTG 62.480 72.222 0.00 0.00 0.00 4.45
1139 1262 2.203126 CCATCGGCTGCTTCTCCC 60.203 66.667 0.00 0.00 0.00 4.30
1260 1838 0.185901 TGCAGGAGCCTGGTTCTTTT 59.814 50.000 17.64 0.00 43.77 2.27
1317 1899 8.032952 TCAGTACAATTAATTGAGAGCACTTG 57.967 34.615 30.18 16.59 40.14 3.16
1351 1933 8.049655 ACACTGCACCAAATTAAACAATTTTT 57.950 26.923 0.00 0.00 30.51 1.94
1352 1934 7.201688 GGACACTGCACCAAATTAAACAATTTT 60.202 33.333 0.00 0.00 30.51 1.82
1353 1935 6.259829 GGACACTGCACCAAATTAAACAATTT 59.740 34.615 0.00 0.00 32.97 1.82
1354 1936 5.757808 GGACACTGCACCAAATTAAACAATT 59.242 36.000 0.00 0.00 0.00 2.32
1355 1937 5.163364 TGGACACTGCACCAAATTAAACAAT 60.163 36.000 0.00 0.00 32.93 2.71
1357 1939 3.701542 TGGACACTGCACCAAATTAAACA 59.298 39.130 0.00 0.00 32.93 2.83
1358 1940 4.298332 CTGGACACTGCACCAAATTAAAC 58.702 43.478 0.00 0.00 35.67 2.01
1427 2009 3.490933 CGGTCATCAACATCGTCTATGGT 60.491 47.826 0.00 0.00 40.16 3.55
1430 2012 2.362397 AGCGGTCATCAACATCGTCTAT 59.638 45.455 0.00 0.00 0.00 1.98
1528 2110 2.700897 AGTGGATTACCTCTGGGAATCG 59.299 50.000 13.55 0.00 38.40 3.34
1591 2173 7.272978 TGTAAAGGCATCTTATAGTCCAAGAC 58.727 38.462 0.00 0.00 34.96 3.01
1619 2201 9.528018 TCTTTGAACCATGATAAAAGTCAAAAC 57.472 29.630 0.00 0.00 0.00 2.43
1633 2224 7.396540 AGCCTTATAGTTTCTTTGAACCATG 57.603 36.000 0.00 0.00 0.00 3.66
1637 2228 7.145323 TGCAAAGCCTTATAGTTTCTTTGAAC 58.855 34.615 14.77 1.95 43.57 3.18
1720 2311 0.247814 GATGCAAGATTGTCACGCGG 60.248 55.000 12.47 0.00 0.00 6.46
1723 2314 1.267235 GCGAGATGCAAGATTGTCACG 60.267 52.381 0.00 0.00 45.45 4.35
2034 2628 0.250901 AAGCACACTAGGGCAGTTGG 60.251 55.000 0.00 0.00 34.26 3.77
2257 2932 0.110056 GTCATGGTTGCTCAACTGCG 60.110 55.000 11.91 2.22 40.94 5.18
2340 3125 4.290155 CATGTTGTTGAACTACAGTTGCC 58.710 43.478 16.71 0.00 37.28 4.52
2347 3132 2.554032 AGCTGCCATGTTGTTGAACTAC 59.446 45.455 2.97 2.97 32.79 2.73
2349 3134 1.338973 CAGCTGCCATGTTGTTGAACT 59.661 47.619 0.00 0.00 32.79 3.01
2355 3140 1.111116 AACTGCAGCTGCCATGTTGT 61.111 50.000 34.64 19.55 41.18 3.32
2366 3151 2.225491 TCCATGTTCGTTTAACTGCAGC 59.775 45.455 15.27 0.00 38.99 5.25
2452 3238 1.684734 GTCCGGCCTCCTACCTCAA 60.685 63.158 0.00 0.00 0.00 3.02
2512 3298 3.066190 CGCGGTCCCTCCTACACA 61.066 66.667 0.00 0.00 0.00 3.72
2541 3327 3.505184 GTAATGCCCACACGCCCG 61.505 66.667 0.00 0.00 0.00 6.13
2619 3405 2.295602 GGGCGTTAAGGGGTCTGGA 61.296 63.158 0.00 0.00 0.00 3.86
2700 3487 9.884814 ACAAGGGATAGTACTTCTAACAGATAT 57.115 33.333 0.00 0.00 31.94 1.63
2701 3488 9.132923 CACAAGGGATAGTACTTCTAACAGATA 57.867 37.037 0.00 0.00 31.94 1.98
2702 3489 7.839705 TCACAAGGGATAGTACTTCTAACAGAT 59.160 37.037 0.00 0.00 31.94 2.90
2703 3490 7.179966 TCACAAGGGATAGTACTTCTAACAGA 58.820 38.462 0.00 0.00 31.94 3.41
2704 3491 7.406031 TCACAAGGGATAGTACTTCTAACAG 57.594 40.000 0.00 0.00 31.94 3.16
2705 3492 7.973048 ATCACAAGGGATAGTACTTCTAACA 57.027 36.000 0.00 0.00 31.94 2.41
2710 3499 5.294552 GCACAATCACAAGGGATAGTACTTC 59.705 44.000 0.00 0.00 0.00 3.01
2719 3508 1.142667 TCACAGCACAATCACAAGGGA 59.857 47.619 0.00 0.00 0.00 4.20
2720 3509 1.267806 GTCACAGCACAATCACAAGGG 59.732 52.381 0.00 0.00 0.00 3.95
2721 3510 2.031420 CAGTCACAGCACAATCACAAGG 60.031 50.000 0.00 0.00 0.00 3.61
2722 3511 2.603892 GCAGTCACAGCACAATCACAAG 60.604 50.000 0.00 0.00 0.00 3.16
2726 3515 0.109153 AGGCAGTCACAGCACAATCA 59.891 50.000 0.00 0.00 0.00 2.57
2750 3539 8.408043 TCAAGGCCATTATCCTATAAATGTTG 57.592 34.615 5.01 0.00 32.34 3.33
2768 3557 6.819284 TCCATGAATTTATCAAATCAAGGCC 58.181 36.000 0.00 0.00 42.54 5.19
2830 3619 5.465935 AGGTATTAACACACGCCAATTTTG 58.534 37.500 0.00 0.00 0.00 2.44
2831 3620 5.715434 AGGTATTAACACACGCCAATTTT 57.285 34.783 0.00 0.00 0.00 1.82
2834 3623 4.328536 TGAAGGTATTAACACACGCCAAT 58.671 39.130 0.00 0.00 0.00 3.16
2919 3709 8.193438 GCCAAGATTTCATTATTTCTTACAGCT 58.807 33.333 0.00 0.00 0.00 4.24
2935 3725 7.063780 CAGACAAATAAACCATGCCAAGATTTC 59.936 37.037 0.00 0.00 0.00 2.17
2936 3726 6.875195 CAGACAAATAAACCATGCCAAGATTT 59.125 34.615 0.00 0.00 0.00 2.17
2942 3732 2.830923 CCCAGACAAATAAACCATGCCA 59.169 45.455 0.00 0.00 0.00 4.92
2943 3733 3.096092 TCCCAGACAAATAAACCATGCC 58.904 45.455 0.00 0.00 0.00 4.40
2961 3751 5.590259 ACAATGAGCTGTACACATTTATCCC 59.410 40.000 7.30 0.00 37.46 3.85
2968 3758 4.292186 AGGAACAATGAGCTGTACACAT 57.708 40.909 0.00 0.00 0.00 3.21
3013 3804 5.472137 GTGGTTACCTCTCACATAAGCAAAA 59.528 40.000 2.07 0.00 37.86 2.44
3045 3853 6.126361 ACAAAGATAGATTCCCCATGCTAGTT 60.126 38.462 0.00 0.00 0.00 2.24
3047 3855 5.874093 ACAAAGATAGATTCCCCATGCTAG 58.126 41.667 0.00 0.00 0.00 3.42
3369 4204 4.530710 TCACAGAATAAGCTTACGGTGT 57.469 40.909 19.46 14.92 32.31 4.16
3370 4205 5.109210 TCATCACAGAATAAGCTTACGGTG 58.891 41.667 8.70 13.57 0.00 4.94
3371 4206 5.339008 TCATCACAGAATAAGCTTACGGT 57.661 39.130 8.70 1.10 0.00 4.83
3372 4207 6.662414 TTTCATCACAGAATAAGCTTACGG 57.338 37.500 8.70 0.43 0.00 4.02
3373 4208 7.688372 ACATTTCATCACAGAATAAGCTTACG 58.312 34.615 8.70 0.51 0.00 3.18
3376 4211 9.846248 GTTAACATTTCATCACAGAATAAGCTT 57.154 29.630 3.48 3.48 0.00 3.74
3377 4212 9.236006 AGTTAACATTTCATCACAGAATAAGCT 57.764 29.630 8.61 0.00 0.00 3.74
3378 4213 9.282247 CAGTTAACATTTCATCACAGAATAAGC 57.718 33.333 8.61 0.00 0.00 3.09
3379 4214 9.282247 GCAGTTAACATTTCATCACAGAATAAG 57.718 33.333 8.61 0.00 0.00 1.73
3380 4215 8.791675 TGCAGTTAACATTTCATCACAGAATAA 58.208 29.630 8.61 0.00 0.00 1.40
3381 4216 8.334263 TGCAGTTAACATTTCATCACAGAATA 57.666 30.769 8.61 0.00 0.00 1.75
3382 4217 7.218228 TGCAGTTAACATTTCATCACAGAAT 57.782 32.000 8.61 0.00 0.00 2.40
3383 4218 6.631971 TGCAGTTAACATTTCATCACAGAA 57.368 33.333 8.61 0.00 0.00 3.02
3384 4219 6.430616 TGATGCAGTTAACATTTCATCACAGA 59.569 34.615 19.07 5.95 36.42 3.41
3385 4220 6.614160 TGATGCAGTTAACATTTCATCACAG 58.386 36.000 19.07 0.00 36.42 3.66
3386 4221 6.572167 TGATGCAGTTAACATTTCATCACA 57.428 33.333 19.07 7.06 36.42 3.58
3387 4222 7.972277 AGAATGATGCAGTTAACATTTCATCAC 59.028 33.333 22.41 15.67 41.74 3.06
3388 4223 8.058667 AGAATGATGCAGTTAACATTTCATCA 57.941 30.769 22.30 22.30 42.68 3.07
3389 4224 8.922058 AAGAATGATGCAGTTAACATTTCATC 57.078 30.769 8.61 13.44 33.92 2.92
3395 4230 9.577110 CACAATTAAGAATGATGCAGTTAACAT 57.423 29.630 8.61 0.00 0.00 2.71
3396 4231 7.541783 GCACAATTAAGAATGATGCAGTTAACA 59.458 33.333 8.61 0.00 0.00 2.41
3397 4232 7.009540 GGCACAATTAAGAATGATGCAGTTAAC 59.990 37.037 0.00 0.00 33.24 2.01
3398 4233 7.035004 GGCACAATTAAGAATGATGCAGTTAA 58.965 34.615 0.00 0.00 33.24 2.01
3402 4237 5.041287 CAGGCACAATTAAGAATGATGCAG 58.959 41.667 0.00 0.70 33.24 4.41
3468 4303 8.974060 AACAAACCAGATTAAGAGTTCAGTAA 57.026 30.769 0.00 0.00 0.00 2.24
3498 4333 4.159135 GCACTTGTGGGATTCTCATTCATT 59.841 41.667 2.81 0.00 0.00 2.57
3500 4335 3.084039 GCACTTGTGGGATTCTCATTCA 58.916 45.455 2.81 0.00 0.00 2.57
3520 4355 6.717084 ACTAAATTAGGCCTCCAGAATATTGC 59.283 38.462 9.68 0.00 0.00 3.56
3521 4356 9.220767 GTACTAAATTAGGCCTCCAGAATATTG 57.779 37.037 9.68 0.00 0.00 1.90
3522 4357 8.945193 TGTACTAAATTAGGCCTCCAGAATATT 58.055 33.333 9.68 3.89 0.00 1.28
3523 4358 8.506196 TGTACTAAATTAGGCCTCCAGAATAT 57.494 34.615 9.68 0.00 0.00 1.28
3524 4359 7.924358 TGTACTAAATTAGGCCTCCAGAATA 57.076 36.000 9.68 0.00 0.00 1.75
3525 4360 6.824958 TGTACTAAATTAGGCCTCCAGAAT 57.175 37.500 9.68 0.00 0.00 2.40
3526 4361 6.630203 TTGTACTAAATTAGGCCTCCAGAA 57.370 37.500 9.68 0.00 0.00 3.02
3527 4362 6.824958 ATTGTACTAAATTAGGCCTCCAGA 57.175 37.500 9.68 0.00 0.00 3.86
3528 4363 7.339466 ACAAATTGTACTAAATTAGGCCTCCAG 59.661 37.037 9.68 2.71 0.00 3.86
3529 4364 7.179269 ACAAATTGTACTAAATTAGGCCTCCA 58.821 34.615 9.68 0.00 0.00 3.86
3530 4365 7.640597 ACAAATTGTACTAAATTAGGCCTCC 57.359 36.000 9.68 0.00 0.00 4.30
3531 4366 9.353999 CAAACAAATTGTACTAAATTAGGCCTC 57.646 33.333 9.68 0.00 34.16 4.70
3532 4367 8.311109 CCAAACAAATTGTACTAAATTAGGCCT 58.689 33.333 11.78 11.78 37.32 5.19
3533 4368 8.092068 ACCAAACAAATTGTACTAAATTAGGCC 58.908 33.333 0.00 0.00 37.32 5.19
3534 4369 8.921670 CACCAAACAAATTGTACTAAATTAGGC 58.078 33.333 0.00 0.00 37.32 3.93
3535 4370 9.974980 ACACCAAACAAATTGTACTAAATTAGG 57.025 29.630 0.00 0.00 37.32 2.69
3538 4373 9.092876 CACACACCAAACAAATTGTACTAAATT 57.907 29.630 0.00 0.00 37.32 1.82
3539 4374 8.254508 ACACACACCAAACAAATTGTACTAAAT 58.745 29.630 0.00 0.00 37.32 1.40
3540 4375 7.603651 ACACACACCAAACAAATTGTACTAAA 58.396 30.769 0.00 0.00 37.32 1.85
3541 4376 7.159322 ACACACACCAAACAAATTGTACTAA 57.841 32.000 0.00 0.00 37.32 2.24
3542 4377 6.761099 ACACACACCAAACAAATTGTACTA 57.239 33.333 0.00 0.00 37.32 1.82
3543 4378 5.652994 ACACACACCAAACAAATTGTACT 57.347 34.783 0.00 0.00 37.32 2.73
3544 4379 5.635700 ACAACACACACCAAACAAATTGTAC 59.364 36.000 0.00 0.00 37.32 2.90
3545 4380 5.635280 CACAACACACACCAAACAAATTGTA 59.365 36.000 0.00 0.00 37.32 2.41
3562 4397 5.484173 TCATGTTTCAGACTTCACAACAC 57.516 39.130 0.00 0.00 30.40 3.32
3675 4510 5.460646 TCTTGTGCAAAGCAAGCTATTTAC 58.539 37.500 9.98 0.00 41.47 2.01
3676 4511 5.703978 TCTTGTGCAAAGCAAGCTATTTA 57.296 34.783 9.98 0.00 41.47 1.40
3831 4666 6.183360 GGGATATAGTGTAAGTGTACAAGGCA 60.183 42.308 0.00 0.00 41.89 4.75
4170 5006 3.465588 TCTTCCTTTTTCCTTTCCCCTCA 59.534 43.478 0.00 0.00 0.00 3.86
4238 5074 0.817654 GTGATAAACTGGCCCCTTGC 59.182 55.000 0.00 0.00 40.16 4.01
4397 5233 6.780031 ACATACTACCACATCAGCTCTAGATT 59.220 38.462 0.00 0.00 0.00 2.40
4401 5237 5.445964 TCACATACTACCACATCAGCTCTA 58.554 41.667 0.00 0.00 0.00 2.43
4520 5360 7.950124 TGTTTCTTCCCCTCTGAAAATTCTATT 59.050 33.333 0.00 0.00 32.50 1.73
4522 5362 6.848069 TGTTTCTTCCCCTCTGAAAATTCTA 58.152 36.000 0.00 0.00 32.50 2.10
4544 5384 3.071312 TGCTTCCATTTTTGCAAGGATGT 59.929 39.130 17.56 0.00 32.12 3.06
4876 5716 1.220749 GCGACTGGGGAGCATTACA 59.779 57.895 0.00 0.00 0.00 2.41
4879 5719 2.270205 CAGCGACTGGGGAGCATT 59.730 61.111 0.00 0.00 0.00 3.56
4895 5735 1.810532 AAAAAGAAACGTGGGCGCA 59.189 47.368 10.83 0.00 42.83 6.09
5035 5909 0.905357 ATGTAGAGCTTCAAGGGCGT 59.095 50.000 0.00 0.00 34.52 5.68
5288 6177 1.725557 GGCGCGAGATGACTACCTCA 61.726 60.000 12.10 0.00 0.00 3.86
5311 6200 1.033746 TTCGACGAGGACGCCCTAAT 61.034 55.000 0.00 0.00 44.53 1.73


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

AutoCloner maintained by Alex Coulton.