Multiple sequence alignment - TraesCS5D01G535300

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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 TraesCS5D01G535300 chr5D 100.000 3576 0 0 1 3576 549307228 549310803 0.000000e+00 6604.0
1 TraesCS5D01G535300 chr5D 81.064 977 111 33 2629 3576 13237869 13238800 0.000000e+00 712.0
2 TraesCS5D01G535300 chr5B 89.896 2118 132 44 423 2497 700916477 700918555 0.000000e+00 2651.0
3 TraesCS5D01G535300 chr5B 81.043 997 102 35 2629 3576 38560798 38559840 0.000000e+00 713.0
4 TraesCS5D01G535300 chr5B 85.489 634 67 10 2956 3576 388385013 388384392 3.890000e-179 638.0
5 TraesCS5D01G535300 chr5B 82.379 454 46 15 1 435 700909188 700909626 7.300000e-97 364.0
6 TraesCS5D01G535300 chr5B 86.047 86 11 1 2636 2720 41386191 41386276 1.370000e-14 91.6
7 TraesCS5D01G535300 chr4A 92.978 1125 46 13 1390 2499 620779333 620780439 0.000000e+00 1609.0
8 TraesCS5D01G535300 chr4A 96.687 483 11 3 619 1096 620778553 620779035 0.000000e+00 798.0
9 TraesCS5D01G535300 chr4A 80.323 991 103 35 2629 3576 166839952 166839011 0.000000e+00 665.0
10 TraesCS5D01G535300 chr4A 95.699 279 11 1 1085 1363 620779056 620779333 7.040000e-122 448.0
11 TraesCS5D01G535300 chr4A 84.793 434 43 9 5 423 620777769 620778194 7.140000e-112 414.0
12 TraesCS5D01G535300 chr4A 85.393 178 10 9 417 586 620778386 620778555 1.710000e-38 171.0
13 TraesCS5D01G535300 chr7A 85.780 654 54 14 2936 3576 734210022 734210649 0.000000e+00 656.0
14 TraesCS5D01G535300 chr7A 79.137 997 111 52 2629 3574 567709587 567708637 1.840000e-167 599.0
15 TraesCS5D01G535300 chr2B 84.912 623 66 15 2961 3576 164022270 164022871 3.950000e-169 604.0
16 TraesCS5D01G535300 chr3B 79.179 999 106 58 2629 3574 105189273 105188324 1.840000e-167 599.0
17 TraesCS5D01G535300 chr3B 81.711 678 77 17 2917 3576 370922935 370922287 4.090000e-144 521.0
18 TraesCS5D01G535300 chr5A 79.095 995 113 50 2629 3574 631367218 631366270 6.610000e-167 597.0
19 TraesCS5D01G535300 chrUn 78.400 1000 123 43 2629 3576 119038412 119039370 6.700000e-157 564.0
20 TraesCS5D01G535300 chr7B 85.166 573 56 12 3009 3576 678659899 678659351 8.670000e-156 560.0
21 TraesCS5D01G535300 chr7B 85.353 553 47 7 3034 3576 710980071 710980599 3.140000e-150 542.0
22 TraesCS5D01G535300 chr7B 81.604 636 64 20 2961 3576 380358183 380357581 8.980000e-131 477.0
23 TraesCS5D01G535300 chr6B 89.563 412 38 3 3170 3576 708242866 708243277 5.290000e-143 518.0
24 TraesCS5D01G535300 chr2D 87.500 112 14 0 50 161 17824627 17824738 2.900000e-26 130.0
25 TraesCS5D01G535300 chr3D 87.736 106 10 1 1941 2046 555772959 555773061 1.740000e-23 121.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G535300 chr5D 549307228 549310803 3575 False 6604 6604 100.000 1 3576 1 chr5D.!!$F2 3575
1 TraesCS5D01G535300 chr5D 13237869 13238800 931 False 712 712 81.064 2629 3576 1 chr5D.!!$F1 947
2 TraesCS5D01G535300 chr5B 700916477 700918555 2078 False 2651 2651 89.896 423 2497 1 chr5B.!!$F3 2074
3 TraesCS5D01G535300 chr5B 38559840 38560798 958 True 713 713 81.043 2629 3576 1 chr5B.!!$R1 947
4 TraesCS5D01G535300 chr5B 388384392 388385013 621 True 638 638 85.489 2956 3576 1 chr5B.!!$R2 620
5 TraesCS5D01G535300 chr4A 620777769 620780439 2670 False 688 1609 91.110 5 2499 5 chr4A.!!$F1 2494
6 TraesCS5D01G535300 chr4A 166839011 166839952 941 True 665 665 80.323 2629 3576 1 chr4A.!!$R1 947
7 TraesCS5D01G535300 chr7A 734210022 734210649 627 False 656 656 85.780 2936 3576 1 chr7A.!!$F1 640
8 TraesCS5D01G535300 chr7A 567708637 567709587 950 True 599 599 79.137 2629 3574 1 chr7A.!!$R1 945
9 TraesCS5D01G535300 chr2B 164022270 164022871 601 False 604 604 84.912 2961 3576 1 chr2B.!!$F1 615
10 TraesCS5D01G535300 chr3B 105188324 105189273 949 True 599 599 79.179 2629 3574 1 chr3B.!!$R1 945
11 TraesCS5D01G535300 chr3B 370922287 370922935 648 True 521 521 81.711 2917 3576 1 chr3B.!!$R2 659
12 TraesCS5D01G535300 chr5A 631366270 631367218 948 True 597 597 79.095 2629 3574 1 chr5A.!!$R1 945
13 TraesCS5D01G535300 chrUn 119038412 119039370 958 False 564 564 78.400 2629 3576 1 chrUn.!!$F1 947
14 TraesCS5D01G535300 chr7B 678659351 678659899 548 True 560 560 85.166 3009 3576 1 chr7B.!!$R2 567
15 TraesCS5D01G535300 chr7B 710980071 710980599 528 False 542 542 85.353 3034 3576 1 chr7B.!!$F1 542
16 TraesCS5D01G535300 chr7B 380357581 380358183 602 True 477 477 81.604 2961 3576 1 chr7B.!!$R1 615

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
572 793 0.250513 AGACCACCATCCTTCTTCGC 59.749 55.0 0.00 0.0 0.0 4.70 F
1407 1682 0.108804 CCCTCGTACGTTCTGCATGT 60.109 55.0 16.05 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 2790 0.107897 ATTTGTATCGCGCAGTCCCA 60.108 50.0 8.75 0.0 0.00 4.37 R
3154 3638 0.035152 TGAGGCCGAAATGAGTGCAT 60.035 50.0 0.00 0.0 35.92 3.96 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.675510 ACGTGGGTATGTTTATGTACTCG 58.324 43.478 0.00 0.00 0.00 4.18
71 72 0.602638 TGCCTCGTGATGGTTGTGAC 60.603 55.000 0.00 0.00 0.00 3.67
73 74 1.945819 GCCTCGTGATGGTTGTGACAT 60.946 52.381 0.00 0.00 0.00 3.06
112 113 1.227089 CGTCTCCTCGCCTTCCATG 60.227 63.158 0.00 0.00 0.00 3.66
151 152 5.681639 AGGTGGGTTTAGCTATGTTGTATC 58.318 41.667 0.00 0.00 0.00 2.24
154 155 5.758784 GTGGGTTTAGCTATGTTGTATCCTC 59.241 44.000 0.00 0.00 0.00 3.71
174 175 1.227002 GTTCGGGTCGAGCATCCTC 60.227 63.158 17.59 0.00 37.08 3.71
175 176 2.423898 TTCGGGTCGAGCATCCTCC 61.424 63.158 17.59 0.00 37.14 4.30
176 177 4.271816 CGGGTCGAGCATCCTCCG 62.272 72.222 17.59 5.62 34.49 4.63
177 178 3.917760 GGGTCGAGCATCCTCCGG 61.918 72.222 17.59 0.00 34.49 5.14
178 179 3.917760 GGTCGAGCATCCTCCGGG 61.918 72.222 10.30 0.00 34.49 5.73
179 180 3.917760 GTCGAGCATCCTCCGGGG 61.918 72.222 0.00 0.00 34.49 5.73
211 225 0.508641 CCTTCTTGCGTTCGTGTCAG 59.491 55.000 0.00 0.00 0.00 3.51
215 229 1.151777 CTTGCGTTCGTGTCAGGTGT 61.152 55.000 0.00 0.00 0.00 4.16
221 235 2.798283 CGTTCGTGTCAGGTGTTGTATT 59.202 45.455 0.00 0.00 0.00 1.89
226 240 4.748102 TCGTGTCAGGTGTTGTATTCTTTC 59.252 41.667 0.00 0.00 0.00 2.62
232 246 7.225931 TGTCAGGTGTTGTATTCTTTCTTGTAC 59.774 37.037 0.00 0.00 0.00 2.90
235 249 7.441157 CAGGTGTTGTATTCTTTCTTGTACTCA 59.559 37.037 0.00 0.00 0.00 3.41
327 343 6.474364 CACGTTGAATTGACATATAAAGCGA 58.526 36.000 0.00 0.00 0.00 4.93
334 350 7.909641 TGAATTGACATATAAAGCGACATGTTG 59.090 33.333 8.88 8.88 31.94 3.33
341 357 5.786401 ATAAAGCGACATGTTGAGAGAAC 57.214 39.130 17.70 0.00 0.00 3.01
351 367 7.971168 CGACATGTTGAGAGAACTAGAATTAGT 59.029 37.037 7.36 0.00 41.91 2.24
389 405 9.422681 AGCTAGGTGTATAAGATTAAGAAGACA 57.577 33.333 0.00 0.00 0.00 3.41
390 406 9.685828 GCTAGGTGTATAAGATTAAGAAGACAG 57.314 37.037 0.00 0.00 0.00 3.51
445 658 3.394606 TGATTCCTATAAAGACCAGGCCC 59.605 47.826 0.00 0.00 0.00 5.80
452 665 1.848886 AAAGACCAGGCCCCGTTAGG 61.849 60.000 0.00 0.00 37.24 2.69
502 715 0.685097 TGTGCTCCAAGAGTACACCC 59.315 55.000 10.88 0.00 46.83 4.61
503 716 0.685097 GTGCTCCAAGAGTACACCCA 59.315 55.000 7.81 0.00 43.09 4.51
504 717 1.279271 GTGCTCCAAGAGTACACCCAT 59.721 52.381 7.81 0.00 43.09 4.00
505 718 1.555075 TGCTCCAAGAGTACACCCATC 59.445 52.381 0.00 0.00 31.39 3.51
506 719 1.834263 GCTCCAAGAGTACACCCATCT 59.166 52.381 0.00 0.00 31.39 2.90
507 720 3.031736 GCTCCAAGAGTACACCCATCTA 58.968 50.000 0.00 0.00 31.39 1.98
572 793 0.250513 AGACCACCATCCTTCTTCGC 59.749 55.000 0.00 0.00 0.00 4.70
581 802 3.190874 CATCCTTCTTCGCACTCCTAAC 58.809 50.000 0.00 0.00 0.00 2.34
595 816 1.001633 TCCTAACAAACTGAGGCCGTC 59.998 52.381 0.00 0.00 0.00 4.79
634 855 0.533308 ACGAACAAGCAGGGCGTTTA 60.533 50.000 0.00 0.00 0.00 2.01
897 1126 5.450965 GCATGATTAAACAATCTCTGTGGGG 60.451 44.000 0.00 0.00 38.67 4.96
1059 1291 6.151985 AGGTAGATGATACTAGGATTCTTGCG 59.848 42.308 0.00 0.00 0.00 4.85
1096 1328 2.364324 AGATTAATTCCCTGTAGCGCGA 59.636 45.455 12.10 0.00 0.00 5.87
1115 1378 2.605818 CGAAAGACGTGTGGAAGAAACA 59.394 45.455 0.00 0.00 37.22 2.83
1131 1394 3.114616 CAGAGCCGAACCAGCGTG 61.115 66.667 0.00 0.00 34.64 5.34
1369 1632 1.385206 GCATCCTTCCTCTCCCCCT 60.385 63.158 0.00 0.00 0.00 4.79
1371 1634 2.022718 CATCCTTCCTCTCCCCCTAG 57.977 60.000 0.00 0.00 0.00 3.02
1372 1635 0.192315 ATCCTTCCTCTCCCCCTAGC 59.808 60.000 0.00 0.00 0.00 3.42
1373 1636 0.931757 TCCTTCCTCTCCCCCTAGCT 60.932 60.000 0.00 0.00 0.00 3.32
1381 1656 2.632512 CTCTCCCCCTAGCTTGATTCTC 59.367 54.545 0.00 0.00 0.00 2.87
1383 1658 1.009552 TCCCCCTAGCTTGATTCTCCA 59.990 52.381 0.00 0.00 0.00 3.86
1385 1660 2.122768 CCCCTAGCTTGATTCTCCAGT 58.877 52.381 0.00 0.00 0.00 4.00
1386 1661 2.507471 CCCCTAGCTTGATTCTCCAGTT 59.493 50.000 0.00 0.00 0.00 3.16
1399 1674 1.271656 CTCCAGTTTCCCTCGTACGTT 59.728 52.381 16.05 0.00 0.00 3.99
1401 1676 1.271656 CCAGTTTCCCTCGTACGTTCT 59.728 52.381 16.05 2.07 0.00 3.01
1405 1680 0.892755 TTCCCTCGTACGTTCTGCAT 59.107 50.000 16.05 0.00 0.00 3.96
1407 1682 0.108804 CCCTCGTACGTTCTGCATGT 60.109 55.000 16.05 0.00 0.00 3.21
1420 1695 1.917955 CTGCATGTACACTACCGTTCG 59.082 52.381 0.00 0.00 0.00 3.95
1582 1868 3.496130 CACAGTTAAGACAGCTCCACTTG 59.504 47.826 6.78 0.00 0.00 3.16
1633 1927 7.998964 ACATTTTCTGTTTAGGAGAAGAAGGAA 59.001 33.333 0.00 0.00 32.90 3.36
1639 1933 5.130477 TGTTTAGGAGAAGAAGGAACACAGT 59.870 40.000 0.00 0.00 0.00 3.55
2211 2539 1.571919 GCACAGACCATATGGACGTC 58.428 55.000 28.77 15.19 38.94 4.34
2212 2540 1.134818 GCACAGACCATATGGACGTCA 60.135 52.381 28.77 3.91 38.94 4.35
2351 2679 3.207669 GAGCTCGCAGGGCAATGG 61.208 66.667 0.00 0.00 0.00 3.16
2352 2680 3.687321 GAGCTCGCAGGGCAATGGA 62.687 63.158 0.00 0.00 0.00 3.41
2353 2681 2.751436 GCTCGCAGGGCAATGGAA 60.751 61.111 0.00 0.00 0.00 3.53
2370 2698 1.228245 AACGGAGCATTGCCAGTGT 60.228 52.632 4.70 0.00 0.00 3.55
2462 2790 4.655963 AGATTGTGTTCAGGCTGTTGTAT 58.344 39.130 15.27 2.16 0.00 2.29
2477 2805 0.031585 TGTATGGGACTGCGCGATAC 59.968 55.000 12.10 7.65 0.00 2.24
2520 2848 8.894768 AAGAGTTACTATTAGAATGTCCATGC 57.105 34.615 0.00 0.00 0.00 4.06
2521 2849 7.148641 AGAGTTACTATTAGAATGTCCATGCG 58.851 38.462 0.00 0.00 0.00 4.73
2522 2850 6.817184 AGTTACTATTAGAATGTCCATGCGT 58.183 36.000 0.00 0.00 0.00 5.24
2523 2851 7.272978 AGTTACTATTAGAATGTCCATGCGTT 58.727 34.615 0.00 0.00 0.00 4.84
2524 2852 5.991328 ACTATTAGAATGTCCATGCGTTG 57.009 39.130 0.00 0.00 0.00 4.10
2525 2853 3.698029 ATTAGAATGTCCATGCGTTGC 57.302 42.857 0.00 0.00 0.00 4.17
2526 2854 1.378531 TAGAATGTCCATGCGTTGCC 58.621 50.000 0.00 0.00 0.00 4.52
2527 2855 0.608856 AGAATGTCCATGCGTTGCCA 60.609 50.000 0.00 0.00 0.00 4.92
2528 2856 0.457035 GAATGTCCATGCGTTGCCAT 59.543 50.000 0.00 0.00 0.00 4.40
2529 2857 0.173935 AATGTCCATGCGTTGCCATG 59.826 50.000 0.00 0.00 41.71 3.66
2549 2877 4.169059 TGGGCCATGGATATATGTATGC 57.831 45.455 18.40 0.00 0.00 3.14
2550 2878 3.787577 TGGGCCATGGATATATGTATGCT 59.212 43.478 18.40 0.00 30.67 3.79
2551 2879 4.139786 GGGCCATGGATATATGTATGCTG 58.860 47.826 18.40 0.00 30.67 4.41
2552 2880 4.139786 GGCCATGGATATATGTATGCTGG 58.860 47.826 18.40 11.87 33.86 4.85
2553 2881 4.385643 GGCCATGGATATATGTATGCTGGT 60.386 45.833 18.40 0.00 33.57 4.00
2554 2882 5.195940 GCCATGGATATATGTATGCTGGTT 58.804 41.667 18.40 0.00 33.57 3.67
2555 2883 5.066893 GCCATGGATATATGTATGCTGGTTG 59.933 44.000 18.40 5.02 33.57 3.77
2556 2884 5.066893 CCATGGATATATGTATGCTGGTTGC 59.933 44.000 5.56 0.00 43.25 4.17
2569 2897 4.928661 GCTGGTTGCATATATACTTCGG 57.071 45.455 0.00 0.00 42.31 4.30
2570 2898 3.684788 GCTGGTTGCATATATACTTCGGG 59.315 47.826 0.00 0.00 42.31 5.14
2571 2899 4.562757 GCTGGTTGCATATATACTTCGGGA 60.563 45.833 0.00 0.00 42.31 5.14
2572 2900 5.147330 TGGTTGCATATATACTTCGGGAG 57.853 43.478 0.00 0.00 0.00 4.30
2573 2901 4.020573 TGGTTGCATATATACTTCGGGAGG 60.021 45.833 0.00 0.00 0.00 4.30
2574 2902 4.222145 GGTTGCATATATACTTCGGGAGGA 59.778 45.833 0.00 0.00 0.00 3.71
2575 2903 5.279809 GGTTGCATATATACTTCGGGAGGAA 60.280 44.000 0.00 0.00 0.00 3.36
2587 2915 5.971763 CTTCGGGAGGAAGGAGATATAATG 58.028 45.833 0.00 0.00 46.89 1.90
2588 2916 3.769844 TCGGGAGGAAGGAGATATAATGC 59.230 47.826 0.00 0.00 0.00 3.56
2589 2917 3.515502 CGGGAGGAAGGAGATATAATGCA 59.484 47.826 0.00 0.00 0.00 3.96
2590 2918 4.163078 CGGGAGGAAGGAGATATAATGCAT 59.837 45.833 0.00 0.00 0.00 3.96
2591 2919 5.435291 GGGAGGAAGGAGATATAATGCATG 58.565 45.833 0.00 0.00 0.00 4.06
2592 2920 5.045286 GGGAGGAAGGAGATATAATGCATGT 60.045 44.000 0.00 0.00 0.00 3.21
2593 2921 6.112058 GGAGGAAGGAGATATAATGCATGTC 58.888 44.000 0.00 0.00 0.00 3.06
2594 2922 6.296087 GGAGGAAGGAGATATAATGCATGTCA 60.296 42.308 0.00 0.00 0.00 3.58
2595 2923 7.083062 AGGAAGGAGATATAATGCATGTCAA 57.917 36.000 0.00 0.00 0.00 3.18
2596 2924 7.696981 AGGAAGGAGATATAATGCATGTCAAT 58.303 34.615 0.00 0.00 0.00 2.57
2597 2925 8.168725 AGGAAGGAGATATAATGCATGTCAATT 58.831 33.333 0.00 0.00 0.00 2.32
2598 2926 8.800332 GGAAGGAGATATAATGCATGTCAATTT 58.200 33.333 0.00 0.00 0.00 1.82
2601 2929 9.976511 AGGAGATATAATGCATGTCAATTTTTG 57.023 29.630 0.00 0.00 0.00 2.44
2602 2930 8.706035 GGAGATATAATGCATGTCAATTTTTGC 58.294 33.333 0.00 0.00 35.67 3.68
2610 2938 7.758613 TGCATGTCAATTTTTGCATGTATAG 57.241 32.000 17.59 2.99 42.16 1.31
2611 2939 7.545489 TGCATGTCAATTTTTGCATGTATAGA 58.455 30.769 17.59 0.00 42.16 1.98
2612 2940 8.033626 TGCATGTCAATTTTTGCATGTATAGAA 58.966 29.630 17.59 0.00 42.16 2.10
2613 2941 8.871862 GCATGTCAATTTTTGCATGTATAGAAA 58.128 29.630 17.59 0.00 42.16 2.52
2616 2944 9.368674 TGTCAATTTTTGCATGTATAGAAATGG 57.631 29.630 0.00 0.00 0.00 3.16
2617 2945 9.369904 GTCAATTTTTGCATGTATAGAAATGGT 57.630 29.630 0.00 0.00 0.00 3.55
2620 2948 9.533253 AATTTTTGCATGTATAGAAATGGTAGC 57.467 29.630 0.00 0.00 0.00 3.58
2621 2949 6.633500 TTTGCATGTATAGAAATGGTAGCC 57.367 37.500 0.00 0.00 0.00 3.93
2622 2950 4.651778 TGCATGTATAGAAATGGTAGCCC 58.348 43.478 0.00 0.00 0.00 5.19
2624 2952 4.455877 GCATGTATAGAAATGGTAGCCCAC 59.544 45.833 0.00 0.00 45.65 4.61
2625 2953 5.620206 CATGTATAGAAATGGTAGCCCACA 58.380 41.667 0.00 0.00 45.65 4.17
2626 2954 5.702065 TGTATAGAAATGGTAGCCCACAA 57.298 39.130 0.00 0.00 45.65 3.33
2627 2955 5.433526 TGTATAGAAATGGTAGCCCACAAC 58.566 41.667 0.00 0.00 45.65 3.32
2640 2968 1.669760 CACAACGGCGGGTGTACAT 60.670 57.895 15.22 0.00 0.00 2.29
2646 2974 2.349755 GCGGGTGTACATGGTGGT 59.650 61.111 0.00 0.00 0.00 4.16
2686 3015 2.556114 CCCTTGGATTTTGAGACAGCCT 60.556 50.000 0.00 0.00 0.00 4.58
2713 3042 7.726033 ATACCTATAGATTCTAACTGGCCAG 57.274 40.000 31.60 31.60 0.00 4.85
2741 3075 1.133513 ACAGCCCAATGAACAGACCAA 60.134 47.619 0.00 0.00 0.00 3.67
2743 3077 0.244721 GCCCAATGAACAGACCAAGC 59.755 55.000 0.00 0.00 0.00 4.01
2759 3093 1.203052 CAAGCCCACATCGAAATTGCT 59.797 47.619 0.00 0.00 0.00 3.91
2760 3094 1.098050 AGCCCACATCGAAATTGCTC 58.902 50.000 0.00 0.00 0.00 4.26
2761 3095 0.248215 GCCCACATCGAAATTGCTCG 60.248 55.000 0.00 0.00 40.25 5.03
2762 3096 1.086696 CCCACATCGAAATTGCTCGT 58.913 50.000 0.00 0.00 39.84 4.18
2763 3097 1.062587 CCCACATCGAAATTGCTCGTC 59.937 52.381 0.00 0.00 39.84 4.20
2764 3098 1.062587 CCACATCGAAATTGCTCGTCC 59.937 52.381 0.00 0.00 39.84 4.79
2765 3099 1.731709 CACATCGAAATTGCTCGTCCA 59.268 47.619 0.00 0.00 39.84 4.02
2766 3100 2.002586 ACATCGAAATTGCTCGTCCAG 58.997 47.619 0.00 0.00 39.84 3.86
2769 3103 1.272490 TCGAAATTGCTCGTCCAGTCT 59.728 47.619 0.00 0.00 39.84 3.24
2803 3154 4.803426 CCTCGCACTGCTCGACCC 62.803 72.222 0.00 0.00 32.08 4.46
2804 3155 3.753434 CTCGCACTGCTCGACCCT 61.753 66.667 0.00 0.00 32.08 4.34
2805 3156 3.978723 CTCGCACTGCTCGACCCTG 62.979 68.421 0.00 0.00 32.08 4.45
2839 3218 4.194720 CGCCTCGCCTCGCTACTT 62.195 66.667 0.00 0.00 0.00 2.24
2841 3220 2.885861 CCTCGCCTCGCTACTTGT 59.114 61.111 0.00 0.00 0.00 3.16
2846 3225 2.662596 CCTCGCTACTTGTGCCCA 59.337 61.111 0.00 0.00 0.00 5.36
2883 3276 2.762043 AGGAAGCTCCCGCCTCTC 60.762 66.667 0.00 0.00 37.19 3.20
2915 3316 3.917760 CCCGACCCTCGATCCAGC 61.918 72.222 0.00 0.00 43.74 4.85
3050 3505 2.828549 CCCCCTTCAAATCCGGCG 60.829 66.667 0.00 0.00 0.00 6.46
3052 3507 3.518068 CCCTTCAAATCCGGCGGC 61.518 66.667 23.83 0.00 0.00 6.53
3053 3508 2.749839 CCTTCAAATCCGGCGGCA 60.750 61.111 23.83 11.08 0.00 5.69
3054 3509 2.764314 CCTTCAAATCCGGCGGCAG 61.764 63.158 23.83 10.73 0.00 4.85
3055 3510 3.401243 CTTCAAATCCGGCGGCAGC 62.401 63.158 23.83 0.00 44.18 5.25
3222 3718 9.080097 AGTACTGATAGAAAGTAGTGTTCTTGT 57.920 33.333 0.00 0.00 36.69 3.16
3245 3742 5.893897 AGAATTGTTGAAGATGAAGAGGC 57.106 39.130 0.00 0.00 0.00 4.70
3249 3746 2.290514 TGTTGAAGATGAAGAGGCCAGG 60.291 50.000 5.01 0.00 0.00 4.45
3268 3767 4.829492 CCAGGGACATTGTTTCTCTTTTCT 59.171 41.667 0.00 0.00 0.00 2.52
3270 3769 6.150140 CCAGGGACATTGTTTCTCTTTTCTAG 59.850 42.308 0.00 0.00 0.00 2.43
3356 3858 2.169832 AGCGAAGTTGTGTGTATGCT 57.830 45.000 0.00 0.00 0.00 3.79
3373 3875 1.344438 TGCTGGTTGTGATCGAAGAGT 59.656 47.619 0.00 0.00 43.63 3.24
3377 3879 4.143094 GCTGGTTGTGATCGAAGAGTAAAC 60.143 45.833 0.00 0.00 43.63 2.01
3410 3912 7.177216 ACCAACATTGTCTATGTCAAATGTGAT 59.823 33.333 0.22 0.00 46.75 3.06
3411 3913 8.030692 CCAACATTGTCTATGTCAAATGTGATT 58.969 33.333 0.22 0.00 46.75 2.57
3441 3943 1.073964 CTGAAGATGTGTCACTGCCG 58.926 55.000 4.27 0.00 0.00 5.69
3448 3950 1.301716 GTGTCACTGCCGTCACCAT 60.302 57.895 0.00 0.00 0.00 3.55
3465 3967 6.199393 GTCACCATCGGTTTATGATTTTAGC 58.801 40.000 0.00 0.00 31.02 3.09
3482 3984 7.335673 TGATTTTAGCCGTCTTAAACATGATCA 59.664 33.333 0.00 0.00 0.00 2.92
3483 3985 7.624360 TTTTAGCCGTCTTAAACATGATCAT 57.376 32.000 1.18 1.18 0.00 2.45
3512 4015 2.290641 GGCTACCCATTGCAAGTTATCG 59.709 50.000 4.94 0.00 0.00 2.92
3519 4022 5.065988 ACCCATTGCAAGTTATCGTATCAAC 59.934 40.000 4.94 0.00 0.00 3.18
3535 4038 4.685169 ATCAACGATCAAGACGCAATTT 57.315 36.364 0.00 0.00 0.00 1.82
3549 4052 9.616634 CAAGACGCAATTTGAATAGCATATATT 57.383 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.440525 CCGAGTACATAAACATACCCACGT 60.441 45.833 0.00 0.00 0.00 4.49
1 2 4.046462 CCGAGTACATAAACATACCCACG 58.954 47.826 0.00 0.00 0.00 4.94
2 3 4.141869 ACCCGAGTACATAAACATACCCAC 60.142 45.833 0.00 0.00 0.00 4.61
3 4 4.032310 ACCCGAGTACATAAACATACCCA 58.968 43.478 0.00 0.00 0.00 4.51
19 20 2.742372 CACGCCTCCAAACCCGAG 60.742 66.667 0.00 0.00 0.00 4.63
22 23 1.966451 CTGTCACGCCTCCAAACCC 60.966 63.158 0.00 0.00 0.00 4.11
45 46 1.812922 CATCACGAGGCACCTCTGC 60.813 63.158 14.58 0.00 43.41 4.26
112 113 2.439104 CCTAGCCCAGACTCCAGCC 61.439 68.421 0.00 0.00 0.00 4.85
151 152 1.949847 ATGCTCGACCCGAACAGAGG 61.950 60.000 0.00 0.00 35.48 3.69
154 155 1.519455 GGATGCTCGACCCGAACAG 60.519 63.158 0.00 0.00 35.48 3.16
174 175 1.006102 GCGTGAGTATGATCCCCGG 60.006 63.158 0.00 0.00 0.00 5.73
175 176 1.006102 GGCGTGAGTATGATCCCCG 60.006 63.158 0.00 0.00 0.00 5.73
176 177 0.759346 AAGGCGTGAGTATGATCCCC 59.241 55.000 0.00 0.00 0.00 4.81
177 178 1.689273 AGAAGGCGTGAGTATGATCCC 59.311 52.381 0.00 0.00 0.00 3.85
178 179 3.126831 CAAGAAGGCGTGAGTATGATCC 58.873 50.000 0.00 0.00 0.00 3.36
179 180 2.541762 GCAAGAAGGCGTGAGTATGATC 59.458 50.000 0.00 0.00 0.00 2.92
180 181 2.555199 GCAAGAAGGCGTGAGTATGAT 58.445 47.619 0.00 0.00 0.00 2.45
181 182 2.010145 GCAAGAAGGCGTGAGTATGA 57.990 50.000 0.00 0.00 0.00 2.15
207 221 6.619801 ACAAGAAAGAATACAACACCTGAC 57.380 37.500 0.00 0.00 0.00 3.51
211 225 7.724305 TGAGTACAAGAAAGAATACAACACC 57.276 36.000 0.00 0.00 0.00 4.16
242 256 5.111989 TGCAGATCTTTCCGTTGATAGAAG 58.888 41.667 0.00 0.00 33.19 2.85
245 259 5.111989 TCTTGCAGATCTTTCCGTTGATAG 58.888 41.667 0.00 0.00 0.00 2.08
287 303 6.206395 TCAACGTGCCATCATGAATTTATT 57.794 33.333 0.00 0.00 33.49 1.40
289 305 5.635417 TTCAACGTGCCATCATGAATTTA 57.365 34.783 0.00 0.00 33.49 1.40
290 306 4.517952 TTCAACGTGCCATCATGAATTT 57.482 36.364 0.00 0.00 33.49 1.82
291 307 4.724074 ATTCAACGTGCCATCATGAATT 57.276 36.364 0.00 0.00 37.42 2.17
292 308 4.158209 TCAATTCAACGTGCCATCATGAAT 59.842 37.500 0.00 4.04 41.20 2.57
293 309 3.505293 TCAATTCAACGTGCCATCATGAA 59.495 39.130 0.00 0.00 34.80 2.57
294 310 3.080319 TCAATTCAACGTGCCATCATGA 58.920 40.909 0.00 0.00 33.49 3.07
302 318 5.169561 CGCTTTATATGTCAATTCAACGTGC 59.830 40.000 0.00 0.00 0.00 5.34
368 384 9.871238 TGTTCTGTCTTCTTAATCTTATACACC 57.129 33.333 0.00 0.00 0.00 4.16
381 397 9.579932 AAAGGATAATCTTTGTTCTGTCTTCTT 57.420 29.630 0.00 0.00 35.83 2.52
423 439 3.394606 GGGCCTGGTCTTTATAGGAATCA 59.605 47.826 0.84 0.00 33.33 2.57
424 440 3.244946 GGGGCCTGGTCTTTATAGGAATC 60.245 52.174 0.84 0.00 33.33 2.52
445 658 1.445871 CGGGGAAGAAAACCTAACGG 58.554 55.000 0.00 0.00 0.00 4.44
452 665 1.577922 GCGAACCGGGGAAGAAAAC 59.422 57.895 6.32 0.00 0.00 2.43
501 714 2.487986 GGGGAAGCAAGATGGTAGATGG 60.488 54.545 0.00 0.00 0.00 3.51
502 715 2.808202 CGGGGAAGCAAGATGGTAGATG 60.808 54.545 0.00 0.00 0.00 2.90
503 716 1.417890 CGGGGAAGCAAGATGGTAGAT 59.582 52.381 0.00 0.00 0.00 1.98
504 717 0.830648 CGGGGAAGCAAGATGGTAGA 59.169 55.000 0.00 0.00 0.00 2.59
505 718 0.179045 CCGGGGAAGCAAGATGGTAG 60.179 60.000 0.00 0.00 0.00 3.18
506 719 1.912220 CCGGGGAAGCAAGATGGTA 59.088 57.895 0.00 0.00 0.00 3.25
507 720 2.677228 CCGGGGAAGCAAGATGGT 59.323 61.111 0.00 0.00 0.00 3.55
572 793 2.427506 GGCCTCAGTTTGTTAGGAGTG 58.572 52.381 0.00 0.00 31.64 3.51
581 802 3.972227 CCAGACGGCCTCAGTTTG 58.028 61.111 0.00 0.00 0.00 2.93
595 816 2.743928 GCGTTGGACTCCAGCCAG 60.744 66.667 6.35 0.00 36.64 4.85
600 821 2.352704 TTCGTTCGCGTTGGACTCCA 62.353 55.000 5.77 0.00 42.11 3.86
606 827 1.721133 GCTTGTTCGTTCGCGTTGG 60.721 57.895 5.77 0.00 42.11 3.77
795 1022 2.282820 GCTCATGCGCTAACTTGTACTC 59.717 50.000 9.73 0.00 0.00 2.59
897 1126 3.866582 CCCCTGATGCCCGTCTCC 61.867 72.222 0.00 0.00 0.00 3.71
1096 1328 3.869065 TCTGTTTCTTCCACACGTCTTT 58.131 40.909 0.00 0.00 0.00 2.52
1131 1394 2.433994 CCTCCTCCTCTGCTCCTGC 61.434 68.421 0.00 0.00 40.20 4.85
1369 1632 3.846588 AGGGAAACTGGAGAATCAAGCTA 59.153 43.478 0.00 0.00 40.94 3.32
1371 1634 3.013219 GAGGGAAACTGGAGAATCAAGC 58.987 50.000 0.00 0.00 40.94 4.01
1372 1635 3.265791 CGAGGGAAACTGGAGAATCAAG 58.734 50.000 0.00 0.00 43.70 3.02
1373 1636 2.637872 ACGAGGGAAACTGGAGAATCAA 59.362 45.455 0.00 0.00 36.25 2.57
1381 1656 1.271656 AGAACGTACGAGGGAAACTGG 59.728 52.381 24.41 0.00 0.00 4.00
1383 1658 1.336609 GCAGAACGTACGAGGGAAACT 60.337 52.381 24.41 6.96 0.00 2.66
1385 1660 0.675083 TGCAGAACGTACGAGGGAAA 59.325 50.000 24.41 0.00 0.00 3.13
1386 1661 0.892755 ATGCAGAACGTACGAGGGAA 59.107 50.000 24.41 3.11 0.00 3.97
1399 1674 2.414957 CGAACGGTAGTGTACATGCAGA 60.415 50.000 0.00 0.00 0.00 4.26
1401 1676 1.540707 TCGAACGGTAGTGTACATGCA 59.459 47.619 0.00 0.00 0.00 3.96
1405 1680 2.598589 GCAATCGAACGGTAGTGTACA 58.401 47.619 0.00 0.00 0.00 2.90
1407 1682 1.468127 TCGCAATCGAACGGTAGTGTA 59.532 47.619 6.10 0.00 42.44 2.90
1420 1695 7.589954 ACAAATACAAGTTGTAACTTCGCAATC 59.410 33.333 19.19 0.00 45.65 2.67
1429 1704 5.593010 TGCCCAACAAATACAAGTTGTAAC 58.407 37.500 19.19 2.67 42.62 2.50
1546 1832 0.114168 ACTGTGACTCCTCCTGAGCT 59.886 55.000 0.00 0.00 45.61 4.09
1582 1868 6.367969 TGCTACTCTGGATAAAAAGAAACGAC 59.632 38.462 0.00 0.00 0.00 4.34
1653 1947 2.245159 TGTGCTGAACTCTGAACTGG 57.755 50.000 0.00 0.00 0.00 4.00
2201 2529 2.557056 CGGGTAGACATGACGTCCATAT 59.443 50.000 14.12 0.00 46.69 1.78
2211 2539 3.458189 GATCTCCAAACGGGTAGACATG 58.542 50.000 0.00 0.00 38.11 3.21
2212 2540 2.100916 CGATCTCCAAACGGGTAGACAT 59.899 50.000 0.00 0.00 38.11 3.06
2217 2545 4.741321 AATAACGATCTCCAAACGGGTA 57.259 40.909 0.00 0.00 38.11 3.69
2255 2583 3.063084 GACAGGGAGCGTCGGAGT 61.063 66.667 0.00 0.00 0.00 3.85
2351 2679 1.237285 ACACTGGCAATGCTCCGTTC 61.237 55.000 4.82 0.00 0.00 3.95
2352 2680 0.823356 AACACTGGCAATGCTCCGTT 60.823 50.000 4.82 1.25 0.00 4.44
2353 2681 1.228245 AACACTGGCAATGCTCCGT 60.228 52.632 4.82 0.00 0.00 4.69
2382 2710 1.787155 CACTGAACTACTCGTGTGCAC 59.213 52.381 10.75 10.75 0.00 4.57
2384 2712 2.031069 TCTCACTGAACTACTCGTGTGC 60.031 50.000 0.00 0.00 33.62 4.57
2462 2790 0.107897 ATTTGTATCGCGCAGTCCCA 60.108 50.000 8.75 0.00 0.00 4.37
2499 2827 7.345192 CAACGCATGGACATTCTAATAGTAAC 58.655 38.462 0.00 0.00 0.00 2.50
2500 2828 6.018262 GCAACGCATGGACATTCTAATAGTAA 60.018 38.462 0.00 0.00 0.00 2.24
2501 2829 5.465390 GCAACGCATGGACATTCTAATAGTA 59.535 40.000 0.00 0.00 0.00 1.82
2502 2830 4.273480 GCAACGCATGGACATTCTAATAGT 59.727 41.667 0.00 0.00 0.00 2.12
2503 2831 4.319766 GGCAACGCATGGACATTCTAATAG 60.320 45.833 0.00 0.00 0.00 1.73
2504 2832 3.563808 GGCAACGCATGGACATTCTAATA 59.436 43.478 0.00 0.00 0.00 0.98
2505 2833 2.358898 GGCAACGCATGGACATTCTAAT 59.641 45.455 0.00 0.00 0.00 1.73
2506 2834 1.742831 GGCAACGCATGGACATTCTAA 59.257 47.619 0.00 0.00 0.00 2.10
2507 2835 1.339535 TGGCAACGCATGGACATTCTA 60.340 47.619 0.00 0.00 42.51 2.10
2508 2836 0.608856 TGGCAACGCATGGACATTCT 60.609 50.000 0.00 0.00 42.51 2.40
2509 2837 0.457035 ATGGCAACGCATGGACATTC 59.543 50.000 0.00 0.00 42.51 2.67
2510 2838 0.173935 CATGGCAACGCATGGACATT 59.826 50.000 0.00 0.00 42.51 2.71
2511 2839 1.811195 CATGGCAACGCATGGACAT 59.189 52.632 0.00 0.00 42.51 3.06
2512 2840 3.276109 CATGGCAACGCATGGACA 58.724 55.556 0.00 0.00 42.51 4.02
2526 2854 4.521639 GCATACATATATCCATGGCCCATG 59.478 45.833 17.16 17.16 41.10 3.66
2527 2855 4.417854 AGCATACATATATCCATGGCCCAT 59.582 41.667 6.96 2.26 0.00 4.00
2528 2856 3.787577 AGCATACATATATCCATGGCCCA 59.212 43.478 6.96 0.00 0.00 5.36
2529 2857 4.139786 CAGCATACATATATCCATGGCCC 58.860 47.826 6.96 0.00 0.00 5.80
2530 2858 4.139786 CCAGCATACATATATCCATGGCC 58.860 47.826 6.96 0.00 0.00 5.36
2531 2859 4.785301 ACCAGCATACATATATCCATGGC 58.215 43.478 6.96 0.00 0.00 4.40
2532 2860 5.066893 GCAACCAGCATACATATATCCATGG 59.933 44.000 4.97 4.97 44.79 3.66
2533 2861 6.127810 GCAACCAGCATACATATATCCATG 57.872 41.667 0.00 0.00 44.79 3.66
2548 2876 3.684788 CCCGAAGTATATATGCAACCAGC 59.315 47.826 3.52 0.00 45.96 4.85
2549 2877 5.147330 TCCCGAAGTATATATGCAACCAG 57.853 43.478 3.52 0.00 0.00 4.00
2550 2878 4.020573 CCTCCCGAAGTATATATGCAACCA 60.021 45.833 3.52 0.00 0.00 3.67
2551 2879 4.222145 TCCTCCCGAAGTATATATGCAACC 59.778 45.833 3.52 0.00 0.00 3.77
2552 2880 5.401531 TCCTCCCGAAGTATATATGCAAC 57.598 43.478 3.52 0.00 0.00 4.17
2553 2881 5.046591 CCTTCCTCCCGAAGTATATATGCAA 60.047 44.000 3.52 0.00 45.75 4.08
2554 2882 4.466370 CCTTCCTCCCGAAGTATATATGCA 59.534 45.833 3.52 0.00 45.75 3.96
2555 2883 4.710375 TCCTTCCTCCCGAAGTATATATGC 59.290 45.833 0.00 0.00 45.75 3.14
2556 2884 6.188407 TCTCCTTCCTCCCGAAGTATATATG 58.812 44.000 0.00 0.00 45.75 1.78
2557 2885 6.404426 TCTCCTTCCTCCCGAAGTATATAT 57.596 41.667 0.00 0.00 45.75 0.86
2558 2886 5.855338 TCTCCTTCCTCCCGAAGTATATA 57.145 43.478 0.00 0.00 45.75 0.86
2559 2887 4.743705 TCTCCTTCCTCCCGAAGTATAT 57.256 45.455 0.00 0.00 45.75 0.86
2560 2888 4.743705 ATCTCCTTCCTCCCGAAGTATA 57.256 45.455 0.00 0.00 45.75 1.47
2561 2889 3.621682 ATCTCCTTCCTCCCGAAGTAT 57.378 47.619 0.00 0.00 45.75 2.12
2562 2890 4.743705 ATATCTCCTTCCTCCCGAAGTA 57.256 45.455 0.00 0.00 45.75 2.24
2563 2891 3.621682 ATATCTCCTTCCTCCCGAAGT 57.378 47.619 0.00 0.00 45.75 3.01
2564 2892 5.625656 GCATTATATCTCCTTCCTCCCGAAG 60.626 48.000 0.00 0.00 46.61 3.79
2565 2893 4.223032 GCATTATATCTCCTTCCTCCCGAA 59.777 45.833 0.00 0.00 0.00 4.30
2566 2894 3.769844 GCATTATATCTCCTTCCTCCCGA 59.230 47.826 0.00 0.00 0.00 5.14
2567 2895 3.515502 TGCATTATATCTCCTTCCTCCCG 59.484 47.826 0.00 0.00 0.00 5.14
2568 2896 5.045286 ACATGCATTATATCTCCTTCCTCCC 60.045 44.000 0.00 0.00 0.00 4.30
2569 2897 6.059787 ACATGCATTATATCTCCTTCCTCC 57.940 41.667 0.00 0.00 0.00 4.30
2570 2898 6.705302 TGACATGCATTATATCTCCTTCCTC 58.295 40.000 0.00 0.00 0.00 3.71
2571 2899 6.692849 TGACATGCATTATATCTCCTTCCT 57.307 37.500 0.00 0.00 0.00 3.36
2572 2900 7.934855 ATTGACATGCATTATATCTCCTTCC 57.065 36.000 0.00 0.00 0.00 3.46
2575 2903 9.976511 CAAAAATTGACATGCATTATATCTCCT 57.023 29.630 0.00 0.00 0.00 3.69
2576 2904 8.706035 GCAAAAATTGACATGCATTATATCTCC 58.294 33.333 0.00 0.00 38.63 3.71
2577 2905 9.251792 TGCAAAAATTGACATGCATTATATCTC 57.748 29.630 0.00 0.00 43.32 2.75
2587 2915 7.990541 TCTATACATGCAAAAATTGACATGC 57.009 32.000 18.56 4.74 43.02 4.06
2590 2918 9.368674 CCATTTCTATACATGCAAAAATTGACA 57.631 29.630 0.00 0.00 0.00 3.58
2591 2919 9.369904 ACCATTTCTATACATGCAAAAATTGAC 57.630 29.630 0.00 0.00 0.00 3.18
2594 2922 9.533253 GCTACCATTTCTATACATGCAAAAATT 57.467 29.630 0.00 0.00 0.00 1.82
2595 2923 8.143835 GGCTACCATTTCTATACATGCAAAAAT 58.856 33.333 0.00 0.00 0.00 1.82
2596 2924 7.417342 GGGCTACCATTTCTATACATGCAAAAA 60.417 37.037 0.00 0.00 36.50 1.94
2597 2925 6.040391 GGGCTACCATTTCTATACATGCAAAA 59.960 38.462 0.00 0.00 36.50 2.44
2598 2926 5.534654 GGGCTACCATTTCTATACATGCAAA 59.465 40.000 0.00 0.00 36.50 3.68
2599 2927 5.070001 GGGCTACCATTTCTATACATGCAA 58.930 41.667 0.00 0.00 36.50 4.08
2600 2928 4.103943 TGGGCTACCATTTCTATACATGCA 59.896 41.667 0.00 0.00 43.37 3.96
2601 2929 4.651778 TGGGCTACCATTTCTATACATGC 58.348 43.478 0.00 0.00 43.37 4.06
2621 2949 3.045492 GTACACCCGCCGTTGTGG 61.045 66.667 8.55 0.00 42.11 4.17
2622 2950 1.669760 ATGTACACCCGCCGTTGTG 60.670 57.895 0.00 2.89 38.44 3.33
2623 2951 1.669760 CATGTACACCCGCCGTTGT 60.670 57.895 0.00 0.00 0.00 3.32
2624 2952 2.395360 CCATGTACACCCGCCGTTG 61.395 63.158 0.00 0.00 0.00 4.10
2625 2953 2.046700 CCATGTACACCCGCCGTT 60.047 61.111 0.00 0.00 0.00 4.44
2626 2954 3.315949 ACCATGTACACCCGCCGT 61.316 61.111 0.00 0.00 0.00 5.68
2627 2955 2.817834 CACCATGTACACCCGCCG 60.818 66.667 0.00 0.00 0.00 6.46
2633 2961 0.690762 ACCCTGACCACCATGTACAC 59.309 55.000 0.00 0.00 0.00 2.90
2661 2989 2.176798 TGTCTCAAAATCCAAGGGTGGT 59.823 45.455 0.00 0.00 46.11 4.16
2669 2998 6.558775 AGGTATATAGGCTGTCTCAAAATCCA 59.441 38.462 0.00 0.00 0.00 3.41
2722 3051 1.542915 CTTGGTCTGTTCATTGGGCTG 59.457 52.381 0.00 0.00 0.00 4.85
2731 3065 1.168714 GATGTGGGCTTGGTCTGTTC 58.831 55.000 0.00 0.00 0.00 3.18
2741 3075 1.098050 GAGCAATTTCGATGTGGGCT 58.902 50.000 0.00 0.00 0.00 5.19
2743 3077 1.062587 GACGAGCAATTTCGATGTGGG 59.937 52.381 6.54 0.00 43.03 4.61
2835 3194 2.749839 GCGGCATGGGCACAAGTA 60.750 61.111 0.00 0.00 43.71 2.24
2860 3239 3.068691 CGGGAGCTTCCTGGACGA 61.069 66.667 10.06 0.00 39.28 4.20
2896 3289 4.458829 TGGATCGAGGGTCGGGCT 62.459 66.667 0.00 0.00 40.88 5.19
3039 3494 4.713735 TGCTGCCGCCGGATTTGA 62.714 61.111 7.68 0.00 34.43 2.69
3050 3505 2.289565 GGTACCTCACTATTTGCTGCC 58.710 52.381 4.06 0.00 0.00 4.85
3052 3507 3.520290 TCGGTACCTCACTATTTGCTG 57.480 47.619 10.90 0.00 0.00 4.41
3053 3508 4.546829 TTTCGGTACCTCACTATTTGCT 57.453 40.909 10.90 0.00 0.00 3.91
3054 3509 4.873827 TGATTTCGGTACCTCACTATTTGC 59.126 41.667 10.90 0.00 0.00 3.68
3055 3510 6.978343 TTGATTTCGGTACCTCACTATTTG 57.022 37.500 10.90 0.00 0.00 2.32
3056 3511 9.106070 GTATTTGATTTCGGTACCTCACTATTT 57.894 33.333 10.90 0.00 0.00 1.40
3057 3512 7.713942 GGTATTTGATTTCGGTACCTCACTATT 59.286 37.037 10.90 0.00 33.63 1.73
3058 3513 7.215085 GGTATTTGATTTCGGTACCTCACTAT 58.785 38.462 10.90 5.79 33.63 2.12
3154 3638 0.035152 TGAGGCCGAAATGAGTGCAT 60.035 50.000 0.00 0.00 35.92 3.96
3222 3718 5.882557 GGCCTCTTCATCTTCAACAATTCTA 59.117 40.000 0.00 0.00 0.00 2.10
3245 3742 4.829492 AGAAAAGAGAAACAATGTCCCTGG 59.171 41.667 0.00 0.00 0.00 4.45
3268 3767 5.103898 TCCCTGTCTTCATAGCTTCTCTCTA 60.104 44.000 0.00 0.00 0.00 2.43
3270 3769 3.957497 TCCCTGTCTTCATAGCTTCTCTC 59.043 47.826 0.00 0.00 0.00 3.20
3333 3835 4.695455 AGCATACACACAACTTCGCTTATT 59.305 37.500 0.00 0.00 0.00 1.40
3336 3838 2.224079 CAGCATACACACAACTTCGCTT 59.776 45.455 0.00 0.00 0.00 4.68
3337 3839 1.800586 CAGCATACACACAACTTCGCT 59.199 47.619 0.00 0.00 0.00 4.93
3356 3858 4.988540 CAGTTTACTCTTCGATCACAACCA 59.011 41.667 0.00 0.00 0.00 3.67
3373 3875 8.783093 CATAGACAATGTTGGTTCTTCAGTTTA 58.217 33.333 0.00 0.00 0.00 2.01
3410 3912 7.331934 GTGACACATCTTCAGTTTGCTCTATAA 59.668 37.037 0.00 0.00 0.00 0.98
3411 3913 6.813649 GTGACACATCTTCAGTTTGCTCTATA 59.186 38.462 0.00 0.00 0.00 1.31
3441 3943 6.199393 GCTAAAATCATAAACCGATGGTGAC 58.801 40.000 0.00 0.00 35.34 3.67
3448 3950 4.761975 AGACGGCTAAAATCATAAACCGA 58.238 39.130 5.44 0.00 41.61 4.69
3465 3967 3.565482 CCCCATGATCATGTTTAAGACGG 59.435 47.826 29.23 20.82 37.11 4.79
3482 3984 4.620673 TGGGTAGCCTTTCCCCAT 57.379 55.556 13.11 0.00 43.51 4.00
3512 4015 4.778842 ATTGCGTCTTGATCGTTGATAC 57.221 40.909 0.00 0.00 0.00 2.24
3519 4022 4.667948 GCTATTCAAATTGCGTCTTGATCG 59.332 41.667 0.00 0.00 31.85 3.69
3535 4038 9.806448 TGGCCTTTTAAGAATATATGCTATTCA 57.194 29.630 3.32 0.00 36.63 2.57
3549 4052 7.610865 CATAAGGTTTGAATGGCCTTTTAAGA 58.389 34.615 3.32 0.00 42.12 2.10


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

AutoCloner maintained by Alex Coulton.