Multiple sequence alignment - TraesCS4A01G458600

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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 TraesCS4A01G458600 chr4A 100.000 5295 0 0 1 5295 723805870 723811164 0.000000e+00 9779.0
1 TraesCS4A01G458600 chr4A 85.839 1144 109 28 3605 4742 723817704 723818800 0.000000e+00 1166.0
2 TraesCS4A01G458600 chr4A 84.311 733 88 12 3846 4572 724117752 724118463 0.000000e+00 691.0
3 TraesCS4A01G458600 chr4A 82.022 178 24 7 4409 4581 724121377 724121551 1.540000e-30 145.0
4 TraesCS4A01G458600 chr4A 78.947 133 16 7 5138 5269 724094526 724094647 4.400000e-11 80.5
5 TraesCS4A01G458600 chr7D 92.680 3907 199 41 744 4638 13298331 13294500 0.000000e+00 5550.0
6 TraesCS4A01G458600 chr7D 88.673 565 56 6 1 562 13299205 13298646 0.000000e+00 682.0
7 TraesCS4A01G458600 chr7D 78.832 685 108 29 138 796 13362903 13362230 1.360000e-115 427.0
8 TraesCS4A01G458600 chr7D 79.685 635 88 24 602 1213 13306202 13305586 2.280000e-113 420.0
9 TraesCS4A01G458600 chr7D 85.227 176 22 2 2629 2804 13185812 13185641 1.520000e-40 178.0
10 TraesCS4A01G458600 chr7D 88.496 113 13 0 1648 1760 13297506 13297394 2.570000e-28 137.0
11 TraesCS4A01G458600 chr7D 88.889 81 7 1 4664 4742 13294500 13294420 1.210000e-16 99.0
12 TraesCS4A01G458600 chr7A 90.093 4310 260 69 350 4574 12760749 12756522 0.000000e+00 5439.0
13 TraesCS4A01G458600 chr7A 86.471 340 27 9 4956 5295 12756126 12755806 6.520000e-94 355.0
14 TraesCS4A01G458600 chr7A 90.066 151 15 0 4799 4949 12756224 12756074 4.180000e-46 196.0
15 TraesCS4A01G458600 chr7A 84.211 190 21 8 133 316 12760933 12760747 5.450000e-40 176.0
16 TraesCS4A01G458600 chr7A 88.889 81 9 0 1584 1664 12759399 12759319 3.370000e-17 100.0
17 TraesCS4A01G458600 chr7B 93.802 242 15 0 1907 2148 427468247 427468488 1.080000e-96 364.0
18 TraesCS4A01G458600 chr7B 88.421 190 22 0 1654 1843 427468054 427468243 4.120000e-56 230.0
19 TraesCS4A01G458600 chr7B 97.222 36 1 0 1637 1672 427468061 427468096 1.590000e-05 62.1


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 TraesCS4A01G458600 chr4A 723805870 723811164 5294 False 9779.0 9779 100.0000 1 5295 1 chr4A.!!$F1 5294
1 TraesCS4A01G458600 chr4A 723817704 723818800 1096 False 1166.0 1166 85.8390 3605 4742 1 chr4A.!!$F2 1137
2 TraesCS4A01G458600 chr4A 724117752 724121551 3799 False 418.0 691 83.1665 3846 4581 2 chr4A.!!$F4 735
3 TraesCS4A01G458600 chr7D 13294420 13299205 4785 True 1617.0 5550 89.6845 1 4742 4 chr7D.!!$R4 4741
4 TraesCS4A01G458600 chr7D 13362230 13362903 673 True 427.0 427 78.8320 138 796 1 chr7D.!!$R3 658
5 TraesCS4A01G458600 chr7D 13305586 13306202 616 True 420.0 420 79.6850 602 1213 1 chr7D.!!$R2 611
6 TraesCS4A01G458600 chr7A 12755806 12760933 5127 True 1253.2 5439 87.9460 133 5295 5 chr7A.!!$R1 5162

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
650 679 0.454957 GACACACATGCATTGTCCGC 60.455 55.0 16.06 4.88 36.00 5.54 F
953 1165 0.478507 CATCCACCCCCTAATCACCC 59.521 60.0 0.00 0.00 0.00 4.61 F
1216 1449 0.729140 GTTTGGCGAATCCGTGCTTG 60.729 55.0 0.00 0.00 37.80 4.01 F
2265 2556 0.252375 AAAGCCCCACCTGCATGATT 60.252 50.0 0.00 0.00 0.00 2.57 F
2627 2920 1.116308 TGGTGACGAGTGGTCTCAAA 58.884 50.0 6.84 0.00 46.24 2.69 F
4006 4308 1.267121 TAGGGCTCAGCGAGAAGTTT 58.733 50.0 9.32 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1693 0.105964 CAACCCGAATCGATAGCCCA 59.894 55.000 3.36 0.0 0.00 5.36 R
2090 2381 0.240945 CTTGACAACAACCATCCGGC 59.759 55.000 0.00 0.0 34.57 6.13 R
2984 3280 0.944386 ACTGTGCTTAAACTGCCACG 59.056 50.000 0.00 0.0 0.00 4.94 R
4006 4308 0.908910 CCACTGTAGTGCCCATGGTA 59.091 55.000 11.73 0.0 44.34 3.25 R
4099 4401 1.005630 GTTGCTCACCGTCTGCTCT 60.006 57.895 0.00 0.0 0.00 4.09 R
4943 5449 1.867233 TCGTGCAGAGAAAGTTCAAGC 59.133 47.619 0.00 0.0 0.00 4.01 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
20 21 2.537633 ATACGAGGTCCCTTGGTGTA 57.462 50.000 5.57 0.00 0.00 2.90
25 26 2.224450 CGAGGTCCCTTGGTGTACTTTT 60.224 50.000 0.00 0.00 0.00 2.27
93 94 6.245115 TCTTAGTCGTCGATGTGTTTAAGA 57.755 37.500 4.21 10.46 0.00 2.10
109 110 2.568623 AAGAGGGTGTACCAAAGCAG 57.431 50.000 3.11 0.00 43.89 4.24
112 113 2.441750 AGAGGGTGTACCAAAGCAGAAA 59.558 45.455 3.11 0.00 43.89 2.52
243 250 8.903820 ACCATATTTATGTAGAAAGGCTGAAAC 58.096 33.333 0.00 0.00 31.82 2.78
260 272 7.449704 AGGCTGAAACTAAAGAATCATTGACTT 59.550 33.333 0.00 0.00 0.00 3.01
280 295 9.959749 TTGACTTAAACCTGTTTGAATAATCAC 57.040 29.630 5.55 0.00 34.61 3.06
309 325 1.265635 TCTCCCGCAATCAAACAAACG 59.734 47.619 0.00 0.00 0.00 3.60
321 337 7.630924 CAATCAAACAAACGTTCTTAGAGACT 58.369 34.615 0.00 0.00 0.00 3.24
326 342 5.855045 ACAAACGTTCTTAGAGACTTCCAT 58.145 37.500 0.00 0.00 0.00 3.41
374 391 6.515272 AAATGATCTCAACAACCATACACC 57.485 37.500 0.00 0.00 0.00 4.16
482 508 3.758554 CCACCTGGTACCAAAAGATGAAG 59.241 47.826 17.11 0.23 0.00 3.02
520 548 8.483218 GCAATACAAAAGAAAAAGAAAGAGAGC 58.517 33.333 0.00 0.00 0.00 4.09
545 573 5.069648 TCATCGCTTCATCTTGAGAATAGGT 59.930 40.000 0.00 0.00 0.00 3.08
580 608 0.745128 AGGCTCAGTACGACTCGGAG 60.745 60.000 2.83 2.83 0.00 4.63
581 609 1.025647 GGCTCAGTACGACTCGGAGT 61.026 60.000 11.09 11.09 31.68 3.85
608 636 3.243002 GCTTAGCATGAAGTGAAGGCATC 60.243 47.826 0.00 0.00 0.00 3.91
625 653 2.298158 ATCGTGTCGAGCCCCATGAC 62.298 60.000 0.00 0.00 39.91 3.06
630 658 0.460987 GTCGAGCCCCATGACTTCTG 60.461 60.000 0.00 0.00 0.00 3.02
643 672 2.224597 TGACTTCTGGACACACATGCAT 60.225 45.455 0.00 0.00 0.00 3.96
650 679 0.454957 GACACACATGCATTGTCCGC 60.455 55.000 16.06 4.88 36.00 5.54
654 683 2.398554 ACATGCATTGTCCGCGGTC 61.399 57.895 27.15 21.30 30.89 4.79
655 684 2.046411 ATGCATTGTCCGCGGTCA 60.046 55.556 27.15 24.07 0.00 4.02
666 695 1.754803 TCCGCGGTCACATATTCTCTT 59.245 47.619 27.15 0.00 0.00 2.85
677 706 7.271511 GTCACATATTCTCTTCATGTCTTCCT 58.728 38.462 0.00 0.00 30.59 3.36
679 708 8.324306 TCACATATTCTCTTCATGTCTTCCTTT 58.676 33.333 0.00 0.00 30.59 3.11
680 709 8.954350 CACATATTCTCTTCATGTCTTCCTTTT 58.046 33.333 0.00 0.00 30.59 2.27
717 746 6.233434 TGTGTTTTCTCTACATGCTTCTCAT 58.767 36.000 0.00 0.00 35.31 2.90
721 750 8.939929 TGTTTTCTCTACATGCTTCTCATAAAG 58.060 33.333 0.00 0.00 33.19 1.85
798 991 4.597075 AGCCCAATATGTTTTCCTTTTGGT 59.403 37.500 0.00 0.00 41.38 3.67
799 992 5.073008 AGCCCAATATGTTTTCCTTTTGGTT 59.927 36.000 0.00 0.00 41.38 3.67
802 995 7.201866 GCCCAATATGTTTTCCTTTTGGTTTTT 60.202 33.333 0.00 0.00 41.38 1.94
803 996 8.134261 CCCAATATGTTTTCCTTTTGGTTTTTG 58.866 33.333 0.00 0.00 41.38 2.44
805 998 8.897752 CAATATGTTTTCCTTTTGGTTTTTGGA 58.102 29.630 0.00 0.00 41.38 3.53
806 999 8.675705 ATATGTTTTCCTTTTGGTTTTTGGAG 57.324 30.769 0.00 0.00 41.38 3.86
808 1001 5.221945 TGTTTTCCTTTTGGTTTTTGGAGGT 60.222 36.000 0.00 0.00 41.38 3.85
809 1002 4.479786 TTCCTTTTGGTTTTTGGAGGTG 57.520 40.909 0.00 0.00 41.38 4.00
857 1052 1.833787 TAACTCCCAAGTCGCCCACC 61.834 60.000 0.00 0.00 33.48 4.61
916 1114 2.059190 GTCGTCTTCCTCCCTCCCC 61.059 68.421 0.00 0.00 0.00 4.81
940 1152 2.549754 CACGCTAATCCAATCCATCCAC 59.450 50.000 0.00 0.00 0.00 4.02
953 1165 0.478507 CATCCACCCCCTAATCACCC 59.521 60.000 0.00 0.00 0.00 4.61
1216 1449 0.729140 GTTTGGCGAATCCGTGCTTG 60.729 55.000 0.00 0.00 37.80 4.01
1220 1453 1.702491 GGCGAATCCGTGCTTGGTAC 61.702 60.000 0.00 0.00 38.24 3.34
1239 1472 2.637383 GGTCGTCGGAGCTGGAAGT 61.637 63.158 0.00 0.00 37.68 3.01
1383 1617 6.958255 TGTTTGATGTCTGTGATTTGTAGTG 58.042 36.000 0.00 0.00 0.00 2.74
1386 1620 4.692155 TGATGTCTGTGATTTGTAGTGCTG 59.308 41.667 0.00 0.00 0.00 4.41
1409 1643 0.737219 GATTAGCTGGGCTTGTGCTG 59.263 55.000 0.00 0.00 40.44 4.41
1463 1697 1.896220 TGTGATGACAAACTCTGGGC 58.104 50.000 0.00 0.00 0.00 5.36
1479 1713 1.228657 GGGCTATCGATTCGGGTTGC 61.229 60.000 1.71 7.99 0.00 4.17
1486 1720 2.436646 ATTCGGGTTGCAGCTCGG 60.437 61.111 23.11 4.46 0.00 4.63
1499 1733 1.958205 GCTCGGGATCGATTGCAGG 60.958 63.158 0.00 0.00 45.04 4.85
1502 1736 3.654020 GGGATCGATTGCAGGCGC 61.654 66.667 0.00 0.00 39.24 6.53
1530 1764 1.411246 AGTTAGTATGCGCCGATTCCA 59.589 47.619 4.18 0.00 0.00 3.53
1536 1770 2.513666 GCGCCGATTCCATGGACA 60.514 61.111 15.91 6.51 0.00 4.02
1537 1771 1.893808 GCGCCGATTCCATGGACAT 60.894 57.895 15.91 11.40 0.00 3.06
1576 1810 3.130340 CGAAACATGGGGAAACTTATGGG 59.870 47.826 0.00 0.00 0.00 4.00
1594 1828 2.698797 TGGGCCTGTACTAGCTGATTAC 59.301 50.000 4.53 0.00 0.00 1.89
1606 1840 2.571653 AGCTGATTACCTGTGGCTTGTA 59.428 45.455 0.00 0.00 0.00 2.41
1609 1843 3.935203 CTGATTACCTGTGGCTTGTACTG 59.065 47.826 0.00 0.00 0.00 2.74
1633 1867 3.538591 TGATTATCTCTGGCTTGTGCTG 58.461 45.455 0.00 0.00 39.59 4.41
1653 1911 4.511527 CTGGCTGATTATCTGTGACTTGT 58.488 43.478 1.32 0.00 0.00 3.16
1696 1954 4.063998 TGTGCTAGCTGATTATCTGTGG 57.936 45.455 17.23 0.00 0.00 4.17
1703 1961 3.199508 AGCTGATTATCTGTGGCTTCTGT 59.800 43.478 0.00 0.00 0.00 3.41
1735 2017 2.434884 TGGCTTGCGCTAGCTGAC 60.435 61.111 35.77 23.24 45.42 3.51
1752 2034 3.257393 CTGACTATCTGTGACTTGTGCC 58.743 50.000 0.00 0.00 0.00 5.01
1818 2100 4.407296 ACTCTGGGATATCAAGTTCAGTCC 59.593 45.833 4.83 0.00 0.00 3.85
1850 2141 1.537202 AGAACCTTGCTTGCGTGATTC 59.463 47.619 0.00 0.00 0.00 2.52
1870 2161 1.806542 CAAGGCTGCTTACGTGTGATT 59.193 47.619 0.00 0.00 0.00 2.57
1876 2167 3.810373 CTGCTTACGTGTGATTTCCAAC 58.190 45.455 0.00 0.00 0.00 3.77
1882 2173 3.541632 ACGTGTGATTTCCAACTTGAGT 58.458 40.909 0.00 0.00 0.00 3.41
1888 2179 6.980397 GTGTGATTTCCAACTTGAGTGAAATT 59.020 34.615 9.46 0.00 37.51 1.82
1932 2223 5.239306 CAGAACACCTTTTGCTTATCTCACA 59.761 40.000 0.00 0.00 0.00 3.58
1963 2254 5.853936 TCTTTGGGTTATATGAGATGACCG 58.146 41.667 0.00 0.00 0.00 4.79
1980 2271 2.073816 ACCGGCAAGTCGATTAACAAG 58.926 47.619 0.00 0.00 0.00 3.16
2065 2356 7.937394 ACCATTTGTAAAGTTCTTAGTGTAGCT 59.063 33.333 0.00 0.00 0.00 3.32
2090 2381 5.047802 AGCATATGTGAGTTGGGAAAAACAG 60.048 40.000 4.29 0.00 32.21 3.16
2098 2389 0.897863 TGGGAAAAACAGCCGGATGG 60.898 55.000 25.79 6.10 38.77 3.51
2107 2398 0.888736 CAGCCGGATGGTTGTTGTCA 60.889 55.000 13.14 0.00 41.25 3.58
2118 2409 4.310769 TGGTTGTTGTCAAGTTTGGTTTG 58.689 39.130 0.00 0.00 33.97 2.93
2132 2423 1.888512 TGGTTTGGAAGATCAAGCTGC 59.111 47.619 0.00 0.00 0.00 5.25
2151 2442 1.227943 TTGAGGTGGCTCACTGTGC 60.228 57.895 2.12 0.00 34.40 4.57
2161 2452 3.408634 GGCTCACTGTGCCTTTTAAGTA 58.591 45.455 13.86 0.00 46.38 2.24
2237 2528 7.891183 TGAGCTTAAGTAGTTTGATTCAGTC 57.109 36.000 4.02 0.00 0.00 3.51
2256 2547 1.005450 TCCATCAACTAAAGCCCCACC 59.995 52.381 0.00 0.00 0.00 4.61
2265 2556 0.252375 AAAGCCCCACCTGCATGATT 60.252 50.000 0.00 0.00 0.00 2.57
2504 2795 5.723295 ACATGTGGATATGAAAAGGTTTGC 58.277 37.500 0.00 0.00 0.00 3.68
2514 2805 9.423061 GATATGAAAAGGTTTGCAAGTTTGTAT 57.577 29.630 0.00 3.26 0.00 2.29
2521 2812 8.956533 AAGGTTTGCAAGTTTGTATTATTTGT 57.043 26.923 0.00 0.00 0.00 2.83
2627 2920 1.116308 TGGTGACGAGTGGTCTCAAA 58.884 50.000 6.84 0.00 46.24 2.69
2712 3005 6.154534 GGTAATTGAAGGCCTTTGTAGGATTT 59.845 38.462 21.54 7.82 45.05 2.17
2713 3006 6.686484 AATTGAAGGCCTTTGTAGGATTTT 57.314 33.333 21.54 0.00 45.05 1.82
2738 3031 4.022603 TCAGCTGCTACAATCTTCTCTCT 58.977 43.478 9.47 0.00 0.00 3.10
2835 3131 5.316167 TGTTTATGCCAGATGTTTCAGACT 58.684 37.500 0.00 0.00 0.00 3.24
3035 3331 7.539034 TTCATAGGATCGACATCTATGGAAA 57.461 36.000 21.24 12.48 0.00 3.13
3036 3332 7.724490 TCATAGGATCGACATCTATGGAAAT 57.276 36.000 21.24 0.00 0.00 2.17
3037 3333 8.823220 TCATAGGATCGACATCTATGGAAATA 57.177 34.615 21.24 7.91 0.00 1.40
3039 3335 9.689976 CATAGGATCGACATCTATGGAAATATC 57.310 37.037 17.10 0.00 0.00 1.63
3040 3336 6.800543 AGGATCGACATCTATGGAAATATCG 58.199 40.000 0.00 0.00 0.00 2.92
3041 3337 6.378564 AGGATCGACATCTATGGAAATATCGT 59.621 38.462 0.00 0.00 0.00 3.73
3042 3338 6.693545 GGATCGACATCTATGGAAATATCGTC 59.306 42.308 0.00 0.00 0.00 4.20
3044 3340 7.215719 TCGACATCTATGGAAATATCGTCTT 57.784 36.000 0.00 0.00 0.00 3.01
3045 3341 7.084486 TCGACATCTATGGAAATATCGTCTTG 58.916 38.462 0.00 0.00 0.00 3.02
3046 3342 6.863645 CGACATCTATGGAAATATCGTCTTGT 59.136 38.462 0.00 0.00 0.00 3.16
3047 3343 7.382488 CGACATCTATGGAAATATCGTCTTGTT 59.618 37.037 0.00 0.00 0.00 2.83
3048 3344 8.594881 ACATCTATGGAAATATCGTCTTGTTC 57.405 34.615 0.00 0.00 0.00 3.18
3052 3348 8.696374 TCTATGGAAATATCGTCTTGTTCTCTT 58.304 33.333 0.00 0.00 0.00 2.85
3078 3376 8.749026 ATGAAAAATATCTCTGAGCAGACATT 57.251 30.769 0.00 0.00 33.22 2.71
3099 3397 8.650143 ACATTTTTATCTCATTGTAACAGGGT 57.350 30.769 0.00 0.00 0.00 4.34
3224 3523 5.596845 TGTTGGCCTGTTTAATTCTTTGTC 58.403 37.500 3.32 0.00 0.00 3.18
3229 3528 6.547880 TGGCCTGTTTAATTCTTTGTCTGTTA 59.452 34.615 3.32 0.00 0.00 2.41
3319 3618 7.972832 AAATTCACTGAAACCGTACTGATTA 57.027 32.000 0.00 0.00 0.00 1.75
3324 3623 6.367695 TCACTGAAACCGTACTGATTATGTTG 59.632 38.462 0.00 0.00 0.00 3.33
3390 3689 6.829229 ATGAGATCAAAGTTGCAATGAAGA 57.171 33.333 0.59 0.00 0.00 2.87
3431 3730 7.823745 AGTTAACAAATGACCATCAGAAACT 57.176 32.000 8.61 0.00 0.00 2.66
3437 3736 3.961480 TGACCATCAGAAACTCGTGAT 57.039 42.857 0.00 0.00 33.52 3.06
3507 3806 1.416772 GGAAGGCATACTCAGTACCCC 59.583 57.143 0.00 0.00 0.00 4.95
3544 3843 7.095017 GCATCCTATTAGTGCTAAACCAGAATC 60.095 40.741 0.00 0.00 36.02 2.52
3546 3845 5.998363 CCTATTAGTGCTAAACCAGAATCCC 59.002 44.000 0.00 0.00 0.00 3.85
3578 3877 5.248477 TCTGGTGTCCTGCTTTTATTAGACT 59.752 40.000 0.00 0.00 0.00 3.24
3579 3878 5.876357 TGGTGTCCTGCTTTTATTAGACTT 58.124 37.500 0.00 0.00 0.00 3.01
3580 3879 7.011499 TGGTGTCCTGCTTTTATTAGACTTA 57.989 36.000 0.00 0.00 0.00 2.24
3581 3880 7.455058 TGGTGTCCTGCTTTTATTAGACTTAA 58.545 34.615 0.00 0.00 0.00 1.85
3582 3881 7.606456 TGGTGTCCTGCTTTTATTAGACTTAAG 59.394 37.037 0.00 0.00 0.00 1.85
3583 3882 7.822822 GGTGTCCTGCTTTTATTAGACTTAAGA 59.177 37.037 10.09 0.00 0.00 2.10
3734 4036 4.980573 TGTTACTGGCAACCTTAGTTCAT 58.019 39.130 0.00 0.00 32.45 2.57
3749 4051 9.227777 ACCTTAGTTCATTAGTAACATGGAAAC 57.772 33.333 0.00 0.00 0.00 2.78
3804 4106 8.408043 AATATTGTCCTGTGTTTTCAGATGAA 57.592 30.769 0.00 0.00 37.61 2.57
3904 4206 3.570212 ACCCTGGGCAAAGACGCT 61.570 61.111 14.08 0.00 0.00 5.07
3910 4212 2.357034 GGCAAAGACGCTGTCGGA 60.357 61.111 3.62 0.00 40.69 4.55
4006 4308 1.267121 TAGGGCTCAGCGAGAAGTTT 58.733 50.000 9.32 0.00 0.00 2.66
4401 4708 2.126882 CACCAGATCACCCCTTCCATA 58.873 52.381 0.00 0.00 0.00 2.74
4402 4709 2.713167 CACCAGATCACCCCTTCCATAT 59.287 50.000 0.00 0.00 0.00 1.78
4403 4710 2.713167 ACCAGATCACCCCTTCCATATG 59.287 50.000 0.00 0.00 0.00 1.78
4404 4711 2.713167 CCAGATCACCCCTTCCATATGT 59.287 50.000 1.24 0.00 0.00 2.29
4405 4712 3.497405 CCAGATCACCCCTTCCATATGTG 60.497 52.174 1.24 0.00 0.00 3.21
4406 4713 3.392285 CAGATCACCCCTTCCATATGTGA 59.608 47.826 1.24 0.00 39.95 3.58
4407 4714 4.047166 AGATCACCCCTTCCATATGTGAA 58.953 43.478 1.24 4.46 39.19 3.18
4408 4715 3.644966 TCACCCCTTCCATATGTGAAC 57.355 47.619 1.24 0.00 33.35 3.18
4409 4716 2.241176 TCACCCCTTCCATATGTGAACC 59.759 50.000 1.24 0.00 33.35 3.62
4410 4717 2.242196 CACCCCTTCCATATGTGAACCT 59.758 50.000 1.24 0.00 0.00 3.50
4411 4718 2.926329 ACCCCTTCCATATGTGAACCTT 59.074 45.455 1.24 0.00 0.00 3.50
4412 4719 3.336694 ACCCCTTCCATATGTGAACCTTT 59.663 43.478 1.24 0.00 0.00 3.11
4413 4720 3.701040 CCCCTTCCATATGTGAACCTTTG 59.299 47.826 1.24 0.00 0.00 2.77
4414 4721 3.131046 CCCTTCCATATGTGAACCTTTGC 59.869 47.826 1.24 0.00 0.00 3.68
4415 4722 3.763360 CCTTCCATATGTGAACCTTTGCA 59.237 43.478 1.24 0.00 0.00 4.08
4416 4723 4.403432 CCTTCCATATGTGAACCTTTGCAT 59.597 41.667 1.24 0.00 0.00 3.96
4440 4747 1.133199 TGAACCTTTGCAACCCAGGAT 60.133 47.619 20.16 10.02 0.00 3.24
4441 4748 1.970640 GAACCTTTGCAACCCAGGATT 59.029 47.619 20.16 11.39 0.00 3.01
4482 4791 5.074746 AGAACAGGAAATTTACCTTGGGT 57.925 39.130 0.00 0.00 40.16 4.51
4492 4802 7.386573 GGAAATTTACCTTGGGTTTTACATGTG 59.613 37.037 9.11 0.00 37.09 3.21
4582 4955 9.716507 GTAATAATATTGCTAGTGTTGTGTTGG 57.283 33.333 0.00 0.00 0.00 3.77
4619 4996 0.845337 TGCCCATGTGCTCCATATGA 59.155 50.000 3.65 0.00 35.47 2.15
4620 4997 1.242076 GCCCATGTGCTCCATATGAC 58.758 55.000 3.65 0.00 35.47 3.06
4650 5027 0.162507 CTCGCACGAAAGCTTCTGTG 59.837 55.000 20.80 20.80 37.30 3.66
4656 5033 3.325870 CACGAAAGCTTCTGTGGTATGA 58.674 45.455 18.51 0.00 33.61 2.15
4668 5051 4.637091 TCTGTGGTATGATTGTTGCATCTG 59.363 41.667 0.00 0.00 0.00 2.90
4738 5123 1.632409 ACTGGATCATGGCTCACAACT 59.368 47.619 0.00 0.00 0.00 3.16
4742 5127 3.519107 TGGATCATGGCTCACAACTAAGA 59.481 43.478 0.00 0.00 0.00 2.10
4750 5197 3.994392 GGCTCACAACTAAGATTTCGTCA 59.006 43.478 0.00 0.00 0.00 4.35
4780 5227 4.051922 GCTCATACTAGCACATACCACAC 58.948 47.826 0.00 0.00 42.30 3.82
4812 5318 2.886862 CAAGGTTTGCAATGGACACA 57.113 45.000 0.00 0.00 0.00 3.72
4819 5325 5.070313 AGGTTTGCAATGGACACAAGTTTAT 59.930 36.000 0.00 0.00 0.00 1.40
4837 5343 9.651718 CAAGTTTATCACTTAGTTGAAACTGAC 57.348 33.333 13.40 0.00 44.60 3.51
4892 5398 1.672881 GACTTGGAAGCATCGGGATTG 59.327 52.381 0.00 0.00 0.00 2.67
4894 5400 0.323269 TTGGAAGCATCGGGATTGCA 60.323 50.000 0.00 0.00 41.66 4.08
4896 5402 0.749454 GGAAGCATCGGGATTGCAGT 60.749 55.000 0.00 0.00 32.98 4.40
4897 5403 0.659957 GAAGCATCGGGATTGCAGTC 59.340 55.000 0.00 0.00 0.00 3.51
4898 5404 0.254178 AAGCATCGGGATTGCAGTCT 59.746 50.000 9.27 0.00 0.00 3.24
4899 5405 0.463295 AGCATCGGGATTGCAGTCTG 60.463 55.000 9.27 0.67 0.00 3.51
4900 5406 2.020131 CATCGGGATTGCAGTCTGC 58.980 57.895 18.32 18.32 45.29 4.26
4913 5419 4.698583 GCAGTCTGCATGATCTTTCTTT 57.301 40.909 20.16 0.00 44.26 2.52
4914 5420 4.660105 GCAGTCTGCATGATCTTTCTTTC 58.340 43.478 20.16 0.00 44.26 2.62
4915 5421 4.438472 GCAGTCTGCATGATCTTTCTTTCC 60.438 45.833 20.16 0.00 44.26 3.13
4916 5422 4.698780 CAGTCTGCATGATCTTTCTTTCCA 59.301 41.667 0.00 0.00 0.00 3.53
4917 5423 5.357314 CAGTCTGCATGATCTTTCTTTCCAT 59.643 40.000 0.00 0.00 0.00 3.41
4918 5424 5.357314 AGTCTGCATGATCTTTCTTTCCATG 59.643 40.000 0.00 0.00 38.04 3.66
4919 5425 5.356190 GTCTGCATGATCTTTCTTTCCATGA 59.644 40.000 0.00 0.00 37.41 3.07
4920 5426 5.947566 TCTGCATGATCTTTCTTTCCATGAA 59.052 36.000 0.00 0.00 37.41 2.57
4921 5427 6.605995 TCTGCATGATCTTTCTTTCCATGAAT 59.394 34.615 0.00 0.00 37.41 2.57
4922 5428 7.123697 TCTGCATGATCTTTCTTTCCATGAATT 59.876 33.333 0.00 0.00 37.41 2.17
4923 5429 7.262772 TGCATGATCTTTCTTTCCATGAATTC 58.737 34.615 0.00 0.00 37.41 2.17
4924 5430 6.700520 GCATGATCTTTCTTTCCATGAATTCC 59.299 38.462 2.27 0.00 37.41 3.01
4925 5431 6.441093 TGATCTTTCTTTCCATGAATTCCG 57.559 37.500 2.27 0.00 0.00 4.30
4926 5432 6.179756 TGATCTTTCTTTCCATGAATTCCGA 58.820 36.000 2.27 0.00 0.00 4.55
4927 5433 6.830324 TGATCTTTCTTTCCATGAATTCCGAT 59.170 34.615 2.27 0.00 0.00 4.18
4928 5434 7.340232 TGATCTTTCTTTCCATGAATTCCGATT 59.660 33.333 2.27 0.00 0.00 3.34
4929 5435 7.466746 TCTTTCTTTCCATGAATTCCGATTT 57.533 32.000 2.27 0.00 0.00 2.17
4930 5436 7.315142 TCTTTCTTTCCATGAATTCCGATTTG 58.685 34.615 2.27 0.00 0.00 2.32
4931 5437 6.588719 TTCTTTCCATGAATTCCGATTTGT 57.411 33.333 2.27 0.00 0.00 2.83
4932 5438 6.194796 TCTTTCCATGAATTCCGATTTGTC 57.805 37.500 2.27 0.00 0.00 3.18
4933 5439 4.614555 TTCCATGAATTCCGATTTGTCG 57.385 40.909 2.27 0.00 0.00 4.35
4934 5440 3.605634 TCCATGAATTCCGATTTGTCGT 58.394 40.909 2.27 0.00 0.00 4.34
4935 5441 3.373748 TCCATGAATTCCGATTTGTCGTG 59.626 43.478 2.27 0.00 0.00 4.35
4936 5442 3.373748 CCATGAATTCCGATTTGTCGTGA 59.626 43.478 2.27 0.00 0.00 4.35
4937 5443 4.035558 CCATGAATTCCGATTTGTCGTGAT 59.964 41.667 2.27 0.00 0.00 3.06
4938 5444 4.598406 TGAATTCCGATTTGTCGTGATG 57.402 40.909 2.27 0.00 0.00 3.07
4939 5445 3.373748 TGAATTCCGATTTGTCGTGATGG 59.626 43.478 2.27 0.00 0.00 3.51
4940 5446 2.465860 TTCCGATTTGTCGTGATGGT 57.534 45.000 0.00 0.00 0.00 3.55
4941 5447 2.465860 TCCGATTTGTCGTGATGGTT 57.534 45.000 0.00 0.00 0.00 3.67
4942 5448 3.596310 TCCGATTTGTCGTGATGGTTA 57.404 42.857 0.00 0.00 0.00 2.85
4943 5449 3.517602 TCCGATTTGTCGTGATGGTTAG 58.482 45.455 0.00 0.00 0.00 2.34
4944 5450 2.030457 CCGATTTGTCGTGATGGTTAGC 59.970 50.000 0.00 0.00 0.00 3.09
4945 5451 2.930040 CGATTTGTCGTGATGGTTAGCT 59.070 45.455 0.00 0.00 0.00 3.32
4946 5452 3.370978 CGATTTGTCGTGATGGTTAGCTT 59.629 43.478 0.00 0.00 0.00 3.74
4947 5453 4.651994 GATTTGTCGTGATGGTTAGCTTG 58.348 43.478 0.00 0.00 0.00 4.01
4948 5454 3.394674 TTGTCGTGATGGTTAGCTTGA 57.605 42.857 0.00 0.00 0.00 3.02
4949 5455 3.394674 TGTCGTGATGGTTAGCTTGAA 57.605 42.857 0.00 0.00 0.00 2.69
4950 5456 3.064207 TGTCGTGATGGTTAGCTTGAAC 58.936 45.455 0.00 0.00 0.00 3.18
4951 5457 3.244078 TGTCGTGATGGTTAGCTTGAACT 60.244 43.478 0.00 0.00 0.00 3.01
4952 5458 3.746492 GTCGTGATGGTTAGCTTGAACTT 59.254 43.478 0.00 0.00 0.00 2.66
4953 5459 4.213482 GTCGTGATGGTTAGCTTGAACTTT 59.787 41.667 0.00 0.00 0.00 2.66
4954 5460 4.451096 TCGTGATGGTTAGCTTGAACTTTC 59.549 41.667 0.00 0.00 0.00 2.62
4989 5665 5.239359 TGCTTTCCATGAATTCAGATTCG 57.761 39.130 14.54 2.19 43.75 3.34
5014 5690 4.125703 GTGATGGTTAGCTTGAGATCAGG 58.874 47.826 0.00 0.00 0.00 3.86
5033 5709 3.318839 CAGGGAATGACTTTTCTTGTGCA 59.681 43.478 0.00 0.00 0.00 4.57
5037 5713 3.715628 ATGACTTTTCTTGTGCACACC 57.284 42.857 21.56 2.21 0.00 4.16
5039 5715 1.400494 GACTTTTCTTGTGCACACCGT 59.600 47.619 21.56 10.07 0.00 4.83
5041 5717 3.011119 ACTTTTCTTGTGCACACCGTTA 58.989 40.909 21.56 3.05 0.00 3.18
5045 5721 1.070914 TCTTGTGCACACCGTTATGGA 59.929 47.619 21.56 0.00 42.00 3.41
5082 5758 8.343168 TGATTCAAATGGTACCGAGTATTTTT 57.657 30.769 7.57 0.00 0.00 1.94
5116 5792 4.130118 CTCTCCACTCCATTTTATTCCGG 58.870 47.826 0.00 0.00 0.00 5.14
5126 5802 4.578516 CCATTTTATTCCGGCAGACACATA 59.421 41.667 0.00 0.00 0.00 2.29
5131 5807 0.172578 TCCGGCAGACACATAGAACG 59.827 55.000 0.00 0.00 0.00 3.95
5133 5809 1.671850 CCGGCAGACACATAGAACGTT 60.672 52.381 0.00 0.00 0.00 3.99
5134 5810 2.416296 CCGGCAGACACATAGAACGTTA 60.416 50.000 0.00 0.00 0.00 3.18
5135 5811 2.852413 CGGCAGACACATAGAACGTTAG 59.148 50.000 0.00 0.00 0.00 2.34
5136 5812 3.672511 CGGCAGACACATAGAACGTTAGT 60.673 47.826 0.00 0.00 0.00 2.24
5137 5813 4.243270 GGCAGACACATAGAACGTTAGTT 58.757 43.478 0.00 0.00 44.47 2.24
5149 5825 9.577110 CATAGAACGTTAGTTAAGTAATGGTGA 57.423 33.333 21.07 9.48 41.34 4.02
5153 5829 8.667076 AACGTTAGTTAAGTAATGGTGACTTT 57.333 30.769 21.07 7.23 39.11 2.66
5208 5884 6.149129 ACATCTATAAGAACATCGACTGCA 57.851 37.500 0.00 0.00 0.00 4.41
5210 5886 4.611943 TCTATAAGAACATCGACTGCAGC 58.388 43.478 15.27 5.81 0.00 5.25
5215 5891 0.944386 AACATCGACTGCAGCGTTTT 59.056 45.000 23.32 14.81 0.00 2.43
5292 6207 7.422465 ACAATTTTGCCATAACCATCATACT 57.578 32.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 8.676401 ACGACTAAGATTACTCCTTACTTCTTC 58.324 37.037 0.00 0.00 0.00 2.87
58 59 6.344500 TCGACGACTAAGATTACTCCTTACT 58.656 40.000 0.00 0.00 0.00 2.24
62 63 5.007823 CACATCGACGACTAAGATTACTCCT 59.992 44.000 0.00 0.00 0.00 3.69
73 74 4.142534 CCCTCTTAAACACATCGACGACTA 60.143 45.833 0.00 0.00 0.00 2.59
93 94 3.157087 CATTTCTGCTTTGGTACACCCT 58.843 45.455 0.00 0.00 39.29 4.34
112 113 8.562892 CGATCCAAGTAGAAAGAATTAATGCAT 58.437 33.333 0.00 0.00 0.00 3.96
215 217 8.677148 TCAGCCTTTCTACATAAATATGGTTC 57.323 34.615 5.48 0.00 38.00 3.62
248 260 9.696917 ATTCAAACAGGTTTAAGTCAATGATTC 57.303 29.630 0.00 0.00 0.00 2.52
289 305 1.265635 CGTTTGTTTGATTGCGGGAGA 59.734 47.619 0.00 0.00 0.00 3.71
340 356 9.624697 GTTGTTGAGATCATTTATTACAAAGCA 57.375 29.630 0.00 0.00 0.00 3.91
341 357 9.076596 GGTTGTTGAGATCATTTATTACAAAGC 57.923 33.333 0.00 0.00 0.00 3.51
374 391 1.665735 GGCATATAAATTGGGCGTGCG 60.666 52.381 0.00 0.00 32.23 5.34
498 526 8.506168 TGAGCTCTCTTTCTTTTTCTTTTGTA 57.494 30.769 16.19 0.00 0.00 2.41
520 548 5.634439 CCTATTCTCAAGATGAAGCGATGAG 59.366 44.000 0.00 0.00 39.04 2.90
545 573 0.601841 GCCTTTTCTTCCCGACGTCA 60.602 55.000 17.16 0.00 0.00 4.35
580 608 2.012673 CACTTCATGCTAAGCAGGGAC 58.987 52.381 0.00 0.00 43.65 4.46
581 609 1.908619 TCACTTCATGCTAAGCAGGGA 59.091 47.619 0.00 0.00 43.65 4.20
608 636 2.507110 AAGTCATGGGGCTCGACACG 62.507 60.000 0.00 0.00 31.92 4.49
625 653 2.555325 ACAATGCATGTGTGTCCAGAAG 59.445 45.455 0.00 0.00 41.93 2.85
643 672 1.206132 AGAATATGTGACCGCGGACAA 59.794 47.619 35.90 21.70 0.00 3.18
650 679 5.595885 AGACATGAAGAGAATATGTGACCG 58.404 41.667 0.00 0.00 35.35 4.79
654 683 8.503458 AAAGGAAGACATGAAGAGAATATGTG 57.497 34.615 0.00 0.00 35.35 3.21
655 684 9.525826 AAAAAGGAAGACATGAAGAGAATATGT 57.474 29.630 0.00 0.00 37.72 2.29
680 709 9.581099 GTAGAGAAAACACATTCCAAAGAAAAA 57.419 29.630 0.00 0.00 35.09 1.94
688 717 5.316167 AGCATGTAGAGAAAACACATTCCA 58.684 37.500 0.00 0.00 30.59 3.53
695 724 8.846943 TTTATGAGAAGCATGTAGAGAAAACA 57.153 30.769 0.00 0.00 37.87 2.83
857 1052 2.301738 GGACTCTTGGAGGGGTGGG 61.302 68.421 0.00 0.00 33.35 4.61
867 1064 3.094484 AGTAGTGGGAGAGGACTCTTG 57.906 52.381 2.97 0.00 40.61 3.02
916 1114 2.620251 TGGATTGGATTAGCGTGGAG 57.380 50.000 0.00 0.00 0.00 3.86
940 1152 3.886001 GCGGGGGTGATTAGGGGG 61.886 72.222 0.00 0.00 0.00 5.40
1133 1366 2.046700 GAAATCACGGGGGTCGCA 60.047 61.111 0.00 0.00 43.89 5.10
1216 1449 3.130160 AGCTCCGACGACCGTACC 61.130 66.667 0.00 0.00 36.31 3.34
1220 1453 3.685214 CTTCCAGCTCCGACGACCG 62.685 68.421 0.00 0.00 38.18 4.79
1271 1504 4.508128 GCCGGCCACGAATCTCGA 62.508 66.667 18.11 0.00 43.74 4.04
1316 1549 2.262774 AATCCTCTTCGGCAGCCCAG 62.263 60.000 5.63 1.93 0.00 4.45
1317 1550 1.852157 AAATCCTCTTCGGCAGCCCA 61.852 55.000 5.63 0.00 0.00 5.36
1459 1693 0.105964 CAACCCGAATCGATAGCCCA 59.894 55.000 3.36 0.00 0.00 5.36
1463 1697 0.861837 GCTGCAACCCGAATCGATAG 59.138 55.000 3.36 0.00 0.00 2.08
1486 1720 2.182842 AAGCGCCTGCAATCGATCC 61.183 57.895 2.29 0.00 46.23 3.36
1499 1733 3.543460 CGCATACTAACTTAACCAAGCGC 60.543 47.826 0.00 0.00 34.94 5.92
1502 1736 3.000925 CGGCGCATACTAACTTAACCAAG 59.999 47.826 10.83 0.00 37.81 3.61
1536 1770 5.589855 TGTTTCGAGCAATCATGTTATCCAT 59.410 36.000 0.00 0.00 0.00 3.41
1537 1771 4.940654 TGTTTCGAGCAATCATGTTATCCA 59.059 37.500 0.00 0.00 0.00 3.41
1544 1778 2.223641 CCCCATGTTTCGAGCAATCATG 60.224 50.000 0.00 0.00 40.09 3.07
1576 1810 3.385111 ACAGGTAATCAGCTAGTACAGGC 59.615 47.826 0.00 0.00 30.09 4.85
1594 1828 0.957395 CAGCCAGTACAAGCCACAGG 60.957 60.000 0.00 0.00 0.00 4.00
1606 1840 2.406559 AGCCAGAGATAATCAGCCAGT 58.593 47.619 0.00 0.00 31.55 4.00
1609 1843 2.877168 CACAAGCCAGAGATAATCAGCC 59.123 50.000 0.00 0.00 31.55 4.85
1633 1867 3.064545 GCACAAGTCACAGATAATCAGCC 59.935 47.826 0.00 0.00 0.00 4.85
1653 1911 2.702478 AGCCACAGATAATCAGCTAGCA 59.298 45.455 18.83 0.00 0.00 3.49
1696 1954 5.236047 CCACAGATAATCAGCTAACAGAAGC 59.764 44.000 0.00 0.00 43.11 3.86
1703 1961 3.879295 GCAAGCCACAGATAATCAGCTAA 59.121 43.478 0.00 0.00 0.00 3.09
1735 2017 2.005451 GCTGGCACAAGTCACAGATAG 58.995 52.381 0.00 0.00 38.70 2.08
1752 2034 8.644619 CAATTCACAGATTAAAAACATCAGCTG 58.355 33.333 7.63 7.63 0.00 4.24
1850 2141 1.442769 ATCACACGTAAGCAGCCTTG 58.557 50.000 0.00 0.00 45.62 3.61
1870 2161 8.502387 CAAACAAAAATTTCACTCAAGTTGGAA 58.498 29.630 2.34 0.00 0.00 3.53
1876 2167 7.745594 CCAACACAAACAAAAATTTCACTCAAG 59.254 33.333 0.00 0.00 0.00 3.02
1882 2173 6.234177 ACTCCCAACACAAACAAAAATTTCA 58.766 32.000 0.00 0.00 0.00 2.69
1888 2179 4.524714 TCTGAACTCCCAACACAAACAAAA 59.475 37.500 0.00 0.00 0.00 2.44
1932 2223 8.090788 TCTCATATAACCCAAAGAACTAGCTT 57.909 34.615 0.00 0.00 0.00 3.74
1963 2254 2.484264 AGCACTTGTTAATCGACTTGCC 59.516 45.455 0.00 0.00 0.00 4.52
1980 2271 8.292448 CCCTAAATCACATATAAACATCAGCAC 58.708 37.037 0.00 0.00 0.00 4.40
2058 2349 4.747108 CCAACTCACATATGCTAGCTACAC 59.253 45.833 17.23 0.00 0.00 2.90
2065 2356 6.007076 TGTTTTTCCCAACTCACATATGCTA 58.993 36.000 1.58 0.00 0.00 3.49
2090 2381 0.240945 CTTGACAACAACCATCCGGC 59.759 55.000 0.00 0.00 34.57 6.13
2098 2389 4.561105 TCCAAACCAAACTTGACAACAAC 58.439 39.130 0.00 0.00 32.27 3.32
2107 2398 4.651045 AGCTTGATCTTCCAAACCAAACTT 59.349 37.500 0.00 0.00 0.00 2.66
2237 2528 1.005924 AGGTGGGGCTTTAGTTGATGG 59.994 52.381 0.00 0.00 0.00 3.51
2256 2547 5.868043 TCAACAGTTGAGTAATCATGCAG 57.132 39.130 12.24 0.00 34.08 4.41
2265 2556 4.202010 GCAAAGGCTTTCAACAGTTGAGTA 60.202 41.667 15.61 7.83 37.80 2.59
2296 2587 2.099756 GCACACTGCATAAGGAAATCCC 59.900 50.000 0.00 0.00 44.26 3.85
2570 2861 6.436261 AGAGCAATCAAAATCTGATAATGCG 58.564 36.000 6.00 0.00 46.38 4.73
2627 2920 9.533253 GGCATCTTTAAAAGTAACATATGCAAT 57.467 29.630 1.58 0.00 39.08 3.56
2712 3005 4.645535 AGAAGATTGTAGCAGCTGAACAA 58.354 39.130 27.13 27.13 37.51 2.83
2713 3006 4.020751 AGAGAAGATTGTAGCAGCTGAACA 60.021 41.667 20.43 17.70 0.00 3.18
2761 3054 4.563580 GCAGAGTTCTGTTGAGGGACAATA 60.564 45.833 10.57 0.00 45.45 1.90
2820 3116 4.163078 AGGTATGGAGTCTGAAACATCTGG 59.837 45.833 0.00 0.00 0.00 3.86
2853 3149 6.767902 ACTACTTCTGTTGAGATGAAAAGCAA 59.232 34.615 0.00 0.00 0.00 3.91
2984 3280 0.944386 ACTGTGCTTAAACTGCCACG 59.056 50.000 0.00 0.00 0.00 4.94
3047 3343 9.761504 CTGCTCAGAGATATTTTTCATAAGAGA 57.238 33.333 0.00 0.00 0.00 3.10
3048 3344 9.761504 TCTGCTCAGAGATATTTTTCATAAGAG 57.238 33.333 0.00 0.00 32.82 2.85
3052 3348 9.842775 AATGTCTGCTCAGAGATATTTTTCATA 57.157 29.630 9.52 0.00 40.10 2.15
3078 3376 6.007076 TGCACCCTGTTACAATGAGATAAAA 58.993 36.000 0.00 0.00 0.00 1.52
3224 3523 5.122869 CCATGTTCAACTCAGGACATAACAG 59.877 44.000 0.00 0.00 31.92 3.16
3229 3528 2.224843 TGCCATGTTCAACTCAGGACAT 60.225 45.455 0.00 0.00 33.27 3.06
3319 3618 6.602803 TGCATAAAGTGTATGATGTCCAACAT 59.397 34.615 4.36 0.00 42.43 2.71
3324 3623 8.454106 GGAATATGCATAAAGTGTATGATGTCC 58.546 37.037 11.13 0.08 34.75 4.02
3390 3689 8.671384 TTGTTAACTACAACTAAGCATGAACT 57.329 30.769 7.22 0.00 41.73 3.01
3437 3736 5.827797 GGCAGATGGAACCTTGTGAAATATA 59.172 40.000 7.79 0.00 0.00 0.86
3507 3806 7.443575 AGCACTAATAGGATGCAAGACATTAAG 59.556 37.037 5.80 0.00 41.97 1.85
3544 3843 3.302347 GACACCAGAGCTCCACGGG 62.302 68.421 10.93 9.85 0.00 5.28
3546 3845 2.262915 GGACACCAGAGCTCCACG 59.737 66.667 10.93 0.00 0.00 4.94
3581 3880 5.990668 ACCAGGCGTAAAAGATCTTAATCT 58.009 37.500 8.75 0.00 44.37 2.40
3582 3881 7.964604 ATACCAGGCGTAAAAGATCTTAATC 57.035 36.000 8.75 1.35 0.00 1.75
3597 3896 2.545526 CAGTTGAGCATAATACCAGGCG 59.454 50.000 0.00 0.00 0.00 5.52
3788 4090 5.009911 TGGTTCCATTCATCTGAAAACACAG 59.990 40.000 0.00 0.00 37.61 3.66
3804 4106 1.909302 CCACTGGTACTCTGGTTCCAT 59.091 52.381 0.00 0.00 41.04 3.41
3904 4206 2.178912 AAGATTTCGCCTTTCCGACA 57.821 45.000 0.00 0.00 36.90 4.35
3910 4212 5.105997 CCTCTCATCAAAAGATTTCGCCTTT 60.106 40.000 0.00 0.00 35.55 3.11
4006 4308 0.908910 CCACTGTAGTGCCCATGGTA 59.091 55.000 11.73 0.00 44.34 3.25
4099 4401 1.005630 GTTGCTCACCGTCTGCTCT 60.006 57.895 0.00 0.00 0.00 4.09
4308 4612 2.237393 GCAAGAGGCACATAGAGGAG 57.763 55.000 0.00 0.00 43.97 3.69
4383 4690 2.713167 ACATATGGAAGGGGTGATCTGG 59.287 50.000 7.80 0.00 0.00 3.86
4401 4708 5.336690 GGTTCACATATGCAAAGGTTCACAT 60.337 40.000 1.58 0.00 0.00 3.21
4402 4709 4.022416 GGTTCACATATGCAAAGGTTCACA 60.022 41.667 1.58 0.00 0.00 3.58
4403 4710 4.218417 AGGTTCACATATGCAAAGGTTCAC 59.782 41.667 1.58 0.00 0.00 3.18
4404 4711 4.406456 AGGTTCACATATGCAAAGGTTCA 58.594 39.130 1.58 0.00 0.00 3.18
4405 4712 5.391312 AAGGTTCACATATGCAAAGGTTC 57.609 39.130 1.58 0.00 0.00 3.62
4406 4713 5.540911 CAAAGGTTCACATATGCAAAGGTT 58.459 37.500 1.58 0.00 0.00 3.50
4407 4714 4.561326 GCAAAGGTTCACATATGCAAAGGT 60.561 41.667 1.58 0.00 34.10 3.50
4408 4715 3.928375 GCAAAGGTTCACATATGCAAAGG 59.072 43.478 1.58 0.00 34.10 3.11
4409 4716 4.558178 TGCAAAGGTTCACATATGCAAAG 58.442 39.130 1.58 0.00 40.47 2.77
4410 4717 4.597404 TGCAAAGGTTCACATATGCAAA 57.403 36.364 1.58 0.00 40.47 3.68
4412 4719 3.305950 GGTTGCAAAGGTTCACATATGCA 60.306 43.478 0.00 0.00 41.57 3.96
4413 4720 3.253230 GGTTGCAAAGGTTCACATATGC 58.747 45.455 0.00 0.00 0.00 3.14
4414 4721 3.257873 TGGGTTGCAAAGGTTCACATATG 59.742 43.478 0.00 0.00 0.00 1.78
4415 4722 3.505386 TGGGTTGCAAAGGTTCACATAT 58.495 40.909 0.00 0.00 0.00 1.78
4416 4723 2.890311 CTGGGTTGCAAAGGTTCACATA 59.110 45.455 0.00 0.00 0.00 2.29
4482 4791 6.993786 TGAACAGTTCTGTCACATGTAAAA 57.006 33.333 14.51 0.00 0.00 1.52
4492 4802 6.073003 CCAATTCTACCTTGAACAGTTCTGTC 60.073 42.308 14.51 1.66 0.00 3.51
4582 4955 3.561725 GGGCATTTCTGTACTGCTATGAC 59.438 47.826 13.97 11.89 36.18 3.06
4619 4996 2.616960 TCGTGCGAGCAATTCAATAGT 58.383 42.857 0.00 0.00 0.00 2.12
4620 4997 3.656651 TTCGTGCGAGCAATTCAATAG 57.343 42.857 0.00 0.00 0.00 1.73
4650 5027 5.124457 ACTTGACAGATGCAACAATCATACC 59.876 40.000 0.00 0.00 0.00 2.73
4656 5033 3.005050 CACCACTTGACAGATGCAACAAT 59.995 43.478 0.00 0.00 0.00 2.71
4668 5051 3.435671 GCACTATTACACCACCACTTGAC 59.564 47.826 0.00 0.00 0.00 3.18
4759 5206 5.262588 TGTGTGGTATGTGCTAGTATGAG 57.737 43.478 0.00 0.00 0.00 2.90
4771 5218 2.159667 CGTGCATCACTTGTGTGGTATG 60.160 50.000 0.00 0.00 43.94 2.39
4780 5227 0.311790 AACCTTGCGTGCATCACTTG 59.688 50.000 0.00 0.00 31.34 3.16
4819 5325 8.780846 TTACAAAGTCAGTTTCAACTAAGTGA 57.219 30.769 0.00 0.00 37.08 3.41
4837 5343 4.973663 GTGGGTTTCGACAACATTACAAAG 59.026 41.667 10.99 0.00 0.00 2.77
4892 5398 4.438472 GGAAAGAAAGATCATGCAGACTGC 60.438 45.833 20.86 20.86 45.29 4.40
4894 5400 4.914983 TGGAAAGAAAGATCATGCAGACT 58.085 39.130 0.00 0.00 0.00 3.24
4896 5402 5.503002 TCATGGAAAGAAAGATCATGCAGA 58.497 37.500 0.00 0.00 36.22 4.26
4897 5403 5.830000 TCATGGAAAGAAAGATCATGCAG 57.170 39.130 0.00 0.00 36.22 4.41
4898 5404 6.785337 ATTCATGGAAAGAAAGATCATGCA 57.215 33.333 0.00 0.00 36.22 3.96
4899 5405 6.700520 GGAATTCATGGAAAGAAAGATCATGC 59.299 38.462 7.93 0.00 36.22 4.06
4900 5406 6.916387 CGGAATTCATGGAAAGAAAGATCATG 59.084 38.462 7.93 0.00 37.23 3.07
4901 5407 6.830324 TCGGAATTCATGGAAAGAAAGATCAT 59.170 34.615 7.93 0.00 0.00 2.45
4902 5408 6.179756 TCGGAATTCATGGAAAGAAAGATCA 58.820 36.000 7.93 0.00 0.00 2.92
4903 5409 6.683974 TCGGAATTCATGGAAAGAAAGATC 57.316 37.500 7.93 0.00 0.00 2.75
4904 5410 7.651027 AATCGGAATTCATGGAAAGAAAGAT 57.349 32.000 7.93 0.00 0.00 2.40
4905 5411 7.039784 ACAAATCGGAATTCATGGAAAGAAAGA 60.040 33.333 7.93 0.00 0.00 2.52
4906 5412 7.092716 ACAAATCGGAATTCATGGAAAGAAAG 58.907 34.615 7.93 0.00 0.00 2.62
4907 5413 6.991938 ACAAATCGGAATTCATGGAAAGAAA 58.008 32.000 7.93 0.00 0.00 2.52
4908 5414 6.588719 ACAAATCGGAATTCATGGAAAGAA 57.411 33.333 7.93 0.00 0.00 2.52
4909 5415 5.163764 CGACAAATCGGAATTCATGGAAAGA 60.164 40.000 7.93 0.00 44.99 2.52
4910 5416 5.030295 CGACAAATCGGAATTCATGGAAAG 58.970 41.667 7.93 0.00 44.99 2.62
4911 5417 4.980590 CGACAAATCGGAATTCATGGAAA 58.019 39.130 7.93 0.00 44.99 3.13
4912 5418 4.614555 CGACAAATCGGAATTCATGGAA 57.385 40.909 7.93 0.00 44.99 3.53
4925 5431 4.391830 TCAAGCTAACCATCACGACAAATC 59.608 41.667 0.00 0.00 0.00 2.17
4926 5432 4.323417 TCAAGCTAACCATCACGACAAAT 58.677 39.130 0.00 0.00 0.00 2.32
4927 5433 3.734463 TCAAGCTAACCATCACGACAAA 58.266 40.909 0.00 0.00 0.00 2.83
4928 5434 3.394674 TCAAGCTAACCATCACGACAA 57.605 42.857 0.00 0.00 0.00 3.18
4929 5435 3.064207 GTTCAAGCTAACCATCACGACA 58.936 45.455 0.00 0.00 0.00 4.35
4930 5436 3.326747 AGTTCAAGCTAACCATCACGAC 58.673 45.455 0.00 0.00 0.00 4.34
4931 5437 3.678056 AGTTCAAGCTAACCATCACGA 57.322 42.857 0.00 0.00 0.00 4.35
4932 5438 4.452455 AGAAAGTTCAAGCTAACCATCACG 59.548 41.667 0.00 0.00 0.00 4.35
4933 5439 5.703130 AGAGAAAGTTCAAGCTAACCATCAC 59.297 40.000 0.00 0.00 0.00 3.06
4934 5440 5.702670 CAGAGAAAGTTCAAGCTAACCATCA 59.297 40.000 0.00 0.00 0.00 3.07
4935 5441 5.391416 GCAGAGAAAGTTCAAGCTAACCATC 60.391 44.000 0.00 0.00 0.00 3.51
4936 5442 4.457257 GCAGAGAAAGTTCAAGCTAACCAT 59.543 41.667 0.00 0.00 0.00 3.55
4937 5443 3.815401 GCAGAGAAAGTTCAAGCTAACCA 59.185 43.478 0.00 0.00 0.00 3.67
4938 5444 3.815401 TGCAGAGAAAGTTCAAGCTAACC 59.185 43.478 0.00 0.00 0.00 2.85
4939 5445 4.609336 CGTGCAGAGAAAGTTCAAGCTAAC 60.609 45.833 0.00 0.00 0.00 2.34
4940 5446 3.494626 CGTGCAGAGAAAGTTCAAGCTAA 59.505 43.478 0.00 0.00 0.00 3.09
4941 5447 3.059884 CGTGCAGAGAAAGTTCAAGCTA 58.940 45.455 0.00 0.00 0.00 3.32
4942 5448 1.869767 CGTGCAGAGAAAGTTCAAGCT 59.130 47.619 0.00 0.00 0.00 3.74
4943 5449 1.867233 TCGTGCAGAGAAAGTTCAAGC 59.133 47.619 0.00 0.00 0.00 4.01
4944 5450 3.993081 AGATCGTGCAGAGAAAGTTCAAG 59.007 43.478 0.00 0.00 0.00 3.02
4945 5451 3.995199 AGATCGTGCAGAGAAAGTTCAA 58.005 40.909 0.00 0.00 0.00 2.69
4946 5452 3.667497 AGATCGTGCAGAGAAAGTTCA 57.333 42.857 0.00 0.00 0.00 3.18
4947 5453 3.424170 GCAAGATCGTGCAGAGAAAGTTC 60.424 47.826 25.91 0.00 44.29 3.01
4948 5454 2.481952 GCAAGATCGTGCAGAGAAAGTT 59.518 45.455 25.91 0.00 44.29 2.66
4949 5455 2.072298 GCAAGATCGTGCAGAGAAAGT 58.928 47.619 25.91 0.00 44.29 2.66
4950 5456 2.802556 GCAAGATCGTGCAGAGAAAG 57.197 50.000 25.91 0.00 44.29 2.62
4989 5665 3.232213 TCTCAAGCTAACCATCACGAC 57.768 47.619 0.00 0.00 0.00 4.34
5014 5690 4.044426 GTGTGCACAAGAAAAGTCATTCC 58.956 43.478 23.59 0.00 0.00 3.01
5033 5709 2.300723 TGTGCTAGTTCCATAACGGTGT 59.699 45.455 0.00 0.00 40.73 4.16
5037 5713 5.794687 TCAAATGTGCTAGTTCCATAACG 57.205 39.130 0.00 0.00 40.73 3.18
5039 5715 7.936496 TGAATCAAATGTGCTAGTTCCATAA 57.064 32.000 0.00 0.00 0.00 1.90
5041 5717 6.839124 TTGAATCAAATGTGCTAGTTCCAT 57.161 33.333 0.00 0.00 0.00 3.41
5104 5780 4.637483 ATGTGTCTGCCGGAATAAAATG 57.363 40.909 5.05 0.00 0.00 2.32
5116 5792 6.585322 ACTTAACTAACGTTCTATGTGTCTGC 59.415 38.462 2.82 0.00 34.59 4.26
5126 5802 7.664758 AGTCACCATTACTTAACTAACGTTCT 58.335 34.615 2.82 0.00 34.59 3.01
5133 5809 9.787435 AACATCAAAGTCACCATTACTTAACTA 57.213 29.630 0.00 0.00 36.17 2.24
5134 5810 8.691661 AACATCAAAGTCACCATTACTTAACT 57.308 30.769 0.00 0.00 36.17 2.24
5135 5811 9.744468 AAAACATCAAAGTCACCATTACTTAAC 57.256 29.630 0.00 0.00 36.17 2.01
5162 5838 3.199727 TGACACCATGCTAGCCAAGATAA 59.800 43.478 13.29 0.00 0.00 1.75
5163 5839 2.771372 TGACACCATGCTAGCCAAGATA 59.229 45.455 13.29 0.00 0.00 1.98
5177 5853 6.756542 CGATGTTCTTATAGATGTTGACACCA 59.243 38.462 0.00 0.00 0.00 4.17
5258 5934 9.516314 GGTTATGGCAAAATTGTAATTCTCTAC 57.484 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.