Multiple sequence alignment - TraesCS3B01G123300

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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 TraesCS3B01G123300 chr3B 100.000 8626 0 0 1 8626 95143960 95152585 0.000000e+00 15930.0
1 TraesCS3B01G123300 chr3B 91.549 142 12 0 2538 2679 95146353 95146494 6.830000e-46 196.0
2 TraesCS3B01G123300 chr3B 93.846 65 4 0 2609 2673 95146352 95146416 1.980000e-16 99.0
3 TraesCS3B01G123300 chr3A 93.813 4655 203 41 3757 8364 68277977 68282593 0.000000e+00 6922.0
4 TraesCS3B01G123300 chr3A 94.042 1393 77 6 2384 3774 68276579 68277967 0.000000e+00 2108.0
5 TraesCS3B01G123300 chr3A 87.259 1554 125 33 748 2280 68274839 68276340 0.000000e+00 1705.0
6 TraesCS3B01G123300 chr3A 94.779 498 26 0 2182 2679 68276305 68276802 0.000000e+00 776.0
7 TraesCS3B01G123300 chr3A 86.667 570 28 21 14 558 68274077 68274623 9.650000e-164 588.0
8 TraesCS3B01G123300 chr3A 89.362 329 28 7 8300 8621 68282619 68282947 2.900000e-109 407.0
9 TraesCS3B01G123300 chr3A 93.023 215 15 0 2393 2607 68276660 68276874 1.810000e-81 315.0
10 TraesCS3B01G123300 chr3A 89.908 218 22 0 2456 2673 68276507 68276724 1.830000e-71 281.0
11 TraesCS3B01G123300 chr3A 90.132 152 15 0 2384 2535 68276723 68276874 1.900000e-46 198.0
12 TraesCS3B01G123300 chr3A 89.437 142 15 0 2538 2679 68276517 68276658 6.880000e-41 180.0
13 TraesCS3B01G123300 chr3A 95.312 64 2 1 5405 5467 34532512 34532449 5.510000e-17 100.0
14 TraesCS3B01G123300 chr3D 91.180 3798 187 75 14 3774 59282100 59285786 0.000000e+00 5022.0
15 TraesCS3B01G123300 chr3D 94.047 2990 129 27 5672 8626 59287547 59290522 0.000000e+00 4490.0
16 TraesCS3B01G123300 chr3D 96.193 1760 64 2 3757 5516 59285797 59287553 0.000000e+00 2876.0
17 TraesCS3B01G123300 chr3D 91.964 224 18 0 2384 2607 59284478 59284701 1.810000e-81 315.0
18 TraesCS3B01G123300 chr3D 89.732 224 23 0 2456 2679 59284406 59284629 3.940000e-73 287.0
19 TraesCS3B01G123300 chr3D 91.549 142 12 0 2394 2535 59284560 59284701 6.830000e-46 196.0
20 TraesCS3B01G123300 chr3D 90.845 142 13 0 2538 2679 59284416 59284557 3.180000e-44 191.0
21 TraesCS3B01G123300 chr3D 95.312 64 3 0 5405 5468 71517741 71517678 1.530000e-17 102.0
22 TraesCS3B01G123300 chr3D 95.312 64 2 1 5405 5467 426451922 426451859 5.510000e-17 100.0
23 TraesCS3B01G123300 chr5D 95.588 68 2 1 5405 5471 241947543 241947610 3.290000e-19 108.0
24 TraesCS3B01G123300 chr5D 95.522 67 2 1 5405 5470 294634425 294634491 1.180000e-18 106.0
25 TraesCS3B01G123300 chr5D 94.000 50 1 1 5965 6012 370554403 370554354 3.340000e-09 75.0
26 TraesCS3B01G123300 chr5A 94.118 68 3 1 5405 5471 311937074 311937141 1.530000e-17 102.0
27 TraesCS3B01G123300 chr5A 91.837 49 3 1 5965 6012 473042755 473042707 5.590000e-07 67.6
28 TraesCS3B01G123300 chr7B 88.462 78 7 2 5405 5481 568676553 568676629 9.220000e-15 93.5
29 TraesCS3B01G123300 chr2A 94.872 39 1 1 5967 6005 678426824 678426861 9.350000e-05 60.2
30 TraesCS3B01G123300 chr2D 94.595 37 1 1 5975 6010 175594172 175594136 1.000000e-03 56.5
31 TraesCS3B01G123300 chr4A 96.875 32 1 0 5980 6011 19952426 19952395 4.000000e-03 54.7
32 TraesCS3B01G123300 chr4A 96.875 32 1 0 5980 6011 20001246 20001215 4.000000e-03 54.7


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 TraesCS3B01G123300 chr3B 95143960 95152585 8625 False 15930 15930 100.000000 1 8626 1 chr3B.!!$F1 8625
1 TraesCS3B01G123300 chr3A 68274077 68282947 8870 False 1348 6922 90.842200 14 8621 10 chr3A.!!$F1 8607
2 TraesCS3B01G123300 chr3D 59282100 59290522 8422 False 1911 5022 92.215714 14 8626 7 chr3D.!!$F1 8612

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
548 586 0.249741 CCGTCTGTCGTTGGTTCCTT 60.250 55.000 0.00 0.0 37.94 3.36 F
771 873 0.341609 CCTTCCCCTCTTCCTCCTCT 59.658 60.000 0.00 0.0 0.00 3.69 F
1606 1741 0.599466 CGTCGGATGATGCAGATGCT 60.599 55.000 6.35 0.0 42.66 3.79 F
3047 3326 0.311790 ATGCACCTCAACAACAAGCG 59.688 50.000 0.00 0.0 0.00 4.68 F
3575 3854 1.002134 ACCCCATGCTCAAGGTTCG 60.002 57.895 0.00 0.0 0.00 3.95 F
4349 4656 0.464452 CGAAGTGGGATCTGGGGTAC 59.536 60.000 0.00 0.0 0.00 3.34 F
5284 5595 1.002868 GGCCTCCGATGCAGCATAT 60.003 57.895 8.22 0.0 0.00 1.78 F
5497 5808 0.535102 AAGCTTCATTATCCCCGGCG 60.535 55.000 0.00 0.0 0.00 6.46 F
5500 5811 0.602905 CTTCATTATCCCCGGCGTCC 60.603 60.000 6.01 0.0 0.00 4.79 F
7335 7655 0.036010 CAGCGAGGGTGATGAAGGTT 60.036 55.000 0.00 0.0 32.22 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2151 1.004745 GGGAGGGTTTGCTGATGAAGA 59.995 52.381 0.00 0.0 0.00 2.87 R
2614 2893 1.203187 TGGAGTAGGAGCCTGAACTGT 60.203 52.381 0.00 0.0 0.00 3.55 R
3229 3508 0.178992 TTCCTTTGGTGGAGGTGCAG 60.179 55.000 0.00 0.0 37.43 4.41 R
4327 4634 1.141881 CCCAGATCCCACTTCGTCG 59.858 63.158 0.00 0.0 0.00 5.12 R
5251 5562 0.543749 AGGCCAAGGCTGTATCTCAC 59.456 55.000 5.01 0.0 41.60 3.51 R
5497 5808 0.625849 ACATGAAGGATGGTGGGGAC 59.374 55.000 0.00 0.0 36.23 4.46 R
6357 6674 1.841277 AGTGTCCCTTGGTACACACAA 59.159 47.619 15.98 0.0 46.71 3.33 R
7335 7655 1.679153 GCTGAAACTTCCCGAACCAAA 59.321 47.619 0.00 0.0 0.00 3.28 R
7495 7815 1.758514 GTCATCAGAGGGCCGGAGA 60.759 63.158 5.05 0.0 0.00 3.71 R
8433 8901 0.583438 CAGTTTCACACCACGCAGAG 59.417 55.000 0.00 0.0 0.00 3.35 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
59 60 3.127533 GATCCACCGGCACAGTGC 61.128 66.667 17.97 17.97 44.08 4.40
111 121 2.032681 GCACGGGCAAGAGAACCT 59.967 61.111 3.77 0.00 40.72 3.50
179 194 4.332637 GGCCACTGCGTTGCACTG 62.333 66.667 0.00 0.00 38.85 3.66
219 241 4.643387 GCGACAAGCTGGGGTGGT 62.643 66.667 0.00 0.00 44.04 4.16
283 310 1.272480 GGATAACCAAAGCCCCACAGT 60.272 52.381 0.00 0.00 35.97 3.55
347 377 1.134699 CAGCGCACTCCCAAAGATCTA 60.135 52.381 11.47 0.00 0.00 1.98
453 489 1.003839 ATTCTTTCGGCCTCGTGCA 60.004 52.632 0.00 0.00 43.89 4.57
454 490 1.021390 ATTCTTTCGGCCTCGTGCAG 61.021 55.000 0.00 0.00 43.89 4.41
455 491 3.793144 CTTTCGGCCTCGTGCAGC 61.793 66.667 0.00 0.00 43.89 5.25
456 492 4.617520 TTTCGGCCTCGTGCAGCA 62.618 61.111 0.00 0.00 43.89 4.41
510 548 4.215613 GGCAGGAAGTAACGAATGTTTTCT 59.784 41.667 0.00 0.00 39.54 2.52
511 549 5.383130 GCAGGAAGTAACGAATGTTTTCTC 58.617 41.667 0.00 0.00 39.54 2.87
512 550 5.049680 GCAGGAAGTAACGAATGTTTTCTCA 60.050 40.000 0.00 0.00 39.54 3.27
513 551 6.363473 CAGGAAGTAACGAATGTTTTCTCAC 58.637 40.000 0.00 0.00 39.54 3.51
514 552 5.176958 AGGAAGTAACGAATGTTTTCTCACG 59.823 40.000 0.00 0.00 39.54 4.35
541 579 2.390599 CCATGGCCGTCTGTCGTTG 61.391 63.158 0.00 0.00 37.94 4.10
545 583 2.315386 GGCCGTCTGTCGTTGGTTC 61.315 63.158 0.00 0.00 37.94 3.62
546 584 2.315386 GCCGTCTGTCGTTGGTTCC 61.315 63.158 0.00 0.00 37.94 3.62
547 585 1.366366 CCGTCTGTCGTTGGTTCCT 59.634 57.895 0.00 0.00 37.94 3.36
548 586 0.249741 CCGTCTGTCGTTGGTTCCTT 60.250 55.000 0.00 0.00 37.94 3.36
549 587 0.859232 CGTCTGTCGTTGGTTCCTTG 59.141 55.000 0.00 0.00 34.52 3.61
550 588 1.537348 CGTCTGTCGTTGGTTCCTTGA 60.537 52.381 0.00 0.00 34.52 3.02
552 590 0.868406 CTGTCGTTGGTTCCTTGAGC 59.132 55.000 0.00 0.00 0.00 4.26
555 625 2.325082 CGTTGGTTCCTTGAGCCGG 61.325 63.158 0.00 0.00 35.65 6.13
559 629 2.666098 GGTTCCTTGAGCCGGGCTA 61.666 63.158 23.92 6.40 39.88 3.93
571 641 3.161450 GGGCTACCAGGATCGCCA 61.161 66.667 16.62 0.00 44.23 5.69
590 660 4.321230 CGCCACTGCTTTCTCCTTTATTTT 60.321 41.667 0.00 0.00 34.43 1.82
628 701 3.280295 GCTAGGGTTCTCTTTTTAGGGC 58.720 50.000 0.00 0.00 0.00 5.19
669 742 3.025262 AGCTGCTACCACTTCTAGTACC 58.975 50.000 0.00 0.00 0.00 3.34
671 744 3.429135 GCTGCTACCACTTCTAGTACCAC 60.429 52.174 0.00 0.00 0.00 4.16
710 783 1.298859 GCGGCCTTCAAGTACTGGTG 61.299 60.000 0.00 0.00 0.00 4.17
762 864 4.332543 TCGGCCACCTTCCCCTCT 62.333 66.667 2.24 0.00 0.00 3.69
771 873 0.341609 CCTTCCCCTCTTCCTCCTCT 59.658 60.000 0.00 0.00 0.00 3.69
798 900 2.202676 GCGCTGCTCTTCGCTACT 60.203 61.111 0.00 0.00 46.92 2.57
801 903 1.813192 GCTGCTCTTCGCTACTCCT 59.187 57.895 0.00 0.00 40.11 3.69
846 950 2.898840 CCGCGATTGCTCATGGCT 60.899 61.111 8.23 0.00 42.39 4.75
855 959 1.077501 GCTCATGGCTTGCTACCCA 60.078 57.895 0.00 0.00 38.06 4.51
949 1053 2.506061 CGCCTCTGATCCCCTCCTG 61.506 68.421 0.00 0.00 0.00 3.86
960 1064 4.411981 CCTCCTGCTGCTGCTGCT 62.412 66.667 27.67 0.00 40.48 4.24
1035 1163 4.099170 GCGCTGGTGCTGCTTCTG 62.099 66.667 0.00 0.00 36.40 3.02
1081 1209 4.917415 GTGAGAAATGTTTTAGCATTGCGT 59.083 37.500 2.38 0.00 38.96 5.24
1159 1287 1.342275 TGGGAAATTGGGGATCAGCTG 60.342 52.381 7.63 7.63 0.00 4.24
1214 1342 4.338879 CTGTTTCTCCATGACATTTCCCT 58.661 43.478 0.00 0.00 0.00 4.20
1215 1343 4.739793 TGTTTCTCCATGACATTTCCCTT 58.260 39.130 0.00 0.00 0.00 3.95
1245 1375 2.890311 TGCCTCGGTTGAACAATTTGAT 59.110 40.909 2.79 0.00 0.00 2.57
1260 1390 0.893270 TTGATGCGGAAACCTGTGGG 60.893 55.000 0.00 0.00 38.88 4.61
1261 1391 2.676471 ATGCGGAAACCTGTGGGC 60.676 61.111 0.00 0.00 35.63 5.36
1269 1399 1.754226 GAAACCTGTGGGCTCAACAAA 59.246 47.619 0.00 0.00 35.63 2.83
1379 1509 4.141620 ACAGGAGAGTTTTCTGAAGCTTGA 60.142 41.667 2.10 0.00 32.53 3.02
1382 1512 6.091986 CAGGAGAGTTTTCTGAAGCTTGATAC 59.908 42.308 2.10 0.00 32.53 2.24
1389 1522 7.719633 AGTTTTCTGAAGCTTGATACCACTAAA 59.280 33.333 2.10 0.00 0.00 1.85
1525 1659 2.670592 TCGCATGTGCTTGCTGCT 60.671 55.556 0.00 0.00 43.37 4.24
1605 1740 1.858041 CGTCGGATGATGCAGATGC 59.142 57.895 0.00 0.00 42.50 3.91
1606 1741 0.599466 CGTCGGATGATGCAGATGCT 60.599 55.000 6.35 0.00 42.66 3.79
1607 1742 0.866427 GTCGGATGATGCAGATGCTG 59.134 55.000 6.35 0.00 42.66 4.41
1609 1744 1.235281 CGGATGATGCAGATGCTGGG 61.235 60.000 6.35 0.00 42.66 4.45
1610 1745 1.524863 GGATGATGCAGATGCTGGGC 61.525 60.000 6.35 0.00 42.66 5.36
1611 1746 0.822121 GATGATGCAGATGCTGGGCA 60.822 55.000 6.35 0.00 44.86 5.36
1728 1867 6.607600 AGCAACCTGTAGATTGTCTGATACTA 59.392 38.462 0.00 0.00 0.00 1.82
1749 1888 7.897575 ACTAAAACTCAGAGCTTAGTCATTG 57.102 36.000 15.41 0.00 30.57 2.82
1762 1901 5.292101 GCTTAGTCATTGCACAGTTAGTAGG 59.708 44.000 0.00 0.00 0.00 3.18
1763 1902 4.891992 AGTCATTGCACAGTTAGTAGGT 57.108 40.909 0.00 0.00 0.00 3.08
1764 1903 5.995565 AGTCATTGCACAGTTAGTAGGTA 57.004 39.130 0.00 0.00 0.00 3.08
1765 1904 6.354794 AGTCATTGCACAGTTAGTAGGTAA 57.645 37.500 0.00 0.00 0.00 2.85
1788 1927 5.477607 TGTACACTGCATACTTTACCTGT 57.522 39.130 0.00 0.00 0.00 4.00
1909 2048 2.042230 GGACCTTCCTCCGCCCTA 60.042 66.667 0.00 0.00 32.53 3.53
2007 2151 2.085343 ATCTGTTGCAGCACCCCCTT 62.085 55.000 0.00 0.00 0.00 3.95
2020 2164 1.428912 ACCCCCTTCTTCATCAGCAAA 59.571 47.619 0.00 0.00 0.00 3.68
2066 2210 2.032528 CCTGCAGTTCCGGCTGAA 59.967 61.111 13.81 1.49 38.70 3.02
2124 2268 3.194542 AGGTAGCTCACATTCAGTCAGAC 59.805 47.826 0.00 0.00 0.00 3.51
2168 2312 5.179929 TGTGTGCATCACTAACTGAATCTTG 59.820 40.000 16.70 0.00 46.27 3.02
2184 2328 8.046708 ACTGAATCTTGTGTAGGTTATAATGCA 58.953 33.333 0.00 0.00 0.00 3.96
2208 2352 4.680237 CCGGTTGAGTCTGCGCCA 62.680 66.667 4.18 0.00 0.00 5.69
2214 2421 4.803426 GAGTCTGCGCCACCTCCG 62.803 72.222 4.18 0.00 0.00 4.63
2223 2430 2.989824 CCACCTCCGGTCGTGTCT 60.990 66.667 18.19 0.00 31.02 3.41
2224 2431 2.258591 CACCTCCGGTCGTGTCTG 59.741 66.667 13.45 0.00 31.02 3.51
2449 2656 3.118629 TGTGAAGCCTAATCTGCCACTAG 60.119 47.826 0.00 0.00 0.00 2.57
2572 2851 1.203441 TCCTGCTCCATCTGTGGCTT 61.203 55.000 0.00 0.00 45.63 4.35
2614 2893 3.205507 AGTGCCTCCTCCTTCACTATCTA 59.794 47.826 0.00 0.00 37.94 1.98
2622 2901 5.888724 TCCTCCTTCACTATCTACAGTTCAG 59.111 44.000 0.00 0.00 0.00 3.02
2629 2908 5.104067 TCACTATCTACAGTTCAGGCTCCTA 60.104 44.000 0.00 0.00 0.00 2.94
2694 2973 2.350772 GCCTTCTGTGAACAATCAACCG 60.351 50.000 0.00 0.00 37.30 4.44
2696 2975 2.631160 TCTGTGAACAATCAACCGGT 57.369 45.000 0.00 0.00 37.30 5.28
2756 3035 3.553828 TTCATAAGCTTAGGTTCCCGG 57.446 47.619 17.04 0.00 0.00 5.73
2775 3054 4.461081 CCCGGATTCTTGATGTACCAAAAA 59.539 41.667 0.73 0.00 0.00 1.94
2776 3055 5.393027 CCCGGATTCTTGATGTACCAAAAAG 60.393 44.000 0.73 0.00 0.00 2.27
2778 3057 6.294508 CCGGATTCTTGATGTACCAAAAAGTT 60.295 38.462 0.00 0.00 0.00 2.66
2780 3059 8.293867 CGGATTCTTGATGTACCAAAAAGTTAA 58.706 33.333 0.00 0.00 0.00 2.01
2810 3089 3.381590 GTGCAAATATGTTCCTTCCCTCC 59.618 47.826 0.00 0.00 0.00 4.30
2862 3141 1.257743 ATGATGTCCCTCCGTATCCG 58.742 55.000 0.00 0.00 0.00 4.18
2882 3161 0.527565 CCACCTGAAGGCATTTTCCG 59.472 55.000 0.00 0.00 39.32 4.30
2912 3191 4.601857 TCCTCCTTCCACTTCAGGTAAATT 59.398 41.667 0.00 0.00 0.00 1.82
2916 3195 6.472887 TCCTTCCACTTCAGGTAAATTACTG 58.527 40.000 2.96 0.55 36.07 2.74
2917 3196 6.271391 TCCTTCCACTTCAGGTAAATTACTGA 59.729 38.462 2.96 2.78 41.63 3.41
2941 3220 7.614974 TGACATGGGATAGATCAAATTTGACAA 59.385 33.333 22.71 11.53 40.49 3.18
2943 3222 6.455360 TGGGATAGATCAAATTTGACAAGC 57.545 37.500 22.71 13.18 40.49 4.01
3009 3288 4.559153 GGAACATGTGAAACCTCCAATTG 58.441 43.478 0.00 0.00 34.36 2.32
3023 3302 4.895297 CCTCCAATTGCACCACCTATTATT 59.105 41.667 0.00 0.00 0.00 1.40
3047 3326 0.311790 ATGCACCTCAACAACAAGCG 59.688 50.000 0.00 0.00 0.00 4.68
3084 3363 4.449068 CCGAGCATAACAATGGTGAGTATC 59.551 45.833 0.00 0.00 31.72 2.24
3129 3408 8.627487 TTTGTTTGACAATGTTCTTACATGTC 57.373 30.769 0.00 0.00 44.14 3.06
3130 3409 7.326968 TGTTTGACAATGTTCTTACATGTCA 57.673 32.000 0.00 14.04 44.14 3.58
3175 3454 5.998981 TCATGTTTATTGTAGGAAACACGGT 59.001 36.000 2.54 0.00 45.56 4.83
3229 3508 3.621715 GGTAAGAACCATGACATTCGACC 59.378 47.826 0.00 5.24 45.98 4.79
3253 3532 2.107552 CACCTCCACCAAAGGAACCTAA 59.892 50.000 0.00 0.00 37.20 2.69
3262 3541 4.042934 ACCAAAGGAACCTAATACTGCACT 59.957 41.667 0.00 0.00 0.00 4.40
3479 3758 3.386932 TCGTTAGGGGTAGCTCCTAAA 57.613 47.619 17.93 6.53 45.26 1.85
3575 3854 1.002134 ACCCCATGCTCAAGGTTCG 60.002 57.895 0.00 0.00 0.00 3.95
3602 3881 3.363341 TGCCTTTTGAAAAACCTAGCG 57.637 42.857 0.00 0.00 0.00 4.26
3653 3932 7.016268 TCTCAAAAGTTCAGTGTTATAGGTCCT 59.984 37.037 0.00 0.00 0.00 3.85
3690 3969 2.528818 CCTCCACAGCAGGTTGGGA 61.529 63.158 0.00 0.00 0.00 4.37
3716 3995 2.181125 AGGCAAAATCATCATGCACCA 58.819 42.857 0.00 0.00 41.80 4.17
3745 4024 6.202954 CCGATGATTCAAGGTAATGGTAGTTC 59.797 42.308 0.00 0.00 0.00 3.01
3783 4090 9.912634 AAACATTGGTTTCATTTCATAGTACTG 57.087 29.630 5.39 0.00 43.60 2.74
3872 4179 2.036256 CACCAAAGGGCCCCTCTG 59.964 66.667 21.43 13.53 37.90 3.35
3889 4196 2.421424 CTCTGATGGCAGCAAAAGTACC 59.579 50.000 6.97 0.00 42.01 3.34
3961 4268 6.426328 CAGTACAGATCTTTGAAGCTTCAGTT 59.574 38.462 27.02 13.10 38.61 3.16
4181 4488 7.553334 TGATTCTTACCTAGTGAAGCGTTAAT 58.447 34.615 0.00 0.00 0.00 1.40
4349 4656 0.464452 CGAAGTGGGATCTGGGGTAC 59.536 60.000 0.00 0.00 0.00 3.34
4485 4792 3.243068 ACTGCCTTGTCGACATTTCAAAC 60.243 43.478 20.80 5.75 0.00 2.93
4685 4996 8.078060 TCTCATAAACATCAGTGGATTCAGTA 57.922 34.615 0.00 0.00 0.00 2.74
4902 5213 2.763249 AGCGTAATTGCTATTGCTGC 57.237 45.000 13.64 13.64 45.14 5.25
4935 5246 9.687210 CACTGTTATAGCATTGATTATTTGCAT 57.313 29.630 1.30 0.00 38.84 3.96
4984 5295 7.576403 TCAAATTCAGGGATTCAGATGACATA 58.424 34.615 0.00 0.00 0.00 2.29
5014 5325 4.702131 GGATATCCACATAGTGCAATTCCC 59.298 45.833 17.34 0.00 35.64 3.97
5144 5455 2.168106 TGCACATTTTCAGCCAAGTGTT 59.832 40.909 0.00 0.00 0.00 3.32
5198 5509 7.350382 TGTGTCCTATAGGCAAATATTTCCAA 58.650 34.615 14.50 0.00 34.44 3.53
5199 5510 7.284489 TGTGTCCTATAGGCAAATATTTCCAAC 59.716 37.037 14.50 2.90 34.44 3.77
5282 5593 3.348554 TTGGCCTCCGATGCAGCAT 62.349 57.895 7.91 7.91 0.00 3.79
5283 5594 1.981951 TTGGCCTCCGATGCAGCATA 61.982 55.000 8.22 0.00 0.00 3.14
5284 5595 1.002868 GGCCTCCGATGCAGCATAT 60.003 57.895 8.22 0.00 0.00 1.78
5327 5638 6.715347 ATAGAAAAACTGCACCCCATAATC 57.285 37.500 0.00 0.00 0.00 1.75
5366 5677 6.140303 TGTCCTGGTCGTATACACTAATTC 57.860 41.667 3.32 0.00 0.00 2.17
5367 5678 5.068198 TGTCCTGGTCGTATACACTAATTCC 59.932 44.000 3.32 0.00 0.00 3.01
5372 5683 5.239306 TGGTCGTATACACTAATTCCTACCG 59.761 44.000 3.32 0.00 0.00 4.02
5388 5699 8.833231 ATTCCTACCGATAAAATAGACATGTG 57.167 34.615 1.15 0.00 0.00 3.21
5395 5706 6.205464 CCGATAAAATAGACATGTGAAGCCAT 59.795 38.462 1.15 0.00 0.00 4.40
5497 5808 0.535102 AAGCTTCATTATCCCCGGCG 60.535 55.000 0.00 0.00 0.00 6.46
5500 5811 0.602905 CTTCATTATCCCCGGCGTCC 60.603 60.000 6.01 0.00 0.00 4.79
5501 5812 2.032071 CATTATCCCCGGCGTCCC 59.968 66.667 6.01 0.00 0.00 4.46
5516 5827 0.625849 GTCCCCACCATCCTTCATGT 59.374 55.000 0.00 0.00 0.00 3.21
5525 5836 5.760253 CCACCATCCTTCATGTAATGTCTAC 59.240 44.000 0.00 0.00 46.80 2.59
5587 5898 1.279271 AGCCACTGCCTCTAAATTCGT 59.721 47.619 0.00 0.00 38.69 3.85
5602 5913 1.640428 TTCGTGCGCTATTCTCAAGG 58.360 50.000 9.73 0.00 0.00 3.61
5603 5914 0.815095 TCGTGCGCTATTCTCAAGGA 59.185 50.000 9.73 0.00 0.00 3.36
5617 5928 9.495572 CTATTCTCAAGGATTTACTTATGGGAC 57.504 37.037 0.00 0.00 0.00 4.46
5628 5939 8.602472 ATTTACTTATGGGACCATTGCTAAAA 57.398 30.769 9.44 5.36 37.82 1.52
5742 6054 7.452880 TTCAGTAGCTGCAAATGTTAGAAAT 57.547 32.000 4.12 0.00 0.00 2.17
5783 6095 6.603095 CAGCTGGTCAGTTAAACATTTCTAC 58.397 40.000 5.57 0.00 0.00 2.59
5821 6133 6.378582 CAAACGTTTTTGTGCTACCATAGAT 58.621 36.000 11.66 0.00 37.85 1.98
6056 6371 4.588528 ACATTTCAAATGCTAACCCACAGT 59.411 37.500 10.21 0.00 0.00 3.55
6067 6382 5.005094 GCTAACCCACAGTGTTTATGGTAA 58.995 41.667 0.00 0.00 0.00 2.85
6083 6398 4.299586 TGGTAACATTTCAGATGAGGCA 57.700 40.909 0.00 0.00 46.17 4.75
6096 6413 4.882427 CAGATGAGGCATTCACTTCTGAAT 59.118 41.667 12.32 0.00 46.36 2.57
6312 6629 4.046938 TGCTGAGATAGAAAAGGCTACG 57.953 45.455 0.00 0.00 0.00 3.51
6357 6674 3.647771 GGGGAAGGTGGCTTCGGT 61.648 66.667 0.00 0.00 34.37 4.69
6471 6788 0.904865 AGGTTGAGATGCTGGGACGA 60.905 55.000 0.00 0.00 0.00 4.20
6596 6913 8.196771 CCATTTGCATGGTAAGTATGTTATTGT 58.803 33.333 0.00 0.00 44.81 2.71
6636 6956 4.272018 GCATATAGAAGTGTCAGCAGTTGG 59.728 45.833 0.00 0.00 38.30 3.77
6902 7222 0.902984 AGCACATCTCCACCCGTGTA 60.903 55.000 0.00 0.00 0.00 2.90
7016 7336 1.980232 ACCGGAGTACGCCATGACA 60.980 57.895 16.39 0.00 42.52 3.58
7223 7543 3.345808 CCACTGGACAACGTGGCG 61.346 66.667 0.00 0.00 43.59 5.69
7331 7651 1.078918 CTGCAGCGAGGGTGATGAA 60.079 57.895 0.00 0.00 32.22 2.57
7335 7655 0.036010 CAGCGAGGGTGATGAAGGTT 60.036 55.000 0.00 0.00 32.22 3.50
7388 7708 2.102357 CGTACGACAGCGGCTCAT 59.898 61.111 10.44 0.00 43.17 2.90
7495 7815 0.035152 TCTTTCCGCATGCAGTCCAT 60.035 50.000 19.57 0.00 33.39 3.41
7499 7819 1.890979 CCGCATGCAGTCCATCTCC 60.891 63.158 19.57 0.00 29.71 3.71
7722 8043 5.810587 AGACCTAGTTTGTGTACATTATGCG 59.189 40.000 0.00 0.00 0.00 4.73
7736 8057 5.670485 ACATTATGCGTGTGGAGATAAAGA 58.330 37.500 0.00 0.00 0.00 2.52
7774 8098 1.000771 AGCAGAGTAGCAGACCGGA 60.001 57.895 9.46 0.00 36.85 5.14
7794 8118 2.928801 TCATGGGTTATGGATCACCG 57.071 50.000 0.00 0.00 39.42 4.94
7834 8168 3.626670 GGCTCAGATCTGGTTCTTCATTG 59.373 47.826 22.42 0.00 0.00 2.82
7895 8229 1.202143 CGCCTGCCTTCCGATTTTTAC 60.202 52.381 0.00 0.00 0.00 2.01
7903 8237 3.181510 CCTTCCGATTTTTACCGCTTCTG 60.182 47.826 0.00 0.00 0.00 3.02
8033 8371 4.619863 GCCATGTGAATTTCAGCTTCATGT 60.620 41.667 18.70 0.00 35.26 3.21
8220 8580 3.253432 GCTGGGAACTTGTTAAGAACTGG 59.747 47.826 0.00 0.00 0.00 4.00
8223 8583 3.004419 GGGAACTTGTTAAGAACTGGTGC 59.996 47.826 0.00 0.00 0.00 5.01
8232 8592 6.039616 TGTTAAGAACTGGTGCATTTTGAAC 58.960 36.000 0.00 0.00 0.00 3.18
8233 8593 6.127479 TGTTAAGAACTGGTGCATTTTGAACT 60.127 34.615 0.00 0.00 0.00 3.01
8246 8606 6.041409 TGCATTTTGAACTGGAAACTTGGATA 59.959 34.615 0.00 0.00 0.00 2.59
8297 8673 4.954875 AGCAGAATACATGAGTTAGCTCC 58.045 43.478 0.00 0.00 40.95 4.70
8337 8713 9.500785 TTTCCTGAAAAGTTTCACTTCATTTTT 57.499 25.926 2.32 0.00 41.88 1.94
8338 8714 8.702163 TCCTGAAAAGTTTCACTTCATTTTTC 57.298 30.769 2.32 0.00 41.88 2.29
8368 8835 1.806542 TCAAAGGTTTCAGCTCGATGC 59.193 47.619 0.00 0.00 43.29 3.91
8413 8880 5.841810 TGTTCATTTCCCATCACAGTTTTC 58.158 37.500 0.00 0.00 0.00 2.29
8417 8884 5.707298 TCATTTCCCATCACAGTTTTCTCTC 59.293 40.000 0.00 0.00 0.00 3.20
8424 8892 4.244425 TCACAGTTTTCTCTCTTCTCCG 57.756 45.455 0.00 0.00 0.00 4.63
8433 8901 1.478916 CTCTCTTCTCCGTTTCCCCTC 59.521 57.143 0.00 0.00 0.00 4.30
8463 8932 1.866601 TGTGAAACTGCTGTCATCACG 59.133 47.619 24.41 0.00 41.66 4.35
8526 8998 4.408182 AACAGAGTAACAGCACAGACTT 57.592 40.909 0.00 0.00 0.00 3.01
8533 9005 6.702282 AGAGTAACAGCACAGACTTTTAGAAC 59.298 38.462 0.00 0.00 0.00 3.01
8541 9013 6.542370 AGCACAGACTTTTAGAACTAGCAAAA 59.458 34.615 0.00 0.00 0.00 2.44
8550 9022 8.756486 TTTTAGAACTAGCAAAACTAAACCCT 57.244 30.769 0.00 0.00 34.35 4.34
8605 9077 5.269505 AGGACACGAAAGGATAATCAGAG 57.730 43.478 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 0.326264 AATTGAGCGCCAGGTTCTCT 59.674 50.000 2.29 0.00 0.00 3.10
111 121 1.678635 CCCCTGAAATTGAGCGCCA 60.679 57.895 2.29 0.00 0.00 5.69
171 186 1.409579 CGTACGTACGCAGTGCAAC 59.590 57.895 32.36 11.52 45.55 4.17
172 187 3.831614 CGTACGTACGCAGTGCAA 58.168 55.556 32.36 0.00 45.55 4.08
219 241 0.107557 GGGAAAATTACCGGCTCCGA 60.108 55.000 10.28 0.00 42.83 4.55
283 310 2.360852 GTCCGTCCGTCCCTCTCA 60.361 66.667 0.00 0.00 0.00 3.27
347 377 1.967762 CGAGACGCAAATGCAAATGT 58.032 45.000 6.18 0.00 42.21 2.71
379 409 3.077359 ACGCTAGTACCACGAACTAGTT 58.923 45.455 8.13 8.13 45.43 2.24
453 489 2.195683 CACCACCACCACCTTGCT 59.804 61.111 0.00 0.00 0.00 3.91
454 490 3.605664 GCACCACCACCACCTTGC 61.606 66.667 0.00 0.00 0.00 4.01
455 491 3.286751 CGCACCACCACCACCTTG 61.287 66.667 0.00 0.00 0.00 3.61
456 492 3.804329 ACGCACCACCACCACCTT 61.804 61.111 0.00 0.00 0.00 3.50
496 534 4.209703 GGTGACGTGAGAAAACATTCGTTA 59.790 41.667 0.00 0.00 33.99 3.18
510 548 4.386951 CATGGCCGGGTGACGTGA 62.387 66.667 2.18 0.00 42.24 4.35
534 572 0.534203 GGCTCAAGGAACCAACGACA 60.534 55.000 0.00 0.00 0.00 4.35
541 579 2.666098 TAGCCCGGCTCAAGGAACC 61.666 63.158 17.40 0.00 40.44 3.62
545 583 3.391665 CTGGTAGCCCGGCTCAAGG 62.392 68.421 17.40 1.48 40.44 3.61
546 584 2.187946 CTGGTAGCCCGGCTCAAG 59.812 66.667 17.40 8.35 40.44 3.02
547 585 3.399181 CCTGGTAGCCCGGCTCAA 61.399 66.667 17.40 0.00 40.44 3.02
548 586 3.696518 ATCCTGGTAGCCCGGCTCA 62.697 63.158 17.40 8.00 40.44 4.26
549 587 2.844839 ATCCTGGTAGCCCGGCTC 60.845 66.667 17.40 7.76 40.44 4.70
550 588 2.844839 GATCCTGGTAGCCCGGCT 60.845 66.667 18.05 18.05 43.41 5.52
552 590 4.301027 GCGATCCTGGTAGCCCGG 62.301 72.222 0.00 0.00 36.81 5.73
628 701 6.669977 GCAGCTACTACAAGTAAATTCACACG 60.670 42.308 0.00 0.00 29.00 4.49
669 742 3.771577 AGGGGAAGAAACTGTGTAGTG 57.228 47.619 0.00 0.00 37.19 2.74
671 744 2.814336 GCAAGGGGAAGAAACTGTGTAG 59.186 50.000 0.00 0.00 0.00 2.74
710 783 5.988561 ACCACTAGTACTCGTACAGTATAGC 59.011 44.000 0.00 0.00 39.90 2.97
762 864 1.939082 CGAGGGAGGGAGAGGAGGAA 61.939 65.000 0.00 0.00 0.00 3.36
793 895 0.325765 AGGGACAGGGAAGGAGTAGC 60.326 60.000 0.00 0.00 0.00 3.58
798 900 2.182858 GAGGGAGGGACAGGGAAGGA 62.183 65.000 0.00 0.00 0.00 3.36
801 903 2.454941 GGAGGGAGGGACAGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
846 950 0.963355 GACCGCCATTTGGGTAGCAA 60.963 55.000 0.00 0.00 39.65 3.91
855 959 2.044946 GGAGCCTGACCGCCATTT 60.045 61.111 0.00 0.00 0.00 2.32
915 1019 4.680237 CGAGTGGGTTCAGGCGCA 62.680 66.667 10.83 0.00 0.00 6.09
930 1034 2.123251 GGAGGGGATCAGAGGCGA 60.123 66.667 0.00 0.00 0.00 5.54
933 1037 1.074623 AGCAGGAGGGGATCAGAGG 60.075 63.158 0.00 0.00 0.00 3.69
972 1076 3.685592 CTCGTAGCAAGAGCAGCG 58.314 61.111 0.00 0.00 45.49 5.18
1035 1163 2.026822 TGTGGATCCAAGAAGAGAAGCC 60.027 50.000 18.20 0.00 0.00 4.35
1125 1253 1.043673 TTCCCACCCCAAACAAACCG 61.044 55.000 0.00 0.00 0.00 4.44
1159 1287 3.503363 GTCCGGCAGCTGCACATC 61.503 66.667 37.63 20.56 44.36 3.06
1236 1366 2.627699 ACAGGTTTCCGCATCAAATTGT 59.372 40.909 0.00 0.00 0.00 2.71
1245 1375 3.842925 GAGCCCACAGGTTTCCGCA 62.843 63.158 0.00 0.00 34.57 5.69
1260 1390 6.138088 GCATTTGGAAGAAAATTTGTTGAGC 58.862 36.000 0.00 0.00 0.00 4.26
1261 1391 6.357198 CGCATTTGGAAGAAAATTTGTTGAG 58.643 36.000 0.00 0.00 0.00 3.02
1269 1399 2.932187 GCCTGCGCATTTGGAAGAAAAT 60.932 45.455 17.65 0.00 34.03 1.82
1306 1436 4.947147 AGCGCGGTTTCCTGGCAA 62.947 61.111 4.23 0.00 0.00 4.52
1353 1483 3.406764 CTTCAGAAAACTCTCCTGTGGG 58.593 50.000 0.00 0.00 0.00 4.61
1525 1659 3.572255 GGCCAAAAACACAGGTAGATGAA 59.428 43.478 0.00 0.00 0.00 2.57
1642 1778 5.849357 TTGCAAAGCAAGAGCAATTATTG 57.151 34.783 0.00 0.00 43.99 1.90
1728 1867 5.049129 GTGCAATGACTAAGCTCTGAGTTTT 60.049 40.000 12.02 6.89 0.00 2.43
1749 1888 6.530534 CAGTGTACATTACCTACTAACTGTGC 59.469 42.308 0.00 0.00 0.00 4.57
1762 1901 7.548075 ACAGGTAAAGTATGCAGTGTACATTAC 59.452 37.037 12.44 12.44 36.36 1.89
1763 1902 7.617225 ACAGGTAAAGTATGCAGTGTACATTA 58.383 34.615 0.00 0.00 0.00 1.90
1764 1903 6.472887 ACAGGTAAAGTATGCAGTGTACATT 58.527 36.000 0.00 0.00 0.00 2.71
1765 1904 6.049955 ACAGGTAAAGTATGCAGTGTACAT 57.950 37.500 0.00 0.00 0.00 2.29
1876 2015 3.617535 TCCAGGAGGACTAGAAGCC 57.382 57.895 0.00 0.00 39.61 4.35
1909 2048 1.903183 GCTGGAAGAGTTACTGGACCT 59.097 52.381 0.00 0.00 34.07 3.85
2007 2151 1.004745 GGGAGGGTTTGCTGATGAAGA 59.995 52.381 0.00 0.00 0.00 2.87
2020 2164 2.456840 CCTTCTGGAGGGGAGGGT 59.543 66.667 0.00 0.00 42.26 4.34
2039 2183 2.744768 GAACTGCAGGGCTCACAGCT 62.745 60.000 19.93 0.00 41.99 4.24
2214 2421 2.126424 GGAGACGCAGACACGACC 60.126 66.667 0.00 0.00 36.70 4.79
2217 2424 2.179517 GGAGGAGACGCAGACACG 59.820 66.667 0.00 0.00 39.50 4.49
2223 2430 2.283173 TCAGCTGGAGGAGACGCA 60.283 61.111 15.13 0.00 0.00 5.24
2224 2431 2.493973 CTCAGCTGGAGGAGACGC 59.506 66.667 15.13 0.00 40.13 5.19
2572 2851 2.584835 AGTGGCACATTAGGCTTCAA 57.415 45.000 21.41 0.00 44.52 2.69
2614 2893 1.203187 TGGAGTAGGAGCCTGAACTGT 60.203 52.381 0.00 0.00 0.00 3.55
2694 2973 2.310538 CCTGATCCAATTGGCCTAACC 58.689 52.381 20.33 5.32 39.84 2.85
2696 2975 6.718593 ATATACCTGATCCAATTGGCCTAA 57.281 37.500 20.33 2.46 34.44 2.69
2700 2979 7.201767 GCAGAATATATACCTGATCCAATTGGC 60.202 40.741 20.33 7.39 34.44 4.52
2728 3007 6.985059 GGAACCTAAGCTTATGAATCGTTACT 59.015 38.462 14.77 0.00 0.00 2.24
2780 3059 9.382275 GGAAGGAACATATTTGCACAATTTTAT 57.618 29.630 0.00 0.00 0.00 1.40
2781 3060 7.821846 GGGAAGGAACATATTTGCACAATTTTA 59.178 33.333 0.00 0.00 0.00 1.52
2810 3089 4.133078 GGGAGAATGCAGGAGTGAATAAG 58.867 47.826 0.00 0.00 0.00 1.73
2912 3191 8.493607 TCAAATTTGATCTATCCCATGTCAGTA 58.506 33.333 16.91 0.00 31.01 2.74
2916 3195 7.572523 TGTCAAATTTGATCTATCCCATGTC 57.427 36.000 23.05 6.86 39.73 3.06
2917 3196 7.417116 GCTTGTCAAATTTGATCTATCCCATGT 60.417 37.037 23.05 0.00 39.73 3.21
2941 3220 6.459573 CGGTAAATGGTAAAACATATGCAGCT 60.460 38.462 1.58 0.00 0.00 4.24
2943 3222 6.791303 ACGGTAAATGGTAAAACATATGCAG 58.209 36.000 1.58 0.00 0.00 4.41
3009 3288 3.796504 GCATGTGCAATAATAGGTGGTGC 60.797 47.826 0.00 0.00 41.59 5.01
3047 3326 1.138247 CTCGGCATTTGGAGCTTGC 59.862 57.895 0.00 0.00 35.64 4.01
3095 3374 7.927629 AGAACATTGTCAAACAAATAGCAACAT 59.072 29.630 0.00 0.00 41.96 2.71
3175 3454 1.567175 GGGAAGTATTTGCTGGGGGTA 59.433 52.381 0.00 0.00 0.00 3.69
3226 3505 0.890996 CTTTGGTGGAGGTGCAGGTC 60.891 60.000 0.00 0.00 0.00 3.85
3229 3508 0.178992 TTCCTTTGGTGGAGGTGCAG 60.179 55.000 0.00 0.00 37.43 4.41
3253 3532 4.216257 GTGATTTGTGAACCAGTGCAGTAT 59.784 41.667 0.00 0.00 0.00 2.12
3262 3541 5.042463 TCTAGTTGGTGATTTGTGAACCA 57.958 39.130 0.00 0.00 42.19 3.67
3300 3579 7.701501 CACAAACAAGCTGCCAATTTTATTTTT 59.298 29.630 0.00 0.00 0.00 1.94
3301 3580 7.066766 TCACAAACAAGCTGCCAATTTTATTTT 59.933 29.630 0.00 0.00 0.00 1.82
3373 3652 1.305633 AGAGGACTAGCTGCAGGCA 60.306 57.895 17.12 0.00 44.79 4.75
3479 3758 0.911525 ATCTGCTAGTGGGTGCTGGT 60.912 55.000 0.00 0.00 0.00 4.00
3540 3819 1.613061 GTGGTGGGTAAGATGGGGG 59.387 63.158 0.00 0.00 0.00 5.40
3690 3969 5.870978 GTGCATGATGATTTTGCCTTTTAGT 59.129 36.000 0.00 0.00 35.51 2.24
3716 3995 3.992943 TTACCTTGAATCATCGGTGGT 57.007 42.857 12.99 6.39 0.00 4.16
3783 4090 6.183360 TGGACAGGAAAAACAATGAAAGTCTC 60.183 38.462 0.00 0.00 0.00 3.36
3961 4268 5.223449 AGAAACACGAGGTCCTGAAAATA 57.777 39.130 0.00 0.00 0.00 1.40
4047 4354 3.516512 TGGTGGTGGGGGCAATGT 61.517 61.111 0.00 0.00 0.00 2.71
4327 4634 1.141881 CCCAGATCCCACTTCGTCG 59.858 63.158 0.00 0.00 0.00 5.12
4485 4792 5.010415 AGAGAAATCTTTTTGCTCCACAAGG 59.990 40.000 0.00 0.00 40.06 3.61
4575 4886 6.176183 CAAATAAGAGAGTCCAAGGACACAT 58.824 40.000 20.52 6.33 46.76 3.21
4685 4996 4.861102 TGAGATATGATGAGCATGACGT 57.139 40.909 0.00 0.00 37.87 4.34
4962 5273 6.002704 GCTATGTCATCTGAATCCCTGAATT 58.997 40.000 0.00 0.00 0.00 2.17
4984 5295 4.262808 GCACTATGTGGATATCCTTGAGCT 60.263 45.833 22.35 0.00 36.82 4.09
5014 5325 2.890945 ACCGGAAGACCTGGAAATTTTG 59.109 45.455 9.46 0.00 35.17 2.44
5077 5388 4.848357 ACAGCTAAGCCAAGTAACATCAT 58.152 39.130 0.00 0.00 0.00 2.45
5090 5401 3.648179 CTGTCAATCGAACAGCTAAGC 57.352 47.619 2.95 0.00 37.88 3.09
5198 5509 4.872293 CCTCCCAAAGGGCATTGT 57.128 55.556 0.00 0.00 43.94 2.71
5251 5562 0.543749 AGGCCAAGGCTGTATCTCAC 59.456 55.000 5.01 0.00 41.60 3.51
5282 5593 8.977412 TCTATATGGGATGTTCGAAAGCATATA 58.023 33.333 0.00 0.00 0.00 0.86
5283 5594 7.851228 TCTATATGGGATGTTCGAAAGCATAT 58.149 34.615 0.00 0.00 0.00 1.78
5284 5595 7.239763 TCTATATGGGATGTTCGAAAGCATA 57.760 36.000 0.00 0.00 0.00 3.14
5327 5638 9.236691 CGACCAGGACAAAATATTGAAAATATG 57.763 33.333 0.00 0.00 38.94 1.78
5366 5677 7.095607 GCTTCACATGTCTATTTTATCGGTAGG 60.096 40.741 0.00 0.00 0.00 3.18
5367 5678 7.095607 GGCTTCACATGTCTATTTTATCGGTAG 60.096 40.741 0.00 0.00 0.00 3.18
5372 5683 8.158169 TCATGGCTTCACATGTCTATTTTATC 57.842 34.615 0.00 0.00 46.39 1.75
5388 5699 3.733337 ACGAGGATAACATCATGGCTTC 58.267 45.455 0.00 0.00 0.00 3.86
5395 5706 7.453439 TGGAAGGATTATACGAGGATAACATCA 59.547 37.037 0.00 0.00 0.00 3.07
5497 5808 0.625849 ACATGAAGGATGGTGGGGAC 59.374 55.000 0.00 0.00 36.23 4.46
5500 5811 3.885297 GACATTACATGAAGGATGGTGGG 59.115 47.826 0.00 0.00 36.23 4.61
5501 5812 4.785301 AGACATTACATGAAGGATGGTGG 58.215 43.478 0.00 0.00 36.23 4.61
5535 5846 5.941058 TCCTCGCAACATTAGTAATTTCCAA 59.059 36.000 0.00 0.00 0.00 3.53
5545 5856 7.078228 GGCTAATTTAATCCTCGCAACATTAG 58.922 38.462 0.00 0.00 0.00 1.73
5554 5865 3.251004 GGCAGTGGCTAATTTAATCCTCG 59.749 47.826 9.90 0.00 40.87 4.63
5587 5898 5.023533 AGTAAATCCTTGAGAATAGCGCA 57.976 39.130 11.47 0.00 0.00 6.09
5602 5913 7.817418 TTAGCAATGGTCCCATAAGTAAATC 57.183 36.000 0.00 0.00 35.31 2.17
5603 5914 8.602472 TTTTAGCAATGGTCCCATAAGTAAAT 57.398 30.769 0.00 0.00 35.31 1.40
5617 5928 5.837437 TGCCCGTTATAATTTTAGCAATGG 58.163 37.500 0.00 0.00 0.00 3.16
5628 5939 4.588951 TGAGAGACAGATGCCCGTTATAAT 59.411 41.667 0.00 0.00 0.00 1.28
5742 6054 4.002982 CAGCTGCACATGTCTAAACCTAA 58.997 43.478 0.00 0.00 0.00 2.69
5753 6065 1.812235 TAACTGACCAGCTGCACATG 58.188 50.000 8.66 7.12 0.00 3.21
5783 6095 2.323959 ACGTTTGTGCAACTTTGTGTG 58.676 42.857 0.00 0.00 38.04 3.82
5816 6128 5.237996 CCGAGTTGCACATCATCAAATCTAT 59.762 40.000 0.00 0.00 35.78 1.98
5821 6133 2.503331 ACCGAGTTGCACATCATCAAA 58.497 42.857 0.00 0.00 0.00 2.69
6056 6371 7.148086 GCCTCATCTGAAATGTTACCATAAACA 60.148 37.037 0.00 0.00 43.16 2.83
6067 6382 4.597004 AGTGAATGCCTCATCTGAAATGT 58.403 39.130 0.00 0.00 36.14 2.71
6169 6486 3.308035 ACATGTCCCTGCAATCATGAT 57.692 42.857 19.48 1.18 39.68 2.45
6312 6629 3.309682 TCGACGAATCATCAAAGCCATTC 59.690 43.478 0.00 0.00 0.00 2.67
6357 6674 1.841277 AGTGTCCCTTGGTACACACAA 59.159 47.619 15.98 0.00 46.71 3.33
6471 6788 3.257873 TGACCAAATTTCGGTGATGCAAT 59.742 39.130 14.53 0.00 36.69 3.56
6525 6842 3.454371 AGTTCATATACCAGACACCGC 57.546 47.619 0.00 0.00 0.00 5.68
6596 6913 3.838244 ATGCTGGCGGAGTTAAATCTA 57.162 42.857 2.56 0.00 0.00 1.98
6902 7222 2.578940 TCCTTACCCGAATGTTCCCATT 59.421 45.455 0.00 0.00 43.97 3.16
6937 7257 8.173130 CCATGTTTAAAACTATACCAAGACGTC 58.827 37.037 7.70 7.70 0.00 4.34
7016 7336 2.641815 ACTCTTGACAAGAAGATGGCCT 59.358 45.455 18.26 0.00 37.02 5.19
7223 7543 2.101770 GCGATGGCAGCTGCTTTC 59.898 61.111 35.82 28.57 41.70 2.62
7331 7651 2.447408 AACTTCCCGAACCAAAACCT 57.553 45.000 0.00 0.00 0.00 3.50
7335 7655 1.679153 GCTGAAACTTCCCGAACCAAA 59.321 47.619 0.00 0.00 0.00 3.28
7388 7708 2.368439 GCTTCCATGCCAGTTACATCA 58.632 47.619 0.00 0.00 0.00 3.07
7495 7815 1.758514 GTCATCAGAGGGCCGGAGA 60.759 63.158 5.05 0.00 0.00 3.71
7499 7819 2.503061 CCTGTCATCAGAGGGCCG 59.497 66.667 0.00 0.00 43.76 6.13
7538 7858 2.069273 CTCGACAAGTTTCGCATCCTT 58.931 47.619 3.51 0.00 38.95 3.36
7633 7954 0.673022 CTGGAAGCTGGACAGAGCAC 60.673 60.000 3.00 0.00 41.83 4.40
7636 7957 1.204467 GAGACTGGAAGCTGGACAGAG 59.796 57.143 16.61 0.00 37.60 3.35
7736 8057 9.332502 CTCTGCTGATCCGTAACTATATATAGT 57.667 37.037 18.01 18.01 45.04 2.12
7774 8098 2.040278 CCGGTGATCCATAACCCATGAT 59.960 50.000 0.00 0.00 36.69 2.45
7794 8118 3.560105 AGCCAATCTTATTCAAGCCTCC 58.440 45.455 0.00 0.00 0.00 4.30
7811 8135 2.259917 TGAAGAACCAGATCTGAGCCA 58.740 47.619 24.62 9.65 0.00 4.75
7812 8136 3.557228 ATGAAGAACCAGATCTGAGCC 57.443 47.619 24.62 11.53 0.00 4.70
7911 8245 5.590259 ACAAACTAACTCAAACTGACATGCT 59.410 36.000 0.00 0.00 0.00 3.79
7995 8333 1.002201 CATGGCCAAATGCAGTCCAAA 59.998 47.619 10.96 0.00 43.89 3.28
7996 8334 0.609151 CATGGCCAAATGCAGTCCAA 59.391 50.000 10.96 0.00 43.89 3.53
7997 8335 0.542467 ACATGGCCAAATGCAGTCCA 60.542 50.000 10.96 0.00 43.89 4.02
8003 8341 3.336468 TGAAATTCACATGGCCAAATGC 58.664 40.909 10.96 1.88 40.16 3.56
8123 8472 6.402222 AGTTAGACTGCATACTTTCTTCAGG 58.598 40.000 0.00 0.00 0.00 3.86
8182 8541 8.782137 AGTTCCCAGCAAAAATTACCATATAT 57.218 30.769 0.00 0.00 0.00 0.86
8220 8580 4.270808 CCAAGTTTCCAGTTCAAAATGCAC 59.729 41.667 0.00 0.00 0.00 4.57
8223 8583 8.090214 ACATATCCAAGTTTCCAGTTCAAAATG 58.910 33.333 0.00 0.00 0.00 2.32
8232 8592 4.885907 AGATGCACATATCCAAGTTTCCAG 59.114 41.667 0.00 0.00 0.00 3.86
8233 8593 4.858850 AGATGCACATATCCAAGTTTCCA 58.141 39.130 0.00 0.00 0.00 3.53
8267 8627 5.738909 ACTCATGTATTCTGCTAAAGTGCT 58.261 37.500 0.00 0.00 0.00 4.40
8268 8628 6.428385 AACTCATGTATTCTGCTAAAGTGC 57.572 37.500 0.00 0.00 0.00 4.40
8269 8629 7.493971 AGCTAACTCATGTATTCTGCTAAAGTG 59.506 37.037 0.00 0.00 0.00 3.16
8270 8630 7.560368 AGCTAACTCATGTATTCTGCTAAAGT 58.440 34.615 0.00 0.00 0.00 2.66
8271 8631 7.170658 GGAGCTAACTCATGTATTCTGCTAAAG 59.829 40.741 0.00 0.00 45.42 1.85
8274 8634 5.598417 TGGAGCTAACTCATGTATTCTGCTA 59.402 40.000 0.00 0.00 45.42 3.49
8275 8635 4.406972 TGGAGCTAACTCATGTATTCTGCT 59.593 41.667 0.00 2.77 45.42 4.24
8276 8636 4.697514 TGGAGCTAACTCATGTATTCTGC 58.302 43.478 0.00 0.00 45.42 4.26
8297 8673 2.958355 TCAGGAAAAGAAAGTGCCCTTG 59.042 45.455 0.00 0.00 0.00 3.61
8337 8713 5.551233 CTGAAACCTTTGATCCACTACTGA 58.449 41.667 0.00 0.00 0.00 3.41
8338 8714 4.154918 GCTGAAACCTTTGATCCACTACTG 59.845 45.833 0.00 0.00 0.00 2.74
8342 8809 3.416156 GAGCTGAAACCTTTGATCCACT 58.584 45.455 0.00 0.00 0.00 4.00
8344 8811 2.038426 TCGAGCTGAAACCTTTGATCCA 59.962 45.455 0.00 0.00 0.00 3.41
8368 8835 4.918810 AAAGGTGTTAGGAAACTTGCAG 57.081 40.909 0.00 0.00 43.67 4.41
8413 8880 1.478916 GAGGGGAAACGGAGAAGAGAG 59.521 57.143 0.00 0.00 0.00 3.20
8417 8884 1.205893 CAGAGAGGGGAAACGGAGAAG 59.794 57.143 0.00 0.00 0.00 2.85
8424 8892 1.376037 CCACGCAGAGAGGGGAAAC 60.376 63.158 0.00 0.00 33.80 2.78
8433 8901 0.583438 CAGTTTCACACCACGCAGAG 59.417 55.000 0.00 0.00 0.00 3.35
8513 8982 5.467063 GCTAGTTCTAAAAGTCTGTGCTGTT 59.533 40.000 0.00 0.00 0.00 3.16
8515 8984 4.991056 TGCTAGTTCTAAAAGTCTGTGCTG 59.009 41.667 0.00 0.00 0.00 4.41
8526 8998 8.626526 CAAGGGTTTAGTTTTGCTAGTTCTAAA 58.373 33.333 0.00 0.00 0.00 1.85
8533 9005 3.509967 CCCCAAGGGTTTAGTTTTGCTAG 59.490 47.826 4.11 0.00 38.25 3.42
8541 9013 4.479156 TTTGATTCCCCAAGGGTTTAGT 57.521 40.909 4.11 0.00 44.74 2.24
8547 9019 1.901833 CAGGTTTTGATTCCCCAAGGG 59.098 52.381 0.00 0.00 46.11 3.95
8550 9022 3.077391 AGATCCAGGTTTTGATTCCCCAA 59.923 43.478 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.