Multiple sequence alignment - TraesCS4B01G272100

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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 TraesCS4B01G272100 chr4B 100.000 3198 0 0 1 3198 548765774 548768971 0.000000e+00 5906.0
1 TraesCS4B01G272100 chr4B 82.658 888 99 31 1034 1920 659689626 659688793 0.000000e+00 736.0
2 TraesCS4B01G272100 chr4B 81.375 698 124 6 1 695 456582621 456583315 5.990000e-157 564.0
3 TraesCS4B01G272100 chr4B 88.496 339 33 4 1582 1920 660090484 660090816 3.840000e-109 405.0
4 TraesCS4B01G272100 chr4B 84.295 312 45 4 1914 2222 660092218 660092528 5.180000e-78 302.0
5 TraesCS4B01G272100 chr4B 86.531 245 33 0 1912 2156 659688437 659688193 1.460000e-68 270.0
6 TraesCS4B01G272100 chr4D 92.462 2640 147 17 1 2602 441899860 441902485 0.000000e+00 3725.0
7 TraesCS4B01G272100 chr4D 81.067 750 115 17 4 741 68486067 68485333 9.950000e-160 573.0
8 TraesCS4B01G272100 chr4D 93.989 366 22 0 2833 3198 441902477 441902842 3.600000e-154 555.0
9 TraesCS4B01G272100 chr4A 90.265 1890 138 23 752 2608 25498048 25496172 0.000000e+00 2429.0
10 TraesCS4B01G272100 chr4A 89.344 366 38 1 2833 3198 25496186 25495822 2.910000e-125 459.0
11 TraesCS4B01G272100 chr4A 84.348 230 29 6 2605 2832 613315049 613315273 5.370000e-53 219.0
12 TraesCS4B01G272100 chr3D 83.737 744 112 7 4 741 522162344 522163084 0.000000e+00 695.0
13 TraesCS4B01G272100 chr3D 82.736 753 109 15 1 745 68832080 68832819 0.000000e+00 651.0
14 TraesCS4B01G272100 chr5A 80.733 955 123 31 986 1920 698888603 698889516 0.000000e+00 688.0
15 TraesCS4B01G272100 chr5A 90.204 245 24 0 1912 2156 698889660 698889904 1.430000e-83 320.0
16 TraesCS4B01G272100 chr5A 88.211 246 24 5 1912 2155 698896135 698896377 4.040000e-74 289.0
17 TraesCS4B01G272100 chr5A 100.000 29 0 0 2574 2602 592056764 592056792 2.000000e-03 54.7
18 TraesCS4B01G272100 chr7B 83.285 688 110 5 4 688 136291216 136290531 2.090000e-176 628.0
19 TraesCS4B01G272100 chr7B 88.158 228 25 2 2605 2830 692342463 692342236 1.460000e-68 270.0
20 TraesCS4B01G272100 chr7D 81.906 724 122 7 16 735 96504308 96505026 1.270000e-168 603.0
21 TraesCS4B01G272100 chr2D 81.497 708 121 5 1 705 421127401 421128101 9.950000e-160 573.0
22 TraesCS4B01G272100 chr2D 87.033 455 59 0 1040 1494 479179254 479179708 6.120000e-142 514.0
23 TraesCS4B01G272100 chr2D 90.080 373 34 1 1551 1920 479180445 479180817 6.200000e-132 481.0
24 TraesCS4B01G272100 chr2D 89.655 232 24 0 1917 2148 479180980 479181211 2.410000e-76 296.0
25 TraesCS4B01G272100 chr1B 81.287 668 117 8 38 701 94043261 94043924 4.700000e-148 534.0
26 TraesCS4B01G272100 chr2A 86.853 464 52 6 1040 1494 621920625 621921088 7.910000e-141 510.0
27 TraesCS4B01G272100 chr2A 90.323 372 33 3 1552 1920 621921797 621922168 4.800000e-133 484.0
28 TraesCS4B01G272100 chr2A 89.451 237 25 0 1912 2148 621922324 621922560 1.860000e-77 300.0
29 TraesCS4B01G272100 chr2B 86.638 464 53 5 1040 1494 562217399 562217862 3.680000e-139 505.0
30 TraesCS4B01G272100 chr2B 90.885 373 31 1 1551 1920 562218574 562218946 6.160000e-137 497.0
31 TraesCS4B01G272100 chr2B 87.149 249 32 0 1917 2165 562219106 562219354 1.880000e-72 283.0
32 TraesCS4B01G272100 chr6D 80.415 337 58 8 1585 1920 302249725 302249396 1.900000e-62 250.0
33 TraesCS4B01G272100 chr6D 81.690 213 39 0 1241 1453 302250960 302250748 9.120000e-41 178.0
34 TraesCS4B01G272100 chr6B 80.357 336 60 6 1585 1920 468010423 468010094 1.900000e-62 250.0
35 TraesCS4B01G272100 chr6B 92.466 146 11 0 2692 2837 675396072 675395927 3.230000e-50 209.0
36 TraesCS4B01G272100 chr6B 80.400 250 49 0 1204 1453 468011517 468011268 1.170000e-44 191.0
37 TraesCS4B01G272100 chr6B 94.624 93 4 1 2601 2692 206445278 206445186 3.330000e-30 143.0
38 TraesCS4B01G272100 chr6B 89.720 107 7 4 2587 2692 675396253 675396150 2.000000e-27 134.0
39 TraesCS4B01G272100 chr6A 79.822 337 60 8 1585 1920 413733926 413734255 4.120000e-59 239.0
40 TraesCS4B01G272100 chr6A 83.117 231 34 4 2604 2832 609794175 609794402 4.180000e-49 206.0
41 TraesCS4B01G272100 chr6A 78.571 266 55 2 1188 1453 413732816 413733079 1.180000e-39 174.0
42 TraesCS4B01G272100 chr5B 87.368 190 23 1 2605 2793 528682828 528683017 1.930000e-52 217.0
43 TraesCS4B01G272100 chr5B 83.117 231 30 6 2607 2832 10072307 10072533 5.410000e-48 202.0
44 TraesCS4B01G272100 chr5B 91.781 146 11 1 2692 2837 482295500 482295644 5.410000e-48 202.0
45 TraesCS4B01G272100 chr5B 91.216 148 12 1 2692 2839 588793859 588794005 1.950000e-47 200.0
46 TraesCS4B01G272100 chr3A 82.759 232 33 7 2605 2832 24052139 24052367 1.950000e-47 200.0
47 TraesCS4B01G272100 chr5D 81.197 234 37 7 2599 2832 386677739 386677513 7.050000e-42 182.0


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 TraesCS4B01G272100 chr4B 548765774 548768971 3197 False 5906.000000 5906 100.000000 1 3198 1 chr4B.!!$F2 3197
1 TraesCS4B01G272100 chr4B 456582621 456583315 694 False 564.000000 564 81.375000 1 695 1 chr4B.!!$F1 694
2 TraesCS4B01G272100 chr4B 659688193 659689626 1433 True 503.000000 736 84.594500 1034 2156 2 chr4B.!!$R1 1122
3 TraesCS4B01G272100 chr4B 660090484 660092528 2044 False 353.500000 405 86.395500 1582 2222 2 chr4B.!!$F3 640
4 TraesCS4B01G272100 chr4D 441899860 441902842 2982 False 2140.000000 3725 93.225500 1 3198 2 chr4D.!!$F1 3197
5 TraesCS4B01G272100 chr4D 68485333 68486067 734 True 573.000000 573 81.067000 4 741 1 chr4D.!!$R1 737
6 TraesCS4B01G272100 chr4A 25495822 25498048 2226 True 1444.000000 2429 89.804500 752 3198 2 chr4A.!!$R1 2446
7 TraesCS4B01G272100 chr3D 522162344 522163084 740 False 695.000000 695 83.737000 4 741 1 chr3D.!!$F2 737
8 TraesCS4B01G272100 chr3D 68832080 68832819 739 False 651.000000 651 82.736000 1 745 1 chr3D.!!$F1 744
9 TraesCS4B01G272100 chr5A 698888603 698889904 1301 False 504.000000 688 85.468500 986 2156 2 chr5A.!!$F3 1170
10 TraesCS4B01G272100 chr7B 136290531 136291216 685 True 628.000000 628 83.285000 4 688 1 chr7B.!!$R1 684
11 TraesCS4B01G272100 chr7D 96504308 96505026 718 False 603.000000 603 81.906000 16 735 1 chr7D.!!$F1 719
12 TraesCS4B01G272100 chr2D 421127401 421128101 700 False 573.000000 573 81.497000 1 705 1 chr2D.!!$F1 704
13 TraesCS4B01G272100 chr2D 479179254 479181211 1957 False 430.333333 514 88.922667 1040 2148 3 chr2D.!!$F2 1108
14 TraesCS4B01G272100 chr1B 94043261 94043924 663 False 534.000000 534 81.287000 38 701 1 chr1B.!!$F1 663
15 TraesCS4B01G272100 chr2A 621920625 621922560 1935 False 431.333333 510 88.875667 1040 2148 3 chr2A.!!$F1 1108
16 TraesCS4B01G272100 chr2B 562217399 562219354 1955 False 428.333333 505 88.224000 1040 2165 3 chr2B.!!$F1 1125
17 TraesCS4B01G272100 chr6D 302249396 302250960 1564 True 214.000000 250 81.052500 1241 1920 2 chr6D.!!$R1 679
18 TraesCS4B01G272100 chr6B 468010094 468011517 1423 True 220.500000 250 80.378500 1204 1920 2 chr6B.!!$R2 716
19 TraesCS4B01G272100 chr6A 413732816 413734255 1439 False 206.500000 239 79.196500 1188 1920 2 chr6A.!!$F2 732

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
886 918 0.179163 GCGATTGGTTTGCTGTAGCC 60.179 55.0 0.8 0.0 41.18 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 5655 0.037232 CAGTGGGAGGAGACGTTTCC 60.037 60.0 17.16 17.16 37.52 3.13 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
90 91 1.746615 GCCACACATCACGGCAGAT 60.747 57.895 0.00 0.00 45.52 2.90
108 109 3.760035 CCAGACCTGGCGTACGCT 61.760 66.667 36.24 19.58 44.73 5.07
170 174 4.373116 TTGTCTCCACCGCCTCGC 62.373 66.667 0.00 0.00 0.00 5.03
282 287 4.003788 CAGCCCACGTCCTCGGTT 62.004 66.667 0.00 0.00 41.85 4.44
551 567 6.183360 ACCGGACGAAATATCATTCAGTTTTC 60.183 38.462 9.46 0.00 0.00 2.29
695 711 2.227089 GACCTCCCGCATTCGTGTCT 62.227 60.000 0.00 0.00 0.00 3.41
701 717 0.948623 CCGCATTCGTGTCTGTGGAA 60.949 55.000 0.00 0.00 44.15 3.53
706 723 2.631160 TTCGTGTCTGTGGAATGGTT 57.369 45.000 0.00 0.00 0.00 3.67
711 728 1.001974 TGTCTGTGGAATGGTTCTCCG 59.998 52.381 0.00 0.00 35.55 4.63
782 814 0.467290 GGAACTGTGTTTGGGGCAGA 60.467 55.000 0.00 0.00 34.60 4.26
786 818 0.890996 CTGTGTTTGGGGCAGAGGTC 60.891 60.000 0.00 0.00 32.39 3.85
801 833 1.007038 GGTCTAACCGTGTGCGACA 60.007 57.895 0.00 0.00 41.33 4.35
837 869 6.114089 TCACTGTCCTATATATACGCCTCTC 58.886 44.000 0.00 0.00 0.00 3.20
880 912 1.210155 GAAGCGCGATTGGTTTGCT 59.790 52.632 17.15 0.00 37.53 3.91
882 914 1.795170 AAGCGCGATTGGTTTGCTGT 61.795 50.000 9.67 0.00 35.77 4.40
883 915 0.953471 AGCGCGATTGGTTTGCTGTA 60.953 50.000 12.10 0.00 33.99 2.74
884 916 0.521242 GCGCGATTGGTTTGCTGTAG 60.521 55.000 12.10 0.00 31.94 2.74
885 917 0.521242 CGCGATTGGTTTGCTGTAGC 60.521 55.000 0.00 0.00 42.50 3.58
886 918 0.179163 GCGATTGGTTTGCTGTAGCC 60.179 55.000 0.80 0.00 41.18 3.93
887 919 1.164411 CGATTGGTTTGCTGTAGCCA 58.836 50.000 0.80 0.00 41.18 4.75
888 920 1.135689 CGATTGGTTTGCTGTAGCCAC 60.136 52.381 0.80 0.00 41.18 5.01
966 998 6.092396 ACGACTCCATCATAAGCTATACGTAG 59.908 42.308 0.08 0.00 0.00 3.51
1095 1127 2.284258 AGAGGCAAGCTCGAGGGT 60.284 61.111 15.58 0.00 0.00 4.34
1418 1471 4.379243 CGGGCAGCTCTCGTGGTT 62.379 66.667 0.00 0.00 0.00 3.67
1469 1522 4.796231 CCGGGAAGACTGCGACCG 62.796 72.222 0.00 0.00 43.89 4.79
1485 1538 4.139420 CGCGGAAAGCTCAGCACG 62.139 66.667 0.00 0.00 42.29 5.34
1528 1686 0.039798 CATGCATGCAAGCCCGTATC 60.040 55.000 26.68 0.00 0.00 2.24
1529 1687 0.179009 ATGCATGCAAGCCCGTATCT 60.179 50.000 26.68 0.00 0.00 1.98
1545 2538 6.223852 CCCGTATCTATGCTTGATTACTTGT 58.776 40.000 0.00 0.00 0.00 3.16
1549 2544 6.851222 ATCTATGCTTGATTACTTGTTCGG 57.149 37.500 0.00 0.00 0.00 4.30
1580 2608 3.438781 TGACGAGCAAAAGTTTTGTCACT 59.561 39.130 25.20 15.93 30.61 3.41
1732 2975 4.626081 ACGTGCTTCCTGCGGCTT 62.626 61.111 0.00 0.00 46.63 4.35
2202 5133 6.109359 CGATGGACCTCTCTTCTTAACATTT 58.891 40.000 0.00 0.00 0.00 2.32
2258 5189 3.243737 TGGCACACCTCGATGATACATAC 60.244 47.826 0.00 0.00 36.63 2.39
2363 5318 7.148222 TGGTACCATTCGGTTATACATTTGTTG 60.148 37.037 11.60 0.00 46.31 3.33
2575 5538 8.481314 GGATATAGGCATCTATGTTGAATCTCA 58.519 37.037 0.00 0.00 36.87 3.27
2602 5565 4.276678 ACAAATCTCAGTGTCATGTTGTGG 59.723 41.667 0.00 0.00 0.00 4.17
2603 5566 3.777106 ATCTCAGTGTCATGTTGTGGT 57.223 42.857 0.00 0.00 0.00 4.16
2604 5567 3.558931 TCTCAGTGTCATGTTGTGGTT 57.441 42.857 0.00 0.00 0.00 3.67
2605 5568 3.884895 TCTCAGTGTCATGTTGTGGTTT 58.115 40.909 0.00 0.00 0.00 3.27
2606 5569 4.269183 TCTCAGTGTCATGTTGTGGTTTT 58.731 39.130 0.00 0.00 0.00 2.43
2607 5570 4.704540 TCTCAGTGTCATGTTGTGGTTTTT 59.295 37.500 0.00 0.00 0.00 1.94
2630 5593 6.993786 TTTTTGAACATCAGTACAGACACA 57.006 33.333 0.00 0.00 0.00 3.72
2631 5594 6.993786 TTTTGAACATCAGTACAGACACAA 57.006 33.333 0.00 0.00 0.00 3.33
2632 5595 6.603237 TTTGAACATCAGTACAGACACAAG 57.397 37.500 0.00 0.00 0.00 3.16
2633 5596 4.058124 TGAACATCAGTACAGACACAAGC 58.942 43.478 0.00 0.00 0.00 4.01
2634 5597 2.677199 ACATCAGTACAGACACAAGCG 58.323 47.619 0.00 0.00 0.00 4.68
2635 5598 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
2636 5599 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
2637 5600 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
2638 5601 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
2639 5602 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
2640 5603 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
2641 5604 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
2642 5605 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
2643 5606 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
2644 5607 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
2645 5608 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
2646 5609 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
2650 5613 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
2651 5614 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
2652 5615 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
2653 5616 2.185262 CGCTCATATACACGCGCATAT 58.815 47.619 5.73 7.02 39.11 1.78
2654 5617 3.359654 CGCTCATATACACGCGCATATA 58.640 45.455 5.73 9.29 39.11 0.86
2655 5618 3.177838 CGCTCATATACACGCGCATATAC 59.822 47.826 5.73 0.29 39.11 1.47
2656 5619 4.352039 GCTCATATACACGCGCATATACT 58.648 43.478 5.73 0.00 0.00 2.12
2657 5620 4.438145 GCTCATATACACGCGCATATACTC 59.562 45.833 5.73 0.00 0.00 2.59
2658 5621 5.554822 TCATATACACGCGCATATACTCA 57.445 39.130 5.73 0.00 0.00 3.41
2659 5622 6.131544 TCATATACACGCGCATATACTCAT 57.868 37.500 5.73 0.00 0.00 2.90
2660 5623 6.199393 TCATATACACGCGCATATACTCATC 58.801 40.000 5.73 0.00 0.00 2.92
2661 5624 4.703645 ATACACGCGCATATACTCATCT 57.296 40.909 5.73 0.00 0.00 2.90
2662 5625 5.813080 ATACACGCGCATATACTCATCTA 57.187 39.130 5.73 0.00 0.00 1.98
2663 5626 4.703645 ACACGCGCATATACTCATCTAT 57.296 40.909 5.73 0.00 0.00 1.98
2664 5627 5.813080 ACACGCGCATATACTCATCTATA 57.187 39.130 5.73 0.00 0.00 1.31
2665 5628 6.378710 ACACGCGCATATACTCATCTATAT 57.621 37.500 5.73 0.00 0.00 0.86
2666 5629 6.202226 ACACGCGCATATACTCATCTATATG 58.798 40.000 5.73 0.00 39.00 1.78
2667 5630 6.038271 ACACGCGCATATACTCATCTATATGA 59.962 38.462 5.73 0.00 38.57 2.15
2668 5631 6.912591 CACGCGCATATACTCATCTATATGAA 59.087 38.462 5.73 0.00 41.57 2.57
2669 5632 7.592903 CACGCGCATATACTCATCTATATGAAT 59.407 37.037 5.73 0.00 41.57 2.57
2670 5633 7.592903 ACGCGCATATACTCATCTATATGAATG 59.407 37.037 5.73 0.00 41.57 2.67
2671 5634 7.410193 CGCGCATATACTCATCTATATGAATGC 60.410 40.741 8.75 12.25 43.22 3.56
2672 5635 7.383300 GCGCATATACTCATCTATATGAATGCA 59.617 37.037 18.20 0.00 45.05 3.96
2673 5636 8.697960 CGCATATACTCATCTATATGAATGCAC 58.302 37.037 18.20 0.00 45.05 4.57
2674 5637 9.538508 GCATATACTCATCTATATGAATGCACA 57.461 33.333 15.37 0.00 44.61 4.57
2677 5640 8.768957 ATACTCATCTATATGAATGCACACAC 57.231 34.615 0.00 0.00 41.57 3.82
2678 5641 5.693555 ACTCATCTATATGAATGCACACACG 59.306 40.000 0.00 0.00 41.57 4.49
2679 5642 4.448732 TCATCTATATGAATGCACACACGC 59.551 41.667 0.00 0.00 39.20 5.34
2680 5643 4.211794 CATCTATATGAATGCACACACGCA 59.788 41.667 0.00 0.00 39.93 5.24
2681 5644 2.830772 ATATGAATGCACACACGCAC 57.169 45.000 0.00 0.00 46.56 5.34
2682 5645 1.517242 TATGAATGCACACACGCACA 58.483 45.000 0.00 0.00 46.56 4.57
2683 5646 0.040157 ATGAATGCACACACGCACAC 60.040 50.000 0.00 0.00 46.56 3.82
2684 5647 1.370414 GAATGCACACACGCACACC 60.370 57.895 0.00 0.00 46.56 4.16
2685 5648 2.731587 GAATGCACACACGCACACCC 62.732 60.000 0.00 0.00 46.56 4.61
2686 5649 3.772853 ATGCACACACGCACACCCT 62.773 57.895 0.00 0.00 46.56 4.34
2687 5650 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
2688 5651 1.671054 GCACACACGCACACCCTAT 60.671 57.895 0.00 0.00 0.00 2.57
2689 5652 1.635663 GCACACACGCACACCCTATC 61.636 60.000 0.00 0.00 0.00 2.08
2690 5653 1.019278 CACACACGCACACCCTATCC 61.019 60.000 0.00 0.00 0.00 2.59
2691 5654 1.449601 CACACGCACACCCTATCCC 60.450 63.158 0.00 0.00 0.00 3.85
2692 5655 2.202878 CACGCACACCCTATCCCG 60.203 66.667 0.00 0.00 0.00 5.14
2693 5656 3.467226 ACGCACACCCTATCCCGG 61.467 66.667 0.00 0.00 0.00 5.73
2694 5657 3.151710 CGCACACCCTATCCCGGA 61.152 66.667 0.73 0.00 0.00 5.14
2695 5658 2.727392 CGCACACCCTATCCCGGAA 61.727 63.158 0.73 0.00 0.00 4.30
2696 5659 1.605453 GCACACCCTATCCCGGAAA 59.395 57.895 0.73 0.00 0.00 3.13
2697 5660 0.746923 GCACACCCTATCCCGGAAAC 60.747 60.000 0.73 0.00 0.00 2.78
2710 5673 2.363297 GGAAACGTCTCCTCCCACT 58.637 57.895 0.00 0.00 32.21 4.00
2711 5674 0.037232 GGAAACGTCTCCTCCCACTG 60.037 60.000 0.00 0.00 32.21 3.66
2712 5675 0.966920 GAAACGTCTCCTCCCACTGA 59.033 55.000 0.00 0.00 0.00 3.41
2713 5676 1.343465 GAAACGTCTCCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
2714 5677 1.645710 AACGTCTCCTCCCACTGAAT 58.354 50.000 0.00 0.00 0.00 2.57
2715 5678 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
2716 5679 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
2717 5680 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
2718 5681 1.817099 CTCCTCCCACTGAATGCGC 60.817 63.158 0.00 0.00 0.00 6.09
2719 5682 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
2720 5683 1.452651 CCTCCCACTGAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
2721 5684 1.442526 CCTCCCACTGAATGCGCATC 61.443 60.000 25.53 17.12 0.00 3.91
2722 5685 1.769098 CTCCCACTGAATGCGCATCG 61.769 60.000 25.53 17.09 0.00 3.84
2733 5696 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
2734 5697 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
2735 5698 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
2736 5699 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
2737 5700 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
2738 5701 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
2739 5702 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
2740 5703 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
2741 5704 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
2742 5705 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
2743 5706 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
2744 5707 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
2745 5708 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
2746 5709 5.163457 GCCGGAAATCCTGAAATAAATCCAA 60.163 40.000 5.05 0.00 0.00 3.53
2747 5710 6.507023 CCGGAAATCCTGAAATAAATCCAAG 58.493 40.000 0.00 0.00 0.00 3.61
2748 5711 6.321181 CCGGAAATCCTGAAATAAATCCAAGA 59.679 38.462 0.00 0.00 0.00 3.02
2749 5712 7.147915 CCGGAAATCCTGAAATAAATCCAAGAA 60.148 37.037 0.00 0.00 0.00 2.52
2750 5713 8.416329 CGGAAATCCTGAAATAAATCCAAGAAT 58.584 33.333 0.00 0.00 0.00 2.40
2757 5720 8.971321 CCTGAAATAAATCCAAGAATAAATGCG 58.029 33.333 0.00 0.00 0.00 4.73
2758 5721 9.734620 CTGAAATAAATCCAAGAATAAATGCGA 57.265 29.630 0.00 0.00 0.00 5.10
2761 5724 9.868277 AAATAAATCCAAGAATAAATGCGAACA 57.132 25.926 0.00 0.00 0.00 3.18
2762 5725 8.856490 ATAAATCCAAGAATAAATGCGAACAC 57.144 30.769 0.00 0.00 0.00 3.32
2763 5726 4.695217 TCCAAGAATAAATGCGAACACC 57.305 40.909 0.00 0.00 0.00 4.16
2764 5727 4.075682 TCCAAGAATAAATGCGAACACCA 58.924 39.130 0.00 0.00 0.00 4.17
2765 5728 4.155826 TCCAAGAATAAATGCGAACACCAG 59.844 41.667 0.00 0.00 0.00 4.00
2766 5729 4.155826 CCAAGAATAAATGCGAACACCAGA 59.844 41.667 0.00 0.00 0.00 3.86
2767 5730 5.335583 CCAAGAATAAATGCGAACACCAGAA 60.336 40.000 0.00 0.00 0.00 3.02
2768 5731 5.957842 AGAATAAATGCGAACACCAGAAA 57.042 34.783 0.00 0.00 0.00 2.52
2769 5732 6.515272 AGAATAAATGCGAACACCAGAAAT 57.485 33.333 0.00 0.00 0.00 2.17
2770 5733 6.924111 AGAATAAATGCGAACACCAGAAATT 58.076 32.000 0.00 0.00 0.00 1.82
2771 5734 8.050778 AGAATAAATGCGAACACCAGAAATTA 57.949 30.769 0.00 0.00 0.00 1.40
2772 5735 8.519526 AGAATAAATGCGAACACCAGAAATTAA 58.480 29.630 0.00 0.00 0.00 1.40
2773 5736 9.134734 GAATAAATGCGAACACCAGAAATTAAA 57.865 29.630 0.00 0.00 0.00 1.52
2774 5737 6.763303 AAATGCGAACACCAGAAATTAAAC 57.237 33.333 0.00 0.00 0.00 2.01
2775 5738 4.231718 TGCGAACACCAGAAATTAAACC 57.768 40.909 0.00 0.00 0.00 3.27
2776 5739 3.004944 TGCGAACACCAGAAATTAAACCC 59.995 43.478 0.00 0.00 0.00 4.11
2777 5740 3.254903 GCGAACACCAGAAATTAAACCCT 59.745 43.478 0.00 0.00 0.00 4.34
2778 5741 4.794169 CGAACACCAGAAATTAAACCCTG 58.206 43.478 0.00 0.00 0.00 4.45
2782 5745 3.592898 CCAGAAATTAAACCCTGGTGC 57.407 47.619 10.51 0.00 40.84 5.01
2783 5746 2.094752 CCAGAAATTAAACCCTGGTGCG 60.095 50.000 10.51 0.00 40.84 5.34
2784 5747 1.544246 AGAAATTAAACCCTGGTGCGC 59.456 47.619 0.00 0.00 0.00 6.09
2785 5748 1.544246 GAAATTAAACCCTGGTGCGCT 59.456 47.619 9.73 0.00 0.00 5.92
2786 5749 0.887933 AATTAAACCCTGGTGCGCTG 59.112 50.000 9.73 0.00 0.00 5.18
2787 5750 0.965363 ATTAAACCCTGGTGCGCTGG 60.965 55.000 9.73 5.63 0.00 4.85
2788 5751 2.058125 TTAAACCCTGGTGCGCTGGA 62.058 55.000 9.73 0.00 0.00 3.86
2789 5752 2.463589 TAAACCCTGGTGCGCTGGAG 62.464 60.000 9.73 0.58 0.00 3.86
2791 5754 3.790437 CCCTGGTGCGCTGGAGAT 61.790 66.667 9.73 0.00 0.00 2.75
2792 5755 2.434843 CCCTGGTGCGCTGGAGATA 61.435 63.158 9.73 0.00 0.00 1.98
2793 5756 1.227380 CCTGGTGCGCTGGAGATAC 60.227 63.158 9.73 0.00 0.00 2.24
2794 5757 1.227380 CTGGTGCGCTGGAGATACC 60.227 63.158 9.73 6.39 39.54 2.73
2796 5759 1.521681 GGTGCGCTGGAGATACCAC 60.522 63.158 9.73 0.00 44.64 4.16
2797 5760 1.218047 GTGCGCTGGAGATACCACA 59.782 57.895 9.73 0.00 44.64 4.17
2798 5761 0.179073 GTGCGCTGGAGATACCACAT 60.179 55.000 9.73 0.00 44.64 3.21
2799 5762 0.541392 TGCGCTGGAGATACCACATT 59.459 50.000 9.73 0.00 44.64 2.71
2800 5763 1.221414 GCGCTGGAGATACCACATTC 58.779 55.000 0.00 0.00 44.64 2.67
2801 5764 1.871080 CGCTGGAGATACCACATTCC 58.129 55.000 0.00 0.00 44.64 3.01
2802 5765 1.541233 CGCTGGAGATACCACATTCCC 60.541 57.143 0.00 0.00 44.64 3.97
2803 5766 1.771255 GCTGGAGATACCACATTCCCT 59.229 52.381 0.00 0.00 44.64 4.20
2804 5767 2.224402 GCTGGAGATACCACATTCCCTC 60.224 54.545 0.00 0.00 44.64 4.30
2805 5768 3.312890 CTGGAGATACCACATTCCCTCT 58.687 50.000 0.00 0.00 44.64 3.69
2806 5769 4.483950 CTGGAGATACCACATTCCCTCTA 58.516 47.826 0.00 0.00 44.64 2.43
2807 5770 4.890988 TGGAGATACCACATTCCCTCTAA 58.109 43.478 0.00 0.00 44.64 2.10
2808 5771 4.654262 TGGAGATACCACATTCCCTCTAAC 59.346 45.833 0.00 0.00 44.64 2.34
2809 5772 4.040584 GGAGATACCACATTCCCTCTAACC 59.959 50.000 0.00 0.00 38.79 2.85
2810 5773 4.631234 AGATACCACATTCCCTCTAACCA 58.369 43.478 0.00 0.00 0.00 3.67
2811 5774 5.227593 AGATACCACATTCCCTCTAACCAT 58.772 41.667 0.00 0.00 0.00 3.55
2812 5775 3.933861 ACCACATTCCCTCTAACCATC 57.066 47.619 0.00 0.00 0.00 3.51
2813 5776 2.509964 ACCACATTCCCTCTAACCATCC 59.490 50.000 0.00 0.00 0.00 3.51
2814 5777 2.509548 CCACATTCCCTCTAACCATCCA 59.490 50.000 0.00 0.00 0.00 3.41
2815 5778 3.053693 CCACATTCCCTCTAACCATCCAA 60.054 47.826 0.00 0.00 0.00 3.53
2816 5779 3.947834 CACATTCCCTCTAACCATCCAAC 59.052 47.826 0.00 0.00 0.00 3.77
2817 5780 3.053619 ACATTCCCTCTAACCATCCAACC 60.054 47.826 0.00 0.00 0.00 3.77
2818 5781 2.352561 TCCCTCTAACCATCCAACCA 57.647 50.000 0.00 0.00 0.00 3.67
2819 5782 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
2820 5783 1.406887 CCCTCTAACCATCCAACCACG 60.407 57.143 0.00 0.00 0.00 4.94
2821 5784 1.553248 CCTCTAACCATCCAACCACGA 59.447 52.381 0.00 0.00 0.00 4.35
2822 5785 2.418746 CCTCTAACCATCCAACCACGAG 60.419 54.545 0.00 0.00 0.00 4.18
2823 5786 2.233922 CTCTAACCATCCAACCACGAGT 59.766 50.000 0.00 0.00 0.00 4.18
2824 5787 2.635915 TCTAACCATCCAACCACGAGTT 59.364 45.455 0.00 0.00 40.16 3.01
2843 5806 2.481289 TGGTTCGCCATGTTGTGATA 57.519 45.000 0.00 0.00 43.56 2.15
2891 5854 5.395486 GCACGTCAGATTTCTAACAAAACAC 59.605 40.000 0.00 0.00 0.00 3.32
2908 5871 1.114722 CACAAGAGGCCCCTTTGCAA 61.115 55.000 0.00 0.00 0.00 4.08
2955 5918 1.730501 CTGGTACTGCATGGTCTGTG 58.269 55.000 0.00 0.00 0.00 3.66
2980 5943 2.674852 CTCCATCTTCCAATGACACACG 59.325 50.000 0.00 0.00 0.00 4.49
2981 5944 1.739466 CCATCTTCCAATGACACACGG 59.261 52.381 0.00 0.00 0.00 4.94
3028 5991 7.653647 ACTTGTCTTTTAACAAAGTTGACACA 58.346 30.769 0.00 0.00 40.47 3.72
3076 6039 5.175127 ACAATGCACACATTATCGTGAGTA 58.825 37.500 0.00 0.00 44.83 2.59
3079 6042 4.816392 TGCACACATTATCGTGAGTAGTT 58.184 39.130 0.00 0.00 39.34 2.24
3117 6080 5.009010 GTCATGAAGCTTTTCACAGAAAGGA 59.991 40.000 0.00 0.00 37.17 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.124612 TGGGATCGACGAGCGGTA 60.125 61.111 7.06 0.00 41.33 4.02
108 109 4.344865 GAGCGGTCCAAGGCCCAA 62.345 66.667 2.39 0.00 0.00 4.12
115 116 4.351938 CGTCACGGAGCGGTCCAA 62.352 66.667 31.39 14.65 44.18 3.53
170 174 0.107361 GTACCTGACCATTTCCCCGG 60.107 60.000 0.00 0.00 0.00 5.73
425 434 2.831333 CTCCTCCTTCATCATCGTTGG 58.169 52.381 0.00 0.00 0.00 3.77
566 582 2.556622 ACGGCGGATTTCATTGAAAGTT 59.443 40.909 13.24 1.80 34.92 2.66
695 711 2.169769 GGATACGGAGAACCATTCCACA 59.830 50.000 0.00 0.00 34.24 4.17
711 728 0.575390 CCGCATTCGTTCGTGGATAC 59.425 55.000 0.00 0.00 34.58 2.24
746 763 1.165907 TCCAAACTGTCGCTTGGCAG 61.166 55.000 5.11 0.00 41.65 4.85
776 808 1.218316 CACGGTTAGACCTCTGCCC 59.782 63.158 0.00 0.00 35.66 5.36
782 814 1.288127 GTCGCACACGGTTAGACCT 59.712 57.895 0.00 0.00 40.63 3.85
786 818 1.334992 CGTCTGTCGCACACGGTTAG 61.335 60.000 0.00 0.00 40.63 2.34
801 833 1.249407 GACAGTGAGGAGAACCGTCT 58.751 55.000 0.00 0.00 41.83 4.18
888 920 2.270205 CCACTGGGCACTGGCTAG 59.730 66.667 13.68 13.68 42.03 3.42
966 998 5.710099 AGAGATAGATGCTAGCTTAGACACC 59.290 44.000 17.23 0.16 0.00 4.16
1056 1088 3.411418 GAGCAGCGCACGGTAGCTA 62.411 63.158 11.47 0.00 42.52 3.32
1284 1337 1.063190 TCCCGCCTCATCTCCTCTAAA 60.063 52.381 0.00 0.00 0.00 1.85
1285 1338 0.556258 TCCCGCCTCATCTCCTCTAA 59.444 55.000 0.00 0.00 0.00 2.10
1287 1340 1.152567 CTCCCGCCTCATCTCCTCT 60.153 63.158 0.00 0.00 0.00 3.69
1418 1471 1.962144 GGAACGTGGAAGGACTCGA 59.038 57.895 0.00 0.00 0.00 4.04
1469 1522 2.607892 AACGTGCTGAGCTTTCCGC 61.608 57.895 5.83 0.00 39.57 5.54
1485 1538 1.198637 ACGCACGTACTCTACCTCAAC 59.801 52.381 0.00 0.00 0.00 3.18
1528 1686 4.572389 AGCCGAACAAGTAATCAAGCATAG 59.428 41.667 0.00 0.00 0.00 2.23
1529 1687 4.332543 CAGCCGAACAAGTAATCAAGCATA 59.667 41.667 0.00 0.00 0.00 3.14
1545 2538 2.125552 CGTCAGCCATCAGCCGAA 60.126 61.111 0.00 0.00 45.47 4.30
1549 2544 1.300971 TTTGCTCGTCAGCCATCAGC 61.301 55.000 0.00 0.00 46.26 4.26
1580 2608 2.725312 GCATCACTCCCCTGCTCGA 61.725 63.158 0.00 0.00 33.15 4.04
1834 3077 2.482839 GGAGTCCTTGATGAGCTGTAGC 60.483 54.545 0.41 0.00 42.49 3.58
1954 4882 0.780637 TGGAATTGGCCACCACCTTA 59.219 50.000 3.88 0.00 30.78 2.69
1984 4912 0.529378 GGAAGTAGGCGACGGAGAAA 59.471 55.000 0.00 0.00 0.00 2.52
2202 5133 1.337071 GACGGTGAGACTGAGTTCACA 59.663 52.381 20.93 6.70 44.23 3.58
2234 5165 1.933853 GTATCATCGAGGTGTGCCAAC 59.066 52.381 0.00 0.00 37.19 3.77
2282 5219 2.816087 TGTCACAAGGTCGTCTACTACC 59.184 50.000 0.00 0.00 35.91 3.18
2283 5220 4.698583 ATGTCACAAGGTCGTCTACTAC 57.301 45.455 0.00 0.00 0.00 2.73
2284 5221 5.247862 TGTATGTCACAAGGTCGTCTACTA 58.752 41.667 0.00 0.00 32.95 1.82
2285 5222 4.077108 TGTATGTCACAAGGTCGTCTACT 58.923 43.478 0.00 0.00 32.95 2.57
2286 5223 4.430137 TGTATGTCACAAGGTCGTCTAC 57.570 45.455 0.00 0.00 32.95 2.59
2287 5224 4.461431 ACATGTATGTCACAAGGTCGTCTA 59.539 41.667 0.00 0.00 41.55 2.59
2363 5318 0.396811 CCACATCGGTTAGGATCCCC 59.603 60.000 8.55 1.20 0.00 4.81
2488 5451 9.716531 AGTCACCATAATATACATCAATGACAG 57.283 33.333 0.00 0.00 36.14 3.51
2529 5492 3.073678 CCCTGAACGATGACAATGAACA 58.926 45.455 0.00 0.00 0.00 3.18
2536 5499 3.258372 GCCTATATCCCTGAACGATGACA 59.742 47.826 0.00 0.00 0.00 3.58
2537 5500 3.258372 TGCCTATATCCCTGAACGATGAC 59.742 47.826 0.00 0.00 0.00 3.06
2575 5538 6.263842 ACAACATGACACTGAGATTTGTTGAT 59.736 34.615 16.95 3.73 43.00 2.57
2607 5570 6.993786 TGTGTCTGTACTGATGTTCAAAAA 57.006 33.333 5.69 0.00 0.00 1.94
2608 5571 6.458206 GCTTGTGTCTGTACTGATGTTCAAAA 60.458 38.462 5.69 0.61 0.00 2.44
2609 5572 5.007626 GCTTGTGTCTGTACTGATGTTCAAA 59.992 40.000 5.69 0.00 0.00 2.69
2610 5573 4.511454 GCTTGTGTCTGTACTGATGTTCAA 59.489 41.667 5.69 8.15 0.00 2.69
2611 5574 4.058124 GCTTGTGTCTGTACTGATGTTCA 58.942 43.478 5.69 0.00 0.00 3.18
2612 5575 3.121944 CGCTTGTGTCTGTACTGATGTTC 59.878 47.826 5.69 0.00 0.00 3.18
2613 5576 3.059884 CGCTTGTGTCTGTACTGATGTT 58.940 45.455 5.69 0.00 0.00 2.71
2614 5577 2.677199 CGCTTGTGTCTGTACTGATGT 58.323 47.619 5.69 0.00 0.00 3.06
2615 5578 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
2616 5579 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
2617 5580 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
2618 5581 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
2619 5582 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
2620 5583 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
2621 5584 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
2622 5585 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
2623 5586 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
2624 5587 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
2625 5588 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
2626 5589 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
2627 5590 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
2628 5591 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
2629 5592 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
2630 5593 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
2631 5594 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
2634 5597 4.352039 AGTATATGCGCGTGTATATGAGC 58.648 43.478 24.28 15.73 38.85 4.26
2635 5598 5.569413 TGAGTATATGCGCGTGTATATGAG 58.431 41.667 24.28 0.00 34.71 2.90
2636 5599 5.554822 TGAGTATATGCGCGTGTATATGA 57.445 39.130 24.28 9.82 34.71 2.15
2637 5600 6.202226 AGATGAGTATATGCGCGTGTATATG 58.798 40.000 24.28 0.00 34.71 1.78
2638 5601 6.378710 AGATGAGTATATGCGCGTGTATAT 57.621 37.500 20.79 20.79 37.23 0.86
2639 5602 5.813080 AGATGAGTATATGCGCGTGTATA 57.187 39.130 13.61 9.23 0.00 1.47
2640 5603 4.703645 AGATGAGTATATGCGCGTGTAT 57.296 40.909 13.61 9.22 0.00 2.29
2641 5604 5.813080 ATAGATGAGTATATGCGCGTGTA 57.187 39.130 13.61 7.27 0.00 2.90
2642 5605 4.703645 ATAGATGAGTATATGCGCGTGT 57.296 40.909 13.61 8.52 0.00 4.49
2643 5606 6.430451 TCATATAGATGAGTATATGCGCGTG 58.570 40.000 13.61 0.00 40.80 5.34
2644 5607 6.619801 TCATATAGATGAGTATATGCGCGT 57.380 37.500 8.43 7.55 40.80 6.01
2645 5608 7.410193 GCATTCATATAGATGAGTATATGCGCG 60.410 40.741 15.28 0.00 43.03 6.86
2646 5609 7.383300 TGCATTCATATAGATGAGTATATGCGC 59.617 37.037 21.11 0.00 46.45 6.09
2647 5610 8.697960 GTGCATTCATATAGATGAGTATATGCG 58.302 37.037 21.11 2.29 46.45 4.73
2648 5611 9.538508 TGTGCATTCATATAGATGAGTATATGC 57.461 33.333 20.34 20.34 45.09 3.14
2651 5614 9.860898 GTGTGTGCATTCATATAGATGAGTATA 57.139 33.333 0.00 0.00 43.03 1.47
2652 5615 7.543520 CGTGTGTGCATTCATATAGATGAGTAT 59.456 37.037 0.00 0.00 43.03 2.12
2653 5616 6.863126 CGTGTGTGCATTCATATAGATGAGTA 59.137 38.462 0.00 0.00 43.03 2.59
2654 5617 5.693555 CGTGTGTGCATTCATATAGATGAGT 59.306 40.000 0.00 0.00 43.03 3.41
2655 5618 5.389202 GCGTGTGTGCATTCATATAGATGAG 60.389 44.000 0.00 0.00 37.85 2.90
2656 5619 4.448732 GCGTGTGTGCATTCATATAGATGA 59.551 41.667 0.00 0.00 36.12 2.92
2657 5620 4.211794 TGCGTGTGTGCATTCATATAGATG 59.788 41.667 0.00 0.00 40.62 2.90
2658 5621 4.379652 TGCGTGTGTGCATTCATATAGAT 58.620 39.130 0.00 0.00 40.62 1.98
2659 5622 3.791245 TGCGTGTGTGCATTCATATAGA 58.209 40.909 0.00 0.00 40.62 1.98
2669 5632 2.390306 ATAGGGTGTGCGTGTGTGCA 62.390 55.000 0.00 0.00 43.95 4.57
2670 5633 1.635663 GATAGGGTGTGCGTGTGTGC 61.636 60.000 0.00 0.00 0.00 4.57
2671 5634 1.019278 GGATAGGGTGTGCGTGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
2672 5635 1.295423 GGATAGGGTGTGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
2673 5636 1.449601 GGGATAGGGTGTGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
2674 5637 2.987125 GGGATAGGGTGTGCGTGT 59.013 61.111 0.00 0.00 0.00 4.49
2675 5638 2.202878 CGGGATAGGGTGTGCGTG 60.203 66.667 0.00 0.00 0.00 5.34
2676 5639 3.467226 CCGGGATAGGGTGTGCGT 61.467 66.667 0.00 0.00 0.00 5.24
2677 5640 2.246761 TTTCCGGGATAGGGTGTGCG 62.247 60.000 0.00 0.00 0.00 5.34
2678 5641 0.746923 GTTTCCGGGATAGGGTGTGC 60.747 60.000 0.00 0.00 0.00 4.57
2679 5642 0.461339 CGTTTCCGGGATAGGGTGTG 60.461 60.000 0.00 0.00 0.00 3.82
2680 5643 0.906282 ACGTTTCCGGGATAGGGTGT 60.906 55.000 0.00 0.00 38.78 4.16
2681 5644 0.179092 GACGTTTCCGGGATAGGGTG 60.179 60.000 0.00 0.00 38.78 4.61
2682 5645 0.325016 AGACGTTTCCGGGATAGGGT 60.325 55.000 0.00 2.30 38.78 4.34
2683 5646 0.388294 GAGACGTTTCCGGGATAGGG 59.612 60.000 0.00 0.00 38.78 3.53
2684 5647 0.388294 GGAGACGTTTCCGGGATAGG 59.612 60.000 9.67 1.11 38.78 2.57
2685 5648 1.337387 GAGGAGACGTTTCCGGGATAG 59.663 57.143 18.59 0.00 42.29 2.08
2686 5649 1.396653 GAGGAGACGTTTCCGGGATA 58.603 55.000 18.59 0.00 42.29 2.59
2687 5650 1.328430 GGAGGAGACGTTTCCGGGAT 61.328 60.000 18.59 1.82 42.29 3.85
2688 5651 1.980772 GGAGGAGACGTTTCCGGGA 60.981 63.158 18.59 0.00 42.29 5.14
2689 5652 2.577593 GGAGGAGACGTTTCCGGG 59.422 66.667 18.59 0.00 42.29 5.73
2690 5653 2.280552 TGGGAGGAGACGTTTCCGG 61.281 63.158 18.59 0.00 42.29 5.14
2691 5654 1.080025 GTGGGAGGAGACGTTTCCG 60.080 63.158 18.59 0.00 42.29 4.30
2692 5655 0.037232 CAGTGGGAGGAGACGTTTCC 60.037 60.000 17.16 17.16 37.52 3.13
2693 5656 0.966920 TCAGTGGGAGGAGACGTTTC 59.033 55.000 0.00 0.00 0.00 2.78
2694 5657 1.420430 TTCAGTGGGAGGAGACGTTT 58.580 50.000 0.00 0.00 0.00 3.60
2695 5658 1.276421 CATTCAGTGGGAGGAGACGTT 59.724 52.381 0.00 0.00 0.00 3.99
2696 5659 0.898320 CATTCAGTGGGAGGAGACGT 59.102 55.000 0.00 0.00 0.00 4.34
2697 5660 0.460987 GCATTCAGTGGGAGGAGACG 60.461 60.000 0.00 0.00 0.00 4.18
2698 5661 0.460987 CGCATTCAGTGGGAGGAGAC 60.461 60.000 0.00 0.00 43.02 3.36
2699 5662 1.900351 CGCATTCAGTGGGAGGAGA 59.100 57.895 0.00 0.00 43.02 3.71
2700 5663 1.817099 GCGCATTCAGTGGGAGGAG 60.817 63.158 0.30 0.00 43.02 3.69
2701 5664 1.913951 ATGCGCATTCAGTGGGAGGA 61.914 55.000 19.28 0.00 43.02 3.71
2702 5665 1.442526 GATGCGCATTCAGTGGGAGG 61.443 60.000 26.12 0.00 43.02 4.30
2703 5666 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
2704 5667 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
2705 5668 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
2716 5679 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
2717 5680 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
2718 5681 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
2719 5682 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
2720 5683 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
2721 5684 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
2722 5685 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
2723 5686 6.321181 TCTTGGATTTATTTCAGGATTTCCGG 59.679 38.462 0.00 0.00 42.08 5.14
2724 5687 7.333528 TCTTGGATTTATTTCAGGATTTCCG 57.666 36.000 0.00 0.00 42.08 4.30
2731 5694 8.971321 CGCATTTATTCTTGGATTTATTTCAGG 58.029 33.333 0.00 0.00 0.00 3.86
2732 5695 9.734620 TCGCATTTATTCTTGGATTTATTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
2735 5698 9.868277 TGTTCGCATTTATTCTTGGATTTATTT 57.132 25.926 0.00 0.00 0.00 1.40
2736 5699 9.301153 GTGTTCGCATTTATTCTTGGATTTATT 57.699 29.630 0.00 0.00 0.00 1.40
2737 5700 7.920682 GGTGTTCGCATTTATTCTTGGATTTAT 59.079 33.333 0.00 0.00 0.00 1.40
2738 5701 7.094162 TGGTGTTCGCATTTATTCTTGGATTTA 60.094 33.333 0.00 0.00 0.00 1.40
2739 5702 6.099341 GGTGTTCGCATTTATTCTTGGATTT 58.901 36.000 0.00 0.00 0.00 2.17
2740 5703 5.184864 TGGTGTTCGCATTTATTCTTGGATT 59.815 36.000 0.00 0.00 0.00 3.01
2741 5704 4.704540 TGGTGTTCGCATTTATTCTTGGAT 59.295 37.500 0.00 0.00 0.00 3.41
2742 5705 4.075682 TGGTGTTCGCATTTATTCTTGGA 58.924 39.130 0.00 0.00 0.00 3.53
2743 5706 4.155826 TCTGGTGTTCGCATTTATTCTTGG 59.844 41.667 0.00 0.00 0.00 3.61
2744 5707 5.295431 TCTGGTGTTCGCATTTATTCTTG 57.705 39.130 0.00 0.00 0.00 3.02
2745 5708 5.957842 TTCTGGTGTTCGCATTTATTCTT 57.042 34.783 0.00 0.00 0.00 2.52
2746 5709 5.957842 TTTCTGGTGTTCGCATTTATTCT 57.042 34.783 0.00 0.00 0.00 2.40
2747 5710 8.682128 TTAATTTCTGGTGTTCGCATTTATTC 57.318 30.769 0.00 0.00 0.00 1.75
2748 5711 8.921670 GTTTAATTTCTGGTGTTCGCATTTATT 58.078 29.630 0.00 0.00 0.00 1.40
2749 5712 7.544217 GGTTTAATTTCTGGTGTTCGCATTTAT 59.456 33.333 0.00 0.00 0.00 1.40
2750 5713 6.864165 GGTTTAATTTCTGGTGTTCGCATTTA 59.136 34.615 0.00 0.00 0.00 1.40
2751 5714 5.694458 GGTTTAATTTCTGGTGTTCGCATTT 59.306 36.000 0.00 0.00 0.00 2.32
2752 5715 5.227152 GGTTTAATTTCTGGTGTTCGCATT 58.773 37.500 0.00 0.00 0.00 3.56
2753 5716 4.321675 GGGTTTAATTTCTGGTGTTCGCAT 60.322 41.667 0.00 0.00 0.00 4.73
2754 5717 3.004944 GGGTTTAATTTCTGGTGTTCGCA 59.995 43.478 0.00 0.00 0.00 5.10
2755 5718 3.254903 AGGGTTTAATTTCTGGTGTTCGC 59.745 43.478 0.00 0.00 0.00 4.70
2756 5719 4.320935 CCAGGGTTTAATTTCTGGTGTTCG 60.321 45.833 0.00 0.00 41.21 3.95
2757 5720 5.134202 CCAGGGTTTAATTTCTGGTGTTC 57.866 43.478 0.00 0.00 41.21 3.18
2763 5726 2.671070 GCGCACCAGGGTTTAATTTCTG 60.671 50.000 0.30 0.00 0.00 3.02
2764 5727 1.544246 GCGCACCAGGGTTTAATTTCT 59.456 47.619 0.30 0.00 0.00 2.52
2765 5728 1.544246 AGCGCACCAGGGTTTAATTTC 59.456 47.619 11.47 0.00 0.00 2.17
2766 5729 1.272212 CAGCGCACCAGGGTTTAATTT 59.728 47.619 11.47 0.00 0.00 1.82
2767 5730 0.887933 CAGCGCACCAGGGTTTAATT 59.112 50.000 11.47 0.00 0.00 1.40
2768 5731 0.965363 CCAGCGCACCAGGGTTTAAT 60.965 55.000 11.47 0.00 0.00 1.40
2769 5732 1.602323 CCAGCGCACCAGGGTTTAA 60.602 57.895 11.47 0.00 0.00 1.52
2770 5733 2.033448 CCAGCGCACCAGGGTTTA 59.967 61.111 11.47 0.00 0.00 2.01
2771 5734 3.850098 CTCCAGCGCACCAGGGTTT 62.850 63.158 11.47 0.00 0.00 3.27
2772 5735 4.335647 CTCCAGCGCACCAGGGTT 62.336 66.667 11.47 0.00 0.00 4.11
2774 5737 2.434843 TATCTCCAGCGCACCAGGG 61.435 63.158 11.47 2.63 0.00 4.45
2775 5738 1.227380 GTATCTCCAGCGCACCAGG 60.227 63.158 11.47 5.96 0.00 4.45
2776 5739 1.227380 GGTATCTCCAGCGCACCAG 60.227 63.158 11.47 0.94 35.97 4.00
2777 5740 1.987306 TGGTATCTCCAGCGCACCA 60.987 57.895 11.47 10.15 41.93 4.17
2778 5741 2.900273 TGGTATCTCCAGCGCACC 59.100 61.111 11.47 7.07 41.93 5.01
2785 5748 3.421394 AGAGGGAATGTGGTATCTCCA 57.579 47.619 0.00 0.00 45.01 3.86
2786 5749 4.040584 GGTTAGAGGGAATGTGGTATCTCC 59.959 50.000 0.00 0.00 0.00 3.71
2787 5750 4.654262 TGGTTAGAGGGAATGTGGTATCTC 59.346 45.833 0.00 0.00 0.00 2.75
2788 5751 4.631234 TGGTTAGAGGGAATGTGGTATCT 58.369 43.478 0.00 0.00 0.00 1.98
2789 5752 5.513267 GGATGGTTAGAGGGAATGTGGTATC 60.513 48.000 0.00 0.00 0.00 2.24
2790 5753 4.351111 GGATGGTTAGAGGGAATGTGGTAT 59.649 45.833 0.00 0.00 0.00 2.73
2791 5754 3.714798 GGATGGTTAGAGGGAATGTGGTA 59.285 47.826 0.00 0.00 0.00 3.25
2792 5755 2.509964 GGATGGTTAGAGGGAATGTGGT 59.490 50.000 0.00 0.00 0.00 4.16
2793 5756 2.509548 TGGATGGTTAGAGGGAATGTGG 59.490 50.000 0.00 0.00 0.00 4.17
2794 5757 3.931907 TGGATGGTTAGAGGGAATGTG 57.068 47.619 0.00 0.00 0.00 3.21
2795 5758 3.053619 GGTTGGATGGTTAGAGGGAATGT 60.054 47.826 0.00 0.00 0.00 2.71
2796 5759 3.053693 TGGTTGGATGGTTAGAGGGAATG 60.054 47.826 0.00 0.00 0.00 2.67
2797 5760 3.053619 GTGGTTGGATGGTTAGAGGGAAT 60.054 47.826 0.00 0.00 0.00 3.01
2798 5761 2.307686 GTGGTTGGATGGTTAGAGGGAA 59.692 50.000 0.00 0.00 0.00 3.97
2799 5762 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
2800 5763 1.406887 CGTGGTTGGATGGTTAGAGGG 60.407 57.143 0.00 0.00 0.00 4.30
2801 5764 1.553248 TCGTGGTTGGATGGTTAGAGG 59.447 52.381 0.00 0.00 0.00 3.69
2802 5765 2.233922 ACTCGTGGTTGGATGGTTAGAG 59.766 50.000 0.00 0.00 0.00 2.43
2803 5766 2.253610 ACTCGTGGTTGGATGGTTAGA 58.746 47.619 0.00 0.00 0.00 2.10
2804 5767 2.762535 ACTCGTGGTTGGATGGTTAG 57.237 50.000 0.00 0.00 0.00 2.34
2825 5788 2.356135 ACTATCACAACATGGCGAACC 58.644 47.619 0.00 0.00 0.00 3.62
2826 5789 3.426159 CCAACTATCACAACATGGCGAAC 60.426 47.826 0.00 0.00 0.00 3.95
2827 5790 2.746904 CCAACTATCACAACATGGCGAA 59.253 45.455 0.00 0.00 0.00 4.70
2828 5791 2.290008 ACCAACTATCACAACATGGCGA 60.290 45.455 0.00 0.00 0.00 5.54
2829 5792 2.083774 ACCAACTATCACAACATGGCG 58.916 47.619 0.00 0.00 0.00 5.69
2830 5793 2.423538 GGACCAACTATCACAACATGGC 59.576 50.000 0.00 0.00 0.00 4.40
2831 5794 3.691118 CAGGACCAACTATCACAACATGG 59.309 47.826 0.00 0.00 0.00 3.66
2832 5795 4.578871 TCAGGACCAACTATCACAACATG 58.421 43.478 0.00 0.00 0.00 3.21
2833 5796 4.908601 TCAGGACCAACTATCACAACAT 57.091 40.909 0.00 0.00 0.00 2.71
2834 5797 4.908601 ATCAGGACCAACTATCACAACA 57.091 40.909 0.00 0.00 0.00 3.33
2835 5798 7.361799 GGTTTTATCAGGACCAACTATCACAAC 60.362 40.741 0.00 0.00 33.61 3.32
2836 5799 6.657541 GGTTTTATCAGGACCAACTATCACAA 59.342 38.462 0.00 0.00 33.61 3.33
2837 5800 6.177610 GGTTTTATCAGGACCAACTATCACA 58.822 40.000 0.00 0.00 33.61 3.58
2838 5801 6.093633 GTGGTTTTATCAGGACCAACTATCAC 59.906 42.308 0.00 0.00 44.43 3.06
2839 5802 6.012858 AGTGGTTTTATCAGGACCAACTATCA 60.013 38.462 0.00 0.00 44.43 2.15
2840 5803 6.316390 CAGTGGTTTTATCAGGACCAACTATC 59.684 42.308 0.00 0.00 44.43 2.08
2843 5806 4.141251 ACAGTGGTTTTATCAGGACCAACT 60.141 41.667 0.00 0.00 44.43 3.16
2891 5854 0.829182 AGTTGCAAAGGGGCCTCTTG 60.829 55.000 21.44 14.32 0.00 3.02
2908 5871 4.220821 CACTATGAGTCTGTGGTGGTAAGT 59.779 45.833 5.20 0.00 0.00 2.24
2955 5918 1.936547 GTCATTGGAAGATGGAGTCGC 59.063 52.381 0.00 0.00 0.00 5.19
2980 5943 5.638596 AAGACCGAATTGATGGTAAAACC 57.361 39.130 0.00 0.00 38.99 3.27
2981 5944 7.373778 AGTAAGACCGAATTGATGGTAAAAC 57.626 36.000 0.00 0.00 38.99 2.43
3028 5991 2.232452 CTCTTCGACAGTGGAATGACCT 59.768 50.000 0.00 0.00 39.86 3.85
3076 6039 8.078596 GCTTCATGACAATTTTTACTCTGAACT 58.921 33.333 0.00 0.00 0.00 3.01
3079 6042 7.750229 AGCTTCATGACAATTTTTACTCTGA 57.250 32.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.