Multiple sequence alignment - TraesCS7B01G121300

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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 TraesCS7B01G121300 chr7B 100.000 3022 0 0 1 3022 141803836 141806857 0.000000e+00 5581.0
1 TraesCS7B01G121300 chr7B 79.780 455 66 12 328 763 80091052 80091499 1.050000e-79 307.0
2 TraesCS7B01G121300 chr7B 79.616 417 60 17 1311 1717 143256926 143256525 2.970000e-70 276.0
3 TraesCS7B01G121300 chr7B 79.570 186 35 3 2488 2673 15939526 15939344 2.450000e-26 130.0
4 TraesCS7B01G121300 chr7B 84.615 130 13 5 2251 2374 72052351 72052479 4.090000e-24 122.0
5 TraesCS7B01G121300 chr7B 80.899 89 11 4 2249 2332 521149076 521149163 6.990000e-07 65.8
6 TraesCS7B01G121300 chr7A 91.968 1519 71 23 721 2205 178023878 178025379 0.000000e+00 2082.0
7 TraesCS7B01G121300 chr7A 87.069 464 52 7 232 690 178021475 178021935 4.470000e-143 518.0
8 TraesCS7B01G121300 chr7A 81.264 459 62 14 332 769 97580315 97579860 1.720000e-92 350.0
9 TraesCS7B01G121300 chr7A 81.955 133 18 4 2250 2378 213796840 213796710 1.150000e-19 108.0
10 TraesCS7B01G121300 chr7D 87.259 1766 120 44 53 1760 175926599 175928317 0.000000e+00 1917.0
11 TraesCS7B01G121300 chr7D 92.326 430 23 4 1782 2205 175930118 175930543 1.200000e-168 603.0
12 TraesCS7B01G121300 chr7D 79.525 547 72 22 327 840 207314613 207314074 1.330000e-93 353.0
13 TraesCS7B01G121300 chr7D 79.661 413 69 11 1311 1717 176881916 176881513 1.770000e-72 283.0
14 TraesCS7B01G121300 chr7D 79.193 322 64 3 2502 2823 1035433 1035115 1.410000e-53 220.0
15 TraesCS7B01G121300 chr7D 83.333 126 18 2 2251 2373 575899118 575898993 2.460000e-21 113.0
16 TraesCS7B01G121300 chr5D 83.612 598 80 3 2443 3022 238902155 238902752 2.050000e-151 545.0
17 TraesCS7B01G121300 chr5D 87.907 215 26 0 2808 3022 456566884 456566670 1.390000e-63 254.0
18 TraesCS7B01G121300 chr3D 82.192 584 97 4 2444 3022 68914559 68915140 2.090000e-136 496.0
19 TraesCS7B01G121300 chr3D 82.008 478 64 16 233 690 141649081 141649556 1.310000e-103 387.0
20 TraesCS7B01G121300 chr3D 82.418 455 60 8 328 763 29493493 29493946 2.200000e-101 379.0
21 TraesCS7B01G121300 chr3D 79.558 543 74 22 328 839 123618509 123619045 1.330000e-93 353.0
22 TraesCS7B01G121300 chr3D 83.969 131 14 4 2251 2376 357424665 357424793 5.290000e-23 119.0
23 TraesCS7B01G121300 chr3D 80.000 160 17 7 694 840 389634348 389634191 1.480000e-18 104.0
24 TraesCS7B01G121300 chr3D 80.153 131 17 5 2251 2375 600656308 600656435 4.150000e-14 89.8
25 TraesCS7B01G121300 chrUn 82.637 455 59 8 328 763 223001840 223002293 4.730000e-103 385.0
26 TraesCS7B01G121300 chrUn 80.147 544 72 19 327 839 92407294 92406756 1.020000e-99 374.0
27 TraesCS7B01G121300 chrUn 79.963 544 72 20 327 839 380756276 380756813 1.710000e-97 366.0
28 TraesCS7B01G121300 chrUn 88.785 214 24 0 2809 3022 288446338 288446551 2.310000e-66 263.0
29 TraesCS7B01G121300 chrUn 88.785 214 24 0 2809 3022 292056701 292056914 2.310000e-66 263.0
30 TraesCS7B01G121300 chrUn 88.785 214 24 0 2809 3022 295041101 295040888 2.310000e-66 263.0
31 TraesCS7B01G121300 chr6D 85.054 368 50 5 328 690 451957823 451958190 1.320000e-98 370.0
32 TraesCS7B01G121300 chr4D 81.897 464 59 15 327 769 354141827 354141368 4.760000e-98 368.0
33 TraesCS7B01G121300 chr6A 84.127 378 51 7 328 700 52848311 52847938 1.030000e-94 357.0
34 TraesCS7B01G121300 chr6A 97.222 36 1 0 1694 1729 612928077 612928042 9.050000e-06 62.1
35 TraesCS7B01G121300 chr1D 81.498 454 64 8 328 763 439108431 439108882 3.710000e-94 355.0
36 TraesCS7B01G121300 chr1A 80.306 457 68 10 328 763 535330764 535331219 2.910000e-85 326.0
37 TraesCS7B01G121300 chr3A 78.431 459 63 21 413 841 1295811 1296263 1.790000e-67 267.0
38 TraesCS7B01G121300 chr3A 81.679 131 16 5 2251 2375 730086831 730086959 5.330000e-18 102.0
39 TraesCS7B01G121300 chr3A 88.889 81 8 1 2296 2375 75567061 75567141 6.890000e-17 99.0
40 TraesCS7B01G121300 chr3B 88.837 215 23 1 2808 3022 436518262 436518475 2.310000e-66 263.0
41 TraesCS7B01G121300 chr3B 89.048 210 23 0 2813 3022 561589572 561589781 8.310000e-66 261.0
42 TraesCS7B01G121300 chr3B 79.389 131 19 4 2251 2375 697706869 697706997 5.370000e-13 86.1
43 TraesCS7B01G121300 chr3B 76.761 142 22 8 2231 2362 697484049 697483909 5.410000e-08 69.4
44 TraesCS7B01G121300 chr4A 88.426 216 23 2 2808 3022 584429814 584429600 2.990000e-65 259.0
45 TraesCS7B01G121300 chr2D 82.166 157 14 8 694 839 593800531 593800684 4.090000e-24 122.0
46 TraesCS7B01G121300 chr5A 97.222 36 1 0 1694 1729 600847828 600847793 9.050000e-06 62.1
47 TraesCS7B01G121300 chr2A 97.222 36 1 0 1694 1729 733312967 733312932 9.050000e-06 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 TraesCS7B01G121300 chr7B 141803836 141806857 3021 False 5581 5581 100.0000 1 3022 1 chr7B.!!$F3 3021
1 TraesCS7B01G121300 chr7A 178021475 178025379 3904 False 1300 2082 89.5185 232 2205 2 chr7A.!!$F1 1973
2 TraesCS7B01G121300 chr7D 175926599 175930543 3944 False 1260 1917 89.7925 53 2205 2 chr7D.!!$F1 2152
3 TraesCS7B01G121300 chr7D 207314074 207314613 539 True 353 353 79.5250 327 840 1 chr7D.!!$R3 513
4 TraesCS7B01G121300 chr5D 238902155 238902752 597 False 545 545 83.6120 2443 3022 1 chr5D.!!$F1 579
5 TraesCS7B01G121300 chr3D 68914559 68915140 581 False 496 496 82.1920 2444 3022 1 chr3D.!!$F2 578
6 TraesCS7B01G121300 chr3D 123618509 123619045 536 False 353 353 79.5580 328 839 1 chr3D.!!$F3 511
7 TraesCS7B01G121300 chrUn 92406756 92407294 538 True 374 374 80.1470 327 839 1 chrUn.!!$R1 512
8 TraesCS7B01G121300 chrUn 380756276 380756813 537 False 366 366 79.9630 327 839 1 chrUn.!!$F4 512

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
123 124 0.250038 CCGGCCCATACAGTGATCTG 60.250 60.0 0.0 0.0 46.18 2.90 F
366 378 0.462225 TCTCGTTGTTTTGGCGGTGA 60.462 50.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 5556 0.252696 AGGCGCATATCTCCCCCATA 60.253 55.0 10.83 0.0 0.0 2.74 R
2022 5788 0.738975 CAGCTTAGTCGACCGGATCA 59.261 55.0 9.46 0.0 0.0 2.92 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
50 51 7.884816 TTAAAAGTCAATGACTAACTCTCCG 57.115 36.000 17.04 0.00 42.59 4.63
51 52 5.723672 AAAGTCAATGACTAACTCTCCGA 57.276 39.130 17.04 0.00 42.59 4.55
58 59 2.818432 TGACTAACTCTCCGAGGTCAAC 59.182 50.000 0.00 0.00 30.01 3.18
65 66 4.351938 CCGAGGTCAACGGTCGCA 62.352 66.667 0.00 0.00 44.57 5.10
90 91 5.170748 GCCCATCAGTCAACCAATTTAAAG 58.829 41.667 0.00 0.00 0.00 1.85
99 100 8.379902 CAGTCAACCAATTTAAAGAAAACACAC 58.620 33.333 0.00 0.00 0.00 3.82
118 119 4.108299 TGGCCGGCCCATACAGTG 62.108 66.667 41.75 0.00 39.18 3.66
119 120 3.792736 GGCCGGCCCATACAGTGA 61.793 66.667 36.64 0.00 0.00 3.41
121 122 1.598130 GCCGGCCCATACAGTGATC 60.598 63.158 18.11 0.00 0.00 2.92
123 124 0.250038 CCGGCCCATACAGTGATCTG 60.250 60.000 0.00 0.00 46.18 2.90
126 127 0.882042 GCCCATACAGTGATCTGGCG 60.882 60.000 0.00 0.00 45.14 5.69
149 150 3.194755 TGAGCGCCAGTTACTCTAATTGA 59.805 43.478 2.29 0.00 0.00 2.57
154 155 4.192317 GCCAGTTACTCTAATTGACCCAG 58.808 47.826 0.00 0.00 0.00 4.45
158 159 7.112779 CCAGTTACTCTAATTGACCCAGATTT 58.887 38.462 0.00 0.00 0.00 2.17
199 200 2.643551 CCGTGGACTGGCAAATTCTAT 58.356 47.619 0.00 0.00 0.00 1.98
228 230 1.672356 CTGTTAAGGGCGCTGCAGT 60.672 57.895 16.64 0.00 0.00 4.40
257 268 4.047627 AGGAAATTTTTGATCCCCTCGT 57.952 40.909 0.00 0.00 33.55 4.18
260 271 4.142381 GGAAATTTTTGATCCCCTCGTCTG 60.142 45.833 0.00 0.00 0.00 3.51
267 278 3.314331 CCCCTCGTCTGTGGCTGT 61.314 66.667 0.00 0.00 0.00 4.40
276 287 1.059098 TCTGTGGCTGTCATCTTGGT 58.941 50.000 0.00 0.00 0.00 3.67
289 300 2.449518 TTGGTGCTGGGAGGTGGA 60.450 61.111 0.00 0.00 0.00 4.02
318 330 6.428159 ACTCGCATTTTCAAGAGTTCTATGTT 59.572 34.615 0.00 0.00 40.64 2.71
334 346 8.137437 AGTTCTATGTTCTTTGTCATTTTGTGG 58.863 33.333 0.00 0.00 0.00 4.17
366 378 0.462225 TCTCGTTGTTTTGGCGGTGA 60.462 50.000 0.00 0.00 0.00 4.02
373 385 0.951558 GTTTTGGCGGTGACATGAGT 59.048 50.000 0.00 0.00 0.00 3.41
384 396 4.859798 CGGTGACATGAGTTTAGAGAGTTC 59.140 45.833 0.00 0.00 0.00 3.01
385 397 5.564848 CGGTGACATGAGTTTAGAGAGTTCA 60.565 44.000 0.00 0.00 0.00 3.18
400 413 6.135454 AGAGAGTTCATGTCCTCACATATCT 58.865 40.000 14.06 7.02 41.69 1.98
468 482 4.399004 TGTTGGTTTGATTCTTTGTGGG 57.601 40.909 0.00 0.00 0.00 4.61
494 510 5.244755 TGAAATCTTTCATCGACACCATGA 58.755 37.500 1.28 0.00 41.88 3.07
511 527 8.529424 ACACCATGATGAAGATATTGTGATTT 57.471 30.769 0.00 0.00 0.00 2.17
539 556 2.702478 CTGCACTTCTAGGGGATGATCA 59.298 50.000 0.00 0.00 0.00 2.92
540 557 3.321039 TGCACTTCTAGGGGATGATCAT 58.679 45.455 8.25 8.25 0.00 2.45
574 591 3.736433 CGTTCATCGATCAAGGCTTCTCT 60.736 47.826 0.00 0.00 42.86 3.10
576 593 4.478206 TCATCGATCAAGGCTTCTCTTT 57.522 40.909 0.00 0.00 0.00 2.52
613 633 6.360681 CGACTAAGAGCTTTCAAAAACCATTG 59.639 38.462 0.00 0.00 0.00 2.82
638 658 4.586421 TGATAATGTTGGTGCAGGTGAAAA 59.414 37.500 0.00 0.00 0.00 2.29
657 677 6.908284 GTGAAAAAGTAACAACATCGTTGCTA 59.092 34.615 6.77 0.00 40.40 3.49
668 688 4.827692 ACATCGTTGCTACAGTCCAATTA 58.172 39.130 0.00 0.00 0.00 1.40
685 705 4.698304 CCAATTACAGCCTCTTTACCGAAA 59.302 41.667 0.00 0.00 0.00 3.46
692 727 5.046520 ACAGCCTCTTTACCGAAATCTTAGT 60.047 40.000 0.00 0.00 0.00 2.24
764 2710 9.588096 AATTCTTAGTCATGGGAGTTACTTTTT 57.412 29.630 0.00 0.00 0.00 1.94
865 2825 2.765705 ATTCCCGGACCTGGTGGACT 62.766 60.000 2.82 0.00 37.04 3.85
879 2839 1.004440 GGACTGCTGGCGTCTCTTT 60.004 57.895 13.63 0.00 0.00 2.52
892 2852 3.312697 GCGTCTCTTTGTTCCTTTCTTGT 59.687 43.478 0.00 0.00 0.00 3.16
912 2872 0.528466 CCATGTACGAGCACGCATCT 60.528 55.000 2.62 0.00 43.96 2.90
924 2884 2.265739 GCATCTGAGCACCGGTCA 59.734 61.111 2.59 0.00 37.74 4.02
1021 2981 1.006571 GTCCACATGACACGGACGT 60.007 57.895 0.00 0.00 43.85 4.34
1038 2998 4.683832 GGACGTCAAGAGCAAGTATACAT 58.316 43.478 18.91 0.00 0.00 2.29
1039 2999 4.504461 GGACGTCAAGAGCAAGTATACATG 59.496 45.833 18.91 4.55 0.00 3.21
1040 3000 3.865745 ACGTCAAGAGCAAGTATACATGC 59.134 43.478 22.30 22.30 40.51 4.06
1041 3001 3.865164 CGTCAAGAGCAAGTATACATGCA 59.135 43.478 28.94 10.23 42.43 3.96
1042 3002 4.259970 CGTCAAGAGCAAGTATACATGCAC 60.260 45.833 28.94 23.91 42.43 4.57
1055 3015 7.329471 AAGTATACATGCACTGCATATACTTCG 59.671 37.037 28.08 15.41 46.47 3.79
1584 3562 3.580319 GGAGGCCAAGGTGGTGGT 61.580 66.667 5.01 0.00 40.46 4.16
1729 3708 3.986572 CGTCTACATCGGAGAGTACGTAT 59.013 47.826 0.00 0.00 43.63 3.06
1730 3709 5.048713 TCGTCTACATCGGAGAGTACGTATA 60.049 44.000 0.00 0.00 43.63 1.47
1732 3711 5.060323 GTCTACATCGGAGAGTACGTATACG 59.940 48.000 23.24 23.24 43.63 3.06
1733 3712 3.982475 ACATCGGAGAGTACGTATACGA 58.018 45.455 30.77 12.26 43.63 3.43
1734 3713 4.564041 ACATCGGAGAGTACGTATACGAT 58.436 43.478 30.77 17.05 43.63 3.73
1735 3714 4.883576 CATCGGAGAGTACGTATACGATG 58.116 47.826 30.77 21.49 46.30 3.84
1736 3715 2.733552 TCGGAGAGTACGTATACGATGC 59.266 50.000 30.77 18.47 43.02 3.91
1738 3717 3.922850 CGGAGAGTACGTATACGATGCTA 59.077 47.826 30.77 10.54 43.02 3.49
1739 3718 4.031539 CGGAGAGTACGTATACGATGCTAG 59.968 50.000 30.77 14.33 43.02 3.42
1752 3731 2.219674 CGATGCTAGCTTCGAACAATCC 59.780 50.000 36.43 8.28 43.36 3.01
1755 3734 2.233676 TGCTAGCTTCGAACAATCCTCA 59.766 45.455 17.23 0.00 0.00 3.86
1756 3735 3.118629 TGCTAGCTTCGAACAATCCTCAT 60.119 43.478 17.23 0.00 0.00 2.90
1757 3736 4.099419 TGCTAGCTTCGAACAATCCTCATA 59.901 41.667 17.23 0.00 0.00 2.15
1758 3737 5.221521 TGCTAGCTTCGAACAATCCTCATAT 60.222 40.000 17.23 0.00 0.00 1.78
1759 3738 6.015434 TGCTAGCTTCGAACAATCCTCATATA 60.015 38.462 17.23 0.00 0.00 0.86
1760 3739 6.309251 GCTAGCTTCGAACAATCCTCATATAC 59.691 42.308 7.70 0.00 0.00 1.47
1761 3740 6.161855 AGCTTCGAACAATCCTCATATACA 57.838 37.500 0.00 0.00 0.00 2.29
1762 3741 5.986135 AGCTTCGAACAATCCTCATATACAC 59.014 40.000 0.00 0.00 0.00 2.90
1764 3743 6.292381 GCTTCGAACAATCCTCATATACACAC 60.292 42.308 0.00 0.00 0.00 3.82
1765 3744 6.215495 TCGAACAATCCTCATATACACACA 57.785 37.500 0.00 0.00 0.00 3.72
1773 3777 9.935682 CAATCCTCATATACACACACAATAAAC 57.064 33.333 0.00 0.00 0.00 2.01
1780 3784 6.729391 ATACACACACAATAAACGTATGCA 57.271 33.333 0.00 0.00 0.00 3.96
1796 5556 1.969862 GCAATGTTCTTGCAGGGCT 59.030 52.632 5.13 0.00 44.34 5.19
1933 5693 1.446272 CGGAGGAACGCAGGAAGAC 60.446 63.158 0.00 0.00 0.00 3.01
1986 5752 4.314440 GCTGTGGGCAGTCACCGA 62.314 66.667 0.00 0.00 44.32 4.69
2001 5767 0.392193 ACCGACGACGTCTGATAGGT 60.392 55.000 23.66 19.58 37.88 3.08
2020 5786 2.959372 CGACGTGGAGGTGCAGTA 59.041 61.111 0.00 0.00 0.00 2.74
2021 5787 1.154016 CGACGTGGAGGTGCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
2022 5788 1.863662 CGACGTGGAGGTGCAGTAGT 61.864 60.000 0.00 0.00 0.00 2.73
2044 5810 0.524862 TCCGGTCGACTAAGCTGTTC 59.475 55.000 16.46 0.00 0.00 3.18
2107 5873 7.009540 CAGACTGTTCATTTGTCTTTGGTTTTC 59.990 37.037 0.00 0.00 38.80 2.29
2109 5875 6.813152 ACTGTTCATTTGTCTTTGGTTTTCTG 59.187 34.615 0.00 0.00 0.00 3.02
2111 5877 5.930837 TCATTTGTCTTTGGTTTTCTGGT 57.069 34.783 0.00 0.00 0.00 4.00
2123 5889 4.116961 GGTTTTCTGGTTGGTTTAGTTGC 58.883 43.478 0.00 0.00 0.00 4.17
2138 5904 2.778299 AGTTGCTTCGTTGCCAAGATA 58.222 42.857 0.62 0.00 0.00 1.98
2148 5914 3.194861 GTTGCCAAGATATGTGCGTCTA 58.805 45.455 0.00 0.00 0.00 2.59
2164 5930 2.673833 GTCTAGGTGAACTTGTCGGTG 58.326 52.381 0.00 0.00 0.00 4.94
2184 5950 5.278364 CGGTGTCTATAAAGGAGCGACTATT 60.278 44.000 0.00 0.00 31.90 1.73
2236 6002 3.996032 GCACTTTTGCTAAGATCGACTG 58.004 45.455 6.22 0.00 46.17 3.51
2237 6003 3.679980 GCACTTTTGCTAAGATCGACTGA 59.320 43.478 6.22 0.00 46.17 3.41
2238 6004 4.201666 GCACTTTTGCTAAGATCGACTGAG 60.202 45.833 6.22 0.00 46.17 3.35
2239 6005 5.164233 CACTTTTGCTAAGATCGACTGAGA 58.836 41.667 6.22 0.00 0.00 3.27
2240 6006 5.061560 CACTTTTGCTAAGATCGACTGAGAC 59.938 44.000 6.22 0.00 0.00 3.36
2241 6007 5.047660 ACTTTTGCTAAGATCGACTGAGACT 60.048 40.000 6.22 0.00 0.00 3.24
2242 6008 5.392767 TTTGCTAAGATCGACTGAGACTT 57.607 39.130 0.00 0.00 0.00 3.01
2243 6009 4.624336 TGCTAAGATCGACTGAGACTTC 57.376 45.455 0.00 0.00 0.00 3.01
2244 6010 4.010349 TGCTAAGATCGACTGAGACTTCA 58.990 43.478 0.00 0.00 0.00 3.02
2257 6023 5.697473 TGAGACTTCAGCTCTTATATCCG 57.303 43.478 0.00 0.00 33.57 4.18
2258 6024 5.133941 TGAGACTTCAGCTCTTATATCCGT 58.866 41.667 0.00 0.00 33.57 4.69
2259 6025 5.009110 TGAGACTTCAGCTCTTATATCCGTG 59.991 44.000 0.00 0.00 33.57 4.94
2260 6026 5.133941 AGACTTCAGCTCTTATATCCGTGA 58.866 41.667 0.00 0.00 0.00 4.35
2261 6027 5.240623 AGACTTCAGCTCTTATATCCGTGAG 59.759 44.000 0.00 0.00 0.00 3.51
2262 6028 5.133941 ACTTCAGCTCTTATATCCGTGAGA 58.866 41.667 0.00 0.00 0.00 3.27
2263 6029 5.772672 ACTTCAGCTCTTATATCCGTGAGAT 59.227 40.000 0.00 0.00 39.15 2.75
2264 6030 5.888691 TCAGCTCTTATATCCGTGAGATC 57.111 43.478 0.00 0.00 36.33 2.75
2265 6031 5.565509 TCAGCTCTTATATCCGTGAGATCT 58.434 41.667 0.00 0.00 36.33 2.75
2266 6032 6.007076 TCAGCTCTTATATCCGTGAGATCTT 58.993 40.000 0.00 0.00 36.33 2.40
2267 6033 7.168905 TCAGCTCTTATATCCGTGAGATCTTA 58.831 38.462 0.00 0.00 36.33 2.10
2268 6034 7.119992 TCAGCTCTTATATCCGTGAGATCTTAC 59.880 40.741 7.56 7.56 36.33 2.34
2269 6035 6.943146 AGCTCTTATATCCGTGAGATCTTACA 59.057 38.462 16.95 0.00 36.33 2.41
2270 6036 7.613801 AGCTCTTATATCCGTGAGATCTTACAT 59.386 37.037 16.95 7.00 36.33 2.29
2271 6037 8.247562 GCTCTTATATCCGTGAGATCTTACATT 58.752 37.037 16.95 4.28 36.33 2.71
2272 6038 9.566530 CTCTTATATCCGTGAGATCTTACATTG 57.433 37.037 16.95 5.64 36.33 2.82
2273 6039 9.297037 TCTTATATCCGTGAGATCTTACATTGA 57.703 33.333 16.95 10.31 36.33 2.57
2274 6040 9.566530 CTTATATCCGTGAGATCTTACATTGAG 57.433 37.037 16.95 1.16 36.33 3.02
2275 6041 7.767250 ATATCCGTGAGATCTTACATTGAGA 57.233 36.000 16.95 8.14 36.33 3.27
2276 6042 6.662865 ATCCGTGAGATCTTACATTGAGAT 57.337 37.500 16.95 7.95 36.60 2.75
2277 6043 6.078202 TCCGTGAGATCTTACATTGAGATC 57.922 41.667 16.95 6.09 46.32 2.75
2278 6044 5.010112 TCCGTGAGATCTTACATTGAGATCC 59.990 44.000 16.95 4.01 46.88 3.36
2279 6045 5.221322 CCGTGAGATCTTACATTGAGATCCA 60.221 44.000 16.95 6.05 46.88 3.41
2280 6046 6.453943 CGTGAGATCTTACATTGAGATCCAT 58.546 40.000 16.95 0.00 46.88 3.41
2281 6047 6.365518 CGTGAGATCTTACATTGAGATCCATG 59.634 42.308 16.95 9.19 46.88 3.66
2282 6048 6.147492 GTGAGATCTTACATTGAGATCCATGC 59.853 42.308 12.50 0.81 46.88 4.06
2283 6049 5.558818 AGATCTTACATTGAGATCCATGCC 58.441 41.667 9.76 0.00 46.88 4.40
2284 6050 4.776435 TCTTACATTGAGATCCATGCCA 57.224 40.909 0.00 0.00 0.00 4.92
2285 6051 5.114764 TCTTACATTGAGATCCATGCCAA 57.885 39.130 0.00 0.00 0.00 4.52
2286 6052 5.508567 TCTTACATTGAGATCCATGCCAAA 58.491 37.500 0.00 0.00 0.00 3.28
2287 6053 5.951148 TCTTACATTGAGATCCATGCCAAAA 59.049 36.000 0.00 0.00 0.00 2.44
2288 6054 6.436847 TCTTACATTGAGATCCATGCCAAAAA 59.563 34.615 0.00 0.00 0.00 1.94
2317 6083 9.783081 ATTATTTTTCCTTTTTCTCTTGCATGT 57.217 25.926 0.00 0.00 0.00 3.21
2318 6084 9.612066 TTATTTTTCCTTTTTCTCTTGCATGTT 57.388 25.926 0.00 0.00 0.00 2.71
2320 6086 9.783081 ATTTTTCCTTTTTCTCTTGCATGTTAT 57.217 25.926 0.00 0.00 0.00 1.89
2321 6087 8.592105 TTTTCCTTTTTCTCTTGCATGTTATG 57.408 30.769 0.00 0.00 0.00 1.90
2322 6088 6.899393 TCCTTTTTCTCTTGCATGTTATGT 57.101 33.333 0.00 0.00 0.00 2.29
2323 6089 6.913170 TCCTTTTTCTCTTGCATGTTATGTC 58.087 36.000 0.00 0.00 0.00 3.06
2324 6090 6.489700 TCCTTTTTCTCTTGCATGTTATGTCA 59.510 34.615 0.00 0.00 0.00 3.58
2325 6091 6.583806 CCTTTTTCTCTTGCATGTTATGTCAC 59.416 38.462 0.00 0.00 0.00 3.67
2326 6092 6.882610 TTTTCTCTTGCATGTTATGTCACT 57.117 33.333 0.00 0.00 0.00 3.41
2327 6093 6.882610 TTTCTCTTGCATGTTATGTCACTT 57.117 33.333 0.00 0.00 0.00 3.16
2328 6094 7.977789 TTTCTCTTGCATGTTATGTCACTTA 57.022 32.000 0.00 0.00 0.00 2.24
2329 6095 7.977789 TTCTCTTGCATGTTATGTCACTTAA 57.022 32.000 0.00 0.00 0.00 1.85
2330 6096 7.364522 TCTCTTGCATGTTATGTCACTTAAC 57.635 36.000 6.63 6.63 0.00 2.01
2331 6097 7.161404 TCTCTTGCATGTTATGTCACTTAACT 58.839 34.615 13.24 0.00 32.09 2.24
2332 6098 7.118245 TCTCTTGCATGTTATGTCACTTAACTG 59.882 37.037 13.24 10.21 32.09 3.16
2333 6099 6.934083 TCTTGCATGTTATGTCACTTAACTGA 59.066 34.615 13.24 0.00 32.09 3.41
2334 6100 7.607607 TCTTGCATGTTATGTCACTTAACTGAT 59.392 33.333 13.24 0.00 32.09 2.90
2335 6101 8.785329 TTGCATGTTATGTCACTTAACTGATA 57.215 30.769 13.24 0.00 32.09 2.15
2336 6102 8.196802 TGCATGTTATGTCACTTAACTGATAC 57.803 34.615 13.24 0.00 32.09 2.24
2337 6103 8.040727 TGCATGTTATGTCACTTAACTGATACT 58.959 33.333 13.24 0.00 32.09 2.12
2338 6104 8.883731 GCATGTTATGTCACTTAACTGATACTT 58.116 33.333 13.24 0.00 32.09 2.24
2354 6120 8.864069 ACTGATACTTGATTAAATCTCAGTCG 57.136 34.615 0.00 0.00 38.05 4.18
2355 6121 8.687242 ACTGATACTTGATTAAATCTCAGTCGA 58.313 33.333 0.00 0.00 38.05 4.20
2356 6122 8.858003 TGATACTTGATTAAATCTCAGTCGAC 57.142 34.615 7.70 7.70 0.00 4.20
2357 6123 8.687242 TGATACTTGATTAAATCTCAGTCGACT 58.313 33.333 13.58 13.58 0.00 4.18
2358 6124 9.522804 GATACTTGATTAAATCTCAGTCGACTT 57.477 33.333 17.26 2.43 0.00 3.01
2360 6126 8.918961 ACTTGATTAAATCTCAGTCGACTTAG 57.081 34.615 17.26 18.13 0.00 2.18
2361 6127 8.740906 ACTTGATTAAATCTCAGTCGACTTAGA 58.259 33.333 26.94 26.94 31.55 2.10
2362 6128 9.743057 CTTGATTAAATCTCAGTCGACTTAGAT 57.257 33.333 28.55 28.55 38.26 1.98
2363 6129 9.737427 TTGATTAAATCTCAGTCGACTTAGATC 57.263 33.333 32.06 23.53 36.28 2.75
2364 6130 9.126151 TGATTAAATCTCAGTCGACTTAGATCT 57.874 33.333 32.06 24.95 36.28 2.75
2367 6133 9.616156 TTAAATCTCAGTCGACTTAGATCTAGT 57.384 33.333 32.06 22.29 36.28 2.57
2368 6134 7.724305 AATCTCAGTCGACTTAGATCTAGTC 57.276 40.000 32.06 16.32 36.28 2.59
2369 6135 6.223351 TCTCAGTCGACTTAGATCTAGTCA 57.777 41.667 22.49 1.46 33.20 3.41
2370 6136 6.044046 TCTCAGTCGACTTAGATCTAGTCAC 58.956 44.000 22.49 18.74 33.20 3.67
2371 6137 5.731591 TCAGTCGACTTAGATCTAGTCACA 58.268 41.667 17.26 11.60 33.20 3.58
2372 6138 5.581479 TCAGTCGACTTAGATCTAGTCACAC 59.419 44.000 17.26 18.28 33.20 3.82
2373 6139 4.877251 AGTCGACTTAGATCTAGTCACACC 59.123 45.833 13.58 11.98 33.20 4.16
2374 6140 4.035441 GTCGACTTAGATCTAGTCACACCC 59.965 50.000 21.75 8.84 33.20 4.61
2375 6141 4.080469 TCGACTTAGATCTAGTCACACCCT 60.080 45.833 21.75 0.00 33.20 4.34
2376 6142 4.641094 CGACTTAGATCTAGTCACACCCTT 59.359 45.833 21.75 0.00 33.20 3.95
2377 6143 5.125739 CGACTTAGATCTAGTCACACCCTTT 59.874 44.000 21.75 0.00 33.20 3.11
2378 6144 6.350277 CGACTTAGATCTAGTCACACCCTTTT 60.350 42.308 21.75 0.00 33.20 2.27
2379 6145 6.937392 ACTTAGATCTAGTCACACCCTTTTC 58.063 40.000 2.02 0.00 0.00 2.29
2380 6146 6.726764 ACTTAGATCTAGTCACACCCTTTTCT 59.273 38.462 2.02 0.00 0.00 2.52
2381 6147 5.669164 AGATCTAGTCACACCCTTTTCTC 57.331 43.478 0.00 0.00 0.00 2.87
2382 6148 4.468153 AGATCTAGTCACACCCTTTTCTCC 59.532 45.833 0.00 0.00 0.00 3.71
2383 6149 3.583228 TCTAGTCACACCCTTTTCTCCA 58.417 45.455 0.00 0.00 0.00 3.86
2384 6150 3.971305 TCTAGTCACACCCTTTTCTCCAA 59.029 43.478 0.00 0.00 0.00 3.53
2385 6151 3.884037 AGTCACACCCTTTTCTCCAAT 57.116 42.857 0.00 0.00 0.00 3.16
2386 6152 3.490348 AGTCACACCCTTTTCTCCAATG 58.510 45.455 0.00 0.00 0.00 2.82
2387 6153 3.117512 AGTCACACCCTTTTCTCCAATGT 60.118 43.478 0.00 0.00 0.00 2.71
2388 6154 4.104102 AGTCACACCCTTTTCTCCAATGTA 59.896 41.667 0.00 0.00 0.00 2.29
2389 6155 4.825085 GTCACACCCTTTTCTCCAATGTAA 59.175 41.667 0.00 0.00 0.00 2.41
2390 6156 5.300792 GTCACACCCTTTTCTCCAATGTAAA 59.699 40.000 0.00 0.00 0.00 2.01
2391 6157 6.015434 GTCACACCCTTTTCTCCAATGTAAAT 60.015 38.462 0.00 0.00 0.00 1.40
2392 6158 6.208599 TCACACCCTTTTCTCCAATGTAAATC 59.791 38.462 0.00 0.00 0.00 2.17
2393 6159 6.209391 CACACCCTTTTCTCCAATGTAAATCT 59.791 38.462 0.00 0.00 0.00 2.40
2394 6160 6.782494 ACACCCTTTTCTCCAATGTAAATCTT 59.218 34.615 0.00 0.00 0.00 2.40
2395 6161 7.290014 ACACCCTTTTCTCCAATGTAAATCTTT 59.710 33.333 0.00 0.00 0.00 2.52
2396 6162 8.150296 CACCCTTTTCTCCAATGTAAATCTTTT 58.850 33.333 0.00 0.00 0.00 2.27
2397 6163 8.713971 ACCCTTTTCTCCAATGTAAATCTTTTT 58.286 29.630 0.00 0.00 0.00 1.94
2491 6258 2.115266 CCCGCCACCACTTTCCTT 59.885 61.111 0.00 0.00 0.00 3.36
2562 6332 2.126463 CGACCTTCTTCTCGCGCA 60.126 61.111 8.75 0.00 0.00 6.09
2565 6335 1.148759 GACCTTCTTCTCGCGCATCC 61.149 60.000 8.75 0.00 0.00 3.51
2567 6337 1.226688 CTTCTTCTCGCGCATCCGA 60.227 57.895 8.75 0.00 36.29 4.55
2584 6354 1.944709 CCGATGCTCAAGATCATTGCA 59.055 47.619 0.00 0.11 38.05 4.08
2585 6355 2.356695 CCGATGCTCAAGATCATTGCAA 59.643 45.455 0.00 0.00 37.20 4.08
2587 6357 3.181504 CGATGCTCAAGATCATTGCAACA 60.182 43.478 0.00 0.00 37.20 3.33
2590 6360 3.189910 TGCTCAAGATCATTGCAACAGTC 59.810 43.478 0.00 0.00 0.00 3.51
2612 6383 1.950216 CGATCTTGATCTCCTCGGTGA 59.050 52.381 8.70 0.00 0.00 4.02
2637 6408 2.029964 GGACAACGACGGCTGGAA 59.970 61.111 0.00 0.00 0.00 3.53
2643 6414 2.047274 CGACGGCTGGAATGTGGT 60.047 61.111 0.00 0.00 0.00 4.16
2653 6424 0.535335 GGAATGTGGTGGCGAGTCTA 59.465 55.000 0.00 0.00 0.00 2.59
2663 6434 1.655329 GCGAGTCTATAGCCGCAGT 59.345 57.895 20.89 0.00 46.04 4.40
2690 6461 1.731613 GCGACGACGACCATGTTGA 60.732 57.895 12.29 0.00 42.66 3.18
2705 6476 3.631453 TTGAAGCCGCTCAACATCT 57.369 47.368 0.00 0.00 30.31 2.90
2722 6493 1.218047 CTGGTTCGGCTTCGGATCA 59.782 57.895 0.00 0.00 30.79 2.92
2725 6496 1.445582 GTTCGGCTTCGGATCACGT 60.446 57.895 0.00 0.00 44.69 4.49
2752 6523 1.164662 CCTGGCCTTGATCTGCATCG 61.165 60.000 3.32 0.00 0.00 3.84
2792 6563 4.722700 CCTGGACTTGGCGGTGGG 62.723 72.222 0.00 0.00 0.00 4.61
2804 6575 1.995626 CGGTGGGGGTCATCTCCTT 60.996 63.158 0.00 0.00 0.00 3.36
2850 6638 1.893801 GATCCGTCATCTATTCCCGGT 59.106 52.381 0.00 0.00 39.62 5.28
2906 6694 3.050339 CCAACGGCAAGCAATGGT 58.950 55.556 0.00 0.00 0.00 3.55
2957 6745 4.421058 GCATCATCGTGTAACTACTGTCA 58.579 43.478 0.00 0.00 31.75 3.58
2965 6753 4.700700 GTGTAACTACTGTCAACCCACTT 58.299 43.478 0.00 0.00 0.00 3.16
2966 6754 5.507817 CGTGTAACTACTGTCAACCCACTTA 60.508 44.000 0.00 0.00 31.75 2.24
2969 6757 5.562298 AACTACTGTCAACCCACTTATGT 57.438 39.130 0.00 0.00 0.00 2.29
2972 6760 4.164843 ACTGTCAACCCACTTATGTTGT 57.835 40.909 0.00 0.00 41.92 3.32
2977 6765 3.142951 CAACCCACTTATGTTGTTCCGA 58.857 45.455 0.00 0.00 37.62 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.770828 CGGAGAGTTAGTCATTGACTTTTAAAA 58.229 33.333 23.53 9.43 40.28 1.52
25 26 8.145767 TCGGAGAGTTAGTCATTGACTTTTAAA 58.854 33.333 23.53 9.79 40.28 1.52
26 27 7.663827 TCGGAGAGTTAGTCATTGACTTTTAA 58.336 34.615 23.53 10.13 40.28 1.52
27 28 7.223260 TCGGAGAGTTAGTCATTGACTTTTA 57.777 36.000 23.53 4.18 40.28 1.52
28 29 6.097915 TCGGAGAGTTAGTCATTGACTTTT 57.902 37.500 23.53 10.26 40.28 2.27
29 30 5.723672 TCGGAGAGTTAGTCATTGACTTT 57.276 39.130 23.53 10.59 40.28 2.66
49 50 2.805353 CTGCGACCGTTGACCTCG 60.805 66.667 0.00 0.00 0.00 4.63
50 51 2.432628 CCTGCGACCGTTGACCTC 60.433 66.667 0.00 0.00 0.00 3.85
51 52 4.681978 GCCTGCGACCGTTGACCT 62.682 66.667 0.00 0.00 0.00 3.85
65 66 0.706433 ATTGGTTGACTGATGGGCCT 59.294 50.000 4.53 0.00 0.00 5.19
90 91 3.039134 CCGGCCAGGTGTGTTTTC 58.961 61.111 2.24 0.00 34.51 2.29
99 100 4.569180 CTGTATGGGCCGGCCAGG 62.569 72.222 44.46 23.08 44.97 4.45
109 110 1.136891 TCACGCCAGATCACTGTATGG 59.863 52.381 0.00 0.00 42.05 2.74
126 127 2.649331 TTAGAGTAACTGGCGCTCAC 57.351 50.000 7.64 0.00 0.00 3.51
140 141 8.792830 TCAGTTTAAATCTGGGTCAATTAGAG 57.207 34.615 14.02 0.00 34.15 2.43
141 142 9.581289 TTTCAGTTTAAATCTGGGTCAATTAGA 57.419 29.630 14.02 0.00 34.15 2.10
180 181 5.811399 TTAATAGAATTTGCCAGTCCACG 57.189 39.130 0.00 0.00 0.00 4.94
199 200 7.254852 CAGCGCCCTTAACAGAATTAATTTAA 58.745 34.615 2.29 0.00 0.00 1.52
207 209 0.322456 TGCAGCGCCCTTAACAGAAT 60.322 50.000 2.29 0.00 0.00 2.40
209 211 1.375908 CTGCAGCGCCCTTAACAGA 60.376 57.895 2.29 0.00 0.00 3.41
213 215 2.625823 GCAACTGCAGCGCCCTTAA 61.626 57.895 15.27 0.00 41.59 1.85
228 230 3.185246 TCAAAAATTTCCTTGCGGCAA 57.815 38.095 15.55 15.55 0.00 4.52
248 259 2.039624 AGCCACAGACGAGGGGAT 59.960 61.111 0.00 0.00 0.00 3.85
257 268 1.059098 ACCAAGATGACAGCCACAGA 58.941 50.000 0.00 0.00 0.00 3.41
260 271 0.607489 AGCACCAAGATGACAGCCAC 60.607 55.000 0.00 0.00 0.00 5.01
267 278 0.842030 ACCTCCCAGCACCAAGATGA 60.842 55.000 0.00 0.00 35.00 2.92
276 287 3.940480 TCCCTCCACCTCCCAGCA 61.940 66.667 0.00 0.00 0.00 4.41
289 300 2.039084 ACTCTTGAAAATGCGAGTCCCT 59.961 45.455 0.00 0.00 31.51 4.20
318 330 9.844257 AAATTTATTCCCACAAAATGACAAAGA 57.156 25.926 0.00 0.00 0.00 2.52
373 385 6.611613 ATGTGAGGACATGAACTCTCTAAA 57.388 37.500 17.68 4.65 41.52 1.85
384 396 7.267857 TGAGTAACAAGATATGTGAGGACATG 58.732 38.462 0.00 0.00 42.99 3.21
385 397 7.343057 TCTGAGTAACAAGATATGTGAGGACAT 59.657 37.037 0.00 0.00 42.99 3.06
426 439 7.279758 CCAACAAATAAAGTTTGACACACCAAT 59.720 33.333 7.44 0.00 33.83 3.16
494 510 5.009010 GGCCGTCAAATCACAATATCTTCAT 59.991 40.000 0.00 0.00 0.00 2.57
511 527 1.591703 CTAGAAGTGCAGGCCGTCA 59.408 57.895 0.00 0.00 0.00 4.35
539 556 0.539986 ATGAACGTACTTGGGCCGAT 59.460 50.000 0.00 0.00 0.00 4.18
540 557 0.108520 GATGAACGTACTTGGGCCGA 60.109 55.000 0.00 0.00 0.00 5.54
583 600 5.845985 TTTGAAAGCTCTTAGTCGTCATG 57.154 39.130 0.00 0.00 0.00 3.07
587 605 4.879545 TGGTTTTTGAAAGCTCTTAGTCGT 59.120 37.500 0.00 0.00 0.00 4.34
593 611 6.405538 TCAACAATGGTTTTTGAAAGCTCTT 58.594 32.000 0.00 0.00 34.21 2.85
595 613 6.849588 ATCAACAATGGTTTTTGAAAGCTC 57.150 33.333 0.00 0.00 34.21 4.09
596 614 8.776470 CATTATCAACAATGGTTTTTGAAAGCT 58.224 29.630 4.53 0.00 34.21 3.74
613 633 3.505680 TCACCTGCACCAACATTATCAAC 59.494 43.478 0.00 0.00 0.00 3.18
638 658 5.054477 ACTGTAGCAACGATGTTGTTACTT 58.946 37.500 26.00 16.11 37.13 2.24
657 677 4.373156 AAAGAGGCTGTAATTGGACTGT 57.627 40.909 0.00 0.00 0.00 3.55
668 688 3.983044 AGATTTCGGTAAAGAGGCTGT 57.017 42.857 0.00 0.00 0.00 4.40
711 746 5.948742 TGAAATTTCTTGGGAACACCTTT 57.051 34.783 18.64 0.00 42.67 3.11
833 2793 4.097437 GGTCCGGGAATAACAGGATTTTTC 59.903 45.833 0.00 0.00 35.00 2.29
865 2825 0.884704 GGAACAAAGAGACGCCAGCA 60.885 55.000 0.00 0.00 0.00 4.41
879 2839 4.062293 CGTACATGGACAAGAAAGGAACA 58.938 43.478 9.21 0.00 0.00 3.18
892 2852 0.527600 GATGCGTGCTCGTACATGGA 60.528 55.000 10.18 0.00 39.49 3.41
912 2872 0.531974 GAACAACTGACCGGTGCTCA 60.532 55.000 14.63 2.16 0.00 4.26
924 2884 7.173390 GTCTTCTATGTTTAGCAAGGAACAACT 59.827 37.037 0.00 0.00 39.03 3.16
1021 2981 4.872124 CAGTGCATGTATACTTGCTCTTGA 59.128 41.667 30.44 16.59 43.53 3.02
1038 2998 3.518634 TGTCGAAGTATATGCAGTGCA 57.481 42.857 22.22 22.22 44.86 4.57
1039 2999 5.235186 AGAAATGTCGAAGTATATGCAGTGC 59.765 40.000 8.58 8.58 0.00 4.40
1040 3000 6.699204 AGAGAAATGTCGAAGTATATGCAGTG 59.301 38.462 0.00 0.00 0.00 3.66
1041 3001 6.810911 AGAGAAATGTCGAAGTATATGCAGT 58.189 36.000 0.00 0.00 0.00 4.40
1042 3002 7.223582 ACAAGAGAAATGTCGAAGTATATGCAG 59.776 37.037 0.00 0.00 0.00 4.41
1055 3015 3.722082 CGCGCTTGTACAAGAGAAATGTC 60.722 47.826 34.61 18.75 40.05 3.06
1090 3050 0.258774 ACATCTTGGTATGGGGTGCC 59.741 55.000 0.00 0.00 0.00 5.01
1091 3051 1.680338 GACATCTTGGTATGGGGTGC 58.320 55.000 0.00 0.00 0.00 5.01
1093 3053 0.837272 CGGACATCTTGGTATGGGGT 59.163 55.000 0.00 0.00 0.00 4.95
1584 3562 0.321919 GAAGGTGGTGAGCATGAGCA 60.322 55.000 0.00 0.00 45.49 4.26
1729 3708 3.497297 TTGTTCGAAGCTAGCATCGTA 57.503 42.857 33.48 25.40 38.18 3.43
1730 3709 2.363788 TTGTTCGAAGCTAGCATCGT 57.636 45.000 33.48 10.66 38.18 3.73
1732 3711 3.462021 AGGATTGTTCGAAGCTAGCATC 58.538 45.455 18.83 14.15 0.00 3.91
1733 3712 3.118629 TGAGGATTGTTCGAAGCTAGCAT 60.119 43.478 18.83 4.30 0.00 3.79
1734 3713 2.233676 TGAGGATTGTTCGAAGCTAGCA 59.766 45.455 18.83 0.00 0.00 3.49
1735 3714 2.893637 TGAGGATTGTTCGAAGCTAGC 58.106 47.619 6.62 6.62 0.00 3.42
1736 3715 7.327275 GTGTATATGAGGATTGTTCGAAGCTAG 59.673 40.741 0.00 0.00 0.00 3.42
1738 3717 5.986135 GTGTATATGAGGATTGTTCGAAGCT 59.014 40.000 0.00 0.00 0.00 3.74
1739 3718 5.753438 TGTGTATATGAGGATTGTTCGAAGC 59.247 40.000 0.00 0.00 0.00 3.86
1755 3734 8.426881 TGCATACGTTTATTGTGTGTGTATAT 57.573 30.769 0.00 0.00 31.85 0.86
1756 3735 7.829378 TGCATACGTTTATTGTGTGTGTATA 57.171 32.000 0.00 0.00 31.85 1.47
1757 3736 6.729391 TGCATACGTTTATTGTGTGTGTAT 57.271 33.333 0.00 0.00 31.85 2.29
1758 3737 6.541111 TTGCATACGTTTATTGTGTGTGTA 57.459 33.333 0.00 0.00 31.85 2.90
1759 3738 5.425577 TTGCATACGTTTATTGTGTGTGT 57.574 34.783 0.00 0.00 31.85 3.72
1760 3739 5.855925 ACATTGCATACGTTTATTGTGTGTG 59.144 36.000 0.00 0.00 31.85 3.82
1761 3740 6.007936 ACATTGCATACGTTTATTGTGTGT 57.992 33.333 0.00 0.00 31.85 3.72
1762 3741 6.801377 AGAACATTGCATACGTTTATTGTGTG 59.199 34.615 0.00 0.00 0.00 3.82
1764 3743 7.656468 CAAGAACATTGCATACGTTTATTGTG 58.344 34.615 0.00 0.00 0.00 3.33
1765 3744 6.307800 GCAAGAACATTGCATACGTTTATTGT 59.692 34.615 7.67 0.00 44.34 2.71
1780 3784 2.381911 CCATAGCCCTGCAAGAACATT 58.618 47.619 0.00 0.00 34.07 2.71
1796 5556 0.252696 AGGCGCATATCTCCCCCATA 60.253 55.000 10.83 0.00 0.00 2.74
1986 5752 1.022982 TCGCACCTATCAGACGTCGT 61.023 55.000 10.46 0.00 0.00 4.34
2001 5767 4.662961 CTGCACCTCCACGTCGCA 62.663 66.667 0.00 0.00 0.00 5.10
2020 5786 0.739561 GCTTAGTCGACCGGATCACT 59.260 55.000 9.46 8.89 0.00 3.41
2021 5787 0.739561 AGCTTAGTCGACCGGATCAC 59.260 55.000 9.46 0.00 0.00 3.06
2022 5788 0.738975 CAGCTTAGTCGACCGGATCA 59.261 55.000 9.46 0.00 0.00 2.92
2044 5810 0.786581 GAGATGATACGTGCATGGCG 59.213 55.000 11.36 1.75 0.00 5.69
2107 5873 2.616842 ACGAAGCAACTAAACCAACCAG 59.383 45.455 0.00 0.00 0.00 4.00
2109 5875 3.368495 CAACGAAGCAACTAAACCAACC 58.632 45.455 0.00 0.00 0.00 3.77
2111 5877 2.223618 GGCAACGAAGCAACTAAACCAA 60.224 45.455 6.23 0.00 35.83 3.67
2123 5889 2.537529 CGCACATATCTTGGCAACGAAG 60.538 50.000 0.00 0.00 42.51 3.79
2138 5904 2.037251 ACAAGTTCACCTAGACGCACAT 59.963 45.455 0.00 0.00 0.00 3.21
2148 5914 1.120530 AGACACCGACAAGTTCACCT 58.879 50.000 0.00 0.00 0.00 4.00
2216 5982 5.061560 GTCTCAGTCGATCTTAGCAAAAGTG 59.938 44.000 0.00 0.00 0.00 3.16
2217 5983 5.047660 AGTCTCAGTCGATCTTAGCAAAAGT 60.048 40.000 0.00 0.00 0.00 2.66
2218 5984 5.406649 AGTCTCAGTCGATCTTAGCAAAAG 58.593 41.667 0.00 0.00 0.00 2.27
2219 5985 5.392767 AGTCTCAGTCGATCTTAGCAAAA 57.607 39.130 0.00 0.00 0.00 2.44
2220 5986 5.048013 TGAAGTCTCAGTCGATCTTAGCAAA 60.048 40.000 0.00 0.00 0.00 3.68
2221 5987 4.459337 TGAAGTCTCAGTCGATCTTAGCAA 59.541 41.667 0.00 0.00 0.00 3.91
2222 5988 4.010349 TGAAGTCTCAGTCGATCTTAGCA 58.990 43.478 0.00 0.00 0.00 3.49
2223 5989 4.597079 CTGAAGTCTCAGTCGATCTTAGC 58.403 47.826 0.00 0.00 43.64 3.09
2235 6001 5.009110 CACGGATATAAGAGCTGAAGTCTCA 59.991 44.000 0.00 0.00 33.15 3.27
2236 6002 5.239744 TCACGGATATAAGAGCTGAAGTCTC 59.760 44.000 0.00 0.00 0.00 3.36
2237 6003 5.133941 TCACGGATATAAGAGCTGAAGTCT 58.866 41.667 0.00 0.00 0.00 3.24
2238 6004 5.239744 TCTCACGGATATAAGAGCTGAAGTC 59.760 44.000 0.00 0.00 0.00 3.01
2239 6005 5.133941 TCTCACGGATATAAGAGCTGAAGT 58.866 41.667 0.00 0.00 0.00 3.01
2240 6006 5.697473 TCTCACGGATATAAGAGCTGAAG 57.303 43.478 0.00 0.00 0.00 3.02
2241 6007 6.007076 AGATCTCACGGATATAAGAGCTGAA 58.993 40.000 0.00 0.00 33.53 3.02
2242 6008 5.565509 AGATCTCACGGATATAAGAGCTGA 58.434 41.667 0.00 0.00 33.53 4.26
2243 6009 5.895636 AGATCTCACGGATATAAGAGCTG 57.104 43.478 0.00 0.00 33.53 4.24
2244 6010 6.943146 TGTAAGATCTCACGGATATAAGAGCT 59.057 38.462 0.00 0.00 36.13 4.09
2245 6011 7.147143 TGTAAGATCTCACGGATATAAGAGC 57.853 40.000 0.00 0.00 34.33 4.09
2246 6012 9.566530 CAATGTAAGATCTCACGGATATAAGAG 57.433 37.037 0.00 0.00 34.33 2.85
2247 6013 9.297037 TCAATGTAAGATCTCACGGATATAAGA 57.703 33.333 0.00 0.00 34.33 2.10
2248 6014 9.566530 CTCAATGTAAGATCTCACGGATATAAG 57.433 37.037 0.00 0.00 34.33 1.73
2249 6015 9.297037 TCTCAATGTAAGATCTCACGGATATAA 57.703 33.333 0.00 0.00 34.33 0.98
2250 6016 8.863872 TCTCAATGTAAGATCTCACGGATATA 57.136 34.615 0.00 0.00 34.33 0.86
2251 6017 7.767250 TCTCAATGTAAGATCTCACGGATAT 57.233 36.000 0.00 0.00 34.33 1.63
2252 6018 7.094162 GGATCTCAATGTAAGATCTCACGGATA 60.094 40.741 11.66 0.00 45.56 2.59
2253 6019 6.295011 GGATCTCAATGTAAGATCTCACGGAT 60.295 42.308 11.66 0.00 45.56 4.18
2254 6020 5.010112 GGATCTCAATGTAAGATCTCACGGA 59.990 44.000 11.66 0.00 45.56 4.69
2255 6021 5.221322 TGGATCTCAATGTAAGATCTCACGG 60.221 44.000 11.66 0.00 45.56 4.94
2256 6022 5.836347 TGGATCTCAATGTAAGATCTCACG 58.164 41.667 11.66 0.00 45.56 4.35
2257 6023 6.147492 GCATGGATCTCAATGTAAGATCTCAC 59.853 42.308 11.66 0.00 45.56 3.51
2258 6024 6.228995 GCATGGATCTCAATGTAAGATCTCA 58.771 40.000 11.66 8.95 45.56 3.27
2259 6025 5.642919 GGCATGGATCTCAATGTAAGATCTC 59.357 44.000 11.66 4.61 45.56 2.75
2260 6026 5.072736 TGGCATGGATCTCAATGTAAGATCT 59.927 40.000 11.66 0.00 45.56 2.75
2261 6027 5.311265 TGGCATGGATCTCAATGTAAGATC 58.689 41.667 4.85 4.85 45.54 2.75
2262 6028 5.314718 TGGCATGGATCTCAATGTAAGAT 57.685 39.130 0.00 0.00 36.19 2.40
2263 6029 4.776435 TGGCATGGATCTCAATGTAAGA 57.224 40.909 0.00 0.00 0.00 2.10
2264 6030 5.840243 TTTGGCATGGATCTCAATGTAAG 57.160 39.130 0.00 0.00 0.00 2.34
2265 6031 6.602410 TTTTTGGCATGGATCTCAATGTAA 57.398 33.333 0.00 0.00 0.00 2.41
2291 6057 9.783081 ACATGCAAGAGAAAAAGGAAAAATAAT 57.217 25.926 0.00 0.00 0.00 1.28
2292 6058 9.612066 AACATGCAAGAGAAAAAGGAAAAATAA 57.388 25.926 0.00 0.00 0.00 1.40
2294 6060 9.783081 ATAACATGCAAGAGAAAAAGGAAAAAT 57.217 25.926 0.00 0.00 0.00 1.82
2295 6061 9.044150 CATAACATGCAAGAGAAAAAGGAAAAA 57.956 29.630 0.00 0.00 0.00 1.94
2296 6062 8.203485 ACATAACATGCAAGAGAAAAAGGAAAA 58.797 29.630 0.00 0.00 0.00 2.29
2297 6063 7.725251 ACATAACATGCAAGAGAAAAAGGAAA 58.275 30.769 0.00 0.00 0.00 3.13
2298 6064 7.014134 TGACATAACATGCAAGAGAAAAAGGAA 59.986 33.333 0.00 0.00 0.00 3.36
2299 6065 6.489700 TGACATAACATGCAAGAGAAAAAGGA 59.510 34.615 0.00 0.00 0.00 3.36
2300 6066 6.583806 GTGACATAACATGCAAGAGAAAAAGG 59.416 38.462 0.00 0.00 0.00 3.11
2301 6067 7.365741 AGTGACATAACATGCAAGAGAAAAAG 58.634 34.615 0.00 0.00 0.00 2.27
2302 6068 7.275888 AGTGACATAACATGCAAGAGAAAAA 57.724 32.000 0.00 0.00 0.00 1.94
2303 6069 6.882610 AGTGACATAACATGCAAGAGAAAA 57.117 33.333 0.00 0.00 0.00 2.29
2304 6070 6.882610 AAGTGACATAACATGCAAGAGAAA 57.117 33.333 0.00 0.00 0.00 2.52
2305 6071 7.661437 AGTTAAGTGACATAACATGCAAGAGAA 59.339 33.333 12.48 0.00 36.04 2.87
2306 6072 7.118245 CAGTTAAGTGACATAACATGCAAGAGA 59.882 37.037 12.48 0.00 36.04 3.10
2307 6073 7.118245 TCAGTTAAGTGACATAACATGCAAGAG 59.882 37.037 12.48 0.00 36.04 2.85
2308 6074 6.934083 TCAGTTAAGTGACATAACATGCAAGA 59.066 34.615 12.48 0.00 36.04 3.02
2309 6075 7.132694 TCAGTTAAGTGACATAACATGCAAG 57.867 36.000 12.48 0.00 36.04 4.01
2310 6076 7.686438 ATCAGTTAAGTGACATAACATGCAA 57.314 32.000 15.17 0.00 36.04 4.08
2311 6077 8.040727 AGTATCAGTTAAGTGACATAACATGCA 58.959 33.333 15.17 0.00 36.04 3.96
2312 6078 8.425577 AGTATCAGTTAAGTGACATAACATGC 57.574 34.615 15.17 1.97 36.04 4.06
2328 6094 9.307121 CGACTGAGATTTAATCAAGTATCAGTT 57.693 33.333 20.20 10.01 46.61 3.16
2330 6096 8.963130 GTCGACTGAGATTTAATCAAGTATCAG 58.037 37.037 8.70 15.18 42.35 2.90
2331 6097 8.687242 AGTCGACTGAGATTTAATCAAGTATCA 58.313 33.333 19.30 1.28 31.25 2.15
2332 6098 9.522804 AAGTCGACTGAGATTTAATCAAGTATC 57.477 33.333 20.85 0.00 31.25 2.24
2335 6101 8.740906 TCTAAGTCGACTGAGATTTAATCAAGT 58.259 33.333 26.12 9.85 28.46 3.16
2336 6102 9.743057 ATCTAAGTCGACTGAGATTTAATCAAG 57.257 33.333 31.94 5.48 40.50 3.02
2337 6103 9.737427 GATCTAAGTCGACTGAGATTTAATCAA 57.263 33.333 35.67 14.11 42.82 2.57
2338 6104 9.126151 AGATCTAAGTCGACTGAGATTTAATCA 57.874 33.333 35.67 14.75 42.82 2.57
2341 6107 9.616156 ACTAGATCTAAGTCGACTGAGATTTAA 57.384 33.333 35.67 25.02 42.82 1.52
2342 6108 9.263538 GACTAGATCTAAGTCGACTGAGATTTA 57.736 37.037 35.67 31.93 42.82 1.40
2343 6109 7.771361 TGACTAGATCTAAGTCGACTGAGATTT 59.229 37.037 35.67 32.42 42.82 2.17
2344 6110 7.225931 GTGACTAGATCTAAGTCGACTGAGATT 59.774 40.741 35.67 27.65 42.82 2.40
2345 6111 6.704493 GTGACTAGATCTAAGTCGACTGAGAT 59.296 42.308 35.88 35.88 44.90 2.75
2346 6112 6.044046 GTGACTAGATCTAAGTCGACTGAGA 58.956 44.000 30.58 30.58 37.84 3.27
2347 6113 5.813157 TGTGACTAGATCTAAGTCGACTGAG 59.187 44.000 22.32 22.32 35.51 3.35
2348 6114 5.581479 GTGTGACTAGATCTAAGTCGACTGA 59.419 44.000 20.85 13.61 35.51 3.41
2349 6115 5.220700 GGTGTGACTAGATCTAAGTCGACTG 60.221 48.000 20.85 7.79 35.51 3.51
2350 6116 4.877251 GGTGTGACTAGATCTAAGTCGACT 59.123 45.833 13.58 13.58 35.51 4.18
2351 6117 4.035441 GGGTGTGACTAGATCTAAGTCGAC 59.965 50.000 7.70 7.70 35.51 4.20
2352 6118 4.080469 AGGGTGTGACTAGATCTAAGTCGA 60.080 45.833 18.98 10.88 35.51 4.20
2353 6119 4.200874 AGGGTGTGACTAGATCTAAGTCG 58.799 47.826 18.98 6.54 35.51 4.18
2354 6120 6.532988 AAAGGGTGTGACTAGATCTAAGTC 57.467 41.667 18.14 18.14 0.00 3.01
2355 6121 6.726764 AGAAAAGGGTGTGACTAGATCTAAGT 59.273 38.462 3.57 4.41 0.00 2.24
2356 6122 7.176589 AGAAAAGGGTGTGACTAGATCTAAG 57.823 40.000 3.57 1.21 0.00 2.18
2357 6123 6.154706 GGAGAAAAGGGTGTGACTAGATCTAA 59.845 42.308 3.57 0.00 0.00 2.10
2358 6124 5.657302 GGAGAAAAGGGTGTGACTAGATCTA 59.343 44.000 1.69 1.69 0.00 1.98
2359 6125 4.468153 GGAGAAAAGGGTGTGACTAGATCT 59.532 45.833 0.00 0.00 0.00 2.75
2360 6126 4.223032 TGGAGAAAAGGGTGTGACTAGATC 59.777 45.833 0.00 0.00 0.00 2.75
2361 6127 4.168101 TGGAGAAAAGGGTGTGACTAGAT 58.832 43.478 0.00 0.00 0.00 1.98
2362 6128 3.583228 TGGAGAAAAGGGTGTGACTAGA 58.417 45.455 0.00 0.00 0.00 2.43
2363 6129 4.351874 TTGGAGAAAAGGGTGTGACTAG 57.648 45.455 0.00 0.00 0.00 2.57
2364 6130 4.104102 ACATTGGAGAAAAGGGTGTGACTA 59.896 41.667 0.00 0.00 0.00 2.59
2365 6131 3.117512 ACATTGGAGAAAAGGGTGTGACT 60.118 43.478 0.00 0.00 0.00 3.41
2366 6132 3.222603 ACATTGGAGAAAAGGGTGTGAC 58.777 45.455 0.00 0.00 0.00 3.67
2367 6133 3.593442 ACATTGGAGAAAAGGGTGTGA 57.407 42.857 0.00 0.00 0.00 3.58
2368 6134 5.782893 TTTACATTGGAGAAAAGGGTGTG 57.217 39.130 0.00 0.00 0.00 3.82
2369 6135 6.314917 AGATTTACATTGGAGAAAAGGGTGT 58.685 36.000 0.00 0.00 0.00 4.16
2370 6136 6.840780 AGATTTACATTGGAGAAAAGGGTG 57.159 37.500 0.00 0.00 0.00 4.61
2371 6137 7.855784 AAAGATTTACATTGGAGAAAAGGGT 57.144 32.000 0.00 0.00 0.00 4.34
2423 6189 9.959721 GCCCTGGTCATTTTTATATATAGAGAA 57.040 33.333 0.00 0.00 0.00 2.87
2424 6190 8.258007 CGCCCTGGTCATTTTTATATATAGAGA 58.742 37.037 0.00 0.00 0.00 3.10
2425 6191 8.041323 ACGCCCTGGTCATTTTTATATATAGAG 58.959 37.037 0.00 0.00 0.00 2.43
2426 6192 7.913789 ACGCCCTGGTCATTTTTATATATAGA 58.086 34.615 0.00 0.00 0.00 1.98
2427 6193 7.280205 GGACGCCCTGGTCATTTTTATATATAG 59.720 40.741 0.00 0.00 38.70 1.31
2428 6194 7.107542 GGACGCCCTGGTCATTTTTATATATA 58.892 38.462 0.00 0.00 38.70 0.86
2429 6195 5.944007 GGACGCCCTGGTCATTTTTATATAT 59.056 40.000 0.00 0.00 38.70 0.86
2430 6196 5.310451 GGACGCCCTGGTCATTTTTATATA 58.690 41.667 0.00 0.00 38.70 0.86
2431 6197 4.142038 GGACGCCCTGGTCATTTTTATAT 58.858 43.478 0.00 0.00 38.70 0.86
2432 6198 3.547746 GGACGCCCTGGTCATTTTTATA 58.452 45.455 0.00 0.00 38.70 0.98
2433 6199 2.375146 GGACGCCCTGGTCATTTTTAT 58.625 47.619 0.00 0.00 38.70 1.40
2434 6200 1.614850 GGGACGCCCTGGTCATTTTTA 60.615 52.381 7.58 0.00 41.34 1.52
2435 6201 0.898326 GGGACGCCCTGGTCATTTTT 60.898 55.000 7.58 0.00 41.34 1.94
2436 6202 1.304134 GGGACGCCCTGGTCATTTT 60.304 57.895 7.58 0.00 41.34 1.82
2437 6203 2.355115 GGGACGCCCTGGTCATTT 59.645 61.111 7.58 0.00 41.34 2.32
2438 6204 3.728373 GGGGACGCCCTGGTCATT 61.728 66.667 13.58 0.00 44.66 2.57
2540 6307 1.214062 CGAGAAGAAGGTCGCTGCT 59.786 57.895 0.00 0.00 0.00 4.24
2547 6314 1.153549 GGATGCGCGAGAAGAAGGT 60.154 57.895 12.10 0.00 0.00 3.50
2549 6316 0.596083 ATCGGATGCGCGAGAAGAAG 60.596 55.000 12.10 0.00 0.00 2.85
2562 6332 2.812591 GCAATGATCTTGAGCATCGGAT 59.187 45.455 1.72 0.00 38.61 4.18
2565 6335 3.181504 TGTTGCAATGATCTTGAGCATCG 60.182 43.478 0.59 0.00 38.61 3.84
2567 6337 3.762288 ACTGTTGCAATGATCTTGAGCAT 59.238 39.130 0.59 0.00 34.87 3.79
2579 6349 2.086869 CAAGATCGGGACTGTTGCAAT 58.913 47.619 0.59 0.00 0.00 3.56
2584 6354 2.432510 GGAGATCAAGATCGGGACTGTT 59.567 50.000 4.54 0.00 42.48 3.16
2585 6355 2.035632 GGAGATCAAGATCGGGACTGT 58.964 52.381 4.54 0.00 42.48 3.55
2587 6357 2.593026 GAGGAGATCAAGATCGGGACT 58.407 52.381 4.54 2.43 42.48 3.85
2612 6383 1.809619 CGTCGTTGTCCGCCATCAT 60.810 57.895 0.00 0.00 36.19 2.45
2637 6408 1.341531 GCTATAGACTCGCCACCACAT 59.658 52.381 3.21 0.00 0.00 3.21
2643 6414 1.796190 CTGCGGCTATAGACTCGCCA 61.796 60.000 23.03 14.65 46.51 5.69
2675 6446 0.949105 GGCTTCAACATGGTCGTCGT 60.949 55.000 0.00 0.00 0.00 4.34
2678 6449 2.325082 GCGGCTTCAACATGGTCGT 61.325 57.895 0.00 0.00 0.00 4.34
2681 6452 0.537143 TTGAGCGGCTTCAACATGGT 60.537 50.000 2.97 0.00 32.39 3.55
2690 6461 0.250901 AACCAGATGTTGAGCGGCTT 60.251 50.000 2.97 0.00 35.31 4.35
2702 6473 0.105039 GATCCGAAGCCGAACCAGAT 59.895 55.000 0.00 0.00 38.22 2.90
2705 6476 1.079405 GTGATCCGAAGCCGAACCA 60.079 57.895 0.00 0.00 38.22 3.67
2738 6509 2.630317 GCGCGATGCAGATCAAGG 59.370 61.111 12.10 0.00 45.45 3.61
2768 6539 4.410400 CCAAGTCCAGGGTCGCCC 62.410 72.222 6.80 6.80 45.90 6.13
2843 6631 4.367023 CCGACTCGCAACCGGGAA 62.367 66.667 6.32 0.00 36.99 3.97
2850 6638 0.681887 TATGTCTCCCCGACTCGCAA 60.682 55.000 0.00 0.00 43.25 4.85
2874 6662 1.153353 GTTGGCTCGGTTTTCATCGA 58.847 50.000 0.00 0.00 0.00 3.59
2877 6665 2.253513 CCGTTGGCTCGGTTTTCAT 58.746 52.632 12.11 0.00 44.77 2.57
2897 6685 0.879839 GCAAAACGCCACCATTGCTT 60.880 50.000 2.33 0.00 43.58 3.91
2898 6686 1.300853 GCAAAACGCCACCATTGCT 60.301 52.632 2.33 0.00 43.58 3.91
2940 6728 3.575256 TGGGTTGACAGTAGTTACACGAT 59.425 43.478 0.00 0.00 0.00 3.73
2957 6745 3.408634 CTCGGAACAACATAAGTGGGTT 58.591 45.455 0.00 0.00 32.10 4.11
2965 6753 2.290450 GGGTTTCCCTCGGAACAACATA 60.290 50.000 0.00 0.00 41.87 2.29
2966 6754 1.546998 GGGTTTCCCTCGGAACAACAT 60.547 52.381 0.00 0.00 41.87 2.71


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

AutoCloner maintained by Alex Coulton.