Multiple sequence alignment - TraesCS3D01G219900

Loading Multiple Alignment...

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 TraesCS3D01G219900 chr3D 100.000 3123 0 0 3048 6170 299908800 299911922 0.000000e+00 5768.0
1 TraesCS3D01G219900 chr3D 100.000 2805 0 0 1 2805 299905753 299908557 0.000000e+00 5180.0
2 TraesCS3D01G219900 chr3D 95.880 631 25 1 1 631 246893657 246893028 0.000000e+00 1020.0
3 TraesCS3D01G219900 chr3D 95.873 630 25 1 2 631 558000923 558000295 0.000000e+00 1018.0
4 TraesCS3D01G219900 chr3A 91.558 1682 68 24 4522 6170 435804271 435802631 0.000000e+00 2252.0
5 TraesCS3D01G219900 chr3A 97.508 1284 31 1 3127 4410 435806638 435805356 0.000000e+00 2193.0
6 TraesCS3D01G219900 chr3A 93.005 1501 55 13 882 2352 435808923 435807443 0.000000e+00 2145.0
7 TraesCS3D01G219900 chr3A 88.163 811 53 10 3899 4688 575786367 575787155 0.000000e+00 926.0
8 TraesCS3D01G219900 chr3A 93.111 450 25 2 3161 3605 511209246 511208798 0.000000e+00 654.0
9 TraesCS3D01G219900 chr3A 91.646 395 20 6 2413 2805 435807435 435807052 9.100000e-148 534.0
10 TraesCS3D01G219900 chr3A 94.203 69 4 0 740 808 435809116 435809048 8.460000e-19 106.0
11 TraesCS3D01G219900 chr3A 95.312 64 3 0 4409 4472 435805082 435805019 1.090000e-17 102.0
12 TraesCS3D01G219900 chr3A 97.059 34 1 0 852 885 435808980 435808947 2.400000e-04 58.4
13 TraesCS3D01G219900 chr3B 94.126 1498 50 10 882 2345 421240460 421238967 0.000000e+00 2244.0
14 TraesCS3D01G219900 chr3B 97.990 1244 18 4 3180 4422 421237777 421236540 0.000000e+00 2152.0
15 TraesCS3D01G219900 chr3B 95.856 724 21 6 4663 5383 421236542 421235825 0.000000e+00 1162.0
16 TraesCS3D01G219900 chr3B 93.647 425 16 3 3633 4057 393256300 393256713 5.250000e-175 625.0
17 TraesCS3D01G219900 chr3B 93.176 425 19 2 3633 4057 430924349 430923935 3.160000e-172 616.0
18 TraesCS3D01G219900 chr3B 92.627 434 19 5 3633 4065 51768893 51769314 4.090000e-171 612.0
19 TraesCS3D01G219900 chr3B 91.879 431 22 4 5571 6001 421229420 421229003 1.920000e-164 590.0
20 TraesCS3D01G219900 chr3B 86.189 391 17 6 2435 2805 421238680 421238307 7.500000e-104 388.0
21 TraesCS3D01G219900 chr3B 95.954 173 7 0 5998 6170 421228956 421228784 1.310000e-71 281.0
22 TraesCS3D01G219900 chr3B 93.243 74 3 2 656 727 421240731 421240658 2.350000e-19 108.0
23 TraesCS3D01G219900 chr3B 93.651 63 3 1 4627 4688 393256715 393256777 6.590000e-15 93.5
24 TraesCS3D01G219900 chr3B 90.476 63 6 0 746 808 421240660 421240598 3.960000e-12 84.2
25 TraesCS3D01G219900 chr3B 97.436 39 1 0 852 890 421240534 421240496 3.990000e-07 67.6
26 TraesCS3D01G219900 chr5D 98.732 631 8 0 1 631 285861080 285860450 0.000000e+00 1122.0
27 TraesCS3D01G219900 chr7D 98.257 631 11 0 1 631 403564639 403565269 0.000000e+00 1105.0
28 TraesCS3D01G219900 chr1B 97.930 628 13 0 2 629 340612814 340612187 0.000000e+00 1088.0
29 TraesCS3D01G219900 chr2A 96.032 630 23 2 2 630 625086729 625087357 0.000000e+00 1024.0
30 TraesCS3D01G219900 chr2A 92.222 630 46 3 1 630 510289087 510288461 0.000000e+00 889.0
31 TraesCS3D01G219900 chr5A 87.004 831 58 20 3892 4688 679161733 679160919 0.000000e+00 891.0
32 TraesCS3D01G219900 chr2D 91.772 632 44 4 1 631 147911917 147912541 0.000000e+00 872.0
33 TraesCS3D01G219900 chr6B 91.139 632 55 1 1 632 189526563 189525933 0.000000e+00 856.0
34 TraesCS3D01G219900 chr1D 95.281 445 20 1 3161 3605 356420417 356420860 0.000000e+00 704.0
35 TraesCS3D01G219900 chr1D 93.548 248 14 2 3161 3407 209727680 209727926 9.770000e-98 368.0
36 TraesCS3D01G219900 chr1D 96.651 209 7 0 3398 3606 209727979 209728187 1.270000e-91 348.0
37 TraesCS3D01G219900 chr7A 93.708 445 27 1 3161 3605 47710519 47710076 0.000000e+00 665.0
38 TraesCS3D01G219900 chr6A 93.556 450 23 2 3161 3605 474449234 474448786 0.000000e+00 665.0
39 TraesCS3D01G219900 chr6A 93.939 429 20 2 3182 3605 474879068 474878641 1.450000e-180 643.0
40 TraesCS3D01G219900 chr2B 93.176 425 19 2 3633 4057 782976096 782975682 3.160000e-172 616.0
41 TraesCS3D01G219900 chr2B 92.706 425 21 2 3633 4057 782991064 782990650 6.840000e-169 604.0
42 TraesCS3D01G219900 chr2B 92.488 426 21 3 3633 4057 782851609 782851194 3.180000e-167 599.0
43 TraesCS3D01G219900 chr7B 92.610 433 20 4 3633 4065 677531254 677531674 4.090000e-171 612.0
44 TraesCS3D01G219900 chr7B 95.238 63 2 1 4627 4688 4990111 4990173 1.420000e-16 99.0
45 TraesCS3D01G219900 chr5B 91.917 433 23 4 3633 4065 686451800 686452220 4.120000e-166 595.0
46 TraesCS3D01G219900 chr5B 94.606 241 12 1 3161 3401 203063629 203063390 7.550000e-99 372.0
47 TraesCS3D01G219900 chr5B 96.135 207 8 0 3398 3604 203063310 203063104 7.660000e-89 339.0
48 TraesCS3D01G219900 chr1A 91.481 270 11 4 3796 4065 58292401 58292144 1.640000e-95 361.0


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 TraesCS3D01G219900 chr3D 299905753 299911922 6169 False 5474.000000 5768 100.000000 1 6170 2 chr3D.!!$F1 6169
1 TraesCS3D01G219900 chr3D 246893028 246893657 629 True 1020.000000 1020 95.880000 1 631 1 chr3D.!!$R1 630
2 TraesCS3D01G219900 chr3D 558000295 558000923 628 True 1018.000000 1018 95.873000 2 631 1 chr3D.!!$R2 629
3 TraesCS3D01G219900 chr3A 435802631 435809116 6485 True 1055.771429 2252 94.327286 740 6170 7 chr3A.!!$R2 5430
4 TraesCS3D01G219900 chr3A 575786367 575787155 788 False 926.000000 926 88.163000 3899 4688 1 chr3A.!!$F1 789
5 TraesCS3D01G219900 chr3B 421235825 421240731 4906 True 886.542857 2244 93.616571 656 5383 7 chr3B.!!$R3 4727
6 TraesCS3D01G219900 chr3B 421228784 421229420 636 True 435.500000 590 93.916500 5571 6170 2 chr3B.!!$R2 599
7 TraesCS3D01G219900 chr5D 285860450 285861080 630 True 1122.000000 1122 98.732000 1 631 1 chr5D.!!$R1 630
8 TraesCS3D01G219900 chr7D 403564639 403565269 630 False 1105.000000 1105 98.257000 1 631 1 chr7D.!!$F1 630
9 TraesCS3D01G219900 chr1B 340612187 340612814 627 True 1088.000000 1088 97.930000 2 629 1 chr1B.!!$R1 627
10 TraesCS3D01G219900 chr2A 625086729 625087357 628 False 1024.000000 1024 96.032000 2 630 1 chr2A.!!$F1 628
11 TraesCS3D01G219900 chr2A 510288461 510289087 626 True 889.000000 889 92.222000 1 630 1 chr2A.!!$R1 629
12 TraesCS3D01G219900 chr5A 679160919 679161733 814 True 891.000000 891 87.004000 3892 4688 1 chr5A.!!$R1 796
13 TraesCS3D01G219900 chr2D 147911917 147912541 624 False 872.000000 872 91.772000 1 631 1 chr2D.!!$F1 630
14 TraesCS3D01G219900 chr6B 189525933 189526563 630 True 856.000000 856 91.139000 1 632 1 chr6B.!!$R1 631
15 TraesCS3D01G219900 chr1D 209727680 209728187 507 False 358.000000 368 95.099500 3161 3606 2 chr1D.!!$F2 445
16 TraesCS3D01G219900 chr5B 203063104 203063629 525 True 355.500000 372 95.370500 3161 3604 2 chr5B.!!$R1 443


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
667 669 0.108019 GTCGGTGGAGTCAAAACCCT 59.892 55.000 0.0 0.0 0.00 4.34 F
777 779 0.185175 AACCACGGAGAAAAGCCCTT 59.815 50.000 0.0 0.0 0.00 3.95 F
2322 2468 0.179048 CTGGCTGGATATGGTTCGCA 60.179 55.000 0.0 0.0 0.00 5.10 F
2339 2485 1.003233 CGCACCTTCTAACCCCTTCTT 59.997 52.381 0.0 0.0 0.00 2.52 F
3104 3648 1.205893 TGTTGCCTTGTTGGTTTGACC 59.794 47.619 0.0 0.0 39.22 4.02 F
4980 6914 1.154413 GTTGGTCATCGTGCTTGCG 60.154 57.895 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2449 0.179048 TGCGAACCATATCCAGCCAG 60.179 55.000 0.00 0.00 0.00 4.85 R
2409 2680 2.308866 ACAAGGTACCCTTCCATTCTGG 59.691 50.000 8.74 0.00 42.67 3.86 R
3125 3669 0.035725 TGCTCTCCAATGGACAGCAG 60.036 55.000 24.99 8.03 45.97 4.24 R
3707 4627 1.218316 GGTAGCAAGGTCCCTCACG 59.782 63.158 0.00 0.00 0.00 4.35 R
5013 6947 1.956477 TCTTTGGCCAAGCTTGAGAAC 59.044 47.619 28.05 14.12 31.70 3.01 R
5841 7797 0.999406 ACGCACGTACATGCAATCTC 59.001 50.000 15.00 0.00 46.47 2.75 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
647 649 2.755952 AAATGATGGCCCTAACCTCC 57.244 50.000 0.00 0.00 0.00 4.30
648 650 0.474184 AATGATGGCCCTAACCTCCG 59.526 55.000 0.00 0.00 0.00 4.63
649 651 0.694444 ATGATGGCCCTAACCTCCGT 60.694 55.000 0.00 0.00 0.00 4.69
650 652 1.335132 TGATGGCCCTAACCTCCGTC 61.335 60.000 0.00 0.00 36.64 4.79
651 653 2.365095 GATGGCCCTAACCTCCGTCG 62.365 65.000 0.00 0.00 0.00 5.12
652 654 3.846430 GGCCCTAACCTCCGTCGG 61.846 72.222 4.39 4.39 0.00 4.79
653 655 3.073101 GCCCTAACCTCCGTCGGT 61.073 66.667 11.88 0.00 39.48 4.69
654 656 2.890371 CCCTAACCTCCGTCGGTG 59.110 66.667 11.88 8.95 37.36 4.94
655 657 2.718073 CCCTAACCTCCGTCGGTGG 61.718 68.421 26.94 26.94 41.65 4.61
656 658 1.679977 CCTAACCTCCGTCGGTGGA 60.680 63.158 33.37 15.02 38.51 4.02
663 665 2.126064 TCCGTCGGTGGAGTCAAAA 58.874 52.632 11.88 0.00 33.05 2.44
666 668 1.226030 CGTCGGTGGAGTCAAAACCC 61.226 60.000 0.00 0.00 0.00 4.11
667 669 0.108019 GTCGGTGGAGTCAAAACCCT 59.892 55.000 0.00 0.00 0.00 4.34
686 688 2.232452 CCTATTCTCGCCCTAGGTCATG 59.768 54.545 8.29 0.00 0.00 3.07
688 690 1.686325 TTCTCGCCCTAGGTCATGGC 61.686 60.000 8.29 2.20 41.85 4.40
692 694 3.142393 CCCTAGGTCATGGCCTCG 58.858 66.667 25.34 17.43 39.94 4.63
724 726 6.749923 ATTCATCAGGTGCTCTTCTAAAAC 57.250 37.500 0.00 0.00 0.00 2.43
725 727 4.579869 TCATCAGGTGCTCTTCTAAAACC 58.420 43.478 0.00 0.00 0.00 3.27
726 728 4.287067 TCATCAGGTGCTCTTCTAAAACCT 59.713 41.667 0.00 0.00 41.99 3.50
727 729 4.706842 TCAGGTGCTCTTCTAAAACCTT 57.293 40.909 0.00 0.00 39.24 3.50
728 730 5.048846 TCAGGTGCTCTTCTAAAACCTTT 57.951 39.130 0.00 0.00 39.24 3.11
729 731 5.445964 TCAGGTGCTCTTCTAAAACCTTTT 58.554 37.500 0.00 0.00 39.24 2.27
730 732 5.891551 TCAGGTGCTCTTCTAAAACCTTTTT 59.108 36.000 0.00 0.00 39.24 1.94
777 779 0.185175 AACCACGGAGAAAAGCCCTT 59.815 50.000 0.00 0.00 0.00 3.95
780 782 1.604604 CACGGAGAAAAGCCCTTGAA 58.395 50.000 0.00 0.00 0.00 2.69
787 789 4.281941 GGAGAAAAGCCCTTGAAGTTGAAT 59.718 41.667 0.00 0.00 0.00 2.57
796 798 5.291971 CCCTTGAAGTTGAATTTGAACTGG 58.708 41.667 1.89 0.00 33.85 4.00
808 810 1.757682 TGAACTGGCTTCCACGTTTT 58.242 45.000 0.00 0.00 29.77 2.43
809 811 2.096248 TGAACTGGCTTCCACGTTTTT 58.904 42.857 0.00 0.00 29.77 1.94
1692 1826 4.283337 TCTTCTACACCGTCATATTCCCA 58.717 43.478 0.00 0.00 0.00 4.37
1710 1844 1.656652 CATTCATCGCCTTCTTCGGT 58.343 50.000 0.00 0.00 0.00 4.69
1963 2097 3.243839 ACCTTGGAATGTGCAAATGTCAC 60.244 43.478 0.00 0.00 35.14 3.67
2064 2198 7.042051 TGGTTATTCGAGAACAAAACTTCTCTG 60.042 37.037 12.65 2.39 42.82 3.35
2066 2200 5.968387 TTCGAGAACAAAACTTCTCTGTC 57.032 39.130 7.22 0.00 42.82 3.51
2082 2216 4.396478 TCTCTGTCTCAGAATGGTTAGACG 59.604 45.833 1.22 0.00 39.53 4.18
2100 2234 4.122776 AGACGGCTGATGATGACATAAAC 58.877 43.478 0.00 0.00 36.82 2.01
2105 2239 4.067896 GCTGATGATGACATAAACGGGAT 58.932 43.478 0.00 0.00 36.82 3.85
2120 2254 2.271800 CGGGATGTGCTCTTTGTAGTC 58.728 52.381 0.00 0.00 0.00 2.59
2213 2359 4.430007 TGCTTTCTGCTACGAATATCGTT 58.570 39.130 10.91 0.00 46.58 3.85
2297 2443 8.980143 ACTGGTTGTGTATATTTGTTTTATGC 57.020 30.769 0.00 0.00 0.00 3.14
2303 2449 8.749841 TGTGTATATTTGTTTTATGCAACACC 57.250 30.769 6.92 0.00 36.36 4.16
2322 2468 0.179048 CTGGCTGGATATGGTTCGCA 60.179 55.000 0.00 0.00 0.00 5.10
2339 2485 1.003233 CGCACCTTCTAACCCCTTCTT 59.997 52.381 0.00 0.00 0.00 2.52
2352 2623 9.589461 TCTAACCCCTTCTTAGATAGTTATGAG 57.411 37.037 0.00 0.00 0.00 2.90
2353 2624 6.673839 ACCCCTTCTTAGATAGTTATGAGC 57.326 41.667 0.00 0.00 0.00 4.26
2355 2626 6.615726 ACCCCTTCTTAGATAGTTATGAGCAA 59.384 38.462 0.00 0.00 0.00 3.91
2356 2627 7.293535 ACCCCTTCTTAGATAGTTATGAGCAAT 59.706 37.037 0.00 0.00 0.00 3.56
2368 2639 7.313951 AGTTATGAGCAATTTAGTCTTGAGC 57.686 36.000 0.00 0.00 0.00 4.26
2369 2640 6.881065 AGTTATGAGCAATTTAGTCTTGAGCA 59.119 34.615 0.00 0.00 0.00 4.26
2370 2641 7.391554 AGTTATGAGCAATTTAGTCTTGAGCAA 59.608 33.333 0.00 0.00 0.00 3.91
2371 2642 6.579666 ATGAGCAATTTAGTCTTGAGCAAA 57.420 33.333 0.00 0.00 0.00 3.68
2372 2643 6.005583 TGAGCAATTTAGTCTTGAGCAAAG 57.994 37.500 0.00 0.00 37.22 2.77
2373 2644 4.802999 AGCAATTTAGTCTTGAGCAAAGC 58.197 39.130 0.00 0.00 35.69 3.51
2374 2645 4.522022 AGCAATTTAGTCTTGAGCAAAGCT 59.478 37.500 0.00 0.00 43.88 3.74
2375 2646 5.707298 AGCAATTTAGTCTTGAGCAAAGCTA 59.293 36.000 0.00 0.00 39.88 3.32
2376 2647 6.207417 AGCAATTTAGTCTTGAGCAAAGCTAA 59.793 34.615 0.00 9.71 39.88 3.09
2377 2648 7.031975 GCAATTTAGTCTTGAGCAAAGCTAAT 58.968 34.615 12.37 0.00 39.88 1.73
2378 2649 7.008992 GCAATTTAGTCTTGAGCAAAGCTAATG 59.991 37.037 12.37 0.00 39.88 1.90
2379 2650 6.500684 TTTAGTCTTGAGCAAAGCTAATGG 57.499 37.500 12.37 0.00 39.88 3.16
2380 2651 4.026356 AGTCTTGAGCAAAGCTAATGGT 57.974 40.909 4.00 4.00 39.88 3.55
2381 2652 5.165961 AGTCTTGAGCAAAGCTAATGGTA 57.834 39.130 4.32 0.00 39.88 3.25
2382 2653 5.181748 AGTCTTGAGCAAAGCTAATGGTAG 58.818 41.667 4.32 0.85 39.88 3.18
2383 2654 4.333926 GTCTTGAGCAAAGCTAATGGTAGG 59.666 45.833 4.32 0.00 39.88 3.18
2384 2655 4.019321 TCTTGAGCAAAGCTAATGGTAGGT 60.019 41.667 4.32 0.00 39.88 3.08
2393 2664 6.358974 AAGCTAATGGTAGGTTTTTGCATT 57.641 33.333 0.00 0.00 43.88 3.56
2394 2665 7.475137 AAGCTAATGGTAGGTTTTTGCATTA 57.525 32.000 0.00 0.00 43.88 1.90
2395 2666 7.660030 AGCTAATGGTAGGTTTTTGCATTAT 57.340 32.000 0.00 0.00 34.31 1.28
2396 2667 7.491682 AGCTAATGGTAGGTTTTTGCATTATG 58.508 34.615 0.00 0.00 34.31 1.90
2397 2668 7.341769 AGCTAATGGTAGGTTTTTGCATTATGA 59.658 33.333 0.00 0.00 34.31 2.15
2398 2669 7.435192 GCTAATGGTAGGTTTTTGCATTATGAC 59.565 37.037 0.00 0.00 0.00 3.06
2399 2670 7.480760 AATGGTAGGTTTTTGCATTATGACT 57.519 32.000 0.00 0.00 0.00 3.41
2400 2671 8.588290 AATGGTAGGTTTTTGCATTATGACTA 57.412 30.769 0.00 0.00 0.00 2.59
2401 2672 7.385778 TGGTAGGTTTTTGCATTATGACTAC 57.614 36.000 0.00 0.00 0.00 2.73
2402 2673 7.172342 TGGTAGGTTTTTGCATTATGACTACT 58.828 34.615 0.00 0.00 0.00 2.57
2403 2674 7.668052 TGGTAGGTTTTTGCATTATGACTACTT 59.332 33.333 0.00 0.00 0.00 2.24
2404 2675 8.182227 GGTAGGTTTTTGCATTATGACTACTTC 58.818 37.037 0.00 0.00 0.00 3.01
2405 2676 8.947115 GTAGGTTTTTGCATTATGACTACTTCT 58.053 33.333 0.00 0.00 0.00 2.85
2406 2677 8.045176 AGGTTTTTGCATTATGACTACTTCTC 57.955 34.615 0.00 0.00 0.00 2.87
2407 2678 7.885399 AGGTTTTTGCATTATGACTACTTCTCT 59.115 33.333 0.00 0.00 0.00 3.10
2408 2679 8.515414 GGTTTTTGCATTATGACTACTTCTCTT 58.485 33.333 0.00 0.00 0.00 2.85
2409 2680 9.548208 GTTTTTGCATTATGACTACTTCTCTTC 57.452 33.333 0.00 0.00 0.00 2.87
2410 2681 7.849804 TTTGCATTATGACTACTTCTCTTCC 57.150 36.000 0.00 0.00 0.00 3.46
2411 2682 6.544928 TGCATTATGACTACTTCTCTTCCA 57.455 37.500 0.00 0.00 0.00 3.53
2513 2909 4.067896 TCAGGACAGCATTTCTGAAACTC 58.932 43.478 4.73 0.47 45.72 3.01
2514 2910 3.817084 CAGGACAGCATTTCTGAAACTCA 59.183 43.478 4.73 0.00 45.72 3.41
2537 2933 9.706691 CTCACTAAAAATAAGTGTACAGAAGGA 57.293 33.333 0.00 0.00 43.88 3.36
2538 2934 9.706691 TCACTAAAAATAAGTGTACAGAAGGAG 57.293 33.333 0.00 0.00 43.88 3.69
2553 2969 6.872920 ACAGAAGGAGAACAGAGATAATGTC 58.127 40.000 0.00 0.00 0.00 3.06
2578 2994 7.528481 TGAAAATATTCAGCATTGCATTGTC 57.472 32.000 11.91 6.64 40.59 3.18
2579 2995 7.097834 TGAAAATATTCAGCATTGCATTGTCA 58.902 30.769 11.91 9.06 40.59 3.58
2580 2996 7.766738 TGAAAATATTCAGCATTGCATTGTCAT 59.233 29.630 11.91 1.91 40.59 3.06
2581 2997 7.477144 AAATATTCAGCATTGCATTGTCATG 57.523 32.000 11.91 0.86 0.00 3.07
2595 3011 3.912496 TGTCATGCTTAGCACCTGTAT 57.088 42.857 9.82 0.00 43.04 2.29
2603 3019 4.824537 TGCTTAGCACCTGTATGTTTTCAA 59.175 37.500 1.39 0.00 31.71 2.69
2652 3068 8.770828 TGGCTATTCTTGTTAAGTTATTATCGC 58.229 33.333 0.00 0.00 0.00 4.58
2766 3182 1.352352 AGCCTGCATTGTGACTTAGGT 59.648 47.619 0.00 0.00 0.00 3.08
3078 3494 3.501349 TGAAGAGTAGGAGCTCACTGTT 58.499 45.455 17.19 15.45 37.94 3.16
3089 3633 2.614057 AGCTCACTGTTGTAGTTGTTGC 59.386 45.455 0.00 0.00 37.60 4.17
3090 3634 2.287009 GCTCACTGTTGTAGTTGTTGCC 60.287 50.000 0.00 0.00 37.60 4.52
3091 3635 3.206150 CTCACTGTTGTAGTTGTTGCCT 58.794 45.455 0.00 0.00 37.60 4.75
3092 3636 3.616219 TCACTGTTGTAGTTGTTGCCTT 58.384 40.909 0.00 0.00 37.60 4.35
3093 3637 3.376859 TCACTGTTGTAGTTGTTGCCTTG 59.623 43.478 0.00 0.00 37.60 3.61
3094 3638 3.128589 CACTGTTGTAGTTGTTGCCTTGT 59.871 43.478 0.00 0.00 37.60 3.16
3095 3639 3.761752 ACTGTTGTAGTTGTTGCCTTGTT 59.238 39.130 0.00 0.00 35.67 2.83
3096 3640 4.103365 TGTTGTAGTTGTTGCCTTGTTG 57.897 40.909 0.00 0.00 0.00 3.33
3097 3641 3.119316 TGTTGTAGTTGTTGCCTTGTTGG 60.119 43.478 0.00 0.00 39.35 3.77
3098 3642 2.729194 TGTAGTTGTTGCCTTGTTGGT 58.271 42.857 0.00 0.00 38.35 3.67
3099 3643 3.093057 TGTAGTTGTTGCCTTGTTGGTT 58.907 40.909 0.00 0.00 38.35 3.67
3100 3644 3.511934 TGTAGTTGTTGCCTTGTTGGTTT 59.488 39.130 0.00 0.00 38.35 3.27
3101 3645 2.971307 AGTTGTTGCCTTGTTGGTTTG 58.029 42.857 0.00 0.00 38.35 2.93
3102 3646 2.564947 AGTTGTTGCCTTGTTGGTTTGA 59.435 40.909 0.00 0.00 38.35 2.69
3103 3647 2.663826 TGTTGCCTTGTTGGTTTGAC 57.336 45.000 0.00 0.00 38.35 3.18
3104 3648 1.205893 TGTTGCCTTGTTGGTTTGACC 59.794 47.619 0.00 0.00 39.22 4.02
3115 3659 2.461695 TGGTTTGACCATGGTGTTTGT 58.538 42.857 25.52 0.00 44.79 2.83
3116 3660 3.632333 TGGTTTGACCATGGTGTTTGTA 58.368 40.909 25.52 1.35 44.79 2.41
3117 3661 4.219115 TGGTTTGACCATGGTGTTTGTAT 58.781 39.130 25.52 0.00 44.79 2.29
3118 3662 4.651503 TGGTTTGACCATGGTGTTTGTATT 59.348 37.500 25.52 0.00 44.79 1.89
3119 3663 4.987912 GGTTTGACCATGGTGTTTGTATTG 59.012 41.667 25.52 0.00 38.42 1.90
3120 3664 3.932545 TGACCATGGTGTTTGTATTGC 57.067 42.857 25.52 3.80 0.00 3.56
3121 3665 3.495331 TGACCATGGTGTTTGTATTGCT 58.505 40.909 25.52 0.00 0.00 3.91
3122 3666 3.255395 TGACCATGGTGTTTGTATTGCTG 59.745 43.478 25.52 0.00 0.00 4.41
3123 3667 3.230134 ACCATGGTGTTTGTATTGCTGT 58.770 40.909 18.99 0.00 0.00 4.40
3124 3668 3.255642 ACCATGGTGTTTGTATTGCTGTC 59.744 43.478 18.99 0.00 0.00 3.51
3125 3669 3.367292 CCATGGTGTTTGTATTGCTGTCC 60.367 47.826 2.57 0.00 0.00 4.02
3196 4031 3.383761 GCTTTGTTTGTCCATGTCCTTG 58.616 45.455 0.00 0.00 0.00 3.61
3767 4687 7.412853 GCATTAGTATCAATCTTGTGGAAGTG 58.587 38.462 0.00 0.00 0.00 3.16
4141 5079 1.241315 GGCTGTTTATGTGGGTGCGT 61.241 55.000 0.00 0.00 0.00 5.24
4188 5126 4.453136 GCAAAGTACAGTTTATTCGACCCA 59.547 41.667 0.00 0.00 0.00 4.51
4327 5269 9.903682 ATTCATTTACTGATGTTCTTTTCTGTG 57.096 29.630 0.00 0.00 32.72 3.66
4447 5664 3.698029 AATTATCGGTTGCTGTCATGC 57.302 42.857 0.00 0.00 0.00 4.06
4493 6414 8.950210 TGATAATCTGTTCAATTTTCTCAGGAC 58.050 33.333 0.00 0.00 0.00 3.85
4498 6419 3.401033 TCAATTTTCTCAGGACGCAGA 57.599 42.857 0.00 0.00 0.00 4.26
4504 6425 2.064434 TCTCAGGACGCAGATGAGAT 57.936 50.000 6.22 0.00 43.36 2.75
4567 6488 4.451900 CATGGTCCTGTAGTTGGATAACC 58.548 47.826 0.00 0.00 37.52 2.85
4592 6513 5.128663 ACATTACTTGTTTTTCCCTGCTGTT 59.871 36.000 0.00 0.00 33.74 3.16
4604 6535 2.287788 CCCTGCTGTTGAATGTGTTGTC 60.288 50.000 0.00 0.00 0.00 3.18
4618 6549 4.765273 TGTGTTGTCATGTGTTGTAGACT 58.235 39.130 0.00 0.00 32.41 3.24
4623 6554 9.151471 GTGTTGTCATGTGTTGTAGACTTATAT 57.849 33.333 0.00 0.00 32.41 0.86
4642 6573 9.062524 ACTTATATGTACTTTCAACAAGTGCAA 57.937 29.630 9.17 1.48 43.92 4.08
4774 6708 8.860780 AGCTAATTCTCAATTCTTCAGAACTT 57.139 30.769 0.00 0.00 36.80 2.66
4805 6739 2.827322 ACCATTGTTATGCTGCACATGT 59.173 40.909 3.57 0.00 40.06 3.21
4822 6756 5.561919 GCACATGTTAACTTTGGTTCGATCA 60.562 40.000 7.22 0.00 36.92 2.92
4890 6824 4.947147 GGCAAGTCGGGTGGTGCA 62.947 66.667 0.00 0.00 38.78 4.57
4953 6887 1.305887 CTCGACCCCCTACCTTGGT 60.306 63.158 0.00 0.00 34.33 3.67
4980 6914 1.154413 GTTGGTCATCGTGCTTGCG 60.154 57.895 0.00 0.00 0.00 4.85
5013 6947 2.159282 GGCAAGATCATTGGACAAGCAG 60.159 50.000 0.00 0.00 0.00 4.24
5095 7029 1.456287 GCACCCAAGGAACCTGAGT 59.544 57.895 0.00 0.00 0.00 3.41
5261 7201 5.468746 TGAAGGAACGATTGACGATTTCTTT 59.531 36.000 0.00 0.00 45.77 2.52
5263 7203 4.392138 AGGAACGATTGACGATTTCTTTCC 59.608 41.667 0.00 0.00 45.77 3.13
5264 7204 4.153475 GGAACGATTGACGATTTCTTTCCA 59.847 41.667 0.00 0.00 45.77 3.53
5265 7205 4.928661 ACGATTGACGATTTCTTTCCAG 57.071 40.909 0.00 0.00 45.77 3.86
5312 7254 4.079253 AGGTGCTGGTTAGTTTGTAATGG 58.921 43.478 0.00 0.00 0.00 3.16
5339 7281 2.086610 ATTTTGACAACTGGCCTGGT 57.913 45.000 14.82 4.00 0.00 4.00
5399 7342 7.840342 TTGCAATTACAACACACAGATTTTT 57.160 28.000 0.00 0.00 0.00 1.94
5400 7343 8.932945 TTGCAATTACAACACACAGATTTTTA 57.067 26.923 0.00 0.00 0.00 1.52
5401 7344 9.539825 TTGCAATTACAACACACAGATTTTTAT 57.460 25.926 0.00 0.00 0.00 1.40
5402 7345 9.539825 TGCAATTACAACACACAGATTTTTATT 57.460 25.926 0.00 0.00 0.00 1.40
5403 7346 9.796062 GCAATTACAACACACAGATTTTTATTG 57.204 29.630 0.00 0.00 0.00 1.90
5416 7359 7.379529 ACAGATTTTTATTGTGTTCTCGCAAAG 59.620 33.333 0.00 0.00 45.23 2.77
5421 7364 4.900635 ATTGTGTTCTCGCAAAGTTTCT 57.099 36.364 0.00 0.00 45.23 2.52
5435 7378 0.531974 GTTTCTGTCACACGGGCTCA 60.532 55.000 0.00 0.00 0.00 4.26
5439 7382 0.946221 CTGTCACACGGGCTCAGAAC 60.946 60.000 0.00 0.00 0.00 3.01
5455 7406 5.392380 GCTCAGAACTTTACCATGTCATTGG 60.392 44.000 0.00 0.00 42.82 3.16
5464 7415 0.813184 CATGTCATTGGTGCCTGGTC 59.187 55.000 0.00 0.00 0.00 4.02
5467 7418 0.036732 GTCATTGGTGCCTGGTCTCA 59.963 55.000 0.00 0.00 0.00 3.27
5471 7422 1.909700 TTGGTGCCTGGTCTCATTTC 58.090 50.000 0.00 0.00 0.00 2.17
5481 7432 2.290896 TGGTCTCATTTCCGCTGGAATT 60.291 45.455 10.19 5.23 41.71 2.17
5495 7446 3.620821 GCTGGAATTGAACTGCTACTCTC 59.379 47.826 0.00 0.00 0.00 3.20
5501 7452 7.014711 TGGAATTGAACTGCTACTCTCTATAGG 59.985 40.741 0.00 0.00 0.00 2.57
5556 7507 6.223852 ACGGTAAGCCAACTATGATATCTTG 58.776 40.000 3.98 0.07 34.09 3.02
5622 7578 4.840401 TCGTATCAAACTTGCAATCTCG 57.160 40.909 0.00 0.00 0.00 4.04
5623 7579 3.062099 TCGTATCAAACTTGCAATCTCGC 59.938 43.478 0.00 0.00 0.00 5.03
5670 7626 3.081804 TCGACTATGACAGACAAGCAGA 58.918 45.455 0.00 0.00 0.00 4.26
5732 7688 1.747355 CAGAAACATGTGAGCCCATCC 59.253 52.381 0.00 0.00 0.00 3.51
5756 7712 1.349688 TGTTGCCCATTTCTAGGTCGT 59.650 47.619 0.00 0.00 0.00 4.34
5823 7779 1.616159 AGCAAACCCCATGTACACAC 58.384 50.000 0.00 0.00 0.00 3.82
5824 7780 1.144913 AGCAAACCCCATGTACACACT 59.855 47.619 0.00 0.00 0.00 3.55
5825 7781 1.539827 GCAAACCCCATGTACACACTC 59.460 52.381 0.00 0.00 0.00 3.51
5826 7782 2.814097 GCAAACCCCATGTACACACTCT 60.814 50.000 0.00 0.00 0.00 3.24
5829 7785 2.897350 ACCCCATGTACACACTCTACA 58.103 47.619 0.00 0.00 0.00 2.74
5841 7797 5.064558 ACACACTCTACATATAGGAGGACG 58.935 45.833 0.00 0.00 0.00 4.79
5958 7914 1.377725 CTCGCCTGACCCATGCTTT 60.378 57.895 0.00 0.00 0.00 3.51
6022 8028 8.763049 AGTATTTGCTTAAATTGCTTCCTTTC 57.237 30.769 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.930040 CACGCGACTTCCATGTTAGATT 59.070 45.455 15.93 0.00 0.00 2.40
509 510 2.177594 CTCAGCACTCACCCACCTCC 62.178 65.000 0.00 0.00 0.00 4.30
632 634 1.446366 GACGGAGGTTAGGGCCATC 59.554 63.158 6.18 0.00 0.00 3.51
633 635 2.432300 CGACGGAGGTTAGGGCCAT 61.432 63.158 6.18 0.00 0.00 4.40
634 636 3.072468 CGACGGAGGTTAGGGCCA 61.072 66.667 6.18 0.00 0.00 5.36
635 637 3.846430 CCGACGGAGGTTAGGGCC 61.846 72.222 8.64 0.00 0.00 5.80
636 638 3.073101 ACCGACGGAGGTTAGGGC 61.073 66.667 23.38 0.00 43.00 5.19
637 639 2.718073 CCACCGACGGAGGTTAGGG 61.718 68.421 23.38 6.12 43.00 3.53
638 640 1.679977 TCCACCGACGGAGGTTAGG 60.680 63.158 26.72 14.76 43.00 2.69
639 641 4.007457 TCCACCGACGGAGGTTAG 57.993 61.111 26.72 4.76 43.00 2.34
645 647 0.249573 GTTTTGACTCCACCGACGGA 60.250 55.000 23.38 0.00 0.00 4.69
646 648 1.226030 GGTTTTGACTCCACCGACGG 61.226 60.000 13.61 13.61 0.00 4.79
647 649 1.226030 GGGTTTTGACTCCACCGACG 61.226 60.000 0.00 0.00 0.00 5.12
648 650 0.108019 AGGGTTTTGACTCCACCGAC 59.892 55.000 0.00 0.00 0.00 4.79
649 651 1.719529 TAGGGTTTTGACTCCACCGA 58.280 50.000 0.00 0.00 0.00 4.69
650 652 2.781681 ATAGGGTTTTGACTCCACCG 57.218 50.000 0.00 0.00 0.00 4.94
651 653 4.262617 GAGAATAGGGTTTTGACTCCACC 58.737 47.826 0.00 0.00 0.00 4.61
652 654 3.933332 CGAGAATAGGGTTTTGACTCCAC 59.067 47.826 0.00 0.00 0.00 4.02
653 655 3.618997 GCGAGAATAGGGTTTTGACTCCA 60.619 47.826 0.00 0.00 0.00 3.86
654 656 2.937149 GCGAGAATAGGGTTTTGACTCC 59.063 50.000 0.00 0.00 0.00 3.85
655 657 2.937149 GGCGAGAATAGGGTTTTGACTC 59.063 50.000 0.00 0.00 0.00 3.36
656 658 2.355818 GGGCGAGAATAGGGTTTTGACT 60.356 50.000 0.00 0.00 0.00 3.41
657 659 2.014857 GGGCGAGAATAGGGTTTTGAC 58.985 52.381 0.00 0.00 0.00 3.18
658 660 1.913419 AGGGCGAGAATAGGGTTTTGA 59.087 47.619 0.00 0.00 0.00 2.69
659 661 2.420058 AGGGCGAGAATAGGGTTTTG 57.580 50.000 0.00 0.00 0.00 2.44
663 665 0.561680 ACCTAGGGCGAGAATAGGGT 59.438 55.000 14.81 0.00 40.40 4.34
666 668 2.232452 CCATGACCTAGGGCGAGAATAG 59.768 54.545 14.81 0.00 0.00 1.73
667 669 2.248248 CCATGACCTAGGGCGAGAATA 58.752 52.381 14.81 0.00 0.00 1.75
686 688 5.221342 CCTGATGAATACCTATATCGAGGCC 60.221 48.000 0.00 0.00 40.65 5.19
688 690 6.681616 GCACCTGATGAATACCTATATCGAGG 60.682 46.154 0.00 0.00 42.89 4.63
692 694 7.416964 AGAGCACCTGATGAATACCTATATC 57.583 40.000 0.00 0.00 0.00 1.63
731 733 4.501743 GGCGGTGAGGGTTTTATTCAAAAA 60.502 41.667 0.00 0.00 35.46 1.94
732 734 3.006003 GGCGGTGAGGGTTTTATTCAAAA 59.994 43.478 0.00 0.00 0.00 2.44
733 735 2.559231 GGCGGTGAGGGTTTTATTCAAA 59.441 45.455 0.00 0.00 0.00 2.69
734 736 2.164338 GGCGGTGAGGGTTTTATTCAA 58.836 47.619 0.00 0.00 0.00 2.69
735 737 1.074084 TGGCGGTGAGGGTTTTATTCA 59.926 47.619 0.00 0.00 0.00 2.57
736 738 1.471287 GTGGCGGTGAGGGTTTTATTC 59.529 52.381 0.00 0.00 0.00 1.75
737 739 1.541379 GTGGCGGTGAGGGTTTTATT 58.459 50.000 0.00 0.00 0.00 1.40
738 740 0.323087 GGTGGCGGTGAGGGTTTTAT 60.323 55.000 0.00 0.00 0.00 1.40
777 779 5.451798 GGAAGCCAGTTCAAATTCAACTTCA 60.452 40.000 0.00 0.00 36.82 3.02
780 782 3.960102 TGGAAGCCAGTTCAAATTCAACT 59.040 39.130 0.00 0.00 36.82 3.16
787 789 1.757682 AACGTGGAAGCCAGTTCAAA 58.242 45.000 0.00 0.00 36.82 2.69
810 812 5.066246 ACGTTACCGAAGTCCAATTCAAAAA 59.934 36.000 0.00 0.00 37.88 1.94
811 813 4.575645 ACGTTACCGAAGTCCAATTCAAAA 59.424 37.500 0.00 0.00 37.88 2.44
812 814 4.024725 CACGTTACCGAAGTCCAATTCAAA 60.025 41.667 0.00 0.00 37.88 2.69
813 815 3.495377 CACGTTACCGAAGTCCAATTCAA 59.505 43.478 0.00 0.00 37.88 2.69
814 816 3.061322 CACGTTACCGAAGTCCAATTCA 58.939 45.455 0.00 0.00 37.88 2.57
815 817 3.319755 TCACGTTACCGAAGTCCAATTC 58.680 45.455 0.00 0.00 37.88 2.17
816 818 3.389925 TCACGTTACCGAAGTCCAATT 57.610 42.857 0.00 0.00 37.88 2.32
817 819 3.389925 TTCACGTTACCGAAGTCCAAT 57.610 42.857 0.00 0.00 37.88 3.16
818 820 2.886862 TTCACGTTACCGAAGTCCAA 57.113 45.000 0.00 0.00 37.88 3.53
819 821 2.886862 TTTCACGTTACCGAAGTCCA 57.113 45.000 0.00 0.00 37.88 4.02
820 822 3.557185 ACTTTTTCACGTTACCGAAGTCC 59.443 43.478 0.00 0.00 37.88 3.85
821 823 4.783959 ACTTTTTCACGTTACCGAAGTC 57.216 40.909 0.00 0.00 37.88 3.01
822 824 5.232838 CACTACTTTTTCACGTTACCGAAGT 59.767 40.000 0.00 0.00 37.88 3.01
823 825 5.332808 CCACTACTTTTTCACGTTACCGAAG 60.333 44.000 0.00 0.00 37.88 3.79
824 826 4.507388 CCACTACTTTTTCACGTTACCGAA 59.493 41.667 0.00 0.00 37.88 4.30
825 827 4.050553 CCACTACTTTTTCACGTTACCGA 58.949 43.478 0.00 0.00 37.88 4.69
826 828 3.184986 CCCACTACTTTTTCACGTTACCG 59.815 47.826 0.00 0.00 40.83 4.02
1176 1304 1.455959 GAGAGAGAGGCCGGGCTTA 60.456 63.158 33.28 0.00 0.00 3.09
1356 1484 0.322975 AAGAGACGCCAGCACTGATT 59.677 50.000 0.00 0.00 0.00 2.57
1358 1486 1.005748 CAAGAGACGCCAGCACTGA 60.006 57.895 0.00 0.00 0.00 3.41
1416 1550 1.122019 ACTTCTTGACCTCCGGCTGT 61.122 55.000 0.00 0.00 0.00 4.40
1458 1592 0.537188 GGGGCACGATCTTCTTGAGA 59.463 55.000 0.00 0.00 39.13 3.27
1692 1826 1.482593 AGACCGAAGAAGGCGATGAAT 59.517 47.619 0.00 0.00 33.69 2.57
1963 2097 1.403780 CCTGGAAACTAACGACGGGAG 60.404 57.143 0.00 0.00 0.00 4.30
2032 2166 3.319755 TGTTCTCGAATAACCAACCGTC 58.680 45.455 7.60 0.00 0.00 4.79
2064 2198 2.166664 AGCCGTCTAACCATTCTGAGAC 59.833 50.000 0.00 0.00 35.91 3.36
2066 2200 2.166459 TCAGCCGTCTAACCATTCTGAG 59.834 50.000 0.00 0.00 0.00 3.35
2082 2216 2.549754 CCCGTTTATGTCATCATCAGCC 59.450 50.000 0.00 0.00 35.70 4.85
2100 2234 2.271800 GACTACAAAGAGCACATCCCG 58.728 52.381 0.00 0.00 0.00 5.14
2105 2239 5.756347 ACAAAATACGACTACAAAGAGCACA 59.244 36.000 0.00 0.00 0.00 4.57
2120 2254 4.394920 ACAATGCAGGACCTACAAAATACG 59.605 41.667 0.00 0.00 0.00 3.06
2297 2443 1.064463 ACCATATCCAGCCAGGTGTTG 60.064 52.381 0.00 0.00 39.02 3.33
2303 2449 0.179048 TGCGAACCATATCCAGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
2322 2468 6.754178 ACTATCTAAGAAGGGGTTAGAAGGT 58.246 40.000 0.00 0.00 39.40 3.50
2352 2623 4.802999 AGCTTTGCTCAAGACTAAATTGC 58.197 39.130 0.79 0.00 30.62 3.56
2353 2624 7.487189 CCATTAGCTTTGCTCAAGACTAAATTG 59.513 37.037 0.00 9.44 40.44 2.32
2355 2626 6.660949 ACCATTAGCTTTGCTCAAGACTAAAT 59.339 34.615 0.00 0.00 40.44 1.40
2356 2627 6.003950 ACCATTAGCTTTGCTCAAGACTAAA 58.996 36.000 0.00 0.00 40.44 1.85
2359 2630 4.026356 ACCATTAGCTTTGCTCAAGACT 57.974 40.909 0.00 1.06 40.44 3.24
2360 2631 4.333926 CCTACCATTAGCTTTGCTCAAGAC 59.666 45.833 0.00 0.00 40.44 3.01
2361 2632 4.019321 ACCTACCATTAGCTTTGCTCAAGA 60.019 41.667 0.00 0.00 40.44 3.02
2362 2633 4.265073 ACCTACCATTAGCTTTGCTCAAG 58.735 43.478 0.00 0.00 40.44 3.02
2363 2634 4.301072 ACCTACCATTAGCTTTGCTCAA 57.699 40.909 0.00 0.00 40.44 3.02
2364 2635 4.301072 AACCTACCATTAGCTTTGCTCA 57.699 40.909 0.00 0.00 40.44 4.26
2365 2636 5.644977 AAAACCTACCATTAGCTTTGCTC 57.355 39.130 0.00 0.00 40.44 4.26
2366 2637 5.783111 CAAAAACCTACCATTAGCTTTGCT 58.217 37.500 0.00 0.00 43.41 3.91
2367 2638 4.388773 GCAAAAACCTACCATTAGCTTTGC 59.611 41.667 0.00 0.00 37.06 3.68
2368 2639 5.537188 TGCAAAAACCTACCATTAGCTTTG 58.463 37.500 0.00 0.00 0.00 2.77
2369 2640 5.799827 TGCAAAAACCTACCATTAGCTTT 57.200 34.783 0.00 0.00 0.00 3.51
2370 2641 6.358974 AATGCAAAAACCTACCATTAGCTT 57.641 33.333 0.00 0.00 0.00 3.74
2371 2642 7.341769 TCATAATGCAAAAACCTACCATTAGCT 59.658 33.333 0.00 0.00 33.46 3.32
2372 2643 7.435192 GTCATAATGCAAAAACCTACCATTAGC 59.565 37.037 0.00 0.00 33.46 3.09
2373 2644 8.686334 AGTCATAATGCAAAAACCTACCATTAG 58.314 33.333 0.00 0.00 33.46 1.73
2374 2645 8.588290 AGTCATAATGCAAAAACCTACCATTA 57.412 30.769 0.00 0.00 34.18 1.90
2375 2646 7.480760 AGTCATAATGCAAAAACCTACCATT 57.519 32.000 0.00 0.00 0.00 3.16
2376 2647 7.834181 AGTAGTCATAATGCAAAAACCTACCAT 59.166 33.333 0.00 0.00 0.00 3.55
2377 2648 7.172342 AGTAGTCATAATGCAAAAACCTACCA 58.828 34.615 0.00 0.00 0.00 3.25
2378 2649 7.625828 AGTAGTCATAATGCAAAAACCTACC 57.374 36.000 0.00 0.00 0.00 3.18
2379 2650 8.947115 AGAAGTAGTCATAATGCAAAAACCTAC 58.053 33.333 0.00 0.00 0.00 3.18
2380 2651 9.162764 GAGAAGTAGTCATAATGCAAAAACCTA 57.837 33.333 0.00 0.00 0.00 3.08
2381 2652 7.885399 AGAGAAGTAGTCATAATGCAAAAACCT 59.115 33.333 0.00 0.00 0.00 3.50
2382 2653 8.045176 AGAGAAGTAGTCATAATGCAAAAACC 57.955 34.615 0.00 0.00 0.00 3.27
2383 2654 9.548208 GAAGAGAAGTAGTCATAATGCAAAAAC 57.452 33.333 0.00 0.00 0.00 2.43
2384 2655 8.730680 GGAAGAGAAGTAGTCATAATGCAAAAA 58.269 33.333 0.00 0.00 0.00 1.94
2385 2656 7.882791 TGGAAGAGAAGTAGTCATAATGCAAAA 59.117 33.333 0.00 0.00 0.00 2.44
2386 2657 7.394016 TGGAAGAGAAGTAGTCATAATGCAAA 58.606 34.615 0.00 0.00 0.00 3.68
2387 2658 6.946340 TGGAAGAGAAGTAGTCATAATGCAA 58.054 36.000 0.00 0.00 0.00 4.08
2388 2659 6.381133 TCTGGAAGAGAAGTAGTCATAATGCA 59.619 38.462 0.00 0.00 38.67 3.96
2389 2660 6.810911 TCTGGAAGAGAAGTAGTCATAATGC 58.189 40.000 0.00 0.00 38.67 3.56
2408 2679 2.576191 CAAGGTACCCTTCCATTCTGGA 59.424 50.000 8.74 0.00 46.61 3.86
2409 2680 2.308866 ACAAGGTACCCTTCCATTCTGG 59.691 50.000 8.74 0.00 42.67 3.86
2410 2681 3.721087 ACAAGGTACCCTTCCATTCTG 57.279 47.619 8.74 0.00 42.67 3.02
2411 2682 3.655777 TGAACAAGGTACCCTTCCATTCT 59.344 43.478 8.74 0.00 42.67 2.40
2513 2909 9.706691 TCTCCTTCTGTACACTTATTTTTAGTG 57.293 33.333 0.00 0.00 46.56 2.74
2528 2924 7.836685 AGACATTATCTCTGTTCTCCTTCTGTA 59.163 37.037 0.00 0.00 28.16 2.74
2532 2928 7.106439 TCAGACATTATCTCTGTTCTCCTTC 57.894 40.000 0.00 0.00 37.12 3.46
2535 2931 8.729805 ATTTTCAGACATTATCTCTGTTCTCC 57.270 34.615 0.00 0.00 37.12 3.71
2572 2988 2.751259 ACAGGTGCTAAGCATGACAATG 59.249 45.455 0.00 0.00 41.91 2.82
2573 2989 3.077484 ACAGGTGCTAAGCATGACAAT 57.923 42.857 0.00 0.00 41.91 2.71
2574 2990 2.566833 ACAGGTGCTAAGCATGACAA 57.433 45.000 0.00 0.00 41.91 3.18
2575 2991 3.055167 ACATACAGGTGCTAAGCATGACA 60.055 43.478 0.00 0.00 41.91 3.58
2578 2994 4.970662 AAACATACAGGTGCTAAGCATG 57.029 40.909 0.00 0.00 41.91 4.06
2579 2995 5.009631 TGAAAACATACAGGTGCTAAGCAT 58.990 37.500 0.00 0.00 41.91 3.79
2580 2996 4.393834 TGAAAACATACAGGTGCTAAGCA 58.606 39.130 0.00 0.00 35.60 3.91
2581 2997 5.371115 TTGAAAACATACAGGTGCTAAGC 57.629 39.130 0.00 0.00 0.00 3.09
2582 2998 6.071952 ACCATTGAAAACATACAGGTGCTAAG 60.072 38.462 0.00 0.00 0.00 2.18
2590 3006 9.559958 GATAACTGAACCATTGAAAACATACAG 57.440 33.333 0.00 0.00 0.00 2.74
2766 3182 7.502895 GTCTTCAGATACATAACTCCCTCACTA 59.497 40.741 0.00 0.00 0.00 2.74
3061 3477 3.759618 ACTACAACAGTGAGCTCCTACTC 59.240 47.826 12.15 0.00 35.62 2.59
3078 3494 2.729194 ACCAACAAGGCAACAACTACA 58.271 42.857 0.00 0.00 43.14 2.74
3096 3640 4.864704 ATACAAACACCATGGTCAAACC 57.135 40.909 16.53 0.00 39.22 3.27
3097 3641 4.447389 GCAATACAAACACCATGGTCAAAC 59.553 41.667 16.53 0.00 0.00 2.93
3098 3642 4.343526 AGCAATACAAACACCATGGTCAAA 59.656 37.500 16.53 0.00 0.00 2.69
3099 3643 3.894427 AGCAATACAAACACCATGGTCAA 59.106 39.130 16.53 0.00 0.00 3.18
3100 3644 3.255395 CAGCAATACAAACACCATGGTCA 59.745 43.478 16.53 0.00 0.00 4.02
3101 3645 3.255642 ACAGCAATACAAACACCATGGTC 59.744 43.478 16.53 0.00 0.00 4.02
3102 3646 3.230134 ACAGCAATACAAACACCATGGT 58.770 40.909 13.00 13.00 0.00 3.55
3103 3647 3.367292 GGACAGCAATACAAACACCATGG 60.367 47.826 11.19 11.19 0.00 3.66
3104 3648 3.507233 AGGACAGCAATACAAACACCATG 59.493 43.478 0.00 0.00 0.00 3.66
3105 3649 3.507233 CAGGACAGCAATACAAACACCAT 59.493 43.478 0.00 0.00 0.00 3.55
3106 3650 2.884012 CAGGACAGCAATACAAACACCA 59.116 45.455 0.00 0.00 0.00 4.17
3107 3651 2.351738 GCAGGACAGCAATACAAACACC 60.352 50.000 0.00 0.00 0.00 4.16
3108 3652 2.554032 AGCAGGACAGCAATACAAACAC 59.446 45.455 0.00 0.00 36.85 3.32
3109 3653 2.553602 CAGCAGGACAGCAATACAAACA 59.446 45.455 0.00 0.00 36.85 2.83
3110 3654 2.554032 ACAGCAGGACAGCAATACAAAC 59.446 45.455 0.00 0.00 36.85 2.93
3111 3655 2.813754 GACAGCAGGACAGCAATACAAA 59.186 45.455 0.00 0.00 36.85 2.83
3112 3656 2.426522 GACAGCAGGACAGCAATACAA 58.573 47.619 0.00 0.00 36.85 2.41
3113 3657 1.339055 GGACAGCAGGACAGCAATACA 60.339 52.381 0.00 0.00 36.85 2.29
3114 3658 1.339055 TGGACAGCAGGACAGCAATAC 60.339 52.381 0.00 0.00 36.85 1.89
3115 3659 0.983467 TGGACAGCAGGACAGCAATA 59.017 50.000 0.00 0.00 36.85 1.90
3116 3660 0.330604 ATGGACAGCAGGACAGCAAT 59.669 50.000 0.00 0.00 36.85 3.56
3117 3661 0.111061 AATGGACAGCAGGACAGCAA 59.889 50.000 0.00 0.00 36.85 3.91
3118 3662 0.607217 CAATGGACAGCAGGACAGCA 60.607 55.000 0.00 0.00 36.85 4.41
3119 3663 1.310933 CCAATGGACAGCAGGACAGC 61.311 60.000 0.00 0.00 0.00 4.40
3120 3664 0.325933 TCCAATGGACAGCAGGACAG 59.674 55.000 0.00 0.00 0.00 3.51
3121 3665 0.325933 CTCCAATGGACAGCAGGACA 59.674 55.000 0.00 0.00 0.00 4.02
3122 3666 0.615331 TCTCCAATGGACAGCAGGAC 59.385 55.000 0.00 0.00 0.00 3.85
3123 3667 0.907486 CTCTCCAATGGACAGCAGGA 59.093 55.000 0.00 0.00 0.00 3.86
3124 3668 0.747283 GCTCTCCAATGGACAGCAGG 60.747 60.000 22.02 1.25 42.12 4.85
3125 3669 0.035725 TGCTCTCCAATGGACAGCAG 60.036 55.000 24.99 8.03 45.97 4.24
3196 4031 1.473258 TTCCATATGGCAGGCACAAC 58.527 50.000 17.58 0.00 34.44 3.32
3707 4627 1.218316 GGTAGCAAGGTCCCTCACG 59.782 63.158 0.00 0.00 0.00 4.35
3767 4687 3.064545 CCTTGAGCTTCGATTTCCATGTC 59.935 47.826 0.00 0.00 0.00 3.06
4141 5079 6.623549 GCACTCTTGCTAAATATGTTCTGCAA 60.624 38.462 11.91 11.91 46.17 4.08
4188 5126 4.774200 GGAATATAGGCCATTTCCTTGCAT 59.226 41.667 5.01 0.00 37.66 3.96
4438 5655 4.319766 CCATACTAAATTCCGCATGACAGC 60.320 45.833 0.00 0.00 0.00 4.40
4447 5664 5.811399 TCAAGTTGCCATACTAAATTCCG 57.189 39.130 0.00 0.00 0.00 4.30
4567 6488 4.984161 CAGCAGGGAAAAACAAGTAATGTG 59.016 41.667 0.00 0.00 42.99 3.21
4592 6513 4.979943 ACAACACATGACAACACATTCA 57.020 36.364 0.00 0.00 0.00 2.57
4623 6554 5.359576 AGGAATTGCACTTGTTGAAAGTACA 59.640 36.000 0.00 0.00 0.00 2.90
4774 6708 3.689161 GCATAACAATGGTGCAGTCAGTA 59.311 43.478 0.00 0.00 38.68 2.74
4805 6739 6.507900 TGCAAATTGATCGAACCAAAGTTAA 58.492 32.000 0.00 0.00 35.94 2.01
4822 6756 3.494924 GCCTTTCCCTTCAACTGCAAATT 60.495 43.478 0.00 0.00 0.00 1.82
4953 6887 3.677700 GCACGATGACCAACAGTATACCA 60.678 47.826 0.00 0.00 0.00 3.25
5013 6947 1.956477 TCTTTGGCCAAGCTTGAGAAC 59.044 47.619 28.05 14.12 31.70 3.01
5095 7029 2.102420 CCACCAATACATCAGTAGCCGA 59.898 50.000 0.00 0.00 32.86 5.54
5197 7131 2.868964 AACCAGTATCCTCCTGCCTA 57.131 50.000 0.00 0.00 0.00 3.93
5209 7143 4.325028 TTTCTGCTCAACGTAACCAGTA 57.675 40.909 0.00 0.00 0.00 2.74
5261 7201 3.133901 TGCTCACTGTTACAAACTCTGGA 59.866 43.478 0.00 0.00 0.00 3.86
5263 7203 3.059325 GCTGCTCACTGTTACAAACTCTG 60.059 47.826 0.00 0.00 0.00 3.35
5264 7204 3.134458 GCTGCTCACTGTTACAAACTCT 58.866 45.455 0.00 0.00 0.00 3.24
5265 7205 2.872245 TGCTGCTCACTGTTACAAACTC 59.128 45.455 0.00 0.00 0.00 3.01
5312 7254 4.211164 GGCCAGTTGTCAAAATTTGCTTAC 59.789 41.667 0.00 0.00 0.00 2.34
5339 7281 4.715130 ACCGGCTCACCAGGCCTA 62.715 66.667 3.98 0.00 46.73 3.93
5389 7332 6.142139 TGCGAGAACACAATAAAAATCTGTG 58.858 36.000 0.08 0.08 44.81 3.66
5390 7333 6.312399 TGCGAGAACACAATAAAAATCTGT 57.688 33.333 0.00 0.00 0.00 3.41
5391 7334 7.379529 ACTTTGCGAGAACACAATAAAAATCTG 59.620 33.333 0.00 0.00 0.00 2.90
5392 7335 7.425606 ACTTTGCGAGAACACAATAAAAATCT 58.574 30.769 0.00 0.00 0.00 2.40
5393 7336 7.623268 ACTTTGCGAGAACACAATAAAAATC 57.377 32.000 0.00 0.00 0.00 2.17
5394 7337 8.419076 AAACTTTGCGAGAACACAATAAAAAT 57.581 26.923 0.00 0.00 0.00 1.82
5396 7339 7.219917 CAGAAACTTTGCGAGAACACAATAAAA 59.780 33.333 0.00 0.00 0.00 1.52
5397 7340 6.690957 CAGAAACTTTGCGAGAACACAATAAA 59.309 34.615 0.00 0.00 0.00 1.40
5398 7341 6.183360 ACAGAAACTTTGCGAGAACACAATAA 60.183 34.615 0.00 0.00 0.00 1.40
5399 7342 5.295787 ACAGAAACTTTGCGAGAACACAATA 59.704 36.000 0.00 0.00 0.00 1.90
5400 7343 4.096382 ACAGAAACTTTGCGAGAACACAAT 59.904 37.500 0.00 0.00 0.00 2.71
5401 7344 3.438781 ACAGAAACTTTGCGAGAACACAA 59.561 39.130 0.00 0.00 0.00 3.33
5402 7345 3.006940 ACAGAAACTTTGCGAGAACACA 58.993 40.909 0.00 0.00 0.00 3.72
5403 7346 3.063452 TGACAGAAACTTTGCGAGAACAC 59.937 43.478 0.00 0.00 0.00 3.32
5404 7347 3.063452 GTGACAGAAACTTTGCGAGAACA 59.937 43.478 0.00 0.00 0.00 3.18
5405 7348 3.063452 TGTGACAGAAACTTTGCGAGAAC 59.937 43.478 0.00 0.00 0.00 3.01
5406 7349 3.063452 GTGTGACAGAAACTTTGCGAGAA 59.937 43.478 0.00 0.00 0.00 2.87
5407 7350 2.607635 GTGTGACAGAAACTTTGCGAGA 59.392 45.455 0.00 0.00 0.00 4.04
5408 7351 2.597505 CGTGTGACAGAAACTTTGCGAG 60.598 50.000 0.00 0.00 0.00 5.03
5409 7352 1.326245 CGTGTGACAGAAACTTTGCGA 59.674 47.619 0.00 0.00 0.00 5.10
5410 7353 1.594518 CCGTGTGACAGAAACTTTGCG 60.595 52.381 0.00 0.00 0.00 4.85
5416 7359 0.531974 TGAGCCCGTGTGACAGAAAC 60.532 55.000 0.00 0.00 0.00 2.78
5421 7364 1.069090 GTTCTGAGCCCGTGTGACA 59.931 57.895 0.00 0.00 0.00 3.58
5455 7406 1.648467 GCGGAAATGAGACCAGGCAC 61.648 60.000 0.00 0.00 0.00 5.01
5467 7418 2.094545 GCAGTTCAATTCCAGCGGAAAT 60.095 45.455 12.83 3.57 45.41 2.17
5471 7422 1.398390 GTAGCAGTTCAATTCCAGCGG 59.602 52.381 0.00 0.00 0.00 5.52
5481 7432 4.793201 TGCCTATAGAGAGTAGCAGTTCA 58.207 43.478 0.00 0.00 0.00 3.18
5495 7446 2.627515 TTGCTTGCTCCTGCCTATAG 57.372 50.000 0.00 0.00 38.71 1.31
5501 7452 2.094390 TGAATTCATTGCTTGCTCCTGC 60.094 45.455 3.38 0.00 40.20 4.85
5622 7578 2.358898 ACACAAAGTGTCAACATGAGGC 59.641 45.455 0.00 0.00 43.92 4.70
5732 7688 4.615912 CGACCTAGAAATGGGCAACAAAAG 60.616 45.833 0.00 0.00 39.74 2.27
5756 7712 2.366301 TTGGGCCGCCCTATGAGA 60.366 61.111 28.97 4.75 45.70 3.27
5823 7779 6.183360 GCAATCTCGTCCTCCTATATGTAGAG 60.183 46.154 0.00 0.00 0.00 2.43
5824 7780 5.648526 GCAATCTCGTCCTCCTATATGTAGA 59.351 44.000 0.00 0.00 0.00 2.59
5825 7781 5.416013 TGCAATCTCGTCCTCCTATATGTAG 59.584 44.000 0.00 0.00 0.00 2.74
5826 7782 5.321927 TGCAATCTCGTCCTCCTATATGTA 58.678 41.667 0.00 0.00 0.00 2.29
5829 7785 4.774726 ACATGCAATCTCGTCCTCCTATAT 59.225 41.667 0.00 0.00 0.00 0.86
5841 7797 0.999406 ACGCACGTACATGCAATCTC 59.001 50.000 15.00 0.00 46.47 2.75
5958 7914 1.037493 AGCCACGCATATAGACCGAA 58.963 50.000 0.00 0.00 0.00 4.30



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

AutoCloner maintained by Alex Coulton.