Multiple sequence alignment - TraesCS4D01G084900

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 TraesCS4D01G084900 chr4D 100.000 3531 0 0 1 3531 58945136 58948666 0.000000e+00 6521.0
1 TraesCS4D01G084900 chr4D 89.991 1119 105 6 1041 2158 59412339 59413451 0.000000e+00 1439.0
2 TraesCS4D01G084900 chr4D 90.638 235 9 6 1599 1825 59024182 59024411 2.060000e-77 300.0
3 TraesCS4D01G084900 chr4D 100.000 36 0 0 2048 2083 59024011 59024046 2.270000e-07 67.6
4 TraesCS4D01G084900 chr4A 91.045 2468 122 45 350 2747 537274818 537272380 0.000000e+00 3241.0
5 TraesCS4D01G084900 chr4A 90.170 1119 103 6 1041 2158 537183984 537182872 0.000000e+00 1450.0
6 TraesCS4D01G084900 chr4A 88.047 343 39 2 1 342 537275204 537274863 4.240000e-109 405.0
7 TraesCS4D01G084900 chr4A 88.889 72 7 1 2745 2816 164491967 164492037 1.750000e-13 87.9
8 TraesCS4D01G084900 chr4A 90.769 65 6 0 2747 2811 523480184 523480248 1.750000e-13 87.9
9 TraesCS4D01G084900 chr4B 94.218 1868 70 14 689 2524 88405136 88403275 0.000000e+00 2817.0
10 TraesCS4D01G084900 chr4B 89.991 1119 105 6 1041 2158 88156535 88155423 0.000000e+00 1439.0
11 TraesCS4D01G084900 chr4B 88.184 694 69 8 2807 3496 656130130 656129446 0.000000e+00 815.0
12 TraesCS4D01G084900 chr4B 86.927 742 52 15 2807 3508 541350434 541351170 0.000000e+00 791.0
13 TraesCS4D01G084900 chr4B 84.457 341 43 6 3 342 88416911 88416580 9.450000e-86 327.0
14 TraesCS4D01G084900 chr1A 92.522 682 50 1 2810 3490 546509803 546509122 0.000000e+00 976.0
15 TraesCS4D01G084900 chr1A 90.000 70 6 1 2747 2816 115501554 115501622 4.850000e-14 89.8
16 TraesCS4D01G084900 chr3D 89.958 707 44 6 2807 3494 361773126 361773824 0.000000e+00 887.0
17 TraesCS4D01G084900 chr3D 89.533 707 51 13 2807 3492 539668958 539668254 0.000000e+00 874.0
18 TraesCS4D01G084900 chr1D 89.773 704 52 4 2807 3490 93503532 93502829 0.000000e+00 883.0
19 TraesCS4D01G084900 chr1D 88.356 292 26 8 3202 3490 469099264 469098978 9.380000e-91 344.0
20 TraesCS4D01G084900 chr5B 89.235 706 52 11 2807 3492 671087476 671086775 0.000000e+00 861.0
21 TraesCS4D01G084900 chr5B 89.706 68 7 0 2745 2812 330753830 330753763 1.750000e-13 87.9
22 TraesCS4D01G084900 chr6D 87.660 705 66 12 2807 3494 3492779 3492079 0.000000e+00 800.0
23 TraesCS4D01G084900 chr3A 87.387 666 66 12 2807 3469 621593620 621592970 0.000000e+00 749.0
24 TraesCS4D01G084900 chr7D 92.585 499 33 4 2807 3302 159881847 159881350 0.000000e+00 713.0
25 TraesCS4D01G084900 chr5A 92.570 498 35 2 2807 3303 574201135 574200639 0.000000e+00 713.0
26 TraesCS4D01G084900 chr2D 86.830 448 39 7 3027 3470 540193166 540192735 1.910000e-132 483.0
27 TraesCS4D01G084900 chr2D 91.445 339 24 4 3156 3490 649834877 649835214 8.930000e-126 460.0
28 TraesCS4D01G084900 chr2D 90.625 64 6 0 2747 2810 650824561 650824498 6.280000e-13 86.1
29 TraesCS4D01G084900 chr7B 93.798 258 15 1 3236 3492 139098326 139098583 1.540000e-103 387.0
30 TraesCS4D01G084900 chr7B 90.909 66 6 0 2747 2812 376806745 376806680 4.850000e-14 89.8
31 TraesCS4D01G084900 chr7B 90.625 64 6 0 2747 2810 727655320 727655257 6.280000e-13 86.1
32 TraesCS4D01G084900 chr7B 84.722 72 10 1 2745 2816 625696059 625695989 1.760000e-08 71.3
33 TraesCS4D01G084900 chr5D 81.763 329 56 4 1811 2135 357018412 357018084 4.490000e-69 272.0
34 TraesCS4D01G084900 chr5D 86.301 73 8 2 2745 2816 216062858 216062787 1.050000e-10 78.7
35 TraesCS4D01G084900 chr5D 85.000 60 9 0 2748 2807 394148853 394148794 1.060000e-05 62.1
36 TraesCS4D01G084900 chr2A 93.750 64 4 0 2747 2810 80886789 80886852 2.900000e-16 97.1
37 TraesCS4D01G084900 chr2B 92.424 66 5 0 2747 2812 438840048 438839983 1.040000e-15 95.3
38 TraesCS4D01G084900 chr3B 91.045 67 6 0 2745 2811 78294261 78294327 1.350000e-14 91.6
39 TraesCS4D01G084900 chr1B 84.848 66 8 2 2747 2812 679040739 679040676 8.180000e-07 65.8
40 TraesCS4D01G084900 chr1B 96.875 32 1 0 2747 2778 467191917 467191886 2.000000e-03 54.7
41 TraesCS4D01G084900 chr1B 100.000 28 0 0 2744 2771 117464299 117464272 6.000000e-03 52.8


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 TraesCS4D01G084900 chr4D 58945136 58948666 3530 False 6521 6521 100.000 1 3531 1 chr4D.!!$F1 3530
1 TraesCS4D01G084900 chr4D 59412339 59413451 1112 False 1439 1439 89.991 1041 2158 1 chr4D.!!$F2 1117
2 TraesCS4D01G084900 chr4A 537272380 537275204 2824 True 1823 3241 89.546 1 2747 2 chr4A.!!$R2 2746
3 TraesCS4D01G084900 chr4A 537182872 537183984 1112 True 1450 1450 90.170 1041 2158 1 chr4A.!!$R1 1117
4 TraesCS4D01G084900 chr4B 88403275 88405136 1861 True 2817 2817 94.218 689 2524 1 chr4B.!!$R2 1835
5 TraesCS4D01G084900 chr4B 88155423 88156535 1112 True 1439 1439 89.991 1041 2158 1 chr4B.!!$R1 1117
6 TraesCS4D01G084900 chr4B 656129446 656130130 684 True 815 815 88.184 2807 3496 1 chr4B.!!$R4 689
7 TraesCS4D01G084900 chr4B 541350434 541351170 736 False 791 791 86.927 2807 3508 1 chr4B.!!$F1 701
8 TraesCS4D01G084900 chr1A 546509122 546509803 681 True 976 976 92.522 2810 3490 1 chr1A.!!$R1 680
9 TraesCS4D01G084900 chr3D 361773126 361773824 698 False 887 887 89.958 2807 3494 1 chr3D.!!$F1 687
10 TraesCS4D01G084900 chr3D 539668254 539668958 704 True 874 874 89.533 2807 3492 1 chr3D.!!$R1 685
11 TraesCS4D01G084900 chr1D 93502829 93503532 703 True 883 883 89.773 2807 3490 1 chr1D.!!$R1 683
12 TraesCS4D01G084900 chr5B 671086775 671087476 701 True 861 861 89.235 2807 3492 1 chr5B.!!$R2 685
13 TraesCS4D01G084900 chr6D 3492079 3492779 700 True 800 800 87.660 2807 3494 1 chr6D.!!$R1 687
14 TraesCS4D01G084900 chr3A 621592970 621593620 650 True 749 749 87.387 2807 3469 1 chr3A.!!$R1 662

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
511 551 0.034896 CCGTACTTTGCTGGACCTGT 59.965 55.0 0.00 0.0 0.0 4.00 F
681 730 0.390735 ACACCGGCGTAGATGGAAAC 60.391 55.0 6.01 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2470 2598 1.124780 TGTCTCCACGAACCCAGAAA 58.875 50.0 0.0 0.0 0.00 2.52 R
2583 2711 0.106708 TCGAGCAAGGCAAACTGACT 59.893 50.0 0.0 0.0 37.28 3.41 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
58 59 2.555757 AGCATGCTTCAAGTTCTTCCAC 59.444 45.455 16.30 0.00 0.00 4.02
60 61 3.365767 GCATGCTTCAAGTTCTTCCACTC 60.366 47.826 11.37 0.00 0.00 3.51
61 62 2.851195 TGCTTCAAGTTCTTCCACTCC 58.149 47.619 0.00 0.00 0.00 3.85
81 82 1.195900 CGGTGGTTTACGAACACATGG 59.804 52.381 0.00 0.00 37.51 3.66
83 84 0.869068 TGGTTTACGAACACATGGCG 59.131 50.000 0.00 0.00 37.51 5.69
102 103 1.063616 CGTCCTTGATACGCGAGAAGA 59.936 52.381 15.93 0.00 33.04 2.87
103 104 2.287069 CGTCCTTGATACGCGAGAAGAT 60.287 50.000 15.93 0.00 33.04 2.40
109 110 2.032808 TGATACGCGAGAAGATCACGAG 60.033 50.000 15.93 0.80 36.94 4.18
111 112 1.298713 CGCGAGAAGATCACGAGGG 60.299 63.158 0.00 0.00 35.45 4.30
112 113 1.715862 CGCGAGAAGATCACGAGGGA 61.716 60.000 0.00 0.00 35.45 4.20
138 140 1.063811 GTAGCCTCCGTGAGCGTAC 59.936 63.158 0.00 0.00 36.15 3.67
140 142 2.825075 TAGCCTCCGTGAGCGTACCA 62.825 60.000 0.00 0.00 36.15 3.25
150 152 1.493446 TGAGCGTACCATCCCTCTCTA 59.507 52.381 0.00 0.00 0.00 2.43
159 161 0.261991 ATCCCTCTCTACCAAGGCGA 59.738 55.000 0.00 0.00 0.00 5.54
161 163 1.123928 CCCTCTCTACCAAGGCGATT 58.876 55.000 0.00 0.00 0.00 3.34
184 186 3.123621 GTCGTCATGCAGAAAAGGTAGTG 59.876 47.826 0.00 0.00 0.00 2.74
187 189 4.201753 CGTCATGCAGAAAAGGTAGTGATG 60.202 45.833 0.00 0.00 0.00 3.07
190 192 1.745653 GCAGAAAAGGTAGTGATGGGC 59.254 52.381 0.00 0.00 0.00 5.36
248 250 1.004918 GTGGGGTGTGTCCTTCTCG 60.005 63.158 0.00 0.00 36.25 4.04
258 260 0.528470 GTCCTTCTCGACCCACTCAG 59.472 60.000 0.00 0.00 0.00 3.35
262 264 0.178973 TTCTCGACCCACTCAGACCA 60.179 55.000 0.00 0.00 0.00 4.02
279 281 2.507471 GACCATTTCCACATCCTCTCCT 59.493 50.000 0.00 0.00 0.00 3.69
280 282 3.711704 GACCATTTCCACATCCTCTCCTA 59.288 47.826 0.00 0.00 0.00 2.94
291 293 6.296145 CCACATCCTCTCCTAAAACTTTCTCT 60.296 42.308 0.00 0.00 0.00 3.10
297 299 2.812011 TCCTAAAACTTTCTCTTGGCGC 59.188 45.455 0.00 0.00 0.00 6.53
299 301 0.310854 AAAACTTTCTCTTGGCGCGG 59.689 50.000 8.83 0.00 0.00 6.46
316 318 1.910688 CGGTCTTCTTTAGTCTCGCC 58.089 55.000 0.00 0.00 0.00 5.54
326 328 1.255667 TAGTCTCGCCGGGAAAAGCT 61.256 55.000 2.18 0.00 0.00 3.74
328 330 1.375523 TCTCGCCGGGAAAAGCTTC 60.376 57.895 2.18 0.00 0.00 3.86
329 331 1.671054 CTCGCCGGGAAAAGCTTCA 60.671 57.895 2.18 0.00 32.75 3.02
342 344 0.106708 AGCTTCACGTGAAAGGCTCA 59.893 50.000 29.25 10.70 32.31 4.26
343 345 0.514691 GCTTCACGTGAAAGGCTCAG 59.485 55.000 29.32 17.86 33.60 3.35
344 346 1.871080 CTTCACGTGAAAGGCTCAGT 58.129 50.000 29.32 0.00 33.60 3.41
346 348 0.750249 TCACGTGAAAGGCTCAGTCA 59.250 50.000 17.62 0.00 33.60 3.41
347 349 1.138069 TCACGTGAAAGGCTCAGTCAA 59.862 47.619 17.62 0.00 33.60 3.18
348 350 1.261619 CACGTGAAAGGCTCAGTCAAC 59.738 52.381 10.90 0.00 33.60 3.18
353 392 0.035458 AAAGGCTCAGTCAACGGGAG 59.965 55.000 0.00 0.00 0.00 4.30
364 403 1.383248 AACGGGAGGATGAGGGAGG 60.383 63.158 0.00 0.00 0.00 4.30
374 413 3.827898 GAGGGAGGAGTGACGCCG 61.828 72.222 0.00 0.00 0.00 6.46
381 420 2.556287 GAGTGACGCCGGCAAAAG 59.444 61.111 28.98 12.87 0.00 2.27
391 430 0.749454 CCGGCAAAAGGAGGAGATGG 60.749 60.000 0.00 0.00 0.00 3.51
397 436 1.589414 AAAGGAGGAGATGGGTGAGG 58.411 55.000 0.00 0.00 0.00 3.86
398 437 0.719015 AAGGAGGAGATGGGTGAGGA 59.281 55.000 0.00 0.00 0.00 3.71
406 445 1.539869 ATGGGTGAGGAGTGGCACT 60.540 57.895 22.26 22.26 35.43 4.40
422 461 1.446907 CACTGCTTAGCAAGAGTGGG 58.553 55.000 14.70 2.14 38.41 4.61
424 463 0.035630 CTGCTTAGCAAGAGTGGGCT 60.036 55.000 8.68 0.00 43.94 5.19
432 471 4.778213 AGCAAGAGTGGGCTGATTTATA 57.222 40.909 0.00 0.00 39.30 0.98
484 523 1.657556 CCGGATTTGGCGTGTTTGT 59.342 52.632 0.00 0.00 0.00 2.83
485 524 0.662970 CCGGATTTGGCGTGTTTGTG 60.663 55.000 0.00 0.00 0.00 3.33
496 535 2.032722 GCGTGTTTGTGTGAATTCCGTA 60.033 45.455 2.27 0.00 0.00 4.02
502 542 3.889196 TGTGTGAATTCCGTACTTTGC 57.111 42.857 2.27 0.00 0.00 3.68
511 551 0.034896 CCGTACTTTGCTGGACCTGT 59.965 55.000 0.00 0.00 0.00 4.00
516 556 3.801114 ACTTTGCTGGACCTGTTTTTC 57.199 42.857 0.00 0.00 0.00 2.29
524 564 3.064207 TGGACCTGTTTTTCGAATCTCG 58.936 45.455 0.00 0.00 42.10 4.04
535 575 2.901249 TCGAATCTCGAATTCCAACCC 58.099 47.619 0.00 0.00 46.90 4.11
634 683 1.267121 AGTACACACGCTTGGGAGAT 58.733 50.000 0.00 0.00 0.00 2.75
681 730 0.390735 ACACCGGCGTAGATGGAAAC 60.391 55.000 6.01 0.00 0.00 2.78
682 731 5.529333 CTACACCGGCGTAGATGGAAACA 62.529 52.174 22.61 0.00 41.21 2.83
737 818 8.961294 AGATGCTTCGAATTTTATATGAATGC 57.039 30.769 0.00 0.00 0.00 3.56
738 819 7.747799 AGATGCTTCGAATTTTATATGAATGCG 59.252 33.333 0.00 7.39 36.98 4.73
739 820 6.724263 TGCTTCGAATTTTATATGAATGCGT 58.276 32.000 0.00 0.00 36.97 5.24
740 821 7.192913 TGCTTCGAATTTTATATGAATGCGTT 58.807 30.769 0.00 0.00 36.97 4.84
746 830 7.149144 CGAATTTTATATGAATGCGTTGCGAAT 60.149 33.333 0.00 0.00 32.21 3.34
754 838 3.755965 ATGCGTTGCGAATGAAATGTA 57.244 38.095 0.00 0.00 0.00 2.29
756 840 4.090138 TGCGTTGCGAATGAAATGTATT 57.910 36.364 0.00 0.00 0.00 1.89
821 906 1.949847 AAGCCACGACAGAGATCGGG 61.950 60.000 0.00 0.00 46.56 5.14
823 908 2.418910 CCACGACAGAGATCGGGCT 61.419 63.158 0.00 0.00 44.38 5.19
824 909 1.226802 CACGACAGAGATCGGGCTG 60.227 63.158 10.45 10.45 46.56 4.85
890 975 1.536766 CGCCAGTGCTCTGAATTTTCA 59.463 47.619 17.19 0.00 43.76 2.69
930 1015 0.463204 CGATGTGTCCTCAGCTCCAT 59.537 55.000 0.00 0.00 0.00 3.41
937 1022 1.220206 CCTCAGCTCCATTCACGCT 59.780 57.895 0.00 0.00 0.00 5.07
1258 1352 2.358737 GCCAACGAGGACCTGGTG 60.359 66.667 10.24 6.00 41.22 4.17
1552 1646 3.998672 TCGGCGCGGTCCTTCTTT 61.999 61.111 15.06 0.00 0.00 2.52
2218 2312 1.657594 CATGTCATGTGTGCGAGAGAC 59.342 52.381 4.53 0.00 0.00 3.36
2368 2491 5.773176 CAGGGGTGTAGTAATCCTTGTTTTT 59.227 40.000 0.00 0.00 0.00 1.94
2409 2533 5.047377 GGATTACCTGATTGTTCTTGGCAAA 60.047 40.000 0.00 0.00 0.00 3.68
2443 2567 4.394795 CGCCTTCTTCAGTCAAAAATACG 58.605 43.478 0.00 0.00 0.00 3.06
2470 2598 4.142026 GGAACAGGTAAAAACAGGCAAACT 60.142 41.667 0.00 0.00 0.00 2.66
2471 2599 5.414789 AACAGGTAAAAACAGGCAAACTT 57.585 34.783 0.00 0.00 0.00 2.66
2482 2610 1.029681 GGCAAACTTTCTGGGTTCGT 58.970 50.000 0.00 0.00 0.00 3.85
2486 2614 2.256117 AACTTTCTGGGTTCGTGGAG 57.744 50.000 0.00 0.00 0.00 3.86
2494 2622 0.895530 GGGTTCGTGGAGACATCTCA 59.104 55.000 10.95 0.00 46.14 3.27
2496 2624 2.544685 GGTTCGTGGAGACATCTCATG 58.455 52.381 10.95 3.46 46.14 3.07
2498 2626 3.443037 GTTCGTGGAGACATCTCATGAG 58.557 50.000 17.07 17.07 46.14 2.90
2499 2627 3.004752 TCGTGGAGACATCTCATGAGA 57.995 47.619 27.03 27.03 46.14 3.27
2500 2628 2.685388 TCGTGGAGACATCTCATGAGAC 59.315 50.000 27.37 14.96 46.14 3.36
2524 2652 3.472652 AGAGTAACAACCAAATGTGCGA 58.527 40.909 0.00 0.00 32.81 5.10
2526 2654 5.242434 AGAGTAACAACCAAATGTGCGATA 58.758 37.500 0.00 0.00 32.81 2.92
2527 2655 5.880332 AGAGTAACAACCAAATGTGCGATAT 59.120 36.000 0.00 0.00 32.81 1.63
2529 2657 7.551262 AGAGTAACAACCAAATGTGCGATATAA 59.449 33.333 0.00 0.00 32.81 0.98
2530 2658 8.046294 AGTAACAACCAAATGTGCGATATAAA 57.954 30.769 0.00 0.00 32.81 1.40
2531 2659 8.181573 AGTAACAACCAAATGTGCGATATAAAG 58.818 33.333 0.00 0.00 32.81 1.85
2532 2660 5.339990 ACAACCAAATGTGCGATATAAAGC 58.660 37.500 0.00 0.00 30.82 3.51
2541 2669 2.283086 TGCGATATAAAGCGAAACACGG 59.717 45.455 0.00 0.00 42.83 4.94
2543 2671 3.361724 GCGATATAAAGCGAAACACGGAG 60.362 47.826 0.00 0.00 42.83 4.63
2545 2673 4.085721 CGATATAAAGCGAAACACGGAGAC 60.086 45.833 0.00 0.00 42.83 3.36
2559 2687 2.256174 CGGAGACATAAAGCGAAACGA 58.744 47.619 0.00 0.00 0.00 3.85
2561 2689 3.241678 CGGAGACATAAAGCGAAACGAAG 60.242 47.826 0.00 0.00 0.00 3.79
2562 2690 3.062234 GGAGACATAAAGCGAAACGAAGG 59.938 47.826 0.00 0.00 0.00 3.46
2563 2691 3.000727 AGACATAAAGCGAAACGAAGGG 58.999 45.455 0.00 0.00 0.00 3.95
2573 2701 1.232119 AAACGAAGGGTTTAGCACGG 58.768 50.000 0.00 0.00 46.76 4.94
2574 2702 0.393820 AACGAAGGGTTTAGCACGGA 59.606 50.000 0.00 0.00 34.41 4.69
2575 2703 0.611714 ACGAAGGGTTTAGCACGGAT 59.388 50.000 0.00 0.00 0.00 4.18
2576 2704 1.002773 ACGAAGGGTTTAGCACGGATT 59.997 47.619 0.00 0.00 0.00 3.01
2577 2705 1.664151 CGAAGGGTTTAGCACGGATTC 59.336 52.381 0.00 0.00 0.00 2.52
2578 2706 2.706890 GAAGGGTTTAGCACGGATTCA 58.293 47.619 0.00 0.00 0.00 2.57
2579 2707 3.279434 GAAGGGTTTAGCACGGATTCAT 58.721 45.455 0.00 0.00 0.00 2.57
2580 2708 2.643551 AGGGTTTAGCACGGATTCATG 58.356 47.619 0.00 0.00 0.00 3.07
2581 2709 2.238646 AGGGTTTAGCACGGATTCATGA 59.761 45.455 0.00 0.00 0.00 3.07
2582 2710 2.614057 GGGTTTAGCACGGATTCATGAG 59.386 50.000 0.00 0.00 0.00 2.90
2583 2711 3.531538 GGTTTAGCACGGATTCATGAGA 58.468 45.455 0.00 0.00 0.00 3.27
2584 2712 3.557595 GGTTTAGCACGGATTCATGAGAG 59.442 47.826 0.00 0.00 0.00 3.20
2585 2713 4.184629 GTTTAGCACGGATTCATGAGAGT 58.815 43.478 0.00 0.00 0.00 3.24
2586 2714 2.593346 AGCACGGATTCATGAGAGTC 57.407 50.000 0.00 0.00 0.00 3.36
2587 2715 1.827344 AGCACGGATTCATGAGAGTCA 59.173 47.619 0.00 0.00 32.55 3.41
2588 2716 2.159128 AGCACGGATTCATGAGAGTCAG 60.159 50.000 0.00 0.00 32.55 3.51
2589 2717 2.417924 GCACGGATTCATGAGAGTCAGT 60.418 50.000 0.00 0.50 38.92 3.41
2597 2725 3.405831 TCATGAGAGTCAGTTTGCCTTG 58.594 45.455 0.00 0.00 0.00 3.61
2747 2876 0.869730 CGGTGTCCGGTTGGTTTAAG 59.130 55.000 0.00 0.00 44.15 1.85
2748 2877 1.241165 GGTGTCCGGTTGGTTTAAGG 58.759 55.000 0.00 0.00 36.30 2.69
2749 2878 0.594602 GTGTCCGGTTGGTTTAAGGC 59.405 55.000 0.00 0.00 36.30 4.35
2750 2879 0.537828 TGTCCGGTTGGTTTAAGGCC 60.538 55.000 0.00 0.00 36.30 5.19
2751 2880 0.537828 GTCCGGTTGGTTTAAGGCCA 60.538 55.000 5.01 0.00 36.30 5.36
2752 2881 0.185416 TCCGGTTGGTTTAAGGCCAA 59.815 50.000 5.01 8.85 43.04 4.52
2757 2886 2.757894 TTGGTTTAAGGCCAACTCCA 57.242 45.000 5.01 3.88 40.69 3.86
2758 2887 1.989706 TGGTTTAAGGCCAACTCCAC 58.010 50.000 5.01 0.00 32.29 4.02
2759 2888 1.254026 GGTTTAAGGCCAACTCCACC 58.746 55.000 5.01 0.00 0.00 4.61
2760 2889 1.479757 GGTTTAAGGCCAACTCCACCA 60.480 52.381 5.01 0.00 0.00 4.17
2761 2890 1.611977 GTTTAAGGCCAACTCCACCAC 59.388 52.381 5.01 0.00 0.00 4.16
2762 2891 0.250553 TTAAGGCCAACTCCACCACG 60.251 55.000 5.01 0.00 0.00 4.94
2763 2892 2.741486 TAAGGCCAACTCCACCACGC 62.741 60.000 5.01 0.00 0.00 5.34
2765 2894 4.980805 GCCAACTCCACCACGCGA 62.981 66.667 15.93 0.00 0.00 5.87
2766 2895 3.041940 CCAACTCCACCACGCGAC 61.042 66.667 15.93 0.00 0.00 5.19
2767 2896 3.041940 CAACTCCACCACGCGACC 61.042 66.667 15.93 0.00 0.00 4.79
2768 2897 4.309950 AACTCCACCACGCGACCC 62.310 66.667 15.93 0.00 0.00 4.46
2775 2904 4.096003 CCACGCGACCCCATCCTT 62.096 66.667 15.93 0.00 0.00 3.36
2776 2905 2.046314 CACGCGACCCCATCCTTT 60.046 61.111 15.93 0.00 0.00 3.11
2777 2906 2.106683 CACGCGACCCCATCCTTTC 61.107 63.158 15.93 0.00 0.00 2.62
2778 2907 2.291043 ACGCGACCCCATCCTTTCT 61.291 57.895 15.93 0.00 0.00 2.52
2779 2908 1.815421 CGCGACCCCATCCTTTCTG 60.815 63.158 0.00 0.00 0.00 3.02
2780 2909 1.452108 GCGACCCCATCCTTTCTGG 60.452 63.158 0.00 0.00 37.10 3.86
2781 2910 1.452108 CGACCCCATCCTTTCTGGC 60.452 63.158 0.00 0.00 35.26 4.85
2782 2911 1.076705 GACCCCATCCTTTCTGGCC 60.077 63.158 0.00 0.00 35.26 5.36
2783 2912 2.280079 CCCCATCCTTTCTGGCCC 59.720 66.667 0.00 0.00 35.26 5.80
2784 2913 2.280079 CCCATCCTTTCTGGCCCC 59.720 66.667 0.00 0.00 35.26 5.80
2785 2914 2.124151 CCATCCTTTCTGGCCCCG 60.124 66.667 0.00 0.00 35.26 5.73
2786 2915 2.677228 CATCCTTTCTGGCCCCGT 59.323 61.111 0.00 0.00 35.26 5.28
2787 2916 1.452108 CATCCTTTCTGGCCCCGTC 60.452 63.158 0.00 0.00 35.26 4.79
2788 2917 2.680370 ATCCTTTCTGGCCCCGTCC 61.680 63.158 0.00 0.00 35.26 4.79
2789 2918 3.646715 CCTTTCTGGCCCCGTCCA 61.647 66.667 0.00 0.00 34.42 4.02
2790 2919 2.677228 CTTTCTGGCCCCGTCCAT 59.323 61.111 0.00 0.00 35.22 3.41
2791 2920 1.000896 CTTTCTGGCCCCGTCCATT 60.001 57.895 0.00 0.00 35.22 3.16
2792 2921 0.611896 CTTTCTGGCCCCGTCCATTT 60.612 55.000 0.00 0.00 35.22 2.32
2793 2922 0.699399 TTTCTGGCCCCGTCCATTTA 59.301 50.000 0.00 0.00 35.22 1.40
2794 2923 0.254747 TTCTGGCCCCGTCCATTTAG 59.745 55.000 0.00 0.00 35.22 1.85
2795 2924 1.152963 CTGGCCCCGTCCATTTAGG 60.153 63.158 0.00 0.00 35.22 2.69
2796 2925 2.194868 GGCCCCGTCCATTTAGGG 59.805 66.667 0.00 0.00 44.67 3.53
2797 2926 2.686572 GGCCCCGTCCATTTAGGGT 61.687 63.158 0.00 0.00 43.58 4.34
2798 2927 1.347243 GGCCCCGTCCATTTAGGGTA 61.347 60.000 0.00 0.00 43.58 3.69
2799 2928 0.547553 GCCCCGTCCATTTAGGGTAA 59.452 55.000 0.00 0.00 43.58 2.85
2800 2929 1.064537 GCCCCGTCCATTTAGGGTAAA 60.065 52.381 0.00 0.00 43.58 2.01
2801 2930 2.621147 GCCCCGTCCATTTAGGGTAAAA 60.621 50.000 0.00 0.00 43.58 1.52
2802 2931 3.284617 CCCCGTCCATTTAGGGTAAAAG 58.715 50.000 0.00 0.00 43.58 2.27
2803 2932 3.284617 CCCGTCCATTTAGGGTAAAAGG 58.715 50.000 0.00 0.00 40.27 3.11
2804 2933 3.284617 CCGTCCATTTAGGGTAAAAGGG 58.715 50.000 1.88 0.00 40.75 3.95
2805 2934 3.054213 CCGTCCATTTAGGGTAAAAGGGA 60.054 47.826 0.00 0.00 44.62 4.20
2808 2937 5.602291 TCCATTTAGGGTAAAAGGGACAA 57.398 39.130 0.00 0.00 42.63 3.18
2846 2975 4.017683 AGGAAGAAGCTTGAAATGGAGGAT 60.018 41.667 2.10 0.00 0.00 3.24
2934 3064 2.596851 AATGTCTCGGCCAGGCAGT 61.597 57.895 15.19 9.21 41.18 4.40
2969 3099 3.683937 GCCACCAATGCCGCAACT 61.684 61.111 0.00 0.00 0.00 3.16
3006 3136 1.011463 CTTGCGATCATGAGCGTGC 60.011 57.895 31.33 18.05 42.87 5.34
3038 3168 1.621992 TGAGCGAGAAGACAAGGAGT 58.378 50.000 0.00 0.00 0.00 3.85
3041 3171 1.964223 AGCGAGAAGACAAGGAGTTGA 59.036 47.619 0.00 0.00 37.10 3.18
3074 3204 1.135257 CAGAAGGAGATGTTCGACGCT 60.135 52.381 0.00 0.00 0.00 5.07
3201 3352 3.259123 ACATTCATTTTGGAGGCTGGTTC 59.741 43.478 0.00 0.00 0.00 3.62
3212 3363 2.594303 CTGGTTCTGTTGCCGGCA 60.594 61.111 29.03 29.03 0.00 5.69
3497 3687 2.092323 GTGGAGTTGGCCTAATGGAAC 58.908 52.381 3.32 0.00 34.57 3.62
3498 3688 1.339631 TGGAGTTGGCCTAATGGAACG 60.340 52.381 3.32 0.00 34.57 3.95
3501 3691 1.349688 AGTTGGCCTAATGGAACGTCA 59.650 47.619 3.32 0.00 34.57 4.35
3508 3698 1.061131 CTAATGGAACGTCAAGCGCAG 59.939 52.381 11.47 0.72 46.11 5.18
3523 3713 0.169009 CGCAGCTACAAAAAGAGGGC 59.831 55.000 0.00 0.00 0.00 5.19
3524 3714 1.247567 GCAGCTACAAAAAGAGGGCA 58.752 50.000 0.00 0.00 0.00 5.36
3525 3715 1.613437 GCAGCTACAAAAAGAGGGCAA 59.387 47.619 0.00 0.00 0.00 4.52
3526 3716 2.035832 GCAGCTACAAAAAGAGGGCAAA 59.964 45.455 0.00 0.00 0.00 3.68
3527 3717 3.858503 GCAGCTACAAAAAGAGGGCAAAG 60.859 47.826 0.00 0.00 0.00 2.77
3528 3718 3.569701 CAGCTACAAAAAGAGGGCAAAGA 59.430 43.478 0.00 0.00 0.00 2.52
3529 3719 3.570125 AGCTACAAAAAGAGGGCAAAGAC 59.430 43.478 0.00 0.00 0.00 3.01
3530 3720 3.609409 GCTACAAAAAGAGGGCAAAGACG 60.609 47.826 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.142474 GTGTTCGTAAACCACCGGAG 58.858 55.000 9.46 0.00 34.28 4.63
60 61 1.195900 CATGTGTTCGTAAACCACCGG 59.804 52.381 0.00 0.00 34.28 5.28
61 62 1.195900 CCATGTGTTCGTAAACCACCG 59.804 52.381 0.00 0.00 34.28 4.94
83 84 2.846039 TCTTCTCGCGTATCAAGGAC 57.154 50.000 5.77 0.00 0.00 3.85
95 96 1.095600 TGTCCCTCGTGATCTTCTCG 58.904 55.000 0.00 0.00 35.02 4.04
102 103 1.481871 ACCGTTATGTCCCTCGTGAT 58.518 50.000 0.00 0.00 0.00 3.06
103 104 2.019249 CTACCGTTATGTCCCTCGTGA 58.981 52.381 0.00 0.00 0.00 4.35
109 110 0.391966 GGAGGCTACCGTTATGTCCC 59.608 60.000 0.00 0.00 0.00 4.46
111 112 3.564455 CGGAGGCTACCGTTATGTC 57.436 57.895 14.64 0.00 46.70 3.06
132 134 1.479021 GGTAGAGAGGGATGGTACGCT 60.479 57.143 0.00 0.00 35.82 5.07
138 140 0.761802 GCCTTGGTAGAGAGGGATGG 59.238 60.000 0.00 0.00 33.52 3.51
140 142 0.261991 TCGCCTTGGTAGAGAGGGAT 59.738 55.000 0.00 0.00 33.52 3.85
150 152 0.036388 ATGACGACAATCGCCTTGGT 60.036 50.000 0.00 0.00 45.12 3.67
159 161 3.149196 ACCTTTTCTGCATGACGACAAT 58.851 40.909 0.00 0.00 0.00 2.71
161 163 2.254546 ACCTTTTCTGCATGACGACA 57.745 45.000 0.00 0.00 0.00 4.35
238 240 0.178973 TGAGTGGGTCGAGAAGGACA 60.179 55.000 0.00 0.00 38.70 4.02
239 241 0.528470 CTGAGTGGGTCGAGAAGGAC 59.472 60.000 0.00 0.00 36.18 3.85
248 250 1.351017 TGGAAATGGTCTGAGTGGGTC 59.649 52.381 0.00 0.00 0.00 4.46
258 260 2.507471 AGGAGAGGATGTGGAAATGGTC 59.493 50.000 0.00 0.00 0.00 4.02
262 264 6.394345 AGTTTTAGGAGAGGATGTGGAAAT 57.606 37.500 0.00 0.00 0.00 2.17
279 281 1.533731 CCGCGCCAAGAGAAAGTTTTA 59.466 47.619 0.00 0.00 0.00 1.52
280 282 0.310854 CCGCGCCAAGAGAAAGTTTT 59.689 50.000 0.00 0.00 0.00 2.43
291 293 0.034337 ACTAAAGAAGACCGCGCCAA 59.966 50.000 0.00 0.00 0.00 4.52
297 299 1.794437 CGGCGAGACTAAAGAAGACCG 60.794 57.143 0.00 0.00 0.00 4.79
299 301 1.469423 CCCGGCGAGACTAAAGAAGAC 60.469 57.143 9.30 0.00 0.00 3.01
316 318 0.941542 TTCACGTGAAGCTTTTCCCG 59.058 50.000 26.53 3.47 0.00 5.14
326 328 1.138069 TGACTGAGCCTTTCACGTGAA 59.862 47.619 26.53 26.53 0.00 3.18
328 330 1.261619 GTTGACTGAGCCTTTCACGTG 59.738 52.381 9.94 9.94 0.00 4.49
329 331 1.583054 GTTGACTGAGCCTTTCACGT 58.417 50.000 0.00 0.00 0.00 4.49
332 334 0.250295 CCCGTTGACTGAGCCTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
342 344 0.978146 CCCTCATCCTCCCGTTGACT 60.978 60.000 0.00 0.00 0.00 3.41
343 345 0.976073 TCCCTCATCCTCCCGTTGAC 60.976 60.000 0.00 0.00 0.00 3.18
344 346 0.687757 CTCCCTCATCCTCCCGTTGA 60.688 60.000 0.00 0.00 0.00 3.18
346 348 1.383248 CCTCCCTCATCCTCCCGTT 60.383 63.158 0.00 0.00 0.00 4.44
347 349 2.283809 CCTCCCTCATCCTCCCGT 59.716 66.667 0.00 0.00 0.00 5.28
348 350 1.532794 CTCCTCCCTCATCCTCCCG 60.533 68.421 0.00 0.00 0.00 5.14
353 392 2.022240 GCGTCACTCCTCCCTCATCC 62.022 65.000 0.00 0.00 0.00 3.51
364 403 2.556287 CTTTTGCCGGCGTCACTC 59.444 61.111 23.90 0.00 0.00 3.51
374 413 0.332972 ACCCATCTCCTCCTTTTGCC 59.667 55.000 0.00 0.00 0.00 4.52
377 416 1.918957 CCTCACCCATCTCCTCCTTTT 59.081 52.381 0.00 0.00 0.00 2.27
381 420 0.031616 ACTCCTCACCCATCTCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
391 430 2.359230 GCAGTGCCACTCCTCACC 60.359 66.667 2.85 0.00 33.90 4.02
397 436 0.801251 CTTGCTAAGCAGTGCCACTC 59.199 55.000 12.58 0.00 40.61 3.51
398 437 0.397941 TCTTGCTAAGCAGTGCCACT 59.602 50.000 12.58 0.00 40.61 4.00
406 445 0.321919 CAGCCCACTCTTGCTAAGCA 60.322 55.000 0.00 0.00 35.69 3.91
410 449 4.778213 ATAAATCAGCCCACTCTTGCTA 57.222 40.909 0.00 0.00 35.69 3.49
422 461 2.488153 GCCATTCCGGGTATAAATCAGC 59.512 50.000 0.00 0.00 34.06 4.26
424 463 3.149005 GGCCATTCCGGGTATAAATCA 57.851 47.619 0.00 0.00 34.06 2.57
447 486 2.972505 CACGTTTGCCGCTGGAGT 60.973 61.111 0.00 0.00 41.42 3.85
448 487 3.726517 CCACGTTTGCCGCTGGAG 61.727 66.667 0.00 0.00 38.94 3.86
457 496 1.080839 CCAAATCCGGCCACGTTTG 60.081 57.895 2.24 9.97 36.44 2.93
467 506 0.030101 ACACAAACACGCCAAATCCG 59.970 50.000 0.00 0.00 0.00 4.18
469 508 2.483583 TCACACAAACACGCCAAATC 57.516 45.000 0.00 0.00 0.00 2.17
479 518 4.439776 GCAAAGTACGGAATTCACACAAAC 59.560 41.667 7.93 0.00 0.00 2.93
484 523 2.811431 CCAGCAAAGTACGGAATTCACA 59.189 45.455 7.93 0.00 0.00 3.58
485 524 3.071479 TCCAGCAAAGTACGGAATTCAC 58.929 45.455 7.93 0.00 0.00 3.18
496 535 2.099098 CGAAAAACAGGTCCAGCAAAGT 59.901 45.455 0.00 0.00 0.00 2.66
502 542 3.123621 CGAGATTCGAAAAACAGGTCCAG 59.876 47.826 0.00 0.00 43.74 3.86
516 556 1.593006 CGGGTTGGAATTCGAGATTCG 59.407 52.381 0.00 0.00 42.10 3.34
535 575 9.688592 AGTACCGAATTCTAATATTAACCTTCG 57.311 33.333 17.55 17.55 35.33 3.79
547 587 9.582431 CAAGTCTCAATAAGTACCGAATTCTAA 57.418 33.333 3.52 0.00 0.00 2.10
548 588 7.705325 GCAAGTCTCAATAAGTACCGAATTCTA 59.295 37.037 3.52 0.00 0.00 2.10
549 589 6.535508 GCAAGTCTCAATAAGTACCGAATTCT 59.464 38.462 3.52 0.00 0.00 2.40
556 596 5.086104 TCTGGCAAGTCTCAATAAGTACC 57.914 43.478 0.00 0.00 0.00 3.34
565 605 6.605471 TTAGAGTAATTCTGGCAAGTCTCA 57.395 37.500 0.00 0.00 36.61 3.27
570 610 7.792374 TTGCTATTAGAGTAATTCTGGCAAG 57.208 36.000 0.00 0.00 35.60 4.01
606 646 4.438200 CCAAGCGTGTGTACTTCTGTTTTT 60.438 41.667 0.00 0.00 0.00 1.94
613 662 1.000506 TCTCCCAAGCGTGTGTACTTC 59.999 52.381 0.00 0.00 0.00 3.01
634 683 2.317900 TGGGAGAGGGAGTAATCTTGGA 59.682 50.000 0.00 0.00 0.00 3.53
641 690 1.292242 AGCAGATGGGAGAGGGAGTAA 59.708 52.381 0.00 0.00 0.00 2.24
684 733 2.555547 GCAAAGCAACAGCCGTCCT 61.556 57.895 0.00 0.00 0.00 3.85
685 734 2.050077 GCAAAGCAACAGCCGTCC 60.050 61.111 0.00 0.00 0.00 4.79
687 736 1.999071 TTTCGCAAAGCAACAGCCGT 61.999 50.000 0.00 0.00 0.00 5.68
735 816 3.755965 ATACATTTCATTCGCAACGCA 57.244 38.095 0.00 0.00 0.00 5.24
736 817 5.434514 AAAATACATTTCATTCGCAACGC 57.565 34.783 0.00 0.00 0.00 4.84
737 818 9.784824 TTTTAAAAATACATTTCATTCGCAACG 57.215 25.926 0.00 0.00 0.00 4.10
754 838 6.989759 ACGATCCAGCCTTTTGTTTTAAAAAT 59.010 30.769 1.31 0.00 0.00 1.82
756 840 5.908341 ACGATCCAGCCTTTTGTTTTAAAA 58.092 33.333 0.00 0.00 0.00 1.52
771 855 4.631377 TGTTTGATTCTTGCTACGATCCAG 59.369 41.667 0.00 0.00 0.00 3.86
773 857 5.545658 TTGTTTGATTCTTGCTACGATCC 57.454 39.130 0.00 0.00 0.00 3.36
821 906 3.106407 GACAGCACCGACGACAGC 61.106 66.667 0.00 0.00 0.00 4.40
823 908 3.531920 GACGACAGCACCGACGACA 62.532 63.158 0.00 0.00 0.00 4.35
824 909 2.799916 GACGACAGCACCGACGAC 60.800 66.667 0.00 0.00 0.00 4.34
825 910 4.379143 CGACGACAGCACCGACGA 62.379 66.667 10.34 0.00 44.84 4.20
890 975 8.147058 ACATCGAAAGCTGTATATTGAAGAGAT 58.853 33.333 0.00 0.00 38.91 2.75
951 1037 2.365293 TGGCATAAATAGAGCGCTGAGA 59.635 45.455 18.48 0.00 0.00 3.27
1258 1352 1.741770 CCCGAACTGCAGCAGGTAC 60.742 63.158 26.38 14.97 35.51 3.34
2218 2312 3.267860 GCATCTGCCTTCCGCTCG 61.268 66.667 0.00 0.00 38.78 5.03
2263 2378 4.396790 ACAGCTGAGCTAACTACACTACTC 59.603 45.833 23.35 0.00 36.40 2.59
2264 2379 4.156922 CACAGCTGAGCTAACTACACTACT 59.843 45.833 23.35 0.00 36.40 2.57
2368 2491 7.463961 GGTAATCCAACCTCTATAGATTCGA 57.536 40.000 2.11 0.00 36.53 3.71
2409 2533 4.331968 TGAAGAAGGCGGATAAATGTTGT 58.668 39.130 0.00 0.00 0.00 3.32
2443 2567 2.551032 CCTGTTTTTACCTGTTCCCGAC 59.449 50.000 0.00 0.00 0.00 4.79
2470 2598 1.124780 TGTCTCCACGAACCCAGAAA 58.875 50.000 0.00 0.00 0.00 2.52
2471 2599 1.275291 GATGTCTCCACGAACCCAGAA 59.725 52.381 0.00 0.00 0.00 3.02
2482 2610 3.973425 TCAGTCTCATGAGATGTCTCCA 58.027 45.455 27.51 7.19 42.20 3.86
2494 2622 5.808366 TTGGTTGTTACTCTCAGTCTCAT 57.192 39.130 0.00 0.00 0.00 2.90
2496 2624 5.992217 ACATTTGGTTGTTACTCTCAGTCTC 59.008 40.000 0.00 0.00 0.00 3.36
2498 2626 5.560953 GCACATTTGGTTGTTACTCTCAGTC 60.561 44.000 0.00 0.00 0.00 3.51
2499 2627 4.275936 GCACATTTGGTTGTTACTCTCAGT 59.724 41.667 0.00 0.00 0.00 3.41
2500 2628 4.611355 CGCACATTTGGTTGTTACTCTCAG 60.611 45.833 0.00 0.00 0.00 3.35
2524 2652 4.751060 TGTCTCCGTGTTTCGCTTTATAT 58.249 39.130 0.00 0.00 38.35 0.86
2526 2654 3.034721 TGTCTCCGTGTTTCGCTTTAT 57.965 42.857 0.00 0.00 38.35 1.40
2527 2655 2.512485 TGTCTCCGTGTTTCGCTTTA 57.488 45.000 0.00 0.00 38.35 1.85
2529 2657 2.736144 TATGTCTCCGTGTTTCGCTT 57.264 45.000 0.00 0.00 38.35 4.68
2530 2658 2.736144 TTATGTCTCCGTGTTTCGCT 57.264 45.000 0.00 0.00 38.35 4.93
2531 2659 2.474032 GCTTTATGTCTCCGTGTTTCGC 60.474 50.000 0.00 0.00 38.35 4.70
2532 2660 2.222508 CGCTTTATGTCTCCGTGTTTCG 60.223 50.000 0.00 0.00 39.52 3.46
2541 2669 3.062234 CCCTTCGTTTCGCTTTATGTCTC 59.938 47.826 0.00 0.00 0.00 3.36
2543 2671 2.740447 ACCCTTCGTTTCGCTTTATGTC 59.260 45.455 0.00 0.00 0.00 3.06
2545 2673 3.824414 AACCCTTCGTTTCGCTTTATG 57.176 42.857 0.00 0.00 0.00 1.90
2559 2687 2.871096 TGAATCCGTGCTAAACCCTT 57.129 45.000 0.00 0.00 0.00 3.95
2561 2689 2.614057 CTCATGAATCCGTGCTAAACCC 59.386 50.000 0.00 0.00 0.00 4.11
2562 2690 3.531538 TCTCATGAATCCGTGCTAAACC 58.468 45.455 0.00 0.00 0.00 3.27
2563 2691 4.184629 ACTCTCATGAATCCGTGCTAAAC 58.815 43.478 0.00 0.00 0.00 2.01
2566 2694 3.023832 TGACTCTCATGAATCCGTGCTA 58.976 45.455 0.00 0.00 0.00 3.49
2570 2698 4.248859 CAAACTGACTCTCATGAATCCGT 58.751 43.478 0.00 0.00 0.00 4.69
2571 2699 3.063180 GCAAACTGACTCTCATGAATCCG 59.937 47.826 0.00 0.00 0.00 4.18
2572 2700 3.376546 GGCAAACTGACTCTCATGAATCC 59.623 47.826 0.00 0.00 0.00 3.01
2573 2701 4.260170 AGGCAAACTGACTCTCATGAATC 58.740 43.478 0.00 0.00 18.29 2.52
2574 2702 4.298103 AGGCAAACTGACTCTCATGAAT 57.702 40.909 0.00 0.00 18.29 2.57
2575 2703 3.777106 AGGCAAACTGACTCTCATGAA 57.223 42.857 0.00 0.00 18.29 2.57
2576 2704 3.405831 CAAGGCAAACTGACTCTCATGA 58.594 45.455 0.00 0.00 31.94 3.07
2577 2705 2.095364 GCAAGGCAAACTGACTCTCATG 60.095 50.000 0.00 0.00 31.94 3.07
2578 2706 2.157738 GCAAGGCAAACTGACTCTCAT 58.842 47.619 0.00 0.00 31.94 2.90
2579 2707 1.141657 AGCAAGGCAAACTGACTCTCA 59.858 47.619 0.00 0.00 31.94 3.27
2580 2708 1.803555 GAGCAAGGCAAACTGACTCTC 59.196 52.381 0.00 0.00 31.94 3.20
2581 2709 1.875576 CGAGCAAGGCAAACTGACTCT 60.876 52.381 0.00 0.00 31.94 3.24
2582 2710 0.514691 CGAGCAAGGCAAACTGACTC 59.485 55.000 0.00 0.00 31.94 3.36
2583 2711 0.106708 TCGAGCAAGGCAAACTGACT 59.893 50.000 0.00 0.00 37.28 3.41
2584 2712 0.235926 GTCGAGCAAGGCAAACTGAC 59.764 55.000 0.00 0.00 0.00 3.51
2585 2713 0.106708 AGTCGAGCAAGGCAAACTGA 59.893 50.000 0.00 0.00 0.00 3.41
2586 2714 0.514691 GAGTCGAGCAAGGCAAACTG 59.485 55.000 0.00 0.00 0.00 3.16
2587 2715 0.394565 AGAGTCGAGCAAGGCAAACT 59.605 50.000 0.00 0.00 0.00 2.66
2588 2716 0.514691 CAGAGTCGAGCAAGGCAAAC 59.485 55.000 0.00 0.00 0.00 2.93
2589 2717 0.106708 ACAGAGTCGAGCAAGGCAAA 59.893 50.000 0.00 0.00 0.00 3.68
2597 2725 2.638556 TGCTAAGAACAGAGTCGAGC 57.361 50.000 0.00 0.00 34.04 5.03
2748 2877 4.980805 TCGCGTGGTGGAGTTGGC 62.981 66.667 5.77 0.00 0.00 4.52
2749 2878 3.041940 GTCGCGTGGTGGAGTTGG 61.042 66.667 5.77 0.00 0.00 3.77
2750 2879 3.041940 GGTCGCGTGGTGGAGTTG 61.042 66.667 5.77 0.00 0.00 3.16
2751 2880 4.309950 GGGTCGCGTGGTGGAGTT 62.310 66.667 5.77 0.00 0.00 3.01
2758 2887 3.622060 AAAGGATGGGGTCGCGTGG 62.622 63.158 5.77 0.00 0.00 4.94
2759 2888 2.046314 AAAGGATGGGGTCGCGTG 60.046 61.111 5.77 0.00 0.00 5.34
2760 2889 2.267961 GAAAGGATGGGGTCGCGT 59.732 61.111 5.77 0.00 0.00 6.01
2761 2890 1.815421 CAGAAAGGATGGGGTCGCG 60.815 63.158 0.00 0.00 0.00 5.87
2762 2891 1.452108 CCAGAAAGGATGGGGTCGC 60.452 63.158 0.00 0.00 41.22 5.19
2763 2892 1.452108 GCCAGAAAGGATGGGGTCG 60.452 63.158 0.00 0.00 41.22 4.79
2764 2893 1.076705 GGCCAGAAAGGATGGGGTC 60.077 63.158 0.00 0.00 41.22 4.46
2765 2894 2.626467 GGGCCAGAAAGGATGGGGT 61.626 63.158 4.39 0.00 41.22 4.95
2766 2895 2.280079 GGGCCAGAAAGGATGGGG 59.720 66.667 4.39 0.00 41.22 4.96
2767 2896 2.280079 GGGGCCAGAAAGGATGGG 59.720 66.667 4.39 0.00 41.22 4.00
2768 2897 2.124151 CGGGGCCAGAAAGGATGG 60.124 66.667 4.39 0.00 41.22 3.51
2769 2898 1.452108 GACGGGGCCAGAAAGGATG 60.452 63.158 11.67 0.00 41.22 3.51
2770 2899 2.680370 GGACGGGGCCAGAAAGGAT 61.680 63.158 11.67 0.00 41.22 3.24
2771 2900 3.327404 GGACGGGGCCAGAAAGGA 61.327 66.667 11.67 0.00 41.22 3.36
2772 2901 2.499303 AATGGACGGGGCCAGAAAGG 62.499 60.000 11.67 0.00 42.15 3.11
2773 2902 0.611896 AAATGGACGGGGCCAGAAAG 60.612 55.000 11.67 0.00 42.15 2.62
2774 2903 0.699399 TAAATGGACGGGGCCAGAAA 59.301 50.000 11.67 0.00 42.15 2.52
2775 2904 0.254747 CTAAATGGACGGGGCCAGAA 59.745 55.000 11.67 0.00 42.15 3.02
2776 2905 1.632018 CCTAAATGGACGGGGCCAGA 61.632 60.000 11.67 0.00 42.15 3.86
2777 2906 1.152963 CCTAAATGGACGGGGCCAG 60.153 63.158 4.39 3.10 42.15 4.85
2778 2907 2.685534 CCCTAAATGGACGGGGCCA 61.686 63.158 4.39 0.00 43.23 5.36
2779 2908 1.347243 TACCCTAAATGGACGGGGCC 61.347 60.000 0.00 0.00 42.44 5.80
2780 2909 0.547553 TTACCCTAAATGGACGGGGC 59.452 55.000 0.00 0.00 42.44 5.80
2781 2910 3.284617 CTTTTACCCTAAATGGACGGGG 58.715 50.000 0.00 0.00 42.44 5.73
2782 2911 3.284617 CCTTTTACCCTAAATGGACGGG 58.715 50.000 0.00 0.00 42.46 5.28
2783 2912 3.054213 TCCCTTTTACCCTAAATGGACGG 60.054 47.826 7.80 0.00 42.46 4.79
2784 2913 3.943381 GTCCCTTTTACCCTAAATGGACG 59.057 47.826 7.48 0.00 42.46 4.79
2785 2914 4.925836 TGTCCCTTTTACCCTAAATGGAC 58.074 43.478 13.31 13.31 42.46 4.02
2786 2915 5.602291 TTGTCCCTTTTACCCTAAATGGA 57.398 39.130 7.80 0.00 42.46 3.41
2787 2916 5.046878 GGTTTGTCCCTTTTACCCTAAATGG 60.047 44.000 0.00 0.00 40.65 3.16
2788 2917 5.778241 AGGTTTGTCCCTTTTACCCTAAATG 59.222 40.000 0.00 0.00 36.75 2.32
2789 2918 5.972698 AGGTTTGTCCCTTTTACCCTAAAT 58.027 37.500 0.00 0.00 36.75 1.40
2790 2919 5.406570 AGGTTTGTCCCTTTTACCCTAAA 57.593 39.130 0.00 0.00 36.75 1.85
2791 2920 5.851138 TCTAGGTTTGTCCCTTTTACCCTAA 59.149 40.000 0.00 0.00 35.97 2.69
2792 2921 5.414171 TCTAGGTTTGTCCCTTTTACCCTA 58.586 41.667 0.00 0.00 35.97 3.53
2793 2922 4.245308 TCTAGGTTTGTCCCTTTTACCCT 58.755 43.478 0.00 0.00 35.97 4.34
2794 2923 4.586884 CTCTAGGTTTGTCCCTTTTACCC 58.413 47.826 0.00 0.00 35.97 3.69
2795 2924 4.008330 GCTCTAGGTTTGTCCCTTTTACC 58.992 47.826 0.00 0.00 35.97 2.85
2796 2925 4.907809 AGCTCTAGGTTTGTCCCTTTTAC 58.092 43.478 0.00 0.00 35.97 2.01
2797 2926 5.072600 TGAAGCTCTAGGTTTGTCCCTTTTA 59.927 40.000 0.00 0.00 35.69 1.52
2798 2927 4.141251 TGAAGCTCTAGGTTTGTCCCTTTT 60.141 41.667 0.00 0.00 35.69 2.27
2799 2928 3.394606 TGAAGCTCTAGGTTTGTCCCTTT 59.605 43.478 0.00 0.00 35.69 3.11
2800 2929 2.979678 TGAAGCTCTAGGTTTGTCCCTT 59.020 45.455 0.00 0.00 35.69 3.95
2801 2930 2.621070 TGAAGCTCTAGGTTTGTCCCT 58.379 47.619 0.00 0.00 35.69 4.20
2802 2931 3.418684 TTGAAGCTCTAGGTTTGTCCC 57.581 47.619 0.00 0.00 35.69 4.46
2803 2932 3.753797 CCTTTGAAGCTCTAGGTTTGTCC 59.246 47.826 0.00 0.00 35.69 4.02
2804 2933 4.642429 TCCTTTGAAGCTCTAGGTTTGTC 58.358 43.478 0.00 0.00 35.69 3.18
2805 2934 4.706842 TCCTTTGAAGCTCTAGGTTTGT 57.293 40.909 0.00 0.00 35.69 2.83
2806 2935 5.308825 TCTTCCTTTGAAGCTCTAGGTTTG 58.691 41.667 0.00 0.00 46.28 2.93
2807 2936 5.568620 TCTTCCTTTGAAGCTCTAGGTTT 57.431 39.130 0.00 0.00 46.28 3.27
2808 2937 5.555966 CTTCTTCCTTTGAAGCTCTAGGTT 58.444 41.667 0.00 0.00 46.28 3.50
2837 2966 1.454479 CTTGGCCGCATCCTCCATT 60.454 57.895 0.00 0.00 0.00 3.16
2846 2975 2.927856 TTCCTCCTCTTGGCCGCA 60.928 61.111 0.00 0.00 0.00 5.69
2969 3099 0.251608 GGGCCACCTCCTTTGCTTTA 60.252 55.000 4.39 0.00 0.00 1.85
3006 3136 3.778618 TCTCGCTCATCTTGATCAAGTG 58.221 45.455 29.80 25.37 39.38 3.16
3038 3168 1.078214 CTGCCTGGCCTCGAATCAA 60.078 57.895 17.53 0.00 0.00 2.57
3041 3171 1.222936 CTTCTGCCTGGCCTCGAAT 59.777 57.895 17.53 0.00 0.00 3.34
3201 3352 0.649993 GTTTTGTTTGCCGGCAACAG 59.350 50.000 40.36 0.00 35.46 3.16
3212 3363 7.442062 CAGCCTCCAAAATGAATAGTTTTGTTT 59.558 33.333 9.60 0.00 42.25 2.83
3498 3688 2.032030 TCTTTTTGTAGCTGCGCTTGAC 60.032 45.455 9.73 1.91 40.44 3.18
3501 3691 1.537202 CCTCTTTTTGTAGCTGCGCTT 59.463 47.619 9.73 0.00 40.44 4.68
3508 3698 3.609409 CGTCTTTGCCCTCTTTTTGTAGC 60.609 47.826 0.00 0.00 0.00 3.58
3509 3699 4.147219 CGTCTTTGCCCTCTTTTTGTAG 57.853 45.455 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.