Multiple sequence alignment - TraesCS2B01G303200

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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 TraesCS2B01G303200 chr2B 100.000 5388 0 0 1 5388 429440848 429435461 0.000000e+00 9950.0
1 TraesCS2B01G303200 chr2B 95.432 810 23 8 4589 5388 780670855 780670050 0.000000e+00 1279.0
2 TraesCS2B01G303200 chr2B 87.109 256 26 3 1410 1665 429438370 429438618 3.180000e-72 283.0
3 TraesCS2B01G303200 chr2B 87.109 256 26 3 2231 2479 429439184 429439439 3.180000e-72 283.0
4 TraesCS2B01G303200 chr2B 89.189 185 13 1 2070 2254 429438699 429438522 1.950000e-54 224.0
5 TraesCS2B01G303200 chr2B 89.189 185 13 1 2150 2327 429438779 429438595 1.950000e-54 224.0
6 TraesCS2B01G303200 chr2D 92.544 2146 91 25 2479 4588 360281489 360283601 0.000000e+00 3013.0
7 TraesCS2B01G303200 chr2D 91.866 836 32 9 606 1411 360280666 360281495 0.000000e+00 1134.0
8 TraesCS2B01G303200 chr2D 97.143 70 2 0 567 636 360275360 360275429 9.480000e-23 119.0
9 TraesCS2B01G303200 chr2D 97.368 38 1 0 567 604 360280671 360280634 1.250000e-06 65.8
10 TraesCS2B01G303200 chr2A 87.986 1440 126 24 1 1410 485259851 485261273 0.000000e+00 1657.0
11 TraesCS2B01G303200 chr2A 89.540 1348 50 28 2477 3741 485261273 485262612 0.000000e+00 1624.0
12 TraesCS2B01G303200 chr2A 94.146 820 25 16 3783 4588 485262610 485263420 0.000000e+00 1227.0
13 TraesCS2B01G303200 chr2A 87.218 266 30 4 1412 1675 115445911 115446174 3.150000e-77 300.0
14 TraesCS2B01G303200 chr2A 82.900 269 44 2 1413 1680 115446783 115446516 1.940000e-59 241.0
15 TraesCS2B01G303200 chr2A 82.946 258 35 7 2228 2477 115446167 115445911 1.950000e-54 224.0
16 TraesCS2B01G303200 chr4D 96.415 809 19 3 4588 5388 358451764 358452570 0.000000e+00 1325.0
17 TraesCS2B01G303200 chr4D 96.040 808 22 3 4589 5388 42240014 42239209 0.000000e+00 1306.0
18 TraesCS2B01G303200 chr3D 96.411 808 20 3 4589 5388 388440439 388439633 0.000000e+00 1323.0
19 TraesCS2B01G303200 chr3D 95.797 809 22 5 4589 5388 579082349 579083154 0.000000e+00 1295.0
20 TraesCS2B01G303200 chr3D 95.787 807 25 2 4589 5388 84657975 84657171 0.000000e+00 1293.0
21 TraesCS2B01G303200 chr3D 90.336 476 41 3 1559 2031 447983827 447983354 2.130000e-173 619.0
22 TraesCS2B01G303200 chr3D 91.463 82 7 0 4136 4217 444486118 444486199 4.410000e-21 113.0
23 TraesCS2B01G303200 chr3D 90.698 43 3 1 4574 4616 42304879 42304920 7.540000e-04 56.5
24 TraesCS2B01G303200 chr5B 95.035 846 30 3 1412 2254 436094393 436095229 0.000000e+00 1319.0
25 TraesCS2B01G303200 chr5B 83.269 783 80 22 1411 2174 587345775 587346525 0.000000e+00 673.0
26 TraesCS2B01G303200 chr5B 94.444 324 18 0 2150 2473 436095052 436095375 2.900000e-137 499.0
27 TraesCS2B01G303200 chr5B 89.375 320 30 4 1410 1727 587346676 587346359 3.020000e-107 399.0
28 TraesCS2B01G303200 chr5B 88.142 253 23 3 1413 1665 436095378 436095133 1.470000e-75 294.0
29 TraesCS2B01G303200 chr5B 87.795 254 22 7 2231 2477 436094644 436094393 6.830000e-74 289.0
30 TraesCS2B01G303200 chr5B 86.667 255 22 8 2228 2473 587346419 587346670 6.880000e-69 272.0
31 TraesCS2B01G303200 chr5B 81.154 260 39 9 2230 2480 232264968 232265226 3.290000e-47 200.0
32 TraesCS2B01G303200 chr6D 96.163 808 20 4 4589 5388 469360806 469360002 0.000000e+00 1310.0
33 TraesCS2B01G303200 chr6D 87.273 55 0 4 4587 4636 60561354 60561302 7.540000e-04 56.5
34 TraesCS2B01G303200 chr1D 95.134 822 28 5 4576 5388 26593497 26594315 0.000000e+00 1286.0
35 TraesCS2B01G303200 chr7D 95.550 809 24 5 4589 5388 387492132 387492937 0.000000e+00 1284.0
36 TraesCS2B01G303200 chr3B 93.292 805 33 4 1410 2210 434729694 434730481 0.000000e+00 1168.0
37 TraesCS2B01G303200 chr3B 94.788 307 16 0 2167 2473 434730358 434730664 3.770000e-131 479.0
38 TraesCS2B01G303200 chr3B 88.538 253 22 3 1413 1665 434730667 434730422 3.150000e-77 300.0
39 TraesCS2B01G303200 chr3B 87.160 257 24 6 2231 2479 434729949 434729694 3.180000e-72 283.0
40 TraesCS2B01G303200 chr3B 89.899 99 10 0 4136 4234 582408390 582408488 1.580000e-25 128.0
41 TraesCS2B01G303200 chr5D 83.892 776 69 26 1412 2174 495490449 495489717 0.000000e+00 689.0
42 TraesCS2B01G303200 chr4B 83.333 762 77 17 1416 2175 541244241 541243528 0.000000e+00 658.0
43 TraesCS2B01G303200 chr4A 88.559 236 22 3 1720 1953 721395119 721395351 1.140000e-71 281.0
44 TraesCS2B01G303200 chr4A 85.887 248 15 8 2230 2468 721396547 721396783 4.170000e-61 246.0
45 TraesCS2B01G303200 chr4A 82.609 230 16 10 1945 2174 721396446 721396651 1.190000e-41 182.0
46 TraesCS2B01G303200 chr4A 90.476 105 10 0 2150 2254 721396547 721396651 7.280000e-29 139.0
47 TraesCS2B01G303200 chr1A 88.333 180 19 2 1412 1590 56598181 56598359 1.180000e-51 215.0
48 TraesCS2B01G303200 chr1A 88.608 158 16 2 2320 2476 376711881 376711725 1.980000e-44 191.0
49 TraesCS2B01G303200 chr3A 86.905 168 14 2 4580 4739 50954680 50954513 1.190000e-41 182.0
50 TraesCS2B01G303200 chr3A 75.339 369 68 14 3856 4217 585331909 585332261 7.230000e-34 156.0
51 TraesCS2B01G303200 chr3A 85.714 63 1 2 4583 4637 257251486 257251548 5.830000e-05 60.2
52 TraesCS2B01G303200 chr6B 79.042 167 25 5 256 412 182593401 182593235 7.380000e-19 106.0
53 TraesCS2B01G303200 chr5A 87.037 54 0 4 4588 4636 423059769 423059718 3.000000e-03 54.7
54 TraesCS2B01G303200 chrUn 89.130 46 0 2 4589 4629 90699930 90699975 1.000000e-02 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 TraesCS2B01G303200 chr2B 429435461 429440848 5387 True 3466.000000 9950 92.792667 1 5388 3 chr2B.!!$R2 5387
1 TraesCS2B01G303200 chr2B 780670050 780670855 805 True 1279.000000 1279 95.432000 4589 5388 1 chr2B.!!$R1 799
2 TraesCS2B01G303200 chr2B 429438370 429439439 1069 False 283.000000 283 87.109000 1410 2479 2 chr2B.!!$F1 1069
3 TraesCS2B01G303200 chr2D 360280666 360283601 2935 False 2073.500000 3013 92.205000 606 4588 2 chr2D.!!$F2 3982
4 TraesCS2B01G303200 chr2A 485259851 485263420 3569 False 1502.666667 1657 90.557333 1 4588 3 chr2A.!!$F2 4587
5 TraesCS2B01G303200 chr2A 115445911 115446783 872 True 232.500000 241 82.923000 1413 2477 2 chr2A.!!$R1 1064
6 TraesCS2B01G303200 chr4D 358451764 358452570 806 False 1325.000000 1325 96.415000 4588 5388 1 chr4D.!!$F1 800
7 TraesCS2B01G303200 chr4D 42239209 42240014 805 True 1306.000000 1306 96.040000 4589 5388 1 chr4D.!!$R1 799
8 TraesCS2B01G303200 chr3D 388439633 388440439 806 True 1323.000000 1323 96.411000 4589 5388 1 chr3D.!!$R2 799
9 TraesCS2B01G303200 chr3D 579082349 579083154 805 False 1295.000000 1295 95.797000 4589 5388 1 chr3D.!!$F3 799
10 TraesCS2B01G303200 chr3D 84657171 84657975 804 True 1293.000000 1293 95.787000 4589 5388 1 chr3D.!!$R1 799
11 TraesCS2B01G303200 chr5B 436094393 436095375 982 False 909.000000 1319 94.739500 1412 2473 2 chr5B.!!$F2 1061
12 TraesCS2B01G303200 chr5B 587345775 587346670 895 False 472.500000 673 84.968000 1411 2473 2 chr5B.!!$F3 1062
13 TraesCS2B01G303200 chr5B 436094393 436095378 985 True 291.500000 294 87.968500 1413 2477 2 chr5B.!!$R2 1064
14 TraesCS2B01G303200 chr6D 469360002 469360806 804 True 1310.000000 1310 96.163000 4589 5388 1 chr6D.!!$R2 799
15 TraesCS2B01G303200 chr1D 26593497 26594315 818 False 1286.000000 1286 95.134000 4576 5388 1 chr1D.!!$F1 812
16 TraesCS2B01G303200 chr7D 387492132 387492937 805 False 1284.000000 1284 95.550000 4589 5388 1 chr7D.!!$F1 799
17 TraesCS2B01G303200 chr3B 434729694 434730664 970 False 823.500000 1168 94.040000 1410 2473 2 chr3B.!!$F2 1063
18 TraesCS2B01G303200 chr3B 434729694 434730667 973 True 291.500000 300 87.849000 1413 2479 2 chr3B.!!$R1 1066
19 TraesCS2B01G303200 chr5D 495489717 495490449 732 True 689.000000 689 83.892000 1412 2174 1 chr5D.!!$R1 762
20 TraesCS2B01G303200 chr4B 541243528 541244241 713 True 658.000000 658 83.333000 1416 2175 1 chr4B.!!$R1 759
21 TraesCS2B01G303200 chr4A 721395119 721396783 1664 False 212.000000 281 86.882750 1720 2468 4 chr4A.!!$F1 748

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
156 158 0.033781 GTTGCAACACATGGGCACAT 59.966 50.0 24.52 0.00 37.26 3.21 F
219 221 0.035036 TCGAGAGACGGAGCCGATAT 59.965 55.0 16.83 0.72 43.21 1.63 F
338 340 0.319813 AGAAAAATGCAAGCACCGGC 60.320 50.0 0.00 0.00 41.61 6.13 F
2209 3995 0.095935 CATTTCGTTCTGCCTCGCTG 59.904 55.0 0.00 0.00 0.00 5.18 F
2918 4788 0.248621 ACTGCAAAAGCGTGAAGTGC 60.249 50.0 0.00 0.00 35.94 4.40 F
3756 5639 0.320946 GCAGGTGTAACAACGGCCTA 60.321 55.0 0.00 0.00 36.33 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1420 0.734889 GGAGTACGTAGTTGCGGCTA 59.265 55.000 4.03 0.0 37.78 3.93 R
2190 3976 0.095935 CAGCGAGGCAGAACGAAATG 59.904 55.000 0.00 0.0 0.00 2.32 R
2269 4055 0.036010 AGTGAGGCAGAACGGAATGG 60.036 55.000 0.00 0.0 0.00 3.16 R
3506 5389 0.450983 GCTGCTAGCTTCTTGCCTTG 59.549 55.000 17.23 0.0 44.23 3.61 R
4066 5949 0.818040 GTCTGGTGCAAACTTCGGGT 60.818 55.000 0.00 0.0 0.00 5.28 R
5253 7164 1.070843 CCGTCTGTGTGTTTTGCTACG 60.071 52.381 0.00 0.0 0.00 3.51 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
33 34 5.011586 GGTAAGCCAATAAAGTGGTTACCA 58.988 41.667 22.18 0.00 44.45 3.25
49 50 5.950549 TGGTTACCAGACAAGTTTTTACCAA 59.049 36.000 0.00 0.00 0.00 3.67
55 56 8.936070 ACCAGACAAGTTTTTACCAAATTTAC 57.064 30.769 0.00 0.00 0.00 2.01
57 58 9.541143 CCAGACAAGTTTTTACCAAATTTACAT 57.459 29.630 0.00 0.00 0.00 2.29
108 110 4.689612 ATATGCTGGTAAATCACGGACT 57.310 40.909 0.00 0.00 0.00 3.85
113 115 2.167693 CTGGTAAATCACGGACTAGCCA 59.832 50.000 0.00 0.00 35.94 4.75
145 147 8.028354 CAGAATATTTATGTTCTGGTTGCAACA 58.972 33.333 29.55 15.29 46.10 3.33
148 150 5.528043 TTTATGTTCTGGTTGCAACACAT 57.472 34.783 29.55 27.86 35.37 3.21
151 153 1.039068 TTCTGGTTGCAACACATGGG 58.961 50.000 29.55 13.64 0.00 4.00
156 158 0.033781 GTTGCAACACATGGGCACAT 59.966 50.000 24.52 0.00 37.26 3.21
174 176 2.355756 ACATCCTATGAAATGCACGCAC 59.644 45.455 0.00 0.00 0.00 5.34
178 180 0.096802 TATGAAATGCACGCACGCAG 59.903 50.000 3.23 0.00 46.99 5.18
185 187 2.809601 CACGCACGCAGACCCTAC 60.810 66.667 0.00 0.00 0.00 3.18
187 189 4.814294 CGCACGCAGACCCTACCC 62.814 72.222 0.00 0.00 0.00 3.69
188 190 3.391382 GCACGCAGACCCTACCCT 61.391 66.667 0.00 0.00 0.00 4.34
195 197 2.679082 GCAGACCCTACCCTTATGAGA 58.321 52.381 0.00 0.00 0.00 3.27
201 203 5.841783 AGACCCTACCCTTATGAGAATCTTC 59.158 44.000 0.00 0.00 34.92 2.87
202 204 4.589374 ACCCTACCCTTATGAGAATCTTCG 59.411 45.833 0.00 0.00 34.92 3.79
217 219 1.440938 CTTCGAGAGACGGAGCCGAT 61.441 60.000 16.83 3.42 40.88 4.18
219 221 0.035036 TCGAGAGACGGAGCCGATAT 59.965 55.000 16.83 0.72 43.21 1.63
228 230 5.437946 AGACGGAGCCGATATATCATCTTA 58.562 41.667 16.83 0.00 42.83 2.10
235 237 8.081633 GGAGCCGATATATCATCTTAAGATCAG 58.918 40.741 15.24 5.78 31.21 2.90
237 239 6.362016 GCCGATATATCATCTTAAGATCAGCG 59.638 42.308 15.24 11.63 31.21 5.18
243 245 6.841443 ATCATCTTAAGATCAGCGAAGTTG 57.159 37.500 15.24 2.26 41.18 3.16
254 256 1.735571 AGCGAAGTTGTCACAAACGTT 59.264 42.857 12.35 0.00 35.13 3.99
291 293 3.833070 AGATGTCTCCTTCCACTAAACGT 59.167 43.478 0.00 0.00 0.00 3.99
297 299 6.209192 TGTCTCCTTCCACTAAACGTACATTA 59.791 38.462 0.00 0.00 0.00 1.90
298 300 6.750963 GTCTCCTTCCACTAAACGTACATTAG 59.249 42.308 11.83 11.83 36.62 1.73
299 301 6.435277 TCTCCTTCCACTAAACGTACATTAGT 59.565 38.462 12.85 12.85 42.73 2.24
337 339 2.228822 ACTAGAAAAATGCAAGCACCGG 59.771 45.455 0.00 0.00 0.00 5.28
338 340 0.319813 AGAAAAATGCAAGCACCGGC 60.320 50.000 0.00 0.00 41.61 6.13
352 354 0.320160 ACCGGCGTCAAGTTTAGGAC 60.320 55.000 6.01 0.00 0.00 3.85
365 367 6.867662 AAGTTTAGGACTTGAACACTGATG 57.132 37.500 0.00 0.00 46.66 3.07
366 368 5.308825 AGTTTAGGACTTGAACACTGATGG 58.691 41.667 0.00 0.00 33.92 3.51
368 370 3.864789 AGGACTTGAACACTGATGGTT 57.135 42.857 0.00 0.00 0.00 3.67
370 372 5.304686 AGGACTTGAACACTGATGGTTAA 57.695 39.130 0.00 0.00 0.00 2.01
371 373 5.308825 AGGACTTGAACACTGATGGTTAAG 58.691 41.667 0.00 0.00 43.20 1.85
377 379 5.741011 TGAACACTGATGGTTAAGGATACC 58.259 41.667 0.00 0.00 36.17 2.73
392 394 4.426704 AGGATACCACTGTCCTTACAACT 58.573 43.478 0.00 0.00 42.09 3.16
394 396 6.203072 AGGATACCACTGTCCTTACAACTAT 58.797 40.000 0.00 0.00 42.09 2.12
399 401 5.250774 ACCACTGTCCTTACAACTATCCAAT 59.749 40.000 0.00 0.00 34.49 3.16
413 415 9.295825 ACAACTATCCAATTACAAGTTGATTCA 57.704 29.630 20.25 0.00 46.29 2.57
418 420 7.681939 TCCAATTACAAGTTGATTCAGTACC 57.318 36.000 10.54 0.00 0.00 3.34
420 422 6.370442 CCAATTACAAGTTGATTCAGTACCGA 59.630 38.462 10.54 0.00 0.00 4.69
424 426 4.202326 ACAAGTTGATTCAGTACCGACCTT 60.202 41.667 10.54 0.00 0.00 3.50
429 431 6.435277 AGTTGATTCAGTACCGACCTTACTTA 59.565 38.462 0.00 0.00 0.00 2.24
433 435 8.316214 TGATTCAGTACCGACCTTACTTAAAAT 58.684 33.333 0.00 0.00 0.00 1.82
436 438 6.211184 TCAGTACCGACCTTACTTAAAATGGA 59.789 38.462 0.00 0.00 0.00 3.41
482 484 2.755650 AGTAACACTTTGCTCCGAGTG 58.244 47.619 0.00 2.22 46.65 3.51
566 574 1.751437 GGCCGCCATCTAGAAAACTT 58.249 50.000 3.91 0.00 0.00 2.66
567 575 1.401905 GGCCGCCATCTAGAAAACTTG 59.598 52.381 3.91 0.00 0.00 3.16
579 587 2.034685 AGAAAACTTGAAGGAAAGCCGC 59.965 45.455 0.00 0.00 39.96 6.53
724 738 2.985282 TAACGCGACCTGTCCCGT 60.985 61.111 15.93 4.29 44.76 5.28
805 819 1.606350 CGAAGACACGGACGAACAGC 61.606 60.000 0.00 0.00 0.00 4.40
856 874 2.659063 CGCCTCTCCCACATCCACA 61.659 63.158 0.00 0.00 0.00 4.17
861 879 1.077930 CTCCCACATCCACAGCCAG 60.078 63.158 0.00 0.00 0.00 4.85
880 898 3.650942 CCAGGCAAGGGTCCATAAGTATA 59.349 47.826 0.00 0.00 0.00 1.47
881 899 4.289672 CCAGGCAAGGGTCCATAAGTATAT 59.710 45.833 0.00 0.00 0.00 0.86
882 900 5.222130 CCAGGCAAGGGTCCATAAGTATATT 60.222 44.000 0.00 0.00 0.00 1.28
884 902 6.207417 CAGGCAAGGGTCCATAAGTATATTTG 59.793 42.308 0.00 0.00 0.00 2.32
886 904 5.048013 GCAAGGGTCCATAAGTATATTTGCC 60.048 44.000 0.00 0.00 33.14 4.52
887 905 4.906618 AGGGTCCATAAGTATATTTGCCG 58.093 43.478 0.00 0.00 0.00 5.69
1159 1201 4.449068 CCTCATTGTATATCTTGTCCGTGC 59.551 45.833 0.00 0.00 0.00 5.34
1303 1345 1.202817 GAGGTGAAGGAGAACTCGGTC 59.797 57.143 0.00 0.00 0.00 4.79
1306 1348 1.153804 GAAGGAGAACTCGGTCCGC 60.154 63.158 6.34 0.00 37.97 5.54
1366 1408 1.442184 CGAGTTCGACGTCCAGGTG 60.442 63.158 10.58 0.00 43.02 4.00
1378 1420 6.263842 TCGACGTCCAGGTGAACTATTATTAT 59.736 38.462 10.58 0.00 0.00 1.28
2184 3970 4.838152 CGGCAGGTCCCACCATCG 62.838 72.222 0.00 0.00 41.95 3.84
2185 3971 4.489771 GGCAGGTCCCACCATCGG 62.490 72.222 0.00 0.00 41.95 4.18
2187 3973 4.489771 CAGGTCCCACCATCGGCC 62.490 72.222 0.00 0.00 41.95 6.13
2188 3974 4.741239 AGGTCCCACCATCGGCCT 62.741 66.667 0.00 0.00 41.95 5.19
2189 3975 4.176752 GGTCCCACCATCGGCCTC 62.177 72.222 0.00 0.00 38.42 4.70
2190 3976 4.176752 GTCCCACCATCGGCCTCC 62.177 72.222 0.00 0.00 0.00 4.30
2191 3977 4.731853 TCCCACCATCGGCCTCCA 62.732 66.667 0.00 0.00 0.00 3.86
2192 3978 3.492353 CCCACCATCGGCCTCCAT 61.492 66.667 0.00 0.00 0.00 3.41
2193 3979 2.597340 CCACCATCGGCCTCCATT 59.403 61.111 0.00 0.00 0.00 3.16
2194 3980 1.076777 CCACCATCGGCCTCCATTT 60.077 57.895 0.00 0.00 0.00 2.32
2195 3981 1.103398 CCACCATCGGCCTCCATTTC 61.103 60.000 0.00 0.00 0.00 2.17
2196 3982 1.153168 ACCATCGGCCTCCATTTCG 60.153 57.895 0.00 0.00 0.00 3.46
2197 3983 1.153168 CCATCGGCCTCCATTTCGT 60.153 57.895 0.00 0.00 0.00 3.85
2198 3984 0.748005 CCATCGGCCTCCATTTCGTT 60.748 55.000 0.00 0.00 0.00 3.85
2199 3985 0.657840 CATCGGCCTCCATTTCGTTC 59.342 55.000 0.00 0.00 0.00 3.95
2200 3986 0.541863 ATCGGCCTCCATTTCGTTCT 59.458 50.000 0.00 0.00 0.00 3.01
2201 3987 0.391130 TCGGCCTCCATTTCGTTCTG 60.391 55.000 0.00 0.00 0.00 3.02
2202 3988 1.803289 GGCCTCCATTTCGTTCTGC 59.197 57.895 0.00 0.00 0.00 4.26
2203 3989 1.657751 GGCCTCCATTTCGTTCTGCC 61.658 60.000 0.00 0.00 0.00 4.85
2204 3990 0.678048 GCCTCCATTTCGTTCTGCCT 60.678 55.000 0.00 0.00 0.00 4.75
2205 3991 1.373570 CCTCCATTTCGTTCTGCCTC 58.626 55.000 0.00 0.00 0.00 4.70
2206 3992 1.002366 CTCCATTTCGTTCTGCCTCG 58.998 55.000 0.00 0.00 0.00 4.63
2207 3993 1.019278 TCCATTTCGTTCTGCCTCGC 61.019 55.000 0.00 0.00 0.00 5.03
2208 3994 1.021390 CCATTTCGTTCTGCCTCGCT 61.021 55.000 0.00 0.00 0.00 4.93
2209 3995 0.095935 CATTTCGTTCTGCCTCGCTG 59.904 55.000 0.00 0.00 0.00 5.18
2210 3996 1.639298 ATTTCGTTCTGCCTCGCTGC 61.639 55.000 0.00 0.00 0.00 5.25
2211 3997 2.715532 TTTCGTTCTGCCTCGCTGCT 62.716 55.000 0.00 0.00 0.00 4.24
2212 3998 3.184683 CGTTCTGCCTCGCTGCTC 61.185 66.667 0.00 0.00 0.00 4.26
2213 3999 3.184683 GTTCTGCCTCGCTGCTCG 61.185 66.667 0.00 0.00 40.15 5.03
2218 4004 4.498520 GCCTCGCTGCTCGCTGTA 62.499 66.667 0.00 0.00 38.27 2.74
2219 4005 2.181777 CCTCGCTGCTCGCTGTAA 59.818 61.111 0.00 0.00 38.27 2.41
2220 4006 1.227089 CCTCGCTGCTCGCTGTAAT 60.227 57.895 0.00 0.00 38.27 1.89
2221 4007 0.807667 CCTCGCTGCTCGCTGTAATT 60.808 55.000 0.00 0.00 38.27 1.40
2222 4008 1.002366 CTCGCTGCTCGCTGTAATTT 58.998 50.000 0.00 0.00 38.27 1.82
2223 4009 0.721154 TCGCTGCTCGCTGTAATTTG 59.279 50.000 0.00 0.00 38.27 2.32
2224 4010 0.721154 CGCTGCTCGCTGTAATTTGA 59.279 50.000 0.00 0.00 36.13 2.69
2225 4011 1.128507 CGCTGCTCGCTGTAATTTGAA 59.871 47.619 0.00 0.00 36.13 2.69
2226 4012 2.778659 GCTGCTCGCTGTAATTTGAAG 58.221 47.619 0.00 0.00 35.14 3.02
2227 4013 2.476854 GCTGCTCGCTGTAATTTGAAGG 60.477 50.000 0.00 0.00 35.14 3.46
2228 4014 1.468520 TGCTCGCTGTAATTTGAAGGC 59.531 47.619 0.00 0.00 0.00 4.35
2229 4015 1.740025 GCTCGCTGTAATTTGAAGGCT 59.260 47.619 0.00 0.00 0.00 4.58
2230 4016 2.476854 GCTCGCTGTAATTTGAAGGCTG 60.477 50.000 0.00 0.00 0.00 4.85
2231 4017 1.468520 TCGCTGTAATTTGAAGGCTGC 59.531 47.619 0.00 0.00 0.00 5.25
2232 4018 1.468054 CGCTGTAATTTGAAGGCTGCC 60.468 52.381 11.65 11.65 0.00 4.85
2233 4019 1.468054 GCTGTAATTTGAAGGCTGCCG 60.468 52.381 13.96 0.00 0.00 5.69
2234 4020 0.525761 TGTAATTTGAAGGCTGCCGC 59.474 50.000 13.96 10.30 0.00 6.53
2264 4050 4.838152 CGGCAGGTCCCACCATCG 62.838 72.222 0.00 0.00 41.95 3.84
2265 4051 4.489771 GGCAGGTCCCACCATCGG 62.490 72.222 0.00 0.00 41.95 4.18
2267 4053 4.489771 CAGGTCCCACCATCGGCC 62.490 72.222 0.00 0.00 41.95 6.13
2268 4054 4.741239 AGGTCCCACCATCGGCCT 62.741 66.667 0.00 0.00 41.95 5.19
2269 4055 4.176752 GGTCCCACCATCGGCCTC 62.177 72.222 0.00 0.00 38.42 4.70
2270 4056 4.176752 GTCCCACCATCGGCCTCC 62.177 72.222 0.00 0.00 0.00 4.30
2271 4057 4.731853 TCCCACCATCGGCCTCCA 62.732 66.667 0.00 0.00 0.00 3.86
2272 4058 3.492353 CCCACCATCGGCCTCCAT 61.492 66.667 0.00 0.00 0.00 3.41
2273 4059 2.597340 CCACCATCGGCCTCCATT 59.403 61.111 0.00 0.00 0.00 3.16
2274 4060 1.526917 CCACCATCGGCCTCCATTC 60.527 63.158 0.00 0.00 0.00 2.67
2275 4061 1.526917 CACCATCGGCCTCCATTCC 60.527 63.158 0.00 0.00 0.00 3.01
2276 4062 2.281070 CCATCGGCCTCCATTCCG 60.281 66.667 0.00 0.00 46.52 4.30
2277 4063 2.505982 CATCGGCCTCCATTCCGT 59.494 61.111 0.00 0.00 45.44 4.69
2278 4064 1.153168 CATCGGCCTCCATTCCGTT 60.153 57.895 0.00 0.00 45.44 4.44
2279 4065 1.146263 ATCGGCCTCCATTCCGTTC 59.854 57.895 0.00 0.00 45.44 3.95
2280 4066 1.338136 ATCGGCCTCCATTCCGTTCT 61.338 55.000 0.00 0.00 45.44 3.01
2281 4067 1.815421 CGGCCTCCATTCCGTTCTG 60.815 63.158 0.00 0.00 40.72 3.02
2282 4068 2.115291 GGCCTCCATTCCGTTCTGC 61.115 63.158 0.00 0.00 0.00 4.26
2283 4069 2.115291 GCCTCCATTCCGTTCTGCC 61.115 63.158 0.00 0.00 0.00 4.85
2284 4070 1.604378 CCTCCATTCCGTTCTGCCT 59.396 57.895 0.00 0.00 0.00 4.75
2285 4071 0.462759 CCTCCATTCCGTTCTGCCTC 60.463 60.000 0.00 0.00 0.00 4.70
2286 4072 0.250234 CTCCATTCCGTTCTGCCTCA 59.750 55.000 0.00 0.00 0.00 3.86
2451 4239 1.118356 TTTGGCAATTCCGTTGGGCT 61.118 50.000 0.00 0.00 38.29 5.19
2642 4433 3.000041 CAGCACTACAAATTAGGCGACA 59.000 45.455 0.00 0.00 0.00 4.35
2661 4491 6.404293 GGCGACATAGTTGGATAACATTTGTT 60.404 38.462 1.08 1.08 39.30 2.83
2679 4509 1.743394 GTTGGGCTCCTAATTTGACCG 59.257 52.381 0.00 0.00 0.00 4.79
2680 4510 0.988832 TGGGCTCCTAATTTGACCGT 59.011 50.000 0.00 0.00 0.00 4.83
2681 4511 1.339631 TGGGCTCCTAATTTGACCGTG 60.340 52.381 0.00 0.00 0.00 4.94
2682 4512 0.733150 GGCTCCTAATTTGACCGTGC 59.267 55.000 0.00 0.00 0.00 5.34
2683 4513 1.448985 GCTCCTAATTTGACCGTGCA 58.551 50.000 0.00 0.00 0.00 4.57
2684 4514 2.017049 GCTCCTAATTTGACCGTGCAT 58.983 47.619 0.00 0.00 0.00 3.96
2685 4515 2.423538 GCTCCTAATTTGACCGTGCATT 59.576 45.455 0.00 0.00 0.00 3.56
2686 4516 3.487544 GCTCCTAATTTGACCGTGCATTC 60.488 47.826 0.00 0.00 0.00 2.67
2687 4517 3.013921 TCCTAATTTGACCGTGCATTCC 58.986 45.455 0.00 0.00 0.00 3.01
2688 4518 2.099098 CCTAATTTGACCGTGCATTCCC 59.901 50.000 0.00 0.00 0.00 3.97
2689 4519 1.923356 AATTTGACCGTGCATTCCCT 58.077 45.000 0.00 0.00 0.00 4.20
2722 4552 2.851263 ATTAGTTCGGTCCAGCACAA 57.149 45.000 0.00 0.00 0.00 3.33
2737 4567 3.817084 CAGCACAAAAGAGACTCCATTCA 59.183 43.478 0.00 0.00 0.00 2.57
2868 4731 4.237724 GCAAGCTATAGATGCGTCACATA 58.762 43.478 8.99 4.58 39.84 2.29
2877 4747 9.617975 CTATAGATGCGTCACATACATATATGG 57.382 37.037 16.96 2.09 42.32 2.74
2895 4765 8.917088 CATATATGGGTTGTTTCATTTTCTCCT 58.083 33.333 4.68 0.00 0.00 3.69
2918 4788 0.248621 ACTGCAAAAGCGTGAAGTGC 60.249 50.000 0.00 0.00 35.94 4.40
2925 4795 3.764049 GCGTGAAGTGCGACGGTC 61.764 66.667 0.00 0.00 36.09 4.79
2952 4823 9.582431 TTTAAAACGTCACATTCCATTTTGTTA 57.418 25.926 0.00 0.00 0.00 2.41
3026 4897 6.540914 TCTTCACCGAACAAGATGTAAGTTTT 59.459 34.615 0.00 0.00 0.00 2.43
3048 4919 5.418310 TCAACTTCCGATCAACTTTTCAC 57.582 39.130 0.00 0.00 0.00 3.18
3112 4995 2.954611 CGACTGCGAGGTCTCACA 59.045 61.111 6.63 0.00 40.82 3.58
3130 5013 6.142320 GTCTCACAAAACAATGACCGAAATTC 59.858 38.462 0.00 0.00 0.00 2.17
3246 5129 2.354510 CAGAACAACCGAGAACTGCAAA 59.645 45.455 0.00 0.00 0.00 3.68
3256 5139 3.684305 CGAGAACTGCAAACATATGACCA 59.316 43.478 10.38 0.00 0.00 4.02
3281 5164 2.836154 GCACCCTCTGGACAACCA 59.164 61.111 0.00 0.00 44.76 3.67
3455 5338 1.452399 GTCGAGCTCAAGTTTGACGAC 59.548 52.381 15.40 15.75 42.61 4.34
3484 5367 1.572689 TACCAGGAGGAGGAGCTCGT 61.573 60.000 9.04 9.04 38.69 4.18
3506 5389 1.817099 CGTCCTGCAAGCCATCCTC 60.817 63.158 0.00 0.00 0.00 3.71
3537 5420 4.096190 AGCTAGCAGCATAATGACCATT 57.904 40.909 18.83 0.64 45.56 3.16
3566 5449 7.203218 TCTTTCTGTAATGGTCTGATGATACG 58.797 38.462 0.00 0.00 0.00 3.06
3756 5639 0.320946 GCAGGTGTAACAACGGCCTA 60.321 55.000 0.00 0.00 36.33 3.93
3823 5706 1.507141 CCGCAAACAGTGACTGACCC 61.507 60.000 20.97 3.64 35.18 4.46
4066 5949 0.390340 CAGCTCAAGTAAGCCAGCGA 60.390 55.000 0.00 0.00 43.56 4.93
4410 6298 3.363182 CGCGTCTTCTTCTCGGATAGTAG 60.363 52.174 0.00 0.00 0.00 2.57
4528 6421 1.202065 CCGTCCGATTGTTTGCATCAG 60.202 52.381 0.00 0.00 0.00 2.90
4572 6468 2.937873 GCCTGTGTAAATCTTGGGCGTA 60.938 50.000 0.00 0.00 0.00 4.42
4574 6470 4.699637 CCTGTGTAAATCTTGGGCGTATA 58.300 43.478 0.00 0.00 0.00 1.47
4637 6540 3.712907 GCCGGTCCAACCCTAGCA 61.713 66.667 1.90 0.00 33.75 3.49
5042 6948 1.003118 AGAAATGCCTCGTGGTAGCAA 59.997 47.619 5.26 0.00 40.46 3.91
5130 7038 5.576384 CGCCATTGTAGCAAACATGTTAATT 59.424 36.000 12.39 2.82 38.10 1.40
5253 7164 1.361271 CATGGCCGCATGAATGGAC 59.639 57.895 0.00 0.00 34.66 4.02
5312 7224 1.144298 ACGGTTGTAGCTTTTCCCCTT 59.856 47.619 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 8.372459 AGTCCGTGATTTACCAGCATATATTAA 58.628 33.333 0.00 0.00 0.00 1.40
90 91 2.418197 GCTAGTCCGTGATTTACCAGCA 60.418 50.000 0.00 0.00 0.00 4.41
92 93 2.167693 TGGCTAGTCCGTGATTTACCAG 59.832 50.000 0.00 0.00 37.80 4.00
145 147 3.668141 TTTCATAGGATGTGCCCATGT 57.332 42.857 0.00 0.00 37.37 3.21
148 150 2.309613 GCATTTCATAGGATGTGCCCA 58.690 47.619 3.85 0.00 37.37 5.36
151 153 2.855953 GCGTGCATTTCATAGGATGTGC 60.856 50.000 7.36 7.36 35.52 4.57
156 158 1.006086 CGTGCGTGCATTTCATAGGA 58.994 50.000 0.00 0.00 0.00 2.94
174 176 1.341531 CTCATAAGGGTAGGGTCTGCG 59.658 57.143 0.00 0.00 0.00 5.18
178 180 5.279056 CGAAGATTCTCATAAGGGTAGGGTC 60.279 48.000 0.00 0.00 0.00 4.46
185 187 5.561919 CGTCTCTCGAAGATTCTCATAAGGG 60.562 48.000 0.00 0.00 42.86 3.95
187 189 5.237561 TCCGTCTCTCGAAGATTCTCATAAG 59.762 44.000 0.00 0.00 42.86 1.73
188 190 5.123936 TCCGTCTCTCGAAGATTCTCATAA 58.876 41.667 0.00 0.00 42.86 1.90
195 197 0.741915 GGCTCCGTCTCTCGAAGATT 59.258 55.000 0.00 0.00 42.86 2.40
201 203 1.723220 TATATCGGCTCCGTCTCTCG 58.277 55.000 8.28 0.00 40.74 4.04
202 204 3.271729 TGATATATCGGCTCCGTCTCTC 58.728 50.000 8.28 1.91 40.74 3.20
217 219 9.631452 CAACTTCGCTGATCTTAAGATGATATA 57.369 33.333 22.61 2.85 34.37 0.86
219 221 7.492524 ACAACTTCGCTGATCTTAAGATGATA 58.507 34.615 22.61 7.90 34.37 2.15
228 230 3.111853 TGTGACAACTTCGCTGATCTT 57.888 42.857 0.00 0.00 35.56 2.40
235 237 2.168201 AACGTTTGTGACAACTTCGC 57.832 45.000 13.62 0.00 35.05 4.70
237 239 4.153256 ACGAAAACGTTTGTGACAACTTC 58.847 39.130 15.46 3.96 29.57 3.01
242 244 3.925299 TGACTACGAAAACGTTTGTGACA 59.075 39.130 15.46 8.23 33.20 3.58
243 245 4.503767 TGACTACGAAAACGTTTGTGAC 57.496 40.909 15.46 6.07 33.20 3.67
268 270 4.082136 ACGTTTAGTGGAAGGAGACATCTC 60.082 45.833 0.00 0.00 42.14 2.75
269 271 3.833070 ACGTTTAGTGGAAGGAGACATCT 59.167 43.478 0.00 0.00 0.00 2.90
270 272 4.189639 ACGTTTAGTGGAAGGAGACATC 57.810 45.455 0.00 0.00 0.00 3.06
272 274 3.890756 TGTACGTTTAGTGGAAGGAGACA 59.109 43.478 0.00 0.00 0.00 3.41
274 276 5.733620 AATGTACGTTTAGTGGAAGGAGA 57.266 39.130 0.00 0.00 0.00 3.71
309 311 8.773645 GGTGCTTGCATTTTTCTAGTTTATTTT 58.226 29.630 0.00 0.00 0.00 1.82
317 319 2.867429 CCGGTGCTTGCATTTTTCTAG 58.133 47.619 0.00 0.00 0.00 2.43
318 320 1.067915 GCCGGTGCTTGCATTTTTCTA 60.068 47.619 1.90 0.00 33.53 2.10
322 324 2.049248 CGCCGGTGCTTGCATTTT 60.049 55.556 0.00 0.00 34.43 1.82
344 346 5.063880 ACCATCAGTGTTCAAGTCCTAAAC 58.936 41.667 0.00 0.00 0.00 2.01
352 354 6.316390 GGTATCCTTAACCATCAGTGTTCAAG 59.684 42.308 0.00 0.00 36.96 3.02
355 357 5.741011 TGGTATCCTTAACCATCAGTGTTC 58.259 41.667 0.00 0.00 42.10 3.18
356 358 5.772393 TGGTATCCTTAACCATCAGTGTT 57.228 39.130 0.00 0.00 42.10 3.32
371 373 4.820894 AGTTGTAAGGACAGTGGTATCC 57.179 45.455 0.00 0.00 36.76 2.59
377 379 7.822334 TGTAATTGGATAGTTGTAAGGACAGTG 59.178 37.037 0.00 0.00 36.76 3.66
381 383 8.788325 ACTTGTAATTGGATAGTTGTAAGGAC 57.212 34.615 0.00 0.00 0.00 3.85
387 389 9.295825 TGAATCAACTTGTAATTGGATAGTTGT 57.704 29.630 16.87 6.19 43.68 3.32
388 390 9.778993 CTGAATCAACTTGTAATTGGATAGTTG 57.221 33.333 13.75 13.75 44.27 3.16
392 394 9.391006 GGTACTGAATCAACTTGTAATTGGATA 57.609 33.333 0.00 0.00 0.00 2.59
394 396 6.370442 CGGTACTGAATCAACTTGTAATTGGA 59.630 38.462 0.00 0.00 0.00 3.53
399 401 5.011329 AGGTCGGTACTGAATCAACTTGTAA 59.989 40.000 5.82 0.00 0.00 2.41
413 415 6.610075 TCCATTTTAAGTAAGGTCGGTACT 57.390 37.500 0.00 0.00 33.12 2.73
417 419 7.501225 ACCATTATCCATTTTAAGTAAGGTCGG 59.499 37.037 0.00 0.00 0.00 4.79
418 420 8.446599 ACCATTATCCATTTTAAGTAAGGTCG 57.553 34.615 0.00 0.00 0.00 4.79
429 431 5.348164 GCGCTTTGTACCATTATCCATTTT 58.652 37.500 0.00 0.00 0.00 1.82
433 435 1.937223 CGCGCTTTGTACCATTATCCA 59.063 47.619 5.56 0.00 0.00 3.41
436 438 2.029970 CGAACGCGCTTTGTACCATTAT 59.970 45.455 5.73 0.00 0.00 1.28
445 447 0.315869 ACTTTCACGAACGCGCTTTG 60.316 50.000 5.73 6.57 42.48 2.77
453 455 4.905269 AGCAAAGTGTTACTTTCACGAAC 58.095 39.130 4.10 0.00 44.47 3.95
479 481 6.615264 AGATATGTCATTCGTACGTACACT 57.385 37.500 24.50 6.22 0.00 3.55
482 484 5.684184 TGCAAGATATGTCATTCGTACGTAC 59.316 40.000 15.90 15.90 0.00 3.67
543 551 0.461339 TTTCTAGATGGCGGCCGAAC 60.461 55.000 33.48 21.72 0.00 3.95
547 555 1.401905 CAAGTTTTCTAGATGGCGGCC 59.598 52.381 13.32 13.32 0.00 6.13
566 574 2.358247 GACGGCGGCTTTCCTTCA 60.358 61.111 13.24 0.00 0.00 3.02
567 575 2.358247 TGACGGCGGCTTTCCTTC 60.358 61.111 16.45 0.00 0.00 3.46
680 694 0.469917 ATGTTGGAGGCGAATCGGAT 59.530 50.000 4.35 0.00 0.00 4.18
724 738 9.472361 GGTTAAGCGATAAGATTTACACATCTA 57.528 33.333 0.00 0.00 32.84 1.98
786 800 1.606350 GCTGTTCGTCCGTGTCTTCG 61.606 60.000 0.00 0.00 0.00 3.79
787 801 1.282930 GGCTGTTCGTCCGTGTCTTC 61.283 60.000 0.00 0.00 0.00 2.87
788 802 1.300697 GGCTGTTCGTCCGTGTCTT 60.301 57.895 0.00 0.00 0.00 3.01
805 819 4.921515 ACGCTATATATACACACGCTTTGG 59.078 41.667 0.00 0.00 0.00 3.28
856 874 1.214305 TTATGGACCCTTGCCTGGCT 61.214 55.000 21.03 0.00 0.00 4.75
861 879 5.048013 GCAAATATACTTATGGACCCTTGCC 60.048 44.000 0.00 0.00 31.53 4.52
954 975 0.249911 AAGCCGAAGAAAGAGCGTGT 60.250 50.000 0.00 0.00 0.00 4.49
1303 1345 3.479269 GCGTCGTTGAAGGAGCGG 61.479 66.667 10.18 0.00 0.00 5.52
1306 1348 3.479269 GCGGCGTCGTTGAAGGAG 61.479 66.667 12.58 0.00 38.89 3.69
1366 1408 7.540055 ACGTAGTTGCGGCTATAATAATAGTTC 59.460 37.037 0.00 0.00 37.78 3.01
1378 1420 0.734889 GGAGTACGTAGTTGCGGCTA 59.265 55.000 4.03 0.00 37.78 3.93
1461 1509 2.918934 TGTCAATTTCATCTGGAGGGGA 59.081 45.455 0.00 0.00 0.00 4.81
1724 2016 0.797249 GTAGTCACGACGCAGCGATT 60.797 55.000 24.65 0.00 36.20 3.34
1823 2118 2.639065 GAACCTGGACAGTCAACAACA 58.361 47.619 0.00 0.00 0.00 3.33
1950 3385 3.532501 CATGCATGCATGGCAGGA 58.467 55.556 40.90 12.42 45.17 3.86
2167 3953 4.838152 CGATGGTGGGACCTGCCG 62.838 72.222 0.00 0.00 39.58 5.69
2168 3954 4.489771 CCGATGGTGGGACCTGCC 62.490 72.222 0.00 0.00 39.58 4.85
2170 3956 4.489771 GGCCGATGGTGGGACCTG 62.490 72.222 0.00 0.00 39.58 4.00
2171 3957 4.741239 AGGCCGATGGTGGGACCT 62.741 66.667 0.00 0.00 39.58 3.85
2172 3958 4.176752 GAGGCCGATGGTGGGACC 62.177 72.222 0.00 0.00 39.22 4.46
2173 3959 4.176752 GGAGGCCGATGGTGGGAC 62.177 72.222 0.00 0.00 0.00 4.46
2174 3960 4.731853 TGGAGGCCGATGGTGGGA 62.732 66.667 0.00 0.00 0.00 4.37
2175 3961 2.572333 AAATGGAGGCCGATGGTGGG 62.572 60.000 0.00 0.00 0.00 4.61
2176 3962 1.076777 AAATGGAGGCCGATGGTGG 60.077 57.895 0.00 0.00 0.00 4.61
2177 3963 1.439353 CGAAATGGAGGCCGATGGTG 61.439 60.000 0.00 0.00 0.00 4.17
2178 3964 1.153168 CGAAATGGAGGCCGATGGT 60.153 57.895 0.00 0.00 0.00 3.55
2179 3965 0.748005 AACGAAATGGAGGCCGATGG 60.748 55.000 0.00 0.00 0.00 3.51
2180 3966 0.657840 GAACGAAATGGAGGCCGATG 59.342 55.000 0.00 0.00 0.00 3.84
2181 3967 0.541863 AGAACGAAATGGAGGCCGAT 59.458 50.000 0.00 0.00 0.00 4.18
2182 3968 0.391130 CAGAACGAAATGGAGGCCGA 60.391 55.000 0.00 0.00 0.00 5.54
2183 3969 1.982073 GCAGAACGAAATGGAGGCCG 61.982 60.000 0.00 0.00 0.00 6.13
2184 3970 1.657751 GGCAGAACGAAATGGAGGCC 61.658 60.000 0.00 0.00 0.00 5.19
2185 3971 0.678048 AGGCAGAACGAAATGGAGGC 60.678 55.000 0.00 0.00 0.00 4.70
2186 3972 1.373570 GAGGCAGAACGAAATGGAGG 58.626 55.000 0.00 0.00 0.00 4.30
2187 3973 1.002366 CGAGGCAGAACGAAATGGAG 58.998 55.000 0.00 0.00 0.00 3.86
2188 3974 1.019278 GCGAGGCAGAACGAAATGGA 61.019 55.000 0.00 0.00 0.00 3.41
2189 3975 1.021390 AGCGAGGCAGAACGAAATGG 61.021 55.000 0.00 0.00 0.00 3.16
2190 3976 0.095935 CAGCGAGGCAGAACGAAATG 59.904 55.000 0.00 0.00 0.00 2.32
2191 3977 1.639298 GCAGCGAGGCAGAACGAAAT 61.639 55.000 0.00 0.00 0.00 2.17
2192 3978 2.317609 GCAGCGAGGCAGAACGAAA 61.318 57.895 0.00 0.00 0.00 3.46
2193 3979 2.738521 GCAGCGAGGCAGAACGAA 60.739 61.111 0.00 0.00 0.00 3.85
2194 3980 3.633094 GAGCAGCGAGGCAGAACGA 62.633 63.158 0.00 0.00 35.83 3.85
2195 3981 3.184683 GAGCAGCGAGGCAGAACG 61.185 66.667 1.57 0.00 35.83 3.95
2196 3982 3.184683 CGAGCAGCGAGGCAGAAC 61.185 66.667 1.57 0.00 44.57 3.01
2207 3993 2.476854 GCCTTCAAATTACAGCGAGCAG 60.477 50.000 0.00 0.00 0.00 4.24
2208 3994 1.468520 GCCTTCAAATTACAGCGAGCA 59.531 47.619 0.00 0.00 0.00 4.26
2209 3995 1.740025 AGCCTTCAAATTACAGCGAGC 59.260 47.619 0.00 0.00 0.00 5.03
2210 3996 2.476854 GCAGCCTTCAAATTACAGCGAG 60.477 50.000 0.00 0.00 0.00 5.03
2211 3997 1.468520 GCAGCCTTCAAATTACAGCGA 59.531 47.619 0.00 0.00 0.00 4.93
2212 3998 1.468054 GGCAGCCTTCAAATTACAGCG 60.468 52.381 3.29 0.00 0.00 5.18
2213 3999 1.468054 CGGCAGCCTTCAAATTACAGC 60.468 52.381 10.54 0.00 0.00 4.40
2214 4000 1.468054 GCGGCAGCCTTCAAATTACAG 60.468 52.381 10.54 0.00 37.42 2.74
2215 4001 0.525761 GCGGCAGCCTTCAAATTACA 59.474 50.000 10.54 0.00 37.42 2.41
2216 4002 3.329114 GCGGCAGCCTTCAAATTAC 57.671 52.632 10.54 0.00 37.42 1.89
2247 4033 4.838152 CGATGGTGGGACCTGCCG 62.838 72.222 0.00 0.00 39.58 5.69
2248 4034 4.489771 CCGATGGTGGGACCTGCC 62.490 72.222 0.00 0.00 39.58 4.85
2250 4036 4.489771 GGCCGATGGTGGGACCTG 62.490 72.222 0.00 0.00 39.58 4.00
2251 4037 4.741239 AGGCCGATGGTGGGACCT 62.741 66.667 0.00 0.00 39.58 3.85
2252 4038 4.176752 GAGGCCGATGGTGGGACC 62.177 72.222 0.00 0.00 39.22 4.46
2253 4039 4.176752 GGAGGCCGATGGTGGGAC 62.177 72.222 0.00 0.00 0.00 4.46
2254 4040 4.731853 TGGAGGCCGATGGTGGGA 62.732 66.667 0.00 0.00 0.00 4.37
2255 4041 2.965716 GAATGGAGGCCGATGGTGGG 62.966 65.000 0.00 0.00 0.00 4.61
2256 4042 1.526917 GAATGGAGGCCGATGGTGG 60.527 63.158 0.00 0.00 0.00 4.61
2257 4043 1.526917 GGAATGGAGGCCGATGGTG 60.527 63.158 0.00 0.00 0.00 4.17
2258 4044 2.919043 GGAATGGAGGCCGATGGT 59.081 61.111 0.00 0.00 0.00 3.55
2264 4050 2.115291 GCAGAACGGAATGGAGGCC 61.115 63.158 0.00 0.00 0.00 5.19
2265 4051 2.115291 GGCAGAACGGAATGGAGGC 61.115 63.158 0.00 0.00 0.00 4.70
2266 4052 0.462759 GAGGCAGAACGGAATGGAGG 60.463 60.000 0.00 0.00 0.00 4.30
2267 4053 0.250234 TGAGGCAGAACGGAATGGAG 59.750 55.000 0.00 0.00 0.00 3.86
2268 4054 0.036388 GTGAGGCAGAACGGAATGGA 60.036 55.000 0.00 0.00 0.00 3.41
2269 4055 0.036010 AGTGAGGCAGAACGGAATGG 60.036 55.000 0.00 0.00 0.00 3.16
2270 4056 1.081892 CAGTGAGGCAGAACGGAATG 58.918 55.000 0.00 0.00 0.00 2.67
2271 4057 0.687354 ACAGTGAGGCAGAACGGAAT 59.313 50.000 0.00 0.00 0.00 3.01
2272 4058 1.334160 TACAGTGAGGCAGAACGGAA 58.666 50.000 0.00 0.00 0.00 4.30
2273 4059 1.000506 GTTACAGTGAGGCAGAACGGA 59.999 52.381 0.00 0.00 0.00 4.69
2274 4060 1.000955 AGTTACAGTGAGGCAGAACGG 59.999 52.381 0.00 0.00 0.00 4.44
2275 4061 2.440539 AGTTACAGTGAGGCAGAACG 57.559 50.000 0.00 0.00 0.00 3.95
2276 4062 3.728845 TCAAGTTACAGTGAGGCAGAAC 58.271 45.455 0.00 0.00 0.00 3.01
2277 4063 4.380531 CTTCAAGTTACAGTGAGGCAGAA 58.619 43.478 0.00 0.00 0.00 3.02
2278 4064 3.244215 CCTTCAAGTTACAGTGAGGCAGA 60.244 47.826 0.00 0.00 0.00 4.26
2279 4065 3.070018 CCTTCAAGTTACAGTGAGGCAG 58.930 50.000 0.00 0.00 0.00 4.85
2280 4066 2.810400 GCCTTCAAGTTACAGTGAGGCA 60.810 50.000 9.67 0.00 37.69 4.75
2281 4067 1.807142 GCCTTCAAGTTACAGTGAGGC 59.193 52.381 0.00 0.00 33.77 4.70
2282 4068 3.070018 CAGCCTTCAAGTTACAGTGAGG 58.930 50.000 0.00 0.00 0.00 3.86
2283 4069 2.481952 GCAGCCTTCAAGTTACAGTGAG 59.518 50.000 0.00 0.00 0.00 3.51
2284 4070 2.104792 AGCAGCCTTCAAGTTACAGTGA 59.895 45.455 0.00 0.00 0.00 3.41
2285 4071 2.225019 CAGCAGCCTTCAAGTTACAGTG 59.775 50.000 0.00 0.00 0.00 3.66
2286 4072 2.498167 CAGCAGCCTTCAAGTTACAGT 58.502 47.619 0.00 0.00 0.00 3.55
2479 4267 3.534056 CCGTCGGGGTCGGCTAAT 61.534 66.667 2.34 0.00 41.48 1.73
2480 4268 4.738998 TCCGTCGGGGTCGGCTAA 62.739 66.667 12.29 0.00 46.49 3.09
2481 4269 4.738998 TTCCGTCGGGGTCGGCTA 62.739 66.667 12.29 0.00 46.49 3.93
2485 4273 3.048941 GAGACTTCCGTCGGGGTCG 62.049 68.421 22.71 9.45 44.93 4.79
2486 4274 2.883621 GAGACTTCCGTCGGGGTC 59.116 66.667 22.03 22.03 44.93 4.46
2642 4433 5.957774 AGCCCAACAAATGTTATCCAACTAT 59.042 36.000 0.00 0.00 36.32 2.12
2661 4491 0.988832 ACGGTCAAATTAGGAGCCCA 59.011 50.000 4.29 0.00 0.00 5.36
2681 4511 0.685458 AGGGAATGCACAGGGAATGC 60.685 55.000 0.00 0.00 43.68 3.56
2682 4512 1.856629 AAGGGAATGCACAGGGAATG 58.143 50.000 0.00 0.00 0.00 2.67
2683 4513 2.629017 AAAGGGAATGCACAGGGAAT 57.371 45.000 0.00 0.00 0.00 3.01
2684 4514 3.756082 ATAAAGGGAATGCACAGGGAA 57.244 42.857 0.00 0.00 0.00 3.97
2685 4515 3.756082 AATAAAGGGAATGCACAGGGA 57.244 42.857 0.00 0.00 0.00 4.20
2686 4516 4.536765 ACTAATAAAGGGAATGCACAGGG 58.463 43.478 0.00 0.00 0.00 4.45
2687 4517 5.220854 CGAACTAATAAAGGGAATGCACAGG 60.221 44.000 0.00 0.00 0.00 4.00
2688 4518 5.220854 CCGAACTAATAAAGGGAATGCACAG 60.221 44.000 0.00 0.00 0.00 3.66
2689 4519 4.638421 CCGAACTAATAAAGGGAATGCACA 59.362 41.667 0.00 0.00 0.00 4.57
2722 4552 3.519510 TCCGGATTGAATGGAGTCTCTTT 59.480 43.478 0.00 0.00 0.00 2.52
2737 4567 7.228706 CCACACTAGCTAAAAATAATCCGGATT 59.771 37.037 31.30 31.30 34.93 3.01
2868 4731 8.695456 GGAGAAAATGAAACAACCCATATATGT 58.305 33.333 11.73 0.00 0.00 2.29
2877 4747 4.320608 TGCAGGAGAAAATGAAACAACC 57.679 40.909 0.00 0.00 0.00 3.77
2925 4795 8.125728 ACAAAATGGAATGTGACGTTTTAAAG 57.874 30.769 0.00 0.00 34.90 1.85
2952 4823 2.042162 AGCCATCTTTGGTCACCTGAAT 59.958 45.455 0.00 0.00 45.57 2.57
3026 4897 5.007626 CAGTGAAAAGTTGATCGGAAGTTGA 59.992 40.000 0.00 0.00 0.00 3.18
3048 4919 4.297299 TGCTTCTTTTCTTCTTGTGCAG 57.703 40.909 0.00 0.00 0.00 4.41
3112 4995 4.262420 CCCTGGAATTTCGGTCATTGTTTT 60.262 41.667 0.00 0.00 0.00 2.43
3246 5129 1.337354 TGCGTGTCGTTGGTCATATGT 60.337 47.619 1.90 0.00 0.00 2.29
3256 5139 2.029073 CAGAGGGTGCGTGTCGTT 59.971 61.111 0.00 0.00 0.00 3.85
3281 5164 5.866159 TCAAGATGCTAGTCAGATGTCAT 57.134 39.130 0.00 0.00 0.00 3.06
3349 5232 2.632544 CGCACGTCCCACCTCAGTA 61.633 63.158 0.00 0.00 0.00 2.74
3422 5305 1.014044 GCTCGACATTGAAGCCGACA 61.014 55.000 0.00 0.00 0.00 4.35
3455 5338 0.663688 CCTCCTGGTACACGAGATCG 59.336 60.000 0.00 0.00 42.66 3.69
3506 5389 0.450983 GCTGCTAGCTTCTTGCCTTG 59.549 55.000 17.23 0.00 44.23 3.61
3537 5420 8.690203 TCATCAGACCATTACAGAAAGAAAAA 57.310 30.769 0.00 0.00 0.00 1.94
3560 5443 3.441163 GGCTGTTAATCGACACGTATCA 58.559 45.455 0.00 0.00 0.00 2.15
3566 5449 0.719465 CCACGGCTGTTAATCGACAC 59.281 55.000 0.00 0.00 0.00 3.67
3756 5639 4.127566 AGAACAATGCAAAAACAGCAGT 57.872 36.364 0.00 0.00 46.36 4.40
3808 5691 1.507140 TGGAGGGTCAGTCACTGTTT 58.493 50.000 4.28 0.00 32.61 2.83
3823 5706 3.915437 ATTTGCACGGTAACTTTGGAG 57.085 42.857 0.00 0.00 0.00 3.86
3915 5798 2.596851 GCCTGACAGCCTCCTCCAA 61.597 63.158 0.00 0.00 0.00 3.53
4066 5949 0.818040 GTCTGGTGCAAACTTCGGGT 60.818 55.000 0.00 0.00 0.00 5.28
4572 6468 1.767759 GCCCAACACAGAATGGCTAT 58.232 50.000 0.00 0.00 43.62 2.97
4574 6470 1.973281 CGCCCAACACAGAATGGCT 60.973 57.895 0.00 0.00 43.62 4.75
4581 6477 1.091771 CCTAGCATCGCCCAACACAG 61.092 60.000 0.00 0.00 0.00 3.66
4582 6478 1.078497 CCTAGCATCGCCCAACACA 60.078 57.895 0.00 0.00 0.00 3.72
4637 6540 1.901085 GGAACAGGCCGATCTGACT 59.099 57.895 11.04 0.00 38.11 3.41
4683 6587 2.868920 GCGAGAGGAAGACGACGT 59.131 61.111 0.00 0.00 0.00 4.34
5025 6931 2.128771 AATTGCTACCACGAGGCATT 57.871 45.000 0.00 0.00 39.06 3.56
5042 6948 2.288579 TGCTACGACTGACACGGAAAAT 60.289 45.455 0.00 0.00 34.93 1.82
5130 7038 2.161410 GCGATGTGTTTTGCTACATCCA 59.839 45.455 10.66 0.00 46.49 3.41
5253 7164 1.070843 CCGTCTGTGTGTTTTGCTACG 60.071 52.381 0.00 0.00 0.00 3.51
5312 7224 3.202829 ACAGAAAAGCTTCCACCGTAA 57.797 42.857 0.00 0.00 31.28 3.18


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

AutoCloner maintained by Alex Coulton.