Multiple sequence alignment - TraesCS2D01G538100

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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 TraesCS2D01G538100 chr2D 100.000 3137 0 0 1 3137 619438430 619435294 0.000000e+00 5794.0
1 TraesCS2D01G538100 chr2D 89.775 1066 65 25 465 1502 619427808 619426759 0.000000e+00 1325.0
2 TraesCS2D01G538100 chr2D 90.649 663 45 9 1842 2495 619426531 619425877 0.000000e+00 865.0
3 TraesCS2D01G538100 chr2D 83.333 546 54 24 1713 2239 620614529 620615056 1.320000e-128 470.0
4 TraesCS2D01G538100 chr2D 87.202 336 32 6 1902 2237 585861014 585861338 3.820000e-99 372.0
5 TraesCS2D01G538100 chr2D 88.780 205 23 0 995 1199 585860382 585860586 5.190000e-63 252.0
6 TraesCS2D01G538100 chr2D 84.279 229 33 3 2910 3136 619420146 619419919 1.460000e-53 220.0
7 TraesCS2D01G538100 chr2D 93.496 123 7 1 1519 1640 155730884 155731006 6.910000e-42 182.0
8 TraesCS2D01G538100 chr2A 97.604 1085 17 3 443 1526 750743971 750745047 0.000000e+00 1851.0
9 TraesCS2D01G538100 chr2A 97.422 1086 18 4 443 1526 750582589 750581512 0.000000e+00 1842.0
10 TraesCS2D01G538100 chr2A 97.934 726 14 1 1784 2508 750581357 750580632 0.000000e+00 1256.0
11 TraesCS2D01G538100 chr2A 97.934 726 14 1 1784 2508 750617402 750616677 0.000000e+00 1256.0
12 TraesCS2D01G538100 chr2A 96.862 733 15 1 1784 2508 750745202 750745934 0.000000e+00 1219.0
13 TraesCS2D01G538100 chr2A 98.065 620 7 1 907 1526 750618171 750617557 0.000000e+00 1074.0
14 TraesCS2D01G538100 chr2A 97.275 477 9 2 443 918 750621081 750620608 0.000000e+00 806.0
15 TraesCS2D01G538100 chr2A 98.232 396 7 0 1 396 750621472 750621077 0.000000e+00 693.0
16 TraesCS2D01G538100 chr2A 98.232 396 7 0 1 396 750743580 750743975 0.000000e+00 693.0
17 TraesCS2D01G538100 chr2A 97.980 396 8 0 1 396 750582980 750582585 0.000000e+00 688.0
18 TraesCS2D01G538100 chr2A 97.945 292 6 0 2612 2903 750580647 750580356 1.000000e-139 507.0
19 TraesCS2D01G538100 chr2A 95.890 292 5 3 2612 2903 750616692 750616408 1.700000e-127 466.0
20 TraesCS2D01G538100 chr2A 96.610 236 7 1 2903 3137 750616345 750616110 1.050000e-104 390.0
21 TraesCS2D01G538100 chr2A 96.186 236 8 1 2903 3137 750580293 750580058 4.910000e-103 385.0
22 TraesCS2D01G538100 chr2A 95.763 236 9 1 2903 3137 750650969 750650734 2.280000e-101 379.0
23 TraesCS2D01G538100 chr2A 97.000 200 6 0 2704 2903 750651231 750651032 1.390000e-88 337.0
24 TraesCS2D01G538100 chr2A 97.938 97 1 1 1695 1791 750581483 750581388 1.940000e-37 167.0
25 TraesCS2D01G538100 chr2A 97.938 97 1 1 1695 1791 750617528 750617433 1.940000e-37 167.0
26 TraesCS2D01G538100 chr2A 97.938 97 1 1 1695 1791 750745076 750745171 1.940000e-37 167.0
27 TraesCS2D01G538100 chr2A 98.925 93 1 0 2612 2704 750745919 750746011 1.940000e-37 167.0
28 TraesCS2D01G538100 chr2A 81.383 188 14 8 2216 2403 750615571 750615405 1.960000e-27 134.0
29 TraesCS2D01G538100 chr2A 80.851 188 15 10 2216 2403 750650195 750650029 9.130000e-26 128.0
30 TraesCS2D01G538100 chr2B 84.563 1030 99 33 236 1225 758151383 758150374 0.000000e+00 966.0
31 TraesCS2D01G538100 chr2B 87.923 828 67 17 1695 2508 758147698 758146890 0.000000e+00 944.0
32 TraesCS2D01G538100 chr2B 87.636 825 76 19 1695 2513 758373273 758372469 0.000000e+00 935.0
33 TraesCS2D01G538100 chr2B 86.288 846 63 19 461 1275 758374516 758373693 0.000000e+00 870.0
34 TraesCS2D01G538100 chr2B 88.295 692 52 13 1695 2373 758390064 758389389 0.000000e+00 802.0
35 TraesCS2D01G538100 chr2B 86.863 510 35 12 782 1261 758390865 758390358 2.750000e-150 542.0
36 TraesCS2D01G538100 chr2B 84.725 563 49 15 260 791 758391595 758391039 2.140000e-146 529.0
37 TraesCS2D01G538100 chr2B 92.754 207 12 2 1318 1524 758373497 758373294 2.370000e-76 296.0
38 TraesCS2D01G538100 chr2B 94.611 167 8 1 236 401 758375127 758374961 1.120000e-64 257.0
39 TraesCS2D01G538100 chr2B 82.492 297 40 6 2616 2905 758146901 758146610 1.870000e-62 250.0
40 TraesCS2D01G538100 chr2B 81.935 310 17 15 1222 1524 758390362 758390085 3.150000e-55 226.0
41 TraesCS2D01G538100 chr2B 80.882 272 17 13 1255 1524 758147957 758147719 6.910000e-42 182.0
42 TraesCS2D01G538100 chr4D 84.282 369 48 7 353 715 465752718 465753082 4.980000e-93 351.0
43 TraesCS2D01G538100 chr4D 89.030 237 24 2 1 236 35599051 35598816 3.060000e-75 292.0
44 TraesCS2D01G538100 chr7A 89.873 237 22 2 1 236 39236057 39235822 1.410000e-78 303.0
45 TraesCS2D01G538100 chr7A 96.117 103 4 0 2510 2612 610117165 610117063 5.380000e-38 169.0
46 TraesCS2D01G538100 chr7A 79.808 104 18 3 2509 2611 575986605 575986706 4.340000e-09 73.1
47 TraesCS2D01G538100 chr1A 89.873 237 22 2 1 236 353653128 353652893 1.410000e-78 303.0
48 TraesCS2D01G538100 chr1A 80.952 105 17 3 2508 2611 551727309 551727411 2.590000e-11 80.5
49 TraesCS2D01G538100 chr3D 89.873 237 21 3 1 236 110308111 110307877 5.080000e-78 302.0
50 TraesCS2D01G538100 chr6A 89.451 237 23 2 1 236 53087722 53087487 6.580000e-77 298.0
51 TraesCS2D01G538100 chr5B 89.451 237 22 3 1 236 275024449 275024683 2.370000e-76 296.0
52 TraesCS2D01G538100 chr5B 93.600 125 8 0 1515 1639 482187712 482187836 1.490000e-43 187.0
53 TraesCS2D01G538100 chr5B 90.977 133 10 2 1509 1640 525131479 525131348 8.940000e-41 178.0
54 TraesCS2D01G538100 chr4A 86.932 176 19 1 544 715 4824421 4824246 8.880000e-46 195.0
55 TraesCS2D01G538100 chr4A 94.958 119 6 0 1523 1641 687177667 687177785 1.490000e-43 187.0
56 TraesCS2D01G538100 chr5A 94.958 119 6 0 1523 1641 615961900 615962018 1.490000e-43 187.0
57 TraesCS2D01G538100 chr5A 93.496 123 6 2 1520 1641 490696668 490696789 6.910000e-42 182.0
58 TraesCS2D01G538100 chr5A 93.519 108 5 2 2507 2612 27698835 27698728 3.240000e-35 159.0
59 TraesCS2D01G538100 chr5A 93.269 104 6 1 2509 2612 11123022 11122920 5.420000e-33 152.0
60 TraesCS2D01G538100 chr3B 98.113 106 2 0 2507 2612 792755595 792755490 5.340000e-43 185.0
61 TraesCS2D01G538100 chr3B 96.226 106 3 1 2507 2612 807741184 807741080 4.160000e-39 172.0
62 TraesCS2D01G538100 chr1D 92.366 131 8 2 1512 1640 453059904 453060034 5.340000e-43 185.0
63 TraesCS2D01G538100 chr1B 98.113 106 2 0 2507 2612 45982330 45982225 5.340000e-43 185.0
64 TraesCS2D01G538100 chr7B 93.443 122 8 0 1520 1641 411754683 411754804 6.910000e-42 182.0
65 TraesCS2D01G538100 chr7B 94.118 119 7 0 1526 1644 712100750 712100632 6.910000e-42 182.0
66 TraesCS2D01G538100 chr6B 82.075 106 17 2 2507 2611 129488209 129488313 4.310000e-14 89.8


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 TraesCS2D01G538100 chr2D 619435294 619438430 3136 True 5794.000000 5794 100.000000 1 3137 1 chr2D.!!$R2 3136
1 TraesCS2D01G538100 chr2D 619425877 619427808 1931 True 1095.000000 1325 90.212000 465 2495 2 chr2D.!!$R3 2030
2 TraesCS2D01G538100 chr2D 620614529 620615056 527 False 470.000000 470 83.333000 1713 2239 1 chr2D.!!$F2 526
3 TraesCS2D01G538100 chr2D 585860382 585861338 956 False 312.000000 372 87.991000 995 2237 2 chr2D.!!$F3 1242
4 TraesCS2D01G538100 chr2A 750743580 750746011 2431 False 819.400000 1851 97.912200 1 2704 5 chr2A.!!$F1 2703
5 TraesCS2D01G538100 chr2A 750580058 750582980 2922 True 807.500000 1842 97.567500 1 3137 6 chr2A.!!$R1 3136
6 TraesCS2D01G538100 chr2A 750615405 750621472 6067 True 623.250000 1256 95.415875 1 3137 8 chr2A.!!$R2 3136
7 TraesCS2D01G538100 chr2A 750650029 750651231 1202 True 281.333333 379 91.204667 2216 3137 3 chr2A.!!$R3 921
8 TraesCS2D01G538100 chr2B 758372469 758375127 2658 True 589.500000 935 90.322250 236 2513 4 chr2B.!!$R2 2277
9 TraesCS2D01G538100 chr2B 758146610 758151383 4773 True 585.500000 966 83.965000 236 2905 4 chr2B.!!$R1 2669
10 TraesCS2D01G538100 chr2B 758389389 758391595 2206 True 524.750000 802 85.454500 260 2373 4 chr2B.!!$R3 2113

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
109 110 0.249489 AGACGAGCGGTGCAATATCC 60.249 55.0 0.0 0.0 0.0 2.59 F
1539 7240 0.038744 ACTAGTCCCTCCGTCCGAAA 59.961 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 7317 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 R
3099 8968 0.036306 CCAAGTAGTGGGTGGTGTCC 59.964 60.0 0.00 0.0 44.64 4.02 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
109 110 0.249489 AGACGAGCGGTGCAATATCC 60.249 55.000 0.00 0.00 0.00 2.59
134 135 0.463620 TTTGCAACCAAGAAGCCACC 59.536 50.000 0.00 0.00 31.52 4.61
170 171 2.749839 TTTTGGCGCCATCTCCCG 60.750 61.111 33.25 0.00 0.00 5.14
182 183 1.516365 ATCTCCCGCCGTGATAGTCG 61.516 60.000 0.00 0.00 0.00 4.18
396 398 4.019950 TGAGCAGGAGAATGTTGAAGATGA 60.020 41.667 0.00 0.00 0.00 2.92
397 399 5.113446 AGCAGGAGAATGTTGAAGATGAT 57.887 39.130 0.00 0.00 0.00 2.45
398 400 5.124645 AGCAGGAGAATGTTGAAGATGATC 58.875 41.667 0.00 0.00 0.00 2.92
399 401 5.104444 AGCAGGAGAATGTTGAAGATGATCT 60.104 40.000 0.00 0.00 0.00 2.75
401 403 6.458478 GCAGGAGAATGTTGAAGATGATCTTG 60.458 42.308 13.18 0.00 36.73 3.02
402 404 6.822170 CAGGAGAATGTTGAAGATGATCTTGA 59.178 38.462 13.18 0.29 36.73 3.02
404 406 7.716123 AGGAGAATGTTGAAGATGATCTTGATC 59.284 37.037 13.18 4.11 36.73 2.92
406 408 8.982091 AGAATGTTGAAGATGATCTTGATCAT 57.018 30.769 21.73 21.73 43.40 2.45
407 409 9.409918 AGAATGTTGAAGATGATCTTGATCATT 57.590 29.630 22.24 22.24 40.29 2.57
410 412 8.570068 TGTTGAAGATGATCTTGATCATTTCA 57.430 30.769 25.49 25.49 41.02 2.69
412 414 9.452065 GTTGAAGATGATCTTGATCATTTCATG 57.548 33.333 27.26 0.00 41.02 3.07
414 416 6.576662 AGATGATCTTGATCATTTCATGCC 57.423 37.500 22.25 11.07 41.02 4.40
415 417 6.068670 AGATGATCTTGATCATTTCATGCCA 58.931 36.000 22.25 0.00 41.02 4.92
418 420 4.976224 TCTTGATCATTTCATGCCACAG 57.024 40.909 0.00 0.00 33.34 3.66
419 421 3.697542 TCTTGATCATTTCATGCCACAGG 59.302 43.478 0.00 0.00 33.34 4.00
420 422 3.369242 TGATCATTTCATGCCACAGGA 57.631 42.857 0.00 0.00 0.00 3.86
421 423 3.905968 TGATCATTTCATGCCACAGGAT 58.094 40.909 0.00 0.00 0.00 3.24
423 425 3.369242 TCATTTCATGCCACAGGATGA 57.631 42.857 0.00 0.00 39.69 2.92
424 426 3.905968 TCATTTCATGCCACAGGATGAT 58.094 40.909 0.00 0.00 39.69 2.45
425 427 3.634910 TCATTTCATGCCACAGGATGATG 59.365 43.478 0.00 0.00 39.69 3.07
426 428 2.812836 TTCATGCCACAGGATGATGT 57.187 45.000 0.00 0.00 39.69 3.06
434 436 2.103771 CCACAGGATGATGTACTGGAGG 59.896 54.545 0.00 0.00 43.63 4.30
435 437 3.033909 CACAGGATGATGTACTGGAGGA 58.966 50.000 0.00 0.00 43.63 3.71
436 438 3.069300 CACAGGATGATGTACTGGAGGAG 59.931 52.174 0.00 0.00 43.63 3.69
437 439 3.052566 ACAGGATGATGTACTGGAGGAGA 60.053 47.826 0.00 0.00 43.63 3.71
440 442 3.964031 GGATGATGTACTGGAGGAGACTT 59.036 47.826 0.00 0.00 44.43 3.01
442 444 4.047627 TGATGTACTGGAGGAGACTTCA 57.952 45.455 0.00 0.00 46.35 3.02
531 983 3.125316 CACGGTAGCTTCAGATTTTGTCC 59.875 47.826 0.00 0.00 0.00 4.02
773 1248 1.593933 TCGCACGTCAACACTTTTACC 59.406 47.619 0.00 0.00 0.00 2.85
938 4044 1.599071 CTGCATATACCACACCAAGCG 59.401 52.381 0.00 0.00 0.00 4.68
1283 6805 7.511354 CGTTAGTTTTAACATGCATATGCGTTG 60.511 37.037 23.30 22.73 40.54 4.10
1284 6806 4.562394 AGTTTTAACATGCATATGCGTTGC 59.438 37.500 23.30 14.00 45.83 4.17
1534 7235 8.798859 TGTATATATTTACTAGTCCCTCCGTC 57.201 38.462 0.00 0.00 0.00 4.79
1535 7236 7.831193 TGTATATATTTACTAGTCCCTCCGTCC 59.169 40.741 0.00 0.00 0.00 4.79
1536 7237 1.755179 TTTACTAGTCCCTCCGTCCG 58.245 55.000 0.00 0.00 0.00 4.79
1537 7238 0.911769 TTACTAGTCCCTCCGTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
1538 7239 0.911769 TACTAGTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
1539 7240 0.038744 ACTAGTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1540 7241 1.341778 ACTAGTCCCTCCGTCCGAAAT 60.342 52.381 0.00 0.00 0.00 2.17
1541 7242 1.755380 CTAGTCCCTCCGTCCGAAATT 59.245 52.381 0.00 0.00 0.00 1.82
1542 7243 1.856629 AGTCCCTCCGTCCGAAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1543 7244 1.479730 AGTCCCTCCGTCCGAAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1546 7247 2.093869 TCCCTCCGTCCGAAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1549 7250 2.597305 CTCCGTCCGAAATTACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
1556 7257 5.627780 GTCCGAAATTACTTGTCGCAAAAAT 59.372 36.000 0.00 0.00 33.46 1.82
1557 7258 5.627367 TCCGAAATTACTTGTCGCAAAAATG 59.373 36.000 0.00 0.00 33.46 2.32
1563 7264 8.586570 AATTACTTGTCGCAAAAATGAATCAA 57.413 26.923 0.00 0.00 0.00 2.57
1564 7265 7.993821 TTACTTGTCGCAAAAATGAATCAAA 57.006 28.000 0.00 0.00 0.00 2.69
1566 7267 7.481275 ACTTGTCGCAAAAATGAATCAAAAT 57.519 28.000 0.00 0.00 0.00 1.82
1567 7268 7.346695 ACTTGTCGCAAAAATGAATCAAAATG 58.653 30.769 0.00 0.00 0.00 2.32
1568 7269 6.225703 TGTCGCAAAAATGAATCAAAATGG 57.774 33.333 0.00 0.00 0.00 3.16
1569 7270 5.987953 TGTCGCAAAAATGAATCAAAATGGA 59.012 32.000 0.00 0.00 0.00 3.41
1570 7271 6.649973 TGTCGCAAAAATGAATCAAAATGGAT 59.350 30.769 0.00 0.00 0.00 3.41
1571 7272 6.957077 GTCGCAAAAATGAATCAAAATGGATG 59.043 34.615 0.00 0.00 0.00 3.51
1572 7273 6.649973 TCGCAAAAATGAATCAAAATGGATGT 59.350 30.769 0.00 0.00 0.00 3.06
1573 7274 7.816513 TCGCAAAAATGAATCAAAATGGATGTA 59.183 29.630 0.00 0.00 0.00 2.29
1575 7276 9.925268 GCAAAAATGAATCAAAATGGATGTATC 57.075 29.630 0.00 0.00 0.00 2.24
1612 7313 6.929625 ACATCTAGATACATCCATTTCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
1613 7314 6.721668 ACATCTAGATACATCCATTTCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
1614 7315 6.576662 TCTAGATACATCCATTTCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
1615 7316 6.068670 TCTAGATACATCCATTTCTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
1616 7317 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
1617 7318 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
1624 7343 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
1625 7344 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
1626 7345 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
1630 7349 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1634 7353 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1641 7360 2.119655 CCGGACGGAGGGAGTACTG 61.120 68.421 4.40 0.00 37.50 2.74
1642 7361 2.772691 CGGACGGAGGGAGTACTGC 61.773 68.421 5.70 5.70 0.00 4.40
1646 7365 1.881324 GACGGAGGGAGTACTGCTATC 59.119 57.143 14.52 12.07 0.00 2.08
1661 7380 4.890581 ACTGCTATCCTGGTATATCGGATC 59.109 45.833 11.19 2.33 38.45 3.36
1662 7381 4.867086 TGCTATCCTGGTATATCGGATCA 58.133 43.478 11.19 4.33 38.45 2.92
1663 7382 5.269189 TGCTATCCTGGTATATCGGATCAA 58.731 41.667 11.19 0.00 38.45 2.57
1664 7383 5.360999 TGCTATCCTGGTATATCGGATCAAG 59.639 44.000 11.19 7.19 38.45 3.02
1665 7384 4.744795 ATCCTGGTATATCGGATCAAGC 57.255 45.455 0.00 0.00 32.17 4.01
1666 7385 3.779444 TCCTGGTATATCGGATCAAGCT 58.221 45.455 0.00 0.00 0.00 3.74
1667 7386 4.930696 TCCTGGTATATCGGATCAAGCTA 58.069 43.478 0.00 0.00 0.00 3.32
1668 7387 5.330233 TCCTGGTATATCGGATCAAGCTAA 58.670 41.667 0.00 0.00 0.00 3.09
1669 7388 5.958380 TCCTGGTATATCGGATCAAGCTAAT 59.042 40.000 0.00 0.00 0.00 1.73
1670 7389 6.440647 TCCTGGTATATCGGATCAAGCTAATT 59.559 38.462 0.00 0.00 0.00 1.40
1671 7390 6.536582 CCTGGTATATCGGATCAAGCTAATTG 59.463 42.308 0.00 0.00 40.52 2.32
1672 7391 5.874810 TGGTATATCGGATCAAGCTAATTGC 59.125 40.000 0.00 0.00 38.89 3.56
1687 7406 4.733405 GCTAATTGCTTCGGTTTAATTCCG 59.267 41.667 11.72 11.72 42.91 4.30
1688 7407 2.622546 TTGCTTCGGTTTAATTCCGC 57.377 45.000 12.74 2.98 46.49 5.54
1689 7408 1.524848 TGCTTCGGTTTAATTCCGCA 58.475 45.000 12.74 3.97 46.49 5.69
1690 7409 1.880675 TGCTTCGGTTTAATTCCGCAA 59.119 42.857 12.74 8.50 46.49 4.85
1691 7410 2.293677 TGCTTCGGTTTAATTCCGCAAA 59.706 40.909 12.74 4.86 46.49 3.68
1692 7411 3.243434 TGCTTCGGTTTAATTCCGCAAAA 60.243 39.130 12.74 4.32 46.49 2.44
1693 7412 3.736759 GCTTCGGTTTAATTCCGCAAAAA 59.263 39.130 12.74 4.05 46.49 1.94
1899 7665 1.133982 ACTTTTTGCGTGTGTGCATGA 59.866 42.857 0.00 0.00 45.78 3.07
2158 7930 2.282040 AGCAAGCTGTCTGGCACC 60.282 61.111 0.00 0.00 41.85 5.01
2313 8101 1.746220 GGCTATCTCGATCGGCAGTAT 59.254 52.381 16.41 4.74 0.00 2.12
2348 8138 2.565210 TATACCGTGTACTTGGTGCG 57.435 50.000 16.80 2.78 39.30 5.34
2501 8304 2.032681 GGGGGTCTGAGTGTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
2502 8305 2.032681 GGGGTCTGAGTGTGTGCC 59.967 66.667 0.00 0.00 0.00 5.01
2503 8306 2.818169 GGGGTCTGAGTGTGTGCCA 61.818 63.158 0.00 0.00 0.00 4.92
2504 8307 1.148273 GGGTCTGAGTGTGTGCCAA 59.852 57.895 0.00 0.00 0.00 4.52
2505 8308 0.886490 GGGTCTGAGTGTGTGCCAAG 60.886 60.000 0.00 0.00 0.00 3.61
2506 8309 0.179045 GGTCTGAGTGTGTGCCAAGT 60.179 55.000 0.00 0.00 0.00 3.16
2507 8310 1.668419 GTCTGAGTGTGTGCCAAGTT 58.332 50.000 0.00 0.00 0.00 2.66
2508 8311 2.017049 GTCTGAGTGTGTGCCAAGTTT 58.983 47.619 0.00 0.00 0.00 2.66
2509 8312 2.423538 GTCTGAGTGTGTGCCAAGTTTT 59.576 45.455 0.00 0.00 0.00 2.43
2510 8313 3.088532 TCTGAGTGTGTGCCAAGTTTTT 58.911 40.909 0.00 0.00 0.00 1.94
2532 8335 2.723322 TTGAGAGAAGGCCATCATGG 57.277 50.000 11.19 0.00 41.55 3.66
2548 8351 6.751157 CCATCATGGCTTGCTTTATTAATCA 58.249 36.000 0.00 0.00 0.00 2.57
2549 8352 7.211573 CCATCATGGCTTGCTTTATTAATCAA 58.788 34.615 0.00 0.00 0.00 2.57
2550 8353 7.876068 CCATCATGGCTTGCTTTATTAATCAAT 59.124 33.333 0.00 0.00 0.00 2.57
2551 8354 8.708742 CATCATGGCTTGCTTTATTAATCAATG 58.291 33.333 0.00 0.00 0.00 2.82
2552 8355 8.009622 TCATGGCTTGCTTTATTAATCAATGA 57.990 30.769 0.00 0.00 0.00 2.57
2553 8356 8.476447 TCATGGCTTGCTTTATTAATCAATGAA 58.524 29.630 0.00 0.00 0.00 2.57
2554 8357 9.100554 CATGGCTTGCTTTATTAATCAATGAAA 57.899 29.630 0.00 0.00 0.00 2.69
2555 8358 8.706492 TGGCTTGCTTTATTAATCAATGAAAG 57.294 30.769 0.00 0.00 0.00 2.62
2556 8359 7.765360 TGGCTTGCTTTATTAATCAATGAAAGG 59.235 33.333 8.87 0.00 0.00 3.11
2557 8360 7.981225 GGCTTGCTTTATTAATCAATGAAAGGA 59.019 33.333 8.87 4.47 0.00 3.36
2558 8361 9.369904 GCTTGCTTTATTAATCAATGAAAGGAA 57.630 29.630 11.66 11.66 35.80 3.36
2567 8370 8.786826 TTAATCAATGAAAGGAAGTACATCGT 57.213 30.769 0.00 0.00 0.00 3.73
2568 8371 6.910536 ATCAATGAAAGGAAGTACATCGTC 57.089 37.500 0.00 0.00 0.00 4.20
2569 8372 6.037786 TCAATGAAAGGAAGTACATCGTCT 57.962 37.500 0.00 0.00 0.00 4.18
2570 8373 7.165460 TCAATGAAAGGAAGTACATCGTCTA 57.835 36.000 0.00 0.00 0.00 2.59
2571 8374 7.782049 TCAATGAAAGGAAGTACATCGTCTAT 58.218 34.615 0.00 0.00 0.00 1.98
2572 8375 7.706607 TCAATGAAAGGAAGTACATCGTCTATG 59.293 37.037 0.00 0.00 41.74 2.23
2573 8376 6.769134 TGAAAGGAAGTACATCGTCTATGA 57.231 37.500 0.00 0.00 39.07 2.15
2574 8377 6.796426 TGAAAGGAAGTACATCGTCTATGAG 58.204 40.000 0.00 0.00 39.07 2.90
2575 8378 6.602009 TGAAAGGAAGTACATCGTCTATGAGA 59.398 38.462 0.00 0.00 39.07 3.27
2576 8379 6.380095 AAGGAAGTACATCGTCTATGAGAC 57.620 41.667 0.00 0.00 41.71 3.36
2586 8389 3.684103 GTCTATGAGACGTGAGACCAG 57.316 52.381 0.00 0.00 35.28 4.00
2587 8390 3.271729 GTCTATGAGACGTGAGACCAGA 58.728 50.000 0.00 0.00 35.28 3.86
2588 8391 3.064271 GTCTATGAGACGTGAGACCAGAC 59.936 52.174 0.00 0.00 35.28 3.51
2589 8392 1.911057 ATGAGACGTGAGACCAGACA 58.089 50.000 0.00 0.00 0.00 3.41
2590 8393 1.239347 TGAGACGTGAGACCAGACAG 58.761 55.000 0.00 0.00 0.00 3.51
2591 8394 0.109504 GAGACGTGAGACCAGACAGC 60.110 60.000 0.00 0.00 0.00 4.40
2592 8395 1.080434 GACGTGAGACCAGACAGCC 60.080 63.158 0.00 0.00 0.00 4.85
2593 8396 2.262915 CGTGAGACCAGACAGCCC 59.737 66.667 0.00 0.00 0.00 5.19
2594 8397 2.262915 GTGAGACCAGACAGCCCG 59.737 66.667 0.00 0.00 0.00 6.13
2595 8398 2.997315 TGAGACCAGACAGCCCGG 60.997 66.667 0.00 0.00 0.00 5.73
2596 8399 2.680352 GAGACCAGACAGCCCGGA 60.680 66.667 0.73 0.00 0.00 5.14
2597 8400 2.681778 AGACCAGACAGCCCGGAG 60.682 66.667 0.73 0.00 0.00 4.63
2609 8412 2.818132 CCGGAGGCTCATCTGTCC 59.182 66.667 17.69 0.00 46.14 4.02
2610 8413 2.060383 CCGGAGGCTCATCTGTCCA 61.060 63.158 17.69 0.00 46.14 4.02
2611 8414 1.440893 CGGAGGCTCATCTGTCCAG 59.559 63.158 17.69 0.00 0.00 3.86
2612 8415 1.039785 CGGAGGCTCATCTGTCCAGA 61.040 60.000 17.69 0.00 42.37 3.86
2613 8416 0.752054 GGAGGCTCATCTGTCCAGAG 59.248 60.000 17.69 0.00 41.33 3.35
2614 8417 1.484038 GAGGCTCATCTGTCCAGAGT 58.516 55.000 10.25 0.00 41.33 3.24
2615 8418 1.136695 GAGGCTCATCTGTCCAGAGTG 59.863 57.143 10.25 2.63 41.33 3.51
2616 8419 0.901124 GGCTCATCTGTCCAGAGTGT 59.099 55.000 3.10 0.00 41.33 3.55
2617 8420 1.405256 GGCTCATCTGTCCAGAGTGTG 60.405 57.143 3.10 0.00 41.33 3.82
2618 8421 1.274728 GCTCATCTGTCCAGAGTGTGT 59.725 52.381 3.10 0.00 41.33 3.72
2619 8422 2.930023 GCTCATCTGTCCAGAGTGTGTG 60.930 54.545 3.10 0.00 41.33 3.82
2663 8466 7.079451 ACTAATAACTATTGGATGGTGAGGG 57.921 40.000 0.37 0.00 0.00 4.30
2752 8555 4.410883 TGGTCTAATAACCGTGGATGGATT 59.589 41.667 0.00 0.00 42.62 3.01
2913 8781 3.069289 GTTGTAACTCTAACCCCCAACG 58.931 50.000 0.00 0.00 0.00 4.10
2978 8846 2.632377 CCTATAACTGTGCCACTGTGG 58.368 52.381 22.46 22.46 41.55 4.17
2979 8847 2.236146 CCTATAACTGTGCCACTGTGGA 59.764 50.000 30.23 12.48 40.96 4.02
2980 8848 2.185004 ATAACTGTGCCACTGTGGAC 57.815 50.000 30.23 22.52 40.96 4.02
3022 8891 1.197721 CATCGCCACACAAAAGGAGAC 59.802 52.381 0.00 0.00 36.54 3.36
3061 8930 1.202940 GCTGAAACCCTCCTTCACCTT 60.203 52.381 0.00 0.00 0.00 3.50
3074 8943 2.381752 TCACCTTGTCAGACTGGAGA 57.618 50.000 16.70 12.44 0.00 3.71
3077 8946 4.416516 TCACCTTGTCAGACTGGAGATAA 58.583 43.478 16.70 0.00 0.00 1.75
3099 8968 6.560253 AACTGCTACACAAAGGACAATAAG 57.440 37.500 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 0.583438 CAAGGATATTGCACCGCTCG 59.417 55.000 0.00 0.00 0.00 5.03
170 171 0.040246 GCCTCTACGACTATCACGGC 60.040 60.000 0.00 0.00 34.93 5.68
182 183 7.148390 GGACTTTGAGTTTTTCTATGCCTCTAC 60.148 40.741 0.00 0.00 0.00 2.59
406 408 3.090210 ACATCATCCTGTGGCATGAAA 57.910 42.857 0.00 0.00 32.76 2.69
407 409 2.812836 ACATCATCCTGTGGCATGAA 57.187 45.000 0.00 0.00 32.76 2.57
408 410 2.773661 AGTACATCATCCTGTGGCATGA 59.226 45.455 0.00 0.00 33.55 3.07
410 412 2.158711 CCAGTACATCATCCTGTGGCAT 60.159 50.000 0.00 0.00 0.00 4.40
412 414 1.486310 TCCAGTACATCATCCTGTGGC 59.514 52.381 0.00 0.00 0.00 5.01
414 416 3.033909 TCCTCCAGTACATCATCCTGTG 58.966 50.000 0.00 0.00 0.00 3.66
415 417 3.052566 TCTCCTCCAGTACATCATCCTGT 60.053 47.826 0.00 0.00 0.00 4.00
418 420 3.571590 AGTCTCCTCCAGTACATCATCC 58.428 50.000 0.00 0.00 0.00 3.51
419 421 4.646945 TGAAGTCTCCTCCAGTACATCATC 59.353 45.833 0.00 0.00 0.00 2.92
420 422 4.614475 TGAAGTCTCCTCCAGTACATCAT 58.386 43.478 0.00 0.00 0.00 2.45
421 423 4.019858 CTGAAGTCTCCTCCAGTACATCA 58.980 47.826 0.00 0.00 0.00 3.07
423 425 4.264172 ACTCTGAAGTCTCCTCCAGTACAT 60.264 45.833 0.00 0.00 0.00 2.29
424 426 3.074687 ACTCTGAAGTCTCCTCCAGTACA 59.925 47.826 0.00 0.00 0.00 2.90
425 427 3.692690 ACTCTGAAGTCTCCTCCAGTAC 58.307 50.000 0.00 0.00 0.00 2.73
426 428 4.536888 AGTACTCTGAAGTCTCCTCCAGTA 59.463 45.833 0.00 0.00 36.92 2.74
434 436 5.493809 ACTACTGGAGTACTCTGAAGTCTC 58.506 45.833 21.88 3.88 36.27 3.36
435 437 5.508280 ACTACTGGAGTACTCTGAAGTCT 57.492 43.478 21.88 9.49 36.27 3.24
436 438 5.474189 ACAACTACTGGAGTACTCTGAAGTC 59.526 44.000 21.88 5.31 37.44 3.01
437 439 5.386924 ACAACTACTGGAGTACTCTGAAGT 58.613 41.667 21.88 21.76 37.44 3.01
440 442 6.377429 CCAATACAACTACTGGAGTACTCTGA 59.623 42.308 21.88 8.66 37.44 3.27
442 444 6.491383 TCCAATACAACTACTGGAGTACTCT 58.509 40.000 21.88 5.62 37.44 3.24
443 445 6.770746 TCCAATACAACTACTGGAGTACTC 57.229 41.667 14.87 14.87 37.44 2.59
444 446 6.668283 ACATCCAATACAACTACTGGAGTACT 59.332 38.462 0.00 0.00 41.17 2.73
531 983 5.220662 CGTTTGGAGTTATAATCTGCACCTG 60.221 44.000 8.15 0.81 33.36 4.00
773 1248 2.686915 AGTACCTGAAAGATACCGGACG 59.313 50.000 9.46 0.00 31.29 4.79
870 1528 4.796231 CGGTGAAGTCCCCTCGCG 62.796 72.222 0.00 0.00 0.00 5.87
895 1553 3.359874 CGGCGTACGTACTGCTATTTATG 59.640 47.826 28.37 11.98 37.93 1.90
938 4044 2.750948 TGAGTTCTGCCTTACGTGAAC 58.249 47.619 0.00 1.80 39.06 3.18
1526 7227 2.277084 CAAGTAATTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1528 7229 2.597305 CGACAAGTAATTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1532 7233 3.799137 TTGCGACAAGTAATTTCGGAC 57.201 42.857 8.68 0.00 32.49 4.79
1534 7235 5.627367 TCATTTTTGCGACAAGTAATTTCGG 59.373 36.000 8.68 0.00 33.28 4.30
1535 7236 6.667981 TCATTTTTGCGACAAGTAATTTCG 57.332 33.333 0.00 4.05 35.82 3.46
1536 7237 8.698854 TGATTCATTTTTGCGACAAGTAATTTC 58.301 29.630 0.00 0.00 0.00 2.17
1537 7238 8.586570 TGATTCATTTTTGCGACAAGTAATTT 57.413 26.923 0.00 0.00 0.00 1.82
1538 7239 8.586570 TTGATTCATTTTTGCGACAAGTAATT 57.413 26.923 0.00 0.00 0.00 1.40
1539 7240 8.586570 TTTGATTCATTTTTGCGACAAGTAAT 57.413 26.923 0.00 0.00 0.00 1.89
1540 7241 7.993821 TTTGATTCATTTTTGCGACAAGTAA 57.006 28.000 0.00 0.00 0.00 2.24
1541 7242 7.993821 TTTTGATTCATTTTTGCGACAAGTA 57.006 28.000 0.00 0.00 0.00 2.24
1542 7243 6.900568 TTTTGATTCATTTTTGCGACAAGT 57.099 29.167 0.00 0.00 0.00 3.16
1543 7244 6.793203 CCATTTTGATTCATTTTTGCGACAAG 59.207 34.615 0.00 0.00 0.00 3.16
1546 7247 6.464895 TCCATTTTGATTCATTTTTGCGAC 57.535 33.333 0.00 0.00 0.00 5.19
1549 7250 9.925268 GATACATCCATTTTGATTCATTTTTGC 57.075 29.630 0.00 0.00 0.00 3.68
1589 7290 7.032580 GTCGGAGAAATGGATGTATCTAGATG 58.967 42.308 15.79 0.00 39.69 2.90
1592 7293 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
1597 7298 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
1598 7299 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
1602 7303 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
1603 7304 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
1605 7306 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
1606 7307 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
1609 7310 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
1611 7312 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1612 7313 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1613 7314 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1614 7315 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1615 7316 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1616 7317 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1617 7318 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1624 7343 2.772691 GCAGTACTCCCTCCGTCCG 61.773 68.421 0.00 0.00 0.00 4.79
1625 7344 0.106819 TAGCAGTACTCCCTCCGTCC 60.107 60.000 0.00 0.00 0.00 4.79
1626 7345 1.881324 GATAGCAGTACTCCCTCCGTC 59.119 57.143 0.00 0.00 0.00 4.79
1630 7349 2.243810 CCAGGATAGCAGTACTCCCTC 58.756 57.143 0.00 0.00 31.26 4.30
1634 7353 5.297278 CCGATATACCAGGATAGCAGTACTC 59.703 48.000 0.00 0.00 0.00 2.59
1641 7360 5.737635 GCTTGATCCGATATACCAGGATAGC 60.738 48.000 0.00 9.85 44.13 2.97
1642 7361 5.596361 AGCTTGATCCGATATACCAGGATAG 59.404 44.000 0.00 3.28 44.13 2.08
1646 7365 5.661056 TTAGCTTGATCCGATATACCAGG 57.339 43.478 0.00 0.00 0.00 4.45
1899 7665 1.376424 CTCGGTTCCTGCATGCAGT 60.376 57.895 38.22 0.00 42.15 4.40
2282 8067 4.744136 TCGAGATAGCCAGTATTACACG 57.256 45.455 0.00 0.00 0.00 4.49
2313 8101 3.491276 CGGTATATTCCGGCACAAGTACA 60.491 47.826 12.62 0.00 45.88 2.90
2431 8229 4.244862 CAAGGGCATAACACATTGTTTCC 58.755 43.478 0.00 0.00 41.45 3.13
2490 8293 3.508744 AAAAACTTGGCACACACTCAG 57.491 42.857 0.00 0.00 39.29 3.35
2510 8313 3.765511 CCATGATGGCCTTCTCTCAAAAA 59.234 43.478 18.67 0.00 0.00 1.94
2511 8314 3.359033 CCATGATGGCCTTCTCTCAAAA 58.641 45.455 18.67 0.00 0.00 2.44
2512 8315 3.008835 CCATGATGGCCTTCTCTCAAA 57.991 47.619 18.67 0.00 0.00 2.69
2513 8316 2.723322 CCATGATGGCCTTCTCTCAA 57.277 50.000 18.67 0.00 0.00 3.02
2524 8327 6.751157 TGATTAATAAAGCAAGCCATGATGG 58.249 36.000 7.21 7.21 41.55 3.51
2525 8328 8.708742 CATTGATTAATAAAGCAAGCCATGATG 58.291 33.333 0.00 0.00 43.66 3.07
2526 8329 8.644216 TCATTGATTAATAAAGCAAGCCATGAT 58.356 29.630 0.00 0.00 43.66 2.45
2527 8330 8.009622 TCATTGATTAATAAAGCAAGCCATGA 57.990 30.769 0.00 0.00 43.66 3.07
2528 8331 8.651391 TTCATTGATTAATAAAGCAAGCCATG 57.349 30.769 0.00 0.00 43.66 3.66
2529 8332 9.321562 CTTTCATTGATTAATAAAGCAAGCCAT 57.678 29.630 0.00 0.00 43.66 4.40
2530 8333 7.765360 CCTTTCATTGATTAATAAAGCAAGCCA 59.235 33.333 3.17 0.00 43.66 4.75
2531 8334 7.981225 TCCTTTCATTGATTAATAAAGCAAGCC 59.019 33.333 3.17 0.00 43.66 4.35
2532 8335 8.931385 TCCTTTCATTGATTAATAAAGCAAGC 57.069 30.769 3.17 0.00 43.66 4.01
2541 8344 9.396022 ACGATGTACTTCCTTTCATTGATTAAT 57.604 29.630 3.35 0.00 0.00 1.40
2542 8345 8.786826 ACGATGTACTTCCTTTCATTGATTAA 57.213 30.769 3.35 0.00 0.00 1.40
2543 8346 8.258007 AGACGATGTACTTCCTTTCATTGATTA 58.742 33.333 3.35 0.00 0.00 1.75
2544 8347 7.106239 AGACGATGTACTTCCTTTCATTGATT 58.894 34.615 3.35 0.00 0.00 2.57
2545 8348 6.644347 AGACGATGTACTTCCTTTCATTGAT 58.356 36.000 3.35 0.00 0.00 2.57
2546 8349 6.037786 AGACGATGTACTTCCTTTCATTGA 57.962 37.500 3.35 0.00 0.00 2.57
2547 8350 7.706607 TCATAGACGATGTACTTCCTTTCATTG 59.293 37.037 3.35 0.00 36.84 2.82
2548 8351 7.782049 TCATAGACGATGTACTTCCTTTCATT 58.218 34.615 3.35 0.00 36.84 2.57
2549 8352 7.285629 TCTCATAGACGATGTACTTCCTTTCAT 59.714 37.037 3.35 0.00 36.84 2.57
2550 8353 6.602009 TCTCATAGACGATGTACTTCCTTTCA 59.398 38.462 3.35 0.00 36.84 2.69
2551 8354 6.913673 GTCTCATAGACGATGTACTTCCTTTC 59.086 42.308 3.35 0.00 35.28 2.62
2552 8355 6.797454 GTCTCATAGACGATGTACTTCCTTT 58.203 40.000 3.35 0.00 35.28 3.11
2553 8356 6.380095 GTCTCATAGACGATGTACTTCCTT 57.620 41.667 3.35 0.00 35.28 3.36
2566 8369 3.064271 GTCTGGTCTCACGTCTCATAGAC 59.936 52.174 0.00 0.00 41.71 2.59
2567 8370 3.271729 GTCTGGTCTCACGTCTCATAGA 58.728 50.000 0.00 0.00 0.00 1.98
2568 8371 3.010420 TGTCTGGTCTCACGTCTCATAG 58.990 50.000 0.00 0.00 0.00 2.23
2569 8372 3.010420 CTGTCTGGTCTCACGTCTCATA 58.990 50.000 0.00 0.00 0.00 2.15
2570 8373 1.815613 CTGTCTGGTCTCACGTCTCAT 59.184 52.381 0.00 0.00 0.00 2.90
2571 8374 1.239347 CTGTCTGGTCTCACGTCTCA 58.761 55.000 0.00 0.00 0.00 3.27
2572 8375 0.109504 GCTGTCTGGTCTCACGTCTC 60.110 60.000 0.00 0.00 0.00 3.36
2573 8376 1.528292 GGCTGTCTGGTCTCACGTCT 61.528 60.000 0.00 0.00 0.00 4.18
2574 8377 1.080434 GGCTGTCTGGTCTCACGTC 60.080 63.158 0.00 0.00 0.00 4.34
2575 8378 2.574955 GGGCTGTCTGGTCTCACGT 61.575 63.158 0.00 0.00 0.00 4.49
2576 8379 2.262915 GGGCTGTCTGGTCTCACG 59.737 66.667 0.00 0.00 0.00 4.35
2577 8380 2.262915 CGGGCTGTCTGGTCTCAC 59.737 66.667 0.00 0.00 0.00 3.51
2578 8381 2.997315 CCGGGCTGTCTGGTCTCA 60.997 66.667 0.00 0.00 37.13 3.27
2579 8382 2.680352 TCCGGGCTGTCTGGTCTC 60.680 66.667 7.07 0.00 42.62 3.36
2580 8383 2.681778 CTCCGGGCTGTCTGGTCT 60.682 66.667 7.07 0.00 42.62 3.85
2581 8384 3.775654 CCTCCGGGCTGTCTGGTC 61.776 72.222 7.07 0.00 42.62 4.02
2591 8394 2.801631 GGACAGATGAGCCTCCGGG 61.802 68.421 0.00 0.00 0.00 5.73
2592 8395 2.025767 CTGGACAGATGAGCCTCCGG 62.026 65.000 0.00 0.00 0.00 5.14
2593 8396 1.039785 TCTGGACAGATGAGCCTCCG 61.040 60.000 0.00 0.00 31.41 4.63
2594 8397 0.752054 CTCTGGACAGATGAGCCTCC 59.248 60.000 2.00 0.00 36.76 4.30
2595 8398 1.136695 CACTCTGGACAGATGAGCCTC 59.863 57.143 2.00 0.00 36.76 4.70
2596 8399 1.193323 CACTCTGGACAGATGAGCCT 58.807 55.000 2.00 0.00 36.76 4.58
2597 8400 0.901124 ACACTCTGGACAGATGAGCC 59.099 55.000 2.00 0.00 36.76 4.70
2598 8401 1.274728 ACACACTCTGGACAGATGAGC 59.725 52.381 2.00 0.00 36.76 4.26
2599 8402 2.930023 GCACACACTCTGGACAGATGAG 60.930 54.545 2.00 5.39 36.76 2.90
2600 8403 1.001293 GCACACACTCTGGACAGATGA 59.999 52.381 2.00 0.00 36.76 2.92
2601 8404 1.436600 GCACACACTCTGGACAGATG 58.563 55.000 2.00 6.39 36.76 2.90
2602 8405 0.322975 GGCACACACTCTGGACAGAT 59.677 55.000 2.00 0.00 36.76 2.90
2603 8406 1.048160 TGGCACACACTCTGGACAGA 61.048 55.000 1.61 1.61 35.85 3.41
2604 8407 0.179048 TTGGCACACACTCTGGACAG 60.179 55.000 0.00 0.00 39.29 3.51
2605 8408 0.179048 CTTGGCACACACTCTGGACA 60.179 55.000 0.00 0.00 39.29 4.02
2606 8409 0.179045 ACTTGGCACACACTCTGGAC 60.179 55.000 0.00 0.00 39.29 4.02
2607 8410 0.546122 AACTTGGCACACACTCTGGA 59.454 50.000 0.00 0.00 39.29 3.86
2608 8411 0.664761 CAACTTGGCACACACTCTGG 59.335 55.000 0.00 0.00 39.29 3.86
2609 8412 1.667236 TCAACTTGGCACACACTCTG 58.333 50.000 0.00 0.00 39.29 3.35
2610 8413 2.620115 CAATCAACTTGGCACACACTCT 59.380 45.455 0.00 0.00 39.29 3.24
2611 8414 2.358898 ACAATCAACTTGGCACACACTC 59.641 45.455 0.00 0.00 39.29 3.51
2612 8415 2.099592 CACAATCAACTTGGCACACACT 59.900 45.455 0.00 0.00 39.29 3.55
2613 8416 2.098934 TCACAATCAACTTGGCACACAC 59.901 45.455 0.00 0.00 39.29 3.82
2614 8417 2.373224 TCACAATCAACTTGGCACACA 58.627 42.857 0.00 0.00 39.29 3.72
2615 8418 3.435105 TTCACAATCAACTTGGCACAC 57.565 42.857 0.00 0.00 39.29 3.82
2616 8419 3.446873 ACTTTCACAATCAACTTGGCACA 59.553 39.130 0.00 0.00 39.30 4.57
2617 8420 4.045636 ACTTTCACAATCAACTTGGCAC 57.954 40.909 0.00 0.00 39.30 5.01
2618 8421 4.887071 AGTACTTTCACAATCAACTTGGCA 59.113 37.500 0.00 0.00 39.30 4.92
2619 8422 5.438761 AGTACTTTCACAATCAACTTGGC 57.561 39.130 0.00 0.00 39.30 4.52
2913 8781 3.660865 TGAAGAAGGAAAAGTAGGCGAC 58.339 45.455 0.00 0.00 0.00 5.19
2978 8846 3.442273 CCATTAGAGCCTAGATCTCCGTC 59.558 52.174 0.00 0.00 28.73 4.79
2979 8847 3.181427 ACCATTAGAGCCTAGATCTCCGT 60.181 47.826 0.00 0.00 28.73 4.69
2980 8848 3.426615 ACCATTAGAGCCTAGATCTCCG 58.573 50.000 0.00 0.00 28.73 4.63
3022 8891 0.664761 CAGCCACCGCTCAATATTGG 59.335 55.000 15.36 7.47 43.95 3.16
3061 8930 3.435275 AGCAGTTATCTCCAGTCTGACA 58.565 45.455 10.88 0.00 0.00 3.58
3074 8943 7.336931 CCTTATTGTCCTTTGTGTAGCAGTTAT 59.663 37.037 0.00 0.00 0.00 1.89
3077 8946 5.003804 CCTTATTGTCCTTTGTGTAGCAGT 58.996 41.667 0.00 0.00 0.00 4.40
3099 8968 0.036306 CCAAGTAGTGGGTGGTGTCC 59.964 60.000 0.00 0.00 44.64 4.02


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

AutoCloner maintained by Alex Coulton.