Multiple sequence alignment - TraesCS2D01G087800

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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 TraesCS2D01G087800 chr2D 100.000 2920 0 0 1 2920 37869017 37871936 0.000000e+00 5393.0
1 TraesCS2D01G087800 chr2D 95.882 510 17 3 1 507 408481900 408481392 0.000000e+00 822.0
2 TraesCS2D01G087800 chr2D 89.466 674 38 19 1702 2349 37929665 37930331 0.000000e+00 821.0
3 TraesCS2D01G087800 chr2D 95.874 509 18 3 1 507 408527158 408526651 0.000000e+00 821.0
4 TraesCS2D01G087800 chr2D 94.086 372 19 3 2550 2920 42737935 42738304 1.960000e-156 562.0
5 TraesCS2D01G087800 chr2D 92.651 381 24 4 2541 2920 52038692 52039069 1.980000e-151 545.0
6 TraesCS2D01G087800 chr2D 85.455 275 22 11 2087 2349 37911708 37911976 1.330000e-68 270.0
7 TraesCS2D01G087800 chr2D 87.273 220 17 7 2101 2320 37960517 37960725 1.050000e-59 241.0
8 TraesCS2D01G087800 chr2D 93.333 135 5 4 2087 2220 37912813 37912944 2.300000e-46 196.0
9 TraesCS2D01G087800 chr2D 86.275 153 18 2 1756 1908 37937384 37937533 2.330000e-36 163.0
10 TraesCS2D01G087800 chr2A 89.892 1850 111 39 547 2349 42784367 42786187 0.000000e+00 2311.0
11 TraesCS2D01G087800 chr2A 88.682 592 41 15 1 577 16582779 16583359 0.000000e+00 699.0
12 TraesCS2D01G087800 chr2A 81.612 397 41 14 1262 1639 42811285 42811668 1.700000e-77 300.0
13 TraesCS2D01G087800 chr2A 91.005 189 14 3 2349 2537 514864226 514864041 4.830000e-63 252.0
14 TraesCS2D01G087800 chr2A 85.000 240 20 10 2093 2320 42932701 42932936 2.260000e-56 230.0
15 TraesCS2D01G087800 chr2A 84.583 240 21 9 2093 2320 42876416 42876651 1.050000e-54 224.0
16 TraesCS2D01G087800 chr2A 83.588 262 20 17 2078 2320 43006344 43006601 1.050000e-54 224.0
17 TraesCS2D01G087800 chr2A 84.167 240 22 10 2093 2320 42839403 42839638 4.900000e-53 219.0
18 TraesCS2D01G087800 chr2A 85.202 223 18 9 2109 2320 42962744 42962962 6.340000e-52 215.0
19 TraesCS2D01G087800 chr2A 87.582 153 19 0 1756 1908 42792054 42792206 8.320000e-41 178.0
20 TraesCS2D01G087800 chr2A 83.226 155 13 6 1485 1639 42932429 42932570 2.360000e-26 130.0
21 TraesCS2D01G087800 chr2B 90.789 1140 50 24 575 1703 66355318 66356413 0.000000e+00 1472.0
22 TraesCS2D01G087800 chr2B 94.410 483 19 6 1697 2177 66356447 66356923 0.000000e+00 736.0
23 TraesCS2D01G087800 chr2B 85.426 645 54 21 1711 2320 66476858 66477497 4.110000e-178 634.0
24 TraesCS2D01G087800 chr2B 83.212 274 21 17 2088 2349 66414057 66414317 8.140000e-56 228.0
25 TraesCS2D01G087800 chr2B 88.387 155 15 2 1485 1637 66492100 66492253 1.790000e-42 183.0
26 TraesCS2D01G087800 chr6D 95.841 577 18 3 1 571 156818078 156818654 0.000000e+00 928.0
27 TraesCS2D01G087800 chr6D 94.624 372 18 2 2550 2920 68582475 68582845 2.520000e-160 575.0
28 TraesCS2D01G087800 chr6D 93.351 376 20 5 2548 2920 464142611 464142238 4.250000e-153 551.0
29 TraesCS2D01G087800 chr6D 80.928 194 29 6 2349 2537 36690240 36690430 2.340000e-31 147.0
30 TraesCS2D01G087800 chr5D 96.094 512 15 3 1 507 501357496 501358007 0.000000e+00 830.0
31 TraesCS2D01G087800 chr5D 94.865 370 14 5 2552 2920 439600083 439600448 9.080000e-160 573.0
32 TraesCS2D01G087800 chr5D 89.070 430 35 9 153 576 260427480 260427057 9.270000e-145 523.0
33 TraesCS2D01G087800 chr1D 96.086 511 15 3 1 507 202963584 202963075 0.000000e+00 828.0
34 TraesCS2D01G087800 chr1D 95.866 508 20 1 1 507 12288777 12289284 0.000000e+00 821.0
35 TraesCS2D01G087800 chr1D 79.474 190 31 8 2349 2536 216035593 216035776 8.490000e-26 128.0
36 TraesCS2D01G087800 chr7D 95.874 509 19 2 1 507 162157870 162157362 0.000000e+00 822.0
37 TraesCS2D01G087800 chr7D 81.915 188 23 10 2349 2532 327406756 327406936 6.520000e-32 148.0
38 TraesCS2D01G087800 chr4A 86.927 589 49 14 1 576 658128224 658127651 1.140000e-178 636.0
39 TraesCS2D01G087800 chr4A 94.355 372 20 1 2550 2920 618022292 618022663 1.170000e-158 569.0
40 TraesCS2D01G087800 chr4A 100.000 31 0 0 797 827 54087389 54087419 1.130000e-04 58.4
41 TraesCS2D01G087800 chr3D 94.070 371 19 3 2550 2919 98568718 98568350 7.070000e-156 560.0
42 TraesCS2D01G087800 chr7A 89.749 439 38 6 151 584 118571470 118571906 3.290000e-154 555.0
43 TraesCS2D01G087800 chr7A 80.447 179 25 10 2349 2523 491576377 491576205 8.490000e-26 128.0
44 TraesCS2D01G087800 chrUn 93.548 372 22 2 2550 2920 334848757 334849127 1.180000e-153 553.0
45 TraesCS2D01G087800 chrUn 93.298 373 21 4 2550 2920 271058934 271058564 5.500000e-152 547.0
46 TraesCS2D01G087800 chr4B 93.194 191 10 2 2349 2539 604533828 604534015 7.970000e-71 278.0
47 TraesCS2D01G087800 chr3B 92.147 191 13 2 2349 2539 755288275 755288463 4.800000e-68 268.0
48 TraesCS2D01G087800 chr3B 82.967 182 26 5 2349 2528 754287750 754287928 3.010000e-35 159.0
49 TraesCS2D01G087800 chr5B 91.710 193 13 2 2349 2539 586628659 586628468 6.200000e-67 265.0
50 TraesCS2D01G087800 chr6B 85.000 180 23 4 2349 2527 693079853 693079677 2.310000e-41 180.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G087800 chr2D 37869017 37871936 2919 False 5393 5393 100.0000 1 2920 1 chr2D.!!$F1 2919
1 TraesCS2D01G087800 chr2D 408481392 408481900 508 True 822 822 95.8820 1 507 1 chr2D.!!$R1 506
2 TraesCS2D01G087800 chr2D 37929665 37930331 666 False 821 821 89.4660 1702 2349 1 chr2D.!!$F2 647
3 TraesCS2D01G087800 chr2D 408526651 408527158 507 True 821 821 95.8740 1 507 1 chr2D.!!$R2 506
4 TraesCS2D01G087800 chr2D 37911708 37912944 1236 False 233 270 89.3940 2087 2349 2 chr2D.!!$F7 262
5 TraesCS2D01G087800 chr2A 42784367 42786187 1820 False 2311 2311 89.8920 547 2349 1 chr2A.!!$F2 1802
6 TraesCS2D01G087800 chr2A 16582779 16583359 580 False 699 699 88.6820 1 577 1 chr2A.!!$F1 576
7 TraesCS2D01G087800 chr2B 66355318 66356923 1605 False 1104 1472 92.5995 575 2177 2 chr2B.!!$F4 1602
8 TraesCS2D01G087800 chr2B 66476858 66477497 639 False 634 634 85.4260 1711 2320 1 chr2B.!!$F2 609
9 TraesCS2D01G087800 chr6D 156818078 156818654 576 False 928 928 95.8410 1 571 1 chr6D.!!$F3 570
10 TraesCS2D01G087800 chr5D 501357496 501358007 511 False 830 830 96.0940 1 507 1 chr5D.!!$F2 506
11 TraesCS2D01G087800 chr1D 202963075 202963584 509 True 828 828 96.0860 1 507 1 chr1D.!!$R1 506
12 TraesCS2D01G087800 chr1D 12288777 12289284 507 False 821 821 95.8660 1 507 1 chr1D.!!$F1 506
13 TraesCS2D01G087800 chr7D 162157362 162157870 508 True 822 822 95.8740 1 507 1 chr7D.!!$R1 506
14 TraesCS2D01G087800 chr4A 658127651 658128224 573 True 636 636 86.9270 1 576 1 chr4A.!!$R1 575

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
738 770 0.759346 ATTTCCTTCCCTCCCGATCG 59.241 55.0 8.51 8.51 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 3484 0.088858 CGATTTTCGCGCCAAAAACG 59.911 50.0 23.1 23.1 35.9 3.6 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
371 390 4.487948 GCAATGCAGTGCAGAATAAAGAA 58.512 39.130 32.30 0.00 43.65 2.52
408 427 4.944048 ACCACCTTCTTTATTTTGTGCAC 58.056 39.130 10.75 10.75 0.00 4.57
419 438 7.448777 TCTTTATTTTGTGCACCAGGTGTATAA 59.551 33.333 21.26 17.79 35.75 0.98
552 577 3.462982 ACAAATTTTCAAAAGCCCGTCC 58.537 40.909 0.00 0.00 0.00 4.79
678 710 2.020720 TGCATACCCCGTTAAGCAATG 58.979 47.619 0.00 0.00 0.00 2.82
702 734 3.056607 CCCTTTTGTCCATCATGTTGGTC 60.057 47.826 19.92 15.72 38.01 4.02
736 768 5.103686 TCAAATTATTTCCTTCCCTCCCGAT 60.104 40.000 0.00 0.00 0.00 4.18
738 770 0.759346 ATTTCCTTCCCTCCCGATCG 59.241 55.000 8.51 8.51 0.00 3.69
810 845 1.601759 ATGTCACAGCCACAGCCAC 60.602 57.895 0.00 0.00 41.25 5.01
811 846 2.203195 GTCACAGCCACAGCCACA 60.203 61.111 0.00 0.00 41.25 4.17
812 847 2.111669 TCACAGCCACAGCCACAG 59.888 61.111 0.00 0.00 41.25 3.66
813 848 3.667282 CACAGCCACAGCCACAGC 61.667 66.667 0.00 0.00 41.25 4.40
814 849 4.962836 ACAGCCACAGCCACAGCC 62.963 66.667 0.00 0.00 41.25 4.85
815 850 4.960866 CAGCCACAGCCACAGCCA 62.961 66.667 0.00 0.00 41.25 4.75
959 994 1.948145 AGTTCTATACACGCTCCTCCG 59.052 52.381 0.00 0.00 0.00 4.63
1048 1087 3.673867 GACGACCACCGCTACGTCC 62.674 68.421 0.00 0.00 45.76 4.79
1390 1435 3.545308 GCGTGCGCGTCATATTATC 57.455 52.632 22.18 0.00 40.81 1.75
1391 1436 0.781787 GCGTGCGCGTCATATTATCA 59.218 50.000 22.18 0.00 40.81 2.15
1393 1438 2.596862 GCGTGCGCGTCATATTATCATA 59.403 45.455 22.18 0.00 40.81 2.15
1394 1439 3.242944 GCGTGCGCGTCATATTATCATAT 59.757 43.478 22.18 0.00 40.81 1.78
1396 1441 4.735338 CGTGCGCGTCATATTATCATATCT 59.265 41.667 12.43 0.00 0.00 1.98
1397 1442 5.907391 CGTGCGCGTCATATTATCATATCTA 59.093 40.000 12.43 0.00 0.00 1.98
1399 1444 7.201190 CGTGCGCGTCATATTATCATATCTATC 60.201 40.741 12.43 0.00 0.00 2.08
1417 1462 1.953138 CCTGCTCGATCGGTCATGC 60.953 63.158 16.41 12.18 0.00 4.06
1419 1464 1.213733 CTGCTCGATCGGTCATGCTG 61.214 60.000 16.41 11.61 0.00 4.41
1426 1471 0.820891 ATCGGTCATGCTGCCATTCC 60.821 55.000 0.00 0.00 0.00 3.01
1430 1475 1.022735 GTCATGCTGCCATTCCTGAG 58.977 55.000 0.00 0.00 0.00 3.35
1433 1478 0.465824 ATGCTGCCATTCCTGAGAGC 60.466 55.000 0.00 0.00 0.00 4.09
1447 1496 2.126734 GAGCGTGCATGGTGTTGC 60.127 61.111 16.75 0.00 43.07 4.17
1456 1505 1.865248 GCATGGTGTTGCACTGTTGAC 60.865 52.381 0.00 0.00 42.31 3.18
1560 1609 0.238553 GCAGGCGTTGAAGAACTTCC 59.761 55.000 11.30 0.00 38.77 3.46
1658 1707 1.404391 CCTAGGCCAGTGTAGTGTACG 59.596 57.143 5.01 0.00 0.00 3.67
1821 1910 4.451150 GCATGAGGTCGGCGGTGA 62.451 66.667 7.21 0.00 0.00 4.02
1966 2071 1.021390 GTCAGCCCATTGTGAGTCGG 61.021 60.000 0.00 0.00 0.00 4.79
1999 2104 7.595819 TCCATGGTTGTTGTAGAAGAAAATT 57.404 32.000 12.58 0.00 0.00 1.82
2000 2105 8.698973 TCCATGGTTGTTGTAGAAGAAAATTA 57.301 30.769 12.58 0.00 0.00 1.40
2001 2106 8.573035 TCCATGGTTGTTGTAGAAGAAAATTAC 58.427 33.333 12.58 0.00 0.00 1.89
2002 2107 8.356657 CCATGGTTGTTGTAGAAGAAAATTACA 58.643 33.333 2.57 0.00 0.00 2.41
2003 2108 9.398170 CATGGTTGTTGTAGAAGAAAATTACAG 57.602 33.333 0.00 0.00 0.00 2.74
2032 2148 5.582689 ACTCCAGGAGAAAAACAAAGTTG 57.417 39.130 24.45 0.00 33.32 3.16
2043 2160 8.056407 AGAAAAACAAAGTTGAGAGTAAGCTT 57.944 30.769 3.48 3.48 0.00 3.74
2065 2182 8.150945 AGCTTGTGAATACTCTTTTGTAGAAGA 58.849 33.333 0.00 0.00 34.63 2.87
2177 2299 2.368875 ACGACCCAAGTTGTCAAGAGAT 59.631 45.455 1.45 0.00 35.57 2.75
2192 2314 6.888088 TGTCAAGAGATCATTTTCATCACCAT 59.112 34.615 0.00 0.00 0.00 3.55
2204 2326 1.550072 CATCACCATTTTGTGGGGGTC 59.450 52.381 0.00 0.00 42.88 4.46
2220 2342 0.252284 GGTCTTGGGGTGAGAGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
2221 2343 1.190643 GTCTTGGGGTGAGAGAGGAG 58.809 60.000 0.00 0.00 0.00 3.69
2222 2344 1.084866 TCTTGGGGTGAGAGAGGAGA 58.915 55.000 0.00 0.00 0.00 3.71
2223 2345 1.648568 TCTTGGGGTGAGAGAGGAGAT 59.351 52.381 0.00 0.00 0.00 2.75
2228 2361 2.358721 GGGGTGAGAGAGGAGATTCAGA 60.359 54.545 0.00 0.00 0.00 3.27
2238 2372 5.271598 AGAGGAGATTCAGAATCACTCACT 58.728 41.667 30.21 19.31 42.08 3.41
2286 2420 3.636929 CTGCGCCACCACCCCAATA 62.637 63.158 4.18 0.00 0.00 1.90
2301 2435 6.016276 CCACCCCAATATTGATTGCTTACTAC 60.016 42.308 17.23 0.00 41.09 2.73
2312 2452 6.414732 TGATTGCTTACTACTAATGCCAACT 58.585 36.000 0.00 0.00 0.00 3.16
2327 2467 9.601217 CTAATGCCAACTTTACTAATCTGTAGT 57.399 33.333 0.00 0.00 0.00 2.73
2349 2489 0.390866 TTATTTGCGACGCCCCGTTA 60.391 50.000 18.69 0.00 41.37 3.18
2350 2490 0.390866 TATTTGCGACGCCCCGTTAA 60.391 50.000 18.69 0.00 41.37 2.01
2351 2491 1.235948 ATTTGCGACGCCCCGTTAAA 61.236 50.000 18.69 10.23 41.37 1.52
2352 2492 1.235948 TTTGCGACGCCCCGTTAAAT 61.236 50.000 18.69 0.00 41.37 1.40
2353 2493 1.235948 TTGCGACGCCCCGTTAAATT 61.236 50.000 18.69 0.00 41.37 1.82
2354 2494 1.226184 GCGACGCCCCGTTAAATTG 60.226 57.895 9.14 0.00 41.37 2.32
2355 2495 1.914531 GCGACGCCCCGTTAAATTGT 61.915 55.000 9.14 0.00 41.37 2.71
2359 2499 3.364764 CGACGCCCCGTTAAATTGTAAAA 60.365 43.478 0.00 0.00 41.37 1.52
2383 2523 9.907229 AAAAACCATCACAATTTAAAACCCTAA 57.093 25.926 0.00 0.00 0.00 2.69
2386 2526 9.719355 AACCATCACAATTTAAAACCCTAATTC 57.281 29.630 0.00 0.00 0.00 2.17
2387 2527 8.875168 ACCATCACAATTTAAAACCCTAATTCA 58.125 29.630 0.00 0.00 0.00 2.57
2388 2528 9.717942 CCATCACAATTTAAAACCCTAATTCAA 57.282 29.630 0.00 0.00 0.00 2.69
2408 3087 1.821216 AAAAACCGCCATCACTCGAT 58.179 45.000 0.00 0.00 0.00 3.59
2409 3088 2.684001 AAAACCGCCATCACTCGATA 57.316 45.000 0.00 0.00 0.00 2.92
2410 3089 2.910688 AAACCGCCATCACTCGATAT 57.089 45.000 0.00 0.00 0.00 1.63
2448 3127 4.122143 CCAACATTGTGGTGACAGTTTT 57.878 40.909 0.00 0.00 44.46 2.43
2450 3129 4.381398 CCAACATTGTGGTGACAGTTTTCA 60.381 41.667 0.00 0.00 44.46 2.69
2451 3130 4.637483 ACATTGTGGTGACAGTTTTCAG 57.363 40.909 0.00 0.00 44.46 3.02
2452 3131 4.269183 ACATTGTGGTGACAGTTTTCAGA 58.731 39.130 0.00 0.00 44.46 3.27
2454 3133 5.184864 ACATTGTGGTGACAGTTTTCAGAAA 59.815 36.000 0.00 0.00 44.46 2.52
2455 3134 5.713792 TTGTGGTGACAGTTTTCAGAAAA 57.286 34.783 4.06 4.06 44.46 2.29
2469 3148 6.940831 TTTCAGAAAACACTGATGACATGA 57.059 33.333 0.00 0.00 44.67 3.07
2470 3149 7.514784 TTTCAGAAAACACTGATGACATGAT 57.485 32.000 0.00 0.00 44.67 2.45
2471 3150 8.620116 TTTCAGAAAACACTGATGACATGATA 57.380 30.769 0.00 0.00 44.67 2.15
2472 3151 8.620116 TTCAGAAAACACTGATGACATGATAA 57.380 30.769 0.00 0.00 44.67 1.75
2473 3152 8.620116 TCAGAAAACACTGATGACATGATAAA 57.380 30.769 0.00 0.00 41.21 1.40
2475 3154 8.291740 CAGAAAACACTGATGACATGATAAACA 58.708 33.333 0.00 0.00 39.94 2.83
2476 3155 8.849168 AGAAAACACTGATGACATGATAAACAA 58.151 29.630 0.00 0.00 0.00 2.83
2477 3156 8.801715 AAAACACTGATGACATGATAAACAAC 57.198 30.769 0.00 0.00 0.00 3.32
2478 3157 6.169419 ACACTGATGACATGATAAACAACG 57.831 37.500 0.00 0.00 0.00 4.10
2481 3160 7.077605 CACTGATGACATGATAAACAACGTTT 58.922 34.615 0.00 0.00 0.00 3.60
2482 3161 7.059831 CACTGATGACATGATAAACAACGTTTG 59.940 37.037 0.00 0.00 0.00 2.93
2483 3162 7.041440 ACTGATGACATGATAAACAACGTTTGA 60.041 33.333 0.00 0.00 0.00 2.69
2484 3163 7.815641 TGATGACATGATAAACAACGTTTGAT 58.184 30.769 0.00 0.00 0.00 2.57
2485 3164 8.940952 TGATGACATGATAAACAACGTTTGATA 58.059 29.630 0.00 0.00 0.00 2.15
2498 3177 2.534349 CGTTTGATACGGAATCTGACGG 59.466 50.000 0.00 0.00 46.42 4.79
2501 3180 3.643159 TGATACGGAATCTGACGGATG 57.357 47.619 0.00 0.00 32.99 3.51
2507 3186 0.106894 GAATCTGACGGATGGGTCCC 59.893 60.000 0.00 0.00 41.83 4.46
2508 3187 0.620410 AATCTGACGGATGGGTCCCA 60.620 55.000 14.64 14.64 41.83 4.37
2510 3189 1.146930 CTGACGGATGGGTCCCATG 59.853 63.158 28.98 16.85 45.26 3.66
2511 3190 1.615124 TGACGGATGGGTCCCATGT 60.615 57.895 28.98 20.08 45.26 3.21
2512 3191 1.153168 GACGGATGGGTCCCATGTG 60.153 63.158 28.98 20.75 45.26 3.21
2513 3192 1.910580 GACGGATGGGTCCCATGTGT 61.911 60.000 28.98 23.72 45.26 3.72
2515 3194 0.544223 CGGATGGGTCCCATGTGTAA 59.456 55.000 28.98 0.00 45.26 2.41
2516 3195 1.475034 CGGATGGGTCCCATGTGTAAG 60.475 57.143 28.98 8.54 45.26 2.34
2517 3196 1.564348 GGATGGGTCCCATGTGTAAGT 59.436 52.381 28.98 1.35 45.26 2.24
2518 3197 2.643551 GATGGGTCCCATGTGTAAGTG 58.356 52.381 28.98 0.00 45.26 3.16
2519 3198 1.735926 TGGGTCCCATGTGTAAGTGA 58.264 50.000 6.47 0.00 0.00 3.41
2520 3199 2.274542 TGGGTCCCATGTGTAAGTGAT 58.725 47.619 6.47 0.00 0.00 3.06
2523 3202 3.270877 GGTCCCATGTGTAAGTGATGAC 58.729 50.000 0.00 0.00 0.00 3.06
2524 3203 3.307410 GGTCCCATGTGTAAGTGATGACA 60.307 47.826 0.00 0.00 0.00 3.58
2525 3204 4.517285 GTCCCATGTGTAAGTGATGACAT 58.483 43.478 0.00 0.00 0.00 3.06
2526 3205 4.333649 GTCCCATGTGTAAGTGATGACATG 59.666 45.833 0.00 0.00 43.49 3.21
2529 3208 5.475273 CATGTGTAAGTGATGACATGGAC 57.525 43.478 0.00 0.00 41.25 4.02
2530 3209 4.615588 TGTGTAAGTGATGACATGGACA 57.384 40.909 0.00 0.00 0.00 4.02
2531 3210 4.967036 TGTGTAAGTGATGACATGGACAA 58.033 39.130 0.00 0.00 0.00 3.18
2533 3212 5.825151 TGTGTAAGTGATGACATGGACAAAA 59.175 36.000 0.00 0.00 0.00 2.44
2534 3213 6.319911 TGTGTAAGTGATGACATGGACAAAAA 59.680 34.615 0.00 0.00 0.00 1.94
2553 3232 4.563140 AAAATAGCCTGGACCGTTAAGA 57.437 40.909 0.00 0.00 0.00 2.10
2554 3233 3.821421 AATAGCCTGGACCGTTAAGAG 57.179 47.619 0.00 0.00 0.00 2.85
2557 3309 0.107654 GCCTGGACCGTTAAGAGCAT 60.108 55.000 0.00 0.00 0.00 3.79
2558 3310 1.941325 CCTGGACCGTTAAGAGCATC 58.059 55.000 0.00 0.00 0.00 3.91
2599 3351 3.196648 CCCCCAGGCGATTTTTCG 58.803 61.111 0.00 0.00 0.00 3.46
2627 3379 3.996614 CCGAAAAATCGGCCCAGT 58.003 55.556 4.12 0.00 46.76 4.00
2628 3380 1.800681 CCGAAAAATCGGCCCAGTC 59.199 57.895 4.12 0.00 46.76 3.51
2629 3381 1.423845 CGAAAAATCGGCCCAGTCG 59.576 57.895 0.00 0.00 0.00 4.18
2630 3382 1.136774 GAAAAATCGGCCCAGTCGC 59.863 57.895 0.00 0.00 0.00 5.19
2649 3401 4.330056 CCCCCAAAGGCCCTTTTT 57.670 55.556 5.84 0.00 30.60 1.94
2679 3431 4.834892 CCGAAATTGGCGCTGGCG 62.835 66.667 7.64 10.80 41.24 5.69
2680 3432 4.834892 CGAAATTGGCGCTGGCGG 62.835 66.667 16.61 0.00 41.24 6.13
2681 3433 3.439540 GAAATTGGCGCTGGCGGA 61.440 61.111 16.61 0.00 41.24 5.54
2682 3434 3.683587 GAAATTGGCGCTGGCGGAC 62.684 63.158 16.61 0.77 41.24 4.79
2695 3447 4.410400 CGGACCCAGGCTGAACCC 62.410 72.222 17.94 12.06 40.58 4.11
2696 3448 4.410400 GGACCCAGGCTGAACCCG 62.410 72.222 17.94 0.00 40.58 5.28
2717 3469 4.489771 CGCTAGGGGGCACTTGGG 62.490 72.222 0.00 0.00 0.00 4.12
2718 3470 4.129148 GCTAGGGGGCACTTGGGG 62.129 72.222 0.00 0.00 0.00 4.96
2719 3471 3.420482 CTAGGGGGCACTTGGGGG 61.420 72.222 0.00 0.00 0.00 5.40
2737 3489 3.795342 CGCCGGCCGAATCGTTTT 61.795 61.111 30.73 0.00 40.02 2.43
2738 3490 2.564458 GCCGGCCGAATCGTTTTT 59.436 55.556 30.73 0.00 0.00 1.94
2739 3491 1.799916 GCCGGCCGAATCGTTTTTG 60.800 57.895 30.73 6.52 0.00 2.44
2740 3492 1.154112 CCGGCCGAATCGTTTTTGG 60.154 57.895 30.73 0.00 0.00 3.28
2741 3493 1.799916 CGGCCGAATCGTTTTTGGC 60.800 57.895 24.07 18.28 44.98 4.52
2742 3494 1.799916 GGCCGAATCGTTTTTGGCG 60.800 57.895 19.21 3.07 46.66 5.69
2743 3495 2.433334 GCCGAATCGTTTTTGGCGC 61.433 57.895 13.77 0.00 35.77 6.53
2744 3496 2.143458 CCGAATCGTTTTTGGCGCG 61.143 57.895 0.00 0.00 0.00 6.86
2745 3497 1.154562 CGAATCGTTTTTGGCGCGA 60.155 52.632 12.10 0.00 39.02 5.87
2746 3498 0.723129 CGAATCGTTTTTGGCGCGAA 60.723 50.000 12.10 0.00 38.17 4.70
2747 3499 1.400550 GAATCGTTTTTGGCGCGAAA 58.599 45.000 13.91 13.91 38.17 3.46
2748 3500 1.781998 GAATCGTTTTTGGCGCGAAAA 59.218 42.857 23.88 23.88 38.17 2.29
2749 3501 2.058913 ATCGTTTTTGGCGCGAAAAT 57.941 40.000 27.22 12.50 38.17 1.82
2750 3502 1.400550 TCGTTTTTGGCGCGAAAATC 58.599 45.000 27.22 24.15 30.72 2.17
2751 3503 0.088858 CGTTTTTGGCGCGAAAATCG 59.911 50.000 31.69 31.69 43.89 3.34
2752 3504 0.433115 GTTTTTGGCGCGAAAATCGG 59.567 50.000 27.22 0.00 40.84 4.18
2761 3513 3.209812 GAAAATCGGCGGGCCCTC 61.210 66.667 22.43 13.01 0.00 4.30
2762 3514 4.815108 AAAATCGGCGGGCCCTCC 62.815 66.667 21.98 21.98 0.00 4.30
2774 3526 3.710722 CCCTCCTTGGCAGCGACT 61.711 66.667 0.00 0.00 0.00 4.18
2775 3527 2.125350 CCTCCTTGGCAGCGACTC 60.125 66.667 0.00 0.00 0.00 3.36
2776 3528 2.507992 CTCCTTGGCAGCGACTCG 60.508 66.667 0.00 0.00 0.00 4.18
2777 3529 3.997064 CTCCTTGGCAGCGACTCGG 62.997 68.421 0.00 0.00 0.00 4.63
2779 3531 4.749310 CTTGGCAGCGACTCGGCT 62.749 66.667 0.00 0.00 46.13 5.52
2780 3532 4.742201 TTGGCAGCGACTCGGCTC 62.742 66.667 0.00 0.00 42.53 4.70
2782 3534 4.443266 GGCAGCGACTCGGCTCTT 62.443 66.667 0.00 0.00 42.53 2.85
2783 3535 2.883253 GCAGCGACTCGGCTCTTC 60.883 66.667 0.00 0.00 42.53 2.87
2784 3536 2.881389 CAGCGACTCGGCTCTTCT 59.119 61.111 0.00 0.00 42.53 2.85
2785 3537 1.226547 CAGCGACTCGGCTCTTCTC 60.227 63.158 0.00 0.00 42.53 2.87
2786 3538 2.277628 GCGACTCGGCTCTTCTCG 60.278 66.667 0.00 0.00 0.00 4.04
2787 3539 2.277628 CGACTCGGCTCTTCTCGC 60.278 66.667 0.00 0.00 0.00 5.03
2788 3540 2.103340 GACTCGGCTCTTCTCGCC 59.897 66.667 0.00 0.00 44.11 5.54
2793 3545 2.888051 GGCTCTTCTCGCCGCTTC 60.888 66.667 0.00 0.00 37.87 3.86
2794 3546 3.251043 GCTCTTCTCGCCGCTTCG 61.251 66.667 0.00 0.00 0.00 3.79
2795 3547 2.179517 CTCTTCTCGCCGCTTCGT 59.820 61.111 0.00 0.00 0.00 3.85
2796 3548 1.870016 CTCTTCTCGCCGCTTCGTC 60.870 63.158 0.00 0.00 0.00 4.20
2797 3549 3.241059 CTTCTCGCCGCTTCGTCG 61.241 66.667 0.00 0.00 0.00 5.12
2798 3550 3.948086 CTTCTCGCCGCTTCGTCGT 62.948 63.158 0.00 0.00 0.00 4.34
2799 3551 3.940975 TTCTCGCCGCTTCGTCGTC 62.941 63.158 0.00 0.00 0.00 4.20
2803 3555 4.415332 GCCGCTTCGTCGTCCTCA 62.415 66.667 0.00 0.00 0.00 3.86
2804 3556 2.490217 CCGCTTCGTCGTCCTCAT 59.510 61.111 0.00 0.00 0.00 2.90
2805 3557 1.586564 CCGCTTCGTCGTCCTCATC 60.587 63.158 0.00 0.00 0.00 2.92
2806 3558 1.934956 CGCTTCGTCGTCCTCATCG 60.935 63.158 0.00 0.00 0.00 3.84
2807 3559 2.224885 GCTTCGTCGTCCTCATCGC 61.225 63.158 0.00 0.00 0.00 4.58
2808 3560 1.586564 CTTCGTCGTCCTCATCGCC 60.587 63.158 0.00 0.00 0.00 5.54
2809 3561 1.994507 CTTCGTCGTCCTCATCGCCT 61.995 60.000 0.00 0.00 0.00 5.52
2810 3562 1.989966 TTCGTCGTCCTCATCGCCTC 61.990 60.000 0.00 0.00 0.00 4.70
2811 3563 2.024871 GTCGTCCTCATCGCCTCG 59.975 66.667 0.00 0.00 0.00 4.63
2812 3564 3.209812 TCGTCCTCATCGCCTCGG 61.210 66.667 0.00 0.00 0.00 4.63
2813 3565 3.518998 CGTCCTCATCGCCTCGGT 61.519 66.667 0.00 0.00 0.00 4.69
2814 3566 2.893398 GTCCTCATCGCCTCGGTT 59.107 61.111 0.00 0.00 0.00 4.44
2815 3567 1.227002 GTCCTCATCGCCTCGGTTC 60.227 63.158 0.00 0.00 0.00 3.62
2816 3568 2.107141 CCTCATCGCCTCGGTTCC 59.893 66.667 0.00 0.00 0.00 3.62
2817 3569 2.107141 CTCATCGCCTCGGTTCCC 59.893 66.667 0.00 0.00 0.00 3.97
2834 3586 4.612536 CGCGGCGGAATCAATGCC 62.613 66.667 15.84 1.03 45.39 4.40
2839 3591 2.669419 GCGGAATCAATGCCAAAGC 58.331 52.632 0.00 0.00 40.48 3.51
2840 3592 0.174162 GCGGAATCAATGCCAAAGCT 59.826 50.000 0.00 0.00 40.80 3.74
2841 3593 1.917273 CGGAATCAATGCCAAAGCTG 58.083 50.000 0.00 0.00 40.80 4.24
2842 3594 1.648504 GGAATCAATGCCAAAGCTGC 58.351 50.000 0.00 0.00 40.80 5.25
2843 3595 1.648504 GAATCAATGCCAAAGCTGCC 58.351 50.000 0.00 0.00 40.80 4.85
2844 3596 0.108520 AATCAATGCCAAAGCTGCCG 60.109 50.000 0.00 0.00 40.80 5.69
2845 3597 2.567564 ATCAATGCCAAAGCTGCCGC 62.568 55.000 0.00 0.00 40.80 6.53
2871 3623 4.459089 GTGCCGGTCAGCCTCCTC 62.459 72.222 1.90 0.00 0.00 3.71
2874 3626 2.765807 CCGGTCAGCCTCCTCCAT 60.766 66.667 0.00 0.00 0.00 3.41
2875 3627 2.370445 CCGGTCAGCCTCCTCCATT 61.370 63.158 0.00 0.00 0.00 3.16
2876 3628 1.153289 CGGTCAGCCTCCTCCATTG 60.153 63.158 0.00 0.00 0.00 2.82
2877 3629 1.617018 CGGTCAGCCTCCTCCATTGA 61.617 60.000 0.00 0.00 0.00 2.57
2878 3630 0.842635 GGTCAGCCTCCTCCATTGAT 59.157 55.000 0.00 0.00 0.00 2.57
2879 3631 1.476471 GGTCAGCCTCCTCCATTGATG 60.476 57.143 0.00 0.00 0.00 3.07
2880 3632 0.182061 TCAGCCTCCTCCATTGATGC 59.818 55.000 0.00 0.00 0.00 3.91
2881 3633 0.822532 CAGCCTCCTCCATTGATGCC 60.823 60.000 0.00 0.00 0.00 4.40
2882 3634 0.992431 AGCCTCCTCCATTGATGCCT 60.992 55.000 0.00 0.00 0.00 4.75
2883 3635 0.536915 GCCTCCTCCATTGATGCCTC 60.537 60.000 0.00 0.00 0.00 4.70
2884 3636 0.841961 CCTCCTCCATTGATGCCTCA 59.158 55.000 0.00 0.00 0.00 3.86
2885 3637 1.424302 CCTCCTCCATTGATGCCTCAT 59.576 52.381 0.00 0.00 0.00 2.90
2886 3638 2.505405 CTCCTCCATTGATGCCTCATG 58.495 52.381 0.00 0.00 0.00 3.07
2887 3639 1.144298 TCCTCCATTGATGCCTCATGG 59.856 52.381 11.54 11.54 34.22 3.66
2888 3640 1.617322 CTCCATTGATGCCTCATGGG 58.383 55.000 15.26 10.23 33.96 4.00
2907 3659 4.373116 GGCGCAGTGAAGACGGGA 62.373 66.667 10.83 0.00 0.00 5.14
2908 3660 3.112709 GCGCAGTGAAGACGGGAC 61.113 66.667 0.30 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 179 3.641437 TGCAATTGGCTGACAAACTAC 57.359 42.857 7.72 0.00 43.46 2.73
408 427 5.909477 TGTAATTCGACCTTATACACCTGG 58.091 41.667 0.00 0.00 0.00 4.45
438 457 4.311606 TCGCTTGCTGTGTACTTTGATAA 58.688 39.130 0.00 0.00 0.00 1.75
452 472 8.947055 AAAATAATTGGAATAATTCGCTTGCT 57.053 26.923 0.00 0.00 0.00 3.91
552 577 0.457337 GTAGACTGCCCGTACGTTGG 60.457 60.000 15.21 10.36 0.00 3.77
558 583 1.283029 ACTACCAGTAGACTGCCCGTA 59.717 52.381 11.71 1.46 42.47 4.02
634 665 3.067106 CGTTCAAGAAAGCAGCTCCTAA 58.933 45.455 0.00 0.00 0.00 2.69
678 710 1.560505 ACATGATGGACAAAAGGGGC 58.439 50.000 0.00 0.00 0.00 5.80
702 734 7.334171 GGAAGGAAATAATTTGAAATGTGTGGG 59.666 37.037 0.00 0.00 0.00 4.61
736 768 0.901827 TGGCTAAGCAATGGACTCGA 59.098 50.000 0.00 0.00 0.00 4.04
824 859 0.391793 CGGGAGAAGAAAGTGAGGGC 60.392 60.000 0.00 0.00 0.00 5.19
959 994 2.991993 GAACGAACGAACGGACGGC 61.992 63.158 15.57 0.00 37.61 5.68
1033 1072 4.139234 GGGGACGTAGCGGTGGTC 62.139 72.222 10.93 10.93 0.00 4.02
1117 1156 2.951745 CGAGACATGCGGCGACTC 60.952 66.667 12.98 9.50 0.00 3.36
1385 1430 7.094420 CCGATCGAGCAGGATAGATATGATAAT 60.094 40.741 18.66 0.00 0.00 1.28
1387 1432 5.703130 CCGATCGAGCAGGATAGATATGATA 59.297 44.000 18.66 0.00 0.00 2.15
1388 1433 4.518590 CCGATCGAGCAGGATAGATATGAT 59.481 45.833 18.66 0.00 0.00 2.45
1389 1434 3.879892 CCGATCGAGCAGGATAGATATGA 59.120 47.826 18.66 0.00 0.00 2.15
1390 1435 3.629855 ACCGATCGAGCAGGATAGATATG 59.370 47.826 18.66 0.00 0.00 1.78
1391 1436 3.880490 GACCGATCGAGCAGGATAGATAT 59.120 47.826 18.66 0.00 0.00 1.63
1393 1438 2.088423 GACCGATCGAGCAGGATAGAT 58.912 52.381 18.66 0.00 0.00 1.98
1394 1439 1.202770 TGACCGATCGAGCAGGATAGA 60.203 52.381 18.66 0.00 0.00 1.98
1396 1441 1.541588 CATGACCGATCGAGCAGGATA 59.458 52.381 18.66 6.72 0.00 2.59
1397 1442 0.316522 CATGACCGATCGAGCAGGAT 59.683 55.000 18.66 0.00 0.00 3.24
1399 1444 1.953138 GCATGACCGATCGAGCAGG 60.953 63.158 18.66 16.09 0.00 4.85
1417 1462 1.088340 CACGCTCTCAGGAATGGCAG 61.088 60.000 0.00 0.00 0.00 4.85
1419 1464 2.467826 GCACGCTCTCAGGAATGGC 61.468 63.158 0.00 0.00 0.00 4.40
1426 1471 0.952497 AACACCATGCACGCTCTCAG 60.952 55.000 0.00 0.00 0.00 3.35
1430 1475 2.126734 GCAACACCATGCACGCTC 60.127 61.111 0.00 0.00 45.70 5.03
1447 1496 1.246056 CCAGCCCATGGTCAACAGTG 61.246 60.000 11.73 0.00 44.91 3.66
1468 1517 1.171549 TCAAGCATGCAAAGCGACCA 61.172 50.000 21.98 0.00 37.01 4.02
1583 1632 0.320771 AATCAAGGAAGCTCGCGTGT 60.321 50.000 5.77 0.00 0.00 4.49
1658 1707 3.485877 GCTGCATCTAAAATGGTCACGTC 60.486 47.826 0.00 0.00 0.00 4.34
1999 2104 7.844493 TTTTCTCCTGGAGTTAACTACTGTA 57.156 36.000 22.50 4.69 37.17 2.74
2000 2105 6.742559 TTTTCTCCTGGAGTTAACTACTGT 57.257 37.500 22.50 0.00 37.17 3.55
2001 2106 6.990349 TGTTTTTCTCCTGGAGTTAACTACTG 59.010 38.462 22.50 17.21 37.17 2.74
2002 2107 7.133133 TGTTTTTCTCCTGGAGTTAACTACT 57.867 36.000 22.50 0.00 40.71 2.57
2003 2108 7.797038 TTGTTTTTCTCCTGGAGTTAACTAC 57.203 36.000 22.50 11.20 0.00 2.73
2011 2116 5.590259 TCTCAACTTTGTTTTTCTCCTGGAG 59.410 40.000 17.84 17.84 0.00 3.86
2032 2148 8.439286 CAAAAGAGTATTCACAAGCTTACTCTC 58.561 37.037 21.71 12.56 46.24 3.20
2065 2182 6.374417 TTGCTCCTGGATCTAACTAGTTTT 57.626 37.500 14.49 0.00 0.00 2.43
2192 2314 1.234529 CCCCAAGACCCCCACAAAA 59.765 57.895 0.00 0.00 0.00 2.44
2202 2324 1.190643 CTCCTCTCTCACCCCAAGAC 58.809 60.000 0.00 0.00 0.00 3.01
2203 2325 1.084866 TCTCCTCTCTCACCCCAAGA 58.915 55.000 0.00 0.00 0.00 3.02
2204 2326 2.173126 ATCTCCTCTCTCACCCCAAG 57.827 55.000 0.00 0.00 0.00 3.61
2220 2342 7.393216 AGCTAAAAGTGAGTGATTCTGAATCT 58.607 34.615 25.83 11.07 38.72 2.40
2221 2343 7.608308 AGCTAAAAGTGAGTGATTCTGAATC 57.392 36.000 20.74 20.74 38.40 2.52
2222 2344 9.107177 CATAGCTAAAAGTGAGTGATTCTGAAT 57.893 33.333 1.81 1.81 0.00 2.57
2223 2345 8.314021 TCATAGCTAAAAGTGAGTGATTCTGAA 58.686 33.333 0.00 0.00 0.00 3.02
2228 2361 7.044798 GGTCTCATAGCTAAAAGTGAGTGATT 58.955 38.462 17.52 0.00 39.22 2.57
2238 2372 3.794475 GCGCGTAGGTCTCATAGCTAAAA 60.794 47.826 8.43 0.00 39.81 1.52
2286 2420 7.557719 AGTTGGCATTAGTAGTAAGCAATCAAT 59.442 33.333 11.42 0.00 0.00 2.57
2301 2435 9.601217 ACTACAGATTAGTAAAGTTGGCATTAG 57.399 33.333 0.00 0.00 0.00 1.73
2327 2467 0.806884 CGGGGCGTCGCAAATAAGTA 60.807 55.000 20.50 0.00 0.00 2.24
2362 2502 9.717942 TTGAATTAGGGTTTTAAATTGTGATGG 57.282 29.630 0.00 0.00 0.00 3.51
2390 2530 2.684001 TATCGAGTGATGGCGGTTTT 57.316 45.000 0.00 0.00 35.99 2.43
2391 2531 2.910688 ATATCGAGTGATGGCGGTTT 57.089 45.000 0.00 0.00 35.99 3.27
2392 2532 2.910688 AATATCGAGTGATGGCGGTT 57.089 45.000 0.00 0.00 35.99 4.44
2393 2533 2.910688 AAATATCGAGTGATGGCGGT 57.089 45.000 0.00 0.00 35.99 5.68
2427 3106 3.799281 AAACTGTCACCACAATGTTGG 57.201 42.857 0.00 1.30 43.04 3.77
2430 3109 4.269183 TCTGAAAACTGTCACCACAATGT 58.731 39.130 0.00 0.00 29.82 2.71
2431 3110 4.898829 TCTGAAAACTGTCACCACAATG 57.101 40.909 0.00 0.00 29.82 2.82
2432 3111 5.913137 TTTCTGAAAACTGTCACCACAAT 57.087 34.783 0.00 0.00 29.82 2.71
2433 3112 5.465935 GTTTTCTGAAAACTGTCACCACAA 58.534 37.500 29.39 0.00 45.55 3.33
2434 3113 5.054390 GTTTTCTGAAAACTGTCACCACA 57.946 39.130 29.39 0.00 45.55 4.17
2445 3124 7.332213 TCATGTCATCAGTGTTTTCTGAAAA 57.668 32.000 11.33 11.33 45.65 2.29
2446 3125 6.940831 TCATGTCATCAGTGTTTTCTGAAA 57.059 33.333 0.00 0.00 45.65 2.69
2448 3127 8.506437 GTTTATCATGTCATCAGTGTTTTCTGA 58.494 33.333 0.00 0.00 46.39 3.27
2450 3129 8.394971 TGTTTATCATGTCATCAGTGTTTTCT 57.605 30.769 0.00 0.00 0.00 2.52
2451 3130 8.905702 GTTGTTTATCATGTCATCAGTGTTTTC 58.094 33.333 0.00 0.00 0.00 2.29
2452 3131 7.591057 CGTTGTTTATCATGTCATCAGTGTTTT 59.409 33.333 0.00 0.00 0.00 2.43
2454 3133 6.204688 ACGTTGTTTATCATGTCATCAGTGTT 59.795 34.615 0.00 0.00 0.00 3.32
2455 3134 5.700832 ACGTTGTTTATCATGTCATCAGTGT 59.299 36.000 0.00 0.00 0.00 3.55
2456 3135 6.169419 ACGTTGTTTATCATGTCATCAGTG 57.831 37.500 0.00 0.00 0.00 3.66
2457 3136 6.801539 AACGTTGTTTATCATGTCATCAGT 57.198 33.333 0.00 0.00 0.00 3.41
2458 3137 7.297391 TCAAACGTTGTTTATCATGTCATCAG 58.703 34.615 0.00 0.00 0.00 2.90
2460 3139 9.210426 GTATCAAACGTTGTTTATCATGTCATC 57.790 33.333 0.00 0.00 0.00 2.92
2462 3141 7.230914 CGTATCAAACGTTGTTTATCATGTCA 58.769 34.615 0.00 0.00 46.72 3.58
2463 3142 7.630689 CGTATCAAACGTTGTTTATCATGTC 57.369 36.000 0.00 0.00 46.72 3.06
2477 3156 7.011219 CATCCGTCAGATTCCGTATCAAACG 62.011 48.000 11.52 11.52 41.73 3.60
2478 3157 3.777478 TCCGTCAGATTCCGTATCAAAC 58.223 45.455 0.00 0.00 35.59 2.93
2481 3160 2.296190 CCATCCGTCAGATTCCGTATCA 59.704 50.000 0.00 0.00 35.59 2.15
2482 3161 2.352814 CCCATCCGTCAGATTCCGTATC 60.353 54.545 0.00 0.00 30.59 2.24
2483 3162 1.618837 CCCATCCGTCAGATTCCGTAT 59.381 52.381 0.00 0.00 30.59 3.06
2484 3163 1.037493 CCCATCCGTCAGATTCCGTA 58.963 55.000 0.00 0.00 30.59 4.02
2485 3164 0.976073 ACCCATCCGTCAGATTCCGT 60.976 55.000 0.00 0.00 30.59 4.69
2487 3166 0.106894 GGACCCATCCGTCAGATTCC 59.893 60.000 0.00 0.00 34.48 3.01
2488 3167 3.688553 GGACCCATCCGTCAGATTC 57.311 57.895 0.00 0.00 34.48 2.52
2498 3177 2.238646 TCACTTACACATGGGACCCATC 59.761 50.000 24.08 0.00 43.15 3.51
2501 3180 2.238646 TCATCACTTACACATGGGACCC 59.761 50.000 0.00 2.45 0.00 4.46
2507 3186 4.937015 TGTCCATGTCATCACTTACACATG 59.063 41.667 4.27 4.27 43.85 3.21
2508 3187 5.164620 TGTCCATGTCATCACTTACACAT 57.835 39.130 0.00 0.00 0.00 3.21
2509 3188 4.615588 TGTCCATGTCATCACTTACACA 57.384 40.909 0.00 0.00 0.00 3.72
2510 3189 5.940192 TTTGTCCATGTCATCACTTACAC 57.060 39.130 0.00 0.00 0.00 2.90
2511 3190 6.951062 TTTTTGTCCATGTCATCACTTACA 57.049 33.333 0.00 0.00 0.00 2.41
2531 3210 4.913784 TCTTAACGGTCCAGGCTATTTTT 58.086 39.130 0.00 0.00 0.00 1.94
2533 3212 3.681874 GCTCTTAACGGTCCAGGCTATTT 60.682 47.826 0.00 0.00 0.00 1.40
2534 3213 2.158943 GCTCTTAACGGTCCAGGCTATT 60.159 50.000 0.00 0.00 0.00 1.73
2535 3214 1.413077 GCTCTTAACGGTCCAGGCTAT 59.587 52.381 0.00 0.00 0.00 2.97
2536 3215 0.822164 GCTCTTAACGGTCCAGGCTA 59.178 55.000 0.00 0.00 0.00 3.93
2537 3216 1.192146 TGCTCTTAACGGTCCAGGCT 61.192 55.000 0.00 0.00 0.00 4.58
2538 3217 0.107654 ATGCTCTTAACGGTCCAGGC 60.108 55.000 0.00 0.00 0.00 4.85
2539 3218 1.482593 AGATGCTCTTAACGGTCCAGG 59.517 52.381 0.00 0.00 0.00 4.45
2541 3220 1.480954 GGAGATGCTCTTAACGGTCCA 59.519 52.381 0.00 0.00 0.00 4.02
2543 3222 2.815478 CTGGAGATGCTCTTAACGGTC 58.185 52.381 0.00 0.00 0.00 4.79
2544 3223 1.134670 GCTGGAGATGCTCTTAACGGT 60.135 52.381 0.00 0.00 0.00 4.83
2545 3224 1.576356 GCTGGAGATGCTCTTAACGG 58.424 55.000 0.00 0.00 0.00 4.44
2547 3226 1.576356 CGGCTGGAGATGCTCTTAAC 58.424 55.000 0.00 0.00 0.00 2.01
2549 3228 1.443407 GCGGCTGGAGATGCTCTTA 59.557 57.895 0.00 0.00 0.00 2.10
2550 3229 2.188994 GCGGCTGGAGATGCTCTT 59.811 61.111 0.00 0.00 0.00 2.85
2551 3230 4.218578 CGCGGCTGGAGATGCTCT 62.219 66.667 0.00 0.00 0.00 4.09
2582 3334 2.414785 CCGAAAAATCGCCTGGGGG 61.415 63.158 11.17 0.78 0.00 5.40
2583 3335 3.063743 GCCGAAAAATCGCCTGGGG 62.064 63.158 4.03 4.03 0.00 4.96
2584 3336 2.489751 GCCGAAAAATCGCCTGGG 59.510 61.111 0.00 0.00 0.00 4.45
2585 3337 2.489751 GGCCGAAAAATCGCCTGG 59.510 61.111 0.00 0.00 0.00 4.45
2586 3338 2.100216 CGGCCGAAAAATCGCCTG 59.900 61.111 24.07 0.00 0.00 4.85
2604 3356 4.530325 CCGATTTTTCGGCGCCGG 62.530 66.667 44.95 27.98 46.76 6.13
2612 3364 1.136774 GCGACTGGGCCGATTTTTC 59.863 57.895 0.00 0.00 0.00 2.29
2613 3365 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
2614 3366 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
2632 3384 4.330056 AAAAAGGGCCTTTGGGGG 57.670 55.556 31.06 0.00 33.64 5.40
2662 3414 4.834892 CGCCAGCGCCAATTTCGG 62.835 66.667 2.29 0.00 0.00 4.30
2663 3415 4.834892 CCGCCAGCGCCAATTTCG 62.835 66.667 2.29 0.00 38.24 3.46
2664 3416 3.439540 TCCGCCAGCGCCAATTTC 61.440 61.111 2.29 0.00 38.24 2.17
2678 3430 4.410400 GGGTTCAGCCTGGGTCCG 62.410 72.222 0.00 0.00 37.43 4.79
2679 3431 4.410400 CGGGTTCAGCCTGGGTCC 62.410 72.222 0.00 0.00 40.02 4.46
2700 3452 4.489771 CCCAAGTGCCCCCTAGCG 62.490 72.222 0.00 0.00 34.65 4.26
2702 3454 3.420482 CCCCCAAGTGCCCCCTAG 61.420 72.222 0.00 0.00 0.00 3.02
2720 3472 3.317153 AAAAACGATTCGGCCGGCG 62.317 57.895 27.83 26.79 0.00 6.46
2721 3473 1.799916 CAAAAACGATTCGGCCGGC 60.800 57.895 27.83 21.18 0.00 6.13
2722 3474 1.154112 CCAAAAACGATTCGGCCGG 60.154 57.895 27.83 11.94 0.00 6.13
2723 3475 1.799916 GCCAAAAACGATTCGGCCG 60.800 57.895 22.12 22.12 36.73 6.13
2724 3476 1.799916 CGCCAAAAACGATTCGGCC 60.800 57.895 11.29 0.00 39.69 6.13
2725 3477 2.433334 GCGCCAAAAACGATTCGGC 61.433 57.895 11.29 8.30 39.45 5.54
2726 3478 2.143458 CGCGCCAAAAACGATTCGG 61.143 57.895 11.29 0.00 0.00 4.30
2727 3479 0.723129 TTCGCGCCAAAAACGATTCG 60.723 50.000 0.00 4.14 35.48 3.34
2728 3480 1.400550 TTTCGCGCCAAAAACGATTC 58.599 45.000 0.00 0.00 35.48 2.52
2729 3481 1.841450 TTTTCGCGCCAAAAACGATT 58.159 40.000 10.58 0.00 35.48 3.34
2730 3482 1.982913 GATTTTCGCGCCAAAAACGAT 59.017 42.857 16.69 0.32 35.48 3.73
2731 3483 1.400550 GATTTTCGCGCCAAAAACGA 58.599 45.000 16.69 0.00 0.00 3.85
2732 3484 0.088858 CGATTTTCGCGCCAAAAACG 59.911 50.000 23.10 23.10 35.90 3.60
2733 3485 0.433115 CCGATTTTCGCGCCAAAAAC 59.567 50.000 16.69 13.00 38.82 2.43
2734 3486 1.278849 GCCGATTTTCGCGCCAAAAA 61.279 50.000 16.69 15.88 38.82 1.94
2735 3487 1.731257 GCCGATTTTCGCGCCAAAA 60.731 52.632 15.19 15.19 38.82 2.44
2736 3488 2.126657 GCCGATTTTCGCGCCAAA 60.127 55.556 0.00 0.00 38.82 3.28
2737 3489 4.453183 CGCCGATTTTCGCGCCAA 62.453 61.111 0.00 0.00 38.82 4.52
2744 3496 3.209812 GAGGGCCCGCCGATTTTC 61.210 66.667 18.44 1.01 36.85 2.29
2745 3497 4.815108 GGAGGGCCCGCCGATTTT 62.815 66.667 30.41 1.01 36.85 1.82
2757 3509 3.672295 GAGTCGCTGCCAAGGAGGG 62.672 68.421 0.00 0.00 38.09 4.30
2758 3510 2.125350 GAGTCGCTGCCAAGGAGG 60.125 66.667 0.00 0.00 41.84 4.30
2759 3511 2.507992 CGAGTCGCTGCCAAGGAG 60.508 66.667 0.00 0.00 0.00 3.69
2760 3512 4.069232 CCGAGTCGCTGCCAAGGA 62.069 66.667 7.12 0.00 0.00 3.36
2762 3514 4.749310 AGCCGAGTCGCTGCCAAG 62.749 66.667 7.12 0.00 37.82 3.61
2763 3515 4.742201 GAGCCGAGTCGCTGCCAA 62.742 66.667 7.12 0.00 39.87 4.52
2765 3517 4.443266 AAGAGCCGAGTCGCTGCC 62.443 66.667 7.12 1.01 39.87 4.85
2766 3518 2.883253 GAAGAGCCGAGTCGCTGC 60.883 66.667 7.12 6.32 39.87 5.25
2767 3519 1.226547 GAGAAGAGCCGAGTCGCTG 60.227 63.158 7.12 0.00 39.87 5.18
2768 3520 2.756025 CGAGAAGAGCCGAGTCGCT 61.756 63.158 7.12 8.14 43.42 4.93
2769 3521 2.277628 CGAGAAGAGCCGAGTCGC 60.278 66.667 7.12 2.73 0.00 5.19
2770 3522 2.277628 GCGAGAAGAGCCGAGTCG 60.278 66.667 5.29 5.29 0.00 4.18
2771 3523 2.103340 GGCGAGAAGAGCCGAGTC 59.897 66.667 0.00 0.00 45.58 3.36
2777 3529 3.251043 CGAAGCGGCGAGAAGAGC 61.251 66.667 12.98 0.00 0.00 4.09
2778 3530 1.870016 GACGAAGCGGCGAGAAGAG 60.870 63.158 12.98 0.00 34.83 2.85
2779 3531 2.178521 GACGAAGCGGCGAGAAGA 59.821 61.111 12.98 0.00 34.83 2.87
2786 3538 3.701604 ATGAGGACGACGAAGCGGC 62.702 63.158 0.00 0.00 38.96 6.53
2787 3539 1.586564 GATGAGGACGACGAAGCGG 60.587 63.158 0.00 0.00 35.12 5.52
2788 3540 1.934956 CGATGAGGACGACGAAGCG 60.935 63.158 0.00 0.00 37.29 4.68
2789 3541 2.224885 GCGATGAGGACGACGAAGC 61.225 63.158 0.00 0.00 0.00 3.86
2790 3542 1.586564 GGCGATGAGGACGACGAAG 60.587 63.158 0.00 0.00 0.00 3.79
2791 3543 1.989966 GAGGCGATGAGGACGACGAA 61.990 60.000 0.00 0.00 44.04 3.85
2792 3544 2.437895 AGGCGATGAGGACGACGA 60.438 61.111 0.00 0.00 44.04 4.20
2793 3545 2.024871 GAGGCGATGAGGACGACG 59.975 66.667 0.00 0.00 44.04 5.12
2794 3546 2.024871 CGAGGCGATGAGGACGAC 59.975 66.667 0.00 0.00 39.24 4.34
2795 3547 3.209812 CCGAGGCGATGAGGACGA 61.210 66.667 0.00 0.00 0.00 4.20
2796 3548 2.938539 GAACCGAGGCGATGAGGACG 62.939 65.000 0.00 0.00 0.00 4.79
2797 3549 1.227002 GAACCGAGGCGATGAGGAC 60.227 63.158 0.00 0.00 0.00 3.85
2798 3550 2.423898 GGAACCGAGGCGATGAGGA 61.424 63.158 0.00 0.00 0.00 3.71
2799 3551 2.107141 GGAACCGAGGCGATGAGG 59.893 66.667 0.00 0.00 0.00 3.86
2800 3552 2.107141 GGGAACCGAGGCGATGAG 59.893 66.667 0.00 0.00 40.86 2.90
2817 3569 4.612536 GGCATTGATTCCGCCGCG 62.613 66.667 5.59 5.59 35.79 6.46
2820 3572 0.807275 GCTTTGGCATTGATTCCGCC 60.807 55.000 0.00 0.00 46.43 6.13
2821 3573 0.174162 AGCTTTGGCATTGATTCCGC 59.826 50.000 0.00 0.00 41.70 5.54
2822 3574 1.917273 CAGCTTTGGCATTGATTCCG 58.083 50.000 0.00 0.00 41.70 4.30
2823 3575 1.648504 GCAGCTTTGGCATTGATTCC 58.351 50.000 0.00 0.00 41.70 3.01
2824 3576 1.648504 GGCAGCTTTGGCATTGATTC 58.351 50.000 0.00 0.00 41.70 2.52
2825 3577 0.108520 CGGCAGCTTTGGCATTGATT 60.109 50.000 0.46 0.00 41.70 2.57
2826 3578 1.514087 CGGCAGCTTTGGCATTGAT 59.486 52.632 0.46 0.00 41.70 2.57
2827 3579 2.964174 CGGCAGCTTTGGCATTGA 59.036 55.556 0.46 0.00 41.70 2.57
2828 3580 2.812178 GCGGCAGCTTTGGCATTG 60.812 61.111 0.00 0.00 41.70 2.82
2854 3606 4.459089 GAGGAGGCTGACCGGCAC 62.459 72.222 0.00 0.00 42.76 5.01
2857 3609 2.370445 AATGGAGGAGGCTGACCGG 61.370 63.158 0.00 0.00 42.76 5.28
2858 3610 1.153289 CAATGGAGGAGGCTGACCG 60.153 63.158 0.00 0.00 42.76 4.79
2859 3611 0.842635 ATCAATGGAGGAGGCTGACC 59.157 55.000 0.00 0.00 0.00 4.02
2860 3612 1.964552 CATCAATGGAGGAGGCTGAC 58.035 55.000 0.00 0.00 0.00 3.51
2861 3613 0.182061 GCATCAATGGAGGAGGCTGA 59.818 55.000 0.00 0.00 38.88 4.26
2862 3614 0.822532 GGCATCAATGGAGGAGGCTG 60.823 60.000 0.00 0.00 41.46 4.85
2863 3615 0.992431 AGGCATCAATGGAGGAGGCT 60.992 55.000 0.00 0.00 41.46 4.58
2864 3616 0.536915 GAGGCATCAATGGAGGAGGC 60.537 60.000 0.00 0.00 41.04 4.70
2865 3617 0.841961 TGAGGCATCAATGGAGGAGG 59.158 55.000 0.00 0.00 30.61 4.30
2866 3618 2.505405 CATGAGGCATCAATGGAGGAG 58.495 52.381 4.62 0.00 39.39 3.69
2867 3619 1.144298 CCATGAGGCATCAATGGAGGA 59.856 52.381 18.91 0.00 39.39 3.71
2868 3620 1.617322 CCATGAGGCATCAATGGAGG 58.383 55.000 18.91 7.96 39.39 4.30
2869 3621 1.617322 CCCATGAGGCATCAATGGAG 58.383 55.000 22.92 13.55 39.39 3.86
2870 3622 3.833729 CCCATGAGGCATCAATGGA 57.166 52.632 22.92 0.00 39.39 3.41
2890 3642 4.373116 TCCCGTCTTCACTGCGCC 62.373 66.667 4.18 0.00 0.00 6.53
2891 3643 3.112709 GTCCCGTCTTCACTGCGC 61.113 66.667 0.00 0.00 0.00 6.09
2892 3644 2.805353 CGTCCCGTCTTCACTGCG 60.805 66.667 0.00 0.00 0.00 5.18
2893 3645 1.733399 GTCGTCCCGTCTTCACTGC 60.733 63.158 0.00 0.00 0.00 4.40
2894 3646 1.442184 CGTCGTCCCGTCTTCACTG 60.442 63.158 0.00 0.00 0.00 3.66
2895 3647 2.952245 CGTCGTCCCGTCTTCACT 59.048 61.111 0.00 0.00 0.00 3.41
2896 3648 2.804090 GCGTCGTCCCGTCTTCAC 60.804 66.667 0.00 0.00 0.00 3.18
2897 3649 4.394078 CGCGTCGTCCCGTCTTCA 62.394 66.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.