Multiple sequence alignment - TraesCS3A01G317400

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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 TraesCS3A01G317400 chr3A 100.000 6486 0 0 1 6486 557956232 557949747 0.000000e+00 11978.0
1 TraesCS3A01G317400 chr3A 94.444 54 2 1 450 502 557955750 557955697 1.500000e-11 82.4
2 TraesCS3A01G317400 chr3A 94.444 54 2 1 483 536 557955783 557955731 1.500000e-11 82.4
3 TraesCS3A01G317400 chr3D 92.426 2469 126 28 2692 5133 427813142 427815576 0.000000e+00 3467.0
4 TraesCS3A01G317400 chr3D 92.543 1502 83 15 482 1971 427810812 427812296 0.000000e+00 2126.0
5 TraesCS3A01G317400 chr3D 95.441 1316 37 4 5192 6486 427815594 427816907 0.000000e+00 2076.0
6 TraesCS3A01G317400 chr3D 89.410 746 50 16 1970 2706 427812402 427813127 0.000000e+00 913.0
7 TraesCS3A01G317400 chr3D 89.646 367 26 2 1 367 427810379 427810733 2.130000e-124 457.0
8 TraesCS3A01G317400 chr3B 93.919 1480 77 5 3071 4546 559337983 559339453 0.000000e+00 2222.0
9 TraesCS3A01G317400 chr3B 95.479 1305 40 6 5192 6478 559340029 559341332 0.000000e+00 2065.0
10 TraesCS3A01G317400 chr3B 89.415 1436 84 25 550 1971 559335346 559336727 0.000000e+00 1748.0
11 TraesCS3A01G317400 chr3B 92.029 1104 50 16 1973 3072 559336832 559337901 0.000000e+00 1517.0
12 TraesCS3A01G317400 chr3B 88.689 610 36 6 4578 5174 559339454 559340043 0.000000e+00 713.0
13 TraesCS3A01G317400 chr3B 88.139 548 42 9 1 547 559334789 559335314 1.190000e-176 630.0
14 TraesCS3A01G317400 chr2B 89.427 227 20 4 6253 6477 751841802 751842026 3.830000e-72 283.0
15 TraesCS3A01G317400 chr2D 89.908 218 18 3 6257 6470 616634858 616635075 1.780000e-70 278.0
16 TraesCS3A01G317400 chr2A 89.450 218 21 2 6254 6470 746851959 746852175 2.300000e-69 274.0
17 TraesCS3A01G317400 chrUn 89.706 136 14 0 6320 6455 98211522 98211657 2.400000e-39 174.0
18 TraesCS3A01G317400 chr6B 89.706 136 14 0 6320 6455 107771734 107771869 2.400000e-39 174.0
19 TraesCS3A01G317400 chr6A 89.706 136 14 0 6320 6455 53156746 53156881 2.400000e-39 174.0
20 TraesCS3A01G317400 chr5B 87.234 141 14 4 6318 6456 562048474 562048336 2.420000e-34 158.0


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 TraesCS3A01G317400 chr3A 557949747 557956232 6485 True 4047.6 11978 96.296000 1 6486 3 chr3A.!!$R1 6485
1 TraesCS3A01G317400 chr3D 427810379 427816907 6528 False 1807.8 3467 91.893200 1 6486 5 chr3D.!!$F1 6485
2 TraesCS3A01G317400 chr3B 559334789 559341332 6543 False 1482.5 2222 91.278333 1 6478 6 chr3B.!!$F1 6477

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
151 152 0.235926 GTCTTCGCTTTCTGTGGTGC 59.764 55.000 0.00 0.0 0.00 5.01 F
667 723 1.003696 CTTCCACTTCCTTCCAGTCCC 59.996 57.143 0.00 0.0 0.00 4.46 F
2538 2723 0.328926 TGCCTCATGCCATTGTGAGA 59.671 50.000 4.08 0.0 43.50 3.27 F
3129 3441 0.409876 TCACTACCCTGCCTCTCAGT 59.590 55.000 0.00 0.0 41.25 3.41 F
4510 4839 1.337167 GGCTAAGCTGCAAAGTTTGGG 60.337 52.381 17.11 0.0 34.04 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1675 0.034896 ACCCGCCAAACTGTGACTAG 59.965 55.0 0.00 0.00 0.00 2.57 R
2550 2735 0.032130 TAAGCGTCGGCATGGAGATC 59.968 55.0 0.00 0.00 43.41 2.75 R
4498 4827 0.175302 CAGTGTGCCCAAACTTTGCA 59.825 50.0 0.00 0.00 0.00 4.08 R
4585 4914 1.917872 TGGTGGTGGTGCCTTTTATC 58.082 50.0 0.00 0.00 38.35 1.75 R
5650 6020 0.268869 ACATGGATCTGGGGCCTAGA 59.731 55.0 22.72 22.72 0.00 2.43 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
82 83 1.381872 ACCGAGGGAGTGGAGATGG 60.382 63.158 0.00 0.00 0.00 3.51
90 91 2.224719 GGGAGTGGAGATGGATGAATGG 60.225 54.545 0.00 0.00 0.00 3.16
95 96 3.073503 GTGGAGATGGATGAATGGATGGA 59.926 47.826 0.00 0.00 0.00 3.41
130 131 2.036862 AGTTTACTCCTGTGTTCGGTCC 59.963 50.000 0.00 0.00 0.00 4.46
139 140 2.808321 GTTCGGTCCGGTCTTCGC 60.808 66.667 12.29 0.00 37.59 4.70
151 152 0.235926 GTCTTCGCTTTCTGTGGTGC 59.764 55.000 0.00 0.00 0.00 5.01
253 254 3.974871 TTGACCGTTCCTTTGTTTAGC 57.025 42.857 0.00 0.00 0.00 3.09
254 255 2.920524 TGACCGTTCCTTTGTTTAGCA 58.079 42.857 0.00 0.00 0.00 3.49
255 256 3.482436 TGACCGTTCCTTTGTTTAGCAT 58.518 40.909 0.00 0.00 0.00 3.79
256 257 3.252215 TGACCGTTCCTTTGTTTAGCATG 59.748 43.478 0.00 0.00 0.00 4.06
257 258 3.482436 ACCGTTCCTTTGTTTAGCATGA 58.518 40.909 0.00 0.00 0.00 3.07
258 259 3.502211 ACCGTTCCTTTGTTTAGCATGAG 59.498 43.478 0.00 0.00 0.00 2.90
259 260 3.751175 CCGTTCCTTTGTTTAGCATGAGA 59.249 43.478 0.00 0.00 0.00 3.27
260 261 4.396166 CCGTTCCTTTGTTTAGCATGAGAT 59.604 41.667 0.00 0.00 0.00 2.75
261 262 5.447818 CCGTTCCTTTGTTTAGCATGAGATC 60.448 44.000 0.00 0.00 0.00 2.75
262 263 5.122239 CGTTCCTTTGTTTAGCATGAGATCA 59.878 40.000 0.00 0.00 0.00 2.92
263 264 6.317857 GTTCCTTTGTTTAGCATGAGATCAC 58.682 40.000 0.00 0.00 0.00 3.06
297 298 4.985409 CCTAGGACTGCTCGTTTGAATATC 59.015 45.833 1.05 0.00 0.00 1.63
409 430 7.333174 CCTTCCTAAAACTCAGCTCTAAGAAAG 59.667 40.741 0.00 0.00 0.00 2.62
436 457 7.721842 TGGGATTCTGTGTAATAAGTTGTTGAA 59.278 33.333 0.00 0.00 0.00 2.69
566 622 4.390048 TGGCGTTTCCAGGTTAGC 57.610 55.556 0.00 0.00 40.72 3.09
578 634 1.856629 AGGTTAGCCTGCATTGCAAT 58.143 45.000 13.18 5.99 45.05 3.56
579 635 1.479323 AGGTTAGCCTGCATTGCAATG 59.521 47.619 30.92 30.92 45.05 2.82
580 636 1.205417 GGTTAGCCTGCATTGCAATGT 59.795 47.619 33.67 19.82 38.41 2.71
581 637 2.354003 GGTTAGCCTGCATTGCAATGTT 60.354 45.455 33.67 19.35 38.41 2.71
582 638 2.658373 TAGCCTGCATTGCAATGTTG 57.342 45.000 33.67 26.05 38.41 3.33
587 643 2.028294 CCTGCATTGCAATGTTGGGTTA 60.028 45.455 33.67 14.74 38.41 2.85
590 646 2.620242 CATTGCAATGTTGGGTTAGGC 58.380 47.619 27.81 0.00 0.00 3.93
644 700 4.523558 TGAATGCCATGTCAGAACAAATCA 59.476 37.500 0.00 0.00 39.30 2.57
661 717 3.990959 ATCAGTCTTCCACTTCCTTCC 57.009 47.619 0.00 0.00 30.26 3.46
667 723 1.003696 CTTCCACTTCCTTCCAGTCCC 59.996 57.143 0.00 0.00 0.00 4.46
718 774 1.408474 CTGAACCCGTACGCGCTAAC 61.408 60.000 10.49 0.53 36.67 2.34
818 875 1.059549 CCACCGCGTCACGTAAATAAC 59.940 52.381 4.92 0.00 41.42 1.89
840 897 1.574702 CCCCGTCTGTCGAAAAAGCC 61.575 60.000 0.00 0.00 42.86 4.35
968 1025 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
971 1028 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
980 1037 3.050835 GAGGAGGAGGAGGAGTAGTACT 58.949 54.545 1.37 1.37 0.00 2.73
1064 1121 4.452733 CCCCTTCGCGGTGAGTCC 62.453 72.222 6.13 0.00 0.00 3.85
1087 1144 5.067544 CCCCTACTCCGTTTCTACTTTCTAG 59.932 48.000 0.00 0.00 0.00 2.43
1150 1207 3.119096 GTCCGCCTTGTCTTCGGC 61.119 66.667 0.00 0.00 42.65 5.54
1240 1299 2.582734 ATAACCCCTCGTTTCGCCGG 62.583 60.000 0.00 0.00 35.79 6.13
1318 1377 4.242475 TCGATGGATGGATGCGTTTATAC 58.758 43.478 0.00 0.00 0.00 1.47
1334 1393 1.289109 ATACGCGTGTCCTGTTGTGC 61.289 55.000 24.59 0.00 0.00 4.57
1430 1489 7.899974 AGAAATGATTCTTAGACACGAAATCG 58.100 34.615 0.48 0.48 43.43 3.34
1432 1491 5.068234 TGATTCTTAGACACGAAATCGGT 57.932 39.130 7.81 2.47 44.95 4.69
1447 1506 3.543680 ATCGGTACTTGAACTGGGATG 57.456 47.619 0.00 0.00 0.00 3.51
1476 1535 4.327898 TGTCTAATTACAACGATGCGGTTC 59.672 41.667 0.00 0.00 0.00 3.62
1534 1593 4.082571 GCTCTTCCAAATTATATGCCGCAT 60.083 41.667 11.38 11.38 0.00 4.73
1551 1610 4.230657 CCGCATACGACAAAATGGAAAAA 58.769 39.130 0.00 0.00 43.93 1.94
1563 1625 6.490721 ACAAAATGGAAAAATACCTCGTACCA 59.509 34.615 0.00 0.00 0.00 3.25
1565 1627 7.712204 AAATGGAAAAATACCTCGTACCATT 57.288 32.000 0.00 0.00 44.97 3.16
1578 1640 2.164219 CGTACCATTTTGCTGGCTGAAT 59.836 45.455 0.00 0.00 40.15 2.57
1613 1675 1.934463 CGTTCAGTGTGACCAGTGC 59.066 57.895 0.00 0.00 41.06 4.40
1619 1681 1.341209 CAGTGTGACCAGTGCTAGTCA 59.659 52.381 0.00 0.00 40.61 3.41
1669 1731 2.163412 GCCGCTGAATGTGTTCCATTTA 59.837 45.455 0.00 0.00 43.87 1.40
1864 1931 1.416401 TCTAATTCTCGGATGCCACCC 59.584 52.381 0.00 0.00 0.00 4.61
2013 2194 2.095718 GGAATTCTTTCACAGCGTGTCC 60.096 50.000 5.23 3.55 34.79 4.02
2028 2209 2.223340 CGTGTCCTTGATTGCTTATGCC 60.223 50.000 0.00 0.00 38.71 4.40
2032 2213 1.745087 CCTTGATTGCTTATGCCGTGT 59.255 47.619 0.00 0.00 38.71 4.49
2037 2218 4.698575 TGATTGCTTATGCCGTGTGTATA 58.301 39.130 0.00 0.00 38.71 1.47
2120 2301 5.370679 AGCTTAACAAACGGGAAAGAGTAA 58.629 37.500 0.00 0.00 0.00 2.24
2178 2359 5.181009 ACACTCACATCACATGTTATCCTG 58.819 41.667 0.00 0.00 42.70 3.86
2188 2369 7.790823 TCACATGTTATCCTGTATGTCATTG 57.209 36.000 0.00 0.00 31.84 2.82
2190 2371 6.543465 CACATGTTATCCTGTATGTCATTGGT 59.457 38.462 0.00 0.00 31.84 3.67
2191 2372 7.714813 CACATGTTATCCTGTATGTCATTGGTA 59.285 37.037 0.00 0.00 31.84 3.25
2194 2375 8.675705 TGTTATCCTGTATGTCATTGGTATTG 57.324 34.615 0.00 0.00 0.00 1.90
2195 2376 7.228507 TGTTATCCTGTATGTCATTGGTATTGC 59.771 37.037 0.00 0.00 0.00 3.56
2236 2420 7.061673 TGTTTTGTGAATTCAGAAGTTGTTTCG 59.938 33.333 16.55 0.00 40.86 3.46
2237 2421 5.811399 TGTGAATTCAGAAGTTGTTTCGT 57.189 34.783 8.80 0.00 40.86 3.85
2238 2422 6.912203 TGTGAATTCAGAAGTTGTTTCGTA 57.088 33.333 8.80 0.00 40.86 3.43
2239 2423 6.711579 TGTGAATTCAGAAGTTGTTTCGTAC 58.288 36.000 8.80 0.00 40.86 3.67
2240 2424 6.537301 TGTGAATTCAGAAGTTGTTTCGTACT 59.463 34.615 8.80 0.00 40.86 2.73
2241 2425 7.065324 TGTGAATTCAGAAGTTGTTTCGTACTT 59.935 33.333 8.80 0.00 40.86 2.24
2242 2426 7.908601 GTGAATTCAGAAGTTGTTTCGTACTTT 59.091 33.333 8.80 0.00 40.86 2.66
2243 2427 8.455682 TGAATTCAGAAGTTGTTTCGTACTTTT 58.544 29.630 3.38 0.00 40.86 2.27
2308 2492 5.561679 ACCTTAAGTTCTCCTGGATGAAAC 58.438 41.667 0.00 2.87 0.00 2.78
2337 2521 4.851639 AGCTTCCCAGATACTGACAAAT 57.148 40.909 0.00 0.00 32.44 2.32
2339 2523 3.557595 GCTTCCCAGATACTGACAAATCG 59.442 47.826 0.00 0.00 32.44 3.34
2357 2541 6.034256 ACAAATCGTTGTGCTTAGATACGTAC 59.966 38.462 0.00 0.00 46.40 3.67
2428 2613 3.286329 AGTAACCATGATGCAGCATGA 57.714 42.857 39.07 21.45 46.64 3.07
2438 2623 1.401761 TGCAGCATGAAAACTGGTGT 58.598 45.000 0.00 0.00 42.58 4.16
2442 2627 1.338973 AGCATGAAAACTGGTGTGCTG 59.661 47.619 0.00 0.00 40.99 4.41
2445 2630 2.121291 TGAAAACTGGTGTGCTGTGA 57.879 45.000 0.00 0.00 0.00 3.58
2463 2648 5.822519 GCTGTGATTGACATGGATTTACCTA 59.177 40.000 0.00 0.00 39.86 3.08
2472 2657 3.145559 TGGATTTACCTAAGGCTCCCT 57.854 47.619 0.00 0.00 39.86 4.20
2480 2665 4.554553 ACCTAAGGCTCCCTTATAGTCA 57.445 45.455 4.33 0.00 44.01 3.41
2532 2717 0.613853 AGTGCTTGCCTCATGCCATT 60.614 50.000 0.00 0.00 40.16 3.16
2538 2723 0.328926 TGCCTCATGCCATTGTGAGA 59.671 50.000 4.08 0.00 43.50 3.27
2544 2729 5.585390 CCTCATGCCATTGTGAGATAAAAC 58.415 41.667 4.08 0.00 43.50 2.43
2545 2730 5.450965 CCTCATGCCATTGTGAGATAAAACC 60.451 44.000 4.08 0.00 43.50 3.27
2546 2731 5.015515 TCATGCCATTGTGAGATAAAACCA 58.984 37.500 0.00 0.00 0.00 3.67
2547 2732 5.657745 TCATGCCATTGTGAGATAAAACCAT 59.342 36.000 0.00 0.00 0.00 3.55
2548 2733 5.327616 TGCCATTGTGAGATAAAACCATG 57.672 39.130 0.00 0.00 0.00 3.66
2549 2734 4.160065 TGCCATTGTGAGATAAAACCATGG 59.840 41.667 11.19 11.19 40.74 3.66
2550 2735 4.441913 GCCATTGTGAGATAAAACCATGGG 60.442 45.833 18.09 0.00 39.08 4.00
2551 2736 4.955450 CCATTGTGAGATAAAACCATGGGA 59.045 41.667 18.09 0.00 36.44 4.37
2552 2737 5.599656 CCATTGTGAGATAAAACCATGGGAT 59.400 40.000 18.09 0.78 36.44 3.85
2553 2738 6.239120 CCATTGTGAGATAAAACCATGGGATC 60.239 42.308 18.09 12.64 36.44 3.36
2554 2739 5.715439 TGTGAGATAAAACCATGGGATCT 57.285 39.130 18.09 16.98 0.00 2.75
2621 2818 5.677091 GCTTGTGGAAACTGCCTATTGTATG 60.677 44.000 0.00 0.00 0.00 2.39
2675 2872 8.152898 TCATTAACCCAGACAATCAGATGATAG 58.847 37.037 0.00 0.00 33.73 2.08
2919 3148 6.924913 TCTTCCTATAGCTGATGCAGTTAT 57.075 37.500 0.00 8.48 40.15 1.89
2920 3149 7.308450 TCTTCCTATAGCTGATGCAGTTATT 57.692 36.000 8.68 0.00 38.48 1.40
2963 3193 6.013032 CCATGATATTGATGGGAAGAGGTAGT 60.013 42.308 0.00 0.00 37.33 2.73
2964 3194 7.180946 CCATGATATTGATGGGAAGAGGTAGTA 59.819 40.741 0.00 0.00 37.33 1.82
2965 3195 7.782897 TGATATTGATGGGAAGAGGTAGTAG 57.217 40.000 0.00 0.00 0.00 2.57
2966 3196 6.726299 TGATATTGATGGGAAGAGGTAGTAGG 59.274 42.308 0.00 0.00 0.00 3.18
3019 3249 8.438676 AGGATATTTATCTGGAAACTTGTTCG 57.561 34.615 0.00 0.00 33.28 3.95
3065 3295 7.325660 TGAATGATTCAGTGAAAGGCTATTC 57.674 36.000 10.14 14.16 34.08 1.75
3104 3416 8.564574 TCATTATGTTCTTGTTGTTACAGTTCC 58.435 33.333 0.00 0.00 35.28 3.62
3128 3440 1.561643 TTCACTACCCTGCCTCTCAG 58.438 55.000 0.00 0.00 42.49 3.35
3129 3441 0.409876 TCACTACCCTGCCTCTCAGT 59.590 55.000 0.00 0.00 41.25 3.41
3297 3609 6.930667 TTGTTGGGTAAGTGTTAGTTCTTC 57.069 37.500 0.00 0.00 0.00 2.87
3301 3613 7.281549 TGTTGGGTAAGTGTTAGTTCTTCTTTC 59.718 37.037 0.00 0.00 0.00 2.62
3387 3699 5.598830 TGCAAACACTATTTTTACTGGGGAA 59.401 36.000 0.00 0.00 0.00 3.97
3443 3755 5.248640 CACTTACTTCACCTGGATCAATGT 58.751 41.667 0.00 0.00 0.00 2.71
3515 3827 6.716628 AGAAGTGGCATGAGAAAACAAGATTA 59.283 34.615 0.00 0.00 0.00 1.75
3653 3965 7.601705 ATTTGGTGATTTCTCTTCTTTTGGA 57.398 32.000 0.00 0.00 0.00 3.53
3954 4267 1.809567 GCCCTGGCACCTGAAACAAG 61.810 60.000 2.58 0.00 41.49 3.16
4038 4351 3.096495 TCCCTGGGGCCTATGTGC 61.096 66.667 14.00 0.00 34.68 4.57
4084 4397 3.305267 GCAATGAGGTTTGTGTACATGCA 60.305 43.478 0.00 0.00 0.00 3.96
4100 4413 8.533965 GTGTACATGCATATGCTTTTGTTATTG 58.466 33.333 27.13 9.86 42.66 1.90
4122 4435 7.949903 TTGTTACAAGTCGCTTCTTTGTATA 57.050 32.000 0.00 0.00 0.00 1.47
4256 4572 8.041323 TCTTCTAGACTAAATGGTTTCCACATC 58.959 37.037 0.00 0.00 35.80 3.06
4258 4574 7.331026 TCTAGACTAAATGGTTTCCACATCTG 58.669 38.462 0.00 0.00 35.80 2.90
4498 4827 7.569240 AGTTATTCACTTATTCTGGCTAAGCT 58.431 34.615 0.00 0.00 27.32 3.74
4510 4839 1.337167 GGCTAAGCTGCAAAGTTTGGG 60.337 52.381 17.11 0.00 34.04 4.12
4564 4893 9.337396 TGTGTGTTGTTATTCTTCAGTATCTTT 57.663 29.630 0.00 0.00 0.00 2.52
4576 4905 9.653287 TTCTTCAGTATCTTTACCATACACAAG 57.347 33.333 0.00 0.00 0.00 3.16
4644 4977 4.155063 TGTTACATATGCTGGATGTGCT 57.845 40.909 1.58 0.00 38.03 4.40
4685 5018 8.389366 ACCCTACTACTTACTAAACTGAGAGAA 58.611 37.037 0.00 0.00 0.00 2.87
4697 5031 9.930693 ACTAAACTGAGAGAAATTACTTAGTGG 57.069 33.333 0.00 0.00 34.20 4.00
4708 5042 2.344093 ACTTAGTGGGTGGGATCAGT 57.656 50.000 0.00 0.00 0.00 3.41
4742 5077 1.135888 TCGATTGACAGTCGGTACACG 60.136 52.381 18.74 0.00 46.11 4.49
4794 5129 4.207891 AGAATAGCAACACCACCTACTG 57.792 45.455 0.00 0.00 0.00 2.74
4962 5304 8.685257 TCAAATCATAGATAGGTGGGTATCAT 57.315 34.615 0.00 0.00 32.57 2.45
4963 5305 8.762645 TCAAATCATAGATAGGTGGGTATCATC 58.237 37.037 0.00 0.00 32.57 2.92
5010 5352 5.580691 TCACATTATCTAACTTTGCCTGTCG 59.419 40.000 0.00 0.00 0.00 4.35
5067 5409 1.438651 TTGACGTCATAGGCAGCAAC 58.561 50.000 20.80 0.00 0.00 4.17
5069 5411 2.025359 GACGTCATAGGCAGCAACGC 62.025 60.000 11.55 0.00 36.85 4.84
5098 5440 6.099269 TGTGGGGGTAAGTATTTCTGTCTATC 59.901 42.308 0.00 0.00 0.00 2.08
5099 5441 6.326843 GTGGGGGTAAGTATTTCTGTCTATCT 59.673 42.308 0.00 0.00 0.00 1.98
5117 5459 6.701841 GTCTATCTCGAGTTAATTTGGCATGA 59.298 38.462 13.13 0.00 0.00 3.07
5146 5488 3.499338 TCTGGGTGTTTGATGAAGCATT 58.501 40.909 0.00 0.00 0.00 3.56
5147 5489 3.896888 TCTGGGTGTTTGATGAAGCATTT 59.103 39.130 0.00 0.00 0.00 2.32
5152 5494 4.448732 GGTGTTTGATGAAGCATTTTCCAC 59.551 41.667 0.00 0.00 0.00 4.02
5159 5501 2.126502 GCATTTTCCACACCCGCG 60.127 61.111 0.00 0.00 0.00 6.46
5160 5502 2.914908 GCATTTTCCACACCCGCGT 61.915 57.895 4.92 0.00 0.00 6.01
5161 5503 1.209127 CATTTTCCACACCCGCGTC 59.791 57.895 4.92 0.00 0.00 5.19
5162 5504 1.072505 ATTTTCCACACCCGCGTCT 59.927 52.632 4.92 0.00 0.00 4.18
5163 5505 0.953960 ATTTTCCACACCCGCGTCTC 60.954 55.000 4.92 0.00 0.00 3.36
5164 5506 2.999739 TTTTCCACACCCGCGTCTCC 63.000 60.000 4.92 0.00 0.00 3.71
5165 5507 4.988716 TCCACACCCGCGTCTCCT 62.989 66.667 4.92 0.00 0.00 3.69
5166 5508 4.436998 CCACACCCGCGTCTCCTC 62.437 72.222 4.92 0.00 0.00 3.71
5167 5509 3.374402 CACACCCGCGTCTCCTCT 61.374 66.667 4.92 0.00 0.00 3.69
5168 5510 3.374402 ACACCCGCGTCTCCTCTG 61.374 66.667 4.92 0.00 0.00 3.35
5169 5511 3.374402 CACCCGCGTCTCCTCTGT 61.374 66.667 4.92 0.00 0.00 3.41
5170 5512 2.044555 CACCCGCGTCTCCTCTGTA 61.045 63.158 4.92 0.00 0.00 2.74
5171 5513 1.749638 ACCCGCGTCTCCTCTGTAG 60.750 63.158 4.92 0.00 0.00 2.74
5172 5514 1.451567 CCCGCGTCTCCTCTGTAGA 60.452 63.158 4.92 0.00 0.00 2.59
5173 5515 0.820074 CCCGCGTCTCCTCTGTAGAT 60.820 60.000 4.92 0.00 0.00 1.98
5174 5516 1.025812 CCGCGTCTCCTCTGTAGATT 58.974 55.000 4.92 0.00 0.00 2.40
5175 5517 1.405821 CCGCGTCTCCTCTGTAGATTT 59.594 52.381 4.92 0.00 0.00 2.17
5176 5518 2.159226 CCGCGTCTCCTCTGTAGATTTT 60.159 50.000 4.92 0.00 0.00 1.82
5177 5519 3.512680 CGCGTCTCCTCTGTAGATTTTT 58.487 45.455 0.00 0.00 0.00 1.94
5305 5658 0.520404 CACTGCTCAGCATTGTGGTC 59.480 55.000 8.83 0.00 38.13 4.02
5386 5746 6.983307 AGAGATTATCATTCTGAACTTGGTCG 59.017 38.462 0.00 0.00 0.00 4.79
5389 5749 2.688507 TCATTCTGAACTTGGTCGCTC 58.311 47.619 0.00 0.00 0.00 5.03
5390 5750 2.300152 TCATTCTGAACTTGGTCGCTCT 59.700 45.455 0.00 0.00 0.00 4.09
5437 5797 0.538287 GTGGAAGTGGAAAGGCTGCT 60.538 55.000 0.00 0.00 0.00 4.24
5476 5836 2.879002 CACGTGGTGCTATGAGATCT 57.121 50.000 7.95 0.00 0.00 2.75
5529 5889 3.072038 TGGATGAGAATAGGATGTGCCAG 59.928 47.826 0.00 0.00 40.02 4.85
5533 5893 1.414181 AGAATAGGATGTGCCAGTCGG 59.586 52.381 0.00 0.00 40.02 4.79
5734 6104 4.440663 CCATCACTATTCTGACGAGCTTGA 60.441 45.833 8.31 0.00 0.00 3.02
5829 6199 6.143438 GCTGAAGCATGTTATTGCATTACATC 59.857 38.462 6.03 3.34 45.23 3.06
5892 6262 6.710295 ACCTTTAAACAAATGAAAATGGGAGC 59.290 34.615 0.00 0.00 0.00 4.70
5909 6282 3.827302 GGGAGCCGAATCTATAACTCTGA 59.173 47.826 0.00 0.00 0.00 3.27
5930 6303 3.786635 ACGTGAGCTGAGATTTCATACC 58.213 45.455 0.00 0.00 31.68 2.73
5939 6312 7.051000 AGCTGAGATTTCATACCCTACTTTTC 58.949 38.462 0.00 0.00 31.68 2.29
5947 6320 2.822701 CCTACTTTTCGGGGCGCC 60.823 66.667 21.18 21.18 0.00 6.53
5948 6321 2.267961 CTACTTTTCGGGGCGCCT 59.732 61.111 28.56 6.02 0.00 5.52
5956 6331 3.597728 CGGGGCGCCTCTCTCTAC 61.598 72.222 26.87 5.51 0.00 2.59
6036 6411 2.060980 GGATGCTCCACGACCTCCT 61.061 63.158 0.00 0.00 36.28 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.678395 CATCCATCTCCACTCCCTCG 59.322 60.000 0.00 0.00 0.00 4.63
107 108 4.262164 GGACCGAACACAGGAGTAAACTAA 60.262 45.833 0.00 0.00 0.00 2.24
115 116 2.261671 CCGGACCGAACACAGGAG 59.738 66.667 17.49 0.00 0.00 3.69
130 131 0.600255 ACCACAGAAAGCGAAGACCG 60.600 55.000 0.00 0.00 42.21 4.79
139 140 0.588252 CGAACCAGCACCACAGAAAG 59.412 55.000 0.00 0.00 0.00 2.62
239 240 6.317857 GTGATCTCATGCTAAACAAAGGAAC 58.682 40.000 0.00 0.00 0.00 3.62
263 264 1.078143 GTCCTAGGCAACCAGCTGG 60.078 63.158 31.60 31.60 44.79 4.85
297 298 7.596749 AGTATGAGTTCACATTTTTAGGACG 57.403 36.000 0.00 0.00 0.00 4.79
375 376 2.917600 GAGTTTTAGGAAGGAGGGGGAA 59.082 50.000 0.00 0.00 0.00 3.97
376 377 2.157911 TGAGTTTTAGGAAGGAGGGGGA 60.158 50.000 0.00 0.00 0.00 4.81
377 378 2.239907 CTGAGTTTTAGGAAGGAGGGGG 59.760 54.545 0.00 0.00 0.00 5.40
378 379 2.356227 GCTGAGTTTTAGGAAGGAGGGG 60.356 54.545 0.00 0.00 0.00 4.79
390 411 5.066593 CCCACTTTCTTAGAGCTGAGTTTT 58.933 41.667 0.00 0.00 0.00 2.43
391 412 4.348168 TCCCACTTTCTTAGAGCTGAGTTT 59.652 41.667 0.00 0.00 0.00 2.66
409 430 7.174253 TCAACAACTTATTACACAGAATCCCAC 59.826 37.037 0.00 0.00 0.00 4.61
456 477 9.236006 ACAGCACATTAAACTTCTCTGATTATT 57.764 29.630 0.00 0.00 0.00 1.40
457 478 8.671921 CACAGCACATTAAACTTCTCTGATTAT 58.328 33.333 0.00 0.00 0.00 1.28
458 479 7.661437 ACACAGCACATTAAACTTCTCTGATTA 59.339 33.333 0.00 0.00 0.00 1.75
461 482 5.368145 ACACAGCACATTAAACTTCTCTGA 58.632 37.500 0.00 0.00 0.00 3.27
462 483 5.679734 ACACAGCACATTAAACTTCTCTG 57.320 39.130 0.00 0.00 0.00 3.35
464 485 8.850454 TTTTTACACAGCACATTAAACTTCTC 57.150 30.769 0.00 0.00 0.00 2.87
533 555 6.308041 GGAAACGCCAAGAAATGTTTAGATTC 59.692 38.462 0.00 0.00 34.89 2.52
538 565 4.920640 TGGAAACGCCAAGAAATGTTTA 57.079 36.364 0.00 0.00 45.87 2.01
566 622 0.322322 ACCCAACATTGCAATGCAGG 59.678 50.000 33.94 31.70 40.61 4.85
572 628 2.008242 AGCCTAACCCAACATTGCAA 57.992 45.000 0.00 0.00 0.00 4.08
574 630 2.024414 CCTAGCCTAACCCAACATTGC 58.976 52.381 0.00 0.00 0.00 3.56
575 631 2.024414 GCCTAGCCTAACCCAACATTG 58.976 52.381 0.00 0.00 0.00 2.82
576 632 1.063942 GGCCTAGCCTAACCCAACATT 60.064 52.381 0.00 0.00 46.69 2.71
578 634 1.996086 GGCCTAGCCTAACCCAACA 59.004 57.895 0.00 0.00 46.69 3.33
579 635 4.979657 GGCCTAGCCTAACCCAAC 57.020 61.111 0.00 0.00 46.69 3.77
590 646 1.280421 GGAGCATTAGATGGGGCCTAG 59.720 57.143 0.84 0.00 0.00 3.02
644 700 2.635427 GACTGGAAGGAAGTGGAAGACT 59.365 50.000 0.00 0.00 39.30 3.24
718 774 1.002134 AAACCTGACTGCCGATGGG 60.002 57.895 0.00 0.00 0.00 4.00
968 1025 3.181441 CCTCCCTGGTAGTACTACTCCTC 60.181 56.522 27.71 14.58 36.36 3.71
971 1028 2.782341 TCCCTCCCTGGTAGTACTACTC 59.218 54.545 27.71 19.42 36.36 2.59
980 1037 3.023045 GCCTCCTCCCTCCCTGGTA 62.023 68.421 0.00 0.00 0.00 3.25
1064 1121 5.450274 GCTAGAAAGTAGAAACGGAGTAGGG 60.450 48.000 0.00 0.00 45.00 3.53
1165 1222 1.632046 CCGGACCAAATTCGACACCG 61.632 60.000 0.00 0.00 38.83 4.94
1167 1224 1.664151 GATCCGGACCAAATTCGACAC 59.336 52.381 6.12 0.00 0.00 3.67
1192 1249 1.008538 CCGCAACAAGCAACTCCAC 60.009 57.895 0.00 0.00 46.13 4.02
1240 1299 4.394712 CCACCGGAGCACCCAGAC 62.395 72.222 9.46 0.00 34.14 3.51
1318 1377 2.967076 AGCACAACAGGACACGCG 60.967 61.111 3.53 3.53 0.00 6.01
1430 1489 6.015434 ACAAAATTCATCCCAGTTCAAGTACC 60.015 38.462 0.00 0.00 0.00 3.34
1432 1491 7.004086 AGACAAAATTCATCCCAGTTCAAGTA 58.996 34.615 0.00 0.00 0.00 2.24
1447 1506 7.044966 CCGCATCGTTGTAATTAGACAAAATTC 60.045 37.037 0.00 0.00 40.88 2.17
1534 1593 6.427547 ACGAGGTATTTTTCCATTTTGTCGTA 59.572 34.615 0.00 0.00 0.00 3.43
1551 1610 3.541632 CCAGCAAAATGGTACGAGGTAT 58.458 45.455 0.00 0.00 35.47 2.73
1563 1625 8.096414 ACTAAAACAATATTCAGCCAGCAAAAT 58.904 29.630 0.00 0.00 0.00 1.82
1565 1627 6.991938 ACTAAAACAATATTCAGCCAGCAAA 58.008 32.000 0.00 0.00 0.00 3.68
1578 1640 6.715344 CTGAACGCCAGTACTAAAACAATA 57.285 37.500 0.00 0.00 38.10 1.90
1613 1675 0.034896 ACCCGCCAAACTGTGACTAG 59.965 55.000 0.00 0.00 0.00 2.57
1619 1681 0.690762 ATAGACACCCGCCAAACTGT 59.309 50.000 0.00 0.00 0.00 3.55
1669 1731 8.251721 GCTGGTATAGATAACGATCCTTGTATT 58.748 37.037 0.00 0.00 31.81 1.89
1773 1840 9.696917 AAATCAGCCAAACAATAGTTAAAAGAG 57.303 29.630 0.00 0.00 36.84 2.85
1864 1931 0.671781 CAGCAGGTTCGTGAGGAAGG 60.672 60.000 0.00 0.00 34.69 3.46
1979 2160 8.572185 TGTGAAAGAATTCCGTAATCAATTTCA 58.428 29.630 0.65 5.82 34.49 2.69
1992 2173 2.095718 GGACACGCTGTGAAAGAATTCC 60.096 50.000 14.18 6.22 36.96 3.01
2013 2194 2.162208 ACACACGGCATAAGCAATCAAG 59.838 45.455 0.00 0.00 44.61 3.02
2120 2301 5.643379 TCAAGTTTCAAGCAAAAGACACT 57.357 34.783 0.00 0.00 0.00 3.55
2178 2359 7.312154 TGAACAAAGCAATACCAATGACATAC 58.688 34.615 0.00 0.00 0.00 2.39
2194 2375 5.794448 CACAAAACAATGGTTTGAACAAAGC 59.206 36.000 28.07 18.47 46.20 3.51
2195 2376 7.126726 TCACAAAACAATGGTTTGAACAAAG 57.873 32.000 28.07 11.30 46.20 2.77
2242 2426 9.859427 GGATTTTGATCACTGAATGAATTACAA 57.141 29.630 0.00 0.00 41.93 2.41
2243 2427 8.469200 GGGATTTTGATCACTGAATGAATTACA 58.531 33.333 0.00 0.00 41.93 2.41
2308 2492 4.394300 CAGTATCTGGGAAGCTTCACAAAG 59.606 45.833 30.22 20.31 40.65 2.77
2337 2521 4.406069 GTGTACGTATCTAAGCACAACGA 58.594 43.478 0.00 0.00 37.04 3.85
2339 2523 3.545078 CCGTGTACGTATCTAAGCACAAC 59.455 47.826 0.00 0.00 37.74 3.32
2353 2537 3.358707 TGTTGGCTATATCCGTGTACG 57.641 47.619 0.00 0.00 39.44 3.67
2357 2541 5.560966 AAACTTTGTTGGCTATATCCGTG 57.439 39.130 0.00 0.00 0.00 4.94
2428 2613 3.023119 TCAATCACAGCACACCAGTTTT 58.977 40.909 0.00 0.00 0.00 2.43
2438 2623 4.398988 GGTAAATCCATGTCAATCACAGCA 59.601 41.667 0.00 0.00 38.85 4.41
2442 2627 6.238759 GCCTTAGGTAAATCCATGTCAATCAC 60.239 42.308 0.00 0.00 39.02 3.06
2445 2630 6.018433 AGCCTTAGGTAAATCCATGTCAAT 57.982 37.500 0.00 0.00 39.02 2.57
2463 2648 5.221742 GCAGTAATGACTATAAGGGAGCCTT 60.222 44.000 0.00 0.00 39.88 4.35
2498 2683 4.573607 GCAAGCACTGTCAATGATCTGATA 59.426 41.667 0.00 0.00 0.00 2.15
2532 2717 5.397899 GGAGATCCCATGGTTTTATCTCACA 60.398 44.000 27.55 0.00 42.76 3.58
2548 2733 2.029666 CGTCGGCATGGAGATCCC 59.970 66.667 0.00 0.00 34.29 3.85
2549 2734 2.650813 AAGCGTCGGCATGGAGATCC 62.651 60.000 0.00 0.00 43.41 3.36
2550 2735 0.032130 TAAGCGTCGGCATGGAGATC 59.968 55.000 0.00 0.00 43.41 2.75
2551 2736 0.681733 ATAAGCGTCGGCATGGAGAT 59.318 50.000 0.00 0.00 43.41 2.75
2552 2737 1.269723 CTATAAGCGTCGGCATGGAGA 59.730 52.381 0.00 0.00 43.41 3.71
2553 2738 1.702886 CTATAAGCGTCGGCATGGAG 58.297 55.000 0.00 0.00 43.41 3.86
2554 2739 0.319555 GCTATAAGCGTCGGCATGGA 60.320 55.000 0.00 0.00 43.41 3.41
2621 2818 8.401490 AGATGATGGCTATATGAAACCTTTTC 57.599 34.615 0.00 0.00 0.00 2.29
2888 3117 9.700831 TGCATCAGCTATAGGAAGAACTATATA 57.299 33.333 1.04 0.00 42.74 0.86
2889 3118 8.601047 TGCATCAGCTATAGGAAGAACTATAT 57.399 34.615 1.04 0.00 42.74 0.86
2963 3193 5.430417 TCAACTTGGGCCAATATCTTACCTA 59.570 40.000 21.25 0.00 0.00 3.08
2964 3194 4.229582 TCAACTTGGGCCAATATCTTACCT 59.770 41.667 21.25 0.00 0.00 3.08
2965 3195 4.532834 TCAACTTGGGCCAATATCTTACC 58.467 43.478 21.25 0.00 0.00 2.85
2966 3196 6.715347 AATCAACTTGGGCCAATATCTTAC 57.285 37.500 21.25 0.00 0.00 2.34
3019 3249 4.353383 AGGTCTTAACTGAAGTTGACCC 57.647 45.455 20.76 10.21 45.13 4.46
3086 3398 9.126151 TGAAATATGGAACTGTAACAACAAGAA 57.874 29.630 0.00 0.00 0.00 2.52
3102 3414 3.391296 GAGGCAGGGTAGTGAAATATGGA 59.609 47.826 0.00 0.00 0.00 3.41
3104 3416 4.101585 TGAGAGGCAGGGTAGTGAAATATG 59.898 45.833 0.00 0.00 0.00 1.78
3128 3440 9.994432 CAAATGAAAAGGAAGATAGTATGACAC 57.006 33.333 0.00 0.00 0.00 3.67
3129 3441 8.677300 GCAAATGAAAAGGAAGATAGTATGACA 58.323 33.333 0.00 0.00 0.00 3.58
3297 3609 8.046107 AGAAGATATTTTGAGGAGAGGTGAAAG 58.954 37.037 0.00 0.00 0.00 2.62
3301 3613 9.103861 GTTTAGAAGATATTTTGAGGAGAGGTG 57.896 37.037 0.00 0.00 0.00 4.00
3387 3699 4.454678 ACAGTGTGAATGTGAATGTGAGT 58.545 39.130 0.00 0.00 0.00 3.41
3443 3755 4.472470 CCCTAGGAGATGATATGGCAATCA 59.528 45.833 11.48 12.51 40.07 2.57
3515 3827 7.913821 GGAAGTTTGTCGAAGTTTTGAAATACT 59.086 33.333 0.00 0.00 31.06 2.12
3531 3843 6.385649 TTGTCAACATAAGGGAAGTTTGTC 57.614 37.500 0.00 0.00 0.00 3.18
3637 3949 5.089434 AGCCCAATCCAAAAGAAGAGAAAT 58.911 37.500 0.00 0.00 0.00 2.17
3653 3965 4.167319 ACCATTGGAAGTTTAAGCCCAAT 58.833 39.130 10.37 6.91 46.84 3.16
3787 4100 6.534059 CATCAAAATTTGCAGAAATCAGCAG 58.466 36.000 0.00 0.00 39.51 4.24
3954 4267 0.391263 ATCGAAAGGAACCGCCAGAC 60.391 55.000 0.00 0.00 40.02 3.51
4038 4351 2.736144 TAAAGCGGCCGATACCATAG 57.264 50.000 33.48 0.00 0.00 2.23
4084 4397 9.554724 CGACTTGTAACAATAACAAAAGCATAT 57.445 29.630 0.00 0.00 36.46 1.78
4100 4413 8.408743 AGATATACAAAGAAGCGACTTGTAAC 57.591 34.615 7.48 4.33 0.00 2.50
4122 4435 9.331282 GAATTCAGTAGCATAAGGTGTAAAGAT 57.669 33.333 0.00 0.00 0.00 2.40
4139 4452 7.239763 TCAGTCCTGTAACATGAATTCAGTA 57.760 36.000 14.54 3.48 0.00 2.74
4256 4572 8.642908 ATCAAATATCAACAAATGCATCACAG 57.357 30.769 0.00 0.00 0.00 3.66
4258 4574 9.309516 AGAATCAAATATCAACAAATGCATCAC 57.690 29.630 0.00 0.00 0.00 3.06
4291 4612 5.353111 TGAATGGAATATTAACTCGTCGCA 58.647 37.500 0.00 0.00 0.00 5.10
4323 4644 2.443255 GGATCTGGAAGGGGCAAAGATA 59.557 50.000 0.00 0.00 0.00 1.98
4498 4827 0.175302 CAGTGTGCCCAAACTTTGCA 59.825 50.000 0.00 0.00 0.00 4.08
4510 4839 3.469899 TTTACGATGCATTCAGTGTGC 57.530 42.857 0.00 0.00 42.81 4.57
4576 4905 6.376018 TGGTGGTGCCTTTTATCAGTAAATAC 59.624 38.462 0.00 0.00 38.35 1.89
4579 4908 4.521256 GTGGTGGTGCCTTTTATCAGTAAA 59.479 41.667 0.00 0.00 38.35 2.01
4585 4914 1.917872 TGGTGGTGGTGCCTTTTATC 58.082 50.000 0.00 0.00 38.35 1.75
4685 5018 4.788617 ACTGATCCCACCCACTAAGTAATT 59.211 41.667 0.00 0.00 0.00 1.40
4697 5031 3.769844 TCTTTGTAGAGACTGATCCCACC 59.230 47.826 0.00 0.00 0.00 4.61
4708 5042 7.378966 ACTGTCAATCGAAATCTTTGTAGAGA 58.621 34.615 0.00 0.00 32.92 3.10
4742 5077 5.057149 AGTATTACCTGCATCAATTCGGTC 58.943 41.667 0.00 0.00 0.00 4.79
4770 5105 5.122396 CAGTAGGTGGTGTTGCTATTCTTTC 59.878 44.000 0.00 0.00 0.00 2.62
4794 5129 5.579718 AGTGCTATACGTGACAATGTACTC 58.420 41.667 0.00 0.00 30.58 2.59
4858 5193 2.026641 ACCGAATTGATCCAGGCAATG 58.973 47.619 0.00 0.00 36.20 2.82
4962 5304 8.055790 TGAATGAGTTGTAGATAAGAGGAGAGA 58.944 37.037 0.00 0.00 0.00 3.10
4963 5305 8.134895 GTGAATGAGTTGTAGATAAGAGGAGAG 58.865 40.741 0.00 0.00 0.00 3.20
5010 5352 5.048991 CCCACTGTAACACCAGAAACAATAC 60.049 44.000 0.00 0.00 36.30 1.89
5067 5409 3.764237 ATACTTACCCCCACAATAGCG 57.236 47.619 0.00 0.00 0.00 4.26
5069 5411 6.659824 ACAGAAATACTTACCCCCACAATAG 58.340 40.000 0.00 0.00 0.00 1.73
5098 5440 4.901814 CAGTCATGCCAAATTAACTCGAG 58.098 43.478 11.84 11.84 0.00 4.04
5099 5441 4.944962 CAGTCATGCCAAATTAACTCGA 57.055 40.909 0.00 0.00 0.00 4.04
5117 5459 2.733956 TCAAACACCCAGAAAAGCAGT 58.266 42.857 0.00 0.00 0.00 4.40
5146 5488 2.029964 GAGACGCGGGTGTGGAAA 59.970 61.111 10.96 0.00 0.00 3.13
5147 5489 3.998672 GGAGACGCGGGTGTGGAA 61.999 66.667 10.96 0.00 0.00 3.53
5152 5494 1.994507 CTACAGAGGAGACGCGGGTG 61.995 65.000 10.96 0.00 34.13 4.61
5174 5516 4.099419 GGGAGACTGGCTCAAAAAGAAAAA 59.901 41.667 13.47 0.00 45.81 1.94
5175 5517 3.636764 GGGAGACTGGCTCAAAAAGAAAA 59.363 43.478 13.47 0.00 45.81 2.29
5176 5518 3.222603 GGGAGACTGGCTCAAAAAGAAA 58.777 45.455 13.47 0.00 45.81 2.52
5177 5519 2.489073 GGGGAGACTGGCTCAAAAAGAA 60.489 50.000 13.47 0.00 45.81 2.52
5178 5520 1.073923 GGGGAGACTGGCTCAAAAAGA 59.926 52.381 13.47 0.00 45.81 2.52
5179 5521 1.074566 AGGGGAGACTGGCTCAAAAAG 59.925 52.381 13.47 0.00 45.81 2.27
5180 5522 1.149101 AGGGGAGACTGGCTCAAAAA 58.851 50.000 13.47 0.00 45.81 1.94
5181 5523 0.401738 CAGGGGAGACTGGCTCAAAA 59.598 55.000 13.47 0.00 45.81 2.44
5182 5524 0.768221 ACAGGGGAGACTGGCTCAAA 60.768 55.000 13.47 0.00 45.81 2.69
5183 5525 0.116342 TACAGGGGAGACTGGCTCAA 59.884 55.000 13.47 0.00 45.81 3.02
5184 5526 0.324738 CTACAGGGGAGACTGGCTCA 60.325 60.000 13.47 0.00 45.81 4.26
5185 5527 0.033011 TCTACAGGGGAGACTGGCTC 60.033 60.000 0.59 0.59 42.75 4.70
5186 5528 0.639392 ATCTACAGGGGAGACTGGCT 59.361 55.000 0.00 0.00 42.75 4.75
5187 5529 0.755686 CATCTACAGGGGAGACTGGC 59.244 60.000 0.00 0.00 42.75 4.85
5188 5530 2.035632 GTCATCTACAGGGGAGACTGG 58.964 57.143 0.00 0.00 42.75 4.00
5189 5531 3.025322 AGTCATCTACAGGGGAGACTG 57.975 52.381 0.00 0.00 44.03 3.51
5190 5532 3.789274 ACTAGTCATCTACAGGGGAGACT 59.211 47.826 0.00 0.00 39.43 3.24
5305 5658 1.093972 TGCATAAACGCACCTGGATG 58.906 50.000 0.00 0.00 36.86 3.51
5386 5746 3.873361 TGTATACTTGCTGCATTCAGAGC 59.127 43.478 1.84 0.00 42.95 4.09
5389 5749 5.746307 ACATGTATACTTGCTGCATTCAG 57.254 39.130 16.47 0.00 43.16 3.02
5390 5750 6.348498 AGTACATGTATACTTGCTGCATTCA 58.652 36.000 16.47 0.00 30.99 2.57
5437 5797 0.540454 CTGCCTCTTGCCTCATCTGA 59.460 55.000 0.00 0.00 40.16 3.27
5467 5827 5.418524 GCTCTATCAGAAGGCAGATCTCATA 59.581 44.000 0.00 0.00 0.00 2.15
5476 5836 0.747255 GACCGCTCTATCAGAAGGCA 59.253 55.000 0.00 0.00 0.00 4.75
5529 5889 1.352156 GACAAGACGCCATCACCGAC 61.352 60.000 0.00 0.00 0.00 4.79
5533 5893 1.873591 ACAAAGACAAGACGCCATCAC 59.126 47.619 0.00 0.00 0.00 3.06
5632 6002 5.809719 CTAGAAAAGGAATGAAGCACTCC 57.190 43.478 0.00 0.00 0.00 3.85
5650 6020 0.268869 ACATGGATCTGGGGCCTAGA 59.731 55.000 22.72 22.72 0.00 2.43
5892 6262 5.419760 TCACGTCAGAGTTATAGATTCGG 57.580 43.478 0.00 0.00 0.00 4.30
5909 6282 3.430929 GGGTATGAAATCTCAGCTCACGT 60.431 47.826 0.00 0.00 34.23 4.49
5930 6303 2.822701 GGCGCCCCGAAAAGTAGG 60.823 66.667 18.11 0.00 0.00 3.18
5939 6312 3.597728 GTAGAGAGAGGCGCCCCG 61.598 72.222 26.15 0.00 35.76 5.73
5947 6320 1.098869 TGAGCGGCAAGTAGAGAGAG 58.901 55.000 1.45 0.00 0.00 3.20
5948 6321 1.406898 CATGAGCGGCAAGTAGAGAGA 59.593 52.381 1.45 0.00 0.00 3.10
6148 6523 1.219124 CGAGGAGGTGGTGATGGTG 59.781 63.158 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.