Multiple sequence alignment - TraesCS4A01G430800

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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 TraesCS4A01G430800 chr4A 100.000 3391 0 0 1 3391 701965190 701961800 0.000000e+00 6263.0
1 TraesCS4A01G430800 chr4A 98.296 763 13 0 2496 3258 650838128 650837366 0.000000e+00 1338.0
2 TraesCS4A01G430800 chr4A 83.140 344 51 6 505 847 697491773 697492110 1.180000e-79 307.0
3 TraesCS4A01G430800 chr4A 100.000 29 0 0 3363 3391 701892668 701892640 2.000000e-03 54.7
4 TraesCS4A01G430800 chr3B 95.666 1569 50 8 830 2395 600905243 600906796 0.000000e+00 2505.0
5 TraesCS4A01G430800 chr3B 92.115 837 57 6 3 831 761204108 761204943 0.000000e+00 1171.0
6 TraesCS4A01G430800 chr1A 98.695 766 10 0 2496 3261 406150091 406150856 0.000000e+00 1360.0
7 TraesCS4A01G430800 chr7A 98.693 765 9 1 2496 3259 720872184 720872948 0.000000e+00 1356.0
8 TraesCS4A01G430800 chr5B 98.691 764 10 0 2496 3259 94273290 94272527 0.000000e+00 1356.0
9 TraesCS4A01G430800 chr5B 98.042 766 15 0 2496 3261 705842357 705841592 0.000000e+00 1332.0
10 TraesCS4A01G430800 chr5B 92.934 835 52 4 3 831 710361249 710360416 0.000000e+00 1208.0
11 TraesCS4A01G430800 chr5B 92.823 836 52 5 3 832 411029045 411028212 0.000000e+00 1205.0
12 TraesCS4A01G430800 chr5B 92.944 822 50 5 3 818 705630914 705631733 0.000000e+00 1190.0
13 TraesCS4A01G430800 chr5B 92.718 824 53 4 14 831 608348842 608349664 0.000000e+00 1182.0
14 TraesCS4A01G430800 chr5B 87.636 275 34 0 573 847 381063193 381062919 1.520000e-83 320.0
15 TraesCS4A01G430800 chr2B 98.691 764 9 1 2496 3259 360850681 360849919 0.000000e+00 1354.0
16 TraesCS4A01G430800 chr2B 98.560 764 11 0 2496 3259 476402354 476403117 0.000000e+00 1351.0
17 TraesCS4A01G430800 chr2B 98.431 765 11 1 2496 3259 53140915 53141679 0.000000e+00 1345.0
18 TraesCS4A01G430800 chr2B 92.601 838 52 8 3 832 406114567 406113732 0.000000e+00 1195.0
19 TraesCS4A01G430800 chr7B 98.429 764 12 0 2496 3259 674191280 674192043 0.000000e+00 1345.0
20 TraesCS4A01G430800 chr4B 93.885 834 42 6 3 829 377799002 377799833 0.000000e+00 1249.0
21 TraesCS4A01G430800 chr2D 93.765 834 44 5 3 829 520039976 520039144 0.000000e+00 1245.0
22 TraesCS4A01G430800 chr2D 80.612 392 67 7 463 849 534727744 534728131 9.200000e-76 294.0
23 TraesCS4A01G430800 chr1B 92.797 833 47 6 3 829 530002239 530003064 0.000000e+00 1194.0
24 TraesCS4A01G430800 chr7D 96.269 134 4 1 3259 3391 28186136 28186003 5.700000e-53 219.0


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 TraesCS4A01G430800 chr4A 701961800 701965190 3390 True 6263 6263 100.000 1 3391 1 chr4A.!!$R3 3390
1 TraesCS4A01G430800 chr4A 650837366 650838128 762 True 1338 1338 98.296 2496 3258 1 chr4A.!!$R1 762
2 TraesCS4A01G430800 chr3B 600905243 600906796 1553 False 2505 2505 95.666 830 2395 1 chr3B.!!$F1 1565
3 TraesCS4A01G430800 chr3B 761204108 761204943 835 False 1171 1171 92.115 3 831 1 chr3B.!!$F2 828
4 TraesCS4A01G430800 chr1A 406150091 406150856 765 False 1360 1360 98.695 2496 3261 1 chr1A.!!$F1 765
5 TraesCS4A01G430800 chr7A 720872184 720872948 764 False 1356 1356 98.693 2496 3259 1 chr7A.!!$F1 763
6 TraesCS4A01G430800 chr5B 94272527 94273290 763 True 1356 1356 98.691 2496 3259 1 chr5B.!!$R1 763
7 TraesCS4A01G430800 chr5B 705841592 705842357 765 True 1332 1332 98.042 2496 3261 1 chr5B.!!$R4 765
8 TraesCS4A01G430800 chr5B 710360416 710361249 833 True 1208 1208 92.934 3 831 1 chr5B.!!$R5 828
9 TraesCS4A01G430800 chr5B 411028212 411029045 833 True 1205 1205 92.823 3 832 1 chr5B.!!$R3 829
10 TraesCS4A01G430800 chr5B 705630914 705631733 819 False 1190 1190 92.944 3 818 1 chr5B.!!$F2 815
11 TraesCS4A01G430800 chr5B 608348842 608349664 822 False 1182 1182 92.718 14 831 1 chr5B.!!$F1 817
12 TraesCS4A01G430800 chr2B 360849919 360850681 762 True 1354 1354 98.691 2496 3259 1 chr2B.!!$R1 763
13 TraesCS4A01G430800 chr2B 476402354 476403117 763 False 1351 1351 98.560 2496 3259 1 chr2B.!!$F2 763
14 TraesCS4A01G430800 chr2B 53140915 53141679 764 False 1345 1345 98.431 2496 3259 1 chr2B.!!$F1 763
15 TraesCS4A01G430800 chr2B 406113732 406114567 835 True 1195 1195 92.601 3 832 1 chr2B.!!$R2 829
16 TraesCS4A01G430800 chr7B 674191280 674192043 763 False 1345 1345 98.429 2496 3259 1 chr7B.!!$F1 763
17 TraesCS4A01G430800 chr4B 377799002 377799833 831 False 1249 1249 93.885 3 829 1 chr4B.!!$F1 826
18 TraesCS4A01G430800 chr2D 520039144 520039976 832 True 1245 1245 93.765 3 829 1 chr2D.!!$R1 826
19 TraesCS4A01G430800 chr1B 530002239 530003064 825 False 1194 1194 92.797 3 829 1 chr1B.!!$F1 826

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
105 108 0.322997 CCGTCTCCTCTCTCACACCT 60.323 60.0 0.00 0.0 0.00 4.00 F
498 510 0.532417 GCAACCATGGCAACTGCAAA 60.532 50.0 13.04 0.0 44.36 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1455 0.608308 GGAACCGGAACCTCTTTGGG 60.608 60.0 9.46 0.0 41.11 4.12 R
2408 2427 0.102481 CGCCGTACTGCCATCTACTT 59.898 55.0 3.50 0.0 0.00 2.24 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
23 25 1.741770 GCGTTGAGAGTTCGCCCAT 60.742 57.895 0.00 0.00 43.41 4.00
98 101 2.752238 CACGCCCGTCTCCTCTCT 60.752 66.667 0.00 0.00 0.00 3.10
105 108 0.322997 CCGTCTCCTCTCTCACACCT 60.323 60.000 0.00 0.00 0.00 4.00
281 286 2.037902 TCTTTACCGAGTTGCCATGTGA 59.962 45.455 0.00 0.00 0.00 3.58
287 292 2.030007 CCGAGTTGCCATGTGATTTTGT 60.030 45.455 0.00 0.00 0.00 2.83
340 349 4.093556 CGTAAGATGGCAACTCTTCCTTTC 59.906 45.833 6.62 0.00 43.02 2.62
347 356 4.041567 TGGCAACTCTTCCTTTCTACATGA 59.958 41.667 0.00 0.00 37.61 3.07
465 477 7.290813 ACTACAGTAGATCAGACCATACATGA 58.709 38.462 14.94 0.00 0.00 3.07
497 509 1.069427 GCAACCATGGCAACTGCAA 59.931 52.632 13.04 0.00 44.36 4.08
498 510 0.532417 GCAACCATGGCAACTGCAAA 60.532 50.000 13.04 0.00 44.36 3.68
695 709 2.359169 GCATGTGAGAGGGACCGGA 61.359 63.158 9.46 0.00 0.00 5.14
746 763 1.140452 TGTTTTGCCCACACGTAGGTA 59.860 47.619 5.59 0.00 0.00 3.08
774 791 5.104900 GGACTGTTCCTCTTATACACCACAT 60.105 44.000 0.00 0.00 39.13 3.21
880 897 3.275617 TTTGACATGTCCGGATAAGGG 57.724 47.619 22.85 1.50 0.00 3.95
881 898 1.874129 TGACATGTCCGGATAAGGGT 58.126 50.000 22.85 5.23 0.00 4.34
888 905 2.290450 TGTCCGGATAAGGGTGAAAACC 60.290 50.000 7.81 0.00 0.00 3.27
922 939 1.073284 ACTACAGCACCGTCCCAATTT 59.927 47.619 0.00 0.00 0.00 1.82
925 942 1.304134 AGCACCGTCCCAATTTCCC 60.304 57.895 0.00 0.00 0.00 3.97
928 945 1.333177 CACCGTCCCAATTTCCCAAA 58.667 50.000 0.00 0.00 0.00 3.28
929 946 1.899142 CACCGTCCCAATTTCCCAAAT 59.101 47.619 0.00 0.00 0.00 2.32
1045 1062 4.373116 GAACCGAGAGCGTGCCCA 62.373 66.667 0.00 0.00 35.23 5.36
1061 1078 3.499737 CAACGCCGATGGAGCCAC 61.500 66.667 0.00 0.00 0.00 5.01
1074 1091 3.730761 GCCACAAGCGTGCAGGAG 61.731 66.667 11.29 1.48 42.17 3.69
1075 1092 3.052082 CCACAAGCGTGCAGGAGG 61.052 66.667 11.29 0.68 42.17 4.30
1076 1093 2.281070 CACAAGCGTGCAGGAGGT 60.281 61.111 11.29 1.35 36.06 3.85
1077 1094 1.893808 CACAAGCGTGCAGGAGGTT 60.894 57.895 11.29 2.90 36.06 3.50
1078 1095 2.949106 CAAGCGTGCAGGAGGTTG 59.051 61.111 11.29 11.88 39.07 3.77
1079 1096 1.893808 CAAGCGTGCAGGAGGTTGT 60.894 57.895 11.29 0.00 39.96 3.32
1080 1097 1.893808 AAGCGTGCAGGAGGTTGTG 60.894 57.895 11.29 0.00 0.00 3.33
1081 1098 4.030452 GCGTGCAGGAGGTTGTGC 62.030 66.667 11.29 0.00 40.29 4.57
1094 1111 2.954684 TTGTGCCTCGAATCGCCCT 61.955 57.895 0.00 0.00 0.00 5.19
1118 1135 1.501741 CGCCGTCCCAAAGAACATG 59.498 57.895 0.00 0.00 0.00 3.21
1119 1136 1.234615 CGCCGTCCCAAAGAACATGT 61.235 55.000 0.00 0.00 0.00 3.21
1146 1163 2.543012 CTGCGATTCTCAGGTATGCAAG 59.457 50.000 0.00 0.00 0.00 4.01
1172 1189 7.118496 AGAAGATCCAGATCTGTTACGATTT 57.882 36.000 21.11 9.02 46.75 2.17
1345 1364 4.410400 CAGGTGGTTCCGGCCCTC 62.410 72.222 10.83 7.37 41.99 4.30
1373 1392 1.001597 CATCGCCGGTACTAGTTCTCC 60.002 57.143 1.90 0.96 0.00 3.71
1378 1397 1.685491 CCGGTACTAGTTCTCCTGGCT 60.685 57.143 0.00 0.00 0.00 4.75
1456 1475 0.109723 CCAAAGAGGTTCCGGTTCCA 59.890 55.000 17.00 0.00 0.00 3.53
1470 1489 3.420206 TTCCATGATCCAGCGGCCC 62.420 63.158 0.00 0.00 0.00 5.80
1545 1564 7.204604 TCTTCGAGATTTTTGCGGTATATACA 58.795 34.615 14.70 0.00 0.00 2.29
1546 1565 7.870954 TCTTCGAGATTTTTGCGGTATATACAT 59.129 33.333 14.70 0.00 0.00 2.29
1603 1622 2.020181 GCATGGCCACACAGATCATCA 61.020 52.381 8.16 0.00 0.00 3.07
1755 1774 5.945466 TGCGATTCACATATATGCATGTT 57.055 34.783 10.16 0.00 37.02 2.71
1787 1806 2.122813 CCTCCTACGGGGCCATCT 60.123 66.667 4.39 0.00 34.39 2.90
1877 1896 2.359900 GAGGTATCCAACAAGCTGGTG 58.640 52.381 0.00 0.00 37.74 4.17
1913 1932 2.673043 GCCCATGTCTGACAAATGCAAG 60.673 50.000 15.31 2.93 0.00 4.01
1932 1951 3.576078 AGTCTGTCACCATCCAAACAA 57.424 42.857 0.00 0.00 0.00 2.83
2012 2031 1.559219 AGTGTATGGCTGTGCATACCA 59.441 47.619 7.64 7.64 37.99 3.25
2085 2104 6.808704 AGACATATTTCATCGTGATATCACCG 59.191 38.462 26.33 20.98 43.66 4.94
2098 2117 2.604046 ATCACCGTATTCACCAGAGC 57.396 50.000 0.00 0.00 0.00 4.09
2152 2171 2.808206 CCCATCCAGTACCGCCCTC 61.808 68.421 0.00 0.00 0.00 4.30
2273 2292 5.298527 CCTAACGATAGGGAAATCCAAAACC 59.701 44.000 10.82 0.00 44.39 3.27
2306 2325 2.412847 GGAAACCGTTCTTCTCAATGCG 60.413 50.000 0.00 0.00 33.92 4.73
2322 2341 0.318699 TGCGGAGGATATTTCGAGCG 60.319 55.000 0.00 0.00 0.00 5.03
2395 2414 0.613853 AGGTGGGCTCGCTAGTGTAA 60.614 55.000 2.66 0.00 0.00 2.41
2396 2415 0.179108 GGTGGGCTCGCTAGTGTAAG 60.179 60.000 2.66 0.00 0.00 2.34
2397 2416 0.531200 GTGGGCTCGCTAGTGTAAGT 59.469 55.000 2.66 0.00 0.00 2.24
2398 2417 0.530744 TGGGCTCGCTAGTGTAAGTG 59.469 55.000 2.66 0.00 0.00 3.16
2399 2418 0.179108 GGGCTCGCTAGTGTAAGTGG 60.179 60.000 2.66 0.00 0.00 4.00
2400 2419 0.815734 GGCTCGCTAGTGTAAGTGGA 59.184 55.000 2.66 0.00 0.00 4.02
2401 2420 1.202313 GGCTCGCTAGTGTAAGTGGAG 60.202 57.143 2.66 0.00 0.00 3.86
2402 2421 1.202313 GCTCGCTAGTGTAAGTGGAGG 60.202 57.143 2.66 0.00 0.00 4.30
2403 2422 2.366533 CTCGCTAGTGTAAGTGGAGGA 58.633 52.381 2.66 0.00 0.00 3.71
2404 2423 2.753452 CTCGCTAGTGTAAGTGGAGGAA 59.247 50.000 2.66 0.00 0.00 3.36
2405 2424 2.490903 TCGCTAGTGTAAGTGGAGGAAC 59.509 50.000 2.66 0.00 0.00 3.62
2406 2425 2.731341 CGCTAGTGTAAGTGGAGGAACG 60.731 54.545 0.00 0.00 0.00 3.95
2407 2426 2.416972 GCTAGTGTAAGTGGAGGAACGG 60.417 54.545 0.00 0.00 0.00 4.44
2408 2427 2.005370 AGTGTAAGTGGAGGAACGGA 57.995 50.000 0.00 0.00 0.00 4.69
2409 2428 2.322658 AGTGTAAGTGGAGGAACGGAA 58.677 47.619 0.00 0.00 0.00 4.30
2410 2429 2.299297 AGTGTAAGTGGAGGAACGGAAG 59.701 50.000 0.00 0.00 0.00 3.46
2424 2443 1.404391 ACGGAAGTAGATGGCAGTACG 59.596 52.381 0.00 0.00 46.88 3.67
2425 2444 1.269102 CGGAAGTAGATGGCAGTACGG 60.269 57.143 0.00 0.00 0.00 4.02
2426 2445 1.538419 GGAAGTAGATGGCAGTACGGC 60.538 57.143 9.73 9.73 41.67 5.68
2427 2446 0.102481 AAGTAGATGGCAGTACGGCG 59.898 55.000 11.93 4.80 45.16 6.46
2428 2447 1.299926 GTAGATGGCAGTACGGCGG 60.300 63.158 13.24 0.00 45.16 6.13
2429 2448 3.146726 TAGATGGCAGTACGGCGGC 62.147 63.158 13.24 4.28 45.16 6.53
2443 2462 4.752879 CGGCGGTGGTGTAGGTGG 62.753 72.222 0.00 0.00 0.00 4.61
2444 2463 4.404098 GGCGGTGGTGTAGGTGGG 62.404 72.222 0.00 0.00 0.00 4.61
2446 2465 3.319198 CGGTGGTGTAGGTGGGCT 61.319 66.667 0.00 0.00 0.00 5.19
2447 2466 2.890766 CGGTGGTGTAGGTGGGCTT 61.891 63.158 0.00 0.00 0.00 4.35
2448 2467 1.002502 GGTGGTGTAGGTGGGCTTC 60.003 63.158 0.00 0.00 0.00 3.86
2449 2468 1.375523 GTGGTGTAGGTGGGCTTCG 60.376 63.158 0.00 0.00 0.00 3.79
2450 2469 1.839747 TGGTGTAGGTGGGCTTCGT 60.840 57.895 0.00 0.00 0.00 3.85
2451 2470 1.373812 GGTGTAGGTGGGCTTCGTT 59.626 57.895 0.00 0.00 0.00 3.85
2452 2471 0.953960 GGTGTAGGTGGGCTTCGTTG 60.954 60.000 0.00 0.00 0.00 4.10
2453 2472 0.250166 GTGTAGGTGGGCTTCGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
2454 2473 1.001181 GTGTAGGTGGGCTTCGTTGTA 59.999 52.381 0.00 0.00 0.00 2.41
2455 2474 1.274167 TGTAGGTGGGCTTCGTTGTAG 59.726 52.381 0.00 0.00 0.00 2.74
2456 2475 0.899720 TAGGTGGGCTTCGTTGTAGG 59.100 55.000 0.00 0.00 0.00 3.18
2457 2476 1.125711 AGGTGGGCTTCGTTGTAGGT 61.126 55.000 0.00 0.00 0.00 3.08
2458 2477 0.953960 GGTGGGCTTCGTTGTAGGTG 60.954 60.000 0.00 0.00 0.00 4.00
2459 2478 0.250166 GTGGGCTTCGTTGTAGGTGT 60.250 55.000 0.00 0.00 0.00 4.16
2460 2479 1.001181 GTGGGCTTCGTTGTAGGTGTA 59.999 52.381 0.00 0.00 0.00 2.90
2461 2480 1.693062 TGGGCTTCGTTGTAGGTGTAA 59.307 47.619 0.00 0.00 0.00 2.41
2462 2481 2.289195 TGGGCTTCGTTGTAGGTGTAAG 60.289 50.000 0.00 0.00 0.00 2.34
2463 2482 2.289257 GGGCTTCGTTGTAGGTGTAAGT 60.289 50.000 0.00 0.00 0.00 2.24
2464 2483 2.735134 GGCTTCGTTGTAGGTGTAAGTG 59.265 50.000 0.00 0.00 0.00 3.16
2465 2484 2.735134 GCTTCGTTGTAGGTGTAAGTGG 59.265 50.000 0.00 0.00 0.00 4.00
2466 2485 3.553508 GCTTCGTTGTAGGTGTAAGTGGA 60.554 47.826 0.00 0.00 0.00 4.02
2467 2486 3.928727 TCGTTGTAGGTGTAAGTGGAG 57.071 47.619 0.00 0.00 0.00 3.86
2468 2487 3.225104 TCGTTGTAGGTGTAAGTGGAGT 58.775 45.455 0.00 0.00 0.00 3.85
2469 2488 3.005050 TCGTTGTAGGTGTAAGTGGAGTG 59.995 47.826 0.00 0.00 0.00 3.51
2470 2489 3.243636 CGTTGTAGGTGTAAGTGGAGTGT 60.244 47.826 0.00 0.00 0.00 3.55
2471 2490 4.056050 GTTGTAGGTGTAAGTGGAGTGTG 58.944 47.826 0.00 0.00 0.00 3.82
2472 2491 3.302161 TGTAGGTGTAAGTGGAGTGTGT 58.698 45.455 0.00 0.00 0.00 3.72
2473 2492 3.319972 TGTAGGTGTAAGTGGAGTGTGTC 59.680 47.826 0.00 0.00 0.00 3.67
2474 2493 1.340248 AGGTGTAAGTGGAGTGTGTCG 59.660 52.381 0.00 0.00 0.00 4.35
2475 2494 1.604693 GGTGTAAGTGGAGTGTGTCGG 60.605 57.143 0.00 0.00 0.00 4.79
2476 2495 1.068127 GTGTAAGTGGAGTGTGTCGGT 59.932 52.381 0.00 0.00 0.00 4.69
2477 2496 1.067974 TGTAAGTGGAGTGTGTCGGTG 59.932 52.381 0.00 0.00 0.00 4.94
2478 2497 0.677288 TAAGTGGAGTGTGTCGGTGG 59.323 55.000 0.00 0.00 0.00 4.61
2479 2498 2.030562 GTGGAGTGTGTCGGTGGG 59.969 66.667 0.00 0.00 0.00 4.61
2480 2499 3.936203 TGGAGTGTGTCGGTGGGC 61.936 66.667 0.00 0.00 0.00 5.36
2481 2500 3.626924 GGAGTGTGTCGGTGGGCT 61.627 66.667 0.00 0.00 0.00 5.19
2482 2501 2.426023 GAGTGTGTCGGTGGGCTT 59.574 61.111 0.00 0.00 0.00 4.35
2483 2502 1.668151 GAGTGTGTCGGTGGGCTTC 60.668 63.158 0.00 0.00 0.00 3.86
2484 2503 3.041940 GTGTGTCGGTGGGCTTCG 61.042 66.667 0.00 0.00 0.00 3.79
2485 2504 3.542676 TGTGTCGGTGGGCTTCGT 61.543 61.111 0.00 0.00 0.00 3.85
2486 2505 3.041940 GTGTCGGTGGGCTTCGTG 61.042 66.667 0.00 0.00 0.00 4.35
2487 2506 4.308458 TGTCGGTGGGCTTCGTGG 62.308 66.667 0.00 0.00 0.00 4.94
2796 2816 3.477530 GTTGCTCTGTTTCAGGTTAGGT 58.522 45.455 0.00 0.00 31.51 3.08
3051 3071 1.407618 GTTTTTGCCTTGGTTCTCGGT 59.592 47.619 0.00 0.00 0.00 4.69
3103 3123 2.421424 GCTTGCTAGCTTGTTGTATGCT 59.579 45.455 17.23 0.00 44.27 3.79
3282 3302 2.813908 GGTACGGCCGTTGAGCTG 60.814 66.667 38.94 1.29 45.09 4.24
3283 3303 2.260434 GTACGGCCGTTGAGCTGA 59.740 61.111 38.94 14.37 42.00 4.26
3284 3304 1.153628 GTACGGCCGTTGAGCTGAT 60.154 57.895 38.94 10.68 42.00 2.90
3285 3305 1.153647 TACGGCCGTTGAGCTGATG 60.154 57.895 38.94 0.00 42.00 3.07
3286 3306 1.600511 TACGGCCGTTGAGCTGATGA 61.601 55.000 38.94 11.67 42.00 2.92
3287 3307 2.456119 CGGCCGTTGAGCTGATGAC 61.456 63.158 19.50 0.00 42.00 3.06
3288 3308 2.109126 GGCCGTTGAGCTGATGACC 61.109 63.158 0.00 0.00 0.00 4.02
3289 3309 1.375908 GCCGTTGAGCTGATGACCA 60.376 57.895 0.00 0.00 0.00 4.02
3290 3310 0.745845 GCCGTTGAGCTGATGACCAT 60.746 55.000 0.00 0.00 0.00 3.55
3291 3311 1.012086 CCGTTGAGCTGATGACCATG 58.988 55.000 0.00 0.00 0.00 3.66
3292 3312 1.405933 CCGTTGAGCTGATGACCATGA 60.406 52.381 0.00 0.00 0.00 3.07
3293 3313 2.349590 CGTTGAGCTGATGACCATGAA 58.650 47.619 0.00 0.00 0.00 2.57
3294 3314 2.743664 CGTTGAGCTGATGACCATGAAA 59.256 45.455 0.00 0.00 0.00 2.69
3295 3315 3.376234 CGTTGAGCTGATGACCATGAAAT 59.624 43.478 0.00 0.00 0.00 2.17
3296 3316 4.495349 CGTTGAGCTGATGACCATGAAATC 60.495 45.833 0.00 0.00 0.00 2.17
3297 3317 4.498894 TGAGCTGATGACCATGAAATCT 57.501 40.909 0.00 0.00 0.00 2.40
3298 3318 4.851843 TGAGCTGATGACCATGAAATCTT 58.148 39.130 0.00 0.00 0.00 2.40
3299 3319 4.880120 TGAGCTGATGACCATGAAATCTTC 59.120 41.667 0.00 0.00 0.00 2.87
3300 3320 4.851843 AGCTGATGACCATGAAATCTTCA 58.148 39.130 0.00 2.56 45.01 3.02
3301 3321 4.882427 AGCTGATGACCATGAAATCTTCAG 59.118 41.667 20.92 20.92 43.98 3.02
3302 3322 4.639310 GCTGATGACCATGAAATCTTCAGT 59.361 41.667 23.28 3.38 43.74 3.41
3303 3323 5.125097 GCTGATGACCATGAAATCTTCAGTT 59.875 40.000 23.28 0.00 43.74 3.16
3304 3324 6.677431 GCTGATGACCATGAAATCTTCAGTTC 60.677 42.308 23.28 13.34 43.74 3.01
3305 3325 6.240145 TGATGACCATGAAATCTTCAGTTCA 58.760 36.000 0.00 0.00 43.98 3.18
3306 3326 6.373495 TGATGACCATGAAATCTTCAGTTCAG 59.627 38.462 0.00 0.00 43.98 3.02
3307 3327 4.456911 TGACCATGAAATCTTCAGTTCAGC 59.543 41.667 0.00 0.00 43.98 4.26
3308 3328 3.760684 ACCATGAAATCTTCAGTTCAGCC 59.239 43.478 0.00 0.00 43.98 4.85
3309 3329 3.760151 CCATGAAATCTTCAGTTCAGCCA 59.240 43.478 0.00 0.00 43.98 4.75
3310 3330 4.219070 CCATGAAATCTTCAGTTCAGCCAA 59.781 41.667 0.00 0.00 43.98 4.52
3311 3331 5.279106 CCATGAAATCTTCAGTTCAGCCAAA 60.279 40.000 0.00 0.00 43.98 3.28
3312 3332 5.850557 TGAAATCTTCAGTTCAGCCAAAA 57.149 34.783 0.00 0.00 34.08 2.44
3313 3333 6.219417 TGAAATCTTCAGTTCAGCCAAAAA 57.781 33.333 0.00 0.00 34.08 1.94
3314 3334 6.819284 TGAAATCTTCAGTTCAGCCAAAAAT 58.181 32.000 0.00 0.00 34.08 1.82
3315 3335 6.702723 TGAAATCTTCAGTTCAGCCAAAAATG 59.297 34.615 0.00 0.00 34.08 2.32
3316 3336 5.796424 ATCTTCAGTTCAGCCAAAAATGT 57.204 34.783 0.00 0.00 0.00 2.71
3317 3337 6.899393 ATCTTCAGTTCAGCCAAAAATGTA 57.101 33.333 0.00 0.00 0.00 2.29
3318 3338 6.072112 TCTTCAGTTCAGCCAAAAATGTAC 57.928 37.500 0.00 0.00 0.00 2.90
3319 3339 5.827797 TCTTCAGTTCAGCCAAAAATGTACT 59.172 36.000 0.00 0.00 0.00 2.73
3320 3340 5.437289 TCAGTTCAGCCAAAAATGTACTG 57.563 39.130 5.83 5.83 42.70 2.74
3321 3341 3.983344 CAGTTCAGCCAAAAATGTACTGC 59.017 43.478 0.00 0.00 37.79 4.40
3322 3342 3.891366 AGTTCAGCCAAAAATGTACTGCT 59.109 39.130 0.00 0.00 0.00 4.24
3323 3343 4.022849 AGTTCAGCCAAAAATGTACTGCTC 60.023 41.667 0.00 0.00 0.00 4.26
3324 3344 2.483877 TCAGCCAAAAATGTACTGCTCG 59.516 45.455 0.00 0.00 0.00 5.03
3325 3345 2.226437 CAGCCAAAAATGTACTGCTCGT 59.774 45.455 0.00 0.00 0.00 4.18
3326 3346 2.484264 AGCCAAAAATGTACTGCTCGTC 59.516 45.455 0.00 0.00 0.00 4.20
3327 3347 2.484264 GCCAAAAATGTACTGCTCGTCT 59.516 45.455 0.00 0.00 0.00 4.18
3328 3348 3.682858 GCCAAAAATGTACTGCTCGTCTA 59.317 43.478 0.00 0.00 0.00 2.59
3329 3349 4.435651 GCCAAAAATGTACTGCTCGTCTAC 60.436 45.833 0.00 0.00 0.00 2.59
3330 3350 4.092968 CCAAAAATGTACTGCTCGTCTACC 59.907 45.833 0.00 0.00 0.00 3.18
3331 3351 4.530710 AAAATGTACTGCTCGTCTACCA 57.469 40.909 0.00 0.00 0.00 3.25
3332 3352 4.737855 AAATGTACTGCTCGTCTACCAT 57.262 40.909 0.00 0.00 0.00 3.55
3333 3353 3.717400 ATGTACTGCTCGTCTACCATG 57.283 47.619 0.00 0.00 0.00 3.66
3334 3354 1.749063 TGTACTGCTCGTCTACCATGG 59.251 52.381 11.19 11.19 0.00 3.66
3335 3355 1.749634 GTACTGCTCGTCTACCATGGT 59.250 52.381 23.55 23.55 0.00 3.55
3336 3356 0.818296 ACTGCTCGTCTACCATGGTC 59.182 55.000 23.76 6.29 0.00 4.02
3337 3357 0.817654 CTGCTCGTCTACCATGGTCA 59.182 55.000 23.76 10.43 0.00 4.02
3338 3358 1.410517 CTGCTCGTCTACCATGGTCAT 59.589 52.381 23.76 0.00 0.00 3.06
3339 3359 1.136891 TGCTCGTCTACCATGGTCATG 59.863 52.381 23.76 14.79 38.51 3.07
3340 3360 1.858091 CTCGTCTACCATGGTCATGC 58.142 55.000 23.76 9.50 37.49 4.06
3341 3361 1.136891 CTCGTCTACCATGGTCATGCA 59.863 52.381 23.76 1.60 37.49 3.96
3342 3362 1.762370 TCGTCTACCATGGTCATGCAT 59.238 47.619 23.76 0.00 37.49 3.96
3343 3363 1.869132 CGTCTACCATGGTCATGCATG 59.131 52.381 23.76 21.07 37.49 4.06
3344 3364 2.483538 CGTCTACCATGGTCATGCATGA 60.484 50.000 25.42 25.42 37.49 3.07
3345 3365 3.748083 GTCTACCATGGTCATGCATGAT 58.252 45.455 30.89 16.93 39.30 2.45
3346 3366 4.139786 GTCTACCATGGTCATGCATGATT 58.860 43.478 30.89 16.68 39.30 2.57
3347 3367 4.214971 GTCTACCATGGTCATGCATGATTC 59.785 45.833 30.89 24.40 39.30 2.52
3348 3368 3.021177 ACCATGGTCATGCATGATTCA 57.979 42.857 30.89 28.39 39.30 2.57
3349 3369 3.367321 ACCATGGTCATGCATGATTCAA 58.633 40.909 30.89 14.30 39.30 2.69
3350 3370 3.383505 ACCATGGTCATGCATGATTCAAG 59.616 43.478 30.89 24.90 39.30 3.02
3351 3371 3.381045 CATGGTCATGCATGATTCAAGC 58.619 45.455 30.89 18.33 39.30 4.01
3352 3372 2.448453 TGGTCATGCATGATTCAAGCA 58.552 42.857 30.89 20.60 42.11 3.91
3353 3373 2.826725 TGGTCATGCATGATTCAAGCAA 59.173 40.909 30.89 9.10 41.28 3.91
3354 3374 3.449377 TGGTCATGCATGATTCAAGCAAT 59.551 39.130 30.89 6.78 41.28 3.56
3355 3375 4.645588 TGGTCATGCATGATTCAAGCAATA 59.354 37.500 30.89 8.65 41.28 1.90
3356 3376 5.303333 TGGTCATGCATGATTCAAGCAATAT 59.697 36.000 30.89 1.96 41.28 1.28
3357 3377 6.183360 TGGTCATGCATGATTCAAGCAATATT 60.183 34.615 30.89 1.61 41.28 1.28
3358 3378 6.704493 GGTCATGCATGATTCAAGCAATATTT 59.296 34.615 30.89 1.25 41.28 1.40
3359 3379 7.868922 GGTCATGCATGATTCAAGCAATATTTA 59.131 33.333 30.89 0.53 41.28 1.40
3360 3380 8.697067 GTCATGCATGATTCAAGCAATATTTAC 58.303 33.333 30.89 9.74 41.28 2.01
3361 3381 7.592164 TCATGCATGATTCAAGCAATATTTACG 59.408 33.333 25.42 3.18 41.28 3.18
3362 3382 6.207928 TGCATGATTCAAGCAATATTTACGG 58.792 36.000 13.73 0.00 35.14 4.02
3363 3383 6.183360 TGCATGATTCAAGCAATATTTACGGT 60.183 34.615 13.73 0.00 35.14 4.83
3364 3384 6.142798 GCATGATTCAAGCAATATTTACGGTG 59.857 38.462 8.90 0.00 0.00 4.94
3365 3385 6.751514 TGATTCAAGCAATATTTACGGTGT 57.248 33.333 0.00 0.00 0.00 4.16
3366 3386 6.550843 TGATTCAAGCAATATTTACGGTGTG 58.449 36.000 0.00 0.00 0.00 3.82
3367 3387 6.372937 TGATTCAAGCAATATTTACGGTGTGA 59.627 34.615 0.00 0.00 0.00 3.58
3368 3388 5.539582 TCAAGCAATATTTACGGTGTGAC 57.460 39.130 0.00 0.00 0.00 3.67
3369 3389 5.242434 TCAAGCAATATTTACGGTGTGACT 58.758 37.500 0.00 0.00 0.00 3.41
3370 3390 5.350365 TCAAGCAATATTTACGGTGTGACTC 59.650 40.000 0.00 0.00 0.00 3.36
3371 3391 5.086104 AGCAATATTTACGGTGTGACTCT 57.914 39.130 0.00 0.00 0.00 3.24
3372 3392 5.488341 AGCAATATTTACGGTGTGACTCTT 58.512 37.500 0.00 0.00 0.00 2.85
3373 3393 5.351465 AGCAATATTTACGGTGTGACTCTTG 59.649 40.000 0.00 0.00 0.00 3.02
3374 3394 5.350365 GCAATATTTACGGTGTGACTCTTGA 59.650 40.000 0.00 0.00 0.00 3.02
3375 3395 6.672357 GCAATATTTACGGTGTGACTCTTGAC 60.672 42.308 0.00 0.00 0.00 3.18
3376 3396 4.602340 ATTTACGGTGTGACTCTTGACT 57.398 40.909 0.00 0.00 0.00 3.41
3377 3397 3.637998 TTACGGTGTGACTCTTGACTC 57.362 47.619 0.00 0.00 0.00 3.36
3378 3398 1.399714 ACGGTGTGACTCTTGACTCA 58.600 50.000 0.00 0.00 0.00 3.41
3379 3399 1.964223 ACGGTGTGACTCTTGACTCAT 59.036 47.619 0.00 0.00 0.00 2.90
3380 3400 2.288457 ACGGTGTGACTCTTGACTCATG 60.288 50.000 0.00 0.00 0.00 3.07
3381 3401 2.029918 CGGTGTGACTCTTGACTCATGA 60.030 50.000 0.00 0.00 0.00 3.07
3382 3402 3.583806 GGTGTGACTCTTGACTCATGAG 58.416 50.000 21.37 21.37 40.17 2.90
3383 3403 3.256879 GGTGTGACTCTTGACTCATGAGA 59.743 47.826 29.27 4.71 37.70 3.27
3384 3404 4.262207 GGTGTGACTCTTGACTCATGAGAA 60.262 45.833 29.27 13.73 37.70 2.87
3385 3405 4.922692 GTGTGACTCTTGACTCATGAGAAG 59.077 45.833 29.27 21.17 37.70 2.85
3386 3406 4.586421 TGTGACTCTTGACTCATGAGAAGT 59.414 41.667 29.27 20.31 37.70 3.01
3387 3407 5.770162 TGTGACTCTTGACTCATGAGAAGTA 59.230 40.000 29.27 11.43 37.70 2.24
3388 3408 6.265422 TGTGACTCTTGACTCATGAGAAGTAA 59.735 38.462 29.27 15.32 37.70 2.24
3389 3409 6.584563 GTGACTCTTGACTCATGAGAAGTAAC 59.415 42.308 29.27 19.27 37.70 2.50
3390 3410 6.265422 TGACTCTTGACTCATGAGAAGTAACA 59.735 38.462 29.27 17.75 37.70 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.459585 GCGAACTCTCAACGCCCATA 60.460 55.000 0.00 0.00 45.35 2.74
1 2 1.741770 GCGAACTCTCAACGCCCAT 60.742 57.895 0.00 0.00 45.35 4.00
10 11 1.591863 GGCGTATGGGCGAACTCTC 60.592 63.158 0.00 0.00 0.00 3.20
23 25 1.957186 GTGCGTGGAAAGTGGCGTA 60.957 57.895 0.00 0.00 0.00 4.42
98 101 2.612972 GCAACTAGCAGCTTAGGTGTGA 60.613 50.000 13.13 0.70 44.79 3.58
281 286 6.183360 GGCAGTTGCTATGTACCATACAAAAT 60.183 38.462 3.88 0.00 40.78 1.82
287 292 3.045634 AGGGCAGTTGCTATGTACCATA 58.954 45.455 3.88 0.00 41.70 2.74
340 349 2.093500 TGCTAGGGCAGTTGTCATGTAG 60.093 50.000 0.00 0.00 44.28 2.74
497 509 0.250793 TACGGTTGCCATGTCGGATT 59.749 50.000 0.00 0.00 36.56 3.01
498 510 0.179084 CTACGGTTGCCATGTCGGAT 60.179 55.000 0.00 0.00 36.56 4.18
588 602 2.658593 GCACGCGTGACAGTCACT 60.659 61.111 41.19 9.80 44.85 3.41
752 769 7.490657 TTATGTGGTGTATAAGAGGAACAGT 57.509 36.000 0.00 0.00 0.00 3.55
774 791 3.153919 GGAAGACTGCCCACACATTTTA 58.846 45.455 0.00 0.00 0.00 1.52
847 864 8.499162 CCGGACATGTCAAATTTATCTCTAATC 58.501 37.037 26.47 2.80 0.00 1.75
848 865 8.210946 TCCGGACATGTCAAATTTATCTCTAAT 58.789 33.333 26.47 0.00 0.00 1.73
849 866 7.561251 TCCGGACATGTCAAATTTATCTCTAA 58.439 34.615 26.47 0.00 0.00 2.10
850 867 7.119709 TCCGGACATGTCAAATTTATCTCTA 57.880 36.000 26.47 0.00 0.00 2.43
851 868 5.989477 TCCGGACATGTCAAATTTATCTCT 58.011 37.500 26.47 0.00 0.00 3.10
852 869 6.867662 ATCCGGACATGTCAAATTTATCTC 57.132 37.500 26.47 4.90 0.00 2.75
866 883 3.617284 GTTTTCACCCTTATCCGGACAT 58.383 45.455 6.12 0.00 0.00 3.06
880 897 1.228154 AGTCCGGCTGGGTTTTCAC 60.228 57.895 12.87 0.53 37.00 3.18
881 898 1.072505 GAGTCCGGCTGGGTTTTCA 59.927 57.895 12.87 0.00 37.00 2.69
888 905 0.965866 TGTAGTCTGAGTCCGGCTGG 60.966 60.000 4.71 4.71 0.00 4.85
889 906 0.453793 CTGTAGTCTGAGTCCGGCTG 59.546 60.000 0.00 0.00 0.00 4.85
922 939 1.567357 GCTGGCCCTTTTATTTGGGA 58.433 50.000 0.00 0.00 46.15 4.37
1023 1040 1.874019 CACGCTCTCGGTTCCATCG 60.874 63.158 0.00 0.00 40.69 3.84
1028 1045 3.876589 TTGGGCACGCTCTCGGTTC 62.877 63.158 0.00 0.00 40.69 3.62
1029 1046 3.936203 TTGGGCACGCTCTCGGTT 61.936 61.111 0.00 0.00 40.69 4.44
1045 1062 3.545124 TTGTGGCTCCATCGGCGTT 62.545 57.895 6.85 0.00 0.00 4.84
1061 1078 1.893808 ACAACCTCCTGCACGCTTG 60.894 57.895 0.00 0.00 0.00 4.01
1074 1091 2.750888 GGCGATTCGAGGCACAACC 61.751 63.158 10.88 0.00 39.61 3.77
1075 1092 2.750888 GGGCGATTCGAGGCACAAC 61.751 63.158 10.88 0.00 35.71 3.32
1076 1093 2.435938 GGGCGATTCGAGGCACAA 60.436 61.111 10.88 0.00 35.71 3.33
1077 1094 3.371097 GAGGGCGATTCGAGGCACA 62.371 63.158 10.88 0.00 34.20 4.57
1078 1095 2.586357 GAGGGCGATTCGAGGCAC 60.586 66.667 10.88 3.80 35.71 5.01
1079 1096 4.207281 CGAGGGCGATTCGAGGCA 62.207 66.667 10.88 0.00 40.36 4.75
1080 1097 4.951963 CCGAGGGCGATTCGAGGC 62.952 72.222 10.88 0.00 40.36 4.70
1081 1098 3.217017 TCCGAGGGCGATTCGAGG 61.217 66.667 10.88 4.64 40.36 4.63
1118 1135 2.815478 CCTGAGAATCGCAGGTAGAAC 58.185 52.381 22.46 0.00 44.47 3.01
1146 1163 4.580995 TCGTAACAGATCTGGATCTTCTCC 59.419 45.833 26.08 3.57 45.31 3.71
1341 1360 2.356793 GCGATGCGGATCAGAGGG 60.357 66.667 17.54 1.08 0.00 4.30
1345 1364 3.207547 TACCGGCGATGCGGATCAG 62.208 63.158 17.54 10.55 0.00 2.90
1388 1407 3.365265 CCCGTGGTGCCTTCTTGC 61.365 66.667 0.00 0.00 0.00 4.01
1436 1455 0.608308 GGAACCGGAACCTCTTTGGG 60.608 60.000 9.46 0.00 41.11 4.12
1439 1458 1.702957 TCATGGAACCGGAACCTCTTT 59.297 47.619 9.46 0.00 0.00 2.52
1456 1475 3.882326 CTGGGGCCGCTGGATCAT 61.882 66.667 21.80 0.00 0.00 2.45
1545 1564 4.141390 ACTTCGCCAATGAGAGGGAAATAT 60.141 41.667 0.00 0.00 34.93 1.28
1546 1565 3.199946 ACTTCGCCAATGAGAGGGAAATA 59.800 43.478 0.00 0.00 34.93 1.40
1603 1622 1.123861 TCCACACTCTTGCTCTGGCT 61.124 55.000 0.00 0.00 39.59 4.75
1669 1688 7.724061 AGAACATACCCTGAAAACATGTTTAGT 59.276 33.333 23.53 16.81 39.31 2.24
1787 1806 3.562182 TGATTCGGCTGAGATGTACCTA 58.438 45.455 0.00 0.00 0.00 3.08
1836 1855 2.227388 CCACAGGTTCATTCTCAGTTGC 59.773 50.000 0.00 0.00 0.00 4.17
1877 1896 1.181786 TGGGCGAATTGAACCAATCC 58.818 50.000 0.00 0.00 32.43 3.01
1932 1951 3.490348 ACACATCTACTTTGCCTTTGCT 58.510 40.909 0.00 0.00 38.71 3.91
2029 2048 4.614946 GGTGATGGAACCGTGTATACTAC 58.385 47.826 4.17 0.36 0.00 2.73
2085 2104 2.113860 TTGGCAGCTCTGGTGAATAC 57.886 50.000 0.66 0.00 32.22 1.89
2098 2117 4.019174 AGGATTAACACCTGAATTGGCAG 58.981 43.478 2.70 0.00 36.30 4.85
2273 2292 3.611766 ACGGTTTCCTTGATACTCAGG 57.388 47.619 0.00 0.00 0.00 3.86
2291 2310 1.002366 CCTCCGCATTGAGAAGAACG 58.998 55.000 0.00 0.00 34.11 3.95
2306 2325 2.608261 CCACTCGCTCGAAATATCCTCC 60.608 54.545 0.00 0.00 0.00 4.30
2322 2341 4.005650 TCATCTTCATGCTTGAACCACTC 58.994 43.478 10.76 0.00 36.94 3.51
2395 2414 2.599408 TCTACTTCCGTTCCTCCACT 57.401 50.000 0.00 0.00 0.00 4.00
2396 2415 2.159085 CCATCTACTTCCGTTCCTCCAC 60.159 54.545 0.00 0.00 0.00 4.02
2397 2416 2.108168 CCATCTACTTCCGTTCCTCCA 58.892 52.381 0.00 0.00 0.00 3.86
2398 2417 1.202545 GCCATCTACTTCCGTTCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
2399 2418 1.480954 TGCCATCTACTTCCGTTCCTC 59.519 52.381 0.00 0.00 0.00 3.71
2400 2419 1.482593 CTGCCATCTACTTCCGTTCCT 59.517 52.381 0.00 0.00 0.00 3.36
2401 2420 1.207329 ACTGCCATCTACTTCCGTTCC 59.793 52.381 0.00 0.00 0.00 3.62
2402 2421 2.674796 ACTGCCATCTACTTCCGTTC 57.325 50.000 0.00 0.00 0.00 3.95
2403 2422 2.159282 CGTACTGCCATCTACTTCCGTT 60.159 50.000 0.00 0.00 0.00 4.44
2404 2423 1.404391 CGTACTGCCATCTACTTCCGT 59.596 52.381 0.00 0.00 0.00 4.69
2405 2424 1.269102 CCGTACTGCCATCTACTTCCG 60.269 57.143 0.00 0.00 0.00 4.30
2406 2425 1.538419 GCCGTACTGCCATCTACTTCC 60.538 57.143 0.00 0.00 0.00 3.46
2407 2426 1.854227 GCCGTACTGCCATCTACTTC 58.146 55.000 0.00 0.00 0.00 3.01
2408 2427 0.102481 CGCCGTACTGCCATCTACTT 59.898 55.000 3.50 0.00 0.00 2.24
2409 2428 1.734137 CGCCGTACTGCCATCTACT 59.266 57.895 3.50 0.00 0.00 2.57
2410 2429 1.299926 CCGCCGTACTGCCATCTAC 60.300 63.158 3.50 0.00 0.00 2.59
2411 2430 3.125607 CCGCCGTACTGCCATCTA 58.874 61.111 3.50 0.00 0.00 1.98
2412 2431 4.530857 GCCGCCGTACTGCCATCT 62.531 66.667 3.50 0.00 0.00 2.90
2426 2445 4.752879 CCACCTACACCACCGCCG 62.753 72.222 0.00 0.00 0.00 6.46
2427 2446 4.404098 CCCACCTACACCACCGCC 62.404 72.222 0.00 0.00 0.00 6.13
2429 2448 2.798148 GAAGCCCACCTACACCACCG 62.798 65.000 0.00 0.00 0.00 4.94
2430 2449 1.002502 GAAGCCCACCTACACCACC 60.003 63.158 0.00 0.00 0.00 4.61
2431 2450 1.375523 CGAAGCCCACCTACACCAC 60.376 63.158 0.00 0.00 0.00 4.16
2432 2451 1.412453 AACGAAGCCCACCTACACCA 61.412 55.000 0.00 0.00 0.00 4.17
2433 2452 0.953960 CAACGAAGCCCACCTACACC 60.954 60.000 0.00 0.00 0.00 4.16
2434 2453 0.250166 ACAACGAAGCCCACCTACAC 60.250 55.000 0.00 0.00 0.00 2.90
2435 2454 1.274167 CTACAACGAAGCCCACCTACA 59.726 52.381 0.00 0.00 0.00 2.74
2436 2455 1.405121 CCTACAACGAAGCCCACCTAC 60.405 57.143 0.00 0.00 0.00 3.18
2437 2456 0.899720 CCTACAACGAAGCCCACCTA 59.100 55.000 0.00 0.00 0.00 3.08
2438 2457 1.125711 ACCTACAACGAAGCCCACCT 61.126 55.000 0.00 0.00 0.00 4.00
2439 2458 0.953960 CACCTACAACGAAGCCCACC 60.954 60.000 0.00 0.00 0.00 4.61
2440 2459 0.250166 ACACCTACAACGAAGCCCAC 60.250 55.000 0.00 0.00 0.00 4.61
2441 2460 1.340088 TACACCTACAACGAAGCCCA 58.660 50.000 0.00 0.00 0.00 5.36
2442 2461 2.289257 ACTTACACCTACAACGAAGCCC 60.289 50.000 0.00 0.00 0.00 5.19
2443 2462 2.735134 CACTTACACCTACAACGAAGCC 59.265 50.000 0.00 0.00 0.00 4.35
2444 2463 2.735134 CCACTTACACCTACAACGAAGC 59.265 50.000 0.00 0.00 0.00 3.86
2445 2464 4.235360 CTCCACTTACACCTACAACGAAG 58.765 47.826 0.00 0.00 0.00 3.79
2446 2465 3.638160 ACTCCACTTACACCTACAACGAA 59.362 43.478 0.00 0.00 0.00 3.85
2447 2466 3.005050 CACTCCACTTACACCTACAACGA 59.995 47.826 0.00 0.00 0.00 3.85
2448 2467 3.243636 ACACTCCACTTACACCTACAACG 60.244 47.826 0.00 0.00 0.00 4.10
2449 2468 4.056050 CACACTCCACTTACACCTACAAC 58.944 47.826 0.00 0.00 0.00 3.32
2450 2469 3.707611 ACACACTCCACTTACACCTACAA 59.292 43.478 0.00 0.00 0.00 2.41
2451 2470 3.302161 ACACACTCCACTTACACCTACA 58.698 45.455 0.00 0.00 0.00 2.74
2452 2471 3.611057 CGACACACTCCACTTACACCTAC 60.611 52.174 0.00 0.00 0.00 3.18
2453 2472 2.555325 CGACACACTCCACTTACACCTA 59.445 50.000 0.00 0.00 0.00 3.08
2454 2473 1.340248 CGACACACTCCACTTACACCT 59.660 52.381 0.00 0.00 0.00 4.00
2455 2474 1.604693 CCGACACACTCCACTTACACC 60.605 57.143 0.00 0.00 0.00 4.16
2456 2475 1.068127 ACCGACACACTCCACTTACAC 59.932 52.381 0.00 0.00 0.00 2.90
2457 2476 1.067974 CACCGACACACTCCACTTACA 59.932 52.381 0.00 0.00 0.00 2.41
2458 2477 1.604693 CCACCGACACACTCCACTTAC 60.605 57.143 0.00 0.00 0.00 2.34
2459 2478 0.677288 CCACCGACACACTCCACTTA 59.323 55.000 0.00 0.00 0.00 2.24
2460 2479 1.445942 CCACCGACACACTCCACTT 59.554 57.895 0.00 0.00 0.00 3.16
2461 2480 2.507854 CCCACCGACACACTCCACT 61.508 63.158 0.00 0.00 0.00 4.00
2462 2481 2.030562 CCCACCGACACACTCCAC 59.969 66.667 0.00 0.00 0.00 4.02
2463 2482 3.936203 GCCCACCGACACACTCCA 61.936 66.667 0.00 0.00 0.00 3.86
2464 2483 3.178540 AAGCCCACCGACACACTCC 62.179 63.158 0.00 0.00 0.00 3.85
2465 2484 1.668151 GAAGCCCACCGACACACTC 60.668 63.158 0.00 0.00 0.00 3.51
2466 2485 2.426023 GAAGCCCACCGACACACT 59.574 61.111 0.00 0.00 0.00 3.55
2467 2486 3.041940 CGAAGCCCACCGACACAC 61.042 66.667 0.00 0.00 0.00 3.82
2468 2487 3.542676 ACGAAGCCCACCGACACA 61.543 61.111 0.00 0.00 0.00 3.72
2469 2488 3.041940 CACGAAGCCCACCGACAC 61.042 66.667 0.00 0.00 0.00 3.67
2470 2489 4.308458 CCACGAAGCCCACCGACA 62.308 66.667 0.00 0.00 0.00 4.35
2491 2510 3.642778 CTCCACCTACACCACGCCG 62.643 68.421 0.00 0.00 0.00 6.46
2492 2511 2.264794 CTCCACCTACACCACGCC 59.735 66.667 0.00 0.00 0.00 5.68
2493 2512 1.374252 CACTCCACCTACACCACGC 60.374 63.158 0.00 0.00 0.00 5.34
2494 2513 0.319555 CACACTCCACCTACACCACG 60.320 60.000 0.00 0.00 0.00 4.94
2829 2849 0.606401 CATCGCAGGAAACCACAGGT 60.606 55.000 0.00 0.00 37.65 4.00
3051 3071 0.397675 TGCCATGAACCCCAAACACA 60.398 50.000 0.00 0.00 0.00 3.72
3103 3123 1.670949 CCTAGGAGCAGCTCGCAGAA 61.671 60.000 16.47 0.00 46.13 3.02
3265 3285 2.573609 ATCAGCTCAACGGCCGTACC 62.574 60.000 34.44 19.34 0.00 3.34
3266 3286 1.153628 ATCAGCTCAACGGCCGTAC 60.154 57.895 34.44 21.02 0.00 3.67
3267 3287 1.153647 CATCAGCTCAACGGCCGTA 60.154 57.895 34.44 16.97 0.00 4.02
3268 3288 2.434884 CATCAGCTCAACGGCCGT 60.435 61.111 28.70 28.70 0.00 5.68
3269 3289 2.125552 TCATCAGCTCAACGGCCG 60.126 61.111 26.86 26.86 0.00 6.13
3270 3290 2.109126 GGTCATCAGCTCAACGGCC 61.109 63.158 0.00 0.00 0.00 6.13
3271 3291 0.745845 ATGGTCATCAGCTCAACGGC 60.746 55.000 0.00 0.00 0.00 5.68
3272 3292 1.012086 CATGGTCATCAGCTCAACGG 58.988 55.000 0.00 0.00 0.00 4.44
3273 3293 2.014335 TCATGGTCATCAGCTCAACG 57.986 50.000 0.00 0.00 0.00 4.10
3274 3294 4.639310 AGATTTCATGGTCATCAGCTCAAC 59.361 41.667 0.00 0.00 0.00 3.18
3275 3295 4.851843 AGATTTCATGGTCATCAGCTCAA 58.148 39.130 0.00 0.00 0.00 3.02
3276 3296 4.498894 AGATTTCATGGTCATCAGCTCA 57.501 40.909 0.00 0.00 0.00 4.26
3277 3297 4.880120 TGAAGATTTCATGGTCATCAGCTC 59.120 41.667 0.00 0.00 34.08 4.09
3278 3298 4.851843 TGAAGATTTCATGGTCATCAGCT 58.148 39.130 0.00 0.00 34.08 4.24
3279 3299 4.639310 ACTGAAGATTTCATGGTCATCAGC 59.361 41.667 19.37 6.75 41.44 4.26
3280 3300 6.373495 TGAACTGAAGATTTCATGGTCATCAG 59.627 38.462 18.54 18.54 42.66 2.90
3281 3301 6.240145 TGAACTGAAGATTTCATGGTCATCA 58.760 36.000 0.00 0.00 39.30 3.07
3282 3302 6.677431 GCTGAACTGAAGATTTCATGGTCATC 60.677 42.308 0.00 0.00 39.30 2.92
3283 3303 5.125097 GCTGAACTGAAGATTTCATGGTCAT 59.875 40.000 0.00 0.00 39.30 3.06
3284 3304 4.456911 GCTGAACTGAAGATTTCATGGTCA 59.543 41.667 0.00 7.97 39.30 4.02
3285 3305 4.142513 GGCTGAACTGAAGATTTCATGGTC 60.143 45.833 0.00 0.00 39.30 4.02
3286 3306 3.760684 GGCTGAACTGAAGATTTCATGGT 59.239 43.478 0.00 0.00 39.30 3.55
3287 3307 3.760151 TGGCTGAACTGAAGATTTCATGG 59.240 43.478 0.00 0.00 39.30 3.66
3288 3308 5.381174 TTGGCTGAACTGAAGATTTCATG 57.619 39.130 0.00 0.00 39.30 3.07
3289 3309 6.409524 TTTTGGCTGAACTGAAGATTTCAT 57.590 33.333 0.00 0.00 39.30 2.57
3290 3310 5.850557 TTTTGGCTGAACTGAAGATTTCA 57.149 34.783 0.00 0.00 38.17 2.69
3291 3311 6.703165 ACATTTTTGGCTGAACTGAAGATTTC 59.297 34.615 0.00 0.00 0.00 2.17
3292 3312 6.585416 ACATTTTTGGCTGAACTGAAGATTT 58.415 32.000 0.00 0.00 0.00 2.17
3293 3313 6.165700 ACATTTTTGGCTGAACTGAAGATT 57.834 33.333 0.00 0.00 0.00 2.40
3294 3314 5.796424 ACATTTTTGGCTGAACTGAAGAT 57.204 34.783 0.00 0.00 0.00 2.40
3295 3315 5.827797 AGTACATTTTTGGCTGAACTGAAGA 59.172 36.000 0.00 0.00 0.00 2.87
3296 3316 5.916883 CAGTACATTTTTGGCTGAACTGAAG 59.083 40.000 0.00 0.00 36.13 3.02
3297 3317 5.735922 GCAGTACATTTTTGGCTGAACTGAA 60.736 40.000 0.00 0.00 36.13 3.02
3298 3318 4.261572 GCAGTACATTTTTGGCTGAACTGA 60.262 41.667 0.00 0.00 36.13 3.41
3299 3319 3.983344 GCAGTACATTTTTGGCTGAACTG 59.017 43.478 0.00 0.00 36.92 3.16
3300 3320 3.891366 AGCAGTACATTTTTGGCTGAACT 59.109 39.130 0.00 0.00 0.00 3.01
3301 3321 4.229876 GAGCAGTACATTTTTGGCTGAAC 58.770 43.478 0.00 0.00 0.00 3.18
3302 3322 3.058293 CGAGCAGTACATTTTTGGCTGAA 60.058 43.478 0.00 0.00 0.00 3.02
3303 3323 2.483877 CGAGCAGTACATTTTTGGCTGA 59.516 45.455 0.00 0.00 0.00 4.26
3304 3324 2.226437 ACGAGCAGTACATTTTTGGCTG 59.774 45.455 0.00 0.00 0.00 4.85
3305 3325 2.484264 GACGAGCAGTACATTTTTGGCT 59.516 45.455 0.00 0.00 0.00 4.75
3306 3326 2.484264 AGACGAGCAGTACATTTTTGGC 59.516 45.455 0.00 0.00 0.00 4.52
3307 3327 4.092968 GGTAGACGAGCAGTACATTTTTGG 59.907 45.833 0.00 0.00 0.00 3.28
3308 3328 4.688879 TGGTAGACGAGCAGTACATTTTTG 59.311 41.667 0.00 0.00 0.00 2.44
3309 3329 4.890088 TGGTAGACGAGCAGTACATTTTT 58.110 39.130 0.00 0.00 0.00 1.94
3310 3330 4.530710 TGGTAGACGAGCAGTACATTTT 57.469 40.909 0.00 0.00 0.00 1.82
3311 3331 4.433615 CATGGTAGACGAGCAGTACATTT 58.566 43.478 0.00 0.00 39.39 2.32
3312 3332 3.181475 CCATGGTAGACGAGCAGTACATT 60.181 47.826 2.57 0.00 39.39 2.71
3313 3333 2.362397 CCATGGTAGACGAGCAGTACAT 59.638 50.000 2.57 0.00 39.39 2.29
3314 3334 1.749063 CCATGGTAGACGAGCAGTACA 59.251 52.381 2.57 0.00 39.39 2.90
3315 3335 1.749634 ACCATGGTAGACGAGCAGTAC 59.250 52.381 18.10 0.00 39.39 2.73
3316 3336 2.022195 GACCATGGTAGACGAGCAGTA 58.978 52.381 19.80 0.00 39.39 2.74
3317 3337 0.818296 GACCATGGTAGACGAGCAGT 59.182 55.000 19.80 0.00 39.39 4.40
3318 3338 0.817654 TGACCATGGTAGACGAGCAG 59.182 55.000 19.80 0.00 39.39 4.24
3319 3339 1.136891 CATGACCATGGTAGACGAGCA 59.863 52.381 19.80 10.18 40.58 4.26
3320 3340 1.858091 CATGACCATGGTAGACGAGC 58.142 55.000 19.80 3.68 35.24 5.03
3321 3341 1.136891 TGCATGACCATGGTAGACGAG 59.863 52.381 19.80 6.13 39.16 4.18
3322 3342 1.190643 TGCATGACCATGGTAGACGA 58.809 50.000 19.80 0.00 39.16 4.20
3323 3343 1.869132 CATGCATGACCATGGTAGACG 59.131 52.381 22.59 8.04 39.08 4.18
3324 3344 3.198409 TCATGCATGACCATGGTAGAC 57.802 47.619 25.42 6.20 42.19 2.59
3325 3345 4.141436 TGAATCATGCATGACCATGGTAGA 60.141 41.667 30.92 8.09 42.19 2.59
3326 3346 4.139038 TGAATCATGCATGACCATGGTAG 58.861 43.478 30.92 12.18 42.19 3.18
3327 3347 4.167652 TGAATCATGCATGACCATGGTA 57.832 40.909 30.92 7.24 42.19 3.25
3328 3348 3.021177 TGAATCATGCATGACCATGGT 57.979 42.857 30.92 19.89 42.19 3.55
3329 3349 3.798889 GCTTGAATCATGCATGACCATGG 60.799 47.826 30.92 22.95 42.19 3.66
3330 3350 3.181480 TGCTTGAATCATGCATGACCATG 60.181 43.478 30.92 27.74 39.10 3.66
3331 3351 3.028130 TGCTTGAATCATGCATGACCAT 58.972 40.909 30.92 19.71 39.10 3.55
3332 3352 2.448453 TGCTTGAATCATGCATGACCA 58.552 42.857 30.92 26.00 39.10 4.02
3333 3353 3.513680 TTGCTTGAATCATGCATGACC 57.486 42.857 30.92 23.91 42.47 4.02
3334 3354 7.709269 AAATATTGCTTGAATCATGCATGAC 57.291 32.000 30.92 19.52 42.47 3.06
3335 3355 7.592164 CGTAAATATTGCTTGAATCATGCATGA 59.408 33.333 30.47 30.47 42.47 3.07
3336 3356 7.148869 CCGTAAATATTGCTTGAATCATGCATG 60.149 37.037 21.69 21.07 42.47 4.06
3337 3357 6.864685 CCGTAAATATTGCTTGAATCATGCAT 59.135 34.615 21.69 14.74 42.47 3.96
3338 3358 6.183360 ACCGTAAATATTGCTTGAATCATGCA 60.183 34.615 18.10 18.10 41.54 3.96
3339 3359 6.142798 CACCGTAAATATTGCTTGAATCATGC 59.857 38.462 13.37 13.37 35.51 4.06
3340 3360 7.166307 CACACCGTAAATATTGCTTGAATCATG 59.834 37.037 0.00 0.00 0.00 3.07
3341 3361 7.066887 TCACACCGTAAATATTGCTTGAATCAT 59.933 33.333 0.00 0.00 0.00 2.45
3342 3362 6.372937 TCACACCGTAAATATTGCTTGAATCA 59.627 34.615 0.00 0.00 0.00 2.57
3343 3363 6.687105 GTCACACCGTAAATATTGCTTGAATC 59.313 38.462 0.00 0.00 0.00 2.52
3344 3364 6.374333 AGTCACACCGTAAATATTGCTTGAAT 59.626 34.615 0.00 0.00 0.00 2.57
3345 3365 5.703592 AGTCACACCGTAAATATTGCTTGAA 59.296 36.000 0.00 0.00 0.00 2.69
3346 3366 5.242434 AGTCACACCGTAAATATTGCTTGA 58.758 37.500 0.00 0.00 0.00 3.02
3347 3367 5.351465 AGAGTCACACCGTAAATATTGCTTG 59.649 40.000 0.00 0.00 0.00 4.01
3348 3368 5.488341 AGAGTCACACCGTAAATATTGCTT 58.512 37.500 0.00 0.00 0.00 3.91
3349 3369 5.086104 AGAGTCACACCGTAAATATTGCT 57.914 39.130 0.00 0.00 0.00 3.91
3350 3370 5.350365 TCAAGAGTCACACCGTAAATATTGC 59.650 40.000 0.00 0.00 0.00 3.56
3351 3371 6.590292 AGTCAAGAGTCACACCGTAAATATTG 59.410 38.462 0.00 0.00 0.00 1.90
3352 3372 6.698380 AGTCAAGAGTCACACCGTAAATATT 58.302 36.000 0.00 0.00 0.00 1.28
3353 3373 6.071560 TGAGTCAAGAGTCACACCGTAAATAT 60.072 38.462 3.54 0.00 35.96 1.28
3354 3374 5.242171 TGAGTCAAGAGTCACACCGTAAATA 59.758 40.000 3.54 0.00 35.96 1.40
3355 3375 4.038763 TGAGTCAAGAGTCACACCGTAAAT 59.961 41.667 3.54 0.00 35.96 1.40
3356 3376 3.382227 TGAGTCAAGAGTCACACCGTAAA 59.618 43.478 3.54 0.00 35.96 2.01
3357 3377 2.953648 TGAGTCAAGAGTCACACCGTAA 59.046 45.455 3.54 0.00 35.96 3.18
3358 3378 2.578786 TGAGTCAAGAGTCACACCGTA 58.421 47.619 3.54 0.00 35.96 4.02
3359 3379 1.399714 TGAGTCAAGAGTCACACCGT 58.600 50.000 3.54 0.00 35.96 4.83
3360 3380 2.029918 TCATGAGTCAAGAGTCACACCG 60.030 50.000 9.61 0.71 42.90 4.94
3361 3381 3.256879 TCTCATGAGTCAAGAGTCACACC 59.743 47.826 21.92 0.00 42.90 4.16
3362 3382 4.511617 TCTCATGAGTCAAGAGTCACAC 57.488 45.455 21.92 0.00 42.90 3.82
3363 3383 4.586421 ACTTCTCATGAGTCAAGAGTCACA 59.414 41.667 23.86 3.31 42.90 3.58
3364 3384 5.132897 ACTTCTCATGAGTCAAGAGTCAC 57.867 43.478 23.86 0.00 42.90 3.67
3365 3385 6.265422 TGTTACTTCTCATGAGTCAAGAGTCA 59.735 38.462 23.86 16.83 44.07 3.41
3366 3386 6.682746 TGTTACTTCTCATGAGTCAAGAGTC 58.317 40.000 23.86 15.21 32.04 3.36
3367 3387 6.656632 TGTTACTTCTCATGAGTCAAGAGT 57.343 37.500 23.86 19.72 32.04 3.24


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

AutoCloner maintained by Alex Coulton.