Multiple sequence alignment - TraesCS3D01G008400

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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 TraesCS3D01G008400 chr3D 100.000 3679 0 0 1 3679 2970414 2966736 0.000000e+00 6794.0
1 TraesCS3D01G008400 chr3D 94.118 221 13 0 3459 3679 5749798 5749578 1.640000e-88 337.0
2 TraesCS3D01G008400 chr3D 77.582 455 71 15 189 638 535509137 535508709 2.840000e-61 246.0
3 TraesCS3D01G008400 chr3D 83.088 136 13 5 3258 3391 2920750 2920877 8.350000e-22 115.0
4 TraesCS3D01G008400 chr3B 91.248 3108 168 34 236 3286 2877378 2880438 0.000000e+00 4137.0
5 TraesCS3D01G008400 chr3B 79.010 505 82 11 189 689 706832594 706832110 1.270000e-84 324.0
6 TraesCS3D01G008400 chr3B 87.083 240 22 6 1 239 2858621 2858852 2.820000e-66 263.0
7 TraesCS3D01G008400 chr3B 92.143 140 7 2 3322 3458 2880699 2880837 1.040000e-45 195.0
8 TraesCS3D01G008400 chr5B 87.383 1490 116 34 1543 3015 664503968 664502534 0.000000e+00 1644.0
9 TraesCS3D01G008400 chr5B 89.219 1076 84 16 1738 2794 664475504 664474442 0.000000e+00 1315.0
10 TraesCS3D01G008400 chr5B 88.992 1081 84 23 1738 2794 664417085 664416016 0.000000e+00 1304.0
11 TraesCS3D01G008400 chr5B 85.818 275 27 6 1001 1273 664475891 664475627 7.780000e-72 281.0
12 TraesCS3D01G008400 chr5B 85.455 275 28 6 1001 1273 664417472 664417208 3.620000e-70 276.0
13 TraesCS3D01G008400 chr5B 92.857 168 8 3 3089 3252 664502248 664502081 1.320000e-59 241.0
14 TraesCS3D01G008400 chr5B 88.785 107 8 4 2801 2905 664474402 664474298 1.070000e-25 128.0
15 TraesCS3D01G008400 chr5A 86.469 1419 129 32 1378 2775 655189702 655188326 0.000000e+00 1498.0
16 TraesCS3D01G008400 chr5A 86.399 1419 130 32 1378 2775 655225864 655224488 0.000000e+00 1493.0
17 TraesCS3D01G008400 chr5A 93.089 709 45 2 1737 2441 654851785 654851077 0.000000e+00 1035.0
18 TraesCS3D01G008400 chr5A 90.780 282 15 6 2530 2800 654851023 654850742 2.090000e-97 366.0
19 TraesCS3D01G008400 chr5A 81.088 386 63 9 192 575 608709576 608709199 2.150000e-77 300.0
20 TraesCS3D01G008400 chr5A 85.030 167 5 8 3086 3252 654849524 654849378 6.360000e-33 152.0
21 TraesCS3D01G008400 chr5A 89.831 118 10 2 2789 2905 655188270 655188154 2.290000e-32 150.0
22 TraesCS3D01G008400 chr5A 89.831 118 10 2 2789 2905 655224432 655224316 2.290000e-32 150.0
23 TraesCS3D01G008400 chr5A 97.297 37 1 0 18 54 3754782 3754818 3.070000e-06 63.9
24 TraesCS3D01G008400 chr7A 89.062 1024 86 19 1761 2764 459210155 459209138 0.000000e+00 1247.0
25 TraesCS3D01G008400 chr7A 88.889 63 7 0 2800 2862 459209063 459209001 1.100000e-10 78.7
26 TraesCS3D01G008400 chr7B 88.834 1021 99 10 1758 2769 411059996 411058982 0.000000e+00 1240.0
27 TraesCS3D01G008400 chr7B 81.061 396 62 8 189 575 144699928 144700319 1.660000e-78 303.0
28 TraesCS3D01G008400 chr7B 77.413 487 93 11 188 668 614064243 614063768 1.300000e-69 274.0
29 TraesCS3D01G008400 chr7B 83.582 67 7 3 2800 2862 411058913 411058847 3.970000e-05 60.2
30 TraesCS3D01G008400 chr7B 100.000 28 0 0 1694 1721 1440968 1440995 7.000000e-03 52.8
31 TraesCS3D01G008400 chr7D 88.625 1011 84 19 1763 2766 401550925 401549939 0.000000e+00 1201.0
32 TraesCS3D01G008400 chr7D 94.570 221 12 0 3459 3679 76527191 76526971 3.520000e-90 342.0
33 TraesCS3D01G008400 chr7D 93.665 221 14 0 3459 3679 10124485 10124705 7.620000e-87 331.0
34 TraesCS3D01G008400 chr7D 89.831 59 6 0 2800 2858 401549866 401549808 3.940000e-10 76.8
35 TraesCS3D01G008400 chr5D 89.597 769 59 14 2121 2885 527841873 527841122 0.000000e+00 957.0
36 TraesCS3D01G008400 chr5D 94.372 231 12 1 3449 3679 57376759 57376988 1.630000e-93 353.0
37 TraesCS3D01G008400 chr5D 94.570 221 12 0 3459 3679 543412484 543412704 3.520000e-90 342.0
38 TraesCS3D01G008400 chr5D 87.814 279 22 5 997 1273 527842916 527842648 2.130000e-82 316.0
39 TraesCS3D01G008400 chr6D 80.943 509 85 8 189 689 361545466 361544962 3.440000e-105 392.0
40 TraesCS3D01G008400 chr6D 94.570 221 12 0 3459 3679 439765269 439765049 3.520000e-90 342.0
41 TraesCS3D01G008400 chr2D 80.550 509 79 13 189 689 648260041 648259545 1.250000e-99 374.0
42 TraesCS3D01G008400 chr2D 93.304 224 15 0 3456 3679 1527459 1527682 7.620000e-87 331.0
43 TraesCS3D01G008400 chr2D 93.665 221 14 0 3459 3679 95273772 95273552 7.620000e-87 331.0
44 TraesCS3D01G008400 chrUn 95.475 221 10 0 3459 3679 96730837 96730617 1.630000e-93 353.0
45 TraesCS3D01G008400 chr1B 84.194 310 40 6 920 1220 628218490 628218799 3.590000e-75 292.0
46 TraesCS3D01G008400 chr1B 96.970 33 0 1 1694 1726 510799089 510799120 2.000000e-03 54.7
47 TraesCS3D01G008400 chr4A 78.756 386 75 7 210 594 73941341 73940962 6.100000e-63 252.0
48 TraesCS3D01G008400 chr2B 77.829 433 74 14 245 661 782573932 782573506 7.890000e-62 248.0
49 TraesCS3D01G008400 chr1D 82.721 272 40 6 188 457 247538208 247537942 6.140000e-58 235.0
50 TraesCS3D01G008400 chr6A 96.970 33 0 1 1694 1726 2752117 2752148 2.000000e-03 54.7


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 TraesCS3D01G008400 chr3D 2966736 2970414 3678 True 6794.000000 6794 100.000000 1 3679 1 chr3D.!!$R1 3678
1 TraesCS3D01G008400 chr3B 2877378 2880837 3459 False 2166.000000 4137 91.695500 236 3458 2 chr3B.!!$F2 3222
2 TraesCS3D01G008400 chr5B 664502081 664503968 1887 True 942.500000 1644 90.120000 1543 3252 2 chr5B.!!$R3 1709
3 TraesCS3D01G008400 chr5B 664416016 664417472 1456 True 790.000000 1304 87.223500 1001 2794 2 chr5B.!!$R1 1793
4 TraesCS3D01G008400 chr5B 664474298 664475891 1593 True 574.666667 1315 87.940667 1001 2905 3 chr5B.!!$R2 1904
5 TraesCS3D01G008400 chr5A 655188154 655189702 1548 True 824.000000 1498 88.150000 1378 2905 2 chr5A.!!$R3 1527
6 TraesCS3D01G008400 chr5A 655224316 655225864 1548 True 821.500000 1493 88.115000 1378 2905 2 chr5A.!!$R4 1527
7 TraesCS3D01G008400 chr5A 654849378 654851785 2407 True 517.666667 1035 89.633000 1737 3252 3 chr5A.!!$R2 1515
8 TraesCS3D01G008400 chr7A 459209001 459210155 1154 True 662.850000 1247 88.975500 1761 2862 2 chr7A.!!$R1 1101
9 TraesCS3D01G008400 chr7B 411058847 411059996 1149 True 650.100000 1240 86.208000 1758 2862 2 chr7B.!!$R2 1104
10 TraesCS3D01G008400 chr7D 401549808 401550925 1117 True 638.900000 1201 89.228000 1763 2858 2 chr7D.!!$R2 1095
11 TraesCS3D01G008400 chr5D 527841122 527842916 1794 True 636.500000 957 88.705500 997 2885 2 chr5D.!!$R1 1888
12 TraesCS3D01G008400 chr6D 361544962 361545466 504 True 392.000000 392 80.943000 189 689 1 chr6D.!!$R1 500

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
665 666 0.106149 GGACGGATGCGGGAGTAAAT 59.894 55.0 12.44 0.0 0.0 1.40 F
1230 1237 0.391130 GCAAGGTACACGCTCATGGA 60.391 55.0 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 2690 4.381292 GCCTCATTCTGACCAATCAAAAGG 60.381 45.833 0.0 0.0 33.30 3.11 R
3144 4476 1.066929 GTGCCCATGATTTGGTTGGAC 60.067 52.381 0.0 0.0 44.83 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.018609 CCTCATGGACGACGATGC 57.981 61.111 0.00 0.00 33.35 3.91
18 19 1.592669 CCTCATGGACGACGATGCC 60.593 63.158 0.00 0.12 33.35 4.40
19 20 1.946156 CTCATGGACGACGATGCCG 60.946 63.158 0.00 0.00 42.50 5.69
20 21 3.630148 CATGGACGACGATGCCGC 61.630 66.667 0.00 0.00 39.95 6.53
21 22 4.891727 ATGGACGACGATGCCGCC 62.892 66.667 0.00 0.00 39.95 6.13
24 25 3.849953 GACGACGATGCCGCCAAC 61.850 66.667 0.00 0.00 39.95 3.77
25 26 4.673298 ACGACGATGCCGCCAACA 62.673 61.111 0.00 0.00 39.95 3.33
26 27 4.147322 CGACGATGCCGCCAACAC 62.147 66.667 0.00 0.00 39.95 3.32
27 28 2.742372 GACGATGCCGCCAACACT 60.742 61.111 0.00 0.00 39.95 3.55
28 29 2.281484 ACGATGCCGCCAACACTT 60.281 55.556 0.00 0.00 39.95 3.16
29 30 2.176546 CGATGCCGCCAACACTTG 59.823 61.111 0.00 0.00 0.00 3.16
86 87 4.705482 GGGGGTAGCAATGCCATT 57.295 55.556 0.00 0.00 0.00 3.16
87 88 2.126951 GGGGGTAGCAATGCCATTG 58.873 57.895 13.11 13.11 43.06 2.82
88 89 0.396974 GGGGGTAGCAATGCCATTGA 60.397 55.000 21.24 0.00 42.83 2.57
89 90 1.484038 GGGGTAGCAATGCCATTGAA 58.516 50.000 21.24 5.26 42.83 2.69
90 91 1.410153 GGGGTAGCAATGCCATTGAAG 59.590 52.381 21.24 0.00 42.83 3.02
91 92 1.202452 GGGTAGCAATGCCATTGAAGC 60.202 52.381 21.24 15.65 42.83 3.86
92 93 1.477700 GGTAGCAATGCCATTGAAGCA 59.522 47.619 21.24 0.00 45.94 3.91
197 198 9.959721 ATGATTTATATATACCACTCCACCAAC 57.040 33.333 0.00 0.00 0.00 3.77
333 334 0.363512 CATCGAACAAGACTGACGCG 59.636 55.000 3.53 3.53 0.00 6.01
352 353 2.897207 CCCTTCGGCGTCATACCA 59.103 61.111 6.85 0.00 0.00 3.25
354 355 1.520787 CCTTCGGCGTCATACCACC 60.521 63.158 6.85 0.00 0.00 4.61
381 382 4.640855 ACCACGACGACGGCACAG 62.641 66.667 12.58 0.00 44.46 3.66
383 384 3.097728 CACGACGACGGCACAGAC 61.098 66.667 12.58 0.00 44.46 3.51
389 390 2.799916 GACGGCACAGACGACGAC 60.800 66.667 0.00 0.00 35.20 4.34
421 422 4.735132 GCAGAGCGGCCACGTGTA 62.735 66.667 15.65 0.00 43.45 2.90
453 454 6.351711 GTTGTCCGGTATAGGGTTTAGATTT 58.648 40.000 0.00 0.00 0.00 2.17
543 544 3.810386 TGAATGAATTCCGTCGTGTTTGA 59.190 39.130 2.27 0.00 35.97 2.69
585 586 8.726650 TGATTCGAATTGTTGTTGAAATGTAG 57.273 30.769 12.81 0.00 0.00 2.74
600 601 1.563924 TGTAGGCGGTCAGTATTGGT 58.436 50.000 0.00 0.00 0.00 3.67
602 603 3.098377 TGTAGGCGGTCAGTATTGGTTA 58.902 45.455 0.00 0.00 0.00 2.85
644 645 0.613260 CGGACTGGTCCCTTCATTCA 59.387 55.000 13.41 0.00 46.96 2.57
650 651 0.739813 GGTCCCTTCATTCACGGACG 60.740 60.000 0.00 0.00 44.80 4.79
665 666 0.106149 GGACGGATGCGGGAGTAAAT 59.894 55.000 12.44 0.00 0.00 1.40
669 670 2.285083 CGGATGCGGGAGTAAATTTGA 58.715 47.619 0.00 0.00 0.00 2.69
678 679 4.625324 CGGGAGTAAATTTGAGGATGACCA 60.625 45.833 0.00 0.00 38.94 4.02
679 680 5.449553 GGGAGTAAATTTGAGGATGACCAT 58.550 41.667 0.00 0.00 38.94 3.55
724 725 4.453480 AGGAAAATCCTTGGTGAACAGA 57.547 40.909 0.00 0.00 46.91 3.41
725 726 4.803452 AGGAAAATCCTTGGTGAACAGAA 58.197 39.130 0.00 0.00 46.91 3.02
726 727 4.829492 AGGAAAATCCTTGGTGAACAGAAG 59.171 41.667 0.00 0.00 46.91 2.85
727 728 4.827284 GGAAAATCCTTGGTGAACAGAAGA 59.173 41.667 0.00 0.00 32.53 2.87
728 729 5.301805 GGAAAATCCTTGGTGAACAGAAGAA 59.698 40.000 0.00 0.00 32.53 2.52
729 730 6.015095 GGAAAATCCTTGGTGAACAGAAGAAT 60.015 38.462 0.00 0.00 32.53 2.40
730 731 6.983906 AAATCCTTGGTGAACAGAAGAATT 57.016 33.333 0.00 0.00 0.00 2.17
735 736 6.043243 TCCTTGGTGAACAGAAGAATTACTCT 59.957 38.462 0.00 0.00 35.13 3.24
738 739 5.997746 TGGTGAACAGAAGAATTACTCTTGG 59.002 40.000 0.00 0.00 44.82 3.61
766 767 5.244626 CCATGATTATCCAATCCCTTGTTCC 59.755 44.000 0.00 0.00 39.97 3.62
768 769 3.680777 TTATCCAATCCCTTGTTCCCC 57.319 47.619 0.00 0.00 0.00 4.81
769 770 0.636647 ATCCAATCCCTTGTTCCCCC 59.363 55.000 0.00 0.00 0.00 5.40
833 834 8.084073 CGGATTGTAACCGGATTAGTATAAGAA 58.916 37.037 9.46 0.00 45.65 2.52
864 869 2.725203 TTCGGCCAAGTCAAGACCCG 62.725 60.000 2.24 8.66 34.96 5.28
916 922 2.632996 TCGACTCACAACTCCCAAATCT 59.367 45.455 0.00 0.00 0.00 2.40
919 925 3.999663 GACTCACAACTCCCAAATCTCAG 59.000 47.826 0.00 0.00 0.00 3.35
969 975 2.541762 CTCGATCGATTCTTTCCCTTGC 59.458 50.000 19.78 0.00 0.00 4.01
973 979 2.500229 TCGATTCTTTCCCTTGCGTTT 58.500 42.857 0.00 0.00 0.00 3.60
994 1001 1.659211 GCGTTCACGTTTGTTAGGCAG 60.659 52.381 0.62 0.00 42.22 4.85
1080 1087 2.025155 GTCTCCTTCGGTGAGATGCTA 58.975 52.381 3.42 0.00 40.73 3.49
1188 1195 3.612247 ATGCGCCGTCTCCAAGCTT 62.612 57.895 4.18 0.00 0.00 3.74
1224 1231 2.048503 GTCGGCAAGGTACACGCT 60.049 61.111 0.00 0.00 0.00 5.07
1227 1234 1.447838 CGGCAAGGTACACGCTCAT 60.448 57.895 0.00 0.00 0.00 2.90
1230 1237 0.391130 GCAAGGTACACGCTCATGGA 60.391 55.000 0.00 0.00 0.00 3.41
1246 1253 3.143728 CATGGATCAAGATCAATCGCCA 58.856 45.455 11.78 0.00 39.54 5.69
1343 1445 2.099098 CCGAAGGCTGTTGACTTGTTTT 59.901 45.455 0.00 0.00 46.14 2.43
1344 1446 3.428862 CCGAAGGCTGTTGACTTGTTTTT 60.429 43.478 0.00 0.00 46.14 1.94
1347 1449 4.799564 AGGCTGTTGACTTGTTTTTGAA 57.200 36.364 0.00 0.00 0.00 2.69
1349 1451 6.463995 AGGCTGTTGACTTGTTTTTGAATA 57.536 33.333 0.00 0.00 0.00 1.75
1351 1453 7.147976 AGGCTGTTGACTTGTTTTTGAATATC 58.852 34.615 0.00 0.00 0.00 1.63
1353 1455 6.398935 GCTGTTGACTTGTTTTTGAATATCGC 60.399 38.462 0.00 0.00 0.00 4.58
1355 1457 6.636447 TGTTGACTTGTTTTTGAATATCGCTG 59.364 34.615 0.00 0.00 0.00 5.18
1356 1458 6.552859 TGACTTGTTTTTGAATATCGCTGA 57.447 33.333 0.00 0.00 0.00 4.26
1358 1460 7.243487 TGACTTGTTTTTGAATATCGCTGATC 58.757 34.615 0.00 0.00 0.00 2.92
1359 1461 7.119699 TGACTTGTTTTTGAATATCGCTGATCT 59.880 33.333 0.00 0.00 0.00 2.75
1360 1462 7.246311 ACTTGTTTTTGAATATCGCTGATCTG 58.754 34.615 0.00 0.00 0.00 2.90
1361 1463 6.983474 TGTTTTTGAATATCGCTGATCTGA 57.017 33.333 3.42 0.00 0.00 3.27
1362 1464 7.558161 TGTTTTTGAATATCGCTGATCTGAT 57.442 32.000 3.42 2.68 0.00 2.90
1363 1465 7.988737 TGTTTTTGAATATCGCTGATCTGATT 58.011 30.769 3.42 0.00 0.00 2.57
1364 1466 8.461222 TGTTTTTGAATATCGCTGATCTGATTT 58.539 29.630 3.42 0.00 0.00 2.17
1365 1467 9.294030 GTTTTTGAATATCGCTGATCTGATTTT 57.706 29.630 3.42 1.92 0.00 1.82
1366 1468 8.845942 TTTTGAATATCGCTGATCTGATTTTG 57.154 30.769 3.42 0.00 0.00 2.44
1367 1469 6.549912 TGAATATCGCTGATCTGATTTTGG 57.450 37.500 3.42 0.00 0.00 3.28
1368 1470 6.290605 TGAATATCGCTGATCTGATTTTGGA 58.709 36.000 3.42 0.00 0.00 3.53
1369 1471 6.426025 TGAATATCGCTGATCTGATTTTGGAG 59.574 38.462 3.42 0.00 0.00 3.86
1370 1472 3.616956 TCGCTGATCTGATTTTGGAGT 57.383 42.857 3.42 0.00 0.00 3.85
1371 1473 4.736126 TCGCTGATCTGATTTTGGAGTA 57.264 40.909 3.42 0.00 0.00 2.59
1372 1474 4.433615 TCGCTGATCTGATTTTGGAGTAC 58.566 43.478 3.42 0.00 0.00 2.73
1373 1475 3.557595 CGCTGATCTGATTTTGGAGTACC 59.442 47.826 3.42 0.00 0.00 3.34
1462 1564 4.743057 AAGCCTCTGCAACTTTCTTTTT 57.257 36.364 0.00 0.00 41.13 1.94
1469 1571 6.036577 TCTGCAACTTTCTTTTTGGTCTTT 57.963 33.333 0.00 0.00 0.00 2.52
1541 1643 6.199908 GTCATCGATCAGTCCAAATCTAACAG 59.800 42.308 0.00 0.00 0.00 3.16
1575 1678 5.869649 AACACAAGAGGCAACCTTTTTAT 57.130 34.783 0.00 0.00 31.76 1.40
1615 1719 9.717942 AGGCTAATGCATTGTTTTTATTAACAA 57.282 25.926 22.27 4.61 42.29 2.83
1723 1830 7.052142 ACTCCCTCCGTAAAGAAATATACAG 57.948 40.000 0.00 0.00 0.00 2.74
1833 1956 1.522806 AAGCAGAACGGCGTGAACA 60.523 52.632 15.70 0.00 39.27 3.18
1854 1977 3.708220 GAGGGCTGCCTCTTCGACG 62.708 68.421 19.68 0.00 34.30 5.12
2457 2599 8.980596 TCTACGTAAGAAACTAATTAATCCCCA 58.019 33.333 0.00 0.00 43.62 4.96
2504 2655 6.095580 AGCTGATTGAATTCTAGTACGAGTGA 59.904 38.462 7.05 0.00 0.00 3.41
2528 2690 7.088589 AGTATGTTGCTAATGGTGATGTTTC 57.911 36.000 0.00 0.00 0.00 2.78
2782 2977 6.811253 TCGTGTGCCAGTCTTAATAAAAAT 57.189 33.333 0.00 0.00 0.00 1.82
2831 3066 3.073062 ACTGATTGTTGTAGCCTTCACCT 59.927 43.478 0.00 0.00 0.00 4.00
2832 3067 3.411446 TGATTGTTGTAGCCTTCACCTG 58.589 45.455 0.00 0.00 0.00 4.00
2833 3068 1.604604 TTGTTGTAGCCTTCACCTGC 58.395 50.000 0.00 0.00 0.00 4.85
2862 3855 2.636830 CGAGCCTTGAATGAATGGACT 58.363 47.619 0.00 0.00 0.00 3.85
3021 4231 6.580041 GCATCAGGCATGTTTTAATAAGATCG 59.420 38.462 0.00 0.00 43.97 3.69
3144 4476 8.790718 CAAATCCCATCTTATCATTCTACAAGG 58.209 37.037 0.00 0.00 0.00 3.61
3170 4502 0.179129 CAAATCATGGGCACGCCTTC 60.179 55.000 8.20 0.00 36.10 3.46
3306 4882 2.288729 TCAACGAGCTATTCATGCATGC 59.711 45.455 22.25 11.82 0.00 4.06
3307 4883 1.957668 ACGAGCTATTCATGCATGCA 58.042 45.000 25.04 25.04 0.00 3.96
3308 4884 1.871676 ACGAGCTATTCATGCATGCAG 59.128 47.619 26.69 17.32 0.00 4.41
3309 4885 1.197036 CGAGCTATTCATGCATGCAGG 59.803 52.381 25.78 25.78 0.00 4.85
3310 4886 1.540267 GAGCTATTCATGCATGCAGGG 59.460 52.381 30.00 21.82 0.00 4.45
3311 4887 1.144298 AGCTATTCATGCATGCAGGGA 59.856 47.619 30.00 24.19 0.00 4.20
3312 4888 1.958579 GCTATTCATGCATGCAGGGAA 59.041 47.619 30.00 29.36 0.00 3.97
3313 4889 2.363038 GCTATTCATGCATGCAGGGAAA 59.637 45.455 29.82 20.68 30.71 3.13
3314 4890 2.973694 ATTCATGCATGCAGGGAAAC 57.026 45.000 29.82 0.00 30.71 2.78
3315 4891 1.927487 TTCATGCATGCAGGGAAACT 58.073 45.000 30.00 7.22 0.00 2.66
3316 4892 1.466856 TCATGCATGCAGGGAAACTC 58.533 50.000 30.00 0.00 0.00 3.01
3317 4893 1.179152 CATGCATGCAGGGAAACTCA 58.821 50.000 26.69 0.00 0.00 3.41
3318 4894 1.135199 CATGCATGCAGGGAAACTCAC 60.135 52.381 26.69 0.00 0.00 3.51
3319 4895 1.236616 TGCATGCAGGGAAACTCACG 61.237 55.000 18.46 0.00 0.00 4.35
3320 4896 1.503542 CATGCAGGGAAACTCACGC 59.496 57.895 0.00 0.00 0.00 5.34
3349 4925 1.422402 GCCCGTATTCCCTTCCCATTA 59.578 52.381 0.00 0.00 0.00 1.90
3350 4926 2.158579 GCCCGTATTCCCTTCCCATTAA 60.159 50.000 0.00 0.00 0.00 1.40
3351 4927 3.688991 GCCCGTATTCCCTTCCCATTAAA 60.689 47.826 0.00 0.00 0.00 1.52
3353 4929 4.957327 CCCGTATTCCCTTCCCATTAAAAA 59.043 41.667 0.00 0.00 0.00 1.94
3399 4978 2.346766 CATGGGCCTAACTACATGCA 57.653 50.000 4.53 0.00 34.94 3.96
3426 5005 2.750237 GCGGGCCATCGGTTTCTT 60.750 61.111 4.39 0.00 0.00 2.52
3435 5014 3.485216 GCCATCGGTTTCTTATTCACACG 60.485 47.826 0.00 0.00 0.00 4.49
3448 5027 7.416817 TCTTATTCACACGGCATTCAAATATG 58.583 34.615 0.00 0.00 0.00 1.78
3467 5046 2.494445 CCGCGTGGCACTATCAGA 59.506 61.111 16.72 0.00 0.00 3.27
3468 5047 1.153647 CCGCGTGGCACTATCAGAA 60.154 57.895 16.72 0.00 0.00 3.02
3469 5048 0.530650 CCGCGTGGCACTATCAGAAT 60.531 55.000 16.72 0.00 0.00 2.40
3470 5049 1.269569 CCGCGTGGCACTATCAGAATA 60.270 52.381 16.72 0.00 0.00 1.75
3471 5050 2.469826 CGCGTGGCACTATCAGAATAA 58.530 47.619 16.72 0.00 0.00 1.40
3472 5051 3.059884 CGCGTGGCACTATCAGAATAAT 58.940 45.455 16.72 0.00 0.00 1.28
3473 5052 3.494626 CGCGTGGCACTATCAGAATAATT 59.505 43.478 16.72 0.00 0.00 1.40
3474 5053 4.609113 CGCGTGGCACTATCAGAATAATTG 60.609 45.833 16.72 0.00 0.00 2.32
3475 5054 4.776743 CGTGGCACTATCAGAATAATTGC 58.223 43.478 16.72 0.00 0.00 3.56
3476 5055 4.512944 CGTGGCACTATCAGAATAATTGCT 59.487 41.667 16.72 0.00 31.47 3.91
3477 5056 5.008019 CGTGGCACTATCAGAATAATTGCTT 59.992 40.000 16.72 0.00 31.47 3.91
3478 5057 6.204359 GTGGCACTATCAGAATAATTGCTTG 58.796 40.000 11.13 0.00 31.47 4.01
3479 5058 5.218139 GGCACTATCAGAATAATTGCTTGC 58.782 41.667 0.00 0.00 31.47 4.01
3480 5059 4.908156 GCACTATCAGAATAATTGCTTGCG 59.092 41.667 0.00 0.00 0.00 4.85
3481 5060 4.908156 CACTATCAGAATAATTGCTTGCGC 59.092 41.667 0.00 0.00 0.00 6.09
3482 5061 2.849880 TCAGAATAATTGCTTGCGCC 57.150 45.000 4.18 0.00 34.43 6.53
3483 5062 1.063912 TCAGAATAATTGCTTGCGCCG 59.936 47.619 4.18 0.00 34.43 6.46
3484 5063 1.063912 CAGAATAATTGCTTGCGCCGA 59.936 47.619 4.18 0.00 34.43 5.54
3485 5064 1.064060 AGAATAATTGCTTGCGCCGAC 59.936 47.619 4.18 0.00 34.43 4.79
3486 5065 0.248054 AATAATTGCTTGCGCCGACG 60.248 50.000 4.18 0.00 44.07 5.12
3487 5066 2.047151 ATAATTGCTTGCGCCGACGG 62.047 55.000 10.29 10.29 40.57 4.79
3497 5076 3.052081 GCCGACGGCCTCATCTAT 58.948 61.111 28.74 0.00 44.06 1.98
3498 5077 1.373497 GCCGACGGCCTCATCTATG 60.373 63.158 28.74 0.00 44.06 2.23
3499 5078 1.373497 CCGACGGCCTCATCTATGC 60.373 63.158 0.00 0.00 0.00 3.14
3500 5079 1.373497 CGACGGCCTCATCTATGCC 60.373 63.158 0.00 0.00 41.85 4.40
3503 5082 4.683432 GGCCTCATCTATGCCGAC 57.317 61.111 0.00 0.00 35.08 4.79
3504 5083 1.373497 GGCCTCATCTATGCCGACG 60.373 63.158 0.00 0.00 35.08 5.12
3505 5084 1.373497 GCCTCATCTATGCCGACGG 60.373 63.158 10.29 10.29 0.00 4.79
3520 5099 4.280494 CGGCCCCCGTCGACATAG 62.280 72.222 17.16 3.21 42.73 2.23
3521 5100 2.836360 GGCCCCCGTCGACATAGA 60.836 66.667 17.16 0.00 0.00 1.98
3522 5101 2.207924 GGCCCCCGTCGACATAGAT 61.208 63.158 17.16 0.00 0.00 1.98
3523 5102 1.006102 GCCCCCGTCGACATAGATG 60.006 63.158 17.16 0.00 0.00 2.90
3524 5103 1.666011 CCCCCGTCGACATAGATGG 59.334 63.158 17.16 7.15 44.79 3.51
3532 5111 3.670895 CGTCGACATAGATGGACCTATGC 60.671 52.174 17.16 4.06 46.09 3.14
3533 5112 2.826128 TCGACATAGATGGACCTATGCC 59.174 50.000 9.96 0.24 46.09 4.40
3534 5113 2.416027 CGACATAGATGGACCTATGCCG 60.416 54.545 9.96 7.73 46.09 5.69
3535 5114 2.826128 GACATAGATGGACCTATGCCGA 59.174 50.000 9.96 0.00 46.09 5.54
3536 5115 2.563179 ACATAGATGGACCTATGCCGAC 59.437 50.000 9.96 0.00 46.09 4.79
3537 5116 1.244816 TAGATGGACCTATGCCGACG 58.755 55.000 0.00 0.00 0.00 5.12
3538 5117 1.006102 GATGGACCTATGCCGACGG 60.006 63.158 10.29 10.29 0.00 4.79
3549 5128 4.760047 CCGACGGCCAAGGACAGG 62.760 72.222 2.24 0.00 0.00 4.00
3555 5134 4.567318 GCCAAGGACAGGCCATAG 57.433 61.111 5.01 0.00 46.50 2.23
3556 5135 1.152881 GCCAAGGACAGGCCATAGG 60.153 63.158 5.01 0.00 46.50 2.57
3586 5165 2.775911 CCATCGGCATACATCCATCT 57.224 50.000 0.00 0.00 0.00 2.90
3587 5166 3.893326 CCATCGGCATACATCCATCTA 57.107 47.619 0.00 0.00 0.00 1.98
3588 5167 4.412796 CCATCGGCATACATCCATCTAT 57.587 45.455 0.00 0.00 0.00 1.98
3589 5168 4.124970 CCATCGGCATACATCCATCTATG 58.875 47.826 0.00 0.00 0.00 2.23
3590 5169 3.251479 TCGGCATACATCCATCTATGC 57.749 47.619 1.72 1.72 43.07 3.14
3593 5172 3.251479 GCATACATCCATCTATGCCGA 57.749 47.619 0.00 0.00 39.51 5.54
3594 5173 2.932614 GCATACATCCATCTATGCCGAC 59.067 50.000 0.00 0.00 39.51 4.79
3595 5174 3.182182 CATACATCCATCTATGCCGACG 58.818 50.000 0.00 0.00 0.00 5.12
3596 5175 0.318441 ACATCCATCTATGCCGACGG 59.682 55.000 10.29 10.29 0.00 4.79
3597 5176 0.390340 CATCCATCTATGCCGACGGG 60.390 60.000 17.22 0.00 0.00 5.28
3598 5177 1.544825 ATCCATCTATGCCGACGGGG 61.545 60.000 17.22 6.38 39.58 5.73
3616 5195 4.343581 CCGTCGGCATAGACATGG 57.656 61.111 0.00 0.00 40.98 3.66
3622 5201 3.630204 GCATAGACATGGCCGTCG 58.370 61.111 0.00 0.00 40.98 5.12
3623 5202 1.956170 GCATAGACATGGCCGTCGG 60.956 63.158 6.99 6.99 40.98 4.79
3624 5203 1.300931 CATAGACATGGCCGTCGGG 60.301 63.158 14.38 0.00 40.98 5.14
3625 5204 1.456892 ATAGACATGGCCGTCGGGA 60.457 57.895 14.38 0.00 40.98 5.14
3626 5205 1.745320 ATAGACATGGCCGTCGGGAC 61.745 60.000 14.38 0.00 44.16 4.46
3627 5206 4.832608 GACATGGCCGTCGGGACC 62.833 72.222 14.38 7.22 42.67 4.46
3637 5216 3.923013 TCGGGACCGCTCGAAATA 58.077 55.556 5.75 0.00 45.56 1.40
3638 5217 2.422303 TCGGGACCGCTCGAAATAT 58.578 52.632 5.75 0.00 45.56 1.28
3639 5218 0.031585 TCGGGACCGCTCGAAATATG 59.968 55.000 5.75 0.00 45.56 1.78
3640 5219 1.557443 CGGGACCGCTCGAAATATGC 61.557 60.000 0.00 0.00 41.67 3.14
3641 5220 1.228657 GGGACCGCTCGAAATATGCC 61.229 60.000 0.00 0.00 0.00 4.40
3642 5221 0.249911 GGACCGCTCGAAATATGCCT 60.250 55.000 0.00 0.00 0.00 4.75
3643 5222 1.000506 GGACCGCTCGAAATATGCCTA 59.999 52.381 0.00 0.00 0.00 3.93
3644 5223 2.353803 GGACCGCTCGAAATATGCCTAT 60.354 50.000 0.00 0.00 0.00 2.57
3645 5224 2.668457 GACCGCTCGAAATATGCCTATG 59.332 50.000 0.00 0.00 0.00 2.23
3646 5225 2.002586 CCGCTCGAAATATGCCTATGG 58.997 52.381 0.00 0.00 0.00 2.74
3647 5226 2.002586 CGCTCGAAATATGCCTATGGG 58.997 52.381 0.00 0.00 0.00 4.00
3648 5227 2.359900 GCTCGAAATATGCCTATGGGG 58.640 52.381 0.00 0.00 38.36 4.96
3649 5228 2.027192 GCTCGAAATATGCCTATGGGGA 60.027 50.000 0.00 0.00 37.23 4.81
3650 5229 3.600388 CTCGAAATATGCCTATGGGGAC 58.400 50.000 0.00 0.00 35.25 4.46
3663 5242 1.153229 GGGGACCGTTGACATAGGC 60.153 63.158 0.00 0.00 40.86 3.93
3664 5243 1.520787 GGGACCGTTGACATAGGCG 60.521 63.158 0.00 0.00 0.00 5.52
3665 5244 2.171725 GGACCGTTGACATAGGCGC 61.172 63.158 0.00 0.00 0.00 6.53
3666 5245 2.508439 ACCGTTGACATAGGCGCG 60.508 61.111 0.00 0.00 0.00 6.86
3667 5246 3.261951 CCGTTGACATAGGCGCGG 61.262 66.667 8.83 0.00 0.00 6.46
3668 5247 3.925238 CGTTGACATAGGCGCGGC 61.925 66.667 27.06 27.06 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.592669 GGCATCGTCGTCCATGAGG 60.593 63.158 0.00 0.00 0.00 3.86
1 2 1.946156 CGGCATCGTCGTCCATGAG 60.946 63.158 0.00 0.00 0.00 2.90
3 4 3.630148 GCGGCATCGTCGTCCATG 61.630 66.667 0.00 0.00 38.89 3.66
4 5 4.891727 GGCGGCATCGTCGTCCAT 62.892 66.667 3.07 0.00 38.89 3.41
7 8 3.849953 GTTGGCGGCATCGTCGTC 61.850 66.667 14.32 0.00 45.11 4.20
8 9 4.673298 TGTTGGCGGCATCGTCGT 62.673 61.111 14.32 0.00 45.11 4.34
9 10 4.147322 GTGTTGGCGGCATCGTCG 62.147 66.667 14.32 0.00 45.11 5.12
10 11 2.325082 AAGTGTTGGCGGCATCGTC 61.325 57.895 14.32 9.51 42.06 4.20
11 12 2.281484 AAGTGTTGGCGGCATCGT 60.281 55.556 14.32 0.17 38.89 3.73
12 13 2.176546 CAAGTGTTGGCGGCATCG 59.823 61.111 14.32 0.00 39.81 3.84
13 14 2.568090 CCAAGTGTTGGCGGCATC 59.432 61.111 14.32 13.42 45.17 3.91
69 70 0.396974 TCAATGGCATTGCTACCCCC 60.397 55.000 30.62 0.00 40.05 5.40
70 71 1.410153 CTTCAATGGCATTGCTACCCC 59.590 52.381 30.62 0.00 40.05 4.95
71 72 1.202452 GCTTCAATGGCATTGCTACCC 60.202 52.381 30.62 15.16 40.05 3.69
72 73 1.477700 TGCTTCAATGGCATTGCTACC 59.522 47.619 30.62 19.44 40.05 3.18
73 74 2.945447 TGCTTCAATGGCATTGCTAC 57.055 45.000 30.62 21.95 40.05 3.58
171 172 9.959721 GTTGGTGGAGTGGTATATATAAATCAT 57.040 33.333 0.00 0.00 0.00 2.45
172 173 8.092068 CGTTGGTGGAGTGGTATATATAAATCA 58.908 37.037 0.00 0.00 0.00 2.57
173 174 7.064253 GCGTTGGTGGAGTGGTATATATAAATC 59.936 40.741 0.00 0.00 0.00 2.17
174 175 6.877322 GCGTTGGTGGAGTGGTATATATAAAT 59.123 38.462 0.00 0.00 0.00 1.40
175 176 6.225318 GCGTTGGTGGAGTGGTATATATAAA 58.775 40.000 0.00 0.00 0.00 1.40
176 177 5.279607 GGCGTTGGTGGAGTGGTATATATAA 60.280 44.000 0.00 0.00 0.00 0.98
177 178 4.221262 GGCGTTGGTGGAGTGGTATATATA 59.779 45.833 0.00 0.00 0.00 0.86
178 179 3.007614 GGCGTTGGTGGAGTGGTATATAT 59.992 47.826 0.00 0.00 0.00 0.86
179 180 2.366266 GGCGTTGGTGGAGTGGTATATA 59.634 50.000 0.00 0.00 0.00 0.86
180 181 1.140252 GGCGTTGGTGGAGTGGTATAT 59.860 52.381 0.00 0.00 0.00 0.86
181 182 0.538118 GGCGTTGGTGGAGTGGTATA 59.462 55.000 0.00 0.00 0.00 1.47
182 183 1.298667 GGCGTTGGTGGAGTGGTAT 59.701 57.895 0.00 0.00 0.00 2.73
183 184 2.745037 GGCGTTGGTGGAGTGGTA 59.255 61.111 0.00 0.00 0.00 3.25
184 185 4.619227 CGGCGTTGGTGGAGTGGT 62.619 66.667 0.00 0.00 0.00 4.16
219 220 1.612442 TAGCCTTCGAAGCCCTGGT 60.612 57.895 19.99 13.46 0.00 4.00
228 229 3.047718 CTGCCGACGTAGCCTTCGA 62.048 63.158 7.52 0.00 37.43 3.71
312 313 1.935300 GCGTCAGTCTTGTTCGATGGT 60.935 52.381 0.00 0.00 0.00 3.55
313 314 0.716108 GCGTCAGTCTTGTTCGATGG 59.284 55.000 0.00 0.00 0.00 3.51
315 316 0.732880 CCGCGTCAGTCTTGTTCGAT 60.733 55.000 4.92 0.00 0.00 3.59
316 317 1.371267 CCGCGTCAGTCTTGTTCGA 60.371 57.895 4.92 0.00 0.00 3.71
318 319 2.668280 GGCCGCGTCAGTCTTGTTC 61.668 63.158 4.92 0.00 0.00 3.18
344 345 0.462047 CCCTTCAGCGGTGGTATGAC 60.462 60.000 15.67 0.00 0.00 3.06
352 353 4.003788 CGTGGTCCCTTCAGCGGT 62.004 66.667 0.00 0.00 0.00 5.68
354 355 2.432628 GTCGTGGTCCCTTCAGCG 60.433 66.667 0.00 0.00 0.00 5.18
408 409 4.415332 CTCGTACACGTGGCCGCT 62.415 66.667 21.57 0.00 40.80 5.52
418 419 1.661480 CGGACAACCACCTCGTACA 59.339 57.895 0.00 0.00 35.59 2.90
420 421 0.251121 TACCGGACAACCACCTCGTA 60.251 55.000 9.46 0.00 35.59 3.43
421 422 0.901580 ATACCGGACAACCACCTCGT 60.902 55.000 9.46 0.00 35.59 4.18
429 430 5.541953 ATCTAAACCCTATACCGGACAAC 57.458 43.478 9.46 0.00 0.00 3.32
585 586 1.283736 CGTAACCAATACTGACCGCC 58.716 55.000 0.00 0.00 31.96 6.13
600 601 3.857038 GGATGCGGGAGGCCGTAA 61.857 66.667 0.00 0.00 42.61 3.18
616 617 4.082523 ACCAGTCCGCGGACATGG 62.083 66.667 42.86 42.86 46.76 3.66
638 639 1.518352 CGCATCCGTCCGTGAATGA 60.518 57.895 0.00 0.00 0.00 2.57
650 651 2.618709 CCTCAAATTTACTCCCGCATCC 59.381 50.000 0.00 0.00 0.00 3.51
665 666 4.529897 CATCTCCAATGGTCATCCTCAAA 58.470 43.478 0.00 0.00 34.23 2.69
669 670 2.133520 AGCATCTCCAATGGTCATCCT 58.866 47.619 0.00 0.00 34.23 3.24
679 680 9.778741 CCTTAAGTACATAATAAGCATCTCCAA 57.221 33.333 0.97 0.00 0.00 3.53
704 705 4.827284 TCTTCTGTTCACCAAGGATTTTCC 59.173 41.667 0.00 0.00 36.58 3.13
725 726 4.922206 TCATGGCAACCAAGAGTAATTCT 58.078 39.130 0.00 0.00 36.95 2.40
726 727 5.841957 ATCATGGCAACCAAGAGTAATTC 57.158 39.130 0.00 0.00 34.67 2.17
727 728 7.014615 GGATAATCATGGCAACCAAGAGTAATT 59.985 37.037 3.54 0.00 35.88 1.40
728 729 6.491403 GGATAATCATGGCAACCAAGAGTAAT 59.509 38.462 3.54 0.00 35.88 1.89
729 730 5.827797 GGATAATCATGGCAACCAAGAGTAA 59.172 40.000 3.54 0.00 35.88 2.24
730 731 5.104151 TGGATAATCATGGCAACCAAGAGTA 60.104 40.000 2.07 2.07 36.50 2.59
735 736 4.344679 GGATTGGATAATCATGGCAACCAA 59.655 41.667 0.00 0.00 43.62 3.67
738 739 4.154942 AGGGATTGGATAATCATGGCAAC 58.845 43.478 0.00 0.00 43.62 4.17
776 777 3.178865 TCGGGTTTGGATAACTCCTCTT 58.821 45.455 0.00 0.00 42.59 2.85
916 922 1.148273 GTGCTGTTGGGTGGACTGA 59.852 57.895 0.00 0.00 0.00 3.41
919 925 0.328258 ATAGGTGCTGTTGGGTGGAC 59.672 55.000 0.00 0.00 0.00 4.02
969 975 1.252235 AACAAACGTGAACGCAAACG 58.748 45.000 2.11 3.18 44.43 3.60
973 979 0.305313 GCCTAACAAACGTGAACGCA 59.695 50.000 2.11 0.00 44.43 5.24
979 985 1.944024 TGAACCTGCCTAACAAACGTG 59.056 47.619 0.00 0.00 0.00 4.49
980 986 2.335316 TGAACCTGCCTAACAAACGT 57.665 45.000 0.00 0.00 0.00 3.99
994 1001 2.464459 CGAGAGGCGCCATTGAACC 61.464 63.158 31.54 8.98 0.00 3.62
1155 1162 2.736995 CATGCGACGTTGACGGGT 60.737 61.111 7.08 0.00 44.95 5.28
1224 1231 3.181452 TGGCGATTGATCTTGATCCATGA 60.181 43.478 7.99 0.00 0.00 3.07
1227 1234 3.405831 GATGGCGATTGATCTTGATCCA 58.594 45.455 7.99 0.00 0.00 3.41
1230 1237 2.374504 AGGGATGGCGATTGATCTTGAT 59.625 45.455 0.00 0.00 0.00 2.57
1246 1253 7.463618 AGGGAGAATCATTATGTTATCAGGGAT 59.536 37.037 0.00 0.00 36.25 3.85
1283 1317 3.055675 CCTACCAAACACCGGATCTAACA 60.056 47.826 9.46 0.00 0.00 2.41
1343 1445 6.767423 TCCAAAATCAGATCAGCGATATTCAA 59.233 34.615 0.00 0.00 0.00 2.69
1344 1446 6.290605 TCCAAAATCAGATCAGCGATATTCA 58.709 36.000 0.00 0.00 0.00 2.57
1347 1449 5.862845 ACTCCAAAATCAGATCAGCGATAT 58.137 37.500 0.00 0.00 0.00 1.63
1349 1451 4.148128 ACTCCAAAATCAGATCAGCGAT 57.852 40.909 0.00 0.00 0.00 4.58
1351 1453 3.557595 GGTACTCCAAAATCAGATCAGCG 59.442 47.826 0.00 0.00 0.00 5.18
1353 1455 8.970859 AATAAGGTACTCCAAAATCAGATCAG 57.029 34.615 0.00 0.00 38.49 2.90
1358 1460 9.262358 GCTACTAATAAGGTACTCCAAAATCAG 57.738 37.037 0.00 0.00 38.49 2.90
1359 1461 7.924412 CGCTACTAATAAGGTACTCCAAAATCA 59.076 37.037 0.00 0.00 38.49 2.57
1360 1462 7.924947 ACGCTACTAATAAGGTACTCCAAAATC 59.075 37.037 0.00 0.00 38.49 2.17
1361 1463 7.789026 ACGCTACTAATAAGGTACTCCAAAAT 58.211 34.615 0.00 0.00 38.49 1.82
1362 1464 7.093814 TGACGCTACTAATAAGGTACTCCAAAA 60.094 37.037 0.00 0.00 38.49 2.44
1363 1465 6.377996 TGACGCTACTAATAAGGTACTCCAAA 59.622 38.462 0.00 0.00 38.49 3.28
1364 1466 5.887598 TGACGCTACTAATAAGGTACTCCAA 59.112 40.000 0.00 0.00 38.49 3.53
1365 1467 5.439721 TGACGCTACTAATAAGGTACTCCA 58.560 41.667 0.00 0.00 38.49 3.86
1366 1468 6.572167 ATGACGCTACTAATAAGGTACTCC 57.428 41.667 0.00 0.00 38.49 3.85
1367 1469 8.115520 CGATATGACGCTACTAATAAGGTACTC 58.884 40.741 0.00 0.00 38.49 2.59
1401 1503 9.330063 TCCAATGATATAACTGAGTGATGAAAC 57.670 33.333 0.00 0.00 0.00 2.78
1462 1564 9.132923 AGACTACGAGATTATATTCAAAGACCA 57.867 33.333 0.00 0.00 0.00 4.02
1541 1643 4.870991 GCCTCTTGTGTTAGAGTGGATTAC 59.129 45.833 0.00 0.00 40.04 1.89
1615 1719 9.070179 TGCACTGCTCATATGAATATAAACAAT 57.930 29.630 6.90 0.00 0.00 2.71
1723 1830 7.681939 TTACAATTTCATGTGTTACTCCCTC 57.318 36.000 0.00 0.00 34.75 4.30
2504 2655 6.095440 GGAAACATCACCATTAGCAACATACT 59.905 38.462 0.00 0.00 0.00 2.12
2528 2690 4.381292 GCCTCATTCTGACCAATCAAAAGG 60.381 45.833 0.00 0.00 33.30 3.11
2782 2977 6.936900 GCCTCCTTAATTATACAGATGCTTGA 59.063 38.462 0.00 0.00 0.00 3.02
2831 3066 2.997980 TCAAGGCTCGGATAAATTGCA 58.002 42.857 0.00 0.00 0.00 4.08
2832 3067 4.036734 TCATTCAAGGCTCGGATAAATTGC 59.963 41.667 0.00 0.00 0.00 3.56
2833 3068 5.756195 TCATTCAAGGCTCGGATAAATTG 57.244 39.130 0.00 0.00 0.00 2.32
2862 3855 8.030106 ACTGTATTTTTCTTTTTCCGAACACAA 58.970 29.630 0.00 0.00 0.00 3.33
3021 4231 5.648330 ACTCCCTCCTTCCCATAAAATAC 57.352 43.478 0.00 0.00 0.00 1.89
3144 4476 1.066929 GTGCCCATGATTTGGTTGGAC 60.067 52.381 0.00 0.00 44.83 4.02
3170 4502 3.432592 TGCAAAATCATTTCATTGGTGCG 59.567 39.130 0.00 0.00 33.32 5.34
3257 4594 5.008712 GGAAGCGAAAGATCCGGAAATTAAT 59.991 40.000 9.01 0.00 0.00 1.40
3306 4882 0.249868 TGACTGCGTGAGTTTCCCTG 60.250 55.000 0.00 0.00 33.83 4.45
3307 4883 0.249911 GTGACTGCGTGAGTTTCCCT 60.250 55.000 0.00 0.00 33.83 4.20
3308 4884 1.557443 CGTGACTGCGTGAGTTTCCC 61.557 60.000 0.00 0.00 33.83 3.97
3309 4885 1.853319 CGTGACTGCGTGAGTTTCC 59.147 57.895 0.00 0.00 33.83 3.13
3310 4886 1.201825 GCGTGACTGCGTGAGTTTC 59.798 57.895 0.00 0.00 33.83 2.78
3311 4887 3.319904 GCGTGACTGCGTGAGTTT 58.680 55.556 0.00 0.00 33.83 2.66
3320 4896 2.508439 AATACGGGCGCGTGACTG 60.508 61.111 35.44 9.69 34.70 3.51
3354 4930 3.652274 CACGATTGGCTGGTTCATTTTT 58.348 40.909 0.00 0.00 0.00 1.94
3426 5005 5.507149 GCCATATTTGAATGCCGTGTGAATA 60.507 40.000 0.00 0.00 0.00 1.75
3435 5014 0.664166 CGCGGCCATATTTGAATGCC 60.664 55.000 2.24 0.00 0.00 4.40
3481 5060 1.373497 GCATAGATGAGGCCGTCGG 60.373 63.158 6.99 6.99 33.59 4.79
3482 5061 1.373497 GGCATAGATGAGGCCGTCG 60.373 63.158 0.00 0.00 46.91 5.12
3483 5062 4.683432 GGCATAGATGAGGCCGTC 57.317 61.111 0.00 0.00 46.91 4.79
3487 5066 1.373497 CCGTCGGCATAGATGAGGC 60.373 63.158 0.00 0.00 0.00 4.70
3488 5067 4.974792 CCGTCGGCATAGATGAGG 57.025 61.111 0.00 0.00 0.00 3.86
3504 5083 2.207924 ATCTATGTCGACGGGGGCC 61.208 63.158 11.62 0.00 0.00 5.80
3505 5084 1.006102 CATCTATGTCGACGGGGGC 60.006 63.158 11.62 0.00 0.00 5.80
3506 5085 0.826256 TCCATCTATGTCGACGGGGG 60.826 60.000 11.62 6.62 0.00 5.40
3507 5086 0.314302 GTCCATCTATGTCGACGGGG 59.686 60.000 11.62 5.91 0.00 5.73
3508 5087 0.314302 GGTCCATCTATGTCGACGGG 59.686 60.000 11.62 5.55 0.00 5.28
3509 5088 1.319541 AGGTCCATCTATGTCGACGG 58.680 55.000 11.62 4.77 0.00 4.79
3510 5089 3.670895 GCATAGGTCCATCTATGTCGACG 60.671 52.174 11.62 0.00 45.01 5.12
3511 5090 3.367498 GGCATAGGTCCATCTATGTCGAC 60.367 52.174 9.11 9.11 45.01 4.20
3512 5091 2.826128 GGCATAGGTCCATCTATGTCGA 59.174 50.000 8.36 0.00 45.01 4.20
3513 5092 3.238108 GGCATAGGTCCATCTATGTCG 57.762 52.381 8.36 0.00 45.01 4.35
3514 5093 2.826128 TCGGCATAGGTCCATCTATGTC 59.174 50.000 8.36 5.25 45.01 3.06
3515 5094 2.563179 GTCGGCATAGGTCCATCTATGT 59.437 50.000 8.36 0.00 45.01 2.29
3516 5095 2.416027 CGTCGGCATAGGTCCATCTATG 60.416 54.545 2.84 2.84 45.62 2.23
3517 5096 1.819288 CGTCGGCATAGGTCCATCTAT 59.181 52.381 0.00 0.00 0.00 1.98
3518 5097 1.244816 CGTCGGCATAGGTCCATCTA 58.755 55.000 0.00 0.00 0.00 1.98
3519 5098 1.464376 CCGTCGGCATAGGTCCATCT 61.464 60.000 0.00 0.00 0.00 2.90
3520 5099 1.006102 CCGTCGGCATAGGTCCATC 60.006 63.158 0.00 0.00 0.00 3.51
3521 5100 3.138625 CCGTCGGCATAGGTCCAT 58.861 61.111 0.00 0.00 0.00 3.41
3532 5111 4.760047 CCTGTCCTTGGCCGTCGG 62.760 72.222 6.99 6.99 0.00 4.79
3539 5118 1.152881 GCCTATGGCCTGTCCTTGG 60.153 63.158 3.32 0.00 44.06 3.61
3540 5119 4.567318 GCCTATGGCCTGTCCTTG 57.433 61.111 3.32 0.00 44.06 3.61
3549 5128 0.945099 GGCTTTTCTACGCCTATGGC 59.055 55.000 0.00 0.00 46.75 4.40
3550 5129 2.325583 TGGCTTTTCTACGCCTATGG 57.674 50.000 0.00 0.00 46.42 2.74
3551 5130 2.476619 CGATGGCTTTTCTACGCCTATG 59.523 50.000 0.00 0.00 46.42 2.23
3552 5131 2.548067 CCGATGGCTTTTCTACGCCTAT 60.548 50.000 0.00 0.00 46.42 2.57
3553 5132 1.202486 CCGATGGCTTTTCTACGCCTA 60.202 52.381 0.00 0.00 46.42 3.93
3554 5133 0.462047 CCGATGGCTTTTCTACGCCT 60.462 55.000 0.00 0.00 46.42 5.52
3555 5134 2.014594 CCGATGGCTTTTCTACGCC 58.985 57.895 0.00 0.00 46.46 5.68
3556 5135 1.352056 GCCGATGGCTTTTCTACGC 59.648 57.895 0.00 0.00 46.69 4.42
3567 5146 2.775911 AGATGGATGTATGCCGATGG 57.224 50.000 0.00 0.00 0.00 3.51
3574 5153 3.182182 CGTCGGCATAGATGGATGTATG 58.818 50.000 0.45 0.45 37.17 2.39
3575 5154 3.510388 CGTCGGCATAGATGGATGTAT 57.490 47.619 0.00 0.00 0.00 2.29
3577 5156 3.894257 CGTCGGCATAGATGGATGT 57.106 52.632 0.00 0.00 0.00 3.06
3581 5160 2.343758 CCCCGTCGGCATAGATGG 59.656 66.667 5.50 7.19 44.79 3.51
3599 5178 1.956170 GCCATGTCTATGCCGACGG 60.956 63.158 10.29 10.29 36.71 4.79
3600 5179 1.956170 GGCCATGTCTATGCCGACG 60.956 63.158 0.00 0.00 36.71 5.12
3601 5180 1.956170 CGGCCATGTCTATGCCGAC 60.956 63.158 22.95 0.00 46.98 4.79
3602 5181 2.363711 GACGGCCATGTCTATGCCGA 62.364 60.000 30.65 0.00 46.98 5.54
3604 5183 1.956170 CGACGGCCATGTCTATGCC 60.956 63.158 2.24 0.17 36.71 4.40
3605 5184 1.956170 CCGACGGCCATGTCTATGC 60.956 63.158 2.24 0.00 36.71 3.14
3606 5185 1.300931 CCCGACGGCCATGTCTATG 60.301 63.158 8.86 0.00 36.71 2.23
3607 5186 1.456892 TCCCGACGGCCATGTCTAT 60.457 57.895 8.86 0.00 36.71 1.98
3608 5187 2.043752 TCCCGACGGCCATGTCTA 60.044 61.111 8.86 0.00 36.71 2.59
3609 5188 3.771160 GTCCCGACGGCCATGTCT 61.771 66.667 8.86 0.00 36.71 3.41
3610 5189 4.832608 GGTCCCGACGGCCATGTC 62.833 72.222 8.86 1.44 35.49 3.06
3618 5197 2.327002 TATTTCGAGCGGTCCCGACG 62.327 60.000 10.46 13.68 42.83 5.12
3619 5198 0.031721 ATATTTCGAGCGGTCCCGAC 59.968 55.000 10.46 0.89 42.83 4.79
3620 5199 0.031585 CATATTTCGAGCGGTCCCGA 59.968 55.000 10.46 1.08 42.83 5.14
3621 5200 1.557443 GCATATTTCGAGCGGTCCCG 61.557 60.000 9.39 0.24 43.09 5.14
3622 5201 1.228657 GGCATATTTCGAGCGGTCCC 61.229 60.000 9.39 0.00 0.00 4.46
3623 5202 0.249911 AGGCATATTTCGAGCGGTCC 60.250 55.000 9.39 0.00 0.00 4.46
3624 5203 2.433868 TAGGCATATTTCGAGCGGTC 57.566 50.000 4.06 4.06 0.00 4.79
3625 5204 2.612972 CCATAGGCATATTTCGAGCGGT 60.613 50.000 0.00 0.00 0.00 5.68
3626 5205 2.002586 CCATAGGCATATTTCGAGCGG 58.997 52.381 0.00 0.00 0.00 5.52
3627 5206 2.002586 CCCATAGGCATATTTCGAGCG 58.997 52.381 0.00 0.00 0.00 5.03
3628 5207 2.027192 TCCCCATAGGCATATTTCGAGC 60.027 50.000 0.00 0.00 34.51 5.03
3629 5208 3.600388 GTCCCCATAGGCATATTTCGAG 58.400 50.000 0.00 0.00 34.51 4.04
3630 5209 2.304761 GGTCCCCATAGGCATATTTCGA 59.695 50.000 0.00 0.00 34.51 3.71
3631 5210 2.711542 GGTCCCCATAGGCATATTTCG 58.288 52.381 0.00 0.00 34.51 3.46
3632 5211 2.039879 ACGGTCCCCATAGGCATATTTC 59.960 50.000 0.00 0.00 34.51 2.17
3633 5212 2.062636 ACGGTCCCCATAGGCATATTT 58.937 47.619 0.00 0.00 34.51 1.40
3634 5213 1.742308 ACGGTCCCCATAGGCATATT 58.258 50.000 0.00 0.00 34.51 1.28
3635 5214 1.351017 CAACGGTCCCCATAGGCATAT 59.649 52.381 0.00 0.00 34.51 1.78
3636 5215 0.762418 CAACGGTCCCCATAGGCATA 59.238 55.000 0.00 0.00 34.51 3.14
3637 5216 0.986019 TCAACGGTCCCCATAGGCAT 60.986 55.000 0.00 0.00 34.51 4.40
3638 5217 1.613928 TCAACGGTCCCCATAGGCA 60.614 57.895 0.00 0.00 34.51 4.75
3639 5218 1.153229 GTCAACGGTCCCCATAGGC 60.153 63.158 0.00 0.00 34.51 3.93
3640 5219 0.837272 ATGTCAACGGTCCCCATAGG 59.163 55.000 0.00 0.00 0.00 2.57
3641 5220 2.037251 CCTATGTCAACGGTCCCCATAG 59.963 54.545 11.15 11.15 36.39 2.23
3642 5221 2.043992 CCTATGTCAACGGTCCCCATA 58.956 52.381 0.00 0.00 0.00 2.74
3643 5222 0.837272 CCTATGTCAACGGTCCCCAT 59.163 55.000 0.00 0.00 0.00 4.00
3644 5223 1.906105 GCCTATGTCAACGGTCCCCA 61.906 60.000 0.00 0.00 0.00 4.96
3645 5224 1.153229 GCCTATGTCAACGGTCCCC 60.153 63.158 0.00 0.00 0.00 4.81
3646 5225 1.520787 CGCCTATGTCAACGGTCCC 60.521 63.158 0.00 0.00 0.00 4.46
3647 5226 2.171725 GCGCCTATGTCAACGGTCC 61.172 63.158 0.00 0.00 0.00 4.46
3648 5227 2.514013 CGCGCCTATGTCAACGGTC 61.514 63.158 0.00 0.00 0.00 4.79
3649 5228 2.508439 CGCGCCTATGTCAACGGT 60.508 61.111 0.00 0.00 0.00 4.83
3650 5229 3.261951 CCGCGCCTATGTCAACGG 61.262 66.667 0.00 0.00 0.00 4.44
3651 5230 3.925238 GCCGCGCCTATGTCAACG 61.925 66.667 0.00 0.00 0.00 4.10
3652 5231 3.573491 GGCCGCGCCTATGTCAAC 61.573 66.667 0.00 0.00 46.69 3.18


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

AutoCloner maintained by Alex Coulton.