Multiple sequence alignment - TraesCS3A01G465400

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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 TraesCS3A01G465400 chr3A 100.000 5679 0 0 1 5679 699757783 699752105 0.000000e+00 10488.0
1 TraesCS3A01G465400 chr3A 87.859 2125 153 40 2865 4969 699767496 699765457 0.000000e+00 2398.0
2 TraesCS3A01G465400 chr3A 85.887 1155 110 24 842 1982 699769907 699768792 0.000000e+00 1181.0
3 TraesCS3A01G465400 chr3A 89.155 793 67 13 2087 2867 699768481 699767696 0.000000e+00 970.0
4 TraesCS3A01G465400 chr3A 81.275 251 28 7 5170 5416 698856084 698856319 9.720000e-43 185.0
5 TraesCS3A01G465400 chr3A 81.385 231 32 6 4544 4772 698762314 698762535 1.630000e-40 178.0
6 TraesCS3A01G465400 chr3A 83.186 113 12 4 1660 1770 290428086 290427979 4.680000e-16 97.1
7 TraesCS3A01G465400 chr3D 96.876 2785 66 6 2087 4861 565562635 565559862 0.000000e+00 4641.0
8 TraesCS3A01G465400 chr3D 88.603 2913 208 41 2087 4968 565609390 565606571 0.000000e+00 3426.0
9 TraesCS3A01G465400 chr3D 85.795 1232 100 38 882 2101 565610572 565609404 0.000000e+00 1236.0
10 TraesCS3A01G465400 chr3D 90.966 797 40 9 4894 5679 565559870 565559095 0.000000e+00 1044.0
11 TraesCS3A01G465400 chr3D 94.143 683 32 6 1140 1820 565563586 565562910 0.000000e+00 1033.0
12 TraesCS3A01G465400 chr3D 84.467 779 104 12 1 776 565565388 565564624 0.000000e+00 752.0
13 TraesCS3A01G465400 chr3D 90.000 250 19 2 1849 2092 565562915 565562666 9.180000e-83 318.0
14 TraesCS3A01G465400 chr3D 87.454 271 29 4 845 1114 565563842 565563576 1.990000e-79 307.0
15 TraesCS3A01G465400 chr3D 80.478 251 30 7 5170 5416 564306274 564306509 2.100000e-39 174.0
16 TraesCS3A01G465400 chr3D 80.952 231 33 6 4544 4772 564202900 564203121 7.560000e-39 172.0
17 TraesCS3A01G465400 chr3D 72.222 612 123 32 49 629 568810059 568809464 1.650000e-30 145.0
18 TraesCS3A01G465400 chr3B 88.729 2910 211 46 2091 4969 753677921 753675098 0.000000e+00 3448.0
19 TraesCS3A01G465400 chr3B 96.823 1920 55 4 2893 4807 753580279 753578361 0.000000e+00 3203.0
20 TraesCS3A01G465400 chr3B 91.812 1661 78 23 1143 2782 753581890 753580267 0.000000e+00 2261.0
21 TraesCS3A01G465400 chr3B 86.204 1109 90 24 882 1980 753679107 753678052 0.000000e+00 1142.0
22 TraesCS3A01G465400 chr3B 90.747 843 44 14 4851 5679 753578366 753577544 0.000000e+00 1094.0
23 TraesCS3A01G465400 chr3B 84.190 778 117 6 2 776 753668314 753667540 0.000000e+00 750.0
24 TraesCS3A01G465400 chr3B 88.382 241 26 2 882 1121 753582116 753581877 7.200000e-74 289.0
25 TraesCS3A01G465400 chr3B 84.314 255 21 11 5174 5416 752047942 752048189 1.230000e-56 231.0
26 TraesCS3A01G465400 chr3B 82.609 253 23 8 5174 5416 752077990 752078231 2.680000e-48 204.0
27 TraesCS3A01G465400 chr3B 81.275 251 28 7 5170 5416 752038863 752039098 9.720000e-43 185.0
28 TraesCS3A01G465400 chr3B 80.000 230 35 6 4544 4771 751953281 751953501 5.890000e-35 159.0
29 TraesCS3A01G465400 chr6D 81.064 2350 325 76 2420 4716 30097456 30095174 0.000000e+00 1764.0
30 TraesCS3A01G465400 chr6D 78.277 2693 394 101 2087 4716 29850993 29853557 0.000000e+00 1555.0
31 TraesCS3A01G465400 chr6D 79.206 2217 317 67 2536 4712 29925599 29927711 0.000000e+00 1408.0
32 TraesCS3A01G465400 chr6D 77.750 2373 346 98 2419 4712 31472174 31474443 0.000000e+00 1290.0
33 TraesCS3A01G465400 chr6D 86.364 88 7 3 1879 1966 31471086 31471168 2.180000e-14 91.6
34 TraesCS3A01G465400 chr6A 80.807 2355 324 78 2420 4716 32741648 32743932 0.000000e+00 1727.0
35 TraesCS3A01G465400 chr6A 80.271 2215 312 61 2536 4712 32812157 32810030 0.000000e+00 1554.0
36 TraesCS3A01G465400 chr6A 79.094 2296 322 80 2478 4716 32885589 32883395 0.000000e+00 1435.0
37 TraesCS3A01G465400 chr6A 83.092 207 29 4 2222 2428 32812758 32812558 3.490000e-42 183.0
38 TraesCS3A01G465400 chr6A 85.965 114 7 6 1660 1770 32887060 32886953 4.650000e-21 113.0
39 TraesCS3A01G465400 chr6A 100.000 49 0 0 2064 2112 409921192 409921240 2.180000e-14 91.6
40 TraesCS3A01G465400 chr6A 77.876 113 13 8 1149 1261 46700802 46700702 6.140000e-05 60.2
41 TraesCS3A01G465400 chr6B 80.587 2349 337 76 2420 4716 57417605 57419886 0.000000e+00 1701.0
42 TraesCS3A01G465400 chr6B 77.798 2806 408 110 2017 4716 50410011 50407315 0.000000e+00 1531.0
43 TraesCS3A01G465400 chr6B 79.315 2219 316 73 2536 4712 57733672 57731555 0.000000e+00 1423.0
44 TraesCS3A01G465400 chr6B 79.755 899 143 23 2536 3423 56397035 56396165 2.910000e-172 616.0
45 TraesCS3A01G465400 chr6B 86.364 88 7 3 1879 1966 56380066 56379984 2.180000e-14 91.6
46 TraesCS3A01G465400 chr2B 90.727 1251 73 20 847 2092 760315880 760317092 0.000000e+00 1628.0
47 TraesCS3A01G465400 chr2B 94.783 115 5 1 2087 2201 760317123 760317236 1.630000e-40 178.0
48 TraesCS3A01G465400 chrUn 80.009 2346 337 64 2420 4712 27473492 27475758 0.000000e+00 1613.0
49 TraesCS3A01G465400 chrUn 78.835 2301 323 92 2087 4308 137913736 137911521 0.000000e+00 1400.0
50 TraesCS3A01G465400 chrUn 89.362 94 8 2 1502 1594 68355833 68355925 3.590000e-22 117.0
51 TraesCS3A01G465400 chrUn 89.362 94 8 2 1502 1594 268239361 268239453 3.590000e-22 117.0
52 TraesCS3A01G465400 chrUn 88.660 97 9 2 1502 1597 312454550 312454455 3.590000e-22 117.0
53 TraesCS3A01G465400 chrUn 100.000 31 0 0 1661 1691 137914369 137914339 2.210000e-04 58.4
54 TraesCS3A01G465400 chr2D 78.938 2298 315 92 2483 4712 48565445 48567641 0.000000e+00 1406.0
55 TraesCS3A01G465400 chr2D 86.667 90 7 3 1877 1966 48563406 48563490 1.680000e-15 95.3
56 TraesCS3A01G465400 chr2A 79.459 370 75 1 397 765 43123963 43123594 1.570000e-65 261.0
57 TraesCS3A01G465400 chr2A 100.000 49 0 0 2064 2112 69153564 69153612 2.180000e-14 91.6
58 TraesCS3A01G465400 chr5B 77.586 348 55 12 2095 2428 660814021 660813683 7.510000e-44 189.0
59 TraesCS3A01G465400 chr4A 79.330 179 34 2 53 229 607180469 607180646 7.730000e-24 122.0
60 TraesCS3A01G465400 chr7A 100.000 49 0 0 2064 2112 646920380 646920332 2.180000e-14 91.6
61 TraesCS3A01G465400 chr7B 87.013 77 10 0 182 258 636938270 636938194 2.820000e-13 87.9
62 TraesCS3A01G465400 chr7D 85.333 75 9 2 175 248 298661377 298661304 6.100000e-10 76.8
63 TraesCS3A01G465400 chr5A 92.308 52 2 2 5223 5274 60246988 60246939 7.890000e-09 73.1
64 TraesCS3A01G465400 chr5D 91.111 45 4 0 5223 5267 69481710 69481666 1.710000e-05 62.1


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 TraesCS3A01G465400 chr3A 699752105 699757783 5678 True 10488.000000 10488 100.000000 1 5679 1 chr3A.!!$R2 5678
1 TraesCS3A01G465400 chr3A 699765457 699769907 4450 True 1516.333333 2398 87.633667 842 4969 3 chr3A.!!$R3 4127
2 TraesCS3A01G465400 chr3D 565606571 565610572 4001 True 2331.000000 3426 87.199000 882 4968 2 chr3D.!!$R3 4086
3 TraesCS3A01G465400 chr3D 565559095 565565388 6293 True 1349.166667 4641 90.651000 1 5679 6 chr3D.!!$R2 5678
4 TraesCS3A01G465400 chr3B 753675098 753679107 4009 True 2295.000000 3448 87.466500 882 4969 2 chr3B.!!$R3 4087
5 TraesCS3A01G465400 chr3B 753577544 753582116 4572 True 1711.750000 3203 91.941000 882 5679 4 chr3B.!!$R2 4797
6 TraesCS3A01G465400 chr3B 753667540 753668314 774 True 750.000000 750 84.190000 2 776 1 chr3B.!!$R1 774
7 TraesCS3A01G465400 chr6D 30095174 30097456 2282 True 1764.000000 1764 81.064000 2420 4716 1 chr6D.!!$R1 2296
8 TraesCS3A01G465400 chr6D 29850993 29853557 2564 False 1555.000000 1555 78.277000 2087 4716 1 chr6D.!!$F1 2629
9 TraesCS3A01G465400 chr6D 29925599 29927711 2112 False 1408.000000 1408 79.206000 2536 4712 1 chr6D.!!$F2 2176
10 TraesCS3A01G465400 chr6D 31471086 31474443 3357 False 690.800000 1290 82.057000 1879 4712 2 chr6D.!!$F3 2833
11 TraesCS3A01G465400 chr6A 32741648 32743932 2284 False 1727.000000 1727 80.807000 2420 4716 1 chr6A.!!$F1 2296
12 TraesCS3A01G465400 chr6A 32810030 32812758 2728 True 868.500000 1554 81.681500 2222 4712 2 chr6A.!!$R2 2490
13 TraesCS3A01G465400 chr6A 32883395 32887060 3665 True 774.000000 1435 82.529500 1660 4716 2 chr6A.!!$R3 3056
14 TraesCS3A01G465400 chr6B 57417605 57419886 2281 False 1701.000000 1701 80.587000 2420 4716 1 chr6B.!!$F1 2296
15 TraesCS3A01G465400 chr6B 50407315 50410011 2696 True 1531.000000 1531 77.798000 2017 4716 1 chr6B.!!$R1 2699
16 TraesCS3A01G465400 chr6B 57731555 57733672 2117 True 1423.000000 1423 79.315000 2536 4712 1 chr6B.!!$R4 2176
17 TraesCS3A01G465400 chr6B 56396165 56397035 870 True 616.000000 616 79.755000 2536 3423 1 chr6B.!!$R3 887
18 TraesCS3A01G465400 chr2B 760315880 760317236 1356 False 903.000000 1628 92.755000 847 2201 2 chr2B.!!$F1 1354
19 TraesCS3A01G465400 chrUn 27473492 27475758 2266 False 1613.000000 1613 80.009000 2420 4712 1 chrUn.!!$F1 2292
20 TraesCS3A01G465400 chrUn 137911521 137914369 2848 True 729.200000 1400 89.417500 1661 4308 2 chrUn.!!$R2 2647
21 TraesCS3A01G465400 chr2D 48563406 48567641 4235 False 750.650000 1406 82.802500 1877 4712 2 chr2D.!!$F1 2835

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
329 331 0.038067 TTAAACTGGCGCGTCAGCTA 60.038 50.000 38.44 26.67 42.32 3.32 F
467 469 0.103208 CCACACCTACGCTCTCCATC 59.897 60.000 0.00 0.00 0.00 3.51 F
486 488 0.181350 CTCCTCTATGCACCCAACCC 59.819 60.000 0.00 0.00 0.00 4.11 F
720 723 0.315568 GCGAGGCATAAGAGGACGAT 59.684 55.000 0.00 0.00 0.00 3.73 F
924 1641 0.405198 TTTCTCCAGATTGCCAGCCA 59.595 50.000 0.00 0.00 0.00 4.75 F
946 1663 0.912486 CCCTCGGGACATTTCTTCCT 59.088 55.000 0.00 0.00 37.50 3.36 F
976 1693 1.091537 ACGTTATCCCAATTGCCACG 58.908 50.000 0.00 5.84 0.00 4.94 F
2041 3820 1.189446 GTACACAGTCGTTGTTGCTCG 59.811 52.381 0.00 0.00 38.16 5.03 F
3484 6111 1.339824 ACTTCAAGCTGGATCTGGCAG 60.340 52.381 8.58 8.58 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1130 1847 1.118838 CGAGAAGGAGGAGGAAGCAT 58.881 55.000 0.00 0.00 0.00 3.79 R
1657 2448 1.812571 CCACATCCCGAACAGAAAAGG 59.187 52.381 0.00 0.00 0.00 3.11 R
2092 3879 2.233676 TGCAGTAATCAGGACACGACAT 59.766 45.455 0.00 0.00 0.00 3.06 R
2384 4220 3.225104 AGACCACAAAATGTGCACATCT 58.775 40.909 31.45 17.13 46.51 2.90 R
2648 4871 7.883391 TGTGATAAAACTTTGAACCTGGTAA 57.117 32.000 0.00 0.00 0.00 2.85 R
2843 5074 8.241367 GGTATTAATTGGTTGTGTTCAGTAAGG 58.759 37.037 0.00 0.00 0.00 2.69 R
3484 6111 7.324616 GCAAATGACAAACAAAGATAGTGAGAC 59.675 37.037 0.00 0.00 0.00 3.36 R
3783 6445 1.618837 AGCTAAGACAACTCGCCTGAA 59.381 47.619 0.00 0.00 0.00 3.02 R
4800 7527 0.031178 GCTGTTTGTGCCAACAGAGG 59.969 55.000 19.50 0.00 46.91 3.69 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
24 25 0.888619 CTCTGGCCAGTTCTGACGTA 59.111 55.000 31.58 8.74 0.00 3.57
30 31 3.886505 TGGCCAGTTCTGACGTAATTTTT 59.113 39.130 0.00 0.00 0.00 1.94
93 94 1.227527 CACACGCCTCTGACAACCA 60.228 57.895 0.00 0.00 0.00 3.67
119 120 1.070134 CACCGAAAACACTCTCCCTCA 59.930 52.381 0.00 0.00 0.00 3.86
193 194 4.802051 TTCATGCCGGCCCAGAGC 62.802 66.667 26.77 0.00 42.60 4.09
202 203 3.112709 GCCCAGAGCGAACACGAC 61.113 66.667 0.00 0.00 0.00 4.34
211 212 0.520404 GCGAACACGACCTCTCACTA 59.480 55.000 0.00 0.00 0.00 2.74
216 217 0.736053 CACGACCTCTCACTAGAGCC 59.264 60.000 0.00 0.00 46.84 4.70
217 218 0.745128 ACGACCTCTCACTAGAGCCG 60.745 60.000 0.00 11.31 46.84 5.52
227 228 0.462759 ACTAGAGCCGGCATTGAAGC 60.463 55.000 31.54 8.32 0.00 3.86
229 230 1.955495 TAGAGCCGGCATTGAAGCGA 61.955 55.000 31.54 1.80 34.64 4.93
230 231 3.100862 GAGCCGGCATTGAAGCGAC 62.101 63.158 31.54 2.51 34.64 5.19
231 232 4.520846 GCCGGCATTGAAGCGACG 62.521 66.667 24.80 0.00 34.64 5.12
246 247 4.180946 ACGCGCTAGCCGAGAGTG 62.181 66.667 25.67 13.85 40.93 3.51
279 280 0.308993 GCGGCTTCTATCCACATTGC 59.691 55.000 0.00 0.00 0.00 3.56
295 296 5.030295 CACATTGCAACGATATTTGTCCTC 58.970 41.667 0.00 0.00 0.00 3.71
299 300 2.682563 GCAACGATATTTGTCCTCCCCA 60.683 50.000 0.00 0.00 0.00 4.96
307 308 0.402861 TTGTCCTCCCCACCTTCCTT 60.403 55.000 0.00 0.00 0.00 3.36
312 313 2.205342 CCTCCCCACCTTCCTTCATTA 58.795 52.381 0.00 0.00 0.00 1.90
329 331 0.038067 TTAAACTGGCGCGTCAGCTA 60.038 50.000 38.44 26.67 42.32 3.32
332 334 3.558411 CTGGCGCGTCAGCTAAGC 61.558 66.667 29.53 0.00 42.32 3.09
344 346 0.824759 AGCTAAGCAACCTACTCCGG 59.175 55.000 0.00 0.00 0.00 5.14
351 353 3.997756 AACCTACTCCGGAGCCCCC 62.998 68.421 31.56 0.00 0.00 5.40
383 385 0.808755 CTGGCCGACATTAAACACCC 59.191 55.000 0.00 0.00 0.00 4.61
430 432 2.887152 CCTCTATTTAACATGGCCAGGC 59.113 50.000 19.26 1.26 0.00 4.85
445 447 4.344865 GGCTCCGGGCAAACTCCA 62.345 66.667 15.49 0.00 44.01 3.86
456 458 1.476110 GCAAACTCCACACCACACCTA 60.476 52.381 0.00 0.00 0.00 3.08
467 469 0.103208 CCACACCTACGCTCTCCATC 59.897 60.000 0.00 0.00 0.00 3.51
476 478 2.513753 ACGCTCTCCATCTCCTCTATG 58.486 52.381 0.00 0.00 0.00 2.23
477 479 1.202114 CGCTCTCCATCTCCTCTATGC 59.798 57.143 0.00 0.00 0.00 3.14
480 482 2.562298 CTCTCCATCTCCTCTATGCACC 59.438 54.545 0.00 0.00 0.00 5.01
483 485 1.770658 CCATCTCCTCTATGCACCCAA 59.229 52.381 0.00 0.00 0.00 4.12
485 487 1.204146 TCTCCTCTATGCACCCAACC 58.796 55.000 0.00 0.00 0.00 3.77
486 488 0.181350 CTCCTCTATGCACCCAACCC 59.819 60.000 0.00 0.00 0.00 4.11
507 509 0.460987 CCATGACCTCGAGCTCCAAC 60.461 60.000 6.99 0.00 0.00 3.77
511 513 4.821589 CCTCGAGCTCCAACGCCC 62.822 72.222 6.99 0.00 0.00 6.13
527 529 2.516930 CCCGTGGGATGGCATCAC 60.517 66.667 27.39 25.22 37.50 3.06
529 531 2.896854 CGTGGGATGGCATCACCG 60.897 66.667 26.07 22.96 43.94 4.94
531 533 1.819632 GTGGGATGGCATCACCGAC 60.820 63.158 26.07 15.15 43.94 4.79
533 535 0.689412 TGGGATGGCATCACCGACTA 60.689 55.000 26.07 4.87 43.94 2.59
564 567 0.392729 AGCTCTCTGACATTGCTGCC 60.393 55.000 0.00 0.00 32.32 4.85
565 568 1.375098 GCTCTCTGACATTGCTGCCC 61.375 60.000 0.00 0.00 0.00 5.36
574 577 2.053865 ATTGCTGCCCGATGGTTGG 61.054 57.895 0.00 0.00 0.00 3.77
575 578 2.497792 ATTGCTGCCCGATGGTTGGA 62.498 55.000 0.00 0.00 0.00 3.53
577 580 2.671070 CTGCCCGATGGTTGGACT 59.329 61.111 0.00 0.00 0.00 3.85
589 592 2.282783 TTGGACTGCCGAGCTAGCA 61.283 57.895 18.83 10.29 38.82 3.49
621 624 3.907260 CTTGCCGGCCAGCTCTTCA 62.907 63.158 26.77 0.00 0.00 3.02
631 634 1.153409 AGCTCTTCAGATGGCAGCG 60.153 57.895 0.00 0.00 35.14 5.18
636 639 0.390866 CTTCAGATGGCAGCGACACT 60.391 55.000 0.00 0.00 0.00 3.55
655 658 2.101249 ACTAACGAACCAACGAAGGACA 59.899 45.455 4.96 0.00 37.03 4.02
677 680 4.740822 GACGCCACCCCCATTGCT 62.741 66.667 0.00 0.00 0.00 3.91
678 681 4.299796 ACGCCACCCCCATTGCTT 62.300 61.111 0.00 0.00 0.00 3.91
679 682 3.762247 CGCCACCCCCATTGCTTG 61.762 66.667 0.00 0.00 0.00 4.01
680 683 2.604382 GCCACCCCCATTGCTTGT 60.604 61.111 0.00 0.00 0.00 3.16
682 685 1.984026 CCACCCCCATTGCTTGTCC 60.984 63.158 0.00 0.00 0.00 4.02
683 686 1.228831 CACCCCCATTGCTTGTCCA 60.229 57.895 0.00 0.00 0.00 4.02
685 688 0.542702 ACCCCCATTGCTTGTCCAAG 60.543 55.000 2.63 2.63 41.24 3.61
717 720 1.069935 GGGCGAGGCATAAGAGGAC 59.930 63.158 0.00 0.00 0.00 3.85
720 723 0.315568 GCGAGGCATAAGAGGACGAT 59.684 55.000 0.00 0.00 0.00 3.73
735 738 3.936203 GATACGGGCATCGGGGCA 61.936 66.667 3.86 0.00 45.66 5.36
744 747 2.507944 ATCGGGGCAGATGAGCAC 59.492 61.111 0.00 0.00 37.14 4.40
766 769 1.626654 GCGCGCAGAGAAGCAAGTTA 61.627 55.000 29.10 0.00 0.00 2.24
768 771 1.462541 CGCGCAGAGAAGCAAGTTAAC 60.463 52.381 8.75 0.00 0.00 2.01
804 915 3.905060 GCCTACGCGAAGATCGAC 58.095 61.111 15.93 0.00 43.74 4.20
805 916 1.063649 GCCTACGCGAAGATCGACA 59.936 57.895 15.93 0.00 43.74 4.35
814 925 2.925162 GAAGATCGACAAGGCGGGGG 62.925 65.000 0.00 0.00 0.00 5.40
828 993 1.379527 CGGGGGCAGAAGTTTATGAC 58.620 55.000 0.00 0.00 0.00 3.06
852 1568 0.893270 CTGGCACGTCCAATTTCCCA 60.893 55.000 7.90 0.00 46.01 4.37
872 1588 3.530910 CTCCGGCCAAACTCACCGT 62.531 63.158 2.24 0.00 45.49 4.83
877 1593 1.134907 CGGCCAAACTCACCGTATACT 60.135 52.381 2.24 0.00 42.01 2.12
924 1641 0.405198 TTTCTCCAGATTGCCAGCCA 59.595 50.000 0.00 0.00 0.00 4.75
943 1660 1.064825 ACACCCTCGGGACATTTCTT 58.935 50.000 9.43 0.00 38.96 2.52
946 1663 0.912486 CCCTCGGGACATTTCTTCCT 59.088 55.000 0.00 0.00 37.50 3.36
950 1667 1.278127 TCGGGACATTTCTTCCTCACC 59.722 52.381 0.00 0.00 33.17 4.02
971 1688 2.297701 CCCCTCACGTTATCCCAATTG 58.702 52.381 0.00 0.00 0.00 2.32
976 1693 1.091537 ACGTTATCCCAATTGCCACG 58.908 50.000 0.00 5.84 0.00 4.94
977 1694 1.339247 ACGTTATCCCAATTGCCACGA 60.339 47.619 15.47 3.63 0.00 4.35
978 1695 1.330521 CGTTATCCCAATTGCCACGAG 59.669 52.381 0.00 0.00 0.00 4.18
979 1696 2.639065 GTTATCCCAATTGCCACGAGA 58.361 47.619 0.00 0.00 0.00 4.04
1145 1931 1.977293 GCCGATGCTTCCTCCTCCTT 61.977 60.000 0.00 0.00 33.53 3.36
1392 2181 4.555709 ACGGCGGTGTTCCAGCAA 62.556 61.111 13.24 0.00 35.88 3.91
1565 2356 1.790623 GAGTGCGTTCTTGAGCGTTTA 59.209 47.619 8.49 0.00 35.87 2.01
1657 2448 5.552870 TTATAGCCTGAATCTTGGACCTC 57.447 43.478 0.00 0.00 0.00 3.85
1721 2515 3.528905 TGAAATCTTGGGGATGATCCAGT 59.471 43.478 14.36 0.00 38.64 4.00
1722 2516 3.872459 AATCTTGGGGATGATCCAGTC 57.128 47.619 14.36 2.93 38.64 3.51
1723 2517 1.511613 TCTTGGGGATGATCCAGTCC 58.488 55.000 14.36 6.06 38.64 3.85
1804 2650 5.254901 AGAAGCAGAATCTTGAGCAAATCT 58.745 37.500 0.00 0.00 0.00 2.40
1806 2652 5.312120 AGCAGAATCTTGAGCAAATCTTG 57.688 39.130 0.00 0.00 0.00 3.02
1807 2653 4.765856 AGCAGAATCTTGAGCAAATCTTGT 59.234 37.500 0.00 0.00 0.00 3.16
1808 2654 4.857588 GCAGAATCTTGAGCAAATCTTGTG 59.142 41.667 0.00 0.00 0.00 3.33
1809 2655 4.857588 CAGAATCTTGAGCAAATCTTGTGC 59.142 41.667 0.00 0.00 42.55 4.57
1969 3549 9.708222 CAAATGTATCAGTTTTCAGTGTATAGC 57.292 33.333 0.00 0.00 0.00 2.97
2007 3593 4.563140 TGTTGGGAGTAGGTTGGTATTC 57.437 45.455 0.00 0.00 0.00 1.75
2041 3820 1.189446 GTACACAGTCGTTGTTGCTCG 59.811 52.381 0.00 0.00 38.16 5.03
2052 3839 2.084610 TGTTGCTCGTGGATCTTCTG 57.915 50.000 0.00 0.00 0.00 3.02
2054 3841 1.728971 GTTGCTCGTGGATCTTCTGTG 59.271 52.381 0.00 0.00 0.00 3.66
2077 3864 6.094603 GTGAGTCTGGCATCATATTTTGAAGT 59.905 38.462 0.00 0.00 38.03 3.01
2083 3870 9.187996 TCTGGCATCATATTTTGAAGTAAATGA 57.812 29.630 0.00 0.00 38.03 2.57
2153 3980 4.458989 GCCTGAAGTCAAATGTATGAACCA 59.541 41.667 0.00 0.00 0.00 3.67
2299 4134 5.696724 CAGTATTTGGTCGAGAAGTTTCACT 59.303 40.000 0.00 0.00 0.00 3.41
2384 4220 7.807977 AGTTGCAGAGAATCAAGAAGTTTTA 57.192 32.000 0.00 0.00 37.82 1.52
2648 4871 6.289834 TGTTTCAAAATGGAAGTGCATGAAT 58.710 32.000 0.00 0.00 0.00 2.57
2665 4890 6.183360 TGCATGAATTACCAGGTTCAAAGTTT 60.183 34.615 0.00 0.00 37.82 2.66
3484 6111 1.339824 ACTTCAAGCTGGATCTGGCAG 60.340 52.381 8.58 8.58 0.00 4.85
3608 6240 5.630661 TTATTGTCATGTTAACAACCCGG 57.369 39.130 13.23 0.00 39.29 5.73
3737 6384 9.929180 GTTATTATTATGTAGCCATCTCACTGA 57.071 33.333 0.00 0.00 32.29 3.41
3831 6493 9.039870 CGTTCTTTCTTATCTTGCTATTGATCT 57.960 33.333 0.00 0.00 0.00 2.75
4353 7059 7.147655 TGTCTCTCTCCTCCCTTTTATTACATG 60.148 40.741 0.00 0.00 0.00 3.21
4579 7303 0.545548 GTCCTGGACCTGGAGTTCCT 60.546 60.000 19.85 0.00 36.82 3.36
4603 7327 3.239449 TGTGAGTGTGACCCTTCTGTAT 58.761 45.455 0.00 0.00 0.00 2.29
4605 7329 5.023452 TGTGAGTGTGACCCTTCTGTATAT 58.977 41.667 0.00 0.00 0.00 0.86
4618 7342 6.296662 CCCTTCTGTATATGGGCATTCACTAT 60.297 42.308 0.00 0.00 32.49 2.12
4621 7345 7.500629 TCTGTATATGGGCATTCACTATGAT 57.499 36.000 0.00 0.00 36.26 2.45
4668 7392 3.717707 CCGAGAGTTCAAGTCAACAGAA 58.282 45.455 0.00 0.00 0.00 3.02
4676 7400 4.437682 TCAAGTCAACAGAATTCCCAGT 57.562 40.909 0.65 0.00 0.00 4.00
4798 7525 5.239525 ACACTTAGTTGTGCATTCTTCTTCC 59.760 40.000 0.00 0.00 41.30 3.46
4799 7526 5.471456 CACTTAGTTGTGCATTCTTCTTCCT 59.529 40.000 0.00 0.00 0.00 3.36
4800 7527 5.703130 ACTTAGTTGTGCATTCTTCTTCCTC 59.297 40.000 0.00 0.00 0.00 3.71
4801 7528 3.416156 AGTTGTGCATTCTTCTTCCTCC 58.584 45.455 0.00 0.00 0.00 4.30
4802 7529 3.073650 AGTTGTGCATTCTTCTTCCTCCT 59.926 43.478 0.00 0.00 0.00 3.69
4803 7530 3.340814 TGTGCATTCTTCTTCCTCCTC 57.659 47.619 0.00 0.00 0.00 3.71
4824 7551 3.524014 TGGCACAAACAGCTGGTG 58.476 55.556 19.93 17.05 31.92 4.17
4827 7554 2.332514 CACAAACAGCTGGTGCCG 59.667 61.111 19.93 6.61 40.80 5.69
4828 7555 2.186160 CACAAACAGCTGGTGCCGA 61.186 57.895 19.93 0.00 40.80 5.54
4829 7556 1.228245 ACAAACAGCTGGTGCCGAT 60.228 52.632 19.93 0.00 40.80 4.18
4830 7557 0.036164 ACAAACAGCTGGTGCCGATA 59.964 50.000 19.93 0.00 40.80 2.92
4831 7558 0.447801 CAAACAGCTGGTGCCGATAC 59.552 55.000 19.93 0.00 40.80 2.24
4832 7559 0.036164 AAACAGCTGGTGCCGATACA 59.964 50.000 19.93 0.00 40.80 2.29
4833 7560 0.253044 AACAGCTGGTGCCGATACAT 59.747 50.000 19.93 0.00 40.80 2.29
4834 7561 0.253044 ACAGCTGGTGCCGATACATT 59.747 50.000 19.93 0.00 40.80 2.71
4835 7562 0.659427 CAGCTGGTGCCGATACATTG 59.341 55.000 5.57 0.00 40.80 2.82
4836 7563 0.541392 AGCTGGTGCCGATACATTGA 59.459 50.000 0.00 0.00 40.80 2.57
4837 7564 1.141657 AGCTGGTGCCGATACATTGAT 59.858 47.619 0.00 0.00 40.80 2.57
4838 7565 1.532868 GCTGGTGCCGATACATTGATC 59.467 52.381 0.00 0.00 0.00 2.92
4839 7566 2.837498 CTGGTGCCGATACATTGATCA 58.163 47.619 0.00 0.00 0.00 2.92
4840 7567 2.804527 CTGGTGCCGATACATTGATCAG 59.195 50.000 0.00 0.00 0.00 2.90
4841 7568 2.170397 TGGTGCCGATACATTGATCAGT 59.830 45.455 0.00 0.00 0.00 3.41
4842 7569 3.386402 TGGTGCCGATACATTGATCAGTA 59.614 43.478 0.00 0.00 0.00 2.74
4941 7688 5.934043 CAGTGAATCTTCTGTGGTCACATTA 59.066 40.000 4.13 0.00 40.83 1.90
5003 7760 4.795469 TGATATCATCCTTGTTGGCATGT 58.205 39.130 0.00 0.00 35.26 3.21
5045 7802 1.880027 GGGCATGATACGAATTGGTCC 59.120 52.381 0.00 0.00 0.00 4.46
5047 7804 2.290641 GGCATGATACGAATTGGTCCAC 59.709 50.000 0.00 0.00 0.00 4.02
5064 7821 4.383335 GGTCCACCGGTATGTTATTTCTGA 60.383 45.833 6.87 0.00 0.00 3.27
5090 7848 2.620115 CACAGGTTTGTCATGTCTTGCT 59.380 45.455 0.00 0.00 39.11 3.91
5094 7852 3.755378 AGGTTTGTCATGTCTTGCTCATC 59.245 43.478 0.00 0.00 0.00 2.92
5106 7864 1.804601 TGCTCATCTGTTCACAGCAG 58.195 50.000 1.74 0.03 43.46 4.24
5161 7919 7.979786 TTCTATCCAAGATTCCTAGTGAAGT 57.020 36.000 0.00 0.00 36.14 3.01
5249 8007 4.025229 GTGCTGAACGTCTGTTTGTGATTA 60.025 41.667 0.00 0.00 38.78 1.75
5259 8017 8.873830 ACGTCTGTTTGTGATTATTTCTATCTG 58.126 33.333 0.00 0.00 0.00 2.90
5270 8028 8.486210 TGATTATTTCTATCTGTGCTGGTTACT 58.514 33.333 0.00 0.00 0.00 2.24
5279 8037 2.222027 GTGCTGGTTACTCTGCTTGTT 58.778 47.619 0.00 0.00 33.58 2.83
5290 8048 3.898123 ACTCTGCTTGTTCCTGAACTAGA 59.102 43.478 20.54 12.89 43.52 2.43
5383 8141 1.444895 GCAGCTGAACAATTGCCCG 60.445 57.895 20.43 0.00 0.00 6.13
5496 8257 3.975035 GGAGCTTTCAACTTGCTTTTACG 59.025 43.478 0.00 0.00 37.16 3.18
5497 8258 3.964909 AGCTTTCAACTTGCTTTTACGG 58.035 40.909 0.00 0.00 32.61 4.02
5508 8269 1.401552 GCTTTTACGGCTGCATCATCA 59.598 47.619 0.50 0.00 0.00 3.07
5513 8274 1.875009 ACGGCTGCATCATCACATAG 58.125 50.000 0.50 0.00 0.00 2.23
5619 8380 5.117355 TGCAAGCAGAGAGAAATGAAAAG 57.883 39.130 0.00 0.00 0.00 2.27
5638 8399 6.324512 TGAAAAGGTCTGGTAGTTACAGTGTA 59.675 38.462 0.00 0.00 37.25 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.851263 AATTACGTCAGAACTGGCCA 57.149 45.000 4.71 4.71 0.00 5.36
76 77 0.603707 CATGGTTGTCAGAGGCGTGT 60.604 55.000 0.00 0.00 0.00 4.49
84 85 1.978617 GGTGGGCCATGGTTGTCAG 60.979 63.158 10.70 0.00 34.09 3.51
93 94 0.893727 GAGTGTTTTCGGTGGGCCAT 60.894 55.000 10.70 0.00 34.09 4.40
133 134 1.522355 CGCTGACTGCTATGGGTGG 60.522 63.158 2.66 0.00 40.11 4.61
193 194 2.074576 TCTAGTGAGAGGTCGTGTTCG 58.925 52.381 0.00 0.00 38.55 3.95
211 212 2.821366 CGCTTCAATGCCGGCTCT 60.821 61.111 29.70 12.59 0.00 4.09
216 217 4.851114 CGCGTCGCTTCAATGCCG 62.851 66.667 16.36 0.00 0.00 5.69
227 228 4.947278 CTCTCGGCTAGCGCGTCG 62.947 72.222 20.20 13.49 36.88 5.12
229 230 4.180946 CACTCTCGGCTAGCGCGT 62.181 66.667 20.20 6.39 36.88 6.01
256 257 0.815213 TGTGGATAGAAGCCGCATGC 60.815 55.000 7.91 7.91 40.74 4.06
261 262 1.667236 TGCAATGTGGATAGAAGCCG 58.333 50.000 0.00 0.00 0.00 5.52
279 280 2.943033 GTGGGGAGGACAAATATCGTTG 59.057 50.000 0.00 0.00 34.52 4.10
295 296 3.763897 CAGTTTAATGAAGGAAGGTGGGG 59.236 47.826 0.00 0.00 0.00 4.96
299 300 3.081804 CGCCAGTTTAATGAAGGAAGGT 58.918 45.455 0.00 0.00 0.00 3.50
307 308 1.075542 CTGACGCGCCAGTTTAATGA 58.924 50.000 14.84 0.00 0.00 2.57
312 313 1.291877 CTTAGCTGACGCGCCAGTTT 61.292 55.000 23.47 14.42 42.32 2.66
329 331 1.597461 GCTCCGGAGTAGGTTGCTT 59.403 57.895 31.43 0.00 0.00 3.91
332 334 2.732619 GGGGCTCCGGAGTAGGTTG 61.733 68.421 31.43 6.80 0.00 3.77
362 364 1.530323 GTGTTTAATGTCGGCCAGGT 58.470 50.000 2.24 0.00 0.00 4.00
363 365 0.808755 GGTGTTTAATGTCGGCCAGG 59.191 55.000 2.24 0.00 0.00 4.45
365 367 0.609681 GGGGTGTTTAATGTCGGCCA 60.610 55.000 2.24 0.00 0.00 5.36
430 432 1.966451 GTGTGGAGTTTGCCCGGAG 60.966 63.158 0.73 0.00 0.00 4.63
441 443 1.374252 GCGTAGGTGTGGTGTGGAG 60.374 63.158 0.00 0.00 0.00 3.86
445 447 1.533469 GGAGAGCGTAGGTGTGGTGT 61.533 60.000 0.00 0.00 39.88 4.16
456 458 2.513753 CATAGAGGAGATGGAGAGCGT 58.486 52.381 0.00 0.00 0.00 5.07
467 469 0.181350 GGGTTGGGTGCATAGAGGAG 59.819 60.000 0.00 0.00 0.00 3.69
477 479 3.061848 GTCATGGCGGGTTGGGTG 61.062 66.667 0.00 0.00 0.00 4.61
480 482 2.438434 GAGGTCATGGCGGGTTGG 60.438 66.667 0.00 0.00 0.00 3.77
483 485 3.461773 CTCGAGGTCATGGCGGGT 61.462 66.667 3.91 0.00 0.00 5.28
485 487 3.781770 GAGCTCGAGGTCATGGCGG 62.782 68.421 33.64 0.00 41.81 6.13
486 488 2.279120 GAGCTCGAGGTCATGGCG 60.279 66.667 33.64 0.00 41.81 5.69
511 513 2.516930 GGTGATGCCATCCCACGG 60.517 66.667 1.49 0.00 37.17 4.94
527 529 2.494073 AGCTCCTTCTTCTGTTAGTCGG 59.506 50.000 0.00 0.00 0.00 4.79
529 531 4.705023 AGAGAGCTCCTTCTTCTGTTAGTC 59.295 45.833 10.93 0.00 0.00 2.59
531 533 4.704540 TCAGAGAGCTCCTTCTTCTGTTAG 59.295 45.833 22.32 4.83 0.00 2.34
533 535 3.258123 GTCAGAGAGCTCCTTCTTCTGTT 59.742 47.826 22.32 0.00 0.00 3.16
564 567 2.819595 CGGCAGTCCAACCATCGG 60.820 66.667 0.00 0.00 0.00 4.18
565 568 1.811266 CTCGGCAGTCCAACCATCG 60.811 63.158 0.00 0.00 0.00 3.84
577 580 1.067669 CTGTATTCTGCTAGCTCGGCA 59.932 52.381 17.23 12.65 38.10 5.69
589 592 3.181526 GCAAGCCAGCCTGTATTCT 57.818 52.632 0.00 0.00 0.00 2.40
608 611 1.523258 CCATCTGAAGAGCTGGCCG 60.523 63.158 0.00 0.00 28.79 6.13
619 622 0.894835 TTAGTGTCGCTGCCATCTGA 59.105 50.000 0.00 0.00 0.00 3.27
621 624 0.458543 CGTTAGTGTCGCTGCCATCT 60.459 55.000 0.00 0.00 0.00 2.90
631 634 2.473984 CCTTCGTTGGTTCGTTAGTGTC 59.526 50.000 0.00 0.00 0.00 3.67
636 639 2.886862 TGTCCTTCGTTGGTTCGTTA 57.113 45.000 0.00 0.00 0.00 3.18
668 671 0.890683 GTCTTGGACAAGCAATGGGG 59.109 55.000 7.18 0.00 38.28 4.96
671 674 1.872952 TGTCGTCTTGGACAAGCAATG 59.127 47.619 7.18 0.00 43.55 2.82
672 675 2.254546 TGTCGTCTTGGACAAGCAAT 57.745 45.000 7.18 0.00 43.55 3.56
673 676 3.770625 TGTCGTCTTGGACAAGCAA 57.229 47.368 7.18 0.00 43.55 3.91
679 682 2.936498 CCATGGTTATGTCGTCTTGGAC 59.064 50.000 2.57 0.00 37.45 4.02
680 683 2.093181 CCCATGGTTATGTCGTCTTGGA 60.093 50.000 11.73 0.00 32.21 3.53
682 685 1.670811 GCCCATGGTTATGTCGTCTTG 59.329 52.381 11.73 0.00 32.21 3.02
683 686 1.742411 CGCCCATGGTTATGTCGTCTT 60.742 52.381 11.73 0.00 32.21 3.01
685 688 0.179094 TCGCCCATGGTTATGTCGTC 60.179 55.000 11.73 0.00 33.21 4.20
751 754 2.800544 TGTCGTTAACTTGCTTCTCTGC 59.199 45.455 3.71 0.00 0.00 4.26
754 757 2.155155 CCGTGTCGTTAACTTGCTTCTC 59.845 50.000 3.71 0.00 0.00 2.87
766 769 1.000496 GTCCTCTTTCTCCGTGTCGTT 60.000 52.381 0.00 0.00 0.00 3.85
768 771 0.454620 CGTCCTCTTTCTCCGTGTCG 60.455 60.000 0.00 0.00 0.00 4.35
796 907 2.584608 CCCCGCCTTGTCGATCTT 59.415 61.111 0.00 0.00 0.00 2.40
802 913 4.344865 TTCTGCCCCCGCCTTGTC 62.345 66.667 0.00 0.00 0.00 3.18
804 915 3.868200 AACTTCTGCCCCCGCCTTG 62.868 63.158 0.00 0.00 0.00 3.61
805 916 1.785353 TAAACTTCTGCCCCCGCCTT 61.785 55.000 0.00 0.00 0.00 4.35
814 925 3.181516 CCAGCTTCGTCATAAACTTCTGC 60.182 47.826 0.00 0.00 0.00 4.26
852 1568 1.299976 GGTGAGTTTGGCCGGAGAT 59.700 57.895 5.05 0.00 0.00 2.75
877 1593 5.821995 GGCGGTTATTTATAAAGGTGGTACA 59.178 40.000 3.94 0.00 0.00 2.90
924 1641 1.003233 GAAGAAATGTCCCGAGGGTGT 59.997 52.381 8.20 0.00 36.47 4.16
950 1667 0.843984 ATTGGGATAACGTGAGGGGG 59.156 55.000 0.00 0.00 0.00 5.40
959 1676 2.614057 CTCTCGTGGCAATTGGGATAAC 59.386 50.000 7.72 0.00 0.00 1.89
971 1688 3.462678 GGGGAGGACTCTCGTGGC 61.463 72.222 0.00 0.00 40.85 5.01
976 1693 3.844090 GCTGCGGGGAGGACTCTC 61.844 72.222 0.00 0.00 39.25 3.20
977 1694 4.704103 TGCTGCGGGGAGGACTCT 62.704 66.667 0.00 0.00 0.00 3.24
978 1695 4.154347 CTGCTGCGGGGAGGACTC 62.154 72.222 0.00 0.00 0.00 3.36
1124 1841 3.798954 GAGGAGGAAGCATCGGCCG 62.799 68.421 22.12 22.12 42.56 6.13
1125 1842 2.110006 GAGGAGGAAGCATCGGCC 59.890 66.667 0.00 0.00 42.56 6.13
1126 1843 1.977293 AAGGAGGAGGAAGCATCGGC 61.977 60.000 0.00 0.00 41.61 5.54
1127 1844 0.105778 GAAGGAGGAGGAAGCATCGG 59.894 60.000 0.00 0.00 0.00 4.18
1128 1845 1.068434 GAGAAGGAGGAGGAAGCATCG 59.932 57.143 0.00 0.00 0.00 3.84
1129 1846 1.068434 CGAGAAGGAGGAGGAAGCATC 59.932 57.143 0.00 0.00 0.00 3.91
1130 1847 1.118838 CGAGAAGGAGGAGGAAGCAT 58.881 55.000 0.00 0.00 0.00 3.79
1131 1848 1.608717 GCGAGAAGGAGGAGGAAGCA 61.609 60.000 0.00 0.00 0.00 3.91
1132 1849 1.142965 GCGAGAAGGAGGAGGAAGC 59.857 63.158 0.00 0.00 0.00 3.86
1133 1850 1.819905 GGCGAGAAGGAGGAGGAAG 59.180 63.158 0.00 0.00 0.00 3.46
1134 1851 2.052690 CGGCGAGAAGGAGGAGGAA 61.053 63.158 0.00 0.00 0.00 3.36
1135 1852 2.440430 CGGCGAGAAGGAGGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
1254 2043 1.626356 CGGAGGGGAGATTCTTGCCA 61.626 60.000 0.00 0.00 0.00 4.92
1657 2448 1.812571 CCACATCCCGAACAGAAAAGG 59.187 52.381 0.00 0.00 0.00 3.11
1721 2515 3.032265 TGCTGCTCCTATTACTCTGGA 57.968 47.619 0.00 0.00 0.00 3.86
1722 2516 3.577848 AGATGCTGCTCCTATTACTCTGG 59.422 47.826 0.00 0.00 0.00 3.86
1723 2517 4.870123 AGATGCTGCTCCTATTACTCTG 57.130 45.455 0.00 0.00 0.00 3.35
1969 3549 3.592059 CAACATTTGCCCAAGATTCCTG 58.408 45.455 0.00 0.00 0.00 3.86
2007 3593 2.738846 CTGTGTACTGCTGGCAAACTAG 59.261 50.000 0.00 0.00 0.00 2.57
2041 3820 2.676463 GCCAGACTCACAGAAGATCCAC 60.676 54.545 0.00 0.00 0.00 4.02
2052 3839 6.094603 ACTTCAAAATATGATGCCAGACTCAC 59.905 38.462 0.00 0.00 38.03 3.51
2054 3841 6.690194 ACTTCAAAATATGATGCCAGACTC 57.310 37.500 0.00 0.00 38.03 3.36
2077 3864 6.978659 GGACACGACATCAAGATAGTCATTTA 59.021 38.462 0.00 0.00 32.68 1.40
2083 3870 4.017126 TCAGGACACGACATCAAGATAGT 58.983 43.478 0.00 0.00 0.00 2.12
2092 3879 2.233676 TGCAGTAATCAGGACACGACAT 59.766 45.455 0.00 0.00 0.00 3.06
2183 4015 9.562583 CAGTCTTGAACTAGTGTCTAGATTAAC 57.437 37.037 15.97 0.00 36.07 2.01
2384 4220 3.225104 AGACCACAAAATGTGCACATCT 58.775 40.909 31.45 17.13 46.51 2.90
2648 4871 7.883391 TGTGATAAAACTTTGAACCTGGTAA 57.117 32.000 0.00 0.00 0.00 2.85
2843 5074 8.241367 GGTATTAATTGGTTGTGTTCAGTAAGG 58.759 37.037 0.00 0.00 0.00 2.69
3484 6111 7.324616 GCAAATGACAAACAAAGATAGTGAGAC 59.675 37.037 0.00 0.00 0.00 3.36
3737 6384 9.944079 AGGATATACTATAGCATAGGAACACAT 57.056 33.333 0.00 0.00 0.00 3.21
3783 6445 1.618837 AGCTAAGACAACTCGCCTGAA 59.381 47.619 0.00 0.00 0.00 3.02
3877 6539 9.817809 AGAATCAGCGACTAAAATAATTCAGTA 57.182 29.630 0.00 0.00 0.00 2.74
4353 7059 3.192466 GGTGCATTGGAAATTCAGCATC 58.808 45.455 0.00 0.00 34.24 3.91
4579 7303 2.103094 CAGAAGGGTCACACTCACAAGA 59.897 50.000 0.00 0.00 0.00 3.02
4603 7327 4.598807 AGGACATCATAGTGAATGCCCATA 59.401 41.667 0.00 0.00 35.38 2.74
4605 7329 2.779430 AGGACATCATAGTGAATGCCCA 59.221 45.455 0.00 0.00 35.38 5.36
4618 7342 1.663379 CGCGTGGGTAGAGGACATCA 61.663 60.000 0.00 0.00 0.00 3.07
4621 7345 3.755628 GCGCGTGGGTAGAGGACA 61.756 66.667 8.43 0.00 0.00 4.02
4668 7392 3.011032 AGCAGGATCTTTTCACTGGGAAT 59.989 43.478 0.00 0.00 34.91 3.01
4676 7400 6.305272 ACTCTAATCAGCAGGATCTTTTCA 57.695 37.500 0.00 0.00 34.28 2.69
4798 7525 1.605710 CTGTTTGTGCCAACAGAGGAG 59.394 52.381 12.89 0.00 46.91 3.69
4799 7526 1.679139 CTGTTTGTGCCAACAGAGGA 58.321 50.000 12.89 0.00 46.91 3.71
4800 7527 0.031178 GCTGTTTGTGCCAACAGAGG 59.969 55.000 19.50 0.00 46.91 3.69
4801 7528 1.027357 AGCTGTTTGTGCCAACAGAG 58.973 50.000 19.50 7.07 46.91 3.35
4802 7529 0.740149 CAGCTGTTTGTGCCAACAGA 59.260 50.000 19.50 0.00 46.91 3.41
4803 7530 0.249155 CCAGCTGTTTGTGCCAACAG 60.249 55.000 13.81 13.58 46.73 3.16
4817 7544 0.541392 TCAATGTATCGGCACCAGCT 59.459 50.000 0.00 0.00 41.70 4.24
4819 7546 2.804527 CTGATCAATGTATCGGCACCAG 59.195 50.000 0.00 0.00 0.00 4.00
4820 7547 2.170397 ACTGATCAATGTATCGGCACCA 59.830 45.455 0.00 0.00 35.95 4.17
4821 7548 2.838736 ACTGATCAATGTATCGGCACC 58.161 47.619 0.00 0.00 35.95 5.01
4822 7549 3.430218 GCTACTGATCAATGTATCGGCAC 59.570 47.826 0.00 0.00 35.95 5.01
4823 7550 3.321968 AGCTACTGATCAATGTATCGGCA 59.678 43.478 0.00 0.00 35.95 5.69
4824 7551 3.677121 CAGCTACTGATCAATGTATCGGC 59.323 47.826 0.00 0.00 35.95 5.54
4825 7552 3.677121 GCAGCTACTGATCAATGTATCGG 59.323 47.826 0.00 0.00 38.09 4.18
4826 7553 4.554292 AGCAGCTACTGATCAATGTATCG 58.446 43.478 0.00 0.00 32.44 2.92
4835 7562 1.484240 ACAAGGGAGCAGCTACTGATC 59.516 52.381 4.10 4.31 44.92 2.92
4836 7563 1.484240 GACAAGGGAGCAGCTACTGAT 59.516 52.381 4.10 0.00 32.44 2.90
4837 7564 0.898320 GACAAGGGAGCAGCTACTGA 59.102 55.000 4.10 0.00 32.44 3.41
4838 7565 0.901124 AGACAAGGGAGCAGCTACTG 59.099 55.000 4.10 0.00 34.12 2.74
4839 7566 0.901124 CAGACAAGGGAGCAGCTACT 59.099 55.000 4.10 0.00 0.00 2.57
4840 7567 0.898320 TCAGACAAGGGAGCAGCTAC 59.102 55.000 0.00 0.00 0.00 3.58
4841 7568 1.552337 CTTCAGACAAGGGAGCAGCTA 59.448 52.381 0.00 0.00 0.00 3.32
4842 7569 0.324285 CTTCAGACAAGGGAGCAGCT 59.676 55.000 0.00 0.00 0.00 4.24
4941 7688 6.655078 AGATGGAAGCAATTAACAAGTTGT 57.345 33.333 1.64 1.64 0.00 3.32
5003 7760 4.142816 CCATGTCAAAAACAAAAACGCCAA 60.143 37.500 0.00 0.00 42.37 4.52
5045 7802 6.370442 TGTCTTTCAGAAATAACATACCGGTG 59.630 38.462 19.93 3.36 0.00 4.94
5047 7804 6.370442 TGTGTCTTTCAGAAATAACATACCGG 59.630 38.462 0.00 0.00 0.00 5.28
5064 7821 4.526970 AGACATGACAAACCTGTGTCTTT 58.473 39.130 0.00 0.00 46.70 2.52
5090 7848 2.916702 ACACTGCTGTGAACAGATGA 57.083 45.000 27.99 0.00 46.59 2.92
5106 7864 6.483640 GGATAGGTAACAAAGATCATCCACAC 59.516 42.308 0.00 0.00 41.41 3.82
5145 7903 8.484214 TGCATATCTACTTCACTAGGAATCTT 57.516 34.615 0.00 0.00 34.32 2.40
5146 7904 8.663209 ATGCATATCTACTTCACTAGGAATCT 57.337 34.615 0.00 0.00 34.32 2.40
5147 7905 8.748412 AGATGCATATCTACTTCACTAGGAATC 58.252 37.037 0.00 0.00 41.82 2.52
5148 7906 8.663209 AGATGCATATCTACTTCACTAGGAAT 57.337 34.615 0.00 0.00 41.82 3.01
5249 8007 6.344500 CAGAGTAACCAGCACAGATAGAAAT 58.656 40.000 0.00 0.00 0.00 2.17
5259 8017 1.884235 ACAAGCAGAGTAACCAGCAC 58.116 50.000 0.00 0.00 0.00 4.40
5270 8028 4.774726 AGATCTAGTTCAGGAACAAGCAGA 59.225 41.667 14.06 10.34 43.47 4.26
5279 8037 7.556996 GGTTGTAGTTCTAGATCTAGTTCAGGA 59.443 40.741 25.54 6.36 34.84 3.86
5290 8048 6.204882 GCACTTGTTTGGTTGTAGTTCTAGAT 59.795 38.462 0.00 0.00 0.00 1.98
5343 8101 7.576477 GCTGCTCAAATCTAGGTTGATCTTTTT 60.576 37.037 9.38 0.00 34.59 1.94
5344 8102 6.127786 GCTGCTCAAATCTAGGTTGATCTTTT 60.128 38.462 9.38 0.00 34.59 2.27
5345 8103 5.356470 GCTGCTCAAATCTAGGTTGATCTTT 59.644 40.000 9.38 0.00 34.59 2.52
5346 8104 4.880696 GCTGCTCAAATCTAGGTTGATCTT 59.119 41.667 9.38 0.00 34.59 2.40
5347 8105 4.163839 AGCTGCTCAAATCTAGGTTGATCT 59.836 41.667 0.00 4.15 34.59 2.75
5350 8108 3.261643 TCAGCTGCTCAAATCTAGGTTGA 59.738 43.478 9.47 8.80 33.97 3.18
5353 8111 3.008375 TGTTCAGCTGCTCAAATCTAGGT 59.992 43.478 9.47 0.00 0.00 3.08
5383 8141 6.018016 TGCATATGTATTATGTGTCAGTGCAC 60.018 38.462 9.40 9.40 39.99 4.57
5429 8190 4.943093 TGTACCATGTGTCATTGAAGGATG 59.057 41.667 0.00 0.00 0.00 3.51
5430 8191 5.178096 TGTACCATGTGTCATTGAAGGAT 57.822 39.130 0.00 0.00 0.00 3.24
5431 8192 4.632327 TGTACCATGTGTCATTGAAGGA 57.368 40.909 0.00 0.00 0.00 3.36
5432 8193 4.439153 GCATGTACCATGTGTCATTGAAGG 60.439 45.833 6.13 0.00 0.00 3.46
5466 8227 6.418101 AGCAAGTTGAAAGCTCCTTATCATA 58.582 36.000 7.16 0.00 32.05 2.15
5471 8232 5.852282 AAAAGCAAGTTGAAAGCTCCTTA 57.148 34.783 7.16 0.00 37.70 2.69
5496 8257 5.471116 TGAATTACTATGTGATGATGCAGCC 59.529 40.000 0.00 0.00 0.00 4.85
5497 8258 6.549912 TGAATTACTATGTGATGATGCAGC 57.450 37.500 0.00 0.00 0.00 5.25
5508 8269 7.126421 AGAGGACAAGACCATGAATTACTATGT 59.874 37.037 0.00 0.00 0.00 2.29
5513 8274 4.333926 GCAGAGGACAAGACCATGAATTAC 59.666 45.833 0.00 0.00 0.00 1.89
5564 8325 3.362706 TCTCCGCTACTACTGGTCAAAT 58.637 45.455 0.00 0.00 0.00 2.32
5619 8380 5.648572 GTGATACACTGTAACTACCAGACC 58.351 45.833 0.00 0.00 0.00 3.85
5638 8399 1.339055 CCACCATGTGTTCCTCGTGAT 60.339 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.