Multiple sequence alignment - TraesCS4A01G321400

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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 TraesCS4A01G321400 chr4A 100.000 5161 0 0 1 5161 609819981 609814821 0.000000e+00 9531.0
1 TraesCS4A01G321400 chr4A 99.306 1008 7 0 4154 5161 585667691 585668698 0.000000e+00 1823.0
2 TraesCS4A01G321400 chr4A 86.329 1441 164 24 1965 3387 609928404 609926979 0.000000e+00 1539.0
3 TraesCS4A01G321400 chr4A 85.543 1418 169 17 2005 3392 609920123 609918712 0.000000e+00 1450.0
4 TraesCS4A01G321400 chr4A 85.305 558 55 11 3603 4153 609918605 609918068 7.550000e-153 551.0
5 TraesCS4A01G321400 chr4A 82.398 517 66 17 3638 4151 610022074 610021580 1.330000e-115 427.0
6 TraesCS4A01G321400 chr4A 85.502 269 36 1 1 266 17396425 17396157 1.420000e-70 278.0
7 TraesCS4A01G321400 chr4A 84.932 219 22 9 3937 4151 609926582 609926371 1.460000e-50 211.0
8 TraesCS4A01G321400 chr4A 86.577 149 14 5 868 1013 609921913 609921768 5.350000e-35 159.0
9 TraesCS4A01G321400 chr5B 89.070 1958 136 37 1461 3392 705271015 705272920 0.000000e+00 2359.0
10 TraesCS4A01G321400 chr5B 99.306 1008 7 0 4154 5161 139343831 139344838 0.000000e+00 1823.0
11 TraesCS4A01G321400 chr5B 83.234 2016 237 63 1426 3387 705137015 705138983 0.000000e+00 1757.0
12 TraesCS4A01G321400 chr5B 85.482 1412 154 18 1976 3370 705065626 705067003 0.000000e+00 1424.0
13 TraesCS4A01G321400 chr5B 91.938 645 39 7 3521 4153 705272984 705273627 0.000000e+00 891.0
14 TraesCS4A01G321400 chr5B 88.193 559 53 7 3600 4151 705259865 705260417 0.000000e+00 654.0
15 TraesCS4A01G321400 chr5B 84.074 653 71 14 1 644 705269481 705270109 2.660000e-167 599.0
16 TraesCS4A01G321400 chr5B 85.395 582 49 23 3574 4151 705067003 705067552 5.800000e-159 571.0
17 TraesCS4A01G321400 chr5B 89.631 434 31 5 833 1262 705270266 705270689 1.630000e-149 540.0
18 TraesCS4A01G321400 chr5B 86.617 269 33 1 1 266 546416713 546416445 1.410000e-75 294.0
19 TraesCS4A01G321400 chr5B 95.513 156 7 0 1304 1459 705270774 705270929 3.090000e-62 250.0
20 TraesCS4A01G321400 chr5B 85.034 147 15 5 867 1010 705065124 705065266 5.390000e-30 143.0
21 TraesCS4A01G321400 chr5B 83.544 158 18 7 861 1012 705256815 705256970 1.940000e-29 141.0
22 TraesCS4A01G321400 chr6B 99.207 1009 8 0 4153 5161 159176244 159175236 0.000000e+00 1820.0
23 TraesCS4A01G321400 chr6B 99.206 1008 8 0 4154 5161 669044078 669045085 0.000000e+00 1818.0
24 TraesCS4A01G321400 chr6B 98.810 1008 12 0 4154 5161 712303142 712302135 0.000000e+00 1796.0
25 TraesCS4A01G321400 chr4B 99.206 1008 8 0 4154 5161 420204594 420205601 0.000000e+00 1818.0
26 TraesCS4A01G321400 chr4B 85.714 147 20 1 544 689 659597638 659597492 2.490000e-33 154.0
27 TraesCS4A01G321400 chr5D 83.640 2011 247 51 1426 3387 557546681 557544704 0.000000e+00 1816.0
28 TraesCS4A01G321400 chr5D 86.447 1424 157 12 1965 3370 558032754 558034159 0.000000e+00 1528.0
29 TraesCS4A01G321400 chr5D 85.311 1416 166 21 2005 3392 557538491 557537090 0.000000e+00 1424.0
30 TraesCS4A01G321400 chr5D 88.330 557 51 10 3603 4151 557536982 557536432 0.000000e+00 656.0
31 TraesCS4A01G321400 chr5D 85.273 550 50 18 3574 4121 558034159 558034679 5.880000e-149 538.0
32 TraesCS4A01G321400 chr5D 84.151 265 29 10 3893 4151 557544379 557544122 1.440000e-60 244.0
33 TraesCS4A01G321400 chr5D 84.659 176 17 5 867 1035 557546955 557546783 3.200000e-37 167.0
34 TraesCS4A01G321400 chr5D 84.302 172 24 3 517 687 286187623 286187454 1.150000e-36 165.0
35 TraesCS4A01G321400 chr5D 85.106 141 15 5 876 1013 557541013 557540876 6.970000e-29 139.0
36 TraesCS4A01G321400 chr2B 98.022 1011 17 1 4154 5161 10802430 10801420 0.000000e+00 1753.0
37 TraesCS4A01G321400 chr2B 91.865 1008 80 2 4154 5161 682793284 682794289 0.000000e+00 1406.0
38 TraesCS4A01G321400 chr3A 97.421 1008 26 0 4154 5161 654384123 654385130 0.000000e+00 1718.0
39 TraesCS4A01G321400 chr3A 81.858 1367 207 16 1967 3326 734128937 734130269 0.000000e+00 1112.0
40 TraesCS4A01G321400 chr3B 82.830 1357 204 13 1994 3347 811446094 811447424 0.000000e+00 1188.0
41 TraesCS4A01G321400 chr3B 81.391 532 73 17 3540 4065 811447532 811448043 1.340000e-110 411.0
42 TraesCS4A01G321400 chr3B 86.989 269 32 1 1 266 378694308 378694576 3.020000e-77 300.0
43 TraesCS4A01G321400 chr6A 81.157 536 72 14 3525 4060 32670247 32670753 2.240000e-108 403.0
44 TraesCS4A01G321400 chr6A 87.361 269 31 1 1 266 549051052 549050784 6.490000e-79 305.0
45 TraesCS4A01G321400 chr6A 82.707 133 20 2 904 1036 32668083 32668212 1.170000e-21 115.0
46 TraesCS4A01G321400 chr7A 87.407 270 29 3 1 266 26772385 26772653 6.490000e-79 305.0
47 TraesCS4A01G321400 chr4D 87.452 263 30 1 7 266 498965828 498965566 3.020000e-77 300.0
48 TraesCS4A01G321400 chr4D 84.524 168 25 1 522 689 406238650 406238816 1.150000e-36 165.0
49 TraesCS4A01G321400 chr1D 87.037 270 30 3 1 266 482920792 482921060 3.020000e-77 300.0
50 TraesCS4A01G321400 chr3D 86.667 270 28 5 1 266 20900588 20900323 5.050000e-75 292.0
51 TraesCS4A01G321400 chr1A 86.452 155 16 3 535 687 47212811 47212660 1.150000e-36 165.0
52 TraesCS4A01G321400 chr2D 82.667 150 24 2 541 689 49400407 49400555 1.170000e-26 132.0
53 TraesCS4A01G321400 chr2A 82.836 134 20 3 514 646 92477292 92477423 3.270000e-22 117.0
54 TraesCS4A01G321400 chr6D 87.755 98 12 0 939 1036 30248355 30248258 1.170000e-21 115.0
55 TraesCS4A01G321400 chr6D 79.641 167 24 7 916 1075 30239561 30239398 1.520000e-20 111.0
56 TraesCS4A01G321400 chr7D 97.143 35 1 0 630 664 566128581 566128615 5.580000e-05 60.2


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 TraesCS4A01G321400 chr4A 609814821 609819981 5160 True 9531.000000 9531 100.000000 1 5161 1 chr4A.!!$R2 5160
1 TraesCS4A01G321400 chr4A 585667691 585668698 1007 False 1823.000000 1823 99.306000 4154 5161 1 chr4A.!!$F1 1007
2 TraesCS4A01G321400 chr4A 609926371 609928404 2033 True 875.000000 1539 85.630500 1965 4151 2 chr4A.!!$R5 2186
3 TraesCS4A01G321400 chr4A 609918068 609921913 3845 True 720.000000 1450 85.808333 868 4153 3 chr4A.!!$R4 3285
4 TraesCS4A01G321400 chr5B 139343831 139344838 1007 False 1823.000000 1823 99.306000 4154 5161 1 chr5B.!!$F1 1007
5 TraesCS4A01G321400 chr5B 705137015 705138983 1968 False 1757.000000 1757 83.234000 1426 3387 1 chr5B.!!$F2 1961
6 TraesCS4A01G321400 chr5B 705269481 705273627 4146 False 927.800000 2359 90.045200 1 4153 5 chr5B.!!$F5 4152
7 TraesCS4A01G321400 chr5B 705065124 705067552 2428 False 712.666667 1424 85.303667 867 4151 3 chr5B.!!$F3 3284
8 TraesCS4A01G321400 chr5B 705256815 705260417 3602 False 397.500000 654 85.868500 861 4151 2 chr5B.!!$F4 3290
9 TraesCS4A01G321400 chr6B 159175236 159176244 1008 True 1820.000000 1820 99.207000 4153 5161 1 chr6B.!!$R1 1008
10 TraesCS4A01G321400 chr6B 669044078 669045085 1007 False 1818.000000 1818 99.206000 4154 5161 1 chr6B.!!$F1 1007
11 TraesCS4A01G321400 chr6B 712302135 712303142 1007 True 1796.000000 1796 98.810000 4154 5161 1 chr6B.!!$R2 1007
12 TraesCS4A01G321400 chr4B 420204594 420205601 1007 False 1818.000000 1818 99.206000 4154 5161 1 chr4B.!!$F1 1007
13 TraesCS4A01G321400 chr5D 558032754 558034679 1925 False 1033.000000 1528 85.860000 1965 4121 2 chr5D.!!$F1 2156
14 TraesCS4A01G321400 chr5D 557536432 557546955 10523 True 741.000000 1816 85.199500 867 4151 6 chr5D.!!$R2 3284
15 TraesCS4A01G321400 chr2B 10801420 10802430 1010 True 1753.000000 1753 98.022000 4154 5161 1 chr2B.!!$R1 1007
16 TraesCS4A01G321400 chr2B 682793284 682794289 1005 False 1406.000000 1406 91.865000 4154 5161 1 chr2B.!!$F1 1007
17 TraesCS4A01G321400 chr3A 654384123 654385130 1007 False 1718.000000 1718 97.421000 4154 5161 1 chr3A.!!$F1 1007
18 TraesCS4A01G321400 chr3A 734128937 734130269 1332 False 1112.000000 1112 81.858000 1967 3326 1 chr3A.!!$F2 1359
19 TraesCS4A01G321400 chr3B 811446094 811448043 1949 False 799.500000 1188 82.110500 1994 4065 2 chr3B.!!$F2 2071
20 TraesCS4A01G321400 chr6A 32668083 32670753 2670 False 259.000000 403 81.932000 904 4060 2 chr6A.!!$F1 3156

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
275 279 0.106519 CCTTTATGGCCCCCTGAGTG 60.107 60.0 0.00 0.0 0.00 3.51 F
729 736 0.167470 CGTACTCGCTCTCCGTTTCA 59.833 55.0 0.00 0.0 38.35 2.69 F
1428 1749 0.034756 AGGCACACACTGTAATGCGA 59.965 50.0 10.14 0.0 39.02 5.10 F
2628 4105 0.179062 GCTGATCTGAACGGCTCCAT 60.179 55.0 11.07 0.0 36.79 3.41 F
3777 13100 0.742281 CCGACAACATGGAGGAGCAG 60.742 60.0 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1351 0.392595 CTCCCCAGTTAGGCGAAACC 60.393 60.000 0.00 0.00 39.61 3.27 R
2566 4043 0.541392 CATCTGGTCCGATCCAACCA 59.459 55.000 12.11 12.11 43.20 3.67 R
2893 4382 1.589993 CAGCCACAGCCGATAGTCG 60.590 63.158 0.00 0.00 41.25 4.18 R
4133 13487 0.460109 CCGACCGATCAATCTGCACA 60.460 55.000 0.00 0.00 0.00 4.57 R
4826 14183 2.174360 GCCCAGAAATCCTCTTGCTTT 58.826 47.619 0.00 0.00 29.07 3.51 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
26 27 0.819582 CCATCACCTTGGCCACAATC 59.180 55.000 3.88 0.00 35.73 2.67
29 30 1.619654 TCACCTTGGCCACAATCTTG 58.380 50.000 3.88 0.00 35.73 3.02
30 31 0.604578 CACCTTGGCCACAATCTTGG 59.395 55.000 3.88 1.66 39.98 3.61
64 65 6.122964 GGATCAAACTGATAGGCCTAAAGTT 58.877 40.000 27.01 27.01 37.20 2.66
122 126 0.109597 CATTTGCGGAGTTGAGCCAC 60.110 55.000 0.00 0.00 0.00 5.01
124 128 1.165907 TTTGCGGAGTTGAGCCACTG 61.166 55.000 0.00 0.00 0.00 3.66
125 129 2.743928 GCGGAGTTGAGCCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
146 150 4.081752 TGGAAGTTCACAACATGCAAACTT 60.082 37.500 9.56 9.56 37.80 2.66
158 162 4.458295 ACATGCAAACTTGAGAAGATGGAG 59.542 41.667 0.00 0.00 0.00 3.86
172 176 7.065120 AGAAGATGGAGATGACCTTCATAAG 57.935 40.000 0.00 0.00 41.20 1.73
176 180 6.786461 AGATGGAGATGACCTTCATAAGATCA 59.214 38.462 0.00 0.00 41.20 2.92
185 189 9.736414 ATGACCTTCATAAGATCATCCTTTATG 57.264 33.333 0.00 0.49 34.88 1.90
197 201 4.646040 TCATCCTTTATGATTGGCCAACAG 59.354 41.667 23.27 9.71 39.77 3.16
209 213 1.268079 GGCCAACAGCTCTTGAAGAAC 59.732 52.381 2.93 0.00 43.05 3.01
210 214 1.949525 GCCAACAGCTCTTGAAGAACA 59.050 47.619 2.93 0.00 38.99 3.18
223 227 2.158871 TGAAGAACACACCGGTAAAGCT 60.159 45.455 6.87 0.00 0.00 3.74
229 233 1.290955 CACCGGTAAAGCTGTCGGA 59.709 57.895 6.87 0.00 44.69 4.55
232 236 1.590147 CGGTAAAGCTGTCGGACCT 59.410 57.895 5.55 0.00 0.00 3.85
236 240 0.609957 TAAAGCTGTCGGACCTCGGA 60.610 55.000 5.55 0.00 39.77 4.55
242 246 1.751927 GTCGGACCTCGGAGCCTTA 60.752 63.158 0.00 0.00 39.77 2.69
274 278 2.321720 CCTTTATGGCCCCCTGAGT 58.678 57.895 0.00 0.00 0.00 3.41
275 279 0.106519 CCTTTATGGCCCCCTGAGTG 60.107 60.000 0.00 0.00 0.00 3.51
276 280 0.753111 CTTTATGGCCCCCTGAGTGC 60.753 60.000 0.00 0.00 0.00 4.40
281 285 0.327095 TGGCCCCCTGAGTGCTTATA 60.327 55.000 0.00 0.00 0.00 0.98
282 286 1.068121 GGCCCCCTGAGTGCTTATAT 58.932 55.000 0.00 0.00 0.00 0.86
283 287 1.003696 GGCCCCCTGAGTGCTTATATC 59.996 57.143 0.00 0.00 0.00 1.63
286 290 3.871463 GCCCCCTGAGTGCTTATATCATG 60.871 52.174 0.00 0.00 0.00 3.07
287 291 3.328931 CCCCCTGAGTGCTTATATCATGT 59.671 47.826 0.00 0.00 0.00 3.21
288 292 4.564406 CCCCCTGAGTGCTTATATCATGTC 60.564 50.000 0.00 0.00 0.00 3.06
289 293 4.040829 CCCCTGAGTGCTTATATCATGTCA 59.959 45.833 0.00 0.00 0.00 3.58
290 294 5.455183 CCCCTGAGTGCTTATATCATGTCAA 60.455 44.000 0.00 0.00 0.00 3.18
330 337 6.975197 TCAAGAGCATTTTCTATAGTCACTCG 59.025 38.462 0.00 0.00 0.00 4.18
366 373 5.808030 TGTAAGCCAAGTACTTTTTGTTTGC 59.192 36.000 5.07 6.37 0.00 3.68
371 378 2.804647 AGTACTTTTTGTTTGCCGTGC 58.195 42.857 0.00 0.00 0.00 5.34
372 379 1.515221 GTACTTTTTGTTTGCCGTGCG 59.485 47.619 0.00 0.00 0.00 5.34
374 381 0.570272 CTTTTTGTTTGCCGTGCGTC 59.430 50.000 0.00 0.00 0.00 5.19
375 382 0.802607 TTTTTGTTTGCCGTGCGTCC 60.803 50.000 0.00 0.00 0.00 4.79
378 385 2.054140 TTGTTTGCCGTGCGTCCTTC 62.054 55.000 0.00 0.00 0.00 3.46
379 386 2.203084 TTTGCCGTGCGTCCTTCA 60.203 55.556 0.00 0.00 0.00 3.02
381 388 1.169661 TTTGCCGTGCGTCCTTCATT 61.170 50.000 0.00 0.00 0.00 2.57
383 390 1.154225 GCCGTGCGTCCTTCATTTG 60.154 57.895 0.00 0.00 0.00 2.32
384 391 1.573829 GCCGTGCGTCCTTCATTTGA 61.574 55.000 0.00 0.00 0.00 2.69
385 392 1.086696 CCGTGCGTCCTTCATTTGAT 58.913 50.000 0.00 0.00 0.00 2.57
386 393 2.276201 CCGTGCGTCCTTCATTTGATA 58.724 47.619 0.00 0.00 0.00 2.15
387 394 2.030457 CCGTGCGTCCTTCATTTGATAC 59.970 50.000 0.00 0.00 0.00 2.24
388 395 2.930040 CGTGCGTCCTTCATTTGATACT 59.070 45.455 0.00 0.00 0.00 2.12
389 396 3.000322 CGTGCGTCCTTCATTTGATACTC 60.000 47.826 0.00 0.00 0.00 2.59
390 397 3.000322 GTGCGTCCTTCATTTGATACTCG 60.000 47.826 0.00 0.00 0.00 4.18
391 398 2.540101 GCGTCCTTCATTTGATACTCGG 59.460 50.000 0.00 0.00 0.00 4.63
406 413 6.811954 TGATACTCGGCTTATGTTGATGTAA 58.188 36.000 0.00 0.00 0.00 2.41
415 422 5.050972 GCTTATGTTGATGTAAGCCGAGTAC 60.051 44.000 5.97 0.00 44.30 2.73
416 423 4.737855 ATGTTGATGTAAGCCGAGTACT 57.262 40.909 0.00 0.00 0.00 2.73
438 445 9.983804 GTACTCATATTTTTACACTTGGCTTAC 57.016 33.333 0.00 0.00 0.00 2.34
439 446 8.630054 ACTCATATTTTTACACTTGGCTTACA 57.370 30.769 0.00 0.00 0.00 2.41
442 449 7.393234 TCATATTTTTACACTTGGCTTACAGCT 59.607 33.333 0.00 0.00 41.99 4.24
473 480 4.154015 TGGCGACATGTGATTTTTCTGTAG 59.846 41.667 1.15 0.00 33.40 2.74
474 481 4.154195 GGCGACATGTGATTTTTCTGTAGT 59.846 41.667 1.15 0.00 0.00 2.73
475 482 5.350365 GGCGACATGTGATTTTTCTGTAGTA 59.650 40.000 1.15 0.00 0.00 1.82
491 498 8.706322 TTCTGTAGTATGACCTCTAATGCATA 57.294 34.615 0.00 0.00 0.00 3.14
492 499 8.885693 TCTGTAGTATGACCTCTAATGCATAT 57.114 34.615 0.00 0.00 0.00 1.78
493 500 8.743714 TCTGTAGTATGACCTCTAATGCATATG 58.256 37.037 0.00 0.00 0.00 1.78
494 501 8.650143 TGTAGTATGACCTCTAATGCATATGA 57.350 34.615 6.97 0.05 0.00 2.15
495 502 9.088987 TGTAGTATGACCTCTAATGCATATGAA 57.911 33.333 6.97 0.00 0.00 2.57
551 558 4.166539 TCATTTTCCCCATTCATGGTTGT 58.833 39.130 5.09 0.00 46.65 3.32
554 561 5.674052 TTTTCCCCATTCATGGTTGTATG 57.326 39.130 5.09 0.00 46.65 2.39
600 607 0.333993 ATTGCATCTTGAGGTGGGCT 59.666 50.000 0.00 0.00 0.00 5.19
607 614 1.564348 TCTTGAGGTGGGCTTTATCCC 59.436 52.381 0.00 0.00 46.73 3.85
637 644 6.720112 AATTGTATAGTGATTTGGCATGCT 57.280 33.333 18.92 0.00 0.00 3.79
638 645 6.720112 ATTGTATAGTGATTTGGCATGCTT 57.280 33.333 18.92 0.00 0.00 3.91
639 646 5.503662 TGTATAGTGATTTGGCATGCTTG 57.496 39.130 18.92 0.00 0.00 4.01
689 696 9.969001 GAGAATGACTCTCTTAGGTATATAGGT 57.031 37.037 0.00 0.00 46.32 3.08
718 725 7.313951 AGGTATATAGGATTAACGTACTCGC 57.686 40.000 0.00 0.00 41.18 5.03
719 726 7.108847 AGGTATATAGGATTAACGTACTCGCT 58.891 38.462 0.00 0.00 41.18 4.93
720 727 7.279758 AGGTATATAGGATTAACGTACTCGCTC 59.720 40.741 0.00 0.00 41.18 5.03
721 728 7.279758 GGTATATAGGATTAACGTACTCGCTCT 59.720 40.741 0.00 0.00 41.18 4.09
722 729 3.967203 AGGATTAACGTACTCGCTCTC 57.033 47.619 0.00 0.00 41.18 3.20
723 730 2.617774 AGGATTAACGTACTCGCTCTCC 59.382 50.000 0.00 0.00 41.18 3.71
724 731 2.601741 GGATTAACGTACTCGCTCTCCG 60.602 54.545 0.00 0.00 41.18 4.63
725 732 1.442769 TTAACGTACTCGCTCTCCGT 58.557 50.000 0.00 0.00 41.18 4.69
726 733 1.442769 TAACGTACTCGCTCTCCGTT 58.557 50.000 0.00 0.00 43.35 4.44
727 734 0.595095 AACGTACTCGCTCTCCGTTT 59.405 50.000 0.00 0.00 38.46 3.60
728 735 0.167689 ACGTACTCGCTCTCCGTTTC 59.832 55.000 0.00 0.00 41.18 2.78
729 736 0.167470 CGTACTCGCTCTCCGTTTCA 59.833 55.000 0.00 0.00 38.35 2.69
730 737 1.615502 GTACTCGCTCTCCGTTTCAC 58.384 55.000 0.00 0.00 38.35 3.18
731 738 1.199558 GTACTCGCTCTCCGTTTCACT 59.800 52.381 0.00 0.00 38.35 3.41
732 739 0.674534 ACTCGCTCTCCGTTTCACTT 59.325 50.000 0.00 0.00 38.35 3.16
733 740 1.068741 ACTCGCTCTCCGTTTCACTTT 59.931 47.619 0.00 0.00 38.35 2.66
734 741 1.721926 CTCGCTCTCCGTTTCACTTTC 59.278 52.381 0.00 0.00 38.35 2.62
735 742 1.340248 TCGCTCTCCGTTTCACTTTCT 59.660 47.619 0.00 0.00 38.35 2.52
736 743 2.555325 TCGCTCTCCGTTTCACTTTCTA 59.445 45.455 0.00 0.00 38.35 2.10
737 744 3.192844 TCGCTCTCCGTTTCACTTTCTAT 59.807 43.478 0.00 0.00 38.35 1.98
738 745 3.927142 CGCTCTCCGTTTCACTTTCTATT 59.073 43.478 0.00 0.00 0.00 1.73
739 746 5.100259 CGCTCTCCGTTTCACTTTCTATTA 58.900 41.667 0.00 0.00 0.00 0.98
740 747 5.230306 CGCTCTCCGTTTCACTTTCTATTAG 59.770 44.000 0.00 0.00 0.00 1.73
741 748 6.100668 GCTCTCCGTTTCACTTTCTATTAGT 58.899 40.000 0.00 0.00 0.00 2.24
742 749 6.590677 GCTCTCCGTTTCACTTTCTATTAGTT 59.409 38.462 0.00 0.00 0.00 2.24
743 750 7.117956 GCTCTCCGTTTCACTTTCTATTAGTTT 59.882 37.037 0.00 0.00 0.00 2.66
744 751 8.530269 TCTCCGTTTCACTTTCTATTAGTTTC 57.470 34.615 0.00 0.00 0.00 2.78
745 752 8.365647 TCTCCGTTTCACTTTCTATTAGTTTCT 58.634 33.333 0.00 0.00 0.00 2.52
746 753 9.635520 CTCCGTTTCACTTTCTATTAGTTTCTA 57.364 33.333 0.00 0.00 0.00 2.10
747 754 9.415544 TCCGTTTCACTTTCTATTAGTTTCTAC 57.584 33.333 0.00 0.00 0.00 2.59
748 755 9.199982 CCGTTTCACTTTCTATTAGTTTCTACA 57.800 33.333 0.00 0.00 0.00 2.74
765 772 8.850156 AGTTTCTACAAATTATTCAGTTGTGCT 58.150 29.630 0.00 0.00 36.23 4.40
766 773 8.905702 GTTTCTACAAATTATTCAGTTGTGCTG 58.094 33.333 0.00 0.00 46.34 4.41
780 787 5.084385 GTTGTGCTGAAGAGACAACTAAC 57.916 43.478 14.11 0.00 43.96 2.34
781 788 4.672587 TGTGCTGAAGAGACAACTAACT 57.327 40.909 0.00 0.00 0.00 2.24
936 1060 2.351418 CTGCTCACAGTCGTCAACAAAA 59.649 45.455 0.00 0.00 39.22 2.44
1082 1219 4.109050 CCTCTATGCTTTCTGTCGACTTC 58.891 47.826 17.92 0.23 0.00 3.01
1105 1258 9.566530 CTTCTATTCGTGACCAATCAGATATAG 57.433 37.037 0.00 0.00 34.75 1.31
1128 1282 4.978580 GTCTCTGATTTGGTGTGCTTTTTC 59.021 41.667 0.00 0.00 0.00 2.29
1159 1324 9.297586 CTCTTGGTAAAAGAAAACTTGGTTAAC 57.702 33.333 0.00 0.00 0.00 2.01
1161 1326 9.297586 CTTGGTAAAAGAAAACTTGGTTAACTC 57.702 33.333 5.42 0.00 0.00 3.01
1177 1342 7.481642 TGGTTAACTCGCACAGAAAAATAAAA 58.518 30.769 5.42 0.00 0.00 1.52
1186 1351 7.596995 TCGCACAGAAAAATAAAATTGGTTAGG 59.403 33.333 0.00 0.00 0.00 2.69
1302 1618 9.723601 TTTTTACAGTAATACCGTTATGAACCT 57.276 29.630 0.00 0.00 0.00 3.50
1366 1687 0.036294 AGGGAAAGCTTCGTAGGCAC 60.036 55.000 0.00 0.00 0.00 5.01
1410 1731 2.557924 TGCTGAATGTTGCCCAAAGTAG 59.442 45.455 0.00 0.00 0.00 2.57
1428 1749 0.034756 AGGCACACACTGTAATGCGA 59.965 50.000 10.14 0.00 39.02 5.10
1443 1764 5.584251 TGTAATGCGATGCAGTTAGATTTCA 59.416 36.000 0.00 0.00 43.65 2.69
1512 1922 3.427193 CCGCAAAACCCAAATCGTAAAAG 59.573 43.478 0.00 0.00 0.00 2.27
1526 1936 3.251487 TCGTAAAAGTTGGCTAAGTTGGC 59.749 43.478 3.38 1.96 30.07 4.52
1626 2567 2.030805 CGGGAGGCTTCAAGACTTTTTG 60.031 50.000 0.00 0.00 30.20 2.44
1628 2569 4.142038 GGGAGGCTTCAAGACTTTTTGTA 58.858 43.478 0.00 0.00 30.20 2.41
1673 2631 4.820173 AGTTTGCTTTGTAACTGGAGGTAC 59.180 41.667 0.00 0.00 33.55 3.34
1683 2641 3.116096 ACTGGAGGTACAGAGGCAATA 57.884 47.619 0.00 0.00 40.97 1.90
1733 2692 6.157820 TGAGGGAGAAATATTGTGACATGGTA 59.842 38.462 0.00 0.00 0.00 3.25
1738 2697 9.429359 GGAGAAATATTGTGACATGGTATCTAG 57.571 37.037 0.00 0.00 0.00 2.43
1758 2717 4.608170 AGGGAATGGGTGTATGTCAATT 57.392 40.909 0.00 0.00 0.00 2.32
1843 3199 4.173256 ACAAGGCGACAAAGAAAAACAAG 58.827 39.130 0.00 0.00 0.00 3.16
1883 3266 3.002038 ACAAGGGTGTTACGGTTTGAA 57.998 42.857 0.00 0.00 32.58 2.69
1889 3272 3.508402 GGGTGTTACGGTTTGAATCCATT 59.492 43.478 0.00 0.00 0.00 3.16
1891 3274 5.183522 GGGTGTTACGGTTTGAATCCATTTA 59.816 40.000 0.00 0.00 0.00 1.40
1893 3276 7.146648 GGTGTTACGGTTTGAATCCATTTAAA 58.853 34.615 0.00 0.00 0.00 1.52
1894 3277 7.652507 GGTGTTACGGTTTGAATCCATTTAAAA 59.347 33.333 0.00 0.00 28.95 1.52
1949 3403 9.841295 TGGTCCTGTTTTACCAATAGTAATATC 57.159 33.333 0.00 0.00 42.74 1.63
1950 3404 9.281371 GGTCCTGTTTTACCAATAGTAATATCC 57.719 37.037 0.00 0.00 40.62 2.59
2193 3667 6.367374 TTCAGGACCAATGTACTACAATGA 57.633 37.500 5.91 0.00 32.28 2.57
2200 3674 8.150945 GGACCAATGTACTACAATGACATCTAT 58.849 37.037 5.91 0.00 30.79 1.98
2566 4043 1.276421 CAGTTCAGGGATCCGACAACT 59.724 52.381 5.45 10.03 0.00 3.16
2586 4063 0.830648 GGTTGGATCGGACCAGATGA 59.169 55.000 10.36 0.00 41.19 2.92
2628 4105 0.179062 GCTGATCTGAACGGCTCCAT 60.179 55.000 11.07 0.00 36.79 3.41
2674 4151 6.931840 GTGAAGACTTCTTGAATTGGACTAGT 59.068 38.462 16.02 0.00 36.11 2.57
2893 4382 4.655762 TGTGCCAGATACTGTCATAGAC 57.344 45.455 0.00 0.00 0.00 2.59
2926 4415 2.300152 GTGGCTGAGGATCGATTATGGA 59.700 50.000 0.00 0.00 38.61 3.41
2968 4457 3.377172 CGTTCTTTGACTCAAAACAGGGT 59.623 43.478 5.72 0.00 32.75 4.34
3005 4494 1.998315 CTTGGAGCAACGAGACAGATG 59.002 52.381 0.00 0.00 0.00 2.90
3131 4630 5.232463 TCGGTGTAACATCTTTAACCTCAC 58.768 41.667 0.00 0.00 39.98 3.51
3248 4757 6.845302 TCGAAGAAATGAAATCAACCATCAG 58.155 36.000 0.00 0.00 0.00 2.90
3290 4799 6.503570 AGGGAGATCTATTTGAGATTAAGGGG 59.496 42.308 0.00 0.00 45.48 4.79
3350 4863 8.362639 ACGTGTTTACTTAGTCTTCCAAAGATA 58.637 33.333 0.00 0.00 40.18 1.98
3351 4864 9.367444 CGTGTTTACTTAGTCTTCCAAAGATAT 57.633 33.333 0.00 0.00 40.18 1.63
3387 4903 1.839424 AGGGTCATGCCAGTAAAAGC 58.161 50.000 8.20 0.00 39.65 3.51
3392 4908 5.073691 AGGGTCATGCCAGTAAAAGCTATAT 59.926 40.000 8.20 0.00 39.65 0.86
3393 4909 6.272324 AGGGTCATGCCAGTAAAAGCTATATA 59.728 38.462 8.20 0.00 39.65 0.86
3394 4910 7.037297 AGGGTCATGCCAGTAAAAGCTATATAT 60.037 37.037 8.20 0.00 39.65 0.86
3396 4912 9.014297 GGTCATGCCAGTAAAAGCTATATATTT 57.986 33.333 0.00 0.00 37.17 1.40
3421 4937 7.765695 AAGGGATATTACATTTACTGGCATG 57.234 36.000 0.00 0.00 0.00 4.06
3422 4938 7.090319 AGGGATATTACATTTACTGGCATGA 57.910 36.000 0.00 0.00 0.00 3.07
3423 4939 6.942576 AGGGATATTACATTTACTGGCATGAC 59.057 38.462 0.00 0.00 0.00 3.06
3424 4940 6.151144 GGGATATTACATTTACTGGCATGACC 59.849 42.308 0.00 0.00 39.84 4.02
3425 4941 6.151144 GGATATTACATTTACTGGCATGACCC 59.849 42.308 0.00 0.00 37.83 4.46
3426 4942 4.584638 TTACATTTACTGGCATGACCCT 57.415 40.909 0.00 0.00 37.83 4.34
3427 4943 3.456380 ACATTTACTGGCATGACCCTT 57.544 42.857 0.00 0.00 37.83 3.95
3428 4944 3.778265 ACATTTACTGGCATGACCCTTT 58.222 40.909 0.00 0.00 37.83 3.11
3429 4945 4.159557 ACATTTACTGGCATGACCCTTTT 58.840 39.130 0.00 0.00 37.83 2.27
3430 4946 4.592778 ACATTTACTGGCATGACCCTTTTT 59.407 37.500 0.00 0.00 37.83 1.94
3431 4947 4.599047 TTTACTGGCATGACCCTTTTTG 57.401 40.909 0.00 0.00 37.83 2.44
3432 4948 2.380064 ACTGGCATGACCCTTTTTGA 57.620 45.000 0.00 0.00 37.83 2.69
3433 4949 2.676748 ACTGGCATGACCCTTTTTGAA 58.323 42.857 0.00 0.00 37.83 2.69
3434 4950 2.629617 ACTGGCATGACCCTTTTTGAAG 59.370 45.455 0.00 0.00 37.83 3.02
3435 4951 2.629617 CTGGCATGACCCTTTTTGAAGT 59.370 45.455 0.00 0.00 37.83 3.01
3436 4952 3.826157 CTGGCATGACCCTTTTTGAAGTA 59.174 43.478 0.00 0.00 37.83 2.24
3437 4953 4.219115 TGGCATGACCCTTTTTGAAGTAA 58.781 39.130 0.00 0.00 37.83 2.24
3438 4954 4.651503 TGGCATGACCCTTTTTGAAGTAAA 59.348 37.500 0.00 0.00 37.83 2.01
3439 4955 5.129485 TGGCATGACCCTTTTTGAAGTAAAA 59.871 36.000 0.00 0.00 37.83 1.52
3440 4956 6.052360 GGCATGACCCTTTTTGAAGTAAAAA 58.948 36.000 0.00 0.00 43.88 1.94
3466 4982 9.479549 AAATATCTTTATGTTTGACATGACCCT 57.520 29.630 0.00 0.00 39.53 4.34
3467 4983 9.479549 AATATCTTTATGTTTGACATGACCCTT 57.520 29.630 0.00 0.00 39.53 3.95
3468 4984 7.781324 ATCTTTATGTTTGACATGACCCTTT 57.219 32.000 0.00 0.00 39.53 3.11
3469 4985 7.595819 TCTTTATGTTTGACATGACCCTTTT 57.404 32.000 0.00 0.00 39.53 2.27
3470 4986 8.017418 TCTTTATGTTTGACATGACCCTTTTT 57.983 30.769 0.00 0.00 39.53 1.94
3471 4987 9.137459 TCTTTATGTTTGACATGACCCTTTTTA 57.863 29.630 0.00 0.00 39.53 1.52
3472 4988 9.191995 CTTTATGTTTGACATGACCCTTTTTAC 57.808 33.333 0.00 0.00 39.53 2.01
3473 4989 6.976934 ATGTTTGACATGACCCTTTTTACT 57.023 33.333 0.00 0.00 37.45 2.24
3474 4990 6.142818 TGTTTGACATGACCCTTTTTACTG 57.857 37.500 0.00 0.00 0.00 2.74
3475 4991 5.068460 TGTTTGACATGACCCTTTTTACTGG 59.932 40.000 0.00 0.00 0.00 4.00
3476 4992 3.153919 TGACATGACCCTTTTTACTGGC 58.846 45.455 0.00 0.00 0.00 4.85
3477 4993 3.153919 GACATGACCCTTTTTACTGGCA 58.846 45.455 0.00 0.00 0.00 4.92
3478 4994 3.763897 GACATGACCCTTTTTACTGGCAT 59.236 43.478 0.00 0.00 0.00 4.40
3479 4995 3.511146 ACATGACCCTTTTTACTGGCATG 59.489 43.478 0.00 2.77 38.49 4.06
3480 4996 3.517296 TGACCCTTTTTACTGGCATGA 57.483 42.857 0.00 0.00 0.00 3.07
3486 5002 5.957774 ACCCTTTTTACTGGCATGATACATT 59.042 36.000 0.00 0.00 0.00 2.71
3488 5004 6.980397 CCCTTTTTACTGGCATGATACATTTC 59.020 38.462 0.00 0.00 0.00 2.17
3491 5007 7.701539 TTTTACTGGCATGATACATTTCTGT 57.298 32.000 0.00 0.00 39.49 3.41
3492 5008 6.925610 TTACTGGCATGATACATTTCTGTC 57.074 37.500 0.00 0.00 36.79 3.51
3497 5013 5.124297 TGGCATGATACATTTCTGTCAACAG 59.876 40.000 3.69 3.69 45.08 3.16
3515 5031 9.929180 TGTCAACAGAAAGATAGGCATATATAC 57.071 33.333 0.00 0.00 0.00 1.47
3517 5033 9.929180 TCAACAGAAAGATAGGCATATATACAC 57.071 33.333 0.00 0.00 0.00 2.90
3518 5034 9.710900 CAACAGAAAGATAGGCATATATACACA 57.289 33.333 0.00 0.00 0.00 3.72
3519 5035 9.712305 AACAGAAAGATAGGCATATATACACAC 57.288 33.333 0.00 0.00 0.00 3.82
3570 5110 9.170584 GTTTTGTGTATTTTCTTAGAGCAAGTC 57.829 33.333 0.00 0.00 35.58 3.01
3572 5112 7.658179 TGTGTATTTTCTTAGAGCAAGTCTG 57.342 36.000 0.00 0.00 36.64 3.51
3598 5267 4.806640 ACCAGGCACATAATTTTCTTGG 57.193 40.909 0.00 0.00 0.00 3.61
3777 13100 0.742281 CCGACAACATGGAGGAGCAG 60.742 60.000 0.00 0.00 0.00 4.24
3904 13237 3.893326 AGCCTTGGTTTCCATAAATGC 57.107 42.857 0.00 0.00 31.53 3.56
4076 13425 1.177401 GGTGAGTTGGGAGGATTTGC 58.823 55.000 0.00 0.00 0.00 3.68
4081 13430 3.245371 TGAGTTGGGAGGATTTGCTTCAT 60.245 43.478 0.00 0.00 0.00 2.57
4116 13469 9.653287 CCAGTTATTTACTTCATGACAGAACTA 57.347 33.333 0.00 0.00 33.85 2.24
4911 14268 0.107508 CGATGGGTGACAAGGATGCT 60.108 55.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.820482 TGATCCATGCCATCGCCAAG 60.820 55.000 0.00 0.00 0.00 3.61
29 30 0.031178 GTTTGATCCATGCCATCGCC 59.969 55.000 0.00 0.00 0.00 5.54
30 31 1.027357 AGTTTGATCCATGCCATCGC 58.973 50.000 0.00 0.00 0.00 4.58
32 33 4.458295 CCTATCAGTTTGATCCATGCCATC 59.542 45.833 0.00 0.00 38.26 3.51
64 65 1.348008 GGGGGCTGAGGTGATCATGA 61.348 60.000 0.00 0.00 37.28 3.07
96 100 1.608590 CAACTCCGCAAATGTGGTTCT 59.391 47.619 12.43 0.00 45.57 3.01
122 126 3.713858 TTGCATGTTGTGAACTTCCAG 57.286 42.857 0.00 0.00 0.00 3.86
124 128 4.045636 AGTTTGCATGTTGTGAACTTCC 57.954 40.909 0.00 0.00 0.00 3.46
125 129 5.101628 TCAAGTTTGCATGTTGTGAACTTC 58.898 37.500 7.32 0.00 0.00 3.01
132 136 5.508489 CCATCTTCTCAAGTTTGCATGTTGT 60.508 40.000 0.00 0.00 0.00 3.32
134 138 4.828939 TCCATCTTCTCAAGTTTGCATGTT 59.171 37.500 0.00 0.00 0.00 2.71
135 139 4.401022 TCCATCTTCTCAAGTTTGCATGT 58.599 39.130 0.00 0.00 0.00 3.21
146 150 4.356436 TGAAGGTCATCTCCATCTTCTCA 58.644 43.478 0.00 0.00 35.98 3.27
172 176 9.810949 GCTGTTGGCCAATCATAAAGGATGATC 62.811 44.444 23.66 2.89 43.46 2.92
176 180 3.385755 GCTGTTGGCCAATCATAAAGGAT 59.614 43.478 23.66 0.00 34.27 3.24
185 189 1.538047 TCAAGAGCTGTTGGCCAATC 58.462 50.000 23.66 15.18 43.05 2.67
197 201 0.868406 CCGGTGTGTTCTTCAAGAGC 59.132 55.000 0.00 0.00 0.00 4.09
209 213 1.289109 CCGACAGCTTTACCGGTGTG 61.289 60.000 19.93 8.19 44.78 3.82
223 227 2.488771 TAAGGCTCCGAGGTCCGACA 62.489 60.000 0.00 0.00 41.76 4.35
229 233 2.588620 CTAGTGATAAGGCTCCGAGGT 58.411 52.381 0.00 0.00 0.00 3.85
305 312 6.975197 CGAGTGACTATAGAAAATGCTCTTGA 59.025 38.462 6.78 0.00 0.00 3.02
312 319 6.978659 TGTAAGCCGAGTGACTATAGAAAATG 59.021 38.462 6.78 0.00 0.00 2.32
321 328 4.703575 ACATAGTTGTAAGCCGAGTGACTA 59.296 41.667 0.00 0.00 33.16 2.59
324 331 5.648178 TTACATAGTTGTAAGCCGAGTGA 57.352 39.130 0.00 0.00 42.10 3.41
350 357 3.183754 GCACGGCAAACAAAAAGTACTT 58.816 40.909 1.12 1.12 0.00 2.24
366 373 1.086696 ATCAAATGAAGGACGCACGG 58.913 50.000 0.00 0.00 0.00 4.94
371 378 2.540101 GCCGAGTATCAAATGAAGGACG 59.460 50.000 0.00 0.00 33.17 4.79
372 379 3.798202 AGCCGAGTATCAAATGAAGGAC 58.202 45.455 0.00 0.00 33.17 3.85
374 381 5.760253 ACATAAGCCGAGTATCAAATGAAGG 59.240 40.000 0.00 0.00 33.17 3.46
375 382 6.851222 ACATAAGCCGAGTATCAAATGAAG 57.149 37.500 0.00 0.00 33.17 3.02
378 385 6.603237 TCAACATAAGCCGAGTATCAAATG 57.397 37.500 0.00 0.00 33.17 2.32
379 386 6.767902 ACATCAACATAAGCCGAGTATCAAAT 59.232 34.615 0.00 0.00 33.17 2.32
381 388 5.670485 ACATCAACATAAGCCGAGTATCAA 58.330 37.500 0.00 0.00 33.17 2.57
383 390 6.128795 GCTTACATCAACATAAGCCGAGTATC 60.129 42.308 4.94 0.00 44.97 2.24
384 391 5.696724 GCTTACATCAACATAAGCCGAGTAT 59.303 40.000 4.94 0.00 44.97 2.12
385 392 5.047847 GCTTACATCAACATAAGCCGAGTA 58.952 41.667 4.94 0.00 44.97 2.59
386 393 3.871594 GCTTACATCAACATAAGCCGAGT 59.128 43.478 4.94 0.00 44.97 4.18
387 394 4.458951 GCTTACATCAACATAAGCCGAG 57.541 45.455 4.94 0.00 44.97 4.63
406 413 6.875076 AGTGTAAAAATATGAGTACTCGGCT 58.125 36.000 17.85 7.87 0.00 5.52
448 455 4.022068 ACAGAAAAATCACATGTCGCCATT 60.022 37.500 0.00 0.00 0.00 3.16
450 457 2.884012 ACAGAAAAATCACATGTCGCCA 59.116 40.909 0.00 0.00 0.00 5.69
457 464 8.543774 AGAGGTCATACTACAGAAAAATCACAT 58.456 33.333 0.00 0.00 0.00 3.21
467 474 8.743714 CATATGCATTAGAGGTCATACTACAGA 58.256 37.037 3.54 0.00 0.00 3.41
515 522 9.841295 ATGGGGAAAATGATTTCTATTCAATTG 57.159 29.630 0.00 0.00 43.65 2.32
584 591 2.128771 TAAAGCCCACCTCAAGATGC 57.871 50.000 0.00 0.00 0.00 3.91
692 699 9.050601 GCGAGTACGTTAATCCTATATACCTAT 57.949 37.037 0.00 0.00 41.98 2.57
693 700 8.260818 AGCGAGTACGTTAATCCTATATACCTA 58.739 37.037 0.00 0.00 41.98 3.08
694 701 7.108847 AGCGAGTACGTTAATCCTATATACCT 58.891 38.462 0.00 0.00 41.98 3.08
695 702 7.279758 AGAGCGAGTACGTTAATCCTATATACC 59.720 40.741 0.00 0.00 41.98 2.73
696 703 8.195617 AGAGCGAGTACGTTAATCCTATATAC 57.804 38.462 0.00 0.00 41.98 1.47
697 704 7.493971 GGAGAGCGAGTACGTTAATCCTATATA 59.506 40.741 0.00 0.00 41.98 0.86
698 705 6.315891 GGAGAGCGAGTACGTTAATCCTATAT 59.684 42.308 0.00 0.00 41.98 0.86
699 706 5.641209 GGAGAGCGAGTACGTTAATCCTATA 59.359 44.000 0.00 0.00 41.98 1.31
700 707 4.455190 GGAGAGCGAGTACGTTAATCCTAT 59.545 45.833 0.00 0.00 41.98 2.57
701 708 3.812053 GGAGAGCGAGTACGTTAATCCTA 59.188 47.826 0.00 0.00 41.98 2.94
702 709 2.617774 GGAGAGCGAGTACGTTAATCCT 59.382 50.000 0.00 0.00 41.98 3.24
703 710 2.601741 CGGAGAGCGAGTACGTTAATCC 60.602 54.545 0.00 0.00 41.98 3.01
704 711 2.031437 ACGGAGAGCGAGTACGTTAATC 59.969 50.000 0.00 0.00 41.98 1.75
705 712 2.012673 ACGGAGAGCGAGTACGTTAAT 58.987 47.619 0.00 0.00 41.98 1.40
706 713 1.442769 ACGGAGAGCGAGTACGTTAA 58.557 50.000 0.00 0.00 41.98 2.01
707 714 1.442769 AACGGAGAGCGAGTACGTTA 58.557 50.000 0.00 0.00 44.69 3.18
708 715 2.251600 AACGGAGAGCGAGTACGTT 58.748 52.632 0.00 0.74 42.17 3.99
709 716 0.167689 GAAACGGAGAGCGAGTACGT 59.832 55.000 0.00 0.00 41.98 3.57
710 717 0.167470 TGAAACGGAGAGCGAGTACG 59.833 55.000 0.00 0.00 42.93 3.67
711 718 1.199558 AGTGAAACGGAGAGCGAGTAC 59.800 52.381 0.00 0.00 45.86 2.73
712 719 1.531423 AGTGAAACGGAGAGCGAGTA 58.469 50.000 0.00 0.00 45.86 2.59
713 720 0.674534 AAGTGAAACGGAGAGCGAGT 59.325 50.000 0.00 0.00 45.86 4.18
714 721 1.721926 GAAAGTGAAACGGAGAGCGAG 59.278 52.381 0.00 0.00 45.86 5.03
715 722 1.340248 AGAAAGTGAAACGGAGAGCGA 59.660 47.619 0.00 0.00 45.86 4.93
716 723 1.784525 AGAAAGTGAAACGGAGAGCG 58.215 50.000 0.00 0.00 45.86 5.03
717 724 6.100668 ACTAATAGAAAGTGAAACGGAGAGC 58.899 40.000 0.00 0.00 45.86 4.09
718 725 8.535690 AAACTAATAGAAAGTGAAACGGAGAG 57.464 34.615 0.00 0.00 45.86 3.20
719 726 8.365647 AGAAACTAATAGAAAGTGAAACGGAGA 58.634 33.333 0.00 0.00 45.86 3.71
720 727 8.535690 AGAAACTAATAGAAAGTGAAACGGAG 57.464 34.615 0.00 0.00 45.86 4.63
721 728 9.415544 GTAGAAACTAATAGAAAGTGAAACGGA 57.584 33.333 0.00 0.00 45.86 4.69
722 729 9.199982 TGTAGAAACTAATAGAAAGTGAAACGG 57.800 33.333 0.00 0.00 45.86 4.44
739 746 8.850156 AGCACAACTGAATAATTTGTAGAAACT 58.150 29.630 0.00 0.00 32.19 2.66
758 765 4.811557 AGTTAGTTGTCTCTTCAGCACAAC 59.188 41.667 6.12 6.12 46.86 3.32
759 766 5.023533 AGTTAGTTGTCTCTTCAGCACAA 57.976 39.130 0.00 0.00 0.00 3.33
760 767 4.672587 AGTTAGTTGTCTCTTCAGCACA 57.327 40.909 0.00 0.00 0.00 4.57
761 768 8.758633 TTATTAGTTAGTTGTCTCTTCAGCAC 57.241 34.615 0.00 0.00 0.00 4.40
762 769 9.944376 AATTATTAGTTAGTTGTCTCTTCAGCA 57.056 29.630 0.00 0.00 0.00 4.41
818 836 9.699703 GGCTCGATCTACTTATAGAAAGAAATT 57.300 33.333 0.00 0.00 40.88 1.82
820 838 8.466617 AGGCTCGATCTACTTATAGAAAGAAA 57.533 34.615 0.00 0.00 40.88 2.52
821 839 9.570468 TTAGGCTCGATCTACTTATAGAAAGAA 57.430 33.333 0.00 0.00 40.88 2.52
822 840 9.742144 ATTAGGCTCGATCTACTTATAGAAAGA 57.258 33.333 0.00 0.00 40.88 2.52
830 848 9.128404 TGAAGTTAATTAGGCTCGATCTACTTA 57.872 33.333 0.00 0.00 0.00 2.24
831 849 8.008513 TGAAGTTAATTAGGCTCGATCTACTT 57.991 34.615 0.00 0.72 0.00 2.24
832 850 7.584122 TGAAGTTAATTAGGCTCGATCTACT 57.416 36.000 0.00 0.00 0.00 2.57
833 851 6.363896 GCTGAAGTTAATTAGGCTCGATCTAC 59.636 42.308 0.00 0.00 0.00 2.59
834 852 6.265649 AGCTGAAGTTAATTAGGCTCGATCTA 59.734 38.462 0.00 0.00 0.00 1.98
836 854 5.293560 AGCTGAAGTTAATTAGGCTCGATC 58.706 41.667 0.00 0.00 0.00 3.69
837 855 5.283457 AGCTGAAGTTAATTAGGCTCGAT 57.717 39.130 0.00 0.00 0.00 3.59
839 857 4.034510 CCAAGCTGAAGTTAATTAGGCTCG 59.965 45.833 0.00 0.00 31.19 5.03
840 858 4.944317 ACCAAGCTGAAGTTAATTAGGCTC 59.056 41.667 0.00 0.00 31.19 4.70
936 1060 1.002069 TGCTGACAATGGAGGGGATT 58.998 50.000 0.00 0.00 0.00 3.01
1041 1172 9.014297 CATAGAGGGAGCTTAAAAAGAAAAGAA 57.986 33.333 0.00 0.00 0.00 2.52
1042 1173 7.121315 GCATAGAGGGAGCTTAAAAAGAAAAGA 59.879 37.037 0.00 0.00 0.00 2.52
1043 1174 7.121907 AGCATAGAGGGAGCTTAAAAAGAAAAG 59.878 37.037 0.00 0.00 34.37 2.27
1059 1196 2.428890 AGTCGACAGAAAGCATAGAGGG 59.571 50.000 19.50 0.00 0.00 4.30
1082 1219 8.735315 AGACTATATCTGATTGGTCACGAATAG 58.265 37.037 14.76 7.81 35.81 1.73
1105 1258 4.574599 AAAAGCACACCAAATCAGAGAC 57.425 40.909 0.00 0.00 0.00 3.36
1128 1282 7.702348 CCAAGTTTTCTTTTACCAAGAGAACAG 59.298 37.037 16.15 10.13 41.25 3.16
1159 1324 7.406799 AACCAATTTTATTTTTCTGTGCGAG 57.593 32.000 0.00 0.00 0.00 5.03
1161 1326 7.148656 CCCTAACCAATTTTATTTTTCTGTGCG 60.149 37.037 0.00 0.00 0.00 5.34
1177 1342 3.724732 TTAGGCGAAACCCTAACCAAT 57.275 42.857 0.00 0.00 41.36 3.16
1186 1351 0.392595 CTCCCCAGTTAGGCGAAACC 60.393 60.000 0.00 0.00 39.61 3.27
1280 1596 7.408756 ACAGGTTCATAACGGTATTACTGTA 57.591 36.000 8.69 0.00 36.53 2.74
1281 1597 6.290294 ACAGGTTCATAACGGTATTACTGT 57.710 37.500 2.31 2.31 39.91 3.55
1282 1598 7.325338 CGATACAGGTTCATAACGGTATTACTG 59.675 40.741 0.00 0.94 34.66 2.74
1284 1600 7.141363 ACGATACAGGTTCATAACGGTATTAC 58.859 38.462 0.00 0.00 34.66 1.89
1285 1601 7.275888 ACGATACAGGTTCATAACGGTATTA 57.724 36.000 0.00 0.00 34.66 0.98
1286 1602 6.152932 ACGATACAGGTTCATAACGGTATT 57.847 37.500 0.00 0.00 34.66 1.89
1287 1603 5.779529 ACGATACAGGTTCATAACGGTAT 57.220 39.130 0.00 0.00 36.14 2.73
1288 1604 5.581126 AACGATACAGGTTCATAACGGTA 57.419 39.130 0.00 0.00 0.00 4.02
1289 1605 4.460948 AACGATACAGGTTCATAACGGT 57.539 40.909 0.00 0.00 0.00 4.83
1290 1606 6.210796 TCATAACGATACAGGTTCATAACGG 58.789 40.000 0.00 0.00 0.00 4.44
1291 1607 7.434307 AGTTCATAACGATACAGGTTCATAACG 59.566 37.037 0.00 0.00 36.23 3.18
1292 1608 8.644318 AGTTCATAACGATACAGGTTCATAAC 57.356 34.615 0.00 0.00 36.23 1.89
1293 1609 9.661563 AAAGTTCATAACGATACAGGTTCATAA 57.338 29.630 0.00 0.00 36.23 1.90
1294 1610 9.661563 AAAAGTTCATAACGATACAGGTTCATA 57.338 29.630 0.00 0.00 36.23 2.15
1295 1611 8.561738 AAAAGTTCATAACGATACAGGTTCAT 57.438 30.769 0.00 0.00 36.23 2.57
1296 1612 7.876068 AGAAAAGTTCATAACGATACAGGTTCA 59.124 33.333 0.00 0.00 36.23 3.18
1297 1613 8.252964 AGAAAAGTTCATAACGATACAGGTTC 57.747 34.615 0.00 0.00 36.23 3.62
1298 1614 8.617290 AAGAAAAGTTCATAACGATACAGGTT 57.383 30.769 0.00 0.00 36.23 3.50
1299 1615 8.504005 CAAAGAAAAGTTCATAACGATACAGGT 58.496 33.333 0.00 0.00 36.23 4.00
1300 1616 8.504005 ACAAAGAAAAGTTCATAACGATACAGG 58.496 33.333 0.00 0.00 36.23 4.00
1301 1617 9.318041 CACAAAGAAAAGTTCATAACGATACAG 57.682 33.333 0.00 0.00 36.23 2.74
1302 1618 8.832521 ACACAAAGAAAAGTTCATAACGATACA 58.167 29.630 0.00 0.00 36.23 2.29
1366 1687 6.694411 GCAACAGATTTGCATAAGTAATCAGG 59.306 38.462 9.99 5.06 44.34 3.86
1410 1731 1.086696 ATCGCATTACAGTGTGTGCC 58.913 50.000 22.15 10.39 34.20 5.01
1512 1922 5.749596 AAAATTTTGCCAACTTAGCCAAC 57.250 34.783 1.75 0.00 0.00 3.77
1535 1946 8.093307 TCAAATGTTTTGCATAAGCTCCAATTA 58.907 29.630 0.00 0.00 42.74 1.40
1594 2359 3.520317 TGAAGCCTCCCGGTTCTATAAAA 59.480 43.478 0.00 0.00 46.97 1.52
1606 2373 2.959030 ACAAAAAGTCTTGAAGCCTCCC 59.041 45.455 0.00 0.00 0.00 4.30
1664 2617 5.808366 TTATATTGCCTCTGTACCTCCAG 57.192 43.478 0.00 0.00 0.00 3.86
1683 2641 6.767524 TTCCGCCACACTTAAATGATTTAT 57.232 33.333 0.00 0.00 0.00 1.40
1696 2654 1.002624 TCCCTCATTTCCGCCACAC 60.003 57.895 0.00 0.00 0.00 3.82
1699 2657 0.695924 TTTCTCCCTCATTTCCGCCA 59.304 50.000 0.00 0.00 0.00 5.69
1733 2692 4.566837 TGACATACACCCATTCCCTAGAT 58.433 43.478 0.00 0.00 0.00 1.98
1738 2697 3.384467 CCAATTGACATACACCCATTCCC 59.616 47.826 7.12 0.00 0.00 3.97
1758 2717 3.399644 TCAACTCCACCTTATTTTCCCCA 59.600 43.478 0.00 0.00 0.00 4.96
1809 2768 2.287103 GTCGCCTTGTTTTCTCTCGTTT 59.713 45.455 0.00 0.00 0.00 3.60
1843 3199 7.435192 CCCTTGTTTCGGCTTTATGATTTTATC 59.565 37.037 0.00 0.00 0.00 1.75
1907 3361 8.970859 AACAGGACCAAAGATATTCTAGATTG 57.029 34.615 0.00 0.00 0.00 2.67
2193 3667 8.948401 ATACTGGTAGAACTCATGATAGATGT 57.052 34.615 0.00 0.00 0.00 3.06
2200 3674 5.601313 GGGGTTATACTGGTAGAACTCATGA 59.399 44.000 16.54 0.00 38.97 3.07
2392 3869 2.099921 GAGACCAGTGTATGTGATCGCT 59.900 50.000 7.94 0.00 0.00 4.93
2395 3872 5.268118 TGATGAGACCAGTGTATGTGATC 57.732 43.478 0.00 0.00 0.00 2.92
2400 3877 4.573607 CCATGTTGATGAGACCAGTGTATG 59.426 45.833 0.00 0.00 0.00 2.39
2566 4043 0.541392 CATCTGGTCCGATCCAACCA 59.459 55.000 12.11 12.11 43.20 3.67
2586 4063 5.431765 CACCAACTGCTATTCTCCATAGTT 58.568 41.667 0.00 0.00 37.74 2.24
2628 4105 6.110033 TCACTCTTGTACAAAAGTGCAGTAA 58.890 36.000 29.36 14.55 39.15 2.24
2674 4151 2.147958 GAATACAGCGGGTGTTCAACA 58.852 47.619 18.81 0.00 44.40 3.33
2893 4382 1.589993 CAGCCACAGCCGATAGTCG 60.590 63.158 0.00 0.00 41.25 4.18
2926 4415 9.696917 AAGAACGATTTTGAAGCATAGAAATTT 57.303 25.926 0.00 0.00 0.00 1.82
2968 4457 3.181396 TCCAAGCCCATATGATCCTCCTA 60.181 47.826 3.65 0.00 0.00 2.94
3005 4494 4.430137 TTGCAACATCATCTGAAGAAGC 57.570 40.909 0.00 0.00 0.00 3.86
3248 4757 1.760029 CCCTTCTTGAGCTCTAGTCCC 59.240 57.143 21.99 0.00 0.00 4.46
3290 4799 5.008613 TGAAACTACCTGCAAAGTGTCAATC 59.991 40.000 11.93 1.32 37.09 2.67
3358 4874 3.037549 TGGCATGACCCTTTTTGAAGTT 58.962 40.909 0.00 0.00 37.83 2.66
3393 4909 9.875708 TGCCAGTAAATGTAATATCCCTTAAAT 57.124 29.630 0.00 0.00 0.00 1.40
3394 4910 9.875708 ATGCCAGTAAATGTAATATCCCTTAAA 57.124 29.630 0.00 0.00 0.00 1.52
3396 4912 8.664992 TCATGCCAGTAAATGTAATATCCCTTA 58.335 33.333 0.00 0.00 0.00 2.69
3397 4913 7.448469 GTCATGCCAGTAAATGTAATATCCCTT 59.552 37.037 0.00 0.00 0.00 3.95
3398 4914 6.942576 GTCATGCCAGTAAATGTAATATCCCT 59.057 38.462 0.00 0.00 0.00 4.20
3399 4915 6.151144 GGTCATGCCAGTAAATGTAATATCCC 59.849 42.308 1.78 0.00 37.17 3.85
3400 4916 6.151144 GGGTCATGCCAGTAAATGTAATATCC 59.849 42.308 8.20 0.00 39.65 2.59
3405 4921 4.584638 AGGGTCATGCCAGTAAATGTAA 57.415 40.909 8.20 0.00 39.65 2.41
3407 4923 3.456380 AAGGGTCATGCCAGTAAATGT 57.544 42.857 8.20 0.00 39.65 2.71
3408 4924 4.806640 AAAAGGGTCATGCCAGTAAATG 57.193 40.909 8.20 0.00 39.65 2.32
3409 4925 4.837860 TCAAAAAGGGTCATGCCAGTAAAT 59.162 37.500 8.20 0.00 39.65 1.40
3411 4927 3.838565 TCAAAAAGGGTCATGCCAGTAA 58.161 40.909 8.20 0.00 39.65 2.24
3412 4928 3.517296 TCAAAAAGGGTCATGCCAGTA 57.483 42.857 8.20 0.00 39.65 2.74
3413 4929 2.380064 TCAAAAAGGGTCATGCCAGT 57.620 45.000 8.20 0.00 39.65 4.00
3414 4930 2.629617 ACTTCAAAAAGGGTCATGCCAG 59.370 45.455 8.20 0.00 39.65 4.85
3415 4931 2.676748 ACTTCAAAAAGGGTCATGCCA 58.323 42.857 8.20 0.00 39.65 4.92
3416 4932 4.864704 TTACTTCAAAAAGGGTCATGCC 57.135 40.909 0.00 0.00 36.78 4.40
3440 4956 9.479549 AGGGTCATGTCAAACATAAAGATATTT 57.520 29.630 0.00 0.00 36.53 1.40
3441 4957 9.479549 AAGGGTCATGTCAAACATAAAGATATT 57.520 29.630 0.00 0.00 36.53 1.28
3442 4958 9.479549 AAAGGGTCATGTCAAACATAAAGATAT 57.520 29.630 0.00 0.00 36.53 1.63
3443 4959 8.877864 AAAGGGTCATGTCAAACATAAAGATA 57.122 30.769 0.00 0.00 36.53 1.98
3444 4960 7.781324 AAAGGGTCATGTCAAACATAAAGAT 57.219 32.000 0.00 0.00 36.53 2.40
3445 4961 7.595819 AAAAGGGTCATGTCAAACATAAAGA 57.404 32.000 0.00 0.00 36.53 2.52
3446 4962 9.191995 GTAAAAAGGGTCATGTCAAACATAAAG 57.808 33.333 0.00 0.00 36.53 1.85
3447 4963 8.919145 AGTAAAAAGGGTCATGTCAAACATAAA 58.081 29.630 0.00 0.00 36.53 1.40
3448 4964 8.356657 CAGTAAAAAGGGTCATGTCAAACATAA 58.643 33.333 0.00 0.00 36.53 1.90
3449 4965 7.040062 CCAGTAAAAAGGGTCATGTCAAACATA 60.040 37.037 0.00 0.00 36.53 2.29
3450 4966 6.239289 CCAGTAAAAAGGGTCATGTCAAACAT 60.239 38.462 0.00 0.00 39.91 2.71
3451 4967 5.068460 CCAGTAAAAAGGGTCATGTCAAACA 59.932 40.000 0.00 0.00 0.00 2.83
3452 4968 5.528870 CCAGTAAAAAGGGTCATGTCAAAC 58.471 41.667 0.00 0.00 0.00 2.93
3453 4969 4.038642 GCCAGTAAAAAGGGTCATGTCAAA 59.961 41.667 0.00 0.00 0.00 2.69
3454 4970 3.572255 GCCAGTAAAAAGGGTCATGTCAA 59.428 43.478 0.00 0.00 0.00 3.18
3455 4971 3.153919 GCCAGTAAAAAGGGTCATGTCA 58.846 45.455 0.00 0.00 0.00 3.58
3456 4972 3.153919 TGCCAGTAAAAAGGGTCATGTC 58.846 45.455 0.00 0.00 0.00 3.06
3457 4973 3.237268 TGCCAGTAAAAAGGGTCATGT 57.763 42.857 0.00 0.00 0.00 3.21
3458 4974 3.763360 TCATGCCAGTAAAAAGGGTCATG 59.237 43.478 0.00 0.00 37.46 3.07
3459 4975 4.046286 TCATGCCAGTAAAAAGGGTCAT 57.954 40.909 0.00 0.00 0.00 3.06
3460 4976 3.517296 TCATGCCAGTAAAAAGGGTCA 57.483 42.857 0.00 0.00 0.00 4.02
3461 4977 4.947388 TGTATCATGCCAGTAAAAAGGGTC 59.053 41.667 0.00 0.00 0.00 4.46
3462 4978 4.929479 TGTATCATGCCAGTAAAAAGGGT 58.071 39.130 0.00 0.00 0.00 4.34
3463 4979 6.469782 AATGTATCATGCCAGTAAAAAGGG 57.530 37.500 0.00 0.00 0.00 3.95
3464 4980 7.703621 CAGAAATGTATCATGCCAGTAAAAAGG 59.296 37.037 0.00 0.00 0.00 3.11
3465 4981 8.246180 ACAGAAATGTATCATGCCAGTAAAAAG 58.754 33.333 0.00 0.00 0.00 2.27
3466 4982 8.121305 ACAGAAATGTATCATGCCAGTAAAAA 57.879 30.769 0.00 0.00 0.00 1.94
3467 4983 7.392953 TGACAGAAATGTATCATGCCAGTAAAA 59.607 33.333 0.00 0.00 0.00 1.52
3468 4984 6.883756 TGACAGAAATGTATCATGCCAGTAAA 59.116 34.615 0.00 0.00 0.00 2.01
3469 4985 6.413892 TGACAGAAATGTATCATGCCAGTAA 58.586 36.000 0.00 0.00 0.00 2.24
3470 4986 5.988287 TGACAGAAATGTATCATGCCAGTA 58.012 37.500 0.00 0.00 0.00 2.74
3471 4987 4.847198 TGACAGAAATGTATCATGCCAGT 58.153 39.130 0.00 0.00 0.00 4.00
3472 4988 5.124297 TGTTGACAGAAATGTATCATGCCAG 59.876 40.000 0.00 0.00 0.00 4.85
3473 4989 5.008980 TGTTGACAGAAATGTATCATGCCA 58.991 37.500 0.00 0.00 0.00 4.92
3474 4990 5.565592 TGTTGACAGAAATGTATCATGCC 57.434 39.130 0.00 0.00 0.00 4.40
3491 5007 9.929180 GTGTATATATGCCTATCTTTCTGTTGA 57.071 33.333 0.00 0.00 0.00 3.18
3492 5008 9.710900 TGTGTATATATGCCTATCTTTCTGTTG 57.289 33.333 0.00 0.00 0.00 3.33
3497 5013 8.926710 GTGTGTGTGTATATATGCCTATCTTTC 58.073 37.037 0.00 0.00 0.00 2.62
3558 5098 3.055819 TGGTTAGCCAGACTTGCTCTAAG 60.056 47.826 3.96 0.00 40.46 2.18
3572 5112 4.402474 AGAAAATTATGTGCCTGGTTAGCC 59.598 41.667 0.00 0.00 0.00 3.93
3598 5267 1.192534 CTCGACGTCAGCCTGTTTTTC 59.807 52.381 17.16 0.00 0.00 2.29
3777 13100 4.558538 AACTCTGAAATGCACAACAGTC 57.441 40.909 13.07 0.00 0.00 3.51
3880 13213 5.660460 CATTTATGGAAACCAAGGCTAACC 58.340 41.667 0.00 0.00 36.95 2.85
3904 13237 9.495572 GTTTCCTTCCAGACATTAATAGATAGG 57.504 37.037 0.00 0.00 0.00 2.57
3914 13251 8.533569 TTCTTTTTAGTTTCCTTCCAGACATT 57.466 30.769 0.00 0.00 0.00 2.71
4131 13485 1.469767 CGACCGATCAATCTGCACAGA 60.470 52.381 2.25 2.25 42.37 3.41
4133 13487 0.460109 CCGACCGATCAATCTGCACA 60.460 55.000 0.00 0.00 0.00 4.57
4826 14183 2.174360 GCCCAGAAATCCTCTTGCTTT 58.826 47.619 0.00 0.00 29.07 3.51


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

AutoCloner maintained by Alex Coulton.