Multiple sequence alignment - TraesCS1D01G043400

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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 TraesCS1D01G043400 chr1D 100.000 3923 0 0 1 3923 22626948 22623026 0.000000e+00 7245.0
1 TraesCS1D01G043400 chr1B 89.447 3525 210 68 474 3909 38831559 38835010 0.000000e+00 4300.0
2 TraesCS1D01G043400 chr1B 88.462 338 30 4 140 470 521185433 521185098 2.200000e-107 399.0
3 TraesCS1D01G043400 chr1B 88.012 342 31 6 136 470 97326931 97326593 2.840000e-106 396.0
4 TraesCS1D01G043400 chr1B 88.686 274 17 5 3054 3319 246423201 246422934 4.890000e-84 322.0
5 TraesCS1D01G043400 chr1B 92.021 188 11 2 3423 3610 246422899 246422716 1.080000e-65 261.0
6 TraesCS1D01G043400 chr1B 90.526 95 9 0 1 95 38831075 38831169 4.120000e-25 126.0
7 TraesCS1D01G043400 chr1B 82.069 145 17 6 3221 3357 38834771 38834914 8.910000e-22 115.0
8 TraesCS1D01G043400 chr1B 86.170 94 12 1 39 131 4789387 4789480 2.490000e-17 100.0
9 TraesCS1D01G043400 chr1A 93.195 2601 108 18 474 3025 23815694 23818274 0.000000e+00 3759.0
10 TraesCS1D01G043400 chr1A 90.071 141 13 1 1 140 23815554 23815694 8.660000e-42 182.0
11 TraesCS1D01G043400 chr1A 88.387 155 11 3 3698 3846 23818494 23818647 3.110000e-41 180.0
12 TraesCS1D01G043400 chr1A 77.493 351 18 24 3032 3369 23818320 23818622 1.890000e-33 154.0
13 TraesCS1D01G043400 chr4A 79.084 1157 191 36 1418 2553 113331632 113330506 0.000000e+00 749.0
14 TraesCS1D01G043400 chr4A 90.754 411 14 11 3445 3834 604196426 604196833 9.650000e-146 527.0
15 TraesCS1D01G043400 chr4A 83.051 118 16 3 25 140 674594886 674594771 1.930000e-18 104.0
16 TraesCS1D01G043400 chr4A 84.000 100 13 2 42 140 674727008 674726911 4.170000e-15 93.5
17 TraesCS1D01G043400 chr4B 78.947 1159 186 42 1424 2553 435486033 435484904 0.000000e+00 736.0
18 TraesCS1D01G043400 chr4B 86.892 679 46 19 2950 3610 663555627 663556280 0.000000e+00 721.0
19 TraesCS1D01G043400 chr4D 78.390 1180 203 38 1397 2550 352118573 352119726 0.000000e+00 719.0
20 TraesCS1D01G043400 chr4D 90.488 410 18 10 3445 3833 60091593 60092002 4.490000e-144 521.0
21 TraesCS1D01G043400 chr5B 86.765 680 47 19 2949 3610 570295378 570294724 0.000000e+00 717.0
22 TraesCS1D01G043400 chr5B 89.053 338 29 3 139 470 229822821 229823156 2.820000e-111 412.0
23 TraesCS1D01G043400 chr5B 88.462 338 31 3 139 470 229891289 229891624 6.110000e-108 401.0
24 TraesCS1D01G043400 chr5B 87.353 340 35 3 137 470 72464221 72464558 2.210000e-102 383.0
25 TraesCS1D01G043400 chr5B 84.444 90 6 6 3030 3115 563670176 563670261 9.030000e-12 82.4
26 TraesCS1D01G043400 chr5B 84.444 90 6 6 3030 3115 563670752 563670837 9.030000e-12 82.4
27 TraesCS1D01G043400 chr5B 83.146 89 8 6 3030 3115 563701319 563701403 1.510000e-09 75.0
28 TraesCS1D01G043400 chr5D 90.054 553 31 9 3381 3909 26628496 26629048 0.000000e+00 695.0
29 TraesCS1D01G043400 chr3A 76.969 1168 221 35 1419 2550 695130679 695131834 1.200000e-174 623.0
30 TraesCS1D01G043400 chr3A 80.193 207 41 0 2690 2896 695132001 695132207 5.250000e-34 156.0
31 TraesCS1D01G043400 chr3A 86.022 93 9 3 42 132 523307646 523307556 3.230000e-16 97.1
32 TraesCS1D01G043400 chr3D 76.884 1168 222 31 1419 2550 558784676 558785831 5.570000e-173 617.0
33 TraesCS1D01G043400 chr3D 81.159 207 39 0 2690 2896 558785998 558786204 2.420000e-37 167.0
34 TraesCS1D01G043400 chr3B 78.419 797 147 18 1419 2204 741601527 741602309 2.720000e-136 496.0
35 TraesCS1D01G043400 chr3B 83.243 185 29 2 2713 2896 741602872 741603055 6.740000e-38 169.0
36 TraesCS1D01G043400 chr6B 88.791 339 29 4 139 470 84860980 84861316 1.310000e-109 407.0
37 TraesCS1D01G043400 chr6B 88.462 338 31 3 139 470 371602326 371602661 6.110000e-108 401.0
38 TraesCS1D01G043400 chr6B 87.870 338 33 3 139 470 36153738 36154073 1.320000e-104 390.0
39 TraesCS1D01G043400 chr6B 88.060 335 32 3 140 468 526777105 526777437 1.320000e-104 390.0
40 TraesCS1D01G043400 chr7B 87.970 133 12 2 1268 1399 33500759 33500888 1.890000e-33 154.0
41 TraesCS1D01G043400 chr7B 82.051 117 16 3 25 139 41034162 41034049 1.160000e-15 95.3
42 TraesCS1D01G043400 chr7B 80.800 125 19 4 19 140 506757888 506758010 4.170000e-15 93.5
43 TraesCS1D01G043400 chr7D 84.000 100 13 2 42 140 481179835 481179932 4.170000e-15 93.5
44 TraesCS1D01G043400 chr2D 85.393 89 6 6 3030 3115 26581009 26580925 6.980000e-13 86.1


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 TraesCS1D01G043400 chr1D 22623026 22626948 3922 True 7245.000000 7245 100.000000 1 3923 1 chr1D.!!$R1 3922
1 TraesCS1D01G043400 chr1B 38831075 38835010 3935 False 1513.666667 4300 87.347333 1 3909 3 chr1B.!!$F2 3908
2 TraesCS1D01G043400 chr1A 23815554 23818647 3093 False 1068.750000 3759 87.286500 1 3846 4 chr1A.!!$F1 3845
3 TraesCS1D01G043400 chr4A 113330506 113331632 1126 True 749.000000 749 79.084000 1418 2553 1 chr4A.!!$R1 1135
4 TraesCS1D01G043400 chr4B 435484904 435486033 1129 True 736.000000 736 78.947000 1424 2553 1 chr4B.!!$R1 1129
5 TraesCS1D01G043400 chr4B 663555627 663556280 653 False 721.000000 721 86.892000 2950 3610 1 chr4B.!!$F1 660
6 TraesCS1D01G043400 chr4D 352118573 352119726 1153 False 719.000000 719 78.390000 1397 2550 1 chr4D.!!$F2 1153
7 TraesCS1D01G043400 chr5B 570294724 570295378 654 True 717.000000 717 86.765000 2949 3610 1 chr5B.!!$R1 661
8 TraesCS1D01G043400 chr5D 26628496 26629048 552 False 695.000000 695 90.054000 3381 3909 1 chr5D.!!$F1 528
9 TraesCS1D01G043400 chr3A 695130679 695132207 1528 False 389.500000 623 78.581000 1419 2896 2 chr3A.!!$F1 1477
10 TraesCS1D01G043400 chr3D 558784676 558786204 1528 False 392.000000 617 79.021500 1419 2896 2 chr3D.!!$F1 1477
11 TraesCS1D01G043400 chr3B 741601527 741603055 1528 False 332.500000 496 80.831000 1419 2896 2 chr3B.!!$F1 1477

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
437 784 0.187117 TTGGTCACCATGCCCAAGAA 59.813 50.000 0.0 0.0 33.43 2.52 F
1215 1625 0.179045 ACCTCCACTTCACACAGCAC 60.179 55.000 0.0 0.0 0.00 4.40 F
2237 2677 1.362237 TCCTGAATTTCCATTGCCCCT 59.638 47.619 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2498 0.329261 CCTTGATGTCCTTGGCCAGA 59.671 55.0 5.11 0.0 0.00 3.86 R
2492 2968 1.101635 TATGAGGTCGAGCGTCCTGG 61.102 60.0 13.08 0.0 33.99 4.45 R
3413 3982 0.247736 CTGGCTCCTGGTCAGTACAC 59.752 60.0 0.00 0.0 42.28 2.90 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
86 88 2.552315 GTTCAACACCAATCATGTCCGT 59.448 45.455 0.00 0.00 0.00 4.69
145 492 8.519799 TTGATAAGATTTGGTTTGATACTCCC 57.480 34.615 0.00 0.00 0.00 4.30
146 493 7.872138 TGATAAGATTTGGTTTGATACTCCCT 58.128 34.615 0.00 0.00 0.00 4.20
147 494 7.993183 TGATAAGATTTGGTTTGATACTCCCTC 59.007 37.037 0.00 0.00 0.00 4.30
148 495 5.117406 AGATTTGGTTTGATACTCCCTCC 57.883 43.478 0.00 0.00 0.00 4.30
149 496 3.343941 TTTGGTTTGATACTCCCTCCG 57.656 47.619 0.00 0.00 0.00 4.63
150 497 1.946984 TGGTTTGATACTCCCTCCGT 58.053 50.000 0.00 0.00 0.00 4.69
151 498 2.262637 TGGTTTGATACTCCCTCCGTT 58.737 47.619 0.00 0.00 0.00 4.44
152 499 2.235402 TGGTTTGATACTCCCTCCGTTC 59.765 50.000 0.00 0.00 0.00 3.95
153 500 2.419713 GGTTTGATACTCCCTCCGTTCC 60.420 54.545 0.00 0.00 0.00 3.62
154 501 2.500504 GTTTGATACTCCCTCCGTTCCT 59.499 50.000 0.00 0.00 0.00 3.36
155 502 2.544844 TGATACTCCCTCCGTTCCTT 57.455 50.000 0.00 0.00 0.00 3.36
156 503 2.829023 TGATACTCCCTCCGTTCCTTT 58.171 47.619 0.00 0.00 0.00 3.11
157 504 3.985127 TGATACTCCCTCCGTTCCTTTA 58.015 45.455 0.00 0.00 0.00 1.85
158 505 4.553678 TGATACTCCCTCCGTTCCTTTAT 58.446 43.478 0.00 0.00 0.00 1.40
159 506 5.708544 TGATACTCCCTCCGTTCCTTTATA 58.291 41.667 0.00 0.00 0.00 0.98
160 507 6.320518 TGATACTCCCTCCGTTCCTTTATAT 58.679 40.000 0.00 0.00 0.00 0.86
161 508 7.472741 TGATACTCCCTCCGTTCCTTTATATA 58.527 38.462 0.00 0.00 0.00 0.86
162 509 7.951806 TGATACTCCCTCCGTTCCTTTATATAA 59.048 37.037 0.00 0.00 0.00 0.98
163 510 6.667558 ACTCCCTCCGTTCCTTTATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
164 511 5.543020 ACTCCCTCCGTTCCTTTATATAAGG 59.457 44.000 0.00 0.00 38.78 2.69
165 512 5.470501 TCCCTCCGTTCCTTTATATAAGGT 58.529 41.667 4.13 0.00 38.55 3.50
166 513 5.907079 TCCCTCCGTTCCTTTATATAAGGTT 59.093 40.000 4.13 0.00 38.55 3.50
167 514 6.387807 TCCCTCCGTTCCTTTATATAAGGTTT 59.612 38.462 4.13 0.00 38.55 3.27
168 515 7.568366 TCCCTCCGTTCCTTTATATAAGGTTTA 59.432 37.037 4.13 0.00 38.55 2.01
169 516 8.380867 CCCTCCGTTCCTTTATATAAGGTTTAT 58.619 37.037 4.13 0.00 38.55 1.40
170 517 9.788889 CCTCCGTTCCTTTATATAAGGTTTATT 57.211 33.333 4.13 0.00 38.55 1.40
216 563 9.643652 GTAAGATGCATTTCTTCTAATTTCTCG 57.356 33.333 5.84 0.00 37.20 4.04
217 564 7.856145 AGATGCATTTCTTCTAATTTCTCGT 57.144 32.000 0.00 0.00 0.00 4.18
218 565 8.948631 AGATGCATTTCTTCTAATTTCTCGTA 57.051 30.769 0.00 0.00 0.00 3.43
219 566 9.383519 AGATGCATTTCTTCTAATTTCTCGTAA 57.616 29.630 0.00 0.00 0.00 3.18
222 569 8.612619 TGCATTTCTTCTAATTTCTCGTAATCC 58.387 33.333 0.00 0.00 0.00 3.01
223 570 8.070769 GCATTTCTTCTAATTTCTCGTAATCCC 58.929 37.037 0.00 0.00 0.00 3.85
224 571 9.331282 CATTTCTTCTAATTTCTCGTAATCCCT 57.669 33.333 0.00 0.00 0.00 4.20
225 572 9.907229 ATTTCTTCTAATTTCTCGTAATCCCTT 57.093 29.630 0.00 0.00 0.00 3.95
226 573 9.734984 TTTCTTCTAATTTCTCGTAATCCCTTT 57.265 29.630 0.00 0.00 0.00 3.11
227 574 9.734984 TTCTTCTAATTTCTCGTAATCCCTTTT 57.265 29.630 0.00 0.00 0.00 2.27
228 575 9.734984 TCTTCTAATTTCTCGTAATCCCTTTTT 57.265 29.630 0.00 0.00 0.00 1.94
265 612 5.346181 AAAAGGAAAGTATCTCTCTCCCG 57.654 43.478 0.00 0.00 0.00 5.14
266 613 3.955524 AGGAAAGTATCTCTCTCCCGA 57.044 47.619 0.00 0.00 0.00 5.14
267 614 4.463050 AGGAAAGTATCTCTCTCCCGAT 57.537 45.455 0.00 0.00 0.00 4.18
268 615 4.810345 AGGAAAGTATCTCTCTCCCGATT 58.190 43.478 0.00 0.00 0.00 3.34
269 616 5.212745 AGGAAAGTATCTCTCTCCCGATTT 58.787 41.667 0.00 0.00 0.00 2.17
270 617 5.663556 AGGAAAGTATCTCTCTCCCGATTTT 59.336 40.000 0.00 0.00 0.00 1.82
271 618 5.986741 GGAAAGTATCTCTCTCCCGATTTTC 59.013 44.000 0.00 0.00 0.00 2.29
272 619 6.183360 GGAAAGTATCTCTCTCCCGATTTTCT 60.183 42.308 0.00 0.00 0.00 2.52
273 620 5.782893 AGTATCTCTCTCCCGATTTTCTG 57.217 43.478 0.00 0.00 0.00 3.02
274 621 5.205056 AGTATCTCTCTCCCGATTTTCTGT 58.795 41.667 0.00 0.00 0.00 3.41
275 622 6.366340 AGTATCTCTCTCCCGATTTTCTGTA 58.634 40.000 0.00 0.00 0.00 2.74
276 623 7.007723 AGTATCTCTCTCCCGATTTTCTGTAT 58.992 38.462 0.00 0.00 0.00 2.29
277 624 5.776173 TCTCTCTCCCGATTTTCTGTATC 57.224 43.478 0.00 0.00 0.00 2.24
278 625 5.450453 TCTCTCTCCCGATTTTCTGTATCT 58.550 41.667 0.00 0.00 0.00 1.98
279 626 5.533154 TCTCTCTCCCGATTTTCTGTATCTC 59.467 44.000 0.00 0.00 0.00 2.75
280 627 5.201243 TCTCTCCCGATTTTCTGTATCTCA 58.799 41.667 0.00 0.00 0.00 3.27
281 628 5.067936 TCTCTCCCGATTTTCTGTATCTCAC 59.932 44.000 0.00 0.00 0.00 3.51
282 629 4.956700 TCTCCCGATTTTCTGTATCTCACT 59.043 41.667 0.00 0.00 0.00 3.41
283 630 5.422331 TCTCCCGATTTTCTGTATCTCACTT 59.578 40.000 0.00 0.00 0.00 3.16
284 631 6.049955 TCCCGATTTTCTGTATCTCACTTT 57.950 37.500 0.00 0.00 0.00 2.66
285 632 7.123697 TCTCCCGATTTTCTGTATCTCACTTTA 59.876 37.037 0.00 0.00 0.00 1.85
286 633 7.792032 TCCCGATTTTCTGTATCTCACTTTAT 58.208 34.615 0.00 0.00 0.00 1.40
287 634 8.920174 TCCCGATTTTCTGTATCTCACTTTATA 58.080 33.333 0.00 0.00 0.00 0.98
288 635 9.197694 CCCGATTTTCTGTATCTCACTTTATAG 57.802 37.037 0.00 0.00 0.00 1.31
289 636 9.967346 CCGATTTTCTGTATCTCACTTTATAGA 57.033 33.333 0.00 0.00 0.00 1.98
319 666 4.855298 AAAGTATTTCCCTCCCGATTGA 57.145 40.909 0.00 0.00 27.08 2.57
320 667 3.840124 AGTATTTCCCTCCCGATTGAC 57.160 47.619 0.00 0.00 0.00 3.18
321 668 3.385115 AGTATTTCCCTCCCGATTGACT 58.615 45.455 0.00 0.00 0.00 3.41
322 669 2.717639 ATTTCCCTCCCGATTGACTG 57.282 50.000 0.00 0.00 0.00 3.51
323 670 1.358152 TTTCCCTCCCGATTGACTGT 58.642 50.000 0.00 0.00 0.00 3.55
324 671 2.241281 TTCCCTCCCGATTGACTGTA 57.759 50.000 0.00 0.00 0.00 2.74
325 672 2.471815 TCCCTCCCGATTGACTGTAT 57.528 50.000 0.00 0.00 0.00 2.29
326 673 2.317040 TCCCTCCCGATTGACTGTATC 58.683 52.381 0.00 0.00 0.00 2.24
327 674 2.091278 TCCCTCCCGATTGACTGTATCT 60.091 50.000 0.00 0.00 0.00 1.98
328 675 2.297597 CCCTCCCGATTGACTGTATCTC 59.702 54.545 0.00 0.00 0.00 2.75
329 676 3.226777 CCTCCCGATTGACTGTATCTCT 58.773 50.000 0.00 0.00 0.00 3.10
330 677 3.639094 CCTCCCGATTGACTGTATCTCTT 59.361 47.826 0.00 0.00 0.00 2.85
331 678 4.100189 CCTCCCGATTGACTGTATCTCTTT 59.900 45.833 0.00 0.00 0.00 2.52
332 679 5.263968 TCCCGATTGACTGTATCTCTTTC 57.736 43.478 0.00 0.00 0.00 2.62
333 680 4.956700 TCCCGATTGACTGTATCTCTTTCT 59.043 41.667 0.00 0.00 0.00 2.52
334 681 5.422331 TCCCGATTGACTGTATCTCTTTCTT 59.578 40.000 0.00 0.00 0.00 2.52
335 682 6.070767 TCCCGATTGACTGTATCTCTTTCTTT 60.071 38.462 0.00 0.00 0.00 2.52
336 683 6.256757 CCCGATTGACTGTATCTCTTTCTTTC 59.743 42.308 0.00 0.00 0.00 2.62
337 684 6.813649 CCGATTGACTGTATCTCTTTCTTTCA 59.186 38.462 0.00 0.00 0.00 2.69
338 685 7.331934 CCGATTGACTGTATCTCTTTCTTTCAA 59.668 37.037 0.00 0.00 0.00 2.69
339 686 8.712363 CGATTGACTGTATCTCTTTCTTTCAAA 58.288 33.333 0.00 0.00 0.00 2.69
341 688 7.426929 TGACTGTATCTCTTTCTTTCAAAGC 57.573 36.000 0.00 0.00 0.00 3.51
342 689 6.428159 TGACTGTATCTCTTTCTTTCAAAGCC 59.572 38.462 0.00 0.00 0.00 4.35
343 690 6.538263 ACTGTATCTCTTTCTTTCAAAGCCT 58.462 36.000 0.00 0.00 0.00 4.58
344 691 7.680730 ACTGTATCTCTTTCTTTCAAAGCCTA 58.319 34.615 0.00 0.00 0.00 3.93
345 692 8.157476 ACTGTATCTCTTTCTTTCAAAGCCTAA 58.843 33.333 0.00 0.00 0.00 2.69
346 693 8.324163 TGTATCTCTTTCTTTCAAAGCCTAAC 57.676 34.615 0.00 0.00 0.00 2.34
347 694 8.157476 TGTATCTCTTTCTTTCAAAGCCTAACT 58.843 33.333 0.00 0.00 0.00 2.24
348 695 6.867662 TCTCTTTCTTTCAAAGCCTAACTG 57.132 37.500 0.00 0.00 0.00 3.16
349 696 6.591935 TCTCTTTCTTTCAAAGCCTAACTGA 58.408 36.000 0.00 0.00 0.00 3.41
350 697 7.227156 TCTCTTTCTTTCAAAGCCTAACTGAT 58.773 34.615 0.00 0.00 0.00 2.90
351 698 7.721399 TCTCTTTCTTTCAAAGCCTAACTGATT 59.279 33.333 0.00 0.00 0.00 2.57
352 699 8.237811 TCTTTCTTTCAAAGCCTAACTGATTT 57.762 30.769 0.00 0.00 0.00 2.17
353 700 9.349713 TCTTTCTTTCAAAGCCTAACTGATTTA 57.650 29.630 0.00 0.00 0.00 1.40
354 701 9.399403 CTTTCTTTCAAAGCCTAACTGATTTAC 57.601 33.333 0.00 0.00 0.00 2.01
355 702 8.691661 TTCTTTCAAAGCCTAACTGATTTACT 57.308 30.769 0.00 0.00 0.00 2.24
356 703 8.691661 TCTTTCAAAGCCTAACTGATTTACTT 57.308 30.769 0.00 0.00 0.00 2.24
357 704 8.567948 TCTTTCAAAGCCTAACTGATTTACTTG 58.432 33.333 0.00 0.00 0.00 3.16
358 705 6.254281 TCAAAGCCTAACTGATTTACTTGC 57.746 37.500 0.00 0.00 0.00 4.01
359 706 5.183140 TCAAAGCCTAACTGATTTACTTGCC 59.817 40.000 0.00 0.00 0.00 4.52
360 707 3.270877 AGCCTAACTGATTTACTTGCCG 58.729 45.455 0.00 0.00 0.00 5.69
361 708 2.354821 GCCTAACTGATTTACTTGCCGG 59.645 50.000 0.00 0.00 0.00 6.13
362 709 2.354821 CCTAACTGATTTACTTGCCGGC 59.645 50.000 22.73 22.73 0.00 6.13
363 710 1.904287 AACTGATTTACTTGCCGGCA 58.096 45.000 29.03 29.03 0.00 5.69
364 711 1.904287 ACTGATTTACTTGCCGGCAA 58.096 45.000 37.78 37.78 0.00 4.52
365 712 2.446435 ACTGATTTACTTGCCGGCAAT 58.554 42.857 40.03 29.61 35.20 3.56
366 713 3.616219 ACTGATTTACTTGCCGGCAATA 58.384 40.909 40.03 28.63 35.20 1.90
367 714 4.013728 ACTGATTTACTTGCCGGCAATAA 58.986 39.130 40.03 31.71 35.20 1.40
368 715 4.461081 ACTGATTTACTTGCCGGCAATAAA 59.539 37.500 40.03 35.97 35.20 1.40
369 716 4.739195 TGATTTACTTGCCGGCAATAAAC 58.261 39.130 40.03 29.62 35.20 2.01
370 717 4.218635 TGATTTACTTGCCGGCAATAAACA 59.781 37.500 40.03 31.08 35.20 2.83
371 718 4.585955 TTTACTTGCCGGCAATAAACAA 57.414 36.364 40.03 24.76 35.20 2.83
372 719 4.585955 TTACTTGCCGGCAATAAACAAA 57.414 36.364 40.03 23.44 35.20 2.83
373 720 3.676291 ACTTGCCGGCAATAAACAAAT 57.324 38.095 40.03 16.17 35.20 2.32
374 721 4.001618 ACTTGCCGGCAATAAACAAATT 57.998 36.364 40.03 10.02 35.20 1.82
375 722 4.384940 ACTTGCCGGCAATAAACAAATTT 58.615 34.783 40.03 12.63 35.20 1.82
376 723 4.213059 ACTTGCCGGCAATAAACAAATTTG 59.787 37.500 40.03 25.37 35.20 2.32
377 724 3.995199 TGCCGGCAATAAACAAATTTGA 58.005 36.364 30.74 2.69 0.00 2.69
378 725 3.743396 TGCCGGCAATAAACAAATTTGAC 59.257 39.130 30.74 0.00 0.00 3.18
379 726 3.743396 GCCGGCAATAAACAAATTTGACA 59.257 39.130 24.80 9.08 0.00 3.58
380 727 4.212214 GCCGGCAATAAACAAATTTGACAA 59.788 37.500 24.80 9.06 0.00 3.18
381 728 5.614449 GCCGGCAATAAACAAATTTGACAAG 60.614 40.000 24.80 9.77 0.00 3.16
382 729 5.107143 CCGGCAATAAACAAATTTGACAAGG 60.107 40.000 24.64 9.95 0.00 3.61
383 730 5.465056 CGGCAATAAACAAATTTGACAAGGT 59.535 36.000 24.64 0.00 0.00 3.50
384 731 6.018343 CGGCAATAAACAAATTTGACAAGGTT 60.018 34.615 24.64 4.48 0.00 3.50
385 732 7.169982 CGGCAATAAACAAATTTGACAAGGTTA 59.830 33.333 24.64 5.37 0.00 2.85
386 733 8.831550 GGCAATAAACAAATTTGACAAGGTTAA 58.168 29.630 24.64 0.45 0.00 2.01
424 771 9.952030 TGTATCTATAATTTGTTGACTTGGTCA 57.048 29.630 0.00 0.00 41.09 4.02
426 773 7.681939 TCTATAATTTGTTGACTTGGTCACC 57.318 36.000 0.00 0.00 42.60 4.02
427 774 7.227873 TCTATAATTTGTTGACTTGGTCACCA 58.772 34.615 0.00 0.00 42.60 4.17
428 775 6.916360 ATAATTTGTTGACTTGGTCACCAT 57.084 33.333 0.00 0.00 42.60 3.55
429 776 4.589216 ATTTGTTGACTTGGTCACCATG 57.411 40.909 8.20 8.20 42.60 3.66
430 777 1.317613 TGTTGACTTGGTCACCATGC 58.682 50.000 9.67 3.79 42.60 4.06
431 778 0.598065 GTTGACTTGGTCACCATGCC 59.402 55.000 9.67 0.00 42.60 4.40
432 779 0.539438 TTGACTTGGTCACCATGCCC 60.539 55.000 9.67 3.08 42.60 5.36
433 780 1.074775 GACTTGGTCACCATGCCCA 59.925 57.895 9.67 0.00 32.73 5.36
434 781 0.539438 GACTTGGTCACCATGCCCAA 60.539 55.000 9.67 0.00 36.80 4.12
435 782 2.269978 CTTGGTCACCATGCCCAAG 58.730 57.895 0.00 4.39 46.57 3.61
436 783 1.849832 TTGGTCACCATGCCCAAGA 59.150 52.632 0.00 0.00 33.43 3.02
437 784 0.187117 TTGGTCACCATGCCCAAGAA 59.813 50.000 0.00 0.00 33.43 2.52
438 785 0.409092 TGGTCACCATGCCCAAGAAT 59.591 50.000 0.00 0.00 0.00 2.40
439 786 1.638070 TGGTCACCATGCCCAAGAATA 59.362 47.619 0.00 0.00 0.00 1.75
440 787 2.244510 TGGTCACCATGCCCAAGAATAT 59.755 45.455 0.00 0.00 0.00 1.28
441 788 3.461458 TGGTCACCATGCCCAAGAATATA 59.539 43.478 0.00 0.00 0.00 0.86
442 789 3.821033 GGTCACCATGCCCAAGAATATAC 59.179 47.826 0.00 0.00 0.00 1.47
443 790 4.460263 GTCACCATGCCCAAGAATATACA 58.540 43.478 0.00 0.00 0.00 2.29
444 791 4.275936 GTCACCATGCCCAAGAATATACAC 59.724 45.833 0.00 0.00 0.00 2.90
445 792 3.569701 CACCATGCCCAAGAATATACACC 59.430 47.826 0.00 0.00 0.00 4.16
446 793 3.463329 ACCATGCCCAAGAATATACACCT 59.537 43.478 0.00 0.00 0.00 4.00
447 794 4.079212 ACCATGCCCAAGAATATACACCTT 60.079 41.667 0.00 0.00 0.00 3.50
448 795 5.133660 ACCATGCCCAAGAATATACACCTTA 59.866 40.000 0.00 0.00 0.00 2.69
449 796 5.707298 CCATGCCCAAGAATATACACCTTAG 59.293 44.000 0.00 0.00 0.00 2.18
450 797 6.465751 CCATGCCCAAGAATATACACCTTAGA 60.466 42.308 0.00 0.00 0.00 2.10
451 798 6.174720 TGCCCAAGAATATACACCTTAGAG 57.825 41.667 0.00 0.00 0.00 2.43
452 799 5.903010 TGCCCAAGAATATACACCTTAGAGA 59.097 40.000 0.00 0.00 0.00 3.10
453 800 6.385759 TGCCCAAGAATATACACCTTAGAGAA 59.614 38.462 0.00 0.00 0.00 2.87
454 801 7.092623 TGCCCAAGAATATACACCTTAGAGAAA 60.093 37.037 0.00 0.00 0.00 2.52
455 802 7.442666 GCCCAAGAATATACACCTTAGAGAAAG 59.557 40.741 0.00 0.00 34.73 2.62
465 812 3.528597 CTTAGAGAAAGGAACGGAGGG 57.471 52.381 0.00 0.00 0.00 4.30
466 813 2.913603 TAGAGAAAGGAACGGAGGGA 57.086 50.000 0.00 0.00 0.00 4.20
467 814 1.562783 AGAGAAAGGAACGGAGGGAG 58.437 55.000 0.00 0.00 0.00 4.30
468 815 1.203199 AGAGAAAGGAACGGAGGGAGT 60.203 52.381 0.00 0.00 0.00 3.85
469 816 2.042706 AGAGAAAGGAACGGAGGGAGTA 59.957 50.000 0.00 0.00 0.00 2.59
470 817 2.166050 GAGAAAGGAACGGAGGGAGTAC 59.834 54.545 0.00 0.00 0.00 2.73
471 818 1.897802 GAAAGGAACGGAGGGAGTACA 59.102 52.381 0.00 0.00 0.00 2.90
472 819 1.264295 AAGGAACGGAGGGAGTACAC 58.736 55.000 0.00 0.00 0.00 2.90
512 860 4.999311 GGAAGGCAATGAAAGCTTTGATTT 59.001 37.500 19.55 7.03 30.99 2.17
524 872 7.964559 TGAAAGCTTTGATTTAGTTGATGATCG 59.035 33.333 18.30 0.00 0.00 3.69
580 929 6.935741 GGAACCCAAGCAAAGTTTTAATTT 57.064 33.333 0.00 0.00 0.00 1.82
586 935 8.261522 ACCCAAGCAAAGTTTTAATTTAGTTCA 58.738 29.630 0.00 0.00 0.00 3.18
633 982 5.372343 TGAGTTAATGCAGGATATGGTGT 57.628 39.130 0.00 0.00 0.00 4.16
642 991 6.191657 TGCAGGATATGGTGTAGAATTGAT 57.808 37.500 0.00 0.00 0.00 2.57
648 997 8.884323 AGGATATGGTGTAGAATTGATGTACAT 58.116 33.333 8.43 8.43 0.00 2.29
656 1005 9.029243 GTGTAGAATTGATGTACATGAGAAGAG 57.971 37.037 14.43 0.00 0.00 2.85
660 1009 9.730705 AGAATTGATGTACATGAGAAGAGAAAA 57.269 29.630 14.43 0.00 0.00 2.29
686 1039 3.024547 CGAAGGAGGGATACAGTTGAGA 58.975 50.000 0.00 0.00 39.74 3.27
714 1067 1.843851 ACAACCACCAACTCTCCAGAA 59.156 47.619 0.00 0.00 0.00 3.02
850 1230 7.908453 AGAAGCTATTATAAAGTCGGGCTATT 58.092 34.615 0.00 0.00 0.00 1.73
927 1310 3.197983 CCGAGAGAAAGTGGGGAATAGTT 59.802 47.826 0.00 0.00 0.00 2.24
928 1311 4.184629 CGAGAGAAAGTGGGGAATAGTTG 58.815 47.826 0.00 0.00 0.00 3.16
951 1334 1.107114 GAGAGAGACTCGGGCATTCA 58.893 55.000 0.00 0.00 35.84 2.57
986 1369 3.878245 GCAACTTGCAGAGTAAAGTGAC 58.122 45.455 8.97 0.00 44.26 3.67
1215 1625 0.179045 ACCTCCACTTCACACAGCAC 60.179 55.000 0.00 0.00 0.00 4.40
2237 2677 1.362237 TCCTGAATTTCCATTGCCCCT 59.638 47.619 0.00 0.00 0.00 4.79
2239 2679 2.625087 CCTGAATTTCCATTGCCCCTCT 60.625 50.000 0.00 0.00 0.00 3.69
2240 2680 2.692041 CTGAATTTCCATTGCCCCTCTC 59.308 50.000 0.00 0.00 0.00 3.20
2241 2681 2.034878 GAATTTCCATTGCCCCTCTCC 58.965 52.381 0.00 0.00 0.00 3.71
2243 2692 2.210144 TTTCCATTGCCCCTCTCCCG 62.210 60.000 0.00 0.00 0.00 5.14
2425 2901 2.046023 CCATGAGCTGCGGGAACA 60.046 61.111 0.00 0.00 0.00 3.18
2715 3224 2.280079 CCCCATTTCCAGGAGCCC 59.720 66.667 0.00 0.00 0.00 5.19
2787 3296 2.031163 AGCTGCACTCCCAACGTC 59.969 61.111 1.02 0.00 0.00 4.34
2928 3437 3.953766 GCAAATCTGTGCATGATGAGAG 58.046 45.455 0.00 0.00 44.29 3.20
2937 3446 0.835276 CATGATGAGAGGGTCCAGCA 59.165 55.000 0.00 0.00 33.01 4.41
2992 3501 3.742640 GCTGTCTGTGAAACTTGGAGACT 60.743 47.826 0.00 0.00 37.15 3.24
3036 3581 5.749109 AGCTAGTGTTCGTGAGCAAATATAC 59.251 40.000 0.00 0.00 37.40 1.47
3037 3582 5.050972 GCTAGTGTTCGTGAGCAAATATACC 60.051 44.000 0.00 0.00 34.96 2.73
3046 3595 5.504010 CGTGAGCAAATATACCGCTTTTCAT 60.504 40.000 0.00 0.00 35.75 2.57
3081 3630 0.325272 GAACCACCTCTCCCCTGAAC 59.675 60.000 0.00 0.00 0.00 3.18
3119 3675 1.765314 CCCCTAGCTAGCTGTTGACAT 59.235 52.381 27.68 0.22 0.00 3.06
3121 3677 3.388024 CCCCTAGCTAGCTGTTGACATTA 59.612 47.826 27.68 2.47 0.00 1.90
3122 3678 4.502259 CCCCTAGCTAGCTGTTGACATTAG 60.502 50.000 27.68 12.55 0.00 1.73
3123 3679 4.100189 CCCTAGCTAGCTGTTGACATTAGT 59.900 45.833 27.68 0.00 0.00 2.24
3124 3680 5.395768 CCCTAGCTAGCTGTTGACATTAGTT 60.396 44.000 27.68 0.00 0.00 2.24
3125 3681 5.751028 CCTAGCTAGCTGTTGACATTAGTTC 59.249 44.000 27.68 0.00 0.00 3.01
3212 3770 6.318900 GGTACAATCTTAAGCAGGCTTATGTT 59.681 38.462 17.91 11.70 38.20 2.71
3217 3775 4.943705 TCTTAAGCAGGCTTATGTTCAAGG 59.056 41.667 19.90 1.58 38.20 3.61
3253 3811 5.789643 TTTAGCCAAGTGATCTTTTGCTT 57.210 34.783 12.08 0.00 38.90 3.91
3259 3817 5.350633 CCAAGTGATCTTTTGCTTTGTCAA 58.649 37.500 0.00 0.00 0.00 3.18
3263 3821 5.069516 AGTGATCTTTTGCTTTGTCAATGGT 59.930 36.000 0.00 0.00 0.00 3.55
3265 3823 6.922957 GTGATCTTTTGCTTTGTCAATGGTTA 59.077 34.615 0.00 0.00 0.00 2.85
3266 3824 6.922957 TGATCTTTTGCTTTGTCAATGGTTAC 59.077 34.615 0.00 0.00 0.00 2.50
3292 3851 2.861462 TTTACAGTGCGCAAAAGCTT 57.139 40.000 14.00 0.00 38.13 3.74
3293 3852 2.118228 TTACAGTGCGCAAAAGCTTG 57.882 45.000 14.00 6.70 38.13 4.01
3340 3899 2.223572 GGTGAACCTGTTTGCTGTTGAG 60.224 50.000 0.00 0.00 0.00 3.02
3413 3982 2.202932 CTTGATCGTCGGGCTGGG 60.203 66.667 0.00 0.00 0.00 4.45
3531 4105 7.170277 TGTACTAGTCAGTCCATGTAGTACAA 58.830 38.462 19.78 9.67 43.71 2.41
3658 4233 1.135489 TGTGTTCGTAGCTCGGCTTAG 60.135 52.381 3.71 0.06 40.44 2.18
3668 4243 1.135944 GCTCGGCTTAGTTGCAGAAAC 60.136 52.381 0.00 0.00 36.78 2.78
3669 4244 1.464997 CTCGGCTTAGTTGCAGAAACC 59.535 52.381 0.00 0.00 39.85 3.27
3692 4267 4.391830 CGCTGTTAGTTGATCTTTTAGCCA 59.608 41.667 0.00 0.00 0.00 4.75
3757 4337 3.914364 CGCAAAAGCTTGAAACCATAGTC 59.086 43.478 0.00 0.00 34.14 2.59
3761 4341 2.076863 AGCTTGAAACCATAGTCGCAC 58.923 47.619 0.00 0.00 0.00 5.34
3787 4378 1.134946 ACAAGTGAACCAGTTTGCTGC 59.865 47.619 0.00 0.00 41.26 5.25
3790 4381 0.740737 GTGAACCAGTTTGCTGCTGT 59.259 50.000 0.00 0.00 41.26 4.40
3909 4507 2.763448 CTCAAAAAGGGTGGTTGGTTGA 59.237 45.455 0.00 0.00 0.00 3.18
3910 4508 3.379452 TCAAAAAGGGTGGTTGGTTGAT 58.621 40.909 0.00 0.00 0.00 2.57
3911 4509 3.133721 TCAAAAAGGGTGGTTGGTTGATG 59.866 43.478 0.00 0.00 0.00 3.07
3912 4510 1.715785 AAAGGGTGGTTGGTTGATGG 58.284 50.000 0.00 0.00 0.00 3.51
3913 4511 0.560688 AAGGGTGGTTGGTTGATGGT 59.439 50.000 0.00 0.00 0.00 3.55
3914 4512 0.560688 AGGGTGGTTGGTTGATGGTT 59.439 50.000 0.00 0.00 0.00 3.67
3915 4513 1.062505 AGGGTGGTTGGTTGATGGTTT 60.063 47.619 0.00 0.00 0.00 3.27
3916 4514 1.343142 GGGTGGTTGGTTGATGGTTTC 59.657 52.381 0.00 0.00 0.00 2.78
3917 4515 2.316108 GGTGGTTGGTTGATGGTTTCT 58.684 47.619 0.00 0.00 0.00 2.52
3918 4516 2.035832 GGTGGTTGGTTGATGGTTTCTG 59.964 50.000 0.00 0.00 0.00 3.02
3919 4517 2.955660 GTGGTTGGTTGATGGTTTCTGA 59.044 45.455 0.00 0.00 0.00 3.27
3920 4518 3.573967 GTGGTTGGTTGATGGTTTCTGAT 59.426 43.478 0.00 0.00 0.00 2.90
3921 4519 3.826157 TGGTTGGTTGATGGTTTCTGATC 59.174 43.478 0.00 0.00 0.00 2.92
3922 4520 3.826157 GGTTGGTTGATGGTTTCTGATCA 59.174 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.892215 TGTATGCCCCATTGTATGCATG 59.108 45.455 10.16 0.00 43.76 4.06
79 81 7.175467 TCGTTGTAAGGTATATATGACGGACAT 59.825 37.037 0.00 0.00 42.39 3.06
133 480 2.500504 AGGAACGGAGGGAGTATCAAAC 59.499 50.000 0.00 0.00 36.25 2.93
139 486 6.723052 CCTTATATAAAGGAACGGAGGGAGTA 59.277 42.308 0.00 0.00 39.81 2.59
140 487 5.543020 CCTTATATAAAGGAACGGAGGGAGT 59.457 44.000 0.00 0.00 39.81 3.85
141 488 5.543020 ACCTTATATAAAGGAACGGAGGGAG 59.457 44.000 10.67 0.00 39.81 4.30
142 489 5.470501 ACCTTATATAAAGGAACGGAGGGA 58.529 41.667 10.67 0.00 39.81 4.20
143 490 5.820404 ACCTTATATAAAGGAACGGAGGG 57.180 43.478 10.67 4.11 39.81 4.30
144 491 9.788889 AATAAACCTTATATAAAGGAACGGAGG 57.211 33.333 10.67 4.52 39.81 4.30
190 537 9.643652 CGAGAAATTAGAAGAAATGCATCTTAC 57.356 33.333 0.00 0.00 39.70 2.34
191 538 9.383519 ACGAGAAATTAGAAGAAATGCATCTTA 57.616 29.630 0.00 0.00 39.70 2.10
192 539 8.273780 ACGAGAAATTAGAAGAAATGCATCTT 57.726 30.769 0.00 0.00 42.24 2.40
193 540 7.856145 ACGAGAAATTAGAAGAAATGCATCT 57.144 32.000 0.00 0.00 0.00 2.90
196 543 8.612619 GGATTACGAGAAATTAGAAGAAATGCA 58.387 33.333 0.00 0.00 0.00 3.96
197 544 8.070769 GGGATTACGAGAAATTAGAAGAAATGC 58.929 37.037 0.00 0.00 0.00 3.56
198 545 9.331282 AGGGATTACGAGAAATTAGAAGAAATG 57.669 33.333 0.00 0.00 0.00 2.32
199 546 9.907229 AAGGGATTACGAGAAATTAGAAGAAAT 57.093 29.630 0.00 0.00 0.00 2.17
200 547 9.734984 AAAGGGATTACGAGAAATTAGAAGAAA 57.265 29.630 0.00 0.00 0.00 2.52
201 548 9.734984 AAAAGGGATTACGAGAAATTAGAAGAA 57.265 29.630 0.00 0.00 0.00 2.52
202 549 9.734984 AAAAAGGGATTACGAGAAATTAGAAGA 57.265 29.630 0.00 0.00 0.00 2.87
242 589 5.484290 TCGGGAGAGAGATACTTTCCTTTTT 59.516 40.000 0.00 0.00 45.70 1.94
243 590 5.024118 TCGGGAGAGAGATACTTTCCTTTT 58.976 41.667 0.00 0.00 45.70 2.27
244 591 4.611367 TCGGGAGAGAGATACTTTCCTTT 58.389 43.478 0.00 0.00 45.70 3.11
245 592 4.252570 TCGGGAGAGAGATACTTTCCTT 57.747 45.455 0.00 0.00 45.70 3.36
246 593 3.955524 TCGGGAGAGAGATACTTTCCT 57.044 47.619 0.00 0.00 45.70 3.36
247 594 5.538849 AAATCGGGAGAGAGATACTTTCC 57.461 43.478 0.00 0.00 45.69 3.13
248 595 6.699642 CAGAAAATCGGGAGAGAGATACTTTC 59.300 42.308 0.00 0.00 45.48 2.62
249 596 6.155393 ACAGAAAATCGGGAGAGAGATACTTT 59.845 38.462 0.00 0.00 45.48 2.66
250 597 5.659079 ACAGAAAATCGGGAGAGAGATACTT 59.341 40.000 0.00 0.00 45.48 2.24
251 598 5.205056 ACAGAAAATCGGGAGAGAGATACT 58.795 41.667 0.00 0.00 45.48 2.12
252 599 5.523438 ACAGAAAATCGGGAGAGAGATAC 57.477 43.478 0.00 0.00 45.48 2.24
253 600 7.235079 AGATACAGAAAATCGGGAGAGAGATA 58.765 38.462 0.00 0.00 45.48 1.98
254 601 6.074648 AGATACAGAAAATCGGGAGAGAGAT 58.925 40.000 0.00 0.00 45.48 2.75
255 602 5.450453 AGATACAGAAAATCGGGAGAGAGA 58.550 41.667 0.00 0.00 45.48 3.10
256 603 5.300539 TGAGATACAGAAAATCGGGAGAGAG 59.699 44.000 0.00 0.00 45.48 3.20
257 604 5.067936 GTGAGATACAGAAAATCGGGAGAGA 59.932 44.000 0.00 0.00 45.48 3.10
258 605 5.068460 AGTGAGATACAGAAAATCGGGAGAG 59.932 44.000 0.00 0.00 45.48 3.20
259 606 4.956700 AGTGAGATACAGAAAATCGGGAGA 59.043 41.667 0.00 0.00 46.90 3.71
260 607 5.269505 AGTGAGATACAGAAAATCGGGAG 57.730 43.478 0.00 0.00 0.00 4.30
261 608 5.677319 AAGTGAGATACAGAAAATCGGGA 57.323 39.130 0.00 0.00 0.00 5.14
262 609 9.197694 CTATAAAGTGAGATACAGAAAATCGGG 57.802 37.037 0.00 0.00 0.00 5.14
263 610 9.967346 TCTATAAAGTGAGATACAGAAAATCGG 57.033 33.333 0.00 0.00 0.00 4.18
297 644 4.575236 GTCAATCGGGAGGGAAATACTTTC 59.425 45.833 0.00 0.00 38.94 2.62
298 645 4.227527 AGTCAATCGGGAGGGAAATACTTT 59.772 41.667 0.00 0.00 0.00 2.66
299 646 3.780850 AGTCAATCGGGAGGGAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
300 647 3.134804 CAGTCAATCGGGAGGGAAATACT 59.865 47.826 0.00 0.00 0.00 2.12
301 648 3.118371 ACAGTCAATCGGGAGGGAAATAC 60.118 47.826 0.00 0.00 0.00 1.89
302 649 3.112263 ACAGTCAATCGGGAGGGAAATA 58.888 45.455 0.00 0.00 0.00 1.40
303 650 1.916181 ACAGTCAATCGGGAGGGAAAT 59.084 47.619 0.00 0.00 0.00 2.17
304 651 1.358152 ACAGTCAATCGGGAGGGAAA 58.642 50.000 0.00 0.00 0.00 3.13
305 652 2.241281 TACAGTCAATCGGGAGGGAA 57.759 50.000 0.00 0.00 0.00 3.97
306 653 2.091278 AGATACAGTCAATCGGGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
307 654 2.297597 GAGATACAGTCAATCGGGAGGG 59.702 54.545 0.00 0.00 0.00 4.30
308 655 3.226777 AGAGATACAGTCAATCGGGAGG 58.773 50.000 0.00 0.00 0.00 4.30
309 656 4.927978 AAGAGATACAGTCAATCGGGAG 57.072 45.455 0.00 0.00 0.00 4.30
310 657 4.956700 AGAAAGAGATACAGTCAATCGGGA 59.043 41.667 0.00 0.00 0.00 5.14
311 658 5.269505 AGAAAGAGATACAGTCAATCGGG 57.730 43.478 0.00 0.00 0.00 5.14
312 659 6.813649 TGAAAGAAAGAGATACAGTCAATCGG 59.186 38.462 0.00 0.00 0.00 4.18
313 660 7.818493 TGAAAGAAAGAGATACAGTCAATCG 57.182 36.000 0.00 0.00 0.00 3.34
315 662 8.510505 GCTTTGAAAGAAAGAGATACAGTCAAT 58.489 33.333 9.48 0.00 0.00 2.57
316 663 7.041098 GGCTTTGAAAGAAAGAGATACAGTCAA 60.041 37.037 9.48 0.00 0.00 3.18
317 664 6.428159 GGCTTTGAAAGAAAGAGATACAGTCA 59.572 38.462 9.48 0.00 0.00 3.41
318 665 6.652900 AGGCTTTGAAAGAAAGAGATACAGTC 59.347 38.462 9.48 0.00 0.00 3.51
319 666 6.538263 AGGCTTTGAAAGAAAGAGATACAGT 58.462 36.000 9.48 0.00 0.00 3.55
320 667 8.447053 GTTAGGCTTTGAAAGAAAGAGATACAG 58.553 37.037 9.48 0.00 0.00 2.74
321 668 8.157476 AGTTAGGCTTTGAAAGAAAGAGATACA 58.843 33.333 9.48 0.00 0.00 2.29
322 669 8.447053 CAGTTAGGCTTTGAAAGAAAGAGATAC 58.553 37.037 9.48 0.00 0.00 2.24
323 670 8.375506 TCAGTTAGGCTTTGAAAGAAAGAGATA 58.624 33.333 9.48 0.00 0.00 1.98
324 671 7.227156 TCAGTTAGGCTTTGAAAGAAAGAGAT 58.773 34.615 9.48 0.00 0.00 2.75
325 672 6.591935 TCAGTTAGGCTTTGAAAGAAAGAGA 58.408 36.000 9.48 0.00 0.00 3.10
326 673 6.867662 TCAGTTAGGCTTTGAAAGAAAGAG 57.132 37.500 9.48 0.00 0.00 2.85
327 674 7.823745 AATCAGTTAGGCTTTGAAAGAAAGA 57.176 32.000 9.48 0.00 0.00 2.52
328 675 9.399403 GTAAATCAGTTAGGCTTTGAAAGAAAG 57.601 33.333 9.48 0.00 0.00 2.62
329 676 9.131791 AGTAAATCAGTTAGGCTTTGAAAGAAA 57.868 29.630 9.48 0.00 0.00 2.52
330 677 8.691661 AGTAAATCAGTTAGGCTTTGAAAGAA 57.308 30.769 9.48 0.00 0.00 2.52
331 678 8.567948 CAAGTAAATCAGTTAGGCTTTGAAAGA 58.432 33.333 9.48 0.00 0.00 2.52
332 679 7.327032 GCAAGTAAATCAGTTAGGCTTTGAAAG 59.673 37.037 0.00 0.00 0.00 2.62
333 680 7.145323 GCAAGTAAATCAGTTAGGCTTTGAAA 58.855 34.615 0.00 0.00 0.00 2.69
334 681 6.294508 GGCAAGTAAATCAGTTAGGCTTTGAA 60.295 38.462 0.00 0.00 0.00 2.69
335 682 5.183140 GGCAAGTAAATCAGTTAGGCTTTGA 59.817 40.000 0.00 0.00 0.00 2.69
336 683 5.402398 GGCAAGTAAATCAGTTAGGCTTTG 58.598 41.667 0.00 0.00 0.00 2.77
337 684 4.156008 CGGCAAGTAAATCAGTTAGGCTTT 59.844 41.667 0.00 0.00 0.00 3.51
338 685 3.689649 CGGCAAGTAAATCAGTTAGGCTT 59.310 43.478 0.00 0.00 0.00 4.35
339 686 3.270877 CGGCAAGTAAATCAGTTAGGCT 58.729 45.455 0.00 0.00 0.00 4.58
340 687 2.354821 CCGGCAAGTAAATCAGTTAGGC 59.645 50.000 0.00 0.00 0.00 3.93
341 688 2.354821 GCCGGCAAGTAAATCAGTTAGG 59.645 50.000 24.80 0.00 0.00 2.69
342 689 3.006940 TGCCGGCAAGTAAATCAGTTAG 58.993 45.455 30.74 0.00 0.00 2.34
343 690 3.060736 TGCCGGCAAGTAAATCAGTTA 57.939 42.857 30.74 0.00 0.00 2.24
344 691 1.904287 TGCCGGCAAGTAAATCAGTT 58.096 45.000 30.74 0.00 0.00 3.16
345 692 1.904287 TTGCCGGCAAGTAAATCAGT 58.096 45.000 37.30 0.00 0.00 3.41
346 693 4.630894 TTATTGCCGGCAAGTAAATCAG 57.369 40.909 41.38 0.00 39.47 2.90
347 694 4.218635 TGTTTATTGCCGGCAAGTAAATCA 59.781 37.500 41.38 32.08 39.47 2.57
348 695 4.739195 TGTTTATTGCCGGCAAGTAAATC 58.261 39.130 41.38 30.40 39.47 2.17
349 696 4.792521 TGTTTATTGCCGGCAAGTAAAT 57.207 36.364 41.38 28.80 39.47 1.40
350 697 4.585955 TTGTTTATTGCCGGCAAGTAAA 57.414 36.364 41.38 35.13 39.47 2.01
351 698 4.585955 TTTGTTTATTGCCGGCAAGTAA 57.414 36.364 41.38 33.02 39.47 2.24
352 699 4.792521 ATTTGTTTATTGCCGGCAAGTA 57.207 36.364 41.38 29.89 39.47 2.24
353 700 3.676291 ATTTGTTTATTGCCGGCAAGT 57.324 38.095 41.38 30.69 39.47 3.16
354 701 4.450419 TCAAATTTGTTTATTGCCGGCAAG 59.550 37.500 41.38 25.20 39.47 4.01
355 702 4.212214 GTCAAATTTGTTTATTGCCGGCAA 59.788 37.500 41.54 41.54 40.47 4.52
356 703 3.743396 GTCAAATTTGTTTATTGCCGGCA 59.257 39.130 29.03 29.03 0.00 5.69
357 704 3.743396 TGTCAAATTTGTTTATTGCCGGC 59.257 39.130 22.73 22.73 0.00 6.13
358 705 5.107143 CCTTGTCAAATTTGTTTATTGCCGG 60.107 40.000 17.47 0.00 0.00 6.13
359 706 5.465056 ACCTTGTCAAATTTGTTTATTGCCG 59.535 36.000 17.47 1.58 0.00 5.69
360 707 6.859420 ACCTTGTCAAATTTGTTTATTGCC 57.141 33.333 17.47 0.00 0.00 4.52
398 745 9.952030 TGACCAAGTCAACAAATTATAGATACA 57.048 29.630 0.00 0.00 39.78 2.29
413 760 3.034924 GGCATGGTGACCAAGTCAA 57.965 52.632 9.06 0.00 44.49 3.18
414 761 4.819783 GGCATGGTGACCAAGTCA 57.180 55.556 9.06 0.00 40.50 3.41
421 768 4.275936 GTGTATATTCTTGGGCATGGTGAC 59.724 45.833 0.00 0.00 0.00 3.67
422 769 4.460263 GTGTATATTCTTGGGCATGGTGA 58.540 43.478 0.00 0.00 0.00 4.02
423 770 3.569701 GGTGTATATTCTTGGGCATGGTG 59.430 47.826 0.00 0.00 0.00 4.17
424 771 3.463329 AGGTGTATATTCTTGGGCATGGT 59.537 43.478 0.00 0.00 0.00 3.55
425 772 4.104383 AGGTGTATATTCTTGGGCATGG 57.896 45.455 0.00 0.00 0.00 3.66
426 773 6.533730 TCTAAGGTGTATATTCTTGGGCATG 58.466 40.000 0.00 0.00 0.00 4.06
427 774 6.558775 TCTCTAAGGTGTATATTCTTGGGCAT 59.441 38.462 0.00 0.00 0.00 4.40
428 775 5.903010 TCTCTAAGGTGTATATTCTTGGGCA 59.097 40.000 0.00 0.00 0.00 5.36
429 776 6.420913 TCTCTAAGGTGTATATTCTTGGGC 57.579 41.667 0.00 0.00 0.00 5.36
430 777 8.894768 CTTTCTCTAAGGTGTATATTCTTGGG 57.105 38.462 0.00 0.00 0.00 4.12
445 792 3.097614 TCCCTCCGTTCCTTTCTCTAAG 58.902 50.000 0.00 0.00 0.00 2.18
446 793 3.097614 CTCCCTCCGTTCCTTTCTCTAA 58.902 50.000 0.00 0.00 0.00 2.10
447 794 2.042706 ACTCCCTCCGTTCCTTTCTCTA 59.957 50.000 0.00 0.00 0.00 2.43
448 795 1.203199 ACTCCCTCCGTTCCTTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
449 796 1.268066 ACTCCCTCCGTTCCTTTCTC 58.732 55.000 0.00 0.00 0.00 2.87
450 797 2.177734 GTACTCCCTCCGTTCCTTTCT 58.822 52.381 0.00 0.00 0.00 2.52
451 798 1.897802 TGTACTCCCTCCGTTCCTTTC 59.102 52.381 0.00 0.00 0.00 2.62
452 799 1.622312 GTGTACTCCCTCCGTTCCTTT 59.378 52.381 0.00 0.00 0.00 3.11
453 800 1.203149 AGTGTACTCCCTCCGTTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
454 801 0.408700 AGTGTACTCCCTCCGTTCCT 59.591 55.000 0.00 0.00 0.00 3.36
455 802 1.264295 AAGTGTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
456 803 4.021632 ACTTAAAGTGTACTCCCTCCGTTC 60.022 45.833 0.00 0.00 0.00 3.95
457 804 3.899980 ACTTAAAGTGTACTCCCTCCGTT 59.100 43.478 0.00 0.00 0.00 4.44
458 805 3.504375 ACTTAAAGTGTACTCCCTCCGT 58.496 45.455 0.00 0.00 0.00 4.69
459 806 5.848833 ATACTTAAAGTGTACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
460 807 6.070366 ACCAATACTTAAAGTGTACTCCCTCC 60.070 42.308 0.00 0.00 0.00 4.30
461 808 6.944096 ACCAATACTTAAAGTGTACTCCCTC 58.056 40.000 0.00 0.00 0.00 4.30
462 809 6.947376 ACCAATACTTAAAGTGTACTCCCT 57.053 37.500 0.00 0.00 0.00 4.20
463 810 7.270779 CCTACCAATACTTAAAGTGTACTCCC 58.729 42.308 0.00 0.00 0.00 4.30
464 811 7.270779 CCCTACCAATACTTAAAGTGTACTCC 58.729 42.308 0.00 0.00 0.00 3.85
465 812 7.124750 TCCCCTACCAATACTTAAAGTGTACTC 59.875 40.741 0.00 0.00 0.00 2.59
466 813 6.961721 TCCCCTACCAATACTTAAAGTGTACT 59.038 38.462 0.00 0.00 0.00 2.73
467 814 7.186570 TCCCCTACCAATACTTAAAGTGTAC 57.813 40.000 0.00 0.00 0.00 2.90
468 815 7.092757 CCTTCCCCTACCAATACTTAAAGTGTA 60.093 40.741 0.00 0.00 0.00 2.90
469 816 6.296836 CCTTCCCCTACCAATACTTAAAGTGT 60.297 42.308 0.00 0.00 0.00 3.55
470 817 6.120220 CCTTCCCCTACCAATACTTAAAGTG 58.880 44.000 0.00 0.00 0.00 3.16
471 818 5.339778 GCCTTCCCCTACCAATACTTAAAGT 60.340 44.000 0.00 0.00 0.00 2.66
472 819 5.131067 GCCTTCCCCTACCAATACTTAAAG 58.869 45.833 0.00 0.00 0.00 1.85
562 911 8.764287 CCTGAACTAAATTAAAACTTTGCTTGG 58.236 33.333 0.00 0.00 0.00 3.61
580 929 8.635765 ATCAAAGCTTATCAAAACCTGAACTA 57.364 30.769 0.00 0.00 37.67 2.24
586 935 9.211485 CAATCAAATCAAAGCTTATCAAAACCT 57.789 29.630 0.00 0.00 0.00 3.50
599 948 8.030692 TCCTGCATTAACTCAATCAAATCAAAG 58.969 33.333 0.00 0.00 0.00 2.77
642 991 6.759356 TCGTTTGTTTTCTCTTCTCATGTACA 59.241 34.615 0.00 0.00 0.00 2.90
648 997 5.424757 TCCTTCGTTTGTTTTCTCTTCTCA 58.575 37.500 0.00 0.00 0.00 3.27
656 1005 4.758165 TGTATCCCTCCTTCGTTTGTTTTC 59.242 41.667 0.00 0.00 0.00 2.29
659 1008 3.326880 ACTGTATCCCTCCTTCGTTTGTT 59.673 43.478 0.00 0.00 0.00 2.83
660 1009 2.904434 ACTGTATCCCTCCTTCGTTTGT 59.096 45.455 0.00 0.00 0.00 2.83
686 1039 1.134729 AGTTGGTGGTTGTACGTTCGT 60.135 47.619 0.00 2.91 0.00 3.85
733 1106 6.591750 TGTAGTTGGGTGTTTTCTCAAAAA 57.408 33.333 0.00 0.00 31.13 1.94
820 1196 6.583050 CCCGACTTTATAATAGCTTCTCGAAG 59.417 42.308 0.00 2.34 41.24 3.79
823 1199 4.621886 GCCCGACTTTATAATAGCTTCTCG 59.378 45.833 0.00 0.00 0.00 4.04
830 1210 9.490379 AAAGACAATAGCCCGACTTTATAATAG 57.510 33.333 0.00 0.00 0.00 1.73
876 1259 8.602472 AAGGCAATGACCCAACTTTATAATAA 57.398 30.769 0.00 0.00 0.00 1.40
891 1274 1.740025 CTCTCGGGAAAAGGCAATGAC 59.260 52.381 0.00 0.00 0.00 3.06
892 1275 1.628340 TCTCTCGGGAAAAGGCAATGA 59.372 47.619 0.00 0.00 0.00 2.57
927 1310 0.107410 GCCCGAGTCTCTCTCTCTCA 60.107 60.000 0.00 0.00 40.75 3.27
928 1311 0.107410 TGCCCGAGTCTCTCTCTCTC 60.107 60.000 0.00 0.00 40.75 3.20
943 1326 3.025619 CCGAATCGCTGAATGCCC 58.974 61.111 0.00 0.00 38.78 5.36
951 1334 2.165301 GTTGCTACGCCGAATCGCT 61.165 57.895 0.00 0.00 0.00 4.93
986 1369 0.725686 CGCCATTGCTCTGTCTCTTG 59.274 55.000 0.00 0.00 34.43 3.02
1035 1418 4.414956 ATCTGCGTGGGGAGGGGA 62.415 66.667 0.00 0.00 31.58 4.81
1114 1500 2.066393 CGAGCTTGGGGATGAGGGA 61.066 63.158 0.00 0.00 0.00 4.20
1186 1596 4.394712 GTGGAGGTGGCCGGTGAG 62.395 72.222 1.90 0.00 0.00 3.51
1189 1599 3.637273 GAAGTGGAGGTGGCCGGT 61.637 66.667 1.90 0.00 0.00 5.28
1215 1625 4.570663 GGGACGGCGTCGATCTGG 62.571 72.222 31.02 0.00 40.11 3.86
1551 1991 4.807039 ATGCGCACGTCCCGGTAC 62.807 66.667 14.90 0.00 0.00 3.34
2058 2498 0.329261 CCTTGATGTCCTTGGCCAGA 59.671 55.000 5.11 0.00 0.00 3.86
2237 2677 3.706373 GCTGCTTCACCCGGGAGA 61.706 66.667 32.02 24.46 0.00 3.71
2239 2679 4.020617 CTGCTGCTTCACCCGGGA 62.021 66.667 32.02 1.07 0.00 5.14
2243 2692 2.282040 AGTGCTGCTGCTTCACCC 60.282 61.111 17.00 0.00 40.48 4.61
2492 2968 1.101635 TATGAGGTCGAGCGTCCTGG 61.102 60.000 13.08 0.00 33.99 4.45
2787 3296 1.531264 CGGACGACATACTGGACGAAG 60.531 57.143 0.00 0.00 0.00 3.79
2937 3446 1.874345 ATCGAGTCGAACCTGGCGTT 61.874 55.000 20.74 0.00 39.99 4.84
3025 3535 6.305693 AGATGAAAAGCGGTATATTTGCTC 57.694 37.500 0.00 0.00 38.17 4.26
3036 3581 3.287312 TCAGCAAAAGATGAAAAGCGG 57.713 42.857 0.00 0.00 0.00 5.52
3037 3582 3.671928 CCTTCAGCAAAAGATGAAAAGCG 59.328 43.478 0.00 0.00 35.14 4.68
3046 3595 3.130340 GTGGTTCAACCTTCAGCAAAAGA 59.870 43.478 8.40 0.00 39.58 2.52
3071 3620 2.104792 TCTGTTTCACAGTTCAGGGGAG 59.895 50.000 3.87 0.00 46.03 4.30
3081 3630 3.667450 GGGCTCCCCTCTGTTTCACAG 62.667 61.905 0.00 0.00 39.84 3.66
3212 3770 9.747898 TGGCTAAAAGATAAACTAAATCCTTGA 57.252 29.630 0.00 0.00 0.00 3.02
3259 3817 7.281324 TGCGCACTGTAAATAATAAGTAACCAT 59.719 33.333 5.66 0.00 0.00 3.55
3263 3821 9.549509 CTTTTGCGCACTGTAAATAATAAGTAA 57.450 29.630 11.12 0.00 31.98 2.24
3265 3823 6.526674 GCTTTTGCGCACTGTAAATAATAAGT 59.473 34.615 11.12 0.00 31.98 2.24
3266 3824 6.911756 GCTTTTGCGCACTGTAAATAATAAG 58.088 36.000 11.12 0.00 31.98 1.73
3292 3851 4.424626 GTGTCTCTGCGACTATGATTTCA 58.575 43.478 0.00 0.00 43.25 2.69
3293 3852 3.799420 GGTGTCTCTGCGACTATGATTTC 59.201 47.826 0.00 0.00 43.25 2.17
3319 3878 1.748493 TCAACAGCAAACAGGTTCACC 59.252 47.619 0.00 0.00 0.00 4.02
3328 3887 6.090129 TCTTACAAACAACTCAACAGCAAAC 58.910 36.000 0.00 0.00 0.00 2.93
3340 3899 6.706055 TCATCGTCATCTCTTACAAACAAC 57.294 37.500 0.00 0.00 0.00 3.32
3413 3982 0.247736 CTGGCTCCTGGTCAGTACAC 59.752 60.000 0.00 0.00 42.28 2.90
3531 4105 5.629622 GCTGTCAGCTCATGTCTCAAACAT 61.630 45.833 17.89 0.00 43.05 2.71
3658 4233 1.602377 ACTAACAGCGGTTTCTGCAAC 59.398 47.619 7.73 0.00 38.45 4.17
3668 4243 4.201822 GGCTAAAAGATCAACTAACAGCGG 60.202 45.833 0.00 0.00 0.00 5.52
3669 4244 4.391830 TGGCTAAAAGATCAACTAACAGCG 59.608 41.667 0.00 0.00 0.00 5.18
3692 4267 4.037208 CACAGACAAGGCAAAAGATCACTT 59.963 41.667 0.00 0.00 38.05 3.16
3757 4337 1.260561 GGTTCACTTGTAGTGTGTGCG 59.739 52.381 6.71 0.00 46.03 5.34
3761 4341 4.730613 GCAAACTGGTTCACTTGTAGTGTG 60.731 45.833 6.71 0.00 46.03 3.82
3778 4369 2.029110 ACAAACAACACAGCAGCAAACT 60.029 40.909 0.00 0.00 0.00 2.66
3787 4378 6.017192 TGACCATCATCTTACAAACAACACAG 60.017 38.462 0.00 0.00 0.00 3.66
3790 4381 6.770303 TCTTGACCATCATCTTACAAACAACA 59.230 34.615 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.