Multiple sequence alignment - TraesCS6B01G271900

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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 TraesCS6B01G271900 chr6B 100.000 3319 0 0 1 3319 490567082 490563764 0.000000e+00 6130.0
1 TraesCS6B01G271900 chr6B 82.743 226 24 7 229 442 569875755 569875533 1.570000e-43 187.0
2 TraesCS6B01G271900 chr6B 98.113 53 1 0 176 228 490566854 490566802 3.530000e-15 93.5
3 TraesCS6B01G271900 chr6B 98.113 53 1 0 229 281 490566907 490566855 3.530000e-15 93.5
4 TraesCS6B01G271900 chr6A 93.633 1759 67 17 820 2566 469109594 469111319 0.000000e+00 2586.0
5 TraesCS6B01G271900 chr6A 86.783 575 40 10 2549 3088 469111360 469111933 2.830000e-170 608.0
6 TraesCS6B01G271900 chr6A 90.506 158 9 4 3165 3319 469111929 469112083 1.560000e-48 204.0
7 TraesCS6B01G271900 chr6D 95.238 1449 53 5 892 2333 329884500 329885939 0.000000e+00 2279.0
8 TraesCS6B01G271900 chr6D 91.090 752 27 14 2371 3085 329887628 329888376 0.000000e+00 981.0
9 TraesCS6B01G271900 chr6D 95.016 321 15 1 229 548 329883570 329883890 1.370000e-138 503.0
10 TraesCS6B01G271900 chr6D 92.258 155 9 1 3165 3319 329888375 329888526 2.010000e-52 217.0
11 TraesCS6B01G271900 chr6D 87.845 181 17 5 8 186 381364446 381364623 1.210000e-49 207.0
12 TraesCS6B01G271900 chr6D 91.781 146 7 4 84 228 329883482 329883623 7.260000e-47 198.0
13 TraesCS6B01G271900 chr6D 77.966 295 45 13 229 507 21985681 21985971 2.050000e-37 167.0
14 TraesCS6B01G271900 chr6D 91.129 124 9 2 262 385 381364634 381364755 2.050000e-37 167.0
15 TraesCS6B01G271900 chr2D 75.964 1011 194 40 1268 2261 517264638 517263660 3.000000e-130 475.0
16 TraesCS6B01G271900 chr2A 75.811 1017 185 47 1268 2261 661585765 661584787 3.020000e-125 459.0
17 TraesCS6B01G271900 chr2A 92.500 40 3 0 468 507 724290598 724290559 1.290000e-04 58.4
18 TraesCS6B01G271900 chr2B 75.296 1012 190 46 1268 2261 609202232 609201263 2.370000e-116 429.0
19 TraesCS6B01G271900 chr2B 92.308 65 5 0 547 611 550168020 550168084 3.530000e-15 93.5
20 TraesCS6B01G271900 chr3B 92.233 103 4 3 614 713 257719113 257719214 3.450000e-30 143.0
21 TraesCS6B01G271900 chr3B 88.732 71 6 2 541 611 828775099 828775167 5.900000e-13 86.1
22 TraesCS6B01G271900 chr3B 90.196 51 5 0 465 515 820509459 820509409 2.140000e-07 67.6
23 TraesCS6B01G271900 chr7B 91.262 103 5 3 614 713 362781661 362781762 1.610000e-28 137.0
24 TraesCS6B01G271900 chr5B 91.176 102 7 1 614 713 684742837 684742938 1.610000e-28 137.0
25 TraesCS6B01G271900 chr5B 93.750 64 3 1 548 611 661040156 661040218 9.800000e-16 95.3
26 TraesCS6B01G271900 chr4B 91.262 103 5 3 614 713 315092567 315092668 1.610000e-28 137.0
27 TraesCS6B01G271900 chr4B 91.262 103 5 3 614 713 323572884 323572985 1.610000e-28 137.0
28 TraesCS6B01G271900 chr4B 81.529 157 27 1 559 713 586943799 586943955 9.660000e-26 128.0
29 TraesCS6B01G271900 chr4B 87.143 70 7 2 553 622 580384151 580384084 9.870000e-11 78.7
30 TraesCS6B01G271900 chr4A 89.908 109 7 3 614 719 688238892 688238785 1.610000e-28 137.0
31 TraesCS6B01G271900 chr4A 90.769 65 6 0 547 611 664180552 664180616 1.640000e-13 87.9
32 TraesCS6B01G271900 chr4A 90.698 43 4 0 465 507 474752970 474753012 1.290000e-04 58.4
33 TraesCS6B01G271900 chr1D 87.931 116 11 2 614 726 124121387 124121502 2.080000e-27 134.0
34 TraesCS6B01G271900 chr1B 88.034 117 9 4 614 726 455649100 455649215 2.080000e-27 134.0
35 TraesCS6B01G271900 chr1B 93.443 61 4 0 551 611 627991749 627991689 1.270000e-14 91.6
36 TraesCS6B01G271900 chr1B 88.889 72 5 3 540 611 657408956 657408888 5.900000e-13 86.1
37 TraesCS6B01G271900 chr3D 94.915 59 3 0 553 611 66739273 66739331 3.530000e-15 93.5
38 TraesCS6B01G271900 chrUn 92.188 64 5 0 548 611 86631373 86631310 1.270000e-14 91.6
39 TraesCS6B01G271900 chrUn 90.196 51 5 0 465 515 310738481 310738431 2.140000e-07 67.6
40 TraesCS6B01G271900 chr4D 89.831 59 6 0 457 515 132919181 132919123 3.550000e-10 76.8
41 TraesCS6B01G271900 chr1A 92.157 51 4 0 465 515 2443890 2443840 4.590000e-09 73.1
42 TraesCS6B01G271900 chr7D 85.714 56 8 0 1508 1563 626438717 626438772 3.580000e-05 60.2
43 TraesCS6B01G271900 chr7A 83.607 61 10 0 447 507 246264823 246264883 1.290000e-04 58.4


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 TraesCS6B01G271900 chr6B 490563764 490567082 3318 True 2105.666667 6130 98.742000 1 3319 3 chr6B.!!$R2 3318
1 TraesCS6B01G271900 chr6A 469109594 469112083 2489 False 1132.666667 2586 90.307333 820 3319 3 chr6A.!!$F1 2499
2 TraesCS6B01G271900 chr6D 329883482 329888526 5044 False 835.600000 2279 93.076600 84 3319 5 chr6D.!!$F2 3235
3 TraesCS6B01G271900 chr2D 517263660 517264638 978 True 475.000000 475 75.964000 1268 2261 1 chr2D.!!$R1 993
4 TraesCS6B01G271900 chr2A 661584787 661585765 978 True 459.000000 459 75.811000 1268 2261 1 chr2A.!!$R1 993
5 TraesCS6B01G271900 chr2B 609201263 609202232 969 True 429.000000 429 75.296000 1268 2261 1 chr2B.!!$R1 993

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
186 187 0.250727 TTTTCGCCAAGGAGACCCAG 60.251 55.0 0.0 0.0 33.88 4.45 F
239 240 0.912486 AGCCACATAAGGAGACCCAC 59.088 55.0 0.0 0.0 33.88 4.61 F
1072 1383 0.110486 ACAAAACGCACCCATCTCCT 59.890 50.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1072 1383 0.616111 GAGCACCTGGAGGAGAAGGA 60.616 60.0 0.00 0.0 37.01 3.36 R
2212 2555 0.038159 GGGAGACTCTGGTGTTGACG 60.038 60.0 1.74 0.0 0.00 4.35 R
2843 4926 0.031917 TTGGGATGCCATTGCCATCT 60.032 50.0 6.84 0.0 36.93 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
24 25 7.433708 TCGCTATCTTCTTTGATTTGTGAAA 57.566 32.000 0.00 0.00 0.00 2.69
25 26 7.870826 TCGCTATCTTCTTTGATTTGTGAAAA 58.129 30.769 0.00 0.00 0.00 2.29
26 27 8.514594 TCGCTATCTTCTTTGATTTGTGAAAAT 58.485 29.630 0.00 0.00 0.00 1.82
27 28 9.132521 CGCTATCTTCTTTGATTTGTGAAAATT 57.867 29.630 0.00 0.00 0.00 1.82
46 47 9.889128 TGAAAATTTTCAAATTTCTCACTCCTT 57.111 25.926 27.22 0.00 45.16 3.36
56 57 9.971922 CAAATTTCTCACTCCTTTCTAATTTGT 57.028 29.630 0.00 0.00 37.15 2.83
57 58 9.971922 AAATTTCTCACTCCTTTCTAATTTGTG 57.028 29.630 0.00 0.00 0.00 3.33
58 59 7.510549 TTTCTCACTCCTTTCTAATTTGTGG 57.489 36.000 0.00 0.00 0.00 4.17
59 60 6.433847 TCTCACTCCTTTCTAATTTGTGGA 57.566 37.500 0.00 0.00 0.00 4.02
60 61 6.231211 TCTCACTCCTTTCTAATTTGTGGAC 58.769 40.000 0.00 0.00 0.00 4.02
61 62 6.043243 TCTCACTCCTTTCTAATTTGTGGACT 59.957 38.462 0.00 0.00 0.00 3.85
62 63 6.601332 TCACTCCTTTCTAATTTGTGGACTT 58.399 36.000 0.00 0.00 0.00 3.01
63 64 7.060421 TCACTCCTTTCTAATTTGTGGACTTT 58.940 34.615 0.00 0.00 0.00 2.66
64 65 7.559897 TCACTCCTTTCTAATTTGTGGACTTTT 59.440 33.333 0.00 0.00 0.00 2.27
65 66 8.846211 CACTCCTTTCTAATTTGTGGACTTTTA 58.154 33.333 0.00 0.00 0.00 1.52
66 67 9.416284 ACTCCTTTCTAATTTGTGGACTTTTAA 57.584 29.630 0.00 0.00 0.00 1.52
142 143 6.810888 AAAAACATCACAACATTTCTCACG 57.189 33.333 0.00 0.00 0.00 4.35
186 187 0.250727 TTTTCGCCAAGGAGACCCAG 60.251 55.000 0.00 0.00 33.88 4.45
188 189 2.046892 CGCCAAGGAGACCCAGTG 60.047 66.667 0.00 0.00 33.88 3.66
192 193 1.754201 GCCAAGGAGACCCAGTGTTTT 60.754 52.381 0.00 0.00 33.88 2.43
197 198 2.781174 AGGAGACCCAGTGTTTTACCAA 59.219 45.455 0.00 0.00 33.88 3.67
198 199 3.397955 AGGAGACCCAGTGTTTTACCAAT 59.602 43.478 0.00 0.00 33.88 3.16
199 200 4.141018 AGGAGACCCAGTGTTTTACCAATT 60.141 41.667 0.00 0.00 33.88 2.32
200 201 4.217767 GGAGACCCAGTGTTTTACCAATTC 59.782 45.833 0.00 0.00 0.00 2.17
201 202 5.061721 AGACCCAGTGTTTTACCAATTCT 57.938 39.130 0.00 0.00 0.00 2.40
202 203 5.454966 AGACCCAGTGTTTTACCAATTCTT 58.545 37.500 0.00 0.00 0.00 2.52
203 204 5.535030 AGACCCAGTGTTTTACCAATTCTTC 59.465 40.000 0.00 0.00 0.00 2.87
204 205 5.205056 ACCCAGTGTTTTACCAATTCTTCA 58.795 37.500 0.00 0.00 0.00 3.02
205 206 5.838521 ACCCAGTGTTTTACCAATTCTTCAT 59.161 36.000 0.00 0.00 0.00 2.57
206 207 7.007723 ACCCAGTGTTTTACCAATTCTTCATA 58.992 34.615 0.00 0.00 0.00 2.15
207 208 7.673926 ACCCAGTGTTTTACCAATTCTTCATAT 59.326 33.333 0.00 0.00 0.00 1.78
208 209 7.975616 CCCAGTGTTTTACCAATTCTTCATATG 59.024 37.037 0.00 0.00 0.00 1.78
209 210 8.522830 CCAGTGTTTTACCAATTCTTCATATGT 58.477 33.333 1.90 0.00 0.00 2.29
219 220 9.631257 ACCAATTCTTCATATGTACATTCATCA 57.369 29.630 14.77 0.00 0.00 3.07
223 224 7.734924 TCTTCATATGTACATTCATCAAGCC 57.265 36.000 14.77 0.00 0.00 4.35
224 225 7.281841 TCTTCATATGTACATTCATCAAGCCA 58.718 34.615 14.77 0.00 0.00 4.75
225 226 6.866010 TCATATGTACATTCATCAAGCCAC 57.134 37.500 14.77 0.00 0.00 5.01
226 227 6.355747 TCATATGTACATTCATCAAGCCACA 58.644 36.000 14.77 0.00 0.00 4.17
227 228 6.999871 TCATATGTACATTCATCAAGCCACAT 59.000 34.615 14.77 0.00 0.00 3.21
228 229 8.156165 TCATATGTACATTCATCAAGCCACATA 58.844 33.333 14.77 0.00 33.55 2.29
229 230 8.785946 CATATGTACATTCATCAAGCCACATAA 58.214 33.333 14.77 0.00 32.97 1.90
230 231 6.682423 TGTACATTCATCAAGCCACATAAG 57.318 37.500 0.00 0.00 0.00 1.73
231 232 5.589855 TGTACATTCATCAAGCCACATAAGG 59.410 40.000 0.00 0.00 0.00 2.69
232 233 4.858850 ACATTCATCAAGCCACATAAGGA 58.141 39.130 0.00 0.00 0.00 3.36
233 234 4.885907 ACATTCATCAAGCCACATAAGGAG 59.114 41.667 0.00 0.00 0.00 3.69
234 235 4.842531 TTCATCAAGCCACATAAGGAGA 57.157 40.909 0.00 0.00 0.00 3.71
235 236 4.142609 TCATCAAGCCACATAAGGAGAC 57.857 45.455 0.00 0.00 0.00 3.36
236 237 3.118261 TCATCAAGCCACATAAGGAGACC 60.118 47.826 0.00 0.00 0.00 3.85
237 238 1.559682 TCAAGCCACATAAGGAGACCC 59.440 52.381 0.00 0.00 0.00 4.46
238 239 1.281867 CAAGCCACATAAGGAGACCCA 59.718 52.381 0.00 0.00 33.88 4.51
239 240 0.912486 AGCCACATAAGGAGACCCAC 59.088 55.000 0.00 0.00 33.88 4.61
240 241 0.912486 GCCACATAAGGAGACCCACT 59.088 55.000 0.00 0.00 33.88 4.00
241 242 1.407437 GCCACATAAGGAGACCCACTG 60.407 57.143 0.00 0.00 33.88 3.66
242 243 1.909302 CCACATAAGGAGACCCACTGT 59.091 52.381 0.00 0.00 33.88 3.55
243 244 2.305927 CCACATAAGGAGACCCACTGTT 59.694 50.000 0.00 0.00 33.88 3.16
244 245 3.244911 CCACATAAGGAGACCCACTGTTT 60.245 47.826 0.00 0.00 33.88 2.83
245 246 4.398319 CACATAAGGAGACCCACTGTTTT 58.602 43.478 0.00 0.00 33.88 2.43
246 247 5.514136 CCACATAAGGAGACCCACTGTTTTA 60.514 44.000 0.00 0.00 33.88 1.52
247 248 5.411669 CACATAAGGAGACCCACTGTTTTAC 59.588 44.000 0.00 0.00 33.88 2.01
248 249 3.503800 AAGGAGACCCACTGTTTTACC 57.496 47.619 0.00 0.00 33.88 2.85
323 324 6.348540 CCAAACTCTAAATGTAGCCAAGTCAC 60.349 42.308 0.00 0.00 0.00 3.67
344 345 1.741770 CACGGGACAAGCTGTAGCC 60.742 63.158 0.00 0.00 43.38 3.93
360 361 1.452833 GCCAGAAGCCCAGATCCAC 60.453 63.158 0.00 0.00 34.35 4.02
414 415 3.403968 ACAACAACAAAACCCAACCAAC 58.596 40.909 0.00 0.00 0.00 3.77
442 443 5.420739 AGAAACAACCAAGACTAAAAAGCCA 59.579 36.000 0.00 0.00 0.00 4.75
443 444 5.669164 AACAACCAAGACTAAAAAGCCAA 57.331 34.783 0.00 0.00 0.00 4.52
463 464 5.048782 GCCAATATTTATCTTCCGATGTGCA 60.049 40.000 0.00 0.00 0.00 4.57
471 472 2.938451 TCTTCCGATGTGCAATGATGTC 59.062 45.455 0.00 0.00 0.00 3.06
486 487 7.440255 TGCAATGATGTCATAGTTAGATGTGAG 59.560 37.037 0.00 0.00 35.10 3.51
487 488 7.654923 GCAATGATGTCATAGTTAGATGTGAGA 59.345 37.037 0.00 0.00 35.10 3.27
553 554 9.899661 ACATATACTGTGTACATTGTAATTGGT 57.100 29.630 12.67 7.92 36.48 3.67
565 566 2.234414 TGTAATTGGTACACCCTCCGTC 59.766 50.000 0.00 0.00 39.29 4.79
567 568 1.610554 ATTGGTACACCCTCCGTCCG 61.611 60.000 0.00 0.00 39.29 4.79
568 569 2.361610 GGTACACCCTCCGTCCGA 60.362 66.667 0.00 0.00 0.00 4.55
579 580 3.311596 CCCTCCGTCCGAAAATATTTGTC 59.688 47.826 0.39 1.54 0.00 3.18
580 581 3.936453 CCTCCGTCCGAAAATATTTGTCA 59.064 43.478 0.39 0.00 0.00 3.58
582 583 5.277345 CCTCCGTCCGAAAATATTTGTCATC 60.277 44.000 0.39 0.00 0.00 2.92
583 584 5.179533 TCCGTCCGAAAATATTTGTCATCA 58.820 37.500 0.39 0.00 0.00 3.07
584 585 5.644206 TCCGTCCGAAAATATTTGTCATCAA 59.356 36.000 0.39 0.00 0.00 2.57
586 587 6.804295 CCGTCCGAAAATATTTGTCATCAAAA 59.196 34.615 0.39 0.00 44.97 2.44
587 588 7.487829 CCGTCCGAAAATATTTGTCATCAAAAT 59.512 33.333 0.39 0.00 44.97 1.82
588 589 8.313227 CGTCCGAAAATATTTGTCATCAAAATG 58.687 33.333 0.39 0.00 44.97 2.32
589 590 8.594687 GTCCGAAAATATTTGTCATCAAAATGG 58.405 33.333 0.39 0.00 44.97 3.16
590 591 8.526978 TCCGAAAATATTTGTCATCAAAATGGA 58.473 29.630 0.39 0.00 44.97 3.41
613 614 8.204160 TGGATGAAAAATGATGTATCTAGACGT 58.796 33.333 0.00 0.00 0.00 4.34
620 621 9.517609 AAAATGATGTATCTAGACGTACTTGTC 57.482 33.333 0.00 0.00 39.21 3.18
621 622 7.803279 ATGATGTATCTAGACGTACTTGTCA 57.197 36.000 0.00 2.64 41.41 3.58
622 623 7.803279 TGATGTATCTAGACGTACTTGTCAT 57.197 36.000 0.00 0.00 41.41 3.06
623 624 7.862648 TGATGTATCTAGACGTACTTGTCATC 58.137 38.462 0.00 0.00 41.41 2.92
624 625 7.497909 TGATGTATCTAGACGTACTTGTCATCA 59.502 37.037 0.00 12.30 41.41 3.07
625 626 7.619964 TGTATCTAGACGTACTTGTCATCAA 57.380 36.000 0.00 0.00 41.41 2.57
627 628 8.517056 TGTATCTAGACGTACTTGTCATCAAAA 58.483 33.333 0.00 0.00 41.41 2.44
628 629 9.517609 GTATCTAGACGTACTTGTCATCAAAAT 57.482 33.333 0.00 0.00 41.41 1.82
629 630 7.812309 TCTAGACGTACTTGTCATCAAAATG 57.188 36.000 0.00 0.00 41.41 2.32
630 631 5.862924 AGACGTACTTGTCATCAAAATGG 57.137 39.130 0.00 0.00 41.41 3.16
631 632 5.547465 AGACGTACTTGTCATCAAAATGGA 58.453 37.500 0.00 0.00 41.41 3.41
633 634 6.092670 AGACGTACTTGTCATCAAAATGGATG 59.907 38.462 0.00 0.00 44.78 3.51
705 746 6.122850 TCATTCTGATGGCAAGTATTTTCG 57.877 37.500 0.00 0.00 33.93 3.46
706 747 5.879777 TCATTCTGATGGCAAGTATTTTCGA 59.120 36.000 0.00 0.00 33.93 3.71
707 748 6.374053 TCATTCTGATGGCAAGTATTTTCGAA 59.626 34.615 0.00 0.00 33.93 3.71
708 749 5.545658 TCTGATGGCAAGTATTTTCGAAC 57.454 39.130 0.00 0.00 0.00 3.95
709 750 4.092821 TCTGATGGCAAGTATTTTCGAACG 59.907 41.667 0.00 0.00 0.00 3.95
710 751 3.126171 TGATGGCAAGTATTTTCGAACGG 59.874 43.478 0.00 0.00 0.00 4.44
711 752 2.768698 TGGCAAGTATTTTCGAACGGA 58.231 42.857 0.00 0.00 0.00 4.69
712 753 2.739913 TGGCAAGTATTTTCGAACGGAG 59.260 45.455 0.00 0.00 0.00 4.63
713 754 2.997986 GGCAAGTATTTTCGAACGGAGA 59.002 45.455 0.00 0.00 0.00 3.71
714 755 3.062234 GGCAAGTATTTTCGAACGGAGAG 59.938 47.826 0.00 0.00 0.00 3.20
715 756 3.924686 GCAAGTATTTTCGAACGGAGAGA 59.075 43.478 0.00 0.00 0.00 3.10
716 757 4.201599 GCAAGTATTTTCGAACGGAGAGAC 60.202 45.833 0.00 0.00 0.00 3.36
722 763 2.469274 TCGAACGGAGAGACTACTGT 57.531 50.000 0.00 0.00 0.00 3.55
765 806 8.593492 AACAGATATTTGGTTTCAAAAAGCTC 57.407 30.769 0.00 0.00 44.83 4.09
778 819 1.280457 AAAGCTCTCGAGGGACCATT 58.720 50.000 18.81 1.28 0.00 3.16
794 837 1.369625 CATTAACACTCACTCCGCCC 58.630 55.000 0.00 0.00 0.00 6.13
810 853 2.619165 CCCGTAACGCCACCAAACC 61.619 63.158 0.00 0.00 0.00 3.27
1001 1312 3.330853 GCCGTGCGATCGATCCAC 61.331 66.667 25.12 25.12 0.00 4.02
1062 1373 1.914700 GCACTTCGAAAACAAAACGCA 59.085 42.857 0.00 0.00 0.00 5.24
1072 1383 0.110486 ACAAAACGCACCCATCTCCT 59.890 50.000 0.00 0.00 0.00 3.69
1318 1640 2.035626 CCATGCCGTTTCCACCCT 59.964 61.111 0.00 0.00 0.00 4.34
1860 2182 3.142838 GTCCATTGCCGCTGCCAT 61.143 61.111 0.00 0.00 36.33 4.40
1906 2228 3.473647 TGCTGGATGCCCTCTCCG 61.474 66.667 0.00 0.00 42.00 4.63
1972 2300 2.883828 CGTCACCACCAAGCCCTCT 61.884 63.158 0.00 0.00 0.00 3.69
2203 2546 2.022129 CAGCGGCGAGAACGTCTTT 61.022 57.895 12.98 0.00 42.31 2.52
2209 2552 3.843985 GAGAACGTCTTTCGCGCT 58.156 55.556 5.56 0.00 44.19 5.92
2212 2555 0.729816 AGAACGTCTTTCGCGCTCTC 60.730 55.000 5.56 0.00 44.19 3.20
2274 2617 4.942852 AGCTTCTGAAGAATAGTGATCCG 58.057 43.478 21.06 0.00 33.01 4.18
2284 2627 1.170442 TAGTGATCCGCAGACGTTGA 58.830 50.000 0.00 0.00 37.70 3.18
2287 2630 0.317160 TGATCCGCAGACGTTGAAGT 59.683 50.000 0.00 0.00 37.70 3.01
2568 4643 1.014352 GTTCATTCCGGATCGTTGGG 58.986 55.000 4.15 0.00 0.00 4.12
2574 4649 2.742116 CCGGATCGTTGGGTGGGAT 61.742 63.158 0.00 0.00 0.00 3.85
2575 4650 1.223487 CGGATCGTTGGGTGGGATT 59.777 57.895 0.00 0.00 0.00 3.01
2611 4688 4.442375 GATGGAATCATACGAGATCGGT 57.558 45.455 7.22 0.00 44.70 4.69
2807 4890 3.644606 CTGGGCAGTGAGGCAGGT 61.645 66.667 0.00 0.00 46.44 4.00
2841 4924 4.806936 TGGCAACAGCAAGGAGAG 57.193 55.556 0.00 0.00 46.17 3.20
2843 4926 1.376466 GGCAACAGCAAGGAGAGGA 59.624 57.895 0.00 0.00 0.00 3.71
2845 4928 0.322975 GCAACAGCAAGGAGAGGAGA 59.677 55.000 0.00 0.00 0.00 3.71
2846 4929 1.065564 GCAACAGCAAGGAGAGGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
2849 4932 0.179051 CAGCAAGGAGAGGAGATGGC 60.179 60.000 0.00 0.00 0.00 4.40
2850 4933 0.619832 AGCAAGGAGAGGAGATGGCA 60.620 55.000 0.00 0.00 0.00 4.92
2947 5032 2.029020 CGACTCTGAAAGTGGTGATCCA 60.029 50.000 0.00 0.00 38.74 3.41
3020 5139 1.857217 CGAGGAATCTGCTGAATCACG 59.143 52.381 10.41 10.66 0.00 4.35
3076 5199 4.702131 GGCAACTTAATCAAGTCCATCACT 59.298 41.667 0.00 0.00 44.41 3.41
3086 5209 0.034896 GTCCATCACTCAACCCACGT 59.965 55.000 0.00 0.00 0.00 4.49
3087 5210 1.274167 GTCCATCACTCAACCCACGTA 59.726 52.381 0.00 0.00 0.00 3.57
3088 5211 1.274167 TCCATCACTCAACCCACGTAC 59.726 52.381 0.00 0.00 0.00 3.67
3089 5212 1.275291 CCATCACTCAACCCACGTACT 59.725 52.381 0.00 0.00 0.00 2.73
3090 5213 2.607187 CATCACTCAACCCACGTACTC 58.393 52.381 0.00 0.00 0.00 2.59
3091 5214 1.694844 TCACTCAACCCACGTACTCA 58.305 50.000 0.00 0.00 0.00 3.41
3092 5215 1.338973 TCACTCAACCCACGTACTCAC 59.661 52.381 0.00 0.00 0.00 3.51
3093 5216 1.340248 CACTCAACCCACGTACTCACT 59.660 52.381 0.00 0.00 0.00 3.41
3094 5217 1.612463 ACTCAACCCACGTACTCACTC 59.388 52.381 0.00 0.00 0.00 3.51
3095 5218 0.963962 TCAACCCACGTACTCACTCC 59.036 55.000 0.00 0.00 0.00 3.85
3096 5219 0.677288 CAACCCACGTACTCACTCCA 59.323 55.000 0.00 0.00 0.00 3.86
3097 5220 1.275291 CAACCCACGTACTCACTCCAT 59.725 52.381 0.00 0.00 0.00 3.41
3098 5221 2.494471 CAACCCACGTACTCACTCCATA 59.506 50.000 0.00 0.00 0.00 2.74
3099 5222 2.811410 ACCCACGTACTCACTCCATAA 58.189 47.619 0.00 0.00 0.00 1.90
3100 5223 2.494870 ACCCACGTACTCACTCCATAAC 59.505 50.000 0.00 0.00 0.00 1.89
3101 5224 2.758979 CCCACGTACTCACTCCATAACT 59.241 50.000 0.00 0.00 0.00 2.24
3102 5225 3.949754 CCCACGTACTCACTCCATAACTA 59.050 47.826 0.00 0.00 0.00 2.24
3103 5226 4.036498 CCCACGTACTCACTCCATAACTAG 59.964 50.000 0.00 0.00 0.00 2.57
3104 5227 4.639310 CCACGTACTCACTCCATAACTAGT 59.361 45.833 0.00 0.00 0.00 2.57
3105 5228 5.819379 CCACGTACTCACTCCATAACTAGTA 59.181 44.000 0.00 0.00 0.00 1.82
3106 5229 6.317140 CCACGTACTCACTCCATAACTAGTAA 59.683 42.308 0.00 0.00 0.00 2.24
3107 5230 7.013083 CCACGTACTCACTCCATAACTAGTAAT 59.987 40.741 0.00 0.00 0.00 1.89
3108 5231 8.404000 CACGTACTCACTCCATAACTAGTAATT 58.596 37.037 0.00 0.00 0.00 1.40
3109 5232 8.619546 ACGTACTCACTCCATAACTAGTAATTC 58.380 37.037 0.00 0.00 0.00 2.17
3110 5233 8.838365 CGTACTCACTCCATAACTAGTAATTCT 58.162 37.037 0.00 0.00 0.00 2.40
3116 5239 9.774742 CACTCCATAACTAGTAATTCTTTTTGC 57.225 33.333 0.00 0.00 0.00 3.68
3117 5240 8.957466 ACTCCATAACTAGTAATTCTTTTTGCC 58.043 33.333 0.00 0.00 0.00 4.52
3118 5241 7.981142 TCCATAACTAGTAATTCTTTTTGCCG 58.019 34.615 0.00 0.00 0.00 5.69
3119 5242 7.825270 TCCATAACTAGTAATTCTTTTTGCCGA 59.175 33.333 0.00 0.00 0.00 5.54
3120 5243 8.455682 CCATAACTAGTAATTCTTTTTGCCGAA 58.544 33.333 0.00 0.00 0.00 4.30
3121 5244 9.834628 CATAACTAGTAATTCTTTTTGCCGAAA 57.165 29.630 0.00 0.00 0.00 3.46
3123 5246 8.965986 AACTAGTAATTCTTTTTGCCGAAATC 57.034 30.769 0.00 0.00 0.00 2.17
3124 5247 7.535997 ACTAGTAATTCTTTTTGCCGAAATCC 58.464 34.615 0.00 0.00 0.00 3.01
3125 5248 5.399013 AGTAATTCTTTTTGCCGAAATCCG 58.601 37.500 0.00 0.00 38.18 4.18
3126 5249 3.934457 ATTCTTTTTGCCGAAATCCGT 57.066 38.095 0.00 0.00 36.31 4.69
3127 5250 5.379732 AATTCTTTTTGCCGAAATCCGTA 57.620 34.783 0.00 0.00 36.31 4.02
3128 5251 4.832590 TTCTTTTTGCCGAAATCCGTAA 57.167 36.364 0.00 0.00 36.31 3.18
3129 5252 4.832590 TCTTTTTGCCGAAATCCGTAAA 57.167 36.364 0.00 0.00 36.31 2.01
3130 5253 4.538917 TCTTTTTGCCGAAATCCGTAAAC 58.461 39.130 0.00 0.00 36.31 2.01
3131 5254 4.276431 TCTTTTTGCCGAAATCCGTAAACT 59.724 37.500 0.00 0.00 36.31 2.66
3132 5255 5.469421 TCTTTTTGCCGAAATCCGTAAACTA 59.531 36.000 0.00 0.00 36.31 2.24
3133 5256 5.686159 TTTTGCCGAAATCCGTAAACTAA 57.314 34.783 0.00 0.00 36.31 2.24
3134 5257 5.883503 TTTGCCGAAATCCGTAAACTAAT 57.116 34.783 0.00 0.00 36.31 1.73
3135 5258 6.981762 TTTGCCGAAATCCGTAAACTAATA 57.018 33.333 0.00 0.00 36.31 0.98
3136 5259 7.556733 TTTGCCGAAATCCGTAAACTAATAT 57.443 32.000 0.00 0.00 36.31 1.28
3137 5260 8.659925 TTTGCCGAAATCCGTAAACTAATATA 57.340 30.769 0.00 0.00 36.31 0.86
3138 5261 8.659925 TTGCCGAAATCCGTAAACTAATATAA 57.340 30.769 0.00 0.00 36.31 0.98
3139 5262 8.659925 TGCCGAAATCCGTAAACTAATATAAA 57.340 30.769 0.00 0.00 36.31 1.40
3140 5263 9.107177 TGCCGAAATCCGTAAACTAATATAAAA 57.893 29.630 0.00 0.00 36.31 1.52
3141 5264 9.590088 GCCGAAATCCGTAAACTAATATAAAAG 57.410 33.333 0.00 0.00 36.31 2.27
3142 5265 9.590088 CCGAAATCCGTAAACTAATATAAAAGC 57.410 33.333 0.00 0.00 36.31 3.51
3143 5266 9.590088 CGAAATCCGTAAACTAATATAAAAGCC 57.410 33.333 0.00 0.00 0.00 4.35
3161 5284 6.831664 AAAGCCTTTAGATAATCAGAGGGA 57.168 37.500 0.00 0.00 0.00 4.20
3162 5285 6.432403 AAGCCTTTAGATAATCAGAGGGAG 57.568 41.667 0.00 0.00 0.00 4.30
3163 5286 5.472347 AGCCTTTAGATAATCAGAGGGAGT 58.528 41.667 0.00 0.00 0.00 3.85
3164 5287 6.625267 AGCCTTTAGATAATCAGAGGGAGTA 58.375 40.000 0.00 0.00 0.00 2.59
3165 5288 6.495526 AGCCTTTAGATAATCAGAGGGAGTAC 59.504 42.308 0.00 0.00 0.00 2.73
3166 5289 6.495526 GCCTTTAGATAATCAGAGGGAGTACT 59.504 42.308 0.00 0.00 0.00 2.73
3202 5328 9.085250 GCTAACATGAAAGTTCTTACTACTACC 57.915 37.037 0.00 0.00 33.17 3.18
3208 5334 5.402997 AAGTTCTTACTACTACCACCAGC 57.597 43.478 0.00 0.00 33.17 4.85
3237 5363 2.897350 CAGGGGATTCGCTTCCGC 60.897 66.667 11.11 11.11 46.32 5.54
3239 5365 2.819550 GGGGATTCGCTTCCGCTA 59.180 61.111 11.61 0.00 43.49 4.26
3298 5424 2.099592 CGCATTGAGGTACAAATGGCAT 59.900 45.455 13.73 0.00 42.03 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.433708 TTTCACAAATCAAAGAAGATAGCGA 57.566 32.000 0.00 0.00 0.00 4.93
1 2 8.679288 ATTTTCACAAATCAAAGAAGATAGCG 57.321 30.769 0.00 0.00 0.00 4.26
18 19 9.097257 GGAGTGAGAAATTTGAAAATTTTCACA 57.903 29.630 28.78 23.88 45.70 3.58
19 20 9.317936 AGGAGTGAGAAATTTGAAAATTTTCAC 57.682 29.630 28.78 25.57 45.70 3.18
20 21 9.889128 AAGGAGTGAGAAATTTGAAAATTTTCA 57.111 25.926 26.01 26.01 45.70 2.69
30 31 9.971922 ACAAATTAGAAAGGAGTGAGAAATTTG 57.028 29.630 12.95 12.95 43.53 2.32
31 32 9.971922 CACAAATTAGAAAGGAGTGAGAAATTT 57.028 29.630 0.00 0.00 0.00 1.82
32 33 8.579863 CCACAAATTAGAAAGGAGTGAGAAATT 58.420 33.333 0.00 0.00 0.00 1.82
33 34 7.944554 TCCACAAATTAGAAAGGAGTGAGAAAT 59.055 33.333 0.00 0.00 0.00 2.17
34 35 7.228706 GTCCACAAATTAGAAAGGAGTGAGAAA 59.771 37.037 0.00 0.00 0.00 2.52
35 36 6.710744 GTCCACAAATTAGAAAGGAGTGAGAA 59.289 38.462 0.00 0.00 0.00 2.87
36 37 6.043243 AGTCCACAAATTAGAAAGGAGTGAGA 59.957 38.462 0.00 0.00 0.00 3.27
37 38 6.234177 AGTCCACAAATTAGAAAGGAGTGAG 58.766 40.000 0.00 0.00 0.00 3.51
38 39 6.187727 AGTCCACAAATTAGAAAGGAGTGA 57.812 37.500 0.00 0.00 0.00 3.41
39 40 6.884280 AAGTCCACAAATTAGAAAGGAGTG 57.116 37.500 0.00 0.00 0.00 3.51
40 41 7.898014 AAAAGTCCACAAATTAGAAAGGAGT 57.102 32.000 0.00 0.00 0.00 3.85
124 125 3.434641 AGCTCGTGAGAAATGTTGTGATG 59.565 43.478 0.00 0.00 41.32 3.07
125 126 3.668447 AGCTCGTGAGAAATGTTGTGAT 58.332 40.909 0.00 0.00 41.32 3.06
142 143 2.289547 GAGGTGTCTCGATGTAGAGCTC 59.710 54.545 5.27 5.27 38.12 4.09
197 198 8.790718 GGCTTGATGAATGTACATATGAAGAAT 58.209 33.333 17.13 0.00 0.00 2.40
198 199 7.774625 TGGCTTGATGAATGTACATATGAAGAA 59.225 33.333 17.13 6.04 0.00 2.52
199 200 7.227314 GTGGCTTGATGAATGTACATATGAAGA 59.773 37.037 17.13 0.73 0.00 2.87
200 201 7.012610 TGTGGCTTGATGAATGTACATATGAAG 59.987 37.037 9.21 10.59 0.00 3.02
201 202 6.827762 TGTGGCTTGATGAATGTACATATGAA 59.172 34.615 9.21 0.00 0.00 2.57
202 203 6.355747 TGTGGCTTGATGAATGTACATATGA 58.644 36.000 9.21 0.00 0.00 2.15
203 204 6.622833 TGTGGCTTGATGAATGTACATATG 57.377 37.500 9.21 0.00 0.00 1.78
204 205 8.922931 TTATGTGGCTTGATGAATGTACATAT 57.077 30.769 9.21 0.00 32.02 1.78
205 206 7.445096 CCTTATGTGGCTTGATGAATGTACATA 59.555 37.037 9.21 0.00 0.00 2.29
206 207 6.263842 CCTTATGTGGCTTGATGAATGTACAT 59.736 38.462 1.41 1.41 0.00 2.29
207 208 5.589855 CCTTATGTGGCTTGATGAATGTACA 59.410 40.000 0.00 0.00 0.00 2.90
208 209 5.822519 TCCTTATGTGGCTTGATGAATGTAC 59.177 40.000 0.00 0.00 0.00 2.90
209 210 6.000246 TCCTTATGTGGCTTGATGAATGTA 58.000 37.500 0.00 0.00 0.00 2.29
210 211 4.858850 TCCTTATGTGGCTTGATGAATGT 58.141 39.130 0.00 0.00 0.00 2.71
211 212 5.008415 GTCTCCTTATGTGGCTTGATGAATG 59.992 44.000 0.00 0.00 0.00 2.67
212 213 5.128919 GTCTCCTTATGTGGCTTGATGAAT 58.871 41.667 0.00 0.00 0.00 2.57
213 214 4.517285 GTCTCCTTATGTGGCTTGATGAA 58.483 43.478 0.00 0.00 0.00 2.57
214 215 3.118261 GGTCTCCTTATGTGGCTTGATGA 60.118 47.826 0.00 0.00 0.00 2.92
215 216 3.209410 GGTCTCCTTATGTGGCTTGATG 58.791 50.000 0.00 0.00 0.00 3.07
216 217 2.173569 GGGTCTCCTTATGTGGCTTGAT 59.826 50.000 0.00 0.00 0.00 2.57
217 218 1.559682 GGGTCTCCTTATGTGGCTTGA 59.440 52.381 0.00 0.00 0.00 3.02
218 219 1.281867 TGGGTCTCCTTATGTGGCTTG 59.718 52.381 0.00 0.00 0.00 4.01
219 220 1.282157 GTGGGTCTCCTTATGTGGCTT 59.718 52.381 0.00 0.00 0.00 4.35
220 221 0.912486 GTGGGTCTCCTTATGTGGCT 59.088 55.000 0.00 0.00 0.00 4.75
221 222 0.912486 AGTGGGTCTCCTTATGTGGC 59.088 55.000 0.00 0.00 0.00 5.01
222 223 1.909302 ACAGTGGGTCTCCTTATGTGG 59.091 52.381 0.00 0.00 0.00 4.17
223 224 3.703001 AACAGTGGGTCTCCTTATGTG 57.297 47.619 0.00 0.00 0.00 3.21
224 225 4.724279 AAAACAGTGGGTCTCCTTATGT 57.276 40.909 0.00 0.00 0.00 2.29
225 226 4.941873 GGTAAAACAGTGGGTCTCCTTATG 59.058 45.833 0.00 0.00 0.00 1.90
226 227 4.600111 TGGTAAAACAGTGGGTCTCCTTAT 59.400 41.667 0.00 0.00 0.00 1.73
227 228 3.975312 TGGTAAAACAGTGGGTCTCCTTA 59.025 43.478 0.00 0.00 0.00 2.69
228 229 2.781174 TGGTAAAACAGTGGGTCTCCTT 59.219 45.455 0.00 0.00 0.00 3.36
229 230 2.414612 TGGTAAAACAGTGGGTCTCCT 58.585 47.619 0.00 0.00 0.00 3.69
230 231 2.943036 TGGTAAAACAGTGGGTCTCC 57.057 50.000 0.00 0.00 0.00 3.71
231 232 5.070685 AGAATTGGTAAAACAGTGGGTCTC 58.929 41.667 0.00 0.00 0.00 3.36
232 233 5.061721 AGAATTGGTAAAACAGTGGGTCT 57.938 39.130 0.00 0.00 0.00 3.85
233 234 5.300792 TGAAGAATTGGTAAAACAGTGGGTC 59.699 40.000 0.00 0.00 0.00 4.46
234 235 5.205056 TGAAGAATTGGTAAAACAGTGGGT 58.795 37.500 0.00 0.00 0.00 4.51
235 236 5.782893 TGAAGAATTGGTAAAACAGTGGG 57.217 39.130 0.00 0.00 0.00 4.61
236 237 8.522830 ACATATGAAGAATTGGTAAAACAGTGG 58.477 33.333 10.38 0.00 0.00 4.00
246 247 9.631257 TGATGAATGTACATATGAAGAATTGGT 57.369 29.630 9.21 0.00 0.00 3.67
269 270 1.563924 ACCATTGCATGTGGCTTGAT 58.436 45.000 16.28 0.00 45.15 2.57
323 324 0.732880 CTACAGCTTGTCCCGTGTCG 60.733 60.000 0.00 0.00 0.00 4.35
344 345 1.225704 GGGTGGATCTGGGCTTCTG 59.774 63.158 0.00 0.00 0.00 3.02
414 415 7.201435 GCTTTTTAGTCTTGGTTGTTTCTGTTG 60.201 37.037 0.00 0.00 0.00 3.33
454 455 3.811497 ACTATGACATCATTGCACATCGG 59.189 43.478 0.00 0.00 37.76 4.18
548 549 1.610554 CGGACGGAGGGTGTACCAAT 61.611 60.000 3.11 0.00 43.89 3.16
549 550 2.277591 CGGACGGAGGGTGTACCAA 61.278 63.158 3.11 0.00 43.89 3.67
550 551 2.677524 CGGACGGAGGGTGTACCA 60.678 66.667 3.11 0.00 43.89 3.25
551 552 1.535204 TTTCGGACGGAGGGTGTACC 61.535 60.000 0.00 0.00 40.67 3.34
552 553 0.318120 TTTTCGGACGGAGGGTGTAC 59.682 55.000 0.00 0.00 0.00 2.90
553 554 1.269012 ATTTTCGGACGGAGGGTGTA 58.731 50.000 0.00 0.00 0.00 2.90
554 555 1.269012 TATTTTCGGACGGAGGGTGT 58.731 50.000 0.00 0.00 0.00 4.16
556 557 3.275999 CAAATATTTTCGGACGGAGGGT 58.724 45.455 0.00 0.00 0.00 4.34
559 560 5.293324 TGATGACAAATATTTTCGGACGGAG 59.707 40.000 0.00 0.00 0.00 4.63
565 566 8.700722 TCCATTTTGATGACAAATATTTTCGG 57.299 30.769 0.00 0.00 43.99 4.30
586 587 9.212641 CGTCTAGATACATCATTTTTCATCCAT 57.787 33.333 0.00 0.00 0.00 3.41
587 588 8.204160 ACGTCTAGATACATCATTTTTCATCCA 58.796 33.333 0.00 0.00 0.00 3.41
588 589 8.594881 ACGTCTAGATACATCATTTTTCATCC 57.405 34.615 0.00 0.00 0.00 3.51
593 594 9.871238 ACAAGTACGTCTAGATACATCATTTTT 57.129 29.630 0.00 0.00 0.00 1.94
597 598 7.803279 TGACAAGTACGTCTAGATACATCAT 57.197 36.000 0.00 0.00 36.82 2.45
598 599 7.497909 TGATGACAAGTACGTCTAGATACATCA 59.502 37.037 13.73 13.73 37.48 3.07
601 602 7.619964 TTGATGACAAGTACGTCTAGATACA 57.380 36.000 0.00 0.00 36.82 2.29
602 603 8.906636 TTTTGATGACAAGTACGTCTAGATAC 57.093 34.615 0.00 0.00 37.32 2.24
603 604 9.516314 CATTTTGATGACAAGTACGTCTAGATA 57.484 33.333 0.00 0.00 37.32 1.98
604 605 7.492669 CCATTTTGATGACAAGTACGTCTAGAT 59.507 37.037 0.00 0.00 37.32 1.98
605 606 6.811665 CCATTTTGATGACAAGTACGTCTAGA 59.188 38.462 0.00 0.00 37.32 2.43
606 607 6.811665 TCCATTTTGATGACAAGTACGTCTAG 59.188 38.462 0.00 0.00 37.32 2.43
607 608 6.693466 TCCATTTTGATGACAAGTACGTCTA 58.307 36.000 0.00 0.00 37.32 2.59
609 610 5.856126 TCCATTTTGATGACAAGTACGTC 57.144 39.130 0.00 0.00 37.32 4.34
683 724 6.122850 TCGAAAATACTTGCCATCAGAATG 57.877 37.500 0.00 0.00 37.54 2.67
684 725 6.555315 GTTCGAAAATACTTGCCATCAGAAT 58.445 36.000 0.00 0.00 0.00 2.40
685 726 5.390461 CGTTCGAAAATACTTGCCATCAGAA 60.390 40.000 0.00 0.00 0.00 3.02
686 727 4.092821 CGTTCGAAAATACTTGCCATCAGA 59.907 41.667 0.00 0.00 0.00 3.27
687 728 4.334443 CGTTCGAAAATACTTGCCATCAG 58.666 43.478 0.00 0.00 0.00 2.90
688 729 3.126171 CCGTTCGAAAATACTTGCCATCA 59.874 43.478 0.00 0.00 0.00 3.07
689 730 3.372822 TCCGTTCGAAAATACTTGCCATC 59.627 43.478 0.00 0.00 0.00 3.51
690 731 3.340034 TCCGTTCGAAAATACTTGCCAT 58.660 40.909 0.00 0.00 0.00 4.40
691 732 2.739913 CTCCGTTCGAAAATACTTGCCA 59.260 45.455 0.00 0.00 0.00 4.92
692 733 2.997986 TCTCCGTTCGAAAATACTTGCC 59.002 45.455 0.00 0.00 0.00 4.52
693 734 3.924686 TCTCTCCGTTCGAAAATACTTGC 59.075 43.478 0.00 0.00 0.00 4.01
694 735 5.162075 AGTCTCTCCGTTCGAAAATACTTG 58.838 41.667 0.00 0.00 0.00 3.16
695 736 5.388408 AGTCTCTCCGTTCGAAAATACTT 57.612 39.130 0.00 0.00 0.00 2.24
696 737 5.647225 AGTAGTCTCTCCGTTCGAAAATACT 59.353 40.000 0.00 0.00 0.00 2.12
697 738 5.738225 CAGTAGTCTCTCCGTTCGAAAATAC 59.262 44.000 0.00 0.00 0.00 1.89
698 739 5.413833 ACAGTAGTCTCTCCGTTCGAAAATA 59.586 40.000 0.00 0.00 0.00 1.40
699 740 4.217983 ACAGTAGTCTCTCCGTTCGAAAAT 59.782 41.667 0.00 0.00 0.00 1.82
700 741 3.567164 ACAGTAGTCTCTCCGTTCGAAAA 59.433 43.478 0.00 0.00 0.00 2.29
701 742 3.144506 ACAGTAGTCTCTCCGTTCGAAA 58.855 45.455 0.00 0.00 0.00 3.46
702 743 2.775890 ACAGTAGTCTCTCCGTTCGAA 58.224 47.619 0.00 0.00 0.00 3.71
703 744 2.469274 ACAGTAGTCTCTCCGTTCGA 57.531 50.000 0.00 0.00 0.00 3.71
704 745 4.879104 AATACAGTAGTCTCTCCGTTCG 57.121 45.455 0.00 0.00 0.00 3.95
705 746 8.976986 TTTTTAATACAGTAGTCTCTCCGTTC 57.023 34.615 0.00 0.00 0.00 3.95
744 785 7.305474 TCGAGAGCTTTTTGAAACCAAATATC 58.695 34.615 0.00 0.00 33.96 1.63
762 803 1.480954 TGTTAATGGTCCCTCGAGAGC 59.519 52.381 15.71 5.37 34.81 4.09
765 806 2.496070 TGAGTGTTAATGGTCCCTCGAG 59.504 50.000 5.13 5.13 0.00 4.04
778 819 0.608856 TACGGGCGGAGTGAGTGTTA 60.609 55.000 0.00 0.00 0.00 2.41
794 837 1.572447 CAGGTTTGGTGGCGTTACG 59.428 57.895 0.00 0.00 0.00 3.18
840 883 3.876255 TTCTAGGTTGGGGCCCGGT 62.876 63.158 19.83 4.41 0.00 5.28
1001 1312 4.506255 GGAAGCCGTGGATGGGGG 62.506 72.222 0.00 0.00 0.00 5.40
1062 1373 1.022903 AGGAGAAGGAGGAGATGGGT 58.977 55.000 0.00 0.00 0.00 4.51
1072 1383 0.616111 GAGCACCTGGAGGAGAAGGA 60.616 60.000 0.00 0.00 37.01 3.36
1118 1434 3.311110 GGATCGGGCGATGGGCTA 61.311 66.667 0.39 0.00 42.94 3.93
1174 1496 2.927856 ACCACCATCCTGCGACCA 60.928 61.111 0.00 0.00 0.00 4.02
1246 1568 4.104183 TTCCCATTCGACCCCGCC 62.104 66.667 0.00 0.00 35.37 6.13
1247 1569 2.513897 CTTCCCATTCGACCCCGC 60.514 66.667 0.00 0.00 35.37 6.13
1248 1570 1.153429 GACTTCCCATTCGACCCCG 60.153 63.158 0.00 0.00 37.07 5.73
1249 1571 1.223763 GGACTTCCCATTCGACCCC 59.776 63.158 0.00 0.00 34.14 4.95
1250 1572 1.153429 CGGACTTCCCATTCGACCC 60.153 63.158 0.00 0.00 34.14 4.46
1303 1625 1.002134 CAGAGGGTGGAAACGGCAT 60.002 57.895 0.00 0.00 0.00 4.40
2203 2546 2.428569 GTGTTGACGAGAGCGCGA 60.429 61.111 12.10 0.00 42.48 5.87
2206 2549 0.730834 CTCTGGTGTTGACGAGAGCG 60.731 60.000 0.00 0.00 44.89 5.03
2209 2552 1.880675 GAGACTCTGGTGTTGACGAGA 59.119 52.381 0.00 0.00 35.77 4.04
2212 2555 0.038159 GGGAGACTCTGGTGTTGACG 60.038 60.000 1.74 0.00 0.00 4.35
2297 2640 7.819415 ACAAATTTCATCACATAAGTCGAGAGA 59.181 33.333 0.00 0.00 38.16 3.10
2298 2641 7.968246 ACAAATTTCATCACATAAGTCGAGAG 58.032 34.615 0.00 0.00 0.00 3.20
2329 2672 3.297830 GCTAAACAAGCCGACCATTTT 57.702 42.857 0.00 0.00 46.25 1.82
2356 4363 3.162666 TGTTCTACTGGTGGTACTGGAG 58.837 50.000 0.00 0.00 0.00 3.86
2358 4365 3.513912 TGATGTTCTACTGGTGGTACTGG 59.486 47.826 0.00 0.00 0.00 4.00
2558 4633 0.751643 CCAATCCCACCCAACGATCC 60.752 60.000 0.00 0.00 0.00 3.36
2568 4643 1.304134 GTGACCCCACCAATCCCAC 60.304 63.158 0.00 0.00 37.33 4.61
2574 4649 2.150719 ATCCACGTGACCCCACCAA 61.151 57.895 19.30 0.00 40.12 3.67
2575 4650 2.528127 ATCCACGTGACCCCACCA 60.528 61.111 19.30 0.00 40.12 4.17
2611 4688 0.529773 GCACGTCCAAGATCGCCATA 60.530 55.000 0.00 0.00 0.00 2.74
2839 4922 1.245732 GATGCCATTGCCATCTCCTC 58.754 55.000 0.50 0.00 36.33 3.71
2840 4923 0.178970 GGATGCCATTGCCATCTCCT 60.179 55.000 7.48 0.00 36.33 3.69
2841 4924 1.183676 GGGATGCCATTGCCATCTCC 61.184 60.000 7.48 4.07 36.33 3.71
2843 4926 0.031917 TTGGGATGCCATTGCCATCT 60.032 50.000 6.84 0.00 36.93 2.90
2845 4928 1.287217 TTTTGGGATGCCATTGCCAT 58.713 45.000 6.84 0.00 36.93 4.40
2846 4929 1.287217 ATTTTGGGATGCCATTGCCA 58.713 45.000 6.84 0.00 35.00 4.92
2849 4932 4.161942 TGGTCTTATTTTGGGATGCCATTG 59.838 41.667 6.84 0.00 0.00 2.82
2850 4933 4.162131 GTGGTCTTATTTTGGGATGCCATT 59.838 41.667 6.84 0.00 0.00 3.16
2947 5032 2.107151 CTCTCGTCGTCGCCGATCAT 62.107 60.000 0.00 0.00 46.30 2.45
2966 5051 8.853469 AAACTACTACACTAATCGCTAATCAC 57.147 34.615 0.00 0.00 0.00 3.06
2967 5052 9.297586 CAAAACTACTACACTAATCGCTAATCA 57.702 33.333 0.00 0.00 0.00 2.57
2968 5053 9.512435 TCAAAACTACTACACTAATCGCTAATC 57.488 33.333 0.00 0.00 0.00 1.75
2969 5054 9.517609 CTCAAAACTACTACACTAATCGCTAAT 57.482 33.333 0.00 0.00 0.00 1.73
2970 5055 8.517878 ACTCAAAACTACTACACTAATCGCTAA 58.482 33.333 0.00 0.00 0.00 3.09
2971 5056 7.966753 CACTCAAAACTACTACACTAATCGCTA 59.033 37.037 0.00 0.00 0.00 4.26
2972 5057 6.807230 CACTCAAAACTACTACACTAATCGCT 59.193 38.462 0.00 0.00 0.00 4.93
3020 5139 2.423577 ACTCCCAAAGATGCACGTAAC 58.576 47.619 0.00 0.00 0.00 2.50
3064 5187 2.154462 GTGGGTTGAGTGATGGACTTG 58.846 52.381 0.00 0.00 33.83 3.16
3076 5199 0.963962 GGAGTGAGTACGTGGGTTGA 59.036 55.000 0.00 0.00 0.00 3.18
3090 5213 9.774742 GCAAAAAGAATTACTAGTTATGGAGTG 57.225 33.333 0.00 0.00 0.00 3.51
3091 5214 8.957466 GGCAAAAAGAATTACTAGTTATGGAGT 58.043 33.333 0.00 0.00 0.00 3.85
3092 5215 8.122952 CGGCAAAAAGAATTACTAGTTATGGAG 58.877 37.037 0.00 0.00 0.00 3.86
3093 5216 7.825270 TCGGCAAAAAGAATTACTAGTTATGGA 59.175 33.333 0.00 0.00 0.00 3.41
3094 5217 7.981142 TCGGCAAAAAGAATTACTAGTTATGG 58.019 34.615 0.00 0.00 0.00 2.74
3095 5218 9.834628 TTTCGGCAAAAAGAATTACTAGTTATG 57.165 29.630 0.00 0.00 0.00 1.90
3098 5221 8.027189 GGATTTCGGCAAAAAGAATTACTAGTT 58.973 33.333 0.00 0.00 0.00 2.24
3099 5222 7.535997 GGATTTCGGCAAAAAGAATTACTAGT 58.464 34.615 0.00 0.00 0.00 2.57
3100 5223 6.687105 CGGATTTCGGCAAAAAGAATTACTAG 59.313 38.462 0.00 0.00 34.75 2.57
3101 5224 6.149807 ACGGATTTCGGCAAAAAGAATTACTA 59.850 34.615 0.00 0.00 44.45 1.82
3102 5225 5.048294 ACGGATTTCGGCAAAAAGAATTACT 60.048 36.000 0.00 0.00 44.45 2.24
3103 5226 5.158494 ACGGATTTCGGCAAAAAGAATTAC 58.842 37.500 0.00 0.00 44.45 1.89
3104 5227 5.379732 ACGGATTTCGGCAAAAAGAATTA 57.620 34.783 0.00 0.00 44.45 1.40
3105 5228 4.251543 ACGGATTTCGGCAAAAAGAATT 57.748 36.364 0.00 0.00 44.45 2.17
3106 5229 3.934457 ACGGATTTCGGCAAAAAGAAT 57.066 38.095 0.00 0.00 44.45 2.40
3107 5230 4.832590 TTACGGATTTCGGCAAAAAGAA 57.167 36.364 0.00 0.00 44.45 2.52
3108 5231 4.276431 AGTTTACGGATTTCGGCAAAAAGA 59.724 37.500 0.00 0.00 44.45 2.52
3109 5232 4.542735 AGTTTACGGATTTCGGCAAAAAG 58.457 39.130 0.00 0.00 44.45 2.27
3110 5233 4.571372 AGTTTACGGATTTCGGCAAAAA 57.429 36.364 0.00 0.00 44.45 1.94
3111 5234 5.686159 TTAGTTTACGGATTTCGGCAAAA 57.314 34.783 0.00 0.00 44.45 2.44
3112 5235 5.883503 ATTAGTTTACGGATTTCGGCAAA 57.116 34.783 0.00 0.00 44.45 3.68
3113 5236 8.659925 TTATATTAGTTTACGGATTTCGGCAA 57.340 30.769 0.00 0.00 44.45 4.52
3114 5237 8.659925 TTTATATTAGTTTACGGATTTCGGCA 57.340 30.769 0.00 0.00 44.45 5.69
3115 5238 9.590088 CTTTTATATTAGTTTACGGATTTCGGC 57.410 33.333 0.00 0.00 44.45 5.54
3116 5239 9.590088 GCTTTTATATTAGTTTACGGATTTCGG 57.410 33.333 0.00 0.00 44.45 4.30
3117 5240 9.590088 GGCTTTTATATTAGTTTACGGATTTCG 57.410 33.333 0.00 0.00 45.88 3.46
3135 5258 8.949421 TCCCTCTGATTATCTAAAGGCTTTTAT 58.051 33.333 18.93 14.10 0.00 1.40
3136 5259 8.331931 TCCCTCTGATTATCTAAAGGCTTTTA 57.668 34.615 18.93 7.48 0.00 1.52
3137 5260 7.092219 ACTCCCTCTGATTATCTAAAGGCTTTT 60.092 37.037 18.93 2.60 0.00 2.27
3138 5261 6.388394 ACTCCCTCTGATTATCTAAAGGCTTT 59.612 38.462 17.76 17.76 0.00 3.51
3139 5262 5.908247 ACTCCCTCTGATTATCTAAAGGCTT 59.092 40.000 0.00 0.00 0.00 4.35
3140 5263 5.472347 ACTCCCTCTGATTATCTAAAGGCT 58.528 41.667 0.00 0.00 0.00 4.58
3141 5264 5.816955 ACTCCCTCTGATTATCTAAAGGC 57.183 43.478 0.00 0.00 0.00 4.35
3142 5265 8.485578 AAGTACTCCCTCTGATTATCTAAAGG 57.514 38.462 0.00 0.00 0.00 3.11
3147 5270 9.308000 CTTCATAAGTACTCCCTCTGATTATCT 57.692 37.037 0.00 0.00 0.00 1.98
3148 5271 8.032451 GCTTCATAAGTACTCCCTCTGATTATC 58.968 40.741 0.00 0.00 0.00 1.75
3149 5272 7.732593 AGCTTCATAAGTACTCCCTCTGATTAT 59.267 37.037 0.00 0.00 0.00 1.28
3150 5273 7.014711 CAGCTTCATAAGTACTCCCTCTGATTA 59.985 40.741 0.00 0.00 0.00 1.75
3151 5274 5.902431 AGCTTCATAAGTACTCCCTCTGATT 59.098 40.000 0.00 0.00 0.00 2.57
3152 5275 5.304101 CAGCTTCATAAGTACTCCCTCTGAT 59.696 44.000 0.00 0.00 0.00 2.90
3153 5276 4.646945 CAGCTTCATAAGTACTCCCTCTGA 59.353 45.833 0.00 0.00 0.00 3.27
3154 5277 4.739137 GCAGCTTCATAAGTACTCCCTCTG 60.739 50.000 0.00 0.00 0.00 3.35
3155 5278 3.386402 GCAGCTTCATAAGTACTCCCTCT 59.614 47.826 0.00 0.00 0.00 3.69
3156 5279 3.386402 AGCAGCTTCATAAGTACTCCCTC 59.614 47.826 0.00 0.00 0.00 4.30
3157 5280 3.379452 AGCAGCTTCATAAGTACTCCCT 58.621 45.455 0.00 0.00 0.00 4.20
3158 5281 3.828875 AGCAGCTTCATAAGTACTCCC 57.171 47.619 0.00 0.00 0.00 4.30
3159 5282 5.661458 TGTTAGCAGCTTCATAAGTACTCC 58.339 41.667 0.00 0.00 0.00 3.85
3160 5283 6.980978 TCATGTTAGCAGCTTCATAAGTACTC 59.019 38.462 0.00 0.00 0.00 2.59
3161 5284 6.878317 TCATGTTAGCAGCTTCATAAGTACT 58.122 36.000 0.00 0.00 0.00 2.73
3162 5285 7.539712 TTCATGTTAGCAGCTTCATAAGTAC 57.460 36.000 0.00 0.00 0.00 2.73
3163 5286 7.824289 ACTTTCATGTTAGCAGCTTCATAAGTA 59.176 33.333 17.54 4.57 0.00 2.24
3164 5287 6.656693 ACTTTCATGTTAGCAGCTTCATAAGT 59.343 34.615 0.00 10.52 0.00 2.24
3165 5288 7.081526 ACTTTCATGTTAGCAGCTTCATAAG 57.918 36.000 0.00 9.95 0.00 1.73
3166 5289 7.391554 AGAACTTTCATGTTAGCAGCTTCATAA 59.608 33.333 0.00 0.00 0.00 1.90
3208 5334 0.987294 ATCCCCTGACCACAACAGAG 59.013 55.000 0.00 0.00 37.54 3.35


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

AutoCloner maintained by Alex Coulton.