Multiple sequence alignment - TraesCS6D01G263000

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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 TraesCS6D01G263000 chr6D 100.000 6257 0 0 1 6257 371524296 371530552 0.000000e+00 11555.0
1 TraesCS6D01G263000 chr6D 87.500 176 16 4 5738 5912 461818360 461818190 1.380000e-46 198.0
2 TraesCS6D01G263000 chr6D 94.488 127 7 0 5127 5253 371529383 371529509 4.950000e-46 196.0
3 TraesCS6D01G263000 chr6D 94.488 127 7 0 5088 5214 371529422 371529548 4.950000e-46 196.0
4 TraesCS6D01G263000 chr6D 93.182 88 6 0 5166 5253 371529383 371529470 5.090000e-26 130.0
5 TraesCS6D01G263000 chr6D 93.182 88 6 0 5088 5175 371529461 371529548 5.090000e-26 130.0
6 TraesCS6D01G263000 chr6A 93.369 5731 238 58 99 5741 512829525 512835201 0.000000e+00 8347.0
7 TraesCS6D01G263000 chr6A 85.008 647 65 19 3 641 512828910 512829532 4.120000e-176 628.0
8 TraesCS6D01G263000 chr6A 91.946 149 9 1 6023 6168 512835398 512835546 8.220000e-49 206.0
9 TraesCS6D01G263000 chr6A 94.488 127 7 0 5127 5253 512834519 512834645 4.950000e-46 196.0
10 TraesCS6D01G263000 chr6A 92.126 127 10 0 5088 5214 512834558 512834684 4.980000e-41 180.0
11 TraesCS6D01G263000 chr6A 91.379 116 8 2 5909 6024 512835198 512835311 2.340000e-34 158.0
12 TraesCS6D01G263000 chr6B 93.705 5020 187 59 789 5741 556752882 556757839 0.000000e+00 7400.0
13 TraesCS6D01G263000 chr6B 93.656 331 16 4 5929 6257 556758203 556758530 2.030000e-134 490.0
14 TraesCS6D01G263000 chr6B 93.564 202 4 2 581 782 556752419 556752611 6.140000e-75 292.0
15 TraesCS6D01G263000 chr6B 95.238 126 6 0 5089 5214 556757226 556757351 3.830000e-47 200.0
16 TraesCS6D01G263000 chr6B 86.982 169 15 4 5748 5916 691796589 691796428 3.850000e-42 183.0
17 TraesCS6D01G263000 chr6B 82.051 78 9 5 293 368 226025854 226025928 1.880000e-05 62.1
18 TraesCS6D01G263000 chr6B 83.582 67 7 3 5880 5946 633647107 633647045 6.770000e-05 60.2
19 TraesCS6D01G263000 chr2A 81.320 803 97 31 1472 2250 735386576 735385803 2.500000e-168 603.0
20 TraesCS6D01G263000 chr2A 85.915 71 6 3 296 365 716349591 716349524 8.700000e-09 73.1
21 TraesCS6D01G263000 chr5A 80.946 803 100 30 1472 2250 197432834 197432061 2.510000e-163 586.0
22 TraesCS6D01G263000 chr5A 82.950 522 65 12 1585 2103 370090419 370090919 3.440000e-122 449.0
23 TraesCS6D01G263000 chr2B 80.542 812 99 30 1473 2250 79123828 79123042 2.530000e-158 569.0
24 TraesCS6D01G263000 chr2B 82.878 549 73 11 1561 2103 225420536 225420003 2.040000e-129 473.0
25 TraesCS6D01G263000 chr2B 86.905 84 8 3 287 368 32122955 32123037 2.400000e-14 91.6
26 TraesCS6D01G263000 chr2B 93.617 47 2 1 297 343 37428178 37428223 1.130000e-07 69.4
27 TraesCS6D01G263000 chr2B 100.000 32 0 0 5880 5911 337014511 337014542 6.770000e-05 60.2
28 TraesCS6D01G263000 chr2B 83.582 67 7 4 5880 5946 406718163 406718101 6.770000e-05 60.2
29 TraesCS6D01G263000 chr2D 83.139 599 77 14 1515 2103 417247740 417247156 5.560000e-145 525.0
30 TraesCS6D01G263000 chr2D 82.000 650 77 24 1615 2250 271976424 271977047 3.340000e-142 516.0
31 TraesCS6D01G263000 chr2D 86.705 173 20 1 5739 5911 628577723 628577892 8.280000e-44 189.0
32 TraesCS6D01G263000 chr2D 100.000 32 0 0 5880 5911 600871872 600871903 6.770000e-05 60.2
33 TraesCS6D01G263000 chr1D 82.805 599 79 14 1515 2103 424896266 424895682 1.200000e-141 514.0
34 TraesCS6D01G263000 chr4B 83.759 548 70 13 1561 2103 17474759 17474226 9.360000e-138 501.0
35 TraesCS6D01G263000 chr4B 84.393 173 21 3 5739 5911 139730657 139730823 1.400000e-36 165.0
36 TraesCS6D01G263000 chr7A 78.989 752 121 27 1515 2249 622250593 622251324 4.390000e-131 479.0
37 TraesCS6D01G263000 chr7A 79.597 397 52 24 1001 1389 194059189 194058814 2.240000e-64 257.0
38 TraesCS6D01G263000 chr7A 77.622 429 70 17 3581 4004 194056251 194055844 2.920000e-58 237.0
39 TraesCS6D01G263000 chr7A 86.127 173 18 3 5739 5911 214303170 214303336 1.390000e-41 182.0
40 TraesCS6D01G263000 chr7D 82.946 516 74 8 1468 1973 603381253 603380742 2.660000e-123 453.0
41 TraesCS6D01G263000 chr7D 80.867 392 51 18 1001 1389 186249037 186248667 2.850000e-73 287.0
42 TraesCS6D01G263000 chr7D 77.681 457 76 17 3553 4004 186246369 186245934 8.050000e-64 255.0
43 TraesCS6D01G263000 chr5B 80.488 574 66 19 1688 2247 492588594 492588053 1.260000e-106 398.0
44 TraesCS6D01G263000 chr3B 82.338 385 44 17 1878 2247 779199802 779199427 4.710000e-81 313.0
45 TraesCS6D01G263000 chr3B 84.971 173 22 2 5739 5911 714622147 714621979 8.340000e-39 172.0
46 TraesCS6D01G263000 chr7B 76.264 455 86 16 3553 4004 328971286 328970851 8.160000e-54 222.0
47 TraesCS6D01G263000 chr7B 85.930 199 25 3 1194 1389 328973754 328973556 6.360000e-50 209.0
48 TraesCS6D01G263000 chr7B 93.204 103 6 1 1001 1103 328973927 328973826 3.910000e-32 150.0
49 TraesCS6D01G263000 chr7B 100.000 38 0 0 296 333 692923800 692923837 3.130000e-08 71.3
50 TraesCS6D01G263000 chr4A 86.286 175 21 1 5737 5911 27645716 27645887 2.980000e-43 187.0
51 TraesCS6D01G263000 chr5D 85.549 173 22 1 5739 5911 15560370 15560539 1.790000e-40 178.0
52 TraesCS6D01G263000 chr5D 89.286 56 6 0 88 143 446076709 446076654 3.130000e-08 71.3
53 TraesCS6D01G263000 chr3D 85.455 165 17 5 5749 5911 574518301 574518142 1.400000e-36 165.0


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 TraesCS6D01G263000 chr6D 371524296 371530552 6256 False 2441.400000 11555 95.06800 1 6257 5 chr6D.!!$F1 6256
1 TraesCS6D01G263000 chr6A 512828910 512835546 6636 False 1619.166667 8347 91.38600 3 6168 6 chr6A.!!$F1 6165
2 TraesCS6D01G263000 chr6B 556752419 556758530 6111 False 2095.500000 7400 94.04075 581 6257 4 chr6B.!!$F2 5676
3 TraesCS6D01G263000 chr2A 735385803 735386576 773 True 603.000000 603 81.32000 1472 2250 1 chr2A.!!$R2 778
4 TraesCS6D01G263000 chr5A 197432061 197432834 773 True 586.000000 586 80.94600 1472 2250 1 chr5A.!!$R1 778
5 TraesCS6D01G263000 chr5A 370090419 370090919 500 False 449.000000 449 82.95000 1585 2103 1 chr5A.!!$F1 518
6 TraesCS6D01G263000 chr2B 79123042 79123828 786 True 569.000000 569 80.54200 1473 2250 1 chr2B.!!$R1 777
7 TraesCS6D01G263000 chr2B 225420003 225420536 533 True 473.000000 473 82.87800 1561 2103 1 chr2B.!!$R2 542
8 TraesCS6D01G263000 chr2D 417247156 417247740 584 True 525.000000 525 83.13900 1515 2103 1 chr2D.!!$R1 588
9 TraesCS6D01G263000 chr2D 271976424 271977047 623 False 516.000000 516 82.00000 1615 2250 1 chr2D.!!$F1 635
10 TraesCS6D01G263000 chr1D 424895682 424896266 584 True 514.000000 514 82.80500 1515 2103 1 chr1D.!!$R1 588
11 TraesCS6D01G263000 chr4B 17474226 17474759 533 True 501.000000 501 83.75900 1561 2103 1 chr4B.!!$R1 542
12 TraesCS6D01G263000 chr7A 622250593 622251324 731 False 479.000000 479 78.98900 1515 2249 1 chr7A.!!$F2 734
13 TraesCS6D01G263000 chr7A 194055844 194059189 3345 True 247.000000 257 78.60950 1001 4004 2 chr7A.!!$R1 3003
14 TraesCS6D01G263000 chr7D 603380742 603381253 511 True 453.000000 453 82.94600 1468 1973 1 chr7D.!!$R1 505
15 TraesCS6D01G263000 chr7D 186245934 186249037 3103 True 271.000000 287 79.27400 1001 4004 2 chr7D.!!$R2 3003
16 TraesCS6D01G263000 chr5B 492588053 492588594 541 True 398.000000 398 80.48800 1688 2247 1 chr5B.!!$R1 559

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
633 1170 0.037160 GTGCCTTAACCCCGAGGAAA 59.963 55.000 0.00 0.00 34.91 3.13 F
887 1699 1.218047 CTGATCTTCGTCCCCGCAA 59.782 57.895 0.00 0.00 0.00 4.85 F
1167 1998 2.368875 GTCAGAAGGGTTTCCTCTGTCA 59.631 50.000 0.00 0.00 44.07 3.58 F
2273 3569 1.625315 ACTGCTGACTGTCCTTATGCA 59.375 47.619 5.17 7.22 0.00 3.96 F
2704 4051 2.178912 TACCTTTGTTTCAGCTCCCG 57.821 50.000 0.00 0.00 0.00 5.14 F
3131 4531 6.085573 TCATTATGTTGTTCTTTGTCATGCG 58.914 36.000 0.00 0.00 0.00 4.73 F
5019 6478 1.227089 CTCGGAGGATGGTGCTTCG 60.227 63.158 0.00 0.00 38.24 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2671 1.744741 GCCTTCTCACCAGAGCAGC 60.745 63.158 0.00 0.00 41.81 5.25 R
2095 3159 3.317149 AGCGCTGCAACATTTATCATGAT 59.683 39.130 10.39 13.81 0.00 2.45 R
3125 4525 1.001293 AGAGCAAGAACAGACGCATGA 59.999 47.619 0.00 0.00 0.00 3.07 R
3214 4629 0.612744 AAGTCTCTGGAGCAAGAGCC 59.387 55.000 6.29 0.00 42.95 4.70 R
4226 5665 2.100197 TCGAGATGTTCTTCCGGATGT 58.900 47.619 16.29 0.00 0.00 3.06 R
5034 6493 0.681733 AGTTTGCCTCTTCGCTCTCA 59.318 50.000 0.00 0.00 0.00 3.27 R
6172 8101 0.902531 TCCAGCAGCTTAGTGGTACC 59.097 55.000 4.43 4.43 32.73 3.34 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
112 113 9.694137 CGGTCAAAGTTTAACCCAAAATATAAA 57.306 29.630 2.11 0.00 0.00 1.40
126 127 9.111519 CCCAAAATATAAAGGGGCCTAATAAAT 57.888 33.333 0.84 0.00 37.66 1.40
132 133 5.686535 AAAGGGGCCTAATAAATCTGGAT 57.313 39.130 0.84 0.00 0.00 3.41
133 134 6.796867 AAAGGGGCCTAATAAATCTGGATA 57.203 37.500 0.84 0.00 0.00 2.59
203 204 8.958175 TTCTTTTATAATTTTGTACCAGCGTG 57.042 30.769 0.00 0.00 0.00 5.34
206 207 9.485591 CTTTTATAATTTTGTACCAGCGTGTAG 57.514 33.333 0.00 0.00 0.00 2.74
210 211 3.671008 TTTGTACCAGCGTGTAGACAT 57.329 42.857 0.00 0.00 0.00 3.06
220 222 5.043903 CAGCGTGTAGACATAAGCAGTAAT 58.956 41.667 9.33 0.00 0.00 1.89
227 229 9.760660 GTGTAGACATAAGCAGTAATCTTTTTG 57.239 33.333 0.00 0.00 0.00 2.44
229 231 9.974750 GTAGACATAAGCAGTAATCTTTTTGTC 57.025 33.333 0.00 0.00 36.63 3.18
238 243 9.005777 AGCAGTAATCTTTTTGTCGGTAATAAA 57.994 29.630 0.00 0.00 0.00 1.40
261 266 7.924103 AAACTAATCCGCTAAAAACAACAAG 57.076 32.000 0.00 0.00 0.00 3.16
262 267 5.458015 ACTAATCCGCTAAAAACAACAAGC 58.542 37.500 0.00 0.00 0.00 4.01
267 272 5.112686 TCCGCTAAAAACAACAAGCAAAAT 58.887 33.333 0.00 0.00 34.60 1.82
281 286 3.571590 AGCAAAATCACACAACCCCTTA 58.428 40.909 0.00 0.00 0.00 2.69
287 292 4.591321 ATCACACAACCCCTTATGACAT 57.409 40.909 0.00 0.00 0.00 3.06
292 297 5.925969 CACACAACCCCTTATGACATTTTTC 59.074 40.000 0.00 0.00 0.00 2.29
297 304 6.840780 ACCCCTTATGACATTTTTCAAGAG 57.159 37.500 0.00 0.00 0.00 2.85
307 314 9.874205 ATGACATTTTTCAAGAGAAACTTTTGA 57.126 25.926 0.00 0.00 43.09 2.69
342 349 6.048732 TCAATCATGGTAGTACAAAGAGCA 57.951 37.500 2.06 0.00 0.00 4.26
347 354 5.700832 TCATGGTAGTACAAAGAGCAACAAG 59.299 40.000 2.06 0.00 0.00 3.16
348 355 4.385825 TGGTAGTACAAAGAGCAACAAGG 58.614 43.478 2.06 0.00 0.00 3.61
349 356 4.101898 TGGTAGTACAAAGAGCAACAAGGA 59.898 41.667 2.06 0.00 0.00 3.36
358 365 6.980397 ACAAAGAGCAACAAGGATAACAAAAG 59.020 34.615 0.00 0.00 0.00 2.27
362 369 8.409358 AGAGCAACAAGGATAACAAAAGTTAT 57.591 30.769 0.84 0.84 32.74 1.89
426 433 0.039437 AGCCGTCACACGTGTTAGAG 60.039 55.000 20.79 8.05 40.58 2.43
446 453 4.674281 AGAAACAGTTCTCCGAAGACTT 57.326 40.909 0.00 0.00 40.18 3.01
452 459 3.184581 CAGTTCTCCGAAGACTTTTTCCG 59.815 47.826 0.00 0.00 0.00 4.30
454 461 1.690352 TCTCCGAAGACTTTTTCCGGT 59.310 47.619 0.00 0.00 0.00 5.28
456 463 2.215196 TCCGAAGACTTTTTCCGGTTG 58.785 47.619 0.00 0.00 0.00 3.77
467 474 4.465512 CCGGTTGTGAGCATGCGC 62.466 66.667 15.17 15.17 38.99 6.09
468 475 3.725459 CGGTTGTGAGCATGCGCA 61.725 61.111 20.84 20.84 42.27 6.09
469 476 2.177531 GGTTGTGAGCATGCGCAG 59.822 61.111 25.10 9.45 42.27 5.18
492 500 5.070714 AGCTAAGCACATCATCAATCTCTCT 59.929 40.000 0.00 0.00 0.00 3.10
589 597 4.877378 TTGATCTCCATTTTGCTTGCTT 57.123 36.364 0.00 0.00 0.00 3.91
590 598 4.182693 TGATCTCCATTTTGCTTGCTTG 57.817 40.909 0.00 0.00 0.00 4.01
591 599 2.443887 TCTCCATTTTGCTTGCTTGC 57.556 45.000 0.00 0.00 0.00 4.01
592 600 1.001181 TCTCCATTTTGCTTGCTTGCC 59.999 47.619 0.00 0.00 0.00 4.52
633 1170 0.037160 GTGCCTTAACCCCGAGGAAA 59.963 55.000 0.00 0.00 34.91 3.13
669 1208 9.493206 GAAGACACAATAAACTAACGAAACAAA 57.507 29.630 0.00 0.00 0.00 2.83
720 1259 2.941583 GCCACTTCCCCCTTCCCT 60.942 66.667 0.00 0.00 0.00 4.20
721 1260 2.985116 GCCACTTCCCCCTTCCCTC 61.985 68.421 0.00 0.00 0.00 4.30
722 1261 2.309504 CCACTTCCCCCTTCCCTCC 61.310 68.421 0.00 0.00 0.00 4.30
723 1262 2.127528 ACTTCCCCCTTCCCTCCC 59.872 66.667 0.00 0.00 0.00 4.30
724 1263 2.461637 CTTCCCCCTTCCCTCCCT 59.538 66.667 0.00 0.00 0.00 4.20
725 1264 1.694525 CTTCCCCCTTCCCTCCCTC 60.695 68.421 0.00 0.00 0.00 4.30
726 1265 3.283467 TTCCCCCTTCCCTCCCTCC 62.283 68.421 0.00 0.00 0.00 4.30
727 1266 4.845307 CCCCCTTCCCTCCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
728 1267 3.711782 CCCCTTCCCTCCCTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
729 1268 2.040359 CCCTTCCCTCCCTCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
730 1269 2.040359 CCTTCCCTCCCTCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
731 1270 2.040359 CTTCCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
732 1271 2.543637 TTCCCTCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
733 1272 2.613576 CTTCCCTCCCTCCCTCCCTC 62.614 70.000 0.00 0.00 0.00 4.30
734 1273 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
735 1274 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
778 1325 4.740822 GGACGCCATTGCCCACCT 62.741 66.667 0.00 0.00 0.00 4.00
820 1632 2.276116 ACGCCAGCGAGAGAAGGAA 61.276 57.895 20.32 0.00 42.83 3.36
869 1681 2.872858 GTGAGCAATTCGGAAGGTATCC 59.127 50.000 0.00 0.00 45.57 2.59
870 1682 2.771943 TGAGCAATTCGGAAGGTATCCT 59.228 45.455 0.00 0.00 46.98 3.24
887 1699 1.218047 CTGATCTTCGTCCCCGCAA 59.782 57.895 0.00 0.00 0.00 4.85
952 1783 2.961741 TCCTCCCTGATCTGAAATCTCG 59.038 50.000 0.38 0.00 0.00 4.04
1146 1977 6.222389 TCTGCTCCAAAAACCACAATTATTG 58.778 36.000 3.07 3.07 0.00 1.90
1147 1978 5.923204 TGCTCCAAAAACCACAATTATTGT 58.077 33.333 4.56 4.56 46.75 2.71
1148 1979 5.988561 TGCTCCAAAAACCACAATTATTGTC 59.011 36.000 7.71 0.00 43.23 3.18
1150 1981 6.146021 GCTCCAAAAACCACAATTATTGTCAG 59.854 38.462 7.71 5.45 43.23 3.51
1152 1983 7.786030 TCCAAAAACCACAATTATTGTCAGAA 58.214 30.769 7.71 0.00 43.23 3.02
1153 1984 7.925483 TCCAAAAACCACAATTATTGTCAGAAG 59.075 33.333 7.71 0.00 43.23 2.85
1155 1986 5.982890 AACCACAATTATTGTCAGAAGGG 57.017 39.130 7.71 7.83 43.23 3.95
1156 1987 4.998051 ACCACAATTATTGTCAGAAGGGT 58.002 39.130 7.71 8.45 43.23 4.34
1158 1989 5.838521 ACCACAATTATTGTCAGAAGGGTTT 59.161 36.000 7.71 0.00 43.23 3.27
1167 1998 2.368875 GTCAGAAGGGTTTCCTCTGTCA 59.631 50.000 0.00 0.00 44.07 3.58
1321 2158 2.909965 GAGGAGGAGATCGCCGCT 60.910 66.667 17.98 5.21 40.51 5.52
1533 2417 2.618816 CCTGAATCTGCAAGCAAGGGTA 60.619 50.000 0.00 0.00 0.00 3.69
1767 2671 5.468540 TCGATCTTATTAGGGATGGTGTG 57.531 43.478 0.00 0.00 0.00 3.82
1868 2822 6.649141 AGTTGTAGCTGATGTTAATTCGTTGA 59.351 34.615 0.00 0.00 0.00 3.18
2095 3159 7.676893 TCCCTACTTGTTATCCTTTCTTGTAGA 59.323 37.037 0.00 0.00 0.00 2.59
2260 3556 9.890629 AATACTGTTCTCATTATTAACTGCTGA 57.109 29.630 0.00 0.00 31.00 4.26
2270 3566 8.486210 TCATTATTAACTGCTGACTGTCCTTAT 58.514 33.333 5.17 0.00 0.00 1.73
2271 3567 8.554528 CATTATTAACTGCTGACTGTCCTTATG 58.445 37.037 5.17 0.00 0.00 1.90
2273 3569 1.625315 ACTGCTGACTGTCCTTATGCA 59.375 47.619 5.17 7.22 0.00 3.96
2341 3645 9.081997 GTTGATTTTCATGTGTCAGTTGTTTTA 57.918 29.630 0.00 0.00 0.00 1.52
2358 3662 5.703310 TGTTTTAAGCCACCTTACCCTAAA 58.297 37.500 0.00 0.00 33.43 1.85
2572 3919 3.394274 TGGTTGAACTCCTCCTTCATCAA 59.606 43.478 0.00 0.00 0.00 2.57
2704 4051 2.178912 TACCTTTGTTTCAGCTCCCG 57.821 50.000 0.00 0.00 0.00 5.14
2979 4332 6.381801 CCTGTTACACATTTGGTTGATCTTC 58.618 40.000 0.00 0.00 0.00 2.87
2981 4334 7.255590 CCTGTTACACATTTGGTTGATCTTCTT 60.256 37.037 0.00 0.00 0.00 2.52
2995 4351 7.922811 GGTTGATCTTCTTGTTGAATTTGAGTT 59.077 33.333 0.00 0.00 33.71 3.01
3125 4525 8.352137 TGATCCATCATTATGTTGTTCTTTGT 57.648 30.769 3.06 0.00 0.00 2.83
3131 4531 6.085573 TCATTATGTTGTTCTTTGTCATGCG 58.914 36.000 0.00 0.00 0.00 4.73
4231 5670 4.260334 GCAAACAGCAAAGTGAAAACATCC 60.260 41.667 0.00 0.00 44.79 3.51
4373 5812 6.944862 AGAGCTTATCAAATGGAGTGTTCTTT 59.055 34.615 0.00 0.00 0.00 2.52
4376 5815 7.449704 AGCTTATCAAATGGAGTGTTCTTTCTT 59.550 33.333 0.00 0.00 0.00 2.52
4421 5860 2.654863 AGGGTTGTGAACTGGAAAGTG 58.345 47.619 0.00 0.00 0.00 3.16
4463 5902 3.076621 TCTGTTCTTGATCCACATGTGC 58.923 45.455 20.81 7.64 0.00 4.57
4464 5903 3.079578 CTGTTCTTGATCCACATGTGCT 58.920 45.455 20.81 9.56 0.00 4.40
4465 5904 4.020307 TCTGTTCTTGATCCACATGTGCTA 60.020 41.667 20.81 10.80 0.00 3.49
4466 5905 4.847198 TGTTCTTGATCCACATGTGCTAT 58.153 39.130 20.81 15.12 0.00 2.97
4467 5906 5.255687 TGTTCTTGATCCACATGTGCTATT 58.744 37.500 20.81 4.12 0.00 1.73
4468 5907 5.711506 TGTTCTTGATCCACATGTGCTATTT 59.288 36.000 20.81 2.30 0.00 1.40
4469 5908 5.823209 TCTTGATCCACATGTGCTATTTG 57.177 39.130 20.81 5.76 0.00 2.32
4470 5909 5.499313 TCTTGATCCACATGTGCTATTTGA 58.501 37.500 20.81 11.22 0.00 2.69
4549 5991 2.050144 ACCATAGTACTGGCTGATGGG 58.950 52.381 20.67 7.61 41.21 4.00
4754 6211 6.042093 TGGATCGGAGCTAAATTCATCTACTT 59.958 38.462 0.00 0.00 0.00 2.24
4755 6212 6.588373 GGATCGGAGCTAAATTCATCTACTTC 59.412 42.308 0.00 0.00 0.00 3.01
4808 6265 6.578163 TGATGCTTGTTGATTGAGAATTGA 57.422 33.333 0.00 0.00 0.00 2.57
4812 6269 6.571605 TGCTTGTTGATTGAGAATTGAAACA 58.428 32.000 0.00 0.00 0.00 2.83
4813 6270 6.476380 TGCTTGTTGATTGAGAATTGAAACAC 59.524 34.615 0.00 0.00 0.00 3.32
5016 6475 3.474570 GGCTCGGAGGATGGTGCT 61.475 66.667 7.20 0.00 0.00 4.40
5019 6478 1.227089 CTCGGAGGATGGTGCTTCG 60.227 63.158 0.00 0.00 38.24 3.79
5150 6609 2.304056 CCACCCCAGATGCTCCACT 61.304 63.158 0.00 0.00 0.00 4.00
5640 7131 4.769688 CTGTACTGCTTGGACCATTATCA 58.230 43.478 0.00 0.00 0.00 2.15
5689 7180 0.035152 GGAGTGTGGACCATGCATGA 60.035 55.000 28.31 4.84 0.00 3.07
5705 7196 6.238814 CCATGCATGATGAGCTGTACATAAAA 60.239 38.462 28.31 0.00 33.31 1.52
5737 7228 1.065273 GCATGCCAAGGAATCGCTG 59.935 57.895 6.36 0.00 0.00 5.18
5738 7229 1.660560 GCATGCCAAGGAATCGCTGT 61.661 55.000 6.36 0.00 0.00 4.40
5739 7230 1.667236 CATGCCAAGGAATCGCTGTA 58.333 50.000 0.00 0.00 0.00 2.74
5740 7231 1.331756 CATGCCAAGGAATCGCTGTAC 59.668 52.381 0.00 0.00 0.00 2.90
5741 7232 0.613260 TGCCAAGGAATCGCTGTACT 59.387 50.000 0.00 0.00 0.00 2.73
5742 7233 1.291132 GCCAAGGAATCGCTGTACTC 58.709 55.000 0.00 0.00 0.00 2.59
5743 7234 1.941325 CCAAGGAATCGCTGTACTCC 58.059 55.000 0.00 0.00 0.00 3.85
5744 7235 1.473434 CCAAGGAATCGCTGTACTCCC 60.473 57.143 0.00 0.00 0.00 4.30
5745 7236 1.482593 CAAGGAATCGCTGTACTCCCT 59.517 52.381 0.00 0.00 0.00 4.20
5746 7237 1.867363 AGGAATCGCTGTACTCCCTT 58.133 50.000 0.00 0.00 0.00 3.95
5747 7238 1.757699 AGGAATCGCTGTACTCCCTTC 59.242 52.381 0.00 0.00 0.00 3.46
5748 7239 1.536284 GGAATCGCTGTACTCCCTTCG 60.536 57.143 0.00 0.00 0.00 3.79
5749 7240 1.134560 GAATCGCTGTACTCCCTTCGT 59.865 52.381 0.00 0.00 0.00 3.85
5750 7241 1.183549 ATCGCTGTACTCCCTTCGTT 58.816 50.000 0.00 0.00 0.00 3.85
5751 7242 0.524862 TCGCTGTACTCCCTTCGTTC 59.475 55.000 0.00 0.00 0.00 3.95
5752 7243 0.458025 CGCTGTACTCCCTTCGTTCC 60.458 60.000 0.00 0.00 0.00 3.62
5753 7244 0.896226 GCTGTACTCCCTTCGTTCCT 59.104 55.000 0.00 0.00 0.00 3.36
5754 7245 2.097825 GCTGTACTCCCTTCGTTCCTA 58.902 52.381 0.00 0.00 0.00 2.94
5755 7246 2.494870 GCTGTACTCCCTTCGTTCCTAA 59.505 50.000 0.00 0.00 0.00 2.69
5756 7247 3.056322 GCTGTACTCCCTTCGTTCCTAAA 60.056 47.826 0.00 0.00 0.00 1.85
5757 7248 4.382793 GCTGTACTCCCTTCGTTCCTAAAT 60.383 45.833 0.00 0.00 0.00 1.40
5758 7249 5.163478 GCTGTACTCCCTTCGTTCCTAAATA 60.163 44.000 0.00 0.00 0.00 1.40
5759 7250 6.462628 GCTGTACTCCCTTCGTTCCTAAATAT 60.463 42.308 0.00 0.00 0.00 1.28
5760 7251 7.255730 GCTGTACTCCCTTCGTTCCTAAATATA 60.256 40.741 0.00 0.00 0.00 0.86
5761 7252 8.537728 TGTACTCCCTTCGTTCCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
5762 7253 8.636213 TGTACTCCCTTCGTTCCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
5763 7254 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5764 7255 8.087303 ACTCCCTTCGTTCCTAAATATAAGTT 57.913 34.615 0.00 0.00 0.00 2.66
5765 7256 8.546322 ACTCCCTTCGTTCCTAAATATAAGTTT 58.454 33.333 0.00 0.00 0.00 2.66
5766 7257 9.392259 CTCCCTTCGTTCCTAAATATAAGTTTT 57.608 33.333 0.00 0.00 0.00 2.43
5767 7258 9.743581 TCCCTTCGTTCCTAAATATAAGTTTTT 57.256 29.630 0.00 0.00 0.00 1.94
5791 7282 7.786046 TTTAGAGATTCCACTACAACCTACA 57.214 36.000 0.00 0.00 0.00 2.74
5792 7283 7.973048 TTAGAGATTCCACTACAACCTACAT 57.027 36.000 0.00 0.00 0.00 2.29
5793 7284 9.483489 TTTAGAGATTCCACTACAACCTACATA 57.517 33.333 0.00 0.00 0.00 2.29
5794 7285 7.349412 AGAGATTCCACTACAACCTACATAC 57.651 40.000 0.00 0.00 0.00 2.39
5795 7286 6.039493 AGAGATTCCACTACAACCTACATACG 59.961 42.308 0.00 0.00 0.00 3.06
5796 7287 4.724074 TTCCACTACAACCTACATACGG 57.276 45.455 0.00 0.00 0.00 4.02
5797 7288 3.966979 TCCACTACAACCTACATACGGA 58.033 45.455 0.00 0.00 0.00 4.69
5798 7289 4.539726 TCCACTACAACCTACATACGGAT 58.460 43.478 0.00 0.00 0.00 4.18
5799 7290 4.340097 TCCACTACAACCTACATACGGATG 59.660 45.833 5.94 5.94 39.16 3.51
5801 7292 5.300034 CCACTACAACCTACATACGGATGTA 59.700 44.000 19.32 19.32 44.77 2.29
5802 7293 6.015688 CCACTACAACCTACATACGGATGTAT 60.016 42.308 20.64 8.38 45.42 2.29
5803 7294 7.175467 CCACTACAACCTACATACGGATGTATA 59.825 40.741 20.64 9.08 45.42 1.47
5804 7295 8.737175 CACTACAACCTACATACGGATGTATAT 58.263 37.037 20.64 9.29 45.42 0.86
5805 7296 9.964354 ACTACAACCTACATACGGATGTATATA 57.036 33.333 20.64 0.52 45.42 0.86
5808 7299 8.954350 ACAACCTACATACGGATGTATATAGAC 58.046 37.037 20.64 0.00 45.42 2.59
5809 7300 8.953313 CAACCTACATACGGATGTATATAGACA 58.047 37.037 20.64 2.07 45.42 3.41
5810 7301 9.696572 AACCTACATACGGATGTATATAGACAT 57.303 33.333 20.64 12.70 45.42 3.06
5853 7344 7.617041 AGTGTAGATTTACTCATTTTGCTCC 57.383 36.000 0.00 0.00 0.00 4.70
5854 7345 6.313905 AGTGTAGATTTACTCATTTTGCTCCG 59.686 38.462 0.00 0.00 0.00 4.63
5855 7346 6.092259 GTGTAGATTTACTCATTTTGCTCCGT 59.908 38.462 0.00 0.00 0.00 4.69
5856 7347 7.277098 GTGTAGATTTACTCATTTTGCTCCGTA 59.723 37.037 0.00 0.00 0.00 4.02
5857 7348 7.985184 TGTAGATTTACTCATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
5858 7349 7.251704 AGATTTACTCATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
5859 7350 6.823689 AGATTTACTCATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
5860 7351 7.985184 AGATTTACTCATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
5861 7352 7.534085 TTTACTCATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
5862 7353 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
5863 7354 5.109903 ACTCATTTTGCTCCGTATGTAGTC 58.890 41.667 0.00 0.00 0.00 2.59
5864 7355 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
5865 7356 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
5866 7357 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
5867 7358 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
5868 7359 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
5869 7360 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
5870 7361 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
5871 7362 3.819337 GCTCCGTATGTAGTCCATAGTGA 59.181 47.826 0.00 0.00 36.71 3.41
5872 7363 4.277672 GCTCCGTATGTAGTCCATAGTGAA 59.722 45.833 0.00 0.00 36.71 3.18
5873 7364 5.221185 GCTCCGTATGTAGTCCATAGTGAAA 60.221 44.000 0.00 0.00 36.71 2.69
5874 7365 6.516860 GCTCCGTATGTAGTCCATAGTGAAAT 60.517 42.308 0.00 0.00 36.71 2.17
5875 7366 7.309012 GCTCCGTATGTAGTCCATAGTGAAATA 60.309 40.741 0.00 0.00 36.71 1.40
5876 7367 8.645814 TCCGTATGTAGTCCATAGTGAAATAT 57.354 34.615 0.00 0.00 36.71 1.28
5877 7368 8.737175 TCCGTATGTAGTCCATAGTGAAATATC 58.263 37.037 0.00 0.00 36.71 1.63
5878 7369 8.740906 CCGTATGTAGTCCATAGTGAAATATCT 58.259 37.037 0.00 0.00 36.71 1.98
5906 7397 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
5907 7398 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
5920 7411 3.838244 TGGAGGGAGTACACATTATGC 57.162 47.619 0.00 0.00 0.00 3.14
5927 7418 6.374588 AGGGAGTACACATTATGCTAGTAGT 58.625 40.000 0.00 0.00 0.00 2.73
5928 7419 7.524290 AGGGAGTACACATTATGCTAGTAGTA 58.476 38.462 0.00 0.00 0.00 1.82
5929 7420 7.666388 AGGGAGTACACATTATGCTAGTAGTAG 59.334 40.741 0.00 0.00 0.00 2.57
6014 7852 4.074526 AGTGAGCGCGAGGTGCAT 62.075 61.111 12.10 0.00 46.97 3.96
6027 7953 3.679980 CGAGGTGCATCGGGAATTATTAG 59.320 47.826 1.69 0.00 39.04 1.73
6125 8054 3.300852 TTGCACCGTACTATTCGTTGA 57.699 42.857 0.00 0.00 0.00 3.18
6172 8101 2.854424 GCATTCCGCATGAACAATACGG 60.854 50.000 0.00 0.00 45.15 4.02
6206 8135 2.625790 TGCTGGAAAATTACTGGCGTTT 59.374 40.909 0.00 0.00 0.00 3.60
6207 8136 3.242518 GCTGGAAAATTACTGGCGTTTC 58.757 45.455 0.00 0.00 0.00 2.78
6212 8141 6.342111 TGGAAAATTACTGGCGTTTCTTTTT 58.658 32.000 0.00 0.00 31.94 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.502145 GAATTGATTTGCAAAATATACGAGACA 57.498 29.630 17.19 1.80 40.48 3.41
63 64 9.730420 ACCGTAGAATTGATTTGCAAAATATAC 57.270 29.630 17.19 10.59 40.48 1.47
112 113 5.676125 TCTATCCAGATTTATTAGGCCCCT 58.324 41.667 0.00 0.00 0.00 4.79
113 114 5.104318 CCTCTATCCAGATTTATTAGGCCCC 60.104 48.000 0.00 0.00 0.00 5.80
126 127 6.849151 TGCAGTTATACTACCTCTATCCAGA 58.151 40.000 0.00 0.00 0.00 3.86
128 129 7.728532 TCATTGCAGTTATACTACCTCTATCCA 59.271 37.037 0.00 0.00 0.00 3.41
196 197 2.196749 CTGCTTATGTCTACACGCTGG 58.803 52.381 0.00 0.00 0.00 4.85
201 202 9.760660 CAAAAAGATTACTGCTTATGTCTACAC 57.239 33.333 0.00 0.00 0.00 2.90
203 204 9.974750 GACAAAAAGATTACTGCTTATGTCTAC 57.025 33.333 0.00 0.00 38.25 2.59
206 207 6.961554 CCGACAAAAAGATTACTGCTTATGTC 59.038 38.462 0.00 0.00 38.10 3.06
210 211 7.966246 TTACCGACAAAAAGATTACTGCTTA 57.034 32.000 0.00 0.00 0.00 3.09
227 229 7.698836 TTAGCGGATTAGTTTTATTACCGAC 57.301 36.000 0.00 0.00 41.09 4.79
229 231 9.213819 GTTTTTAGCGGATTAGTTTTATTACCG 57.786 33.333 0.00 0.00 41.44 4.02
238 243 5.918576 GCTTGTTGTTTTTAGCGGATTAGTT 59.081 36.000 0.00 0.00 0.00 2.24
261 266 2.908688 AAGGGGTTGTGTGATTTTGC 57.091 45.000 0.00 0.00 0.00 3.68
262 267 5.010516 TGTCATAAGGGGTTGTGTGATTTTG 59.989 40.000 0.00 0.00 0.00 2.44
267 272 4.380843 AATGTCATAAGGGGTTGTGTGA 57.619 40.909 0.00 0.00 0.00 3.58
281 286 9.874205 TCAAAAGTTTCTCTTGAAAAATGTCAT 57.126 25.926 0.00 0.00 42.94 3.06
329 336 7.446769 TGTTATCCTTGTTGCTCTTTGTACTA 58.553 34.615 0.00 0.00 0.00 1.82
334 341 6.980397 ACTTTTGTTATCCTTGTTGCTCTTTG 59.020 34.615 0.00 0.00 0.00 2.77
362 369 9.953565 GGCTTAGGATTTACATGTATATGGTTA 57.046 33.333 12.80 1.70 38.66 2.85
376 383 3.818773 GCATTAAGGCGGCTTAGGATTTA 59.181 43.478 27.58 14.97 0.00 1.40
399 406 1.078759 CGTGTGACGGCTGAATCCTC 61.079 60.000 0.00 0.00 38.08 3.71
426 433 5.736486 AAAAGTCTTCGGAGAACTGTTTC 57.264 39.130 0.00 0.00 45.90 2.78
432 439 2.479275 CCGGAAAAAGTCTTCGGAGAAC 59.521 50.000 0.00 0.00 45.90 3.01
433 440 2.103601 ACCGGAAAAAGTCTTCGGAGAA 59.896 45.455 9.46 0.00 45.90 2.87
446 453 0.313672 GCATGCTCACAACCGGAAAA 59.686 50.000 9.46 0.00 0.00 2.29
452 459 2.177531 CTGCGCATGCTCACAACC 59.822 61.111 12.24 0.00 43.34 3.77
454 461 0.954938 TTAGCTGCGCATGCTCACAA 60.955 50.000 29.09 19.04 43.34 3.33
456 463 1.351012 CTTAGCTGCGCATGCTCAC 59.649 57.895 29.09 8.93 43.34 3.51
467 474 5.057819 AGAGATTGATGATGTGCTTAGCTG 58.942 41.667 5.60 0.00 0.00 4.24
468 475 5.070714 AGAGAGATTGATGATGTGCTTAGCT 59.929 40.000 5.60 0.00 0.00 3.32
469 476 5.299148 AGAGAGATTGATGATGTGCTTAGC 58.701 41.667 0.00 0.00 0.00 3.09
470 477 5.927689 GGAGAGAGATTGATGATGTGCTTAG 59.072 44.000 0.00 0.00 0.00 2.18
471 478 5.364735 TGGAGAGAGATTGATGATGTGCTTA 59.635 40.000 0.00 0.00 0.00 3.09
563 571 7.562135 AGCAAGCAAAATGGAGATCAATAAAT 58.438 30.769 0.00 0.00 0.00 1.40
589 597 1.133325 TGGAAAGGGTAAAAGCAGGCA 60.133 47.619 0.00 0.00 0.00 4.75
590 598 1.627864 TGGAAAGGGTAAAAGCAGGC 58.372 50.000 0.00 0.00 0.00 4.85
591 599 2.760650 GGATGGAAAGGGTAAAAGCAGG 59.239 50.000 0.00 0.00 0.00 4.85
592 600 3.430453 TGGATGGAAAGGGTAAAAGCAG 58.570 45.455 0.00 0.00 0.00 4.24
633 1170 6.485648 AGTTTATTGTGTCTTCGCTTTAGGTT 59.514 34.615 0.00 0.00 0.00 3.50
669 1208 0.546988 GAGGTAAGGGTGGGGTCTGT 60.547 60.000 0.00 0.00 0.00 3.41
731 1270 4.060667 ATTTGGTGGGGGCGGGAG 62.061 66.667 0.00 0.00 0.00 4.30
732 1271 4.055227 GATTTGGTGGGGGCGGGA 62.055 66.667 0.00 0.00 0.00 5.14
733 1272 4.060667 AGATTTGGTGGGGGCGGG 62.061 66.667 0.00 0.00 0.00 6.13
734 1273 2.755469 CAGATTTGGTGGGGGCGG 60.755 66.667 0.00 0.00 0.00 6.13
735 1274 2.755469 CCAGATTTGGTGGGGGCG 60.755 66.667 0.00 0.00 39.79 6.13
928 1740 1.885049 TTTCAGATCAGGGAGGAGGG 58.115 55.000 0.00 0.00 0.00 4.30
1111 1942 2.936919 TGGAGCAGAGAAGCAAAGAA 57.063 45.000 0.00 0.00 36.85 2.52
1146 1977 2.368875 TGACAGAGGAAACCCTTCTGAC 59.631 50.000 10.47 5.66 35.18 3.51
1147 1978 2.368875 GTGACAGAGGAAACCCTTCTGA 59.631 50.000 10.47 0.00 35.18 3.27
1148 1979 2.551071 GGTGACAGAGGAAACCCTTCTG 60.551 54.545 0.00 0.00 36.21 3.02
1150 1981 1.700186 AGGTGACAGAGGAAACCCTTC 59.300 52.381 0.00 0.00 33.25 3.46
1152 1983 1.353091 GAGGTGACAGAGGAAACCCT 58.647 55.000 0.00 0.00 36.57 4.34
1153 1984 0.325272 GGAGGTGACAGAGGAAACCC 59.675 60.000 0.00 0.00 32.85 4.11
1155 1986 0.670854 GCGGAGGTGACAGAGGAAAC 60.671 60.000 0.00 0.00 0.00 2.78
1156 1987 0.832135 AGCGGAGGTGACAGAGGAAA 60.832 55.000 0.00 0.00 36.17 3.13
1158 1989 1.679305 GAGCGGAGGTGACAGAGGA 60.679 63.158 0.00 0.00 39.88 3.71
1167 1998 2.282958 TCGAGTTGGAGCGGAGGT 60.283 61.111 0.00 0.00 46.54 3.85
1321 2158 1.270550 GGGTACGACTCCGACAAGAAA 59.729 52.381 0.00 0.00 39.50 2.52
1533 2417 1.973812 GCTTCCTTCCTTGGCGCTT 60.974 57.895 7.64 0.00 0.00 4.68
1767 2671 1.744741 GCCTTCTCACCAGAGCAGC 60.745 63.158 0.00 0.00 41.81 5.25
1864 2807 7.440523 ACTTACTGACAAAAGATCCATCAAC 57.559 36.000 4.62 0.00 0.00 3.18
1868 2822 7.884877 TGATCAACTTACTGACAAAAGATCCAT 59.115 33.333 0.00 0.00 30.96 3.41
2095 3159 3.317149 AGCGCTGCAACATTTATCATGAT 59.683 39.130 10.39 13.81 0.00 2.45
2260 3556 6.054860 AGTGATAAAGTGCATAAGGACAGT 57.945 37.500 0.00 0.00 38.75 3.55
2311 3615 7.601886 ACAACTGACACATGAAAATCAACAAAA 59.398 29.630 0.00 0.00 0.00 2.44
2331 3635 4.261867 GGGTAAGGTGGCTTAAAACAACTG 60.262 45.833 0.00 0.00 34.29 3.16
2334 3638 4.187506 AGGGTAAGGTGGCTTAAAACAA 57.812 40.909 0.00 0.00 0.00 2.83
2416 3754 4.894784 AGTATGTGTAAGTCACCACTTGG 58.105 43.478 0.00 0.00 43.17 3.61
2704 4051 5.181690 TGTTTTGAGCAAAGATGTACACC 57.818 39.130 0.00 0.00 0.00 4.16
2979 4332 5.220643 GCCCACAAAACTCAAATTCAACAAG 60.221 40.000 0.00 0.00 0.00 3.16
2981 4334 4.187694 GCCCACAAAACTCAAATTCAACA 58.812 39.130 0.00 0.00 0.00 3.33
2995 4351 1.140589 CTGTTGCGTTGCCCACAAA 59.859 52.632 0.00 0.00 37.58 2.83
3125 4525 1.001293 AGAGCAAGAACAGACGCATGA 59.999 47.619 0.00 0.00 0.00 3.07
3131 4531 3.873952 AGTTGAACAGAGCAAGAACAGAC 59.126 43.478 0.00 0.00 0.00 3.51
3214 4629 0.612744 AAGTCTCTGGAGCAAGAGCC 59.387 55.000 6.29 0.00 42.95 4.70
3340 4755 0.846693 AGTTGGCAGAACCCTCAGTT 59.153 50.000 0.00 0.00 43.07 3.16
3551 4990 3.130516 TCACTAGTTAGACCATTCCTGCG 59.869 47.826 0.00 0.00 0.00 5.18
4226 5665 2.100197 TCGAGATGTTCTTCCGGATGT 58.900 47.619 16.29 0.00 0.00 3.06
4231 5670 3.165058 TCCATTCGAGATGTTCTTCCG 57.835 47.619 6.77 0.00 0.00 4.30
4421 5860 2.224793 ACCAGCTTCTCCCTTTGTAACC 60.225 50.000 0.00 0.00 0.00 2.85
4466 5905 9.695526 CAGAAACCAATTCATGAAATAGTCAAA 57.304 29.630 13.09 0.00 40.72 2.69
4467 5906 9.076781 TCAGAAACCAATTCATGAAATAGTCAA 57.923 29.630 13.09 0.00 40.72 3.18
4468 5907 8.634335 TCAGAAACCAATTCATGAAATAGTCA 57.366 30.769 13.09 0.00 40.72 3.41
4549 5991 8.280909 TCGTCTGCAAAATCAAAAGAAATTAC 57.719 30.769 0.00 0.00 0.00 1.89
4812 6269 4.272489 ACCAACAATATATGCACAGCAGT 58.728 39.130 0.00 0.00 43.65 4.40
4813 6270 4.906065 ACCAACAATATATGCACAGCAG 57.094 40.909 0.00 0.00 43.65 4.24
5034 6493 0.681733 AGTTTGCCTCTTCGCTCTCA 59.318 50.000 0.00 0.00 0.00 3.27
5150 6609 0.658897 GTCGTTCCCGTTTTCTGCAA 59.341 50.000 0.00 0.00 35.01 4.08
5219 6678 0.235926 GTTTTCTGCAGGTCGAGCAC 59.764 55.000 18.15 9.03 37.02 4.40
5225 6684 0.591659 GTTCCCGTTTTCTGCAGGTC 59.408 55.000 15.13 1.28 0.00 3.85
5448 6910 5.298777 TCTCTTTCTCCCGTATAGTACTTGC 59.701 44.000 0.00 0.00 0.00 4.01
5449 6911 6.766944 TCTCTCTTTCTCCCGTATAGTACTTG 59.233 42.308 0.00 0.00 0.00 3.16
5705 7196 2.568062 TGGCATGCCAGAAATCAACATT 59.432 40.909 35.59 0.00 41.89 2.71
5737 7228 8.637099 ACTTATATTTAGGAACGAAGGGAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
5738 7229 8.773033 ACTTATATTTAGGAACGAAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
5739 7230 7.672122 ACTTATATTTAGGAACGAAGGGAGT 57.328 36.000 0.00 0.00 0.00 3.85
5740 7231 8.959705 AAACTTATATTTAGGAACGAAGGGAG 57.040 34.615 0.00 0.00 0.00 4.30
5741 7232 9.743581 AAAAACTTATATTTAGGAACGAAGGGA 57.256 29.630 0.00 0.00 0.00 4.20
5765 7256 8.653191 TGTAGGTTGTAGTGGAATCTCTAAAAA 58.347 33.333 0.00 0.00 0.00 1.94
5766 7257 8.197592 TGTAGGTTGTAGTGGAATCTCTAAAA 57.802 34.615 0.00 0.00 0.00 1.52
5767 7258 7.786046 TGTAGGTTGTAGTGGAATCTCTAAA 57.214 36.000 0.00 0.00 0.00 1.85
5768 7259 7.973048 ATGTAGGTTGTAGTGGAATCTCTAA 57.027 36.000 0.00 0.00 0.00 2.10
5769 7260 7.228108 CGTATGTAGGTTGTAGTGGAATCTCTA 59.772 40.741 0.00 0.00 0.00 2.43
5770 7261 6.039493 CGTATGTAGGTTGTAGTGGAATCTCT 59.961 42.308 0.00 0.00 0.00 3.10
5771 7262 6.207213 CGTATGTAGGTTGTAGTGGAATCTC 58.793 44.000 0.00 0.00 0.00 2.75
5772 7263 5.068723 CCGTATGTAGGTTGTAGTGGAATCT 59.931 44.000 0.00 0.00 0.00 2.40
5773 7264 5.068198 TCCGTATGTAGGTTGTAGTGGAATC 59.932 44.000 0.00 0.00 0.00 2.52
5774 7265 4.957954 TCCGTATGTAGGTTGTAGTGGAAT 59.042 41.667 0.00 0.00 0.00 3.01
5775 7266 4.343231 TCCGTATGTAGGTTGTAGTGGAA 58.657 43.478 0.00 0.00 0.00 3.53
5776 7267 3.966979 TCCGTATGTAGGTTGTAGTGGA 58.033 45.455 0.00 0.00 0.00 4.02
5777 7268 4.098960 ACATCCGTATGTAGGTTGTAGTGG 59.901 45.833 0.00 0.00 44.66 4.00
5778 7269 5.258456 ACATCCGTATGTAGGTTGTAGTG 57.742 43.478 0.00 0.00 44.66 2.74
5827 7318 8.515414 GGAGCAAAATGAGTAAATCTACACTTT 58.485 33.333 0.00 0.00 0.00 2.66
5828 7319 7.148407 CGGAGCAAAATGAGTAAATCTACACTT 60.148 37.037 0.00 0.00 0.00 3.16
5829 7320 6.313905 CGGAGCAAAATGAGTAAATCTACACT 59.686 38.462 0.00 0.00 0.00 3.55
5830 7321 6.092259 ACGGAGCAAAATGAGTAAATCTACAC 59.908 38.462 0.00 0.00 0.00 2.90
5831 7322 6.170506 ACGGAGCAAAATGAGTAAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
5832 7323 6.663944 ACGGAGCAAAATGAGTAAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
5833 7324 7.985184 ACATACGGAGCAAAATGAGTAAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
5834 7325 6.823689 ACATACGGAGCAAAATGAGTAAATCT 59.176 34.615 0.00 0.00 0.00 2.40
5835 7326 7.016361 ACATACGGAGCAAAATGAGTAAATC 57.984 36.000 0.00 0.00 0.00 2.17
5836 7327 7.769044 ACTACATACGGAGCAAAATGAGTAAAT 59.231 33.333 0.00 0.00 0.00 1.40
5837 7328 7.101054 ACTACATACGGAGCAAAATGAGTAAA 58.899 34.615 0.00 0.00 0.00 2.01
5838 7329 6.636705 ACTACATACGGAGCAAAATGAGTAA 58.363 36.000 0.00 0.00 0.00 2.24
5839 7330 6.216801 ACTACATACGGAGCAAAATGAGTA 57.783 37.500 0.00 0.00 0.00 2.59
5840 7331 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
5841 7332 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
5842 7333 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
5843 7334 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
5844 7335 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
5845 7336 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
5846 7337 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
5847 7338 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
5848 7339 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
5849 7340 3.819337 TCACTATGGACTACATACGGAGC 59.181 47.826 0.00 0.00 41.03 4.70
5850 7341 6.387041 TTTCACTATGGACTACATACGGAG 57.613 41.667 0.00 0.00 41.03 4.63
5851 7342 6.971726 ATTTCACTATGGACTACATACGGA 57.028 37.500 0.00 0.00 41.03 4.69
5852 7343 8.740906 AGATATTTCACTATGGACTACATACGG 58.259 37.037 0.00 0.00 41.03 4.02
5880 7371 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
5881 7372 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
5882 7373 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
5883 7374 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
5884 7375 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
5885 7376 9.102453 GTACTCCCTCCATTCCTAAATATAAGT 57.898 37.037 0.00 0.00 0.00 2.24
5886 7377 9.101325 TGTACTCCCTCCATTCCTAAATATAAG 57.899 37.037 0.00 0.00 0.00 1.73
5887 7378 8.877195 GTGTACTCCCTCCATTCCTAAATATAA 58.123 37.037 0.00 0.00 0.00 0.98
5888 7379 8.014263 TGTGTACTCCCTCCATTCCTAAATATA 58.986 37.037 0.00 0.00 0.00 0.86
5889 7380 6.849697 TGTGTACTCCCTCCATTCCTAAATAT 59.150 38.462 0.00 0.00 0.00 1.28
5890 7381 6.206787 TGTGTACTCCCTCCATTCCTAAATA 58.793 40.000 0.00 0.00 0.00 1.40
5891 7382 5.036916 TGTGTACTCCCTCCATTCCTAAAT 58.963 41.667 0.00 0.00 0.00 1.40
5892 7383 4.431378 TGTGTACTCCCTCCATTCCTAAA 58.569 43.478 0.00 0.00 0.00 1.85
5893 7384 4.069312 TGTGTACTCCCTCCATTCCTAA 57.931 45.455 0.00 0.00 0.00 2.69
5894 7385 3.769189 TGTGTACTCCCTCCATTCCTA 57.231 47.619 0.00 0.00 0.00 2.94
5895 7386 2.642171 TGTGTACTCCCTCCATTCCT 57.358 50.000 0.00 0.00 0.00 3.36
5896 7387 3.933861 AATGTGTACTCCCTCCATTCC 57.066 47.619 0.00 0.00 0.00 3.01
5897 7388 4.757149 GCATAATGTGTACTCCCTCCATTC 59.243 45.833 0.00 0.00 0.00 2.67
5898 7389 4.413520 AGCATAATGTGTACTCCCTCCATT 59.586 41.667 0.00 0.00 0.00 3.16
5899 7390 3.976654 AGCATAATGTGTACTCCCTCCAT 59.023 43.478 0.00 0.00 0.00 3.41
5900 7391 3.384168 AGCATAATGTGTACTCCCTCCA 58.616 45.455 0.00 0.00 0.00 3.86
5901 7392 4.589374 ACTAGCATAATGTGTACTCCCTCC 59.411 45.833 0.00 0.00 0.00 4.30
5902 7393 5.793030 ACTAGCATAATGTGTACTCCCTC 57.207 43.478 0.00 0.00 0.00 4.30
5903 7394 6.374588 ACTACTAGCATAATGTGTACTCCCT 58.625 40.000 0.00 0.00 0.00 4.20
5904 7395 6.651975 ACTACTAGCATAATGTGTACTCCC 57.348 41.667 0.00 0.00 0.00 4.30
5905 7396 8.618702 TCTACTACTAGCATAATGTGTACTCC 57.381 38.462 0.00 0.00 0.00 3.85
5907 7398 9.629878 ACTTCTACTACTAGCATAATGTGTACT 57.370 33.333 0.00 0.00 0.00 2.73
5920 7411 6.097839 TGCCCCAACAATACTTCTACTACTAG 59.902 42.308 0.00 0.00 0.00 2.57
5927 7418 5.450818 AGAATGCCCCAACAATACTTCTA 57.549 39.130 0.00 0.00 0.00 2.10
5928 7419 4.322057 AGAATGCCCCAACAATACTTCT 57.678 40.909 0.00 0.00 0.00 2.85
5929 7420 4.220602 ACAAGAATGCCCCAACAATACTTC 59.779 41.667 0.00 0.00 0.00 3.01
5937 7775 1.632589 AGGAACAAGAATGCCCCAAC 58.367 50.000 0.00 0.00 0.00 3.77
6014 7852 7.592885 AACAGCTACTACTAATAATTCCCGA 57.407 36.000 0.00 0.00 0.00 5.14
6027 7953 6.985188 TGATCCATTTCAAACAGCTACTAC 57.015 37.500 0.00 0.00 0.00 2.73
6125 8054 2.158652 CCTGGGTCTCATTCATGCAGAT 60.159 50.000 0.00 0.00 0.00 2.90
6172 8101 0.902531 TCCAGCAGCTTAGTGGTACC 59.097 55.000 4.43 4.43 32.73 3.34
6177 8106 5.392380 CCAGTAATTTTCCAGCAGCTTAGTG 60.392 44.000 0.00 0.00 0.00 2.74
6179 8108 4.439289 GCCAGTAATTTTCCAGCAGCTTAG 60.439 45.833 0.00 0.00 0.00 2.18
6181 8110 2.232208 GCCAGTAATTTTCCAGCAGCTT 59.768 45.455 0.00 0.00 0.00 3.74
6187 8116 4.766404 AGAAACGCCAGTAATTTTCCAG 57.234 40.909 0.00 0.00 0.00 3.86
6212 8141 5.552178 GCCCTTGTCTTTCTCTTCTAAGAA 58.448 41.667 0.00 0.00 34.03 2.52
6214 8143 3.929610 CGCCCTTGTCTTTCTCTTCTAAG 59.070 47.826 0.00 0.00 0.00 2.18
6215 8144 3.864921 GCGCCCTTGTCTTTCTCTTCTAA 60.865 47.826 0.00 0.00 0.00 2.10
6216 8145 2.353803 GCGCCCTTGTCTTTCTCTTCTA 60.354 50.000 0.00 0.00 0.00 2.10
6217 8146 1.609320 GCGCCCTTGTCTTTCTCTTCT 60.609 52.381 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.