Multiple sequence alignment - TraesCS7D01G044100

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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 TraesCS7D01G044100 chr7D 100.000 5544 0 0 1 5544 22580173 22585716 0.000000e+00 10238
1 TraesCS7D01G044100 chr4A 93.062 4641 197 56 1 4557 705503777 705508376 0.000000e+00 6671
2 TraesCS7D01G044100 chr4A 79.931 578 45 26 5002 5541 705508761 705509305 5.280000e-95 359
3 TraesCS7D01G044100 chr7A 94.022 2526 83 32 1 2499 22931369 22933853 0.000000e+00 3766
4 TraesCS7D01G044100 chr7A 90.171 2218 146 35 2680 4841 22934166 22936367 0.000000e+00 2822
5 TraesCS7D01G044100 chr7A 98.578 211 3 0 2472 2682 22933853 22934063 1.890000e-99 374
6 TraesCS7D01G044100 chr7A 81.507 146 11 12 4974 5115 22936456 22936589 7.600000e-19 106
7 TraesCS7D01G044100 chr7A 95.522 67 2 1 5385 5451 22936791 22936856 7.600000e-19 106


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 TraesCS7D01G044100 chr7D 22580173 22585716 5543 False 10238.0 10238 100.0000 1 5544 1 chr7D.!!$F1 5543
1 TraesCS7D01G044100 chr4A 705503777 705509305 5528 False 3515.0 6671 86.4965 1 5541 2 chr4A.!!$F1 5540
2 TraesCS7D01G044100 chr7A 22931369 22936856 5487 False 1434.8 3766 91.9600 1 5451 5 chr7A.!!$F1 5450

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
671 676 2.138320 AGTGTGCACTGTTCTTCATCG 58.862 47.619 19.41 0.0 40.75 3.84 F
1196 1207 0.983467 TATGTCACTCTGCTTGCCCA 59.017 50.000 0.00 0.0 0.00 5.36 F
1858 1890 1.028905 CCGGAACTGGTGCTTTCAAA 58.971 50.000 0.00 0.0 0.00 2.69 F
2315 2360 0.110464 GCTTGCTCTTGACAGAACGC 60.110 55.000 0.00 0.0 0.00 4.84 F
3322 3524 0.534427 GCAGCTGGCAGCATCTATCA 60.534 55.000 38.09 0.0 45.56 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 2341 0.110464 GCGTTCTGTCAAGAGCAAGC 60.110 55.000 0.00 0.00 33.47 4.01 R
2313 2358 0.249280 TATATCCCACAGTGCACGCG 60.249 55.000 12.01 3.53 0.00 6.01 R
2970 3166 1.067060 GGGCACAACAACCAAGAGAAC 59.933 52.381 0.00 0.00 0.00 3.01 R
4182 4406 0.039617 CAAAACGGAAGCGCCATTCA 60.040 50.000 2.29 0.00 35.94 2.57 R
5317 5659 0.179006 GAGACCATCTGGGGAATGCC 60.179 60.000 0.54 0.00 42.91 4.40 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
36 39 3.120546 CCATGTCACACGTTTTCAGCTAG 60.121 47.826 0.00 0.00 0.00 3.42
61 64 4.515432 GTCTGTTGCTTACGAACAACTTC 58.485 43.478 7.32 0.00 45.07 3.01
302 305 2.439507 CCATGCTACTGGACATTAGGGT 59.560 50.000 0.00 0.00 38.69 4.34
491 494 6.486056 TCTAGGTATGCTCTTATCCGAGAAT 58.514 40.000 0.00 0.00 33.78 2.40
492 495 6.948886 TCTAGGTATGCTCTTATCCGAGAATT 59.051 38.462 0.00 0.00 31.66 2.17
498 501 6.465439 TGCTCTTATCCGAGAATTCAGTAA 57.535 37.500 8.44 0.00 32.74 2.24
612 617 3.909732 CTCTCTTCTCCCCTATCACTGT 58.090 50.000 0.00 0.00 0.00 3.55
671 676 2.138320 AGTGTGCACTGTTCTTCATCG 58.862 47.619 19.41 0.00 40.75 3.84
788 794 5.295431 TGTGAACATTAGCATTTCTTCCG 57.705 39.130 0.00 0.00 0.00 4.30
1057 1064 7.994911 TGTAAGATGATAATGAGCTTCCAACAT 59.005 33.333 0.00 0.00 0.00 2.71
1169 1180 4.324402 CGTGCAATCAATAAAGAAAGTGGC 59.676 41.667 0.00 0.00 0.00 5.01
1196 1207 0.983467 TATGTCACTCTGCTTGCCCA 59.017 50.000 0.00 0.00 0.00 5.36
1279 1290 1.149174 GCTAGCATGCTTGGGGCTA 59.851 57.895 28.02 4.49 42.39 3.93
1294 1305 7.344352 TGCTTGGGGCTATTTATTGTATTTCTT 59.656 33.333 0.00 0.00 42.39 2.52
1295 1306 8.856103 GCTTGGGGCTATTTATTGTATTTCTTA 58.144 33.333 0.00 0.00 38.06 2.10
1297 1308 9.930158 TTGGGGCTATTTATTGTATTTCTTACT 57.070 29.630 0.00 0.00 0.00 2.24
1348 1359 7.490962 TTCAGTTTGTATTGTTACACTCTGG 57.509 36.000 12.50 0.00 38.05 3.86
1382 1393 7.444629 ACGACTAGCCGATATTCTTATGTTA 57.555 36.000 5.13 0.00 0.00 2.41
1434 1445 5.009310 CCTTGTTGACATATATGCACATGCT 59.991 40.000 12.79 0.00 42.66 3.79
1512 1523 2.744202 GTGCATCAATCTCCGTGAAGTT 59.256 45.455 0.00 0.00 0.00 2.66
1523 1534 7.611213 ATCTCCGTGAAGTTAAGGTATTTTG 57.389 36.000 0.00 0.00 0.00 2.44
1664 1687 6.843333 TCAAGGAGGTCATAAGAGAGAATGAT 59.157 38.462 0.00 0.00 34.77 2.45
1767 1799 8.717821 GTTGACTAATGTTTTATGTGCTCTACA 58.282 33.333 0.00 0.00 44.87 2.74
1858 1890 1.028905 CCGGAACTGGTGCTTTCAAA 58.971 50.000 0.00 0.00 0.00 2.69
1961 1993 9.573133 GGACTCTGGAATTGTTAATAATGTTTG 57.427 33.333 0.00 0.00 0.00 2.93
2107 2145 7.475840 AGAACAGTTTGAGAACATCTTTTGTC 58.524 34.615 0.00 0.00 37.68 3.18
2118 2156 9.741647 GAGAACATCTTTTGTCTTTCATCTTTT 57.258 29.630 0.00 0.00 37.68 2.27
2125 2163 8.621286 TCTTTTGTCTTTCATCTTTTCACCTAC 58.379 33.333 0.00 0.00 0.00 3.18
2313 2358 1.502231 TCGCTTGCTCTTGACAGAAC 58.498 50.000 0.00 0.00 0.00 3.01
2315 2360 0.110464 GCTTGCTCTTGACAGAACGC 60.110 55.000 0.00 0.00 0.00 4.84
2367 2426 7.038941 GGTAGCAGTAATGACAGATAATAGGGT 60.039 40.741 0.00 0.00 0.00 4.34
2398 2457 9.999009 TGAAAGACTAGTTGTATATGACTAACG 57.001 33.333 0.00 0.00 0.00 3.18
2401 2460 7.416022 AGACTAGTTGTATATGACTAACGTGC 58.584 38.462 0.00 0.00 0.00 5.34
2455 2517 4.911390 AGCCTTAAATGCTACTGTGTTCT 58.089 39.130 0.00 0.00 37.28 3.01
2531 2620 6.076981 TCATCTTTTGCTCTTTTGACCTTC 57.923 37.500 0.00 0.00 0.00 3.46
2682 2873 9.719355 TCAGTCTTAAACAGCTTAAATCATACA 57.281 29.630 0.00 0.00 0.00 2.29
2805 2999 8.041323 TGGTGAGTAGAGAATATTTGTTCCTTC 58.959 37.037 0.00 0.00 0.00 3.46
2858 3052 2.036217 TGCTGATTCCCTGTTGCTTTTG 59.964 45.455 0.00 0.00 0.00 2.44
2939 3135 2.437281 CCTGGCTCAAGGTACATGATCT 59.563 50.000 0.00 0.00 34.79 2.75
2942 3138 5.396772 CCTGGCTCAAGGTACATGATCTTTA 60.397 44.000 0.00 0.00 34.79 1.85
2953 3149 8.216423 AGGTACATGATCTTTATTCTGCTGAAT 58.784 33.333 20.75 20.75 44.32 2.57
2954 3150 8.288208 GGTACATGATCTTTATTCTGCTGAATG 58.712 37.037 24.38 11.25 42.34 2.67
2955 3151 6.736123 ACATGATCTTTATTCTGCTGAATGC 58.264 36.000 24.38 10.12 42.34 3.56
2957 3153 4.274214 TGATCTTTATTCTGCTGAATGCCG 59.726 41.667 24.38 13.83 42.34 5.69
2970 3166 1.184970 AATGCCGTTTGGTTCCCCTG 61.185 55.000 0.00 0.00 37.67 4.45
2992 3188 1.133513 TCTCTTGGTTGTTGTGCCCAT 60.134 47.619 0.00 0.00 0.00 4.00
3005 3202 6.397272 TGTTGTGCCCATTTAATTGAAGATC 58.603 36.000 0.00 0.00 0.00 2.75
3007 3204 7.395772 TGTTGTGCCCATTTAATTGAAGATCTA 59.604 33.333 0.00 0.00 0.00 1.98
3200 3402 4.074970 CAAGTAATTGCTCAAGTGAGGGT 58.925 43.478 10.25 0.00 42.29 4.34
3207 3409 7.775053 AATTGCTCAAGTGAGGGTATTTTTA 57.225 32.000 10.25 0.00 42.29 1.52
3237 3439 1.211703 TCTTTGTCCCACAGTGAAGCA 59.788 47.619 0.62 0.00 0.00 3.91
3322 3524 0.534427 GCAGCTGGCAGCATCTATCA 60.534 55.000 38.09 0.00 45.56 2.15
3499 3707 7.254353 GCTGAACCTTATTTCGGTAAGTATCAC 60.254 40.741 0.00 0.00 34.74 3.06
3511 3719 5.351465 CGGTAAGTATCACATCAGCAGTTTT 59.649 40.000 0.00 0.00 0.00 2.43
3527 3735 4.740205 GCAGTTTTTGTCTGTCCTTAAAGC 59.260 41.667 0.00 0.00 35.60 3.51
3614 3822 1.734163 CTCATGGGACCCACGTAAAC 58.266 55.000 17.78 0.00 35.80 2.01
3678 3886 9.342308 TCAGGTCATAATATTTCCAATGTCTTC 57.658 33.333 0.00 0.00 0.00 2.87
3681 3889 7.308589 GGTCATAATATTTCCAATGTCTTCCCG 60.309 40.741 0.00 0.00 0.00 5.14
3690 3898 2.936498 CAATGTCTTCCCGTACCACATC 59.064 50.000 0.00 0.00 0.00 3.06
3709 3917 3.531934 TCAGATGATGCATTGACTCGT 57.468 42.857 0.00 0.00 0.00 4.18
3713 3921 4.093850 CAGATGATGCATTGACTCGTTTCA 59.906 41.667 0.00 0.00 0.00 2.69
3725 3934 2.303022 ACTCGTTTCATGACCTGACCAT 59.697 45.455 0.00 0.00 32.17 3.55
3728 3937 4.250464 TCGTTTCATGACCTGACCATAAC 58.750 43.478 0.00 0.00 32.17 1.89
3843 4052 8.539770 AATATTCTCACGCTTATATGACTTGG 57.460 34.615 0.00 0.00 0.00 3.61
3872 4081 7.416154 TTTTCACTAGAATACCGTTGTTGAG 57.584 36.000 0.00 0.00 32.89 3.02
3884 4093 3.429543 CCGTTGTTGAGGCAATTCAAATG 59.570 43.478 0.00 0.00 38.69 2.32
3936 4145 1.210478 TGGACCAGAAGAATGCTAGGC 59.790 52.381 0.00 0.00 0.00 3.93
3990 4199 2.159282 CCGGCAGTCAATAACTCGTACT 60.159 50.000 0.00 0.00 35.45 2.73
4097 4306 1.080434 GCTGACGAAGGAGAACGCT 60.080 57.895 0.00 0.00 0.00 5.07
4211 4436 2.781646 GCTTCCGTTTTGTTCAAAGTCG 59.218 45.455 13.32 13.32 0.00 4.18
4215 4440 1.530236 CGTTTTGTTCAAAGTCGCGGT 60.530 47.619 6.13 0.00 0.00 5.68
4219 4444 2.461897 TGTTCAAAGTCGCGGTTTTC 57.538 45.000 6.13 1.19 0.00 2.29
4235 4461 3.305064 GGTTTTCCGCTTCTGTAATGCAA 60.305 43.478 0.00 0.00 0.00 4.08
4238 4464 4.355543 TTCCGCTTCTGTAATGCAAATC 57.644 40.909 0.00 0.00 0.00 2.17
4240 4466 3.755905 TCCGCTTCTGTAATGCAAATCAA 59.244 39.130 0.00 0.00 0.00 2.57
4245 4471 6.101332 GCTTCTGTAATGCAAATCAATTCCA 58.899 36.000 0.00 0.00 0.00 3.53
4256 4485 2.601240 TCAATTCCATTGTGCAGGGA 57.399 45.000 0.00 0.00 41.02 4.20
4257 4486 2.886913 TCAATTCCATTGTGCAGGGAA 58.113 42.857 10.43 10.43 44.22 3.97
4258 4487 2.562298 TCAATTCCATTGTGCAGGGAAC 59.438 45.455 10.28 0.00 43.01 3.62
4267 4496 1.493022 TGTGCAGGGAACAACTACCTT 59.507 47.619 0.00 0.00 30.66 3.50
4273 4502 0.881796 GGAACAACTACCTTGCTGCC 59.118 55.000 0.00 0.00 32.41 4.85
4495 4727 3.861797 CCCTTCCGGCGCACCTAT 61.862 66.667 10.83 0.00 0.00 2.57
4563 4795 4.715523 ACCATCCCACCAACGCCG 62.716 66.667 0.00 0.00 0.00 6.46
4564 4796 4.715523 CCATCCCACCAACGCCGT 62.716 66.667 0.00 0.00 0.00 5.68
4568 4800 4.715523 CCCACCAACGCCGTCCAT 62.716 66.667 0.00 0.00 0.00 3.41
4570 4802 2.047274 CACCAACGCCGTCCATCT 60.047 61.111 0.00 0.00 0.00 2.90
4571 4803 2.047274 ACCAACGCCGTCCATCTG 60.047 61.111 0.00 0.00 0.00 2.90
4578 4827 2.124570 CCGTCCATCTGCCCCTTG 60.125 66.667 0.00 0.00 0.00 3.61
4668 4925 2.290641 CCAAGTTTGTGTCTCCCTTTCG 59.709 50.000 0.00 0.00 0.00 3.46
4670 4927 4.124238 CAAGTTTGTGTCTCCCTTTCGTA 58.876 43.478 0.00 0.00 0.00 3.43
4674 4931 3.380479 TGTGTCTCCCTTTCGTAGTTG 57.620 47.619 0.00 0.00 0.00 3.16
4685 4943 4.274950 CCTTTCGTAGTTGGTGTTGTGATT 59.725 41.667 0.00 0.00 0.00 2.57
4686 4944 5.220970 CCTTTCGTAGTTGGTGTTGTGATTT 60.221 40.000 0.00 0.00 0.00 2.17
4687 4945 4.804608 TCGTAGTTGGTGTTGTGATTTG 57.195 40.909 0.00 0.00 0.00 2.32
4688 4946 4.443621 TCGTAGTTGGTGTTGTGATTTGA 58.556 39.130 0.00 0.00 0.00 2.69
4692 4950 6.695278 CGTAGTTGGTGTTGTGATTTGAAAAT 59.305 34.615 0.00 0.00 0.00 1.82
4693 4951 7.858382 CGTAGTTGGTGTTGTGATTTGAAAATA 59.142 33.333 0.00 0.00 0.00 1.40
4697 4955 9.701355 GTTGGTGTTGTGATTTGAAAATAAAAG 57.299 29.630 0.00 0.00 0.00 2.27
4702 4960 7.011857 TGTTGTGATTTGAAAATAAAAGGCCAC 59.988 33.333 5.01 0.00 0.00 5.01
4740 5015 2.646175 CGGCGGGGAGAGTGAAGAA 61.646 63.158 0.00 0.00 0.00 2.52
4741 5016 1.677552 GGCGGGGAGAGTGAAGAAA 59.322 57.895 0.00 0.00 0.00 2.52
4742 5017 0.673956 GGCGGGGAGAGTGAAGAAAC 60.674 60.000 0.00 0.00 0.00 2.78
4746 5021 1.608283 GGGGAGAGTGAAGAAACGTGG 60.608 57.143 0.00 0.00 0.00 4.94
4747 5022 1.343465 GGGAGAGTGAAGAAACGTGGA 59.657 52.381 0.00 0.00 0.00 4.02
4748 5023 2.224209 GGGAGAGTGAAGAAACGTGGAA 60.224 50.000 0.00 0.00 0.00 3.53
4750 5025 3.492829 GGAGAGTGAAGAAACGTGGAACT 60.493 47.826 0.00 0.00 31.75 3.01
4752 5027 3.871594 AGAGTGAAGAAACGTGGAACTTG 59.128 43.478 0.00 0.00 31.75 3.16
4754 5029 4.007659 AGTGAAGAAACGTGGAACTTGTT 58.992 39.130 0.00 0.00 31.75 2.83
4755 5030 4.095610 GTGAAGAAACGTGGAACTTGTTG 58.904 43.478 0.00 0.00 31.75 3.33
4756 5031 4.004314 TGAAGAAACGTGGAACTTGTTGA 58.996 39.130 0.00 0.00 31.75 3.18
4759 5034 5.576447 AGAAACGTGGAACTTGTTGATTT 57.424 34.783 0.00 0.00 31.75 2.17
4761 5036 4.974368 AACGTGGAACTTGTTGATTTGA 57.026 36.364 0.00 0.00 31.75 2.69
4762 5037 4.552166 ACGTGGAACTTGTTGATTTGAG 57.448 40.909 0.00 0.00 31.75 3.02
4763 5038 3.243068 ACGTGGAACTTGTTGATTTGAGC 60.243 43.478 0.00 0.00 31.75 4.26
4766 5041 5.351458 GTGGAACTTGTTGATTTGAGCTTT 58.649 37.500 0.00 0.00 0.00 3.51
4768 5043 5.105392 TGGAACTTGTTGATTTGAGCTTTGT 60.105 36.000 0.00 0.00 0.00 2.83
4769 5044 5.460091 GGAACTTGTTGATTTGAGCTTTGTC 59.540 40.000 0.00 0.00 0.00 3.18
4788 5067 3.934579 TGTCAGAAACGTGGATGATGATG 59.065 43.478 0.00 0.00 0.00 3.07
4789 5068 3.935203 GTCAGAAACGTGGATGATGATGT 59.065 43.478 0.00 0.00 0.00 3.06
4815 5097 0.306228 TGTGATTTGTGTGCGAACCG 59.694 50.000 0.00 0.00 0.00 4.44
4816 5098 0.584396 GTGATTTGTGTGCGAACCGA 59.416 50.000 0.00 0.00 0.00 4.69
4817 5099 0.584396 TGATTTGTGTGCGAACCGAC 59.416 50.000 0.00 0.00 0.00 4.79
4818 5100 0.110373 GATTTGTGTGCGAACCGACC 60.110 55.000 0.00 0.00 0.00 4.79
4819 5101 1.837538 ATTTGTGTGCGAACCGACCG 61.838 55.000 0.00 0.00 0.00 4.79
4831 5113 2.202440 CGACCGACGATCGCTTGT 60.202 61.111 16.60 9.45 45.77 3.16
4832 5114 1.800315 CGACCGACGATCGCTTGTT 60.800 57.895 16.60 0.00 45.77 2.83
4835 5117 0.108804 ACCGACGATCGCTTGTTCAT 60.109 50.000 16.60 0.00 38.82 2.57
4836 5118 0.298707 CCGACGATCGCTTGTTCATG 59.701 55.000 16.60 0.00 38.82 3.07
4838 5120 1.266550 CGACGATCGCTTGTTCATGTG 60.267 52.381 16.60 0.00 31.14 3.21
4840 5122 1.726791 ACGATCGCTTGTTCATGTGAC 59.273 47.619 16.60 0.00 0.00 3.67
4841 5123 1.061131 CGATCGCTTGTTCATGTGACC 59.939 52.381 0.26 0.00 0.00 4.02
4846 5138 1.949525 GCTTGTTCATGTGACCTGTGT 59.050 47.619 0.00 0.00 0.00 3.72
4851 5143 0.246360 TCATGTGACCTGTGTAGCCG 59.754 55.000 0.00 0.00 0.00 5.52
4859 5151 0.459899 CCTGTGTAGCCGCTGATGTA 59.540 55.000 2.16 0.00 0.00 2.29
4881 5173 5.705609 ATCGTGGCTAAACTTGTTGATTT 57.294 34.783 0.00 0.00 0.00 2.17
4883 5175 6.621316 TCGTGGCTAAACTTGTTGATTTTA 57.379 33.333 0.00 0.00 0.00 1.52
4886 5178 6.915843 CGTGGCTAAACTTGTTGATTTTACTT 59.084 34.615 0.00 0.00 0.00 2.24
4903 5195 6.642707 TTTACTTTGGTCGTTGATCCATTT 57.357 33.333 0.00 0.00 33.50 2.32
4930 5223 2.099062 GCTTGCTCGCATGGTTCG 59.901 61.111 6.87 0.00 0.00 3.95
4931 5224 2.787249 CTTGCTCGCATGGTTCGG 59.213 61.111 0.00 0.00 0.00 4.30
4932 5225 3.386867 CTTGCTCGCATGGTTCGGC 62.387 63.158 0.00 0.00 0.00 5.54
4933 5226 4.695993 TGCTCGCATGGTTCGGCA 62.696 61.111 0.00 0.00 33.29 5.69
4934 5227 3.204827 GCTCGCATGGTTCGGCAT 61.205 61.111 0.00 0.00 0.00 4.40
4935 5228 2.711311 CTCGCATGGTTCGGCATG 59.289 61.111 0.00 0.00 0.00 4.06
4937 5230 2.040213 CTCGCATGGTTCGGCATGTC 62.040 60.000 0.00 0.00 0.00 3.06
4938 5231 2.800736 GCATGGTTCGGCATGTCC 59.199 61.111 0.00 0.00 0.00 4.02
4967 5265 3.076621 TCTGCATGACTGGTGATGTTTC 58.923 45.455 0.00 0.00 0.00 2.78
4968 5266 3.079578 CTGCATGACTGGTGATGTTTCT 58.920 45.455 0.00 0.00 0.00 2.52
4969 5267 3.489355 TGCATGACTGGTGATGTTTCTT 58.511 40.909 0.00 0.00 0.00 2.52
4970 5268 3.503363 TGCATGACTGGTGATGTTTCTTC 59.497 43.478 0.00 0.00 0.00 2.87
4971 5269 3.755378 GCATGACTGGTGATGTTTCTTCT 59.245 43.478 0.00 0.00 0.00 2.85
4972 5270 4.142730 GCATGACTGGTGATGTTTCTTCTC 60.143 45.833 0.00 0.00 0.00 2.87
4993 5291 2.475098 TACGCGGTTGCTGCTTCGTA 62.475 55.000 12.47 4.99 39.65 3.43
5004 5302 4.684877 TGCTGCTTCGTATCCGTATTTTA 58.315 39.130 0.00 0.00 35.01 1.52
5020 5321 6.037830 CCGTATTTTATTTACTCCTGTGGGTG 59.962 42.308 0.00 0.00 0.00 4.61
5028 5329 2.690840 ACTCCTGTGGGTGTTACTCTT 58.309 47.619 0.00 0.00 36.05 2.85
5029 5330 3.853207 ACTCCTGTGGGTGTTACTCTTA 58.147 45.455 0.00 0.00 36.05 2.10
5030 5331 4.426704 ACTCCTGTGGGTGTTACTCTTAT 58.573 43.478 0.00 0.00 36.05 1.73
5031 5332 4.466726 ACTCCTGTGGGTGTTACTCTTATC 59.533 45.833 0.00 0.00 36.05 1.75
5032 5333 4.684724 TCCTGTGGGTGTTACTCTTATCT 58.315 43.478 0.00 0.00 0.00 1.98
5033 5334 5.834460 TCCTGTGGGTGTTACTCTTATCTA 58.166 41.667 0.00 0.00 0.00 1.98
5034 5335 5.655532 TCCTGTGGGTGTTACTCTTATCTAC 59.344 44.000 0.00 0.00 0.00 2.59
5035 5336 5.657302 CCTGTGGGTGTTACTCTTATCTACT 59.343 44.000 0.00 0.00 0.00 2.57
5036 5337 6.183360 CCTGTGGGTGTTACTCTTATCTACTC 60.183 46.154 0.00 0.00 0.00 2.59
5038 5339 4.885907 TGGGTGTTACTCTTATCTACTCCG 59.114 45.833 0.00 0.00 0.00 4.63
5039 5340 4.886489 GGGTGTTACTCTTATCTACTCCGT 59.114 45.833 0.00 0.00 0.00 4.69
5040 5341 6.058183 GGGTGTTACTCTTATCTACTCCGTA 58.942 44.000 0.00 0.00 0.00 4.02
5041 5342 6.017523 GGGTGTTACTCTTATCTACTCCGTAC 60.018 46.154 0.00 0.00 0.00 3.67
5042 5343 6.765512 GGTGTTACTCTTATCTACTCCGTACT 59.234 42.308 0.00 0.00 0.00 2.73
5073 5374 3.584586 CGAGAGCTGTCATGGATCC 57.415 57.895 11.90 4.20 0.00 3.36
5081 5382 2.499205 TCATGGATCCCGTGACGC 59.501 61.111 9.90 0.00 43.70 5.19
5090 5391 1.062365 CCCGTGACGCGACGTATTA 59.938 57.895 15.93 0.00 41.37 0.98
5111 5432 2.512485 TTTTCAGTTGCGAGTACCGA 57.488 45.000 7.77 0.00 41.76 4.69
5150 5477 3.181500 GGATTGATTTCTGTGGGCGTTAC 60.181 47.826 0.00 0.00 0.00 2.50
5155 5482 2.433664 CTGTGGGCGTTACGGTCC 60.434 66.667 6.94 0.00 0.00 4.46
5200 5536 2.074547 TGTTTGACTACGTAGCAGCC 57.925 50.000 22.40 14.01 0.00 4.85
5201 5537 1.337447 TGTTTGACTACGTAGCAGCCC 60.337 52.381 22.40 8.61 0.00 5.19
5205 5541 1.000019 ACTACGTAGCAGCCCCAGA 60.000 57.895 22.40 0.00 0.00 3.86
5210 5546 3.790437 TAGCAGCCCCAGAGCAGC 61.790 66.667 0.00 0.00 44.85 5.25
5217 5553 2.746671 CCCAGAGCAGCAGCAGTG 60.747 66.667 3.17 0.00 45.49 3.66
5218 5554 2.346365 CCAGAGCAGCAGCAGTGA 59.654 61.111 3.17 0.00 45.49 3.41
5219 5555 1.302271 CCAGAGCAGCAGCAGTGAA 60.302 57.895 3.17 0.00 45.49 3.18
5245 5584 1.804601 ACAGTACGTAGGCCTTTTGC 58.195 50.000 12.58 0.00 40.16 3.68
5279 5621 3.793144 GCCGCTGCCGAAACTGAG 61.793 66.667 0.00 0.00 36.29 3.35
5281 5623 3.793144 CGCTGCCGAAACTGAGCC 61.793 66.667 0.00 0.00 36.29 4.70
5282 5624 2.359230 GCTGCCGAAACTGAGCCT 60.359 61.111 0.00 0.00 0.00 4.58
5283 5625 2.684843 GCTGCCGAAACTGAGCCTG 61.685 63.158 0.00 0.00 0.00 4.85
5284 5626 1.004560 CTGCCGAAACTGAGCCTGA 60.005 57.895 0.00 0.00 0.00 3.86
5285 5627 1.004560 TGCCGAAACTGAGCCTGAG 60.005 57.895 0.00 0.00 0.00 3.35
5302 5644 1.492176 TGAGCCTCCATCCATCCTTTC 59.508 52.381 0.00 0.00 0.00 2.62
5309 5651 1.524621 ATCCATCCTTTCGCCGCTG 60.525 57.895 0.00 0.00 0.00 5.18
5311 5653 2.436646 CATCCTTTCGCCGCTGGT 60.437 61.111 0.00 0.00 0.00 4.00
5312 5654 2.040544 CATCCTTTCGCCGCTGGTT 61.041 57.895 0.00 0.00 0.00 3.67
5313 5655 1.745489 ATCCTTTCGCCGCTGGTTC 60.745 57.895 0.00 0.00 0.00 3.62
5315 5657 3.041940 CTTTCGCCGCTGGTTCGT 61.042 61.111 0.00 0.00 0.00 3.85
5317 5659 1.683790 CTTTCGCCGCTGGTTCGTAG 61.684 60.000 0.00 0.00 0.00 3.51
5318 5660 3.636313 TTCGCCGCTGGTTCGTAGG 62.636 63.158 0.00 0.00 0.00 3.18
5321 5663 2.186903 CCGCTGGTTCGTAGGCAT 59.813 61.111 0.00 0.00 0.00 4.40
5322 5664 1.449601 CCGCTGGTTCGTAGGCATT 60.450 57.895 0.00 0.00 0.00 3.56
5323 5665 1.429148 CCGCTGGTTCGTAGGCATTC 61.429 60.000 0.00 0.00 0.00 2.67
5324 5666 1.429148 CGCTGGTTCGTAGGCATTCC 61.429 60.000 0.00 0.00 0.00 3.01
5325 5667 1.095807 GCTGGTTCGTAGGCATTCCC 61.096 60.000 0.00 0.00 0.00 3.97
5333 5676 0.846693 GTAGGCATTCCCCAGATGGT 59.153 55.000 0.00 0.00 0.00 3.55
5429 5772 4.073293 TCTTCTTGACCAGGAGAAACAC 57.927 45.455 0.00 0.00 33.62 3.32
5451 5798 2.604174 CGTCCCGTGTGCCTTGTTC 61.604 63.158 0.00 0.00 0.00 3.18
5478 5831 1.503542 CTGCGTGCTGGGTCATTTC 59.496 57.895 0.00 0.00 0.00 2.17
5513 5866 6.127253 CCAGCTTTGAATCCATGGTAAGATTT 60.127 38.462 12.58 0.00 32.91 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.990092 TCTAGCTGAAAACGTGTGACAT 58.010 40.909 0.00 0.00 0.00 3.06
36 39 2.750948 TGTTCGTAAGCAACAGACCTC 58.249 47.619 0.00 0.00 34.22 3.85
61 64 5.215160 GTGTTGAAACCTGCAAGAATACAG 58.785 41.667 0.00 0.00 34.07 2.74
302 305 0.457853 GCACCGCAATCACTAGTCGA 60.458 55.000 0.00 0.00 0.00 4.20
491 494 8.363390 TGCCATGAAAATTATTGTGTTACTGAA 58.637 29.630 0.00 0.00 0.00 3.02
492 495 7.812191 GTGCCATGAAAATTATTGTGTTACTGA 59.188 33.333 0.00 0.00 0.00 3.41
498 501 6.869913 CAGAAGTGCCATGAAAATTATTGTGT 59.130 34.615 0.00 0.00 0.00 3.72
612 617 1.673920 GCCGGACAAACTGAAAACTCA 59.326 47.619 5.05 0.00 0.00 3.41
671 676 1.372087 CGCCATCAGAAGTGAAGCCC 61.372 60.000 0.00 0.00 35.88 5.19
788 794 6.790285 TTAAACAAAGTGGATTAGACCGTC 57.210 37.500 0.00 0.00 0.00 4.79
1169 1180 2.094494 AGCAGAGTGACATACCACTTCG 60.094 50.000 0.00 0.00 46.45 3.79
1225 1236 6.765989 ACAACATAAACAAGAGTTGCTACTGA 59.234 34.615 5.27 0.00 43.74 3.41
1230 1241 6.863126 GCATAACAACATAAACAAGAGTTGCT 59.137 34.615 0.00 0.00 43.74 3.91
1236 1247 5.004448 TCCGGCATAACAACATAAACAAGA 58.996 37.500 0.00 0.00 0.00 3.02
1237 1248 5.303747 TCCGGCATAACAACATAAACAAG 57.696 39.130 0.00 0.00 0.00 3.16
1348 1359 9.649024 GAATATCGGCTAGTCGTAAAGATATAC 57.351 37.037 17.56 0.00 31.84 1.47
1357 1368 7.444629 AACATAAGAATATCGGCTAGTCGTA 57.555 36.000 17.56 8.92 29.74 3.43
1434 1445 3.637714 GCGACCTGCGAAGAACAA 58.362 55.556 0.00 0.00 44.57 2.83
1590 1613 1.343465 TCGGAGGGACTGTTGAAGTTC 59.657 52.381 0.00 0.00 41.55 3.01
1664 1687 9.979578 ATGTATTCAAAAACAAAGAACAGCATA 57.020 25.926 0.00 0.00 0.00 3.14
1767 1799 5.025453 AGATTGCATTCCTAACAAACCCAT 58.975 37.500 5.00 0.00 0.00 4.00
1772 1804 7.012704 GCTGATAGAGATTGCATTCCTAACAAA 59.987 37.037 5.00 0.00 0.00 2.83
1858 1890 6.825213 TGCATGTGACTAAGAGCTTGAAATAT 59.175 34.615 0.00 0.00 0.00 1.28
1987 2019 3.449018 AGGCTCTAACACTAGACCACATG 59.551 47.826 0.00 0.00 32.22 3.21
2107 2145 4.093556 GGAGCGTAGGTGAAAAGATGAAAG 59.906 45.833 0.00 0.00 39.88 2.62
2118 2156 1.557099 ATGACAAGGAGCGTAGGTGA 58.443 50.000 0.00 0.00 39.88 4.02
2125 2163 1.662629 CACAGCTTATGACAAGGAGCG 59.337 52.381 0.00 0.00 39.99 5.03
2296 2341 0.110464 GCGTTCTGTCAAGAGCAAGC 60.110 55.000 0.00 0.00 33.47 4.01
2313 2358 0.249280 TATATCCCACAGTGCACGCG 60.249 55.000 12.01 3.53 0.00 6.01
2315 2360 4.820897 ACATATATATCCCACAGTGCACG 58.179 43.478 12.01 9.15 0.00 5.34
2367 2426 9.856488 GTCATATACAACTAGTCTTTCAAGTGA 57.144 33.333 0.00 0.00 0.00 3.41
2455 2517 4.103153 AGGTCAATCTGAACTCTCCAAACA 59.897 41.667 0.00 0.00 41.32 2.83
2681 2872 8.310382 AGTATCCTTGCTTTAGTGCTCTATATG 58.690 37.037 0.00 0.00 0.00 1.78
2682 2873 8.429237 AGTATCCTTGCTTTAGTGCTCTATAT 57.571 34.615 0.00 0.00 0.00 0.86
2683 2874 7.841282 AGTATCCTTGCTTTAGTGCTCTATA 57.159 36.000 0.00 0.00 0.00 1.31
2684 2875 6.739331 AGTATCCTTGCTTTAGTGCTCTAT 57.261 37.500 0.00 0.00 0.00 1.98
2685 2876 7.655521 TTAGTATCCTTGCTTTAGTGCTCTA 57.344 36.000 0.00 0.00 0.00 2.43
2686 2877 6.546428 TTAGTATCCTTGCTTTAGTGCTCT 57.454 37.500 0.00 0.00 0.00 4.09
2687 2878 6.763610 ACATTAGTATCCTTGCTTTAGTGCTC 59.236 38.462 0.00 0.00 0.00 4.26
2858 3052 1.543429 GCCCATAGCCCACATGTCTAC 60.543 57.143 0.00 0.00 34.35 2.59
2970 3166 1.067060 GGGCACAACAACCAAGAGAAC 59.933 52.381 0.00 0.00 0.00 3.01
2992 3188 9.807921 AGGACCAAACTTAGATCTTCAATTAAA 57.192 29.630 0.00 0.00 0.00 1.52
3005 3202 6.316390 CCAGCAACTATTAGGACCAAACTTAG 59.684 42.308 0.00 0.00 0.00 2.18
3007 3204 5.010282 CCAGCAACTATTAGGACCAAACTT 58.990 41.667 0.00 0.00 0.00 2.66
3081 3280 7.194962 TGGTTTTACTTGTTAAAATGGTCGAC 58.805 34.615 7.13 7.13 40.88 4.20
3227 3429 4.640647 TGTATATCTCGTCTGCTTCACTGT 59.359 41.667 0.00 0.00 0.00 3.55
3237 3439 7.941919 TGCTACAGATTTTGTATATCTCGTCT 58.058 34.615 0.00 0.00 41.30 4.18
3322 3524 8.166726 AGATTCTACCTGAGGAAACTGAAAATT 58.833 33.333 4.99 0.00 44.43 1.82
3499 3707 3.567164 AGGACAGACAAAAACTGCTGATG 59.433 43.478 0.00 0.00 38.74 3.07
3511 3719 3.476552 CCACTGCTTTAAGGACAGACAA 58.523 45.455 13.28 0.00 35.38 3.18
3527 3735 1.730501 ACATGATCACTTCGCCACTG 58.269 50.000 0.00 0.00 0.00 3.66
3678 3886 2.759191 CATCATCTGATGTGGTACGGG 58.241 52.381 16.66 0.00 45.10 5.28
3690 3898 4.093850 TGAAACGAGTCAATGCATCATCTG 59.906 41.667 0.00 0.00 0.00 2.90
3705 3913 2.455674 TGGTCAGGTCATGAAACGAG 57.544 50.000 0.00 0.00 40.43 4.18
3709 3917 5.241403 ACAGTTATGGTCAGGTCATGAAA 57.759 39.130 0.00 0.00 40.43 2.69
3725 3934 4.155826 GCATGGCTGTGACATAAACAGTTA 59.844 41.667 5.55 0.00 45.58 2.24
3728 3937 2.751259 AGCATGGCTGTGACATAAACAG 59.249 45.455 0.00 0.00 46.39 3.16
3815 4024 8.539770 AGTCATATAAGCGTGAGAATATTTGG 57.460 34.615 0.00 0.00 0.00 3.28
3843 4052 8.197988 ACAACGGTATTCTAGTGAAAATGATC 57.802 34.615 0.00 0.00 35.63 2.92
3872 4081 4.510340 GCAGAATCCATCATTTGAATTGCC 59.490 41.667 0.00 0.00 0.00 4.52
3884 4093 1.396653 CCCCAACTGCAGAATCCATC 58.603 55.000 23.35 0.00 0.00 3.51
3962 4171 0.616395 TATTGACTGCCGGTCTCCCA 60.616 55.000 1.90 0.00 44.74 4.37
3990 4199 3.857052 CTGGGACGTTATTAGTGCTCAA 58.143 45.455 0.00 0.00 0.00 3.02
4068 4277 2.350522 CTTCGTCAGCTTATGGTTGCT 58.649 47.619 0.00 0.00 40.54 3.91
4145 4354 9.802039 TTAGGAACAAAACAATAATACTCACCT 57.198 29.630 0.00 0.00 0.00 4.00
4179 4394 0.671251 AACGGAAGCGCCATTCAAAA 59.329 45.000 2.29 0.00 35.94 2.44
4182 4406 0.039617 CAAAACGGAAGCGCCATTCA 60.040 50.000 2.29 0.00 35.94 2.57
4215 4440 4.576216 TTTGCATTACAGAAGCGGAAAA 57.424 36.364 0.00 0.00 0.00 2.29
4219 4444 3.763097 TGATTTGCATTACAGAAGCGG 57.237 42.857 0.00 0.00 0.00 5.52
4240 4466 2.299867 GTTGTTCCCTGCACAATGGAAT 59.700 45.455 5.76 0.00 40.11 3.01
4245 4471 2.108250 AGGTAGTTGTTCCCTGCACAAT 59.892 45.455 0.00 0.00 36.54 2.71
4256 4485 1.956477 CTTGGCAGCAAGGTAGTTGTT 59.044 47.619 0.00 0.00 38.55 2.83
4257 4486 1.609208 CTTGGCAGCAAGGTAGTTGT 58.391 50.000 0.00 0.00 38.55 3.32
4258 4487 0.883833 CCTTGGCAGCAAGGTAGTTG 59.116 55.000 12.28 0.00 44.99 3.16
4273 4502 1.445095 CCGAGGGATCTGCTCCTTG 59.555 63.158 0.00 0.00 44.28 3.61
4495 4727 3.531207 CTCTCGCCCGGCATCTCA 61.531 66.667 10.77 0.00 0.00 3.27
4646 4903 3.288092 GAAAGGGAGACACAAACTTGGT 58.712 45.455 0.00 0.00 0.00 3.67
4668 4925 9.522804 TTATTTTCAAATCACAACACCAACTAC 57.477 29.630 0.00 0.00 0.00 2.73
4670 4927 9.442047 TTTTATTTTCAAATCACAACACCAACT 57.558 25.926 0.00 0.00 0.00 3.16
4674 4931 7.351981 GCCTTTTATTTTCAAATCACAACACC 58.648 34.615 0.00 0.00 0.00 4.16
4685 4943 4.526650 GGGAGAGTGGCCTTTTATTTTCAA 59.473 41.667 3.32 0.00 0.00 2.69
4686 4944 4.086457 GGGAGAGTGGCCTTTTATTTTCA 58.914 43.478 3.32 0.00 0.00 2.69
4687 4945 3.447586 GGGGAGAGTGGCCTTTTATTTTC 59.552 47.826 3.32 0.00 0.00 2.29
4688 4946 3.441101 GGGGAGAGTGGCCTTTTATTTT 58.559 45.455 3.32 0.00 0.00 1.82
4692 4950 1.559065 CGGGGGAGAGTGGCCTTTTA 61.559 60.000 3.32 0.00 0.00 1.52
4693 4951 2.907179 CGGGGGAGAGTGGCCTTTT 61.907 63.158 3.32 0.00 0.00 2.27
4740 5015 4.733523 GCTCAAATCAACAAGTTCCACGTT 60.734 41.667 0.00 0.00 0.00 3.99
4741 5016 3.243068 GCTCAAATCAACAAGTTCCACGT 60.243 43.478 0.00 0.00 0.00 4.49
4742 5017 3.003689 AGCTCAAATCAACAAGTTCCACG 59.996 43.478 0.00 0.00 0.00 4.94
4746 5021 6.035843 TGACAAAGCTCAAATCAACAAGTTC 58.964 36.000 0.00 0.00 0.00 3.01
4747 5022 5.964758 TGACAAAGCTCAAATCAACAAGTT 58.035 33.333 0.00 0.00 0.00 2.66
4748 5023 5.357878 TCTGACAAAGCTCAAATCAACAAGT 59.642 36.000 0.00 0.00 0.00 3.16
4750 5025 5.833406 TCTGACAAAGCTCAAATCAACAA 57.167 34.783 0.00 0.00 0.00 2.83
4752 5027 5.172053 CGTTTCTGACAAAGCTCAAATCAAC 59.828 40.000 0.00 0.00 0.00 3.18
4754 5029 4.335315 ACGTTTCTGACAAAGCTCAAATCA 59.665 37.500 0.00 0.00 0.00 2.57
4755 5030 4.672413 CACGTTTCTGACAAAGCTCAAATC 59.328 41.667 0.00 0.00 0.00 2.17
4756 5031 4.498009 CCACGTTTCTGACAAAGCTCAAAT 60.498 41.667 0.00 0.00 0.00 2.32
4759 5034 1.939934 CCACGTTTCTGACAAAGCTCA 59.060 47.619 0.00 0.00 0.00 4.26
4761 5036 2.325583 TCCACGTTTCTGACAAAGCT 57.674 45.000 0.00 0.00 0.00 3.74
4762 5037 2.548057 TCATCCACGTTTCTGACAAAGC 59.452 45.455 0.00 0.00 0.00 3.51
4763 5038 4.452114 TCATCATCCACGTTTCTGACAAAG 59.548 41.667 0.00 0.00 0.00 2.77
4766 5041 3.676291 TCATCATCCACGTTTCTGACA 57.324 42.857 0.00 0.00 0.00 3.58
4768 5043 4.206477 ACATCATCATCCACGTTTCTGA 57.794 40.909 0.00 0.00 0.00 3.27
4769 5044 5.559608 GCATACATCATCATCCACGTTTCTG 60.560 44.000 0.00 0.00 0.00 3.02
4788 5067 3.361644 CGCACACAAATCACAAAGCATAC 59.638 43.478 0.00 0.00 0.00 2.39
4789 5068 3.251972 TCGCACACAAATCACAAAGCATA 59.748 39.130 0.00 0.00 0.00 3.14
4817 5099 0.298707 CATGAACAAGCGATCGTCGG 59.701 55.000 17.81 8.62 40.84 4.79
4818 5100 0.992072 ACATGAACAAGCGATCGTCG 59.008 50.000 17.81 7.94 43.89 5.12
4819 5101 1.992667 TCACATGAACAAGCGATCGTC 59.007 47.619 17.81 9.17 0.00 4.20
4831 5113 1.337728 CGGCTACACAGGTCACATGAA 60.338 52.381 0.00 0.00 0.00 2.57
4832 5114 0.246360 CGGCTACACAGGTCACATGA 59.754 55.000 0.00 0.00 0.00 3.07
4835 5117 2.207229 AGCGGCTACACAGGTCACA 61.207 57.895 0.00 0.00 0.00 3.58
4836 5118 1.738099 CAGCGGCTACACAGGTCAC 60.738 63.158 0.26 0.00 0.00 3.67
4838 5120 0.807667 CATCAGCGGCTACACAGGTC 60.808 60.000 0.26 0.00 0.00 3.85
4840 5122 0.459899 TACATCAGCGGCTACACAGG 59.540 55.000 0.26 0.00 0.00 4.00
4841 5123 2.398498 GATACATCAGCGGCTACACAG 58.602 52.381 0.26 0.00 0.00 3.66
4846 5138 0.313987 CCACGATACATCAGCGGCTA 59.686 55.000 0.26 0.00 41.38 3.93
4851 5143 3.458189 AGTTTAGCCACGATACATCAGC 58.542 45.455 0.00 0.00 0.00 4.26
4859 5151 5.705609 AAATCAACAAGTTTAGCCACGAT 57.294 34.783 0.00 0.00 0.00 3.73
4881 5173 5.048364 CCAAATGGATCAACGACCAAAGTAA 60.048 40.000 0.00 0.00 39.69 2.24
4883 5175 3.255642 CCAAATGGATCAACGACCAAAGT 59.744 43.478 0.00 0.00 39.69 2.66
4886 5178 3.147553 TCCAAATGGATCAACGACCAA 57.852 42.857 0.00 0.00 39.78 3.67
4903 5195 1.878070 CGAGCAAGCAAAGCATCCA 59.122 52.632 0.00 0.00 0.00 3.41
4932 5225 2.704108 GCAGATGCAGGAGGACATG 58.296 57.895 0.00 0.00 41.59 3.21
4967 5265 0.716108 CAGCAACCGCGTAAGAGAAG 59.284 55.000 4.92 0.00 45.49 2.85
4968 5266 1.289109 GCAGCAACCGCGTAAGAGAA 61.289 55.000 4.92 0.00 45.49 2.87
4969 5267 1.736645 GCAGCAACCGCGTAAGAGA 60.737 57.895 4.92 0.00 45.49 3.10
4970 5268 1.291877 AAGCAGCAACCGCGTAAGAG 61.292 55.000 4.92 0.00 45.49 2.85
4971 5269 1.289109 GAAGCAGCAACCGCGTAAGA 61.289 55.000 4.92 0.00 45.49 2.10
4972 5270 1.132640 GAAGCAGCAACCGCGTAAG 59.867 57.895 4.92 0.00 45.49 2.34
4993 5291 6.996282 CCCACAGGAGTAAATAAAATACGGAT 59.004 38.462 0.00 0.00 33.47 4.18
5004 5302 4.844655 AGAGTAACACCCACAGGAGTAAAT 59.155 41.667 0.00 0.00 35.69 1.40
5031 5332 7.260570 GCAGCATCTGTCTAGTACGGAGTAG 62.261 52.000 2.77 2.77 46.66 2.57
5032 5333 4.127907 CAGCATCTGTCTAGTACGGAGTA 58.872 47.826 8.97 0.00 46.66 2.59
5033 5334 2.946329 CAGCATCTGTCTAGTACGGAGT 59.054 50.000 8.97 0.00 46.66 3.85
5034 5335 2.287308 GCAGCATCTGTCTAGTACGGAG 60.287 54.545 8.97 0.00 46.66 4.63
5036 5337 1.598183 CGCAGCATCTGTCTAGTACGG 60.598 57.143 0.00 0.00 33.43 4.02
5038 5339 2.614520 TCTCGCAGCATCTGTCTAGTAC 59.385 50.000 0.00 0.00 33.43 2.73
5039 5340 2.875317 CTCTCGCAGCATCTGTCTAGTA 59.125 50.000 0.00 0.00 33.43 1.82
5040 5341 1.675483 CTCTCGCAGCATCTGTCTAGT 59.325 52.381 0.00 0.00 33.43 2.57
5041 5342 2.404265 CTCTCGCAGCATCTGTCTAG 57.596 55.000 0.00 0.00 33.43 2.43
5073 5374 1.469917 AATAATACGTCGCGTCACGG 58.530 50.000 21.96 6.74 44.41 4.94
5079 5380 4.199575 GCAACTGAAAAATAATACGTCGCG 59.800 41.667 0.00 0.00 0.00 5.87
5081 5382 5.543716 TCGCAACTGAAAAATAATACGTCG 58.456 37.500 0.00 0.00 0.00 5.12
5090 5391 3.185797 GTCGGTACTCGCAACTGAAAAAT 59.814 43.478 0.00 0.00 39.05 1.82
5111 5432 4.129737 CATCACCCCTCGCGTCGT 62.130 66.667 5.77 0.00 0.00 4.34
5200 5536 2.743126 TTCACTGCTGCTGCTCTGGG 62.743 60.000 17.00 8.20 40.48 4.45
5201 5537 0.887836 TTTCACTGCTGCTGCTCTGG 60.888 55.000 17.00 6.95 40.48 3.86
5205 5541 1.071385 ACTAGTTTCACTGCTGCTGCT 59.929 47.619 17.00 0.00 40.48 4.24
5210 5546 4.852104 CGTACTGTACTAGTTTCACTGCTG 59.148 45.833 15.35 0.00 40.89 4.41
5212 5548 4.791974 ACGTACTGTACTAGTTTCACTGC 58.208 43.478 15.35 0.00 40.89 4.40
5213 5549 6.541086 CCTACGTACTGTACTAGTTTCACTG 58.459 44.000 15.35 0.00 40.89 3.66
5215 5551 5.327891 GCCTACGTACTGTACTAGTTTCAC 58.672 45.833 15.35 0.00 40.89 3.18
5217 5553 4.637977 AGGCCTACGTACTGTACTAGTTTC 59.362 45.833 1.29 0.00 40.89 2.78
5218 5554 4.593956 AGGCCTACGTACTGTACTAGTTT 58.406 43.478 1.29 0.00 40.89 2.66
5219 5555 4.227864 AGGCCTACGTACTGTACTAGTT 57.772 45.455 1.29 0.97 40.89 2.24
5228 5564 0.604578 TCGCAAAAGGCCTACGTACT 59.395 50.000 5.16 0.00 40.31 2.73
5278 5620 1.385631 ATGGATGGAGGCTCAGGCT 60.386 57.895 17.69 0.00 42.48 4.58
5279 5621 1.072852 GATGGATGGAGGCTCAGGC 59.927 63.158 17.69 4.02 37.82 4.85
5281 5623 1.138568 AAGGATGGATGGAGGCTCAG 58.861 55.000 17.69 0.00 0.00 3.35
5282 5624 1.492176 GAAAGGATGGATGGAGGCTCA 59.508 52.381 17.69 2.84 0.00 4.26
5283 5625 1.542108 CGAAAGGATGGATGGAGGCTC 60.542 57.143 5.78 5.78 0.00 4.70
5284 5626 0.471617 CGAAAGGATGGATGGAGGCT 59.528 55.000 0.00 0.00 0.00 4.58
5285 5627 1.169034 GCGAAAGGATGGATGGAGGC 61.169 60.000 0.00 0.00 0.00 4.70
5309 5651 0.463833 CTGGGGAATGCCTACGAACC 60.464 60.000 0.00 0.00 0.00 3.62
5311 5653 1.140852 CATCTGGGGAATGCCTACGAA 59.859 52.381 0.00 0.00 0.00 3.85
5312 5654 0.758734 CATCTGGGGAATGCCTACGA 59.241 55.000 0.00 0.00 0.00 3.43
5313 5655 0.250467 CCATCTGGGGAATGCCTACG 60.250 60.000 0.00 0.00 0.00 3.51
5315 5657 1.140312 GACCATCTGGGGAATGCCTA 58.860 55.000 0.54 0.00 42.91 3.93
5317 5659 0.179006 GAGACCATCTGGGGAATGCC 60.179 60.000 0.54 0.00 42.91 4.40
5318 5660 0.548031 TGAGACCATCTGGGGAATGC 59.452 55.000 0.54 0.00 42.91 3.56
5321 5663 0.547471 TGCTGAGACCATCTGGGGAA 60.547 55.000 0.54 0.00 42.91 3.97
5322 5664 1.080907 TGCTGAGACCATCTGGGGA 59.919 57.895 0.54 0.00 42.91 4.81
5323 5665 1.222936 GTGCTGAGACCATCTGGGG 59.777 63.158 0.54 0.00 42.91 4.96
5324 5666 1.222936 GGTGCTGAGACCATCTGGG 59.777 63.158 0.54 0.00 44.81 4.45
5325 5667 0.325933 TTGGTGCTGAGACCATCTGG 59.674 55.000 4.94 0.00 45.64 3.86
5377 5720 2.293934 GATGATGGGGGAGGGGGA 59.706 66.667 0.00 0.00 0.00 4.81
5385 5728 0.179037 AGATGCACGTGATGATGGGG 60.179 55.000 22.23 0.00 0.00 4.96
5386 5729 1.600957 GAAGATGCACGTGATGATGGG 59.399 52.381 22.23 0.00 0.00 4.00
5387 5730 2.558378 AGAAGATGCACGTGATGATGG 58.442 47.619 22.23 0.00 0.00 3.51
5388 5731 3.869832 AGAAGAAGATGCACGTGATGATG 59.130 43.478 22.23 0.00 0.00 3.07
5389 5732 4.134379 AGAAGAAGATGCACGTGATGAT 57.866 40.909 22.23 7.33 0.00 2.45
5445 5792 1.148310 CGCAGGGTAGTGTGAACAAG 58.852 55.000 0.00 0.00 0.00 3.16
5478 5831 7.161773 TGGATTCAAAGCTGGAAAAGAATAG 57.838 36.000 5.30 0.00 0.00 1.73
5513 5866 4.081254 TGCAAATTAGTATTTGGCATGCCA 60.081 37.500 35.59 35.59 46.93 4.92


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

AutoCloner maintained by Alex Coulton.