Multiple sequence alignment - TraesCS7D01G143300

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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 TraesCS7D01G143300 chr7D 100.000 4970 0 0 1 4970 91657700 91662669 0.000000e+00 9178.0
1 TraesCS7D01G143300 chr7D 88.258 792 82 7 1 784 395845025 395844237 0.000000e+00 937.0
2 TraesCS7D01G143300 chr7A 94.649 1850 63 11 876 2694 93131927 93133771 0.000000e+00 2835.0
3 TraesCS7D01G143300 chr7A 94.557 1525 71 7 2692 4207 93133885 93135406 0.000000e+00 2346.0
4 TraesCS7D01G143300 chr7A 93.333 105 4 1 2719 2820 93134011 93134115 8.620000e-33 152.0
5 TraesCS7D01G143300 chr7B 91.288 1894 104 24 674 2522 43553673 43551796 0.000000e+00 2527.0
6 TraesCS7D01G143300 chr7B 89.940 1332 92 17 2911 4210 43551491 43550170 0.000000e+00 1679.0
7 TraesCS7D01G143300 chr7B 87.042 409 40 8 3974 4377 43528076 43527676 2.730000e-122 449.0
8 TraesCS7D01G143300 chr7B 87.773 229 24 4 4710 4937 43549448 43549223 1.060000e-66 265.0
9 TraesCS7D01G143300 chr7B 88.550 131 15 0 2532 2662 43551734 43551604 5.150000e-35 159.0
10 TraesCS7D01G143300 chr7B 85.586 111 5 3 2692 2791 43551606 43551496 6.800000e-19 106.0
11 TraesCS7D01G143300 chr7B 90.698 43 2 2 790 832 560508117 560508077 6.950000e-04 56.5
12 TraesCS7D01G143300 chr6D 89.899 792 67 9 1 784 246055531 246054745 0.000000e+00 1007.0
13 TraesCS7D01G143300 chr5D 89.367 790 78 4 1 784 206609185 206608396 0.000000e+00 989.0
14 TraesCS7D01G143300 chr5D 90.244 41 2 2 791 831 408650770 408650732 9.000000e-03 52.8
15 TraesCS7D01G143300 chr3D 89.413 784 77 4 1 778 208982600 208983383 0.000000e+00 983.0
16 TraesCS7D01G143300 chr3D 89.796 49 0 4 786 833 57193923 57193879 1.930000e-04 58.4
17 TraesCS7D01G143300 chrUn 88.805 795 74 9 2 784 93311541 93310750 0.000000e+00 961.0
18 TraesCS7D01G143300 chr4A 88.691 787 83 3 1 781 76949080 76949866 0.000000e+00 955.0
19 TraesCS7D01G143300 chr2D 88.539 794 77 8 1 784 424749611 424750400 0.000000e+00 950.0
20 TraesCS7D01G143300 chr6B 88.161 794 74 14 1 784 672002425 672001642 0.000000e+00 928.0
21 TraesCS7D01G143300 chr1B 88.005 792 86 7 1 784 495524354 495525144 0.000000e+00 928.0


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 TraesCS7D01G143300 chr7D 91657700 91662669 4969 False 9178.000000 9178 100.000000 1 4970 1 chr7D.!!$F1 4969
1 TraesCS7D01G143300 chr7D 395844237 395845025 788 True 937.000000 937 88.258000 1 784 1 chr7D.!!$R1 783
2 TraesCS7D01G143300 chr7A 93131927 93135406 3479 False 1777.666667 2835 94.179667 876 4207 3 chr7A.!!$F1 3331
3 TraesCS7D01G143300 chr7B 43549223 43553673 4450 True 947.200000 2527 88.627400 674 4937 5 chr7B.!!$R3 4263
4 TraesCS7D01G143300 chr6D 246054745 246055531 786 True 1007.000000 1007 89.899000 1 784 1 chr6D.!!$R1 783
5 TraesCS7D01G143300 chr5D 206608396 206609185 789 True 989.000000 989 89.367000 1 784 1 chr5D.!!$R1 783
6 TraesCS7D01G143300 chr3D 208982600 208983383 783 False 983.000000 983 89.413000 1 778 1 chr3D.!!$F1 777
7 TraesCS7D01G143300 chrUn 93310750 93311541 791 True 961.000000 961 88.805000 2 784 1 chrUn.!!$R1 782
8 TraesCS7D01G143300 chr4A 76949080 76949866 786 False 955.000000 955 88.691000 1 781 1 chr4A.!!$F1 780
9 TraesCS7D01G143300 chr2D 424749611 424750400 789 False 950.000000 950 88.539000 1 784 1 chr2D.!!$F1 783
10 TraesCS7D01G143300 chr6B 672001642 672002425 783 True 928.000000 928 88.161000 1 784 1 chr6B.!!$R1 783
11 TraesCS7D01G143300 chr1B 495524354 495525144 790 False 928.000000 928 88.005000 1 784 1 chr1B.!!$F1 783

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
473 484 0.031994 AAACTTGCAACACCGCCATC 59.968 50.000 0.00 0.00 0.00 3.51 F
886 905 0.399949 ACCTTCCACTGACAGGGTGA 60.400 55.000 7.51 0.00 36.89 4.02 F
1349 1371 1.064758 CCCCTCATTCATTTCGTGGGA 60.065 52.381 0.00 0.00 35.40 4.37 F
1590 1617 1.069358 GGGTAGCAGTGCAGTATCTCC 59.931 57.143 19.20 8.06 0.00 3.71 F
1874 1905 1.672881 GCATAAGTCATCACCACTGCC 59.327 52.381 0.00 0.00 0.00 4.85 F
3639 3914 1.340017 GGTGCAGCCTGAACATTCCTA 60.340 52.381 4.94 0.00 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 1341 0.398318 GAATGAGGGGAGGGGAATCG 59.602 60.000 0.00 0.0 0.00 3.34 R
2512 2581 0.240945 GCTTGTTACGTGCCAATGCT 59.759 50.000 0.00 0.0 38.71 3.79 R
2888 3136 3.450457 AGCTAGTTCAGATGGAGTTCAGG 59.550 47.826 0.00 0.0 0.00 3.86 R
3489 3764 3.903360 ACTCAAGAAGACACTAGAACGC 58.097 45.455 0.00 0.0 0.00 4.84 R
3771 4047 3.428063 AGGAGGGAATGATCTTCCTGA 57.572 47.619 17.88 0.0 37.85 3.86 R
4787 5332 0.734309 GCATGCATCAATGACCACGA 59.266 50.000 14.21 0.0 0.00 4.35 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
37 41 7.170320 GCTACTGTTACAACTGCTACAAAACTA 59.830 37.037 0.00 0.00 0.00 2.24
75 79 1.341531 ACCGCTGCTATCATCACTACC 59.658 52.381 0.00 0.00 0.00 3.18
77 81 2.224042 CCGCTGCTATCATCACTACCAA 60.224 50.000 0.00 0.00 0.00 3.67
142 147 8.547481 TGTAGATATTTAATCTCCAGGTGTGA 57.453 34.615 0.00 0.00 0.00 3.58
248 254 3.092334 ACCCTCAAAAATTGTTGCGAC 57.908 42.857 3.24 0.00 0.00 5.19
280 288 5.535030 ACTTGTGGGTTATCAAGACCTTTTC 59.465 40.000 11.07 0.00 42.22 2.29
287 295 2.978156 TCAAGACCTTTTCCTGGCAT 57.022 45.000 0.00 0.00 0.00 4.40
468 479 3.684103 TTGAGTAAACTTGCAACACCG 57.316 42.857 0.00 0.00 0.00 4.94
472 483 1.000717 GTAAACTTGCAACACCGCCAT 60.001 47.619 0.00 0.00 0.00 4.40
473 484 0.031994 AAACTTGCAACACCGCCATC 59.968 50.000 0.00 0.00 0.00 3.51
484 495 3.820557 ACACCGCCATCTGCTATTAATT 58.179 40.909 0.00 0.00 38.05 1.40
485 496 4.207165 ACACCGCCATCTGCTATTAATTT 58.793 39.130 0.00 0.00 38.05 1.82
515 526 8.687292 ATGTCACAAGTTATTGATGATGCTAT 57.313 30.769 0.00 0.00 38.83 2.97
518 529 9.229784 GTCACAAGTTATTGATGATGCTATTTG 57.770 33.333 0.00 0.00 38.83 2.32
550 564 8.374743 TGAATAATGCTTATGATGCTAGTACCA 58.625 33.333 0.00 0.00 0.00 3.25
568 582 6.359804 AGTACCATGCTTGATGATAATGTGT 58.640 36.000 0.22 0.00 33.31 3.72
599 613 7.068593 AGGTGAATTTCTTGATGAACAACTTGA 59.931 33.333 0.00 0.00 33.88 3.02
612 626 8.715191 ATGAACAACTTGATAGAGCTAAAGAG 57.285 34.615 0.00 0.00 0.00 2.85
614 628 8.367911 TGAACAACTTGATAGAGCTAAAGAGAA 58.632 33.333 0.00 0.00 0.00 2.87
647 663 8.303156 TGTTGAAACTGATGAAGTCTTTGAAAA 58.697 29.630 0.00 0.00 38.56 2.29
754 771 5.483811 AGGTAGCTAGAGACTTTTTGCTTC 58.516 41.667 0.00 0.00 32.72 3.86
763 780 7.823745 AGAGACTTTTTGCTTCCAAAGATAA 57.176 32.000 0.00 0.00 41.58 1.75
874 893 1.207089 CTCGGCATTCTGTACCTTCCA 59.793 52.381 0.00 0.00 0.00 3.53
886 905 0.399949 ACCTTCCACTGACAGGGTGA 60.400 55.000 7.51 0.00 36.89 4.02
1029 1048 1.064946 GCTCGAGGTGGAGATCGTG 59.935 63.158 15.58 0.00 39.86 4.35
1205 1227 3.755628 GTCGCTGCTGTCCCGGTA 61.756 66.667 0.00 0.00 0.00 4.02
1207 1229 4.063967 CGCTGCTGTCCCGGTACA 62.064 66.667 0.00 0.00 0.00 2.90
1309 1331 1.497991 CCGTTCGTGTCTGATGTGTT 58.502 50.000 0.00 0.00 0.00 3.32
1315 1337 2.002586 CGTGTCTGATGTGTTCCCATC 58.997 52.381 0.00 0.00 41.32 3.51
1319 1341 1.207089 TCTGATGTGTTCCCATCGACC 59.793 52.381 0.00 0.00 43.39 4.79
1349 1371 1.064758 CCCCTCATTCATTTCGTGGGA 60.065 52.381 0.00 0.00 35.40 4.37
1350 1372 2.017049 CCCTCATTCATTTCGTGGGAC 58.983 52.381 0.00 0.00 35.40 4.46
1352 1374 2.939103 CCTCATTCATTTCGTGGGACTC 59.061 50.000 0.00 0.00 0.00 3.36
1359 1381 1.878953 TTTCGTGGGACTCTTCTTGC 58.121 50.000 0.00 0.00 0.00 4.01
1361 1383 2.383527 CGTGGGACTCTTCTTGCGC 61.384 63.158 0.00 0.00 0.00 6.09
1375 1397 4.664677 GCGCGACAGGAGTGGTGT 62.665 66.667 12.10 0.00 36.49 4.16
1396 1418 3.799420 GTGATAAGCAGATGGAGTTCGTC 59.201 47.826 0.00 0.00 0.00 4.20
1559 1586 6.718912 TGAAACCCAACACTGAATGATAATGA 59.281 34.615 0.00 0.00 0.00 2.57
1590 1617 1.069358 GGGTAGCAGTGCAGTATCTCC 59.931 57.143 19.20 8.06 0.00 3.71
1598 1625 3.620374 CAGTGCAGTATCTCCATGTGTTC 59.380 47.826 0.00 0.00 0.00 3.18
1655 1682 5.741011 ACAAATCGCTCCAGGTTAAGAATA 58.259 37.500 0.00 0.00 0.00 1.75
1874 1905 1.672881 GCATAAGTCATCACCACTGCC 59.327 52.381 0.00 0.00 0.00 4.85
1960 2008 9.023967 GGTTGGAGAATGAAATCGATTTAAATG 57.976 33.333 22.78 0.00 0.00 2.32
2171 2235 5.862924 TTAAACTTGCAGCTCTGTATCAC 57.137 39.130 0.00 0.00 0.00 3.06
2223 2289 3.326297 GGAGGAAGTCTGGAATGGATAGG 59.674 52.174 0.00 0.00 0.00 2.57
2491 2560 2.477245 ACCATTAAAAATGGGGAGGCC 58.523 47.619 19.92 0.00 43.32 5.19
2512 2581 2.355444 CGGCAAATCATCACATGCTGTA 59.645 45.455 0.00 0.00 39.69 2.74
2841 3089 5.078256 AGTTATGGTATCTCCTTCCTACGG 58.922 45.833 0.00 0.00 37.07 4.02
2864 3112 7.441458 ACGGCAGGATTTATCTTTCAGTTATAC 59.559 37.037 0.00 0.00 0.00 1.47
3061 3326 7.959651 CAGATTTATTATTATGTGGAGCTTCGC 59.040 37.037 0.00 0.00 0.00 4.70
3556 3831 4.344104 ACTTTCGGGGATGTGATGAAATT 58.656 39.130 0.00 0.00 0.00 1.82
3639 3914 1.340017 GGTGCAGCCTGAACATTCCTA 60.340 52.381 4.94 0.00 0.00 2.94
3665 3940 6.495872 ACCTGTAGTGATTACTGAACACCTAA 59.504 38.462 0.00 0.00 37.78 2.69
3679 3954 7.037586 ACTGAACACCTAATATCTGAAAAGGGA 60.038 37.037 0.00 0.00 0.00 4.20
3708 3983 4.231439 GTTAATACCGCCAGTTTGTTTGG 58.769 43.478 0.00 0.00 38.78 3.28
3751 4027 9.503399 AAACTTATAACCTACTTCAGTTTCCTG 57.497 33.333 0.00 0.00 40.25 3.86
3759 4035 8.147244 ACCTACTTCAGTTTCCTGTATATTGT 57.853 34.615 0.00 0.00 39.82 2.71
3789 4065 4.769345 ACTTCAGGAAGATCATTCCCTC 57.231 45.455 15.51 0.00 40.79 4.30
3852 4128 2.095461 GGTCAAATCCAAGAAGCCCTC 58.905 52.381 0.00 0.00 0.00 4.30
3854 4130 2.751806 GTCAAATCCAAGAAGCCCTCAG 59.248 50.000 0.00 0.00 0.00 3.35
3948 4224 0.742990 CGCCGAGTTGCCCAAAGATA 60.743 55.000 0.00 0.00 0.00 1.98
3949 4225 1.017387 GCCGAGTTGCCCAAAGATAG 58.983 55.000 0.00 0.00 0.00 2.08
3977 4253 4.916983 CCTCAAGGTGTTGACATTCAAA 57.083 40.909 0.00 0.00 38.22 2.69
3991 4267 5.021033 ACATTCAAAGTTGCAAATGGACA 57.979 34.783 0.00 0.00 0.00 4.02
3997 4273 1.884579 AGTTGCAAATGGACAGCTCTG 59.115 47.619 0.00 0.00 0.00 3.35
4005 4282 0.550914 TGGACAGCTCTGTTTGGGTT 59.449 50.000 3.83 0.00 45.05 4.11
4012 4289 4.246458 CAGCTCTGTTTGGGTTAGTAGAC 58.754 47.826 0.00 0.00 0.00 2.59
4013 4290 4.021016 CAGCTCTGTTTGGGTTAGTAGACT 60.021 45.833 0.00 0.00 0.00 3.24
4018 4297 3.073356 TGTTTGGGTTAGTAGACTTGGGG 59.927 47.826 0.00 0.00 0.00 4.96
4020 4299 3.278987 TGGGTTAGTAGACTTGGGGAA 57.721 47.619 0.00 0.00 0.00 3.97
4032 4313 4.584743 AGACTTGGGGAATTTTTCTGACAC 59.415 41.667 0.00 0.00 0.00 3.67
4041 4322 5.473504 GGAATTTTTCTGACACTAGGCTGAA 59.526 40.000 0.00 0.00 0.00 3.02
4051 4332 1.002087 ACTAGGCTGAAGAACCAACCG 59.998 52.381 0.00 0.00 0.00 4.44
4052 4333 1.002087 CTAGGCTGAAGAACCAACCGT 59.998 52.381 0.00 0.00 0.00 4.83
4066 4347 3.386402 ACCAACCGTTTTGATGAACCATT 59.614 39.130 0.00 0.00 0.00 3.16
4095 4376 3.064900 AGTGCCTCCATCTGTTCTTTC 57.935 47.619 0.00 0.00 0.00 2.62
4113 4394 5.256474 TCTTTCCTTCTTTCCATGGCTAAG 58.744 41.667 6.96 13.00 0.00 2.18
4119 4400 7.410174 TCCTTCTTTCCATGGCTAAGATTTAA 58.590 34.615 22.21 11.61 0.00 1.52
4120 4401 7.339466 TCCTTCTTTCCATGGCTAAGATTTAAC 59.661 37.037 22.21 0.00 0.00 2.01
4123 4404 7.402054 TCTTTCCATGGCTAAGATTTAACTCA 58.598 34.615 19.39 1.67 0.00 3.41
4124 4405 7.888021 TCTTTCCATGGCTAAGATTTAACTCAA 59.112 33.333 19.39 0.00 0.00 3.02
4129 4410 7.756722 CCATGGCTAAGATTTAACTCAAAAGTG 59.243 37.037 0.00 0.00 35.36 3.16
4132 4413 9.077885 TGGCTAAGATTTAACTCAAAAGTGAAT 57.922 29.630 0.00 0.00 35.36 2.57
4140 4421 4.937201 ACTCAAAAGTGAATTTCCACCC 57.063 40.909 0.00 0.00 37.76 4.61
4157 4438 4.471747 TCCACCCTATGTAGCATTGTAACA 59.528 41.667 0.00 0.00 0.00 2.41
4163 4444 7.017155 ACCCTATGTAGCATTGTAACATGGATA 59.983 37.037 14.18 0.00 34.95 2.59
4191 4472 5.481105 TGATTGGCAAGTGAATTTCATTCC 58.519 37.500 5.96 2.97 38.50 3.01
4198 4479 6.446318 GCAAGTGAATTTCATTCCTGTTGTA 58.554 36.000 1.78 0.00 38.50 2.41
4207 4488 5.304686 TCATTCCTGTTGTATGTATCCCC 57.695 43.478 0.00 0.00 0.00 4.81
4208 4489 4.724293 TCATTCCTGTTGTATGTATCCCCA 59.276 41.667 0.00 0.00 0.00 4.96
4209 4490 5.372363 TCATTCCTGTTGTATGTATCCCCAT 59.628 40.000 0.00 0.00 0.00 4.00
4210 4491 4.974645 TCCTGTTGTATGTATCCCCATC 57.025 45.455 0.00 0.00 0.00 3.51
4211 4492 3.323691 TCCTGTTGTATGTATCCCCATCG 59.676 47.826 0.00 0.00 0.00 3.84
4212 4493 3.557054 CCTGTTGTATGTATCCCCATCGG 60.557 52.174 0.00 0.00 0.00 4.18
4213 4494 3.042682 TGTTGTATGTATCCCCATCGGT 58.957 45.455 0.00 0.00 0.00 4.69
4214 4495 3.456644 TGTTGTATGTATCCCCATCGGTT 59.543 43.478 0.00 0.00 0.00 4.44
4215 4496 4.062991 GTTGTATGTATCCCCATCGGTTC 58.937 47.826 0.00 0.00 0.00 3.62
4216 4497 3.583228 TGTATGTATCCCCATCGGTTCT 58.417 45.455 0.00 0.00 0.00 3.01
4217 4498 3.971305 TGTATGTATCCCCATCGGTTCTT 59.029 43.478 0.00 0.00 0.00 2.52
4218 4499 4.410883 TGTATGTATCCCCATCGGTTCTTT 59.589 41.667 0.00 0.00 0.00 2.52
4219 4500 4.519906 ATGTATCCCCATCGGTTCTTTT 57.480 40.909 0.00 0.00 0.00 2.27
4220 4501 4.310022 TGTATCCCCATCGGTTCTTTTT 57.690 40.909 0.00 0.00 0.00 1.94
4221 4502 4.266714 TGTATCCCCATCGGTTCTTTTTC 58.733 43.478 0.00 0.00 0.00 2.29
4222 4503 2.209690 TCCCCATCGGTTCTTTTTCC 57.790 50.000 0.00 0.00 0.00 3.13
4223 4504 1.425831 TCCCCATCGGTTCTTTTTCCA 59.574 47.619 0.00 0.00 0.00 3.53
4224 4505 2.158445 TCCCCATCGGTTCTTTTTCCAA 60.158 45.455 0.00 0.00 0.00 3.53
4225 4506 2.029380 CCCCATCGGTTCTTTTTCCAAC 60.029 50.000 0.00 0.00 0.00 3.77
4226 4507 2.625790 CCCATCGGTTCTTTTTCCAACA 59.374 45.455 0.00 0.00 0.00 3.33
4227 4508 3.068873 CCCATCGGTTCTTTTTCCAACAA 59.931 43.478 0.00 0.00 0.00 2.83
4228 4509 4.442192 CCCATCGGTTCTTTTTCCAACAAA 60.442 41.667 0.00 0.00 0.00 2.83
4229 4510 4.744631 CCATCGGTTCTTTTTCCAACAAAG 59.255 41.667 0.00 0.00 33.22 2.77
4230 4511 5.451242 CCATCGGTTCTTTTTCCAACAAAGA 60.451 40.000 0.00 0.00 38.27 2.52
4231 4512 5.845391 TCGGTTCTTTTTCCAACAAAGAT 57.155 34.783 0.00 0.00 39.46 2.40
4232 4513 5.587289 TCGGTTCTTTTTCCAACAAAGATG 58.413 37.500 0.00 0.00 39.46 2.90
4233 4514 5.126384 TCGGTTCTTTTTCCAACAAAGATGT 59.874 36.000 0.00 0.00 39.46 3.06
4234 4515 6.319152 TCGGTTCTTTTTCCAACAAAGATGTA 59.681 34.615 0.00 0.00 39.46 2.29
4235 4516 6.975772 CGGTTCTTTTTCCAACAAAGATGTAA 59.024 34.615 0.00 0.00 39.46 2.41
4236 4517 7.489757 CGGTTCTTTTTCCAACAAAGATGTAAA 59.510 33.333 0.00 0.00 39.46 2.01
4244 4525 5.011533 TCCAACAAAGATGTAAACCCAATGG 59.988 40.000 0.00 0.00 39.40 3.16
4246 4527 6.295802 CCAACAAAGATGTAAACCCAATGGAT 60.296 38.462 0.00 0.00 39.40 3.41
4250 4531 8.875168 ACAAAGATGTAAACCCAATGGATAAAA 58.125 29.630 0.00 0.00 38.24 1.52
4270 4551 5.984695 AAATAACTTCCTGGAGGCTTTTC 57.015 39.130 5.63 0.00 34.44 2.29
4276 4557 3.634397 TCCTGGAGGCTTTTCTATGTG 57.366 47.619 0.00 0.00 34.44 3.21
4278 4559 2.019984 CTGGAGGCTTTTCTATGTGGC 58.980 52.381 0.00 0.00 0.00 5.01
4281 4562 2.356135 GAGGCTTTTCTATGTGGCGAA 58.644 47.619 0.00 0.00 0.00 4.70
4284 4565 3.378427 AGGCTTTTCTATGTGGCGAATTC 59.622 43.478 0.00 0.00 0.00 2.17
4285 4566 3.128589 GGCTTTTCTATGTGGCGAATTCA 59.871 43.478 6.22 0.00 0.00 2.57
4287 4568 5.008613 GGCTTTTCTATGTGGCGAATTCATA 59.991 40.000 6.22 0.00 0.00 2.15
4289 4570 5.673337 TTTCTATGTGGCGAATTCATAGC 57.327 39.130 6.22 0.59 40.12 2.97
4290 4571 4.335400 TCTATGTGGCGAATTCATAGCA 57.665 40.909 6.22 0.00 40.12 3.49
4291 4572 4.058124 TCTATGTGGCGAATTCATAGCAC 58.942 43.478 6.22 3.57 40.12 4.40
4293 4574 1.065491 TGTGGCGAATTCATAGCACCT 60.065 47.619 6.22 0.00 0.00 4.00
4295 4576 2.544267 GTGGCGAATTCATAGCACCTAC 59.456 50.000 6.22 0.00 0.00 3.18
4297 4578 2.484770 GGCGAATTCATAGCACCTACCA 60.485 50.000 6.22 0.00 0.00 3.25
4298 4579 3.403038 GCGAATTCATAGCACCTACCAT 58.597 45.455 6.22 0.00 0.00 3.55
4299 4580 4.562757 GGCGAATTCATAGCACCTACCATA 60.563 45.833 6.22 0.00 0.00 2.74
4300 4581 5.178797 GCGAATTCATAGCACCTACCATAT 58.821 41.667 6.22 0.00 0.00 1.78
4301 4582 5.292101 GCGAATTCATAGCACCTACCATATC 59.708 44.000 6.22 0.00 0.00 1.63
4302 4583 6.634805 CGAATTCATAGCACCTACCATATCT 58.365 40.000 6.22 0.00 0.00 1.98
4323 4609 3.386543 GTGGTGGCTATAGCACTGG 57.613 57.895 25.53 0.00 43.67 4.00
4332 4618 6.070767 GGTGGCTATAGCACTGGATAATTCTA 60.071 42.308 25.53 0.00 44.36 2.10
4334 4620 8.043710 GTGGCTATAGCACTGGATAATTCTATT 58.956 37.037 25.53 0.00 44.36 1.73
4336 4622 9.535878 GGCTATAGCACTGGATAATTCTATTAC 57.464 37.037 25.53 0.00 44.36 1.89
4374 4663 6.111382 TCCTCTTGATCAGTCATCATTTGTC 58.889 40.000 0.00 0.00 41.42 3.18
4435 4724 4.532126 TCTGTCTTATTTCTTCAGCCAGGA 59.468 41.667 0.00 0.00 0.00 3.86
4437 4726 5.630121 TGTCTTATTTCTTCAGCCAGGAAA 58.370 37.500 0.00 0.00 34.22 3.13
4442 4731 2.260844 TCTTCAGCCAGGAAAGTGTG 57.739 50.000 0.00 0.00 0.00 3.82
4445 4734 2.260844 TCAGCCAGGAAAGTGTGAAG 57.739 50.000 0.00 0.00 0.00 3.02
4448 4737 3.135712 TCAGCCAGGAAAGTGTGAAGTTA 59.864 43.478 0.00 0.00 0.00 2.24
4452 4741 4.338400 GCCAGGAAAGTGTGAAGTTACTTT 59.662 41.667 0.00 2.56 46.54 2.66
4453 4742 5.529800 GCCAGGAAAGTGTGAAGTTACTTTA 59.470 40.000 0.00 0.00 44.59 1.85
4454 4743 6.038936 GCCAGGAAAGTGTGAAGTTACTTTAA 59.961 38.462 0.00 0.00 44.59 1.52
4455 4744 7.639945 CCAGGAAAGTGTGAAGTTACTTTAAG 58.360 38.462 0.00 0.00 44.59 1.85
4460 4749 9.322773 GAAAGTGTGAAGTTACTTTAAGTAGGT 57.677 33.333 4.94 0.00 44.59 3.08
4506 4795 6.828273 TCAGATTTCATGTGTAGTAATTGGGG 59.172 38.462 0.00 0.00 0.00 4.96
4509 4798 3.616219 TCATGTGTAGTAATTGGGGTGC 58.384 45.455 0.00 0.00 0.00 5.01
4517 4806 3.697166 AGTAATTGGGGTGCCTTTGTAG 58.303 45.455 0.00 0.00 0.00 2.74
4520 4809 4.331159 AATTGGGGTGCCTTTGTAGTAT 57.669 40.909 0.00 0.00 0.00 2.12
4521 4810 3.818295 TTGGGGTGCCTTTGTAGTATT 57.182 42.857 0.00 0.00 0.00 1.89
4522 4811 4.931027 TTGGGGTGCCTTTGTAGTATTA 57.069 40.909 0.00 0.00 0.00 0.98
4523 4812 4.224991 TGGGGTGCCTTTGTAGTATTAC 57.775 45.455 0.00 0.00 0.00 1.89
4524 4813 3.587951 TGGGGTGCCTTTGTAGTATTACA 59.412 43.478 0.00 0.00 38.00 2.41
4525 4814 4.228666 TGGGGTGCCTTTGTAGTATTACAT 59.771 41.667 0.00 0.00 39.43 2.29
4526 4815 4.820173 GGGGTGCCTTTGTAGTATTACATC 59.180 45.833 0.00 0.00 39.43 3.06
4528 4817 5.114081 GGTGCCTTTGTAGTATTACATCGT 58.886 41.667 0.00 0.00 39.43 3.73
4530 4819 6.757947 GGTGCCTTTGTAGTATTACATCGTTA 59.242 38.462 0.00 0.00 39.43 3.18
4531 4820 7.042925 GGTGCCTTTGTAGTATTACATCGTTAG 60.043 40.741 0.00 0.00 39.43 2.34
4532 4821 7.490402 GTGCCTTTGTAGTATTACATCGTTAGT 59.510 37.037 0.00 0.00 39.43 2.24
4533 4822 7.703621 TGCCTTTGTAGTATTACATCGTTAGTC 59.296 37.037 0.00 0.00 39.43 2.59
4534 4823 7.919621 GCCTTTGTAGTATTACATCGTTAGTCT 59.080 37.037 0.00 0.00 39.43 3.24
4570 4859 3.797039 TCTTGGCTGTATGAGATTTCCG 58.203 45.455 0.00 0.00 0.00 4.30
4573 4862 1.869767 GGCTGTATGAGATTTCCGCAG 59.130 52.381 0.00 0.00 0.00 5.18
4578 4867 5.739752 TGTATGAGATTTCCGCAGAATTG 57.260 39.130 0.00 0.00 0.00 2.32
4589 4878 5.694231 TCCGCAGAATTGGATATTTCATG 57.306 39.130 0.00 0.00 0.00 3.07
4604 4894 9.736023 GGATATTTCATGTTCAAAATCTACCAC 57.264 33.333 0.00 0.00 0.00 4.16
4607 4897 5.627499 TCATGTTCAAAATCTACCACAGC 57.373 39.130 0.00 0.00 0.00 4.40
4608 4898 4.154015 TCATGTTCAAAATCTACCACAGCG 59.846 41.667 0.00 0.00 0.00 5.18
4609 4899 3.734463 TGTTCAAAATCTACCACAGCGA 58.266 40.909 0.00 0.00 0.00 4.93
4610 4900 4.323417 TGTTCAAAATCTACCACAGCGAT 58.677 39.130 0.00 0.00 0.00 4.58
4622 5132 2.577450 CACAGCGATGTTTGTGATGTG 58.423 47.619 2.11 0.00 45.79 3.21
4625 5135 3.228749 CAGCGATGTTTGTGATGTGAAC 58.771 45.455 0.00 0.00 0.00 3.18
4629 5139 4.846137 GCGATGTTTGTGATGTGAACTTAC 59.154 41.667 0.00 0.00 0.00 2.34
4641 5151 8.015658 GTGATGTGAACTTACATAACAACCTTC 58.984 37.037 0.00 0.00 40.62 3.46
4642 5152 6.870971 TGTGAACTTACATAACAACCTTCC 57.129 37.500 0.00 0.00 0.00 3.46
4643 5153 5.766174 TGTGAACTTACATAACAACCTTCCC 59.234 40.000 0.00 0.00 0.00 3.97
4644 5154 5.182570 GTGAACTTACATAACAACCTTCCCC 59.817 44.000 0.00 0.00 0.00 4.81
4645 5155 4.311520 ACTTACATAACAACCTTCCCCC 57.688 45.455 0.00 0.00 0.00 5.40
4648 5158 3.169512 ACATAACAACCTTCCCCCAAG 57.830 47.619 0.00 0.00 0.00 3.61
4652 5162 2.858787 ACAACCTTCCCCCAAGAAAA 57.141 45.000 0.00 0.00 33.29 2.29
4654 5164 2.023404 ACAACCTTCCCCCAAGAAAAGT 60.023 45.455 0.00 0.00 33.29 2.66
4657 5167 3.840991 ACCTTCCCCCAAGAAAAGTTAC 58.159 45.455 0.00 0.00 33.29 2.50
4660 5170 2.056359 TCCCCCAAGAAAAGTTACGGA 58.944 47.619 0.00 0.00 0.00 4.69
4663 5173 3.192633 CCCCCAAGAAAAGTTACGGAATG 59.807 47.826 0.00 0.00 0.00 2.67
4681 5191 8.567285 ACGGAATGACTTTTCTATTTTGAGAT 57.433 30.769 0.00 0.00 0.00 2.75
4702 5212 7.875041 TGAGATAAGGTATATGAAAAGAGCTGC 59.125 37.037 0.00 0.00 0.00 5.25
4725 5270 2.158711 TGCATTATGAAGCTAGCCTGCT 60.159 45.455 12.13 0.00 46.40 4.24
4727 5272 3.474600 CATTATGAAGCTAGCCTGCTGT 58.525 45.455 12.13 0.00 43.24 4.40
4728 5273 2.609427 TATGAAGCTAGCCTGCTGTG 57.391 50.000 12.13 0.00 43.24 3.66
4730 5275 0.036952 TGAAGCTAGCCTGCTGTGAC 60.037 55.000 12.13 0.00 43.24 3.67
4742 5287 1.001974 TGCTGTGACGCTGAGGTTATT 59.998 47.619 0.00 0.00 0.00 1.40
4745 5290 3.491267 GCTGTGACGCTGAGGTTATTATC 59.509 47.826 0.00 0.00 0.00 1.75
4756 5301 5.984725 TGAGGTTATTATCGGCAGAAAGAA 58.015 37.500 0.00 0.00 0.00 2.52
4759 5304 6.357367 AGGTTATTATCGGCAGAAAGAACAT 58.643 36.000 15.17 9.37 0.00 2.71
4763 5308 9.651718 GTTATTATCGGCAGAAAGAACATTTAG 57.348 33.333 11.30 0.00 0.00 1.85
4765 5310 5.803020 ATCGGCAGAAAGAACATTTAGAC 57.197 39.130 0.00 0.00 0.00 2.59
4766 5311 4.637276 TCGGCAGAAAGAACATTTAGACA 58.363 39.130 0.00 0.00 0.00 3.41
4768 5313 4.378459 CGGCAGAAAGAACATTTAGACACC 60.378 45.833 0.00 0.00 0.00 4.16
4769 5314 4.518970 GGCAGAAAGAACATTTAGACACCA 59.481 41.667 0.00 0.00 0.00 4.17
4782 5327 3.641434 AGACACCAGAGATGGGAAATG 57.359 47.619 0.00 0.00 0.00 2.32
4783 5328 2.915604 AGACACCAGAGATGGGAAATGT 59.084 45.455 0.00 0.00 0.00 2.71
4787 5332 2.379907 ACCAGAGATGGGAAATGTTGGT 59.620 45.455 0.00 0.00 33.10 3.67
4789 5334 2.679837 CAGAGATGGGAAATGTTGGTCG 59.320 50.000 0.00 0.00 0.00 4.79
4794 5339 0.879090 GGGAAATGTTGGTCGTGGTC 59.121 55.000 0.00 0.00 0.00 4.02
4809 5354 1.411246 GTGGTCATTGATGCATGCCAT 59.589 47.619 16.68 8.81 36.70 4.40
4812 5357 1.864711 GTCATTGATGCATGCCATTGC 59.135 47.619 16.68 6.42 43.07 3.56
4829 5374 4.561938 CCATTGCATTTTCTGTCCATGTGT 60.562 41.667 0.00 0.00 0.00 3.72
4847 5392 4.905429 TGTGTTGGTGTATCAATGCTACT 58.095 39.130 0.00 0.00 0.00 2.57
4855 5400 4.509600 GTGTATCAATGCTACTGAGAAGGC 59.490 45.833 0.00 0.00 0.00 4.35
4875 5420 1.136695 CTTTGGCCACAACAGAAGCAA 59.863 47.619 3.88 0.00 36.06 3.91
4880 5425 1.266989 GCCACAACAGAAGCAAGTACC 59.733 52.381 0.00 0.00 0.00 3.34
4888 5433 4.973168 ACAGAAGCAAGTACCAGAAATGA 58.027 39.130 0.00 0.00 0.00 2.57
4898 5443 7.750903 GCAAGTACCAGAAATGATTTGACTTAC 59.249 37.037 0.00 0.00 0.00 2.34
4934 5479 2.209838 TGGCTAATTCGAAGCGAGAG 57.790 50.000 3.35 0.00 41.03 3.20
4937 5482 2.479730 GGCTAATTCGAAGCGAGAGTGA 60.480 50.000 3.35 0.00 41.03 3.41
4938 5483 3.179830 GCTAATTCGAAGCGAGAGTGAA 58.820 45.455 3.35 0.00 37.14 3.18
4939 5484 3.000575 GCTAATTCGAAGCGAGAGTGAAC 60.001 47.826 3.35 0.00 37.14 3.18
4940 5485 3.305398 AATTCGAAGCGAGAGTGAACT 57.695 42.857 3.35 0.00 37.14 3.01
4941 5486 4.436242 AATTCGAAGCGAGAGTGAACTA 57.564 40.909 3.35 0.00 37.14 2.24
4942 5487 4.640789 ATTCGAAGCGAGAGTGAACTAT 57.359 40.909 3.35 0.00 37.14 2.12
4943 5488 3.406728 TCGAAGCGAGAGTGAACTATG 57.593 47.619 0.00 0.00 0.00 2.23
4944 5489 2.747989 TCGAAGCGAGAGTGAACTATGT 59.252 45.455 0.00 0.00 0.00 2.29
4945 5490 3.190744 TCGAAGCGAGAGTGAACTATGTT 59.809 43.478 0.00 0.00 0.00 2.71
4946 5491 4.393990 TCGAAGCGAGAGTGAACTATGTTA 59.606 41.667 0.00 0.00 0.00 2.41
4947 5492 5.093457 CGAAGCGAGAGTGAACTATGTTAA 58.907 41.667 0.00 0.00 0.00 2.01
4948 5493 5.003590 CGAAGCGAGAGTGAACTATGTTAAC 59.996 44.000 0.00 0.00 0.00 2.01
4949 5494 5.386958 AGCGAGAGTGAACTATGTTAACA 57.613 39.130 11.41 11.41 0.00 2.41
4950 5495 5.967088 AGCGAGAGTGAACTATGTTAACAT 58.033 37.500 23.80 23.80 40.22 2.71
4951 5496 5.807520 AGCGAGAGTGAACTATGTTAACATG 59.192 40.000 27.62 19.59 37.15 3.21
4952 5497 5.805486 GCGAGAGTGAACTATGTTAACATGA 59.195 40.000 27.62 12.75 37.15 3.07
4953 5498 6.237595 GCGAGAGTGAACTATGTTAACATGAC 60.238 42.308 27.62 16.21 37.15 3.06
4954 5499 6.806739 CGAGAGTGAACTATGTTAACATGACA 59.193 38.462 27.62 18.45 37.15 3.58
4955 5500 7.328493 CGAGAGTGAACTATGTTAACATGACAA 59.672 37.037 27.62 9.62 37.15 3.18
4956 5501 9.155975 GAGAGTGAACTATGTTAACATGACAAT 57.844 33.333 27.62 19.64 37.15 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 147 5.779529 AGCAGTTGAGTTGTCAATTCAAT 57.220 34.783 21.92 11.35 44.58 2.57
468 479 9.565213 GACATATCAAAATTAATAGCAGATGGC 57.435 33.333 0.00 0.00 45.30 4.40
550 564 6.709397 CCTAGTGACACATTATCATCAAGCAT 59.291 38.462 8.59 0.00 0.00 3.79
568 582 7.223584 TGTTCATCAAGAAATTCACCTAGTGA 58.776 34.615 0.00 0.00 38.21 3.41
612 626 9.252962 ACTTCATCAGTTTCAACAATTTCATTC 57.747 29.630 0.00 0.00 27.32 2.67
614 628 8.636213 AGACTTCATCAGTTTCAACAATTTCAT 58.364 29.630 0.00 0.00 35.01 2.57
706 722 8.033178 TCTTCATCCATAACATAACCATCAGA 57.967 34.615 0.00 0.00 0.00 3.27
711 727 6.575244 ACCTCTTCATCCATAACATAACCA 57.425 37.500 0.00 0.00 0.00 3.67
842 861 2.988010 ATGCCGAGCTAGATCAAACA 57.012 45.000 8.99 3.00 0.00 2.83
1029 1048 2.026879 GCCATCTCCTCGTCGCTC 59.973 66.667 0.00 0.00 0.00 5.03
1152 1171 2.413765 GAGTCCTCGATGTCGGCC 59.586 66.667 2.25 0.00 40.29 6.13
1154 1173 2.716244 CGGAGTCCTCGATGTCGG 59.284 66.667 7.77 0.00 40.29 4.79
1309 1331 2.138179 GGGGAATCGGTCGATGGGA 61.138 63.158 6.63 0.00 34.70 4.37
1315 1337 3.547513 GGGGAGGGGAATCGGTCG 61.548 72.222 0.00 0.00 0.00 4.79
1319 1341 0.398318 GAATGAGGGGAGGGGAATCG 59.602 60.000 0.00 0.00 0.00 3.34
1349 1371 1.373497 CCTGTCGCGCAAGAAGAGT 60.373 57.895 8.75 0.00 43.02 3.24
1350 1372 1.075425 CTCCTGTCGCGCAAGAAGAG 61.075 60.000 8.75 3.59 43.02 2.85
1352 1374 1.373497 ACTCCTGTCGCGCAAGAAG 60.373 57.895 8.75 0.00 43.02 2.85
1359 1381 2.492449 ATCACACCACTCCTGTCGCG 62.492 60.000 0.00 0.00 0.00 5.87
1361 1383 2.881074 CTTATCACACCACTCCTGTCG 58.119 52.381 0.00 0.00 0.00 4.35
1375 1397 3.181475 GGACGAACTCCATCTGCTTATCA 60.181 47.826 0.00 0.00 39.21 2.15
1559 1586 1.705186 ACTGCTACCCATGGAAACTGT 59.295 47.619 15.22 4.37 0.00 3.55
1590 1617 4.696899 AATGTCATGCTGAGAACACATG 57.303 40.909 0.00 0.00 42.01 3.21
1598 1625 6.292757 GCACTGTATTCTAATGTCATGCTGAG 60.293 42.308 0.00 0.00 0.00 3.35
1639 1666 3.454812 TCCCTGTATTCTTAACCTGGAGC 59.545 47.826 0.00 0.00 0.00 4.70
1655 1682 8.749354 GGAGTGATTTGTTAATAAAATCCCTGT 58.251 33.333 17.33 5.90 41.37 4.00
1695 1723 5.125097 GCTCAATGACAAGATCCAATCAGTT 59.875 40.000 0.00 0.00 0.00 3.16
1874 1905 6.596309 TGATTAGGATATGACTAGCAGTGG 57.404 41.667 0.00 0.00 0.00 4.00
2171 2235 8.761575 AACCAATATTACACAAGCATTTTCAG 57.238 30.769 0.00 0.00 0.00 3.02
2461 2530 6.754675 CCCCATTTTTAATGGTTAGTAAAGCG 59.245 38.462 15.28 0.00 37.48 4.68
2491 2560 1.835121 CAGCATGTGATGATTTGCCG 58.165 50.000 0.00 0.00 35.71 5.69
2512 2581 0.240945 GCTTGTTACGTGCCAATGCT 59.759 50.000 0.00 0.00 38.71 3.79
2841 3089 9.331282 ACTGTATAACTGAAAGATAAATCCTGC 57.669 33.333 0.00 0.00 37.43 4.85
2864 3112 8.960591 AGGTGAAATTTAAGTATCATTCCACTG 58.039 33.333 0.00 0.00 0.00 3.66
2888 3136 3.450457 AGCTAGTTCAGATGGAGTTCAGG 59.550 47.826 0.00 0.00 0.00 3.86
2987 3249 6.922957 TCACCAATTTCAGCAATAGTTTTGTC 59.077 34.615 0.00 0.00 0.00 3.18
3061 3326 7.436080 AGTGCATGAGAAATAAAACAAGTTGTG 59.564 33.333 9.79 0.00 0.00 3.33
3489 3764 3.903360 ACTCAAGAAGACACTAGAACGC 58.097 45.455 0.00 0.00 0.00 4.84
3556 3831 7.447545 ACAGCGTATGACAGGTAATCTTATAGA 59.552 37.037 0.00 0.00 0.00 1.98
3636 3911 6.812160 GTGTTCAGTAATCACTACAGGTTAGG 59.188 42.308 0.00 0.00 32.21 2.69
3639 3914 5.307196 AGGTGTTCAGTAATCACTACAGGTT 59.693 40.000 0.00 0.00 32.21 3.50
3665 3940 9.927081 ATTAACAGTGAATCCCTTTTCAGATAT 57.073 29.630 0.00 0.00 36.34 1.63
3679 3954 4.216411 ACTGGCGGTATTAACAGTGAAT 57.784 40.909 0.00 0.00 42.14 2.57
3708 3983 5.905480 AAGTTTTTCATTTGCCGAACATC 57.095 34.783 0.00 0.00 0.00 3.06
3771 4047 3.428063 AGGAGGGAATGATCTTCCTGA 57.572 47.619 17.88 0.00 37.85 3.86
3789 4065 9.137459 TCATAAGAGAACTGGTATTCTTCTAGG 57.863 37.037 0.00 0.00 39.08 3.02
3863 4139 4.660611 TAGGTTCCCGTGCCCCCA 62.661 66.667 0.00 0.00 0.00 4.96
3873 4149 6.763610 CCTCTTCAGTCACATATTTAGGTTCC 59.236 42.308 0.00 0.00 0.00 3.62
3971 4247 4.060205 GCTGTCCATTTGCAACTTTGAAT 58.940 39.130 0.00 0.00 0.00 2.57
3977 4253 1.884579 CAGAGCTGTCCATTTGCAACT 59.115 47.619 0.00 0.00 0.00 3.16
3991 4267 4.161102 AGTCTACTAACCCAAACAGAGCT 58.839 43.478 0.00 0.00 0.00 4.09
3997 4273 3.328637 TCCCCAAGTCTACTAACCCAAAC 59.671 47.826 0.00 0.00 0.00 2.93
4005 4282 7.166167 GTCAGAAAAATTCCCCAAGTCTACTA 58.834 38.462 0.00 0.00 0.00 1.82
4012 4289 5.183904 CCTAGTGTCAGAAAAATTCCCCAAG 59.816 44.000 0.00 0.00 0.00 3.61
4013 4290 5.076873 CCTAGTGTCAGAAAAATTCCCCAA 58.923 41.667 0.00 0.00 0.00 4.12
4018 4297 6.428159 TCTTCAGCCTAGTGTCAGAAAAATTC 59.572 38.462 0.00 0.00 0.00 2.17
4020 4299 5.869579 TCTTCAGCCTAGTGTCAGAAAAAT 58.130 37.500 0.00 0.00 0.00 1.82
4032 4313 1.002087 ACGGTTGGTTCTTCAGCCTAG 59.998 52.381 0.00 0.00 36.12 3.02
4041 4322 3.067601 GGTTCATCAAAACGGTTGGTTCT 59.932 43.478 0.00 0.00 38.08 3.01
4051 4332 6.325919 TCCAGTGTAATGGTTCATCAAAAC 57.674 37.500 0.00 0.00 41.43 2.43
4052 4333 6.549364 ACTTCCAGTGTAATGGTTCATCAAAA 59.451 34.615 0.00 0.00 41.43 2.44
4079 4360 4.566426 AGAAGGAAAGAACAGATGGAGG 57.434 45.455 0.00 0.00 0.00 4.30
4082 4363 5.072741 TGGAAAGAAGGAAAGAACAGATGG 58.927 41.667 0.00 0.00 0.00 3.51
4095 4376 7.340487 AGTTAAATCTTAGCCATGGAAAGAAGG 59.660 37.037 25.24 6.98 33.26 3.46
4113 4394 8.978539 GGTGGAAATTCACTTTTGAGTTAAATC 58.021 33.333 0.00 0.00 37.75 2.17
4119 4400 4.546674 AGGGTGGAAATTCACTTTTGAGT 58.453 39.130 0.00 0.00 37.75 3.41
4120 4401 6.209391 ACATAGGGTGGAAATTCACTTTTGAG 59.791 38.462 0.00 0.00 37.75 3.02
4123 4404 6.152831 GCTACATAGGGTGGAAATTCACTTTT 59.847 38.462 0.00 0.00 37.75 2.27
4124 4405 5.652452 GCTACATAGGGTGGAAATTCACTTT 59.348 40.000 0.00 0.00 37.75 2.66
4129 4410 5.594317 ACAATGCTACATAGGGTGGAAATTC 59.406 40.000 0.00 0.00 0.00 2.17
4132 4413 4.584638 ACAATGCTACATAGGGTGGAAA 57.415 40.909 0.00 0.00 0.00 3.13
4135 4416 4.776349 TGTTACAATGCTACATAGGGTGG 58.224 43.478 0.00 0.00 0.00 4.61
4184 4465 5.192722 TGGGGATACATACAACAGGAATGAA 59.807 40.000 0.00 0.00 39.74 2.57
4191 4472 3.071023 ACCGATGGGGATACATACAACAG 59.929 47.826 0.00 0.00 39.97 3.16
4198 4479 4.519906 AAAAGAACCGATGGGGATACAT 57.480 40.909 0.00 0.00 39.97 2.29
4207 4488 5.587289 TCTTTGTTGGAAAAAGAACCGATG 58.413 37.500 0.00 0.00 39.94 3.84
4208 4489 5.845391 TCTTTGTTGGAAAAAGAACCGAT 57.155 34.783 0.00 0.00 39.94 4.18
4209 4490 5.126384 ACATCTTTGTTGGAAAAAGAACCGA 59.874 36.000 2.99 0.00 44.49 4.69
4210 4491 5.348164 ACATCTTTGTTGGAAAAAGAACCG 58.652 37.500 2.99 0.00 44.49 4.44
4211 4492 8.600625 GTTTACATCTTTGTTGGAAAAAGAACC 58.399 33.333 2.99 0.00 44.49 3.62
4212 4493 8.600625 GGTTTACATCTTTGTTGGAAAAAGAAC 58.399 33.333 2.99 0.00 44.49 3.01
4213 4494 7.766738 GGGTTTACATCTTTGTTGGAAAAAGAA 59.233 33.333 2.99 0.00 44.49 2.52
4214 4495 7.093289 TGGGTTTACATCTTTGTTGGAAAAAGA 60.093 33.333 1.45 1.45 45.17 2.52
4215 4496 7.044798 TGGGTTTACATCTTTGTTGGAAAAAG 58.955 34.615 0.00 0.00 37.28 2.27
4216 4497 6.947464 TGGGTTTACATCTTTGTTGGAAAAA 58.053 32.000 0.00 0.00 37.28 1.94
4217 4498 6.546428 TGGGTTTACATCTTTGTTGGAAAA 57.454 33.333 0.00 0.00 37.28 2.29
4218 4499 6.546428 TTGGGTTTACATCTTTGTTGGAAA 57.454 33.333 0.00 0.00 37.28 3.13
4219 4500 6.463614 CCATTGGGTTTACATCTTTGTTGGAA 60.464 38.462 0.00 0.00 37.28 3.53
4220 4501 5.011533 CCATTGGGTTTACATCTTTGTTGGA 59.988 40.000 0.00 0.00 37.28 3.53
4221 4502 5.011533 TCCATTGGGTTTACATCTTTGTTGG 59.988 40.000 2.09 0.00 34.77 3.77
4222 4503 6.095432 TCCATTGGGTTTACATCTTTGTTG 57.905 37.500 2.09 0.00 34.77 3.33
4223 4504 6.933514 ATCCATTGGGTTTACATCTTTGTT 57.066 33.333 2.09 0.00 34.77 2.83
4224 4505 8.429237 TTTATCCATTGGGTTTACATCTTTGT 57.571 30.769 2.09 0.00 36.23 2.83
4225 4506 9.889128 ATTTTATCCATTGGGTTTACATCTTTG 57.111 29.630 2.09 0.00 34.93 2.77
4232 4513 9.811995 GGAAGTTATTTTATCCATTGGGTTTAC 57.188 33.333 2.09 0.00 34.93 2.01
4233 4514 9.777008 AGGAAGTTATTTTATCCATTGGGTTTA 57.223 29.630 2.09 0.00 34.30 2.01
4234 4515 8.539544 CAGGAAGTTATTTTATCCATTGGGTTT 58.460 33.333 2.09 0.00 34.30 3.27
4235 4516 7.125659 CCAGGAAGTTATTTTATCCATTGGGTT 59.874 37.037 2.09 0.00 34.30 4.11
4236 4517 6.611236 CCAGGAAGTTATTTTATCCATTGGGT 59.389 38.462 2.09 0.00 34.30 4.51
4244 4525 7.646548 AAAGCCTCCAGGAAGTTATTTTATC 57.353 36.000 0.00 0.00 37.39 1.75
4246 4527 7.238710 AGAAAAGCCTCCAGGAAGTTATTTTA 58.761 34.615 0.00 0.00 37.39 1.52
4250 4531 4.936685 AGAAAAGCCTCCAGGAAGTTAT 57.063 40.909 0.00 0.00 37.39 1.89
4252 4533 4.043435 ACATAGAAAAGCCTCCAGGAAGTT 59.957 41.667 0.00 0.00 37.39 2.66
4255 4536 3.308402 CCACATAGAAAAGCCTCCAGGAA 60.308 47.826 0.00 0.00 37.39 3.36
4270 4551 3.187227 GGTGCTATGAATTCGCCACATAG 59.813 47.826 14.99 0.00 43.33 2.23
4276 4557 2.143925 GGTAGGTGCTATGAATTCGCC 58.856 52.381 0.04 0.00 0.00 5.54
4278 4559 6.634805 AGATATGGTAGGTGCTATGAATTCG 58.365 40.000 0.04 0.00 0.00 3.34
4281 4562 8.535335 CACTTAGATATGGTAGGTGCTATGAAT 58.465 37.037 0.00 0.00 0.00 2.57
4284 4565 6.634805 CCACTTAGATATGGTAGGTGCTATG 58.365 44.000 0.00 0.00 0.00 2.23
4285 4566 6.859112 CCACTTAGATATGGTAGGTGCTAT 57.141 41.667 0.00 0.00 0.00 2.97
4293 4574 7.969905 TGCTATAGCCACCACTTAGATATGGTA 60.970 40.741 21.84 0.00 43.31 3.25
4295 4576 5.187772 TGCTATAGCCACCACTTAGATATGG 59.812 44.000 21.84 0.00 40.21 2.74
4297 4578 6.019748 AGTGCTATAGCCACCACTTAGATAT 58.980 40.000 21.84 0.00 41.18 1.63
4298 4579 5.243954 CAGTGCTATAGCCACCACTTAGATA 59.756 44.000 21.84 0.00 41.18 1.98
4299 4580 4.039730 CAGTGCTATAGCCACCACTTAGAT 59.960 45.833 21.84 0.15 41.18 1.98
4300 4581 3.384789 CAGTGCTATAGCCACCACTTAGA 59.615 47.826 21.84 0.00 41.18 2.10
4301 4582 3.493350 CCAGTGCTATAGCCACCACTTAG 60.493 52.174 21.84 8.40 41.18 2.18
4302 4583 2.434336 CCAGTGCTATAGCCACCACTTA 59.566 50.000 21.84 0.00 41.18 2.24
4336 4622 9.205719 CTGATCAAGAGGAAGATACACATATTG 57.794 37.037 0.00 0.00 0.00 1.90
4352 4641 6.980051 TGACAAATGATGACTGATCAAGAG 57.020 37.500 0.00 0.00 44.50 2.85
4384 4673 7.554959 AAAAAGAGGATAGAGTTCACACCTA 57.445 36.000 0.00 0.00 0.00 3.08
4413 4702 4.836825 TCCTGGCTGAAGAAATAAGACAG 58.163 43.478 0.00 0.00 45.14 3.51
4415 4704 5.707764 ACTTTCCTGGCTGAAGAAATAAGAC 59.292 40.000 10.05 0.00 0.00 3.01
4417 4706 5.474876 ACACTTTCCTGGCTGAAGAAATAAG 59.525 40.000 10.05 0.00 0.00 1.73
4418 4707 5.241506 CACACTTTCCTGGCTGAAGAAATAA 59.758 40.000 10.05 0.00 0.00 1.40
4419 4708 4.761739 CACACTTTCCTGGCTGAAGAAATA 59.238 41.667 10.05 0.00 0.00 1.40
4420 4709 3.571401 CACACTTTCCTGGCTGAAGAAAT 59.429 43.478 10.05 0.00 0.00 2.17
4421 4710 2.951642 CACACTTTCCTGGCTGAAGAAA 59.048 45.455 10.05 0.00 0.00 2.52
4422 4711 2.172505 TCACACTTTCCTGGCTGAAGAA 59.827 45.455 10.05 0.00 0.00 2.52
4423 4712 1.768275 TCACACTTTCCTGGCTGAAGA 59.232 47.619 10.05 0.00 0.00 2.87
4424 4713 2.260844 TCACACTTTCCTGGCTGAAG 57.739 50.000 0.00 0.00 0.00 3.02
4437 4726 9.140874 AGTACCTACTTAAAGTAACTTCACACT 57.859 33.333 0.00 0.00 31.13 3.55
4442 4731 9.971922 TTGTCAGTACCTACTTAAAGTAACTTC 57.028 33.333 0.00 0.00 33.46 3.01
4482 4771 6.603201 ACCCCAATTACTACACATGAAATCTG 59.397 38.462 0.00 0.00 0.00 2.90
4483 4772 6.603201 CACCCCAATTACTACACATGAAATCT 59.397 38.462 0.00 0.00 0.00 2.40
4506 4795 6.657836 AACGATGTAATACTACAAAGGCAC 57.342 37.500 0.00 0.00 41.36 5.01
4530 4819 9.692325 AGCCAAGAATATTTGAAGAAATAGACT 57.308 29.630 0.00 0.00 37.44 3.24
4531 4820 9.727627 CAGCCAAGAATATTTGAAGAAATAGAC 57.272 33.333 0.00 0.00 37.44 2.59
4532 4821 9.466497 ACAGCCAAGAATATTTGAAGAAATAGA 57.534 29.630 0.00 0.00 37.44 1.98
4536 4825 9.241919 TCATACAGCCAAGAATATTTGAAGAAA 57.758 29.630 0.00 0.00 0.00 2.52
4537 4826 8.806429 TCATACAGCCAAGAATATTTGAAGAA 57.194 30.769 0.00 0.00 0.00 2.52
4539 4828 8.442632 TCTCATACAGCCAAGAATATTTGAAG 57.557 34.615 0.00 0.00 0.00 3.02
4540 4829 8.985315 ATCTCATACAGCCAAGAATATTTGAA 57.015 30.769 0.00 0.00 0.00 2.69
4541 4830 8.985315 AATCTCATACAGCCAAGAATATTTGA 57.015 30.769 0.00 0.00 0.00 2.69
4542 4831 9.674824 GAAATCTCATACAGCCAAGAATATTTG 57.325 33.333 0.00 0.00 0.00 2.32
4544 4833 7.173907 CGGAAATCTCATACAGCCAAGAATATT 59.826 37.037 0.00 0.00 0.00 1.28
4545 4834 6.652481 CGGAAATCTCATACAGCCAAGAATAT 59.348 38.462 0.00 0.00 0.00 1.28
4561 4850 6.566197 AATATCCAATTCTGCGGAAATCTC 57.434 37.500 12.96 0.00 34.22 2.75
4570 4859 8.706492 TTTGAACATGAAATATCCAATTCTGC 57.294 30.769 0.00 0.00 0.00 4.26
4578 4867 9.736023 GTGGTAGATTTTGAACATGAAATATCC 57.264 33.333 0.00 0.08 0.00 2.59
4589 4878 4.154195 ACATCGCTGTGGTAGATTTTGAAC 59.846 41.667 0.00 0.00 33.22 3.18
4600 4890 1.536766 CATCACAAACATCGCTGTGGT 59.463 47.619 0.00 0.00 42.62 4.16
4604 4894 3.058708 AGTTCACATCACAAACATCGCTG 60.059 43.478 0.00 0.00 0.00 5.18
4605 4895 3.141398 AGTTCACATCACAAACATCGCT 58.859 40.909 0.00 0.00 0.00 4.93
4606 4896 3.542712 AGTTCACATCACAAACATCGC 57.457 42.857 0.00 0.00 0.00 4.58
4607 4897 5.984627 TGTAAGTTCACATCACAAACATCG 58.015 37.500 0.00 0.00 0.00 3.84
4608 4898 9.329913 GTTATGTAAGTTCACATCACAAACATC 57.670 33.333 0.00 0.00 39.77 3.06
4609 4899 8.845227 TGTTATGTAAGTTCACATCACAAACAT 58.155 29.630 1.79 0.00 39.09 2.71
4610 4900 8.214721 TGTTATGTAAGTTCACATCACAAACA 57.785 30.769 1.79 1.11 39.09 2.83
4622 5132 4.703575 GGGGGAAGGTTGTTATGTAAGTTC 59.296 45.833 0.00 0.00 0.00 3.01
4625 5135 4.310022 TGGGGGAAGGTTGTTATGTAAG 57.690 45.455 0.00 0.00 0.00 2.34
4629 5139 3.449746 TCTTGGGGGAAGGTTGTTATG 57.550 47.619 0.00 0.00 31.85 1.90
4641 5151 2.572209 TCCGTAACTTTTCTTGGGGG 57.428 50.000 0.00 0.00 0.00 5.40
4642 5152 4.076394 TCATTCCGTAACTTTTCTTGGGG 58.924 43.478 0.00 0.00 0.00 4.96
4643 5153 4.760204 AGTCATTCCGTAACTTTTCTTGGG 59.240 41.667 0.00 0.00 0.00 4.12
4644 5154 5.941948 AGTCATTCCGTAACTTTTCTTGG 57.058 39.130 0.00 0.00 0.00 3.61
4652 5162 9.280174 TCAAAATAGAAAAGTCATTCCGTAACT 57.720 29.630 0.00 0.00 0.00 2.24
4654 5164 9.496873 TCTCAAAATAGAAAAGTCATTCCGTAA 57.503 29.630 0.00 0.00 0.00 3.18
4681 5191 6.291377 CAGGCAGCTCTTTTCATATACCTTA 58.709 40.000 0.00 0.00 0.00 2.69
4702 5212 2.812591 CAGGCTAGCTTCATAATGCAGG 59.187 50.000 15.72 0.00 0.00 4.85
4725 5270 3.490249 CCGATAATAACCTCAGCGTCACA 60.490 47.826 0.00 0.00 0.00 3.58
4727 5272 2.545113 GCCGATAATAACCTCAGCGTCA 60.545 50.000 0.00 0.00 0.00 4.35
4728 5273 2.059541 GCCGATAATAACCTCAGCGTC 58.940 52.381 0.00 0.00 0.00 5.19
4730 5275 2.061773 CTGCCGATAATAACCTCAGCG 58.938 52.381 0.00 0.00 0.00 5.18
4742 5287 6.312918 GTGTCTAAATGTTCTTTCTGCCGATA 59.687 38.462 0.00 0.00 0.00 2.92
4745 5290 4.378459 GGTGTCTAAATGTTCTTTCTGCCG 60.378 45.833 0.00 0.00 0.00 5.69
4756 5301 4.104086 TCCCATCTCTGGTGTCTAAATGT 58.896 43.478 0.00 0.00 41.37 2.71
4759 5304 5.014123 ACATTTCCCATCTCTGGTGTCTAAA 59.986 40.000 0.00 0.00 41.37 1.85
4763 5308 3.356529 ACATTTCCCATCTCTGGTGTC 57.643 47.619 0.00 0.00 41.37 3.67
4765 5310 2.756760 CCAACATTTCCCATCTCTGGTG 59.243 50.000 0.00 0.00 41.37 4.17
4766 5311 2.379907 ACCAACATTTCCCATCTCTGGT 59.620 45.455 0.00 0.00 41.37 4.00
4768 5313 2.679837 CGACCAACATTTCCCATCTCTG 59.320 50.000 0.00 0.00 0.00 3.35
4769 5314 2.305927 ACGACCAACATTTCCCATCTCT 59.694 45.455 0.00 0.00 0.00 3.10
4782 5327 1.135689 GCATCAATGACCACGACCAAC 60.136 52.381 0.00 0.00 0.00 3.77
4783 5328 1.164411 GCATCAATGACCACGACCAA 58.836 50.000 0.00 0.00 0.00 3.67
4787 5332 0.734309 GCATGCATCAATGACCACGA 59.266 50.000 14.21 0.00 0.00 4.35
4789 5334 0.818938 TGGCATGCATCAATGACCAC 59.181 50.000 21.36 0.00 34.38 4.16
4809 5354 4.370049 CAACACATGGACAGAAAATGCAA 58.630 39.130 0.00 0.00 0.00 4.08
4829 5374 5.675684 TCTCAGTAGCATTGATACACCAA 57.324 39.130 14.03 0.00 0.00 3.67
4855 5400 0.746063 TGCTTCTGTTGTGGCCAAAG 59.254 50.000 7.24 7.76 30.94 2.77
4875 5420 8.375506 TCTGTAAGTCAAATCATTTCTGGTACT 58.624 33.333 0.00 0.00 33.76 2.73
4880 5425 7.388776 TGGTCTCTGTAAGTCAAATCATTTCTG 59.611 37.037 0.00 0.00 33.76 3.02
4888 5433 6.263168 CCACTTTTGGTCTCTGTAAGTCAAAT 59.737 38.462 0.00 0.00 38.23 2.32
4898 5443 1.815003 GCCATCCACTTTTGGTCTCTG 59.185 52.381 0.00 0.00 44.35 3.35


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

AutoCloner maintained by Alex Coulton.