Multiple sequence alignment - TraesCS6B01G180100

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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 TraesCS6B01G180100 chr6B 100.000 5037 0 0 1 5037 200309980 200315016 0.000000e+00 9302.0
1 TraesCS6B01G180100 chr6D 96.409 2228 53 12 2818 5037 111437809 111440017 0.000000e+00 3646.0
2 TraesCS6B01G180100 chr6D 93.818 2378 80 25 486 2820 111435424 111437777 0.000000e+00 3515.0
3 TraesCS6B01G180100 chr6D 79.167 216 26 11 37 238 111434879 111435089 1.140000e-26 132.0
4 TraesCS6B01G180100 chr6D 94.444 36 2 0 4826 4861 111439771 111439806 7.040000e-04 56.5
5 TraesCS6B01G180100 chr6A 93.190 1762 86 10 2855 4611 136992737 136991005 0.000000e+00 2558.0
6 TraesCS6B01G180100 chr6A 94.997 1439 36 10 1414 2820 136994967 136993533 0.000000e+00 2226.0
7 TraesCS6B01G180100 chr6A 85.915 71 8 2 362 430 137384811 137384881 1.940000e-09 75.0
8 TraesCS6B01G180100 chr4D 87.129 202 20 4 3411 3607 258893453 258893653 1.820000e-54 224.0
9 TraesCS6B01G180100 chr4D 97.143 35 1 0 4622 4656 123476870 123476904 5.450000e-05 60.2
10 TraesCS6B01G180100 chr4D 97.143 35 1 0 4622 4656 450990625 450990591 5.450000e-05 60.2
11 TraesCS6B01G180100 chr4D 97.143 35 1 0 4622 4656 451011269 451011303 5.450000e-05 60.2
12 TraesCS6B01G180100 chr1D 87.374 198 19 5 3413 3605 296894305 296894501 6.560000e-54 222.0
13 TraesCS6B01G180100 chr5B 86.700 203 21 3 3410 3607 30632705 30632906 2.360000e-53 220.0
14 TraesCS6B01G180100 chr5B 86.700 203 22 2 3410 3607 412385083 412384881 2.360000e-53 220.0
15 TraesCS6B01G180100 chr5B 85.577 208 23 4 3406 3608 352576673 352576878 1.420000e-50 211.0
16 TraesCS6B01G180100 chr5B 77.907 172 27 8 37 198 31270727 31270897 4.150000e-16 97.1
17 TraesCS6B01G180100 chr5B 77.326 172 28 8 37 198 31185565 31185735 1.930000e-14 91.6
18 TraesCS6B01G180100 chrUn 86.207 203 22 4 3410 3607 27663857 27664058 1.100000e-51 215.0
19 TraesCS6B01G180100 chrUn 95.122 41 2 0 426 466 473849813 473849853 1.170000e-06 65.8
20 TraesCS6B01G180100 chrUn 97.143 35 1 0 4622 4656 237093983 237093949 5.450000e-05 60.2
21 TraesCS6B01G180100 chr5D 86.207 203 21 4 3411 3607 455764893 455764692 3.950000e-51 213.0
22 TraesCS6B01G180100 chr5D 97.143 35 1 0 4622 4656 464500482 464500448 5.450000e-05 60.2
23 TraesCS6B01G180100 chr5D 97.143 35 1 0 4622 4656 464527912 464527878 5.450000e-05 60.2
24 TraesCS6B01G180100 chr1B 80.198 101 14 5 307 407 653819213 653819119 2.520000e-08 71.3
25 TraesCS6B01G180100 chr1B 97.222 36 0 1 253 287 532486954 532486919 5.450000e-05 60.2
26 TraesCS6B01G180100 chr1A 94.872 39 2 0 429 467 536208118 536208080 1.510000e-05 62.1
27 TraesCS6B01G180100 chr3D 97.143 35 1 0 4622 4656 308588054 308588020 5.450000e-05 60.2
28 TraesCS6B01G180100 chr2D 97.143 35 1 0 4622 4656 635005618 635005652 5.450000e-05 60.2
29 TraesCS6B01G180100 chr2D 86.792 53 5 2 59 110 400296574 400296523 1.960000e-04 58.4
30 TraesCS6B01G180100 chr7B 92.500 40 3 0 426 465 579832029 579832068 1.960000e-04 58.4
31 TraesCS6B01G180100 chr7B 94.444 36 2 0 62 97 663601264 663601299 7.040000e-04 56.5
32 TraesCS6B01G180100 chr7B 94.444 36 2 0 62 97 663634101 663634136 7.040000e-04 56.5
33 TraesCS6B01G180100 chr7B 94.444 36 2 0 62 97 663655042 663655077 7.040000e-04 56.5
34 TraesCS6B01G180100 chr7B 94.444 36 2 0 62 97 663687262 663687297 7.040000e-04 56.5
35 TraesCS6B01G180100 chr3B 92.500 40 3 0 426 465 204806657 204806696 1.960000e-04 58.4
36 TraesCS6B01G180100 chr3B 96.970 33 1 0 433 465 577723849 577723817 7.040000e-04 56.5


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 TraesCS6B01G180100 chr6B 200309980 200315016 5036 False 9302.000 9302 100.0000 1 5037 1 chr6B.!!$F1 5036
1 TraesCS6B01G180100 chr6D 111434879 111440017 5138 False 1837.375 3646 90.9595 37 5037 4 chr6D.!!$F1 5000
2 TraesCS6B01G180100 chr6A 136991005 136994967 3962 True 2392.000 2558 94.0935 1414 4611 2 chr6A.!!$R1 3197

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
141 149 0.109132 GGAGGCACGGATTTGCTTTG 60.109 55.000 0.00 0.00 42.56 2.77 F
559 659 0.109226 AAGTTGCGCTAGACTCGACC 60.109 55.000 9.73 0.00 0.00 4.79 F
562 662 0.109272 TTGCGCTAGACTCGACCTTG 60.109 55.000 9.73 0.00 0.00 3.61 F
944 1056 0.169009 GAAGTCGGTTGATTGCAGGC 59.831 55.000 0.00 0.00 0.00 4.85 F
1557 1673 0.250727 CCCAAGTTGACCCACGTGAT 60.251 55.000 19.30 4.23 0.00 3.06 F
1558 1674 1.002659 CCCAAGTTGACCCACGTGATA 59.997 52.381 19.30 0.00 0.00 2.15 F
3010 3918 1.615883 GAAGGCTATGAGATGGCGAGA 59.384 52.381 0.00 0.00 37.67 4.04 F
3710 4622 0.315568 GCGATCGGACCATCTAGCTT 59.684 55.000 18.30 0.00 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 1129 0.734942 AGTAAATGTGACCGTCGGCG 60.735 55.000 12.28 0.29 37.95 6.46 R
1989 2135 1.071071 CCCGTTAGGAAGTGAACCACA 59.929 52.381 0.00 0.00 41.02 4.17 R
2372 2518 8.154856 AGCAGTAGGAAAGACAGTAACAAAATA 58.845 33.333 0.00 0.00 0.00 1.40 R
2761 2908 1.611977 GTTGTTGCCCCAACTTCTACC 59.388 52.381 9.23 0.00 43.85 3.18 R
3477 4389 0.815615 CTCCTGCGGAAATAGGCACC 60.816 60.000 0.00 0.00 34.97 5.01 R
3518 4430 2.912956 ACCAGTGCTTATTTGGAGAGGA 59.087 45.455 0.00 0.00 35.89 3.71 R
4032 4944 0.037326 GCGGTCCATGTCTTCTCACA 60.037 55.000 0.00 0.00 0.00 3.58 R
4735 5649 0.613777 AACCTCTTAGGCCCTGTTCG 59.386 55.000 0.00 0.00 39.63 3.95 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
20 21 3.690475 GTCTCTCGGAAAAGGGGTAAA 57.310 47.619 0.00 0.00 0.00 2.01
21 22 3.332919 GTCTCTCGGAAAAGGGGTAAAC 58.667 50.000 0.00 0.00 0.00 2.01
22 23 2.974099 TCTCTCGGAAAAGGGGTAAACA 59.026 45.455 0.00 0.00 0.00 2.83
23 24 3.072211 CTCTCGGAAAAGGGGTAAACAC 58.928 50.000 0.00 0.00 0.00 3.32
24 25 2.438763 TCTCGGAAAAGGGGTAAACACA 59.561 45.455 0.00 0.00 0.00 3.72
25 26 3.073356 TCTCGGAAAAGGGGTAAACACAT 59.927 43.478 0.00 0.00 0.00 3.21
26 27 3.824443 CTCGGAAAAGGGGTAAACACATT 59.176 43.478 0.00 0.00 0.00 2.71
27 28 4.216708 TCGGAAAAGGGGTAAACACATTT 58.783 39.130 0.00 0.00 34.42 2.32
28 29 4.650131 TCGGAAAAGGGGTAAACACATTTT 59.350 37.500 7.39 7.39 44.60 1.82
29 30 5.128991 TCGGAAAAGGGGTAAACACATTTTT 59.871 36.000 8.89 3.48 42.39 1.94
64 65 6.183360 ACAAATTTAGTTTCCATGAAGGCACA 60.183 34.615 0.00 0.00 37.29 4.57
76 77 1.806542 GAAGGCACAGATTTGCTTCGA 59.193 47.619 0.00 0.00 42.56 3.71
78 79 0.179215 GGCACAGATTTGCTTCGACG 60.179 55.000 0.00 0.00 42.56 5.12
93 101 1.413767 CGACGAGAGGCACGGATTTG 61.414 60.000 0.00 0.00 41.50 2.32
99 107 1.003839 AGGCACGGATTTGCTTCGA 60.004 52.632 0.00 0.00 42.56 3.71
103 111 0.366871 CACGGATTTGCTTCGACGAG 59.633 55.000 0.00 0.00 0.00 4.18
111 119 4.467232 CTTCGACGAGAGGCACAG 57.533 61.111 0.00 0.00 41.50 3.66
112 120 1.876664 CTTCGACGAGAGGCACAGA 59.123 57.895 0.00 0.00 41.50 3.41
113 121 0.453793 CTTCGACGAGAGGCACAGAT 59.546 55.000 0.00 0.00 41.50 2.90
114 122 0.888619 TTCGACGAGAGGCACAGATT 59.111 50.000 0.00 0.00 41.50 2.40
116 124 2.089201 TCGACGAGAGGCACAGATTTA 58.911 47.619 0.00 0.00 41.50 1.40
118 126 2.159366 CGACGAGAGGCACAGATTTACT 60.159 50.000 0.00 0.00 41.50 2.24
120 128 4.438336 CGACGAGAGGCACAGATTTACTTA 60.438 45.833 0.00 0.00 41.50 2.24
122 130 5.352284 ACGAGAGGCACAGATTTACTTATG 58.648 41.667 0.00 0.00 0.00 1.90
123 131 4.747108 CGAGAGGCACAGATTTACTTATGG 59.253 45.833 0.00 0.00 0.00 2.74
124 132 5.451937 CGAGAGGCACAGATTTACTTATGGA 60.452 44.000 0.00 0.00 0.00 3.41
125 133 5.923204 AGAGGCACAGATTTACTTATGGAG 58.077 41.667 0.00 0.00 0.00 3.86
126 134 5.041191 AGGCACAGATTTACTTATGGAGG 57.959 43.478 0.00 0.00 0.00 4.30
127 135 3.565902 GGCACAGATTTACTTATGGAGGC 59.434 47.826 0.00 0.00 0.00 4.70
128 136 4.199310 GCACAGATTTACTTATGGAGGCA 58.801 43.478 0.00 0.00 0.00 4.75
129 137 4.035675 GCACAGATTTACTTATGGAGGCAC 59.964 45.833 0.00 0.00 0.00 5.01
131 139 3.809832 CAGATTTACTTATGGAGGCACGG 59.190 47.826 0.00 0.00 0.00 4.94
133 141 4.348168 AGATTTACTTATGGAGGCACGGAT 59.652 41.667 0.00 0.00 0.00 4.18
134 142 4.497291 TTTACTTATGGAGGCACGGATT 57.503 40.909 0.00 0.00 0.00 3.01
138 146 0.546122 TATGGAGGCACGGATTTGCT 59.454 50.000 0.00 0.00 42.56 3.91
140 148 0.539438 TGGAGGCACGGATTTGCTTT 60.539 50.000 0.00 0.00 42.56 3.51
141 149 0.109132 GGAGGCACGGATTTGCTTTG 60.109 55.000 0.00 0.00 42.56 2.77
143 151 1.737735 GGCACGGATTTGCTTTGGC 60.738 57.895 0.00 0.00 42.56 4.52
178 186 3.593442 TGCCTCTCAGAAAGGGAAAAA 57.407 42.857 0.00 0.00 34.26 1.94
179 187 4.118168 TGCCTCTCAGAAAGGGAAAAAT 57.882 40.909 0.00 0.00 34.26 1.82
180 188 3.828451 TGCCTCTCAGAAAGGGAAAAATG 59.172 43.478 0.00 0.00 34.26 2.32
181 189 3.829026 GCCTCTCAGAAAGGGAAAAATGT 59.171 43.478 0.00 0.00 34.26 2.71
182 190 4.321527 GCCTCTCAGAAAGGGAAAAATGTG 60.322 45.833 0.00 0.00 34.26 3.21
208 220 3.275143 TCTTTCTTTCACGAAAGCCACA 58.725 40.909 13.55 0.00 45.90 4.17
223 235 5.644977 AAGCCACAAATTTACTTCTAGGC 57.355 39.130 0.00 0.00 39.82 3.93
225 237 4.459337 AGCCACAAATTTACTTCTAGGCAC 59.541 41.667 0.00 0.00 41.88 5.01
238 250 1.667724 CTAGGCACGGATTTGCTTCTG 59.332 52.381 0.00 0.00 42.56 3.02
239 251 1.153958 GGCACGGATTTGCTTCTGC 60.154 57.895 0.00 0.00 42.56 4.26
240 252 1.512734 GCACGGATTTGCTTCTGCG 60.513 57.895 0.00 0.00 43.34 5.18
241 253 1.911293 GCACGGATTTGCTTCTGCGA 61.911 55.000 0.00 0.00 43.34 5.10
242 254 0.179215 CACGGATTTGCTTCTGCGAC 60.179 55.000 0.00 0.00 43.34 5.19
260 319 2.473984 CGACCAGTCGTACCTTGAAAAC 59.526 50.000 11.94 0.00 46.99 2.43
267 326 5.675444 CAGTCGTACCTTGAAAACGAAAAAG 59.325 40.000 0.00 0.00 46.08 2.27
271 330 6.742264 TCGTACCTTGAAAACGAAAAAGAAAC 59.258 34.615 0.00 0.00 42.18 2.78
371 430 0.604578 TCGTACCTGTTCGGAAAGGG 59.395 55.000 4.49 13.26 37.94 3.95
396 455 3.963383 AACGTGCTCCTAGTTTGTTTG 57.037 42.857 0.00 0.00 0.00 2.93
401 460 4.279659 GTGCTCCTAGTTTGTTTGTTTCG 58.720 43.478 0.00 0.00 0.00 3.46
407 466 7.090953 TCCTAGTTTGTTTGTTTCGTGAAAT 57.909 32.000 0.00 0.00 32.36 2.17
408 467 7.540299 TCCTAGTTTGTTTGTTTCGTGAAATT 58.460 30.769 0.00 0.00 32.36 1.82
431 490 8.937634 ATTAGTTTATCGAAACCTATCAACGT 57.062 30.769 0.00 0.00 45.21 3.99
434 493 6.530534 AGTTTATCGAAACCTATCAACGTGAG 59.469 38.462 0.00 0.00 45.21 3.51
458 517 4.927978 ATCCAACAATGAAAACGGTTCA 57.072 36.364 6.30 6.30 0.00 3.18
467 526 6.183360 ACAATGAAAACGGTTCAAAATTTGGG 60.183 34.615 5.83 0.00 31.55 4.12
471 530 0.669012 CGGTTCAAAATTTGGGCGGG 60.669 55.000 5.83 0.00 0.00 6.13
472 531 0.682292 GGTTCAAAATTTGGGCGGGA 59.318 50.000 5.83 0.00 0.00 5.14
473 532 1.277842 GGTTCAAAATTTGGGCGGGAT 59.722 47.619 5.83 0.00 0.00 3.85
475 534 1.930251 TCAAAATTTGGGCGGGATGA 58.070 45.000 5.83 0.00 0.00 2.92
477 536 2.430332 TCAAAATTTGGGCGGGATGATC 59.570 45.455 5.83 0.00 0.00 2.92
478 537 2.431782 CAAAATTTGGGCGGGATGATCT 59.568 45.455 0.00 0.00 0.00 2.75
479 538 2.459555 AATTTGGGCGGGATGATCTT 57.540 45.000 0.00 0.00 0.00 2.40
480 539 2.459555 ATTTGGGCGGGATGATCTTT 57.540 45.000 0.00 0.00 0.00 2.52
481 540 1.473258 TTTGGGCGGGATGATCTTTG 58.527 50.000 0.00 0.00 0.00 2.77
482 541 1.037030 TTGGGCGGGATGATCTTTGC 61.037 55.000 0.00 0.00 0.00 3.68
484 543 1.037030 GGGCGGGATGATCTTTGCAA 61.037 55.000 0.00 0.00 0.00 4.08
509 609 5.388944 GCAAAGAGCACTTCTTAATCAGTG 58.611 41.667 9.02 9.02 45.41 3.66
559 659 0.109226 AAGTTGCGCTAGACTCGACC 60.109 55.000 9.73 0.00 0.00 4.79
560 660 0.961358 AGTTGCGCTAGACTCGACCT 60.961 55.000 9.73 0.00 0.00 3.85
561 661 0.109226 GTTGCGCTAGACTCGACCTT 60.109 55.000 9.73 0.00 0.00 3.50
562 662 0.109272 TTGCGCTAGACTCGACCTTG 60.109 55.000 9.73 0.00 0.00 3.61
563 663 1.241990 TGCGCTAGACTCGACCTTGT 61.242 55.000 9.73 0.00 0.00 3.16
564 664 0.731417 GCGCTAGACTCGACCTTGTA 59.269 55.000 0.00 0.00 0.00 2.41
565 665 1.334243 GCGCTAGACTCGACCTTGTAT 59.666 52.381 0.00 0.00 0.00 2.29
566 666 2.855187 GCGCTAGACTCGACCTTGTATG 60.855 54.545 0.00 0.00 0.00 2.39
567 667 2.287069 CGCTAGACTCGACCTTGTATGG 60.287 54.545 0.00 0.00 0.00 2.74
568 668 2.688958 GCTAGACTCGACCTTGTATGGT 59.311 50.000 0.00 0.00 44.10 3.55
596 699 3.584848 CCATAATAAGCTAGTCCAGGGCT 59.415 47.826 0.00 0.00 37.99 5.19
641 753 2.509336 CCTTGTCAGTAGCCGGCG 60.509 66.667 23.20 6.78 0.00 6.46
649 761 2.125673 GTAGCCGGCGCTTTCTCA 60.126 61.111 23.20 0.00 45.55 3.27
650 762 2.167861 GTAGCCGGCGCTTTCTCAG 61.168 63.158 23.20 0.00 45.55 3.35
651 763 2.348104 TAGCCGGCGCTTTCTCAGA 61.348 57.895 23.20 0.00 45.55 3.27
652 764 2.558554 TAGCCGGCGCTTTCTCAGAC 62.559 60.000 23.20 0.00 45.55 3.51
653 765 3.181967 CCGGCGCTTTCTCAGACG 61.182 66.667 7.64 0.00 0.00 4.18
654 766 3.181967 CGGCGCTTTCTCAGACGG 61.182 66.667 7.64 0.00 0.00 4.79
655 767 2.815647 GGCGCTTTCTCAGACGGG 60.816 66.667 7.64 0.00 0.00 5.28
656 768 3.491652 GCGCTTTCTCAGACGGGC 61.492 66.667 0.00 0.00 0.00 6.13
657 769 2.048222 CGCTTTCTCAGACGGGCA 60.048 61.111 0.00 0.00 0.00 5.36
658 770 2.383527 CGCTTTCTCAGACGGGCAC 61.384 63.158 0.00 0.00 0.00 5.01
660 772 2.357034 TTTCTCAGACGGGCACGC 60.357 61.111 9.12 0.14 46.04 5.34
661 773 3.876589 TTTCTCAGACGGGCACGCC 62.877 63.158 9.12 0.00 46.04 5.68
754 866 0.875728 CGTCTCTACCAGATAGGCCG 59.124 60.000 0.00 0.00 43.14 6.13
775 887 2.423446 CCGCATCCTCCTAGCCAC 59.577 66.667 0.00 0.00 0.00 5.01
779 891 2.150051 CATCCTCCTAGCCACCCCC 61.150 68.421 0.00 0.00 0.00 5.40
818 930 2.592287 GGCGACCGGTCAAACCAA 60.592 61.111 32.80 0.00 38.47 3.67
820 932 2.900167 GCGACCGGTCAAACCAACC 61.900 63.158 32.80 4.66 38.47 3.77
834 946 4.733725 AACCTAGCGGCCCTCCCA 62.734 66.667 0.00 0.00 0.00 4.37
859 971 0.768221 TGGTGAGTTCCTTGCCCTCT 60.768 55.000 0.00 0.00 0.00 3.69
907 1019 1.156736 CCCGCTTGAACACTAGGTTG 58.843 55.000 0.00 0.00 40.63 3.77
930 1042 3.449018 TCCTGCTGTAGATTGGAGAAGTC 59.551 47.826 0.00 0.00 0.00 3.01
934 1046 3.368531 GCTGTAGATTGGAGAAGTCGGTT 60.369 47.826 0.00 0.00 0.00 4.44
943 1055 1.734465 GAGAAGTCGGTTGATTGCAGG 59.266 52.381 0.00 0.00 0.00 4.85
944 1056 0.169009 GAAGTCGGTTGATTGCAGGC 59.831 55.000 0.00 0.00 0.00 4.85
971 1083 7.175990 TGGACAAGTTGGTTGATATTTTACTCC 59.824 37.037 7.96 0.44 38.60 3.85
972 1084 7.141100 ACAAGTTGGTTGATATTTTACTCCG 57.859 36.000 7.96 0.00 38.60 4.63
983 1095 8.018537 TGATATTTTACTCCGAATCTTCTCCA 57.981 34.615 0.00 0.00 0.00 3.86
1017 1129 7.502561 AGCCTTTTCATGGACTATACATTTACC 59.497 37.037 0.00 0.00 0.00 2.85
1058 1170 1.985473 TCACTTCCATGTTTGCAGCT 58.015 45.000 0.00 0.00 0.00 4.24
1062 1174 5.252547 TCACTTCCATGTTTGCAGCTTATA 58.747 37.500 0.00 0.00 0.00 0.98
1136 1248 7.043565 CCTTGTTGCCAATTATTCTAAATGCT 58.956 34.615 0.00 0.00 0.00 3.79
1169 1281 0.603707 AGGTGTTCGTGTCCATGCAG 60.604 55.000 0.00 0.00 0.00 4.41
1175 1287 2.104859 CGTGTCCATGCAGCAGAGG 61.105 63.158 9.89 9.89 0.00 3.69
1185 1297 3.694043 TGCAGCAGAGGTTGTAATGTA 57.306 42.857 0.00 0.00 0.00 2.29
1198 1310 3.745799 TGTAATGTACCCAACACCACTG 58.254 45.455 0.00 0.00 42.09 3.66
1203 1315 0.323629 TACCCAACACCACTGCTAGC 59.676 55.000 8.10 8.10 0.00 3.42
1208 1320 1.001974 CAACACCACTGCTAGCCACTA 59.998 52.381 13.29 0.00 0.00 2.74
1237 1349 3.777106 TGAAGCTTCTTCACATCCAGT 57.223 42.857 26.09 0.00 0.00 4.00
1289 1404 8.964476 TCGCAAAAGAGGAATAGAAATCTTAT 57.036 30.769 0.00 0.00 31.90 1.73
1313 1428 7.475786 ATGTTCATACAACCTGGGAAAGGAAC 61.476 42.308 0.00 5.10 42.72 3.62
1331 1446 3.190744 GGAACGATATATCCGTGCTCTGA 59.809 47.826 7.15 0.00 40.44 3.27
1487 1603 5.813672 CCTTTCTTGTTATGGATGCCAATTG 59.186 40.000 0.00 0.00 36.95 2.32
1550 1666 1.613437 CATGTTGACCCAAGTTGACCC 59.387 52.381 3.87 0.00 0.00 4.46
1552 1668 1.029681 GTTGACCCAAGTTGACCCAC 58.970 55.000 3.87 0.00 0.00 4.61
1553 1669 0.464735 TTGACCCAAGTTGACCCACG 60.465 55.000 3.87 0.00 0.00 4.94
1554 1670 1.147600 GACCCAAGTTGACCCACGT 59.852 57.895 3.87 0.00 0.00 4.49
1555 1671 1.153046 ACCCAAGTTGACCCACGTG 60.153 57.895 9.08 9.08 0.00 4.49
1556 1672 1.147376 CCCAAGTTGACCCACGTGA 59.853 57.895 19.30 0.00 0.00 4.35
1557 1673 0.250727 CCCAAGTTGACCCACGTGAT 60.251 55.000 19.30 4.23 0.00 3.06
1558 1674 1.002659 CCCAAGTTGACCCACGTGATA 59.997 52.381 19.30 0.00 0.00 2.15
1559 1675 2.355716 CCCAAGTTGACCCACGTGATAT 60.356 50.000 19.30 0.75 0.00 1.63
1561 1677 2.936498 CAAGTTGACCCACGTGATATCC 59.064 50.000 19.30 1.83 0.00 2.59
1638 1770 6.767902 TGACTTCAGATTTTGCTAGAGTGTTT 59.232 34.615 0.00 0.00 0.00 2.83
1989 2135 7.616935 ACTCCATCAACAATGAAATATGACCTT 59.383 33.333 0.00 0.00 39.49 3.50
2562 2709 7.381766 TGAATCAGAACAACTCATATGGTTG 57.618 36.000 24.00 24.00 46.42 3.77
2731 2878 3.544834 CGTTGCTTAAGCCAATCTCGATG 60.545 47.826 24.30 2.81 41.18 3.84
2853 3761 2.669569 CACCACTGCCCTCAACCG 60.670 66.667 0.00 0.00 0.00 4.44
3010 3918 1.615883 GAAGGCTATGAGATGGCGAGA 59.384 52.381 0.00 0.00 37.67 4.04
3011 3919 1.709578 AGGCTATGAGATGGCGAGAA 58.290 50.000 0.00 0.00 37.67 2.87
3012 3920 2.255406 AGGCTATGAGATGGCGAGAAT 58.745 47.619 0.00 0.00 37.67 2.40
3013 3921 2.233431 AGGCTATGAGATGGCGAGAATC 59.767 50.000 0.00 0.00 37.67 2.52
3014 3922 2.233431 GGCTATGAGATGGCGAGAATCT 59.767 50.000 0.00 0.00 37.67 2.40
3015 3923 3.252400 GCTATGAGATGGCGAGAATCTG 58.748 50.000 0.00 0.00 34.50 2.90
3016 3924 3.056962 GCTATGAGATGGCGAGAATCTGA 60.057 47.826 0.00 0.00 34.50 3.27
3017 3925 2.879002 TGAGATGGCGAGAATCTGAC 57.121 50.000 0.00 0.00 34.50 3.51
3028 3936 4.676546 CGAGAATCTGACAATCTGTAGCA 58.323 43.478 0.00 0.00 0.00 3.49
3085 3993 8.029522 GCTAAAGTAGATCACCATCATCGATAA 58.970 37.037 0.00 0.00 0.00 1.75
3113 4021 2.679092 CAAGAGGGATGCTGGGCA 59.321 61.111 0.00 0.00 44.86 5.36
3283 4191 4.305956 CAAAGGGCCCCAGCAGGT 62.306 66.667 21.43 0.00 42.56 4.00
3518 4430 4.532521 AGGGATGCCTAATTAAGCGTCTAT 59.467 41.667 21.85 11.82 43.21 1.98
3615 4527 1.631405 ACAAGGCCTAAAGCATGCAA 58.369 45.000 21.98 3.70 46.50 4.08
3619 4531 3.303351 AGGCCTAAAGCATGCAACTAT 57.697 42.857 21.98 3.21 46.50 2.12
3674 4586 1.399791 ACGTCCGACGATTTAGAGTCC 59.600 52.381 27.03 0.00 46.05 3.85
3684 4596 3.243877 CGATTTAGAGTCCGATGCTTGTG 59.756 47.826 0.00 0.00 0.00 3.33
3710 4622 0.315568 GCGATCGGACCATCTAGCTT 59.684 55.000 18.30 0.00 0.00 3.74
3711 4623 1.540267 GCGATCGGACCATCTAGCTTA 59.460 52.381 18.30 0.00 0.00 3.09
3761 4673 3.827876 TGGTAGGTGTCGTACAAAGATCA 59.172 43.478 0.00 0.00 0.00 2.92
3782 4694 3.852536 CAGACCAGAATTTCTCGTACGTC 59.147 47.826 16.05 4.09 0.00 4.34
3884 4796 7.277760 CGATAACGGCTGATTCCATATTTGATA 59.722 37.037 0.00 0.00 35.72 2.15
4032 4944 2.373335 ACCGAGATAGAGGATGCAGT 57.627 50.000 0.00 0.00 0.00 4.40
4176 5090 4.469657 ACATGTTTGGTTGTACTGGTGAT 58.530 39.130 0.00 0.00 0.00 3.06
4596 5510 7.447853 TGGTTGTAAAATAATACGGAGGTGTTT 59.552 33.333 0.00 0.00 0.00 2.83
4665 5579 3.985925 GCACCTTTCTTTGAGCAATTCTG 59.014 43.478 0.00 0.00 0.00 3.02
4735 5649 7.146648 TGTATTTAAAACGAAAATGGTGACCC 58.853 34.615 0.00 0.00 0.00 4.46
4761 5675 4.223953 CAGGGCCTAAGAGGTTGACTATA 58.776 47.826 5.28 0.00 37.80 1.31
4762 5676 4.841246 CAGGGCCTAAGAGGTTGACTATAT 59.159 45.833 5.28 0.00 37.80 0.86
4800 5714 8.116753 CGATAAATTCTTTTAGTGCAAGTCGAT 58.883 33.333 0.00 0.00 31.07 3.59
4843 5757 8.613060 TTTCCTCGTGTAAGTCGACTATATAT 57.387 34.615 20.39 5.08 33.71 0.86
4844 5758 9.710900 TTTCCTCGTGTAAGTCGACTATATATA 57.289 33.333 20.39 3.95 33.71 0.86
4846 5760 9.363763 TCCTCGTGTAAGTCGACTATATATAAG 57.636 37.037 20.39 8.59 33.71 1.73
4847 5761 9.363763 CCTCGTGTAAGTCGACTATATATAAGA 57.636 37.037 20.39 12.22 33.71 2.10
4850 5764 9.752274 CGTGTAAGTCGACTATATATAAGAACC 57.248 37.037 20.39 0.00 0.00 3.62
4852 5766 9.236006 TGTAAGTCGACTATATATAAGAACCCC 57.764 37.037 20.39 0.00 0.00 4.95
4878 5792 2.747855 CTCCAGCCGCCCAACTTC 60.748 66.667 0.00 0.00 0.00 3.01
4895 5809 0.959553 TTCTCTCTCGTCGTTGCCTT 59.040 50.000 0.00 0.00 0.00 4.35
4942 5857 1.194781 ACCGACAATGCCTCCTCTGT 61.195 55.000 0.00 0.00 0.00 3.41
4972 5887 3.415212 TCCTCTCTGCAAAATCAAGGTG 58.585 45.455 0.00 0.00 0.00 4.00
4974 5889 3.415212 CTCTCTGCAAAATCAAGGTGGA 58.585 45.455 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.244318 TGTTTACCCCTTTTCCGAGAGAC 60.244 47.826 0.00 0.00 0.00 3.36
1 2 2.974099 TGTTTACCCCTTTTCCGAGAGA 59.026 45.455 0.00 0.00 0.00 3.10
2 3 3.072211 GTGTTTACCCCTTTTCCGAGAG 58.928 50.000 0.00 0.00 0.00 3.20
3 4 2.438763 TGTGTTTACCCCTTTTCCGAGA 59.561 45.455 0.00 0.00 0.00 4.04
4 5 2.853705 TGTGTTTACCCCTTTTCCGAG 58.146 47.619 0.00 0.00 0.00 4.63
5 6 3.512219 ATGTGTTTACCCCTTTTCCGA 57.488 42.857 0.00 0.00 0.00 4.55
6 7 4.594123 AAATGTGTTTACCCCTTTTCCG 57.406 40.909 0.00 0.00 0.00 4.30
28 29 7.607991 TGGAAACTAAATTTGTGCCAAGAAAAA 59.392 29.630 0.00 0.00 0.00 1.94
29 30 7.106239 TGGAAACTAAATTTGTGCCAAGAAAA 58.894 30.769 0.00 0.00 0.00 2.29
30 31 6.644347 TGGAAACTAAATTTGTGCCAAGAAA 58.356 32.000 0.00 0.00 0.00 2.52
31 32 6.227298 TGGAAACTAAATTTGTGCCAAGAA 57.773 33.333 0.00 0.00 0.00 2.52
32 33 5.860941 TGGAAACTAAATTTGTGCCAAGA 57.139 34.783 0.00 0.00 0.00 3.02
33 34 6.222389 TCATGGAAACTAAATTTGTGCCAAG 58.778 36.000 0.00 6.44 0.00 3.61
34 35 6.166984 TCATGGAAACTAAATTTGTGCCAA 57.833 33.333 0.00 0.00 0.00 4.52
35 36 5.798125 TCATGGAAACTAAATTTGTGCCA 57.202 34.783 0.00 8.86 0.00 4.92
41 42 6.267471 TCTGTGCCTTCATGGAAACTAAATTT 59.733 34.615 0.00 0.00 38.35 1.82
48 49 4.240096 CAAATCTGTGCCTTCATGGAAAC 58.760 43.478 0.00 0.00 38.35 2.78
51 52 1.820519 GCAAATCTGTGCCTTCATGGA 59.179 47.619 0.00 0.00 38.66 3.41
52 53 1.822990 AGCAAATCTGTGCCTTCATGG 59.177 47.619 0.00 0.00 46.14 3.66
64 65 1.737363 GCCTCTCGTCGAAGCAAATCT 60.737 52.381 0.00 0.00 0.00 2.40
76 77 1.741770 GCAAATCCGTGCCTCTCGT 60.742 57.895 0.00 0.00 38.66 4.18
78 79 0.729690 GAAGCAAATCCGTGCCTCTC 59.270 55.000 0.00 0.00 46.14 3.20
93 101 1.803519 CTGTGCCTCTCGTCGAAGC 60.804 63.158 0.00 0.38 0.00 3.86
99 107 3.963428 AAGTAAATCTGTGCCTCTCGT 57.037 42.857 0.00 0.00 0.00 4.18
103 111 5.059833 CCTCCATAAGTAAATCTGTGCCTC 58.940 45.833 0.00 0.00 0.00 4.70
111 119 4.067972 TCCGTGCCTCCATAAGTAAATC 57.932 45.455 0.00 0.00 0.00 2.17
112 120 4.706842 ATCCGTGCCTCCATAAGTAAAT 57.293 40.909 0.00 0.00 0.00 1.40
113 121 4.497291 AATCCGTGCCTCCATAAGTAAA 57.503 40.909 0.00 0.00 0.00 2.01
114 122 4.196193 CAAATCCGTGCCTCCATAAGTAA 58.804 43.478 0.00 0.00 0.00 2.24
116 124 2.643551 CAAATCCGTGCCTCCATAAGT 58.356 47.619 0.00 0.00 0.00 2.24
118 126 1.064758 AGCAAATCCGTGCCTCCATAA 60.065 47.619 0.00 0.00 46.14 1.90
120 128 0.323725 AAGCAAATCCGTGCCTCCAT 60.324 50.000 0.00 0.00 46.14 3.41
122 130 0.109132 CAAAGCAAATCCGTGCCTCC 60.109 55.000 0.00 0.00 46.14 4.30
123 131 0.109132 CCAAAGCAAATCCGTGCCTC 60.109 55.000 0.00 0.00 46.14 4.70
124 132 1.966762 CCAAAGCAAATCCGTGCCT 59.033 52.632 0.00 0.00 46.14 4.75
125 133 1.737735 GCCAAAGCAAATCCGTGCC 60.738 57.895 0.00 0.00 46.14 5.01
126 134 3.860717 GCCAAAGCAAATCCGTGC 58.139 55.556 0.00 0.00 45.28 5.34
138 146 1.189752 TGACTGTGCCTTTTGCCAAA 58.810 45.000 0.00 0.00 40.16 3.28
140 148 0.675083 CATGACTGTGCCTTTTGCCA 59.325 50.000 0.00 0.00 40.16 4.92
141 149 0.668401 GCATGACTGTGCCTTTTGCC 60.668 55.000 0.00 0.00 39.18 4.52
197 209 5.767816 AGAAGTAAATTTGTGGCTTTCGT 57.232 34.783 0.00 0.00 0.00 3.85
208 220 6.625081 GCAAATCCGTGCCTAGAAGTAAATTT 60.625 38.462 0.00 0.00 38.66 1.82
223 235 0.179215 GTCGCAGAAGCAAATCCGTG 60.179 55.000 0.00 0.00 39.69 4.94
225 237 1.298157 TGGTCGCAGAAGCAAATCCG 61.298 55.000 0.00 0.00 39.69 4.18
240 252 2.473984 CGTTTTCAAGGTACGACTGGTC 59.526 50.000 0.00 0.00 37.47 4.02
241 253 2.101249 TCGTTTTCAAGGTACGACTGGT 59.899 45.455 0.00 0.00 39.15 4.00
242 254 2.746269 TCGTTTTCAAGGTACGACTGG 58.254 47.619 0.00 0.00 39.15 4.00
254 313 8.983724 AGAAAACATGTTTCTTTTTCGTTTTCA 58.016 25.926 23.47 0.00 46.57 2.69
316 375 2.254546 AGCAAATCCGTGTCTTCACA 57.745 45.000 0.00 0.00 44.02 3.58
320 379 2.969443 CGAAAGCAAATCCGTGTCTT 57.031 45.000 0.00 0.00 0.00 3.01
347 406 4.487948 CTTTCCGAACAGGTACGAATGTA 58.512 43.478 0.00 0.00 41.99 2.29
351 410 1.001181 CCCTTTCCGAACAGGTACGAA 59.999 52.381 0.00 0.00 41.99 3.85
356 415 2.740506 TTTTCCCTTTCCGAACAGGT 57.259 45.000 7.93 0.00 41.99 4.00
379 438 4.201881 ACGAAACAAACAAACTAGGAGCAC 60.202 41.667 0.00 0.00 0.00 4.40
380 439 3.942748 ACGAAACAAACAAACTAGGAGCA 59.057 39.130 0.00 0.00 0.00 4.26
381 440 4.034742 TCACGAAACAAACAAACTAGGAGC 59.965 41.667 0.00 0.00 0.00 4.70
382 441 5.728351 TCACGAAACAAACAAACTAGGAG 57.272 39.130 0.00 0.00 0.00 3.69
383 442 6.497785 TTTCACGAAACAAACAAACTAGGA 57.502 33.333 0.00 0.00 0.00 2.94
384 443 7.749539 AATTTCACGAAACAAACAAACTAGG 57.250 32.000 0.00 0.00 32.51 3.02
386 445 9.843334 AACTAATTTCACGAAACAAACAAACTA 57.157 25.926 0.00 0.00 32.51 2.24
387 446 8.751302 AACTAATTTCACGAAACAAACAAACT 57.249 26.923 0.00 0.00 32.51 2.66
392 451 9.372541 TCGATAAACTAATTTCACGAAACAAAC 57.627 29.630 0.00 0.00 34.73 2.93
407 466 8.028354 TCACGTTGATAGGTTTCGATAAACTAA 58.972 33.333 8.50 0.00 43.76 2.24
408 467 7.537715 TCACGTTGATAGGTTTCGATAAACTA 58.462 34.615 7.31 7.31 43.76 2.24
431 490 4.022416 CCGTTTTCATTGTTGGATTCCTCA 60.022 41.667 3.95 0.91 0.00 3.86
434 493 4.251543 ACCGTTTTCATTGTTGGATTCC 57.748 40.909 0.00 0.00 0.00 3.01
458 517 2.750814 AGATCATCCCGCCCAAATTTT 58.249 42.857 0.00 0.00 0.00 1.82
467 526 1.866880 GCATTGCAAAGATCATCCCGC 60.867 52.381 1.71 0.00 0.00 6.13
494 594 6.414408 AGCGAAATCACTGATTAAGAAGTG 57.586 37.500 12.13 12.13 44.23 3.16
505 605 5.634859 AGCCAAAATTTAAGCGAAATCACTG 59.365 36.000 6.69 0.44 36.71 3.66
507 607 6.145371 TGAAGCCAAAATTTAAGCGAAATCAC 59.855 34.615 6.69 0.00 36.71 3.06
509 609 6.704512 TGAAGCCAAAATTTAAGCGAAATC 57.295 33.333 6.69 5.61 36.71 2.17
544 644 1.241990 ACAAGGTCGAGTCTAGCGCA 61.242 55.000 11.47 0.00 0.00 6.09
565 665 2.135189 AGCTTATTATGGGCCAGACCA 58.865 47.619 13.78 0.00 46.24 4.02
566 666 2.959465 AGCTTATTATGGGCCAGACC 57.041 50.000 13.78 0.00 37.93 3.85
567 667 4.563786 GGACTAGCTTATTATGGGCCAGAC 60.564 50.000 13.78 0.00 0.00 3.51
568 668 3.583086 GGACTAGCTTATTATGGGCCAGA 59.417 47.826 13.78 3.79 0.00 3.86
596 699 2.673775 TGGGCCTTTTGATGTCTTCA 57.326 45.000 4.53 0.00 0.00 3.02
641 753 2.383527 CGTGCCCGTCTGAGAAAGC 61.384 63.158 0.00 0.00 0.00 3.51
754 866 2.423446 CTAGGAGGATGCGGTGGC 59.577 66.667 0.00 0.00 40.52 5.01
779 891 3.986572 CGTAGATCTGCTGATGCTTAAGG 59.013 47.826 11.21 0.00 40.48 2.69
812 924 2.035155 GGGCCGCTAGGTTGGTTT 59.965 61.111 0.00 0.00 40.50 3.27
818 930 4.733725 TTGGGAGGGCCGCTAGGT 62.734 66.667 7.35 0.00 40.50 3.08
820 932 4.554036 GCTTGGGAGGGCCGCTAG 62.554 72.222 7.35 3.87 34.62 3.42
834 946 1.915141 CAAGGAACTCACCATGGCTT 58.085 50.000 13.04 1.82 38.49 4.35
859 971 4.584325 CACTTTCAATTTGGTGAGGAAGGA 59.416 41.667 0.00 0.00 32.12 3.36
907 1019 3.196685 ACTTCTCCAATCTACAGCAGGAC 59.803 47.826 0.00 0.00 0.00 3.85
930 1042 1.675310 TCCAGCCTGCAATCAACCG 60.675 57.895 0.00 0.00 0.00 4.44
934 1046 0.111061 ACTTGTCCAGCCTGCAATCA 59.889 50.000 0.00 0.00 0.00 2.57
943 1055 5.391312 AAATATCAACCAACTTGTCCAGC 57.609 39.130 0.00 0.00 0.00 4.85
944 1056 8.110860 AGTAAAATATCAACCAACTTGTCCAG 57.889 34.615 0.00 0.00 0.00 3.86
971 1083 3.623510 GCTAGGGTTTTGGAGAAGATTCG 59.376 47.826 0.00 0.00 0.00 3.34
972 1084 3.948473 GGCTAGGGTTTTGGAGAAGATTC 59.052 47.826 0.00 0.00 0.00 2.52
983 1095 3.832490 GTCCATGAAAAGGCTAGGGTTTT 59.168 43.478 0.00 0.00 0.00 2.43
1017 1129 0.734942 AGTAAATGTGACCGTCGGCG 60.735 55.000 12.28 0.29 37.95 6.46
1093 1205 9.649167 GCAACAAGGGTATAATACGTAATCTAT 57.351 33.333 0.00 0.11 0.00 1.98
1136 1248 3.613193 CGAACACCTAACACGAGGATTCA 60.613 47.826 0.00 0.00 39.15 2.57
1169 1281 3.343941 TGGGTACATTACAACCTCTGC 57.656 47.619 0.00 0.00 35.97 4.26
1175 1287 4.023536 CAGTGGTGTTGGGTACATTACAAC 60.024 45.833 12.26 12.26 43.47 3.32
1185 1297 1.073199 GCTAGCAGTGGTGTTGGGT 59.927 57.895 10.63 0.00 0.00 4.51
1198 1310 5.178438 GCTTCATCATACTTTAGTGGCTAGC 59.822 44.000 6.04 6.04 0.00 3.42
1203 1315 7.550551 TGAAGAAGCTTCATCATACTTTAGTGG 59.449 37.037 26.10 0.00 30.81 4.00
1208 1320 7.066766 GGATGTGAAGAAGCTTCATCATACTTT 59.933 37.037 30.60 17.12 37.27 2.66
1260 1375 6.481954 TTTCTATTCCTCTTTTGCGAGTTC 57.518 37.500 0.00 0.00 0.00 3.01
1289 1404 3.396276 TCCTTTCCCAGGTTGTATGAACA 59.604 43.478 0.00 0.00 44.37 3.18
1294 1409 2.640826 TCGTTCCTTTCCCAGGTTGTAT 59.359 45.455 0.00 0.00 44.37 2.29
1302 1417 3.899360 ACGGATATATCGTTCCTTTCCCA 59.101 43.478 6.64 0.00 37.61 4.37
1313 1428 4.564372 CCATTTCAGAGCACGGATATATCG 59.436 45.833 6.64 5.08 0.00 2.92
1317 1432 4.285517 AGATCCATTTCAGAGCACGGATAT 59.714 41.667 0.00 0.00 33.44 1.63
1331 1446 7.366913 CCCTCTTACCCTTCTAAAGATCCATTT 60.367 40.741 0.00 0.00 0.00 2.32
1401 1516 7.764443 AGATGTGTTGTCGCTACTTTATAATGT 59.236 33.333 8.83 8.83 0.00 2.71
1408 1523 4.377021 TCAAGATGTGTTGTCGCTACTTT 58.623 39.130 0.00 0.00 0.00 2.66
1439 1554 4.067896 AGGTGCAACAAGATCACTAACAG 58.932 43.478 3.64 0.00 39.98 3.16
1440 1555 4.085357 AGGTGCAACAAGATCACTAACA 57.915 40.909 3.64 0.00 39.98 2.41
1487 1603 3.940209 TCACAATCACTTGAAATGGCC 57.060 42.857 0.00 0.00 36.20 5.36
1550 1666 4.876125 ACTGATGCTAAGGATATCACGTG 58.124 43.478 9.94 9.94 0.00 4.49
1552 1668 5.176406 CACAACTGATGCTAAGGATATCACG 59.824 44.000 4.83 0.00 0.00 4.35
1553 1669 6.051717 ACACAACTGATGCTAAGGATATCAC 58.948 40.000 4.83 0.00 0.00 3.06
1554 1670 6.239217 ACACAACTGATGCTAAGGATATCA 57.761 37.500 4.83 0.00 0.00 2.15
1555 1671 6.367422 GCTACACAACTGATGCTAAGGATATC 59.633 42.308 0.00 0.00 0.00 1.63
1556 1672 6.042552 AGCTACACAACTGATGCTAAGGATAT 59.957 38.462 0.00 0.00 31.30 1.63
1557 1673 5.363868 AGCTACACAACTGATGCTAAGGATA 59.636 40.000 0.00 0.00 31.30 2.59
1558 1674 4.163078 AGCTACACAACTGATGCTAAGGAT 59.837 41.667 0.00 0.00 31.30 3.24
1559 1675 3.515502 AGCTACACAACTGATGCTAAGGA 59.484 43.478 0.00 0.00 31.30 3.36
1561 1677 4.093998 CCAAGCTACACAACTGATGCTAAG 59.906 45.833 0.00 0.00 32.24 2.18
1638 1770 6.286758 TGATTTAAGTGCAAAATTTGGAGCA 58.713 32.000 7.89 8.59 34.10 4.26
1683 1815 4.048504 AGCAAACAAAAACGCCTGAATAC 58.951 39.130 0.00 0.00 0.00 1.89
1989 2135 1.071071 CCCGTTAGGAAGTGAACCACA 59.929 52.381 0.00 0.00 41.02 4.17
2372 2518 8.154856 AGCAGTAGGAAAGACAGTAACAAAATA 58.845 33.333 0.00 0.00 0.00 1.40
2731 2878 3.270877 AGTTGTTTCACAGTCTGGACAC 58.729 45.455 4.53 3.23 0.00 3.67
2761 2908 1.611977 GTTGTTGCCCCAACTTCTACC 59.388 52.381 9.23 0.00 43.85 3.18
2782 2929 2.310779 TCTGTTCCCTAGCACACTCT 57.689 50.000 0.00 0.00 0.00 3.24
2853 3761 2.811317 CGGACTCGCTTGGTGCTC 60.811 66.667 0.00 0.00 40.11 4.26
2930 3838 1.739371 GCTCTTTGGCTCGACGGTATT 60.739 52.381 0.00 0.00 0.00 1.89
3010 3918 4.867047 CGTCTTGCTACAGATTGTCAGATT 59.133 41.667 0.00 0.00 0.00 2.40
3011 3919 4.081972 ACGTCTTGCTACAGATTGTCAGAT 60.082 41.667 0.00 0.00 0.00 2.90
3012 3920 3.255888 ACGTCTTGCTACAGATTGTCAGA 59.744 43.478 0.00 0.00 0.00 3.27
3013 3921 3.579709 ACGTCTTGCTACAGATTGTCAG 58.420 45.455 0.00 0.00 0.00 3.51
3014 3922 3.660501 ACGTCTTGCTACAGATTGTCA 57.339 42.857 0.00 0.00 0.00 3.58
3015 3923 3.987868 TCAACGTCTTGCTACAGATTGTC 59.012 43.478 0.00 0.00 0.00 3.18
3016 3924 3.990092 TCAACGTCTTGCTACAGATTGT 58.010 40.909 0.00 0.00 0.00 2.71
3017 3925 4.237724 TCTCAACGTCTTGCTACAGATTG 58.762 43.478 0.00 0.00 0.00 2.67
3028 3936 3.357203 TCTATGCTCCTCTCAACGTCTT 58.643 45.455 0.00 0.00 0.00 3.01
3056 3964 6.145209 CGATGATGGTGATCTACTTTAGCAAG 59.855 42.308 0.00 0.00 35.92 4.01
3085 3993 2.925966 TCCCTCTTGCCAAATCCAAT 57.074 45.000 0.00 0.00 0.00 3.16
3113 4021 2.741612 CGTTGTTCACACAATTGCCAT 58.258 42.857 5.05 0.00 44.85 4.40
3117 4025 1.851666 GTGGCGTTGTTCACACAATTG 59.148 47.619 3.24 3.24 44.85 2.32
3283 4191 4.202451 TGTTGATCTTGACTGGGTCATTCA 60.202 41.667 1.10 3.59 42.40 2.57
3299 4207 8.356533 ACAATTTTCTGATTGTGTTGTTGATC 57.643 30.769 2.73 0.00 45.75 2.92
3477 4389 0.815615 CTCCTGCGGAAATAGGCACC 60.816 60.000 0.00 0.00 34.97 5.01
3518 4430 2.912956 ACCAGTGCTTATTTGGAGAGGA 59.087 45.455 0.00 0.00 35.89 3.71
3577 4489 3.081061 TGTACAATGCAAGGTGCTTAGG 58.919 45.455 9.81 0.00 45.31 2.69
3578 4490 4.726416 CTTGTACAATGCAAGGTGCTTAG 58.274 43.478 9.13 4.87 45.31 2.18
3579 4491 4.764679 CTTGTACAATGCAAGGTGCTTA 57.235 40.909 9.13 0.00 45.31 3.09
3619 4531 8.095792 TCCGGTAAAATTTAGAACACATAGTGA 58.904 33.333 0.00 0.00 36.96 3.41
3684 4596 1.394917 GATGGTCCGATCGCATATTGC 59.605 52.381 10.32 0.00 40.69 3.56
3711 4623 9.017509 CAGCCATCCATCACATTATTAGTTTAT 57.982 33.333 0.00 0.00 0.00 1.40
3761 4673 3.757493 AGACGTACGAGAAATTCTGGTCT 59.243 43.478 24.41 6.53 36.78 3.85
3782 4694 6.674694 ACAATAAAACATGAGAGCTGCTAG 57.325 37.500 0.15 0.00 0.00 3.42
4032 4944 0.037326 GCGGTCCATGTCTTCTCACA 60.037 55.000 0.00 0.00 0.00 3.58
4176 5090 7.857389 CAGACGATTGAAAACTGAAAAATCTGA 59.143 33.333 0.00 0.00 0.00 3.27
4492 5406 4.337555 CCCTGAACTATTGAAATCCTGCTG 59.662 45.833 0.00 0.00 0.00 4.41
4596 5510 5.831997 CAGATGATGTACACCTGTAATCGA 58.168 41.667 0.00 0.00 35.51 3.59
4624 5538 7.186570 AGGTGCAAATAAGCCATTTTATTCT 57.813 32.000 0.00 0.00 34.49 2.40
4665 5579 2.337170 CCGTTTTGTTTCCGGCCC 59.663 61.111 0.00 0.00 34.62 5.80
4735 5649 0.613777 AACCTCTTAGGCCCTGTTCG 59.386 55.000 0.00 0.00 39.63 3.95
4800 5714 9.162733 ACGAGGAAAAGGGGTTCTTATATATAA 57.837 33.333 5.10 5.10 34.78 0.98
4821 5735 9.363763 TCTTATATATAGTCGACTTACACGAGG 57.636 37.037 25.44 9.29 40.37 4.63
4843 5757 2.917600 GGAGGAGGAAAAGGGGTTCTTA 59.082 50.000 0.00 0.00 34.78 2.10
4844 5758 1.711375 GGAGGAGGAAAAGGGGTTCTT 59.289 52.381 0.00 0.00 37.28 2.52
4846 5760 1.004862 CTGGAGGAGGAAAAGGGGTTC 59.995 57.143 0.00 0.00 0.00 3.62
4847 5761 1.076438 CTGGAGGAGGAAAAGGGGTT 58.924 55.000 0.00 0.00 0.00 4.11
4848 5762 1.501654 GCTGGAGGAGGAAAAGGGGT 61.502 60.000 0.00 0.00 0.00 4.95
4850 5764 1.304617 GGCTGGAGGAGGAAAAGGG 59.695 63.158 0.00 0.00 0.00 3.95
4851 5765 1.078143 CGGCTGGAGGAGGAAAAGG 60.078 63.158 0.00 0.00 0.00 3.11
4852 5766 1.746991 GCGGCTGGAGGAGGAAAAG 60.747 63.158 0.00 0.00 0.00 2.27
4878 5792 1.347817 GCAAGGCAACGACGAGAGAG 61.348 60.000 0.00 0.00 46.39 3.20
4942 5857 4.897509 TTTGCAGAGAGGAAGATGAAGA 57.102 40.909 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.