Multiple sequence alignment - TraesCS6B01G285300

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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 TraesCS6B01G285300 chr6B 100.000 3540 0 0 1 3540 514480577 514477038 0.000000e+00 6538.0
1 TraesCS6B01G285300 chr6D 93.399 2621 89 26 880 3443 312557694 312560287 0.000000e+00 3805.0
2 TraesCS6B01G285300 chr6D 94.326 282 13 3 305 584 312556839 312557119 2.530000e-116 429.0
3 TraesCS6B01G285300 chr6D 88.889 108 9 3 585 689 312557146 312557253 2.870000e-26 130.0
4 TraesCS6B01G285300 chr6A 91.915 2647 100 47 880 3440 449180627 449183245 0.000000e+00 3598.0
5 TraesCS6B01G285300 chr6A 95.745 282 9 3 305 584 449180023 449180303 5.390000e-123 451.0
6 TraesCS6B01G285300 chr6A 88.591 149 14 1 17 165 449179772 449179917 1.010000e-40 178.0
7 TraesCS6B01G285300 chr6A 90.566 106 9 1 585 689 449180330 449180435 4.770000e-29 139.0
8 TraesCS6B01G285300 chr2D 78.341 651 83 42 1926 2541 491193870 491194497 5.580000e-98 368.0
9 TraesCS6B01G285300 chr2A 78.321 655 83 43 1926 2544 635511719 635512350 5.580000e-98 368.0
10 TraesCS6B01G285300 chr2A 98.990 99 1 0 3442 3540 734654552 734654454 1.010000e-40 178.0
11 TraesCS6B01G285300 chr2A 83.673 98 11 5 694 787 24117310 24117406 1.750000e-13 87.9
12 TraesCS6B01G285300 chr2B 77.356 658 87 42 1926 2544 575836135 575836769 2.040000e-87 333.0
13 TraesCS6B01G285300 chr2B 97.143 105 2 1 3436 3540 784526716 784526613 3.630000e-40 176.0
14 TraesCS6B01G285300 chr4A 99.000 100 1 0 3441 3540 674449205 674449106 2.810000e-41 180.0
15 TraesCS6B01G285300 chr7B 98.990 99 1 0 3442 3540 72768470 72768372 1.010000e-40 178.0
16 TraesCS6B01G285300 chr7A 98.039 102 2 0 3439 3540 120591626 120591525 1.010000e-40 178.0
17 TraesCS6B01G285300 chr7A 98.020 101 2 0 3440 3540 17485380 17485280 3.630000e-40 176.0
18 TraesCS6B01G285300 chr7A 86.364 88 12 0 697 784 133087699 133087786 2.910000e-16 97.1
19 TraesCS6B01G285300 chr3A 98.990 99 1 0 3442 3540 98833151 98833249 1.010000e-40 178.0
20 TraesCS6B01G285300 chr1B 98.990 99 1 0 3442 3540 373630749 373630847 1.010000e-40 178.0
21 TraesCS6B01G285300 chr3B 98.020 101 2 0 3440 3540 157766631 157766531 3.630000e-40 176.0
22 TraesCS6B01G285300 chr3B 80.000 210 34 8 2280 2485 496615093 496615298 7.920000e-32 148.0
23 TraesCS6B01G285300 chr3B 87.500 80 5 3 703 778 9404057 9403979 1.750000e-13 87.9
24 TraesCS6B01G285300 chr3B 84.884 86 13 0 700 785 398965959 398966044 1.750000e-13 87.9
25 TraesCS6B01G285300 chr4B 89.024 82 7 2 700 780 628229652 628229732 2.250000e-17 100.0
26 TraesCS6B01G285300 chr4B 87.805 82 8 2 700 780 628260120 628260200 1.050000e-15 95.3
27 TraesCS6B01G285300 chr7D 87.805 82 10 0 703 784 411331688 411331607 2.910000e-16 97.1
28 TraesCS6B01G285300 chr5D 86.047 86 10 2 694 779 510442748 510442831 1.350000e-14 91.6
29 TraesCS6B01G285300 chr1D 83.696 92 15 0 693 784 456271665 456271756 1.750000e-13 87.9


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 TraesCS6B01G285300 chr6B 514477038 514480577 3539 True 6538.000000 6538 100.000000 1 3540 1 chr6B.!!$R1 3539
1 TraesCS6B01G285300 chr6D 312556839 312560287 3448 False 1454.666667 3805 92.204667 305 3443 3 chr6D.!!$F1 3138
2 TraesCS6B01G285300 chr6A 449179772 449183245 3473 False 1091.500000 3598 91.704250 17 3440 4 chr6A.!!$F1 3423
3 TraesCS6B01G285300 chr2D 491193870 491194497 627 False 368.000000 368 78.341000 1926 2541 1 chr2D.!!$F1 615
4 TraesCS6B01G285300 chr2A 635511719 635512350 631 False 368.000000 368 78.321000 1926 2544 1 chr2A.!!$F2 618
5 TraesCS6B01G285300 chr2B 575836135 575836769 634 False 333.000000 333 77.356000 1926 2544 1 chr2B.!!$F1 618

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
312 374 0.095417 GATCTGAAGCGGCGAACAAC 59.905 55.0 12.98 0.0 0.0 3.32 F
1299 1686 0.037697 AGACGTGTGTGTGTGTGTGT 60.038 50.0 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2610 0.038801 GCTTCTTGGCCTTGTGCTTC 60.039 55.0 3.32 0.0 40.92 3.86 R
3144 3639 0.733909 GGTTCCGCTTTGAATGCAGC 60.734 55.0 3.94 0.0 0.00 5.25 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
33 34 7.945664 CCCTACTAGTACTATCCAAACAGATCT 59.054 40.741 2.33 0.00 0.00 2.75
35 36 7.826918 ACTAGTACTATCCAAACAGATCTCC 57.173 40.000 2.33 0.00 0.00 3.71
42 43 1.276421 CCAAACAGATCTCCACTCGGT 59.724 52.381 0.00 0.00 0.00 4.69
54 55 2.158957 TCCACTCGGTCAAATATGGAGC 60.159 50.000 0.00 0.00 32.50 4.70
60 61 3.450817 TCGGTCAAATATGGAGCAGAAGA 59.549 43.478 7.39 0.00 33.16 2.87
66 67 7.363268 GGTCAAATATGGAGCAGAAGATTTGTT 60.363 37.037 10.46 0.00 36.27 2.83
67 68 8.677300 GTCAAATATGGAGCAGAAGATTTGTTA 58.323 33.333 10.46 0.00 36.27 2.41
83 84 1.271102 TGTTAACCCGATTTGGCAAGC 59.729 47.619 2.48 0.00 35.87 4.01
85 86 1.309499 TAACCCGATTTGGCAAGCCG 61.309 55.000 13.87 13.87 39.42 5.52
101 102 4.389687 GCAAGCCGAATTTGTGATTTCATT 59.610 37.500 0.00 0.00 0.00 2.57
102 103 5.576384 GCAAGCCGAATTTGTGATTTCATTA 59.424 36.000 0.00 0.00 0.00 1.90
103 104 6.237648 GCAAGCCGAATTTGTGATTTCATTAG 60.238 38.462 0.00 0.00 0.00 1.73
165 166 4.155449 CAACGAATAAACACCGAACATGG 58.845 43.478 0.00 0.00 0.00 3.66
166 167 2.160813 ACGAATAAACACCGAACATGGC 59.839 45.455 0.00 0.00 0.00 4.40
167 168 2.780993 GAATAAACACCGAACATGGCG 58.219 47.619 0.00 0.00 0.00 5.69
168 169 2.102070 ATAAACACCGAACATGGCGA 57.898 45.000 11.20 0.00 0.00 5.54
169 170 1.434555 TAAACACCGAACATGGCGAG 58.565 50.000 11.20 6.49 0.00 5.03
170 171 1.852067 AAACACCGAACATGGCGAGC 61.852 55.000 11.20 0.00 0.00 5.03
193 255 4.301505 ATTGCTTGACGCGATGGT 57.698 50.000 15.93 0.00 41.27 3.55
199 261 3.263261 TGCTTGACGCGATGGTTTATTA 58.737 40.909 15.93 0.00 43.27 0.98
201 263 3.308866 GCTTGACGCGATGGTTTATTACT 59.691 43.478 15.93 0.00 0.00 2.24
223 285 1.401539 GCCTGAAGCGGACAAATTCAC 60.402 52.381 0.00 0.00 0.00 3.18
224 286 2.154462 CCTGAAGCGGACAAATTCACT 58.846 47.619 0.00 0.00 0.00 3.41
225 287 2.095567 CCTGAAGCGGACAAATTCACTG 60.096 50.000 0.00 0.00 0.00 3.66
226 288 2.549754 CTGAAGCGGACAAATTCACTGT 59.450 45.455 0.00 0.00 0.00 3.55
227 289 2.948979 TGAAGCGGACAAATTCACTGTT 59.051 40.909 0.00 0.00 0.00 3.16
228 290 3.380004 TGAAGCGGACAAATTCACTGTTT 59.620 39.130 0.00 0.00 0.00 2.83
229 291 4.142271 TGAAGCGGACAAATTCACTGTTTT 60.142 37.500 0.00 0.00 0.00 2.43
230 292 3.705604 AGCGGACAAATTCACTGTTTTG 58.294 40.909 2.72 2.72 38.49 2.44
231 293 2.218530 GCGGACAAATTCACTGTTTTGC 59.781 45.455 3.93 0.00 36.51 3.68
232 294 2.794350 CGGACAAATTCACTGTTTTGCC 59.206 45.455 3.93 5.56 36.51 4.52
233 295 3.130633 GGACAAATTCACTGTTTTGCCC 58.869 45.455 3.93 0.00 36.51 5.36
234 296 3.181466 GGACAAATTCACTGTTTTGCCCT 60.181 43.478 3.93 0.00 36.51 5.19
235 297 4.441792 GACAAATTCACTGTTTTGCCCTT 58.558 39.130 3.93 0.00 36.51 3.95
236 298 4.842574 ACAAATTCACTGTTTTGCCCTTT 58.157 34.783 3.93 0.00 36.51 3.11
237 299 5.252547 ACAAATTCACTGTTTTGCCCTTTT 58.747 33.333 3.93 0.00 36.51 2.27
238 300 5.709631 ACAAATTCACTGTTTTGCCCTTTTT 59.290 32.000 3.93 0.00 36.51 1.94
296 358 7.851822 TTTTGAAAATAACTTCAGCACGATC 57.148 32.000 0.00 0.00 36.69 3.69
297 359 6.801539 TTGAAAATAACTTCAGCACGATCT 57.198 33.333 0.00 0.00 36.69 2.75
298 360 6.169419 TGAAAATAACTTCAGCACGATCTG 57.831 37.500 0.00 0.00 31.67 2.90
299 361 5.931724 TGAAAATAACTTCAGCACGATCTGA 59.068 36.000 7.16 7.16 40.99 3.27
303 365 2.741930 TTCAGCACGATCTGAAGCG 58.258 52.632 16.09 2.38 45.21 4.68
304 366 0.737367 TTCAGCACGATCTGAAGCGG 60.737 55.000 16.09 0.00 45.21 5.52
305 367 2.510238 AGCACGATCTGAAGCGGC 60.510 61.111 7.92 0.00 38.99 6.53
306 368 3.918220 GCACGATCTGAAGCGGCG 61.918 66.667 0.51 0.51 38.99 6.46
307 369 2.202610 CACGATCTGAAGCGGCGA 60.203 61.111 12.98 0.00 38.99 5.54
308 370 1.805539 CACGATCTGAAGCGGCGAA 60.806 57.895 12.98 0.00 38.99 4.70
309 371 1.805945 ACGATCTGAAGCGGCGAAC 60.806 57.895 12.98 0.60 38.99 3.95
310 372 1.805539 CGATCTGAAGCGGCGAACA 60.806 57.895 12.98 5.97 0.00 3.18
311 373 1.351430 CGATCTGAAGCGGCGAACAA 61.351 55.000 12.98 0.00 0.00 2.83
312 374 0.095417 GATCTGAAGCGGCGAACAAC 59.905 55.000 12.98 0.00 0.00 3.32
313 375 0.320771 ATCTGAAGCGGCGAACAACT 60.321 50.000 12.98 0.00 0.00 3.16
314 376 0.944311 TCTGAAGCGGCGAACAACTC 60.944 55.000 12.98 0.00 0.00 3.01
315 377 1.221466 CTGAAGCGGCGAACAACTCA 61.221 55.000 12.98 1.94 0.00 3.41
316 378 1.221466 TGAAGCGGCGAACAACTCAG 61.221 55.000 12.98 0.00 0.00 3.35
317 379 0.944311 GAAGCGGCGAACAACTCAGA 60.944 55.000 12.98 0.00 0.00 3.27
318 380 0.320771 AAGCGGCGAACAACTCAGAT 60.321 50.000 12.98 0.00 0.00 2.90
325 387 3.059188 GGCGAACAACTCAGATTTTTCGA 60.059 43.478 10.10 0.00 38.44 3.71
331 393 6.436843 ACAACTCAGATTTTTCGAAACAGT 57.563 33.333 10.79 3.40 0.00 3.55
336 398 9.450807 AACTCAGATTTTTCGAAACAGTATTTG 57.549 29.630 10.79 7.65 0.00 2.32
341 403 4.759516 TTTCGAAACAGTATTTGCTCCC 57.240 40.909 6.47 0.00 0.00 4.30
344 406 3.500680 TCGAAACAGTATTTGCTCCCAAC 59.499 43.478 0.00 0.00 0.00 3.77
422 485 1.069513 CCGTAGTAATCAATCGCCCCA 59.930 52.381 0.00 0.00 0.00 4.96
525 588 1.630244 GCAGTGCGCGAATCTGTTCT 61.630 55.000 12.10 0.00 32.00 3.01
622 712 8.082242 AGCATCACTTCACTTAAAATAAACCAC 58.918 33.333 0.00 0.00 0.00 4.16
678 770 2.831333 CTTAGAGATGCTCGGCAACAT 58.169 47.619 2.68 0.00 43.62 2.71
689 781 3.791353 GCTCGGCAACATGTTTATTAAGC 59.209 43.478 8.77 8.06 0.00 3.09
692 784 4.457603 TCGGCAACATGTTTATTAAGCTGT 59.542 37.500 19.02 0.00 0.00 4.40
693 785 5.644206 TCGGCAACATGTTTATTAAGCTGTA 59.356 36.000 19.02 8.28 0.00 2.74
694 786 6.149640 TCGGCAACATGTTTATTAAGCTGTAA 59.850 34.615 19.02 4.51 0.00 2.41
696 788 8.126074 CGGCAACATGTTTATTAAGCTGTAATA 58.874 33.333 8.77 0.00 0.00 0.98
711 803 6.456501 AGCTGTAATATGTATTCCTTCCGTC 58.543 40.000 0.00 0.00 0.00 4.79
712 804 5.638234 GCTGTAATATGTATTCCTTCCGTCC 59.362 44.000 0.00 0.00 0.00 4.79
714 806 5.603395 TGTAATATGTATTCCTTCCGTCCCA 59.397 40.000 0.00 0.00 0.00 4.37
715 807 5.843019 AATATGTATTCCTTCCGTCCCAT 57.157 39.130 0.00 0.00 0.00 4.00
717 809 6.945636 ATATGTATTCCTTCCGTCCCATAA 57.054 37.500 0.00 0.00 0.00 1.90
718 810 5.843019 ATGTATTCCTTCCGTCCCATAAT 57.157 39.130 0.00 0.00 0.00 1.28
719 811 6.945636 ATGTATTCCTTCCGTCCCATAATA 57.054 37.500 0.00 0.00 0.00 0.98
721 813 8.618240 ATGTATTCCTTCCGTCCCATAATATA 57.382 34.615 0.00 0.00 0.00 0.86
722 814 8.438618 TGTATTCCTTCCGTCCCATAATATAA 57.561 34.615 0.00 0.00 0.00 0.98
777 1028 8.446599 AAACACTTTTATATTATGGGACGGAG 57.553 34.615 0.00 0.00 0.00 4.63
778 1029 6.531021 ACACTTTTATATTATGGGACGGAGG 58.469 40.000 0.00 0.00 0.00 4.30
779 1030 5.938125 CACTTTTATATTATGGGACGGAGGG 59.062 44.000 0.00 0.00 0.00 4.30
780 1031 5.013808 ACTTTTATATTATGGGACGGAGGGG 59.986 44.000 0.00 0.00 0.00 4.79
781 1032 1.966845 ATATTATGGGACGGAGGGGG 58.033 55.000 0.00 0.00 0.00 5.40
784 1035 0.105349 TTATGGGACGGAGGGGGTAG 60.105 60.000 0.00 0.00 0.00 3.18
785 1036 1.000590 TATGGGACGGAGGGGGTAGA 61.001 60.000 0.00 0.00 0.00 2.59
786 1037 1.893588 ATGGGACGGAGGGGGTAGAA 61.894 60.000 0.00 0.00 0.00 2.10
787 1038 1.306397 GGGACGGAGGGGGTAGAAA 60.306 63.158 0.00 0.00 0.00 2.52
789 1040 1.210538 GGACGGAGGGGGTAGAAAAT 58.789 55.000 0.00 0.00 0.00 1.82
790 1041 2.401568 GGACGGAGGGGGTAGAAAATA 58.598 52.381 0.00 0.00 0.00 1.40
791 1042 2.773661 GGACGGAGGGGGTAGAAAATAA 59.226 50.000 0.00 0.00 0.00 1.40
792 1043 3.393609 GGACGGAGGGGGTAGAAAATAAT 59.606 47.826 0.00 0.00 0.00 1.28
794 1045 5.512060 GGACGGAGGGGGTAGAAAATAATAC 60.512 48.000 0.00 0.00 0.00 1.89
795 1046 4.349048 ACGGAGGGGGTAGAAAATAATACC 59.651 45.833 0.00 0.00 40.69 2.73
796 1047 4.596212 CGGAGGGGGTAGAAAATAATACCT 59.404 45.833 1.74 0.00 41.10 3.08
798 1049 6.442885 CGGAGGGGGTAGAAAATAATACCTAT 59.557 42.308 1.74 0.00 41.10 2.57
799 1050 7.037802 CGGAGGGGGTAGAAAATAATACCTATT 60.038 40.741 1.74 0.00 41.10 1.73
800 1051 8.676020 GGAGGGGGTAGAAAATAATACCTATTT 58.324 37.037 1.74 0.00 41.16 1.40
865 1126 8.793592 CAGCTAAATATTTTAATAGACCCCCAC 58.206 37.037 5.91 0.00 0.00 4.61
868 1129 7.907841 AAATATTTTAATAGACCCCCACCAC 57.092 36.000 0.00 0.00 0.00 4.16
870 1131 3.724732 TTTAATAGACCCCCACCACAC 57.275 47.619 0.00 0.00 0.00 3.82
871 1132 2.345782 TAATAGACCCCCACCACACA 57.654 50.000 0.00 0.00 0.00 3.72
872 1133 0.696501 AATAGACCCCCACCACACAC 59.303 55.000 0.00 0.00 0.00 3.82
873 1134 0.474854 ATAGACCCCCACCACACACA 60.475 55.000 0.00 0.00 0.00 3.72
874 1135 1.412453 TAGACCCCCACCACACACAC 61.412 60.000 0.00 0.00 0.00 3.82
875 1136 4.183858 ACCCCCACCACACACACG 62.184 66.667 0.00 0.00 0.00 4.49
878 1139 3.582120 CCCACCACACACACGCAC 61.582 66.667 0.00 0.00 0.00 5.34
913 1261 2.622064 ATTCATCCGGGAACTAGCAC 57.378 50.000 0.00 0.00 0.00 4.40
975 1325 6.387041 TGACTATTGACCGGTAGTATTCTG 57.613 41.667 7.34 0.00 31.61 3.02
977 1327 6.379133 TGACTATTGACCGGTAGTATTCTGTT 59.621 38.462 7.34 0.00 31.61 3.16
1193 1567 0.646055 CCTACCCTTTCCCCCTCCTA 59.354 60.000 0.00 0.00 0.00 2.94
1299 1686 0.037697 AGACGTGTGTGTGTGTGTGT 60.038 50.000 0.00 0.00 0.00 3.72
1323 1711 3.056465 ACGGTTTCTAGCAAGAGAGAAGG 60.056 47.826 0.00 0.00 33.38 3.46
1324 1712 3.056465 CGGTTTCTAGCAAGAGAGAAGGT 60.056 47.826 0.00 0.00 33.38 3.50
1326 1714 4.249661 GTTTCTAGCAAGAGAGAAGGTGG 58.750 47.826 0.00 0.00 33.38 4.61
1327 1715 3.176924 TCTAGCAAGAGAGAAGGTGGT 57.823 47.619 0.00 0.00 0.00 4.16
1328 1716 3.511477 TCTAGCAAGAGAGAAGGTGGTT 58.489 45.455 0.00 0.00 0.00 3.67
1329 1717 2.849294 AGCAAGAGAGAAGGTGGTTC 57.151 50.000 0.00 0.00 35.08 3.62
1340 1728 5.263872 AGAAGGTGGTTCTCTTCTCTAGA 57.736 43.478 0.00 0.00 42.26 2.43
1391 1779 3.670377 GTGGGTGCGGTTTCAGGC 61.670 66.667 0.00 0.00 0.00 4.85
1814 2203 1.004918 GAACTGGAGTGGGTGTCGG 60.005 63.158 0.00 0.00 0.00 4.79
1834 2223 1.202371 GGTATCATGGACGACTCGCAA 60.202 52.381 0.00 0.00 0.00 4.85
2185 2610 2.077413 AGAGCAAGAGCAAGAAGTCG 57.923 50.000 0.00 0.00 45.49 4.18
2512 2955 4.492160 GTCGTCATCGAGGCCGCA 62.492 66.667 7.44 0.00 46.96 5.69
2716 3159 4.097589 AGTCTATTAGGTCGTGTTAGGTGC 59.902 45.833 0.00 0.00 0.00 5.01
2748 3191 2.166664 ACTGCTCTACTAAGCTTTCGGG 59.833 50.000 3.20 0.00 42.94 5.14
2803 3246 1.241315 TGGCGCCTTTTTAGTGGAGC 61.241 55.000 29.70 0.00 46.09 4.70
2845 3289 2.489329 AGTTGTTTGAATCATGCGAGGG 59.511 45.455 0.00 0.00 0.00 4.30
2846 3290 1.462616 TGTTTGAATCATGCGAGGGG 58.537 50.000 0.00 0.00 0.00 4.79
2866 3310 1.133790 GCAGAAGTGGCAATGTCCATC 59.866 52.381 0.00 0.00 38.57 3.51
2942 3386 0.667993 TTTCAAGGAAGCTGCCAACG 59.332 50.000 15.05 0.00 0.00 4.10
2948 3397 1.425428 GAAGCTGCCAACGATTCCG 59.575 57.895 0.00 0.00 42.50 4.30
2958 3407 2.870411 CCAACGATTCCGGAAGAATACC 59.130 50.000 23.47 6.27 45.52 2.73
3067 3535 0.108329 ACGGCCCTTCGTCATTACTG 60.108 55.000 0.00 0.00 39.34 2.74
3069 3540 0.392461 GGCCCTTCGTCATTACTGCA 60.392 55.000 0.00 0.00 0.00 4.41
3078 3549 4.740268 TCGTCATTACTGCAAACTCGTAT 58.260 39.130 0.00 0.00 0.00 3.06
3079 3550 4.796830 TCGTCATTACTGCAAACTCGTATC 59.203 41.667 0.00 0.00 0.00 2.24
3081 3552 5.275927 CGTCATTACTGCAAACTCGTATCTG 60.276 44.000 0.00 0.00 0.00 2.90
3106 3577 2.226330 GATTAATGGCCACCGCACATA 58.774 47.619 8.16 0.00 36.38 2.29
3113 3584 1.227147 CCACCGCACATAGGGTACG 60.227 63.158 0.00 0.00 36.01 3.67
3119 3590 1.135199 CGCACATAGGGTACGAACAGT 60.135 52.381 0.00 0.00 38.58 3.55
3136 3631 0.815734 AGTTCCATCTACGACACCCG 59.184 55.000 0.00 0.00 45.44 5.28
3144 3639 3.770263 TCTACGACACCCGAATTACTG 57.230 47.619 0.00 0.00 41.76 2.74
3157 3652 3.545078 CGAATTACTGCTGCATTCAAAGC 59.455 43.478 1.31 0.00 39.96 3.51
3203 3699 1.000385 TGCCAGCCAAAAATCTTCACG 60.000 47.619 0.00 0.00 0.00 4.35
3339 3836 4.943508 ACTTCGAAAGAACGTTTCTACG 57.056 40.909 0.46 7.35 46.92 3.51
3340 3837 3.732721 ACTTCGAAAGAACGTTTCTACGG 59.267 43.478 0.46 0.00 46.92 4.02
3443 3944 1.163554 ACTCCGTTCGGACAGAGTAC 58.836 55.000 11.15 0.00 40.78 2.73
3444 3945 1.271271 ACTCCGTTCGGACAGAGTACT 60.271 52.381 11.15 0.00 40.78 2.73
3445 3946 1.397692 CTCCGTTCGGACAGAGTACTC 59.602 57.143 15.41 15.41 0.00 2.59
3446 3947 0.450983 CCGTTCGGACAGAGTACTCC 59.549 60.000 19.38 3.98 0.00 3.85
3447 3948 0.450983 CGTTCGGACAGAGTACTCCC 59.549 60.000 19.38 12.35 0.00 4.30
3448 3949 1.836802 GTTCGGACAGAGTACTCCCT 58.163 55.000 19.38 4.38 0.00 4.20
3449 3950 1.744522 GTTCGGACAGAGTACTCCCTC 59.255 57.143 19.38 13.15 0.00 4.30
3450 3951 0.255318 TCGGACAGAGTACTCCCTCC 59.745 60.000 19.38 19.77 31.53 4.30
3451 3952 1.096386 CGGACAGAGTACTCCCTCCG 61.096 65.000 30.16 30.16 40.51 4.63
3452 3953 0.034283 GGACAGAGTACTCCCTCCGT 60.034 60.000 19.38 8.95 31.53 4.69
3453 3954 1.616456 GGACAGAGTACTCCCTCCGTT 60.616 57.143 19.38 0.00 31.53 4.44
3454 3955 1.744522 GACAGAGTACTCCCTCCGTTC 59.255 57.143 19.38 2.31 31.53 3.95
3455 3956 1.104630 CAGAGTACTCCCTCCGTTCC 58.895 60.000 19.38 0.00 31.53 3.62
3456 3957 0.702902 AGAGTACTCCCTCCGTTCCA 59.297 55.000 19.38 0.00 31.53 3.53
3457 3958 1.076677 AGAGTACTCCCTCCGTTCCAA 59.923 52.381 19.38 0.00 31.53 3.53
3458 3959 1.897802 GAGTACTCCCTCCGTTCCAAA 59.102 52.381 12.13 0.00 0.00 3.28
3459 3960 2.301009 GAGTACTCCCTCCGTTCCAAAA 59.699 50.000 12.13 0.00 0.00 2.44
3460 3961 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3461 3962 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
3462 3963 4.720273 AGTACTCCCTCCGTTCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
3463 3964 5.901276 AGTACTCCCTCCGTTCCAAAATATA 59.099 40.000 0.00 0.00 0.00 0.86
3464 3965 5.291905 ACTCCCTCCGTTCCAAAATATAG 57.708 43.478 0.00 0.00 0.00 1.31
3465 3966 4.065789 CTCCCTCCGTTCCAAAATATAGC 58.934 47.826 0.00 0.00 0.00 2.97
3466 3967 2.806244 CCCTCCGTTCCAAAATATAGCG 59.194 50.000 0.00 0.00 0.00 4.26
3467 3968 2.223377 CCTCCGTTCCAAAATATAGCGC 59.777 50.000 0.00 0.00 0.00 5.92
3468 3969 1.862201 TCCGTTCCAAAATATAGCGCG 59.138 47.619 0.00 0.00 0.00 6.86
3469 3970 1.658968 CGTTCCAAAATATAGCGCGC 58.341 50.000 26.66 26.66 0.00 6.86
3470 3971 1.659211 CGTTCCAAAATATAGCGCGCC 60.659 52.381 30.33 10.31 0.00 6.53
3471 3972 0.948678 TTCCAAAATATAGCGCGCCC 59.051 50.000 30.33 0.16 0.00 6.13
3472 3973 0.179043 TCCAAAATATAGCGCGCCCA 60.179 50.000 30.33 17.44 0.00 5.36
3473 3974 0.040425 CCAAAATATAGCGCGCCCAC 60.040 55.000 30.33 0.00 0.00 4.61
3474 3975 0.384230 CAAAATATAGCGCGCCCACG 60.384 55.000 30.33 4.40 44.07 4.94
3475 3976 0.812412 AAAATATAGCGCGCCCACGT 60.812 50.000 30.33 11.88 42.83 4.49
3476 3977 0.812412 AAATATAGCGCGCCCACGTT 60.812 50.000 30.33 14.39 42.83 3.99
3477 3978 0.812412 AATATAGCGCGCCCACGTTT 60.812 50.000 30.33 10.14 42.83 3.60
3478 3979 0.812412 ATATAGCGCGCCCACGTTTT 60.812 50.000 30.33 9.26 42.83 2.43
3479 3980 1.020333 TATAGCGCGCCCACGTTTTT 61.020 50.000 30.33 8.40 42.83 1.94
3480 3981 2.248274 ATAGCGCGCCCACGTTTTTC 62.248 55.000 30.33 0.00 42.83 2.29
3482 3983 4.003011 CGCGCCCACGTTTTTCGA 62.003 61.111 0.00 0.00 42.83 3.71
3483 3984 2.127383 GCGCCCACGTTTTTCGAG 60.127 61.111 0.00 0.00 42.83 4.04
3484 3985 2.554272 CGCCCACGTTTTTCGAGG 59.446 61.111 0.00 0.00 46.86 4.63
3485 3986 2.248835 CGCCCACGTTTTTCGAGGT 61.249 57.895 0.00 0.00 46.11 3.85
3486 3987 1.778027 CGCCCACGTTTTTCGAGGTT 61.778 55.000 0.00 0.00 46.11 3.50
3487 3988 0.040692 GCCCACGTTTTTCGAGGTTC 60.041 55.000 0.00 0.00 46.11 3.62
3488 3989 1.301423 CCCACGTTTTTCGAGGTTCA 58.699 50.000 0.00 0.00 46.11 3.18
3489 3990 1.671845 CCCACGTTTTTCGAGGTTCAA 59.328 47.619 0.00 0.00 46.11 2.69
3490 3991 2.540157 CCCACGTTTTTCGAGGTTCAAC 60.540 50.000 0.00 0.00 46.11 3.18
3491 3992 2.353579 CCACGTTTTTCGAGGTTCAACT 59.646 45.455 0.00 0.00 43.41 3.16
3492 3993 3.181504 CCACGTTTTTCGAGGTTCAACTT 60.182 43.478 0.00 0.00 43.41 2.66
3493 3994 4.408694 CACGTTTTTCGAGGTTCAACTTT 58.591 39.130 0.00 0.00 42.86 2.66
3494 3995 4.262045 CACGTTTTTCGAGGTTCAACTTTG 59.738 41.667 0.00 0.00 42.86 2.77
3495 3996 4.154556 ACGTTTTTCGAGGTTCAACTTTGA 59.845 37.500 0.00 0.00 42.86 2.69
3496 3997 4.494410 CGTTTTTCGAGGTTCAACTTTGAC 59.506 41.667 0.00 0.00 42.86 3.18
3497 3998 4.625972 TTTTCGAGGTTCAACTTTGACC 57.374 40.909 0.00 0.00 36.83 4.02
3498 3999 2.992124 TCGAGGTTCAACTTTGACCA 57.008 45.000 11.01 0.00 36.83 4.02
3499 4000 3.485463 TCGAGGTTCAACTTTGACCAT 57.515 42.857 11.01 0.00 36.83 3.55
3500 4001 4.610605 TCGAGGTTCAACTTTGACCATA 57.389 40.909 11.01 0.00 36.83 2.74
3501 4002 4.963373 TCGAGGTTCAACTTTGACCATAA 58.037 39.130 11.01 0.00 36.83 1.90
3502 4003 5.369833 TCGAGGTTCAACTTTGACCATAAA 58.630 37.500 11.01 0.00 36.83 1.40
3503 4004 6.001460 TCGAGGTTCAACTTTGACCATAAAT 58.999 36.000 11.01 0.00 36.83 1.40
3504 4005 6.488683 TCGAGGTTCAACTTTGACCATAAATT 59.511 34.615 11.01 0.00 36.83 1.82
3505 4006 7.013846 TCGAGGTTCAACTTTGACCATAAATTT 59.986 33.333 0.00 0.00 36.83 1.82
3506 4007 8.293867 CGAGGTTCAACTTTGACCATAAATTTA 58.706 33.333 0.00 0.00 36.83 1.40
3507 4008 9.974980 GAGGTTCAACTTTGACCATAAATTTAA 57.025 29.630 1.21 0.00 36.83 1.52
3508 4009 9.758651 AGGTTCAACTTTGACCATAAATTTAAC 57.241 29.630 1.21 0.00 36.83 2.01
3509 4010 8.984764 GGTTCAACTTTGACCATAAATTTAACC 58.015 33.333 1.21 0.00 36.83 2.85
3510 4011 8.984764 GTTCAACTTTGACCATAAATTTAACCC 58.015 33.333 1.21 0.00 36.83 4.11
3511 4012 8.251383 TCAACTTTGACCATAAATTTAACCCA 57.749 30.769 1.21 0.00 31.01 4.51
3512 4013 8.145122 TCAACTTTGACCATAAATTTAACCCAC 58.855 33.333 1.21 0.00 31.01 4.61
3513 4014 6.683715 ACTTTGACCATAAATTTAACCCACG 58.316 36.000 1.21 0.00 0.00 4.94
3514 4015 6.490721 ACTTTGACCATAAATTTAACCCACGA 59.509 34.615 1.21 0.00 0.00 4.35
3515 4016 6.503589 TTGACCATAAATTTAACCCACGAG 57.496 37.500 1.21 0.00 0.00 4.18
3516 4017 5.806818 TGACCATAAATTTAACCCACGAGA 58.193 37.500 1.21 0.00 0.00 4.04
3517 4018 5.644636 TGACCATAAATTTAACCCACGAGAC 59.355 40.000 1.21 0.00 0.00 3.36
3518 4019 4.945543 ACCATAAATTTAACCCACGAGACC 59.054 41.667 1.21 0.00 0.00 3.85
3519 4020 4.034742 CCATAAATTTAACCCACGAGACCG 59.965 45.833 1.21 0.00 42.50 4.79
3520 4021 3.405823 AAATTTAACCCACGAGACCGA 57.594 42.857 0.00 0.00 39.50 4.69
3521 4022 2.375173 ATTTAACCCACGAGACCGAC 57.625 50.000 0.00 0.00 39.50 4.79
3522 4023 1.331214 TTTAACCCACGAGACCGACT 58.669 50.000 0.00 0.00 39.50 4.18
3523 4024 0.599558 TTAACCCACGAGACCGACTG 59.400 55.000 0.00 0.00 39.50 3.51
3524 4025 1.870055 TAACCCACGAGACCGACTGC 61.870 60.000 0.00 0.00 39.50 4.40
3525 4026 4.778415 CCCACGAGACCGACTGCG 62.778 72.222 0.00 0.00 39.50 5.18
3535 4036 2.202824 CGACTGCGGCGGGATAAA 60.203 61.111 14.26 0.00 0.00 1.40
3536 4037 1.812093 CGACTGCGGCGGGATAAAA 60.812 57.895 14.26 0.00 0.00 1.52
3537 4038 1.363145 CGACTGCGGCGGGATAAAAA 61.363 55.000 14.26 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.799106 GTTTGGATAGTACTAGTAGGGTATGTA 57.201 37.037 8.85 0.00 0.00 2.29
2 3 8.284435 TGTTTGGATAGTACTAGTAGGGTATGT 58.716 37.037 8.85 0.00 0.00 2.29
3 4 8.701908 TGTTTGGATAGTACTAGTAGGGTATG 57.298 38.462 8.85 0.00 0.00 2.39
5 6 8.106017 TCTGTTTGGATAGTACTAGTAGGGTA 57.894 38.462 8.85 0.00 0.00 3.69
6 7 6.978261 TCTGTTTGGATAGTACTAGTAGGGT 58.022 40.000 8.85 0.00 0.00 4.34
7 8 7.945664 AGATCTGTTTGGATAGTACTAGTAGGG 59.054 40.741 8.85 0.00 0.00 3.53
8 9 8.927675 AGATCTGTTTGGATAGTACTAGTAGG 57.072 38.462 8.85 0.00 0.00 3.18
9 10 9.005777 GGAGATCTGTTTGGATAGTACTAGTAG 57.994 40.741 8.85 0.00 0.00 2.57
10 11 8.500238 TGGAGATCTGTTTGGATAGTACTAGTA 58.500 37.037 8.85 0.00 0.00 1.82
11 12 7.285858 GTGGAGATCTGTTTGGATAGTACTAGT 59.714 40.741 8.85 0.00 0.00 2.57
12 13 7.504238 AGTGGAGATCTGTTTGGATAGTACTAG 59.496 40.741 8.85 0.00 0.00 2.57
13 14 7.355101 AGTGGAGATCTGTTTGGATAGTACTA 58.645 38.462 4.77 4.77 0.00 1.82
14 15 6.198639 AGTGGAGATCTGTTTGGATAGTACT 58.801 40.000 0.00 0.00 0.00 2.73
15 16 6.472686 AGTGGAGATCTGTTTGGATAGTAC 57.527 41.667 0.00 0.00 0.00 2.73
16 17 5.299531 CGAGTGGAGATCTGTTTGGATAGTA 59.700 44.000 0.00 0.00 0.00 1.82
17 18 4.098654 CGAGTGGAGATCTGTTTGGATAGT 59.901 45.833 0.00 0.00 0.00 2.12
18 19 4.500545 CCGAGTGGAGATCTGTTTGGATAG 60.501 50.000 0.00 0.00 37.49 2.08
19 20 3.384789 CCGAGTGGAGATCTGTTTGGATA 59.615 47.826 0.00 0.00 37.49 2.59
20 21 2.169352 CCGAGTGGAGATCTGTTTGGAT 59.831 50.000 0.00 0.00 37.49 3.41
21 22 1.550524 CCGAGTGGAGATCTGTTTGGA 59.449 52.381 0.00 0.00 37.49 3.53
33 34 2.158957 GCTCCATATTTGACCGAGTGGA 60.159 50.000 0.00 0.00 39.21 4.02
35 36 2.868583 CTGCTCCATATTTGACCGAGTG 59.131 50.000 0.00 0.00 0.00 3.51
42 43 7.707624 AACAAATCTTCTGCTCCATATTTGA 57.292 32.000 16.08 0.00 37.61 2.69
54 55 6.092748 CCAAATCGGGTTAACAAATCTTCTG 58.907 40.000 8.10 0.00 0.00 3.02
60 61 4.565022 CTTGCCAAATCGGGTTAACAAAT 58.435 39.130 8.10 0.00 34.06 2.32
66 67 1.309499 CGGCTTGCCAAATCGGGTTA 61.309 55.000 12.45 0.00 34.06 2.85
67 68 2.635443 CGGCTTGCCAAATCGGGTT 61.635 57.895 12.45 0.00 34.06 4.11
101 102 1.326245 GCATCGCGTGTGCAATAACTA 59.674 47.619 26.01 0.00 42.97 2.24
102 103 0.096976 GCATCGCGTGTGCAATAACT 59.903 50.000 26.01 0.00 42.97 2.24
103 104 2.554656 GCATCGCGTGTGCAATAAC 58.445 52.632 26.01 3.81 42.97 1.89
109 110 4.170062 AGCATGCATCGCGTGTGC 62.170 61.111 21.98 24.86 46.10 4.57
140 141 0.791422 TCGGTGTTTATTCGTTGCCG 59.209 50.000 0.00 0.00 39.13 5.69
147 148 2.417239 TCGCCATGTTCGGTGTTTATTC 59.583 45.455 5.03 0.00 37.81 1.75
169 170 2.502510 CGTCAAGCAATGCCGTGC 60.503 61.111 0.00 0.53 45.28 5.34
187 249 3.713288 TCAGGCGAGTAATAAACCATCG 58.287 45.455 0.00 0.00 36.51 3.84
191 253 3.946308 GCTTCAGGCGAGTAATAAACC 57.054 47.619 0.00 0.00 0.00 3.27
213 275 4.058721 AGGGCAAAACAGTGAATTTGTC 57.941 40.909 19.73 18.37 39.72 3.18
271 333 8.134895 AGATCGTGCTGAAGTTATTTTCAAAAA 58.865 29.630 0.00 0.00 36.69 1.94
272 334 7.591057 CAGATCGTGCTGAAGTTATTTTCAAAA 59.409 33.333 1.86 0.00 38.14 2.44
273 335 7.041440 TCAGATCGTGCTGAAGTTATTTTCAAA 60.041 33.333 7.36 0.00 41.65 2.69
274 336 6.426633 TCAGATCGTGCTGAAGTTATTTTCAA 59.573 34.615 7.36 0.00 41.65 2.69
275 337 5.931724 TCAGATCGTGCTGAAGTTATTTTCA 59.068 36.000 7.36 0.00 41.65 2.69
276 338 6.408858 TCAGATCGTGCTGAAGTTATTTTC 57.591 37.500 7.36 0.00 41.65 2.29
277 339 6.801539 TTCAGATCGTGCTGAAGTTATTTT 57.198 33.333 15.29 0.00 46.73 1.82
286 348 1.153765 CCGCTTCAGATCGTGCTGA 60.154 57.895 6.00 6.00 42.81 4.26
287 349 2.806856 GCCGCTTCAGATCGTGCTG 61.807 63.158 1.67 1.67 37.24 4.41
288 350 2.510238 GCCGCTTCAGATCGTGCT 60.510 61.111 0.00 0.00 0.00 4.40
289 351 3.918220 CGCCGCTTCAGATCGTGC 61.918 66.667 0.00 0.00 0.00 5.34
290 352 1.805539 TTCGCCGCTTCAGATCGTG 60.806 57.895 0.00 0.00 0.00 4.35
291 353 1.805945 GTTCGCCGCTTCAGATCGT 60.806 57.895 0.00 0.00 0.00 3.73
292 354 1.351430 TTGTTCGCCGCTTCAGATCG 61.351 55.000 0.00 0.00 0.00 3.69
293 355 0.095417 GTTGTTCGCCGCTTCAGATC 59.905 55.000 0.00 0.00 0.00 2.75
294 356 0.320771 AGTTGTTCGCCGCTTCAGAT 60.321 50.000 0.00 0.00 0.00 2.90
295 357 0.944311 GAGTTGTTCGCCGCTTCAGA 60.944 55.000 0.00 0.00 0.00 3.27
296 358 1.221466 TGAGTTGTTCGCCGCTTCAG 61.221 55.000 0.00 0.00 0.00 3.02
297 359 1.221466 CTGAGTTGTTCGCCGCTTCA 61.221 55.000 0.00 0.00 0.00 3.02
298 360 0.944311 TCTGAGTTGTTCGCCGCTTC 60.944 55.000 0.00 0.00 0.00 3.86
299 361 0.320771 ATCTGAGTTGTTCGCCGCTT 60.321 50.000 0.00 0.00 0.00 4.68
300 362 0.320771 AATCTGAGTTGTTCGCCGCT 60.321 50.000 0.00 0.00 0.00 5.52
301 363 0.517316 AAATCTGAGTTGTTCGCCGC 59.483 50.000 0.00 0.00 0.00 6.53
302 364 2.969443 AAAATCTGAGTTGTTCGCCG 57.031 45.000 0.00 0.00 0.00 6.46
303 365 3.059188 TCGAAAAATCTGAGTTGTTCGCC 60.059 43.478 19.86 0.00 38.14 5.54
304 366 4.128554 TCGAAAAATCTGAGTTGTTCGC 57.871 40.909 19.86 0.00 38.14 4.70
305 367 5.963004 TGTTTCGAAAAATCTGAGTTGTTCG 59.037 36.000 13.10 19.20 39.26 3.95
306 368 6.967199 ACTGTTTCGAAAAATCTGAGTTGTTC 59.033 34.615 13.10 0.00 0.00 3.18
307 369 6.852664 ACTGTTTCGAAAAATCTGAGTTGTT 58.147 32.000 13.10 0.00 0.00 2.83
308 370 6.436843 ACTGTTTCGAAAAATCTGAGTTGT 57.563 33.333 13.10 0.00 0.00 3.32
309 371 9.450807 AAATACTGTTTCGAAAAATCTGAGTTG 57.549 29.630 13.10 0.00 0.00 3.16
310 372 9.450807 CAAATACTGTTTCGAAAAATCTGAGTT 57.549 29.630 13.10 0.00 0.00 3.01
311 373 7.591426 GCAAATACTGTTTCGAAAAATCTGAGT 59.409 33.333 13.10 9.92 0.00 3.41
312 374 7.805071 AGCAAATACTGTTTCGAAAAATCTGAG 59.195 33.333 13.10 4.73 0.00 3.35
313 375 7.648142 AGCAAATACTGTTTCGAAAAATCTGA 58.352 30.769 13.10 0.00 0.00 3.27
314 376 7.061094 GGAGCAAATACTGTTTCGAAAAATCTG 59.939 37.037 13.10 7.19 0.00 2.90
315 377 7.084486 GGAGCAAATACTGTTTCGAAAAATCT 58.916 34.615 13.10 0.00 0.00 2.40
316 378 6.308041 GGGAGCAAATACTGTTTCGAAAAATC 59.692 38.462 13.10 0.75 0.00 2.17
317 379 6.156519 GGGAGCAAATACTGTTTCGAAAAAT 58.843 36.000 13.10 3.65 0.00 1.82
318 380 5.067936 TGGGAGCAAATACTGTTTCGAAAAA 59.932 36.000 13.10 6.34 0.00 1.94
325 387 3.482436 TCGTTGGGAGCAAATACTGTTT 58.518 40.909 0.00 0.00 0.00 2.83
331 393 3.334691 CTCTGTTCGTTGGGAGCAAATA 58.665 45.455 0.00 0.00 35.31 1.40
336 398 1.376037 CCCTCTGTTCGTTGGGAGC 60.376 63.158 0.00 0.00 42.11 4.70
341 403 2.143925 GTCCTTTCCCTCTGTTCGTTG 58.856 52.381 0.00 0.00 0.00 4.10
344 406 0.036294 GGGTCCTTTCCCTCTGTTCG 60.036 60.000 0.00 0.00 43.85 3.95
477 540 1.451387 AGTTTATTCGCCGGGGCAG 60.451 57.895 14.85 2.98 42.06 4.85
525 588 2.035961 CTCCCCGAAATGAGCGAATCTA 59.964 50.000 0.00 0.00 0.00 1.98
628 719 4.826733 TCATGCCGATATTGCCACTATTTT 59.173 37.500 0.00 0.00 0.00 1.82
640 731 3.482156 AAGCTTGACTCATGCCGATAT 57.518 42.857 12.18 0.00 35.53 1.63
689 781 6.164176 GGGACGGAAGGAATACATATTACAG 58.836 44.000 0.00 0.00 0.00 2.74
692 784 6.945636 ATGGGACGGAAGGAATACATATTA 57.054 37.500 0.00 0.00 0.00 0.98
693 785 5.843019 ATGGGACGGAAGGAATACATATT 57.157 39.130 0.00 0.00 0.00 1.28
694 786 6.945636 TTATGGGACGGAAGGAATACATAT 57.054 37.500 0.00 0.00 0.00 1.78
696 788 5.843019 ATTATGGGACGGAAGGAATACAT 57.157 39.130 0.00 0.00 0.00 2.29
700 792 7.808279 TCTTATATTATGGGACGGAAGGAAT 57.192 36.000 0.00 0.00 0.00 3.01
702 794 7.808279 ATTCTTATATTATGGGACGGAAGGA 57.192 36.000 0.00 0.00 0.00 3.36
751 1002 8.810990 TCCGTCCCATAATATAAAAGTGTTTT 57.189 30.769 0.00 0.00 36.67 2.43
752 1003 7.501225 CCTCCGTCCCATAATATAAAAGTGTTT 59.499 37.037 0.00 0.00 0.00 2.83
753 1004 6.996282 CCTCCGTCCCATAATATAAAAGTGTT 59.004 38.462 0.00 0.00 0.00 3.32
754 1005 6.465321 CCCTCCGTCCCATAATATAAAAGTGT 60.465 42.308 0.00 0.00 0.00 3.55
755 1006 5.938125 CCCTCCGTCCCATAATATAAAAGTG 59.062 44.000 0.00 0.00 0.00 3.16
756 1007 5.013808 CCCCTCCGTCCCATAATATAAAAGT 59.986 44.000 0.00 0.00 0.00 2.66
757 1008 5.497474 CCCCTCCGTCCCATAATATAAAAG 58.503 45.833 0.00 0.00 0.00 2.27
758 1009 4.290196 CCCCCTCCGTCCCATAATATAAAA 59.710 45.833 0.00 0.00 0.00 1.52
759 1010 3.847780 CCCCCTCCGTCCCATAATATAAA 59.152 47.826 0.00 0.00 0.00 1.40
760 1011 3.181392 ACCCCCTCCGTCCCATAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
761 1012 2.387861 ACCCCCTCCGTCCCATAATATA 59.612 50.000 0.00 0.00 0.00 0.86
762 1013 1.153565 ACCCCCTCCGTCCCATAATAT 59.846 52.381 0.00 0.00 0.00 1.28
764 1015 0.569204 TACCCCCTCCGTCCCATAAT 59.431 55.000 0.00 0.00 0.00 1.28
765 1016 0.105349 CTACCCCCTCCGTCCCATAA 60.105 60.000 0.00 0.00 0.00 1.90
766 1017 1.000590 TCTACCCCCTCCGTCCCATA 61.001 60.000 0.00 0.00 0.00 2.74
767 1018 1.893588 TTCTACCCCCTCCGTCCCAT 61.894 60.000 0.00 0.00 0.00 4.00
769 1020 0.911045 TTTTCTACCCCCTCCGTCCC 60.911 60.000 0.00 0.00 0.00 4.46
771 1022 4.701651 ATTATTTTCTACCCCCTCCGTC 57.298 45.455 0.00 0.00 0.00 4.79
772 1023 4.349048 GGTATTATTTTCTACCCCCTCCGT 59.651 45.833 0.00 0.00 32.79 4.69
774 1025 7.825983 ATAGGTATTATTTTCTACCCCCTCC 57.174 40.000 0.00 0.00 38.54 4.30
790 1041 9.393786 ACCACCTGATCTATGTAAATAGGTATT 57.606 33.333 0.00 0.00 35.45 1.89
791 1042 8.816894 CACCACCTGATCTATGTAAATAGGTAT 58.183 37.037 0.00 0.00 35.45 2.73
792 1043 8.008332 TCACCACCTGATCTATGTAAATAGGTA 58.992 37.037 0.00 0.00 35.45 3.08
794 1045 7.303182 TCACCACCTGATCTATGTAAATAGG 57.697 40.000 0.00 0.00 0.00 2.57
795 1046 9.784531 ATTTCACCACCTGATCTATGTAAATAG 57.215 33.333 0.00 0.00 0.00 1.73
796 1047 9.559732 CATTTCACCACCTGATCTATGTAAATA 57.440 33.333 0.00 0.00 0.00 1.40
798 1049 6.828273 CCATTTCACCACCTGATCTATGTAAA 59.172 38.462 0.00 0.00 0.00 2.01
799 1050 6.069673 ACCATTTCACCACCTGATCTATGTAA 60.070 38.462 0.00 0.00 0.00 2.41
800 1051 5.428457 ACCATTTCACCACCTGATCTATGTA 59.572 40.000 0.00 0.00 0.00 2.29
801 1052 4.228210 ACCATTTCACCACCTGATCTATGT 59.772 41.667 0.00 0.00 0.00 2.29
802 1053 4.785301 ACCATTTCACCACCTGATCTATG 58.215 43.478 0.00 0.00 0.00 2.23
803 1054 6.329986 TGATACCATTTCACCACCTGATCTAT 59.670 38.462 0.00 0.00 0.00 1.98
804 1055 5.665360 TGATACCATTTCACCACCTGATCTA 59.335 40.000 0.00 0.00 0.00 1.98
805 1056 4.474651 TGATACCATTTCACCACCTGATCT 59.525 41.667 0.00 0.00 0.00 2.75
808 1059 4.860802 ATGATACCATTTCACCACCTGA 57.139 40.909 0.00 0.00 0.00 3.86
809 1060 5.885352 TGTAATGATACCATTTCACCACCTG 59.115 40.000 0.00 0.00 42.56 4.00
810 1061 6.073447 TGTAATGATACCATTTCACCACCT 57.927 37.500 0.00 0.00 42.56 4.00
811 1062 6.772716 AGATGTAATGATACCATTTCACCACC 59.227 38.462 0.00 0.00 40.95 4.61
854 1115 0.474854 TGTGTGTGGTGGGGGTCTAT 60.475 55.000 0.00 0.00 0.00 1.98
857 1118 2.203294 GTGTGTGTGGTGGGGGTC 60.203 66.667 0.00 0.00 0.00 4.46
858 1119 4.183858 CGTGTGTGTGGTGGGGGT 62.184 66.667 0.00 0.00 0.00 4.95
860 1121 4.866224 TGCGTGTGTGTGGTGGGG 62.866 66.667 0.00 0.00 0.00 4.96
861 1122 3.582120 GTGCGTGTGTGTGGTGGG 61.582 66.667 0.00 0.00 0.00 4.61
865 1126 1.919918 AAAAATGTGCGTGTGTGTGG 58.080 45.000 0.00 0.00 0.00 4.17
889 1237 6.097839 GGTGCTAGTTCCCGGATGAATATATA 59.902 42.308 0.73 0.00 0.00 0.86
913 1261 4.097741 TCCATTCGTTATGATGCTTTTGGG 59.902 41.667 2.54 0.00 36.26 4.12
983 1333 4.719273 ACCCCATTTCTTTTTCCTGTCAAA 59.281 37.500 0.00 0.00 0.00 2.69
1004 1354 0.798776 CTCAATCACGTTGCTCCACC 59.201 55.000 0.00 0.00 37.74 4.61
1131 1505 1.642952 GAGCAGAGGAAAAGGCAGCG 61.643 60.000 0.00 0.00 0.00 5.18
1299 1686 3.154710 TCTCTCTTGCTAGAAACCGTCA 58.845 45.455 0.00 0.00 0.00 4.35
1330 1718 3.263681 TCGTCAGTTCCCTCTAGAGAAGA 59.736 47.826 21.76 14.07 0.00 2.87
1331 1719 3.611970 TCGTCAGTTCCCTCTAGAGAAG 58.388 50.000 21.76 11.93 0.00 2.85
1337 1725 1.282447 AGCTCTCGTCAGTTCCCTCTA 59.718 52.381 0.00 0.00 0.00 2.43
1338 1726 0.039035 AGCTCTCGTCAGTTCCCTCT 59.961 55.000 0.00 0.00 0.00 3.69
1340 1728 0.605589 CAAGCTCTCGTCAGTTCCCT 59.394 55.000 0.00 0.00 0.00 4.20
1814 2203 0.384309 TGCGAGTCGTCCATGATACC 59.616 55.000 15.08 0.00 0.00 2.73
2185 2610 0.038801 GCTTCTTGGCCTTGTGCTTC 60.039 55.000 3.32 0.00 40.92 3.86
2692 3135 5.393896 GCACCTAACACGACCTAATAGACTT 60.394 44.000 0.00 0.00 0.00 3.01
2716 3159 3.034635 AGTAGAGCAGTGGTAATCCCTG 58.965 50.000 0.00 0.00 36.10 4.45
2748 3191 8.398665 CAATATCCTAACAGACCAAAGCTAAAC 58.601 37.037 0.00 0.00 0.00 2.01
2803 3246 1.079503 CGAAAGCTTTCTTCCCGAGG 58.920 55.000 30.91 13.37 35.07 4.63
2845 3289 0.895100 TGGACATTGCCACTTCTGCC 60.895 55.000 0.00 0.00 31.66 4.85
2846 3290 1.133790 GATGGACATTGCCACTTCTGC 59.866 52.381 2.52 0.00 41.56 4.26
2866 3310 3.761897 TCACACCAAAGATAACCCAAGG 58.238 45.455 0.00 0.00 0.00 3.61
2907 3351 1.754226 TGAAAGAAAAACAAGGCCGCT 59.246 42.857 0.00 0.00 0.00 5.52
2908 3352 2.217429 TGAAAGAAAAACAAGGCCGC 57.783 45.000 0.00 0.00 0.00 6.53
2942 3386 4.752101 CAGACATGGTATTCTTCCGGAATC 59.248 45.833 19.21 8.18 42.96 2.52
2958 3407 4.686972 CCATGACACTACTACCAGACATG 58.313 47.826 0.00 0.00 35.26 3.21
3067 3535 7.700322 TTAATCAGATCAGATACGAGTTTGC 57.300 36.000 0.45 0.00 0.00 3.68
3069 3540 7.386299 GCCATTAATCAGATCAGATACGAGTTT 59.614 37.037 0.45 0.00 0.00 2.66
3078 3549 3.494924 CGGTGGCCATTAATCAGATCAGA 60.495 47.826 9.72 0.00 0.00 3.27
3079 3550 2.810274 CGGTGGCCATTAATCAGATCAG 59.190 50.000 9.72 0.00 0.00 2.90
3081 3552 1.537202 GCGGTGGCCATTAATCAGATC 59.463 52.381 9.72 0.00 0.00 2.75
3106 3577 2.537143 AGATGGAACTGTTCGTACCCT 58.463 47.619 13.89 4.55 0.00 4.34
3113 3584 3.251571 GGTGTCGTAGATGGAACTGTTC 58.748 50.000 12.05 12.05 40.67 3.18
3119 3590 1.548081 TTCGGGTGTCGTAGATGGAA 58.452 50.000 0.00 0.00 40.67 3.53
3136 3631 3.545078 CGCTTTGAATGCAGCAGTAATTC 59.455 43.478 0.00 0.00 35.60 2.17
3144 3639 0.733909 GGTTCCGCTTTGAATGCAGC 60.734 55.000 3.94 0.00 0.00 5.25
3157 3652 0.745468 GGCCTAGTCTACTGGTTCCG 59.255 60.000 0.00 0.00 0.00 4.30
3203 3699 6.621316 TCTCGTATACAATTCAGGACTCTC 57.379 41.667 3.32 0.00 0.00 3.20
3215 3711 7.609760 ACAATTGCATTCTTCTCGTATACAA 57.390 32.000 5.05 0.00 0.00 2.41
3339 3836 4.038883 CCAATGGCCAGTAGTACTAGTACC 59.961 50.000 25.97 13.92 36.75 3.34
3340 3837 4.891756 TCCAATGGCCAGTAGTACTAGTAC 59.108 45.833 23.03 23.03 36.35 2.73
3342 3839 3.961408 CTCCAATGGCCAGTAGTACTAGT 59.039 47.826 13.05 3.18 0.00 2.57
3343 3840 3.243907 GCTCCAATGGCCAGTAGTACTAG 60.244 52.174 13.05 0.00 0.00 2.57
3346 3847 1.486726 AGCTCCAATGGCCAGTAGTAC 59.513 52.381 13.05 0.00 0.00 2.73
3443 3944 4.065789 GCTATATTTTGGAACGGAGGGAG 58.934 47.826 0.00 0.00 0.00 4.30
3444 3945 3.493699 CGCTATATTTTGGAACGGAGGGA 60.494 47.826 0.00 0.00 0.00 4.20
3445 3946 2.806244 CGCTATATTTTGGAACGGAGGG 59.194 50.000 0.00 0.00 0.00 4.30
3446 3947 2.223377 GCGCTATATTTTGGAACGGAGG 59.777 50.000 0.00 0.00 0.00 4.30
3447 3948 2.096909 CGCGCTATATTTTGGAACGGAG 60.097 50.000 5.56 0.00 0.00 4.63
3448 3949 1.862201 CGCGCTATATTTTGGAACGGA 59.138 47.619 5.56 0.00 0.00 4.69
3449 3950 1.659211 GCGCGCTATATTTTGGAACGG 60.659 52.381 26.67 0.00 0.00 4.44
3450 3951 1.658968 GCGCGCTATATTTTGGAACG 58.341 50.000 26.67 0.00 0.00 3.95
3451 3952 1.334689 GGGCGCGCTATATTTTGGAAC 60.335 52.381 32.29 8.93 0.00 3.62
3452 3953 0.948678 GGGCGCGCTATATTTTGGAA 59.051 50.000 32.29 0.00 0.00 3.53
3453 3954 0.179043 TGGGCGCGCTATATTTTGGA 60.179 50.000 32.29 0.00 0.00 3.53
3454 3955 0.040425 GTGGGCGCGCTATATTTTGG 60.040 55.000 32.29 0.00 0.00 3.28
3455 3956 0.384230 CGTGGGCGCGCTATATTTTG 60.384 55.000 32.29 9.06 0.00 2.44
3456 3957 0.812412 ACGTGGGCGCGCTATATTTT 60.812 50.000 32.29 6.70 42.83 1.82
3457 3958 0.812412 AACGTGGGCGCGCTATATTT 60.812 50.000 32.29 15.90 42.83 1.40
3458 3959 0.812412 AAACGTGGGCGCGCTATATT 60.812 50.000 32.29 15.95 42.83 1.28
3459 3960 0.812412 AAAACGTGGGCGCGCTATAT 60.812 50.000 32.29 10.39 42.83 0.86
3460 3961 1.020333 AAAAACGTGGGCGCGCTATA 61.020 50.000 32.29 14.73 42.83 1.31
3461 3962 2.248274 GAAAAACGTGGGCGCGCTAT 62.248 55.000 32.29 9.20 42.83 2.97
3462 3963 2.957052 GAAAAACGTGGGCGCGCTA 61.957 57.895 32.29 17.92 42.83 4.26
3463 3964 4.322385 GAAAAACGTGGGCGCGCT 62.322 61.111 32.29 7.69 42.83 5.92
3465 3966 3.904233 CTCGAAAAACGTGGGCGCG 62.904 63.158 0.00 0.00 42.83 6.86
3466 3967 2.127383 CTCGAAAAACGTGGGCGC 60.127 61.111 0.00 0.00 42.83 6.53
3470 3971 8.744110 TCAAAGTTGAACCTCGAAAAACGTGG 62.744 42.308 0.00 0.00 44.47 4.94
3471 3972 3.668596 AGTTGAACCTCGAAAAACGTG 57.331 42.857 0.00 0.00 43.13 4.49
3472 3973 4.154556 TCAAAGTTGAACCTCGAAAAACGT 59.845 37.500 0.00 0.00 37.49 3.99
3473 3974 4.494410 GTCAAAGTTGAACCTCGAAAAACG 59.506 41.667 0.00 0.00 39.21 3.60
3474 3975 4.796830 GGTCAAAGTTGAACCTCGAAAAAC 59.203 41.667 0.00 0.00 38.96 2.43
3475 3976 4.459685 TGGTCAAAGTTGAACCTCGAAAAA 59.540 37.500 6.62 0.00 44.20 1.94
3476 3977 4.011023 TGGTCAAAGTTGAACCTCGAAAA 58.989 39.130 6.62 0.00 44.20 2.29
3477 3978 3.611970 TGGTCAAAGTTGAACCTCGAAA 58.388 40.909 6.62 0.00 44.20 3.46
3478 3979 3.269538 TGGTCAAAGTTGAACCTCGAA 57.730 42.857 6.62 0.00 44.20 3.71
3479 3980 2.992124 TGGTCAAAGTTGAACCTCGA 57.008 45.000 6.62 0.00 44.20 4.04
3480 3981 5.682943 TTTATGGTCAAAGTTGAACCTCG 57.317 39.130 6.62 0.00 44.20 4.63
3481 3982 9.974980 TTAAATTTATGGTCAAAGTTGAACCTC 57.025 29.630 6.62 0.00 44.20 3.85
3482 3983 9.758651 GTTAAATTTATGGTCAAAGTTGAACCT 57.241 29.630 6.62 0.00 44.20 3.50
3483 3984 8.984764 GGTTAAATTTATGGTCAAAGTTGAACC 58.015 33.333 6.62 6.25 44.20 3.62
3484 3985 8.984764 GGGTTAAATTTATGGTCAAAGTTGAAC 58.015 33.333 1.98 1.98 45.04 3.18
3485 3986 8.705594 TGGGTTAAATTTATGGTCAAAGTTGAA 58.294 29.630 0.00 0.00 39.21 2.69
3486 3987 8.145122 GTGGGTTAAATTTATGGTCAAAGTTGA 58.855 33.333 0.00 0.00 34.20 3.18
3487 3988 7.115663 CGTGGGTTAAATTTATGGTCAAAGTTG 59.884 37.037 0.00 0.00 29.44 3.16
3488 3989 7.014422 TCGTGGGTTAAATTTATGGTCAAAGTT 59.986 33.333 0.00 0.00 31.36 2.66
3489 3990 6.490721 TCGTGGGTTAAATTTATGGTCAAAGT 59.509 34.615 0.00 0.00 0.00 2.66
3490 3991 6.915349 TCGTGGGTTAAATTTATGGTCAAAG 58.085 36.000 0.00 0.00 0.00 2.77
3491 3992 6.715718 TCTCGTGGGTTAAATTTATGGTCAAA 59.284 34.615 0.00 0.00 0.00 2.69
3492 3993 6.149807 GTCTCGTGGGTTAAATTTATGGTCAA 59.850 38.462 0.00 0.00 0.00 3.18
3493 3994 5.644636 GTCTCGTGGGTTAAATTTATGGTCA 59.355 40.000 0.00 0.00 0.00 4.02
3494 3995 5.065602 GGTCTCGTGGGTTAAATTTATGGTC 59.934 44.000 0.00 0.00 0.00 4.02
3495 3996 4.945543 GGTCTCGTGGGTTAAATTTATGGT 59.054 41.667 0.00 0.00 0.00 3.55
3496 3997 4.034742 CGGTCTCGTGGGTTAAATTTATGG 59.965 45.833 0.00 0.00 0.00 2.74
3497 3998 4.871557 TCGGTCTCGTGGGTTAAATTTATG 59.128 41.667 0.00 0.00 37.69 1.90
3498 3999 4.872124 GTCGGTCTCGTGGGTTAAATTTAT 59.128 41.667 0.00 0.00 37.69 1.40
3499 4000 4.021192 AGTCGGTCTCGTGGGTTAAATTTA 60.021 41.667 0.00 0.00 37.69 1.40
3500 4001 3.069289 GTCGGTCTCGTGGGTTAAATTT 58.931 45.455 0.00 0.00 37.69 1.82
3501 4002 2.301009 AGTCGGTCTCGTGGGTTAAATT 59.699 45.455 0.00 0.00 37.69 1.82
3502 4003 1.897802 AGTCGGTCTCGTGGGTTAAAT 59.102 47.619 0.00 0.00 37.69 1.40
3503 4004 1.000060 CAGTCGGTCTCGTGGGTTAAA 60.000 52.381 0.00 0.00 37.69 1.52
3504 4005 0.599558 CAGTCGGTCTCGTGGGTTAA 59.400 55.000 0.00 0.00 37.69 2.01
3505 4006 1.870055 GCAGTCGGTCTCGTGGGTTA 61.870 60.000 0.00 0.00 37.69 2.85
3506 4007 3.048602 CAGTCGGTCTCGTGGGTT 58.951 61.111 0.00 0.00 37.69 4.11
3507 4008 3.681835 GCAGTCGGTCTCGTGGGT 61.682 66.667 0.00 0.00 37.69 4.51
3508 4009 4.778415 CGCAGTCGGTCTCGTGGG 62.778 72.222 0.00 0.00 37.69 4.61
3518 4019 1.363145 TTTTTATCCCGCCGCAGTCG 61.363 55.000 0.00 0.00 0.00 4.18
3519 4020 2.473457 TTTTTATCCCGCCGCAGTC 58.527 52.632 0.00 0.00 0.00 3.51
3520 4021 4.726334 TTTTTATCCCGCCGCAGT 57.274 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.