Multiple sequence alignment - TraesCS1B01G065900

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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 TraesCS1B01G065900 chr1B 100.000 4520 0 0 1 4520 50187297 50182778 0.000000e+00 8347
1 TraesCS1B01G065900 chr1D 93.069 3073 149 33 716 3753 32546921 32543878 0.000000e+00 4436
2 TraesCS1B01G065900 chr1D 80.754 743 100 25 2 711 32547989 32547257 1.430000e-149 540
3 TraesCS1B01G065900 chr1D 85.437 103 10 3 3776 3878 32543828 32543731 8.000000e-18 102
4 TraesCS1B01G065900 chr1A 93.113 2875 146 22 923 3762 31779107 31781964 0.000000e+00 4165
5 TraesCS1B01G065900 chr5A 83.951 648 60 12 3886 4497 466617627 466618266 8.430000e-162 580
6 TraesCS1B01G065900 chr5B 82.111 682 70 13 3886 4517 431078225 431078904 1.850000e-148 536
7 TraesCS1B01G065900 chr5B 83.645 214 17 6 4319 4520 431349667 431349874 7.720000e-43 185
8 TraesCS1B01G065900 chr5D 82.198 646 56 23 3886 4497 365129414 365130034 6.750000e-138 501


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 TraesCS1B01G065900 chr1B 50182778 50187297 4519 True 8347.000000 8347 100.000 1 4520 1 chr1B.!!$R1 4519
1 TraesCS1B01G065900 chr1D 32543731 32547989 4258 True 1692.666667 4436 86.420 2 3878 3 chr1D.!!$R1 3876
2 TraesCS1B01G065900 chr1A 31779107 31781964 2857 False 4165.000000 4165 93.113 923 3762 1 chr1A.!!$F1 2839
3 TraesCS1B01G065900 chr5A 466617627 466618266 639 False 580.000000 580 83.951 3886 4497 1 chr5A.!!$F1 611
4 TraesCS1B01G065900 chr5B 431078225 431078904 679 False 536.000000 536 82.111 3886 4517 1 chr5B.!!$F1 631
5 TraesCS1B01G065900 chr5D 365129414 365130034 620 False 501.000000 501 82.198 3886 4497 1 chr5D.!!$F1 611

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
195 196 0.099082 CGTACGGCTCTCTGGTTCTC 59.901 60.000 7.57 0.0 0.00 2.87 F
861 1243 0.252375 AGCCCCATGAAATTGGCTGT 60.252 50.000 4.06 0.0 46.96 4.40 F
862 1244 1.006998 AGCCCCATGAAATTGGCTGTA 59.993 47.619 4.06 0.0 46.96 2.74 F
863 1245 1.136891 GCCCCATGAAATTGGCTGTAC 59.863 52.381 0.00 0.0 38.36 2.90 F
1063 1445 1.225908 CGTTATGGAAACGCACGCC 60.226 57.895 0.00 0.0 36.82 5.68 F
2979 3389 1.032114 GTATGCTGAGCAACCCACCC 61.032 60.000 12.69 0.0 43.62 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1530 0.026803 GCCGAACTCTTAATGCGCAG 59.973 55.000 18.32 2.85 0.00 5.18 R
2770 3178 1.133513 TGCAATGGAGGTGACCAAAGT 60.134 47.619 3.63 0.00 43.47 2.66 R
2776 3186 2.945668 GGAGTATTGCAATGGAGGTGAC 59.054 50.000 22.27 9.97 0.00 3.67 R
2787 3197 3.429492 TCAAGCCATTTGGAGTATTGCA 58.571 40.909 0.00 0.00 37.39 4.08 R
3037 3447 0.105593 GATCGGCTGATTGCAGGAGA 59.894 55.000 9.98 0.00 45.15 3.71 R
4427 4935 0.178964 CCAGCCCCTTGTCCTTTTCA 60.179 55.000 0.00 0.00 0.00 2.69 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
24 25 0.608308 GTGGGGTTTGTAGTCTGGGC 60.608 60.000 0.00 0.00 0.00 5.36
28 29 0.250727 GGTTTGTAGTCTGGGCTGCA 60.251 55.000 0.50 0.00 0.00 4.41
70 71 0.536460 TTTCGAGTTCCTGTTGGGGC 60.536 55.000 0.00 0.00 35.33 5.80
75 76 1.341209 GAGTTCCTGTTGGGGCTTTTG 59.659 52.381 0.00 0.00 35.33 2.44
95 96 2.159212 TGCGAATTTCGGTCGGATCTAA 60.159 45.455 19.53 0.00 40.84 2.10
104 105 2.030185 CGGTCGGATCTAATTGGATCGT 60.030 50.000 21.37 0.00 41.99 3.73
109 110 4.023107 TCGGATCTAATTGGATCGTCTGTC 60.023 45.833 21.37 8.87 41.99 3.51
117 118 1.428219 GATCGTCTGTCGGCGAGAA 59.572 57.895 11.20 0.00 40.56 2.87
126 127 1.014564 GTCGGCGAGAAAAGGAGGTG 61.015 60.000 11.20 0.00 0.00 4.00
132 133 1.071699 CGAGAAAAGGAGGTGGGTTGA 59.928 52.381 0.00 0.00 0.00 3.18
138 139 0.251787 AGGAGGTGGGTTGATTTGGC 60.252 55.000 0.00 0.00 0.00 4.52
156 157 2.126071 CCGTCGTGCCGTGATTCT 60.126 61.111 0.00 0.00 0.00 2.40
157 158 1.736645 CCGTCGTGCCGTGATTCTT 60.737 57.895 0.00 0.00 0.00 2.52
190 191 2.337749 ATTCGCGTACGGCTCTCTGG 62.338 60.000 18.39 0.00 40.44 3.86
195 196 0.099082 CGTACGGCTCTCTGGTTCTC 59.901 60.000 7.57 0.00 0.00 2.87
199 200 2.202676 GCTCTCTGGTTCTCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
201 202 3.708220 CTCTCTGGTTCTCGCCGGC 62.708 68.421 19.07 19.07 34.92 6.13
212 213 3.264897 CGCCGGCGAGATTTCCTG 61.265 66.667 44.86 10.04 42.83 3.86
214 215 1.745489 GCCGGCGAGATTTCCTGTT 60.745 57.895 12.58 0.00 0.00 3.16
219 220 2.369394 GGCGAGATTTCCTGTTTGGAT 58.631 47.619 0.00 0.00 45.68 3.41
221 222 2.098117 GCGAGATTTCCTGTTTGGATGG 59.902 50.000 0.00 0.00 45.68 3.51
227 228 3.951563 TTCCTGTTTGGATGGGGATAG 57.048 47.619 0.00 0.00 45.68 2.08
230 231 3.652869 TCCTGTTTGGATGGGGATAGATC 59.347 47.826 0.00 0.00 40.56 2.75
242 243 3.319122 GGGGATAGATCAGCGCAATTTTT 59.681 43.478 11.47 0.00 0.00 1.94
243 244 4.293415 GGGATAGATCAGCGCAATTTTTG 58.707 43.478 11.47 0.00 0.00 2.44
245 246 4.736793 GGATAGATCAGCGCAATTTTTGTG 59.263 41.667 11.47 0.00 43.79 3.33
247 248 3.568538 AGATCAGCGCAATTTTTGTGTC 58.431 40.909 11.47 1.45 42.92 3.67
251 252 0.508213 GCGCAATTTTTGTGTCTGCC 59.492 50.000 0.30 0.00 42.92 4.85
275 276 5.494863 AAGCGCGAATTTGAATTTTACAC 57.505 34.783 12.10 0.00 0.00 2.90
280 281 5.562248 CGCGAATTTGAATTTTACACGAGAA 59.438 36.000 0.00 0.00 0.00 2.87
284 285 7.408290 CGAATTTGAATTTTACACGAGAACTGC 60.408 37.037 0.00 0.00 0.00 4.40
288 289 7.060600 TGAATTTTACACGAGAACTGCATAG 57.939 36.000 0.00 0.00 0.00 2.23
353 354 9.579768 GTCATACATAATCTTGGCTATACAGAG 57.420 37.037 0.00 0.00 0.00 3.35
354 355 9.533831 TCATACATAATCTTGGCTATACAGAGA 57.466 33.333 0.00 0.00 0.00 3.10
374 413 7.014422 ACAGAGAGGGTAGTTAGTGCATAATAC 59.986 40.741 0.00 0.00 0.00 1.89
375 414 7.231722 CAGAGAGGGTAGTTAGTGCATAATACT 59.768 40.741 0.00 0.00 0.00 2.12
376 415 7.785506 AGAGAGGGTAGTTAGTGCATAATACTT 59.214 37.037 0.00 0.00 0.00 2.24
377 416 9.075678 GAGAGGGTAGTTAGTGCATAATACTTA 57.924 37.037 0.00 0.00 0.00 2.24
410 449 9.628500 GGTCAGATATATTTGTAAAAGGGAGTT 57.372 33.333 3.39 0.00 0.00 3.01
412 451 9.627123 TCAGATATATTTGTAAAAGGGAGTTGG 57.373 33.333 3.39 0.00 0.00 3.77
424 463 7.490657 AAAAGGGAGTTGGTAAAAAGACTTT 57.509 32.000 0.00 0.00 0.00 2.66
430 469 9.256477 GGGAGTTGGTAAAAAGACTTTATTTTG 57.744 33.333 0.00 0.00 30.52 2.44
457 496 7.047891 TGAGTAAATAGGATGTGATGTTGGTC 58.952 38.462 0.00 0.00 0.00 4.02
465 504 7.991084 AGGATGTGATGTTGGTCATATAATG 57.009 36.000 0.00 0.00 36.83 1.90
467 506 7.663081 AGGATGTGATGTTGGTCATATAATGTC 59.337 37.037 0.00 0.00 36.83 3.06
472 511 6.826231 TGATGTTGGTCATATAATGTCGGTTT 59.174 34.615 0.00 0.00 36.83 3.27
511 550 6.089417 GGTTTTACATCTTGCTGAAATTTCCG 59.911 38.462 15.48 10.32 0.00 4.30
517 556 3.008594 TCTTGCTGAAATTTCCGTCCCTA 59.991 43.478 15.48 0.00 0.00 3.53
532 571 6.752168 TCCGTCCCTAAAAGTACATAATAGC 58.248 40.000 0.00 0.00 0.00 2.97
535 574 5.407691 GTCCCTAAAAGTACATAATAGCGGC 59.592 44.000 0.00 0.00 0.00 6.53
540 579 6.693315 AAAAGTACATAATAGCGGCATTGT 57.307 33.333 1.45 0.85 0.00 2.71
543 582 6.097915 AGTACATAATAGCGGCATTGTAGT 57.902 37.500 1.45 3.00 0.00 2.73
548 587 6.934645 ACATAATAGCGGCATTGTAGTGTATT 59.065 34.615 1.45 0.00 0.00 1.89
566 605 8.508883 AGTGTATTAACTGTTTTTGTGGTGTA 57.491 30.769 0.00 0.00 0.00 2.90
568 607 9.389570 GTGTATTAACTGTTTTTGTGGTGTATC 57.610 33.333 0.00 0.00 0.00 2.24
577 616 8.918202 TGTTTTTGTGGTGTATCTTATTCTCT 57.082 30.769 0.00 0.00 0.00 3.10
659 698 5.998454 AAATGAGATGAGCGGTCAATAAG 57.002 39.130 22.64 0.00 35.88 1.73
662 701 5.282055 TGAGATGAGCGGTCAATAAGAAT 57.718 39.130 22.64 2.39 35.88 2.40
663 702 6.405278 TGAGATGAGCGGTCAATAAGAATA 57.595 37.500 22.64 0.00 35.88 1.75
664 703 6.997655 TGAGATGAGCGGTCAATAAGAATAT 58.002 36.000 22.64 0.70 35.88 1.28
666 705 7.933577 TGAGATGAGCGGTCAATAAGAATATTT 59.066 33.333 22.64 0.00 35.88 1.40
668 707 9.778741 AGATGAGCGGTCAATAAGAATATTTTA 57.221 29.630 22.64 0.00 35.88 1.52
670 709 9.778741 ATGAGCGGTCAATAAGAATATTTTAGA 57.221 29.630 22.64 0.00 35.88 2.10
703 752 7.014711 TGGAATGTGGATACTTGCAACTTAAAA 59.985 33.333 0.00 0.00 37.61 1.52
704 753 7.542130 GGAATGTGGATACTTGCAACTTAAAAG 59.458 37.037 0.00 0.00 37.61 2.27
705 754 6.952773 TGTGGATACTTGCAACTTAAAAGT 57.047 33.333 0.00 0.00 38.19 2.66
706 755 6.966021 TGTGGATACTTGCAACTTAAAAGTC 58.034 36.000 0.00 0.00 36.13 3.01
707 756 6.544197 TGTGGATACTTGCAACTTAAAAGTCA 59.456 34.615 0.00 0.00 36.13 3.41
708 757 7.230510 TGTGGATACTTGCAACTTAAAAGTCAT 59.769 33.333 0.00 0.00 36.13 3.06
709 758 7.538678 GTGGATACTTGCAACTTAAAAGTCATG 59.461 37.037 0.00 0.00 36.13 3.07
772 1151 6.041637 TGTCTGGTATATTCGGTTTGCTATCT 59.958 38.462 0.00 0.00 0.00 1.98
774 1153 8.086522 GTCTGGTATATTCGGTTTGCTATCTAA 58.913 37.037 0.00 0.00 0.00 2.10
821 1203 6.283694 TGTCTCTATGCTGAATCACAATACC 58.716 40.000 0.00 0.00 0.00 2.73
845 1227 2.744202 CCACAGTGAGTACATTCAAGCC 59.256 50.000 0.62 0.00 0.00 4.35
847 1229 2.290323 ACAGTGAGTACATTCAAGCCCC 60.290 50.000 0.00 0.00 0.00 5.80
848 1230 1.985159 AGTGAGTACATTCAAGCCCCA 59.015 47.619 0.00 0.00 0.00 4.96
849 1231 2.578021 AGTGAGTACATTCAAGCCCCAT 59.422 45.455 0.00 0.00 0.00 4.00
850 1232 2.684881 GTGAGTACATTCAAGCCCCATG 59.315 50.000 0.00 0.00 0.00 3.66
851 1233 2.575735 TGAGTACATTCAAGCCCCATGA 59.424 45.455 0.00 0.00 0.00 3.07
852 1234 3.010027 TGAGTACATTCAAGCCCCATGAA 59.990 43.478 0.00 0.00 40.76 2.57
853 1235 4.016444 GAGTACATTCAAGCCCCATGAAA 58.984 43.478 0.00 0.00 39.98 2.69
854 1236 4.613437 AGTACATTCAAGCCCCATGAAAT 58.387 39.130 0.00 0.00 39.98 2.17
855 1237 5.025453 AGTACATTCAAGCCCCATGAAATT 58.975 37.500 0.00 0.00 39.98 1.82
856 1238 4.210724 ACATTCAAGCCCCATGAAATTG 57.789 40.909 0.00 0.00 39.98 2.32
857 1239 3.054948 ACATTCAAGCCCCATGAAATTGG 60.055 43.478 0.00 0.00 39.98 3.16
858 1240 0.903942 TCAAGCCCCATGAAATTGGC 59.096 50.000 0.00 0.00 40.97 4.52
860 1242 2.599216 AGCCCCATGAAATTGGCTG 58.401 52.632 4.06 0.00 46.96 4.85
861 1243 0.252375 AGCCCCATGAAATTGGCTGT 60.252 50.000 4.06 0.00 46.96 4.40
862 1244 1.006998 AGCCCCATGAAATTGGCTGTA 59.993 47.619 4.06 0.00 46.96 2.74
863 1245 1.136891 GCCCCATGAAATTGGCTGTAC 59.863 52.381 0.00 0.00 38.36 2.90
864 1246 2.455557 CCCCATGAAATTGGCTGTACA 58.544 47.619 0.00 0.00 35.29 2.90
865 1247 3.033184 CCCCATGAAATTGGCTGTACAT 58.967 45.455 0.00 0.00 35.29 2.29
866 1248 3.068590 CCCCATGAAATTGGCTGTACATC 59.931 47.826 0.00 0.00 35.29 3.06
867 1249 3.700539 CCCATGAAATTGGCTGTACATCA 59.299 43.478 0.00 0.00 35.29 3.07
868 1250 4.342951 CCCATGAAATTGGCTGTACATCAT 59.657 41.667 0.00 0.00 35.29 2.45
869 1251 5.535783 CCCATGAAATTGGCTGTACATCATA 59.464 40.000 0.00 0.00 35.29 2.15
873 1255 9.999009 CATGAAATTGGCTGTACATCATATATC 57.001 33.333 0.00 0.00 0.00 1.63
950 1332 4.416516 AGTAGCCTTTGCCAGGTTATTTT 58.583 39.130 1.18 0.00 46.07 1.82
956 1338 6.878923 AGCCTTTGCCAGGTTATTTTAATTTC 59.121 34.615 1.18 0.00 46.07 2.17
964 1346 9.713713 GCCAGGTTATTTTAATTTCTTGGTTTA 57.286 29.630 0.00 0.00 0.00 2.01
990 1372 5.094812 GCTTGTCATATTTGTTCATTGCGA 58.905 37.500 0.00 0.00 0.00 5.10
1016 1398 4.695928 GGGACTGATGGAGTGTTTTCTTAC 59.304 45.833 0.00 0.00 33.83 2.34
1026 1408 7.060421 TGGAGTGTTTTCTTACTTTTCAGGAT 58.940 34.615 0.00 0.00 0.00 3.24
1063 1445 1.225908 CGTTATGGAAACGCACGCC 60.226 57.895 0.00 0.00 36.82 5.68
1083 1465 4.680708 CGCCTGTATGTTGGTAGATTGTCT 60.681 45.833 0.00 0.00 0.00 3.41
1152 1534 4.508124 GGAAGGTAATGACAATACTCTGCG 59.492 45.833 0.85 0.00 0.00 5.18
1173 1555 3.364964 CGCATTAAGAGTTCGGCAAAAGT 60.365 43.478 0.00 0.00 0.00 2.66
1184 1566 2.098443 TCGGCAAAAGTTTTCTGGTGTC 59.902 45.455 0.00 0.00 0.00 3.67
1187 1569 2.851824 GCAAAAGTTTTCTGGTGTCACG 59.148 45.455 0.00 0.00 0.00 4.35
1193 1575 2.234300 TTTCTGGTGTCACGGACTTC 57.766 50.000 0.00 0.54 33.15 3.01
1202 1586 4.117685 GTGTCACGGACTTCTTTACAAGT 58.882 43.478 5.77 0.00 39.43 3.16
1265 1650 9.146984 CTTGTGAATATGATTCTGCACAAATTT 57.853 29.630 0.00 0.00 43.14 1.82
1319 1704 7.283127 CACCATTATTGGACTAGTGCTTGTTAT 59.717 37.037 15.92 4.33 46.92 1.89
1320 1705 7.499232 ACCATTATTGGACTAGTGCTTGTTATC 59.501 37.037 15.92 0.00 46.92 1.75
1333 1718 5.411361 GTGCTTGTTATCATAGTTGACACCA 59.589 40.000 0.00 0.00 33.85 4.17
1391 1776 2.849646 ATAAGCCGCTCCCTCCCC 60.850 66.667 0.00 0.00 0.00 4.81
1405 1790 2.037381 CCCTCCCCGCTTATTCTAGAAC 59.963 54.545 7.48 0.00 0.00 3.01
1406 1791 2.288273 CCTCCCCGCTTATTCTAGAACG 60.288 54.545 7.48 6.78 0.00 3.95
1408 1793 1.411612 CCCCGCTTATTCTAGAACGGT 59.588 52.381 23.16 6.85 38.99 4.83
1410 1795 2.382519 CCGCTTATTCTAGAACGGTCG 58.617 52.381 19.12 14.61 35.99 4.79
1418 1803 2.280823 CTAGAACGGTCGCTCCCCAC 62.281 65.000 0.00 0.00 0.00 4.61
1432 1817 3.371595 GCTCCCCACCTTATTCTAAAGCA 60.372 47.826 0.00 0.00 0.00 3.91
1433 1818 4.455606 CTCCCCACCTTATTCTAAAGCAG 58.544 47.826 0.00 0.00 0.00 4.24
1471 1856 3.136077 GGGGCTTCTAAACTAGGTAAGGG 59.864 52.174 0.00 0.00 0.00 3.95
1514 1916 4.083565 CAAAAATTTTAGGGTCGGGGAGA 58.916 43.478 3.34 0.00 0.00 3.71
1593 1995 5.064558 TCGGTCAAACAATTTAGGCTGTTA 58.935 37.500 0.00 0.00 34.71 2.41
1647 2049 7.028962 GCATGTCTTCTGCTATATAGAGTGAG 58.971 42.308 14.16 5.77 36.68 3.51
1652 2054 3.761218 TCTGCTATATAGAGTGAGCCAGC 59.239 47.826 14.16 0.00 33.87 4.85
1657 2059 1.577736 ATAGAGTGAGCCAGCCAGTT 58.422 50.000 0.00 0.00 0.00 3.16
1681 2083 6.963117 TTCTTGGATTTCTTCCTACCCTTA 57.037 37.500 0.00 0.00 45.68 2.69
1696 2098 2.466846 CCCTTATTTTTCCTGGGTGGG 58.533 52.381 0.00 0.00 36.20 4.61
1713 2115 3.427573 GTGGGTTATACAAGCTGGGTTT 58.572 45.455 0.00 0.00 32.59 3.27
1783 2187 5.885352 CCATGTATGTGTGGAAATTGGACTA 59.115 40.000 0.00 0.00 37.72 2.59
1801 2205 2.508300 ACTACCAGGTCCTGTGTGTTTT 59.492 45.455 17.85 0.00 0.00 2.43
1818 2222 6.019881 GTGTGTTTTAACTTGAATGGTCTTGC 60.020 38.462 0.00 0.00 0.00 4.01
2241 2645 9.023967 GCATTCATTGTATGTGAATTTTACTCC 57.976 33.333 5.34 0.00 42.08 3.85
2325 2731 2.429250 AGGTACACTGTTTGTTTTGCCC 59.571 45.455 0.00 0.00 39.91 5.36
2374 2780 2.631545 TGATCCTCGTGATGCTGATGAT 59.368 45.455 0.00 0.00 32.41 2.45
2386 2792 2.224597 TGCTGATGATGCCCGATACAAT 60.225 45.455 0.00 0.00 0.00 2.71
2490 2896 7.176515 ACTTTGCGGGCATAATGATAATGATAA 59.823 33.333 0.00 0.00 0.00 1.75
2494 2900 7.975058 TGCGGGCATAATGATAATGATAATTTG 59.025 33.333 0.00 0.00 0.00 2.32
2533 2939 7.335924 TGAAGCTACTAGAAACTTTGTTGTGTT 59.664 33.333 0.00 0.00 0.00 3.32
2542 2948 8.281212 AGAAACTTTGTTGTGTTGTCTCTTAT 57.719 30.769 0.00 0.00 0.00 1.73
2606 3014 2.213499 CGTGAATATGTGGGAAGAGGC 58.787 52.381 0.00 0.00 0.00 4.70
2654 3062 4.323417 TCAACTGTGGTATTGATGGTCAC 58.677 43.478 0.00 0.00 29.89 3.67
2764 3172 3.025262 GTCCGAGGAGTCTCAGGTATTT 58.975 50.000 1.47 0.00 39.95 1.40
2765 3173 3.024547 TCCGAGGAGTCTCAGGTATTTG 58.975 50.000 1.47 0.00 39.95 2.32
2766 3174 3.024547 CCGAGGAGTCTCAGGTATTTGA 58.975 50.000 1.47 0.00 39.95 2.69
2768 3176 4.827835 CCGAGGAGTCTCAGGTATTTGATA 59.172 45.833 1.47 0.00 39.95 2.15
2770 3178 6.183360 CCGAGGAGTCTCAGGTATTTGATAAA 60.183 42.308 1.47 0.00 39.95 1.40
2776 3186 8.567285 AGTCTCAGGTATTTGATAAACTTTGG 57.433 34.615 0.00 0.00 0.00 3.28
2787 3197 5.640147 TGATAAACTTTGGTCACCTCCATT 58.360 37.500 0.00 0.00 37.33 3.16
2811 3221 4.627035 GCAATACTCCAAATGGCTTGAAAC 59.373 41.667 0.00 0.00 37.17 2.78
2816 3226 2.690497 TCCAAATGGCTTGAAACGTTCA 59.310 40.909 0.00 0.00 37.17 3.18
2818 3228 3.429543 CCAAATGGCTTGAAACGTTCATG 59.570 43.478 0.00 5.39 39.84 3.07
2823 3233 3.438781 TGGCTTGAAACGTTCATGTATCC 59.561 43.478 0.00 0.00 39.84 2.59
2855 3265 7.859325 TGGGAGTTCTTATTTAATCTTTCGG 57.141 36.000 0.00 0.00 0.00 4.30
2979 3389 1.032114 GTATGCTGAGCAACCCACCC 61.032 60.000 12.69 0.00 43.62 4.61
2982 3392 4.335647 CTGAGCAACCCACCCGCT 62.336 66.667 0.00 0.00 39.12 5.52
3000 3410 2.418976 CGCTACTCTTGGGCTTTTTACC 59.581 50.000 0.00 0.00 0.00 2.85
3001 3411 3.687125 GCTACTCTTGGGCTTTTTACCT 58.313 45.455 0.00 0.00 0.00 3.08
3003 3413 4.876679 GCTACTCTTGGGCTTTTTACCTAG 59.123 45.833 0.00 0.00 0.00 3.02
3004 3414 3.687125 ACTCTTGGGCTTTTTACCTAGC 58.313 45.455 0.00 0.00 36.66 3.42
3009 3419 3.839778 TGGGCTTTTTACCTAGCAGTTT 58.160 40.909 0.00 0.00 39.15 2.66
3069 3479 1.427368 AGCCGATCTAGGTCCAGATCT 59.573 52.381 20.14 0.00 45.89 2.75
3129 3539 2.964464 TGAGAGGAGATCAAGGAGCATC 59.036 50.000 0.00 0.00 0.00 3.91
3303 3713 1.227674 CCCTTCTGATGGCTACCGC 60.228 63.158 4.12 0.00 0.00 5.68
3350 3763 0.251742 AGCCCTGCTAACAATGGCAA 60.252 50.000 8.56 0.00 42.95 4.52
3395 3808 3.322466 CAGTCCAAGCCCGAGGGT 61.322 66.667 10.26 0.00 37.65 4.34
3417 3830 1.508256 ACAATGGTAGCCCTAGTCCC 58.492 55.000 0.00 0.00 0.00 4.46
3474 3887 0.029834 GCAATGGTGACGATGATGGC 59.970 55.000 0.00 0.00 0.00 4.40
3616 4029 5.998363 GTCAGTGAATTTCCTACCTGTTTCT 59.002 40.000 0.00 0.00 0.00 2.52
3643 4056 4.529377 ACCTGTTATTTAGTTCCTGGACGA 59.471 41.667 0.00 0.00 0.00 4.20
3647 4060 5.244402 TGTTATTTAGTTCCTGGACGACTCA 59.756 40.000 4.34 0.00 0.00 3.41
3662 4075 5.278660 GGACGACTCAGAAGGTTTGTTACTA 60.279 44.000 0.00 0.00 0.00 1.82
3668 4081 7.970102 ACTCAGAAGGTTTGTTACTATGGTTA 58.030 34.615 0.00 0.00 0.00 2.85
3776 4193 3.532950 GTCTCTGCTTCGAAACGTTTTC 58.467 45.455 15.89 7.60 0.00 2.29
3777 4194 3.000925 GTCTCTGCTTCGAAACGTTTTCA 59.999 43.478 15.89 1.68 0.00 2.69
3778 4195 3.807622 TCTCTGCTTCGAAACGTTTTCAT 59.192 39.130 15.89 0.00 0.00 2.57
3792 4245 3.632189 GTTTTCATGCACTGGACTGAAC 58.368 45.455 0.00 0.00 0.00 3.18
3799 4252 6.413892 TCATGCACTGGACTGAACATATTTA 58.586 36.000 0.00 0.00 0.00 1.40
3803 4256 8.121305 TGCACTGGACTGAACATATTTAATTT 57.879 30.769 0.00 0.00 0.00 1.82
3826 4279 8.578308 TTTCAAAAGCAAAATCATCTACACTG 57.422 30.769 0.00 0.00 0.00 3.66
3829 4282 6.882610 AAAGCAAAATCATCTACACTGTCA 57.117 33.333 0.00 0.00 0.00 3.58
3830 4283 6.882610 AAGCAAAATCATCTACACTGTCAA 57.117 33.333 0.00 0.00 0.00 3.18
3831 4284 6.246420 AGCAAAATCATCTACACTGTCAAC 57.754 37.500 0.00 0.00 0.00 3.18
3832 4285 6.000219 AGCAAAATCATCTACACTGTCAACT 59.000 36.000 0.00 0.00 0.00 3.16
3833 4286 6.488006 AGCAAAATCATCTACACTGTCAACTT 59.512 34.615 0.00 0.00 0.00 2.66
3834 4287 7.013655 AGCAAAATCATCTACACTGTCAACTTT 59.986 33.333 0.00 0.00 0.00 2.66
3835 4288 7.113965 GCAAAATCATCTACACTGTCAACTTTG 59.886 37.037 0.00 0.00 0.00 2.77
3836 4289 8.344831 CAAAATCATCTACACTGTCAACTTTGA 58.655 33.333 0.00 0.00 34.20 2.69
3837 4290 8.627208 AAATCATCTACACTGTCAACTTTGAT 57.373 30.769 0.00 0.00 39.73 2.57
3838 4291 9.725019 AAATCATCTACACTGTCAACTTTGATA 57.275 29.630 0.00 0.00 39.73 2.15
3839 4292 9.896645 AATCATCTACACTGTCAACTTTGATAT 57.103 29.630 0.00 0.00 39.73 1.63
3840 4293 8.932945 TCATCTACACTGTCAACTTTGATATC 57.067 34.615 0.00 0.00 39.73 1.63
3841 4294 8.753133 TCATCTACACTGTCAACTTTGATATCT 58.247 33.333 3.98 0.00 39.73 1.98
3842 4295 9.376075 CATCTACACTGTCAACTTTGATATCTT 57.624 33.333 3.98 0.00 39.73 2.40
3878 4331 4.014406 TGCTTCATGTCATCTCAAATGCT 58.986 39.130 0.00 0.00 0.00 3.79
3879 4332 4.142469 TGCTTCATGTCATCTCAAATGCTG 60.142 41.667 0.00 0.00 0.00 4.41
3880 4333 4.352039 CTTCATGTCATCTCAAATGCTGC 58.648 43.478 0.00 0.00 0.00 5.25
3881 4334 2.686405 TCATGTCATCTCAAATGCTGCC 59.314 45.455 0.00 0.00 0.00 4.85
3882 4335 2.203470 TGTCATCTCAAATGCTGCCA 57.797 45.000 0.00 0.00 0.00 4.92
3883 4336 1.814394 TGTCATCTCAAATGCTGCCAC 59.186 47.619 0.00 0.00 0.00 5.01
3884 4337 2.089980 GTCATCTCAAATGCTGCCACT 58.910 47.619 0.00 0.00 0.00 4.00
3893 4346 2.015736 ATGCTGCCACTAGAGAAACG 57.984 50.000 0.00 0.00 0.00 3.60
3904 4357 5.354234 CCACTAGAGAAACGGCATAAACATT 59.646 40.000 0.00 0.00 0.00 2.71
3936 4392 5.531287 GGAACTGTCAAAAACCTACTCACAT 59.469 40.000 0.00 0.00 0.00 3.21
3944 4400 7.955864 GTCAAAAACCTACTCACATACGAATTC 59.044 37.037 0.00 0.00 0.00 2.17
4019 4492 4.308526 CGCAGCAATCCAGAACCT 57.691 55.556 0.00 0.00 0.00 3.50
4046 4519 1.653151 GTTACGCCTCCCAGATTCAC 58.347 55.000 0.00 0.00 0.00 3.18
4047 4520 0.539986 TTACGCCTCCCAGATTCACC 59.460 55.000 0.00 0.00 0.00 4.02
4048 4521 1.335132 TACGCCTCCCAGATTCACCC 61.335 60.000 0.00 0.00 0.00 4.61
4049 4522 2.370445 CGCCTCCCAGATTCACCCT 61.370 63.158 0.00 0.00 0.00 4.34
4055 4534 2.104451 CTCCCAGATTCACCCTGATCTG 59.896 54.545 6.41 6.41 39.98 2.90
4064 4543 4.656100 TCACCCTGATCTGAAATCCAAA 57.344 40.909 0.38 0.00 0.00 3.28
4171 4675 2.526873 ACCTCGTCCCAACCAGCT 60.527 61.111 0.00 0.00 0.00 4.24
4173 4677 2.583441 CCTCGTCCCAACCAGCTGA 61.583 63.158 17.39 0.00 0.00 4.26
4194 4698 2.687902 CTCCCGACCTCCCACCTA 59.312 66.667 0.00 0.00 0.00 3.08
4202 4706 1.082206 CCTCCCACCTAACCCCTCA 59.918 63.158 0.00 0.00 0.00 3.86
4312 4816 3.324930 CCAGGGTCCTGCTCAGCA 61.325 66.667 11.36 0.00 42.35 4.41
4313 4817 2.677289 CCAGGGTCCTGCTCAGCAT 61.677 63.158 0.00 0.00 42.35 3.79
4337 4841 2.498077 CCATGAGAGAGGCAGACGA 58.502 57.895 0.00 0.00 0.00 4.20
4343 4847 4.104417 AGAGGCAGACGACGTCGC 62.104 66.667 35.92 27.05 44.43 5.19
4402 4910 0.519961 GTTCGGATGGTTTGGGTTCG 59.480 55.000 0.00 0.00 0.00 3.95
4405 4913 1.076014 GGATGGTTTGGGTTCGGGT 59.924 57.895 0.00 0.00 0.00 5.28
4415 4923 2.652530 GTTCGGGTGCGGTGTCTA 59.347 61.111 0.00 0.00 0.00 2.59
4427 4935 0.563672 GGTGTCTAGGAGGGGGAGAT 59.436 60.000 0.00 0.00 0.00 2.75
4429 4937 1.218196 GTGTCTAGGAGGGGGAGATGA 59.782 57.143 0.00 0.00 0.00 2.92
4436 4944 1.213182 GGAGGGGGAGATGAAAAGGAC 59.787 57.143 0.00 0.00 0.00 3.85
4443 4951 2.095461 GAGATGAAAAGGACAAGGGGC 58.905 52.381 0.00 0.00 0.00 5.80
4444 4952 1.713078 AGATGAAAAGGACAAGGGGCT 59.287 47.619 0.00 0.00 0.00 5.19
4493 5006 2.314215 GGAGGGTGGGTTTAGGGGG 61.314 68.421 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321034 GACTACAAACCCCACCGGAC 60.321 60.000 9.46 0.00 34.64 4.79
1 2 0.472352 AGACTACAAACCCCACCGGA 60.472 55.000 9.46 0.00 34.64 5.14
4 5 0.037734 CCCAGACTACAAACCCCACC 59.962 60.000 0.00 0.00 0.00 4.61
51 52 0.536460 GCCCCAACAGGAACTCGAAA 60.536 55.000 0.00 0.00 34.60 3.46
54 55 0.537371 AAAGCCCCAACAGGAACTCG 60.537 55.000 0.00 0.00 34.60 4.18
55 56 1.341209 CAAAAGCCCCAACAGGAACTC 59.659 52.381 0.00 0.00 34.60 3.01
60 61 1.743321 TTCGCAAAAGCCCCAACAGG 61.743 55.000 0.00 0.00 0.00 4.00
62 63 0.755686 AATTCGCAAAAGCCCCAACA 59.244 45.000 0.00 0.00 0.00 3.33
64 65 1.604185 CGAAATTCGCAAAAGCCCCAA 60.604 47.619 1.35 0.00 31.14 4.12
70 71 1.195900 TCCGACCGAAATTCGCAAAAG 59.804 47.619 10.24 0.00 38.82 2.27
75 76 2.129823 TAGATCCGACCGAAATTCGC 57.870 50.000 10.24 0.00 38.82 4.70
78 79 5.031066 TCCAATTAGATCCGACCGAAATT 57.969 39.130 0.00 0.00 0.00 1.82
95 96 1.226974 CGCCGACAGACGATCCAAT 60.227 57.895 0.00 0.00 45.77 3.16
104 105 0.243907 CTCCTTTTCTCGCCGACAGA 59.756 55.000 0.00 0.00 0.00 3.41
109 110 1.741770 CCACCTCCTTTTCTCGCCG 60.742 63.158 0.00 0.00 0.00 6.46
117 118 2.608623 CCAAATCAACCCACCTCCTTT 58.391 47.619 0.00 0.00 0.00 3.11
126 127 2.696759 CGACGGGCCAAATCAACCC 61.697 63.158 4.39 0.00 40.51 4.11
156 157 2.643551 GCGAATCTCCAATTCTCCCAA 58.356 47.619 0.00 0.00 0.00 4.12
157 158 1.473257 CGCGAATCTCCAATTCTCCCA 60.473 52.381 0.00 0.00 0.00 4.37
195 196 3.264897 CAGGAAATCTCGCCGGCG 61.265 66.667 42.13 42.13 41.35 6.46
199 200 1.821216 TCCAAACAGGAAATCTCGCC 58.179 50.000 0.00 0.00 45.65 5.54
212 213 3.416156 GCTGATCTATCCCCATCCAAAC 58.584 50.000 0.00 0.00 0.00 2.93
214 215 1.625315 CGCTGATCTATCCCCATCCAA 59.375 52.381 0.00 0.00 0.00 3.53
219 220 1.059098 ATTGCGCTGATCTATCCCCA 58.941 50.000 9.73 0.00 0.00 4.96
221 222 4.202050 ACAAAAATTGCGCTGATCTATCCC 60.202 41.667 9.73 0.00 0.00 3.85
227 228 3.362831 CAGACACAAAAATTGCGCTGATC 59.637 43.478 9.73 1.25 31.90 2.92
230 231 1.190763 GCAGACACAAAAATTGCGCTG 59.809 47.619 9.73 0.00 32.78 5.18
245 246 2.240612 AAATTCGCGCTTCGGCAGAC 62.241 55.000 5.56 0.00 41.88 3.51
247 248 1.864750 CAAATTCGCGCTTCGGCAG 60.865 57.895 5.56 0.00 41.88 4.85
251 252 3.952174 AAAATTCAAATTCGCGCTTCG 57.048 38.095 5.56 0.00 40.15 3.79
318 319 9.224267 GCCAAGATTATGTATGACTAACATCAT 57.776 33.333 0.00 0.00 42.13 2.45
319 320 8.432013 AGCCAAGATTATGTATGACTAACATCA 58.568 33.333 0.00 0.00 38.49 3.07
320 321 8.839310 AGCCAAGATTATGTATGACTAACATC 57.161 34.615 0.00 0.00 38.49 3.06
326 327 9.314133 TCTGTATAGCCAAGATTATGTATGACT 57.686 33.333 0.00 0.00 0.00 3.41
327 328 9.579768 CTCTGTATAGCCAAGATTATGTATGAC 57.420 37.037 0.00 0.00 0.00 3.06
328 329 9.533831 TCTCTGTATAGCCAAGATTATGTATGA 57.466 33.333 0.00 0.00 0.00 2.15
329 330 9.800433 CTCTCTGTATAGCCAAGATTATGTATG 57.200 37.037 0.00 0.00 0.00 2.39
330 331 8.976353 CCTCTCTGTATAGCCAAGATTATGTAT 58.024 37.037 0.00 0.00 0.00 2.29
331 332 7.397476 CCCTCTCTGTATAGCCAAGATTATGTA 59.603 40.741 0.00 0.00 0.00 2.29
332 333 6.212388 CCCTCTCTGTATAGCCAAGATTATGT 59.788 42.308 0.00 0.00 0.00 2.29
333 334 6.212388 ACCCTCTCTGTATAGCCAAGATTATG 59.788 42.308 0.00 0.00 0.00 1.90
334 335 6.326970 ACCCTCTCTGTATAGCCAAGATTAT 58.673 40.000 0.00 0.00 0.00 1.28
343 344 5.048573 GCACTAACTACCCTCTCTGTATAGC 60.049 48.000 0.00 0.00 0.00 2.97
349 350 5.854010 TTATGCACTAACTACCCTCTCTG 57.146 43.478 0.00 0.00 0.00 3.35
396 435 7.616542 AGTCTTTTTACCAACTCCCTTTTACAA 59.383 33.333 0.00 0.00 0.00 2.41
397 436 7.120716 AGTCTTTTTACCAACTCCCTTTTACA 58.879 34.615 0.00 0.00 0.00 2.41
398 437 7.578310 AGTCTTTTTACCAACTCCCTTTTAC 57.422 36.000 0.00 0.00 0.00 2.01
399 438 8.598202 AAAGTCTTTTTACCAACTCCCTTTTA 57.402 30.769 0.00 0.00 0.00 1.52
400 439 7.490657 AAAGTCTTTTTACCAACTCCCTTTT 57.509 32.000 0.00 0.00 0.00 2.27
430 469 7.336931 ACCAACATCACATCCTATTTACTCAAC 59.663 37.037 0.00 0.00 0.00 3.18
432 471 6.957631 ACCAACATCACATCCTATTTACTCA 58.042 36.000 0.00 0.00 0.00 3.41
433 472 7.047891 TGACCAACATCACATCCTATTTACTC 58.952 38.462 0.00 0.00 0.00 2.59
440 479 8.659527 ACATTATATGACCAACATCACATCCTA 58.340 33.333 0.00 0.00 40.07 2.94
484 523 7.603784 GGAAATTTCAGCAAGATGTAAAACCAT 59.396 33.333 19.49 0.00 0.00 3.55
487 526 6.640907 ACGGAAATTTCAGCAAGATGTAAAAC 59.359 34.615 19.49 0.00 0.00 2.43
493 532 3.428045 GGGACGGAAATTTCAGCAAGATG 60.428 47.826 19.49 1.94 0.00 2.90
503 542 8.866970 TTATGTACTTTTAGGGACGGAAATTT 57.133 30.769 0.00 0.00 0.00 1.82
507 546 7.212274 GCTATTATGTACTTTTAGGGACGGAA 58.788 38.462 0.00 0.00 0.00 4.30
511 550 5.407691 GCCGCTATTATGTACTTTTAGGGAC 59.592 44.000 12.73 3.44 0.00 4.46
517 556 6.693315 ACAATGCCGCTATTATGTACTTTT 57.307 33.333 0.00 0.00 0.00 2.27
532 571 6.417191 AACAGTTAATACACTACAATGCCG 57.583 37.500 0.00 0.00 0.00 5.69
540 579 8.508883 ACACCACAAAAACAGTTAATACACTA 57.491 30.769 0.00 0.00 0.00 2.74
543 582 9.344772 AGATACACCACAAAAACAGTTAATACA 57.655 29.630 0.00 0.00 0.00 2.29
577 616 8.183104 TCTCTTCTTCTGTACTGAATCAGAAA 57.817 34.615 18.20 1.48 45.75 2.52
579 618 7.667635 TCTTCTCTTCTTCTGTACTGAATCAGA 59.332 37.037 18.20 15.76 38.66 3.27
621 660 9.113838 TCATCTCATTTACTTTTGAATAGAGGC 57.886 33.333 0.00 0.00 0.00 4.70
626 665 7.552687 ACCGCTCATCTCATTTACTTTTGAATA 59.447 33.333 0.00 0.00 0.00 1.75
632 671 4.832248 TGACCGCTCATCTCATTTACTTT 58.168 39.130 0.00 0.00 0.00 2.66
668 707 8.416329 GCAAGTATCCACATTCCAAAATAATCT 58.584 33.333 0.00 0.00 0.00 2.40
669 708 8.196771 TGCAAGTATCCACATTCCAAAATAATC 58.803 33.333 0.00 0.00 0.00 1.75
670 709 8.076910 TGCAAGTATCCACATTCCAAAATAAT 57.923 30.769 0.00 0.00 0.00 1.28
724 1103 8.354711 ACAGTTCAACTATCACTCTATCAGAA 57.645 34.615 0.00 0.00 0.00 3.02
725 1104 7.831690 AGACAGTTCAACTATCACTCTATCAGA 59.168 37.037 0.00 0.00 0.00 3.27
772 1151 7.684317 TGGTAAGATGACATTAGATGGGTTA 57.316 36.000 0.00 0.00 33.60 2.85
774 1153 6.101734 ACATGGTAAGATGACATTAGATGGGT 59.898 38.462 0.00 0.00 33.60 4.51
821 1203 3.961480 TGAATGTACTCACTGTGGAGG 57.039 47.619 8.11 1.76 39.27 4.30
845 1227 3.700539 TGATGTACAGCCAATTTCATGGG 59.299 43.478 8.95 0.00 41.01 4.00
847 1229 9.999009 GATATATGATGTACAGCCAATTTCATG 57.001 33.333 8.95 0.00 0.00 3.07
848 1230 9.970553 AGATATATGATGTACAGCCAATTTCAT 57.029 29.630 8.95 9.57 0.00 2.57
849 1231 9.223099 CAGATATATGATGTACAGCCAATTTCA 57.777 33.333 8.95 1.93 0.00 2.69
850 1232 8.671921 CCAGATATATGATGTACAGCCAATTTC 58.328 37.037 8.95 6.85 0.00 2.17
851 1233 8.385491 TCCAGATATATGATGTACAGCCAATTT 58.615 33.333 8.95 0.00 0.00 1.82
852 1234 7.921304 TCCAGATATATGATGTACAGCCAATT 58.079 34.615 8.95 0.96 0.00 2.32
853 1235 7.500629 TCCAGATATATGATGTACAGCCAAT 57.499 36.000 8.95 4.68 0.00 3.16
854 1236 6.933514 TCCAGATATATGATGTACAGCCAA 57.066 37.500 8.95 0.00 0.00 4.52
855 1237 6.441604 ACATCCAGATATATGATGTACAGCCA 59.558 38.462 8.95 5.93 45.31 4.75
856 1238 6.760298 CACATCCAGATATATGATGTACAGCC 59.240 42.308 8.95 0.00 45.37 4.85
857 1239 6.257411 GCACATCCAGATATATGATGTACAGC 59.743 42.308 13.82 3.61 45.37 4.40
858 1240 6.760298 GGCACATCCAGATATATGATGTACAG 59.240 42.308 13.82 6.52 45.37 2.74
859 1241 6.441604 AGGCACATCCAGATATATGATGTACA 59.558 38.462 13.82 0.00 45.37 2.90
860 1242 6.882656 AGGCACATCCAGATATATGATGTAC 58.117 40.000 13.82 10.03 45.37 2.90
861 1243 7.841222 ACTAGGCACATCCAGATATATGATGTA 59.159 37.037 13.82 2.55 45.37 2.29
863 1245 7.122138 ACTAGGCACATCCAGATATATGATG 57.878 40.000 0.00 9.05 41.26 3.07
864 1246 8.064389 AGTACTAGGCACATCCAGATATATGAT 58.936 37.037 0.00 0.00 37.29 2.45
865 1247 7.414266 AGTACTAGGCACATCCAGATATATGA 58.586 38.462 0.00 0.00 37.29 2.15
866 1248 7.559533 AGAGTACTAGGCACATCCAGATATATG 59.440 40.741 0.00 0.00 37.29 1.78
867 1249 7.647827 AGAGTACTAGGCACATCCAGATATAT 58.352 38.462 0.00 0.00 37.29 0.86
868 1250 7.033782 AGAGTACTAGGCACATCCAGATATA 57.966 40.000 0.00 0.00 37.29 0.86
869 1251 5.898120 AGAGTACTAGGCACATCCAGATAT 58.102 41.667 0.00 0.00 37.29 1.63
873 1255 3.254657 GCTAGAGTACTAGGCACATCCAG 59.745 52.174 0.00 0.00 44.33 3.86
956 1338 8.761575 ACAAATATGACAAGCATTAAACCAAG 57.238 30.769 0.00 0.00 38.44 3.61
964 1346 6.035220 CGCAATGAACAAATATGACAAGCATT 59.965 34.615 0.00 0.00 38.44 3.56
990 1372 3.884037 AAACACTCCATCAGTCCCTTT 57.116 42.857 0.00 0.00 30.26 3.11
1026 1408 4.783764 ACGATCATCATAACGAGGCATA 57.216 40.909 0.00 0.00 0.00 3.14
1063 1445 5.817816 GGGAAGACAATCTACCAACATACAG 59.182 44.000 0.00 0.00 0.00 2.74
1083 1465 2.176546 CGCGAACGAGTACGGGAA 59.823 61.111 0.00 0.00 43.93 3.97
1148 1530 0.026803 GCCGAACTCTTAATGCGCAG 59.973 55.000 18.32 2.85 0.00 5.18
1152 1534 4.160736 ACTTTTGCCGAACTCTTAATGC 57.839 40.909 0.00 0.00 0.00 3.56
1164 1546 2.159310 TGACACCAGAAAACTTTTGCCG 60.159 45.455 0.00 0.00 0.00 5.69
1173 1555 2.169769 AGAAGTCCGTGACACCAGAAAA 59.830 45.455 0.00 0.00 34.60 2.29
1236 1621 7.920160 TGTGCAGAATCATATTCACAAGTTA 57.080 32.000 0.00 0.00 32.35 2.24
1265 1650 8.445275 TCACAACTCTAGAAAAGCACATTTTA 57.555 30.769 0.00 0.00 41.24 1.52
1266 1651 7.333528 TCACAACTCTAGAAAAGCACATTTT 57.666 32.000 0.00 0.00 43.88 1.82
1319 1704 8.692710 CCTAAGTACTTATGGTGTCAACTATGA 58.307 37.037 15.57 0.00 0.00 2.15
1320 1705 7.438459 GCCTAAGTACTTATGGTGTCAACTATG 59.562 40.741 15.57 0.00 0.00 2.23
1333 1718 6.638021 AAAGAACTGGGCCTAAGTACTTAT 57.362 37.500 15.57 0.00 0.00 1.73
1391 1776 1.779724 GCGACCGTTCTAGAATAAGCG 59.220 52.381 8.75 11.52 0.00 4.68
1405 1790 1.968050 AATAAGGTGGGGAGCGACCG 61.968 60.000 0.00 0.00 40.11 4.79
1406 1791 0.179054 GAATAAGGTGGGGAGCGACC 60.179 60.000 0.00 0.00 38.08 4.79
1408 1793 2.464796 TAGAATAAGGTGGGGAGCGA 57.535 50.000 0.00 0.00 0.00 4.93
1410 1795 3.215151 GCTTTAGAATAAGGTGGGGAGC 58.785 50.000 0.00 0.00 0.00 4.70
1418 1803 2.091885 TGGGGGCTGCTTTAGAATAAGG 60.092 50.000 0.00 0.00 0.00 2.69
1471 1856 7.470935 TTTGGGGGCTTCTAAAGTAATTAAC 57.529 36.000 0.00 0.00 0.00 2.01
1479 1864 6.878923 CCTAAAATTTTTGGGGGCTTCTAAAG 59.121 38.462 19.92 2.85 30.82 1.85
1514 1916 1.758862 GCTGCCAAAATAATCTGCCCT 59.241 47.619 0.00 0.00 0.00 5.19
1608 2010 3.668447 AGACATGCACCTTACAGTTCAG 58.332 45.455 0.00 0.00 0.00 3.02
1647 2049 1.260544 ATCCAAGAAAACTGGCTGGC 58.739 50.000 0.00 0.00 33.63 4.85
1681 2083 5.278127 TGTATAACCCACCCAGGAAAAAT 57.722 39.130 0.00 0.00 41.22 1.82
1783 2187 3.053917 AGTTAAAACACACAGGACCTGGT 60.054 43.478 25.34 16.63 35.51 4.00
1801 2205 5.239306 CACTCAAGCAAGACCATTCAAGTTA 59.761 40.000 0.00 0.00 0.00 2.24
2241 2645 7.775561 ACTTGAAAGAGCATAAATAAGGTAGGG 59.224 37.037 0.00 0.00 0.00 3.53
2325 2731 8.188799 TGTATTCCTGTTAGATAGACAAGAACG 58.811 37.037 0.00 0.00 32.16 3.95
2374 2780 2.028112 GCCATCTAGATTGTATCGGGCA 60.028 50.000 18.39 0.00 38.71 5.36
2386 2792 2.763039 TCAACATCCCTGCCATCTAGA 58.237 47.619 0.00 0.00 0.00 2.43
2490 2896 7.885399 AGTAGCTTCATAAAGAGGACAACAAAT 59.115 33.333 0.00 0.00 34.14 2.32
2494 2900 7.773149 TCTAGTAGCTTCATAAAGAGGACAAC 58.227 38.462 0.00 0.00 34.14 3.32
2497 2903 8.471609 AGTTTCTAGTAGCTTCATAAAGAGGAC 58.528 37.037 0.00 0.00 34.14 3.85
2498 2904 8.596781 AGTTTCTAGTAGCTTCATAAAGAGGA 57.403 34.615 0.00 0.00 34.14 3.71
2499 2905 9.660180 AAAGTTTCTAGTAGCTTCATAAAGAGG 57.340 33.333 0.00 0.00 34.14 3.69
2501 2907 9.998106 ACAAAGTTTCTAGTAGCTTCATAAAGA 57.002 29.630 0.00 0.00 34.14 2.52
2533 2939 5.063204 CCTGAACACAAACCATAAGAGACA 58.937 41.667 0.00 0.00 0.00 3.41
2542 2948 2.096248 GTGGAACCTGAACACAAACCA 58.904 47.619 0.00 0.00 35.30 3.67
2606 3014 2.674220 GCCTGTTCCTGGAGGAGGG 61.674 68.421 19.40 11.86 46.36 4.30
2654 3062 3.933048 CTTGCAGTCCCTGGCCCAG 62.933 68.421 2.91 2.91 31.21 4.45
2744 3152 3.024547 CAAATACCTGAGACTCCTCGGA 58.975 50.000 0.00 0.00 46.42 4.55
2764 3172 4.715534 TGGAGGTGACCAAAGTTTATCA 57.284 40.909 3.63 0.00 36.96 2.15
2765 3173 5.622233 GCAATGGAGGTGACCAAAGTTTATC 60.622 44.000 3.63 0.00 43.47 1.75
2766 3174 4.220602 GCAATGGAGGTGACCAAAGTTTAT 59.779 41.667 3.63 0.00 43.47 1.40
2768 3176 2.365293 GCAATGGAGGTGACCAAAGTTT 59.635 45.455 3.63 0.00 43.47 2.66
2770 3178 1.133513 TGCAATGGAGGTGACCAAAGT 60.134 47.619 3.63 0.00 43.47 2.66
2776 3186 2.945668 GGAGTATTGCAATGGAGGTGAC 59.054 50.000 22.27 9.97 0.00 3.67
2787 3197 3.429492 TCAAGCCATTTGGAGTATTGCA 58.571 40.909 0.00 0.00 37.39 4.08
2823 3233 8.980481 ATTAAATAAGAACTCCCATGTACTGG 57.020 34.615 0.00 0.00 45.51 4.00
2853 3263 6.435428 GCCTAACAAAACATATCCATTACCG 58.565 40.000 0.00 0.00 0.00 4.02
2855 3265 6.910433 CACGCCTAACAAAACATATCCATTAC 59.090 38.462 0.00 0.00 0.00 1.89
2871 3281 3.719173 ATAGCTTCTCTCACGCCTAAC 57.281 47.619 0.00 0.00 0.00 2.34
2979 3389 2.418976 GGTAAAAAGCCCAAGAGTAGCG 59.581 50.000 0.00 0.00 0.00 4.26
2982 3392 4.287585 TGCTAGGTAAAAAGCCCAAGAGTA 59.712 41.667 0.00 0.00 37.97 2.59
3000 3410 8.856490 AACAGAATACAAAACAAAACTGCTAG 57.144 30.769 0.00 0.00 0.00 3.42
3001 3411 9.646427 AAAACAGAATACAAAACAAAACTGCTA 57.354 25.926 0.00 0.00 0.00 3.49
3003 3413 8.655970 AGAAAACAGAATACAAAACAAAACTGC 58.344 29.630 0.00 0.00 0.00 4.40
3037 3447 0.105593 GATCGGCTGATTGCAGGAGA 59.894 55.000 9.98 0.00 45.15 3.71
3129 3539 2.188994 GGGCTCCTGCTGTAGCTG 59.811 66.667 8.04 4.66 42.66 4.24
3327 3737 1.616725 CCATTGTTAGCAGGGCTTGGA 60.617 52.381 0.00 0.00 40.44 3.53
3395 3808 2.504175 GGACTAGGGCTACCATTGTTGA 59.496 50.000 0.00 0.00 40.13 3.18
3417 3830 2.053865 ACCATCGCCATTGCCCTTG 61.054 57.895 0.00 0.00 0.00 3.61
3480 3893 1.733402 CTCTAGGTGAGCCTGAGCCG 61.733 65.000 0.00 0.00 46.47 5.52
3539 3952 2.076100 CCACATGTAGCGAGCAGAAAA 58.924 47.619 0.00 0.00 0.00 2.29
3616 4029 6.713450 GTCCAGGAACTAAATAACAGGTTCAA 59.287 38.462 0.00 0.00 39.55 2.69
3643 4056 6.435292 ACCATAGTAACAAACCTTCTGAGT 57.565 37.500 0.00 0.00 0.00 3.41
3662 4075 6.544197 TCCATTACGCACAACATAATAACCAT 59.456 34.615 0.00 0.00 0.00 3.55
3668 4081 6.691754 TCAATCCATTACGCACAACATAAT 57.308 33.333 0.00 0.00 0.00 1.28
3714 4131 7.118390 GGCTGTCACAAACTGATACCATATATC 59.882 40.741 0.00 0.00 0.00 1.63
3730 4147 0.254462 TCAACCACAGGCTGTCACAA 59.746 50.000 19.13 0.00 0.00 3.33
3776 4193 5.571784 AAATATGTTCAGTCCAGTGCATG 57.428 39.130 0.00 0.00 0.00 4.06
3777 4194 7.886629 ATTAAATATGTTCAGTCCAGTGCAT 57.113 32.000 0.00 0.00 0.00 3.96
3778 4195 7.701539 AATTAAATATGTTCAGTCCAGTGCA 57.298 32.000 0.00 0.00 0.00 4.57
3799 4252 9.768662 AGTGTAGATGATTTTGCTTTTGAAATT 57.231 25.926 0.00 0.00 0.00 1.82
3803 4256 7.013178 TGACAGTGTAGATGATTTTGCTTTTGA 59.987 33.333 0.00 0.00 0.00 2.69
3826 4279 8.656849 ACACGACAATAAGATATCAAAGTTGAC 58.343 33.333 5.32 4.52 40.49 3.18
3829 4282 9.825972 CAAACACGACAATAAGATATCAAAGTT 57.174 29.630 5.32 0.00 0.00 2.66
3830 4283 8.999431 ACAAACACGACAATAAGATATCAAAGT 58.001 29.630 5.32 0.00 0.00 2.66
3831 4284 9.265938 CACAAACACGACAATAAGATATCAAAG 57.734 33.333 5.32 0.00 0.00 2.77
3832 4285 7.748683 GCACAAACACGACAATAAGATATCAAA 59.251 33.333 5.32 0.00 0.00 2.69
3833 4286 7.119116 AGCACAAACACGACAATAAGATATCAA 59.881 33.333 5.32 0.00 0.00 2.57
3834 4287 6.593770 AGCACAAACACGACAATAAGATATCA 59.406 34.615 5.32 0.00 0.00 2.15
3835 4288 7.005062 AGCACAAACACGACAATAAGATATC 57.995 36.000 0.00 0.00 0.00 1.63
3836 4289 6.985188 AGCACAAACACGACAATAAGATAT 57.015 33.333 0.00 0.00 0.00 1.63
3837 4290 6.425417 TGAAGCACAAACACGACAATAAGATA 59.575 34.615 0.00 0.00 0.00 1.98
3838 4291 5.238432 TGAAGCACAAACACGACAATAAGAT 59.762 36.000 0.00 0.00 0.00 2.40
3839 4292 4.572795 TGAAGCACAAACACGACAATAAGA 59.427 37.500 0.00 0.00 0.00 2.10
3840 4293 4.843147 TGAAGCACAAACACGACAATAAG 58.157 39.130 0.00 0.00 0.00 1.73
3841 4294 4.884458 TGAAGCACAAACACGACAATAA 57.116 36.364 0.00 0.00 0.00 1.40
3842 4295 4.274705 ACATGAAGCACAAACACGACAATA 59.725 37.500 0.00 0.00 0.00 1.90
3846 4299 2.031560 TGACATGAAGCACAAACACGAC 59.968 45.455 0.00 0.00 0.00 4.34
3879 4332 2.596904 TATGCCGTTTCTCTAGTGGC 57.403 50.000 0.00 0.00 45.91 5.01
3880 4333 4.250464 TGTTTATGCCGTTTCTCTAGTGG 58.750 43.478 0.00 0.00 0.00 4.00
3881 4334 6.092122 TGAATGTTTATGCCGTTTCTCTAGTG 59.908 38.462 0.00 0.00 0.00 2.74
3882 4335 6.170506 TGAATGTTTATGCCGTTTCTCTAGT 58.829 36.000 0.00 0.00 0.00 2.57
3883 4336 6.662414 TGAATGTTTATGCCGTTTCTCTAG 57.338 37.500 0.00 0.00 0.00 2.43
3884 4337 7.201696 GGATTGAATGTTTATGCCGTTTCTCTA 60.202 37.037 0.00 0.00 0.00 2.43
3893 4346 5.127682 AGTTCCAGGATTGAATGTTTATGCC 59.872 40.000 0.00 0.00 0.00 4.40
3904 4357 4.340950 GGTTTTTGACAGTTCCAGGATTGA 59.659 41.667 8.18 0.00 0.00 2.57
3944 4400 5.235186 CAGGATAAATTGAGAGGCTGTTACG 59.765 44.000 0.00 0.00 0.00 3.18
3946 4402 6.313519 ACAGGATAAATTGAGAGGCTGTTA 57.686 37.500 0.00 0.00 0.00 2.41
4019 4492 1.315257 GGGAGGCGTAACGACCAGTA 61.315 60.000 0.00 0.00 34.11 2.74
4046 4519 2.684881 CCGTTTGGATTTCAGATCAGGG 59.315 50.000 0.00 0.00 37.49 4.45
4047 4520 3.609853 TCCGTTTGGATTTCAGATCAGG 58.390 45.455 0.00 0.00 40.17 3.86
4048 4521 4.095483 CCTTCCGTTTGGATTTCAGATCAG 59.905 45.833 0.00 0.00 45.91 2.90
4049 4522 4.009675 CCTTCCGTTTGGATTTCAGATCA 58.990 43.478 0.00 0.00 45.91 2.92
4055 4534 3.816523 TGTGTACCTTCCGTTTGGATTTC 59.183 43.478 0.00 0.00 45.91 2.17
4064 4543 2.290071 CCAATCCTTGTGTACCTTCCGT 60.290 50.000 0.00 0.00 0.00 4.69
4105 4585 2.125773 GAGGAGTTCGAGTACCAGGA 57.874 55.000 0.00 0.00 0.00 3.86
4151 4655 3.164977 TGGTTGGGACGAGGTGCA 61.165 61.111 0.00 0.00 0.00 4.57
4160 4664 3.256960 GGGGTCAGCTGGTTGGGA 61.257 66.667 15.13 0.00 0.00 4.37
4164 4668 2.936032 GGGAGGGGTCAGCTGGTT 60.936 66.667 15.13 0.00 0.00 3.67
4171 4675 4.393778 GGAGGTCGGGAGGGGTCA 62.394 72.222 0.00 0.00 0.00 4.02
4183 4687 1.082392 GAGGGGTTAGGTGGGAGGT 59.918 63.158 0.00 0.00 0.00 3.85
4312 4816 2.815945 CCTCTCTCATGGCGCCCAT 61.816 63.158 26.77 14.88 46.37 4.00
4313 4817 3.473647 CCTCTCTCATGGCGCCCA 61.474 66.667 26.77 12.96 38.19 5.36
4324 4828 2.392181 CGACGTCGTCTGCCTCTCT 61.392 63.158 29.08 0.00 34.11 3.10
4363 4867 4.988598 CCAACCACCAGCGAGCGT 62.989 66.667 0.00 0.00 0.00 5.07
4402 4910 2.722201 CCTCCTAGACACCGCACCC 61.722 68.421 0.00 0.00 0.00 4.61
4405 4913 2.363795 CCCCTCCTAGACACCGCA 60.364 66.667 0.00 0.00 0.00 5.69
4415 4923 1.082879 TCCTTTTCATCTCCCCCTCCT 59.917 52.381 0.00 0.00 0.00 3.69
4427 4935 0.178964 CCAGCCCCTTGTCCTTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
4429 4937 1.533994 GCCAGCCCCTTGTCCTTTT 60.534 57.895 0.00 0.00 0.00 2.27
4436 4944 2.155197 AAACCCTAGCCAGCCCCTTG 62.155 60.000 0.00 0.00 0.00 3.61
4443 4951 3.714798 TCCCAAGTATAAACCCTAGCCAG 59.285 47.826 0.00 0.00 0.00 4.85
4444 4952 3.738434 TCCCAAGTATAAACCCTAGCCA 58.262 45.455 0.00 0.00 0.00 4.75
4493 5006 1.010574 CGCTCTCATCGTCGTCTCC 60.011 63.158 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.