Multiple sequence alignment - TraesCS5A01G341800

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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 TraesCS5A01G341800 chr5A 100.000 3660 0 0 1 3660 547611856 547615515 0.000000e+00 6759.0
1 TraesCS5A01G341800 chr5A 76.917 1265 214 40 998 2211 447547050 447545813 0.000000e+00 647.0
2 TraesCS5A01G341800 chr5A 82.042 529 79 12 2218 2743 547597604 547598119 1.560000e-118 436.0
3 TraesCS5A01G341800 chr5A 82.394 426 64 8 1050 1468 547590322 547590743 9.660000e-96 361.0
4 TraesCS5A01G341800 chr5A 80.499 441 70 10 1041 1469 547508927 547509363 1.270000e-84 324.0
5 TraesCS5A01G341800 chr5A 84.663 163 19 3 2913 3070 547598245 547598406 1.360000e-34 158.0
6 TraesCS5A01G341800 chr5B 94.699 1396 45 8 2256 3639 526576179 526577557 0.000000e+00 2141.0
7 TraesCS5A01G341800 chr5B 95.542 1301 55 1 963 2263 526574688 526575985 0.000000e+00 2078.0
8 TraesCS5A01G341800 chr5B 85.509 904 100 18 16 899 526572209 526573101 0.000000e+00 915.0
9 TraesCS5A01G341800 chr5B 78.219 1258 195 47 998 2220 525447612 525448825 0.000000e+00 732.0
10 TraesCS5A01G341800 chr5B 77.026 1271 203 48 998 2219 407241814 407240584 0.000000e+00 647.0
11 TraesCS5A01G341800 chr5B 79.866 596 80 18 2235 2821 526249941 526250505 2.050000e-107 399.0
12 TraesCS5A01G341800 chr5B 77.851 605 78 25 2302 2884 526438847 526439417 1.270000e-84 324.0
13 TraesCS5A01G341800 chr5B 82.540 126 17 4 2765 2888 526175982 526176104 5.000000e-19 106.0
14 TraesCS5A01G341800 chr5B 97.436 39 1 0 3173 3211 526439739 526439777 2.360000e-07 67.6
15 TraesCS5A01G341800 chr6D 81.111 1260 188 29 979 2207 31479678 31480918 0.000000e+00 963.0
16 TraesCS5A01G341800 chr6A 80.994 1268 189 31 985 2220 31745519 31744272 0.000000e+00 959.0
17 TraesCS5A01G341800 chr5D 78.000 1250 199 46 1000 2211 344534316 344535527 0.000000e+00 715.0
18 TraesCS5A01G341800 chr5D 77.885 1248 199 42 998 2211 432781795 432782999 0.000000e+00 704.0
19 TraesCS5A01G341800 chr5D 80.030 661 87 29 2422 3059 432925131 432925769 7.210000e-122 448.0
20 TraesCS5A01G341800 chr5D 81.853 529 80 12 2218 2743 433012455 433012970 7.260000e-117 431.0
21 TraesCS5A01G341800 chr5D 80.967 331 45 11 2889 3207 433004996 433005320 2.820000e-61 246.0
22 TraesCS5A01G341800 chr5D 84.663 163 19 3 2913 3070 433013105 433013266 1.360000e-34 158.0
23 TraesCS5A01G341800 chrUn 77.627 1256 206 45 998 2220 63282944 63281731 0.000000e+00 693.0
24 TraesCS5A01G341800 chrUn 77.627 1256 206 45 998 2220 327299180 327297967 0.000000e+00 693.0
25 TraesCS5A01G341800 chrUn 92.157 51 4 0 2164 2214 296014006 296013956 5.070000e-09 73.1
26 TraesCS5A01G341800 chrUn 97.059 34 1 0 2164 2197 81877754 81877721 1.420000e-04 58.4
27 TraesCS5A01G341800 chr6B 79.667 841 130 25 1256 2074 56316825 56316004 5.300000e-158 568.0
28 TraesCS5A01G341800 chr6B 89.756 205 18 2 979 1180 56317250 56317046 3.630000e-65 259.0
29 TraesCS5A01G341800 chr4A 82.353 170 28 2 1071 1239 623952131 623951963 2.950000e-31 147.0
30 TraesCS5A01G341800 chr4A 97.143 35 1 0 2163 2197 702028840 702028806 3.950000e-05 60.2
31 TraesCS5A01G341800 chr1A 82.353 170 28 2 1071 1239 569949623 569949455 2.950000e-31 147.0
32 TraesCS5A01G341800 chr1B 92.157 51 4 0 2164 2214 395253954 395253904 5.070000e-09 73.1
33 TraesCS5A01G341800 chr1B 92.157 51 4 0 2164 2214 395259063 395259013 5.070000e-09 73.1


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 TraesCS5A01G341800 chr5A 547611856 547615515 3659 False 6759.000000 6759 100.000000 1 3660 1 chr5A.!!$F3 3659
1 TraesCS5A01G341800 chr5A 447545813 447547050 1237 True 647.000000 647 76.917000 998 2211 1 chr5A.!!$R1 1213
2 TraesCS5A01G341800 chr5A 547597604 547598406 802 False 297.000000 436 83.352500 2218 3070 2 chr5A.!!$F4 852
3 TraesCS5A01G341800 chr5B 526572209 526577557 5348 False 1711.333333 2141 91.916667 16 3639 3 chr5B.!!$F5 3623
4 TraesCS5A01G341800 chr5B 525447612 525448825 1213 False 732.000000 732 78.219000 998 2220 1 chr5B.!!$F1 1222
5 TraesCS5A01G341800 chr5B 407240584 407241814 1230 True 647.000000 647 77.026000 998 2219 1 chr5B.!!$R1 1221
6 TraesCS5A01G341800 chr5B 526249941 526250505 564 False 399.000000 399 79.866000 2235 2821 1 chr5B.!!$F3 586
7 TraesCS5A01G341800 chr6D 31479678 31480918 1240 False 963.000000 963 81.111000 979 2207 1 chr6D.!!$F1 1228
8 TraesCS5A01G341800 chr6A 31744272 31745519 1247 True 959.000000 959 80.994000 985 2220 1 chr6A.!!$R1 1235
9 TraesCS5A01G341800 chr5D 344534316 344535527 1211 False 715.000000 715 78.000000 1000 2211 1 chr5D.!!$F1 1211
10 TraesCS5A01G341800 chr5D 432781795 432782999 1204 False 704.000000 704 77.885000 998 2211 1 chr5D.!!$F2 1213
11 TraesCS5A01G341800 chr5D 432925131 432925769 638 False 448.000000 448 80.030000 2422 3059 1 chr5D.!!$F3 637
12 TraesCS5A01G341800 chr5D 433012455 433013266 811 False 294.500000 431 83.258000 2218 3070 2 chr5D.!!$F5 852
13 TraesCS5A01G341800 chrUn 63281731 63282944 1213 True 693.000000 693 77.627000 998 2220 1 chrUn.!!$R1 1222
14 TraesCS5A01G341800 chrUn 327297967 327299180 1213 True 693.000000 693 77.627000 998 2220 1 chrUn.!!$R4 1222
15 TraesCS5A01G341800 chr6B 56316004 56317250 1246 True 413.500000 568 84.711500 979 2074 2 chr6B.!!$R1 1095

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
845 849 0.031178 AGCAAAAGCGAGGCAAACAG 59.969 50.0 0.0 0.0 0.0 3.16 F
846 850 0.249031 GCAAAAGCGAGGCAAACAGT 60.249 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 3429 0.456312 GCCTTACTCGTGTGTCTCCG 60.456 60.0 0.0 0.0 0.00 4.63 R
2776 4758 0.473755 ATGCTGTTGTCTCCACACCA 59.526 50.0 0.0 0.0 29.76 4.17 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
68 69 3.595819 GCTGGCTTGCCAACTAGG 58.404 61.111 15.63 4.75 41.84 3.02
87 88 3.021177 GGCTAGAGTTCCTAGTCTGGT 57.979 52.381 0.00 0.00 44.64 4.00
98 99 2.159028 CCTAGTCTGGTTAGAAGCTGCC 60.159 54.545 0.00 0.00 34.01 4.85
101 102 0.615331 TCTGGTTAGAAGCTGCCCAG 59.385 55.000 8.80 8.80 43.26 4.45
121 122 2.087646 GGAGCCTCTTTGGAATGACAC 58.912 52.381 0.00 0.00 38.35 3.67
143 144 4.835615 ACCACCCTTTGTTTGCATGTATTA 59.164 37.500 0.00 0.00 0.00 0.98
150 151 6.928492 CCTTTGTTTGCATGTATTAGTGGTTT 59.072 34.615 0.00 0.00 0.00 3.27
151 152 7.095691 CCTTTGTTTGCATGTATTAGTGGTTTG 60.096 37.037 0.00 0.00 0.00 2.93
157 158 6.821388 TGCATGTATTAGTGGTTTGGTTTTT 58.179 32.000 0.00 0.00 0.00 1.94
195 196 9.973450 AACAAACATGTGCTAATTTTACATACA 57.027 25.926 0.00 0.00 33.57 2.29
256 257 1.909700 TTGTCCTCATTTGTCTGGGC 58.090 50.000 0.00 0.00 0.00 5.36
274 275 1.941812 CAGACAACCCGAACTGTGC 59.058 57.895 0.00 0.00 0.00 4.57
276 277 2.203294 ACAACCCGAACTGTGCCC 60.203 61.111 0.00 0.00 0.00 5.36
278 279 3.868985 AACCCGAACTGTGCCCGT 61.869 61.111 0.00 0.00 0.00 5.28
282 283 2.126071 CGAACTGTGCCCGTCGAT 60.126 61.111 0.00 0.00 0.00 3.59
288 289 0.738975 CTGTGCCCGTCGATAAGAGA 59.261 55.000 0.00 0.00 0.00 3.10
295 296 3.696898 CCCGTCGATAAGAGAGACAAAG 58.303 50.000 0.00 0.00 34.80 2.77
296 297 3.128938 CCCGTCGATAAGAGAGACAAAGT 59.871 47.826 0.00 0.00 34.80 2.66
297 298 4.344448 CCGTCGATAAGAGAGACAAAGTC 58.656 47.826 0.00 0.00 34.80 3.01
316 317 8.960591 ACAAAGTCTATCCAATTTGACCATTAG 58.039 33.333 0.00 0.00 36.41 1.73
332 333 8.463930 TGACCATTAGATTGTTCCCATTAATC 57.536 34.615 0.00 0.00 0.00 1.75
335 336 6.071952 CCATTAGATTGTTCCCATTAATCCGG 60.072 42.308 0.00 0.00 32.59 5.14
345 346 3.761752 CCCATTAATCCGGTTGTCAAACT 59.238 43.478 0.00 0.00 36.48 2.66
347 348 4.700213 CCATTAATCCGGTTGTCAAACTCT 59.300 41.667 0.00 0.00 36.48 3.24
349 350 3.485463 AATCCGGTTGTCAAACTCTCA 57.515 42.857 0.00 0.00 36.48 3.27
356 357 5.008217 CCGGTTGTCAAACTCTCAAATACAA 59.992 40.000 0.00 0.00 36.48 2.41
357 358 5.907391 CGGTTGTCAAACTCTCAAATACAAC 59.093 40.000 0.00 0.00 42.65 3.32
359 360 7.027778 GTTGTCAAACTCTCAAATACAACCT 57.972 36.000 0.00 0.00 39.34 3.50
360 361 6.618287 TGTCAAACTCTCAAATACAACCTG 57.382 37.500 0.00 0.00 0.00 4.00
362 363 7.276658 TGTCAAACTCTCAAATACAACCTGTA 58.723 34.615 0.00 0.00 37.24 2.74
370 371 6.821665 TCTCAAATACAACCTGTATGTAAGGC 59.178 38.462 0.22 0.00 42.29 4.35
387 388 1.633945 AGGCGAAAATTAGGGTGTCCT 59.366 47.619 0.00 0.00 46.96 3.85
393 394 4.382685 CGAAAATTAGGGTGTCCTAGCAGA 60.383 45.833 0.00 0.00 45.60 4.26
394 395 5.497474 GAAAATTAGGGTGTCCTAGCAGAA 58.503 41.667 0.00 0.00 45.60 3.02
407 408 2.844146 CAGAACGCCACGTCGAAC 59.156 61.111 0.00 0.00 39.99 3.95
410 411 2.202770 AACGCCACGTCGAACACA 60.203 55.556 0.00 0.00 39.99 3.72
411 412 1.754436 GAACGCCACGTCGAACACAA 61.754 55.000 0.00 0.00 39.99 3.33
418 419 0.108041 ACGTCGAACACAACCCAACT 60.108 50.000 0.00 0.00 0.00 3.16
419 420 1.011333 CGTCGAACACAACCCAACTT 58.989 50.000 0.00 0.00 0.00 2.66
423 424 2.680841 TCGAACACAACCCAACTTGAAG 59.319 45.455 0.00 0.00 0.00 3.02
425 426 3.623960 CGAACACAACCCAACTTGAAGTA 59.376 43.478 0.00 0.00 0.00 2.24
427 428 3.958018 ACACAACCCAACTTGAAGTACA 58.042 40.909 0.00 0.00 0.00 2.90
469 473 4.210611 TCTCTCTCTCCATCCCATCAAT 57.789 45.455 0.00 0.00 0.00 2.57
470 474 5.345307 TCTCTCTCTCCATCCCATCAATA 57.655 43.478 0.00 0.00 0.00 1.90
471 475 5.083122 TCTCTCTCTCCATCCCATCAATAC 58.917 45.833 0.00 0.00 0.00 1.89
476 480 6.326161 TCTCTCCATCCCATCAATACTATGT 58.674 40.000 0.00 0.00 0.00 2.29
480 484 6.653020 TCCATCCCATCAATACTATGTATGC 58.347 40.000 0.00 0.00 0.00 3.14
484 488 5.480422 TCCCATCAATACTATGTATGCGTCT 59.520 40.000 0.00 0.00 0.00 4.18
487 491 6.089954 CCATCAATACTATGTATGCGTCTGTG 59.910 42.308 0.00 0.00 0.00 3.66
511 515 1.327690 GGGAGGGTATGACTGCGTGA 61.328 60.000 0.00 0.00 0.00 4.35
513 517 1.471676 GGAGGGTATGACTGCGTGAAG 60.472 57.143 0.00 0.00 0.00 3.02
514 518 1.204941 GAGGGTATGACTGCGTGAAGT 59.795 52.381 0.00 0.00 0.00 3.01
516 520 0.721718 GGTATGACTGCGTGAAGTGC 59.278 55.000 0.00 0.00 0.00 4.40
517 521 1.428448 GTATGACTGCGTGAAGTGCA 58.572 50.000 0.00 0.00 40.70 4.57
518 522 1.126846 GTATGACTGCGTGAAGTGCAC 59.873 52.381 9.40 9.40 44.21 4.57
557 561 3.878160 AGGGTTTGAAGCGAAACAAAA 57.122 38.095 10.08 0.00 37.53 2.44
564 568 2.285371 TGAAGCGAAACAAAACGACGAG 60.285 45.455 0.00 0.00 0.00 4.18
573 577 2.801679 ACAAAACGACGAGCCGAATTAA 59.198 40.909 0.00 0.00 0.00 1.40
577 581 0.458889 CGACGAGCCGAATTAACCCA 60.459 55.000 1.50 0.00 0.00 4.51
599 603 5.649395 CCAGTTTGATTGGAGATGCTCTAAA 59.351 40.000 0.00 0.00 34.82 1.85
606 610 7.394016 TGATTGGAGATGCTCTAAACTTTGTA 58.606 34.615 0.00 0.00 34.82 2.41
612 616 8.198109 GGAGATGCTCTAAACTTTGTATAGTGA 58.802 37.037 0.00 0.00 0.00 3.41
626 630 1.623163 TAGTGACGGTGTGACCATCA 58.377 50.000 0.00 0.00 38.25 3.07
639 643 3.933332 GTGACCATCAGTAAGTAGCAACC 59.067 47.826 0.00 0.00 0.00 3.77
651 655 3.034635 AGTAGCAACCCACTCTATCCTG 58.965 50.000 0.00 0.00 0.00 3.86
653 657 0.543749 GCAACCCACTCTATCCTGCT 59.456 55.000 0.00 0.00 0.00 4.24
655 659 2.224161 GCAACCCACTCTATCCTGCTAG 60.224 54.545 0.00 0.00 0.00 3.42
670 674 2.764128 TAGGAGGAGCAAGCCCCG 60.764 66.667 0.00 0.00 0.00 5.73
680 684 3.692406 AAGCCCCGTGGTCGTCTC 61.692 66.667 0.00 0.00 35.01 3.36
684 688 3.450115 CCCGTGGTCGTCTCTCCC 61.450 72.222 0.00 0.00 35.01 4.30
686 690 2.745100 CGTGGTCGTCTCTCCCGA 60.745 66.667 0.00 0.00 0.00 5.14
711 715 2.328099 CCACTCGCAACTCTTGGCC 61.328 63.158 0.00 0.00 0.00 5.36
713 717 0.886490 CACTCGCAACTCTTGGCCTT 60.886 55.000 3.32 0.00 0.00 4.35
714 718 0.886490 ACTCGCAACTCTTGGCCTTG 60.886 55.000 3.32 0.00 0.00 3.61
755 759 3.371087 GAGTGCTTCGAATCCTCCC 57.629 57.895 0.00 0.00 0.00 4.30
757 761 0.250513 AGTGCTTCGAATCCTCCCAC 59.749 55.000 0.00 0.20 0.00 4.61
762 766 1.956629 TTCGAATCCTCCCACGCCTC 61.957 60.000 0.00 0.00 0.00 4.70
768 772 2.422231 CCTCCCACGCCTCTCTCAG 61.422 68.421 0.00 0.00 0.00 3.35
778 782 1.964344 GCCTCTCTCAGGGACATGTCT 60.964 57.143 24.50 3.64 43.70 3.41
789 793 2.440539 GACATGTCTGTCGTCCTTGT 57.559 50.000 18.83 0.00 42.24 3.16
809 813 2.860735 GTGATGTAGATGTCGGTGAAGC 59.139 50.000 0.00 0.00 0.00 3.86
811 815 3.056179 TGATGTAGATGTCGGTGAAGCAA 60.056 43.478 0.00 0.00 0.00 3.91
817 821 2.270352 TGTCGGTGAAGCAAAGGAAT 57.730 45.000 0.00 0.00 0.00 3.01
819 823 3.950397 TGTCGGTGAAGCAAAGGAATAT 58.050 40.909 0.00 0.00 0.00 1.28
820 824 3.938963 TGTCGGTGAAGCAAAGGAATATC 59.061 43.478 0.00 0.00 0.00 1.63
821 825 3.938963 GTCGGTGAAGCAAAGGAATATCA 59.061 43.478 0.00 0.00 0.00 2.15
822 826 4.394920 GTCGGTGAAGCAAAGGAATATCAA 59.605 41.667 0.00 0.00 0.00 2.57
823 827 5.066505 GTCGGTGAAGCAAAGGAATATCAAT 59.933 40.000 0.00 0.00 0.00 2.57
824 828 5.652014 TCGGTGAAGCAAAGGAATATCAATT 59.348 36.000 0.00 0.00 0.00 2.32
826 830 6.404623 CGGTGAAGCAAAGGAATATCAATTGA 60.405 38.462 11.26 11.26 0.00 2.57
829 833 6.153170 TGAAGCAAAGGAATATCAATTGAGCA 59.847 34.615 14.54 4.67 0.00 4.26
830 834 6.534475 AGCAAAGGAATATCAATTGAGCAA 57.466 33.333 14.54 2.44 0.00 3.91
833 837 7.548075 AGCAAAGGAATATCAATTGAGCAAAAG 59.452 33.333 14.54 0.06 0.00 2.27
834 838 7.675637 GCAAAGGAATATCAATTGAGCAAAAGC 60.676 37.037 14.54 6.09 0.00 3.51
838 842 2.995466 TCAATTGAGCAAAAGCGAGG 57.005 45.000 3.38 0.00 0.00 4.63
839 843 1.068333 TCAATTGAGCAAAAGCGAGGC 60.068 47.619 3.38 0.00 0.00 4.70
840 844 0.961019 AATTGAGCAAAAGCGAGGCA 59.039 45.000 0.00 0.00 0.00 4.75
842 846 0.743688 TTGAGCAAAAGCGAGGCAAA 59.256 45.000 0.00 0.00 0.00 3.68
845 849 0.031178 AGCAAAAGCGAGGCAAACAG 59.969 50.000 0.00 0.00 0.00 3.16
846 850 0.249031 GCAAAAGCGAGGCAAACAGT 60.249 50.000 0.00 0.00 0.00 3.55
868 885 3.216292 GGTGTTTGCGTGTGGGCT 61.216 61.111 0.00 0.00 0.00 5.19
876 893 2.111043 CGTGTGGGCTCAGGTTGT 59.889 61.111 0.00 0.00 0.00 3.32
888 905 1.425066 TCAGGTTGTCAGGGAGCAAAT 59.575 47.619 0.00 0.00 0.00 2.32
890 907 0.890683 GGTTGTCAGGGAGCAAATGG 59.109 55.000 0.00 0.00 0.00 3.16
891 908 1.620822 GTTGTCAGGGAGCAAATGGT 58.379 50.000 0.00 0.00 0.00 3.55
899 916 4.018506 TCAGGGAGCAAATGGTAATGAGAA 60.019 41.667 0.00 0.00 0.00 2.87
900 917 4.891756 CAGGGAGCAAATGGTAATGAGAAT 59.108 41.667 0.00 0.00 0.00 2.40
903 920 6.441604 AGGGAGCAAATGGTAATGAGAATTTT 59.558 34.615 0.00 0.00 0.00 1.82
904 921 6.758416 GGGAGCAAATGGTAATGAGAATTTTC 59.242 38.462 0.00 0.00 0.00 2.29
905 922 6.473455 GGAGCAAATGGTAATGAGAATTTTCG 59.527 38.462 0.00 0.00 0.00 3.46
907 924 5.807011 GCAAATGGTAATGAGAATTTTCGCT 59.193 36.000 0.00 0.00 0.00 4.93
908 925 6.020360 GCAAATGGTAATGAGAATTTTCGCTC 60.020 38.462 0.00 0.00 0.00 5.03
910 927 5.545658 TGGTAATGAGAATTTTCGCTCAC 57.454 39.130 0.00 0.00 43.26 3.51
911 928 5.000591 TGGTAATGAGAATTTTCGCTCACA 58.999 37.500 0.00 0.00 43.26 3.58
913 930 6.016693 TGGTAATGAGAATTTTCGCTCACAAA 60.017 34.615 0.00 0.00 43.26 2.83
914 931 6.524586 GGTAATGAGAATTTTCGCTCACAAAG 59.475 38.462 0.00 0.00 43.26 2.77
915 932 5.947228 ATGAGAATTTTCGCTCACAAAGA 57.053 34.783 0.00 0.00 43.26 2.52
916 933 5.749596 TGAGAATTTTCGCTCACAAAGAA 57.250 34.783 0.00 0.00 36.31 2.52
918 935 6.201517 TGAGAATTTTCGCTCACAAAGAAAG 58.798 36.000 0.00 0.00 36.31 2.62
920 1576 3.708563 TTTTCGCTCACAAAGAAAGGG 57.291 42.857 0.00 0.00 35.62 3.95
926 1582 2.162408 GCTCACAAAGAAAGGGAATCGG 59.838 50.000 0.00 0.00 0.00 4.18
928 1584 3.146066 TCACAAAGAAAGGGAATCGGTG 58.854 45.455 0.00 0.00 0.00 4.94
930 1586 3.189287 CACAAAGAAAGGGAATCGGTGAG 59.811 47.826 0.00 0.00 0.00 3.51
931 1587 3.181443 ACAAAGAAAGGGAATCGGTGAGT 60.181 43.478 0.00 0.00 0.00 3.41
932 1588 2.770164 AGAAAGGGAATCGGTGAGTG 57.230 50.000 0.00 0.00 0.00 3.51
933 1589 2.257207 AGAAAGGGAATCGGTGAGTGA 58.743 47.619 0.00 0.00 0.00 3.41
937 1593 3.721087 AGGGAATCGGTGAGTGAAAAT 57.279 42.857 0.00 0.00 0.00 1.82
938 1594 4.034285 AGGGAATCGGTGAGTGAAAATT 57.966 40.909 0.00 0.00 0.00 1.82
939 1595 4.010349 AGGGAATCGGTGAGTGAAAATTC 58.990 43.478 0.00 0.00 0.00 2.17
943 1599 5.355350 GGAATCGGTGAGTGAAAATTCTCAT 59.645 40.000 0.00 0.00 41.67 2.90
944 1600 6.127897 GGAATCGGTGAGTGAAAATTCTCATT 60.128 38.462 0.00 0.00 41.67 2.57
945 1601 5.611796 TCGGTGAGTGAAAATTCTCATTG 57.388 39.130 0.00 0.00 41.67 2.82
948 1604 5.563475 CGGTGAGTGAAAATTCTCATTGCTT 60.563 40.000 0.00 0.00 41.67 3.91
950 1606 5.860716 GTGAGTGAAAATTCTCATTGCTTCC 59.139 40.000 0.00 0.00 41.67 3.46
951 1607 5.047802 TGAGTGAAAATTCTCATTGCTTCCC 60.048 40.000 0.00 0.00 36.04 3.97
1068 2611 2.049767 CCCCACCACAATTACCGCC 61.050 63.158 0.00 0.00 0.00 6.13
1375 3066 2.505982 CCGGGTGGCACATAGAGG 59.494 66.667 20.82 10.46 44.52 3.69
1501 3192 1.066587 GAGATCCTCGTCAAGGGCG 59.933 63.158 0.00 0.00 46.23 6.13
1509 3200 2.045926 GTCAAGGGCGTGCCTGAT 60.046 61.111 11.25 0.00 36.10 2.90
1519 3210 2.352617 GGCGTGCCTGATTTCATTTTCA 60.353 45.455 2.98 0.00 0.00 2.69
1527 3218 6.145535 GCCTGATTTCATTTTCATATCCGAC 58.854 40.000 0.00 0.00 0.00 4.79
1732 3429 5.122396 ACACAGCTGAAAGGATTCGTTTATC 59.878 40.000 23.35 0.00 38.46 1.75
1749 3446 4.611310 TTATCGGAGACACACGAGTAAG 57.389 45.455 0.00 0.00 42.51 2.34
1817 3514 0.532115 GATTTGCCGCCATTCTTGGT 59.468 50.000 0.00 0.00 45.57 3.67
1843 3540 4.900054 AGATGGACCCTACGCTATTTAGTT 59.100 41.667 0.00 0.00 0.00 2.24
1846 3543 4.124970 GGACCCTACGCTATTTAGTTTGG 58.875 47.826 0.00 0.00 0.00 3.28
1847 3544 4.141869 GGACCCTACGCTATTTAGTTTGGA 60.142 45.833 0.00 0.00 0.00 3.53
1894 3606 2.361757 CTCTGTCTGGCTGTCATAGAGG 59.638 54.545 9.24 0.00 30.70 3.69
1937 3649 3.306613 TCTGGAGAGCTGATGATGATGT 58.693 45.455 0.00 0.00 0.00 3.06
1993 3705 4.641954 GCTGAGTACATTTGTTGATGACG 58.358 43.478 0.00 0.00 0.00 4.35
2006 3718 5.237815 TGTTGATGACGCTAAGATTTCAGT 58.762 37.500 0.00 0.00 0.00 3.41
2078 3802 6.632035 GTGTACGTGTCTACTAAGTATGATGC 59.368 42.308 0.00 0.00 0.00 3.91
2203 3942 2.076863 CTCCTTCTTTGGTAGGCAACG 58.923 52.381 0.00 0.00 46.39 4.10
2238 3977 6.374578 GTCCTTATTTCACTTCTGTTGCTTC 58.625 40.000 0.00 0.00 0.00 3.86
2296 4237 7.041098 TGCACCTTGTTTCTTAAGATCTTTCTC 60.041 37.037 14.36 0.29 0.00 2.87
2297 4238 7.041098 GCACCTTGTTTCTTAAGATCTTTCTCA 60.041 37.037 14.36 2.81 0.00 3.27
2299 4240 9.007901 ACCTTGTTTCTTAAGATCTTTCTCATG 57.992 33.333 14.36 7.26 0.00 3.07
2310 4253 6.950842 AGATCTTTCTCATGTCATTGGTGTA 58.049 36.000 0.00 0.00 0.00 2.90
2367 4311 7.827819 TGAATCCTTACTTACACTGAAATCG 57.172 36.000 0.00 0.00 0.00 3.34
2389 4333 7.596749 TCGTTTTATGTCTCAGGAAGATTTC 57.403 36.000 0.00 0.00 36.11 2.17
2746 4721 5.539979 TCTTCTGATGAGATGAGCTTATGC 58.460 41.667 0.00 0.00 40.05 3.14
2776 4758 1.270550 CTGGCGCTTCAGTTTTTGGAT 59.729 47.619 7.64 0.00 0.00 3.41
2885 4921 7.169982 GCTAATGAGTGTAACCATCAGTATGTC 59.830 40.741 0.00 0.00 37.80 3.06
2973 5016 6.987404 GGTCCACTATATCTTTTCTTGGTCTC 59.013 42.308 0.00 0.00 0.00 3.36
2988 5042 7.696992 TCTTGGTCTCGCCTTTTTATTATTT 57.303 32.000 0.00 0.00 38.35 1.40
3070 5125 8.806429 TCTGCTTGGTTTTATATCTGAAATGA 57.194 30.769 0.00 0.00 0.00 2.57
3100 5155 1.526917 ACTGAAGGTGCAGCGCTTT 60.527 52.632 7.50 2.40 39.51 3.51
3132 5191 5.678132 ACCAGTAACCATTTGACGTTTAC 57.322 39.130 0.00 0.00 0.00 2.01
3146 5205 6.564709 TGACGTTTACTAAGCAGAGAAGTA 57.435 37.500 0.00 0.00 0.00 2.24
3158 5217 3.059884 CAGAGAAGTAAGCTCGTTTGCA 58.940 45.455 0.00 0.00 37.46 4.08
3227 5293 6.043474 ACATACAAGTACAAGGTCCCAAACTA 59.957 38.462 0.00 0.00 0.00 2.24
3244 5310 5.106396 CCAAACTAGTGCTTCTTCATCCTTG 60.106 44.000 0.00 0.00 0.00 3.61
3248 5314 4.843220 AGTGCTTCTTCATCCTTGTTTG 57.157 40.909 0.00 0.00 0.00 2.93
3252 5318 6.491403 AGTGCTTCTTCATCCTTGTTTGTAAT 59.509 34.615 0.00 0.00 0.00 1.89
3269 5335 8.526978 TGTTTGTAATTTTAGCCTATTGATGCA 58.473 29.630 0.00 0.00 0.00 3.96
3270 5336 9.023967 GTTTGTAATTTTAGCCTATTGATGCAG 57.976 33.333 0.00 0.00 0.00 4.41
3271 5337 6.738114 TGTAATTTTAGCCTATTGATGCAGC 58.262 36.000 0.00 0.00 0.00 5.25
3272 5338 6.547141 TGTAATTTTAGCCTATTGATGCAGCT 59.453 34.615 2.53 0.98 37.58 4.24
3273 5339 7.719193 TGTAATTTTAGCCTATTGATGCAGCTA 59.281 33.333 2.53 0.00 35.03 3.32
3274 5340 7.587037 AATTTTAGCCTATTGATGCAGCTAA 57.413 32.000 2.53 6.86 42.58 3.09
3275 5341 6.377327 TTTTAGCCTATTGATGCAGCTAAC 57.623 37.500 12.32 0.00 43.61 2.34
3276 5342 3.853355 AGCCTATTGATGCAGCTAACT 57.147 42.857 2.53 0.00 30.46 2.24
3277 5343 4.162040 AGCCTATTGATGCAGCTAACTT 57.838 40.909 2.53 0.00 30.46 2.66
3278 5344 3.881688 AGCCTATTGATGCAGCTAACTTG 59.118 43.478 2.53 0.00 30.46 3.16
3279 5345 3.879295 GCCTATTGATGCAGCTAACTTGA 59.121 43.478 2.53 0.00 0.00 3.02
3280 5346 4.024218 GCCTATTGATGCAGCTAACTTGAG 60.024 45.833 2.53 0.00 0.00 3.02
3281 5347 5.363101 CCTATTGATGCAGCTAACTTGAGA 58.637 41.667 2.53 0.00 0.00 3.27
3282 5348 5.996513 CCTATTGATGCAGCTAACTTGAGAT 59.003 40.000 2.53 0.00 0.00 2.75
3283 5349 6.485984 CCTATTGATGCAGCTAACTTGAGATT 59.514 38.462 2.53 0.00 0.00 2.40
3284 5350 5.556355 TTGATGCAGCTAACTTGAGATTG 57.444 39.130 2.53 0.00 0.00 2.67
3285 5351 3.376234 TGATGCAGCTAACTTGAGATTGC 59.624 43.478 2.53 0.00 32.36 3.56
3315 5381 7.624360 TGATACGTTTTTCAGGCTATTCAAT 57.376 32.000 0.00 0.00 0.00 2.57
3335 5401 3.929955 TCCATTGATGACATACAGGCA 57.070 42.857 0.00 0.00 41.62 4.75
3376 5442 7.011773 CGGCTATTCATCTAATCAAATGTTCG 58.988 38.462 0.00 0.00 0.00 3.95
3413 5480 0.540923 ACAGATCTGGCAGCTCTTCC 59.459 55.000 26.08 0.00 34.19 3.46
3483 5550 4.471904 TTCTGTATCAGGTGGTCATCAC 57.528 45.455 0.00 0.00 45.34 3.06
3554 5621 9.751542 CGTCTGGTATCTATCTTTCTTAATTGT 57.248 33.333 0.00 0.00 0.00 2.71
3572 5639 2.695359 TGTTTCCGTATCTGCTGTTCC 58.305 47.619 0.00 0.00 0.00 3.62
3586 5653 5.363580 TCTGCTGTTCCCTTCTTTGATTTTT 59.636 36.000 0.00 0.00 0.00 1.94
3591 5658 7.301868 TGTTCCCTTCTTTGATTTTTAGCAT 57.698 32.000 0.00 0.00 0.00 3.79
3659 5726 8.822652 ATTCTAATTTTGTGCTTTTCTTGAGG 57.177 30.769 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.134789 TAGAACTACAGTCGGGGTCC 57.865 55.000 0.00 0.00 0.00 4.46
3 4 4.401837 AGATTTAGAACTACAGTCGGGGTC 59.598 45.833 0.00 0.00 0.00 4.46
4 5 4.351127 AGATTTAGAACTACAGTCGGGGT 58.649 43.478 0.00 0.00 0.00 4.95
5 6 5.340439 AAGATTTAGAACTACAGTCGGGG 57.660 43.478 0.00 0.00 0.00 5.73
6 7 6.631962 AGAAAGATTTAGAACTACAGTCGGG 58.368 40.000 0.00 0.00 0.00 5.14
41 42 0.319405 GCAAGCCAGCCAGATGTTTT 59.681 50.000 0.00 0.00 0.00 2.43
87 88 1.604378 GCTCCTGGGCAGCTTCTAA 59.396 57.895 0.37 0.00 33.75 2.10
98 99 1.283029 TCATTCCAAAGAGGCTCCTGG 59.717 52.381 21.73 21.73 37.29 4.45
101 102 2.087646 GTGTCATTCCAAAGAGGCTCC 58.912 52.381 11.71 0.00 37.29 4.70
121 122 3.959535 ATACATGCAAACAAAGGGTGG 57.040 42.857 0.00 0.00 0.00 4.61
157 158 3.703556 ACATGTTTGTTCCACACCATCAA 59.296 39.130 0.00 0.00 29.55 2.57
158 159 3.067883 CACATGTTTGTTCCACACCATCA 59.932 43.478 0.00 0.00 32.34 3.07
162 163 1.408702 AGCACATGTTTGTTCCACACC 59.591 47.619 0.00 0.00 32.34 4.16
205 206 4.437682 TCAGTTGAAGATGGTGTTTCCT 57.562 40.909 0.00 0.00 37.07 3.36
223 224 0.310854 GGACAAAGTGCGGGTTTCAG 59.689 55.000 0.00 0.00 0.00 3.02
256 257 1.507141 GGCACAGTTCGGGTTGTCTG 61.507 60.000 0.00 0.00 0.00 3.51
274 275 3.128938 ACTTTGTCTCTCTTATCGACGGG 59.871 47.826 0.00 0.00 0.00 5.28
276 277 5.224562 AGACTTTGTCTCTCTTATCGACG 57.775 43.478 0.00 0.00 38.71 5.12
278 279 7.054751 TGGATAGACTTTGTCTCTCTTATCGA 58.945 38.462 3.30 0.00 42.40 3.59
282 283 9.658799 CAAATTGGATAGACTTTGTCTCTCTTA 57.341 33.333 3.30 0.00 42.40 2.10
288 289 6.542821 TGGTCAAATTGGATAGACTTTGTCT 58.457 36.000 5.53 5.53 45.54 3.41
295 296 9.125026 ACAATCTAATGGTCAAATTGGATAGAC 57.875 33.333 0.00 0.00 36.92 2.59
296 297 9.699410 AACAATCTAATGGTCAAATTGGATAGA 57.301 29.630 0.00 0.00 36.92 1.98
297 298 9.956720 GAACAATCTAATGGTCAAATTGGATAG 57.043 33.333 0.00 0.00 36.92 2.08
332 333 4.513692 TGTATTTGAGAGTTTGACAACCGG 59.486 41.667 0.00 0.00 32.70 5.28
335 336 6.912591 CAGGTTGTATTTGAGAGTTTGACAAC 59.087 38.462 6.47 6.47 42.69 3.32
345 346 6.821665 GCCTTACATACAGGTTGTATTTGAGA 59.178 38.462 8.06 0.00 40.40 3.27
347 348 5.583061 CGCCTTACATACAGGTTGTATTTGA 59.417 40.000 0.00 0.00 40.40 2.69
349 350 5.736813 TCGCCTTACATACAGGTTGTATTT 58.263 37.500 0.00 0.00 40.40 1.40
356 357 5.820947 CCTAATTTTCGCCTTACATACAGGT 59.179 40.000 0.00 0.00 33.40 4.00
357 358 5.238650 CCCTAATTTTCGCCTTACATACAGG 59.761 44.000 0.00 0.00 34.08 4.00
358 359 5.820947 ACCCTAATTTTCGCCTTACATACAG 59.179 40.000 0.00 0.00 0.00 2.74
359 360 5.587043 CACCCTAATTTTCGCCTTACATACA 59.413 40.000 0.00 0.00 0.00 2.29
360 361 5.587443 ACACCCTAATTTTCGCCTTACATAC 59.413 40.000 0.00 0.00 0.00 2.39
362 363 4.595986 ACACCCTAATTTTCGCCTTACAT 58.404 39.130 0.00 0.00 0.00 2.29
370 371 3.869065 TGCTAGGACACCCTAATTTTCG 58.131 45.455 0.00 0.00 44.06 3.46
387 388 2.126618 CGACGTGGCGTTCTGCTA 60.127 61.111 0.00 0.00 41.37 3.49
393 394 1.810441 TTGTGTTCGACGTGGCGTT 60.810 52.632 0.00 0.00 41.37 4.84
394 395 2.202770 TTGTGTTCGACGTGGCGT 60.203 55.556 0.00 0.00 45.10 5.68
407 408 5.514274 AATGTACTTCAAGTTGGGTTGTG 57.486 39.130 0.00 0.00 0.00 3.33
410 411 7.418337 AAGAAAATGTACTTCAAGTTGGGTT 57.582 32.000 0.00 0.00 0.00 4.11
411 412 7.418337 AAAGAAAATGTACTTCAAGTTGGGT 57.582 32.000 0.00 5.44 0.00 4.51
439 440 5.200483 GGATGGAGAGAGAGAAGAGAAAGA 58.800 45.833 0.00 0.00 0.00 2.52
440 441 4.342092 GGGATGGAGAGAGAGAAGAGAAAG 59.658 50.000 0.00 0.00 0.00 2.62
443 444 2.855599 TGGGATGGAGAGAGAGAAGAGA 59.144 50.000 0.00 0.00 0.00 3.10
444 445 3.311167 TGGGATGGAGAGAGAGAAGAG 57.689 52.381 0.00 0.00 0.00 2.85
445 446 3.206185 TGATGGGATGGAGAGAGAGAAGA 59.794 47.826 0.00 0.00 0.00 2.87
469 473 4.379339 TTGCACAGACGCATACATAGTA 57.621 40.909 0.00 0.00 42.62 1.82
470 474 2.959507 TGCACAGACGCATACATAGT 57.040 45.000 0.00 0.00 36.86 2.12
471 475 3.059393 CCATTGCACAGACGCATACATAG 60.059 47.826 0.00 0.00 42.62 2.23
476 480 0.251634 TCCCATTGCACAGACGCATA 59.748 50.000 0.00 0.00 42.62 3.14
480 484 1.746615 CCCTCCCATTGCACAGACG 60.747 63.158 0.00 0.00 0.00 4.18
484 488 1.064758 GTCATACCCTCCCATTGCACA 60.065 52.381 0.00 0.00 0.00 4.57
487 491 1.972872 CAGTCATACCCTCCCATTGC 58.027 55.000 0.00 0.00 0.00 3.56
519 523 6.564709 AACCCTTATTTCCTCGTTTTGTAC 57.435 37.500 0.00 0.00 0.00 2.90
520 524 6.771749 TCAAACCCTTATTTCCTCGTTTTGTA 59.228 34.615 0.00 0.00 0.00 2.41
521 525 5.595133 TCAAACCCTTATTTCCTCGTTTTGT 59.405 36.000 0.00 0.00 0.00 2.83
522 526 6.079424 TCAAACCCTTATTTCCTCGTTTTG 57.921 37.500 0.00 0.00 0.00 2.44
535 539 4.985538 TTTGTTTCGCTTCAAACCCTTA 57.014 36.364 0.00 0.00 35.69 2.69
557 561 0.459063 GGGTTAATTCGGCTCGTCGT 60.459 55.000 0.00 0.00 0.00 4.34
564 568 4.173256 CAATCAAACTGGGTTAATTCGGC 58.827 43.478 0.00 0.00 0.00 5.54
573 577 2.042162 AGCATCTCCAATCAAACTGGGT 59.958 45.455 0.00 0.00 34.46 4.51
599 603 4.553323 GTCACACCGTCACTATACAAAGT 58.447 43.478 0.00 0.00 0.00 2.66
612 616 1.968493 ACTTACTGATGGTCACACCGT 59.032 47.619 0.00 0.00 42.58 4.83
626 630 4.650131 GGATAGAGTGGGTTGCTACTTACT 59.350 45.833 7.43 7.43 0.00 2.24
639 643 2.109128 TCCTCCTAGCAGGATAGAGTGG 59.891 54.545 0.00 3.41 44.81 4.00
651 655 2.508436 GGGCTTGCTCCTCCTAGC 59.492 66.667 0.00 0.00 43.08 3.42
653 657 2.764128 CGGGGCTTGCTCCTCCTA 60.764 66.667 10.05 0.00 0.00 2.94
655 659 4.785453 CACGGGGCTTGCTCCTCC 62.785 72.222 10.05 0.00 0.00 4.30
667 671 3.450115 GGGAGAGACGACCACGGG 61.450 72.222 0.00 0.00 44.46 5.28
680 684 1.755008 GAGTGGAGGAGGTCGGGAG 60.755 68.421 0.00 0.00 0.00 4.30
684 688 2.636412 TTGCGAGTGGAGGAGGTCG 61.636 63.158 0.00 0.00 35.51 4.79
686 690 1.534235 AGTTGCGAGTGGAGGAGGT 60.534 57.895 0.00 0.00 0.00 3.85
711 715 0.179073 ATCGGATCGGAGTTGGCAAG 60.179 55.000 0.00 0.00 0.00 4.01
713 717 1.143838 CATCGGATCGGAGTTGGCA 59.856 57.895 9.03 0.00 0.00 4.92
714 718 0.034059 ATCATCGGATCGGAGTTGGC 59.966 55.000 9.03 0.00 0.00 4.52
737 741 0.537188 TGGGAGGATTCGAAGCACTC 59.463 55.000 16.24 17.31 0.00 3.51
753 757 3.465403 CCCTGAGAGAGGCGTGGG 61.465 72.222 0.00 0.00 41.19 4.61
755 759 1.326213 ATGTCCCTGAGAGAGGCGTG 61.326 60.000 0.00 0.00 41.19 5.34
757 761 1.326213 ACATGTCCCTGAGAGAGGCG 61.326 60.000 0.00 0.00 41.19 5.52
778 782 3.509967 ACATCTACATCACAAGGACGACA 59.490 43.478 0.00 0.00 0.00 4.35
789 793 2.495669 TGCTTCACCGACATCTACATCA 59.504 45.455 0.00 0.00 0.00 3.07
809 813 7.463648 CGCTTTTGCTCAATTGATATTCCTTTG 60.464 37.037 8.96 0.00 44.80 2.77
811 815 6.038356 CGCTTTTGCTCAATTGATATTCCTT 58.962 36.000 8.96 0.00 44.80 3.36
817 821 3.181497 GCCTCGCTTTTGCTCAATTGATA 60.181 43.478 8.96 0.00 44.80 2.15
819 823 1.068333 GCCTCGCTTTTGCTCAATTGA 60.068 47.619 8.12 8.12 44.80 2.57
820 824 1.336148 TGCCTCGCTTTTGCTCAATTG 60.336 47.619 0.00 0.00 44.80 2.32
821 825 0.961019 TGCCTCGCTTTTGCTCAATT 59.039 45.000 0.00 0.00 44.80 2.32
822 826 0.961019 TTGCCTCGCTTTTGCTCAAT 59.039 45.000 0.00 0.00 44.80 2.57
823 827 0.743688 TTTGCCTCGCTTTTGCTCAA 59.256 45.000 0.00 0.00 44.80 3.02
824 828 0.030638 GTTTGCCTCGCTTTTGCTCA 59.969 50.000 0.00 0.00 44.80 4.26
826 830 0.031178 CTGTTTGCCTCGCTTTTGCT 59.969 50.000 0.00 0.00 44.80 3.91
829 833 0.249031 GCACTGTTTGCCTCGCTTTT 60.249 50.000 0.00 0.00 46.63 2.27
830 834 1.360192 GCACTGTTTGCCTCGCTTT 59.640 52.632 0.00 0.00 46.63 3.51
839 843 1.925229 CAAACACCTGGCACTGTTTG 58.075 50.000 22.24 22.24 46.45 2.93
840 844 0.175531 GCAAACACCTGGCACTGTTT 59.824 50.000 11.15 11.15 40.47 2.83
842 846 2.480610 CGCAAACACCTGGCACTGT 61.481 57.895 0.00 0.00 0.00 3.55
845 849 2.026014 CACGCAAACACCTGGCAC 59.974 61.111 0.00 0.00 0.00 5.01
846 850 2.439338 ACACGCAAACACCTGGCA 60.439 55.556 0.00 0.00 0.00 4.92
849 853 2.721231 CCCACACGCAAACACCTG 59.279 61.111 0.00 0.00 0.00 4.00
868 885 0.843309 TTTGCTCCCTGACAACCTGA 59.157 50.000 0.00 0.00 0.00 3.86
876 893 3.523157 TCTCATTACCATTTGCTCCCTGA 59.477 43.478 0.00 0.00 0.00 3.86
888 905 5.000591 TGTGAGCGAAAATTCTCATTACCA 58.999 37.500 0.00 0.00 40.89 3.25
890 907 7.298122 TCTTTGTGAGCGAAAATTCTCATTAC 58.702 34.615 0.00 0.00 40.89 1.89
891 908 7.433708 TCTTTGTGAGCGAAAATTCTCATTA 57.566 32.000 0.00 0.00 40.89 1.90
899 916 3.888930 TCCCTTTCTTTGTGAGCGAAAAT 59.111 39.130 0.00 0.00 0.00 1.82
900 917 3.283751 TCCCTTTCTTTGTGAGCGAAAA 58.716 40.909 0.00 0.00 0.00 2.29
903 920 2.631160 TTCCCTTTCTTTGTGAGCGA 57.369 45.000 0.00 0.00 0.00 4.93
904 921 2.159653 CGATTCCCTTTCTTTGTGAGCG 60.160 50.000 0.00 0.00 0.00 5.03
905 922 2.162408 CCGATTCCCTTTCTTTGTGAGC 59.838 50.000 0.00 0.00 0.00 4.26
907 924 3.146066 CACCGATTCCCTTTCTTTGTGA 58.854 45.455 0.00 0.00 0.00 3.58
908 925 3.146066 TCACCGATTCCCTTTCTTTGTG 58.854 45.455 0.00 0.00 0.00 3.33
910 927 3.189287 CACTCACCGATTCCCTTTCTTTG 59.811 47.826 0.00 0.00 0.00 2.77
911 928 3.072476 TCACTCACCGATTCCCTTTCTTT 59.928 43.478 0.00 0.00 0.00 2.52
913 930 2.257207 TCACTCACCGATTCCCTTTCT 58.743 47.619 0.00 0.00 0.00 2.52
914 931 2.762535 TCACTCACCGATTCCCTTTC 57.237 50.000 0.00 0.00 0.00 2.62
915 932 3.502123 TTTCACTCACCGATTCCCTTT 57.498 42.857 0.00 0.00 0.00 3.11
916 933 3.502123 TTTTCACTCACCGATTCCCTT 57.498 42.857 0.00 0.00 0.00 3.95
918 935 4.010349 AGAATTTTCACTCACCGATTCCC 58.990 43.478 0.00 0.00 0.00 3.97
920 1576 5.862924 TGAGAATTTTCACTCACCGATTC 57.137 39.130 0.00 0.00 38.08 2.52
926 1582 5.860716 GGAAGCAATGAGAATTTTCACTCAC 59.139 40.000 0.00 0.00 44.18 3.51
928 1584 5.184671 AGGGAAGCAATGAGAATTTTCACTC 59.815 40.000 0.00 0.00 0.00 3.51
930 1586 5.397142 AGGGAAGCAATGAGAATTTTCAC 57.603 39.130 0.00 0.00 0.00 3.18
931 1587 7.537596 TTAAGGGAAGCAATGAGAATTTTCA 57.462 32.000 0.54 0.54 0.00 2.69
932 1588 8.831715 TTTTAAGGGAAGCAATGAGAATTTTC 57.168 30.769 0.00 0.00 0.00 2.29
959 1615 7.821846 AGCTCGAGAGTAATGAGAATTTTCTTT 59.178 33.333 18.75 0.48 37.73 2.52
960 1616 7.327214 AGCTCGAGAGTAATGAGAATTTTCTT 58.673 34.615 18.75 0.00 37.73 2.52
961 1617 6.872920 AGCTCGAGAGTAATGAGAATTTTCT 58.127 36.000 18.75 0.00 41.00 2.52
1497 3188 0.532115 AAATGAAATCAGGCACGCCC 59.468 50.000 3.95 0.00 36.58 6.13
1501 3192 5.916883 CGGATATGAAAATGAAATCAGGCAC 59.083 40.000 0.00 0.00 0.00 5.01
1509 3200 5.522460 GTCCTCGTCGGATATGAAAATGAAA 59.478 40.000 0.00 0.00 45.44 2.69
1519 3210 0.477204 TCCTGGTCCTCGTCGGATAT 59.523 55.000 0.00 0.00 45.44 1.63
1685 3382 1.117142 AGGGAGAAACGTGGGAACGA 61.117 55.000 5.12 0.00 36.85 3.85
1732 3429 0.456312 GCCTTACTCGTGTGTCTCCG 60.456 60.000 0.00 0.00 0.00 4.63
1749 3446 5.701290 AGTGTTGAGAACAAGTACATAAGCC 59.299 40.000 0.00 0.00 44.16 4.35
1817 3514 4.383931 AATAGCGTAGGGTCCATCTCTA 57.616 45.455 0.00 0.00 0.00 2.43
1843 3540 3.011144 TCCTTGCTATGACCCAAATCCAA 59.989 43.478 0.00 0.00 0.00 3.53
1846 3543 3.571401 CCATCCTTGCTATGACCCAAATC 59.429 47.826 0.00 0.00 0.00 2.17
1847 3544 3.205056 TCCATCCTTGCTATGACCCAAAT 59.795 43.478 0.00 0.00 0.00 2.32
1894 3606 2.408368 GCCAAACAATAAGCGTTTCTGC 59.592 45.455 0.00 0.00 34.40 4.26
1937 3649 3.765381 TCCTGCATCCATTTCTCAACAA 58.235 40.909 0.00 0.00 0.00 2.83
1993 3705 9.863845 GGTATAATCCTCTACTGAAATCTTAGC 57.136 37.037 0.00 0.00 0.00 3.09
2006 3718 5.454966 TCTGCACTGTGGTATAATCCTCTA 58.545 41.667 10.21 0.00 0.00 2.43
2155 3894 3.877559 CCATGATGTAAGGACAAGCAGA 58.122 45.455 0.00 0.00 39.59 4.26
2161 3900 1.406751 CCACGCCATGATGTAAGGACA 60.407 52.381 0.00 0.00 40.72 4.02
2162 3901 1.299541 CCACGCCATGATGTAAGGAC 58.700 55.000 0.00 0.00 0.00 3.85
2203 3942 3.194968 TGAAATAAGGACGGACTCACCTC 59.805 47.826 0.00 0.00 36.31 3.85
2238 3977 9.470490 GATTTATTTAGCAATGATCGAAGATCG 57.530 33.333 5.68 0.00 45.12 3.69
2296 4237 7.013178 TGCAAGGTTATATACACCAATGACATG 59.987 37.037 13.30 0.00 36.67 3.21
2297 4238 7.013274 GTGCAAGGTTATATACACCAATGACAT 59.987 37.037 13.30 0.00 36.67 3.06
2299 4240 6.317642 TGTGCAAGGTTATATACACCAATGAC 59.682 38.462 13.30 11.52 36.67 3.06
2367 4311 7.596749 TCGAAATCTTCCTGAGACATAAAAC 57.403 36.000 0.00 0.00 37.17 2.43
2389 4333 4.053295 TCTCTCCGGTAACTTTGTTTTCG 58.947 43.478 0.00 0.00 0.00 3.46
2598 4543 4.588951 TGTCGGCACTTATCCTCAAGATAT 59.411 41.667 0.00 0.00 37.31 1.63
2776 4758 0.473755 ATGCTGTTGTCTCCACACCA 59.526 50.000 0.00 0.00 29.76 4.17
2885 4921 5.640783 TCTCAACTCAATGATGCACAGTTAG 59.359 40.000 0.00 0.00 0.00 2.34
3009 5063 9.920946 ACTACCATTATGGAAGAACAATGTTAT 57.079 29.630 19.23 0.00 40.96 1.89
3116 5175 5.761234 TCTGCTTAGTAAACGTCAAATGGTT 59.239 36.000 0.00 0.00 0.00 3.67
3126 5185 6.094061 AGCTTACTTCTCTGCTTAGTAAACG 58.906 40.000 0.00 0.00 34.86 3.60
3132 5191 4.364415 ACGAGCTTACTTCTCTGCTTAG 57.636 45.455 0.00 0.00 35.76 2.18
3146 5205 6.204882 AGTCTTTAAAGTATGCAAACGAGCTT 59.795 34.615 14.74 0.00 34.99 3.74
3227 5293 4.210331 ACAAACAAGGATGAAGAAGCACT 58.790 39.130 0.00 0.00 0.00 4.40
3244 5310 8.925161 TGCATCAATAGGCTAAAATTACAAAC 57.075 30.769 0.00 0.00 32.35 2.93
3248 5314 6.974965 AGCTGCATCAATAGGCTAAAATTAC 58.025 36.000 1.02 0.00 32.35 1.89
3252 5318 6.122277 AGTTAGCTGCATCAATAGGCTAAAA 58.878 36.000 13.83 0.00 43.79 1.52
3269 5335 2.005451 CGCTGCAATCTCAAGTTAGCT 58.995 47.619 0.00 0.00 0.00 3.32
3270 5336 1.734465 ACGCTGCAATCTCAAGTTAGC 59.266 47.619 0.00 0.00 0.00 3.09
3271 5337 3.433274 TCAACGCTGCAATCTCAAGTTAG 59.567 43.478 0.00 0.00 0.00 2.34
3272 5338 3.398406 TCAACGCTGCAATCTCAAGTTA 58.602 40.909 0.00 0.00 0.00 2.24
3273 5339 2.221169 TCAACGCTGCAATCTCAAGTT 58.779 42.857 0.00 0.00 0.00 2.66
3274 5340 1.882912 TCAACGCTGCAATCTCAAGT 58.117 45.000 0.00 0.00 0.00 3.16
3275 5341 3.542875 CGTATCAACGCTGCAATCTCAAG 60.543 47.826 0.00 0.00 43.12 3.02
3276 5342 2.348362 CGTATCAACGCTGCAATCTCAA 59.652 45.455 0.00 0.00 43.12 3.02
3277 5343 1.926510 CGTATCAACGCTGCAATCTCA 59.073 47.619 0.00 0.00 43.12 3.27
3278 5344 2.635141 CGTATCAACGCTGCAATCTC 57.365 50.000 0.00 0.00 43.12 2.75
3315 5381 3.929955 TGCCTGTATGTCATCAATGGA 57.070 42.857 0.00 0.00 0.00 3.41
3335 5401 0.601057 GCCGTTGCTTGTACCCATTT 59.399 50.000 0.00 0.00 33.53 2.32
3413 5480 9.635520 AAATGCTTTCTGAAGTTCTGATTAATG 57.364 29.630 12.62 3.29 35.25 1.90
3554 5621 1.906574 AGGGAACAGCAGATACGGAAA 59.093 47.619 0.00 0.00 0.00 3.13
3572 5639 8.619546 CCTAGAGATGCTAAAAATCAAAGAAGG 58.380 37.037 0.00 0.00 0.00 3.46
3586 5653 6.849151 TGTATTGTAGACCCTAGAGATGCTA 58.151 40.000 0.00 0.00 0.00 3.49
3591 5658 7.943447 GGAACTATGTATTGTAGACCCTAGAGA 59.057 40.741 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.