Multiple sequence alignment - TraesCS6D01G230600

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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 TraesCS6D01G230600 chr6D 100.000 4440 0 0 1 4440 323797169 323801608 0.000000e+00 8200.0
1 TraesCS6D01G230600 chr6D 93.929 280 9 5 575 846 444359924 444359645 2.470000e-112 416.0
2 TraesCS6D01G230600 chr6D 90.722 291 26 1 55 345 323741363 323741652 1.940000e-103 387.0
3 TraesCS6D01G230600 chr6D 98.246 57 1 0 1 57 429468355 429468299 2.830000e-17 100.0
4 TraesCS6D01G230600 chr6D 98.214 56 1 0 1 56 262189586 262189531 1.020000e-16 99.0
5 TraesCS6D01G230600 chr6A 96.615 1536 36 9 853 2377 461425865 461427395 0.000000e+00 2534.0
6 TraesCS6D01G230600 chr6A 98.424 952 15 0 2375 3326 461427449 461428400 0.000000e+00 1676.0
7 TraesCS6D01G230600 chr6A 96.617 473 13 2 3333 3802 461428803 461429275 0.000000e+00 782.0
8 TraesCS6D01G230600 chr6A 95.593 295 10 2 3993 4286 461429837 461430129 1.870000e-128 470.0
9 TraesCS6D01G230600 chr6A 94.245 278 10 3 575 846 122055861 122056138 1.910000e-113 420.0
10 TraesCS6D01G230600 chr6A 93.929 280 9 5 575 846 408156868 408156589 2.470000e-112 416.0
11 TraesCS6D01G230600 chr6A 94.681 188 7 2 396 580 461425660 461425847 5.620000e-74 289.0
12 TraesCS6D01G230600 chr6A 94.558 147 5 2 3856 3999 461429661 461429807 1.610000e-54 224.0
13 TraesCS6D01G230600 chr6A 87.179 156 11 5 4285 4440 461430253 461430399 7.640000e-38 169.0
14 TraesCS6D01G230600 chr6A 97.727 44 1 0 841 884 461425839 461425882 4.760000e-10 76.8
15 TraesCS6D01G230600 chr6B 95.198 1541 50 8 841 2377 499894690 499893170 0.000000e+00 2414.0
16 TraesCS6D01G230600 chr6B 97.372 647 15 1 2377 3021 499893113 499892467 0.000000e+00 1099.0
17 TraesCS6D01G230600 chr6B 89.578 403 11 9 3332 3721 499892027 499891643 2.400000e-132 483.0
18 TraesCS6D01G230600 chr6B 89.855 276 15 7 3994 4266 499891224 499890959 4.250000e-90 342.0
19 TraesCS6D01G230600 chr6B 97.810 137 3 0 3190 3326 499892447 499892311 2.060000e-58 237.0
20 TraesCS6D01G230600 chr6B 95.139 144 6 1 438 580 499894825 499894682 4.470000e-55 226.0
21 TraesCS6D01G230600 chr6B 91.034 145 11 2 3856 3999 499891398 499891255 1.260000e-45 195.0
22 TraesCS6D01G230600 chr6B 97.183 71 1 1 3741 3810 499891557 499891487 7.800000e-23 119.0
23 TraesCS6D01G230600 chr6B 98.214 56 1 0 3611 3666 499891557 499891502 1.020000e-16 99.0
24 TraesCS6D01G230600 chr7B 95.784 759 27 5 1294 2051 606062324 606061570 0.000000e+00 1219.0
25 TraesCS6D01G230600 chr7B 94.109 645 22 4 2377 3021 606061253 606060625 0.000000e+00 966.0
26 TraesCS6D01G230600 chr7B 93.680 538 16 6 3340 3861 606060092 606059557 0.000000e+00 789.0
27 TraesCS6D01G230600 chr7B 95.865 266 9 2 2112 2377 606061572 606061309 3.170000e-116 429.0
28 TraesCS6D01G230600 chr7B 90.580 276 12 7 3994 4265 606059344 606059079 1.960000e-93 353.0
29 TraesCS6D01G230600 chr7B 95.620 137 6 0 3190 3326 606060605 606060469 2.080000e-53 220.0
30 TraesCS6D01G230600 chr7B 93.333 135 6 2 3534 3666 606059756 606059623 3.500000e-46 196.0
31 TraesCS6D01G230600 chr7B 92.366 131 9 1 3870 3999 606059503 606059373 7.580000e-43 185.0
32 TraesCS6D01G230600 chr3A 94.286 280 8 5 575 846 206528652 206528373 5.310000e-114 422.0
33 TraesCS6D01G230600 chr3A 88.358 335 38 1 55 389 151162941 151163274 6.920000e-108 401.0
34 TraesCS6D01G230600 chr3A 88.201 339 36 3 55 391 151165729 151166065 6.920000e-108 401.0
35 TraesCS6D01G230600 chr3A 89.773 88 8 1 4346 4432 593351713 593351626 1.310000e-20 111.0
36 TraesCS6D01G230600 chr1A 94.245 278 10 3 575 846 108423634 108423357 1.910000e-113 420.0
37 TraesCS6D01G230600 chr5A 93.929 280 9 5 575 846 408978670 408978949 2.470000e-112 416.0
38 TraesCS6D01G230600 chr5A 93.929 280 8 6 575 846 304480249 304479971 8.890000e-112 414.0
39 TraesCS6D01G230600 chr5A 93.907 279 10 4 575 846 650906875 650907153 8.890000e-112 414.0
40 TraesCS6D01G230600 chr5A 88.955 335 36 1 55 389 632759071 632758738 3.200000e-111 412.0
41 TraesCS6D01G230600 chr5A 88.922 334 36 1 55 388 632753488 632753156 1.150000e-110 411.0
42 TraesCS6D01G230600 chr5A 88.657 335 37 1 55 389 632756279 632755946 1.490000e-109 407.0
43 TraesCS6D01G230600 chr3D 93.031 287 10 7 570 846 164112540 164112826 1.150000e-110 411.0
44 TraesCS6D01G230600 chr3D 98.214 56 1 0 1 56 432025754 432025809 1.020000e-16 99.0
45 TraesCS6D01G230600 chr3B 96.610 59 2 0 1 59 532665685 532665743 1.020000e-16 99.0
46 TraesCS6D01G230600 chr4D 98.182 55 1 0 1 55 365184061 365184115 3.660000e-16 97.1
47 TraesCS6D01G230600 chr7D 98.148 54 1 0 1 54 201160687 201160740 1.310000e-15 95.3
48 TraesCS6D01G230600 chr4B 98.148 54 1 0 1 54 48101632 48101685 1.310000e-15 95.3
49 TraesCS6D01G230600 chr2D 96.552 58 1 1 1 57 21932704 21932761 1.310000e-15 95.3
50 TraesCS6D01G230600 chr2D 98.148 54 1 0 1 54 618082869 618082922 1.310000e-15 95.3


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 TraesCS6D01G230600 chr6D 323797169 323801608 4439 False 8200.000000 8200 100.000000 1 4440 1 chr6D.!!$F2 4439
1 TraesCS6D01G230600 chr6A 461425660 461430399 4739 False 777.600000 2534 95.174250 396 4440 8 chr6A.!!$F2 4044
2 TraesCS6D01G230600 chr6B 499890959 499894825 3866 True 579.333333 2414 94.598111 438 4266 9 chr6B.!!$R1 3828
3 TraesCS6D01G230600 chr7B 606059079 606062324 3245 True 544.625000 1219 93.917125 1294 4265 8 chr7B.!!$R1 2971
4 TraesCS6D01G230600 chr3A 151162941 151166065 3124 False 401.000000 401 88.279500 55 391 2 chr3A.!!$F1 336
5 TraesCS6D01G230600 chr5A 632753156 632759071 5915 True 410.000000 412 88.844667 55 389 3 chr5A.!!$R2 334

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
177 178 0.239347 CGACGTCTCGTAGGGTTTGT 59.761 55.000 14.70 0.0 41.37 2.83 F
838 841 0.532196 GTTACCCCACTATCGCCAGC 60.532 60.000 0.00 0.0 0.00 4.85 F
852 855 0.753867 GCCAGCCTTAGGACTACCTC 59.246 60.000 0.69 0.0 46.43 3.85 F
1973 3948 1.734465 CCGCAAACTGAGCCTTAGAAG 59.266 52.381 0.00 0.0 0.00 2.85 F
2219 5193 2.420022 CTGGTTTTGGAAGGCATACTCG 59.580 50.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 2971 1.747355 CATCCATCCCAGCACTTTGAC 59.253 52.381 0.00 0.00 0.00 3.18 R
2767 6071 2.734492 GCATGAGTTCAAGCTGATTGCC 60.734 50.000 0.00 0.00 44.23 4.52 R
2966 6270 1.201965 GCAGTAATGACAGCGTTCTGC 60.202 52.381 0.00 0.00 44.10 4.26 R
3021 6325 0.178068 ATACCAGTAGCCCACAAGCG 59.822 55.000 0.00 0.00 38.01 4.68 R
3947 8094 0.665298 GCCGAATCCATTTGAGGCTC 59.335 55.000 7.79 7.79 41.21 4.70 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
21 22 1.926561 ATCATGTCGTGTGTGGATCG 58.073 50.000 0.00 0.00 0.00 3.69
22 23 0.601057 TCATGTCGTGTGTGGATCGT 59.399 50.000 0.00 0.00 0.00 3.73
23 24 0.715551 CATGTCGTGTGTGGATCGTG 59.284 55.000 0.00 0.00 0.00 4.35
24 25 1.014044 ATGTCGTGTGTGGATCGTGC 61.014 55.000 0.00 0.00 0.00 5.34
25 26 1.663388 GTCGTGTGTGGATCGTGCA 60.663 57.895 0.00 0.00 0.00 4.57
26 27 1.014044 GTCGTGTGTGGATCGTGCAT 61.014 55.000 0.00 0.00 0.00 3.96
27 28 1.013524 TCGTGTGTGGATCGTGCATG 61.014 55.000 0.00 0.00 0.00 4.06
28 29 1.135315 GTGTGTGGATCGTGCATGC 59.865 57.895 11.82 11.82 0.00 4.06
29 30 1.302351 TGTGTGGATCGTGCATGCA 60.302 52.632 18.46 18.46 0.00 3.96
46 47 3.637714 ACGGATCGTGTGCACAAC 58.362 55.556 23.59 14.69 39.18 3.32
47 48 1.227409 ACGGATCGTGTGCACAACA 60.227 52.632 23.59 11.55 39.18 3.33
57 58 1.544686 GTGCACAACACTTCCGTTTG 58.455 50.000 13.17 0.00 46.41 2.93
84 85 7.113658 GAGAATCCATCTAAGGTCTGTGTTA 57.886 40.000 0.00 0.00 38.96 2.41
89 90 5.105310 TCCATCTAAGGTCTGTGTTAGCTTC 60.105 44.000 0.00 0.00 36.22 3.86
103 104 1.447838 GCTTCGCGTGGAGGATTGA 60.448 57.895 5.77 0.00 0.00 2.57
105 106 1.438651 CTTCGCGTGGAGGATTGAAA 58.561 50.000 5.77 0.00 0.00 2.69
108 109 1.644786 CGCGTGGAGGATTGAAACCC 61.645 60.000 0.00 0.00 0.00 4.11
118 119 2.484264 GGATTGAAACCCGTGACTTCTG 59.516 50.000 0.00 0.00 0.00 3.02
128 129 2.164422 CCGTGACTTCTGATCTGCTACA 59.836 50.000 0.00 0.00 0.00 2.74
150 151 1.671379 GTCCAAAGGGCTCGTCCAC 60.671 63.158 0.00 0.00 36.21 4.02
160 161 1.504900 CTCGTCCACGTGATTCCGA 59.495 57.895 19.30 16.31 40.80 4.55
168 169 1.134075 CGTGATTCCGACGTCTCGT 59.866 57.895 14.70 0.00 45.10 4.18
177 178 0.239347 CGACGTCTCGTAGGGTTTGT 59.761 55.000 14.70 0.00 41.37 2.83
187 188 5.467399 TCTCGTAGGGTTTGTATGTTGTTTG 59.533 40.000 0.00 0.00 0.00 2.93
192 193 8.291032 CGTAGGGTTTGTATGTTGTTTGATTAA 58.709 33.333 0.00 0.00 0.00 1.40
228 229 8.378115 AGTAAGTCTAGTTCTGGAGTAGTCTA 57.622 38.462 0.00 0.00 31.92 2.59
232 233 8.097791 AGTCTAGTTCTGGAGTAGTCTAGATT 57.902 38.462 13.80 8.57 39.82 2.40
243 244 6.404513 GGAGTAGTCTAGATTGTTGTTACGCT 60.405 42.308 0.00 0.00 0.00 5.07
252 253 1.472878 TGTTGTTACGCTGGTTTGCAA 59.527 42.857 0.00 0.00 0.00 4.08
271 272 4.742438 CAAATTGATTTGCTGCTGCTTT 57.258 36.364 17.00 4.21 40.42 3.51
272 273 5.849357 CAAATTGATTTGCTGCTGCTTTA 57.151 34.783 17.00 2.49 40.42 1.85
273 274 5.614760 CAAATTGATTTGCTGCTGCTTTAC 58.385 37.500 17.00 6.77 40.42 2.01
274 275 4.524316 ATTGATTTGCTGCTGCTTTACA 57.476 36.364 17.00 9.08 40.48 2.41
280 281 0.804989 GCTGCTGCTTTACACGGATT 59.195 50.000 8.53 0.00 36.03 3.01
281 282 1.200020 GCTGCTGCTTTACACGGATTT 59.800 47.619 8.53 0.00 36.03 2.17
290 291 2.083167 TACACGGATTTGGGAACGAC 57.917 50.000 0.00 0.00 0.00 4.34
291 292 0.604511 ACACGGATTTGGGAACGACC 60.605 55.000 0.00 0.00 38.08 4.79
342 343 2.159430 TGAATTGTGCCGTGAAAGATCG 59.841 45.455 0.00 0.00 0.00 3.69
355 356 6.349033 CCGTGAAAGATCGGGAAAAGTTATTT 60.349 38.462 0.00 0.00 42.61 1.40
360 361 3.926821 TCGGGAAAAGTTATTTGCACC 57.073 42.857 0.00 0.00 0.00 5.01
363 364 3.551250 CGGGAAAAGTTATTTGCACCGTT 60.551 43.478 0.00 0.00 36.14 4.44
389 390 1.078497 TGTCGAAGGGCGCATCAAT 60.078 52.632 10.83 0.00 40.61 2.57
391 392 1.295792 GTCGAAGGGCGCATCAATTA 58.704 50.000 10.83 0.00 40.61 1.40
392 393 1.873591 GTCGAAGGGCGCATCAATTAT 59.126 47.619 10.83 0.00 40.61 1.28
393 394 1.872952 TCGAAGGGCGCATCAATTATG 59.127 47.619 10.83 0.00 40.61 1.90
502 505 1.450312 CCTGCGTCCAAGGATGACC 60.450 63.158 12.42 0.00 33.22 4.02
512 515 3.217231 GGATGACCATCCGACGGT 58.783 61.111 14.79 0.00 46.84 4.83
576 579 4.530857 CCGGCCGTGCTCCTTAGG 62.531 72.222 26.12 0.00 0.00 2.69
579 582 3.217231 GCCGTGCTCCTTAGGCTA 58.783 61.111 0.00 0.00 45.67 3.93
581 584 1.677637 GCCGTGCTCCTTAGGCTAGT 61.678 60.000 0.00 0.00 45.67 2.57
584 587 1.683917 CGTGCTCCTTAGGCTAGTCAT 59.316 52.381 0.00 0.00 0.00 3.06
585 588 2.885266 CGTGCTCCTTAGGCTAGTCATA 59.115 50.000 0.00 0.00 0.00 2.15
586 589 3.057876 CGTGCTCCTTAGGCTAGTCATAG 60.058 52.174 0.00 0.00 0.00 2.23
587 590 3.892588 GTGCTCCTTAGGCTAGTCATAGT 59.107 47.826 0.00 0.00 0.00 2.12
588 591 3.891977 TGCTCCTTAGGCTAGTCATAGTG 59.108 47.826 0.00 0.00 0.00 2.74
589 592 3.257127 GCTCCTTAGGCTAGTCATAGTGG 59.743 52.174 0.00 0.00 0.00 4.00
591 594 2.900546 CCTTAGGCTAGTCATAGTGGGG 59.099 54.545 0.00 0.00 0.00 4.96
592 595 3.438078 CCTTAGGCTAGTCATAGTGGGGA 60.438 52.174 0.00 0.00 0.00 4.81
594 597 1.576272 AGGCTAGTCATAGTGGGGAGT 59.424 52.381 0.00 0.00 0.00 3.85
597 600 3.764972 GGCTAGTCATAGTGGGGAGTATC 59.235 52.174 0.00 0.00 0.00 2.24
598 601 4.408276 GCTAGTCATAGTGGGGAGTATCA 58.592 47.826 0.00 0.00 36.25 2.15
600 603 6.188407 GCTAGTCATAGTGGGGAGTATCATA 58.812 44.000 0.00 0.00 36.25 2.15
604 607 5.423610 GTCATAGTGGGGAGTATCATATGCT 59.576 44.000 0.00 0.00 36.25 3.79
606 609 6.836007 TCATAGTGGGGAGTATCATATGCTAG 59.164 42.308 0.00 0.00 36.25 3.42
609 612 6.562228 AGTGGGGAGTATCATATGCTAGTAA 58.438 40.000 0.00 0.00 36.25 2.24
610 613 6.437793 AGTGGGGAGTATCATATGCTAGTAAC 59.562 42.308 0.00 0.00 36.25 2.50
611 614 6.210784 GTGGGGAGTATCATATGCTAGTAACA 59.789 42.308 0.00 0.00 36.25 2.41
613 616 7.093333 TGGGGAGTATCATATGCTAGTAACATG 60.093 40.741 0.00 0.00 36.25 3.21
614 617 6.758886 GGGAGTATCATATGCTAGTAACATGC 59.241 42.308 0.00 0.00 36.25 4.06
615 618 7.323420 GGAGTATCATATGCTAGTAACATGCA 58.677 38.462 0.00 0.00 37.81 3.96
616 619 7.984050 GGAGTATCATATGCTAGTAACATGCAT 59.016 37.037 0.00 0.00 43.07 3.96
643 646 9.908747 ATGATACTAGTGTATGATACTACCTCC 57.091 37.037 5.39 0.00 39.29 4.30
645 648 9.908747 GATACTAGTGTATGATACTACCTCCAT 57.091 37.037 5.39 0.00 39.29 3.41
648 651 8.892530 ACTAGTGTATGATACTACCTCCATAGT 58.107 37.037 4.03 2.61 38.89 2.12
649 652 9.168451 CTAGTGTATGATACTACCTCCATAGTG 57.832 40.741 4.03 0.00 36.09 2.74
650 653 6.434652 AGTGTATGATACTACCTCCATAGTGC 59.565 42.308 4.03 0.00 36.09 4.40
651 654 6.208797 GTGTATGATACTACCTCCATAGTGCA 59.791 42.308 4.03 0.00 36.09 4.57
652 655 6.954102 TGTATGATACTACCTCCATAGTGCAT 59.046 38.462 4.03 0.00 36.09 3.96
653 656 8.113462 TGTATGATACTACCTCCATAGTGCATA 58.887 37.037 4.03 0.00 36.09 3.14
654 657 7.652524 ATGATACTACCTCCATAGTGCATAG 57.347 40.000 0.00 0.00 36.09 2.23
655 658 6.552932 TGATACTACCTCCATAGTGCATAGT 58.447 40.000 0.00 0.00 36.09 2.12
656 659 7.696017 TGATACTACCTCCATAGTGCATAGTA 58.304 38.462 0.00 0.00 36.09 1.82
657 660 8.336987 TGATACTACCTCCATAGTGCATAGTAT 58.663 37.037 9.49 9.49 37.18 2.12
658 661 8.754991 ATACTACCTCCATAGTGCATAGTATC 57.245 38.462 0.00 0.00 36.09 2.24
659 662 6.552932 ACTACCTCCATAGTGCATAGTATCA 58.447 40.000 0.00 0.00 34.02 2.15
660 663 7.185565 ACTACCTCCATAGTGCATAGTATCAT 58.814 38.462 0.00 0.00 34.02 2.45
661 664 8.336987 ACTACCTCCATAGTGCATAGTATCATA 58.663 37.037 0.00 0.00 34.02 2.15
662 665 9.190317 CTACCTCCATAGTGCATAGTATCATAA 57.810 37.037 0.00 0.00 0.00 1.90
663 666 8.435931 ACCTCCATAGTGCATAGTATCATAAA 57.564 34.615 0.00 0.00 0.00 1.40
664 667 8.314751 ACCTCCATAGTGCATAGTATCATAAAC 58.685 37.037 0.00 0.00 0.00 2.01
665 668 8.535335 CCTCCATAGTGCATAGTATCATAAACT 58.465 37.037 0.00 0.00 0.00 2.66
697 700 9.678941 CATAGATGATCATATTTATTGCCATGC 57.321 33.333 8.54 0.00 0.00 4.06
698 701 7.712204 AGATGATCATATTTATTGCCATGCA 57.288 32.000 8.54 0.00 36.47 3.96
699 702 8.306313 AGATGATCATATTTATTGCCATGCAT 57.694 30.769 8.54 0.00 38.76 3.96
700 703 8.197439 AGATGATCATATTTATTGCCATGCATG 58.803 33.333 20.19 20.19 38.76 4.06
701 704 7.469537 TGATCATATTTATTGCCATGCATGA 57.530 32.000 28.31 8.76 38.76 3.07
702 705 7.317390 TGATCATATTTATTGCCATGCATGAC 58.683 34.615 28.31 17.77 38.76 3.06
703 706 6.651975 TCATATTTATTGCCATGCATGACA 57.348 33.333 28.31 20.53 38.76 3.58
704 707 6.448852 TCATATTTATTGCCATGCATGACAC 58.551 36.000 28.31 16.49 38.76 3.67
705 708 4.739587 ATTTATTGCCATGCATGACACA 57.260 36.364 28.31 18.81 38.76 3.72
706 709 4.532314 TTTATTGCCATGCATGACACAA 57.468 36.364 28.31 25.14 38.76 3.33
707 710 4.532314 TTATTGCCATGCATGACACAAA 57.468 36.364 28.31 15.45 38.76 2.83
708 711 2.442212 TTGCCATGCATGACACAAAG 57.558 45.000 28.31 10.23 38.76 2.77
709 712 1.330234 TGCCATGCATGACACAAAGT 58.670 45.000 28.31 0.00 31.71 2.66
710 713 2.512705 TGCCATGCATGACACAAAGTA 58.487 42.857 28.31 5.91 31.71 2.24
711 714 2.488937 TGCCATGCATGACACAAAGTAG 59.511 45.455 28.31 8.01 31.71 2.57
712 715 2.733227 GCCATGCATGACACAAAGTAGC 60.733 50.000 28.31 14.15 0.00 3.58
713 716 2.488937 CCATGCATGACACAAAGTAGCA 59.511 45.455 28.31 0.00 37.13 3.49
714 717 3.129813 CCATGCATGACACAAAGTAGCAT 59.870 43.478 28.31 0.00 41.24 3.79
715 718 4.336153 CCATGCATGACACAAAGTAGCATA 59.664 41.667 28.31 0.00 39.67 3.14
716 719 5.505159 CCATGCATGACACAAAGTAGCATAG 60.505 44.000 28.31 0.74 39.67 2.23
717 720 3.374988 TGCATGACACAAAGTAGCATAGC 59.625 43.478 0.00 0.00 30.65 2.97
718 721 3.374988 GCATGACACAAAGTAGCATAGCA 59.625 43.478 0.00 0.00 0.00 3.49
719 722 4.036027 GCATGACACAAAGTAGCATAGCAT 59.964 41.667 0.00 0.00 0.00 3.79
720 723 5.449588 GCATGACACAAAGTAGCATAGCATT 60.450 40.000 0.00 0.00 0.00 3.56
721 724 6.558009 CATGACACAAAGTAGCATAGCATTT 58.442 36.000 0.00 0.00 0.00 2.32
722 725 7.679400 GCATGACACAAAGTAGCATAGCATTTA 60.679 37.037 0.00 0.00 0.00 1.40
723 726 7.680442 TGACACAAAGTAGCATAGCATTTAA 57.320 32.000 0.00 0.00 0.00 1.52
724 727 7.526608 TGACACAAAGTAGCATAGCATTTAAC 58.473 34.615 0.00 0.00 0.00 2.01
725 728 7.174080 TGACACAAAGTAGCATAGCATTTAACA 59.826 33.333 0.00 0.00 0.00 2.41
726 729 8.055279 ACACAAAGTAGCATAGCATTTAACAT 57.945 30.769 0.00 0.00 0.00 2.71
727 730 7.970061 ACACAAAGTAGCATAGCATTTAACATG 59.030 33.333 0.00 0.00 0.00 3.21
728 731 8.183536 CACAAAGTAGCATAGCATTTAACATGA 58.816 33.333 0.00 0.00 0.00 3.07
729 732 8.906867 ACAAAGTAGCATAGCATTTAACATGAT 58.093 29.630 0.00 0.00 0.00 2.45
732 735 8.244494 AGTAGCATAGCATTTAACATGATACG 57.756 34.615 0.00 0.00 42.29 3.06
733 736 6.486253 AGCATAGCATTTAACATGATACGG 57.514 37.500 0.00 0.00 0.00 4.02
734 737 5.997746 AGCATAGCATTTAACATGATACGGT 59.002 36.000 0.00 0.00 0.00 4.83
735 738 7.158697 AGCATAGCATTTAACATGATACGGTA 58.841 34.615 0.00 0.00 0.00 4.02
736 739 7.824289 AGCATAGCATTTAACATGATACGGTAT 59.176 33.333 0.00 0.00 0.00 2.73
737 740 8.116753 GCATAGCATTTAACATGATACGGTATC 58.883 37.037 18.97 18.97 35.74 2.24
738 741 9.371136 CATAGCATTTAACATGATACGGTATCT 57.629 33.333 24.27 10.32 36.17 1.98
741 744 9.587772 AGCATTTAACATGATACGGTATCTATC 57.412 33.333 24.27 5.80 36.17 2.08
742 745 9.587772 GCATTTAACATGATACGGTATCTATCT 57.412 33.333 24.27 12.01 36.17 1.98
796 799 4.487948 ATGTGTCACATAAGCATGTTTGC 58.512 39.130 16.99 0.00 42.98 3.68
797 800 4.219070 ATGTGTCACATAAGCATGTTTGCT 59.781 37.500 16.99 0.00 45.67 3.91
798 801 5.415389 ATGTGTCACATAAGCATGTTTGCTA 59.585 36.000 16.99 0.00 46.65 3.49
799 802 6.403964 ATGTGTCACATAAGCATGTTTGCTAG 60.404 38.462 16.99 0.00 46.65 3.42
800 803 8.705810 ATGTGTCACATAAGCATGTTTGCTAGT 61.706 37.037 16.99 0.00 46.65 2.57
808 811 3.545703 GCATGTTTGCTAGTCCCTATGT 58.454 45.455 0.00 0.00 45.77 2.29
809 812 3.947834 GCATGTTTGCTAGTCCCTATGTT 59.052 43.478 0.00 0.00 45.77 2.71
810 813 5.123227 GCATGTTTGCTAGTCCCTATGTTA 58.877 41.667 0.00 0.00 45.77 2.41
811 814 5.007724 GCATGTTTGCTAGTCCCTATGTTAC 59.992 44.000 0.00 0.00 45.77 2.50
812 815 5.093849 TGTTTGCTAGTCCCTATGTTACC 57.906 43.478 0.00 0.00 0.00 2.85
813 816 4.532916 TGTTTGCTAGTCCCTATGTTACCA 59.467 41.667 0.00 0.00 0.00 3.25
814 817 5.190925 TGTTTGCTAGTCCCTATGTTACCAT 59.809 40.000 0.00 0.00 34.97 3.55
815 818 5.968676 TTGCTAGTCCCTATGTTACCATT 57.031 39.130 0.00 0.00 32.29 3.16
816 819 5.968676 TGCTAGTCCCTATGTTACCATTT 57.031 39.130 0.00 0.00 32.29 2.32
817 820 7.440505 TTGCTAGTCCCTATGTTACCATTTA 57.559 36.000 0.00 0.00 32.29 1.40
818 821 7.626999 TGCTAGTCCCTATGTTACCATTTAT 57.373 36.000 0.00 0.00 32.29 1.40
819 822 7.450074 TGCTAGTCCCTATGTTACCATTTATG 58.550 38.462 0.00 0.00 32.29 1.90
820 823 7.071950 TGCTAGTCCCTATGTTACCATTTATGT 59.928 37.037 0.00 0.00 32.29 2.29
821 824 7.937394 GCTAGTCCCTATGTTACCATTTATGTT 59.063 37.037 0.00 0.00 32.29 2.71
824 827 8.215736 AGTCCCTATGTTACCATTTATGTTACC 58.784 37.037 0.00 0.00 32.29 2.85
825 828 7.446319 GTCCCTATGTTACCATTTATGTTACCC 59.554 40.741 0.00 0.00 32.29 3.69
826 829 6.717997 CCCTATGTTACCATTTATGTTACCCC 59.282 42.308 0.00 0.00 32.29 4.95
827 830 7.291566 CCTATGTTACCATTTATGTTACCCCA 58.708 38.462 0.00 0.00 32.29 4.96
828 831 7.229907 CCTATGTTACCATTTATGTTACCCCAC 59.770 40.741 0.00 0.00 32.29 4.61
829 832 6.142259 TGTTACCATTTATGTTACCCCACT 57.858 37.500 0.00 0.00 0.00 4.00
830 833 7.268212 TGTTACCATTTATGTTACCCCACTA 57.732 36.000 0.00 0.00 0.00 2.74
831 834 7.874252 TGTTACCATTTATGTTACCCCACTAT 58.126 34.615 0.00 0.00 0.00 2.12
832 835 7.994334 TGTTACCATTTATGTTACCCCACTATC 59.006 37.037 0.00 0.00 0.00 2.08
833 836 5.617252 ACCATTTATGTTACCCCACTATCG 58.383 41.667 0.00 0.00 0.00 2.92
834 837 4.454504 CCATTTATGTTACCCCACTATCGC 59.545 45.833 0.00 0.00 0.00 4.58
835 838 3.756933 TTATGTTACCCCACTATCGCC 57.243 47.619 0.00 0.00 0.00 5.54
836 839 1.502690 ATGTTACCCCACTATCGCCA 58.497 50.000 0.00 0.00 0.00 5.69
837 840 0.828022 TGTTACCCCACTATCGCCAG 59.172 55.000 0.00 0.00 0.00 4.85
838 841 0.532196 GTTACCCCACTATCGCCAGC 60.532 60.000 0.00 0.00 0.00 4.85
839 842 1.692173 TTACCCCACTATCGCCAGCC 61.692 60.000 0.00 0.00 0.00 4.85
852 855 0.753867 GCCAGCCTTAGGACTACCTC 59.246 60.000 0.69 0.00 46.43 3.85
1524 2912 7.745620 TCATTTGAACTTAGAAAAGAGTCCC 57.254 36.000 0.00 0.00 36.50 4.46
1583 2971 3.879295 AGATGTGACATGCTAAAATCGGG 59.121 43.478 1.23 0.00 0.00 5.14
1584 2972 3.066291 TGTGACATGCTAAAATCGGGT 57.934 42.857 0.00 0.00 0.00 5.28
1659 3047 9.692325 ATTCATTAGCTTAAGAATCTTTGACCT 57.308 29.630 6.67 0.00 0.00 3.85
1749 3137 9.763465 GAAGCCATTGATGTAATTTGATTTTTG 57.237 29.630 0.00 0.00 0.00 2.44
1771 3161 5.509498 TGCTCTGCATACTCCCTTAATTTT 58.491 37.500 0.00 0.00 31.71 1.82
1799 3189 4.111375 ACTCAGGTGATGTCGTATGTTC 57.889 45.455 0.00 0.00 0.00 3.18
1814 3204 4.386049 CGTATGTTCGCTCCAATTCCTATC 59.614 45.833 0.00 0.00 0.00 2.08
1973 3948 1.734465 CCGCAAACTGAGCCTTAGAAG 59.266 52.381 0.00 0.00 0.00 2.85
2219 5193 2.420022 CTGGTTTTGGAAGGCATACTCG 59.580 50.000 0.00 0.00 0.00 4.18
2254 5228 5.570320 AGCAGTTTGGATGGTGTAATAAGT 58.430 37.500 0.00 0.00 0.00 2.24
2256 5231 6.493458 AGCAGTTTGGATGGTGTAATAAGTTT 59.507 34.615 0.00 0.00 0.00 2.66
2322 5297 3.196469 TGGAATCGCAAATTTTGGGCATA 59.804 39.130 18.46 5.21 42.68 3.14
2323 5298 4.141756 TGGAATCGCAAATTTTGGGCATAT 60.142 37.500 18.46 7.06 42.68 1.78
2409 5517 4.624015 CCATCATTGGCATATTGTTGGTC 58.376 43.478 11.59 0.00 35.85 4.02
2563 5725 5.554822 TTGATGATAAAGTGCGGTTAACC 57.445 39.130 15.13 15.13 0.00 2.85
2767 6071 5.005779 AGCAAAGAAGAATATGAGCGTTACG 59.994 40.000 0.00 0.00 0.00 3.18
2966 6270 7.869429 AGTCTTGCAGTCATTTCCATTTTAAAG 59.131 33.333 0.00 0.00 0.00 1.85
3021 6325 6.308282 CACGTCCTCTGAACTGAAGTTTATAC 59.692 42.308 0.00 0.00 38.56 1.47
3036 6340 2.882927 TATACGCTTGTGGGCTACTG 57.117 50.000 1.79 0.00 0.00 2.74
3287 6591 5.333798 CGTTTTTGCTTCTGGATTCGAACTA 60.334 40.000 0.00 0.00 0.00 2.24
3326 6630 6.313411 TGCCTGAATTAGCATTAATTTTGTGC 59.687 34.615 0.00 2.29 39.10 4.57
3328 6632 7.043565 CCTGAATTAGCATTAATTTTGTGCCT 58.956 34.615 5.96 0.00 39.10 4.75
3330 6634 7.609960 TGAATTAGCATTAATTTTGTGCCTGA 58.390 30.769 5.96 0.00 39.10 3.86
3331 6635 8.093307 TGAATTAGCATTAATTTTGTGCCTGAA 58.907 29.630 5.96 1.01 39.10 3.02
3334 6638 6.730960 AGCATTAATTTTGTGCCTGAATTG 57.269 33.333 5.96 0.00 39.62 2.32
3505 7232 6.148811 CGACAATACCTGTAACCAGTTGAAAT 59.851 38.462 0.00 0.00 38.84 2.17
3639 7366 6.375455 AGCAAAGTAAGTCTGTTTGGATATGG 59.625 38.462 0.00 0.00 32.78 2.74
3734 7463 7.663493 TGTCATATTTGGTTCAGTTGATGTACA 59.337 33.333 0.00 0.00 31.17 2.90
3769 7563 5.123820 GCAAAGTAGTCTGTTTGGATATGCA 59.876 40.000 0.00 0.00 34.75 3.96
3854 7648 3.252944 TGCATTCATCTTCGTGCTTTTCA 59.747 39.130 0.00 0.00 38.37 2.69
3947 8094 8.407832 TGAGAATGACAATGTAGCCAATAATTG 58.592 33.333 0.00 0.00 36.35 2.32
3990 8139 7.358105 GGCACGCTCAAAATAAAAAGTAAACTC 60.358 37.037 0.00 0.00 0.00 3.01
4058 8243 1.539827 GGCATACAGTGGGTTGTCAAC 59.460 52.381 7.20 7.20 32.56 3.18
4061 8246 4.069304 GCATACAGTGGGTTGTCAACTTA 58.931 43.478 15.17 2.41 32.56 2.24
4062 8247 4.517453 GCATACAGTGGGTTGTCAACTTAA 59.483 41.667 15.17 0.00 32.56 1.85
4070 8255 5.298276 GTGGGTTGTCAACTTAAGTCATTGA 59.702 40.000 15.17 6.48 0.00 2.57
4071 8256 5.888724 TGGGTTGTCAACTTAAGTCATTGAA 59.111 36.000 15.17 0.00 34.28 2.69
4166 8351 4.397481 TGACATCCATAGCAGAACTCAG 57.603 45.455 0.00 0.00 0.00 3.35
4287 8477 6.899393 AACCCATACAATTAGGCACATATG 57.101 37.500 0.00 0.00 0.00 1.78
4342 8721 2.941720 GTCCAAGAACTGATCAGGCATC 59.058 50.000 26.08 19.40 0.00 3.91
4365 8744 7.698836 TCATAAAGAAAAAGAAACTGCTTGC 57.301 32.000 0.00 0.00 0.00 4.01
4368 8747 4.454728 AGAAAAAGAAACTGCTTGCACA 57.545 36.364 0.00 0.00 0.00 4.57
4379 8758 3.885297 ACTGCTTGCACAAATCTTAGTGT 59.115 39.130 0.00 0.00 38.02 3.55
4380 8759 5.063204 ACTGCTTGCACAAATCTTAGTGTA 58.937 37.500 0.00 0.00 38.02 2.90
4383 8762 6.800543 TGCTTGCACAAATCTTAGTGTAAAA 58.199 32.000 0.00 0.00 39.28 1.52
4384 8763 7.432869 TGCTTGCACAAATCTTAGTGTAAAAT 58.567 30.769 0.00 0.00 39.28 1.82
4385 8764 7.594758 TGCTTGCACAAATCTTAGTGTAAAATC 59.405 33.333 0.00 0.00 39.28 2.17
4387 8766 9.462174 CTTGCACAAATCTTAGTGTAAAATCAA 57.538 29.630 0.00 0.00 39.28 2.57
4389 8768 9.409312 TGCACAAATCTTAGTGTAAAATCAATG 57.591 29.630 0.00 0.00 38.02 2.82
4392 8771 8.584157 ACAAATCTTAGTGTAAAATCAATGCCA 58.416 29.630 0.00 0.00 0.00 4.92
4393 8772 9.590451 CAAATCTTAGTGTAAAATCAATGCCAT 57.410 29.630 0.00 0.00 0.00 4.40
4397 8776 9.625747 TCTTAGTGTAAAATCAATGCCATATGA 57.374 29.630 3.65 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.672874 CGATCCACACACGACATGATTT 59.327 45.455 0.00 0.00 0.00 2.17
1 2 2.270923 CGATCCACACACGACATGATT 58.729 47.619 0.00 0.00 0.00 2.57
2 3 1.204704 ACGATCCACACACGACATGAT 59.795 47.619 0.00 0.00 0.00 2.45
4 5 0.715551 CACGATCCACACACGACATG 59.284 55.000 0.00 0.00 0.00 3.21
5 6 1.014044 GCACGATCCACACACGACAT 61.014 55.000 0.00 0.00 0.00 3.06
6 7 1.663388 GCACGATCCACACACGACA 60.663 57.895 0.00 0.00 0.00 4.35
7 8 1.014044 ATGCACGATCCACACACGAC 61.014 55.000 0.00 0.00 0.00 4.34
8 9 1.013524 CATGCACGATCCACACACGA 61.014 55.000 0.00 0.00 0.00 4.35
9 10 1.421093 CATGCACGATCCACACACG 59.579 57.895 0.00 0.00 0.00 4.49
10 11 1.135315 GCATGCACGATCCACACAC 59.865 57.895 14.21 0.00 0.00 3.82
11 12 1.302351 TGCATGCACGATCCACACA 60.302 52.632 18.46 0.00 0.00 3.72
12 13 1.135315 GTGCATGCACGATCCACAC 59.865 57.895 33.20 9.23 37.19 3.82
13 14 3.577229 GTGCATGCACGATCCACA 58.423 55.556 33.20 0.00 37.19 4.17
29 30 1.227409 TGTTGTGCACACGATCCGT 60.227 52.632 21.56 0.00 42.36 4.69
30 31 1.204062 GTGTTGTGCACACGATCCG 59.796 57.895 21.56 0.00 46.51 4.18
43 44 7.491161 GGATTCTCCACAAACGGAAGTGTTG 62.491 48.000 0.00 0.00 39.89 3.33
44 45 5.518755 GGATTCTCCACAAACGGAAGTGTT 61.519 45.833 0.00 0.00 39.89 3.32
45 46 4.055214 GGATTCTCCACAAACGGAAGTGT 61.055 47.826 0.00 0.00 39.89 3.55
46 47 2.484264 GGATTCTCCACAAACGGAAGTG 59.516 50.000 0.00 0.00 39.89 3.16
47 48 2.105821 TGGATTCTCCACAAACGGAAGT 59.894 45.455 0.00 0.00 45.18 3.01
48 49 2.778299 TGGATTCTCCACAAACGGAAG 58.222 47.619 0.00 0.00 42.67 3.46
49 50 2.940994 TGGATTCTCCACAAACGGAA 57.059 45.000 0.00 0.00 42.67 4.30
89 90 1.644786 GGGTTTCAATCCTCCACGCG 61.645 60.000 3.53 3.53 0.00 6.01
103 104 2.872038 GCAGATCAGAAGTCACGGGTTT 60.872 50.000 0.00 0.00 0.00 3.27
105 106 0.247736 GCAGATCAGAAGTCACGGGT 59.752 55.000 0.00 0.00 0.00 5.28
108 109 3.494045 TGTAGCAGATCAGAAGTCACG 57.506 47.619 0.00 0.00 0.00 4.35
118 119 4.125703 CCTTTGGACTCATGTAGCAGATC 58.874 47.826 0.00 0.00 0.00 2.75
128 129 0.250513 GACGAGCCCTTTGGACTCAT 59.749 55.000 0.00 0.00 35.66 2.90
150 151 3.963841 CGAGACGTCGGAATCACG 58.036 61.111 10.46 5.21 42.87 4.35
160 161 2.821969 ACATACAAACCCTACGAGACGT 59.178 45.455 0.00 0.00 44.35 4.34
228 229 3.550030 GCAAACCAGCGTAACAACAATCT 60.550 43.478 0.00 0.00 0.00 2.40
232 233 1.095600 TGCAAACCAGCGTAACAACA 58.904 45.000 0.00 0.00 37.31 3.33
252 253 4.687483 GTGTAAAGCAGCAGCAAATCAATT 59.313 37.500 3.17 0.00 45.49 2.32
271 272 1.338011 GGTCGTTCCCAAATCCGTGTA 60.338 52.381 0.00 0.00 0.00 2.90
272 273 0.604511 GGTCGTTCCCAAATCCGTGT 60.605 55.000 0.00 0.00 0.00 4.49
273 274 1.632046 CGGTCGTTCCCAAATCCGTG 61.632 60.000 0.00 0.00 34.38 4.94
274 275 1.375013 CGGTCGTTCCCAAATCCGT 60.375 57.895 0.00 0.00 34.38 4.69
280 281 3.592059 CTTAATCTTCGGTCGTTCCCAA 58.408 45.455 0.00 0.00 0.00 4.12
281 282 2.093869 CCTTAATCTTCGGTCGTTCCCA 60.094 50.000 0.00 0.00 0.00 4.37
290 291 8.768955 CAATCAGTATTTCTCCTTAATCTTCGG 58.231 37.037 0.00 0.00 0.00 4.30
291 292 8.279103 GCAATCAGTATTTCTCCTTAATCTTCG 58.721 37.037 0.00 0.00 0.00 3.79
342 343 3.653539 ACGGTGCAAATAACTTTTCCC 57.346 42.857 0.00 0.00 0.00 3.97
355 356 1.202087 CGACAGAAAAACAACGGTGCA 60.202 47.619 0.00 0.00 0.00 4.57
360 361 2.853281 GCCCTTCGACAGAAAAACAACG 60.853 50.000 0.00 0.00 35.71 4.10
363 364 0.941542 CGCCCTTCGACAGAAAAACA 59.058 50.000 0.00 0.00 41.67 2.83
391 392 7.141363 GCACAAAATATCGCCTTAGATTTCAT 58.859 34.615 0.00 0.00 32.39 2.57
392 393 6.459573 GGCACAAAATATCGCCTTAGATTTCA 60.460 38.462 0.00 0.00 41.50 2.69
393 394 5.915196 GGCACAAAATATCGCCTTAGATTTC 59.085 40.000 0.00 0.00 41.50 2.17
502 505 1.772182 GCTATCTCAACCGTCGGATG 58.228 55.000 20.51 17.47 0.00 3.51
541 544 1.529309 GCAGTGGATCCCTTCTCCC 59.471 63.158 9.90 0.00 31.32 4.30
571 574 3.829601 CTCCCCACTATGACTAGCCTAAG 59.170 52.174 0.00 0.00 0.00 2.18
572 575 3.206866 ACTCCCCACTATGACTAGCCTAA 59.793 47.826 0.00 0.00 0.00 2.69
573 576 2.789992 ACTCCCCACTATGACTAGCCTA 59.210 50.000 0.00 0.00 0.00 3.93
574 577 1.576272 ACTCCCCACTATGACTAGCCT 59.424 52.381 0.00 0.00 0.00 4.58
575 578 2.089600 ACTCCCCACTATGACTAGCC 57.910 55.000 0.00 0.00 0.00 3.93
576 579 4.408276 TGATACTCCCCACTATGACTAGC 58.592 47.826 0.00 0.00 0.00 3.42
577 580 7.201866 GCATATGATACTCCCCACTATGACTAG 60.202 44.444 6.97 0.00 0.00 2.57
578 581 6.607600 GCATATGATACTCCCCACTATGACTA 59.392 42.308 6.97 0.00 0.00 2.59
579 582 5.423610 GCATATGATACTCCCCACTATGACT 59.576 44.000 6.97 0.00 0.00 3.41
581 584 5.593786 AGCATATGATACTCCCCACTATGA 58.406 41.667 6.97 0.00 0.00 2.15
584 587 6.153942 ACTAGCATATGATACTCCCCACTA 57.846 41.667 6.97 0.00 0.00 2.74
585 588 5.017093 ACTAGCATATGATACTCCCCACT 57.983 43.478 6.97 0.00 0.00 4.00
586 589 6.210784 TGTTACTAGCATATGATACTCCCCAC 59.789 42.308 6.97 0.00 0.00 4.61
587 590 6.319715 TGTTACTAGCATATGATACTCCCCA 58.680 40.000 6.97 0.00 0.00 4.96
588 591 6.852420 TGTTACTAGCATATGATACTCCCC 57.148 41.667 6.97 0.00 0.00 4.81
589 592 6.758886 GCATGTTACTAGCATATGATACTCCC 59.241 42.308 6.97 0.00 0.00 4.30
591 594 8.939201 ATGCATGTTACTAGCATATGATACTC 57.061 34.615 6.97 0.00 46.27 2.59
617 620 9.908747 GGAGGTAGTATCATACACTAGTATCAT 57.091 37.037 0.00 0.00 38.88 2.45
619 622 9.908747 ATGGAGGTAGTATCATACACTAGTATC 57.091 37.037 0.00 0.00 38.88 2.24
622 625 8.892530 ACTATGGAGGTAGTATCATACACTAGT 58.107 37.037 0.00 0.00 33.29 2.57
623 626 9.168451 CACTATGGAGGTAGTATCATACACTAG 57.832 40.741 0.00 0.00 33.29 2.57
624 627 7.610692 GCACTATGGAGGTAGTATCATACACTA 59.389 40.741 0.00 0.00 33.29 2.74
625 628 6.434652 GCACTATGGAGGTAGTATCATACACT 59.565 42.308 0.00 0.00 33.29 3.55
626 629 6.208797 TGCACTATGGAGGTAGTATCATACAC 59.791 42.308 0.00 0.00 33.29 2.90
627 630 6.311735 TGCACTATGGAGGTAGTATCATACA 58.688 40.000 0.00 0.00 33.29 2.29
630 633 7.185565 ACTATGCACTATGGAGGTAGTATCAT 58.814 38.462 0.00 0.00 33.29 2.45
631 634 6.552932 ACTATGCACTATGGAGGTAGTATCA 58.447 40.000 0.00 0.00 33.29 2.15
632 635 8.754991 ATACTATGCACTATGGAGGTAGTATC 57.245 38.462 0.00 0.00 31.70 2.24
634 637 7.696017 TGATACTATGCACTATGGAGGTAGTA 58.304 38.462 0.00 0.00 33.29 1.82
635 638 6.552932 TGATACTATGCACTATGGAGGTAGT 58.447 40.000 0.00 0.00 35.34 2.73
636 639 7.652524 ATGATACTATGCACTATGGAGGTAG 57.347 40.000 0.00 0.00 0.00 3.18
637 640 9.541884 TTTATGATACTATGCACTATGGAGGTA 57.458 33.333 0.00 0.00 0.00 3.08
638 641 8.314751 GTTTATGATACTATGCACTATGGAGGT 58.685 37.037 0.00 0.00 0.00 3.85
639 642 8.535335 AGTTTATGATACTATGCACTATGGAGG 58.465 37.037 0.00 0.00 0.00 4.30
671 674 9.678941 GCATGGCAATAAATATGATCATCTATG 57.321 33.333 12.53 9.66 0.00 2.23
672 675 9.416284 TGCATGGCAATAAATATGATCATCTAT 57.584 29.630 12.53 5.37 34.76 1.98
673 676 8.810990 TGCATGGCAATAAATATGATCATCTA 57.189 30.769 12.53 3.11 34.76 1.98
674 677 7.712204 TGCATGGCAATAAATATGATCATCT 57.288 32.000 12.53 0.00 34.76 2.90
675 678 8.194769 TCATGCATGGCAATAAATATGATCATC 58.805 33.333 25.97 0.00 43.62 2.92
676 679 7.979537 GTCATGCATGGCAATAAATATGATCAT 59.020 33.333 26.04 13.81 43.62 2.45
677 680 7.039644 TGTCATGCATGGCAATAAATATGATCA 60.040 33.333 30.82 2.65 43.62 2.92
678 681 7.274904 GTGTCATGCATGGCAATAAATATGATC 59.725 37.037 34.01 14.19 44.94 2.92
679 682 7.094631 GTGTCATGCATGGCAATAAATATGAT 58.905 34.615 34.01 0.00 44.94 2.45
680 683 6.040616 TGTGTCATGCATGGCAATAAATATGA 59.959 34.615 34.01 6.03 44.94 2.15
681 684 6.217294 TGTGTCATGCATGGCAATAAATATG 58.783 36.000 34.01 1.77 44.94 1.78
682 685 6.408107 TGTGTCATGCATGGCAATAAATAT 57.592 33.333 34.01 0.00 44.94 1.28
683 686 5.848833 TGTGTCATGCATGGCAATAAATA 57.151 34.783 34.01 14.13 44.94 1.40
684 687 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
685 688 4.532314 TTGTGTCATGCATGGCAATAAA 57.468 36.364 34.01 24.20 44.94 1.40
686 689 4.021280 ACTTTGTGTCATGCATGGCAATAA 60.021 37.500 34.01 26.82 44.94 1.40
687 690 3.510753 ACTTTGTGTCATGCATGGCAATA 59.489 39.130 34.01 22.99 44.94 1.90
688 691 2.300723 ACTTTGTGTCATGCATGGCAAT 59.699 40.909 34.01 15.19 44.94 3.56
689 692 1.687660 ACTTTGTGTCATGCATGGCAA 59.312 42.857 34.01 25.74 44.94 4.52
690 693 1.330234 ACTTTGTGTCATGCATGGCA 58.670 45.000 29.45 29.45 44.86 4.92
691 694 2.733227 GCTACTTTGTGTCATGCATGGC 60.733 50.000 24.40 24.40 0.00 4.40
692 695 2.488937 TGCTACTTTGTGTCATGCATGG 59.511 45.455 25.97 10.76 0.00 3.66
693 696 3.835378 TGCTACTTTGTGTCATGCATG 57.165 42.857 21.07 21.07 0.00 4.06
694 697 4.036027 GCTATGCTACTTTGTGTCATGCAT 59.964 41.667 0.00 0.00 40.50 3.96
695 698 3.374988 GCTATGCTACTTTGTGTCATGCA 59.625 43.478 0.00 0.00 35.34 3.96
696 699 3.374988 TGCTATGCTACTTTGTGTCATGC 59.625 43.478 0.00 0.00 0.00 4.06
697 700 5.746307 ATGCTATGCTACTTTGTGTCATG 57.254 39.130 0.00 0.00 0.00 3.07
698 701 6.764308 AAATGCTATGCTACTTTGTGTCAT 57.236 33.333 0.00 0.00 0.00 3.06
699 702 7.174080 TGTTAAATGCTATGCTACTTTGTGTCA 59.826 33.333 0.00 0.00 0.00 3.58
700 703 7.526608 TGTTAAATGCTATGCTACTTTGTGTC 58.473 34.615 0.00 0.00 0.00 3.67
701 704 7.447374 TGTTAAATGCTATGCTACTTTGTGT 57.553 32.000 0.00 0.00 0.00 3.72
702 705 8.183536 TCATGTTAAATGCTATGCTACTTTGTG 58.816 33.333 0.00 0.00 0.00 3.33
703 706 8.279970 TCATGTTAAATGCTATGCTACTTTGT 57.720 30.769 0.00 0.00 0.00 2.83
706 709 8.712363 CGTATCATGTTAAATGCTATGCTACTT 58.288 33.333 0.00 0.00 0.00 2.24
707 710 7.331934 CCGTATCATGTTAAATGCTATGCTACT 59.668 37.037 0.00 0.00 0.00 2.57
708 711 7.117812 ACCGTATCATGTTAAATGCTATGCTAC 59.882 37.037 0.00 0.00 0.00 3.58
709 712 7.158697 ACCGTATCATGTTAAATGCTATGCTA 58.841 34.615 0.00 0.00 0.00 3.49
710 713 5.997746 ACCGTATCATGTTAAATGCTATGCT 59.002 36.000 0.00 0.00 0.00 3.79
711 714 6.241207 ACCGTATCATGTTAAATGCTATGC 57.759 37.500 0.00 0.00 0.00 3.14
712 715 9.371136 AGATACCGTATCATGTTAAATGCTATG 57.629 33.333 18.67 0.00 37.65 2.23
715 718 9.587772 GATAGATACCGTATCATGTTAAATGCT 57.412 33.333 18.67 0.00 37.65 3.79
716 719 9.587772 AGATAGATACCGTATCATGTTAAATGC 57.412 33.333 18.67 0.00 37.65 3.56
769 772 9.786105 CAAACATGCTTATGTGACACATAATTA 57.214 29.630 31.38 24.63 46.38 1.40
770 773 7.276218 GCAAACATGCTTATGTGACACATAATT 59.724 33.333 31.38 22.47 46.38 1.40
771 774 6.753279 GCAAACATGCTTATGTGACACATAAT 59.247 34.615 31.38 19.54 46.38 1.28
772 775 6.072008 AGCAAACATGCTTATGTGACACATAA 60.072 34.615 29.99 29.99 45.70 1.90
773 776 5.415389 AGCAAACATGCTTATGTGACACATA 59.585 36.000 21.76 21.76 43.52 2.29
774 777 4.219070 AGCAAACATGCTTATGTGACACAT 59.781 37.500 23.83 23.83 43.52 3.21
775 778 3.569277 AGCAAACATGCTTATGTGACACA 59.431 39.130 11.41 11.41 43.52 3.72
776 779 4.164822 AGCAAACATGCTTATGTGACAC 57.835 40.909 0.00 0.00 43.52 3.67
777 780 5.003160 ACTAGCAAACATGCTTATGTGACA 58.997 37.500 8.79 0.00 43.52 3.58
778 781 5.447818 GGACTAGCAAACATGCTTATGTGAC 60.448 44.000 8.79 0.00 43.52 3.67
779 782 4.635765 GGACTAGCAAACATGCTTATGTGA 59.364 41.667 8.79 0.00 43.52 3.58
780 783 4.201950 GGGACTAGCAAACATGCTTATGTG 60.202 45.833 8.79 0.00 43.52 3.21
781 784 3.947834 GGGACTAGCAAACATGCTTATGT 59.052 43.478 8.79 6.15 43.52 2.29
782 785 4.202441 AGGGACTAGCAAACATGCTTATG 58.798 43.478 8.79 3.17 43.52 1.90
783 786 4.510167 AGGGACTAGCAAACATGCTTAT 57.490 40.909 8.79 0.00 43.52 1.73
785 788 2.887151 AGGGACTAGCAAACATGCTT 57.113 45.000 8.79 0.00 43.52 3.91
807 810 7.172019 CGATAGTGGGGTAACATAAATGGTAAC 59.828 40.741 0.00 0.00 36.94 2.50
808 811 7.218614 CGATAGTGGGGTAACATAAATGGTAA 58.781 38.462 0.00 0.00 30.66 2.85
809 812 6.742082 GCGATAGTGGGGTAACATAAATGGTA 60.742 42.308 0.00 0.00 36.77 3.25
810 813 5.617252 CGATAGTGGGGTAACATAAATGGT 58.383 41.667 0.00 0.00 39.74 3.55
811 814 4.454504 GCGATAGTGGGGTAACATAAATGG 59.545 45.833 0.00 0.00 36.77 3.16
812 815 4.454504 GGCGATAGTGGGGTAACATAAATG 59.545 45.833 0.00 0.00 36.77 2.32
813 816 4.103469 TGGCGATAGTGGGGTAACATAAAT 59.897 41.667 0.00 0.00 36.77 1.40
814 817 3.455177 TGGCGATAGTGGGGTAACATAAA 59.545 43.478 0.00 0.00 36.77 1.40
815 818 3.039743 TGGCGATAGTGGGGTAACATAA 58.960 45.455 0.00 0.00 36.77 1.90
816 819 2.631062 CTGGCGATAGTGGGGTAACATA 59.369 50.000 0.00 0.00 36.77 2.29
817 820 1.416401 CTGGCGATAGTGGGGTAACAT 59.584 52.381 0.00 0.00 36.77 2.71
818 821 0.828022 CTGGCGATAGTGGGGTAACA 59.172 55.000 0.00 0.00 36.77 2.41
819 822 0.532196 GCTGGCGATAGTGGGGTAAC 60.532 60.000 0.00 0.00 39.35 2.50
820 823 1.692173 GGCTGGCGATAGTGGGGTAA 61.692 60.000 0.00 0.00 39.35 2.85
821 824 2.138179 GGCTGGCGATAGTGGGGTA 61.138 63.158 0.00 0.00 39.35 3.69
822 825 3.480133 GGCTGGCGATAGTGGGGT 61.480 66.667 0.00 0.00 39.35 4.95
823 826 1.407656 TAAGGCTGGCGATAGTGGGG 61.408 60.000 0.00 0.00 39.35 4.96
824 827 0.034059 CTAAGGCTGGCGATAGTGGG 59.966 60.000 0.00 0.00 39.35 4.61
825 828 0.034059 CCTAAGGCTGGCGATAGTGG 59.966 60.000 13.22 1.92 39.35 4.00
826 829 1.040646 TCCTAAGGCTGGCGATAGTG 58.959 55.000 13.22 7.37 39.35 2.74
827 830 1.041437 GTCCTAAGGCTGGCGATAGT 58.959 55.000 13.22 0.00 39.35 2.12
828 831 1.333177 AGTCCTAAGGCTGGCGATAG 58.667 55.000 9.18 9.18 0.00 2.08
829 832 2.236766 GTAGTCCTAAGGCTGGCGATA 58.763 52.381 0.00 0.00 0.00 2.92
830 833 1.041437 GTAGTCCTAAGGCTGGCGAT 58.959 55.000 0.00 0.00 0.00 4.58
831 834 1.041447 GGTAGTCCTAAGGCTGGCGA 61.041 60.000 0.00 0.00 0.00 5.54
832 835 1.043673 AGGTAGTCCTAAGGCTGGCG 61.044 60.000 0.00 0.00 43.12 5.69
833 836 0.753867 GAGGTAGTCCTAAGGCTGGC 59.246 60.000 0.00 0.00 45.24 4.85
834 837 1.033574 CGAGGTAGTCCTAAGGCTGG 58.966 60.000 0.00 0.00 45.24 4.85
835 838 0.386113 GCGAGGTAGTCCTAAGGCTG 59.614 60.000 0.00 0.00 45.24 4.85
836 839 0.756070 GGCGAGGTAGTCCTAAGGCT 60.756 60.000 0.00 0.00 45.24 4.58
837 840 0.756070 AGGCGAGGTAGTCCTAAGGC 60.756 60.000 0.00 7.36 45.24 4.35
838 841 1.133730 AGAGGCGAGGTAGTCCTAAGG 60.134 57.143 0.00 0.00 45.24 2.69
839 842 1.950909 CAGAGGCGAGGTAGTCCTAAG 59.049 57.143 0.00 0.00 45.24 2.18
1197 1224 4.957684 CGATGCCGATGCCTCGCT 62.958 66.667 5.81 0.00 45.97 4.93
1583 2971 1.747355 CATCCATCCCAGCACTTTGAC 59.253 52.381 0.00 0.00 0.00 3.18
1584 2972 1.956636 GCATCCATCCCAGCACTTTGA 60.957 52.381 0.00 0.00 0.00 2.69
1656 3044 9.809395 AGGAAAAACTAAATTAGCTTTCTAGGT 57.191 29.630 19.09 1.08 34.16 3.08
1749 3137 7.751768 ATAAAATTAAGGGAGTATGCAGAGC 57.248 36.000 0.00 0.00 0.00 4.09
1771 3161 4.715713 ACGACATCACCTGAGTAGCTATA 58.284 43.478 0.00 0.00 0.00 1.31
1799 3189 3.797039 TGACAAGATAGGAATTGGAGCG 58.203 45.455 0.00 0.00 0.00 5.03
1814 3204 5.353938 CCAGGCATATCCAAAATTGACAAG 58.646 41.667 0.00 0.00 37.29 3.16
1973 3948 4.674281 AAAACCCTCTGATATCTCCGTC 57.326 45.455 3.98 0.00 0.00 4.79
2219 5193 8.034804 ACCATCCAAACTGCTATTCAATTTAAC 58.965 33.333 0.00 0.00 0.00 2.01
2254 5228 4.701651 CACATGTTCTAGGATTGGAGCAAA 59.298 41.667 0.00 0.00 0.00 3.68
2256 5231 3.519107 TCACATGTTCTAGGATTGGAGCA 59.481 43.478 0.00 0.00 0.00 4.26
2322 5297 5.301835 ACTTCTTAGCAGTATCCATGCAT 57.698 39.130 0.00 0.00 46.31 3.96
2323 5298 4.760530 ACTTCTTAGCAGTATCCATGCA 57.239 40.909 0.00 0.00 46.31 3.96
2767 6071 2.734492 GCATGAGTTCAAGCTGATTGCC 60.734 50.000 0.00 0.00 44.23 4.52
2966 6270 1.201965 GCAGTAATGACAGCGTTCTGC 60.202 52.381 0.00 0.00 44.10 4.26
3021 6325 0.178068 ATACCAGTAGCCCACAAGCG 59.822 55.000 0.00 0.00 38.01 4.68
3287 6591 1.630369 TCAGGCAGCCTATTGTCTTGT 59.370 47.619 15.64 0.00 28.61 3.16
3326 6630 1.843368 AGGGTGTGCATCAATTCAGG 58.157 50.000 0.00 0.00 0.00 3.86
3328 6632 5.999205 AAATAAGGGTGTGCATCAATTCA 57.001 34.783 0.00 0.00 0.00 2.57
3330 6634 6.437162 AGTGTAAATAAGGGTGTGCATCAATT 59.563 34.615 0.00 0.00 0.00 2.32
3331 6635 5.951747 AGTGTAAATAAGGGTGTGCATCAAT 59.048 36.000 0.00 0.00 0.00 2.57
3334 6638 4.941263 TCAGTGTAAATAAGGGTGTGCATC 59.059 41.667 0.00 0.00 0.00 3.91
3505 7232 9.243637 CTTCACAAATAATCCAACGAAAAGAAA 57.756 29.630 0.00 0.00 0.00 2.52
3528 7255 5.975410 ACGTTTTATATCTGCAGAGCTTC 57.025 39.130 22.96 7.58 0.00 3.86
3854 7648 5.549742 TCAAGCATTTCTTTTGTTCCCAT 57.450 34.783 0.00 0.00 31.27 4.00
3866 8012 5.695851 TTCTTCAGACCTTCAAGCATTTC 57.304 39.130 0.00 0.00 0.00 2.17
3947 8094 0.665298 GCCGAATCCATTTGAGGCTC 59.335 55.000 7.79 7.79 41.21 4.70
3990 8139 3.813724 AGGAGATTTCATGCACATGATCG 59.186 43.478 13.77 0.00 46.12 3.69
3999 8148 1.009829 AACGCGAGGAGATTTCATGC 58.990 50.000 15.93 0.00 0.00 4.06
4058 8243 8.131100 AGTGTTCAATGTGTTCAATGACTTAAG 58.869 33.333 0.00 0.00 33.83 1.85
4061 8246 6.095300 TGAGTGTTCAATGTGTTCAATGACTT 59.905 34.615 0.00 0.00 33.83 3.01
4062 8247 5.589855 TGAGTGTTCAATGTGTTCAATGACT 59.410 36.000 0.00 0.00 33.83 3.41
4287 8477 9.822185 TGGCTGAACATGTATATGTGATATATC 57.178 33.333 5.81 5.73 46.54 1.63
4324 8703 6.541278 TCTTTATGATGCCTGATCAGTTCTTG 59.459 38.462 21.11 6.76 44.54 3.02
4328 8707 7.707624 TTTTCTTTATGATGCCTGATCAGTT 57.292 32.000 21.11 5.90 44.54 3.16
4342 8721 7.010367 TGTGCAAGCAGTTTCTTTTTCTTTATG 59.990 33.333 0.00 0.00 0.00 1.90
4365 8744 8.863049 GGCATTGATTTTACACTAAGATTTGTG 58.137 33.333 5.75 5.75 39.32 3.33
4383 8762 8.886719 CGTACATCTAAATCATATGGCATTGAT 58.113 33.333 4.78 11.75 34.08 2.57
4384 8763 8.093927 TCGTACATCTAAATCATATGGCATTGA 58.906 33.333 4.78 9.89 0.00 2.57
4385 8764 8.255394 TCGTACATCTAAATCATATGGCATTG 57.745 34.615 4.78 4.31 0.00 2.82
4387 8766 9.534565 GTATCGTACATCTAAATCATATGGCAT 57.465 33.333 4.88 4.88 0.00 4.40
4389 8768 9.587772 AAGTATCGTACATCTAAATCATATGGC 57.412 33.333 2.13 0.00 0.00 4.40
4395 8774 9.063615 TGCTCTAAGTATCGTACATCTAAATCA 57.936 33.333 0.00 0.00 0.00 2.57
4397 8776 8.847196 TGTGCTCTAAGTATCGTACATCTAAAT 58.153 33.333 0.00 0.00 0.00 1.40
4408 8787 6.642540 TGCATTTAGATGTGCTCTAAGTATCG 59.357 38.462 0.00 0.00 45.07 2.92


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

AutoCloner maintained by Alex Coulton.