Multiple sequence alignment - TraesCS5A01G309800

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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 TraesCS5A01G309800 chr5A 100.000 4501 0 0 1 4501 522059796 522055296 0.000000e+00 8312.0
1 TraesCS5A01G309800 chr5A 88.060 67 4 4 3684 3747 112312133 112312068 4.830000e-10 76.8
2 TraesCS5A01G309800 chr5D 95.153 1898 57 12 1759 3648 410422051 410420181 0.000000e+00 2963.0
3 TraesCS5A01G309800 chr5D 89.901 1109 72 20 593 1690 410423241 410422162 0.000000e+00 1391.0
4 TraesCS5A01G309800 chr5D 93.072 332 19 3 1 331 410423572 410423244 2.430000e-132 483.0
5 TraesCS5A01G309800 chr5D 79.902 204 32 8 3684 3882 489307161 489306962 1.690000e-29 141.0
6 TraesCS5A01G309800 chr5B 95.831 1823 59 10 1759 3565 492537894 492536073 0.000000e+00 2929.0
7 TraesCS5A01G309800 chr5B 92.147 573 42 3 1119 1690 492538606 492538036 0.000000e+00 806.0
8 TraesCS5A01G309800 chr5B 87.129 505 34 11 590 1087 492539091 492538611 1.100000e-150 544.0
9 TraesCS5A01G309800 chr5B 97.059 136 4 0 199 334 492539223 492539088 3.500000e-56 230.0
10 TraesCS5A01G309800 chr5B 92.857 56 4 0 3692 3747 264838274 264838329 1.040000e-11 82.4
11 TraesCS5A01G309800 chr3A 92.151 637 28 4 3886 4501 703299548 703298913 0.000000e+00 880.0
12 TraesCS5A01G309800 chr3A 94.834 271 14 0 329 599 686900006 686899736 1.500000e-114 424.0
13 TraesCS5A01G309800 chr3A 92.308 195 13 2 3696 3888 703300168 703299974 4.440000e-70 276.0
14 TraesCS5A01G309800 chr3A 88.333 60 4 3 3683 3740 703381982 703382040 8.080000e-08 69.4
15 TraesCS5A01G309800 chr3A 90.000 50 2 3 3700 3747 535176097 535176049 1.350000e-05 62.1
16 TraesCS5A01G309800 chr6B 86.499 637 57 12 3886 4499 544463344 544463974 0.000000e+00 673.0
17 TraesCS5A01G309800 chr6B 94.203 276 12 3 323 594 706113833 706114108 6.960000e-113 418.0
18 TraesCS5A01G309800 chr6B 100.000 31 0 0 3858 3888 544462888 544462918 1.750000e-04 58.4
19 TraesCS5A01G309800 chr3B 94.565 276 13 2 330 603 49226432 49226707 4.160000e-115 425.0
20 TraesCS5A01G309800 chr7B 94.853 272 13 1 328 598 717149511 717149240 1.500000e-114 424.0
21 TraesCS5A01G309800 chr7B 94.853 272 13 1 328 598 717224983 717224712 1.500000e-114 424.0
22 TraesCS5A01G309800 chr4A 95.472 265 12 0 330 594 677437425 677437689 1.500000e-114 424.0
23 TraesCS5A01G309800 chr4A 89.904 208 18 3 3683 3888 586429534 586429740 9.600000e-67 265.0
24 TraesCS5A01G309800 chr4A 93.671 79 4 1 3886 3964 586430165 586430242 2.840000e-22 117.0
25 TraesCS5A01G309800 chr4B 94.815 270 14 0 331 600 416649503 416649234 5.380000e-114 422.0
26 TraesCS5A01G309800 chr1B 96.109 257 10 0 339 595 302760066 302759810 1.940000e-113 420.0
27 TraesCS5A01G309800 chr2B 94.776 268 14 0 333 600 376496764 376497031 6.960000e-113 418.0
28 TraesCS5A01G309800 chr1A 85.714 70 6 4 3681 3747 544043539 544043607 2.250000e-08 71.3


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 TraesCS5A01G309800 chr5A 522055296 522059796 4500 True 8312.000000 8312 100.000000 1 4501 1 chr5A.!!$R2 4500
1 TraesCS5A01G309800 chr5D 410420181 410423572 3391 True 1612.333333 2963 92.708667 1 3648 3 chr5D.!!$R2 3647
2 TraesCS5A01G309800 chr5B 492536073 492539223 3150 True 1127.250000 2929 93.041500 199 3565 4 chr5B.!!$R1 3366
3 TraesCS5A01G309800 chr3A 703298913 703300168 1255 True 578.000000 880 92.229500 3696 4501 2 chr3A.!!$R3 805
4 TraesCS5A01G309800 chr6B 544462888 544463974 1086 False 365.700000 673 93.249500 3858 4499 2 chr6B.!!$F2 641

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
837 842 0.106819 CCAAGAATCTGCCTGGGAGG 60.107 60.0 15.66 0.0 38.8 4.30 F
957 967 0.319727 AAAACCGTATCGTCGCACCA 60.320 50.0 0.00 0.0 0.0 4.17 F
2719 2818 0.247460 TGGCTGTGGATCTCGTTCAG 59.753 55.0 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2423 1.153549 CCAGGCGCTGAAGTAGACC 60.154 63.158 7.64 0.0 32.44 3.85 R
2804 2903 2.252072 GATACTCACCCGCAAGCCCA 62.252 60.000 0.00 0.0 0.00 5.36 R
3692 3808 0.098200 CGCCATTGACGTACTCTCGA 59.902 55.000 0.00 0.0 34.70 4.04 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
44 45 7.312154 CCAATGGTCGATGAAAGAAACATTTA 58.688 34.615 0.00 0.00 30.33 1.40
46 47 8.800972 CAATGGTCGATGAAAGAAACATTTATG 58.199 33.333 0.00 0.00 30.33 1.90
50 51 7.905493 GGTCGATGAAAGAAACATTTATGAGTC 59.095 37.037 0.00 0.00 0.00 3.36
107 108 5.298276 TCTGTTGTCAACTCCACCAAATTAC 59.702 40.000 16.45 0.00 0.00 1.89
117 118 3.130869 TCCACCAAATTACAGATGCATGC 59.869 43.478 11.82 11.82 0.00 4.06
121 122 3.005050 CCAAATTACAGATGCATGCGGAT 59.995 43.478 14.09 0.91 0.00 4.18
126 127 0.321387 CAGATGCATGCGGATAGGCT 60.321 55.000 14.09 0.00 0.00 4.58
146 147 5.074115 GGCTCCATGTAGATGTAGTAGTCT 58.926 45.833 0.00 0.00 0.00 3.24
148 149 6.294286 GGCTCCATGTAGATGTAGTAGTCTTC 60.294 46.154 0.00 0.00 0.00 2.87
219 221 7.549134 TGAACTATATTCTTTGCAGGTGTGTAG 59.451 37.037 0.00 0.00 0.00 2.74
240 242 2.029649 GTCTGTTGCTGGTCGGTTAGTA 60.030 50.000 0.00 0.00 0.00 1.82
333 335 2.901338 AGCTGGACCTGACACTAGTA 57.099 50.000 1.91 0.00 0.00 1.82
334 336 2.448453 AGCTGGACCTGACACTAGTAC 58.552 52.381 1.91 0.00 0.00 2.73
335 337 2.041891 AGCTGGACCTGACACTAGTACT 59.958 50.000 0.00 0.00 0.00 2.73
336 338 2.826725 GCTGGACCTGACACTAGTACTT 59.173 50.000 0.00 0.00 0.00 2.24
337 339 3.258622 GCTGGACCTGACACTAGTACTTT 59.741 47.826 0.00 0.00 0.00 2.66
338 340 4.618693 GCTGGACCTGACACTAGTACTTTC 60.619 50.000 0.00 0.00 0.00 2.62
339 341 4.737578 TGGACCTGACACTAGTACTTTCT 58.262 43.478 0.00 0.00 0.00 2.52
340 342 4.765856 TGGACCTGACACTAGTACTTTCTC 59.234 45.833 0.00 0.00 0.00 2.87
341 343 4.158209 GGACCTGACACTAGTACTTTCTCC 59.842 50.000 0.00 0.00 0.00 3.71
342 344 3.757493 ACCTGACACTAGTACTTTCTCCG 59.243 47.826 0.00 0.00 0.00 4.63
343 345 3.757493 CCTGACACTAGTACTTTCTCCGT 59.243 47.826 0.00 0.00 0.00 4.69
344 346 4.217983 CCTGACACTAGTACTTTCTCCGTT 59.782 45.833 0.00 0.00 0.00 4.44
345 347 5.278858 CCTGACACTAGTACTTTCTCCGTTT 60.279 44.000 0.00 0.00 0.00 3.60
346 348 5.766222 TGACACTAGTACTTTCTCCGTTTC 58.234 41.667 0.00 0.00 0.00 2.78
347 349 5.300034 TGACACTAGTACTTTCTCCGTTTCA 59.700 40.000 0.00 0.00 0.00 2.69
348 350 5.527033 ACACTAGTACTTTCTCCGTTTCAC 58.473 41.667 0.00 0.00 0.00 3.18
349 351 5.068198 ACACTAGTACTTTCTCCGTTTCACA 59.932 40.000 0.00 0.00 0.00 3.58
350 352 5.981315 CACTAGTACTTTCTCCGTTTCACAA 59.019 40.000 0.00 0.00 0.00 3.33
351 353 6.645415 CACTAGTACTTTCTCCGTTTCACAAT 59.355 38.462 0.00 0.00 0.00 2.71
352 354 5.924475 AGTACTTTCTCCGTTTCACAATG 57.076 39.130 0.00 0.00 0.00 2.82
353 355 5.365619 AGTACTTTCTCCGTTTCACAATGT 58.634 37.500 0.00 0.00 0.00 2.71
354 356 6.518493 AGTACTTTCTCCGTTTCACAATGTA 58.482 36.000 0.00 0.00 0.00 2.29
355 357 5.924475 ACTTTCTCCGTTTCACAATGTAG 57.076 39.130 0.00 0.00 0.00 2.74
356 358 4.213482 ACTTTCTCCGTTTCACAATGTAGC 59.787 41.667 0.00 0.00 0.00 3.58
357 359 2.333926 TCTCCGTTTCACAATGTAGCG 58.666 47.619 0.00 0.00 0.00 4.26
358 360 0.793861 TCCGTTTCACAATGTAGCGC 59.206 50.000 0.00 0.00 0.00 5.92
359 361 0.515127 CCGTTTCACAATGTAGCGCA 59.485 50.000 11.47 0.00 0.00 6.09
360 362 1.130373 CCGTTTCACAATGTAGCGCAT 59.870 47.619 11.47 0.00 40.03 4.73
361 363 2.350192 CCGTTTCACAATGTAGCGCATA 59.650 45.455 11.47 0.00 36.67 3.14
362 364 3.002246 CCGTTTCACAATGTAGCGCATAT 59.998 43.478 11.47 0.00 36.67 1.78
363 365 4.210328 CCGTTTCACAATGTAGCGCATATA 59.790 41.667 11.47 0.00 36.67 0.86
364 366 5.107104 CCGTTTCACAATGTAGCGCATATAT 60.107 40.000 11.47 0.00 36.67 0.86
365 367 6.090223 CCGTTTCACAATGTAGCGCATATATA 59.910 38.462 11.47 0.00 36.67 0.86
366 368 7.201522 CCGTTTCACAATGTAGCGCATATATAT 60.202 37.037 11.47 0.00 36.67 0.86
367 369 8.168626 CGTTTCACAATGTAGCGCATATATATT 58.831 33.333 11.47 0.31 36.67 1.28
368 370 9.825972 GTTTCACAATGTAGCGCATATATATTT 57.174 29.630 11.47 0.00 36.67 1.40
404 406 9.495572 TCAAACTTTGTAAAATTTGACCAAGTT 57.504 25.926 23.22 23.22 41.01 2.66
407 409 8.840833 ACTTTGTAAAATTTGACCAAGTTTGT 57.159 26.923 16.11 0.00 29.79 2.83
408 410 9.930693 ACTTTGTAAAATTTGACCAAGTTTGTA 57.069 25.926 16.11 0.00 29.79 2.41
411 413 9.796120 TTGTAAAATTTGACCAAGTTTGTAGAG 57.204 29.630 3.10 0.00 31.87 2.43
412 414 9.179909 TGTAAAATTTGACCAAGTTTGTAGAGA 57.820 29.630 3.10 0.00 31.87 3.10
415 417 9.936759 AAAATTTGACCAAGTTTGTAGAGAAAA 57.063 25.926 4.40 0.00 31.87 2.29
417 419 9.750125 AATTTGACCAAGTTTGTAGAGAAAATC 57.250 29.630 0.00 0.00 0.00 2.17
418 420 7.873719 TTGACCAAGTTTGTAGAGAAAATCA 57.126 32.000 0.00 0.00 0.00 2.57
419 421 8.463930 TTGACCAAGTTTGTAGAGAAAATCAT 57.536 30.769 0.00 0.00 0.00 2.45
420 422 9.567776 TTGACCAAGTTTGTAGAGAAAATCATA 57.432 29.630 0.00 0.00 0.00 2.15
421 423 9.739276 TGACCAAGTTTGTAGAGAAAATCATAT 57.261 29.630 0.00 0.00 0.00 1.78
447 449 8.383318 ACATCTAGAATACCAAATACATGTGC 57.617 34.615 9.11 0.00 0.00 4.57
448 450 8.213679 ACATCTAGAATACCAAATACATGTGCT 58.786 33.333 9.11 0.00 0.00 4.40
449 451 9.060347 CATCTAGAATACCAAATACATGTGCTT 57.940 33.333 9.11 0.00 0.00 3.91
451 453 9.764363 TCTAGAATACCAAATACATGTGCTTAG 57.236 33.333 9.11 0.00 0.00 2.18
452 454 9.764363 CTAGAATACCAAATACATGTGCTTAGA 57.236 33.333 9.11 0.00 0.00 2.10
456 458 9.845740 AATACCAAATACATGTGCTTAGATACA 57.154 29.630 9.11 0.00 0.00 2.29
458 460 8.383318 ACCAAATACATGTGCTTAGATACATC 57.617 34.615 9.11 0.00 35.46 3.06
459 461 7.992608 ACCAAATACATGTGCTTAGATACATCA 59.007 33.333 9.11 0.00 35.46 3.07
460 462 8.285394 CCAAATACATGTGCTTAGATACATCAC 58.715 37.037 9.11 0.00 35.46 3.06
461 463 8.829612 CAAATACATGTGCTTAGATACATCACA 58.170 33.333 9.11 0.00 41.18 3.58
462 464 8.962884 AATACATGTGCTTAGATACATCACAA 57.037 30.769 9.11 0.00 40.46 3.33
463 465 6.915544 ACATGTGCTTAGATACATCACAAG 57.084 37.500 0.00 0.00 40.46 3.16
464 466 6.643388 ACATGTGCTTAGATACATCACAAGA 58.357 36.000 0.00 0.00 40.46 3.02
465 467 6.536582 ACATGTGCTTAGATACATCACAAGAC 59.463 38.462 0.00 4.73 40.46 3.01
466 468 6.036577 TGTGCTTAGATACATCACAAGACA 57.963 37.500 7.43 6.40 35.08 3.41
467 469 6.643388 TGTGCTTAGATACATCACAAGACAT 58.357 36.000 7.43 0.00 35.08 3.06
468 470 7.781056 TGTGCTTAGATACATCACAAGACATA 58.219 34.615 7.43 2.88 35.08 2.29
469 471 7.706607 TGTGCTTAGATACATCACAAGACATAC 59.293 37.037 7.43 0.00 35.08 2.39
470 472 7.923344 GTGCTTAGATACATCACAAGACATACT 59.077 37.037 7.43 0.00 0.00 2.12
471 473 8.478066 TGCTTAGATACATCACAAGACATACTT 58.522 33.333 7.43 0.00 39.70 2.24
472 474 9.319143 GCTTAGATACATCACAAGACATACTTT 57.681 33.333 7.43 0.00 36.61 2.66
568 570 8.948853 TTGACTTTGTAGAAAATCTAAATGCG 57.051 30.769 0.00 0.00 29.58 4.73
569 571 7.021196 TGACTTTGTAGAAAATCTAAATGCGC 58.979 34.615 0.00 0.00 29.58 6.09
570 572 7.094805 TGACTTTGTAGAAAATCTAAATGCGCT 60.095 33.333 9.73 0.00 29.58 5.92
571 573 8.263940 ACTTTGTAGAAAATCTAAATGCGCTA 57.736 30.769 9.73 0.00 29.58 4.26
572 574 8.893727 ACTTTGTAGAAAATCTAAATGCGCTAT 58.106 29.630 9.73 0.00 29.58 2.97
583 585 7.520119 TCTAAATGCGCTATATTATGGAACG 57.480 36.000 9.73 0.00 0.00 3.95
584 586 5.545658 AAATGCGCTATATTATGGAACGG 57.454 39.130 9.73 0.00 0.00 4.44
585 587 3.945981 TGCGCTATATTATGGAACGGA 57.054 42.857 9.73 0.00 0.00 4.69
586 588 3.845178 TGCGCTATATTATGGAACGGAG 58.155 45.455 9.73 0.00 0.00 4.63
587 589 3.187700 GCGCTATATTATGGAACGGAGG 58.812 50.000 0.00 0.00 0.00 4.30
588 590 3.782046 CGCTATATTATGGAACGGAGGG 58.218 50.000 0.00 0.00 0.00 4.30
589 591 3.446161 CGCTATATTATGGAACGGAGGGA 59.554 47.826 0.00 0.00 0.00 4.20
590 592 4.440250 CGCTATATTATGGAACGGAGGGAG 60.440 50.000 0.00 0.00 0.00 4.30
591 593 4.466726 GCTATATTATGGAACGGAGGGAGT 59.533 45.833 0.00 0.00 0.00 3.85
602 604 6.126594 TGGAACGGAGGGAGTATGATTTAATT 60.127 38.462 0.00 0.00 0.00 1.40
658 663 6.704289 AATACATATGCAATTGTCTGCTGT 57.296 33.333 7.40 7.50 43.07 4.40
691 696 5.525378 GCGTATCAAACTTGATCTCCATCTT 59.475 40.000 8.19 0.00 44.17 2.40
692 697 6.510799 GCGTATCAAACTTGATCTCCATCTTG 60.511 42.308 8.19 0.00 44.17 3.02
719 724 3.635373 AGCATGGATTTATTCAGCACTGG 59.365 43.478 0.00 0.00 0.00 4.00
734 739 6.711277 TCAGCACTGGTTAATAATCAGTTCT 58.289 36.000 15.62 13.59 39.43 3.01
788 793 9.522804 GGAAAGCTATATATACTGAGCACATAC 57.477 37.037 13.02 0.44 37.40 2.39
806 811 1.952621 ACTAGTAGCACACCACCCAT 58.047 50.000 0.00 0.00 0.00 4.00
808 813 1.139058 CTAGTAGCACACCACCCATCC 59.861 57.143 0.00 0.00 0.00 3.51
810 815 0.255890 GTAGCACACCACCCATCCAT 59.744 55.000 0.00 0.00 0.00 3.41
825 830 5.672194 ACCCATCCATCTTACTACCAAGAAT 59.328 40.000 0.00 0.00 38.03 2.40
826 831 6.183361 ACCCATCCATCTTACTACCAAGAATC 60.183 42.308 0.00 0.00 38.03 2.52
827 832 6.043706 CCCATCCATCTTACTACCAAGAATCT 59.956 42.308 0.00 0.00 38.03 2.40
828 833 6.933521 CCATCCATCTTACTACCAAGAATCTG 59.066 42.308 0.00 0.00 38.03 2.90
829 834 5.918608 TCCATCTTACTACCAAGAATCTGC 58.081 41.667 0.00 0.00 38.03 4.26
830 835 5.059833 CCATCTTACTACCAAGAATCTGCC 58.940 45.833 0.00 0.00 38.03 4.85
831 836 5.163258 CCATCTTACTACCAAGAATCTGCCT 60.163 44.000 0.00 0.00 38.03 4.75
832 837 5.344743 TCTTACTACCAAGAATCTGCCTG 57.655 43.478 0.00 0.00 31.63 4.85
833 838 4.162320 TCTTACTACCAAGAATCTGCCTGG 59.838 45.833 0.00 0.00 31.63 4.45
834 839 1.561542 ACTACCAAGAATCTGCCTGGG 59.438 52.381 4.66 0.00 0.00 4.45
835 840 1.839994 CTACCAAGAATCTGCCTGGGA 59.160 52.381 4.66 0.00 0.00 4.37
836 841 0.622665 ACCAAGAATCTGCCTGGGAG 59.377 55.000 9.21 9.21 0.00 4.30
837 842 0.106819 CCAAGAATCTGCCTGGGAGG 60.107 60.000 15.66 0.00 38.80 4.30
838 843 0.914644 CAAGAATCTGCCTGGGAGGA 59.085 55.000 15.66 2.71 37.67 3.71
839 844 1.134159 CAAGAATCTGCCTGGGAGGAG 60.134 57.143 15.66 0.00 37.67 3.69
840 845 1.148048 GAATCTGCCTGGGAGGAGC 59.852 63.158 15.66 1.15 37.67 4.70
841 846 2.336484 GAATCTGCCTGGGAGGAGCC 62.336 65.000 15.66 0.00 37.67 4.70
857 862 3.782523 AGGAGCCCAAGAACTAATCATCA 59.217 43.478 0.00 0.00 0.00 3.07
859 864 3.549794 AGCCCAAGAACTAATCATCAGC 58.450 45.455 0.00 0.00 0.00 4.26
890 895 2.335681 TCCTGGTATGGTTCACCTCA 57.664 50.000 0.00 0.00 36.96 3.86
957 967 0.319727 AAAACCGTATCGTCGCACCA 60.320 50.000 0.00 0.00 0.00 4.17
982 992 2.426024 GGTGTGCTCGTCTTATAGGTCA 59.574 50.000 0.00 0.00 0.00 4.02
993 1003 6.827251 TCGTCTTATAGGTCATCTTACACTGT 59.173 38.462 0.00 0.00 0.00 3.55
1036 1047 4.500887 CCAAGAAACTAACGACAGACCAGA 60.501 45.833 0.00 0.00 0.00 3.86
1041 1052 2.163815 ACTAACGACAGACCAGATTCCG 59.836 50.000 0.00 0.00 0.00 4.30
1089 1101 7.928307 TTTCCTCATTTTCTGATCAACTAGG 57.072 36.000 0.00 0.00 32.10 3.02
1092 1104 7.865820 TCCTCATTTTCTGATCAACTAGGATT 58.134 34.615 0.00 0.00 32.10 3.01
1093 1105 7.772292 TCCTCATTTTCTGATCAACTAGGATTG 59.228 37.037 0.00 0.00 32.10 2.67
1094 1106 7.325660 TCATTTTCTGATCAACTAGGATTGC 57.674 36.000 0.00 0.00 0.00 3.56
1098 1110 3.389329 TCTGATCAACTAGGATTGCCTCC 59.611 47.826 0.00 0.00 45.54 4.30
1141 1153 5.947228 TTTCAGTCCTGATGAAACATCAC 57.053 39.130 9.88 2.47 40.72 3.06
1220 1232 1.443872 GGTGTACACGGAGCAGACG 60.444 63.158 19.41 0.00 37.36 4.18
1269 1281 6.316390 ACGTGTTCTGAAAGATTTCTCAAAGT 59.684 34.615 6.84 3.50 46.36 2.66
1274 1286 6.963796 TCTGAAAGATTTCTCAAAGTTGCTC 58.036 36.000 6.84 0.00 38.67 4.26
1302 1314 3.119101 TGAGGTTCCAACTTCTCGATAGC 60.119 47.826 3.53 0.00 36.15 2.97
1336 1348 4.044426 CACGCGTCATGAATCTCTCATTA 58.956 43.478 9.86 0.00 42.46 1.90
1363 1376 2.762535 TCTCATGTCGTTCCCCTTTC 57.237 50.000 0.00 0.00 0.00 2.62
1367 1380 3.821033 CTCATGTCGTTCCCCTTTCTTTT 59.179 43.478 0.00 0.00 0.00 2.27
1386 1399 9.784531 TTTCTTTTCAGATTGAGAAGATAGTGT 57.215 29.630 11.37 0.00 43.95 3.55
1466 1479 2.125512 GCGGTGCTCGAGGACATT 60.126 61.111 33.73 0.00 42.43 2.71
1475 1488 1.751351 CTCGAGGACATTCCACTGCTA 59.249 52.381 3.91 0.00 39.61 3.49
1559 1572 0.793478 AGTTCGTCGATCTCAACGCG 60.793 55.000 3.53 3.53 38.72 6.01
1668 1681 1.473258 CTACTCTCAGCTCCAGCAGT 58.527 55.000 0.48 0.00 45.16 4.40
1699 1716 1.143889 TGTGGTGAGTTGGCCAACATA 59.856 47.619 41.88 29.80 43.47 2.29
1701 1718 3.009584 TGTGGTGAGTTGGCCAACATATA 59.990 43.478 41.88 25.31 43.47 0.86
1704 1721 4.165950 TGGTGAGTTGGCCAACATATATCT 59.834 41.667 41.88 24.80 43.47 1.98
1707 1724 4.165950 TGAGTTGGCCAACATATATCTGGT 59.834 41.667 41.88 22.70 43.47 4.00
1710 1727 5.594317 AGTTGGCCAACATATATCTGGTTTC 59.406 40.000 41.88 16.09 43.47 2.78
1711 1728 5.122707 TGGCCAACATATATCTGGTTTCA 57.877 39.130 0.61 5.99 32.46 2.69
1712 1729 5.514169 TGGCCAACATATATCTGGTTTCAA 58.486 37.500 0.61 0.00 32.46 2.69
1714 1731 6.438741 TGGCCAACATATATCTGGTTTCAAAA 59.561 34.615 0.61 0.00 32.46 2.44
1717 1734 8.819974 GCCAACATATATCTGGTTTCAAAATTG 58.180 33.333 10.69 0.00 32.46 2.32
1773 1859 9.859427 TTTCATTCGAGCATTTGAATTTTAGAT 57.141 25.926 0.00 0.00 35.63 1.98
1774 1860 9.507280 TTCATTCGAGCATTTGAATTTTAGATC 57.493 29.630 0.00 0.00 35.63 2.75
1805 1891 2.766263 TGAGTAGGGTATTGGAGCTGTG 59.234 50.000 0.00 0.00 0.00 3.66
1913 1999 3.214328 TCCAAAGGTTCTTCAGTCTTGC 58.786 45.455 0.00 0.00 0.00 4.01
1935 2021 5.470098 TGCGCTTTCTCTTTTCAGTAGAAAT 59.530 36.000 9.73 0.00 42.90 2.17
1945 2031 8.287439 TCTTTTCAGTAGAAATCCACAAACAA 57.713 30.769 0.00 0.00 42.90 2.83
1947 2033 8.696410 TTTTCAGTAGAAATCCACAAACAAAC 57.304 30.769 0.00 0.00 42.90 2.93
1948 2034 7.639113 TTCAGTAGAAATCCACAAACAAACT 57.361 32.000 0.00 0.00 0.00 2.66
2543 2642 2.447379 AGGATCCGGATGCAGGCT 60.447 61.111 33.93 13.80 0.00 4.58
2675 2774 3.736224 CCTGGCTGGGTCATGGCT 61.736 66.667 1.84 0.00 0.00 4.75
2676 2775 2.124403 CTGGCTGGGTCATGGCTC 60.124 66.667 0.00 0.00 0.00 4.70
2719 2818 0.247460 TGGCTGTGGATCTCGTTCAG 59.753 55.000 0.00 0.00 0.00 3.02
2759 2858 2.126031 GACGAGGAAGGTCACCGC 60.126 66.667 0.00 0.00 34.56 5.68
2804 2903 2.037772 CAGCTTAGGATACCGGAAGCAT 59.962 50.000 21.28 7.47 44.28 3.79
2819 2918 3.136123 CATGGGCTTGCGGGTGAG 61.136 66.667 0.00 0.00 0.00 3.51
2822 2921 1.635817 ATGGGCTTGCGGGTGAGTAT 61.636 55.000 0.00 0.00 0.00 2.12
2973 3072 1.280133 TGCTCAAGTTCTCCATGGAGG 59.720 52.381 35.95 22.11 42.20 4.30
2990 3089 2.574399 GTCCTGCTGTCGGAGTCC 59.426 66.667 0.00 0.00 0.00 3.85
3083 3182 2.045926 GTGCTCCCCATCAACGCT 60.046 61.111 0.00 0.00 0.00 5.07
3509 3608 1.068434 CTCTTCTACTAGCCAGCCAGC 59.932 57.143 0.00 0.00 0.00 4.85
3510 3609 0.105778 CTTCTACTAGCCAGCCAGCC 59.894 60.000 0.00 0.00 0.00 4.85
3511 3610 0.617535 TTCTACTAGCCAGCCAGCCA 60.618 55.000 0.00 0.00 0.00 4.75
3578 3694 1.065851 TGTTTGTGACTCGCGAGTGTA 59.934 47.619 43.61 28.97 42.66 2.90
3589 3705 1.801913 CGAGTGTAGGCGTGTGCTC 60.802 63.158 0.00 0.00 42.25 4.26
3656 3772 3.406361 GGTGCGTCACAGCGTCAG 61.406 66.667 11.20 0.00 40.67 3.51
3657 3773 4.064491 GTGCGTCACAGCGTCAGC 62.064 66.667 5.30 0.00 45.58 4.26
3669 3785 2.927553 GCGTCAGCTTGGATTCATTT 57.072 45.000 0.00 0.00 41.01 2.32
3670 3786 3.221964 GCGTCAGCTTGGATTCATTTT 57.778 42.857 0.00 0.00 41.01 1.82
3671 3787 2.919229 GCGTCAGCTTGGATTCATTTTG 59.081 45.455 0.00 0.00 41.01 2.44
3672 3788 2.919229 CGTCAGCTTGGATTCATTTTGC 59.081 45.455 0.00 0.00 0.00 3.68
3673 3789 3.612241 CGTCAGCTTGGATTCATTTTGCA 60.612 43.478 0.00 0.00 0.00 4.08
3674 3790 3.924686 GTCAGCTTGGATTCATTTTGCAG 59.075 43.478 0.00 0.00 0.00 4.41
3675 3791 2.671396 CAGCTTGGATTCATTTTGCAGC 59.329 45.455 0.00 0.00 0.00 5.25
3676 3792 1.657094 GCTTGGATTCATTTTGCAGCG 59.343 47.619 0.00 0.00 0.00 5.18
3677 3793 2.671914 GCTTGGATTCATTTTGCAGCGA 60.672 45.455 0.00 0.00 0.00 4.93
3678 3794 3.777478 CTTGGATTCATTTTGCAGCGAT 58.223 40.909 0.00 0.00 0.00 4.58
3679 3795 3.153676 TGGATTCATTTTGCAGCGATG 57.846 42.857 0.00 0.00 0.00 3.84
3680 3796 2.492881 TGGATTCATTTTGCAGCGATGT 59.507 40.909 1.22 0.00 0.00 3.06
3681 3797 3.111098 GGATTCATTTTGCAGCGATGTC 58.889 45.455 1.22 0.00 0.00 3.06
3682 3798 3.181493 GGATTCATTTTGCAGCGATGTCT 60.181 43.478 1.22 0.00 0.00 3.41
3683 3799 3.921119 TTCATTTTGCAGCGATGTCTT 57.079 38.095 1.22 0.00 0.00 3.01
3684 3800 3.921119 TCATTTTGCAGCGATGTCTTT 57.079 38.095 1.22 0.00 0.00 2.52
3685 3801 4.241590 TCATTTTGCAGCGATGTCTTTT 57.758 36.364 1.22 0.00 0.00 2.27
3686 3802 4.619973 TCATTTTGCAGCGATGTCTTTTT 58.380 34.783 1.22 0.00 0.00 1.94
3714 3830 2.286831 CGAGAGTACGTCAATGGCGTAT 60.287 50.000 22.98 11.99 44.83 3.06
3823 3941 5.940470 CACTCCAATTACAAAGCCTACTCTT 59.060 40.000 0.00 0.00 0.00 2.85
3844 3962 7.390718 ACTCTTTCACAAATCTATTTAACGCCT 59.609 33.333 0.00 0.00 0.00 5.52
3855 3973 2.088950 TTAACGCCTCAGCACCTAAC 57.911 50.000 0.00 0.00 39.83 2.34
3856 3974 0.970640 TAACGCCTCAGCACCTAACA 59.029 50.000 0.00 0.00 39.83 2.41
3901 4447 2.114616 CAGACATAAGGCACCCTCTCT 58.885 52.381 0.00 0.00 30.89 3.10
3909 4455 2.403561 AGGCACCCTCTCTAATCCTTC 58.596 52.381 0.00 0.00 0.00 3.46
3945 4491 0.246635 ACAGAGCGAGCCGTGTATTT 59.753 50.000 0.00 0.00 0.00 1.40
4033 4579 1.337167 GGCATGGCAAAGGTGAAGAAC 60.337 52.381 15.47 0.00 0.00 3.01
4046 4604 2.097056 GTGAAGAACCGTAAACGTGAGC 60.097 50.000 1.41 0.00 37.74 4.26
4063 4621 0.339859 AGCTCACCCTCCACATCCTA 59.660 55.000 0.00 0.00 0.00 2.94
4133 4700 2.421424 GTCCACCATGTCAAGAATGAGC 59.579 50.000 0.00 0.00 35.88 4.26
4238 4807 4.241681 TGACCAAACTGTCAAAAACTTGC 58.758 39.130 0.00 0.00 42.06 4.01
4242 4811 5.046950 ACCAAACTGTCAAAAACTTGCCTTA 60.047 36.000 0.00 0.00 0.00 2.69
4271 4840 9.812347 TCCTTATCCACTATCATATGCAAATTT 57.188 29.630 0.00 0.00 0.00 1.82
4321 4890 1.656587 AGCCACTCCCATCTAACACA 58.343 50.000 0.00 0.00 0.00 3.72
4365 4934 1.484653 GGTTTTTGACACCAAGCCCTT 59.515 47.619 0.00 0.00 34.04 3.95
4366 4935 2.093181 GGTTTTTGACACCAAGCCCTTT 60.093 45.455 0.00 0.00 34.04 3.11
4404 4973 4.165180 TGCAAATAGTATCCCAAGCCACTA 59.835 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.760092 CGACCATTGGGGATTGACAATT 59.240 45.455 7.78 0.00 41.15 2.32
16 17 1.912731 TCTTTCATCGACCATTGGGGA 59.087 47.619 7.78 4.42 41.15 4.81
107 108 0.321387 AGCCTATCCGCATGCATCTG 60.321 55.000 19.57 0.26 0.00 2.90
121 122 6.044520 AGACTACTACATCTACATGGAGCCTA 59.955 42.308 0.00 0.00 44.26 3.93
126 127 6.589135 TCGAAGACTACTACATCTACATGGA 58.411 40.000 0.00 0.00 33.82 3.41
146 147 8.710835 TCTTTTGCTACATACATAATGTCGAA 57.289 30.769 0.00 0.00 46.15 3.71
148 149 9.767684 TTTTCTTTTGCTACATACATAATGTCG 57.232 29.630 0.00 0.00 46.15 4.35
194 196 6.743575 ACACACCTGCAAAGAATATAGTTC 57.256 37.500 0.00 0.00 0.00 3.01
196 198 6.947464 ACTACACACCTGCAAAGAATATAGT 58.053 36.000 0.00 0.00 0.00 2.12
219 221 1.270147 ACTAACCGACCAGCAACAGAC 60.270 52.381 0.00 0.00 0.00 3.51
240 242 7.565190 TCATCCTATTGAGAAATAGCCATCT 57.435 36.000 0.80 0.00 32.69 2.90
333 335 4.213482 GCTACATTGTGAAACGGAGAAAGT 59.787 41.667 0.00 0.00 42.39 2.66
334 336 4.666655 CGCTACATTGTGAAACGGAGAAAG 60.667 45.833 0.00 0.00 42.39 2.62
335 337 3.185594 CGCTACATTGTGAAACGGAGAAA 59.814 43.478 0.00 0.00 42.39 2.52
336 338 2.734606 CGCTACATTGTGAAACGGAGAA 59.265 45.455 0.00 0.00 42.39 2.87
337 339 2.333926 CGCTACATTGTGAAACGGAGA 58.666 47.619 0.00 0.00 42.39 3.71
338 340 1.201921 GCGCTACATTGTGAAACGGAG 60.202 52.381 0.00 0.00 42.39 4.63
339 341 0.793861 GCGCTACATTGTGAAACGGA 59.206 50.000 0.00 0.00 42.39 4.69
340 342 0.515127 TGCGCTACATTGTGAAACGG 59.485 50.000 9.73 0.00 42.39 4.44
341 343 2.525750 ATGCGCTACATTGTGAAACG 57.474 45.000 9.73 0.00 42.39 3.60
342 344 9.825972 AAATATATATGCGCTACATTGTGAAAC 57.174 29.630 9.73 0.00 40.38 2.78
378 380 9.495572 AACTTGGTCAAATTTTACAAAGTTTGA 57.504 25.926 23.51 16.68 43.94 2.69
381 383 9.278978 ACAAACTTGGTCAAATTTTACAAAGTT 57.721 25.926 23.51 23.51 46.81 2.66
382 384 8.840833 ACAAACTTGGTCAAATTTTACAAAGT 57.159 26.923 16.34 16.34 40.77 2.66
385 387 9.796120 CTCTACAAACTTGGTCAAATTTTACAA 57.204 29.630 4.96 2.61 0.00 2.41
386 388 9.179909 TCTCTACAAACTTGGTCAAATTTTACA 57.820 29.630 4.96 0.00 0.00 2.41
389 391 9.936759 TTTTCTCTACAAACTTGGTCAAATTTT 57.063 25.926 0.00 0.00 0.00 1.82
391 393 9.750125 GATTTTCTCTACAAACTTGGTCAAATT 57.250 29.630 0.00 0.00 0.00 1.82
392 394 8.912988 TGATTTTCTCTACAAACTTGGTCAAAT 58.087 29.630 0.00 0.00 0.00 2.32
393 395 8.287439 TGATTTTCTCTACAAACTTGGTCAAA 57.713 30.769 0.00 0.00 0.00 2.69
394 396 7.873719 TGATTTTCTCTACAAACTTGGTCAA 57.126 32.000 0.00 0.00 0.00 3.18
395 397 9.739276 ATATGATTTTCTCTACAAACTTGGTCA 57.261 29.630 0.00 0.00 0.00 4.02
421 423 9.489084 GCACATGTATTTGGTATTCTAGATGTA 57.511 33.333 0.00 0.00 29.88 2.29
422 424 8.213679 AGCACATGTATTTGGTATTCTAGATGT 58.786 33.333 0.00 0.00 30.73 3.06
423 425 8.613060 AGCACATGTATTTGGTATTCTAGATG 57.387 34.615 0.00 0.00 0.00 2.90
425 427 9.764363 CTAAGCACATGTATTTGGTATTCTAGA 57.236 33.333 0.00 0.00 0.00 2.43
426 428 9.764363 TCTAAGCACATGTATTTGGTATTCTAG 57.236 33.333 0.00 0.00 0.00 2.43
430 432 9.845740 TGTATCTAAGCACATGTATTTGGTATT 57.154 29.630 0.00 0.00 0.00 1.89
432 434 9.489084 GATGTATCTAAGCACATGTATTTGGTA 57.511 33.333 0.00 0.00 35.55 3.25
433 435 7.992608 TGATGTATCTAAGCACATGTATTTGGT 59.007 33.333 0.00 0.00 35.55 3.67
434 436 8.285394 GTGATGTATCTAAGCACATGTATTTGG 58.715 37.037 0.00 0.00 35.55 3.28
435 437 8.829612 TGTGATGTATCTAAGCACATGTATTTG 58.170 33.333 0.00 0.00 35.55 2.32
436 438 8.962884 TGTGATGTATCTAAGCACATGTATTT 57.037 30.769 0.00 0.00 35.55 1.40
437 439 8.962884 TTGTGATGTATCTAAGCACATGTATT 57.037 30.769 0.00 0.00 39.00 1.89
438 440 8.424133 TCTTGTGATGTATCTAAGCACATGTAT 58.576 33.333 0.00 0.00 39.00 2.29
439 441 7.706607 GTCTTGTGATGTATCTAAGCACATGTA 59.293 37.037 0.00 0.00 39.00 2.29
440 442 6.536582 GTCTTGTGATGTATCTAAGCACATGT 59.463 38.462 0.00 0.00 39.00 3.21
441 443 6.536224 TGTCTTGTGATGTATCTAAGCACATG 59.464 38.462 0.00 0.00 39.00 3.21
442 444 6.643388 TGTCTTGTGATGTATCTAAGCACAT 58.357 36.000 0.00 0.00 39.00 3.21
443 445 6.036577 TGTCTTGTGATGTATCTAAGCACA 57.963 37.500 0.00 0.00 37.66 4.57
444 446 7.923344 AGTATGTCTTGTGATGTATCTAAGCAC 59.077 37.037 0.00 0.00 0.00 4.40
445 447 8.011844 AGTATGTCTTGTGATGTATCTAAGCA 57.988 34.615 0.00 0.00 0.00 3.91
446 448 8.879342 AAGTATGTCTTGTGATGTATCTAAGC 57.121 34.615 0.00 0.00 34.77 3.09
542 544 9.393249 CGCATTTAGATTTTCTACAAAGTCAAA 57.607 29.630 0.00 0.00 32.03 2.69
543 545 7.537306 GCGCATTTAGATTTTCTACAAAGTCAA 59.463 33.333 0.30 0.00 32.03 3.18
544 546 7.021196 GCGCATTTAGATTTTCTACAAAGTCA 58.979 34.615 0.30 0.00 32.03 3.41
545 547 7.244192 AGCGCATTTAGATTTTCTACAAAGTC 58.756 34.615 11.47 0.00 0.00 3.01
546 548 7.145932 AGCGCATTTAGATTTTCTACAAAGT 57.854 32.000 11.47 0.00 0.00 2.66
557 559 8.604035 CGTTCCATAATATAGCGCATTTAGATT 58.396 33.333 11.47 5.18 0.00 2.40
558 560 7.224753 CCGTTCCATAATATAGCGCATTTAGAT 59.775 37.037 11.47 0.00 0.00 1.98
559 561 6.533723 CCGTTCCATAATATAGCGCATTTAGA 59.466 38.462 11.47 0.00 0.00 2.10
560 562 6.533723 TCCGTTCCATAATATAGCGCATTTAG 59.466 38.462 11.47 0.00 0.00 1.85
561 563 6.399743 TCCGTTCCATAATATAGCGCATTTA 58.600 36.000 11.47 1.79 0.00 1.40
562 564 5.242434 TCCGTTCCATAATATAGCGCATTT 58.758 37.500 11.47 0.00 0.00 2.32
563 565 4.827692 TCCGTTCCATAATATAGCGCATT 58.172 39.130 11.47 2.98 0.00 3.56
564 566 4.433615 CTCCGTTCCATAATATAGCGCAT 58.566 43.478 11.47 3.63 0.00 4.73
565 567 3.368013 CCTCCGTTCCATAATATAGCGCA 60.368 47.826 11.47 0.00 0.00 6.09
566 568 3.187700 CCTCCGTTCCATAATATAGCGC 58.812 50.000 0.00 0.00 0.00 5.92
567 569 3.446161 TCCCTCCGTTCCATAATATAGCG 59.554 47.826 0.00 0.00 0.00 4.26
568 570 4.466726 ACTCCCTCCGTTCCATAATATAGC 59.533 45.833 0.00 0.00 0.00 2.97
569 571 7.560262 TCATACTCCCTCCGTTCCATAATATAG 59.440 40.741 0.00 0.00 0.00 1.31
570 572 7.415908 TCATACTCCCTCCGTTCCATAATATA 58.584 38.462 0.00 0.00 0.00 0.86
571 573 6.261435 TCATACTCCCTCCGTTCCATAATAT 58.739 40.000 0.00 0.00 0.00 1.28
572 574 5.647230 TCATACTCCCTCCGTTCCATAATA 58.353 41.667 0.00 0.00 0.00 0.98
573 575 4.489737 TCATACTCCCTCCGTTCCATAAT 58.510 43.478 0.00 0.00 0.00 1.28
574 576 3.918566 TCATACTCCCTCCGTTCCATAA 58.081 45.455 0.00 0.00 0.00 1.90
575 577 3.605726 TCATACTCCCTCCGTTCCATA 57.394 47.619 0.00 0.00 0.00 2.74
576 578 2.471815 TCATACTCCCTCCGTTCCAT 57.528 50.000 0.00 0.00 0.00 3.41
577 579 2.471815 ATCATACTCCCTCCGTTCCA 57.528 50.000 0.00 0.00 0.00 3.53
578 580 3.840124 AAATCATACTCCCTCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
579 581 6.990349 TGAATTAAATCATACTCCCTCCGTTC 59.010 38.462 0.00 0.00 0.00 3.95
580 582 6.895782 TGAATTAAATCATACTCCCTCCGTT 58.104 36.000 0.00 0.00 0.00 4.44
581 583 6.494666 TGAATTAAATCATACTCCCTCCGT 57.505 37.500 0.00 0.00 0.00 4.69
582 584 6.372659 CCATGAATTAAATCATACTCCCTCCG 59.627 42.308 5.70 0.00 37.96 4.63
583 585 7.461749 TCCATGAATTAAATCATACTCCCTCC 58.538 38.462 5.70 0.00 37.96 4.30
584 586 8.378565 TCTCCATGAATTAAATCATACTCCCTC 58.621 37.037 5.70 0.00 37.96 4.30
585 587 8.280258 TCTCCATGAATTAAATCATACTCCCT 57.720 34.615 5.70 0.00 37.96 4.20
586 588 8.924511 TTCTCCATGAATTAAATCATACTCCC 57.075 34.615 5.70 0.00 37.96 4.30
587 589 9.566432 ACTTCTCCATGAATTAAATCATACTCC 57.434 33.333 5.70 0.00 37.96 3.85
658 663 1.001974 AGTTTGATACGCACAGCTGGA 59.998 47.619 19.93 0.00 0.00 3.86
691 696 7.035004 GTGCTGAATAAATCCATGCTAAAACA 58.965 34.615 0.00 0.00 0.00 2.83
692 697 7.221452 CAGTGCTGAATAAATCCATGCTAAAAC 59.779 37.037 0.00 0.00 0.00 2.43
719 724 6.741358 GCACGTTGGAAGAACTGATTATTAAC 59.259 38.462 0.00 0.00 0.00 2.01
758 763 7.433719 GTGCTCAGTATATATAGCTTTCCATCG 59.566 40.741 12.92 0.00 35.95 3.84
788 793 1.139058 GGATGGGTGGTGTGCTACTAG 59.861 57.143 0.00 0.00 0.00 2.57
806 811 5.163301 GGCAGATTCTTGGTAGTAAGATGGA 60.163 44.000 0.00 0.00 36.63 3.41
808 813 5.757320 CAGGCAGATTCTTGGTAGTAAGATG 59.243 44.000 0.00 0.00 36.63 2.90
810 815 4.162320 CCAGGCAGATTCTTGGTAGTAAGA 59.838 45.833 0.00 0.00 35.02 2.10
833 838 2.505819 TGATTAGTTCTTGGGCTCCTCC 59.494 50.000 0.00 0.00 0.00 4.30
834 839 3.914426 TGATTAGTTCTTGGGCTCCTC 57.086 47.619 0.00 0.00 0.00 3.71
835 840 3.782523 TGATGATTAGTTCTTGGGCTCCT 59.217 43.478 0.00 0.00 0.00 3.69
836 841 4.133078 CTGATGATTAGTTCTTGGGCTCC 58.867 47.826 0.00 0.00 0.00 4.70
837 842 3.563390 GCTGATGATTAGTTCTTGGGCTC 59.437 47.826 0.00 0.00 0.00 4.70
838 843 3.201708 AGCTGATGATTAGTTCTTGGGCT 59.798 43.478 0.00 0.00 0.00 5.19
839 844 3.549794 AGCTGATGATTAGTTCTTGGGC 58.450 45.455 0.00 0.00 0.00 5.36
840 845 5.435291 AGAAGCTGATGATTAGTTCTTGGG 58.565 41.667 0.00 0.00 0.00 4.12
841 846 6.783162 CAAGAAGCTGATGATTAGTTCTTGG 58.217 40.000 20.94 11.36 43.53 3.61
843 848 7.574592 GCAACAAGAAGCTGATGATTAGTTCTT 60.575 37.037 0.00 8.10 35.20 2.52
844 849 6.128063 GCAACAAGAAGCTGATGATTAGTTCT 60.128 38.462 0.00 0.00 0.00 3.01
845 850 6.026513 GCAACAAGAAGCTGATGATTAGTTC 58.973 40.000 0.00 0.00 0.00 3.01
846 851 5.474532 TGCAACAAGAAGCTGATGATTAGTT 59.525 36.000 0.00 0.00 0.00 2.24
847 852 5.005740 TGCAACAAGAAGCTGATGATTAGT 58.994 37.500 0.00 0.00 0.00 2.24
857 862 1.202976 ACCAGGATGCAACAAGAAGCT 60.203 47.619 0.00 0.00 31.97 3.74
859 864 3.379372 CCATACCAGGATGCAACAAGAAG 59.621 47.826 0.00 0.00 31.97 2.85
943 953 2.581409 GGGTGGTGCGACGATACG 60.581 66.667 0.00 0.00 0.00 3.06
957 967 1.255667 ATAAGACGAGCACACCGGGT 61.256 55.000 6.32 0.00 0.00 5.28
969 979 7.028926 ACAGTGTAAGATGACCTATAAGACG 57.971 40.000 0.00 0.00 0.00 4.18
970 980 9.339850 TCTACAGTGTAAGATGACCTATAAGAC 57.660 37.037 4.21 0.00 0.00 3.01
982 992 7.482169 TCACCATTCTTCTACAGTGTAAGAT 57.518 36.000 8.89 0.00 0.00 2.40
993 1003 7.689299 TCTTGGAGAAATTCACCATTCTTCTA 58.311 34.615 12.70 0.00 37.00 2.10
998 1009 6.986250 AGTTTCTTGGAGAAATTCACCATTC 58.014 36.000 12.70 3.31 44.94 2.67
1036 1047 0.566176 TACTCCTCCCATCCCGGAAT 59.434 55.000 0.73 0.00 36.56 3.01
1041 1052 1.417890 CACACATACTCCTCCCATCCC 59.582 57.143 0.00 0.00 0.00 3.85
1089 1101 3.064900 AGAACAACAGAGGAGGCAATC 57.935 47.619 0.00 0.00 0.00 2.67
1092 1104 2.563179 GAGTAGAACAACAGAGGAGGCA 59.437 50.000 0.00 0.00 0.00 4.75
1093 1105 2.829120 AGAGTAGAACAACAGAGGAGGC 59.171 50.000 0.00 0.00 0.00 4.70
1094 1106 3.829601 ACAGAGTAGAACAACAGAGGAGG 59.170 47.826 0.00 0.00 0.00 4.30
1141 1153 4.037208 ACCTGAAAGAAACAAGCAGACATG 59.963 41.667 0.00 0.00 34.07 3.21
1220 1232 1.087501 GGTCGTGATTGCCTTCCTTC 58.912 55.000 0.00 0.00 0.00 3.46
1269 1281 0.108804 GGAACCTCATCGTCGAGCAA 60.109 55.000 0.00 0.00 0.00 3.91
1274 1286 1.993370 GAAGTTGGAACCTCATCGTCG 59.007 52.381 0.00 0.00 0.00 5.12
1302 1314 3.864686 CGCGTGAAGCCGATTGGG 61.865 66.667 0.00 0.00 44.76 4.12
1336 1348 4.221703 GGGGAACGACATGAGATCATCTAT 59.778 45.833 0.00 0.00 33.61 1.98
1363 1376 8.997323 ACAACACTATCTTCTCAATCTGAAAAG 58.003 33.333 0.00 0.00 0.00 2.27
1367 1380 7.670364 TGAACAACACTATCTTCTCAATCTGA 58.330 34.615 0.00 0.00 0.00 3.27
1457 1470 1.204704 TGTAGCAGTGGAATGTCCTCG 59.795 52.381 0.00 0.00 37.46 4.63
1466 1479 3.701542 CAGTTATCTCCTGTAGCAGTGGA 59.298 47.826 0.00 0.00 0.00 4.02
1475 1488 3.772025 CCCTCAGTTCAGTTATCTCCTGT 59.228 47.826 0.00 0.00 0.00 4.00
1559 1572 1.419107 GGATCTTCCGAACCGCGTTC 61.419 60.000 4.92 8.32 38.97 3.95
1568 1581 3.119459 CGAACTTCTTCAGGATCTTCCGA 60.119 47.826 0.00 0.00 42.75 4.55
1668 1681 4.431809 CAACTCACCACATGCTTGAAAAA 58.568 39.130 6.60 0.00 0.00 1.94
1732 1749 9.943465 GCTCGAATGAAAATAATTTTGAACTTC 57.057 29.630 0.00 0.00 31.94 3.01
1734 1751 9.643693 ATGCTCGAATGAAAATAATTTTGAACT 57.356 25.926 0.00 0.00 31.94 3.01
1747 1833 9.859427 ATCTAAAATTCAAATGCTCGAATGAAA 57.141 25.926 0.00 0.00 35.62 2.69
1750 1836 8.133627 AGGATCTAAAATTCAAATGCTCGAATG 58.866 33.333 0.00 0.00 32.27 2.67
1751 1837 8.230472 AGGATCTAAAATTCAAATGCTCGAAT 57.770 30.769 0.00 0.00 33.27 3.34
1755 1841 9.080915 GTTCAAGGATCTAAAATTCAAATGCTC 57.919 33.333 0.00 0.00 0.00 4.26
1757 1843 8.866956 CAGTTCAAGGATCTAAAATTCAAATGC 58.133 33.333 0.00 0.00 0.00 3.56
1763 1849 8.329203 ACTCACAGTTCAAGGATCTAAAATTC 57.671 34.615 0.00 0.00 0.00 2.17
1771 1857 3.515901 ACCCTACTCACAGTTCAAGGATC 59.484 47.826 0.00 0.00 0.00 3.36
1773 1859 2.972348 ACCCTACTCACAGTTCAAGGA 58.028 47.619 0.00 0.00 0.00 3.36
1774 1860 5.178797 CAATACCCTACTCACAGTTCAAGG 58.821 45.833 0.00 0.00 0.00 3.61
1805 1891 2.438434 CGAGACAATGCCCCCACC 60.438 66.667 0.00 0.00 0.00 4.61
1835 1921 3.509757 CCTTCGCGCTCCTCGAGA 61.510 66.667 15.71 0.00 44.98 4.04
1913 1999 6.147821 TGGATTTCTACTGAAAAGAGAAAGCG 59.852 38.462 5.95 0.00 43.29 4.68
1935 2021 3.064682 CACGATCACAGTTTGTTTGTGGA 59.935 43.478 5.64 0.00 44.63 4.02
1945 2031 7.602644 ACATATAAGAACAACACGATCACAGTT 59.397 33.333 0.00 0.00 0.00 3.16
1947 2033 7.394099 CACATATAAGAACAACACGATCACAG 58.606 38.462 0.00 0.00 0.00 3.66
1948 2034 6.312672 CCACATATAAGAACAACACGATCACA 59.687 38.462 0.00 0.00 0.00 3.58
2324 2423 1.153549 CCAGGCGCTGAAGTAGACC 60.154 63.158 7.64 0.00 32.44 3.85
2462 2561 4.489771 GACCCCATCCCGCACAGG 62.490 72.222 0.00 0.00 40.63 4.00
2675 2774 3.378602 TACGCGAGCCAGCCAAGA 61.379 61.111 15.93 0.00 0.00 3.02
2676 2775 3.188786 GTACGCGAGCCAGCCAAG 61.189 66.667 15.93 0.00 0.00 3.61
2735 2834 3.744719 CCTTCCTCGTCGGCGTCA 61.745 66.667 10.18 0.00 39.49 4.35
2747 2846 4.410400 CCCTGGCGGTGACCTTCC 62.410 72.222 0.00 1.07 0.00 3.46
2759 2858 3.465403 CCACGAGAGGAGCCCTGG 61.465 72.222 0.00 0.00 31.76 4.45
2804 2903 2.252072 GATACTCACCCGCAAGCCCA 62.252 60.000 0.00 0.00 0.00 5.36
2973 3072 2.219325 CTGGACTCCGACAGCAGGAC 62.219 65.000 0.00 0.00 33.58 3.85
2990 3089 1.801913 GTAGCTCGTCACCACGCTG 60.802 63.158 0.00 0.00 46.28 5.18
3059 3158 2.284625 ATGGGGAGCACGGTGAGA 60.285 61.111 13.29 0.00 0.00 3.27
3062 3161 2.040544 GTTGATGGGGAGCACGGTG 61.041 63.158 3.15 3.15 0.00 4.94
3065 3164 3.499737 GCGTTGATGGGGAGCACG 61.500 66.667 0.00 0.00 0.00 5.34
3511 3610 4.749310 CTCGCTCGCTGGTTGGCT 62.749 66.667 0.00 0.00 0.00 4.75
3589 3705 1.686325 ATCCATCCCACGTTCCGAGG 61.686 60.000 0.00 0.00 37.35 4.63
3625 3741 1.652563 GCACCGTCCAGTTGGTTTC 59.347 57.895 0.00 0.00 35.96 2.78
3650 3766 2.919229 CAAAATGAATCCAAGCTGACGC 59.081 45.455 0.00 0.00 0.00 5.19
3651 3767 2.919229 GCAAAATGAATCCAAGCTGACG 59.081 45.455 0.00 0.00 0.00 4.35
3652 3768 3.916761 TGCAAAATGAATCCAAGCTGAC 58.083 40.909 0.00 0.00 0.00 3.51
3653 3769 3.615592 GCTGCAAAATGAATCCAAGCTGA 60.616 43.478 0.00 0.00 0.00 4.26
3654 3770 2.671396 GCTGCAAAATGAATCCAAGCTG 59.329 45.455 0.00 0.00 0.00 4.24
3655 3771 2.673043 CGCTGCAAAATGAATCCAAGCT 60.673 45.455 0.00 0.00 0.00 3.74
3656 3772 1.657094 CGCTGCAAAATGAATCCAAGC 59.343 47.619 0.00 0.00 0.00 4.01
3657 3773 3.220507 TCGCTGCAAAATGAATCCAAG 57.779 42.857 0.00 0.00 0.00 3.61
3658 3774 3.056678 ACATCGCTGCAAAATGAATCCAA 60.057 39.130 11.99 0.00 0.00 3.53
3659 3775 2.492881 ACATCGCTGCAAAATGAATCCA 59.507 40.909 11.99 0.00 0.00 3.41
3660 3776 3.111098 GACATCGCTGCAAAATGAATCC 58.889 45.455 11.99 0.00 0.00 3.01
3661 3777 4.025015 AGACATCGCTGCAAAATGAATC 57.975 40.909 11.99 2.83 0.00 2.52
3662 3778 4.445452 AAGACATCGCTGCAAAATGAAT 57.555 36.364 11.99 0.38 0.00 2.57
3663 3779 3.921119 AAGACATCGCTGCAAAATGAA 57.079 38.095 11.99 0.00 0.00 2.57
3664 3780 3.921119 AAAGACATCGCTGCAAAATGA 57.079 38.095 11.99 0.00 0.00 2.57
3665 3781 4.977741 AAAAAGACATCGCTGCAAAATG 57.022 36.364 0.00 2.87 0.00 2.32
3685 3801 5.404366 CCATTGACGTACTCTCGAAGAAAAA 59.596 40.000 0.00 0.00 34.09 1.94
3686 3802 4.921515 CCATTGACGTACTCTCGAAGAAAA 59.078 41.667 0.00 0.00 34.09 2.29
3687 3803 4.482386 CCATTGACGTACTCTCGAAGAAA 58.518 43.478 0.00 0.00 34.09 2.52
3688 3804 3.672511 GCCATTGACGTACTCTCGAAGAA 60.673 47.826 0.00 0.00 34.09 2.52
3689 3805 2.159421 GCCATTGACGTACTCTCGAAGA 60.159 50.000 0.00 0.00 34.70 2.87
3690 3806 2.186076 GCCATTGACGTACTCTCGAAG 58.814 52.381 0.00 0.00 34.70 3.79
3691 3807 1.466866 CGCCATTGACGTACTCTCGAA 60.467 52.381 0.00 0.00 34.70 3.71
3692 3808 0.098200 CGCCATTGACGTACTCTCGA 59.902 55.000 0.00 0.00 34.70 4.04
3693 3809 0.179171 ACGCCATTGACGTACTCTCG 60.179 55.000 0.00 0.00 43.02 4.04
3694 3810 2.838386 TACGCCATTGACGTACTCTC 57.162 50.000 0.82 0.00 44.55 3.20
3730 3846 9.816354 ACTCAACTTTTTGTACATATTTTTGCT 57.184 25.926 0.00 0.00 34.02 3.91
3747 3863 2.942376 TGTTCGCATCACACTCAACTTT 59.058 40.909 0.00 0.00 0.00 2.66
3778 3894 2.237643 GGGTGTGGGTGGTTTTTCTTTT 59.762 45.455 0.00 0.00 0.00 2.27
3823 3941 6.403200 GCTGAGGCGTTAAATAGATTTGTGAA 60.403 38.462 0.00 0.00 0.00 3.18
3844 3962 0.391130 GATGCCGTGTTAGGTGCTGA 60.391 55.000 0.00 0.00 0.00 4.26
3855 3973 3.191162 TCAAAGAATGGAAAGATGCCGTG 59.809 43.478 0.00 0.00 0.00 4.94
3856 3974 3.420893 TCAAAGAATGGAAAGATGCCGT 58.579 40.909 0.00 0.00 0.00 5.68
3901 4447 3.838244 AACAGGCTATGCGAAGGATTA 57.162 42.857 0.00 0.00 40.68 1.75
4004 4550 3.961225 TTGCCATGCCCTCGCCAAT 62.961 57.895 0.00 0.00 0.00 3.16
4005 4551 4.675161 TTGCCATGCCCTCGCCAA 62.675 61.111 0.00 0.00 0.00 4.52
4006 4552 4.675161 TTTGCCATGCCCTCGCCA 62.675 61.111 0.00 0.00 0.00 5.69
4046 4604 2.092914 GGTTTAGGATGTGGAGGGTGAG 60.093 54.545 0.00 0.00 0.00 3.51
4063 4621 2.297033 CAGCATGCTTACAGTTGGGTTT 59.703 45.455 19.98 0.00 0.00 3.27
4108 4675 2.566833 TCTTGACATGGTGGACTTGG 57.433 50.000 0.00 0.00 0.00 3.61
4133 4700 1.334059 GCCATTGTTGATATCGCACCG 60.334 52.381 0.00 0.00 0.00 4.94
4238 4807 8.700051 CATATGATAGTGGATAAGGAGGTAAGG 58.300 40.741 0.00 0.00 0.00 2.69
4242 4811 6.025539 TGCATATGATAGTGGATAAGGAGGT 58.974 40.000 6.97 0.00 0.00 3.85
4292 4861 1.545706 GGGAGTGGCTTCGGAGAACT 61.546 60.000 0.00 0.00 45.90 3.01
4321 4890 2.880890 CAGTTACAAGCTTTGGCACTCT 59.119 45.455 0.00 0.00 41.70 3.24
4365 4934 2.855514 GCAGGCCGGTTTGCTTCAA 61.856 57.895 20.58 0.00 37.35 2.69
4366 4935 3.294493 GCAGGCCGGTTTGCTTCA 61.294 61.111 20.58 0.00 37.35 3.02
4404 4973 5.310857 AGAAAGTAAATGGAGGGAAGTGTCT 59.689 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.