Multiple sequence alignment - TraesCS4D01G004300

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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 TraesCS4D01G004300 chr4D 100.000 4484 0 0 1 4484 1994347 1998830 0.000000e+00 8281.0
1 TraesCS4D01G004300 chr4D 89.490 314 26 4 56 366 2967828 2967519 1.510000e-104 390.0
2 TraesCS4D01G004300 chr5B 95.831 1727 60 8 2174 3891 14705912 14707635 0.000000e+00 2780.0
3 TraesCS4D01G004300 chr5B 82.742 1634 237 22 2232 3845 113676934 113675326 0.000000e+00 1413.0
4 TraesCS4D01G004300 chr5B 81.353 1582 252 30 673 2238 113683985 113682431 0.000000e+00 1247.0
5 TraesCS4D01G004300 chr5B 81.760 1398 218 24 889 2268 515184000 515185378 0.000000e+00 1134.0
6 TraesCS4D01G004300 chr5B 94.059 707 33 5 596 1294 14702983 14703688 0.000000e+00 1064.0
7 TraesCS4D01G004300 chr5B 93.284 402 25 2 56 456 14702594 14702994 3.860000e-165 592.0
8 TraesCS4D01G004300 chr5B 91.867 332 17 5 4162 4484 14711044 14711374 5.290000e-124 455.0
9 TraesCS4D01G004300 chr5B 93.182 176 5 3 3945 4119 14707815 14707984 7.450000e-63 252.0
10 TraesCS4D01G004300 chr5B 96.226 53 2 0 3888 3940 14707665 14707717 2.220000e-13 87.9
11 TraesCS4D01G004300 chr5D 82.231 3281 502 48 600 3845 104257947 104254713 0.000000e+00 2754.0
12 TraesCS4D01G004300 chr5D 93.750 128 7 1 467 593 217748354 217748481 1.650000e-44 191.0
13 TraesCS4D01G004300 chr3A 81.484 2965 463 51 604 3507 44709432 44712371 0.000000e+00 2355.0
14 TraesCS4D01G004300 chr3A 80.752 2951 490 51 623 3513 44639124 44642056 0.000000e+00 2231.0
15 TraesCS4D01G004300 chrUn 82.189 2796 438 42 753 3512 47549283 47546512 0.000000e+00 2350.0
16 TraesCS4D01G004300 chr3D 81.063 2973 459 49 618 3512 32299196 32302142 0.000000e+00 2276.0
17 TraesCS4D01G004300 chr3D 80.695 2963 480 51 604 3501 32278493 32281428 0.000000e+00 2218.0
18 TraesCS4D01G004300 chr3D 96.694 121 4 0 467 587 173713050 173713170 7.610000e-48 202.0
19 TraesCS4D01G004300 chr4B 93.377 1525 61 4 596 2109 2337626 2336131 0.000000e+00 2220.0
20 TraesCS4D01G004300 chr4B 93.970 1194 60 8 2453 3636 2336123 2334932 0.000000e+00 1796.0
21 TraesCS4D01G004300 chr4B 92.822 404 27 2 56 458 2338015 2337613 6.460000e-163 584.0
22 TraesCS4D01G004300 chr4B 83.925 535 35 20 3945 4433 2330970 2330441 8.790000e-127 464.0
23 TraesCS4D01G004300 chr4B 95.331 257 11 1 3638 3894 2331404 2331149 1.500000e-109 407.0
24 TraesCS4D01G004300 chr4B 89.668 271 18 5 4173 4433 3212871 3213141 2.000000e-88 337.0
25 TraesCS4D01G004300 chr4B 87.083 240 17 7 3945 4174 3212611 3212846 4.450000e-65 259.0
26 TraesCS4D01G004300 chr4B 100.000 53 0 0 3888 3940 2331122 2331070 1.030000e-16 99.0
27 TraesCS4D01G004300 chr4B 96.364 55 2 0 4430 4484 2317296 2317242 1.720000e-14 91.6
28 TraesCS4D01G004300 chr4B 94.231 52 3 0 4430 4481 3228757 3228808 3.720000e-11 80.5
29 TraesCS4D01G004300 chr3B 80.538 2975 492 55 604 3512 54793902 54796855 0.000000e+00 2206.0
30 TraesCS4D01G004300 chr3B 81.387 1644 263 27 604 2221 54784416 54786042 0.000000e+00 1301.0
31 TraesCS4D01G004300 chr3B 83.568 1205 162 18 2342 3512 54786097 54787299 0.000000e+00 1096.0
32 TraesCS4D01G004300 chr3B 94.400 125 7 0 467 591 820413733 820413609 4.580000e-45 193.0
33 TraesCS4D01G004300 chr5A 81.804 1286 194 28 1000 2268 540052000 540053262 0.000000e+00 1042.0
34 TraesCS4D01G004300 chr5A 96.800 125 4 0 467 591 36244906 36245030 4.550000e-50 209.0
35 TraesCS4D01G004300 chr5A 94.531 128 7 0 467 594 343986077 343986204 9.840000e-47 198.0
36 TraesCS4D01G004300 chr5A 95.161 124 6 0 468 591 400672255 400672132 3.540000e-46 196.0
37 TraesCS4D01G004300 chr7B 94.488 127 7 0 467 593 149966224 149966350 3.540000e-46 196.0
38 TraesCS4D01G004300 chr7A 94.488 127 7 0 467 593 445250623 445250749 3.540000e-46 196.0
39 TraesCS4D01G004300 chr6D 95.868 121 5 0 467 587 436684094 436684214 3.540000e-46 196.0


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 TraesCS4D01G004300 chr4D 1994347 1998830 4483 False 8281.000000 8281 100.000000 1 4484 1 chr4D.!!$F1 4483
1 TraesCS4D01G004300 chr5B 113675326 113676934 1608 True 1413.000000 1413 82.742000 2232 3845 1 chr5B.!!$R1 1613
2 TraesCS4D01G004300 chr5B 113682431 113683985 1554 True 1247.000000 1247 81.353000 673 2238 1 chr5B.!!$R2 1565
3 TraesCS4D01G004300 chr5B 515184000 515185378 1378 False 1134.000000 1134 81.760000 889 2268 1 chr5B.!!$F1 1379
4 TraesCS4D01G004300 chr5B 14702594 14711374 8780 False 871.816667 2780 94.074833 56 4484 6 chr5B.!!$F2 4428
5 TraesCS4D01G004300 chr5D 104254713 104257947 3234 True 2754.000000 2754 82.231000 600 3845 1 chr5D.!!$R1 3245
6 TraesCS4D01G004300 chr3A 44709432 44712371 2939 False 2355.000000 2355 81.484000 604 3507 1 chr3A.!!$F2 2903
7 TraesCS4D01G004300 chr3A 44639124 44642056 2932 False 2231.000000 2231 80.752000 623 3513 1 chr3A.!!$F1 2890
8 TraesCS4D01G004300 chrUn 47546512 47549283 2771 True 2350.000000 2350 82.189000 753 3512 1 chrUn.!!$R1 2759
9 TraesCS4D01G004300 chr3D 32299196 32302142 2946 False 2276.000000 2276 81.063000 618 3512 1 chr3D.!!$F2 2894
10 TraesCS4D01G004300 chr3D 32278493 32281428 2935 False 2218.000000 2218 80.695000 604 3501 1 chr3D.!!$F1 2897
11 TraesCS4D01G004300 chr4B 2330441 2338015 7574 True 928.333333 2220 93.237500 56 4433 6 chr4B.!!$R2 4377
12 TraesCS4D01G004300 chr4B 3212611 3213141 530 False 298.000000 337 88.375500 3945 4433 2 chr4B.!!$F2 488
13 TraesCS4D01G004300 chr3B 54793902 54796855 2953 False 2206.000000 2206 80.538000 604 3512 1 chr3B.!!$F1 2908
14 TraesCS4D01G004300 chr3B 54784416 54787299 2883 False 1198.500000 1301 82.477500 604 3512 2 chr3B.!!$F2 2908
15 TraesCS4D01G004300 chr5A 540052000 540053262 1262 False 1042.000000 1042 81.804000 1000 2268 1 chr5A.!!$F3 1268

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
579 581 0.035056 CCCCCAACCAGTTGAGCTAG 60.035 60.0 12.06 0.00 42.93 3.42 F
580 582 0.035056 CCCCAACCAGTTGAGCTAGG 60.035 60.0 12.06 4.24 42.93 3.02 F
594 596 0.107459 GCTAGGCTCACTCCCCAAAG 60.107 60.0 0.00 0.00 0.00 2.77 F
2245 3917 0.400213 ACCGAACAATCTTGCTGGGA 59.600 50.0 1.98 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1897 0.534203 ACTTTGGCACTACGGGTGTG 60.534 55.000 11.35 6.52 46.86 3.82 R
2112 2197 0.979187 TATCCACCTGACCGGAACCC 60.979 60.000 9.46 0.00 34.22 4.11 R
2407 4097 1.801178 GGTCTTGCAAGAACTCTTCCG 59.199 52.381 32.62 2.97 39.66 4.30 R
3861 9146 0.680061 AGTCCTTCACTTGACCGGAC 59.320 55.000 9.46 14.78 41.51 4.79 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
23 24 6.926630 CCCTATTAAAGAGCTCCTCATACT 57.073 41.667 10.93 0.00 32.06 2.12
24 25 7.309770 CCCTATTAAAGAGCTCCTCATACTT 57.690 40.000 10.93 0.00 32.06 2.24
25 26 7.158021 CCCTATTAAAGAGCTCCTCATACTTG 58.842 42.308 10.93 0.00 32.06 3.16
26 27 7.158021 CCTATTAAAGAGCTCCTCATACTTGG 58.842 42.308 10.93 0.00 32.06 3.61
27 28 2.998316 AAGAGCTCCTCATACTTGGC 57.002 50.000 10.93 0.00 32.06 4.52
28 29 0.749649 AGAGCTCCTCATACTTGGCG 59.250 55.000 10.93 0.00 32.06 5.69
29 30 0.461961 GAGCTCCTCATACTTGGCGT 59.538 55.000 0.87 0.00 0.00 5.68
30 31 1.681793 GAGCTCCTCATACTTGGCGTA 59.318 52.381 0.87 0.00 0.00 4.42
31 32 2.100916 GAGCTCCTCATACTTGGCGTAA 59.899 50.000 0.87 0.00 0.00 3.18
32 33 2.700897 AGCTCCTCATACTTGGCGTAAT 59.299 45.455 0.00 0.00 0.00 1.89
33 34 3.134804 AGCTCCTCATACTTGGCGTAATT 59.865 43.478 0.00 0.00 0.00 1.40
34 35 3.877508 GCTCCTCATACTTGGCGTAATTT 59.122 43.478 0.00 0.00 0.00 1.82
35 36 4.024809 GCTCCTCATACTTGGCGTAATTTC 60.025 45.833 0.00 0.00 0.00 2.17
36 37 5.092554 TCCTCATACTTGGCGTAATTTCA 57.907 39.130 0.00 0.00 0.00 2.69
37 38 5.116180 TCCTCATACTTGGCGTAATTTCAG 58.884 41.667 0.00 0.00 0.00 3.02
38 39 4.260784 CCTCATACTTGGCGTAATTTCAGC 60.261 45.833 0.00 0.00 0.00 4.26
39 40 4.513442 TCATACTTGGCGTAATTTCAGCT 58.487 39.130 0.00 0.00 0.00 4.24
40 41 4.570772 TCATACTTGGCGTAATTTCAGCTC 59.429 41.667 0.00 0.00 0.00 4.09
41 42 2.084546 ACTTGGCGTAATTTCAGCTCC 58.915 47.619 0.00 0.00 0.00 4.70
42 43 2.083774 CTTGGCGTAATTTCAGCTCCA 58.916 47.619 0.00 0.00 0.00 3.86
43 44 1.448985 TGGCGTAATTTCAGCTCCAC 58.551 50.000 0.00 0.00 0.00 4.02
44 45 0.733150 GGCGTAATTTCAGCTCCACC 59.267 55.000 0.00 0.00 0.00 4.61
45 46 1.448985 GCGTAATTTCAGCTCCACCA 58.551 50.000 0.00 0.00 0.00 4.17
46 47 1.398390 GCGTAATTTCAGCTCCACCAG 59.602 52.381 0.00 0.00 0.00 4.00
47 48 2.935238 GCGTAATTTCAGCTCCACCAGA 60.935 50.000 0.00 0.00 0.00 3.86
48 49 3.334691 CGTAATTTCAGCTCCACCAGAA 58.665 45.455 0.00 0.00 0.00 3.02
49 50 3.941483 CGTAATTTCAGCTCCACCAGAAT 59.059 43.478 0.00 0.00 0.00 2.40
50 51 5.116180 CGTAATTTCAGCTCCACCAGAATA 58.884 41.667 0.00 0.00 0.00 1.75
51 52 5.584649 CGTAATTTCAGCTCCACCAGAATAA 59.415 40.000 0.00 0.00 0.00 1.40
52 53 6.260936 CGTAATTTCAGCTCCACCAGAATAAT 59.739 38.462 0.00 0.00 0.00 1.28
53 54 6.705863 AATTTCAGCTCCACCAGAATAATC 57.294 37.500 0.00 0.00 0.00 1.75
54 55 3.845781 TCAGCTCCACCAGAATAATCC 57.154 47.619 0.00 0.00 0.00 3.01
152 153 5.103686 AGCATCTTTCTAGTCTCTAGGGAGT 60.104 44.000 5.05 5.05 40.29 3.85
189 190 4.567959 GCATGTATGAACCAATTTTCAGCC 59.432 41.667 0.00 0.00 38.87 4.85
200 201 8.922931 AACCAATTTTCAGCCTGATTATTTTT 57.077 26.923 0.00 0.00 0.00 1.94
351 352 5.041191 AGGAAAAGTGTGATCAAGAGTGT 57.959 39.130 0.00 0.00 0.00 3.55
354 355 6.483640 AGGAAAAGTGTGATCAAGAGTGTTAC 59.516 38.462 0.00 0.00 0.00 2.50
396 398 6.345803 GGCTAAATTCTCGCAAGTTTTGTTTC 60.346 38.462 0.00 0.00 39.48 2.78
407 409 6.695278 CGCAAGTTTTGTTTCTCCTTATTTGA 59.305 34.615 0.00 0.00 0.00 2.69
443 445 9.273016 TGTTGTAAGGAAAGTTAGAATTCAGAG 57.727 33.333 8.44 0.00 0.00 3.35
444 446 9.490379 GTTGTAAGGAAAGTTAGAATTCAGAGA 57.510 33.333 8.44 0.00 0.00 3.10
445 447 9.712305 TTGTAAGGAAAGTTAGAATTCAGAGAG 57.288 33.333 8.44 0.00 0.00 3.20
446 448 9.090103 TGTAAGGAAAGTTAGAATTCAGAGAGA 57.910 33.333 8.44 0.00 0.00 3.10
447 449 9.581099 GTAAGGAAAGTTAGAATTCAGAGAGAG 57.419 37.037 8.44 0.00 0.00 3.20
448 450 6.639563 AGGAAAGTTAGAATTCAGAGAGAGC 58.360 40.000 8.44 0.00 0.00 4.09
449 451 6.440328 AGGAAAGTTAGAATTCAGAGAGAGCT 59.560 38.462 8.44 0.00 0.00 4.09
450 452 6.756542 GGAAAGTTAGAATTCAGAGAGAGCTC 59.243 42.308 5.27 5.27 41.62 4.09
451 453 5.852282 AGTTAGAATTCAGAGAGAGCTCC 57.148 43.478 10.93 1.70 42.30 4.70
452 454 5.268387 AGTTAGAATTCAGAGAGAGCTCCA 58.732 41.667 10.93 0.00 42.30 3.86
453 455 5.898972 AGTTAGAATTCAGAGAGAGCTCCAT 59.101 40.000 10.93 0.00 42.30 3.41
454 456 6.383726 AGTTAGAATTCAGAGAGAGCTCCATT 59.616 38.462 10.93 0.00 42.30 3.16
455 457 7.563188 AGTTAGAATTCAGAGAGAGCTCCATTA 59.437 37.037 10.93 0.00 42.30 1.90
456 458 6.409524 AGAATTCAGAGAGAGCTCCATTAG 57.590 41.667 10.93 0.00 42.30 1.73
457 459 5.898972 AGAATTCAGAGAGAGCTCCATTAGT 59.101 40.000 10.93 0.00 42.30 2.24
458 460 6.383726 AGAATTCAGAGAGAGCTCCATTAGTT 59.616 38.462 10.93 0.00 42.30 2.24
459 461 6.558488 ATTCAGAGAGAGCTCCATTAGTTT 57.442 37.500 10.93 0.00 42.30 2.66
460 462 6.365970 TTCAGAGAGAGCTCCATTAGTTTT 57.634 37.500 10.93 0.00 42.30 2.43
461 463 6.365970 TCAGAGAGAGCTCCATTAGTTTTT 57.634 37.500 10.93 0.00 42.30 1.94
483 485 6.817765 TTTTTAGAGTACCTGGAAAGCATG 57.182 37.500 0.00 0.00 0.00 4.06
484 486 4.487714 TTAGAGTACCTGGAAAGCATGG 57.512 45.455 0.00 0.00 0.00 3.66
485 487 2.269940 AGAGTACCTGGAAAGCATGGT 58.730 47.619 0.00 0.00 36.66 3.55
486 488 2.237392 AGAGTACCTGGAAAGCATGGTC 59.763 50.000 0.00 0.00 34.33 4.02
487 489 1.282157 AGTACCTGGAAAGCATGGTCC 59.718 52.381 0.00 0.00 34.33 4.46
488 490 1.282157 GTACCTGGAAAGCATGGTCCT 59.718 52.381 0.00 0.00 34.77 3.85
489 491 0.329596 ACCTGGAAAGCATGGTCCTC 59.670 55.000 0.00 0.00 34.77 3.71
490 492 0.329261 CCTGGAAAGCATGGTCCTCA 59.671 55.000 0.00 0.00 34.77 3.86
491 493 1.272092 CCTGGAAAGCATGGTCCTCAA 60.272 52.381 0.00 0.00 34.77 3.02
492 494 2.089980 CTGGAAAGCATGGTCCTCAAG 58.910 52.381 0.00 0.00 34.77 3.02
493 495 1.704628 TGGAAAGCATGGTCCTCAAGA 59.295 47.619 0.00 0.00 34.77 3.02
494 496 2.108075 TGGAAAGCATGGTCCTCAAGAA 59.892 45.455 0.00 0.00 34.77 2.52
495 497 3.245371 TGGAAAGCATGGTCCTCAAGAAT 60.245 43.478 0.00 0.00 34.77 2.40
496 498 4.018506 TGGAAAGCATGGTCCTCAAGAATA 60.019 41.667 0.00 0.00 34.77 1.75
497 499 4.949856 GGAAAGCATGGTCCTCAAGAATAA 59.050 41.667 0.00 0.00 0.00 1.40
498 500 5.418840 GGAAAGCATGGTCCTCAAGAATAAA 59.581 40.000 0.00 0.00 0.00 1.40
499 501 6.097412 GGAAAGCATGGTCCTCAAGAATAAAT 59.903 38.462 0.00 0.00 0.00 1.40
500 502 7.285401 GGAAAGCATGGTCCTCAAGAATAAATA 59.715 37.037 0.00 0.00 0.00 1.40
501 503 7.814264 AAGCATGGTCCTCAAGAATAAATAG 57.186 36.000 0.00 0.00 0.00 1.73
502 504 6.302269 AGCATGGTCCTCAAGAATAAATAGG 58.698 40.000 0.00 0.00 0.00 2.57
503 505 6.101734 AGCATGGTCCTCAAGAATAAATAGGA 59.898 38.462 0.00 0.00 33.97 2.94
504 506 6.772716 GCATGGTCCTCAAGAATAAATAGGAA 59.227 38.462 0.00 0.00 38.06 3.36
505 507 7.255277 GCATGGTCCTCAAGAATAAATAGGAAC 60.255 40.741 0.00 0.00 43.16 3.62
506 508 6.659824 TGGTCCTCAAGAATAAATAGGAACC 58.340 40.000 0.00 0.00 42.35 3.62
507 509 6.447084 TGGTCCTCAAGAATAAATAGGAACCT 59.553 38.462 0.00 0.00 42.35 3.50
508 510 7.626084 TGGTCCTCAAGAATAAATAGGAACCTA 59.374 37.037 2.93 2.93 42.35 3.08
509 511 8.491958 GGTCCTCAAGAATAAATAGGAACCTAA 58.508 37.037 4.63 0.00 37.98 2.69
510 512 9.901172 GTCCTCAAGAATAAATAGGAACCTAAA 57.099 33.333 4.63 0.00 38.06 1.85
515 517 9.665264 CAAGAATAAATAGGAACCTAAATTCGC 57.335 33.333 17.79 6.04 34.74 4.70
516 518 8.392372 AGAATAAATAGGAACCTAAATTCGCC 57.608 34.615 17.79 0.00 34.74 5.54
517 519 8.218488 AGAATAAATAGGAACCTAAATTCGCCT 58.782 33.333 17.79 0.00 34.74 5.52
518 520 7.981102 ATAAATAGGAACCTAAATTCGCCTC 57.019 36.000 4.63 0.00 31.73 4.70
519 521 2.711978 AGGAACCTAAATTCGCCTCC 57.288 50.000 0.00 0.00 0.00 4.30
520 522 1.134491 AGGAACCTAAATTCGCCTCCG 60.134 52.381 0.00 0.00 0.00 4.63
521 523 1.406477 GGAACCTAAATTCGCCTCCGT 60.406 52.381 0.00 0.00 35.54 4.69
522 524 1.664151 GAACCTAAATTCGCCTCCGTG 59.336 52.381 0.00 0.00 35.54 4.94
523 525 0.899720 ACCTAAATTCGCCTCCGTGA 59.100 50.000 0.00 0.00 35.54 4.35
524 526 1.134788 ACCTAAATTCGCCTCCGTGAG 60.135 52.381 0.00 0.00 35.54 3.51
537 539 3.050703 CGTGAGGATTCGAACCCAG 57.949 57.895 12.20 0.00 0.00 4.45
538 540 0.460284 CGTGAGGATTCGAACCCAGG 60.460 60.000 12.20 10.92 0.00 4.45
539 541 0.613777 GTGAGGATTCGAACCCAGGT 59.386 55.000 12.20 0.00 0.00 4.00
540 542 0.613260 TGAGGATTCGAACCCAGGTG 59.387 55.000 12.20 0.00 0.00 4.00
541 543 0.613777 GAGGATTCGAACCCAGGTGT 59.386 55.000 12.20 0.00 0.00 4.16
542 544 1.003233 GAGGATTCGAACCCAGGTGTT 59.997 52.381 12.20 0.00 0.00 3.32
543 545 1.165270 GGATTCGAACCCAGGTGTTG 58.835 55.000 2.75 0.00 0.00 3.33
553 555 2.060050 CCAGGTGTTGGGTTTGTACA 57.940 50.000 0.00 0.00 43.75 2.90
554 556 2.593026 CCAGGTGTTGGGTTTGTACAT 58.407 47.619 0.00 0.00 43.75 2.29
555 557 2.556622 CCAGGTGTTGGGTTTGTACATC 59.443 50.000 0.00 0.00 43.75 3.06
556 558 2.556622 CAGGTGTTGGGTTTGTACATCC 59.443 50.000 0.00 2.58 0.00 3.51
557 559 2.175931 AGGTGTTGGGTTTGTACATCCA 59.824 45.455 16.09 12.45 0.00 3.41
558 560 2.295070 GGTGTTGGGTTTGTACATCCAC 59.705 50.000 16.09 9.30 0.00 4.02
559 561 3.219281 GTGTTGGGTTTGTACATCCACT 58.781 45.455 16.09 0.00 0.00 4.00
560 562 3.252458 GTGTTGGGTTTGTACATCCACTC 59.748 47.826 16.09 6.61 0.00 3.51
561 563 2.817844 GTTGGGTTTGTACATCCACTCC 59.182 50.000 16.09 9.13 0.00 3.85
562 564 1.353022 TGGGTTTGTACATCCACTCCC 59.647 52.381 16.09 12.49 34.77 4.30
563 565 1.340697 GGGTTTGTACATCCACTCCCC 60.341 57.143 16.09 6.58 0.00 4.81
564 566 1.340697 GGTTTGTACATCCACTCCCCC 60.341 57.143 0.00 0.00 0.00 5.40
565 567 1.353022 GTTTGTACATCCACTCCCCCA 59.647 52.381 0.00 0.00 0.00 4.96
566 568 1.748732 TTGTACATCCACTCCCCCAA 58.251 50.000 0.00 0.00 0.00 4.12
567 569 0.988832 TGTACATCCACTCCCCCAAC 59.011 55.000 0.00 0.00 0.00 3.77
568 570 0.255033 GTACATCCACTCCCCCAACC 59.745 60.000 0.00 0.00 0.00 3.77
569 571 0.178858 TACATCCACTCCCCCAACCA 60.179 55.000 0.00 0.00 0.00 3.67
570 572 1.304282 CATCCACTCCCCCAACCAG 59.696 63.158 0.00 0.00 0.00 4.00
571 573 1.151587 ATCCACTCCCCCAACCAGT 60.152 57.895 0.00 0.00 0.00 4.00
572 574 0.776080 ATCCACTCCCCCAACCAGTT 60.776 55.000 0.00 0.00 0.00 3.16
573 575 1.228552 CCACTCCCCCAACCAGTTG 60.229 63.158 3.47 3.47 40.13 3.16
574 576 1.715019 CCACTCCCCCAACCAGTTGA 61.715 60.000 12.06 0.00 42.93 3.18
575 577 0.250901 CACTCCCCCAACCAGTTGAG 60.251 60.000 12.06 4.06 42.93 3.02
576 578 1.303643 CTCCCCCAACCAGTTGAGC 60.304 63.158 12.06 0.00 42.93 4.26
577 579 1.774217 TCCCCCAACCAGTTGAGCT 60.774 57.895 12.06 0.00 42.93 4.09
578 580 0.474854 TCCCCCAACCAGTTGAGCTA 60.475 55.000 12.06 0.00 42.93 3.32
579 581 0.035056 CCCCCAACCAGTTGAGCTAG 60.035 60.000 12.06 0.00 42.93 3.42
580 582 0.035056 CCCCAACCAGTTGAGCTAGG 60.035 60.000 12.06 4.24 42.93 3.02
581 583 0.678048 CCCAACCAGTTGAGCTAGGC 60.678 60.000 12.06 0.00 42.93 3.93
582 584 0.326264 CCAACCAGTTGAGCTAGGCT 59.674 55.000 12.06 0.00 42.93 4.58
591 593 2.780693 AGCTAGGCTCACTCCCCA 59.219 61.111 0.00 0.00 30.62 4.96
592 594 1.081092 AGCTAGGCTCACTCCCCAA 59.919 57.895 0.00 0.00 30.62 4.12
593 595 0.547712 AGCTAGGCTCACTCCCCAAA 60.548 55.000 0.00 0.00 30.62 3.28
594 596 0.107459 GCTAGGCTCACTCCCCAAAG 60.107 60.000 0.00 0.00 0.00 2.77
680 686 7.988737 TGGTGATATCAGAAACTATTTTGCTG 58.011 34.615 5.42 0.00 0.00 4.41
758 768 5.433855 CCTGCAAAAATCAATTGTTGTTCG 58.566 37.500 5.13 0.00 37.33 3.95
849 871 3.746492 GGCGTGTCTTCTTCACTAAACAT 59.254 43.478 0.00 0.00 34.14 2.71
918 947 8.306038 TCCCATAAAGAAAATCACAATGTTCTG 58.694 33.333 0.00 0.00 38.32 3.02
946 983 3.365472 TGCAACTGCTCCTAGAGACATA 58.635 45.455 2.95 0.00 42.66 2.29
1042 1096 5.163723 CCAATTACACTCACATGCCTTACAG 60.164 44.000 0.00 0.00 0.00 2.74
1095 1152 1.534175 GCTAACGACTCCATGGACTCG 60.534 57.143 30.57 30.57 36.82 4.18
1259 1328 3.521126 CCCTCCATGGTCCCTTATATGAG 59.479 52.174 12.58 0.00 0.00 2.90
1410 1479 5.069781 CACCTTAGGAAATCTAGTCCTCCTG 59.930 48.000 4.77 4.97 42.02 3.86
1716 1788 0.909623 TTTCCCCCGAGAATGACTCC 59.090 55.000 0.00 0.00 42.18 3.85
2130 2215 2.298661 GGGTTCCGGTCAGGTGGAT 61.299 63.158 0.00 0.00 41.99 3.41
2170 2255 5.829924 CACCCTGATATTTCAACTAAGCCAT 59.170 40.000 0.00 0.00 0.00 4.40
2184 3847 0.949397 AGCCATGCTATGTTGATGCG 59.051 50.000 0.00 0.00 36.99 4.73
2245 3917 0.400213 ACCGAACAATCTTGCTGGGA 59.600 50.000 1.98 0.00 0.00 4.37
2464 4172 1.417288 TCATCCCGCATGTGATCTCT 58.583 50.000 8.11 0.00 33.66 3.10
2478 4186 2.181205 GATCTCTTGCGTCAGTTCTCG 58.819 52.381 0.00 0.00 0.00 4.04
2662 4370 5.677852 GCTGAAATTGAGATGCTGTGCAATA 60.678 40.000 0.00 0.00 43.62 1.90
2730 4438 9.722056 GACAATAATGAGATGATTTTGGTGTAC 57.278 33.333 0.00 0.00 0.00 2.90
2777 4485 3.430236 CGTGAGCATCTGTACAATACCCA 60.430 47.826 0.00 0.00 34.92 4.51
3423 5161 2.403252 AACCATCGACCCACTCAATC 57.597 50.000 0.00 0.00 0.00 2.67
3535 5273 8.472007 TTGAAAGGTTCATTGTTACCTAATGT 57.528 30.769 11.74 1.94 43.88 2.71
3536 5274 8.472007 TGAAAGGTTCATTGTTACCTAATGTT 57.528 30.769 11.74 5.05 43.88 2.71
3537 5275 8.573035 TGAAAGGTTCATTGTTACCTAATGTTC 58.427 33.333 11.74 11.67 43.88 3.18
3539 5277 8.472007 AAGGTTCATTGTTACCTAATGTTCAA 57.528 30.769 11.74 0.00 43.88 2.69
3541 5279 9.747898 AGGTTCATTGTTACCTAATGTTCAATA 57.252 29.630 10.25 0.00 42.87 1.90
3593 5344 1.604604 ATGTTCCGGTGACTTTGGTG 58.395 50.000 0.00 0.00 0.00 4.17
3725 9003 7.393796 GGTGCTAGAGCCTGAATATACTTAGTA 59.606 40.741 0.00 0.00 41.18 1.82
3861 9146 1.476891 TGGTCAGGTTTAGCTCGCTAG 59.523 52.381 0.00 0.00 0.00 3.42
3940 9258 7.129816 ACCCAGGGTGGTTTATTTGTACTATAT 59.870 37.037 11.70 0.00 33.91 0.86
3965 9379 5.736951 AGGATATTAGCTAGGCTTGTGAG 57.263 43.478 0.00 0.00 40.44 3.51
3989 9403 5.009410 GCAATGCAGAATATATATGAGGCCC 59.991 44.000 0.00 0.00 0.00 5.80
4044 9458 0.378962 GACTACGTGCTCAGCGAGAT 59.621 55.000 0.00 0.00 0.00 2.75
4055 9469 4.122776 GCTCAGCGAGATAAAAATCCTGA 58.877 43.478 9.32 0.00 0.00 3.86
4056 9470 4.572389 GCTCAGCGAGATAAAAATCCTGAA 59.428 41.667 9.32 0.00 0.00 3.02
4057 9471 5.277250 GCTCAGCGAGATAAAAATCCTGAAG 60.277 44.000 9.32 0.00 0.00 3.02
4150 12556 1.486310 AGCTGTGGTTGTGAAGTGAGA 59.514 47.619 0.00 0.00 0.00 3.27
4187 12619 6.262273 ACAGGCAAGATTCGTTTCTCTTTTAA 59.738 34.615 0.00 0.00 29.34 1.52
4231 12663 5.650703 GGTTATTAGGCCTGTGTTGTATGTT 59.349 40.000 17.99 0.00 0.00 2.71
4235 12675 1.339610 GGCCTGTGTTGTATGTTTGCA 59.660 47.619 0.00 0.00 0.00 4.08
4355 12795 2.554462 GGAACAAGGAAAGAAGCTCCAC 59.446 50.000 0.00 0.00 35.20 4.02
4398 12838 5.221925 ACTCCATCCACATTGACTTGTAACT 60.222 40.000 0.00 0.00 0.00 2.24
4422 12864 6.808829 TGTCCATGATCAAATTAATTCTGGC 58.191 36.000 0.00 0.00 0.00 4.85
4423 12865 5.916883 GTCCATGATCAAATTAATTCTGGCG 59.083 40.000 0.00 0.00 0.00 5.69
4443 12885 3.679083 GCGGGTTGTAAGTCTTATCTGCT 60.679 47.826 0.00 0.00 0.00 4.24
4459 12901 3.963665 TCTGCTTATGTTTTGTGCACAC 58.036 40.909 21.56 9.20 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.926630 AGTATGAGGAGCTCTTTAATAGGG 57.073 41.667 14.64 0.00 0.00 3.53
1 2 7.158021 CCAAGTATGAGGAGCTCTTTAATAGG 58.842 42.308 14.64 2.49 0.00 2.57
2 3 6.648725 GCCAAGTATGAGGAGCTCTTTAATAG 59.351 42.308 14.64 0.00 0.00 1.73
3 4 6.525629 GCCAAGTATGAGGAGCTCTTTAATA 58.474 40.000 14.64 5.93 0.00 0.98
4 5 5.372373 GCCAAGTATGAGGAGCTCTTTAAT 58.628 41.667 14.64 6.92 0.00 1.40
5 6 4.680708 CGCCAAGTATGAGGAGCTCTTTAA 60.681 45.833 14.64 0.00 0.00 1.52
6 7 3.181475 CGCCAAGTATGAGGAGCTCTTTA 60.181 47.826 14.64 2.58 0.00 1.85
7 8 2.419297 CGCCAAGTATGAGGAGCTCTTT 60.419 50.000 14.64 1.93 0.00 2.52
8 9 1.137872 CGCCAAGTATGAGGAGCTCTT 59.862 52.381 14.64 5.66 0.00 2.85
9 10 0.749649 CGCCAAGTATGAGGAGCTCT 59.250 55.000 14.64 0.00 0.00 4.09
10 11 0.461961 ACGCCAAGTATGAGGAGCTC 59.538 55.000 4.71 4.71 0.00 4.09
11 12 1.776662 TACGCCAAGTATGAGGAGCT 58.223 50.000 0.00 0.00 0.00 4.09
12 13 2.596904 TTACGCCAAGTATGAGGAGC 57.403 50.000 0.00 0.00 34.88 4.70
13 14 5.116180 TGAAATTACGCCAAGTATGAGGAG 58.884 41.667 0.00 0.00 34.88 3.69
14 15 5.092554 TGAAATTACGCCAAGTATGAGGA 57.907 39.130 0.00 0.00 34.88 3.71
15 16 4.260784 GCTGAAATTACGCCAAGTATGAGG 60.261 45.833 0.00 0.00 34.88 3.86
16 17 4.572389 AGCTGAAATTACGCCAAGTATGAG 59.428 41.667 0.00 0.00 34.88 2.90
17 18 4.513442 AGCTGAAATTACGCCAAGTATGA 58.487 39.130 0.00 0.00 34.88 2.15
18 19 4.260784 GGAGCTGAAATTACGCCAAGTATG 60.261 45.833 0.00 0.00 34.88 2.39
19 20 3.877508 GGAGCTGAAATTACGCCAAGTAT 59.122 43.478 0.00 0.00 34.88 2.12
20 21 3.267483 GGAGCTGAAATTACGCCAAGTA 58.733 45.455 0.00 0.00 0.00 2.24
21 22 2.084546 GGAGCTGAAATTACGCCAAGT 58.915 47.619 0.00 0.00 0.00 3.16
22 23 2.083774 TGGAGCTGAAATTACGCCAAG 58.916 47.619 0.00 0.00 0.00 3.61
23 24 1.810151 GTGGAGCTGAAATTACGCCAA 59.190 47.619 0.00 0.00 0.00 4.52
24 25 1.448985 GTGGAGCTGAAATTACGCCA 58.551 50.000 0.00 0.00 0.00 5.69
25 26 0.733150 GGTGGAGCTGAAATTACGCC 59.267 55.000 0.00 0.00 0.00 5.68
26 27 1.398390 CTGGTGGAGCTGAAATTACGC 59.602 52.381 0.00 0.00 0.00 4.42
27 28 2.972625 TCTGGTGGAGCTGAAATTACG 58.027 47.619 0.00 0.00 0.00 3.18
28 29 7.255277 GGATTATTCTGGTGGAGCTGAAATTAC 60.255 40.741 0.00 0.00 0.00 1.89
29 30 6.772716 GGATTATTCTGGTGGAGCTGAAATTA 59.227 38.462 0.00 0.00 0.00 1.40
30 31 5.595952 GGATTATTCTGGTGGAGCTGAAATT 59.404 40.000 0.00 0.00 0.00 1.82
31 32 5.136105 GGATTATTCTGGTGGAGCTGAAAT 58.864 41.667 0.00 0.00 0.00 2.17
32 33 4.018506 TGGATTATTCTGGTGGAGCTGAAA 60.019 41.667 0.00 0.00 0.00 2.69
33 34 3.523157 TGGATTATTCTGGTGGAGCTGAA 59.477 43.478 0.00 1.35 0.00 3.02
34 35 3.114606 TGGATTATTCTGGTGGAGCTGA 58.885 45.455 0.00 0.00 0.00 4.26
35 36 3.209410 GTGGATTATTCTGGTGGAGCTG 58.791 50.000 0.00 0.00 0.00 4.24
36 37 2.173569 GGTGGATTATTCTGGTGGAGCT 59.826 50.000 0.00 0.00 0.00 4.09
37 38 2.173569 AGGTGGATTATTCTGGTGGAGC 59.826 50.000 0.00 0.00 0.00 4.70
38 39 3.713764 AGAGGTGGATTATTCTGGTGGAG 59.286 47.826 0.00 0.00 0.00 3.86
39 40 3.736094 AGAGGTGGATTATTCTGGTGGA 58.264 45.455 0.00 0.00 0.00 4.02
40 41 4.510167 AAGAGGTGGATTATTCTGGTGG 57.490 45.455 0.00 0.00 0.00 4.61
41 42 6.653989 AGTAAAGAGGTGGATTATTCTGGTG 58.346 40.000 0.00 0.00 0.00 4.17
42 43 6.893020 AGTAAAGAGGTGGATTATTCTGGT 57.107 37.500 0.00 0.00 0.00 4.00
43 44 8.581253 AAAAGTAAAGAGGTGGATTATTCTGG 57.419 34.615 0.00 0.00 0.00 3.86
51 52 9.981114 CACAAAATTAAAAGTAAAGAGGTGGAT 57.019 29.630 0.00 0.00 0.00 3.41
52 53 8.973182 ACACAAAATTAAAAGTAAAGAGGTGGA 58.027 29.630 0.00 0.00 0.00 4.02
53 54 9.030301 CACACAAAATTAAAAGTAAAGAGGTGG 57.970 33.333 0.00 0.00 0.00 4.61
54 55 8.539674 GCACACAAAATTAAAAGTAAAGAGGTG 58.460 33.333 0.00 0.00 0.00 4.00
117 118 7.179338 AGACTAGAAAGATGCTACTTCAAAGGA 59.821 37.037 0.00 0.00 0.00 3.36
130 131 6.264518 GGAACTCCCTAGAGACTAGAAAGATG 59.735 46.154 0.00 0.00 43.39 2.90
171 172 6.855763 AATCAGGCTGAAAATTGGTTCATA 57.144 33.333 22.84 0.00 36.92 2.15
232 233 4.816126 AGGCTGGGTGTAATCAGTATCTA 58.184 43.478 0.00 0.00 33.81 1.98
240 241 0.253044 TGCAGAGGCTGGGTGTAATC 59.747 55.000 0.00 0.00 41.91 1.75
351 352 9.781633 TTTAGCCAAACAAAGTATCTACTGTAA 57.218 29.630 0.00 0.00 36.50 2.41
354 355 9.774742 GAATTTAGCCAAACAAAGTATCTACTG 57.225 33.333 0.00 0.00 36.50 2.74
460 462 5.710099 CCATGCTTTCCAGGTACTCTAAAAA 59.290 40.000 0.00 0.00 34.60 1.94
461 463 5.222048 ACCATGCTTTCCAGGTACTCTAAAA 60.222 40.000 0.00 0.00 34.60 1.52
462 464 4.288626 ACCATGCTTTCCAGGTACTCTAAA 59.711 41.667 0.00 0.00 34.60 1.85
463 465 3.844211 ACCATGCTTTCCAGGTACTCTAA 59.156 43.478 0.00 0.00 34.60 2.10
464 466 3.450904 ACCATGCTTTCCAGGTACTCTA 58.549 45.455 0.00 0.00 34.60 2.43
465 467 2.237392 GACCATGCTTTCCAGGTACTCT 59.763 50.000 0.00 0.00 34.60 3.24
466 468 2.633488 GACCATGCTTTCCAGGTACTC 58.367 52.381 0.00 0.00 34.60 2.59
467 469 1.282157 GGACCATGCTTTCCAGGTACT 59.718 52.381 0.00 0.00 43.88 2.73
468 470 1.282157 AGGACCATGCTTTCCAGGTAC 59.718 52.381 8.48 0.00 35.11 3.34
469 471 1.559682 GAGGACCATGCTTTCCAGGTA 59.440 52.381 8.48 0.00 33.77 3.08
470 472 0.329596 GAGGACCATGCTTTCCAGGT 59.670 55.000 8.48 0.00 37.00 4.00
471 473 0.329261 TGAGGACCATGCTTTCCAGG 59.671 55.000 8.48 0.00 33.92 4.45
472 474 2.089980 CTTGAGGACCATGCTTTCCAG 58.910 52.381 8.48 0.00 33.92 3.86
473 475 1.704628 TCTTGAGGACCATGCTTTCCA 59.295 47.619 8.48 0.00 33.92 3.53
474 476 2.496899 TCTTGAGGACCATGCTTTCC 57.503 50.000 0.00 0.00 0.00 3.13
475 477 6.515272 TTTATTCTTGAGGACCATGCTTTC 57.485 37.500 0.00 0.00 0.00 2.62
476 478 7.286316 CCTATTTATTCTTGAGGACCATGCTTT 59.714 37.037 0.00 0.00 0.00 3.51
477 479 6.774656 CCTATTTATTCTTGAGGACCATGCTT 59.225 38.462 0.00 0.00 0.00 3.91
478 480 6.101734 TCCTATTTATTCTTGAGGACCATGCT 59.898 38.462 0.00 0.00 31.25 3.79
479 481 6.299141 TCCTATTTATTCTTGAGGACCATGC 58.701 40.000 0.00 0.00 31.25 4.06
480 482 7.229506 GGTTCCTATTTATTCTTGAGGACCATG 59.770 40.741 0.00 0.00 36.04 3.66
481 483 7.129504 AGGTTCCTATTTATTCTTGAGGACCAT 59.870 37.037 0.00 0.00 36.04 3.55
482 484 6.447084 AGGTTCCTATTTATTCTTGAGGACCA 59.553 38.462 0.00 0.00 36.04 4.02
483 485 6.901300 AGGTTCCTATTTATTCTTGAGGACC 58.099 40.000 0.00 0.00 36.04 4.46
484 486 9.901172 TTTAGGTTCCTATTTATTCTTGAGGAC 57.099 33.333 0.00 0.00 36.04 3.85
489 491 9.665264 GCGAATTTAGGTTCCTATTTATTCTTG 57.335 33.333 16.98 10.01 0.00 3.02
490 492 8.847196 GGCGAATTTAGGTTCCTATTTATTCTT 58.153 33.333 16.98 2.44 0.00 2.52
491 493 8.218488 AGGCGAATTTAGGTTCCTATTTATTCT 58.782 33.333 16.98 0.00 0.00 2.40
492 494 8.392372 AGGCGAATTTAGGTTCCTATTTATTC 57.608 34.615 0.00 8.38 0.00 1.75
493 495 7.447545 GGAGGCGAATTTAGGTTCCTATTTATT 59.552 37.037 0.00 1.48 0.00 1.40
494 496 6.940867 GGAGGCGAATTTAGGTTCCTATTTAT 59.059 38.462 0.00 0.00 0.00 1.40
495 497 6.293698 GGAGGCGAATTTAGGTTCCTATTTA 58.706 40.000 0.00 0.00 0.00 1.40
496 498 5.131067 GGAGGCGAATTTAGGTTCCTATTT 58.869 41.667 0.00 0.00 0.00 1.40
497 499 4.715713 GGAGGCGAATTTAGGTTCCTATT 58.284 43.478 0.00 0.00 0.00 1.73
498 500 3.244112 CGGAGGCGAATTTAGGTTCCTAT 60.244 47.826 0.00 0.00 0.00 2.57
499 501 2.101917 CGGAGGCGAATTTAGGTTCCTA 59.898 50.000 0.00 0.00 0.00 2.94
500 502 1.134491 CGGAGGCGAATTTAGGTTCCT 60.134 52.381 0.00 0.00 0.00 3.36
501 503 1.296727 CGGAGGCGAATTTAGGTTCC 58.703 55.000 0.00 0.00 0.00 3.62
502 504 1.664151 CACGGAGGCGAATTTAGGTTC 59.336 52.381 0.00 0.00 0.00 3.62
503 505 1.276989 TCACGGAGGCGAATTTAGGTT 59.723 47.619 0.00 0.00 0.00 3.50
504 506 0.899720 TCACGGAGGCGAATTTAGGT 59.100 50.000 0.00 0.00 0.00 3.08
505 507 1.571919 CTCACGGAGGCGAATTTAGG 58.428 55.000 0.00 0.00 0.00 2.69
506 508 1.571919 CCTCACGGAGGCGAATTTAG 58.428 55.000 6.97 0.00 43.29 1.85
507 509 3.752796 CCTCACGGAGGCGAATTTA 57.247 52.632 6.97 0.00 43.29 1.40
508 510 4.617875 CCTCACGGAGGCGAATTT 57.382 55.556 6.97 0.00 43.29 1.82
516 518 0.179108 GGGTTCGAATCCTCACGGAG 60.179 60.000 20.59 0.00 44.06 4.63
517 519 0.901114 TGGGTTCGAATCCTCACGGA 60.901 55.000 27.18 3.80 45.16 4.69
518 520 0.460284 CTGGGTTCGAATCCTCACGG 60.460 60.000 27.18 4.57 0.00 4.94
519 521 0.460284 CCTGGGTTCGAATCCTCACG 60.460 60.000 27.18 13.01 0.00 4.35
520 522 0.613777 ACCTGGGTTCGAATCCTCAC 59.386 55.000 27.18 3.79 0.00 3.51
521 523 0.613260 CACCTGGGTTCGAATCCTCA 59.387 55.000 27.18 8.55 0.00 3.86
522 524 0.613777 ACACCTGGGTTCGAATCCTC 59.386 55.000 27.18 3.71 0.00 3.71
523 525 1.064825 AACACCTGGGTTCGAATCCT 58.935 50.000 27.18 5.38 0.00 3.24
524 526 1.165270 CAACACCTGGGTTCGAATCC 58.835 55.000 21.05 21.05 0.00 3.01
525 527 1.165270 CCAACACCTGGGTTCGAATC 58.835 55.000 0.00 0.00 42.17 2.52
526 528 3.339547 CCAACACCTGGGTTCGAAT 57.660 52.632 0.00 0.00 42.17 3.34
527 529 4.889807 CCAACACCTGGGTTCGAA 57.110 55.556 0.00 0.00 42.17 3.71
534 536 2.060050 TGTACAAACCCAACACCTGG 57.940 50.000 0.00 0.00 45.97 4.45
535 537 2.556622 GGATGTACAAACCCAACACCTG 59.443 50.000 0.00 0.00 0.00 4.00
536 538 2.175931 TGGATGTACAAACCCAACACCT 59.824 45.455 16.34 0.00 0.00 4.00
537 539 2.295070 GTGGATGTACAAACCCAACACC 59.705 50.000 14.17 2.24 0.00 4.16
538 540 3.219281 AGTGGATGTACAAACCCAACAC 58.781 45.455 14.17 9.16 0.00 3.32
539 541 3.482436 GAGTGGATGTACAAACCCAACA 58.518 45.455 14.17 0.00 0.00 3.33
540 542 2.817844 GGAGTGGATGTACAAACCCAAC 59.182 50.000 14.17 9.51 0.00 3.77
541 543 2.224917 GGGAGTGGATGTACAAACCCAA 60.225 50.000 14.17 0.00 37.68 4.12
542 544 1.353022 GGGAGTGGATGTACAAACCCA 59.647 52.381 16.34 13.27 37.68 4.51
543 545 1.340697 GGGGAGTGGATGTACAAACCC 60.341 57.143 16.34 13.70 37.30 4.11
544 546 1.340697 GGGGGAGTGGATGTACAAACC 60.341 57.143 13.39 13.39 0.00 3.27
545 547 1.353022 TGGGGGAGTGGATGTACAAAC 59.647 52.381 0.00 0.00 0.00 2.93
546 548 1.748732 TGGGGGAGTGGATGTACAAA 58.251 50.000 0.00 0.00 0.00 2.83
547 549 1.353022 GTTGGGGGAGTGGATGTACAA 59.647 52.381 0.00 0.00 0.00 2.41
548 550 0.988832 GTTGGGGGAGTGGATGTACA 59.011 55.000 0.00 0.00 0.00 2.90
549 551 0.255033 GGTTGGGGGAGTGGATGTAC 59.745 60.000 0.00 0.00 0.00 2.90
550 552 0.178858 TGGTTGGGGGAGTGGATGTA 60.179 55.000 0.00 0.00 0.00 2.29
551 553 1.465188 TGGTTGGGGGAGTGGATGT 60.465 57.895 0.00 0.00 0.00 3.06
552 554 1.304282 CTGGTTGGGGGAGTGGATG 59.696 63.158 0.00 0.00 0.00 3.51
553 555 0.776080 AACTGGTTGGGGGAGTGGAT 60.776 55.000 0.00 0.00 0.00 3.41
554 556 1.386772 AACTGGTTGGGGGAGTGGA 60.387 57.895 0.00 0.00 0.00 4.02
555 557 1.228552 CAACTGGTTGGGGGAGTGG 60.229 63.158 5.64 0.00 36.95 4.00
556 558 0.250901 CTCAACTGGTTGGGGGAGTG 60.251 60.000 12.65 0.00 40.78 3.51
557 559 2.069165 GCTCAACTGGTTGGGGGAGT 62.069 60.000 14.16 0.00 41.25 3.85
558 560 1.303643 GCTCAACTGGTTGGGGGAG 60.304 63.158 14.16 5.72 41.25 4.30
559 561 0.474854 TAGCTCAACTGGTTGGGGGA 60.475 55.000 14.16 0.00 41.25 4.81
560 562 0.035056 CTAGCTCAACTGGTTGGGGG 60.035 60.000 14.16 6.57 41.25 5.40
561 563 0.035056 CCTAGCTCAACTGGTTGGGG 60.035 60.000 14.16 8.58 41.25 4.96
562 564 0.678048 GCCTAGCTCAACTGGTTGGG 60.678 60.000 12.65 10.80 43.71 4.12
563 565 0.326264 AGCCTAGCTCAACTGGTTGG 59.674 55.000 12.65 5.82 40.78 3.77
564 566 3.944476 AGCCTAGCTCAACTGGTTG 57.056 52.632 7.10 7.10 41.71 3.77
574 576 0.547712 TTTGGGGAGTGAGCCTAGCT 60.548 55.000 0.00 0.00 43.88 3.32
575 577 0.107459 CTTTGGGGAGTGAGCCTAGC 60.107 60.000 0.00 0.00 0.00 3.42
576 578 1.484240 CTCTTTGGGGAGTGAGCCTAG 59.516 57.143 0.00 0.00 0.00 3.02
577 579 1.078823 TCTCTTTGGGGAGTGAGCCTA 59.921 52.381 0.00 0.00 35.11 3.93
578 580 0.178891 TCTCTTTGGGGAGTGAGCCT 60.179 55.000 0.00 0.00 35.11 4.58
579 581 0.251634 CTCTCTTTGGGGAGTGAGCC 59.748 60.000 0.00 0.00 32.51 4.70
580 582 3.851051 CTCTCTTTGGGGAGTGAGC 57.149 57.895 0.00 0.00 32.51 4.26
581 583 1.206849 GAGCTCTCTTTGGGGAGTGAG 59.793 57.143 6.43 0.00 39.23 3.51
582 584 1.270907 GAGCTCTCTTTGGGGAGTGA 58.729 55.000 6.43 0.00 35.11 3.41
583 585 0.251634 GGAGCTCTCTTTGGGGAGTG 59.748 60.000 14.64 0.00 35.11 3.51
584 586 0.178891 TGGAGCTCTCTTTGGGGAGT 60.179 55.000 14.64 0.00 35.11 3.85
585 587 1.211456 ATGGAGCTCTCTTTGGGGAG 58.789 55.000 14.64 0.00 34.88 4.30
586 588 1.673767 AATGGAGCTCTCTTTGGGGA 58.326 50.000 14.64 0.00 0.00 4.81
587 589 2.507471 ACTAATGGAGCTCTCTTTGGGG 59.493 50.000 14.64 6.32 0.00 4.96
588 590 3.198635 TCACTAATGGAGCTCTCTTTGGG 59.801 47.826 14.64 9.50 0.00 4.12
589 591 4.081198 ACTCACTAATGGAGCTCTCTTTGG 60.081 45.833 14.64 11.89 35.79 3.28
590 592 5.083533 ACTCACTAATGGAGCTCTCTTTG 57.916 43.478 14.64 10.52 35.79 2.77
591 593 5.163457 GCTACTCACTAATGGAGCTCTCTTT 60.163 44.000 14.64 10.43 35.79 2.52
592 594 4.340950 GCTACTCACTAATGGAGCTCTCTT 59.659 45.833 14.64 9.85 35.79 2.85
593 595 3.888930 GCTACTCACTAATGGAGCTCTCT 59.111 47.826 14.64 0.74 35.79 3.10
594 596 3.304391 CGCTACTCACTAATGGAGCTCTC 60.304 52.174 14.64 4.40 35.79 3.20
667 669 9.822185 ATTTCAAGAACTTCAGCAAAATAGTTT 57.178 25.926 0.00 0.00 31.41 2.66
749 759 4.837896 TTCATGGCAATACGAACAACAA 57.162 36.364 0.00 0.00 0.00 2.83
758 768 6.318648 TCCACTAAACTGATTCATGGCAATAC 59.681 38.462 0.00 0.00 0.00 1.89
849 871 9.457436 GTCAGGGAAATTGGAAAATAGTACTAA 57.543 33.333 6.70 0.00 0.00 2.24
859 881 6.516527 CGAGAAAATGTCAGGGAAATTGGAAA 60.517 38.462 0.00 0.00 0.00 3.13
869 898 1.339055 TGGAGCGAGAAAATGTCAGGG 60.339 52.381 0.00 0.00 0.00 4.45
918 947 0.543749 AGGAGCAGTTGCATAGGGTC 59.456 55.000 6.90 0.00 45.16 4.46
946 983 4.973168 TGGAGACTTCTGTTTGCTACAAT 58.027 39.130 0.00 0.00 36.02 2.71
1042 1096 4.403453 GCAATCGACAAGAATACCAACAC 58.597 43.478 0.00 0.00 0.00 3.32
1095 1152 2.379005 CAATTTAGGAGGACAAGGCCC 58.621 52.381 0.00 0.00 0.00 5.80
1259 1328 0.867746 TGAAGTGAAGATGCGTGCAC 59.132 50.000 6.82 6.82 0.00 4.57
1365 1434 0.804989 CACCAAAGAAGGCATCGGAC 59.195 55.000 0.00 0.00 0.00 4.79
1410 1479 5.284660 CGTTTGTGAAGCATTGAAGCTATTC 59.715 40.000 0.00 0.00 45.89 1.75
1812 1897 0.534203 ACTTTGGCACTACGGGTGTG 60.534 55.000 11.35 6.52 46.86 3.82
2098 2183 2.305927 CGGAACCCCTAGCCATGATAAT 59.694 50.000 0.00 0.00 0.00 1.28
2112 2197 0.979187 TATCCACCTGACCGGAACCC 60.979 60.000 9.46 0.00 34.22 4.11
2170 2255 4.320608 TCAGTATCGCATCAACATAGCA 57.679 40.909 0.00 0.00 0.00 3.49
2184 3847 5.606348 AGACCTCAAGACCATTCAGTATC 57.394 43.478 0.00 0.00 0.00 2.24
2245 3917 6.071165 GGATTTTGTTGAAGTGGAGGATTGAT 60.071 38.462 0.00 0.00 0.00 2.57
2407 4097 1.801178 GGTCTTGCAAGAACTCTTCCG 59.199 52.381 32.62 2.97 39.66 4.30
2464 4172 2.029970 GTGAAAACGAGAACTGACGCAA 59.970 45.455 0.00 0.00 0.00 4.85
2478 4186 5.970612 GGTGGCAATTTGAATTTGTGAAAAC 59.029 36.000 0.00 0.00 0.00 2.43
2662 4370 3.743017 AAGGTGGCCATGGCGGAT 61.743 61.111 29.90 13.28 43.06 4.18
2730 4438 2.205074 GTTCCATGAGCCATGTAGTCG 58.795 52.381 12.36 0.37 39.94 4.18
2864 4572 2.216046 CATCACGGTGGATGATTCCTG 58.784 52.381 8.50 0.00 46.00 3.86
3285 4993 1.077068 TCCCATTGTTGGCCGATCC 60.077 57.895 0.00 0.00 42.15 3.36
3303 5011 5.413309 CCTCAAGGTTCTGAAGTACATCT 57.587 43.478 0.00 0.00 0.00 2.90
3423 5161 0.723414 CCTGTGCAGCGACACTAATG 59.277 55.000 12.44 2.40 41.30 1.90
3587 5338 7.587037 AAATGATCTGAGAGTTTTCACCAAA 57.413 32.000 0.00 0.00 0.00 3.28
3745 9026 8.634335 TGGAATTGAATCAACAAGAAGTGATA 57.366 30.769 0.00 0.00 33.22 2.15
3861 9146 0.680061 AGTCCTTCACTTGACCGGAC 59.320 55.000 9.46 14.78 41.51 4.79
3940 9258 7.068839 GCTCACAAGCCTAGCTAATATCCTATA 59.931 40.741 0.00 0.00 43.10 1.31
3942 9260 5.186021 GCTCACAAGCCTAGCTAATATCCTA 59.814 44.000 0.00 0.00 43.10 2.94
3943 9261 4.020662 GCTCACAAGCCTAGCTAATATCCT 60.021 45.833 0.00 0.00 43.10 3.24
3965 9379 5.009410 GGGCCTCATATATATTCTGCATTGC 59.991 44.000 0.84 0.46 0.00 3.56
3989 9403 3.569701 AGTTGGCATATTTAATCCCTGCG 59.430 43.478 0.00 0.00 33.69 5.18
4055 9469 8.837389 GTGAAGTGTGAACTAATTAACTTCCTT 58.163 33.333 17.01 7.25 41.68 3.36
4056 9470 7.990886 TGTGAAGTGTGAACTAATTAACTTCCT 59.009 33.333 17.01 1.14 41.68 3.36
4057 9471 8.149973 TGTGAAGTGTGAACTAATTAACTTCC 57.850 34.615 17.01 11.59 41.68 3.46
4062 9476 7.985184 ACTGACTGTGAAGTGTGAACTAATTAA 59.015 33.333 0.00 0.00 0.00 1.40
4063 9477 7.497595 ACTGACTGTGAAGTGTGAACTAATTA 58.502 34.615 0.00 0.00 0.00 1.40
4065 9479 5.918608 ACTGACTGTGAAGTGTGAACTAAT 58.081 37.500 0.00 0.00 0.00 1.73
4122 9536 8.870116 TCACTTCACAACCACAGCTATATATAT 58.130 33.333 0.00 0.00 0.00 0.86
4124 9538 7.069950 TCTCACTTCACAACCACAGCTATATAT 59.930 37.037 0.00 0.00 0.00 0.86
4125 9539 6.379988 TCTCACTTCACAACCACAGCTATATA 59.620 38.462 0.00 0.00 0.00 0.86
4136 12542 5.847670 GTGAACTATCTCACTTCACAACC 57.152 43.478 5.15 0.00 42.22 3.77
4150 12556 6.313905 CGAATCTTGCCTGTTAAGTGAACTAT 59.686 38.462 0.00 0.00 38.98 2.12
4187 12619 1.665735 CGCGGCTAGTGCAAACAAATT 60.666 47.619 0.00 0.00 41.91 1.82
4235 12675 2.938756 GCAGTTCATTCCAGCAGCTAGT 60.939 50.000 0.00 0.00 0.00 2.57
4355 12795 4.201930 GGAGTACGTCTGAATCAGTACCAG 60.202 50.000 10.36 1.64 39.99 4.00
4398 12838 6.459985 CGCCAGAATTAATTTGATCATGGACA 60.460 38.462 9.80 0.00 0.00 4.02
4422 12864 4.124851 AGCAGATAAGACTTACAACCCG 57.875 45.455 0.00 0.00 0.00 5.28
4423 12865 7.048512 ACATAAGCAGATAAGACTTACAACCC 58.951 38.462 0.00 0.00 0.00 4.11
4443 12885 5.268118 TCCAATGTGTGCACAAAACATAA 57.732 34.783 23.59 7.63 45.41 1.90
4459 12901 5.170748 GCCTTAGTTTGACCAATTCCAATG 58.829 41.667 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.