Multiple sequence alignment - TraesCS1D01G194700

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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 TraesCS1D01G194700 chr1D 100.000 5707 0 0 1 5707 272186967 272192673 0.000000e+00 10539
1 TraesCS1D01G194700 chr1D 98.214 168 1 1 5540 5707 272208988 272209153 5.590000e-75 292
2 TraesCS1D01G194700 chr1A 93.243 3922 152 39 1685 5540 344291297 344295171 0.000000e+00 5670
3 TraesCS1D01G194700 chr1A 92.636 1711 86 13 1 1690 344289352 344291043 0.000000e+00 2425
4 TraesCS1D01G194700 chr1B 94.365 1739 44 23 3361 5087 371141187 371142883 0.000000e+00 2619
5 TraesCS1D01G194700 chr1B 90.081 1845 92 31 1 1802 371137863 371139659 0.000000e+00 2309
6 TraesCS1D01G194700 chr1B 92.647 476 21 5 5075 5540 371144548 371145019 0.000000e+00 673
7 TraesCS1D01G194700 chr1B 86.449 642 37 12 1879 2485 371139655 371140281 0.000000e+00 658
8 TraesCS1D01G194700 chr5A 88.448 831 70 7 865 1679 49741165 49740345 0.000000e+00 979
9 TraesCS1D01G194700 chr5A 87.349 830 83 4 865 1679 49851327 49850505 0.000000e+00 931
10 TraesCS1D01G194700 chr5A 88.345 695 63 8 865 1553 49741898 49741216 0.000000e+00 819
11 TraesCS1D01G194700 chr5A 94.186 172 7 2 5539 5707 464103755 464103584 5.670000e-65 259
12 TraesCS1D01G194700 chr7A 96.471 170 3 2 5539 5707 236107101 236106934 1.570000e-70 278
13 TraesCS1D01G194700 chr7A 96.471 170 3 2 5539 5707 236127359 236127192 1.570000e-70 278
14 TraesCS1D01G194700 chr7A 94.857 175 5 3 5535 5707 236111872 236111700 2.620000e-68 270
15 TraesCS1D01G194700 chr7A 94.857 175 5 3 5535 5707 236132127 236131955 2.620000e-68 270
16 TraesCS1D01G194700 chr6A 95.858 169 4 2 5540 5707 596311415 596311581 2.620000e-68 270
17 TraesCS1D01G194700 chr2A 95.294 170 5 2 5539 5707 765057597 765057430 3.390000e-67 267
18 TraesCS1D01G194700 chr2B 95.294 170 3 2 5539 5707 236844088 236843923 1.220000e-66 265


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 TraesCS1D01G194700 chr1D 272186967 272192673 5706 False 10539.00 10539 100.0000 1 5707 1 chr1D.!!$F1 5706
1 TraesCS1D01G194700 chr1A 344289352 344295171 5819 False 4047.50 5670 92.9395 1 5540 2 chr1A.!!$F1 5539
2 TraesCS1D01G194700 chr1B 371137863 371145019 7156 False 1564.75 2619 90.8855 1 5540 4 chr1B.!!$F1 5539
3 TraesCS1D01G194700 chr5A 49850505 49851327 822 True 931.00 931 87.3490 865 1679 1 chr5A.!!$R1 814
4 TraesCS1D01G194700 chr5A 49740345 49741898 1553 True 899.00 979 88.3965 865 1679 2 chr5A.!!$R3 814

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
486 502 0.112412 ATTGGTGGTGGTGGAGTTCC 59.888 55.0 0.00 0.00 0.00 3.62 F
997 1021 0.389166 GCTCTCTGTCGGACTTGTGG 60.389 60.0 9.88 0.00 0.00 4.17 F
2632 3804 0.176680 GTGCTGATCGTGGATCCACT 59.823 55.0 35.84 22.70 44.16 4.00 F
2955 4136 0.106708 ATAGCATTCCACGTGGCGAT 59.893 50.0 30.25 21.64 34.44 4.58 F
3052 4247 0.327000 AAGTAGAGCCAGGGGAGCAT 60.327 55.0 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 2140 2.756400 GCCATCTCCACACCACCA 59.244 61.111 0.00 0.0 0.00 4.17 R
2919 4100 2.009051 CTATCAGCATTTGACGGCACA 58.991 47.619 0.00 0.0 38.99 4.57 R
3869 5169 0.514691 GAGACTTCAGCTGGTTTGCG 59.485 55.000 15.13 0.0 38.13 4.85 R
4548 5851 0.823356 ACCGCCTGACATGCAAAAGT 60.823 50.000 3.55 0.0 0.00 2.66 R
4706 6009 2.175878 ACAGACGAAATGCTTCAGCT 57.824 45.000 0.00 0.0 42.66 4.24 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
41 46 1.066286 GCTGATCTGTCCTGCAGTCTT 60.066 52.381 13.81 0.00 45.23 3.01
59 64 2.755655 TCTTCTCCTAGGAAAGCGTCAG 59.244 50.000 13.77 0.00 0.00 3.51
109 114 4.101448 CCTGGCTCCCGTCCAAGG 62.101 72.222 0.00 0.00 32.41 3.61
120 125 1.852067 CGTCCAAGGCCCTCGTTTTG 61.852 60.000 0.00 0.00 0.00 2.44
202 207 3.016736 GTGTCCAATTATCCAGTGGGTG 58.983 50.000 9.92 0.31 34.93 4.61
338 343 3.414700 CGTGCGCCTGTCTGTTCC 61.415 66.667 4.18 0.00 0.00 3.62
426 442 2.814336 CCACTTGGAGAGTTAACAAGGC 59.186 50.000 8.61 0.00 44.35 4.35
431 447 2.158682 TGGAGAGTTAACAAGGCAGCAA 60.159 45.455 8.61 0.00 0.00 3.91
434 450 3.555966 AGAGTTAACAAGGCAGCAACTT 58.444 40.909 8.61 0.00 29.89 2.66
476 492 8.292444 TCCTAGATCATTTTTAATTGGTGGTG 57.708 34.615 0.00 0.00 0.00 4.17
477 493 7.341769 TCCTAGATCATTTTTAATTGGTGGTGG 59.658 37.037 0.00 0.00 0.00 4.61
479 495 6.700352 AGATCATTTTTAATTGGTGGTGGTG 58.300 36.000 0.00 0.00 0.00 4.17
480 496 5.220710 TCATTTTTAATTGGTGGTGGTGG 57.779 39.130 0.00 0.00 0.00 4.61
481 497 4.901849 TCATTTTTAATTGGTGGTGGTGGA 59.098 37.500 0.00 0.00 0.00 4.02
482 498 4.946478 TTTTTAATTGGTGGTGGTGGAG 57.054 40.909 0.00 0.00 0.00 3.86
483 499 3.603965 TTTAATTGGTGGTGGTGGAGT 57.396 42.857 0.00 0.00 0.00 3.85
484 500 3.603965 TTAATTGGTGGTGGTGGAGTT 57.396 42.857 0.00 0.00 0.00 3.01
485 501 1.995376 AATTGGTGGTGGTGGAGTTC 58.005 50.000 0.00 0.00 0.00 3.01
486 502 0.112412 ATTGGTGGTGGTGGAGTTCC 59.888 55.000 0.00 0.00 0.00 3.62
487 503 1.282653 TTGGTGGTGGTGGAGTTCCA 61.283 55.000 0.00 0.00 45.30 3.53
511 527 2.911484 CAAGCCCCAGATCAACTAGAC 58.089 52.381 0.00 0.00 0.00 2.59
572 588 5.050091 ACTGCAATTTACTCAGTCAAACTCG 60.050 40.000 0.00 0.00 36.42 4.18
582 598 5.009710 ACTCAGTCAAACTCGTGATCAGTTA 59.990 40.000 0.00 0.00 32.71 2.24
583 599 6.025749 TCAGTCAAACTCGTGATCAGTTAT 57.974 37.500 0.00 0.00 32.71 1.89
584 600 7.094334 ACTCAGTCAAACTCGTGATCAGTTATA 60.094 37.037 0.00 0.00 32.71 0.98
586 602 8.085909 TCAGTCAAACTCGTGATCAGTTATAAA 58.914 33.333 0.00 0.00 32.71 1.40
588 604 9.436957 AGTCAAACTCGTGATCAGTTATAAAAT 57.563 29.630 0.00 0.00 32.71 1.82
680 704 0.868406 GAGCGGTGAGTGGAGTTTTG 59.132 55.000 0.00 0.00 0.00 2.44
687 711 2.032178 GTGAGTGGAGTTTTGACAGTGC 59.968 50.000 0.00 0.00 0.00 4.40
690 714 2.159014 AGTGGAGTTTTGACAGTGCGTA 60.159 45.455 0.00 0.00 0.00 4.42
737 761 2.359354 TGGTGCGATTGGGAACGG 60.359 61.111 0.00 0.00 0.00 4.44
779 803 1.449423 CATCCCGATGCGGTGACAA 60.449 57.895 5.06 0.00 46.80 3.18
833 857 1.667467 GCCTACGCATTTTGCCGAAAA 60.667 47.619 0.00 0.00 41.12 2.29
969 993 4.541648 GGCCCGCTCCCCTCTCTA 62.542 72.222 0.00 0.00 0.00 2.43
988 1012 1.317613 ATAGGCTCTGCTCTCTGTCG 58.682 55.000 0.00 0.00 0.00 4.35
990 1014 2.049185 GGCTCTGCTCTCTGTCGGA 61.049 63.158 0.00 0.00 0.00 4.55
993 1017 1.173043 CTCTGCTCTCTGTCGGACTT 58.827 55.000 9.88 0.00 0.00 3.01
995 1019 0.600557 CTGCTCTCTGTCGGACTTGT 59.399 55.000 9.88 0.00 0.00 3.16
997 1021 0.389166 GCTCTCTGTCGGACTTGTGG 60.389 60.000 9.88 0.00 0.00 4.17
999 1023 1.201181 CTCTCTGTCGGACTTGTGGAG 59.799 57.143 9.88 8.86 0.00 3.86
1525 2294 2.736995 TTTCGTCCCTGCTTCGCG 60.737 61.111 0.00 0.00 0.00 5.87
1574 2352 0.248866 CTTCGGCTTTGCGTTGGTTT 60.249 50.000 0.00 0.00 0.00 3.27
1679 2460 4.789012 TGTTGGAATCAGGAAATCTTGC 57.211 40.909 0.00 0.00 0.00 4.01
1828 2869 6.128063 CCACTTTATTTCTCTCTGCCTCTTTG 60.128 42.308 0.00 0.00 0.00 2.77
2037 3086 6.952773 ACTTGCTATTGTTTGTTTGGAGTA 57.047 33.333 0.00 0.00 0.00 2.59
2092 3141 8.610896 CATTTTTCTAGAGAATGAAAGCGATCT 58.389 33.333 18.85 0.00 34.29 2.75
2178 3229 9.116054 CCATTTTTGTTGTAATTTGCATTTAGC 57.884 29.630 0.00 0.00 45.96 3.09
2232 3293 5.461078 CCATTTGACTTCTGAGCTGTTTTTG 59.539 40.000 0.00 0.00 0.00 2.44
2435 3511 4.707448 TCTCTTGGCTCTAGGAAACACTAG 59.293 45.833 0.00 0.00 41.41 2.57
2626 3798 0.599991 GTGTGTGTGCTGATCGTGGA 60.600 55.000 0.00 0.00 0.00 4.02
2632 3804 0.176680 GTGCTGATCGTGGATCCACT 59.823 55.000 35.84 22.70 44.16 4.00
2669 3841 2.103263 GGTAGCTGGACCCACTATGAAG 59.897 54.545 0.00 0.00 32.88 3.02
2674 3846 3.244044 GCTGGACCCACTATGAAGAGATC 60.244 52.174 0.00 0.00 0.00 2.75
2677 3849 5.970289 TGGACCCACTATGAAGAGATCTAT 58.030 41.667 0.00 0.00 0.00 1.98
2679 3851 5.420739 GGACCCACTATGAAGAGATCTATCC 59.579 48.000 0.00 0.00 0.00 2.59
2694 3866 3.899726 TCTATCCTTGGCTTCTCGTACT 58.100 45.455 0.00 0.00 0.00 2.73
2702 3874 5.522824 CCTTGGCTTCTCGTACTAATTTACC 59.477 44.000 0.00 0.00 0.00 2.85
2712 3884 8.511321 TCTCGTACTAATTTACCGTGAAACTTA 58.489 33.333 0.00 0.00 31.75 2.24
2715 3887 9.075519 CGTACTAATTTACCGTGAAACTTATCA 57.924 33.333 0.00 0.00 31.75 2.15
2719 3891 9.537848 CTAATTTACCGTGAAACTTATCAACAC 57.462 33.333 0.00 0.00 31.75 3.32
2722 3894 2.158841 CCGTGAAACTTATCAACACCCG 59.841 50.000 0.00 0.00 31.75 5.28
2735 3907 3.816523 TCAACACCCGAAGTTAATTCACC 59.183 43.478 0.00 0.00 37.83 4.02
2818 3997 0.741915 GGCAAAAACCGGTTGACTCA 59.258 50.000 23.08 0.00 30.83 3.41
2836 4015 4.796606 ACTCAATTGGATACCCATCTTGG 58.203 43.478 5.42 0.00 43.12 3.61
2871 4050 7.391148 TGAGCAGAAATACCATTAAAAGGAC 57.609 36.000 4.48 0.00 0.00 3.85
2873 4052 7.669722 TGAGCAGAAATACCATTAAAAGGACTT 59.330 33.333 4.48 0.00 0.00 3.01
2903 4084 9.169592 GCACTTAAATACCACCAAGTCTTATAA 57.830 33.333 0.00 0.00 0.00 0.98
2955 4136 0.106708 ATAGCATTCCACGTGGCGAT 59.893 50.000 30.25 21.64 34.44 4.58
2956 4137 0.809636 TAGCATTCCACGTGGCGATG 60.810 55.000 30.63 30.63 34.04 3.84
2957 4138 2.404789 CATTCCACGTGGCGATGC 59.595 61.111 30.25 0.00 34.44 3.91
3033 4228 1.377987 GCCAACCGTTGCCCATAGA 60.378 57.895 5.68 0.00 0.00 1.98
3052 4247 0.327000 AAGTAGAGCCAGGGGAGCAT 60.327 55.000 0.00 0.00 0.00 3.79
3059 4254 1.383664 CCAGGGGAGCATGAGGAGA 60.384 63.158 0.00 0.00 0.00 3.71
3071 4266 1.323271 TGAGGAGACGGATGTGGCTC 61.323 60.000 0.00 0.00 0.00 4.70
3072 4267 1.305297 AGGAGACGGATGTGGCTCA 60.305 57.895 0.00 0.00 0.00 4.26
3094 4307 3.683802 AGAGAAGAAGGCCAATCACTTG 58.316 45.455 5.01 0.00 0.00 3.16
3136 4349 2.959465 AAGAAGGCCACTTGCTAGTT 57.041 45.000 5.01 0.00 40.92 2.24
3143 4356 1.801178 GCCACTTGCTAGTTGTCTGTC 59.199 52.381 0.00 0.00 36.87 3.51
3215 4429 9.336171 TCACATTATTCATATTGAATTCCGACA 57.664 29.630 7.94 0.00 44.03 4.35
3228 4442 9.787532 ATTGAATTCCGACAAAATATGTAACAG 57.212 29.630 2.27 0.00 44.12 3.16
3229 4443 8.554835 TGAATTCCGACAAAATATGTAACAGA 57.445 30.769 2.27 0.00 44.12 3.41
3230 4444 8.664798 TGAATTCCGACAAAATATGTAACAGAG 58.335 33.333 2.27 0.00 44.12 3.35
3231 4445 8.786826 AATTCCGACAAAATATGTAACAGAGA 57.213 30.769 0.00 0.00 44.12 3.10
3232 4446 8.964476 ATTCCGACAAAATATGTAACAGAGAT 57.036 30.769 0.00 0.00 44.12 2.75
3233 4447 8.786826 TTCCGACAAAATATGTAACAGAGATT 57.213 30.769 0.00 0.00 44.12 2.40
3234 4448 8.786826 TCCGACAAAATATGTAACAGAGATTT 57.213 30.769 0.00 0.00 44.12 2.17
3235 4449 9.226606 TCCGACAAAATATGTAACAGAGATTTT 57.773 29.630 0.00 0.00 44.12 1.82
3236 4450 9.840427 CCGACAAAATATGTAACAGAGATTTTT 57.160 29.630 0.00 0.00 44.12 1.94
3275 4489 5.485353 ACAGAGAGAAATTCTGGTGGTATCA 59.515 40.000 0.00 0.00 44.96 2.15
3288 4502 4.764823 TGGTGGTATCAGTGTTGAAATTCC 59.235 41.667 0.00 0.00 36.78 3.01
3352 4566 5.134339 AGGCATAGATAGTCAATTTTCCCCA 59.866 40.000 0.00 0.00 0.00 4.96
3355 4569 6.016777 GCATAGATAGTCAATTTTCCCCACTG 60.017 42.308 0.00 0.00 0.00 3.66
3369 4667 5.702065 TCCCCACTGCACTGTATTAATTA 57.298 39.130 0.00 0.00 0.00 1.40
3372 4670 6.545666 TCCCCACTGCACTGTATTAATTATTG 59.454 38.462 0.00 0.00 0.00 1.90
3375 4673 8.250332 CCCACTGCACTGTATTAATTATTGTTT 58.750 33.333 0.00 0.00 0.00 2.83
3528 4828 3.122445 CGTTTTGAGCTTCCGGTACTTAC 59.878 47.826 0.00 0.00 0.00 2.34
3543 4843 5.867716 CGGTACTTACTGTAACTCATGCTTT 59.132 40.000 0.00 0.00 36.72 3.51
3548 4848 8.220755 ACTTACTGTAACTCATGCTTTTGAAA 57.779 30.769 0.00 0.00 0.00 2.69
3635 4935 1.556911 TCATCAGCAAAGAGAGGGACC 59.443 52.381 0.00 0.00 0.00 4.46
3869 5169 8.400947 TCTAGCTTAATTGATCTTGATTTGCAC 58.599 33.333 0.00 0.00 0.00 4.57
4163 5463 3.253188 TGCACTACAACAGAATCAAAGGC 59.747 43.478 0.00 0.00 0.00 4.35
4421 5721 4.764679 TGCAAAGCTTCGTGTATTTCAT 57.235 36.364 0.00 0.00 0.00 2.57
4424 5724 4.726416 CAAAGCTTCGTGTATTTCATGCT 58.274 39.130 0.00 0.00 33.44 3.79
4625 5928 2.883386 AGCAAGCCAGAAGAAAACAGAG 59.117 45.455 0.00 0.00 0.00 3.35
4656 5959 4.115199 GGGCCTGGTTCCGCTCAT 62.115 66.667 0.84 0.00 0.00 2.90
4861 6164 8.837389 GTGTAGTTTTCTTGTAAAGGTTCATCT 58.163 33.333 0.00 0.00 46.24 2.90
4897 6200 9.645059 TCTTCAAGAACTAGTCATATTCACTTG 57.355 33.333 0.00 0.00 35.19 3.16
4999 6307 5.277925 GCGATCTGTCTTAAGTACTAGTCCC 60.278 48.000 0.00 0.00 0.00 4.46
5039 6347 7.227512 CCTTCCATATTAAGATGTTCAGTGTCC 59.772 40.741 9.13 0.00 0.00 4.02
5056 6364 5.581085 CAGTGTCCTACAAATAAGTACTGCC 59.419 44.000 0.00 0.00 0.00 4.85
5070 6378 1.737735 CTGCCTGATCGCGTCAACA 60.738 57.895 5.77 9.41 36.14 3.33
5134 8120 6.237516 GCGAGAGATGACAATGATGATATTCG 60.238 42.308 0.00 0.00 0.00 3.34
5236 8223 7.358931 CGACCTAACGCACTGGTATTATTATTG 60.359 40.741 0.00 0.00 33.74 1.90
5238 8225 8.423349 ACCTAACGCACTGGTATTATTATTGTA 58.577 33.333 0.00 0.00 31.50 2.41
5239 8226 9.263538 CCTAACGCACTGGTATTATTATTGTAA 57.736 33.333 0.00 0.00 0.00 2.41
5344 8338 0.252479 CAAGACTGATGGCTCCAGCT 59.748 55.000 5.72 0.00 41.70 4.24
5398 8392 1.726853 ACATGGCGTAGAGACTTTGC 58.273 50.000 0.00 0.00 0.00 3.68
5407 8401 3.365064 CGTAGAGACTTTGCGTTGAGAGA 60.365 47.826 0.00 0.00 0.00 3.10
5433 8427 8.087136 ACAGATATAGTGTCACATCAGCAATAG 58.913 37.037 5.62 0.00 0.00 1.73
5479 8473 5.509670 GGTGAAAGCAATCTAAGCCTTGTTT 60.510 40.000 0.00 0.00 0.00 2.83
5540 8536 2.166254 CCTCACAACTTTGTTTGCTGGT 59.834 45.455 0.00 0.00 39.91 4.00
5541 8537 3.181397 CTCACAACTTTGTTTGCTGGTG 58.819 45.455 0.00 0.00 39.91 4.17
5542 8538 2.560542 TCACAACTTTGTTTGCTGGTGT 59.439 40.909 0.00 0.00 39.91 4.16
5543 8539 3.006323 TCACAACTTTGTTTGCTGGTGTT 59.994 39.130 0.00 0.00 39.91 3.32
5544 8540 4.218635 TCACAACTTTGTTTGCTGGTGTTA 59.781 37.500 0.00 0.00 39.91 2.41
5545 8541 4.562394 CACAACTTTGTTTGCTGGTGTTAG 59.438 41.667 0.00 0.00 39.91 2.34
5546 8542 4.461081 ACAACTTTGTTTGCTGGTGTTAGA 59.539 37.500 0.00 0.00 38.47 2.10
5547 8543 5.047660 ACAACTTTGTTTGCTGGTGTTAGAA 60.048 36.000 0.00 0.00 38.47 2.10
5548 8544 4.993905 ACTTTGTTTGCTGGTGTTAGAAC 58.006 39.130 0.00 0.00 0.00 3.01
5549 8545 4.461081 ACTTTGTTTGCTGGTGTTAGAACA 59.539 37.500 0.00 0.00 36.38 3.18
5550 8546 5.047660 ACTTTGTTTGCTGGTGTTAGAACAA 60.048 36.000 0.00 0.00 41.21 2.83
5551 8547 5.392767 TTGTTTGCTGGTGTTAGAACAAA 57.607 34.783 0.00 0.00 41.21 2.83
5552 8548 5.590530 TGTTTGCTGGTGTTAGAACAAAT 57.409 34.783 0.00 0.00 41.21 2.32
5553 8549 5.587289 TGTTTGCTGGTGTTAGAACAAATC 58.413 37.500 0.00 0.00 41.21 2.17
5554 8550 5.359576 TGTTTGCTGGTGTTAGAACAAATCT 59.640 36.000 0.00 0.00 41.21 2.40
5555 8551 5.689383 TTGCTGGTGTTAGAACAAATCTC 57.311 39.130 0.00 0.00 41.21 2.75
5556 8552 4.713553 TGCTGGTGTTAGAACAAATCTCA 58.286 39.130 0.00 0.00 41.21 3.27
5557 8553 5.316167 TGCTGGTGTTAGAACAAATCTCAT 58.684 37.500 0.00 0.00 41.21 2.90
5558 8554 6.472016 TGCTGGTGTTAGAACAAATCTCATA 58.528 36.000 0.00 0.00 41.21 2.15
5559 8555 7.112122 TGCTGGTGTTAGAACAAATCTCATAT 58.888 34.615 0.00 0.00 41.21 1.78
5560 8556 7.280876 TGCTGGTGTTAGAACAAATCTCATATC 59.719 37.037 0.00 0.00 41.21 1.63
5561 8557 7.517417 GCTGGTGTTAGAACAAATCTCATATCG 60.517 40.741 0.00 0.00 41.21 2.92
5562 8558 7.327975 TGGTGTTAGAACAAATCTCATATCGT 58.672 34.615 0.00 0.00 41.21 3.73
5563 8559 7.822334 TGGTGTTAGAACAAATCTCATATCGTT 59.178 33.333 0.00 0.00 41.21 3.85
5564 8560 8.116753 GGTGTTAGAACAAATCTCATATCGTTG 58.883 37.037 0.00 0.00 41.21 4.10
5565 8561 8.656849 GTGTTAGAACAAATCTCATATCGTTGT 58.343 33.333 0.00 0.00 41.21 3.32
5566 8562 9.863845 TGTTAGAACAAATCTCATATCGTTGTA 57.136 29.630 0.00 0.00 39.71 2.41
5570 8566 9.823647 AGAACAAATCTCATATCGTTGTAATCT 57.176 29.630 0.00 0.00 30.46 2.40
5572 8568 9.599866 AACAAATCTCATATCGTTGTAATCTCA 57.400 29.630 0.00 0.00 32.32 3.27
5573 8569 9.599866 ACAAATCTCATATCGTTGTAATCTCAA 57.400 29.630 0.00 0.00 30.88 3.02
5574 8570 9.855361 CAAATCTCATATCGTTGTAATCTCAAC 57.145 33.333 0.00 0.00 42.67 3.18
5575 8571 8.594881 AATCTCATATCGTTGTAATCTCAACC 57.405 34.615 4.39 0.00 43.02 3.77
5576 8572 7.348080 TCTCATATCGTTGTAATCTCAACCT 57.652 36.000 4.39 0.00 43.02 3.50
5577 8573 7.426410 TCTCATATCGTTGTAATCTCAACCTC 58.574 38.462 4.39 0.00 43.02 3.85
5578 8574 7.285629 TCTCATATCGTTGTAATCTCAACCTCT 59.714 37.037 4.39 0.00 43.02 3.69
5579 8575 7.782049 TCATATCGTTGTAATCTCAACCTCTT 58.218 34.615 4.39 0.00 43.02 2.85
5580 8576 7.921214 TCATATCGTTGTAATCTCAACCTCTTC 59.079 37.037 4.39 0.00 43.02 2.87
5581 8577 4.817517 TCGTTGTAATCTCAACCTCTTCC 58.182 43.478 4.39 0.00 43.02 3.46
5582 8578 4.527038 TCGTTGTAATCTCAACCTCTTCCT 59.473 41.667 4.39 0.00 43.02 3.36
5583 8579 4.865365 CGTTGTAATCTCAACCTCTTCCTC 59.135 45.833 4.39 0.00 43.02 3.71
5584 8580 5.336849 CGTTGTAATCTCAACCTCTTCCTCT 60.337 44.000 4.39 0.00 43.02 3.69
5585 8581 6.127703 CGTTGTAATCTCAACCTCTTCCTCTA 60.128 42.308 4.39 0.00 43.02 2.43
5586 8582 7.416890 CGTTGTAATCTCAACCTCTTCCTCTAT 60.417 40.741 4.39 0.00 43.02 1.98
5587 8583 7.589958 TGTAATCTCAACCTCTTCCTCTATC 57.410 40.000 0.00 0.00 0.00 2.08
5588 8584 7.358263 TGTAATCTCAACCTCTTCCTCTATCT 58.642 38.462 0.00 0.00 0.00 1.98
5589 8585 6.976934 AATCTCAACCTCTTCCTCTATCTC 57.023 41.667 0.00 0.00 0.00 2.75
5590 8586 4.798882 TCTCAACCTCTTCCTCTATCTCC 58.201 47.826 0.00 0.00 0.00 3.71
5591 8587 4.480537 TCTCAACCTCTTCCTCTATCTCCT 59.519 45.833 0.00 0.00 0.00 3.69
5592 8588 5.672653 TCTCAACCTCTTCCTCTATCTCCTA 59.327 44.000 0.00 0.00 0.00 2.94
5593 8589 6.334237 TCTCAACCTCTTCCTCTATCTCCTAT 59.666 42.308 0.00 0.00 0.00 2.57
5594 8590 6.928202 TCAACCTCTTCCTCTATCTCCTATT 58.072 40.000 0.00 0.00 0.00 1.73
5595 8591 6.780031 TCAACCTCTTCCTCTATCTCCTATTG 59.220 42.308 0.00 0.00 0.00 1.90
5596 8592 6.288096 ACCTCTTCCTCTATCTCCTATTGT 57.712 41.667 0.00 0.00 0.00 2.71
5597 8593 7.409408 ACCTCTTCCTCTATCTCCTATTGTA 57.591 40.000 0.00 0.00 0.00 2.41
5598 8594 8.006967 ACCTCTTCCTCTATCTCCTATTGTAT 57.993 38.462 0.00 0.00 0.00 2.29
5599 8595 8.461033 ACCTCTTCCTCTATCTCCTATTGTATT 58.539 37.037 0.00 0.00 0.00 1.89
5600 8596 8.966868 CCTCTTCCTCTATCTCCTATTGTATTC 58.033 40.741 0.00 0.00 0.00 1.75
5601 8597 9.527157 CTCTTCCTCTATCTCCTATTGTATTCA 57.473 37.037 0.00 0.00 0.00 2.57
5602 8598 9.883293 TCTTCCTCTATCTCCTATTGTATTCAA 57.117 33.333 0.00 0.00 37.98 2.69
5605 8601 9.661954 TCCTCTATCTCCTATTGTATTCAAACT 57.338 33.333 0.00 0.00 37.11 2.66
5606 8602 9.921637 CCTCTATCTCCTATTGTATTCAAACTC 57.078 37.037 0.00 0.00 37.11 3.01
5612 8608 9.871238 TCTCCTATTGTATTCAAACTCTTGTAC 57.129 33.333 0.00 0.00 37.11 2.90
5613 8609 9.877178 CTCCTATTGTATTCAAACTCTTGTACT 57.123 33.333 0.00 0.00 37.11 2.73
5614 8610 9.871238 TCCTATTGTATTCAAACTCTTGTACTC 57.129 33.333 0.00 0.00 37.11 2.59
5615 8611 9.653287 CCTATTGTATTCAAACTCTTGTACTCA 57.347 33.333 0.00 0.00 37.11 3.41
5618 8614 8.547967 TTGTATTCAAACTCTTGTACTCATCC 57.452 34.615 0.00 0.00 33.94 3.51
5619 8615 7.907389 TGTATTCAAACTCTTGTACTCATCCT 58.093 34.615 0.00 0.00 33.94 3.24
5620 8616 8.375506 TGTATTCAAACTCTTGTACTCATCCTT 58.624 33.333 0.00 0.00 33.94 3.36
5621 8617 7.678947 ATTCAAACTCTTGTACTCATCCTTG 57.321 36.000 0.00 0.00 33.94 3.61
5622 8618 6.174720 TCAAACTCTTGTACTCATCCTTGT 57.825 37.500 0.00 0.00 33.94 3.16
5623 8619 5.991606 TCAAACTCTTGTACTCATCCTTGTG 59.008 40.000 0.00 0.00 33.94 3.33
5624 8620 3.931578 ACTCTTGTACTCATCCTTGTGC 58.068 45.455 0.00 0.00 0.00 4.57
5625 8621 2.926200 CTCTTGTACTCATCCTTGTGCG 59.074 50.000 0.00 0.00 0.00 5.34
5626 8622 1.394917 CTTGTACTCATCCTTGTGCGC 59.605 52.381 0.00 0.00 0.00 6.09
5627 8623 0.391130 TGTACTCATCCTTGTGCGCC 60.391 55.000 4.18 0.00 0.00 6.53
5628 8624 0.391130 GTACTCATCCTTGTGCGCCA 60.391 55.000 4.18 0.00 0.00 5.69
5629 8625 0.323302 TACTCATCCTTGTGCGCCAA 59.677 50.000 4.18 8.10 0.00 4.52
5635 8631 2.049802 CTTGTGCGCCAAGGCAAG 60.050 61.111 23.11 16.54 45.70 4.01
5636 8632 2.832661 TTGTGCGCCAAGGCAAGT 60.833 55.556 12.19 0.00 45.93 3.16
5637 8633 2.737932 CTTGTGCGCCAAGGCAAGTC 62.738 60.000 23.11 0.00 45.70 3.01
5638 8634 4.043200 GTGCGCCAAGGCAAGTCC 62.043 66.667 12.19 0.00 45.93 3.85
5646 8642 4.035102 AGGCAAGTCCTTCGGCCC 62.035 66.667 0.00 0.00 44.75 5.80
5647 8643 4.035102 GGCAAGTCCTTCGGCCCT 62.035 66.667 0.00 0.00 40.55 5.19
5648 8644 2.666098 GGCAAGTCCTTCGGCCCTA 61.666 63.158 0.00 0.00 40.55 3.53
5649 8645 1.527370 GCAAGTCCTTCGGCCCTAT 59.473 57.895 0.00 0.00 0.00 2.57
5650 8646 0.533085 GCAAGTCCTTCGGCCCTATC 60.533 60.000 0.00 0.00 0.00 2.08
5651 8647 0.830648 CAAGTCCTTCGGCCCTATCA 59.169 55.000 0.00 0.00 0.00 2.15
5652 8648 1.209504 CAAGTCCTTCGGCCCTATCAA 59.790 52.381 0.00 0.00 0.00 2.57
5653 8649 1.807814 AGTCCTTCGGCCCTATCAAT 58.192 50.000 0.00 0.00 0.00 2.57
5654 8650 2.972348 AGTCCTTCGGCCCTATCAATA 58.028 47.619 0.00 0.00 0.00 1.90
5655 8651 3.521727 AGTCCTTCGGCCCTATCAATAT 58.478 45.455 0.00 0.00 0.00 1.28
5656 8652 4.684724 AGTCCTTCGGCCCTATCAATATA 58.315 43.478 0.00 0.00 0.00 0.86
5657 8653 5.281314 AGTCCTTCGGCCCTATCAATATAT 58.719 41.667 0.00 0.00 0.00 0.86
5658 8654 6.441222 AGTCCTTCGGCCCTATCAATATATA 58.559 40.000 0.00 0.00 0.00 0.86
5659 8655 7.076446 AGTCCTTCGGCCCTATCAATATATAT 58.924 38.462 0.00 0.00 0.00 0.86
5660 8656 8.232412 AGTCCTTCGGCCCTATCAATATATATA 58.768 37.037 0.00 0.00 0.00 0.86
5661 8657 9.036980 GTCCTTCGGCCCTATCAATATATATAT 57.963 37.037 0.00 0.00 0.00 0.86
5665 8661 7.993101 TCGGCCCTATCAATATATATATACGC 58.007 38.462 5.66 1.34 0.00 4.42
5666 8662 7.612633 TCGGCCCTATCAATATATATATACGCA 59.387 37.037 5.66 0.00 0.00 5.24
5667 8663 7.701078 CGGCCCTATCAATATATATATACGCAC 59.299 40.741 5.66 0.00 0.00 5.34
5668 8664 7.701078 GGCCCTATCAATATATATATACGCACG 59.299 40.741 5.66 0.00 0.00 5.34
5669 8665 7.220300 GCCCTATCAATATATATATACGCACGC 59.780 40.741 5.66 0.58 0.00 5.34
5670 8666 7.428472 CCCTATCAATATATATATACGCACGCG 59.572 40.741 10.36 10.36 46.03 6.01
5671 8667 7.428472 CCTATCAATATATATATACGCACGCGG 59.572 40.741 16.70 0.00 44.69 6.46
5672 8668 4.913345 TCAATATATATATACGCACGCGGC 59.087 41.667 16.70 10.52 44.69 6.53
5673 8669 4.761235 ATATATATATACGCACGCGGCT 57.239 40.909 16.70 4.86 44.69 5.52
5674 8670 2.463553 TATATATACGCACGCGGCTC 57.536 50.000 16.70 0.00 44.69 4.70
5675 8671 0.179145 ATATATACGCACGCGGCTCC 60.179 55.000 16.70 0.00 44.69 4.70
5676 8672 2.203972 TATATACGCACGCGGCTCCC 62.204 60.000 16.70 0.00 44.69 4.30
5694 8690 2.406205 CCTCGAGGGAGTAGGAACG 58.594 63.158 24.62 0.00 38.70 3.95
5695 8691 1.726533 CCTCGAGGGAGTAGGAACGC 61.727 65.000 24.62 0.00 38.70 4.84
5696 8692 0.748729 CTCGAGGGAGTAGGAACGCT 60.749 60.000 3.91 0.00 35.48 5.07
5697 8693 0.323178 TCGAGGGAGTAGGAACGCTT 60.323 55.000 0.00 0.00 0.00 4.68
5698 8694 0.100861 CGAGGGAGTAGGAACGCTTC 59.899 60.000 0.00 0.00 0.00 3.86
5699 8695 1.183549 GAGGGAGTAGGAACGCTTCA 58.816 55.000 0.00 0.00 0.00 3.02
5700 8696 1.757699 GAGGGAGTAGGAACGCTTCAT 59.242 52.381 0.00 0.00 0.00 2.57
5701 8697 2.957006 GAGGGAGTAGGAACGCTTCATA 59.043 50.000 0.00 0.00 0.00 2.15
5702 8698 2.694109 AGGGAGTAGGAACGCTTCATAC 59.306 50.000 11.84 11.84 44.75 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 46 1.272536 ACCTGACGCTTTCCTAGGAGA 60.273 52.381 12.26 6.72 32.86 3.71
109 114 2.710902 GGGATGGCAAAACGAGGGC 61.711 63.158 0.00 0.00 0.00 5.19
120 125 1.005037 TGCGTATCATCGGGATGGC 60.005 57.895 8.68 5.04 39.24 4.40
161 166 2.211761 GACGAAACGACAGCGGCTTC 62.212 60.000 0.00 0.82 43.17 3.86
202 207 0.030908 GTCCTCGGTGTGATCGATCC 59.969 60.000 22.31 13.85 36.01 3.36
431 447 3.877508 GGAAGCTTCTGTACAACACAAGT 59.122 43.478 25.05 0.00 36.48 3.16
434 450 3.838244 AGGAAGCTTCTGTACAACACA 57.162 42.857 25.05 0.00 35.30 3.72
476 492 1.518903 GCTTGCACTGGAACTCCACC 61.519 60.000 0.00 0.00 42.01 4.61
477 493 1.518903 GGCTTGCACTGGAACTCCAC 61.519 60.000 0.00 0.00 42.01 4.02
479 495 1.973812 GGGCTTGCACTGGAACTCC 60.974 63.158 0.00 0.00 0.00 3.85
480 496 1.973812 GGGGCTTGCACTGGAACTC 60.974 63.158 0.00 0.00 0.00 3.01
481 497 2.116125 GGGGCTTGCACTGGAACT 59.884 61.111 0.00 0.00 0.00 3.01
482 498 2.203480 TGGGGCTTGCACTGGAAC 60.203 61.111 0.00 0.00 0.00 3.62
483 499 1.792757 ATCTGGGGCTTGCACTGGAA 61.793 55.000 0.00 0.00 0.00 3.53
484 500 2.202236 GATCTGGGGCTTGCACTGGA 62.202 60.000 0.00 0.00 0.00 3.86
485 501 1.751927 GATCTGGGGCTTGCACTGG 60.752 63.158 0.00 0.00 0.00 4.00
486 502 0.609957 TTGATCTGGGGCTTGCACTG 60.610 55.000 0.00 0.00 0.00 3.66
487 503 0.610232 GTTGATCTGGGGCTTGCACT 60.610 55.000 0.00 0.00 0.00 4.40
511 527 0.737367 TGAGCCGCATTGTCTCTTCG 60.737 55.000 0.00 0.00 0.00 3.79
584 600 9.236691 CTGCAAATAATCGCAACATAGTATTTT 57.763 29.630 0.00 0.00 37.76 1.82
586 602 6.857964 GCTGCAAATAATCGCAACATAGTATT 59.142 34.615 0.00 0.00 37.76 1.89
588 604 5.295540 TGCTGCAAATAATCGCAACATAGTA 59.704 36.000 0.00 0.00 37.76 1.82
590 606 4.600032 TGCTGCAAATAATCGCAACATAG 58.400 39.130 0.00 0.00 37.76 2.23
595 611 1.912001 GCTGCTGCAAATAATCGCAA 58.088 45.000 11.11 0.00 37.76 4.85
596 612 3.628005 GCTGCTGCAAATAATCGCA 57.372 47.368 11.11 0.00 39.41 5.10
655 672 4.662961 CACTCACCGCTCCACGCA 62.663 66.667 0.00 0.00 41.76 5.24
680 704 2.097038 CCAGCTGCTACGCACTGTC 61.097 63.158 8.66 0.00 36.62 3.51
687 711 1.446792 CTGTGTCCCAGCTGCTACG 60.447 63.158 8.66 0.00 33.59 3.51
833 857 1.202940 GCTCAAAAAGAGTGAGGGGGT 60.203 52.381 3.79 0.00 46.47 4.95
969 993 1.317613 CGACAGAGAGCAGAGCCTAT 58.682 55.000 0.00 0.00 0.00 2.57
988 1012 1.450312 CCGCCATCTCCACAAGTCC 60.450 63.158 0.00 0.00 0.00 3.85
990 1014 2.045926 GCCGCCATCTCCACAAGT 60.046 61.111 0.00 0.00 0.00 3.16
1019 1784 1.004440 GTGAGCTCCTCCACCACAC 60.004 63.158 12.15 0.00 0.00 3.82
1278 2044 3.500642 CGCCTCTCGAGCTCGACA 61.501 66.667 33.84 23.65 44.22 4.35
1374 2140 2.756400 GCCATCTCCACACCACCA 59.244 61.111 0.00 0.00 0.00 4.17
1525 2294 7.923414 AAGTAAAATCACCTGTAGAACCATC 57.077 36.000 0.00 0.00 0.00 3.51
1679 2460 8.977267 ACTACCACTACTACAGGAGTATAAAG 57.023 38.462 0.00 0.00 39.98 1.85
2037 3086 5.529060 GGATATGAAACCTGCGAAGAATTCT 59.471 40.000 0.88 0.88 44.75 2.40
2178 3229 7.390996 AGCTTCTGCATTCAAGATATTAGGATG 59.609 37.037 4.74 0.00 42.74 3.51
2232 3293 6.354130 TGCCAAAGGAATCTATTAGGTGTAC 58.646 40.000 0.00 0.00 0.00 2.90
2425 3501 8.678199 CAAGGAGGAAATAATTCTAGTGTTTCC 58.322 37.037 10.40 10.40 45.07 3.13
2501 3585 4.008074 TCTGACTCTGTCCAATGGTTTC 57.992 45.455 0.00 0.00 0.00 2.78
2626 3798 2.761786 CATTGGGGAATGGAGTGGAT 57.238 50.000 0.00 0.00 0.00 3.41
2669 3841 3.572255 ACGAGAAGCCAAGGATAGATCTC 59.428 47.826 0.00 0.00 0.00 2.75
2674 3846 5.769484 TTAGTACGAGAAGCCAAGGATAG 57.231 43.478 0.00 0.00 0.00 2.08
2677 3849 5.416271 AAATTAGTACGAGAAGCCAAGGA 57.584 39.130 0.00 0.00 0.00 3.36
2679 3851 5.231568 CGGTAAATTAGTACGAGAAGCCAAG 59.768 44.000 0.00 0.00 0.00 3.61
2694 3866 8.505625 GGTGTTGATAAGTTTCACGGTAAATTA 58.494 33.333 0.00 0.00 0.00 1.40
2702 3874 3.061322 TCGGGTGTTGATAAGTTTCACG 58.939 45.455 0.00 0.00 0.00 4.35
2712 3884 4.457949 GGTGAATTAACTTCGGGTGTTGAT 59.542 41.667 0.00 0.00 36.60 2.57
2715 3887 3.818773 CAGGTGAATTAACTTCGGGTGTT 59.181 43.478 0.00 0.00 36.60 3.32
2719 3891 5.447624 AAAACAGGTGAATTAACTTCGGG 57.552 39.130 0.00 0.00 36.60 5.14
2781 3959 6.712179 TTTGCCATGCTTCATATCACAATA 57.288 33.333 0.00 0.00 0.00 1.90
2818 3997 7.088236 GGTGTTACCAAGATGGGTATCCAATT 61.088 42.308 0.00 0.00 43.37 2.32
2836 4015 5.106673 GGTATTTCTGCTCAAGTGGTGTTAC 60.107 44.000 0.00 0.00 0.00 2.50
2871 4050 3.823873 TGGTGGTATTTAAGTGCACCAAG 59.176 43.478 14.63 0.00 42.48 3.61
2873 4052 3.510531 TGGTGGTATTTAAGTGCACCA 57.489 42.857 14.63 0.00 38.72 4.17
2903 4084 5.521544 ACGGCACAACAAATACGTTAAATT 58.478 33.333 0.00 0.00 0.00 1.82
2919 4100 2.009051 CTATCAGCATTTGACGGCACA 58.991 47.619 0.00 0.00 38.99 4.57
3026 4221 1.974236 CCCTGGCTCTACTTCTATGGG 59.026 57.143 0.00 0.00 0.00 4.00
3033 4228 0.327000 ATGCTCCCCTGGCTCTACTT 60.327 55.000 0.00 0.00 0.00 2.24
3052 4247 1.305297 AGCCACATCCGTCTCCTCA 60.305 57.895 0.00 0.00 0.00 3.86
3059 4254 0.976641 TTCTCTTGAGCCACATCCGT 59.023 50.000 0.00 0.00 0.00 4.69
3071 4266 3.683802 AGTGATTGGCCTTCTTCTCTTG 58.316 45.455 3.32 0.00 0.00 3.02
3072 4267 4.077822 CAAGTGATTGGCCTTCTTCTCTT 58.922 43.478 3.32 5.43 0.00 2.85
3136 4349 2.160205 CTCTCAACCTACGGACAGACA 58.840 52.381 0.00 0.00 0.00 3.41
3143 4356 1.962100 GGGGTATCTCTCAACCTACGG 59.038 57.143 0.00 0.00 35.97 4.02
3239 4453 9.838339 AGAATTTCTCTCTGTTAGTTTCTCAAA 57.162 29.630 0.00 0.00 0.00 2.69
3240 4454 9.265901 CAGAATTTCTCTCTGTTAGTTTCTCAA 57.734 33.333 0.00 0.00 36.38 3.02
3241 4455 7.875041 CCAGAATTTCTCTCTGTTAGTTTCTCA 59.125 37.037 0.00 0.00 38.96 3.27
3242 4456 7.875554 ACCAGAATTTCTCTCTGTTAGTTTCTC 59.124 37.037 0.00 0.00 38.96 2.87
3243 4457 7.659390 CACCAGAATTTCTCTCTGTTAGTTTCT 59.341 37.037 0.00 0.00 38.96 2.52
3244 4458 7.095017 CCACCAGAATTTCTCTCTGTTAGTTTC 60.095 40.741 0.00 0.00 38.96 2.78
3245 4459 6.712547 CCACCAGAATTTCTCTCTGTTAGTTT 59.287 38.462 0.00 0.00 38.96 2.66
3246 4460 6.183361 ACCACCAGAATTTCTCTCTGTTAGTT 60.183 38.462 0.00 0.00 38.96 2.24
3247 4461 5.308237 ACCACCAGAATTTCTCTCTGTTAGT 59.692 40.000 0.00 0.00 38.96 2.24
3275 4489 4.536765 ACCAACTGAGGAATTTCAACACT 58.463 39.130 0.00 0.00 0.00 3.55
3288 4502 5.181748 AGCTCTAGCAAAATACCAACTGAG 58.818 41.667 4.54 0.00 45.16 3.35
3369 4667 8.674607 GCCTATACTACAAAGCACTTAAACAAT 58.325 33.333 0.00 0.00 0.00 2.71
3372 4670 6.822170 AGGCCTATACTACAAAGCACTTAAAC 59.178 38.462 1.29 0.00 0.00 2.01
3375 4673 7.664552 TTAGGCCTATACTACAAAGCACTTA 57.335 36.000 14.74 0.00 0.00 2.24
3377 4675 6.070424 TGTTTAGGCCTATACTACAAAGCACT 60.070 38.462 27.17 0.00 0.00 4.40
3467 4767 8.365399 TGTCACTGTTACAAACTGATCTTTAG 57.635 34.615 0.00 0.00 34.78 1.85
3517 4817 4.142315 GCATGAGTTACAGTAAGTACCGGA 60.142 45.833 9.46 0.00 30.91 5.14
3518 4818 4.110482 GCATGAGTTACAGTAAGTACCGG 58.890 47.826 0.00 0.00 30.91 5.28
3528 4828 6.583806 GGATGTTTCAAAAGCATGAGTTACAG 59.416 38.462 0.00 0.00 0.00 2.74
3543 4843 1.250328 CTGCCTGCAGGATGTTTCAA 58.750 50.000 37.21 9.03 40.17 2.69
3869 5169 0.514691 GAGACTTCAGCTGGTTTGCG 59.485 55.000 15.13 0.00 38.13 4.85
4163 5463 2.095263 CGAACCAATTGTTGTAGGCAGG 60.095 50.000 4.43 0.00 37.29 4.85
4421 5721 1.003233 TCTAGTGGAGTCTCGTCAGCA 59.997 52.381 0.00 0.00 0.00 4.41
4424 5724 3.420300 ACTTCTAGTGGAGTCTCGTCA 57.580 47.619 0.00 0.00 0.00 4.35
4535 5838 9.755804 TGACATGCAAAAGTAAACATAATTCAA 57.244 25.926 0.00 0.00 0.00 2.69
4541 5844 5.618863 CGCCTGACATGCAAAAGTAAACATA 60.619 40.000 3.55 0.00 0.00 2.29
4548 5851 0.823356 ACCGCCTGACATGCAAAAGT 60.823 50.000 3.55 0.00 0.00 2.66
4556 5859 2.927856 TGGACCACCGCCTGACAT 60.928 61.111 0.00 0.00 39.42 3.06
4625 5928 2.361737 GCCCAGAAGCTTGTCCCC 60.362 66.667 2.10 0.00 0.00 4.81
4706 6009 2.175878 ACAGACGAAATGCTTCAGCT 57.824 45.000 0.00 0.00 42.66 4.24
4897 6200 2.614829 ACAGGTGGAGTTACACACAC 57.385 50.000 11.16 4.54 43.08 3.82
4971 6274 8.624367 ACTAGTACTTAAGACAGATCGCATAT 57.376 34.615 10.09 0.00 0.00 1.78
4999 6307 2.426522 TGGAAGGAAAAGAGTGCATCG 58.573 47.619 0.00 0.00 0.00 3.84
5039 6347 5.175856 GCGATCAGGCAGTACTTATTTGTAG 59.824 44.000 0.00 0.00 0.00 2.74
5056 6364 3.439293 AGATAACTGTTGACGCGATCAG 58.561 45.455 15.93 16.78 38.99 2.90
5210 8197 2.288961 AATACCAGTGCGTTAGGTCG 57.711 50.000 0.00 0.00 36.87 4.79
5240 8227 8.526147 AGCATAAACATATGAAAAGTCAAGCTT 58.474 29.630 10.38 0.00 37.30 3.74
5253 8240 6.425735 TGGATGGGGATAGCATAAACATATG 58.574 40.000 0.00 0.00 0.00 1.78
5263 8250 1.479205 GCAACATGGATGGGGATAGCA 60.479 52.381 0.00 0.00 0.00 3.49
5344 8338 5.877491 TCCGGATAAGTAATAGAGAGCTCA 58.123 41.667 17.77 0.00 0.00 4.26
5398 8392 6.183360 TGTGACACTATATCTGTCTCTCAACG 60.183 42.308 7.20 0.00 39.11 4.10
5407 8401 5.859205 TGCTGATGTGACACTATATCTGT 57.141 39.130 7.20 0.00 0.00 3.41
5433 8427 4.633565 CCAAGGATTAGCACTGACTTCTTC 59.366 45.833 0.00 0.00 0.00 2.87
5473 8467 9.630098 AACAGCTTATTGTCATATTCAAACAAG 57.370 29.630 0.00 0.00 36.44 3.16
5540 8536 8.771920 ACAACGATATGAGATTTGTTCTAACA 57.228 30.769 0.00 0.00 33.74 2.41
5544 8540 9.823647 AGATTACAACGATATGAGATTTGTTCT 57.176 29.630 0.00 0.00 37.41 3.01
5546 8542 9.599866 TGAGATTACAACGATATGAGATTTGTT 57.400 29.630 0.00 0.00 32.73 2.83
5547 8543 9.599866 TTGAGATTACAACGATATGAGATTTGT 57.400 29.630 0.00 0.00 34.79 2.83
5548 8544 9.855361 GTTGAGATTACAACGATATGAGATTTG 57.145 33.333 0.00 0.00 40.17 2.32
5561 8557 6.043854 AGAGGAAGAGGTTGAGATTACAAC 57.956 41.667 0.00 0.00 46.20 3.32
5562 8558 7.841729 AGATAGAGGAAGAGGTTGAGATTACAA 59.158 37.037 0.00 0.00 0.00 2.41
5563 8559 7.358263 AGATAGAGGAAGAGGTTGAGATTACA 58.642 38.462 0.00 0.00 0.00 2.41
5564 8560 7.039993 GGAGATAGAGGAAGAGGTTGAGATTAC 60.040 44.444 0.00 0.00 0.00 1.89
5565 8561 7.007723 GGAGATAGAGGAAGAGGTTGAGATTA 58.992 42.308 0.00 0.00 0.00 1.75
5566 8562 5.838521 GGAGATAGAGGAAGAGGTTGAGATT 59.161 44.000 0.00 0.00 0.00 2.40
5567 8563 5.136048 AGGAGATAGAGGAAGAGGTTGAGAT 59.864 44.000 0.00 0.00 0.00 2.75
5568 8564 4.480537 AGGAGATAGAGGAAGAGGTTGAGA 59.519 45.833 0.00 0.00 0.00 3.27
5569 8565 4.803452 AGGAGATAGAGGAAGAGGTTGAG 58.197 47.826 0.00 0.00 0.00 3.02
5570 8566 4.890499 AGGAGATAGAGGAAGAGGTTGA 57.110 45.455 0.00 0.00 0.00 3.18
5571 8567 6.553100 ACAATAGGAGATAGAGGAAGAGGTTG 59.447 42.308 0.00 0.00 0.00 3.77
5572 8568 6.688554 ACAATAGGAGATAGAGGAAGAGGTT 58.311 40.000 0.00 0.00 0.00 3.50
5573 8569 6.288096 ACAATAGGAGATAGAGGAAGAGGT 57.712 41.667 0.00 0.00 0.00 3.85
5574 8570 8.893563 AATACAATAGGAGATAGAGGAAGAGG 57.106 38.462 0.00 0.00 0.00 3.69
5575 8571 9.527157 TGAATACAATAGGAGATAGAGGAAGAG 57.473 37.037 0.00 0.00 0.00 2.85
5576 8572 9.883293 TTGAATACAATAGGAGATAGAGGAAGA 57.117 33.333 0.00 0.00 0.00 2.87
5579 8575 9.661954 AGTTTGAATACAATAGGAGATAGAGGA 57.338 33.333 0.00 0.00 35.85 3.71
5580 8576 9.921637 GAGTTTGAATACAATAGGAGATAGAGG 57.078 37.037 0.00 0.00 35.85 3.69
5586 8582 9.871238 GTACAAGAGTTTGAATACAATAGGAGA 57.129 33.333 0.00 0.00 37.73 3.71
5587 8583 9.877178 AGTACAAGAGTTTGAATACAATAGGAG 57.123 33.333 0.00 0.00 37.73 3.69
5588 8584 9.871238 GAGTACAAGAGTTTGAATACAATAGGA 57.129 33.333 0.00 0.00 37.73 2.94
5589 8585 9.653287 TGAGTACAAGAGTTTGAATACAATAGG 57.347 33.333 0.00 0.00 37.73 2.57
5592 8588 9.167311 GGATGAGTACAAGAGTTTGAATACAAT 57.833 33.333 0.00 0.00 37.73 2.71
5593 8589 8.375506 AGGATGAGTACAAGAGTTTGAATACAA 58.624 33.333 0.00 0.00 37.73 2.41
5594 8590 7.907389 AGGATGAGTACAAGAGTTTGAATACA 58.093 34.615 0.00 0.00 37.73 2.29
5595 8591 8.660373 CAAGGATGAGTACAAGAGTTTGAATAC 58.340 37.037 0.00 0.00 37.73 1.89
5596 8592 8.375506 ACAAGGATGAGTACAAGAGTTTGAATA 58.624 33.333 0.00 0.00 37.73 1.75
5597 8593 7.173907 CACAAGGATGAGTACAAGAGTTTGAAT 59.826 37.037 0.00 0.00 37.73 2.57
5598 8594 6.483307 CACAAGGATGAGTACAAGAGTTTGAA 59.517 38.462 0.00 0.00 37.73 2.69
5599 8595 5.991606 CACAAGGATGAGTACAAGAGTTTGA 59.008 40.000 0.00 0.00 37.73 2.69
5600 8596 5.334414 GCACAAGGATGAGTACAAGAGTTTG 60.334 44.000 0.00 0.00 40.24 2.93
5601 8597 4.757149 GCACAAGGATGAGTACAAGAGTTT 59.243 41.667 0.00 0.00 0.00 2.66
5602 8598 4.319177 GCACAAGGATGAGTACAAGAGTT 58.681 43.478 0.00 0.00 0.00 3.01
5603 8599 3.615110 CGCACAAGGATGAGTACAAGAGT 60.615 47.826 0.00 0.00 0.00 3.24
5604 8600 2.926200 CGCACAAGGATGAGTACAAGAG 59.074 50.000 0.00 0.00 0.00 2.85
5605 8601 2.930887 GCGCACAAGGATGAGTACAAGA 60.931 50.000 0.30 0.00 0.00 3.02
5606 8602 1.394917 GCGCACAAGGATGAGTACAAG 59.605 52.381 0.30 0.00 0.00 3.16
5607 8603 1.438651 GCGCACAAGGATGAGTACAA 58.561 50.000 0.30 0.00 0.00 2.41
5608 8604 0.391130 GGCGCACAAGGATGAGTACA 60.391 55.000 10.83 0.00 0.00 2.90
5609 8605 0.391130 TGGCGCACAAGGATGAGTAC 60.391 55.000 10.83 0.00 0.00 2.73
5610 8606 0.323302 TTGGCGCACAAGGATGAGTA 59.677 50.000 10.83 0.00 33.18 2.59
5611 8607 1.073025 TTGGCGCACAAGGATGAGT 59.927 52.632 10.83 0.00 33.18 3.41
5612 8608 3.985877 TTGGCGCACAAGGATGAG 58.014 55.556 10.83 0.00 33.18 2.90
5619 8615 2.832661 ACTTGCCTTGGCGCACAA 60.833 55.556 10.83 10.48 38.83 3.33
5620 8616 3.286751 GACTTGCCTTGGCGCACA 61.287 61.111 10.83 1.22 38.83 4.57
5621 8617 4.043200 GGACTTGCCTTGGCGCAC 62.043 66.667 10.83 0.00 38.83 5.34
5639 8635 8.464404 GCGTATATATATATTGATAGGGCCGAA 58.536 37.037 10.48 0.00 0.00 4.30
5640 8636 7.612633 TGCGTATATATATATTGATAGGGCCGA 59.387 37.037 10.48 0.00 0.00 5.54
5641 8637 7.701078 GTGCGTATATATATATTGATAGGGCCG 59.299 40.741 10.48 2.60 0.00 6.13
5642 8638 7.701078 CGTGCGTATATATATATTGATAGGGCC 59.299 40.741 10.48 0.00 0.00 5.80
5643 8639 7.220300 GCGTGCGTATATATATATTGATAGGGC 59.780 40.741 10.48 4.18 0.00 5.19
5644 8640 7.428472 CGCGTGCGTATATATATATTGATAGGG 59.572 40.741 10.48 4.26 34.35 3.53
5645 8641 7.428472 CCGCGTGCGTATATATATATTGATAGG 59.572 40.741 13.70 1.50 37.81 2.57
5646 8642 7.044901 GCCGCGTGCGTATATATATATTGATAG 60.045 40.741 13.70 1.30 37.81 2.08
5647 8643 6.744082 GCCGCGTGCGTATATATATATTGATA 59.256 38.462 13.70 0.00 37.81 2.15
5648 8644 5.571741 GCCGCGTGCGTATATATATATTGAT 59.428 40.000 13.70 0.00 37.81 2.57
5649 8645 4.913345 GCCGCGTGCGTATATATATATTGA 59.087 41.667 13.70 0.00 37.81 2.57
5650 8646 5.173525 GCCGCGTGCGTATATATATATTG 57.826 43.478 13.70 5.62 37.81 1.90
5676 8672 1.726533 GCGTTCCTACTCCCTCGAGG 61.727 65.000 25.36 25.36 40.77 4.63
5677 8673 0.748729 AGCGTTCCTACTCCCTCGAG 60.749 60.000 5.13 5.13 42.32 4.04
5678 8674 0.323178 AAGCGTTCCTACTCCCTCGA 60.323 55.000 0.00 0.00 0.00 4.04
5679 8675 0.100861 GAAGCGTTCCTACTCCCTCG 59.899 60.000 0.00 0.00 0.00 4.63
5680 8676 1.183549 TGAAGCGTTCCTACTCCCTC 58.816 55.000 0.00 0.00 0.00 4.30
5681 8677 1.867363 ATGAAGCGTTCCTACTCCCT 58.133 50.000 0.00 0.00 0.00 4.20
5682 8678 2.694109 AGTATGAAGCGTTCCTACTCCC 59.306 50.000 8.66 0.00 36.72 4.30
5683 8679 4.388378 AAGTATGAAGCGTTCCTACTCC 57.612 45.455 12.40 0.00 39.27 3.85


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

AutoCloner maintained by Alex Coulton.