Multiple sequence alignment - TraesCS7B01G223400

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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 TraesCS7B01G223400 chr7B 100.000 4485 0 0 1 4485 421700840 421696356 0.000000e+00 8283.0
1 TraesCS7B01G223400 chr7B 97.335 3265 72 4 520 3774 420072712 420075971 0.000000e+00 5533.0
2 TraesCS7B01G223400 chr7B 99.368 475 3 0 47 521 420072291 420072765 0.000000e+00 861.0
3 TraesCS7B01G223400 chr7B 89.320 309 25 7 4179 4485 420077194 420077496 9.100000e-102 381.0
4 TraesCS7B01G223400 chr7B 97.826 92 1 1 520 610 463050449 463050358 1.670000e-34 158.0
5 TraesCS7B01G223400 chr7B 95.652 92 0 3 433 521 58655883 58655973 1.300000e-30 145.0
6 TraesCS7B01G223400 chr7B 98.462 65 1 0 1 65 420068904 420068968 1.020000e-21 115.0
7 TraesCS7B01G223400 chr7B 96.296 54 2 0 4104 4157 420077093 420077146 6.180000e-14 89.8
8 TraesCS7B01G223400 chr7B 97.143 35 1 0 4145 4179 361790114 361790148 4.850000e-05 60.2
9 TraesCS7B01G223400 chr7B 94.737 38 2 0 4145 4182 516807370 516807333 4.850000e-05 60.2
10 TraesCS7B01G223400 chr7A 85.821 1467 179 18 601 2051 466884910 466886363 0.000000e+00 1530.0
11 TraesCS7B01G223400 chr7A 85.942 1067 109 20 2075 3132 466886353 466887387 0.000000e+00 1101.0
12 TraesCS7B01G223400 chr7A 96.517 402 13 1 1 401 466884439 466884840 0.000000e+00 664.0
13 TraesCS7B01G223400 chr7A 85.091 275 32 5 3352 3626 466887788 466888053 5.720000e-69 272.0
14 TraesCS7B01G223400 chr7A 82.819 227 19 6 3130 3336 466887475 466887701 7.660000e-43 185.0
15 TraesCS7B01G223400 chr7A 90.370 135 9 2 3623 3754 466888127 466888260 1.660000e-39 174.0
16 TraesCS7B01G223400 chr5D 87.273 220 20 8 4226 4442 548985875 548985661 1.250000e-60 244.0
17 TraesCS7B01G223400 chr5D 90.566 159 15 0 446 604 390354599 390354441 1.260000e-50 211.0
18 TraesCS7B01G223400 chr5D 94.059 101 6 0 3740 3840 373835044 373834944 2.160000e-33 154.0
19 TraesCS7B01G223400 chr5D 96.667 90 3 0 520 609 399621865 399621954 2.790000e-32 150.0
20 TraesCS7B01G223400 chr5D 81.065 169 28 4 439 605 390354434 390354600 1.010000e-26 132.0
21 TraesCS7B01G223400 chr5A 87.097 217 21 6 4227 4440 565483150 565482938 5.800000e-59 239.0
22 TraesCS7B01G223400 chr4B 87.097 217 20 8 4227 4440 561393676 561393465 5.800000e-59 239.0
23 TraesCS7B01G223400 chr4B 86.239 218 25 5 4227 4442 460159401 460159187 9.700000e-57 231.0
24 TraesCS7B01G223400 chr4B 96.739 92 2 1 431 521 60204685 60204594 7.770000e-33 152.0
25 TraesCS7B01G223400 chr1B 86.239 218 24 6 4226 4442 644541325 644541537 9.700000e-57 231.0
26 TraesCS7B01G223400 chr1B 85.789 190 19 8 4226 4414 644334264 644334082 1.270000e-45 195.0
27 TraesCS7B01G223400 chr1B 94.059 101 5 1 421 521 88542218 88542119 7.770000e-33 152.0
28 TraesCS7B01G223400 chr1B 96.739 92 2 1 520 610 572442149 572442058 7.770000e-33 152.0
29 TraesCS7B01G223400 chr1B 92.929 99 7 0 3748 3846 118420570 118420668 1.300000e-30 145.0
30 TraesCS7B01G223400 chr1B 96.875 32 1 0 4151 4182 189722771 189722740 2.000000e-03 54.7
31 TraesCS7B01G223400 chr2B 85.253 217 27 5 4227 4442 393108183 393108395 7.550000e-53 219.0
32 TraesCS7B01G223400 chr2B 96.739 92 2 1 520 610 734295926 734296017 7.770000e-33 152.0
33 TraesCS7B01G223400 chr2B 91.176 102 7 2 3751 3852 142245673 142245574 2.180000e-28 137.0
34 TraesCS7B01G223400 chr2B 89.091 110 10 2 3734 3843 799001952 799002059 7.830000e-28 135.0
35 TraesCS7B01G223400 chr2B 97.143 35 0 1 4145 4179 693884220 693884253 1.740000e-04 58.4
36 TraesCS7B01G223400 chr4A 84.259 216 25 8 4228 4442 17670001 17670208 7.610000e-48 202.0
37 TraesCS7B01G223400 chr4D 97.753 89 2 0 520 608 441486730 441486818 2.160000e-33 154.0
38 TraesCS7B01G223400 chr1D 97.778 90 1 1 433 521 43822678 43822767 2.160000e-33 154.0
39 TraesCS7B01G223400 chr1D 96.629 89 3 0 433 521 44274597 44274685 1.010000e-31 148.0
40 TraesCS7B01G223400 chr1D 96.629 89 3 0 433 521 44309795 44309883 1.010000e-31 148.0
41 TraesCS7B01G223400 chr3A 94.845 97 3 2 3745 3839 38264436 38264532 2.790000e-32 150.0
42 TraesCS7B01G223400 chr3A 91.089 101 8 1 3741 3840 210592069 210591969 7.830000e-28 135.0
43 TraesCS7B01G223400 chr3A 97.143 35 1 0 4145 4179 175774442 175774476 4.850000e-05 60.2
44 TraesCS7B01G223400 chr2A 93.204 103 5 2 3750 3851 18339609 18339508 2.790000e-32 150.0
45 TraesCS7B01G223400 chr7D 93.069 101 7 0 3745 3845 540714215 540714315 1.010000e-31 148.0
46 TraesCS7B01G223400 chr7D 100.000 29 0 0 4151 4179 433079315 433079343 2.000000e-03 54.7
47 TraesCS7B01G223400 chr6D 96.667 90 2 1 520 609 456557380 456557468 1.010000e-31 148.0
48 TraesCS7B01G223400 chr6D 96.875 32 1 0 4151 4182 386524482 386524451 2.000000e-03 54.7
49 TraesCS7B01G223400 chr2D 90.654 107 9 1 3735 3840 54963989 54963883 1.680000e-29 141.0
50 TraesCS7B01G223400 chr3B 100.000 31 0 0 4152 4182 290776361 290776391 1.740000e-04 58.4
51 TraesCS7B01G223400 chr3B 96.875 32 1 0 4151 4182 814638550 814638581 2.000000e-03 54.7


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 TraesCS7B01G223400 chr7B 421696356 421700840 4484 True 8283.000000 8283 100.0000 1 4485 1 chr7B.!!$R1 4484
1 TraesCS7B01G223400 chr7B 420068904 420077496 8592 False 1395.960000 5533 96.1562 1 4485 5 chr7B.!!$F3 4484
2 TraesCS7B01G223400 chr7A 466884439 466888260 3821 False 654.333333 1530 87.7600 1 3754 6 chr7A.!!$F1 3753

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
236 3579 5.173854 GTCTTTTCAGATTTGTGGCTTTTCG 59.826 40.000 0.00 0.00 0.00 3.46 F
1293 4663 0.732538 CAAAGCCCATTTCCGTTCGC 60.733 55.000 0.00 0.00 0.00 4.70 F
1486 4856 0.886490 CTTGGCGAGGAAGTGCACTT 60.886 55.000 31.57 31.57 39.23 3.16 F
2433 5817 1.398390 GCAATACCTTCAGCACGGAAG 59.602 52.381 3.85 3.85 43.09 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 5050 0.456221 TCCCTTTCTCACTCGCGATC 59.544 55.000 10.36 0.0 0.0 3.69 R
2847 6233 1.889530 AAACCGCTCCCTCTTCCTCG 61.890 60.000 0.00 0.0 0.0 4.63 R
3002 6389 5.053145 GTGGGTTCTGCTAATCTGATGTAG 58.947 45.833 0.00 0.0 0.0 2.74 R
3969 7694 0.250166 ATATACGCCGGCCACTTTCC 60.250 55.000 23.46 0.0 0.0 3.13 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
236 3579 5.173854 GTCTTTTCAGATTTGTGGCTTTTCG 59.826 40.000 0.00 0.00 0.00 3.46
301 3644 5.390885 CCGATTTGTATGTGTCCACTCTTTG 60.391 44.000 0.00 0.00 0.00 2.77
524 3894 9.529325 TTTAGTTCTAGATACATCCATTTGTCG 57.471 33.333 0.00 0.00 0.00 4.35
525 3895 7.113658 AGTTCTAGATACATCCATTTGTCGT 57.886 36.000 0.00 0.00 0.00 4.34
526 3896 8.234136 AGTTCTAGATACATCCATTTGTCGTA 57.766 34.615 0.00 0.00 0.00 3.43
527 3897 8.353684 AGTTCTAGATACATCCATTTGTCGTAG 58.646 37.037 0.00 0.00 0.00 3.51
528 3898 8.350722 GTTCTAGATACATCCATTTGTCGTAGA 58.649 37.037 0.00 0.00 0.00 2.59
529 3899 8.459911 TCTAGATACATCCATTTGTCGTAGAA 57.540 34.615 0.00 0.00 39.69 2.10
530 3900 8.909923 TCTAGATACATCCATTTGTCGTAGAAA 58.090 33.333 0.00 0.00 39.69 2.52
531 3901 9.698309 CTAGATACATCCATTTGTCGTAGAAAT 57.302 33.333 0.00 0.00 39.69 2.17
532 3902 8.370493 AGATACATCCATTTGTCGTAGAAATG 57.630 34.615 0.00 0.00 39.69 2.32
541 3911 8.370493 CATTTGTCGTAGAAATGGATGTATCT 57.630 34.615 0.00 0.00 39.69 1.98
542 3912 9.476202 CATTTGTCGTAGAAATGGATGTATCTA 57.524 33.333 0.00 0.00 39.69 1.98
543 3913 9.698309 ATTTGTCGTAGAAATGGATGTATCTAG 57.302 33.333 0.00 0.00 39.69 2.43
544 3914 8.459911 TTGTCGTAGAAATGGATGTATCTAGA 57.540 34.615 0.00 0.00 39.69 2.43
545 3915 7.872881 TGTCGTAGAAATGGATGTATCTAGAC 58.127 38.462 0.00 0.00 39.69 2.59
546 3916 7.501225 TGTCGTAGAAATGGATGTATCTAGACA 59.499 37.037 0.00 0.00 39.69 3.41
547 3917 8.516234 GTCGTAGAAATGGATGTATCTAGACAT 58.484 37.037 0.00 0.00 40.04 3.06
548 3918 9.078990 TCGTAGAAATGGATGTATCTAGACATT 57.921 33.333 0.00 0.00 40.18 2.71
549 3919 9.698309 CGTAGAAATGGATGTATCTAGACATTT 57.302 33.333 13.59 13.59 40.18 2.32
1099 4469 4.531854 TGTGAATGTCTTTCCCAACTTGA 58.468 39.130 0.00 0.00 33.04 3.02
1110 4480 6.542370 TCTTTCCCAACTTGAACTACAAAGAG 59.458 38.462 0.00 0.00 38.08 2.85
1187 4557 1.270550 GGTGCTGAAACAGGGACAATG 59.729 52.381 0.00 0.00 31.21 2.82
1293 4663 0.732538 CAAAGCCCATTTCCGTTCGC 60.733 55.000 0.00 0.00 0.00 4.70
1378 4748 2.636830 CTGGGCAAAGGAGACATAGTG 58.363 52.381 0.00 0.00 0.00 2.74
1384 4754 3.127721 GCAAAGGAGACATAGTGAAAGGC 59.872 47.826 0.00 0.00 0.00 4.35
1429 4799 1.672881 GCATAGATTGTGCACAGGACC 59.327 52.381 20.59 10.28 42.08 4.46
1463 4833 2.543861 CCGTCCCACGAGTGAATATCAG 60.544 54.545 4.59 0.00 46.05 2.90
1484 4854 1.166531 AACTTGGCGAGGAAGTGCAC 61.167 55.000 9.40 9.40 33.85 4.57
1486 4856 0.886490 CTTGGCGAGGAAGTGCACTT 60.886 55.000 31.57 31.57 39.23 3.16
1606 4976 6.097839 GGTTAAGGGTAGTATCTGTCACATGA 59.902 42.308 0.00 0.00 0.00 3.07
1680 5050 5.591472 TGGGATGAATCTCATGCAAGTAAAG 59.409 40.000 9.88 0.00 45.52 1.85
1784 5162 5.936956 CCATTCTCTTACTTTGTCTTGCTCT 59.063 40.000 0.00 0.00 0.00 4.09
1811 5189 5.116882 GCATACTACCGTTCCTGAGAAAAT 58.883 41.667 0.00 0.00 32.58 1.82
1826 5204 6.114187 TGAGAAAATATGGCATAGATCCGT 57.886 37.500 13.39 0.00 0.00 4.69
2114 5492 9.040939 GCTGTTTCTTTATGTTGTTAATTGGTT 57.959 29.630 0.00 0.00 0.00 3.67
2130 5508 6.660887 AATTGGTTGTGTTACAAAGCAAAG 57.339 33.333 19.69 0.00 40.15 2.77
2401 5785 8.138365 TGGTATGTACAAAATAAAGAGCGATC 57.862 34.615 0.00 0.00 0.00 3.69
2408 5792 9.136952 GTACAAAATAAAGAGCGATCGGTATAT 57.863 33.333 21.30 15.35 0.00 0.86
2433 5817 1.398390 GCAATACCTTCAGCACGGAAG 59.602 52.381 3.85 3.85 43.09 3.46
2786 6172 8.518430 TGGTATGCACATATTGTTAAGAATGT 57.482 30.769 8.05 0.00 32.91 2.71
2980 6367 3.731728 GATGGTGCAGAGGGGGCA 61.732 66.667 0.00 0.00 39.32 5.36
3002 6389 1.379176 GAGGAAAGGGGCCAGAAGC 60.379 63.158 4.39 0.00 42.60 3.86
3500 7068 2.622942 TCTTGACAGCAATGTTGGTTCC 59.377 45.455 1.55 0.00 36.65 3.62
3501 7069 0.950836 TGACAGCAATGTTGGTTCCG 59.049 50.000 1.55 0.00 36.65 4.30
3502 7070 1.234821 GACAGCAATGTTGGTTCCGA 58.765 50.000 1.55 0.00 36.65 4.55
3503 7071 1.812571 GACAGCAATGTTGGTTCCGAT 59.187 47.619 1.55 0.00 36.65 4.18
3556 7124 0.035152 CCACCCTGCAGCAGTTCATA 60.035 55.000 21.26 0.00 0.00 2.15
3566 7134 3.503748 GCAGCAGTTCATAAAGTTGGAGT 59.496 43.478 0.00 0.00 0.00 3.85
3761 7409 9.508642 GCTATTTTGCTTAAGATATACTCCCTT 57.491 33.333 6.67 0.00 0.00 3.95
3764 7412 5.135508 TGCTTAAGATATACTCCCTTCGC 57.864 43.478 6.67 0.00 0.00 4.70
3774 7422 3.268023 ACTCCCTTCGCTCCAAAATAG 57.732 47.619 0.00 0.00 0.00 1.73
3776 7424 3.456277 ACTCCCTTCGCTCCAAAATAGAT 59.544 43.478 0.00 0.00 0.00 1.98
3778 7426 3.454447 TCCCTTCGCTCCAAAATAGATGA 59.546 43.478 0.00 0.00 0.00 2.92
3780 7428 3.561725 CCTTCGCTCCAAAATAGATGACC 59.438 47.826 0.00 0.00 0.00 4.02
3781 7429 3.194005 TCGCTCCAAAATAGATGACCC 57.806 47.619 0.00 0.00 0.00 4.46
3782 7430 2.503765 TCGCTCCAAAATAGATGACCCA 59.496 45.455 0.00 0.00 0.00 4.51
3783 7431 3.054728 TCGCTCCAAAATAGATGACCCAA 60.055 43.478 0.00 0.00 0.00 4.12
3784 7432 3.065371 CGCTCCAAAATAGATGACCCAAC 59.935 47.826 0.00 0.00 0.00 3.77
3785 7433 4.273318 GCTCCAAAATAGATGACCCAACT 58.727 43.478 0.00 0.00 0.00 3.16
3786 7434 4.706962 GCTCCAAAATAGATGACCCAACTT 59.293 41.667 0.00 0.00 0.00 2.66
3787 7435 5.185828 GCTCCAAAATAGATGACCCAACTTT 59.814 40.000 0.00 0.00 0.00 2.66
3789 7437 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
3790 7438 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3791 7439 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3793 7441 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3795 7443 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3796 7444 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
3797 7445 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
3799 7447 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3800 7448 8.983702 ATGACCCAACTTTGTACTAAAGTTAA 57.016 30.769 23.56 13.94 45.57 2.01
3801 7449 8.983702 TGACCCAACTTTGTACTAAAGTTAAT 57.016 30.769 23.56 16.51 45.57 1.40
3837 7562 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
3859 7584 3.262420 ACGTATGACTTTCTGCATGGTC 58.738 45.455 0.00 0.00 0.00 4.02
3860 7585 3.261580 CGTATGACTTTCTGCATGGTCA 58.738 45.455 11.54 11.54 41.84 4.02
3861 7586 3.308053 CGTATGACTTTCTGCATGGTCAG 59.692 47.826 13.58 1.01 41.11 3.51
3862 7587 2.936919 TGACTTTCTGCATGGTCAGT 57.063 45.000 0.00 0.00 34.38 3.41
3863 7588 3.213206 TGACTTTCTGCATGGTCAGTT 57.787 42.857 0.00 0.00 34.38 3.16
3864 7589 3.141398 TGACTTTCTGCATGGTCAGTTC 58.859 45.455 0.00 0.00 34.38 3.01
3866 7591 3.817647 GACTTTCTGCATGGTCAGTTCTT 59.182 43.478 0.00 0.00 35.63 2.52
3867 7592 4.210331 ACTTTCTGCATGGTCAGTTCTTT 58.790 39.130 0.00 0.00 35.63 2.52
3868 7593 4.646492 ACTTTCTGCATGGTCAGTTCTTTT 59.354 37.500 0.00 0.00 35.63 2.27
3869 7594 5.127682 ACTTTCTGCATGGTCAGTTCTTTTT 59.872 36.000 0.00 0.00 35.63 1.94
3890 7615 7.610580 TTTTTCTGGGTTTAATCTGAATGGT 57.389 32.000 0.00 0.00 0.00 3.55
3891 7616 8.713708 TTTTTCTGGGTTTAATCTGAATGGTA 57.286 30.769 0.00 0.00 0.00 3.25
3892 7617 8.893563 TTTTCTGGGTTTAATCTGAATGGTAT 57.106 30.769 0.00 0.00 0.00 2.73
3893 7618 8.519799 TTTCTGGGTTTAATCTGAATGGTATC 57.480 34.615 0.00 0.00 0.00 2.24
3894 7619 6.601332 TCTGGGTTTAATCTGAATGGTATCC 58.399 40.000 0.00 0.00 0.00 2.59
3895 7620 5.701224 TGGGTTTAATCTGAATGGTATCCC 58.299 41.667 0.00 0.00 0.00 3.85
3897 7622 4.760204 GGTTTAATCTGAATGGTATCCCCG 59.240 45.833 0.00 0.00 35.15 5.73
3898 7623 5.374071 GTTTAATCTGAATGGTATCCCCGT 58.626 41.667 0.00 0.00 35.15 5.28
3900 7625 3.492102 ATCTGAATGGTATCCCCGTTG 57.508 47.619 0.00 0.00 42.76 4.10
3903 7628 2.436542 CTGAATGGTATCCCCGTTGGTA 59.563 50.000 0.00 0.00 42.76 3.25
3904 7629 3.050089 TGAATGGTATCCCCGTTGGTAT 58.950 45.455 0.00 0.00 42.76 2.73
3907 7632 2.479340 TGGTATCCCCGTTGGTATTGA 58.521 47.619 0.00 0.00 35.15 2.57
3908 7633 2.171027 TGGTATCCCCGTTGGTATTGAC 59.829 50.000 0.00 0.00 35.15 3.18
3909 7634 2.436911 GGTATCCCCGTTGGTATTGACT 59.563 50.000 0.00 0.00 34.77 3.41
3910 7635 3.118149 GGTATCCCCGTTGGTATTGACTT 60.118 47.826 0.00 0.00 34.77 3.01
3913 7638 2.640826 TCCCCGTTGGTATTGACTTCTT 59.359 45.455 0.00 0.00 34.77 2.52
3915 7640 2.747446 CCCGTTGGTATTGACTTCTTGG 59.253 50.000 0.00 0.00 0.00 3.61
3916 7641 3.558321 CCCGTTGGTATTGACTTCTTGGA 60.558 47.826 0.00 0.00 0.00 3.53
3917 7642 4.069304 CCGTTGGTATTGACTTCTTGGAA 58.931 43.478 0.00 0.00 0.00 3.53
3918 7643 4.700213 CCGTTGGTATTGACTTCTTGGAAT 59.300 41.667 0.00 0.00 0.00 3.01
3919 7644 5.391950 CCGTTGGTATTGACTTCTTGGAATG 60.392 44.000 0.00 0.00 0.00 2.67
3920 7645 5.411361 CGTTGGTATTGACTTCTTGGAATGA 59.589 40.000 0.00 0.00 0.00 2.57
3921 7646 6.094048 CGTTGGTATTGACTTCTTGGAATGAT 59.906 38.462 0.00 0.00 0.00 2.45
3923 7648 8.306761 GTTGGTATTGACTTCTTGGAATGATTT 58.693 33.333 0.00 0.00 0.00 2.17
3924 7649 9.527157 TTGGTATTGACTTCTTGGAATGATTTA 57.473 29.630 0.00 0.00 0.00 1.40
3925 7650 9.699410 TGGTATTGACTTCTTGGAATGATTTAT 57.301 29.630 0.00 0.00 0.00 1.40
3951 7676 4.481195 GGCATATGTGGCCGTGAT 57.519 55.556 4.52 0.00 44.61 3.06
3952 7677 2.719376 GGCATATGTGGCCGTGATT 58.281 52.632 4.52 0.00 44.61 2.57
3953 7678 1.032014 GGCATATGTGGCCGTGATTT 58.968 50.000 4.52 0.00 44.61 2.17
3954 7679 1.269206 GGCATATGTGGCCGTGATTTG 60.269 52.381 4.52 0.00 44.61 2.32
3956 7681 1.404748 CATATGTGGCCGTGATTTGCA 59.595 47.619 0.00 0.00 0.00 4.08
3957 7682 1.539157 TATGTGGCCGTGATTTGCAA 58.461 45.000 0.00 0.00 0.00 4.08
3958 7683 0.038343 ATGTGGCCGTGATTTGCAAC 60.038 50.000 0.00 0.00 31.84 4.17
3959 7684 1.106351 TGTGGCCGTGATTTGCAACT 61.106 50.000 0.00 0.00 32.46 3.16
3960 7685 0.664166 GTGGCCGTGATTTGCAACTG 60.664 55.000 0.00 0.00 0.00 3.16
3962 7687 0.313672 GGCCGTGATTTGCAACTGAA 59.686 50.000 0.00 0.00 0.00 3.02
3963 7688 1.666888 GGCCGTGATTTGCAACTGAAG 60.667 52.381 0.00 0.00 0.00 3.02
3964 7689 1.266718 GCCGTGATTTGCAACTGAAGA 59.733 47.619 0.00 0.00 0.00 2.87
3966 7691 3.795150 GCCGTGATTTGCAACTGAAGAAA 60.795 43.478 0.00 0.00 0.00 2.52
3967 7692 4.549458 CCGTGATTTGCAACTGAAGAAAT 58.451 39.130 0.00 0.00 0.00 2.17
3968 7693 4.984161 CCGTGATTTGCAACTGAAGAAATT 59.016 37.500 0.00 0.00 0.00 1.82
3969 7694 5.107760 CCGTGATTTGCAACTGAAGAAATTG 60.108 40.000 0.00 0.00 0.00 2.32
3970 7695 5.107760 CGTGATTTGCAACTGAAGAAATTGG 60.108 40.000 0.00 0.00 0.00 3.16
3971 7696 5.984926 GTGATTTGCAACTGAAGAAATTGGA 59.015 36.000 0.00 0.00 0.00 3.53
3972 7697 6.479660 GTGATTTGCAACTGAAGAAATTGGAA 59.520 34.615 0.00 0.00 32.65 3.53
3974 7699 6.907206 TTTGCAACTGAAGAAATTGGAAAG 57.093 33.333 0.00 0.00 38.31 2.62
3976 7701 5.350633 TGCAACTGAAGAAATTGGAAAGTG 58.649 37.500 0.00 0.00 0.00 3.16
3977 7702 4.746611 GCAACTGAAGAAATTGGAAAGTGG 59.253 41.667 0.00 0.00 0.00 4.00
3978 7703 4.590850 ACTGAAGAAATTGGAAAGTGGC 57.409 40.909 0.00 0.00 0.00 5.01
3979 7704 3.321968 ACTGAAGAAATTGGAAAGTGGCC 59.678 43.478 0.00 0.00 0.00 5.36
3980 7705 2.295909 TGAAGAAATTGGAAAGTGGCCG 59.704 45.455 0.00 0.00 0.00 6.13
3981 7706 1.256812 AGAAATTGGAAAGTGGCCGG 58.743 50.000 0.00 0.00 0.00 6.13
3982 7707 0.389817 GAAATTGGAAAGTGGCCGGC 60.390 55.000 21.18 21.18 0.00 6.13
3983 7708 2.153547 AAATTGGAAAGTGGCCGGCG 62.154 55.000 22.54 0.00 0.00 6.46
3984 7709 3.860930 ATTGGAAAGTGGCCGGCGT 62.861 57.895 22.54 4.20 0.00 5.68
3985 7710 2.472414 ATTGGAAAGTGGCCGGCGTA 62.472 55.000 22.54 9.49 0.00 4.42
3987 7712 1.144496 GGAAAGTGGCCGGCGTATA 59.856 57.895 22.54 3.46 0.00 1.47
3988 7713 0.250166 GGAAAGTGGCCGGCGTATAT 60.250 55.000 22.54 6.33 0.00 0.86
3990 7715 2.548493 GGAAAGTGGCCGGCGTATATAA 60.548 50.000 22.54 0.00 0.00 0.98
3991 7716 2.159327 AAGTGGCCGGCGTATATAAC 57.841 50.000 22.54 9.52 0.00 1.89
3992 7717 0.319405 AGTGGCCGGCGTATATAACC 59.681 55.000 22.54 3.09 0.00 2.85
3994 7719 1.078918 GGCCGGCGTATATAACCCC 60.079 63.158 22.54 0.00 0.00 4.95
3996 7721 0.322648 GCCGGCGTATATAACCCCTT 59.677 55.000 12.58 0.00 0.00 3.95
3997 7722 1.673923 GCCGGCGTATATAACCCCTTC 60.674 57.143 12.58 0.00 0.00 3.46
3998 7723 1.403249 CCGGCGTATATAACCCCTTCG 60.403 57.143 6.01 0.00 0.00 3.79
3999 7724 1.403249 CGGCGTATATAACCCCTTCGG 60.403 57.143 0.00 0.00 37.81 4.30
4007 7732 3.643398 ACCCCTTCGGTATCTGCC 58.357 61.111 0.00 0.00 45.97 4.85
4008 7733 1.003051 ACCCCTTCGGTATCTGCCT 59.997 57.895 0.00 0.00 45.97 4.75
4010 7735 0.760945 CCCCTTCGGTATCTGCCTCT 60.761 60.000 0.00 0.00 0.00 3.69
4013 7738 1.889829 CCTTCGGTATCTGCCTCTAGG 59.110 57.143 0.00 0.00 38.53 3.02
4014 7739 2.588620 CTTCGGTATCTGCCTCTAGGT 58.411 52.381 0.00 0.00 37.57 3.08
4015 7740 2.273538 TCGGTATCTGCCTCTAGGTC 57.726 55.000 0.00 0.00 37.57 3.85
4016 7741 1.202903 TCGGTATCTGCCTCTAGGTCC 60.203 57.143 0.00 0.00 37.57 4.46
4017 7742 1.249407 GGTATCTGCCTCTAGGTCCG 58.751 60.000 0.00 0.00 37.57 4.79
4018 7743 1.202903 GGTATCTGCCTCTAGGTCCGA 60.203 57.143 0.00 0.00 37.57 4.55
4019 7744 2.584236 GTATCTGCCTCTAGGTCCGAA 58.416 52.381 0.00 0.00 37.57 4.30
4020 7745 1.404843 ATCTGCCTCTAGGTCCGAAC 58.595 55.000 0.00 0.00 37.57 3.95
4021 7746 0.331954 TCTGCCTCTAGGTCCGAACT 59.668 55.000 0.00 0.00 37.57 3.01
4022 7747 0.457851 CTGCCTCTAGGTCCGAACTG 59.542 60.000 0.00 0.00 37.57 3.16
4023 7748 0.970937 TGCCTCTAGGTCCGAACTGG 60.971 60.000 0.00 0.00 37.57 4.00
4024 7749 0.683504 GCCTCTAGGTCCGAACTGGA 60.684 60.000 0.00 0.00 39.25 3.86
4031 7756 4.123571 TCCGAACTGGAATCCCGT 57.876 55.556 0.00 0.00 46.38 5.28
4033 7758 1.449601 CCGAACTGGAATCCCGTGG 60.450 63.158 0.00 0.00 42.00 4.94
4034 7759 1.295423 CGAACTGGAATCCCGTGGT 59.705 57.895 0.00 0.00 34.29 4.16
4035 7760 1.019278 CGAACTGGAATCCCGTGGTG 61.019 60.000 0.00 0.00 34.29 4.17
4036 7761 0.676782 GAACTGGAATCCCGTGGTGG 60.677 60.000 0.00 0.00 34.29 4.61
4046 7771 4.619227 CGTGGTGGGGCTTCACGT 62.619 66.667 6.89 0.00 46.04 4.49
4047 7772 2.978010 GTGGTGGGGCTTCACGTG 60.978 66.667 9.94 9.94 38.46 4.49
4048 7773 4.947147 TGGTGGGGCTTCACGTGC 62.947 66.667 11.67 0.00 38.46 5.34
4073 7798 4.338539 GTCGACGTCCGTGCCACT 62.339 66.667 10.58 0.00 39.75 4.00
4074 7799 3.598715 TCGACGTCCGTGCCACTT 61.599 61.111 10.58 0.00 39.75 3.16
4075 7800 3.103911 CGACGTCCGTGCCACTTC 61.104 66.667 10.58 0.00 0.00 3.01
4076 7801 2.737376 GACGTCCGTGCCACTTCC 60.737 66.667 3.51 0.00 0.00 3.46
4077 7802 3.509137 GACGTCCGTGCCACTTCCA 62.509 63.158 3.51 0.00 0.00 3.53
4078 7803 2.047274 CGTCCGTGCCACTTCCAT 60.047 61.111 0.00 0.00 0.00 3.41
4079 7804 1.216977 CGTCCGTGCCACTTCCATA 59.783 57.895 0.00 0.00 0.00 2.74
4081 7806 1.090052 GTCCGTGCCACTTCCATAGC 61.090 60.000 0.00 0.00 0.00 2.97
4082 7807 2.173669 CCGTGCCACTTCCATAGCG 61.174 63.158 0.00 0.00 0.00 4.26
4085 7810 2.902343 GCCACTTCCATAGCGGCC 60.902 66.667 0.00 0.00 44.74 6.13
4086 7811 2.911143 CCACTTCCATAGCGGCCT 59.089 61.111 0.00 0.00 33.14 5.19
4087 7812 1.524621 CCACTTCCATAGCGGCCTG 60.525 63.158 0.00 0.00 33.14 4.85
4091 7816 1.971505 CTTCCATAGCGGCCTGGTCA 61.972 60.000 16.18 6.44 34.03 4.02
4094 7819 3.075005 ATAGCGGCCTGGTCACGT 61.075 61.111 0.00 0.00 0.00 4.49
4098 7823 3.991051 CGGCCTGGTCACGTCAGT 61.991 66.667 0.00 0.00 0.00 3.41
4136 8576 1.003112 AACAGGCGCGGTTGGAATA 60.003 52.632 14.27 0.00 0.00 1.75
4137 8577 0.606944 AACAGGCGCGGTTGGAATAA 60.607 50.000 14.27 0.00 0.00 1.40
4157 8597 7.867909 GGAATAACTTATTTTATGCTTGCTCCC 59.132 37.037 0.00 0.00 0.00 4.30
4158 8598 8.539117 AATAACTTATTTTATGCTTGCTCCCT 57.461 30.769 0.00 0.00 0.00 4.20
4159 8599 6.857437 AACTTATTTTATGCTTGCTCCCTT 57.143 33.333 0.00 0.00 0.00 3.95
4160 8600 6.456795 ACTTATTTTATGCTTGCTCCCTTC 57.543 37.500 0.00 0.00 0.00 3.46
4162 8602 7.346471 ACTTATTTTATGCTTGCTCCCTTCTA 58.654 34.615 0.00 0.00 0.00 2.10
4163 8603 8.001292 ACTTATTTTATGCTTGCTCCCTTCTAT 58.999 33.333 0.00 0.00 0.00 1.98
4164 8604 9.507329 CTTATTTTATGCTTGCTCCCTTCTATA 57.493 33.333 0.00 0.00 0.00 1.31
4166 8606 8.766994 ATTTTATGCTTGCTCCCTTCTATAAA 57.233 30.769 0.00 0.00 0.00 1.40
4167 8607 8.588290 TTTTATGCTTGCTCCCTTCTATAAAA 57.412 30.769 0.00 0.00 0.00 1.52
4168 8608 8.588290 TTTATGCTTGCTCCCTTCTATAAAAA 57.412 30.769 0.00 0.00 0.00 1.94
4169 8609 8.766994 TTATGCTTGCTCCCTTCTATAAAAAT 57.233 30.769 0.00 0.00 0.00 1.82
4171 8611 8.946797 ATGCTTGCTCCCTTCTATAAAAATAT 57.053 30.769 0.00 0.00 0.00 1.28
4173 8613 7.231317 TGCTTGCTCCCTTCTATAAAAATATGG 59.769 37.037 0.00 0.00 0.00 2.74
4175 8615 9.793259 CTTGCTCCCTTCTATAAAAATATGGTA 57.207 33.333 0.00 0.00 0.00 3.25
4176 8616 9.569122 TTGCTCCCTTCTATAAAAATATGGTAC 57.431 33.333 0.00 0.00 0.00 3.34
4177 8617 7.876068 TGCTCCCTTCTATAAAAATATGGTACG 59.124 37.037 0.00 0.00 0.00 3.67
4195 8661 7.912949 TGGTACGCTATAAAAATACAGTACG 57.087 36.000 0.00 0.00 35.42 3.67
4196 8662 6.417635 TGGTACGCTATAAAAATACAGTACGC 59.582 38.462 0.00 0.00 35.42 4.42
4212 8678 4.195308 GCCGTTGGCGTATTCTCA 57.805 55.556 0.00 0.00 39.62 3.27
4213 8679 2.006772 GCCGTTGGCGTATTCTCAG 58.993 57.895 0.00 0.00 39.62 3.35
4259 8726 9.959749 AAACAACATTTCTCGCTTAAAATAGAA 57.040 25.926 0.00 0.00 0.00 2.10
4381 8849 8.076178 AGTTCAACAATACAACATCAAACTAGC 58.924 33.333 0.00 0.00 0.00 3.42
4389 8857 2.076863 ACATCAAACTAGCCTTGTCGC 58.923 47.619 5.36 0.00 0.00 5.19
4390 8858 2.289694 ACATCAAACTAGCCTTGTCGCT 60.290 45.455 5.36 0.00 43.09 4.93
4395 8863 2.770164 ACTAGCCTTGTCGCTCATTT 57.230 45.000 0.00 0.00 40.39 2.32
4402 8870 1.469703 CTTGTCGCTCATTTCATGCCA 59.530 47.619 0.00 0.00 0.00 4.92
4403 8871 0.804364 TGTCGCTCATTTCATGCCAC 59.196 50.000 0.00 0.00 0.00 5.01
4405 8873 0.322366 TCGCTCATTTCATGCCACCA 60.322 50.000 0.00 0.00 0.00 4.17
4406 8874 0.179156 CGCTCATTTCATGCCACCAC 60.179 55.000 0.00 0.00 0.00 4.16
4407 8875 1.180029 GCTCATTTCATGCCACCACT 58.820 50.000 0.00 0.00 0.00 4.00
4408 8876 1.547372 GCTCATTTCATGCCACCACTT 59.453 47.619 0.00 0.00 0.00 3.16
4409 8877 2.416431 GCTCATTTCATGCCACCACTTC 60.416 50.000 0.00 0.00 0.00 3.01
4410 8878 3.087031 CTCATTTCATGCCACCACTTCT 58.913 45.455 0.00 0.00 0.00 2.85
4411 8879 3.499338 TCATTTCATGCCACCACTTCTT 58.501 40.909 0.00 0.00 0.00 2.52
4427 8895 8.571336 CACCACTTCTTGATTAGATTCTTTTGT 58.429 33.333 0.00 0.00 31.54 2.83
4452 8920 1.453155 ATCATGCGTCCCAACAACTC 58.547 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 3644 7.331934 ACGTCATGGCATGTTACATCTTATATC 59.668 37.037 25.62 0.00 0.00 1.63
502 3872 8.350722 TCTACGACAAATGGATGTATCTAGAAC 58.649 37.037 0.00 0.00 32.57 3.01
503 3873 8.459911 TCTACGACAAATGGATGTATCTAGAA 57.540 34.615 0.00 0.00 32.57 2.10
504 3874 8.459911 TTCTACGACAAATGGATGTATCTAGA 57.540 34.615 0.00 0.00 32.57 2.43
505 3875 9.698309 ATTTCTACGACAAATGGATGTATCTAG 57.302 33.333 0.00 0.00 32.57 2.43
506 3876 9.476202 CATTTCTACGACAAATGGATGTATCTA 57.524 33.333 0.00 0.00 37.51 1.98
507 3877 8.370493 CATTTCTACGACAAATGGATGTATCT 57.630 34.615 0.00 0.00 37.51 1.98
516 3886 8.370493 AGATACATCCATTTCTACGACAAATG 57.630 34.615 0.00 0.35 39.84 2.32
517 3887 9.698309 CTAGATACATCCATTTCTACGACAAAT 57.302 33.333 0.00 0.00 0.00 2.32
518 3888 8.909923 TCTAGATACATCCATTTCTACGACAAA 58.090 33.333 0.00 0.00 0.00 2.83
519 3889 8.350722 GTCTAGATACATCCATTTCTACGACAA 58.649 37.037 0.00 0.00 0.00 3.18
520 3890 7.501225 TGTCTAGATACATCCATTTCTACGACA 59.499 37.037 0.00 0.00 32.64 4.35
521 3891 7.872881 TGTCTAGATACATCCATTTCTACGAC 58.127 38.462 0.00 0.00 0.00 4.34
522 3892 8.637196 ATGTCTAGATACATCCATTTCTACGA 57.363 34.615 0.00 0.00 35.08 3.43
523 3893 9.698309 AAATGTCTAGATACATCCATTTCTACG 57.302 33.333 9.70 0.00 39.16 3.51
550 3920 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
551 3921 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
552 3922 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
553 3923 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
595 3965 5.552371 AGCATGTCTCCTATACTACTCCCTA 59.448 44.000 0.00 0.00 0.00 3.53
964 4334 7.867909 GGAAAAAGGAAAGACAATGGTTTAGAG 59.132 37.037 0.00 0.00 0.00 2.43
1099 4469 8.712228 AGATTTTCCAAATCCTCTTTGTAGTT 57.288 30.769 5.73 0.00 0.00 2.24
1110 4480 5.052481 GCAGCCATAAGATTTTCCAAATCC 58.948 41.667 5.73 0.00 0.00 3.01
1187 4557 1.526917 ACAACAGAGCCAGTGCCAC 60.527 57.895 0.00 0.00 38.69 5.01
1293 4663 5.852755 TGTATAGAAATACGTATTGGCGTCG 59.147 40.000 21.00 0.00 44.55 5.12
1378 4748 1.723870 CTGCGCCATACTGCCTTTC 59.276 57.895 4.18 0.00 0.00 2.62
1384 4754 1.586422 ATTGTAGCTGCGCCATACTG 58.414 50.000 4.18 0.00 0.00 2.74
1429 4799 1.739049 GGACGGAGATGAGGAGCAG 59.261 63.158 0.00 0.00 0.00 4.24
1463 4833 1.578206 GCACTTCCTCGCCAAGTTCC 61.578 60.000 0.00 0.00 31.40 3.62
1484 4854 4.657969 AGGTAAGAGGAGGATGATTGGAAG 59.342 45.833 0.00 0.00 0.00 3.46
1486 4856 4.286813 AGGTAAGAGGAGGATGATTGGA 57.713 45.455 0.00 0.00 0.00 3.53
1606 4976 9.160496 CTTCACTAAATCATAGAGTGCTCTTTT 57.840 33.333 7.05 4.76 40.35 2.27
1680 5050 0.456221 TCCCTTTCTCACTCGCGATC 59.544 55.000 10.36 0.00 0.00 3.69
1784 5162 1.133598 CAGGAACGGTAGTATGCGACA 59.866 52.381 0.00 0.00 0.00 4.35
1811 5189 5.801531 AACTTACACGGATCTATGCCATA 57.198 39.130 0.00 0.00 0.00 2.74
2076 5454 9.167311 ACATAAAGAAACAGCCAACTAGAATAG 57.833 33.333 0.00 0.00 46.50 1.73
2397 5781 6.042777 AGGTATTGCAATCATATACCGATCG 58.957 40.000 16.86 8.51 45.42 3.69
2401 5785 6.402550 GCTGAAGGTATTGCAATCATATACCG 60.403 42.308 16.86 5.97 45.42 4.02
2408 5792 2.419673 CGTGCTGAAGGTATTGCAATCA 59.580 45.455 16.86 7.38 37.17 2.57
2433 5817 2.415697 ACAACTGGCAATAACAACGC 57.584 45.000 0.00 0.00 0.00 4.84
2847 6233 1.889530 AAACCGCTCCCTCTTCCTCG 61.890 60.000 0.00 0.00 0.00 4.63
3002 6389 5.053145 GTGGGTTCTGCTAATCTGATGTAG 58.947 45.833 0.00 0.00 0.00 2.74
3155 6632 8.752187 ACAACATACAAAATGAGCCAATTAGAT 58.248 29.630 0.00 0.00 0.00 1.98
3311 6808 9.771534 GATCTTAGTATCTTATGCTGTTTTCCT 57.228 33.333 0.00 0.00 0.00 3.36
3403 6971 9.461312 AGAATTAAAGCAACATCAGGTTATGTA 57.539 29.630 0.00 0.00 39.16 2.29
3556 7124 7.158021 CAGAGAGATAACTTGACTCCAACTTT 58.842 38.462 0.00 0.00 0.00 2.66
3566 7134 7.272244 TGTTTGTCAACAGAGAGATAACTTGA 58.728 34.615 0.00 0.00 38.03 3.02
3761 7409 2.503765 TGGGTCATCTATTTTGGAGCGA 59.496 45.455 0.00 0.00 0.00 4.93
3764 7412 6.209391 ACAAAGTTGGGTCATCTATTTTGGAG 59.791 38.462 0.00 0.00 0.00 3.86
3774 7422 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3776 7424 8.983702 ATTAACTTTAGTACAAAGTTGGGTCA 57.016 30.769 27.85 15.73 46.41 4.02
3778 7426 9.850198 TGTATTAACTTTAGTACAAAGTTGGGT 57.150 29.630 27.85 20.50 46.41 4.51
3799 7447 9.927668 CCAAAATAGATGAACCAACTTTGTATT 57.072 29.630 0.00 0.00 0.00 1.89
3800 7448 9.308000 TCCAAAATAGATGAACCAACTTTGTAT 57.692 29.630 0.00 0.00 0.00 2.29
3801 7449 8.698973 TCCAAAATAGATGAACCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
3802 7450 7.595819 TCCAAAATAGATGAACCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
3803 7451 7.114811 CGTTCCAAAATAGATGAACCAACTTTG 59.885 37.037 0.00 0.00 34.93 2.77
3805 7453 6.294508 CCGTTCCAAAATAGATGAACCAACTT 60.295 38.462 0.00 0.00 34.93 2.66
3807 7455 5.182380 TCCGTTCCAAAATAGATGAACCAAC 59.818 40.000 0.00 0.00 34.93 3.77
3808 7456 5.317808 TCCGTTCCAAAATAGATGAACCAA 58.682 37.500 0.00 0.00 34.93 3.67
3812 7460 4.226394 TCCCTCCGTTCCAAAATAGATGAA 59.774 41.667 0.00 0.00 0.00 2.57
3814 7462 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3815 7463 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3816 7464 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3817 7465 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3823 7548 0.327924 TACGTACTCCCTCCGTTCCA 59.672 55.000 0.00 0.00 36.12 3.53
3837 7562 4.081917 TGACCATGCAGAAAGTCATACGTA 60.082 41.667 0.00 0.00 34.44 3.57
3866 7591 7.610580 ACCATTCAGATTAAACCCAGAAAAA 57.389 32.000 0.00 0.00 0.00 1.94
3867 7592 8.893563 ATACCATTCAGATTAAACCCAGAAAA 57.106 30.769 0.00 0.00 0.00 2.29
3868 7593 7.559897 GGATACCATTCAGATTAAACCCAGAAA 59.440 37.037 0.00 0.00 0.00 2.52
3869 7594 7.060421 GGATACCATTCAGATTAAACCCAGAA 58.940 38.462 0.00 0.00 0.00 3.02
3870 7595 6.601332 GGATACCATTCAGATTAAACCCAGA 58.399 40.000 0.00 0.00 0.00 3.86
3890 7615 4.035112 AGAAGTCAATACCAACGGGGATA 58.965 43.478 2.06 0.00 36.37 2.59
3891 7616 2.844348 AGAAGTCAATACCAACGGGGAT 59.156 45.455 2.06 0.00 40.54 3.85
3892 7617 2.262637 AGAAGTCAATACCAACGGGGA 58.737 47.619 2.06 0.00 41.15 4.81
3893 7618 2.747446 CAAGAAGTCAATACCAACGGGG 59.253 50.000 0.00 0.00 44.81 5.73
3894 7619 2.747446 CCAAGAAGTCAATACCAACGGG 59.253 50.000 0.00 0.00 41.29 5.28
3895 7620 3.670625 TCCAAGAAGTCAATACCAACGG 58.329 45.455 0.00 0.00 0.00 4.44
3897 7622 6.817765 TCATTCCAAGAAGTCAATACCAAC 57.182 37.500 0.00 0.00 0.00 3.77
3898 7623 8.421249 AAATCATTCCAAGAAGTCAATACCAA 57.579 30.769 0.00 0.00 0.00 3.67
3919 7644 9.956720 GCCACATATGCCATAGATAAATAAATC 57.043 33.333 1.58 0.00 0.00 2.17
3934 7659 1.032014 AAATCACGGCCACATATGCC 58.968 50.000 2.24 0.00 45.70 4.40
3935 7660 1.865248 GCAAATCACGGCCACATATGC 60.865 52.381 2.24 1.70 0.00 3.14
3936 7661 1.404748 TGCAAATCACGGCCACATATG 59.595 47.619 2.24 0.00 0.00 1.78
3938 7663 1.201181 GTTGCAAATCACGGCCACATA 59.799 47.619 0.00 0.00 0.00 2.29
3940 7665 1.106351 AGTTGCAAATCACGGCCACA 61.106 50.000 0.00 0.00 0.00 4.17
3941 7666 0.664166 CAGTTGCAAATCACGGCCAC 60.664 55.000 0.00 0.00 0.00 5.01
3944 7669 1.266718 TCTTCAGTTGCAAATCACGGC 59.733 47.619 0.00 0.00 0.00 5.68
3947 7672 5.984926 TCCAATTTCTTCAGTTGCAAATCAC 59.015 36.000 0.00 0.00 0.00 3.06
3948 7673 6.159299 TCCAATTTCTTCAGTTGCAAATCA 57.841 33.333 0.00 0.00 0.00 2.57
3949 7674 7.225341 ACTTTCCAATTTCTTCAGTTGCAAATC 59.775 33.333 0.00 0.00 0.00 2.17
3950 7675 7.011669 CACTTTCCAATTTCTTCAGTTGCAAAT 59.988 33.333 0.00 0.00 0.00 2.32
3951 7676 6.313411 CACTTTCCAATTTCTTCAGTTGCAAA 59.687 34.615 0.00 0.00 0.00 3.68
3952 7677 5.811613 CACTTTCCAATTTCTTCAGTTGCAA 59.188 36.000 0.00 0.00 0.00 4.08
3953 7678 5.350633 CACTTTCCAATTTCTTCAGTTGCA 58.649 37.500 0.00 0.00 0.00 4.08
3954 7679 4.746611 CCACTTTCCAATTTCTTCAGTTGC 59.253 41.667 0.00 0.00 0.00 4.17
3956 7681 4.202253 GGCCACTTTCCAATTTCTTCAGTT 60.202 41.667 0.00 0.00 0.00 3.16
3957 7682 3.321968 GGCCACTTTCCAATTTCTTCAGT 59.678 43.478 0.00 0.00 0.00 3.41
3958 7683 3.612479 CGGCCACTTTCCAATTTCTTCAG 60.612 47.826 2.24 0.00 0.00 3.02
3959 7684 2.295909 CGGCCACTTTCCAATTTCTTCA 59.704 45.455 2.24 0.00 0.00 3.02
3960 7685 2.352715 CCGGCCACTTTCCAATTTCTTC 60.353 50.000 2.24 0.00 0.00 2.87
3962 7687 1.256812 CCGGCCACTTTCCAATTTCT 58.743 50.000 2.24 0.00 0.00 2.52
3963 7688 0.389817 GCCGGCCACTTTCCAATTTC 60.390 55.000 18.11 0.00 0.00 2.17
3964 7689 1.671166 GCCGGCCACTTTCCAATTT 59.329 52.632 18.11 0.00 0.00 1.82
3966 7691 2.472414 TACGCCGGCCACTTTCCAAT 62.472 55.000 23.46 0.00 0.00 3.16
3967 7692 2.472414 ATACGCCGGCCACTTTCCAA 62.472 55.000 23.46 0.00 0.00 3.53
3968 7693 1.615165 TATACGCCGGCCACTTTCCA 61.615 55.000 23.46 0.00 0.00 3.53
3969 7694 0.250166 ATATACGCCGGCCACTTTCC 60.250 55.000 23.46 0.00 0.00 3.13
3970 7695 2.443887 TATATACGCCGGCCACTTTC 57.556 50.000 23.46 0.00 0.00 2.62
3971 7696 2.486918 GTTATATACGCCGGCCACTTT 58.513 47.619 23.46 5.92 0.00 2.66
3972 7697 1.270465 GGTTATATACGCCGGCCACTT 60.270 52.381 23.46 5.92 0.00 3.16
3974 7699 0.671472 GGGTTATATACGCCGGCCAC 60.671 60.000 23.46 0.01 33.80 5.01
3976 7701 4.604114 GGGTTATATACGCCGGCC 57.396 61.111 23.46 3.23 33.80 6.13
3994 7719 2.554893 GACCTAGAGGCAGATACCGAAG 59.445 54.545 0.00 0.00 39.32 3.79
3996 7721 1.202903 GGACCTAGAGGCAGATACCGA 60.203 57.143 0.00 0.00 39.32 4.69
3997 7722 1.249407 GGACCTAGAGGCAGATACCG 58.751 60.000 0.00 0.00 39.32 4.02
3998 7723 1.202903 TCGGACCTAGAGGCAGATACC 60.203 57.143 0.00 0.00 39.32 2.73
3999 7724 2.273538 TCGGACCTAGAGGCAGATAC 57.726 55.000 0.00 0.00 39.32 2.24
4000 7725 2.175069 AGTTCGGACCTAGAGGCAGATA 59.825 50.000 0.00 0.00 39.32 1.98
4001 7726 1.063567 AGTTCGGACCTAGAGGCAGAT 60.064 52.381 0.00 0.00 39.32 2.90
4003 7728 0.457851 CAGTTCGGACCTAGAGGCAG 59.542 60.000 0.00 0.00 39.32 4.85
4004 7729 0.970937 CCAGTTCGGACCTAGAGGCA 60.971 60.000 0.00 0.00 39.32 4.75
4005 7730 0.683504 TCCAGTTCGGACCTAGAGGC 60.684 60.000 0.00 0.00 39.64 4.70
4006 7731 1.848652 TTCCAGTTCGGACCTAGAGG 58.151 55.000 0.00 0.00 46.36 3.69
4007 7732 2.362717 GGATTCCAGTTCGGACCTAGAG 59.637 54.545 0.00 0.00 46.36 2.43
4008 7733 2.385803 GGATTCCAGTTCGGACCTAGA 58.614 52.381 0.00 0.00 46.36 2.43
4010 7735 1.492764 GGGATTCCAGTTCGGACCTA 58.507 55.000 4.80 0.00 46.36 3.08
4013 7738 0.739813 CACGGGATTCCAGTTCGGAC 60.740 60.000 5.68 0.00 46.36 4.79
4014 7739 1.594833 CACGGGATTCCAGTTCGGA 59.405 57.895 5.68 0.00 44.40 4.55
4015 7740 1.449601 CCACGGGATTCCAGTTCGG 60.450 63.158 5.68 2.07 0.00 4.30
4016 7741 1.019278 CACCACGGGATTCCAGTTCG 61.019 60.000 5.68 1.74 0.00 3.95
4017 7742 0.676782 CCACCACGGGATTCCAGTTC 60.677 60.000 5.68 0.00 0.00 3.01
4018 7743 1.378762 CCACCACGGGATTCCAGTT 59.621 57.895 5.68 0.00 0.00 3.16
4019 7744 3.077907 CCACCACGGGATTCCAGT 58.922 61.111 4.80 3.52 0.00 4.00
4030 7755 2.978010 CACGTGAAGCCCCACCAC 60.978 66.667 10.90 0.00 33.67 4.16
4031 7756 4.947147 GCACGTGAAGCCCCACCA 62.947 66.667 22.23 0.00 33.67 4.17
4056 7781 3.836176 AAGTGGCACGGACGTCGAC 62.836 63.158 12.71 5.18 42.43 4.20
4058 7783 3.103911 GAAGTGGCACGGACGTCG 61.104 66.667 12.71 7.64 45.88 5.12
4060 7785 1.537814 TATGGAAGTGGCACGGACGT 61.538 55.000 12.71 9.85 0.00 4.34
4063 7788 1.220749 GCTATGGAAGTGGCACGGA 59.779 57.895 12.71 0.00 0.00 4.69
4065 7790 3.398920 CGCTATGGAAGTGGCACG 58.601 61.111 12.71 0.00 31.67 5.34
4070 7795 1.524621 CCAGGCCGCTATGGAAGTG 60.525 63.158 2.49 0.00 42.00 3.16
4072 7797 1.227674 GACCAGGCCGCTATGGAAG 60.228 63.158 15.38 0.00 42.00 3.46
4073 7798 1.992834 TGACCAGGCCGCTATGGAA 60.993 57.895 15.38 0.83 42.00 3.53
4074 7799 2.364973 TGACCAGGCCGCTATGGA 60.365 61.111 15.38 0.00 42.00 3.41
4075 7800 2.203070 GTGACCAGGCCGCTATGG 60.203 66.667 7.20 7.20 42.60 2.74
4076 7801 2.586079 CGTGACCAGGCCGCTATG 60.586 66.667 0.00 0.00 0.00 2.23
4077 7802 3.075005 ACGTGACCAGGCCGCTAT 61.075 61.111 0.00 0.00 0.00 2.97
4078 7803 3.755628 GACGTGACCAGGCCGCTA 61.756 66.667 0.00 0.00 0.00 4.26
4081 7806 3.991051 ACTGACGTGACCAGGCCG 61.991 66.667 0.00 0.00 36.03 6.13
4082 7807 2.357517 CACTGACGTGACCAGGCC 60.358 66.667 0.00 0.00 43.97 5.19
4085 7810 2.734723 CGCCACTGACGTGACCAG 60.735 66.667 0.00 0.00 43.97 4.00
4086 7811 3.493830 GACGCCACTGACGTGACCA 62.494 63.158 0.00 0.00 45.24 4.02
4087 7812 2.694829 AAGACGCCACTGACGTGACC 62.695 60.000 0.00 0.00 45.24 4.02
4094 7819 1.135139 GATGCTCTAAGACGCCACTGA 59.865 52.381 0.00 0.00 0.00 3.41
4096 7821 1.407258 GAGATGCTCTAAGACGCCACT 59.593 52.381 0.00 0.00 0.00 4.00
4097 7822 1.537135 GGAGATGCTCTAAGACGCCAC 60.537 57.143 0.00 0.00 0.00 5.01
4098 7823 0.747255 GGAGATGCTCTAAGACGCCA 59.253 55.000 0.00 0.00 0.00 5.69
4099 7824 0.747255 TGGAGATGCTCTAAGACGCC 59.253 55.000 0.00 0.00 0.00 5.68
4102 7827 3.791245 CCTGTTGGAGATGCTCTAAGAC 58.209 50.000 0.00 0.00 31.92 3.01
4136 8576 6.665248 AGAAGGGAGCAAGCATAAAATAAGTT 59.335 34.615 0.00 0.00 0.00 2.66
4137 8577 6.190587 AGAAGGGAGCAAGCATAAAATAAGT 58.809 36.000 0.00 0.00 0.00 2.24
4169 8609 9.611284 CGTACTGTATTTTTATAGCGTACCATA 57.389 33.333 0.00 0.00 0.00 2.74
4171 8611 6.417635 GCGTACTGTATTTTTATAGCGTACCA 59.582 38.462 0.00 0.00 0.00 3.25
4173 8613 6.397894 CGGCGTACTGTATTTTTATAGCGTAC 60.398 42.308 0.00 0.00 0.00 3.67
4175 8615 4.442073 CGGCGTACTGTATTTTTATAGCGT 59.558 41.667 0.00 0.00 0.00 5.07
4176 8616 4.442073 ACGGCGTACTGTATTTTTATAGCG 59.558 41.667 12.58 0.00 31.99 4.26
4177 8617 5.895216 ACGGCGTACTGTATTTTTATAGC 57.105 39.130 12.58 0.00 31.99 2.97
4195 8661 0.459585 TCTGAGAATACGCCAACGGC 60.460 55.000 0.00 0.00 46.75 5.68
4196 8662 2.004583 TTCTGAGAATACGCCAACGG 57.995 50.000 0.00 0.00 46.04 4.44
4204 8670 5.985781 TGAACACGCTTTTTCTGAGAATAC 58.014 37.500 0.00 0.00 0.00 1.89
4207 8673 3.242739 GCTGAACACGCTTTTTCTGAGAA 60.243 43.478 0.00 0.00 0.00 2.87
4211 8677 2.111756 GTGCTGAACACGCTTTTTCTG 58.888 47.619 0.00 0.00 40.07 3.02
4212 8678 2.475200 GTGCTGAACACGCTTTTTCT 57.525 45.000 0.00 0.00 40.07 2.52
4395 8863 2.885135 ATCAAGAAGTGGTGGCATGA 57.115 45.000 0.00 0.00 0.00 3.07
4402 8870 8.697507 ACAAAAGAATCTAATCAAGAAGTGGT 57.302 30.769 0.00 0.00 37.89 4.16
4427 8895 4.681074 TGTTGGGACGCATGATAATCTA 57.319 40.909 0.00 0.00 0.00 1.98
4432 8900 2.027653 TGAGTTGTTGGGACGCATGATA 60.028 45.455 0.00 0.00 0.00 2.15
4439 8907 5.515797 TCTCTATATGAGTTGTTGGGACG 57.484 43.478 0.00 0.00 43.13 4.79


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

AutoCloner maintained by Alex Coulton.