Multiple sequence alignment - TraesCS4B01G189000

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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 TraesCS4B01G189000 chr4B 100.000 6288 0 0 1 6288 411530723 411537010 0.000000e+00 11612.0
1 TraesCS4B01G189000 chr4B 99.444 540 3 0 5749 6288 18256910 18256371 0.000000e+00 981.0
2 TraesCS4B01G189000 chr4B 99.217 511 4 0 1 511 35512266 35511756 0.000000e+00 922.0
3 TraesCS4B01G189000 chr4B 98.830 513 6 0 1 513 386042821 386042309 0.000000e+00 915.0
4 TraesCS4B01G189000 chr4B 91.935 124 8 2 4666 4788 482619946 482619824 8.380000e-39 172.0
5 TraesCS4B01G189000 chr4A 94.308 4234 155 27 512 4681 140284078 140279867 0.000000e+00 6405.0
6 TraesCS4B01G189000 chr4A 97.417 968 21 3 4780 5747 140279873 140278910 0.000000e+00 1646.0
7 TraesCS4B01G189000 chr4A 99.444 540 3 0 5749 6288 637924391 637924930 0.000000e+00 981.0
8 TraesCS4B01G189000 chr4A 99.081 544 5 0 5745 6288 210984974 210985517 0.000000e+00 977.0
9 TraesCS4B01G189000 chr4D 94.553 4112 147 16 620 4678 333069369 333073456 0.000000e+00 6281.0
10 TraesCS4B01G189000 chr4D 95.248 968 21 2 4780 5747 333073453 333074395 0.000000e+00 1509.0
11 TraesCS4B01G189000 chr4D 98.077 52 1 0 512 563 333069318 333069369 2.410000e-14 91.6
12 TraesCS4B01G189000 chrUn 99.445 541 3 0 5748 6288 49783969 49783429 0.000000e+00 983.0
13 TraesCS4B01G189000 chr7A 99.443 539 3 0 5750 6288 229021553 229022091 0.000000e+00 979.0
14 TraesCS4B01G189000 chr7A 99.259 540 4 0 5749 6288 730476584 730476045 0.000000e+00 976.0
15 TraesCS4B01G189000 chr7A 95.690 116 4 1 4669 4784 501070666 501070780 1.080000e-42 185.0
16 TraesCS4B01G189000 chr7A 94.118 119 5 2 4675 4792 192671856 192671973 5.010000e-41 180.0
17 TraesCS4B01G189000 chr5B 99.443 539 3 0 5750 6288 375662920 375662382 0.000000e+00 979.0
18 TraesCS4B01G189000 chr5B 98.239 511 9 0 1 511 678521184 678521694 0.000000e+00 894.0
19 TraesCS4B01G189000 chr5A 99.443 539 3 0 5750 6288 609263844 609264382 0.000000e+00 979.0
20 TraesCS4B01G189000 chr5A 98.826 511 6 0 1 511 324964961 324964451 0.000000e+00 911.0
21 TraesCS4B01G189000 chr5A 98.043 511 10 0 1 511 328723114 328723624 0.000000e+00 889.0
22 TraesCS4B01G189000 chr3A 99.443 539 3 0 5750 6288 301773755 301773217 0.000000e+00 979.0
23 TraesCS4B01G189000 chr3A 89.781 137 12 2 4661 4797 427104443 427104309 2.330000e-39 174.0
24 TraesCS4B01G189000 chr1A 99.219 512 4 0 1 512 425731388 425731899 0.000000e+00 924.0
25 TraesCS4B01G189000 chr1A 90.909 132 10 2 4665 4795 6706845 6706975 6.480000e-40 176.0
26 TraesCS4B01G189000 chr7B 98.821 509 6 0 1 509 221916030 221915522 0.000000e+00 907.0
27 TraesCS4B01G189000 chr7B 98.630 511 6 1 1 511 595536042 595536551 0.000000e+00 904.0
28 TraesCS4B01G189000 chr7B 86.842 114 10 4 4569 4681 149352757 149352648 8.560000e-24 122.0
29 TraesCS4B01G189000 chr6A 98.242 512 9 0 1 512 418951769 418951258 0.000000e+00 896.0
30 TraesCS4B01G189000 chr6A 94.118 119 6 1 4665 4782 436115588 436115470 5.010000e-41 180.0
31 TraesCS4B01G189000 chr1D 95.652 115 4 1 4673 4787 220211112 220210999 3.870000e-42 183.0
32 TraesCS4B01G189000 chr5D 94.783 115 4 2 4667 4781 522142254 522142142 1.800000e-40 178.0
33 TraesCS4B01G189000 chr5D 95.556 45 2 0 4603 4647 269731792 269731748 8.740000e-09 73.1
34 TraesCS4B01G189000 chr6B 91.270 126 10 1 4656 4781 37764436 37764560 3.010000e-38 171.0
35 TraesCS4B01G189000 chr3D 97.500 40 1 0 4608 4647 309674506 309674545 1.130000e-07 69.4


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 TraesCS4B01G189000 chr4B 411530723 411537010 6287 False 11612.0 11612 100.000000 1 6288 1 chr4B.!!$F1 6287
1 TraesCS4B01G189000 chr4B 18256371 18256910 539 True 981.0 981 99.444000 5749 6288 1 chr4B.!!$R1 539
2 TraesCS4B01G189000 chr4B 35511756 35512266 510 True 922.0 922 99.217000 1 511 1 chr4B.!!$R2 510
3 TraesCS4B01G189000 chr4B 386042309 386042821 512 True 915.0 915 98.830000 1 513 1 chr4B.!!$R3 512
4 TraesCS4B01G189000 chr4A 140278910 140284078 5168 True 4025.5 6405 95.862500 512 5747 2 chr4A.!!$R1 5235
5 TraesCS4B01G189000 chr4A 637924391 637924930 539 False 981.0 981 99.444000 5749 6288 1 chr4A.!!$F2 539
6 TraesCS4B01G189000 chr4A 210984974 210985517 543 False 977.0 977 99.081000 5745 6288 1 chr4A.!!$F1 543
7 TraesCS4B01G189000 chr4D 333069318 333074395 5077 False 2627.2 6281 95.959333 512 5747 3 chr4D.!!$F1 5235
8 TraesCS4B01G189000 chrUn 49783429 49783969 540 True 983.0 983 99.445000 5748 6288 1 chrUn.!!$R1 540
9 TraesCS4B01G189000 chr7A 229021553 229022091 538 False 979.0 979 99.443000 5750 6288 1 chr7A.!!$F2 538
10 TraesCS4B01G189000 chr7A 730476045 730476584 539 True 976.0 976 99.259000 5749 6288 1 chr7A.!!$R1 539
11 TraesCS4B01G189000 chr5B 375662382 375662920 538 True 979.0 979 99.443000 5750 6288 1 chr5B.!!$R1 538
12 TraesCS4B01G189000 chr5B 678521184 678521694 510 False 894.0 894 98.239000 1 511 1 chr5B.!!$F1 510
13 TraesCS4B01G189000 chr5A 609263844 609264382 538 False 979.0 979 99.443000 5750 6288 1 chr5A.!!$F2 538
14 TraesCS4B01G189000 chr5A 324964451 324964961 510 True 911.0 911 98.826000 1 511 1 chr5A.!!$R1 510
15 TraesCS4B01G189000 chr5A 328723114 328723624 510 False 889.0 889 98.043000 1 511 1 chr5A.!!$F1 510
16 TraesCS4B01G189000 chr3A 301773217 301773755 538 True 979.0 979 99.443000 5750 6288 1 chr3A.!!$R1 538
17 TraesCS4B01G189000 chr1A 425731388 425731899 511 False 924.0 924 99.219000 1 512 1 chr1A.!!$F2 511
18 TraesCS4B01G189000 chr7B 221915522 221916030 508 True 907.0 907 98.821000 1 509 1 chr7B.!!$R2 508
19 TraesCS4B01G189000 chr7B 595536042 595536551 509 False 904.0 904 98.630000 1 511 1 chr7B.!!$F1 510
20 TraesCS4B01G189000 chr6A 418951258 418951769 511 True 896.0 896 98.242000 1 512 1 chr6A.!!$R1 511

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
856 858 0.109723 GGGTGGGTTCAGCACTGTAA 59.890 55.0 0.00 0.00 42.72 2.41 F
2388 2435 0.330604 TAGCTACCGAGTCCAGTGGT 59.669 55.0 9.54 0.00 39.80 4.16 F
2805 2852 0.543749 GCCAGCTGGAAGTAGTGGAT 59.456 55.0 37.21 0.00 37.39 3.41 F
3333 3416 0.036732 CAGTAGCAAGTGAAGGCCCA 59.963 55.0 0.00 0.00 0.00 5.36 F
4690 4791 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.0 13.34 13.34 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2488 0.190815 AACATTGTTCCCCTTGGCCT 59.809 50.0 3.32 0.0 0.00 5.19 R
3237 3320 0.104855 TGGATGAAATCGGCGAGGAG 59.895 55.0 17.22 0.0 46.86 3.69 R
3820 3903 0.694444 AGAGGTGGAAGTGGTGGTGT 60.694 55.0 0.00 0.0 0.00 4.16 R
5132 5233 0.323957 GCGAGAGGGTTTAACCTGGT 59.676 55.0 14.27 0.0 42.10 4.00 R
5797 5898 0.107066 TCCTATCCACCGCGACTACA 60.107 55.0 8.23 0.0 0.00 2.74 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
214 215 1.008403 ACTCTACCAGGTCTAGGGCA 58.992 55.000 0.00 0.00 0.00 5.36
563 564 4.687948 TCTTCTGAGACGAAATTTCTGCAG 59.312 41.667 15.92 7.63 0.00 4.41
578 579 5.528043 TTCTGCAGCCACTTCAATTTTTA 57.472 34.783 9.47 0.00 0.00 1.52
629 630 6.037610 GGAAGACGCATCAGAATTCATAACTT 59.962 38.462 8.44 2.51 0.00 2.66
669 671 4.611310 CCATCGTATGGCATCATCATTC 57.389 45.455 1.65 0.00 44.70 2.67
693 695 1.798735 CAGATTTGCGGCAGAGGTG 59.201 57.895 1.67 0.00 0.00 4.00
772 774 4.025858 GGGTGCAGCAGCTGGAGA 62.026 66.667 24.13 0.00 42.74 3.71
854 856 2.515901 GGGTGGGTTCAGCACTGT 59.484 61.111 0.00 0.00 42.72 3.55
855 857 1.758592 GGGTGGGTTCAGCACTGTA 59.241 57.895 0.00 0.00 42.72 2.74
856 858 0.109723 GGGTGGGTTCAGCACTGTAA 59.890 55.000 0.00 0.00 42.72 2.41
859 861 1.607148 GTGGGTTCAGCACTGTAAACC 59.393 52.381 11.12 11.12 32.10 3.27
1103 1125 3.130693 GGAGGTAGTGAAGCGATGTACTT 59.869 47.826 0.00 0.00 0.00 2.24
1142 1164 8.739972 GTTTGGTCAACTTTCAGGTATGATATT 58.260 33.333 0.00 0.00 31.73 1.28
1232 1254 2.099263 CAGAATGCTGCAGGAAGGAATG 59.901 50.000 13.45 3.49 34.95 2.67
1287 1309 7.764443 TGGTAATCAACTGTTAATCTCTAGTGC 59.236 37.037 0.00 0.00 0.00 4.40
1310 1332 8.961092 GTGCTGTTATTGCATTAAGTTCATATG 58.039 33.333 1.35 0.00 42.69 1.78
1311 1333 7.648908 TGCTGTTATTGCATTAAGTTCATATGC 59.351 33.333 0.00 9.43 43.74 3.14
1649 1675 5.046591 TCAAGACTGATTTATCGGGTGAAGT 60.047 40.000 3.76 0.00 37.50 3.01
1659 1685 1.418264 TCGGGTGAAGTGTTGGATGAA 59.582 47.619 0.00 0.00 0.00 2.57
1678 1704 4.257654 TCCCGACAAGGCGCCAAA 62.258 61.111 31.54 0.71 39.21 3.28
1740 1766 1.145598 CAGACCGCAGATGCAGGAT 59.854 57.895 18.21 7.25 42.21 3.24
1748 1774 3.396560 CGCAGATGCAGGATCTTTATGA 58.603 45.455 0.71 0.00 39.64 2.15
1832 1858 0.529119 GACTCACCCGACACAAACGT 60.529 55.000 0.00 0.00 0.00 3.99
1886 1912 0.768221 ACCACTGAGAAGGGCAAGGA 60.768 55.000 0.00 0.00 0.00 3.36
2159 2206 2.630158 CTCTTCAGATGTTGGCTCAGG 58.370 52.381 0.00 0.00 0.00 3.86
2271 2318 3.004315 GCTCGTTGGAGGAATTGTTTTCA 59.996 43.478 0.00 0.00 40.80 2.69
2358 2405 5.396213 GGACATACTTCTTTCAGAGCCTGAT 60.396 44.000 5.83 0.00 40.39 2.90
2388 2435 0.330604 TAGCTACCGAGTCCAGTGGT 59.669 55.000 9.54 0.00 39.80 4.16
2571 2618 1.280133 CTCTCCAAGAAGCATGACCCA 59.720 52.381 0.00 0.00 0.00 4.51
2583 2630 2.883386 GCATGACCCATTCTCTGATTCC 59.117 50.000 0.00 0.00 0.00 3.01
2717 2764 2.026262 TGGCTCACCCTCCTATTGAAAC 60.026 50.000 0.00 0.00 33.59 2.78
2727 2774 5.116084 CTCCTATTGAAACCATGGAGGAA 57.884 43.478 21.47 5.73 41.22 3.36
2760 2807 5.397142 AGAGCATTTCTTTTGATTCACCC 57.603 39.130 0.00 0.00 29.61 4.61
2764 2811 4.692155 GCATTTCTTTTGATTCACCCCAAG 59.308 41.667 0.00 0.00 0.00 3.61
2765 2812 5.511202 GCATTTCTTTTGATTCACCCCAAGA 60.511 40.000 0.00 0.00 0.00 3.02
2766 2813 6.704310 CATTTCTTTTGATTCACCCCAAGAT 58.296 36.000 0.00 0.00 0.00 2.40
2805 2852 0.543749 GCCAGCTGGAAGTAGTGGAT 59.456 55.000 37.21 0.00 37.39 3.41
2815 2862 4.838423 TGGAAGTAGTGGATCAAGAGTCAA 59.162 41.667 0.00 0.00 0.00 3.18
2823 2870 4.394300 GTGGATCAAGAGTCAAACCATGAG 59.606 45.833 0.00 0.00 39.19 2.90
2875 2922 4.449743 CAGTGCCTGATGAAAATGGTTTTG 59.550 41.667 0.00 0.00 32.44 2.44
2882 2929 5.856156 TGATGAAAATGGTTTTGAGCACAT 58.144 33.333 0.00 0.00 27.68 3.21
2928 2975 2.257207 TCACCGAGTCCCAAAGAAGAT 58.743 47.619 0.00 0.00 0.00 2.40
2929 2976 2.028112 TCACCGAGTCCCAAAGAAGATG 60.028 50.000 0.00 0.00 0.00 2.90
2930 2977 1.279271 ACCGAGTCCCAAAGAAGATGG 59.721 52.381 0.00 0.00 37.71 3.51
2949 2996 5.422012 AGATGGAGAAGAGGAAGAAGAAGAC 59.578 44.000 0.00 0.00 0.00 3.01
3140 3223 2.300787 GCGAAGAGCGTGTGAACGT 61.301 57.895 0.00 0.00 43.41 3.99
3174 3257 3.805207 TGGATGCAGTGAATCTGATGAG 58.195 45.455 11.05 0.00 46.27 2.90
3189 3272 2.224137 TGATGAGAATGCATCGGAGGAC 60.224 50.000 0.00 0.00 45.93 3.85
3206 3289 4.499183 GAGGACGAAATCACAGAGAACAT 58.501 43.478 0.00 0.00 0.00 2.71
3213 3296 5.976534 CGAAATCACAGAGAACATAGGAGAG 59.023 44.000 0.00 0.00 0.00 3.20
3237 3320 4.597404 TGTGGCTCTAGATGATGTGATC 57.403 45.455 0.00 0.00 0.00 2.92
3238 3321 4.221530 TGTGGCTCTAGATGATGTGATCT 58.778 43.478 0.00 0.00 36.61 2.75
3239 3322 4.280425 TGTGGCTCTAGATGATGTGATCTC 59.720 45.833 0.00 0.00 34.42 2.75
3279 3362 2.891580 GCAATCTGATGATCCTTGCCAT 59.108 45.455 11.22 0.00 31.34 4.40
3310 3393 6.053650 CCATTCACTCTCAAAGATGCAGATA 58.946 40.000 0.00 0.00 0.00 1.98
3332 3415 1.308783 GCAGTAGCAAGTGAAGGCCC 61.309 60.000 0.00 0.00 41.58 5.80
3333 3416 0.036732 CAGTAGCAAGTGAAGGCCCA 59.963 55.000 0.00 0.00 0.00 5.36
3344 3427 1.347707 TGAAGGCCCAGACAACTACAG 59.652 52.381 0.00 0.00 0.00 2.74
3346 3429 1.127567 AGGCCCAGACAACTACAGCA 61.128 55.000 0.00 0.00 0.00 4.41
3366 3449 2.815503 CACTGAAATGGAGCATGTCACA 59.184 45.455 0.00 0.00 33.67 3.58
3416 3499 6.229936 ACTACCTAAAGTTGTGACTGAACA 57.770 37.500 0.00 0.00 35.91 3.18
3464 3547 2.676839 CAGATGATGAACAGTGCTGTCC 59.323 50.000 5.22 0.00 44.13 4.02
3495 3578 7.876068 CCAGAAACTAGTTTACCACAAGATACA 59.124 37.037 20.58 0.00 32.11 2.29
3501 3584 8.305317 ACTAGTTTACCACAAGATACAGTTCTC 58.695 37.037 0.00 0.00 0.00 2.87
3555 3638 2.552802 GCAACTGCACAGCTCATCT 58.447 52.632 0.00 0.00 41.59 2.90
3588 3671 4.003648 CCACTCCAGATCCAACTGTAAAC 58.996 47.826 0.00 0.00 36.30 2.01
3675 3758 1.097232 TTGCAGATCAATTGGCTCCG 58.903 50.000 5.42 0.00 0.00 4.63
3684 3767 1.201429 AATTGGCTCCGGACTCCACT 61.201 55.000 17.82 11.48 0.00 4.00
3966 4049 7.288810 AGAAAATGAAAATAACTCTGCACCA 57.711 32.000 0.00 0.00 0.00 4.17
4018 4101 4.934356 TCAGGAAATAGGCTGGAACAATT 58.066 39.130 0.00 0.00 38.70 2.32
4224 4307 0.041312 GCGACGACATGCACACTTTT 60.041 50.000 0.00 0.00 0.00 2.27
4385 4468 3.559655 GGTTTGCCAATTGAAAAGACCAC 59.440 43.478 7.12 0.00 34.09 4.16
4386 4469 4.441792 GTTTGCCAATTGAAAAGACCACT 58.558 39.130 7.12 0.00 0.00 4.00
4387 4470 3.731652 TGCCAATTGAAAAGACCACTG 57.268 42.857 7.12 0.00 0.00 3.66
4388 4471 3.030291 TGCCAATTGAAAAGACCACTGT 58.970 40.909 7.12 0.00 0.00 3.55
4389 4472 3.181477 TGCCAATTGAAAAGACCACTGTG 60.181 43.478 7.12 0.00 0.00 3.66
4390 4473 3.799917 GCCAATTGAAAAGACCACTGTGG 60.800 47.826 24.80 24.80 45.02 4.17
4391 4474 3.636300 CCAATTGAAAAGACCACTGTGGA 59.364 43.478 32.30 8.44 40.96 4.02
4392 4475 4.261741 CCAATTGAAAAGACCACTGTGGAG 60.262 45.833 32.30 8.17 40.96 3.86
4393 4476 1.967319 TGAAAAGACCACTGTGGAGC 58.033 50.000 32.30 21.93 40.96 4.70
4394 4477 1.211703 TGAAAAGACCACTGTGGAGCA 59.788 47.619 32.30 16.30 40.96 4.26
4395 4478 2.158623 TGAAAAGACCACTGTGGAGCAT 60.159 45.455 32.30 10.75 40.96 3.79
4396 4479 1.901591 AAAGACCACTGTGGAGCATG 58.098 50.000 32.30 5.89 40.96 4.06
4397 4480 1.059098 AAGACCACTGTGGAGCATGA 58.941 50.000 32.30 0.00 40.96 3.07
4398 4481 1.059098 AGACCACTGTGGAGCATGAA 58.941 50.000 32.30 0.00 40.96 2.57
4399 4482 1.421268 AGACCACTGTGGAGCATGAAA 59.579 47.619 32.30 0.00 40.96 2.69
4400 4483 1.808945 GACCACTGTGGAGCATGAAAG 59.191 52.381 32.30 2.89 40.96 2.62
4401 4484 0.524862 CCACTGTGGAGCATGAAAGC 59.475 55.000 22.33 0.00 40.96 3.51
4521 4622 3.055963 AGAATCCTGACTTCTCAGTGCAG 60.056 47.826 0.00 0.00 42.36 4.41
4554 4655 5.408079 AATCCAATGACATGGTTAGGGAT 57.592 39.130 0.00 1.09 41.46 3.85
4613 4714 1.072806 TGCTCATTCAGTGCCAGAACT 59.927 47.619 0.00 0.00 35.92 3.01
4680 4781 8.759782 AGCATGGTATACAATATAACTACTCCC 58.240 37.037 5.01 0.00 0.00 4.30
4681 4782 8.759782 GCATGGTATACAATATAACTACTCCCT 58.240 37.037 5.01 0.00 0.00 4.20
4683 4784 8.890410 TGGTATACAATATAACTACTCCCTCC 57.110 38.462 5.01 0.00 0.00 4.30
4684 4785 7.613022 TGGTATACAATATAACTACTCCCTCCG 59.387 40.741 5.01 0.00 0.00 4.63
4685 4786 7.613411 GGTATACAATATAACTACTCCCTCCGT 59.387 40.741 5.01 0.00 0.00 4.69
4686 4787 9.018582 GTATACAATATAACTACTCCCTCCGTT 57.981 37.037 0.00 0.00 0.00 4.44
4687 4788 6.402456 ACAATATAACTACTCCCTCCGTTC 57.598 41.667 0.00 0.00 0.00 3.95
4688 4789 5.009410 ACAATATAACTACTCCCTCCGTTCG 59.991 44.000 0.00 0.00 0.00 3.95
4689 4790 1.755179 TAACTACTCCCTCCGTTCGG 58.245 55.000 4.74 4.74 0.00 4.30
4690 4791 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
4691 4792 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
4692 4793 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
4693 4794 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
4694 4795 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4695 4796 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4696 4797 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4697 4798 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4698 4799 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4699 4800 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4700 4801 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4701 4802 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
4702 4803 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
4703 4804 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
4704 4805 3.122948 CCGTTCGGAATTACTTGTCACAG 59.877 47.826 5.19 0.00 0.00 3.66
4705 4806 3.985279 CGTTCGGAATTACTTGTCACAGA 59.015 43.478 0.00 0.00 0.00 3.41
4706 4807 4.446385 CGTTCGGAATTACTTGTCACAGAA 59.554 41.667 0.00 0.00 0.00 3.02
4707 4808 5.050634 CGTTCGGAATTACTTGTCACAGAAA 60.051 40.000 0.00 0.00 0.00 2.52
4708 4809 6.347402 CGTTCGGAATTACTTGTCACAGAAAT 60.347 38.462 0.00 0.00 0.00 2.17
4709 4810 6.480524 TCGGAATTACTTGTCACAGAAATG 57.519 37.500 0.00 0.00 0.00 2.32
4710 4811 5.411361 TCGGAATTACTTGTCACAGAAATGG 59.589 40.000 0.00 0.00 0.00 3.16
4711 4812 5.411361 CGGAATTACTTGTCACAGAAATGGA 59.589 40.000 0.00 0.00 0.00 3.41
4712 4813 6.094048 CGGAATTACTTGTCACAGAAATGGAT 59.906 38.462 0.00 0.00 0.00 3.41
4713 4814 7.253422 GGAATTACTTGTCACAGAAATGGATG 58.747 38.462 0.00 0.00 0.00 3.51
4714 4815 7.094205 GGAATTACTTGTCACAGAAATGGATGT 60.094 37.037 0.00 0.00 0.00 3.06
4715 4816 8.862325 AATTACTTGTCACAGAAATGGATGTA 57.138 30.769 0.00 0.00 0.00 2.29
4716 4817 9.466497 AATTACTTGTCACAGAAATGGATGTAT 57.534 29.630 0.00 0.00 0.00 2.29
4717 4818 6.992063 ACTTGTCACAGAAATGGATGTATC 57.008 37.500 0.00 0.00 0.00 2.24
4718 4819 6.715280 ACTTGTCACAGAAATGGATGTATCT 58.285 36.000 0.00 0.00 0.00 1.98
4719 4820 6.820656 ACTTGTCACAGAAATGGATGTATCTC 59.179 38.462 0.00 0.00 0.00 2.75
4720 4821 5.351458 TGTCACAGAAATGGATGTATCTCG 58.649 41.667 0.00 0.00 0.00 4.04
4721 4822 5.127031 TGTCACAGAAATGGATGTATCTCGA 59.873 40.000 0.00 0.00 0.00 4.04
4722 4823 5.460419 GTCACAGAAATGGATGTATCTCGAC 59.540 44.000 0.00 0.00 0.00 4.20
4723 4824 4.442403 CACAGAAATGGATGTATCTCGACG 59.558 45.833 0.00 0.00 0.00 5.12
4724 4825 4.098044 ACAGAAATGGATGTATCTCGACGT 59.902 41.667 0.00 0.00 0.00 4.34
4725 4826 5.298527 ACAGAAATGGATGTATCTCGACGTA 59.701 40.000 0.00 0.00 0.00 3.57
4726 4827 6.016192 ACAGAAATGGATGTATCTCGACGTAT 60.016 38.462 0.00 0.00 0.00 3.06
4727 4828 6.863645 CAGAAATGGATGTATCTCGACGTATT 59.136 38.462 0.00 0.00 0.00 1.89
4728 4829 7.382488 CAGAAATGGATGTATCTCGACGTATTT 59.618 37.037 0.00 0.00 0.00 1.40
4729 4830 7.926555 AGAAATGGATGTATCTCGACGTATTTT 59.073 33.333 0.00 0.00 0.00 1.82
4730 4831 9.188588 GAAATGGATGTATCTCGACGTATTTTA 57.811 33.333 0.00 0.00 0.00 1.52
4731 4832 8.744008 AATGGATGTATCTCGACGTATTTTAG 57.256 34.615 0.00 0.00 0.00 1.85
4732 4833 7.268199 TGGATGTATCTCGACGTATTTTAGT 57.732 36.000 0.00 0.00 0.00 2.24
4733 4834 7.709947 TGGATGTATCTCGACGTATTTTAGTT 58.290 34.615 0.00 0.00 0.00 2.24
4734 4835 7.859377 TGGATGTATCTCGACGTATTTTAGTTC 59.141 37.037 0.00 0.00 0.00 3.01
4735 4836 8.074972 GGATGTATCTCGACGTATTTTAGTTCT 58.925 37.037 0.00 0.00 0.00 3.01
4738 4839 9.317936 TGTATCTCGACGTATTTTAGTTCTAGA 57.682 33.333 0.00 0.00 0.00 2.43
4742 4843 9.317936 TCTCGACGTATTTTAGTTCTAGATACA 57.682 33.333 0.00 0.00 0.00 2.29
4745 4846 9.327529 CGACGTATTTTAGTTCTAGATACATCC 57.672 37.037 0.00 0.00 0.00 3.51
4754 4855 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
4755 4856 8.239038 AGTTCTAGATACATCCATTTTCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
4756 4857 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
4757 4858 6.669278 TCTAGATACATCCATTTTCGAGACG 58.331 40.000 0.00 0.00 0.00 4.18
4758 4859 5.515797 AGATACATCCATTTTCGAGACGA 57.484 39.130 0.00 0.00 0.00 4.20
4759 4860 5.524284 AGATACATCCATTTTCGAGACGAG 58.476 41.667 0.00 0.00 37.14 4.18
4760 4861 3.594603 ACATCCATTTTCGAGACGAGT 57.405 42.857 0.00 0.00 37.14 4.18
4761 4862 4.713824 ACATCCATTTTCGAGACGAGTA 57.286 40.909 0.00 0.00 37.14 2.59
4762 4863 5.068234 ACATCCATTTTCGAGACGAGTAA 57.932 39.130 0.00 0.00 37.14 2.24
4763 4864 5.661458 ACATCCATTTTCGAGACGAGTAAT 58.339 37.500 0.00 0.00 37.14 1.89
4764 4865 6.106673 ACATCCATTTTCGAGACGAGTAATT 58.893 36.000 0.00 0.00 37.14 1.40
4765 4866 6.255887 ACATCCATTTTCGAGACGAGTAATTC 59.744 38.462 0.00 0.00 37.14 2.17
4766 4867 5.107133 TCCATTTTCGAGACGAGTAATTCC 58.893 41.667 0.00 0.00 37.14 3.01
4767 4868 4.026804 CCATTTTCGAGACGAGTAATTCCG 60.027 45.833 0.00 0.00 37.14 4.30
4768 4869 4.424061 TTTTCGAGACGAGTAATTCCGA 57.576 40.909 0.00 0.00 37.14 4.55
4769 4870 4.424061 TTTCGAGACGAGTAATTCCGAA 57.576 40.909 0.00 0.00 37.14 4.30
4770 4871 3.395858 TCGAGACGAGTAATTCCGAAC 57.604 47.619 0.00 0.00 0.00 3.95
4771 4872 2.099621 CGAGACGAGTAATTCCGAACG 58.900 52.381 0.00 0.00 0.00 3.95
4772 4873 2.222886 CGAGACGAGTAATTCCGAACGA 60.223 50.000 0.00 0.00 0.00 3.85
4773 4874 3.725895 CGAGACGAGTAATTCCGAACGAA 60.726 47.826 0.00 0.00 34.14 3.85
4774 4875 3.756069 AGACGAGTAATTCCGAACGAAG 58.244 45.455 0.00 0.00 32.78 3.79
4775 4876 2.850647 GACGAGTAATTCCGAACGAAGG 59.149 50.000 0.00 0.00 32.78 3.46
4776 4877 2.190981 CGAGTAATTCCGAACGAAGGG 58.809 52.381 0.00 0.00 32.78 3.95
4777 4878 2.159338 CGAGTAATTCCGAACGAAGGGA 60.159 50.000 0.00 0.00 32.78 4.20
4778 4879 3.445857 GAGTAATTCCGAACGAAGGGAG 58.554 50.000 0.00 0.00 32.78 4.30
4779 4880 2.830321 AGTAATTCCGAACGAAGGGAGT 59.170 45.455 0.00 0.00 32.78 3.85
5002 5103 8.580720 ACATCGTTGTTCAGCTAGATTATATCT 58.419 33.333 0.00 0.00 36.67 1.98
5004 5105 9.988815 ATCGTTGTTCAGCTAGATTATATCTTT 57.011 29.630 0.00 0.00 40.76 2.52
5053 5154 5.183522 ACTTTCAACTTGAAACCGGTTGTTA 59.816 36.000 23.08 7.50 41.02 2.41
5132 5233 2.435938 GAGGGCCAACGCGATTCA 60.436 61.111 15.93 0.00 35.02 2.57
5191 5292 3.657634 TGCTAGAAGTTTCAGCTGACAG 58.342 45.455 18.03 6.23 34.58 3.51
5707 5808 4.763073 CAACAGATGATCCAGCAAGACTA 58.237 43.478 0.00 0.00 0.00 2.59
5797 5898 2.746362 CAGGACCTCGACTACGTAGTTT 59.254 50.000 27.96 7.59 37.78 2.66
5925 6026 6.862090 GCTAACTATCCGATATATAAAGGCCG 59.138 42.308 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 2.236893 GGTATCAGGTAACCGGGTTTCA 59.763 50.000 19.02 0.00 37.17 2.69
214 215 3.050564 TCCATCCTTCCCTTACCACCTAT 60.051 47.826 0.00 0.00 0.00 2.57
563 564 7.248437 ACGTTATAGCTAAAAATTGAAGTGGC 58.752 34.615 0.00 0.00 0.00 5.01
595 596 6.161855 TCTGATGCGTCTTCCTATAATTGT 57.838 37.500 7.58 0.00 0.00 2.71
610 611 5.193216 CGTCAAGTTATGAATTCTGATGCG 58.807 41.667 7.05 0.00 40.50 4.73
629 630 1.675714 GGCATCATGGTCAAGACGTCA 60.676 52.381 19.50 0.00 0.00 4.35
661 663 3.064408 GCAAATCTGCTCACGAATGATGA 59.936 43.478 0.00 0.00 45.74 2.92
693 695 1.134521 TCATCATACAGCCCGTGGAAC 60.135 52.381 0.00 0.00 0.00 3.62
783 785 1.889829 CAGACGTCTTTCTCCAGGAGT 59.110 52.381 17.26 0.00 0.00 3.85
852 854 3.820467 CAGTCCAAAGATGCAGGTTTACA 59.180 43.478 0.00 0.00 0.00 2.41
854 856 2.819608 GCAGTCCAAAGATGCAGGTTTA 59.180 45.455 0.00 0.00 39.75 2.01
855 857 1.615392 GCAGTCCAAAGATGCAGGTTT 59.385 47.619 0.00 0.00 39.75 3.27
856 858 1.202976 AGCAGTCCAAAGATGCAGGTT 60.203 47.619 0.00 0.00 42.45 3.50
859 861 1.884579 ACAAGCAGTCCAAAGATGCAG 59.115 47.619 0.00 0.00 42.45 4.41
991 1012 4.173290 TGATGGAATCCATGATGAAGCA 57.827 40.909 21.01 6.49 45.26 3.91
1232 1254 8.499967 GTTCTAATTGGTCTTCTTTCTGTTCTC 58.500 37.037 0.00 0.00 0.00 2.87
1310 1332 6.159988 AGATTACAACTGAGTGAACTAGTGC 58.840 40.000 0.00 0.00 0.00 4.40
1311 1333 8.491152 CAAAGATTACAACTGAGTGAACTAGTG 58.509 37.037 0.00 0.00 0.00 2.74
1352 1374 8.993121 CCAGAATGTTATTCTGATTTACGCTAT 58.007 33.333 25.33 0.00 46.57 2.97
1356 1378 8.331022 CAGTCCAGAATGTTATTCTGATTTACG 58.669 37.037 25.33 12.43 46.57 3.18
1489 1511 1.538047 TTGTTGGCTCCATCAGAAGC 58.462 50.000 0.61 0.00 0.00 3.86
1678 1704 0.753262 AGTTGTCGGTGCTTCAGTCT 59.247 50.000 0.00 0.00 0.00 3.24
1740 1766 5.630121 TCTGGTGAAGCCTTTTCATAAAGA 58.370 37.500 0.00 0.00 42.78 2.52
1748 1774 2.057922 TCTCCTCTGGTGAAGCCTTTT 58.942 47.619 0.00 0.00 38.35 2.27
1832 1858 4.764308 CCACCATGATATCTCTCTCTTCGA 59.236 45.833 3.98 0.00 0.00 3.71
1868 1894 0.401738 TTCCTTGCCCTTCTCAGTGG 59.598 55.000 0.00 0.00 0.00 4.00
2063 2101 6.774163 GAGCATCAGAGCACATCTTGCCTA 62.774 50.000 0.00 0.00 44.35 3.93
2159 2206 2.094494 TGATCAGCCTCGTCTCTGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
2197 2244 1.270147 GGCTTCCGTTACACAGACAGT 60.270 52.381 0.00 0.00 0.00 3.55
2214 2261 0.823460 CACCACCAACAAGTTTGGCT 59.177 50.000 2.85 0.00 43.23 4.75
2220 2267 1.091537 CGTGTTCACCACCAACAAGT 58.908 50.000 0.00 0.00 41.26 3.16
2328 2375 5.338632 TCTGAAAGAAGTATGTCCCCAGTA 58.661 41.667 0.00 0.00 42.31 2.74
2358 2405 4.284178 ACTCGGTAGCTAATTCCCTTGTA 58.716 43.478 0.00 0.00 0.00 2.41
2388 2435 9.208022 GATGTAGCATTACTGACAATAGCATTA 57.792 33.333 0.00 0.00 0.00 1.90
2441 2488 0.190815 AACATTGTTCCCCTTGGCCT 59.809 50.000 3.32 0.00 0.00 5.19
2571 2618 4.030913 TGTTACGGAGGGAATCAGAGAAT 58.969 43.478 0.00 0.00 0.00 2.40
2583 2630 1.094785 CCTTTGCCATGTTACGGAGG 58.905 55.000 0.00 0.00 0.00 4.30
2717 2764 3.439857 TCCTGAAACTTTCCTCCATGG 57.560 47.619 4.97 4.97 37.10 3.66
2727 2774 6.721704 AAAGAAATGCTCTTCCTGAAACTT 57.278 33.333 0.00 0.00 44.00 2.66
2760 2807 3.194116 CCCTTGAACCAACATCATCTTGG 59.806 47.826 0.00 0.00 43.49 3.61
2764 2811 4.678840 GCATTCCCTTGAACCAACATCATC 60.679 45.833 0.00 0.00 32.13 2.92
2765 2812 3.196254 GCATTCCCTTGAACCAACATCAT 59.804 43.478 0.00 0.00 32.13 2.45
2766 2813 2.562298 GCATTCCCTTGAACCAACATCA 59.438 45.455 0.00 0.00 32.13 3.07
2875 2922 2.359214 TCAGGTAGACATCGATGTGCTC 59.641 50.000 34.48 20.17 41.95 4.26
2905 2952 3.194968 TCTTCTTTGGGACTCGGTGATAC 59.805 47.826 0.00 0.00 0.00 2.24
2906 2953 3.437213 TCTTCTTTGGGACTCGGTGATA 58.563 45.455 0.00 0.00 0.00 2.15
2928 2975 3.508012 CGTCTTCTTCTTCCTCTTCTCCA 59.492 47.826 0.00 0.00 0.00 3.86
2929 2976 3.759618 TCGTCTTCTTCTTCCTCTTCTCC 59.240 47.826 0.00 0.00 0.00 3.71
2930 2977 5.124776 TCATCGTCTTCTTCTTCCTCTTCTC 59.875 44.000 0.00 0.00 0.00 2.87
2949 2996 4.727507 TCCTTCCTCTTCTTCTTCATCG 57.272 45.455 0.00 0.00 0.00 3.84
3138 3221 1.871676 CATCCATCAGCATCTTCCACG 59.128 52.381 0.00 0.00 0.00 4.94
3140 3223 1.213430 TGCATCCATCAGCATCTTCCA 59.787 47.619 0.00 0.00 35.51 3.53
3174 3257 1.651987 TTTCGTCCTCCGATGCATTC 58.348 50.000 0.00 0.00 46.75 2.67
3189 3272 5.895928 TCTCCTATGTTCTCTGTGATTTCG 58.104 41.667 0.00 0.00 0.00 3.46
3213 3296 2.806818 CACATCATCTAGAGCCACATGC 59.193 50.000 0.00 0.00 41.71 4.06
3224 3307 2.822561 GGCGAGGAGATCACATCATCTA 59.177 50.000 5.68 0.00 32.94 1.98
3237 3320 0.104855 TGGATGAAATCGGCGAGGAG 59.895 55.000 17.22 0.00 46.86 3.69
3238 3321 0.539518 TTGGATGAAATCGGCGAGGA 59.460 50.000 17.22 0.00 46.86 3.71
3239 3322 0.940126 CTTGGATGAAATCGGCGAGG 59.060 55.000 17.22 0.00 46.86 4.63
3279 3362 6.419484 TCTTTGAGAGTGAATGGAGTTACA 57.581 37.500 0.00 0.00 0.00 2.41
3317 3400 0.324943 GTCTGGGCCTTCACTTGCTA 59.675 55.000 4.53 0.00 0.00 3.49
3324 3407 1.347707 CTGTAGTTGTCTGGGCCTTCA 59.652 52.381 4.53 0.00 0.00 3.02
3332 3415 4.083643 CCATTTCAGTGCTGTAGTTGTCTG 60.084 45.833 0.00 0.00 0.00 3.51
3333 3416 4.067896 CCATTTCAGTGCTGTAGTTGTCT 58.932 43.478 0.00 0.00 0.00 3.41
3344 3427 1.814394 TGACATGCTCCATTTCAGTGC 59.186 47.619 0.00 0.00 28.96 4.40
3346 3429 3.144657 TGTGACATGCTCCATTTCAGT 57.855 42.857 0.00 0.00 32.29 3.41
3366 3449 1.577328 CCGCGACTGTTTCCAGCAAT 61.577 55.000 8.23 0.00 42.81 3.56
3383 3466 2.232208 ACTTTAGGTAGTCCCGTTTCCG 59.768 50.000 0.00 0.00 38.74 4.30
3416 3499 1.638529 AGCCTCACTGCTGACTACTT 58.361 50.000 0.00 0.00 40.90 2.24
3439 3522 1.814394 GCACTGTTCATCATCTGGCAA 59.186 47.619 0.00 0.00 0.00 4.52
3464 3547 5.995282 TGTGGTAAACTAGTTTCTGGATGTG 59.005 40.000 23.76 0.00 34.23 3.21
3495 3578 2.240279 AGTTCACAGCTACCGAGAACT 58.760 47.619 8.81 8.81 42.77 3.01
3501 3584 3.427773 GGTCTAGAAGTTCACAGCTACCG 60.428 52.174 5.50 0.00 0.00 4.02
3555 3638 2.750814 TCTGGAGTGGCAGACATCATA 58.249 47.619 0.00 0.00 0.00 2.15
3588 3671 4.160065 TGCAATTCATGTATTTCCCCTGTG 59.840 41.667 0.00 0.00 0.00 3.66
3675 3758 1.648467 GCGGCAAATCAGTGGAGTCC 61.648 60.000 0.73 0.73 0.00 3.85
3684 3767 3.063704 CTGGGCAGCGGCAAATCA 61.064 61.111 11.88 2.42 43.71 2.57
3820 3903 0.694444 AGAGGTGGAAGTGGTGGTGT 60.694 55.000 0.00 0.00 0.00 4.16
3966 4049 4.761739 TCAGATTCTTGATTTGTTTCGCCT 59.238 37.500 0.00 0.00 0.00 5.52
4006 4089 4.679654 CGAACTAAAACAATTGTTCCAGCC 59.320 41.667 23.47 15.70 37.25 4.85
4018 4101 5.278266 CCATTTCCTTCTGCGAACTAAAACA 60.278 40.000 0.00 0.00 0.00 2.83
4390 4473 7.558034 CCTTTTGGTCAGAGCTTTCATGCTC 62.558 48.000 8.28 8.28 45.71 4.26
4391 4474 5.823885 CCTTTTGGTCAGAGCTTTCATGCT 61.824 45.833 0.38 0.00 39.47 3.79
4392 4475 3.572584 CTTTTGGTCAGAGCTTTCATGC 58.427 45.455 0.38 0.00 0.00 4.06
4393 4476 3.822735 TCCTTTTGGTCAGAGCTTTCATG 59.177 43.478 0.38 0.00 41.38 3.07
4394 4477 4.077822 CTCCTTTTGGTCAGAGCTTTCAT 58.922 43.478 0.38 0.00 41.38 2.57
4395 4478 3.480470 CTCCTTTTGGTCAGAGCTTTCA 58.520 45.455 0.38 0.00 41.38 2.69
4396 4479 2.816672 CCTCCTTTTGGTCAGAGCTTTC 59.183 50.000 0.38 0.00 41.38 2.62
4397 4480 2.443255 TCCTCCTTTTGGTCAGAGCTTT 59.557 45.455 0.38 0.00 41.38 3.51
4398 4481 2.057922 TCCTCCTTTTGGTCAGAGCTT 58.942 47.619 0.38 0.00 41.38 3.74
4399 4482 1.734655 TCCTCCTTTTGGTCAGAGCT 58.265 50.000 0.38 0.00 41.38 4.09
4400 4483 2.568623 TTCCTCCTTTTGGTCAGAGC 57.431 50.000 0.00 0.00 41.38 4.09
4401 4484 4.401925 ACAATTCCTCCTTTTGGTCAGAG 58.598 43.478 0.00 0.00 41.38 3.35
4402 4485 4.141274 TGACAATTCCTCCTTTTGGTCAGA 60.141 41.667 0.00 0.00 41.38 3.27
4521 4622 6.444633 CATGTCATTGGATTTATCTTCCTGC 58.555 40.000 0.00 0.00 34.17 4.85
4613 4714 6.615617 ACTTGAAGCAGAGGATATCTAGGTA 58.384 40.000 2.05 0.00 36.10 3.08
4675 4776 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4676 4777 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4677 4778 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4678 4779 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
4679 4780 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4680 4781 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
4681 4782 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
4682 4783 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
4683 4784 3.985279 TCTGTGACAAGTAATTCCGAACG 59.015 43.478 0.00 0.00 0.00 3.95
4684 4785 5.917541 TTCTGTGACAAGTAATTCCGAAC 57.082 39.130 0.00 0.00 0.00 3.95
4685 4786 6.072728 CCATTTCTGTGACAAGTAATTCCGAA 60.073 38.462 0.00 0.00 0.00 4.30
4686 4787 5.411361 CCATTTCTGTGACAAGTAATTCCGA 59.589 40.000 0.00 0.00 0.00 4.55
4687 4788 5.411361 TCCATTTCTGTGACAAGTAATTCCG 59.589 40.000 0.00 0.00 0.00 4.30
4688 4789 6.817765 TCCATTTCTGTGACAAGTAATTCC 57.182 37.500 0.00 0.00 0.00 3.01
4689 4790 7.820648 ACATCCATTTCTGTGACAAGTAATTC 58.179 34.615 0.00 0.00 0.00 2.17
4690 4791 7.765695 ACATCCATTTCTGTGACAAGTAATT 57.234 32.000 0.00 0.00 0.00 1.40
4691 4792 9.113838 GATACATCCATTTCTGTGACAAGTAAT 57.886 33.333 0.00 0.00 0.00 1.89
4692 4793 8.321353 AGATACATCCATTTCTGTGACAAGTAA 58.679 33.333 0.00 0.00 0.00 2.24
4693 4794 7.851228 AGATACATCCATTTCTGTGACAAGTA 58.149 34.615 0.00 0.00 0.00 2.24
4694 4795 6.715280 AGATACATCCATTTCTGTGACAAGT 58.285 36.000 0.00 0.00 0.00 3.16
4695 4796 6.019237 CGAGATACATCCATTTCTGTGACAAG 60.019 42.308 0.00 0.00 0.00 3.16
4696 4797 5.812127 CGAGATACATCCATTTCTGTGACAA 59.188 40.000 0.00 0.00 0.00 3.18
4697 4798 5.127031 TCGAGATACATCCATTTCTGTGACA 59.873 40.000 0.00 0.00 0.00 3.58
4698 4799 5.460419 GTCGAGATACATCCATTTCTGTGAC 59.540 44.000 0.00 0.00 0.00 3.67
4699 4800 5.592054 GTCGAGATACATCCATTTCTGTGA 58.408 41.667 0.00 0.00 0.00 3.58
4700 4801 4.442403 CGTCGAGATACATCCATTTCTGTG 59.558 45.833 0.00 0.00 0.00 3.66
4701 4802 4.098044 ACGTCGAGATACATCCATTTCTGT 59.902 41.667 0.00 0.00 0.00 3.41
4702 4803 4.611943 ACGTCGAGATACATCCATTTCTG 58.388 43.478 0.00 0.00 0.00 3.02
4703 4804 4.920640 ACGTCGAGATACATCCATTTCT 57.079 40.909 0.00 0.00 0.00 2.52
4704 4805 7.639162 AAATACGTCGAGATACATCCATTTC 57.361 36.000 0.00 0.00 0.00 2.17
4705 4806 9.193133 CTAAAATACGTCGAGATACATCCATTT 57.807 33.333 0.00 0.00 0.00 2.32
4706 4807 8.358148 ACTAAAATACGTCGAGATACATCCATT 58.642 33.333 0.00 0.00 0.00 3.16
4707 4808 7.883217 ACTAAAATACGTCGAGATACATCCAT 58.117 34.615 0.00 0.00 0.00 3.41
4708 4809 7.268199 ACTAAAATACGTCGAGATACATCCA 57.732 36.000 0.00 0.00 0.00 3.41
4709 4810 8.074972 AGAACTAAAATACGTCGAGATACATCC 58.925 37.037 0.00 0.00 0.00 3.51
4712 4813 9.317936 TCTAGAACTAAAATACGTCGAGATACA 57.682 33.333 0.00 0.00 0.00 2.29
4716 4817 9.317936 TGTATCTAGAACTAAAATACGTCGAGA 57.682 33.333 0.00 0.00 0.00 4.04
4719 4820 9.327529 GGATGTATCTAGAACTAAAATACGTCG 57.672 37.037 17.86 0.00 38.69 5.12
4728 4829 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
4729 4830 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
4730 4831 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
4731 4832 7.113684 CGTCTCGAAAATGGATGTATCTAGAAC 59.886 40.741 0.00 0.00 0.00 3.01
4732 4833 7.012989 TCGTCTCGAAAATGGATGTATCTAGAA 59.987 37.037 0.00 0.00 31.06 2.10
4733 4834 6.485648 TCGTCTCGAAAATGGATGTATCTAGA 59.514 38.462 0.00 0.00 31.06 2.43
4734 4835 6.669278 TCGTCTCGAAAATGGATGTATCTAG 58.331 40.000 0.00 0.00 31.06 2.43
4735 4836 6.262496 ACTCGTCTCGAAAATGGATGTATCTA 59.738 38.462 0.00 0.00 34.74 1.98
4736 4837 5.067936 ACTCGTCTCGAAAATGGATGTATCT 59.932 40.000 0.00 0.00 34.74 1.98
4737 4838 5.282510 ACTCGTCTCGAAAATGGATGTATC 58.717 41.667 0.00 0.00 34.74 2.24
4738 4839 5.263968 ACTCGTCTCGAAAATGGATGTAT 57.736 39.130 0.00 0.00 34.74 2.29
4739 4840 4.713824 ACTCGTCTCGAAAATGGATGTA 57.286 40.909 0.00 0.00 34.74 2.29
4740 4841 3.594603 ACTCGTCTCGAAAATGGATGT 57.405 42.857 0.00 0.00 34.74 3.06
4741 4842 6.292381 GGAATTACTCGTCTCGAAAATGGATG 60.292 42.308 0.00 0.00 34.74 3.51
4742 4843 5.753921 GGAATTACTCGTCTCGAAAATGGAT 59.246 40.000 0.00 0.00 34.74 3.41
4743 4844 5.107133 GGAATTACTCGTCTCGAAAATGGA 58.893 41.667 0.00 0.00 34.74 3.41
4744 4845 4.026804 CGGAATTACTCGTCTCGAAAATGG 60.027 45.833 0.00 0.00 34.74 3.16
4745 4846 4.796830 TCGGAATTACTCGTCTCGAAAATG 59.203 41.667 0.00 0.00 34.74 2.32
4746 4847 4.990257 TCGGAATTACTCGTCTCGAAAAT 58.010 39.130 0.00 0.00 34.74 1.82
4747 4848 4.424061 TCGGAATTACTCGTCTCGAAAA 57.576 40.909 0.00 0.00 34.74 2.29
4748 4849 4.161333 GTTCGGAATTACTCGTCTCGAAA 58.839 43.478 0.00 0.00 37.00 3.46
4749 4850 3.725895 CGTTCGGAATTACTCGTCTCGAA 60.726 47.826 0.00 0.00 34.74 3.71
4750 4851 2.222886 CGTTCGGAATTACTCGTCTCGA 60.223 50.000 0.00 0.00 0.00 4.04
4751 4852 2.099621 CGTTCGGAATTACTCGTCTCG 58.900 52.381 0.00 0.00 0.00 4.04
4752 4853 3.395858 TCGTTCGGAATTACTCGTCTC 57.604 47.619 0.00 0.00 0.00 3.36
4753 4854 3.427233 CCTTCGTTCGGAATTACTCGTCT 60.427 47.826 0.00 0.00 33.26 4.18
4754 4855 2.850647 CCTTCGTTCGGAATTACTCGTC 59.149 50.000 0.00 0.00 33.26 4.20
4755 4856 2.416431 CCCTTCGTTCGGAATTACTCGT 60.416 50.000 0.00 0.00 33.26 4.18
4756 4857 2.159338 TCCCTTCGTTCGGAATTACTCG 60.159 50.000 0.00 0.00 33.26 4.18
4757 4858 3.119209 ACTCCCTTCGTTCGGAATTACTC 60.119 47.826 0.00 0.00 33.26 2.59
4758 4859 2.830321 ACTCCCTTCGTTCGGAATTACT 59.170 45.455 0.00 0.00 33.26 2.24
4759 4860 3.242549 ACTCCCTTCGTTCGGAATTAC 57.757 47.619 0.00 0.00 33.26 1.89
4760 4861 4.019174 AGTACTCCCTTCGTTCGGAATTA 58.981 43.478 0.00 0.00 33.26 1.40
4761 4862 2.830321 AGTACTCCCTTCGTTCGGAATT 59.170 45.455 0.00 0.00 33.26 2.17
4762 4863 2.454538 AGTACTCCCTTCGTTCGGAAT 58.545 47.619 0.00 0.00 33.26 3.01
4763 4864 1.915141 AGTACTCCCTTCGTTCGGAA 58.085 50.000 0.00 0.00 0.00 4.30
4764 4865 1.815003 GAAGTACTCCCTTCGTTCGGA 59.185 52.381 0.00 0.00 32.23 4.55
4765 4866 1.135170 GGAAGTACTCCCTTCGTTCGG 60.135 57.143 0.00 0.00 41.44 4.30
4766 4867 1.542915 TGGAAGTACTCCCTTCGTTCG 59.457 52.381 0.00 0.00 44.69 3.95
4767 4868 3.056035 ACATGGAAGTACTCCCTTCGTTC 60.056 47.826 0.00 0.00 44.69 3.95
4768 4869 2.904434 ACATGGAAGTACTCCCTTCGTT 59.096 45.455 0.00 0.00 44.69 3.85
4769 4870 2.537143 ACATGGAAGTACTCCCTTCGT 58.463 47.619 0.00 0.00 44.69 3.85
4770 4871 3.195825 AGAACATGGAAGTACTCCCTTCG 59.804 47.826 0.00 0.00 44.69 3.79
4771 4872 4.508662 CAGAACATGGAAGTACTCCCTTC 58.491 47.826 0.00 0.00 44.69 3.46
4772 4873 3.307762 GCAGAACATGGAAGTACTCCCTT 60.308 47.826 0.00 0.00 44.69 3.95
4773 4874 2.237392 GCAGAACATGGAAGTACTCCCT 59.763 50.000 0.00 0.00 44.69 4.20
4774 4875 2.633488 GCAGAACATGGAAGTACTCCC 58.367 52.381 0.00 0.00 44.69 4.30
4775 4876 2.271800 CGCAGAACATGGAAGTACTCC 58.728 52.381 0.00 0.00 45.64 3.85
4776 4877 2.960819 ACGCAGAACATGGAAGTACTC 58.039 47.619 0.00 0.00 0.00 2.59
4777 4878 3.402628 AACGCAGAACATGGAAGTACT 57.597 42.857 0.00 0.00 0.00 2.73
4778 4879 4.483476 AAAACGCAGAACATGGAAGTAC 57.517 40.909 0.00 0.00 0.00 2.73
5004 5105 9.352784 GTCTGCAAACAAAGCATGTTAATATTA 57.647 29.630 8.14 0.00 45.86 0.98
5010 5111 4.916983 AGTCTGCAAACAAAGCATGTTA 57.083 36.364 8.14 0.00 45.86 2.41
5053 5154 3.828451 CCCATCACATTTGGTCTCTTTGT 59.172 43.478 0.00 0.00 31.99 2.83
5132 5233 0.323957 GCGAGAGGGTTTAACCTGGT 59.676 55.000 14.27 0.00 42.10 4.00
5191 5292 4.315803 ACCGTGCCATATGATAAAGCTAC 58.684 43.478 3.65 0.00 0.00 3.58
5200 5301 0.671796 CTCGGTACCGTGCCATATGA 59.328 55.000 32.16 10.17 40.74 2.15
5390 5491 5.922544 CGAGATGAAGAAAAAGGTGCATTTT 59.077 36.000 0.00 0.00 33.86 1.82
5619 5720 3.392616 TCTCCTTGGCTTCAGAAGACTTT 59.607 43.478 17.38 0.00 37.45 2.66
5707 5808 4.323562 GGTGGCTAAGATGTAGAAGGTTGT 60.324 45.833 0.00 0.00 0.00 3.32
5797 5898 0.107066 TCCTATCCACCGCGACTACA 60.107 55.000 8.23 0.00 0.00 2.74
5910 6011 2.872245 CCCATGCGGCCTTTATATATCG 59.128 50.000 0.00 0.00 0.00 2.92
5925 6026 6.693315 TTCTAGTTTGTTATTAGCCCATGC 57.307 37.500 0.00 0.00 37.95 4.06


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

AutoCloner maintained by Alex Coulton.