Multiple sequence alignment - TraesCS4A01G406400

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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 TraesCS4A01G406400 chr4A 100.000 5015 0 0 1 5015 679260902 679255888 0.000000e+00 9262.0
1 TraesCS4A01G406400 chr4A 94.690 113 2 3 4276 4388 17385845 17385953 6.670000e-39 172.0
2 TraesCS4A01G406400 chr4B 87.545 2770 151 79 599 3281 594848861 594846199 0.000000e+00 3025.0
3 TraesCS4A01G406400 chr4B 90.240 707 53 10 3356 4058 594846020 594845326 0.000000e+00 909.0
4 TraesCS4A01G406400 chr4B 85.650 446 32 15 163 599 594849378 594848956 1.660000e-119 440.0
5 TraesCS4A01G406400 chr4B 90.448 335 25 2 4687 5015 594844216 594843883 7.710000e-118 435.0
6 TraesCS4A01G406400 chr4B 88.991 218 19 4 4260 4473 594844793 594844577 1.070000e-66 265.0
7 TraesCS4A01G406400 chr4B 85.246 183 23 3 4069 4250 594845040 594844861 8.570000e-43 185.0
8 TraesCS4A01G406400 chr4B 98.077 104 1 1 4294 4396 562057983 562057880 3.990000e-41 180.0
9 TraesCS4A01G406400 chr7D 90.817 1873 94 40 1036 2861 78420240 78418399 0.000000e+00 2435.0
10 TraesCS4A01G406400 chr7D 88.798 732 48 17 3356 4067 78417911 78417194 0.000000e+00 867.0
11 TraesCS4A01G406400 chr7D 82.445 638 43 35 1 603 78421347 78420744 1.250000e-135 494.0
12 TraesCS4A01G406400 chr7D 87.097 434 19 17 599 1024 78420708 78420304 1.650000e-124 457.0
13 TraesCS4A01G406400 chr7D 84.938 405 44 11 4258 4661 78416599 78416211 1.310000e-105 394.0
14 TraesCS4A01G406400 chr7D 84.173 417 19 18 2885 3287 78418402 78418019 1.330000e-95 361.0
15 TraesCS4A01G406400 chr7D 86.257 342 27 4 4675 5015 78416224 78415902 2.220000e-93 353.0
16 TraesCS4A01G406400 chr7D 78.182 220 33 12 4061 4279 78416936 78416731 5.270000e-25 126.0
17 TraesCS4A01G406400 chr4D 90.550 1873 99 40 1036 2861 472491214 472489373 0.000000e+00 2407.0
18 TraesCS4A01G406400 chr4D 89.208 732 45 17 3356 4067 472488885 472488168 0.000000e+00 883.0
19 TraesCS4A01G406400 chr4D 82.677 635 46 32 1 603 472492316 472491714 5.790000e-139 505.0
20 TraesCS4A01G406400 chr4D 92.507 347 20 1 4675 5015 30895457 30895111 4.510000e-135 492.0
21 TraesCS4A01G406400 chr4D 87.531 409 34 10 4258 4661 472487571 472487175 1.650000e-124 457.0
22 TraesCS4A01G406400 chr4D 86.636 434 17 17 599 1024 472491678 472491278 4.610000e-120 442.0
23 TraesCS4A01G406400 chr4D 84.804 408 20 16 3356 3740 30898642 30898254 6.130000e-99 372.0
24 TraesCS4A01G406400 chr4D 84.173 417 19 21 2885 3287 472489376 472488993 1.330000e-95 361.0
25 TraesCS4A01G406400 chr4D 85.965 342 28 4 4675 5015 472487188 472486866 1.030000e-91 348.0
26 TraesCS4A01G406400 chr4D 90.514 253 24 0 4274 4526 30897396 30897144 8.040000e-88 335.0
27 TraesCS4A01G406400 chr4D 86.585 246 21 10 1525 1763 30903214 30902974 1.380000e-65 261.0
28 TraesCS4A01G406400 chr4D 78.733 221 32 11 4061 4279 472487910 472487703 3.150000e-27 134.0
29 TraesCS4A01G406400 chr4D 81.000 100 19 0 2471 2570 327048039 327048138 4.160000e-11 80.5
30 TraesCS4A01G406400 chr5A 90.722 291 27 0 3443 3733 650649432 650649142 6.090000e-104 388.0
31 TraesCS4A01G406400 chr5A 88.966 145 16 0 2427 2571 650649944 650649800 3.990000e-41 180.0
32 TraesCS4A01G406400 chr5D 90.378 291 28 0 3443 3733 524449934 524449644 2.830000e-102 383.0
33 TraesCS4A01G406400 chr5B 90.034 291 29 0 3443 3733 658925668 658925378 1.320000e-100 377.0
34 TraesCS4A01G406400 chr1A 98.058 103 2 0 4288 4390 480566428 480566326 3.990000e-41 180.0
35 TraesCS4A01G406400 chr1D 98.039 102 2 0 4288 4389 379472688 379472587 1.430000e-40 178.0
36 TraesCS4A01G406400 chr6B 93.860 114 5 2 4280 4393 611459686 611459797 2.400000e-38 171.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G406400 chr4A 679255888 679260902 5014 True 9262.000000 9262 100.000000 1 5015 1 chr4A.!!$R1 5014
1 TraesCS4A01G406400 chr4B 594843883 594849378 5495 True 876.500000 3025 88.020000 163 5015 6 chr4B.!!$R2 4852
2 TraesCS4A01G406400 chr7D 78415902 78421347 5445 True 685.875000 2435 85.338375 1 5015 8 chr7D.!!$R1 5014
3 TraesCS4A01G406400 chr4D 472486866 472492316 5450 True 692.125000 2407 85.684125 1 5015 8 chr4D.!!$R3 5014
4 TraesCS4A01G406400 chr4D 30895111 30898642 3531 True 399.666667 492 89.275000 3356 5015 3 chr4D.!!$R2 1659
5 TraesCS4A01G406400 chr5A 650649142 650649944 802 True 284.000000 388 89.844000 2427 3733 2 chr5A.!!$R1 1306

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
517 559 0.105039 CCAGGTAATGGCCTCGTCTC 59.895 60.0 3.32 0.0 43.83 3.36 F
1033 1192 0.111061 TGATTGAGCACCTGCACCTT 59.889 50.0 0.00 0.0 45.16 3.50 F
2579 2823 0.179084 CGGTAAGCACACCCGATGAT 60.179 55.0 1.48 0.0 44.41 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2531 0.677098 TCCACTCCTCTTCCTCGTCG 60.677 60.0 0.00 0.0 0.00 5.12 R
2864 3148 0.114954 AAGGAAGGAAGGGCATGCAA 59.885 50.0 21.36 0.0 0.00 4.08 R
4180 4964 0.042131 AGGATTACCCACGGTCTCCA 59.958 55.0 12.47 0.0 39.01 3.86 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
19 21 1.586154 CCTCTCGTGCCGCCAAAAAT 61.586 55.000 0.00 0.00 0.00 1.82
20 22 1.083489 CTCTCGTGCCGCCAAAAATA 58.917 50.000 0.00 0.00 0.00 1.40
23 25 2.490115 TCTCGTGCCGCCAAAAATAAAT 59.510 40.909 0.00 0.00 0.00 1.40
25 27 4.156190 TCTCGTGCCGCCAAAAATAAATTA 59.844 37.500 0.00 0.00 0.00 1.40
27 29 5.411781 TCGTGCCGCCAAAAATAAATTAAT 58.588 33.333 0.00 0.00 0.00 1.40
31 40 5.460419 TGCCGCCAAAAATAAATTAATAGCG 59.540 36.000 0.00 0.00 39.54 4.26
35 44 7.307101 CCGCCAAAAATAAATTAATAGCGCAAT 60.307 33.333 11.47 0.00 38.59 3.56
53 62 1.928868 ATGTCCCAAAGCCAGAAAGG 58.071 50.000 0.00 0.00 41.84 3.11
54 63 0.850100 TGTCCCAAAGCCAGAAAGGA 59.150 50.000 0.00 0.00 41.22 3.36
59 68 1.331214 CAAAGCCAGAAAGGAGCCAA 58.669 50.000 0.00 0.00 41.22 4.52
73 82 0.463295 AGCCAATGTCTCCATGCGAG 60.463 55.000 5.18 5.18 40.30 5.03
100 113 4.679372 CGAAGTCAAACCCCAAACAAACAT 60.679 41.667 0.00 0.00 0.00 2.71
102 115 3.133901 AGTCAAACCCCAAACAAACATCC 59.866 43.478 0.00 0.00 0.00 3.51
111 124 2.098298 CAAACATCCGCGCTTCCG 59.902 61.111 5.56 0.00 37.57 4.30
196 222 2.856988 GGTTGGGTCCTGGGTGGA 60.857 66.667 0.00 0.00 43.86 4.02
277 308 2.983930 CTCCTCCGATCGATCCCGC 61.984 68.421 18.66 0.00 35.37 6.13
282 313 4.702081 CGATCGATCCCGCCCGAC 62.702 72.222 19.51 0.00 37.64 4.79
283 314 4.359455 GATCGATCCCGCCCGACC 62.359 72.222 14.76 0.00 37.64 4.79
294 325 4.862823 CCCGACCCCTCTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
304 340 4.179599 CTCCCTCCCTCCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
357 393 3.374402 CCGCTCCCACTCACTCGT 61.374 66.667 0.00 0.00 0.00 4.18
358 394 2.179517 CGCTCCCACTCACTCGTC 59.820 66.667 0.00 0.00 0.00 4.20
365 405 3.063084 ACTCACTCGTCCTCCCGC 61.063 66.667 0.00 0.00 0.00 6.13
474 516 1.680249 GGTTCCCTGACTGATCCTTGC 60.680 57.143 0.00 0.00 0.00 4.01
475 517 1.280421 GTTCCCTGACTGATCCTTGCT 59.720 52.381 0.00 0.00 0.00 3.91
517 559 0.105039 CCAGGTAATGGCCTCGTCTC 59.895 60.000 3.32 0.00 43.83 3.36
540 582 5.299279 TCCCTGATATTTTTCTCGCCATTTC 59.701 40.000 0.00 0.00 0.00 2.17
551 596 2.110296 GCCATTTCTAGGCCACAGC 58.890 57.895 5.01 0.00 46.50 4.40
593 638 5.046529 ACATCACAGAAAGACGATGATAGC 58.953 41.667 5.31 0.00 38.85 2.97
661 801 3.635510 GGCCGGAATGGACTCTCT 58.364 61.111 5.05 0.00 45.46 3.10
667 807 2.366916 CCGGAATGGACTCTCTGCTATT 59.633 50.000 0.00 0.00 42.00 1.73
762 902 2.034305 AGCGGTATAGAACATGACGGAC 59.966 50.000 0.00 0.00 0.00 4.79
763 903 2.223641 GCGGTATAGAACATGACGGACA 60.224 50.000 0.00 0.00 0.00 4.02
764 904 3.369385 CGGTATAGAACATGACGGACAC 58.631 50.000 0.00 0.00 0.00 3.67
765 905 3.181494 CGGTATAGAACATGACGGACACA 60.181 47.826 0.00 0.00 0.00 3.72
788 930 1.471287 GTTTTCCTGCCATTACCCGAC 59.529 52.381 0.00 0.00 0.00 4.79
789 931 0.391927 TTTCCTGCCATTACCCGACG 60.392 55.000 0.00 0.00 0.00 5.12
790 932 1.259142 TTCCTGCCATTACCCGACGA 61.259 55.000 0.00 0.00 0.00 4.20
817 959 4.998033 CGAGATGCTGATAGGACACTACTA 59.002 45.833 0.00 0.00 30.59 1.82
818 960 5.121611 CGAGATGCTGATAGGACACTACTAG 59.878 48.000 0.00 0.00 30.59 2.57
819 961 4.764823 AGATGCTGATAGGACACTACTAGC 59.235 45.833 0.00 0.00 39.79 3.42
821 963 3.117474 TGCTGATAGGACACTACTAGCCT 60.117 47.826 0.00 0.00 39.16 4.58
822 964 4.104261 TGCTGATAGGACACTACTAGCCTA 59.896 45.833 0.00 0.00 39.16 3.93
824 966 5.746656 GCTGATAGGACACTACTAGCCTACT 60.747 48.000 0.00 0.00 36.36 2.57
839 981 1.005512 TACTCTGCGCTGCGGAAAA 60.006 52.632 24.61 10.95 43.76 2.29
841 983 3.031964 CTCTGCGCTGCGGAAAAGG 62.032 63.158 24.61 9.21 43.76 3.11
842 984 4.766088 CTGCGCTGCGGAAAAGGC 62.766 66.667 24.61 5.29 37.02 4.35
845 987 4.107051 CGCTGCGGAAAAGGCCTG 62.107 66.667 15.40 0.00 0.00 4.85
846 988 2.672996 GCTGCGGAAAAGGCCTGA 60.673 61.111 5.69 0.00 0.00 3.86
847 989 2.268076 GCTGCGGAAAAGGCCTGAA 61.268 57.895 5.69 0.00 0.00 3.02
855 997 2.615912 GGAAAAGGCCTGAATCTGATCG 59.384 50.000 5.69 0.00 0.00 3.69
1018 1177 2.225068 CCGATAGACAACGGCTGATT 57.775 50.000 0.00 0.00 42.55 2.57
1020 1179 2.481276 CCGATAGACAACGGCTGATTGA 60.481 50.000 0.00 0.00 42.55 2.57
1032 1191 0.322277 CTGATTGAGCACCTGCACCT 60.322 55.000 0.00 0.00 45.16 4.00
1033 1192 0.111061 TGATTGAGCACCTGCACCTT 59.889 50.000 0.00 0.00 45.16 3.50
1072 1283 1.885887 CAAGAAGAATTGGGGCGTGAA 59.114 47.619 0.00 0.00 0.00 3.18
1073 1284 1.826385 AGAAGAATTGGGGCGTGAAG 58.174 50.000 0.00 0.00 0.00 3.02
1100 1312 0.319728 ATCCGAGATGGCCAAGATCG 59.680 55.000 23.39 23.39 37.80 3.69
1140 1352 0.686789 GGTGGCAAGGGCAAGAAATT 59.313 50.000 0.00 0.00 43.71 1.82
1154 1366 4.500375 GCAAGAAATTCAAGGTCAGTGCTT 60.500 41.667 0.00 0.00 0.00 3.91
1155 1367 4.843220 AGAAATTCAAGGTCAGTGCTTG 57.157 40.909 4.58 4.58 0.00 4.01
1156 1368 4.464008 AGAAATTCAAGGTCAGTGCTTGA 58.536 39.130 8.59 8.59 35.60 3.02
1157 1369 5.075493 AGAAATTCAAGGTCAGTGCTTGAT 58.925 37.500 12.27 0.96 38.29 2.57
1158 1370 5.182760 AGAAATTCAAGGTCAGTGCTTGATC 59.817 40.000 12.27 8.45 38.29 2.92
1160 1372 3.325293 TCAAGGTCAGTGCTTGATCTC 57.675 47.619 8.59 0.00 46.68 2.75
1166 1378 1.206610 TCAGTGCTTGATCTCCTCTGC 59.793 52.381 0.00 0.00 0.00 4.26
1179 1391 9.685276 TTGATCTCCTCTGCTTTTCATTAATTA 57.315 29.630 0.00 0.00 0.00 1.40
1180 1392 9.857656 TGATCTCCTCTGCTTTTCATTAATTAT 57.142 29.630 0.00 0.00 0.00 1.28
1206 1418 9.689976 TCAATGATTAATTAACCAGTTTGTGTG 57.310 29.630 0.00 0.00 0.00 3.82
1207 1419 9.474920 CAATGATTAATTAACCAGTTTGTGTGT 57.525 29.630 0.00 0.00 0.00 3.72
1210 1422 2.834574 TTAACCAGTTTGTGTGTGCG 57.165 45.000 0.00 0.00 0.00 5.34
1211 1423 1.740297 TAACCAGTTTGTGTGTGCGT 58.260 45.000 0.00 0.00 0.00 5.24
1247 1459 4.792521 CTGTACACAGGCTCTTTAGTCT 57.207 45.455 1.21 0.00 38.57 3.24
1248 1460 5.140747 CTGTACACAGGCTCTTTAGTCTT 57.859 43.478 1.21 0.00 34.68 3.01
1249 1461 5.542779 CTGTACACAGGCTCTTTAGTCTTT 58.457 41.667 1.21 0.00 34.68 2.52
1250 1462 6.659745 TGTACACAGGCTCTTTAGTCTTTA 57.340 37.500 0.00 0.00 34.68 1.85
1256 1468 5.071923 ACAGGCTCTTTAGTCTTTACCAAGT 59.928 40.000 0.00 0.00 34.68 3.16
1323 1548 7.329717 GTGTTGACCTCTGTAGATTTCAACTAG 59.670 40.741 22.83 0.00 41.48 2.57
1324 1549 7.015292 TGTTGACCTCTGTAGATTTCAACTAGT 59.985 37.037 22.83 0.00 41.48 2.57
1325 1550 8.521176 GTTGACCTCTGTAGATTTCAACTAGTA 58.479 37.037 18.94 0.00 39.78 1.82
1388 1614 1.289800 GGACGTGAAGAAGGTTCCGC 61.290 60.000 0.00 0.00 0.00 5.54
1507 1745 2.050533 GCATGCCGCGACACAAAA 60.051 55.556 8.23 0.00 0.00 2.44
1518 1756 2.825086 GACACAAAAGTTGTCGCAGT 57.175 45.000 0.00 0.00 43.23 4.40
1567 1805 2.126031 GACGACGACAAGGCCTCC 60.126 66.667 5.23 0.00 0.00 4.30
2057 2295 1.398692 GGACACACACCACCAAATGT 58.601 50.000 0.00 0.00 0.00 2.71
2068 2306 2.528564 CACCAAATGTTCCACTCCCAT 58.471 47.619 0.00 0.00 0.00 4.00
2070 2308 1.745087 CCAAATGTTCCACTCCCATCG 59.255 52.381 0.00 0.00 0.00 3.84
2101 2339 2.259511 GGGTACACGTCCGACACC 59.740 66.667 0.00 0.00 0.00 4.16
2148 2386 0.741221 AAGAACAAGGAGATCGCCGC 60.741 55.000 10.07 0.00 0.00 6.53
2271 2509 3.260483 CTCGCTGCTGATCCACGC 61.260 66.667 0.00 0.00 0.00 5.34
2293 2531 1.760480 GGAGCAGGAGGAGGAGGAC 60.760 68.421 0.00 0.00 0.00 3.85
2302 2540 1.378250 GGAGGAGGACGACGAGGAA 60.378 63.158 0.00 0.00 0.00 3.36
2309 2547 0.677414 GGACGACGAGGAAGAGGAGT 60.677 60.000 0.00 0.00 0.00 3.85
2571 2815 2.412847 GCAACTTCATCGGTAAGCACAC 60.413 50.000 0.00 0.00 0.00 3.82
2573 2817 1.338769 ACTTCATCGGTAAGCACACCC 60.339 52.381 1.48 0.00 34.90 4.61
2574 2818 0.390603 TTCATCGGTAAGCACACCCG 60.391 55.000 1.48 0.00 43.03 5.28
2576 2820 3.702802 TCGGTAAGCACACCCGAT 58.297 55.556 0.00 0.00 45.20 4.18
2577 2821 1.216977 TCGGTAAGCACACCCGATG 59.783 57.895 0.00 0.00 45.20 3.84
2578 2822 1.216977 CGGTAAGCACACCCGATGA 59.783 57.895 1.48 0.00 44.41 2.92
2579 2823 0.179084 CGGTAAGCACACCCGATGAT 60.179 55.000 1.48 0.00 44.41 2.45
2582 2826 1.134521 GTAAGCACACCCGATGATCCA 60.135 52.381 0.00 0.00 0.00 3.41
2583 2827 0.392998 AAGCACACCCGATGATCCAC 60.393 55.000 0.00 0.00 0.00 4.02
2584 2828 1.819632 GCACACCCGATGATCCACC 60.820 63.158 0.00 0.00 0.00 4.61
2585 2829 1.521457 CACACCCGATGATCCACCG 60.521 63.158 0.00 0.00 0.00 4.94
2586 2830 2.108976 CACCCGATGATCCACCGG 59.891 66.667 0.00 0.00 42.64 5.28
2587 2831 3.861797 ACCCGATGATCCACCGGC 61.862 66.667 0.00 0.00 41.74 6.13
2589 2833 2.280389 CCGATGATCCACCGGCAG 60.280 66.667 0.00 0.00 36.62 4.85
2590 2834 2.501128 CGATGATCCACCGGCAGT 59.499 61.111 0.00 0.00 0.00 4.40
2835 3119 0.240945 CTTGGCAACGGACCATGAAC 59.759 55.000 0.00 0.00 36.96 3.18
2837 3121 1.602323 GGCAACGGACCATGAACCA 60.602 57.895 0.00 0.00 0.00 3.67
2839 3123 0.887933 GCAACGGACCATGAACCAAT 59.112 50.000 0.00 0.00 0.00 3.16
2858 3142 4.854924 CACCATGGATCGCGCCCA 62.855 66.667 21.47 19.54 38.19 5.36
2864 3148 1.541147 CATGGATCGCGCCCATTATTT 59.459 47.619 23.97 7.21 42.18 1.40
2883 3168 0.114954 TTGCATGCCCTTCCTTCCTT 59.885 50.000 16.68 0.00 0.00 3.36
2898 3183 4.401519 TCCTTCCTTCATTCCAGTACTACG 59.598 45.833 0.00 0.00 0.00 3.51
2899 3184 4.159879 CCTTCCTTCATTCCAGTACTACGT 59.840 45.833 0.00 0.00 0.00 3.57
2954 3239 4.578928 GGGGCTATACCTTGTACATTGTTG 59.421 45.833 0.00 0.00 39.10 3.33
2956 3241 6.062095 GGGCTATACCTTGTACATTGTTGAT 58.938 40.000 0.00 0.00 39.10 2.57
2962 3247 6.707440 ACCTTGTACATTGTTGATTGTTCA 57.293 33.333 0.00 0.00 0.00 3.18
2963 3248 6.738114 ACCTTGTACATTGTTGATTGTTCAG 58.262 36.000 0.00 0.00 32.27 3.02
2964 3249 6.321181 ACCTTGTACATTGTTGATTGTTCAGT 59.679 34.615 0.00 0.00 32.27 3.41
2965 3250 6.638063 CCTTGTACATTGTTGATTGTTCAGTG 59.362 38.462 0.00 0.00 32.27 3.66
2966 3251 6.691754 TGTACATTGTTGATTGTTCAGTGT 57.308 33.333 0.00 0.00 32.27 3.55
2967 3252 6.724263 TGTACATTGTTGATTGTTCAGTGTC 58.276 36.000 0.00 0.00 32.27 3.67
2968 3253 4.847633 ACATTGTTGATTGTTCAGTGTCG 58.152 39.130 0.00 0.00 32.27 4.35
2980 3265 3.036084 GTGTCGCCGTGTCCACAG 61.036 66.667 0.00 0.00 0.00 3.66
3041 3340 3.871395 GGCCCAGCCTAGCTCTGG 61.871 72.222 17.64 17.64 46.69 3.86
3044 3343 2.041508 CCAGCCTAGCTCTGGGGA 60.042 66.667 17.08 0.00 45.62 4.81
3049 3348 1.768077 CCTAGCTCTGGGGAAGGGG 60.768 68.421 0.00 0.00 0.00 4.79
3114 3413 0.469917 ATTGATGAGCGTACAGGGGG 59.530 55.000 0.00 0.00 0.00 5.40
3117 3416 2.650813 GATGAGCGTACAGGGGGCAG 62.651 65.000 0.00 0.00 0.00 4.85
3118 3417 3.391382 GAGCGTACAGGGGGCAGT 61.391 66.667 0.00 0.00 0.00 4.40
3142 3446 2.106332 GTCATCGGCCGGTACCAG 59.894 66.667 27.83 6.14 0.00 4.00
3166 3470 2.391389 CGCGCTGGAAAGAACCTCC 61.391 63.158 5.56 0.00 0.00 4.30
3268 3578 4.156190 CACTCACACAGTACCTGGTACTAG 59.844 50.000 32.88 28.53 46.08 2.57
3269 3579 4.042560 ACTCACACAGTACCTGGTACTAGA 59.957 45.833 32.88 25.33 46.08 2.43
3339 3734 0.038618 CACATCGTGGTCCACTCGAA 60.039 55.000 19.82 3.34 46.53 3.71
3354 3782 1.189446 CTCGAACGTCGTCCTTTGTTG 59.811 52.381 0.00 0.00 41.35 3.33
3406 3851 5.811613 CACCAAACATCTTTGAGCTTTCAAA 59.188 36.000 1.65 1.65 39.43 2.69
3415 3860 3.558931 TGAGCTTTCAAAGACTGACCA 57.441 42.857 0.00 0.00 32.21 4.02
3416 3861 3.884895 TGAGCTTTCAAAGACTGACCAA 58.115 40.909 0.00 0.00 32.21 3.67
3417 3862 4.464008 TGAGCTTTCAAAGACTGACCAAT 58.536 39.130 0.00 0.00 32.21 3.16
3418 3863 5.620206 TGAGCTTTCAAAGACTGACCAATA 58.380 37.500 0.00 0.00 32.21 1.90
3419 3864 6.061441 TGAGCTTTCAAAGACTGACCAATAA 58.939 36.000 0.00 0.00 32.21 1.40
3420 3865 6.017109 TGAGCTTTCAAAGACTGACCAATAAC 60.017 38.462 0.00 0.00 32.21 1.89
3422 3867 5.564848 GCTTTCAAAGACTGACCAATAACCC 60.565 44.000 0.00 0.00 32.21 4.11
3423 3868 4.993705 TCAAAGACTGACCAATAACCCT 57.006 40.909 0.00 0.00 0.00 4.34
3425 3870 6.636454 TCAAAGACTGACCAATAACCCTAT 57.364 37.500 0.00 0.00 0.00 2.57
3426 3871 6.650120 TCAAAGACTGACCAATAACCCTATC 58.350 40.000 0.00 0.00 0.00 2.08
3427 3872 5.632034 AAGACTGACCAATAACCCTATCC 57.368 43.478 0.00 0.00 0.00 2.59
3727 4196 0.959372 CTCAACAAGCAGGCCCTCAG 60.959 60.000 0.00 0.00 0.00 3.35
3898 4368 3.465403 CCGGAGCAGGTCCCTGAG 61.465 72.222 17.49 4.83 46.30 3.35
3912 4383 4.329545 TGAGCGGGGTTCAGGCAC 62.330 66.667 0.00 0.00 0.00 5.01
3977 4452 2.380084 TAGATGGCCTTGTCACGTTC 57.620 50.000 3.32 0.00 0.00 3.95
4028 4503 8.534866 GAGTTGAGACTCGAGTCAAGATAGACT 61.535 44.444 39.05 29.58 45.36 3.24
4048 4545 0.042188 CTGCAAACGTTGTGAGACCG 60.042 55.000 0.00 0.00 0.00 4.79
4050 4547 1.938861 CAAACGTTGTGAGACCGGG 59.061 57.895 6.32 0.00 0.00 5.73
4088 4871 2.766400 GGCGCTAGAGCTCGAGTGT 61.766 63.158 30.02 8.29 39.32 3.55
4092 4875 0.811915 GCTAGAGCTCGAGTGTCCAA 59.188 55.000 22.72 2.44 38.21 3.53
4117 4900 3.133362 AGGTTAGTTGTTCTTGTCCGTCA 59.867 43.478 0.00 0.00 0.00 4.35
4125 4908 1.205064 CTTGTCCGTCAAAGCGCTG 59.795 57.895 12.58 0.00 35.48 5.18
4188 4972 5.880054 ACAAAATCTAATTGTGGAGACCG 57.120 39.130 0.00 0.00 39.43 4.79
4252 5043 8.924511 TGAGAAAAGGAAAATATCAGACACTT 57.075 30.769 0.00 0.00 0.00 3.16
4253 5044 8.786898 TGAGAAAAGGAAAATATCAGACACTTG 58.213 33.333 0.00 0.00 0.00 3.16
4254 5045 8.924511 AGAAAAGGAAAATATCAGACACTTGA 57.075 30.769 0.00 0.00 0.00 3.02
4255 5046 9.354673 AGAAAAGGAAAATATCAGACACTTGAA 57.645 29.630 0.00 0.00 0.00 2.69
4256 5047 9.965824 GAAAAGGAAAATATCAGACACTTGAAA 57.034 29.630 0.00 0.00 0.00 2.69
4295 5234 8.224389 ACTTGGCAAAAAGAAGCAAAAATAAT 57.776 26.923 0.00 0.00 0.00 1.28
4391 5330 2.876550 GAGCTAAGGTCGGTTTGTGTTT 59.123 45.455 0.00 0.00 0.00 2.83
4392 5331 2.876550 AGCTAAGGTCGGTTTGTGTTTC 59.123 45.455 0.00 0.00 0.00 2.78
4395 5334 2.358322 AGGTCGGTTTGTGTTTCCAT 57.642 45.000 0.00 0.00 0.00 3.41
4396 5335 2.661718 AGGTCGGTTTGTGTTTCCATT 58.338 42.857 0.00 0.00 0.00 3.16
4409 5348 5.221422 TGTGTTTCCATTTGGATCAGAAACC 60.221 40.000 10.44 4.33 44.98 3.27
4423 5363 6.772716 GGATCAGAAACCATAAATCTAAGGCA 59.227 38.462 0.00 0.00 0.00 4.75
4424 5364 7.449704 GGATCAGAAACCATAAATCTAAGGCAT 59.550 37.037 0.00 0.00 0.00 4.40
4450 5394 5.316987 AGGACAAAGACAGGAATACCAAAG 58.683 41.667 0.00 0.00 38.94 2.77
4459 5407 6.158695 AGACAGGAATACCAAAGACCATATGT 59.841 38.462 1.24 0.00 38.94 2.29
4470 5615 2.158711 AGACCATATGTGCATCAGGGTG 60.159 50.000 6.27 0.77 31.95 4.61
4473 5618 3.117398 ACCATATGTGCATCAGGGTGAAT 60.117 43.478 1.24 0.00 31.07 2.57
4516 7237 0.179032 TGAACGGATGCACCACAAGT 60.179 50.000 0.00 0.00 38.90 3.16
4545 7266 2.879103 ATCCTTGGGTCAATGTTCGT 57.121 45.000 0.00 0.00 0.00 3.85
4555 7276 3.545633 GTCAATGTTCGTCTGTCTTTGC 58.454 45.455 0.00 0.00 0.00 3.68
4573 7294 5.416639 TCTTTGCATGCAAGTCAATCATACT 59.583 36.000 30.25 0.00 37.24 2.12
4655 7377 7.753309 ATGTACTAACATTTTACTGTTGGCA 57.247 32.000 0.00 0.00 44.07 4.92
4656 7378 6.961576 TGTACTAACATTTTACTGTTGGCAC 58.038 36.000 0.00 0.00 40.20 5.01
4657 7379 6.768861 TGTACTAACATTTTACTGTTGGCACT 59.231 34.615 0.00 0.00 40.20 4.40
4658 7380 6.313744 ACTAACATTTTACTGTTGGCACTC 57.686 37.500 0.00 0.00 40.20 3.51
4659 7381 4.584327 AACATTTTACTGTTGGCACTCC 57.416 40.909 0.00 0.00 37.93 3.85
4660 7382 3.832527 ACATTTTACTGTTGGCACTCCT 58.167 40.909 0.00 0.00 0.00 3.69
4661 7383 4.215109 ACATTTTACTGTTGGCACTCCTT 58.785 39.130 0.00 0.00 0.00 3.36
4662 7384 4.649218 ACATTTTACTGTTGGCACTCCTTT 59.351 37.500 0.00 0.00 0.00 3.11
4663 7385 5.128663 ACATTTTACTGTTGGCACTCCTTTT 59.871 36.000 0.00 0.00 0.00 2.27
4664 7386 5.669164 TTTTACTGTTGGCACTCCTTTTT 57.331 34.783 0.00 0.00 0.00 1.94
4693 7415 3.244249 ACTCTGTTGGCACTCCTCTAAAC 60.244 47.826 0.00 0.00 0.00 2.01
4730 7452 4.142687 GCTTAGTTGCATGATGGTACGTTT 60.143 41.667 0.00 0.00 0.00 3.60
4884 7612 0.383949 GACTGAGCTCGTGAGATCCC 59.616 60.000 14.47 0.00 42.79 3.85
4900 7628 4.152248 CCCCCTCTGTGATGGTGA 57.848 61.111 0.00 0.00 0.00 4.02
4924 7652 6.532119 AAGGTGATATACTCCACTCTCCTA 57.468 41.667 0.00 0.00 32.75 2.94
4936 7664 2.557056 CACTCTCCTAGGACAACGACAA 59.443 50.000 7.62 0.00 0.00 3.18
4941 7669 1.060713 CTAGGACAACGACAAGTGCG 58.939 55.000 0.00 0.00 0.00 5.34
4964 7692 0.250467 ATATGATGGTGGCGTCCTGC 60.250 55.000 0.00 0.00 45.38 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 6.701145 TTGGGACATTGCGCTATTAATTTA 57.299 33.333 9.73 0.00 39.30 1.40
20 22 5.590530 TTGGGACATTGCGCTATTAATTT 57.409 34.783 9.73 0.00 39.30 1.82
23 25 3.181491 GCTTTGGGACATTGCGCTATTAA 60.181 43.478 9.73 0.00 39.30 1.40
25 27 1.134946 GCTTTGGGACATTGCGCTATT 59.865 47.619 9.73 0.00 39.30 1.73
27 29 1.312371 GGCTTTGGGACATTGCGCTA 61.312 55.000 9.73 0.00 39.30 4.26
31 40 0.968405 TTCTGGCTTTGGGACATTGC 59.032 50.000 0.00 0.00 39.30 3.56
35 44 0.850100 TCCTTTCTGGCTTTGGGACA 59.150 50.000 0.00 0.00 35.26 4.02
73 82 3.733960 GGGGTTTGACTTCGGCGC 61.734 66.667 0.00 0.00 0.00 6.53
78 87 4.195225 TGTTTGTTTGGGGTTTGACTTC 57.805 40.909 0.00 0.00 0.00 3.01
277 308 4.862823 GGAGGGAGAGGGGTCGGG 62.863 77.778 0.00 0.00 0.00 5.14
280 311 2.284151 GAGGGAGGGAGAGGGGTC 59.716 72.222 0.00 0.00 0.00 4.46
281 312 3.369388 GGAGGGAGGGAGAGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
282 313 4.179599 GGGAGGGAGGGAGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
283 314 4.179599 GGGGAGGGAGGGAGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
304 340 1.199558 GGTAGTTATAGGCGAGCGAGG 59.800 57.143 0.00 0.00 0.00 4.63
357 393 4.916314 GGGGATCGAGCGGGAGGA 62.916 72.222 0.00 0.00 0.00 3.71
365 405 1.729470 CGAGGAGTGTGGGGATCGAG 61.729 65.000 0.00 0.00 32.13 4.04
438 480 3.387947 CCTAGAACCGGTGGCCGT 61.388 66.667 8.52 0.00 46.80 5.68
441 483 1.078637 GGAACCTAGAACCGGTGGC 60.079 63.158 8.52 3.13 34.33 5.01
455 497 1.280421 AGCAAGGATCAGTCAGGGAAC 59.720 52.381 0.00 0.00 0.00 3.62
474 516 4.637489 CCGAGCCGGCGAGATCAG 62.637 72.222 23.20 9.25 41.17 2.90
513 555 3.810386 GGCGAGAAAAATATCAGGGAGAC 59.190 47.826 0.00 0.00 0.00 3.36
517 559 5.300286 AGAAATGGCGAGAAAAATATCAGGG 59.700 40.000 0.00 0.00 0.00 4.45
540 582 3.121030 GTGCGTGCTGTGGCCTAG 61.121 66.667 3.32 3.44 37.74 3.02
593 638 2.485814 TGCTGATCTAGGATCGTCGATG 59.514 50.000 13.54 0.00 0.00 3.84
661 801 0.393077 GGCGCCTAGGAAGAATAGCA 59.607 55.000 22.15 0.00 0.00 3.49
745 885 6.736123 ACTATGTGTCCGTCATGTTCTATAC 58.264 40.000 0.00 0.00 0.00 1.47
762 902 4.097892 GGGTAATGGCAGGAAAACTATGTG 59.902 45.833 0.00 0.00 0.00 3.21
763 903 4.278310 GGGTAATGGCAGGAAAACTATGT 58.722 43.478 0.00 0.00 0.00 2.29
764 904 3.315191 CGGGTAATGGCAGGAAAACTATG 59.685 47.826 0.00 0.00 0.00 2.23
765 905 3.201266 TCGGGTAATGGCAGGAAAACTAT 59.799 43.478 0.00 0.00 0.00 2.12
800 942 3.492337 AGGCTAGTAGTGTCCTATCAGC 58.508 50.000 0.00 0.00 34.51 4.26
817 959 4.504916 CGCAGCGCAGAGTAGGCT 62.505 66.667 11.47 0.00 37.55 4.58
819 961 2.835701 TTTCCGCAGCGCAGAGTAGG 62.836 60.000 11.47 3.95 0.00 3.18
821 963 1.005512 TTTTCCGCAGCGCAGAGTA 60.006 52.632 11.47 0.00 0.00 2.59
822 964 2.280797 TTTTCCGCAGCGCAGAGT 60.281 55.556 11.47 0.00 0.00 3.24
824 966 3.049674 CCTTTTCCGCAGCGCAGA 61.050 61.111 11.47 0.00 0.00 4.26
835 977 3.274288 ACGATCAGATTCAGGCCTTTTC 58.726 45.455 0.00 0.00 0.00 2.29
839 981 0.755686 GGACGATCAGATTCAGGCCT 59.244 55.000 0.00 0.00 0.00 5.19
841 983 2.411904 GATGGACGATCAGATTCAGGC 58.588 52.381 0.00 0.00 0.00 4.85
842 984 2.670479 CGATGGACGATCAGATTCAGG 58.330 52.381 0.00 0.00 45.77 3.86
843 985 2.057316 GCGATGGACGATCAGATTCAG 58.943 52.381 0.00 0.00 45.77 3.02
844 986 1.600413 CGCGATGGACGATCAGATTCA 60.600 52.381 0.00 0.00 45.77 2.57
845 987 1.056103 CGCGATGGACGATCAGATTC 58.944 55.000 0.00 0.00 45.77 2.52
846 988 0.941463 GCGCGATGGACGATCAGATT 60.941 55.000 12.10 0.00 45.77 2.40
847 989 1.372251 GCGCGATGGACGATCAGAT 60.372 57.895 12.10 0.00 45.77 2.90
855 997 0.179124 AGAAGAAGAGCGCGATGGAC 60.179 55.000 12.10 0.00 0.00 4.02
1018 1177 0.321919 GATGAAGGTGCAGGTGCTCA 60.322 55.000 3.18 0.00 42.66 4.26
1020 1179 0.322277 CTGATGAAGGTGCAGGTGCT 60.322 55.000 3.18 0.00 42.66 4.40
1024 1183 2.507484 TGTTTCTGATGAAGGTGCAGG 58.493 47.619 0.00 0.00 33.28 4.85
1026 1185 3.554934 ACTTGTTTCTGATGAAGGTGCA 58.445 40.909 0.00 0.00 33.28 4.57
1030 1189 8.786898 TCTTGAATTACTTGTTTCTGATGAAGG 58.213 33.333 0.00 0.00 33.28 3.46
1033 1192 9.559732 TCTTCTTGAATTACTTGTTTCTGATGA 57.440 29.630 0.00 0.00 0.00 2.92
1064 1275 1.646189 GATCAAGACTCTTCACGCCC 58.354 55.000 0.00 0.00 0.00 6.13
1072 1283 1.686052 GCCATCTCGGATCAAGACTCT 59.314 52.381 0.00 0.00 36.56 3.24
1073 1284 1.270041 GGCCATCTCGGATCAAGACTC 60.270 57.143 0.00 0.00 36.56 3.36
1100 1312 2.688794 GCAGAGCACAGAAGCAGCC 61.689 63.158 0.00 0.00 36.85 4.85
1154 1366 9.857656 ATAATTAATGAAAAGCAGAGGAGATCA 57.142 29.630 0.00 0.00 0.00 2.92
1156 1368 9.857656 TGATAATTAATGAAAAGCAGAGGAGAT 57.142 29.630 0.00 0.00 0.00 2.75
1157 1369 9.685276 TTGATAATTAATGAAAAGCAGAGGAGA 57.315 29.630 0.00 0.00 0.00 3.71
1180 1392 9.689976 CACACAAACTGGTTAATTAATCATTGA 57.310 29.630 22.72 0.41 0.00 2.57
1181 1393 9.474920 ACACACAAACTGGTTAATTAATCATTG 57.525 29.630 17.48 17.48 0.00 2.82
1210 1422 2.430921 AGTAGTGCACGCGCTGAC 60.431 61.111 15.13 9.11 39.64 3.51
1211 1423 1.858372 TACAGTAGTGCACGCGCTGA 61.858 55.000 30.42 18.21 39.64 4.26
1372 1598 1.860078 GTGCGGAACCTTCTTCACG 59.140 57.895 0.00 0.00 0.00 4.35
1466 1692 4.681978 AGGGGCGCTGTTGTCGAC 62.682 66.667 9.11 9.11 0.00 4.20
1750 1988 3.426568 GGCAGCAGCAGGTCGAAC 61.427 66.667 2.65 0.00 44.61 3.95
1912 2150 1.216710 GCTGGACGACCTCCTCTTG 59.783 63.158 5.33 0.00 40.26 3.02
1967 2205 2.401766 GGCTCCACATGAACAGCCG 61.402 63.158 14.84 0.00 42.10 5.52
2040 2278 1.754226 GGAACATTTGGTGGTGTGTGT 59.246 47.619 0.00 0.00 0.00 3.72
2045 2283 1.613437 GGAGTGGAACATTTGGTGGTG 59.387 52.381 0.00 0.00 44.52 4.17
2057 2295 2.989639 CTGGCGATGGGAGTGGAA 59.010 61.111 0.00 0.00 0.00 3.53
2124 2362 2.693069 CGATCTCCTTGTTCTTGCAGT 58.307 47.619 0.00 0.00 0.00 4.40
2125 2363 1.396301 GCGATCTCCTTGTTCTTGCAG 59.604 52.381 0.00 0.00 0.00 4.41
2126 2364 1.442769 GCGATCTCCTTGTTCTTGCA 58.557 50.000 0.00 0.00 0.00 4.08
2127 2365 0.729690 GGCGATCTCCTTGTTCTTGC 59.270 55.000 0.00 0.00 0.00 4.01
2128 2366 1.002366 CGGCGATCTCCTTGTTCTTG 58.998 55.000 0.00 0.00 0.00 3.02
2129 2367 0.741221 GCGGCGATCTCCTTGTTCTT 60.741 55.000 12.98 0.00 0.00 2.52
2148 2386 3.068691 TCGGCTCTTCCTCCACCG 61.069 66.667 0.00 0.00 45.15 4.94
2202 2440 3.429141 GGTCCAGCGACGACGAGA 61.429 66.667 12.29 1.12 40.17 4.04
2255 2493 4.819761 GGCGTGGATCAGCAGCGA 62.820 66.667 8.86 0.00 34.54 4.93
2257 2495 4.819761 TCGGCGTGGATCAGCAGC 62.820 66.667 6.85 2.08 34.54 5.25
2258 2496 2.584418 CTCGGCGTGGATCAGCAG 60.584 66.667 6.85 5.41 34.54 4.24
2259 2497 4.147449 CCTCGGCGTGGATCAGCA 62.147 66.667 22.66 0.00 34.54 4.41
2271 2509 2.837291 CCTCCTCCTGCTCCTCGG 60.837 72.222 0.00 0.00 0.00 4.63
2293 2531 0.677098 TCCACTCCTCTTCCTCGTCG 60.677 60.000 0.00 0.00 0.00 5.12
2302 2540 0.904865 TGATGCCGTTCCACTCCTCT 60.905 55.000 0.00 0.00 0.00 3.69
2573 2817 1.884464 CACTGCCGGTGGATCATCG 60.884 63.158 1.90 0.00 41.90 3.84
2574 2818 4.131376 CACTGCCGGTGGATCATC 57.869 61.111 1.90 0.00 41.90 2.92
2582 2826 1.671742 CTCTGTTACCACTGCCGGT 59.328 57.895 1.90 0.00 43.46 5.28
2583 2827 1.079127 CCTCTGTTACCACTGCCGG 60.079 63.158 0.00 0.00 0.00 6.13
2584 2828 0.670546 CACCTCTGTTACCACTGCCG 60.671 60.000 0.00 0.00 0.00 5.69
2585 2829 0.955919 GCACCTCTGTTACCACTGCC 60.956 60.000 0.00 0.00 0.00 4.85
2586 2830 0.250295 TGCACCTCTGTTACCACTGC 60.250 55.000 0.00 0.00 0.00 4.40
2587 2831 2.146342 CTTGCACCTCTGTTACCACTG 58.854 52.381 0.00 0.00 0.00 3.66
2589 2833 1.873591 CACTTGCACCTCTGTTACCAC 59.126 52.381 0.00 0.00 0.00 4.16
2590 2834 1.765904 TCACTTGCACCTCTGTTACCA 59.234 47.619 0.00 0.00 0.00 3.25
2595 2855 1.123077 TCAGTCACTTGCACCTCTGT 58.877 50.000 0.00 0.00 0.00 3.41
2598 2858 0.394565 AGGTCAGTCACTTGCACCTC 59.605 55.000 0.00 0.00 31.41 3.85
2810 3094 0.955919 GGTCCGTTGCCAAGAGAAGG 60.956 60.000 0.00 0.00 0.00 3.46
2857 3141 4.411256 AGGAAGGGCATGCAAAATAATG 57.589 40.909 21.36 0.00 0.00 1.90
2858 3142 4.141642 GGAAGGAAGGGCATGCAAAATAAT 60.142 41.667 21.36 0.00 0.00 1.28
2864 3148 0.114954 AAGGAAGGAAGGGCATGCAA 59.885 50.000 21.36 0.00 0.00 4.08
2898 3183 1.792949 CTTTCACCAGAGCACGTACAC 59.207 52.381 0.00 0.00 0.00 2.90
2899 3184 1.872237 GCTTTCACCAGAGCACGTACA 60.872 52.381 0.00 0.00 38.73 2.90
2926 3211 0.551396 ACAAGGTATAGCCCCAAGCC 59.449 55.000 0.00 0.00 45.47 4.35
2954 3239 0.163788 CACGGCGACACTGAACAATC 59.836 55.000 16.62 0.00 0.00 2.67
2956 3241 1.149361 GACACGGCGACACTGAACAA 61.149 55.000 16.62 0.00 0.00 2.83
2962 3247 3.499929 CTGTGGACACGGCGACACT 62.500 63.158 16.62 0.00 35.02 3.55
2963 3248 3.036084 CTGTGGACACGGCGACAC 61.036 66.667 16.62 16.77 0.00 3.67
2964 3249 4.293648 CCTGTGGACACGGCGACA 62.294 66.667 16.62 5.97 36.39 4.35
3031 3320 1.768077 CCCCTTCCCCAGAGCTAGG 60.768 68.421 0.00 0.00 0.00 3.02
3037 3336 2.127297 CCCTTCCCCTTCCCCAGA 59.873 66.667 0.00 0.00 0.00 3.86
3041 3340 2.534533 ACCACCCTTCCCCTTCCC 60.535 66.667 0.00 0.00 0.00 3.97
3042 3341 2.613482 GGACCACCCTTCCCCTTCC 61.613 68.421 0.00 0.00 0.00 3.46
3044 3343 2.933834 CGGACCACCCTTCCCCTT 60.934 66.667 0.00 0.00 0.00 3.95
3049 3348 1.080025 CTCGTTCGGACCACCCTTC 60.080 63.158 0.00 0.00 0.00 3.46
3082 3381 4.641954 GCTCATCAATTTGTGTGTACGAG 58.358 43.478 0.00 0.00 0.00 4.18
3114 3413 2.094659 CCGATGACACGACCACTGC 61.095 63.158 0.00 0.00 35.09 4.40
3117 3416 2.813908 GGCCGATGACACGACCAC 60.814 66.667 0.00 0.00 35.95 4.16
3118 3417 4.429212 CGGCCGATGACACGACCA 62.429 66.667 24.07 0.00 35.65 4.02
3142 3446 3.849953 CTTTCCAGCGCGGCGTAC 61.850 66.667 24.46 8.13 33.14 3.67
3166 3470 4.807039 CGGTCGGGCGTAACCAGG 62.807 72.222 3.05 0.00 42.05 4.45
3176 3486 1.267261 GAGATGTCTATGTCGGTCGGG 59.733 57.143 0.00 0.00 0.00 5.14
3217 3527 0.103755 GGATCGTCAGAGCAGCATCA 59.896 55.000 0.00 0.00 33.76 3.07
3268 3578 0.174389 TGCTGCTGCTGCTACTACTC 59.826 55.000 27.67 1.98 40.48 2.59
3269 3579 0.175302 CTGCTGCTGCTGCTACTACT 59.825 55.000 27.67 0.00 40.48 2.57
3338 3733 0.375803 GCACAACAAAGGACGACGTT 59.624 50.000 0.13 0.00 0.00 3.99
3339 3734 0.741574 TGCACAACAAAGGACGACGT 60.742 50.000 0.00 0.00 0.00 4.34
3406 3851 4.656112 CAGGATAGGGTTATTGGTCAGTCT 59.344 45.833 0.00 0.00 0.00 3.24
3407 3852 4.409247 ACAGGATAGGGTTATTGGTCAGTC 59.591 45.833 0.00 0.00 0.00 3.51
3408 3853 4.371681 ACAGGATAGGGTTATTGGTCAGT 58.628 43.478 0.00 0.00 0.00 3.41
3411 3856 5.367945 TCAACAGGATAGGGTTATTGGTC 57.632 43.478 0.00 0.00 0.00 4.02
3413 3858 6.435904 TGTTTTCAACAGGATAGGGTTATTGG 59.564 38.462 0.00 0.00 36.25 3.16
3415 3860 8.664669 AATGTTTTCAACAGGATAGGGTTATT 57.335 30.769 0.00 0.00 45.95 1.40
3416 3861 7.342026 GGAATGTTTTCAACAGGATAGGGTTAT 59.658 37.037 0.00 0.00 45.95 1.89
3417 3862 6.661805 GGAATGTTTTCAACAGGATAGGGTTA 59.338 38.462 0.00 0.00 45.95 2.85
3418 3863 5.480422 GGAATGTTTTCAACAGGATAGGGTT 59.520 40.000 0.00 0.00 45.95 4.11
3419 3864 5.016831 GGAATGTTTTCAACAGGATAGGGT 58.983 41.667 0.00 0.00 45.95 4.34
3420 3865 5.016173 TGGAATGTTTTCAACAGGATAGGG 58.984 41.667 0.00 0.00 45.95 3.53
3422 3867 5.393461 GCCTGGAATGTTTTCAACAGGATAG 60.393 44.000 12.31 0.28 45.95 2.08
3423 3868 4.462483 GCCTGGAATGTTTTCAACAGGATA 59.538 41.667 12.31 0.00 45.95 2.59
3425 3870 2.627699 GCCTGGAATGTTTTCAACAGGA 59.372 45.455 12.31 0.00 45.95 3.86
3426 3871 2.289010 GGCCTGGAATGTTTTCAACAGG 60.289 50.000 0.00 0.00 45.95 4.00
3427 3872 2.629617 AGGCCTGGAATGTTTTCAACAG 59.370 45.455 3.11 0.00 45.95 3.16
3776 4245 1.376037 CCAGAGGTTGTTCCCGAGC 60.376 63.158 0.00 0.00 36.75 5.03
3882 4352 4.154347 GCTCAGGGACCTGCTCCG 62.154 72.222 13.51 3.48 43.31 4.63
3912 4383 2.716244 CCGATCGTCTCACCTCCG 59.284 66.667 15.09 0.00 0.00 4.63
3940 4411 5.638657 CCATCTATCTTGTAGCATCTGAAGC 59.361 44.000 0.00 0.00 0.00 3.86
3954 4425 2.501723 ACGTGACAAGGCCATCTATCTT 59.498 45.455 5.01 0.00 0.00 2.40
3955 4426 2.111384 ACGTGACAAGGCCATCTATCT 58.889 47.619 5.01 0.00 0.00 1.98
3956 4427 2.604046 ACGTGACAAGGCCATCTATC 57.396 50.000 5.01 0.00 0.00 2.08
3957 4428 2.236146 TGAACGTGACAAGGCCATCTAT 59.764 45.455 5.01 0.00 0.00 1.98
3958 4429 1.621317 TGAACGTGACAAGGCCATCTA 59.379 47.619 5.01 0.00 0.00 1.98
3977 4452 0.254178 CCTCCAAGTCCAGGGTGATG 59.746 60.000 0.00 0.00 0.00 3.07
4017 4492 4.521130 ACGTTTGCAGAGTCTATCTTGA 57.479 40.909 0.00 0.00 35.47 3.02
4018 4493 4.449068 ACAACGTTTGCAGAGTCTATCTTG 59.551 41.667 0.00 0.00 35.47 3.02
4019 4494 4.449068 CACAACGTTTGCAGAGTCTATCTT 59.551 41.667 0.00 0.00 35.47 2.40
4020 4495 3.990469 CACAACGTTTGCAGAGTCTATCT 59.010 43.478 0.00 0.00 39.56 1.98
4021 4496 3.987868 TCACAACGTTTGCAGAGTCTATC 59.012 43.478 0.00 0.00 0.00 2.08
4022 4497 3.990092 TCACAACGTTTGCAGAGTCTAT 58.010 40.909 0.00 0.00 0.00 1.98
4023 4498 3.067601 TCTCACAACGTTTGCAGAGTCTA 59.932 43.478 0.00 0.00 37.38 2.59
4025 4500 2.033662 GTCTCACAACGTTTGCAGAGTC 60.034 50.000 0.00 0.00 37.38 3.36
4026 4501 1.933853 GTCTCACAACGTTTGCAGAGT 59.066 47.619 0.00 0.00 37.38 3.24
4027 4502 1.261619 GGTCTCACAACGTTTGCAGAG 59.738 52.381 0.00 3.93 37.42 3.35
4028 4503 1.295792 GGTCTCACAACGTTTGCAGA 58.704 50.000 0.00 0.00 0.00 4.26
4048 4545 4.022329 CCAACTTCAAATGTACACCTTCCC 60.022 45.833 0.00 0.00 0.00 3.97
4050 4547 4.546570 GCCAACTTCAAATGTACACCTTC 58.453 43.478 0.00 0.00 0.00 3.46
4092 4875 4.141779 ACGGACAAGAACAACTAACCTTCT 60.142 41.667 0.00 0.00 0.00 2.85
4117 4900 1.675552 AAACCAGTACACAGCGCTTT 58.324 45.000 7.50 0.00 0.00 3.51
4125 4908 6.203808 AGGAAAAACAGAAAACCAGTACAC 57.796 37.500 0.00 0.00 0.00 2.90
4163 4947 6.370442 CGGTCTCCACAATTAGATTTTGTACA 59.630 38.462 0.00 0.00 35.61 2.90
4167 4951 5.391950 CCACGGTCTCCACAATTAGATTTTG 60.392 44.000 0.00 0.00 0.00 2.44
4180 4964 0.042131 AGGATTACCCACGGTCTCCA 59.958 55.000 12.47 0.00 39.01 3.86
4181 4965 1.201424 AAGGATTACCCACGGTCTCC 58.799 55.000 4.81 4.81 37.70 3.71
4241 5032 9.177608 CCCTTCATTATTTTCAAGTGTCTGATA 57.822 33.333 0.00 0.00 0.00 2.15
4250 5041 7.542025 CCAAGTCTCCCTTCATTATTTTCAAG 58.458 38.462 0.00 0.00 0.00 3.02
4252 5043 5.418840 GCCAAGTCTCCCTTCATTATTTTCA 59.581 40.000 0.00 0.00 0.00 2.69
4253 5044 5.418840 TGCCAAGTCTCCCTTCATTATTTTC 59.581 40.000 0.00 0.00 0.00 2.29
4254 5045 5.332743 TGCCAAGTCTCCCTTCATTATTTT 58.667 37.500 0.00 0.00 0.00 1.82
4255 5046 4.934356 TGCCAAGTCTCCCTTCATTATTT 58.066 39.130 0.00 0.00 0.00 1.40
4256 5047 4.591321 TGCCAAGTCTCCCTTCATTATT 57.409 40.909 0.00 0.00 0.00 1.40
4258 5049 4.380843 TTTGCCAAGTCTCCCTTCATTA 57.619 40.909 0.00 0.00 0.00 1.90
4259 5050 2.978156 TTGCCAAGTCTCCCTTCATT 57.022 45.000 0.00 0.00 0.00 2.57
4260 5051 2.978156 TTTGCCAAGTCTCCCTTCAT 57.022 45.000 0.00 0.00 0.00 2.57
4261 5052 2.746279 TTTTGCCAAGTCTCCCTTCA 57.254 45.000 0.00 0.00 0.00 3.02
4263 5054 3.312736 TCTTTTTGCCAAGTCTCCCTT 57.687 42.857 0.00 0.00 0.00 3.95
4264 5055 3.225940 CTTCTTTTTGCCAAGTCTCCCT 58.774 45.455 0.00 0.00 0.00 4.20
4265 5056 2.288457 GCTTCTTTTTGCCAAGTCTCCC 60.288 50.000 0.00 0.00 0.00 4.30
4392 5331 8.015185 AGATTTATGGTTTCTGATCCAAATGG 57.985 34.615 6.26 0.00 37.27 3.16
4395 5334 9.189156 CCTTAGATTTATGGTTTCTGATCCAAA 57.811 33.333 6.26 0.00 37.27 3.28
4396 5335 7.285401 GCCTTAGATTTATGGTTTCTGATCCAA 59.715 37.037 6.26 0.00 37.27 3.53
4409 5348 9.956720 CTTTGTCCTTTATGCCTTAGATTTATG 57.043 33.333 0.00 0.00 0.00 1.90
4423 5363 7.027874 TGGTATTCCTGTCTTTGTCCTTTAT 57.972 36.000 0.00 0.00 34.23 1.40
4424 5364 6.442541 TGGTATTCCTGTCTTTGTCCTTTA 57.557 37.500 0.00 0.00 34.23 1.85
4450 5394 2.158769 TCACCCTGATGCACATATGGTC 60.159 50.000 7.80 0.00 0.00 4.02
4459 5407 1.210234 ACGATCATTCACCCTGATGCA 59.790 47.619 0.00 0.00 33.56 3.96
4470 5615 2.089121 CGTATAGCGTGCACGATCATTC 59.911 50.000 41.19 23.79 43.02 2.67
4473 5618 0.317519 CCGTATAGCGTGCACGATCA 60.318 55.000 41.19 24.14 43.02 2.92
4516 7237 7.007723 ACATTGACCCAAGGATAACAAGTTTA 58.992 34.615 0.00 0.00 0.00 2.01
4523 7244 4.007659 ACGAACATTGACCCAAGGATAAC 58.992 43.478 0.00 0.00 0.00 1.89
4545 7266 2.574450 TGACTTGCATGCAAAGACAGA 58.426 42.857 31.37 10.11 35.33 3.41
4582 7303 2.205022 TGAATGACTTCCCTTGCAGG 57.795 50.000 0.00 0.00 34.30 4.85
4583 7304 4.701651 TGTTATGAATGACTTCCCTTGCAG 59.298 41.667 0.00 0.00 0.00 4.41
4587 7308 9.699410 TCAAATATGTTATGAATGACTTCCCTT 57.301 29.630 0.00 0.00 0.00 3.95
4629 7350 9.456147 TGCCAACAGTAAAATGTTAGTACATAT 57.544 29.630 0.00 0.00 44.14 1.78
4630 7351 8.723311 GTGCCAACAGTAAAATGTTAGTACATA 58.277 33.333 5.44 0.00 44.14 2.29
4631 7352 7.447238 AGTGCCAACAGTAAAATGTTAGTACAT 59.553 33.333 10.97 0.00 46.85 2.29
4632 7353 6.768861 AGTGCCAACAGTAAAATGTTAGTACA 59.231 34.615 10.97 0.00 41.41 2.90
4633 7354 7.198306 AGTGCCAACAGTAAAATGTTAGTAC 57.802 36.000 2.83 2.83 41.41 2.73
4663 7385 2.233431 AGTGCCAACAGAGTTGCAAAAA 59.767 40.909 0.00 0.00 35.16 1.94
4664 7386 1.824230 AGTGCCAACAGAGTTGCAAAA 59.176 42.857 0.00 0.00 35.16 2.44
4665 7387 1.405105 GAGTGCCAACAGAGTTGCAAA 59.595 47.619 0.00 0.00 35.16 3.68
4666 7388 1.024271 GAGTGCCAACAGAGTTGCAA 58.976 50.000 0.00 0.00 35.16 4.08
4667 7389 0.819259 GGAGTGCCAACAGAGTTGCA 60.819 55.000 4.42 4.14 0.00 4.08
4668 7390 0.536006 AGGAGTGCCAACAGAGTTGC 60.536 55.000 4.42 1.78 36.29 4.17
4669 7391 1.071385 AGAGGAGTGCCAACAGAGTTG 59.929 52.381 3.00 3.00 36.29 3.16
4670 7392 1.428869 AGAGGAGTGCCAACAGAGTT 58.571 50.000 0.00 0.00 36.29 3.01
4671 7393 2.310779 TAGAGGAGTGCCAACAGAGT 57.689 50.000 0.00 0.00 36.29 3.24
4672 7394 3.007398 AGTTTAGAGGAGTGCCAACAGAG 59.993 47.826 0.00 0.00 36.29 3.35
4673 7395 2.972713 AGTTTAGAGGAGTGCCAACAGA 59.027 45.455 0.00 0.00 36.29 3.41
4884 7612 1.340405 CCTTTCACCATCACAGAGGGG 60.340 57.143 2.59 0.00 37.87 4.79
4890 7618 6.408092 GGAGTATATCACCTTTCACCATCACA 60.408 42.308 0.00 0.00 0.00 3.58
4891 7619 5.992217 GGAGTATATCACCTTTCACCATCAC 59.008 44.000 0.00 0.00 0.00 3.06
4900 7628 5.782925 AGGAGAGTGGAGTATATCACCTTT 58.217 41.667 0.00 0.00 29.76 3.11
4924 7652 2.244651 GCGCACTTGTCGTTGTCCT 61.245 57.895 0.30 0.00 0.00 3.85
4936 7664 1.605457 CCACCATCATATACGCGCACT 60.605 52.381 5.73 0.00 0.00 4.40
4941 7669 1.068474 GACGCCACCATCATATACGC 58.932 55.000 0.00 0.00 0.00 4.42
4964 7692 1.321474 TGAAGCACCTTTTGGCAGAG 58.679 50.000 0.00 0.00 45.59 3.35


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

AutoCloner maintained by Alex Coulton.