Multiple sequence alignment - TraesCS4A01G096800

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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 TraesCS4A01G096800 chr4A 100.000 4911 0 0 1 4911 106338293 106343203 0.000000e+00 9070.0
1 TraesCS4A01G096800 chr4A 89.873 790 55 15 1 790 106190726 106191490 0.000000e+00 992.0
2 TraesCS4A01G096800 chr4A 92.222 90 7 0 822 911 106191487 106191576 1.430000e-25 128.0
3 TraesCS4A01G096800 chr4A 97.917 48 1 0 2177 2224 106340422 106340469 3.150000e-12 84.2
4 TraesCS4A01G096800 chr4A 97.917 48 1 0 2130 2177 106340469 106340516 3.150000e-12 84.2
5 TraesCS4A01G096800 chr4A 92.308 52 4 0 3069 3120 572539213 572539264 1.900000e-09 75.0
6 TraesCS4A01G096800 chr4D 89.517 2175 143 55 2799 4911 359123445 359121294 0.000000e+00 2675.0
7 TraesCS4A01G096800 chr4D 95.994 624 21 4 1554 2176 359125004 359124384 0.000000e+00 1011.0
8 TraesCS4A01G096800 chr4D 87.273 715 54 21 427 1134 359126347 359125663 0.000000e+00 782.0
9 TraesCS4A01G096800 chr4D 94.928 414 15 1 1128 1541 359125482 359125075 1.150000e-180 643.0
10 TraesCS4A01G096800 chr4D 86.431 538 26 17 2177 2704 359124429 359123929 3.340000e-151 545.0
11 TraesCS4A01G096800 chr4D 100.000 29 0 0 1274 1302 39980576 39980548 2.000000e-03 54.7
12 TraesCS4A01G096800 chr4D 100.000 28 0 0 1274 1301 71294267 71294240 9.000000e-03 52.8
13 TraesCS4A01G096800 chr4B 89.254 1247 75 30 3203 4427 443452017 443450808 0.000000e+00 1506.0
14 TraesCS4A01G096800 chr4B 88.362 1117 68 28 456 1541 443455104 443454019 0.000000e+00 1286.0
15 TraesCS4A01G096800 chr4B 94.409 626 25 4 1554 2177 443453944 443453327 0.000000e+00 953.0
16 TraesCS4A01G096800 chr4B 93.878 490 23 4 4425 4911 443450548 443450063 0.000000e+00 732.0
17 TraesCS4A01G096800 chr4B 90.000 530 25 9 2177 2704 443453374 443452871 0.000000e+00 660.0
18 TraesCS4A01G096800 chr4B 78.068 383 47 7 2799 3146 443452395 443452015 1.790000e-49 207.0
19 TraesCS4A01G096800 chr4B 100.000 28 0 0 1274 1301 105002635 105002662 9.000000e-03 52.8
20 TraesCS4A01G096800 chr1A 84.884 344 38 10 3 339 483681323 483681659 7.880000e-88 335.0
21 TraesCS4A01G096800 chr3B 84.566 311 40 5 26 330 258169865 258169557 7.990000e-78 302.0
22 TraesCS4A01G096800 chr2A 84.354 294 38 6 42 330 587021085 587021375 1.040000e-71 281.0
23 TraesCS4A01G096800 chr2A 92.683 41 3 0 2700 2740 401220739 401220779 5.310000e-05 60.2
24 TraesCS4A01G096800 chr2A 92.683 41 3 0 2700 2740 403188483 403188523 5.310000e-05 60.2
25 TraesCS4A01G096800 chr3D 84.375 288 36 7 49 330 615476154 615475870 1.740000e-69 274.0
26 TraesCS4A01G096800 chr2D 82.692 312 43 8 26 330 30739644 30739337 2.910000e-67 267.0
27 TraesCS4A01G096800 chr2D 81.928 332 45 11 1 324 47320091 47319767 2.910000e-67 267.0
28 TraesCS4A01G096800 chr2D 100.000 28 0 0 3100 3127 27061398 27061425 9.000000e-03 52.8
29 TraesCS4A01G096800 chr1D 81.381 333 49 11 2 327 226471361 226471035 4.880000e-65 259.0
30 TraesCS4A01G096800 chr1D 81.194 335 48 12 1 330 401176088 401176412 6.310000e-64 255.0
31 TraesCS4A01G096800 chr5D 100.000 29 0 0 1272 1300 518921018 518921046 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 TraesCS4A01G096800 chr4A 106338293 106343203 4910 False 3079.466667 9070 98.611333 1 4911 3 chr4A.!!$F3 4910
1 TraesCS4A01G096800 chr4A 106190726 106191576 850 False 560.000000 992 91.047500 1 911 2 chr4A.!!$F2 910
2 TraesCS4A01G096800 chr4D 359121294 359126347 5053 True 1131.200000 2675 90.828600 427 4911 5 chr4D.!!$R3 4484
3 TraesCS4A01G096800 chr4B 443450063 443455104 5041 True 890.666667 1506 88.995167 456 4911 6 chr4B.!!$R1 4455

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
930 976 0.108424 CTCTCGAGTGAAAGCTGGGG 60.108 60.0 13.13 0.00 0.00 4.96 F
1557 1837 0.180642 TACCCACACGCCTGTTTCAA 59.819 50.0 0.00 0.00 0.00 2.69 F
2685 2989 0.036388 CTCCAACGCTCTGCCCTTAA 60.036 55.0 0.00 0.00 0.00 1.85 F
3568 4317 0.179111 TATTGGCACTTCGAGCTCGG 60.179 55.0 33.98 21.94 40.29 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2360 0.253327 GGCAGGTAGGAAGGACAAGG 59.747 60.0 0.00 0.00 0.00 3.61 R
3047 3763 0.321564 CGGAAGCAGACATCCAACCA 60.322 55.0 0.00 0.00 33.01 3.67 R
3832 4584 0.726827 GCTCAAAACCATGATCGCGA 59.273 50.0 13.09 13.09 0.00 5.87 R
4799 5822 0.693049 ACAAGTAGGGAGGGTTGCTG 59.307 55.0 0.00 0.00 0.00 4.41 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
67 68 6.036626 ACCAATTTTCAAAACAATGTTCGTCC 59.963 34.615 0.00 0.00 0.00 4.79
83 84 6.227522 TGTTCGTCCATTCTAGAAATGTTCA 58.772 36.000 9.71 0.00 0.00 3.18
94 95 7.737972 TCTAGAAATGTTCACCGATTCAAAA 57.262 32.000 0.00 0.00 0.00 2.44
203 204 9.760660 TTGGAAATGTTTGAAAATTTGTAAACG 57.239 25.926 18.16 0.00 36.18 3.60
288 289 7.823665 TCATGATTTCAGAAAATTGAGAGTGG 58.176 34.615 0.00 0.00 35.21 4.00
291 292 8.099364 TGATTTCAGAAAATTGAGAGTGGTAC 57.901 34.615 0.00 0.00 35.21 3.34
294 295 6.419484 TCAGAAAATTGAGAGTGGTACTGA 57.581 37.500 0.00 0.00 0.00 3.41
295 296 6.459066 TCAGAAAATTGAGAGTGGTACTGAG 58.541 40.000 0.00 0.00 0.00 3.35
297 298 7.232737 TCAGAAAATTGAGAGTGGTACTGAGTA 59.767 37.037 0.00 0.00 0.00 2.59
300 301 5.759506 ATTGAGAGTGGTACTGAGTATCG 57.240 43.478 0.00 0.00 38.61 2.92
321 322 2.733026 GGTGATGCAGCAAAATGTGAAC 59.267 45.455 6.05 0.00 0.00 3.18
330 331 3.514706 AGCAAAATGTGAACATGGCCATA 59.485 39.130 20.30 1.02 36.56 2.74
334 335 6.675971 GCAAAATGTGAACATGGCCATATTTG 60.676 38.462 20.30 17.72 35.36 2.32
336 337 5.680594 ATGTGAACATGGCCATATTTGTT 57.319 34.783 20.30 20.03 34.83 2.83
337 338 5.480642 TGTGAACATGGCCATATTTGTTT 57.519 34.783 20.30 4.79 32.73 2.83
338 339 5.862845 TGTGAACATGGCCATATTTGTTTT 58.137 33.333 20.30 0.00 32.73 2.43
339 340 5.699915 TGTGAACATGGCCATATTTGTTTTG 59.300 36.000 20.30 6.80 32.73 2.44
340 341 5.931146 GTGAACATGGCCATATTTGTTTTGA 59.069 36.000 20.30 5.64 32.73 2.69
341 342 6.091169 GTGAACATGGCCATATTTGTTTTGAG 59.909 38.462 20.30 3.64 32.73 3.02
342 343 5.999205 ACATGGCCATATTTGTTTTGAGA 57.001 34.783 20.30 0.00 0.00 3.27
343 344 5.723295 ACATGGCCATATTTGTTTTGAGAC 58.277 37.500 20.30 0.00 0.00 3.36
344 345 5.245751 ACATGGCCATATTTGTTTTGAGACA 59.754 36.000 20.30 0.00 0.00 3.41
362 363 6.472016 TGAGACAATGAACATAGCCACTAAA 58.528 36.000 0.00 0.00 0.00 1.85
430 431 5.981315 GCTAGCGTTATATTACAGGTTCACA 59.019 40.000 0.00 0.00 0.00 3.58
431 432 6.074463 GCTAGCGTTATATTACAGGTTCACAC 60.074 42.308 0.00 0.00 0.00 3.82
473 474 2.674563 TATTGAGGATTGGGCCGCCG 62.675 60.000 2.55 0.00 0.00 6.46
684 688 5.416013 CCTTTCTCTTTCTTTTTATCCGCCT 59.584 40.000 0.00 0.00 0.00 5.52
692 696 3.070590 TCTTTTTATCCGCCTACCCTAGC 59.929 47.826 0.00 0.00 0.00 3.42
702 706 2.294170 CTACCCTAGCAGACGGGGGA 62.294 65.000 3.72 0.00 45.07 4.81
748 752 1.658717 GCGCGTGTATCTGATCGCT 60.659 57.895 16.67 0.00 45.25 4.93
786 790 0.806492 GACCTAGCGTGGCTGCTAAC 60.806 60.000 11.99 0.00 46.17 2.34
790 794 0.534873 TAGCGTGGCTGCTAACATGA 59.465 50.000 0.00 0.00 45.14 3.07
791 795 0.321564 AGCGTGGCTGCTAACATGAA 60.322 50.000 0.00 0.00 45.14 2.57
792 796 0.734889 GCGTGGCTGCTAACATGAAT 59.265 50.000 0.00 0.00 0.00 2.57
793 797 1.133025 GCGTGGCTGCTAACATGAATT 59.867 47.619 0.00 0.00 0.00 2.17
794 798 2.415893 GCGTGGCTGCTAACATGAATTT 60.416 45.455 0.00 0.00 0.00 1.82
795 799 3.429085 CGTGGCTGCTAACATGAATTTC 58.571 45.455 0.00 0.00 0.00 2.17
796 800 3.127548 CGTGGCTGCTAACATGAATTTCT 59.872 43.478 0.00 0.00 0.00 2.52
797 801 4.379813 CGTGGCTGCTAACATGAATTTCTT 60.380 41.667 0.00 0.00 0.00 2.52
798 802 5.473039 GTGGCTGCTAACATGAATTTCTTT 58.527 37.500 0.00 0.00 0.00 2.52
799 803 5.928264 GTGGCTGCTAACATGAATTTCTTTT 59.072 36.000 0.00 0.00 0.00 2.27
800 804 6.089954 GTGGCTGCTAACATGAATTTCTTTTC 59.910 38.462 0.00 0.00 0.00 2.29
801 805 6.015180 TGGCTGCTAACATGAATTTCTTTTCT 60.015 34.615 0.00 0.00 0.00 2.52
802 806 6.870439 GGCTGCTAACATGAATTTCTTTTCTT 59.130 34.615 0.00 0.00 0.00 2.52
803 807 7.062722 GGCTGCTAACATGAATTTCTTTTCTTC 59.937 37.037 0.00 0.00 0.00 2.87
804 808 7.062722 GCTGCTAACATGAATTTCTTTTCTTCC 59.937 37.037 0.00 0.00 0.00 3.46
805 809 7.378181 TGCTAACATGAATTTCTTTTCTTCCC 58.622 34.615 0.00 0.00 0.00 3.97
806 810 6.528072 GCTAACATGAATTTCTTTTCTTCCCG 59.472 38.462 0.00 0.00 0.00 5.14
807 811 4.809673 ACATGAATTTCTTTTCTTCCCGC 58.190 39.130 0.00 0.00 0.00 6.13
808 812 4.280677 ACATGAATTTCTTTTCTTCCCGCA 59.719 37.500 0.00 0.00 0.00 5.69
809 813 4.927978 TGAATTTCTTTTCTTCCCGCAA 57.072 36.364 0.00 0.00 0.00 4.85
810 814 5.269505 TGAATTTCTTTTCTTCCCGCAAA 57.730 34.783 0.00 0.00 0.00 3.68
811 815 5.665459 TGAATTTCTTTTCTTCCCGCAAAA 58.335 33.333 0.00 0.00 0.00 2.44
812 816 6.109359 TGAATTTCTTTTCTTCCCGCAAAAA 58.891 32.000 0.00 0.00 0.00 1.94
837 841 3.913089 ACATGAATTTCTTTTCGGTGGC 58.087 40.909 0.00 0.00 0.00 5.01
902 948 1.357258 CTGCTAGCAGCGGTCTGTTG 61.357 60.000 30.62 5.33 46.26 3.33
930 976 0.108424 CTCTCGAGTGAAAGCTGGGG 60.108 60.000 13.13 0.00 0.00 4.96
963 1009 0.886490 CTGTGGCACCGAGAAGCTTT 60.886 55.000 16.26 0.00 0.00 3.51
1020 1067 3.249799 TGATGGTGTTTGTTCATGACGAC 59.750 43.478 0.00 0.00 0.00 4.34
1074 1124 5.576774 GGTAGTATTTGCTGATTTTGTTGGC 59.423 40.000 0.00 0.00 0.00 4.52
1077 1127 2.593346 TTGCTGATTTTGTTGGCGTT 57.407 40.000 0.00 0.00 0.00 4.84
1094 1144 5.672503 TGGCGTTATAAAGTTGCATACCTA 58.327 37.500 0.35 0.00 0.00 3.08
1140 1378 6.609876 TCATAATATGGTAGTTTGGCATGGT 58.390 36.000 0.00 0.00 0.00 3.55
1180 1418 4.279982 TGCATTCATTTGGCCTAGATTGA 58.720 39.130 3.32 0.00 0.00 2.57
1202 1440 7.026631 TGATAATTTGGCCGTTCAATCTTAG 57.973 36.000 0.00 0.00 0.00 2.18
1240 1478 4.959596 TGTTACCAACGTTGTTGCTTTA 57.040 36.364 25.63 5.43 0.00 1.85
1272 1510 2.691409 TTCAGGTTAGAATGAGGCGG 57.309 50.000 0.00 0.00 0.00 6.13
1289 1527 3.721706 GCAGGGACAGGGACAGGG 61.722 72.222 0.00 0.00 0.00 4.45
1290 1528 2.122729 CAGGGACAGGGACAGGGA 59.877 66.667 0.00 0.00 0.00 4.20
1291 1529 2.122954 AGGGACAGGGACAGGGAC 59.877 66.667 0.00 0.00 0.00 4.46
1292 1530 2.203938 GGGACAGGGACAGGGACA 60.204 66.667 0.00 0.00 0.00 4.02
1293 1531 2.294078 GGGACAGGGACAGGGACAG 61.294 68.421 0.00 0.00 0.00 3.51
1294 1532 2.294078 GGACAGGGACAGGGACAGG 61.294 68.421 0.00 0.00 0.00 4.00
1335 1573 5.242393 GGATCCTAACATCAATTCCATGGTG 59.758 44.000 12.58 2.68 37.45 4.17
1383 1621 3.882888 CTCAGCAAAGGGTTCAACAACTA 59.117 43.478 0.00 0.00 32.50 2.24
1488 1726 2.047179 GACAGAGGTGGGCCGAAC 60.047 66.667 0.00 0.00 40.50 3.95
1493 1731 2.933287 AGGTGGGCCGAACATCCA 60.933 61.111 5.28 0.00 40.50 3.41
1557 1837 0.180642 TACCCACACGCCTGTTTCAA 59.819 50.000 0.00 0.00 0.00 2.69
1647 1947 6.267471 ACTTTGGACAGATTAGCATTTTTCCA 59.733 34.615 0.00 0.00 0.00 3.53
1653 1953 8.037166 GGACAGATTAGCATTTTTCCAAGAAAT 58.963 33.333 0.00 0.00 0.00 2.17
1833 2133 8.133627 CCTTTTATGATGGACAACAATCTGATC 58.866 37.037 0.00 0.00 0.00 2.92
1870 2170 6.239217 AGAAAAGCAACCAAGAAAGGAATT 57.761 33.333 0.00 0.00 0.00 2.17
1909 2209 2.032549 CCGATAAGATTGAAGCAAGGCG 60.033 50.000 0.00 0.00 0.00 5.52
2059 2360 8.806177 TGTTCAAATATATTGCATGATTCTGC 57.194 30.769 0.00 0.00 42.62 4.26
2066 2367 1.466856 TGCATGATTCTGCCTTGTCC 58.533 50.000 0.00 0.00 41.58 4.02
2081 2382 1.440618 TGTCCTTCCTACCTGCCAAA 58.559 50.000 0.00 0.00 0.00 3.28
2103 2404 7.301054 CAAAAGTAGATTAACTGGACTTGCAG 58.699 38.462 0.00 0.00 30.63 4.41
2169 2470 7.973048 ACTATTGACAGGAAGTACTTATCCA 57.027 36.000 14.68 4.50 38.23 3.41
2170 2471 8.554490 ACTATTGACAGGAAGTACTTATCCAT 57.446 34.615 14.68 3.77 38.23 3.41
2171 2472 8.993424 ACTATTGACAGGAAGTACTTATCCATT 58.007 33.333 14.68 2.30 38.23 3.16
2172 2473 9.838339 CTATTGACAGGAAGTACTTATCCATTT 57.162 33.333 14.68 0.09 38.23 2.32
2176 2477 9.613428 TGACAGGAAGTACTTATCCATTTTATG 57.387 33.333 14.68 6.57 38.23 1.90
2177 2478 9.614792 GACAGGAAGTACTTATCCATTTTATGT 57.385 33.333 14.68 9.23 38.23 2.29
2178 2479 9.614792 ACAGGAAGTACTTATCCATTTTATGTC 57.385 33.333 14.68 0.00 38.23 3.06
2179 2480 9.613428 CAGGAAGTACTTATCCATTTTATGTCA 57.387 33.333 14.68 0.00 38.23 3.58
2191 2492 9.818270 ATCCATTTTATGTCATTGATATGTCCT 57.182 29.630 6.19 0.00 33.34 3.85
2203 2504 9.948964 TCATTGATATGTCCTATTATTGACAGG 57.051 33.333 0.00 0.00 44.07 4.00
2204 2505 9.948964 CATTGATATGTCCTATTATTGACAGGA 57.051 33.333 0.00 0.00 44.07 3.86
2207 2508 9.159254 TGATATGTCCTATTATTGACAGGAAGT 57.841 33.333 0.00 0.00 44.07 3.01
2280 2581 5.112129 AGTTTCTGTTTGGTCCTGTTAGT 57.888 39.130 0.00 0.00 0.00 2.24
2285 2586 5.690865 TCTGTTTGGTCCTGTTAGTCAATT 58.309 37.500 0.00 0.00 0.00 2.32
2286 2587 5.530915 TCTGTTTGGTCCTGTTAGTCAATTG 59.469 40.000 0.00 0.00 0.00 2.32
2316 2617 7.391148 TGATTAGCCTTTTGAGTAACAATCC 57.609 36.000 0.00 0.00 38.36 3.01
2339 2640 4.335416 CACAGGTAGATGTTGGGAAACAT 58.665 43.478 3.84 3.84 45.32 2.71
2361 2662 8.671384 ACATCTAGTTTTGTGTTGCTACTTAA 57.329 30.769 0.00 0.00 0.00 1.85
2414 2715 6.463360 TCAGTTATGTGCATAGACTTGTCAA 58.537 36.000 3.49 0.00 0.00 3.18
2418 2719 8.454106 AGTTATGTGCATAGACTTGTCAATTTC 58.546 33.333 3.49 0.00 0.00 2.17
2454 2755 4.717233 TTTTGCATGCCAATACCAGTAG 57.283 40.909 16.68 0.00 32.49 2.57
2455 2756 3.364460 TTGCATGCCAATACCAGTAGT 57.636 42.857 16.68 0.00 0.00 2.73
2456 2757 2.917933 TGCATGCCAATACCAGTAGTC 58.082 47.619 16.68 0.00 0.00 2.59
2457 2758 2.505407 TGCATGCCAATACCAGTAGTCT 59.495 45.455 16.68 0.00 0.00 3.24
2458 2759 3.709141 TGCATGCCAATACCAGTAGTCTA 59.291 43.478 16.68 0.00 0.00 2.59
2459 2760 4.202253 TGCATGCCAATACCAGTAGTCTAG 60.202 45.833 16.68 0.00 0.00 2.43
2460 2761 4.202264 GCATGCCAATACCAGTAGTCTAGT 60.202 45.833 6.36 0.00 0.00 2.57
2461 2762 5.010719 GCATGCCAATACCAGTAGTCTAGTA 59.989 44.000 6.36 0.00 0.00 1.82
2466 2767 6.679884 GCCAATACCAGTAGTCTAGTACACAC 60.680 46.154 0.00 0.00 0.00 3.82
2491 2792 7.824289 ACCCACATTAATCCATATTAGTCATCG 59.176 37.037 0.00 0.00 0.00 3.84
2506 2807 0.601576 CATCGGACGTGAACAACCCA 60.602 55.000 0.00 0.00 0.00 4.51
2522 2823 4.236935 CAACCCACATCTTGCAATGTAAC 58.763 43.478 5.40 0.00 37.78 2.50
2543 2844 0.096628 GCAGAGAACATGCAAGCTCG 59.903 55.000 0.00 0.00 43.31 5.03
2546 2847 0.373024 GAGAACATGCAAGCTCGAGC 59.627 55.000 30.01 30.01 42.49 5.03
2672 2976 4.965200 ACTCTATTAGGGCATCTCCAAC 57.035 45.455 0.00 0.00 36.21 3.77
2676 2980 0.178068 TTAGGGCATCTCCAACGCTC 59.822 55.000 0.00 0.00 36.21 5.03
2685 2989 0.036388 CTCCAACGCTCTGCCCTTAA 60.036 55.000 0.00 0.00 0.00 1.85
2687 2991 0.521735 CCAACGCTCTGCCCTTAAAC 59.478 55.000 0.00 0.00 0.00 2.01
2712 3373 1.017701 CAAACGTCCGGGAAGCCTAC 61.018 60.000 10.02 0.00 0.00 3.18
2715 3376 1.753463 CGTCCGGGAAGCCTACTCT 60.753 63.158 0.00 0.00 0.00 3.24
2725 3386 4.880537 CCTACTCTGGCCGCTGCG 62.881 72.222 16.34 16.34 38.85 5.18
2744 3405 3.707156 CTGCATTGAAGCGGCGTCG 62.707 63.158 4.29 4.29 37.31 5.12
2769 3430 1.410224 GCCTGCCCAGCCTATTTAAGT 60.410 52.381 0.00 0.00 0.00 2.24
2776 3437 4.575236 GCCCAGCCTATTTAAGTAGTGTTC 59.425 45.833 4.51 0.00 0.00 3.18
2778 3439 5.338871 CCCAGCCTATTTAAGTAGTGTTCCA 60.339 44.000 4.51 0.00 0.00 3.53
2789 3474 4.069232 TGTTCCAGCGCCTCCTCG 62.069 66.667 2.29 0.00 0.00 4.63
2812 3497 0.615850 CAAACCCTCTCCACTCCTCC 59.384 60.000 0.00 0.00 0.00 4.30
2813 3498 0.193574 AAACCCTCTCCACTCCTCCA 59.806 55.000 0.00 0.00 0.00 3.86
2815 3500 1.079256 CCCTCTCCACTCCTCCACA 59.921 63.158 0.00 0.00 0.00 4.17
2821 3516 2.745698 CACTCCTCCACAGCAGCA 59.254 61.111 0.00 0.00 0.00 4.41
2874 3569 1.666011 CTAGGACGGCCATGCGTAT 59.334 57.895 11.69 0.00 36.29 3.06
2884 3579 0.465705 CCATGCGTATGAGGTCACCT 59.534 55.000 15.64 0.00 36.36 4.00
2896 3591 1.611474 GGTCACCTTCCGGTACCTCC 61.611 65.000 10.90 0.00 43.24 4.30
2897 3592 1.305549 TCACCTTCCGGTACCTCCC 60.306 63.158 10.90 0.00 43.24 4.30
2963 3658 9.377383 CAAAATATCGTCCGGTTTATGTAAATC 57.623 33.333 0.00 0.00 0.00 2.17
2968 3663 8.842358 ATCGTCCGGTTTATGTAAATCATATT 57.158 30.769 0.00 0.00 38.59 1.28
2995 3711 7.239763 ACTTTTATCCGGTTCCATGAAATTT 57.760 32.000 0.00 0.00 0.00 1.82
3005 3721 4.250116 TCCATGAAATTTGTCCGTTTGG 57.750 40.909 0.00 0.00 0.00 3.28
3011 3727 5.665459 TGAAATTTGTCCGTTTGGTTCAAT 58.335 33.333 0.00 0.00 36.30 2.57
3015 3731 6.597262 ATTTGTCCGTTTGGTTCAATTTTC 57.403 33.333 0.00 0.00 36.30 2.29
3016 3732 3.696898 TGTCCGTTTGGTTCAATTTTCG 58.303 40.909 0.00 0.00 36.30 3.46
3018 3734 4.106909 GTCCGTTTGGTTCAATTTTCGTT 58.893 39.130 0.00 0.00 36.30 3.85
3020 3736 5.742926 GTCCGTTTGGTTCAATTTTCGTTTA 59.257 36.000 0.00 0.00 36.30 2.01
3047 3763 1.227556 GCGGACGATTAGGGCACAT 60.228 57.895 0.00 0.00 0.00 3.21
3057 3773 0.998928 TAGGGCACATGGTTGGATGT 59.001 50.000 0.00 0.00 37.01 3.06
3059 3775 0.323725 GGGCACATGGTTGGATGTCT 60.324 55.000 0.00 0.00 34.18 3.41
3062 3778 1.830279 CACATGGTTGGATGTCTGCT 58.170 50.000 0.00 0.00 34.18 4.24
3066 3782 0.321564 TGGTTGGATGTCTGCTTCCG 60.322 55.000 0.00 0.00 40.64 4.30
3067 3783 0.321653 GGTTGGATGTCTGCTTCCGT 60.322 55.000 0.00 0.00 40.64 4.69
3084 3813 1.589196 GTGTCTGCGGACGGATAGC 60.589 63.158 20.49 3.27 44.83 2.97
3086 3815 2.515290 TCTGCGGACGGATAGCGA 60.515 61.111 0.00 0.00 0.00 4.93
3090 3819 4.344474 CGGACGGATAGCGAGGCC 62.344 72.222 0.00 0.00 0.00 5.19
3099 3828 2.397413 ATAGCGAGGCCGATTTGGGG 62.397 60.000 0.00 0.00 38.63 4.96
3108 3838 2.360726 GATTTGGGGGACGGCGTT 60.361 61.111 16.19 0.00 0.00 4.84
3124 3854 1.138266 GCGTTGGAGATGCCCTTAGTA 59.862 52.381 0.00 0.00 34.03 1.82
3125 3855 2.419574 GCGTTGGAGATGCCCTTAGTAA 60.420 50.000 0.00 0.00 34.03 2.24
3128 3858 2.764269 TGGAGATGCCCTTAGTAAGCT 58.236 47.619 4.22 0.00 34.97 3.74
3151 3881 7.497249 AGCTTAGATTTATCTTAGTGCTTGGTG 59.503 37.037 7.38 0.00 36.30 4.17
3155 3885 7.168219 AGATTTATCTTAGTGCTTGGTGTTGA 58.832 34.615 0.00 0.00 31.97 3.18
3161 3891 5.705441 TCTTAGTGCTTGGTGTTGATTAAGG 59.295 40.000 0.00 0.00 0.00 2.69
3168 3898 6.095377 GCTTGGTGTTGATTAAGGAATTGAG 58.905 40.000 0.00 0.00 0.00 3.02
3175 3905 7.389053 GTGTTGATTAAGGAATTGAGTCACTCT 59.611 37.037 6.33 0.00 0.00 3.24
3188 3918 6.609237 TGAGTCACTCTGAAGATTTTTGTG 57.391 37.500 6.33 0.00 0.00 3.33
3192 3922 4.276678 TCACTCTGAAGATTTTTGTGCCTG 59.723 41.667 0.00 0.00 0.00 4.85
3207 3937 3.452474 GTGCCTGTGTTAAAATTGCACA 58.548 40.909 6.83 4.57 45.08 4.57
3211 3941 3.389221 CTGTGTTAAAATTGCACACCCC 58.611 45.455 10.85 0.00 40.16 4.95
3212 3942 2.766263 TGTGTTAAAATTGCACACCCCA 59.234 40.909 10.85 0.00 40.16 4.96
3215 3945 3.181471 TGTTAAAATTGCACACCCCACAG 60.181 43.478 0.00 0.00 0.00 3.66
3217 3947 1.047596 AAATTGCACACCCCACAGCA 61.048 50.000 0.00 0.00 34.79 4.41
3231 3961 3.219176 CACAGCATATGGTGGATCCTT 57.781 47.619 32.09 12.67 46.90 3.36
3232 3962 2.882761 CACAGCATATGGTGGATCCTTG 59.117 50.000 32.09 19.32 46.90 3.61
3233 3963 2.511218 ACAGCATATGGTGGATCCTTGT 59.489 45.455 32.09 11.35 46.90 3.16
3234 3964 3.716353 ACAGCATATGGTGGATCCTTGTA 59.284 43.478 32.09 1.42 46.90 2.41
3252 3982 8.679344 TCCTTGTATATATGCCTTTCCTATGA 57.321 34.615 0.00 0.00 0.00 2.15
3331 4061 5.531634 ACAATGGAACTTGTTGCAGTAATG 58.468 37.500 12.71 10.80 35.90 1.90
3361 4091 8.393366 CCTCAACTACAATCATACTTGTCAATG 58.607 37.037 0.00 0.00 39.88 2.82
3388 4133 5.072055 CCCCAATTACAGCATGACATCATA 58.928 41.667 0.00 0.00 39.69 2.15
3389 4134 5.048504 CCCCAATTACAGCATGACATCATAC 60.049 44.000 0.00 0.00 39.69 2.39
3401 4146 7.718314 AGCATGACATCATACTGTTGATAATGT 59.282 33.333 0.00 0.00 34.59 2.71
3411 4156 4.163458 TGTTGATAATGTTGCAGCACTG 57.837 40.909 5.00 0.00 0.00 3.66
3413 4158 4.161333 GTTGATAATGTTGCAGCACTGTC 58.839 43.478 5.00 3.23 0.00 3.51
3416 4161 2.267174 AATGTTGCAGCACTGTCTCT 57.733 45.000 5.00 0.00 0.00 3.10
3417 4162 1.520494 ATGTTGCAGCACTGTCTCTG 58.480 50.000 5.00 3.06 0.00 3.35
3418 4163 0.465287 TGTTGCAGCACTGTCTCTGA 59.535 50.000 0.00 0.00 32.26 3.27
3419 4164 1.134431 TGTTGCAGCACTGTCTCTGAA 60.134 47.619 0.00 0.00 32.26 3.02
3420 4165 2.149578 GTTGCAGCACTGTCTCTGAAT 58.850 47.619 0.00 0.00 32.26 2.57
3421 4166 2.090400 TGCAGCACTGTCTCTGAATC 57.910 50.000 9.89 0.00 32.26 2.52
3422 4167 1.345415 TGCAGCACTGTCTCTGAATCA 59.655 47.619 9.89 0.00 32.26 2.57
3423 4168 2.027469 TGCAGCACTGTCTCTGAATCAT 60.027 45.455 9.89 0.00 32.26 2.45
3425 4170 3.803231 GCAGCACTGTCTCTGAATCATAG 59.197 47.826 9.89 0.00 32.26 2.23
3428 4173 4.955450 AGCACTGTCTCTGAATCATAGAGT 59.045 41.667 0.00 0.00 41.83 3.24
3429 4174 5.421693 AGCACTGTCTCTGAATCATAGAGTT 59.578 40.000 0.00 0.00 41.83 3.01
3432 4181 7.201513 GCACTGTCTCTGAATCATAGAGTTTTC 60.202 40.741 0.00 0.00 41.83 2.29
3492 4241 4.836125 AGACAACTGCTGTTTTACATGG 57.164 40.909 6.20 0.00 38.84 3.66
3538 4287 8.677300 AGATTGAACGAAATAAATGCACAGTAT 58.323 29.630 0.00 0.00 0.00 2.12
3568 4317 0.179111 TATTGGCACTTCGAGCTCGG 60.179 55.000 33.98 21.94 40.29 4.63
3574 4323 2.268802 ACTTCGAGCTCGGCAGACA 61.269 57.895 33.98 12.67 40.29 3.41
3619 4368 1.048601 AAGAGTCTCTGGAACGCCAA 58.951 50.000 2.28 0.00 45.41 4.52
3639 4388 1.895131 ACAGCAATACCAAAAGGCCAG 59.105 47.619 5.01 0.00 0.00 4.85
3737 4486 2.964310 GCTGCTGCTCCCTCTGGAA 61.964 63.158 8.53 0.00 41.17 3.53
3832 4584 3.996621 CATGGTGGGGGCCAAGGT 61.997 66.667 4.39 0.00 42.48 3.50
3878 4630 0.916086 TCATCAATACCCTGGCGGTT 59.084 50.000 0.00 0.00 45.36 4.44
3921 4673 3.003068 CGCAGATTCTAAAGATGGCTTGG 59.997 47.826 0.00 0.00 33.79 3.61
3965 4717 3.772025 CCTCACTTCACCTGGTCTTATCT 59.228 47.826 0.00 0.00 0.00 1.98
3994 4746 7.326063 CCGTGGAAAGCTTAAAGTAAATTTCTG 59.674 37.037 0.00 0.00 32.01 3.02
4054 4806 7.486870 ACACTTGTAAAACCTGTTTTTCGATTC 59.513 33.333 12.73 0.58 42.22 2.52
4099 4851 5.757320 CGATGATCATTTTCTTCAGTAGCCT 59.243 40.000 10.14 0.00 0.00 4.58
4121 4873 5.220931 CCTGCCTAAAATTCTCCAATTCTCG 60.221 44.000 0.00 0.00 30.37 4.04
4130 4882 2.562738 TCTCCAATTCTCGACTCTTGCA 59.437 45.455 0.00 0.00 0.00 4.08
4184 4936 5.460646 CAGTGTTGCTTTGGATTCGTAATT 58.539 37.500 0.00 0.00 0.00 1.40
4186 4938 6.420604 CAGTGTTGCTTTGGATTCGTAATTTT 59.579 34.615 0.00 0.00 0.00 1.82
4187 4939 7.593273 CAGTGTTGCTTTGGATTCGTAATTTTA 59.407 33.333 0.00 0.00 0.00 1.52
4188 4940 8.303876 AGTGTTGCTTTGGATTCGTAATTTTAT 58.696 29.630 0.00 0.00 0.00 1.40
4210 4962 9.947189 TTTATAGAGGAGAAAGGGAACACTATA 57.053 33.333 0.00 0.00 0.00 1.31
4243 4995 2.580783 TGGCTAGGCTTTGGGTTTCTAT 59.419 45.455 18.18 0.00 0.00 1.98
4325 5078 6.899393 TCAAAGCAATGTGAATACTCCTTT 57.101 33.333 0.00 0.00 0.00 3.11
4326 5079 7.288810 TCAAAGCAATGTGAATACTCCTTTT 57.711 32.000 0.00 0.00 0.00 2.27
4508 5524 2.364647 CTCTGACATGGCTCTCAGCATA 59.635 50.000 0.00 0.00 44.75 3.14
4510 5526 3.198417 TCTGACATGGCTCTCAGCATAAA 59.802 43.478 0.00 0.00 44.75 1.40
4577 5596 3.120041 CCAACTTGTTTTACAAAGCCGG 58.880 45.455 0.00 0.00 37.69 6.13
4626 5645 2.618241 CAGGCTGACAGCAAAGTAACAA 59.382 45.455 27.87 0.00 44.75 2.83
4627 5646 2.618709 AGGCTGACAGCAAAGTAACAAC 59.381 45.455 27.87 7.29 44.75 3.32
4628 5647 2.357637 GGCTGACAGCAAAGTAACAACA 59.642 45.455 27.87 0.00 44.75 3.33
4629 5648 3.548818 GGCTGACAGCAAAGTAACAACAG 60.549 47.826 27.87 0.00 44.75 3.16
4630 5649 3.065371 GCTGACAGCAAAGTAACAACAGT 59.935 43.478 22.62 0.00 41.89 3.55
4714 5733 2.203938 TTCCCCTCAAGTCCGGCT 60.204 61.111 0.00 0.00 0.00 5.52
4799 5822 3.434940 AAAGGAGTACACATGGAACCC 57.565 47.619 0.00 0.00 0.00 4.11
4800 5823 2.038863 AGGAGTACACATGGAACCCA 57.961 50.000 0.00 0.00 38.19 4.51
4801 5824 1.909302 AGGAGTACACATGGAACCCAG 59.091 52.381 0.00 0.00 36.75 4.45
4802 5825 1.679032 GGAGTACACATGGAACCCAGC 60.679 57.143 0.00 0.00 36.75 4.85
4804 5827 1.423541 AGTACACATGGAACCCAGCAA 59.576 47.619 0.00 0.00 36.75 3.91
4807 5830 1.228862 ACATGGAACCCAGCAACCC 60.229 57.895 0.00 0.00 36.75 4.11
4808 5831 1.077265 CATGGAACCCAGCAACCCT 59.923 57.895 0.00 0.00 36.75 4.34
4904 5927 2.690778 GGCGTCCATTGACAGGCAC 61.691 63.158 9.26 0.00 41.85 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 7.307493 TGAATCGGTGAACATTTCTAGAATG 57.693 36.000 5.89 9.27 0.00 2.67
258 259 7.176165 TCTCAATTTTCTGAAATCATGAGCAGT 59.824 33.333 22.38 0.54 38.65 4.40
259 260 7.535997 TCTCAATTTTCTGAAATCATGAGCAG 58.464 34.615 22.38 13.82 38.65 4.24
261 262 7.485277 CACTCTCAATTTTCTGAAATCATGAGC 59.515 37.037 22.38 0.00 38.65 4.26
262 263 7.968956 CCACTCTCAATTTTCTGAAATCATGAG 59.031 37.037 21.77 21.77 39.38 2.90
263 264 7.449395 ACCACTCTCAATTTTCTGAAATCATGA 59.551 33.333 3.31 0.00 34.44 3.07
274 275 7.221067 CGATACTCAGTACCACTCTCAATTTTC 59.779 40.741 0.00 0.00 0.00 2.29
288 289 3.633235 CTGCATCACCGATACTCAGTAC 58.367 50.000 0.00 0.00 0.00 2.73
291 292 1.202452 TGCTGCATCACCGATACTCAG 60.202 52.381 0.00 0.00 0.00 3.35
294 295 2.401583 TTTGCTGCATCACCGATACT 57.598 45.000 1.84 0.00 0.00 2.12
295 296 3.181497 ACATTTTGCTGCATCACCGATAC 60.181 43.478 1.84 0.00 0.00 2.24
297 298 1.820519 ACATTTTGCTGCATCACCGAT 59.179 42.857 1.84 0.00 0.00 4.18
300 301 2.728690 TCACATTTTGCTGCATCACC 57.271 45.000 1.84 0.00 0.00 4.02
301 302 3.382855 TGTTCACATTTTGCTGCATCAC 58.617 40.909 1.84 0.00 0.00 3.06
307 308 2.070783 GGCCATGTTCACATTTTGCTG 58.929 47.619 0.00 0.00 33.61 4.41
321 322 5.722263 TGTCTCAAAACAAATATGGCCATG 58.278 37.500 29.04 15.73 0.00 3.66
330 331 7.599998 GGCTATGTTCATTGTCTCAAAACAAAT 59.400 33.333 4.60 0.00 42.10 2.32
334 335 5.858581 GTGGCTATGTTCATTGTCTCAAAAC 59.141 40.000 1.45 0.00 0.00 2.43
336 337 5.316167 AGTGGCTATGTTCATTGTCTCAAA 58.684 37.500 1.45 0.00 0.00 2.69
337 338 4.910195 AGTGGCTATGTTCATTGTCTCAA 58.090 39.130 1.45 0.00 0.00 3.02
338 339 4.558226 AGTGGCTATGTTCATTGTCTCA 57.442 40.909 1.45 0.00 0.00 3.27
339 340 6.818644 TCTTTAGTGGCTATGTTCATTGTCTC 59.181 38.462 1.45 0.00 0.00 3.36
340 341 6.711277 TCTTTAGTGGCTATGTTCATTGTCT 58.289 36.000 1.45 0.00 0.00 3.41
341 342 6.985188 TCTTTAGTGGCTATGTTCATTGTC 57.015 37.500 0.00 0.00 0.00 3.18
342 343 7.944729 AATCTTTAGTGGCTATGTTCATTGT 57.055 32.000 0.00 0.00 0.00 2.71
343 344 9.888878 CATAATCTTTAGTGGCTATGTTCATTG 57.111 33.333 0.00 0.00 0.00 2.82
344 345 9.851686 TCATAATCTTTAGTGGCTATGTTCATT 57.148 29.630 0.00 0.00 0.00 2.57
378 379 2.883574 CCCGTGCGTTATAACAGAAGA 58.116 47.619 15.67 0.00 0.00 2.87
379 380 1.326548 GCCCGTGCGTTATAACAGAAG 59.673 52.381 15.67 3.63 0.00 2.85
396 397 0.678684 TAACGCTAGCAAAAGGGCCC 60.679 55.000 16.46 16.46 32.92 5.80
586 589 2.417516 GCAGCGGCGATAGAGGAA 59.582 61.111 12.98 0.00 39.76 3.36
684 688 1.877672 TTCCCCCGTCTGCTAGGGTA 61.878 60.000 0.00 0.00 46.17 3.69
692 696 1.452108 GCCTGATTTCCCCCGTCTG 60.452 63.158 0.00 0.00 0.00 3.51
748 752 2.997986 GTCGAGAAACCCTAATTTCGCA 59.002 45.455 0.00 0.00 42.37 5.10
786 790 4.808558 TGCGGGAAGAAAAGAAATTCATG 58.191 39.130 0.00 0.00 0.00 3.07
812 816 6.238347 GCCACCGAAAAGAAATTCATGTTTTT 60.238 34.615 0.00 0.00 0.00 1.94
813 817 5.236263 GCCACCGAAAAGAAATTCATGTTTT 59.764 36.000 0.00 0.00 0.00 2.43
814 818 4.749598 GCCACCGAAAAGAAATTCATGTTT 59.250 37.500 0.00 0.00 0.00 2.83
815 819 4.306600 GCCACCGAAAAGAAATTCATGTT 58.693 39.130 0.00 0.00 0.00 2.71
816 820 3.611530 CGCCACCGAAAAGAAATTCATGT 60.612 43.478 0.00 0.00 36.29 3.21
817 821 2.916716 CGCCACCGAAAAGAAATTCATG 59.083 45.455 0.00 0.00 36.29 3.07
818 822 2.671070 GCGCCACCGAAAAGAAATTCAT 60.671 45.455 0.00 0.00 36.29 2.57
819 823 1.335506 GCGCCACCGAAAAGAAATTCA 60.336 47.619 0.00 0.00 36.29 2.57
820 824 1.336877 GCGCCACCGAAAAGAAATTC 58.663 50.000 0.00 0.00 36.29 2.17
837 841 3.062466 TCCAGTCTCAGTCCCGCG 61.062 66.667 0.00 0.00 0.00 6.46
902 948 1.803519 CACTCGAGAGCACCGAAGC 60.804 63.158 21.68 0.00 35.48 3.86
930 976 1.875813 CACAGATCTCGGCGCTGTC 60.876 63.158 17.37 6.67 40.63 3.51
963 1009 2.350964 GGGCGCAAATTTCGAGTGTAAA 60.351 45.455 10.83 0.00 0.00 2.01
1074 1124 8.138365 ACACATAGGTATGCAACTTTATAACG 57.862 34.615 0.00 0.00 37.19 3.18
1094 1144 5.466058 TGATTCCGTAACAACGTTTACACAT 59.534 36.000 0.00 0.00 32.32 3.21
1120 1170 7.364320 GGTTTTACCATGCCAAACTACCATATT 60.364 37.037 10.62 0.00 38.42 1.28
1140 1378 6.889177 TGAATGCATCATCAGGTAAGGTTTTA 59.111 34.615 0.00 0.00 31.50 1.52
1180 1418 7.639113 TTCTAAGATTGAACGGCCAAATTAT 57.361 32.000 2.24 0.00 0.00 1.28
1240 1478 6.299805 TCTAACCTGAATGTGCAAGATACT 57.700 37.500 0.00 0.00 0.00 2.12
1272 1510 3.721706 CCCTGTCCCTGTCCCTGC 61.722 72.222 0.00 0.00 0.00 4.85
1284 1522 2.203998 CCCTGTCCCTGTCCCTGT 60.204 66.667 0.00 0.00 0.00 4.00
1289 1527 0.107165 GTATTGCCCCTGTCCCTGTC 60.107 60.000 0.00 0.00 0.00 3.51
1290 1528 1.910580 CGTATTGCCCCTGTCCCTGT 61.911 60.000 0.00 0.00 0.00 4.00
1291 1529 1.153168 CGTATTGCCCCTGTCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
1292 1530 2.375345 CCGTATTGCCCCTGTCCCT 61.375 63.158 0.00 0.00 0.00 4.20
1293 1531 2.192175 CCGTATTGCCCCTGTCCC 59.808 66.667 0.00 0.00 0.00 4.46
1294 1532 2.192175 CCCGTATTGCCCCTGTCC 59.808 66.667 0.00 0.00 0.00 4.02
1335 1573 2.191128 AGTGATGCAACTGGGAAGAC 57.809 50.000 0.00 0.00 0.00 3.01
1383 1621 6.449956 TCTTCCAGGGTAACTATTATCAGGT 58.550 40.000 0.00 0.00 0.00 4.00
1482 1720 2.315925 TCTGATTCTGGATGTTCGGC 57.684 50.000 0.00 0.00 0.00 5.54
1488 1726 7.575155 GCATATGGTGAAATCTGATTCTGGATG 60.575 40.741 4.56 3.56 0.00 3.51
1521 1759 6.041182 GTGTGGGTACATACTACATACCATCA 59.959 42.308 0.00 0.00 40.23 3.07
1524 1762 4.338964 CGTGTGGGTACATACTACATACCA 59.661 45.833 0.00 0.00 40.23 3.25
1539 1819 0.467290 ATTGAAACAGGCGTGTGGGT 60.467 50.000 13.63 1.42 36.84 4.51
1608 1907 2.640332 TCCAAAGTGTAGGGTGCACATA 59.360 45.455 20.43 8.09 39.17 2.29
1611 1910 1.235724 GTCCAAAGTGTAGGGTGCAC 58.764 55.000 8.80 8.80 37.13 4.57
1647 1947 9.927668 CAACCACTAATATGTCCAAAATTTCTT 57.072 29.630 0.00 0.00 0.00 2.52
1653 1953 7.094549 GCTACACAACCACTAATATGTCCAAAA 60.095 37.037 0.00 0.00 0.00 2.44
1762 2062 3.361794 CTACATCAGGATCCGTCAGTG 57.638 52.381 5.98 5.21 0.00 3.66
1833 2133 4.389374 TGCTTTTCTAGACCAACCTTCAG 58.611 43.478 0.00 0.00 0.00 3.02
1909 2209 5.049398 ACGAGGAAGATTATAGTCATCGC 57.951 43.478 10.25 0.00 46.32 4.58
2059 2360 0.253327 GGCAGGTAGGAAGGACAAGG 59.747 60.000 0.00 0.00 0.00 3.61
2066 2367 4.553330 TCTACTTTTGGCAGGTAGGAAG 57.447 45.455 17.69 7.47 35.15 3.46
2081 2382 6.360370 TCTGCAAGTCCAGTTAATCTACTT 57.640 37.500 0.00 0.00 34.47 2.24
2177 2478 9.948964 CCTGTCAATAATAGGACATATCAATGA 57.051 33.333 0.00 0.00 42.62 2.57
2178 2479 9.948964 TCCTGTCAATAATAGGACATATCAATG 57.051 33.333 0.00 0.00 40.14 2.82
2181 2482 9.159254 ACTTCCTGTCAATAATAGGACATATCA 57.841 33.333 0.00 0.00 44.30 2.15
2184 2485 9.656323 AGTACTTCCTGTCAATAATAGGACATA 57.344 33.333 0.00 0.00 44.30 2.29
2185 2486 8.554490 AGTACTTCCTGTCAATAATAGGACAT 57.446 34.615 0.00 0.00 44.30 3.06
2186 2487 7.973048 AGTACTTCCTGTCAATAATAGGACA 57.027 36.000 0.00 0.00 44.30 4.02
2189 2490 9.930693 GGATAAGTACTTCCTGTCAATAATAGG 57.069 37.037 12.39 0.00 37.60 2.57
2197 2498 9.613428 CATAAAATGGATAAGTACTTCCTGTCA 57.387 33.333 12.39 5.56 32.95 3.58
2198 2499 9.832445 TCATAAAATGGATAAGTACTTCCTGTC 57.168 33.333 12.39 6.54 32.95 3.51
2225 2526 9.933723 GCAAAAGGCATATGATATTAAATCCTT 57.066 29.630 6.97 3.37 43.97 3.36
2280 2581 7.395772 TCAAAAGGCTAATCATACCACAATTGA 59.604 33.333 13.59 0.00 0.00 2.57
2285 2586 5.815581 ACTCAAAAGGCTAATCATACCACA 58.184 37.500 0.00 0.00 0.00 4.17
2286 2587 7.335924 TGTTACTCAAAAGGCTAATCATACCAC 59.664 37.037 0.00 0.00 0.00 4.16
2316 2617 3.081804 GTTTCCCAACATCTACCTGTGG 58.918 50.000 0.00 0.00 32.54 4.17
2339 2640 9.777575 GTTTTTAAGTAGCAACACAAAACTAGA 57.222 29.630 0.00 0.00 33.07 2.43
2340 2641 9.783256 AGTTTTTAAGTAGCAACACAAAACTAG 57.217 29.630 5.54 0.00 38.39 2.57
2357 2658 9.549078 GGGGAGAAGACATCTATAGTTTTTAAG 57.451 37.037 0.00 0.00 38.96 1.85
2358 2659 9.280456 AGGGGAGAAGACATCTATAGTTTTTAA 57.720 33.333 0.00 0.00 38.96 1.52
2361 2662 7.182930 ACAAGGGGAGAAGACATCTATAGTTTT 59.817 37.037 0.00 0.00 38.96 2.43
2418 2719 6.639686 GGCATGCAAAATGAGAATGTACATAG 59.360 38.462 21.36 0.00 0.00 2.23
2454 2755 6.047231 GGATTAATGTGGGTGTGTACTAGAC 58.953 44.000 0.00 0.00 0.00 2.59
2455 2756 5.722441 TGGATTAATGTGGGTGTGTACTAGA 59.278 40.000 0.00 0.00 0.00 2.43
2456 2757 5.984725 TGGATTAATGTGGGTGTGTACTAG 58.015 41.667 0.00 0.00 0.00 2.57
2457 2758 6.569127 ATGGATTAATGTGGGTGTGTACTA 57.431 37.500 0.00 0.00 0.00 1.82
2458 2759 4.919774 TGGATTAATGTGGGTGTGTACT 57.080 40.909 0.00 0.00 0.00 2.73
2459 2760 7.817418 AATATGGATTAATGTGGGTGTGTAC 57.183 36.000 0.00 0.00 0.00 2.90
2460 2761 8.719596 ACTAATATGGATTAATGTGGGTGTGTA 58.280 33.333 0.00 0.00 0.00 2.90
2461 2762 7.582719 ACTAATATGGATTAATGTGGGTGTGT 58.417 34.615 0.00 0.00 0.00 3.72
2466 2767 7.280876 CCGATGACTAATATGGATTAATGTGGG 59.719 40.741 0.00 0.00 0.00 4.61
2491 2792 0.872388 GATGTGGGTTGTTCACGTCC 59.128 55.000 5.42 0.00 42.30 4.79
2495 2796 1.680735 TGCAAGATGTGGGTTGTTCAC 59.319 47.619 0.00 0.00 35.82 3.18
2543 2844 9.515226 TGGTATTAAATCCTATATTGGTTGCTC 57.485 33.333 3.01 0.00 0.00 4.26
2586 2888 7.751768 GGAGAACCCCATTTCAATATCTAAG 57.248 40.000 0.00 0.00 0.00 2.18
2672 2976 2.750888 GGCGTTTAAGGGCAGAGCG 61.751 63.158 6.34 0.00 0.00 5.03
2676 2980 3.810896 GCGGGCGTTTAAGGGCAG 61.811 66.667 12.87 9.88 0.00 4.85
2725 3386 4.107051 ACGCCGCTTCAATGCAGC 62.107 61.111 0.00 0.00 33.43 5.25
2727 3388 3.787676 CGACGCCGCTTCAATGCA 61.788 61.111 0.00 0.00 0.00 3.96
2757 3418 5.429130 GCTGGAACACTACTTAAATAGGCT 58.571 41.667 0.00 0.00 0.00 4.58
2769 3430 1.605058 GAGGAGGCGCTGGAACACTA 61.605 60.000 7.64 0.00 0.00 2.74
2789 3474 3.056328 GTGGAGAGGGTTTGCGGC 61.056 66.667 0.00 0.00 0.00 6.53
2791 3476 1.376037 GGAGTGGAGAGGGTTTGCG 60.376 63.158 0.00 0.00 0.00 4.85
2813 3498 4.731612 CTCCGTCGCTGCTGCTGT 62.732 66.667 14.03 0.00 36.97 4.40
2856 3551 0.667487 CATACGCATGGCCGTCCTAG 60.667 60.000 0.00 0.00 42.20 3.02
2861 3556 2.108976 CCTCATACGCATGGCCGT 59.891 61.111 0.00 0.00 44.62 5.68
2922 3617 9.977762 GACGATATTTTGTCCGTTTAACTATTT 57.022 29.630 0.00 0.00 35.22 1.40
2923 3618 8.606602 GGACGATATTTTGTCCGTTTAACTATT 58.393 33.333 6.80 0.00 44.68 1.73
2924 3619 8.134905 GGACGATATTTTGTCCGTTTAACTAT 57.865 34.615 6.80 0.00 44.68 2.12
2963 3658 7.328277 TGGAACCGGATAAAAGTTGAATATG 57.672 36.000 9.46 0.00 0.00 1.78
2968 3663 4.912586 TCATGGAACCGGATAAAAGTTGA 58.087 39.130 9.46 0.00 0.00 3.18
2995 3711 3.128938 ACGAAAATTGAACCAAACGGACA 59.871 39.130 0.00 0.00 0.00 4.02
3005 3721 6.083137 GCACGCATTTTAAACGAAAATTGAAC 59.917 34.615 3.97 0.00 43.83 3.18
3011 3727 2.468040 CCGCACGCATTTTAAACGAAAA 59.532 40.909 3.97 0.00 41.24 2.29
3015 3731 0.972013 GTCCGCACGCATTTTAAACG 59.028 50.000 0.00 0.00 0.00 3.60
3016 3732 0.972013 CGTCCGCACGCATTTTAAAC 59.028 50.000 0.00 0.00 39.69 2.01
3018 3734 1.080298 ATCGTCCGCACGCATTTTAA 58.920 45.000 0.00 0.00 46.28 1.52
3020 3736 1.062002 CTAATCGTCCGCACGCATTTT 59.938 47.619 0.00 0.00 46.28 1.82
3036 3752 2.024080 ACATCCAACCATGTGCCCTAAT 60.024 45.455 0.00 0.00 35.57 1.73
3047 3763 0.321564 CGGAAGCAGACATCCAACCA 60.322 55.000 0.00 0.00 33.01 3.67
3057 3773 2.049156 CGCAGACACGGAAGCAGA 60.049 61.111 0.00 0.00 0.00 4.26
3066 3782 1.589196 GCTATCCGTCCGCAGACAC 60.589 63.158 0.20 0.00 43.73 3.67
3067 3783 2.805546 GCTATCCGTCCGCAGACA 59.194 61.111 0.20 0.00 43.73 3.41
3084 3813 3.792736 TCCCCCAAATCGGCCTCG 61.793 66.667 0.00 0.00 37.82 4.63
3086 3815 4.109675 CGTCCCCCAAATCGGCCT 62.110 66.667 0.00 0.00 0.00 5.19
3090 3819 4.770874 ACGCCGTCCCCCAAATCG 62.771 66.667 0.00 0.00 0.00 3.34
3099 3828 3.195698 GCATCTCCAACGCCGTCC 61.196 66.667 0.00 0.00 0.00 4.79
3108 3838 2.764269 AGCTTACTAAGGGCATCTCCA 58.236 47.619 0.00 0.00 36.21 3.86
3124 3854 8.049721 ACCAAGCACTAAGATAAATCTAAGCTT 58.950 33.333 3.48 3.48 38.73 3.74
3125 3855 7.497249 CACCAAGCACTAAGATAAATCTAAGCT 59.503 37.037 0.00 0.00 35.76 3.74
3128 3858 8.946085 CAACACCAAGCACTAAGATAAATCTAA 58.054 33.333 0.00 0.00 35.76 2.10
3151 3881 7.604164 TCAGAGTGACTCAATTCCTTAATCAAC 59.396 37.037 15.86 0.00 32.06 3.18
3155 3885 7.911651 TCTTCAGAGTGACTCAATTCCTTAAT 58.088 34.615 15.86 0.00 32.06 1.40
3161 3891 8.348507 ACAAAAATCTTCAGAGTGACTCAATTC 58.651 33.333 15.86 0.00 32.06 2.17
3168 3898 4.276926 AGGCACAAAAATCTTCAGAGTGAC 59.723 41.667 0.00 0.00 33.86 3.67
3175 3905 4.734398 AACACAGGCACAAAAATCTTCA 57.266 36.364 0.00 0.00 0.00 3.02
3188 3918 2.799978 GGTGTGCAATTTTAACACAGGC 59.200 45.455 13.97 0.00 44.41 4.85
3192 3922 3.127589 GTGGGGTGTGCAATTTTAACAC 58.872 45.455 0.00 6.53 42.75 3.32
3207 3937 1.614711 CCACCATATGCTGTGGGGT 59.385 57.895 18.54 0.00 46.67 4.95
3211 3941 2.882761 CAAGGATCCACCATATGCTGTG 59.117 50.000 15.82 1.12 42.04 3.66
3212 3942 2.511218 ACAAGGATCCACCATATGCTGT 59.489 45.455 15.82 0.10 42.04 4.40
3215 3945 7.173907 GCATATATACAAGGATCCACCATATGC 59.826 40.741 23.20 23.20 41.60 3.14
3217 3947 7.573994 AGGCATATATACAAGGATCCACCATAT 59.426 37.037 15.82 12.66 42.04 1.78
3231 3961 8.880244 AGTTGTCATAGGAAAGGCATATATACA 58.120 33.333 0.00 0.00 0.00 2.29
3232 3962 9.726438 AAGTTGTCATAGGAAAGGCATATATAC 57.274 33.333 0.00 0.00 0.00 1.47
3234 3964 9.646522 AAAAGTTGTCATAGGAAAGGCATATAT 57.353 29.630 0.00 0.00 0.00 0.86
3331 4061 6.149474 ACAAGTATGATTGTAGTTGAGGCAAC 59.851 38.462 8.11 2.22 41.53 4.17
3361 4091 1.824230 TCATGCTGTAATTGGGGCAAC 59.176 47.619 5.44 0.00 38.21 4.17
3388 4133 3.822735 AGTGCTGCAACATTATCAACAGT 59.177 39.130 2.77 0.00 0.00 3.55
3389 4134 4.163552 CAGTGCTGCAACATTATCAACAG 58.836 43.478 2.77 0.00 0.00 3.16
3393 4138 3.678289 AGACAGTGCTGCAACATTATCA 58.322 40.909 2.77 0.00 0.00 2.15
3401 4146 2.224354 TGATTCAGAGACAGTGCTGCAA 60.224 45.455 2.77 0.00 32.27 4.08
3460 4209 8.798859 AAACAGCAGTTGTCTTTGATAGATAT 57.201 30.769 0.00 0.00 39.73 1.63
3463 4212 6.942532 AAAACAGCAGTTGTCTTTGATAGA 57.057 33.333 0.00 0.00 39.73 1.98
3464 4213 7.639039 TGTAAAACAGCAGTTGTCTTTGATAG 58.361 34.615 0.00 0.00 39.73 2.08
3465 4214 7.561021 TGTAAAACAGCAGTTGTCTTTGATA 57.439 32.000 0.00 0.00 39.73 2.15
3466 4215 6.449635 TGTAAAACAGCAGTTGTCTTTGAT 57.550 33.333 0.00 0.00 39.73 2.57
3467 4216 5.888691 TGTAAAACAGCAGTTGTCTTTGA 57.111 34.783 0.00 0.00 39.73 2.69
3468 4217 5.459762 CCATGTAAAACAGCAGTTGTCTTTG 59.540 40.000 0.00 0.00 39.73 2.77
3469 4218 5.127031 ACCATGTAAAACAGCAGTTGTCTTT 59.873 36.000 0.00 0.00 39.73 2.52
3470 4219 4.644685 ACCATGTAAAACAGCAGTTGTCTT 59.355 37.500 0.00 0.00 39.73 3.01
3538 4287 4.631377 CGAAGTGCCAATAGTTTCTCATGA 59.369 41.667 0.00 0.00 0.00 3.07
3568 4317 1.678627 TCTTCTCGATAGGCTGTCTGC 59.321 52.381 9.66 0.00 41.94 4.26
3574 4323 3.244044 GCAGGAATTCTTCTCGATAGGCT 60.244 47.826 5.23 0.00 0.00 4.58
3619 4368 1.895131 CTGGCCTTTTGGTATTGCTGT 59.105 47.619 3.32 0.00 42.99 4.40
3664 4413 1.839747 ACGTGGTTCCCTAGGCACA 60.840 57.895 15.06 4.03 0.00 4.57
3711 4460 2.187424 GAGCAGCAGCAGGAGGAG 59.813 66.667 3.17 0.00 45.49 3.69
3712 4461 3.397439 GGAGCAGCAGCAGGAGGA 61.397 66.667 3.17 0.00 45.49 3.71
3713 4462 4.486503 GGGAGCAGCAGCAGGAGG 62.487 72.222 3.17 0.00 45.49 4.30
3737 4486 3.320541 CGATGAGCCTCTCCATAAGAACT 59.679 47.826 0.00 0.00 32.23 3.01
3832 4584 0.726827 GCTCAAAACCATGATCGCGA 59.273 50.000 13.09 13.09 0.00 5.87
3878 4630 1.134521 CCCGCCAGAGTTATAAGCACA 60.135 52.381 0.00 0.00 0.00 4.57
3921 4673 3.383761 CCAAAATGGCTGACTGTTCAAC 58.616 45.455 0.00 0.00 0.00 3.18
3965 4717 6.696441 TTTACTTTAAGCTTTCCACGGAAA 57.304 33.333 3.20 10.72 41.22 3.13
3994 4746 3.431068 GGAGGCTGGAACTAAGCTTCTAC 60.431 52.174 0.00 0.00 44.00 2.59
4054 4806 3.621794 GCTTGAATAAATAGCGGCACAG 58.378 45.455 1.45 0.00 0.00 3.66
4099 4851 5.354234 GTCGAGAATTGGAGAATTTTAGGCA 59.646 40.000 0.00 0.00 31.58 4.75
4121 4873 2.693069 ACAGCTACATGTGCAAGAGTC 58.307 47.619 9.11 0.00 30.46 3.36
4130 4882 3.796504 GCAAAGCACAAACAGCTACATGT 60.797 43.478 2.69 2.69 42.53 3.21
4184 4936 8.855804 ATAGTGTTCCCTTTCTCCTCTATAAA 57.144 34.615 0.00 0.00 0.00 1.40
4186 4938 9.535170 CATATAGTGTTCCCTTTCTCCTCTATA 57.465 37.037 0.00 0.00 0.00 1.31
4187 4939 7.456269 CCATATAGTGTTCCCTTTCTCCTCTAT 59.544 40.741 0.00 0.00 0.00 1.98
4188 4940 6.782988 CCATATAGTGTTCCCTTTCTCCTCTA 59.217 42.308 0.00 0.00 0.00 2.43
4195 4947 5.112129 ACACCCATATAGTGTTCCCTTTC 57.888 43.478 5.15 0.00 46.07 2.62
4210 4962 1.923356 CCTAGCCAAACAACACCCAT 58.077 50.000 0.00 0.00 0.00 4.00
4243 4995 8.270030 AGCAGATAAGCCATATGATATAAGCAA 58.730 33.333 3.65 0.00 34.23 3.91
4508 5524 2.309528 TTCTCACTCAGTGCGTGTTT 57.690 45.000 12.73 0.00 32.98 2.83
4510 5526 1.788258 CATTCTCACTCAGTGCGTGT 58.212 50.000 12.73 0.00 32.98 4.49
4577 5596 7.586300 CGCCTGTTTTATATATTTGCAGTACAC 59.414 37.037 0.00 0.00 0.00 2.90
4714 5733 5.011125 CAGGGAGTAGAAACAGTGAAGAGAA 59.989 44.000 0.00 0.00 0.00 2.87
4762 5781 2.223923 CCTTTACCTCTCTGGAGCATCG 60.224 54.545 0.00 0.00 38.21 3.84
4799 5822 0.693049 ACAAGTAGGGAGGGTTGCTG 59.307 55.000 0.00 0.00 0.00 4.41
4800 5823 2.337359 TACAAGTAGGGAGGGTTGCT 57.663 50.000 0.00 0.00 0.00 3.91
4801 5824 2.238898 ACATACAAGTAGGGAGGGTTGC 59.761 50.000 0.00 0.00 0.00 4.17
4802 5825 4.569719 AACATACAAGTAGGGAGGGTTG 57.430 45.455 0.00 0.00 0.00 3.77
4804 5827 4.850386 AGAAAACATACAAGTAGGGAGGGT 59.150 41.667 0.00 0.00 0.00 4.34
4807 5830 6.371825 GGTGAAGAAAACATACAAGTAGGGAG 59.628 42.308 0.00 0.00 0.00 4.30
4808 5831 6.043938 AGGTGAAGAAAACATACAAGTAGGGA 59.956 38.462 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.