Multiple sequence alignment - TraesCS5D01G299700

Loading Multiple Alignment...

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 TraesCS5D01G299700 chr5D 100.000 4004 0 0 1 4004 397026286 397030289 0.000000e+00 7395.0
1 TraesCS5D01G299700 chr5D 96.907 485 13 2 3520 4002 342525685 342526169 0.000000e+00 811.0
2 TraesCS5D01G299700 chr5A 92.268 1914 108 15 1640 3519 502581596 502583503 0.000000e+00 2678.0
3 TraesCS5D01G299700 chr5A 89.645 1014 83 13 602 1597 502580577 502581586 0.000000e+00 1271.0
4 TraesCS5D01G299700 chr5A 86.434 258 32 1 285 542 502580365 502580619 3.050000e-71 279.0
5 TraesCS5D01G299700 chr5A 79.288 309 30 19 16 293 502555608 502555913 6.830000e-43 185.0
6 TraesCS5D01G299700 chr5A 87.097 155 5 8 2561 2700 51477788 51477634 1.150000e-35 161.0
7 TraesCS5D01G299700 chr5A 95.918 98 2 1 709 804 702637727 702637630 1.490000e-34 158.0
8 TraesCS5D01G299700 chr5A 80.952 168 11 10 2556 2708 409327621 409327460 3.270000e-21 113.0
9 TraesCS5D01G299700 chr5B 86.256 2401 222 67 189 2542 477422328 477424667 0.000000e+00 2507.0
10 TraesCS5D01G299700 chr5B 95.976 497 17 3 3511 4004 318172790 318173286 0.000000e+00 804.0
11 TraesCS5D01G299700 chr5B 80.322 559 76 22 2720 3262 477424677 477425217 3.750000e-105 392.0
12 TraesCS5D01G299700 chr5B 91.954 174 12 1 1 174 477421308 477421479 4.000000e-60 243.0
13 TraesCS5D01G299700 chr5B 86.486 185 8 6 2535 2704 6651892 6651710 1.900000e-43 187.0
14 TraesCS5D01G299700 chr5B 77.419 279 39 11 1999 2273 477960247 477959989 1.160000e-30 145.0
15 TraesCS5D01G299700 chr4D 97.143 490 12 2 3517 4004 50231536 50231047 0.000000e+00 826.0
16 TraesCS5D01G299700 chr4D 95.749 494 19 2 3510 4001 108101228 108101721 0.000000e+00 795.0
17 TraesCS5D01G299700 chr4D 84.615 182 11 6 2542 2706 341523972 341523791 8.900000e-37 165.0
18 TraesCS5D01G299700 chr4D 96.000 100 2 2 712 811 482238094 482238191 1.150000e-35 161.0
19 TraesCS5D01G299700 chr4D 94.231 104 2 4 710 809 506979842 506979739 5.360000e-34 156.0
20 TraesCS5D01G299700 chr4D 91.892 111 6 3 692 800 506899213 506899322 6.930000e-33 152.0
21 TraesCS5D01G299700 chr4D 95.604 91 2 2 710 798 506930250 506930340 1.160000e-30 145.0
22 TraesCS5D01G299700 chr4D 93.814 97 3 3 709 802 506366834 506366738 4.170000e-30 143.0
23 TraesCS5D01G299700 chr1D 97.131 488 12 2 3519 4004 250741387 250740900 0.000000e+00 822.0
24 TraesCS5D01G299700 chr1D 96.667 90 0 2 711 797 412087592 412087681 3.220000e-31 147.0
25 TraesCS5D01G299700 chr1D 96.512 86 3 0 722 807 75541296 75541381 4.170000e-30 143.0
26 TraesCS5D01G299700 chr1D 95.556 90 2 2 716 804 324621762 324621850 4.170000e-30 143.0
27 TraesCS5D01G299700 chr7D 96.721 488 14 2 3519 4004 136708147 136707660 0.000000e+00 811.0
28 TraesCS5D01G299700 chr1B 96.516 488 15 2 3519 4004 305284872 305284385 0.000000e+00 806.0
29 TraesCS5D01G299700 chr1B 87.500 176 7 7 2543 2704 246770874 246770700 5.280000e-44 189.0
30 TraesCS5D01G299700 chr1B 96.739 92 1 2 711 801 119050026 119050116 6.930000e-33 152.0
31 TraesCS5D01G299700 chr1B 96.667 90 1 2 710 797 555636601 555636690 8.970000e-32 148.0
32 TraesCS5D01G299700 chr3D 96.334 491 14 4 3518 4004 89546405 89546895 0.000000e+00 804.0
33 TraesCS5D01G299700 chr3D 86.170 188 10 5 2534 2705 422475509 422475696 5.280000e-44 189.0
34 TraesCS5D01G299700 chr7B 83.174 523 68 19 3495 4004 350882142 350881627 1.010000e-125 460.0
35 TraesCS5D01G299700 chrUn 94.309 123 7 0 2540 2662 237212880 237212758 5.280000e-44 189.0
36 TraesCS5D01G299700 chrUn 95.349 86 2 1 713 796 5443412 5443497 6.980000e-28 135.0
37 TraesCS5D01G299700 chr6B 87.151 179 8 7 2542 2706 602841102 602840925 5.280000e-44 189.0
38 TraesCS5D01G299700 chr6B 86.857 175 9 3 2535 2695 432492789 432492963 2.460000e-42 183.0
39 TraesCS5D01G299700 chr1A 88.166 169 6 3 2542 2696 208903790 208903958 5.280000e-44 189.0
40 TraesCS5D01G299700 chr1A 87.429 175 8 2 2542 2702 249045036 249045210 5.280000e-44 189.0
41 TraesCS5D01G299700 chr1A 97.778 90 0 2 710 797 508639727 508639816 1.930000e-33 154.0
42 TraesCS5D01G299700 chr7A 94.309 123 6 1 2541 2662 602713459 602713581 1.900000e-43 187.0
43 TraesCS5D01G299700 chr7A 85.870 184 9 9 2543 2709 223677550 223677367 3.180000e-41 180.0
44 TraesCS5D01G299700 chr2A 91.603 131 10 1 2533 2662 482696519 482696649 3.180000e-41 180.0
45 TraesCS5D01G299700 chr2A 95.789 95 3 1 711 804 501848384 501848290 6.930000e-33 152.0
46 TraesCS5D01G299700 chr4B 84.699 183 10 6 2542 2706 423360087 423359905 2.480000e-37 167.0
47 TraesCS5D01G299700 chr4B 97.826 92 1 1 712 803 612029770 612029860 1.490000e-34 158.0
48 TraesCS5D01G299700 chr2D 100.000 89 0 0 716 804 371161173 371161085 8.900000e-37 165.0
49 TraesCS5D01G299700 chr2D 93.878 98 5 1 700 796 626127255 626127352 3.220000e-31 147.0
50 TraesCS5D01G299700 chr2B 97.826 92 1 1 711 802 440215634 440215544 1.490000e-34 158.0
51 TraesCS5D01G299700 chr2B 95.000 100 4 1 700 798 767745192 767745291 5.360000e-34 156.0
52 TraesCS5D01G299700 chr6D 94.624 93 3 2 709 800 407474578 407474669 4.170000e-30 143.0
53 TraesCS5D01G299700 chr4A 97.561 41 0 1 2665 2705 18116760 18116799 7.180000e-08 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 TraesCS5D01G299700 chr5D 397026286 397030289 4003 False 7395.000000 7395 100.000000 1 4004 1 chr5D.!!$F2 4003
1 TraesCS5D01G299700 chr5A 502580365 502583503 3138 False 1409.333333 2678 89.449000 285 3519 3 chr5A.!!$F2 3234
2 TraesCS5D01G299700 chr5B 477421308 477425217 3909 False 1047.333333 2507 86.177333 1 3262 3 chr5B.!!$F2 3261
3 TraesCS5D01G299700 chr7B 350881627 350882142 515 True 460.000000 460 83.174000 3495 4004 1 chr7B.!!$R1 509

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
412 1249 1.112113 TAGAGGCTTCATCGACCCAC 58.888 55.0 0.00 0.0 0.0 4.61 F
1183 2064 0.818445 CCTGCCATGGTCTGATCTGC 60.818 60.0 14.67 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 2220 1.152881 CGGGTAGTAGTAGGGCGGT 60.153 63.158 0.00 0.0 0.00 5.68 R
3051 4004 0.541392 TTCACTGGATACTGCGGCAT 59.459 50.000 1.75 0.0 39.52 4.40 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
27 28 1.895798 CCAGAGTGGCAAGTAGAGTGA 59.104 52.381 0.00 0.00 0.00 3.41
50 51 1.922545 GTGTATTCACGGGTTCGCTAC 59.077 52.381 0.00 0.00 40.63 3.58
51 52 1.820519 TGTATTCACGGGTTCGCTACT 59.179 47.619 0.00 0.00 40.63 2.57
83 84 1.598130 GTTGAGTGCCTTGGACGCT 60.598 57.895 0.00 0.00 0.00 5.07
91 92 2.356313 CTTGGACGCTGCAGTCGT 60.356 61.111 27.93 27.93 41.81 4.34
140 141 3.873952 GGGAGTCTCATGTGCATACTTTC 59.126 47.826 1.47 0.00 0.00 2.62
147 148 3.818210 TCATGTGCATACTTTCGTTTGGT 59.182 39.130 0.00 0.00 0.00 3.67
174 175 8.565416 CGAGAACCAACCTTTTTAGTAGAAAAT 58.435 33.333 0.00 0.00 0.00 1.82
175 176 9.678941 GAGAACCAACCTTTTTAGTAGAAAATG 57.321 33.333 0.00 0.00 0.00 2.32
178 179 8.990163 ACCAACCTTTTTAGTAGAAAATGAGA 57.010 30.769 0.00 0.00 0.00 3.27
189 190 7.454260 AGTAGAAAATGAGAAATGACCAACC 57.546 36.000 0.00 0.00 0.00 3.77
190 191 7.004086 AGTAGAAAATGAGAAATGACCAACCA 58.996 34.615 0.00 0.00 0.00 3.67
233 1068 7.936496 TGTTTTGGTGTCATATATGTGTCAT 57.064 32.000 12.42 0.00 0.00 3.06
283 1118 7.976175 CCAAGGATTTAAGCTTTAATTCTGGTC 59.024 37.037 17.56 3.31 0.00 4.02
314 1150 4.753516 AAAAGGCCAAGCAGTACTTTTT 57.246 36.364 5.01 0.00 37.93 1.94
399 1236 4.886489 AGCATTCAAAAGGAAGATAGAGGC 59.114 41.667 0.00 0.00 39.30 4.70
412 1249 1.112113 TAGAGGCTTCATCGACCCAC 58.888 55.000 0.00 0.00 0.00 4.61
423 1260 2.754946 TCGACCCACATACAAGGTTC 57.245 50.000 0.00 0.00 32.81 3.62
431 1269 4.218417 CCCACATACAAGGTTCAGAAAAGG 59.782 45.833 0.00 0.00 0.00 3.11
442 1280 4.454847 GGTTCAGAAAAGGCCAAGTAGTAC 59.545 45.833 5.01 0.00 0.00 2.73
489 1327 7.900352 GCAATATTTTTGAACGAAAACAACACA 59.100 29.630 0.00 0.00 33.09 3.72
499 1337 3.989167 CGAAAACAACACATCATGGCAAT 59.011 39.130 0.00 0.00 0.00 3.56
546 1384 2.761767 TCTCATGTGATGGCAAAATGGG 59.238 45.455 0.00 0.00 0.00 4.00
548 1386 2.761767 TCATGTGATGGCAAAATGGGAG 59.238 45.455 0.00 0.00 0.00 4.30
549 1387 2.601240 TGTGATGGCAAAATGGGAGA 57.399 45.000 0.00 0.00 0.00 3.71
550 1388 2.886913 TGTGATGGCAAAATGGGAGAA 58.113 42.857 0.00 0.00 0.00 2.87
551 1389 3.443052 TGTGATGGCAAAATGGGAGAAT 58.557 40.909 0.00 0.00 0.00 2.40
552 1390 3.839490 TGTGATGGCAAAATGGGAGAATT 59.161 39.130 0.00 0.00 0.00 2.17
553 1391 4.186159 GTGATGGCAAAATGGGAGAATTG 58.814 43.478 0.00 0.00 0.00 2.32
554 1392 4.081531 GTGATGGCAAAATGGGAGAATTGA 60.082 41.667 0.00 0.00 0.00 2.57
555 1393 4.531339 TGATGGCAAAATGGGAGAATTGAA 59.469 37.500 0.00 0.00 0.00 2.69
556 1394 5.190132 TGATGGCAAAATGGGAGAATTGAAT 59.810 36.000 0.00 0.00 0.00 2.57
557 1395 4.834534 TGGCAAAATGGGAGAATTGAATG 58.165 39.130 0.00 0.00 0.00 2.67
558 1396 4.531339 TGGCAAAATGGGAGAATTGAATGA 59.469 37.500 0.00 0.00 0.00 2.57
566 1404 9.796180 AAATGGGAGAATTGAATGAAAATGAAA 57.204 25.926 0.00 0.00 0.00 2.69
576 1414 8.713737 TTGAATGAAAATGAAACATTGTGTCA 57.286 26.923 11.99 11.99 34.03 3.58
584 1422 5.199024 TGAAACATTGTGTCATGGGAAAG 57.801 39.130 5.53 0.00 0.00 2.62
590 1428 5.128499 ACATTGTGTCATGGGAAAGTGAAAA 59.872 36.000 0.00 0.00 0.00 2.29
597 1435 5.691754 GTCATGGGAAAGTGAAAAATGACAC 59.308 40.000 7.76 0.00 41.18 3.67
614 1452 4.580868 TGACACGGGCAATATTAGTTTGA 58.419 39.130 0.00 0.00 0.00 2.69
616 1454 5.473846 TGACACGGGCAATATTAGTTTGAAA 59.526 36.000 0.00 0.00 0.00 2.69
617 1455 6.016192 TGACACGGGCAATATTAGTTTGAAAA 60.016 34.615 0.00 0.00 0.00 2.29
646 1486 5.794945 CGACATGTCATGTGATGGTAAAAAC 59.205 40.000 23.08 3.32 45.03 2.43
687 1527 4.778534 ACATCTGAAGTGATGGCAAAAG 57.221 40.909 8.96 0.00 45.78 2.27
688 1528 3.508793 ACATCTGAAGTGATGGCAAAAGG 59.491 43.478 8.96 0.00 45.78 3.11
697 1537 2.985311 TGATGGCAAAAGGGGGAAAAAT 59.015 40.909 0.00 0.00 0.00 1.82
699 1539 4.599241 TGATGGCAAAAGGGGGAAAAATTA 59.401 37.500 0.00 0.00 0.00 1.40
701 1541 5.590976 TGGCAAAAGGGGGAAAAATTAAT 57.409 34.783 0.00 0.00 0.00 1.40
703 1543 6.377080 TGGCAAAAGGGGGAAAAATTAATTT 58.623 32.000 7.64 7.64 0.00 1.82
811 1665 2.100584 CCAGCTTTGTTGGTTAGTTGCA 59.899 45.455 0.00 0.00 0.00 4.08
821 1675 3.215975 TGGTTAGTTGCAGTGGTAAACC 58.784 45.455 0.00 7.93 36.33 3.27
829 1683 9.826574 TTAGTTGCAGTGGTAAACCTTATATAG 57.173 33.333 0.02 0.00 36.82 1.31
832 1686 6.288294 TGCAGTGGTAAACCTTATATAGCAG 58.712 40.000 0.02 0.00 36.82 4.24
940 1807 2.635338 GTCAACCAAACGACCCGC 59.365 61.111 0.00 0.00 0.00 6.13
1111 1992 3.638592 AACCCTCCCCAAATCGGCG 62.639 63.158 0.00 0.00 0.00 6.46
1154 2035 2.200170 GATTGGGGAGCGTGTGTTGC 62.200 60.000 0.00 0.00 0.00 4.17
1164 2045 1.971695 GTGTGTTGCTGGGTAGGGC 60.972 63.158 0.00 0.00 0.00 5.19
1183 2064 0.818445 CCTGCCATGGTCTGATCTGC 60.818 60.000 14.67 0.00 0.00 4.26
1356 2241 2.205843 GCCCTACTACTACCCGCCC 61.206 68.421 0.00 0.00 0.00 6.13
1464 2349 2.184167 CCACCACCACCACAACGAC 61.184 63.158 0.00 0.00 0.00 4.34
1522 2408 4.908601 TGTTAATTCAGGCCTTCTCTCA 57.091 40.909 0.00 0.00 0.00 3.27
1524 2410 5.819991 TGTTAATTCAGGCCTTCTCTCAAT 58.180 37.500 0.00 0.00 0.00 2.57
1544 2430 9.066892 TCTCAATATGTATTATGAGTTTTGGGC 57.933 33.333 0.00 0.00 0.00 5.36
1561 2447 1.382522 GGCATGTGATTCGGATGTGT 58.617 50.000 0.00 0.00 0.00 3.72
1564 2450 2.789208 CATGTGATTCGGATGTGTTGC 58.211 47.619 0.00 0.00 0.00 4.17
1578 2464 1.407258 GTGTTGCTGGCTGTGGTTAAA 59.593 47.619 0.00 0.00 0.00 1.52
1589 2475 7.296628 TGGCTGTGGTTAAATTCTTGTTTAT 57.703 32.000 0.00 0.00 0.00 1.40
1591 2477 8.301002 TGGCTGTGGTTAAATTCTTGTTTATAC 58.699 33.333 0.00 0.00 0.00 1.47
1599 2485 9.341899 GTTAAATTCTTGTTTATACTGCACCAG 57.658 33.333 0.00 0.00 37.52 4.00
1615 2501 6.204882 ACTGCACCAGTAATGTAGTTTTTCTC 59.795 38.462 0.00 0.00 43.46 2.87
1661 2547 4.428294 TGAGAATTGAGATCATGGGGTC 57.572 45.455 0.00 0.00 0.00 4.46
1677 2563 4.479158 TGGGGTCATGCTTAGTTTTTCTT 58.521 39.130 0.00 0.00 0.00 2.52
1694 2580 3.325293 TCTTGAGCTAGCTCTTTGGTG 57.675 47.619 37.42 22.56 43.12 4.17
1722 2608 1.068352 AGAGGGGCTTGGTTGGTTCT 61.068 55.000 0.00 0.00 0.00 3.01
1737 2623 6.920758 TGGTTGGTTCTTTATGAAATCGTTTG 59.079 34.615 0.00 0.00 36.30 2.93
1745 2631 8.766493 TCTTTATGAAATCGTTTGCATATTCG 57.234 30.769 7.57 1.46 0.00 3.34
1825 2712 8.190122 TGCTGGCTGAATTTGTGTAATAAATAG 58.810 33.333 0.00 0.00 36.59 1.73
1867 2755 6.756074 TGCCTAAACAAAAACTTCACAATGAG 59.244 34.615 0.00 0.00 0.00 2.90
1920 2809 6.052840 CAAAGCATTGTGTAGAAGCGATAT 57.947 37.500 0.00 0.00 0.00 1.63
2021 2919 3.774528 CGCTGTAGCAGGAGCCCA 61.775 66.667 4.59 0.00 43.56 5.36
2185 3087 3.499157 GGTAGGATACGTCTGCTAGACTG 59.501 52.174 2.34 9.27 44.28 3.51
2242 3145 0.905357 ATTGACCTTAGACAGCGGCT 59.095 50.000 0.00 0.00 0.00 5.52
2283 3203 4.794278 TGCTCATGTTCATCAATGCTTT 57.206 36.364 0.00 0.00 0.00 3.51
2308 3229 4.093743 GTCCACCCAAAATACATCCCTTT 58.906 43.478 0.00 0.00 0.00 3.11
2317 3238 6.258160 CAAAATACATCCCTTTAGAAGTGCG 58.742 40.000 0.00 0.00 0.00 5.34
2319 3240 5.864418 ATACATCCCTTTAGAAGTGCGTA 57.136 39.130 0.00 0.00 0.00 4.42
2350 3271 7.259290 ACTTGTTTGAATGTACTACCTGTTG 57.741 36.000 0.00 0.00 0.00 3.33
2402 3324 2.034558 GTGTGTTATGCAAGCACCTGTT 59.965 45.455 13.56 0.00 32.62 3.16
2472 3394 3.650139 TGTGGACTAGCGAAGAGTTTTC 58.350 45.455 0.00 0.00 0.00 2.29
2548 3472 2.167693 TGTAAGGTAATCACTGAGGGCG 59.832 50.000 0.00 0.00 0.00 6.13
2553 3477 1.271840 TAATCACTGAGGGCGGGCTT 61.272 55.000 0.26 0.00 0.00 4.35
2554 3478 2.826777 AATCACTGAGGGCGGGCTTG 62.827 60.000 0.26 0.00 0.00 4.01
2568 3492 2.844451 GCTTGGCGCAGTGGTGAAA 61.844 57.895 10.83 0.00 38.92 2.69
2583 3507 2.307686 GGTGAAATCCTCCCCACTTGTA 59.692 50.000 0.00 0.00 0.00 2.41
2590 3514 1.702957 CCTCCCCACTTGTACCAAGAA 59.297 52.381 10.73 0.00 0.00 2.52
2639 3563 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
2640 3564 0.881796 GCACTTTGCAGGGGTAAGAC 59.118 55.000 2.16 0.00 44.26 3.01
2657 3581 6.380414 GGTAAGACTAGGTTCCTATAACCCT 58.620 44.000 3.33 0.00 41.18 4.34
2662 3586 3.816967 AGGTTCCTATAACCCTTCCCT 57.183 47.619 3.33 0.00 41.18 4.20
2663 3587 4.104051 AGGTTCCTATAACCCTTCCCTT 57.896 45.455 3.33 0.00 41.18 3.95
2696 3633 1.064017 TGCACTGGGTCTGTCCTTTTT 60.064 47.619 0.00 0.00 36.25 1.94
2801 3741 8.306313 AGTGTCAATTCATACTACACAGGATA 57.694 34.615 0.00 0.00 42.21 2.59
2810 3750 7.726216 TCATACTACACAGGATAATGTCTTGG 58.274 38.462 0.00 0.00 38.19 3.61
2820 3760 7.770897 ACAGGATAATGTCTTGGTACAGATTTC 59.229 37.037 0.00 0.00 42.39 2.17
2848 3792 7.607607 TGTTTGACAAAGATGTGTATAGATGCT 59.392 33.333 0.00 0.00 40.74 3.79
2852 3796 9.098355 TGACAAAGATGTGTATAGATGCTTAAC 57.902 33.333 0.00 0.00 40.74 2.01
2860 3806 6.483307 TGTGTATAGATGCTTAACTCAATGGC 59.517 38.462 0.00 0.00 0.00 4.40
2887 3836 3.860641 CATTTTATTGCACAAGACCCCC 58.139 45.455 0.00 0.00 0.00 5.40
2895 3844 1.746470 CACAAGACCCCCGGTATTTC 58.254 55.000 0.00 0.00 34.68 2.17
2901 3850 1.493446 GACCCCCGGTATTTCCATTCT 59.507 52.381 0.00 0.00 35.25 2.40
2926 3875 7.581011 ATTTTCCTGTTTTCATCGCATTAAC 57.419 32.000 0.00 0.00 0.00 2.01
3002 3955 0.108396 TGCTGCTGCTGTTTCTGGTA 59.892 50.000 17.00 0.00 40.48 3.25
3037 3990 2.001812 AGCTACTCGTGTCTTGCATG 57.998 50.000 0.00 0.00 35.47 4.06
3051 4004 0.892814 TGCATGTTCGACATTGGGCA 60.893 50.000 0.00 0.00 36.53 5.36
3064 4017 2.980233 GGGCATGCCGCAGTATCC 60.980 66.667 29.90 10.13 45.17 2.59
3214 4167 5.714806 TGTACATGATCCAGACTTGACTGTA 59.285 40.000 0.00 0.00 36.30 2.74
3218 4171 7.170965 ACATGATCCAGACTTGACTGTATTTT 58.829 34.615 0.00 0.00 36.30 1.82
3310 4269 4.467795 ACAGTAACTGATAGGTCATGCTGT 59.532 41.667 0.00 0.00 35.18 4.40
3314 4273 7.712639 CAGTAACTGATAGGTCATGCTGTTAAT 59.287 37.037 0.00 0.00 32.44 1.40
3319 4278 7.443575 ACTGATAGGTCATGCTGTTAATTGATC 59.556 37.037 0.00 0.00 32.98 2.92
3320 4279 6.424812 TGATAGGTCATGCTGTTAATTGATCG 59.575 38.462 0.00 0.00 0.00 3.69
3379 4338 1.136305 TGGCGAATTAGAACTCTCCCG 59.864 52.381 0.00 0.00 0.00 5.14
3402 4361 6.403200 CCGTGACATATTCAAAAGTAGGGTTG 60.403 42.308 0.00 0.00 35.39 3.77
3406 4365 7.893302 TGACATATTCAAAAGTAGGGTTGGAAT 59.107 33.333 0.00 0.00 0.00 3.01
3411 4370 6.457159 TCAAAAGTAGGGTTGGAATCCTAA 57.543 37.500 0.00 0.00 37.38 2.69
3418 4378 7.475299 AGTAGGGTTGGAATCCTAAAATCAAA 58.525 34.615 0.00 0.00 37.38 2.69
3424 4384 8.581578 GGTTGGAATCCTAAAATCAAACAAGTA 58.418 33.333 0.00 0.00 30.19 2.24
3432 4392 3.565905 AATCAAACAAGTAGCTGCTGC 57.434 42.857 13.43 11.60 40.05 5.25
3437 4397 0.179020 ACAAGTAGCTGCTGCCACAA 60.179 50.000 13.43 0.00 40.80 3.33
3442 4402 0.603707 TAGCTGCTGCCACAACTGAC 60.604 55.000 13.43 0.00 40.80 3.51
3455 4415 2.036475 ACAACTGACTACTCTGTGCCAG 59.964 50.000 0.00 0.00 0.00 4.85
3459 4419 1.229336 ACTACTCTGTGCCAGGGCT 60.229 57.895 12.19 0.00 42.51 5.19
3470 4430 1.144913 TGCCAGGGCTCTAGTGTTTTT 59.855 47.619 12.19 0.00 42.51 1.94
3481 4441 5.408909 GCTCTAGTGTTTTTACCTGAAGACC 59.591 44.000 0.00 0.00 0.00 3.85
3483 4443 6.285990 TCTAGTGTTTTTACCTGAAGACCAC 58.714 40.000 0.00 0.00 0.00 4.16
3495 4455 4.131596 CTGAAGACCACGGGTTCTTTTTA 58.868 43.478 0.00 0.00 35.25 1.52
3501 4462 4.925836 ACCACGGGTTCTTTTTATACCAT 58.074 39.130 0.00 0.00 33.51 3.55
3502 4463 4.703093 ACCACGGGTTCTTTTTATACCATG 59.297 41.667 0.00 0.00 33.51 3.66
3504 4465 5.592688 CCACGGGTTCTTTTTATACCATGAT 59.407 40.000 0.00 0.00 33.51 2.45
3506 4467 7.255001 CCACGGGTTCTTTTTATACCATGATAC 60.255 40.741 0.00 0.00 33.51 2.24
3507 4468 6.769341 ACGGGTTCTTTTTATACCATGATACC 59.231 38.462 0.00 0.00 33.51 2.73
3521 4482 2.609747 TGATACCCACTCCTATGAGGC 58.390 52.381 0.00 0.00 43.29 4.70
3525 4486 1.992557 ACCCACTCCTATGAGGCAAAA 59.007 47.619 0.00 0.00 43.29 2.44
3539 4500 7.989416 ATGAGGCAAAATTGACAAATTTGAT 57.011 28.000 25.81 16.03 43.63 2.57
3542 4503 8.366401 TGAGGCAAAATTGACAAATTTGATCTA 58.634 29.630 25.81 14.22 43.63 1.98
3572 4533 6.033196 CGAAATCAAATCACAGAATGAACTGC 59.967 38.462 0.00 0.00 41.93 4.40
3577 4538 1.621317 TCACAGAATGAACTGCCCGTA 59.379 47.619 0.00 0.00 39.69 4.02
3581 4542 3.252458 ACAGAATGAACTGCCCGTAAAAC 59.748 43.478 0.00 0.00 39.69 2.43
3590 4551 4.391155 ACTGCCCGTAAAACTATTTCACA 58.609 39.130 0.00 0.00 0.00 3.58
3636 4597 2.048503 ACGAAGGCGCCACACTAC 60.049 61.111 31.54 11.50 42.48 2.73
3638 4599 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
3653 4614 0.878523 TACACTGTGCAACGCCTCAC 60.879 55.000 7.90 0.00 42.39 3.51
3660 4621 0.108186 TGCAACGCCTCACAGATAGG 60.108 55.000 0.00 0.00 37.17 2.57
3668 4629 3.495670 CCTCACAGATAGGCGCTATAC 57.504 52.381 7.64 0.00 0.00 1.47
3678 4639 3.038417 CGCTATACGCCTGCCAGC 61.038 66.667 0.00 0.00 34.21 4.85
3697 4658 4.429212 TCGCACCCGTGTGATCCG 62.429 66.667 0.90 0.00 45.76 4.18
3704 4667 3.004171 CACCCGTGTGATCCGAAAATTA 58.996 45.455 0.00 0.00 45.76 1.40
3713 4676 7.462856 CGTGTGATCCGAAAATTACTAAGTCAG 60.463 40.741 0.00 0.00 0.00 3.51
3721 4684 5.613358 AAATTACTAAGTCAGTGTGCAGC 57.387 39.130 0.00 0.00 38.24 5.25
3726 4689 3.720193 GTCAGTGTGCAGCGCCTG 61.720 66.667 2.29 14.85 34.12 4.85
3740 4703 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
3745 4708 1.379977 AGAGCTAGGCGCCACACTA 60.380 57.895 31.54 11.42 40.39 2.74
3748 4711 0.674534 AGCTAGGCGCCACACTATAC 59.325 55.000 31.54 8.64 40.39 1.47
3765 4728 5.228145 ACTATACAGTGTAGCGCCTAGCTT 61.228 45.833 2.29 0.00 43.79 3.74
3766 4729 6.996034 ACTATACAGTGTAGCGCCTAGCTTC 61.996 48.000 2.29 0.00 43.79 3.86
3789 4752 1.507141 GCGTTGCACTAGTGGTTGCT 61.507 55.000 23.95 0.00 0.00 3.91
3790 4753 0.944386 CGTTGCACTAGTGGTTGCTT 59.056 50.000 23.95 0.00 0.00 3.91
3791 4754 1.069906 CGTTGCACTAGTGGTTGCTTC 60.070 52.381 23.95 6.25 0.00 3.86
3793 4756 2.554032 GTTGCACTAGTGGTTGCTTCAT 59.446 45.455 23.95 0.00 0.00 2.57
3794 4757 2.862541 TGCACTAGTGGTTGCTTCATT 58.137 42.857 23.95 0.00 0.00 2.57
3795 4758 3.221771 TGCACTAGTGGTTGCTTCATTT 58.778 40.909 23.95 0.00 0.00 2.32
3796 4759 3.636300 TGCACTAGTGGTTGCTTCATTTT 59.364 39.130 23.95 0.00 0.00 1.82
3797 4760 3.983344 GCACTAGTGGTTGCTTCATTTTG 59.017 43.478 23.95 0.00 0.00 2.44
3799 4762 5.278266 GCACTAGTGGTTGCTTCATTTTGTA 60.278 40.000 23.95 0.00 0.00 2.41
3800 4763 6.373779 CACTAGTGGTTGCTTCATTTTGTAG 58.626 40.000 15.49 0.00 0.00 2.74
3801 4764 6.017109 CACTAGTGGTTGCTTCATTTTGTAGT 60.017 38.462 15.49 0.00 0.00 2.73
3823 4786 2.816958 CCACTAGTGCAGCGCCTG 60.817 66.667 17.86 2.69 34.12 4.85
3824 4787 2.262603 CACTAGTGCAGCGCCTGA 59.737 61.111 10.54 0.00 32.44 3.86
3825 4788 1.808799 CACTAGTGCAGCGCCTGAG 60.809 63.158 10.54 0.34 32.44 3.35
3837 4800 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
3842 4805 1.379977 AGAGCTAGGCGCCACACTA 60.380 57.895 31.54 11.42 40.39 2.74
3845 4808 0.674534 AGCTAGGCGCCACACTATAC 59.325 55.000 31.54 8.64 40.39 1.47
3846 4809 0.663568 GCTAGGCGCCACACTATACG 60.664 60.000 31.54 6.38 0.00 3.06
3850 4813 3.700961 CGCCACACTATACGGTGC 58.299 61.111 0.00 0.00 40.52 5.01
3851 4814 1.153726 CGCCACACTATACGGTGCA 60.154 57.895 0.00 0.00 40.52 4.57
3876 4839 1.753649 CTAGCTCTTAGGCTCTGCACA 59.246 52.381 0.00 0.00 42.97 4.57
3877 4840 0.979665 AGCTCTTAGGCTCTGCACAA 59.020 50.000 0.00 0.00 38.24 3.33
3886 4849 1.399791 GGCTCTGCACAATGACTTAGC 59.600 52.381 0.00 0.00 0.00 3.09
3893 4856 6.514947 TCTGCACAATGACTTAGCAATTTTT 58.485 32.000 0.00 0.00 34.45 1.94
3894 4857 7.656412 TCTGCACAATGACTTAGCAATTTTTA 58.344 30.769 0.00 0.00 34.45 1.52
3896 4859 6.867816 TGCACAATGACTTAGCAATTTTTAGG 59.132 34.615 0.00 0.00 31.42 2.69
3897 4860 6.183360 GCACAATGACTTAGCAATTTTTAGGC 60.183 38.462 0.00 0.00 0.00 3.93
3898 4861 6.867816 CACAATGACTTAGCAATTTTTAGGCA 59.132 34.615 0.00 0.00 0.00 4.75
3899 4862 7.062605 CACAATGACTTAGCAATTTTTAGGCAG 59.937 37.037 0.00 0.00 0.00 4.85
3900 4863 6.840780 ATGACTTAGCAATTTTTAGGCAGT 57.159 33.333 0.00 0.00 0.00 4.40
3901 4864 6.254281 TGACTTAGCAATTTTTAGGCAGTC 57.746 37.500 0.00 0.00 33.59 3.51
3902 4865 6.003950 TGACTTAGCAATTTTTAGGCAGTCT 58.996 36.000 0.00 0.00 33.92 3.24
3903 4866 6.072508 TGACTTAGCAATTTTTAGGCAGTCTG 60.073 38.462 0.00 0.00 33.92 3.51
3941 4904 2.873367 CGTGTAGCGCCTATCTGTG 58.127 57.895 2.29 0.00 0.00 3.66
3987 4950 3.215597 TTCGTGTCGGGCGTCACAT 62.216 57.895 0.00 0.00 34.69 3.21
3992 4956 1.532007 GTGTCGGGCGTCACATAAAAA 59.468 47.619 0.00 0.00 35.02 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.942586 GCGAACCCGTGAATACACCTT 60.943 52.381 0.00 0.00 43.34 3.50
50 51 2.157738 CTCAACCCCTTCAAGCTTCAG 58.842 52.381 0.00 0.00 0.00 3.02
51 52 1.494721 ACTCAACCCCTTCAAGCTTCA 59.505 47.619 0.00 0.00 0.00 3.02
58 59 0.178992 CAAGGCACTCAACCCCTTCA 60.179 55.000 0.00 0.00 38.49 3.02
60 61 1.153756 CCAAGGCACTCAACCCCTT 59.846 57.895 0.00 0.00 38.49 3.95
66 67 1.597854 CAGCGTCCAAGGCACTCAA 60.598 57.895 0.00 0.00 38.49 3.02
83 84 1.533033 TTCCCCTCTCACGACTGCA 60.533 57.895 0.00 0.00 0.00 4.41
91 92 1.152271 AGGGTTTCTCTTCCCCTCTCA 59.848 52.381 0.00 0.00 45.98 3.27
120 121 4.177026 ACGAAAGTATGCACATGAGACTC 58.823 43.478 0.00 0.00 46.88 3.36
147 148 6.409524 TCTACTAAAAAGGTTGGTTCTCGA 57.590 37.500 0.00 0.00 0.00 4.04
174 175 1.144708 TGGCTGGTTGGTCATTTCTCA 59.855 47.619 0.00 0.00 0.00 3.27
175 176 1.909700 TGGCTGGTTGGTCATTTCTC 58.090 50.000 0.00 0.00 0.00 2.87
178 179 2.380064 TCTTGGCTGGTTGGTCATTT 57.620 45.000 0.00 0.00 0.00 2.32
180 181 2.610438 ATTCTTGGCTGGTTGGTCAT 57.390 45.000 0.00 0.00 0.00 3.06
181 182 2.238521 GAATTCTTGGCTGGTTGGTCA 58.761 47.619 0.00 0.00 0.00 4.02
182 183 2.238521 TGAATTCTTGGCTGGTTGGTC 58.761 47.619 7.05 0.00 0.00 4.02
183 184 2.365293 GTTGAATTCTTGGCTGGTTGGT 59.635 45.455 7.05 0.00 0.00 3.67
185 186 3.571401 AGAGTTGAATTCTTGGCTGGTTG 59.429 43.478 7.05 0.00 0.00 3.77
186 187 3.837355 AGAGTTGAATTCTTGGCTGGTT 58.163 40.909 7.05 0.00 0.00 3.67
189 190 6.506500 AACATAGAGTTGAATTCTTGGCTG 57.493 37.500 7.05 0.00 39.49 4.85
190 191 7.373493 CAAAACATAGAGTTGAATTCTTGGCT 58.627 34.615 7.05 2.33 41.19 4.75
227 1062 8.739972 AGAAATGATAACCCACTTTAATGACAC 58.260 33.333 0.00 0.00 0.00 3.67
233 1068 9.589461 TGGTAAAGAAATGATAACCCACTTTAA 57.411 29.630 0.00 0.00 32.74 1.52
277 1112 4.517285 GCCTTTTATCACATGAGACCAGA 58.483 43.478 0.00 0.00 0.00 3.86
278 1113 3.629398 GGCCTTTTATCACATGAGACCAG 59.371 47.826 0.00 0.00 0.00 4.00
283 1118 3.444742 TGCTTGGCCTTTTATCACATGAG 59.555 43.478 3.32 0.00 0.00 2.90
327 1163 4.803329 ATGAATAAATGAGCCTGAGGGT 57.197 40.909 1.18 1.18 35.46 4.34
334 1170 6.409524 TCATTGGGAATGAATAAATGAGCC 57.590 37.500 0.00 0.00 44.47 4.70
399 1236 3.198068 CCTTGTATGTGGGTCGATGAAG 58.802 50.000 0.00 0.00 0.00 3.02
412 1249 3.826157 TGGCCTTTTCTGAACCTTGTATG 59.174 43.478 3.32 0.00 0.00 2.39
423 1260 6.635030 AAAAGTACTACTTGGCCTTTTCTG 57.365 37.500 3.32 0.00 38.66 3.02
442 1280 7.644986 TTGCCCGTGTCATTTTTATTAAAAG 57.355 32.000 2.12 0.00 36.73 2.27
489 1327 9.550406 CATCCAAACTATTTTTATTGCCATGAT 57.450 29.630 0.00 0.00 0.00 2.45
550 1388 9.327628 TGACACAATGTTTCATTTTCATTCAAT 57.672 25.926 0.00 0.00 30.74 2.57
551 1389 8.713737 TGACACAATGTTTCATTTTCATTCAA 57.286 26.923 0.00 0.00 30.74 2.69
552 1390 8.766151 CATGACACAATGTTTCATTTTCATTCA 58.234 29.630 11.87 0.00 31.65 2.57
553 1391 8.225107 CCATGACACAATGTTTCATTTTCATTC 58.775 33.333 11.87 0.00 31.65 2.67
554 1392 7.173562 CCCATGACACAATGTTTCATTTTCATT 59.826 33.333 11.87 0.00 31.65 2.57
555 1393 6.651643 CCCATGACACAATGTTTCATTTTCAT 59.348 34.615 11.87 0.00 31.65 2.57
556 1394 5.990386 CCCATGACACAATGTTTCATTTTCA 59.010 36.000 11.87 0.00 31.65 2.69
557 1395 6.222389 TCCCATGACACAATGTTTCATTTTC 58.778 36.000 11.87 0.00 31.65 2.29
558 1396 6.172136 TCCCATGACACAATGTTTCATTTT 57.828 33.333 11.87 0.00 31.65 1.82
566 1404 3.831323 TCACTTTCCCATGACACAATGT 58.169 40.909 0.00 0.00 0.00 2.71
573 1411 5.691754 GTGTCATTTTTCACTTTCCCATGAC 59.308 40.000 0.00 0.00 39.56 3.06
576 1414 4.261994 CCGTGTCATTTTTCACTTTCCCAT 60.262 41.667 0.00 0.00 33.07 4.00
584 1422 2.500509 TTGCCCGTGTCATTTTTCAC 57.499 45.000 0.00 0.00 0.00 3.18
590 1428 5.650266 TCAAACTAATATTGCCCGTGTCATT 59.350 36.000 0.00 0.00 0.00 2.57
617 1455 4.278170 ACCATCACATGACATGTCGTTTTT 59.722 37.500 18.27 2.97 42.70 1.94
620 1458 3.057969 ACCATCACATGACATGTCGTT 57.942 42.857 18.27 6.56 42.70 3.85
627 1465 8.402798 ACTATTGTTTTTACCATCACATGACA 57.597 30.769 0.00 0.00 0.00 3.58
646 1486 9.277565 CAGATGTCGGTTTAATCAAAACTATTG 57.722 33.333 1.14 0.00 45.70 1.90
663 1503 1.293924 GCCATCACTTCAGATGTCGG 58.706 55.000 0.00 0.00 43.00 4.79
811 1665 9.080097 CTCTACTGCTATATAAGGTTTACCACT 57.920 37.037 1.13 0.00 38.89 4.00
821 1675 4.142359 CCGTGGGCTCTACTGCTATATAAG 60.142 50.000 0.00 0.00 0.00 1.73
829 1683 2.579684 CTTCCCGTGGGCTCTACTGC 62.580 65.000 0.00 0.00 34.68 4.40
832 1686 2.187163 GCTTCCCGTGGGCTCTAC 59.813 66.667 0.00 0.00 34.68 2.59
1111 1992 3.774702 GGAAAGTGACGCGTCGGC 61.775 66.667 31.88 26.05 34.27 5.54
1154 2035 3.099170 ATGGCAGGCCCTACCCAG 61.099 66.667 8.02 0.00 40.58 4.45
1164 2045 0.818445 GCAGATCAGACCATGGCAGG 60.818 60.000 13.04 0.57 0.00 4.85
1183 2064 3.088608 CCGCGCGGAACAAAAACG 61.089 61.111 44.86 12.52 37.50 3.60
1335 2220 1.152881 CGGGTAGTAGTAGGGCGGT 60.153 63.158 0.00 0.00 0.00 5.68
1440 2325 1.348775 TGTGGTGGTGGTGGTGATGA 61.349 55.000 0.00 0.00 0.00 2.92
1464 2349 2.758089 GCCAAGGCAGCAGTCATCG 61.758 63.158 6.14 0.00 41.49 3.84
1522 2408 9.146586 ACATGCCCAAAACTCATAATACATATT 57.853 29.630 0.00 0.00 0.00 1.28
1524 2410 7.777440 TCACATGCCCAAAACTCATAATACATA 59.223 33.333 0.00 0.00 0.00 2.29
1544 2430 2.421073 AGCAACACATCCGAATCACATG 59.579 45.455 0.00 0.00 0.00 3.21
1561 2447 3.230134 AGAATTTAACCACAGCCAGCAA 58.770 40.909 0.00 0.00 0.00 3.91
1564 2450 4.853924 ACAAGAATTTAACCACAGCCAG 57.146 40.909 0.00 0.00 0.00 4.85
1578 2464 8.677300 CATTACTGGTGCAGTATAAACAAGAAT 58.323 33.333 0.00 0.00 44.85 2.40
1589 2475 7.221450 AGAAAAACTACATTACTGGTGCAGTA 58.779 34.615 0.00 0.00 43.46 2.74
1591 2477 6.428159 AGAGAAAAACTACATTACTGGTGCAG 59.572 38.462 0.00 0.00 37.52 4.41
1615 2501 5.639506 ACAATGAGTTCCAAGTTCGTCATAG 59.360 40.000 0.00 0.00 0.00 2.23
1656 2542 4.522789 TCAAGAAAAACTAAGCATGACCCC 59.477 41.667 0.00 0.00 0.00 4.95
1661 2547 6.026513 GCTAGCTCAAGAAAAACTAAGCATG 58.973 40.000 7.70 0.00 32.25 4.06
1677 2563 2.251818 AGACACCAAAGAGCTAGCTCA 58.748 47.619 38.86 0.00 44.99 4.26
1694 2580 1.889170 CCAAGCCCCTCTCAAAAAGAC 59.111 52.381 0.00 0.00 0.00 3.01
1722 2608 9.561270 TTTCGAATATGCAAACGATTTCATAAA 57.439 25.926 0.00 0.00 34.85 1.40
1737 2623 9.031360 TCAGACATACTTTAGTTTCGAATATGC 57.969 33.333 0.00 0.00 0.00 3.14
1745 2631 6.252869 TCGCGATTCAGACATACTTTAGTTTC 59.747 38.462 3.71 0.00 0.00 2.78
1797 2683 1.401761 ACACAAATTCAGCCAGCACA 58.598 45.000 0.00 0.00 0.00 4.57
1825 2712 8.726988 TGTTTAGGCAACAACTACTGAATTATC 58.273 33.333 0.00 0.00 42.76 1.75
1867 2755 6.702716 AGGTGCTAGTAGATACAAGACTTC 57.297 41.667 0.00 0.00 0.00 3.01
2061 2960 8.912988 ACCATGATAAACAATGGATTTAACGAT 58.087 29.630 8.62 0.00 37.60 3.73
2185 3087 1.174712 ATCAGGCAACAGTGTGCACC 61.175 55.000 15.69 5.76 46.81 5.01
2242 3145 8.206126 TGAGCATCTATTGGTTATTCCAGATA 57.794 34.615 0.00 0.00 41.44 1.98
2283 3203 3.426615 GGATGTATTTTGGGTGGACACA 58.573 45.455 4.69 0.00 0.00 3.72
2350 3271 3.552132 TTTTTCCTTTTGGGTTCAGCC 57.448 42.857 0.00 0.00 40.87 4.85
2402 3324 1.832998 TGTGCAGCTATCAGTCATCCA 59.167 47.619 0.00 0.00 0.00 3.41
2524 3447 4.101741 GCCCTCAGTGATTACCTTACATCT 59.898 45.833 0.00 0.00 0.00 2.90
2553 3477 1.971167 GGATTTCACCACTGCGCCA 60.971 57.895 4.18 0.00 0.00 5.69
2554 3478 1.648467 GAGGATTTCACCACTGCGCC 61.648 60.000 4.18 0.00 0.00 6.53
2568 3492 3.828418 TGGTACAAGTGGGGAGGAT 57.172 52.632 0.00 0.00 31.92 3.24
2583 3507 1.518367 TGAACCCAGGACTTCTTGGT 58.482 50.000 6.64 0.00 42.69 3.67
2602 3526 1.542492 CAATGCAGAGAGGCTGGTTT 58.458 50.000 0.00 0.00 45.03 3.27
2637 3561 5.465901 GGAAGGGTTATAGGAACCTAGTCT 58.534 45.833 6.44 0.00 40.15 3.24
2638 3562 4.592351 GGGAAGGGTTATAGGAACCTAGTC 59.408 50.000 6.44 2.35 40.15 2.59
2639 3563 4.237059 AGGGAAGGGTTATAGGAACCTAGT 59.763 45.833 6.44 0.00 40.15 2.57
2640 3564 4.828963 AGGGAAGGGTTATAGGAACCTAG 58.171 47.826 6.44 0.00 40.15 3.02
2662 3586 2.618816 CCAGTGCATAGAAGCTCCCAAA 60.619 50.000 0.00 0.00 34.99 3.28
2663 3587 1.065199 CCAGTGCATAGAAGCTCCCAA 60.065 52.381 0.00 0.00 34.99 4.12
2696 3633 9.256477 CTTTCAGCTACGGATTACATTACATAA 57.744 33.333 0.00 0.00 0.00 1.90
2702 3639 5.978814 AGACTTTCAGCTACGGATTACATT 58.021 37.500 0.00 0.00 0.00 2.71
2704 3641 5.416639 TGTAGACTTTCAGCTACGGATTACA 59.583 40.000 0.00 0.00 39.79 2.41
2712 3649 4.130286 AGGCATGTAGACTTTCAGCTAC 57.870 45.455 0.00 0.00 37.94 3.58
2718 3655 7.989826 ACATTGATTAAGGCATGTAGACTTTC 58.010 34.615 0.00 0.00 45.75 2.62
2749 3686 3.405823 TGGTGTAAGTCTAAAACCCCG 57.594 47.619 0.00 0.00 0.00 5.73
2801 3741 7.823745 AACAAGAAATCTGTACCAAGACATT 57.176 32.000 0.00 0.00 0.00 2.71
2810 3750 9.173939 CATCTTTGTCAAACAAGAAATCTGTAC 57.826 33.333 0.00 0.00 39.53 2.90
2820 3760 9.764870 CATCTATACACATCTTTGTCAAACAAG 57.235 33.333 0.00 0.00 39.53 3.16
2848 3792 5.726980 AAATGCTTCAGCCATTGAGTTAA 57.273 34.783 0.00 0.00 41.18 2.01
2852 3796 5.006358 GCAATAAAATGCTTCAGCCATTGAG 59.994 40.000 0.00 0.00 43.06 3.02
2860 3806 5.346822 GGTCTTGTGCAATAAAATGCTTCAG 59.653 40.000 0.00 0.00 46.54 3.02
2887 3836 7.568199 ACAGGAAAATAGAATGGAAATACCG 57.432 36.000 0.00 0.00 42.61 4.02
2895 3844 6.473455 GCGATGAAAACAGGAAAATAGAATGG 59.527 38.462 0.00 0.00 0.00 3.16
2901 3850 7.757624 GGTTAATGCGATGAAAACAGGAAAATA 59.242 33.333 0.00 0.00 0.00 1.40
2926 3875 1.490621 CTGCAAAAGGAAACGCAAGG 58.509 50.000 0.00 0.00 46.39 3.61
3037 3990 1.139520 GGCATGCCCAATGTCGAAC 59.860 57.895 27.24 0.00 38.65 3.95
3051 4004 0.541392 TTCACTGGATACTGCGGCAT 59.459 50.000 1.75 0.00 39.52 4.40
3064 4017 6.506500 AATAACAAGCCAGAAGATTCACTG 57.493 37.500 0.00 0.00 0.00 3.66
3106 4059 9.048446 GTTTATTTGACACAGGTAACAGACTAA 57.952 33.333 0.00 0.00 41.41 2.24
3109 4062 7.012044 ACAGTTTATTTGACACAGGTAACAGAC 59.988 37.037 0.00 0.00 41.41 3.51
3214 4167 9.054922 CAAGTTTCCACAATCAACCAATAAAAT 57.945 29.630 0.00 0.00 0.00 1.82
3218 4171 5.600484 ACCAAGTTTCCACAATCAACCAATA 59.400 36.000 0.00 0.00 0.00 1.90
3356 4315 4.500887 CGGGAGAGTTCTAATTCGCCAATA 60.501 45.833 9.53 0.00 36.55 1.90
3379 4338 6.657541 TCCAACCCTACTTTTGAATATGTCAC 59.342 38.462 0.00 0.00 35.39 3.67
3402 4361 7.970614 CAGCTACTTGTTTGATTTTAGGATTCC 59.029 37.037 0.00 0.00 0.00 3.01
3406 4365 6.003950 AGCAGCTACTTGTTTGATTTTAGGA 58.996 36.000 0.00 0.00 0.00 2.94
3411 4370 3.305608 GGCAGCAGCTACTTGTTTGATTT 60.306 43.478 0.00 0.00 41.70 2.17
3424 4384 1.895707 GTCAGTTGTGGCAGCAGCT 60.896 57.895 0.00 0.00 41.70 4.24
3432 4392 2.408050 GCACAGAGTAGTCAGTTGTGG 58.592 52.381 16.11 0.00 39.50 4.17
3455 4415 4.281898 TCAGGTAAAAACACTAGAGCCC 57.718 45.455 0.00 0.00 0.00 5.19
3459 4419 6.285990 GTGGTCTTCAGGTAAAAACACTAGA 58.714 40.000 0.00 0.00 0.00 2.43
3470 4430 0.971386 GAACCCGTGGTCTTCAGGTA 59.029 55.000 0.00 0.00 33.12 3.08
3481 4441 6.693315 ATCATGGTATAAAAAGAACCCGTG 57.307 37.500 0.00 0.00 31.97 4.94
3483 4443 6.206048 GGGTATCATGGTATAAAAAGAACCCG 59.794 42.308 0.00 0.00 32.96 5.28
3495 4455 5.915628 TCATAGGAGTGGGTATCATGGTAT 58.084 41.667 0.00 0.00 0.00 2.73
3501 4462 2.090775 TGCCTCATAGGAGTGGGTATCA 60.091 50.000 3.36 0.00 37.67 2.15
3502 4463 2.609747 TGCCTCATAGGAGTGGGTATC 58.390 52.381 3.36 0.00 37.67 2.24
3504 4465 2.561209 TTGCCTCATAGGAGTGGGTA 57.439 50.000 3.36 0.00 37.67 3.69
3506 4467 2.806945 TTTTGCCTCATAGGAGTGGG 57.193 50.000 3.36 0.00 37.67 4.61
3507 4468 4.096984 GTCAATTTTGCCTCATAGGAGTGG 59.903 45.833 3.36 0.00 37.67 4.00
3525 4486 7.864108 TCGTCCATAGATCAAATTTGTCAAT 57.136 32.000 17.47 4.40 0.00 2.57
3539 4500 6.639563 TCTGTGATTTGATTTCGTCCATAGA 58.360 36.000 0.00 0.00 0.00 1.98
3542 4503 6.375174 TCATTCTGTGATTTGATTTCGTCCAT 59.625 34.615 0.00 0.00 0.00 3.41
3572 4533 3.425227 GCCGTGTGAAATAGTTTTACGGG 60.425 47.826 20.22 12.20 41.22 5.28
3577 4538 3.252458 GGTCAGCCGTGTGAAATAGTTTT 59.748 43.478 0.00 0.00 0.00 2.43
3581 4542 2.386661 AGGTCAGCCGTGTGAAATAG 57.613 50.000 0.00 0.00 40.50 1.73
3590 4551 0.738389 CACACAAAAAGGTCAGCCGT 59.262 50.000 0.00 0.00 40.50 5.68
3628 4589 0.581529 CGTTGCACAGTGTAGTGTGG 59.418 55.000 18.52 1.81 46.73 4.17
3636 4597 2.179547 TGTGAGGCGTTGCACAGTG 61.180 57.895 0.00 0.00 39.86 3.66
3678 4639 3.179265 GATCACACGGGTGCGACG 61.179 66.667 14.50 0.00 44.87 5.12
3679 4640 2.813908 GGATCACACGGGTGCGAC 60.814 66.667 14.50 6.54 44.87 5.19
3680 4641 4.429212 CGGATCACACGGGTGCGA 62.429 66.667 14.50 0.00 44.87 5.10
3681 4642 3.925362 TTCGGATCACACGGGTGCG 62.925 63.158 14.50 11.68 44.87 5.34
3682 4643 1.231958 TTTTCGGATCACACGGGTGC 61.232 55.000 14.50 0.00 44.87 5.01
3683 4644 1.448985 ATTTTCGGATCACACGGGTG 58.551 50.000 12.84 12.84 46.66 4.61
3684 4645 2.194201 AATTTTCGGATCACACGGGT 57.806 45.000 0.00 0.00 0.00 5.28
3685 4646 3.267483 AGTAATTTTCGGATCACACGGG 58.733 45.455 0.00 0.00 0.00 5.28
3686 4647 5.579511 ACTTAGTAATTTTCGGATCACACGG 59.420 40.000 0.00 0.00 0.00 4.94
3688 4649 7.331193 ACTGACTTAGTAATTTTCGGATCACAC 59.669 37.037 0.00 0.00 38.04 3.82
3689 4650 7.330946 CACTGACTTAGTAATTTTCGGATCACA 59.669 37.037 0.00 0.00 37.60 3.58
3690 4651 7.331193 ACACTGACTTAGTAATTTTCGGATCAC 59.669 37.037 0.00 0.00 37.60 3.06
3691 4652 7.330946 CACACTGACTTAGTAATTTTCGGATCA 59.669 37.037 0.00 0.00 37.60 2.92
3692 4653 7.674240 GCACACTGACTTAGTAATTTTCGGATC 60.674 40.741 0.00 0.00 37.60 3.36
3693 4654 6.092259 GCACACTGACTTAGTAATTTTCGGAT 59.908 38.462 0.00 0.00 37.60 4.18
3695 4656 5.178623 TGCACACTGACTTAGTAATTTTCGG 59.821 40.000 0.00 0.00 37.60 4.30
3697 4658 6.080406 GCTGCACACTGACTTAGTAATTTTC 58.920 40.000 0.00 0.00 37.60 2.29
3704 4667 0.946221 GCGCTGCACACTGACTTAGT 60.946 55.000 0.00 0.00 41.36 2.24
3713 4676 3.117171 CTCTCAGGCGCTGCACAC 61.117 66.667 7.64 0.00 0.00 3.82
3765 4728 0.530744 CCACTAGTGCAACGCCTAGA 59.469 55.000 17.86 0.00 45.86 2.43
3766 4729 0.246635 ACCACTAGTGCAACGCCTAG 59.753 55.000 17.86 7.38 45.86 3.02
3767 4730 0.682852 AACCACTAGTGCAACGCCTA 59.317 50.000 17.86 0.00 45.86 3.93
3769 4732 1.574428 CAACCACTAGTGCAACGCC 59.426 57.895 17.86 0.00 45.86 5.68
3772 4735 1.946768 TGAAGCAACCACTAGTGCAAC 59.053 47.619 17.86 6.35 0.00 4.17
3773 4736 2.340210 TGAAGCAACCACTAGTGCAA 57.660 45.000 17.86 0.00 0.00 4.08
3789 4752 5.825679 ACTAGTGGTTGCACTACAAAATGAA 59.174 36.000 0.00 0.00 40.82 2.57
3790 4753 5.238432 CACTAGTGGTTGCACTACAAAATGA 59.762 40.000 15.49 0.00 40.82 2.57
3791 4754 5.451908 CACTAGTGGTTGCACTACAAAATG 58.548 41.667 15.49 0.00 40.82 2.32
3793 4756 3.314080 GCACTAGTGGTTGCACTACAAAA 59.686 43.478 23.95 0.00 40.82 2.44
3794 4757 2.875933 GCACTAGTGGTTGCACTACAAA 59.124 45.455 23.95 0.00 40.82 2.83
3795 4758 2.158885 TGCACTAGTGGTTGCACTACAA 60.159 45.455 23.95 0.00 36.68 2.41
3796 4759 1.414550 TGCACTAGTGGTTGCACTACA 59.585 47.619 23.95 7.41 36.68 2.74
3797 4760 2.069273 CTGCACTAGTGGTTGCACTAC 58.931 52.381 23.95 4.83 36.68 2.73
3799 4762 0.886490 GCTGCACTAGTGGTTGCACT 60.886 55.000 23.95 0.00 39.08 4.40
3800 4763 1.576421 GCTGCACTAGTGGTTGCAC 59.424 57.895 23.95 6.97 32.03 4.57
3801 4764 1.960763 CGCTGCACTAGTGGTTGCA 60.961 57.895 23.95 14.47 33.19 4.08
3830 4793 2.056223 ACCGTATAGTGTGGCGCCT 61.056 57.895 29.70 9.99 0.00 5.52
3836 4799 0.457853 ACGCTGCACCGTATAGTGTG 60.458 55.000 5.00 0.00 40.08 3.82
3837 4800 0.179145 GACGCTGCACCGTATAGTGT 60.179 55.000 7.11 0.00 42.24 3.55
3842 4805 1.065928 GCTAGACGCTGCACCGTAT 59.934 57.895 7.11 7.01 42.24 3.06
3864 4827 3.679917 GCTAAGTCATTGTGCAGAGCCTA 60.680 47.826 0.00 0.00 0.00 3.93
3869 4832 5.710513 AAATTGCTAAGTCATTGTGCAGA 57.289 34.783 0.00 0.00 33.13 4.26
3876 4839 7.177392 AGACTGCCTAAAAATTGCTAAGTCATT 59.823 33.333 0.00 0.00 33.10 2.57
3877 4840 6.660949 AGACTGCCTAAAAATTGCTAAGTCAT 59.339 34.615 0.00 0.00 33.10 3.06
3886 4849 3.056607 CACCCCAGACTGCCTAAAAATTG 60.057 47.826 0.00 0.00 0.00 2.32
3893 4856 1.845664 TTGCACCCCAGACTGCCTA 60.846 57.895 0.00 0.00 31.97 3.93
3894 4857 3.177884 TTGCACCCCAGACTGCCT 61.178 61.111 0.00 0.00 31.97 4.75
3896 4859 3.357079 CGTTGCACCCCAGACTGC 61.357 66.667 0.00 0.00 0.00 4.40
3897 4860 3.357079 GCGTTGCACCCCAGACTG 61.357 66.667 0.00 0.00 0.00 3.51
3898 4861 3.560251 AGCGTTGCACCCCAGACT 61.560 61.111 0.00 0.00 0.00 3.24
3899 4862 3.357079 CAGCGTTGCACCCCAGAC 61.357 66.667 0.00 0.00 0.00 3.51
3900 4863 4.641645 CCAGCGTTGCACCCCAGA 62.642 66.667 0.00 0.00 0.00 3.86
3941 4904 0.600255 ACTACACTGTGCAACGCCTC 60.600 55.000 7.90 0.00 42.39 4.70
3979 4942 2.724839 CGGCTGACTTTTTATGTGACGC 60.725 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.