Multiple sequence alignment - TraesCS1D01G097600

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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 TraesCS1D01G097600 chr1D 100.000 4200 0 0 1 4200 84609768 84613967 0.000000e+00 7757.0
1 TraesCS1D01G097600 chr1D 88.295 1085 89 17 2353 3431 84724655 84725707 0.000000e+00 1266.0
2 TraesCS1D01G097600 chr1D 89.181 1026 87 10 2239 3255 84569334 84570344 0.000000e+00 1258.0
3 TraesCS1D01G097600 chr1D 87.719 627 51 16 3576 4198 84725911 84726515 0.000000e+00 708.0
4 TraesCS1D01G097600 chr1D 90.108 465 35 7 1731 2190 84566320 84566778 1.010000e-165 593.0
5 TraesCS1D01G097600 chr1D 87.061 541 28 17 1803 2326 84723532 84724047 1.310000e-159 573.0
6 TraesCS1D01G097600 chr1D 91.045 335 22 6 1794 2127 84568830 84569157 2.980000e-121 446.0
7 TraesCS1D01G097600 chr1D 82.343 572 43 21 983 1536 84722925 84723456 1.070000e-120 444.0
8 TraesCS1D01G097600 chr1D 81.560 564 64 23 996 1537 84565726 84566271 3.000000e-116 429.0
9 TraesCS1D01G097600 chr1D 88.410 371 23 9 3834 4200 84571116 84571470 3.000000e-116 429.0
10 TraesCS1D01G097600 chr1D 90.030 331 30 1 626 953 84573568 84573898 3.880000e-115 425.0
11 TraesCS1D01G097600 chr1D 94.819 193 10 0 432 624 84597727 84597919 6.820000e-78 302.0
12 TraesCS1D01G097600 chr1D 88.660 97 9 2 4105 4200 12330334 12330239 2.650000e-22 117.0
13 TraesCS1D01G097600 chr1D 92.647 68 5 0 3364 3431 84570467 84570534 9.610000e-17 99.0
14 TraesCS1D01G097600 chr1D 87.692 65 7 1 1598 1662 97132466 97132529 1.620000e-09 75.0
15 TraesCS1D01G097600 chr1B 91.914 2090 117 20 1584 3638 137173880 137175952 0.000000e+00 2876.0
16 TraesCS1D01G097600 chr1B 85.250 1478 145 35 2319 3777 137178974 137180397 0.000000e+00 1454.0
17 TraesCS1D01G097600 chr1B 87.962 1163 90 16 2279 3431 137153033 137154155 0.000000e+00 1327.0
18 TraesCS1D01G097600 chr1B 90.662 921 38 11 625 1536 137172985 137173866 0.000000e+00 1181.0
19 TraesCS1D01G097600 chr1B 87.226 1049 86 21 2353 3394 137447068 137448075 0.000000e+00 1151.0
20 TraesCS1D01G097600 chr1B 91.061 537 32 10 1692 2219 137152394 137152923 0.000000e+00 712.0
21 TraesCS1D01G097600 chr1B 87.742 620 50 14 3586 4198 137448325 137448925 0.000000e+00 701.0
22 TraesCS1D01G097600 chr1B 83.217 572 38 18 983 1536 137445304 137445835 4.920000e-129 472.0
23 TraesCS1D01G097600 chr1B 80.282 568 44 26 983 1536 137177368 137177881 2.390000e-97 366.0
24 TraesCS1D01G097600 chr1B 86.297 343 26 8 3861 4200 137154855 137155179 1.860000e-93 353.0
25 TraesCS1D01G097600 chr1B 86.975 238 21 3 984 1217 137151808 137152039 4.170000e-65 259.0
26 TraesCS1D01G097600 chr1B 91.743 109 6 3 4093 4200 137180436 137180542 9.410000e-32 148.0
27 TraesCS1D01G097600 chr1B 100.000 28 0 0 2225 2252 137152942 137152969 8.000000e-03 52.8
28 TraesCS1D01G097600 chr1A 90.492 1809 131 19 1739 3537 78546680 78548457 0.000000e+00 2350.0
29 TraesCS1D01G097600 chr1A 88.896 1486 126 26 1772 3255 78337973 78339421 0.000000e+00 1794.0
30 TraesCS1D01G097600 chr1A 87.268 1131 92 19 2319 3431 78955004 78956100 0.000000e+00 1243.0
31 TraesCS1D01G097600 chr1A 87.122 629 56 13 3576 4200 78956300 78956907 0.000000e+00 689.0
32 TraesCS1D01G097600 chr1A 89.892 554 26 7 983 1536 78543222 78543745 0.000000e+00 686.0
33 TraesCS1D01G097600 chr1A 85.197 635 57 18 1587 2190 78336181 78336809 5.970000e-173 617.0
34 TraesCS1D01G097600 chr1A 94.865 370 19 0 626 995 78542815 78543184 2.820000e-161 579.0
35 TraesCS1D01G097600 chr1A 85.958 527 41 14 1803 2326 78953955 78954451 2.220000e-147 532.0
36 TraesCS1D01G097600 chr1A 82.153 678 58 33 3551 4200 78548522 78549164 1.340000e-144 523.0
37 TraesCS1D01G097600 chr1A 86.583 477 37 16 3728 4200 78339431 78339884 6.270000e-138 501.0
38 TraesCS1D01G097600 chr1A 88.788 330 28 5 625 952 78348779 78349101 3.040000e-106 396.0
39 TraesCS1D01G097600 chr1A 81.644 523 47 20 1028 1536 78953400 78953887 5.090000e-104 388.0
40 TraesCS1D01G097600 chr1A 80.841 214 26 5 3999 4200 14163245 14163035 2.020000e-33 154.0
41 TraesCS1D01G097600 chr7B 91.520 625 39 8 1 624 122895198 122894587 0.000000e+00 848.0
42 TraesCS1D01G097600 chr7A 84.953 638 78 13 1 624 657436721 657436088 7.660000e-177 630.0
43 TraesCS1D01G097600 chr7A 82.879 514 48 13 2044 2545 583787780 583787295 3.880000e-115 425.0
44 TraesCS1D01G097600 chr7A 81.959 194 30 5 432 624 657441213 657441024 4.350000e-35 159.0
45 TraesCS1D01G097600 chr7A 90.476 63 6 0 1600 1662 634877709 634877771 2.690000e-12 84.2
46 TraesCS1D01G097600 chr6B 90.201 398 24 9 228 624 29753338 29753721 4.850000e-139 505.0
47 TraesCS1D01G097600 chr6B 92.609 230 17 0 1 230 29744364 29744593 8.700000e-87 331.0
48 TraesCS1D01G097600 chr6B 81.967 305 41 11 284 581 550588742 550588445 3.240000e-61 246.0
49 TraesCS1D01G097600 chr6B 89.691 194 9 7 432 624 29739995 29740178 1.950000e-58 237.0
50 TraesCS1D01G097600 chr6B 91.304 69 6 0 1248 1316 21052052 21051984 1.240000e-15 95.3
51 TraesCS1D01G097600 chr6D 84.264 197 20 7 432 624 12134572 12134761 9.280000e-42 182.0
52 TraesCS1D01G097600 chr5D 85.987 157 15 6 477 630 550446231 550446383 1.210000e-35 161.0
53 TraesCS1D01G097600 chr5D 87.719 57 7 0 1602 1658 297753739 297753683 2.710000e-07 67.6
54 TraesCS1D01G097600 chrUn 88.235 85 10 0 1248 1332 248122 248038 7.430000e-18 102.0
55 TraesCS1D01G097600 chr2B 86.905 84 8 3 1268 1349 706923973 706924055 1.610000e-14 91.6
56 TraesCS1D01G097600 chr5A 82.143 84 13 2 1268 1350 645680550 645680632 2.090000e-08 71.3
57 TraesCS1D01G097600 chr3A 89.091 55 6 0 1603 1657 502098336 502098282 7.530000e-08 69.4
58 TraesCS1D01G097600 chr5B 87.719 57 6 1 1593 1648 457984256 457984312 9.750000e-07 65.8


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 TraesCS1D01G097600 chr1D 84609768 84613967 4199 False 7757.000000 7757 100.000000 1 4200 1 chr1D.!!$F2 4199
1 TraesCS1D01G097600 chr1D 84722925 84726515 3590 False 747.750000 1266 86.354500 983 4198 4 chr1D.!!$F5 3215
2 TraesCS1D01G097600 chr1D 84565726 84573898 8172 False 525.571429 1258 88.997286 626 4200 7 chr1D.!!$F4 3574
3 TraesCS1D01G097600 chr1B 137172985 137180542 7557 False 1205.000000 2876 87.970200 625 4200 5 chr1B.!!$F2 3575
4 TraesCS1D01G097600 chr1B 137445304 137448925 3621 False 774.666667 1151 86.061667 983 4198 3 chr1B.!!$F3 3215
5 TraesCS1D01G097600 chr1B 137151808 137155179 3371 False 540.760000 1327 90.459000 984 4200 5 chr1B.!!$F1 3216
6 TraesCS1D01G097600 chr1A 78542815 78549164 6349 False 1034.500000 2350 89.350500 626 4200 4 chr1A.!!$F3 3574
7 TraesCS1D01G097600 chr1A 78336181 78339884 3703 False 970.666667 1794 86.892000 1587 4200 3 chr1A.!!$F2 2613
8 TraesCS1D01G097600 chr1A 78953400 78956907 3507 False 713.000000 1243 85.498000 1028 4200 4 chr1A.!!$F4 3172
9 TraesCS1D01G097600 chr7B 122894587 122895198 611 True 848.000000 848 91.520000 1 624 1 chr7B.!!$R1 623
10 TraesCS1D01G097600 chr7A 657436088 657436721 633 True 630.000000 630 84.953000 1 624 1 chr7A.!!$R2 623

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
281 294 0.755686 GATCGCTGGATTGAGGGAGT 59.244 55.0 0.00 0.00 38.23 3.85 F
1167 1242 0.102481 TCCGCTACTTCTTCGATGGC 59.898 55.0 0.00 0.00 0.00 4.40 F
2715 14756 0.179034 GGGAGGACTGTCCATGATGC 60.179 60.0 27.48 12.55 39.61 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1362 0.704664 ACCTCAATCCCCTCCAAACC 59.295 55.000 0.00 0.00 0.00 3.27 R
2870 14911 0.833949 GGACCCTGAAGGATCCTGAC 59.166 60.000 17.02 13.36 39.89 3.51 R
3964 16577 1.610522 GTTCATCCAGTGCAGCAGTTT 59.389 47.619 0.00 0.00 0.00 2.66 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
189 190 2.119029 TCGAGGACGCCGATGATGT 61.119 57.895 0.00 0.00 39.58 3.06
205 206 3.407967 GTTGGCCGGGATGGGAGA 61.408 66.667 2.18 0.00 38.63 3.71
273 286 2.224402 GCTAAGGGAAGATCGCTGGATT 60.224 50.000 0.00 0.00 39.75 3.01
281 294 0.755686 GATCGCTGGATTGAGGGAGT 59.244 55.000 0.00 0.00 38.23 3.85
463 480 3.901222 TGAATCACCGCATCTATTCCCTA 59.099 43.478 0.00 0.00 0.00 3.53
562 580 1.912417 CCCTACACTCTAGGCGCTAT 58.088 55.000 7.64 0.00 33.41 2.97
577 595 4.124238 GGCGCTATGGTTACAACAGAATA 58.876 43.478 7.64 0.00 0.00 1.75
579 597 5.238650 GGCGCTATGGTTACAACAGAATAAT 59.761 40.000 7.64 0.00 0.00 1.28
582 600 6.346598 CGCTATGGTTACAACAGAATAATCGG 60.347 42.308 0.00 0.00 0.00 4.18
583 601 6.482308 GCTATGGTTACAACAGAATAATCGGT 59.518 38.462 0.00 0.00 35.36 4.69
584 602 7.654520 GCTATGGTTACAACAGAATAATCGGTA 59.345 37.037 0.00 0.00 32.50 4.02
585 603 7.781548 ATGGTTACAACAGAATAATCGGTAC 57.218 36.000 0.00 0.00 32.50 3.34
587 605 7.160049 TGGTTACAACAGAATAATCGGTACAA 58.840 34.615 0.00 0.00 32.50 2.41
588 606 7.825270 TGGTTACAACAGAATAATCGGTACAAT 59.175 33.333 0.00 0.00 32.50 2.71
589 607 8.120465 GGTTACAACAGAATAATCGGTACAATG 58.880 37.037 0.00 0.00 32.50 2.82
592 610 8.780846 ACAACAGAATAATCGGTACAATGTTA 57.219 30.769 0.00 0.00 32.50 2.41
596 614 8.826710 ACAGAATAATCGGTACAATGTTACATG 58.173 33.333 0.00 0.00 31.87 3.21
597 615 9.040939 CAGAATAATCGGTACAATGTTACATGA 57.959 33.333 0.00 0.00 0.00 3.07
631 649 4.816385 ACGTGACAGTTCAACAATCAGATT 59.184 37.500 0.00 0.00 31.90 2.40
635 653 6.634436 GTGACAGTTCAACAATCAGATTTGAC 59.366 38.462 0.00 0.00 32.27 3.18
723 741 5.759059 TCCAGAAATGCATAATGGTCTTCT 58.241 37.500 18.94 11.62 32.68 2.85
802 820 5.840940 AACGAGATGTGCTACAGTAAAAC 57.159 39.130 0.00 0.00 0.00 2.43
909 928 5.298347 GTCAAGCTACAGTTAACTGAACCT 58.702 41.667 36.14 24.61 46.59 3.50
1164 1239 1.093159 ACGTCCGCTACTTCTTCGAT 58.907 50.000 0.00 0.00 0.00 3.59
1167 1242 0.102481 TCCGCTACTTCTTCGATGGC 59.898 55.000 0.00 0.00 0.00 4.40
1202 1280 0.179205 GACGAGGAGTGTACGTTCCG 60.179 60.000 0.00 0.00 40.29 4.30
1203 1281 0.886490 ACGAGGAGTGTACGTTCCGT 60.886 55.000 0.00 0.00 44.35 4.69
1211 1289 1.728425 GTGTACGTTCCGTTCCAATCC 59.272 52.381 0.00 0.00 41.54 3.01
1212 1290 1.343789 TGTACGTTCCGTTCCAATCCA 59.656 47.619 0.00 0.00 41.54 3.41
1213 1291 2.224233 TGTACGTTCCGTTCCAATCCAA 60.224 45.455 0.00 0.00 41.54 3.53
1214 1292 2.194201 ACGTTCCGTTCCAATCCAAT 57.806 45.000 0.00 0.00 36.35 3.16
1215 1293 2.081462 ACGTTCCGTTCCAATCCAATC 58.919 47.619 0.00 0.00 36.35 2.67
1219 1297 2.442413 TCCGTTCCAATCCAATCCAAC 58.558 47.619 0.00 0.00 0.00 3.77
1272 1360 3.502123 TCGGTTGAACCTCTTTTGGAT 57.498 42.857 13.18 0.00 35.66 3.41
1274 1362 4.575885 TCGGTTGAACCTCTTTTGGATAG 58.424 43.478 13.18 0.00 35.66 2.08
1348 1436 4.088634 CAATCCACTCAAATCCCCTTCAA 58.911 43.478 0.00 0.00 0.00 2.69
1391 1479 0.541863 AGCCCTTACCGATCCTTGTG 59.458 55.000 0.00 0.00 0.00 3.33
1458 1614 6.718454 AGTGTCACTTCATTCCTCAAAATCAT 59.282 34.615 0.00 0.00 0.00 2.45
1485 1644 6.522054 TGAAGGTTACTTTCACTTCCTACTG 58.478 40.000 5.80 0.00 38.78 2.74
1537 1696 7.271223 ACTTTCAAATTCATTCGTCAATTAGCG 59.729 33.333 0.00 0.00 0.00 4.26
1538 1697 5.027737 TCAAATTCATTCGTCAATTAGCGC 58.972 37.500 0.00 0.00 0.00 5.92
1539 1698 4.614555 AATTCATTCGTCAATTAGCGCA 57.385 36.364 11.47 0.00 0.00 6.09
1541 1700 4.614555 TTCATTCGTCAATTAGCGCATT 57.385 36.364 11.47 0.00 0.00 3.56
1544 1703 5.027737 TCATTCGTCAATTAGCGCATTTTC 58.972 37.500 11.47 0.00 0.00 2.29
1545 1704 4.678509 TTCGTCAATTAGCGCATTTTCT 57.321 36.364 11.47 0.00 0.00 2.52
1546 1705 4.678509 TCGTCAATTAGCGCATTTTCTT 57.321 36.364 11.47 0.00 0.00 2.52
1550 1709 5.631026 GTCAATTAGCGCATTTTCTTCTGA 58.369 37.500 11.47 0.00 0.00 3.27
1551 1710 6.086222 GTCAATTAGCGCATTTTCTTCTGAA 58.914 36.000 11.47 0.00 0.00 3.02
1553 1712 6.968904 TCAATTAGCGCATTTTCTTCTGAATC 59.031 34.615 11.47 0.00 31.56 2.52
1556 1715 3.436704 AGCGCATTTTCTTCTGAATCGAA 59.563 39.130 11.47 0.00 31.56 3.71
1557 1716 4.095483 AGCGCATTTTCTTCTGAATCGAAT 59.905 37.500 11.47 0.00 31.56 3.34
1558 1717 4.203764 GCGCATTTTCTTCTGAATCGAATG 59.796 41.667 0.30 11.92 33.99 2.67
1559 1718 5.327091 CGCATTTTCTTCTGAATCGAATGT 58.673 37.500 15.12 0.00 33.67 2.71
1560 1719 5.796935 CGCATTTTCTTCTGAATCGAATGTT 59.203 36.000 15.12 0.00 33.67 2.71
1561 1720 6.021939 CGCATTTTCTTCTGAATCGAATGTTC 60.022 38.462 15.12 0.00 33.67 3.18
1562 1721 7.025963 GCATTTTCTTCTGAATCGAATGTTCT 58.974 34.615 15.12 0.00 33.67 3.01
1563 1722 8.177663 GCATTTTCTTCTGAATCGAATGTTCTA 58.822 33.333 15.12 0.00 33.67 2.10
1566 1725 7.596749 TTCTTCTGAATCGAATGTTCTAACC 57.403 36.000 0.00 0.00 0.00 2.85
1567 1726 6.936279 TCTTCTGAATCGAATGTTCTAACCT 58.064 36.000 0.00 0.00 0.00 3.50
1568 1727 7.386851 TCTTCTGAATCGAATGTTCTAACCTT 58.613 34.615 0.00 0.00 0.00 3.50
1569 1728 7.878127 TCTTCTGAATCGAATGTTCTAACCTTT 59.122 33.333 0.00 0.00 0.00 3.11
1570 1729 7.979444 TCTGAATCGAATGTTCTAACCTTTT 57.021 32.000 0.00 0.00 0.00 2.27
1571 1730 8.391075 TCTGAATCGAATGTTCTAACCTTTTT 57.609 30.769 0.00 0.00 0.00 1.94
1572 1731 8.504005 TCTGAATCGAATGTTCTAACCTTTTTC 58.496 33.333 0.00 0.00 0.00 2.29
1573 1732 8.391075 TGAATCGAATGTTCTAACCTTTTTCT 57.609 30.769 0.00 0.00 0.00 2.52
1574 1733 8.289618 TGAATCGAATGTTCTAACCTTTTTCTG 58.710 33.333 0.00 0.00 0.00 3.02
1575 1734 7.979444 ATCGAATGTTCTAACCTTTTTCTGA 57.021 32.000 0.00 0.00 0.00 3.27
1576 1735 7.795482 TCGAATGTTCTAACCTTTTTCTGAA 57.205 32.000 0.00 0.00 0.00 3.02
1577 1736 8.391075 TCGAATGTTCTAACCTTTTTCTGAAT 57.609 30.769 0.00 0.00 0.00 2.57
1578 1737 8.504005 TCGAATGTTCTAACCTTTTTCTGAATC 58.496 33.333 0.00 0.00 0.00 2.52
1579 1738 7.478667 CGAATGTTCTAACCTTTTTCTGAATCG 59.521 37.037 0.00 0.00 0.00 3.34
1580 1739 7.979444 ATGTTCTAACCTTTTTCTGAATCGA 57.021 32.000 0.00 0.00 0.00 3.59
1581 1740 7.795482 TGTTCTAACCTTTTTCTGAATCGAA 57.205 32.000 0.00 0.00 0.00 3.71
1582 1741 8.215926 TGTTCTAACCTTTTTCTGAATCGAAA 57.784 30.769 0.00 0.00 0.00 3.46
1607 4475 9.702494 AAACGCACTACTTTTAATTACTACTCT 57.298 29.630 0.00 0.00 0.00 3.24
1667 4556 6.542735 TCTGAGTAGGATGTATGTAGTGTGTC 59.457 42.308 0.00 0.00 0.00 3.67
1762 4674 0.252479 AAGATGAGAGCACAGCCTGG 59.748 55.000 0.00 0.00 0.00 4.45
1836 6354 2.299297 CTCGTCTTGTTACCCTCCTTGT 59.701 50.000 0.00 0.00 0.00 3.16
1846 6364 5.710099 TGTTACCCTCCTTGTTTGATTGATC 59.290 40.000 0.00 0.00 0.00 2.92
1847 6365 3.347216 ACCCTCCTTGTTTGATTGATCG 58.653 45.455 0.00 0.00 0.00 3.69
1848 6366 3.009033 ACCCTCCTTGTTTGATTGATCGA 59.991 43.478 0.00 0.00 0.00 3.59
1849 6367 4.202441 CCCTCCTTGTTTGATTGATCGAT 58.798 43.478 0.00 0.00 0.00 3.59
1851 6369 6.000219 CCCTCCTTGTTTGATTGATCGATAT 59.000 40.000 0.00 0.00 0.00 1.63
1852 6370 6.072838 CCCTCCTTGTTTGATTGATCGATATG 60.073 42.308 0.00 0.00 0.00 1.78
1853 6371 6.304356 TCCTTGTTTGATTGATCGATATGC 57.696 37.500 0.00 0.00 0.00 3.14
1854 6372 5.821995 TCCTTGTTTGATTGATCGATATGCA 59.178 36.000 0.00 0.00 0.00 3.96
1855 6373 6.487668 TCCTTGTTTGATTGATCGATATGCAT 59.512 34.615 3.79 3.79 0.00 3.96
1930 6448 0.545787 TCAAAGAGGGGTTCCGGCTA 60.546 55.000 0.00 0.00 38.33 3.93
2174 6697 8.185506 TGTACTGGTACTTTCTCATTTCAGTA 57.814 34.615 11.44 0.00 37.00 2.74
2317 9424 6.540914 TGAATAACGGATCTGGTTTTGTATCC 59.459 38.462 6.47 0.00 35.54 2.59
2367 10066 8.057011 TGATACTTGTCTTGTAGGGTATAGTGA 58.943 37.037 0.00 0.00 0.00 3.41
2440 10140 6.158598 GCAATCTGCACAATAAGAAAAGGAA 58.841 36.000 0.00 0.00 44.26 3.36
2512 10212 6.727824 ATTACCTTGTTTCGTCATTCAGAG 57.272 37.500 0.00 0.00 0.00 3.35
2628 14669 6.051179 TGATTCATTGATTTTGATTGGCCA 57.949 33.333 0.00 0.00 0.00 5.36
2629 14670 6.473758 TGATTCATTGATTTTGATTGGCCAA 58.526 32.000 23.00 23.00 0.00 4.52
2708 14749 1.078143 GTGCATGGGAGGACTGTCC 60.078 63.158 19.20 19.20 36.58 4.02
2715 14756 0.179034 GGGAGGACTGTCCATGATGC 60.179 60.000 27.48 12.55 39.61 3.91
2719 14760 2.036992 GAGGACTGTCCATGATGCTAGG 59.963 54.545 27.48 0.00 39.61 3.02
2769 14810 4.001248 CCGCAGGCTGGAATTTGA 57.999 55.556 17.64 0.00 46.14 2.69
2800 14841 2.420722 TGTGGTTGAAACGGAAACACTC 59.579 45.455 0.00 0.00 40.93 3.51
2833 14874 7.479980 TGCACAGCATATTGGATTTAAACTAC 58.520 34.615 0.00 0.00 31.71 2.73
2870 14911 1.302832 GTGGAGGGCACTGTTGAGG 60.303 63.158 0.00 0.00 0.00 3.86
2882 14924 2.569404 ACTGTTGAGGTCAGGATCCTTC 59.431 50.000 13.00 7.96 37.25 3.46
2887 14929 0.419459 AGGTCAGGATCCTTCAGGGT 59.581 55.000 13.00 0.00 36.25 4.34
2911 14953 4.765856 CCTGATGAATTCCATGGGAAGATC 59.234 45.833 13.02 7.09 45.48 2.75
2913 14955 2.575532 TGAATTCCATGGGAAGATCGC 58.424 47.619 13.02 0.00 45.48 4.58
3001 15043 1.271597 GCAGGTGACAATGGAGTCCTT 60.272 52.381 11.33 0.19 37.73 3.36
3043 15085 4.805140 AGGAGTCTCTGTGGATGAGATA 57.195 45.455 0.00 0.00 41.79 1.98
3076 15118 3.418068 GCTGCTGCTGTCGGTGAC 61.418 66.667 8.53 0.00 36.03 3.67
3077 15119 2.341543 CTGCTGCTGTCGGTGACT 59.658 61.111 0.00 0.00 33.15 3.41
3080 15122 1.405463 CTGCTGCTGTCGGTGACTATA 59.595 52.381 0.00 0.00 33.15 1.31
3132 15174 1.298339 GGCGCAATGGTTACGATGC 60.298 57.895 10.83 0.00 35.49 3.91
3138 15180 2.874701 GCAATGGTTACGATGCTGAGAT 59.125 45.455 0.00 0.00 35.93 2.75
3144 15186 6.101650 TGGTTACGATGCTGAGATTATCAT 57.898 37.500 0.00 0.00 37.28 2.45
3145 15187 7.227049 TGGTTACGATGCTGAGATTATCATA 57.773 36.000 0.00 0.00 37.28 2.15
3151 15193 3.264947 TGCTGAGATTATCATATGCGGC 58.735 45.455 0.00 0.00 37.28 6.53
3152 15194 3.264947 GCTGAGATTATCATATGCGGCA 58.735 45.455 4.58 4.58 37.28 5.69
3158 15200 5.178797 AGATTATCATATGCGGCAACTACC 58.821 41.667 6.82 0.00 0.00 3.18
3160 15202 2.928801 TCATATGCGGCAACTACCAT 57.071 45.000 6.82 0.00 0.00 3.55
3174 15216 4.078639 ACTACCATATGCTTCTGAAGGC 57.921 45.455 18.38 11.24 0.00 4.35
3205 15252 7.768582 TGGTCGATTGTGTATTTCTGATGTAAT 59.231 33.333 0.00 0.00 0.00 1.89
3278 15325 8.511604 TTTTAGCAATCCTCTAGATCCTTTTG 57.488 34.615 0.00 0.00 32.47 2.44
3279 15326 5.965033 AGCAATCCTCTAGATCCTTTTGA 57.035 39.130 0.00 0.00 32.47 2.69
3280 15327 6.512514 AGCAATCCTCTAGATCCTTTTGAT 57.487 37.500 0.00 0.00 32.47 2.57
3288 15335 5.111989 TCTAGATCCTTTTGATGCAACGAG 58.888 41.667 0.00 0.00 32.41 4.18
3292 15339 1.135575 CCTTTTGATGCAACGAGGCTC 60.136 52.381 3.87 3.87 34.04 4.70
3305 15352 1.417890 CGAGGCTCCATTATGGGAACT 59.582 52.381 11.76 6.78 38.32 3.01
3346 15393 5.734855 AACAATATATGTGTTCCAGCGTC 57.265 39.130 7.19 0.00 42.99 5.19
3355 15402 5.585820 TGTGTTCCAGCGTCTATTGTATA 57.414 39.130 0.00 0.00 0.00 1.47
3396 15483 5.294552 GCTGATGTAAGCTAGTTTTACTGGG 59.705 44.000 15.59 8.15 40.20 4.45
3433 15654 7.878477 ACATGCATGAAATTTAAGAGTTGTG 57.122 32.000 32.75 1.41 0.00 3.33
3434 15655 6.366877 ACATGCATGAAATTTAAGAGTTGTGC 59.633 34.615 32.75 0.00 0.00 4.57
3447 15668 5.135508 AGAGTTGTGCTATTTACGTCAGT 57.864 39.130 0.00 0.00 0.00 3.41
3468 15689 5.008811 CAGTATAGTCAGGTTTACTCGGAGG 59.991 48.000 10.23 0.00 0.00 4.30
3473 15694 3.744942 GTCAGGTTTACTCGGAGGAAAAC 59.255 47.826 20.80 20.80 0.00 2.43
3474 15695 2.735134 CAGGTTTACTCGGAGGAAAACG 59.265 50.000 21.79 14.31 33.61 3.60
3477 15698 3.370061 GGTTTACTCGGAGGAAAACGATG 59.630 47.826 16.71 0.00 38.56 3.84
3480 15701 2.960819 ACTCGGAGGAAAACGATGAAG 58.039 47.619 10.23 0.00 38.56 3.02
3481 15702 2.299297 ACTCGGAGGAAAACGATGAAGT 59.701 45.455 10.23 0.00 38.56 3.01
3482 15703 2.668457 CTCGGAGGAAAACGATGAAGTG 59.332 50.000 0.00 0.00 38.56 3.16
3483 15704 2.036733 TCGGAGGAAAACGATGAAGTGT 59.963 45.455 0.00 0.00 33.69 3.55
3487 15710 1.810755 GGAAAACGATGAAGTGTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
3491 15714 2.649531 ACGATGAAGTGTCCCCAAAA 57.350 45.000 0.00 0.00 0.00 2.44
3492 15715 2.227194 ACGATGAAGTGTCCCCAAAAC 58.773 47.619 0.00 0.00 0.00 2.43
3507 15730 4.202409 CCCCAAAACTTGCCATCCTAAAAA 60.202 41.667 0.00 0.00 0.00 1.94
3508 15731 4.996758 CCCAAAACTTGCCATCCTAAAAAG 59.003 41.667 0.00 0.00 0.00 2.27
3515 15738 5.774690 ACTTGCCATCCTAAAAAGAATGTCA 59.225 36.000 0.00 0.00 0.00 3.58
3595 15917 8.768501 ATATACAAGATCTGAAGACCTGTGTA 57.231 34.615 0.00 0.00 0.00 2.90
3717 16194 8.567948 TGTTTTTGGTTAGAATCAAGATCTCAC 58.432 33.333 0.00 0.00 29.47 3.51
3897 16509 8.987890 TCAGAATTTAAGCAACTTTAAAATGCC 58.012 29.630 17.49 5.39 40.93 4.40
3964 16577 3.376859 CACTAACAAGCGCCCATCAATAA 59.623 43.478 2.29 0.00 0.00 1.40
3988 16601 2.230508 CTGCTGCACTGGATGAACAAAT 59.769 45.455 0.00 0.00 0.00 2.32
3990 16603 3.248266 GCTGCACTGGATGAACAAATTC 58.752 45.455 0.00 0.00 35.18 2.17
3991 16604 3.057033 GCTGCACTGGATGAACAAATTCT 60.057 43.478 0.00 0.00 35.69 2.40
3992 16605 4.482386 CTGCACTGGATGAACAAATTCTG 58.518 43.478 0.00 0.00 35.69 3.02
3993 16606 3.256383 TGCACTGGATGAACAAATTCTGG 59.744 43.478 0.00 0.00 35.69 3.86
3994 16607 3.256631 GCACTGGATGAACAAATTCTGGT 59.743 43.478 0.00 0.00 35.69 4.00
3995 16608 4.262164 GCACTGGATGAACAAATTCTGGTT 60.262 41.667 0.00 0.00 35.69 3.67
3996 16609 5.048083 GCACTGGATGAACAAATTCTGGTTA 60.048 40.000 0.00 0.00 35.69 2.85
4134 16756 4.033009 TGCAGAGTTTGGATATCTCAGGA 58.967 43.478 2.05 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.249322 CGACAACACCCTCGTCTTGT 60.249 55.000 0.00 0.00 34.26 3.16
189 190 3.089874 CTCTCCCATCCCGGCCAA 61.090 66.667 2.24 0.00 0.00 4.52
273 286 0.041833 CTCTCCCCTGAACTCCCTCA 59.958 60.000 0.00 0.00 0.00 3.86
281 294 2.903357 GCATCGCTCTCCCCTGAA 59.097 61.111 0.00 0.00 0.00 3.02
326 342 1.966451 CGGTGCAAACCTCTCCACC 60.966 63.158 0.00 0.00 43.27 4.61
327 343 1.966451 CCGGTGCAAACCTCTCCAC 60.966 63.158 0.00 0.00 0.00 4.02
328 344 2.429930 CCGGTGCAAACCTCTCCA 59.570 61.111 0.00 0.00 0.00 3.86
484 501 0.902984 TGTAGGGATCACGCCTGTGT 60.903 55.000 0.00 0.00 46.49 3.72
562 580 6.699366 TGTACCGATTATTCTGTTGTAACCA 58.301 36.000 0.00 0.00 0.00 3.67
577 595 9.168451 TGTATTTCATGTAACATTGTACCGATT 57.832 29.630 0.00 0.00 0.00 3.34
579 597 8.725405 ATGTATTTCATGTAACATTGTACCGA 57.275 30.769 0.00 0.00 35.19 4.69
584 602 9.767684 CGTTGTATGTATTTCATGTAACATTGT 57.232 29.630 9.18 0.00 37.91 2.71
585 603 9.767684 ACGTTGTATGTATTTCATGTAACATTG 57.232 29.630 9.18 0.00 37.91 2.82
587 605 9.157104 TCACGTTGTATGTATTTCATGTAACAT 57.843 29.630 0.00 1.86 37.91 2.71
588 606 8.436970 GTCACGTTGTATGTATTTCATGTAACA 58.563 33.333 0.00 0.00 37.91 2.41
589 607 8.436970 TGTCACGTTGTATGTATTTCATGTAAC 58.563 33.333 0.00 0.00 37.91 2.50
592 610 6.649141 ACTGTCACGTTGTATGTATTTCATGT 59.351 34.615 0.00 0.00 37.91 3.21
596 614 7.112528 TGAACTGTCACGTTGTATGTATTTC 57.887 36.000 0.00 0.00 0.00 2.17
597 615 7.011576 TGTTGAACTGTCACGTTGTATGTATTT 59.988 33.333 0.00 0.00 31.90 1.40
631 649 5.450818 ACTTGCTCCCCAATTATAGTCAA 57.549 39.130 0.00 0.00 31.91 3.18
635 653 6.187727 TCCTTACTTGCTCCCCAATTATAG 57.812 41.667 0.00 0.00 31.91 1.31
871 890 3.641906 AGCTTGACCTACAATACCGCTAT 59.358 43.478 0.00 0.00 35.53 2.97
872 891 3.028850 AGCTTGACCTACAATACCGCTA 58.971 45.455 0.00 0.00 35.53 4.26
1202 1280 2.534990 TGGGTTGGATTGGATTGGAAC 58.465 47.619 0.00 0.00 0.00 3.62
1203 1281 3.266477 TTGGGTTGGATTGGATTGGAA 57.734 42.857 0.00 0.00 0.00 3.53
1211 1289 2.252535 AGGGGAATTGGGTTGGATTG 57.747 50.000 0.00 0.00 0.00 2.67
1212 1290 4.642489 ATAAGGGGAATTGGGTTGGATT 57.358 40.909 0.00 0.00 0.00 3.01
1213 1291 4.235164 AGAATAAGGGGAATTGGGTTGGAT 59.765 41.667 0.00 0.00 0.00 3.41
1214 1292 3.600617 AGAATAAGGGGAATTGGGTTGGA 59.399 43.478 0.00 0.00 0.00 3.53
1215 1293 3.994317 AGAATAAGGGGAATTGGGTTGG 58.006 45.455 0.00 0.00 0.00 3.77
1219 1297 6.013554 TGAACTAGAATAAGGGGAATTGGG 57.986 41.667 0.00 0.00 0.00 4.12
1272 1360 2.205342 CCTCAATCCCCTCCAAACCTA 58.795 52.381 0.00 0.00 0.00 3.08
1274 1362 0.704664 ACCTCAATCCCCTCCAAACC 59.295 55.000 0.00 0.00 0.00 3.27
1348 1436 2.371897 CTGTTGCAAGGGGAGGGGTT 62.372 60.000 0.00 0.00 0.00 4.11
1391 1479 1.668419 AGACATGCATAACGAAGGCC 58.332 50.000 0.00 0.00 0.00 5.19
1458 1614 6.248569 AGGAAGTGAAAGTAACCTTCAGAA 57.751 37.500 0.00 0.00 36.00 3.02
1485 1644 3.706698 GCCTTTGCTTCGGAATAAATCC 58.293 45.455 0.00 0.00 38.61 3.01
1537 1696 7.025963 AGAACATTCGATTCAGAAGAAAATGC 58.974 34.615 11.42 0.00 34.84 3.56
1541 1700 7.878127 AGGTTAGAACATTCGATTCAGAAGAAA 59.122 33.333 0.47 0.00 37.29 2.52
1544 1703 7.602517 AAGGTTAGAACATTCGATTCAGAAG 57.397 36.000 0.47 0.00 33.19 2.85
1545 1704 7.979444 AAAGGTTAGAACATTCGATTCAGAA 57.021 32.000 0.47 0.00 30.85 3.02
1546 1705 7.979444 AAAAGGTTAGAACATTCGATTCAGA 57.021 32.000 0.47 0.00 30.85 3.27
1550 1709 8.391075 TCAGAAAAAGGTTAGAACATTCGATT 57.609 30.769 0.00 0.00 30.85 3.34
1551 1710 7.979444 TCAGAAAAAGGTTAGAACATTCGAT 57.021 32.000 0.00 0.00 30.85 3.59
1553 1712 7.478667 CGATTCAGAAAAAGGTTAGAACATTCG 59.521 37.037 0.00 0.00 30.85 3.34
1556 1715 7.979444 TCGATTCAGAAAAAGGTTAGAACAT 57.021 32.000 0.00 0.00 0.00 2.71
1557 1716 7.795482 TTCGATTCAGAAAAAGGTTAGAACA 57.205 32.000 0.00 0.00 0.00 3.18
1581 1740 9.702494 AGAGTAGTAATTAAAAGTAGTGCGTTT 57.298 29.630 0.00 0.00 33.56 3.60
1582 1741 9.351570 GAGAGTAGTAATTAAAAGTAGTGCGTT 57.648 33.333 0.00 0.00 0.00 4.84
1607 4475 6.494666 ACATCTTATAATTGGGAACGGAGA 57.505 37.500 0.00 0.00 0.00 3.71
1647 4515 6.452494 ACAGACACACTACATACATCCTAC 57.548 41.667 0.00 0.00 0.00 3.18
1649 4517 5.480422 TGAACAGACACACTACATACATCCT 59.520 40.000 0.00 0.00 0.00 3.24
1667 4556 4.836125 ACAGGCTAAAATGTGTGAACAG 57.164 40.909 0.00 0.00 0.00 3.16
1714 4626 9.458727 GCATAGTAATATACTACCACCTCTGTA 57.541 37.037 0.00 0.00 43.46 2.74
1762 4674 1.339929 ACCATTGAAAACCGAACCAGC 59.660 47.619 0.00 0.00 0.00 4.85
1836 6354 9.806203 AAGAAAAATGCATATCGATCAATCAAA 57.194 25.926 0.00 0.00 0.00 2.69
1846 6364 8.740369 GTCAAATGAGAAGAAAAATGCATATCG 58.260 33.333 0.00 0.00 0.00 2.92
1847 6365 9.577110 TGTCAAATGAGAAGAAAAATGCATATC 57.423 29.630 0.00 0.00 0.00 1.63
1848 6366 9.582431 CTGTCAAATGAGAAGAAAAATGCATAT 57.418 29.630 0.00 0.00 0.00 1.78
1849 6367 7.543172 GCTGTCAAATGAGAAGAAAAATGCATA 59.457 33.333 0.00 0.00 0.00 3.14
1851 6369 5.693104 GCTGTCAAATGAGAAGAAAAATGCA 59.307 36.000 0.00 0.00 0.00 3.96
1852 6370 5.693104 TGCTGTCAAATGAGAAGAAAAATGC 59.307 36.000 0.00 0.00 0.00 3.56
1853 6371 6.145048 GGTGCTGTCAAATGAGAAGAAAAATG 59.855 38.462 0.00 0.00 0.00 2.32
1854 6372 6.041296 AGGTGCTGTCAAATGAGAAGAAAAAT 59.959 34.615 0.00 0.00 0.00 1.82
1855 6373 5.360714 AGGTGCTGTCAAATGAGAAGAAAAA 59.639 36.000 0.00 0.00 0.00 1.94
2290 9396 6.834168 ACAAAACCAGATCCGTTATTCAAT 57.166 33.333 0.00 0.00 0.00 2.57
2317 9424 9.949174 TCATTAAAATCAACATCATATGGAACG 57.051 29.630 2.13 0.00 33.60 3.95
2367 10066 2.711547 GTGATAAACCCCTGGCTCCTAT 59.288 50.000 0.00 0.00 0.00 2.57
2512 10212 5.337578 TTGGGGTTCATTTTTAGCTATGC 57.662 39.130 0.00 0.00 0.00 3.14
2600 14641 8.145767 GCCAATCAAAATCAATGAATCATCCTA 58.854 33.333 0.00 0.00 0.00 2.94
2622 14663 3.524095 TGAATCCTCTCTTTTGGCCAA 57.476 42.857 16.05 16.05 0.00 4.52
2628 14669 4.818546 CGCATACCATGAATCCTCTCTTTT 59.181 41.667 0.00 0.00 0.00 2.27
2629 14670 4.101585 TCGCATACCATGAATCCTCTCTTT 59.898 41.667 0.00 0.00 0.00 2.52
2708 14749 4.063689 CCTTTACTGAGCCTAGCATCATG 58.936 47.826 0.00 0.00 0.00 3.07
2719 14760 1.210478 TCCATCAGGCCTTTACTGAGC 59.790 52.381 0.00 0.00 46.98 4.26
2768 14809 4.273480 CGTTTCAACCACATATCTGGGATC 59.727 45.833 1.80 0.00 35.34 3.36
2769 14810 4.199310 CGTTTCAACCACATATCTGGGAT 58.801 43.478 1.80 0.00 35.34 3.85
2833 14874 2.666508 CACCGACCTTCTTACGAATGTG 59.333 50.000 0.00 0.00 29.72 3.21
2870 14911 0.833949 GGACCCTGAAGGATCCTGAC 59.166 60.000 17.02 13.36 39.89 3.51
2882 14924 3.220110 CATGGAATTCATCAGGACCCTG 58.780 50.000 9.74 9.74 44.86 4.45
2887 14929 3.787577 TCTTCCCATGGAATTCATCAGGA 59.212 43.478 15.22 5.19 41.23 3.86
2911 14953 4.192000 CTGGTAGTGGAAGCAGCG 57.808 61.111 0.00 0.00 38.08 5.18
2962 15004 1.004918 AGTTAGCGCACCACTCACC 60.005 57.895 11.47 0.00 0.00 4.02
3043 15085 1.382522 CAGCAACAGTCAACACCAGT 58.617 50.000 0.00 0.00 0.00 4.00
3076 15118 5.833082 ACAGTGCCGACAGATAACTTATAG 58.167 41.667 0.00 0.00 0.00 1.31
3077 15119 5.847111 ACAGTGCCGACAGATAACTTATA 57.153 39.130 0.00 0.00 0.00 0.98
3080 15122 3.067106 CAACAGTGCCGACAGATAACTT 58.933 45.455 0.00 0.00 0.00 2.66
3132 15174 4.934001 AGTTGCCGCATATGATAATCTCAG 59.066 41.667 6.97 0.00 37.28 3.35
3138 15180 4.344359 TGGTAGTTGCCGCATATGATAA 57.656 40.909 6.97 0.00 0.00 1.75
3144 15186 2.038426 AGCATATGGTAGTTGCCGCATA 59.962 45.455 5.40 0.00 37.07 3.14
3145 15187 1.202806 AGCATATGGTAGTTGCCGCAT 60.203 47.619 5.40 0.00 37.07 4.73
3151 15193 4.274459 GCCTTCAGAAGCATATGGTAGTTG 59.726 45.833 8.04 7.27 0.00 3.16
3152 15194 4.455606 GCCTTCAGAAGCATATGGTAGTT 58.544 43.478 8.04 0.00 0.00 2.24
3158 15200 2.928334 AGTGGCCTTCAGAAGCATATG 58.072 47.619 3.32 0.00 0.00 1.78
3160 15202 2.618816 CCAAGTGGCCTTCAGAAGCATA 60.619 50.000 3.32 0.00 0.00 3.14
3174 15216 4.695455 AGAAATACACAATCGACCAAGTGG 59.305 41.667 11.45 0.00 42.17 4.00
3205 15252 3.184541 GCCGCGACTGAATAACTAAGAA 58.815 45.455 8.23 0.00 0.00 2.52
3255 15302 7.437713 TCAAAAGGATCTAGAGGATTGCTAA 57.562 36.000 0.00 0.00 34.33 3.09
3257 15304 5.965033 TCAAAAGGATCTAGAGGATTGCT 57.035 39.130 0.00 0.00 34.33 3.91
3258 15305 5.048852 GCATCAAAAGGATCTAGAGGATTGC 60.049 44.000 0.00 0.00 34.33 3.56
3259 15306 6.060136 TGCATCAAAAGGATCTAGAGGATTG 58.940 40.000 0.00 0.00 34.33 2.67
3260 15307 6.257994 TGCATCAAAAGGATCTAGAGGATT 57.742 37.500 0.00 0.00 34.33 3.01
3261 15308 5.901413 TGCATCAAAAGGATCTAGAGGAT 57.099 39.130 0.00 0.00 37.37 3.24
3262 15309 5.431765 GTTGCATCAAAAGGATCTAGAGGA 58.568 41.667 0.00 0.00 32.57 3.71
3263 15310 4.272018 CGTTGCATCAAAAGGATCTAGAGG 59.728 45.833 0.00 0.00 32.57 3.69
3264 15311 5.111989 TCGTTGCATCAAAAGGATCTAGAG 58.888 41.667 0.00 0.00 32.57 2.43
3265 15312 5.084818 TCGTTGCATCAAAAGGATCTAGA 57.915 39.130 0.00 0.00 32.57 2.43
3266 15313 4.272018 CCTCGTTGCATCAAAAGGATCTAG 59.728 45.833 0.00 0.00 33.18 2.43
3267 15314 4.191544 CCTCGTTGCATCAAAAGGATCTA 58.808 43.478 0.00 0.00 33.18 1.98
3268 15315 3.012518 CCTCGTTGCATCAAAAGGATCT 58.987 45.455 0.00 0.00 33.18 2.75
3269 15316 2.478539 GCCTCGTTGCATCAAAAGGATC 60.479 50.000 10.51 0.00 33.18 3.36
3270 15317 1.474077 GCCTCGTTGCATCAAAAGGAT 59.526 47.619 10.51 0.00 33.18 3.24
3271 15318 0.881118 GCCTCGTTGCATCAAAAGGA 59.119 50.000 10.51 0.00 33.18 3.36
3272 15319 0.883833 AGCCTCGTTGCATCAAAAGG 59.116 50.000 0.00 0.00 33.99 3.11
3273 15320 1.135575 GGAGCCTCGTTGCATCAAAAG 60.136 52.381 0.00 0.00 0.00 2.27
3274 15321 0.881118 GGAGCCTCGTTGCATCAAAA 59.119 50.000 0.00 0.00 0.00 2.44
3275 15322 0.250684 TGGAGCCTCGTTGCATCAAA 60.251 50.000 0.00 0.00 0.00 2.69
3276 15323 0.035152 ATGGAGCCTCGTTGCATCAA 60.035 50.000 0.00 0.00 0.00 2.57
3277 15324 0.035152 AATGGAGCCTCGTTGCATCA 60.035 50.000 0.00 0.61 0.00 3.07
3278 15325 1.953559 TAATGGAGCCTCGTTGCATC 58.046 50.000 0.00 0.00 0.00 3.91
3279 15326 2.224606 CATAATGGAGCCTCGTTGCAT 58.775 47.619 0.00 0.00 0.00 3.96
3280 15327 1.667236 CATAATGGAGCCTCGTTGCA 58.333 50.000 2.08 0.00 0.00 4.08
3288 15335 4.439253 AACTAGTTCCCATAATGGAGCC 57.561 45.455 1.12 0.00 40.96 4.70
3355 15402 6.887013 ACATCAGCAAGAAGAGTCAGAATAT 58.113 36.000 0.00 0.00 0.00 1.28
3371 15418 5.874810 CCAGTAAAACTAGCTTACATCAGCA 59.125 40.000 14.54 0.00 42.84 4.41
3396 15483 1.522668 TGCATGTACCACAAGCAGTC 58.477 50.000 5.20 0.00 46.19 3.51
3433 15654 6.968250 ACCTGACTATACTGACGTAAATAGC 58.032 40.000 0.00 0.00 0.00 2.97
3447 15668 5.378230 TCCTCCGAGTAAACCTGACTATA 57.622 43.478 0.00 0.00 0.00 1.31
3468 15689 2.500229 TGGGGACACTTCATCGTTTTC 58.500 47.619 0.00 0.00 33.40 2.29
3473 15694 2.504367 AGTTTTGGGGACACTTCATCG 58.496 47.619 0.00 0.00 42.67 3.84
3474 15695 3.552890 GCAAGTTTTGGGGACACTTCATC 60.553 47.826 0.00 0.00 42.67 2.92
3477 15698 1.068588 GGCAAGTTTTGGGGACACTTC 59.931 52.381 0.00 0.00 42.67 3.01
3480 15701 1.000843 GATGGCAAGTTTTGGGGACAC 59.999 52.381 0.00 0.00 42.67 3.67
3481 15702 1.337118 GATGGCAAGTTTTGGGGACA 58.663 50.000 0.00 0.00 39.83 4.02
3482 15703 0.608130 GGATGGCAAGTTTTGGGGAC 59.392 55.000 0.00 0.00 0.00 4.46
3483 15704 0.486879 AGGATGGCAAGTTTTGGGGA 59.513 50.000 0.00 0.00 0.00 4.81
3487 15710 7.442062 ACATTCTTTTTAGGATGGCAAGTTTTG 59.558 33.333 0.00 0.00 0.00 2.44
3491 15714 5.774690 TGACATTCTTTTTAGGATGGCAAGT 59.225 36.000 0.00 0.00 0.00 3.16
3492 15715 6.271488 TGACATTCTTTTTAGGATGGCAAG 57.729 37.500 0.00 0.00 0.00 4.01
3507 15730 9.082313 AGGTGAAAAACTTCATATTGACATTCT 57.918 29.630 0.00 0.00 33.02 2.40
3508 15731 9.696917 AAGGTGAAAAACTTCATATTGACATTC 57.303 29.630 0.00 0.00 33.02 2.67
3530 15753 4.942761 ACATCTTGCAATTCAACAAGGT 57.057 36.364 0.00 3.37 42.82 3.50
3583 15905 7.593273 CGATCTGATTCTAATACACAGGTCTTC 59.407 40.741 0.00 0.00 36.81 2.87
3584 15906 7.429633 CGATCTGATTCTAATACACAGGTCTT 58.570 38.462 0.00 0.00 36.81 3.01
3595 15917 4.679373 ACACAGGCGATCTGATTCTAAT 57.321 40.909 12.18 0.00 46.18 1.73
3692 16168 8.787852 AGTGAGATCTTGATTCTAACCAAAAAC 58.212 33.333 0.00 0.00 0.00 2.43
3723 16200 9.998106 AAGTATCAAAAGAACTGAAAGCTAGTA 57.002 29.630 0.00 0.00 37.60 1.82
3724 16201 8.910351 AAGTATCAAAAGAACTGAAAGCTAGT 57.090 30.769 0.00 0.00 37.60 2.57
3725 16202 8.447053 GGAAGTATCAAAAGAACTGAAAGCTAG 58.553 37.037 0.00 0.00 37.60 3.42
3964 16577 1.610522 GTTCATCCAGTGCAGCAGTTT 59.389 47.619 0.00 0.00 0.00 2.66
3988 16601 3.222173 TCAGGCTTTGCTTAACCAGAA 57.778 42.857 0.00 0.00 0.00 3.02
3990 16603 5.643379 TTAATCAGGCTTTGCTTAACCAG 57.357 39.130 0.00 0.00 0.00 4.00
3991 16604 4.082245 GCTTAATCAGGCTTTGCTTAACCA 60.082 41.667 0.00 0.00 0.00 3.67
3992 16605 4.082245 TGCTTAATCAGGCTTTGCTTAACC 60.082 41.667 0.00 0.00 0.00 2.85
3993 16606 5.059404 TGCTTAATCAGGCTTTGCTTAAC 57.941 39.130 0.00 0.00 0.00 2.01
3994 16607 5.920193 ATGCTTAATCAGGCTTTGCTTAA 57.080 34.783 0.00 0.00 0.00 1.85
3995 16608 5.920193 AATGCTTAATCAGGCTTTGCTTA 57.080 34.783 0.00 0.00 0.00 3.09
3996 16609 4.813750 AATGCTTAATCAGGCTTTGCTT 57.186 36.364 0.00 0.00 0.00 3.91
4103 16724 5.640189 ATCCAAACTCTGCAGATGAAAAG 57.360 39.130 18.63 6.87 0.00 2.27


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

AutoCloner maintained by Alex Coulton.