Multiple sequence alignment - TraesCS1B01G175900

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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 TraesCS1B01G175900 chr1B 100.000 7613 0 0 1 7613 317417097 317424709 0.000000e+00 14059.0
1 TraesCS1B01G175900 chr1B 94.000 200 9 3 1304 1501 538865418 538865220 4.470000e-77 300.0
2 TraesCS1B01G175900 chr1B 75.806 248 50 10 1537 1779 317418875 317418633 4.830000e-22 117.0
3 TraesCS1B01G175900 chr1B 97.500 40 0 1 2834 2872 317419896 317419935 4.930000e-07 67.6
4 TraesCS1B01G175900 chr1B 97.500 40 0 1 2800 2839 317419930 317419968 4.930000e-07 67.6
5 TraesCS1B01G175900 chr1D 96.142 4847 111 21 2834 7613 221097154 221101991 0.000000e+00 7845.0
6 TraesCS1B01G175900 chr1D 95.301 1362 55 8 1482 2839 221095836 221097192 0.000000e+00 2152.0
7 TraesCS1B01G175900 chr1D 94.824 1024 32 13 27 1034 221094443 221095461 0.000000e+00 1578.0
8 TraesCS1B01G175900 chr1D 92.143 280 12 4 1033 1309 221095572 221095844 3.330000e-103 387.0
9 TraesCS1B01G175900 chr1D 75.814 215 44 8 1551 1760 221096120 221095909 1.350000e-17 102.0
10 TraesCS1B01G175900 chr1A 96.093 4838 121 23 2834 7613 285982913 285987740 0.000000e+00 7825.0
11 TraesCS1B01G175900 chr1A 94.233 1023 27 11 20 1034 285980435 285981433 0.000000e+00 1533.0
12 TraesCS1B01G175900 chr1A 97.215 754 16 4 2086 2839 285982203 285982951 0.000000e+00 1271.0
13 TraesCS1B01G175900 chr1A 93.929 280 10 3 1033 1309 285981544 285981819 4.250000e-112 416.0
14 TraesCS1B01G175900 chr1A 96.226 212 7 1 1872 2082 285981953 285982164 5.650000e-91 346.0
15 TraesCS1B01G175900 chr1A 84.783 92 9 4 1688 1779 285981953 285981867 3.780000e-13 87.9
16 TraesCS1B01G175900 chr1A 94.737 38 2 0 6271 6308 285986391 285986428 8.250000e-05 60.2
17 TraesCS1B01G175900 chr3A 84.248 838 94 25 4513 5335 12380480 12381294 0.000000e+00 782.0
18 TraesCS1B01G175900 chr3A 87.097 651 73 8 388 1034 12376056 12376699 0.000000e+00 726.0
19 TraesCS1B01G175900 chr3A 81.458 782 105 24 3700 4470 12379424 12380176 8.450000e-169 604.0
20 TraesCS1B01G175900 chr3D 81.573 928 138 27 3557 4473 8503165 8502260 0.000000e+00 736.0
21 TraesCS1B01G175900 chr3D 83.394 825 96 24 4543 5351 8520586 8519787 0.000000e+00 726.0
22 TraesCS1B01G175900 chr3D 83.071 827 101 22 4513 5325 8501971 8501170 0.000000e+00 715.0
23 TraesCS1B01G175900 chr3D 87.400 627 73 4 410 1033 8509163 8508540 0.000000e+00 715.0
24 TraesCS1B01G175900 chr3D 80.589 917 130 36 3559 4466 8521801 8520924 0.000000e+00 664.0
25 TraesCS1B01G175900 chr3D 81.021 764 110 24 5406 6148 8499951 8499202 6.630000e-160 575.0
26 TraesCS1B01G175900 chr3D 76.281 527 100 19 1868 2379 8523319 8522803 2.730000e-64 257.0
27 TraesCS1B01G175900 chr3B 82.803 849 95 28 4522 5344 10327986 10327163 0.000000e+00 712.0
28 TraesCS1B01G175900 chr3B 81.236 906 128 34 3577 4466 10329202 10328323 0.000000e+00 693.0
29 TraesCS1B01G175900 chr3B 80.947 908 139 27 3577 4470 10305847 10304960 0.000000e+00 688.0
30 TraesCS1B01G175900 chr3B 86.603 627 73 10 410 1033 10309026 10308408 0.000000e+00 682.0
31 TraesCS1B01G175900 chr3B 85.846 650 68 13 4522 5160 10304477 10303841 0.000000e+00 669.0
32 TraesCS1B01G175900 chr3B 85.355 437 61 2 5509 5942 10301981 10301545 4.190000e-122 449.0
33 TraesCS1B01G175900 chr3B 95.722 187 7 1 1303 1488 758070262 758070448 4.470000e-77 300.0
34 TraesCS1B01G175900 chr7D 87.584 298 26 3 4971 5259 611273384 611273089 1.220000e-87 335.0
35 TraesCS1B01G175900 chr2A 96.842 190 5 1 1299 1487 72943264 72943075 4.430000e-82 316.0
36 TraesCS1B01G175900 chr2A 84.483 116 13 5 1677 1792 725255886 725255776 8.080000e-20 110.0
37 TraesCS1B01G175900 chr2A 83.333 72 7 5 1696 1764 763482943 763483012 2.290000e-05 62.1
38 TraesCS1B01G175900 chr2B 96.825 189 5 1 1299 1486 385773164 385772976 1.590000e-81 315.0
39 TraesCS1B01G175900 chr6B 95.361 194 7 2 1297 1488 213152367 213152560 2.670000e-79 307.0
40 TraesCS1B01G175900 chr6B 94.595 37 2 0 1688 1724 717955495 717955531 2.970000e-04 58.4
41 TraesCS1B01G175900 chr6A 96.757 185 4 2 1304 1486 586032885 586033069 2.670000e-79 307.0
42 TraesCS1B01G175900 chr4B 95.238 189 8 1 1296 1483 123497732 123497920 1.610000e-76 298.0
43 TraesCS1B01G175900 chr4B 95.238 189 8 1 1304 1491 592626513 592626701 1.610000e-76 298.0
44 TraesCS1B01G175900 chrUn 94.792 192 6 4 1300 1489 54266919 54266730 5.780000e-76 296.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G175900 chr1B 317417097 317424709 7612 False 14059.000000 14059 100.000000 1 7613 1 chr1B.!!$F1 7612
1 TraesCS1B01G175900 chr1D 221094443 221101991 7548 False 2990.500000 7845 94.602500 27 7613 4 chr1D.!!$F1 7586
2 TraesCS1B01G175900 chr1A 285980435 285987740 7305 False 1908.533333 7825 95.405500 20 7613 6 chr1A.!!$F1 7593
3 TraesCS1B01G175900 chr3A 12376056 12381294 5238 False 704.000000 782 84.267667 388 5335 3 chr3A.!!$F1 4947
4 TraesCS1B01G175900 chr3D 8508540 8509163 623 True 715.000000 715 87.400000 410 1033 1 chr3D.!!$R1 623
5 TraesCS1B01G175900 chr3D 8499202 8503165 3963 True 675.333333 736 81.888333 3557 6148 3 chr3D.!!$R2 2591
6 TraesCS1B01G175900 chr3D 8519787 8523319 3532 True 549.000000 726 80.088000 1868 5351 3 chr3D.!!$R3 3483
7 TraesCS1B01G175900 chr3B 10327163 10329202 2039 True 702.500000 712 82.019500 3577 5344 2 chr3B.!!$R2 1767
8 TraesCS1B01G175900 chr3B 10301545 10309026 7481 True 622.000000 688 84.687750 410 5942 4 chr3B.!!$R1 5532

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
646 664 0.111446 TCAATTCCACCTTCGCCCAA 59.889 50.000 0.00 0.0 0.00 4.12 F
1416 1555 0.108615 GTGCTGACGTGGCTGTATCT 60.109 55.000 0.00 0.0 0.00 1.98 F
1843 2011 0.622665 ATGCTTCTGTTCCAGGGAGG 59.377 55.000 0.00 0.0 39.47 4.30 F
2886 3497 0.908910 TTCATAGTCGTGCCCCACAT 59.091 50.000 0.00 0.0 33.40 3.21 F
3183 3831 1.073763 TGCAAGGGTATGTGCTTGAGT 59.926 47.619 0.00 0.0 41.48 3.41 F
3186 3834 3.756434 GCAAGGGTATGTGCTTGAGTTTA 59.244 43.478 0.00 0.0 37.78 2.01 F
4534 5721 5.147767 AGTTTTTGGGAAGGCAATTACTCT 58.852 37.500 0.00 0.0 0.00 3.24 F
6042 8972 2.353269 GTGACATCGACGATCTGAGACT 59.647 50.000 7.54 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1709 2.234414 CTGGGTAATTGCTGCCACAAAT 59.766 45.455 0.00 0.0 32.27 2.32 R
3186 3834 1.686587 GCACAAGTAGGCAAAAACCCT 59.313 47.619 0.00 0.0 36.47 4.34 R
3658 4353 3.258123 ACCTGGTTGTTGTGAATAATGCC 59.742 43.478 0.00 0.0 0.00 4.40 R
4080 4799 1.796459 GCATTGCCTTTTGTCTGCAAG 59.204 47.619 0.00 0.0 46.90 4.01 R
5042 6238 0.250640 CTGTGTTTCAGGCTCCAGCT 60.251 55.000 0.00 0.0 40.23 4.24 R
5201 6398 6.320164 ACAGCACAAAATTAGTTAGTGGAACA 59.680 34.615 0.00 0.0 41.43 3.18 R
6449 9381 1.003839 TTGGCTGAGGCTTGTACGG 60.004 57.895 7.74 0.0 38.73 4.02 R
7157 10113 1.374947 GGCACACACTAAGGCAGGA 59.625 57.895 0.00 0.0 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 135 1.470098 GCTAGTGCCCAACAATCACAG 59.530 52.381 0.00 0.00 33.44 3.66
134 136 2.875672 GCTAGTGCCCAACAATCACAGA 60.876 50.000 0.00 0.00 33.44 3.41
136 138 2.880443 AGTGCCCAACAATCACAGAAT 58.120 42.857 0.00 0.00 33.44 2.40
168 179 4.922026 ACACGCCACCGAACACCC 62.922 66.667 0.00 0.00 38.29 4.61
169 180 4.619227 CACGCCACCGAACACCCT 62.619 66.667 0.00 0.00 38.29 4.34
170 181 4.309950 ACGCCACCGAACACCCTC 62.310 66.667 0.00 0.00 38.29 4.30
171 182 4.308458 CGCCACCGAACACCCTCA 62.308 66.667 0.00 0.00 36.29 3.86
172 183 2.112297 GCCACCGAACACCCTCAA 59.888 61.111 0.00 0.00 0.00 3.02
174 185 1.450211 CCACCGAACACCCTCAACT 59.550 57.895 0.00 0.00 0.00 3.16
175 186 0.884704 CCACCGAACACCCTCAACTG 60.885 60.000 0.00 0.00 0.00 3.16
180 191 2.285083 CGAACACCCTCAACTGTTTCA 58.715 47.619 0.00 0.00 30.59 2.69
181 192 2.680841 CGAACACCCTCAACTGTTTCAA 59.319 45.455 0.00 0.00 30.59 2.69
182 193 3.242739 CGAACACCCTCAACTGTTTCAAG 60.243 47.826 0.00 0.00 30.59 3.02
183 194 3.366052 ACACCCTCAACTGTTTCAAGT 57.634 42.857 0.00 0.00 0.00 3.16
187 198 5.129815 ACACCCTCAACTGTTTCAAGTAGTA 59.870 40.000 0.00 0.00 0.00 1.82
208 225 7.759489 AGTACTGATTAAACAAAGGCATTCA 57.241 32.000 0.00 0.00 0.00 2.57
294 311 1.114627 CGTGACAGAGGATCATCCCA 58.885 55.000 3.23 0.00 37.19 4.37
348 365 0.393077 CTGTTCCACACTTCCCGACT 59.607 55.000 0.00 0.00 0.00 4.18
386 404 1.921748 TCAATCCATCCCCATCACACA 59.078 47.619 0.00 0.00 0.00 3.72
442 460 1.210413 CACGGCGATATCTCCTCCG 59.790 63.158 16.62 13.53 45.04 4.63
644 662 1.032114 CCTCAATTCCACCTTCGCCC 61.032 60.000 0.00 0.00 0.00 6.13
646 664 0.111446 TCAATTCCACCTTCGCCCAA 59.889 50.000 0.00 0.00 0.00 4.12
1137 1270 3.560068 GTGAGTTCATCCTCGTGTTTTGT 59.440 43.478 0.00 0.00 34.04 2.83
1174 1313 7.324178 ACATACTAGCTTCGAGATGTTTTCTT 58.676 34.615 0.00 0.00 33.74 2.52
1176 1315 8.660373 CATACTAGCTTCGAGATGTTTTCTTTT 58.340 33.333 0.00 0.00 33.74 2.27
1179 1318 9.871238 ACTAGCTTCGAGATGTTTTCTTTTATA 57.129 29.630 0.00 0.00 33.74 0.98
1224 1363 0.674895 ATCTTTGGCTCGCTGTCCAC 60.675 55.000 0.00 0.00 30.97 4.02
1235 1374 0.592247 GCTGTCCACGTTTGTTGCTG 60.592 55.000 0.00 0.00 0.00 4.41
1261 1400 3.122948 CGACCGGCATAGATTTTTATCGG 59.877 47.826 0.00 0.00 41.65 4.18
1309 1448 6.313411 TGCAGCATATCCTTGTTTAAAATTGC 59.687 34.615 0.00 0.00 0.00 3.56
1311 1450 7.464977 GCAGCATATCCTTGTTTAAAATTGCAG 60.465 37.037 0.00 0.00 0.00 4.41
1314 1453 8.720562 GCATATCCTTGTTTAAAATTGCAGTTT 58.279 29.630 0.65 0.65 0.00 2.66
1358 1497 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
1359 1498 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
1360 1499 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
1369 1508 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
1370 1509 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
1372 1511 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
1374 1513 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
1375 1514 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
1381 1520 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
1382 1521 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
1385 1524 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
1386 1525 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
1387 1526 4.989277 AGCCATTGGATGTGATGCTATAA 58.011 39.130 6.95 0.00 0.00 0.98
1388 1527 5.008331 AGCCATTGGATGTGATGCTATAAG 58.992 41.667 6.95 0.00 0.00 1.73
1389 1528 5.005740 GCCATTGGATGTGATGCTATAAGA 58.994 41.667 6.95 0.00 0.00 2.10
1390 1529 5.651139 GCCATTGGATGTGATGCTATAAGAT 59.349 40.000 6.95 0.00 0.00 2.40
1391 1530 6.404403 GCCATTGGATGTGATGCTATAAGATG 60.404 42.308 6.95 0.00 0.00 2.90
1392 1531 6.404403 CCATTGGATGTGATGCTATAAGATGC 60.404 42.308 0.00 0.00 0.00 3.91
1393 1532 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
1394 1533 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
1395 1534 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
1397 1536 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
1398 1537 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
1399 1538 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
1400 1539 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
1401 1540 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
1402 1541 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
1403 1542 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
1404 1543 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
1405 1544 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
1406 1545 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
1407 1546 2.484631 GATGCGTGTGTGCTGACGTG 62.485 60.000 0.00 0.00 37.89 4.49
1408 1547 4.000557 GCGTGTGTGCTGACGTGG 62.001 66.667 0.00 0.00 37.89 4.94
1409 1548 4.000557 CGTGTGTGCTGACGTGGC 62.001 66.667 0.00 0.00 0.00 5.01
1410 1549 2.588877 GTGTGTGCTGACGTGGCT 60.589 61.111 0.00 0.00 0.00 4.75
1411 1550 2.588596 TGTGTGCTGACGTGGCTG 60.589 61.111 0.00 0.00 0.00 4.85
1412 1551 2.588877 GTGTGCTGACGTGGCTGT 60.589 61.111 0.00 0.00 0.00 4.40
1413 1552 1.300620 GTGTGCTGACGTGGCTGTA 60.301 57.895 0.00 0.00 0.00 2.74
1414 1553 0.670546 GTGTGCTGACGTGGCTGTAT 60.671 55.000 0.00 0.00 0.00 2.29
1415 1554 0.389817 TGTGCTGACGTGGCTGTATC 60.390 55.000 0.00 0.00 0.00 2.24
1416 1555 0.108615 GTGCTGACGTGGCTGTATCT 60.109 55.000 0.00 0.00 0.00 1.98
1417 1556 1.134367 GTGCTGACGTGGCTGTATCTA 59.866 52.381 0.00 0.00 0.00 1.98
1418 1557 2.031870 TGCTGACGTGGCTGTATCTAT 58.968 47.619 0.00 0.00 0.00 1.98
1419 1558 2.430694 TGCTGACGTGGCTGTATCTATT 59.569 45.455 0.00 0.00 0.00 1.73
1420 1559 3.053455 GCTGACGTGGCTGTATCTATTC 58.947 50.000 0.00 0.00 0.00 1.75
1421 1560 3.243569 GCTGACGTGGCTGTATCTATTCT 60.244 47.826 0.00 0.00 0.00 2.40
1422 1561 4.737946 GCTGACGTGGCTGTATCTATTCTT 60.738 45.833 0.00 0.00 0.00 2.52
1423 1562 4.682787 TGACGTGGCTGTATCTATTCTTG 58.317 43.478 0.00 0.00 0.00 3.02
1424 1563 4.159693 TGACGTGGCTGTATCTATTCTTGT 59.840 41.667 0.00 0.00 0.00 3.16
1425 1564 5.086104 ACGTGGCTGTATCTATTCTTGTT 57.914 39.130 0.00 0.00 0.00 2.83
1426 1565 5.488341 ACGTGGCTGTATCTATTCTTGTTT 58.512 37.500 0.00 0.00 0.00 2.83
1427 1566 5.938125 ACGTGGCTGTATCTATTCTTGTTTT 59.062 36.000 0.00 0.00 0.00 2.43
1428 1567 6.092259 ACGTGGCTGTATCTATTCTTGTTTTC 59.908 38.462 0.00 0.00 0.00 2.29
1429 1568 6.092122 CGTGGCTGTATCTATTCTTGTTTTCA 59.908 38.462 0.00 0.00 0.00 2.69
1430 1569 7.360861 CGTGGCTGTATCTATTCTTGTTTTCAA 60.361 37.037 0.00 0.00 38.21 2.69
1431 1570 8.296713 GTGGCTGTATCTATTCTTGTTTTCAAA 58.703 33.333 0.00 0.00 39.47 2.69
1432 1571 8.514594 TGGCTGTATCTATTCTTGTTTTCAAAG 58.485 33.333 0.00 0.00 39.47 2.77
1433 1572 8.515414 GGCTGTATCTATTCTTGTTTTCAAAGT 58.485 33.333 0.00 0.00 39.47 2.66
1434 1573 9.334693 GCTGTATCTATTCTTGTTTTCAAAGTG 57.665 33.333 0.00 0.00 39.47 3.16
1442 1581 8.862550 ATTCTTGTTTTCAAAGTGAATGAGAC 57.137 30.769 0.00 0.00 39.47 3.36
1443 1582 6.795399 TCTTGTTTTCAAAGTGAATGAGACC 58.205 36.000 0.00 0.00 39.47 3.85
1444 1583 6.376864 TCTTGTTTTCAAAGTGAATGAGACCA 59.623 34.615 0.00 0.00 39.47 4.02
1445 1584 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
1446 1585 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
1447 1586 7.555087 TGTTTTCAAAGTGAATGAGACCAAAT 58.445 30.769 0.00 0.00 36.11 2.32
1448 1587 8.040132 TGTTTTCAAAGTGAATGAGACCAAATT 58.960 29.630 0.00 0.00 36.11 1.82
1449 1588 9.528018 GTTTTCAAAGTGAATGAGACCAAATTA 57.472 29.630 0.00 0.00 36.11 1.40
1479 1618 7.455058 TCATCTAGATGAGTTCTAGGTACTCC 58.545 42.308 27.93 8.04 44.99 3.85
1480 1619 6.657541 CATCTAGATGAGTTCTAGGTACTCCC 59.342 46.154 25.78 12.05 44.99 4.30
1481 1620 7.475654 CATCTAGATGAGTTCTAGGTACTCCCT 60.476 44.444 25.78 16.34 44.99 4.20
1482 1621 5.475398 AGATGAGTTCTAGGTACTCCCTT 57.525 43.478 17.72 7.62 42.73 3.95
1483 1622 6.593759 AGATGAGTTCTAGGTACTCCCTTA 57.406 41.667 17.72 5.36 42.73 2.69
1484 1623 6.982899 AGATGAGTTCTAGGTACTCCCTTAA 58.017 40.000 17.72 5.09 42.73 1.85
1485 1624 7.420029 AGATGAGTTCTAGGTACTCCCTTAAA 58.580 38.462 17.72 4.58 42.73 1.52
1486 1625 7.899709 AGATGAGTTCTAGGTACTCCCTTAAAA 59.100 37.037 17.72 4.06 42.73 1.52
1487 1626 8.625467 ATGAGTTCTAGGTACTCCCTTAAAAT 57.375 34.615 17.72 5.65 42.73 1.82
1488 1627 8.445361 TGAGTTCTAGGTACTCCCTTAAAATT 57.555 34.615 17.72 0.00 42.73 1.82
1489 1628 8.319146 TGAGTTCTAGGTACTCCCTTAAAATTG 58.681 37.037 17.72 0.00 42.73 2.32
1490 1629 8.215954 AGTTCTAGGTACTCCCTTAAAATTGT 57.784 34.615 0.00 0.00 42.73 2.71
1491 1630 8.319881 AGTTCTAGGTACTCCCTTAAAATTGTC 58.680 37.037 0.00 0.00 42.73 3.18
1492 1631 7.191593 TCTAGGTACTCCCTTAAAATTGTCC 57.808 40.000 0.00 0.00 42.73 4.02
1493 1632 6.964086 TCTAGGTACTCCCTTAAAATTGTCCT 59.036 38.462 0.00 0.00 42.73 3.85
1543 1682 8.728088 ACGTTGCAAATTAGAAATAGAGTTTG 57.272 30.769 0.00 0.00 0.00 2.93
1564 1703 7.398047 AGTTTGTTTCACTTTTTACCCCTAAGT 59.602 33.333 0.00 0.00 32.60 2.24
1570 1709 6.424883 TCACTTTTTACCCCTAAGTTTCACA 58.575 36.000 0.00 0.00 30.08 3.58
1650 1790 3.763897 AGACTTGTGCCACATTTTATCCC 59.236 43.478 0.00 0.00 0.00 3.85
1658 1798 7.327214 TGTGCCACATTTTATCCCTTTTATTC 58.673 34.615 0.00 0.00 0.00 1.75
1693 1833 5.222631 GTTCTGACAGGTTTGCTTAAATGG 58.777 41.667 1.81 0.00 0.00 3.16
1769 1937 4.669700 ACTTAGGGGGTAACAAATGGAAC 58.330 43.478 0.00 0.00 39.74 3.62
1843 2011 0.622665 ATGCTTCTGTTCCAGGGAGG 59.377 55.000 0.00 0.00 39.47 4.30
1856 2024 2.173569 CCAGGGAGGTTTGAATCTAGGG 59.826 54.545 0.00 0.00 0.00 3.53
1960 2183 7.148018 GCAAATGAGGACTTCATGGAGAATTAA 60.148 37.037 8.39 0.00 45.82 1.40
2046 2374 7.782897 TGGTACATTTGGAATCCAATGTTTA 57.217 32.000 24.28 9.76 43.55 2.01
2047 2375 8.372877 TGGTACATTTGGAATCCAATGTTTAT 57.627 30.769 24.28 11.32 43.55 1.40
2204 2577 7.864108 AAAGAAAAAGGTTCCAATTCAAAGG 57.136 32.000 0.00 0.00 0.00 3.11
2206 2579 6.957631 AGAAAAAGGTTCCAATTCAAAGGTT 58.042 32.000 0.00 0.00 0.00 3.50
2408 2796 5.499139 TGTGAAGTTAAAGCTCTTTGGTG 57.501 39.130 5.21 0.00 34.23 4.17
2428 2819 4.496507 GGTGCTTGTCAAGTTTTCAGTCTC 60.497 45.833 14.03 0.00 0.00 3.36
2584 3189 1.799544 TGACATGCAGTGTGTAGCTG 58.200 50.000 0.00 0.00 42.36 4.24
2743 3351 8.726870 TTTGATTACTAAGGCAGGTATGTAAC 57.273 34.615 0.00 0.00 0.00 2.50
2828 3439 4.431416 TTTCCAAAGGCAGAAGTAGACA 57.569 40.909 0.00 0.00 0.00 3.41
2829 3440 4.640771 TTCCAAAGGCAGAAGTAGACAT 57.359 40.909 0.00 0.00 0.00 3.06
2830 3441 3.942829 TCCAAAGGCAGAAGTAGACATG 58.057 45.455 0.00 0.00 0.00 3.21
2831 3442 3.327757 TCCAAAGGCAGAAGTAGACATGT 59.672 43.478 0.00 0.00 0.00 3.21
2832 3443 4.074970 CCAAAGGCAGAAGTAGACATGTT 58.925 43.478 0.00 0.00 0.00 2.71
2833 3444 4.520492 CCAAAGGCAGAAGTAGACATGTTT 59.480 41.667 0.00 0.00 0.00 2.83
2834 3445 5.010012 CCAAAGGCAGAAGTAGACATGTTTT 59.990 40.000 0.00 0.00 0.00 2.43
2835 3446 5.695851 AAGGCAGAAGTAGACATGTTTTG 57.304 39.130 0.00 0.00 0.00 2.44
2836 3447 3.503748 AGGCAGAAGTAGACATGTTTTGC 59.496 43.478 0.00 0.20 0.00 3.68
2837 3448 3.253188 GGCAGAAGTAGACATGTTTTGCA 59.747 43.478 10.92 0.00 0.00 4.08
2838 3449 4.082571 GGCAGAAGTAGACATGTTTTGCAT 60.083 41.667 10.92 0.00 38.60 3.96
2839 3450 5.464168 GCAGAAGTAGACATGTTTTGCATT 58.536 37.500 0.00 0.00 35.19 3.56
2875 3486 7.201565 GGCAGAAGTAGACATGTTTTCATAGTC 60.202 40.741 0.00 0.00 38.64 2.59
2886 3497 0.908910 TTCATAGTCGTGCCCCACAT 59.091 50.000 0.00 0.00 33.40 3.21
3172 3787 2.158871 GGATTCCGTACATGCAAGGGTA 60.159 50.000 0.00 0.00 0.00 3.69
3183 3831 1.073763 TGCAAGGGTATGTGCTTGAGT 59.926 47.619 0.00 0.00 41.48 3.41
3186 3834 3.756434 GCAAGGGTATGTGCTTGAGTTTA 59.244 43.478 0.00 0.00 37.78 2.01
3243 3891 5.630680 CCTCAAAATGTTTACAGATGTGCAC 59.369 40.000 10.75 10.75 0.00 4.57
3788 4504 9.539825 TTGTTTGACATTTGCAAGTGTTATTAT 57.460 25.926 25.92 4.71 0.00 1.28
4080 4799 8.514594 TCAAATGTTTAATCCACTCATGAAGAC 58.485 33.333 0.00 0.00 0.00 3.01
4534 5721 5.147767 AGTTTTTGGGAAGGCAATTACTCT 58.852 37.500 0.00 0.00 0.00 3.24
5223 6470 7.995463 TTTGTTCCACTAACTAATTTTGTGC 57.005 32.000 0.00 0.00 39.00 4.57
5275 6530 3.287312 TGCACTGCTGATTTAACAAGC 57.713 42.857 1.98 0.00 0.00 4.01
5506 8421 4.944962 TTTCTTATGCCTGTCGATTGTG 57.055 40.909 0.00 0.00 0.00 3.33
5891 8809 9.676195 TGATTGATTTGTAACTACAATTGTGTG 57.324 29.630 21.42 15.20 44.72 3.82
6042 8972 2.353269 GTGACATCGACGATCTGAGACT 59.647 50.000 7.54 0.00 0.00 3.24
6132 9064 4.399219 AGGTATTCTAGCTCGTATGCTGA 58.601 43.478 0.00 4.24 43.87 4.26
6381 9313 5.037598 ACTTTAGCTGACCCCTAATTAGGT 58.962 41.667 26.38 12.76 42.03 3.08
6673 9605 7.944729 ATACAAAAAGTACATGAAGCTCCAT 57.055 32.000 0.00 0.00 35.05 3.41
6681 9613 7.847711 AGTACATGAAGCTCCATCTAACTAT 57.152 36.000 0.00 0.00 0.00 2.12
6889 9841 2.490903 CAGGATTGCTGAGAAAGTTGGG 59.509 50.000 0.00 0.00 0.00 4.12
7074 10026 4.035091 TGTGTTGGTCAAGAAATTCTGACG 59.965 41.667 14.59 1.83 30.55 4.35
7077 10029 3.476552 TGGTCAAGAAATTCTGACGCTT 58.523 40.909 14.59 0.00 30.55 4.68
7203 10159 2.471743 GCTGACTTCACTACACAACGTC 59.528 50.000 0.00 0.00 0.00 4.34
7207 10163 2.691526 ACTTCACTACACAACGTCCAGA 59.308 45.455 0.00 0.00 0.00 3.86
7248 10204 6.089476 TGTTGCACACCAATATATTGTTTCG 58.911 36.000 21.20 10.36 35.55 3.46
7604 10581 0.738389 CCGTTTGTGTTTCAGCCACT 59.262 50.000 0.00 0.00 33.92 4.00
7608 10585 0.257328 TTGTGTTTCAGCCACTGGGA 59.743 50.000 0.00 0.00 35.59 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.912956 AGTAGGAGTGATTTGGGAGCAA 59.087 45.455 0.00 0.00 0.00 3.91
1 2 2.501723 GAGTAGGAGTGATTTGGGAGCA 59.498 50.000 0.00 0.00 0.00 4.26
2 3 2.769095 AGAGTAGGAGTGATTTGGGAGC 59.231 50.000 0.00 0.00 0.00 4.70
6 7 5.997746 TGTGAAAAGAGTAGGAGTGATTTGG 59.002 40.000 0.00 0.00 0.00 3.28
7 8 6.708054 AGTGTGAAAAGAGTAGGAGTGATTTG 59.292 38.462 0.00 0.00 0.00 2.32
8 9 6.831976 AGTGTGAAAAGAGTAGGAGTGATTT 58.168 36.000 0.00 0.00 0.00 2.17
9 10 6.426646 AGTGTGAAAAGAGTAGGAGTGATT 57.573 37.500 0.00 0.00 0.00 2.57
10 11 6.493802 TGTAGTGTGAAAAGAGTAGGAGTGAT 59.506 38.462 0.00 0.00 0.00 3.06
11 12 5.831525 TGTAGTGTGAAAAGAGTAGGAGTGA 59.168 40.000 0.00 0.00 0.00 3.41
12 13 6.085555 TGTAGTGTGAAAAGAGTAGGAGTG 57.914 41.667 0.00 0.00 0.00 3.51
13 14 6.726490 TTGTAGTGTGAAAAGAGTAGGAGT 57.274 37.500 0.00 0.00 0.00 3.85
15 16 6.015688 ACGATTGTAGTGTGAAAAGAGTAGGA 60.016 38.462 0.00 0.00 0.00 2.94
16 17 6.157211 ACGATTGTAGTGTGAAAAGAGTAGG 58.843 40.000 0.00 0.00 0.00 3.18
17 18 7.502339 CAACGATTGTAGTGTGAAAAGAGTAG 58.498 38.462 0.00 0.00 0.00 2.57
18 19 6.073980 GCAACGATTGTAGTGTGAAAAGAGTA 60.074 38.462 0.00 0.00 0.00 2.59
133 135 2.281762 GTGTGTTGACGATCGGCTATTC 59.718 50.000 23.76 12.02 0.00 1.75
134 136 2.268298 GTGTGTTGACGATCGGCTATT 58.732 47.619 23.76 0.00 0.00 1.73
136 138 0.455464 CGTGTGTTGACGATCGGCTA 60.455 55.000 23.76 12.65 42.10 3.93
168 179 8.594881 AATCAGTACTACTTGAAACAGTTGAG 57.405 34.615 0.00 0.00 0.00 3.02
172 183 9.826574 TGTTTAATCAGTACTACTTGAAACAGT 57.173 29.630 13.80 0.00 0.00 3.55
180 191 8.863872 ATGCCTTTGTTTAATCAGTACTACTT 57.136 30.769 0.00 0.00 0.00 2.24
181 192 8.863872 AATGCCTTTGTTTAATCAGTACTACT 57.136 30.769 0.00 0.00 0.00 2.57
182 193 8.726988 TGAATGCCTTTGTTTAATCAGTACTAC 58.273 33.333 0.00 0.00 0.00 2.73
183 194 8.856153 TGAATGCCTTTGTTTAATCAGTACTA 57.144 30.769 0.00 0.00 0.00 1.82
187 198 5.567423 GCCTGAATGCCTTTGTTTAATCAGT 60.567 40.000 0.00 0.00 33.04 3.41
208 225 0.961857 TCTTGCATTGCATGTCGCCT 60.962 50.000 20.16 0.00 38.76 5.52
294 311 6.271391 TCGAGGTGGTATAAATATTGGGATGT 59.729 38.462 0.00 0.00 0.00 3.06
348 365 4.412796 TTGATTTGTGTTGAATGGCCAA 57.587 36.364 10.96 0.00 0.00 4.52
644 662 3.423154 GAGGTTGGCGCGGAGTTG 61.423 66.667 8.83 0.00 0.00 3.16
646 664 4.070552 GAGAGGTTGGCGCGGAGT 62.071 66.667 8.83 0.00 0.00 3.85
1137 1270 6.584942 CGAAGCTAGTATGTTAACAACTCACA 59.415 38.462 13.23 2.87 0.00 3.58
1176 1315 9.970395 CCTCGGTACAACACAAAACTATATATA 57.030 33.333 0.00 0.00 0.00 0.86
1179 1318 5.583457 GCCTCGGTACAACACAAAACTATAT 59.417 40.000 0.00 0.00 0.00 0.86
1190 1329 0.981183 AAGATGGCCTCGGTACAACA 59.019 50.000 3.32 0.00 0.00 3.33
1224 1363 1.654137 GTCGTGCCAGCAACAAACG 60.654 57.895 0.00 0.00 35.64 3.60
1235 1374 0.814010 AAATCTATGCCGGTCGTGCC 60.814 55.000 1.90 0.00 0.00 5.01
1246 1385 5.107065 GGGAACTCGCCGATAAAAATCTATG 60.107 44.000 0.00 0.00 0.00 2.23
1261 1400 2.100605 ATGAGACTTTGGGAACTCGC 57.899 50.000 0.00 0.00 32.81 5.03
1334 1473 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
1335 1474 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
1341 1480 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
1342 1481 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
1343 1482 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
1344 1483 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
1346 1485 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
1347 1486 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
1349 1488 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
1350 1489 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
1351 1490 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
1352 1491 6.840705 ACATCCAATGGCTATAAAAGGTGAAT 59.159 34.615 0.00 0.00 33.60 2.57
1353 1492 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
1354 1493 5.593909 CACATCCAATGGCTATAAAAGGTGA 59.406 40.000 0.00 0.00 33.60 4.02
1355 1494 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
1356 1495 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
1357 1496 6.684686 CATCACATCCAATGGCTATAAAAGG 58.315 40.000 0.00 0.00 33.60 3.11
1358 1497 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
1359 1498 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
1360 1499 5.387788 AGCATCACATCCAATGGCTATAAA 58.612 37.500 0.00 0.00 33.60 1.40
1362 1501 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
1363 1502 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
1364 1503 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
1365 1504 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
1366 1505 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40
1369 1508 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
1370 1509 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
1372 1511 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
1374 1513 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
1375 1514 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
1381 1520 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
1382 1521 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
1385 1524 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
1386 1525 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
1387 1526 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
1388 1527 2.310233 ACGTCAGCACACACGCATC 61.310 57.895 0.00 0.00 39.73 3.91
1389 1528 2.280119 ACGTCAGCACACACGCAT 60.280 55.556 0.00 0.00 39.73 4.73
1390 1529 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
1391 1530 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
1392 1531 4.000557 GCCACGTCAGCACACACG 62.001 66.667 2.25 0.00 41.90 4.49
1393 1532 2.588877 AGCCACGTCAGCACACAC 60.589 61.111 9.59 0.00 0.00 3.82
1394 1533 2.022240 TACAGCCACGTCAGCACACA 62.022 55.000 9.59 0.00 0.00 3.72
1395 1534 0.670546 ATACAGCCACGTCAGCACAC 60.671 55.000 9.59 0.00 0.00 3.82
1397 1536 0.108615 AGATACAGCCACGTCAGCAC 60.109 55.000 9.59 0.00 0.00 4.40
1398 1537 1.470051 TAGATACAGCCACGTCAGCA 58.530 50.000 9.59 0.00 0.00 4.41
1399 1538 2.802787 ATAGATACAGCCACGTCAGC 57.197 50.000 0.00 0.00 0.00 4.26
1400 1539 4.576216 AGAATAGATACAGCCACGTCAG 57.424 45.455 0.00 0.00 0.00 3.51
1401 1540 4.159693 ACAAGAATAGATACAGCCACGTCA 59.840 41.667 0.00 0.00 0.00 4.35
1402 1541 4.683832 ACAAGAATAGATACAGCCACGTC 58.316 43.478 0.00 0.00 0.00 4.34
1403 1542 4.737855 ACAAGAATAGATACAGCCACGT 57.262 40.909 0.00 0.00 0.00 4.49
1404 1543 6.092122 TGAAAACAAGAATAGATACAGCCACG 59.908 38.462 0.00 0.00 0.00 4.94
1405 1544 7.377766 TGAAAACAAGAATAGATACAGCCAC 57.622 36.000 0.00 0.00 0.00 5.01
1406 1545 7.994425 TTGAAAACAAGAATAGATACAGCCA 57.006 32.000 0.00 0.00 0.00 4.75
1407 1546 8.515414 ACTTTGAAAACAAGAATAGATACAGCC 58.485 33.333 0.00 0.00 0.00 4.85
1408 1547 9.334693 CACTTTGAAAACAAGAATAGATACAGC 57.665 33.333 0.00 0.00 0.00 4.40
1416 1555 9.950680 GTCTCATTCACTTTGAAAACAAGAATA 57.049 29.630 0.00 0.00 40.12 1.75
1417 1556 7.922811 GGTCTCATTCACTTTGAAAACAAGAAT 59.077 33.333 0.00 0.00 40.12 2.40
1418 1557 7.093988 TGGTCTCATTCACTTTGAAAACAAGAA 60.094 33.333 0.00 0.00 40.12 2.52
1419 1558 6.376864 TGGTCTCATTCACTTTGAAAACAAGA 59.623 34.615 0.00 0.00 40.12 3.02
1420 1559 6.563422 TGGTCTCATTCACTTTGAAAACAAG 58.437 36.000 0.00 0.00 40.12 3.16
1421 1560 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
1422 1561 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
1423 1562 8.424274 AATTTGGTCTCATTCACTTTGAAAAC 57.576 30.769 0.00 0.00 40.12 2.43
1472 1611 7.803131 AGATAGGACAATTTTAAGGGAGTACC 58.197 38.462 0.00 0.00 40.67 3.34
1473 1612 9.682465 AAAGATAGGACAATTTTAAGGGAGTAC 57.318 33.333 0.00 0.00 0.00 2.73
1475 1614 9.244292 GAAAAGATAGGACAATTTTAAGGGAGT 57.756 33.333 0.00 0.00 0.00 3.85
1476 1615 8.687242 GGAAAAGATAGGACAATTTTAAGGGAG 58.313 37.037 0.00 0.00 0.00 4.30
1477 1616 7.338449 CGGAAAAGATAGGACAATTTTAAGGGA 59.662 37.037 0.00 0.00 0.00 4.20
1478 1617 7.338449 TCGGAAAAGATAGGACAATTTTAAGGG 59.662 37.037 0.00 0.00 0.00 3.95
1479 1618 8.276252 TCGGAAAAGATAGGACAATTTTAAGG 57.724 34.615 0.00 0.00 0.00 2.69
1480 1619 9.774742 CTTCGGAAAAGATAGGACAATTTTAAG 57.225 33.333 0.00 0.00 0.00 1.85
1481 1620 9.292195 ACTTCGGAAAAGATAGGACAATTTTAA 57.708 29.630 0.00 0.00 0.00 1.52
1482 1621 8.857694 ACTTCGGAAAAGATAGGACAATTTTA 57.142 30.769 0.00 0.00 0.00 1.52
1483 1622 7.761038 ACTTCGGAAAAGATAGGACAATTTT 57.239 32.000 0.00 0.00 0.00 1.82
1484 1623 7.761038 AACTTCGGAAAAGATAGGACAATTT 57.239 32.000 0.00 0.00 0.00 1.82
1485 1624 9.462606 AATAACTTCGGAAAAGATAGGACAATT 57.537 29.630 0.00 0.00 0.00 2.32
1487 1626 9.595823 CTAATAACTTCGGAAAAGATAGGACAA 57.404 33.333 0.00 0.00 0.00 3.18
1488 1627 8.755977 ACTAATAACTTCGGAAAAGATAGGACA 58.244 33.333 0.00 0.00 0.00 4.02
1489 1628 9.247126 GACTAATAACTTCGGAAAAGATAGGAC 57.753 37.037 0.00 0.00 0.00 3.85
1490 1629 8.419442 GGACTAATAACTTCGGAAAAGATAGGA 58.581 37.037 0.00 0.00 0.00 2.94
1491 1630 8.422566 AGGACTAATAACTTCGGAAAAGATAGG 58.577 37.037 0.00 0.00 0.00 2.57
1542 1681 7.396623 TGAAACTTAGGGGTAAAAAGTGAAACA 59.603 33.333 0.00 0.00 41.43 2.83
1543 1682 7.703621 GTGAAACTTAGGGGTAAAAAGTGAAAC 59.296 37.037 0.00 0.00 0.00 2.78
1570 1709 2.234414 CTGGGTAATTGCTGCCACAAAT 59.766 45.455 0.00 0.00 32.27 2.32
1693 1833 8.825667 TTAGCAGATTTTTCACATTTTTACCC 57.174 30.769 0.00 0.00 0.00 3.69
1870 2091 2.431419 TGGCCAATCGATGCATCAAATT 59.569 40.909 25.70 19.86 0.00 1.82
2046 2374 6.530019 AACTTCAAAGTTCAAACTCACCAT 57.470 33.333 2.30 0.00 45.65 3.55
2047 2375 5.975693 AACTTCAAAGTTCAAACTCACCA 57.024 34.783 2.30 0.00 45.65 4.17
2082 2410 9.919348 GCAAATAAACATGCCTTTACATTAATG 57.081 29.630 14.01 14.01 0.00 1.90
2084 2447 9.364989 GAGCAAATAAACATGCCTTTACATTAA 57.635 29.630 0.00 0.00 0.00 1.40
2204 2577 5.292765 TGTGAGATCTGAACTGAAGACAAC 58.707 41.667 0.00 0.00 0.00 3.32
2206 2579 5.535753 TTGTGAGATCTGAACTGAAGACA 57.464 39.130 0.00 0.00 0.00 3.41
2408 2796 4.882671 TGAGACTGAAAACTTGACAAGC 57.117 40.909 15.24 0.00 0.00 4.01
2428 2819 7.023575 GCAACTTTGACCATGTTACTAAGATG 58.976 38.462 10.23 0.00 32.35 2.90
2584 3189 4.885907 AGATGATTGATGACCATTGGTGAC 59.114 41.667 14.44 0.00 35.25 3.67
2701 3309 9.988815 AGTAATCAAAGGCAGTCTAGTTATATG 57.011 33.333 0.00 0.00 0.00 1.78
2743 3351 7.653713 AGGATGTAAGTTATCAACTGCGATTAG 59.346 37.037 0.00 0.00 41.91 1.73
2839 3450 5.197451 TGTCTACTTCTGCCTTTGGAAAAA 58.803 37.500 0.00 0.00 0.00 1.94
2844 3455 3.679389 ACATGTCTACTTCTGCCTTTGG 58.321 45.455 0.00 0.00 0.00 3.28
2847 3458 5.376625 TGAAAACATGTCTACTTCTGCCTT 58.623 37.500 0.00 0.00 0.00 4.35
2875 3486 1.750193 ATCAAAGTATGTGGGGCACG 58.250 50.000 0.00 0.00 37.14 5.34
2886 3497 8.593679 TGATACAACAGAGAGGAAATCAAAGTA 58.406 33.333 0.00 0.00 0.00 2.24
3143 3758 5.189928 TGCATGTACGGAATCCACTTTATT 58.810 37.500 0.00 0.00 0.00 1.40
3172 3787 5.600696 CAAAAACCCTAAACTCAAGCACAT 58.399 37.500 0.00 0.00 0.00 3.21
3183 3831 4.202172 GCACAAGTAGGCAAAAACCCTAAA 60.202 41.667 0.00 0.00 36.74 1.85
3186 3834 1.686587 GCACAAGTAGGCAAAAACCCT 59.313 47.619 0.00 0.00 36.47 4.34
3243 3891 5.163530 TGCAGGTGCTCATTTTATAACATGG 60.164 40.000 10.88 4.43 42.66 3.66
3446 4096 4.576873 GCTCCTGGCTAGAAAATAGTTTCC 59.423 45.833 11.81 0.00 39.92 3.13
3658 4353 3.258123 ACCTGGTTGTTGTGAATAATGCC 59.742 43.478 0.00 0.00 0.00 4.40
3732 4433 7.716799 AATGTTCATGGCTAAACTCCAATAA 57.283 32.000 0.00 0.00 37.13 1.40
4080 4799 1.796459 GCATTGCCTTTTGTCTGCAAG 59.204 47.619 0.00 0.00 46.90 4.01
4534 5721 4.576873 TCAACTCGGTTTGCAAGATAAACA 59.423 37.500 0.00 0.00 39.24 2.83
5042 6238 0.250640 CTGTGTTTCAGGCTCCAGCT 60.251 55.000 0.00 0.00 40.23 4.24
5201 6398 6.320164 ACAGCACAAAATTAGTTAGTGGAACA 59.680 34.615 0.00 0.00 41.43 3.18
5210 6407 6.925165 CAGGAATTCACAGCACAAAATTAGTT 59.075 34.615 7.93 0.00 0.00 2.24
5211 6408 6.449698 CAGGAATTCACAGCACAAAATTAGT 58.550 36.000 7.93 0.00 0.00 2.24
5223 6470 0.038744 ACCAGCCCAGGAATTCACAG 59.961 55.000 7.93 0.00 0.00 3.66
5506 8421 5.772825 TTTCATATAACTTCCATGCCTGC 57.227 39.130 0.00 0.00 0.00 4.85
6042 8972 4.884668 AGAACAAGGGACACGAAGAATA 57.115 40.909 0.00 0.00 0.00 1.75
6333 9265 1.133513 TGAACCACATGAAAGGGTGCT 60.134 47.619 0.00 0.00 34.51 4.40
6381 9313 1.488812 ACCAGTCACTTGTTAGCACCA 59.511 47.619 0.00 0.00 0.00 4.17
6449 9381 1.003839 TTGGCTGAGGCTTGTACGG 60.004 57.895 7.74 0.00 38.73 4.02
6673 9605 8.618240 TTCAACAAAGAGGGGATATAGTTAGA 57.382 34.615 0.00 0.00 0.00 2.10
6681 9613 6.073447 TGCTAATTCAACAAAGAGGGGATA 57.927 37.500 0.00 0.00 0.00 2.59
6878 9830 4.142600 CGACAAATCATCCCCAACTTTCTC 60.143 45.833 0.00 0.00 0.00 2.87
6889 9841 4.113354 GTCTGTAGGACGACAAATCATCC 58.887 47.826 0.00 0.00 37.48 3.51
7157 10113 1.374947 GGCACACACTAAGGCAGGA 59.625 57.895 0.00 0.00 0.00 3.86
7203 10159 3.834489 ACTTGGATGCTCACTATCTGG 57.166 47.619 0.00 0.00 0.00 3.86
7207 10163 3.441572 GCAACAACTTGGATGCTCACTAT 59.558 43.478 12.25 0.00 33.42 2.12
7248 10204 6.381481 TGAATTGTCTCCATCACATAATGC 57.619 37.500 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.