Multiple sequence alignment - TraesCS3D01G389100

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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 TraesCS3D01G389100 chr3D 100.000 7688 0 0 1 7688 504727169 504734856 0.000000e+00 14198.0
1 TraesCS3D01G389100 chr3D 100.000 58 0 0 4507 4564 360634040 360634097 2.930000e-19 108.0
2 TraesCS3D01G389100 chr3D 94.118 68 3 1 4507 4574 589761279 589761213 1.360000e-17 102.0
3 TraesCS3D01G389100 chr3B 92.721 3558 165 35 1752 5263 666442661 666446170 0.000000e+00 5049.0
4 TraesCS3D01G389100 chr3B 95.159 1797 56 13 5320 7090 666446367 666448158 0.000000e+00 2808.0
5 TraesCS3D01G389100 chr3B 85.525 1285 85 50 501 1717 666441413 666442664 0.000000e+00 1249.0
6 TraesCS3D01G389100 chr3B 97.143 455 12 1 5 458 666440884 666441338 0.000000e+00 767.0
7 TraesCS3D01G389100 chr3A 90.258 2135 143 38 2342 4442 642918280 642920383 0.000000e+00 2730.0
8 TraesCS3D01G389100 chr3A 93.103 1682 94 10 5413 7091 642921647 642923309 0.000000e+00 2444.0
9 TraesCS3D01G389100 chr3A 91.062 1309 46 32 1 1283 642915962 642917225 0.000000e+00 1703.0
10 TraesCS3D01G389100 chr3A 92.121 1028 46 28 1332 2343 642917219 642918227 0.000000e+00 1417.0
11 TraesCS3D01G389100 chr3A 85.678 796 78 20 4568 5339 642920437 642921220 0.000000e+00 806.0
12 TraesCS3D01G389100 chr3A 96.825 63 1 1 4507 4568 434000917 434000979 3.790000e-18 104.0
13 TraesCS3D01G389100 chr3A 77.717 184 23 10 5169 5339 642921456 642921634 6.350000e-16 97.1
14 TraesCS3D01G389100 chr1D 92.574 404 23 3 7290 7688 365431186 365431587 2.410000e-159 573.0
15 TraesCS3D01G389100 chr1D 92.857 378 25 2 7123 7499 365430815 365431191 1.460000e-151 547.0
16 TraesCS3D01G389100 chr7A 92.519 401 24 3 7294 7688 412567789 412568189 3.110000e-158 569.0
17 TraesCS3D01G389100 chr7A 92.000 375 26 4 7123 7494 412567415 412567788 2.460000e-144 523.0
18 TraesCS3D01G389100 chr6B 93.103 377 19 5 7126 7499 550725408 550725780 5.250000e-151 545.0
19 TraesCS3D01G389100 chr6B 90.558 233 12 4 7460 7688 550743143 550743369 4.510000e-77 300.0
20 TraesCS3D01G389100 chr4A 89.731 409 38 4 7282 7688 377547995 377548401 3.180000e-143 520.0
21 TraesCS3D01G389100 chr4A 85.124 121 16 2 5762 5881 6635061 6634942 1.050000e-23 122.0
22 TraesCS3D01G389100 chr4A 92.857 70 4 1 4507 4575 626981553 626981484 4.910000e-17 100.0
23 TraesCS3D01G389100 chr4D 89.563 412 37 4 7279 7688 98531802 98531395 1.140000e-142 518.0
24 TraesCS3D01G389100 chr4D 85.124 121 16 2 5762 5881 462744652 462744533 1.050000e-23 122.0
25 TraesCS3D01G389100 chr2A 88.626 422 38 8 7274 7688 47204355 47204773 8.900000e-139 505.0
26 TraesCS3D01G389100 chr2A 87.923 414 40 6 7279 7686 46355952 46356361 5.400000e-131 479.0
27 TraesCS3D01G389100 chr7B 90.526 190 16 2 7091 7279 154571430 154571242 4.610000e-62 250.0
28 TraesCS3D01G389100 chr4B 86.607 112 13 2 5762 5872 578227121 578227231 1.050000e-23 122.0
29 TraesCS3D01G389100 chr2D 83.471 121 20 0 5762 5882 600319062 600318942 6.310000e-21 113.0
30 TraesCS3D01G389100 chr6D 96.825 63 2 0 4507 4569 24554584 24554522 1.060000e-18 106.0
31 TraesCS3D01G389100 chr5B 96.774 62 2 0 4507 4568 279098288 279098349 3.790000e-18 104.0
32 TraesCS3D01G389100 chr1B 88.636 88 7 2 4477 4564 421538158 421538074 3.790000e-18 104.0
33 TraesCS3D01G389100 chr5A 89.610 77 6 2 4498 4572 364712645 364712721 6.350000e-16 97.1
34 TraesCS3D01G389100 chr1A 97.143 35 0 1 7087 7120 157413303 157413269 3.000000e-04 58.4


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 TraesCS3D01G389100 chr3D 504727169 504734856 7687 False 14198.00 14198 100.000000 1 7688 1 chr3D.!!$F2 7687
1 TraesCS3D01G389100 chr3B 666440884 666448158 7274 False 2468.25 5049 92.637000 5 7090 4 chr3B.!!$F1 7085
2 TraesCS3D01G389100 chr3A 642915962 642923309 7347 False 1532.85 2730 88.323167 1 7091 6 chr3A.!!$F2 7090
3 TraesCS3D01G389100 chr1D 365430815 365431587 772 False 560.00 573 92.715500 7123 7688 2 chr1D.!!$F1 565
4 TraesCS3D01G389100 chr7A 412567415 412568189 774 False 546.00 569 92.259500 7123 7688 2 chr7A.!!$F1 565

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
458 464 0.453950 AAGCGCACGTACGTGTCTAG 60.454 55.0 39.56 29.69 46.9 2.43 F
1590 1712 0.179116 TGCCATTGTGTGTGTGTTGC 60.179 50.0 0.00 0.00 0.0 4.17 F
2954 3149 0.172578 TCGGCGGCATATCCTATTCG 59.827 55.0 10.53 0.00 0.0 3.34 F
3393 3594 0.459585 GCCGGAGTTAGCGATTGTCA 60.460 55.0 5.05 0.00 0.0 3.58 F
4975 5225 0.963856 TCGTATGGTGCAGAGGTCGT 60.964 55.0 0.00 0.00 0.0 4.34 F
5685 6553 0.519077 GCTAGCTTGTCACACCTTGC 59.481 55.0 7.70 0.00 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1814 0.455815 CAATTAAGTCTTGGCCGGCC 59.544 55.000 39.40 39.4 0.00 6.13 R
3518 3722 0.533308 AAGTTCGCTGCCCAAACGTA 60.533 50.000 0.00 0.0 0.00 3.57 R
4733 4980 0.767375 ACTCCTGCCTTGTCATGTGT 59.233 50.000 0.00 0.0 0.00 3.72 R
5368 6207 1.064979 CCTACGTATGGGTTGGCCTTT 60.065 52.381 3.32 0.0 34.45 3.11 R
5979 6847 1.153842 CATGTCGTAGCCGCTCACA 60.154 57.895 0.00 0.0 0.00 3.58 R
7104 7980 0.033228 TACCCCGTTGTAACACACGG 59.967 55.000 15.50 15.5 40.17 4.94 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
444 450 6.703165 TCATATCATATCATACCATCAAGCGC 59.297 38.462 0.00 0.00 0.00 5.92
455 461 1.342082 ATCAAGCGCACGTACGTGTC 61.342 55.000 39.56 31.72 46.90 3.67
456 462 2.014554 CAAGCGCACGTACGTGTCT 61.015 57.895 39.56 33.02 46.90 3.41
457 463 0.726787 CAAGCGCACGTACGTGTCTA 60.727 55.000 39.56 0.00 46.90 2.59
458 464 0.453950 AAGCGCACGTACGTGTCTAG 60.454 55.000 39.56 29.69 46.90 2.43
469 475 5.582269 ACGTACGTGTCTAGCTAATTAGTCA 59.418 40.000 22.14 1.73 0.00 3.41
475 481 8.464404 ACGTGTCTAGCTAATTAGTCAACAATA 58.536 33.333 13.91 0.00 0.00 1.90
540 586 5.398711 GCGTACGTATACTTCATTTCTGAGG 59.601 44.000 17.90 0.00 34.76 3.86
587 633 7.118825 CCACCTTATGATAGCATATTCACACTG 59.881 40.741 0.71 0.00 36.89 3.66
600 650 3.339253 TCACACTGCCGAGTAGTACTA 57.661 47.619 1.88 0.00 0.00 1.82
601 651 3.268330 TCACACTGCCGAGTAGTACTAG 58.732 50.000 1.87 2.84 0.00 2.57
602 652 3.008330 CACACTGCCGAGTAGTACTAGT 58.992 50.000 10.09 10.09 0.00 2.57
603 653 4.081476 TCACACTGCCGAGTAGTACTAGTA 60.081 45.833 10.28 0.00 0.00 1.82
929 986 0.670546 GTACTGGCGCTTGCTTCTCA 60.671 55.000 7.64 0.00 39.13 3.27
950 1013 5.502079 TCACTCTAGTCTTGTTAGGGAGAG 58.498 45.833 0.00 0.00 36.01 3.20
951 1014 5.251005 TCACTCTAGTCTTGTTAGGGAGAGA 59.749 44.000 3.16 0.00 34.41 3.10
1144 1210 3.556004 GCAGGTAGCACATTATCTCCTCC 60.556 52.174 0.00 0.00 44.79 4.30
1159 1225 1.383803 CTCCCCTCTTCCTCCCCAG 60.384 68.421 0.00 0.00 0.00 4.45
1160 1226 3.093172 CCCCTCTTCCTCCCCAGC 61.093 72.222 0.00 0.00 0.00 4.85
1161 1227 3.474570 CCCTCTTCCTCCCCAGCG 61.475 72.222 0.00 0.00 0.00 5.18
1170 1236 4.804420 TCCCCAGCGCCCTCTCAT 62.804 66.667 2.29 0.00 0.00 2.90
1177 1243 1.146930 GCGCCCTCTCATCCATCAA 59.853 57.895 0.00 0.00 0.00 2.57
1180 1246 1.071228 CGCCCTCTCATCCATCAATCA 59.929 52.381 0.00 0.00 0.00 2.57
1181 1247 2.502295 GCCCTCTCATCCATCAATCAC 58.498 52.381 0.00 0.00 0.00 3.06
1182 1248 2.106166 GCCCTCTCATCCATCAATCACT 59.894 50.000 0.00 0.00 0.00 3.41
1184 1250 3.647113 CCCTCTCATCCATCAATCACTCT 59.353 47.826 0.00 0.00 0.00 3.24
1185 1251 4.837298 CCCTCTCATCCATCAATCACTCTA 59.163 45.833 0.00 0.00 0.00 2.43
1186 1252 5.279406 CCCTCTCATCCATCAATCACTCTAC 60.279 48.000 0.00 0.00 0.00 2.59
1187 1253 5.539574 CCTCTCATCCATCAATCACTCTACT 59.460 44.000 0.00 0.00 0.00 2.57
1188 1254 6.718912 CCTCTCATCCATCAATCACTCTACTA 59.281 42.308 0.00 0.00 0.00 1.82
1189 1255 7.309133 CCTCTCATCCATCAATCACTCTACTAC 60.309 44.444 0.00 0.00 0.00 2.73
1190 1256 7.293828 TCTCATCCATCAATCACTCTACTACT 58.706 38.462 0.00 0.00 0.00 2.57
1191 1257 8.440771 TCTCATCCATCAATCACTCTACTACTA 58.559 37.037 0.00 0.00 0.00 1.82
1192 1258 8.628630 TCATCCATCAATCACTCTACTACTAG 57.371 38.462 0.00 0.00 0.00 2.57
1193 1259 8.221251 TCATCCATCAATCACTCTACTACTAGT 58.779 37.037 0.00 0.00 0.00 2.57
1196 1262 8.715842 TCCATCAATCACTCTACTACTAGTAGT 58.284 37.037 32.39 32.39 46.31 2.73
1228 1300 1.078143 CCCCTTTTCCAGCCTCTCG 60.078 63.158 0.00 0.00 0.00 4.04
1278 1354 3.451526 GCTTATGCTTTCCATTGAAGCC 58.548 45.455 6.40 0.00 46.85 4.35
1289 1365 4.355549 TCCATTGAAGCCAAATGAATCCT 58.644 39.130 5.43 0.00 35.67 3.24
1297 1373 3.722728 CCAAATGAATCCTTGGCTAGC 57.277 47.619 6.04 6.04 35.97 3.42
1298 1374 3.294214 CCAAATGAATCCTTGGCTAGCT 58.706 45.455 15.72 0.00 35.97 3.32
1299 1375 3.703052 CCAAATGAATCCTTGGCTAGCTT 59.297 43.478 15.72 0.00 35.97 3.74
1300 1376 4.202090 CCAAATGAATCCTTGGCTAGCTTC 60.202 45.833 15.72 9.78 35.97 3.86
1301 1377 3.939740 ATGAATCCTTGGCTAGCTTCA 57.060 42.857 15.72 15.19 32.21 3.02
1302 1378 3.939740 TGAATCCTTGGCTAGCTTCAT 57.060 42.857 15.72 0.00 0.00 2.57
1303 1379 4.240881 TGAATCCTTGGCTAGCTTCATT 57.759 40.909 15.72 6.20 0.00 2.57
1304 1380 4.603131 TGAATCCTTGGCTAGCTTCATTT 58.397 39.130 15.72 2.02 0.00 2.32
1305 1381 4.641989 TGAATCCTTGGCTAGCTTCATTTC 59.358 41.667 15.72 11.30 0.00 2.17
1306 1382 3.004752 TCCTTGGCTAGCTTCATTTCC 57.995 47.619 15.72 0.00 0.00 3.13
1307 1383 2.308570 TCCTTGGCTAGCTTCATTTCCA 59.691 45.455 15.72 0.00 0.00 3.53
1308 1384 3.053395 TCCTTGGCTAGCTTCATTTCCAT 60.053 43.478 15.72 0.00 0.00 3.41
1309 1385 3.317430 CCTTGGCTAGCTTCATTTCCATC 59.683 47.826 15.72 0.00 0.00 3.51
1310 1386 3.650281 TGGCTAGCTTCATTTCCATCA 57.350 42.857 15.72 0.00 0.00 3.07
1311 1387 4.174704 TGGCTAGCTTCATTTCCATCAT 57.825 40.909 15.72 0.00 0.00 2.45
1312 1388 3.887110 TGGCTAGCTTCATTTCCATCATG 59.113 43.478 15.72 0.00 0.00 3.07
1313 1389 3.887716 GGCTAGCTTCATTTCCATCATGT 59.112 43.478 15.72 0.00 0.00 3.21
1314 1390 4.340381 GGCTAGCTTCATTTCCATCATGTT 59.660 41.667 15.72 0.00 0.00 2.71
1315 1391 5.163478 GGCTAGCTTCATTTCCATCATGTTT 60.163 40.000 15.72 0.00 0.00 2.83
1316 1392 6.335777 GCTAGCTTCATTTCCATCATGTTTT 58.664 36.000 7.70 0.00 0.00 2.43
1317 1393 6.474751 GCTAGCTTCATTTCCATCATGTTTTC 59.525 38.462 7.70 0.00 0.00 2.29
1318 1394 6.349243 AGCTTCATTTCCATCATGTTTTCA 57.651 33.333 0.00 0.00 0.00 2.69
1319 1395 6.942976 AGCTTCATTTCCATCATGTTTTCAT 58.057 32.000 0.00 0.00 41.78 2.57
1320 1396 7.039882 AGCTTCATTTCCATCATGTTTTCATC 58.960 34.615 0.00 0.00 38.64 2.92
1321 1397 7.039882 GCTTCATTTCCATCATGTTTTCATCT 58.960 34.615 0.00 0.00 38.64 2.90
1322 1398 7.548075 GCTTCATTTCCATCATGTTTTCATCTT 59.452 33.333 0.00 0.00 38.64 2.40
1327 1403 5.323581 TCCATCATGTTTTCATCTTCACCA 58.676 37.500 0.00 0.00 38.64 4.17
1337 1413 4.572985 TCATCTTCACCACAAGCAAAAG 57.427 40.909 0.00 0.00 0.00 2.27
1457 1538 2.741517 TCATGTGTATTGTCACTTGCGG 59.258 45.455 0.00 0.00 40.71 5.69
1458 1539 2.248280 TGTGTATTGTCACTTGCGGT 57.752 45.000 0.00 0.00 38.90 5.68
1459 1540 1.870402 TGTGTATTGTCACTTGCGGTG 59.130 47.619 3.61 3.61 46.60 4.94
1463 1555 2.113860 ATTGTCACTTGCGGTGCTAT 57.886 45.000 4.97 1.75 44.98 2.97
1466 1558 2.616960 TGTCACTTGCGGTGCTATTAG 58.383 47.619 4.97 0.00 44.98 1.73
1467 1559 1.327764 GTCACTTGCGGTGCTATTAGC 59.672 52.381 8.80 8.80 44.98 3.09
1587 1709 1.180907 TTGTGCCATTGTGTGTGTGT 58.819 45.000 0.00 0.00 0.00 3.72
1588 1710 1.180907 TGTGCCATTGTGTGTGTGTT 58.819 45.000 0.00 0.00 0.00 3.32
1589 1711 1.135170 TGTGCCATTGTGTGTGTGTTG 60.135 47.619 0.00 0.00 0.00 3.33
1590 1712 0.179116 TGCCATTGTGTGTGTGTTGC 60.179 50.000 0.00 0.00 0.00 4.17
1607 1729 2.664081 GCTGTGTCAGGAGGAGGGG 61.664 68.421 0.00 0.00 31.21 4.79
1637 1760 5.651530 GCCTAGGGCTTTGAAAGAAATAAC 58.348 41.667 11.72 0.00 46.69 1.89
1691 1814 4.974399 AGTGGTTTTAGGGTTTGAGAGAG 58.026 43.478 0.00 0.00 0.00 3.20
1722 1848 6.403200 CCAAGACTTAATTGTTCATACGTGGG 60.403 42.308 0.00 0.00 0.00 4.61
1727 1853 4.759516 AATTGTTCATACGTGGGTTCAC 57.240 40.909 0.00 0.00 40.36 3.18
1765 1891 3.419264 TTGGCGCATAGTTAGCAATTG 57.581 42.857 10.83 0.00 0.00 2.32
1772 1898 6.430451 GCGCATAGTTAGCAATTGATTAACT 58.570 36.000 25.76 25.76 39.96 2.24
1984 2114 6.818644 AGCTAGATCTTGCGACATTTCTTAAA 59.181 34.615 20.91 0.00 36.47 1.52
2121 2251 1.904865 CATGCAGGCAACAGGGTGT 60.905 57.895 0.00 0.00 41.41 4.16
2130 2260 2.504367 GCAACAGGGTGTACTCATGTT 58.496 47.619 11.82 11.82 34.56 2.71
2311 2444 4.202284 TGTGGAAAAAGCTTCCTACTACGT 60.202 41.667 0.00 0.00 39.31 3.57
2551 2746 1.972660 CTCCTAACCTTGGGCTCCCG 61.973 65.000 0.00 0.00 39.42 5.14
2621 2816 4.873746 ACAGCAAGCTTAAGTAGAGACA 57.126 40.909 0.00 0.00 0.00 3.41
2754 2949 1.972223 CTCAGGTGACGTCTCCGGT 60.972 63.158 27.95 13.17 38.78 5.28
2850 3045 5.517770 GCATCAAGCAGTTGTATGAAAATCC 59.482 40.000 0.00 0.00 44.79 3.01
2954 3149 0.172578 TCGGCGGCATATCCTATTCG 59.827 55.000 10.53 0.00 0.00 3.34
3296 3497 4.828925 GAGCAGCAGAGGGCCGAC 62.829 72.222 0.00 0.00 46.50 4.79
3383 3584 4.728102 CGTGGCGTGCCGGAGTTA 62.728 66.667 5.05 0.00 39.42 2.24
3393 3594 0.459585 GCCGGAGTTAGCGATTGTCA 60.460 55.000 5.05 0.00 0.00 3.58
3434 3635 4.711949 AGCAGCGCTGGTTCTGGG 62.712 66.667 34.85 9.65 38.24 4.45
3518 3722 1.828660 ATCGAGGAAGACGGCCGAT 60.829 57.895 35.90 17.82 35.46 4.18
3533 3737 1.807981 CGATACGTTTGGGCAGCGA 60.808 57.895 0.00 0.00 0.00 4.93
3853 4091 6.488006 AGTGAGTATGTCATTTGCTTTTGAGT 59.512 34.615 0.00 0.00 37.56 3.41
3917 4155 1.401761 TATGTGGGCATGATTGTGGC 58.598 50.000 0.00 0.00 43.34 5.01
4121 4362 7.732222 TCCCCTTCAATGTTGCTAATTAAAT 57.268 32.000 0.00 0.00 0.00 1.40
4165 4406 2.357952 ACTTTGTTTGAACTCGGCCTTC 59.642 45.455 0.00 0.00 0.00 3.46
4168 4409 1.140052 TGTTTGAACTCGGCCTTCTCA 59.860 47.619 0.00 0.00 0.00 3.27
4206 4447 6.603940 ATCTAGGTAAGCAAGATCCAGATC 57.396 41.667 0.00 0.00 38.09 2.75
4208 4449 2.366916 AGGTAAGCAAGATCCAGATCGG 59.633 50.000 2.08 0.85 42.48 4.18
4229 4470 9.834628 GATCGGAGTAATTACATTTGTTTTTGA 57.165 29.630 17.65 1.87 0.00 2.69
4438 4679 3.047796 GCTGCTCTTGTTGTCATTGTTG 58.952 45.455 0.00 0.00 0.00 3.33
4439 4680 3.489738 GCTGCTCTTGTTGTCATTGTTGT 60.490 43.478 0.00 0.00 0.00 3.32
4440 4681 4.675510 CTGCTCTTGTTGTCATTGTTGTT 58.324 39.130 0.00 0.00 0.00 2.83
4441 4682 4.422840 TGCTCTTGTTGTCATTGTTGTTG 58.577 39.130 0.00 0.00 0.00 3.33
4442 4683 4.082300 TGCTCTTGTTGTCATTGTTGTTGT 60.082 37.500 0.00 0.00 0.00 3.32
4443 4684 4.500477 GCTCTTGTTGTCATTGTTGTTGTC 59.500 41.667 0.00 0.00 0.00 3.18
4444 4685 5.635417 TCTTGTTGTCATTGTTGTTGTCA 57.365 34.783 0.00 0.00 0.00 3.58
4445 4686 6.206395 TCTTGTTGTCATTGTTGTTGTCAT 57.794 33.333 0.00 0.00 0.00 3.06
4446 4687 6.629128 TCTTGTTGTCATTGTTGTTGTCATT 58.371 32.000 0.00 0.00 0.00 2.57
4447 4688 6.530887 TCTTGTTGTCATTGTTGTTGTCATTG 59.469 34.615 0.00 0.00 0.00 2.82
4448 4689 5.718146 TGTTGTCATTGTTGTTGTCATTGT 58.282 33.333 0.00 0.00 0.00 2.71
4449 4690 6.162079 TGTTGTCATTGTTGTTGTCATTGTT 58.838 32.000 0.00 0.00 0.00 2.83
4450 4691 6.648310 TGTTGTCATTGTTGTTGTCATTGTTT 59.352 30.769 0.00 0.00 0.00 2.83
4466 4707 7.492020 TGTCATTGTTTTTGGAAGAAGTCATTG 59.508 33.333 0.00 0.00 0.00 2.82
4469 4710 9.311916 CATTGTTTTTGGAAGAAGTCATTGTTA 57.688 29.630 0.00 0.00 0.00 2.41
4604 4845 5.937540 TCGTTGATCAATGTAATGGTGAACT 59.062 36.000 23.63 0.00 0.00 3.01
4733 4980 7.009179 TGAAAAAGAGCTAGAGGAGATGAAA 57.991 36.000 0.00 0.00 0.00 2.69
4931 5181 3.129988 GTGGAGTAACTAGGTATGCACGT 59.870 47.826 0.00 0.00 0.00 4.49
4933 5183 3.114065 GAGTAACTAGGTATGCACGTGC 58.886 50.000 33.11 33.11 42.50 5.34
4975 5225 0.963856 TCGTATGGTGCAGAGGTCGT 60.964 55.000 0.00 0.00 0.00 4.34
5068 5318 1.978617 GCACCACCAACATGGGAGG 60.979 63.158 0.00 0.00 44.81 4.30
5141 5391 6.380190 GGCACCTTCAGTAAGTATAGATACG 58.620 44.000 0.00 0.00 38.28 3.06
5145 5395 6.544931 ACCTTCAGTAAGTATAGATACGCACA 59.455 38.462 8.47 0.00 38.28 4.57
5163 5644 5.038683 CGCACAATCAATTGCACTGAATAT 58.961 37.500 0.00 0.00 41.38 1.28
5167 5648 7.488792 GCACAATCAATTGCACTGAATATGTTA 59.511 33.333 0.00 0.00 41.38 2.41
5168 5649 9.356433 CACAATCAATTGCACTGAATATGTTAA 57.644 29.630 0.00 0.00 41.38 2.01
5206 5687 4.487714 TTGCCACCTTAACTATCAGAGG 57.512 45.455 0.00 0.00 35.39 3.69
5307 5993 6.820656 AGTCATTCATTGCGAACTAATCTCTT 59.179 34.615 0.00 0.00 36.12 2.85
5329 6168 5.833406 TTACGGATGGTACTCGTTGATTA 57.167 39.130 8.68 0.00 38.19 1.75
5344 6183 8.190784 ACTCGTTGATTATCCAAATTCAAATCC 58.809 33.333 0.00 0.00 0.00 3.01
5349 6188 9.820725 TTGATTATCCAAATTCAAATCCATGTC 57.179 29.630 0.00 0.00 0.00 3.06
5365 6204 2.024319 GTCCAGCTGACGTGTGAGC 61.024 63.158 17.39 3.09 40.20 4.26
5368 6207 3.233980 AGCTGACGTGTGAGCCCA 61.234 61.111 7.85 0.00 40.81 5.36
5384 6223 1.319614 CCCAAAGGCCAACCCATACG 61.320 60.000 5.01 0.00 36.11 3.06
5386 6225 1.340211 CCAAAGGCCAACCCATACGTA 60.340 52.381 5.01 0.00 36.11 3.57
5387 6226 2.014128 CAAAGGCCAACCCATACGTAG 58.986 52.381 5.01 0.00 36.11 3.51
5388 6227 0.544697 AAGGCCAACCCATACGTAGG 59.455 55.000 5.01 0.00 36.11 3.18
5393 6232 1.134220 CCAACCCATACGTAGGCATGT 60.134 52.381 0.71 0.00 0.00 3.21
5414 6253 3.058914 GTGAGAAATGGAGTGACAAACCG 60.059 47.826 0.00 0.00 0.00 4.44
5683 6551 2.938956 AAGCTAGCTTGTCACACCTT 57.061 45.000 28.83 0.20 34.60 3.50
5684 6552 2.175878 AGCTAGCTTGTCACACCTTG 57.824 50.000 12.68 0.00 0.00 3.61
5685 6553 0.519077 GCTAGCTTGTCACACCTTGC 59.481 55.000 7.70 0.00 0.00 4.01
5686 6554 1.879796 GCTAGCTTGTCACACCTTGCT 60.880 52.381 7.70 0.00 34.92 3.91
5687 6555 2.498167 CTAGCTTGTCACACCTTGCTT 58.502 47.619 0.00 0.00 32.72 3.91
5688 6556 1.027357 AGCTTGTCACACCTTGCTTG 58.973 50.000 0.00 0.00 0.00 4.01
5689 6557 0.595825 GCTTGTCACACCTTGCTTGC 60.596 55.000 0.00 0.00 0.00 4.01
5690 6558 0.740149 CTTGTCACACCTTGCTTGCA 59.260 50.000 0.00 0.00 0.00 4.08
6105 6973 2.348998 CCGCCTCAGCAGGTTTCT 59.651 61.111 0.00 0.00 42.74 2.52
6240 7108 2.516888 CCACCACCTCAACCTCGGT 61.517 63.158 0.00 0.00 0.00 4.69
6243 7111 2.743718 CACCTCAACCTCGGTGCT 59.256 61.111 0.00 0.00 43.59 4.40
6422 7290 1.592400 CTGCCAATGAGCACCACCAG 61.592 60.000 0.00 0.00 38.00 4.00
6588 7456 2.686106 GAAGCCTACGGTGGGGGA 60.686 66.667 12.78 0.00 0.00 4.81
6816 7688 1.541588 GTTGGGATGGTGTTCTTCTGC 59.458 52.381 0.00 0.00 0.00 4.26
6876 7748 4.586001 ACTGCATTGTTCTTGGATCAGTTT 59.414 37.500 0.00 0.00 30.30 2.66
6877 7749 5.069516 ACTGCATTGTTCTTGGATCAGTTTT 59.930 36.000 0.00 0.00 30.30 2.43
6881 7753 6.680810 CATTGTTCTTGGATCAGTTTTGCTA 58.319 36.000 0.00 0.00 0.00 3.49
7022 7897 3.896133 GGCACTGCATGATGGCGG 61.896 66.667 2.82 0.00 45.74 6.13
7041 7916 2.159585 CGGTCAATGCGCAAATGAGTTA 60.160 45.455 24.35 5.72 0.00 2.24
7095 7971 8.374327 TCTGTTTCCTTTAGTGTTTTACTAGC 57.626 34.615 0.00 0.00 42.57 3.42
7096 7972 7.988599 TCTGTTTCCTTTAGTGTTTTACTAGCA 59.011 33.333 0.00 0.00 42.57 3.49
7097 7973 8.508883 TGTTTCCTTTAGTGTTTTACTAGCAA 57.491 30.769 0.00 0.00 42.57 3.91
7098 7974 8.958506 TGTTTCCTTTAGTGTTTTACTAGCAAA 58.041 29.630 0.00 0.00 42.57 3.68
7099 7975 9.791820 GTTTCCTTTAGTGTTTTACTAGCAAAA 57.208 29.630 0.00 0.00 42.57 2.44
7102 7978 9.959749 TCCTTTAGTGTTTTACTAGCAAAAATG 57.040 29.630 2.37 0.00 42.57 2.32
7103 7979 8.699749 CCTTTAGTGTTTTACTAGCAAAAATGC 58.300 33.333 2.37 0.00 42.57 3.56
7104 7980 8.582433 TTTAGTGTTTTACTAGCAAAAATGCC 57.418 30.769 2.37 0.00 42.57 4.40
7105 7981 5.538118 AGTGTTTTACTAGCAAAAATGCCC 58.462 37.500 2.37 0.00 38.04 5.36
7106 7982 4.384547 GTGTTTTACTAGCAAAAATGCCCG 59.615 41.667 2.37 0.00 34.90 6.13
7107 7983 4.038162 TGTTTTACTAGCAAAAATGCCCGT 59.962 37.500 2.37 0.00 34.90 5.28
7108 7984 3.840890 TTACTAGCAAAAATGCCCGTG 57.159 42.857 0.00 0.00 34.90 4.94
7109 7985 1.616159 ACTAGCAAAAATGCCCGTGT 58.384 45.000 0.00 0.00 34.90 4.49
7110 7986 1.269448 ACTAGCAAAAATGCCCGTGTG 59.731 47.619 0.00 0.00 34.90 3.82
7111 7987 1.269448 CTAGCAAAAATGCCCGTGTGT 59.731 47.619 0.00 0.00 34.90 3.72
7112 7988 0.463620 AGCAAAAATGCCCGTGTGTT 59.536 45.000 0.00 0.00 34.90 3.32
7113 7989 1.683917 AGCAAAAATGCCCGTGTGTTA 59.316 42.857 0.00 0.00 34.90 2.41
7114 7990 1.790043 GCAAAAATGCCCGTGTGTTAC 59.210 47.619 0.00 0.00 0.00 2.50
7115 7991 2.799917 GCAAAAATGCCCGTGTGTTACA 60.800 45.455 0.00 0.00 0.00 2.41
7116 7992 3.448686 CAAAAATGCCCGTGTGTTACAA 58.551 40.909 0.00 0.00 0.00 2.41
7117 7993 2.785713 AAATGCCCGTGTGTTACAAC 57.214 45.000 0.00 0.00 0.00 3.32
7118 7994 0.589223 AATGCCCGTGTGTTACAACG 59.411 50.000 11.15 11.15 0.00 4.10
7119 7995 1.231958 ATGCCCGTGTGTTACAACGG 61.232 55.000 22.54 22.54 40.17 4.44
7121 7997 3.645286 CCGTGTGTTACAACGGGG 58.355 61.111 22.08 5.30 38.33 5.73
7177 8053 4.083537 TCACACTGTTGACGCCATTTATTC 60.084 41.667 0.00 0.00 0.00 1.75
7182 8058 0.923358 TGACGCCATTTATTCCCCCT 59.077 50.000 0.00 0.00 0.00 4.79
7216 8092 5.428253 TCATAGTGGTTGTTATCCTGCTTC 58.572 41.667 0.00 0.00 0.00 3.86
7238 8115 2.009774 CCCATCAATGACGTTGGTCTC 58.990 52.381 7.54 0.00 43.79 3.36
7239 8116 2.009774 CCATCAATGACGTTGGTCTCC 58.990 52.381 7.54 0.00 43.79 3.71
7253 8130 2.912295 TGGTCTCCCATCTCATCAACAA 59.088 45.455 0.00 0.00 35.17 2.83
7276 8153 7.041098 ACAAGTCTAAATGTGGTCAATCTCAAC 60.041 37.037 0.00 0.00 0.00 3.18
7279 8156 6.204688 GTCTAAATGTGGTCAATCTCAACACA 59.795 38.462 0.00 0.00 44.91 3.72
7370 8248 6.734137 TGTTGCTCATTTTACAAATCGACTT 58.266 32.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 440 2.092291 ACGTACGTGCGCTTGATGG 61.092 57.895 26.01 0.00 34.88 3.51
475 481 9.668497 TCATGAGCGTATATATCTACTAAGTGT 57.332 33.333 0.00 0.00 0.00 3.55
540 586 2.545106 GAGACGTACTCCTCGAGATTCC 59.455 54.545 15.71 0.00 39.53 3.01
600 650 9.525409 CGCTGTTAATTAATTACCAGTACTACT 57.475 33.333 25.00 0.00 35.83 2.57
601 651 8.271487 GCGCTGTTAATTAATTACCAGTACTAC 58.729 37.037 25.00 12.80 35.83 2.73
602 652 7.167968 CGCGCTGTTAATTAATTACCAGTACTA 59.832 37.037 25.00 2.29 35.83 1.82
603 653 6.019318 CGCGCTGTTAATTAATTACCAGTACT 60.019 38.462 25.00 0.00 35.83 2.73
608 658 3.940221 ACCGCGCTGTTAATTAATTACCA 59.060 39.130 5.56 6.36 0.00 3.25
609 659 4.541085 ACCGCGCTGTTAATTAATTACC 57.459 40.909 5.56 1.63 0.00 2.85
618 668 2.690786 ACTGATTAACCGCGCTGTTAA 58.309 42.857 30.55 30.55 42.91 2.01
623 673 3.592059 TCTTTTACTGATTAACCGCGCT 58.408 40.909 5.56 0.00 0.00 5.92
624 674 4.033587 TCATCTTTTACTGATTAACCGCGC 59.966 41.667 0.00 0.00 0.00 6.86
929 986 5.489637 TCTCTCTCCCTAACAAGACTAGAGT 59.510 44.000 0.00 0.00 32.67 3.24
950 1013 2.627699 CCACCCAGCTAATCTCTCTCTC 59.372 54.545 0.00 0.00 0.00 3.20
951 1014 2.676748 CCACCCAGCTAATCTCTCTCT 58.323 52.381 0.00 0.00 0.00 3.10
1144 1210 3.474570 CGCTGGGGAGGAAGAGGG 61.475 72.222 0.00 0.00 0.00 4.30
1159 1225 0.250640 ATTGATGGATGAGAGGGCGC 60.251 55.000 0.00 0.00 0.00 6.53
1160 1226 1.071228 TGATTGATGGATGAGAGGGCG 59.929 52.381 0.00 0.00 0.00 6.13
1161 1227 2.106166 AGTGATTGATGGATGAGAGGGC 59.894 50.000 0.00 0.00 0.00 5.19
1165 1231 7.293828 AGTAGTAGAGTGATTGATGGATGAGA 58.706 38.462 0.00 0.00 0.00 3.27
1186 1252 9.984190 GGGGAAAGAAAATCATACTACTAGTAG 57.016 37.037 25.30 25.30 33.66 2.57
1187 1253 8.931568 GGGGGAAAGAAAATCATACTACTAGTA 58.068 37.037 1.89 1.89 34.82 1.82
1188 1254 7.628101 AGGGGGAAAGAAAATCATACTACTAGT 59.372 37.037 0.00 0.00 0.00 2.57
1189 1255 8.035448 AGGGGGAAAGAAAATCATACTACTAG 57.965 38.462 0.00 0.00 0.00 2.57
1190 1256 8.401955 AAGGGGGAAAGAAAATCATACTACTA 57.598 34.615 0.00 0.00 0.00 1.82
1191 1257 6.910259 AGGGGGAAAGAAAATCATACTACT 57.090 37.500 0.00 0.00 0.00 2.57
1192 1258 7.956328 AAAGGGGGAAAGAAAATCATACTAC 57.044 36.000 0.00 0.00 0.00 2.73
1193 1259 7.618117 GGAAAAGGGGGAAAGAAAATCATACTA 59.382 37.037 0.00 0.00 0.00 1.82
1195 1261 6.212589 TGGAAAAGGGGGAAAGAAAATCATAC 59.787 38.462 0.00 0.00 0.00 2.39
1196 1262 6.326970 TGGAAAAGGGGGAAAGAAAATCATA 58.673 36.000 0.00 0.00 0.00 2.15
1228 1300 8.958175 CTACATATAGCTAGTAGCAGAACAAC 57.042 38.462 23.77 0.00 45.56 3.32
1278 1354 4.400251 TGAAGCTAGCCAAGGATTCATTTG 59.600 41.667 12.13 0.00 33.77 2.32
1289 1365 3.966979 TGATGGAAATGAAGCTAGCCAA 58.033 40.909 12.13 0.00 0.00 4.52
1297 1373 8.997621 AAGATGAAAACATGATGGAAATGAAG 57.002 30.769 0.00 0.00 0.00 3.02
1298 1374 8.586744 TGAAGATGAAAACATGATGGAAATGAA 58.413 29.630 0.00 0.00 0.00 2.57
1299 1375 8.030692 GTGAAGATGAAAACATGATGGAAATGA 58.969 33.333 0.00 0.00 0.00 2.57
1300 1376 7.277098 GGTGAAGATGAAAACATGATGGAAATG 59.723 37.037 0.00 0.00 0.00 2.32
1301 1377 7.038870 TGGTGAAGATGAAAACATGATGGAAAT 60.039 33.333 0.00 0.00 0.00 2.17
1302 1378 6.267242 TGGTGAAGATGAAAACATGATGGAAA 59.733 34.615 0.00 0.00 0.00 3.13
1303 1379 5.774184 TGGTGAAGATGAAAACATGATGGAA 59.226 36.000 0.00 0.00 0.00 3.53
1304 1380 5.183713 GTGGTGAAGATGAAAACATGATGGA 59.816 40.000 0.00 0.00 0.00 3.41
1305 1381 5.047872 TGTGGTGAAGATGAAAACATGATGG 60.048 40.000 0.00 0.00 0.00 3.51
1306 1382 6.016213 TGTGGTGAAGATGAAAACATGATG 57.984 37.500 0.00 0.00 0.00 3.07
1307 1383 6.653526 TTGTGGTGAAGATGAAAACATGAT 57.346 33.333 0.00 0.00 0.00 2.45
1308 1384 5.507817 GCTTGTGGTGAAGATGAAAACATGA 60.508 40.000 0.00 0.00 0.00 3.07
1309 1385 4.682860 GCTTGTGGTGAAGATGAAAACATG 59.317 41.667 0.00 0.00 0.00 3.21
1310 1386 4.341806 TGCTTGTGGTGAAGATGAAAACAT 59.658 37.500 0.00 0.00 0.00 2.71
1311 1387 3.698539 TGCTTGTGGTGAAGATGAAAACA 59.301 39.130 0.00 0.00 0.00 2.83
1312 1388 4.305989 TGCTTGTGGTGAAGATGAAAAC 57.694 40.909 0.00 0.00 0.00 2.43
1313 1389 4.998671 TTGCTTGTGGTGAAGATGAAAA 57.001 36.364 0.00 0.00 0.00 2.29
1314 1390 4.998671 TTTGCTTGTGGTGAAGATGAAA 57.001 36.364 0.00 0.00 0.00 2.69
1315 1391 4.402155 ACTTTTGCTTGTGGTGAAGATGAA 59.598 37.500 0.00 0.00 0.00 2.57
1316 1392 3.953612 ACTTTTGCTTGTGGTGAAGATGA 59.046 39.130 0.00 0.00 0.00 2.92
1317 1393 4.311816 ACTTTTGCTTGTGGTGAAGATG 57.688 40.909 0.00 0.00 0.00 2.90
1318 1394 7.944729 ATATACTTTTGCTTGTGGTGAAGAT 57.055 32.000 0.00 0.00 0.00 2.40
1319 1395 7.759489 AATATACTTTTGCTTGTGGTGAAGA 57.241 32.000 0.00 0.00 0.00 2.87
1320 1396 8.702438 CAAAATATACTTTTGCTTGTGGTGAAG 58.298 33.333 7.15 0.00 33.38 3.02
1321 1397 8.586570 CAAAATATACTTTTGCTTGTGGTGAA 57.413 30.769 7.15 0.00 33.38 3.18
1405 1486 5.796350 AACTCTGTAATTCGCACATAACC 57.204 39.130 0.00 0.00 0.00 2.85
1466 1558 8.847567 CGCTGATAATAATCTCATGAAAAATGC 58.152 33.333 0.00 0.00 32.93 3.56
1483 1575 6.757010 ACAACTTAGACGAAATCGCTGATAAT 59.243 34.615 2.15 0.00 44.43 1.28
1489 1581 4.304110 TCAACAACTTAGACGAAATCGCT 58.696 39.130 2.15 4.13 44.43 4.93
1587 1709 1.483595 CCCTCCTCCTGACACAGCAA 61.484 60.000 0.00 0.00 0.00 3.91
1588 1710 1.915266 CCCTCCTCCTGACACAGCA 60.915 63.158 0.00 0.00 0.00 4.41
1589 1711 2.664081 CCCCTCCTCCTGACACAGC 61.664 68.421 0.00 0.00 0.00 4.40
1590 1712 1.992277 CCCCCTCCTCCTGACACAG 60.992 68.421 0.00 0.00 0.00 3.66
1691 1814 0.455815 CAATTAAGTCTTGGCCGGCC 59.544 55.000 39.40 39.40 0.00 6.13
1874 2004 2.819608 TCCTCTCTTTTTCAATTGCGGG 59.180 45.455 0.00 0.00 0.00 6.13
1984 2114 4.132122 ACTGATCACCCCCTTGAAAAAT 57.868 40.909 0.00 0.00 0.00 1.82
2121 2251 7.508687 ACATGTAAGATATGCCAACATGAGTA 58.491 34.615 17.80 0.00 46.57 2.59
2130 2260 5.128499 CCCCAAAAACATGTAAGATATGCCA 59.872 40.000 0.00 0.00 0.00 4.92
2344 2531 6.042437 TGAGACTACTGTGGATGATTATGCAT 59.958 38.462 3.79 3.79 36.99 3.96
2352 2539 3.759086 GAGTGTGAGACTACTGTGGATGA 59.241 47.826 0.00 0.00 33.83 2.92
2465 2660 4.021894 ACTTGAGGAACTGTGTGCTACTAG 60.022 45.833 0.00 0.00 41.55 2.57
2469 2664 2.965831 AGACTTGAGGAACTGTGTGCTA 59.034 45.455 0.00 0.00 41.55 3.49
2470 2665 1.765314 AGACTTGAGGAACTGTGTGCT 59.235 47.619 0.00 0.00 41.55 4.40
2471 2666 2.139118 GAGACTTGAGGAACTGTGTGC 58.861 52.381 0.00 0.00 41.55 4.57
2472 2667 2.103094 TGGAGACTTGAGGAACTGTGTG 59.897 50.000 0.00 0.00 41.55 3.82
2473 2668 2.398588 TGGAGACTTGAGGAACTGTGT 58.601 47.619 0.00 0.00 41.55 3.72
2551 2746 2.494870 AGATCAAGAAGCCATTGTTGCC 59.505 45.455 0.00 0.00 39.05 4.52
2621 2816 5.694910 CACAGTACGTGGAAGTGATTAACTT 59.305 40.000 0.00 0.00 43.70 2.66
2754 2949 1.372499 GTTGTAGCAGACGTCGGCA 60.372 57.895 35.89 21.94 39.54 5.69
2811 3006 4.622740 GCTTGATGCACTTAAACCAATCAC 59.377 41.667 0.00 0.00 42.31 3.06
2850 3045 3.044986 CTGCGAAACAAACCAATCACAG 58.955 45.455 0.00 0.00 0.00 3.66
2954 3149 1.002134 CTGGTGGTGGTGATGGTCC 60.002 63.158 0.00 0.00 0.00 4.46
2996 3191 2.731571 GCCTGCAGGGACGACCATA 61.732 63.158 33.46 0.00 43.89 2.74
3170 3365 1.379309 ACCGTTGGCTGTGGTGTTT 60.379 52.632 0.00 0.00 33.91 2.83
3383 3584 1.833630 TCATCCTTCCTGACAATCGCT 59.166 47.619 0.00 0.00 0.00 4.93
3393 3594 2.990479 GGCCGTGTCATCCTTCCT 59.010 61.111 0.00 0.00 0.00 3.36
3494 3698 1.227089 CGTCTTCCTCGATGCTGGG 60.227 63.158 0.00 0.00 0.00 4.45
3500 3704 0.536687 TATCGGCCGTCTTCCTCGAT 60.537 55.000 27.15 10.34 42.22 3.59
3518 3722 0.533308 AAGTTCGCTGCCCAAACGTA 60.533 50.000 0.00 0.00 0.00 3.57
3533 3737 1.073177 CGCCACGGTAAATCGAAGTT 58.927 50.000 0.00 0.00 0.00 2.66
3815 4053 8.675705 TGACATACTCACTTGATTCAAAGAAA 57.324 30.769 0.01 0.00 0.00 2.52
3835 4073 6.645790 AAGAGACTCAAAAGCAAATGACAT 57.354 33.333 5.02 0.00 0.00 3.06
3836 4074 6.455360 AAAGAGACTCAAAAGCAAATGACA 57.545 33.333 5.02 0.00 0.00 3.58
3853 4091 7.994425 TGCACCTACATTATTCAAAAAGAGA 57.006 32.000 0.00 0.00 0.00 3.10
3873 4111 3.491447 GGCATTCCACATTTCCTATGCAC 60.491 47.826 0.00 0.00 39.96 4.57
3917 4155 3.067106 AGAATCACACGTTGTAAGCCTG 58.933 45.455 0.00 0.00 0.00 4.85
3946 4184 7.177392 GTCCATCTATGCCTATTAAAGCCAATT 59.823 37.037 0.00 0.00 0.00 2.32
4165 4406 5.067153 CCTAGATAGACTGTGTGGAGTTGAG 59.933 48.000 0.00 0.00 0.00 3.02
4168 4409 4.936802 ACCTAGATAGACTGTGTGGAGTT 58.063 43.478 0.00 0.00 0.00 3.01
4206 4447 8.687301 GTGTCAAAAACAAATGTAATTACTCCG 58.313 33.333 16.33 5.48 40.31 4.63
4229 4470 4.502171 TGAATGCATCGACAAAATGTGT 57.498 36.364 0.00 0.00 45.74 3.72
4276 4517 7.928908 TTCAAGATTAGAACATGCACAAAAC 57.071 32.000 0.00 0.00 0.00 2.43
4317 4558 4.094146 GCAGCTTTCTCCTCTTTGTCATAC 59.906 45.833 0.00 0.00 0.00 2.39
4438 4679 6.811170 TGACTTCTTCCAAAAACAATGACAAC 59.189 34.615 0.00 0.00 0.00 3.32
4439 4680 6.929625 TGACTTCTTCCAAAAACAATGACAA 58.070 32.000 0.00 0.00 0.00 3.18
4440 4681 6.522625 TGACTTCTTCCAAAAACAATGACA 57.477 33.333 0.00 0.00 0.00 3.58
4441 4682 7.492344 ACAATGACTTCTTCCAAAAACAATGAC 59.508 33.333 0.00 0.00 0.00 3.06
4442 4683 7.555087 ACAATGACTTCTTCCAAAAACAATGA 58.445 30.769 0.00 0.00 0.00 2.57
4443 4684 7.775397 ACAATGACTTCTTCCAAAAACAATG 57.225 32.000 0.00 0.00 0.00 2.82
4445 4686 9.883142 AATAACAATGACTTCTTCCAAAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
4446 4687 9.883142 AAATAACAATGACTTCTTCCAAAAACA 57.117 25.926 0.00 0.00 0.00 2.83
4555 4796 7.957929 ATAATAAAATGGTACCCCCTCTGTA 57.042 36.000 10.07 0.00 0.00 2.74
4659 4904 9.638300 GAGAAAATATGCATGACTTTAAGTACG 57.362 33.333 10.16 0.00 0.00 3.67
4733 4980 0.767375 ACTCCTGCCTTGTCATGTGT 59.233 50.000 0.00 0.00 0.00 3.72
4799 5046 4.018870 TGATTTGCTAACCATGTACCTGGA 60.019 41.667 22.41 1.61 39.73 3.86
4800 5047 4.269183 TGATTTGCTAACCATGTACCTGG 58.731 43.478 14.97 14.97 42.35 4.45
4801 5048 5.895636 TTGATTTGCTAACCATGTACCTG 57.104 39.130 0.00 0.00 0.00 4.00
4810 5060 8.650714 GTTGATTTGAAGATTGATTTGCTAACC 58.349 33.333 0.00 0.00 0.00 2.85
4842 5092 9.566530 GCACATACACACATCAAATAACATTAA 57.433 29.630 0.00 0.00 0.00 1.40
4931 5181 1.066908 CGCAACCAAGAAAAGGAAGCA 59.933 47.619 0.00 0.00 32.53 3.91
4933 5183 2.731217 CACGCAACCAAGAAAAGGAAG 58.269 47.619 0.00 0.00 0.00 3.46
5068 5318 1.227674 CCCTATCCTCGCTTGCCAC 60.228 63.158 0.00 0.00 0.00 5.01
5141 5391 5.808540 ACATATTCAGTGCAATTGATTGTGC 59.191 36.000 10.34 0.00 39.88 4.57
5153 5403 8.122952 GTGTAACCAGATTAACATATTCAGTGC 58.877 37.037 0.00 0.00 0.00 4.40
5163 5644 7.367285 GCAATTTCAGTGTAACCAGATTAACA 58.633 34.615 0.00 0.00 37.80 2.41
5167 5648 4.832266 TGGCAATTTCAGTGTAACCAGATT 59.168 37.500 0.00 0.00 37.80 2.40
5168 5649 4.218417 GTGGCAATTTCAGTGTAACCAGAT 59.782 41.667 0.00 0.00 37.80 2.90
5169 5650 3.568007 GTGGCAATTTCAGTGTAACCAGA 59.432 43.478 0.00 0.00 37.80 3.86
5170 5651 3.305335 GGTGGCAATTTCAGTGTAACCAG 60.305 47.826 0.00 0.00 37.80 4.00
5187 5668 2.170607 TGCCTCTGATAGTTAAGGTGGC 59.829 50.000 0.00 0.00 35.48 5.01
5206 5687 2.030457 ACAAACGCATACGCTCTAATGC 59.970 45.455 0.00 0.00 45.53 3.56
5250 5731 4.776349 TGTCAGCATAAAATGTATCCGGT 58.224 39.130 0.00 0.00 0.00 5.28
5283 5963 6.595772 AGAGATTAGTTCGCAATGAATGAC 57.404 37.500 0.00 0.00 39.21 3.06
5286 5966 7.254455 CCGTAAAGAGATTAGTTCGCAATGAAT 60.254 37.037 0.00 0.00 39.21 2.57
5288 5968 5.518847 CCGTAAAGAGATTAGTTCGCAATGA 59.481 40.000 0.00 0.00 0.00 2.57
5301 5981 4.205587 ACGAGTACCATCCGTAAAGAGAT 58.794 43.478 0.00 0.00 34.52 2.75
5307 5993 4.724074 AATCAACGAGTACCATCCGTAA 57.276 40.909 0.00 0.00 35.28 3.18
5329 6168 5.395990 GCTGGACATGGATTTGAATTTGGAT 60.396 40.000 0.00 0.00 0.00 3.41
5349 6188 2.740055 GGCTCACACGTCAGCTGG 60.740 66.667 15.13 0.36 35.82 4.85
5365 6204 1.319614 CGTATGGGTTGGCCTTTGGG 61.320 60.000 3.32 0.00 34.45 4.12
5368 6207 1.064979 CCTACGTATGGGTTGGCCTTT 60.065 52.381 3.32 0.00 34.45 3.11
5384 6223 3.624861 CACTCCATTTCTCACATGCCTAC 59.375 47.826 0.00 0.00 0.00 3.18
5386 6225 2.306805 TCACTCCATTTCTCACATGCCT 59.693 45.455 0.00 0.00 0.00 4.75
5387 6226 2.421424 GTCACTCCATTTCTCACATGCC 59.579 50.000 0.00 0.00 0.00 4.40
5388 6227 3.076621 TGTCACTCCATTTCTCACATGC 58.923 45.455 0.00 0.00 0.00 4.06
5393 6232 3.138304 CGGTTTGTCACTCCATTTCTCA 58.862 45.455 0.00 0.00 0.00 3.27
5662 6530 3.601443 AGGTGTGACAAGCTAGCTTAG 57.399 47.619 28.87 23.13 34.50 2.18
5979 6847 1.153842 CATGTCGTAGCCGCTCACA 60.154 57.895 0.00 0.00 0.00 3.58
6255 7123 1.950098 GCTGCGAGAAGAAGTCGTGC 61.950 60.000 0.00 0.00 39.69 5.34
6735 7603 4.202599 ACCTTAATGGCCATCTCATGCATA 60.203 41.667 21.08 1.52 40.22 3.14
6876 7748 8.602472 ACTTAACCCCAAAATGATAATAGCAA 57.398 30.769 0.00 0.00 0.00 3.91
6877 7749 8.602472 AACTTAACCCCAAAATGATAATAGCA 57.398 30.769 0.00 0.00 0.00 3.49
6881 7753 8.893563 TCTGAACTTAACCCCAAAATGATAAT 57.106 30.769 0.00 0.00 0.00 1.28
6918 7790 1.607225 ATTCCCTAGTCAATGCCCCA 58.393 50.000 0.00 0.00 0.00 4.96
7022 7897 6.393720 AAAATAACTCATTTGCGCATTGAC 57.606 33.333 12.75 0.00 36.93 3.18
7091 7967 1.269448 ACACACGGGCATTTTTGCTAG 59.731 47.619 0.00 0.00 34.73 3.42
7092 7968 1.323412 ACACACGGGCATTTTTGCTA 58.677 45.000 0.00 0.00 34.73 3.49
7093 7969 0.463620 AACACACGGGCATTTTTGCT 59.536 45.000 0.00 0.00 34.73 3.91
7094 7970 1.790043 GTAACACACGGGCATTTTTGC 59.210 47.619 0.00 0.00 0.00 3.68
7095 7971 3.085443 TGTAACACACGGGCATTTTTG 57.915 42.857 0.00 0.00 0.00 2.44
7096 7972 3.449632 GTTGTAACACACGGGCATTTTT 58.550 40.909 0.00 0.00 0.00 1.94
7097 7973 2.541999 CGTTGTAACACACGGGCATTTT 60.542 45.455 0.00 0.00 0.00 1.82
7098 7974 1.002251 CGTTGTAACACACGGGCATTT 60.002 47.619 0.00 0.00 0.00 2.32
7099 7975 0.589223 CGTTGTAACACACGGGCATT 59.411 50.000 0.00 0.00 0.00 3.56
7100 7976 1.231958 CCGTTGTAACACACGGGCAT 61.232 55.000 14.99 0.00 38.33 4.40
7101 7977 1.888172 CCGTTGTAACACACGGGCA 60.888 57.895 14.99 0.00 38.33 5.36
7102 7978 2.940561 CCGTTGTAACACACGGGC 59.059 61.111 14.99 0.00 38.33 6.13
7104 7980 0.033228 TACCCCGTTGTAACACACGG 59.967 55.000 15.50 15.50 40.17 4.94
7105 7981 1.863267 TTACCCCGTTGTAACACACG 58.137 50.000 0.00 0.00 0.00 4.49
7106 7982 7.608308 TTATTATTACCCCGTTGTAACACAC 57.392 36.000 0.00 0.00 33.78 3.82
7107 7983 9.896645 TTATTATTATTACCCCGTTGTAACACA 57.103 29.630 0.00 0.00 33.78 3.72
7144 8020 1.051812 AACAGTGTGACAGAGGAGGG 58.948 55.000 0.00 0.00 0.00 4.30
7177 8053 3.420482 GATGGGGGTGTCAGGGGG 61.420 72.222 0.00 0.00 0.00 5.40
7182 8058 1.212375 CCACTATGATGGGGGTGTCA 58.788 55.000 0.00 0.00 35.95 3.58
7216 8092 0.323360 ACCAACGTCATTGATGGGGG 60.323 55.000 17.83 15.73 41.23 5.40
7238 8115 6.600822 ACATTTAGACTTGTTGATGAGATGGG 59.399 38.462 0.00 0.00 0.00 4.00
7239 8116 7.414873 CCACATTTAGACTTGTTGATGAGATGG 60.415 40.741 0.00 0.00 0.00 3.51
7253 8130 6.428159 GTGTTGAGATTGACCACATTTAGACT 59.572 38.462 0.00 0.00 0.00 3.24
7279 8156 4.698651 CAACGCGCGGGCATTTGT 62.699 61.111 35.22 11.03 39.92 2.83
7370 8248 0.613260 ATAGAAGAAGTGGCGCACCA 59.387 50.000 10.83 0.00 46.51 4.17
7410 8288 8.578151 ACGTTCCCTTCTTCTATCTATATTCAC 58.422 37.037 0.00 0.00 0.00 3.18
7544 8628 2.437651 TGAAACTCTGGTGGACATGACA 59.562 45.455 0.00 0.00 0.00 3.58
7592 8676 8.359642 CCACAAGTTTTTCTTTCCATCATTCTA 58.640 33.333 0.00 0.00 33.63 2.10
7600 8684 5.478679 TGAGTTCCACAAGTTTTTCTTTCCA 59.521 36.000 0.00 0.00 33.63 3.53
7602 8686 6.871044 GTGAGTTCCACAAGTTTTTCTTTC 57.129 37.500 0.00 0.00 45.03 2.62


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

AutoCloner maintained by Alex Coulton.