Multiple sequence alignment - TraesCS4D01G179700

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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 TraesCS4D01G179700 chr4D 100.000 5627 0 0 1 5627 312791041 312796667 0.000000e+00 10392.0
1 TraesCS4D01G179700 chr4A 93.041 3492 158 37 1529 4974 163828924 163825472 0.000000e+00 5024.0
2 TraesCS4D01G179700 chr4A 88.793 928 46 22 7 895 163830343 163829435 0.000000e+00 1085.0
3 TraesCS4D01G179700 chr4A 92.873 449 27 3 894 1341 163829397 163828953 0.000000e+00 647.0
4 TraesCS4D01G179700 chr4A 82.466 519 45 25 5113 5611 163825341 163824849 4.060000e-111 412.0
5 TraesCS4D01G179700 chr4A 93.407 91 2 2 4982 5068 163825426 163825336 1.270000e-26 132.0
6 TraesCS4D01G179700 chr4B 92.981 2365 116 22 1529 3856 389464429 389466780 0.000000e+00 3402.0
7 TraesCS4D01G179700 chr4B 94.444 1134 40 12 3855 4978 389466942 389468062 0.000000e+00 1724.0
8 TraesCS4D01G179700 chr4B 86.588 932 45 37 7 895 389462964 389463858 0.000000e+00 955.0
9 TraesCS4D01G179700 chr4B 92.494 453 26 3 895 1347 389463896 389464340 4.750000e-180 641.0
10 TraesCS4D01G179700 chr4B 90.541 148 11 2 5113 5257 389468183 389468330 5.750000e-45 193.0
11 TraesCS4D01G179700 chr4B 95.402 87 4 0 4982 5068 389468102 389468188 7.600000e-29 139.0
12 TraesCS4D01G179700 chr7A 100.000 35 0 0 5079 5113 110116156 110116190 1.310000e-06 65.8
13 TraesCS4D01G179700 chr5B 100.000 33 0 0 5079 5111 377342297 377342265 1.690000e-05 62.1
14 TraesCS4D01G179700 chr5B 94.872 39 1 1 5075 5113 106354530 106354493 6.090000e-05 60.2
15 TraesCS4D01G179700 chr2B 100.000 33 0 0 5079 5111 494277021 494277053 1.690000e-05 62.1
16 TraesCS4D01G179700 chr7D 100.000 32 0 0 5079 5110 533955330 533955299 6.090000e-05 60.2
17 TraesCS4D01G179700 chr7B 97.222 36 0 1 5075 5110 585987183 585987149 6.090000e-05 60.2
18 TraesCS4D01G179700 chr1B 94.872 39 0 2 5079 5115 445192492 445192530 6.090000e-05 60.2
19 TraesCS4D01G179700 chr5D 97.059 34 1 0 5079 5112 268927857 268927890 2.190000e-04 58.4
20 TraesCS4D01G179700 chrUn 97.059 34 0 1 5075 5108 87231355 87231387 7.880000e-04 56.5


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 TraesCS4D01G179700 chr4D 312791041 312796667 5626 False 10392.000000 10392 100.000 1 5627 1 chr4D.!!$F1 5626
1 TraesCS4D01G179700 chr4A 163824849 163830343 5494 True 1460.000000 5024 90.116 7 5611 5 chr4A.!!$R1 5604
2 TraesCS4D01G179700 chr4B 389462964 389468330 5366 False 1175.666667 3402 92.075 7 5257 6 chr4B.!!$F1 5250

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
897 972 1.216064 AGGCTGCCTCATGATACCAA 58.784 50.000 17.22 0.0 0.00 3.67 F
1395 1510 0.319728 CCGGCCTCTACATCCTCATG 59.680 60.000 0.00 0.0 35.92 3.07 F
1407 1522 0.393402 TCCTCATGATGCACACAGCC 60.393 55.000 0.00 0.0 44.83 4.85 F
2513 2654 0.447801 CCGTTGACTATTGCCACAGC 59.552 55.000 0.00 0.0 40.48 4.40 F
2852 3008 2.256158 CTGCACACAACATGCGGG 59.744 61.111 0.00 0.0 46.49 6.13 F
2886 3042 4.469657 TGTTGCTCCTGAGGTAATTTTGT 58.530 39.130 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 2633 0.250510 TGTGGCAATAGTCAACGGCA 60.251 50.000 0.00 0.00 0.00 5.69 R
2946 3104 1.829849 TCCTCAATCACCTGCAGAGAG 59.170 52.381 17.39 11.47 0.00 3.20 R
2950 3108 3.244146 CCTCTATCCTCAATCACCTGCAG 60.244 52.174 6.78 6.78 0.00 4.41 R
4202 4527 0.181350 GGGTTCTCCATCCGCATCTT 59.819 55.000 0.00 0.00 35.00 2.40 R
4557 4885 1.079750 GTCCTTGAGCTGGGTCGAC 60.080 63.158 7.13 7.13 0.00 4.20 R
4710 5041 3.264104 ACAAACCAACGAAAGAACTCGA 58.736 40.909 0.00 0.00 41.44 4.04 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
32 33 2.426183 GCGAGCACGTACGTGTCAG 61.426 63.158 39.56 31.10 46.90 3.51
136 150 1.668101 CTCAGACCCACCCTCGCTAC 61.668 65.000 0.00 0.00 0.00 3.58
169 183 2.587473 GCTGCTAAGCTCCGCCTC 60.587 66.667 4.92 0.00 46.60 4.70
170 184 2.107953 CTGCTAAGCTCCGCCTCC 59.892 66.667 4.92 0.00 0.00 4.30
171 185 2.683572 TGCTAAGCTCCGCCTCCA 60.684 61.111 4.92 0.00 0.00 3.86
172 186 2.202946 GCTAAGCTCCGCCTCCAC 60.203 66.667 0.00 0.00 0.00 4.02
364 401 2.307496 TGGTTTCATGCCCTGTGAAT 57.693 45.000 0.00 0.00 35.68 2.57
373 435 4.096231 TCATGCCCTGTGAATGATTTTACG 59.904 41.667 0.00 0.00 0.00 3.18
416 478 6.591834 GCTCTGTTCATTTGAGTAGTACACAT 59.408 38.462 2.52 0.00 0.00 3.21
420 482 9.424319 CTGTTCATTTGAGTAGTACACATACTT 57.576 33.333 2.52 0.00 41.99 2.24
421 483 9.419297 TGTTCATTTGAGTAGTACACATACTTC 57.581 33.333 2.52 0.00 41.99 3.01
438 505 6.703607 ACATACTTCTTTGAGCGAGGATTATG 59.296 38.462 0.00 0.00 0.00 1.90
450 517 4.280174 GCGAGGATTATGTACCTTACTCCA 59.720 45.833 10.21 0.00 36.57 3.86
482 549 7.435488 CAGCAGTAACCAGTACATATCTGTAAC 59.565 40.741 0.00 0.00 39.51 2.50
617 685 5.647658 CCTGCCATGTACTACTTTTCATGAA 59.352 40.000 3.38 3.38 39.68 2.57
785 857 8.439971 ACTAGGCTGGTCATTTTATATTGATGA 58.560 33.333 0.00 0.00 0.00 2.92
815 887 3.815401 CAGGTGTTGTTTAGTCTTCCTGG 59.185 47.826 0.00 0.00 37.94 4.45
895 970 2.355010 AAAGGCTGCCTCATGATACC 57.645 50.000 23.61 0.00 30.89 2.73
897 972 1.216064 AGGCTGCCTCATGATACCAA 58.784 50.000 17.22 0.00 0.00 3.67
900 975 2.555757 GGCTGCCTCATGATACCAAATC 59.444 50.000 12.43 0.00 0.00 2.17
914 1028 8.821686 TGATACCAAATCAATACCAAGTTCAT 57.178 30.769 0.00 0.00 0.00 2.57
977 1091 4.214310 TCAGGAGCATTTTGAAGGTTGAA 58.786 39.130 0.00 0.00 0.00 2.69
990 1104 2.983402 GGTTGAAAGTAACCTTCGGC 57.017 50.000 0.00 0.00 45.29 5.54
1221 1335 4.441792 TCACACAATTCCCTCATATGACG 58.558 43.478 0.00 0.00 0.00 4.35
1225 1339 4.635765 CACAATTCCCTCATATGACGTTGT 59.364 41.667 0.00 6.07 0.00 3.32
1227 1341 2.979814 TCCCTCATATGACGTTGTGG 57.020 50.000 0.00 0.21 0.00 4.17
1238 1352 4.395959 TGACGTTGTGGTAGTTTCTTCT 57.604 40.909 0.00 0.00 0.00 2.85
1240 1354 4.569162 TGACGTTGTGGTAGTTTCTTCTTG 59.431 41.667 0.00 0.00 0.00 3.02
1247 1361 6.184789 TGTGGTAGTTTCTTCTTGTTCCTTT 58.815 36.000 0.00 0.00 0.00 3.11
1249 1363 7.830201 TGTGGTAGTTTCTTCTTGTTCCTTTTA 59.170 33.333 0.00 0.00 0.00 1.52
1284 1398 7.819900 ACATATCATGTCACAGATCAGATCATG 59.180 37.037 13.14 10.22 39.92 3.07
1331 1446 5.443283 AGTTCAGTCAACCATGCATATCAT 58.557 37.500 0.00 0.00 35.28 2.45
1336 1451 6.604396 TCAGTCAACCATGCATATCATCTTTT 59.396 34.615 0.00 0.00 31.79 2.27
1385 1500 2.042230 GGAAGACCCCGGCCTCTA 60.042 66.667 0.00 0.00 0.00 2.43
1386 1501 2.433146 GGAAGACCCCGGCCTCTAC 61.433 68.421 0.00 0.00 0.00 2.59
1387 1502 1.684734 GAAGACCCCGGCCTCTACA 60.685 63.158 0.00 0.00 0.00 2.74
1388 1503 1.003051 AAGACCCCGGCCTCTACAT 59.997 57.895 0.00 0.00 0.00 2.29
1389 1504 1.049289 AAGACCCCGGCCTCTACATC 61.049 60.000 0.00 0.00 0.00 3.06
1390 1505 2.446036 ACCCCGGCCTCTACATCC 60.446 66.667 0.00 0.00 0.00 3.51
1391 1506 2.122813 CCCCGGCCTCTACATCCT 60.123 66.667 0.00 0.00 0.00 3.24
1392 1507 2.210711 CCCCGGCCTCTACATCCTC 61.211 68.421 0.00 0.00 0.00 3.71
1393 1508 1.457643 CCCGGCCTCTACATCCTCA 60.458 63.158 0.00 0.00 0.00 3.86
1394 1509 0.833834 CCCGGCCTCTACATCCTCAT 60.834 60.000 0.00 0.00 0.00 2.90
1395 1510 0.319728 CCGGCCTCTACATCCTCATG 59.680 60.000 0.00 0.00 35.92 3.07
1396 1511 1.332195 CGGCCTCTACATCCTCATGA 58.668 55.000 0.00 0.00 33.72 3.07
1397 1512 1.898472 CGGCCTCTACATCCTCATGAT 59.102 52.381 0.00 0.00 33.72 2.45
1406 1521 1.333931 CATCCTCATGATGCACACAGC 59.666 52.381 0.00 0.00 44.16 4.40
1407 1522 0.393402 TCCTCATGATGCACACAGCC 60.393 55.000 0.00 0.00 44.83 4.85
1408 1523 0.678684 CCTCATGATGCACACAGCCA 60.679 55.000 0.00 0.00 44.83 4.75
1409 1524 1.389555 CTCATGATGCACACAGCCAT 58.610 50.000 0.00 0.00 44.83 4.40
1410 1525 1.749063 CTCATGATGCACACAGCCATT 59.251 47.619 0.00 0.00 44.83 3.16
1411 1526 2.165641 CTCATGATGCACACAGCCATTT 59.834 45.455 0.00 0.00 44.83 2.32
1412 1527 2.563620 TCATGATGCACACAGCCATTTT 59.436 40.909 0.00 0.00 44.83 1.82
1413 1528 2.728690 TGATGCACACAGCCATTTTC 57.271 45.000 0.00 0.00 44.83 2.29
1414 1529 1.962100 TGATGCACACAGCCATTTTCA 59.038 42.857 0.00 0.00 44.83 2.69
1415 1530 2.563620 TGATGCACACAGCCATTTTCAT 59.436 40.909 0.00 0.00 44.83 2.57
1416 1531 2.442212 TGCACACAGCCATTTTCATG 57.558 45.000 0.00 0.00 44.83 3.07
1417 1532 1.962100 TGCACACAGCCATTTTCATGA 59.038 42.857 0.00 0.00 44.83 3.07
1418 1533 2.364647 TGCACACAGCCATTTTCATGAA 59.635 40.909 3.38 3.38 44.83 2.57
1419 1534 3.007074 TGCACACAGCCATTTTCATGAAT 59.993 39.130 9.40 0.00 44.83 2.57
1420 1535 3.369756 GCACACAGCCATTTTCATGAATG 59.630 43.478 9.40 5.51 37.23 2.67
1421 1536 4.562082 CACACAGCCATTTTCATGAATGT 58.438 39.130 9.40 6.63 35.68 2.71
1422 1537 4.992319 CACACAGCCATTTTCATGAATGTT 59.008 37.500 9.40 0.00 35.68 2.71
1423 1538 6.157904 CACACAGCCATTTTCATGAATGTTA 58.842 36.000 9.40 0.00 35.68 2.41
1424 1539 6.309494 CACACAGCCATTTTCATGAATGTTAG 59.691 38.462 9.40 1.79 35.68 2.34
1425 1540 6.015180 ACACAGCCATTTTCATGAATGTTAGT 60.015 34.615 9.40 2.38 35.68 2.24
1426 1541 7.176515 ACACAGCCATTTTCATGAATGTTAGTA 59.823 33.333 9.40 0.00 35.68 1.82
1427 1542 8.028354 CACAGCCATTTTCATGAATGTTAGTAA 58.972 33.333 9.40 0.00 35.68 2.24
1428 1543 8.028938 ACAGCCATTTTCATGAATGTTAGTAAC 58.971 33.333 9.40 6.06 35.68 2.50
1429 1544 7.489113 CAGCCATTTTCATGAATGTTAGTAACC 59.511 37.037 9.40 0.00 35.68 2.85
1430 1545 7.178274 AGCCATTTTCATGAATGTTAGTAACCA 59.822 33.333 9.40 2.08 35.68 3.67
1431 1546 7.816995 GCCATTTTCATGAATGTTAGTAACCAA 59.183 33.333 9.40 0.00 35.68 3.67
1450 1565 3.328505 CAATAACCAAGCCAGCAAAAGG 58.671 45.455 0.00 0.00 0.00 3.11
1459 1574 5.240121 CAAGCCAGCAAAAGGATTATGTTT 58.760 37.500 0.00 0.00 32.02 2.83
1642 1760 1.228675 GCATGGGGGCATAGGAAGG 60.229 63.158 0.00 0.00 0.00 3.46
1694 1812 9.088512 GTATCTACATACTTGCATTACATAGCC 57.911 37.037 0.00 0.00 33.22 3.93
1695 1813 6.464222 TCTACATACTTGCATTACATAGCCC 58.536 40.000 0.00 0.00 0.00 5.19
1696 1814 4.398319 ACATACTTGCATTACATAGCCCC 58.602 43.478 0.00 0.00 0.00 5.80
1697 1815 1.967319 ACTTGCATTACATAGCCCCG 58.033 50.000 0.00 0.00 0.00 5.73
1698 1816 0.593128 CTTGCATTACATAGCCCCGC 59.407 55.000 0.00 0.00 0.00 6.13
1699 1817 1.163420 TTGCATTACATAGCCCCGCG 61.163 55.000 0.00 0.00 0.00 6.46
1700 1818 1.301401 GCATTACATAGCCCCGCGA 60.301 57.895 8.23 0.00 0.00 5.87
1717 1835 2.135933 GCGATCTTACCCACATAGTGC 58.864 52.381 0.00 0.00 31.34 4.40
1722 1840 5.009710 CGATCTTACCCACATAGTGCTCTTA 59.990 44.000 0.00 0.00 31.34 2.10
1736 1854 6.734104 AGTGCTCTTACAATTGAAGTCATC 57.266 37.500 13.59 8.62 0.00 2.92
1748 1866 4.897509 TGAAGTCATCTCACCAACTCAT 57.102 40.909 0.00 0.00 0.00 2.90
1812 1932 5.233225 TGAACTTTGTGCAAATTGAACACA 58.767 33.333 6.24 4.35 35.19 3.72
1846 1976 2.681976 GCACTTCAGCATATGTGTCCCT 60.682 50.000 4.29 0.00 33.44 4.20
1856 1986 2.949177 ATGTGTCCCTTGTTGCACTA 57.051 45.000 0.00 0.00 33.44 2.74
1858 1988 2.778299 TGTGTCCCTTGTTGCACTATC 58.222 47.619 0.00 0.00 33.44 2.08
1872 2002 1.120530 ACTATCGGGTGTCCATGTCC 58.879 55.000 0.00 0.00 0.00 4.02
1876 2006 0.834261 TCGGGTGTCCATGTCCTCAA 60.834 55.000 0.00 0.00 0.00 3.02
1883 2013 5.059833 GGTGTCCATGTCCTCAATTCTATC 58.940 45.833 0.00 0.00 0.00 2.08
1897 2027 7.040823 CCTCAATTCTATCTAATTGCCTTCACC 60.041 40.741 4.77 0.00 43.49 4.02
1898 2028 7.345691 TCAATTCTATCTAATTGCCTTCACCA 58.654 34.615 4.77 0.00 43.49 4.17
1904 2034 8.494433 TCTATCTAATTGCCTTCACCATACTTT 58.506 33.333 0.00 0.00 0.00 2.66
1922 2052 5.053978 ACTTTGGTGATCTTCCAAGTTCT 57.946 39.130 17.51 5.02 44.26 3.01
1931 2061 8.095169 GGTGATCTTCCAAGTTCTAAGTTCTAA 58.905 37.037 0.00 0.00 0.00 2.10
1943 2073 7.674772 AGTTCTAAGTTCTAACCATACAGTCCT 59.325 37.037 0.00 0.00 0.00 3.85
1950 2080 6.428083 TCTAACCATACAGTCCTCAAACAA 57.572 37.500 0.00 0.00 0.00 2.83
1965 2095 4.134563 TCAAACAAGGACTTCTGTTAGCC 58.865 43.478 0.00 0.00 0.00 3.93
1967 2097 3.127425 ACAAGGACTTCTGTTAGCCAC 57.873 47.619 0.00 0.00 0.00 5.01
1985 2124 5.244755 AGCCACAAAAACATTGACAAAACT 58.755 33.333 0.00 0.00 0.00 2.66
2132 2273 1.241165 TCGACTGCACGAGGTAAAGA 58.759 50.000 0.00 0.00 37.37 2.52
2155 2296 4.172505 CCAAAAATCAATCGGCGATTCAA 58.827 39.130 30.51 21.69 31.90 2.69
2159 2300 4.739046 AATCAATCGGCGATTCAAGATC 57.261 40.909 30.51 0.00 28.87 2.75
2173 2314 6.587990 CGATTCAAGATCTATCGCCATACTTT 59.412 38.462 12.17 0.00 35.36 2.66
2175 2316 8.994429 ATTCAAGATCTATCGCCATACTTTAG 57.006 34.615 0.00 0.00 0.00 1.85
2201 2342 2.917701 TGTGTTTATTCATGGCTGCG 57.082 45.000 0.00 0.00 0.00 5.18
2208 2349 1.668419 ATTCATGGCTGCGGTCTTAC 58.332 50.000 0.00 0.00 0.00 2.34
2213 2354 0.613853 TGGCTGCGGTCTTACTACCT 60.614 55.000 0.00 0.00 37.39 3.08
2214 2355 0.535797 GGCTGCGGTCTTACTACCTT 59.464 55.000 0.00 0.00 37.39 3.50
2334 2475 7.510549 ACCATTGTAAGTGCCAATATATCAC 57.489 36.000 0.00 0.00 31.52 3.06
2346 2487 6.444816 TGCCAATATATCACCCATCTATCTGT 59.555 38.462 0.00 0.00 0.00 3.41
2365 2506 9.764363 CTATCTGTAATTGCTGAGGTTGTATTA 57.236 33.333 8.88 0.00 0.00 0.98
2371 2512 4.054780 TGCTGAGGTTGTATTATCGGTC 57.945 45.455 0.00 0.00 0.00 4.79
2390 2531 7.072177 TCGGTCAGATTTTCATTCATGTTAC 57.928 36.000 0.00 0.00 0.00 2.50
2462 2603 4.357918 TGGAAGGTTGAAAGAAGAGGAG 57.642 45.455 0.00 0.00 0.00 3.69
2480 2621 2.159517 GGAGGCACGCAAATACTTTCAG 60.160 50.000 0.00 0.00 0.00 3.02
2483 2624 2.606795 GGCACGCAAATACTTTCAGCAA 60.607 45.455 0.00 0.00 0.00 3.91
2492 2633 7.485913 CGCAAATACTTTCAGCAACTGATAAAT 59.514 33.333 0.00 0.00 40.39 1.40
2513 2654 0.447801 CCGTTGACTATTGCCACAGC 59.552 55.000 0.00 0.00 40.48 4.40
2624 2766 6.275335 ACAGGAAAGTGACAAAATGATGTTG 58.725 36.000 0.00 0.00 32.57 3.33
2628 2770 6.200854 GGAAAGTGACAAAATGATGTTGAACC 59.799 38.462 1.66 0.00 32.57 3.62
2726 2868 7.522236 GCTTTAACTGAGCAAGTGAAGGTATTT 60.522 37.037 13.25 0.00 39.81 1.40
2730 2872 7.817418 ACTGAGCAAGTGAAGGTATTTTTAA 57.183 32.000 0.00 0.00 37.88 1.52
2731 2873 7.875971 ACTGAGCAAGTGAAGGTATTTTTAAG 58.124 34.615 0.00 0.00 37.88 1.85
2733 2875 8.635765 TGAGCAAGTGAAGGTATTTTTAAGAT 57.364 30.769 0.00 0.00 0.00 2.40
2767 2923 8.313944 ACTTTGGGTAAAAATTTCTAACTGGT 57.686 30.769 0.00 0.00 0.00 4.00
2782 2938 6.166279 TCTAACTGGTCACATCATTGTCTTC 58.834 40.000 0.00 0.00 32.34 2.87
2852 3008 2.256158 CTGCACACAACATGCGGG 59.744 61.111 0.00 0.00 46.49 6.13
2881 3037 5.675538 GAACTATGTTGCTCCTGAGGTAAT 58.324 41.667 0.00 0.00 0.00 1.89
2882 3038 5.700402 ACTATGTTGCTCCTGAGGTAATT 57.300 39.130 0.00 0.00 0.00 1.40
2883 3039 6.067217 ACTATGTTGCTCCTGAGGTAATTT 57.933 37.500 0.00 0.00 0.00 1.82
2884 3040 6.485171 ACTATGTTGCTCCTGAGGTAATTTT 58.515 36.000 0.00 0.00 0.00 1.82
2885 3041 5.649782 ATGTTGCTCCTGAGGTAATTTTG 57.350 39.130 0.00 0.00 0.00 2.44
2886 3042 4.469657 TGTTGCTCCTGAGGTAATTTTGT 58.530 39.130 0.00 0.00 0.00 2.83
2953 3111 8.846211 ACTATTGTCTAACTTAGATCTCTCTGC 58.154 37.037 0.00 0.00 37.13 4.26
3422 3581 9.092876 CAGTAGTCCTTAATTTCATTCTCAGTC 57.907 37.037 0.00 0.00 0.00 3.51
3574 3733 8.997621 TTGACGATAAGTATGAAACTAGCTTT 57.002 30.769 0.00 0.00 37.50 3.51
3849 4008 4.808077 AATATTTCTGCTGCAGACATCG 57.192 40.909 30.47 4.84 40.46 3.84
3923 4245 9.346725 GTTGCCTATGATTTTCTTTAGAAACTG 57.653 33.333 4.48 0.00 43.01 3.16
4327 4652 7.557719 ACACTAAAGAAGGATTACCCATTCATG 59.442 37.037 0.00 0.00 37.41 3.07
4503 4831 8.627487 TTAACTACTGTCAAAGCATTGTTTTG 57.373 30.769 17.03 17.03 37.79 2.44
4557 4885 7.116090 CTGTGAAAACAGTTCTACAGATCTCTG 59.884 40.741 14.74 5.66 39.93 3.35
4612 4940 1.925068 GCGGCGAGGTAGAAGATAACG 60.925 57.143 12.98 0.00 0.00 3.18
4655 4984 5.751990 CGTTTTCCATGTACATAGTCCCTAC 59.248 44.000 8.32 1.06 0.00 3.18
4656 4985 6.406624 CGTTTTCCATGTACATAGTCCCTACT 60.407 42.308 8.32 0.00 39.91 2.57
4657 4986 6.479972 TTTCCATGTACATAGTCCCTACTG 57.520 41.667 8.32 0.00 36.36 2.74
4658 4987 5.138758 TCCATGTACATAGTCCCTACTGT 57.861 43.478 8.32 0.00 36.36 3.55
4659 4988 6.270219 TCCATGTACATAGTCCCTACTGTA 57.730 41.667 8.32 0.00 36.36 2.74
4710 5041 1.315257 GCGGAATGGGTTGTGCAGAT 61.315 55.000 0.00 0.00 0.00 2.90
4732 5063 3.685756 TCGAGTTCTTTCGTTGGTTTGTT 59.314 39.130 0.00 0.00 41.22 2.83
4733 5064 4.869297 TCGAGTTCTTTCGTTGGTTTGTTA 59.131 37.500 0.00 0.00 41.22 2.41
4734 5065 5.350914 TCGAGTTCTTTCGTTGGTTTGTTAA 59.649 36.000 0.00 0.00 41.22 2.01
4735 5066 6.037391 TCGAGTTCTTTCGTTGGTTTGTTAAT 59.963 34.615 0.00 0.00 41.22 1.40
4736 5067 6.140108 CGAGTTCTTTCGTTGGTTTGTTAATG 59.860 38.462 0.00 0.00 35.91 1.90
4737 5068 7.090953 AGTTCTTTCGTTGGTTTGTTAATGA 57.909 32.000 0.00 0.00 0.00 2.57
4828 5162 6.995511 ATGGCTTCGTTAGTTTGCTTATTA 57.004 33.333 0.00 0.00 0.00 0.98
4829 5163 6.995511 TGGCTTCGTTAGTTTGCTTATTAT 57.004 33.333 0.00 0.00 0.00 1.28
4862 5196 2.774809 GGTCCAGAGGGAGATTAAAGCT 59.225 50.000 0.00 0.00 46.12 3.74
4978 5322 3.497103 TGTACTGTAGCTATAGCCGGA 57.503 47.619 21.17 4.30 43.38 5.14
4979 5323 3.824133 TGTACTGTAGCTATAGCCGGAA 58.176 45.455 21.17 4.14 43.38 4.30
4980 5324 4.404640 TGTACTGTAGCTATAGCCGGAAT 58.595 43.478 21.17 4.88 43.38 3.01
5027 5407 4.152625 GGCGATGCTGCGTGTGTC 62.153 66.667 0.00 0.00 35.06 3.67
5028 5408 4.489795 GCGATGCTGCGTGTGTCG 62.490 66.667 0.00 3.10 43.12 4.35
5066 5450 4.202274 TGGAATCGTAACTGACCAGTGAAA 60.202 41.667 3.13 0.00 41.58 2.69
5067 5451 4.753107 GGAATCGTAACTGACCAGTGAAAA 59.247 41.667 3.13 0.00 41.58 2.29
5068 5452 5.237779 GGAATCGTAACTGACCAGTGAAAAA 59.762 40.000 3.13 0.00 41.58 1.94
5069 5453 5.668558 ATCGTAACTGACCAGTGAAAAAC 57.331 39.130 3.13 0.00 41.58 2.43
5070 5454 4.761975 TCGTAACTGACCAGTGAAAAACT 58.238 39.130 3.13 0.00 41.58 2.66
5085 5469 7.301054 AGTGAAAAACTGAGAATGATAAAGCG 58.699 34.615 0.00 0.00 37.88 4.68
5086 5470 6.524586 GTGAAAAACTGAGAATGATAAAGCGG 59.475 38.462 0.00 0.00 0.00 5.52
5087 5471 5.567138 AAAACTGAGAATGATAAAGCGGG 57.433 39.130 0.00 0.00 0.00 6.13
5088 5472 3.199880 ACTGAGAATGATAAAGCGGGG 57.800 47.619 0.00 0.00 0.00 5.73
5089 5473 1.876156 CTGAGAATGATAAAGCGGGGC 59.124 52.381 0.00 0.00 0.00 5.80
5090 5474 0.868406 GAGAATGATAAAGCGGGGCG 59.132 55.000 0.00 0.00 0.00 6.13
5091 5475 0.468226 AGAATGATAAAGCGGGGCGA 59.532 50.000 0.00 0.00 0.00 5.54
5092 5476 1.134220 AGAATGATAAAGCGGGGCGAA 60.134 47.619 0.00 0.00 0.00 4.70
5093 5477 1.673920 GAATGATAAAGCGGGGCGAAA 59.326 47.619 0.00 0.00 0.00 3.46
5094 5478 1.308998 ATGATAAAGCGGGGCGAAAG 58.691 50.000 0.00 0.00 0.00 2.62
5095 5479 0.035820 TGATAAAGCGGGGCGAAAGT 60.036 50.000 0.00 0.00 0.00 2.66
5096 5480 0.656259 GATAAAGCGGGGCGAAAGTC 59.344 55.000 0.00 0.00 0.00 3.01
5097 5481 0.252197 ATAAAGCGGGGCGAAAGTCT 59.748 50.000 0.00 0.00 34.89 3.24
5098 5482 0.035739 TAAAGCGGGGCGAAAGTCTT 59.964 50.000 0.00 0.00 34.89 3.01
5099 5483 0.822121 AAAGCGGGGCGAAAGTCTTT 60.822 50.000 0.00 0.00 34.89 2.52
5100 5484 0.822121 AAGCGGGGCGAAAGTCTTTT 60.822 50.000 0.00 0.00 34.89 2.27
5101 5485 0.822121 AGCGGGGCGAAAGTCTTTTT 60.822 50.000 0.00 0.00 34.89 1.94
5102 5486 0.386858 GCGGGGCGAAAGTCTTTTTC 60.387 55.000 0.00 0.00 34.89 2.29
5113 5497 7.133443 CGAAAGTCTTTTTCGGTAAAAACTG 57.867 36.000 12.72 0.00 45.17 3.16
5114 5498 6.962678 CGAAAGTCTTTTTCGGTAAAAACTGA 59.037 34.615 12.72 0.00 45.17 3.41
5130 5514 7.504924 AAAAACTGAGAATGAAACCGATGTA 57.495 32.000 0.00 0.00 0.00 2.29
5137 5521 5.547465 AGAATGAAACCGATGTAAGTGTGA 58.453 37.500 0.00 0.00 0.00 3.58
5155 5542 3.820467 TGTGAATCTCCAAATTGCGAACT 59.180 39.130 0.00 0.00 0.00 3.01
5180 5567 1.318158 ATGTAGTCGGACCACGGACC 61.318 60.000 4.14 0.00 44.01 4.46
5214 5601 1.750193 CCGGCAAAGATGAAAGCCTA 58.250 50.000 0.00 0.00 44.85 3.93
5230 5617 1.021390 CCTAGCAAGTTGTGAGCCGG 61.021 60.000 4.48 0.00 0.00 6.13
5351 5738 2.586357 GTGGCGCCGATCTTCTCC 60.586 66.667 23.90 0.00 0.00 3.71
5374 5761 2.867472 CGGTTAGTGCCGCTTTGG 59.133 61.111 0.00 0.00 45.47 3.28
5418 5806 1.552719 GGAGGGGATTCTATAGGGCGT 60.553 57.143 0.00 0.00 0.00 5.68
5423 5811 1.618837 GGATTCTATAGGGCGTGCAGA 59.381 52.381 0.00 0.00 0.00 4.26
5471 5859 2.511373 CTCACGCGCTGGGCATTA 60.511 61.111 17.13 0.00 43.84 1.90
5472 5860 2.813179 CTCACGCGCTGGGCATTAC 61.813 63.158 17.13 0.00 43.84 1.89
5477 5865 0.599991 CGCGCTGGGCATTACTATGA 60.600 55.000 17.13 0.00 43.84 2.15
5484 5872 0.955919 GGCATTACTATGAGCCGGCC 60.956 60.000 26.15 15.80 37.41 6.13
5485 5873 0.955919 GCATTACTATGAGCCGGCCC 60.956 60.000 26.15 13.59 33.37 5.80
5486 5874 0.670546 CATTACTATGAGCCGGCCCG 60.671 60.000 26.15 9.73 33.37 6.13
5487 5875 1.119574 ATTACTATGAGCCGGCCCGT 61.120 55.000 26.15 16.98 0.00 5.28
5488 5876 1.332144 TTACTATGAGCCGGCCCGTT 61.332 55.000 26.15 3.43 0.00 4.44
5489 5877 1.332144 TACTATGAGCCGGCCCGTTT 61.332 55.000 26.15 2.91 0.00 3.60
5490 5878 1.887707 CTATGAGCCGGCCCGTTTC 60.888 63.158 26.15 14.83 0.00 2.78
5498 5886 2.204461 CGGCCCGTTTCCCCTTTTT 61.204 57.895 0.00 0.00 0.00 1.94
5500 5888 1.669440 GCCCGTTTCCCCTTTTTCC 59.331 57.895 0.00 0.00 0.00 3.13
5501 5889 1.116536 GCCCGTTTCCCCTTTTTCCA 61.117 55.000 0.00 0.00 0.00 3.53
5503 5891 1.974957 CCCGTTTCCCCTTTTTCCATT 59.025 47.619 0.00 0.00 0.00 3.16
5504 5892 2.028476 CCCGTTTCCCCTTTTTCCATTC 60.028 50.000 0.00 0.00 0.00 2.67
5580 5987 9.489393 CTTCTTTAATTTTCCACTTTTGTTTGC 57.511 29.630 0.00 0.00 0.00 3.68
5581 5988 7.680062 TCTTTAATTTTCCACTTTTGTTTGCG 58.320 30.769 0.00 0.00 0.00 4.85
5602 6009 7.993821 TGCGAATTTTCTTTTTAATGTCACA 57.006 28.000 0.00 0.00 0.00 3.58
5604 6011 9.039870 TGCGAATTTTCTTTTTAATGTCACAAT 57.960 25.926 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.542825 GCTCGCACAGCTAGAGTAG 57.457 57.895 0.00 0.00 45.83 2.57
136 150 0.249953 CAGCAGATGCAGCTAGGAGG 60.250 60.000 3.06 0.00 45.16 4.30
319 356 4.489249 GCAAATGCGCATGAAGCT 57.511 50.000 26.09 4.31 42.61 3.74
364 401 6.387465 AGAGAAATGAGTCGTCGTAAAATCA 58.613 36.000 0.00 0.00 0.00 2.57
373 435 4.091220 CAGAGCAAAGAGAAATGAGTCGTC 59.909 45.833 0.00 0.00 0.00 4.20
416 478 6.222038 ACATAATCCTCGCTCAAAGAAGTA 57.778 37.500 0.00 0.00 0.00 2.24
420 482 4.649674 AGGTACATAATCCTCGCTCAAAGA 59.350 41.667 0.00 0.00 0.00 2.52
421 483 4.950050 AGGTACATAATCCTCGCTCAAAG 58.050 43.478 0.00 0.00 0.00 2.77
425 487 5.335819 GGAGTAAGGTACATAATCCTCGCTC 60.336 48.000 13.93 0.00 42.51 5.03
438 505 3.818773 TGCTGCTTTTTGGAGTAAGGTAC 59.181 43.478 0.00 0.00 36.43 3.34
450 517 4.204012 TGTACTGGTTACTGCTGCTTTTT 58.796 39.130 0.00 0.00 0.00 1.94
482 549 5.811613 TGACAAAACATTTTCAGAAAGCAGG 59.188 36.000 0.00 0.00 0.00 4.85
640 708 3.823873 TCATCCCAAACTAAACGCATGTT 59.176 39.130 0.00 0.00 40.98 2.71
646 714 4.336433 AGATGCATCATCCCAAACTAAACG 59.664 41.667 27.81 0.00 41.36 3.60
652 720 3.005472 CCATGAGATGCATCATCCCAAAC 59.995 47.826 27.81 9.17 41.36 2.93
695 763 6.525629 AGGTGGCATAGACATATCTACAAAC 58.474 40.000 0.00 0.00 40.32 2.93
785 857 6.715280 AGACTAAACAACACCTGATCATCAT 58.285 36.000 0.00 0.00 0.00 2.45
895 970 8.184192 GGACACTATGAACTTGGTATTGATTTG 58.816 37.037 0.00 0.00 0.00 2.32
897 972 7.402054 TGGACACTATGAACTTGGTATTGATT 58.598 34.615 0.00 0.00 0.00 2.57
900 975 7.447374 TTTGGACACTATGAACTTGGTATTG 57.553 36.000 0.00 0.00 0.00 1.90
914 1028 4.365514 TGAAATCAGGCTTTGGACACTA 57.634 40.909 0.00 0.00 0.00 2.74
955 1069 3.831323 TCAACCTTCAAAATGCTCCTGA 58.169 40.909 0.00 0.00 0.00 3.86
958 1072 4.948847 ACTTTCAACCTTCAAAATGCTCC 58.051 39.130 0.00 0.00 0.00 4.70
990 1104 2.213499 GCCCGATACATCTTCCAACAG 58.787 52.381 0.00 0.00 0.00 3.16
1221 1335 5.589050 AGGAACAAGAAGAAACTACCACAAC 59.411 40.000 0.00 0.00 0.00 3.32
1225 1339 8.990163 ATAAAAGGAACAAGAAGAAACTACCA 57.010 30.769 0.00 0.00 0.00 3.25
1267 1381 7.062022 CGTTCATATCATGATCTGATCTGTGAC 59.938 40.741 20.70 14.59 43.70 3.67
1271 1385 6.310711 CCACGTTCATATCATGATCTGATCTG 59.689 42.308 20.70 17.44 43.70 2.90
1290 1404 9.292846 GACTGAACTTTAAAATTTTACCACGTT 57.707 29.630 10.18 10.42 0.00 3.99
1368 1483 2.042230 TAGAGGCCGGGGTCTTCC 60.042 66.667 2.18 0.00 0.00 3.46
1369 1484 1.049289 ATGTAGAGGCCGGGGTCTTC 61.049 60.000 2.18 0.00 0.00 2.87
1370 1485 1.003051 ATGTAGAGGCCGGGGTCTT 59.997 57.895 2.18 0.00 0.00 3.01
1371 1486 1.457831 GATGTAGAGGCCGGGGTCT 60.458 63.158 2.18 0.00 0.00 3.85
1372 1487 2.508751 GGATGTAGAGGCCGGGGTC 61.509 68.421 2.18 0.00 0.00 4.46
1373 1488 2.446036 GGATGTAGAGGCCGGGGT 60.446 66.667 2.18 0.00 0.00 4.95
1374 1489 2.122813 AGGATGTAGAGGCCGGGG 60.123 66.667 2.18 0.00 0.00 5.73
1375 1490 0.833834 ATGAGGATGTAGAGGCCGGG 60.834 60.000 2.18 0.00 0.00 5.73
1376 1491 0.319728 CATGAGGATGTAGAGGCCGG 59.680 60.000 0.00 0.00 0.00 6.13
1377 1492 1.332195 TCATGAGGATGTAGAGGCCG 58.668 55.000 0.00 0.00 0.00 6.13
1378 1493 3.331478 CATCATGAGGATGTAGAGGCC 57.669 52.381 0.00 0.00 46.81 5.19
1387 1502 1.676746 GCTGTGTGCATCATGAGGAT 58.323 50.000 12.39 0.00 42.31 3.24
1388 1503 0.393402 GGCTGTGTGCATCATGAGGA 60.393 55.000 12.39 0.00 45.15 3.71
1389 1504 0.678684 TGGCTGTGTGCATCATGAGG 60.679 55.000 2.22 2.22 45.15 3.86
1390 1505 1.389555 ATGGCTGTGTGCATCATGAG 58.610 50.000 0.09 0.00 45.15 2.90
1391 1506 1.842052 AATGGCTGTGTGCATCATGA 58.158 45.000 0.00 0.00 45.15 3.07
1392 1507 2.665649 AAATGGCTGTGTGCATCATG 57.334 45.000 0.00 0.00 45.15 3.07
1393 1508 2.563620 TGAAAATGGCTGTGTGCATCAT 59.436 40.909 0.00 0.00 45.15 2.45
1394 1509 1.962100 TGAAAATGGCTGTGTGCATCA 59.038 42.857 0.00 0.00 45.15 3.07
1395 1510 2.728690 TGAAAATGGCTGTGTGCATC 57.271 45.000 0.00 0.00 45.15 3.91
1396 1511 2.563620 TCATGAAAATGGCTGTGTGCAT 59.436 40.909 0.00 0.00 45.15 3.96
1397 1512 1.962100 TCATGAAAATGGCTGTGTGCA 59.038 42.857 0.00 0.00 45.15 4.57
1398 1513 2.728690 TCATGAAAATGGCTGTGTGC 57.271 45.000 0.00 0.00 41.94 4.57
1399 1514 4.562082 ACATTCATGAAAATGGCTGTGTG 58.438 39.130 13.09 4.59 40.28 3.82
1400 1515 4.877378 ACATTCATGAAAATGGCTGTGT 57.123 36.364 13.09 6.73 40.28 3.72
1401 1516 6.392354 ACTAACATTCATGAAAATGGCTGTG 58.608 36.000 13.09 6.07 40.28 3.66
1402 1517 6.594788 ACTAACATTCATGAAAATGGCTGT 57.405 33.333 13.09 8.23 40.28 4.40
1403 1518 7.489113 GGTTACTAACATTCATGAAAATGGCTG 59.511 37.037 13.09 7.56 40.28 4.85
1404 1519 7.178274 TGGTTACTAACATTCATGAAAATGGCT 59.822 33.333 13.09 2.19 40.28 4.75
1405 1520 7.319646 TGGTTACTAACATTCATGAAAATGGC 58.680 34.615 13.09 0.00 40.28 4.40
1406 1521 9.874205 ATTGGTTACTAACATTCATGAAAATGG 57.126 29.630 13.09 6.30 40.28 3.16
1411 1526 9.521841 TGGTTATTGGTTACTAACATTCATGAA 57.478 29.630 11.26 11.26 30.98 2.57
1412 1527 9.521841 TTGGTTATTGGTTACTAACATTCATGA 57.478 29.630 0.00 0.00 30.98 3.07
1413 1528 9.787532 CTTGGTTATTGGTTACTAACATTCATG 57.212 33.333 1.40 0.00 30.98 3.07
1414 1529 8.466798 GCTTGGTTATTGGTTACTAACATTCAT 58.533 33.333 1.40 0.00 30.98 2.57
1415 1530 7.094118 GGCTTGGTTATTGGTTACTAACATTCA 60.094 37.037 1.40 0.00 30.98 2.57
1416 1531 7.094118 TGGCTTGGTTATTGGTTACTAACATTC 60.094 37.037 1.40 0.00 30.98 2.67
1417 1532 6.722129 TGGCTTGGTTATTGGTTACTAACATT 59.278 34.615 1.40 0.00 30.98 2.71
1418 1533 6.249951 TGGCTTGGTTATTGGTTACTAACAT 58.750 36.000 1.40 0.00 30.98 2.71
1419 1534 5.632118 TGGCTTGGTTATTGGTTACTAACA 58.368 37.500 1.40 0.00 30.98 2.41
1420 1535 5.392703 GCTGGCTTGGTTATTGGTTACTAAC 60.393 44.000 0.00 0.00 0.00 2.34
1421 1536 4.703093 GCTGGCTTGGTTATTGGTTACTAA 59.297 41.667 0.00 0.00 0.00 2.24
1422 1537 4.263550 TGCTGGCTTGGTTATTGGTTACTA 60.264 41.667 0.00 0.00 0.00 1.82
1423 1538 3.089284 GCTGGCTTGGTTATTGGTTACT 58.911 45.455 0.00 0.00 0.00 2.24
1424 1539 2.823154 TGCTGGCTTGGTTATTGGTTAC 59.177 45.455 0.00 0.00 0.00 2.50
1425 1540 3.162147 TGCTGGCTTGGTTATTGGTTA 57.838 42.857 0.00 0.00 0.00 2.85
1426 1541 2.008242 TGCTGGCTTGGTTATTGGTT 57.992 45.000 0.00 0.00 0.00 3.67
1427 1542 2.008242 TTGCTGGCTTGGTTATTGGT 57.992 45.000 0.00 0.00 0.00 3.67
1428 1543 3.328505 CTTTTGCTGGCTTGGTTATTGG 58.671 45.455 0.00 0.00 0.00 3.16
1429 1544 3.006752 TCCTTTTGCTGGCTTGGTTATTG 59.993 43.478 0.00 0.00 0.00 1.90
1430 1545 3.238597 TCCTTTTGCTGGCTTGGTTATT 58.761 40.909 0.00 0.00 0.00 1.40
1431 1546 2.888212 TCCTTTTGCTGGCTTGGTTAT 58.112 42.857 0.00 0.00 0.00 1.89
1471 1586 3.967332 TCACATCTGTGCATCTCAGAA 57.033 42.857 9.31 0.00 45.25 3.02
1472 1587 3.705072 AGATCACATCTGTGCATCTCAGA 59.295 43.478 7.85 7.85 45.25 3.27
1642 1760 8.226448 CAGAATCATTCTTAACTGAAGTCACAC 58.774 37.037 0.00 0.00 38.11 3.82
1679 1797 0.593128 GCGGGGCTATGTAATGCAAG 59.407 55.000 0.00 0.00 0.00 4.01
1694 1812 0.677288 TATGTGGGTAAGATCGCGGG 59.323 55.000 6.13 0.00 0.00 6.13
1695 1813 1.340248 ACTATGTGGGTAAGATCGCGG 59.660 52.381 6.13 0.00 0.00 6.46
1696 1814 2.394708 CACTATGTGGGTAAGATCGCG 58.605 52.381 0.00 0.00 0.00 5.87
1697 1815 2.135933 GCACTATGTGGGTAAGATCGC 58.864 52.381 0.00 0.00 33.64 4.58
1698 1816 3.319405 AGAGCACTATGTGGGTAAGATCG 59.681 47.826 0.00 0.00 33.64 3.69
1699 1817 4.946478 AGAGCACTATGTGGGTAAGATC 57.054 45.455 0.00 0.00 33.64 2.75
1700 1818 5.661312 TGTAAGAGCACTATGTGGGTAAGAT 59.339 40.000 0.00 0.00 33.64 2.40
1717 1835 6.875726 TGGTGAGATGACTTCAATTGTAAGAG 59.124 38.462 18.50 10.31 0.00 2.85
1722 1840 5.380043 AGTTGGTGAGATGACTTCAATTGT 58.620 37.500 5.13 0.00 0.00 2.71
1736 1854 6.824305 AGGAAAACATAATGAGTTGGTGAG 57.176 37.500 0.00 0.00 0.00 3.51
1770 1888 5.829924 AGTTCAGACATCAATTGGAAACTGT 59.170 36.000 5.42 2.34 0.00 3.55
1812 1932 6.100404 TGCTGAAGTGCAGGAAATAATTTT 57.900 33.333 0.00 0.00 42.41 1.82
1846 1976 1.609580 GGACACCCGATAGTGCAACAA 60.610 52.381 0.00 0.00 41.67 2.83
1856 1986 0.617535 TGAGGACATGGACACCCGAT 60.618 55.000 0.00 0.00 34.29 4.18
1858 1988 0.253044 ATTGAGGACATGGACACCCG 59.747 55.000 0.00 0.00 34.29 5.28
1872 2002 7.500227 TGGTGAAGGCAATTAGATAGAATTGAG 59.500 37.037 11.95 0.00 45.70 3.02
1876 2006 8.664079 AGTATGGTGAAGGCAATTAGATAGAAT 58.336 33.333 0.00 0.00 0.00 2.40
1883 2013 5.894807 CCAAAGTATGGTGAAGGCAATTAG 58.105 41.667 0.00 0.00 44.85 1.73
1897 2027 6.656693 AGAACTTGGAAGATCACCAAAGTATG 59.343 38.462 19.70 12.81 45.05 2.39
1898 2028 6.784031 AGAACTTGGAAGATCACCAAAGTAT 58.216 36.000 19.70 9.34 45.05 2.12
1904 2034 5.825593 ACTTAGAACTTGGAAGATCACCA 57.174 39.130 7.43 7.43 35.47 4.17
1909 2039 7.974504 TGGTTAGAACTTAGAACTTGGAAGAT 58.025 34.615 0.00 0.00 0.00 2.40
1922 2052 7.786046 TTGAGGACTGTATGGTTAGAACTTA 57.214 36.000 0.00 0.00 0.00 2.24
1931 2061 3.650942 TCCTTGTTTGAGGACTGTATGGT 59.349 43.478 0.00 0.00 40.87 3.55
1943 2073 4.134563 GGCTAACAGAAGTCCTTGTTTGA 58.865 43.478 3.64 0.00 0.00 2.69
1950 2080 3.857157 TTTGTGGCTAACAGAAGTCCT 57.143 42.857 0.00 0.00 40.74 3.85
1965 2095 8.066595 TGTTTCAGTTTTGTCAATGTTTTTGTG 58.933 29.630 0.00 0.00 0.00 3.33
2025 2166 9.688091 TGAGGATAGTATTAGGACACAGATATC 57.312 37.037 0.00 0.00 0.00 1.63
2034 2175 7.600752 GCATTGAGTTGAGGATAGTATTAGGAC 59.399 40.741 0.00 0.00 0.00 3.85
2132 2273 3.192422 TGAATCGCCGATTGATTTTTGGT 59.808 39.130 18.32 0.00 36.24 3.67
2155 2296 9.469097 AATCTACTAAAGTATGGCGATAGATCT 57.531 33.333 0.00 0.00 39.76 2.75
2159 2300 8.916654 CACAAATCTACTAAAGTATGGCGATAG 58.083 37.037 0.00 0.00 0.00 2.08
2173 2314 8.892723 CAGCCATGAATAAACACAAATCTACTA 58.107 33.333 0.00 0.00 0.00 1.82
2175 2316 6.473455 GCAGCCATGAATAAACACAAATCTAC 59.527 38.462 0.00 0.00 0.00 2.59
2191 2332 1.136305 GTAGTAAGACCGCAGCCATGA 59.864 52.381 0.00 0.00 0.00 3.07
2235 2376 2.188817 ACTTCCCATCACCTGAGGTAC 58.811 52.381 2.59 0.00 32.11 3.34
2334 2475 5.221803 ACCTCAGCAATTACAGATAGATGGG 60.222 44.000 0.00 0.00 0.00 4.00
2346 2487 6.588204 ACCGATAATACAACCTCAGCAATTA 58.412 36.000 0.00 0.00 0.00 1.40
2365 2506 6.764308 AACATGAATGAAAATCTGACCGAT 57.236 33.333 0.00 0.00 0.00 4.18
2427 2568 3.886123 ACCTTCCATTGGTATACTGTGC 58.114 45.455 1.86 0.00 35.80 4.57
2462 2603 1.068610 TGCTGAAAGTATTTGCGTGCC 60.069 47.619 0.00 0.00 39.27 5.01
2480 2621 3.119849 AGTCAACGGCATTTATCAGTTGC 60.120 43.478 2.18 0.00 41.15 4.17
2483 2624 5.220854 GCAATAGTCAACGGCATTTATCAGT 60.221 40.000 0.00 0.00 0.00 3.41
2492 2633 0.250510 TGTGGCAATAGTCAACGGCA 60.251 50.000 0.00 0.00 0.00 5.69
2558 2700 5.698741 ATCATAGAAGAACACATGACCCA 57.301 39.130 0.00 0.00 30.64 4.51
2590 2732 6.169557 TGTCACTTTCCTGTACTTGTATGT 57.830 37.500 0.00 0.00 0.00 2.29
2602 2744 6.713762 TCAACATCATTTTGTCACTTTCCT 57.286 33.333 0.00 0.00 0.00 3.36
2604 2746 6.980397 AGGTTCAACATCATTTTGTCACTTTC 59.020 34.615 0.00 0.00 0.00 2.62
2740 2896 9.908152 CCAGTTAGAAATTTTTACCCAAAGTAG 57.092 33.333 0.00 0.00 30.92 2.57
2754 2910 7.667219 AGACAATGATGTGACCAGTTAGAAATT 59.333 33.333 0.00 0.00 40.74 1.82
2755 2911 7.170965 AGACAATGATGTGACCAGTTAGAAAT 58.829 34.615 0.00 0.00 40.74 2.17
2757 2913 6.114187 AGACAATGATGTGACCAGTTAGAA 57.886 37.500 0.00 0.00 40.74 2.10
2758 2914 5.745312 AGACAATGATGTGACCAGTTAGA 57.255 39.130 0.00 0.00 40.74 2.10
2759 2915 6.091849 CAGAAGACAATGATGTGACCAGTTAG 59.908 42.308 0.00 0.00 40.74 2.34
2760 2916 5.934043 CAGAAGACAATGATGTGACCAGTTA 59.066 40.000 0.00 0.00 40.74 2.24
2767 2923 6.938596 AGAATCAACAGAAGACAATGATGTGA 59.061 34.615 0.00 0.00 40.74 3.58
2852 3008 2.166664 AGGAGCAACATAGTTCGGAGTC 59.833 50.000 0.00 0.00 0.00 3.36
2899 3057 5.190528 AGTGGATTGGACACATGATCTTACT 59.809 40.000 0.00 0.00 41.21 2.24
2900 3058 5.431765 AGTGGATTGGACACATGATCTTAC 58.568 41.667 0.00 0.00 41.21 2.34
2946 3104 1.829849 TCCTCAATCACCTGCAGAGAG 59.170 52.381 17.39 11.47 0.00 3.20
2950 3108 3.244146 CCTCTATCCTCAATCACCTGCAG 60.244 52.174 6.78 6.78 0.00 4.41
2953 3111 6.268617 TCATAACCTCTATCCTCAATCACCTG 59.731 42.308 0.00 0.00 0.00 4.00
3422 3581 8.678199 GTTGGGATTCTATAACTTCTTTTCAGG 58.322 37.037 0.00 0.00 0.00 3.86
3574 3733 4.277423 CCAAATGCAGCATAGACATCATCA 59.723 41.667 8.75 0.00 0.00 3.07
3789 3948 1.160137 CCTCCTTTGCCTCGAACAAG 58.840 55.000 1.34 0.00 0.00 3.16
3923 4245 8.509690 ACAGATAAGTACATTGCAATGATATGC 58.490 33.333 38.99 23.15 46.58 3.14
4106 4428 3.802866 TGTAACAGAAGATGTGTGCACA 58.197 40.909 17.42 17.42 43.00 4.57
4202 4527 0.181350 GGGTTCTCCATCCGCATCTT 59.819 55.000 0.00 0.00 35.00 2.40
4335 4663 5.151297 CCTGAAGGTTGCCACATAAAAAT 57.849 39.130 0.00 0.00 0.00 1.82
4503 4831 9.516314 AAAATAAACTCTTGTTACTTGCTTGTC 57.484 29.630 0.00 0.00 34.96 3.18
4557 4885 1.079750 GTCCTTGAGCTGGGTCGAC 60.080 63.158 7.13 7.13 0.00 4.20
4632 4960 6.761714 CAGTAGGGACTATGTACATGGAAAAC 59.238 42.308 24.30 13.91 45.60 2.43
4655 4984 5.551305 TCCATCCCACATATGAACTACAG 57.449 43.478 10.38 0.00 0.00 2.74
4656 4985 5.221904 CCATCCATCCCACATATGAACTACA 60.222 44.000 10.38 0.00 0.00 2.74
4657 4986 5.248640 CCATCCATCCCACATATGAACTAC 58.751 45.833 10.38 0.00 0.00 2.73
4658 4987 4.263462 GCCATCCATCCCACATATGAACTA 60.263 45.833 10.38 0.00 0.00 2.24
4659 4988 3.499202 GCCATCCATCCCACATATGAACT 60.499 47.826 10.38 0.00 0.00 3.01
4710 5041 3.264104 ACAAACCAACGAAAGAACTCGA 58.736 40.909 0.00 0.00 41.44 4.04
4732 5063 9.338622 GCCTATTCATCATCATCATCATCATTA 57.661 33.333 0.00 0.00 0.00 1.90
4733 5064 8.055790 AGCCTATTCATCATCATCATCATCATT 58.944 33.333 0.00 0.00 0.00 2.57
4734 5065 7.578203 AGCCTATTCATCATCATCATCATCAT 58.422 34.615 0.00 0.00 0.00 2.45
4735 5066 6.958767 AGCCTATTCATCATCATCATCATCA 58.041 36.000 0.00 0.00 0.00 3.07
4736 5067 6.483974 GGAGCCTATTCATCATCATCATCATC 59.516 42.308 0.00 0.00 0.00 2.92
4737 5068 6.358178 GGAGCCTATTCATCATCATCATCAT 58.642 40.000 0.00 0.00 0.00 2.45
4786 5120 3.900601 CCATAGATAGGCTCTTCCACAGT 59.099 47.826 0.00 0.00 37.29 3.55
4828 5162 5.851693 TCCCTCTGGACCATGAATATGTAAT 59.148 40.000 0.00 0.00 35.03 1.89
4829 5163 5.223655 TCCCTCTGGACCATGAATATGTAA 58.776 41.667 0.00 0.00 35.03 2.41
5027 5407 0.826715 TCCATGAGCTTCCTTCCTCG 59.173 55.000 0.00 0.00 0.00 4.63
5028 5408 3.475575 GATTCCATGAGCTTCCTTCCTC 58.524 50.000 0.00 0.00 0.00 3.71
5066 5450 3.947834 CCCCGCTTTATCATTCTCAGTTT 59.052 43.478 0.00 0.00 0.00 2.66
5067 5451 3.545703 CCCCGCTTTATCATTCTCAGTT 58.454 45.455 0.00 0.00 0.00 3.16
5068 5452 2.746472 GCCCCGCTTTATCATTCTCAGT 60.746 50.000 0.00 0.00 0.00 3.41
5069 5453 1.876156 GCCCCGCTTTATCATTCTCAG 59.124 52.381 0.00 0.00 0.00 3.35
5070 5454 1.810031 CGCCCCGCTTTATCATTCTCA 60.810 52.381 0.00 0.00 0.00 3.27
5071 5455 0.868406 CGCCCCGCTTTATCATTCTC 59.132 55.000 0.00 0.00 0.00 2.87
5072 5456 0.468226 TCGCCCCGCTTTATCATTCT 59.532 50.000 0.00 0.00 0.00 2.40
5073 5457 1.305201 TTCGCCCCGCTTTATCATTC 58.695 50.000 0.00 0.00 0.00 2.67
5074 5458 1.676006 CTTTCGCCCCGCTTTATCATT 59.324 47.619 0.00 0.00 0.00 2.57
5075 5459 1.308998 CTTTCGCCCCGCTTTATCAT 58.691 50.000 0.00 0.00 0.00 2.45
5076 5460 0.035820 ACTTTCGCCCCGCTTTATCA 60.036 50.000 0.00 0.00 0.00 2.15
5077 5461 0.656259 GACTTTCGCCCCGCTTTATC 59.344 55.000 0.00 0.00 0.00 1.75
5078 5462 0.252197 AGACTTTCGCCCCGCTTTAT 59.748 50.000 0.00 0.00 0.00 1.40
5079 5463 0.035739 AAGACTTTCGCCCCGCTTTA 59.964 50.000 0.00 0.00 0.00 1.85
5080 5464 0.822121 AAAGACTTTCGCCCCGCTTT 60.822 50.000 0.00 0.00 0.00 3.51
5081 5465 0.822121 AAAAGACTTTCGCCCCGCTT 60.822 50.000 0.00 0.00 0.00 4.68
5082 5466 0.822121 AAAAAGACTTTCGCCCCGCT 60.822 50.000 0.00 0.00 0.00 5.52
5083 5467 0.386858 GAAAAAGACTTTCGCCCCGC 60.387 55.000 0.00 0.00 0.00 6.13
5084 5468 0.110373 CGAAAAAGACTTTCGCCCCG 60.110 55.000 0.00 0.00 43.52 5.73
5085 5469 0.240145 CCGAAAAAGACTTTCGCCCC 59.760 55.000 12.82 0.00 46.89 5.80
5086 5470 0.949397 ACCGAAAAAGACTTTCGCCC 59.051 50.000 12.82 0.00 46.89 6.13
5087 5471 3.883631 TTACCGAAAAAGACTTTCGCC 57.116 42.857 12.82 0.00 46.89 5.54
5088 5472 5.740569 AGTTTTTACCGAAAAAGACTTTCGC 59.259 36.000 12.82 0.00 46.89 4.70
5089 5473 6.962678 TCAGTTTTTACCGAAAAAGACTTTCG 59.037 34.615 11.62 11.62 43.48 3.46
5090 5474 8.179615 TCTCAGTTTTTACCGAAAAAGACTTTC 58.820 33.333 0.00 0.00 43.48 2.62
5091 5475 8.047413 TCTCAGTTTTTACCGAAAAAGACTTT 57.953 30.769 0.00 0.00 43.48 2.66
5092 5476 7.619964 TCTCAGTTTTTACCGAAAAAGACTT 57.380 32.000 3.82 0.00 43.48 3.01
5093 5477 7.619964 TTCTCAGTTTTTACCGAAAAAGACT 57.380 32.000 0.00 0.00 43.48 3.24
5094 5478 8.126700 TCATTCTCAGTTTTTACCGAAAAAGAC 58.873 33.333 0.00 0.00 43.48 3.01
5095 5479 8.215926 TCATTCTCAGTTTTTACCGAAAAAGA 57.784 30.769 0.00 0.00 43.48 2.52
5096 5480 8.850454 TTCATTCTCAGTTTTTACCGAAAAAG 57.150 30.769 0.00 0.00 43.48 2.27
5097 5481 9.078753 GTTTCATTCTCAGTTTTTACCGAAAAA 57.921 29.630 0.00 0.00 41.24 1.94
5098 5482 7.703197 GGTTTCATTCTCAGTTTTTACCGAAAA 59.297 33.333 0.00 0.00 34.93 2.29
5099 5483 7.197703 GGTTTCATTCTCAGTTTTTACCGAAA 58.802 34.615 0.00 0.00 0.00 3.46
5100 5484 6.512091 CGGTTTCATTCTCAGTTTTTACCGAA 60.512 38.462 0.00 0.00 45.46 4.30
5101 5485 5.049954 CGGTTTCATTCTCAGTTTTTACCGA 60.050 40.000 0.00 0.00 45.46 4.69
5102 5486 5.049954 TCGGTTTCATTCTCAGTTTTTACCG 60.050 40.000 0.00 0.00 44.37 4.02
5103 5487 6.308371 TCGGTTTCATTCTCAGTTTTTACC 57.692 37.500 0.00 0.00 0.00 2.85
5104 5488 7.360361 ACATCGGTTTCATTCTCAGTTTTTAC 58.640 34.615 0.00 0.00 0.00 2.01
5105 5489 7.504924 ACATCGGTTTCATTCTCAGTTTTTA 57.495 32.000 0.00 0.00 0.00 1.52
5106 5490 6.391227 ACATCGGTTTCATTCTCAGTTTTT 57.609 33.333 0.00 0.00 0.00 1.94
5107 5491 7.228706 ACTTACATCGGTTTCATTCTCAGTTTT 59.771 33.333 0.00 0.00 0.00 2.43
5108 5492 6.710744 ACTTACATCGGTTTCATTCTCAGTTT 59.289 34.615 0.00 0.00 0.00 2.66
5109 5493 6.147821 CACTTACATCGGTTTCATTCTCAGTT 59.852 38.462 0.00 0.00 0.00 3.16
5110 5494 5.639506 CACTTACATCGGTTTCATTCTCAGT 59.360 40.000 0.00 0.00 0.00 3.41
5111 5495 5.639506 ACACTTACATCGGTTTCATTCTCAG 59.360 40.000 0.00 0.00 0.00 3.35
5112 5496 5.408299 CACACTTACATCGGTTTCATTCTCA 59.592 40.000 0.00 0.00 0.00 3.27
5113 5497 5.637810 TCACACTTACATCGGTTTCATTCTC 59.362 40.000 0.00 0.00 0.00 2.87
5114 5498 5.547465 TCACACTTACATCGGTTTCATTCT 58.453 37.500 0.00 0.00 0.00 2.40
5130 5514 3.820467 TCGCAATTTGGAGATTCACACTT 59.180 39.130 0.00 0.00 0.00 3.16
5137 5521 5.452078 TTTCAGTTCGCAATTTGGAGATT 57.548 34.783 0.00 0.00 0.00 2.40
5155 5542 3.061322 CGTGGTCCGACTACATTTTTCA 58.939 45.455 14.61 0.00 39.56 2.69
5180 5567 1.135315 CCGGCAAATGCGAGAGTTG 59.865 57.895 0.00 0.00 43.26 3.16
5214 5601 2.281761 CCCGGCTCACAACTTGCT 60.282 61.111 0.00 0.00 0.00 3.91
5296 5683 3.486383 TCAAAGCTGAGAAAAATCCGGT 58.514 40.909 0.00 0.00 0.00 5.28
5335 5722 4.207281 CGGAGAAGATCGGCGCCA 62.207 66.667 28.98 14.46 0.00 5.69
5373 5760 3.680786 GCCGGGTTTGGAAGTGCC 61.681 66.667 2.18 0.00 37.10 5.01
5374 5761 3.680786 GGCCGGGTTTGGAAGTGC 61.681 66.667 2.18 0.00 0.00 4.40
5375 5762 1.530655 AAGGCCGGGTTTGGAAGTG 60.531 57.895 2.18 0.00 0.00 3.16
5376 5763 1.530655 CAAGGCCGGGTTTGGAAGT 60.531 57.895 2.18 0.00 0.00 3.01
5377 5764 1.228429 TCAAGGCCGGGTTTGGAAG 60.228 57.895 2.18 0.00 0.00 3.46
5378 5765 1.529713 GTCAAGGCCGGGTTTGGAA 60.530 57.895 2.18 0.00 0.00 3.53
5379 5766 2.114411 GTCAAGGCCGGGTTTGGA 59.886 61.111 2.18 0.00 0.00 3.53
5380 5767 2.989253 GGTCAAGGCCGGGTTTGG 60.989 66.667 2.18 0.00 0.00 3.28
5457 5845 0.880278 CATAGTAATGCCCAGCGCGT 60.880 55.000 8.43 0.00 42.08 6.01
5468 5856 1.119574 ACGGGCCGGCTCATAGTAAT 61.120 55.000 31.78 0.20 0.00 1.89
5471 5859 2.588856 GAAACGGGCCGGCTCATAGT 62.589 60.000 31.78 14.05 0.00 2.12
5472 5860 1.887707 GAAACGGGCCGGCTCATAG 60.888 63.158 31.78 13.26 0.00 2.23
5484 5872 2.897326 AGAATGGAAAAAGGGGAAACGG 59.103 45.455 0.00 0.00 0.00 4.44
5485 5873 4.600692 AAGAATGGAAAAAGGGGAAACG 57.399 40.909 0.00 0.00 0.00 3.60
5557 5964 7.680062 TCGCAAACAAAAGTGGAAAATTAAAG 58.320 30.769 0.00 0.00 0.00 1.85
5559 5966 7.596749 TTCGCAAACAAAAGTGGAAAATTAA 57.403 28.000 0.00 0.00 0.00 1.40
5560 5967 7.778470 ATTCGCAAACAAAAGTGGAAAATTA 57.222 28.000 0.00 0.00 0.00 1.40
5568 5975 8.433585 AAAAAGAAAATTCGCAAACAAAAGTG 57.566 26.923 0.00 0.00 0.00 3.16
5575 5982 9.142993 GTGACATTAAAAAGAAAATTCGCAAAC 57.857 29.630 0.00 0.00 0.00 2.93
5579 5986 9.862585 AATTGTGACATTAAAAAGAAAATTCGC 57.137 25.926 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.