Multiple sequence alignment - TraesCS7D01G231000

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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 TraesCS7D01G231000 chr7D 100.000 6375 0 0 1 6375 192152508 192158882 0.000000e+00 11773
1 TraesCS7D01G231000 chr7B 93.801 3920 205 16 2477 6375 337636155 337640057 0.000000e+00 5858
2 TraesCS7D01G231000 chr7B 82.653 2058 182 73 489 2510 337634236 337636154 0.000000e+00 1661
3 TraesCS7D01G231000 chr7B 89.744 390 17 4 1 390 337633837 337634203 1.610000e-130 477
4 TraesCS7D01G231000 chr7A 94.882 3009 133 7 2477 5480 201539447 201542439 0.000000e+00 4684
5 TraesCS7D01G231000 chr7A 87.819 1839 132 48 691 2510 201537681 201539446 0.000000e+00 2071
6 TraesCS7D01G231000 chr7A 92.700 863 44 8 5519 6375 201542597 201543446 0.000000e+00 1227
7 TraesCS7D01G231000 chr7A 87.638 542 50 13 1 536 201536924 201537454 1.170000e-171 614
8 TraesCS7D01G231000 chr3A 81.780 1202 183 16 3848 5037 57890842 57889665 0.000000e+00 974
9 TraesCS7D01G231000 chr2B 87.797 295 34 2 1 295 510351060 510351352 1.700000e-90 344
10 TraesCS7D01G231000 chr2B 82.492 297 41 6 1 294 799413174 799412886 3.820000e-62 250
11 TraesCS7D01G231000 chr3D 87.542 297 33 3 1 296 456644628 456644335 2.200000e-89 340
12 TraesCS7D01G231000 chr6D 85.762 302 38 5 1 301 377335662 377335365 1.330000e-81 315
13 TraesCS7D01G231000 chr2A 87.243 243 30 1 4 246 71691424 71691183 6.300000e-70 276
14 TraesCS7D01G231000 chr1B 82.432 296 49 3 1 296 17411735 17411443 8.200000e-64 255
15 TraesCS7D01G231000 chr1B 82.432 296 49 3 1 296 17420261 17419969 8.200000e-64 255
16 TraesCS7D01G231000 chr5D 85.490 255 20 7 2547 2797 179720636 179720877 3.820000e-62 250
17 TraesCS7D01G231000 chr5D 91.597 119 9 1 2838 2955 179720880 179720998 5.110000e-36 163
18 TraesCS7D01G231000 chr4A 85.039 254 20 9 2547 2796 391386538 391386299 6.390000e-60 243
19 TraesCS7D01G231000 chr4B 85.841 226 18 9 2571 2796 465958183 465957972 1.790000e-55 228
20 TraesCS7D01G231000 chr4B 85.333 225 19 9 2572 2796 465836947 465836737 2.990000e-53 220
21 TraesCS7D01G231000 chr5A 90.511 137 13 0 2563 2699 579876231 579876095 1.410000e-41 182
22 TraesCS7D01G231000 chr5A 90.400 125 9 3 2834 2955 579968158 579968034 1.840000e-35 161
23 TraesCS7D01G231000 chr5A 88.800 125 11 3 2834 2955 579956427 579956303 3.980000e-32 150


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 TraesCS7D01G231000 chr7D 192152508 192158882 6374 False 11773.000000 11773 100.000000 1 6375 1 chr7D.!!$F1 6374
1 TraesCS7D01G231000 chr7B 337633837 337640057 6220 False 2665.333333 5858 88.732667 1 6375 3 chr7B.!!$F1 6374
2 TraesCS7D01G231000 chr7A 201536924 201543446 6522 False 2149.000000 4684 90.759750 1 6375 4 chr7A.!!$F1 6374
3 TraesCS7D01G231000 chr3A 57889665 57890842 1177 True 974.000000 974 81.780000 3848 5037 1 chr3A.!!$R1 1189

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
584 589 0.250597 GGTTCAACTAGGTGCCGGTT 60.251 55.000 1.76 0.00 0.00 4.44 F
1090 1176 0.033796 CATCCCACTTGCACCCATCT 60.034 55.000 0.00 0.00 0.00 2.90 F
1094 1180 0.033796 CCACTTGCACCCATCTCCAT 60.034 55.000 0.00 0.00 0.00 3.41 F
1173 1260 0.103572 TAGTTATTCGTCCCGCTGCC 59.896 55.000 0.00 0.00 0.00 4.85 F
1591 1690 0.179086 TGCTCTGCAGTGAACGTTCA 60.179 50.000 26.53 26.53 33.32 3.18 F
1771 1872 0.236187 CTAGCTACTACGCGCCTCAG 59.764 60.000 5.73 0.30 34.40 3.35 F
2832 2996 0.250234 TCAGTGGCTCGGAAATGGAG 59.750 55.000 0.00 0.00 34.62 3.86 F
3213 3377 0.529378 GCCAAAGCTTCAGTGATGGG 59.471 55.000 13.21 3.91 35.50 4.00 F
3219 3383 1.211457 AGCTTCAGTGATGGGATGACC 59.789 52.381 8.02 0.00 40.81 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1671 0.179086 TGAACGTTCACTGCAGAGCA 60.179 50.0 26.53 0.00 32.42 4.26 R
2296 2423 0.323087 GTAAAACGTGATGGCCCCCT 60.323 55.0 0.00 0.00 0.00 4.79 R
2321 2448 0.615331 TGCCTGGTAGCTTTCTGAGG 59.385 55.0 0.00 0.00 0.00 3.86 R
2871 3035 0.744281 AACCAAAGCCAAACACCGAG 59.256 50.0 0.00 0.00 0.00 4.63 R
3270 3434 0.035439 ACAACATCATGTCCCCGGAC 60.035 55.0 0.73 6.95 44.77 4.79 R
3471 3635 0.176680 CACCGAGGACAGCAGCTAAT 59.823 55.0 0.00 0.00 0.00 1.73 R
3641 3805 0.391793 GTTTGGAGAAGAGCCGAGGG 60.392 60.0 0.00 0.00 0.00 4.30 R
4977 5150 0.036010 CGAGCATCTGGACCACCTTT 60.036 55.0 0.00 0.00 37.04 3.11 R
5459 5636 5.321102 ACACTGATTATGCCACAGGTTTAA 58.679 37.5 0.00 0.00 36.17 1.52 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
133 138 5.352569 CACGAACATCTAGCAAATTTCTCCT 59.647 40.000 0.00 0.00 0.00 3.69
137 142 7.043059 CGAACATCTAGCAAATTTCTCCTCTAC 60.043 40.741 0.00 0.00 0.00 2.59
172 177 9.277783 CAATATACTCTTCTTCCCAATACCAAG 57.722 37.037 0.00 0.00 0.00 3.61
189 194 5.121380 ACCAAGACTTGCATTCATCCTAT 57.879 39.130 9.85 0.00 0.00 2.57
436 441 2.363795 AGGCCGGAGTGGATTCGA 60.364 61.111 5.05 0.00 42.00 3.71
437 442 1.749334 GAGGCCGGAGTGGATTCGAT 61.749 60.000 5.05 0.00 42.00 3.59
438 443 1.595382 GGCCGGAGTGGATTCGATG 60.595 63.158 5.05 0.00 42.00 3.84
439 444 1.144057 GCCGGAGTGGATTCGATGT 59.856 57.895 5.05 0.00 42.00 3.06
441 446 0.459899 CCGGAGTGGATTCGATGTGA 59.540 55.000 0.00 0.00 42.00 3.58
476 481 2.851588 GAGGGGAGAGGGGGCATC 60.852 72.222 0.00 0.00 0.00 3.91
479 484 2.009302 GGGGAGAGGGGGCATCTTT 61.009 63.158 0.00 0.00 0.00 2.52
497 502 2.554370 TTTTTACTCGGGTGGGTGAG 57.446 50.000 0.00 0.00 38.21 3.51
498 503 1.426751 TTTTACTCGGGTGGGTGAGT 58.573 50.000 0.00 0.22 46.60 3.41
501 506 4.394712 CTCGGGTGGGTGAGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
522 527 3.505293 GCCGAGTAAATATAGGAGTCCGT 59.495 47.826 2.76 0.00 0.00 4.69
555 560 8.745464 AGAAGTAGAATTTGTTCTCGTCTAAC 57.255 34.615 0.00 0.00 32.72 2.34
570 575 3.181501 CGTCTAACGGTTATACGGGTTCA 60.182 47.826 23.22 0.00 38.08 3.18
581 586 1.740296 CGGGTTCAACTAGGTGCCG 60.740 63.158 10.36 10.36 0.00 5.69
583 588 1.373812 GGTTCAACTAGGTGCCGGT 59.626 57.895 1.76 0.00 0.00 5.28
584 589 0.250597 GGTTCAACTAGGTGCCGGTT 60.251 55.000 1.76 0.00 0.00 4.44
586 591 2.355412 GGTTCAACTAGGTGCCGGTTAT 60.355 50.000 1.76 0.00 0.00 1.89
593 598 3.890147 ACTAGGTGCCGGTTATAGAAGAG 59.110 47.826 1.90 0.00 0.00 2.85
599 604 4.989168 GTGCCGGTTATAGAAGAGTAATGG 59.011 45.833 1.90 0.00 0.00 3.16
657 736 2.783828 AGTGATCGGTTAGAGATGCG 57.216 50.000 0.00 0.00 0.00 4.73
689 768 3.771216 TCCTACGAGTATATTCCACCCC 58.229 50.000 0.00 0.00 0.00 4.95
715 794 6.749139 AGTGATGCTATACATACGACACATT 58.251 36.000 0.00 0.00 39.84 2.71
730 809 4.441744 CGACACATTTGCGTCCGTATATTA 59.558 41.667 0.00 0.00 0.00 0.98
751 830 3.323751 AAAAATCGTAGGCGGTGTAGT 57.676 42.857 0.00 0.00 38.89 2.73
754 833 1.602311 ATCGTAGGCGGTGTAGTAGG 58.398 55.000 0.00 0.00 38.89 3.18
776 855 2.707257 TCCGTTCCACTTTTTACTCCCT 59.293 45.455 0.00 0.00 0.00 4.20
777 856 3.903090 TCCGTTCCACTTTTTACTCCCTA 59.097 43.478 0.00 0.00 0.00 3.53
778 857 3.999001 CCGTTCCACTTTTTACTCCCTAC 59.001 47.826 0.00 0.00 0.00 3.18
779 858 4.262765 CCGTTCCACTTTTTACTCCCTACT 60.263 45.833 0.00 0.00 0.00 2.57
780 859 5.047092 CCGTTCCACTTTTTACTCCCTACTA 60.047 44.000 0.00 0.00 0.00 1.82
797 876 6.543831 TCCCTACTATAGTTGACGTTTACCTC 59.456 42.308 11.40 0.00 0.00 3.85
802 881 3.648339 AGTTGACGTTTACCTCGCTTA 57.352 42.857 0.00 0.00 0.00 3.09
803 882 3.981211 AGTTGACGTTTACCTCGCTTAA 58.019 40.909 0.00 0.00 0.00 1.85
806 885 4.713854 TGACGTTTACCTCGCTTAAAAC 57.286 40.909 0.00 0.00 0.00 2.43
807 886 4.370917 TGACGTTTACCTCGCTTAAAACT 58.629 39.130 0.00 0.00 31.25 2.66
817 898 1.145803 GCTTAAAACTCTGACCGCGT 58.854 50.000 4.92 0.00 0.00 6.01
879 962 1.815212 CGCGCACGATCTCCAAGATG 61.815 60.000 8.75 0.00 43.93 2.90
895 978 7.335673 TCTCCAAGATGTACGAAATTTAATGCA 59.664 33.333 0.00 0.00 0.00 3.96
897 980 6.472163 CCAAGATGTACGAAATTTAATGCACC 59.528 38.462 0.00 0.00 0.00 5.01
1003 1089 1.465777 GGCCGTACGCACTAAACAAAT 59.534 47.619 10.49 0.00 40.31 2.32
1004 1090 2.672381 GGCCGTACGCACTAAACAAATA 59.328 45.455 10.49 0.00 40.31 1.40
1005 1091 3.484065 GGCCGTACGCACTAAACAAATAC 60.484 47.826 10.49 0.00 40.31 1.89
1006 1092 3.368843 GCCGTACGCACTAAACAAATACT 59.631 43.478 10.49 0.00 37.47 2.12
1007 1093 4.491441 GCCGTACGCACTAAACAAATACTC 60.491 45.833 10.49 0.00 37.47 2.59
1008 1094 4.032104 CCGTACGCACTAAACAAATACTCC 59.968 45.833 10.49 0.00 0.00 3.85
1011 1097 6.195983 CGTACGCACTAAACAAATACTCCTAG 59.804 42.308 0.52 0.00 0.00 3.02
1090 1176 0.033796 CATCCCACTTGCACCCATCT 60.034 55.000 0.00 0.00 0.00 2.90
1091 1177 0.257039 ATCCCACTTGCACCCATCTC 59.743 55.000 0.00 0.00 0.00 2.75
1092 1178 1.379044 CCCACTTGCACCCATCTCC 60.379 63.158 0.00 0.00 0.00 3.71
1093 1179 1.379916 CCACTTGCACCCATCTCCA 59.620 57.895 0.00 0.00 0.00 3.86
1094 1180 0.033796 CCACTTGCACCCATCTCCAT 60.034 55.000 0.00 0.00 0.00 3.41
1095 1181 1.386533 CACTTGCACCCATCTCCATC 58.613 55.000 0.00 0.00 0.00 3.51
1096 1182 0.257039 ACTTGCACCCATCTCCATCC 59.743 55.000 0.00 0.00 0.00 3.51
1097 1183 0.816825 CTTGCACCCATCTCCATCCG 60.817 60.000 0.00 0.00 0.00 4.18
1098 1184 1.561769 TTGCACCCATCTCCATCCGT 61.562 55.000 0.00 0.00 0.00 4.69
1099 1185 1.227674 GCACCCATCTCCATCCGTC 60.228 63.158 0.00 0.00 0.00 4.79
1100 1186 1.447643 CACCCATCTCCATCCGTCC 59.552 63.158 0.00 0.00 0.00 4.79
1101 1187 1.002921 ACCCATCTCCATCCGTCCA 59.997 57.895 0.00 0.00 0.00 4.02
1102 1188 0.400525 ACCCATCTCCATCCGTCCAT 60.401 55.000 0.00 0.00 0.00 3.41
1110 1196 0.601046 CCATCCGTCCATGTCCATCG 60.601 60.000 0.00 0.00 0.00 3.84
1122 1208 3.141767 TGTCCATCGATCGATCTACCT 57.858 47.619 27.20 4.02 31.62 3.08
1130 1216 0.539901 ATCGATCTACCTCCACCCCG 60.540 60.000 0.00 0.00 0.00 5.73
1173 1260 0.103572 TAGTTATTCGTCCCGCTGCC 59.896 55.000 0.00 0.00 0.00 4.85
1174 1261 2.202824 TTATTCGTCCCGCTGCCG 60.203 61.111 0.00 0.00 0.00 5.69
1175 1262 4.884257 TATTCGTCCCGCTGCCGC 62.884 66.667 0.00 0.00 0.00 6.53
1245 1335 4.465446 CCGCCTCCTCCTCCTCCA 62.465 72.222 0.00 0.00 0.00 3.86
1269 1359 2.675423 CGTCGAGTCTCCCCACCA 60.675 66.667 0.00 0.00 0.00 4.17
1322 1412 1.215647 CTTCCTCGTCCTCCCGTTG 59.784 63.158 0.00 0.00 0.00 4.10
1368 1460 1.192146 TCTTCTTGTCCTGTCCGGGG 61.192 60.000 0.00 0.00 0.00 5.73
1369 1461 2.804828 CTTCTTGTCCTGTCCGGGGC 62.805 65.000 0.00 0.00 0.00 5.80
1395 1487 2.171840 CGAGTTCTTCCTCCTCCTTGA 58.828 52.381 0.00 0.00 0.00 3.02
1397 1489 3.169908 GAGTTCTTCCTCCTCCTTGACT 58.830 50.000 0.00 0.00 0.00 3.41
1414 1506 1.049289 ACTCCTTCCCCTATCCGTGC 61.049 60.000 0.00 0.00 0.00 5.34
1463 1555 1.071605 CCGTGGCTCTCTTTCTTTCG 58.928 55.000 0.00 0.00 0.00 3.46
1547 1646 0.383949 TCCGGTTGCTGTTTTCTTGC 59.616 50.000 0.00 0.00 0.00 4.01
1551 1650 1.269778 GGTTGCTGTTTTCTTGCTCCC 60.270 52.381 0.00 0.00 0.00 4.30
1572 1671 1.577328 CGAATTTGGCGTCTGGCTGT 61.577 55.000 0.00 0.00 42.94 4.40
1580 1679 2.031616 GTCTGGCTGTGCTCTGCA 59.968 61.111 17.64 5.18 39.69 4.41
1581 1680 2.033755 GTCTGGCTGTGCTCTGCAG 61.034 63.158 17.64 7.63 40.08 4.41
1582 1681 2.032223 CTGGCTGTGCTCTGCAGT 59.968 61.111 14.67 0.00 40.08 4.40
1590 1689 0.233332 GTGCTCTGCAGTGAACGTTC 59.767 55.000 21.42 21.42 40.08 3.95
1591 1690 0.179086 TGCTCTGCAGTGAACGTTCA 60.179 50.000 26.53 26.53 33.32 3.18
1605 1704 4.819630 TGAACGTTCAGTGAAATTAGGCTT 59.180 37.500 26.53 0.00 32.50 4.35
1630 1730 6.038825 TGAATTAAGCAAGAAACAAACGAGGA 59.961 34.615 0.00 0.00 0.00 3.71
1631 1731 6.575162 ATTAAGCAAGAAACAAACGAGGAT 57.425 33.333 0.00 0.00 0.00 3.24
1634 1734 5.262588 AGCAAGAAACAAACGAGGATTTT 57.737 34.783 0.00 0.00 0.00 1.82
1636 1736 6.801575 AGCAAGAAACAAACGAGGATTTTAA 58.198 32.000 0.00 0.00 0.00 1.52
1637 1737 6.695713 AGCAAGAAACAAACGAGGATTTTAAC 59.304 34.615 0.00 0.00 0.00 2.01
1639 1739 7.222031 GCAAGAAACAAACGAGGATTTTAACTT 59.778 33.333 0.00 0.00 0.00 2.66
1640 1740 9.083080 CAAGAAACAAACGAGGATTTTAACTTT 57.917 29.630 0.00 0.00 0.00 2.66
1641 1741 8.628882 AGAAACAAACGAGGATTTTAACTTTG 57.371 30.769 0.00 0.00 0.00 2.77
1642 1742 8.248253 AGAAACAAACGAGGATTTTAACTTTGT 58.752 29.630 0.00 0.00 33.00 2.83
1643 1743 7.980742 AACAAACGAGGATTTTAACTTTGTC 57.019 32.000 0.00 0.00 30.96 3.18
1644 1744 7.090953 ACAAACGAGGATTTTAACTTTGTCA 57.909 32.000 0.00 0.00 0.00 3.58
1645 1745 7.193595 ACAAACGAGGATTTTAACTTTGTCAG 58.806 34.615 0.00 0.00 0.00 3.51
1660 1761 8.514330 AACTTTGTCAGTTTAGTTTGGATGTA 57.486 30.769 0.00 0.00 43.89 2.29
1661 1762 8.691661 ACTTTGTCAGTTTAGTTTGGATGTAT 57.308 30.769 0.00 0.00 27.32 2.29
1662 1763 9.131791 ACTTTGTCAGTTTAGTTTGGATGTATT 57.868 29.630 0.00 0.00 27.32 1.89
1663 1764 9.612620 CTTTGTCAGTTTAGTTTGGATGTATTC 57.387 33.333 0.00 0.00 0.00 1.75
1664 1765 7.359262 TGTCAGTTTAGTTTGGATGTATTCG 57.641 36.000 0.00 0.00 0.00 3.34
1665 1766 6.932400 TGTCAGTTTAGTTTGGATGTATTCGT 59.068 34.615 0.00 0.00 0.00 3.85
1666 1767 7.442969 TGTCAGTTTAGTTTGGATGTATTCGTT 59.557 33.333 0.00 0.00 0.00 3.85
1678 1779 2.809119 TGTATTCGTTTCGTTGGCATGT 59.191 40.909 0.00 0.00 0.00 3.21
1701 1802 1.520342 GCTGCCTCGAATTCTCGCT 60.520 57.895 3.52 0.00 45.04 4.93
1728 1829 7.439056 GCAATGGAAATGTGTAGAATTAATGGG 59.561 37.037 0.00 0.00 0.00 4.00
1734 1835 2.685897 GTGTAGAATTAATGGGGCGCAA 59.314 45.455 10.83 0.00 0.00 4.85
1771 1872 0.236187 CTAGCTACTACGCGCCTCAG 59.764 60.000 5.73 0.30 34.40 3.35
1773 1874 1.586564 GCTACTACGCGCCTCAGTG 60.587 63.158 5.73 1.53 0.00 3.66
1881 1990 4.142491 TGTGTTCATTTTCAGTGAAACGCT 60.142 37.500 17.85 3.50 45.86 5.07
1899 2008 0.600057 CTGGCCTTTCTCCAACTTGC 59.400 55.000 3.32 0.00 32.41 4.01
1925 2039 1.251251 AACTGCTGTGCTTTCCCATC 58.749 50.000 0.00 0.00 0.00 3.51
1938 2052 9.420118 TGTGCTTTCCCATCACTAATTATTATT 57.580 29.630 0.00 0.00 0.00 1.40
2002 2116 9.410556 GTGCAAAACTATCAAATGTTTGTAGAT 57.589 29.630 15.48 6.89 39.18 1.98
2084 2198 1.407989 CCCAGCTCTCTTCCAACCATC 60.408 57.143 0.00 0.00 0.00 3.51
2117 2238 9.277783 ACCAGTATCATGATTTATTCTTGTAGC 57.722 33.333 14.65 0.00 32.65 3.58
2137 2258 7.723324 TGTAGCAGTAGTCCCTTAAATCATAC 58.277 38.462 0.00 0.00 0.00 2.39
2138 2259 7.563924 TGTAGCAGTAGTCCCTTAAATCATACT 59.436 37.037 0.00 0.00 0.00 2.12
2139 2260 6.821388 AGCAGTAGTCCCTTAAATCATACTG 58.179 40.000 5.34 5.34 40.85 2.74
2146 2267 7.112779 AGTCCCTTAAATCATACTGTTTCAGG 58.887 38.462 1.90 0.00 35.51 3.86
2167 2288 6.976934 AGGGTTTGTAACACTGAATCAAAT 57.023 33.333 0.00 0.00 45.20 2.32
2264 2390 5.760743 TGTTGGAAGTCATGAAAACGATGTA 59.239 36.000 0.00 0.00 0.00 2.29
2284 2411 4.396790 TGTATATTGGTTCCTTTTCCGTGC 59.603 41.667 0.00 0.00 0.00 5.34
2296 2423 0.395862 TTCCGTGCACAAAAGGGGAA 60.396 50.000 18.64 16.60 0.00 3.97
2303 2430 2.284625 CAAAAGGGGAAGGGGGCC 60.285 66.667 0.00 0.00 0.00 5.80
2308 2435 4.143301 GGGGAAGGGGGCCATCAC 62.143 72.222 4.39 0.68 0.00 3.06
2310 2437 3.728373 GGAAGGGGGCCATCACGT 61.728 66.667 4.39 0.00 0.00 4.49
2321 2448 3.561503 GGCCATCACGTTTTACACTTTC 58.438 45.455 0.00 0.00 0.00 2.62
2323 2450 3.252458 GCCATCACGTTTTACACTTTCCT 59.748 43.478 0.00 0.00 0.00 3.36
2345 2472 0.517316 GAAAGCTACCAGGCAACACG 59.483 55.000 0.00 0.00 41.41 4.49
2352 2479 3.726517 CAGGCAACACGGGCTTCG 61.727 66.667 0.00 0.00 42.46 3.79
2369 2496 5.763204 GGGCTTCGGTATCAAGATCAAATAA 59.237 40.000 0.00 0.00 0.00 1.40
2374 2501 6.345298 TCGGTATCAAGATCAAATAACTGCA 58.655 36.000 0.00 0.00 0.00 4.41
2435 2562 4.184079 AGTGAAGCTCGTAACCGTTATT 57.816 40.909 0.00 0.00 35.01 1.40
2449 2577 8.642020 CGTAACCGTTATTAATCCTATAGTTGC 58.358 37.037 0.00 0.00 0.00 4.17
2454 2582 9.871238 CCGTTATTAATCCTATAGTTGCTGTAT 57.129 33.333 0.00 0.00 0.00 2.29
2465 2593 8.554528 CCTATAGTTGCTGTATCAAGACATTTG 58.445 37.037 0.00 0.00 0.00 2.32
2466 2594 7.928307 ATAGTTGCTGTATCAAGACATTTGT 57.072 32.000 0.00 0.00 0.00 2.83
2495 2623 5.529791 TCTGTGCTAGAACAGTTGTTAGTC 58.470 41.667 26.97 0.00 46.33 2.59
2502 2630 7.010023 GCTAGAACAGTTGTTAGTCGAATTTG 58.990 38.462 0.00 0.00 38.56 2.32
2505 2665 6.537301 AGAACAGTTGTTAGTCGAATTTGTCA 59.463 34.615 0.00 0.00 38.56 3.58
2537 2697 5.147330 TGTTATAATATGGAGACTGCCCG 57.853 43.478 0.00 0.00 0.00 6.13
2551 2711 1.519898 GCCCGCCAGCAATTCAATG 60.520 57.895 0.00 0.00 0.00 2.82
2576 2740 7.545265 TGTCTAATTTTGCTTGCATATGAAACC 59.455 33.333 6.97 0.00 0.00 3.27
2578 2742 8.093307 TCTAATTTTGCTTGCATATGAAACCAA 58.907 29.630 6.97 3.31 0.00 3.67
2587 2751 7.383300 GCTTGCATATGAAACCAATATTTCCTC 59.617 37.037 6.97 0.00 37.72 3.71
2596 2760 8.607713 TGAAACCAATATTTCCTCTACCAACTA 58.392 33.333 0.00 0.00 37.72 2.24
2633 2797 3.390135 TGTGAACATTTCAGAGGACGTC 58.610 45.455 7.13 7.13 41.01 4.34
2659 2823 6.331369 TGACTGGATGGTTTTTGAAGATTC 57.669 37.500 0.00 0.00 0.00 2.52
2663 2827 4.527816 TGGATGGTTTTTGAAGATTCCCAG 59.472 41.667 0.00 0.00 0.00 4.45
2676 2840 4.479993 CCCAGCTGGAAGGGCTCG 62.480 72.222 34.91 10.80 38.44 5.03
2688 2852 0.618458 AGGGCTCGCCTTTCATACAA 59.382 50.000 8.00 0.00 36.10 2.41
2701 2865 3.419264 TCATACAAATGAATGCACGGC 57.581 42.857 0.00 0.00 39.20 5.68
2712 2876 2.179018 GCACGGCGCAAATGTCAT 59.821 55.556 10.83 0.00 41.79 3.06
2714 2878 1.209898 CACGGCGCAAATGTCATGT 59.790 52.632 10.83 0.00 0.00 3.21
2743 2907 5.242171 TCATTATGCTTCATTATGCTGTGGG 59.758 40.000 2.07 0.00 32.88 4.61
2804 2968 6.205658 GGCAGTATTCAGAAATATGTTCTCCC 59.794 42.308 0.00 0.00 30.28 4.30
2805 2969 6.767902 GCAGTATTCAGAAATATGTTCTCCCA 59.232 38.462 0.00 0.00 30.28 4.37
2823 2987 2.046892 CCAGGGTTCAGTGGCTCG 60.047 66.667 0.00 0.00 0.00 5.03
2832 2996 0.250234 TCAGTGGCTCGGAAATGGAG 59.750 55.000 0.00 0.00 34.62 3.86
2868 3032 7.044798 ACAGTGGAATATTTCTGCTCTCTAAC 58.955 38.462 12.76 0.00 0.00 2.34
2871 3035 4.449405 GGAATATTTCTGCTCTCTAACGGC 59.551 45.833 0.00 0.00 0.00 5.68
2893 3057 2.758979 TCGGTGTTTGGCTTTGGTTTTA 59.241 40.909 0.00 0.00 0.00 1.52
2894 3058 3.385111 TCGGTGTTTGGCTTTGGTTTTAT 59.615 39.130 0.00 0.00 0.00 1.40
2897 3061 4.509970 GGTGTTTGGCTTTGGTTTTATCAC 59.490 41.667 0.00 0.00 0.00 3.06
2932 3096 2.103941 GAGAGCCCATCCTACCTTCTTG 59.896 54.545 0.00 0.00 0.00 3.02
2933 3097 0.548510 AGCCCATCCTACCTTCTTGC 59.451 55.000 0.00 0.00 0.00 4.01
2973 3137 0.881796 CTACTGTCGTCTGGACTGCA 59.118 55.000 0.00 0.00 45.52 4.41
3056 3220 2.745492 GCAGTCTGCAGGCTCCAC 60.745 66.667 20.28 7.36 44.26 4.02
3213 3377 0.529378 GCCAAAGCTTCAGTGATGGG 59.471 55.000 13.21 3.91 35.50 4.00
3219 3383 1.211457 AGCTTCAGTGATGGGATGACC 59.789 52.381 8.02 0.00 40.81 4.02
3239 3403 1.303236 TTGTGAGCCATTCCACCGG 60.303 57.895 0.00 0.00 32.61 5.28
3270 3434 7.587629 ACATGACACATACACTTCAAATCAAG 58.412 34.615 0.00 0.00 0.00 3.02
3291 3455 2.123589 TCCGGGGACATGATGTTGTAT 58.876 47.619 0.00 0.00 0.00 2.29
3349 3513 4.020396 CACTGCAGGATAATAGGCTGATCT 60.020 45.833 19.93 0.00 0.00 2.75
3358 3522 8.938883 AGGATAATAGGCTGATCTTTAACAAGA 58.061 33.333 0.00 0.00 43.45 3.02
3527 3691 3.661944 CCTTCTATATGCTGCAGAGTGG 58.338 50.000 20.43 8.54 0.00 4.00
3591 3755 2.203153 GACACGCCAACCCACTGT 60.203 61.111 0.00 0.00 0.00 3.55
3611 3775 5.867716 ACTGTAAACCGTACTCTATTTGCAG 59.132 40.000 16.76 16.76 45.02 4.41
3641 3805 1.440476 GATGCCAATGCCCTTCAGC 59.560 57.895 0.00 0.00 36.33 4.26
3750 3914 6.658391 GTGGAGTTGGATATATCGGTACTAGT 59.342 42.308 6.64 0.00 0.00 2.57
4341 4514 2.457813 TAATTGGCAGCATCCACCAT 57.542 45.000 0.00 0.00 35.50 3.55
4587 4760 2.163211 GCCTGAGAATTTCCTGCTTGAC 59.837 50.000 0.00 0.00 0.00 3.18
4857 5030 3.378399 GAAGCTGGAGGAGGGCGAC 62.378 68.421 0.00 0.00 0.00 5.19
4977 5150 2.659063 CCAGAGGCCGTCCATGTCA 61.659 63.158 0.00 0.00 33.74 3.58
5435 5612 4.705507 CAGCTTAGGACTCCTTGTGTACTA 59.294 45.833 1.94 0.00 34.61 1.82
5437 5614 5.778750 AGCTTAGGACTCCTTGTGTACTAAA 59.221 40.000 1.94 0.00 39.49 1.85
5483 5676 4.568072 AACCTGTGGCATAATCAGTGTA 57.432 40.909 0.00 0.00 0.00 2.90
5541 5843 9.314133 TGCTAGTATATATCCACTGTTTCAGAT 57.686 33.333 3.70 0.00 35.18 2.90
5649 5952 5.046910 ACTAATTTTCACCTGCATCAACG 57.953 39.130 0.00 0.00 0.00 4.10
5658 5961 1.664016 CCTGCATCAACGAAACTGCAC 60.664 52.381 0.00 0.00 39.54 4.57
5680 5983 6.568653 GCACAACTATTGAAGGGAAAGAGAAC 60.569 42.308 0.00 0.00 0.00 3.01
5740 6045 1.657751 GCCGATGCAGGAAAACTCCC 61.658 60.000 0.00 0.00 37.47 4.30
5846 6151 3.434984 GCAGCGAGAGAAAAGAAAGATGT 59.565 43.478 0.00 0.00 0.00 3.06
5849 6154 5.350914 CAGCGAGAGAAAAGAAAGATGTGAT 59.649 40.000 0.00 0.00 0.00 3.06
5911 6216 3.584250 CTGCGCCTGAAACACAGCG 62.584 63.158 4.18 0.00 44.52 5.18
5922 6227 2.974148 CACAGCGGCAACAGCAGA 60.974 61.111 1.45 0.00 38.34 4.26
5946 6251 0.403271 AGATCAAAGCACCTGCCTGT 59.597 50.000 0.00 0.00 43.38 4.00
5995 6300 9.440773 TGACCATGATATAGCAGAAAATGATAC 57.559 33.333 0.00 0.00 31.30 2.24
5997 6302 7.550551 ACCATGATATAGCAGAAAATGATACGG 59.449 37.037 0.00 0.00 31.30 4.02
5998 6303 7.765819 CCATGATATAGCAGAAAATGATACGGA 59.234 37.037 0.00 0.00 31.30 4.69
5999 6304 8.815189 CATGATATAGCAGAAAATGATACGGAG 58.185 37.037 0.00 0.00 31.30 4.63
6057 6362 3.743521 TCAGGTGAACAGGAAATCAGTG 58.256 45.455 0.00 0.00 0.00 3.66
6104 6409 2.066262 ACACAATTCCGCTGTTACTCG 58.934 47.619 0.00 0.00 0.00 4.18
6348 6653 2.216898 GGGATATCACAAGACAGCAGC 58.783 52.381 4.83 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 142 9.883142 GGGAAGAAGAGTATATTGATCTATTGG 57.117 37.037 0.00 0.00 0.00 3.16
436 441 1.228552 GCACCCACCAACCTCACAT 60.229 57.895 0.00 0.00 0.00 3.21
437 442 2.194597 GCACCCACCAACCTCACA 59.805 61.111 0.00 0.00 0.00 3.58
438 443 2.978010 CGCACCCACCAACCTCAC 60.978 66.667 0.00 0.00 0.00 3.51
439 444 4.263572 CCGCACCCACCAACCTCA 62.264 66.667 0.00 0.00 0.00 3.86
479 484 1.071071 CACTCACCCACCCGAGTAAAA 59.929 52.381 0.00 0.00 40.50 1.52
494 499 4.476297 TCCTATATTTACTCGGCCACTCA 58.524 43.478 2.24 0.00 0.00 3.41
495 500 4.523558 ACTCCTATATTTACTCGGCCACTC 59.476 45.833 2.24 0.00 0.00 3.51
496 501 4.481072 ACTCCTATATTTACTCGGCCACT 58.519 43.478 2.24 0.00 0.00 4.00
497 502 4.321824 GGACTCCTATATTTACTCGGCCAC 60.322 50.000 2.24 0.00 0.00 5.01
498 503 3.830755 GGACTCCTATATTTACTCGGCCA 59.169 47.826 2.24 0.00 0.00 5.36
501 506 4.082895 CCACGGACTCCTATATTTACTCGG 60.083 50.000 0.00 0.00 0.00 4.63
522 527 3.244422 ACAAATTCTACTTCTCGGCACCA 60.244 43.478 0.00 0.00 0.00 4.17
555 560 3.131046 ACCTAGTTGAACCCGTATAACCG 59.869 47.826 0.00 0.00 0.00 4.44
570 575 4.284178 TCTTCTATAACCGGCACCTAGTT 58.716 43.478 0.00 0.00 0.00 2.24
608 613 6.760770 GTGTGAGAGAAGGATTGATAAAGGAG 59.239 42.308 0.00 0.00 0.00 3.69
612 617 7.244886 TGAGTGTGAGAGAAGGATTGATAAA 57.755 36.000 0.00 0.00 0.00 1.40
613 618 6.857437 TGAGTGTGAGAGAAGGATTGATAA 57.143 37.500 0.00 0.00 0.00 1.75
689 768 4.846677 GTGTCGTATGTATAGCATCACTCG 59.153 45.833 0.00 0.00 38.94 4.18
751 830 4.262592 GGAGTAAAAAGTGGAACGGACCTA 60.263 45.833 2.17 0.00 45.86 3.08
754 833 2.810274 GGGAGTAAAAAGTGGAACGGAC 59.190 50.000 0.00 0.00 45.86 4.79
776 855 5.586243 AGCGAGGTAAACGTCAACTATAGTA 59.414 40.000 5.65 0.00 0.00 1.82
777 856 4.397417 AGCGAGGTAAACGTCAACTATAGT 59.603 41.667 0.00 0.00 0.00 2.12
778 857 4.918037 AGCGAGGTAAACGTCAACTATAG 58.082 43.478 0.00 0.00 0.00 1.31
779 858 4.970662 AGCGAGGTAAACGTCAACTATA 57.029 40.909 0.00 0.00 0.00 1.31
780 859 3.863142 AGCGAGGTAAACGTCAACTAT 57.137 42.857 0.00 0.00 0.00 2.12
797 876 0.093026 CGCGGTCAGAGTTTTAAGCG 59.907 55.000 0.00 0.00 40.37 4.68
802 881 0.884704 ATGCACGCGGTCAGAGTTTT 60.885 50.000 12.47 0.00 0.00 2.43
803 882 0.884704 AATGCACGCGGTCAGAGTTT 60.885 50.000 12.47 0.00 0.00 2.66
806 885 1.075542 TAAAATGCACGCGGTCAGAG 58.924 50.000 12.47 0.00 0.00 3.35
807 886 0.793861 GTAAAATGCACGCGGTCAGA 59.206 50.000 12.47 0.00 0.00 3.27
817 898 7.759489 AGTGTAAAATCTGGAGTAAAATGCA 57.241 32.000 0.00 0.00 0.00 3.96
864 945 3.692791 TCGTACATCTTGGAGATCGTG 57.307 47.619 0.00 0.00 31.32 4.35
865 946 4.713824 TTTCGTACATCTTGGAGATCGT 57.286 40.909 0.00 0.00 31.32 3.73
879 962 4.728534 TGCTGGTGCATTAAATTTCGTAC 58.271 39.130 0.00 0.00 45.31 3.67
895 978 1.538047 ATTGCGAGTGATTTGCTGGT 58.462 45.000 0.00 0.00 37.09 4.00
897 980 6.082338 GGATTATATTGCGAGTGATTTGCTG 58.918 40.000 0.00 0.00 37.09 4.41
908 991 6.018588 CACTTGTTTACCGGATTATATTGCGA 60.019 38.462 9.46 0.00 31.44 5.10
910 993 7.254227 TCACTTGTTTACCGGATTATATTGC 57.746 36.000 9.46 0.00 0.00 3.56
1003 1089 5.389520 TCTAGCTCGGTACTACTAGGAGTA 58.610 45.833 11.03 11.03 34.24 2.59
1004 1090 4.222336 TCTAGCTCGGTACTACTAGGAGT 58.778 47.826 13.42 13.42 34.24 3.85
1005 1091 4.523943 TCTCTAGCTCGGTACTACTAGGAG 59.476 50.000 0.00 0.00 34.24 3.69
1006 1092 4.478203 TCTCTAGCTCGGTACTACTAGGA 58.522 47.826 0.00 0.00 34.24 2.94
1007 1093 4.870123 TCTCTAGCTCGGTACTACTAGG 57.130 50.000 0.00 0.00 34.24 3.02
1008 1094 8.830201 TTATTTCTCTAGCTCGGTACTACTAG 57.170 38.462 0.00 0.00 34.66 2.57
1011 1097 7.701445 TGTTTATTTCTCTAGCTCGGTACTAC 58.299 38.462 0.00 0.00 0.00 2.73
1090 1176 0.758734 GATGGACATGGACGGATGGA 59.241 55.000 0.00 0.00 0.00 3.41
1091 1177 0.601046 CGATGGACATGGACGGATGG 60.601 60.000 0.00 0.00 0.00 3.51
1092 1178 0.389025 TCGATGGACATGGACGGATG 59.611 55.000 0.00 0.00 0.00 3.51
1093 1179 1.273606 GATCGATGGACATGGACGGAT 59.726 52.381 0.54 0.00 0.00 4.18
1094 1180 0.673985 GATCGATGGACATGGACGGA 59.326 55.000 0.54 0.00 0.00 4.69
1095 1181 0.664466 CGATCGATGGACATGGACGG 60.664 60.000 10.26 0.00 0.00 4.79
1096 1182 0.310854 TCGATCGATGGACATGGACG 59.689 55.000 15.15 0.00 0.00 4.79
1097 1183 2.230025 AGATCGATCGATGGACATGGAC 59.770 50.000 33.86 16.16 34.60 4.02
1098 1184 2.519013 AGATCGATCGATGGACATGGA 58.481 47.619 33.86 1.34 34.60 3.41
1099 1185 3.428180 GGTAGATCGATCGATGGACATGG 60.428 52.174 33.86 0.00 34.60 3.66
1100 1186 3.441922 AGGTAGATCGATCGATGGACATG 59.558 47.826 33.86 0.00 34.60 3.21
1101 1187 3.691575 AGGTAGATCGATCGATGGACAT 58.308 45.455 33.86 23.78 34.60 3.06
1102 1188 3.075148 GAGGTAGATCGATCGATGGACA 58.925 50.000 33.86 13.43 34.60 4.02
1110 1196 1.258676 GGGGTGGAGGTAGATCGATC 58.741 60.000 17.91 17.91 0.00 3.69
1122 1208 2.431454 CGGATGACATCGGGGTGGA 61.431 63.158 13.73 0.00 0.00 4.02
1148 1235 0.390492 GGGACGAATAACTACGGGGG 59.610 60.000 0.00 0.00 0.00 5.40
1181 1268 4.803908 GGTGGTAGCAGGCAGGGC 62.804 72.222 0.00 0.00 0.00 5.19
1182 1269 3.011517 AGGTGGTAGCAGGCAGGG 61.012 66.667 0.00 0.00 0.00 4.45
1228 1315 4.465446 TGGAGGAGGAGGAGGCGG 62.465 72.222 0.00 0.00 0.00 6.13
1280 1370 4.828296 GGGGAGGCGAGGACCGTA 62.828 72.222 0.00 0.00 41.15 4.02
1322 1412 0.603975 GTGGTCACCTCACCTGAAGC 60.604 60.000 0.00 0.00 37.34 3.86
1395 1487 1.049289 GCACGGATAGGGGAAGGAGT 61.049 60.000 0.00 0.00 0.00 3.85
1397 1489 1.002403 TGCACGGATAGGGGAAGGA 59.998 57.895 0.00 0.00 0.00 3.36
1414 1506 1.813513 ACCAGCAAGAAAGATCCGTG 58.186 50.000 0.00 0.00 0.00 4.94
1450 1542 3.662973 GCAAAGCGACGAAAGAAAGAGAG 60.663 47.826 0.00 0.00 0.00 3.20
1452 1544 2.565005 GCAAAGCGACGAAAGAAAGAG 58.435 47.619 0.00 0.00 0.00 2.85
1463 1555 1.082104 CAGAAACCGGCAAAGCGAC 60.082 57.895 0.00 0.00 0.00 5.19
1547 1646 0.673644 AGACGCCAAATTCGTGGGAG 60.674 55.000 0.00 0.00 40.59 4.30
1551 1650 1.154225 GCCAGACGCCAAATTCGTG 60.154 57.895 0.00 0.00 40.59 4.35
1572 1671 0.179086 TGAACGTTCACTGCAGAGCA 60.179 50.000 26.53 0.00 32.42 4.26
1580 1679 4.213482 GCCTAATTTCACTGAACGTTCACT 59.787 41.667 26.53 15.25 32.90 3.41
1581 1680 4.213482 AGCCTAATTTCACTGAACGTTCAC 59.787 41.667 26.53 12.25 32.90 3.18
1582 1681 4.385825 AGCCTAATTTCACTGAACGTTCA 58.614 39.130 28.07 28.07 35.57 3.18
1605 1704 6.038825 TCCTCGTTTGTTTCTTGCTTAATTCA 59.961 34.615 0.00 0.00 0.00 2.57
1621 1720 7.193595 ACTGACAAAGTTAAAATCCTCGTTTG 58.806 34.615 0.00 0.00 34.57 2.93
1622 1721 7.329588 ACTGACAAAGTTAAAATCCTCGTTT 57.670 32.000 0.00 0.00 34.57 3.60
1623 1722 6.937436 ACTGACAAAGTTAAAATCCTCGTT 57.063 33.333 0.00 0.00 34.57 3.85
1636 1736 8.691661 ATACATCCAAACTAAACTGACAAAGT 57.308 30.769 0.00 0.00 42.60 2.66
1637 1737 9.612620 GAATACATCCAAACTAAACTGACAAAG 57.387 33.333 0.00 0.00 0.00 2.77
1639 1739 7.442969 ACGAATACATCCAAACTAAACTGACAA 59.557 33.333 0.00 0.00 0.00 3.18
1640 1740 6.932400 ACGAATACATCCAAACTAAACTGACA 59.068 34.615 0.00 0.00 0.00 3.58
1641 1741 7.360575 ACGAATACATCCAAACTAAACTGAC 57.639 36.000 0.00 0.00 0.00 3.51
1642 1742 7.972832 AACGAATACATCCAAACTAAACTGA 57.027 32.000 0.00 0.00 0.00 3.41
1643 1743 7.477422 CGAAACGAATACATCCAAACTAAACTG 59.523 37.037 0.00 0.00 0.00 3.16
1644 1744 7.172019 ACGAAACGAATACATCCAAACTAAACT 59.828 33.333 0.00 0.00 0.00 2.66
1645 1745 7.293018 ACGAAACGAATACATCCAAACTAAAC 58.707 34.615 0.00 0.00 0.00 2.01
1660 1761 3.243234 TGAAACATGCCAACGAAACGAAT 60.243 39.130 0.00 0.00 0.00 3.34
1661 1762 2.097629 TGAAACATGCCAACGAAACGAA 59.902 40.909 0.00 0.00 0.00 3.85
1662 1763 1.671328 TGAAACATGCCAACGAAACGA 59.329 42.857 0.00 0.00 0.00 3.85
1663 1764 2.043411 CTGAAACATGCCAACGAAACG 58.957 47.619 0.00 0.00 0.00 3.60
1664 1765 1.786579 GCTGAAACATGCCAACGAAAC 59.213 47.619 0.00 0.00 0.00 2.78
1665 1766 1.680735 AGCTGAAACATGCCAACGAAA 59.319 42.857 0.00 0.00 0.00 3.46
1666 1767 1.001487 CAGCTGAAACATGCCAACGAA 60.001 47.619 8.42 0.00 0.00 3.85
1678 1779 2.350522 GAGAATTCGAGGCAGCTGAAA 58.649 47.619 20.43 3.13 0.00 2.69
1701 1802 7.980662 CCATTAATTCTACACATTTCCATTGCA 59.019 33.333 0.00 0.00 0.00 4.08
1771 1872 9.654663 AGTAGTTCTAATTAATCTGGAACACAC 57.345 33.333 20.18 17.56 38.78 3.82
1807 1914 9.069082 TCCTTTTTCCATTTTTGTATTCGTCTA 57.931 29.630 0.00 0.00 0.00 2.59
1881 1990 1.172180 CGCAAGTTGGAGAAAGGCCA 61.172 55.000 5.01 0.00 0.00 5.36
1899 2008 3.545633 GAAAGCACAGCAGTTAAGAACG 58.454 45.455 0.00 0.00 36.23 3.95
1938 2052 5.048083 GGATCCTGCAGTCAAAAACATACAA 60.048 40.000 13.81 0.00 0.00 2.41
1951 2065 1.289231 TCCTAGACAGGATCCTGCAGT 59.711 52.381 36.78 24.59 46.58 4.40
2002 2116 2.495270 TGCTGTTGGTTTCTTCAAAGCA 59.505 40.909 0.00 0.00 46.01 3.91
2084 2198 8.627208 AATAAATCATGATACTGGTAGCAAGG 57.373 34.615 9.04 0.00 34.93 3.61
2117 2238 9.099454 GAAACAGTATGATTTAAGGGACTACTG 57.901 37.037 0.00 0.00 35.46 2.74
2137 2258 4.638421 TCAGTGTTACAAACCCTGAAACAG 59.362 41.667 3.00 0.00 41.80 3.16
2138 2259 4.590918 TCAGTGTTACAAACCCTGAAACA 58.409 39.130 3.00 0.00 41.80 2.83
2146 2267 7.379529 CACTCATTTGATTCAGTGTTACAAACC 59.620 37.037 11.17 0.00 34.21 3.27
2167 2288 1.674359 ACAAACGTTGATGGCACTCA 58.326 45.000 0.00 0.00 0.00 3.41
2264 2390 3.192633 GTGCACGGAAAAGGAACCAATAT 59.807 43.478 0.00 0.00 0.00 1.28
2284 2411 1.913262 GCCCCCTTCCCCTTTTGTG 60.913 63.158 0.00 0.00 0.00 3.33
2296 2423 0.323087 GTAAAACGTGATGGCCCCCT 60.323 55.000 0.00 0.00 0.00 4.79
2303 2430 5.465390 TCTGAGGAAAGTGTAAAACGTGATG 59.535 40.000 0.00 0.00 0.00 3.07
2321 2448 0.615331 TGCCTGGTAGCTTTCTGAGG 59.385 55.000 0.00 0.00 0.00 3.86
2323 2450 1.419762 TGTTGCCTGGTAGCTTTCTGA 59.580 47.619 0.00 0.00 0.00 3.27
2331 2458 2.746277 GCCCGTGTTGCCTGGTAG 60.746 66.667 0.00 0.00 0.00 3.18
2345 2472 2.910688 TGATCTTGATACCGAAGCCC 57.089 50.000 0.00 0.00 0.00 5.19
2352 2479 9.884465 GTAATGCAGTTATTTGATCTTGATACC 57.116 33.333 0.00 0.00 0.00 2.73
2412 2539 2.521105 ACGGTTACGAGCTTCACTTT 57.479 45.000 0.00 0.00 44.60 2.66
2414 2541 3.863142 ATAACGGTTACGAGCTTCACT 57.137 42.857 2.10 0.00 44.60 3.41
2416 2543 5.750067 GGATTAATAACGGTTACGAGCTTCA 59.250 40.000 2.10 0.00 44.60 3.02
2418 2545 5.910614 AGGATTAATAACGGTTACGAGCTT 58.089 37.500 2.10 0.00 44.60 3.74
2435 2562 9.143155 TGTCTTGATACAGCAACTATAGGATTA 57.857 33.333 4.43 0.00 0.00 1.75
2465 2593 4.310769 ACTGTTCTAGCACAGATGACAAC 58.689 43.478 26.32 3.40 46.29 3.32
2466 2594 4.607293 ACTGTTCTAGCACAGATGACAA 57.393 40.909 26.32 0.00 46.29 3.18
2472 2600 5.529791 GACTAACAACTGTTCTAGCACAGA 58.470 41.667 26.32 5.27 46.29 3.41
2495 2623 3.498397 ACAGCTGTAGGTTGACAAATTCG 59.502 43.478 20.16 0.00 0.00 3.34
2502 2630 8.148351 TCCATATTATAACAGCTGTAGGTTGAC 58.852 37.037 22.01 0.00 0.00 3.18
2505 2665 8.368668 GTCTCCATATTATAACAGCTGTAGGTT 58.631 37.037 22.01 6.93 0.00 3.50
2537 2697 6.673796 GCAAAATTAGACATTGAATTGCTGGC 60.674 38.462 0.00 0.00 38.96 4.85
2551 2711 7.545265 TGGTTTCATATGCAAGCAAAATTAGAC 59.455 33.333 15.98 0.00 0.00 2.59
2614 2778 3.744238 TGACGTCCTCTGAAATGTTCA 57.256 42.857 14.12 0.00 38.17 3.18
2633 2797 6.088016 TCTTCAAAAACCATCCAGTCATTG 57.912 37.500 0.00 0.00 0.00 2.82
2659 2823 4.479993 CGAGCCCTTCCAGCTGGG 62.480 72.222 32.23 17.72 41.75 4.45
2671 2835 2.682856 TCATTTGTATGAAAGGCGAGCC 59.317 45.455 5.89 5.89 37.83 4.70
2701 2865 4.611310 ATGAAGAGACATGACATTTGCG 57.389 40.909 0.00 0.00 0.00 4.85
2707 2871 6.408869 TGAAGCATAATGAAGAGACATGACA 58.591 36.000 0.00 0.00 0.00 3.58
2712 2876 7.718314 AGCATAATGAAGCATAATGAAGAGACA 59.282 33.333 0.00 0.00 0.00 3.41
2714 2878 7.718314 ACAGCATAATGAAGCATAATGAAGAGA 59.282 33.333 0.00 0.00 0.00 3.10
2743 2907 1.607148 GAGGTTGGGTAACACAAGCAC 59.393 52.381 16.45 8.10 43.32 4.40
2771 2935 6.016527 ATATTTCTGAATACTGCCACTGCATG 60.017 38.462 0.00 0.00 36.91 4.06
2778 2942 6.767902 GGAGAACATATTTCTGAATACTGCCA 59.232 38.462 5.29 0.00 30.87 4.92
2804 2968 1.302832 GAGCCACTGAACCCTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
2805 2969 2.883828 CGAGCCACTGAACCCTGGT 61.884 63.158 0.00 0.00 0.00 4.00
2823 2987 7.201732 CCACTGTTATCAATGTACTCCATTTCC 60.202 40.741 0.00 0.00 41.93 3.13
2846 3010 5.463724 CCGTTAGAGAGCAGAAATATTCCAC 59.536 44.000 0.00 0.00 0.00 4.02
2868 3032 2.551912 AAAGCCAAACACCGAGCCG 61.552 57.895 0.00 0.00 0.00 5.52
2871 3035 0.744281 AACCAAAGCCAAACACCGAG 59.256 50.000 0.00 0.00 0.00 4.63
2893 3057 4.214310 CTCTCTGATAGACCACTGGTGAT 58.786 47.826 5.10 0.00 35.25 3.06
2894 3058 3.625853 CTCTCTGATAGACCACTGGTGA 58.374 50.000 5.10 0.00 35.25 4.02
2897 3061 1.686052 GGCTCTCTGATAGACCACTGG 59.314 57.143 0.00 0.00 0.00 4.00
2902 3066 1.899142 GGATGGGCTCTCTGATAGACC 59.101 57.143 7.96 7.96 43.12 3.85
2905 3069 3.096092 GGTAGGATGGGCTCTCTGATAG 58.904 54.545 0.00 0.00 0.00 2.08
2906 3070 2.724672 AGGTAGGATGGGCTCTCTGATA 59.275 50.000 0.00 0.00 0.00 2.15
2907 3071 1.507300 AGGTAGGATGGGCTCTCTGAT 59.493 52.381 0.00 0.00 0.00 2.90
2917 3081 2.636830 CACTGCAAGAAGGTAGGATGG 58.363 52.381 0.00 0.00 37.43 3.51
2933 3097 3.569210 TGCCCAGGTGGACCACTG 61.569 66.667 23.72 18.09 38.89 3.66
2958 3122 1.511850 CATTTGCAGTCCAGACGACA 58.488 50.000 0.00 0.00 44.66 4.35
2962 3126 3.077359 AGTTAGCATTTGCAGTCCAGAC 58.923 45.455 5.20 0.00 45.16 3.51
2973 3137 3.437049 GCGAAACAGGAGAGTTAGCATTT 59.563 43.478 0.00 0.00 36.18 2.32
3056 3220 3.387374 AGAGATATTGGCAGTCCAGACAG 59.613 47.826 0.00 0.00 44.53 3.51
3086 3250 1.153208 AGCAGCTGCATAGAGGCAC 60.153 57.895 38.24 7.01 45.16 5.01
3087 3251 1.153229 CAGCAGCTGCATAGAGGCA 60.153 57.895 38.24 0.00 45.16 4.75
3088 3252 1.892862 CCAGCAGCTGCATAGAGGC 60.893 63.158 38.24 11.06 45.16 4.70
3151 3315 2.928801 TAGCTGAAACTCTGCCACAA 57.071 45.000 0.00 0.00 41.50 3.33
3213 3377 2.019984 GAATGGCTCACAAGGGTCATC 58.980 52.381 0.00 0.00 0.00 2.92
3219 3383 1.308069 CGGTGGAATGGCTCACAAGG 61.308 60.000 0.00 0.00 35.74 3.61
3239 3403 5.696270 TGAAGTGTATGTGTCATGTTCTGTC 59.304 40.000 0.00 0.00 0.00 3.51
3270 3434 0.035439 ACAACATCATGTCCCCGGAC 60.035 55.000 0.73 6.95 44.77 4.79
3349 3513 4.782019 AGATTGCGCCATTCTTGTTAAA 57.218 36.364 4.18 0.00 0.00 1.52
3358 3522 1.303309 GCAGAGTAGATTGCGCCATT 58.697 50.000 4.18 0.00 0.00 3.16
3471 3635 0.176680 CACCGAGGACAGCAGCTAAT 59.823 55.000 0.00 0.00 0.00 1.73
3527 3691 2.620585 GGCAGATTAGTCTTGCCATTCC 59.379 50.000 17.72 0.00 42.87 3.01
3591 3755 7.031372 CACTACTGCAAATAGAGTACGGTTTA 58.969 38.462 10.84 0.00 0.00 2.01
3611 3775 0.618458 TTGGCATCCTGTCCCACTAC 59.382 55.000 0.00 0.00 0.00 2.73
3641 3805 0.391793 GTTTGGAGAAGAGCCGAGGG 60.392 60.000 0.00 0.00 0.00 4.30
3651 3815 1.142870 CCAGGGTCACAGTTTGGAGAA 59.857 52.381 0.00 0.00 0.00 2.87
3750 3914 1.429930 TAGGCACAGGTGAGGTGAAA 58.570 50.000 3.10 0.00 38.54 2.69
4107 4280 4.022416 GTCTGCAGATATCCATCGTCTTCT 60.022 45.833 21.47 0.00 36.20 2.85
4341 4514 6.371278 ACCTCGGAGTTTAACTAGATGGATA 58.629 40.000 16.70 0.00 0.00 2.59
4857 5030 0.867753 CGTCAAGGATCTCGCGAAGG 60.868 60.000 11.33 0.00 0.00 3.46
4977 5150 0.036010 CGAGCATCTGGACCACCTTT 60.036 55.000 0.00 0.00 37.04 3.11
5459 5636 5.321102 ACACTGATTATGCCACAGGTTTAA 58.679 37.500 0.00 0.00 36.17 1.52
5631 5934 4.037923 AGTTTCGTTGATGCAGGTGAAAAT 59.962 37.500 0.00 0.00 0.00 1.82
5649 5952 4.518970 TCCCTTCAATAGTTGTGCAGTTTC 59.481 41.667 0.00 0.00 0.00 2.78
5658 5961 5.390991 GCGTTCTCTTTCCCTTCAATAGTTG 60.391 44.000 0.00 0.00 0.00 3.16
5680 5983 2.287608 GGAACTGGAAGAAAACCAAGCG 60.288 50.000 0.00 0.00 36.95 4.68
5833 6138 9.741647 AAAGAAGTTCATCACATCTTTCTTTTC 57.258 29.630 5.50 0.00 46.00 2.29
5846 6151 2.108075 TGGCCCTGAAAGAAGTTCATCA 59.892 45.455 0.00 8.25 45.27 3.07
5849 6154 2.517959 CATGGCCCTGAAAGAAGTTCA 58.482 47.619 0.97 0.00 44.20 3.18
5911 6216 0.815734 ATCTGCATTCTGCTGTTGCC 59.184 50.000 14.84 3.08 45.31 4.52
5995 6300 7.079182 TGGCAAATGTTTAGTTAATACTCCG 57.921 36.000 0.00 0.00 35.78 4.63
5997 6302 8.903820 AGGATGGCAAATGTTTAGTTAATACTC 58.096 33.333 0.00 0.00 35.78 2.59
5998 6303 8.686334 CAGGATGGCAAATGTTTAGTTAATACT 58.314 33.333 0.00 0.00 38.44 2.12
5999 6304 7.435192 GCAGGATGGCAAATGTTTAGTTAATAC 59.565 37.037 0.00 0.00 35.86 1.89
6000 6305 7.488322 GCAGGATGGCAAATGTTTAGTTAATA 58.512 34.615 0.00 0.00 35.86 0.98
6001 6306 6.340522 GCAGGATGGCAAATGTTTAGTTAAT 58.659 36.000 0.00 0.00 35.86 1.40
6002 6307 5.621104 CGCAGGATGGCAAATGTTTAGTTAA 60.621 40.000 0.00 0.00 35.86 2.01
6003 6308 4.142491 CGCAGGATGGCAAATGTTTAGTTA 60.142 41.667 0.00 0.00 35.86 2.24
6057 6362 6.207417 ACATAATAGGAAATGCTACACATGCC 59.793 38.462 0.00 0.00 39.60 4.40
6208 6513 4.200092 GGAAGGACAGGCTAAATCGATTT 58.800 43.478 25.48 25.48 0.00 2.17
6348 6653 3.133464 ACGGAATGCGTGCATGGG 61.133 61.111 8.30 3.56 36.68 4.00


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

AutoCloner maintained by Alex Coulton.