Multiple sequence alignment - TraesCS7D01G153400

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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 TraesCS7D01G153400 chr7D 100.000 2819 0 0 1 2819 101669415 101672233 0.000000e+00 5206.0
1 TraesCS7D01G153400 chr7D 89.349 169 6 3 1581 1743 360553809 360553971 4.760000e-48 202.0
2 TraesCS7D01G153400 chr7D 93.103 58 4 0 2258 2315 101671544 101671601 5.000000e-13 86.1
3 TraesCS7D01G153400 chr7D 93.103 58 4 0 2130 2187 101671672 101671729 5.000000e-13 86.1
4 TraesCS7D01G153400 chr7D 97.059 34 1 0 2069 2102 91104874 91104907 1.090000e-04 58.4
5 TraesCS7D01G153400 chr7B 82.648 1677 148 43 2 1579 58873408 58875040 0.000000e+00 1352.0
6 TraesCS7D01G153400 chr7B 88.475 295 27 7 1812 2103 58875419 58875709 1.610000e-92 350.0
7 TraesCS7D01G153400 chr7B 89.011 182 17 3 2306 2484 58875821 58876002 3.660000e-54 222.0
8 TraesCS7D01G153400 chr7B 86.517 178 15 6 1576 1744 478480054 478480231 1.330000e-43 187.0
9 TraesCS7D01G153400 chr7A 84.682 1273 78 41 378 1582 105401226 105402449 0.000000e+00 1162.0
10 TraesCS7D01G153400 chr7A 92.750 400 17 2 2390 2788 105406893 105407281 4.080000e-158 568.0
11 TraesCS7D01G153400 chr7A 86.686 353 37 9 1754 2103 105402715 105403060 1.580000e-102 383.0
12 TraesCS7D01G153400 chr7A 81.132 371 35 16 485 832 105382726 105383084 5.990000e-67 265.0
13 TraesCS7D01G153400 chr7A 97.297 37 1 0 2064 2100 612363956 612363992 2.340000e-06 63.9
14 TraesCS7D01G153400 chr7A 97.059 34 1 0 2070 2103 684935961 684935994 1.090000e-04 58.4
15 TraesCS7D01G153400 chr2B 78.075 374 71 7 114 484 659729916 659730281 2.830000e-55 226.0
16 TraesCS7D01G153400 chr2B 76.812 345 63 13 106 441 673610702 673610366 8.020000e-41 178.0
17 TraesCS7D01G153400 chr2B 97.059 34 1 0 2070 2103 28351900 28351867 1.090000e-04 58.4
18 TraesCS7D01G153400 chr4D 90.123 162 4 4 1587 1742 2070809 2070964 1.710000e-47 200.0
19 TraesCS7D01G153400 chr4D 100.000 31 0 0 2074 2104 363578335 363578305 1.090000e-04 58.4
20 TraesCS7D01G153400 chr5D 78.730 315 53 11 130 441 363885002 363885305 6.160000e-47 198.0
21 TraesCS7D01G153400 chr4B 78.859 298 58 5 116 410 32262179 32262474 2.220000e-46 196.0
22 TraesCS7D01G153400 chr4B 100.000 28 0 0 1093 1120 641571098 641571071 5.000000e-03 52.8
23 TraesCS7D01G153400 chr1A 88.372 172 8 2 1577 1742 282055923 282056088 2.220000e-46 196.0
24 TraesCS7D01G153400 chr6D 77.955 313 65 3 130 441 471484110 471483801 2.870000e-45 193.0
25 TraesCS7D01G153400 chr6D 77.019 322 66 8 121 438 414037363 414037680 8.020000e-41 178.0
26 TraesCS7D01G153400 chr6B 88.166 169 8 6 1581 1743 601199595 601199433 1.030000e-44 191.0
27 TraesCS7D01G153400 chr3D 88.166 169 9 3 1579 1742 397162708 397162546 1.030000e-44 191.0
28 TraesCS7D01G153400 chr3D 77.287 317 71 1 114 429 606746498 606746814 4.800000e-43 185.0
29 TraesCS7D01G153400 chr3D 94.872 39 1 1 2063 2100 325515645 325515683 3.030000e-05 60.2
30 TraesCS7D01G153400 chr3D 97.059 34 1 0 2070 2103 132162990 132163023 1.090000e-04 58.4
31 TraesCS7D01G153400 chr3A 87.791 172 9 5 1577 1742 151465469 151465634 1.030000e-44 191.0
32 TraesCS7D01G153400 chr3A 77.987 318 60 9 130 441 727002302 727002615 1.030000e-44 191.0
33 TraesCS7D01G153400 chr5B 86.592 179 12 7 1576 1749 199658107 199658278 1.330000e-43 187.0
34 TraesCS7D01G153400 chr2D 87.135 171 11 3 1580 1745 600300695 600300531 1.720000e-42 183.0
35 TraesCS7D01G153400 chr5A 76.972 317 70 3 127 441 636287614 636287929 8.020000e-41 178.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G153400 chr7D 101669415 101672233 2818 False 1792.733333 5206 95.402000 1 2819 3 chr7D.!!$F3 2818
1 TraesCS7D01G153400 chr7B 58873408 58876002 2594 False 641.333333 1352 86.711333 2 2484 3 chr7B.!!$F2 2482
2 TraesCS7D01G153400 chr7A 105401226 105407281 6055 False 704.333333 1162 88.039333 378 2788 3 chr7A.!!$F4 2410

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
642 707 0.027979 TCGTACGCGTATTTCCGGAG 59.972 55.0 23.56 6.89 39.49 4.63 F
705 770 0.108662 TGTGACGCAGATGTAGGCAG 60.109 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1648 1.135575 GCTGCAAACATACTCCTGCAC 60.136 52.381 0.00 0.0 39.77 4.57 R
2688 6774 0.866427 GGTGAGATCAGCATGCATCG 59.134 55.000 21.98 8.0 43.34 3.84 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
26 27 2.298729 TGGGCCAGCAATTCAAAAGTAC 59.701 45.455 0.00 0.00 0.00 2.73
29 30 3.578688 GCCAGCAATTCAAAAGTACTGG 58.421 45.455 0.00 0.00 44.80 4.00
33 34 2.989166 GCAATTCAAAAGTACTGGCAGC 59.011 45.455 15.89 0.00 0.00 5.25
37 38 6.389091 CAATTCAAAAGTACTGGCAGCAATA 58.611 36.000 15.89 0.00 0.00 1.90
47 48 3.392285 ACTGGCAGCAATAGGATGTATGA 59.608 43.478 15.89 0.00 34.68 2.15
62 63 7.782049 AGGATGTATGAAGTCGTAAATCAAGA 58.218 34.615 11.24 0.00 34.97 3.02
64 65 7.707035 GGATGTATGAAGTCGTAAATCAAGACT 59.293 37.037 11.24 0.00 46.41 3.24
76 77 9.764363 TCGTAAATCAAGACTATATTGATGCTT 57.236 29.630 2.20 0.00 44.57 3.91
123 124 5.665360 TCCTTCTTTTGGGGAACTTTTGATT 59.335 36.000 0.00 0.00 0.00 2.57
163 164 9.906660 TCATGGTATTTTAATGAACACAAGAAC 57.093 29.630 0.00 0.00 0.00 3.01
180 181 9.744468 ACACAAGAACTAACAAAAATTGTATCC 57.256 29.630 0.00 0.00 44.59 2.59
181 182 9.743057 CACAAGAACTAACAAAAATTGTATCCA 57.257 29.630 0.00 0.00 44.59 3.41
182 183 9.965824 ACAAGAACTAACAAAAATTGTATCCAG 57.034 29.630 0.00 0.00 44.59 3.86
186 187 9.788960 GAACTAACAAAAATTGTATCCAGATCC 57.211 33.333 0.00 0.00 44.59 3.36
187 188 7.985476 ACTAACAAAAATTGTATCCAGATCCG 58.015 34.615 0.00 0.00 44.59 4.18
188 189 6.834168 AACAAAAATTGTATCCAGATCCGT 57.166 33.333 0.00 0.00 44.59 4.69
189 190 7.931578 AACAAAAATTGTATCCAGATCCGTA 57.068 32.000 0.00 0.00 44.59 4.02
190 191 7.553881 ACAAAAATTGTATCCAGATCCGTAG 57.446 36.000 0.00 0.00 43.27 3.51
192 193 7.280205 ACAAAAATTGTATCCAGATCCGTAGAC 59.720 37.037 0.00 0.00 43.27 2.59
193 194 5.470047 AATTGTATCCAGATCCGTAGACC 57.530 43.478 0.00 0.00 0.00 3.85
194 195 3.588210 TGTATCCAGATCCGTAGACCA 57.412 47.619 0.00 0.00 0.00 4.02
195 196 3.220110 TGTATCCAGATCCGTAGACCAC 58.780 50.000 0.00 0.00 0.00 4.16
196 197 1.705873 ATCCAGATCCGTAGACCACC 58.294 55.000 0.00 0.00 0.00 4.61
198 199 1.848388 TCCAGATCCGTAGACCACCTA 59.152 52.381 0.00 0.00 0.00 3.08
199 200 2.158652 TCCAGATCCGTAGACCACCTAG 60.159 54.545 0.00 0.00 0.00 3.02
200 201 2.423088 CCAGATCCGTAGACCACCTAGT 60.423 54.545 0.00 0.00 0.00 2.57
202 203 2.508716 AGATCCGTAGACCACCTAGTGA 59.491 50.000 0.00 0.00 35.23 3.41
203 204 2.119801 TCCGTAGACCACCTAGTGAC 57.880 55.000 0.00 0.00 35.23 3.67
204 205 0.731417 CCGTAGACCACCTAGTGACG 59.269 60.000 0.00 0.00 35.23 4.35
205 206 1.676916 CCGTAGACCACCTAGTGACGA 60.677 57.143 7.89 0.00 33.83 4.20
206 207 1.396301 CGTAGACCACCTAGTGACGAC 59.604 57.143 0.00 0.00 33.83 4.34
213 216 2.163815 CCACCTAGTGACGACTACAAGG 59.836 54.545 0.00 0.00 35.23 3.61
215 218 3.080319 ACCTAGTGACGACTACAAGGAC 58.920 50.000 0.00 0.00 31.92 3.85
217 220 4.019860 ACCTAGTGACGACTACAAGGACTA 60.020 45.833 0.00 0.00 31.92 2.59
218 221 4.571580 CCTAGTGACGACTACAAGGACTAG 59.428 50.000 0.00 0.00 29.71 2.57
230 233 1.064458 GGACTAGAGCGAGCCGAAC 59.936 63.158 0.00 0.00 0.00 3.95
231 234 1.297745 GACTAGAGCGAGCCGAACG 60.298 63.158 0.00 0.00 0.00 3.95
253 257 1.515020 GCAGCTGTCATCGTCCTCT 59.485 57.895 16.64 0.00 0.00 3.69
255 259 0.813821 CAGCTGTCATCGTCCTCTGA 59.186 55.000 5.25 0.00 0.00 3.27
259 263 2.417924 GCTGTCATCGTCCTCTGATGTT 60.418 50.000 3.21 0.00 42.96 2.71
264 268 1.924731 TCGTCCTCTGATGTTGGAGT 58.075 50.000 0.00 0.00 0.00 3.85
268 272 2.303022 GTCCTCTGATGTTGGAGTTGGA 59.697 50.000 0.00 0.00 0.00 3.53
271 275 3.332919 CTCTGATGTTGGAGTTGGACAG 58.667 50.000 0.00 0.00 0.00 3.51
274 278 3.997021 CTGATGTTGGAGTTGGACAGTAC 59.003 47.826 0.00 0.00 0.00 2.73
275 279 3.646162 TGATGTTGGAGTTGGACAGTACT 59.354 43.478 0.00 0.00 0.00 2.73
278 282 2.543777 TGGAGTTGGACAGTACTTGC 57.456 50.000 0.00 0.00 0.00 4.01
314 318 2.632987 AAAGTCGTTGTGCTAAGGGT 57.367 45.000 0.00 0.00 0.00 4.34
316 320 0.320697 AGTCGTTGTGCTAAGGGTCC 59.679 55.000 0.00 0.00 0.00 4.46
319 323 1.086696 CGTTGTGCTAAGGGTCCATG 58.913 55.000 0.00 0.00 0.00 3.66
325 329 1.998530 CTAAGGGTCCATGGCACCA 59.001 57.895 25.45 11.44 35.35 4.17
344 348 0.675633 AATGCACCAGAACAGCAACC 59.324 50.000 0.00 0.00 42.15 3.77
346 350 1.891919 GCACCAGAACAGCAACCGA 60.892 57.895 0.00 0.00 0.00 4.69
349 353 1.594293 CCAGAACAGCAACCGACGT 60.594 57.895 0.00 0.00 0.00 4.34
351 355 0.874175 CAGAACAGCAACCGACGTCA 60.874 55.000 17.16 0.00 0.00 4.35
431 435 3.613193 CGAATACCGGATCCGAGCAAATA 60.613 47.826 35.42 16.29 42.83 1.40
434 441 1.416401 ACCGGATCCGAGCAAATACAT 59.584 47.619 35.42 4.20 42.83 2.29
449 456 5.048083 GCAAATACATCAAAGAGAACCACCA 60.048 40.000 0.00 0.00 0.00 4.17
484 491 0.968901 ATTCGCCGGAGACACACCTA 60.969 55.000 7.66 0.00 0.00 3.08
557 589 6.846283 GCGTGCAGATGACACTATTAAATTAC 59.154 38.462 0.00 0.00 35.84 1.89
614 654 2.794103 ACATCAAGCCTGCACATGTTA 58.206 42.857 0.00 0.00 0.00 2.41
642 707 0.027979 TCGTACGCGTATTTCCGGAG 59.972 55.000 23.56 6.89 39.49 4.63
663 728 9.341899 CCGGAGTTTTGAAGAATTAACATTTAG 57.658 33.333 0.00 0.00 0.00 1.85
705 770 0.108662 TGTGACGCAGATGTAGGCAG 60.109 55.000 0.00 0.00 0.00 4.85
719 784 2.334946 GGCAGCAGCAATTCGTCCA 61.335 57.895 2.65 0.00 44.61 4.02
735 805 0.250467 TCCACAAGGAAGCAGAGCAC 60.250 55.000 0.00 0.00 42.23 4.40
755 825 2.003301 CTTCCGCTAGCAAGAAGGTTC 58.997 52.381 26.16 0.00 34.63 3.62
756 826 0.108804 TCCGCTAGCAAGAAGGTTCG 60.109 55.000 16.45 0.00 0.00 3.95
757 827 0.108804 CCGCTAGCAAGAAGGTTCGA 60.109 55.000 16.45 0.00 0.00 3.71
758 828 0.992802 CGCTAGCAAGAAGGTTCGAC 59.007 55.000 16.45 0.00 0.00 4.20
759 829 1.668919 CGCTAGCAAGAAGGTTCGACA 60.669 52.381 16.45 0.00 0.00 4.35
760 830 1.727335 GCTAGCAAGAAGGTTCGACAC 59.273 52.381 10.63 0.00 0.00 3.67
761 831 2.610727 GCTAGCAAGAAGGTTCGACACT 60.611 50.000 10.63 0.00 0.00 3.55
831 901 0.399075 CCTACCTTTTCCACCACGGT 59.601 55.000 0.00 0.00 35.57 4.83
832 902 1.609841 CCTACCTTTTCCACCACGGTC 60.610 57.143 0.00 0.00 35.57 4.79
834 904 2.613506 CCTTTTCCACCACGGTCGC 61.614 63.158 0.00 0.00 35.57 5.19
895 965 1.801332 CCAGGTAGTCGTCAGTCCG 59.199 63.158 0.00 0.00 0.00 4.79
1014 1114 4.978099 ACTAACCCATCATCATCATCCAC 58.022 43.478 0.00 0.00 0.00 4.02
1018 1118 2.042569 CCCATCATCATCATCCACCCAT 59.957 50.000 0.00 0.00 0.00 4.00
1021 1121 2.709966 TCATCATCATCCACCCATCCT 58.290 47.619 0.00 0.00 0.00 3.24
1105 1209 1.203994 GCAATGGAGAGCAACAGCAAT 59.796 47.619 0.00 0.00 0.00 3.56
1108 1215 4.418392 CAATGGAGAGCAACAGCAATAAC 58.582 43.478 0.00 0.00 0.00 1.89
1120 1227 6.468484 CAACAGCAATAACAACAACAACAAG 58.532 36.000 0.00 0.00 0.00 3.16
1132 1239 1.301401 CAACAAGGCGAAGGTCGGA 60.301 57.895 0.00 0.00 40.84 4.55
1355 1465 3.458163 CGGCGAAGGGCAGGAGTA 61.458 66.667 0.00 0.00 46.16 2.59
1358 1468 3.019003 GCGAAGGGCAGGAGTAGCA 62.019 63.158 0.00 0.00 42.87 3.49
1359 1469 1.142748 CGAAGGGCAGGAGTAGCAG 59.857 63.158 0.00 0.00 0.00 4.24
1430 1540 4.457496 CATGGGCCGACGAGTGCT 62.457 66.667 0.00 0.00 0.00 4.40
1431 1541 2.758327 ATGGGCCGACGAGTGCTA 60.758 61.111 0.00 0.00 0.00 3.49
1432 1542 2.786495 ATGGGCCGACGAGTGCTAG 61.786 63.158 0.00 0.00 0.00 3.42
1433 1543 4.208686 GGGCCGACGAGTGCTAGG 62.209 72.222 0.00 0.00 0.00 3.02
1434 1544 4.874977 GGCCGACGAGTGCTAGGC 62.875 72.222 0.00 0.00 46.51 3.93
1498 1609 4.695928 GCCTTGTTACTAGCAAGCTTAGTT 59.304 41.667 5.71 0.00 41.27 2.24
1523 1634 2.367030 TTTGTACATGGACGTACCGG 57.633 50.000 3.00 0.00 40.91 5.28
1586 1709 3.425492 GGTTCCGTTCGTGTACTACTCTC 60.425 52.174 0.00 0.00 0.00 3.20
1592 1715 3.325293 TCGTGTACTACTCTCTCCGTT 57.675 47.619 0.00 0.00 0.00 4.44
1595 1718 3.608796 GTGTACTACTCTCTCCGTTCCT 58.391 50.000 0.00 0.00 0.00 3.36
1601 1724 8.216423 TGTACTACTCTCTCCGTTCCTAAATAT 58.784 37.037 0.00 0.00 0.00 1.28
1602 1725 9.717942 GTACTACTCTCTCCGTTCCTAAATATA 57.282 37.037 0.00 0.00 0.00 0.86
1607 1730 8.000127 ACTCTCTCCGTTCCTAAATATAAGTCT 59.000 37.037 0.00 0.00 0.00 3.24
1608 1731 8.763984 TCTCTCCGTTCCTAAATATAAGTCTT 57.236 34.615 0.00 0.00 0.00 3.01
1646 1769 4.866508 TGGACTACATTCGGATGTATCC 57.133 45.455 24.37 24.37 45.20 2.59
1669 1792 9.950496 ATCCGAATATAGATGCATTTTAGAGTT 57.050 29.630 0.00 0.00 0.00 3.01
1670 1793 9.424319 TCCGAATATAGATGCATTTTAGAGTTC 57.576 33.333 0.00 0.00 0.00 3.01
1681 1813 8.020861 TGCATTTTAGAGTTCATTCATTTTGC 57.979 30.769 0.00 0.00 0.00 3.68
1682 1814 7.874016 TGCATTTTAGAGTTCATTCATTTTGCT 59.126 29.630 0.00 0.00 0.00 3.91
1683 1815 8.378421 GCATTTTAGAGTTCATTCATTTTGCTC 58.622 33.333 0.00 0.00 0.00 4.26
1684 1816 8.866956 CATTTTAGAGTTCATTCATTTTGCTCC 58.133 33.333 0.00 0.00 0.00 4.70
1685 1817 4.691860 AGAGTTCATTCATTTTGCTCCG 57.308 40.909 0.00 0.00 0.00 4.63
1686 1818 4.074970 AGAGTTCATTCATTTTGCTCCGT 58.925 39.130 0.00 0.00 0.00 4.69
1688 1820 5.882557 AGAGTTCATTCATTTTGCTCCGTAT 59.117 36.000 0.00 0.00 0.00 3.06
1689 1821 5.883661 AGTTCATTCATTTTGCTCCGTATG 58.116 37.500 0.00 0.00 0.00 2.39
1690 1822 5.415701 AGTTCATTCATTTTGCTCCGTATGT 59.584 36.000 0.00 0.00 0.00 2.29
1691 1823 6.597672 AGTTCATTCATTTTGCTCCGTATGTA 59.402 34.615 0.00 0.00 0.00 2.29
1692 1824 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
1693 1825 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
1694 1826 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
1695 1827 5.339008 TCATTTTGCTCCGTATGTAGTCT 57.661 39.130 0.00 0.00 0.00 3.24
1696 1828 6.459670 TCATTTTGCTCCGTATGTAGTCTA 57.540 37.500 0.00 0.00 0.00 2.59
1697 1829 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
1698 1830 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
1707 1839 9.221933 CTCCGTATGTAGTCTATAGTGAAATCT 57.778 37.037 0.00 0.00 0.00 2.40
1740 1989 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1741 1990 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1742 1991 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
1743 1992 9.471702 CTTATATTTAGGAACGGAGGGAGTATA 57.528 37.037 0.00 0.00 0.00 1.47
1744 1993 9.827198 TTATATTTAGGAACGGAGGGAGTATAA 57.173 33.333 0.00 0.00 0.00 0.98
1745 1994 8.912614 ATATTTAGGAACGGAGGGAGTATAAT 57.087 34.615 0.00 0.00 0.00 1.28
1746 1995 6.415206 TTTAGGAACGGAGGGAGTATAATG 57.585 41.667 0.00 0.00 0.00 1.90
1747 1996 3.240302 AGGAACGGAGGGAGTATAATGG 58.760 50.000 0.00 0.00 0.00 3.16
1748 1997 3.116862 AGGAACGGAGGGAGTATAATGGA 60.117 47.826 0.00 0.00 0.00 3.41
1749 1998 3.258622 GGAACGGAGGGAGTATAATGGAG 59.741 52.174 0.00 0.00 0.00 3.86
1750 1999 3.614568 ACGGAGGGAGTATAATGGAGT 57.385 47.619 0.00 0.00 0.00 3.85
1751 2000 4.736611 ACGGAGGGAGTATAATGGAGTA 57.263 45.455 0.00 0.00 0.00 2.59
1752 2001 5.272405 ACGGAGGGAGTATAATGGAGTAT 57.728 43.478 0.00 0.00 0.00 2.12
1808 2057 1.471829 TTCCGCTGAGCTGAGAACCA 61.472 55.000 3.62 0.00 0.00 3.67
1848 2290 9.726232 CACTTCAGTATATCATCACATTTTTGG 57.274 33.333 0.00 0.00 0.00 3.28
1849 2291 9.466497 ACTTCAGTATATCATCACATTTTTGGT 57.534 29.630 0.00 0.00 0.00 3.67
1859 2301 9.632638 ATCATCACATTTTTGGTAGTATAAGCT 57.367 29.630 0.00 0.00 0.00 3.74
1864 2306 9.906660 CACATTTTTGGTAGTATAAGCTTTTCA 57.093 29.630 3.20 0.00 0.00 2.69
1915 2358 7.094508 TGAACTAAAGTTTTGATTGCTCACA 57.905 32.000 4.00 0.00 38.56 3.58
1942 2385 4.299155 ACGCCACTTGATAATAGATCACG 58.701 43.478 0.00 0.00 0.00 4.35
2049 2492 7.231467 AACAGAGGAAGTGTTATTGGTACAAT 58.769 34.615 0.00 0.00 39.07 2.71
2103 2546 4.232091 GGTTGGATGGTTAGGAGGATAGA 58.768 47.826 0.00 0.00 0.00 1.98
2104 2547 4.040584 GGTTGGATGGTTAGGAGGATAGAC 59.959 50.000 0.00 0.00 0.00 2.59
2105 2548 3.858135 TGGATGGTTAGGAGGATAGACC 58.142 50.000 0.00 0.00 39.35 3.85
2106 2549 3.208922 TGGATGGTTAGGAGGATAGACCA 59.791 47.826 0.00 0.00 43.82 4.02
2107 2550 4.232091 GGATGGTTAGGAGGATAGACCAA 58.768 47.826 0.00 0.00 43.02 3.67
2108 2551 4.284746 GGATGGTTAGGAGGATAGACCAAG 59.715 50.000 0.00 0.00 43.02 3.61
2109 2552 4.620086 TGGTTAGGAGGATAGACCAAGA 57.380 45.455 0.00 0.00 42.04 3.02
2110 2553 4.955335 TGGTTAGGAGGATAGACCAAGAA 58.045 43.478 0.00 0.00 42.04 2.52
2111 2554 5.347124 TGGTTAGGAGGATAGACCAAGAAA 58.653 41.667 0.00 0.00 42.04 2.52
2112 2555 5.970640 TGGTTAGGAGGATAGACCAAGAAAT 59.029 40.000 0.00 0.00 42.04 2.17
2113 2556 7.136885 TGGTTAGGAGGATAGACCAAGAAATA 58.863 38.462 0.00 0.00 42.04 1.40
2114 2557 7.794683 TGGTTAGGAGGATAGACCAAGAAATAT 59.205 37.037 0.00 0.00 42.04 1.28
2115 2558 8.661345 GGTTAGGAGGATAGACCAAGAAATATT 58.339 37.037 0.00 0.00 42.04 1.28
2116 2559 9.495572 GTTAGGAGGATAGACCAAGAAATATTG 57.504 37.037 0.00 0.00 42.04 1.90
2117 2560 7.937700 AGGAGGATAGACCAAGAAATATTGA 57.062 36.000 0.00 0.00 42.04 2.57
2118 2561 8.337118 AGGAGGATAGACCAAGAAATATTGAA 57.663 34.615 0.00 0.00 42.04 2.69
2119 2562 8.953665 AGGAGGATAGACCAAGAAATATTGAAT 58.046 33.333 0.00 0.00 42.04 2.57
2120 2563 9.225436 GGAGGATAGACCAAGAAATATTGAATC 57.775 37.037 0.00 0.00 42.04 2.52
2121 2564 9.784531 GAGGATAGACCAAGAAATATTGAATCA 57.215 33.333 0.00 0.00 42.04 2.57
2125 2568 9.927081 ATAGACCAAGAAATATTGAATCAACCT 57.073 29.630 0.00 0.00 31.55 3.50
2127 2570 9.927081 AGACCAAGAAATATTGAATCAACCTAT 57.073 29.630 0.00 0.00 31.55 2.57
2128 2571 9.956720 GACCAAGAAATATTGAATCAACCTATG 57.043 33.333 0.00 0.00 31.55 2.23
2129 2572 9.479549 ACCAAGAAATATTGAATCAACCTATGT 57.520 29.630 0.00 0.00 31.55 2.29
2137 2580 6.528537 TTGAATCAACCTATGTTTGGATGG 57.471 37.500 0.00 0.00 30.42 3.51
2138 2581 5.579047 TGAATCAACCTATGTTTGGATGGT 58.421 37.500 0.00 0.00 30.42 3.55
2139 2582 5.652014 TGAATCAACCTATGTTTGGATGGTC 59.348 40.000 0.00 0.00 30.42 4.02
2140 2583 4.649267 TCAACCTATGTTTGGATGGTCA 57.351 40.909 0.00 0.00 30.42 4.02
2141 2584 4.588899 TCAACCTATGTTTGGATGGTCAG 58.411 43.478 0.00 0.00 30.42 3.51
2142 2585 3.652057 ACCTATGTTTGGATGGTCAGG 57.348 47.619 0.00 0.00 0.00 3.86
2143 2586 3.189606 ACCTATGTTTGGATGGTCAGGA 58.810 45.455 0.00 0.00 0.00 3.86
2144 2587 3.200825 ACCTATGTTTGGATGGTCAGGAG 59.799 47.826 0.00 0.00 0.00 3.69
2145 2588 2.814805 ATGTTTGGATGGTCAGGAGG 57.185 50.000 0.00 0.00 0.00 4.30
2146 2589 1.741028 TGTTTGGATGGTCAGGAGGA 58.259 50.000 0.00 0.00 0.00 3.71
2147 2590 2.278245 TGTTTGGATGGTCAGGAGGAT 58.722 47.619 0.00 0.00 0.00 3.24
2148 2591 3.459828 TGTTTGGATGGTCAGGAGGATA 58.540 45.455 0.00 0.00 0.00 2.59
2149 2592 3.455910 TGTTTGGATGGTCAGGAGGATAG 59.544 47.826 0.00 0.00 0.00 2.08
2158 2601 6.672266 TGGTCAGGAGGATAGTGATATTTC 57.328 41.667 0.00 0.00 0.00 2.17
2163 2606 6.043243 TCAGGAGGATAGTGATATTTCCAACC 59.957 42.308 0.00 0.00 0.00 3.77
2188 2631 8.678199 CCCATCAAGGTTTAAATTCTAGACTTC 58.322 37.037 0.00 0.00 34.66 3.01
2200 2643 7.440523 AATTCTAGACTTCACATTGGTGTTC 57.559 36.000 0.00 0.00 45.45 3.18
2233 2678 4.495844 CGGATTTATTTCAGACCTTTCGGC 60.496 45.833 0.00 0.00 0.00 5.54
2250 2695 2.962786 CGGTGTGCGTTCAACGGA 60.963 61.111 12.81 5.91 43.61 4.69
2257 2702 0.320374 TGCGTTCAACGGAAGGAGAT 59.680 50.000 12.81 0.00 39.47 2.75
2258 2703 1.270625 TGCGTTCAACGGAAGGAGATT 60.271 47.619 12.81 0.00 39.47 2.40
2261 2706 2.092211 CGTTCAACGGAAGGAGATTTCG 59.908 50.000 0.61 0.00 46.01 3.46
2262 2707 2.380084 TCAACGGAAGGAGATTTCGG 57.620 50.000 0.00 0.00 44.75 4.30
2263 2708 1.621814 TCAACGGAAGGAGATTTCGGT 59.378 47.619 0.00 0.00 41.91 4.69
2264 2709 2.094762 AACGGAAGGAGATTTCGGTG 57.905 50.000 0.69 0.00 44.75 4.94
2265 2710 0.249398 ACGGAAGGAGATTTCGGTGG 59.751 55.000 0.00 0.00 44.75 4.61
2266 2711 0.249398 CGGAAGGAGATTTCGGTGGT 59.751 55.000 0.00 0.00 36.15 4.16
2267 2712 1.338769 CGGAAGGAGATTTCGGTGGTT 60.339 52.381 0.00 0.00 36.15 3.67
2268 2713 2.093869 CGGAAGGAGATTTCGGTGGTTA 60.094 50.000 0.00 0.00 36.15 2.85
2269 2714 3.532542 GGAAGGAGATTTCGGTGGTTAG 58.467 50.000 0.00 0.00 0.00 2.34
2270 2715 3.532542 GAAGGAGATTTCGGTGGTTAGG 58.467 50.000 0.00 0.00 0.00 2.69
2271 2716 2.829023 AGGAGATTTCGGTGGTTAGGA 58.171 47.619 0.00 0.00 0.00 2.94
2272 2717 2.766828 AGGAGATTTCGGTGGTTAGGAG 59.233 50.000 0.00 0.00 0.00 3.69
2273 2718 2.158943 GGAGATTTCGGTGGTTAGGAGG 60.159 54.545 0.00 0.00 0.00 4.30
2274 2719 2.764572 GAGATTTCGGTGGTTAGGAGGA 59.235 50.000 0.00 0.00 0.00 3.71
2275 2720 3.385115 AGATTTCGGTGGTTAGGAGGAT 58.615 45.455 0.00 0.00 0.00 3.24
2276 2721 4.553678 AGATTTCGGTGGTTAGGAGGATA 58.446 43.478 0.00 0.00 0.00 2.59
2277 2722 4.589374 AGATTTCGGTGGTTAGGAGGATAG 59.411 45.833 0.00 0.00 0.00 2.08
2278 2723 3.393426 TTCGGTGGTTAGGAGGATAGT 57.607 47.619 0.00 0.00 0.00 2.12
2279 2724 2.662866 TCGGTGGTTAGGAGGATAGTG 58.337 52.381 0.00 0.00 0.00 2.74
2280 2725 2.242965 TCGGTGGTTAGGAGGATAGTGA 59.757 50.000 0.00 0.00 0.00 3.41
2281 2726 3.117246 TCGGTGGTTAGGAGGATAGTGAT 60.117 47.826 0.00 0.00 0.00 3.06
2282 2727 4.105217 TCGGTGGTTAGGAGGATAGTGATA 59.895 45.833 0.00 0.00 0.00 2.15
2283 2728 5.017490 CGGTGGTTAGGAGGATAGTGATAT 58.983 45.833 0.00 0.00 0.00 1.63
2284 2729 5.480772 CGGTGGTTAGGAGGATAGTGATATT 59.519 44.000 0.00 0.00 0.00 1.28
2285 2730 6.014499 CGGTGGTTAGGAGGATAGTGATATTT 60.014 42.308 0.00 0.00 0.00 1.40
2286 2731 7.387643 GGTGGTTAGGAGGATAGTGATATTTC 58.612 42.308 0.00 0.00 0.00 2.17
2287 2732 7.387643 GTGGTTAGGAGGATAGTGATATTTCC 58.612 42.308 0.00 0.00 0.00 3.13
2288 2733 7.016268 GTGGTTAGGAGGATAGTGATATTTCCA 59.984 40.741 0.00 0.00 0.00 3.53
2289 2734 7.570982 TGGTTAGGAGGATAGTGATATTTCCAA 59.429 37.037 0.00 0.00 0.00 3.53
2290 2735 7.878644 GGTTAGGAGGATAGTGATATTTCCAAC 59.121 40.741 0.00 0.00 0.00 3.77
2291 2736 6.441088 AGGAGGATAGTGATATTTCCAACC 57.559 41.667 0.00 0.00 0.00 3.77
2292 2737 5.310857 AGGAGGATAGTGATATTTCCAACCC 59.689 44.000 0.00 0.00 31.68 4.11
2293 2738 5.073144 GGAGGATAGTGATATTTCCAACCCA 59.927 44.000 0.00 0.00 0.00 4.51
2294 2739 6.240292 GGAGGATAGTGATATTTCCAACCCAT 60.240 42.308 0.00 0.00 0.00 4.00
2295 2740 6.784031 AGGATAGTGATATTTCCAACCCATC 58.216 40.000 0.00 0.00 0.00 3.51
2296 2741 6.332635 AGGATAGTGATATTTCCAACCCATCA 59.667 38.462 0.00 0.00 0.00 3.07
2297 2742 6.656693 GGATAGTGATATTTCCAACCCATCAG 59.343 42.308 0.00 0.00 0.00 2.90
2298 2743 4.796606 AGTGATATTTCCAACCCATCAGG 58.203 43.478 0.00 0.00 43.78 3.86
2318 2763 9.667107 CATCAGGGTTTAAATTCTAGACTACAA 57.333 33.333 0.00 0.00 0.00 2.41
2324 2769 9.201127 GGTTTAAATTCTAGACTACAAAGACGT 57.799 33.333 0.00 0.00 0.00 4.34
2327 2772 9.622004 TTAAATTCTAGACTACAAAGACGTCTG 57.378 33.333 20.85 11.25 38.39 3.51
2378 3067 2.666508 CCGGTCTTGAAACGAGTGTATG 59.333 50.000 0.00 0.00 0.00 2.39
2499 6585 2.280628 CCTAATCACAAGGAGGTTCGC 58.719 52.381 0.00 0.00 36.08 4.70
2542 6628 1.548269 TGAGTATCACATGCCACGTCA 59.452 47.619 0.00 0.00 42.56 4.35
2572 6658 4.043200 GCTCCACGTTTGCAGCCC 62.043 66.667 0.00 0.00 0.00 5.19
2671 6757 0.112995 GCTGATGGATGGGCCCAATA 59.887 55.000 32.58 18.75 40.04 1.90
2681 6767 0.818040 GGGCCCAATACGTGATGACC 60.818 60.000 19.95 2.37 0.00 4.02
2682 6768 0.818040 GGCCCAATACGTGATGACCC 60.818 60.000 0.00 0.00 0.00 4.46
2688 6774 1.696097 ATACGTGATGACCCCTGGCC 61.696 60.000 0.00 0.00 0.00 5.36
2699 6785 3.592814 CCTGGCCGATGCATGCTG 61.593 66.667 20.33 8.67 40.13 4.41
2700 6786 2.515290 CTGGCCGATGCATGCTGA 60.515 61.111 20.33 0.00 40.13 4.26
2767 6853 0.250295 CAGCCTTGAACTCACCGGAA 60.250 55.000 9.46 0.00 0.00 4.30
2788 6874 2.687935 ACAGAAATCGCACAACCAGTTT 59.312 40.909 0.00 0.00 0.00 2.66
2789 6875 3.130340 ACAGAAATCGCACAACCAGTTTT 59.870 39.130 0.00 0.00 0.00 2.43
2790 6876 4.111916 CAGAAATCGCACAACCAGTTTTT 58.888 39.130 0.00 0.00 0.00 1.94
2813 6899 5.476091 TTTTTGAAGTTCCACAACCAGTT 57.524 34.783 0.00 0.00 32.22 3.16
2814 6900 6.591750 TTTTTGAAGTTCCACAACCAGTTA 57.408 33.333 0.00 0.00 32.22 2.24
2815 6901 6.783708 TTTTGAAGTTCCACAACCAGTTAT 57.216 33.333 0.00 0.00 32.22 1.89
2816 6902 6.783708 TTTGAAGTTCCACAACCAGTTATT 57.216 33.333 0.00 0.00 32.22 1.40
2817 6903 7.883391 TTTGAAGTTCCACAACCAGTTATTA 57.117 32.000 0.00 0.00 32.22 0.98
2818 6904 7.883391 TTGAAGTTCCACAACCAGTTATTAA 57.117 32.000 0.00 0.00 32.22 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.011966 TCATACATCCTATTGCTGCCAG 57.988 45.455 0.00 0.00 0.00 4.85
29 30 4.151335 CGACTTCATACATCCTATTGCTGC 59.849 45.833 0.00 0.00 0.00 5.25
33 34 9.476202 TGATTTACGACTTCATACATCCTATTG 57.524 33.333 0.00 0.00 0.00 1.90
37 38 7.707035 GTCTTGATTTACGACTTCATACATCCT 59.293 37.037 0.00 0.00 0.00 3.24
96 97 4.536295 AAGTTCCCCAAAAGAAGGAGAA 57.464 40.909 0.00 0.00 0.00 2.87
98 99 4.649218 TCAAAAGTTCCCCAAAAGAAGGAG 59.351 41.667 0.00 0.00 0.00 3.69
99 100 4.615513 TCAAAAGTTCCCCAAAAGAAGGA 58.384 39.130 0.00 0.00 0.00 3.36
100 101 5.551305 ATCAAAAGTTCCCCAAAAGAAGG 57.449 39.130 0.00 0.00 0.00 3.46
150 151 9.651913 ACAATTTTTGTTAGTTCTTGTGTTCAT 57.348 25.926 0.00 0.00 42.22 2.57
175 176 2.557490 GGTGGTCTACGGATCTGGATAC 59.443 54.545 6.47 0.00 0.00 2.24
176 177 2.445905 AGGTGGTCTACGGATCTGGATA 59.554 50.000 6.47 0.00 0.00 2.59
177 178 1.218196 AGGTGGTCTACGGATCTGGAT 59.782 52.381 6.47 0.00 0.00 3.41
178 179 0.629596 AGGTGGTCTACGGATCTGGA 59.370 55.000 6.47 0.00 0.00 3.86
180 181 2.619177 CACTAGGTGGTCTACGGATCTG 59.381 54.545 0.00 0.00 0.00 2.90
181 182 2.508716 TCACTAGGTGGTCTACGGATCT 59.491 50.000 0.00 0.00 33.87 2.75
182 183 2.617774 GTCACTAGGTGGTCTACGGATC 59.382 54.545 0.00 0.00 33.87 3.36
183 184 2.652590 GTCACTAGGTGGTCTACGGAT 58.347 52.381 0.00 0.00 33.87 4.18
184 185 1.676916 CGTCACTAGGTGGTCTACGGA 60.677 57.143 0.00 0.00 33.87 4.69
185 186 0.731417 CGTCACTAGGTGGTCTACGG 59.269 60.000 0.00 0.00 33.87 4.02
186 187 1.396301 GTCGTCACTAGGTGGTCTACG 59.604 57.143 0.00 0.00 33.87 3.51
187 188 2.709213 AGTCGTCACTAGGTGGTCTAC 58.291 52.381 0.00 0.00 33.87 2.59
188 189 3.261643 TGTAGTCGTCACTAGGTGGTCTA 59.738 47.826 0.00 0.00 35.67 2.59
189 190 2.039480 TGTAGTCGTCACTAGGTGGTCT 59.961 50.000 0.00 0.00 35.67 3.85
190 191 2.430465 TGTAGTCGTCACTAGGTGGTC 58.570 52.381 0.00 0.00 35.67 4.02
192 193 2.163815 CCTTGTAGTCGTCACTAGGTGG 59.836 54.545 0.00 0.00 35.67 4.61
193 194 3.079578 TCCTTGTAGTCGTCACTAGGTG 58.920 50.000 11.48 0.00 39.19 4.00
194 195 3.080319 GTCCTTGTAGTCGTCACTAGGT 58.920 50.000 11.48 0.00 39.19 3.08
195 196 3.345414 AGTCCTTGTAGTCGTCACTAGG 58.655 50.000 0.00 7.54 39.41 3.02
196 197 5.417811 TCTAGTCCTTGTAGTCGTCACTAG 58.582 45.833 0.00 0.00 35.67 2.57
198 199 4.255301 CTCTAGTCCTTGTAGTCGTCACT 58.745 47.826 0.00 0.00 36.55 3.41
199 200 3.181508 GCTCTAGTCCTTGTAGTCGTCAC 60.182 52.174 0.00 0.00 0.00 3.67
200 201 3.008330 GCTCTAGTCCTTGTAGTCGTCA 58.992 50.000 0.00 0.00 0.00 4.35
202 203 2.008329 CGCTCTAGTCCTTGTAGTCGT 58.992 52.381 0.00 0.00 0.00 4.34
203 204 2.277969 TCGCTCTAGTCCTTGTAGTCG 58.722 52.381 0.00 0.00 0.00 4.18
204 205 2.032426 GCTCGCTCTAGTCCTTGTAGTC 59.968 54.545 0.00 0.00 0.00 2.59
205 206 2.018515 GCTCGCTCTAGTCCTTGTAGT 58.981 52.381 0.00 0.00 0.00 2.73
206 207 1.335496 GGCTCGCTCTAGTCCTTGTAG 59.665 57.143 0.00 0.00 0.00 2.74
213 216 1.297745 CGTTCGGCTCGCTCTAGTC 60.298 63.158 0.00 0.00 0.00 2.59
235 238 0.805322 CAGAGGACGATGACAGCTGC 60.805 60.000 15.27 7.45 0.00 5.25
237 240 1.408340 CATCAGAGGACGATGACAGCT 59.592 52.381 0.00 0.00 42.39 4.24
240 243 2.094026 CCAACATCAGAGGACGATGACA 60.094 50.000 7.12 0.00 42.39 3.58
241 244 2.166459 TCCAACATCAGAGGACGATGAC 59.834 50.000 7.12 0.00 42.39 3.06
247 250 2.303022 TCCAACTCCAACATCAGAGGAC 59.697 50.000 0.00 0.00 34.27 3.85
253 257 3.646162 AGTACTGTCCAACTCCAACATCA 59.354 43.478 0.00 0.00 0.00 3.07
255 259 4.389374 CAAGTACTGTCCAACTCCAACAT 58.611 43.478 0.00 0.00 0.00 2.71
259 263 2.047061 AGCAAGTACTGTCCAACTCCA 58.953 47.619 0.00 0.00 0.00 3.86
283 287 6.482308 AGCACAACGACTTTTTAACTGTCTAT 59.518 34.615 0.00 0.00 0.00 1.98
292 296 4.453751 ACCCTTAGCACAACGACTTTTTA 58.546 39.130 0.00 0.00 0.00 1.52
293 297 3.284617 ACCCTTAGCACAACGACTTTTT 58.715 40.909 0.00 0.00 0.00 1.94
294 298 2.876550 GACCCTTAGCACAACGACTTTT 59.123 45.455 0.00 0.00 0.00 2.27
295 299 2.490991 GACCCTTAGCACAACGACTTT 58.509 47.619 0.00 0.00 0.00 2.66
296 300 1.270678 GGACCCTTAGCACAACGACTT 60.271 52.381 0.00 0.00 0.00 3.01
297 301 0.320697 GGACCCTTAGCACAACGACT 59.679 55.000 0.00 0.00 0.00 4.18
298 302 0.034337 TGGACCCTTAGCACAACGAC 59.966 55.000 0.00 0.00 0.00 4.34
299 303 0.981183 ATGGACCCTTAGCACAACGA 59.019 50.000 0.00 0.00 0.00 3.85
300 304 1.086696 CATGGACCCTTAGCACAACG 58.913 55.000 0.00 0.00 0.00 4.10
301 305 1.463674 CCATGGACCCTTAGCACAAC 58.536 55.000 5.56 0.00 0.00 3.32
302 306 0.323360 GCCATGGACCCTTAGCACAA 60.323 55.000 18.40 0.00 0.00 3.33
303 307 1.302949 GCCATGGACCCTTAGCACA 59.697 57.895 18.40 0.00 0.00 4.57
304 308 1.032114 GTGCCATGGACCCTTAGCAC 61.032 60.000 18.40 9.86 43.14 4.40
325 329 0.675633 GGTTGCTGTTCTGGTGCATT 59.324 50.000 0.00 0.00 36.55 3.56
339 343 2.991190 TCTCTTTATTGACGTCGGTTGC 59.009 45.455 11.62 0.00 0.00 4.17
344 348 2.915463 ACGCTTCTCTTTATTGACGTCG 59.085 45.455 11.62 0.00 0.00 5.12
346 350 5.306532 TCTACGCTTCTCTTTATTGACGT 57.693 39.130 0.00 0.00 36.38 4.34
349 353 6.373186 TCGATCTACGCTTCTCTTTATTGA 57.627 37.500 0.00 0.00 42.26 2.57
351 355 7.974501 TCTTTTCGATCTACGCTTCTCTTTATT 59.025 33.333 0.00 0.00 42.26 1.40
431 435 3.753272 CGATTGGTGGTTCTCTTTGATGT 59.247 43.478 0.00 0.00 0.00 3.06
434 441 3.762407 TCGATTGGTGGTTCTCTTTGA 57.238 42.857 0.00 0.00 0.00 2.69
484 491 2.779755 TTGATTATCTGGTGGTGCGT 57.220 45.000 0.00 0.00 0.00 5.24
557 589 1.464997 GCAAACTCCGTCAAGCTTAGG 59.535 52.381 0.00 3.36 0.00 2.69
614 654 1.302366 TACGCGTACGATGGATCAGT 58.698 50.000 21.65 7.28 43.93 3.41
642 707 9.777843 CGTTGCTAAATGTTAATTCTTCAAAAC 57.222 29.630 0.00 0.00 0.00 2.43
663 728 2.320587 CCTCACTGGCTCACGTTGC 61.321 63.158 1.99 1.99 0.00 4.17
686 751 0.108662 CTGCCTACATCTGCGTCACA 60.109 55.000 0.00 0.00 0.00 3.58
705 770 0.109597 CCTTGTGGACGAATTGCTGC 60.110 55.000 0.00 0.00 34.57 5.25
719 784 1.889545 GAAGTGCTCTGCTTCCTTGT 58.110 50.000 0.00 0.00 37.08 3.16
735 805 2.003301 GAACCTTCTTGCTAGCGGAAG 58.997 52.381 28.44 28.44 39.66 3.46
759 829 2.645567 CCTGCGTCACTGTCGAGT 59.354 61.111 0.00 0.00 0.00 4.18
760 830 2.807045 GCCTGCGTCACTGTCGAG 60.807 66.667 0.00 0.00 0.00 4.04
761 831 4.700365 CGCCTGCGTCACTGTCGA 62.700 66.667 2.83 0.00 34.35 4.20
834 904 2.401766 GCATCACGCCTCCACCTTG 61.402 63.158 0.00 0.00 32.94 3.61
895 965 1.218316 CGTGTCAGGGGCTTAGGTC 59.782 63.158 0.00 0.00 0.00 3.85
900 970 2.847234 TCACCGTGTCAGGGGCTT 60.847 61.111 15.79 0.00 33.82 4.35
989 1082 3.751479 TGATGATGATGGGTTAGTCGG 57.249 47.619 0.00 0.00 0.00 4.79
1014 1114 0.766288 GGAGGGAGAGGAAGGATGGG 60.766 65.000 0.00 0.00 0.00 4.00
1105 1209 3.181495 CCTTCGCCTTGTTGTTGTTGTTA 60.181 43.478 0.00 0.00 0.00 2.41
1108 1215 1.134175 ACCTTCGCCTTGTTGTTGTTG 59.866 47.619 0.00 0.00 0.00 3.33
1120 1227 3.116531 CCGTTTCCGACCTTCGCC 61.117 66.667 0.00 0.00 38.82 5.54
1340 1450 2.202946 GCTACTCCTGCCCTTCGC 60.203 66.667 0.00 0.00 38.31 4.70
1355 1465 2.513204 CATGCTGCCGCTACTGCT 60.513 61.111 0.70 0.00 36.97 4.24
1358 1468 2.503061 CTCCATGCTGCCGCTACT 59.497 61.111 0.70 0.00 36.97 2.57
1359 1469 3.275338 GCTCCATGCTGCCGCTAC 61.275 66.667 0.70 0.00 38.95 3.58
1523 1634 4.017877 GCACGCACACAGCAGGTC 62.018 66.667 0.00 0.00 46.13 3.85
1537 1648 1.135575 GCTGCAAACATACTCCTGCAC 60.136 52.381 0.00 0.00 39.77 4.57
1586 1709 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
1613 1736 7.390996 TCCGAATGTAGTCCATAGTAGAATCTC 59.609 40.741 0.00 0.00 31.97 2.75
1614 1737 7.232188 TCCGAATGTAGTCCATAGTAGAATCT 58.768 38.462 0.00 0.00 31.97 2.40
1615 1738 7.450124 TCCGAATGTAGTCCATAGTAGAATC 57.550 40.000 0.00 0.00 31.97 2.52
1616 1739 7.451877 ACATCCGAATGTAGTCCATAGTAGAAT 59.548 37.037 0.00 0.00 44.38 2.40
1619 1742 6.576662 ACATCCGAATGTAGTCCATAGTAG 57.423 41.667 0.00 0.00 44.38 2.57
1657 1780 8.248117 AGCAAAATGAATGAACTCTAAAATGC 57.752 30.769 0.00 0.00 0.00 3.56
1658 1781 8.866956 GGAGCAAAATGAATGAACTCTAAAATG 58.133 33.333 0.00 0.00 0.00 2.32
1667 1790 5.640732 ACATACGGAGCAAAATGAATGAAC 58.359 37.500 0.00 0.00 0.00 3.18
1669 1792 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
1670 1793 6.258727 AGACTACATACGGAGCAAAATGAATG 59.741 38.462 0.00 0.00 0.00 2.67
1680 1812 6.798315 TTCACTATAGACTACATACGGAGC 57.202 41.667 6.78 0.00 0.00 4.70
1681 1813 9.221933 AGATTTCACTATAGACTACATACGGAG 57.778 37.037 6.78 0.00 0.00 4.63
1712 1844 7.015001 TCCCTCCGTTCCTAAATATAAGTCTTC 59.985 40.741 0.00 0.00 0.00 2.87
1714 1846 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1715 1847 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1717 1849 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1718 1850 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
1720 1852 8.759782 CATTATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
1726 1858 3.116862 TCCATTATACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
1728 1860 3.896272 ACTCCATTATACTCCCTCCGTTC 59.104 47.826 0.00 0.00 0.00 3.95
1729 1861 3.924922 ACTCCATTATACTCCCTCCGTT 58.075 45.455 0.00 0.00 0.00 4.44
1845 2287 8.956426 CCTTTCATGAAAAGCTTATACTACCAA 58.044 33.333 20.82 0.00 42.63 3.67
1847 2289 8.507524 ACCTTTCATGAAAAGCTTATACTACC 57.492 34.615 20.82 0.00 42.63 3.18
1848 2290 9.989869 GAACCTTTCATGAAAAGCTTATACTAC 57.010 33.333 20.82 1.60 42.63 2.73
1849 2291 9.959721 AGAACCTTTCATGAAAAGCTTATACTA 57.040 29.630 20.82 0.00 42.63 1.82
1850 2292 8.870075 AGAACCTTTCATGAAAAGCTTATACT 57.130 30.769 20.82 9.84 42.63 2.12
1851 2293 9.914131 AAAGAACCTTTCATGAAAAGCTTATAC 57.086 29.630 20.82 8.08 42.63 1.47
1855 2297 9.836864 AAATAAAGAACCTTTCATGAAAAGCTT 57.163 25.926 20.82 16.75 42.63 3.74
1915 2358 7.761704 GTGATCTATTATCAAGTGGCGTATGAT 59.238 37.037 0.00 4.50 37.54 2.45
2057 2500 8.210946 ACCATAGGTTGATTCAATATTTCTCGA 58.789 33.333 1.78 0.00 27.29 4.04
2103 2546 9.479549 ACATAGGTTGATTCAATATTTCTTGGT 57.520 29.630 1.78 0.00 0.00 3.67
2111 2554 8.863086 CCATCCAAACATAGGTTGATTCAATAT 58.137 33.333 1.78 0.00 37.30 1.28
2112 2555 7.838696 ACCATCCAAACATAGGTTGATTCAATA 59.161 33.333 1.78 0.00 37.30 1.90
2113 2556 6.669154 ACCATCCAAACATAGGTTGATTCAAT 59.331 34.615 1.78 0.00 37.30 2.57
2114 2557 6.015918 ACCATCCAAACATAGGTTGATTCAA 58.984 36.000 0.00 0.00 37.30 2.69
2115 2558 5.579047 ACCATCCAAACATAGGTTGATTCA 58.421 37.500 0.00 0.00 37.30 2.57
2116 2559 5.652014 TGACCATCCAAACATAGGTTGATTC 59.348 40.000 0.00 0.00 37.30 2.52
2117 2560 5.579047 TGACCATCCAAACATAGGTTGATT 58.421 37.500 0.00 0.00 37.30 2.57
2118 2561 5.191727 TGACCATCCAAACATAGGTTGAT 57.808 39.130 0.00 0.00 37.30 2.57
2119 2562 4.567537 CCTGACCATCCAAACATAGGTTGA 60.568 45.833 0.00 0.00 37.30 3.18
2120 2563 3.696051 CCTGACCATCCAAACATAGGTTG 59.304 47.826 0.00 0.00 37.30 3.77
2121 2564 3.591527 TCCTGACCATCCAAACATAGGTT 59.408 43.478 0.00 0.00 39.43 3.50
2122 2565 3.189606 TCCTGACCATCCAAACATAGGT 58.810 45.455 0.00 0.00 34.76 3.08
2123 2566 3.434167 CCTCCTGACCATCCAAACATAGG 60.434 52.174 0.00 0.00 0.00 2.57
2124 2567 3.455910 TCCTCCTGACCATCCAAACATAG 59.544 47.826 0.00 0.00 0.00 2.23
2125 2568 3.459828 TCCTCCTGACCATCCAAACATA 58.540 45.455 0.00 0.00 0.00 2.29
2126 2569 2.278245 TCCTCCTGACCATCCAAACAT 58.722 47.619 0.00 0.00 0.00 2.71
2127 2570 1.741028 TCCTCCTGACCATCCAAACA 58.259 50.000 0.00 0.00 0.00 2.83
2128 2571 3.456277 ACTATCCTCCTGACCATCCAAAC 59.544 47.826 0.00 0.00 0.00 2.93
2129 2572 3.455910 CACTATCCTCCTGACCATCCAAA 59.544 47.826 0.00 0.00 0.00 3.28
2130 2573 3.041211 CACTATCCTCCTGACCATCCAA 58.959 50.000 0.00 0.00 0.00 3.53
2131 2574 2.247372 TCACTATCCTCCTGACCATCCA 59.753 50.000 0.00 0.00 0.00 3.41
2132 2575 2.964209 TCACTATCCTCCTGACCATCC 58.036 52.381 0.00 0.00 0.00 3.51
2133 2576 6.865834 AATATCACTATCCTCCTGACCATC 57.134 41.667 0.00 0.00 0.00 3.51
2134 2577 6.214412 GGAAATATCACTATCCTCCTGACCAT 59.786 42.308 0.00 0.00 0.00 3.55
2135 2578 5.544176 GGAAATATCACTATCCTCCTGACCA 59.456 44.000 0.00 0.00 0.00 4.02
2136 2579 5.544176 TGGAAATATCACTATCCTCCTGACC 59.456 44.000 0.00 0.00 33.02 4.02
2137 2580 6.672266 TGGAAATATCACTATCCTCCTGAC 57.328 41.667 0.00 0.00 33.02 3.51
2138 2581 6.043243 GGTTGGAAATATCACTATCCTCCTGA 59.957 42.308 0.00 0.00 33.02 3.86
2139 2582 6.234177 GGTTGGAAATATCACTATCCTCCTG 58.766 44.000 0.00 0.00 33.02 3.86
2140 2583 5.310857 GGGTTGGAAATATCACTATCCTCCT 59.689 44.000 0.00 0.00 33.02 3.69
2141 2584 5.073144 TGGGTTGGAAATATCACTATCCTCC 59.927 44.000 0.00 0.00 33.02 4.30
2142 2585 6.187727 TGGGTTGGAAATATCACTATCCTC 57.812 41.667 0.00 0.00 33.02 3.71
2143 2586 6.332635 TGATGGGTTGGAAATATCACTATCCT 59.667 38.462 0.00 0.00 33.02 3.24
2144 2587 6.542821 TGATGGGTTGGAAATATCACTATCC 58.457 40.000 0.00 0.00 0.00 2.59
2145 2588 7.175641 CCTTGATGGGTTGGAAATATCACTATC 59.824 40.741 0.00 0.00 0.00 2.08
2146 2589 7.006509 CCTTGATGGGTTGGAAATATCACTAT 58.993 38.462 0.00 0.00 0.00 2.12
2147 2590 6.069088 ACCTTGATGGGTTGGAAATATCACTA 60.069 38.462 0.00 0.00 41.11 2.74
2148 2591 5.203528 CCTTGATGGGTTGGAAATATCACT 58.796 41.667 0.00 0.00 0.00 3.41
2149 2592 4.956075 ACCTTGATGGGTTGGAAATATCAC 59.044 41.667 0.00 0.00 41.11 3.06
2163 2606 9.231297 TGAAGTCTAGAATTTAAACCTTGATGG 57.769 33.333 6.91 0.00 42.93 3.51
2183 2626 1.601903 TGCGAACACCAATGTGAAGTC 59.398 47.619 0.00 0.00 45.76 3.01
2233 2678 2.424576 CTTCCGTTGAACGCACACCG 62.425 60.000 12.95 0.00 40.91 4.94
2250 2695 3.178865 TCCTAACCACCGAAATCTCCTT 58.821 45.455 0.00 0.00 0.00 3.36
2257 2702 3.449737 CACTATCCTCCTAACCACCGAAA 59.550 47.826 0.00 0.00 0.00 3.46
2258 2703 3.028850 CACTATCCTCCTAACCACCGAA 58.971 50.000 0.00 0.00 0.00 4.30
2261 2706 6.936968 AATATCACTATCCTCCTAACCACC 57.063 41.667 0.00 0.00 0.00 4.61
2262 2707 7.016268 TGGAAATATCACTATCCTCCTAACCAC 59.984 40.741 0.00 0.00 33.02 4.16
2263 2708 7.079700 TGGAAATATCACTATCCTCCTAACCA 58.920 38.462 0.00 0.00 33.02 3.67
2264 2709 7.554959 TGGAAATATCACTATCCTCCTAACC 57.445 40.000 0.00 0.00 33.02 2.85
2265 2710 7.878644 GGTTGGAAATATCACTATCCTCCTAAC 59.121 40.741 0.00 0.00 33.02 2.34
2266 2711 7.017254 GGGTTGGAAATATCACTATCCTCCTAA 59.983 40.741 0.00 0.00 33.02 2.69
2267 2712 6.500751 GGGTTGGAAATATCACTATCCTCCTA 59.499 42.308 0.00 0.00 33.02 2.94
2268 2713 5.310857 GGGTTGGAAATATCACTATCCTCCT 59.689 44.000 0.00 0.00 33.02 3.69
2269 2714 5.073144 TGGGTTGGAAATATCACTATCCTCC 59.927 44.000 0.00 0.00 33.02 4.30
2270 2715 6.187727 TGGGTTGGAAATATCACTATCCTC 57.812 41.667 0.00 0.00 33.02 3.71
2271 2716 6.332635 TGATGGGTTGGAAATATCACTATCCT 59.667 38.462 0.00 0.00 33.02 3.24
2272 2717 6.542821 TGATGGGTTGGAAATATCACTATCC 58.457 40.000 0.00 0.00 0.00 2.59
2273 2718 6.656693 CCTGATGGGTTGGAAATATCACTATC 59.343 42.308 0.00 0.00 0.00 2.08
2274 2719 6.546484 CCTGATGGGTTGGAAATATCACTAT 58.454 40.000 0.00 0.00 0.00 2.12
2275 2720 5.940617 CCTGATGGGTTGGAAATATCACTA 58.059 41.667 0.00 0.00 0.00 2.74
2276 2721 4.796606 CCTGATGGGTTGGAAATATCACT 58.203 43.478 0.00 0.00 0.00 3.41
2291 2736 8.265055 TGTAGTCTAGAATTTAAACCCTGATGG 58.735 37.037 0.00 0.00 41.37 3.51
2292 2737 9.667107 TTGTAGTCTAGAATTTAAACCCTGATG 57.333 33.333 0.00 0.00 0.00 3.07
2294 2739 9.720769 CTTTGTAGTCTAGAATTTAAACCCTGA 57.279 33.333 0.00 0.00 0.00 3.86
2295 2740 9.720769 TCTTTGTAGTCTAGAATTTAAACCCTG 57.279 33.333 0.00 0.00 0.00 4.45
2296 2741 9.722184 GTCTTTGTAGTCTAGAATTTAAACCCT 57.278 33.333 0.00 0.00 0.00 4.34
2297 2742 8.654215 CGTCTTTGTAGTCTAGAATTTAAACCC 58.346 37.037 0.00 0.00 0.00 4.11
2298 2743 9.201127 ACGTCTTTGTAGTCTAGAATTTAAACC 57.799 33.333 0.00 0.00 0.00 3.27
2301 2746 9.622004 CAGACGTCTTTGTAGTCTAGAATTTAA 57.378 33.333 17.26 0.00 42.65 1.52
2302 2747 8.790718 ACAGACGTCTTTGTAGTCTAGAATTTA 58.209 33.333 17.26 0.00 42.65 1.40
2303 2748 7.595502 CACAGACGTCTTTGTAGTCTAGAATTT 59.404 37.037 21.03 0.00 42.65 1.82
2304 2749 7.040617 TCACAGACGTCTTTGTAGTCTAGAATT 60.041 37.037 26.33 0.00 42.65 2.17
2308 2753 5.383958 GTCACAGACGTCTTTGTAGTCTAG 58.616 45.833 26.33 10.47 42.65 2.43
2310 2755 4.226113 GTCACAGACGTCTTTGTAGTCT 57.774 45.455 26.33 0.00 45.07 3.24
2338 2784 4.129380 CCGGCACATCATCTTAGATTGAA 58.871 43.478 1.39 0.00 0.00 2.69
2357 3046 2.427232 TACACTCGTTTCAAGACCGG 57.573 50.000 0.00 0.00 0.00 5.28
2378 3067 3.000322 GCACAAGACGCTCATATACACAC 60.000 47.826 0.00 0.00 0.00 3.82
2499 6585 2.035961 TCTTTCGTGGACTGGACTGAAG 59.964 50.000 0.00 0.00 0.00 3.02
2607 6693 3.108144 CTGCTTTGTTTGTCTTGGTTCG 58.892 45.455 0.00 0.00 0.00 3.95
2609 6695 2.418609 GGCTGCTTTGTTTGTCTTGGTT 60.419 45.455 0.00 0.00 0.00 3.67
2616 6702 1.319614 ACACGGGCTGCTTTGTTTGT 61.320 50.000 0.00 0.00 0.00 2.83
2671 6757 3.717294 GGCCAGGGGTCATCACGT 61.717 66.667 0.00 0.00 0.00 4.49
2681 6767 4.889112 AGCATGCATCGGCCAGGG 62.889 66.667 21.98 0.00 40.13 4.45
2682 6768 3.592814 CAGCATGCATCGGCCAGG 61.593 66.667 21.98 0.00 40.13 4.45
2688 6774 0.866427 GGTGAGATCAGCATGCATCG 59.134 55.000 21.98 8.00 43.34 3.84
2730 6816 2.916640 CTGGGTGCACAAACCATTTTT 58.083 42.857 20.43 0.00 42.47 1.94
2731 6817 1.474855 GCTGGGTGCACAAACCATTTT 60.475 47.619 20.43 0.00 42.47 1.82
2732 6818 0.106521 GCTGGGTGCACAAACCATTT 59.893 50.000 20.43 0.00 42.47 2.32
2733 6819 1.747774 GCTGGGTGCACAAACCATT 59.252 52.632 20.43 0.00 42.47 3.16
2734 6820 2.209315 GGCTGGGTGCACAAACCAT 61.209 57.895 20.43 0.00 45.15 3.55
2735 6821 2.837291 GGCTGGGTGCACAAACCA 60.837 61.111 20.43 15.70 45.15 3.67
2767 6853 1.967319 ACTGGTTGTGCGATTTCTGT 58.033 45.000 0.00 0.00 0.00 3.41
2791 6877 5.476091 AACTGGTTGTGGAACTTCAAAAA 57.524 34.783 0.00 0.00 38.04 1.94
2792 6878 6.783708 ATAACTGGTTGTGGAACTTCAAAA 57.216 33.333 0.00 0.00 38.04 2.44
2793 6879 6.783708 AATAACTGGTTGTGGAACTTCAAA 57.216 33.333 0.00 0.00 38.04 2.69
2794 6880 7.883391 TTAATAACTGGTTGTGGAACTTCAA 57.117 32.000 0.00 0.00 38.04 2.69


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

AutoCloner maintained by Alex Coulton.