Multiple sequence alignment - TraesCS2D01G421700

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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 TraesCS2D01G421700 chr2D 100.000 4367 0 0 1 4367 535110676 535106310 0.000000e+00 8065.0
1 TraesCS2D01G421700 chr2B 89.066 3631 177 71 18 3524 636484032 636480498 0.000000e+00 4303.0
2 TraesCS2D01G421700 chr2B 80.879 387 51 17 3740 4124 636480240 636479875 2.570000e-72 283.0
3 TraesCS2D01G421700 chr2B 93.478 46 3 0 4281 4326 636479821 636479776 7.840000e-08 69.4
4 TraesCS2D01G421700 chr2A 92.484 1876 69 34 1839 3705 678372426 678370614 0.000000e+00 2617.0
5 TraesCS2D01G421700 chr2A 80.023 881 73 40 847 1665 678373475 678372636 1.370000e-154 556.0
6 TraesCS2D01G421700 chr2A 87.685 406 31 10 250 647 678373938 678373544 5.150000e-124 455.0
7 TraesCS2D01G421700 chr2A 93.491 169 3 3 3748 3909 678370390 678370223 1.210000e-60 244.0
8 TraesCS2D01G421700 chr2A 83.168 202 20 11 4106 4306 678368415 678368227 5.810000e-39 172.0
9 TraesCS2D01G421700 chr2A 85.496 131 13 3 3948 4078 678368621 678368497 9.850000e-27 132.0
10 TraesCS2D01G421700 chr2A 88.000 100 6 4 168 267 678374046 678373953 3.570000e-21 113.0


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 TraesCS2D01G421700 chr2D 535106310 535110676 4366 True 8065.000000 8065 100.000000 1 4367 1 chr2D.!!$R1 4366
1 TraesCS2D01G421700 chr2B 636479776 636484032 4256 True 1551.800000 4303 87.807667 18 4326 3 chr2B.!!$R1 4308
2 TraesCS2D01G421700 chr2A 678368227 678374046 5819 True 612.714286 2617 87.192429 168 4306 7 chr2A.!!$R1 4138

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
722 822 0.031111 CTCCCTCCCTCCCACACATA 60.031 60.0 0.00 0.0 0.0 2.29 F
1697 1907 0.384309 CCGTGCGCCTGAATCTACTA 59.616 55.0 4.18 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2205 0.179936 AGCCCGAGTAGTACGTAGCT 59.820 55.000 0.00 0.0 35.05 3.32 R
3426 3725 2.436469 AATGACGCCATGCTCGCA 60.436 55.556 5.65 0.0 32.36 5.10 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
22 23 5.306532 CAAAGAAGAAGGGACATGACATG 57.693 43.478 14.02 14.02 0.00 3.21
23 24 4.916041 AAGAAGAAGGGACATGACATGA 57.084 40.909 22.19 0.00 0.00 3.07
24 25 5.447778 AAGAAGAAGGGACATGACATGAT 57.552 39.130 22.19 6.35 0.00 2.45
25 26 4.778579 AGAAGAAGGGACATGACATGATG 58.221 43.478 22.19 0.00 0.00 3.07
26 27 3.572632 AGAAGGGACATGACATGATGG 57.427 47.619 22.19 0.00 0.00 3.51
64 65 4.943705 GGAAAGAATAATGAGAGCACACCA 59.056 41.667 0.00 0.00 0.00 4.17
67 68 7.363268 GGAAAGAATAATGAGAGCACACCAAAT 60.363 37.037 0.00 0.00 0.00 2.32
106 107 2.026636 TCCTTGGACCCGATTAAACAGG 60.027 50.000 0.00 0.00 0.00 4.00
134 135 3.725459 CACACCAAGATGCGCGCA 61.725 61.111 38.27 38.27 0.00 6.09
142 143 4.741781 GATGCGCGCACACACACC 62.742 66.667 39.05 15.18 0.00 4.16
153 154 3.018193 ACACACCACCCACCCACA 61.018 61.111 0.00 0.00 0.00 4.17
195 196 8.694540 TCTTCTCCTTCTTCTAGATTCATTCAG 58.305 37.037 0.00 0.00 0.00 3.02
202 203 7.953005 TCTTCTAGATTCATTCAGAGTCACT 57.047 36.000 0.00 0.00 35.57 3.41
203 204 8.359875 TCTTCTAGATTCATTCAGAGTCACTT 57.640 34.615 0.00 0.00 35.57 3.16
204 205 8.465999 TCTTCTAGATTCATTCAGAGTCACTTC 58.534 37.037 0.00 0.00 35.57 3.01
206 207 5.096443 AGATTCATTCAGAGTCACTTCCC 57.904 43.478 0.00 0.00 35.57 3.97
207 208 4.533707 AGATTCATTCAGAGTCACTTCCCA 59.466 41.667 0.00 0.00 35.57 4.37
208 209 3.685139 TCATTCAGAGTCACTTCCCAC 57.315 47.619 0.00 0.00 0.00 4.61
209 210 2.972021 TCATTCAGAGTCACTTCCCACA 59.028 45.455 0.00 0.00 0.00 4.17
210 211 2.910688 TTCAGAGTCACTTCCCACAC 57.089 50.000 0.00 0.00 0.00 3.82
211 212 0.673985 TCAGAGTCACTTCCCACACG 59.326 55.000 0.00 0.00 0.00 4.49
212 213 0.319900 CAGAGTCACTTCCCACACGG 60.320 60.000 0.00 0.00 0.00 4.94
213 214 0.469331 AGAGTCACTTCCCACACGGA 60.469 55.000 0.00 0.00 39.68 4.69
214 215 0.319641 GAGTCACTTCCCACACGGAC 60.320 60.000 0.00 0.00 41.83 4.79
288 349 3.432051 CTGGTCGGCACCTCGATCC 62.432 68.421 7.47 0.00 44.17 3.36
301 363 2.511373 GATCCATGCACGCGGTGA 60.511 61.111 12.47 0.00 35.23 4.02
302 364 1.889105 GATCCATGCACGCGGTGAT 60.889 57.895 12.47 2.40 35.23 3.06
303 365 0.599991 GATCCATGCACGCGGTGATA 60.600 55.000 12.47 0.03 35.23 2.15
315 377 3.118884 ACGCGGTGATAATAAACTGGTCT 60.119 43.478 12.47 0.00 0.00 3.85
321 383 5.396884 GGTGATAATAAACTGGTCTCTGCCT 60.397 44.000 0.00 0.00 0.00 4.75
332 394 1.227205 CTCTGCCTGACGGATCTGC 60.227 63.158 0.00 0.00 31.63 4.26
378 440 2.799412 TGACATTGCAAAATTTCCACGC 59.201 40.909 1.71 0.00 0.00 5.34
448 522 3.900601 ACTGTGACAGTCTCAGGAAAGAT 59.099 43.478 28.16 10.32 41.21 2.40
483 563 1.799933 ATTTCTGTTGCCAAACCCCA 58.200 45.000 0.00 0.00 35.25 4.96
484 564 1.118838 TTTCTGTTGCCAAACCCCAG 58.881 50.000 0.00 0.00 35.25 4.45
516 600 2.350458 ACGATGGCCCCATTGTTGC 61.350 57.895 13.31 0.00 45.82 4.17
615 703 1.280457 TTCTTCCTTCAGGCTCCTCC 58.720 55.000 0.00 0.00 34.44 4.30
620 708 2.041265 TTCAGGCTCCTCCCCTCC 59.959 66.667 0.00 0.00 34.51 4.30
621 709 2.543978 CTTCAGGCTCCTCCCCTCCT 62.544 65.000 0.00 0.00 34.51 3.69
622 710 2.445654 CAGGCTCCTCCCCTCCTC 60.446 72.222 0.00 0.00 34.51 3.71
626 714 2.710826 GCTCCTCCCCTCCTCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
627 715 2.023532 CTCCTCCCCTCCTCTCCTT 58.976 63.158 0.00 0.00 0.00 3.36
716 816 3.368501 CTCCCTCCCTCCCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
718 818 4.024984 CCCTCCCTCCCTCCCACA 62.025 72.222 0.00 0.00 0.00 4.17
720 820 2.122729 CTCCCTCCCTCCCACACA 59.877 66.667 0.00 0.00 0.00 3.72
721 821 1.307343 CTCCCTCCCTCCCACACAT 60.307 63.158 0.00 0.00 0.00 3.21
722 822 0.031111 CTCCCTCCCTCCCACACATA 60.031 60.000 0.00 0.00 0.00 2.29
729 845 3.648067 CTCCCTCCCACACATACATACAT 59.352 47.826 0.00 0.00 0.00 2.29
733 849 5.013079 CCCTCCCACACATACATACATACAT 59.987 44.000 0.00 0.00 0.00 2.29
781 902 1.654105 GCACGACACCTATATATGCGC 59.346 52.381 0.00 0.00 0.00 6.09
842 967 3.869272 CGCTAGCGGGCAAGCAAG 61.869 66.667 29.29 0.00 38.70 4.01
843 968 4.185059 GCTAGCGGGCAAGCAAGC 62.185 66.667 0.00 3.35 38.63 4.01
844 969 2.747460 CTAGCGGGCAAGCAAGCA 60.747 61.111 12.17 0.51 40.15 3.91
845 970 2.747460 TAGCGGGCAAGCAAGCAG 60.747 61.111 12.17 0.00 40.15 4.24
849 974 4.065281 GGGCAAGCAAGCAGGCAG 62.065 66.667 11.76 0.00 35.83 4.85
850 975 4.065281 GGCAAGCAAGCAGGCAGG 62.065 66.667 9.55 0.00 35.83 4.85
851 976 4.736896 GCAAGCAAGCAGGCAGGC 62.737 66.667 2.37 0.00 35.83 4.85
852 977 3.299977 CAAGCAAGCAGGCAGGCA 61.300 61.111 9.31 0.00 35.83 4.75
853 978 2.989824 AAGCAAGCAGGCAGGCAG 60.990 61.111 9.31 0.00 35.83 4.85
985 1124 2.045926 CAAGGACGGGCCCAAGAG 60.046 66.667 24.92 7.89 37.37 2.85
987 1126 2.294078 AAGGACGGGCCCAAGAGAG 61.294 63.158 24.92 6.57 37.37 3.20
988 1127 2.683933 GGACGGGCCCAAGAGAGA 60.684 66.667 24.92 0.00 0.00 3.10
989 1128 2.291043 GGACGGGCCCAAGAGAGAA 61.291 63.158 24.92 0.00 0.00 2.87
990 1129 1.219393 GACGGGCCCAAGAGAGAAG 59.781 63.158 24.92 3.98 0.00 2.85
991 1130 2.245438 GACGGGCCCAAGAGAGAAGG 62.245 65.000 24.92 3.12 0.00 3.46
992 1131 3.002371 GGGCCCAAGAGAGAAGGG 58.998 66.667 19.95 0.00 45.68 3.95
993 1132 2.684499 GGGCCCAAGAGAGAAGGGG 61.684 68.421 19.95 0.00 43.04 4.79
994 1133 2.684499 GGCCCAAGAGAGAAGGGGG 61.684 68.421 0.00 0.00 43.04 5.40
1055 1208 0.455633 CTGCATGCGGTTCTTCTTGC 60.456 55.000 18.84 0.00 34.96 4.01
1056 1209 1.512734 GCATGCGGTTCTTCTTGCG 60.513 57.895 0.00 0.00 0.00 4.85
1229 1391 2.095372 GGCTTGCAACGGTCAGTATTAC 59.905 50.000 0.00 0.00 0.00 1.89
1256 1426 1.748122 ATGCCTGCTGCTTCTTCCG 60.748 57.895 0.00 0.00 42.00 4.30
1274 1446 3.327626 TCCGTTTGCGCTAATTAGTTCA 58.672 40.909 9.73 9.06 36.67 3.18
1276 1448 4.028383 CCGTTTGCGCTAATTAGTTCATG 58.972 43.478 9.73 0.00 36.67 3.07
1278 1450 4.662145 GTTTGCGCTAATTAGTTCATGCT 58.338 39.130 9.73 0.00 0.00 3.79
1279 1451 4.536364 TTGCGCTAATTAGTTCATGCTC 57.464 40.909 9.73 0.00 0.00 4.26
1280 1452 3.797039 TGCGCTAATTAGTTCATGCTCT 58.203 40.909 9.73 0.00 0.00 4.09
1281 1453 3.557185 TGCGCTAATTAGTTCATGCTCTG 59.443 43.478 9.73 0.00 0.00 3.35
1284 1456 4.210120 CGCTAATTAGTTCATGCTCTGTCC 59.790 45.833 13.91 0.00 0.00 4.02
1285 1457 5.363939 GCTAATTAGTTCATGCTCTGTCCT 58.636 41.667 13.91 0.00 0.00 3.85
1287 1459 6.018343 GCTAATTAGTTCATGCTCTGTCCTTC 60.018 42.308 13.91 0.00 0.00 3.46
1288 1460 5.690464 ATTAGTTCATGCTCTGTCCTTCT 57.310 39.130 0.00 0.00 0.00 2.85
1289 1461 6.798427 ATTAGTTCATGCTCTGTCCTTCTA 57.202 37.500 0.00 0.00 0.00 2.10
1290 1462 4.734398 AGTTCATGCTCTGTCCTTCTAG 57.266 45.455 0.00 0.00 0.00 2.43
1306 1479 8.836413 TGTCCTTCTAGTAATCACTTTGTTTTG 58.164 33.333 0.00 0.00 36.14 2.44
1307 1480 9.052759 GTCCTTCTAGTAATCACTTTGTTTTGA 57.947 33.333 0.00 0.00 36.14 2.69
1308 1481 9.621629 TCCTTCTAGTAATCACTTTGTTTTGAA 57.378 29.630 0.00 0.00 36.14 2.69
1327 1502 4.138290 TGAATTAAAACGGGAGCAGTTCA 58.862 39.130 0.00 0.00 0.00 3.18
1351 1526 6.453926 TGGAATCATGTGGTTACATTCATG 57.546 37.500 0.00 0.00 45.01 3.07
1413 1588 4.321480 GCAGTTGTTGTTAACGTTCGTTTT 59.679 37.500 15.40 0.00 35.73 2.43
1415 1590 4.782533 AGTTGTTGTTAACGTTCGTTTTCG 59.217 37.500 15.40 0.00 38.90 3.46
1418 1618 2.691836 TGTTAACGTTCGTTTTCGTGC 58.308 42.857 15.40 2.35 44.46 5.34
1473 1676 2.484947 GGAACAGAGGAAGTGTCGGTTT 60.485 50.000 0.00 0.00 33.24 3.27
1485 1688 1.202359 TGTCGGTTTGCTTTGCTTTCC 60.202 47.619 0.00 0.00 0.00 3.13
1500 1703 3.454447 TGCTTTCCGGGAGATTTCTCATA 59.546 43.478 0.00 0.00 44.60 2.15
1543 1746 0.693049 ATGAGCCGTTCCTTTCACCT 59.307 50.000 0.00 0.00 0.00 4.00
1591 1798 5.415221 AGTTGAAAAGAAAACGCAAATGGA 58.585 33.333 0.00 0.00 0.00 3.41
1613 1823 4.618920 AGTAGAACATCTTCCCGTTGTT 57.381 40.909 0.00 0.00 38.04 2.83
1646 1856 0.737715 ATTTGCGTCAGGTCTCGAGC 60.738 55.000 7.81 2.69 0.00 5.03
1669 1879 3.909662 CTGGAAATCAGGGGCACG 58.090 61.111 0.00 0.00 39.76 5.34
1696 1906 1.141881 CCGTGCGCCTGAATCTACT 59.858 57.895 4.18 0.00 0.00 2.57
1697 1907 0.384309 CCGTGCGCCTGAATCTACTA 59.616 55.000 4.18 0.00 0.00 1.82
1735 1945 4.402474 TCTCTTCATTCATCCGTCAGCTTA 59.598 41.667 0.00 0.00 0.00 3.09
1736 1946 5.069648 TCTCTTCATTCATCCGTCAGCTTAT 59.930 40.000 0.00 0.00 0.00 1.73
1737 1947 5.674525 TCTTCATTCATCCGTCAGCTTATT 58.325 37.500 0.00 0.00 0.00 1.40
1755 1998 6.149474 AGCTTATTACAAATGCAGTTTCGTCT 59.851 34.615 0.00 0.00 0.00 4.18
1770 2013 5.812642 AGTTTCGTCTAGAATGTTAGGCATG 59.187 40.000 0.00 0.00 38.86 4.06
1821 2064 2.292257 TGATTCTCCCTTCTCTTCCCGA 60.292 50.000 0.00 0.00 0.00 5.14
1829 2072 2.613223 CCTTCTCTTCCCGAGTTTGGTC 60.613 54.545 0.00 0.00 40.75 4.02
1846 2132 4.471904 TGGTCATGCCAGTAGTAGAAAG 57.528 45.455 4.93 0.00 43.61 2.62
1847 2133 3.838317 TGGTCATGCCAGTAGTAGAAAGT 59.162 43.478 4.93 0.00 43.61 2.66
1848 2134 5.020795 TGGTCATGCCAGTAGTAGAAAGTA 58.979 41.667 4.93 0.00 43.61 2.24
1849 2135 5.127194 TGGTCATGCCAGTAGTAGAAAGTAG 59.873 44.000 4.93 0.00 43.61 2.57
1850 2136 5.044558 GTCATGCCAGTAGTAGAAAGTAGC 58.955 45.833 0.00 0.00 0.00 3.58
1851 2137 4.709886 TCATGCCAGTAGTAGAAAGTAGCA 59.290 41.667 0.00 0.00 0.00 3.49
1911 2197 1.453015 TCAAACGCTTGGGTGCAGT 60.453 52.632 0.00 0.00 33.01 4.40
1912 2198 1.299316 CAAACGCTTGGGTGCAGTG 60.299 57.895 0.00 0.00 0.00 3.66
1913 2199 3.137637 AAACGCTTGGGTGCAGTGC 62.138 57.895 8.58 8.58 0.00 4.40
1914 2200 4.873810 ACGCTTGGGTGCAGTGCA 62.874 61.111 15.37 15.37 35.60 4.57
1915 2201 4.034258 CGCTTGGGTGCAGTGCAG 62.034 66.667 20.42 7.56 40.08 4.41
1916 2202 2.908940 GCTTGGGTGCAGTGCAGT 60.909 61.111 20.42 0.00 40.08 4.40
1917 2203 3.036577 CTTGGGTGCAGTGCAGTG 58.963 61.111 20.42 17.56 40.08 3.66
1918 2204 3.203546 CTTGGGTGCAGTGCAGTGC 62.204 63.158 34.65 34.65 40.08 4.40
1935 2222 1.012086 TGCAGCTACGTACTACTCGG 58.988 55.000 0.00 0.00 0.00 4.63
1945 2232 0.178970 TACTACTCGGGCTCCCATCC 60.179 60.000 5.70 0.00 35.37 3.51
1946 2233 1.457643 CTACTCGGGCTCCCATCCA 60.458 63.158 5.70 0.00 35.37 3.41
1947 2234 0.833834 CTACTCGGGCTCCCATCCAT 60.834 60.000 5.70 0.00 35.37 3.41
1948 2235 0.832135 TACTCGGGCTCCCATCCATC 60.832 60.000 5.70 0.00 35.37 3.51
1959 2246 1.521450 CCATCCATCATTGGCCGCTC 61.521 60.000 0.00 0.00 43.29 5.03
2001 2288 2.359850 TGACCACCAGCCGATTGC 60.360 61.111 0.00 0.00 41.71 3.56
2235 2522 3.366739 CTACCTCGTCAACGGCCCC 62.367 68.421 0.00 0.00 40.29 5.80
2324 2618 0.241749 ACAATGTGCCAATGCGTGAG 59.758 50.000 0.00 0.00 41.78 3.51
2342 2636 3.786576 GTGAGTACATTGTCTGACGATCG 59.213 47.826 14.88 14.88 0.00 3.69
2347 2641 0.179100 ATTGTCTGACGATCGCTGGG 60.179 55.000 16.60 3.31 0.00 4.45
2852 3147 2.350895 CACCGGCATCCACCTCAA 59.649 61.111 0.00 0.00 0.00 3.02
3306 3601 2.737376 GGCAACCAGGTCGTCGTC 60.737 66.667 0.00 0.00 0.00 4.20
3309 3604 4.695231 AACCAGGTCGTCGTCGCG 62.695 66.667 0.00 0.00 36.96 5.87
3469 3768 6.510478 CGTTCGTTTGTTCCTAGTGAAATGAA 60.510 38.462 0.00 0.00 33.94 2.57
3499 3801 4.176752 GACACCCGGATCTGGCCC 62.177 72.222 15.84 0.00 0.00 5.80
3520 3822 4.048241 CGAGAGGATTTGAACCTAGGTC 57.952 50.000 16.64 9.55 37.93 3.85
3555 3857 3.947868 CCAAATCTTGGCAGAGAGAAGA 58.052 45.455 5.78 0.00 45.17 2.87
3556 3858 4.525024 CCAAATCTTGGCAGAGAGAAGAT 58.475 43.478 0.00 0.00 45.17 2.40
3557 3859 5.678583 CCAAATCTTGGCAGAGAGAAGATA 58.321 41.667 0.00 0.00 45.17 1.98
3558 3860 5.526846 CCAAATCTTGGCAGAGAGAAGATAC 59.473 44.000 0.00 0.00 45.17 2.24
3559 3861 6.347696 CAAATCTTGGCAGAGAGAAGATACT 58.652 40.000 0.00 0.00 35.78 2.12
3560 3862 7.418368 CCAAATCTTGGCAGAGAGAAGATACTA 60.418 40.741 0.00 0.00 45.17 1.82
3561 3863 6.648879 ATCTTGGCAGAGAGAAGATACTAC 57.351 41.667 0.00 0.00 35.20 2.73
3562 3864 5.761205 TCTTGGCAGAGAGAAGATACTACT 58.239 41.667 0.00 0.00 0.00 2.57
3563 3865 6.901300 TCTTGGCAGAGAGAAGATACTACTA 58.099 40.000 0.00 0.00 0.00 1.82
3572 3874 8.148351 AGAGAGAAGATACTACTACTGCTACTG 58.852 40.741 0.00 0.00 0.00 2.74
3650 4046 1.267806 AGCTTGCTCGTCCAAAATGTG 59.732 47.619 0.00 0.00 0.00 3.21
3651 4047 1.689959 CTTGCTCGTCCAAAATGTGC 58.310 50.000 0.00 0.00 34.63 4.57
3698 4094 6.037830 ACGCTTAATTAGTTGTGCCGATAAAT 59.962 34.615 0.00 0.00 0.00 1.40
3723 4312 7.910441 AAATAAAGAAAACAATGGAGCCATG 57.090 32.000 2.18 0.66 36.68 3.66
3725 4314 3.173953 AGAAAACAATGGAGCCATGGA 57.826 42.857 18.40 0.00 36.68 3.41
3726 4315 3.094572 AGAAAACAATGGAGCCATGGAG 58.905 45.455 18.40 3.55 36.68 3.86
3727 4316 1.856629 AAACAATGGAGCCATGGAGG 58.143 50.000 18.40 0.00 36.68 4.30
3738 4327 1.325355 CCATGGAGGCATCATCAACC 58.675 55.000 5.56 0.00 0.00 3.77
3742 4331 2.449464 TGGAGGCATCATCAACCTTTG 58.551 47.619 0.00 0.00 32.67 2.77
3807 4396 5.634859 GTGCACCAACTTTCATTCAAATAGG 59.365 40.000 5.22 0.00 0.00 2.57
3848 4441 4.631377 CACCGAGCTTGTCTTAATCATTCA 59.369 41.667 0.00 0.00 0.00 2.57
3875 4471 3.843422 TCTGATTCAGGAAGGCCAAAAA 58.157 40.909 13.59 0.00 36.29 1.94
3878 4474 4.735369 TGATTCAGGAAGGCCAAAAAGTA 58.265 39.130 5.01 0.00 36.29 2.24
3909 4508 1.670380 GGCGGTTCAGTCTCAACTCTC 60.670 57.143 0.00 0.00 31.71 3.20
3910 4509 1.000163 GCGGTTCAGTCTCAACTCTCA 60.000 52.381 0.00 0.00 31.71 3.27
3911 4510 2.545952 GCGGTTCAGTCTCAACTCTCAA 60.546 50.000 0.00 0.00 31.71 3.02
3919 5684 1.294659 CTCAACTCTCAAGGGCACGC 61.295 60.000 0.00 0.00 0.00 5.34
3926 5691 3.055719 CAAGGGCACGCGTCCAAT 61.056 61.111 23.07 12.24 40.51 3.16
3927 5692 2.746277 AAGGGCACGCGTCCAATC 60.746 61.111 23.07 10.62 40.51 2.67
3928 5693 3.545124 AAGGGCACGCGTCCAATCA 62.545 57.895 23.07 0.00 40.51 2.57
3929 5694 3.053291 GGGCACGCGTCCAATCAA 61.053 61.111 23.07 0.00 36.65 2.57
3930 5695 2.622011 GGGCACGCGTCCAATCAAA 61.622 57.895 23.07 0.00 36.65 2.69
3932 5697 0.730265 GGCACGCGTCCAATCAAATA 59.270 50.000 9.86 0.00 0.00 1.40
3933 5698 1.531058 GGCACGCGTCCAATCAAATAC 60.531 52.381 9.86 0.00 0.00 1.89
3934 5699 1.396996 GCACGCGTCCAATCAAATACT 59.603 47.619 9.86 0.00 0.00 2.12
3935 5700 2.605818 GCACGCGTCCAATCAAATACTA 59.394 45.455 9.86 0.00 0.00 1.82
3937 5702 3.863424 CACGCGTCCAATCAAATACTAGT 59.137 43.478 9.86 0.00 0.00 2.57
3941 5706 5.163893 CGCGTCCAATCAAATACTAGTGTTT 60.164 40.000 11.45 11.45 0.00 2.83
3942 5707 6.035220 CGCGTCCAATCAAATACTAGTGTTTA 59.965 38.462 16.15 6.92 0.00 2.01
3990 6152 5.702349 CAGCTTTTCTGGTTGATTCTTCT 57.298 39.130 0.00 0.00 39.15 2.85
3991 6153 6.081872 CAGCTTTTCTGGTTGATTCTTCTT 57.918 37.500 0.00 0.00 39.15 2.52
3992 6154 6.148264 CAGCTTTTCTGGTTGATTCTTCTTC 58.852 40.000 0.00 0.00 39.15 2.87
3993 6155 6.016443 CAGCTTTTCTGGTTGATTCTTCTTCT 60.016 38.462 0.00 0.00 39.15 2.85
3994 6156 6.206438 AGCTTTTCTGGTTGATTCTTCTTCTC 59.794 38.462 0.00 0.00 0.00 2.87
3995 6157 6.545504 TTTTCTGGTTGATTCTTCTTCTCG 57.454 37.500 0.00 0.00 0.00 4.04
3996 6158 4.873746 TCTGGTTGATTCTTCTTCTCGT 57.126 40.909 0.00 0.00 0.00 4.18
3999 6161 6.936279 TCTGGTTGATTCTTCTTCTCGTAAT 58.064 36.000 0.00 0.00 0.00 1.89
4001 6163 8.528643 TCTGGTTGATTCTTCTTCTCGTAATAA 58.471 33.333 0.00 0.00 0.00 1.40
4048 6210 2.507769 GCAGCGGCCATTTCTTGC 60.508 61.111 2.24 0.00 0.00 4.01
4075 6237 0.455464 CACGCGTGATCCAACTACGA 60.455 55.000 34.93 0.00 40.01 3.43
4124 6339 8.434661 GTGTTACCAAAATTGTCAATAAGCATG 58.565 33.333 0.00 0.00 0.00 4.06
4139 6354 7.823799 TCAATAAGCATGACAGACAAGACATAA 59.176 33.333 0.00 0.00 0.00 1.90
4150 6365 5.120208 CAGACAAGACATAACCAGTTTACCG 59.880 44.000 0.00 0.00 0.00 4.02
4168 6383 8.456471 AGTTTACCGGTTCTATATTTTTCTTGC 58.544 33.333 15.04 0.00 0.00 4.01
4170 6385 9.669887 TTTACCGGTTCTATATTTTTCTTGCTA 57.330 29.630 15.04 0.00 0.00 3.49
4185 6400 6.882610 TTCTTGCTAGTTGTCATCATTTGT 57.117 33.333 0.00 0.00 0.00 2.83
4207 6422 3.867493 TCAATCTGTCATGCATCTCGAAC 59.133 43.478 0.00 0.00 0.00 3.95
4210 6425 2.493278 TCTGTCATGCATCTCGAACTGA 59.507 45.455 0.00 0.00 0.00 3.41
4241 6456 4.260985 TGCTTCAACTTCACTCAACTCAA 58.739 39.130 0.00 0.00 0.00 3.02
4242 6457 4.094887 TGCTTCAACTTCACTCAACTCAAC 59.905 41.667 0.00 0.00 0.00 3.18
4263 6478 3.759618 ACGTCTGAACAACCAAAGGAAAA 59.240 39.130 0.00 0.00 0.00 2.29
4264 6479 4.401202 ACGTCTGAACAACCAAAGGAAAAT 59.599 37.500 0.00 0.00 0.00 1.82
4265 6480 5.591067 ACGTCTGAACAACCAAAGGAAAATA 59.409 36.000 0.00 0.00 0.00 1.40
4266 6481 6.095720 ACGTCTGAACAACCAAAGGAAAATAA 59.904 34.615 0.00 0.00 0.00 1.40
4267 6482 6.975772 CGTCTGAACAACCAAAGGAAAATAAA 59.024 34.615 0.00 0.00 0.00 1.40
4268 6483 7.489757 CGTCTGAACAACCAAAGGAAAATAAAA 59.510 33.333 0.00 0.00 0.00 1.52
4269 6484 9.157104 GTCTGAACAACCAAAGGAAAATAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
4272 6487 8.940952 TGAACAACCAAAGGAAAATAAAAACAG 58.059 29.630 0.00 0.00 0.00 3.16
4277 6492 8.028652 ACCAAAGGAAAATAAAAACAGGATCA 57.971 30.769 0.00 0.00 0.00 2.92
4279 6494 9.154847 CCAAAGGAAAATAAAAACAGGATCATC 57.845 33.333 0.00 0.00 0.00 2.92
4317 6532 5.123186 TCACCATTTTTAGTACAGAATGCCG 59.877 40.000 0.00 0.00 42.53 5.69
4322 6537 8.402472 CCATTTTTAGTACAGAATGCCGAATTA 58.598 33.333 0.00 0.00 42.53 1.40
4326 6541 5.086104 AGTACAGAATGCCGAATTACACT 57.914 39.130 0.00 0.00 42.53 3.55
4327 6542 5.488341 AGTACAGAATGCCGAATTACACTT 58.512 37.500 0.00 0.00 42.53 3.16
4328 6543 5.938125 AGTACAGAATGCCGAATTACACTTT 59.062 36.000 0.00 0.00 42.53 2.66
4329 6544 5.046910 ACAGAATGCCGAATTACACTTTG 57.953 39.130 0.00 0.00 42.53 2.77
4330 6545 3.853671 CAGAATGCCGAATTACACTTTGC 59.146 43.478 0.00 0.00 0.00 3.68
4331 6546 2.939460 ATGCCGAATTACACTTTGCC 57.061 45.000 0.00 0.00 0.00 4.52
4332 6547 1.904287 TGCCGAATTACACTTTGCCT 58.096 45.000 0.00 0.00 0.00 4.75
4333 6548 2.235016 TGCCGAATTACACTTTGCCTT 58.765 42.857 0.00 0.00 0.00 4.35
4334 6549 2.227865 TGCCGAATTACACTTTGCCTTC 59.772 45.455 0.00 0.00 0.00 3.46
4335 6550 2.488153 GCCGAATTACACTTTGCCTTCT 59.512 45.455 0.00 0.00 0.00 2.85
4336 6551 3.057526 GCCGAATTACACTTTGCCTTCTT 60.058 43.478 0.00 0.00 0.00 2.52
4337 6552 4.558697 GCCGAATTACACTTTGCCTTCTTT 60.559 41.667 0.00 0.00 0.00 2.52
4338 6553 5.528870 CCGAATTACACTTTGCCTTCTTTT 58.471 37.500 0.00 0.00 0.00 2.27
4339 6554 5.983118 CCGAATTACACTTTGCCTTCTTTTT 59.017 36.000 0.00 0.00 0.00 1.94
4365 6580 9.862371 TTCTTCTACTAGTTCTGATGAAATGTC 57.138 33.333 0.00 0.00 33.52 3.06
4366 6581 9.025041 TCTTCTACTAGTTCTGATGAAATGTCA 57.975 33.333 0.00 0.00 38.41 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.005740 TCATGTCATGTCCCTTCTTCTTTG 58.994 41.667 12.54 0.00 0.00 2.77
2 3 4.916041 TCATGTCATGTCCCTTCTTCTT 57.084 40.909 12.54 0.00 0.00 2.52
4 5 3.881688 CCATCATGTCATGTCCCTTCTTC 59.118 47.826 12.54 0.00 0.00 2.87
5 6 3.372349 CCCATCATGTCATGTCCCTTCTT 60.372 47.826 12.54 0.00 0.00 2.52
7 8 2.579873 CCCATCATGTCATGTCCCTTC 58.420 52.381 12.54 0.00 0.00 3.46
8 9 1.216175 CCCCATCATGTCATGTCCCTT 59.784 52.381 12.54 0.00 0.00 3.95
10 11 0.846015 TCCCCATCATGTCATGTCCC 59.154 55.000 12.54 0.00 0.00 4.46
11 12 2.173356 TCTTCCCCATCATGTCATGTCC 59.827 50.000 12.54 0.00 0.00 4.02
12 13 3.474600 CTCTTCCCCATCATGTCATGTC 58.525 50.000 12.54 0.00 0.00 3.06
13 14 2.174210 CCTCTTCCCCATCATGTCATGT 59.826 50.000 12.54 0.00 0.00 3.21
14 15 2.440627 TCCTCTTCCCCATCATGTCATG 59.559 50.000 6.47 6.47 0.00 3.07
15 16 2.709934 CTCCTCTTCCCCATCATGTCAT 59.290 50.000 0.00 0.00 0.00 3.06
16 17 2.121948 CTCCTCTTCCCCATCATGTCA 58.878 52.381 0.00 0.00 0.00 3.58
17 18 2.368221 CTCTCCTCTTCCCCATCATGTC 59.632 54.545 0.00 0.00 0.00 3.06
18 19 2.406559 CTCTCCTCTTCCCCATCATGT 58.593 52.381 0.00 0.00 0.00 3.21
19 20 1.698532 CCTCTCCTCTTCCCCATCATG 59.301 57.143 0.00 0.00 0.00 3.07
20 21 1.582624 TCCTCTCCTCTTCCCCATCAT 59.417 52.381 0.00 0.00 0.00 2.45
21 22 1.018840 TCCTCTCCTCTTCCCCATCA 58.981 55.000 0.00 0.00 0.00 3.07
22 23 1.715785 CTCCTCTCCTCTTCCCCATC 58.284 60.000 0.00 0.00 0.00 3.51
23 24 0.267356 CCTCCTCTCCTCTTCCCCAT 59.733 60.000 0.00 0.00 0.00 4.00
24 25 0.855855 TCCTCCTCTCCTCTTCCCCA 60.856 60.000 0.00 0.00 0.00 4.96
25 26 0.340208 TTCCTCCTCTCCTCTTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
26 27 2.115427 CTTTCCTCCTCTCCTCTTCCC 58.885 57.143 0.00 0.00 0.00 3.97
64 65 1.478105 GAGCCGATGAAAAGCCCATTT 59.522 47.619 0.00 0.00 0.00 2.32
67 68 0.392998 GAGAGCCGATGAAAAGCCCA 60.393 55.000 0.00 0.00 0.00 5.36
118 119 3.726517 GTGCGCGCATCTTGGTGT 61.727 61.111 38.62 0.00 0.00 4.16
134 135 3.018193 TGGGTGGGTGGTGTGTGT 61.018 61.111 0.00 0.00 0.00 3.72
153 154 1.276705 GAAGAAGAAGGAAGGGAGCGT 59.723 52.381 0.00 0.00 0.00 5.07
195 196 2.046938 TCCGTGTGGGAAGTGACTC 58.953 57.895 0.00 0.00 43.62 3.36
203 204 3.208623 TAGTCCGGTCCGTGTGGGA 62.209 63.158 11.06 0.00 44.68 4.37
204 205 2.677524 TAGTCCGGTCCGTGTGGG 60.678 66.667 11.06 0.00 35.24 4.61
206 207 0.316204 AAAGTAGTCCGGTCCGTGTG 59.684 55.000 11.06 0.00 0.00 3.82
207 208 1.909700 TAAAGTAGTCCGGTCCGTGT 58.090 50.000 11.06 0.00 0.00 4.49
208 209 3.119388 TGAATAAAGTAGTCCGGTCCGTG 60.119 47.826 11.06 1.77 0.00 4.94
209 210 3.091545 TGAATAAAGTAGTCCGGTCCGT 58.908 45.455 11.06 0.00 0.00 4.69
210 211 3.442100 GTGAATAAAGTAGTCCGGTCCG 58.558 50.000 3.60 3.60 0.00 4.79
211 212 3.196254 TGGTGAATAAAGTAGTCCGGTCC 59.804 47.826 0.00 0.00 0.00 4.46
212 213 4.179298 GTGGTGAATAAAGTAGTCCGGTC 58.821 47.826 0.00 0.00 0.00 4.79
213 214 3.055602 GGTGGTGAATAAAGTAGTCCGGT 60.056 47.826 0.00 0.00 0.00 5.28
214 215 3.055675 TGGTGGTGAATAAAGTAGTCCGG 60.056 47.826 0.00 0.00 0.00 5.14
288 349 3.002246 AGTTTATTATCACCGCGTGCATG 59.998 43.478 4.92 0.09 32.98 4.06
301 363 5.675538 GTCAGGCAGAGACCAGTTTATTAT 58.324 41.667 0.00 0.00 0.00 1.28
302 364 4.381612 CGTCAGGCAGAGACCAGTTTATTA 60.382 45.833 0.00 0.00 32.41 0.98
303 365 3.617531 CGTCAGGCAGAGACCAGTTTATT 60.618 47.826 0.00 0.00 32.41 1.40
315 377 1.984026 TGCAGATCCGTCAGGCAGA 60.984 57.895 0.00 0.00 37.47 4.26
321 383 2.481969 GCAATCTAGTGCAGATCCGTCA 60.482 50.000 0.64 0.00 43.56 4.35
332 394 1.556911 ACAGACAGGGGCAATCTAGTG 59.443 52.381 0.00 0.00 0.00 2.74
373 435 5.173312 CGAAAATGATACTACTACTGCGTGG 59.827 44.000 0.00 0.00 0.00 4.94
378 440 9.175060 CTGATCACGAAAATGATACTACTACTG 57.825 37.037 0.00 0.00 39.48 2.74
448 522 5.701224 ACAGAAATACAAAACCTTCTGGGA 58.299 37.500 13.52 0.00 45.88 4.37
483 563 0.537188 ATCGTCGTGCCAGAATTCCT 59.463 50.000 0.65 0.00 0.00 3.36
484 564 0.652592 CATCGTCGTGCCAGAATTCC 59.347 55.000 0.65 0.00 0.00 3.01
516 600 1.135315 CCCGACCATTCAATGCAACAG 60.135 52.381 0.00 0.00 0.00 3.16
566 654 0.682855 ATGGCGTGTGGTTAATGGGG 60.683 55.000 0.00 0.00 0.00 4.96
615 703 1.007721 TGAAGGAGAAGGAGAGGAGGG 59.992 57.143 0.00 0.00 0.00 4.30
620 708 5.478679 TCAAGTAACTGAAGGAGAAGGAGAG 59.521 44.000 0.00 0.00 0.00 3.20
621 709 5.244178 GTCAAGTAACTGAAGGAGAAGGAGA 59.756 44.000 0.00 0.00 0.00 3.71
622 710 5.474825 GTCAAGTAACTGAAGGAGAAGGAG 58.525 45.833 0.00 0.00 0.00 3.69
626 714 3.326880 GGGGTCAAGTAACTGAAGGAGAA 59.673 47.826 0.00 0.00 0.00 2.87
627 715 2.904434 GGGGTCAAGTAACTGAAGGAGA 59.096 50.000 0.00 0.00 0.00 3.71
716 816 7.787028 TGGTGTGTATGTATGTATGTATGTGT 58.213 34.615 0.00 0.00 0.00 3.72
718 818 7.441157 GCTTGGTGTGTATGTATGTATGTATGT 59.559 37.037 0.00 0.00 0.00 2.29
720 820 7.735917 AGCTTGGTGTGTATGTATGTATGTAT 58.264 34.615 0.00 0.00 0.00 2.29
721 821 7.119709 AGCTTGGTGTGTATGTATGTATGTA 57.880 36.000 0.00 0.00 0.00 2.29
722 822 5.989477 AGCTTGGTGTGTATGTATGTATGT 58.011 37.500 0.00 0.00 0.00 2.29
729 845 3.195610 CAGAGGAGCTTGGTGTGTATGTA 59.804 47.826 0.00 0.00 0.00 2.29
733 849 0.321671 GCAGAGGAGCTTGGTGTGTA 59.678 55.000 0.00 0.00 0.00 2.90
781 902 2.732658 GGGGCGGTGTAGGATACG 59.267 66.667 0.00 0.00 46.99 3.06
842 967 4.368543 GTTTGCCTGCCTGCCTGC 62.369 66.667 0.00 0.00 0.00 4.85
843 968 3.688159 GGTTTGCCTGCCTGCCTG 61.688 66.667 0.00 0.00 0.00 4.85
846 971 3.994853 GTGGGTTTGCCTGCCTGC 61.995 66.667 0.00 0.00 34.45 4.85
847 972 3.673484 CGTGGGTTTGCCTGCCTG 61.673 66.667 0.00 0.00 34.45 4.85
848 973 4.974721 CCGTGGGTTTGCCTGCCT 62.975 66.667 0.00 0.00 34.45 4.75
973 1112 2.294078 CCTTCTCTCTTGGGCCCGT 61.294 63.158 19.37 0.00 0.00 5.28
991 1130 2.276740 CACCTCCATGCTTCCCCC 59.723 66.667 0.00 0.00 0.00 5.40
992 1131 2.440980 GCACCTCCATGCTTCCCC 60.441 66.667 0.00 0.00 42.62 4.81
1256 1426 4.662145 AGCATGAACTAATTAGCGCAAAC 58.338 39.130 11.47 7.33 0.00 2.93
1274 1446 5.896678 AGTGATTACTAGAAGGACAGAGCAT 59.103 40.000 0.00 0.00 34.74 3.79
1276 1448 5.845391 AGTGATTACTAGAAGGACAGAGC 57.155 43.478 0.00 0.00 34.74 4.09
1278 1450 7.540474 ACAAAGTGATTACTAGAAGGACAGA 57.460 36.000 0.00 0.00 35.69 3.41
1279 1451 8.608844 AAACAAAGTGATTACTAGAAGGACAG 57.391 34.615 0.00 0.00 35.69 3.51
1280 1452 8.836413 CAAAACAAAGTGATTACTAGAAGGACA 58.164 33.333 0.00 0.00 35.69 4.02
1281 1453 9.052759 TCAAAACAAAGTGATTACTAGAAGGAC 57.947 33.333 0.00 0.00 35.69 3.85
1306 1479 4.759516 TGAACTGCTCCCGTTTTAATTC 57.240 40.909 0.00 0.00 0.00 2.17
1307 1480 4.082245 CCATGAACTGCTCCCGTTTTAATT 60.082 41.667 0.00 0.00 0.00 1.40
1308 1481 3.443681 CCATGAACTGCTCCCGTTTTAAT 59.556 43.478 0.00 0.00 0.00 1.40
1327 1502 6.041182 CCATGAATGTAACCACATGATTCCAT 59.959 38.462 0.00 0.00 44.83 3.41
1351 1526 2.176314 AACGGAACTACGGAAGGGCC 62.176 60.000 0.00 0.00 38.39 5.80
1473 1676 0.038166 ATCTCCCGGAAAGCAAAGCA 59.962 50.000 0.73 0.00 0.00 3.91
1485 1688 3.430218 GCGAATGTATGAGAAATCTCCCG 59.570 47.826 7.91 0.00 42.20 5.14
1500 1703 3.451141 TCCTTTTGCAAAAGCGAATGT 57.549 38.095 36.00 0.00 43.07 2.71
1515 1718 3.230976 AGGAACGGCTCATTTTTCCTTT 58.769 40.909 0.00 0.00 44.54 3.11
1569 1776 5.710613 TCCATTTGCGTTTTCTTTTCAAC 57.289 34.783 0.00 0.00 0.00 3.18
1572 1779 5.966636 ACTTCCATTTGCGTTTTCTTTTC 57.033 34.783 0.00 0.00 0.00 2.29
1591 1798 4.618920 ACAACGGGAAGATGTTCTACTT 57.381 40.909 2.24 0.00 31.36 2.24
1613 1823 2.035704 ACGCAAATGCAGACATGGAAAA 59.964 40.909 6.18 0.00 42.21 2.29
1646 1856 1.957113 GCCCCTGATTTCCAGTCAAGG 60.957 57.143 0.00 0.00 41.33 3.61
1696 1906 3.314307 AGAGATCAACACGGGGAGATA 57.686 47.619 0.00 0.00 0.00 1.98
1697 1907 2.166907 AGAGATCAACACGGGGAGAT 57.833 50.000 0.00 0.00 0.00 2.75
1735 1945 7.667043 TTCTAGACGAAACTGCATTTGTAAT 57.333 32.000 0.00 0.00 0.00 1.89
1736 1946 7.172532 ACATTCTAGACGAAACTGCATTTGTAA 59.827 33.333 0.00 0.00 34.79 2.41
1737 1947 6.649141 ACATTCTAGACGAAACTGCATTTGTA 59.351 34.615 0.00 0.00 34.79 2.41
1755 1998 5.744171 TCTTTGCTCATGCCTAACATTCTA 58.256 37.500 0.00 0.00 36.64 2.10
1770 2013 2.031069 GGGACGGAAAGTTTCTTTGCTC 60.031 50.000 15.05 3.55 0.00 4.26
1829 2072 5.011090 TGCTACTTTCTACTACTGGCATG 57.989 43.478 0.00 0.00 0.00 4.06
1911 2197 1.135489 GTAGTACGTAGCTGCACTGCA 60.135 52.381 3.11 3.11 36.92 4.41
1912 2198 1.132643 AGTAGTACGTAGCTGCACTGC 59.867 52.381 1.02 2.52 0.00 4.40
1913 2199 2.537128 CGAGTAGTACGTAGCTGCACTG 60.537 54.545 1.02 0.00 0.00 3.66
1914 2200 1.664659 CGAGTAGTACGTAGCTGCACT 59.335 52.381 1.02 1.16 0.00 4.40
1915 2201 1.267932 CCGAGTAGTACGTAGCTGCAC 60.268 57.143 1.02 0.00 0.00 4.57
1916 2202 1.012086 CCGAGTAGTACGTAGCTGCA 58.988 55.000 1.02 0.00 0.00 4.41
1917 2203 0.307146 CCCGAGTAGTACGTAGCTGC 59.693 60.000 0.00 0.00 0.00 5.25
1918 2204 0.307146 GCCCGAGTAGTACGTAGCTG 59.693 60.000 0.00 0.00 0.00 4.24
1919 2205 0.179936 AGCCCGAGTAGTACGTAGCT 59.820 55.000 0.00 0.00 35.05 3.32
1920 2206 0.585838 GAGCCCGAGTAGTACGTAGC 59.414 60.000 0.00 0.00 0.00 3.58
1945 2232 2.514592 ACCGAGCGGCCAATGATG 60.515 61.111 9.14 0.00 39.32 3.07
1946 2233 2.514592 CACCGAGCGGCCAATGAT 60.515 61.111 9.14 0.00 39.32 2.45
2022 2309 0.234884 CCGAGGACTGCAACGAAAAC 59.765 55.000 0.00 0.00 0.00 2.43
2319 2613 3.197434 TCGTCAGACAATGTACTCACG 57.803 47.619 0.41 3.77 0.00 4.35
2324 2618 2.531912 CAGCGATCGTCAGACAATGTAC 59.468 50.000 17.81 0.00 0.00 2.90
2446 2741 0.538516 TAGCTCGATGAGGAGGAGGC 60.539 60.000 0.00 0.00 34.56 4.70
2447 2742 1.243902 GTAGCTCGATGAGGAGGAGG 58.756 60.000 0.00 0.00 34.56 4.30
2448 2743 1.243902 GGTAGCTCGATGAGGAGGAG 58.756 60.000 0.00 0.00 34.56 3.69
2449 2744 0.551396 TGGTAGCTCGATGAGGAGGA 59.449 55.000 0.00 0.00 34.56 3.71
2450 2745 0.671251 GTGGTAGCTCGATGAGGAGG 59.329 60.000 0.00 0.00 34.56 4.30
2451 2746 1.686355 AGTGGTAGCTCGATGAGGAG 58.314 55.000 0.00 0.00 37.11 3.69
2452 2747 2.573369 GTAGTGGTAGCTCGATGAGGA 58.427 52.381 0.00 0.00 0.00 3.71
2453 2748 1.264557 CGTAGTGGTAGCTCGATGAGG 59.735 57.143 0.00 0.00 0.00 3.86
2457 2752 2.328819 ACTCGTAGTGGTAGCTCGAT 57.671 50.000 0.00 0.00 0.00 3.59
2882 3177 2.673368 GTGTAGTCCATGTAGCAGTTGC 59.327 50.000 0.00 0.00 42.49 4.17
2943 3238 2.496817 CCGAGGAAGAAGGAGCCG 59.503 66.667 0.00 0.00 0.00 5.52
3309 3604 2.737376 GACACGGCCTTGTCGGTC 60.737 66.667 24.79 4.86 36.79 4.79
3373 3668 4.829518 GAACGCGCCGCCATTTCC 62.830 66.667 5.73 0.00 0.00 3.13
3426 3725 2.436469 AATGACGCCATGCTCGCA 60.436 55.556 5.65 0.00 32.36 5.10
3479 3778 2.903357 CCAGATCCGGGTGTCCAG 59.097 66.667 0.00 0.00 0.00 3.86
3499 3801 3.489398 CGACCTAGGTTCAAATCCTCTCG 60.489 52.174 17.53 6.35 36.60 4.04
3600 3903 7.948357 TCCAAATGATCCATTCTGAATCATTC 58.052 34.615 14.10 6.69 40.00 2.67
3650 4046 2.800544 GCAATTGCATGATGATCTTGGC 59.199 45.455 25.36 4.00 41.59 4.52
3675 4071 9.724839 TTTATTTATCGGCACAACTAATTAAGC 57.275 29.630 0.00 0.00 0.00 3.09
3698 4094 8.040132 CCATGGCTCCATTGTTTTCTTTATTTA 58.960 33.333 0.00 0.00 33.90 1.40
3721 4310 3.028850 CAAAGGTTGATGATGCCTCCAT 58.971 45.455 0.00 0.00 0.00 3.41
3723 4312 1.753073 CCAAAGGTTGATGATGCCTCC 59.247 52.381 0.00 0.00 0.00 4.30
3725 4314 2.905415 TCCAAAGGTTGATGATGCCT 57.095 45.000 0.00 0.00 0.00 4.75
3726 4315 3.294214 AGATCCAAAGGTTGATGATGCC 58.706 45.455 0.00 0.00 0.00 4.40
3727 4316 4.276926 GGTAGATCCAAAGGTTGATGATGC 59.723 45.833 0.00 0.00 35.97 3.91
3729 4318 4.708177 CGGTAGATCCAAAGGTTGATGAT 58.292 43.478 0.00 0.00 35.57 2.45
3730 4319 3.681594 GCGGTAGATCCAAAGGTTGATGA 60.682 47.826 0.00 0.00 35.57 2.92
3732 4321 2.505819 AGCGGTAGATCCAAAGGTTGAT 59.494 45.455 0.00 0.00 35.57 2.57
3733 4322 1.906574 AGCGGTAGATCCAAAGGTTGA 59.093 47.619 0.00 0.00 35.57 3.18
3734 4323 2.403252 AGCGGTAGATCCAAAGGTTG 57.597 50.000 0.00 0.00 35.57 3.77
3735 4324 3.081804 CAAAGCGGTAGATCCAAAGGTT 58.918 45.455 0.00 0.00 35.57 3.50
3736 4325 2.039879 ACAAAGCGGTAGATCCAAAGGT 59.960 45.455 0.00 0.00 35.57 3.50
3737 4326 2.420022 CACAAAGCGGTAGATCCAAAGG 59.580 50.000 0.00 0.00 35.57 3.11
3738 4327 2.159517 GCACAAAGCGGTAGATCCAAAG 60.160 50.000 0.00 0.00 35.57 2.77
3807 4396 3.014036 CGTGCATGTACGGATGGC 58.986 61.111 26.18 0.00 40.22 4.40
3848 4441 2.814336 GCCTTCCTGAATCAGAAAACGT 59.186 45.455 12.53 0.00 32.44 3.99
3909 4508 3.039202 GATTGGACGCGTGCCCTTG 62.039 63.158 28.22 0.00 0.00 3.61
3910 4509 2.746277 GATTGGACGCGTGCCCTT 60.746 61.111 28.22 12.51 0.00 3.95
3911 4510 3.545124 TTGATTGGACGCGTGCCCT 62.545 57.895 28.22 15.05 0.00 5.19
3930 5695 8.173130 GCAACGCTTTTGTATAAACACTAGTAT 58.827 33.333 0.00 0.00 34.61 2.12
3932 5697 6.017770 TGCAACGCTTTTGTATAAACACTAGT 60.018 34.615 0.00 0.00 34.61 2.57
3933 5698 6.367421 TGCAACGCTTTTGTATAAACACTAG 58.633 36.000 0.00 0.00 34.61 2.57
3934 5699 6.301687 TGCAACGCTTTTGTATAAACACTA 57.698 33.333 0.00 0.00 34.61 2.74
3935 5700 5.176407 TGCAACGCTTTTGTATAAACACT 57.824 34.783 0.00 0.00 34.61 3.55
3937 5702 5.583495 ACTTGCAACGCTTTTGTATAAACA 58.417 33.333 0.00 0.00 0.00 2.83
3941 5706 4.693566 AGCTACTTGCAACGCTTTTGTATA 59.306 37.500 0.00 0.00 45.94 1.47
3942 5707 3.502211 AGCTACTTGCAACGCTTTTGTAT 59.498 39.130 0.00 0.00 45.94 2.29
3945 5710 2.286950 TGAGCTACTTGCAACGCTTTTG 60.287 45.455 12.70 0.00 45.94 2.44
3989 6151 6.371825 AGCCAGGAAACTTTTATTACGAGAAG 59.628 38.462 0.00 0.00 40.21 2.85
3990 6152 6.235664 AGCCAGGAAACTTTTATTACGAGAA 58.764 36.000 0.00 0.00 40.21 2.87
3991 6153 5.801380 AGCCAGGAAACTTTTATTACGAGA 58.199 37.500 0.00 0.00 40.21 4.04
3992 6154 7.605410 TTAGCCAGGAAACTTTTATTACGAG 57.395 36.000 0.00 0.00 40.21 4.18
3993 6155 8.570068 AATTAGCCAGGAAACTTTTATTACGA 57.430 30.769 0.00 0.00 40.21 3.43
3994 6156 9.634163 AAAATTAGCCAGGAAACTTTTATTACG 57.366 29.630 0.00 0.00 40.21 3.18
3999 6161 8.245195 ACTGAAAATTAGCCAGGAAACTTTTA 57.755 30.769 0.00 0.00 40.21 1.52
4001 6163 6.551227 AGACTGAAAATTAGCCAGGAAACTTT 59.449 34.615 0.00 0.00 40.21 2.66
4048 6210 3.432051 GATCACGCGTGAGAGGGGG 62.432 68.421 40.50 14.99 43.61 5.40
4075 6237 8.103305 ACACAATCCACAAAGAATGATACTACT 58.897 33.333 0.00 0.00 0.00 2.57
4124 6339 6.147328 GGTAAACTGGTTATGTCTTGTCTGTC 59.853 42.308 0.00 0.00 0.00 3.51
4150 6365 9.989869 GACAACTAGCAAGAAAAATATAGAACC 57.010 33.333 0.00 0.00 0.00 3.62
4168 6383 8.037382 ACAGATTGACAAATGATGACAACTAG 57.963 34.615 9.94 0.00 44.33 2.57
4170 6385 6.487668 TGACAGATTGACAAATGATGACAACT 59.512 34.615 9.94 0.00 44.33 3.16
4181 6396 4.093850 CGAGATGCATGACAGATTGACAAA 59.906 41.667 2.46 0.00 0.00 2.83
4185 6400 3.806625 TCGAGATGCATGACAGATTGA 57.193 42.857 2.46 0.00 0.00 2.57
4207 6422 2.230508 AGTTGAAGCATGCACCAATCAG 59.769 45.455 21.98 0.00 0.00 2.90
4210 6425 2.629137 TGAAGTTGAAGCATGCACCAAT 59.371 40.909 21.98 8.94 0.00 3.16
4241 6456 2.702592 TCCTTTGGTTGTTCAGACGT 57.297 45.000 0.00 0.00 0.00 4.34
4242 6457 4.364415 TTTTCCTTTGGTTGTTCAGACG 57.636 40.909 0.00 0.00 0.00 4.18
4263 6478 7.058525 TGAGCATCAGATGATCCTGTTTTTAT 58.941 34.615 23.03 0.00 44.67 1.40
4264 6479 6.417258 TGAGCATCAGATGATCCTGTTTTTA 58.583 36.000 23.03 2.04 44.67 1.52
4265 6480 5.258841 TGAGCATCAGATGATCCTGTTTTT 58.741 37.500 23.03 0.00 44.67 1.94
4266 6481 4.851843 TGAGCATCAGATGATCCTGTTTT 58.148 39.130 23.03 0.00 44.67 2.43
4267 6482 4.498894 TGAGCATCAGATGATCCTGTTT 57.501 40.909 23.03 0.00 44.67 2.83
4311 6526 2.825532 AGGCAAAGTGTAATTCGGCATT 59.174 40.909 0.00 0.00 0.00 3.56
4339 6554 9.862371 GACATTTCATCAGAACTAGTAGAAGAA 57.138 33.333 3.59 1.42 32.39 2.52
4340 6555 9.025041 TGACATTTCATCAGAACTAGTAGAAGA 57.975 33.333 3.59 0.00 32.39 2.87


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

AutoCloner maintained by Alex Coulton.