Multiple sequence alignment - TraesCS2D01G471900

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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 TraesCS2D01G471900 chr2D 100.000 4018 0 0 1 4018 575759320 575763337 0.000000e+00 7420.0
1 TraesCS2D01G471900 chr2D 91.356 671 35 9 567 1219 575690060 575690725 0.000000e+00 896.0
2 TraesCS2D01G471900 chr2D 96.667 150 3 1 529 678 575689731 575689878 8.620000e-62 248.0
3 TraesCS2D01G471900 chr2D 91.250 80 3 1 475 550 575689650 575689729 5.490000e-19 106.0
4 TraesCS2D01G471900 chr2B 88.475 1935 158 31 2062 3960 691778292 691780197 0.000000e+00 2278.0
5 TraesCS2D01G471900 chr2B 88.907 1217 84 27 839 2031 691776908 691778097 0.000000e+00 1452.0
6 TraesCS2D01G471900 chr2A 87.460 1244 90 24 836 2031 713916121 713917346 0.000000e+00 1373.0
7 TraesCS2D01G471900 chr2A 89.321 1105 86 14 2028 3113 713917379 713918470 0.000000e+00 1358.0
8 TraesCS2D01G471900 chr2A 87.995 883 76 18 3106 3981 713930579 713931438 0.000000e+00 1016.0
9 TraesCS2D01G471900 chr2A 90.705 312 28 1 166 476 713915390 713915701 8.030000e-112 414.0
10 TraesCS2D01G471900 chr2A 84.472 161 17 4 476 634 713914195 713914349 6.960000e-33 152.0
11 TraesCS2D01G471900 chr7A 91.111 45 4 0 321 365 127083448 127083492 1.210000e-05 62.1


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 TraesCS2D01G471900 chr2D 575759320 575763337 4017 False 7420.000000 7420 100.0000 1 4018 1 chr2D.!!$F1 4017
1 TraesCS2D01G471900 chr2D 575689650 575690725 1075 False 416.666667 896 93.0910 475 1219 3 chr2D.!!$F2 744
2 TraesCS2D01G471900 chr2B 691776908 691780197 3289 False 1865.000000 2278 88.6910 839 3960 2 chr2B.!!$F1 3121
3 TraesCS2D01G471900 chr2A 713930579 713931438 859 False 1016.000000 1016 87.9950 3106 3981 1 chr2A.!!$F1 875
4 TraesCS2D01G471900 chr2A 713914195 713918470 4275 False 824.250000 1373 87.9895 166 3113 4 chr2A.!!$F2 2947

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
156 157 0.598065 GGAGTGTTGAATGGTGGCAC 59.402 55.0 9.7 9.7 0.00 5.01 F
1294 2887 0.103208 CCTCCTTCCCACTCGATTCG 59.897 60.0 0.0 0.0 0.00 3.34 F
1348 2942 0.107993 TGCAGCAGGCTCATGTAGTC 60.108 55.0 0.0 0.0 45.15 2.59 F
2259 4043 0.409484 AGCTTATGGTGGGGTTGCTT 59.591 50.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 3230 0.657840 GCTAAGCCCGCACACATAAG 59.342 55.0 0.0 0.0 0.0 1.73 R
2399 4184 0.798776 CACACGAGCCTGAAATGGAC 59.201 55.0 0.0 0.0 0.0 4.02 R
2582 4379 0.871722 GCAGACACACCATAAACGCA 59.128 50.0 0.0 0.0 0.0 5.24 R
3128 4931 1.608055 TCCATTATGCCATTGAGCCG 58.392 50.0 0.0 0.0 0.0 5.52 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
26 27 8.428063 GGTAAGCCATCTATATGCATCTTAGAT 58.572 37.037 19.27 19.27 33.92 1.98
27 28 9.258826 GTAAGCCATCTATATGCATCTTAGATG 57.741 37.037 30.61 30.61 44.51 2.90
28 29 7.672122 AGCCATCTATATGCATCTTAGATGA 57.328 36.000 34.59 16.94 46.37 2.92
29 30 8.087303 AGCCATCTATATGCATCTTAGATGAA 57.913 34.615 34.59 15.87 46.37 2.57
30 31 8.205512 AGCCATCTATATGCATCTTAGATGAAG 58.794 37.037 34.59 26.65 46.37 3.02
31 32 7.041916 GCCATCTATATGCATCTTAGATGAAGC 60.042 40.741 34.59 29.54 46.37 3.86
32 33 7.985752 CCATCTATATGCATCTTAGATGAAGCA 59.014 37.037 34.59 15.91 46.37 3.91
33 34 9.036671 CATCTATATGCATCTTAGATGAAGCAG 57.963 37.037 32.18 17.61 46.37 4.24
34 35 8.131847 TCTATATGCATCTTAGATGAAGCAGT 57.868 34.615 24.63 11.21 42.58 4.40
36 37 9.518906 CTATATGCATCTTAGATGAAGCAGTAG 57.481 37.037 24.63 15.96 42.58 2.57
37 38 4.375272 TGCATCTTAGATGAAGCAGTAGC 58.625 43.478 24.63 7.34 36.04 3.58
51 52 4.408182 GCAGTAGCTAATTCTCCTCCAA 57.592 45.455 0.00 0.00 37.91 3.53
53 54 4.813697 GCAGTAGCTAATTCTCCTCCAAAG 59.186 45.833 0.00 0.00 37.91 2.77
54 55 5.627968 GCAGTAGCTAATTCTCCTCCAAAGT 60.628 44.000 0.00 0.00 37.91 2.66
56 57 4.495690 AGCTAATTCTCCTCCAAAGTCC 57.504 45.455 0.00 0.00 0.00 3.85
57 58 3.846588 AGCTAATTCTCCTCCAAAGTCCA 59.153 43.478 0.00 0.00 0.00 4.02
59 60 5.667626 AGCTAATTCTCCTCCAAAGTCCATA 59.332 40.000 0.00 0.00 0.00 2.74
60 61 5.760743 GCTAATTCTCCTCCAAAGTCCATAC 59.239 44.000 0.00 0.00 0.00 2.39
77 78 9.807649 AAGTCCATACTTTTATGATTGAAATGC 57.192 29.630 0.00 0.00 43.60 3.56
78 79 8.970020 AGTCCATACTTTTATGATTGAAATGCA 58.030 29.630 0.00 0.00 37.86 3.96
79 80 9.754382 GTCCATACTTTTATGATTGAAATGCAT 57.246 29.630 0.00 0.00 37.86 3.96
135 136 6.540438 ACTCCAAACTTGTAGATAATCGGA 57.460 37.500 0.00 0.00 0.00 4.55
136 137 6.338937 ACTCCAAACTTGTAGATAATCGGAC 58.661 40.000 0.00 0.00 0.00 4.79
138 139 4.506654 CCAAACTTGTAGATAATCGGACGG 59.493 45.833 0.00 0.00 0.00 4.79
140 141 4.832590 ACTTGTAGATAATCGGACGGAG 57.167 45.455 0.00 0.00 0.00 4.63
153 154 3.322514 ACGGAGTGTTGAATGGTGG 57.677 52.632 0.00 0.00 42.51 4.61
154 155 0.889186 ACGGAGTGTTGAATGGTGGC 60.889 55.000 0.00 0.00 42.51 5.01
156 157 0.598065 GGAGTGTTGAATGGTGGCAC 59.402 55.000 9.70 9.70 0.00 5.01
157 158 1.317613 GAGTGTTGAATGGTGGCACA 58.682 50.000 20.82 6.09 32.99 4.57
159 160 1.032014 GTGTTGAATGGTGGCACAGT 58.968 50.000 20.82 4.81 41.80 3.55
160 161 2.158682 AGTGTTGAATGGTGGCACAGTA 60.159 45.455 20.82 5.41 41.80 2.74
161 162 2.031157 GTGTTGAATGGTGGCACAGTAC 60.031 50.000 20.82 8.41 41.80 2.73
163 164 2.884639 GTTGAATGGTGGCACAGTACTT 59.115 45.455 20.82 4.61 41.80 2.24
164 165 2.778299 TGAATGGTGGCACAGTACTTC 58.222 47.619 20.82 13.44 41.80 3.01
165 166 2.105649 TGAATGGTGGCACAGTACTTCA 59.894 45.455 20.82 15.62 41.80 3.02
166 167 3.244875 TGAATGGTGGCACAGTACTTCAT 60.245 43.478 20.82 8.64 41.80 2.57
167 168 4.019771 TGAATGGTGGCACAGTACTTCATA 60.020 41.667 20.82 0.00 41.80 2.15
168 169 4.568072 ATGGTGGCACAGTACTTCATAA 57.432 40.909 20.82 0.00 41.80 1.90
169 170 3.670625 TGGTGGCACAGTACTTCATAAC 58.329 45.455 20.82 0.00 41.80 1.89
179 1210 9.765795 GCACAGTACTTCATAACTCCTTATAAT 57.234 33.333 0.00 0.00 0.00 1.28
181 1212 9.765795 ACAGTACTTCATAACTCCTTATAATGC 57.234 33.333 0.00 0.00 0.00 3.56
202 1233 6.919775 TGCTCTTTATAGAAGGTATCCTCC 57.080 41.667 0.00 0.00 30.89 4.30
203 1234 6.382087 TGCTCTTTATAGAAGGTATCCTCCA 58.618 40.000 0.00 0.00 30.89 3.86
207 1238 8.019656 TCTTTATAGAAGGTATCCTCCACAAC 57.980 38.462 0.00 0.00 30.89 3.32
220 1251 4.164221 TCCTCCACAACTCTTTGAACTTCT 59.836 41.667 0.00 0.00 36.48 2.85
226 1257 6.763610 CCACAACTCTTTGAACTTCTACTTCT 59.236 38.462 0.00 0.00 36.48 2.85
233 1264 2.178783 GAACTTCTACTTCTCGCGCTC 58.821 52.381 5.56 0.00 0.00 5.03
239 1270 2.466520 TACTTCTCGCGCTCGCAACA 62.467 55.000 14.80 0.00 42.06 3.33
243 1274 3.411703 CTCGCGCTCGCAACACATC 62.412 63.158 14.80 0.00 42.06 3.06
303 1334 6.112927 TGCTAGGCAAATCAAGGAAATTTT 57.887 33.333 0.00 0.00 34.76 1.82
304 1335 7.238486 TGCTAGGCAAATCAAGGAAATTTTA 57.762 32.000 0.00 0.00 34.76 1.52
318 1349 4.690748 GGAAATTTTACTTCAAGCCCAAGC 59.309 41.667 0.00 0.00 40.32 4.01
324 1355 2.601905 ACTTCAAGCCCAAGCAAGAAT 58.398 42.857 0.00 0.00 43.56 2.40
326 1357 2.291209 TCAAGCCCAAGCAAGAATGA 57.709 45.000 0.00 0.00 43.56 2.57
327 1358 2.596346 TCAAGCCCAAGCAAGAATGAA 58.404 42.857 0.00 0.00 43.56 2.57
367 1398 8.539117 AGAAAAGGAAGGAAAGAGAATTTCAA 57.461 30.769 0.00 0.00 0.00 2.69
414 1446 4.394920 CGCAACCCTACAAACATGAGTATT 59.605 41.667 0.00 0.00 0.00 1.89
424 1456 2.972625 ACATGAGTATTCACCACCACG 58.027 47.619 0.00 0.00 35.83 4.94
444 1476 5.643777 CCACGTGGAAATTCACTCTAGATTT 59.356 40.000 31.31 0.00 37.39 2.17
451 1483 8.932791 TGGAAATTCACTCTAGATTTTACGAAC 58.067 33.333 0.00 0.00 28.80 3.95
453 1485 7.845066 AATTCACTCTAGATTTTACGAACCC 57.155 36.000 0.00 0.00 0.00 4.11
454 1486 5.988310 TCACTCTAGATTTTACGAACCCA 57.012 39.130 0.00 0.00 0.00 4.51
519 1555 4.079958 TGAAACCCTAGCTAATTCCCCTTC 60.080 45.833 0.00 0.00 0.00 3.46
520 1556 3.145559 ACCCTAGCTAATTCCCCTTCA 57.854 47.619 0.00 0.00 0.00 3.02
571 1659 9.390795 CATATTCAGTAGCATTGTAATTTCAGC 57.609 33.333 0.00 0.00 0.00 4.26
640 2019 5.761003 CACAATACTTCATTTCACACAGCA 58.239 37.500 0.00 0.00 0.00 4.41
660 2039 7.881643 CAGCATGTAGTTCCTGATTATCTAC 57.118 40.000 0.00 0.00 33.76 2.59
746 2125 3.372206 AGAAATTGTCATCCTCGCGAAAG 59.628 43.478 11.33 4.64 0.00 2.62
822 2250 8.635983 GTTTGATTTGTAGCGAAATCCTTTTAC 58.364 33.333 13.17 4.62 40.31 2.01
825 2253 8.181573 TGATTTGTAGCGAAATCCTTTTACATC 58.818 33.333 13.17 0.00 40.31 3.06
843 2271 8.601845 TTTACATCGATCTTGTCTTCTTGAAA 57.398 30.769 0.00 0.00 0.00 2.69
844 2272 8.777865 TTACATCGATCTTGTCTTCTTGAAAT 57.222 30.769 0.00 0.00 0.00 2.17
845 2273 9.869757 TTACATCGATCTTGTCTTCTTGAAATA 57.130 29.630 0.00 0.00 0.00 1.40
850 2414 8.721478 TCGATCTTGTCTTCTTGAAATAAAAGG 58.279 33.333 0.00 0.00 0.00 3.11
852 2416 9.833182 GATCTTGTCTTCTTGAAATAAAAGGTC 57.167 33.333 0.00 0.00 0.00 3.85
871 2435 3.003068 GGTCTATAAGCTGCTTCGTACGA 59.997 47.826 19.62 15.28 0.00 3.43
937 2506 2.874648 CTTGCTGGCCCATGAGCGTA 62.875 60.000 0.00 0.00 38.09 4.42
1084 2655 4.063967 CAGCCGCAGTCCACCGTA 62.064 66.667 0.00 0.00 0.00 4.02
1294 2887 0.103208 CCTCCTTCCCACTCGATTCG 59.897 60.000 0.00 0.00 0.00 3.34
1300 2893 3.326747 CTTCCCACTCGATTCGTTTTCT 58.673 45.455 5.89 0.00 0.00 2.52
1303 2896 3.508793 TCCCACTCGATTCGTTTTCTAGT 59.491 43.478 5.89 0.00 0.00 2.57
1307 2900 4.559251 CACTCGATTCGTTTTCTAGTGAGG 59.441 45.833 14.64 0.00 38.50 3.86
1335 2929 1.065199 CCCTAATCTCCAGTTGCAGCA 60.065 52.381 2.55 0.00 0.00 4.41
1347 2941 0.325933 TTGCAGCAGGCTCATGTAGT 59.674 50.000 0.00 0.00 45.15 2.73
1348 2942 0.107993 TGCAGCAGGCTCATGTAGTC 60.108 55.000 0.00 0.00 45.15 2.59
1349 2943 0.813210 GCAGCAGGCTCATGTAGTCC 60.813 60.000 0.00 0.00 40.25 3.85
1350 2944 0.829333 CAGCAGGCTCATGTAGTCCT 59.171 55.000 0.00 0.00 33.54 3.85
1351 2945 0.829333 AGCAGGCTCATGTAGTCCTG 59.171 55.000 19.27 19.27 45.19 3.86
1352 2946 0.826715 GCAGGCTCATGTAGTCCTGA 59.173 55.000 23.38 0.00 45.22 3.86
1353 2947 1.208052 GCAGGCTCATGTAGTCCTGAA 59.792 52.381 23.38 0.00 45.22 3.02
1391 2985 6.121776 TGGAGCAATCCAGTTAGTTTTCTA 57.878 37.500 0.00 0.00 34.33 2.10
1394 2988 8.325787 TGGAGCAATCCAGTTAGTTTTCTATAA 58.674 33.333 0.00 0.00 34.33 0.98
1395 2989 9.343539 GGAGCAATCCAGTTAGTTTTCTATAAT 57.656 33.333 0.00 0.00 31.96 1.28
1411 3021 5.407502 TCTATAATGATGCGTACCCAATCG 58.592 41.667 0.00 0.00 0.00 3.34
1416 3026 2.210116 GATGCGTACCCAATCGAATGT 58.790 47.619 0.00 0.00 0.00 2.71
1452 3062 7.828712 AGAACTCGTCAGTTTAGCTAGTAAAT 58.171 34.615 0.00 0.00 43.37 1.40
1453 3063 8.954350 AGAACTCGTCAGTTTAGCTAGTAAATA 58.046 33.333 0.00 0.00 43.37 1.40
1470 3080 7.715265 AGTAAATAATAATGTCCTGCTCACG 57.285 36.000 0.00 0.00 0.00 4.35
1478 3088 0.946221 GTCCTGCTCACGTGAACCAG 60.946 60.000 26.85 26.85 0.00 4.00
1493 3103 5.611844 CGTGAACCAGTCGTTAATTCAGTTC 60.612 44.000 0.00 0.00 33.74 3.01
1513 3123 8.540388 TCAGTTCTTATGCTCTACAAGGTTATT 58.460 33.333 0.00 0.00 0.00 1.40
1528 3138 6.860080 CAAGGTTATTCTTGTCATGCTGATT 58.140 36.000 0.00 0.00 39.27 2.57
1529 3139 7.988737 CAAGGTTATTCTTGTCATGCTGATTA 58.011 34.615 0.00 0.00 39.27 1.75
1539 3149 5.886992 TGTCATGCTGATTAATTGCTGAAG 58.113 37.500 13.15 4.12 0.00 3.02
1549 3160 3.855689 AATTGCTGAAGGGTTCATTCG 57.144 42.857 0.00 0.00 39.30 3.34
1574 3185 6.036517 GCGATCTATTGCTTCCAATGGTATAG 59.963 42.308 0.00 0.00 41.58 1.31
1619 3230 1.953559 TCCGCCTGATATGTTGCTTC 58.046 50.000 0.00 0.00 0.00 3.86
1658 3277 4.335416 AGCCTTGCAGTTGTATACACATT 58.665 39.130 4.68 0.00 33.76 2.71
1716 3335 3.117701 TGACTTGTCCATCCTGAAACCAA 60.118 43.478 0.00 0.00 0.00 3.67
1750 3369 7.334921 GTGTACTCTGTTGACTAGATCTACACT 59.665 40.741 0.00 0.00 38.02 3.55
1759 3378 5.926542 TGACTAGATCTACACTGTTTTGTGC 59.073 40.000 0.00 0.00 41.30 4.57
1844 3463 4.778213 AAAGCCTTCTACTGATATGCCA 57.222 40.909 0.00 0.00 0.00 4.92
1847 3466 2.746362 GCCTTCTACTGATATGCCATGC 59.254 50.000 0.00 0.00 0.00 4.06
1859 3478 5.184287 TGATATGCCATGCCTATGATTGTTG 59.816 40.000 0.00 0.00 36.36 3.33
1889 3508 5.466819 AGTTGATCTTTGCATTCATGTGTG 58.533 37.500 0.00 0.00 0.00 3.82
1975 3594 5.391310 GCCAATATACTCTGCCATCATTTCG 60.391 44.000 0.00 0.00 0.00 3.46
2145 3929 8.517056 TCACTACATCTTTTTACGAGACACATA 58.483 33.333 0.00 0.00 0.00 2.29
2225 4009 1.743394 GGAGGCATAAAACTGGGAACG 59.257 52.381 0.00 0.00 0.00 3.95
2259 4043 0.409484 AGCTTATGGTGGGGTTGCTT 59.591 50.000 0.00 0.00 0.00 3.91
2297 4081 4.415881 TGCTCCTACTTGTCTTGTGAAA 57.584 40.909 0.00 0.00 0.00 2.69
2307 4091 2.025793 TGTCTTGTGAAACCCAAGGTGA 60.026 45.455 0.00 0.00 39.78 4.02
2312 4096 3.636679 TGTGAAACCCAAGGTGATCAAA 58.363 40.909 0.00 0.00 35.26 2.69
2318 4102 4.118168 ACCCAAGGTGATCAAACTCAAT 57.882 40.909 0.00 0.00 32.98 2.57
2352 4137 4.021229 TGCTCTTTCCTGATTCATGCAAT 58.979 39.130 0.00 0.00 0.00 3.56
2353 4138 4.464951 TGCTCTTTCCTGATTCATGCAATT 59.535 37.500 0.00 0.00 0.00 2.32
2366 4151 5.900865 TCATGCAATTATGTGAAGAAGCA 57.099 34.783 0.00 0.00 35.03 3.91
2368 4153 5.648960 TCATGCAATTATGTGAAGAAGCAGA 59.351 36.000 0.00 0.00 33.94 4.26
2371 4156 6.927416 TGCAATTATGTGAAGAAGCAGAAAT 58.073 32.000 0.00 0.00 0.00 2.17
2377 4162 4.923893 TGTGAAGAAGCAGAAATTGTGTG 58.076 39.130 0.00 0.00 0.00 3.82
2385 4170 7.588512 AGAAGCAGAAATTGTGTGTAATTCTC 58.411 34.615 0.00 0.00 30.33 2.87
2393 4178 8.458573 AAATTGTGTGTAATTCTCACTTGGTA 57.541 30.769 12.64 0.00 40.09 3.25
2399 4184 7.277981 GTGTGTAATTCTCACTTGGTAGGTATG 59.722 40.741 12.64 0.00 37.51 2.39
2401 4186 7.491696 GTGTAATTCTCACTTGGTAGGTATGTC 59.508 40.741 6.48 0.00 33.59 3.06
2430 4215 1.300971 CTCGTGTGGGCATGGAAGTG 61.301 60.000 0.00 0.00 32.65 3.16
2448 4233 0.776810 TGCCATTTGACCTCTTGGGA 59.223 50.000 0.00 0.00 38.76 4.37
2451 4236 2.875296 CCATTTGACCTCTTGGGAACA 58.125 47.619 0.00 0.00 38.76 3.18
2454 4239 4.506625 CCATTTGACCTCTTGGGAACAGTA 60.507 45.833 0.00 0.00 44.54 2.74
2457 4242 5.416271 TTGACCTCTTGGGAACAGTATAC 57.584 43.478 0.00 0.00 44.54 1.47
2471 4256 8.305317 GGGAACAGTATACAATCAGGTATAGTC 58.695 40.741 5.50 0.00 37.64 2.59
2482 4267 8.870116 ACAATCAGGTATAGTCAGCATATACAA 58.130 33.333 5.71 0.00 37.69 2.41
2503 4291 6.827727 ACAAAATAGTTGTACTGGAGACACT 58.172 36.000 0.00 0.00 35.60 3.55
2504 4292 6.706270 ACAAAATAGTTGTACTGGAGACACTG 59.294 38.462 0.00 0.00 35.60 3.66
2505 4293 5.407407 AATAGTTGTACTGGAGACACTGG 57.593 43.478 0.00 0.00 35.60 4.00
2516 4313 4.469657 TGGAGACACTGGCACTTATTTTT 58.530 39.130 0.00 0.00 33.40 1.94
2520 4317 6.599638 GGAGACACTGGCACTTATTTTTAGAT 59.400 38.462 0.00 0.00 0.00 1.98
2521 4318 7.383102 AGACACTGGCACTTATTTTTAGATG 57.617 36.000 0.00 0.00 0.00 2.90
2572 4369 6.365970 TTGCCATTATAAACATTTGTGGGT 57.634 33.333 2.14 0.00 0.00 4.51
2573 4370 7.482169 TTGCCATTATAAACATTTGTGGGTA 57.518 32.000 2.14 0.00 0.00 3.69
2574 4371 7.667575 TGCCATTATAAACATTTGTGGGTAT 57.332 32.000 2.14 0.00 0.00 2.73
2575 4372 8.768501 TGCCATTATAAACATTTGTGGGTATA 57.231 30.769 2.14 0.00 0.00 1.47
2576 4373 9.373450 TGCCATTATAAACATTTGTGGGTATAT 57.627 29.630 2.14 0.00 0.00 0.86
2577 4374 9.855021 GCCATTATAAACATTTGTGGGTATATC 57.145 33.333 2.14 0.00 0.00 1.63
2584 4381 6.147864 ACATTTGTGGGTATATCATGTTGC 57.852 37.500 0.00 0.00 0.00 4.17
2585 4382 4.891627 TTTGTGGGTATATCATGTTGCG 57.108 40.909 0.00 0.00 0.00 4.85
2603 4400 1.135972 GCGTTTATGGTGTGTCTGCTG 60.136 52.381 0.00 0.00 0.00 4.41
2605 4402 2.157668 CGTTTATGGTGTGTCTGCTGAC 59.842 50.000 16.18 16.18 43.20 3.51
2610 4407 1.613925 TGGTGTGTCTGCTGACTAGAC 59.386 52.381 22.31 16.29 43.29 2.59
2634 4431 7.826260 CACAATTGTGTTGAAAAACCTAAGT 57.174 32.000 27.08 0.00 40.96 2.24
2635 4432 8.918961 CACAATTGTGTTGAAAAACCTAAGTA 57.081 30.769 27.08 0.00 40.96 2.24
2636 4433 9.528018 CACAATTGTGTTGAAAAACCTAAGTAT 57.472 29.630 27.08 0.00 40.96 2.12
2637 4434 9.528018 ACAATTGTGTTGAAAAACCTAAGTATG 57.472 29.630 11.07 0.00 32.58 2.39
2638 4435 8.977505 CAATTGTGTTGAAAAACCTAAGTATGG 58.022 33.333 0.00 0.00 0.00 2.74
2640 4437 7.266922 TGTGTTGAAAAACCTAAGTATGGTC 57.733 36.000 0.00 0.00 36.69 4.02
2652 4450 8.375493 ACCTAAGTATGGTCATCTAGTTTGAA 57.625 34.615 0.66 0.00 31.03 2.69
2660 4458 5.580691 TGGTCATCTAGTTTGAATACTTGCG 59.419 40.000 0.66 0.00 0.00 4.85
2665 4463 3.980646 AGTTTGAATACTTGCGTGCAA 57.019 38.095 7.12 7.12 0.00 4.08
2676 4474 2.354109 TGCGTGCAACAAAGTGAAAA 57.646 40.000 0.00 0.00 35.74 2.29
2677 4475 2.677199 TGCGTGCAACAAAGTGAAAAA 58.323 38.095 0.00 0.00 35.74 1.94
2678 4476 2.665537 TGCGTGCAACAAAGTGAAAAAG 59.334 40.909 0.00 0.00 35.74 2.27
2689 4487 7.816945 ACAAAGTGAAAAAGAAATCACAGTG 57.183 32.000 8.43 0.00 46.55 3.66
2694 4492 5.978919 GTGAAAAAGAAATCACAGTGCATCA 59.021 36.000 0.00 0.00 44.19 3.07
2696 4494 7.010367 GTGAAAAAGAAATCACAGTGCATCAAA 59.990 33.333 0.00 0.00 44.19 2.69
2697 4495 6.833342 AAAAGAAATCACAGTGCATCAAAC 57.167 33.333 0.00 0.00 0.00 2.93
2714 4512 5.673337 TCAAACTGTTCTGCTGTATGTTC 57.327 39.130 0.00 0.00 0.00 3.18
2716 4514 6.521162 TCAAACTGTTCTGCTGTATGTTCTA 58.479 36.000 0.00 0.00 0.00 2.10
2762 4561 8.823220 ACCAGTAAGTTAATTCCAAGCAATAT 57.177 30.769 0.00 0.00 0.00 1.28
2795 4594 7.278868 GTCTTCTGGAGGTTATTCATGTACTTG 59.721 40.741 2.36 2.36 0.00 3.16
2838 4641 5.277047 GTTATGATTTGCTGAAGCCTAAGC 58.723 41.667 0.00 0.00 41.18 3.09
2845 4648 1.679944 GCTGAAGCCTAAGCATGACCA 60.680 52.381 0.00 0.00 43.56 4.02
2846 4649 2.928334 CTGAAGCCTAAGCATGACCAT 58.072 47.619 0.00 0.00 43.56 3.55
3032 4835 2.019984 CAATAAGCAGAGGGGACAAGC 58.980 52.381 0.00 0.00 0.00 4.01
3033 4836 0.548510 ATAAGCAGAGGGGACAAGCC 59.451 55.000 0.00 0.00 0.00 4.35
3039 4842 1.005215 CAGAGGGGACAAGCCTGATTT 59.995 52.381 0.00 0.00 36.66 2.17
3053 4856 6.165700 AGCCTGATTTTTCAGTTTCAATGT 57.834 33.333 2.61 0.00 36.06 2.71
3071 4874 8.475331 TTCAATGTTTAACTAGCAGCTAGTAC 57.525 34.615 31.28 25.33 45.28 2.73
3104 4907 8.545420 AGTTTGTTGAGTGTAAGTATTTGTACG 58.455 33.333 0.00 0.00 0.00 3.67
3124 4927 4.855340 ACGATCTAATCCCACCATGTTTT 58.145 39.130 0.00 0.00 0.00 2.43
3125 4928 4.881850 ACGATCTAATCCCACCATGTTTTC 59.118 41.667 0.00 0.00 0.00 2.29
3128 4931 6.238484 CGATCTAATCCCACCATGTTTTCTTC 60.238 42.308 0.00 0.00 0.00 2.87
3140 4943 1.269448 GTTTTCTTCGGCTCAATGGCA 59.731 47.619 0.00 0.00 41.89 4.92
3159 4962 7.658525 ATGGCATAATGGAAATTAGTTCACA 57.341 32.000 0.00 0.00 38.06 3.58
3174 4977 3.834231 AGTTCACATGGGCTTAAAGCAAT 59.166 39.130 0.00 0.00 44.75 3.56
3176 4979 3.700538 TCACATGGGCTTAAAGCAATCT 58.299 40.909 0.00 0.00 44.75 2.40
3193 4996 5.104982 AGCAATCTGTTGACCTTTCCAAAAA 60.105 36.000 0.00 0.00 37.53 1.94
3222 5025 5.239525 GCCATATGTACTTCCAAGCCTTTAG 59.760 44.000 1.24 0.00 0.00 1.85
3242 5047 9.827411 CCTTTAGTTCTGCTTTGTTTTATACTC 57.173 33.333 0.00 0.00 0.00 2.59
3270 5075 1.379642 GGCATGTAGGCACCAGAAGC 61.380 60.000 0.00 0.00 43.51 3.86
3280 5085 2.436417 GCACCAGAAGCATTTACTCCA 58.564 47.619 0.00 0.00 0.00 3.86
3296 5101 9.469807 CATTTACTCCATAGTCTCACTGTAATC 57.530 37.037 0.00 0.00 37.15 1.75
3343 5149 2.286935 AACCCTACATCCACCTCCAT 57.713 50.000 0.00 0.00 0.00 3.41
3344 5150 1.511613 ACCCTACATCCACCTCCATG 58.488 55.000 0.00 0.00 0.00 3.66
3397 5203 8.545229 AGATATATTAGCTTCAGTTCACATGC 57.455 34.615 0.00 0.00 0.00 4.06
3543 5350 9.853555 TTATCACCATGTTAACATCAAATTGTC 57.146 29.630 18.25 0.00 33.61 3.18
3560 5368 4.430137 TTGTCATCTCTTGCTTCAATGC 57.570 40.909 0.00 0.00 0.00 3.56
3562 5370 2.674852 GTCATCTCTTGCTTCAATGCGA 59.325 45.455 0.00 0.00 35.36 5.10
3636 5445 8.760980 TTCCTTTCCTTTTTCTGTTCTCATTA 57.239 30.769 0.00 0.00 0.00 1.90
3707 5524 2.428491 CTACGAGTCCGAGATAGCCAT 58.572 52.381 0.00 0.00 39.50 4.40
3710 5527 1.621992 GAGTCCGAGATAGCCATGGA 58.378 55.000 18.40 0.00 0.00 3.41
3717 5534 3.499918 CCGAGATAGCCATGGAATTTGTC 59.500 47.826 18.40 5.50 0.00 3.18
3814 5631 4.686091 GCTTCTTGCTGGTGTTTATTTTCC 59.314 41.667 0.00 0.00 38.95 3.13
3885 5702 7.169158 TCTTTCCATTCTGTCAAACAAAAGT 57.831 32.000 0.00 0.00 0.00 2.66
3933 5757 8.609478 TTTTTCTGTCAAACAAGATAAACGTC 57.391 30.769 0.00 0.00 0.00 4.34
3981 5805 2.076863 GACAGTTGACACCATGCTACC 58.923 52.381 0.00 0.00 0.00 3.18
3982 5806 1.419762 ACAGTTGACACCATGCTACCA 59.580 47.619 0.00 0.00 0.00 3.25
3983 5807 2.040278 ACAGTTGACACCATGCTACCAT 59.960 45.455 0.00 0.00 0.00 3.55
3984 5808 3.084039 CAGTTGACACCATGCTACCATT 58.916 45.455 0.00 0.00 0.00 3.16
3985 5809 3.127548 CAGTTGACACCATGCTACCATTC 59.872 47.826 0.00 0.00 0.00 2.67
3986 5810 3.081061 GTTGACACCATGCTACCATTCA 58.919 45.455 0.00 0.00 0.00 2.57
3987 5811 3.431673 TGACACCATGCTACCATTCAA 57.568 42.857 0.00 0.00 0.00 2.69
3988 5812 3.760738 TGACACCATGCTACCATTCAAA 58.239 40.909 0.00 0.00 0.00 2.69
3989 5813 4.148079 TGACACCATGCTACCATTCAAAA 58.852 39.130 0.00 0.00 0.00 2.44
3990 5814 4.771577 TGACACCATGCTACCATTCAAAAT 59.228 37.500 0.00 0.00 0.00 1.82
3991 5815 5.948758 TGACACCATGCTACCATTCAAAATA 59.051 36.000 0.00 0.00 0.00 1.40
3992 5816 6.095300 TGACACCATGCTACCATTCAAAATAG 59.905 38.462 0.00 0.00 0.00 1.73
3993 5817 5.360714 ACACCATGCTACCATTCAAAATAGG 59.639 40.000 0.00 0.00 0.00 2.57
3994 5818 5.593909 CACCATGCTACCATTCAAAATAGGA 59.406 40.000 0.00 0.00 0.00 2.94
3995 5819 6.096705 CACCATGCTACCATTCAAAATAGGAA 59.903 38.462 0.00 0.00 0.00 3.36
3996 5820 6.840705 ACCATGCTACCATTCAAAATAGGAAT 59.159 34.615 0.00 0.00 35.43 3.01
3997 5821 7.345392 ACCATGCTACCATTCAAAATAGGAATT 59.655 33.333 0.00 0.00 32.86 2.17
3998 5822 7.869429 CCATGCTACCATTCAAAATAGGAATTC 59.131 37.037 0.00 0.00 32.86 2.17
3999 5823 7.953005 TGCTACCATTCAAAATAGGAATTCA 57.047 32.000 7.93 0.00 32.86 2.57
4000 5824 7.771183 TGCTACCATTCAAAATAGGAATTCAC 58.229 34.615 7.93 0.00 32.86 3.18
4001 5825 6.912591 GCTACCATTCAAAATAGGAATTCACG 59.087 38.462 7.93 0.00 32.86 4.35
4002 5826 7.201696 GCTACCATTCAAAATAGGAATTCACGA 60.202 37.037 7.93 0.00 32.86 4.35
4003 5827 7.645058 ACCATTCAAAATAGGAATTCACGAT 57.355 32.000 7.93 0.00 32.86 3.73
4004 5828 8.066612 ACCATTCAAAATAGGAATTCACGATT 57.933 30.769 7.93 2.62 32.86 3.34
4005 5829 8.190784 ACCATTCAAAATAGGAATTCACGATTC 58.809 33.333 7.93 0.00 42.84 2.52
4006 5830 8.408601 CCATTCAAAATAGGAATTCACGATTCT 58.591 33.333 7.93 0.00 43.08 2.40
4007 5831 9.793252 CATTCAAAATAGGAATTCACGATTCTT 57.207 29.630 7.93 0.00 43.08 2.52
4011 5835 9.884465 CAAAATAGGAATTCACGATTCTTATCC 57.116 33.333 7.93 0.00 42.76 2.59
4012 5836 9.853177 AAAATAGGAATTCACGATTCTTATCCT 57.147 29.630 7.93 0.00 42.76 3.24
4013 5837 9.853177 AAATAGGAATTCACGATTCTTATCCTT 57.147 29.630 7.93 0.00 42.76 3.36
4014 5838 9.853177 AATAGGAATTCACGATTCTTATCCTTT 57.147 29.630 7.93 0.00 42.76 3.11
4015 5839 7.559590 AGGAATTCACGATTCTTATCCTTTG 57.440 36.000 7.93 0.00 43.08 2.77
4016 5840 6.038714 AGGAATTCACGATTCTTATCCTTTGC 59.961 38.462 7.93 0.00 43.08 3.68
4017 5841 6.183360 GGAATTCACGATTCTTATCCTTTGCA 60.183 38.462 7.93 0.00 43.08 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.258826 CATCTAAGATGCATATAGATGGCTTAC 57.741 37.037 31.57 8.80 44.65 2.34
2 3 9.205513 TCATCTAAGATGCATATAGATGGCTTA 57.794 33.333 34.46 24.06 46.71 3.09
4 5 7.672122 TCATCTAAGATGCATATAGATGGCT 57.328 36.000 34.46 17.36 46.71 4.75
5 6 7.041916 GCTTCATCTAAGATGCATATAGATGGC 60.042 40.741 34.46 30.13 46.71 4.40
6 7 7.985752 TGCTTCATCTAAGATGCATATAGATGG 59.014 37.037 34.46 27.28 46.71 3.51
8 9 8.760735 ACTGCTTCATCTAAGATGCATATAGAT 58.239 33.333 20.84 20.84 44.41 1.98
9 10 8.131847 ACTGCTTCATCTAAGATGCATATAGA 57.868 34.615 18.82 18.82 44.41 1.98
10 11 9.518906 CTACTGCTTCATCTAAGATGCATATAG 57.481 37.037 0.00 5.91 44.41 1.31
11 12 7.978414 GCTACTGCTTCATCTAAGATGCATATA 59.022 37.037 0.00 0.00 44.41 0.86
12 13 6.817641 GCTACTGCTTCATCTAAGATGCATAT 59.182 38.462 0.00 0.00 44.41 1.78
13 14 6.162079 GCTACTGCTTCATCTAAGATGCATA 58.838 40.000 0.00 0.00 44.41 3.14
14 15 4.996122 GCTACTGCTTCATCTAAGATGCAT 59.004 41.667 0.00 0.00 44.41 3.96
15 16 4.375272 GCTACTGCTTCATCTAAGATGCA 58.625 43.478 5.70 5.70 43.64 3.96
16 17 4.988708 GCTACTGCTTCATCTAAGATGC 57.011 45.455 0.00 1.49 37.38 3.91
30 31 4.408182 TTGGAGGAGAATTAGCTACTGC 57.592 45.455 0.00 0.00 37.66 4.40
31 32 5.983540 ACTTTGGAGGAGAATTAGCTACTG 58.016 41.667 0.00 0.00 0.00 2.74
32 33 5.129650 GGACTTTGGAGGAGAATTAGCTACT 59.870 44.000 0.00 0.00 0.00 2.57
33 34 5.104900 TGGACTTTGGAGGAGAATTAGCTAC 60.105 44.000 0.00 0.00 0.00 3.58
34 35 5.030147 TGGACTTTGGAGGAGAATTAGCTA 58.970 41.667 0.00 0.00 0.00 3.32
36 37 4.222124 TGGACTTTGGAGGAGAATTAGC 57.778 45.455 0.00 0.00 0.00 3.09
37 38 7.130681 AGTATGGACTTTGGAGGAGAATTAG 57.869 40.000 0.00 0.00 28.61 1.73
38 39 7.510675 AAGTATGGACTTTGGAGGAGAATTA 57.489 36.000 0.00 0.00 43.70 1.40
39 40 6.394345 AAGTATGGACTTTGGAGGAGAATT 57.606 37.500 0.00 0.00 43.70 2.17
53 54 9.754382 ATGCATTTCAATCATAAAAGTATGGAC 57.246 29.630 0.00 0.00 38.15 4.02
107 108 9.968743 CGATTATCTACAAGTTTGGAGTTTAAC 57.031 33.333 4.12 0.00 40.14 2.01
108 109 9.158233 CCGATTATCTACAAGTTTGGAGTTTAA 57.842 33.333 4.12 4.89 40.14 1.52
109 110 8.533657 TCCGATTATCTACAAGTTTGGAGTTTA 58.466 33.333 4.12 0.00 40.14 2.01
110 111 7.333672 GTCCGATTATCTACAAGTTTGGAGTTT 59.666 37.037 4.12 0.00 40.14 2.66
111 112 6.817140 GTCCGATTATCTACAAGTTTGGAGTT 59.183 38.462 4.12 0.00 40.14 3.01
112 113 6.338937 GTCCGATTATCTACAAGTTTGGAGT 58.661 40.000 4.12 0.00 40.14 3.85
113 114 5.459107 CGTCCGATTATCTACAAGTTTGGAG 59.541 44.000 0.00 0.00 40.61 3.86
115 116 4.506654 CCGTCCGATTATCTACAAGTTTGG 59.493 45.833 0.00 0.00 0.00 3.28
116 117 5.345702 TCCGTCCGATTATCTACAAGTTTG 58.654 41.667 0.00 0.00 0.00 2.93
117 118 5.126707 ACTCCGTCCGATTATCTACAAGTTT 59.873 40.000 0.00 0.00 0.00 2.66
118 119 4.643784 ACTCCGTCCGATTATCTACAAGTT 59.356 41.667 0.00 0.00 0.00 2.66
121 122 3.949754 ACACTCCGTCCGATTATCTACAA 59.050 43.478 0.00 0.00 0.00 2.41
122 123 3.548770 ACACTCCGTCCGATTATCTACA 58.451 45.455 0.00 0.00 0.00 2.74
123 124 4.036027 TCAACACTCCGTCCGATTATCTAC 59.964 45.833 0.00 0.00 0.00 2.59
124 125 4.201657 TCAACACTCCGTCCGATTATCTA 58.798 43.478 0.00 0.00 0.00 1.98
125 126 3.021695 TCAACACTCCGTCCGATTATCT 58.978 45.455 0.00 0.00 0.00 1.98
127 128 3.880047 TTCAACACTCCGTCCGATTAT 57.120 42.857 0.00 0.00 0.00 1.28
129 130 2.346803 CATTCAACACTCCGTCCGATT 58.653 47.619 0.00 0.00 0.00 3.34
131 132 0.037697 CCATTCAACACTCCGTCCGA 60.038 55.000 0.00 0.00 0.00 4.55
132 133 0.320421 ACCATTCAACACTCCGTCCG 60.320 55.000 0.00 0.00 0.00 4.79
135 136 0.889186 GCCACCATTCAACACTCCGT 60.889 55.000 0.00 0.00 0.00 4.69
136 137 0.888736 TGCCACCATTCAACACTCCG 60.889 55.000 0.00 0.00 0.00 4.63
138 139 1.267806 CTGTGCCACCATTCAACACTC 59.732 52.381 0.00 0.00 32.49 3.51
140 141 1.032014 ACTGTGCCACCATTCAACAC 58.968 50.000 0.00 0.00 0.00 3.32
141 142 2.158682 AGTACTGTGCCACCATTCAACA 60.159 45.455 0.00 0.00 0.00 3.33
142 143 2.504367 AGTACTGTGCCACCATTCAAC 58.496 47.619 0.00 0.00 0.00 3.18
144 145 2.105649 TGAAGTACTGTGCCACCATTCA 59.894 45.455 0.00 0.00 0.00 2.57
145 146 2.778299 TGAAGTACTGTGCCACCATTC 58.222 47.619 0.00 0.00 0.00 2.67
146 147 2.949177 TGAAGTACTGTGCCACCATT 57.051 45.000 0.00 0.00 0.00 3.16
147 148 4.019321 AGTTATGAAGTACTGTGCCACCAT 60.019 41.667 0.00 0.00 0.00 3.55
148 149 3.326588 AGTTATGAAGTACTGTGCCACCA 59.673 43.478 0.00 0.00 0.00 4.17
149 150 3.933332 GAGTTATGAAGTACTGTGCCACC 59.067 47.826 0.00 0.00 0.00 4.61
150 151 3.933332 GGAGTTATGAAGTACTGTGCCAC 59.067 47.826 0.00 0.00 0.00 5.01
152 153 4.473477 AGGAGTTATGAAGTACTGTGCC 57.527 45.455 0.00 0.00 0.00 5.01
153 154 9.765795 ATTATAAGGAGTTATGAAGTACTGTGC 57.234 33.333 0.00 0.00 31.04 4.57
156 157 9.988815 AGCATTATAAGGAGTTATGAAGTACTG 57.011 33.333 0.32 0.00 31.04 2.74
179 1210 6.267928 GTGGAGGATACCTTCTATAAAGAGCA 59.732 42.308 0.00 0.00 31.76 4.26
181 1212 7.841282 TGTGGAGGATACCTTCTATAAAGAG 57.159 40.000 0.00 0.00 31.76 2.85
189 1220 4.067944 AGAGTTGTGGAGGATACCTTCT 57.932 45.455 0.00 0.00 31.76 2.85
195 1226 5.825593 AGTTCAAAGAGTTGTGGAGGATA 57.174 39.130 0.00 0.00 36.07 2.59
202 1233 7.306283 CGAGAAGTAGAAGTTCAAAGAGTTGTG 60.306 40.741 5.50 0.00 36.07 3.33
203 1234 6.697892 CGAGAAGTAGAAGTTCAAAGAGTTGT 59.302 38.462 5.50 0.00 36.07 3.32
207 1238 4.322274 CGCGAGAAGTAGAAGTTCAAAGAG 59.678 45.833 0.00 0.00 30.04 2.85
220 1251 1.800315 GTTGCGAGCGCGAGAAGTA 60.800 57.895 15.92 0.00 45.51 2.24
226 1257 3.478394 GATGTGTTGCGAGCGCGA 61.478 61.111 15.92 5.45 45.51 5.87
233 1264 3.247411 TGTTGTAGTTCAGATGTGTTGCG 59.753 43.478 0.00 0.00 0.00 4.85
303 1334 2.949177 TCTTGCTTGGGCTTGAAGTA 57.051 45.000 0.00 0.00 39.59 2.24
304 1335 2.071778 TTCTTGCTTGGGCTTGAAGT 57.928 45.000 0.00 0.00 39.59 3.01
324 1355 9.733556 TCCTTTTCTTATTAGCATAGTGTTTCA 57.266 29.630 0.00 0.00 0.00 2.69
327 1358 9.178758 CCTTCCTTTTCTTATTAGCATAGTGTT 57.821 33.333 0.00 0.00 0.00 3.32
367 1398 4.511527 CTGATGTAAGCATGTCTTCTGGT 58.488 43.478 5.78 0.00 36.25 4.00
424 1456 8.475331 TCGTAAAATCTAGAGTGAATTTCCAC 57.525 34.615 0.00 0.00 37.32 4.02
427 1459 8.388853 GGGTTCGTAAAATCTAGAGTGAATTTC 58.611 37.037 0.00 0.00 0.00 2.17
430 1462 6.942976 TGGGTTCGTAAAATCTAGAGTGAAT 58.057 36.000 0.00 0.00 0.00 2.57
444 1476 2.253610 AGGACACAGATGGGTTCGTAA 58.746 47.619 0.00 0.00 30.39 3.18
451 1483 1.442769 CGTTCAAGGACACAGATGGG 58.557 55.000 0.00 0.00 0.00 4.00
453 1485 0.439985 CGCGTTCAAGGACACAGATG 59.560 55.000 0.00 0.00 0.00 2.90
454 1486 0.033504 ACGCGTTCAAGGACACAGAT 59.966 50.000 5.58 0.00 0.00 2.90
571 1659 7.378995 CCGATTATCTACAAGTTCGGAGTTTAG 59.621 40.741 3.17 0.00 46.84 1.85
640 2019 7.928706 GCTTGTGTAGATAATCAGGAACTACAT 59.071 37.037 0.00 0.00 42.92 2.29
657 2036 0.242017 GCTTGCTTGGGCTTGTGTAG 59.758 55.000 0.00 0.00 39.59 2.74
659 2038 1.117142 ATGCTTGCTTGGGCTTGTGT 61.117 50.000 0.00 0.00 39.59 3.72
660 2039 0.669318 CATGCTTGCTTGGGCTTGTG 60.669 55.000 1.19 0.00 39.59 3.33
712 2091 7.398332 AGGATGACAATTTCTTTTAGGAAGCAT 59.602 33.333 0.00 0.00 0.00 3.79
724 2103 2.672961 TCGCGAGGATGACAATTTCT 57.327 45.000 3.71 0.00 0.00 2.52
746 2125 8.772705 TCAAACACTTTTGATGGAAAATTATGC 58.227 29.630 0.00 0.00 45.08 3.14
825 2253 8.507249 ACCTTTTATTTCAAGAAGACAAGATCG 58.493 33.333 0.00 0.00 0.00 3.69
843 2271 6.583562 ACGAAGCAGCTTATAGACCTTTTAT 58.416 36.000 7.92 0.00 0.00 1.40
844 2272 5.974108 ACGAAGCAGCTTATAGACCTTTTA 58.026 37.500 7.92 0.00 0.00 1.52
845 2273 4.833390 ACGAAGCAGCTTATAGACCTTTT 58.167 39.130 7.92 0.00 0.00 2.27
849 2413 3.003068 TCGTACGAAGCAGCTTATAGACC 59.997 47.826 17.11 0.00 0.00 3.85
850 2414 4.206698 TCGTACGAAGCAGCTTATAGAC 57.793 45.455 17.11 3.43 0.00 2.59
852 2416 2.974536 GCTCGTACGAAGCAGCTTATAG 59.025 50.000 24.93 5.44 0.00 1.31
854 2418 1.841450 GCTCGTACGAAGCAGCTTAT 58.159 50.000 24.93 1.84 0.00 1.73
1110 2696 2.447714 GGAGGAGGAGGACATGGCC 61.448 68.421 10.65 10.65 0.00 5.36
1149 2739 3.352338 GAGCGTCGTGTAGGGGGTG 62.352 68.421 0.00 0.00 0.00 4.61
1274 2864 1.486211 GAATCGAGTGGGAAGGAGGA 58.514 55.000 0.00 0.00 0.00 3.71
1307 2900 3.108376 ACTGGAGATTAGGGGTCAAGAC 58.892 50.000 0.00 0.00 0.00 3.01
1335 2929 2.703007 GGATTCAGGACTACATGAGCCT 59.297 50.000 0.00 0.00 38.07 4.58
1391 2985 4.265904 TCGATTGGGTACGCATCATTAT 57.734 40.909 13.97 3.56 0.00 1.28
1394 2988 2.613026 TTCGATTGGGTACGCATCAT 57.387 45.000 13.97 5.10 0.00 2.45
1395 2989 2.209273 CATTCGATTGGGTACGCATCA 58.791 47.619 13.97 0.00 0.00 3.07
1452 3062 4.729227 TCACGTGAGCAGGACATTATTA 57.271 40.909 15.76 0.00 0.00 0.98
1453 3063 3.610040 TCACGTGAGCAGGACATTATT 57.390 42.857 15.76 0.00 0.00 1.40
1455 3065 2.611971 GGTTCACGTGAGCAGGACATTA 60.612 50.000 29.72 4.98 0.00 1.90
1456 3066 1.512926 GTTCACGTGAGCAGGACATT 58.487 50.000 25.21 0.00 0.00 2.71
1461 3071 0.946221 GACTGGTTCACGTGAGCAGG 60.946 60.000 31.45 25.13 44.62 4.85
1470 3080 5.465724 AGAACTGAATTAACGACTGGTTCAC 59.534 40.000 0.00 0.00 40.09 3.18
1478 3088 7.527084 AGAGCATAAGAACTGAATTAACGAC 57.473 36.000 0.00 0.00 0.00 4.34
1528 3138 3.128589 GCGAATGAACCCTTCAGCAATTA 59.871 43.478 0.00 0.00 43.98 1.40
1529 3139 2.094545 GCGAATGAACCCTTCAGCAATT 60.095 45.455 0.00 0.00 43.98 2.32
1539 3149 2.096218 GCAATAGATCGCGAATGAACCC 60.096 50.000 15.24 0.00 0.00 4.11
1549 3160 2.880890 ACCATTGGAAGCAATAGATCGC 59.119 45.455 10.37 0.00 0.00 4.58
1580 3191 5.245531 CGGAATGCTTATAAATCCTAGCCA 58.754 41.667 0.00 0.00 32.73 4.75
1601 3212 1.959042 AGAAGCAACATATCAGGCGG 58.041 50.000 0.00 0.00 0.00 6.13
1619 3230 0.657840 GCTAAGCCCGCACACATAAG 59.342 55.000 0.00 0.00 0.00 1.73
1663 3282 5.163530 TGCTAGTATGGTCCAAATGCAAATG 60.164 40.000 0.00 0.00 0.00 2.32
1679 3298 7.620880 TGGACAAGTCATAAGTTTGCTAGTAT 58.379 34.615 2.29 0.00 0.00 2.12
1716 3335 5.978814 AGTCAACAGAGTACACAGAAGTTT 58.021 37.500 0.00 0.00 0.00 2.66
1750 3369 5.235850 TCCTTGACCTATAGCACAAAACA 57.764 39.130 9.78 0.00 0.00 2.83
1759 3378 3.057174 GCACGAGGATCCTTGACCTATAG 60.057 52.174 32.26 14.36 36.57 1.31
1844 3463 4.795469 TCACCATCAACAATCATAGGCAT 58.205 39.130 0.00 0.00 0.00 4.40
1847 3466 5.882000 TCAACTCACCATCAACAATCATAGG 59.118 40.000 0.00 0.00 0.00 2.57
1859 3478 4.978083 ATGCAAAGATCAACTCACCATC 57.022 40.909 0.00 0.00 0.00 3.51
1889 3508 2.615747 GGAACTGTTCTCCCACCTAAGC 60.616 54.545 19.05 0.00 0.00 3.09
1927 3546 0.886490 CAGCCGTGCTTGAAGGTTCT 60.886 55.000 0.00 0.00 36.40 3.01
1975 3594 4.019860 ACCATGACCATATCTATGCCAGAC 60.020 45.833 0.00 0.00 35.62 3.51
2145 3929 8.798859 AGCATAAAGAAGTAATCACATGAACT 57.201 30.769 0.00 0.00 0.00 3.01
2259 4043 3.369892 GGAGCATCTTTAAGGCACTCAGA 60.370 47.826 9.79 0.00 32.43 3.27
2297 4081 3.593442 TTGAGTTTGATCACCTTGGGT 57.407 42.857 0.00 0.00 35.62 4.51
2352 4137 7.140705 CACACAATTTCTGCTTCTTCACATAA 58.859 34.615 0.00 0.00 0.00 1.90
2353 4138 6.262944 ACACACAATTTCTGCTTCTTCACATA 59.737 34.615 0.00 0.00 0.00 2.29
2366 4151 7.285401 ACCAAGTGAGAATTACACACAATTTCT 59.715 33.333 14.70 0.00 41.32 2.52
2368 4153 7.346751 ACCAAGTGAGAATTACACACAATTT 57.653 32.000 14.70 1.43 41.32 1.82
2371 4156 5.995282 CCTACCAAGTGAGAATTACACACAA 59.005 40.000 14.70 0.00 41.32 3.33
2377 4162 6.985059 GGACATACCTACCAAGTGAGAATTAC 59.015 42.308 0.00 0.00 35.41 1.89
2385 4170 5.496556 TGAAATGGACATACCTACCAAGTG 58.503 41.667 0.00 0.00 39.86 3.16
2393 4178 2.158900 CGAGCCTGAAATGGACATACCT 60.159 50.000 0.00 0.00 39.86 3.08
2399 4184 0.798776 CACACGAGCCTGAAATGGAC 59.201 55.000 0.00 0.00 0.00 4.02
2401 4186 1.308069 CCCACACGAGCCTGAAATGG 61.308 60.000 0.00 0.00 0.00 3.16
2430 4215 1.546029 GTTCCCAAGAGGTCAAATGGC 59.454 52.381 0.00 0.00 36.75 4.40
2439 4224 5.989477 TGATTGTATACTGTTCCCAAGAGG 58.011 41.667 4.17 0.00 0.00 3.69
2448 4233 8.361139 GCTGACTATACCTGATTGTATACTGTT 58.639 37.037 4.17 0.00 33.58 3.16
2451 4236 8.657387 ATGCTGACTATACCTGATTGTATACT 57.343 34.615 4.17 0.00 33.58 2.12
2457 4242 9.710900 TTTGTATATGCTGACTATACCTGATTG 57.289 33.333 0.00 0.00 33.14 2.67
2471 4256 9.325198 TCCAGTACAACTATTTTGTATATGCTG 57.675 33.333 0.00 3.72 37.25 4.41
2482 4267 5.794894 CCAGTGTCTCCAGTACAACTATTT 58.205 41.667 0.00 0.00 0.00 1.40
2485 4270 2.561419 GCCAGTGTCTCCAGTACAACTA 59.439 50.000 0.00 0.00 0.00 2.24
2548 4345 6.956497 ACCCACAAATGTTTATAATGGCAAT 58.044 32.000 0.00 0.00 0.00 3.56
2572 4369 6.540551 ACACACCATAAACGCAACATGATATA 59.459 34.615 0.00 0.00 0.00 0.86
2573 4370 5.356751 ACACACCATAAACGCAACATGATAT 59.643 36.000 0.00 0.00 0.00 1.63
2574 4371 4.697828 ACACACCATAAACGCAACATGATA 59.302 37.500 0.00 0.00 0.00 2.15
2575 4372 3.505680 ACACACCATAAACGCAACATGAT 59.494 39.130 0.00 0.00 0.00 2.45
2576 4373 2.881513 ACACACCATAAACGCAACATGA 59.118 40.909 0.00 0.00 0.00 3.07
2577 4374 3.058293 AGACACACCATAAACGCAACATG 60.058 43.478 0.00 0.00 0.00 3.21
2578 4375 3.058293 CAGACACACCATAAACGCAACAT 60.058 43.478 0.00 0.00 0.00 2.71
2579 4376 2.289274 CAGACACACCATAAACGCAACA 59.711 45.455 0.00 0.00 0.00 3.33
2580 4377 2.916111 CAGACACACCATAAACGCAAC 58.084 47.619 0.00 0.00 0.00 4.17
2581 4378 1.265635 GCAGACACACCATAAACGCAA 59.734 47.619 0.00 0.00 0.00 4.85
2582 4379 0.871722 GCAGACACACCATAAACGCA 59.128 50.000 0.00 0.00 0.00 5.24
2583 4380 1.135972 CAGCAGACACACCATAAACGC 60.136 52.381 0.00 0.00 0.00 4.84
2584 4381 2.157668 GTCAGCAGACACACCATAAACG 59.842 50.000 4.10 0.00 44.34 3.60
2585 4382 3.813529 GTCAGCAGACACACCATAAAC 57.186 47.619 4.10 0.00 44.34 2.01
2611 4408 9.528018 CATACTTAGGTTTTTCAACACAATTGT 57.472 29.630 4.92 4.92 37.67 2.71
2634 4431 7.438160 CGCAAGTATTCAAACTAGATGACCATA 59.562 37.037 0.00 0.00 0.00 2.74
2635 4432 6.258727 CGCAAGTATTCAAACTAGATGACCAT 59.741 38.462 0.00 0.00 0.00 3.55
2636 4433 5.580691 CGCAAGTATTCAAACTAGATGACCA 59.419 40.000 0.00 0.00 0.00 4.02
2637 4434 6.037423 CGCAAGTATTCAAACTAGATGACC 57.963 41.667 0.00 0.00 0.00 4.02
2660 4458 6.955407 GTGATTTCTTTTTCACTTTGTTGCAC 59.045 34.615 0.00 0.00 39.30 4.57
2665 4463 6.311200 GCACTGTGATTTCTTTTTCACTTTGT 59.689 34.615 12.86 0.00 42.17 2.83
2676 4474 5.526115 CAGTTTGATGCACTGTGATTTCTT 58.474 37.500 12.86 0.00 37.47 2.52
2677 4475 5.117355 CAGTTTGATGCACTGTGATTTCT 57.883 39.130 12.86 0.00 37.47 2.52
2689 4487 4.083110 ACATACAGCAGAACAGTTTGATGC 60.083 41.667 11.34 10.62 34.23 3.91
2694 4492 7.661437 TCAATAGAACATACAGCAGAACAGTTT 59.339 33.333 0.00 0.00 0.00 2.66
2696 4494 6.701340 TCAATAGAACATACAGCAGAACAGT 58.299 36.000 0.00 0.00 0.00 3.55
2697 4495 7.783090 ATCAATAGAACATACAGCAGAACAG 57.217 36.000 0.00 0.00 0.00 3.16
2716 4514 9.632638 ACTGGTCACATTAAGCTATAAATCAAT 57.367 29.630 0.00 0.00 0.00 2.57
2725 4524 9.953565 AATTAACTTACTGGTCACATTAAGCTA 57.046 29.630 0.00 0.00 41.16 3.32
2729 4528 9.575868 TTGGAATTAACTTACTGGTCACATTAA 57.424 29.630 0.00 0.00 0.00 1.40
2736 4535 6.569179 TTGCTTGGAATTAACTTACTGGTC 57.431 37.500 0.00 0.00 0.00 4.02
2745 4544 8.532977 ACACACAAATATTGCTTGGAATTAAC 57.467 30.769 0.00 0.00 0.00 2.01
2762 4561 3.644966 AACCTCCAGAAGACACACAAA 57.355 42.857 0.00 0.00 0.00 2.83
2806 4609 3.684305 CAGCAAATCATAACGACTCACCA 59.316 43.478 0.00 0.00 0.00 4.17
2812 4615 3.375299 AGGCTTCAGCAAATCATAACGAC 59.625 43.478 0.30 0.00 44.36 4.34
2814 4617 5.484173 TTAGGCTTCAGCAAATCATAACG 57.516 39.130 0.30 0.00 44.36 3.18
2838 4641 5.575606 GCTGTTCAAAGATTCAATGGTCATG 59.424 40.000 0.00 0.00 0.00 3.07
2845 4648 4.806330 CTGCAGCTGTTCAAAGATTCAAT 58.194 39.130 16.64 0.00 0.00 2.57
2846 4649 3.551454 GCTGCAGCTGTTCAAAGATTCAA 60.551 43.478 31.33 0.00 38.21 2.69
2957 4760 2.414481 CACTGCATTTCCAAGACTCTCG 59.586 50.000 0.00 0.00 0.00 4.04
2971 4774 1.890489 TGCAAGCTGAATTCACTGCAT 59.110 42.857 22.25 10.19 37.23 3.96
2972 4775 1.268625 CTGCAAGCTGAATTCACTGCA 59.731 47.619 23.57 23.57 37.23 4.41
3039 4842 7.647715 GCTGCTAGTTAAACATTGAAACTGAAA 59.352 33.333 11.43 0.00 35.23 2.69
3071 4874 5.065218 ACTTACACTCAACAAACTGAAGCTG 59.935 40.000 0.00 0.00 0.00 4.24
3078 4881 8.545420 CGTACAAATACTTACACTCAACAAACT 58.455 33.333 0.00 0.00 0.00 2.66
3104 4907 6.238484 CGAAGAAAACATGGTGGGATTAGATC 60.238 42.308 0.00 0.00 0.00 2.75
3124 4927 2.708216 TTATGCCATTGAGCCGAAGA 57.292 45.000 0.00 0.00 0.00 2.87
3125 4928 2.030540 CCATTATGCCATTGAGCCGAAG 60.031 50.000 0.00 0.00 0.00 3.79
3128 4931 1.608055 TCCATTATGCCATTGAGCCG 58.392 50.000 0.00 0.00 0.00 5.52
3140 4943 6.840705 AGCCCATGTGAACTAATTTCCATTAT 59.159 34.615 0.00 0.00 32.58 1.28
3159 4962 4.082026 GTCAACAGATTGCTTTAAGCCCAT 60.082 41.667 14.80 6.47 41.51 4.00
3193 4996 5.711976 GGCTTGGAAGTACATATGGCATATT 59.288 40.000 17.19 11.24 0.00 1.28
3199 5002 6.357367 ACTAAAGGCTTGGAAGTACATATGG 58.643 40.000 7.80 0.00 0.00 2.74
3210 5013 3.508845 AAGCAGAACTAAAGGCTTGGA 57.491 42.857 0.00 0.00 44.29 3.53
3222 5025 5.086727 GCCGAGTATAAAACAAAGCAGAAC 58.913 41.667 0.00 0.00 0.00 3.01
3242 5047 1.789078 GCCTACATGCCATTGAGCCG 61.789 60.000 0.00 0.00 0.00 5.52
3270 5075 9.469807 GATTACAGTGAGACTATGGAGTAAATG 57.530 37.037 0.00 0.00 35.45 2.32
3280 5085 7.946381 TGAGTTGAGATTACAGTGAGACTAT 57.054 36.000 0.00 0.00 0.00 2.12
3296 5101 2.499289 AGGCACTCCAGTATGAGTTGAG 59.501 50.000 0.00 0.00 42.92 3.02
3447 5254 6.016718 GCACTAACACGCGATAACAAAATTA 58.983 36.000 15.93 0.00 0.00 1.40
3459 5266 1.693467 TAAGACAGCACTAACACGCG 58.307 50.000 3.53 3.53 0.00 6.01
3460 5267 2.222819 GCATAAGACAGCACTAACACGC 60.223 50.000 0.00 0.00 0.00 5.34
3461 5268 3.254060 AGCATAAGACAGCACTAACACG 58.746 45.455 0.00 0.00 0.00 4.49
3504 5311 8.945195 AACATGGTGATAATGAACATGGATAT 57.055 30.769 8.35 0.00 42.28 1.63
3526 5333 7.809331 GCAAGAGATGACAATTTGATGTTAACA 59.191 33.333 11.41 11.41 32.57 2.41
3542 5349 2.674852 GTCGCATTGAAGCAAGAGATGA 59.325 45.455 0.00 0.00 0.00 2.92
3543 5350 2.417586 TGTCGCATTGAAGCAAGAGATG 59.582 45.455 0.00 0.00 0.00 2.90
3560 5368 7.493971 AGAGAAGATTTATCCATCAAACTGTCG 59.506 37.037 0.00 0.00 0.00 4.35
3562 5370 8.954350 CAAGAGAAGATTTATCCATCAAACTGT 58.046 33.333 0.00 0.00 0.00 3.55
3596 5404 5.104982 AGGAAAGGAAAACAAACATTGAGCA 60.105 36.000 0.00 0.00 0.00 4.26
3608 5417 7.320399 TGAGAACAGAAAAAGGAAAGGAAAAC 58.680 34.615 0.00 0.00 0.00 2.43
3636 5445 5.251700 ACAAGATACTCCTGGACTTCCAAAT 59.748 40.000 0.00 0.00 46.97 2.32
3710 5527 4.162131 AGCTTTGGTGTTTCTGGACAAATT 59.838 37.500 0.00 0.00 31.51 1.82
3717 5534 4.520492 AGATGTAAGCTTTGGTGTTTCTGG 59.480 41.667 3.20 0.00 0.00 3.86
3748 5565 3.244665 CCAGGACATGCTATATGGCAAGA 60.245 47.826 21.09 0.00 45.68 3.02
3858 5675 9.918630 CTTTTGTTTGACAGAATGGAAAGATAT 57.081 29.630 0.00 0.00 43.62 1.63
3868 5685 5.964758 TGCTCAACTTTTGTTTGACAGAAT 58.035 33.333 0.00 0.00 41.35 2.40
3885 5702 3.111484 TGATACCACCTACCATGCTCAA 58.889 45.455 0.00 0.00 0.00 3.02
3944 5768 6.826231 TCAACTGTCAACAGAAAAGAATGGTA 59.174 34.615 16.71 0.00 46.59 3.25
3946 5770 5.973565 GTCAACTGTCAACAGAAAAGAATGG 59.026 40.000 16.71 0.00 46.59 3.16
3981 5805 9.793252 AAGAATCGTGAATTCCTATTTTGAATG 57.207 29.630 2.27 0.00 44.20 2.67
3985 5809 9.884465 GGATAAGAATCGTGAATTCCTATTTTG 57.116 33.333 2.27 0.00 44.20 2.44
3986 5810 9.853177 AGGATAAGAATCGTGAATTCCTATTTT 57.147 29.630 2.27 0.00 44.20 1.82
3987 5811 9.853177 AAGGATAAGAATCGTGAATTCCTATTT 57.147 29.630 2.27 0.00 44.20 1.40
3988 5812 9.853177 AAAGGATAAGAATCGTGAATTCCTATT 57.147 29.630 2.27 0.05 44.20 1.73
3989 5813 9.277783 CAAAGGATAAGAATCGTGAATTCCTAT 57.722 33.333 2.27 0.00 44.20 2.57
3990 5814 7.226720 GCAAAGGATAAGAATCGTGAATTCCTA 59.773 37.037 2.27 0.00 44.20 2.94
3991 5815 6.038714 GCAAAGGATAAGAATCGTGAATTCCT 59.961 38.462 2.27 0.00 44.20 3.36
3992 5816 6.183360 TGCAAAGGATAAGAATCGTGAATTCC 60.183 38.462 2.27 0.00 44.20 3.01
3993 5817 6.785191 TGCAAAGGATAAGAATCGTGAATTC 58.215 36.000 0.00 0.00 43.58 2.17
3994 5818 6.757897 TGCAAAGGATAAGAATCGTGAATT 57.242 33.333 0.00 0.00 32.44 2.17


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

AutoCloner maintained by Alex Coulton.