Multiple sequence alignment - TraesCS2A01G393500

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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 TraesCS2A01G393500 chr2A 100.000 2843 0 0 1 2843 643232184 643229342 0.000000e+00 5251.0
1 TraesCS2A01G393500 chr2A 82.873 362 46 7 57 402 49942104 49942465 7.650000e-81 311.0
2 TraesCS2A01G393500 chr2D 91.558 2144 127 19 10 2129 498533989 498531876 0.000000e+00 2907.0
3 TraesCS2A01G393500 chr2D 84.685 555 49 19 2311 2843 498531018 498530478 3.250000e-144 521.0
4 TraesCS2A01G393500 chr2D 83.208 399 54 8 409 798 628263681 628264075 1.250000e-93 353.0
5 TraesCS2A01G393500 chr2D 86.207 174 24 0 1396 1569 569853853 569853680 3.740000e-44 189.0
6 TraesCS2A01G393500 chr2D 97.561 41 1 0 2129 2169 622496518 622496558 1.410000e-08 71.3
7 TraesCS2A01G393500 chr2B 95.238 1050 46 3 795 1843 585757650 585756604 0.000000e+00 1659.0
8 TraesCS2A01G393500 chr4A 80.695 777 98 35 1037 1793 613544311 613543567 8.900000e-155 556.0
9 TraesCS2A01G393500 chr4A 85.882 170 24 0 1396 1565 571971976 571972145 6.260000e-42 182.0
10 TraesCS2A01G393500 chr1A 82.363 601 61 27 1383 1958 517520072 517520652 5.510000e-132 481.0
11 TraesCS2A01G393500 chr1A 82.197 264 25 14 1025 1269 517519743 517520003 1.030000e-49 207.0
12 TraesCS2A01G393500 chr1D 85.294 476 54 10 1383 1844 421226617 421227090 7.130000e-131 477.0
13 TraesCS2A01G393500 chr1D 82.000 250 30 12 1023 1266 421464869 421465109 6.210000e-47 198.0
14 TraesCS2A01G393500 chr1D 80.065 306 28 16 995 1268 421226243 421226547 2.230000e-46 196.0
15 TraesCS2A01G393500 chr1B 84.679 483 60 7 1369 1844 570526244 570526719 1.190000e-128 470.0
16 TraesCS2A01G393500 chr1B 80.156 257 35 13 1023 1268 570525940 570526191 8.090000e-41 178.0
17 TraesCS2A01G393500 chr5D 85.908 369 35 7 57 408 349067442 349067810 7.430000e-101 377.0
18 TraesCS2A01G393500 chr5D 85.054 368 38 6 58 408 130698593 130698226 2.690000e-95 359.0
19 TraesCS2A01G393500 chr5D 80.810 469 68 14 1385 1843 556449729 556450185 5.830000e-92 348.0
20 TraesCS2A01G393500 chr5D 78.322 143 29 1 2281 2423 505398029 505397889 1.080000e-14 91.6
21 TraesCS2A01G393500 chr7A 85.870 368 35 7 58 408 32931227 32930860 2.670000e-100 375.0
22 TraesCS2A01G393500 chr6D 85.870 368 34 8 58 408 392115216 392115582 2.670000e-100 375.0
23 TraesCS2A01G393500 chr6D 97.619 42 1 0 2128 2169 6483417 6483376 3.930000e-09 73.1
24 TraesCS2A01G393500 chr6D 97.500 40 1 0 2130 2169 11489858 11489819 5.080000e-08 69.4
25 TraesCS2A01G393500 chr7D 85.598 368 36 7 58 408 315498741 315499108 1.240000e-98 370.0
26 TraesCS2A01G393500 chr7D 84.636 371 38 11 57 408 183692298 183692668 4.510000e-93 351.0
27 TraesCS2A01G393500 chr7D 79.630 324 37 17 57 363 266902853 266903164 3.710000e-49 206.0
28 TraesCS2A01G393500 chr7D 80.193 207 29 10 1881 2080 586834607 586834808 8.210000e-31 145.0
29 TraesCS2A01G393500 chr3B 84.595 370 39 9 57 408 623393164 623393533 4.510000e-93 351.0
30 TraesCS2A01G393500 chr3B 82.203 354 54 8 57 402 503601613 503601261 2.140000e-76 296.0
31 TraesCS2A01G393500 chr3B 95.455 44 2 0 2126 2169 802746390 802746433 1.410000e-08 71.3
32 TraesCS2A01G393500 chr3A 81.616 359 51 11 57 402 599776846 599777202 1.670000e-72 283.0
33 TraesCS2A01G393500 chr4D 79.630 324 42 12 57 363 360327008 360326692 7.980000e-51 211.0
34 TraesCS2A01G393500 chr5B 84.358 179 27 1 1385 1563 491173622 491173445 1.050000e-39 174.0
35 TraesCS2A01G393500 chr6B 77.636 313 44 16 57 363 372871249 372871541 1.750000e-37 167.0
36 TraesCS2A01G393500 chr3D 81.379 145 26 1 2281 2425 411006228 411006371 1.790000e-22 117.0
37 TraesCS2A01G393500 chrUn 97.561 41 1 0 2129 2169 227962052 227962092 1.410000e-08 71.3
38 TraesCS2A01G393500 chrUn 97.500 40 1 0 2130 2169 109108883 109108922 5.080000e-08 69.4
39 TraesCS2A01G393500 chrUn 95.455 44 1 1 2126 2169 113191558 113191516 5.080000e-08 69.4
40 TraesCS2A01G393500 chrUn 93.478 46 2 1 2124 2169 50621653 50621609 1.830000e-07 67.6
41 TraesCS2A01G393500 chr5A 90.741 54 4 1 2116 2169 663579119 663579067 1.410000e-08 71.3
42 TraesCS2A01G393500 chr4B 96.875 32 1 0 20 51 131437997 131438028 1.000000e-03 54.7


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 TraesCS2A01G393500 chr2A 643229342 643232184 2842 True 5251.0 5251 100.0000 1 2843 1 chr2A.!!$R1 2842
1 TraesCS2A01G393500 chr2D 498530478 498533989 3511 True 1714.0 2907 88.1215 10 2843 2 chr2D.!!$R2 2833
2 TraesCS2A01G393500 chr2B 585756604 585757650 1046 True 1659.0 1659 95.2380 795 1843 1 chr2B.!!$R1 1048
3 TraesCS2A01G393500 chr4A 613543567 613544311 744 True 556.0 556 80.6950 1037 1793 1 chr4A.!!$R1 756
4 TraesCS2A01G393500 chr1A 517519743 517520652 909 False 344.0 481 82.2800 1025 1958 2 chr1A.!!$F1 933
5 TraesCS2A01G393500 chr1D 421226243 421227090 847 False 336.5 477 82.6795 995 1844 2 chr1D.!!$F2 849
6 TraesCS2A01G393500 chr1B 570525940 570526719 779 False 324.0 470 82.4175 1023 1844 2 chr1B.!!$F1 821

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
645 669 0.029834 CTGCACTGTGGAGTTGCAAC 59.97 55.0 22.17 22.17 36.46 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2314 0.03759 TGGCGCCAAAGAGGTTACAT 59.962 50.0 30.74 0.0 40.61 2.29 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
34 35 1.002087 AGATGTTTCGGGTCTCGCTTT 59.998 47.619 0.00 0.00 39.05 3.51
35 36 1.128692 GATGTTTCGGGTCTCGCTTTG 59.871 52.381 0.00 0.00 39.05 2.77
43 44 1.605753 GGTCTCGCTTTGAGGGTTTT 58.394 50.000 0.00 0.00 45.32 2.43
44 45 2.551504 GGGTCTCGCTTTGAGGGTTTTA 60.552 50.000 0.00 0.00 45.32 1.52
52 53 5.065988 TCGCTTTGAGGGTTTTAGAATATGC 59.934 40.000 0.00 0.00 0.00 3.14
65 66 6.554334 TTAGAATATGCGGGAATACTTTGC 57.446 37.500 0.00 0.00 0.00 3.68
68 69 1.014352 ATGCGGGAATACTTTGCGTC 58.986 50.000 0.00 0.00 0.00 5.19
71 72 1.202031 GCGGGAATACTTTGCGTCAAG 60.202 52.381 0.00 0.00 0.00 3.02
79 80 3.126001 ACTTTGCGTCAAGAAGATGGA 57.874 42.857 3.09 0.00 33.68 3.41
81 82 1.442769 TTGCGTCAAGAAGATGGAGC 58.557 50.000 0.00 0.00 34.88 4.70
131 132 6.096695 GGATGGCGTTCTTTAGCATTTTTAA 58.903 36.000 0.00 0.00 34.54 1.52
136 137 7.095439 TGGCGTTCTTTAGCATTTTTAATTTGG 60.095 33.333 0.00 0.00 34.54 3.28
150 164 3.799281 AATTTGGATGTTGGTATGCCG 57.201 42.857 0.00 0.00 37.67 5.69
165 179 5.989168 TGGTATGCCGAAGTATTAATGTCTG 59.011 40.000 0.00 0.00 37.67 3.51
173 189 7.572353 GCCGAAGTATTAATGTCTGTGTCAAAA 60.572 37.037 0.00 0.00 0.00 2.44
264 280 6.624352 ACATGTTATGTAGCATTCCACATC 57.376 37.500 0.00 0.00 42.78 3.06
267 283 7.286087 ACATGTTATGTAGCATTCCACATCAAT 59.714 33.333 0.00 0.00 42.78 2.57
270 286 9.353431 TGTTATGTAGCATTCCACATCAATAAT 57.647 29.630 0.00 0.00 36.74 1.28
274 290 8.922931 TGTAGCATTCCACATCAATAATATGT 57.077 30.769 0.00 0.00 38.08 2.29
276 292 9.831737 GTAGCATTCCACATCAATAATATGTTC 57.168 33.333 0.00 0.00 35.39 3.18
317 334 2.352960 GGACGAGCAGGAATTAAGCTTG 59.647 50.000 9.86 10.41 43.74 4.01
323 340 3.463329 AGCAGGAATTAAGCTTGGGGATA 59.537 43.478 9.86 0.00 34.37 2.59
332 349 1.985159 AGCTTGGGGATACTTGACACA 59.015 47.619 0.00 0.00 0.00 3.72
336 353 4.446371 CTTGGGGATACTTGACACATCTC 58.554 47.826 0.00 0.00 0.00 2.75
460 478 4.843147 TCTTCACTTTTGCAACATACGTG 58.157 39.130 0.00 0.00 0.00 4.49
461 479 4.334203 TCTTCACTTTTGCAACATACGTGT 59.666 37.500 0.00 0.00 41.28 4.49
555 577 6.952773 TTTTTGCAACAGAGGTTATGTAGT 57.047 33.333 0.00 0.00 34.87 2.73
557 579 7.429636 TTTTGCAACAGAGGTTATGTAGTAC 57.570 36.000 0.00 0.00 34.87 2.73
589 613 4.959596 ACAGAGCTTATGTTGCAGATTG 57.040 40.909 0.00 0.00 0.00 2.67
594 618 6.643770 CAGAGCTTATGTTGCAGATTGTTTTT 59.356 34.615 0.00 0.00 0.00 1.94
632 656 4.797275 GCTGCAAAAGGAATAAACTGCACT 60.797 41.667 0.00 0.00 35.02 4.40
634 658 4.099266 TGCAAAAGGAATAAACTGCACTGT 59.901 37.500 0.00 0.00 35.02 3.55
635 659 4.445385 GCAAAAGGAATAAACTGCACTGTG 59.555 41.667 2.76 2.76 0.00 3.66
636 660 4.853924 AAAGGAATAAACTGCACTGTGG 57.146 40.909 10.21 0.00 0.00 4.17
637 661 3.788227 AGGAATAAACTGCACTGTGGA 57.212 42.857 10.21 5.79 0.00 4.02
638 662 3.679389 AGGAATAAACTGCACTGTGGAG 58.321 45.455 25.09 25.09 41.93 3.86
643 667 4.146058 CTGCACTGTGGAGTTGCA 57.854 55.556 19.70 4.79 35.92 4.08
644 668 2.407268 CTGCACTGTGGAGTTGCAA 58.593 52.632 19.70 0.00 36.46 4.08
645 669 0.029834 CTGCACTGTGGAGTTGCAAC 59.970 55.000 22.17 22.17 36.46 4.17
646 670 1.360192 GCACTGTGGAGTTGCAACC 59.640 57.895 25.62 16.44 0.00 3.77
647 671 1.648720 CACTGTGGAGTTGCAACCG 59.351 57.895 25.62 9.93 0.00 4.44
648 672 2.186826 ACTGTGGAGTTGCAACCGC 61.187 57.895 25.62 18.07 37.22 5.68
659 683 2.499214 GCAACCGCAATATTCCCCA 58.501 52.632 0.00 0.00 38.36 4.96
666 690 4.735369 ACCGCAATATTCCCCATATTTCA 58.265 39.130 0.00 0.00 36.10 2.69
671 695 7.309990 CCGCAATATTCCCCATATTTCAGAAAT 60.310 37.037 13.06 13.06 36.10 2.17
696 720 5.214417 TGAACGATGTTGCAAAATCTTGAG 58.786 37.500 23.92 12.85 34.14 3.02
721 745 0.109226 GTGCGTGGGACTAGACTGAC 60.109 60.000 0.00 0.00 0.00 3.51
739 763 0.615331 ACACATGGTTGGCTCTCGAT 59.385 50.000 0.00 0.00 0.00 3.59
742 766 1.522355 ATGGTTGGCTCTCGATGCG 60.522 57.895 4.79 0.00 0.00 4.73
776 800 3.614150 GCGTAGAATCGGCCAGATGATTA 60.614 47.826 2.24 0.00 40.02 1.75
780 804 6.253727 CGTAGAATCGGCCAGATGATTATAAC 59.746 42.308 2.24 2.40 40.02 1.89
933 958 3.005472 TCATTCTCAACGAACGAGGAAGT 59.995 43.478 0.14 0.00 33.72 3.01
945 970 4.329545 GGAAGTCAGCCGCCACCA 62.330 66.667 0.00 0.00 0.00 4.17
947 972 4.335647 AAGTCAGCCGCCACCAGG 62.336 66.667 0.00 0.00 38.23 4.45
952 977 3.391382 AGCCGCCACCAGGACTAC 61.391 66.667 0.00 0.00 36.89 2.73
1245 1333 1.808799 CGACGAGATGCTGCTGCTT 60.809 57.895 17.00 10.47 40.48 3.91
1352 1458 1.309499 CGAGAGGTCAGCGAAGAGGT 61.309 60.000 0.00 0.00 0.00 3.85
1482 1591 3.216292 GTGTGGCTGGGCACGTTT 61.216 61.111 19.46 0.00 0.00 3.60
1575 1684 4.700448 TTCCCCGCCGACCAGGTA 62.700 66.667 0.00 0.00 43.70 3.08
1698 1807 3.611057 CGTCTACAACACGAAAGGCTAGT 60.611 47.826 0.00 0.00 39.75 2.57
1857 2003 4.880120 TCCATCTGATTCTGAAATCTGCAC 59.120 41.667 0.00 0.00 41.63 4.57
1933 2090 1.761449 TTCTTGCCTGTTGCTGTTGA 58.239 45.000 0.00 0.00 42.00 3.18
1980 2137 5.070001 AGTTCAGCTGGACTAGATAGCTAG 58.930 45.833 26.78 13.47 45.37 3.42
2009 2166 6.017605 CGAGCATTAGGTTCTTTAGCATTGAT 60.018 38.462 0.00 0.00 0.00 2.57
2013 2170 7.975616 GCATTAGGTTCTTTAGCATTGATGAAA 59.024 33.333 0.00 0.00 0.00 2.69
2049 2206 2.608546 TCGGTTGTGTACGTTTTGAAGG 59.391 45.455 0.00 0.00 0.00 3.46
2052 2209 3.129113 GGTTGTGTACGTTTTGAAGGGTT 59.871 43.478 0.00 0.00 0.00 4.11
2056 2213 6.062434 TGTGTACGTTTTGAAGGGTTAATG 57.938 37.500 0.00 0.00 0.00 1.90
2068 2225 5.069781 TGAAGGGTTAATGTTTGGGTTTGAG 59.930 40.000 0.00 0.00 0.00 3.02
2077 2234 4.082845 TGTTTGGGTTTGAGTTCAGTCAA 58.917 39.130 0.00 0.00 34.56 3.18
2090 2247 7.054124 TGAGTTCAGTCAAAACTAATGGTTCT 58.946 34.615 0.00 0.00 37.10 3.01
2098 2255 8.695456 AGTCAAAACTAATGGTTCTTTCACATT 58.305 29.630 0.00 0.00 37.12 2.71
2111 2268 8.884726 GGTTCTTTCACATTATCTTAAGAGACC 58.115 37.037 11.53 0.00 33.99 3.85
2126 2283 3.382278 AGAGACCCTCATGACATGACAT 58.618 45.455 14.24 4.76 35.06 3.06
2127 2284 3.779183 AGAGACCCTCATGACATGACATT 59.221 43.478 14.24 1.12 35.06 2.71
2128 2285 3.875727 GAGACCCTCATGACATGACATTG 59.124 47.826 14.24 4.86 35.06 2.82
2129 2286 2.357009 GACCCTCATGACATGACATTGC 59.643 50.000 14.24 0.22 35.06 3.56
2130 2287 2.291089 ACCCTCATGACATGACATTGCA 60.291 45.455 14.24 0.00 35.06 4.08
2131 2288 2.098607 CCCTCATGACATGACATTGCAC 59.901 50.000 14.24 0.00 35.06 4.57
2132 2289 2.750712 CCTCATGACATGACATTGCACA 59.249 45.455 14.24 0.00 35.06 4.57
2133 2290 3.191791 CCTCATGACATGACATTGCACAA 59.808 43.478 14.24 0.00 35.06 3.33
2134 2291 4.321378 CCTCATGACATGACATTGCACAAA 60.321 41.667 14.24 0.00 35.06 2.83
2135 2292 4.800784 TCATGACATGACATTGCACAAAG 58.199 39.130 14.24 0.00 33.59 2.77
2136 2293 4.278919 TCATGACATGACATTGCACAAAGT 59.721 37.500 14.24 0.00 33.59 2.66
2137 2294 4.652421 TGACATGACATTGCACAAAGTT 57.348 36.364 0.00 0.00 0.00 2.66
2138 2295 4.609947 TGACATGACATTGCACAAAGTTC 58.390 39.130 0.00 0.00 0.00 3.01
2139 2296 3.981211 ACATGACATTGCACAAAGTTCC 58.019 40.909 0.00 0.00 0.00 3.62
2140 2297 3.638160 ACATGACATTGCACAAAGTTCCT 59.362 39.130 0.00 0.00 0.00 3.36
2141 2298 4.099881 ACATGACATTGCACAAAGTTCCTT 59.900 37.500 0.00 0.00 0.00 3.36
2142 2299 4.734398 TGACATTGCACAAAGTTCCTTT 57.266 36.364 0.00 0.00 33.58 3.11
2152 2309 4.756084 CAAAGTTCCTTTGTAGCTCAGG 57.244 45.455 8.25 0.00 43.85 3.86
2153 2310 2.481289 AGTTCCTTTGTAGCTCAGGC 57.519 50.000 0.00 0.00 39.06 4.85
2154 2311 3.181439 AAAGTTCCTTTGTAGCTCAGGCT 60.181 43.478 0.00 0.00 41.04 4.58
2155 2312 4.041691 AAAGTTCCTTTGTAGCTCAGGCTA 59.958 41.667 0.00 0.00 39.78 3.93
2165 2322 2.990066 GCTCAGGCTACATGTAACCT 57.010 50.000 20.06 20.06 32.15 3.50
2166 2323 2.827652 GCTCAGGCTACATGTAACCTC 58.172 52.381 22.40 10.11 29.65 3.85
2167 2324 2.432510 GCTCAGGCTACATGTAACCTCT 59.567 50.000 22.40 3.28 29.65 3.69
2192 2349 2.674177 GCGCCAAGCTTGTACTTCTCTA 60.674 50.000 24.35 0.00 44.04 2.43
2202 2364 3.357203 TGTACTTCTCTAGACCAGGCTG 58.643 50.000 7.75 7.75 0.00 4.85
2209 2371 2.173782 CTCTAGACCAGGCTGTCTCCTA 59.826 54.545 18.55 10.85 44.30 2.94
2215 2377 2.975489 ACCAGGCTGTCTCCTAATATGG 59.025 50.000 14.43 0.00 33.95 2.74
2252 2414 8.885494 AATGCAGTATATTTGTTGTTGTTGTT 57.115 26.923 0.00 0.00 0.00 2.83
2253 2415 7.691430 TGCAGTATATTTGTTGTTGTTGTTG 57.309 32.000 0.00 0.00 0.00 3.33
2254 2416 7.261325 TGCAGTATATTTGTTGTTGTTGTTGT 58.739 30.769 0.00 0.00 0.00 3.32
2255 2417 7.761704 TGCAGTATATTTGTTGTTGTTGTTGTT 59.238 29.630 0.00 0.00 0.00 2.83
2256 2418 8.055402 GCAGTATATTTGTTGTTGTTGTTGTTG 58.945 33.333 0.00 0.00 0.00 3.33
2257 2419 9.081997 CAGTATATTTGTTGTTGTTGTTGTTGT 57.918 29.630 0.00 0.00 0.00 3.32
2258 2420 9.646427 AGTATATTTGTTGTTGTTGTTGTTGTT 57.354 25.926 0.00 0.00 0.00 2.83
2259 2421 9.682298 GTATATTTGTTGTTGTTGTTGTTGTTG 57.318 29.630 0.00 0.00 0.00 3.33
2260 2422 6.610741 ATTTGTTGTTGTTGTTGTTGTTGT 57.389 29.167 0.00 0.00 0.00 3.32
2261 2423 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
2262 2424 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2263 2425 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2264 2426 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2265 2427 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2266 2428 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2267 2429 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2268 2430 6.533723 TGTTGTTGTTGTTGTTGTTGTTGTTA 59.466 30.769 0.00 0.00 0.00 2.41
2269 2431 6.755461 TGTTGTTGTTGTTGTTGTTGTTAG 57.245 33.333 0.00 0.00 0.00 2.34
2270 2432 6.273825 TGTTGTTGTTGTTGTTGTTGTTAGT 58.726 32.000 0.00 0.00 0.00 2.24
2271 2433 6.757010 TGTTGTTGTTGTTGTTGTTGTTAGTT 59.243 30.769 0.00 0.00 0.00 2.24
2272 2434 7.277981 TGTTGTTGTTGTTGTTGTTGTTAGTTT 59.722 29.630 0.00 0.00 0.00 2.66
2273 2435 7.772332 TGTTGTTGTTGTTGTTGTTAGTTTT 57.228 28.000 0.00 0.00 0.00 2.43
2274 2436 7.621991 TGTTGTTGTTGTTGTTGTTAGTTTTG 58.378 30.769 0.00 0.00 0.00 2.44
2275 2437 7.491372 TGTTGTTGTTGTTGTTGTTAGTTTTGA 59.509 29.630 0.00 0.00 0.00 2.69
2284 2446 9.692749 TGTTGTTGTTAGTTTTGATGTGTTTTA 57.307 25.926 0.00 0.00 0.00 1.52
2304 2466 8.198778 TGTTTTATAACACAGTACAGACACAGA 58.801 33.333 0.22 0.00 39.29 3.41
2305 2467 9.204570 GTTTTATAACACAGTACAGACACAGAT 57.795 33.333 0.00 0.00 34.31 2.90
2307 2469 3.032017 ACACAGTACAGACACAGATGC 57.968 47.619 0.00 0.00 0.00 3.91
2316 2478 5.859205 ACAGACACAGATGCTCATACATA 57.141 39.130 0.00 0.00 0.00 2.29
2317 2479 6.416631 ACAGACACAGATGCTCATACATAT 57.583 37.500 0.00 0.00 0.00 1.78
2328 3239 9.473007 AGATGCTCATACATATGTATCTACAGT 57.527 33.333 22.81 9.75 39.06 3.55
2342 3253 9.601810 ATGTATCTACAGTCATCCCTATAAACA 57.398 33.333 0.00 0.00 39.92 2.83
2346 3257 9.601810 ATCTACAGTCATCCCTATAAACACATA 57.398 33.333 0.00 0.00 0.00 2.29
2353 3264 7.438459 GTCATCCCTATAAACACATACTCACAC 59.562 40.741 0.00 0.00 0.00 3.82
2356 3267 5.815740 CCCTATAAACACATACTCACACACC 59.184 44.000 0.00 0.00 0.00 4.16
2363 3274 2.565834 ACATACTCACACACCCTACCAC 59.434 50.000 0.00 0.00 0.00 4.16
2366 3277 2.245582 ACTCACACACCCTACCACTAC 58.754 52.381 0.00 0.00 0.00 2.73
2367 3278 1.201647 CTCACACACCCTACCACTACG 59.798 57.143 0.00 0.00 0.00 3.51
2368 3279 0.245539 CACACACCCTACCACTACGG 59.754 60.000 0.00 0.00 42.50 4.02
2369 3280 0.112995 ACACACCCTACCACTACGGA 59.887 55.000 0.00 0.00 38.63 4.69
2370 3281 0.529378 CACACCCTACCACTACGGAC 59.471 60.000 0.00 0.00 38.63 4.79
2371 3282 0.112995 ACACCCTACCACTACGGACA 59.887 55.000 0.00 0.00 38.63 4.02
2372 3283 0.529378 CACCCTACCACTACGGACAC 59.471 60.000 0.00 0.00 38.63 3.67
2375 3286 1.897802 CCCTACCACTACGGACACTTT 59.102 52.381 0.00 0.00 38.63 2.66
2377 3288 2.415090 CCTACCACTACGGACACTTTCG 60.415 54.545 0.00 0.00 38.63 3.46
2387 3298 2.413502 CGGACACTTTCGAGAGACTGAG 60.414 54.545 10.37 0.00 41.84 3.35
2390 3301 0.523966 ACTTTCGAGAGACTGAGCCG 59.476 55.000 10.37 0.00 41.84 5.52
2397 3308 0.684479 AGAGACTGAGCCGGCACATA 60.684 55.000 31.54 10.56 0.00 2.29
2398 3309 0.175760 GAGACTGAGCCGGCACATAA 59.824 55.000 31.54 5.61 0.00 1.90
2410 3321 3.879295 CCGGCACATAATCTTGAGATTGT 59.121 43.478 14.82 6.80 43.90 2.71
2417 3328 7.616673 CACATAATCTTGAGATTGTCGAAGTC 58.383 38.462 14.82 0.00 43.90 3.01
2424 3335 1.611977 AGATTGTCGAAGTCACCACGA 59.388 47.619 0.00 0.00 0.00 4.35
2425 3336 1.986378 GATTGTCGAAGTCACCACGAG 59.014 52.381 0.00 0.00 36.74 4.18
2426 3337 0.596600 TTGTCGAAGTCACCACGAGC 60.597 55.000 0.00 0.00 36.74 5.03
2427 3338 2.081212 GTCGAAGTCACCACGAGCG 61.081 63.158 0.00 0.00 36.74 5.03
2428 3339 2.050351 CGAAGTCACCACGAGCGT 60.050 61.111 0.00 0.00 0.00 5.07
2444 3355 0.944311 GCGTCCAGAAAAGTGCGAGA 60.944 55.000 0.00 0.00 0.00 4.04
2448 3359 1.140052 TCCAGAAAAGTGCGAGAACCA 59.860 47.619 0.00 0.00 0.00 3.67
2466 3392 2.281761 GTGTCACCTGGTGGGCTG 60.282 66.667 25.67 0.60 39.10 4.85
2467 3393 2.447572 TGTCACCTGGTGGGCTGA 60.448 61.111 25.67 3.94 39.10 4.26
2473 3399 0.251341 ACCTGGTGGGCTGATTTCAC 60.251 55.000 0.00 0.00 39.10 3.18
2493 3419 1.457346 CACAAGGAAGCTGACCATCC 58.543 55.000 11.89 3.30 0.00 3.51
2496 3422 0.984230 AAGGAAGCTGACCATCCGAA 59.016 50.000 11.89 0.00 38.31 4.30
2510 3436 3.432186 CCATCCGAACTAGGCTCAATTCA 60.432 47.826 0.00 0.00 0.00 2.57
2515 3441 3.181530 CGAACTAGGCTCAATTCACGTTG 60.182 47.826 0.00 0.00 0.00 4.10
2516 3442 3.402628 ACTAGGCTCAATTCACGTTGT 57.597 42.857 0.00 0.00 0.00 3.32
2517 3443 3.740115 ACTAGGCTCAATTCACGTTGTT 58.260 40.909 0.00 0.00 0.00 2.83
2536 3462 6.313252 GTTGTTAGTTTTGGTGTTGACGTTA 58.687 36.000 0.00 0.00 0.00 3.18
2542 3468 0.107081 TGGTGTTGACGTTACCAGGG 59.893 55.000 9.82 0.00 39.43 4.45
2543 3469 0.604511 GGTGTTGACGTTACCAGGGG 60.605 60.000 0.00 0.00 34.61 4.79
2565 3491 4.749598 GGAAAATCCAAACATGTTGGTGAC 59.250 41.667 12.82 7.53 40.40 3.67
2592 3518 2.557805 GGCATGCAGTCACGTGTG 59.442 61.111 21.36 8.70 0.00 3.82
2593 3519 1.960763 GGCATGCAGTCACGTGTGA 60.961 57.895 21.36 0.00 37.24 3.58
2594 3520 1.494628 GCATGCAGTCACGTGTGAG 59.505 57.895 16.51 7.44 40.75 3.51
2608 3539 5.467063 TCACGTGTGAGCATAATAAACAACA 59.533 36.000 16.51 0.00 34.14 3.33
2628 3559 4.469657 ACAATTAGTGATGTTGTGTGGGT 58.530 39.130 0.00 0.00 34.98 4.51
2646 3577 8.325787 TGTGTGGGTATTCAAGTTAATGACTAT 58.674 33.333 0.00 0.00 37.72 2.12
2746 3677 8.615211 TCATAGCAAATAAGATGTCACACATTC 58.385 33.333 0.00 0.00 39.27 2.67
2785 3716 6.533730 AGAGACATGTCATTTGGTTTGTAGA 58.466 36.000 27.02 0.00 0.00 2.59
2788 3719 8.862325 AGACATGTCATTTGGTTTGTAGAATA 57.138 30.769 27.02 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.238942 AACATCTTATCGCCATCGCA 57.761 45.000 0.00 0.00 35.26 5.10
2 3 2.410262 CGAAACATCTTATCGCCATCGC 60.410 50.000 0.00 0.00 35.26 4.58
3 4 2.155732 CCGAAACATCTTATCGCCATCG 59.844 50.000 0.00 0.00 35.35 3.84
4 5 2.480419 CCCGAAACATCTTATCGCCATC 59.520 50.000 0.00 0.00 35.35 3.51
5 6 2.158813 ACCCGAAACATCTTATCGCCAT 60.159 45.455 0.00 0.00 35.35 4.40
6 7 1.208535 ACCCGAAACATCTTATCGCCA 59.791 47.619 0.00 0.00 35.35 5.69
7 8 1.865340 GACCCGAAACATCTTATCGCC 59.135 52.381 0.00 0.00 35.35 5.54
8 9 2.795470 GAGACCCGAAACATCTTATCGC 59.205 50.000 0.00 0.00 35.35 4.58
15 16 1.128692 CAAAGCGAGACCCGAAACATC 59.871 52.381 0.00 0.00 41.76 3.06
34 35 3.456644 TCCCGCATATTCTAAAACCCTCA 59.543 43.478 0.00 0.00 0.00 3.86
35 36 4.081322 TCCCGCATATTCTAAAACCCTC 57.919 45.455 0.00 0.00 0.00 4.30
43 44 4.688879 CGCAAAGTATTCCCGCATATTCTA 59.311 41.667 0.00 0.00 0.00 2.10
44 45 3.498397 CGCAAAGTATTCCCGCATATTCT 59.502 43.478 0.00 0.00 0.00 2.40
52 53 2.343101 TCTTGACGCAAAGTATTCCCG 58.657 47.619 0.00 0.00 0.00 5.14
65 66 2.606725 GTCATGCTCCATCTTCTTGACG 59.393 50.000 0.00 0.00 0.00 4.35
68 69 4.094590 GTCTTGTCATGCTCCATCTTCTTG 59.905 45.833 0.00 0.00 0.00 3.02
71 72 3.871485 AGTCTTGTCATGCTCCATCTTC 58.129 45.455 0.00 0.00 0.00 2.87
111 112 7.117092 TCCAAATTAAAAATGCTAAAGAACGCC 59.883 33.333 0.00 0.00 0.00 5.68
131 132 3.011566 TCGGCATACCAACATCCAAAT 57.988 42.857 0.00 0.00 34.57 2.32
136 137 6.854496 TTAATACTTCGGCATACCAACATC 57.146 37.500 0.00 0.00 34.57 3.06
236 252 5.942826 TGGAATGCTACATAACATGTTCACA 59.057 36.000 15.85 6.02 41.63 3.58
250 266 9.831737 GAACATATTATTGATGTGGAATGCTAC 57.168 33.333 0.00 0.00 37.59 3.58
274 290 9.529325 CGTCCTTGAGTATGTAAATGATAAGAA 57.471 33.333 0.00 0.00 0.00 2.52
276 292 9.186323 CTCGTCCTTGAGTATGTAAATGATAAG 57.814 37.037 0.00 0.00 0.00 1.73
286 303 1.478510 CCTGCTCGTCCTTGAGTATGT 59.521 52.381 0.00 0.00 38.28 2.29
288 305 2.145397 TCCTGCTCGTCCTTGAGTAT 57.855 50.000 0.00 0.00 38.28 2.12
294 311 2.237392 AGCTTAATTCCTGCTCGTCCTT 59.763 45.455 0.00 0.00 30.41 3.36
297 314 2.352960 CCAAGCTTAATTCCTGCTCGTC 59.647 50.000 0.00 0.00 35.85 4.20
317 334 2.771943 TGGAGATGTGTCAAGTATCCCC 59.228 50.000 0.00 0.00 0.00 4.81
323 340 2.910688 ACGTTGGAGATGTGTCAAGT 57.089 45.000 0.00 0.00 0.00 3.16
432 450 4.241681 TGTTGCAAAAGTGAAGAACAACC 58.758 39.130 0.00 0.00 36.08 3.77
435 453 5.163703 ACGTATGTTGCAAAAGTGAAGAACA 60.164 36.000 0.00 0.00 0.00 3.18
491 513 9.762933 ACAACATTTGCTACAAATATTTTCTGT 57.237 25.926 5.30 0.00 0.00 3.41
603 627 7.064966 GCAGTTTATTCCTTTTGCAGCATAAAT 59.935 33.333 0.00 0.00 0.00 1.40
619 643 4.787598 CAACTCCACAGTGCAGTTTATTC 58.212 43.478 7.18 0.00 31.06 1.75
620 644 3.004734 GCAACTCCACAGTGCAGTTTATT 59.995 43.478 7.18 0.00 31.06 1.40
623 647 0.740737 GCAACTCCACAGTGCAGTTT 59.259 50.000 7.18 0.00 31.06 2.66
641 665 1.039856 ATGGGGAATATTGCGGTTGC 58.960 50.000 0.46 0.00 43.20 4.17
642 666 5.010516 TGAAATATGGGGAATATTGCGGTTG 59.989 40.000 0.46 0.00 40.00 3.77
643 667 5.144100 TGAAATATGGGGAATATTGCGGTT 58.856 37.500 0.46 0.00 40.00 4.44
644 668 4.735369 TGAAATATGGGGAATATTGCGGT 58.265 39.130 0.46 0.00 40.00 5.68
645 669 5.009631 TCTGAAATATGGGGAATATTGCGG 58.990 41.667 0.46 0.16 41.81 5.69
646 670 6.573664 TTCTGAAATATGGGGAATATTGCG 57.426 37.500 0.46 0.00 40.00 4.85
659 683 9.669353 GCAACATCGTTCATATTTCTGAAATAT 57.331 29.630 23.43 23.43 43.10 1.28
666 690 8.246180 AGATTTTGCAACATCGTTCATATTTCT 58.754 29.630 17.55 0.00 0.00 2.52
671 695 6.907741 TCAAGATTTTGCAACATCGTTCATA 58.092 32.000 17.55 2.19 34.21 2.15
696 720 3.869473 TAGTCCCACGCACCGCAAC 62.869 63.158 0.00 0.00 0.00 4.17
710 734 3.589988 CCAACCATGTGTCAGTCTAGTC 58.410 50.000 0.00 0.00 0.00 2.59
721 745 1.012086 CATCGAGAGCCAACCATGTG 58.988 55.000 0.00 0.00 0.00 3.21
752 776 0.753262 ATCTGGCCGATTCTACGCTT 59.247 50.000 0.00 0.00 0.00 4.68
756 780 6.535508 GGTTATAATCATCTGGCCGATTCTAC 59.464 42.308 6.85 4.89 33.90 2.59
761 785 4.908601 TGGTTATAATCATCTGGCCGAT 57.091 40.909 0.00 0.60 0.00 4.18
826 850 7.145985 TCCTAACAGATAATTGTGATAGCGAC 58.854 38.462 0.00 0.00 0.00 5.19
933 958 3.897681 TAGTCCTGGTGGCGGCTGA 62.898 63.158 11.43 0.00 0.00 4.26
945 970 6.409349 GCCTCCATGGTTTTTATAGTAGTCCT 60.409 42.308 12.58 0.00 38.35 3.85
947 972 5.465724 CGCCTCCATGGTTTTTATAGTAGTC 59.534 44.000 12.58 0.00 38.35 2.59
952 977 2.948979 TGCGCCTCCATGGTTTTTATAG 59.051 45.455 12.58 0.00 38.35 1.31
1220 1299 4.831307 GCATCTCGTCGGCGTCGT 62.831 66.667 24.03 4.42 39.49 4.34
1668 1777 2.813908 GTTGTAGACGCCCGCCTG 60.814 66.667 0.00 0.00 0.00 4.85
1857 2003 0.179103 GCCATCGCCATTTTTCTGGG 60.179 55.000 0.00 0.00 36.75 4.45
1933 2090 1.530013 AACGAACGAGACCGGACCAT 61.530 55.000 9.46 0.00 40.78 3.55
1980 2137 4.260415 GCTAAAGAACCTAATGCTCGAAGC 60.260 45.833 0.00 0.00 42.82 3.86
2009 2166 2.546368 CGACGATTTCCACAACCTTTCA 59.454 45.455 0.00 0.00 0.00 2.69
2013 2170 0.395312 ACCGACGATTTCCACAACCT 59.605 50.000 0.00 0.00 0.00 3.50
2049 2206 5.908341 TGAACTCAAACCCAAACATTAACC 58.092 37.500 0.00 0.00 0.00 2.85
2052 2209 5.888724 TGACTGAACTCAAACCCAAACATTA 59.111 36.000 0.00 0.00 0.00 1.90
2056 2213 4.712122 TTGACTGAACTCAAACCCAAAC 57.288 40.909 0.00 0.00 0.00 2.93
2068 2225 8.188139 TGAAAGAACCATTAGTTTTGACTGAAC 58.812 33.333 0.00 0.00 39.40 3.18
2090 2247 8.146053 TGAGGGTCTCTTAAGATAATGTGAAA 57.854 34.615 5.44 0.00 33.08 2.69
2098 2255 7.014711 GTCATGTCATGAGGGTCTCTTAAGATA 59.985 40.741 15.96 0.00 40.53 1.98
2111 2268 2.750712 TGTGCAATGTCATGTCATGAGG 59.249 45.455 15.96 7.41 40.53 3.86
2133 2290 2.784347 GCCTGAGCTACAAAGGAACTT 58.216 47.619 8.11 0.00 44.29 2.66
2134 2291 2.481289 GCCTGAGCTACAAAGGAACT 57.519 50.000 8.11 0.00 36.38 3.01
2146 2303 2.432510 AGAGGTTACATGTAGCCTGAGC 59.567 50.000 37.10 25.25 45.12 4.26
2147 2304 4.744795 AAGAGGTTACATGTAGCCTGAG 57.255 45.455 37.10 0.00 45.12 3.35
2148 2305 4.323485 CCAAAGAGGTTACATGTAGCCTGA 60.323 45.833 37.10 8.01 45.12 3.86
2149 2306 3.941483 CCAAAGAGGTTACATGTAGCCTG 59.059 47.826 37.10 25.32 45.12 4.85
2151 2308 2.683362 GCCAAAGAGGTTACATGTAGCC 59.317 50.000 26.52 26.52 40.61 3.93
2152 2309 2.351726 CGCCAAAGAGGTTACATGTAGC 59.648 50.000 10.99 10.99 40.61 3.58
2153 2310 2.351726 GCGCCAAAGAGGTTACATGTAG 59.648 50.000 5.56 0.00 40.61 2.74
2154 2311 2.352388 GCGCCAAAGAGGTTACATGTA 58.648 47.619 0.08 0.08 40.61 2.29
2155 2312 1.165270 GCGCCAAAGAGGTTACATGT 58.835 50.000 2.69 2.69 40.61 3.21
2156 2313 0.451783 GGCGCCAAAGAGGTTACATG 59.548 55.000 24.80 0.00 40.61 3.21
2157 2314 0.037590 TGGCGCCAAAGAGGTTACAT 59.962 50.000 30.74 0.00 40.61 2.29
2158 2315 0.179015 TTGGCGCCAAAGAGGTTACA 60.179 50.000 38.61 13.20 40.61 2.41
2159 2316 0.521735 CTTGGCGCCAAAGAGGTTAC 59.478 55.000 38.96 3.98 40.61 2.50
2160 2317 1.241315 GCTTGGCGCCAAAGAGGTTA 61.241 55.000 38.96 17.82 40.61 2.85
2161 2318 2.564721 GCTTGGCGCCAAAGAGGTT 61.565 57.895 38.96 0.00 40.61 3.50
2162 2319 2.983725 AAGCTTGGCGCCAAAGAGGT 62.984 55.000 38.96 30.44 40.39 3.85
2163 2320 2.270986 AAGCTTGGCGCCAAAGAGG 61.271 57.895 38.96 28.58 40.39 3.69
2164 2321 1.080974 CAAGCTTGGCGCCAAAGAG 60.081 57.895 38.96 29.47 40.39 2.85
2165 2322 0.536233 TACAAGCTTGGCGCCAAAGA 60.536 50.000 38.96 20.94 40.39 2.52
2166 2323 0.387239 GTACAAGCTTGGCGCCAAAG 60.387 55.000 38.96 31.18 40.39 2.77
2167 2324 0.821711 AGTACAAGCTTGGCGCCAAA 60.822 50.000 38.96 23.00 40.39 3.28
2235 2397 8.316640 ACAACAACAACAACAACAACAAATAT 57.683 26.923 0.00 0.00 0.00 1.28
2237 2399 6.610741 ACAACAACAACAACAACAACAAAT 57.389 29.167 0.00 0.00 0.00 2.32
2238 2400 6.128282 ACAACAACAACAACAACAACAACAAA 60.128 30.769 0.00 0.00 0.00 2.83
2239 2401 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2240 2402 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2241 2403 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2242 2404 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2243 2405 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2244 2406 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2245 2407 6.757010 ACTAACAACAACAACAACAACAACAA 59.243 30.769 0.00 0.00 0.00 2.83
2246 2408 6.273825 ACTAACAACAACAACAACAACAACA 58.726 32.000 0.00 0.00 0.00 3.33
2247 2409 6.757026 ACTAACAACAACAACAACAACAAC 57.243 33.333 0.00 0.00 0.00 3.32
2248 2410 7.772332 AAACTAACAACAACAACAACAACAA 57.228 28.000 0.00 0.00 0.00 2.83
2249 2411 7.491372 TCAAAACTAACAACAACAACAACAACA 59.509 29.630 0.00 0.00 0.00 3.33
2250 2412 7.842484 TCAAAACTAACAACAACAACAACAAC 58.158 30.769 0.00 0.00 0.00 3.32
2251 2413 8.491152 CATCAAAACTAACAACAACAACAACAA 58.509 29.630 0.00 0.00 0.00 2.83
2252 2414 7.653713 ACATCAAAACTAACAACAACAACAACA 59.346 29.630 0.00 0.00 0.00 3.33
2253 2415 7.949428 CACATCAAAACTAACAACAACAACAAC 59.051 33.333 0.00 0.00 0.00 3.32
2254 2416 7.653713 ACACATCAAAACTAACAACAACAACAA 59.346 29.630 0.00 0.00 0.00 2.83
2255 2417 7.148641 ACACATCAAAACTAACAACAACAACA 58.851 30.769 0.00 0.00 0.00 3.33
2256 2418 7.575332 ACACATCAAAACTAACAACAACAAC 57.425 32.000 0.00 0.00 0.00 3.32
2257 2419 8.594881 AAACACATCAAAACTAACAACAACAA 57.405 26.923 0.00 0.00 0.00 2.83
2258 2420 8.594881 AAAACACATCAAAACTAACAACAACA 57.405 26.923 0.00 0.00 0.00 3.33
2284 2446 5.047021 AGCATCTGTGTCTGTACTGTGTTAT 60.047 40.000 0.00 0.00 0.00 1.89
2290 2452 3.582714 TGAGCATCTGTGTCTGTACTG 57.417 47.619 0.00 0.00 34.92 2.74
2299 2461 9.513727 GTAGATACATATGTATGAGCATCTGTG 57.486 37.037 28.82 0.00 40.99 3.66
2300 2462 9.247861 TGTAGATACATATGTATGAGCATCTGT 57.752 33.333 28.82 8.12 40.99 3.41
2304 2466 9.247861 TGACTGTAGATACATATGTATGAGCAT 57.752 33.333 28.82 9.46 40.99 3.79
2305 2467 8.635765 TGACTGTAGATACATATGTATGAGCA 57.364 34.615 28.82 21.11 40.99 4.26
2316 2478 9.601810 TGTTTATAGGGATGACTGTAGATACAT 57.398 33.333 0.00 0.00 35.36 2.29
2317 2479 8.857098 GTGTTTATAGGGATGACTGTAGATACA 58.143 37.037 0.00 0.00 34.56 2.29
2319 2481 9.601810 ATGTGTTTATAGGGATGACTGTAGATA 57.398 33.333 0.00 0.00 0.00 1.98
2320 2482 7.914427 TGTGTTTATAGGGATGACTGTAGAT 57.086 36.000 0.00 0.00 0.00 1.98
2322 2484 8.861086 AGTATGTGTTTATAGGGATGACTGTAG 58.139 37.037 0.00 0.00 0.00 2.74
2325 3236 7.653713 GTGAGTATGTGTTTATAGGGATGACTG 59.346 40.741 0.00 0.00 0.00 3.51
2328 3239 7.125053 TGTGTGAGTATGTGTTTATAGGGATGA 59.875 37.037 0.00 0.00 0.00 2.92
2342 3253 2.565834 GTGGTAGGGTGTGTGAGTATGT 59.434 50.000 0.00 0.00 0.00 2.29
2346 3257 2.245582 GTAGTGGTAGGGTGTGTGAGT 58.754 52.381 0.00 0.00 0.00 3.41
2353 3264 0.529378 GTGTCCGTAGTGGTAGGGTG 59.471 60.000 0.00 0.00 39.52 4.61
2356 3267 2.415090 CGAAAGTGTCCGTAGTGGTAGG 60.415 54.545 0.00 0.00 39.52 3.18
2363 3274 2.743126 AGTCTCTCGAAAGTGTCCGTAG 59.257 50.000 0.00 0.00 0.00 3.51
2366 3277 1.535896 TCAGTCTCTCGAAAGTGTCCG 59.464 52.381 0.00 0.00 0.00 4.79
2367 3278 2.669950 GCTCAGTCTCTCGAAAGTGTCC 60.670 54.545 0.00 0.00 0.00 4.02
2368 3279 2.591133 GCTCAGTCTCTCGAAAGTGTC 58.409 52.381 0.00 0.00 0.00 3.67
2369 3280 1.271102 GGCTCAGTCTCTCGAAAGTGT 59.729 52.381 0.00 0.00 0.00 3.55
2370 3281 1.730772 CGGCTCAGTCTCTCGAAAGTG 60.731 57.143 0.00 0.00 0.00 3.16
2371 3282 0.523966 CGGCTCAGTCTCTCGAAAGT 59.476 55.000 0.00 0.00 0.00 2.66
2372 3283 0.179150 CCGGCTCAGTCTCTCGAAAG 60.179 60.000 0.00 0.00 0.00 2.62
2375 3286 3.134792 GCCGGCTCAGTCTCTCGA 61.135 66.667 22.15 0.00 0.00 4.04
2377 3288 1.954362 ATGTGCCGGCTCAGTCTCTC 61.954 60.000 32.06 10.69 0.00 3.20
2387 3298 1.953559 TCTCAAGATTATGTGCCGGC 58.046 50.000 22.73 22.73 0.00 6.13
2390 3301 4.811024 TCGACAATCTCAAGATTATGTGCC 59.189 41.667 4.98 0.00 42.41 5.01
2397 3308 4.932200 GGTGACTTCGACAATCTCAAGATT 59.068 41.667 0.00 0.00 44.93 2.40
2398 3309 4.021104 TGGTGACTTCGACAATCTCAAGAT 60.021 41.667 0.00 0.00 36.07 2.40
2410 3321 2.254350 CGCTCGTGGTGACTTCGA 59.746 61.111 3.35 3.35 36.42 3.71
2417 3328 0.878523 TTTTCTGGACGCTCGTGGTG 60.879 55.000 0.00 0.00 0.00 4.17
2424 3335 0.946221 CTCGCACTTTTCTGGACGCT 60.946 55.000 0.00 0.00 0.00 5.07
2425 3336 0.944311 TCTCGCACTTTTCTGGACGC 60.944 55.000 0.00 0.00 0.00 5.19
2426 3337 1.192534 GTTCTCGCACTTTTCTGGACG 59.807 52.381 0.00 0.00 0.00 4.79
2427 3338 1.531578 GGTTCTCGCACTTTTCTGGAC 59.468 52.381 0.00 0.00 0.00 4.02
2428 3339 1.140052 TGGTTCTCGCACTTTTCTGGA 59.860 47.619 0.00 0.00 0.00 3.86
2448 3359 2.448542 AGCCCACCAGGTGACACT 60.449 61.111 22.37 11.81 38.26 3.55
2466 3392 3.057946 GTCAGCTTCCTTGTGGTGAAATC 60.058 47.826 0.00 0.00 41.41 2.17
2467 3393 2.887152 GTCAGCTTCCTTGTGGTGAAAT 59.113 45.455 0.00 0.00 41.41 2.17
2473 3399 1.457346 GATGGTCAGCTTCCTTGTGG 58.543 55.000 6.31 0.00 0.00 4.17
2474 3400 1.457346 GGATGGTCAGCTTCCTTGTG 58.543 55.000 1.47 0.00 0.00 3.33
2493 3419 2.607187 ACGTGAATTGAGCCTAGTTCG 58.393 47.619 0.00 0.00 0.00 3.95
2496 3422 3.402628 ACAACGTGAATTGAGCCTAGT 57.597 42.857 0.00 0.00 33.57 2.57
2510 3436 4.669708 CGTCAACACCAAAACTAACAACGT 60.670 41.667 0.00 0.00 0.00 3.99
2515 3441 5.163774 TGGTAACGTCAACACCAAAACTAAC 60.164 40.000 8.36 0.00 39.36 2.34
2516 3442 4.940046 TGGTAACGTCAACACCAAAACTAA 59.060 37.500 8.36 0.00 39.36 2.24
2517 3443 4.511527 TGGTAACGTCAACACCAAAACTA 58.488 39.130 8.36 0.00 39.36 2.24
2536 3462 2.785357 TGTTTGGATTTTCCCCTGGT 57.215 45.000 0.00 0.00 35.03 4.00
2542 3468 4.749598 GTCACCAACATGTTTGGATTTTCC 59.250 41.667 24.75 9.36 42.06 3.13
2543 3469 4.749598 GGTCACCAACATGTTTGGATTTTC 59.250 41.667 24.75 13.76 42.06 2.29
2581 3507 5.120053 TGTTTATTATGCTCACACGTGACTG 59.880 40.000 25.01 11.50 35.46 3.51
2608 3539 6.945435 TGAATACCCACACAACATCACTAATT 59.055 34.615 0.00 0.00 0.00 1.40
2715 3646 9.013229 TGTGACATCTTATTTGCTATGACTTTT 57.987 29.630 0.00 0.00 0.00 2.27
2721 3652 7.859377 GGAATGTGTGACATCTTATTTGCTATG 59.141 37.037 0.00 0.00 37.97 2.23


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

AutoCloner maintained by Alex Coulton.