Multiple sequence alignment - TraesCS2D01G115200

Loading Multiple Alignment...

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 TraesCS2D01G115200 chr2D 100.000 3046 0 0 1 3046 63708932 63711977 0.000000e+00 5626.0
1 TraesCS2D01G115200 chr2D 87.449 494 43 8 1 478 263487417 263487907 4.440000e-153 551.0
2 TraesCS2D01G115200 chr2D 99.194 124 1 0 2245 2368 620514379 620514502 1.100000e-54 224.0
3 TraesCS2D01G115200 chr2B 91.325 1291 63 25 722 1965 99959887 99961175 0.000000e+00 1718.0
4 TraesCS2D01G115200 chr2B 87.793 213 8 5 72 266 99954064 99954276 1.830000e-57 233.0
5 TraesCS2D01G115200 chr2B 95.082 122 6 0 2247 2368 620863469 620863348 3.100000e-45 193.0
6 TraesCS2D01G115200 chr2B 86.111 180 18 6 364 539 99954596 99954772 1.440000e-43 187.0
7 TraesCS2D01G115200 chr2B 92.857 126 7 1 143 266 99954477 99954602 6.710000e-42 182.0
8 TraesCS2D01G115200 chr2B 93.388 121 6 1 143 261 99954315 99954435 8.680000e-41 178.0
9 TraesCS2D01G115200 chr2B 88.276 145 17 0 557 701 99959688 99959832 1.120000e-39 174.0
10 TraesCS2D01G115200 chr2B 98.750 80 1 0 552 631 99961220 99961299 3.170000e-30 143.0
11 TraesCS2D01G115200 chr2B 87.097 62 6 2 364 423 99954270 99954331 5.450000e-08 69.4
12 TraesCS2D01G115200 chr2B 87.097 62 4 4 364 423 99954434 99954493 1.960000e-07 67.6
13 TraesCS2D01G115200 chr2A 94.041 1074 35 14 813 1876 65402541 65403595 0.000000e+00 1602.0
14 TraesCS2D01G115200 chr2A 93.023 817 44 3 1 810 65401488 65402298 0.000000e+00 1181.0
15 TraesCS2D01G115200 chr2A 91.089 101 6 3 533 631 65403908 65404007 1.910000e-27 134.0
16 TraesCS2D01G115200 chr6A 89.835 423 42 1 70 492 256665401 256664980 2.670000e-150 542.0
17 TraesCS2D01G115200 chr7B 92.988 328 22 1 2637 2964 665690227 665690553 7.640000e-131 477.0
18 TraesCS2D01G115200 chr7B 94.574 129 7 0 2463 2591 665689749 665689877 1.850000e-47 200.0
19 TraesCS2D01G115200 chr5B 79.582 622 65 25 2462 3046 670015912 670015316 3.680000e-104 388.0
20 TraesCS2D01G115200 chr5B 95.161 124 6 0 2244 2367 294553610 294553487 2.400000e-46 196.0
21 TraesCS2D01G115200 chr5B 91.346 104 6 3 531 633 632129866 632129765 4.100000e-29 139.0
22 TraesCS2D01G115200 chr7A 84.492 374 35 12 2694 3046 107470141 107469770 6.250000e-92 348.0
23 TraesCS2D01G115200 chr1A 100.000 126 0 0 2244 2369 488074850 488074725 1.830000e-57 233.0
24 TraesCS2D01G115200 chr5A 98.438 128 1 1 2244 2370 581930710 581930837 1.100000e-54 224.0
25 TraesCS2D01G115200 chr5A 97.531 81 2 0 555 635 130120770 130120850 4.100000e-29 139.0
26 TraesCS2D01G115200 chr5A 96.154 78 3 0 2170 2247 631646594 631646517 8.860000e-26 128.0
27 TraesCS2D01G115200 chr4A 99.187 123 1 0 2245 2367 681900367 681900489 3.950000e-54 222.0
28 TraesCS2D01G115200 chr4A 98.400 125 2 0 2244 2368 596004150 596004274 1.420000e-53 220.0
29 TraesCS2D01G115200 chr4A 95.161 124 6 0 2245 2368 604853677 604853554 2.400000e-46 196.0
30 TraesCS2D01G115200 chr4A 96.250 80 0 3 2166 2244 655448476 655448553 8.860000e-26 128.0
31 TraesCS2D01G115200 chr4A 96.104 77 3 0 2168 2244 656488682 656488758 3.190000e-25 126.0
32 TraesCS2D01G115200 chr1B 84.255 235 21 5 1 219 322725321 322725555 6.610000e-52 215.0
33 TraesCS2D01G115200 chr3B 96.748 123 4 0 2245 2367 500539531 500539409 3.980000e-49 206.0
34 TraesCS2D01G115200 chr5D 94.624 93 3 2 552 642 503655936 503655844 3.170000e-30 143.0
35 TraesCS2D01G115200 chrUn 96.471 85 1 2 550 633 48984656 48984573 4.100000e-29 139.0
36 TraesCS2D01G115200 chrUn 96.250 80 0 3 2166 2244 48992575 48992652 8.860000e-26 128.0
37 TraesCS2D01G115200 chr7D 94.444 90 3 2 546 633 45271811 45271722 1.470000e-28 137.0
38 TraesCS2D01G115200 chr7D 95.000 80 2 2 2166 2244 44403114 44403192 1.150000e-24 124.0
39 TraesCS2D01G115200 chr7D 95.000 80 2 2 2166 2244 44571331 44571409 1.150000e-24 124.0
40 TraesCS2D01G115200 chr3A 90.625 96 7 2 2165 2260 739732965 739733058 3.190000e-25 126.0
41 TraesCS2D01G115200 chr3A 93.976 83 4 1 2165 2247 739324521 739324440 1.150000e-24 124.0
42 TraesCS2D01G115200 chr6B 95.000 80 3 1 2166 2244 216505923 216506002 1.150000e-24 124.0


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 TraesCS2D01G115200 chr2D 63708932 63711977 3045 False 5626.000000 5626 100.000000 1 3046 1 chr2D.!!$F1 3045
1 TraesCS2D01G115200 chr2B 99959688 99961299 1611 False 678.333333 1718 92.783667 552 1965 3 chr2B.!!$F2 1413
2 TraesCS2D01G115200 chr2A 65401488 65404007 2519 False 972.333333 1602 92.717667 1 1876 3 chr2A.!!$F1 1875
3 TraesCS2D01G115200 chr7B 665689749 665690553 804 False 338.500000 477 93.781000 2463 2964 2 chr7B.!!$F1 501
4 TraesCS2D01G115200 chr5B 670015316 670015912 596 True 388.000000 388 79.582000 2462 3046 1 chr5B.!!$R3 584

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
360 361 0.327924 CTCTTGGTACCACATGGGCA 59.672 55.0 16.04 0.0 42.05 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2671 0.035056 CCACCTGTCAGGGATGGAAC 60.035 60.0 23.06 0.0 40.58 3.62 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
44 45 4.380550 GCAGTTTTTATACAGGGCAAGGAC 60.381 45.833 0.00 0.00 0.00 3.85
53 54 1.223487 GGGCAAGGACAAGCGGATA 59.777 57.895 0.00 0.00 0.00 2.59
56 57 1.230324 GCAAGGACAAGCGGATATCC 58.770 55.000 12.14 12.14 0.00 2.59
156 157 7.870954 TCGTGTGAACTGTGAACTAAAGATTAT 59.129 33.333 0.00 0.00 0.00 1.28
194 195 2.159379 CGCTTGGAGCCCTAATTGTTTC 60.159 50.000 0.00 0.00 38.18 2.78
265 266 1.247567 CCCTGGTTTCATCACGCTTT 58.752 50.000 0.00 0.00 0.00 3.51
345 346 6.115448 AGACAAACATTAGCCACTACTCTT 57.885 37.500 0.00 0.00 0.00 2.85
353 354 1.900486 AGCCACTACTCTTGGTACCAC 59.100 52.381 16.04 0.00 36.40 4.16
360 361 0.327924 CTCTTGGTACCACATGGGCA 59.672 55.000 16.04 0.00 42.05 5.36
370 371 1.003580 CCACATGGGCAGTACTCTTGT 59.996 52.381 0.00 0.00 0.00 3.16
426 427 3.758554 GCCAGGACAAAACATATGACTGT 59.241 43.478 10.38 9.05 0.00 3.55
435 436 9.438291 GACAAAACATATGACTGTATACATTGC 57.562 33.333 10.38 0.00 0.00 3.56
492 499 4.946160 ATTCCAATTCCAAGGTCAGGTA 57.054 40.909 0.00 0.00 0.00 3.08
493 500 4.301072 TTCCAATTCCAAGGTCAGGTAG 57.699 45.455 0.00 0.00 0.00 3.18
494 501 2.026262 TCCAATTCCAAGGTCAGGTAGC 60.026 50.000 0.00 0.00 0.00 3.58
495 502 2.290896 CCAATTCCAAGGTCAGGTAGCA 60.291 50.000 0.00 0.00 0.00 3.49
496 503 3.624777 CAATTCCAAGGTCAGGTAGCAT 58.375 45.455 0.00 0.00 0.00 3.79
589 597 2.159085 GGAATCGAACCCTGGTCAGTAG 60.159 54.545 0.00 0.00 0.00 2.57
630 638 0.723414 CACTACACCAGATGCGCTTG 59.277 55.000 9.73 4.45 0.00 4.01
635 643 2.180017 CCAGATGCGCTTGGTTGC 59.820 61.111 9.73 0.00 0.00 4.17
636 644 2.180017 CAGATGCGCTTGGTTGCC 59.820 61.111 9.73 0.00 0.00 4.52
639 647 1.181098 AGATGCGCTTGGTTGCCTTT 61.181 50.000 9.73 0.00 0.00 3.11
656 664 3.769536 CCTTTTGACCATTGATTACGGC 58.230 45.455 0.00 0.00 0.00 5.68
787 835 3.924686 ACGCCTTTAGAAACGTCATGTAG 59.075 43.478 0.00 0.00 32.37 2.74
790 838 5.444218 CGCCTTTAGAAACGTCATGTAGTTC 60.444 44.000 8.51 0.00 0.00 3.01
921 1227 1.270518 CGTGAGGATAATGGGAGCCAG 60.271 57.143 0.00 0.00 36.75 4.85
1039 1345 4.177026 TCAAAAACAAAACCATCACCACG 58.823 39.130 0.00 0.00 0.00 4.94
1064 1372 4.704833 CCCCTGAGGCCACACACG 62.705 72.222 5.01 0.00 0.00 4.49
1078 1386 3.919386 CACGCGCACGAACACACA 61.919 61.111 5.73 0.00 43.93 3.72
1082 1390 2.625906 CGCACGAACACACACCAG 59.374 61.111 0.00 0.00 0.00 4.00
1083 1391 1.880796 CGCACGAACACACACCAGA 60.881 57.895 0.00 0.00 0.00 3.86
1084 1392 1.221466 CGCACGAACACACACCAGAT 61.221 55.000 0.00 0.00 0.00 2.90
1085 1393 0.512952 GCACGAACACACACCAGATC 59.487 55.000 0.00 0.00 0.00 2.75
1099 1410 4.524328 ACACCAGATCAATCAAGAAAACCC 59.476 41.667 0.00 0.00 0.00 4.11
1361 1672 2.716424 TGTTTCCTTCCTTCCCTGTCAT 59.284 45.455 0.00 0.00 0.00 3.06
1362 1673 3.244911 TGTTTCCTTCCTTCCCTGTCATC 60.245 47.826 0.00 0.00 0.00 2.92
1363 1674 2.342406 TCCTTCCTTCCCTGTCATCA 57.658 50.000 0.00 0.00 0.00 3.07
1369 1680 0.608130 CTTCCCTGTCATCACCGTCA 59.392 55.000 0.00 0.00 0.00 4.35
1389 1704 5.561532 CGTCAGTTTGTTGCTCATTTCTCAT 60.562 40.000 0.00 0.00 0.00 2.90
1398 1725 3.686241 TGCTCATTTCTCATCGGAGTTTG 59.314 43.478 0.00 0.00 42.05 2.93
1399 1726 3.935203 GCTCATTTCTCATCGGAGTTTGA 59.065 43.478 0.00 0.00 42.05 2.69
1400 1727 4.201763 GCTCATTTCTCATCGGAGTTTGAC 60.202 45.833 0.00 0.00 42.05 3.18
1401 1728 3.926527 TCATTTCTCATCGGAGTTTGACG 59.073 43.478 0.00 0.00 42.05 4.35
1402 1729 3.653539 TTTCTCATCGGAGTTTGACGA 57.346 42.857 0.00 0.00 42.05 4.20
1404 1731 3.422417 TCTCATCGGAGTTTGACGATC 57.578 47.619 0.00 0.00 45.76 3.69
1405 1732 3.017442 TCTCATCGGAGTTTGACGATCT 58.983 45.455 0.00 0.00 45.76 2.75
1406 1733 3.444034 TCTCATCGGAGTTTGACGATCTT 59.556 43.478 0.00 0.00 45.76 2.40
1407 1734 4.082190 TCTCATCGGAGTTTGACGATCTTT 60.082 41.667 0.00 0.00 45.76 2.52
1408 1735 4.566004 TCATCGGAGTTTGACGATCTTTT 58.434 39.130 0.00 0.00 45.76 2.27
1642 1973 3.369147 CGATCATGTCTTCTTGTGTGGTC 59.631 47.826 0.00 0.00 0.00 4.02
1741 2072 3.438434 GTCTTCTGGAAATGGTGAAGCTC 59.562 47.826 0.00 0.00 36.72 4.09
1742 2073 3.072915 TCTTCTGGAAATGGTGAAGCTCA 59.927 43.478 0.00 0.00 36.72 4.26
1780 2111 2.517450 GGCGAGTGCTGATGTACGC 61.517 63.158 0.00 0.00 44.18 4.42
1806 2137 1.135199 CACCGCGTGTACCTAGATGTT 60.135 52.381 4.92 0.00 0.00 2.71
1819 2153 0.239347 AGATGTTCAAAGCTGCGCAC 59.761 50.000 5.66 3.54 0.00 5.34
1957 2327 4.122776 GCTTAGGCAAATTCGAGATCAGA 58.877 43.478 0.00 0.00 38.54 3.27
1959 2329 5.928839 GCTTAGGCAAATTCGAGATCAGATA 59.071 40.000 0.00 0.00 38.54 1.98
1967 2337 7.340699 CAAATTCGAGATCAGATAGGAAAACG 58.659 38.462 0.00 0.00 0.00 3.60
1970 2340 4.112634 CGAGATCAGATAGGAAAACGCAA 58.887 43.478 0.00 0.00 0.00 4.85
1972 2342 5.063438 CGAGATCAGATAGGAAAACGCAAAA 59.937 40.000 0.00 0.00 0.00 2.44
2006 2376 8.968969 ACTCCTACATAGTAACACCTAAAGAAG 58.031 37.037 0.00 0.00 0.00 2.85
2007 2377 9.186837 CTCCTACATAGTAACACCTAAAGAAGA 57.813 37.037 0.00 0.00 0.00 2.87
2008 2378 9.710818 TCCTACATAGTAACACCTAAAGAAGAT 57.289 33.333 0.00 0.00 0.00 2.40
2052 2422 9.480053 AAGAAATATTCATGTTGTTGAACCTTG 57.520 29.630 0.00 0.00 38.37 3.61
2053 2423 8.859090 AGAAATATTCATGTTGTTGAACCTTGA 58.141 29.630 0.00 0.00 38.37 3.02
2054 2424 9.643693 GAAATATTCATGTTGTTGAACCTTGAT 57.356 29.630 0.00 0.00 38.37 2.57
2061 2431 9.906660 TCATGTTGTTGAACCTTGATTAAATAC 57.093 29.630 0.00 0.00 0.00 1.89
2062 2432 9.139174 CATGTTGTTGAACCTTGATTAAATACC 57.861 33.333 0.00 0.00 0.00 2.73
2070 2440 4.210331 CCTTGATTAAATACCTGCCAGCT 58.790 43.478 0.00 0.00 0.00 4.24
2076 2446 1.191535 AATACCTGCCAGCTACGTCA 58.808 50.000 0.00 0.00 0.00 4.35
2077 2447 1.414158 ATACCTGCCAGCTACGTCAT 58.586 50.000 0.00 0.00 0.00 3.06
2078 2448 0.744874 TACCTGCCAGCTACGTCATC 59.255 55.000 0.00 0.00 0.00 2.92
2079 2449 1.227380 CCTGCCAGCTACGTCATCC 60.227 63.158 0.00 0.00 0.00 3.51
2080 2450 1.517361 CTGCCAGCTACGTCATCCA 59.483 57.895 0.00 0.00 0.00 3.41
2081 2451 0.529337 CTGCCAGCTACGTCATCCAG 60.529 60.000 0.00 0.00 0.00 3.86
2082 2452 1.227380 GCCAGCTACGTCATCCAGG 60.227 63.158 0.00 0.00 0.00 4.45
2083 2453 1.676678 GCCAGCTACGTCATCCAGGA 61.677 60.000 0.00 0.00 0.00 3.86
2084 2454 1.043816 CCAGCTACGTCATCCAGGAT 58.956 55.000 0.00 0.00 0.00 3.24
2085 2455 2.239400 CCAGCTACGTCATCCAGGATA 58.761 52.381 0.00 0.00 0.00 2.59
2086 2456 2.628178 CCAGCTACGTCATCCAGGATAA 59.372 50.000 0.00 0.00 0.00 1.75
2087 2457 3.259374 CCAGCTACGTCATCCAGGATAAT 59.741 47.826 0.00 0.00 0.00 1.28
2088 2458 4.262635 CCAGCTACGTCATCCAGGATAATT 60.263 45.833 0.00 0.00 0.00 1.40
2089 2459 4.926238 CAGCTACGTCATCCAGGATAATTC 59.074 45.833 0.00 0.00 0.00 2.17
2090 2460 4.021016 AGCTACGTCATCCAGGATAATTCC 60.021 45.833 0.00 0.00 42.96 3.01
2165 2548 7.707774 TTTGATTATACGAATGAGCAATCGA 57.292 32.000 14.15 0.00 41.43 3.59
2244 2638 4.217118 GGGTACTATGATACCACTACACCG 59.783 50.000 8.92 0.00 45.72 4.94
2245 2639 4.217118 GGTACTATGATACCACTACACCGG 59.783 50.000 0.00 0.00 43.69 5.28
2246 2640 4.174704 ACTATGATACCACTACACCGGA 57.825 45.455 9.46 0.00 0.00 5.14
2247 2641 3.887716 ACTATGATACCACTACACCGGAC 59.112 47.826 9.46 0.00 0.00 4.79
2248 2642 1.097232 TGATACCACTACACCGGACG 58.903 55.000 9.46 0.00 0.00 4.79
2249 2643 1.339920 TGATACCACTACACCGGACGA 60.340 52.381 9.46 0.00 0.00 4.20
2250 2644 1.332997 GATACCACTACACCGGACGAG 59.667 57.143 9.46 3.80 0.00 4.18
2251 2645 0.677731 TACCACTACACCGGACGAGG 60.678 60.000 9.46 4.53 37.30 4.63
2252 2646 2.181021 CACTACACCGGACGAGGC 59.819 66.667 9.46 0.00 33.69 4.70
2253 2647 2.035312 ACTACACCGGACGAGGCT 59.965 61.111 9.46 0.00 33.69 4.58
2254 2648 2.045131 ACTACACCGGACGAGGCTC 61.045 63.158 9.46 3.87 33.69 4.70
2255 2649 2.753043 TACACCGGACGAGGCTCC 60.753 66.667 9.46 0.00 33.69 4.70
2256 2650 3.278072 TACACCGGACGAGGCTCCT 62.278 63.158 9.46 0.00 33.69 3.69
2257 2651 3.827898 CACCGGACGAGGCTCCTC 61.828 72.222 9.46 6.95 39.55 3.71
2258 2652 4.049817 ACCGGACGAGGCTCCTCT 62.050 66.667 9.46 1.64 40.69 3.69
2259 2653 3.522731 CCGGACGAGGCTCCTCTG 61.523 72.222 9.32 11.82 40.69 3.35
2260 2654 4.200283 CGGACGAGGCTCCTCTGC 62.200 72.222 9.32 5.56 40.69 4.26
2267 2661 4.821589 GGCTCCTCTGCCGTTCGG 62.822 72.222 6.90 6.90 43.74 4.30
2284 2678 3.134127 GCAGGGTGCCGTTCCATC 61.134 66.667 0.00 0.00 37.42 3.51
2285 2679 2.438434 CAGGGTGCCGTTCCATCC 60.438 66.667 0.00 0.00 36.19 3.51
2286 2680 3.728373 AGGGTGCCGTTCCATCCC 61.728 66.667 0.00 0.00 36.63 3.85
2287 2681 3.728373 GGGTGCCGTTCCATCCCT 61.728 66.667 0.00 0.00 35.63 4.20
2288 2682 2.438434 GGTGCCGTTCCATCCCTG 60.438 66.667 0.00 0.00 0.00 4.45
2289 2683 2.668632 GTGCCGTTCCATCCCTGA 59.331 61.111 0.00 0.00 0.00 3.86
2290 2684 1.745489 GTGCCGTTCCATCCCTGAC 60.745 63.158 0.00 0.00 0.00 3.51
2291 2685 2.220586 TGCCGTTCCATCCCTGACA 61.221 57.895 0.00 0.00 0.00 3.58
2292 2686 1.450312 GCCGTTCCATCCCTGACAG 60.450 63.158 0.00 0.00 0.00 3.51
2293 2687 1.221840 CCGTTCCATCCCTGACAGG 59.778 63.158 15.15 15.15 34.30 4.00
2294 2688 1.553690 CCGTTCCATCCCTGACAGGT 61.554 60.000 20.24 0.00 31.93 4.00
2295 2689 0.391661 CGTTCCATCCCTGACAGGTG 60.392 60.000 20.24 12.39 31.93 4.00
2296 2690 0.035056 GTTCCATCCCTGACAGGTGG 60.035 60.000 20.50 20.50 31.93 4.61
2297 2691 1.207488 TTCCATCCCTGACAGGTGGG 61.207 60.000 24.18 19.31 44.66 4.61
2298 2692 2.273449 CATCCCTGACAGGTGGGC 59.727 66.667 20.24 0.00 43.04 5.36
2299 2693 2.125912 ATCCCTGACAGGTGGGCT 59.874 61.111 20.24 0.00 43.04 5.19
2300 2694 1.997874 ATCCCTGACAGGTGGGCTC 60.998 63.158 20.24 0.00 43.04 4.70
2301 2695 2.770868 ATCCCTGACAGGTGGGCTCA 62.771 60.000 20.24 0.00 43.04 4.26
2302 2696 2.304056 CCCTGACAGGTGGGCTCAT 61.304 63.158 20.24 0.00 36.61 2.90
2303 2697 1.687612 CCTGACAGGTGGGCTCATT 59.312 57.895 13.84 0.00 0.00 2.57
2304 2698 0.911769 CCTGACAGGTGGGCTCATTA 59.088 55.000 13.84 0.00 0.00 1.90
2305 2699 1.281867 CCTGACAGGTGGGCTCATTAA 59.718 52.381 13.84 0.00 0.00 1.40
2306 2700 2.290896 CCTGACAGGTGGGCTCATTAAA 60.291 50.000 13.84 0.00 0.00 1.52
2307 2701 3.420893 CTGACAGGTGGGCTCATTAAAA 58.579 45.455 0.00 0.00 0.00 1.52
2308 2702 3.826157 CTGACAGGTGGGCTCATTAAAAA 59.174 43.478 0.00 0.00 0.00 1.94
2340 2734 3.036577 CAGTGCCACAACTGCAGG 58.963 61.111 19.93 3.21 41.05 4.85
2341 2735 1.825191 CAGTGCCACAACTGCAGGT 60.825 57.895 19.93 9.19 41.05 4.00
2342 2736 1.825191 AGTGCCACAACTGCAGGTG 60.825 57.895 30.07 30.07 39.87 4.00
2343 2737 1.823470 GTGCCACAACTGCAGGTGA 60.823 57.895 37.55 13.17 39.87 4.02
2344 2738 1.151221 TGCCACAACTGCAGGTGAT 59.849 52.632 37.55 18.98 37.18 3.06
2345 2739 1.174078 TGCCACAACTGCAGGTGATG 61.174 55.000 37.55 27.69 37.18 3.07
2346 2740 1.174712 GCCACAACTGCAGGTGATGT 61.175 55.000 37.55 22.17 37.18 3.06
2347 2741 1.881925 GCCACAACTGCAGGTGATGTA 60.882 52.381 37.55 0.00 37.18 2.29
2348 2742 1.806542 CCACAACTGCAGGTGATGTAC 59.193 52.381 37.55 0.00 37.18 2.90
2349 2743 1.460743 CACAACTGCAGGTGATGTACG 59.539 52.381 37.55 10.30 37.18 3.67
2350 2744 1.070134 ACAACTGCAGGTGATGTACGT 59.930 47.619 37.55 11.11 0.00 3.57
2351 2745 1.726791 CAACTGCAGGTGATGTACGTC 59.273 52.381 28.20 8.21 0.00 4.34
2352 2746 0.966179 ACTGCAGGTGATGTACGTCA 59.034 50.000 19.93 13.87 0.00 4.35
2353 2747 1.067565 ACTGCAGGTGATGTACGTCAG 60.068 52.381 18.11 8.10 33.03 3.51
2354 2748 0.246360 TGCAGGTGATGTACGTCAGG 59.754 55.000 18.11 11.59 0.00 3.86
2355 2749 0.460284 GCAGGTGATGTACGTCAGGG 60.460 60.000 18.11 11.26 0.00 4.45
2356 2750 0.175760 CAGGTGATGTACGTCAGGGG 59.824 60.000 18.11 6.70 0.00 4.79
2357 2751 0.040646 AGGTGATGTACGTCAGGGGA 59.959 55.000 18.11 0.00 0.00 4.81
2358 2752 0.460311 GGTGATGTACGTCAGGGGAG 59.540 60.000 18.11 0.00 0.00 4.30
2359 2753 0.179108 GTGATGTACGTCAGGGGAGC 60.179 60.000 18.11 1.85 0.00 4.70
2360 2754 1.327690 TGATGTACGTCAGGGGAGCC 61.328 60.000 13.87 0.00 0.00 4.70
2361 2755 2.351336 GATGTACGTCAGGGGAGCCG 62.351 65.000 10.30 0.00 0.00 5.52
2362 2756 4.509737 GTACGTCAGGGGAGCCGC 62.510 72.222 0.00 0.00 0.00 6.53
2363 2757 4.753662 TACGTCAGGGGAGCCGCT 62.754 66.667 0.00 0.00 39.92 5.52
2365 2759 4.821589 CGTCAGGGGAGCCGCTTC 62.822 72.222 3.01 0.00 37.10 3.86
2366 2760 4.475135 GTCAGGGGAGCCGCTTCC 62.475 72.222 9.56 9.56 37.10 3.46
2372 2766 2.187163 GGAGCCGCTTCCCACTAC 59.813 66.667 0.00 0.00 0.00 2.73
2373 2767 2.656069 GGAGCCGCTTCCCACTACA 61.656 63.158 0.00 0.00 0.00 2.74
2374 2768 1.448013 GAGCCGCTTCCCACTACAC 60.448 63.158 0.00 0.00 0.00 2.90
2375 2769 2.436115 GCCGCTTCCCACTACACC 60.436 66.667 0.00 0.00 0.00 4.16
2387 2781 0.321671 ACTACACCAGATGCGCTTGT 59.678 50.000 9.73 0.00 0.00 3.16
2388 2782 1.002366 CTACACCAGATGCGCTTGTC 58.998 55.000 9.73 4.30 0.00 3.18
2389 2783 0.608130 TACACCAGATGCGCTTGTCT 59.392 50.000 9.73 6.84 0.00 3.41
2390 2784 0.952497 ACACCAGATGCGCTTGTCTG 60.952 55.000 22.55 22.55 41.13 3.51
2392 2786 2.789917 CAGATGCGCTTGTCTGGC 59.210 61.111 22.07 0.83 38.50 4.85
2393 2787 2.036571 CAGATGCGCTTGTCTGGCA 61.037 57.895 22.07 0.00 38.50 4.92
2394 2788 2.037136 AGATGCGCTTGTCTGGCAC 61.037 57.895 9.73 0.00 39.84 5.01
2395 2789 2.033141 ATGCGCTTGTCTGGCACT 59.967 55.556 9.73 0.00 39.84 4.40
2396 2790 2.249557 GATGCGCTTGTCTGGCACTG 62.250 60.000 9.73 0.00 39.84 3.66
2397 2791 2.666190 GCGCTTGTCTGGCACTGA 60.666 61.111 0.00 0.00 0.00 3.41
2398 2792 2.253758 GCGCTTGTCTGGCACTGAA 61.254 57.895 0.00 0.00 38.22 3.02
2399 2793 1.571460 CGCTTGTCTGGCACTGAAC 59.429 57.895 0.00 0.00 38.22 3.18
2400 2794 1.845809 CGCTTGTCTGGCACTGAACC 61.846 60.000 0.00 0.00 38.22 3.62
2401 2795 0.536006 GCTTGTCTGGCACTGAACCT 60.536 55.000 0.00 0.00 38.22 3.50
2402 2796 1.972872 CTTGTCTGGCACTGAACCTT 58.027 50.000 0.00 0.00 38.22 3.50
2403 2797 1.605710 CTTGTCTGGCACTGAACCTTG 59.394 52.381 0.00 0.00 38.22 3.61
2404 2798 0.836606 TGTCTGGCACTGAACCTTGA 59.163 50.000 0.00 0.00 38.22 3.02
2405 2799 1.421268 TGTCTGGCACTGAACCTTGAT 59.579 47.619 0.00 0.00 38.22 2.57
2406 2800 1.808945 GTCTGGCACTGAACCTTGATG 59.191 52.381 0.00 0.00 38.22 3.07
2407 2801 1.699083 TCTGGCACTGAACCTTGATGA 59.301 47.619 0.00 0.00 32.07 2.92
2408 2802 2.106338 TCTGGCACTGAACCTTGATGAA 59.894 45.455 0.00 0.00 32.07 2.57
2409 2803 2.486982 CTGGCACTGAACCTTGATGAAG 59.513 50.000 0.00 0.00 0.00 3.02
2410 2804 1.200948 GGCACTGAACCTTGATGAAGC 59.799 52.381 0.00 0.00 0.00 3.86
2411 2805 2.157738 GCACTGAACCTTGATGAAGCT 58.842 47.619 0.00 0.00 0.00 3.74
2412 2806 3.338249 GCACTGAACCTTGATGAAGCTA 58.662 45.455 0.00 0.00 0.00 3.32
2413 2807 3.753272 GCACTGAACCTTGATGAAGCTAA 59.247 43.478 0.00 0.00 0.00 3.09
2414 2808 4.378874 GCACTGAACCTTGATGAAGCTAAC 60.379 45.833 0.00 0.00 0.00 2.34
2415 2809 4.999950 CACTGAACCTTGATGAAGCTAACT 59.000 41.667 0.00 0.00 0.00 2.24
2416 2810 4.999950 ACTGAACCTTGATGAAGCTAACTG 59.000 41.667 0.00 0.00 0.00 3.16
2417 2811 4.973168 TGAACCTTGATGAAGCTAACTGT 58.027 39.130 0.00 0.00 0.00 3.55
2418 2812 6.109156 TGAACCTTGATGAAGCTAACTGTA 57.891 37.500 0.00 0.00 0.00 2.74
2419 2813 6.166279 TGAACCTTGATGAAGCTAACTGTAG 58.834 40.000 0.00 0.00 0.00 2.74
2420 2814 5.746990 ACCTTGATGAAGCTAACTGTAGT 57.253 39.130 0.00 0.00 0.00 2.73
2421 2815 5.482908 ACCTTGATGAAGCTAACTGTAGTG 58.517 41.667 0.00 0.00 0.00 2.74
2422 2816 5.012148 ACCTTGATGAAGCTAACTGTAGTGT 59.988 40.000 0.00 0.00 0.00 3.55
2423 2817 6.210784 ACCTTGATGAAGCTAACTGTAGTGTA 59.789 38.462 0.00 0.00 0.00 2.90
2424 2818 6.531948 CCTTGATGAAGCTAACTGTAGTGTAC 59.468 42.308 0.00 0.00 0.00 2.90
2425 2819 6.584185 TGATGAAGCTAACTGTAGTGTACA 57.416 37.500 0.00 0.00 37.13 2.90
2441 2835 9.787435 TGTAGTGTACAGAATAAATTCCAAAGT 57.213 29.630 0.00 0.00 37.51 2.66
2443 2837 8.336801 AGTGTACAGAATAAATTCCAAAGTCC 57.663 34.615 0.00 0.00 37.51 3.85
2444 2838 7.119262 AGTGTACAGAATAAATTCCAAAGTCCG 59.881 37.037 0.00 0.00 37.51 4.79
2445 2839 6.938030 TGTACAGAATAAATTCCAAAGTCCGT 59.062 34.615 0.00 0.00 37.51 4.69
2446 2840 6.894339 ACAGAATAAATTCCAAAGTCCGTT 57.106 33.333 0.00 0.00 37.51 4.44
2447 2841 6.677913 ACAGAATAAATTCCAAAGTCCGTTG 58.322 36.000 0.00 0.00 37.51 4.10
2448 2842 6.264518 ACAGAATAAATTCCAAAGTCCGTTGT 59.735 34.615 0.00 0.00 37.51 3.32
2449 2843 7.446013 ACAGAATAAATTCCAAAGTCCGTTGTA 59.554 33.333 0.00 0.00 37.51 2.41
2450 2844 7.749126 CAGAATAAATTCCAAAGTCCGTTGTAC 59.251 37.037 0.00 0.00 37.51 2.90
2451 2845 7.446013 AGAATAAATTCCAAAGTCCGTTGTACA 59.554 33.333 0.00 0.00 37.51 2.90
2452 2846 5.838531 AAATTCCAAAGTCCGTTGTACAA 57.161 34.783 3.59 3.59 0.00 2.41
2453 2847 4.823790 ATTCCAAAGTCCGTTGTACAAC 57.176 40.909 25.73 25.73 37.92 3.32
2454 2848 3.547054 TCCAAAGTCCGTTGTACAACT 57.453 42.857 30.47 13.78 39.08 3.16
2455 2849 3.876341 TCCAAAGTCCGTTGTACAACTT 58.124 40.909 30.47 18.44 39.08 2.66
2456 2850 3.623960 TCCAAAGTCCGTTGTACAACTTG 59.376 43.478 30.47 25.65 39.08 3.16
2457 2851 3.623960 CCAAAGTCCGTTGTACAACTTGA 59.376 43.478 30.47 24.09 39.08 3.02
2458 2852 4.095185 CCAAAGTCCGTTGTACAACTTGAA 59.905 41.667 30.47 14.04 39.08 2.69
2459 2853 4.870221 AAGTCCGTTGTACAACTTGAAC 57.130 40.909 30.47 22.27 39.08 3.18
2460 2854 2.861935 AGTCCGTTGTACAACTTGAACG 59.138 45.455 30.47 19.78 40.62 3.95
2600 3000 8.870075 ACCTTTATGCTTTGTTTCTTATCTCT 57.130 30.769 0.00 0.00 0.00 3.10
2601 3001 8.951243 ACCTTTATGCTTTGTTTCTTATCTCTC 58.049 33.333 0.00 0.00 0.00 3.20
2602 3002 9.171877 CCTTTATGCTTTGTTTCTTATCTCTCT 57.828 33.333 0.00 0.00 0.00 3.10
2604 3004 8.723942 TTATGCTTTGTTTCTTATCTCTCTCC 57.276 34.615 0.00 0.00 0.00 3.71
2605 3005 5.491982 TGCTTTGTTTCTTATCTCTCTCCC 58.508 41.667 0.00 0.00 0.00 4.30
2606 3006 4.878971 GCTTTGTTTCTTATCTCTCTCCCC 59.121 45.833 0.00 0.00 0.00 4.81
2607 3007 5.432645 CTTTGTTTCTTATCTCTCTCCCCC 58.567 45.833 0.00 0.00 0.00 5.40
2675 3382 0.765519 ACTCCTACCGTGGGTGGTTT 60.766 55.000 7.77 0.00 43.56 3.27
2685 3392 2.547642 CGTGGGTGGTTTTGATGCAAAT 60.548 45.455 0.00 0.00 33.19 2.32
2714 3421 6.529463 AAAGTTTTGTTTAGTGATGCATGC 57.471 33.333 11.82 11.82 0.00 4.06
2719 3426 6.468333 TTTGTTTAGTGATGCATGCCATAT 57.532 33.333 16.68 1.15 33.29 1.78
2855 3580 8.609478 AAAAACGTAATATTCTGCATAAACGG 57.391 30.769 10.33 0.00 36.11 4.44
2882 3617 4.463891 AGAGTTTGGCCACATAAAATCCTG 59.536 41.667 3.88 0.00 32.93 3.86
2893 3628 7.148086 GCCACATAAAATCCTGTGATGTCTTTA 60.148 37.037 4.34 0.00 44.35 1.85
2937 3672 0.397941 CCACACACACCATCCTCTGT 59.602 55.000 0.00 0.00 0.00 3.41
2968 3703 3.017048 TGGCCACAAGAAATCCTATGG 57.983 47.619 0.00 0.00 0.00 2.74
2975 3710 5.066505 CCACAAGAAATCCTATGGTGCTAAC 59.933 44.000 0.00 0.00 0.00 2.34
2979 3714 6.420913 AGAAATCCTATGGTGCTAACGTAT 57.579 37.500 0.00 0.00 0.00 3.06
2986 3721 5.009710 CCTATGGTGCTAACGTATGAGAAGA 59.990 44.000 0.00 0.00 0.00 2.87
2988 3723 4.933330 TGGTGCTAACGTATGAGAAGATC 58.067 43.478 0.00 0.00 0.00 2.75
2989 3724 4.401202 TGGTGCTAACGTATGAGAAGATCA 59.599 41.667 0.00 0.00 43.70 2.92
2990 3725 5.105513 TGGTGCTAACGTATGAGAAGATCAA 60.106 40.000 0.00 0.00 42.53 2.57
2999 3734 6.097554 ACGTATGAGAAGATCAAAGAGTGGAT 59.902 38.462 0.00 0.00 42.53 3.41
3004 3739 5.732633 AGAAGATCAAAGAGTGGATCACAG 58.267 41.667 0.00 0.00 41.84 3.66
3005 3740 5.483231 AGAAGATCAAAGAGTGGATCACAGA 59.517 40.000 0.00 0.00 41.84 3.41
3026 3761 1.529244 ACTGGAGTGGCTGCAAACC 60.529 57.895 0.50 0.00 30.12 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.648059 ACTGCAGAATACAGAATGGCC 58.352 47.619 23.35 0.00 43.62 5.36
6 7 4.708726 AAACTGCAGAATACAGAATGGC 57.291 40.909 23.35 0.00 43.62 4.40
56 57 1.189403 GAACTACTCCGCAACGATCG 58.811 55.000 14.88 14.88 0.00 3.69
63 64 0.175760 GCCATCAGAACTACTCCGCA 59.824 55.000 0.00 0.00 0.00 5.69
66 67 8.910351 AAATTTATAGCCATCAGAACTACTCC 57.090 34.615 0.00 0.00 0.00 3.85
118 119 4.625311 CAGTTCACACGATACAATGCAGTA 59.375 41.667 0.00 0.00 0.00 2.74
156 157 7.280876 GCTCCAAGCGGAAATATATCATTATCA 59.719 37.037 0.00 0.00 42.21 2.15
165 166 2.054799 AGGGCTCCAAGCGGAAATATA 58.945 47.619 0.00 0.00 43.62 0.86
167 168 1.502690 TAGGGCTCCAAGCGGAAATA 58.497 50.000 0.00 0.00 43.62 1.40
174 175 3.092301 AGAAACAATTAGGGCTCCAAGC 58.908 45.455 0.00 0.00 41.46 4.01
194 195 9.916397 GGTAAGTAATTTGTCGATCAAACATAG 57.084 33.333 13.04 0.00 46.77 2.23
217 218 3.551259 GCAGGTTAGCTTGCTGGTA 57.449 52.632 6.42 0.00 43.35 3.25
333 334 1.900486 GTGGTACCAAGAGTAGTGGCT 59.100 52.381 18.31 0.00 40.02 4.75
345 346 0.616371 GTACTGCCCATGTGGTACCA 59.384 55.000 11.60 11.60 36.04 3.25
353 354 5.003804 AGTAAAACAAGAGTACTGCCCATG 58.996 41.667 0.00 0.00 0.00 3.66
360 361 9.074576 CCCCATAAAAAGTAAAACAAGAGTACT 57.925 33.333 0.00 0.00 0.00 2.73
370 371 6.519213 GCCATGTCACCCCATAAAAAGTAAAA 60.519 38.462 0.00 0.00 0.00 1.52
426 427 6.301486 AGATCAAATCTGCTGGCAATGTATA 58.699 36.000 0.00 0.00 38.44 1.47
435 436 4.259356 TCACTGAAGATCAAATCTGCTGG 58.741 43.478 0.00 0.00 40.13 4.85
535 543 6.156519 GCAATTTTTCTCCTCACCGTATTTT 58.843 36.000 0.00 0.00 0.00 1.82
541 549 1.729149 GCGCAATTTTTCTCCTCACCG 60.729 52.381 0.30 0.00 0.00 4.94
543 551 2.704725 TGCGCAATTTTTCTCCTCAC 57.295 45.000 8.16 0.00 0.00 3.51
589 597 1.339097 ATCATAGTACCCTCCCACGC 58.661 55.000 0.00 0.00 0.00 5.34
630 638 3.683365 ATCAATGGTCAAAAGGCAACC 57.317 42.857 0.00 0.00 37.17 3.77
635 643 3.443681 AGCCGTAATCAATGGTCAAAAGG 59.556 43.478 0.00 0.00 36.53 3.11
636 644 4.701956 AGCCGTAATCAATGGTCAAAAG 57.298 40.909 0.00 0.00 36.53 2.27
639 647 7.337184 TGTTTATTAGCCGTAATCAATGGTCAA 59.663 33.333 0.00 0.00 36.53 3.18
720 768 9.765795 CTCCGACCACTAATTAGAATCTTTTAT 57.234 33.333 19.38 0.00 0.00 1.40
803 851 6.960468 TGAGCTCTCACGAAACATATACTAG 58.040 40.000 16.19 0.00 34.14 2.57
810 858 2.613977 CCCTTGAGCTCTCACGAAACAT 60.614 50.000 16.19 0.00 39.66 2.71
871 1177 4.961511 TGCGACACGTGGCAGGAC 62.962 66.667 23.63 8.02 39.36 3.85
904 1210 0.321122 CGCTGGCTCCCATTATCCTC 60.321 60.000 0.00 0.00 30.82 3.71
932 1238 2.759149 CATTCCATTGGCCGGCCA 60.759 61.111 44.23 44.23 45.63 5.36
937 1243 0.903942 TTGCTTCCATTCCATTGGCC 59.096 50.000 0.00 0.00 36.66 5.36
1064 1372 3.506312 CTGGTGTGTGTTCGTGCGC 62.506 63.158 0.00 0.00 0.00 6.09
1070 1378 4.756642 TCTTGATTGATCTGGTGTGTGTTC 59.243 41.667 0.00 0.00 0.00 3.18
1071 1379 4.717877 TCTTGATTGATCTGGTGTGTGTT 58.282 39.130 0.00 0.00 0.00 3.32
1078 1386 4.089361 GGGGTTTTCTTGATTGATCTGGT 58.911 43.478 0.00 0.00 0.00 4.00
1082 1390 4.261801 TCTCGGGGTTTTCTTGATTGATC 58.738 43.478 0.00 0.00 0.00 2.92
1083 1391 4.265073 CTCTCGGGGTTTTCTTGATTGAT 58.735 43.478 0.00 0.00 0.00 2.57
1084 1392 3.559171 CCTCTCGGGGTTTTCTTGATTGA 60.559 47.826 0.00 0.00 0.00 2.57
1085 1393 2.749621 CCTCTCGGGGTTTTCTTGATTG 59.250 50.000 0.00 0.00 0.00 2.67
1099 1410 2.341543 CGGCCATGATCCTCTCGG 59.658 66.667 2.24 0.00 0.00 4.63
1361 1672 1.295792 GAGCAACAAACTGACGGTGA 58.704 50.000 0.00 0.00 0.00 4.02
1362 1673 1.013596 TGAGCAACAAACTGACGGTG 58.986 50.000 0.00 0.00 0.00 4.94
1363 1674 1.967319 ATGAGCAACAAACTGACGGT 58.033 45.000 0.00 0.00 0.00 4.83
1369 1680 4.083110 CCGATGAGAAATGAGCAACAAACT 60.083 41.667 0.00 0.00 0.00 2.66
1407 1734 3.444916 TCACGCGCAAAAACCATAAAAA 58.555 36.364 5.73 0.00 0.00 1.94
1408 1735 3.079960 TCACGCGCAAAAACCATAAAA 57.920 38.095 5.73 0.00 0.00 1.52
1411 1738 1.807142 TGATCACGCGCAAAAACCATA 59.193 42.857 5.73 0.00 0.00 2.74
1642 1973 0.721718 GATGAACGGGACTTTCTGCG 59.278 55.000 0.00 0.00 37.50 5.18
1741 2072 2.174363 TATTGCCTGGCAGATCGATG 57.826 50.000 22.17 0.00 40.61 3.84
1742 2073 2.617276 CCATATTGCCTGGCAGATCGAT 60.617 50.000 22.17 14.28 40.61 3.59
1819 2153 4.431214 CGATAACTTCACAGTCGAAACACG 60.431 45.833 0.00 0.00 44.09 4.49
1979 2349 9.979897 TTCTTTAGGTGTTACTATGTAGGAGTA 57.020 33.333 0.00 0.00 0.00 2.59
1981 2351 9.186837 TCTTCTTTAGGTGTTACTATGTAGGAG 57.813 37.037 0.00 0.00 0.00 3.69
2026 2396 9.480053 CAAGGTTCAACAACATGAATATTTCTT 57.520 29.630 0.00 0.00 41.09 2.52
2028 2398 9.643693 ATCAAGGTTCAACAACATGAATATTTC 57.356 29.630 0.00 0.00 41.09 2.17
2036 2406 9.139174 GGTATTTAATCAAGGTTCAACAACATG 57.861 33.333 0.00 0.00 33.70 3.21
2037 2407 9.088987 AGGTATTTAATCAAGGTTCAACAACAT 57.911 29.630 0.00 0.00 33.70 2.71
2038 2408 8.356657 CAGGTATTTAATCAAGGTTCAACAACA 58.643 33.333 0.00 0.00 33.70 3.33
2039 2409 7.328493 GCAGGTATTTAATCAAGGTTCAACAAC 59.672 37.037 0.00 0.00 0.00 3.32
2041 2411 6.071616 GGCAGGTATTTAATCAAGGTTCAACA 60.072 38.462 0.00 0.00 0.00 3.33
2042 2412 6.071616 TGGCAGGTATTTAATCAAGGTTCAAC 60.072 38.462 0.00 0.00 0.00 3.18
2043 2413 6.013379 TGGCAGGTATTTAATCAAGGTTCAA 58.987 36.000 0.00 0.00 0.00 2.69
2044 2414 5.575157 TGGCAGGTATTTAATCAAGGTTCA 58.425 37.500 0.00 0.00 0.00 3.18
2045 2415 5.450550 GCTGGCAGGTATTTAATCAAGGTTC 60.451 44.000 17.64 0.00 0.00 3.62
2046 2416 4.402474 GCTGGCAGGTATTTAATCAAGGTT 59.598 41.667 17.64 0.00 0.00 3.50
2050 2420 4.814234 CGTAGCTGGCAGGTATTTAATCAA 59.186 41.667 27.17 2.77 30.21 2.57
2051 2421 4.141801 ACGTAGCTGGCAGGTATTTAATCA 60.142 41.667 27.17 3.53 30.21 2.57
2052 2422 4.377897 ACGTAGCTGGCAGGTATTTAATC 58.622 43.478 27.17 13.43 30.21 1.75
2053 2423 4.141801 TGACGTAGCTGGCAGGTATTTAAT 60.142 41.667 27.17 12.46 30.21 1.40
2054 2424 3.196039 TGACGTAGCTGGCAGGTATTTAA 59.804 43.478 27.17 12.58 30.21 1.52
2055 2425 2.761767 TGACGTAGCTGGCAGGTATTTA 59.238 45.455 27.17 12.85 30.21 1.40
2056 2426 1.553248 TGACGTAGCTGGCAGGTATTT 59.447 47.619 27.17 17.64 30.21 1.40
2057 2427 1.191535 TGACGTAGCTGGCAGGTATT 58.808 50.000 27.17 17.97 30.21 1.89
2061 2431 1.227380 GGATGACGTAGCTGGCAGG 60.227 63.158 17.64 1.38 0.00 4.85
2062 2432 0.529337 CTGGATGACGTAGCTGGCAG 60.529 60.000 10.94 10.94 0.00 4.85
2081 2451 8.445588 TGGGAATTTAACTAGGAGGAATTATCC 58.554 37.037 0.00 1.59 46.98 2.59
2082 2452 9.862149 TTGGGAATTTAACTAGGAGGAATTATC 57.138 33.333 0.00 0.00 0.00 1.75
2083 2453 9.868160 CTTGGGAATTTAACTAGGAGGAATTAT 57.132 33.333 0.00 0.00 0.00 1.28
2084 2454 8.279361 CCTTGGGAATTTAACTAGGAGGAATTA 58.721 37.037 0.00 0.00 0.00 1.40
2085 2455 7.126061 CCTTGGGAATTTAACTAGGAGGAATT 58.874 38.462 0.00 0.00 0.00 2.17
2086 2456 6.219772 ACCTTGGGAATTTAACTAGGAGGAAT 59.780 38.462 10.65 0.00 0.00 3.01
2087 2457 5.554350 ACCTTGGGAATTTAACTAGGAGGAA 59.446 40.000 10.65 0.00 0.00 3.36
2088 2458 5.105853 ACCTTGGGAATTTAACTAGGAGGA 58.894 41.667 10.65 0.00 0.00 3.71
2089 2459 5.452341 ACCTTGGGAATTTAACTAGGAGG 57.548 43.478 10.65 0.00 0.00 4.30
2090 2460 7.054751 CCTAACCTTGGGAATTTAACTAGGAG 58.945 42.308 10.65 2.15 0.00 3.69
2091 2461 6.506413 ACCTAACCTTGGGAATTTAACTAGGA 59.494 38.462 10.65 0.00 32.43 2.94
2100 2470 5.537295 GTGTTGTAACCTAACCTTGGGAATT 59.463 40.000 0.00 0.00 32.43 2.17
2104 2474 3.822940 TGTGTTGTAACCTAACCTTGGG 58.177 45.455 0.00 0.00 34.56 4.12
2136 2515 9.853555 ATTGCTCATTCGTATAATCAAAAACAA 57.146 25.926 0.00 0.00 0.00 2.83
2138 2517 8.673275 CGATTGCTCATTCGTATAATCAAAAAC 58.327 33.333 6.13 0.00 31.76 2.43
2170 2553 4.183101 CCTGGATGCGCATATTTTTGTTT 58.817 39.130 25.40 0.00 0.00 2.83
2173 2556 2.361757 TCCCTGGATGCGCATATTTTTG 59.638 45.455 25.40 10.70 0.00 2.44
2267 2661 3.134127 GATGGAACGGCACCCTGC 61.134 66.667 0.00 0.00 44.08 4.85
2268 2662 2.438434 GGATGGAACGGCACCCTG 60.438 66.667 0.00 0.00 0.00 4.45
2269 2663 3.728373 GGGATGGAACGGCACCCT 61.728 66.667 0.00 0.00 37.75 4.34
2270 2664 3.728373 AGGGATGGAACGGCACCC 61.728 66.667 0.00 0.00 40.71 4.61
2271 2665 2.438434 CAGGGATGGAACGGCACC 60.438 66.667 0.00 0.00 0.00 5.01
2272 2666 1.745489 GTCAGGGATGGAACGGCAC 60.745 63.158 0.00 0.00 0.00 5.01
2273 2667 2.184020 CTGTCAGGGATGGAACGGCA 62.184 60.000 0.00 0.00 0.00 5.69
2274 2668 1.450312 CTGTCAGGGATGGAACGGC 60.450 63.158 0.00 0.00 0.00 5.68
2275 2669 1.221840 CCTGTCAGGGATGGAACGG 59.778 63.158 11.46 0.00 0.00 4.44
2276 2670 0.391661 CACCTGTCAGGGATGGAACG 60.392 60.000 23.06 0.00 40.58 3.95
2277 2671 0.035056 CCACCTGTCAGGGATGGAAC 60.035 60.000 23.06 0.00 40.58 3.62
2278 2672 2.386864 CCACCTGTCAGGGATGGAA 58.613 57.895 23.06 0.00 40.58 3.53
2279 2673 4.152248 CCACCTGTCAGGGATGGA 57.848 61.111 23.06 0.00 40.58 3.41
2281 2675 2.262774 GAGCCCACCTGTCAGGGATG 62.263 65.000 23.06 12.62 45.39 3.51
2285 2679 0.911769 TAATGAGCCCACCTGTCAGG 59.088 55.000 17.88 17.88 42.49 3.86
2286 2680 2.787473 TTAATGAGCCCACCTGTCAG 57.213 50.000 0.00 0.00 0.00 3.51
2287 2681 3.517296 TTTTAATGAGCCCACCTGTCA 57.483 42.857 0.00 0.00 0.00 3.58
2323 2717 1.825191 ACCTGCAGTTGTGGCACTG 60.825 57.895 19.83 10.08 46.15 3.66
2324 2718 1.825191 CACCTGCAGTTGTGGCACT 60.825 57.895 19.83 0.00 36.11 4.40
2325 2719 1.174712 ATCACCTGCAGTTGTGGCAC 61.175 55.000 19.13 11.55 36.11 5.01
2326 2720 1.151221 ATCACCTGCAGTTGTGGCA 59.849 52.632 19.13 5.42 39.32 4.92
2327 2721 1.174712 ACATCACCTGCAGTTGTGGC 61.175 55.000 19.13 0.00 33.29 5.01
2328 2722 1.806542 GTACATCACCTGCAGTTGTGG 59.193 52.381 19.13 11.79 33.29 4.17
2329 2723 1.460743 CGTACATCACCTGCAGTTGTG 59.539 52.381 13.81 14.41 0.00 3.33
2330 2724 1.070134 ACGTACATCACCTGCAGTTGT 59.930 47.619 13.81 12.59 0.00 3.32
2331 2725 1.726791 GACGTACATCACCTGCAGTTG 59.273 52.381 13.81 9.31 0.00 3.16
2332 2726 1.343142 TGACGTACATCACCTGCAGTT 59.657 47.619 13.81 0.00 0.00 3.16
2333 2727 0.966179 TGACGTACATCACCTGCAGT 59.034 50.000 13.81 0.00 0.00 4.40
2334 2728 1.633561 CTGACGTACATCACCTGCAG 58.366 55.000 6.78 6.78 0.00 4.41
2335 2729 0.246360 CCTGACGTACATCACCTGCA 59.754 55.000 0.00 0.00 0.00 4.41
2336 2730 0.460284 CCCTGACGTACATCACCTGC 60.460 60.000 0.00 0.00 0.00 4.85
2337 2731 0.175760 CCCCTGACGTACATCACCTG 59.824 60.000 0.00 0.00 0.00 4.00
2338 2732 0.040646 TCCCCTGACGTACATCACCT 59.959 55.000 0.00 0.00 0.00 4.00
2339 2733 0.460311 CTCCCCTGACGTACATCACC 59.540 60.000 0.00 0.00 0.00 4.02
2340 2734 0.179108 GCTCCCCTGACGTACATCAC 60.179 60.000 0.00 0.00 0.00 3.06
2341 2735 1.327690 GGCTCCCCTGACGTACATCA 61.328 60.000 0.00 0.00 0.00 3.07
2342 2736 1.442148 GGCTCCCCTGACGTACATC 59.558 63.158 0.00 0.00 0.00 3.06
2343 2737 2.423898 CGGCTCCCCTGACGTACAT 61.424 63.158 0.00 0.00 33.11 2.29
2344 2738 3.066190 CGGCTCCCCTGACGTACA 61.066 66.667 0.00 0.00 33.11 2.90
2345 2739 4.509737 GCGGCTCCCCTGACGTAC 62.510 72.222 0.00 0.00 41.16 3.67
2346 2740 4.753662 AGCGGCTCCCCTGACGTA 62.754 66.667 0.00 0.00 41.16 3.57
2348 2742 4.821589 GAAGCGGCTCCCCTGACG 62.822 72.222 1.45 0.00 42.16 4.35
2349 2743 4.475135 GGAAGCGGCTCCCCTGAC 62.475 72.222 1.45 0.00 0.00 3.51
2355 2749 2.187163 GTAGTGGGAAGCGGCTCC 59.813 66.667 1.45 6.44 34.41 4.70
2356 2750 1.448013 GTGTAGTGGGAAGCGGCTC 60.448 63.158 1.45 0.00 0.00 4.70
2357 2751 2.663196 GTGTAGTGGGAAGCGGCT 59.337 61.111 0.00 0.00 0.00 5.52
2358 2752 2.436115 GGTGTAGTGGGAAGCGGC 60.436 66.667 0.00 0.00 0.00 6.53
2359 2753 1.079127 CTGGTGTAGTGGGAAGCGG 60.079 63.158 0.00 0.00 0.00 5.52
2360 2754 0.537188 ATCTGGTGTAGTGGGAAGCG 59.463 55.000 0.00 0.00 0.00 4.68
2361 2755 2.014068 GCATCTGGTGTAGTGGGAAGC 61.014 57.143 0.00 0.00 0.00 3.86
2362 2756 1.740380 CGCATCTGGTGTAGTGGGAAG 60.740 57.143 0.00 0.00 0.00 3.46
2363 2757 0.249120 CGCATCTGGTGTAGTGGGAA 59.751 55.000 0.00 0.00 0.00 3.97
2364 2758 1.897423 CGCATCTGGTGTAGTGGGA 59.103 57.895 0.00 0.00 0.00 4.37
2365 2759 1.815421 GCGCATCTGGTGTAGTGGG 60.815 63.158 0.30 0.00 0.00 4.61
2366 2760 0.391661 AAGCGCATCTGGTGTAGTGG 60.392 55.000 11.47 0.00 0.00 4.00
2367 2761 0.723414 CAAGCGCATCTGGTGTAGTG 59.277 55.000 11.47 0.00 0.00 2.74
2368 2762 0.321671 ACAAGCGCATCTGGTGTAGT 59.678 50.000 11.47 0.00 0.00 2.73
2369 2763 1.002366 GACAAGCGCATCTGGTGTAG 58.998 55.000 11.47 0.00 0.00 2.74
2370 2764 0.608130 AGACAAGCGCATCTGGTGTA 59.392 50.000 11.47 0.00 0.00 2.90
2371 2765 0.952497 CAGACAAGCGCATCTGGTGT 60.952 55.000 21.97 11.18 38.97 4.16
2372 2766 1.792301 CAGACAAGCGCATCTGGTG 59.208 57.895 21.97 10.06 38.97 4.17
2373 2767 4.291047 CAGACAAGCGCATCTGGT 57.709 55.556 21.97 8.42 38.97 4.00
2375 2769 2.036571 TGCCAGACAAGCGCATCTG 61.037 57.895 22.49 22.49 41.75 2.90
2387 2781 1.699083 TCATCAAGGTTCAGTGCCAGA 59.301 47.619 0.00 0.00 0.00 3.86
2388 2782 2.189594 TCATCAAGGTTCAGTGCCAG 57.810 50.000 0.00 0.00 0.00 4.85
2389 2783 2.507484 CTTCATCAAGGTTCAGTGCCA 58.493 47.619 0.00 0.00 0.00 4.92
2390 2784 1.200948 GCTTCATCAAGGTTCAGTGCC 59.799 52.381 0.00 0.00 0.00 5.01
2391 2785 2.157738 AGCTTCATCAAGGTTCAGTGC 58.842 47.619 0.00 0.00 36.99 4.40
2392 2786 4.999950 AGTTAGCTTCATCAAGGTTCAGTG 59.000 41.667 0.00 0.00 40.85 3.66
2393 2787 4.999950 CAGTTAGCTTCATCAAGGTTCAGT 59.000 41.667 0.00 0.00 40.85 3.41
2394 2788 4.999950 ACAGTTAGCTTCATCAAGGTTCAG 59.000 41.667 0.00 0.00 40.85 3.02
2395 2789 4.973168 ACAGTTAGCTTCATCAAGGTTCA 58.027 39.130 0.00 0.00 40.85 3.18
2396 2790 6.091441 CACTACAGTTAGCTTCATCAAGGTTC 59.909 42.308 0.00 0.00 40.85 3.62
2397 2791 5.934625 CACTACAGTTAGCTTCATCAAGGTT 59.065 40.000 0.00 0.00 40.85 3.50
2398 2792 5.012148 ACACTACAGTTAGCTTCATCAAGGT 59.988 40.000 0.00 0.00 43.04 3.50
2399 2793 5.482908 ACACTACAGTTAGCTTCATCAAGG 58.517 41.667 0.00 0.00 0.00 3.61
2400 2794 7.090808 TGTACACTACAGTTAGCTTCATCAAG 58.909 38.462 0.00 0.00 34.06 3.02
2401 2795 6.988522 TGTACACTACAGTTAGCTTCATCAA 58.011 36.000 0.00 0.00 34.06 2.57
2402 2796 6.584185 TGTACACTACAGTTAGCTTCATCA 57.416 37.500 0.00 0.00 34.06 3.07
2415 2809 9.787435 ACTTTGGAATTTATTCTGTACACTACA 57.213 29.630 0.00 0.00 37.00 2.74
2417 2811 9.444600 GGACTTTGGAATTTATTCTGTACACTA 57.555 33.333 0.00 0.00 37.00 2.74
2418 2812 7.119262 CGGACTTTGGAATTTATTCTGTACACT 59.881 37.037 0.00 0.00 37.00 3.55
2419 2813 7.094933 ACGGACTTTGGAATTTATTCTGTACAC 60.095 37.037 0.00 0.00 37.00 2.90
2420 2814 6.938030 ACGGACTTTGGAATTTATTCTGTACA 59.062 34.615 0.00 0.00 37.00 2.90
2421 2815 7.373778 ACGGACTTTGGAATTTATTCTGTAC 57.626 36.000 2.77 0.00 37.00 2.90
2422 2816 7.446013 ACAACGGACTTTGGAATTTATTCTGTA 59.554 33.333 2.77 0.00 37.00 2.74
2423 2817 6.264518 ACAACGGACTTTGGAATTTATTCTGT 59.735 34.615 2.77 0.00 37.00 3.41
2424 2818 6.677913 ACAACGGACTTTGGAATTTATTCTG 58.322 36.000 2.77 0.00 37.00 3.02
2425 2819 6.894339 ACAACGGACTTTGGAATTTATTCT 57.106 33.333 2.77 0.00 37.00 2.40
2426 2820 7.586747 TGTACAACGGACTTTGGAATTTATTC 58.413 34.615 0.00 0.00 36.08 1.75
2427 2821 7.513371 TGTACAACGGACTTTGGAATTTATT 57.487 32.000 0.00 0.00 0.00 1.40
2428 2822 7.229907 AGTTGTACAACGGACTTTGGAATTTAT 59.770 33.333 28.21 6.28 45.50 1.40
2429 2823 6.543100 AGTTGTACAACGGACTTTGGAATTTA 59.457 34.615 28.21 0.00 45.50 1.40
2430 2824 5.358725 AGTTGTACAACGGACTTTGGAATTT 59.641 36.000 28.21 7.23 45.50 1.82
2431 2825 4.885325 AGTTGTACAACGGACTTTGGAATT 59.115 37.500 28.21 7.63 45.50 2.17
2432 2826 4.457466 AGTTGTACAACGGACTTTGGAAT 58.543 39.130 28.21 7.82 45.50 3.01
2433 2827 3.876341 AGTTGTACAACGGACTTTGGAA 58.124 40.909 28.21 0.00 45.50 3.53
2434 2828 3.547054 AGTTGTACAACGGACTTTGGA 57.453 42.857 28.21 0.00 45.50 3.53
2435 2829 3.623960 TCAAGTTGTACAACGGACTTTGG 59.376 43.478 28.21 11.38 45.50 3.28
2436 2830 4.868450 TCAAGTTGTACAACGGACTTTG 57.132 40.909 28.21 24.89 45.50 2.77
2437 2831 4.201744 CGTTCAAGTTGTACAACGGACTTT 60.202 41.667 28.21 16.49 45.50 2.66
2438 2832 3.307782 CGTTCAAGTTGTACAACGGACTT 59.692 43.478 28.21 16.99 45.50 3.01
2439 2833 2.861935 CGTTCAAGTTGTACAACGGACT 59.138 45.455 28.21 12.09 45.50 3.85
2440 2834 2.604462 ACGTTCAAGTTGTACAACGGAC 59.396 45.455 28.21 22.52 44.63 4.79
2441 2835 2.891112 ACGTTCAAGTTGTACAACGGA 58.109 42.857 28.21 25.64 44.63 4.69
2442 2836 3.798337 AGTACGTTCAAGTTGTACAACGG 59.202 43.478 28.21 24.11 44.63 4.44
2443 2837 5.682862 ACTAGTACGTTCAAGTTGTACAACG 59.317 40.000 28.21 20.42 45.50 4.10
2444 2838 7.986426 GTACTAGTACGTTCAAGTTGTACAAC 58.014 38.462 27.72 27.72 40.64 3.32
2460 2854 1.004927 CACGTACCGGCGTACTAGTAC 60.005 57.143 21.06 21.06 43.83 2.73
2484 2878 4.836125 ATCCATGAATTGAATACGTGCC 57.164 40.909 0.00 0.00 0.00 5.01
2515 2914 8.417780 TTTTTCTTTTGCGAAAAATCAGATGA 57.582 26.923 0.72 0.00 43.84 2.92
2621 3021 9.169468 GTATGATAACTGTCACAACAACTTTTG 57.831 33.333 0.00 0.00 34.24 2.44
2837 3562 7.990886 ACTCTTTCCCGTTTATGCAGAATATTA 59.009 33.333 0.00 0.00 0.00 0.98
2849 3574 2.232399 GGCCAAACTCTTTCCCGTTTA 58.768 47.619 0.00 0.00 32.52 2.01
2853 3578 0.821711 TGTGGCCAAACTCTTTCCCG 60.822 55.000 7.24 0.00 0.00 5.14
2855 3580 4.864704 TTTATGTGGCCAAACTCTTTCC 57.135 40.909 7.24 0.00 0.00 3.13
2882 3617 3.386486 TCACGTGTGGTAAAGACATCAC 58.614 45.455 16.51 0.00 0.00 3.06
2893 3628 1.169577 TGTTGCTTTTCACGTGTGGT 58.830 45.000 16.51 0.00 0.00 4.16
2937 3672 3.348119 TCTTGTGGCCATACGCAAATAA 58.652 40.909 9.72 0.00 40.00 1.40
2968 3703 6.752351 TCTTTGATCTTCTCATACGTTAGCAC 59.248 38.462 0.00 0.00 32.72 4.40
2975 3710 5.895928 TCCACTCTTTGATCTTCTCATACG 58.104 41.667 0.00 0.00 32.72 3.06
2979 3714 5.246883 TGTGATCCACTCTTTGATCTTCTCA 59.753 40.000 0.00 0.00 38.53 3.27
2986 3721 4.999950 GTGTTCTGTGATCCACTCTTTGAT 59.000 41.667 0.00 0.00 35.11 2.57
2988 3723 4.212847 CAGTGTTCTGTGATCCACTCTTTG 59.787 45.833 0.00 0.00 36.06 2.77
2989 3724 4.384056 CAGTGTTCTGTGATCCACTCTTT 58.616 43.478 0.00 0.00 36.06 2.52
2990 3725 3.244353 CCAGTGTTCTGTGATCCACTCTT 60.244 47.826 0.00 0.00 39.82 2.85
2999 3734 0.106708 GCCACTCCAGTGTTCTGTGA 59.893 55.000 5.99 0.00 44.21 3.58
3004 3739 0.819259 TTGCAGCCACTCCAGTGTTC 60.819 55.000 5.99 0.00 44.21 3.18
3005 3740 0.395586 TTTGCAGCCACTCCAGTGTT 60.396 50.000 5.99 0.00 44.21 3.32


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

AutoCloner maintained by Alex Coulton.