Multiple sequence alignment - TraesCS2B01G151800

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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 TraesCS2B01G151800 chr2B 100.000 6704 0 0 1 6704 118609361 118602658 0.000000e+00 12381
1 TraesCS2B01G151800 chr2B 96.751 708 22 1 1 707 316103957 316103250 0.000000e+00 1179
2 TraesCS2B01G151800 chr2B 96.229 716 24 3 1 713 631607091 631606376 0.000000e+00 1170
3 TraesCS2B01G151800 chr2B 93.750 96 4 2 4648 4743 723358721 723358628 7.010000e-30 143
4 TraesCS2B01G151800 chr2D 90.224 2762 160 31 704 3417 76863972 76861273 0.000000e+00 3504
5 TraesCS2B01G151800 chr2D 91.456 2013 89 38 4733 6703 76860081 76858110 0.000000e+00 2687
6 TraesCS2B01G151800 chr2D 96.330 1199 38 6 3458 4652 76861272 76860076 0.000000e+00 1965
7 TraesCS2B01G151800 chr2A 95.336 1951 76 9 2686 4625 77531372 77529426 0.000000e+00 3085
8 TraesCS2B01G151800 chr2A 92.431 1995 101 24 4731 6703 77529402 77527436 0.000000e+00 2802
9 TraesCS2B01G151800 chr2A 88.567 2038 136 46 704 2699 77533433 77531451 0.000000e+00 2383
10 TraesCS2B01G151800 chr2A 93.258 89 6 0 4647 4735 56937884 56937972 1.520000e-26 132
11 TraesCS2B01G151800 chr2A 93.182 88 6 0 4651 4738 71793878 71793791 5.460000e-26 130
12 TraesCS2B01G151800 chr1B 96.639 714 22 2 1 712 295769441 295768728 0.000000e+00 1184
13 TraesCS2B01G151800 chr1B 96.738 705 21 2 1 703 9416979 9417683 0.000000e+00 1173
14 TraesCS2B01G151800 chr1B 96.591 704 24 0 1 704 561625405 561626108 0.000000e+00 1168
15 TraesCS2B01G151800 chr1B 92.079 101 4 4 4644 4742 240710046 240710144 9.070000e-29 139
16 TraesCS2B01G151800 chr6B 96.884 706 22 0 1 706 179996078 179995373 0.000000e+00 1182
17 TraesCS2B01G151800 chr6B 96.489 712 23 2 1 711 67946110 67945400 0.000000e+00 1175
18 TraesCS2B01G151800 chr7B 96.879 705 20 1 1 705 667781650 667782352 0.000000e+00 1179
19 TraesCS2B01G151800 chr5B 96.474 709 22 3 1 706 150043724 150043016 0.000000e+00 1168
20 TraesCS2B01G151800 chr3A 100.000 83 0 0 1279 1361 653839767 653839685 3.240000e-33 154
21 TraesCS2B01G151800 chr1A 95.745 94 4 0 1278 1371 571359298 571359391 1.160000e-32 152
22 TraesCS2B01G151800 chr1A 92.233 103 4 4 1273 1372 571561466 571561567 7.010000e-30 143
23 TraesCS2B01G151800 chr7D 97.727 88 1 1 1279 1366 476701407 476701493 4.190000e-32 150
24 TraesCS2B01G151800 chr7D 93.684 95 5 1 4648 4742 572186284 572186191 2.520000e-29 141
25 TraesCS2B01G151800 chr3D 93.939 99 3 3 1276 1371 417381200 417381298 5.420000e-31 147
26 TraesCS2B01G151800 chr1D 91.589 107 5 4 1273 1375 475490187 475490081 1.950000e-30 145
27 TraesCS2B01G151800 chrUn 93.000 100 3 4 1275 1371 32916325 32916423 7.010000e-30 143
28 TraesCS2B01G151800 chrUn 91.398 93 8 0 4644 4736 27127834 27127742 1.960000e-25 128
29 TraesCS2B01G151800 chr4B 93.617 94 6 0 4648 4741 471155209 471155302 2.520000e-29 141
30 TraesCS2B01G151800 chr3B 94.505 91 4 1 4648 4737 26648722 26648632 9.070000e-29 139
31 TraesCS2B01G151800 chr5A 89.216 102 11 0 4643 4744 678203565 678203666 1.960000e-25 128


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 TraesCS2B01G151800 chr2B 118602658 118609361 6703 True 12381.000000 12381 100.000000 1 6704 1 chr2B.!!$R1 6703
1 TraesCS2B01G151800 chr2B 316103250 316103957 707 True 1179.000000 1179 96.751000 1 707 1 chr2B.!!$R2 706
2 TraesCS2B01G151800 chr2B 631606376 631607091 715 True 1170.000000 1170 96.229000 1 713 1 chr2B.!!$R3 712
3 TraesCS2B01G151800 chr2D 76858110 76863972 5862 True 2718.666667 3504 92.670000 704 6703 3 chr2D.!!$R1 5999
4 TraesCS2B01G151800 chr2A 77527436 77533433 5997 True 2756.666667 3085 92.111333 704 6703 3 chr2A.!!$R2 5999
5 TraesCS2B01G151800 chr1B 295768728 295769441 713 True 1184.000000 1184 96.639000 1 712 1 chr1B.!!$R1 711
6 TraesCS2B01G151800 chr1B 9416979 9417683 704 False 1173.000000 1173 96.738000 1 703 1 chr1B.!!$F1 702
7 TraesCS2B01G151800 chr1B 561625405 561626108 703 False 1168.000000 1168 96.591000 1 704 1 chr1B.!!$F3 703
8 TraesCS2B01G151800 chr6B 179995373 179996078 705 True 1182.000000 1182 96.884000 1 706 1 chr6B.!!$R2 705
9 TraesCS2B01G151800 chr6B 67945400 67946110 710 True 1175.000000 1175 96.489000 1 711 1 chr6B.!!$R1 710
10 TraesCS2B01G151800 chr7B 667781650 667782352 702 False 1179.000000 1179 96.879000 1 705 1 chr7B.!!$F1 704
11 TraesCS2B01G151800 chr5B 150043016 150043724 708 True 1168.000000 1168 96.474000 1 706 1 chr5B.!!$R1 705

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
922 945 1.792118 ATCGGAATCGCCATCGTCGA 61.792 55.000 0.00 0.0 40.45 4.20 F
1145 1182 0.977395 CCAGGTTTTCCCTCGAGTCT 59.023 55.000 12.31 0.0 43.86 3.24 F
1890 1944 0.824109 TCGATGTCCTGCGGAAGAAT 59.176 50.000 0.00 0.0 31.38 2.40 F
1994 2053 1.541588 GTGTTGCTCCCTGTTCCATTC 59.458 52.381 0.00 0.0 0.00 2.67 F
3017 3199 2.041485 TGCCAATCAGATCAAAGGACCA 59.959 45.455 0.00 0.0 0.00 4.02 F
4402 4590 1.416772 GCACTACAGGTATCCCTTCCC 59.583 57.143 0.00 0.0 39.89 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1944 2.815684 ATACTCGGACAGGCACCCCA 62.816 60.000 0.00 0.0 0.00 4.96 R
3068 3250 1.882623 CTCAGCCCAACACTTTCCTTC 59.117 52.381 0.00 0.0 0.00 3.46 R
3847 4035 3.864789 AAAAGTCCATGTCCAGACAGT 57.135 42.857 6.63 0.0 45.48 3.55 R
3986 4174 2.423185 TGCTTCCAGTGACAAAACACAG 59.577 45.455 0.00 0.0 42.45 3.66 R
4648 4848 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.0 0.00 2.73 R
6157 6370 0.548510 AGGAGGCTGGGATAACTTGC 59.451 55.000 0.00 0.0 0.00 4.01 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
360 366 8.996024 AATTCCCCGTTTTATAAATGTCAAAG 57.004 30.769 0.00 0.00 0.00 2.77
497 504 8.308851 TCATCAAAACATATCAACATGGGATT 57.691 30.769 7.35 0.00 0.00 3.01
645 653 3.120321 TGACGTGGCAATCTGTTTACT 57.880 42.857 0.00 0.00 0.00 2.24
651 659 6.797454 ACGTGGCAATCTGTTTACTTTAAAA 58.203 32.000 0.00 0.00 0.00 1.52
716 724 3.422655 CGCGACCCAAATAAAAAGCTAC 58.577 45.455 0.00 0.00 0.00 3.58
722 730 5.262009 ACCCAAATAAAAAGCTACTCCTCC 58.738 41.667 0.00 0.00 0.00 4.30
730 738 4.439253 AAAGCTACTCCTCCAAAACTGT 57.561 40.909 0.00 0.00 0.00 3.55
733 741 4.417437 AGCTACTCCTCCAAAACTGTAGA 58.583 43.478 0.00 0.00 31.82 2.59
809 821 3.488090 CTCGAAAACGGGCGAGCC 61.488 66.667 5.37 5.37 45.97 4.70
922 945 1.792118 ATCGGAATCGCCATCGTCGA 61.792 55.000 0.00 0.00 40.45 4.20
923 946 2.293627 CGGAATCGCCATCGTCGAC 61.294 63.158 5.18 5.18 38.88 4.20
924 947 2.293627 GGAATCGCCATCGTCGACG 61.294 63.158 31.30 31.30 38.88 5.12
995 1025 4.831307 CGCCGTCCGTCCGAGAAG 62.831 72.222 0.00 0.00 0.00 2.85
1022 1055 2.041928 CTGCCCCTCCTCCTCCTT 59.958 66.667 0.00 0.00 0.00 3.36
1067 1100 2.438434 CAATCCCCGGGTGAGTGC 60.438 66.667 21.85 0.00 0.00 4.40
1145 1182 0.977395 CCAGGTTTTCCCTCGAGTCT 59.023 55.000 12.31 0.00 43.86 3.24
1158 1195 3.489229 CCTCGAGTCTTCATGCGTGAATA 60.489 47.826 21.24 12.02 43.08 1.75
1163 1200 5.674148 CGAGTCTTCATGCGTGAATATTTTG 59.326 40.000 21.24 9.13 43.08 2.44
1169 1206 6.188400 TCATGCGTGAATATTTTGCTGTTA 57.812 33.333 6.04 0.00 0.00 2.41
1228 1265 8.922931 AATCAATAAACCAAGGCAAATCTTTT 57.077 26.923 0.00 0.00 0.00 2.27
1231 1268 3.769739 AACCAAGGCAAATCTTTTCCC 57.230 42.857 0.00 0.00 0.00 3.97
1232 1269 2.976440 ACCAAGGCAAATCTTTTCCCT 58.024 42.857 0.00 0.00 0.00 4.20
1234 1271 2.234661 CCAAGGCAAATCTTTTCCCTCC 59.765 50.000 0.00 0.00 0.00 4.30
1235 1272 1.839424 AGGCAAATCTTTTCCCTCCG 58.161 50.000 0.00 0.00 0.00 4.63
1240 1277 3.255888 GCAAATCTTTTCCCTCCGTTTCT 59.744 43.478 0.00 0.00 0.00 2.52
1253 1290 9.609346 TTCCCTCCGTTTCTAAAAGAATATTAG 57.391 33.333 0.00 0.00 33.67 1.73
1353 1391 1.185618 TCAAGTCTCGGTGGGACCTG 61.186 60.000 0.00 0.00 35.66 4.00
1354 1392 1.152312 AAGTCTCGGTGGGACCTGT 60.152 57.895 0.00 0.00 35.66 4.00
1384 1423 4.561606 GCATTATTTTTGCTCAGCTCAGTG 59.438 41.667 0.00 0.00 37.14 3.66
1415 1462 5.527582 CCAATGCTTACTACTGGTACCAATC 59.472 44.000 17.11 0.00 0.00 2.67
1424 1471 9.871175 TTACTACTGGTACCAATCATATCACTA 57.129 33.333 17.11 0.00 0.00 2.74
1491 1538 3.341823 CTGCTAGTTGCTCCACAAGAAT 58.658 45.455 0.00 0.00 39.50 2.40
1503 1550 5.799213 CTCCACAAGAATAACTCAGAAGGT 58.201 41.667 0.00 0.00 0.00 3.50
1523 1570 2.293399 GTGCATTTCTTCGGTTCAAGGT 59.707 45.455 0.00 0.00 0.00 3.50
1567 1614 2.164017 CCCAACATCATCGCATTTGTCA 59.836 45.455 0.00 0.00 0.00 3.58
1598 1645 2.478335 AATCGCCTTGGCCGGAAAGA 62.478 55.000 5.05 0.00 0.00 2.52
1609 1656 2.379005 GCCGGAAAGAAATCTTGGGAT 58.621 47.619 5.05 0.00 36.12 3.85
1700 1749 4.026356 ACTTGACATTTCCCCTCTTCTG 57.974 45.455 0.00 0.00 0.00 3.02
1706 1755 5.015178 TGACATTTCCCCTCTTCTGGTTAAT 59.985 40.000 0.00 0.00 0.00 1.40
1714 1763 6.099269 TCCCCTCTTCTGGTTAATATGTGTAC 59.901 42.308 0.00 0.00 0.00 2.90
1723 1772 4.102681 GGTTAATATGTGTACCTCTGGGCT 59.897 45.833 0.00 0.00 35.63 5.19
1869 1923 2.202453 GGCGTCGGACGAAGAGTC 60.202 66.667 32.48 14.08 46.05 3.36
1890 1944 0.824109 TCGATGTCCTGCGGAAGAAT 59.176 50.000 0.00 0.00 31.38 2.40
1921 1975 4.028131 TGTCCGAGTATTGGTATTCCACT 58.972 43.478 0.00 0.00 44.22 4.00
1994 2053 1.541588 GTGTTGCTCCCTGTTCCATTC 59.458 52.381 0.00 0.00 0.00 2.67
2019 2078 6.348868 CCATTTTCTCGCTTTTCTTAGAGCTT 60.349 38.462 0.00 0.00 36.76 3.74
2116 2175 2.775384 TGTGGACTTGGTAGGTCACTTT 59.225 45.455 0.00 0.00 35.61 2.66
2153 2220 9.042450 AGTTATGTATCGTGGGGATATTTCATA 57.958 33.333 0.00 0.00 39.71 2.15
2168 2235 8.086522 GGATATTTCATAAGCTACGGTTAGACA 58.913 37.037 0.00 0.00 0.00 3.41
2183 2250 5.411977 CGGTTAGACAGTTAGTTCAGAGAGA 59.588 44.000 0.00 0.00 0.00 3.10
2184 2251 6.094325 CGGTTAGACAGTTAGTTCAGAGAGAT 59.906 42.308 0.00 0.00 0.00 2.75
2185 2252 7.477494 GGTTAGACAGTTAGTTCAGAGAGATC 58.523 42.308 0.00 0.00 0.00 2.75
2186 2253 7.121463 GGTTAGACAGTTAGTTCAGAGAGATCA 59.879 40.741 0.00 0.00 0.00 2.92
2187 2254 8.516234 GTTAGACAGTTAGTTCAGAGAGATCAA 58.484 37.037 0.00 0.00 0.00 2.57
2188 2255 7.156876 AGACAGTTAGTTCAGAGAGATCAAG 57.843 40.000 0.00 0.00 0.00 3.02
2189 2256 5.719173 ACAGTTAGTTCAGAGAGATCAAGC 58.281 41.667 0.00 0.00 0.00 4.01
2190 2257 5.244851 ACAGTTAGTTCAGAGAGATCAAGCA 59.755 40.000 0.00 0.00 0.00 3.91
2191 2258 6.162079 CAGTTAGTTCAGAGAGATCAAGCAA 58.838 40.000 0.00 0.00 0.00 3.91
2192 2259 6.090628 CAGTTAGTTCAGAGAGATCAAGCAAC 59.909 42.308 0.00 0.00 0.00 4.17
2193 2260 4.613925 AGTTCAGAGAGATCAAGCAACA 57.386 40.909 0.00 0.00 0.00 3.33
2194 2261 4.965814 AGTTCAGAGAGATCAAGCAACAA 58.034 39.130 0.00 0.00 0.00 2.83
2195 2262 5.558818 AGTTCAGAGAGATCAAGCAACAAT 58.441 37.500 0.00 0.00 0.00 2.71
2196 2263 6.705302 AGTTCAGAGAGATCAAGCAACAATA 58.295 36.000 0.00 0.00 0.00 1.90
2197 2264 7.337167 AGTTCAGAGAGATCAAGCAACAATAT 58.663 34.615 0.00 0.00 0.00 1.28
2198 2265 8.481314 AGTTCAGAGAGATCAAGCAACAATATA 58.519 33.333 0.00 0.00 0.00 0.86
2199 2266 9.270640 GTTCAGAGAGATCAAGCAACAATATAT 57.729 33.333 0.00 0.00 0.00 0.86
2200 2267 9.486497 TTCAGAGAGATCAAGCAACAATATATC 57.514 33.333 0.00 0.00 0.00 1.63
2201 2268 8.645110 TCAGAGAGATCAAGCAACAATATATCA 58.355 33.333 0.00 0.00 0.00 2.15
2202 2269 8.710551 CAGAGAGATCAAGCAACAATATATCAC 58.289 37.037 0.00 0.00 0.00 3.06
2203 2270 7.598118 AGAGAGATCAAGCAACAATATATCACG 59.402 37.037 0.00 0.00 0.00 4.35
2204 2271 7.436933 AGAGATCAAGCAACAATATATCACGA 58.563 34.615 0.00 0.00 0.00 4.35
2205 2272 7.598118 AGAGATCAAGCAACAATATATCACGAG 59.402 37.037 0.00 0.00 0.00 4.18
2206 2273 7.436933 AGATCAAGCAACAATATATCACGAGA 58.563 34.615 0.00 0.00 0.00 4.04
2207 2274 6.828502 TCAAGCAACAATATATCACGAGAC 57.171 37.500 0.00 0.00 0.00 3.36
2208 2275 5.753438 TCAAGCAACAATATATCACGAGACC 59.247 40.000 0.00 0.00 0.00 3.85
2209 2276 5.537300 AGCAACAATATATCACGAGACCT 57.463 39.130 0.00 0.00 0.00 3.85
2210 2277 6.650427 AGCAACAATATATCACGAGACCTA 57.350 37.500 0.00 0.00 0.00 3.08
2211 2278 7.233389 AGCAACAATATATCACGAGACCTAT 57.767 36.000 0.00 0.00 0.00 2.57
2351 2435 4.237724 GGGCTGAAAAGCTGTTAATTGTC 58.762 43.478 0.00 0.00 34.73 3.18
2421 2505 9.477484 GCAAAGGACACGGATATATTATATAGG 57.523 37.037 0.00 0.00 0.00 2.57
2534 2618 9.121658 AGCATCATGTCATCCATATATGAATTC 57.878 33.333 14.54 0.00 37.61 2.17
2699 2783 7.861372 TCGCAAGTAAGTCATCTAGTAAATAGC 59.139 37.037 0.00 0.00 39.48 2.97
2733 2913 8.945195 TCTATGATCATCCATTGGCTAAATTT 57.055 30.769 12.53 0.00 0.00 1.82
2749 2929 6.260050 GGCTAAATTTGACGATCTCAACCATA 59.740 38.462 0.00 2.20 38.70 2.74
2979 3161 8.956446 TTCATTCCCTCTCTTTAAAATTCCTT 57.044 30.769 0.00 0.00 0.00 3.36
3017 3199 2.041485 TGCCAATCAGATCAAAGGACCA 59.959 45.455 0.00 0.00 0.00 4.02
3068 3250 6.715344 ATGCAAAACTTGATTAATGCTGTG 57.285 33.333 0.00 0.00 35.37 3.66
3175 3357 6.807708 ACATTCAAGTCATATTCGTCGTAC 57.192 37.500 0.00 0.00 0.00 3.67
3244 3429 4.216257 GTCATACTCTGGCTTTTTGCTTCA 59.784 41.667 0.00 0.00 42.39 3.02
3266 3451 6.299141 TCACTGCTCTGAAGTTTTTCCTAAT 58.701 36.000 0.00 0.00 32.09 1.73
3469 3656 4.262164 CCTTTGGTGTAAAAGCTGCAAGAT 60.262 41.667 1.02 0.00 36.10 2.40
3473 3660 5.500234 TGGTGTAAAAGCTGCAAGATATCT 58.500 37.500 1.02 0.00 34.07 1.98
3475 3662 7.109501 TGGTGTAAAAGCTGCAAGATATCTAA 58.890 34.615 5.46 0.00 34.07 2.10
3584 3771 7.713507 CGTAAATCATTCCCTGACCTACATAAA 59.286 37.037 0.00 0.00 36.48 1.40
3646 3833 6.453943 TCATACAACATGTTGGTCATTTTGG 58.546 36.000 35.20 17.19 44.05 3.28
3847 4035 7.549147 TCCTTTGAGTAGTCTTTAGCCTAAA 57.451 36.000 0.00 0.00 0.00 1.85
3855 4043 5.153950 AGTCTTTAGCCTAAACTGTCTGG 57.846 43.478 0.00 0.00 0.00 3.86
3977 4165 9.002600 TGGAAATTACTCATACATGCATATCAC 57.997 33.333 0.00 0.00 0.00 3.06
4041 4229 3.386768 TCTGAACTGGTCTGTGTAAGC 57.613 47.619 0.00 0.00 0.00 3.09
4402 4590 1.416772 GCACTACAGGTATCCCTTCCC 59.583 57.143 0.00 0.00 39.89 3.97
4407 4595 5.427481 CACTACAGGTATCCCTTCCCTTTTA 59.573 44.000 0.00 0.00 39.89 1.52
4488 4679 9.675464 ACCCGAAACACTCATCTAAATTTATTA 57.325 29.630 0.00 0.00 0.00 0.98
4656 4856 8.843262 ACAAGTTTTGTTTTATGTACTACTCCC 58.157 33.333 0.00 0.00 42.22 4.30
4657 4857 9.063615 CAAGTTTTGTTTTATGTACTACTCCCT 57.936 33.333 0.00 0.00 0.00 4.20
4658 4858 8.843885 AGTTTTGTTTTATGTACTACTCCCTC 57.156 34.615 0.00 0.00 0.00 4.30
4659 4859 7.881751 AGTTTTGTTTTATGTACTACTCCCTCC 59.118 37.037 0.00 0.00 0.00 4.30
4660 4860 5.587388 TGTTTTATGTACTACTCCCTCCG 57.413 43.478 0.00 0.00 0.00 4.63
4661 4861 5.018809 TGTTTTATGTACTACTCCCTCCGT 58.981 41.667 0.00 0.00 0.00 4.69
4662 4862 5.126061 TGTTTTATGTACTACTCCCTCCGTC 59.874 44.000 0.00 0.00 0.00 4.79
4663 4863 2.361643 ATGTACTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
4664 4864 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
4665 4865 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
4666 4866 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4667 4867 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
4668 4868 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
4669 4869 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
4670 4870 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
4671 4871 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
4672 4872 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
4673 4873 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
4674 4874 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
4675 4875 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
4676 4876 3.007635 CCTCCGTCCCAAAATGTAAGAC 58.992 50.000 0.00 0.00 0.00 3.01
4678 4878 2.037511 TCCGTCCCAAAATGTAAGACGT 59.962 45.455 9.63 0.00 46.62 4.34
4679 4879 2.809696 CCGTCCCAAAATGTAAGACGTT 59.190 45.455 9.63 0.00 46.62 3.99
4680 4880 3.251487 CCGTCCCAAAATGTAAGACGTTT 59.749 43.478 9.63 0.00 46.62 3.60
4681 4881 4.261280 CCGTCCCAAAATGTAAGACGTTTT 60.261 41.667 9.63 4.14 45.25 2.43
4682 4882 5.275494 CGTCCCAAAATGTAAGACGTTTTT 58.725 37.500 6.77 0.00 42.72 1.94
4730 4930 6.374565 CGTCTTATATTATAGGACGGAGGG 57.625 45.833 27.66 10.18 43.69 4.30
4731 4931 6.118170 CGTCTTATATTATAGGACGGAGGGA 58.882 44.000 27.66 0.00 43.69 4.20
4732 4932 6.260493 CGTCTTATATTATAGGACGGAGGGAG 59.740 46.154 27.66 9.15 43.69 4.30
4733 4933 7.118060 GTCTTATATTATAGGACGGAGGGAGT 58.882 42.308 9.42 0.00 0.00 3.85
4734 4934 8.270744 GTCTTATATTATAGGACGGAGGGAGTA 58.729 40.741 9.42 0.00 0.00 2.59
4735 4935 8.270744 TCTTATATTATAGGACGGAGGGAGTAC 58.729 40.741 0.00 0.00 0.00 2.73
4738 4938 5.495926 TTATAGGACGGAGGGAGTACTAG 57.504 47.826 0.00 0.00 38.32 2.57
4753 4953 8.851876 AGGGAGTACTAGATATCAGGACATTAT 58.148 37.037 15.58 0.86 28.37 1.28
4803 5003 6.609212 TCCAGTTCTACAGAGCTCATAAAGAT 59.391 38.462 17.77 0.00 33.18 2.40
5094 5296 4.433186 TGCTTGCACGTAAATGCTTAAT 57.567 36.364 0.00 0.00 46.28 1.40
5179 5381 2.741228 GCCATGTGCTCTAACTGAGGAG 60.741 54.545 0.00 0.00 43.81 3.69
5247 5449 5.853936 TGTAAGTAGAGACAGCATTGTGTT 58.146 37.500 0.00 0.00 37.76 3.32
5447 5650 4.633980 GCAACCCACTTGCGAAAG 57.366 55.556 0.10 0.10 45.88 2.62
5457 5660 4.360563 CCACTTGCGAAAGAGATACGTAT 58.639 43.478 11.02 8.05 0.00 3.06
5473 5676 8.179509 AGATACGTATGGCAGTAGAACTTTAT 57.820 34.615 13.97 0.00 0.00 1.40
5474 5677 9.293404 AGATACGTATGGCAGTAGAACTTTATA 57.707 33.333 13.97 0.00 0.00 0.98
5583 5791 0.373716 GCACCGTTCCATTTAGCGAG 59.626 55.000 0.00 0.00 0.00 5.03
5589 5797 1.062148 GTTCCATTTAGCGAGCCGTTC 59.938 52.381 0.00 0.00 0.00 3.95
5616 5824 0.691413 ATCCTTCGAACCCTCCTCCC 60.691 60.000 0.00 0.00 0.00 4.30
5628 5836 1.682740 CTCCTCCCGAGAAGGACTAC 58.317 60.000 0.00 0.00 45.00 2.73
5679 5887 1.183549 TCACGGGTAAAGAGGCTCTC 58.816 55.000 19.03 5.23 0.00 3.20
5871 6079 2.041620 AGCTTCCTGGTAATTTCCTGCA 59.958 45.455 2.53 0.00 0.00 4.41
5879 6087 5.453198 CCTGGTAATTTCCTGCAGTTGTTTT 60.453 40.000 13.81 2.43 0.00 2.43
6065 6278 0.592247 CGCAACTTGCAACTGTGGAC 60.592 55.000 14.10 0.00 45.36 4.02
6157 6370 7.704047 TGATATCAGTCGATTTTCAGACAAGAG 59.296 37.037 0.00 0.00 39.67 2.85
6165 6378 6.650807 TCGATTTTCAGACAAGAGCAAGTTAT 59.349 34.615 0.00 0.00 0.00 1.89
6166 6379 6.958193 CGATTTTCAGACAAGAGCAAGTTATC 59.042 38.462 0.00 0.00 0.00 1.75
6180 6393 1.847088 AGTTATCCCAGCCTCCTTTCC 59.153 52.381 0.00 0.00 0.00 3.13
6195 6408 6.608610 CCTCCTTTCCAAATACAGTAAAACG 58.391 40.000 0.00 0.00 0.00 3.60
6201 6414 5.976586 TCCAAATACAGTAAAACGTCAACG 58.023 37.500 0.12 0.12 46.33 4.10
6202 6415 5.752472 TCCAAATACAGTAAAACGTCAACGA 59.248 36.000 9.88 0.00 43.02 3.85
6337 6568 5.242434 GGAACAACTACACACATATGACCA 58.758 41.667 10.38 0.00 0.00 4.02
6382 6613 0.673644 CTCGAGGGTGAAAATGGCGT 60.674 55.000 3.91 0.00 0.00 5.68
6521 6758 4.564041 CAGAAGGATCTATGAACATCCCG 58.436 47.826 0.00 0.00 39.73 5.14
6536 6773 2.478746 CCGATTGCCCGAAACACG 59.521 61.111 0.00 0.00 42.18 4.49
6539 6776 0.452122 CGATTGCCCGAAACACGAAC 60.452 55.000 0.00 0.00 45.77 3.95
6636 6882 3.894427 TCTCAAGTCTCAGCTCTCAAGTT 59.106 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 409 5.048782 GCCATGATGTTTACACTGAAGTTGA 60.049 40.000 0.00 0.00 0.00 3.18
497 504 4.035684 CGCGATGAGATCTTCGAAACTAA 58.964 43.478 18.67 0.00 43.48 2.24
617 625 1.026182 ATTGCCACGTCATCGCATGT 61.026 50.000 0.00 0.00 41.18 3.21
645 653 2.419324 AGACGCACCACACGTTTTTAAA 59.581 40.909 0.00 0.00 45.24 1.52
651 659 2.279918 GGAGACGCACCACACGTT 60.280 61.111 0.00 0.00 45.24 3.99
716 724 3.330267 GCACTCTACAGTTTTGGAGGAG 58.670 50.000 0.00 0.00 35.82 3.69
722 730 0.517316 GCCGGCACTCTACAGTTTTG 59.483 55.000 24.80 0.00 0.00 2.44
761 769 3.052082 CTCAGTGCCACAAGCCGG 61.052 66.667 0.00 0.00 42.71 6.13
766 774 2.195567 GGCTTGCTCAGTGCCACAA 61.196 57.895 0.00 0.00 45.46 3.33
796 808 2.668550 GAGTGGCTCGCCCGTTTT 60.669 61.111 5.33 0.00 35.87 2.43
809 821 2.055042 AGCCTGGAGCCTACGAGTG 61.055 63.158 0.00 0.00 45.47 3.51
845 857 3.618019 GCCACACAAAATCCTACGGTCTA 60.618 47.826 0.00 0.00 0.00 2.59
851 863 0.170339 GCGGCCACACAAAATCCTAC 59.830 55.000 2.24 0.00 0.00 3.18
852 864 1.302383 CGCGGCCACACAAAATCCTA 61.302 55.000 2.24 0.00 0.00 2.94
854 866 2.126502 CGCGGCCACACAAAATCC 60.127 61.111 2.24 0.00 0.00 3.01
884 896 0.835971 TGCTACTGGAGGCTTGGACA 60.836 55.000 0.00 0.00 0.00 4.02
922 945 1.660560 AGGTACTTATCGCACGGCGT 61.661 55.000 6.77 6.77 46.35 5.68
924 947 1.488261 GCAGGTACTTATCGCACGGC 61.488 60.000 0.00 0.00 34.60 5.68
995 1025 1.034292 GGAGGGGCAGTTCATCTTGC 61.034 60.000 0.00 0.00 0.00 4.01
1022 1055 3.134792 GAGGAGAGACGCCGCAGA 61.135 66.667 0.00 0.00 0.00 4.26
1067 1100 0.813210 GATTGAGGAGGGCAAGAGCG 60.813 60.000 0.00 0.00 43.41 5.03
1113 1146 1.534729 AACCTGGCCGATTTCTGAAC 58.465 50.000 0.00 0.00 0.00 3.18
1158 1195 7.613585 TCAATCATCACCAATAACAGCAAAAT 58.386 30.769 0.00 0.00 0.00 1.82
1163 1200 7.887996 TTTTTCAATCATCACCAATAACAGC 57.112 32.000 0.00 0.00 0.00 4.40
1211 1248 3.317406 AGGGAAAAGATTTGCCTTGGTT 58.683 40.909 9.75 0.00 36.86 3.67
1212 1249 2.899900 GAGGGAAAAGATTTGCCTTGGT 59.100 45.455 15.66 0.00 40.50 3.67
1213 1250 2.234661 GGAGGGAAAAGATTTGCCTTGG 59.765 50.000 15.66 0.00 40.50 3.61
1220 1257 7.504574 TCTTTTAGAAACGGAGGGAAAAGATTT 59.495 33.333 10.76 0.00 37.76 2.17
1223 1260 5.932455 TCTTTTAGAAACGGAGGGAAAAGA 58.068 37.500 10.76 10.76 39.39 2.52
1224 1261 6.628919 TTCTTTTAGAAACGGAGGGAAAAG 57.371 37.500 7.43 7.43 35.96 2.27
1225 1262 8.873186 ATATTCTTTTAGAAACGGAGGGAAAA 57.127 30.769 0.00 0.00 37.82 2.29
1228 1265 8.765517 ACTAATATTCTTTTAGAAACGGAGGGA 58.234 33.333 0.00 0.00 37.82 4.20
1234 1271 9.851043 GCAGCTACTAATATTCTTTTAGAAACG 57.149 33.333 0.00 0.00 37.82 3.60
1264 1301 5.511363 TGGGACCTTTTTGTTCTACAAGAA 58.489 37.500 0.00 0.00 39.53 2.52
1265 1302 5.118729 TGGGACCTTTTTGTTCTACAAGA 57.881 39.130 0.00 0.00 39.53 3.02
1266 1303 5.278957 CCATGGGACCTTTTTGTTCTACAAG 60.279 44.000 2.85 0.00 39.53 3.16
1280 1318 0.417841 ACCACTAGACCATGGGACCT 59.582 55.000 18.09 12.33 40.59 3.85
1362 1401 5.946298 TCACTGAGCTGAGCAAAAATAATG 58.054 37.500 7.39 0.00 0.00 1.90
1363 1402 6.770746 ATCACTGAGCTGAGCAAAAATAAT 57.229 33.333 7.39 0.00 0.00 1.28
1364 1403 6.654582 TGTATCACTGAGCTGAGCAAAAATAA 59.345 34.615 7.39 0.00 0.00 1.40
1446 1493 4.808895 CGAATTCACCCTGATAACGATGAA 59.191 41.667 6.22 0.00 0.00 2.57
1447 1494 4.368315 CGAATTCACCCTGATAACGATGA 58.632 43.478 6.22 0.00 0.00 2.92
1448 1495 3.059597 GCGAATTCACCCTGATAACGATG 60.060 47.826 6.22 0.00 0.00 3.84
1449 1496 3.131396 GCGAATTCACCCTGATAACGAT 58.869 45.455 6.22 0.00 0.00 3.73
1450 1497 2.167693 AGCGAATTCACCCTGATAACGA 59.832 45.455 6.22 0.00 0.00 3.85
1451 1498 2.285220 CAGCGAATTCACCCTGATAACG 59.715 50.000 6.22 0.00 0.00 3.18
1452 1499 2.032178 GCAGCGAATTCACCCTGATAAC 59.968 50.000 17.20 1.70 0.00 1.89
1491 1538 4.690748 CGAAGAAATGCACCTTCTGAGTTA 59.309 41.667 12.43 0.00 37.29 2.24
1503 1550 2.552315 GACCTTGAACCGAAGAAATGCA 59.448 45.455 0.00 0.00 0.00 3.96
1523 1570 4.202398 GCTGTAGATGATTTGGGAGGATGA 60.202 45.833 0.00 0.00 0.00 2.92
1567 1614 1.038130 AGGCGATTACAGCTCTCCGT 61.038 55.000 0.00 0.00 34.52 4.69
1598 1645 2.443255 ACCTGCCGATATCCCAAGATTT 59.557 45.455 0.00 0.00 33.67 2.17
1690 1739 5.373812 ACACATATTAACCAGAAGAGGGG 57.626 43.478 0.00 0.00 0.00 4.79
1700 1749 4.102681 AGCCCAGAGGTACACATATTAACC 59.897 45.833 0.00 0.00 34.57 2.85
1706 1755 2.236146 CACAAGCCCAGAGGTACACATA 59.764 50.000 0.00 0.00 34.57 2.29
1714 1763 1.030488 CATGAGCACAAGCCCAGAGG 61.030 60.000 0.00 0.00 43.56 3.69
1890 1944 2.815684 ATACTCGGACAGGCACCCCA 62.816 60.000 0.00 0.00 0.00 4.96
1921 1975 8.740123 TGGATAGTTGACAAAACAGAAAGTAA 57.260 30.769 0.00 0.00 0.00 2.24
1994 2053 5.123027 AGCTCTAAGAAAAGCGAGAAAATGG 59.877 40.000 0.00 0.00 43.37 3.16
2121 2180 5.202765 TCCCCACGATACATAACTCAAGTA 58.797 41.667 0.00 0.00 0.00 2.24
2122 2181 4.028131 TCCCCACGATACATAACTCAAGT 58.972 43.478 0.00 0.00 0.00 3.16
2123 2182 4.665833 TCCCCACGATACATAACTCAAG 57.334 45.455 0.00 0.00 0.00 3.02
2125 2184 6.928348 AATATCCCCACGATACATAACTCA 57.072 37.500 0.00 0.00 36.26 3.41
2126 2185 7.383687 TGAAATATCCCCACGATACATAACTC 58.616 38.462 0.00 0.00 36.26 3.01
2128 2187 9.661563 TTATGAAATATCCCCACGATACATAAC 57.338 33.333 0.00 0.00 36.26 1.89
2131 2190 6.823689 GCTTATGAAATATCCCCACGATACAT 59.176 38.462 0.00 0.00 36.26 2.29
2132 2191 6.013725 AGCTTATGAAATATCCCCACGATACA 60.014 38.462 0.00 0.00 36.26 2.29
2133 2192 6.407202 AGCTTATGAAATATCCCCACGATAC 58.593 40.000 0.00 0.00 36.26 2.24
2134 2193 6.620877 AGCTTATGAAATATCCCCACGATA 57.379 37.500 0.00 0.00 37.85 2.92
2135 2194 5.505181 AGCTTATGAAATATCCCCACGAT 57.495 39.130 0.00 0.00 34.73 3.73
2136 2195 4.974645 AGCTTATGAAATATCCCCACGA 57.025 40.909 0.00 0.00 0.00 4.35
2137 2196 4.625742 CGTAGCTTATGAAATATCCCCACG 59.374 45.833 0.00 0.00 0.00 4.94
2138 2197 4.935808 CCGTAGCTTATGAAATATCCCCAC 59.064 45.833 0.00 0.00 0.00 4.61
2139 2198 4.595781 ACCGTAGCTTATGAAATATCCCCA 59.404 41.667 0.00 0.00 0.00 4.96
2140 2199 5.161943 ACCGTAGCTTATGAAATATCCCC 57.838 43.478 0.00 0.00 0.00 4.81
2153 2220 5.242393 TGAACTAACTGTCTAACCGTAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2168 2235 5.991933 TGCTTGATCTCTCTGAACTAACT 57.008 39.130 0.00 0.00 0.00 2.24
2183 2250 6.425114 GGTCTCGTGATATATTGTTGCTTGAT 59.575 38.462 0.00 0.00 0.00 2.57
2184 2251 5.753438 GGTCTCGTGATATATTGTTGCTTGA 59.247 40.000 0.00 0.00 0.00 3.02
2185 2252 5.755375 AGGTCTCGTGATATATTGTTGCTTG 59.245 40.000 0.00 0.00 0.00 4.01
2186 2253 5.918608 AGGTCTCGTGATATATTGTTGCTT 58.081 37.500 0.00 0.00 0.00 3.91
2187 2254 5.537300 AGGTCTCGTGATATATTGTTGCT 57.463 39.130 0.00 0.00 0.00 3.91
2188 2255 9.239002 GATATAGGTCTCGTGATATATTGTTGC 57.761 37.037 0.00 0.00 0.00 4.17
2191 2258 9.462606 TGTGATATAGGTCTCGTGATATATTGT 57.537 33.333 0.00 0.00 0.00 2.71
2192 2259 9.943163 CTGTGATATAGGTCTCGTGATATATTG 57.057 37.037 0.00 0.00 0.00 1.90
2193 2260 9.907229 TCTGTGATATAGGTCTCGTGATATATT 57.093 33.333 0.00 0.00 0.00 1.28
2196 2263 9.907229 TTATCTGTGATATAGGTCTCGTGATAT 57.093 33.333 0.00 0.00 0.00 1.63
2197 2264 9.907229 ATTATCTGTGATATAGGTCTCGTGATA 57.093 33.333 0.00 0.00 0.00 2.15
2198 2265 8.681806 CATTATCTGTGATATAGGTCTCGTGAT 58.318 37.037 0.00 0.00 0.00 3.06
2199 2266 7.883311 TCATTATCTGTGATATAGGTCTCGTGA 59.117 37.037 0.00 0.00 0.00 4.35
2200 2267 8.045176 TCATTATCTGTGATATAGGTCTCGTG 57.955 38.462 0.00 0.00 0.00 4.35
2201 2268 7.338196 CCTCATTATCTGTGATATAGGTCTCGT 59.662 40.741 0.00 0.00 0.00 4.18
2202 2269 7.554476 TCCTCATTATCTGTGATATAGGTCTCG 59.446 40.741 0.00 0.00 0.00 4.04
2203 2270 8.682710 GTCCTCATTATCTGTGATATAGGTCTC 58.317 40.741 0.00 0.00 0.00 3.36
2204 2271 8.397957 AGTCCTCATTATCTGTGATATAGGTCT 58.602 37.037 0.00 0.00 0.00 3.85
2205 2272 8.465999 CAGTCCTCATTATCTGTGATATAGGTC 58.534 40.741 0.00 0.00 0.00 3.85
2206 2273 7.093552 GCAGTCCTCATTATCTGTGATATAGGT 60.094 40.741 0.00 0.00 0.00 3.08
2207 2274 7.093596 TGCAGTCCTCATTATCTGTGATATAGG 60.094 40.741 0.00 0.00 0.00 2.57
2208 2275 7.834803 TGCAGTCCTCATTATCTGTGATATAG 58.165 38.462 0.00 0.00 0.00 1.31
2209 2276 7.452813 ACTGCAGTCCTCATTATCTGTGATATA 59.547 37.037 15.25 0.00 0.00 0.86
2210 2277 6.269538 ACTGCAGTCCTCATTATCTGTGATAT 59.730 38.462 15.25 0.00 0.00 1.63
2211 2278 5.600069 ACTGCAGTCCTCATTATCTGTGATA 59.400 40.000 15.25 0.00 0.00 2.15
2276 2360 3.008923 TGTGACAATGAGGTAGGCAATGA 59.991 43.478 0.00 0.00 0.00 2.57
2362 2446 7.453393 AGAATGTCAGGATAGTGAACTTCAAA 58.547 34.615 0.00 0.00 0.00 2.69
2420 2504 7.443575 GGATCCATTGTAGATATATGCATCACC 59.556 40.741 6.95 0.00 0.00 4.02
2421 2505 8.209584 AGGATCCATTGTAGATATATGCATCAC 58.790 37.037 15.82 0.00 0.00 3.06
2534 2618 9.149225 GTAACATCTCCTATGATCTGCAATAAG 57.851 37.037 0.00 0.00 0.00 1.73
2699 2783 8.252417 CCAATGGATGATCATAGAAGACTCTAG 58.748 40.741 8.54 0.00 37.58 2.43
2701 2785 6.520401 GCCAATGGATGATCATAGAAGACTCT 60.520 42.308 8.54 0.00 35.52 3.24
2702 2786 5.642919 GCCAATGGATGATCATAGAAGACTC 59.357 44.000 8.54 0.00 0.00 3.36
2703 2787 5.310068 AGCCAATGGATGATCATAGAAGACT 59.690 40.000 8.54 0.00 0.00 3.24
2704 2788 5.558818 AGCCAATGGATGATCATAGAAGAC 58.441 41.667 8.54 0.00 0.00 3.01
2733 2913 8.459911 TTTAGAGTATATGGTTGAGATCGTCA 57.540 34.615 0.00 0.00 0.00 4.35
2979 3161 9.421806 CTGATTGGCAAAACAAATATAGTGAAA 57.578 29.630 3.01 0.00 33.48 2.69
3068 3250 1.882623 CTCAGCCCAACACTTTCCTTC 59.117 52.381 0.00 0.00 0.00 3.46
3152 3334 6.561614 AGTACGACGAATATGACTTGAATGT 58.438 36.000 0.00 0.00 0.00 2.71
3244 3429 5.474876 CCATTAGGAAAAACTTCAGAGCAGT 59.525 40.000 0.00 0.00 36.89 4.40
3391 3577 9.739276 AGATAATCAGTTTTACCAGATCAACAA 57.261 29.630 0.00 0.00 0.00 2.83
3441 3628 4.320275 GCAGCTTTTACACCAAAGGACTAC 60.320 45.833 0.00 0.00 34.75 2.73
3469 3656 7.918562 GCCAGCGTAAATTCCAAAAATTAGATA 59.081 33.333 0.00 0.00 0.00 1.98
3473 3660 6.031751 AGCCAGCGTAAATTCCAAAAATTA 57.968 33.333 0.00 0.00 0.00 1.40
3475 3662 4.535526 AGCCAGCGTAAATTCCAAAAAT 57.464 36.364 0.00 0.00 0.00 1.82
3646 3833 6.267496 ACTTTCCACATAAATTGCCTACAC 57.733 37.500 0.00 0.00 0.00 2.90
3847 4035 3.864789 AAAAGTCCATGTCCAGACAGT 57.135 42.857 6.63 0.00 45.48 3.55
3855 4043 4.390909 CACGGTACCTAAAAAGTCCATGTC 59.609 45.833 10.90 0.00 0.00 3.06
3977 4165 6.692681 CCAGTGACAAAACACAGAATTAACAG 59.307 38.462 0.00 0.00 42.45 3.16
3986 4174 2.423185 TGCTTCCAGTGACAAAACACAG 59.577 45.455 0.00 0.00 42.45 3.66
4041 4229 1.135402 GGCACGGTAAAATTCTGCAGG 60.135 52.381 15.13 0.00 0.00 4.85
4436 4627 3.327757 TCCTCAAGTTTACACAGGAGCAT 59.672 43.478 0.00 0.00 0.00 3.79
4488 4679 4.460263 TGAGCTACAAAATTGTCACACCT 58.540 39.130 1.37 0.00 42.35 4.00
4643 4843 2.107204 GGGACGGAGGGAGTAGTACATA 59.893 54.545 2.52 0.00 0.00 2.29
4645 4845 0.257039 GGGACGGAGGGAGTAGTACA 59.743 60.000 2.52 0.00 0.00 2.90
4646 4846 0.257039 TGGGACGGAGGGAGTAGTAC 59.743 60.000 0.00 0.00 0.00 2.73
4647 4847 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
4648 4848 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
4649 4849 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
4650 4850 1.557832 CATTTTGGGACGGAGGGAGTA 59.442 52.381 0.00 0.00 0.00 2.59
4651 4851 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
4652 4852 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
4654 4854 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4655 4855 3.007635 GTCTTACATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4656 4856 2.671396 CGTCTTACATTTTGGGACGGAG 59.329 50.000 0.00 0.00 43.69 4.63
4657 4857 2.690786 CGTCTTACATTTTGGGACGGA 58.309 47.619 0.00 0.00 43.69 4.69
4702 4902 9.688592 CTCCGTCCTATAATATAAGACGTTTTT 57.311 33.333 22.33 0.00 46.62 1.94
4703 4903 8.302438 CCTCCGTCCTATAATATAAGACGTTTT 58.698 37.037 22.33 0.00 46.62 2.43
4704 4904 7.094032 CCCTCCGTCCTATAATATAAGACGTTT 60.094 40.741 22.33 0.00 46.62 3.60
4705 4905 6.376581 CCCTCCGTCCTATAATATAAGACGTT 59.623 42.308 22.33 0.00 46.62 3.99
4706 4906 5.884792 CCCTCCGTCCTATAATATAAGACGT 59.115 44.000 22.33 0.00 46.62 4.34
4708 4908 7.118060 ACTCCCTCCGTCCTATAATATAAGAC 58.882 42.308 0.12 0.12 0.00 3.01
4709 4909 7.281366 ACTCCCTCCGTCCTATAATATAAGA 57.719 40.000 0.00 0.00 0.00 2.10
4710 4910 8.273605 AGTACTCCCTCCGTCCTATAATATAAG 58.726 40.741 0.00 0.00 0.00 1.73
4711 4911 8.167691 AGTACTCCCTCCGTCCTATAATATAA 57.832 38.462 0.00 0.00 0.00 0.98
4712 4912 7.761981 AGTACTCCCTCCGTCCTATAATATA 57.238 40.000 0.00 0.00 0.00 0.86
4713 4913 6.655376 AGTACTCCCTCCGTCCTATAATAT 57.345 41.667 0.00 0.00 0.00 1.28
4714 4914 6.962311 TCTAGTACTCCCTCCGTCCTATAATA 59.038 42.308 0.00 0.00 0.00 0.98
4715 4915 5.789575 TCTAGTACTCCCTCCGTCCTATAAT 59.210 44.000 0.00 0.00 0.00 1.28
4716 4916 5.158141 TCTAGTACTCCCTCCGTCCTATAA 58.842 45.833 0.00 0.00 0.00 0.98
4717 4917 4.756564 TCTAGTACTCCCTCCGTCCTATA 58.243 47.826 0.00 0.00 0.00 1.31
4718 4918 3.596101 TCTAGTACTCCCTCCGTCCTAT 58.404 50.000 0.00 0.00 0.00 2.57
4719 4919 3.051940 TCTAGTACTCCCTCCGTCCTA 57.948 52.381 0.00 0.00 0.00 2.94
4720 4920 1.890552 TCTAGTACTCCCTCCGTCCT 58.109 55.000 0.00 0.00 0.00 3.85
4721 4921 2.955342 ATCTAGTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
4722 4922 5.163281 TGATATCTAGTACTCCCTCCGTC 57.837 47.826 0.00 0.00 0.00 4.79
4723 4923 4.019141 CCTGATATCTAGTACTCCCTCCGT 60.019 50.000 0.00 0.00 0.00 4.69
4724 4924 4.225492 TCCTGATATCTAGTACTCCCTCCG 59.775 50.000 0.00 0.00 0.00 4.63
4725 4925 5.014333 TGTCCTGATATCTAGTACTCCCTCC 59.986 48.000 0.00 0.00 0.00 4.30
4726 4926 6.129414 TGTCCTGATATCTAGTACTCCCTC 57.871 45.833 0.00 0.00 0.00 4.30
4727 4927 6.728366 ATGTCCTGATATCTAGTACTCCCT 57.272 41.667 0.00 0.00 0.00 4.20
4766 4966 9.092876 CTCTGTAGAACTGGAAAATAAAGCTAG 57.907 37.037 0.00 0.00 0.00 3.42
4874 5074 2.478872 TGCTTAGATCTAGCCCTGGT 57.521 50.000 16.59 0.00 0.00 4.00
5094 5296 5.044919 TCCTCTCCCTGAAAGCATTCAAATA 60.045 40.000 5.79 0.00 44.64 1.40
5247 5449 6.817641 GTGACATGGAATTTCATTTGGCAATA 59.182 34.615 0.00 0.00 35.20 1.90
5394 5597 0.846693 AAGTCTTCCCCACTGCACTT 59.153 50.000 0.00 0.00 0.00 3.16
5447 5650 5.692613 AGTTCTACTGCCATACGTATCTC 57.307 43.478 4.74 0.89 0.00 2.75
5616 5824 3.683822 AGTACACTTCGTAGTCCTTCTCG 59.316 47.826 0.00 0.00 30.26 4.04
5679 5887 1.546476 ACTAGAGCAGGTGTTCCTTCG 59.454 52.381 0.00 0.00 43.07 3.79
5782 5990 2.489722 GCAGTTTCATGGGGACTTCTTC 59.510 50.000 0.00 0.00 0.00 2.87
5866 6074 3.996150 ATCAGTGAAAACAACTGCAGG 57.004 42.857 19.93 3.21 43.88 4.85
5919 6127 8.408043 TGATTCTCACTTCACATTACCAAAAT 57.592 30.769 0.00 0.00 0.00 1.82
5946 6154 5.966742 AAACCTCCTTTTTCTATGCACTC 57.033 39.130 0.00 0.00 0.00 3.51
6065 6278 4.428294 TCTGAGGGCATTAATCTTCAGG 57.572 45.455 13.17 0.83 0.00 3.86
6157 6370 0.548510 AGGAGGCTGGGATAACTTGC 59.451 55.000 0.00 0.00 0.00 4.01
6165 6378 1.084018 ATTTGGAAAGGAGGCTGGGA 58.916 50.000 0.00 0.00 0.00 4.37
6166 6379 2.291540 TGTATTTGGAAAGGAGGCTGGG 60.292 50.000 0.00 0.00 0.00 4.45
6180 6393 9.033262 GTAATCGTTGACGTTTTACTGTATTTG 57.967 33.333 16.86 0.00 40.80 2.32
6195 6408 1.435577 AAGCGGTGGTAATCGTTGAC 58.564 50.000 0.00 0.00 0.00 3.18
6201 6414 4.913345 GTGTTGTAAAAAGCGGTGGTAATC 59.087 41.667 0.00 0.00 0.00 1.75
6202 6415 4.261698 GGTGTTGTAAAAAGCGGTGGTAAT 60.262 41.667 0.00 0.00 0.00 1.89
6271 6484 2.778679 GACGGCGTTCATGCACTC 59.221 61.111 16.19 0.00 36.28 3.51
6272 6485 3.112075 CGACGGCGTTCATGCACT 61.112 61.111 16.19 0.00 36.28 4.40
6317 6548 4.253685 GCTGGTCATATGTGTGTAGTTGT 58.746 43.478 1.90 0.00 0.00 3.32
6521 6758 0.452122 CGTTCGTGTTTCGGGCAATC 60.452 55.000 0.00 0.00 40.32 2.67
6536 6773 2.277501 GACATGCATGCGCCGTTC 60.278 61.111 26.53 11.55 37.32 3.95
6539 6776 4.541482 GGTGACATGCATGCGCCG 62.541 66.667 26.53 6.23 37.32 6.46
6614 6860 3.495331 ACTTGAGAGCTGAGACTTGAGA 58.505 45.455 0.00 0.00 0.00 3.27
6620 6866 4.122776 TGTTGAAACTTGAGAGCTGAGAC 58.877 43.478 0.00 0.00 0.00 3.36
6636 6882 3.646650 GCAAGTGCAAGCTGTTGAA 57.353 47.368 9.99 0.00 41.59 2.69
6657 6903 2.637872 AGGAAGGTTAGTAGCACTGCAA 59.362 45.455 3.30 0.00 0.00 4.08
6658 6904 2.257207 AGGAAGGTTAGTAGCACTGCA 58.743 47.619 3.30 0.00 0.00 4.41
6659 6905 3.055747 AGAAGGAAGGTTAGTAGCACTGC 60.056 47.826 0.00 0.00 0.00 4.40
6660 6906 4.382147 GGAGAAGGAAGGTTAGTAGCACTG 60.382 50.000 0.00 0.00 0.00 3.66
6661 6907 3.770388 GGAGAAGGAAGGTTAGTAGCACT 59.230 47.826 0.00 0.00 0.00 4.40
6662 6908 3.514309 TGGAGAAGGAAGGTTAGTAGCAC 59.486 47.826 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.