Multiple sequence alignment - TraesCS2B01G122300

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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 TraesCS2B01G122300 chr2B 100.000 3883 0 0 1 3883 89550229 89554111 0.000000e+00 7171.0
1 TraesCS2B01G122300 chr2D 87.198 2898 221 71 707 3513 56575341 56578179 0.000000e+00 3158.0
2 TraesCS2B01G122300 chr2D 91.629 657 50 4 45 698 56541154 56541808 0.000000e+00 904.0
3 TraesCS2B01G122300 chr2D 94.860 214 6 4 3671 3883 56578286 56578495 2.890000e-86 329.0
4 TraesCS2B01G122300 chr2D 94.000 150 7 2 2132 2280 500648629 500648481 3.900000e-55 226.0
5 TraesCS2B01G122300 chr2D 92.727 110 6 2 1649 1758 525935523 525935416 1.440000e-34 158.0
6 TraesCS2B01G122300 chr2D 97.872 47 1 0 1 47 56540950 56540996 8.940000e-12 82.4
7 TraesCS2B01G122300 chr2A 83.646 1119 125 33 2292 3383 57999726 58000813 0.000000e+00 1000.0
8 TraesCS2B01G122300 chr2A 89.456 607 46 8 172 764 57997312 57997914 0.000000e+00 750.0
9 TraesCS2B01G122300 chr2A 89.709 515 43 4 786 1290 57997971 57998485 0.000000e+00 649.0
10 TraesCS2B01G122300 chr2A 89.726 292 14 3 3594 3883 58001040 58001317 3.690000e-95 359.0
11 TraesCS2B01G122300 chr2A 97.122 139 4 0 2138 2276 604991504 604991642 6.490000e-58 235.0
12 TraesCS2B01G122300 chr2A 90.909 143 6 3 1 143 57996763 57996898 6.630000e-43 185.0
13 TraesCS2B01G122300 chr4A 97.260 146 2 2 2127 2271 448099241 448099097 3.000000e-61 246.0
14 TraesCS2B01G122300 chr4A 99.254 134 1 0 2145 2278 513375882 513376015 3.880000e-60 243.0
15 TraesCS2B01G122300 chr4A 90.265 113 9 2 1645 1757 692657457 692657347 3.130000e-31 147.0
16 TraesCS2B01G122300 chr3A 97.810 137 3 0 2137 2273 686910094 686909958 1.800000e-58 237.0
17 TraesCS2B01G122300 chr1A 97.163 141 1 2 2144 2281 12159684 12159824 6.490000e-58 235.0
18 TraesCS2B01G122300 chr1A 95.139 144 6 1 2145 2288 311814211 311814069 3.900000e-55 226.0
19 TraesCS2B01G122300 chr6A 96.479 142 3 2 2144 2285 594970385 594970524 2.330000e-57 233.0
20 TraesCS2B01G122300 chr7A 95.804 143 5 1 2130 2271 442842990 442843132 3.020000e-56 230.0
21 TraesCS2B01G122300 chr5A 81.107 307 38 11 1813 2103 64808971 64809273 1.090000e-55 228.0
22 TraesCS2B01G122300 chr5A 76.289 388 47 17 2296 2673 64809377 64809729 8.630000e-37 165.0
23 TraesCS2B01G122300 chr7B 91.071 112 8 2 1648 1759 420072797 420072688 2.420000e-32 150.0
24 TraesCS2B01G122300 chr4D 90.909 110 8 2 1649 1758 441486814 441486707 3.130000e-31 147.0
25 TraesCS2B01G122300 chr4D 90.826 109 8 2 1649 1757 13244480 13244586 1.120000e-30 145.0
26 TraesCS2B01G122300 chr6D 90.826 109 8 2 1649 1757 249445908 249445802 1.120000e-30 145.0
27 TraesCS2B01G122300 chr1D 88.983 118 11 2 1642 1759 95869696 95869811 1.120000e-30 145.0
28 TraesCS2B01G122300 chr1D 90.826 109 9 1 1649 1757 169065403 169065296 1.120000e-30 145.0


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 TraesCS2B01G122300 chr2B 89550229 89554111 3882 False 7171.0 7171 100.0000 1 3883 1 chr2B.!!$F1 3882
1 TraesCS2B01G122300 chr2D 56575341 56578495 3154 False 1743.5 3158 91.0290 707 3883 2 chr2D.!!$F2 3176
2 TraesCS2B01G122300 chr2D 56540950 56541808 858 False 493.2 904 94.7505 1 698 2 chr2D.!!$F1 697
3 TraesCS2B01G122300 chr2A 57996763 58001317 4554 False 588.6 1000 88.6892 1 3883 5 chr2A.!!$F2 3882

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
894 1493 0.546122 AATAGGCCCATCAGAACGCA 59.454 50.0 0.0 0.0 0.0 5.24 F
1657 2601 0.537653 GGCACACTTCTACTCCCTCC 59.462 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2707 0.171903 CACCGTCCGGAATTACTCGT 59.828 55.0 5.23 0.0 38.96 4.18 R
3206 4286 0.036388 TGGGCTTCTTCTTTCGCGAT 60.036 50.0 10.88 0.0 0.00 4.58 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
161 322 2.177888 AGGAAGAGCCCTTCTTTGGTTT 59.822 45.455 7.98 0.00 46.12 3.27
166 327 2.229062 GAGCCCTTCTTTGGTTTAGTGC 59.771 50.000 0.00 0.00 0.00 4.40
168 329 2.229062 GCCCTTCTTTGGTTTAGTGCTC 59.771 50.000 0.00 0.00 0.00 4.26
169 330 2.484264 CCCTTCTTTGGTTTAGTGCTCG 59.516 50.000 0.00 0.00 0.00 5.03
170 331 2.484264 CCTTCTTTGGTTTAGTGCTCGG 59.516 50.000 0.00 0.00 0.00 4.63
281 827 9.319143 CCAAGTTAAAAGAGTGAATATCTCGAT 57.681 33.333 0.00 0.00 37.07 3.59
377 926 3.260380 CCCACCAATGTATTTTCTTGCCA 59.740 43.478 0.00 0.00 0.00 4.92
410 959 6.022821 GTCTCTCACTATAAGTTGTGTCGTC 58.977 44.000 0.00 0.00 35.82 4.20
481 1036 1.218875 GGGCAAAAGGTTTTTCCGCG 61.219 55.000 0.00 0.00 41.99 6.46
493 1048 5.404066 AGGTTTTTCCGCGTTTCATTAATTG 59.596 36.000 4.92 0.00 41.99 2.32
562 1117 4.282703 TGGCCTTAAAAGAACTACTCTCGT 59.717 41.667 3.32 0.00 31.02 4.18
564 1119 5.228665 GCCTTAAAAGAACTACTCTCGTGT 58.771 41.667 0.00 0.00 31.02 4.49
570 1125 5.906113 AAGAACTACTCTCGTGTCATCAT 57.094 39.130 0.00 0.00 31.02 2.45
642 1197 1.512926 CGGATTTTGGCGAGGATAGG 58.487 55.000 0.00 0.00 0.00 2.57
651 1206 1.290324 CGAGGATAGGCATCGGTGG 59.710 63.158 0.00 0.00 46.18 4.61
687 1242 0.853530 AACACCCTTGCCTTCCTCTT 59.146 50.000 0.00 0.00 0.00 2.85
691 1247 1.251251 CCCTTGCCTTCCTCTTGTTG 58.749 55.000 0.00 0.00 0.00 3.33
699 1255 3.006217 GCCTTCCTCTTGTTGCAGATTTT 59.994 43.478 0.00 0.00 0.00 1.82
705 1261 4.021719 CCTCTTGTTGCAGATTTTCCATGT 60.022 41.667 0.00 0.00 0.00 3.21
706 1262 5.183713 CCTCTTGTTGCAGATTTTCCATGTA 59.816 40.000 0.00 0.00 0.00 2.29
707 1263 6.294675 CCTCTTGTTGCAGATTTTCCATGTAA 60.295 38.462 0.00 0.00 0.00 2.41
708 1264 7.048629 TCTTGTTGCAGATTTTCCATGTAAA 57.951 32.000 0.00 0.00 0.00 2.01
709 1265 7.495901 TCTTGTTGCAGATTTTCCATGTAAAA 58.504 30.769 0.00 0.00 33.15 1.52
730 1292 1.481871 AGAGGGATGCCAATGCTTTG 58.518 50.000 5.86 5.37 38.71 2.77
779 1341 4.378770 CGTCATTCCACCAATCTTTGACAG 60.379 45.833 0.00 0.00 33.38 3.51
799 1396 1.595093 CGTGGAATGGTTTGGGCCTC 61.595 60.000 4.53 0.00 0.00 4.70
835 1432 4.631813 GCTAGATACGATTTTAGGCCCATG 59.368 45.833 0.00 0.00 0.00 3.66
853 1450 0.920763 TGAGATGGACTGGGCCCATT 60.921 55.000 28.82 22.24 43.96 3.16
856 1455 0.753111 GATGGACTGGGCCCATTCAC 60.753 60.000 35.45 26.27 43.96 3.18
863 1462 1.076705 GGGCCCATTCACCTTCCTC 60.077 63.158 19.95 0.00 0.00 3.71
894 1493 0.546122 AATAGGCCCATCAGAACGCA 59.454 50.000 0.00 0.00 0.00 5.24
897 1496 2.401766 GGCCCATCAGAACGCACAG 61.402 63.158 0.00 0.00 0.00 3.66
904 1503 0.880278 TCAGAACGCACAGGAAGCAC 60.880 55.000 0.00 0.00 0.00 4.40
976 1575 5.335583 CGAGAAGAGAGAGAGAGAAAAGCAA 60.336 44.000 0.00 0.00 0.00 3.91
991 1590 0.666274 AGCAACGAGACGCGAATCAA 60.666 50.000 15.93 0.00 44.57 2.57
1143 1742 1.875514 GTCCAGGTCCGTGTTAAAACC 59.124 52.381 0.00 0.00 0.00 3.27
1151 1750 4.213059 GGTCCGTGTTAAAACCGTCAATTA 59.787 41.667 0.00 0.00 0.00 1.40
1152 1751 5.376537 GTCCGTGTTAAAACCGTCAATTAG 58.623 41.667 0.00 0.00 0.00 1.73
1171 1770 3.710233 CGATTACGCCTTCGATTGC 57.290 52.632 0.00 0.00 37.55 3.56
1173 1772 1.332028 CGATTACGCCTTCGATTGCAC 60.332 52.381 7.36 0.00 37.55 4.57
1204 1811 1.682854 CCACTTTTGAGCCTTGCTTCA 59.317 47.619 0.00 0.00 39.88 3.02
1216 1823 1.431488 TTGCTTCATCTCGCATCCGC 61.431 55.000 0.00 0.00 35.85 5.54
1241 1848 1.067425 CGATCCGTGGGTAGTTTGTCA 60.067 52.381 0.00 0.00 0.00 3.58
1267 1875 2.889045 GGTGTTAGGGTTTGGTTTCTCC 59.111 50.000 0.00 0.00 0.00 3.71
1300 1913 0.679002 CCATGCCTGTGTAGCTGCTT 60.679 55.000 7.79 0.00 0.00 3.91
1307 1920 2.287188 CCTGTGTAGCTGCTTGTTGTTG 60.287 50.000 7.79 0.00 0.00 3.33
1340 1953 2.432628 GTGCTGGGTCGGTCTTCG 60.433 66.667 0.00 0.00 40.90 3.79
1362 1975 4.559229 CGGCGATCTGAGCTGCGA 62.559 66.667 0.00 0.00 33.94 5.10
1363 1976 2.028778 GGCGATCTGAGCTGCGAT 59.971 61.111 0.00 0.00 34.52 4.58
1364 1977 2.308769 GGCGATCTGAGCTGCGATG 61.309 63.158 0.00 0.00 34.52 3.84
1365 1978 2.308769 GCGATCTGAGCTGCGATGG 61.309 63.158 0.00 0.00 0.00 3.51
1387 2000 3.906846 GTGTGATCTGGGAGGGATTATCT 59.093 47.826 0.00 0.00 0.00 1.98
1409 2338 7.789273 TCTGAAGTTTATTACGTGGTCAAAA 57.211 32.000 0.00 0.00 0.00 2.44
1425 2354 6.538381 GTGGTCAAAATTGTTGTTTGGATCTT 59.462 34.615 0.00 0.00 36.75 2.40
1427 2356 8.260818 TGGTCAAAATTGTTGTTTGGATCTTAA 58.739 29.630 0.00 0.00 36.75 1.85
1437 2366 5.116180 TGTTTGGATCTTAATAGTGCTCCG 58.884 41.667 0.00 0.00 0.00 4.63
1468 2405 4.891566 CGGTGAAGGAGAAGACCG 57.108 61.111 0.00 0.00 44.86 4.79
1480 2417 4.712337 AGGAGAAGACCGAAGTGATTATGT 59.288 41.667 0.00 0.00 34.73 2.29
1518 2455 1.515521 CTGGCGAACCCCTGTTTGTC 61.516 60.000 0.00 0.00 40.31 3.18
1657 2601 0.537653 GGCACACTTCTACTCCCTCC 59.462 60.000 0.00 0.00 0.00 4.30
1662 2606 1.075896 CTTCTACTCCCTCCGCCCT 60.076 63.158 0.00 0.00 0.00 5.19
1675 2619 1.626321 TCCGCCCTGAATTACTTGTCA 59.374 47.619 0.00 0.00 0.00 3.58
1731 2707 5.753438 GTCTAACATACATCCATTTCTGCGA 59.247 40.000 0.00 0.00 0.00 5.10
1749 2746 0.453390 GACGAGTAATTCCGGACGGT 59.547 55.000 1.83 0.00 36.47 4.83
1758 2755 2.362120 CCGGACGGTGGGAGTACT 60.362 66.667 0.00 0.00 0.00 2.73
1772 2769 5.244626 GTGGGAGTACTGGTTAGAACACTTA 59.755 44.000 0.00 0.00 0.00 2.24
1773 2770 6.021030 TGGGAGTACTGGTTAGAACACTTAT 58.979 40.000 0.00 0.00 0.00 1.73
1774 2771 6.070995 TGGGAGTACTGGTTAGAACACTTATG 60.071 42.308 0.00 0.00 0.00 1.90
1805 2803 3.438087 CAGAACCTGGATGCAAAGTACAG 59.562 47.826 0.00 0.00 0.00 2.74
1808 2806 3.412386 ACCTGGATGCAAAGTACAGTTC 58.588 45.455 0.00 0.00 0.00 3.01
1810 2808 2.416547 CTGGATGCAAAGTACAGTTCCG 59.583 50.000 0.00 0.00 0.00 4.30
1820 2818 3.018149 AGTACAGTTCCGGTTTTGCAAA 58.982 40.909 8.05 8.05 0.00 3.68
1835 2833 8.716909 CGGTTTTGCAAAATTTTGATAGGTAAT 58.283 29.630 30.40 0.00 40.55 1.89
2068 3073 9.884465 GTATTCCATTATTTCTGACTGTTATGC 57.116 33.333 0.00 0.00 0.00 3.14
2069 3074 7.936496 TTCCATTATTTCTGACTGTTATGCA 57.064 32.000 0.00 0.00 0.00 3.96
2070 3075 8.523915 TTCCATTATTTCTGACTGTTATGCAT 57.476 30.769 3.79 3.79 0.00 3.96
2071 3076 7.933396 TCCATTATTTCTGACTGTTATGCATG 58.067 34.615 10.16 0.00 0.00 4.06
2085 3090 6.408035 TGTTATGCATGAAAATTTGGAGCAT 58.592 32.000 10.16 18.41 42.98 3.79
2089 3094 5.979993 TGCATGAAAATTTGGAGCATGTAT 58.020 33.333 17.43 0.00 38.76 2.29
2095 3100 7.890515 TGAAAATTTGGAGCATGTATGTGTAA 58.109 30.769 0.00 0.00 0.00 2.41
2159 3169 1.878734 GTATCTACTCCCTCCGTTCCG 59.121 57.143 0.00 0.00 0.00 4.30
2165 3175 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2173 3183 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
2174 3184 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
2175 3185 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
2176 3186 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
2177 3187 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
2178 3188 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
2179 3189 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
2180 3190 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
2181 3191 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2183 3193 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
2184 3194 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2196 3220 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2214 3238 9.130312 CGGATGTATCTAGACTTATTTTAGTGC 57.870 37.037 0.00 0.00 0.00 4.40
2225 3249 8.862085 AGACTTATTTTAGTGCTAGATACCTCC 58.138 37.037 0.00 0.00 0.00 4.30
2226 3250 7.659186 ACTTATTTTAGTGCTAGATACCTCCG 58.341 38.462 0.00 0.00 0.00 4.63
2228 3252 8.696043 TTATTTTAGTGCTAGATACCTCCGTA 57.304 34.615 0.00 0.00 0.00 4.02
2241 3265 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
2249 3295 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2257 3303 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
2277 3323 2.169330 GAACGGAGGGAGTAGTTCTGT 58.831 52.381 0.55 0.00 39.66 3.41
2282 3328 4.080129 ACGGAGGGAGTAGTTCTGTACATA 60.080 45.833 0.00 0.00 0.00 2.29
2329 3376 3.068873 TGTTGCCGGCTTTAAAGTCAAAT 59.931 39.130 29.70 0.00 0.00 2.32
2377 3424 2.280628 GTACCTACTGCCTTGTGATGC 58.719 52.381 0.00 0.00 0.00 3.91
2403 3450 7.436673 CGATGGAACTTTATTTCCTCTACTCTG 59.563 40.741 3.66 0.00 44.89 3.35
2447 3495 3.346315 TGCCATAGTCAACATTCAGTGG 58.654 45.455 0.00 0.00 0.00 4.00
2493 3541 5.302313 GGCCTAGCTACTTTACATAGTGAGT 59.698 44.000 0.00 0.00 0.00 3.41
2574 3622 4.646945 TGGTCTTTGCTGTATTGGTGAAAA 59.353 37.500 0.00 0.00 0.00 2.29
2642 3690 7.532884 GCTGTTTGTGTTAACTCTATTTAACCG 59.467 37.037 7.22 3.41 40.03 4.44
2675 3723 5.183904 AGTTGCTTGATCAATTCCAAGTACC 59.816 40.000 8.96 2.26 41.21 3.34
2678 3726 4.201822 GCTTGATCAATTCCAAGTACCGTC 60.202 45.833 8.96 0.00 41.21 4.79
2679 3727 3.517602 TGATCAATTCCAAGTACCGTCG 58.482 45.455 0.00 0.00 0.00 5.12
2680 3728 1.717194 TCAATTCCAAGTACCGTCGC 58.283 50.000 0.00 0.00 0.00 5.19
2681 3729 1.001068 TCAATTCCAAGTACCGTCGCA 59.999 47.619 0.00 0.00 0.00 5.10
2682 3730 1.127951 CAATTCCAAGTACCGTCGCAC 59.872 52.381 0.00 0.00 0.00 5.34
2719 3767 5.708736 TGCCCTCCTCAAAGTCATAATTA 57.291 39.130 0.00 0.00 0.00 1.40
2723 3771 6.547510 GCCCTCCTCAAAGTCATAATTATTGT 59.452 38.462 0.00 0.00 0.00 2.71
2726 3774 7.917505 CCTCCTCAAAGTCATAATTATTGTTGC 59.082 37.037 0.00 0.00 0.00 4.17
2740 3788 7.867445 ATTATTGTTGCTAACCTGTTTTTCG 57.133 32.000 0.00 0.00 0.00 3.46
2760 3809 5.611796 TCGTCTGAATTTTCTTGTCATGG 57.388 39.130 0.00 0.00 0.00 3.66
2766 3815 6.944290 TCTGAATTTTCTTGTCATGGTCATCT 59.056 34.615 0.00 0.00 0.00 2.90
2768 3817 5.808042 ATTTTCTTGTCATGGTCATCTCG 57.192 39.130 0.00 0.00 0.00 4.04
2785 3834 7.394872 GTCATCTCGCTATTAGTTTCAGTTTG 58.605 38.462 0.00 0.00 0.00 2.93
2788 3837 6.452242 TCTCGCTATTAGTTTCAGTTTGTCA 58.548 36.000 0.00 0.00 0.00 3.58
2793 3842 7.410942 CGCTATTAGTTTCAGTTTGTCAGTCTC 60.411 40.741 0.00 0.00 0.00 3.36
2794 3843 7.600752 GCTATTAGTTTCAGTTTGTCAGTCTCT 59.399 37.037 0.00 0.00 0.00 3.10
2796 3845 8.819643 ATTAGTTTCAGTTTGTCAGTCTCTAC 57.180 34.615 0.00 0.00 0.00 2.59
2800 3849 6.812879 TTCAGTTTGTCAGTCTCTACGATA 57.187 37.500 0.00 0.00 0.00 2.92
2821 3870 8.454106 ACGATACTGAAGATCCTTTTGATTTTG 58.546 33.333 0.00 0.00 32.41 2.44
2834 3884 5.831702 TTTGATTTTGTTTGCAGCCATTT 57.168 30.435 0.00 0.00 0.00 2.32
2858 3908 5.765182 TGACTGGATCAAGAAAACCTTCTTC 59.235 40.000 3.42 0.00 46.88 2.87
2873 3923 2.680352 TTCGAGAAGCCCGAGCCT 60.680 61.111 0.00 0.00 41.25 4.58
2892 3942 4.000331 CCTGAGGCATAAGTGTCTATGG 58.000 50.000 0.00 0.00 41.25 2.74
2896 3946 1.774856 GGCATAAGTGTCTATGGGGGT 59.225 52.381 0.00 0.00 31.10 4.95
2897 3947 2.487265 GGCATAAGTGTCTATGGGGGTG 60.487 54.545 0.00 0.00 31.10 4.61
2898 3948 2.851195 CATAAGTGTCTATGGGGGTGC 58.149 52.381 0.00 0.00 0.00 5.01
2899 3949 1.959710 TAAGTGTCTATGGGGGTGCA 58.040 50.000 0.00 0.00 0.00 4.57
2900 3950 0.328258 AAGTGTCTATGGGGGTGCAC 59.672 55.000 8.80 8.80 0.00 4.57
2901 3951 1.449601 GTGTCTATGGGGGTGCACG 60.450 63.158 11.45 0.00 0.00 5.34
2902 3952 2.189521 GTCTATGGGGGTGCACGG 59.810 66.667 11.45 0.00 0.00 4.94
2903 3953 3.792736 TCTATGGGGGTGCACGGC 61.793 66.667 11.45 0.00 0.00 5.68
2904 3954 3.797353 CTATGGGGGTGCACGGCT 61.797 66.667 11.45 0.00 0.00 5.52
2905 3955 2.365768 TATGGGGGTGCACGGCTA 60.366 61.111 11.45 0.00 0.00 3.93
2906 3956 2.660258 CTATGGGGGTGCACGGCTAC 62.660 65.000 11.45 0.00 0.00 3.58
2908 3958 4.778143 GGGGGTGCACGGCTACAG 62.778 72.222 11.45 0.00 0.00 2.74
2983 4038 6.740401 GCCAATAATATACAAGACCCTCGTGA 60.740 42.308 0.00 0.00 30.40 4.35
3088 4147 7.812648 TGTAAATTTATTTTCCGTCACAGAGG 58.187 34.615 0.31 0.00 0.00 3.69
3103 4162 3.891049 ACAGAGGAAAGAAACTGTGCTT 58.109 40.909 0.00 0.00 41.16 3.91
3104 4163 4.273318 ACAGAGGAAAGAAACTGTGCTTT 58.727 39.130 8.18 8.18 41.16 3.51
3123 4187 8.359642 TGTGCTTTTGTTTATTTCTCTTGCTAT 58.640 29.630 0.00 0.00 0.00 2.97
3163 4243 4.129737 GCTCGCTCAGCCGTGGTA 62.130 66.667 0.00 0.00 43.17 3.25
3172 4252 2.147958 TCAGCCGTGGTATTTTGTGTC 58.852 47.619 0.00 0.00 0.00 3.67
3173 4253 1.136085 CAGCCGTGGTATTTTGTGTCG 60.136 52.381 0.00 0.00 0.00 4.35
3185 4265 2.048127 GTGTCGAGCCTGGTGTCC 60.048 66.667 0.00 0.00 0.00 4.02
3186 4266 3.311110 TGTCGAGCCTGGTGTCCC 61.311 66.667 0.00 0.00 0.00 4.46
3189 4269 2.046892 CGAGCCTGGTGTCCCTTG 60.047 66.667 0.00 0.00 0.00 3.61
3201 4281 4.409574 TGGTGTCCCTTGTTGAACTAACTA 59.590 41.667 0.00 0.00 40.05 2.24
3204 4284 6.053650 GTGTCCCTTGTTGAACTAACTAACT 58.946 40.000 0.00 0.00 40.05 2.24
3205 4285 6.202379 GTGTCCCTTGTTGAACTAACTAACTC 59.798 42.308 0.00 0.00 40.05 3.01
3206 4286 6.126997 TGTCCCTTGTTGAACTAACTAACTCA 60.127 38.462 0.00 0.00 40.05 3.41
3207 4287 6.935208 GTCCCTTGTTGAACTAACTAACTCAT 59.065 38.462 0.00 0.00 40.05 2.90
3208 4288 7.117956 GTCCCTTGTTGAACTAACTAACTCATC 59.882 40.741 0.00 0.00 40.05 2.92
3209 4289 6.090898 CCCTTGTTGAACTAACTAACTCATCG 59.909 42.308 0.00 0.00 40.05 3.84
3212 4292 4.690184 TGAACTAACTAACTCATCGCGA 57.310 40.909 13.09 13.09 0.00 5.87
3214 4294 5.463286 TGAACTAACTAACTCATCGCGAAA 58.537 37.500 15.24 3.16 0.00 3.46
3215 4295 5.571741 TGAACTAACTAACTCATCGCGAAAG 59.428 40.000 15.24 16.63 0.00 2.62
3216 4296 5.306532 ACTAACTAACTCATCGCGAAAGA 57.693 39.130 23.72 18.57 0.00 2.52
3217 4297 5.706916 ACTAACTAACTCATCGCGAAAGAA 58.293 37.500 23.72 12.69 0.00 2.52
3218 4298 5.800941 ACTAACTAACTCATCGCGAAAGAAG 59.199 40.000 23.72 20.52 0.00 2.85
3233 4313 4.397417 CGAAAGAAGAAGCCCATGAGATTT 59.603 41.667 0.00 0.00 0.00 2.17
3234 4314 5.586243 CGAAAGAAGAAGCCCATGAGATTTA 59.414 40.000 0.00 0.00 0.00 1.40
3236 4316 4.786425 AGAAGAAGCCCATGAGATTTACC 58.214 43.478 0.00 0.00 0.00 2.85
3237 4317 4.476479 AGAAGAAGCCCATGAGATTTACCT 59.524 41.667 0.00 0.00 0.00 3.08
3239 4319 3.137360 AGAAGCCCATGAGATTTACCTCC 59.863 47.826 0.00 0.00 32.32 4.30
3240 4320 1.417890 AGCCCATGAGATTTACCTCCG 59.582 52.381 0.00 0.00 32.32 4.63
3242 4322 1.543429 CCCATGAGATTTACCTCCGCC 60.543 57.143 0.00 0.00 32.32 6.13
3243 4323 1.502231 CATGAGATTTACCTCCGCCG 58.498 55.000 0.00 0.00 32.32 6.46
3244 4324 1.120530 ATGAGATTTACCTCCGCCGT 58.879 50.000 0.00 0.00 32.32 5.68
3245 4325 1.766494 TGAGATTTACCTCCGCCGTA 58.234 50.000 0.00 0.00 32.32 4.02
3246 4326 1.679680 TGAGATTTACCTCCGCCGTAG 59.320 52.381 0.00 0.00 32.32 3.51
3247 4327 3.592051 TGAGATTTACCTCCGCCGTAGG 61.592 54.545 0.00 0.00 41.08 3.18
3249 4329 6.748409 TGAGATTTACCTCCGCCGTAGGTA 62.748 50.000 4.27 4.27 45.69 3.08
3268 4348 7.434602 CGTAGGTAGCCTTAACAAGATTCTAAC 59.565 40.741 0.00 0.00 34.61 2.34
3271 4351 7.824779 AGGTAGCCTTAACAAGATTCTAACAAG 59.175 37.037 0.00 0.00 0.00 3.16
3274 4354 6.717084 AGCCTTAACAAGATTCTAACAAGCTT 59.283 34.615 0.00 0.00 0.00 3.74
3280 4361 7.608308 ACAAGATTCTAACAAGCTTGAGATC 57.392 36.000 32.50 22.57 43.96 2.75
3306 4387 6.771188 AATCACTTGTAGAACTCGACAAAG 57.229 37.500 6.81 3.68 40.10 2.77
3307 4388 5.509716 TCACTTGTAGAACTCGACAAAGA 57.490 39.130 6.81 5.53 40.10 2.52
3309 4390 6.150318 TCACTTGTAGAACTCGACAAAGATC 58.850 40.000 6.81 0.00 40.10 2.75
3316 4397 4.563184 AGAACTCGACAAAGATCATAACGC 59.437 41.667 0.00 0.00 0.00 4.84
3326 4407 1.517276 GATCATAACGCCGTGTTCTCG 59.483 52.381 0.00 0.00 42.09 4.04
3330 4411 2.424705 TAACGCCGTGTTCTCGCCTT 62.425 55.000 0.00 0.00 42.09 4.35
3368 4449 5.856126 TTGAGAACGATGTGTACCAAATC 57.144 39.130 0.00 0.00 0.00 2.17
3377 4458 0.871722 TGTACCAAATCGCAGCACAC 59.128 50.000 0.00 0.00 0.00 3.82
3383 4464 1.135859 CAAATCGCAGCACACTTCTCC 60.136 52.381 0.00 0.00 0.00 3.71
3384 4465 1.016130 AATCGCAGCACACTTCTCCG 61.016 55.000 0.00 0.00 0.00 4.63
3396 4477 0.173708 CTTCTCCGGTGGTAGTCTGC 59.826 60.000 0.00 0.00 0.00 4.26
3403 4484 1.402984 CGGTGGTAGTCTGCACTCTTC 60.403 57.143 0.00 0.00 33.62 2.87
3404 4485 1.618837 GGTGGTAGTCTGCACTCTTCA 59.381 52.381 0.00 0.00 33.62 3.02
3415 4496 1.268079 GCACTCTTCAGCCAGAAAACC 59.732 52.381 0.00 0.00 35.40 3.27
3439 4520 5.054477 GCACCTTTGTAGTCTCAGTTACAA 58.946 41.667 1.84 1.84 37.84 2.41
3441 4522 6.046593 CACCTTTGTAGTCTCAGTTACAACA 58.953 40.000 4.64 0.00 38.94 3.33
3451 4532 4.569162 TCTCAGTTACAACAACAAAGACGG 59.431 41.667 0.00 0.00 0.00 4.79
3453 4534 4.569162 TCAGTTACAACAACAAAGACGGAG 59.431 41.667 0.00 0.00 0.00 4.63
3479 4560 3.103911 CGCACCGACTCGAACCAC 61.104 66.667 0.00 0.00 0.00 4.16
3513 4597 5.248640 CACAGTCATATTCCCAACAACTCT 58.751 41.667 0.00 0.00 0.00 3.24
3514 4598 5.122869 CACAGTCATATTCCCAACAACTCTG 59.877 44.000 0.00 0.00 0.00 3.35
3517 4601 2.107950 TATTCCCAACAACTCTGCCG 57.892 50.000 0.00 0.00 0.00 5.69
3519 4603 3.365265 CCCAACAACTCTGCCGCC 61.365 66.667 0.00 0.00 0.00 6.13
3523 4607 3.429372 AACAACTCTGCCGCCCCAA 62.429 57.895 0.00 0.00 0.00 4.12
3526 4610 2.606587 AACTCTGCCGCCCCAAGAT 61.607 57.895 0.00 0.00 0.00 2.40
3527 4611 2.515523 CTCTGCCGCCCCAAGATG 60.516 66.667 0.00 0.00 0.00 2.90
3528 4612 3.329889 TCTGCCGCCCCAAGATGT 61.330 61.111 0.00 0.00 0.00 3.06
3529 4613 2.361610 CTGCCGCCCCAAGATGTT 60.362 61.111 0.00 0.00 0.00 2.71
3533 4617 0.751643 GCCGCCCCAAGATGTTGTAT 60.752 55.000 1.49 0.00 30.95 2.29
3534 4618 1.762708 CCGCCCCAAGATGTTGTATT 58.237 50.000 1.49 0.00 30.95 1.89
3535 4619 1.676006 CCGCCCCAAGATGTTGTATTC 59.324 52.381 1.49 0.00 30.95 1.75
3550 4680 6.851609 TGTTGTATTCATCAAGGAAAATCCG 58.148 36.000 0.00 0.00 42.75 4.18
3558 4688 2.362375 GGAAAATCCGCCTGCCCA 60.362 61.111 0.00 0.00 0.00 5.36
3559 4689 1.758122 GGAAAATCCGCCTGCCCAT 60.758 57.895 0.00 0.00 0.00 4.00
3560 4690 1.438814 GAAAATCCGCCTGCCCATG 59.561 57.895 0.00 0.00 0.00 3.66
3563 4693 2.803593 AAATCCGCCTGCCCATGGTT 62.804 55.000 11.73 0.00 0.00 3.67
3564 4694 2.803593 AATCCGCCTGCCCATGGTTT 62.804 55.000 11.73 0.00 0.00 3.27
3573 4711 1.414550 TGCCCATGGTTTCGATCGATA 59.585 47.619 20.18 11.85 0.00 2.92
3577 4715 3.243737 CCCATGGTTTCGATCGATACTGA 60.244 47.826 29.26 20.02 0.00 3.41
3586 4724 0.661552 ATCGATACTGACCGTCCACG 59.338 55.000 0.00 0.00 39.44 4.94
3587 4725 0.674581 TCGATACTGACCGTCCACGT 60.675 55.000 0.00 0.00 37.74 4.49
3588 4726 1.009078 CGATACTGACCGTCCACGTA 58.991 55.000 0.00 0.00 37.74 3.57
3589 4727 1.267732 CGATACTGACCGTCCACGTAC 60.268 57.143 0.00 0.00 37.74 3.67
3590 4728 0.729116 ATACTGACCGTCCACGTACG 59.271 55.000 15.01 15.01 42.49 3.67
3591 4729 1.911293 TACTGACCGTCCACGTACGC 61.911 60.000 16.72 0.00 41.51 4.42
3592 4730 3.958822 CTGACCGTCCACGTACGCC 62.959 68.421 16.72 0.00 41.51 5.68
3616 4754 2.679837 CCATTGCTAGATCCACACACAC 59.320 50.000 0.00 0.00 0.00 3.82
3617 4755 2.078849 TTGCTAGATCCACACACACG 57.921 50.000 0.00 0.00 0.00 4.49
3618 4756 0.389817 TGCTAGATCCACACACACGC 60.390 55.000 0.00 0.00 0.00 5.34
3619 4757 0.389817 GCTAGATCCACACACACGCA 60.390 55.000 0.00 0.00 0.00 5.24
3664 4802 4.457496 CTCCCTCACGCGCACCAT 62.457 66.667 5.73 0.00 0.00 3.55
3726 4864 1.799403 GGATGAGCATGAGAATGAGCG 59.201 52.381 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 322 1.480789 TGGATAGTTGCCGAGCACTA 58.519 50.000 0.00 4.89 38.71 2.74
309 858 6.263168 CCCAACAATAAATCTGGTATGAGGTC 59.737 42.308 0.00 0.00 0.00 3.85
348 897 3.569194 AATACATTGGTGGGCGTGATA 57.431 42.857 0.00 0.00 0.00 2.15
377 926 1.557099 TAGTGAGAGACAACGGGCAT 58.443 50.000 0.00 0.00 0.00 4.40
410 959 5.212532 AGAGGTCTGCAAAGCTATATCTG 57.787 43.478 0.00 0.00 0.00 2.90
493 1048 9.653067 GTGTTCTAACTTTTAAAGCTTCTTCTC 57.347 33.333 0.00 0.00 0.00 2.87
532 1087 5.887214 AGTTCTTTTAAGGCCATTTTGGT 57.113 34.783 5.01 0.00 40.46 3.67
562 1117 4.762956 TTTCAACGCAATCATGATGACA 57.237 36.364 9.46 0.00 0.00 3.58
564 1119 5.313520 ACATTTCAACGCAATCATGATGA 57.686 34.783 9.46 0.00 0.00 2.92
570 1125 2.723658 GCGAAACATTTCAACGCAATCA 59.276 40.909 0.00 0.00 46.75 2.57
642 1197 2.165301 GTGTACGCTCCACCGATGC 61.165 63.158 0.00 0.00 0.00 3.91
649 1204 1.262417 TCCAGAATGTGTACGCTCCA 58.738 50.000 8.10 0.00 0.00 3.86
651 1206 2.412089 GTGTTCCAGAATGTGTACGCTC 59.588 50.000 8.10 0.00 0.00 5.03
707 1263 2.543635 AGCATTGGCATCCCTCTTTTT 58.456 42.857 0.00 0.00 44.61 1.94
708 1264 2.242882 AGCATTGGCATCCCTCTTTT 57.757 45.000 0.00 0.00 44.61 2.27
709 1265 2.235402 CAAAGCATTGGCATCCCTCTTT 59.765 45.455 0.00 0.00 44.61 2.52
718 1280 2.339348 CCGTGCAAAGCATTGGCA 59.661 55.556 3.55 0.00 41.91 4.92
730 1292 2.114670 CATCCATGGACACCCGTGC 61.115 63.158 18.99 0.00 45.97 5.34
779 1341 2.261361 GCCCAAACCATTCCACGC 59.739 61.111 0.00 0.00 0.00 5.34
835 1432 0.179006 GAATGGGCCCAGTCCATCTC 60.179 60.000 36.98 15.56 45.91 2.75
847 1444 1.076705 GGGAGGAAGGTGAATGGGC 60.077 63.158 0.00 0.00 0.00 5.36
853 1450 1.150135 AGAGACAAGGGAGGAAGGTGA 59.850 52.381 0.00 0.00 0.00 4.02
856 1455 1.944177 TCAGAGACAAGGGAGGAAGG 58.056 55.000 0.00 0.00 0.00 3.46
863 1462 1.141858 GGGCCTATTCAGAGACAAGGG 59.858 57.143 0.84 0.00 0.00 3.95
894 1493 4.781934 AGACTTGTTAAAGTGCTTCCTGT 58.218 39.130 0.00 0.00 46.84 4.00
897 1496 5.049336 GGAGAAGACTTGTTAAAGTGCTTCC 60.049 44.000 17.50 12.77 46.84 3.46
904 1503 6.764379 AGAGGAAGGAGAAGACTTGTTAAAG 58.236 40.000 0.00 0.00 39.49 1.85
976 1575 1.800315 CCGTTGATTCGCGTCTCGT 60.800 57.895 5.77 0.00 39.67 4.18
1162 1761 1.635663 GACGGTGGGTGCAATCGAAG 61.636 60.000 0.00 0.00 0.00 3.79
1173 1772 4.636435 AAAGTGGCGGACGGTGGG 62.636 66.667 0.00 0.00 0.00 4.61
1204 1811 4.654412 GAGCGGCGGATGCGAGAT 62.654 66.667 12.10 1.04 44.10 2.75
1216 1823 3.195591 CTACCCACGGATCGAGCGG 62.196 68.421 6.70 6.70 0.00 5.52
1229 1836 4.133013 ACACCGATATGACAAACTACCC 57.867 45.455 0.00 0.00 0.00 3.69
1231 1838 5.751990 CCCTAACACCGATATGACAAACTAC 59.248 44.000 0.00 0.00 0.00 2.73
1241 1848 4.579647 AACCAAACCCTAACACCGATAT 57.420 40.909 0.00 0.00 0.00 1.63
1267 1875 0.873054 GCATGGCAAGATCGGATCTG 59.127 55.000 20.57 14.94 40.13 2.90
1300 1913 1.675714 CGCAGATCTAGGCCAACAACA 60.676 52.381 5.01 0.00 0.00 3.33
1353 1966 0.460811 GATCACACCATCGCAGCTCA 60.461 55.000 0.00 0.00 0.00 4.26
1358 1971 1.221566 CCCAGATCACACCATCGCA 59.778 57.895 0.00 0.00 0.00 5.10
1359 1972 0.531532 CTCCCAGATCACACCATCGC 60.532 60.000 0.00 0.00 0.00 4.58
1360 1973 0.105593 CCTCCCAGATCACACCATCG 59.894 60.000 0.00 0.00 0.00 3.84
1362 1975 0.044702 TCCCTCCCAGATCACACCAT 59.955 55.000 0.00 0.00 0.00 3.55
1363 1976 0.044702 ATCCCTCCCAGATCACACCA 59.955 55.000 0.00 0.00 0.00 4.17
1364 1977 1.216990 AATCCCTCCCAGATCACACC 58.783 55.000 0.00 0.00 0.00 4.16
1365 1978 3.906846 AGATAATCCCTCCCAGATCACAC 59.093 47.826 0.00 0.00 0.00 3.82
1387 2000 8.407064 ACAATTTTGACCACGTAATAAACTTCA 58.593 29.630 0.00 0.00 0.00 3.02
1409 2338 8.353423 AGCACTATTAAGATCCAAACAACAAT 57.647 30.769 0.00 0.00 0.00 2.71
1425 2354 3.199071 ACAATCCCAACGGAGCACTATTA 59.801 43.478 0.00 0.00 43.12 0.98
1427 2356 1.559682 ACAATCCCAACGGAGCACTAT 59.440 47.619 0.00 0.00 43.12 2.12
1437 2366 3.875134 CCTTCACCGTATACAATCCCAAC 59.125 47.826 3.32 0.00 0.00 3.77
1468 2405 5.355071 TCTGTTGCCATCACATAATCACTTC 59.645 40.000 0.00 0.00 0.00 3.01
1614 2558 5.261209 TGTGCTAAACTTGCTTGTCAAAT 57.739 34.783 0.00 0.00 33.65 2.32
1657 2601 2.416547 CTGTGACAAGTAATTCAGGGCG 59.583 50.000 0.00 0.00 0.00 6.13
1662 2606 7.448161 ACATCCATTTCTGTGACAAGTAATTCA 59.552 33.333 0.00 0.00 0.00 2.57
1713 2689 3.123050 TCGTCGCAGAAATGGATGTATG 58.877 45.455 0.00 0.00 39.69 2.39
1731 2707 0.171903 CACCGTCCGGAATTACTCGT 59.828 55.000 5.23 0.00 38.96 4.18
1749 2746 3.853207 AGTGTTCTAACCAGTACTCCCA 58.147 45.455 0.00 0.00 0.00 4.37
1772 2769 2.371841 TCCAGGTTCTGTTACACTGCAT 59.628 45.455 0.00 0.00 0.00 3.96
1773 2770 1.765904 TCCAGGTTCTGTTACACTGCA 59.234 47.619 0.00 0.00 0.00 4.41
1774 2771 2.543777 TCCAGGTTCTGTTACACTGC 57.456 50.000 0.00 0.00 0.00 4.40
1805 2803 5.223225 TCAAAATTTTGCAAAACCGGAAC 57.777 34.783 26.05 0.00 38.05 3.62
1808 2806 5.468409 ACCTATCAAAATTTTGCAAAACCGG 59.532 36.000 26.05 17.46 38.05 5.28
1957 2955 2.038295 CCTTCCAGGAGCTATTAGGCAG 59.962 54.545 0.00 0.00 37.67 4.85
2032 3033 7.432252 CAGAAATAATGGAATACGCCAGAAAAC 59.568 37.037 0.00 0.00 42.15 2.43
2068 3073 6.814644 ACACATACATGCTCCAAATTTTCATG 59.185 34.615 13.53 13.53 40.07 3.07
2069 3074 6.938507 ACACATACATGCTCCAAATTTTCAT 58.061 32.000 0.00 0.00 0.00 2.57
2070 3075 6.343716 ACACATACATGCTCCAAATTTTCA 57.656 33.333 0.00 0.00 0.00 2.69
2071 3076 8.931385 ATTACACATACATGCTCCAAATTTTC 57.069 30.769 0.00 0.00 0.00 2.29
2124 3134 7.449086 GGGAGTAGATACTAAGTTCATAGCAGT 59.551 40.741 0.00 0.00 36.50 4.40
2159 3169 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
2165 3175 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2203 3227 7.592885 ACGGAGGTATCTAGCACTAAAATAA 57.407 36.000 0.00 0.00 0.00 1.40
2218 3242 9.233649 CTTAGATTTGTCTAGATACGGAGGTAT 57.766 37.037 0.00 0.00 42.01 2.73
2220 3244 7.229106 GTCTTAGATTTGTCTAGATACGGAGGT 59.771 40.741 0.00 0.00 0.00 3.85
2221 3245 7.228906 TGTCTTAGATTTGTCTAGATACGGAGG 59.771 40.741 0.00 0.00 0.00 4.30
2222 3246 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
2231 3255 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
2232 3256 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
2233 3257 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
2234 3258 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
2235 3259 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
2236 3260 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
2238 3262 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
2239 3263 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
2240 3264 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
2241 3265 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
2249 3295 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2252 3298 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
2255 3301 0.455005 GAACTACTCCCTCCGTTCCG 59.545 60.000 0.00 0.00 31.89 4.30
2257 3303 2.169330 ACAGAACTACTCCCTCCGTTC 58.831 52.381 0.00 0.00 36.81 3.95
2282 3328 5.563592 AGCCCGTAAAACCTAATAAACAGT 58.436 37.500 0.00 0.00 0.00 3.55
2314 3360 9.489084 AAATTCCTAACATTTGACTTTAAAGCC 57.511 29.630 15.24 4.72 0.00 4.35
2329 3376 8.536175 AGTTTCAACCAAAAGAAATTCCTAACA 58.464 29.630 0.00 0.00 36.29 2.41
2403 3450 7.199078 GCAGAATGGATCCTTAGATTTTTGTC 58.801 38.462 14.23 0.00 35.86 3.18
2447 3495 5.644644 CCAAGTCATAGAAATTGCCTCAAC 58.355 41.667 0.00 0.00 0.00 3.18
2493 3541 1.257743 GTACCAGACAGGCAGACTCA 58.742 55.000 0.00 0.00 43.14 3.41
2574 3622 7.405292 TCTTCATCATGATTTTAGTTCCAGGT 58.595 34.615 5.16 0.00 0.00 4.00
2642 3690 7.650903 GGAATTGATCAAGCAACTAATGGAATC 59.349 37.037 14.54 0.00 0.00 2.52
2679 3727 2.931969 GGCAAATAAAGATGCAAGGTGC 59.068 45.455 0.00 0.00 44.32 5.01
2680 3728 3.196254 AGGGCAAATAAAGATGCAAGGTG 59.804 43.478 0.00 0.00 44.32 4.00
2681 3729 3.444029 AGGGCAAATAAAGATGCAAGGT 58.556 40.909 0.00 0.00 44.32 3.50
2682 3730 3.181472 GGAGGGCAAATAAAGATGCAAGG 60.181 47.826 0.00 0.00 44.32 3.61
2719 3767 5.067283 AGACGAAAAACAGGTTAGCAACAAT 59.933 36.000 0.00 0.00 0.00 2.71
2723 3771 4.193090 TCAGACGAAAAACAGGTTAGCAA 58.807 39.130 0.00 0.00 0.00 3.91
2726 3774 8.129211 AGAAAATTCAGACGAAAAACAGGTTAG 58.871 33.333 0.00 0.00 34.01 2.34
2730 3778 6.751888 ACAAGAAAATTCAGACGAAAAACAGG 59.248 34.615 0.00 0.00 34.01 4.00
2740 3788 6.317789 TGACCATGACAAGAAAATTCAGAC 57.682 37.500 0.00 0.00 0.00 3.51
2760 3809 7.063544 ACAAACTGAAACTAATAGCGAGATGAC 59.936 37.037 0.00 0.00 0.00 3.06
2766 3815 6.220930 ACTGACAAACTGAAACTAATAGCGA 58.779 36.000 0.00 0.00 0.00 4.93
2768 3817 7.600752 AGAGACTGACAAACTGAAACTAATAGC 59.399 37.037 0.00 0.00 0.00 2.97
2793 3842 8.879342 AATCAAAAGGATCTTCAGTATCGTAG 57.121 34.615 0.00 0.00 34.28 3.51
2794 3843 9.667107 AAAATCAAAAGGATCTTCAGTATCGTA 57.333 29.630 0.00 0.00 34.28 3.43
2796 3845 8.454106 ACAAAATCAAAAGGATCTTCAGTATCG 58.546 33.333 0.00 0.00 34.28 2.92
2800 3849 7.225341 GCAAACAAAATCAAAAGGATCTTCAGT 59.775 33.333 0.00 0.00 34.28 3.41
2821 3870 1.340889 TCCAGTCAAATGGCTGCAAAC 59.659 47.619 9.49 0.00 45.86 2.93
2834 3884 5.310409 AGAAGGTTTTCTTGATCCAGTCA 57.690 39.130 0.00 0.00 40.79 3.41
2858 3908 3.423162 CTCAGGCTCGGGCTTCTCG 62.423 68.421 7.48 0.00 35.88 4.04
2873 3923 2.705658 CCCCATAGACACTTATGCCTCA 59.294 50.000 0.00 0.00 31.15 3.86
2881 3931 0.328258 GTGCACCCCCATAGACACTT 59.672 55.000 5.22 0.00 0.00 3.16
2888 3938 2.365768 TAGCCGTGCACCCCCATA 60.366 61.111 12.15 0.00 0.00 2.74
2889 3939 4.109675 GTAGCCGTGCACCCCCAT 62.110 66.667 12.15 0.00 0.00 4.00
2891 3941 4.778143 CTGTAGCCGTGCACCCCC 62.778 72.222 12.15 0.00 0.00 5.40
2896 3946 0.533978 TCAAAAGCTGTAGCCGTGCA 60.534 50.000 0.00 0.00 43.38 4.57
2897 3947 0.804989 ATCAAAAGCTGTAGCCGTGC 59.195 50.000 0.00 0.00 43.38 5.34
2898 3948 1.466360 GCATCAAAAGCTGTAGCCGTG 60.466 52.381 0.00 0.00 43.38 4.94
2899 3949 0.804989 GCATCAAAAGCTGTAGCCGT 59.195 50.000 0.00 0.00 43.38 5.68
2900 3950 0.247814 CGCATCAAAAGCTGTAGCCG 60.248 55.000 0.00 0.00 43.38 5.52
2901 3951 0.804989 ACGCATCAAAAGCTGTAGCC 59.195 50.000 0.00 0.00 43.38 3.93
2902 3952 2.415168 TGTACGCATCAAAAGCTGTAGC 59.585 45.455 0.00 0.00 42.49 3.58
2903 3953 4.864916 ATGTACGCATCAAAAGCTGTAG 57.135 40.909 0.00 0.00 0.00 2.74
2904 3954 5.621197 AAATGTACGCATCAAAAGCTGTA 57.379 34.783 0.00 0.00 33.50 2.74
2905 3955 4.503741 AAATGTACGCATCAAAAGCTGT 57.496 36.364 0.00 0.00 33.50 4.40
2906 3956 4.916831 TGAAAATGTACGCATCAAAAGCTG 59.083 37.500 0.00 0.00 33.50 4.24
2907 3957 5.119931 TGAAAATGTACGCATCAAAAGCT 57.880 34.783 0.00 0.00 33.50 3.74
2908 3958 4.324402 CCTGAAAATGTACGCATCAAAAGC 59.676 41.667 0.00 0.00 33.50 3.51
2983 4038 5.092968 TGGATGGAAAATCAAACAAGGGAT 58.907 37.500 0.00 0.00 0.00 3.85
3088 4147 9.689075 GAAATAAACAAAAGCACAGTTTCTTTC 57.311 29.630 13.51 13.51 39.18 2.62
3103 4162 8.296713 GTGACCATAGCAAGAGAAATAAACAAA 58.703 33.333 0.00 0.00 0.00 2.83
3104 4163 7.094377 GGTGACCATAGCAAGAGAAATAAACAA 60.094 37.037 0.00 0.00 0.00 2.83
3123 4187 1.131638 AGCTCACTCTTTGGTGACCA 58.868 50.000 0.00 0.00 40.72 4.02
3150 4214 1.135689 CACAAAATACCACGGCTGAGC 60.136 52.381 0.00 0.00 0.00 4.26
3151 4215 2.151202 ACACAAAATACCACGGCTGAG 58.849 47.619 0.00 0.00 0.00 3.35
3152 4216 2.147958 GACACAAAATACCACGGCTGA 58.852 47.619 0.00 0.00 0.00 4.26
3153 4217 1.136085 CGACACAAAATACCACGGCTG 60.136 52.381 0.00 0.00 0.00 4.85
3154 4218 1.153353 CGACACAAAATACCACGGCT 58.847 50.000 0.00 0.00 0.00 5.52
3155 4219 1.127951 CTCGACACAAAATACCACGGC 59.872 52.381 0.00 0.00 0.00 5.68
3156 4220 1.127951 GCTCGACACAAAATACCACGG 59.872 52.381 0.00 0.00 0.00 4.94
3163 4243 1.238439 CACCAGGCTCGACACAAAAT 58.762 50.000 0.00 0.00 0.00 1.82
3172 4252 2.046892 CAAGGGACACCAGGCTCG 60.047 66.667 0.00 0.00 40.13 5.03
3173 4253 0.890996 CAACAAGGGACACCAGGCTC 60.891 60.000 0.00 0.00 40.13 4.70
3185 4265 6.401153 GCGATGAGTTAGTTAGTTCAACAAGG 60.401 42.308 0.00 0.00 39.81 3.61
3186 4266 6.526222 GCGATGAGTTAGTTAGTTCAACAAG 58.474 40.000 0.00 0.00 39.81 3.16
3189 4269 4.855388 TCGCGATGAGTTAGTTAGTTCAAC 59.145 41.667 3.71 0.00 37.41 3.18
3201 4281 2.413453 GCTTCTTCTTTCGCGATGAGTT 59.587 45.455 10.88 0.00 0.00 3.01
3204 4284 1.359848 GGCTTCTTCTTTCGCGATGA 58.640 50.000 10.88 9.11 0.00 2.92
3205 4285 0.375106 GGGCTTCTTCTTTCGCGATG 59.625 55.000 10.88 6.45 0.00 3.84
3206 4286 0.036388 TGGGCTTCTTCTTTCGCGAT 60.036 50.000 10.88 0.00 0.00 4.58
3207 4287 0.036388 ATGGGCTTCTTCTTTCGCGA 60.036 50.000 3.71 3.71 0.00 5.87
3208 4288 0.097674 CATGGGCTTCTTCTTTCGCG 59.902 55.000 0.00 0.00 0.00 5.87
3209 4289 1.399791 CTCATGGGCTTCTTCTTTCGC 59.600 52.381 0.00 0.00 0.00 4.70
3212 4292 5.654209 GGTAAATCTCATGGGCTTCTTCTTT 59.346 40.000 0.00 0.00 0.00 2.52
3214 4294 4.476479 AGGTAAATCTCATGGGCTTCTTCT 59.524 41.667 0.00 0.00 0.00 2.85
3215 4295 4.786425 AGGTAAATCTCATGGGCTTCTTC 58.214 43.478 0.00 0.00 0.00 2.87
3216 4296 4.385754 GGAGGTAAATCTCATGGGCTTCTT 60.386 45.833 0.00 0.00 35.58 2.52
3217 4297 3.137360 GGAGGTAAATCTCATGGGCTTCT 59.863 47.826 0.00 0.00 35.58 2.85
3218 4298 3.481453 GGAGGTAAATCTCATGGGCTTC 58.519 50.000 0.00 0.00 35.58 3.86
3233 4313 1.526917 GCTACCTACGGCGGAGGTA 60.527 63.158 40.28 40.28 45.82 3.08
3236 4316 0.820891 TAAGGCTACCTACGGCGGAG 60.821 60.000 13.43 13.43 31.13 4.63
3237 4317 0.395586 TTAAGGCTACCTACGGCGGA 60.396 55.000 13.24 0.00 31.13 5.54
3239 4319 0.457035 TGTTAAGGCTACCTACGGCG 59.543 55.000 4.80 4.80 31.13 6.46
3240 4320 2.167075 TCTTGTTAAGGCTACCTACGGC 59.833 50.000 0.00 0.00 31.13 5.68
3242 4322 5.903810 AGAATCTTGTTAAGGCTACCTACG 58.096 41.667 0.00 0.00 31.13 3.51
3243 4323 8.255905 TGTTAGAATCTTGTTAAGGCTACCTAC 58.744 37.037 0.00 0.00 31.13 3.18
3244 4324 8.370266 TGTTAGAATCTTGTTAAGGCTACCTA 57.630 34.615 0.00 0.00 31.13 3.08
3245 4325 7.253905 TGTTAGAATCTTGTTAAGGCTACCT 57.746 36.000 0.00 0.00 33.87 3.08
3246 4326 7.414208 GCTTGTTAGAATCTTGTTAAGGCTACC 60.414 40.741 0.00 0.00 0.00 3.18
3247 4327 7.334671 AGCTTGTTAGAATCTTGTTAAGGCTAC 59.665 37.037 0.00 0.00 0.00 3.58
3248 4328 7.394816 AGCTTGTTAGAATCTTGTTAAGGCTA 58.605 34.615 0.00 0.00 0.00 3.93
3249 4329 6.241645 AGCTTGTTAGAATCTTGTTAAGGCT 58.758 36.000 0.00 0.00 0.00 4.58
3253 4333 8.902540 TCTCAAGCTTGTTAGAATCTTGTTAA 57.097 30.769 25.19 0.00 36.47 2.01
3255 4335 7.148507 CGATCTCAAGCTTGTTAGAATCTTGTT 60.149 37.037 25.19 5.73 36.47 2.83
3256 4336 6.312426 CGATCTCAAGCTTGTTAGAATCTTGT 59.688 38.462 25.19 6.40 36.47 3.16
3268 4348 5.106791 ACAAGTGATTTCGATCTCAAGCTTG 60.107 40.000 20.81 20.81 36.61 4.01
3271 4351 4.935885 ACAAGTGATTTCGATCTCAAGC 57.064 40.909 0.00 0.00 0.00 4.01
3274 4354 6.925211 AGTTCTACAAGTGATTTCGATCTCA 58.075 36.000 0.00 0.00 0.00 3.27
3280 4361 4.915667 TGTCGAGTTCTACAAGTGATTTCG 59.084 41.667 0.00 0.00 0.00 3.46
3306 4387 1.517276 CGAGAACACGGCGTTATGATC 59.483 52.381 11.19 3.73 38.19 2.92
3307 4388 1.556564 CGAGAACACGGCGTTATGAT 58.443 50.000 11.19 0.00 38.19 2.45
3309 4390 1.343821 GCGAGAACACGGCGTTATG 59.656 57.895 11.19 1.08 38.19 1.90
3316 4397 1.463444 CCTTTTAAGGCGAGAACACGG 59.537 52.381 0.00 0.00 39.76 4.94
3326 4407 7.045416 TCTCAAAACCTTTTTCCTTTTAAGGC 58.955 34.615 3.56 0.00 46.06 4.35
3330 4411 7.828712 TCGTTCTCAAAACCTTTTTCCTTTTA 58.171 30.769 0.00 0.00 0.00 1.52
3344 4425 6.627395 ATTTGGTACACATCGTTCTCAAAA 57.373 33.333 0.00 0.00 39.29 2.44
3345 4426 6.236017 GATTTGGTACACATCGTTCTCAAA 57.764 37.500 0.00 0.00 35.75 2.69
3368 4449 3.114616 CCGGAGAAGTGTGCTGCG 61.115 66.667 0.00 0.00 45.12 5.18
3369 4450 2.031163 ACCGGAGAAGTGTGCTGC 59.969 61.111 9.46 0.00 0.00 5.25
3370 4451 1.669115 CCACCGGAGAAGTGTGCTG 60.669 63.158 9.46 0.00 33.20 4.41
3377 4458 0.173708 GCAGACTACCACCGGAGAAG 59.826 60.000 9.46 3.84 0.00 2.85
3383 4464 0.603569 AAGAGTGCAGACTACCACCG 59.396 55.000 0.00 0.00 30.16 4.94
3384 4465 1.618837 TGAAGAGTGCAGACTACCACC 59.381 52.381 0.00 0.00 30.16 4.61
3396 4477 1.532868 CGGTTTTCTGGCTGAAGAGTG 59.467 52.381 6.91 0.00 35.89 3.51
3403 4484 1.455383 AAGGTGCGGTTTTCTGGCTG 61.455 55.000 0.00 0.00 0.00 4.85
3404 4485 0.755327 AAAGGTGCGGTTTTCTGGCT 60.755 50.000 0.00 0.00 0.00 4.75
3415 4496 2.440539 ACTGAGACTACAAAGGTGCG 57.559 50.000 0.00 0.00 0.00 5.34
3439 4520 0.249741 CCCGTCTCCGTCTTTGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
3441 4522 1.331214 TACCCGTCTCCGTCTTTGTT 58.669 50.000 0.00 0.00 0.00 2.83
3479 4560 5.574055 GGAATATGACTGTGCACAACAAATG 59.426 40.000 21.98 10.48 38.67 2.32
3490 4571 5.122869 CAGAGTTGTTGGGAATATGACTGTG 59.877 44.000 0.00 0.00 0.00 3.66
3492 4573 4.095483 GCAGAGTTGTTGGGAATATGACTG 59.905 45.833 0.00 0.00 0.00 3.51
3513 4597 2.130821 TACAACATCTTGGGGCGGCA 62.131 55.000 12.47 0.00 0.00 5.69
3514 4598 0.751643 ATACAACATCTTGGGGCGGC 60.752 55.000 0.00 0.00 0.00 6.53
3517 4601 3.953612 TGATGAATACAACATCTTGGGGC 59.046 43.478 0.00 0.00 42.89 5.80
3519 4603 5.887598 TCCTTGATGAATACAACATCTTGGG 59.112 40.000 0.00 0.00 42.89 4.12
3523 4607 8.689972 GGATTTTCCTTGATGAATACAACATCT 58.310 33.333 0.00 0.00 38.20 2.90
3526 4610 6.624861 GCGGATTTTCCTTGATGAATACAACA 60.625 38.462 0.00 0.00 33.30 3.33
3527 4611 5.743872 GCGGATTTTCCTTGATGAATACAAC 59.256 40.000 0.00 0.00 33.30 3.32
3528 4612 5.163561 GGCGGATTTTCCTTGATGAATACAA 60.164 40.000 0.00 0.00 33.30 2.41
3529 4613 4.338118 GGCGGATTTTCCTTGATGAATACA 59.662 41.667 0.00 0.00 33.30 2.29
3533 4617 2.754552 CAGGCGGATTTTCCTTGATGAA 59.245 45.455 0.00 0.00 33.30 2.57
3534 4618 2.368439 CAGGCGGATTTTCCTTGATGA 58.632 47.619 0.00 0.00 33.30 2.92
3535 4619 1.202336 GCAGGCGGATTTTCCTTGATG 60.202 52.381 0.00 0.00 33.30 3.07
3550 4680 1.728490 GATCGAAACCATGGGCAGGC 61.728 60.000 18.09 0.00 0.00 4.85
3558 4688 3.550233 CGGTCAGTATCGATCGAAACCAT 60.550 47.826 23.50 7.71 42.18 3.55
3559 4689 2.223409 CGGTCAGTATCGATCGAAACCA 60.223 50.000 23.50 4.94 42.18 3.67
3560 4690 2.223433 ACGGTCAGTATCGATCGAAACC 60.223 50.000 23.50 20.57 42.18 3.27
3563 4693 1.600957 GGACGGTCAGTATCGATCGAA 59.399 52.381 23.50 8.85 42.18 3.71
3564 4694 1.224075 GGACGGTCAGTATCGATCGA 58.776 55.000 21.86 21.86 42.18 3.59
3573 4711 2.949106 CGTACGTGGACGGTCAGT 59.051 61.111 7.22 9.09 44.95 3.41
3592 4730 0.846015 TGTGGATCTAGCAATGGGGG 59.154 55.000 0.00 0.00 0.00 5.40
3605 4743 1.795170 GCCTTTGCGTGTGTGTGGAT 61.795 55.000 0.00 0.00 0.00 3.41
3650 4788 1.521457 ATGTATGGTGCGCGTGAGG 60.521 57.895 8.43 0.00 0.00 3.86
3692 4830 1.746220 CTCATCCGAGGAGAAAGACGT 59.254 52.381 3.92 0.00 35.44 4.34
3693 4831 1.535015 GCTCATCCGAGGAGAAAGACG 60.535 57.143 14.18 0.00 39.88 4.18
3726 4864 0.234884 CCTTTTTCGGACGCTGTCAC 59.765 55.000 10.14 0.92 33.68 3.67


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

AutoCloner maintained by Alex Coulton.