Multiple sequence alignment - TraesCS4A01G077800

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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 TraesCS4A01G077800 chr4A 100.000 4508 0 0 1 4508 76944797 76940290 0.000000e+00 8325.0
1 TraesCS4A01G077800 chr4A 75.079 955 193 37 2227 3148 595417817 595418759 1.950000e-108 403.0
2 TraesCS4A01G077800 chr4A 91.176 68 6 0 252 319 211380433 211380366 4.800000e-15 93.5
3 TraesCS4A01G077800 chr4D 95.275 2349 83 11 2171 4508 395382960 395380629 0.000000e+00 3698.0
4 TraesCS4A01G077800 chr4D 92.676 751 40 8 166 915 395384971 395384235 0.000000e+00 1068.0
5 TraesCS4A01G077800 chr4D 79.161 787 69 42 1377 2144 395383772 395383062 1.480000e-124 457.0
6 TraesCS4A01G077800 chr4D 74.526 950 201 35 2227 3148 7898553 7897617 4.260000e-100 375.0
7 TraesCS4A01G077800 chr4D 92.245 245 9 5 946 1190 395384059 395383825 5.590000e-89 339.0
8 TraesCS4A01G077800 chr4D 94.444 162 7 2 1 161 395385200 395385040 9.680000e-62 248.0
9 TraesCS4A01G077800 chr4D 87.059 85 9 2 159 242 114579237 114579154 1.340000e-15 95.3
10 TraesCS4A01G077800 chr4D 93.651 63 4 0 256 318 271771875 271771937 1.340000e-15 95.3
11 TraesCS4A01G077800 chr4D 93.651 63 4 0 256 318 421190648 421190710 1.340000e-15 95.3
12 TraesCS4A01G077800 chr4B 94.668 1144 45 10 2595 3728 486284818 486283681 0.000000e+00 1760.0
13 TraesCS4A01G077800 chr4B 88.138 1273 77 28 1376 2594 486286160 486284908 0.000000e+00 1447.0
14 TraesCS4A01G077800 chr4B 95.796 785 29 3 3727 4508 486283598 486282815 0.000000e+00 1264.0
15 TraesCS4A01G077800 chr4B 89.028 638 40 8 166 795 486287700 486287085 0.000000e+00 763.0
16 TraesCS4A01G077800 chr4B 75.157 958 190 40 2227 3148 14266422 14267367 1.510000e-109 407.0
17 TraesCS4A01G077800 chr4B 94.156 154 9 0 3 156 486287946 486287793 7.540000e-58 235.0
18 TraesCS4A01G077800 chr6A 98.095 105 2 0 1188 1292 269572189 269572293 2.770000e-42 183.0
19 TraesCS4A01G077800 chr6A 92.647 68 5 0 253 320 557984856 557984923 1.030000e-16 99.0
20 TraesCS4A01G077800 chr2A 92.500 120 7 2 1181 1299 120719739 120719857 2.160000e-38 171.0
21 TraesCS4A01G077800 chr2A 100.000 43 0 0 1335 1377 39971404 39971446 3.740000e-11 80.5
22 TraesCS4A01G077800 chr5D 94.495 109 6 0 1189 1297 560426192 560426084 7.760000e-38 169.0
23 TraesCS4A01G077800 chr5D 95.312 64 3 0 179 242 418946192 418946129 7.980000e-18 102.0
24 TraesCS4A01G077800 chr3A 94.495 109 6 0 1189 1297 517028744 517028636 7.760000e-38 169.0
25 TraesCS4A01G077800 chr1A 94.444 108 6 0 1191 1298 499985356 499985463 2.790000e-37 167.0
26 TraesCS4A01G077800 chr1A 93.694 111 7 0 1188 1298 587607300 587607410 2.790000e-37 167.0
27 TraesCS4A01G077800 chr1A 93.694 111 7 0 1188 1298 587610182 587610292 2.790000e-37 167.0
28 TraesCS4A01G077800 chr1A 90.278 72 6 1 171 242 287694042 287693972 4.800000e-15 93.5
29 TraesCS4A01G077800 chr1A 89.796 49 5 0 1337 1385 272648073 272648121 3.760000e-06 63.9
30 TraesCS4A01G077800 chr3D 93.636 110 7 0 1190 1299 571704748 571704857 1.000000e-36 165.0
31 TraesCS4A01G077800 chr3D 91.304 69 6 0 174 242 151444893 151444961 1.340000e-15 95.3
32 TraesCS4A01G077800 chr3D 93.651 63 4 0 256 318 264003532 264003594 1.340000e-15 95.3
33 TraesCS4A01G077800 chr3D 97.561 41 1 0 1337 1377 606566317 606566357 2.250000e-08 71.3
34 TraesCS4A01G077800 chr3D 97.561 41 1 0 1337 1377 606595332 606595372 2.250000e-08 71.3
35 TraesCS4A01G077800 chr2D 91.597 119 10 0 1182 1300 87030968 87031086 1.000000e-36 165.0
36 TraesCS4A01G077800 chr2D 98.113 53 0 1 1337 1389 601712113 601712164 1.730000e-14 91.6
37 TraesCS4A01G077800 chr3B 91.667 72 5 1 171 242 538816112 538816042 1.030000e-16 99.0
38 TraesCS4A01G077800 chr1B 93.750 64 4 0 179 242 562894165 562894102 3.710000e-16 97.1
39 TraesCS4A01G077800 chr1B 91.304 69 6 0 252 320 430157906 430157974 1.340000e-15 95.3
40 TraesCS4A01G077800 chr7A 90.411 73 5 2 171 242 648845254 648845183 1.340000e-15 95.3
41 TraesCS4A01G077800 chr7A 97.561 41 1 0 1337 1377 558749130 558749170 2.250000e-08 71.3
42 TraesCS4A01G077800 chr6D 91.176 68 6 0 252 319 266648439 266648506 4.800000e-15 93.5
43 TraesCS4A01G077800 chr6B 90.141 71 6 1 173 242 623180260 623180330 1.730000e-14 91.6
44 TraesCS4A01G077800 chr2B 95.918 49 1 1 1337 1385 32871525 32871572 1.340000e-10 78.7
45 TraesCS4A01G077800 chr7D 93.617 47 2 1 1337 1383 451616839 451616884 8.090000e-08 69.4
46 TraesCS4A01G077800 chrUn 93.023 43 3 0 1343 1385 325927217 325927175 3.760000e-06 63.9


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 TraesCS4A01G077800 chr4A 76940290 76944797 4507 True 8325.0 8325 100.0000 1 4508 1 chr4A.!!$R1 4507
1 TraesCS4A01G077800 chr4A 595417817 595418759 942 False 403.0 403 75.0790 2227 3148 1 chr4A.!!$F1 921
2 TraesCS4A01G077800 chr4D 395380629 395385200 4571 True 1162.0 3698 90.7602 1 4508 5 chr4D.!!$R3 4507
3 TraesCS4A01G077800 chr4D 7897617 7898553 936 True 375.0 375 74.5260 2227 3148 1 chr4D.!!$R1 921
4 TraesCS4A01G077800 chr4B 486282815 486287946 5131 True 1093.8 1760 92.3572 3 4508 5 chr4B.!!$R1 4505
5 TraesCS4A01G077800 chr4B 14266422 14267367 945 False 407.0 407 75.1570 2227 3148 1 chr4B.!!$F1 921

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
156 157 0.038455 CAAACCGTAATCCACCCCCA 59.962 55.0 0.00 0.0 0.00 4.96 F
161 162 0.464452 CGTAATCCACCCCCAGAGAC 59.536 60.0 0.00 0.0 0.00 3.36 F
877 1020 0.536260 AGAGCATTGCGAGAGAAGCT 59.464 50.0 2.38 0.0 35.28 3.74 F
1207 1680 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.0 0.00 0.0 0.00 4.30 F
1798 2344 0.318107 AAGCAAACTCACATGCACGC 60.318 50.0 0.00 0.0 44.95 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 1442 0.463295 CCTGAAGATCACAGCGGCAT 60.463 55.0 1.45 0.00 34.47 4.40 R
1098 1512 0.830444 TACTGAACGGCACTGGGAGT 60.830 55.0 0.00 0.00 0.00 3.85 R
1809 2359 0.949105 AAGTCACGTCGTGCCAATCC 60.949 55.0 20.56 4.08 32.98 3.01 R
2016 2566 1.093159 ACTTCTAGGTAGCGACGGTG 58.907 55.0 10.33 0.00 0.00 4.94 R
3644 4423 0.990374 AGAGAGATGCAAGGTGGCTT 59.010 50.0 0.00 0.00 34.04 4.35 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
20 21 1.406539 CCTCAAGGCATTTCCATTCCG 59.593 52.381 0.00 0.00 37.29 4.30
22 23 2.754552 CTCAAGGCATTTCCATTCCGAA 59.245 45.455 0.00 0.00 37.29 4.30
27 28 2.223180 GGCATTTCCATTCCGAACGTAC 60.223 50.000 0.00 0.00 34.01 3.67
84 85 1.302832 CCATGCCTCTATTCCCGCC 60.303 63.158 0.00 0.00 0.00 6.13
156 157 0.038455 CAAACCGTAATCCACCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
161 162 0.464452 CGTAATCCACCCCCAGAGAC 59.536 60.000 0.00 0.00 0.00 3.36
162 163 0.837940 GTAATCCACCCCCAGAGACC 59.162 60.000 0.00 0.00 0.00 3.85
164 165 4.715130 TCCACCCCCAGAGACCGG 62.715 72.222 0.00 0.00 0.00 5.28
182 266 6.127793 AGACCGGAGTAGTATGTTGATACTT 58.872 40.000 9.46 0.00 41.86 2.24
184 268 5.889853 ACCGGAGTAGTATGTTGATACTTCA 59.110 40.000 9.46 0.00 41.86 3.02
187 271 6.363626 CGGAGTAGTATGTTGATACTTCATGC 59.636 42.308 0.00 0.00 41.86 4.06
196 280 3.950397 TGATACTTCATGCGGTCCTTTT 58.050 40.909 0.00 0.00 0.00 2.27
342 434 1.018752 TATCACGCACAGCACGCATT 61.019 50.000 0.00 0.00 0.00 3.56
404 497 3.222603 AGATTTGGGACGGCCAAATATC 58.777 45.455 11.00 10.44 44.60 1.63
416 509 5.758296 ACGGCCAAATATCACTAGTATGTTG 59.242 40.000 2.24 0.00 0.00 3.33
417 510 5.989168 CGGCCAAATATCACTAGTATGTTGA 59.011 40.000 2.24 0.00 0.00 3.18
418 511 6.650807 CGGCCAAATATCACTAGTATGTTGAT 59.349 38.462 2.24 0.00 0.00 2.57
419 512 7.173218 CGGCCAAATATCACTAGTATGTTGATT 59.827 37.037 2.24 0.00 0.00 2.57
497 590 2.727544 GTGGCAGGCGCTTTTCAA 59.272 55.556 7.64 0.00 38.60 2.69
540 633 3.757184 CATGTTGAAAAATCGATCGCCA 58.243 40.909 11.09 0.00 0.00 5.69
559 652 3.084786 CCACCCTTTTCATCTTGACCTC 58.915 50.000 0.00 0.00 0.00 3.85
681 774 2.582226 CGGCGTCGATGCTGCTTA 60.582 61.111 27.56 0.00 39.00 3.09
682 775 2.164663 CGGCGTCGATGCTGCTTAA 61.165 57.895 27.56 0.00 39.00 1.85
683 776 1.638467 GGCGTCGATGCTGCTTAAG 59.362 57.895 27.56 0.00 34.52 1.85
684 777 0.806102 GGCGTCGATGCTGCTTAAGA 60.806 55.000 27.56 0.00 34.52 2.10
685 778 0.574454 GCGTCGATGCTGCTTAAGAG 59.426 55.000 22.31 2.23 0.00 2.85
686 779 1.914634 CGTCGATGCTGCTTAAGAGT 58.085 50.000 6.67 0.00 0.00 3.24
687 780 1.585668 CGTCGATGCTGCTTAAGAGTG 59.414 52.381 6.67 0.00 0.00 3.51
718 818 4.202524 ACACAATTGCTAGGAACCAAGGTA 60.203 41.667 5.05 0.00 0.00 3.08
722 822 6.325286 ACAATTGCTAGGAACCAAGGTAAAAA 59.675 34.615 5.05 0.00 0.00 1.94
726 826 5.222254 TGCTAGGAACCAAGGTAAAAATCCT 60.222 40.000 12.66 12.66 39.13 3.24
813 922 3.525537 CAGCTAAATTCTGCGAGGAGAA 58.474 45.455 9.38 9.38 36.41 2.87
877 1020 0.536260 AGAGCATTGCGAGAGAAGCT 59.464 50.000 2.38 0.00 35.28 3.74
915 1058 3.362706 TCGGGTGGCTATATATCTGTCC 58.637 50.000 0.00 0.00 0.00 4.02
917 1060 3.381908 CGGGTGGCTATATATCTGTCCTC 59.618 52.174 0.00 0.00 0.00 3.71
918 1061 4.615513 GGGTGGCTATATATCTGTCCTCT 58.384 47.826 0.00 0.00 0.00 3.69
919 1062 5.026790 GGGTGGCTATATATCTGTCCTCTT 58.973 45.833 0.00 0.00 0.00 2.85
923 1066 5.420421 TGGCTATATATCTGTCCTCTTCTGC 59.580 44.000 0.00 0.00 0.00 4.26
924 1067 5.163457 GGCTATATATCTGTCCTCTTCTGCC 60.163 48.000 0.00 0.00 0.00 4.85
925 1068 5.656416 GCTATATATCTGTCCTCTTCTGCCT 59.344 44.000 0.00 0.00 0.00 4.75
926 1069 6.183360 GCTATATATCTGTCCTCTTCTGCCTC 60.183 46.154 0.00 0.00 0.00 4.70
927 1070 2.548464 ATCTGTCCTCTTCTGCCTCT 57.452 50.000 0.00 0.00 0.00 3.69
981 1395 0.664166 CGGCATCAAAGTGGTTGCAC 60.664 55.000 0.00 0.00 37.13 4.57
1028 1442 1.203441 AGAAGGTGGCAGCTGGATGA 61.203 55.000 21.35 0.00 0.00 2.92
1098 1512 2.170166 CAATTGGCAAGTAAGCTCCCA 58.830 47.619 5.96 0.00 34.17 4.37
1123 1537 2.159707 CCAGTGCCGTTCAGTAATTTCG 60.160 50.000 0.00 0.00 0.00 3.46
1124 1538 1.463444 AGTGCCGTTCAGTAATTTCGC 59.537 47.619 0.00 0.00 0.00 4.70
1125 1539 1.463444 GTGCCGTTCAGTAATTTCGCT 59.537 47.619 0.00 0.00 0.00 4.93
1127 1541 1.730064 GCCGTTCAGTAATTTCGCTCA 59.270 47.619 0.00 0.00 0.00 4.26
1128 1542 2.222819 GCCGTTCAGTAATTTCGCTCAG 60.223 50.000 0.00 0.00 0.00 3.35
1130 1544 3.250744 CGTTCAGTAATTTCGCTCAGGA 58.749 45.455 0.00 0.00 0.00 3.86
1131 1545 3.304559 CGTTCAGTAATTTCGCTCAGGAG 59.695 47.826 0.00 0.00 0.00 3.69
1146 1619 5.124138 CGCTCAGGAGACTTCTTACTTAAGA 59.876 44.000 10.09 0.00 40.21 2.10
1147 1620 6.349445 CGCTCAGGAGACTTCTTACTTAAGAA 60.349 42.308 10.09 10.35 46.70 2.52
1192 1665 5.424121 TGCTTGCTCTTTTTGAGAACTAC 57.576 39.130 0.00 0.00 45.39 2.73
1194 1667 5.237344 TGCTTGCTCTTTTTGAGAACTACTC 59.763 40.000 0.00 0.00 45.39 2.59
1195 1668 5.334491 GCTTGCTCTTTTTGAGAACTACTCC 60.334 44.000 0.00 0.00 45.39 3.85
1196 1669 4.642429 TGCTCTTTTTGAGAACTACTCCC 58.358 43.478 0.00 0.00 45.39 4.30
1197 1670 4.348168 TGCTCTTTTTGAGAACTACTCCCT 59.652 41.667 0.00 0.00 45.39 4.20
1198 1671 4.932799 GCTCTTTTTGAGAACTACTCCCTC 59.067 45.833 0.00 0.00 45.39 4.30
1200 1673 3.955650 TTTTGAGAACTACTCCCTCCG 57.044 47.619 0.00 0.00 44.34 4.63
1201 1674 2.599408 TTGAGAACTACTCCCTCCGT 57.401 50.000 0.00 0.00 44.34 4.69
1202 1675 2.599408 TGAGAACTACTCCCTCCGTT 57.401 50.000 0.00 0.00 44.34 4.44
1203 1676 2.444421 TGAGAACTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 44.34 3.95
1204 1677 1.750206 GAGAACTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 39.53 3.62
1205 1678 0.455005 GAACTACTCCCTCCGTTCCG 59.545 60.000 0.00 0.00 31.89 4.30
1207 1680 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
1208 1681 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
1209 1682 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
1210 1683 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1211 1684 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1212 1685 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1213 1686 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1214 1687 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1216 1689 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1217 1690 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1218 1691 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
1220 1693 3.919804 CCGTTCCGAATTACTTGTCGTAA 59.080 43.478 0.00 0.00 41.97 3.18
1222 1695 4.618489 CGTTCCGAATTACTTGTCGTAAGT 59.382 41.667 11.39 11.39 41.13 2.24
1223 1696 5.794945 CGTTCCGAATTACTTGTCGTAAGTA 59.205 40.000 9.78 9.78 41.13 2.24
1224 1697 6.470235 CGTTCCGAATTACTTGTCGTAAGTAT 59.530 38.462 13.13 3.29 41.13 2.12
1226 1699 6.267817 TCCGAATTACTTGTCGTAAGTATGG 58.732 40.000 13.13 12.45 41.13 2.74
1227 1700 6.095300 TCCGAATTACTTGTCGTAAGTATGGA 59.905 38.462 13.13 13.82 41.13 3.41
1229 1702 7.096189 CCGAATTACTTGTCGTAAGTATGGATG 60.096 40.741 13.13 5.92 41.13 3.51
1231 1704 9.740239 GAATTACTTGTCGTAAGTATGGATGTA 57.260 33.333 13.13 1.59 41.13 2.29
1235 1708 8.687292 ACTTGTCGTAAGTATGGATGTATCTA 57.313 34.615 6.13 0.00 39.48 1.98
1239 1712 9.908152 TGTCGTAAGTATGGATGTATCTAAATG 57.092 33.333 0.00 0.00 39.48 2.32
1287 1760 9.893305 AATTTCTAAGACAAGTAATTTGGAACG 57.107 29.630 0.00 0.00 41.25 3.95
1288 1761 7.429636 TTCTAAGACAAGTAATTTGGAACGG 57.570 36.000 0.00 0.00 41.25 4.44
1289 1762 6.761312 TCTAAGACAAGTAATTTGGAACGGA 58.239 36.000 0.00 0.00 41.25 4.69
1290 1763 5.941948 AAGACAAGTAATTTGGAACGGAG 57.058 39.130 0.00 0.00 41.25 4.63
1291 1764 4.324267 AGACAAGTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 41.25 4.30
1293 1766 4.721132 ACAAGTAATTTGGAACGGAGGAA 58.279 39.130 0.00 0.00 41.25 3.36
1294 1767 4.760204 ACAAGTAATTTGGAACGGAGGAAG 59.240 41.667 0.00 0.00 41.25 3.46
1295 1768 4.635699 AGTAATTTGGAACGGAGGAAGT 57.364 40.909 0.00 0.00 0.00 3.01
1296 1769 5.750352 AGTAATTTGGAACGGAGGAAGTA 57.250 39.130 0.00 0.00 0.00 2.24
1297 1770 6.309389 AGTAATTTGGAACGGAGGAAGTAT 57.691 37.500 0.00 0.00 0.00 2.12
1298 1771 6.718294 AGTAATTTGGAACGGAGGAAGTATT 58.282 36.000 0.00 0.00 0.00 1.89
1300 1773 5.897377 ATTTGGAACGGAGGAAGTATTTG 57.103 39.130 0.00 0.00 0.00 2.32
1305 1778 5.009210 TGGAACGGAGGAAGTATTTGTTTTG 59.991 40.000 0.00 0.00 0.00 2.44
1309 1782 4.261825 CGGAGGAAGTATTTGTTTTGGCAA 60.262 41.667 0.00 0.00 0.00 4.52
1310 1783 5.606505 GGAGGAAGTATTTGTTTTGGCAAA 58.393 37.500 8.93 8.93 41.77 3.68
1318 1791 7.702386 AGTATTTGTTTTGGCAAATTTGGTTC 58.298 30.769 19.47 3.20 43.97 3.62
1321 1794 7.687941 TTTGTTTTGGCAAATTTGGTTCTAA 57.312 28.000 19.47 4.85 33.91 2.10
1322 1839 7.687941 TTGTTTTGGCAAATTTGGTTCTAAA 57.312 28.000 19.47 10.24 0.00 1.85
1323 1840 7.313951 TGTTTTGGCAAATTTGGTTCTAAAG 57.686 32.000 19.47 0.00 0.00 1.85
1327 1844 3.428534 GGCAAATTTGGTTCTAAAGTGCG 59.571 43.478 19.47 0.00 36.30 5.34
1332 1849 7.518211 GCAAATTTGGTTCTAAAGTGCGAAAAT 60.518 33.333 19.47 0.00 30.15 1.82
1333 1850 8.334632 CAAATTTGGTTCTAAAGTGCGAAAATT 58.665 29.630 10.49 0.00 0.00 1.82
1341 1858 8.706035 GTTCTAAAGTGCGAAAATTAGTAGTGA 58.294 33.333 0.00 0.00 0.00 3.41
1343 1860 9.084164 TCTAAAGTGCGAAAATTAGTAGTGATC 57.916 33.333 0.00 0.00 0.00 2.92
1345 1862 8.997621 AAAGTGCGAAAATTAGTAGTGATCTA 57.002 30.769 0.00 0.00 0.00 1.98
1346 1863 8.997621 AAGTGCGAAAATTAGTAGTGATCTAA 57.002 30.769 0.00 0.00 32.96 2.10
1349 1866 7.839837 GTGCGAAAATTAGTAGTGATCTAAACG 59.160 37.037 0.00 0.00 32.32 3.60
1351 1868 7.254017 GCGAAAATTAGTAGTGATCTAAACGCT 60.254 37.037 0.00 0.00 37.14 5.07
1352 1869 8.592998 CGAAAATTAGTAGTGATCTAAACGCTT 58.407 33.333 0.00 0.00 32.32 4.68
1357 1874 9.865321 ATTAGTAGTGATCTAAACGCTTTTACA 57.135 29.630 0.00 0.00 32.32 2.41
1358 1875 9.865321 TTAGTAGTGATCTAAACGCTTTTACAT 57.135 29.630 0.00 0.00 0.00 2.29
1359 1876 8.773404 AGTAGTGATCTAAACGCTTTTACATT 57.227 30.769 0.00 0.00 0.00 2.71
1360 1877 9.865321 AGTAGTGATCTAAACGCTTTTACATTA 57.135 29.630 0.00 0.00 0.00 1.90
1362 1879 8.773404 AGTGATCTAAACGCTTTTACATTAGT 57.227 30.769 0.00 0.00 0.00 2.24
1363 1880 9.216117 AGTGATCTAAACGCTTTTACATTAGTT 57.784 29.630 0.00 0.00 0.00 2.24
1364 1881 9.821662 GTGATCTAAACGCTTTTACATTAGTTT 57.178 29.630 0.00 0.00 36.11 2.66
1367 1884 9.962759 ATCTAAACGCTTTTACATTAGTTTACG 57.037 29.630 0.00 0.00 34.29 3.18
1368 1885 8.434661 TCTAAACGCTTTTACATTAGTTTACGG 58.565 33.333 0.00 0.00 34.29 4.02
1369 1886 6.783892 AACGCTTTTACATTAGTTTACGGA 57.216 33.333 0.00 0.00 0.00 4.69
1370 1887 6.399204 ACGCTTTTACATTAGTTTACGGAG 57.601 37.500 0.00 0.00 0.00 4.63
1371 1888 5.349543 ACGCTTTTACATTAGTTTACGGAGG 59.650 40.000 0.00 0.00 0.00 4.30
1372 1889 5.220529 CGCTTTTACATTAGTTTACGGAGGG 60.221 44.000 0.00 0.00 0.00 4.30
1373 1890 5.876460 GCTTTTACATTAGTTTACGGAGGGA 59.124 40.000 0.00 0.00 0.00 4.20
1374 1891 6.036844 GCTTTTACATTAGTTTACGGAGGGAG 59.963 42.308 0.00 0.00 0.00 4.30
1380 1897 7.065504 ACATTAGTTTACGGAGGGAGTACTAT 58.934 38.462 0.00 0.00 0.00 2.12
1382 1899 9.240734 CATTAGTTTACGGAGGGAGTACTATAT 57.759 37.037 0.00 0.00 0.00 0.86
1394 1911 5.163343 GGGAGTACTATATGTGGCAAGTCAA 60.163 44.000 0.00 0.00 0.00 3.18
1422 1942 2.706890 TCTTCAGGTTACGGAAATGGC 58.293 47.619 0.00 0.00 30.49 4.40
1424 1944 0.391927 TCAGGTTACGGAAATGGCGG 60.392 55.000 0.00 0.00 0.00 6.13
1448 1972 6.463897 GGTGGCATATGCTAACCTAAAGTAGA 60.464 42.308 30.18 0.00 41.38 2.59
1503 2034 4.344104 TCAGATCAAATGAACTTTCCCCC 58.656 43.478 0.00 0.00 0.00 5.40
1521 2052 3.528532 CCCCACGGTAGAGAAATACAAC 58.471 50.000 0.00 0.00 0.00 3.32
1522 2053 3.055675 CCCCACGGTAGAGAAATACAACA 60.056 47.826 0.00 0.00 0.00 3.33
1556 2097 2.751806 CTGAAGTTCCTCCTTGAATGCC 59.248 50.000 0.00 0.00 0.00 4.40
1569 2110 4.390909 CCTTGAATGCCATTTTTCTTCTGC 59.609 41.667 0.00 0.00 0.00 4.26
1574 2115 1.402852 GCCATTTTTCTTCTGCCGTCC 60.403 52.381 0.00 0.00 0.00 4.79
1586 2132 4.422073 TCTGCCGTCCTGATCATATTTT 57.578 40.909 0.00 0.00 0.00 1.82
1623 2169 3.555966 AGAAAGGAGTCACTTTTGGGTG 58.444 45.455 7.69 0.00 40.55 4.61
1625 2171 4.165372 AGAAAGGAGTCACTTTTGGGTGTA 59.835 41.667 7.69 0.00 40.55 2.90
1644 2190 2.820059 ACTGTCAAAGACGATGCTCA 57.180 45.000 0.00 0.00 34.95 4.26
1663 2209 5.009911 TGCTCAATAAAAATCATGATCCCGG 59.990 40.000 9.06 0.00 0.00 5.73
1706 2252 0.884704 ACGGCACCTTAACTGCACTG 60.885 55.000 3.40 0.00 36.27 3.66
1716 2262 4.034510 CCTTAACTGCACTGCATTAGTAGC 59.965 45.833 3.64 0.00 38.13 3.58
1764 2310 6.238049 GCTGATGTGCTGAAAGTAAGTGATAG 60.238 42.308 0.00 0.00 35.30 2.08
1798 2344 0.318107 AAGCAAACTCACATGCACGC 60.318 50.000 0.00 0.00 44.95 5.34
1809 2359 2.911484 ATGCACGCTGTGTTGGCTG 61.911 57.895 9.76 0.00 35.75 4.85
1881 2431 1.653151 GGTTGGTCACGGAATCTAGC 58.347 55.000 0.00 0.00 0.00 3.42
1883 2433 0.459585 TTGGTCACGGAATCTAGCGC 60.460 55.000 0.00 0.00 0.00 5.92
1899 2449 3.004752 AGCGCTGGGAGTATCAAATTT 57.995 42.857 10.39 0.00 36.25 1.82
1959 2509 2.075837 GGTCCAGCACCTAAACCCT 58.924 57.895 0.00 0.00 42.84 4.34
1961 2511 0.322546 GTCCAGCACCTAAACCCTGG 60.323 60.000 0.00 0.00 44.84 4.45
2032 2582 1.377594 TGCACCGTCGCTACCTAGA 60.378 57.895 0.00 0.00 0.00 2.43
2034 2584 0.248539 GCACCGTCGCTACCTAGAAG 60.249 60.000 0.00 0.00 0.00 2.85
2035 2585 1.093159 CACCGTCGCTACCTAGAAGT 58.907 55.000 0.00 0.00 0.00 3.01
2036 2586 2.283298 CACCGTCGCTACCTAGAAGTA 58.717 52.381 0.00 0.00 0.00 2.24
2037 2587 2.287373 CACCGTCGCTACCTAGAAGTAG 59.713 54.545 0.00 0.00 42.25 2.57
2146 2704 4.272991 TGCATTCCAAAAGTTTGCATGTTC 59.727 37.500 12.29 2.86 38.32 3.18
2147 2705 4.512571 GCATTCCAAAAGTTTGCATGTTCT 59.487 37.500 12.29 0.00 36.86 3.01
2156 2714 5.869753 AGTTTGCATGTTCTGACATACTC 57.130 39.130 0.00 0.00 44.55 2.59
2208 2864 3.181491 CCACTTGGACGTGTTCAATGTTT 60.181 43.478 0.00 0.00 37.39 2.83
2487 3152 3.209812 TCCGTCTCCGCCATCTCG 61.210 66.667 0.00 0.00 0.00 4.04
3424 4202 4.329545 TCCCGGGAACAGCAGCAC 62.330 66.667 24.50 0.00 0.00 4.40
3509 4287 1.207329 GGTGGCCGAAAGTAGATGACT 59.793 52.381 0.00 0.00 41.56 3.41
3518 4296 5.632764 CCGAAAGTAGATGACTGCATAGATG 59.367 44.000 0.00 0.00 38.87 2.90
3562 4340 1.464734 TGACTTTTGGAACGCAACCA 58.535 45.000 0.00 0.00 35.47 3.67
3623 4402 2.706339 AAATGGCCAAACTTGCACAA 57.294 40.000 10.96 0.00 0.00 3.33
3675 4454 6.461788 CCTTGCATCTCTCTACCCTTAGTTAC 60.462 46.154 0.00 0.00 0.00 2.50
3806 4669 2.895062 CTTCAGCAAAACGCAAAATGC 58.105 42.857 0.00 0.00 46.13 3.56
3827 4690 1.571460 CAGCCAGCAACAAGACGTC 59.429 57.895 7.70 7.70 0.00 4.34
3889 4754 0.865769 ACGATCGTGCTGTTTTGGTC 59.134 50.000 22.06 0.00 0.00 4.02
3899 4764 4.072131 TGCTGTTTTGGTCACCTATCTTC 58.928 43.478 0.00 0.00 0.00 2.87
3900 4765 3.440522 GCTGTTTTGGTCACCTATCTTCC 59.559 47.826 0.00 0.00 0.00 3.46
3924 4789 3.829066 GCAATTATGCGCACATTCTTG 57.171 42.857 14.90 13.48 43.83 3.02
3926 4791 4.350346 GCAATTATGCGCACATTCTTGTA 58.650 39.130 14.90 0.00 43.83 2.41
3927 4792 4.797868 GCAATTATGCGCACATTCTTGTAA 59.202 37.500 14.90 5.08 43.83 2.41
3971 4836 5.330295 GCATCATCATGACTCAAGTTTGTC 58.670 41.667 0.00 0.00 30.57 3.18
3975 4840 4.163441 TCATGACTCAAGTTTGTCCCAA 57.837 40.909 0.00 0.00 32.67 4.12
4304 5170 3.072184 ACTCATCCCTTAGCAGGCTAATG 59.928 47.826 13.62 10.96 39.20 1.90
4358 5224 6.996282 TGAAAGAAGACGGTTAGGAAGAAAAT 59.004 34.615 0.00 0.00 0.00 1.82
4451 5317 3.633986 ACAGCTTCTCAACCTTTTCCTTG 59.366 43.478 0.00 0.00 0.00 3.61
4452 5318 3.633986 CAGCTTCTCAACCTTTTCCTTGT 59.366 43.478 0.00 0.00 0.00 3.16
4493 5359 8.414778 AGAACTCTACTGGAATAAATTACTCGG 58.585 37.037 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.763465 ACAATAATAAAATTTGAGTACGTTCGG 57.237 29.630 0.00 0.00 0.00 4.30
156 157 4.232188 TCAACATACTACTCCGGTCTCT 57.768 45.455 0.00 0.00 0.00 3.10
161 162 6.387041 TGAAGTATCAACATACTACTCCGG 57.613 41.667 0.00 0.00 43.94 5.14
162 163 6.363626 GCATGAAGTATCAACATACTACTCCG 59.636 42.308 0.00 0.00 43.94 4.63
164 165 6.363626 CCGCATGAAGTATCAACATACTACTC 59.636 42.308 0.00 0.00 43.94 2.59
182 266 3.334691 CAGACTAAAAAGGACCGCATGA 58.665 45.455 0.00 0.00 0.00 3.07
184 268 2.084546 GCAGACTAAAAAGGACCGCAT 58.915 47.619 0.00 0.00 0.00 4.73
187 271 6.761714 ACTTATATGCAGACTAAAAAGGACCG 59.238 38.462 0.00 0.00 0.00 4.79
305 397 6.513230 GCGTGATAGTGGCAATATTGATTTGA 60.513 38.462 19.73 1.24 0.00 2.69
342 434 1.270094 ACTGACGTCAAATTCCTCGCA 60.270 47.619 20.49 0.00 0.00 5.10
404 497 9.933723 TGGATATCATCAATCAACATACTAGTG 57.066 33.333 5.39 0.00 0.00 2.74
416 509 5.178061 TGGCGTGTATGGATATCATCAATC 58.822 41.667 4.83 0.00 37.30 2.67
417 510 5.164620 TGGCGTGTATGGATATCATCAAT 57.835 39.130 4.83 0.00 37.30 2.57
418 511 4.615588 TGGCGTGTATGGATATCATCAA 57.384 40.909 4.83 0.00 37.30 2.57
419 512 4.506758 CATGGCGTGTATGGATATCATCA 58.493 43.478 4.83 0.00 37.30 3.07
423 516 2.698803 TGCATGGCGTGTATGGATATC 58.301 47.619 8.75 0.00 0.00 1.63
497 590 0.851469 AGGGAGAGCATGATGGCAAT 59.149 50.000 0.00 0.00 35.83 3.56
540 633 2.372172 ACGAGGTCAAGATGAAAAGGGT 59.628 45.455 0.00 0.00 0.00 4.34
559 652 2.138320 CAATCATCATCCCCTTCGACG 58.862 52.381 0.00 0.00 0.00 5.12
647 740 2.723746 GGATTTGCGCGATGGCAT 59.276 55.556 12.10 0.00 43.52 4.40
648 741 3.875039 CGGATTTGCGCGATGGCA 61.875 61.111 12.10 0.00 42.12 4.92
669 762 3.193479 TCTTCACTCTTAAGCAGCATCGA 59.807 43.478 0.00 0.00 0.00 3.59
681 774 4.201950 GCAATTGTGTGTGTCTTCACTCTT 60.202 41.667 7.40 0.00 44.14 2.85
682 775 3.313526 GCAATTGTGTGTGTCTTCACTCT 59.686 43.478 7.40 0.00 44.14 3.24
683 776 3.313526 AGCAATTGTGTGTGTCTTCACTC 59.686 43.478 7.40 0.00 44.14 3.51
684 777 3.282021 AGCAATTGTGTGTGTCTTCACT 58.718 40.909 7.40 0.00 44.14 3.41
685 778 3.698029 AGCAATTGTGTGTGTCTTCAC 57.302 42.857 7.40 0.00 44.08 3.18
686 779 3.814842 CCTAGCAATTGTGTGTGTCTTCA 59.185 43.478 7.40 0.00 0.00 3.02
687 780 4.065088 TCCTAGCAATTGTGTGTGTCTTC 58.935 43.478 7.40 0.00 0.00 2.87
718 818 3.070878 ACGGGATTTTGCACAGGATTTTT 59.929 39.130 0.00 0.00 0.00 1.94
722 822 1.176527 CACGGGATTTTGCACAGGAT 58.823 50.000 0.00 0.00 0.00 3.24
726 826 2.569354 GGCCACGGGATTTTGCACA 61.569 57.895 0.00 0.00 0.00 4.57
807 916 2.435059 GCGGCGCTTTCTTCTCCT 60.435 61.111 26.86 0.00 0.00 3.69
808 917 3.854459 CGCGGCGCTTTCTTCTCC 61.854 66.667 30.54 0.00 0.00 3.71
895 1038 3.366396 AGGACAGATATATAGCCACCCG 58.634 50.000 0.00 0.00 0.00 5.28
923 1066 3.126831 GACGACTATGGAAATGCAGAGG 58.873 50.000 1.73 0.00 0.00 3.69
924 1067 3.126831 GGACGACTATGGAAATGCAGAG 58.873 50.000 0.00 0.00 0.00 3.35
925 1068 2.499693 TGGACGACTATGGAAATGCAGA 59.500 45.455 0.00 0.00 0.00 4.26
926 1069 2.905075 TGGACGACTATGGAAATGCAG 58.095 47.619 0.00 0.00 0.00 4.41
927 1070 3.270027 CTTGGACGACTATGGAAATGCA 58.730 45.455 0.00 0.00 0.00 3.96
981 1395 0.746923 TGCTATGCTCTGCTGCCTTG 60.747 55.000 0.00 0.00 0.00 3.61
989 1403 4.815489 CCCCCATGCTATGCTCTG 57.185 61.111 0.00 0.00 0.00 3.35
1028 1442 0.463295 CCTGAAGATCACAGCGGCAT 60.463 55.000 1.45 0.00 34.47 4.40
1098 1512 0.830444 TACTGAACGGCACTGGGAGT 60.830 55.000 0.00 0.00 0.00 3.85
1123 1537 6.518208 TCTTAAGTAAGAAGTCTCCTGAGC 57.482 41.667 1.63 0.00 39.22 4.26
1146 1619 3.205338 TGCTGAACATATGCGCATACTT 58.795 40.909 31.17 23.64 0.00 2.24
1147 1620 2.837498 TGCTGAACATATGCGCATACT 58.163 42.857 31.17 18.68 0.00 2.12
1198 1671 3.500982 TACGACAAGTAATTCGGAACGG 58.499 45.455 0.00 0.00 42.34 4.44
1200 1673 7.253883 CCATACTTACGACAAGTAATTCGGAAC 60.254 40.741 15.02 0.00 43.64 3.62
1201 1674 6.753279 CCATACTTACGACAAGTAATTCGGAA 59.247 38.462 15.02 0.00 43.64 4.30
1202 1675 6.095300 TCCATACTTACGACAAGTAATTCGGA 59.905 38.462 15.02 14.52 43.64 4.55
1203 1676 6.267817 TCCATACTTACGACAAGTAATTCGG 58.732 40.000 15.02 13.14 43.64 4.30
1204 1677 7.434307 ACATCCATACTTACGACAAGTAATTCG 59.566 37.037 15.02 0.00 43.64 3.34
1205 1678 8.644318 ACATCCATACTTACGACAAGTAATTC 57.356 34.615 15.02 0.00 43.64 2.17
1207 1680 9.909644 GATACATCCATACTTACGACAAGTAAT 57.090 33.333 15.02 5.84 43.64 1.89
1208 1681 9.128404 AGATACATCCATACTTACGACAAGTAA 57.872 33.333 15.02 3.84 42.56 2.24
1209 1682 8.687292 AGATACATCCATACTTACGACAAGTA 57.313 34.615 13.91 13.91 37.18 2.24
1210 1683 7.584122 AGATACATCCATACTTACGACAAGT 57.416 36.000 11.00 11.00 0.00 3.16
1211 1684 9.961265 TTTAGATACATCCATACTTACGACAAG 57.039 33.333 0.00 0.00 0.00 3.16
1213 1686 9.908152 CATTTAGATACATCCATACTTACGACA 57.092 33.333 0.00 0.00 0.00 4.35
1214 1687 9.909644 ACATTTAGATACATCCATACTTACGAC 57.090 33.333 0.00 0.00 0.00 4.34
1261 1734 9.893305 CGTTCCAAATTACTTGTCTTAGAAATT 57.107 29.630 0.00 0.00 32.65 1.82
1263 1736 7.716123 TCCGTTCCAAATTACTTGTCTTAGAAA 59.284 33.333 0.00 0.00 32.65 2.52
1264 1737 7.218614 TCCGTTCCAAATTACTTGTCTTAGAA 58.781 34.615 0.00 0.00 32.65 2.10
1266 1739 6.092259 CCTCCGTTCCAAATTACTTGTCTTAG 59.908 42.308 0.00 0.00 32.65 2.18
1267 1740 5.935789 CCTCCGTTCCAAATTACTTGTCTTA 59.064 40.000 0.00 0.00 32.65 2.10
1268 1741 4.760204 CCTCCGTTCCAAATTACTTGTCTT 59.240 41.667 0.00 0.00 32.65 3.01
1269 1742 4.041198 TCCTCCGTTCCAAATTACTTGTCT 59.959 41.667 0.00 0.00 32.65 3.41
1270 1743 4.320870 TCCTCCGTTCCAAATTACTTGTC 58.679 43.478 0.00 0.00 32.65 3.18
1272 1745 4.760204 ACTTCCTCCGTTCCAAATTACTTG 59.240 41.667 0.00 0.00 34.52 3.16
1273 1746 4.981812 ACTTCCTCCGTTCCAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
1274 1747 4.635699 ACTTCCTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1275 1748 6.997239 AATACTTCCTCCGTTCCAAATTAC 57.003 37.500 0.00 0.00 0.00 1.89
1276 1749 6.943718 ACAAATACTTCCTCCGTTCCAAATTA 59.056 34.615 0.00 0.00 0.00 1.40
1277 1750 5.773176 ACAAATACTTCCTCCGTTCCAAATT 59.227 36.000 0.00 0.00 0.00 1.82
1278 1751 5.321927 ACAAATACTTCCTCCGTTCCAAAT 58.678 37.500 0.00 0.00 0.00 2.32
1279 1752 4.721132 ACAAATACTTCCTCCGTTCCAAA 58.279 39.130 0.00 0.00 0.00 3.28
1280 1753 4.360951 ACAAATACTTCCTCCGTTCCAA 57.639 40.909 0.00 0.00 0.00 3.53
1281 1754 4.360951 AACAAATACTTCCTCCGTTCCA 57.639 40.909 0.00 0.00 0.00 3.53
1282 1755 5.458015 CAAAACAAATACTTCCTCCGTTCC 58.542 41.667 0.00 0.00 0.00 3.62
1283 1756 5.458015 CCAAAACAAATACTTCCTCCGTTC 58.542 41.667 0.00 0.00 0.00 3.95
1284 1757 4.261867 GCCAAAACAAATACTTCCTCCGTT 60.262 41.667 0.00 0.00 0.00 4.44
1286 1759 3.254657 TGCCAAAACAAATACTTCCTCCG 59.745 43.478 0.00 0.00 0.00 4.63
1287 1760 4.864704 TGCCAAAACAAATACTTCCTCC 57.135 40.909 0.00 0.00 0.00 4.30
1288 1761 7.728847 AATTTGCCAAAACAAATACTTCCTC 57.271 32.000 0.00 0.00 46.80 3.71
1289 1762 7.013178 CCAAATTTGCCAAAACAAATACTTCCT 59.987 33.333 12.92 0.00 46.80 3.36
1290 1763 7.138081 CCAAATTTGCCAAAACAAATACTTCC 58.862 34.615 12.92 0.00 46.80 3.46
1291 1764 7.702386 ACCAAATTTGCCAAAACAAATACTTC 58.298 30.769 12.92 0.00 46.80 3.01
1293 1766 7.555914 AGAACCAAATTTGCCAAAACAAATACT 59.444 29.630 12.92 0.00 46.80 2.12
1294 1767 7.702386 AGAACCAAATTTGCCAAAACAAATAC 58.298 30.769 12.92 0.00 46.80 1.89
1295 1768 7.872113 AGAACCAAATTTGCCAAAACAAATA 57.128 28.000 12.92 0.00 46.80 1.40
1297 1770 7.687941 TTAGAACCAAATTTGCCAAAACAAA 57.312 28.000 12.92 0.00 43.27 2.83
1298 1771 7.391833 ACTTTAGAACCAAATTTGCCAAAACAA 59.608 29.630 12.92 0.00 0.00 2.83
1300 1773 7.186128 CACTTTAGAACCAAATTTGCCAAAAC 58.814 34.615 12.92 1.21 0.00 2.43
1305 1778 3.428534 CGCACTTTAGAACCAAATTTGCC 59.571 43.478 12.92 4.27 0.00 4.52
1309 1782 9.191995 CTAATTTTCGCACTTTAGAACCAAATT 57.808 29.630 0.00 0.00 0.00 1.82
1310 1783 8.357402 ACTAATTTTCGCACTTTAGAACCAAAT 58.643 29.630 0.00 0.00 0.00 2.32
1318 1791 9.088512 AGATCACTACTAATTTTCGCACTTTAG 57.911 33.333 0.00 0.00 0.00 1.85
1321 1794 8.997621 TTAGATCACTACTAATTTTCGCACTT 57.002 30.769 0.00 0.00 0.00 3.16
1322 1839 8.870879 GTTTAGATCACTACTAATTTTCGCACT 58.129 33.333 0.00 0.00 31.34 4.40
1323 1840 7.839837 CGTTTAGATCACTACTAATTTTCGCAC 59.160 37.037 0.00 0.00 31.34 5.34
1332 1849 9.865321 ATGTAAAAGCGTTTAGATCACTACTAA 57.135 29.630 8.62 0.00 29.51 2.24
1333 1850 9.865321 AATGTAAAAGCGTTTAGATCACTACTA 57.135 29.630 13.63 0.00 33.31 1.82
1341 1858 9.962759 CGTAAACTAATGTAAAAGCGTTTAGAT 57.037 29.630 8.62 8.62 35.33 1.98
1343 1860 8.434661 TCCGTAAACTAATGTAAAAGCGTTTAG 58.565 33.333 5.01 0.00 30.36 1.85
1345 1862 7.188468 TCCGTAAACTAATGTAAAAGCGTTT 57.812 32.000 2.53 2.53 0.00 3.60
1346 1863 6.128472 CCTCCGTAAACTAATGTAAAAGCGTT 60.128 38.462 0.00 0.00 0.00 4.84
1349 1866 5.876460 TCCCTCCGTAAACTAATGTAAAAGC 59.124 40.000 0.00 0.00 0.00 3.51
1351 1868 7.008021 ACTCCCTCCGTAAACTAATGTAAAA 57.992 36.000 0.00 0.00 0.00 1.52
1352 1869 6.610075 ACTCCCTCCGTAAACTAATGTAAA 57.390 37.500 0.00 0.00 0.00 2.01
1353 1870 6.891908 AGTACTCCCTCCGTAAACTAATGTAA 59.108 38.462 0.00 0.00 0.00 2.41
1354 1871 6.426587 AGTACTCCCTCCGTAAACTAATGTA 58.573 40.000 0.00 0.00 0.00 2.29
1355 1872 5.267587 AGTACTCCCTCCGTAAACTAATGT 58.732 41.667 0.00 0.00 0.00 2.71
1356 1873 5.848833 AGTACTCCCTCCGTAAACTAATG 57.151 43.478 0.00 0.00 0.00 1.90
1357 1874 9.240734 CATATAGTACTCCCTCCGTAAACTAAT 57.759 37.037 0.00 0.00 0.00 1.73
1358 1875 8.220559 ACATATAGTACTCCCTCCGTAAACTAA 58.779 37.037 0.00 0.00 0.00 2.24
1359 1876 7.663081 CACATATAGTACTCCCTCCGTAAACTA 59.337 40.741 0.00 0.00 0.00 2.24
1360 1877 6.489361 CACATATAGTACTCCCTCCGTAAACT 59.511 42.308 0.00 0.00 0.00 2.66
1361 1878 6.294397 CCACATATAGTACTCCCTCCGTAAAC 60.294 46.154 0.00 0.00 0.00 2.01
1362 1879 5.771666 CCACATATAGTACTCCCTCCGTAAA 59.228 44.000 0.00 0.00 0.00 2.01
1363 1880 5.319453 CCACATATAGTACTCCCTCCGTAA 58.681 45.833 0.00 0.00 0.00 3.18
1364 1881 4.808665 GCCACATATAGTACTCCCTCCGTA 60.809 50.000 0.00 0.00 0.00 4.02
1365 1882 3.764218 CCACATATAGTACTCCCTCCGT 58.236 50.000 0.00 0.00 0.00 4.69
1366 1883 2.492484 GCCACATATAGTACTCCCTCCG 59.508 54.545 0.00 0.00 0.00 4.63
1367 1884 3.507411 TGCCACATATAGTACTCCCTCC 58.493 50.000 0.00 0.00 0.00 4.30
1368 1885 4.589374 ACTTGCCACATATAGTACTCCCTC 59.411 45.833 0.00 0.00 0.00 4.30
1369 1886 4.557705 ACTTGCCACATATAGTACTCCCT 58.442 43.478 0.00 0.00 0.00 4.20
1370 1887 4.344102 TGACTTGCCACATATAGTACTCCC 59.656 45.833 0.00 0.00 0.00 4.30
1371 1888 5.531122 TGACTTGCCACATATAGTACTCC 57.469 43.478 0.00 0.00 0.00 3.85
1372 1889 7.210174 TCATTGACTTGCCACATATAGTACTC 58.790 38.462 0.00 0.00 0.00 2.59
1373 1890 7.124573 TCATTGACTTGCCACATATAGTACT 57.875 36.000 0.00 0.00 0.00 2.73
1374 1891 7.495934 AGTTCATTGACTTGCCACATATAGTAC 59.504 37.037 0.00 0.00 0.00 2.73
1380 1897 5.769662 AGAAAGTTCATTGACTTGCCACATA 59.230 36.000 0.00 0.00 39.68 2.29
1382 1899 3.953612 AGAAAGTTCATTGACTTGCCACA 59.046 39.130 0.00 0.00 39.68 4.17
1394 1911 5.223449 TCCGTAACCTGAAGAAAGTTCAT 57.777 39.130 0.00 0.00 0.00 2.57
1422 1942 2.831685 TAGGTTAGCATATGCCACCG 57.168 50.000 28.61 0.00 45.09 4.94
1424 1944 6.522054 TCTACTTTAGGTTAGCATATGCCAC 58.478 40.000 23.96 19.54 43.38 5.01
1503 2034 5.121768 CCCTTTGTTGTATTTCTCTACCGTG 59.878 44.000 0.00 0.00 0.00 4.94
1535 2072 2.751806 GGCATTCAAGGAGGAACTTCAG 59.248 50.000 0.00 0.00 41.55 3.02
1538 2075 2.978156 TGGCATTCAAGGAGGAACTT 57.022 45.000 0.00 0.00 41.55 2.66
1556 2097 2.813754 TCAGGACGGCAGAAGAAAAATG 59.186 45.455 0.00 0.00 0.00 2.32
1569 2110 4.024893 CGTTGGAAAATATGATCAGGACGG 60.025 45.833 0.09 0.00 0.00 4.79
1574 2115 3.631686 TGGGCGTTGGAAAATATGATCAG 59.368 43.478 0.09 0.00 0.00 2.90
1586 2132 1.860641 TTCTCTATCTGGGCGTTGGA 58.139 50.000 0.00 0.00 0.00 3.53
1623 2169 3.575630 TGAGCATCGTCTTTGACAGTAC 58.424 45.455 0.00 0.00 38.61 2.73
1625 2171 2.820059 TGAGCATCGTCTTTGACAGT 57.180 45.000 0.00 0.00 38.61 3.55
1644 2190 3.255642 CGGCCGGGATCATGATTTTTATT 59.744 43.478 20.10 0.00 0.00 1.40
1706 2252 4.122776 ACATACAGCAGTGCTACTAATGC 58.877 43.478 19.26 0.00 41.59 3.56
1716 2262 2.700371 TCCCCTGATACATACAGCAGTG 59.300 50.000 0.00 0.00 34.47 3.66
1798 2344 1.180456 TGCCAATCCAGCCAACACAG 61.180 55.000 0.00 0.00 0.00 3.66
1809 2359 0.949105 AAGTCACGTCGTGCCAATCC 60.949 55.000 20.56 4.08 32.98 3.01
1842 2392 2.112297 TTGGGTTGGGTGAGCGTC 59.888 61.111 0.00 0.00 0.00 5.19
1871 2421 1.006805 CTCCCAGCGCTAGATTCCG 60.007 63.158 10.99 0.00 0.00 4.30
1881 2431 6.293626 CCTTCATAAATTTGATACTCCCAGCG 60.294 42.308 0.00 0.00 0.00 5.18
1883 2433 8.790718 CATCCTTCATAAATTTGATACTCCCAG 58.209 37.037 0.00 0.00 0.00 4.45
1899 2449 2.135139 GATTCGCACGCATCCTTCATA 58.865 47.619 0.00 0.00 0.00 2.15
1946 2496 1.767692 CACCCAGGGTTTAGGTGCT 59.232 57.895 9.12 0.00 44.21 4.40
1959 2509 1.278985 GACACCATGATCTGTCACCCA 59.721 52.381 7.71 0.00 37.14 4.51
1961 2511 1.278985 TGGACACCATGATCTGTCACC 59.721 52.381 13.11 0.87 38.89 4.02
2016 2566 1.093159 ACTTCTAGGTAGCGACGGTG 58.907 55.000 10.33 0.00 0.00 4.94
2032 2582 6.579666 CATGCAAATATACCCATGCTACTT 57.420 37.500 0.00 0.00 39.49 2.24
2038 2588 4.926832 CACATGCATGCAAATATACCCATG 59.073 41.667 26.68 16.21 38.41 3.66
2039 2589 4.020928 CCACATGCATGCAAATATACCCAT 60.021 41.667 26.68 0.00 0.00 4.00
2040 2590 3.321396 CCACATGCATGCAAATATACCCA 59.679 43.478 26.68 0.00 0.00 4.51
2041 2591 3.861886 GCCACATGCATGCAAATATACCC 60.862 47.826 26.68 4.90 40.77 3.69
2146 2704 2.430694 TGATCGTTGGGGAGTATGTCAG 59.569 50.000 0.00 0.00 0.00 3.51
2147 2705 2.462723 TGATCGTTGGGGAGTATGTCA 58.537 47.619 0.00 0.00 0.00 3.58
2156 2714 4.279169 AGAATGCATATTTGATCGTTGGGG 59.721 41.667 0.00 0.00 0.00 4.96
2208 2864 1.441515 GAACGACTGCGACGCTGTA 60.442 57.895 28.76 5.23 40.59 2.74
2487 3152 3.991536 GAGGAGCTCGTTGCCGACC 62.992 68.421 10.79 0.00 44.23 4.79
3105 3874 3.264866 GAACGACCGCTCCGACACT 62.265 63.158 0.00 0.00 0.00 3.55
3509 4287 6.017687 CCATTCAGAAAACGATCATCTATGCA 60.018 38.462 0.00 0.00 0.00 3.96
3518 4296 4.725169 GCGAGTTCCATTCAGAAAACGATC 60.725 45.833 0.00 0.00 32.27 3.69
3562 4340 8.131100 CGGTGAATTCTTATGCACAAAGATAAT 58.869 33.333 12.72 3.86 41.46 1.28
3644 4423 0.990374 AGAGAGATGCAAGGTGGCTT 59.010 50.000 0.00 0.00 34.04 4.35
3806 4669 2.979676 TCTTGTTGCTGGCTGCCG 60.980 61.111 14.98 10.05 42.00 5.69
3827 4690 1.839994 TCAGCCATACCCAAGGAGAAG 59.160 52.381 0.00 0.00 0.00 2.85
3889 4754 0.532862 ATTGCGCGGGAAGATAGGTG 60.533 55.000 8.83 0.00 0.00 4.00
3915 4780 7.946655 TTCAGTAGTGACTTACAAGAATGTG 57.053 36.000 0.00 0.00 35.28 3.21
3943 4808 4.141459 ACTTGAGTCATGATGATGCCAGAT 60.141 41.667 12.65 0.00 0.00 2.90
3971 4836 5.248640 TCAGAAGAGCTTTGTATCTTTGGG 58.751 41.667 0.00 0.00 35.93 4.12
3975 4840 8.675504 CAAATCATCAGAAGAGCTTTGTATCTT 58.324 33.333 0.00 0.00 38.46 2.40
4304 5170 6.575162 ACTGAATTCCACCATCTTTTGTAC 57.425 37.500 2.27 0.00 0.00 2.90
4358 5224 2.944129 ACTCTGCAAAAGCCTGGTAAA 58.056 42.857 0.00 0.00 0.00 2.01
4451 5317 4.525100 AGAGTTCTTCCCTACTGTTCTCAC 59.475 45.833 0.00 0.00 0.00 3.51
4452 5318 4.742012 AGAGTTCTTCCCTACTGTTCTCA 58.258 43.478 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.