Multiple sequence alignment - TraesCS2B01G558400

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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 TraesCS2B01G558400 chr2B 100.000 4589 0 0 1 4589 752784199 752788787 0.000000e+00 8475.0
1 TraesCS2B01G558400 chr2B 92.568 1036 74 1 2577 3612 24089835 24090867 0.000000e+00 1483.0
2 TraesCS2B01G558400 chr2B 89.751 1044 99 6 2572 3613 17873746 17872709 0.000000e+00 1328.0
3 TraesCS2B01G558400 chr2B 95.939 197 8 0 997 1193 17883301 17883105 2.060000e-83 320.0
4 TraesCS2B01G558400 chr2B 89.575 259 16 10 937 1192 24089478 24089728 7.410000e-83 318.0
5 TraesCS2B01G558400 chr2B 81.818 242 23 14 606 843 17883607 17883383 2.820000e-42 183.0
6 TraesCS2B01G558400 chr2B 94.845 97 5 0 1261 1357 200473733 200473637 7.950000e-33 152.0
7 TraesCS2B01G558400 chr2A 92.191 2113 89 40 1931 3998 747088028 747090109 0.000000e+00 2918.0
8 TraesCS2B01G558400 chr2A 90.630 1302 70 20 1 1259 747086058 747087350 0.000000e+00 1681.0
9 TraesCS2B01G558400 chr2A 90.675 1126 88 9 2577 3699 15395163 15396274 0.000000e+00 1482.0
10 TraesCS2B01G558400 chr2A 89.228 1049 107 4 2568 3615 12048319 12047276 0.000000e+00 1306.0
11 TraesCS2B01G558400 chr2A 94.240 434 15 2 4166 4589 747090198 747090631 0.000000e+00 654.0
12 TraesCS2B01G558400 chr2A 79.293 594 66 36 606 1193 12103651 12103109 3.370000e-96 363.0
13 TraesCS2B01G558400 chr2A 89.888 267 10 7 1344 1604 747087352 747087607 1.230000e-85 327.0
14 TraesCS2B01G558400 chr2A 91.597 238 15 3 958 1193 12073522 12073288 1.590000e-84 324.0
15 TraesCS2B01G558400 chr2A 89.030 237 21 4 958 1192 12048634 12048401 5.810000e-74 289.0
16 TraesCS2B01G558400 chr2A 93.939 99 6 0 1253 1351 407739276 407739178 2.860000e-32 150.0
17 TraesCS2B01G558400 chr2A 92.308 65 1 2 1686 1746 747087879 747087943 6.320000e-14 89.8
18 TraesCS2B01G558400 chr2A 100.000 39 0 0 1779 1817 747087957 747087995 6.370000e-09 73.1
19 TraesCS2B01G558400 chr2A 90.741 54 2 1 1865 1915 747087992 747088045 8.240000e-08 69.4
20 TraesCS2B01G558400 chr2D 93.783 1866 53 31 2221 4052 617052304 617054140 0.000000e+00 2745.0
21 TraesCS2B01G558400 chr2D 93.070 1241 60 12 1 1234 617050377 617051598 0.000000e+00 1792.0
22 TraesCS2B01G558400 chr2D 92.589 1039 74 1 2577 3615 13421739 13422774 0.000000e+00 1489.0
23 TraesCS2B01G558400 chr2D 89.971 1047 99 5 2568 3613 11509635 11508594 0.000000e+00 1347.0
24 TraesCS2B01G558400 chr2D 89.323 1049 106 4 2568 3615 11477728 11476685 0.000000e+00 1312.0
25 TraesCS2B01G558400 chr2D 88.136 708 31 15 1345 2040 617051620 617052286 0.000000e+00 793.0
26 TraesCS2B01G558400 chr2D 93.427 426 21 2 4170 4589 617054156 617054580 3.900000e-175 625.0
27 TraesCS2B01G558400 chr2D 90.310 258 18 2 939 1192 11509965 11509711 9.520000e-87 331.0
28 TraesCS2B01G558400 chr2D 87.986 283 24 6 916 1193 11478132 11477855 4.430000e-85 326.0
29 TraesCS2B01G558400 chr2D 99.020 102 1 0 4488 4589 617057579 617057680 2.820000e-42 183.0
30 TraesCS2B01G558400 chr2D 79.498 239 27 11 597 828 11510264 11510041 2.860000e-32 150.0
31 TraesCS2B01G558400 chr2D 79.310 174 18 11 685 849 11496815 11496651 6.280000e-19 106.0
32 TraesCS2B01G558400 chr2D 80.882 136 14 10 637 767 11478348 11478220 3.780000e-16 97.1
33 TraesCS2B01G558400 chr5A 96.809 94 3 0 1256 1349 247191150 247191243 1.710000e-34 158.0
34 TraesCS2B01G558400 chr1A 95.876 97 4 0 1256 1352 31314898 31314994 1.710000e-34 158.0
35 TraesCS2B01G558400 chr6B 96.774 93 3 0 1263 1355 22906143 22906235 6.150000e-34 156.0
36 TraesCS2B01G558400 chr6B 93.069 101 7 0 1256 1356 639915317 639915417 1.030000e-31 148.0
37 TraesCS2B01G558400 chr7D 94.000 100 6 0 1253 1352 406244533 406244632 7.950000e-33 152.0
38 TraesCS2B01G558400 chr7D 85.714 56 3 3 4085 4136 440005162 440005108 2.000000e-03 54.7
39 TraesCS2B01G558400 chr3A 95.699 93 4 0 1256 1348 66362271 66362363 2.860000e-32 150.0
40 TraesCS2B01G558400 chr3A 93.878 98 5 1 1256 1352 658636779 658636876 3.700000e-31 147.0
41 TraesCS2B01G558400 chr1B 84.946 93 13 1 4160 4252 32399906 32399997 4.890000e-15 93.5


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 TraesCS2B01G558400 chr2B 752784199 752788787 4588 False 8475.000000 8475 100.000000 1 4589 1 chr2B.!!$F1 4588
1 TraesCS2B01G558400 chr2B 17872709 17873746 1037 True 1328.000000 1328 89.751000 2572 3613 1 chr2B.!!$R1 1041
2 TraesCS2B01G558400 chr2B 24089478 24090867 1389 False 900.500000 1483 91.071500 937 3612 2 chr2B.!!$F2 2675
3 TraesCS2B01G558400 chr2B 17883105 17883607 502 True 251.500000 320 88.878500 606 1193 2 chr2B.!!$R3 587
4 TraesCS2B01G558400 chr2A 15395163 15396274 1111 False 1482.000000 1482 90.675000 2577 3699 1 chr2A.!!$F1 1122
5 TraesCS2B01G558400 chr2A 747086058 747090631 4573 False 830.328571 2918 92.856857 1 4589 7 chr2A.!!$F2 4588
6 TraesCS2B01G558400 chr2A 12047276 12048634 1358 True 797.500000 1306 89.129000 958 3615 2 chr2A.!!$R4 2657
7 TraesCS2B01G558400 chr2A 12103109 12103651 542 True 363.000000 363 79.293000 606 1193 1 chr2A.!!$R2 587
8 TraesCS2B01G558400 chr2D 13421739 13422774 1035 False 1489.000000 1489 92.589000 2577 3615 1 chr2D.!!$F1 1038
9 TraesCS2B01G558400 chr2D 617050377 617057680 7303 False 1227.600000 2745 93.487200 1 4589 5 chr2D.!!$F2 4588
10 TraesCS2B01G558400 chr2D 11508594 11510264 1670 True 609.333333 1347 86.593000 597 3613 3 chr2D.!!$R3 3016
11 TraesCS2B01G558400 chr2D 11476685 11478348 1663 True 578.366667 1312 86.063667 637 3615 3 chr2D.!!$R2 2978

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
397 405 0.332293 TTCCAGGCTTGGCATCATCA 59.668 50.000 10.65 0.0 44.63 3.07 F
398 406 0.554305 TCCAGGCTTGGCATCATCAT 59.446 50.000 10.65 0.0 44.63 2.45 F
2350 2624 0.250295 TGGGCCACTCGACAAAGAAG 60.250 55.000 0.00 0.0 0.00 2.85 F
2848 3218 1.220206 CTCACCAAGATGCTCGGCT 59.780 57.895 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 2002 0.530744 TCTTGGTCGAACCGATCCAG 59.469 55.00 0.00 0.00 42.58 3.86 R
2364 2638 5.022282 TCATGGATTCGCTCATGTTTCTA 57.978 39.13 0.00 0.00 40.94 2.10 R
3246 3616 0.179059 GCTTGAAGGCCTCCTCTAGC 60.179 60.00 20.32 20.32 30.89 3.42 R
4110 4529 0.249868 CTGCACCCTGACGAGAACAA 60.250 55.00 0.00 0.00 0.00 2.83 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
48 51 2.500442 CGACTAGCACAGAAGCGCG 61.500 63.158 0.00 0.00 40.15 6.86
55 58 0.732880 GCACAGAAGCGCGAAGAGTA 60.733 55.000 12.10 0.00 0.00 2.59
66 69 4.326548 AGCGCGAAGAGTATGTTTTCTTAC 59.673 41.667 12.10 0.00 33.97 2.34
79 82 3.335729 CTTACCAGGGGCCGGGTT 61.336 66.667 21.66 8.13 41.59 4.11
100 103 2.882324 GCTACAAGCAGAGTACCACTC 58.118 52.381 0.00 0.00 45.38 3.51
118 121 4.345257 CCACTCTATGGCTAATACAGTGGT 59.655 45.833 18.00 0.00 45.80 4.16
124 127 8.257602 TCTATGGCTAATACAGTGGTTGAATA 57.742 34.615 0.00 0.00 0.00 1.75
127 130 7.801716 TGGCTAATACAGTGGTTGAATATTC 57.198 36.000 8.60 8.60 0.00 1.75
146 149 3.695830 TCTTGACTCCGGCAATTACTT 57.304 42.857 0.00 0.00 0.00 2.24
151 154 2.673368 GACTCCGGCAATTACTTGTCAG 59.327 50.000 0.00 0.00 36.77 3.51
207 210 3.349488 TCTGCGACAATGTATCTACCG 57.651 47.619 0.00 0.00 0.00 4.02
209 212 2.789339 CTGCGACAATGTATCTACCGTG 59.211 50.000 0.00 0.00 0.00 4.94
219 222 1.964552 ATCTACCGTGTACCTCTCCG 58.035 55.000 0.00 0.00 0.00 4.63
221 224 1.003580 TCTACCGTGTACCTCTCCGTT 59.996 52.381 0.00 0.00 0.00 4.44
227 230 2.174360 GTGTACCTCTCCGTTAACCCT 58.826 52.381 0.00 0.00 0.00 4.34
264 267 5.750547 CGTACACATTGAGCTAGACATTCAT 59.249 40.000 0.00 0.00 0.00 2.57
299 302 5.559148 AATGTCTCTCTCTTGGACAGTTT 57.441 39.130 0.00 0.00 42.13 2.66
352 360 5.167121 CAGATATCATGACGAAAGGGCTAG 58.833 45.833 5.32 0.00 0.00 3.42
376 384 3.440522 GTCGGCAAGCTTAGAAGGATTTT 59.559 43.478 0.00 0.00 0.00 1.82
384 392 5.012893 AGCTTAGAAGGATTTTGTTCCAGG 58.987 41.667 0.00 0.00 38.32 4.45
397 405 0.332293 TTCCAGGCTTGGCATCATCA 59.668 50.000 10.65 0.00 44.63 3.07
398 406 0.554305 TCCAGGCTTGGCATCATCAT 59.446 50.000 10.65 0.00 44.63 2.45
399 407 1.776063 TCCAGGCTTGGCATCATCATA 59.224 47.619 10.65 0.00 44.63 2.15
400 408 2.175284 TCCAGGCTTGGCATCATCATAA 59.825 45.455 10.65 0.00 44.63 1.90
401 409 2.295349 CCAGGCTTGGCATCATCATAAC 59.705 50.000 0.13 0.00 37.73 1.89
403 411 3.252701 CAGGCTTGGCATCATCATAACTC 59.747 47.826 0.00 0.00 0.00 3.01
433 446 3.099905 TGGGTGGTGTGAGAGAAGATAG 58.900 50.000 0.00 0.00 0.00 2.08
456 469 0.557238 TGGGGCTCCATATTGCATGT 59.443 50.000 0.00 0.00 38.32 3.21
558 598 7.175119 CGTGATTAGATGTAGAGATTAGGTGGA 59.825 40.741 0.00 0.00 0.00 4.02
744 788 2.737180 CATCCATCCTCCCGTCCG 59.263 66.667 0.00 0.00 0.00 4.79
781 830 3.737172 CCCAACGGCCAGCTTTCG 61.737 66.667 2.24 0.00 0.00 3.46
852 901 4.868116 ACCACACCACACCACGCC 62.868 66.667 0.00 0.00 0.00 5.68
853 902 4.866224 CCACACCACACCACGCCA 62.866 66.667 0.00 0.00 0.00 5.69
890 940 3.338249 CCTGTCATTTGTCTACCACCTG 58.662 50.000 0.00 0.00 0.00 4.00
891 941 2.744202 CTGTCATTTGTCTACCACCTGC 59.256 50.000 0.00 0.00 0.00 4.85
892 942 2.371841 TGTCATTTGTCTACCACCTGCT 59.628 45.455 0.00 0.00 0.00 4.24
893 943 3.580895 TGTCATTTGTCTACCACCTGCTA 59.419 43.478 0.00 0.00 0.00 3.49
914 964 3.376935 TAGCTGCTTCCCTCTGCGC 62.377 63.158 7.79 0.00 34.25 6.09
930 980 1.375523 CGCCCCGCAAACTTAGACT 60.376 57.895 0.00 0.00 0.00 3.24
1119 1180 2.042639 TACCAGGCCGACTACCCC 60.043 66.667 0.00 0.00 0.00 4.95
1208 1269 6.398095 TGTGTAAGTCTATGTTCACCATCTG 58.602 40.000 0.00 0.00 34.86 2.90
1211 1272 3.866651 AGTCTATGTTCACCATCTGTGC 58.133 45.455 0.00 0.00 45.03 4.57
1242 1303 2.275380 ATGCACGGCTTGTTTCCCC 61.275 57.895 0.00 0.00 0.00 4.81
1261 1322 3.065925 CCCCTAACGGCGCTACTATATAC 59.934 52.174 6.90 0.00 0.00 1.47
1265 1326 5.814705 CCTAACGGCGCTACTATATACTACT 59.185 44.000 6.90 0.00 0.00 2.57
1266 1327 5.793026 AACGGCGCTACTATATACTACTC 57.207 43.478 6.90 0.00 0.00 2.59
1267 1328 4.187694 ACGGCGCTACTATATACTACTCC 58.812 47.826 6.90 0.00 0.00 3.85
1268 1329 3.559242 CGGCGCTACTATATACTACTCCC 59.441 52.174 7.64 0.00 0.00 4.30
1269 1330 4.682859 CGGCGCTACTATATACTACTCCCT 60.683 50.000 7.64 0.00 0.00 4.20
1270 1331 4.815846 GGCGCTACTATATACTACTCCCTC 59.184 50.000 7.64 0.00 0.00 4.30
1271 1332 5.396660 GGCGCTACTATATACTACTCCCTCT 60.397 48.000 7.64 0.00 0.00 3.69
1272 1333 5.524646 GCGCTACTATATACTACTCCCTCTG 59.475 48.000 0.00 0.00 0.00 3.35
1273 1334 6.642430 CGCTACTATATACTACTCCCTCTGT 58.358 44.000 0.00 0.00 0.00 3.41
1274 1335 7.632462 GCGCTACTATATACTACTCCCTCTGTA 60.632 44.444 0.00 0.00 0.00 2.74
1275 1336 8.256605 CGCTACTATATACTACTCCCTCTGTAA 58.743 40.741 0.00 0.00 0.00 2.41
1276 1337 9.956640 GCTACTATATACTACTCCCTCTGTAAA 57.043 37.037 0.00 0.00 0.00 2.01
1289 1350 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1290 1351 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
1291 1352 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
1420 1481 7.884354 TCCCCGTAAACTTTTGTTGATAGTTAT 59.116 33.333 0.00 0.00 42.67 1.89
1476 1543 6.049149 GCAATAAGCCAAGATGTGTACTAGA 58.951 40.000 0.00 0.00 37.23 2.43
1498 1565 5.358442 AGACATGGATCGGAGTAGCATATAC 59.642 44.000 0.00 0.00 0.00 1.47
1499 1566 5.016831 ACATGGATCGGAGTAGCATATACA 58.983 41.667 0.00 0.00 0.00 2.29
1500 1567 5.658634 ACATGGATCGGAGTAGCATATACAT 59.341 40.000 0.00 0.00 0.00 2.29
1501 1568 6.833933 ACATGGATCGGAGTAGCATATACATA 59.166 38.462 0.00 0.00 0.00 2.29
1502 1569 7.507277 ACATGGATCGGAGTAGCATATACATAT 59.493 37.037 0.00 0.00 0.00 1.78
1503 1570 9.014297 CATGGATCGGAGTAGCATATACATATA 57.986 37.037 0.00 0.00 0.00 0.86
1536 1606 1.758280 ACACAATAAGCATGGCCATGG 59.242 47.619 39.72 26.62 39.16 3.66
1748 2015 1.887854 TGTTACACTGGATCGGTTCGA 59.112 47.619 0.00 0.00 41.13 3.71
1768 2035 7.966753 GGTTCGACCAAGAATTAATTCCTAAAC 59.033 37.037 21.86 15.69 38.42 2.01
1818 2086 8.548721 GTGTTTATATGTGGACTAATTTCCTCG 58.451 37.037 0.00 0.00 36.51 4.63
1819 2087 8.262227 TGTTTATATGTGGACTAATTTCCTCGT 58.738 33.333 0.00 0.00 36.51 4.18
1848 2116 7.164122 TGGCACATCTAAATCATCCTTAGATC 58.836 38.462 2.79 0.00 41.88 2.75
1849 2117 6.597280 GGCACATCTAAATCATCCTTAGATCC 59.403 42.308 2.79 0.00 41.88 3.36
1850 2118 6.597280 GCACATCTAAATCATCCTTAGATCCC 59.403 42.308 2.79 0.00 41.88 3.85
1851 2119 6.815641 CACATCTAAATCATCCTTAGATCCCG 59.184 42.308 2.79 0.00 41.88 5.14
1852 2120 6.498651 ACATCTAAATCATCCTTAGATCCCGT 59.501 38.462 2.79 0.00 41.88 5.28
1853 2121 7.674348 ACATCTAAATCATCCTTAGATCCCGTA 59.326 37.037 2.79 0.00 41.88 4.02
1854 2122 8.531982 CATCTAAATCATCCTTAGATCCCGTAA 58.468 37.037 2.79 0.00 41.88 3.18
1855 2123 8.486942 TCTAAATCATCCTTAGATCCCGTAAA 57.513 34.615 0.00 0.00 31.84 2.01
1856 2124 8.930527 TCTAAATCATCCTTAGATCCCGTAAAA 58.069 33.333 0.00 0.00 31.84 1.52
1857 2125 9.555727 CTAAATCATCCTTAGATCCCGTAAAAA 57.444 33.333 0.00 0.00 0.00 1.94
2059 2330 5.015391 TGGCAGGGTAAAGGGAGTTTTATTA 59.985 40.000 0.00 0.00 0.00 0.98
2060 2331 6.134055 GGCAGGGTAAAGGGAGTTTTATTAT 58.866 40.000 0.00 0.00 0.00 1.28
2061 2332 6.610020 GGCAGGGTAAAGGGAGTTTTATTATT 59.390 38.462 0.00 0.00 0.00 1.40
2062 2333 7.201884 GGCAGGGTAAAGGGAGTTTTATTATTC 60.202 40.741 0.00 0.00 0.00 1.75
2063 2334 7.468220 GCAGGGTAAAGGGAGTTTTATTATTCG 60.468 40.741 0.00 0.00 0.00 3.34
2073 2344 8.979574 GGGAGTTTTATTATTCGATAGTGACAG 58.020 37.037 0.00 0.00 37.40 3.51
2084 2355 6.961360 TCGATAGTGACAGGATTACATTCT 57.039 37.500 0.00 0.00 37.40 2.40
2085 2356 6.739112 TCGATAGTGACAGGATTACATTCTG 58.261 40.000 0.00 0.00 37.40 3.02
2086 2357 5.403766 CGATAGTGACAGGATTACATTCTGC 59.596 44.000 0.00 0.00 32.19 4.26
2103 2376 7.041721 ACATTCTGCTAATACAAGATCGTGAA 58.958 34.615 15.90 0.00 0.00 3.18
2203 2477 0.678395 TGTTTGCATGAACCGCCAAT 59.322 45.000 0.00 0.00 0.00 3.16
2206 2480 3.056250 TGTTTGCATGAACCGCCAATAAT 60.056 39.130 0.00 0.00 0.00 1.28
2207 2481 3.883830 TTGCATGAACCGCCAATAATT 57.116 38.095 0.00 0.00 0.00 1.40
2210 2484 4.677584 TGCATGAACCGCCAATAATTTAC 58.322 39.130 0.00 0.00 0.00 2.01
2212 2486 5.590663 TGCATGAACCGCCAATAATTTACTA 59.409 36.000 0.00 0.00 0.00 1.82
2213 2487 5.912955 GCATGAACCGCCAATAATTTACTAC 59.087 40.000 0.00 0.00 0.00 2.73
2214 2488 5.721876 TGAACCGCCAATAATTTACTACG 57.278 39.130 0.00 0.00 0.00 3.51
2215 2489 5.177326 TGAACCGCCAATAATTTACTACGT 58.823 37.500 0.00 0.00 0.00 3.57
2216 2490 6.336566 TGAACCGCCAATAATTTACTACGTA 58.663 36.000 0.00 0.00 0.00 3.57
2217 2491 6.476380 TGAACCGCCAATAATTTACTACGTAG 59.524 38.462 20.97 20.97 0.00 3.51
2219 2493 7.038154 ACCGCCAATAATTTACTACGTAGTA 57.962 36.000 27.51 27.51 45.11 1.82
2220 2494 7.488322 ACCGCCAATAATTTACTACGTAGTAA 58.512 34.615 33.82 33.82 45.13 2.24
2350 2624 0.250295 TGGGCCACTCGACAAAGAAG 60.250 55.000 0.00 0.00 0.00 2.85
2363 2637 5.474532 TCGACAAAGAAGGTACTAGCAAGTA 59.525 40.000 0.00 0.00 38.49 2.24
2364 2638 6.152323 TCGACAAAGAAGGTACTAGCAAGTAT 59.848 38.462 0.00 0.00 40.30 2.12
2848 3218 1.220206 CTCACCAAGATGCTCGGCT 59.780 57.895 0.00 0.00 0.00 5.52
3150 3520 3.140225 GACGATCCTGCCGGACTCC 62.140 68.421 5.05 0.00 43.51 3.85
3246 3616 1.057822 CAAGAACATCGAGCGTGCG 59.942 57.895 0.00 0.00 0.00 5.34
3616 3991 4.393834 GCTCCTTCTCCATTTATCTTCCC 58.606 47.826 0.00 0.00 0.00 3.97
3641 4019 4.720046 TGCATGGAAAACAACCTACTACA 58.280 39.130 0.00 0.00 0.00 2.74
3649 4035 6.653740 GGAAAACAACCTACTACATACAGCTT 59.346 38.462 0.00 0.00 0.00 3.74
3654 4040 6.890814 ACAACCTACTACATACAGCTTCTACT 59.109 38.462 0.00 0.00 0.00 2.57
3717 4108 6.649155 TGTACTATGTGTTGGTAGATGCATT 58.351 36.000 0.00 0.00 0.00 3.56
3718 4109 6.761242 TGTACTATGTGTTGGTAGATGCATTC 59.239 38.462 0.00 0.00 0.00 2.67
3719 4110 4.811024 ACTATGTGTTGGTAGATGCATTCG 59.189 41.667 0.00 0.00 0.00 3.34
3720 4111 3.326836 TGTGTTGGTAGATGCATTCGA 57.673 42.857 0.00 0.00 0.00 3.71
3838 4229 4.640771 ATGTGGAGTGTGAGGTGTATTT 57.359 40.909 0.00 0.00 0.00 1.40
3955 4346 8.674925 TTCTCCTATCTCCTACCTTTTGTTTA 57.325 34.615 0.00 0.00 0.00 2.01
3956 4347 8.855804 TCTCCTATCTCCTACCTTTTGTTTAT 57.144 34.615 0.00 0.00 0.00 1.40
3957 4348 8.705594 TCTCCTATCTCCTACCTTTTGTTTATG 58.294 37.037 0.00 0.00 0.00 1.90
4026 4443 7.927048 GGTACAAACCATAATGAACATACTCC 58.073 38.462 0.00 0.00 45.98 3.85
4052 4471 3.054065 CCTCTAAAAGAACCCAGCCTCAT 60.054 47.826 0.00 0.00 0.00 2.90
4053 4472 3.944015 CTCTAAAAGAACCCAGCCTCATG 59.056 47.826 0.00 0.00 0.00 3.07
4054 4473 1.260544 AAAAGAACCCAGCCTCATGC 58.739 50.000 0.00 0.00 41.71 4.06
4055 4474 0.112995 AAAGAACCCAGCCTCATGCA 59.887 50.000 0.00 0.00 44.83 3.96
4056 4475 0.333993 AAGAACCCAGCCTCATGCAT 59.666 50.000 0.00 0.00 44.83 3.96
4057 4476 0.106819 AGAACCCAGCCTCATGCATC 60.107 55.000 0.00 0.00 44.83 3.91
4058 4477 0.394762 GAACCCAGCCTCATGCATCA 60.395 55.000 0.00 0.00 44.83 3.07
4062 4481 1.760613 CCCAGCCTCATGCATCAAATT 59.239 47.619 0.00 0.00 44.83 1.82
4065 4484 4.321750 CCCAGCCTCATGCATCAAATTATC 60.322 45.833 0.00 0.00 44.83 1.75
4067 4486 5.708697 CCAGCCTCATGCATCAAATTATCTA 59.291 40.000 0.00 0.00 44.83 1.98
4068 4487 6.349115 CCAGCCTCATGCATCAAATTATCTAC 60.349 42.308 0.00 0.00 44.83 2.59
4069 4488 5.709164 AGCCTCATGCATCAAATTATCTACC 59.291 40.000 0.00 0.00 44.83 3.18
4070 4489 5.474532 GCCTCATGCATCAAATTATCTACCA 59.525 40.000 0.00 0.00 40.77 3.25
4071 4490 6.569226 GCCTCATGCATCAAATTATCTACCAC 60.569 42.308 0.00 0.00 40.77 4.16
4072 4491 6.487668 CCTCATGCATCAAATTATCTACCACA 59.512 38.462 0.00 0.00 0.00 4.17
4073 4492 7.263100 TCATGCATCAAATTATCTACCACAC 57.737 36.000 0.00 0.00 0.00 3.82
4074 4493 6.827762 TCATGCATCAAATTATCTACCACACA 59.172 34.615 0.00 0.00 0.00 3.72
4075 4494 6.435430 TGCATCAAATTATCTACCACACAC 57.565 37.500 0.00 0.00 0.00 3.82
4076 4495 5.942826 TGCATCAAATTATCTACCACACACA 59.057 36.000 0.00 0.00 0.00 3.72
4077 4496 6.128035 TGCATCAAATTATCTACCACACACAC 60.128 38.462 0.00 0.00 0.00 3.82
4078 4497 6.128035 GCATCAAATTATCTACCACACACACA 60.128 38.462 0.00 0.00 0.00 3.72
4079 4498 6.795098 TCAAATTATCTACCACACACACAC 57.205 37.500 0.00 0.00 0.00 3.82
4080 4499 6.292150 TCAAATTATCTACCACACACACACA 58.708 36.000 0.00 0.00 0.00 3.72
4081 4500 6.768381 TCAAATTATCTACCACACACACACAA 59.232 34.615 0.00 0.00 0.00 3.33
4082 4501 7.283354 TCAAATTATCTACCACACACACACAAA 59.717 33.333 0.00 0.00 0.00 2.83
4083 4502 7.575414 AATTATCTACCACACACACACAAAA 57.425 32.000 0.00 0.00 0.00 2.44
4084 4503 7.759489 ATTATCTACCACACACACACAAAAT 57.241 32.000 0.00 0.00 0.00 1.82
4085 4504 7.575414 TTATCTACCACACACACACAAAATT 57.425 32.000 0.00 0.00 0.00 1.82
4086 4505 5.242069 TCTACCACACACACACAAAATTG 57.758 39.130 0.00 0.00 0.00 2.32
4087 4506 4.944317 TCTACCACACACACACAAAATTGA 59.056 37.500 0.00 0.00 0.00 2.57
4088 4507 4.527509 ACCACACACACACAAAATTGAA 57.472 36.364 0.00 0.00 0.00 2.69
4089 4508 5.083533 ACCACACACACACAAAATTGAAT 57.916 34.783 0.00 0.00 0.00 2.57
4090 4509 4.869297 ACCACACACACACAAAATTGAATG 59.131 37.500 0.00 0.66 0.00 2.67
4091 4510 4.869297 CCACACACACACAAAATTGAATGT 59.131 37.500 0.00 1.26 32.71 2.71
4092 4511 5.350914 CCACACACACACAAAATTGAATGTT 59.649 36.000 0.00 0.00 31.06 2.71
4093 4512 6.128336 CCACACACACACAAAATTGAATGTTT 60.128 34.615 0.00 0.00 31.06 2.83
4094 4513 6.954852 CACACACACACAAAATTGAATGTTTC 59.045 34.615 0.00 0.00 31.06 2.78
4095 4514 6.873076 ACACACACACAAAATTGAATGTTTCT 59.127 30.769 0.00 0.00 31.06 2.52
4096 4515 8.031864 ACACACACACAAAATTGAATGTTTCTA 58.968 29.630 0.00 0.00 31.06 2.10
4097 4516 8.533965 CACACACACAAAATTGAATGTTTCTAG 58.466 33.333 0.00 0.00 31.06 2.43
4098 4517 8.250332 ACACACACAAAATTGAATGTTTCTAGT 58.750 29.630 0.00 0.00 31.06 2.57
4099 4518 9.729023 CACACACAAAATTGAATGTTTCTAGTA 57.271 29.630 0.00 0.00 31.06 1.82
4123 4542 9.490663 GTATTTATTTTGATTGTTCTCGTCAGG 57.509 33.333 0.00 0.00 0.00 3.86
4124 4543 6.494893 TTATTTTGATTGTTCTCGTCAGGG 57.505 37.500 0.00 0.00 0.00 4.45
4125 4544 3.485463 TTTGATTGTTCTCGTCAGGGT 57.515 42.857 0.00 0.00 0.00 4.34
4126 4545 2.455674 TGATTGTTCTCGTCAGGGTG 57.544 50.000 0.00 0.00 0.00 4.61
4127 4546 1.079503 GATTGTTCTCGTCAGGGTGC 58.920 55.000 0.00 0.00 0.00 5.01
4128 4547 0.396435 ATTGTTCTCGTCAGGGTGCA 59.604 50.000 0.00 0.00 0.00 4.57
4129 4548 0.249868 TTGTTCTCGTCAGGGTGCAG 60.250 55.000 0.00 0.00 0.00 4.41
4130 4549 2.029844 GTTCTCGTCAGGGTGCAGC 61.030 63.158 7.55 7.55 0.00 5.25
4131 4550 2.210013 TTCTCGTCAGGGTGCAGCT 61.210 57.895 16.65 0.00 0.00 4.24
4132 4551 2.433838 CTCGTCAGGGTGCAGCTG 60.434 66.667 16.65 10.11 0.00 4.24
4133 4552 2.917227 TCGTCAGGGTGCAGCTGA 60.917 61.111 20.43 13.99 0.00 4.26
4134 4553 2.433838 CGTCAGGGTGCAGCTGAG 60.434 66.667 20.43 6.17 0.00 3.35
4135 4554 2.745492 GTCAGGGTGCAGCTGAGC 60.745 66.667 20.43 12.09 0.00 4.26
4136 4555 4.025858 TCAGGGTGCAGCTGAGCC 62.026 66.667 20.43 20.29 0.00 4.70
4137 4556 4.031129 CAGGGTGCAGCTGAGCCT 62.031 66.667 20.43 22.13 42.19 4.58
4138 4557 2.284921 AGGGTGCAGCTGAGCCTA 60.285 61.111 25.69 3.69 39.60 3.93
4139 4558 2.188994 GGGTGCAGCTGAGCCTAG 59.811 66.667 20.43 0.00 0.00 3.02
4140 4559 2.188994 GGTGCAGCTGAGCCTAGG 59.811 66.667 20.43 3.67 0.00 3.02
4141 4560 2.513435 GTGCAGCTGAGCCTAGGC 60.513 66.667 27.19 27.19 42.33 3.93
4151 4570 2.501610 GCCTAGGCTCGGAAGTGG 59.498 66.667 27.17 0.00 38.26 4.00
4152 4571 2.058595 GCCTAGGCTCGGAAGTGGA 61.059 63.158 27.17 0.00 38.26 4.02
4153 4572 1.403687 GCCTAGGCTCGGAAGTGGAT 61.404 60.000 27.17 0.00 38.26 3.41
4154 4573 1.123928 CCTAGGCTCGGAAGTGGATT 58.876 55.000 0.00 0.00 0.00 3.01
4155 4574 2.317040 CCTAGGCTCGGAAGTGGATTA 58.683 52.381 0.00 0.00 0.00 1.75
4156 4575 2.036089 CCTAGGCTCGGAAGTGGATTAC 59.964 54.545 0.00 0.00 0.00 1.89
4157 4576 0.831307 AGGCTCGGAAGTGGATTACC 59.169 55.000 0.00 0.00 0.00 2.85
4158 4577 0.529992 GGCTCGGAAGTGGATTACCG 60.530 60.000 0.00 0.00 45.61 4.02
4168 4587 8.798748 CGGAAGTGGATTACCGATATATAATC 57.201 38.462 0.00 5.73 46.94 1.75
4272 4701 2.620115 ACAACACTCTCCAACAAGCATG 59.380 45.455 0.00 0.00 0.00 4.06
4362 4791 7.386573 CCAAGAACAAGTTTAAAACCAACAAGT 59.613 33.333 0.00 0.00 0.00 3.16
4374 4803 3.585862 ACCAACAAGTAGCATAGACACG 58.414 45.455 0.00 0.00 0.00 4.49
4375 4804 3.006537 ACCAACAAGTAGCATAGACACGT 59.993 43.478 0.00 0.00 0.00 4.49
4397 4826 5.408356 GTCAAGAAATGCAATGAGCTTCAT 58.592 37.500 0.00 0.00 45.94 2.57
4446 4875 4.074259 ACAAGTTCAGAAGCACATGCATA 58.926 39.130 6.64 0.00 45.16 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 3.368236 AGAAAACATACTCTTCGCGCTTC 59.632 43.478 5.56 0.00 0.00 3.86
48 51 5.880887 CCCCTGGTAAGAAAACATACTCTTC 59.119 44.000 0.00 0.00 33.89 2.87
55 58 1.615919 CGGCCCCTGGTAAGAAAACAT 60.616 52.381 0.00 0.00 0.00 2.71
100 103 9.507329 AATATTCAACCACTGTATTAGCCATAG 57.493 33.333 0.00 0.00 0.00 2.23
102 105 8.220559 AGAATATTCAACCACTGTATTAGCCAT 58.779 33.333 17.56 0.00 0.00 4.40
104 107 8.345565 CAAGAATATTCAACCACTGTATTAGCC 58.654 37.037 17.56 0.00 0.00 3.93
114 117 4.332819 CCGGAGTCAAGAATATTCAACCAC 59.667 45.833 17.56 8.16 0.00 4.16
118 121 4.214986 TGCCGGAGTCAAGAATATTCAA 57.785 40.909 17.56 0.03 0.00 2.69
124 127 4.222124 AGTAATTGCCGGAGTCAAGAAT 57.778 40.909 5.05 0.00 0.00 2.40
127 130 3.074412 ACAAGTAATTGCCGGAGTCAAG 58.926 45.455 5.05 0.00 0.00 3.02
146 149 1.351076 TGGAGCAATGGAGTCTGACA 58.649 50.000 10.88 0.00 0.00 3.58
151 154 2.715046 TGTTGATGGAGCAATGGAGTC 58.285 47.619 0.00 0.00 0.00 3.36
207 210 2.094338 CAGGGTTAACGGAGAGGTACAC 60.094 54.545 0.00 0.00 0.00 2.90
209 212 2.174360 ACAGGGTTAACGGAGAGGTAC 58.826 52.381 0.00 0.00 0.00 3.34
219 222 3.306166 CGTCGATGATGAACAGGGTTAAC 59.694 47.826 0.00 0.00 0.00 2.01
221 224 2.494471 ACGTCGATGATGAACAGGGTTA 59.506 45.455 12.58 0.00 0.00 2.85
227 230 3.562567 TGTGTACGTCGATGATGAACA 57.437 42.857 12.58 7.29 0.00 3.18
279 282 3.004839 CGAAACTGTCCAAGAGAGAGACA 59.995 47.826 0.00 0.00 38.14 3.41
299 302 1.582968 GGAGTAGGCACGTGAACGA 59.417 57.895 22.23 4.43 43.02 3.85
352 360 1.696832 CCTTCTAAGCTTGCCGACGC 61.697 60.000 9.86 0.00 0.00 5.19
376 384 0.040058 ATGATGCCAAGCCTGGAACA 59.960 50.000 5.23 1.82 46.92 3.18
384 392 2.225019 CGGAGTTATGATGATGCCAAGC 59.775 50.000 0.00 0.00 0.00 4.01
397 405 1.066143 CACCCAAGCAGTCGGAGTTAT 60.066 52.381 0.00 0.00 0.00 1.89
398 406 0.320374 CACCCAAGCAGTCGGAGTTA 59.680 55.000 0.00 0.00 0.00 2.24
399 407 1.071471 CACCCAAGCAGTCGGAGTT 59.929 57.895 0.00 0.00 0.00 3.01
400 408 2.743718 CACCCAAGCAGTCGGAGT 59.256 61.111 0.00 0.00 0.00 3.85
401 409 2.046892 CCACCCAAGCAGTCGGAG 60.047 66.667 0.00 0.00 0.00 4.63
403 411 2.669569 CACCACCCAAGCAGTCGG 60.670 66.667 0.00 0.00 0.00 4.79
456 469 6.781014 AGATATAGGATTGGTACGGAGAAACA 59.219 38.462 0.00 0.00 0.00 2.83
558 598 0.040942 TGCCCAGCCCATTGTACAAT 59.959 50.000 15.47 15.47 0.00 2.71
744 788 1.769465 GAGAAGGGGGTTAGGTCCATC 59.231 57.143 0.00 0.00 0.00 3.51
781 830 1.064906 GGGAAGGGTGGGTAAGTAAGC 60.065 57.143 0.00 0.00 0.00 3.09
852 901 3.788766 GCGCCGCTTGTACTGGTG 61.789 66.667 0.00 0.00 36.36 4.17
914 964 1.804748 GTGAAGTCTAAGTTTGCGGGG 59.195 52.381 0.00 0.00 0.00 5.73
930 980 3.872603 AGTGGCCGGCTGTGTGAA 61.873 61.111 28.56 0.22 0.00 3.18
1119 1180 5.562506 TGGTGATCTTGAAGTAGTAGTCG 57.437 43.478 0.00 0.00 0.00 4.18
1242 1303 6.019156 GGAGTAGTATATAGTAGCGCCGTTAG 60.019 46.154 2.29 0.00 0.00 2.34
1265 1326 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
1330 1391 9.435570 ACATGTATAGTACTCCCTCTGTAAATT 57.564 33.333 0.00 0.00 0.00 1.82
1331 1392 8.861086 CACATGTATAGTACTCCCTCTGTAAAT 58.139 37.037 0.00 0.00 0.00 1.40
1332 1393 7.837689 ACACATGTATAGTACTCCCTCTGTAAA 59.162 37.037 0.00 0.00 0.00 2.01
1333 1394 7.351952 ACACATGTATAGTACTCCCTCTGTAA 58.648 38.462 0.00 0.00 0.00 2.41
1334 1395 6.907961 ACACATGTATAGTACTCCCTCTGTA 58.092 40.000 0.00 0.00 0.00 2.74
1335 1396 5.767670 ACACATGTATAGTACTCCCTCTGT 58.232 41.667 0.00 0.00 0.00 3.41
1336 1397 6.016693 CAGACACATGTATAGTACTCCCTCTG 60.017 46.154 0.00 0.00 0.00 3.35
1337 1398 6.065374 CAGACACATGTATAGTACTCCCTCT 58.935 44.000 0.00 0.00 0.00 3.69
1338 1399 5.278561 GCAGACACATGTATAGTACTCCCTC 60.279 48.000 0.00 0.00 0.00 4.30
1339 1400 4.585162 GCAGACACATGTATAGTACTCCCT 59.415 45.833 0.00 0.00 0.00 4.20
1340 1401 4.341235 TGCAGACACATGTATAGTACTCCC 59.659 45.833 0.00 0.00 0.00 4.30
1341 1402 5.515797 TGCAGACACATGTATAGTACTCC 57.484 43.478 0.00 0.00 0.00 3.85
1342 1403 5.923114 CCATGCAGACACATGTATAGTACTC 59.077 44.000 0.00 0.00 44.88 2.59
1347 1408 5.303165 ACATCCATGCAGACACATGTATAG 58.697 41.667 0.00 0.00 44.88 1.31
1420 1481 7.839907 TCGTTTGCCTCCTAGTACTTATTTTA 58.160 34.615 0.00 0.00 0.00 1.52
1467 1529 3.884091 ACTCCGATCCATGTCTAGTACAC 59.116 47.826 0.00 0.00 42.09 2.90
1469 1531 4.154556 GCTACTCCGATCCATGTCTAGTAC 59.845 50.000 0.00 0.00 0.00 2.73
1476 1543 5.016831 TGTATATGCTACTCCGATCCATGT 58.983 41.667 0.00 0.00 0.00 3.21
1500 1567 9.027129 GCTTATTGTGTCAGTTTCACGTATATA 57.973 33.333 0.00 0.00 38.48 0.86
1501 1568 7.547722 TGCTTATTGTGTCAGTTTCACGTATAT 59.452 33.333 0.00 0.00 38.48 0.86
1502 1569 6.869388 TGCTTATTGTGTCAGTTTCACGTATA 59.131 34.615 0.00 0.00 38.48 1.47
1503 1570 5.699001 TGCTTATTGTGTCAGTTTCACGTAT 59.301 36.000 0.00 0.00 38.48 3.06
1514 1581 2.212812 TGGCCATGCTTATTGTGTCA 57.787 45.000 0.00 0.00 0.00 3.58
1515 1582 2.223876 CCATGGCCATGCTTATTGTGTC 60.224 50.000 36.08 0.00 37.49 3.67
1536 1606 2.683859 GCGGCCGTTACCCAGTTTC 61.684 63.158 28.70 0.32 0.00 2.78
1735 2002 0.530744 TCTTGGTCGAACCGATCCAG 59.469 55.000 0.00 0.00 42.58 3.86
1748 2015 8.502105 CGTAGGTTTAGGAATTAATTCTTGGT 57.498 34.615 23.85 11.44 37.00 3.67
1818 2086 7.516198 AGGATGATTTAGATGTGCCATTAAC 57.484 36.000 0.00 0.00 0.00 2.01
1819 2087 9.288576 CTAAGGATGATTTAGATGTGCCATTAA 57.711 33.333 0.00 0.00 0.00 1.40
1821 2089 7.520798 TCTAAGGATGATTTAGATGTGCCATT 58.479 34.615 0.00 0.00 0.00 3.16
1863 2131 8.373220 CCGGTAATTAAAGGTACATCTAAGGAT 58.627 37.037 0.00 0.00 0.00 3.24
1864 2132 7.345392 ACCGGTAATTAAAGGTACATCTAAGGA 59.655 37.037 4.49 0.00 34.83 3.36
1865 2133 7.503549 ACCGGTAATTAAAGGTACATCTAAGG 58.496 38.462 4.49 0.00 34.83 2.69
1866 2134 8.823818 CAACCGGTAATTAAAGGTACATCTAAG 58.176 37.037 8.00 0.00 35.68 2.18
1867 2135 7.769970 CCAACCGGTAATTAAAGGTACATCTAA 59.230 37.037 8.00 0.00 35.68 2.10
1868 2136 7.092935 ACCAACCGGTAATTAAAGGTACATCTA 60.093 37.037 8.00 0.00 46.71 1.98
1869 2137 6.117488 CCAACCGGTAATTAAAGGTACATCT 58.883 40.000 8.00 0.00 35.68 2.90
1870 2138 5.882000 ACCAACCGGTAATTAAAGGTACATC 59.118 40.000 8.00 0.00 46.71 3.06
1871 2139 5.818887 ACCAACCGGTAATTAAAGGTACAT 58.181 37.500 8.00 0.00 46.71 2.29
1872 2140 5.240013 ACCAACCGGTAATTAAAGGTACA 57.760 39.130 8.00 0.00 46.71 2.90
2059 2330 7.869937 CAGAATGTAATCCTGTCACTATCGAAT 59.130 37.037 0.00 0.00 0.00 3.34
2060 2331 7.203218 CAGAATGTAATCCTGTCACTATCGAA 58.797 38.462 0.00 0.00 0.00 3.71
2061 2332 6.735968 GCAGAATGTAATCCTGTCACTATCGA 60.736 42.308 0.00 0.00 39.31 3.59
2062 2333 5.403766 GCAGAATGTAATCCTGTCACTATCG 59.596 44.000 0.00 0.00 39.31 2.92
2063 2334 6.520272 AGCAGAATGTAATCCTGTCACTATC 58.480 40.000 0.00 0.00 39.31 2.08
2073 2344 8.651588 CGATCTTGTATTAGCAGAATGTAATCC 58.348 37.037 0.00 0.00 39.31 3.01
2078 2349 6.573434 TCACGATCTTGTATTAGCAGAATGT 58.427 36.000 0.00 0.00 39.31 2.71
2081 2352 7.763985 TCAATTCACGATCTTGTATTAGCAGAA 59.236 33.333 4.15 0.00 0.00 3.02
2084 2355 6.816140 TGTCAATTCACGATCTTGTATTAGCA 59.184 34.615 4.15 4.32 0.00 3.49
2085 2356 7.234187 TGTCAATTCACGATCTTGTATTAGC 57.766 36.000 4.15 2.28 0.00 3.09
2086 2357 9.642312 CATTGTCAATTCACGATCTTGTATTAG 57.358 33.333 4.15 1.20 0.00 1.73
2132 2405 8.948853 TTTTCAAGAAATCAACGCAATACTAG 57.051 30.769 0.00 0.00 0.00 2.57
2213 2487 9.314501 GCTTGTCTTTAGAAATTGTTTACTACG 57.685 33.333 0.00 0.00 0.00 3.51
2350 2624 7.382759 GCTCATGTTTCTATACTTGCTAGTACC 59.617 40.741 10.26 0.00 39.59 3.34
2355 2629 6.144078 TCGCTCATGTTTCTATACTTGCTA 57.856 37.500 0.00 0.00 0.00 3.49
2363 2637 5.614308 TCATGGATTCGCTCATGTTTCTAT 58.386 37.500 0.00 0.00 40.94 1.98
2364 2638 5.022282 TCATGGATTCGCTCATGTTTCTA 57.978 39.130 0.00 0.00 40.94 2.10
2435 2715 6.713731 TTCTCCCTTTAATGTAGGAGGTTT 57.286 37.500 5.14 0.00 45.04 3.27
2453 2737 6.204882 CCGATGTCTATATTTGGGTTTTCTCC 59.795 42.308 0.00 0.00 0.00 3.71
2848 3218 4.697756 CTTGACGGAGGGGCGCAA 62.698 66.667 10.83 0.00 0.00 4.85
3186 3556 1.376553 GAGCAGGTGGAAGGTGAGC 60.377 63.158 0.00 0.00 0.00 4.26
3246 3616 0.179059 GCTTGAAGGCCTCCTCTAGC 60.179 60.000 20.32 20.32 30.89 3.42
3480 3850 3.467226 TCCATTCCCTCGCCGGTC 61.467 66.667 1.90 0.00 0.00 4.79
3630 4005 7.197017 CAGTAGAAGCTGTATGTAGTAGGTTG 58.803 42.308 0.00 0.00 32.85 3.77
3641 4019 2.379972 ACTCGGCAGTAGAAGCTGTAT 58.620 47.619 0.00 0.00 39.38 2.29
3649 4035 2.241160 TGGTACAAACTCGGCAGTAGA 58.759 47.619 0.00 0.00 31.92 2.59
3717 4108 3.687125 ACACAGACTAACAGGAGATCGA 58.313 45.455 0.00 0.00 0.00 3.59
3718 4109 3.486043 CGACACAGACTAACAGGAGATCG 60.486 52.174 0.00 0.00 0.00 3.69
3719 4110 3.732471 GCGACACAGACTAACAGGAGATC 60.732 52.174 0.00 0.00 0.00 2.75
3720 4111 2.164624 GCGACACAGACTAACAGGAGAT 59.835 50.000 0.00 0.00 0.00 2.75
3838 4229 3.998341 GCCAATCTTTTCGTACACAGGTA 59.002 43.478 0.00 0.00 0.00 3.08
3937 4328 9.927081 ATTCATCATAAACAAAAGGTAGGAGAT 57.073 29.630 0.00 0.00 0.00 2.75
3973 4364 9.385902 CCTTGACGCTACATTATGAATTAAATG 57.614 33.333 0.00 6.24 38.71 2.32
4015 4432 2.145397 AGAGGCGAGGAGTATGTTCA 57.855 50.000 0.00 0.00 0.00 3.18
4021 4438 3.446516 GGTTCTTTTAGAGGCGAGGAGTA 59.553 47.826 0.00 0.00 0.00 2.59
4026 4443 2.622436 CTGGGTTCTTTTAGAGGCGAG 58.378 52.381 0.00 0.00 0.00 5.03
4052 4471 5.942826 TGTGTGTGGTAGATAATTTGATGCA 59.057 36.000 0.00 0.00 0.00 3.96
4053 4472 6.128035 TGTGTGTGTGGTAGATAATTTGATGC 60.128 38.462 0.00 0.00 0.00 3.91
4054 4473 7.094848 TGTGTGTGTGTGGTAGATAATTTGATG 60.095 37.037 0.00 0.00 0.00 3.07
4055 4474 6.939730 TGTGTGTGTGTGGTAGATAATTTGAT 59.060 34.615 0.00 0.00 0.00 2.57
4056 4475 6.292150 TGTGTGTGTGTGGTAGATAATTTGA 58.708 36.000 0.00 0.00 0.00 2.69
4057 4476 6.552859 TGTGTGTGTGTGGTAGATAATTTG 57.447 37.500 0.00 0.00 0.00 2.32
4058 4477 7.575414 TTTGTGTGTGTGTGGTAGATAATTT 57.425 32.000 0.00 0.00 0.00 1.82
4062 4481 6.768381 TCAATTTTGTGTGTGTGTGGTAGATA 59.232 34.615 0.00 0.00 0.00 1.98
4065 4484 5.242069 TCAATTTTGTGTGTGTGTGGTAG 57.758 39.130 0.00 0.00 0.00 3.18
4067 4486 4.527509 TTCAATTTTGTGTGTGTGTGGT 57.472 36.364 0.00 0.00 0.00 4.16
4068 4487 4.869297 ACATTCAATTTTGTGTGTGTGTGG 59.131 37.500 3.70 0.00 0.00 4.17
4069 4488 6.406093 AACATTCAATTTTGTGTGTGTGTG 57.594 33.333 4.84 0.00 31.23 3.82
4070 4489 6.873076 AGAAACATTCAATTTTGTGTGTGTGT 59.127 30.769 4.84 0.00 31.23 3.72
4071 4490 7.293402 AGAAACATTCAATTTTGTGTGTGTG 57.707 32.000 4.84 0.00 31.23 3.82
4072 4491 8.250332 ACTAGAAACATTCAATTTTGTGTGTGT 58.750 29.630 0.00 0.87 31.23 3.72
4073 4492 8.633075 ACTAGAAACATTCAATTTTGTGTGTG 57.367 30.769 0.00 0.00 31.23 3.82
4097 4516 9.490663 CCTGACGAGAACAATCAAAATAAATAC 57.509 33.333 0.00 0.00 0.00 1.89
4098 4517 8.673711 CCCTGACGAGAACAATCAAAATAAATA 58.326 33.333 0.00 0.00 0.00 1.40
4099 4518 7.176690 ACCCTGACGAGAACAATCAAAATAAAT 59.823 33.333 0.00 0.00 0.00 1.40
4100 4519 6.488683 ACCCTGACGAGAACAATCAAAATAAA 59.511 34.615 0.00 0.00 0.00 1.40
4101 4520 6.001460 ACCCTGACGAGAACAATCAAAATAA 58.999 36.000 0.00 0.00 0.00 1.40
4102 4521 5.411361 CACCCTGACGAGAACAATCAAAATA 59.589 40.000 0.00 0.00 0.00 1.40
4103 4522 4.216257 CACCCTGACGAGAACAATCAAAAT 59.784 41.667 0.00 0.00 0.00 1.82
4104 4523 3.563808 CACCCTGACGAGAACAATCAAAA 59.436 43.478 0.00 0.00 0.00 2.44
4105 4524 3.138304 CACCCTGACGAGAACAATCAAA 58.862 45.455 0.00 0.00 0.00 2.69
4106 4525 2.766313 CACCCTGACGAGAACAATCAA 58.234 47.619 0.00 0.00 0.00 2.57
4107 4526 1.608025 GCACCCTGACGAGAACAATCA 60.608 52.381 0.00 0.00 0.00 2.57
4108 4527 1.079503 GCACCCTGACGAGAACAATC 58.920 55.000 0.00 0.00 0.00 2.67
4109 4528 0.396435 TGCACCCTGACGAGAACAAT 59.604 50.000 0.00 0.00 0.00 2.71
4110 4529 0.249868 CTGCACCCTGACGAGAACAA 60.250 55.000 0.00 0.00 0.00 2.83
4111 4530 1.367471 CTGCACCCTGACGAGAACA 59.633 57.895 0.00 0.00 0.00 3.18
4112 4531 2.029844 GCTGCACCCTGACGAGAAC 61.030 63.158 0.00 0.00 0.00 3.01
4113 4532 2.210013 AGCTGCACCCTGACGAGAA 61.210 57.895 1.02 0.00 0.00 2.87
4114 4533 2.601666 AGCTGCACCCTGACGAGA 60.602 61.111 1.02 0.00 0.00 4.04
4115 4534 2.433838 CAGCTGCACCCTGACGAG 60.434 66.667 0.00 0.00 32.03 4.18
4116 4535 2.917227 TCAGCTGCACCCTGACGA 60.917 61.111 9.47 0.00 34.59 4.20
4117 4536 2.433838 CTCAGCTGCACCCTGACG 60.434 66.667 9.47 2.84 35.60 4.35
4118 4537 2.745492 GCTCAGCTGCACCCTGAC 60.745 66.667 9.47 3.50 35.60 3.51
4119 4538 4.025858 GGCTCAGCTGCACCCTGA 62.026 66.667 9.47 10.86 37.71 3.86
4120 4539 2.590391 CTAGGCTCAGCTGCACCCTG 62.590 65.000 22.22 12.45 34.04 4.45
4121 4540 2.284921 TAGGCTCAGCTGCACCCT 60.285 61.111 18.16 18.67 34.04 4.34
4122 4541 2.188994 CTAGGCTCAGCTGCACCC 59.811 66.667 18.16 13.37 34.04 4.61
4123 4542 2.188994 CCTAGGCTCAGCTGCACC 59.811 66.667 9.47 12.84 34.04 5.01
4124 4543 2.513435 GCCTAGGCTCAGCTGCAC 60.513 66.667 27.17 2.69 38.26 4.57
4134 4553 1.403687 ATCCACTTCCGAGCCTAGGC 61.404 60.000 27.19 27.19 42.33 3.93
4135 4554 1.123928 AATCCACTTCCGAGCCTAGG 58.876 55.000 3.67 3.67 0.00 3.02
4136 4555 2.036089 GGTAATCCACTTCCGAGCCTAG 59.964 54.545 0.00 0.00 0.00 3.02
4137 4556 2.037144 GGTAATCCACTTCCGAGCCTA 58.963 52.381 0.00 0.00 0.00 3.93
4138 4557 0.831307 GGTAATCCACTTCCGAGCCT 59.169 55.000 0.00 0.00 0.00 4.58
4139 4558 0.529992 CGGTAATCCACTTCCGAGCC 60.530 60.000 0.00 0.00 44.86 4.70
4140 4559 0.458669 TCGGTAATCCACTTCCGAGC 59.541 55.000 0.97 0.00 45.49 5.03
4143 4562 8.410912 TGATTATATATCGGTAATCCACTTCCG 58.589 37.037 10.50 0.00 43.65 4.30
4168 4587 9.144747 GCTGAGTAATATGTGTTGGACTATATG 57.855 37.037 0.00 0.00 0.00 1.78
4272 4701 7.440556 CCTATATGAGGTTGTCATGCTATATGC 59.559 40.741 0.00 0.00 46.09 3.14
4362 4791 4.566759 GCATTTCTTGACGTGTCTATGCTA 59.433 41.667 0.00 0.00 0.00 3.49
4374 4803 4.801891 TGAAGCTCATTGCATTTCTTGAC 58.198 39.130 0.00 0.00 45.94 3.18
4375 4804 5.647589 GATGAAGCTCATTGCATTTCTTGA 58.352 37.500 0.00 0.00 45.94 3.02
4446 4875 6.400940 CGTTTGACATTTGAACTTGCAAACTT 60.401 34.615 0.00 0.00 40.23 2.66


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

AutoCloner maintained by Alex Coulton.