Multiple sequence alignment - TraesCS3B01G484500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G484500 chr3B 100.000 4236 0 0 1 4236 730936833 730941068 0.000000e+00 7823.0
1 TraesCS3B01G484500 chr3B 88.372 731 63 12 2635 3347 731264914 731265640 0.000000e+00 859.0
2 TraesCS3B01G484500 chr3B 82.471 696 81 21 1331 1989 731263506 731264197 4.750000e-159 571.0
3 TraesCS3B01G484500 chr3B 86.398 522 58 6 1987 2504 731264263 731264775 3.700000e-155 558.0
4 TraesCS3B01G484500 chr3B 89.189 74 5 2 522 595 731262628 731262698 5.830000e-14 89.8
5 TraesCS3B01G484500 chr3A 87.353 2127 154 41 1626 3689 688579113 688581187 0.000000e+00 2331.0
6 TraesCS3B01G484500 chr3A 83.452 1263 131 32 1330 2524 688616293 688617545 0.000000e+00 1103.0
7 TraesCS3B01G484500 chr3A 87.500 720 72 10 2580 3298 688618150 688618852 0.000000e+00 815.0
8 TraesCS3B01G484500 chr3A 90.385 312 22 3 46 351 688576661 688576970 1.830000e-108 403.0
9 TraesCS3B01G484500 chr3A 80.093 643 45 40 515 1144 688578152 688578724 6.600000e-108 401.0
10 TraesCS3B01G484500 chr3A 88.485 330 27 6 1301 1625 688578749 688579072 5.140000e-104 388.0
11 TraesCS3B01G484500 chr3A 88.934 244 19 2 3729 3971 688581563 688581799 1.150000e-75 294.0
12 TraesCS3B01G484500 chr3A 82.373 295 22 12 3966 4235 688581983 688582272 3.290000e-56 230.0
13 TraesCS3B01G484500 chr3A 91.597 119 7 1 365 483 688578044 688578159 1.220000e-35 161.0
14 TraesCS3B01G484500 chr3D 90.643 1742 113 23 1622 3347 551272272 551273979 0.000000e+00 2268.0
15 TraesCS3B01G484500 chr3D 88.959 1114 79 20 46 1144 551270816 551271900 0.000000e+00 1336.0
16 TraesCS3B01G484500 chr3D 85.776 921 85 25 3346 4230 551274010 551274920 0.000000e+00 933.0
17 TraesCS3B01G484500 chr3D 86.702 752 68 16 2580 3315 551392281 551391546 0.000000e+00 806.0
18 TraesCS3B01G484500 chr3D 82.663 721 78 16 1331 2005 551393669 551392950 2.820000e-166 595.0
19 TraesCS3B01G484500 chr3D 86.151 491 59 4 1978 2466 551392947 551392464 4.850000e-144 521.0
20 TraesCS3B01G484500 chr3D 90.060 332 20 7 1301 1625 551271912 551272237 6.550000e-113 418.0
21 TraesCS3B01G484500 chr4A 91.758 728 33 10 2233 2934 11173973 11174699 0.000000e+00 987.0
22 TraesCS3B01G484500 chr4A 91.525 59 3 2 3692 3750 15491643 15491699 3.510000e-11 80.5
23 TraesCS3B01G484500 chr4A 97.143 35 1 0 3716 3750 680953121 680953087 4.570000e-05 60.2
24 TraesCS3B01G484500 chr7D 91.358 729 36 10 2233 2935 165953481 165952754 0.000000e+00 972.0
25 TraesCS3B01G484500 chr7D 90.000 60 4 2 3691 3750 5526421 5526364 4.540000e-10 76.8
26 TraesCS3B01G484500 chr7A 85.714 140 13 3 3346 3478 715930087 715930226 1.590000e-29 141.0
27 TraesCS3B01G484500 chr7A 72.772 202 45 9 4038 4234 622347587 622347783 4.570000e-05 60.2
28 TraesCS3B01G484500 chr7B 89.655 58 2 4 3694 3750 611806112 611806058 2.110000e-08 71.3
29 TraesCS3B01G484500 chr7B 87.273 55 4 3 3700 3754 625892560 625892611 4.570000e-05 60.2
30 TraesCS3B01G484500 chr1B 76.812 138 24 7 4034 4165 610039278 610039413 2.110000e-08 71.3
31 TraesCS3B01G484500 chr1B 100.000 31 0 0 2905 2935 29769018 29768988 1.650000e-04 58.4
32 TraesCS3B01G484500 chr1B 100.000 31 0 0 2905 2935 322465877 322465847 1.650000e-04 58.4
33 TraesCS3B01G484500 chr6B 97.436 39 1 0 4118 4156 664696620 664696658 2.730000e-07 67.6
34 TraesCS3B01G484500 chr6B 100.000 31 0 0 2905 2935 38071627 38071657 1.650000e-04 58.4


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 TraesCS3B01G484500 chr3B 730936833 730941068 4235 False 7823.000000 7823 100.000000 1 4236 1 chr3B.!!$F1 4235
1 TraesCS3B01G484500 chr3B 731262628 731265640 3012 False 519.450000 859 86.607500 522 3347 4 chr3B.!!$F2 2825
2 TraesCS3B01G484500 chr3A 688616293 688618852 2559 False 959.000000 1103 85.476000 1330 3298 2 chr3A.!!$F2 1968
3 TraesCS3B01G484500 chr3A 688576661 688582272 5611 False 601.142857 2331 87.031429 46 4235 7 chr3A.!!$F1 4189
4 TraesCS3B01G484500 chr3D 551270816 551274920 4104 False 1238.750000 2268 88.859500 46 4230 4 chr3D.!!$F1 4184
5 TraesCS3B01G484500 chr3D 551391546 551393669 2123 True 640.666667 806 85.172000 1331 3315 3 chr3D.!!$R1 1984
6 TraesCS3B01G484500 chr4A 11173973 11174699 726 False 987.000000 987 91.758000 2233 2934 1 chr4A.!!$F1 701
7 TraesCS3B01G484500 chr7D 165952754 165953481 727 True 972.000000 972 91.358000 2233 2935 1 chr7D.!!$R2 702

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
708 1891 0.036952 GTAGCTTGGCTGCTCTCACA 60.037 55.000 8.68 0.0 42.97 3.58 F
1165 2434 0.036577 CTGCTCTTCTCCCACACCAG 60.037 60.000 0.00 0.0 0.00 4.00 F
1220 2493 0.250510 TGAGTATGTGGTTGGCGCAA 60.251 50.000 10.83 0.0 0.00 4.85 F
1221 2494 0.447801 GAGTATGTGGTTGGCGCAAG 59.552 55.000 10.83 0.0 43.44 4.01 F
1324 2597 1.352352 AGCCCAGTTATGTGCTTGTCT 59.648 47.619 0.00 0.0 36.70 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 3991 0.034616 AGCTCTGTTCCTCTGTGCAC 59.965 55.000 10.75 10.75 37.10 4.57 R
2510 3998 2.278854 GCAGAATGAGCTCTGTTCCTC 58.721 52.381 21.21 13.36 44.04 3.71 R
3046 5116 3.378742 CGACTACACTGCCAGATAGAGTT 59.621 47.826 12.62 0.00 0.00 3.01 R
3211 5281 5.991933 ACTTGAAAGAGCTCTCTATGTCA 57.008 39.130 18.55 12.49 39.39 3.58 R
3306 5377 0.458543 CTATCACAAGTCAGCCGCGT 60.459 55.000 4.92 0.00 0.00 6.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 4.929808 AGTAGACCACATGAAAATGTCGAC 59.070 41.667 9.11 9.11 33.51 4.20
61 62 3.074412 GACCACATGAAAATGTCGACCT 58.926 45.455 14.12 0.00 31.37 3.85
66 67 6.049149 CCACATGAAAATGTCGACCTATACT 58.951 40.000 14.12 0.00 31.37 2.12
94 95 5.185454 CAGTGAGTGGCAGTGGAATATTTA 58.815 41.667 0.00 0.00 42.95 1.40
141 142 3.015516 ACGAAAAATGCCGTGGTCT 57.984 47.368 0.00 0.00 37.64 3.85
146 147 0.598065 AAAATGCCGTGGTCTTGAGC 59.402 50.000 0.00 0.00 0.00 4.26
163 164 2.158856 TGAGCCTGATCATGATGGTGTC 60.159 50.000 14.30 10.46 0.00 3.67
177 182 1.363885 GGTGTCGCATTAACCGGGTC 61.364 60.000 6.32 0.00 0.00 4.46
214 219 5.119588 ACAATGTCAAACCGTAACGTATGAG 59.880 40.000 0.00 0.00 0.00 2.90
220 225 0.102481 CCGTAACGTATGAGCTGCCT 59.898 55.000 0.00 0.00 0.00 4.75
231 236 7.996385 ACGTATGAGCTGCCTATTTTAATTTT 58.004 30.769 0.00 0.00 0.00 1.82
275 286 3.303593 GCACACAAAGTCATCAGTGTCAG 60.304 47.826 0.00 0.00 42.79 3.51
351 362 6.615316 TCCAATGAGGATAGAGACAATGGTTA 59.385 38.462 0.00 0.00 43.07 2.85
353 364 8.597167 CCAATGAGGATAGAGACAATGGTTATA 58.403 37.037 0.00 0.00 41.22 0.98
359 370 9.482175 AGGATAGAGACAATGGTTATATACTCC 57.518 37.037 0.00 0.00 0.00 3.85
360 371 9.482175 GGATAGAGACAATGGTTATATACTCCT 57.518 37.037 0.00 0.00 0.00 3.69
407 1478 2.095263 CGCGGAATGATTTGTTTGACCT 60.095 45.455 0.00 0.00 0.00 3.85
483 1554 4.441792 TGATGTTCTATTATGTGCGCTGT 58.558 39.130 9.73 0.00 0.00 4.40
502 1574 0.339859 TGACTGCAGGGGGTAGATCT 59.660 55.000 19.93 0.00 32.90 2.75
516 1588 4.548991 GTAGATCTACCCACTACACGTG 57.451 50.000 20.40 15.48 43.41 4.49
519 1591 0.606130 TCTACCCACTACACGTGCGA 60.606 55.000 17.22 2.57 42.42 5.10
520 1592 0.455633 CTACCCACTACACGTGCGAC 60.456 60.000 17.22 0.00 42.42 5.19
612 1684 1.142870 CCCTCCACAGAAACTGGAACA 59.857 52.381 0.00 0.00 37.36 3.18
613 1685 2.224867 CCCTCCACAGAAACTGGAACAT 60.225 50.000 0.00 0.00 37.36 2.71
615 1687 3.496692 CCTCCACAGAAACTGGAACATCA 60.497 47.826 0.00 0.00 37.36 3.07
616 1688 4.330250 CTCCACAGAAACTGGAACATCAT 58.670 43.478 0.00 0.00 37.36 2.45
629 1781 2.277501 ATCATTTTGCTCGCGCGC 60.278 55.556 27.95 23.91 39.65 6.86
646 1798 2.626780 GCCGGCTGGTTTCAGGTTC 61.627 63.158 22.15 0.00 41.19 3.62
647 1799 1.228124 CCGGCTGGTTTCAGGTTCA 60.228 57.895 2.29 0.00 41.19 3.18
648 1800 1.237285 CCGGCTGGTTTCAGGTTCAG 61.237 60.000 2.29 0.00 41.19 3.02
649 1801 1.237285 CGGCTGGTTTCAGGTTCAGG 61.237 60.000 0.00 0.00 41.19 3.86
650 1802 0.178990 GGCTGGTTTCAGGTTCAGGT 60.179 55.000 0.00 0.00 41.19 4.00
651 1803 1.692411 GCTGGTTTCAGGTTCAGGTT 58.308 50.000 0.00 0.00 41.19 3.50
704 1887 1.904032 GAGGTAGCTTGGCTGCTCT 59.096 57.895 8.68 2.18 42.97 4.09
705 1888 0.179086 GAGGTAGCTTGGCTGCTCTC 60.179 60.000 8.68 7.25 42.97 3.20
706 1889 0.906756 AGGTAGCTTGGCTGCTCTCA 60.907 55.000 8.68 0.00 42.97 3.27
707 1890 0.742635 GGTAGCTTGGCTGCTCTCAC 60.743 60.000 8.68 3.15 42.97 3.51
708 1891 0.036952 GTAGCTTGGCTGCTCTCACA 60.037 55.000 8.68 0.00 42.97 3.58
716 1899 1.373497 CTGCTCTCACACCACCGAC 60.373 63.158 0.00 0.00 0.00 4.79
717 1900 2.048127 GCTCTCACACCACCGACC 60.048 66.667 0.00 0.00 0.00 4.79
811 2052 2.036992 CTCTGGTTCTGTCTTCTGTGCT 59.963 50.000 0.00 0.00 0.00 4.40
828 2069 0.716108 GCTGAGATGAACCAACGACG 59.284 55.000 0.00 0.00 0.00 5.12
839 2080 1.275657 CAACGACGCACACCTCAAC 59.724 57.895 0.00 0.00 0.00 3.18
865 2107 4.660168 ACCTGCTCTGTTTCTGAATTCAT 58.340 39.130 8.96 0.00 0.00 2.57
943 2196 8.712285 AAATGAATGGATTCTGCTACAATTTG 57.288 30.769 1.26 0.00 37.67 2.32
991 2247 6.073819 GCCACTTATTGTTTTTGCAGTTTAGG 60.074 38.462 0.00 0.00 0.00 2.69
1056 2312 0.749049 GGGCAGCAAATGATCCTTCC 59.251 55.000 0.00 0.00 0.00 3.46
1133 2402 9.231297 CTCCCTTGTGAGATTTTATTTACAAGA 57.769 33.333 14.43 0.00 44.59 3.02
1144 2413 9.989394 GATTTTATTTACAAGAAAACTCAACGC 57.011 29.630 0.00 0.00 0.00 4.84
1146 2415 8.776680 TTTATTTACAAGAAAACTCAACGCTC 57.223 30.769 0.00 0.00 0.00 5.03
1147 2416 6.619801 ATTTACAAGAAAACTCAACGCTCT 57.380 33.333 0.00 0.00 0.00 4.09
1148 2417 3.951979 ACAAGAAAACTCAACGCTCTG 57.048 42.857 0.00 0.00 0.00 3.35
1149 2418 2.032178 ACAAGAAAACTCAACGCTCTGC 59.968 45.455 0.00 0.00 0.00 4.26
1150 2419 2.246719 AGAAAACTCAACGCTCTGCT 57.753 45.000 0.00 0.00 0.00 4.24
1151 2420 2.139118 AGAAAACTCAACGCTCTGCTC 58.861 47.619 0.00 0.00 0.00 4.26
1153 2422 2.246719 AAACTCAACGCTCTGCTCTT 57.753 45.000 0.00 0.00 0.00 2.85
1154 2423 1.789506 AACTCAACGCTCTGCTCTTC 58.210 50.000 0.00 0.00 0.00 2.87
1155 2424 0.965439 ACTCAACGCTCTGCTCTTCT 59.035 50.000 0.00 0.00 0.00 2.85
1156 2425 1.067915 ACTCAACGCTCTGCTCTTCTC 60.068 52.381 0.00 0.00 0.00 2.87
1157 2426 0.244994 TCAACGCTCTGCTCTTCTCC 59.755 55.000 0.00 0.00 0.00 3.71
1160 2429 1.153667 CGCTCTGCTCTTCTCCCAC 60.154 63.158 0.00 0.00 0.00 4.61
1161 2430 1.881903 CGCTCTGCTCTTCTCCCACA 61.882 60.000 0.00 0.00 0.00 4.17
1162 2431 0.390998 GCTCTGCTCTTCTCCCACAC 60.391 60.000 0.00 0.00 0.00 3.82
1163 2432 0.248843 CTCTGCTCTTCTCCCACACC 59.751 60.000 0.00 0.00 0.00 4.16
1164 2433 0.471780 TCTGCTCTTCTCCCACACCA 60.472 55.000 0.00 0.00 0.00 4.17
1165 2434 0.036577 CTGCTCTTCTCCCACACCAG 60.037 60.000 0.00 0.00 0.00 4.00
1167 2436 0.321122 GCTCTTCTCCCACACCAGTG 60.321 60.000 0.00 0.00 45.47 3.66
1200 2473 5.607119 TTAGCAAACGATCCTTCTGAAAC 57.393 39.130 0.00 0.00 0.00 2.78
1204 2477 4.377841 GCAAACGATCCTTCTGAAACTGAG 60.378 45.833 0.00 0.00 0.00 3.35
1205 2478 4.608948 AACGATCCTTCTGAAACTGAGT 57.391 40.909 0.00 0.00 0.00 3.41
1207 2480 5.923733 ACGATCCTTCTGAAACTGAGTAT 57.076 39.130 0.00 0.00 0.00 2.12
1208 2481 5.655488 ACGATCCTTCTGAAACTGAGTATG 58.345 41.667 0.00 0.00 0.00 2.39
1209 2482 5.186021 ACGATCCTTCTGAAACTGAGTATGT 59.814 40.000 0.00 0.00 0.00 2.29
1210 2483 5.518128 CGATCCTTCTGAAACTGAGTATGTG 59.482 44.000 0.00 0.00 0.00 3.21
1212 2485 4.593206 TCCTTCTGAAACTGAGTATGTGGT 59.407 41.667 0.00 0.00 0.00 4.16
1213 2486 5.071788 TCCTTCTGAAACTGAGTATGTGGTT 59.928 40.000 0.00 0.00 0.00 3.67
1214 2487 5.180117 CCTTCTGAAACTGAGTATGTGGTTG 59.820 44.000 0.00 0.00 0.00 3.77
1215 2488 4.641396 TCTGAAACTGAGTATGTGGTTGG 58.359 43.478 0.00 0.00 0.00 3.77
1216 2489 3.146066 TGAAACTGAGTATGTGGTTGGC 58.854 45.455 0.00 0.00 0.00 4.52
1220 2493 0.250510 TGAGTATGTGGTTGGCGCAA 60.251 50.000 10.83 0.00 0.00 4.85
1221 2494 0.447801 GAGTATGTGGTTGGCGCAAG 59.552 55.000 10.83 0.00 43.44 4.01
1233 2506 3.339731 CGCAAGCTCCCGTGAAAA 58.660 55.556 0.00 0.00 0.00 2.29
1234 2507 1.652012 CGCAAGCTCCCGTGAAAAA 59.348 52.632 0.00 0.00 0.00 1.94
1253 2526 5.637006 AAAAAGCCGTCATAATAGTGCAA 57.363 34.783 0.00 0.00 0.00 4.08
1258 2531 6.727824 AGCCGTCATAATAGTGCAATTATC 57.272 37.500 0.00 0.00 31.17 1.75
1259 2532 6.467677 AGCCGTCATAATAGTGCAATTATCT 58.532 36.000 0.00 0.00 31.17 1.98
1269 2542 3.835378 TGCAATTATCTGTGCAGTGTG 57.165 42.857 0.00 0.00 45.52 3.82
1270 2543 3.148412 TGCAATTATCTGTGCAGTGTGT 58.852 40.909 0.00 0.00 45.52 3.72
1274 2547 5.740569 GCAATTATCTGTGCAGTGTGTTATG 59.259 40.000 0.00 0.00 40.58 1.90
1275 2548 4.944962 TTATCTGTGCAGTGTGTTATGC 57.055 40.909 0.00 0.00 42.86 3.14
1285 2558 6.470557 GCAGTGTGTTATGCAATTCATTTT 57.529 33.333 0.00 0.00 42.11 1.82
1318 2591 2.939103 CTCTGTTAGCCCAGTTATGTGC 59.061 50.000 0.00 0.00 34.02 4.57
1323 2596 1.826385 AGCCCAGTTATGTGCTTGTC 58.174 50.000 0.00 0.00 36.70 3.18
1324 2597 1.352352 AGCCCAGTTATGTGCTTGTCT 59.648 47.619 0.00 0.00 36.70 3.41
1325 2598 2.162681 GCCCAGTTATGTGCTTGTCTT 58.837 47.619 0.00 0.00 0.00 3.01
1326 2599 3.009033 AGCCCAGTTATGTGCTTGTCTTA 59.991 43.478 0.00 0.00 36.70 2.10
1327 2600 3.756434 GCCCAGTTATGTGCTTGTCTTAA 59.244 43.478 0.00 0.00 0.00 1.85
1328 2601 4.142600 GCCCAGTTATGTGCTTGTCTTAAG 60.143 45.833 0.00 0.00 0.00 1.85
1345 2618 8.539770 TGTCTTAAGCTTTGTTCTCTGAATAG 57.460 34.615 3.20 0.00 0.00 1.73
1385 2665 3.132111 TGCTAGTCCAGTTATTCATCGCA 59.868 43.478 0.00 0.00 0.00 5.10
1395 2675 9.990360 TCCAGTTATTCATCGCAGTAAATTATA 57.010 29.630 0.00 0.00 0.00 0.98
1424 2705 1.970917 CTTGCCGATGCCGACTGAAC 61.971 60.000 0.00 0.00 38.22 3.18
1425 2706 2.125512 GCCGATGCCGACTGAACT 60.126 61.111 0.00 0.00 38.22 3.01
1436 2738 2.731976 CCGACTGAACTACTGCTTTGTC 59.268 50.000 0.00 0.00 0.00 3.18
1447 2749 3.748021 GCTTTGTCAGCGTGTTACC 57.252 52.632 0.00 0.00 39.29 2.85
1461 2763 6.035758 CAGCGTGTTACCTTCTTCTTATAACC 59.964 42.308 0.00 0.00 0.00 2.85
1470 2781 7.104290 ACCTTCTTCTTATAACCAGTGCTTAC 58.896 38.462 0.00 0.00 0.00 2.34
1491 2806 4.968259 ACGCATATGCTACCCTGATTAAA 58.032 39.130 24.56 0.00 39.32 1.52
1503 2818 2.887152 CCTGATTAAATACCAGGGCTGC 59.113 50.000 0.00 0.00 42.75 5.25
1625 2940 2.062636 TCCCTGGGTAAGCTTTTCAGT 58.937 47.619 13.56 0.00 0.00 3.41
1626 2941 2.162681 CCCTGGGTAAGCTTTTCAGTG 58.837 52.381 3.20 0.00 0.00 3.66
1651 3012 6.703165 GCATTTTTCTTTCTGTTGATTGACCT 59.297 34.615 0.00 0.00 0.00 3.85
1717 3085 1.523758 CTGGGTGCCTACTGTTCAAC 58.476 55.000 0.00 0.00 0.00 3.18
1902 3270 6.951062 TTCACTTTCAATGGTGTTGATACA 57.049 33.333 0.00 0.00 35.26 2.29
1908 3276 2.024176 ATGGTGTTGATACAGACGGC 57.976 50.000 0.00 0.00 34.24 5.68
1926 3294 1.518903 GCACTGTCACAAAGGGAGGC 61.519 60.000 0.00 0.00 0.00 4.70
1959 3327 6.224584 TCACATTGTAGTTCATGAACGGTAA 58.775 36.000 28.18 23.18 45.50 2.85
1966 3334 2.325583 TCATGAACGGTAAGGATGCC 57.674 50.000 0.00 0.00 0.00 4.40
1999 3367 4.142381 GGATGTTCTGAATTTGGTGTAGGC 60.142 45.833 0.00 0.00 0.00 3.93
2034 3493 8.538409 ACAAATAGTCATGGCAATTCTTTTTC 57.462 30.769 0.00 0.00 0.00 2.29
2057 3516 3.003793 GCCTCCAAGTCAAAACTCACTTC 59.996 47.826 0.00 0.00 33.48 3.01
2318 3786 6.260050 TGACAGTTTTGAGTACAAGTGAATCC 59.740 38.462 5.71 0.00 37.32 3.01
2348 3816 3.347216 TGAAGCTATCAACCTTCTTGGC 58.653 45.455 0.00 0.00 38.55 4.52
2469 3942 5.877012 AGCACAACAAGTACATATCTCCTTG 59.123 40.000 0.00 0.00 40.05 3.61
2490 3970 7.054124 CCTTGCCTTATGTTAGATTCCAACTA 58.946 38.462 0.00 0.00 0.00 2.24
2541 4439 4.056740 AGCTCATTCTGCAATCGATACTG 58.943 43.478 0.00 0.00 0.00 2.74
2577 4626 6.462073 TTTTGTGCGAGAGACAATTAGTAC 57.538 37.500 0.00 0.00 33.47 2.73
2578 4627 3.754955 TGTGCGAGAGACAATTAGTACG 58.245 45.455 0.00 0.00 0.00 3.67
2582 4631 3.003068 GCGAGAGACAATTAGTACGGCTA 59.997 47.826 0.00 0.00 0.00 3.93
2614 4663 6.072783 GCTTGTTATTCTTCTCACTCTGCTTT 60.073 38.462 0.00 0.00 0.00 3.51
2639 4688 8.697846 TGTACTAAGTGAGAATAACGAAATGG 57.302 34.615 0.00 0.00 0.00 3.16
2781 4830 3.938334 GCTTTCCTGGAGAAATCAGAGTC 59.062 47.826 0.00 0.00 43.50 3.36
2947 5016 5.544176 ACTTGGTGAAGAGTTGAGGATCTAA 59.456 40.000 0.00 0.00 32.04 2.10
2955 5024 7.667219 TGAAGAGTTGAGGATCTAAAAGCATTT 59.333 33.333 0.00 0.00 36.05 2.32
3137 5207 9.177608 CAAACAAAATCTACCCAGATATTGAGA 57.822 33.333 0.00 0.00 40.81 3.27
3211 5281 5.413523 GGATGTGAAGTACCGGTTTGTAATT 59.586 40.000 15.04 0.00 32.23 1.40
3318 5389 0.248458 CAAACAAACGCGGCTGACTT 60.248 50.000 12.47 3.76 0.00 3.01
3347 5420 4.388577 AGGGCTTTCCTCTGTAATGTTT 57.611 40.909 0.00 0.00 44.06 2.83
3352 5457 6.015772 GGGCTTTCCTCTGTAATGTTTTTGTA 60.016 38.462 0.00 0.00 0.00 2.41
3418 5527 7.315890 TCCTATGAATGCTCAATGTAGTATCG 58.684 38.462 0.00 0.00 34.49 2.92
3454 5563 3.452755 TTGACTGATCAACACGTGAGT 57.547 42.857 25.01 14.05 42.44 3.41
3476 5585 5.960811 AGTAATGGTCAGATTGAAGAGAGGA 59.039 40.000 0.00 0.00 0.00 3.71
3482 5592 6.213397 TGGTCAGATTGAAGAGAGGAAATACA 59.787 38.462 0.00 0.00 0.00 2.29
3505 5615 1.269413 CCAAAACAGCTGAAGCCAGTG 60.269 52.381 23.35 7.88 42.35 3.66
3562 5672 3.782523 TCACTTATTTCTGGGGCTGATCT 59.217 43.478 0.00 0.00 0.00 2.75
3572 5682 1.127343 GGGCTGATCTAGAACCTGCT 58.873 55.000 19.26 0.00 0.00 4.24
3602 5712 9.264719 CAGAAGCAAATATCATGTCAGTATACA 57.735 33.333 5.50 0.00 0.00 2.29
3626 5736 7.920682 ACATTTCAAGCTTCGACAAACTATTTT 59.079 29.630 0.00 0.00 0.00 1.82
3628 5738 5.757886 TCAAGCTTCGACAAACTATTTTGG 58.242 37.500 9.99 0.00 45.65 3.28
3629 5739 4.766404 AGCTTCGACAAACTATTTTGGG 57.234 40.909 9.99 2.43 45.65 4.12
3632 5742 4.215613 GCTTCGACAAACTATTTTGGGACT 59.784 41.667 9.99 0.00 45.65 3.85
3689 5799 8.691797 TCCAATTTTAACTACAAAACAAGAGCT 58.308 29.630 0.00 0.00 30.57 4.09
3707 5817 2.183555 CCGCTTCGGTACACCCTC 59.816 66.667 0.00 0.00 42.73 4.30
3708 5818 2.183555 CGCTTCGGTACACCCTCC 59.816 66.667 0.00 0.00 0.00 4.30
3709 5819 2.582978 GCTTCGGTACACCCTCCC 59.417 66.667 0.00 0.00 0.00 4.30
3712 5822 0.324460 CTTCGGTACACCCTCCCTCT 60.324 60.000 0.00 0.00 0.00 3.69
3714 5824 1.000019 CGGTACACCCTCCCTCTCA 60.000 63.158 0.00 0.00 0.00 3.27
3715 5825 1.321074 CGGTACACCCTCCCTCTCAC 61.321 65.000 0.00 0.00 0.00 3.51
3716 5826 0.252103 GGTACACCCTCCCTCTCACA 60.252 60.000 0.00 0.00 0.00 3.58
3717 5827 1.640917 GTACACCCTCCCTCTCACAA 58.359 55.000 0.00 0.00 0.00 3.33
3718 5828 1.975680 GTACACCCTCCCTCTCACAAA 59.024 52.381 0.00 0.00 0.00 2.83
3719 5829 0.765510 ACACCCTCCCTCTCACAAAC 59.234 55.000 0.00 0.00 0.00 2.93
3720 5830 0.036875 CACCCTCCCTCTCACAAACC 59.963 60.000 0.00 0.00 0.00 3.27
3721 5831 1.296715 CCCTCCCTCTCACAAACCG 59.703 63.158 0.00 0.00 0.00 4.44
3741 6187 4.349930 ACCGTATAAAGGGCAATATGGACT 59.650 41.667 7.43 0.00 37.90 3.85
3756 6202 8.721478 GCAATATGGACTTTTGACATATCGTAT 58.279 33.333 0.00 0.00 36.94 3.06
3801 6247 1.844003 CGTATATGGACGTGCGTGC 59.156 57.895 12.54 9.23 38.04 5.34
3803 6249 0.528901 GTATATGGACGTGCGTGCCA 60.529 55.000 12.54 13.99 35.53 4.92
3807 6253 3.490759 GGACGTGCGTGCCATCAG 61.491 66.667 0.67 0.00 0.00 2.90
3954 6403 4.321008 CGTGCTACAGTACTTCTTTCCTCA 60.321 45.833 0.00 0.00 0.00 3.86
3997 6636 2.153547 AAAAAGCATGCGTTCCCGGG 62.154 55.000 19.22 16.85 33.68 5.73
4005 6644 1.450669 GCGTTCCCGGGCTGATTTA 60.451 57.895 18.49 0.00 33.68 1.40
4033 6672 2.442413 TCAGCCGTTTTTATTCTGGGG 58.558 47.619 0.00 0.00 0.00 4.96
4095 6734 9.855021 TTCATTTTCCTTTCTTAAATCGGAATC 57.145 29.630 0.00 0.00 34.08 2.52
4101 6740 8.051901 TCCTTTCTTAAATCGGAATCCTTTTC 57.948 34.615 0.00 0.00 0.00 2.29
4107 6746 8.802267 TCTTAAATCGGAATCCTTTTCAAATGT 58.198 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.928979 TTTTCATGTGGTCTACTCGAAAAA 57.071 33.333 11.36 1.94 37.28 1.94
30 31 6.485313 ACATTTTCATGTGGTCTACTCGAAAA 59.515 34.615 14.26 14.26 42.46 2.29
31 32 5.995282 ACATTTTCATGTGGTCTACTCGAAA 59.005 36.000 0.00 1.47 42.46 3.46
32 33 5.547465 ACATTTTCATGTGGTCTACTCGAA 58.453 37.500 0.00 0.00 42.46 3.71
33 34 5.147330 ACATTTTCATGTGGTCTACTCGA 57.853 39.130 0.00 0.00 42.46 4.04
34 35 4.031765 CGACATTTTCATGTGGTCTACTCG 59.968 45.833 0.00 0.00 44.22 4.18
35 36 5.062308 GTCGACATTTTCATGTGGTCTACTC 59.938 44.000 11.55 0.00 44.22 2.59
36 37 4.929808 GTCGACATTTTCATGTGGTCTACT 59.070 41.667 11.55 0.00 44.22 2.57
37 38 4.092968 GGTCGACATTTTCATGTGGTCTAC 59.907 45.833 18.91 0.00 44.22 2.59
38 39 4.020573 AGGTCGACATTTTCATGTGGTCTA 60.021 41.667 18.91 0.00 44.22 2.59
39 40 3.074412 GGTCGACATTTTCATGTGGTCT 58.926 45.455 18.91 0.00 44.22 3.85
40 41 3.074412 AGGTCGACATTTTCATGTGGTC 58.926 45.455 18.91 0.00 44.22 4.02
41 42 3.140325 AGGTCGACATTTTCATGTGGT 57.860 42.857 18.91 0.00 44.22 4.16
42 43 6.018751 CAGTATAGGTCGACATTTTCATGTGG 60.019 42.308 18.91 0.00 44.22 4.17
43 44 6.535150 ACAGTATAGGTCGACATTTTCATGTG 59.465 38.462 18.91 5.76 44.22 3.21
44 45 7.578763 TGACAGTATAGGTCGACATTTTCATGT 60.579 37.037 18.91 12.78 38.50 3.21
94 95 8.267183 TGTCAGGACAGTGAATGATTTATATGT 58.733 33.333 0.00 0.00 36.21 2.29
141 142 2.240414 ACACCATCATGATCAGGCTCAA 59.760 45.455 4.86 0.00 0.00 3.02
146 147 1.224075 GCGACACCATCATGATCAGG 58.776 55.000 4.86 7.89 0.00 3.86
163 164 1.078708 ACCTGACCCGGTTAATGCG 60.079 57.895 0.00 0.00 31.94 4.73
177 182 2.289631 TGACATTGTGCTACTCCACCTG 60.290 50.000 0.00 0.00 34.85 4.00
214 219 7.547227 TCTGGAAGAAAATTAAAATAGGCAGC 58.453 34.615 0.00 0.00 42.31 5.25
231 236 5.061853 GCATGCTGATCTATTTCTGGAAGA 58.938 41.667 11.37 0.00 44.68 2.87
298 309 6.473397 AGTGACTGAAAGATCAAACGAATC 57.527 37.500 0.00 0.00 37.43 2.52
353 364 8.648693 GGACAAAGGTTACATACATAGGAGTAT 58.351 37.037 0.00 0.00 35.14 2.12
355 366 6.126854 GGGACAAAGGTTACATACATAGGAGT 60.127 42.308 0.00 0.00 0.00 3.85
356 367 6.289064 GGGACAAAGGTTACATACATAGGAG 58.711 44.000 0.00 0.00 0.00 3.69
358 369 5.054477 CGGGACAAAGGTTACATACATAGG 58.946 45.833 0.00 0.00 0.00 2.57
359 370 5.909477 TCGGGACAAAGGTTACATACATAG 58.091 41.667 0.00 0.00 0.00 2.23
360 371 5.936187 TCGGGACAAAGGTTACATACATA 57.064 39.130 0.00 0.00 0.00 2.29
362 373 4.563993 CCTTCGGGACAAAGGTTACATACA 60.564 45.833 0.00 0.00 37.25 2.29
363 374 3.937079 CCTTCGGGACAAAGGTTACATAC 59.063 47.826 0.00 0.00 37.25 2.39
472 1543 1.005156 TGCAGTCACAGCGCACATA 60.005 52.632 11.47 0.00 33.85 2.29
473 1544 2.281002 TGCAGTCACAGCGCACAT 60.281 55.556 11.47 0.00 33.85 3.21
474 1545 2.968697 CTGCAGTCACAGCGCACA 60.969 61.111 11.47 0.00 33.85 4.57
483 1554 0.339859 AGATCTACCCCCTGCAGTCA 59.660 55.000 13.81 0.00 0.00 3.41
537 1609 0.031449 GGCCGTTTTAACTTGCAGCA 59.969 50.000 0.00 0.00 0.00 4.41
538 1610 0.031449 TGGCCGTTTTAACTTGCAGC 59.969 50.000 0.00 0.00 0.00 5.25
539 1611 1.766069 GTGGCCGTTTTAACTTGCAG 58.234 50.000 0.00 0.00 0.00 4.41
580 1652 1.074471 TGGAGGGTAGGGGAGATGC 60.074 63.158 0.00 0.00 0.00 3.91
629 1781 1.228124 TGAACCTGAAACCAGCCGG 60.228 57.895 0.00 0.00 38.77 6.13
704 1887 3.552384 GGTGGGTCGGTGGTGTGA 61.552 66.667 0.00 0.00 0.00 3.58
705 1888 4.636435 GGGTGGGTCGGTGGTGTG 62.636 72.222 0.00 0.00 0.00 3.82
706 1889 4.892291 AGGGTGGGTCGGTGGTGT 62.892 66.667 0.00 0.00 0.00 4.16
707 1890 3.128032 AAAGGGTGGGTCGGTGGTG 62.128 63.158 0.00 0.00 0.00 4.17
708 1891 2.775219 AAAGGGTGGGTCGGTGGT 60.775 61.111 0.00 0.00 0.00 4.16
716 1899 0.897621 GCAGGAAATGAAAGGGTGGG 59.102 55.000 0.00 0.00 0.00 4.61
717 1900 0.897621 GGCAGGAAATGAAAGGGTGG 59.102 55.000 0.00 0.00 0.00 4.61
783 2024 1.001641 ACAGAACCAGAGGCATGGC 60.002 57.895 12.14 12.14 44.80 4.40
811 2052 0.032815 TGCGTCGTTGGTTCATCTCA 59.967 50.000 0.00 0.00 0.00 3.27
828 2069 0.385390 CAGGTTTGGTTGAGGTGTGC 59.615 55.000 0.00 0.00 0.00 4.57
839 2080 2.575532 TCAGAAACAGAGCAGGTTTGG 58.424 47.619 5.32 0.00 38.50 3.28
921 2168 5.185442 TGCAAATTGTAGCAGAATCCATTCA 59.815 36.000 2.21 0.00 39.23 2.57
933 2186 6.040247 GGGGTTAAGTTATGCAAATTGTAGC 58.960 40.000 0.00 0.00 0.00 3.58
934 2187 7.404671 AGGGGTTAAGTTATGCAAATTGTAG 57.595 36.000 0.00 0.00 0.00 2.74
1133 2402 2.246719 AGAGCAGAGCGTTGAGTTTT 57.753 45.000 0.00 0.00 0.00 2.43
1137 2406 1.627879 GAGAAGAGCAGAGCGTTGAG 58.372 55.000 0.00 0.00 0.00 3.02
1138 2407 0.244994 GGAGAAGAGCAGAGCGTTGA 59.755 55.000 0.00 0.00 0.00 3.18
1139 2408 0.739112 GGGAGAAGAGCAGAGCGTTG 60.739 60.000 0.00 0.00 0.00 4.10
1140 2409 1.188219 TGGGAGAAGAGCAGAGCGTT 61.188 55.000 0.00 0.00 0.00 4.84
1142 2411 1.153667 GTGGGAGAAGAGCAGAGCG 60.154 63.158 0.00 0.00 0.00 5.03
1143 2412 0.390998 GTGTGGGAGAAGAGCAGAGC 60.391 60.000 0.00 0.00 0.00 4.09
1144 2413 0.248843 GGTGTGGGAGAAGAGCAGAG 59.751 60.000 0.00 0.00 0.00 3.35
1146 2415 0.036577 CTGGTGTGGGAGAAGAGCAG 60.037 60.000 0.00 0.00 33.38 4.24
1147 2416 0.764369 ACTGGTGTGGGAGAAGAGCA 60.764 55.000 0.00 0.00 0.00 4.26
1148 2417 0.321122 CACTGGTGTGGGAGAAGAGC 60.321 60.000 0.00 0.00 40.33 4.09
1149 2418 3.923354 CACTGGTGTGGGAGAAGAG 57.077 57.895 0.00 0.00 40.33 2.85
1175 2444 6.627395 TTCAGAAGGATCGTTTGCTAAAAA 57.373 33.333 1.57 0.00 0.00 1.94
1176 2445 6.262273 AGTTTCAGAAGGATCGTTTGCTAAAA 59.738 34.615 1.57 0.00 0.00 1.52
1200 2473 0.673333 TGCGCCAACCACATACTCAG 60.673 55.000 4.18 0.00 0.00 3.35
1204 2477 1.154035 GCTTGCGCCAACCACATAC 60.154 57.895 4.18 0.00 0.00 2.39
1205 2478 1.303236 AGCTTGCGCCAACCACATA 60.303 52.632 4.18 0.00 36.60 2.29
1207 2480 3.286751 GAGCTTGCGCCAACCACA 61.287 61.111 4.18 0.00 36.60 4.17
1208 2481 4.043200 GGAGCTTGCGCCAACCAC 62.043 66.667 4.18 0.00 36.60 4.16
1215 2488 2.400896 TTTTTCACGGGAGCTTGCGC 62.401 55.000 0.00 0.00 0.00 6.09
1216 2489 1.652012 TTTTTCACGGGAGCTTGCG 59.348 52.632 0.00 0.00 0.00 4.85
1231 2504 5.637006 TTGCACTATTATGACGGCTTTTT 57.363 34.783 0.00 0.00 0.00 1.94
1232 2505 5.835113 ATTGCACTATTATGACGGCTTTT 57.165 34.783 0.00 0.00 0.00 2.27
1233 2506 5.835113 AATTGCACTATTATGACGGCTTT 57.165 34.783 0.00 0.00 0.00 3.51
1234 2507 6.936900 AGATAATTGCACTATTATGACGGCTT 59.063 34.615 8.11 0.00 32.30 4.35
1235 2508 6.369890 CAGATAATTGCACTATTATGACGGCT 59.630 38.462 8.11 0.00 32.30 5.52
1236 2509 6.147821 ACAGATAATTGCACTATTATGACGGC 59.852 38.462 8.11 0.00 32.30 5.68
1237 2510 7.513132 CACAGATAATTGCACTATTATGACGG 58.487 38.462 8.11 0.45 32.30 4.79
1238 2511 7.011773 GCACAGATAATTGCACTATTATGACG 58.988 38.462 8.11 0.91 38.68 4.35
1239 2512 7.864686 TGCACAGATAATTGCACTATTATGAC 58.135 34.615 8.11 0.00 43.79 3.06
1240 2513 7.716560 ACTGCACAGATAATTGCACTATTATGA 59.283 33.333 8.11 0.00 43.79 2.15
1241 2514 7.801783 CACTGCACAGATAATTGCACTATTATG 59.198 37.037 8.11 0.72 43.79 1.90
1242 2515 7.500227 ACACTGCACAGATAATTGCACTATTAT 59.500 33.333 4.31 3.75 43.79 1.28
1248 2521 3.058016 ACACACTGCACAGATAATTGCAC 60.058 43.478 4.31 0.00 43.79 4.57
1253 2526 4.943093 TGCATAACACACTGCACAGATAAT 59.057 37.500 4.31 0.00 43.11 1.28
1318 2591 6.851222 TCAGAGAACAAAGCTTAAGACAAG 57.149 37.500 6.67 0.00 0.00 3.16
1345 2618 8.508875 GGACTAGCAAGTACAGAAGTCTATATC 58.491 40.741 14.78 0.00 36.47 1.63
1361 2637 4.210120 GCGATGAATAACTGGACTAGCAAG 59.790 45.833 0.00 0.00 0.00 4.01
1362 2638 4.119862 GCGATGAATAACTGGACTAGCAA 58.880 43.478 0.00 0.00 0.00 3.91
1369 2649 8.902540 ATAATTTACTGCGATGAATAACTGGA 57.097 30.769 0.00 0.00 0.00 3.86
1385 2665 7.709613 CGGCAAGGTGTCTACTTATAATTTACT 59.290 37.037 0.00 0.00 0.00 2.24
1395 2675 1.676014 GCATCGGCAAGGTGTCTACTT 60.676 52.381 0.00 0.00 40.72 2.24
1436 2738 6.035758 GGTTATAAGAAGAAGGTAACACGCTG 59.964 42.308 0.00 0.00 41.41 5.18
1447 2749 7.223058 CGTAAGCACTGGTTATAAGAAGAAG 57.777 40.000 4.06 0.00 0.00 2.85
1491 2806 1.626356 ATGTCGTGCAGCCCTGGTAT 61.626 55.000 0.00 0.00 0.00 2.73
1503 2818 5.930405 TCAAAGAAACATCATCATGTCGTG 58.070 37.500 0.00 0.00 42.89 4.35
1625 2940 6.479660 GGTCAATCAACAGAAAGAAAAATGCA 59.520 34.615 0.00 0.00 0.00 3.96
1626 2941 6.703165 AGGTCAATCAACAGAAAGAAAAATGC 59.297 34.615 0.00 0.00 0.00 3.56
1677 3045 6.431234 CCCAGGTTAGCACATAATCCTTTATC 59.569 42.308 0.00 0.00 0.00 1.75
1717 3085 2.998670 CAATCTCATGCCTATAGCCACG 59.001 50.000 0.00 0.00 42.71 4.94
1902 3270 0.532862 CCTTTGTGACAGTGCCGTCT 60.533 55.000 0.00 0.00 36.82 4.18
1908 3276 0.109342 AGCCTCCCTTTGTGACAGTG 59.891 55.000 0.00 0.00 0.00 3.66
1926 3294 7.765819 TCATGAACTACAATGTGAGTGGAATAG 59.234 37.037 0.00 0.00 0.00 1.73
1959 3327 2.260639 TCCAGAAGAGAAGGCATCCT 57.739 50.000 0.00 0.00 33.87 3.24
1966 3334 7.361885 CCAAATTCAGAACATCCAGAAGAGAAG 60.362 40.741 0.00 0.00 0.00 2.85
2015 3474 3.578688 GCGAAAAAGAATTGCCATGACT 58.421 40.909 0.00 0.00 0.00 3.41
2034 3493 1.264288 GTGAGTTTTGACTTGGAGGCG 59.736 52.381 0.00 0.00 0.00 5.52
2057 3516 9.838339 AGGAAACACAATATTCTTATACCAGAG 57.162 33.333 0.00 0.00 0.00 3.35
2076 3538 9.474920 GTCATGAAAATGAATTAACAGGAAACA 57.525 29.630 0.00 0.00 31.60 2.83
2077 3539 9.474920 TGTCATGAAAATGAATTAACAGGAAAC 57.525 29.630 0.00 0.00 31.60 2.78
2089 3551 5.316167 AGCAGTACCTGTCATGAAAATGAA 58.684 37.500 0.00 0.00 33.43 2.57
2090 3552 4.910195 AGCAGTACCTGTCATGAAAATGA 58.090 39.130 0.00 0.00 33.43 2.57
2091 3553 6.932356 ATAGCAGTACCTGTCATGAAAATG 57.068 37.500 0.00 0.00 33.43 2.32
2092 3554 9.461312 TTTTATAGCAGTACCTGTCATGAAAAT 57.539 29.630 0.00 0.00 33.43 1.82
2093 3555 8.856153 TTTTATAGCAGTACCTGTCATGAAAA 57.144 30.769 0.00 0.00 33.43 2.29
2135 3603 4.056125 GGTGCGGCCTTTTCCAGC 62.056 66.667 0.00 0.00 0.00 4.85
2270 3738 0.250727 TCAGTCCAAAGGCTTTCCCG 60.251 55.000 10.08 0.00 39.21 5.14
2318 3786 6.998968 AGGTTGATAGCTTCATCTCTTTTG 57.001 37.500 0.00 0.00 33.34 2.44
2348 3816 6.958255 TGATGATACCACAAAATTATCTGCG 58.042 36.000 0.00 0.00 0.00 5.18
2381 3849 2.832129 GGTGTTCAGTACCTCCATCTGA 59.168 50.000 0.00 0.00 36.59 3.27
2446 3919 5.447818 GCAAGGAGATATGTACTTGTTGTGC 60.448 44.000 22.27 8.08 41.65 4.57
2503 3991 0.034616 AGCTCTGTTCCTCTGTGCAC 59.965 55.000 10.75 10.75 37.10 4.57
2510 3998 2.278854 GCAGAATGAGCTCTGTTCCTC 58.721 52.381 21.21 13.36 44.04 3.71
2541 4439 3.807622 TCGCACAAAATAGTATAGGCAGC 59.192 43.478 0.00 0.00 0.00 5.25
2577 4626 6.124088 AGAATAACAAGCAGAATTTAGCCG 57.876 37.500 0.08 0.00 0.00 5.52
2578 4627 7.766283 AGAAGAATAACAAGCAGAATTTAGCC 58.234 34.615 0.08 0.00 0.00 3.93
2582 4631 8.401490 AGTGAGAAGAATAACAAGCAGAATTT 57.599 30.769 0.00 0.00 0.00 1.82
2614 4663 8.308931 ACCATTTCGTTATTCTCACTTAGTACA 58.691 33.333 0.00 0.00 0.00 2.90
2781 4830 3.379372 CCAGATTAAGTGTTGCAGGATGG 59.621 47.826 0.00 0.00 35.86 3.51
2947 5016 5.040635 CCAGTAACAACGTTCAAATGCTTT 58.959 37.500 0.00 0.00 0.00 3.51
2955 5024 4.379603 CCAAAACACCAGTAACAACGTTCA 60.380 41.667 0.00 0.00 0.00 3.18
3046 5116 3.378742 CGACTACACTGCCAGATAGAGTT 59.621 47.826 12.62 0.00 0.00 3.01
3211 5281 5.991933 ACTTGAAAGAGCTCTCTATGTCA 57.008 39.130 18.55 12.49 39.39 3.58
3306 5377 0.458543 CTATCACAAGTCAGCCGCGT 60.459 55.000 4.92 0.00 0.00 6.01
3400 5505 9.113838 AGAAAATTCGATACTACATTGAGCATT 57.886 29.630 0.00 0.00 0.00 3.56
3434 5543 3.452755 ACTCACGTGTTGATCAGTCAA 57.547 42.857 16.51 0.00 41.89 3.18
3435 5544 4.577834 TTACTCACGTGTTGATCAGTCA 57.422 40.909 16.51 0.00 32.17 3.41
3454 5563 6.874278 TTCCTCTCTTCAATCTGACCATTA 57.126 37.500 0.00 0.00 0.00 1.90
3476 5585 5.507985 GCTTCAGCTGTTTTGGACTGTATTT 60.508 40.000 14.67 0.00 38.21 1.40
3482 5592 1.322442 GGCTTCAGCTGTTTTGGACT 58.678 50.000 14.67 0.00 41.70 3.85
3505 5615 6.601332 TCCAATATTGTCTATCAAAGGTCCC 58.399 40.000 14.25 0.00 39.62 4.46
3562 5672 3.045601 GCTTCTGTGAAGCAGGTTCTA 57.954 47.619 22.54 2.39 45.08 2.10
3572 5682 6.656270 ACTGACATGATATTTGCTTCTGTGAA 59.344 34.615 0.00 0.00 0.00 3.18
3602 5712 7.382218 CCAAAATAGTTTGTCGAAGCTTGAAAT 59.618 33.333 14.02 0.00 42.26 2.17
3607 5717 4.825085 TCCCAAAATAGTTTGTCGAAGCTT 59.175 37.500 14.02 0.00 42.26 3.74
3703 5813 1.296715 CGGTTTGTGAGAGGGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
3704 5814 1.263356 TACGGTTTGTGAGAGGGAGG 58.737 55.000 0.00 0.00 0.00 4.30
3705 5815 4.730949 TTATACGGTTTGTGAGAGGGAG 57.269 45.455 0.00 0.00 0.00 4.30
3706 5816 4.081309 CCTTTATACGGTTTGTGAGAGGGA 60.081 45.833 0.00 0.00 0.00 4.20
3707 5817 4.189231 CCTTTATACGGTTTGTGAGAGGG 58.811 47.826 0.00 0.00 0.00 4.30
3708 5818 4.189231 CCCTTTATACGGTTTGTGAGAGG 58.811 47.826 0.00 0.00 0.00 3.69
3709 5819 3.621715 GCCCTTTATACGGTTTGTGAGAG 59.378 47.826 0.00 0.00 0.00 3.20
3712 5822 3.420300 TGCCCTTTATACGGTTTGTGA 57.580 42.857 0.00 0.00 0.00 3.58
3714 5824 5.300792 CCATATTGCCCTTTATACGGTTTGT 59.699 40.000 0.00 0.00 0.00 2.83
3715 5825 5.533154 TCCATATTGCCCTTTATACGGTTTG 59.467 40.000 0.00 0.00 0.00 2.93
3716 5826 5.533528 GTCCATATTGCCCTTTATACGGTTT 59.466 40.000 0.00 0.00 0.00 3.27
3717 5827 5.067954 GTCCATATTGCCCTTTATACGGTT 58.932 41.667 0.00 0.00 0.00 4.44
3718 5828 4.349930 AGTCCATATTGCCCTTTATACGGT 59.650 41.667 0.00 0.00 0.00 4.83
3719 5829 4.906618 AGTCCATATTGCCCTTTATACGG 58.093 43.478 0.00 0.00 0.00 4.02
3720 5830 6.877611 AAAGTCCATATTGCCCTTTATACG 57.122 37.500 0.00 0.00 0.00 3.06
3721 5831 8.135529 GTCAAAAGTCCATATTGCCCTTTATAC 58.864 37.037 0.00 0.00 0.00 1.47
3756 6202 5.250200 GGTGACCCATCATACAAAACTGTA 58.750 41.667 0.00 0.00 37.14 2.74
3789 6235 4.306967 TGATGGCACGCACGTCCA 62.307 61.111 13.89 13.89 32.77 4.02
3796 6242 0.670546 ACACTGTACTGATGGCACGC 60.671 55.000 6.77 0.00 0.00 5.34
3801 6247 4.093408 GTGCACATAACACTGTACTGATGG 59.907 45.833 13.17 0.00 35.12 3.51
3803 6249 4.020218 AGGTGCACATAACACTGTACTGAT 60.020 41.667 20.43 0.00 38.14 2.90
3807 6253 3.188460 CCAAGGTGCACATAACACTGTAC 59.812 47.826 20.43 0.00 38.14 2.90
3891 6340 2.165030 TGGTTAGCGCCTTCAGTACTAC 59.835 50.000 2.29 0.00 0.00 2.73
3931 6380 4.167268 GAGGAAAGAAGTACTGTAGCACG 58.833 47.826 0.00 0.00 0.00 5.34
4005 6644 6.863126 CAGAATAAAAACGGCTGAACTGAAAT 59.137 34.615 0.00 0.00 0.00 2.17
4072 6711 8.595362 AGGATTCCGATTTAAGAAAGGAAAAT 57.405 30.769 0.00 0.00 38.36 1.82
4125 6788 9.859427 TCATGGATTTGAAAATAAGTTCATGAC 57.141 29.630 0.00 0.00 37.36 3.06


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

AutoCloner maintained by Alex Coulton.