Multiple sequence alignment - TraesCS2B01G147800

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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 TraesCS2B01G147800 chr2B 100.000 3879 0 0 1 3879 114045931 114049809 0.000000e+00 7164.0
1 TraesCS2B01G147800 chr2B 93.548 62 2 1 3077 3136 12709696 12709635 1.480000e-14 91.6
2 TraesCS2B01G147800 chr2A 91.898 3098 196 20 53 3123 74105484 74108553 0.000000e+00 4279.0
3 TraesCS2B01G147800 chr2A 96.682 211 5 2 3669 3879 74108633 74108841 2.220000e-92 350.0
4 TraesCS2B01G147800 chr2A 88.950 181 18 2 53 232 490351024 490351203 5.040000e-54 222.0
5 TraesCS2B01G147800 chr2A 95.349 86 3 1 3158 3242 74108549 74108634 6.760000e-28 135.0
6 TraesCS2B01G147800 chr2D 92.255 3047 171 28 53 3065 74935695 74938710 0.000000e+00 4259.0
7 TraesCS2B01G147800 chr2D 90.180 611 27 12 3077 3665 74938694 74939293 0.000000e+00 765.0
8 TraesCS2B01G147800 chr2D 83.864 471 29 16 3151 3610 365349106 365349540 4.670000e-109 405.0
9 TraesCS2B01G147800 chr1D 87.943 705 48 13 3184 3873 459049210 459049892 0.000000e+00 797.0
10 TraesCS2B01G147800 chr1D 85.307 456 25 17 3151 3597 215043299 215042877 2.140000e-117 433.0
11 TraesCS2B01G147800 chr1D 86.446 332 28 11 3290 3610 339905557 339905232 7.980000e-92 348.0
12 TraesCS2B01G147800 chr1D 83.924 367 29 3 2619 2984 459048580 459048917 1.340000e-84 324.0
13 TraesCS2B01G147800 chr1D 93.548 62 2 1 3077 3136 66760371 66760310 1.480000e-14 91.6
14 TraesCS2B01G147800 chr1A 85.167 809 61 28 3092 3873 551483752 551484528 0.000000e+00 774.0
15 TraesCS2B01G147800 chr1A 89.706 136 9 2 2764 2894 551483278 551483413 6.670000e-38 169.0
16 TraesCS2B01G147800 chr1A 85.593 118 7 4 2887 2995 551483613 551483729 8.810000e-22 115.0
17 TraesCS2B01G147800 chr1B 86.444 509 34 22 3389 3873 631228578 631229075 3.430000e-145 525.0
18 TraesCS2B01G147800 chr1B 78.571 546 43 12 2462 2995 631227858 631228341 3.790000e-75 292.0
19 TraesCS2B01G147800 chr1B 88.950 181 18 2 53 232 280475863 280475684 5.040000e-54 222.0
20 TraesCS2B01G147800 chr1B 80.000 295 32 10 1694 1981 631227316 631227590 3.960000e-45 193.0
21 TraesCS2B01G147800 chr1B 93.548 62 2 1 3077 3136 513973833 513973772 1.480000e-14 91.6
22 TraesCS2B01G147800 chr1B 94.444 36 0 2 2031 2066 631227630 631227663 2.000000e-03 54.7
23 TraesCS2B01G147800 chr6D 90.395 177 11 4 3439 3610 101398234 101398409 1.080000e-55 228.0
24 TraesCS2B01G147800 chr4A 89.503 181 17 2 53 232 428994985 428994806 1.080000e-55 228.0
25 TraesCS2B01G147800 chr4A 88.889 180 18 2 53 231 708069866 708069688 1.810000e-53 220.0
26 TraesCS2B01G147800 chr4A 88.889 180 18 2 53 231 708092521 708092343 1.810000e-53 220.0
27 TraesCS2B01G147800 chr4A 88.398 181 19 2 53 232 29364775 29364954 2.350000e-52 217.0
28 TraesCS2B01G147800 chr4B 88.950 181 18 2 53 232 458279148 458278969 5.040000e-54 222.0
29 TraesCS2B01G147800 chr4B 88.298 188 19 3 53 239 631792116 631791931 5.040000e-54 222.0
30 TraesCS2B01G147800 chrUn 88.889 180 18 2 53 231 50448678 50448500 1.810000e-53 220.0
31 TraesCS2B01G147800 chrUn 93.548 62 2 1 3077 3136 93959193 93959132 1.480000e-14 91.6
32 TraesCS2B01G147800 chr7A 93.548 62 2 1 3077 3136 727859941 727859880 1.480000e-14 91.6
33 TraesCS2B01G147800 chr5B 93.548 62 2 1 3077 3136 43858170 43858231 1.480000e-14 91.6


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 TraesCS2B01G147800 chr2B 114045931 114049809 3878 False 7164.000000 7164 100.00000 1 3879 1 chr2B.!!$F1 3878
1 TraesCS2B01G147800 chr2A 74105484 74108841 3357 False 1588.000000 4279 94.64300 53 3879 3 chr2A.!!$F2 3826
2 TraesCS2B01G147800 chr2D 74935695 74939293 3598 False 2512.000000 4259 91.21750 53 3665 2 chr2D.!!$F2 3612
3 TraesCS2B01G147800 chr1D 459048580 459049892 1312 False 560.500000 797 85.93350 2619 3873 2 chr1D.!!$F1 1254
4 TraesCS2B01G147800 chr1A 551483278 551484528 1250 False 352.666667 774 86.82200 2764 3873 3 chr1A.!!$F1 1109
5 TraesCS2B01G147800 chr1B 631227316 631229075 1759 False 266.175000 525 84.86475 1694 3873 4 chr1B.!!$F1 2179

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
50 51 0.475906 AGCTCAAGTGCTCAAACCCT 59.524 50.0 0.00 0.0 39.34 4.34 F
881 896 0.543410 TCCCTGGGAAAGCTACACGA 60.543 55.0 14.48 0.0 0.00 4.35 F
1453 1476 0.035439 TCTTCCCCCAATCTCGTTGC 60.035 55.0 0.00 0.0 36.46 4.17 F
1924 1957 0.163788 CTTTCGAAGCGAATGTGCGT 59.836 50.0 2.92 0.0 45.28 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1458 0.035056 AGCAACGAGATTGGGGGAAG 60.035 55.0 0.00 0.0 38.88 3.46 R
2122 2164 0.039437 CGTATGCCCGCTTATCGAGT 60.039 55.0 0.00 0.0 41.67 4.18 R
2515 2567 0.109689 CGTTCTCTTCGAGCTCCGTT 60.110 55.0 8.47 0.0 39.75 4.44 R
3158 3472 0.384669 GCATGAATTGAGGAGCCTGC 59.615 55.0 0.00 0.0 0.00 4.85 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
43 44 3.261933 GCCACAGCTCAAGTGCTC 58.738 61.111 0.00 0.00 41.98 4.26
44 45 1.598962 GCCACAGCTCAAGTGCTCA 60.599 57.895 0.00 0.00 41.98 4.26
45 46 1.168407 GCCACAGCTCAAGTGCTCAA 61.168 55.000 0.00 0.00 41.98 3.02
46 47 1.311859 CCACAGCTCAAGTGCTCAAA 58.688 50.000 0.00 0.00 41.98 2.69
47 48 1.002033 CCACAGCTCAAGTGCTCAAAC 60.002 52.381 0.00 0.00 41.98 2.93
48 49 1.002033 CACAGCTCAAGTGCTCAAACC 60.002 52.381 0.00 0.00 41.98 3.27
49 50 0.595095 CAGCTCAAGTGCTCAAACCC 59.405 55.000 0.00 0.00 41.98 4.11
50 51 0.475906 AGCTCAAGTGCTCAAACCCT 59.524 50.000 0.00 0.00 39.34 4.34
51 52 0.877743 GCTCAAGTGCTCAAACCCTC 59.122 55.000 0.00 0.00 0.00 4.30
63 64 0.555769 AAACCCTCACCTTGGAAGCA 59.444 50.000 0.00 0.00 0.00 3.91
110 111 2.883267 GATGCACTCACCCCAGAGGC 62.883 65.000 0.00 0.00 40.58 4.70
139 140 3.427161 GGAACCTGCATAATCAGCAAC 57.573 47.619 0.00 0.00 42.17 4.17
140 141 2.754552 GGAACCTGCATAATCAGCAACA 59.245 45.455 0.00 0.00 42.17 3.33
141 142 3.382546 GGAACCTGCATAATCAGCAACAT 59.617 43.478 0.00 0.00 42.17 2.71
142 143 4.580167 GGAACCTGCATAATCAGCAACATA 59.420 41.667 0.00 0.00 42.17 2.29
143 144 5.242393 GGAACCTGCATAATCAGCAACATAT 59.758 40.000 0.00 0.00 42.17 1.78
144 145 5.700722 ACCTGCATAATCAGCAACATATG 57.299 39.130 0.00 0.00 42.17 1.78
148 150 5.765176 TGCATAATCAGCAACATATGAAGC 58.235 37.500 10.38 12.43 39.39 3.86
154 156 3.191162 TCAGCAACATATGAAGCAACCAC 59.809 43.478 20.43 0.00 0.00 4.16
167 169 4.725556 AGCAACCACGCATATAATTACG 57.274 40.909 0.00 0.00 0.00 3.18
170 172 2.419667 ACCACGCATATAATTACGCCC 58.580 47.619 0.00 0.00 0.00 6.13
171 173 2.224329 ACCACGCATATAATTACGCCCA 60.224 45.455 0.00 0.00 0.00 5.36
174 176 3.063452 CACGCATATAATTACGCCCATCC 59.937 47.826 0.00 0.00 0.00 3.51
178 180 5.050363 CGCATATAATTACGCCCATCCATAC 60.050 44.000 0.00 0.00 0.00 2.39
180 182 2.178912 AATTACGCCCATCCATACGG 57.821 50.000 0.00 0.00 0.00 4.02
186 188 0.674895 GCCCATCCATACGGCAGATC 60.675 60.000 0.00 0.00 42.52 2.75
213 215 3.209410 GCCAAGCTTAGTGACAGCATAT 58.791 45.455 0.00 0.00 39.99 1.78
218 220 6.017605 CCAAGCTTAGTGACAGCATATTAAGG 60.018 42.308 0.00 0.00 39.99 2.69
229 231 6.414732 ACAGCATATTAAGGTAGAACAGCAA 58.585 36.000 0.00 0.00 0.00 3.91
230 232 6.540189 ACAGCATATTAAGGTAGAACAGCAAG 59.460 38.462 0.00 0.00 0.00 4.01
231 233 5.529060 AGCATATTAAGGTAGAACAGCAAGC 59.471 40.000 0.00 0.00 0.00 4.01
245 255 1.618837 AGCAAGCTCGTACCTTGAAGA 59.381 47.619 12.79 0.00 41.64 2.87
249 259 2.673833 AGCTCGTACCTTGAAGAAACG 58.326 47.619 11.39 11.39 34.99 3.60
379 389 3.365364 GCAGAAGCATCACAAACACTACC 60.365 47.826 0.00 0.00 41.58 3.18
380 390 3.067106 AGAAGCATCACAAACACTACCG 58.933 45.455 0.00 0.00 0.00 4.02
395 405 4.242475 CACTACCGATAAGCAAACACAGA 58.758 43.478 0.00 0.00 0.00 3.41
397 407 2.066262 ACCGATAAGCAAACACAGACG 58.934 47.619 0.00 0.00 0.00 4.18
398 408 1.201921 CCGATAAGCAAACACAGACGC 60.202 52.381 0.00 0.00 0.00 5.19
401 411 0.941542 TAAGCAAACACAGACGCCAC 59.058 50.000 0.00 0.00 0.00 5.01
402 412 2.047151 AAGCAAACACAGACGCCACG 62.047 55.000 0.00 0.00 0.00 4.94
404 414 3.276846 AAACACAGACGCCACGCC 61.277 61.111 0.00 0.00 0.00 5.68
410 420 4.344865 AGACGCCACGCCCCAAAT 62.345 61.111 0.00 0.00 0.00 2.32
411 421 3.810896 GACGCCACGCCCCAAATC 61.811 66.667 0.00 0.00 0.00 2.17
413 423 3.814268 CGCCACGCCCCAAATCAG 61.814 66.667 0.00 0.00 0.00 2.90
414 424 2.676471 GCCACGCCCCAAATCAGT 60.676 61.111 0.00 0.00 0.00 3.41
417 427 1.501741 CACGCCCCAAATCAGTTCG 59.498 57.895 0.00 0.00 0.00 3.95
438 448 2.848302 GCCAGATTTGCGAAATTCGAAG 59.152 45.455 20.38 0.00 43.74 3.79
448 458 3.000423 GCGAAATTCGAAGCTAAGGAGAC 60.000 47.826 20.38 0.00 43.74 3.36
497 509 1.333619 GCAGAGCGGAACAGTTCAAAA 59.666 47.619 15.36 0.00 0.00 2.44
502 514 3.139077 AGCGGAACAGTTCAAAACTAGG 58.861 45.455 15.36 0.00 40.46 3.02
503 515 2.350484 GCGGAACAGTTCAAAACTAGGC 60.350 50.000 15.36 1.81 40.46 3.93
569 581 1.035932 GCGAGTGAGTAGGGTAGGCA 61.036 60.000 0.00 0.00 0.00 4.75
799 814 2.289565 GCCGCCTATTTATATCTGGCC 58.710 52.381 0.00 0.00 40.40 5.36
881 896 0.543410 TCCCTGGGAAAGCTACACGA 60.543 55.000 14.48 0.00 0.00 4.35
910 925 2.261586 CGCTCGATCGGATCTCCCA 61.262 63.158 16.41 0.00 34.14 4.37
911 926 1.590610 CGCTCGATCGGATCTCCCAT 61.591 60.000 16.41 0.00 34.14 4.00
977 992 1.970352 CTCCTTGCTCAGCTCCCTCC 61.970 65.000 0.00 0.00 0.00 4.30
1037 1058 2.045926 GGCATTCCACTCGCTGGT 60.046 61.111 0.00 0.00 41.52 4.00
1039 1060 2.456119 GCATTCCACTCGCTGGTCG 61.456 63.158 0.00 0.00 41.52 4.79
1170 1191 3.462678 GTGGAGGCGGAGGAGACC 61.463 72.222 0.00 0.00 0.00 3.85
1435 1458 4.612932 GCTGAGGTCAGTGATCATTTTC 57.387 45.455 6.10 0.00 45.45 2.29
1437 1460 4.699257 GCTGAGGTCAGTGATCATTTTCTT 59.301 41.667 6.10 0.00 45.45 2.52
1442 1465 3.696548 GTCAGTGATCATTTTCTTCCCCC 59.303 47.826 0.00 0.00 0.00 5.40
1453 1476 0.035439 TCTTCCCCCAATCTCGTTGC 60.035 55.000 0.00 0.00 36.46 4.17
1455 1478 1.209504 CTTCCCCCAATCTCGTTGCTA 59.790 52.381 0.00 0.00 36.46 3.49
1469 1492 3.436704 TCGTTGCTAAATCTTTGGAGCAG 59.563 43.478 0.00 0.00 45.14 4.24
1472 1495 5.392380 CGTTGCTAAATCTTTGGAGCAGATT 60.392 40.000 0.00 0.00 45.14 2.40
1473 1496 6.183360 CGTTGCTAAATCTTTGGAGCAGATTA 60.183 38.462 0.00 0.00 45.14 1.75
1544 1567 7.128418 TGAAGTACTAGAATCACCTAGGGAGTA 59.872 40.741 14.81 5.98 40.24 2.59
1546 1569 7.289310 AGTACTAGAATCACCTAGGGAGTAAC 58.711 42.308 14.81 0.00 40.24 2.50
1551 1574 5.367060 AGAATCACCTAGGGAGTAACCATTC 59.633 44.000 14.81 9.54 41.20 2.67
1557 1581 4.656112 CCTAGGGAGTAACCATTCTCATGT 59.344 45.833 0.00 0.00 41.20 3.21
1600 1626 7.313951 AGCTATACTTGAGAAACTGAAATGC 57.686 36.000 0.00 0.00 0.00 3.56
1601 1627 7.108847 AGCTATACTTGAGAAACTGAAATGCT 58.891 34.615 0.00 0.00 0.00 3.79
1617 1643 2.552802 GCTCTCTGCATGTTGCTGT 58.447 52.632 0.75 0.00 45.31 4.40
1628 1654 3.125316 GCATGTTGCTGTACTAGGTTGAC 59.875 47.826 0.00 0.00 40.96 3.18
1785 1815 6.825721 AGCTCCTTACTGAACATTGAATTAGG 59.174 38.462 0.00 0.00 0.00 2.69
1790 1820 9.177608 CCTTACTGAACATTGAATTAGGAATGA 57.822 33.333 10.00 0.00 34.31 2.57
1821 1851 7.611467 ACTTCTAATTTGCATCAATGGTGACTA 59.389 33.333 0.00 0.00 36.31 2.59
1824 1854 9.625747 TCTAATTTGCATCAATGGTGACTATTA 57.374 29.630 0.00 0.00 36.31 0.98
1840 1870 7.376072 GGTGACTATTAGCATTAATTTTGTCGC 59.624 37.037 0.00 0.00 35.50 5.19
1842 1872 6.427150 ACTATTAGCATTAATTTTGTCGCCG 58.573 36.000 0.00 0.00 31.97 6.46
1924 1957 0.163788 CTTTCGAAGCGAATGTGCGT 59.836 50.000 2.92 0.00 45.28 5.24
2104 2146 5.617751 CGCAAAGGAAACATTCGAAGAGATT 60.618 40.000 3.35 0.00 38.43 2.40
2113 2155 4.153117 ACATTCGAAGAGATTGTGTTGCTC 59.847 41.667 3.35 0.00 40.65 4.26
2122 2164 2.046009 TTGTGTTGCTCGGCCTACCA 62.046 55.000 0.00 0.00 34.57 3.25
2134 2176 0.318784 GCCTACCACTCGATAAGCGG 60.319 60.000 0.00 0.00 41.33 5.52
2161 2203 3.181440 ACGGTTCAATGATCATGGCCTAT 60.181 43.478 9.46 0.00 0.00 2.57
2254 2306 3.118920 GGAAAGAGGTCTACAAGGCTCTC 60.119 52.174 0.00 0.00 0.00 3.20
2257 2309 1.754226 GAGGTCTACAAGGCTCTCCTG 59.246 57.143 0.00 0.00 43.40 3.86
2287 2339 4.304110 ACTCGTACAAAAGCGATTCAGAA 58.696 39.130 0.00 0.00 36.50 3.02
2302 2354 3.119096 GAAGGGGCGCAACGAGTC 61.119 66.667 10.83 0.00 0.00 3.36
2329 2381 1.669440 GGTACAGTTCGCAGGGACA 59.331 57.895 0.00 0.00 0.00 4.02
2428 2480 0.321564 CCCGAAACATGAGGAGTGCA 60.322 55.000 0.00 0.00 0.00 4.57
2439 2491 0.472734 AGGAGTGCAGGACTGGAACT 60.473 55.000 0.00 0.00 33.83 3.01
2515 2567 2.567615 GGAAGGAGCACTGGAGTTTCTA 59.432 50.000 0.00 0.00 0.00 2.10
2516 2568 3.008049 GGAAGGAGCACTGGAGTTTCTAA 59.992 47.826 0.00 0.00 0.00 2.10
2707 2767 1.141053 AGGAAGAGCAAAGACGGTGTT 59.859 47.619 0.00 0.00 0.00 3.32
2708 2768 1.264288 GGAAGAGCAAAGACGGTGTTG 59.736 52.381 0.00 0.00 0.00 3.33
2735 2795 3.194329 GGAATGGAGAAAAGGCAGAAAGG 59.806 47.826 0.00 0.00 0.00 3.11
2737 2797 1.499007 TGGAGAAAAGGCAGAAAGGGT 59.501 47.619 0.00 0.00 0.00 4.34
2739 2799 3.139397 TGGAGAAAAGGCAGAAAGGGTAA 59.861 43.478 0.00 0.00 0.00 2.85
2740 2800 4.149598 GGAGAAAAGGCAGAAAGGGTAAA 58.850 43.478 0.00 0.00 0.00 2.01
2741 2801 4.022242 GGAGAAAAGGCAGAAAGGGTAAAC 60.022 45.833 0.00 0.00 0.00 2.01
2742 2802 4.542697 AGAAAAGGCAGAAAGGGTAAACA 58.457 39.130 0.00 0.00 0.00 2.83
2743 2803 4.341235 AGAAAAGGCAGAAAGGGTAAACAC 59.659 41.667 0.00 0.00 0.00 3.32
2744 2804 3.306472 AAGGCAGAAAGGGTAAACACA 57.694 42.857 0.00 0.00 0.00 3.72
2745 2805 2.863809 AGGCAGAAAGGGTAAACACAG 58.136 47.619 0.00 0.00 0.00 3.66
2746 2806 1.269723 GGCAGAAAGGGTAAACACAGC 59.730 52.381 0.00 0.00 0.00 4.40
2747 2807 1.953686 GCAGAAAGGGTAAACACAGCA 59.046 47.619 0.00 0.00 0.00 4.41
2748 2808 2.558359 GCAGAAAGGGTAAACACAGCAT 59.442 45.455 0.00 0.00 0.00 3.79
2749 2809 3.005791 GCAGAAAGGGTAAACACAGCATT 59.994 43.478 0.00 0.00 0.00 3.56
2750 2810 4.501400 GCAGAAAGGGTAAACACAGCATTT 60.501 41.667 0.00 0.00 33.13 2.32
2751 2811 5.222631 CAGAAAGGGTAAACACAGCATTTC 58.777 41.667 4.76 4.76 43.37 2.17
2752 2812 4.892934 AGAAAGGGTAAACACAGCATTTCA 59.107 37.500 12.88 0.00 44.67 2.69
2753 2813 4.853924 AAGGGTAAACACAGCATTTCAG 57.146 40.909 0.00 0.00 0.00 3.02
2754 2814 3.832527 AGGGTAAACACAGCATTTCAGT 58.167 40.909 0.00 0.00 0.00 3.41
2755 2815 4.980573 AGGGTAAACACAGCATTTCAGTA 58.019 39.130 0.00 0.00 0.00 2.74
2756 2816 4.760204 AGGGTAAACACAGCATTTCAGTAC 59.240 41.667 0.00 0.00 0.00 2.73
2757 2817 4.517453 GGGTAAACACAGCATTTCAGTACA 59.483 41.667 0.00 0.00 0.00 2.90
2758 2818 5.449304 GGTAAACACAGCATTTCAGTACAC 58.551 41.667 0.00 0.00 0.00 2.90
2759 2819 4.568152 AAACACAGCATTTCAGTACACC 57.432 40.909 0.00 0.00 0.00 4.16
2760 2820 3.207265 ACACAGCATTTCAGTACACCA 57.793 42.857 0.00 0.00 0.00 4.17
2761 2821 3.550820 ACACAGCATTTCAGTACACCAA 58.449 40.909 0.00 0.00 0.00 3.67
2762 2822 3.315191 ACACAGCATTTCAGTACACCAAC 59.685 43.478 0.00 0.00 0.00 3.77
2766 2826 3.317993 AGCATTTCAGTACACCAACAACC 59.682 43.478 0.00 0.00 0.00 3.77
2857 2923 6.374333 GCAAAATCACTAAGTCCATTACCTCA 59.626 38.462 0.00 0.00 0.00 3.86
2942 3214 4.803613 CAGAAATCACATGCACAATCATGG 59.196 41.667 8.38 0.00 46.02 3.66
2947 3219 2.432874 CACATGCACAATCATGGGGAAT 59.567 45.455 8.38 0.00 46.02 3.01
2995 3278 7.289084 TGCCAGGATCTATGTAAGTGTATGTAA 59.711 37.037 0.00 0.00 0.00 2.41
3048 3331 1.471327 CCACAAAACCAGGCAACAGTG 60.471 52.381 0.00 0.00 41.41 3.66
3057 3369 1.267806 CAGGCAACAGTGATGTCAACC 59.732 52.381 7.79 0.00 41.41 3.77
3058 3370 1.143684 AGGCAACAGTGATGTCAACCT 59.856 47.619 7.79 0.00 41.41 3.50
3059 3371 2.371841 AGGCAACAGTGATGTCAACCTA 59.628 45.455 7.79 0.00 41.41 3.08
3060 3372 3.146066 GGCAACAGTGATGTCAACCTAA 58.854 45.455 0.00 0.00 0.00 2.69
3061 3373 3.058224 GGCAACAGTGATGTCAACCTAAC 60.058 47.826 0.00 0.00 0.00 2.34
3062 3374 3.563808 GCAACAGTGATGTCAACCTAACA 59.436 43.478 0.00 0.00 0.00 2.41
3063 3375 4.216257 GCAACAGTGATGTCAACCTAACAT 59.784 41.667 0.00 0.00 39.99 2.71
3064 3376 5.278463 GCAACAGTGATGTCAACCTAACATT 60.278 40.000 0.00 0.00 37.47 2.71
3065 3377 6.735694 GCAACAGTGATGTCAACCTAACATTT 60.736 38.462 0.00 0.00 37.47 2.32
3066 3378 6.560253 ACAGTGATGTCAACCTAACATTTC 57.440 37.500 0.00 0.00 37.47 2.17
3067 3379 6.299141 ACAGTGATGTCAACCTAACATTTCT 58.701 36.000 0.00 0.00 37.47 2.52
3068 3380 6.428159 ACAGTGATGTCAACCTAACATTTCTC 59.572 38.462 0.00 0.00 37.47 2.87
3069 3381 6.652481 CAGTGATGTCAACCTAACATTTCTCT 59.348 38.462 0.00 0.00 37.47 3.10
3070 3382 6.652481 AGTGATGTCAACCTAACATTTCTCTG 59.348 38.462 0.00 0.00 37.47 3.35
3071 3383 5.939883 TGATGTCAACCTAACATTTCTCTGG 59.060 40.000 0.00 0.00 37.47 3.86
3072 3384 5.560722 TGTCAACCTAACATTTCTCTGGA 57.439 39.130 0.00 0.00 0.00 3.86
3073 3385 5.935945 TGTCAACCTAACATTTCTCTGGAA 58.064 37.500 0.00 0.00 0.00 3.53
3074 3386 6.361433 TGTCAACCTAACATTTCTCTGGAAA 58.639 36.000 0.00 0.00 44.26 3.13
3075 3387 6.831353 TGTCAACCTAACATTTCTCTGGAAAA 59.169 34.615 0.00 0.00 43.51 2.29
3076 3388 7.340743 TGTCAACCTAACATTTCTCTGGAAAAA 59.659 33.333 0.00 0.00 43.51 1.94
3138 3452 1.301677 GCAGACTAGTGCAACAGGGC 61.302 60.000 0.00 0.00 43.41 5.19
3139 3453 0.322975 CAGACTAGTGCAACAGGGCT 59.677 55.000 0.00 0.00 41.43 5.19
3140 3454 1.550524 CAGACTAGTGCAACAGGGCTA 59.449 52.381 0.00 0.00 41.43 3.93
3142 3456 1.550976 GACTAGTGCAACAGGGCTACT 59.449 52.381 0.00 0.00 41.43 2.57
3235 3715 4.034048 TGCAGAGAGAAACAACTTCGAAAC 59.966 41.667 0.00 0.00 39.22 2.78
3339 3823 3.299340 AGACCAAACTACTGTAGTGCG 57.701 47.619 20.34 13.93 39.39 5.34
3353 3841 3.888093 GTGCGACAGGACTACTTGT 57.112 52.632 0.00 0.00 39.00 3.16
3356 3844 2.985139 GTGCGACAGGACTACTTGTTAC 59.015 50.000 0.00 0.00 36.49 2.50
3399 3890 5.835113 AAACATGCTCTAAACGGCAATAT 57.165 34.783 0.00 0.00 41.90 1.28
3426 3917 0.536915 GCCTCCTCAATCCATGCTCC 60.537 60.000 0.00 0.00 0.00 4.70
3430 3921 0.250209 CCTCAATCCATGCTCCTCCG 60.250 60.000 0.00 0.00 0.00 4.63
3606 4119 1.535896 GCCTCGGTTTTGGACTTCTTC 59.464 52.381 0.00 0.00 0.00 2.87
3610 4123 4.023963 CCTCGGTTTTGGACTTCTTCTTTC 60.024 45.833 0.00 0.00 0.00 2.62
3612 4125 5.190677 TCGGTTTTGGACTTCTTCTTTCTT 58.809 37.500 0.00 0.00 0.00 2.52
3614 4127 5.971792 CGGTTTTGGACTTCTTCTTTCTTTC 59.028 40.000 0.00 0.00 0.00 2.62
3636 4160 1.731720 GCTGTCTTAGGCTCAACAGG 58.268 55.000 19.32 7.16 39.57 4.00
3657 4181 0.671472 TCTGCAGCATCACGGTTCTG 60.671 55.000 9.47 0.00 0.00 3.02
3673 4197 6.090763 CACGGTTCTGCTTTTTCTTTTTCTTT 59.909 34.615 0.00 0.00 0.00 2.52
3682 4206 7.035612 GCTTTTTCTTTTTCTTTGGAGTCTCA 58.964 34.615 1.47 0.00 0.00 3.27
3698 4222 2.014093 CTCATCTTGTTCGCCGTCGC 62.014 60.000 0.00 0.00 35.26 5.19
3717 4244 1.751733 GCCATTGGCTGCCATCTCTTA 60.752 52.381 24.03 6.57 46.69 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.599343 GGCTTTTATTTGCCCTTGAAGG 58.401 45.455 3.69 3.69 43.11 3.46
26 27 1.168407 TTGAGCACTTGAGCTGTGGC 61.168 55.000 0.00 0.00 46.75 5.01
27 28 1.002033 GTTTGAGCACTTGAGCTGTGG 60.002 52.381 0.00 0.00 46.75 4.17
28 29 1.002033 GGTTTGAGCACTTGAGCTGTG 60.002 52.381 0.00 0.00 46.75 3.66
29 30 1.312815 GGTTTGAGCACTTGAGCTGT 58.687 50.000 0.00 0.00 46.75 4.40
30 31 0.595095 GGGTTTGAGCACTTGAGCTG 59.405 55.000 0.00 0.00 46.75 4.24
32 33 0.877743 GAGGGTTTGAGCACTTGAGC 59.122 55.000 0.00 0.00 0.00 4.26
33 34 1.876156 GTGAGGGTTTGAGCACTTGAG 59.124 52.381 0.00 0.00 0.00 3.02
34 35 1.476833 GGTGAGGGTTTGAGCACTTGA 60.477 52.381 0.00 0.00 0.00 3.02
35 36 0.954452 GGTGAGGGTTTGAGCACTTG 59.046 55.000 0.00 0.00 0.00 3.16
36 37 0.846693 AGGTGAGGGTTTGAGCACTT 59.153 50.000 0.00 0.00 0.00 3.16
37 38 0.846693 AAGGTGAGGGTTTGAGCACT 59.153 50.000 0.00 0.00 0.00 4.40
38 39 0.954452 CAAGGTGAGGGTTTGAGCAC 59.046 55.000 0.00 0.00 0.00 4.40
39 40 0.178992 CCAAGGTGAGGGTTTGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
40 41 0.110486 TCCAAGGTGAGGGTTTGAGC 59.890 55.000 0.00 0.00 0.00 4.26
41 42 2.508526 CTTCCAAGGTGAGGGTTTGAG 58.491 52.381 0.00 0.00 0.00 3.02
42 43 1.478654 GCTTCCAAGGTGAGGGTTTGA 60.479 52.381 0.00 0.00 0.00 2.69
43 44 0.961753 GCTTCCAAGGTGAGGGTTTG 59.038 55.000 0.00 0.00 0.00 2.93
44 45 0.555769 TGCTTCCAAGGTGAGGGTTT 59.444 50.000 0.00 0.00 0.00 3.27
45 46 0.111253 CTGCTTCCAAGGTGAGGGTT 59.889 55.000 0.00 0.00 0.00 4.11
46 47 1.763770 CTGCTTCCAAGGTGAGGGT 59.236 57.895 0.00 0.00 0.00 4.34
47 48 1.676967 GCTGCTTCCAAGGTGAGGG 60.677 63.158 0.00 0.00 0.00 4.30
48 49 0.959372 CTGCTGCTTCCAAGGTGAGG 60.959 60.000 0.00 0.00 0.00 3.86
49 50 0.959372 CCTGCTGCTTCCAAGGTGAG 60.959 60.000 0.00 0.00 0.00 3.51
50 51 1.073722 CCTGCTGCTTCCAAGGTGA 59.926 57.895 0.00 0.00 0.00 4.02
51 52 0.959372 CTCCTGCTGCTTCCAAGGTG 60.959 60.000 0.00 0.00 0.00 4.00
90 91 1.222936 CTCTGGGGTGAGTGCATCC 59.777 63.158 0.00 0.00 45.04 3.51
131 132 4.018490 TGGTTGCTTCATATGTTGCTGAT 58.982 39.130 18.14 0.00 0.00 2.90
139 140 4.754372 ATATGCGTGGTTGCTTCATATG 57.246 40.909 0.00 0.00 31.40 1.78
140 141 7.452880 AATTATATGCGTGGTTGCTTCATAT 57.547 32.000 0.00 0.00 35.35 1.78
141 142 6.875948 AATTATATGCGTGGTTGCTTCATA 57.124 33.333 0.00 0.00 35.36 2.15
142 143 5.772825 AATTATATGCGTGGTTGCTTCAT 57.227 34.783 0.00 0.00 35.36 2.57
143 144 5.277106 CGTAATTATATGCGTGGTTGCTTCA 60.277 40.000 0.00 0.00 35.36 3.02
144 145 5.137403 CGTAATTATATGCGTGGTTGCTTC 58.863 41.667 0.00 0.00 35.36 3.86
148 150 3.364565 GGGCGTAATTATATGCGTGGTTG 60.365 47.826 0.00 0.00 43.64 3.77
154 156 3.266636 TGGATGGGCGTAATTATATGCG 58.733 45.455 0.00 0.00 43.64 4.73
170 172 3.683340 CAGATTGATCTGCCGTATGGATG 59.317 47.826 4.73 0.00 46.63 3.51
171 173 3.935315 CAGATTGATCTGCCGTATGGAT 58.065 45.455 4.73 0.00 46.63 3.41
186 188 3.076621 TGTCACTAAGCTTGGCAGATTG 58.923 45.455 9.86 0.00 29.24 2.67
196 198 6.240549 ACCTTAATATGCTGTCACTAAGCT 57.759 37.500 0.00 0.00 41.42 3.74
200 202 8.301252 TGTTCTACCTTAATATGCTGTCACTA 57.699 34.615 0.00 0.00 0.00 2.74
213 215 3.006537 ACGAGCTTGCTGTTCTACCTTAA 59.993 43.478 0.00 0.00 0.00 1.85
218 220 2.094649 AGGTACGAGCTTGCTGTTCTAC 60.095 50.000 0.00 0.00 0.00 2.59
229 231 2.609737 CCGTTTCTTCAAGGTACGAGCT 60.610 50.000 12.11 0.00 34.36 4.09
230 232 1.725164 CCGTTTCTTCAAGGTACGAGC 59.275 52.381 12.11 0.00 34.36 5.03
231 233 1.725164 GCCGTTTCTTCAAGGTACGAG 59.275 52.381 12.11 5.53 34.36 4.18
379 389 1.201921 GGCGTCTGTGTTTGCTTATCG 60.202 52.381 0.00 0.00 0.00 2.92
380 390 1.804151 TGGCGTCTGTGTTTGCTTATC 59.196 47.619 0.00 0.00 0.00 1.75
395 405 4.652131 TGATTTGGGGCGTGGCGT 62.652 61.111 0.00 0.00 0.00 5.68
397 407 2.212900 GAACTGATTTGGGGCGTGGC 62.213 60.000 0.00 0.00 0.00 5.01
398 408 1.883021 GAACTGATTTGGGGCGTGG 59.117 57.895 0.00 0.00 0.00 4.94
401 411 2.485122 GCGAACTGATTTGGGGCG 59.515 61.111 0.00 0.00 0.00 6.13
402 412 1.937546 CTGGCGAACTGATTTGGGGC 61.938 60.000 0.00 0.00 0.00 5.80
404 414 1.755179 ATCTGGCGAACTGATTTGGG 58.245 50.000 0.00 0.00 34.50 4.12
417 427 2.542766 TCGAATTTCGCAAATCTGGC 57.457 45.000 13.86 0.00 40.21 4.85
428 438 4.421948 TCGTCTCCTTAGCTTCGAATTTC 58.578 43.478 0.00 0.00 0.00 2.17
448 458 2.634982 GCCTAGAGCATGAGATCTCG 57.365 55.000 17.76 5.78 40.26 4.04
484 496 4.911514 TTGCCTAGTTTTGAACTGTTCC 57.088 40.909 17.26 2.55 42.84 3.62
487 499 4.469657 TGGATTGCCTAGTTTTGAACTGT 58.530 39.130 3.70 0.00 42.84 3.55
497 509 1.630369 TCTGCAGTTGGATTGCCTAGT 59.370 47.619 14.67 0.00 40.81 2.57
502 514 0.242017 GTGGTCTGCAGTTGGATTGC 59.758 55.000 14.67 0.00 41.86 3.56
503 515 1.901591 AGTGGTCTGCAGTTGGATTG 58.098 50.000 14.67 0.00 0.00 2.67
569 581 1.194781 ATCTCCGGGTGAGCACAGTT 61.195 55.000 0.00 0.00 41.18 3.16
835 850 0.668535 CACCGTAGATGCCAGATCGA 59.331 55.000 0.00 0.00 0.00 3.59
910 925 2.618053 GAATCTGAACCGTCCAACGAT 58.382 47.619 0.24 0.00 46.05 3.73
911 926 1.667756 CGAATCTGAACCGTCCAACGA 60.668 52.381 0.24 0.00 46.05 3.85
1037 1058 2.345991 CCCTGGAGGTTTTCGCGA 59.654 61.111 3.71 3.71 0.00 5.87
1039 1060 3.062466 GGCCCTGGAGGTTTTCGC 61.062 66.667 0.00 0.00 38.26 4.70
1042 1063 2.118294 GCAGGCCCTGGAGGTTTT 59.882 61.111 13.78 0.00 38.26 2.43
1427 1448 4.210331 CGAGATTGGGGGAAGAAAATGAT 58.790 43.478 0.00 0.00 0.00 2.45
1428 1449 3.010138 ACGAGATTGGGGGAAGAAAATGA 59.990 43.478 0.00 0.00 0.00 2.57
1435 1458 0.035056 AGCAACGAGATTGGGGGAAG 60.035 55.000 0.00 0.00 38.88 3.46
1437 1460 1.281419 TTAGCAACGAGATTGGGGGA 58.719 50.000 0.00 0.00 38.88 4.81
1442 1465 6.182039 TCCAAAGATTTAGCAACGAGATTG 57.818 37.500 0.00 0.00 41.69 2.67
1469 1492 6.310224 AGCAAACGCACCATGTAATTTTAATC 59.690 34.615 0.00 0.00 0.00 1.75
1472 1495 4.920340 CAGCAAACGCACCATGTAATTTTA 59.080 37.500 0.00 0.00 0.00 1.52
1473 1496 3.740321 CAGCAAACGCACCATGTAATTTT 59.260 39.130 0.00 0.00 0.00 1.82
1551 1574 9.459640 CTAATTCAATTGCCTCATAAACATGAG 57.540 33.333 0.00 7.52 45.69 2.90
1564 1588 8.383318 TCTCAAGTATAGCTAATTCAATTGCC 57.617 34.615 0.00 0.00 0.00 4.52
1608 1634 4.617253 TGTCAACCTAGTACAGCAACAT 57.383 40.909 0.00 0.00 0.00 2.71
1617 1643 8.836268 AAAATAACAACGATGTCAACCTAGTA 57.164 30.769 0.00 0.00 39.40 1.82
1660 1686 6.092670 TCTCCAAGCAAATAAAATCTCACTCG 59.907 38.462 0.00 0.00 0.00 4.18
1744 1770 3.448301 AGGAGCTCAGATCAGAAGTTCAG 59.552 47.826 17.19 0.00 0.00 3.02
1785 1815 8.239314 TGATGCAAATTAGAAGTTCAGTCATTC 58.761 33.333 5.50 0.00 0.00 2.67
1790 1820 7.039504 ACCATTGATGCAAATTAGAAGTTCAGT 60.040 33.333 5.50 0.00 0.00 3.41
1801 1831 7.147863 TGCTAATAGTCACCATTGATGCAAATT 60.148 33.333 0.00 0.00 33.11 1.82
1803 1833 5.651576 TGCTAATAGTCACCATTGATGCAAA 59.348 36.000 0.00 0.00 33.11 3.68
1821 1851 5.493133 TCGGCGACAAAATTAATGCTAAT 57.507 34.783 4.99 0.00 0.00 1.73
1824 1854 3.128589 ACATCGGCGACAAAATTAATGCT 59.871 39.130 13.76 0.00 0.00 3.79
1836 1866 1.138047 CGTAAGGTCACATCGGCGAC 61.138 60.000 13.76 0.00 0.00 5.19
1840 1870 2.159156 TCCATTCGTAAGGTCACATCGG 60.159 50.000 0.00 0.00 38.47 4.18
1842 1872 3.865745 CAGTCCATTCGTAAGGTCACATC 59.134 47.826 0.00 0.00 38.47 3.06
1924 1957 3.483808 TGCATCAGTTTGGTGTAGTCA 57.516 42.857 0.00 0.00 29.39 3.41
2104 2146 2.345991 GGTAGGCCGAGCAACACA 59.654 61.111 10.45 0.00 0.00 3.72
2113 2155 0.318784 GCTTATCGAGTGGTAGGCCG 60.319 60.000 0.00 0.00 37.67 6.13
2122 2164 0.039437 CGTATGCCCGCTTATCGAGT 60.039 55.000 0.00 0.00 41.67 4.18
2134 2176 3.058016 CCATGATCATTGAACCGTATGCC 60.058 47.826 5.16 0.00 0.00 4.40
2137 2179 3.149196 GGCCATGATCATTGAACCGTAT 58.851 45.455 10.85 0.00 0.00 3.06
2146 2188 5.191124 TGCTCTGATATAGGCCATGATCATT 59.809 40.000 5.16 0.00 0.00 2.57
2161 2203 4.956075 TGGTCTAACATGTCTGCTCTGATA 59.044 41.667 0.00 0.00 0.00 2.15
2233 2285 3.118920 GGAGAGCCTTGTAGACCTCTTTC 60.119 52.174 0.00 0.00 34.98 2.62
2254 2306 4.371855 TTTGTACGAGTATGCTCTCAGG 57.628 45.455 9.26 0.00 39.53 3.86
2257 2309 3.240861 CGCTTTTGTACGAGTATGCTCTC 59.759 47.826 9.26 0.71 39.53 3.20
2276 2328 2.187946 CGCCCCTTCTGAATCGCT 59.812 61.111 0.00 0.00 0.00 4.93
2287 2339 3.591254 GAAGACTCGTTGCGCCCCT 62.591 63.158 4.18 0.00 0.00 4.79
2302 2354 0.914551 CGAACTGTACCGCATCGAAG 59.085 55.000 7.11 0.00 32.93 3.79
2323 2375 2.872388 CGTGTCTGGCACTGTCCCT 61.872 63.158 11.02 0.00 45.57 4.20
2329 2381 1.301244 CAGCTTCGTGTCTGGCACT 60.301 57.895 11.02 0.00 45.57 4.40
2350 2402 2.747460 GCATTCACCAGGAGCGCA 60.747 61.111 11.47 0.00 0.00 6.09
2428 2480 1.367840 GTCGCACAGTTCCAGTCCT 59.632 57.895 0.00 0.00 0.00 3.85
2458 2510 1.526617 CGTACGCGCCGAGTATCAAC 61.527 60.000 5.73 0.00 33.17 3.18
2515 2567 0.109689 CGTTCTCTTCGAGCTCCGTT 60.110 55.000 8.47 0.00 39.75 4.44
2516 2568 1.502640 CGTTCTCTTCGAGCTCCGT 59.497 57.895 8.47 0.00 39.75 4.69
2670 2726 0.739561 CCTACTCTTCGTCCCTTCCG 59.260 60.000 0.00 0.00 0.00 4.30
2707 2767 3.074390 TGCCTTTTCTCCATTCCTTCTCA 59.926 43.478 0.00 0.00 0.00 3.27
2708 2768 3.690460 TGCCTTTTCTCCATTCCTTCTC 58.310 45.455 0.00 0.00 0.00 2.87
2735 2795 5.449304 GTGTACTGAAATGCTGTGTTTACC 58.551 41.667 0.00 0.00 0.00 2.85
2737 2797 5.126779 TGGTGTACTGAAATGCTGTGTTTA 58.873 37.500 0.00 0.00 0.00 2.01
2739 2799 3.550820 TGGTGTACTGAAATGCTGTGTT 58.449 40.909 0.00 0.00 0.00 3.32
2740 2800 3.207265 TGGTGTACTGAAATGCTGTGT 57.793 42.857 0.00 0.00 0.00 3.72
2741 2801 3.314913 TGTTGGTGTACTGAAATGCTGTG 59.685 43.478 0.00 0.00 0.00 3.66
2742 2802 3.550820 TGTTGGTGTACTGAAATGCTGT 58.449 40.909 0.00 0.00 0.00 4.40
2743 2803 4.290155 GTTGTTGGTGTACTGAAATGCTG 58.710 43.478 0.00 0.00 0.00 4.41
2744 2804 3.317993 GGTTGTTGGTGTACTGAAATGCT 59.682 43.478 0.00 0.00 0.00 3.79
2745 2805 3.552068 GGGTTGTTGGTGTACTGAAATGC 60.552 47.826 0.00 0.00 0.00 3.56
2746 2806 3.634448 TGGGTTGTTGGTGTACTGAAATG 59.366 43.478 0.00 0.00 0.00 2.32
2747 2807 3.888930 CTGGGTTGTTGGTGTACTGAAAT 59.111 43.478 0.00 0.00 0.00 2.17
2748 2808 3.283751 CTGGGTTGTTGGTGTACTGAAA 58.716 45.455 0.00 0.00 0.00 2.69
2749 2809 2.925724 CTGGGTTGTTGGTGTACTGAA 58.074 47.619 0.00 0.00 0.00 3.02
2750 2810 1.476110 GCTGGGTTGTTGGTGTACTGA 60.476 52.381 0.00 0.00 0.00 3.41
2751 2811 0.951558 GCTGGGTTGTTGGTGTACTG 59.048 55.000 0.00 0.00 0.00 2.74
2752 2812 0.548989 TGCTGGGTTGTTGGTGTACT 59.451 50.000 0.00 0.00 0.00 2.73
2753 2813 1.616159 ATGCTGGGTTGTTGGTGTAC 58.384 50.000 0.00 0.00 0.00 2.90
2754 2814 2.373335 AATGCTGGGTTGTTGGTGTA 57.627 45.000 0.00 0.00 0.00 2.90
2755 2815 1.412343 GAAATGCTGGGTTGTTGGTGT 59.588 47.619 0.00 0.00 0.00 4.16
2756 2816 1.411977 TGAAATGCTGGGTTGTTGGTG 59.588 47.619 0.00 0.00 0.00 4.17
2757 2817 1.688197 CTGAAATGCTGGGTTGTTGGT 59.312 47.619 0.00 0.00 0.00 3.67
2758 2818 1.688197 ACTGAAATGCTGGGTTGTTGG 59.312 47.619 0.00 0.00 0.00 3.77
2759 2819 3.317711 TGTACTGAAATGCTGGGTTGTTG 59.682 43.478 0.00 0.00 0.00 3.33
2760 2820 3.317993 GTGTACTGAAATGCTGGGTTGTT 59.682 43.478 0.00 0.00 0.00 2.83
2761 2821 2.884639 GTGTACTGAAATGCTGGGTTGT 59.115 45.455 0.00 0.00 0.00 3.32
2762 2822 2.228822 GGTGTACTGAAATGCTGGGTTG 59.771 50.000 0.00 0.00 0.00 3.77
2766 2826 1.470098 GCTGGTGTACTGAAATGCTGG 59.530 52.381 0.00 0.00 0.00 4.85
2857 2923 6.238759 GGAGTTACAAAATCACTTCAGTTGCT 60.239 38.462 0.00 0.00 0.00 3.91
2942 3214 2.562738 CCTCTTGTGGTTTTGGATTCCC 59.437 50.000 0.00 0.00 0.00 3.97
2947 3219 1.691196 CTGCCTCTTGTGGTTTTGGA 58.309 50.000 0.00 0.00 0.00 3.53
2950 3222 2.242043 CATCCTGCCTCTTGTGGTTTT 58.758 47.619 0.00 0.00 0.00 2.43
2951 3223 1.915141 CATCCTGCCTCTTGTGGTTT 58.085 50.000 0.00 0.00 0.00 3.27
3014 3297 7.227049 TGGTTTTGTGGAATCTTATTTCTCC 57.773 36.000 0.00 0.00 0.00 3.71
3048 3331 6.173339 TCCAGAGAAATGTTAGGTTGACATC 58.827 40.000 0.00 0.00 36.76 3.06
3126 3438 1.550976 GTAGAGTAGCCCTGTTGCACT 59.449 52.381 0.00 0.00 0.00 4.40
3158 3472 0.384669 GCATGAATTGAGGAGCCTGC 59.615 55.000 0.00 0.00 0.00 4.85
3194 3674 3.023119 TGCACTTGGACACATTTTGAGT 58.977 40.909 0.00 0.00 0.00 3.41
3235 3715 2.886523 TGCCTGGTTCTGTCAAATCTTG 59.113 45.455 0.00 0.00 0.00 3.02
3339 3823 7.545362 TCGTATAGTAACAAGTAGTCCTGTC 57.455 40.000 0.00 0.00 0.00 3.51
3352 3840 7.157050 TGCGATTCATGTTTCGTATAGTAAC 57.843 36.000 17.07 0.00 37.66 2.50
3353 3841 7.758613 TTGCGATTCATGTTTCGTATAGTAA 57.241 32.000 17.07 0.79 37.66 2.24
3356 3844 6.958752 TGTTTTGCGATTCATGTTTCGTATAG 59.041 34.615 17.07 0.00 37.66 1.31
3399 3890 2.108075 TGGATTGAGGAGGCTGTTCAAA 59.892 45.455 12.58 0.00 34.80 2.69
3426 3917 9.823647 ATTTTGAGGTCTATATATAATGCGGAG 57.176 33.333 0.00 0.00 0.00 4.63
3456 3948 1.486310 TCATCCTATGGTGGTGCTGAC 59.514 52.381 0.00 0.00 0.00 3.51
3560 4063 4.579869 TGATTAGACCAGAACCTCTTTGC 58.420 43.478 0.00 0.00 0.00 3.68
3606 4119 3.438434 GCCTAAGACAGCCAGAAAGAAAG 59.562 47.826 0.00 0.00 0.00 2.62
3610 4123 2.027745 TGAGCCTAAGACAGCCAGAAAG 60.028 50.000 0.00 0.00 0.00 2.62
3612 4125 1.644509 TGAGCCTAAGACAGCCAGAA 58.355 50.000 0.00 0.00 0.00 3.02
3614 4127 1.002430 TGTTGAGCCTAAGACAGCCAG 59.998 52.381 0.00 0.00 0.00 4.85
3636 4160 1.975363 GAACCGTGATGCTGCAGAGC 61.975 60.000 20.43 3.99 46.44 4.09
3657 4181 7.035612 TGAGACTCCAAAGAAAAAGAAAAAGC 58.964 34.615 0.00 0.00 0.00 3.51
3673 4197 1.066858 GGCGAACAAGATGAGACTCCA 60.067 52.381 0.00 0.00 0.00 3.86
3682 4206 2.813908 GGCGACGGCGAACAAGAT 60.814 61.111 18.90 0.00 41.24 2.40
3698 4222 2.353357 TAAGAGATGGCAGCCAATGG 57.647 50.000 20.84 0.00 36.95 3.16
3717 4244 0.766288 GCTAGAGGAGCCCCAGGATT 60.766 60.000 0.00 0.00 46.41 3.01


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

AutoCloner maintained by Alex Coulton.