Multiple sequence alignment - TraesCS2A01G381700

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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 TraesCS2A01G381700 chr2A 100.000 4340 0 0 2989 7328 625022817 625018478 0.000000e+00 8015
1 TraesCS2A01G381700 chr2A 100.000 2595 0 0 1 2595 625025805 625023211 0.000000e+00 4793
2 TraesCS2A01G381700 chr2A 88.961 154 15 1 1 152 79316012 79316165 9.710000e-44 189
3 TraesCS2A01G381700 chr2D 95.817 1817 62 14 3023 4835 482659983 482658177 0.000000e+00 2922
4 TraesCS2A01G381700 chr2D 92.381 1982 85 24 1 1954 482662626 482660683 0.000000e+00 2763
5 TraesCS2A01G381700 chr2D 93.263 1039 50 12 4873 5898 482657945 482656914 0.000000e+00 1513
6 TraesCS2A01G381700 chr2D 92.593 945 38 12 5896 6819 482656876 482655943 0.000000e+00 1328
7 TraesCS2A01G381700 chr2D 93.303 657 22 7 1929 2577 482660641 482659999 0.000000e+00 950
8 TraesCS2A01G381700 chr2D 88.610 518 30 16 6809 7318 482481681 482481185 2.920000e-168 603
9 TraesCS2A01G381700 chr2D 90.260 154 13 1 1 152 79056174 79056327 4.480000e-47 200
10 TraesCS2A01G381700 chr2B 95.309 1620 57 11 3222 4837 566621976 566620372 0.000000e+00 2553
11 TraesCS2A01G381700 chr2B 94.114 1529 67 12 1 1520 566624961 566623447 0.000000e+00 2303
12 TraesCS2A01G381700 chr2B 91.313 990 41 19 5675 6631 566619216 566618239 0.000000e+00 1310
13 TraesCS2A01G381700 chr2B 94.709 756 33 5 4914 5667 566620372 566619622 0.000000e+00 1168
14 TraesCS2A01G381700 chr2B 94.018 652 33 4 1929 2580 566623025 566622380 0.000000e+00 983
15 TraesCS2A01G381700 chr2B 93.005 386 20 4 1561 1946 566623452 566623074 2.310000e-154 556
16 TraesCS2A01G381700 chr2B 93.590 234 13 2 2997 3229 566622393 566622161 1.510000e-91 348
17 TraesCS2A01G381700 chr2B 88.550 262 18 4 6630 6880 566617933 566617673 2.570000e-79 307
18 TraesCS2A01G381700 chr2B 92.135 178 10 2 7151 7328 566614077 566613904 1.580000e-61 248
19 TraesCS2A01G381700 chr2B 85.957 235 16 12 6931 7163 566617671 566617452 1.230000e-57 235
20 TraesCS2A01G381700 chr6D 85.388 219 23 7 1128 1345 298911337 298911547 1.240000e-52 219
21 TraesCS2A01G381700 chr3D 91.781 146 11 1 2 146 288550603 288550458 1.250000e-47 202
22 TraesCS2A01G381700 chr7B 88.889 153 17 0 1 153 505937321 505937473 9.710000e-44 189
23 TraesCS2A01G381700 chr3A 89.333 150 14 2 1 149 383691077 383690929 3.490000e-43 187
24 TraesCS2A01G381700 chr6B 88.387 155 16 2 1 154 345218703 345218550 1.260000e-42 185
25 TraesCS2A01G381700 chr7D 88.387 155 14 2 1 152 265692979 265692826 4.520000e-42 183


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 TraesCS2A01G381700 chr2A 625018478 625025805 7327 True 6404.0 8015 100.0000 1 7328 2 chr2A.!!$R1 7327
1 TraesCS2A01G381700 chr2D 482655943 482662626 6683 True 1895.2 2922 93.4714 1 6819 5 chr2D.!!$R2 6818
2 TraesCS2A01G381700 chr2B 566613904 566624961 11057 True 1001.1 2553 92.2700 1 7328 10 chr2B.!!$R1 7327

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
233 234 0.244721 GCACTCCAATTTCAGGTGCC 59.755 55.000 0.00 0.00 44.87 5.01 F
663 672 0.326238 ACGAGTATGTCCATGGGGGT 60.326 55.000 13.02 0.14 38.11 4.95 F
1560 1585 0.739462 TAGGTTCGCGCAGAATGGTG 60.739 55.000 8.75 0.00 41.49 4.17 F
2383 2485 1.071605 AAACTTGAGAGCGATCGCAC 58.928 50.000 38.60 32.85 44.88 5.34 F
3257 3560 0.820891 CTTGTGGCTGCAGAACCTGT 60.821 55.000 20.43 0.00 33.43 4.00 F
3782 4086 1.019673 CTTGATACTGCATGCGCCTT 58.980 50.000 14.09 0.00 37.32 4.35 F
4080 4385 1.962807 TGCTTTGTTTGGGACTCATGG 59.037 47.619 0.00 0.00 0.00 3.66 F
5735 6663 2.104111 CCGGCATTTCCATAGGACTACA 59.896 50.000 0.00 0.00 34.01 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1348 0.739112 CAGCAAACCTCGAGGAGCTC 60.739 60.000 37.69 21.49 38.50 4.09 R
2374 2476 1.254570 CGTTTAGGTAAGTGCGATCGC 59.745 52.381 32.48 32.48 42.35 4.58 R
3006 3116 0.185901 AAGGTGGTGGATGTGCAACT 59.814 50.000 0.00 0.00 38.04 3.16 R
3433 3736 1.133513 ACTTCCAACTGGGCATCACAA 60.134 47.619 0.00 0.00 36.21 3.33 R
4865 5386 0.696501 GGTGGTCCCTTTAGGCTTCA 59.303 55.000 0.00 0.00 34.51 3.02 R
5502 6027 1.086696 AAAATGTCGCCTCCATGTCG 58.913 50.000 0.00 0.00 0.00 4.35 R
5795 6723 0.253044 GTCATAGCTCCCACCAGCAA 59.747 55.000 0.00 0.00 42.40 3.91 R
7190 11880 0.320073 TCGGTCCACCATTTCACGAC 60.320 55.000 0.00 0.00 35.14 4.34 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
78 79 6.074195 GCACGTTTTAGTGTGTATGTTCACTA 60.074 38.462 0.00 0.00 43.39 2.74
233 234 0.244721 GCACTCCAATTTCAGGTGCC 59.755 55.000 0.00 0.00 44.87 5.01
258 259 5.311913 AGAGGGGGAAATCTAATCTGATTCC 59.688 44.000 6.10 1.57 35.82 3.01
291 292 7.765695 ACAACATTTTTCACTGTCATCCTAT 57.234 32.000 0.00 0.00 0.00 2.57
292 293 7.820648 ACAACATTTTTCACTGTCATCCTATC 58.179 34.615 0.00 0.00 0.00 2.08
294 295 7.856145 ACATTTTTCACTGTCATCCTATCTC 57.144 36.000 0.00 0.00 0.00 2.75
295 296 6.536582 ACATTTTTCACTGTCATCCTATCTCG 59.463 38.462 0.00 0.00 0.00 4.04
296 297 5.661056 TTTTCACTGTCATCCTATCTCGT 57.339 39.130 0.00 0.00 0.00 4.18
297 298 4.639135 TTCACTGTCATCCTATCTCGTG 57.361 45.455 0.00 0.00 0.00 4.35
323 332 0.743345 GTAATCCTGGTCGGCACACC 60.743 60.000 0.00 0.00 36.90 4.16
330 339 2.040544 GGTCGGCACACCAAGGATG 61.041 63.158 0.00 0.00 36.32 3.51
360 369 4.142622 CGATGCAAGCCTGAAAGTTCATAA 60.143 41.667 0.00 0.00 36.46 1.90
391 400 7.081857 ACAGTAGTAACCACAAGGGAAAATA 57.918 36.000 0.00 0.00 41.15 1.40
392 401 6.938596 ACAGTAGTAACCACAAGGGAAAATAC 59.061 38.462 0.00 0.00 41.15 1.89
411 420 3.802948 ACAGAAGGCTTACAGATACGG 57.197 47.619 0.00 0.00 0.00 4.02
413 422 1.413077 AGAAGGCTTACAGATACGGCC 59.587 52.381 0.00 0.00 42.74 6.13
625 634 3.067833 GAGTAGGGATAAAGGATTGCGC 58.932 50.000 0.00 0.00 0.00 6.09
663 672 0.326238 ACGAGTATGTCCATGGGGGT 60.326 55.000 13.02 0.14 38.11 4.95
679 688 4.415332 GTGCGACGCGGAGAGGAA 62.415 66.667 16.14 0.00 0.00 3.36
811 828 3.516615 GATTCCAACTCCTCTTCTGTCG 58.483 50.000 0.00 0.00 0.00 4.35
942 963 1.676635 ATTCCCTCGACGACCGTCA 60.677 57.895 20.43 8.44 44.77 4.35
1004 1025 1.899142 TGACCGAACACATCTCCATCA 59.101 47.619 0.00 0.00 0.00 3.07
1005 1026 2.271800 GACCGAACACATCTCCATCAC 58.728 52.381 0.00 0.00 0.00 3.06
1006 1027 1.066143 ACCGAACACATCTCCATCACC 60.066 52.381 0.00 0.00 0.00 4.02
1007 1028 1.066215 CCGAACACATCTCCATCACCA 60.066 52.381 0.00 0.00 0.00 4.17
1008 1029 2.420547 CCGAACACATCTCCATCACCAT 60.421 50.000 0.00 0.00 0.00 3.55
1009 1030 2.868583 CGAACACATCTCCATCACCATC 59.131 50.000 0.00 0.00 0.00 3.51
1393 1415 3.056107 AGCGGTAGATTAAGTGTGCTTCA 60.056 43.478 0.00 0.00 36.22 3.02
1510 1535 2.543037 TAGGGGTGCTCACTGTGATA 57.457 50.000 11.45 0.82 0.00 2.15
1513 1538 1.765314 GGGGTGCTCACTGTGATATCT 59.235 52.381 11.45 0.00 0.00 1.98
1520 1545 4.038361 GCTCACTGTGATATCTGTGTACG 58.962 47.826 11.45 0.00 38.07 3.67
1529 1554 8.352752 TGTGATATCTGTGTACGAAATTCATC 57.647 34.615 3.98 0.00 0.00 2.92
1560 1585 0.739462 TAGGTTCGCGCAGAATGGTG 60.739 55.000 8.75 0.00 41.49 4.17
1561 1586 2.325082 GGTTCGCGCAGAATGGTGT 61.325 57.895 8.75 0.00 41.49 4.16
1562 1587 1.154413 GTTCGCGCAGAATGGTGTG 60.154 57.895 8.75 0.00 41.49 3.82
1563 1588 2.324330 TTCGCGCAGAATGGTGTGG 61.324 57.895 8.75 0.00 35.86 4.17
1601 1626 9.886132 AATTTTGTCATTCTAGTCCGTATTACT 57.114 29.630 0.00 0.00 0.00 2.24
1602 1627 8.697846 TTTTGTCATTCTAGTCCGTATTACTG 57.302 34.615 0.00 0.00 0.00 2.74
1603 1628 7.400599 TTGTCATTCTAGTCCGTATTACTGT 57.599 36.000 0.00 0.00 0.00 3.55
1604 1629 8.510243 TTGTCATTCTAGTCCGTATTACTGTA 57.490 34.615 0.00 0.00 0.00 2.74
1877 1914 3.562557 ACAAGCTACAAAAAGGGTACGTG 59.437 43.478 0.00 0.00 0.00 4.49
1899 1936 8.067784 ACGTGCCGATAATAATTTAAGTGATTG 58.932 33.333 1.50 0.00 0.00 2.67
2333 2435 7.919091 ACATCTATTAAATTTCAGTGCATGCTG 59.081 33.333 20.33 10.07 37.81 4.41
2344 2446 3.884693 CAGTGCATGCTGGTCCATATAAA 59.115 43.478 20.33 0.00 33.11 1.40
2374 2476 8.807667 AAATTCTTGTGCAATAAACTTGAGAG 57.192 30.769 0.00 0.00 0.00 3.20
2375 2477 5.362556 TCTTGTGCAATAAACTTGAGAGC 57.637 39.130 0.00 0.00 0.00 4.09
2383 2485 1.071605 AAACTTGAGAGCGATCGCAC 58.928 50.000 38.60 32.85 44.88 5.34
2393 2495 2.534757 GAGCGATCGCACTTACCTAAAC 59.465 50.000 38.60 7.62 44.88 2.01
2458 2560 3.187842 CGGGTAACTTGGTAAGTGCTTTC 59.812 47.826 0.00 0.00 41.91 2.62
2468 2570 4.816385 TGGTAAGTGCTTTCAGAGACTTTG 59.184 41.667 0.00 0.00 32.10 2.77
2480 2582 4.584743 TCAGAGACTTTGCTCTCACACTTA 59.415 41.667 3.79 0.00 43.15 2.24
2553 2655 4.700268 TTGGCATGTTAGTGCATGTAAG 57.300 40.909 7.71 0.00 46.81 2.34
3115 3226 6.902341 TGATTTGTTAGTCTTCTTCATGCAC 58.098 36.000 0.00 0.00 0.00 4.57
3116 3227 6.712095 TGATTTGTTAGTCTTCTTCATGCACT 59.288 34.615 0.00 0.00 0.00 4.40
3132 3243 2.703536 TGCACTGTCAGGTCCTCTTTTA 59.296 45.455 4.53 0.00 0.00 1.52
3160 3271 1.459158 TGGCAACACCAGGGCAATT 60.459 52.632 0.00 0.00 46.36 2.32
3165 3276 1.542915 CAACACCAGGGCAATTCTCAG 59.457 52.381 0.00 0.00 0.00 3.35
3191 3302 2.848694 TCCCATCCTCTGCAGAAATTCT 59.151 45.455 18.85 0.00 0.00 2.40
3197 3308 3.328931 TCCTCTGCAGAAATTCTCCACTT 59.671 43.478 18.85 0.00 0.00 3.16
3257 3560 0.820891 CTTGTGGCTGCAGAACCTGT 60.821 55.000 20.43 0.00 33.43 4.00
3258 3561 1.102809 TTGTGGCTGCAGAACCTGTG 61.103 55.000 20.43 0.00 33.43 3.66
3268 3571 3.255888 TGCAGAACCTGTGTGTAGAGTAG 59.744 47.826 0.00 0.00 33.43 2.57
3377 3680 3.387962 TGTTCAAGATAGAGGAGGGCAT 58.612 45.455 0.00 0.00 0.00 4.40
3388 3691 2.300152 GAGGAGGGCATTACGATCATCA 59.700 50.000 0.00 0.00 0.00 3.07
3427 3730 2.990740 ACTTAGCCCATGGTTTTGGA 57.009 45.000 11.73 0.00 39.25 3.53
3433 3736 3.250617 AGCCCATGGTTTTGGAAAGATT 58.749 40.909 11.73 0.00 39.25 2.40
3435 3738 3.752747 GCCCATGGTTTTGGAAAGATTTG 59.247 43.478 11.73 0.00 39.25 2.32
3462 3765 3.306710 GCCCAGTTGGAAGTTATTTTGGG 60.307 47.826 0.00 1.89 45.39 4.12
3519 3822 7.867305 TTTTATGTGCTGTATTTAATCGGGA 57.133 32.000 0.00 0.00 0.00 5.14
3562 3865 6.437162 CAGGGGATCAAGGTTTTCTTAATTCA 59.563 38.462 0.00 0.00 33.68 2.57
3782 4086 1.019673 CTTGATACTGCATGCGCCTT 58.980 50.000 14.09 0.00 37.32 4.35
3833 4138 3.254166 GCCAGCCATTACTGTATTCCATG 59.746 47.826 0.00 0.00 35.83 3.66
3850 4155 9.498307 GTATTCCATGTTATTTAAACCTTGTCG 57.502 33.333 0.00 0.00 0.00 4.35
4080 4385 1.962807 TGCTTTGTTTGGGACTCATGG 59.037 47.619 0.00 0.00 0.00 3.66
4112 4417 4.979335 TGTTGTAGTGGATGGTTGATGAA 58.021 39.130 0.00 0.00 0.00 2.57
4287 4593 8.338259 GTGAATTAGTAGCATGTTGGTGATAAG 58.662 37.037 0.00 0.00 0.00 1.73
4459 4765 6.258230 TCATGCTTTCAGGTTAAATCACAG 57.742 37.500 0.00 0.00 0.00 3.66
4466 4772 7.581213 TTTCAGGTTAAATCACAGTTCATGT 57.419 32.000 0.00 0.00 45.43 3.21
4523 4831 9.614792 ACATGTTCTTATAGGAGTTTATTGACC 57.385 33.333 0.00 0.00 0.00 4.02
4560 4868 4.097892 GGGTGTGATGTTTTTGACAGAACT 59.902 41.667 5.67 0.00 42.62 3.01
4622 4930 4.740934 GCAAGAAGAGGCCGTCATAAGTAT 60.741 45.833 0.00 0.00 0.00 2.12
4682 4990 8.299570 GTTGGTGTTTCATCATCTACATTTTCT 58.700 33.333 0.00 0.00 0.00 2.52
4724 5032 4.816925 AGTTACTCCTCTTCAACAGCAAAC 59.183 41.667 0.00 0.00 0.00 2.93
4727 5035 4.016444 ACTCCTCTTCAACAGCAAACAAA 58.984 39.130 0.00 0.00 0.00 2.83
4729 5037 3.761218 TCCTCTTCAACAGCAAACAAACA 59.239 39.130 0.00 0.00 0.00 2.83
4837 5358 2.552599 TGAACGTTGACTATTGGGCA 57.447 45.000 5.00 0.00 0.00 5.36
4849 5370 6.466812 TGACTATTGGGCATGTATGTATCAG 58.533 40.000 0.00 0.00 0.00 2.90
4858 5379 6.486657 GGGCATGTATGTATCAGCTTTAAGAA 59.513 38.462 0.00 0.00 0.00 2.52
4860 5381 8.019669 GGCATGTATGTATCAGCTTTAAGAATG 58.980 37.037 0.00 0.00 0.00 2.67
4861 5382 8.777413 GCATGTATGTATCAGCTTTAAGAATGA 58.223 33.333 0.00 0.00 0.00 2.57
4871 5392 7.934457 TCAGCTTTAAGAATGAATATGAAGCC 58.066 34.615 0.00 0.00 39.11 4.35
4872 5393 7.776969 TCAGCTTTAAGAATGAATATGAAGCCT 59.223 33.333 0.00 0.00 39.11 4.58
4873 5394 9.060347 CAGCTTTAAGAATGAATATGAAGCCTA 57.940 33.333 0.00 0.00 39.11 3.93
4874 5395 9.632638 AGCTTTAAGAATGAATATGAAGCCTAA 57.367 29.630 0.00 0.00 39.11 2.69
5076 5600 4.378356 CCGAAATGTGTTGACGATCATGTT 60.378 41.667 0.00 0.00 0.00 2.71
5082 5606 9.720667 AAATGTGTTGACGATCATGTTATATTG 57.279 29.630 0.00 0.00 0.00 1.90
5092 5616 6.038603 CGATCATGTTATATTGGCCTAATGGG 59.961 42.308 3.32 0.00 38.36 4.00
5405 5929 6.433847 TGGCTACAGGCATGTTATACTATT 57.566 37.500 10.25 0.00 46.12 1.73
5496 6021 3.875727 GCCATCATCAGCGCAATATATCT 59.124 43.478 11.47 0.00 0.00 1.98
5502 6027 5.866092 TCATCAGCGCAATATATCTGACTTC 59.134 40.000 11.47 0.00 38.25 3.01
5620 6145 2.903926 AGTAAGACACTTACTGGCCCT 58.096 47.619 19.07 0.00 34.25 5.19
5635 6161 2.447047 TGGCCCTTCTCTTTTCTTTCCT 59.553 45.455 0.00 0.00 0.00 3.36
5667 6194 3.603697 AGAAAGAAGGGGGAGAAACTCT 58.396 45.455 0.00 0.00 0.00 3.24
5708 6633 5.570234 TCTTGAATACGTAAAAATGGGGC 57.430 39.130 0.00 0.00 0.00 5.80
5735 6663 2.104111 CCGGCATTTCCATAGGACTACA 59.896 50.000 0.00 0.00 34.01 2.74
5741 6669 5.629133 GCATTTCCATAGGACTACAGGAACA 60.629 44.000 12.17 6.96 38.03 3.18
5795 6723 1.731324 CGAGAGGGGATAGGAGGGGT 61.731 65.000 0.00 0.00 0.00 4.95
5866 6799 5.179368 CACATAATTATCTTGGGGTAGCACG 59.821 44.000 0.00 0.00 0.00 5.34
5881 6814 4.698780 GGTAGCACGGACCTTTTCTATTTT 59.301 41.667 0.00 0.00 33.86 1.82
5882 6815 4.766404 AGCACGGACCTTTTCTATTTTG 57.234 40.909 0.00 0.00 0.00 2.44
5898 6831 7.894376 TCTATTTTGTTCGTAAAGGGTAGTG 57.106 36.000 0.00 0.00 0.00 2.74
5945 6918 9.877178 ACTTACTCCTGTAGAAATGTAGATTTG 57.123 33.333 2.01 0.00 31.58 2.32
6056 7029 1.037579 GGCTAGGGTTGATGGTTGCC 61.038 60.000 0.00 0.00 0.00 4.52
6170 7143 7.360185 GGGTCGAGAACTAGAAGAATTTGTTTC 60.360 40.741 0.00 0.00 34.31 2.78
6193 7166 5.295787 TCTGGTGTTTGTAGTAAGCTTTGTG 59.704 40.000 3.20 0.00 0.00 3.33
6197 7170 4.036262 TGTTTGTAGTAAGCTTTGTGCCTG 59.964 41.667 3.20 0.00 44.23 4.85
6205 7180 1.962807 AGCTTTGTGCCTGCATTGTTA 59.037 42.857 0.00 0.00 44.23 2.41
6257 7232 3.068873 TCAAGGAAATTTTGGTGGTTCCG 59.931 43.478 0.00 0.00 43.60 4.30
6275 7250 1.670811 CCGTTGGCACAGATATTCCAC 59.329 52.381 0.00 0.00 42.39 4.02
6398 7380 1.950216 TGCCATTTGCTCGTTGTACAA 59.050 42.857 3.59 3.59 42.00 2.41
6399 7381 2.556189 TGCCATTTGCTCGTTGTACAAT 59.444 40.909 12.26 0.00 42.00 2.71
6415 7397 4.278919 TGTACAATATGATCGGCGGTTCTA 59.721 41.667 7.21 0.00 0.00 2.10
6490 7472 6.616774 AGTATTAGCCAGAGAACTACGTAC 57.383 41.667 0.00 0.00 0.00 3.67
6497 7479 4.155644 GCCAGAGAACTACGTACAGTAACT 59.844 45.833 0.00 0.00 34.45 2.24
6524 7506 6.853872 CGGTTTCATTTATTTCAACGTTCTGA 59.146 34.615 0.00 0.00 0.00 3.27
6573 7556 9.513906 TGTATTGAATCTCCAAAACTAACATGA 57.486 29.630 0.00 0.00 0.00 3.07
6574 7557 9.994432 GTATTGAATCTCCAAAACTAACATGAG 57.006 33.333 0.00 0.00 0.00 2.90
6575 7558 6.500684 TGAATCTCCAAAACTAACATGAGC 57.499 37.500 0.00 0.00 0.00 4.26
6576 7559 6.240894 TGAATCTCCAAAACTAACATGAGCT 58.759 36.000 0.00 0.00 0.00 4.09
6577 7560 6.149973 TGAATCTCCAAAACTAACATGAGCTG 59.850 38.462 0.00 0.00 0.00 4.24
6637 7927 4.584327 AAACGCCAGCAGATAAAAGTTT 57.416 36.364 0.00 0.00 0.00 2.66
6680 7970 0.593128 AGAAATCTGCACGTTGGCAC 59.407 50.000 0.00 0.00 39.25 5.01
6724 8015 3.610585 GCATCATTTTTCGGTTTCGTGGA 60.611 43.478 0.00 0.00 37.69 4.02
6725 8016 3.889196 TCATTTTTCGGTTTCGTGGAG 57.111 42.857 0.00 0.00 37.69 3.86
6726 8017 2.550606 TCATTTTTCGGTTTCGTGGAGG 59.449 45.455 0.00 0.00 37.69 4.30
6727 8018 2.041251 TTTTTCGGTTTCGTGGAGGT 57.959 45.000 0.00 0.00 37.69 3.85
6782 8084 5.293814 CCATGTTTTGCAGTTGTTTGATTGA 59.706 36.000 0.00 0.00 0.00 2.57
6783 8085 6.017770 CCATGTTTTGCAGTTGTTTGATTGAT 60.018 34.615 0.00 0.00 0.00 2.57
6784 8086 6.981762 TGTTTTGCAGTTGTTTGATTGATT 57.018 29.167 0.00 0.00 0.00 2.57
6798 8101 3.131577 TGATTGATTGCATTGCCTCTTCC 59.868 43.478 6.12 0.00 0.00 3.46
6821 8124 0.239347 AGATGCAGAAACGCAAGCAC 59.761 50.000 0.00 0.00 46.87 4.40
6824 8127 2.427410 CAGAAACGCAAGCACGGC 60.427 61.111 0.00 0.00 45.62 5.68
6825 8128 2.899838 AGAAACGCAAGCACGGCA 60.900 55.556 0.00 0.00 45.62 5.69
6839 8142 2.666022 GCACGGCATTTGGTTGTATTTC 59.334 45.455 0.00 0.00 0.00 2.17
6863 8166 1.725931 GCTTCCAAGATGCAACGTTCG 60.726 52.381 0.00 0.00 33.71 3.95
6877 8180 3.931285 ACGTTCGGTTGTCTGTTTTAC 57.069 42.857 0.00 0.00 0.00 2.01
6878 8181 2.282290 ACGTTCGGTTGTCTGTTTTACG 59.718 45.455 0.00 0.00 0.00 3.18
6879 8182 2.282290 CGTTCGGTTGTCTGTTTTACGT 59.718 45.455 0.00 0.00 0.00 3.57
6880 8183 3.600011 CGTTCGGTTGTCTGTTTTACGTC 60.600 47.826 0.00 0.00 0.00 4.34
6881 8184 2.118683 TCGGTTGTCTGTTTTACGTCG 58.881 47.619 0.00 0.00 0.00 5.12
6882 8185 1.396316 CGGTTGTCTGTTTTACGTCGC 60.396 52.381 0.00 0.00 0.00 5.19
6883 8186 1.593933 GGTTGTCTGTTTTACGTCGCA 59.406 47.619 0.00 0.00 0.00 5.10
6884 8187 2.598205 GGTTGTCTGTTTTACGTCGCAC 60.598 50.000 0.00 0.00 0.00 5.34
6885 8188 2.212869 TGTCTGTTTTACGTCGCACT 57.787 45.000 0.00 0.00 0.00 4.40
6886 8189 1.855978 TGTCTGTTTTACGTCGCACTG 59.144 47.619 0.00 0.00 0.00 3.66
6887 8190 2.121786 GTCTGTTTTACGTCGCACTGA 58.878 47.619 0.00 0.00 0.00 3.41
6888 8191 2.729882 GTCTGTTTTACGTCGCACTGAT 59.270 45.455 0.00 0.00 0.00 2.90
6889 8192 2.729360 TCTGTTTTACGTCGCACTGATG 59.271 45.455 0.00 0.00 39.64 3.07
6890 8193 1.795872 TGTTTTACGTCGCACTGATGG 59.204 47.619 0.00 0.00 37.96 3.51
6891 8194 1.796459 GTTTTACGTCGCACTGATGGT 59.204 47.619 0.00 0.00 37.96 3.55
6892 8195 2.157834 TTTACGTCGCACTGATGGTT 57.842 45.000 0.00 0.00 37.96 3.67
6893 8196 3.300852 TTTACGTCGCACTGATGGTTA 57.699 42.857 0.00 0.00 37.96 2.85
6894 8197 2.267188 TACGTCGCACTGATGGTTAC 57.733 50.000 0.00 0.00 37.96 2.50
6895 8198 0.601558 ACGTCGCACTGATGGTTACT 59.398 50.000 0.00 0.00 37.96 2.24
6896 8199 1.000506 ACGTCGCACTGATGGTTACTT 59.999 47.619 0.00 0.00 37.96 2.24
6897 8200 1.390123 CGTCGCACTGATGGTTACTTG 59.610 52.381 0.00 0.00 0.00 3.16
6898 8201 1.128692 GTCGCACTGATGGTTACTTGC 59.871 52.381 0.00 0.00 0.00 4.01
6899 8202 1.155889 CGCACTGATGGTTACTTGCA 58.844 50.000 0.00 0.00 0.00 4.08
6900 8203 1.135972 CGCACTGATGGTTACTTGCAC 60.136 52.381 0.00 0.00 0.00 4.57
6901 8204 2.154462 GCACTGATGGTTACTTGCACT 58.846 47.619 0.00 0.00 0.00 4.40
6902 8205 2.095567 GCACTGATGGTTACTTGCACTG 60.096 50.000 0.00 0.00 0.00 3.66
6903 8206 3.402110 CACTGATGGTTACTTGCACTGA 58.598 45.455 0.00 0.00 0.00 3.41
6904 8207 4.005650 CACTGATGGTTACTTGCACTGAT 58.994 43.478 0.00 0.00 0.00 2.90
6905 8208 5.178061 CACTGATGGTTACTTGCACTGATA 58.822 41.667 0.00 0.00 0.00 2.15
6906 8209 5.643348 CACTGATGGTTACTTGCACTGATAA 59.357 40.000 0.00 0.00 0.00 1.75
6907 8210 6.317140 CACTGATGGTTACTTGCACTGATAAT 59.683 38.462 0.00 0.00 0.00 1.28
6908 8211 6.886459 ACTGATGGTTACTTGCACTGATAATT 59.114 34.615 0.00 0.00 0.00 1.40
6909 8212 8.046708 ACTGATGGTTACTTGCACTGATAATTA 58.953 33.333 0.00 0.00 0.00 1.40
6910 8213 8.208718 TGATGGTTACTTGCACTGATAATTAC 57.791 34.615 0.00 0.00 0.00 1.89
6911 8214 8.046708 TGATGGTTACTTGCACTGATAATTACT 58.953 33.333 0.00 0.00 0.00 2.24
6912 8215 7.843490 TGGTTACTTGCACTGATAATTACTC 57.157 36.000 0.00 0.00 0.00 2.59
6913 8216 7.620880 TGGTTACTTGCACTGATAATTACTCT 58.379 34.615 0.00 0.00 0.00 3.24
6914 8217 7.764443 TGGTTACTTGCACTGATAATTACTCTC 59.236 37.037 0.00 0.00 0.00 3.20
6915 8218 7.764443 GGTTACTTGCACTGATAATTACTCTCA 59.236 37.037 0.00 0.00 0.00 3.27
6916 8219 8.596380 GTTACTTGCACTGATAATTACTCTCAC 58.404 37.037 0.00 0.00 0.00 3.51
6917 8220 6.109359 ACTTGCACTGATAATTACTCTCACC 58.891 40.000 0.00 0.00 0.00 4.02
6918 8221 5.939764 TGCACTGATAATTACTCTCACCT 57.060 39.130 0.00 0.00 0.00 4.00
6919 8222 7.124298 ACTTGCACTGATAATTACTCTCACCTA 59.876 37.037 0.00 0.00 0.00 3.08
6920 8223 6.806751 TGCACTGATAATTACTCTCACCTAC 58.193 40.000 0.00 0.00 0.00 3.18
6921 8224 6.379988 TGCACTGATAATTACTCTCACCTACA 59.620 38.462 0.00 0.00 0.00 2.74
6922 8225 6.697892 GCACTGATAATTACTCTCACCTACAC 59.302 42.308 0.00 0.00 0.00 2.90
6923 8226 6.913132 CACTGATAATTACTCTCACCTACACG 59.087 42.308 0.00 0.00 0.00 4.49
6924 8227 6.039493 ACTGATAATTACTCTCACCTACACGG 59.961 42.308 0.00 0.00 39.35 4.94
6937 8240 3.240069 CCTACACGGTGAACTTAACTCG 58.760 50.000 16.29 0.00 0.00 4.18
6966 8269 9.426837 CCATCACACTTGAACAATTTCATTTAT 57.573 29.630 0.00 0.00 41.50 1.40
6971 8274 8.143193 ACACTTGAACAATTTCATTTATGAGCA 58.857 29.630 0.00 0.00 41.50 4.26
7027 8330 5.465724 GTGGAACAACGAGATGAAACTAAGT 59.534 40.000 0.00 0.00 44.16 2.24
7028 8331 5.465390 TGGAACAACGAGATGAAACTAAGTG 59.535 40.000 0.00 0.00 31.92 3.16
7030 8333 6.369065 GGAACAACGAGATGAAACTAAGTGAT 59.631 38.462 0.00 0.00 0.00 3.06
7031 8334 6.952935 ACAACGAGATGAAACTAAGTGATC 57.047 37.500 0.00 0.00 0.00 2.92
7032 8335 6.455647 ACAACGAGATGAAACTAAGTGATCA 58.544 36.000 0.00 0.00 0.00 2.92
7034 8337 7.441157 ACAACGAGATGAAACTAAGTGATCAAA 59.559 33.333 0.00 0.00 0.00 2.69
7035 8338 7.588143 ACGAGATGAAACTAAGTGATCAAAG 57.412 36.000 0.00 0.00 0.00 2.77
7037 8340 6.813649 CGAGATGAAACTAAGTGATCAAAGGA 59.186 38.462 0.00 0.00 0.00 3.36
7039 8342 7.911651 AGATGAAACTAAGTGATCAAAGGAGA 58.088 34.615 0.00 0.00 0.00 3.71
7040 8343 8.547173 AGATGAAACTAAGTGATCAAAGGAGAT 58.453 33.333 0.00 0.00 0.00 2.75
7041 8344 8.729805 ATGAAACTAAGTGATCAAAGGAGATC 57.270 34.615 0.00 0.00 43.69 2.75
7051 8354 6.871844 TGATCAAAGGAGATCACTTAGACTG 58.128 40.000 0.00 0.00 46.92 3.51
7052 8355 6.665248 TGATCAAAGGAGATCACTTAGACTGA 59.335 38.462 0.00 0.66 46.92 3.41
7053 8356 6.274157 TCAAAGGAGATCACTTAGACTGAC 57.726 41.667 0.00 0.00 0.00 3.51
7054 8357 6.013379 TCAAAGGAGATCACTTAGACTGACT 58.987 40.000 0.00 0.00 0.00 3.41
7055 8358 5.913137 AAGGAGATCACTTAGACTGACTG 57.087 43.478 0.00 0.00 0.00 3.51
7056 8359 4.277476 AGGAGATCACTTAGACTGACTGG 58.723 47.826 0.00 0.00 0.00 4.00
7057 8360 4.020543 GGAGATCACTTAGACTGACTGGT 58.979 47.826 0.00 0.00 0.00 4.00
7058 8361 4.142271 GGAGATCACTTAGACTGACTGGTG 60.142 50.000 0.00 8.03 36.13 4.17
7120 8423 4.223032 ACATGAAATCGAGGAGTTACCACT 59.777 41.667 0.00 0.00 42.04 4.00
7137 8440 4.243270 ACCACTAAGGAAACTCGAAATCG 58.757 43.478 0.00 0.00 42.68 3.34
7190 11880 5.461407 CCACATCTTCTTCATGTAGACATCG 59.539 44.000 0.90 0.00 32.48 3.84
7193 11883 4.909894 TCTTCTTCATGTAGACATCGTCG 58.090 43.478 0.90 0.00 37.67 5.12
7208 11898 1.623081 CGTCGTGAAATGGTGGACCG 61.623 60.000 0.00 0.00 39.43 4.79
7220 11910 2.028476 TGGTGGACCGACAAAGTAGATG 60.028 50.000 0.00 0.00 39.43 2.90
7233 11923 9.619316 CGACAAAGTAGATGATAAAGAGGATAG 57.381 37.037 0.00 0.00 0.00 2.08
7238 11928 8.644374 AGTAGATGATAAAGAGGATAGGTGAC 57.356 38.462 0.00 0.00 0.00 3.67
7243 11933 6.673583 TGATAAAGAGGATAGGTGACAGAGA 58.326 40.000 0.00 0.00 0.00 3.10
7244 11934 6.775142 TGATAAAGAGGATAGGTGACAGAGAG 59.225 42.308 0.00 0.00 0.00 3.20
7245 11935 3.593442 AGAGGATAGGTGACAGAGAGG 57.407 52.381 0.00 0.00 0.00 3.69
7246 11936 2.176798 AGAGGATAGGTGACAGAGAGGG 59.823 54.545 0.00 0.00 0.00 4.30
7247 11937 2.175931 GAGGATAGGTGACAGAGAGGGA 59.824 54.545 0.00 0.00 0.00 4.20
7253 11943 1.283613 GGTGACAGAGAGGGAGAGAGA 59.716 57.143 0.00 0.00 0.00 3.10
7257 11947 1.846439 ACAGAGAGGGAGAGAGAGAGG 59.154 57.143 0.00 0.00 0.00 3.69
7261 11951 1.158007 GAGGGAGAGAGAGAGGGGAT 58.842 60.000 0.00 0.00 0.00 3.85
7265 11955 2.316108 GGAGAGAGAGAGGGGATGAAC 58.684 57.143 0.00 0.00 0.00 3.18
7301 11991 7.804600 TCACGTACACACACAAAGTATAGTAAG 59.195 37.037 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.684613 GCCTGCATACATCCATTTCAGAAAAT 60.685 38.462 0.00 0.00 35.43 1.82
39 40 0.181114 ACGTGCCTGCATACATCCAT 59.819 50.000 0.00 0.00 0.00 3.41
40 41 0.035534 AACGTGCCTGCATACATCCA 60.036 50.000 0.00 0.00 0.00 3.41
49 50 0.661020 ACACACTAAAACGTGCCTGC 59.339 50.000 0.00 0.00 38.45 4.85
78 79 3.270877 GGACTGCATACGGACTGAAATT 58.729 45.455 0.00 0.00 0.00 1.82
233 234 5.839517 ATCAGATTAGATTTCCCCCTCTG 57.160 43.478 0.00 0.00 0.00 3.35
291 292 0.108520 GGATTACGCCCAACACGAGA 60.109 55.000 0.00 0.00 0.00 4.04
292 293 0.108329 AGGATTACGCCCAACACGAG 60.108 55.000 0.00 0.00 0.00 4.18
294 295 1.366111 CCAGGATTACGCCCAACACG 61.366 60.000 0.00 0.00 0.00 4.49
295 296 0.322187 ACCAGGATTACGCCCAACAC 60.322 55.000 0.00 0.00 0.00 3.32
296 297 0.035820 GACCAGGATTACGCCCAACA 60.036 55.000 0.00 0.00 0.00 3.33
297 298 1.087771 CGACCAGGATTACGCCCAAC 61.088 60.000 0.00 0.00 0.00 3.77
360 369 6.769341 CCCTTGTGGTTACTACTGTAGTTTTT 59.231 38.462 24.09 3.54 40.14 1.94
368 377 6.938030 TGTATTTTCCCTTGTGGTTACTACTG 59.062 38.462 0.00 0.00 34.77 2.74
369 378 7.016858 TCTGTATTTTCCCTTGTGGTTACTACT 59.983 37.037 0.00 0.00 34.77 2.57
370 379 7.163441 TCTGTATTTTCCCTTGTGGTTACTAC 58.837 38.462 0.00 0.00 34.77 2.73
371 380 7.319052 TCTGTATTTTCCCTTGTGGTTACTA 57.681 36.000 0.00 0.00 34.77 1.82
372 381 6.195600 TCTGTATTTTCCCTTGTGGTTACT 57.804 37.500 0.00 0.00 34.77 2.24
391 400 2.159085 GCCGTATCTGTAAGCCTTCTGT 60.159 50.000 0.00 0.00 0.00 3.41
392 401 2.474816 GCCGTATCTGTAAGCCTTCTG 58.525 52.381 0.00 0.00 0.00 3.02
599 608 1.577242 TCCTTTATCCCTACTCCCCGT 59.423 52.381 0.00 0.00 0.00 5.28
663 672 3.411418 GATTCCTCTCCGCGTCGCA 62.411 63.158 18.75 0.00 0.00 5.10
679 688 1.187087 AAGGAAGAAGACGAGGCGAT 58.813 50.000 0.00 0.00 0.00 4.58
811 828 3.015293 CTCACACGGCGACACATGC 62.015 63.158 16.62 0.00 0.00 4.06
916 933 3.781307 TCGAGGGAATGGGCCGTG 61.781 66.667 0.00 0.00 0.00 4.94
1004 1025 1.764723 TGATCTTCTCATGGCGATGGT 59.235 47.619 8.98 0.00 0.00 3.55
1005 1026 2.141517 GTGATCTTCTCATGGCGATGG 58.858 52.381 8.98 0.15 35.97 3.51
1006 1027 2.141517 GGTGATCTTCTCATGGCGATG 58.858 52.381 1.66 1.66 35.97 3.84
1007 1028 1.764723 TGGTGATCTTCTCATGGCGAT 59.235 47.619 0.00 0.00 35.97 4.58
1008 1029 1.194218 TGGTGATCTTCTCATGGCGA 58.806 50.000 0.00 0.00 35.97 5.54
1009 1030 2.251409 ATGGTGATCTTCTCATGGCG 57.749 50.000 0.00 0.00 35.97 5.69
1281 1302 1.805945 GACGAGCACGACCATGTCC 60.806 63.158 11.40 0.00 42.66 4.02
1327 1348 0.739112 CAGCAAACCTCGAGGAGCTC 60.739 60.000 37.69 21.49 38.50 4.09
1393 1415 2.611518 CGCTAAAGCTGCTACTTCACT 58.388 47.619 0.90 0.00 39.32 3.41
1510 1535 5.528690 CCCATGATGAATTTCGTACACAGAT 59.471 40.000 0.00 0.00 0.00 2.90
1513 1538 4.584874 ACCCATGATGAATTTCGTACACA 58.415 39.130 0.00 0.00 0.00 3.72
1529 1554 2.736721 CGCGAACCTATCATAACCCATG 59.263 50.000 0.00 0.00 35.81 3.66
1547 1572 2.741985 TCCACACCATTCTGCGCG 60.742 61.111 0.00 0.00 0.00 6.86
1560 1585 5.213891 ACAAAATTTTCATCCAGGTCCAC 57.786 39.130 0.00 0.00 0.00 4.02
1561 1586 4.898265 TGACAAAATTTTCATCCAGGTCCA 59.102 37.500 0.00 0.00 0.00 4.02
1562 1587 5.467035 TGACAAAATTTTCATCCAGGTCC 57.533 39.130 0.00 0.00 0.00 4.46
1563 1588 7.381323 AGAATGACAAAATTTTCATCCAGGTC 58.619 34.615 0.00 4.61 30.96 3.85
1600 1625 7.382110 TCTTTCAGGAATCTTCTGAACTACAG 58.618 38.462 6.08 0.00 46.84 2.74
1601 1626 7.303182 TCTTTCAGGAATCTTCTGAACTACA 57.697 36.000 6.08 0.00 46.84 2.74
1602 1627 8.608844 TTTCTTTCAGGAATCTTCTGAACTAC 57.391 34.615 6.08 0.00 46.84 2.73
1603 1628 9.627123 TTTTTCTTTCAGGAATCTTCTGAACTA 57.373 29.630 6.08 0.00 46.84 2.24
1604 1629 8.525290 TTTTTCTTTCAGGAATCTTCTGAACT 57.475 30.769 6.08 0.00 46.84 3.01
1877 1914 8.076178 AGCACAATCACTTAAATTATTATCGGC 58.924 33.333 0.00 0.00 0.00 5.54
1899 1936 3.500680 TGGTGACGGAAATAAAGAAGCAC 59.499 43.478 0.00 0.00 0.00 4.40
2349 2451 7.383300 GCTCTCAAGTTTATTGCACAAGAATTT 59.617 33.333 0.00 0.00 0.00 1.82
2374 2476 1.254570 CGTTTAGGTAAGTGCGATCGC 59.745 52.381 32.48 32.48 42.35 4.58
2375 2477 1.850441 CCGTTTAGGTAAGTGCGATCG 59.150 52.381 11.69 11.69 34.51 3.69
2430 2532 5.481105 CACTTACCAAGTTACCCGTATGAA 58.519 41.667 0.00 0.00 40.46 2.57
2431 2533 4.621274 GCACTTACCAAGTTACCCGTATGA 60.621 45.833 0.00 0.00 40.46 2.15
2458 2560 3.383620 AGTGTGAGAGCAAAGTCTCTG 57.616 47.619 0.00 0.00 43.05 3.35
2468 2570 7.639945 ACTTTACATTTTGTAAGTGTGAGAGC 58.360 34.615 0.91 0.00 42.93 4.09
2505 2607 6.989759 TCTATGAAAAGTAACACACTGAAGCA 59.010 34.615 0.00 0.00 37.63 3.91
2988 3098 9.891828 TGTGCAACTGTCTATTATGTTTTTAAG 57.108 29.630 0.00 0.00 38.04 1.85
2991 3101 8.028938 GGATGTGCAACTGTCTATTATGTTTTT 58.971 33.333 0.00 0.00 38.04 1.94
2992 3102 7.176515 TGGATGTGCAACTGTCTATTATGTTTT 59.823 33.333 0.00 0.00 38.04 2.43
2993 3103 6.658816 TGGATGTGCAACTGTCTATTATGTTT 59.341 34.615 0.00 0.00 38.04 2.83
2994 3104 6.094048 GTGGATGTGCAACTGTCTATTATGTT 59.906 38.462 0.00 0.00 38.04 2.71
2995 3105 5.586243 GTGGATGTGCAACTGTCTATTATGT 59.414 40.000 0.00 0.00 38.04 2.29
2996 3106 5.008019 GGTGGATGTGCAACTGTCTATTATG 59.992 44.000 0.00 0.00 38.04 1.90
2997 3107 5.126067 GGTGGATGTGCAACTGTCTATTAT 58.874 41.667 0.00 0.00 38.04 1.28
2998 3108 4.019771 TGGTGGATGTGCAACTGTCTATTA 60.020 41.667 0.00 0.00 38.04 0.98
2999 3109 3.244875 TGGTGGATGTGCAACTGTCTATT 60.245 43.478 0.00 0.00 38.04 1.73
3000 3110 2.305635 TGGTGGATGTGCAACTGTCTAT 59.694 45.455 0.00 0.00 38.04 1.98
3001 3111 1.696884 TGGTGGATGTGCAACTGTCTA 59.303 47.619 0.00 0.00 38.04 2.59
3002 3112 0.473755 TGGTGGATGTGCAACTGTCT 59.526 50.000 0.00 0.00 38.04 3.41
3003 3113 0.593128 GTGGTGGATGTGCAACTGTC 59.407 55.000 0.00 0.00 38.04 3.51
3004 3114 0.823356 GGTGGTGGATGTGCAACTGT 60.823 55.000 0.00 0.00 38.04 3.55
3005 3115 0.538057 AGGTGGTGGATGTGCAACTG 60.538 55.000 0.00 0.00 38.04 3.16
3006 3116 0.185901 AAGGTGGTGGATGTGCAACT 59.814 50.000 0.00 0.00 38.04 3.16
3007 3117 1.000274 GAAAGGTGGTGGATGTGCAAC 60.000 52.381 0.00 0.00 37.35 4.17
3008 3118 1.327303 GAAAGGTGGTGGATGTGCAA 58.673 50.000 0.00 0.00 0.00 4.08
3052 3162 1.002379 AGGCCAAAGAGAGCAGCAG 60.002 57.895 5.01 0.00 0.00 4.24
3106 3217 1.002888 AGGACCTGACAGTGCATGAAG 59.997 52.381 0.00 0.00 0.00 3.02
3115 3226 6.990349 TGTAAACTTAAAAGAGGACCTGACAG 59.010 38.462 0.00 0.00 0.00 3.51
3116 3227 6.891388 TGTAAACTTAAAAGAGGACCTGACA 58.109 36.000 0.00 0.00 0.00 3.58
3165 3276 0.324285 CTGCAGAGGATGGGATAGCC 59.676 60.000 8.42 0.00 34.09 3.93
3197 3308 3.415457 TGATGGTGTGTATGAACTGCA 57.585 42.857 0.00 0.00 0.00 4.41
3257 3560 8.678199 CATAAGAAGATGTGACTACTCTACACA 58.322 37.037 0.00 0.00 46.04 3.72
3258 3561 8.894731 TCATAAGAAGATGTGACTACTCTACAC 58.105 37.037 0.00 0.00 35.45 2.90
3268 3571 5.684704 TGGGGAATCATAAGAAGATGTGAC 58.315 41.667 0.00 0.00 0.00 3.67
3377 3680 6.447162 AGACTATTTCGCATGATGATCGTAA 58.553 36.000 0.00 0.00 0.00 3.18
3427 3730 3.007182 CCAACTGGGCATCACAAATCTTT 59.993 43.478 0.00 0.00 0.00 2.52
3433 3736 1.133513 ACTTCCAACTGGGCATCACAA 60.134 47.619 0.00 0.00 36.21 3.33
3435 3738 1.620822 AACTTCCAACTGGGCATCAC 58.379 50.000 0.00 0.00 36.21 3.06
3462 3765 9.918630 ACAATGCTAAATATAATCATCAAAGGC 57.081 29.630 0.00 0.00 0.00 4.35
3519 3822 4.039973 CCCCTGCATTGATTAATTCAGCAT 59.960 41.667 4.63 0.00 36.58 3.79
3562 3865 7.094634 CGGGAGTTAGCAAAATCAGCATAATAT 60.095 37.037 0.00 0.00 31.29 1.28
3749 4052 5.175673 GCAGTATCAAGTTTGCAAAAAGGTC 59.824 40.000 14.67 0.55 36.59 3.85
3804 4109 8.210946 GGAATACAGTAATGGCTGGCATATATA 58.789 37.037 17.59 3.60 40.59 0.86
3806 4111 6.012945 TGGAATACAGTAATGGCTGGCATATA 60.013 38.462 17.59 9.13 40.59 0.86
3833 4138 7.432838 TCTTTGCAACGACAAGGTTTAAATAAC 59.567 33.333 0.00 0.00 0.00 1.89
3850 4155 7.970614 CCTTACTGGAATCTATTTCTTTGCAAC 59.029 37.037 0.00 0.00 38.35 4.17
3963 4268 6.684686 AGCACGAGACAACAAATAAGTAGTA 58.315 36.000 0.00 0.00 0.00 1.82
3964 4269 5.539048 AGCACGAGACAACAAATAAGTAGT 58.461 37.500 0.00 0.00 0.00 2.73
3965 4270 5.633601 TGAGCACGAGACAACAAATAAGTAG 59.366 40.000 0.00 0.00 0.00 2.57
4080 4385 8.732746 ACCATCCACTACAACATAAATTAGAC 57.267 34.615 0.00 0.00 0.00 2.59
4112 4417 9.708092 GTGTAGTGAATAACTCTAAGTTCCTTT 57.292 33.333 0.00 0.00 39.51 3.11
4287 4593 6.291377 TCCTGGAATCATACAGAGCATAAAC 58.709 40.000 0.00 0.00 36.86 2.01
4523 4831 3.534554 TCACACCCATGATCGATCAAAG 58.465 45.455 30.41 23.90 40.69 2.77
4560 4868 6.245408 ACTGCACACTTGGAAAATCCTTATA 58.755 36.000 0.00 0.00 37.46 0.98
4601 4909 6.324254 ACTTATACTTATGACGGCCTCTTCTT 59.676 38.462 0.00 0.00 0.00 2.52
4724 5032 5.978919 ACACATGCTACAAATTCAGTGTTTG 59.021 36.000 5.01 5.01 41.22 2.93
4727 5035 5.772825 AACACATGCTACAAATTCAGTGT 57.227 34.783 0.00 0.00 40.32 3.55
4729 5037 7.510549 ACTTAACACATGCTACAAATTCAGT 57.489 32.000 0.00 0.00 0.00 3.41
4858 5379 5.134339 TGGTCCCTTTAGGCTTCATATTCAT 59.866 40.000 0.00 0.00 34.51 2.57
4860 5381 4.822350 GTGGTCCCTTTAGGCTTCATATTC 59.178 45.833 0.00 0.00 34.51 1.75
4861 5382 4.386424 GGTGGTCCCTTTAGGCTTCATATT 60.386 45.833 0.00 0.00 34.51 1.28
4862 5383 3.138468 GGTGGTCCCTTTAGGCTTCATAT 59.862 47.826 0.00 0.00 34.51 1.78
4863 5384 2.508300 GGTGGTCCCTTTAGGCTTCATA 59.492 50.000 0.00 0.00 34.51 2.15
4864 5385 1.285078 GGTGGTCCCTTTAGGCTTCAT 59.715 52.381 0.00 0.00 34.51 2.57
4865 5386 0.696501 GGTGGTCCCTTTAGGCTTCA 59.303 55.000 0.00 0.00 34.51 3.02
4866 5387 3.571748 GGTGGTCCCTTTAGGCTTC 57.428 57.895 0.00 0.00 34.51 3.86
4877 5398 3.303351 AATCATCATGAAGGGTGGTCC 57.697 47.619 0.00 0.00 0.00 4.46
4944 5465 3.945285 CAGGGTGAACGCTTTACCAATAT 59.055 43.478 11.68 0.00 37.00 1.28
5040 5561 8.286800 TCAACACATTTCGGTAAGAACATTAAG 58.713 33.333 0.00 0.00 38.83 1.85
5046 5567 4.209703 TCGTCAACACATTTCGGTAAGAAC 59.790 41.667 0.00 0.00 38.83 3.01
5076 5600 7.285858 GTGTTAAACACCCATTAGGCCAATATA 59.714 37.037 5.01 0.00 43.05 0.86
5082 5606 3.861276 GTGTTAAACACCCATTAGGCC 57.139 47.619 0.00 0.00 43.05 5.19
5405 5929 6.959639 AGATGAACCTTTGCAAGAAGTTAA 57.040 33.333 0.00 0.00 0.00 2.01
5479 6004 5.220172 CGAAGTCAGATATATTGCGCTGATG 60.220 44.000 9.73 0.00 39.33 3.07
5480 6005 4.861462 CGAAGTCAGATATATTGCGCTGAT 59.139 41.667 9.73 5.45 39.33 2.90
5481 6006 4.023193 TCGAAGTCAGATATATTGCGCTGA 60.023 41.667 9.73 0.00 35.22 4.26
5496 6021 1.215382 CGCCTCCATGTCGAAGTCA 59.785 57.895 0.00 0.00 0.00 3.41
5502 6027 1.086696 AAAATGTCGCCTCCATGTCG 58.913 50.000 0.00 0.00 0.00 4.35
5611 6136 4.506802 GGAAAGAAAAGAGAAGGGCCAGTA 60.507 45.833 6.18 0.00 0.00 2.74
5635 6161 9.460413 TCTCCCCCTTCTTTCTTCATATTAATA 57.540 33.333 0.00 0.00 0.00 0.98
5648 6175 2.376855 CCAGAGTTTCTCCCCCTTCTTT 59.623 50.000 0.00 0.00 0.00 2.52
5741 6669 2.243736 TCCCAAGTTTTCAACAGTCCCT 59.756 45.455 0.00 0.00 0.00 4.20
5752 6680 5.070685 GTGTAGTCCTCAATCCCAAGTTTT 58.929 41.667 0.00 0.00 0.00 2.43
5795 6723 0.253044 GTCATAGCTCCCACCAGCAA 59.747 55.000 0.00 0.00 42.40 3.91
5866 6799 7.806487 CCTTTACGAACAAAATAGAAAAGGTCC 59.194 37.037 0.00 0.00 37.83 4.46
5881 6814 2.037511 CCACCACTACCCTTTACGAACA 59.962 50.000 0.00 0.00 0.00 3.18
5882 6815 2.037641 ACCACCACTACCCTTTACGAAC 59.962 50.000 0.00 0.00 0.00 3.95
5898 6831 5.501156 AGTCAGAATCCTTAAATCACCACC 58.499 41.667 0.00 0.00 0.00 4.61
5945 6918 7.750903 GCCTTTCAGACAGTTTGTGAAATATAC 59.249 37.037 2.43 0.00 39.00 1.47
6056 7029 3.357079 GCCAGCAGAACACCACCG 61.357 66.667 0.00 0.00 0.00 4.94
6128 7101 5.188948 TCTCGACCCATTCCTATCTTTTTGA 59.811 40.000 0.00 0.00 0.00 2.69
6131 7104 5.189934 AGTTCTCGACCCATTCCTATCTTTT 59.810 40.000 0.00 0.00 0.00 2.27
6170 7143 5.510671 CACAAAGCTTACTACAAACACCAG 58.489 41.667 0.00 0.00 0.00 4.00
6193 7166 6.813152 ACATGAACTAAATTAACAATGCAGGC 59.187 34.615 0.00 0.00 0.00 4.85
6197 7170 9.796062 CAACAACATGAACTAAATTAACAATGC 57.204 29.630 0.00 0.00 0.00 3.56
6235 7210 3.068873 CGGAACCACCAAAATTTCCTTGA 59.931 43.478 0.00 0.00 36.18 3.02
6257 7232 5.163513 CAAAAGTGGAATATCTGTGCCAAC 58.836 41.667 0.00 0.00 31.18 3.77
6275 7250 6.215121 TGATTTGGCATCAGTGTTACAAAAG 58.785 36.000 0.00 0.00 33.12 2.27
6398 7380 5.362717 TCCAATATAGAACCGCCGATCATAT 59.637 40.000 0.00 0.00 0.00 1.78
6399 7381 4.707934 TCCAATATAGAACCGCCGATCATA 59.292 41.667 0.00 0.00 0.00 2.15
6415 7397 8.274322 TCAGTTCATGTTCCATAGTTCCAATAT 58.726 33.333 0.00 0.00 0.00 1.28
6490 7472 7.081349 TGAAATAAATGAAACCGCAGTTACTG 58.919 34.615 8.18 8.18 34.19 2.74
6497 7479 4.861210 ACGTTGAAATAAATGAAACCGCA 58.139 34.783 0.00 0.00 0.00 5.69
6575 7558 2.203167 AGGCCGCATGCTCATCAG 60.203 61.111 17.13 0.00 40.92 2.90
6576 7559 2.203112 GAGGCCGCATGCTCATCA 60.203 61.111 17.13 0.00 40.92 3.07
6577 7560 2.110627 AGAGGCCGCATGCTCATC 59.889 61.111 17.13 13.97 40.92 2.92
6631 7614 4.443913 ACAACGTGCCTGTTTAAACTTT 57.556 36.364 18.72 0.00 0.00 2.66
6637 7927 2.335316 AGGAACAACGTGCCTGTTTA 57.665 45.000 5.63 0.00 40.73 2.01
6680 7970 1.035139 GCATCCAAACAGGCCCATAG 58.965 55.000 0.00 0.00 37.29 2.23
6782 8084 2.519771 TGAGGAAGAGGCAATGCAAT 57.480 45.000 7.79 0.00 0.00 3.56
6783 8085 2.165167 CTTGAGGAAGAGGCAATGCAA 58.835 47.619 7.79 0.00 0.00 4.08
6784 8086 1.352017 TCTTGAGGAAGAGGCAATGCA 59.648 47.619 7.79 0.00 32.98 3.96
6798 8101 2.847901 CTTGCGTTTCTGCATCTTGAG 58.152 47.619 0.00 0.00 45.78 3.02
6821 8124 3.919804 CACAGAAATACAACCAAATGCCG 59.080 43.478 0.00 0.00 0.00 5.69
6824 8127 5.634859 GGAAGCACAGAAATACAACCAAATG 59.365 40.000 0.00 0.00 0.00 2.32
6825 8128 5.304101 TGGAAGCACAGAAATACAACCAAAT 59.696 36.000 0.00 0.00 0.00 2.32
6839 8142 1.400629 CGTTGCATCTTGGAAGCACAG 60.401 52.381 0.00 0.00 36.00 3.66
6863 8166 1.593933 TGCGACGTAAAACAGACAACC 59.406 47.619 0.00 0.00 0.00 3.77
6868 8171 2.495409 TCAGTGCGACGTAAAACAGA 57.505 45.000 0.00 0.00 0.00 3.41
6869 8172 2.159841 CCATCAGTGCGACGTAAAACAG 60.160 50.000 0.00 0.00 0.00 3.16
6875 8178 1.814394 AGTAACCATCAGTGCGACGTA 59.186 47.619 0.00 0.00 0.00 3.57
6876 8179 0.601558 AGTAACCATCAGTGCGACGT 59.398 50.000 0.00 0.00 0.00 4.34
6877 8180 1.390123 CAAGTAACCATCAGTGCGACG 59.610 52.381 0.00 0.00 0.00 5.12
6878 8181 1.128692 GCAAGTAACCATCAGTGCGAC 59.871 52.381 0.00 0.00 0.00 5.19
6879 8182 1.270571 TGCAAGTAACCATCAGTGCGA 60.271 47.619 0.00 0.00 34.73 5.10
6880 8183 1.135972 GTGCAAGTAACCATCAGTGCG 60.136 52.381 0.00 0.00 34.73 5.34
6881 8184 2.095567 CAGTGCAAGTAACCATCAGTGC 60.096 50.000 0.00 0.00 0.00 4.40
6882 8185 3.402110 TCAGTGCAAGTAACCATCAGTG 58.598 45.455 0.00 0.00 0.00 3.66
6883 8186 3.769739 TCAGTGCAAGTAACCATCAGT 57.230 42.857 0.00 0.00 0.00 3.41
6884 8187 6.932356 ATTATCAGTGCAAGTAACCATCAG 57.068 37.500 0.00 0.00 0.00 2.90
6885 8188 8.046708 AGTAATTATCAGTGCAAGTAACCATCA 58.953 33.333 0.00 0.00 0.00 3.07
6886 8189 8.438676 AGTAATTATCAGTGCAAGTAACCATC 57.561 34.615 0.00 0.00 0.00 3.51
6887 8190 8.267894 AGAGTAATTATCAGTGCAAGTAACCAT 58.732 33.333 0.00 0.00 0.00 3.55
6888 8191 7.620880 AGAGTAATTATCAGTGCAAGTAACCA 58.379 34.615 0.00 0.00 0.00 3.67
6889 8192 7.764443 TGAGAGTAATTATCAGTGCAAGTAACC 59.236 37.037 0.00 0.00 0.00 2.85
6890 8193 8.596380 GTGAGAGTAATTATCAGTGCAAGTAAC 58.404 37.037 0.00 0.00 0.00 2.50
6891 8194 7.764443 GGTGAGAGTAATTATCAGTGCAAGTAA 59.236 37.037 0.00 0.00 0.00 2.24
6892 8195 7.124298 AGGTGAGAGTAATTATCAGTGCAAGTA 59.876 37.037 0.00 0.00 0.00 2.24
6893 8196 6.070538 AGGTGAGAGTAATTATCAGTGCAAGT 60.071 38.462 0.00 0.00 0.00 3.16
6894 8197 6.344500 AGGTGAGAGTAATTATCAGTGCAAG 58.656 40.000 0.00 0.00 0.00 4.01
6895 8198 6.299805 AGGTGAGAGTAATTATCAGTGCAA 57.700 37.500 0.00 0.00 0.00 4.08
6896 8199 5.939764 AGGTGAGAGTAATTATCAGTGCA 57.060 39.130 0.00 0.00 0.00 4.57
6897 8200 6.697892 GTGTAGGTGAGAGTAATTATCAGTGC 59.302 42.308 0.00 0.00 0.00 4.40
6898 8201 6.913132 CGTGTAGGTGAGAGTAATTATCAGTG 59.087 42.308 0.00 0.00 0.00 3.66
6899 8202 6.039493 CCGTGTAGGTGAGAGTAATTATCAGT 59.961 42.308 0.00 0.00 34.51 3.41
6900 8203 6.439599 CCGTGTAGGTGAGAGTAATTATCAG 58.560 44.000 0.00 0.00 34.51 2.90
6901 8204 6.387041 CCGTGTAGGTGAGAGTAATTATCA 57.613 41.667 0.00 0.00 34.51 2.15
6917 8220 2.660236 GCGAGTTAAGTTCACCGTGTAG 59.340 50.000 0.00 0.00 0.00 2.74
6918 8221 2.034432 TGCGAGTTAAGTTCACCGTGTA 59.966 45.455 0.00 0.00 0.00 2.90
6919 8222 1.202440 TGCGAGTTAAGTTCACCGTGT 60.202 47.619 0.00 0.00 0.00 4.49
6920 8223 1.191647 GTGCGAGTTAAGTTCACCGTG 59.808 52.381 0.00 0.00 0.00 4.94
6921 8224 1.494824 GTGCGAGTTAAGTTCACCGT 58.505 50.000 0.00 0.00 0.00 4.83
6922 8225 0.788391 GGTGCGAGTTAAGTTCACCG 59.212 55.000 15.50 3.21 37.96 4.94
6923 8226 1.873698 TGGTGCGAGTTAAGTTCACC 58.126 50.000 20.31 20.31 45.43 4.02
6924 8227 3.064207 TGATGGTGCGAGTTAAGTTCAC 58.936 45.455 7.66 7.66 0.00 3.18
6925 8228 3.064207 GTGATGGTGCGAGTTAAGTTCA 58.936 45.455 0.00 0.00 0.00 3.18
6926 8229 3.064207 TGTGATGGTGCGAGTTAAGTTC 58.936 45.455 0.00 0.00 0.00 3.01
6927 8230 2.806244 GTGTGATGGTGCGAGTTAAGTT 59.194 45.455 0.00 0.00 0.00 2.66
6928 8231 2.037251 AGTGTGATGGTGCGAGTTAAGT 59.963 45.455 0.00 0.00 0.00 2.24
6929 8232 2.688507 AGTGTGATGGTGCGAGTTAAG 58.311 47.619 0.00 0.00 0.00 1.85
6937 8240 3.648339 ATTGTTCAAGTGTGATGGTGC 57.352 42.857 0.00 0.00 32.48 5.01
6966 8269 7.978414 TGTTGTGAGTTTTTATTTGAATGCTCA 59.022 29.630 0.00 0.00 0.00 4.26
7016 8319 8.324306 TGATCTCCTTTGATCACTTAGTTTCAT 58.676 33.333 0.00 0.00 45.29 2.57
7017 8320 7.679783 TGATCTCCTTTGATCACTTAGTTTCA 58.320 34.615 0.00 0.00 45.29 2.69
7028 8331 6.978080 GTCAGTCTAAGTGATCTCCTTTGATC 59.022 42.308 10.91 0.00 42.19 2.92
7030 8333 6.013379 AGTCAGTCTAAGTGATCTCCTTTGA 58.987 40.000 3.98 5.10 29.14 2.69
7031 8334 6.098679 CAGTCAGTCTAAGTGATCTCCTTTG 58.901 44.000 3.98 3.15 29.14 2.77
7032 8335 5.186797 CCAGTCAGTCTAAGTGATCTCCTTT 59.813 44.000 3.98 0.00 29.14 3.11
7034 8337 4.264172 ACCAGTCAGTCTAAGTGATCTCCT 60.264 45.833 0.00 0.00 29.14 3.69
7035 8338 4.020543 ACCAGTCAGTCTAAGTGATCTCC 58.979 47.826 0.00 0.00 29.14 3.71
7037 8340 4.667573 TCACCAGTCAGTCTAAGTGATCT 58.332 43.478 0.00 0.00 35.27 2.75
7039 8342 6.365970 AATTCACCAGTCAGTCTAAGTGAT 57.634 37.500 0.00 0.00 37.97 3.06
7040 8343 5.808366 AATTCACCAGTCAGTCTAAGTGA 57.192 39.130 0.00 0.00 37.07 3.41
7041 8344 5.991606 TCAAATTCACCAGTCAGTCTAAGTG 59.008 40.000 0.00 0.00 33.53 3.16
7042 8345 6.174720 TCAAATTCACCAGTCAGTCTAAGT 57.825 37.500 0.00 0.00 0.00 2.24
7043 8346 6.875726 TCATCAAATTCACCAGTCAGTCTAAG 59.124 38.462 0.00 0.00 0.00 2.18
7046 8349 5.233083 TCATCAAATTCACCAGTCAGTCT 57.767 39.130 0.00 0.00 0.00 3.24
7047 8350 5.947228 TTCATCAAATTCACCAGTCAGTC 57.053 39.130 0.00 0.00 0.00 3.51
7048 8351 6.906157 ATTTCATCAAATTCACCAGTCAGT 57.094 33.333 0.00 0.00 0.00 3.41
7049 8352 7.654520 ACAAATTTCATCAAATTCACCAGTCAG 59.345 33.333 0.00 0.00 40.68 3.51
7050 8353 7.499292 ACAAATTTCATCAAATTCACCAGTCA 58.501 30.769 0.00 0.00 40.68 3.41
7051 8354 7.869429 AGACAAATTTCATCAAATTCACCAGTC 59.131 33.333 0.00 0.00 40.68 3.51
7052 8355 7.729116 AGACAAATTTCATCAAATTCACCAGT 58.271 30.769 0.00 0.00 40.68 4.00
7053 8356 9.695526 TTAGACAAATTTCATCAAATTCACCAG 57.304 29.630 0.00 0.00 40.68 4.00
7105 8408 3.726557 TCCTTAGTGGTAACTCCTCGA 57.273 47.619 0.00 0.00 37.88 4.04
7106 8409 4.492611 GTTTCCTTAGTGGTAACTCCTCG 58.507 47.826 0.00 0.00 41.22 4.63
7137 8440 4.996788 AAGTGATTCCATTCTGGCAATC 57.003 40.909 0.00 9.50 37.47 2.67
7144 8447 6.012113 TGGATCAACAAAGTGATTCCATTCT 58.988 36.000 0.00 0.00 38.38 2.40
7190 11880 0.320073 TCGGTCCACCATTTCACGAC 60.320 55.000 0.00 0.00 35.14 4.34
7193 11883 1.600023 TTGTCGGTCCACCATTTCAC 58.400 50.000 0.00 0.00 35.14 3.18
7208 11898 9.921637 CCTATCCTCTTTATCATCTACTTTGTC 57.078 37.037 0.00 0.00 0.00 3.18
7220 11910 6.208599 CCTCTCTGTCACCTATCCTCTTTATC 59.791 46.154 0.00 0.00 0.00 1.75
7233 11923 1.283613 TCTCTCTCCCTCTCTGTCACC 59.716 57.143 0.00 0.00 0.00 4.02
7238 11928 1.143684 CCCTCTCTCTCTCCCTCTCTG 59.856 61.905 0.00 0.00 0.00 3.35
7243 11933 0.859760 CATCCCCTCTCTCTCTCCCT 59.140 60.000 0.00 0.00 0.00 4.20
7244 11934 0.856982 TCATCCCCTCTCTCTCTCCC 59.143 60.000 0.00 0.00 0.00 4.30
7245 11935 2.316108 GTTCATCCCCTCTCTCTCTCC 58.684 57.143 0.00 0.00 0.00 3.71
7246 11936 3.025322 TGTTCATCCCCTCTCTCTCTC 57.975 52.381 0.00 0.00 0.00 3.20
7247 11937 3.481559 TTGTTCATCCCCTCTCTCTCT 57.518 47.619 0.00 0.00 0.00 3.10
7253 11943 2.447047 AGGTGTTTTGTTCATCCCCTCT 59.553 45.455 0.00 0.00 0.00 3.69
7257 11947 3.550030 CGTGAAGGTGTTTTGTTCATCCC 60.550 47.826 0.00 0.00 32.98 3.85
7261 11951 4.001652 TGTACGTGAAGGTGTTTTGTTCA 58.998 39.130 0.00 0.00 0.00 3.18
7265 11955 3.125487 TGTGTGTACGTGAAGGTGTTTTG 59.875 43.478 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.