Multiple sequence alignment - TraesCS5B01G296600

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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 TraesCS5B01G296600 chr5B 100.000 7766 0 0 1 7766 479733830 479726065 0.000000e+00 14342.0
1 TraesCS5B01G296600 chr5B 93.182 44 3 0 2021 2064 19791260 19791217 1.810000e-06 65.8
2 TraesCS5B01G296600 chr5D 95.257 3310 77 31 4490 7766 399617011 399613749 0.000000e+00 5169.0
3 TraesCS5B01G296600 chr5D 97.284 2872 57 8 1 2861 399621319 399618458 0.000000e+00 4852.0
4 TraesCS5B01G296600 chr5D 97.109 1107 27 3 3238 4339 399618409 399617303 0.000000e+00 1862.0
5 TraesCS5B01G296600 chr5D 93.443 61 1 1 4337 4394 416804001 416804061 3.860000e-13 87.9
6 TraesCS5B01G296600 chr5A 93.238 2647 111 31 1 2613 505024552 505021940 0.000000e+00 3834.0
7 TraesCS5B01G296600 chr5A 91.134 1455 103 14 5000 6434 505020880 505019432 0.000000e+00 1949.0
8 TraesCS5B01G296600 chr5A 88.088 1276 82 24 6419 7670 505019252 505018023 0.000000e+00 1450.0
9 TraesCS5B01G296600 chr5A 90.103 1071 80 11 2767 3820 505021935 505020874 0.000000e+00 1367.0
10 TraesCS5B01G296600 chr3A 95.266 169 5 2 6830 6998 675873017 675873182 1.660000e-66 265.0
11 TraesCS5B01G296600 chr3A 93.413 167 10 1 6833 6999 405691670 405691505 6.020000e-61 246.0
12 TraesCS5B01G296600 chr3A 84.874 119 16 2 2620 2736 690218448 690218566 1.370000e-22 119.0
13 TraesCS5B01G296600 chr3B 94.012 167 10 0 6833 6999 399973281 399973115 3.600000e-63 254.0
14 TraesCS5B01G296600 chr3B 91.566 83 6 1 2670 2751 61801315 61801397 6.370000e-21 113.0
15 TraesCS5B01G296600 chr3B 88.372 86 9 1 2670 2754 224964877 224964962 1.380000e-17 102.0
16 TraesCS5B01G296600 chr3B 93.443 61 1 1 4337 4394 51954461 51954521 3.860000e-13 87.9
17 TraesCS5B01G296600 chr3B 93.220 59 3 1 4337 4394 670026650 670026708 1.390000e-12 86.1
18 TraesCS5B01G296600 chr4D 93.452 168 11 0 6834 7001 32019614 32019447 4.650000e-62 250.0
19 TraesCS5B01G296600 chr4D 93.452 168 11 0 6834 7001 32019796 32019629 4.650000e-62 250.0
20 TraesCS5B01G296600 chr3D 93.413 167 11 0 6833 6999 320429812 320429978 1.670000e-61 248.0
21 TraesCS5B01G296600 chr6A 93.902 164 7 2 6833 6996 47466950 47466790 2.160000e-60 244.0
22 TraesCS5B01G296600 chr1A 86.441 118 13 3 2632 2747 582655698 582655582 8.180000e-25 126.0
23 TraesCS5B01G296600 chr2A 90.476 84 7 1 2670 2752 448298270 448298353 8.240000e-20 110.0
24 TraesCS5B01G296600 chr2A 90.476 63 4 1 4337 4397 778925490 778925428 1.800000e-11 82.4
25 TraesCS5B01G296600 chr2B 87.500 80 9 1 2620 2698 425214697 425214776 2.980000e-14 91.6
26 TraesCS5B01G296600 chr2B 91.667 60 3 1 4337 4394 393857157 393857216 1.800000e-11 82.4
27 TraesCS5B01G296600 chr6B 96.154 52 2 0 4348 4399 506028540 506028489 1.390000e-12 86.1
28 TraesCS5B01G296600 chr6B 94.444 54 3 0 4343 4396 665734416 665734363 4.990000e-12 84.2
29 TraesCS5B01G296600 chr6B 89.394 66 2 2 4334 4394 36205551 36205616 2.320000e-10 78.7
30 TraesCS5B01G296600 chr4B 91.667 60 2 2 4337 4394 358188501 358188443 6.460000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G296600 chr5B 479726065 479733830 7765 True 14342 14342 100.00000 1 7766 1 chr5B.!!$R2 7765
1 TraesCS5B01G296600 chr5D 399613749 399621319 7570 True 3961 5169 96.55000 1 7766 3 chr5D.!!$R1 7765
2 TraesCS5B01G296600 chr5A 505018023 505024552 6529 True 2150 3834 90.64075 1 7670 4 chr5A.!!$R1 7669

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
97 99 1.381928 TAGTCAAGCCGGCTACCTCG 61.382 60.000 33.07 16.01 0.00 4.63 F
710 714 2.356125 CCACAGCTACAACTAGGCCATT 60.356 50.000 5.01 0.00 0.00 3.16 F
1919 1950 0.392998 ACTGCTTCCCACTATTGCGG 60.393 55.000 0.00 0.00 36.24 5.69 F
2254 2286 0.465097 ATTGGAATGCAGCCCTCTCG 60.465 55.000 8.41 0.00 0.00 4.04 F
2619 2654 0.544697 GCCCTCAATAAGGTTCCGGA 59.455 55.000 0.00 0.00 44.56 5.14 F
4350 4409 1.041437 CCTCATACTCCCTCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62 F
4450 4509 0.104120 TGTGTGCCGCGCTCTAATAT 59.896 50.000 5.56 0.00 0.00 1.28 F
4452 4511 0.104120 TGTGCCGCGCTCTAATATGT 59.896 50.000 5.56 0.00 0.00 2.29 F
4454 4513 0.387565 TGCCGCGCTCTAATATGTGA 59.612 50.000 5.56 0.00 0.00 3.58 F
4455 4514 0.784778 GCCGCGCTCTAATATGTGAC 59.215 55.000 5.56 0.00 0.00 3.67 F
4473 4532 1.198637 GACTGCACCTGTCTTTGATGC 59.801 52.381 0.00 0.00 36.81 3.91 F
4474 4533 1.241165 CTGCACCTGTCTTTGATGCA 58.759 50.000 0.00 0.00 43.70 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1010 2.614013 AAAGGATCCCTGCCCCGT 60.614 61.111 8.55 0.00 32.13 5.28 R
2619 2654 0.101399 CGCATGCTCTCGGTAACTCT 59.899 55.000 17.13 0.00 0.00 3.24 R
3193 3247 1.154430 TTACTGGAAGGCCAAAGGGT 58.846 50.000 5.01 0.19 45.41 4.34 R
3648 3705 1.224965 GCGTTACCCACCAAAACGTA 58.775 50.000 8.40 0.00 45.74 3.57 R
4431 4490 0.104120 ATATTAGAGCGCGGCACACA 59.896 50.000 8.83 0.00 0.00 3.72 R
6294 6568 4.464008 TCAGCAATCTCCAGAAACTGTTT 58.536 39.130 5.29 5.29 0.00 2.83 R
6555 7050 9.593565 TGTGTATATATCAAGAGAGGAGAACAT 57.406 33.333 0.00 0.00 0.00 2.71 R
6601 7096 2.842208 TTGTCGCCACTGTTTTTGAG 57.158 45.000 0.00 0.00 0.00 3.02 R
6616 7111 8.753497 AGATAAAGGGATGGTATTCTTTTGTC 57.247 34.615 0.00 0.00 32.53 3.18 R
6626 7121 6.661805 GGTGTTTTGAAGATAAAGGGATGGTA 59.338 38.462 0.00 0.00 0.00 3.25 R
6731 7230 7.614192 GTCCTTGGAACCTATTAATCCAGAAAA 59.386 37.037 0.00 0.00 43.69 2.29 R
6780 7279 0.107459 CTGCCTTGTTCTAGAGCCCC 60.107 60.000 3.94 0.00 0.00 5.80 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
97 99 1.381928 TAGTCAAGCCGGCTACCTCG 61.382 60.000 33.07 16.01 0.00 4.63
301 303 2.805099 GTGAAGCCTCTCTGACTGTTTG 59.195 50.000 0.00 0.00 0.00 2.93
353 355 5.334421 ACAACTCTGTAAGATAGGACCTGT 58.666 41.667 3.53 0.00 45.62 4.00
407 410 7.649973 CGAAGTACTAGATACTACCATTGCTT 58.350 38.462 0.00 0.00 43.79 3.91
679 683 4.130118 CCATACAGGCCATTCACTAAGAC 58.870 47.826 5.01 0.00 0.00 3.01
710 714 2.356125 CCACAGCTACAACTAGGCCATT 60.356 50.000 5.01 0.00 0.00 3.16
893 897 5.041191 ACTCTGTTCTTCCACACAGAAAT 57.959 39.130 3.75 0.00 46.86 2.17
1017 1022 0.986019 TTATGTCACGGGGCAGGGAT 60.986 55.000 0.00 0.00 0.00 3.85
1137 1142 1.043816 CTGGGGTACGATCATCTGCT 58.956 55.000 0.00 0.00 0.00 4.24
1357 1370 1.004862 AGATGACTCTCGTGTGAGGGA 59.995 52.381 0.00 0.00 46.36 4.20
1442 1455 3.149981 GCTCCTTACTCAAAGCAACCTT 58.850 45.455 0.00 0.00 34.86 3.50
1609 1622 5.713025 AGAACATCACACAATAACCATTGC 58.287 37.500 0.00 0.00 44.62 3.56
1739 1752 5.173774 TCTGTCTGCTTTGCTTAAAGTTG 57.826 39.130 0.00 0.00 32.52 3.16
1918 1949 0.729116 CACTGCTTCCCACTATTGCG 59.271 55.000 0.00 0.00 0.00 4.85
1919 1950 0.392998 ACTGCTTCCCACTATTGCGG 60.393 55.000 0.00 0.00 36.24 5.69
2254 2286 0.465097 ATTGGAATGCAGCCCTCTCG 60.465 55.000 8.41 0.00 0.00 4.04
2544 2579 3.385111 CACCTTCTCATGGACTAGGTACC 59.615 52.174 2.73 2.73 34.04 3.34
2555 2590 6.208840 TGGACTAGGTACCCTGAAAATTTT 57.791 37.500 8.74 2.28 34.61 1.82
2556 2591 7.332433 TGGACTAGGTACCCTGAAAATTTTA 57.668 36.000 8.74 0.00 34.61 1.52
2557 2592 7.935405 TGGACTAGGTACCCTGAAAATTTTAT 58.065 34.615 8.74 0.00 34.61 1.40
2558 2593 8.395605 TGGACTAGGTACCCTGAAAATTTTATT 58.604 33.333 8.74 0.00 34.61 1.40
2559 2594 9.251440 GGACTAGGTACCCTGAAAATTTTATTT 57.749 33.333 8.74 0.00 34.61 1.40
2605 2640 3.636153 AGTAGTGAAAAGATGGCCCTC 57.364 47.619 0.00 0.00 0.00 4.30
2619 2654 0.544697 GCCCTCAATAAGGTTCCGGA 59.455 55.000 0.00 0.00 44.56 5.14
2620 2655 1.475213 GCCCTCAATAAGGTTCCGGAG 60.475 57.143 3.34 0.00 44.56 4.63
2621 2656 2.116238 CCCTCAATAAGGTTCCGGAGA 58.884 52.381 3.34 0.00 44.56 3.71
2622 2657 2.103263 CCCTCAATAAGGTTCCGGAGAG 59.897 54.545 3.34 5.12 44.56 3.20
2627 2663 4.161001 TCAATAAGGTTCCGGAGAGTTACC 59.839 45.833 13.49 13.49 0.00 2.85
2905 2946 7.275920 ACAGAGACTATTCAACAGAAACAAGT 58.724 34.615 0.00 0.00 0.00 3.16
2964 3010 6.019801 ACGTATTGCTCAGACGACATTTATTC 60.020 38.462 10.07 0.00 39.81 1.75
2965 3011 6.019881 CGTATTGCTCAGACGACATTTATTCA 60.020 38.462 0.00 0.00 38.88 2.57
3025 3071 5.632244 AATGAATGCCAAAAATTTCTGCC 57.368 34.783 0.00 0.00 0.00 4.85
3035 3081 6.631088 GCCAAAAATTTCTGCCAGGAATATCT 60.631 38.462 0.00 0.00 0.00 1.98
3052 3098 6.995091 GGAATATCTAGAAGCAAACCACAGAT 59.005 38.462 0.00 0.00 0.00 2.90
3053 3099 8.150945 GGAATATCTAGAAGCAAACCACAGATA 58.849 37.037 0.00 0.00 0.00 1.98
3139 3185 9.923143 GATTACATATAAGTGCTGTGTATACCA 57.077 33.333 0.00 0.00 0.00 3.25
3157 3211 4.259933 ACCAATTGTATAAGGGGTTCCC 57.740 45.455 4.43 0.00 45.90 3.97
3179 3233 4.202503 CCAGCATATTTCCCTCACCTGTAT 60.203 45.833 0.00 0.00 0.00 2.29
3183 3237 5.799213 CATATTTCCCTCACCTGTATCTCC 58.201 45.833 0.00 0.00 0.00 3.71
3193 3247 7.619698 CCCTCACCTGTATCTCCATATATACAA 59.380 40.741 0.00 0.00 37.94 2.41
3194 3248 8.470805 CCTCACCTGTATCTCCATATATACAAC 58.529 40.741 0.00 0.00 37.94 3.32
3207 3261 2.231716 ATACAACCCTTTGGCCTTCC 57.768 50.000 3.32 0.00 37.00 3.46
3215 3269 3.335484 ACCCTTTGGCCTTCCAGTAATAA 59.665 43.478 3.32 0.00 44.53 1.40
3223 3277 3.064958 GCCTTCCAGTAATAAAAGTCGCC 59.935 47.826 0.00 0.00 0.00 5.54
3229 3283 5.818857 TCCAGTAATAAAAGTCGCCATTACC 59.181 40.000 0.00 0.00 35.43 2.85
3230 3284 5.277154 CCAGTAATAAAAGTCGCCATTACCG 60.277 44.000 0.00 0.00 35.43 4.02
3315 3369 2.014857 TCCATACGTTCCTCTGACTCG 58.985 52.381 0.00 0.00 0.00 4.18
3407 3461 8.677148 TGCTATTAAGAAAGTATCACCAATCC 57.323 34.615 0.00 0.00 0.00 3.01
3530 3585 9.639563 TTAATTTGACATGATTTAGGCATAGGA 57.360 29.630 0.00 0.00 0.00 2.94
3578 3635 3.213206 ACAGTCCTGTTGCTGATCAAA 57.787 42.857 0.00 0.00 41.83 2.69
3601 3658 7.497925 AAGATCTAAAGGTGTTGTCTTGTTC 57.502 36.000 0.00 0.00 0.00 3.18
3602 3659 6.591935 AGATCTAAAGGTGTTGTCTTGTTCA 58.408 36.000 0.00 0.00 0.00 3.18
3648 3705 1.064906 CATCCCAGAGGCAACAGATGT 60.065 52.381 0.00 0.00 41.41 3.06
3704 3761 6.705825 TCCAATAGTCGAACAATCATACATGG 59.294 38.462 0.00 0.00 0.00 3.66
3788 3845 8.519799 TTTGGGTATCAATATCTTTCCTCAAC 57.480 34.615 0.00 0.00 34.98 3.18
3806 3863 3.119316 TCAACTGTTCCACGCACAAAAAT 60.119 39.130 0.00 0.00 0.00 1.82
3809 3866 5.195001 ACTGTTCCACGCACAAAAATAAT 57.805 34.783 0.00 0.00 0.00 1.28
3856 3915 3.071874 TCCTTTGGCTCGAACAATCAT 57.928 42.857 3.39 0.00 0.00 2.45
3898 3957 6.681777 TGAACTACTACCTCCGTTCTAAAAC 58.318 40.000 0.00 0.00 37.31 2.43
3928 3987 1.327690 TTGGTAGGCTAGCGGAGGTG 61.328 60.000 18.00 0.00 40.22 4.00
3952 4011 9.935682 GTGGTATATGACAAATGACAACATAAG 57.064 33.333 0.00 0.00 35.50 1.73
4189 4248 3.816994 AGGCATTTTCGTTCTATACCCC 58.183 45.455 0.00 0.00 0.00 4.95
4336 4395 7.623999 ACCATCTCAAATACAGATACCTCAT 57.376 36.000 0.00 0.00 0.00 2.90
4337 4396 8.727100 ACCATCTCAAATACAGATACCTCATA 57.273 34.615 0.00 0.00 0.00 2.15
4338 4397 8.589338 ACCATCTCAAATACAGATACCTCATAC 58.411 37.037 0.00 0.00 0.00 2.39
4339 4398 8.811017 CCATCTCAAATACAGATACCTCATACT 58.189 37.037 0.00 0.00 0.00 2.12
4340 4399 9.853555 CATCTCAAATACAGATACCTCATACTC 57.146 37.037 0.00 0.00 0.00 2.59
4341 4400 8.410673 TCTCAAATACAGATACCTCATACTCC 57.589 38.462 0.00 0.00 0.00 3.85
4342 4401 7.451877 TCTCAAATACAGATACCTCATACTCCC 59.548 40.741 0.00 0.00 0.00 4.30
4343 4402 7.306013 TCAAATACAGATACCTCATACTCCCT 58.694 38.462 0.00 0.00 0.00 4.20
4344 4403 7.451877 TCAAATACAGATACCTCATACTCCCTC 59.548 40.741 0.00 0.00 0.00 4.30
4345 4404 4.120946 ACAGATACCTCATACTCCCTCC 57.879 50.000 0.00 0.00 0.00 4.30
4346 4405 3.085533 CAGATACCTCATACTCCCTCCG 58.914 54.545 0.00 0.00 0.00 4.63
4347 4406 2.717515 AGATACCTCATACTCCCTCCGT 59.282 50.000 0.00 0.00 0.00 4.69
4348 4407 3.140519 AGATACCTCATACTCCCTCCGTT 59.859 47.826 0.00 0.00 0.00 4.44
4349 4408 1.777941 ACCTCATACTCCCTCCGTTC 58.222 55.000 0.00 0.00 0.00 3.95
4350 4409 1.041437 CCTCATACTCCCTCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62
4351 4410 1.411787 CCTCATACTCCCTCCGTTCCT 60.412 57.143 0.00 0.00 0.00 3.36
4352 4411 2.389715 CTCATACTCCCTCCGTTCCTT 58.610 52.381 0.00 0.00 0.00 3.36
4353 4412 2.766828 CTCATACTCCCTCCGTTCCTTT 59.233 50.000 0.00 0.00 0.00 3.11
4354 4413 2.500098 TCATACTCCCTCCGTTCCTTTG 59.500 50.000 0.00 0.00 0.00 2.77
4355 4414 2.314071 TACTCCCTCCGTTCCTTTGA 57.686 50.000 0.00 0.00 0.00 2.69
4356 4415 1.430992 ACTCCCTCCGTTCCTTTGAA 58.569 50.000 0.00 0.00 0.00 2.69
4357 4416 1.071857 ACTCCCTCCGTTCCTTTGAAC 59.928 52.381 0.00 0.00 46.05 3.18
4368 4427 5.488645 GTTCCTTTGAACTAAAACCACGA 57.511 39.130 0.00 0.00 46.03 4.35
4369 4428 5.268544 GTTCCTTTGAACTAAAACCACGAC 58.731 41.667 0.00 0.00 46.03 4.34
4370 4429 3.556775 TCCTTTGAACTAAAACCACGACG 59.443 43.478 0.00 0.00 0.00 5.12
4371 4430 3.556775 CCTTTGAACTAAAACCACGACGA 59.443 43.478 0.00 0.00 0.00 4.20
4372 4431 4.318546 CCTTTGAACTAAAACCACGACGAG 60.319 45.833 0.00 0.00 0.00 4.18
4373 4432 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4374 4433 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4375 4434 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4376 4435 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
4377 4436 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
4378 4437 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
4412 4471 5.048782 GGAGTACATGTGAGTCAAATGCAAA 60.049 40.000 21.20 6.38 32.69 3.68
4413 4472 6.005583 AGTACATGTGAGTCAAATGCAAAG 57.994 37.500 21.20 0.00 32.69 2.77
4414 4473 3.645884 ACATGTGAGTCAAATGCAAAGC 58.354 40.909 21.20 0.00 32.69 3.51
4415 4474 3.068448 ACATGTGAGTCAAATGCAAAGCA 59.932 39.130 21.20 0.15 44.86 3.91
4416 4475 3.082698 TGTGAGTCAAATGCAAAGCAC 57.917 42.857 0.00 0.00 43.04 4.40
4417 4476 2.223782 TGTGAGTCAAATGCAAAGCACC 60.224 45.455 0.00 0.00 43.04 5.01
4418 4477 2.035066 GTGAGTCAAATGCAAAGCACCT 59.965 45.455 0.00 0.00 43.04 4.00
4419 4478 2.694628 TGAGTCAAATGCAAAGCACCTT 59.305 40.909 0.00 0.00 43.04 3.50
4420 4479 3.888323 TGAGTCAAATGCAAAGCACCTTA 59.112 39.130 0.00 0.00 43.04 2.69
4421 4480 4.022935 TGAGTCAAATGCAAAGCACCTTAG 60.023 41.667 0.00 0.00 43.04 2.18
4422 4481 4.144297 AGTCAAATGCAAAGCACCTTAGA 58.856 39.130 0.00 0.00 43.04 2.10
4423 4482 4.217118 AGTCAAATGCAAAGCACCTTAGAG 59.783 41.667 0.00 0.00 43.04 2.43
4424 4483 4.216257 GTCAAATGCAAAGCACCTTAGAGA 59.784 41.667 0.00 0.00 43.04 3.10
4425 4484 4.456911 TCAAATGCAAAGCACCTTAGAGAG 59.543 41.667 0.00 0.00 43.04 3.20
4426 4485 3.988976 ATGCAAAGCACCTTAGAGAGA 57.011 42.857 0.00 0.00 43.04 3.10
4427 4486 3.325293 TGCAAAGCACCTTAGAGAGAG 57.675 47.619 0.00 0.00 31.71 3.20
4428 4487 2.027745 TGCAAAGCACCTTAGAGAGAGG 60.028 50.000 0.00 0.00 40.24 3.69
4429 4488 2.679349 GCAAAGCACCTTAGAGAGAGGG 60.679 54.545 0.00 0.00 38.65 4.30
4430 4489 1.872773 AAGCACCTTAGAGAGAGGGG 58.127 55.000 0.00 0.00 40.81 4.79
4431 4490 0.713579 AGCACCTTAGAGAGAGGGGT 59.286 55.000 0.00 0.00 39.98 4.95
4433 4492 1.897647 GCACCTTAGAGAGAGGGGTGT 60.898 57.143 11.27 0.00 46.27 4.16
4434 4493 1.827969 CACCTTAGAGAGAGGGGTGTG 59.172 57.143 0.00 0.00 41.52 3.82
4435 4494 1.433592 ACCTTAGAGAGAGGGGTGTGT 59.566 52.381 0.00 0.00 38.65 3.72
4436 4495 1.827969 CCTTAGAGAGAGGGGTGTGTG 59.172 57.143 0.00 0.00 0.00 3.82
4437 4496 1.205893 CTTAGAGAGAGGGGTGTGTGC 59.794 57.143 0.00 0.00 0.00 4.57
4438 4497 0.614979 TAGAGAGAGGGGTGTGTGCC 60.615 60.000 0.00 0.00 0.00 5.01
4439 4498 3.302347 GAGAGAGGGGTGTGTGCCG 62.302 68.421 0.00 0.00 0.00 5.69
4446 4505 4.735132 GGTGTGTGCCGCGCTCTA 62.735 66.667 5.56 0.00 0.00 2.43
4447 4506 2.736995 GTGTGTGCCGCGCTCTAA 60.737 61.111 5.56 0.00 0.00 2.10
4448 4507 2.100631 GTGTGTGCCGCGCTCTAAT 61.101 57.895 5.56 0.00 0.00 1.73
4449 4508 0.804544 GTGTGTGCCGCGCTCTAATA 60.805 55.000 5.56 0.00 0.00 0.98
4450 4509 0.104120 TGTGTGCCGCGCTCTAATAT 59.896 50.000 5.56 0.00 0.00 1.28
4451 4510 0.508641 GTGTGCCGCGCTCTAATATG 59.491 55.000 5.56 0.00 0.00 1.78
4452 4511 0.104120 TGTGCCGCGCTCTAATATGT 59.896 50.000 5.56 0.00 0.00 2.29
4453 4512 0.508641 GTGCCGCGCTCTAATATGTG 59.491 55.000 5.56 0.00 0.00 3.21
4454 4513 0.387565 TGCCGCGCTCTAATATGTGA 59.612 50.000 5.56 0.00 0.00 3.58
4455 4514 0.784778 GCCGCGCTCTAATATGTGAC 59.215 55.000 5.56 0.00 0.00 3.67
4456 4515 1.603172 GCCGCGCTCTAATATGTGACT 60.603 52.381 5.56 0.00 0.00 3.41
4457 4516 2.054363 CCGCGCTCTAATATGTGACTG 58.946 52.381 5.56 0.00 0.00 3.51
4458 4517 1.453524 CGCGCTCTAATATGTGACTGC 59.546 52.381 5.56 0.00 0.00 4.40
4459 4518 2.473816 GCGCTCTAATATGTGACTGCA 58.526 47.619 0.00 0.00 0.00 4.41
4460 4519 2.219674 GCGCTCTAATATGTGACTGCAC 59.780 50.000 0.00 0.00 45.35 4.57
4461 4520 2.797156 CGCTCTAATATGTGACTGCACC 59.203 50.000 0.00 0.00 44.51 5.01
4462 4521 3.491619 CGCTCTAATATGTGACTGCACCT 60.492 47.826 0.00 0.00 44.51 4.00
4463 4522 3.806521 GCTCTAATATGTGACTGCACCTG 59.193 47.826 0.00 0.00 44.51 4.00
4464 4523 4.681781 GCTCTAATATGTGACTGCACCTGT 60.682 45.833 0.00 0.00 44.51 4.00
4465 4524 5.011090 TCTAATATGTGACTGCACCTGTC 57.989 43.478 0.00 0.00 44.51 3.51
4466 4525 3.988976 AATATGTGACTGCACCTGTCT 57.011 42.857 6.20 0.00 44.51 3.41
4467 4526 3.988976 ATATGTGACTGCACCTGTCTT 57.011 42.857 6.20 0.00 44.51 3.01
4468 4527 2.645838 ATGTGACTGCACCTGTCTTT 57.354 45.000 6.20 0.00 44.51 2.52
4469 4528 1.667236 TGTGACTGCACCTGTCTTTG 58.333 50.000 6.20 0.00 44.51 2.77
4470 4529 1.209261 TGTGACTGCACCTGTCTTTGA 59.791 47.619 6.20 0.00 44.51 2.69
4471 4530 2.158769 TGTGACTGCACCTGTCTTTGAT 60.159 45.455 6.20 0.00 44.51 2.57
4472 4531 2.225019 GTGACTGCACCTGTCTTTGATG 59.775 50.000 6.20 0.00 39.14 3.07
4473 4532 1.198637 GACTGCACCTGTCTTTGATGC 59.801 52.381 0.00 0.00 36.81 3.91
4474 4533 1.241165 CTGCACCTGTCTTTGATGCA 58.759 50.000 0.00 0.00 43.70 3.96
4475 4534 1.241165 TGCACCTGTCTTTGATGCAG 58.759 50.000 0.00 0.00 41.18 4.41
4481 4540 4.691860 CCTGTCTTTGATGCAGGTTAAG 57.308 45.455 0.00 0.00 43.42 1.85
4482 4541 3.119708 CCTGTCTTTGATGCAGGTTAAGC 60.120 47.826 0.00 0.00 43.42 3.09
4484 4543 3.503363 TGTCTTTGATGCAGGTTAAGCAG 59.497 43.478 7.52 0.00 46.36 4.24
4485 4544 3.503748 GTCTTTGATGCAGGTTAAGCAGT 59.496 43.478 7.52 0.00 46.36 4.40
4486 4545 4.022849 GTCTTTGATGCAGGTTAAGCAGTT 60.023 41.667 7.52 0.00 46.36 3.16
4487 4546 3.921119 TTGATGCAGGTTAAGCAGTTG 57.079 42.857 7.52 0.00 46.36 3.16
4488 4547 2.161855 TGATGCAGGTTAAGCAGTTGG 58.838 47.619 7.52 0.00 46.36 3.77
4677 4933 5.689835 TGTGGCCAGCATAAATACAAGATA 58.310 37.500 5.11 0.00 0.00 1.98
4747 5003 5.301805 GGAACTTCCATTTCCAAGTGAAGAA 59.698 40.000 2.62 0.00 42.04 2.52
4786 5042 7.173218 TGCCACTTAGAACACTAATCTGAAAAG 59.827 37.037 0.00 0.00 0.00 2.27
4794 5050 9.778741 AGAACACTAATCTGAAAAGTTATCACA 57.221 29.630 0.00 0.00 0.00 3.58
4802 5058 6.959361 TCTGAAAAGTTATCACAGTGCTTTC 58.041 36.000 0.00 0.00 0.00 2.62
4827 5083 2.038295 CCTCCCTTAAGATGCTGCCTAG 59.962 54.545 3.36 0.00 0.00 3.02
5061 5318 5.221224 GCTACAGATAGACATGCTTCTCTGT 60.221 44.000 22.79 22.79 44.19 3.41
5394 5656 8.621286 GTTTGAGAAGAAGGTCAACAAATAAGA 58.379 33.333 0.00 0.00 32.40 2.10
5525 5789 2.890945 AGCTTGTCGCCCAAAATAGTTT 59.109 40.909 0.00 0.00 40.39 2.66
5548 5812 2.991250 ACAGTGGCAGTCCATATTGTC 58.009 47.619 0.00 0.00 45.62 3.18
5789 6057 4.021544 GCATTTTACAATCTTGGACCACCA 60.022 41.667 0.00 0.00 45.34 4.17
5902 6170 8.510283 AGGATAGATATGATATAGGCAGTGACT 58.490 37.037 2.72 2.72 0.00 3.41
6294 6568 3.381335 GGGTTACTAAGGTGATCTGGGA 58.619 50.000 0.00 0.00 0.00 4.37
6477 6948 7.461182 TTCATCCCTTTAACGATGAACAATT 57.539 32.000 13.81 0.00 45.82 2.32
6478 6949 7.461182 TCATCCCTTTAACGATGAACAATTT 57.539 32.000 6.60 0.00 41.40 1.82
6479 6950 8.568676 TCATCCCTTTAACGATGAACAATTTA 57.431 30.769 6.60 0.00 41.40 1.40
6555 7050 8.098912 GGTAGAACAATACAAAGAAGGTTAGGA 58.901 37.037 0.00 0.00 0.00 2.94
6601 7096 3.746492 ACAAGAATGAGCCACGTAGAAAC 59.254 43.478 0.00 0.00 0.00 2.78
6616 7111 3.420839 AGAAACTCAAAAACAGTGGCG 57.579 42.857 0.00 0.00 0.00 5.69
6626 7121 4.385358 AAAACAGTGGCGACAAAAGAAT 57.615 36.364 0.00 0.00 46.06 2.40
6731 7230 8.383175 TCATTACCAGTTCTAAACAGATTCCTT 58.617 33.333 0.00 0.00 0.00 3.36
6780 7279 1.454976 CTGAGGGATGGATGCAGGG 59.545 63.158 0.00 0.00 0.00 4.45
6839 7338 1.742308 TAGTCCACCAAAGAAGGGCT 58.258 50.000 0.00 0.00 41.05 5.19
7025 7524 9.515226 TTATATAGTTCACCAAAGCTTTTGAGT 57.485 29.630 16.58 8.62 0.00 3.41
7079 7579 3.310774 CCAGTAGTCCAGCAATTGATTCG 59.689 47.826 10.34 0.00 0.00 3.34
7225 7725 4.584743 ACTGTGAGTGTAAGTGTGATCAGA 59.415 41.667 0.00 0.00 0.00 3.27
7242 7742 3.617284 TCAGATGTCGTGGAGCTTAGTA 58.383 45.455 0.00 0.00 0.00 1.82
7299 7799 8.753497 ACATGTATCTCTCTTCTGTACATACA 57.247 34.615 0.00 0.00 35.03 2.29
7300 7800 9.190317 ACATGTATCTCTCTTCTGTACATACAA 57.810 33.333 0.00 0.00 35.03 2.41
7317 7817 7.042797 ACATACAATACTTTGCAATCCCATC 57.957 36.000 0.00 0.00 36.22 3.51
7336 7839 2.520069 TCAAGACTGGTCCTCTCTGTC 58.480 52.381 0.00 0.00 34.62 3.51
7352 7855 3.114558 GTCAACTGGACAGAGCTCG 57.885 57.895 8.37 6.04 46.19 5.03
7360 7863 2.601666 ACAGAGCTCGGCCACTGA 60.602 61.111 14.20 0.00 37.10 3.41
7380 7883 1.470051 TGATCGGATCACTCGGTTGA 58.530 50.000 16.44 0.00 33.59 3.18
7383 7886 3.004419 TGATCGGATCACTCGGTTGATAC 59.996 47.826 16.44 0.40 36.30 2.24
7404 7907 2.880890 CTGCAAGTGGTACTGCTTTTCT 59.119 45.455 6.41 0.00 0.00 2.52
7408 7911 5.358442 TGCAAGTGGTACTGCTTTTCTTTTA 59.642 36.000 6.41 0.00 0.00 1.52
7411 7914 7.480810 CAAGTGGTACTGCTTTTCTTTTACTT 58.519 34.615 0.00 0.00 0.00 2.24
7413 7916 7.704271 AGTGGTACTGCTTTTCTTTTACTTTC 58.296 34.615 0.00 0.00 0.00 2.62
7439 7942 2.084546 GTGTGGATGTAAACCAGAGCC 58.915 52.381 0.00 0.00 40.56 4.70
7440 7943 1.985159 TGTGGATGTAAACCAGAGCCT 59.015 47.619 0.00 0.00 40.56 4.58
7442 7945 2.027192 GTGGATGTAAACCAGAGCCTGA 60.027 50.000 4.00 0.00 40.56 3.86
7647 8168 3.627123 TCCAAACCATGCATACTCGAATG 59.373 43.478 0.00 0.00 0.00 2.67
7651 8172 3.470709 ACCATGCATACTCGAATGGAAG 58.529 45.455 16.55 3.18 41.84 3.46
7655 8176 1.789464 GCATACTCGAATGGAAGAGCG 59.211 52.381 0.00 0.00 37.99 5.03
7673 8194 2.124901 CCATTCGGCGCCCACTAA 60.125 61.111 23.46 10.82 0.00 2.24
7674 8195 1.525995 CCATTCGGCGCCCACTAAT 60.526 57.895 23.46 12.76 0.00 1.73
7675 8196 1.507141 CCATTCGGCGCCCACTAATC 61.507 60.000 23.46 0.00 0.00 1.75
7676 8197 0.813610 CATTCGGCGCCCACTAATCA 60.814 55.000 23.46 0.00 0.00 2.57
7677 8198 0.107410 ATTCGGCGCCCACTAATCAA 60.107 50.000 23.46 0.96 0.00 2.57
7678 8199 1.022451 TTCGGCGCCCACTAATCAAC 61.022 55.000 23.46 0.00 0.00 3.18
7683 8204 1.539827 GCGCCCACTAATCAACAAGTT 59.460 47.619 0.00 0.00 0.00 2.66
7684 8205 2.414161 GCGCCCACTAATCAACAAGTTC 60.414 50.000 0.00 0.00 0.00 3.01
7700 8221 0.529992 GTTCGATTACTCCAGCCCCG 60.530 60.000 0.00 0.00 0.00 5.73
7701 8222 2.280186 CGATTACTCCAGCCCCGC 60.280 66.667 0.00 0.00 0.00 6.13
7716 8242 1.021390 CCCGCAGTTGGTGTCTCATC 61.021 60.000 0.00 0.00 0.00 2.92
7727 8253 2.289320 GGTGTCTCATCTCAGCAACTGT 60.289 50.000 0.00 0.00 32.61 3.55
7728 8254 2.735663 GTGTCTCATCTCAGCAACTGTG 59.264 50.000 0.00 0.00 32.61 3.66
7742 8268 0.534877 ACTGTGCCACATTGAGCGAA 60.535 50.000 0.00 0.00 0.00 4.70
7743 8269 0.592637 CTGTGCCACATTGAGCGAAA 59.407 50.000 0.00 0.00 0.00 3.46
7751 8277 3.189080 CCACATTGAGCGAAAATCTGTGA 59.811 43.478 0.00 0.00 0.00 3.58
7753 8279 3.120546 ACATTGAGCGAAAATCTGTGACG 60.121 43.478 0.00 0.00 0.00 4.35
7757 8283 4.052608 TGAGCGAAAATCTGTGACGTTAA 58.947 39.130 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 303 2.092968 TGAGGCTTCACATGGACCATAC 60.093 50.000 6.67 0.00 0.00 2.39
353 355 5.070001 CACCCTTGAGTGGAAAAGTATTCA 58.930 41.667 0.00 0.00 33.95 2.57
407 410 9.761504 TCATAAGCAATTTTCATTGTTCTTGAA 57.238 25.926 0.00 0.00 41.84 2.69
519 523 7.900352 GTCATTTCATGTTCAACGATACTTCTC 59.100 37.037 0.00 0.00 0.00 2.87
710 714 4.019411 TGTTGAGCACCTATCAATCTCCAA 60.019 41.667 0.00 0.00 38.81 3.53
893 897 0.105760 TGGAAGGGCTGGCTGAAAAA 60.106 50.000 0.00 0.00 0.00 1.94
933 937 0.038526 ACACTTTGGTCGACTAGGCG 60.039 55.000 13.16 13.16 0.00 5.52
983 988 8.126700 CCCGTGACATAACTTGGTTTTATTATC 58.873 37.037 0.00 0.00 0.00 1.75
1005 1010 2.614013 AAAGGATCCCTGCCCCGT 60.614 61.111 8.55 0.00 32.13 5.28
1267 1273 8.453238 TCTAACACAATAAACCTGCAAACTAA 57.547 30.769 0.00 0.00 0.00 2.24
1357 1370 9.386122 ACCTTATCTGATTATTCTAGACACCAT 57.614 33.333 0.00 0.00 0.00 3.55
1392 1405 2.967599 TCAGCGTATGCATCACTCTT 57.032 45.000 10.11 0.00 46.23 2.85
1393 1406 2.627221 AGATCAGCGTATGCATCACTCT 59.373 45.455 10.11 0.00 46.23 3.24
1394 1407 3.023946 AGATCAGCGTATGCATCACTC 57.976 47.619 10.11 0.00 46.23 3.51
1400 1413 4.021981 AGCTTGTATAGATCAGCGTATGCA 60.022 41.667 10.11 0.00 46.23 3.96
1442 1455 6.719370 ACTTGTGCATAAGGGTTTCTAAATGA 59.281 34.615 24.73 0.00 31.94 2.57
1609 1622 9.066939 GTAGCATGTACTATACTTGATCATTCG 57.933 37.037 0.00 0.00 36.31 3.34
1739 1752 3.936564 ACATGAGAGAGCTTCAAACTCC 58.063 45.455 0.00 0.00 34.56 3.85
1918 1949 5.301555 ACTCTACAGAGCAAAAAGAAGACC 58.698 41.667 6.15 0.00 45.79 3.85
1919 1950 6.258947 ACAACTCTACAGAGCAAAAAGAAGAC 59.741 38.462 6.15 0.00 45.79 3.01
2605 2640 4.439968 GGTAACTCTCCGGAACCTTATTG 58.560 47.826 13.98 0.00 0.00 1.90
2619 2654 0.101399 CGCATGCTCTCGGTAACTCT 59.899 55.000 17.13 0.00 0.00 3.24
2620 2655 1.483424 GCGCATGCTCTCGGTAACTC 61.483 60.000 17.13 0.00 38.39 3.01
2621 2656 1.519455 GCGCATGCTCTCGGTAACT 60.519 57.895 17.13 0.00 38.39 2.24
2622 2657 1.154205 ATGCGCATGCTCTCGGTAAC 61.154 55.000 24.69 0.00 43.34 2.50
2627 2663 1.149964 TCTTCATGCGCATGCTCTCG 61.150 55.000 39.11 24.97 43.34 4.04
2736 2773 7.952930 CCAGCTCACCATATCCTATATACCTAT 59.047 40.741 0.00 0.00 0.00 2.57
2905 2946 4.327982 CATTAGCTGCTTAGCTCTACCA 57.672 45.455 7.79 0.00 45.00 3.25
2933 2974 4.561606 GTCGTCTGAGCAATACGTGTTAAT 59.438 41.667 0.00 0.00 37.83 1.40
2964 3010 9.520204 ACAGAATGAGTTTTCAGTTTTAACATG 57.480 29.630 0.00 0.00 39.69 3.21
2973 3019 6.949352 ACATGAACAGAATGAGTTTTCAGT 57.051 33.333 0.00 0.00 39.69 3.41
3003 3049 5.071370 TGGCAGAAATTTTTGGCATTCATT 58.929 33.333 27.45 0.00 43.78 2.57
3017 3063 6.183361 TGCTTCTAGATATTCCTGGCAGAAAT 60.183 38.462 17.94 10.69 0.00 2.17
3021 3067 4.613925 TGCTTCTAGATATTCCTGGCAG 57.386 45.455 7.75 7.75 0.00 4.85
3025 3071 6.115446 TGTGGTTTGCTTCTAGATATTCCTG 58.885 40.000 0.00 0.00 0.00 3.86
3035 3081 4.222810 TCTGCTATCTGTGGTTTGCTTCTA 59.777 41.667 0.00 0.00 0.00 2.10
3052 3098 6.040842 AGCAAGTTCCTTCAATTTTTCTGCTA 59.959 34.615 0.00 0.00 0.00 3.49
3053 3099 5.052481 GCAAGTTCCTTCAATTTTTCTGCT 58.948 37.500 0.00 0.00 0.00 4.24
3093 3139 8.590204 TGTAATCTAACAATGACCACTGTTCTA 58.410 33.333 0.00 0.00 37.05 2.10
3107 3153 9.884636 ACACAGCACTTATATGTAATCTAACAA 57.115 29.630 0.00 0.00 32.02 2.83
3157 3211 3.287867 ACAGGTGAGGGAAATATGCTG 57.712 47.619 0.00 0.00 0.00 4.41
3179 3233 5.222048 GGCCAAAGGGTTGTATATATGGAGA 60.222 44.000 0.00 0.00 36.17 3.71
3183 3237 5.476945 GGAAGGCCAAAGGGTTGTATATATG 59.523 44.000 5.01 0.00 36.17 1.78
3193 3247 1.154430 TTACTGGAAGGCCAAAGGGT 58.846 50.000 5.01 0.19 45.41 4.34
3194 3248 2.532250 ATTACTGGAAGGCCAAAGGG 57.468 50.000 5.01 0.00 45.41 3.95
3207 3261 5.292589 ACGGTAATGGCGACTTTTATTACTG 59.707 40.000 13.73 13.73 43.21 2.74
3215 3269 2.997986 CTGTTACGGTAATGGCGACTTT 59.002 45.455 3.59 0.00 0.00 2.66
3223 3277 5.642063 AGGAAATGTGACTGTTACGGTAATG 59.358 40.000 3.59 3.50 0.00 1.90
3229 3283 3.067106 AGCAGGAAATGTGACTGTTACG 58.933 45.455 0.00 0.00 34.79 3.18
3230 3284 3.189287 CCAGCAGGAAATGTGACTGTTAC 59.811 47.826 0.00 0.00 36.89 2.50
3315 3369 2.749076 TGTCACAAATAGGCAGCATGTC 59.251 45.455 0.00 0.00 44.67 3.06
3578 3635 6.591935 TGAACAAGACAACACCTTTAGATCT 58.408 36.000 0.00 0.00 0.00 2.75
3601 3658 6.976088 TGTCACCAACCTGTACAAAATAATG 58.024 36.000 0.00 0.00 0.00 1.90
3602 3659 7.001674 TCTGTCACCAACCTGTACAAAATAAT 58.998 34.615 0.00 0.00 0.00 1.28
3648 3705 1.224965 GCGTTACCCACCAAAACGTA 58.775 50.000 8.40 0.00 45.74 3.57
3704 3761 1.737236 TGTTCAACCGTCTGCATATGC 59.263 47.619 21.09 21.09 42.50 3.14
3788 3845 7.810766 ATTATTATTTTTGTGCGTGGAACAG 57.189 32.000 0.00 0.00 41.80 3.16
3835 3894 2.857483 TGATTGTTCGAGCCAAAGGAA 58.143 42.857 0.00 0.00 0.00 3.36
3856 3915 6.415206 AGTTCATTAAGTAGCGGGCTTATA 57.585 37.500 0.00 0.00 0.00 0.98
3898 3957 5.106948 CGCTAGCCTACCAAAACATCATATG 60.107 44.000 9.66 0.00 0.00 1.78
3952 4011 7.097087 CGCTTGCAAATTTTATTTTGTTGGAAC 60.097 33.333 0.00 0.00 38.55 3.62
4040 4099 4.142182 ACGATGGCTTGAATTAACCATTGG 60.142 41.667 11.73 0.00 44.97 3.16
4139 4198 5.914085 AGACAAATAATCTCAGCATACGC 57.086 39.130 0.00 0.00 38.99 4.42
4154 4213 9.705290 AACGAAAATGCCTAATTAAAGACAAAT 57.295 25.926 0.00 0.00 0.00 2.32
4336 4395 2.301009 GTTCAAAGGAACGGAGGGAGTA 59.699 50.000 0.00 0.00 43.54 2.59
4337 4396 1.071857 GTTCAAAGGAACGGAGGGAGT 59.928 52.381 0.00 0.00 43.54 3.85
4338 4397 1.809684 GTTCAAAGGAACGGAGGGAG 58.190 55.000 0.00 0.00 43.54 4.30
4347 4406 4.034279 CGTCGTGGTTTTAGTTCAAAGGAA 59.966 41.667 0.00 0.00 0.00 3.36
4348 4407 3.556775 CGTCGTGGTTTTAGTTCAAAGGA 59.443 43.478 0.00 0.00 0.00 3.36
4349 4408 3.556775 TCGTCGTGGTTTTAGTTCAAAGG 59.443 43.478 0.00 0.00 0.00 3.11
4350 4409 4.269363 ACTCGTCGTGGTTTTAGTTCAAAG 59.731 41.667 0.00 0.00 0.00 2.77
4351 4410 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4352 4411 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4353 4412 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4354 4413 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
4355 4414 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
4356 4415 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
4357 4416 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
4358 4417 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
4359 4418 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
4360 4419 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
4361 4420 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
4362 4421 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
4363 4422 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
4364 4423 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
4365 4424 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
4366 4425 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
4367 4426 2.549633 TCCGTTCCGATTTACTCGTC 57.450 50.000 0.00 0.00 46.18 4.20
4368 4427 2.480759 CCATCCGTTCCGATTTACTCGT 60.481 50.000 0.00 0.00 46.18 4.18
4370 4429 3.181478 ACTCCATCCGTTCCGATTTACTC 60.181 47.826 0.00 0.00 0.00 2.59
4371 4430 2.764572 ACTCCATCCGTTCCGATTTACT 59.235 45.455 0.00 0.00 0.00 2.24
4372 4431 3.175109 ACTCCATCCGTTCCGATTTAC 57.825 47.619 0.00 0.00 0.00 2.01
4373 4432 3.700539 TGTACTCCATCCGTTCCGATTTA 59.299 43.478 0.00 0.00 0.00 1.40
4374 4433 2.498481 TGTACTCCATCCGTTCCGATTT 59.502 45.455 0.00 0.00 0.00 2.17
4375 4434 2.104967 TGTACTCCATCCGTTCCGATT 58.895 47.619 0.00 0.00 0.00 3.34
4376 4435 1.771565 TGTACTCCATCCGTTCCGAT 58.228 50.000 0.00 0.00 0.00 4.18
4377 4436 1.407618 CATGTACTCCATCCGTTCCGA 59.592 52.381 0.00 0.00 0.00 4.55
4378 4437 1.136305 ACATGTACTCCATCCGTTCCG 59.864 52.381 0.00 0.00 0.00 4.30
4379 4438 2.167693 TCACATGTACTCCATCCGTTCC 59.832 50.000 0.00 0.00 0.00 3.62
4380 4439 3.119101 ACTCACATGTACTCCATCCGTTC 60.119 47.826 0.00 0.00 0.00 3.95
4381 4440 2.832129 ACTCACATGTACTCCATCCGTT 59.168 45.455 0.00 0.00 0.00 4.44
4382 4441 2.427453 GACTCACATGTACTCCATCCGT 59.573 50.000 0.00 0.00 0.00 4.69
4383 4442 2.427095 TGACTCACATGTACTCCATCCG 59.573 50.000 0.00 0.00 0.00 4.18
4384 4443 4.471904 TTGACTCACATGTACTCCATCC 57.528 45.455 0.00 0.00 0.00 3.51
4385 4444 5.220739 GCATTTGACTCACATGTACTCCATC 60.221 44.000 0.00 0.00 0.00 3.51
4386 4445 4.637534 GCATTTGACTCACATGTACTCCAT 59.362 41.667 0.00 0.00 0.00 3.41
4387 4446 4.002982 GCATTTGACTCACATGTACTCCA 58.997 43.478 0.00 0.00 0.00 3.86
4388 4447 4.002982 TGCATTTGACTCACATGTACTCC 58.997 43.478 0.00 0.00 0.00 3.85
4389 4448 5.611796 TTGCATTTGACTCACATGTACTC 57.388 39.130 0.00 0.00 0.00 2.59
4390 4449 5.563475 GCTTTGCATTTGACTCACATGTACT 60.563 40.000 0.00 0.00 0.00 2.73
4391 4450 4.618489 GCTTTGCATTTGACTCACATGTAC 59.382 41.667 0.00 0.00 0.00 2.90
4412 4471 0.713579 ACCCCTCTCTCTAAGGTGCT 59.286 55.000 0.00 0.00 31.51 4.40
4413 4472 0.827368 CACCCCTCTCTCTAAGGTGC 59.173 60.000 0.00 0.00 41.38 5.01
4415 4474 1.433592 ACACACCCCTCTCTCTAAGGT 59.566 52.381 0.00 0.00 31.51 3.50
4416 4475 1.827969 CACACACCCCTCTCTCTAAGG 59.172 57.143 0.00 0.00 0.00 2.69
4417 4476 1.205893 GCACACACCCCTCTCTCTAAG 59.794 57.143 0.00 0.00 0.00 2.18
4418 4477 1.267121 GCACACACCCCTCTCTCTAA 58.733 55.000 0.00 0.00 0.00 2.10
4419 4478 0.614979 GGCACACACCCCTCTCTCTA 60.615 60.000 0.00 0.00 0.00 2.43
4420 4479 1.915769 GGCACACACCCCTCTCTCT 60.916 63.158 0.00 0.00 0.00 3.10
4421 4480 2.665603 GGCACACACCCCTCTCTC 59.334 66.667 0.00 0.00 0.00 3.20
4422 4481 3.314331 CGGCACACACCCCTCTCT 61.314 66.667 0.00 0.00 0.00 3.10
4429 4488 4.735132 TAGAGCGCGGCACACACC 62.735 66.667 8.83 0.00 0.00 4.16
4430 4489 0.804544 TATTAGAGCGCGGCACACAC 60.805 55.000 8.83 0.00 0.00 3.82
4431 4490 0.104120 ATATTAGAGCGCGGCACACA 59.896 50.000 8.83 0.00 0.00 3.72
4432 4491 0.508641 CATATTAGAGCGCGGCACAC 59.491 55.000 8.83 0.00 0.00 3.82
4433 4492 0.104120 ACATATTAGAGCGCGGCACA 59.896 50.000 8.83 0.00 0.00 4.57
4434 4493 0.508641 CACATATTAGAGCGCGGCAC 59.491 55.000 8.83 0.00 0.00 5.01
4435 4494 0.387565 TCACATATTAGAGCGCGGCA 59.612 50.000 8.83 0.00 0.00 5.69
4436 4495 0.784778 GTCACATATTAGAGCGCGGC 59.215 55.000 8.83 0.00 0.00 6.53
4437 4496 2.054363 CAGTCACATATTAGAGCGCGG 58.946 52.381 8.83 0.00 0.00 6.46
4438 4497 1.453524 GCAGTCACATATTAGAGCGCG 59.546 52.381 0.00 0.00 0.00 6.86
4439 4498 2.219674 GTGCAGTCACATATTAGAGCGC 59.780 50.000 0.00 0.00 42.66 5.92
4440 4499 2.797156 GGTGCAGTCACATATTAGAGCG 59.203 50.000 0.00 0.00 44.87 5.03
4441 4500 3.806521 CAGGTGCAGTCACATATTAGAGC 59.193 47.826 0.00 0.00 44.87 4.09
4442 4501 5.016051 ACAGGTGCAGTCACATATTAGAG 57.984 43.478 0.00 0.00 44.87 2.43
4443 4502 4.711846 AGACAGGTGCAGTCACATATTAGA 59.288 41.667 7.27 0.00 44.87 2.10
4444 4503 5.016051 AGACAGGTGCAGTCACATATTAG 57.984 43.478 7.27 0.00 44.87 1.73
4445 4504 5.420725 AAGACAGGTGCAGTCACATATTA 57.579 39.130 7.27 0.00 44.87 0.98
4446 4505 3.988976 AGACAGGTGCAGTCACATATT 57.011 42.857 7.27 0.00 44.87 1.28
4447 4506 3.988976 AAGACAGGTGCAGTCACATAT 57.011 42.857 7.27 0.00 44.87 1.78
4448 4507 3.070878 TCAAAGACAGGTGCAGTCACATA 59.929 43.478 7.27 0.00 44.87 2.29
4449 4508 2.158769 TCAAAGACAGGTGCAGTCACAT 60.159 45.455 7.27 0.00 44.87 3.21
4450 4509 1.209261 TCAAAGACAGGTGCAGTCACA 59.791 47.619 7.27 0.00 44.87 3.58
4451 4510 1.953559 TCAAAGACAGGTGCAGTCAC 58.046 50.000 7.27 0.00 42.40 3.67
4452 4511 2.497138 CATCAAAGACAGGTGCAGTCA 58.503 47.619 7.27 0.00 38.46 3.41
4453 4512 1.198637 GCATCAAAGACAGGTGCAGTC 59.801 52.381 0.00 0.00 35.93 3.51
4454 4513 1.242076 GCATCAAAGACAGGTGCAGT 58.758 50.000 0.00 0.00 35.93 4.40
4455 4514 1.241165 TGCATCAAAGACAGGTGCAG 58.759 50.000 0.00 0.00 40.51 4.41
4456 4515 1.241165 CTGCATCAAAGACAGGTGCA 58.759 50.000 0.90 0.90 42.86 4.57
4457 4516 0.524862 CCTGCATCAAAGACAGGTGC 59.475 55.000 0.00 0.00 44.91 5.01
4461 4520 3.503363 TGCTTAACCTGCATCAAAGACAG 59.497 43.478 0.00 0.00 35.31 3.51
4462 4521 3.485394 TGCTTAACCTGCATCAAAGACA 58.515 40.909 0.00 0.00 35.31 3.41
4463 4522 3.503748 ACTGCTTAACCTGCATCAAAGAC 59.496 43.478 0.00 0.00 39.86 3.01
4464 4523 3.754965 ACTGCTTAACCTGCATCAAAGA 58.245 40.909 0.00 0.00 39.86 2.52
4465 4524 4.232221 CAACTGCTTAACCTGCATCAAAG 58.768 43.478 0.00 0.00 39.86 2.77
4466 4525 3.005684 CCAACTGCTTAACCTGCATCAAA 59.994 43.478 0.00 0.00 39.86 2.69
4467 4526 2.557924 CCAACTGCTTAACCTGCATCAA 59.442 45.455 0.00 0.00 39.86 2.57
4468 4527 2.161855 CCAACTGCTTAACCTGCATCA 58.838 47.619 0.00 0.00 39.86 3.07
4469 4528 2.162408 GTCCAACTGCTTAACCTGCATC 59.838 50.000 0.00 0.00 39.86 3.91
4470 4529 2.162681 GTCCAACTGCTTAACCTGCAT 58.837 47.619 0.00 0.00 39.86 3.96
4471 4530 1.133945 TGTCCAACTGCTTAACCTGCA 60.134 47.619 0.00 0.00 38.81 4.41
4472 4531 1.537202 CTGTCCAACTGCTTAACCTGC 59.463 52.381 0.00 0.00 0.00 4.85
4473 4532 2.851195 ACTGTCCAACTGCTTAACCTG 58.149 47.619 0.00 0.00 0.00 4.00
4474 4533 4.910458 ATACTGTCCAACTGCTTAACCT 57.090 40.909 0.00 0.00 0.00 3.50
4475 4534 5.959618 AAATACTGTCCAACTGCTTAACC 57.040 39.130 0.00 0.00 0.00 2.85
4476 4535 8.391106 CAGATAAATACTGTCCAACTGCTTAAC 58.609 37.037 0.00 0.00 0.00 2.01
4477 4536 7.065803 GCAGATAAATACTGTCCAACTGCTTAA 59.934 37.037 0.00 0.00 42.85 1.85
4478 4537 6.538742 GCAGATAAATACTGTCCAACTGCTTA 59.461 38.462 0.00 0.00 42.85 3.09
4479 4538 5.355350 GCAGATAAATACTGTCCAACTGCTT 59.645 40.000 0.00 0.00 42.85 3.91
4480 4539 4.878397 GCAGATAAATACTGTCCAACTGCT 59.122 41.667 0.00 0.00 42.85 4.24
4481 4540 4.035675 GGCAGATAAATACTGTCCAACTGC 59.964 45.833 0.00 0.00 44.57 4.40
4482 4541 5.185454 TGGCAGATAAATACTGTCCAACTG 58.815 41.667 0.00 0.00 38.95 3.16
4483 4542 5.435686 TGGCAGATAAATACTGTCCAACT 57.564 39.130 0.00 0.00 38.95 3.16
4485 4544 5.565509 TGTTGGCAGATAAATACTGTCCAA 58.434 37.500 1.46 1.46 42.68 3.53
4486 4545 5.172687 TGTTGGCAGATAAATACTGTCCA 57.827 39.130 0.00 0.00 38.95 4.02
4487 4546 5.065218 CACTGTTGGCAGATAAATACTGTCC 59.935 44.000 1.30 0.00 45.28 4.02
4488 4547 5.447818 GCACTGTTGGCAGATAAATACTGTC 60.448 44.000 1.30 0.00 45.28 3.51
4747 5003 9.515226 TGTTCTAAGTGGCATTCTAGTATTTTT 57.485 29.630 0.00 0.00 0.00 1.94
4827 5083 7.165483 GTGCTAATACGTATGTGTGAACTCTAC 59.835 40.741 9.24 0.00 0.00 2.59
5061 5318 5.184287 TCTGCTTGCAATCTTGATTGAATGA 59.816 36.000 22.85 9.09 33.55 2.57
5471 5735 7.386299 CAGTTTGACATAGATATTCCCTGTAGC 59.614 40.741 0.00 0.00 0.00 3.58
5548 5812 9.492973 AAGGTGAAGAATAAATTTGACCATTTG 57.507 29.630 0.00 0.00 0.00 2.32
5789 6057 5.706916 CAGTTGAAGAATAATGCAGCAACT 58.293 37.500 0.00 0.00 43.48 3.16
5902 6170 5.511202 GCCCCTGATTTTTCATTGAAACTCA 60.511 40.000 11.30 14.67 30.83 3.41
6206 6480 6.215023 TCCTAGTCTAGTACTTCTCAACTGGA 59.785 42.308 0.00 5.60 39.80 3.86
6207 6481 6.316890 GTCCTAGTCTAGTACTTCTCAACTGG 59.683 46.154 0.00 0.51 39.80 4.00
6294 6568 4.464008 TCAGCAATCTCCAGAAACTGTTT 58.536 39.130 5.29 5.29 0.00 2.83
6555 7050 9.593565 TGTGTATATATCAAGAGAGGAGAACAT 57.406 33.333 0.00 0.00 0.00 2.71
6601 7096 2.842208 TTGTCGCCACTGTTTTTGAG 57.158 45.000 0.00 0.00 0.00 3.02
6616 7111 8.753497 AGATAAAGGGATGGTATTCTTTTGTC 57.247 34.615 0.00 0.00 32.53 3.18
6626 7121 6.661805 GGTGTTTTGAAGATAAAGGGATGGTA 59.338 38.462 0.00 0.00 0.00 3.25
6731 7230 7.614192 GTCCTTGGAACCTATTAATCCAGAAAA 59.386 37.037 0.00 0.00 43.69 2.29
6780 7279 0.107459 CTGCCTTGTTCTAGAGCCCC 60.107 60.000 3.94 0.00 0.00 5.80
6839 7338 2.851588 TACCACTGTGCCAGGCCA 60.852 61.111 9.64 5.67 35.51 5.36
7008 7507 5.167845 GTCAAAACTCAAAAGCTTTGGTGA 58.832 37.500 19.91 15.85 38.53 4.02
7025 7524 3.287222 GGTGCTATATGGGCTGTCAAAA 58.713 45.455 4.57 0.00 0.00 2.44
7203 7703 5.126396 TCTGATCACACTTACACTCACAG 57.874 43.478 0.00 0.00 0.00 3.66
7225 7725 2.427453 CCTGTACTAAGCTCCACGACAT 59.573 50.000 0.00 0.00 0.00 3.06
7242 7742 7.016268 TCTCACTCTAATTTACTTTGACCCTGT 59.984 37.037 0.00 0.00 0.00 4.00
7297 7797 5.716228 TCTTGATGGGATTGCAAAGTATTGT 59.284 36.000 1.71 0.00 38.85 2.71
7298 7798 6.038356 GTCTTGATGGGATTGCAAAGTATTG 58.962 40.000 1.71 0.00 39.65 1.90
7299 7799 5.954150 AGTCTTGATGGGATTGCAAAGTATT 59.046 36.000 1.71 0.00 0.00 1.89
7300 7800 5.359009 CAGTCTTGATGGGATTGCAAAGTAT 59.641 40.000 1.71 0.00 0.00 2.12
7301 7801 4.701651 CAGTCTTGATGGGATTGCAAAGTA 59.298 41.667 1.71 0.00 0.00 2.24
7317 7817 2.242926 TGACAGAGAGGACCAGTCTTG 58.757 52.381 0.00 0.00 0.00 3.02
7336 7839 1.739562 GCCGAGCTCTGTCCAGTTG 60.740 63.158 12.85 0.00 0.00 3.16
7352 7855 0.394192 TGATCCGATCATCAGTGGCC 59.606 55.000 7.00 0.00 33.59 5.36
7360 7863 2.031870 TCAACCGAGTGATCCGATCAT 58.968 47.619 14.15 4.04 42.04 2.45
7380 7883 3.703001 AAGCAGTACCACTTGCAGTAT 57.297 42.857 7.48 0.00 0.00 2.12
7383 7886 2.880890 AGAAAAGCAGTACCACTTGCAG 59.119 45.455 7.48 0.00 0.00 4.41
7411 7914 4.141597 TGGTTTACATCCACACTCACTGAA 60.142 41.667 0.00 0.00 0.00 3.02
7413 7916 3.738982 TGGTTTACATCCACACTCACTG 58.261 45.455 0.00 0.00 0.00 3.66
7439 7942 2.037641 TCCCAGACATGAGTGTTGTCAG 59.962 50.000 0.00 0.00 44.73 3.51
7440 7943 2.046292 TCCCAGACATGAGTGTTGTCA 58.954 47.619 0.00 0.00 44.73 3.58
7442 7945 1.768275 TGTCCCAGACATGAGTGTTGT 59.232 47.619 0.00 0.00 37.67 3.32
7672 8193 5.122396 GCTGGAGTAATCGAACTTGTTGATT 59.878 40.000 0.00 12.22 42.21 2.57
7673 8194 4.631813 GCTGGAGTAATCGAACTTGTTGAT 59.368 41.667 0.00 0.00 30.87 2.57
7674 8195 3.994392 GCTGGAGTAATCGAACTTGTTGA 59.006 43.478 0.00 0.00 0.00 3.18
7675 8196 3.125316 GGCTGGAGTAATCGAACTTGTTG 59.875 47.826 0.00 0.00 0.00 3.33
7676 8197 3.335579 GGCTGGAGTAATCGAACTTGTT 58.664 45.455 0.00 0.00 0.00 2.83
7677 8198 2.354805 GGGCTGGAGTAATCGAACTTGT 60.355 50.000 0.00 0.00 0.00 3.16
7678 8199 2.280628 GGGCTGGAGTAATCGAACTTG 58.719 52.381 0.00 0.00 0.00 3.16
7683 8204 2.792947 GCGGGGCTGGAGTAATCGA 61.793 63.158 0.00 0.00 0.00 3.59
7684 8205 2.280186 GCGGGGCTGGAGTAATCG 60.280 66.667 0.00 0.00 0.00 3.34
7700 8221 2.344950 CTGAGATGAGACACCAACTGC 58.655 52.381 0.00 0.00 0.00 4.40
7701 8222 2.289257 TGCTGAGATGAGACACCAACTG 60.289 50.000 0.00 0.00 0.00 3.16
7727 8253 2.095110 CAGATTTTCGCTCAATGTGGCA 60.095 45.455 0.00 0.00 0.00 4.92
7728 8254 2.095059 ACAGATTTTCGCTCAATGTGGC 60.095 45.455 0.00 0.00 30.84 5.01
7731 8257 3.120546 CGTCACAGATTTTCGCTCAATGT 60.121 43.478 0.00 0.00 0.00 2.71
7734 8260 2.479837 ACGTCACAGATTTTCGCTCAA 58.520 42.857 0.00 0.00 0.00 3.02
7742 8268 6.784068 CGTTGTTTTTAACGTCACAGATTT 57.216 33.333 0.00 0.00 46.02 2.17


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

AutoCloner maintained by Alex Coulton.