Multiple sequence alignment - TraesCS5B01G411800

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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 TraesCS5B01G411800 chr5B 100.000 4175 0 0 1 4175 586823957 586819783 0.000000e+00 7710.0
1 TraesCS5B01G411800 chr5B 87.417 151 13 4 91 240 299013883 299014028 7.180000e-38 169.0
2 TraesCS5B01G411800 chr5D 91.789 2862 163 30 1 2824 478964798 478961971 0.000000e+00 3917.0
3 TraesCS5B01G411800 chr5D 90.945 508 35 3 2822 3320 478961266 478960761 0.000000e+00 673.0
4 TraesCS5B01G411800 chr5D 91.067 403 20 5 3381 3783 478960763 478960377 7.950000e-147 531.0
5 TraesCS5B01G411800 chr5D 83.854 192 23 6 91 280 281848723 281848908 4.290000e-40 176.0
6 TraesCS5B01G411800 chr5D 86.000 150 19 1 91 240 265661198 265661345 4.320000e-35 159.0
7 TraesCS5B01G411800 chr5A 95.027 2051 87 8 785 2824 597797114 597795068 0.000000e+00 3208.0
8 TraesCS5B01G411800 chr5A 84.648 697 89 10 2 683 597797806 597797113 0.000000e+00 678.0
9 TraesCS5B01G411800 chr5A 90.196 510 34 7 2821 3317 597794031 597793525 0.000000e+00 651.0
10 TraesCS5B01G411800 chr5A 85.629 334 27 9 3651 3967 597792642 597792313 8.650000e-87 331.0
11 TraesCS5B01G411800 chr5A 87.273 220 8 3 3381 3600 597793454 597793255 2.510000e-57 233.0
12 TraesCS5B01G411800 chr5A 88.000 150 14 2 91 240 353156258 353156403 1.540000e-39 174.0
13 TraesCS5B01G411800 chr5A 86.275 153 14 4 4026 4175 597792362 597792214 4.320000e-35 159.0
14 TraesCS5B01G411800 chr5A 97.143 70 2 0 3383 3452 597793522 597793453 7.330000e-23 119.0
15 TraesCS5B01G411800 chrUn 83.954 349 27 17 3382 3725 35321966 35321642 1.460000e-79 307.0
16 TraesCS5B01G411800 chrUn 82.521 349 34 15 3382 3725 34660997 34660671 8.840000e-72 281.0
17 TraesCS5B01G411800 chrUn 84.716 229 17 10 3504 3726 32295443 32295227 3.270000e-51 213.0
18 TraesCS5B01G411800 chrUn 84.746 177 22 4 2570 2745 35322714 35322542 5.550000e-39 172.0
19 TraesCS5B01G411800 chr3A 83.381 349 35 13 3382 3725 11351998 11352328 6.780000e-78 302.0
20 TraesCS5B01G411800 chr3A 84.868 152 21 2 89 238 489305181 489305030 7.230000e-33 152.0
21 TraesCS5B01G411800 chr4A 87.742 155 19 0 91 245 693393145 693392991 9.220000e-42 182.0
22 TraesCS5B01G411800 chr4D 86.000 150 19 2 91 240 427944469 427944616 4.320000e-35 159.0
23 TraesCS5B01G411800 chr7A 85.882 85 8 3 3884 3967 352907411 352907492 2.070000e-13 87.9
24 TraesCS5B01G411800 chr6A 84.146 82 13 0 3 84 168086918 168086837 3.460000e-11 80.5
25 TraesCS5B01G411800 chr3B 82.105 95 9 5 2397 2483 28368222 28368128 1.610000e-09 75.0
26 TraesCS5B01G411800 chr2D 97.436 39 1 0 3348 3386 580114088 580114126 2.690000e-07 67.6
27 TraesCS5B01G411800 chr7D 95.000 40 2 0 3931 3970 342626281 342626242 3.480000e-06 63.9
28 TraesCS5B01G411800 chr6B 100.000 28 0 0 3358 3385 162217350 162217323 8.000000e-03 52.8


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 TraesCS5B01G411800 chr5B 586819783 586823957 4174 True 7710.000000 7710 100.000000 1 4175 1 chr5B.!!$R1 4174
1 TraesCS5B01G411800 chr5D 478960377 478964798 4421 True 1707.000000 3917 91.267000 1 3783 3 chr5D.!!$R1 3782
2 TraesCS5B01G411800 chr5A 597792214 597797806 5592 True 768.428571 3208 89.455857 2 4175 7 chr5A.!!$R1 4173
3 TraesCS5B01G411800 chrUn 35321642 35322714 1072 True 239.500000 307 84.350000 2570 3725 2 chrUn.!!$R3 1155

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
400 413 1.064239 TACTCCCCTAGGCGGCTAGA 61.064 60.0 39.08 23.01 0.0 2.43 F
1462 1510 0.324943 CACCGACCCCAACTTCATCT 59.675 55.0 0.00 0.00 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1837 1.303561 AGTGGCCGTGCACATGATT 60.304 52.632 18.64 0.0 0.0 2.57 R
3320 4512 0.687354 CATTATGGGACGGGAGGGAG 59.313 60.000 0.00 0.0 0.0 4.30 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
58 59 2.280592 AGTCCAAACCGTCGCCAC 60.281 61.111 0.00 0.00 0.00 5.01
230 232 8.650490 TCTTCAGTGATTTGATATGCCACTATA 58.350 33.333 0.00 0.00 36.44 1.31
242 244 1.603172 GCCACTATATTGAGCTCGCGT 60.603 52.381 9.64 0.00 0.00 6.01
290 303 4.410400 GGGACAAGGCCTCCCACG 62.410 72.222 21.18 4.36 46.30 4.94
310 323 3.168528 ACTGCCCGTGGACTGGTT 61.169 61.111 0.00 0.00 0.00 3.67
318 331 1.544537 CCGTGGACTGGTTTGGATCAA 60.545 52.381 0.00 0.00 0.00 2.57
338 351 4.868171 TCAATCTACAGACAAATACCGTGC 59.132 41.667 0.00 0.00 0.00 5.34
365 378 1.918262 TGAGGGTCAGCATTGGAGATT 59.082 47.619 0.00 0.00 0.00 2.40
368 381 2.042162 AGGGTCAGCATTGGAGATTTGT 59.958 45.455 0.00 0.00 0.00 2.83
370 383 2.416431 GGTCAGCATTGGAGATTTGTGC 60.416 50.000 0.00 0.00 36.11 4.57
390 403 1.457643 AGCAGCGCATACTCCCCTA 60.458 57.895 11.47 0.00 0.00 3.53
400 413 1.064239 TACTCCCCTAGGCGGCTAGA 61.064 60.000 39.08 23.01 0.00 2.43
437 450 2.963782 GGTCCTATCAAGGTCGGTATGT 59.036 50.000 0.00 0.00 44.09 2.29
508 521 5.242838 TCTTTTAACACCGGCTCATTCAATT 59.757 36.000 0.00 0.00 0.00 2.32
511 524 2.513753 ACACCGGCTCATTCAATTTGA 58.486 42.857 0.00 0.00 0.00 2.69
514 527 3.191162 CACCGGCTCATTCAATTTGAAGA 59.809 43.478 16.34 12.37 40.05 2.87
549 562 7.040494 GGTAGGAATTAGGAGTGTACAAGAAC 58.960 42.308 0.00 0.00 0.00 3.01
565 578 5.491982 ACAAGAACTTGATAGGATGACACC 58.508 41.667 19.35 0.00 42.93 4.16
567 580 6.440647 ACAAGAACTTGATAGGATGACACCTA 59.559 38.462 19.35 0.00 43.08 3.08
580 593 5.221541 GGATGACACCTACCATTCTAAGGAG 60.222 48.000 0.00 0.00 34.34 3.69
588 601 6.272558 ACCTACCATTCTAAGGAGTTGTCTTT 59.727 38.462 0.00 0.00 34.34 2.52
602 615 5.741011 AGTTGTCTTTGACTTGTTCCTACA 58.259 37.500 0.00 0.00 33.15 2.74
673 692 9.520515 ACACAGAAAATGAATAGTATTTCCACT 57.479 29.630 0.00 0.00 33.35 4.00
715 734 7.246674 TCTTACAAAACCGAATGCATCTATC 57.753 36.000 0.00 0.00 0.00 2.08
721 740 4.156455 ACCGAATGCATCTATCCTTGTT 57.844 40.909 0.00 0.00 0.00 2.83
723 742 4.949856 ACCGAATGCATCTATCCTTGTTTT 59.050 37.500 0.00 0.00 0.00 2.43
749 772 8.243961 TGTGTTTTTCTATGAAAATCCTCCAA 57.756 30.769 6.35 0.00 31.80 3.53
783 806 6.380079 AACCTGGAGATAATTGTCTCAACT 57.620 37.500 27.24 9.04 45.12 3.16
791 814 7.094634 GGAGATAATTGTCTCAACTTGCTTTCA 60.095 37.037 27.24 0.00 45.12 2.69
858 889 3.947041 AGGTGGGGCCTCCAGAGT 61.947 66.667 12.75 0.00 46.96 3.24
920 953 1.083329 CCCTAACCCCTACCCACCA 59.917 63.158 0.00 0.00 0.00 4.17
991 1030 4.799949 TCGTCTATGACCGAATAAAAACCG 59.200 41.667 0.00 0.00 0.00 4.44
1178 1220 4.821589 GGCAAGCGAGGAGGACGG 62.822 72.222 0.00 0.00 0.00 4.79
1383 1431 1.416030 GAGATCCTTCTCCTTCTGCCC 59.584 57.143 0.00 0.00 42.26 5.36
1462 1510 0.324943 CACCGACCCCAACTTCATCT 59.675 55.000 0.00 0.00 0.00 2.90
1570 1618 4.682334 TGCACCCTCCCGACCGTA 62.682 66.667 0.00 0.00 0.00 4.02
1579 1627 2.728817 CCGACCGTATCCCTGCTC 59.271 66.667 0.00 0.00 0.00 4.26
1765 1813 2.520982 CCATCCTCTACGGGGCGA 60.521 66.667 0.00 0.00 0.00 5.54
1865 1913 4.323333 CCACAGAAGAGATCATCAACCACT 60.323 45.833 0.00 0.00 0.00 4.00
1866 1914 4.869297 CACAGAAGAGATCATCAACCACTC 59.131 45.833 0.00 0.00 0.00 3.51
1995 2043 2.289694 ACTCTATTGGCTGCTTTCGTGT 60.290 45.455 0.00 0.00 0.00 4.49
2198 2246 2.634815 ATTGCCACATGGTTTTTGCA 57.365 40.000 0.00 0.00 37.57 4.08
2283 2331 2.084546 GACAAAGTGCTGGGGTATGAC 58.915 52.381 0.00 0.00 0.00 3.06
2297 2345 3.673809 GGGTATGACGAAGATAACGATGC 59.326 47.826 0.00 0.00 34.70 3.91
2304 2352 4.299155 ACGAAGATAACGATGCGATCATT 58.701 39.130 0.00 0.00 31.96 2.57
2388 2436 4.295141 TGGAACCCGTTCTATGAAACAT 57.705 40.909 7.47 0.00 39.45 2.71
2403 2451 6.653526 ATGAAACATTGTCATCCTTTCACA 57.346 33.333 2.37 0.00 34.53 3.58
2560 2612 4.096732 AGCAATTGTCGCTGATAAAACC 57.903 40.909 7.40 0.00 38.60 3.27
2621 2673 3.131046 AGTTGGCAAGTTTGAAACCTCAG 59.869 43.478 0.00 0.00 31.69 3.35
2624 2676 2.952310 GGCAAGTTTGAAACCTCAGAGT 59.048 45.455 4.14 0.00 31.69 3.24
2768 2821 1.280746 CTTCTGCTGGTGCGTGTTG 59.719 57.895 0.00 0.00 43.34 3.33
2810 2865 1.544724 TTGAATTTCTTGCCTCGGGG 58.455 50.000 0.00 0.00 0.00 5.73
2854 4001 8.116651 TGCTAGACTTTATTGTTTTGGCATAA 57.883 30.769 0.00 0.00 0.00 1.90
2898 4045 8.059798 ACAAGGGATGATCTTACATGAAAAAG 57.940 34.615 0.00 0.10 0.00 2.27
2939 4090 8.553459 TTCTTCTTCTTGGTAGCTAAATTCTG 57.447 34.615 0.00 0.00 0.00 3.02
2964 4115 4.569761 TCGAAGGTAGCTAAGTATGCTG 57.430 45.455 0.00 0.00 41.32 4.41
2973 4124 6.483640 GGTAGCTAAGTATGCTGCTTTTATGT 59.516 38.462 0.00 0.00 41.68 2.29
3023 4176 8.980143 TGTGGCTTTTTAAAATCTATTGCTAC 57.020 30.769 0.55 8.23 0.00 3.58
3024 4177 8.032451 TGTGGCTTTTTAAAATCTATTGCTACC 58.968 33.333 0.55 0.00 0.00 3.18
3041 4194 3.367498 GCTACCACTGTAAGGAGTGAGTG 60.367 52.174 0.00 0.00 45.39 3.51
3051 4204 7.577807 ACTGTAAGGAGTGAGTGATAACACATC 60.578 40.741 5.87 1.54 43.85 3.06
3096 4272 6.740002 CGATGTTTCTGATTGTCTCATTGTTC 59.260 38.462 0.00 0.00 32.10 3.18
3119 4296 4.699257 CCCTTTTCTCTCCATTTGTCTCTG 59.301 45.833 0.00 0.00 0.00 3.35
3129 4306 5.499313 TCCATTTGTCTCTGCATCATAACA 58.501 37.500 0.00 0.00 0.00 2.41
3133 4310 6.486253 TTTGTCTCTGCATCATAACAGTTC 57.514 37.500 0.00 0.00 35.37 3.01
3134 4311 5.411831 TGTCTCTGCATCATAACAGTTCT 57.588 39.130 0.00 0.00 35.37 3.01
3255 4441 1.702182 TTTCCAGAAACAGCCATGCA 58.298 45.000 0.00 0.00 0.00 3.96
3283 4474 9.403110 GGATGCAGCAAGTATATAAATGAAAAG 57.597 33.333 3.51 0.00 0.00 2.27
3308 4500 4.968812 CAGCATGTGATGTAATGTGGAA 57.031 40.909 0.00 0.00 0.00 3.53
3327 4519 8.431910 TGTGGAAAATAGTATATACTCCCTCC 57.568 38.462 18.68 18.25 37.73 4.30
3328 4520 7.456902 TGTGGAAAATAGTATATACTCCCTCCC 59.543 40.741 18.68 15.04 37.73 4.30
3329 4521 6.666546 TGGAAAATAGTATATACTCCCTCCCG 59.333 42.308 18.68 0.00 37.73 5.14
3330 4522 6.666980 GGAAAATAGTATATACTCCCTCCCGT 59.333 42.308 18.68 0.00 37.73 5.28
3331 4523 7.147932 GGAAAATAGTATATACTCCCTCCCGTC 60.148 44.444 18.68 7.09 37.73 4.79
3332 4524 3.735720 AGTATATACTCCCTCCCGTCC 57.264 52.381 9.71 0.00 0.00 4.79
3333 4525 2.311243 AGTATATACTCCCTCCCGTCCC 59.689 54.545 9.71 0.00 0.00 4.46
3334 4526 1.164313 ATATACTCCCTCCCGTCCCA 58.836 55.000 0.00 0.00 0.00 4.37
3335 4527 1.164313 TATACTCCCTCCCGTCCCAT 58.836 55.000 0.00 0.00 0.00 4.00
3336 4528 1.164313 ATACTCCCTCCCGTCCCATA 58.836 55.000 0.00 0.00 0.00 2.74
3337 4529 0.935942 TACTCCCTCCCGTCCCATAA 59.064 55.000 0.00 0.00 0.00 1.90
3338 4530 0.267960 ACTCCCTCCCGTCCCATAAT 59.732 55.000 0.00 0.00 0.00 1.28
3339 4531 0.687354 CTCCCTCCCGTCCCATAATG 59.313 60.000 0.00 0.00 0.00 1.90
3340 4532 0.030501 TCCCTCCCGTCCCATAATGT 60.031 55.000 0.00 0.00 0.00 2.71
3341 4533 1.221007 TCCCTCCCGTCCCATAATGTA 59.779 52.381 0.00 0.00 0.00 2.29
3347 4539 4.485875 TCCCGTCCCATAATGTATAGTGT 58.514 43.478 0.00 0.00 0.00 3.55
3348 4540 4.903049 TCCCGTCCCATAATGTATAGTGTT 59.097 41.667 0.00 0.00 0.00 3.32
3349 4541 6.076653 TCCCGTCCCATAATGTATAGTGTTA 58.923 40.000 0.00 0.00 0.00 2.41
3351 4543 7.070946 TCCCGTCCCATAATGTATAGTGTTAAA 59.929 37.037 0.00 0.00 0.00 1.52
3352 4544 7.716123 CCCGTCCCATAATGTATAGTGTTAAAA 59.284 37.037 0.00 0.00 0.00 1.52
3353 4545 9.111613 CCGTCCCATAATGTATAGTGTTAAAAA 57.888 33.333 0.00 0.00 0.00 1.94
3374 4566 4.957684 AAGGTCTTAGATTATGGGACGG 57.042 45.455 0.00 0.00 0.00 4.79
3376 4568 4.153411 AGGTCTTAGATTATGGGACGGAG 58.847 47.826 0.00 0.00 0.00 4.63
3377 4569 3.258622 GGTCTTAGATTATGGGACGGAGG 59.741 52.174 0.00 0.00 0.00 4.30
3378 4570 3.258622 GTCTTAGATTATGGGACGGAGGG 59.741 52.174 0.00 0.00 0.00 4.30
3379 4571 3.141460 TCTTAGATTATGGGACGGAGGGA 59.859 47.826 0.00 0.00 0.00 4.20
3433 4632 1.040339 TTTGTTGTCTGCGGGCCTTT 61.040 50.000 0.84 0.00 0.00 3.11
3454 4653 3.226777 TGTTTCCCTGTTTGTATGTGGG 58.773 45.455 0.00 0.00 39.22 4.61
3657 5450 5.524284 TGGTTTCATTTCCACGTTTGTATG 58.476 37.500 0.00 0.00 0.00 2.39
3709 5502 1.002134 GTGGGATGGTGTGACTGGG 60.002 63.158 0.00 0.00 0.00 4.45
3743 5536 6.378280 GTCAAGATCAATATGTTCTGGGGTTT 59.622 38.462 0.00 0.00 0.00 3.27
3783 5576 2.499685 GCGCGTATGAGGGTCCTT 59.500 61.111 8.43 0.00 0.00 3.36
3787 5580 1.904771 CGTATGAGGGTCCTTGCCA 59.095 57.895 0.00 0.00 0.00 4.92
3788 5581 0.469917 CGTATGAGGGTCCTTGCCAT 59.530 55.000 0.00 0.00 0.00 4.40
3808 5601 2.176273 GCATGAATGAGCGCTCCGT 61.176 57.895 33.23 21.45 0.00 4.69
3811 5604 2.202623 GAATGAGCGCTCCGTCGT 60.203 61.111 33.23 14.39 0.00 4.34
3812 5605 1.805945 GAATGAGCGCTCCGTCGTT 60.806 57.895 33.23 17.56 0.00 3.85
3813 5606 2.014093 GAATGAGCGCTCCGTCGTTG 62.014 60.000 33.23 0.00 0.00 4.10
3822 5615 1.074423 TCCGTCGTTGGGAGAGTCT 59.926 57.895 0.00 0.00 0.00 3.24
3823 5616 0.959372 TCCGTCGTTGGGAGAGTCTC 60.959 60.000 12.01 12.01 0.00 3.36
3851 5644 2.989253 TCGAGAACGCTGCCTCCA 60.989 61.111 0.00 0.00 39.58 3.86
3852 5645 2.507992 CGAGAACGCTGCCTCCAG 60.508 66.667 0.00 0.00 42.13 3.86
3889 5698 7.392953 TCTCACCAATGCTGATAATGTGTTTAA 59.607 33.333 0.00 0.00 0.00 1.52
3944 5754 7.933215 TCTTTGTTGATGATGATGATGAACT 57.067 32.000 0.00 0.00 0.00 3.01
3945 5755 9.452287 TTCTTTGTTGATGATGATGATGAACTA 57.548 29.630 0.00 0.00 0.00 2.24
3946 5756 9.623000 TCTTTGTTGATGATGATGATGAACTAT 57.377 29.630 0.00 0.00 0.00 2.12
3958 5768 8.565896 TGATGATGAACTATTTATACATGCCC 57.434 34.615 0.00 0.00 0.00 5.36
3959 5769 8.162746 TGATGATGAACTATTTATACATGCCCA 58.837 33.333 0.00 0.00 0.00 5.36
3960 5770 8.938801 ATGATGAACTATTTATACATGCCCAA 57.061 30.769 0.00 0.00 0.00 4.12
3961 5771 8.759481 TGATGAACTATTTATACATGCCCAAA 57.241 30.769 0.00 0.00 0.00 3.28
3962 5772 8.849168 TGATGAACTATTTATACATGCCCAAAG 58.151 33.333 0.00 0.00 0.00 2.77
3963 5773 7.581213 TGAACTATTTATACATGCCCAAAGG 57.419 36.000 0.00 0.00 0.00 3.11
3981 5791 3.512516 GCATGTGCCTCCCTTCGC 61.513 66.667 0.00 0.00 34.31 4.70
3982 5792 2.825836 CATGTGCCTCCCTTCGCC 60.826 66.667 0.00 0.00 0.00 5.54
3983 5793 3.011517 ATGTGCCTCCCTTCGCCT 61.012 61.111 0.00 0.00 0.00 5.52
3984 5794 2.606587 ATGTGCCTCCCTTCGCCTT 61.607 57.895 0.00 0.00 0.00 4.35
3985 5795 2.034221 GTGCCTCCCTTCGCCTTT 59.966 61.111 0.00 0.00 0.00 3.11
3986 5796 1.603739 GTGCCTCCCTTCGCCTTTT 60.604 57.895 0.00 0.00 0.00 2.27
3987 5797 1.303317 TGCCTCCCTTCGCCTTTTC 60.303 57.895 0.00 0.00 0.00 2.29
3988 5798 1.002011 GCCTCCCTTCGCCTTTTCT 60.002 57.895 0.00 0.00 0.00 2.52
3989 5799 1.027255 GCCTCCCTTCGCCTTTTCTC 61.027 60.000 0.00 0.00 0.00 2.87
3990 5800 0.615850 CCTCCCTTCGCCTTTTCTCT 59.384 55.000 0.00 0.00 0.00 3.10
3991 5801 1.003696 CCTCCCTTCGCCTTTTCTCTT 59.996 52.381 0.00 0.00 0.00 2.85
3992 5802 2.079925 CTCCCTTCGCCTTTTCTCTTG 58.920 52.381 0.00 0.00 0.00 3.02
3993 5803 0.523519 CCCTTCGCCTTTTCTCTTGC 59.476 55.000 0.00 0.00 0.00 4.01
3994 5804 1.238439 CCTTCGCCTTTTCTCTTGCA 58.762 50.000 0.00 0.00 0.00 4.08
3995 5805 1.608590 CCTTCGCCTTTTCTCTTGCAA 59.391 47.619 0.00 0.00 0.00 4.08
3996 5806 2.034558 CCTTCGCCTTTTCTCTTGCAAA 59.965 45.455 0.00 0.00 0.00 3.68
3997 5807 3.305608 CCTTCGCCTTTTCTCTTGCAAAT 60.306 43.478 0.00 0.00 0.00 2.32
3998 5808 3.287312 TCGCCTTTTCTCTTGCAAATG 57.713 42.857 0.00 0.00 0.00 2.32
3999 5809 1.723003 CGCCTTTTCTCTTGCAAATGC 59.277 47.619 0.00 0.00 42.50 3.56
4000 5810 2.608752 CGCCTTTTCTCTTGCAAATGCT 60.609 45.455 0.00 0.00 42.66 3.79
4001 5811 2.735134 GCCTTTTCTCTTGCAAATGCTG 59.265 45.455 0.00 0.23 42.66 4.41
4002 5812 3.553508 GCCTTTTCTCTTGCAAATGCTGA 60.554 43.478 0.00 4.53 42.66 4.26
4003 5813 4.817517 CCTTTTCTCTTGCAAATGCTGAT 58.182 39.130 0.00 0.00 42.66 2.90
4004 5814 5.622914 GCCTTTTCTCTTGCAAATGCTGATA 60.623 40.000 0.00 0.00 42.66 2.15
4005 5815 6.392354 CCTTTTCTCTTGCAAATGCTGATAA 58.608 36.000 0.00 2.25 42.66 1.75
4006 5816 7.039882 CCTTTTCTCTTGCAAATGCTGATAAT 58.960 34.615 0.00 0.00 42.66 1.28
4007 5817 7.010183 CCTTTTCTCTTGCAAATGCTGATAATG 59.990 37.037 0.00 5.48 42.66 1.90
4008 5818 6.519679 TTCTCTTGCAAATGCTGATAATGT 57.480 33.333 0.00 0.00 42.66 2.71
4009 5819 5.886992 TCTCTTGCAAATGCTGATAATGTG 58.113 37.500 0.00 0.00 42.66 3.21
4010 5820 5.416639 TCTCTTGCAAATGCTGATAATGTGT 59.583 36.000 0.00 0.00 42.66 3.72
4011 5821 6.028146 TCTTGCAAATGCTGATAATGTGTT 57.972 33.333 0.00 0.00 42.66 3.32
4012 5822 6.457355 TCTTGCAAATGCTGATAATGTGTTT 58.543 32.000 0.00 0.00 42.66 2.83
4013 5823 7.600960 TCTTGCAAATGCTGATAATGTGTTTA 58.399 30.769 0.00 0.00 42.66 2.01
4014 5824 7.756272 TCTTGCAAATGCTGATAATGTGTTTAG 59.244 33.333 0.00 0.00 42.66 1.85
4015 5825 7.155655 TGCAAATGCTGATAATGTGTTTAGA 57.844 32.000 6.97 0.00 42.66 2.10
4016 5826 7.600960 TGCAAATGCTGATAATGTGTTTAGAA 58.399 30.769 6.97 0.00 42.66 2.10
4017 5827 8.252417 TGCAAATGCTGATAATGTGTTTAGAAT 58.748 29.630 6.97 0.00 42.66 2.40
4018 5828 8.537223 GCAAATGCTGATAATGTGTTTAGAATG 58.463 33.333 0.00 0.00 38.21 2.67
4019 5829 9.791820 CAAATGCTGATAATGTGTTTAGAATGA 57.208 29.630 0.00 0.00 0.00 2.57
4023 5833 9.844790 TGCTGATAATGTGTTTAGAATGAAAAG 57.155 29.630 0.00 0.00 0.00 2.27
4024 5834 9.846248 GCTGATAATGTGTTTAGAATGAAAAGT 57.154 29.630 0.00 0.00 0.00 2.66
4078 5888 2.824041 CCCAAAGGGCACGATCCG 60.824 66.667 0.00 0.00 35.35 4.18
4079 5889 2.046314 CCAAAGGGCACGATCCGT 60.046 61.111 0.00 0.00 42.36 4.69
4080 5890 1.219664 CCAAAGGGCACGATCCGTA 59.780 57.895 0.00 0.00 38.32 4.02
4089 5899 1.470285 GCACGATCCGTAGCCTTTACA 60.470 52.381 0.00 0.00 38.32 2.41
4090 5900 2.460918 CACGATCCGTAGCCTTTACAG 58.539 52.381 0.00 0.00 38.32 2.74
4101 5911 4.264460 AGCCTTTACAGAGAGTCACAAG 57.736 45.455 0.00 0.00 0.00 3.16
4106 5916 5.694006 CCTTTACAGAGAGTCACAAGTGAAG 59.306 44.000 4.20 9.17 41.85 3.02
4110 5920 3.247173 CAGAGAGTCACAAGTGAAGCAAC 59.753 47.826 4.20 0.00 41.85 4.17
4117 5927 0.111089 CAAGTGAAGCAACGCGACTC 60.111 55.000 15.93 0.00 0.00 3.36
4118 5928 1.222115 AAGTGAAGCAACGCGACTCC 61.222 55.000 15.93 0.00 0.00 3.85
4142 5952 3.365969 GCCCAATGACGGTTTAGACAAAG 60.366 47.826 0.00 0.00 0.00 2.77
4143 5953 3.365969 CCCAATGACGGTTTAGACAAAGC 60.366 47.826 0.00 0.00 38.50 3.51
4145 5955 4.261405 CCAATGACGGTTTAGACAAAGCAA 60.261 41.667 0.00 0.00 41.27 3.91
4146 5956 4.749245 ATGACGGTTTAGACAAAGCAAG 57.251 40.909 0.00 0.00 41.27 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.617959 GCAAAGTCCCCTAGTTTGTTTTC 58.382 43.478 7.05 0.00 46.22 2.29
58 59 1.746517 GGGGTGCCATAGTCCTACG 59.253 63.158 0.00 0.00 0.00 3.51
85 86 2.450609 TGTTCTAGTTGTCCCTTCGC 57.549 50.000 0.00 0.00 0.00 4.70
87 88 5.294552 GCACATATGTTCTAGTTGTCCCTTC 59.705 44.000 5.37 0.00 0.00 3.46
209 211 9.445878 CTCAATATAGTGGCATATCAAATCACT 57.554 33.333 0.00 0.00 41.02 3.41
210 212 8.180267 GCTCAATATAGTGGCATATCAAATCAC 58.820 37.037 0.00 0.00 0.00 3.06
267 269 0.927029 GGAGGCCTTGTCCCCTAATT 59.073 55.000 6.77 0.00 0.00 1.40
268 270 2.634100 GGAGGCCTTGTCCCCTAAT 58.366 57.895 6.77 0.00 0.00 1.73
282 284 4.394712 GGGCAGTGACGTGGGAGG 62.395 72.222 0.00 0.00 0.00 4.30
310 323 6.761242 CGGTATTTGTCTGTAGATTGATCCAA 59.239 38.462 0.00 0.00 0.00 3.53
318 331 3.431766 GGGCACGGTATTTGTCTGTAGAT 60.432 47.826 0.00 0.00 0.00 1.98
354 367 1.738030 GCTGGCACAAATCTCCAATGC 60.738 52.381 0.00 0.00 38.70 3.56
365 378 2.359726 TATGCGCTGCTGGCACAA 60.360 55.556 9.73 0.00 44.23 3.33
368 381 2.512286 GAGTATGCGCTGCTGGCA 60.512 61.111 9.73 4.73 45.71 4.92
370 383 2.590007 GGGAGTATGCGCTGCTGG 60.590 66.667 9.73 0.00 0.00 4.85
390 403 2.930777 ATCGAAGGGTCTAGCCGCCT 62.931 60.000 0.00 0.00 38.44 5.52
437 450 4.746535 AGCAATGGCATGATGATTTTGA 57.253 36.364 0.00 0.00 44.61 2.69
511 524 9.822727 TCCTAATTCCTACCTTTTGATTTTCTT 57.177 29.630 0.00 0.00 0.00 2.52
514 527 9.025041 CACTCCTAATTCCTACCTTTTGATTTT 57.975 33.333 0.00 0.00 0.00 1.82
524 537 6.786967 TCTTGTACACTCCTAATTCCTACC 57.213 41.667 0.00 0.00 0.00 3.18
565 578 7.332182 GTCAAAGACAACTCCTTAGAATGGTAG 59.668 40.741 0.00 0.00 32.09 3.18
567 580 5.998363 GTCAAAGACAACTCCTTAGAATGGT 59.002 40.000 0.00 0.00 32.09 3.55
580 593 5.353123 TGTGTAGGAACAAGTCAAAGACAAC 59.647 40.000 0.00 0.00 37.36 3.32
611 624 3.619929 CACATCGCATCACTCAAATCTCA 59.380 43.478 0.00 0.00 0.00 3.27
700 719 3.845781 ACAAGGATAGATGCATTCGGT 57.154 42.857 0.00 0.00 0.00 4.69
703 722 7.092716 ACACAAAAACAAGGATAGATGCATTC 58.907 34.615 0.00 0.00 0.00 2.67
721 740 9.541143 GGAGGATTTTCATAGAAAAACACAAAA 57.459 29.630 8.75 0.00 31.35 2.44
723 742 8.243961 TGGAGGATTTTCATAGAAAAACACAA 57.756 30.769 8.75 0.00 31.35 3.33
749 772 1.428912 TCTCCAGGTTTGGCCTCATTT 59.571 47.619 3.32 0.00 46.96 2.32
764 787 5.809001 AGCAAGTTGAGACAATTATCTCCA 58.191 37.500 11.17 0.00 43.94 3.86
765 788 6.749923 AAGCAAGTTGAGACAATTATCTCC 57.250 37.500 11.17 0.00 43.94 3.71
767 790 7.094463 CCTGAAAGCAAGTTGAGACAATTATCT 60.094 37.037 7.16 0.00 0.00 1.98
768 791 7.025963 CCTGAAAGCAAGTTGAGACAATTATC 58.974 38.462 7.16 0.00 0.00 1.75
769 792 6.071728 CCCTGAAAGCAAGTTGAGACAATTAT 60.072 38.462 7.16 0.00 0.00 1.28
770 793 5.241506 CCCTGAAAGCAAGTTGAGACAATTA 59.758 40.000 7.16 0.00 0.00 1.40
771 794 4.038402 CCCTGAAAGCAAGTTGAGACAATT 59.962 41.667 7.16 0.00 0.00 2.32
772 795 3.571401 CCCTGAAAGCAAGTTGAGACAAT 59.429 43.478 7.16 0.00 0.00 2.71
773 796 2.951642 CCCTGAAAGCAAGTTGAGACAA 59.048 45.455 7.16 0.00 0.00 3.18
774 797 2.092429 ACCCTGAAAGCAAGTTGAGACA 60.092 45.455 7.16 0.10 0.00 3.41
775 798 2.291741 CACCCTGAAAGCAAGTTGAGAC 59.708 50.000 7.16 0.00 0.00 3.36
783 806 1.110442 CCACAACACCCTGAAAGCAA 58.890 50.000 0.00 0.00 0.00 3.91
791 814 0.106217 CCAAAGACCCACAACACCCT 60.106 55.000 0.00 0.00 0.00 4.34
858 889 4.081642 GGATGACACTGCTACCAAGTTCTA 60.082 45.833 0.00 0.00 0.00 2.10
991 1030 2.492088 GGTAGGTTTTCATTCTGGTGGC 59.508 50.000 0.00 0.00 0.00 5.01
1214 1256 4.951963 CCTCGCTCGCCCCGATTC 62.952 72.222 0.00 0.00 34.61 2.52
1254 1299 4.821589 GGCGCCTCCGGAGAGTTG 62.822 72.222 33.39 16.83 38.58 3.16
1440 1488 4.280019 AAGTTGGGGTCGGTGGCC 62.280 66.667 0.00 0.00 0.00 5.36
1579 1627 3.274586 CGGGATGTGGATGCGCTG 61.275 66.667 9.73 0.00 0.00 5.18
1789 1837 1.303561 AGTGGCCGTGCACATGATT 60.304 52.632 18.64 0.00 0.00 2.57
1791 1839 2.669229 CAGTGGCCGTGCACATGA 60.669 61.111 18.64 0.00 0.00 3.07
2198 2246 5.005740 TGCTATGCATTTCAACAGTCTTCT 58.994 37.500 3.54 0.00 31.71 2.85
2283 2331 4.618912 AGAATGATCGCATCGTTATCTTCG 59.381 41.667 4.30 0.00 38.56 3.79
2297 2345 5.776744 TGTCATCCACATAGAGAATGATCG 58.223 41.667 0.00 0.00 39.07 3.69
2304 2352 2.432146 GGCACTGTCATCCACATAGAGA 59.568 50.000 0.00 0.00 33.23 3.10
2388 2436 7.174946 GGATAGAAACTTGTGAAAGGATGACAA 59.825 37.037 0.00 0.00 0.00 3.18
2403 2451 4.772886 ATTACCTGGCGGATAGAAACTT 57.227 40.909 0.00 0.00 0.00 2.66
2592 2644 5.906113 TTCAAACTTGCCAACTGACTTAA 57.094 34.783 0.00 0.00 0.00 1.85
2747 2800 3.241530 ACGCACCAGCAGAAGGGA 61.242 61.111 0.00 0.00 42.27 4.20
2803 2858 3.359695 TTGAATAAAAGGACCCCGAGG 57.640 47.619 0.00 0.00 40.04 4.63
2810 2865 9.561270 GTCTAGCAGAAAATTGAATAAAAGGAC 57.439 33.333 0.00 0.00 0.00 3.85
2854 4001 4.652421 TGTCATGTCAAGCAAACAACAT 57.348 36.364 0.00 0.00 32.73 2.71
2898 4045 8.794335 AGAAGAAGAAAACATGTCCTATAACC 57.206 34.615 0.00 0.00 0.00 2.85
2916 4063 6.372659 TGCAGAATTTAGCTACCAAGAAGAAG 59.627 38.462 0.00 0.00 0.00 2.85
2939 4090 4.150804 GCATACTTAGCTACCTTCGAATGC 59.849 45.833 0.00 1.38 0.00 3.56
3023 4176 5.047306 TGTTATCACTCACTCCTTACAGTGG 60.047 44.000 0.00 0.00 43.59 4.00
3024 4177 5.864474 GTGTTATCACTCACTCCTTACAGTG 59.136 44.000 0.00 0.00 40.98 3.66
3032 4185 9.817809 TTTTATAGATGTGTTATCACTCACTCC 57.182 33.333 5.57 0.00 44.14 3.85
3071 4227 6.174451 ACAATGAGACAATCAGAAACATCG 57.826 37.500 0.00 0.00 42.53 3.84
3081 4257 6.432472 AGAGAAAAGGGAACAATGAGACAATC 59.568 38.462 0.00 0.00 0.00 2.67
3096 4272 4.699257 CAGAGACAAATGGAGAGAAAAGGG 59.301 45.833 0.00 0.00 0.00 3.95
3119 4296 8.668353 TCAGACAATTAAGAACTGTTATGATGC 58.332 33.333 0.00 0.00 0.00 3.91
3129 4306 8.317679 AGCATAGAAGTCAGACAATTAAGAACT 58.682 33.333 2.66 0.00 0.00 3.01
3133 4310 8.715191 AGAAGCATAGAAGTCAGACAATTAAG 57.285 34.615 2.66 0.00 0.00 1.85
3134 4311 9.809096 CTAGAAGCATAGAAGTCAGACAATTAA 57.191 33.333 2.66 0.00 0.00 1.40
3149 4327 6.528537 AGATGGCTATGTCTAGAAGCATAG 57.471 41.667 19.21 19.21 44.31 2.23
3255 4441 6.782986 TCATTTATATACTTGCTGCATCCCT 58.217 36.000 1.84 0.00 0.00 4.20
3283 4474 4.035558 CCACATTACATCACATGCTGTACC 59.964 45.833 0.00 0.00 0.00 3.34
3304 4495 6.666546 CGGGAGGGAGTATATACTATTTTCCA 59.333 42.308 23.17 0.00 36.50 3.53
3308 4500 6.193504 GGACGGGAGGGAGTATATACTATTT 58.806 44.000 15.42 4.05 36.50 1.40
3317 4509 1.164313 TATGGGACGGGAGGGAGTAT 58.836 55.000 0.00 0.00 0.00 2.12
3320 4512 0.687354 CATTATGGGACGGGAGGGAG 59.313 60.000 0.00 0.00 0.00 4.30
3322 4514 1.724545 TACATTATGGGACGGGAGGG 58.275 55.000 0.00 0.00 0.00 4.30
3323 4515 4.081642 CACTATACATTATGGGACGGGAGG 60.082 50.000 0.00 0.00 0.00 4.30
3324 4516 4.527038 ACACTATACATTATGGGACGGGAG 59.473 45.833 0.00 0.00 0.00 4.30
3325 4517 4.485875 ACACTATACATTATGGGACGGGA 58.514 43.478 0.00 0.00 0.00 5.14
3326 4518 4.884668 ACACTATACATTATGGGACGGG 57.115 45.455 0.00 0.00 0.00 5.28
3327 4519 8.665643 TTTTAACACTATACATTATGGGACGG 57.334 34.615 0.00 0.00 0.00 4.79
3351 4543 5.427481 TCCGTCCCATAATCTAAGACCTTTT 59.573 40.000 0.00 0.00 0.00 2.27
3352 4544 4.966805 TCCGTCCCATAATCTAAGACCTTT 59.033 41.667 0.00 0.00 0.00 3.11
3353 4545 4.553678 TCCGTCCCATAATCTAAGACCTT 58.446 43.478 0.00 0.00 0.00 3.50
3354 4546 4.153411 CTCCGTCCCATAATCTAAGACCT 58.847 47.826 0.00 0.00 0.00 3.85
3355 4547 3.258622 CCTCCGTCCCATAATCTAAGACC 59.741 52.174 0.00 0.00 0.00 3.85
3356 4548 3.258622 CCCTCCGTCCCATAATCTAAGAC 59.741 52.174 0.00 0.00 0.00 3.01
3357 4549 3.141460 TCCCTCCGTCCCATAATCTAAGA 59.859 47.826 0.00 0.00 0.00 2.10
3358 4550 3.507411 TCCCTCCGTCCCATAATCTAAG 58.493 50.000 0.00 0.00 0.00 2.18
3359 4551 3.116862 ACTCCCTCCGTCCCATAATCTAA 60.117 47.826 0.00 0.00 0.00 2.10
3361 4553 1.220750 ACTCCCTCCGTCCCATAATCT 59.779 52.381 0.00 0.00 0.00 2.40
3362 4554 1.718280 ACTCCCTCCGTCCCATAATC 58.282 55.000 0.00 0.00 0.00 1.75
3363 4555 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3364 4556 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3365 4557 2.969950 CAAATACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
3366 4558 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
3367 4559 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
3368 4560 1.201424 ACAAATACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
3369 4561 3.703052 TCTTACAAATACTCCCTCCGTCC 59.297 47.826 0.00 0.00 0.00 4.79
3370 4562 4.996788 TCTTACAAATACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
3371 4563 4.715297 ACATCTTACAAATACTCCCTCCGT 59.285 41.667 0.00 0.00 0.00 4.69
3372 4564 5.277857 ACATCTTACAAATACTCCCTCCG 57.722 43.478 0.00 0.00 0.00 4.63
3373 4565 8.019656 TCTTACATCTTACAAATACTCCCTCC 57.980 38.462 0.00 0.00 0.00 4.30
3374 4566 9.699703 GATCTTACATCTTACAAATACTCCCTC 57.300 37.037 0.00 0.00 0.00 4.30
3376 4568 9.832445 TTGATCTTACATCTTACAAATACTCCC 57.168 33.333 0.00 0.00 0.00 4.30
3433 4632 3.226777 CCCACATACAAACAGGGAAACA 58.773 45.455 0.00 0.00 42.25 2.83
3606 5399 8.575649 TGATCTCACATCTTACAACTACAGTA 57.424 34.615 0.00 0.00 0.00 2.74
3607 5400 7.468141 TGATCTCACATCTTACAACTACAGT 57.532 36.000 0.00 0.00 0.00 3.55
3608 5401 8.939201 AATGATCTCACATCTTACAACTACAG 57.061 34.615 0.00 0.00 0.00 2.74
3609 5402 9.154847 CAAATGATCTCACATCTTACAACTACA 57.845 33.333 0.00 0.00 0.00 2.74
3610 5403 8.607459 CCAAATGATCTCACATCTTACAACTAC 58.393 37.037 0.00 0.00 0.00 2.73
3657 5450 2.095869 CAGCTGCATTGAGTTCAGTCAC 60.096 50.000 0.00 0.00 0.00 3.67
3690 5483 1.760527 CCAGTCACACCATCCCACA 59.239 57.895 0.00 0.00 0.00 4.17
3709 5502 8.715191 AACATATTGATCTTGACTCTGTCTTC 57.285 34.615 0.00 0.00 33.15 2.87
3743 5536 1.798223 CGCTCGACAAAATCCAACTCA 59.202 47.619 0.00 0.00 0.00 3.41
3773 5566 3.089838 CCATGGCAAGGACCCTCA 58.910 61.111 1.66 0.00 0.00 3.86
3787 5580 1.170919 GGAGCGCTCATTCATGCCAT 61.171 55.000 36.27 0.00 0.00 4.40
3788 5581 1.820906 GGAGCGCTCATTCATGCCA 60.821 57.895 36.27 0.00 0.00 4.92
3795 5588 2.094659 CAACGACGGAGCGCTCATT 61.095 57.895 36.27 23.41 33.86 2.57
3797 5590 4.717629 CCAACGACGGAGCGCTCA 62.718 66.667 36.27 0.00 33.86 4.26
3819 5612 0.523966 CTCGACACAGTCCAGGAGAC 59.476 60.000 0.00 0.00 46.71 3.36
3822 5615 0.959553 GTTCTCGACACAGTCCAGGA 59.040 55.000 0.00 0.00 0.00 3.86
3823 5616 0.387367 CGTTCTCGACACAGTCCAGG 60.387 60.000 0.00 0.00 39.71 4.45
3824 5617 1.004277 GCGTTCTCGACACAGTCCAG 61.004 60.000 0.00 0.00 39.71 3.86
3825 5618 1.007734 GCGTTCTCGACACAGTCCA 60.008 57.895 0.00 0.00 39.71 4.02
3862 5655 5.255687 ACACATTATCAGCATTGGTGAGAA 58.744 37.500 23.35 23.35 43.48 2.87
3865 5658 5.981088 AAACACATTATCAGCATTGGTGA 57.019 34.783 19.85 19.85 44.17 4.02
3867 5660 9.723601 AATTTTAAACACATTATCAGCATTGGT 57.276 25.926 0.00 0.00 0.00 3.67
3964 5774 3.512516 GCGAAGGGAGGCACATGC 61.513 66.667 0.00 0.00 41.14 4.06
3965 5775 2.825836 GGCGAAGGGAGGCACATG 60.826 66.667 0.00 0.00 0.00 3.21
3966 5776 2.142292 AAAGGCGAAGGGAGGCACAT 62.142 55.000 0.00 0.00 36.55 3.21
3967 5777 2.351924 AAAAGGCGAAGGGAGGCACA 62.352 55.000 0.00 0.00 36.55 4.57
3968 5778 1.587043 GAAAAGGCGAAGGGAGGCAC 61.587 60.000 0.00 0.00 36.55 5.01
3969 5779 1.303317 GAAAAGGCGAAGGGAGGCA 60.303 57.895 0.00 0.00 36.55 4.75
3970 5780 1.002011 AGAAAAGGCGAAGGGAGGC 60.002 57.895 0.00 0.00 0.00 4.70
3971 5781 0.615850 AGAGAAAAGGCGAAGGGAGG 59.384 55.000 0.00 0.00 0.00 4.30
3972 5782 2.079925 CAAGAGAAAAGGCGAAGGGAG 58.920 52.381 0.00 0.00 0.00 4.30
3973 5783 1.882352 GCAAGAGAAAAGGCGAAGGGA 60.882 52.381 0.00 0.00 0.00 4.20
3974 5784 0.523519 GCAAGAGAAAAGGCGAAGGG 59.476 55.000 0.00 0.00 0.00 3.95
3975 5785 1.238439 TGCAAGAGAAAAGGCGAAGG 58.762 50.000 0.00 0.00 0.00 3.46
3976 5786 3.354089 TTTGCAAGAGAAAAGGCGAAG 57.646 42.857 0.00 0.00 0.00 3.79
3977 5787 3.641648 CATTTGCAAGAGAAAAGGCGAA 58.358 40.909 0.00 0.00 34.42 4.70
3978 5788 2.607771 GCATTTGCAAGAGAAAAGGCGA 60.608 45.455 0.00 0.00 39.93 5.54
3979 5789 1.723003 GCATTTGCAAGAGAAAAGGCG 59.277 47.619 0.00 0.00 39.93 5.52
3981 5791 4.247267 TCAGCATTTGCAAGAGAAAAGG 57.753 40.909 5.20 0.00 45.16 3.11
3982 5792 7.544566 ACATTATCAGCATTTGCAAGAGAAAAG 59.455 33.333 5.20 6.15 45.16 2.27
3983 5793 7.329962 CACATTATCAGCATTTGCAAGAGAAAA 59.670 33.333 5.20 0.56 45.16 2.29
3984 5794 6.809689 CACATTATCAGCATTTGCAAGAGAAA 59.190 34.615 5.20 2.66 45.16 2.52
3985 5795 6.071784 ACACATTATCAGCATTTGCAAGAGAA 60.072 34.615 5.20 6.45 45.16 2.87
3986 5796 5.416639 ACACATTATCAGCATTTGCAAGAGA 59.583 36.000 5.20 0.00 45.16 3.10
3987 5797 5.647589 ACACATTATCAGCATTTGCAAGAG 58.352 37.500 5.20 0.00 45.16 2.85
3988 5798 5.648178 ACACATTATCAGCATTTGCAAGA 57.352 34.783 5.20 2.92 45.16 3.02
3989 5799 6.715344 AAACACATTATCAGCATTTGCAAG 57.285 33.333 5.20 0.00 45.16 4.01
3990 5800 7.600960 TCTAAACACATTATCAGCATTTGCAA 58.399 30.769 5.20 0.00 45.16 4.08
3991 5801 7.155655 TCTAAACACATTATCAGCATTTGCA 57.844 32.000 5.20 0.00 45.16 4.08
3992 5802 8.537223 CATTCTAAACACATTATCAGCATTTGC 58.463 33.333 0.00 0.00 42.49 3.68
3993 5803 9.791820 TCATTCTAAACACATTATCAGCATTTG 57.208 29.630 0.00 0.00 0.00 2.32
3997 5807 9.844790 CTTTTCATTCTAAACACATTATCAGCA 57.155 29.630 0.00 0.00 0.00 4.41
3998 5808 9.846248 ACTTTTCATTCTAAACACATTATCAGC 57.154 29.630 0.00 0.00 0.00 4.26
4038 5848 9.585369 TGGGCATGTATAAATAATTCTTCATCA 57.415 29.630 0.00 0.00 0.00 3.07
4042 5852 9.696917 CCTTTGGGCATGTATAAATAATTCTTC 57.303 33.333 0.00 0.00 0.00 2.87
4043 5853 8.650490 CCCTTTGGGCATGTATAAATAATTCTT 58.350 33.333 0.00 0.00 35.35 2.52
4044 5854 8.193953 CCCTTTGGGCATGTATAAATAATTCT 57.806 34.615 0.00 0.00 35.35 2.40
4074 5884 3.633065 GACTCTCTGTAAAGGCTACGGAT 59.367 47.826 0.00 0.00 32.94 4.18
4075 5885 3.015327 GACTCTCTGTAAAGGCTACGGA 58.985 50.000 0.00 0.00 0.00 4.69
4077 5887 3.190744 TGTGACTCTCTGTAAAGGCTACG 59.809 47.826 0.00 0.00 0.00 3.51
4078 5888 4.785511 TGTGACTCTCTGTAAAGGCTAC 57.214 45.455 0.00 0.00 0.00 3.58
4079 5889 4.833380 ACTTGTGACTCTCTGTAAAGGCTA 59.167 41.667 0.00 0.00 0.00 3.93
4080 5890 3.643792 ACTTGTGACTCTCTGTAAAGGCT 59.356 43.478 0.00 0.00 0.00 4.58
4089 5899 3.462021 GTTGCTTCACTTGTGACTCTCT 58.538 45.455 2.62 0.00 0.00 3.10
4090 5900 2.219674 CGTTGCTTCACTTGTGACTCTC 59.780 50.000 2.62 0.00 0.00 3.20
4101 5911 1.664965 AGGAGTCGCGTTGCTTCAC 60.665 57.895 5.77 0.00 0.00 3.18
4110 5920 3.197790 CATTGGGCAGGAGTCGCG 61.198 66.667 0.00 0.00 0.00 5.87
4117 5927 1.094785 CTAAACCGTCATTGGGCAGG 58.905 55.000 0.00 0.00 0.00 4.85
4118 5928 1.737793 GTCTAAACCGTCATTGGGCAG 59.262 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.