Multiple sequence alignment - TraesCS6A01G279200

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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 TraesCS6A01G279200 chr6A 100.000 7106 0 0 1 7106 506646358 506639253 0.000000e+00 13123
1 TraesCS6A01G279200 chr6D 96.415 3180 85 14 932 4091 365849487 365846317 0.000000e+00 5214
2 TraesCS6A01G279200 chr6D 95.731 2881 75 20 4081 6923 365845516 365842646 0.000000e+00 4595
3 TraesCS6A01G279200 chr6D 91.636 538 43 2 1 536 365850755 365850218 0.000000e+00 743
4 TraesCS6A01G279200 chr6D 89.235 353 36 2 3178 3530 267533165 267532815 2.350000e-119 440
5 TraesCS6A01G279200 chr6D 96.067 178 4 1 697 871 365850134 365849957 3.240000e-73 287
6 TraesCS6A01G279200 chr6B 95.660 3180 117 7 933 4091 551980372 551977193 0.000000e+00 5088
7 TraesCS6A01G279200 chr6B 96.409 2785 75 13 4081 6856 551976697 551973929 0.000000e+00 4566
8 TraesCS6A01G279200 chr6B 89.045 639 63 6 1 634 551984467 551983831 0.000000e+00 785
9 TraesCS6A01G279200 chr6B 93.993 283 10 7 662 943 551980906 551980630 8.520000e-114 422
10 TraesCS6A01G279200 chr6B 91.892 148 9 2 508 652 551986830 551986683 3.360000e-48 204
11 TraesCS6A01G279200 chr3B 90.449 356 30 4 3177 3531 71401512 71401864 3.880000e-127 466
12 TraesCS6A01G279200 chr3B 89.356 357 31 6 3178 3530 694031267 694031620 6.540000e-120 442
13 TraesCS6A01G279200 chr3B 86.555 119 15 1 3013 3131 812340466 812340349 5.780000e-26 130
14 TraesCS6A01G279200 chr5A 90.028 351 29 6 3178 3527 9842865 9843210 3.910000e-122 449
15 TraesCS6A01G279200 chr5A 88.158 152 16 2 6956 7106 656675631 656675481 5.660000e-41 180
16 TraesCS6A01G279200 chr2D 89.235 353 34 4 3178 3530 380416879 380416531 8.460000e-119 438
17 TraesCS6A01G279200 chr2D 90.066 151 13 2 6957 7106 72159573 72159722 2.020000e-45 195
18 TraesCS6A01G279200 chr2D 92.233 103 7 1 3016 3118 340262181 340262080 2.070000e-30 145
19 TraesCS6A01G279200 chr5D 88.983 354 36 3 3178 3530 360542210 360541859 1.090000e-117 435
20 TraesCS6A01G279200 chr5D 88.128 219 24 2 5033 5250 479457133 479456916 7.070000e-65 259
21 TraesCS6A01G279200 chr5D 89.262 149 13 3 6960 7106 478597505 478597358 4.380000e-42 183
22 TraesCS6A01G279200 chr1A 87.500 368 42 4 3178 3545 477661044 477660681 8.520000e-114 422
23 TraesCS6A01G279200 chr1A 90.909 110 10 0 3017 3126 334203607 334203716 1.600000e-31 148
24 TraesCS6A01G279200 chr5B 88.073 218 26 0 5033 5250 587125089 587124872 7.070000e-65 259
25 TraesCS6A01G279200 chr3A 90.260 154 12 3 6955 7106 521554444 521554596 1.560000e-46 198
26 TraesCS6A01G279200 chr3A 88.816 152 14 3 6957 7106 623608320 623608470 4.380000e-42 183
27 TraesCS6A01G279200 chr3D 88.742 151 15 2 6957 7106 434949469 434949618 4.380000e-42 183
28 TraesCS6A01G279200 chr3D 85.950 121 17 0 3004 3124 73896335 73896455 5.780000e-26 130
29 TraesCS6A01G279200 chr3D 83.607 122 15 5 2818 2935 157038399 157038519 7.540000e-20 110
30 TraesCS6A01G279200 chr1B 88.816 152 14 3 6957 7106 86778509 86778659 4.380000e-42 183
31 TraesCS6A01G279200 chr1B 90.351 114 10 1 3013 3126 151093183 151093071 1.600000e-31 148
32 TraesCS6A01G279200 chr7D 88.514 148 15 2 6960 7106 568468323 568468177 2.040000e-40 178
33 TraesCS6A01G279200 chr4D 87.742 155 16 3 6954 7106 499679740 499679893 2.040000e-40 178
34 TraesCS6A01G279200 chr1D 91.228 114 9 1 3013 3126 100458982 100459094 3.430000e-33 154
35 TraesCS6A01G279200 chrUn 88.496 113 12 1 3011 3123 3061873 3061984 1.240000e-27 135


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 TraesCS6A01G279200 chr6A 506639253 506646358 7105 True 13123.00 13123 100.00000 1 7106 1 chr6A.!!$R1 7105
1 TraesCS6A01G279200 chr6D 365842646 365850755 8109 True 2709.75 5214 94.96225 1 6923 4 chr6D.!!$R2 6922
2 TraesCS6A01G279200 chr6B 551973929 551986830 12901 True 2213.00 5088 93.39980 1 6856 5 chr6B.!!$R1 6855

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
600 2972 0.099613 CCACTCGTCGTCATCAGAGG 59.900 60.000 0.00 0.0 35.22 3.69 F
671 5940 1.846007 ACCGCCATGCTTAAAATCCA 58.154 45.000 0.00 0.0 0.00 3.41 F
1783 7482 2.134287 AGGCACAGACTGGACACGT 61.134 57.895 7.51 0.0 0.00 4.49 F
2230 7932 2.541762 GGTGATAGATTGCTCGCAGAAC 59.458 50.000 0.00 0.0 34.09 3.01 F
3551 9260 1.696832 GATGCCGCCTCGTCAGTTTC 61.697 60.000 0.00 0.0 0.00 2.78 F
4207 10833 1.133356 CATCCCCTTCCCATCCCTTTC 60.133 57.143 0.00 0.0 0.00 2.62 F
5238 11874 1.693606 TGCTCTCCGAATATGGCATGA 59.306 47.619 10.98 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 7367 0.884704 GGAACAGAACAGCGCAAGGA 60.885 55.000 11.47 0.00 38.28 3.36 R
1814 7513 2.173519 TCCACCCTTTCACGGTACTAG 58.826 52.381 0.00 0.00 30.42 2.57 R
2906 8612 1.684450 CTGGTTTAAAAGCCCCACGTT 59.316 47.619 0.00 0.00 0.00 3.99 R
3934 9648 0.235926 GTGGCGACAGAACAAGAAGC 59.764 55.000 0.00 0.00 44.46 3.86 R
5388 12026 1.992557 TCCCTGAAATTGGGCAGTACT 59.007 47.619 0.00 0.00 44.23 2.73 R
5858 12507 1.493446 GGGTCCCCAGTTATAACCAGG 59.507 57.143 12.05 13.61 35.81 4.45 R
6948 13608 0.899720 ACGGAGGGAATAAACGAGCA 59.100 50.000 0.00 0.00 0.00 4.26 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
23 2387 6.761731 GTGATCAGAAACCTATTCTCATCG 57.238 41.667 0.00 0.00 29.98 3.84
77 2442 1.278985 AGATCGGACCAAGTGCATTCA 59.721 47.619 0.00 0.00 0.00 2.57
105 2470 0.527565 TACGCGTAGGTGGGTTTCTC 59.472 55.000 16.41 0.00 36.35 2.87
130 2495 0.930726 TCAACTTCCCCACCACCTTT 59.069 50.000 0.00 0.00 0.00 3.11
163 2528 4.202567 ACTCCCACTTTGCCAAAATCTCTA 60.203 41.667 0.00 0.00 0.00 2.43
167 2532 4.520492 CCACTTTGCCAAAATCTCTACACT 59.480 41.667 0.00 0.00 0.00 3.55
171 2536 2.301870 TGCCAAAATCTCTACACTCGGT 59.698 45.455 0.00 0.00 0.00 4.69
195 2560 1.002773 GACCCCCTTCTTCTACGCAAA 59.997 52.381 0.00 0.00 0.00 3.68
208 2573 2.010817 CGCAAACGCCAGTTTCAGC 61.011 57.895 0.00 0.00 46.73 4.26
246 2613 3.054948 CACCCCATCCGTACTCCTTTTTA 60.055 47.826 0.00 0.00 0.00 1.52
278 2645 8.877195 TGTAGTCCAAAACTCTATCTAGGTTTT 58.123 33.333 0.00 0.00 41.77 2.43
308 2675 5.023533 ACGATCACATACTTTAGCCACAT 57.976 39.130 0.00 0.00 0.00 3.21
315 2682 4.457603 ACATACTTTAGCCACATGCGAAAA 59.542 37.500 0.00 0.00 42.79 2.29
320 2687 3.389741 GCCACATGCGAAAAGTCTG 57.610 52.632 0.00 0.00 0.00 3.51
329 2696 1.484356 CGAAAAGTCTGGAACGACGT 58.516 50.000 0.00 0.00 37.07 4.34
419 2786 7.072961 ACCAAAGGGACATATCAAGACTATCAT 59.927 37.037 0.00 0.00 38.05 2.45
458 2825 0.660595 AACAAGAGCAGTCGACGACG 60.661 55.000 21.44 16.80 37.67 5.12
482 2849 3.127030 CGATCAAACTTGGAAACCTAGCC 59.873 47.826 0.00 0.00 29.74 3.93
485 2852 2.180432 AACTTGGAAACCTAGCCGAC 57.820 50.000 0.00 0.00 29.74 4.79
500 2867 1.952133 CGACGCACCCGAGTTTTCA 60.952 57.895 0.00 0.00 38.29 2.69
546 2915 4.816385 TCCACTTGTTGTCATCAGAGTTTC 59.184 41.667 0.00 0.00 0.00 2.78
553 2922 4.535526 TGTCATCAGAGTTTCGATGGAA 57.464 40.909 0.00 0.00 39.60 3.53
600 2972 0.099613 CCACTCGTCGTCATCAGAGG 59.900 60.000 0.00 0.00 35.22 3.69
640 3012 5.918011 TCGCCATCTTGATGTTTTTACAAAC 59.082 36.000 9.41 0.00 42.49 2.93
658 3030 4.279671 ACAAACAGAAATGATAAACCGCCA 59.720 37.500 0.00 0.00 0.00 5.69
660 3032 4.637483 ACAGAAATGATAAACCGCCATG 57.363 40.909 0.00 0.00 0.00 3.66
665 5934 5.359576 AGAAATGATAAACCGCCATGCTTAA 59.640 36.000 0.00 0.00 0.00 1.85
671 5940 1.846007 ACCGCCATGCTTAAAATCCA 58.154 45.000 0.00 0.00 0.00 3.41
675 5944 3.368323 CCGCCATGCTTAAAATCCAAACT 60.368 43.478 0.00 0.00 0.00 2.66
682 5951 6.150396 TGCTTAAAATCCAAACTTCCGAAA 57.850 33.333 0.00 0.00 0.00 3.46
683 5952 5.980715 TGCTTAAAATCCAAACTTCCGAAAC 59.019 36.000 0.00 0.00 0.00 2.78
685 5954 6.700081 GCTTAAAATCCAAACTTCCGAAACTT 59.300 34.615 0.00 0.00 0.00 2.66
686 5955 7.863877 GCTTAAAATCCAAACTTCCGAAACTTA 59.136 33.333 0.00 0.00 0.00 2.24
687 5956 9.177304 CTTAAAATCCAAACTTCCGAAACTTAC 57.823 33.333 0.00 0.00 0.00 2.34
688 5957 5.700722 AATCCAAACTTCCGAAACTTACC 57.299 39.130 0.00 0.00 0.00 2.85
692 5961 2.180432 ACTTCCGAAACTTACCAGGC 57.820 50.000 0.00 0.00 0.00 4.85
730 5999 7.091443 CCTACTAGTGACTTCCAAAACAGTAG 58.909 42.308 5.39 7.57 40.18 2.57
928 6218 4.150454 CCCCTCCCTCTCTCCGCT 62.150 72.222 0.00 0.00 0.00 5.52
929 6219 2.520741 CCCTCCCTCTCTCCGCTC 60.521 72.222 0.00 0.00 0.00 5.03
930 6220 2.520741 CCTCCCTCTCTCCGCTCC 60.521 72.222 0.00 0.00 0.00 4.70
931 6221 2.600731 CTCCCTCTCTCCGCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
1293 6974 4.760047 GCCATGAGCCACGACGGT 62.760 66.667 0.00 0.00 36.97 4.83
1399 7098 3.068691 CGAGGGCGGAGGTGAAGA 61.069 66.667 0.00 0.00 0.00 2.87
1783 7482 2.134287 AGGCACAGACTGGACACGT 61.134 57.895 7.51 0.00 0.00 4.49
1814 7513 6.145338 TCCCGATACTACAGAGTGATTTTC 57.855 41.667 0.00 0.00 36.28 2.29
1829 7528 6.164176 AGTGATTTTCTAGTACCGTGAAAGG 58.836 40.000 0.00 0.00 32.36 3.11
1957 7657 6.825213 TGCTCATCTTCTATTGTAAATGCTGT 59.175 34.615 0.00 0.00 0.00 4.40
2103 7805 6.469139 TTTCAGCGATACATGTTAAACGAA 57.531 33.333 2.30 0.00 0.00 3.85
2203 7905 8.237267 GTGTCTTGGTCATTTCGAATTTTCTAT 58.763 33.333 0.00 0.00 0.00 1.98
2230 7932 2.541762 GGTGATAGATTGCTCGCAGAAC 59.458 50.000 0.00 0.00 34.09 3.01
2325 8027 9.365906 TCTTGAAACAATATTATGGCATATGGT 57.634 29.630 8.24 0.00 0.00 3.55
2509 8212 9.683069 GCTTCTTTTTCATTTCATAGAAACTGA 57.317 29.630 0.00 0.00 33.82 3.41
2724 8427 3.555956 GCATGTAGCGTTAGTATGCTGTT 59.444 43.478 16.28 0.00 46.01 3.16
2728 8431 5.104374 TGTAGCGTTAGTATGCTGTTTACC 58.896 41.667 7.48 0.00 46.01 2.85
2816 8519 8.402472 ACAAATTGTATGTCATAAACGGTATGG 58.598 33.333 0.00 0.00 0.00 2.74
2902 8608 6.655003 ACGTTGATCAAATTGTCAATCTAGGT 59.345 34.615 10.35 5.99 36.79 3.08
2925 8631 1.777941 AACGTGGGGCTTTTAAACCA 58.222 45.000 0.00 0.00 0.00 3.67
2944 8650 3.072622 ACCAGAAAGGAAGTAGAACCACC 59.927 47.826 0.00 0.00 41.22 4.61
2955 8661 7.037514 AGGAAGTAGAACCACCTAATTAGCTTT 60.038 37.037 6.99 0.00 28.51 3.51
3046 8752 6.413783 TCTGTCCCATATTAATTGACGCTA 57.586 37.500 0.00 0.00 0.00 4.26
3128 8834 4.931661 TGTGACGGAGGGAGTATTTATC 57.068 45.455 0.00 0.00 0.00 1.75
3185 8891 5.316327 GAGATGCCATCTCGTGATATACA 57.684 43.478 18.33 0.00 45.50 2.29
3373 9079 2.684374 GGAGTCCGTAAAGAGAGACCTC 59.316 54.545 0.00 0.00 39.72 3.85
3392 9098 3.493350 CCTCAAGGACTGGAATATCACCG 60.493 52.174 0.00 0.00 37.39 4.94
3400 9106 5.823045 GGACTGGAATATCACCGAAGATTTT 59.177 40.000 0.00 0.00 0.00 1.82
3413 9119 2.905415 AGATTTTGCCATGGACAGGA 57.095 45.000 18.40 6.03 0.00 3.86
3551 9260 1.696832 GATGCCGCCTCGTCAGTTTC 61.697 60.000 0.00 0.00 0.00 2.78
4111 10737 3.256879 CAGAGTGAGGCTAACAGAACTCA 59.743 47.826 4.46 0.00 37.18 3.41
4122 10748 6.472486 GGCTAACAGAACTCAAAACAAACTTC 59.528 38.462 0.00 0.00 0.00 3.01
4207 10833 1.133356 CATCCCCTTCCCATCCCTTTC 60.133 57.143 0.00 0.00 0.00 2.62
4212 10838 2.357569 CCCTTCCCATCCCTTTCTTCAG 60.358 54.545 0.00 0.00 0.00 3.02
4259 10885 3.626028 AAGCGACAACCAAATTCTGAC 57.374 42.857 0.00 0.00 0.00 3.51
4416 11050 7.360438 GCCTTTAAGATATCTAACATTGCCGAG 60.360 40.741 5.46 0.00 0.00 4.63
4641 11275 8.353423 ACTTGCACATACTTTGATTTTCCTAT 57.647 30.769 0.00 0.00 0.00 2.57
5052 11687 5.212194 TCGTTTTAAAGTGCAAGCAGAATC 58.788 37.500 0.00 0.00 0.00 2.52
5128 11764 4.183865 TGTTGCCTATGTTCAAGAGATCG 58.816 43.478 0.00 0.00 0.00 3.69
5238 11874 1.693606 TGCTCTCCGAATATGGCATGA 59.306 47.619 10.98 0.00 0.00 3.07
5269 11905 2.558359 GACAACTTGACCCCTGAAATGG 59.442 50.000 0.00 0.00 0.00 3.16
5332 11970 7.844779 AGGACCTTATAGTAGGATTGAACTTGA 59.155 37.037 0.00 0.00 38.73 3.02
5518 12161 8.734218 TTAATAAGGTGGTGCACGAATATTAA 57.266 30.769 19.90 19.90 34.83 1.40
5858 12507 1.520342 GTCTGATCCTGCTGGACGC 60.520 63.158 15.36 10.59 46.51 5.19
5979 12628 4.964593 TGGGTACTTCCTCAACTTAACAC 58.035 43.478 0.00 0.00 36.25 3.32
6015 12664 1.980765 TCTCAGGTGATCAACTTGCCT 59.019 47.619 11.57 2.86 35.87 4.75
6081 12730 1.137404 CCAGCTATTTGTGCGTGCC 59.863 57.895 0.00 0.00 35.28 5.01
6109 12758 1.623811 GGCACCCGGACATGTAGATAT 59.376 52.381 0.73 0.00 0.00 1.63
6136 12785 5.496556 TCCTGTTCACTTCAGTTTTCTTCA 58.503 37.500 0.00 0.00 0.00 3.02
6394 13043 8.101654 TGGTACACATAAATTAGTTGGTTCAC 57.898 34.615 0.00 0.00 0.00 3.18
6415 13064 9.952188 GTTCACTCCTGGATTTTAATATTTAGC 57.048 33.333 0.00 0.00 0.00 3.09
6477 13126 6.321181 AGAAACAACACAAAGCTGGAAATAGA 59.679 34.615 0.00 0.00 0.00 1.98
6629 13280 7.601073 TGAGTAGCACTGTTCATTAATCTTG 57.399 36.000 0.00 0.00 0.00 3.02
6654 13305 4.100963 TGGTTGCTGTCTCAAGAAAGTCTA 59.899 41.667 0.00 0.00 31.96 2.59
6656 13307 5.121454 GGTTGCTGTCTCAAGAAAGTCTATG 59.879 44.000 0.00 0.00 31.96 2.23
6657 13308 5.728637 TGCTGTCTCAAGAAAGTCTATGA 57.271 39.130 0.00 0.00 31.96 2.15
6659 13310 6.705302 TGCTGTCTCAAGAAAGTCTATGAAT 58.295 36.000 0.00 0.00 31.96 2.57
6661 13312 8.481314 TGCTGTCTCAAGAAAGTCTATGAATAT 58.519 33.333 0.00 0.00 31.96 1.28
6662 13313 8.977505 GCTGTCTCAAGAAAGTCTATGAATATC 58.022 37.037 0.00 0.00 31.96 1.63
6663 13314 9.474920 CTGTCTCAAGAAAGTCTATGAATATCC 57.525 37.037 0.00 0.00 0.00 2.59
6664 13315 8.138074 TGTCTCAAGAAAGTCTATGAATATCCG 58.862 37.037 0.00 0.00 0.00 4.18
6665 13316 7.115663 GTCTCAAGAAAGTCTATGAATATCCGC 59.884 40.741 0.00 0.00 0.00 5.54
6756 13407 5.798434 GGTAGCAACCAAAAGCGTTAAATAG 59.202 40.000 0.00 0.00 45.98 1.73
6799 13450 7.826252 TGAGAGGTTGAGGAAATTAGAAATCTG 59.174 37.037 0.00 0.00 0.00 2.90
6881 13541 5.286438 GGACTAAAAGTTTTTGCGGATTGT 58.714 37.500 6.10 0.00 0.00 2.71
6882 13542 5.174943 GGACTAAAAGTTTTTGCGGATTGTG 59.825 40.000 6.10 0.00 0.00 3.33
6892 13552 7.440856 AGTTTTTGCGGATTGTGACATATTTTT 59.559 29.630 0.00 0.00 0.00 1.94
6918 13578 0.690077 AATGGTACTCCCTCCGTCCC 60.690 60.000 0.00 0.00 0.00 4.46
6923 13583 2.169330 GTACTCCCTCCGTCCCATATC 58.831 57.143 0.00 0.00 0.00 1.63
6924 13584 0.178929 ACTCCCTCCGTCCCATATCC 60.179 60.000 0.00 0.00 0.00 2.59
6925 13585 0.115349 CTCCCTCCGTCCCATATCCT 59.885 60.000 0.00 0.00 0.00 3.24
6926 13586 1.358103 CTCCCTCCGTCCCATATCCTA 59.642 57.143 0.00 0.00 0.00 2.94
6927 13587 1.076677 TCCCTCCGTCCCATATCCTAC 59.923 57.143 0.00 0.00 0.00 3.18
6928 13588 1.077334 CCCTCCGTCCCATATCCTACT 59.923 57.143 0.00 0.00 0.00 2.57
6929 13589 2.492940 CCCTCCGTCCCATATCCTACTT 60.493 54.545 0.00 0.00 0.00 2.24
6930 13590 2.563179 CCTCCGTCCCATATCCTACTTG 59.437 54.545 0.00 0.00 0.00 3.16
6931 13591 3.231818 CTCCGTCCCATATCCTACTTGT 58.768 50.000 0.00 0.00 0.00 3.16
6932 13592 4.404640 CTCCGTCCCATATCCTACTTGTA 58.595 47.826 0.00 0.00 0.00 2.41
6933 13593 4.147321 TCCGTCCCATATCCTACTTGTAC 58.853 47.826 0.00 0.00 0.00 2.90
6934 13594 3.257624 CCGTCCCATATCCTACTTGTACC 59.742 52.174 0.00 0.00 0.00 3.34
6935 13595 3.257624 CGTCCCATATCCTACTTGTACCC 59.742 52.174 0.00 0.00 0.00 3.69
6936 13596 4.490706 GTCCCATATCCTACTTGTACCCT 58.509 47.826 0.00 0.00 0.00 4.34
6937 13597 5.648247 GTCCCATATCCTACTTGTACCCTA 58.352 45.833 0.00 0.00 0.00 3.53
6938 13598 6.262207 GTCCCATATCCTACTTGTACCCTAT 58.738 44.000 0.00 0.00 0.00 2.57
6939 13599 6.380560 GTCCCATATCCTACTTGTACCCTATC 59.619 46.154 0.00 0.00 0.00 2.08
6940 13600 6.279682 TCCCATATCCTACTTGTACCCTATCT 59.720 42.308 0.00 0.00 0.00 1.98
6941 13601 7.466539 TCCCATATCCTACTTGTACCCTATCTA 59.533 40.741 0.00 0.00 0.00 1.98
6942 13602 7.560626 CCCATATCCTACTTGTACCCTATCTAC 59.439 44.444 0.00 0.00 0.00 2.59
6943 13603 8.114102 CCATATCCTACTTGTACCCTATCTACA 58.886 40.741 0.00 0.00 0.00 2.74
6944 13604 9.179909 CATATCCTACTTGTACCCTATCTACAG 57.820 40.741 0.00 0.00 0.00 2.74
6945 13605 6.836714 TCCTACTTGTACCCTATCTACAGA 57.163 41.667 0.00 0.00 0.00 3.41
6946 13606 6.839454 TCCTACTTGTACCCTATCTACAGAG 58.161 44.000 0.00 0.00 0.00 3.35
6947 13607 6.389278 TCCTACTTGTACCCTATCTACAGAGT 59.611 42.308 0.00 0.00 0.00 3.24
6948 13608 7.061688 CCTACTTGTACCCTATCTACAGAGTT 58.938 42.308 0.00 0.00 0.00 3.01
6949 13609 6.777213 ACTTGTACCCTATCTACAGAGTTG 57.223 41.667 0.00 0.00 0.00 3.16
6950 13610 5.127356 ACTTGTACCCTATCTACAGAGTTGC 59.873 44.000 0.00 0.00 0.00 4.17
6951 13611 4.868268 TGTACCCTATCTACAGAGTTGCT 58.132 43.478 0.00 0.00 0.00 3.91
6952 13612 4.888239 TGTACCCTATCTACAGAGTTGCTC 59.112 45.833 0.00 0.00 0.00 4.26
6953 13613 2.952978 ACCCTATCTACAGAGTTGCTCG 59.047 50.000 0.00 0.00 35.36 5.03
6954 13614 2.952978 CCCTATCTACAGAGTTGCTCGT 59.047 50.000 0.00 0.00 35.36 4.18
6955 13615 3.381908 CCCTATCTACAGAGTTGCTCGTT 59.618 47.826 0.00 0.00 35.36 3.85
6956 13616 4.142138 CCCTATCTACAGAGTTGCTCGTTT 60.142 45.833 0.00 0.00 35.36 3.60
6957 13617 5.067413 CCCTATCTACAGAGTTGCTCGTTTA 59.933 44.000 0.00 0.00 35.36 2.01
6958 13618 6.239064 CCCTATCTACAGAGTTGCTCGTTTAT 60.239 42.308 0.00 0.00 35.36 1.40
6959 13619 7.203910 CCTATCTACAGAGTTGCTCGTTTATT 58.796 38.462 0.00 0.00 35.36 1.40
6960 13620 7.380065 CCTATCTACAGAGTTGCTCGTTTATTC 59.620 40.741 0.00 0.00 35.36 1.75
6961 13621 5.408356 TCTACAGAGTTGCTCGTTTATTCC 58.592 41.667 0.00 0.00 35.36 3.01
6962 13622 3.335579 ACAGAGTTGCTCGTTTATTCCC 58.664 45.455 0.00 0.00 35.36 3.97
6963 13623 3.008049 ACAGAGTTGCTCGTTTATTCCCT 59.992 43.478 0.00 0.00 35.36 4.20
6964 13624 3.619038 CAGAGTTGCTCGTTTATTCCCTC 59.381 47.826 0.00 0.00 35.36 4.30
6965 13625 2.937149 GAGTTGCTCGTTTATTCCCTCC 59.063 50.000 0.00 0.00 0.00 4.30
6966 13626 1.664151 GTTGCTCGTTTATTCCCTCCG 59.336 52.381 0.00 0.00 0.00 4.63
6967 13627 0.899720 TGCTCGTTTATTCCCTCCGT 59.100 50.000 0.00 0.00 0.00 4.69
6968 13628 1.134907 TGCTCGTTTATTCCCTCCGTC 60.135 52.381 0.00 0.00 0.00 4.79
6969 13629 1.136500 GCTCGTTTATTCCCTCCGTCT 59.864 52.381 0.00 0.00 0.00 4.18
6970 13630 2.810650 CTCGTTTATTCCCTCCGTCTG 58.189 52.381 0.00 0.00 0.00 3.51
6971 13631 1.479323 TCGTTTATTCCCTCCGTCTGG 59.521 52.381 0.00 0.00 0.00 3.86
6972 13632 1.206371 CGTTTATTCCCTCCGTCTGGT 59.794 52.381 0.00 0.00 36.30 4.00
6973 13633 2.428171 CGTTTATTCCCTCCGTCTGGTA 59.572 50.000 0.00 0.00 36.30 3.25
6974 13634 3.119029 CGTTTATTCCCTCCGTCTGGTAA 60.119 47.826 0.00 0.00 36.30 2.85
6975 13635 4.621274 CGTTTATTCCCTCCGTCTGGTAAA 60.621 45.833 0.00 0.00 36.30 2.01
6976 13636 4.748277 TTATTCCCTCCGTCTGGTAAAG 57.252 45.455 0.00 0.00 36.30 1.85
6977 13637 2.314071 TTCCCTCCGTCTGGTAAAGA 57.686 50.000 0.00 0.00 36.30 2.52
6978 13638 1.848652 TCCCTCCGTCTGGTAAAGAG 58.151 55.000 0.00 0.00 34.84 2.85
6979 13639 1.076677 TCCCTCCGTCTGGTAAAGAGT 59.923 52.381 0.00 0.00 34.84 3.24
6980 13640 1.204941 CCCTCCGTCTGGTAAAGAGTG 59.795 57.143 0.00 0.00 34.84 3.51
6981 13641 1.893801 CCTCCGTCTGGTAAAGAGTGT 59.106 52.381 0.00 0.00 34.84 3.55
6982 13642 3.087031 CCTCCGTCTGGTAAAGAGTGTA 58.913 50.000 0.00 0.00 34.84 2.90
6983 13643 3.119566 CCTCCGTCTGGTAAAGAGTGTAC 60.120 52.174 0.00 0.00 34.84 2.90
6984 13644 3.489355 TCCGTCTGGTAAAGAGTGTACA 58.511 45.455 0.00 0.00 34.84 2.90
6985 13645 4.084287 TCCGTCTGGTAAAGAGTGTACAT 58.916 43.478 0.00 0.00 34.84 2.29
6986 13646 4.157289 TCCGTCTGGTAAAGAGTGTACATC 59.843 45.833 0.00 0.00 34.84 3.06
6987 13647 4.158025 CCGTCTGGTAAAGAGTGTACATCT 59.842 45.833 0.00 0.27 34.84 2.90
6988 13648 5.356190 CCGTCTGGTAAAGAGTGTACATCTA 59.644 44.000 0.00 0.00 34.84 1.98
6989 13649 6.458478 CCGTCTGGTAAAGAGTGTACATCTAG 60.458 46.154 0.00 0.00 34.84 2.43
6990 13650 6.267070 GTCTGGTAAAGAGTGTACATCTAGC 58.733 44.000 0.00 0.55 34.84 3.42
6991 13651 6.095720 GTCTGGTAAAGAGTGTACATCTAGCT 59.904 42.308 0.00 0.00 34.84 3.32
6992 13652 6.663953 TCTGGTAAAGAGTGTACATCTAGCTT 59.336 38.462 0.00 0.00 0.00 3.74
6993 13653 7.178628 TCTGGTAAAGAGTGTACATCTAGCTTT 59.821 37.037 0.00 7.55 0.00 3.51
6994 13654 8.357290 TGGTAAAGAGTGTACATCTAGCTTTA 57.643 34.615 0.00 6.66 0.00 1.85
6995 13655 8.809066 TGGTAAAGAGTGTACATCTAGCTTTAA 58.191 33.333 0.00 0.00 30.88 1.52
6996 13656 9.649167 GGTAAAGAGTGTACATCTAGCTTTAAA 57.351 33.333 0.00 0.00 30.88 1.52
7030 13690 8.834749 ACAAAAGAGTGTACTTCTATCTTTCC 57.165 34.615 0.00 0.00 38.82 3.13
7031 13691 8.429641 ACAAAAGAGTGTACTTCTATCTTTCCA 58.570 33.333 0.00 0.00 38.82 3.53
7032 13692 9.273016 CAAAAGAGTGTACTTCTATCTTTCCAA 57.727 33.333 0.00 0.00 38.82 3.53
7034 13694 9.442047 AAAGAGTGTACTTCTATCTTTCCAATG 57.558 33.333 0.00 0.00 35.82 2.82
7035 13695 7.044798 AGAGTGTACTTCTATCTTTCCAATGC 58.955 38.462 0.00 0.00 0.00 3.56
7036 13696 6.711277 AGTGTACTTCTATCTTTCCAATGCA 58.289 36.000 0.00 0.00 0.00 3.96
7037 13697 6.595716 AGTGTACTTCTATCTTTCCAATGCAC 59.404 38.462 0.00 0.00 0.00 4.57
7038 13698 6.595716 GTGTACTTCTATCTTTCCAATGCACT 59.404 38.462 0.00 0.00 0.00 4.40
7039 13699 7.119846 GTGTACTTCTATCTTTCCAATGCACTT 59.880 37.037 0.00 0.00 0.00 3.16
7040 13700 7.665559 TGTACTTCTATCTTTCCAATGCACTTT 59.334 33.333 0.00 0.00 0.00 2.66
7041 13701 9.162764 GTACTTCTATCTTTCCAATGCACTTTA 57.837 33.333 0.00 0.00 0.00 1.85
7042 13702 8.635765 ACTTCTATCTTTCCAATGCACTTTAA 57.364 30.769 0.00 0.00 0.00 1.52
7043 13703 9.077885 ACTTCTATCTTTCCAATGCACTTTAAA 57.922 29.630 0.00 0.00 0.00 1.52
7044 13704 9.912634 CTTCTATCTTTCCAATGCACTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
7049 13709 8.415950 TCTTTCCAATGCACTTTAAAATAGGA 57.584 30.769 0.00 0.00 0.00 2.94
7050 13710 8.865090 TCTTTCCAATGCACTTTAAAATAGGAA 58.135 29.630 0.00 0.00 0.00 3.36
7051 13711 9.487790 CTTTCCAATGCACTTTAAAATAGGAAA 57.512 29.630 0.00 0.00 38.62 3.13
7052 13712 9.838339 TTTCCAATGCACTTTAAAATAGGAAAA 57.162 25.926 0.00 0.00 38.16 2.29
7053 13713 9.838339 TTCCAATGCACTTTAAAATAGGAAAAA 57.162 25.926 0.00 0.00 0.00 1.94
7086 13746 9.904198 TTCTTTATCACATGATAATCAAGACCA 57.096 29.630 13.68 0.65 43.93 4.02
7087 13747 9.904198 TCTTTATCACATGATAATCAAGACCAA 57.096 29.630 13.68 0.00 43.93 3.67
7092 13752 9.631257 ATCACATGATAATCAAGACCAATAACA 57.369 29.630 0.00 0.00 32.01 2.41
7093 13753 9.460019 TCACATGATAATCAAGACCAATAACAA 57.540 29.630 0.00 0.00 0.00 2.83
7101 13761 8.862325 AATCAAGACCAATAACAATCTACACA 57.138 30.769 0.00 0.00 0.00 3.72
7102 13762 9.466497 AATCAAGACCAATAACAATCTACACAT 57.534 29.630 0.00 0.00 0.00 3.21
7103 13763 8.267620 TCAAGACCAATAACAATCTACACATG 57.732 34.615 0.00 0.00 0.00 3.21
7104 13764 7.336679 TCAAGACCAATAACAATCTACACATGG 59.663 37.037 0.00 0.00 0.00 3.66
7105 13765 6.721318 AGACCAATAACAATCTACACATGGT 58.279 36.000 0.00 0.00 41.10 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 2470 0.463833 GGTGGGGAAGTTGATAGCCG 60.464 60.000 0.00 0.00 0.00 5.52
130 2495 1.352622 AAGTGGGAGTGGTGGAAGCA 61.353 55.000 0.00 0.00 45.41 3.91
167 2532 1.057851 AAGAAGGGGGTCAACACCGA 61.058 55.000 0.00 0.00 44.91 4.69
171 2536 1.621814 CGTAGAAGAAGGGGGTCAACA 59.378 52.381 0.00 0.00 0.00 3.33
195 2560 2.594592 GTGGGCTGAAACTGGCGT 60.595 61.111 0.00 0.00 0.00 5.68
208 2573 2.046285 GTGGAAGGAATGCCGTGGG 61.046 63.158 0.00 0.00 39.96 4.61
278 2645 7.650504 GGCTAAAGTATGTGATCGTAATACACA 59.349 37.037 0.00 0.00 46.04 3.72
308 2675 1.214367 GTCGTTCCAGACTTTTCGCA 58.786 50.000 0.00 0.00 38.09 5.10
315 2682 1.830279 TCCATACGTCGTTCCAGACT 58.170 50.000 1.78 0.00 38.90 3.24
320 2687 4.743644 CCTAGAAAATCCATACGTCGTTCC 59.256 45.833 1.78 0.00 0.00 3.62
329 2696 5.883673 CCGTCAAAACCCTAGAAAATCCATA 59.116 40.000 0.00 0.00 0.00 2.74
366 2733 1.408405 CCCTGCTCGTAGTCTCCACTA 60.408 57.143 0.00 0.00 33.62 2.74
368 2735 0.680280 TCCCTGCTCGTAGTCTCCAC 60.680 60.000 0.00 0.00 0.00 4.02
419 2786 3.904800 TCTCATTAGCGATTGTTCCCA 57.095 42.857 0.00 0.00 0.00 4.37
426 2793 4.507710 TGCTCTTGTTCTCATTAGCGATT 58.492 39.130 0.00 0.00 35.68 3.34
458 2825 1.886542 AGGTTTCCAAGTTTGATCGCC 59.113 47.619 0.00 0.00 0.00 5.54
482 2849 1.289109 ATGAAAACTCGGGTGCGTCG 61.289 55.000 0.00 0.00 0.00 5.12
485 2852 1.396996 CCTAATGAAAACTCGGGTGCG 59.603 52.381 0.00 0.00 0.00 5.34
500 2867 6.791466 GGATAAGGTCCTTAAGGTACCCTAAT 59.209 42.308 26.65 20.47 44.16 1.73
523 2890 4.422073 AACTCTGATGACAACAAGTGGA 57.578 40.909 2.84 0.00 0.00 4.02
553 2922 2.575279 ACCAACATCAAGCTGGAGAGAT 59.425 45.455 0.00 0.00 36.93 2.75
600 2972 2.035321 TGGCGAAAAGTCCATCAAAACC 59.965 45.455 0.00 0.00 0.00 3.27
640 3012 3.067180 AGCATGGCGGTTTATCATTTCTG 59.933 43.478 0.00 0.00 0.00 3.02
641 3013 3.290710 AGCATGGCGGTTTATCATTTCT 58.709 40.909 0.00 0.00 0.00 2.52
642 3014 3.715628 AGCATGGCGGTTTATCATTTC 57.284 42.857 0.00 0.00 0.00 2.17
643 3015 5.590530 TTAAGCATGGCGGTTTATCATTT 57.409 34.783 0.00 0.00 36.52 2.32
645 3017 5.590530 TTTTAAGCATGGCGGTTTATCAT 57.409 34.783 0.00 0.00 36.52 2.45
647 3019 4.982295 GGATTTTAAGCATGGCGGTTTATC 59.018 41.667 0.00 0.00 36.52 1.75
648 3020 4.404073 TGGATTTTAAGCATGGCGGTTTAT 59.596 37.500 0.00 0.00 36.52 1.40
651 3023 2.175202 TGGATTTTAAGCATGGCGGTT 58.825 42.857 0.00 0.00 39.17 4.44
652 3024 1.846007 TGGATTTTAAGCATGGCGGT 58.154 45.000 0.00 0.00 0.00 5.68
655 3027 4.631377 GGAAGTTTGGATTTTAAGCATGGC 59.369 41.667 0.00 0.00 0.00 4.40
658 3030 5.975693 TCGGAAGTTTGGATTTTAAGCAT 57.024 34.783 0.00 0.00 0.00 3.79
660 3032 6.213677 AGTTTCGGAAGTTTGGATTTTAAGC 58.786 36.000 0.00 0.00 0.00 3.09
665 5934 5.595133 TGGTAAGTTTCGGAAGTTTGGATTT 59.405 36.000 0.89 0.00 31.14 2.17
671 5940 2.882761 GCCTGGTAAGTTTCGGAAGTTT 59.117 45.455 0.89 0.00 31.14 2.66
675 5944 1.002773 GGAGCCTGGTAAGTTTCGGAA 59.997 52.381 0.00 0.00 0.00 4.30
682 5951 4.717279 TTTGTAAAGGAGCCTGGTAAGT 57.283 40.909 0.00 0.00 0.00 2.24
683 5952 4.217767 GGTTTTGTAAAGGAGCCTGGTAAG 59.782 45.833 0.00 0.00 0.00 2.34
685 5954 3.396611 AGGTTTTGTAAAGGAGCCTGGTA 59.603 43.478 0.00 0.00 0.00 3.25
686 5955 2.177016 AGGTTTTGTAAAGGAGCCTGGT 59.823 45.455 0.00 0.00 0.00 4.00
687 5956 2.876581 AGGTTTTGTAAAGGAGCCTGG 58.123 47.619 0.00 0.00 0.00 4.45
688 5957 4.652822 AGTAGGTTTTGTAAAGGAGCCTG 58.347 43.478 0.00 0.00 0.00 4.85
692 5961 7.668492 AGTCACTAGTAGGTTTTGTAAAGGAG 58.332 38.462 1.45 0.00 0.00 3.69
1668 7367 0.884704 GGAACAGAACAGCGCAAGGA 60.885 55.000 11.47 0.00 38.28 3.36
1783 7482 2.889045 CTGTAGTATCGGGATTCGGGAA 59.111 50.000 0.00 0.00 39.77 3.97
1814 7513 2.173519 TCCACCCTTTCACGGTACTAG 58.826 52.381 0.00 0.00 30.42 2.57
1832 7531 2.224769 TGGAACATGTGGAGGAACTTCC 60.225 50.000 0.00 0.00 41.55 3.46
2103 7805 9.667989 GCAAAATTTAAATCTTTCACTGCAAAT 57.332 25.926 0.10 0.00 0.00 2.32
2203 7905 3.491619 GCGAGCAATCTATCACCTTCTCA 60.492 47.826 0.00 0.00 0.00 3.27
2230 7932 7.850982 GTGAGACAAGTACAACATGTAACAAAG 59.149 37.037 0.00 0.00 34.21 2.77
2267 7969 2.494627 CCCAGCTACCATAGTGGGGATA 60.495 54.545 12.28 0.00 43.37 2.59
2325 8027 6.647481 TCAGCGAGTAAATTTACAGTAAAGCA 59.353 34.615 26.06 7.85 36.12 3.91
2356 8059 9.726438 CTAGTAGGTTTTAATGGCATATAGCTT 57.274 33.333 0.00 0.00 44.79 3.74
2711 8414 5.128991 AGGAGGAGGTAAACAGCATACTAAC 59.871 44.000 0.00 0.00 0.00 2.34
2720 8423 2.354805 CCGGAAAGGAGGAGGTAAACAG 60.355 54.545 0.00 0.00 45.00 3.16
2724 8427 2.034436 AACCGGAAAGGAGGAGGTAA 57.966 50.000 9.46 0.00 45.00 2.85
2902 8608 5.075493 TGGTTTAAAAGCCCCACGTTTATA 58.925 37.500 0.00 0.00 33.17 0.98
2906 8612 1.684450 CTGGTTTAAAAGCCCCACGTT 59.316 47.619 0.00 0.00 0.00 3.99
2925 8631 6.954352 ATTAGGTGGTTCTACTTCCTTTCT 57.046 37.500 0.00 0.00 0.00 2.52
2944 8650 6.914757 GCAGCAACCAAGATAAAGCTAATTAG 59.085 38.462 8.20 8.20 0.00 1.73
2955 8661 3.119531 CCAAAATCGCAGCAACCAAGATA 60.120 43.478 0.00 0.00 0.00 1.98
3046 8752 5.339008 TCAGTGCTAGATACATCCGTTTT 57.661 39.130 0.00 0.00 0.00 2.43
3139 8845 9.109393 CTCACGAAATAAGGAAATTGAAGGATA 57.891 33.333 0.00 0.00 0.00 2.59
3185 8891 1.903877 CGCCACCCCAACTCTCTCAT 61.904 60.000 0.00 0.00 0.00 2.90
3303 9009 5.609423 GACCTCTCTTGACATTATCAGCAT 58.391 41.667 0.00 0.00 38.99 3.79
3373 9079 3.819564 TCGGTGATATTCCAGTCCTTG 57.180 47.619 0.00 0.00 0.00 3.61
3392 9098 3.091545 TCCTGTCCATGGCAAAATCTTC 58.908 45.455 6.96 0.00 0.00 2.87
3400 9106 2.352422 GCACTCCTGTCCATGGCA 59.648 61.111 6.96 7.80 0.00 4.92
3413 9119 2.159085 GGATAGCTAACTTCCACGCACT 60.159 50.000 6.95 0.00 0.00 4.40
3551 9260 7.328493 GTGTTTTTCTTCTTTTATTCCATCCGG 59.672 37.037 0.00 0.00 0.00 5.14
3924 9634 6.076981 ACAGAACAAGAAGCCAGTATTTTG 57.923 37.500 0.00 0.00 0.00 2.44
3934 9648 0.235926 GTGGCGACAGAACAAGAAGC 59.764 55.000 0.00 0.00 44.46 3.86
4111 10737 3.127895 TGTGTAGCTGCGAAGTTTGTTTT 59.872 39.130 0.00 0.00 0.00 2.43
4122 10748 1.713597 TCTGTGATTGTGTAGCTGCG 58.286 50.000 0.00 0.00 0.00 5.18
4172 10798 2.683362 GGGGATGAAATCTGTCGTTTCC 59.317 50.000 0.00 0.00 44.71 3.13
4367 11001 7.449704 AGGCATTCATTGAAATAGTTCCTATCC 59.550 37.037 2.68 0.00 32.28 2.59
4388 11022 7.094634 CGGCAATGTTAGATATCTTAAAGGCAT 60.095 37.037 11.25 0.00 0.00 4.40
4416 11050 2.035066 AGCAGGTGACAGCAAAACATTC 59.965 45.455 7.50 0.00 46.80 2.67
5052 11687 7.992180 AATGCAACTTCTTCACAGTAAAAAG 57.008 32.000 0.00 0.00 0.00 2.27
5128 11764 4.813697 GTCCATTCAGCAGGTAAGATTCTC 59.186 45.833 0.00 0.00 0.00 2.87
5238 11874 3.758554 GGGTCAAGTTGTCTATTGCATGT 59.241 43.478 2.11 0.00 0.00 3.21
5269 11905 9.521503 GATTTTCCTTATTAAATTGAGGAGTGC 57.478 33.333 0.00 0.00 39.33 4.40
5332 11970 5.197224 TCCAAATCCATGGATTCTTCTGT 57.803 39.130 34.67 18.80 44.52 3.41
5388 12026 1.992557 TCCCTGAAATTGGGCAGTACT 59.007 47.619 0.00 0.00 44.23 2.73
5491 12134 5.968528 ATTCGTGCACCACCTTATTAAAA 57.031 34.783 12.15 0.00 0.00 1.52
5858 12507 1.493446 GGGTCCCCAGTTATAACCAGG 59.507 57.143 12.05 13.61 35.81 4.45
5955 12604 5.237996 GTGTTAAGTTGAGGAAGTACCCAAC 59.762 44.000 0.00 0.00 43.51 3.77
6015 12664 5.417266 TGTTTGATGCGGATCAATCCTTAAA 59.583 36.000 29.41 12.70 45.91 1.52
6093 12742 3.525537 GATGCATATCTACATGTCCGGG 58.474 50.000 0.00 0.00 0.00 5.73
6109 12758 2.936919 ACTGAAGTGAACAGGATGCA 57.063 45.000 0.00 0.00 42.53 3.96
6394 13043 8.378172 TGTCGCTAAATATTAAAATCCAGGAG 57.622 34.615 0.00 0.00 0.00 3.69
6583 13234 2.678336 ACTCGAAAAATGAGGGAATCGC 59.322 45.455 0.00 0.00 37.79 4.58
6629 13280 3.378427 ACTTTCTTGAGACAGCAACCAAC 59.622 43.478 0.00 0.00 0.00 3.77
6654 13305 4.279145 AGTACCGGATAGCGGATATTCAT 58.721 43.478 9.46 0.00 0.00 2.57
6656 13307 4.715527 AAGTACCGGATAGCGGATATTC 57.284 45.455 9.46 0.00 0.00 1.75
6657 13308 4.525487 TGAAAGTACCGGATAGCGGATATT 59.475 41.667 9.46 0.00 0.00 1.28
6659 13310 3.489355 TGAAAGTACCGGATAGCGGATA 58.511 45.455 9.46 0.00 0.00 2.59
6661 13312 1.766494 TGAAAGTACCGGATAGCGGA 58.234 50.000 9.46 0.00 0.00 5.54
6662 13313 2.159142 AGTTGAAAGTACCGGATAGCGG 60.159 50.000 9.46 0.00 0.00 5.52
6663 13314 3.114065 GAGTTGAAAGTACCGGATAGCG 58.886 50.000 9.46 0.00 0.00 4.26
6664 13315 3.114065 CGAGTTGAAAGTACCGGATAGC 58.886 50.000 9.46 0.00 0.00 2.97
6665 13316 4.349501 GTCGAGTTGAAAGTACCGGATAG 58.650 47.826 9.46 0.00 0.00 2.08
6756 13407 6.410540 ACCTCTCAACATTAGACTTGATTCC 58.589 40.000 0.00 0.00 0.00 3.01
6831 13482 6.455360 TTTAGAATGTGCATTTCCCTCATC 57.545 37.500 8.30 0.00 0.00 2.92
6832 13483 6.855763 TTTTAGAATGTGCATTTCCCTCAT 57.144 33.333 8.30 0.00 0.00 2.90
6833 13484 6.404623 CGATTTTAGAATGTGCATTTCCCTCA 60.405 38.462 8.30 0.00 0.00 3.86
6892 13552 3.054948 CGGAGGGAGTACCATTTTACCAA 60.055 47.826 0.00 0.00 43.89 3.67
6903 13563 2.169330 GATATGGGACGGAGGGAGTAC 58.831 57.143 0.00 0.00 0.00 2.73
6918 13578 9.179909 CTGTAGATAGGGTACAAGTAGGATATG 57.820 40.741 0.00 0.00 30.04 1.78
6923 13583 6.603224 ACTCTGTAGATAGGGTACAAGTAGG 58.397 44.000 0.00 0.00 30.04 3.18
6924 13584 7.468906 GCAACTCTGTAGATAGGGTACAAGTAG 60.469 44.444 0.00 0.00 29.34 2.57
6925 13585 6.320672 GCAACTCTGTAGATAGGGTACAAGTA 59.679 42.308 0.00 0.00 29.34 2.24
6926 13586 5.127356 GCAACTCTGTAGATAGGGTACAAGT 59.873 44.000 0.00 0.00 29.34 3.16
6927 13587 5.361285 AGCAACTCTGTAGATAGGGTACAAG 59.639 44.000 0.00 0.00 29.34 3.16
6928 13588 5.269991 AGCAACTCTGTAGATAGGGTACAA 58.730 41.667 0.00 0.00 29.34 2.41
6929 13589 4.868268 AGCAACTCTGTAGATAGGGTACA 58.132 43.478 0.00 0.00 29.34 2.90
6930 13590 4.023878 CGAGCAACTCTGTAGATAGGGTAC 60.024 50.000 0.00 0.00 29.34 3.34
6931 13591 4.135306 CGAGCAACTCTGTAGATAGGGTA 58.865 47.826 0.00 0.00 29.34 3.69
6932 13592 2.952978 CGAGCAACTCTGTAGATAGGGT 59.047 50.000 0.00 0.00 31.16 4.34
6933 13593 2.952978 ACGAGCAACTCTGTAGATAGGG 59.047 50.000 0.00 0.00 0.00 3.53
6934 13594 4.640789 AACGAGCAACTCTGTAGATAGG 57.359 45.455 0.00 0.00 0.00 2.57
6935 13595 7.380065 GGAATAAACGAGCAACTCTGTAGATAG 59.620 40.741 0.00 0.00 0.00 2.08
6936 13596 7.201145 GGAATAAACGAGCAACTCTGTAGATA 58.799 38.462 0.00 0.00 0.00 1.98
6937 13597 6.043411 GGAATAAACGAGCAACTCTGTAGAT 58.957 40.000 0.00 0.00 0.00 1.98
6938 13598 5.408356 GGAATAAACGAGCAACTCTGTAGA 58.592 41.667 0.00 0.00 0.00 2.59
6939 13599 4.567159 GGGAATAAACGAGCAACTCTGTAG 59.433 45.833 0.00 0.00 0.00 2.74
6940 13600 4.222145 AGGGAATAAACGAGCAACTCTGTA 59.778 41.667 0.00 0.00 0.00 2.74
6941 13601 3.008049 AGGGAATAAACGAGCAACTCTGT 59.992 43.478 0.00 0.00 0.00 3.41
6942 13602 3.600388 AGGGAATAAACGAGCAACTCTG 58.400 45.455 0.00 0.00 0.00 3.35
6943 13603 3.369576 GGAGGGAATAAACGAGCAACTCT 60.370 47.826 0.00 0.00 0.00 3.24
6944 13604 2.937149 GGAGGGAATAAACGAGCAACTC 59.063 50.000 0.00 0.00 0.00 3.01
6945 13605 2.677037 CGGAGGGAATAAACGAGCAACT 60.677 50.000 0.00 0.00 0.00 3.16
6946 13606 1.664151 CGGAGGGAATAAACGAGCAAC 59.336 52.381 0.00 0.00 0.00 4.17
6947 13607 1.276989 ACGGAGGGAATAAACGAGCAA 59.723 47.619 0.00 0.00 0.00 3.91
6948 13608 0.899720 ACGGAGGGAATAAACGAGCA 59.100 50.000 0.00 0.00 0.00 4.26
6949 13609 1.136500 AGACGGAGGGAATAAACGAGC 59.864 52.381 0.00 0.00 0.00 5.03
6950 13610 2.481449 CCAGACGGAGGGAATAAACGAG 60.481 54.545 0.00 0.00 0.00 4.18
6951 13611 1.479323 CCAGACGGAGGGAATAAACGA 59.521 52.381 0.00 0.00 0.00 3.85
6952 13612 1.206371 ACCAGACGGAGGGAATAAACG 59.794 52.381 0.00 0.00 35.59 3.60
6953 13613 4.476628 TTACCAGACGGAGGGAATAAAC 57.523 45.455 0.00 0.00 35.59 2.01
6954 13614 4.778958 TCTTTACCAGACGGAGGGAATAAA 59.221 41.667 0.00 0.00 35.59 1.40
6955 13615 4.355549 TCTTTACCAGACGGAGGGAATAA 58.644 43.478 0.00 0.00 35.59 1.40
6956 13616 3.958798 CTCTTTACCAGACGGAGGGAATA 59.041 47.826 0.00 0.00 35.59 1.75
6957 13617 2.766828 CTCTTTACCAGACGGAGGGAAT 59.233 50.000 0.00 0.00 35.59 3.01
6958 13618 2.176889 CTCTTTACCAGACGGAGGGAA 58.823 52.381 0.00 0.00 35.59 3.97
6959 13619 1.076677 ACTCTTTACCAGACGGAGGGA 59.923 52.381 0.00 0.00 35.59 4.20
6960 13620 1.204941 CACTCTTTACCAGACGGAGGG 59.795 57.143 0.00 0.00 35.59 4.30
6961 13621 1.893801 ACACTCTTTACCAGACGGAGG 59.106 52.381 0.00 0.00 35.59 4.30
6962 13622 3.504906 TGTACACTCTTTACCAGACGGAG 59.495 47.826 0.00 0.00 35.59 4.63
6963 13623 3.489355 TGTACACTCTTTACCAGACGGA 58.511 45.455 0.00 0.00 35.59 4.69
6964 13624 3.928727 TGTACACTCTTTACCAGACGG 57.071 47.619 0.00 0.00 38.77 4.79
6965 13625 5.312120 AGATGTACACTCTTTACCAGACG 57.688 43.478 0.00 0.00 0.00 4.18
6966 13626 6.095720 AGCTAGATGTACACTCTTTACCAGAC 59.904 42.308 0.00 0.00 0.00 3.51
6967 13627 6.188407 AGCTAGATGTACACTCTTTACCAGA 58.812 40.000 0.00 0.00 0.00 3.86
6968 13628 6.458232 AGCTAGATGTACACTCTTTACCAG 57.542 41.667 0.00 0.00 0.00 4.00
6969 13629 6.852420 AAGCTAGATGTACACTCTTTACCA 57.148 37.500 0.00 0.00 0.00 3.25
6970 13630 9.649167 TTTAAAGCTAGATGTACACTCTTTACC 57.351 33.333 0.00 0.00 0.00 2.85
7004 13664 9.274206 GGAAAGATAGAAGTACACTCTTTTGTT 57.726 33.333 3.13 0.00 36.56 2.83
7005 13665 8.429641 TGGAAAGATAGAAGTACACTCTTTTGT 58.570 33.333 3.13 0.00 36.56 2.83
7006 13666 8.833231 TGGAAAGATAGAAGTACACTCTTTTG 57.167 34.615 3.13 0.00 36.56 2.44
7008 13668 9.442047 CATTGGAAAGATAGAAGTACACTCTTT 57.558 33.333 3.13 5.62 38.50 2.52
7009 13669 7.550906 GCATTGGAAAGATAGAAGTACACTCTT 59.449 37.037 3.13 0.00 0.00 2.85
7010 13670 7.044798 GCATTGGAAAGATAGAAGTACACTCT 58.955 38.462 0.00 0.00 0.00 3.24
7011 13671 6.818644 TGCATTGGAAAGATAGAAGTACACTC 59.181 38.462 0.00 0.00 0.00 3.51
7012 13672 6.595716 GTGCATTGGAAAGATAGAAGTACACT 59.404 38.462 0.00 0.00 0.00 3.55
7013 13673 6.595716 AGTGCATTGGAAAGATAGAAGTACAC 59.404 38.462 0.00 0.00 0.00 2.90
7014 13674 6.711277 AGTGCATTGGAAAGATAGAAGTACA 58.289 36.000 0.00 0.00 0.00 2.90
7015 13675 7.617041 AAGTGCATTGGAAAGATAGAAGTAC 57.383 36.000 0.00 0.00 0.00 2.73
7016 13676 9.733556 TTAAAGTGCATTGGAAAGATAGAAGTA 57.266 29.630 0.00 0.00 0.00 2.24
7017 13677 8.635765 TTAAAGTGCATTGGAAAGATAGAAGT 57.364 30.769 0.00 0.00 0.00 3.01
7018 13678 9.912634 TTTTAAAGTGCATTGGAAAGATAGAAG 57.087 29.630 0.00 0.00 0.00 2.85
7023 13683 9.034800 TCCTATTTTAAAGTGCATTGGAAAGAT 57.965 29.630 0.00 0.00 0.00 2.40
7024 13684 8.415950 TCCTATTTTAAAGTGCATTGGAAAGA 57.584 30.769 0.00 0.00 0.00 2.52
7025 13685 9.487790 TTTCCTATTTTAAAGTGCATTGGAAAG 57.512 29.630 15.97 0.00 36.34 2.62
7026 13686 9.838339 TTTTCCTATTTTAAAGTGCATTGGAAA 57.162 25.926 15.97 15.97 38.17 3.13
7027 13687 9.838339 TTTTTCCTATTTTAAAGTGCATTGGAA 57.162 25.926 8.53 8.53 31.33 3.53
7060 13720 9.904198 TGGTCTTGATTATCATGTGATAAAGAA 57.096 29.630 16.76 11.98 46.39 2.52
7061 13721 9.904198 TTGGTCTTGATTATCATGTGATAAAGA 57.096 29.630 16.76 12.93 46.39 2.52
7066 13726 9.631257 TGTTATTGGTCTTGATTATCATGTGAT 57.369 29.630 7.76 0.68 38.51 3.06
7067 13727 9.460019 TTGTTATTGGTCTTGATTATCATGTGA 57.540 29.630 7.76 0.00 0.00 3.58
7075 13735 9.952030 TGTGTAGATTGTTATTGGTCTTGATTA 57.048 29.630 0.00 0.00 0.00 1.75
7076 13736 8.862325 TGTGTAGATTGTTATTGGTCTTGATT 57.138 30.769 0.00 0.00 0.00 2.57
7077 13737 8.896744 CATGTGTAGATTGTTATTGGTCTTGAT 58.103 33.333 0.00 0.00 0.00 2.57
7078 13738 7.336679 CCATGTGTAGATTGTTATTGGTCTTGA 59.663 37.037 0.00 0.00 0.00 3.02
7079 13739 7.121168 ACCATGTGTAGATTGTTATTGGTCTTG 59.879 37.037 0.00 0.00 0.00 3.02
7080 13740 7.175104 ACCATGTGTAGATTGTTATTGGTCTT 58.825 34.615 0.00 0.00 0.00 3.01
7081 13741 6.721318 ACCATGTGTAGATTGTTATTGGTCT 58.279 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.