Multiple sequence alignment - TraesCS4B01G180100

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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 TraesCS4B01G180100 chr4B 100.000 6487 0 0 1 6487 394547071 394553557 0.000000e+00 11980.0
1 TraesCS4B01G180100 chr4B 97.500 40 1 0 5255 5294 394552290 394552329 1.170000e-07 69.4
2 TraesCS4B01G180100 chr4B 97.500 40 1 0 5220 5259 394552325 394552364 1.170000e-07 69.4
3 TraesCS4B01G180100 chr4D 95.078 4815 127 28 496 5259 317513147 317517902 0.000000e+00 7478.0
4 TraesCS4B01G180100 chr4D 91.425 723 53 6 5768 6485 317531916 317532634 0.000000e+00 983.0
5 TraesCS4B01G180100 chr4D 93.725 510 23 3 5264 5773 317517872 317518372 0.000000e+00 756.0
6 TraesCS4B01G180100 chr4D 86.028 501 59 5 1 492 441072730 441072232 1.600000e-145 527.0
7 TraesCS4B01G180100 chr4D 83.111 225 33 5 3711 3934 449830067 449829847 3.970000e-47 200.0
8 TraesCS4B01G180100 chr4A 94.147 2221 80 20 1212 3404 157336680 157334482 0.000000e+00 3336.0
9 TraesCS4B01G180100 chr4A 96.648 1820 43 7 3443 5258 157328960 157327155 0.000000e+00 3007.0
10 TraesCS4B01G180100 chr4A 89.291 1242 90 17 5265 6485 157327186 157325967 0.000000e+00 1517.0
11 TraesCS4B01G180100 chr4A 86.283 729 69 21 1 711 157338379 157337664 0.000000e+00 763.0
12 TraesCS4B01G180100 chr4A 93.684 475 14 2 705 1163 157337568 157337094 0.000000e+00 697.0
13 TraesCS4B01G180100 chrUn 82.609 506 49 14 185 657 109054955 109055454 1.680000e-110 411.0
14 TraesCS4B01G180100 chrUn 81.333 375 50 7 185 540 357022000 357021627 2.960000e-73 287.0
15 TraesCS4B01G180100 chr7D 82.766 441 44 11 253 661 547682235 547682675 1.330000e-96 364.0
16 TraesCS4B01G180100 chr5A 80.196 510 63 17 185 657 704089775 704089267 1.340000e-91 348.0
17 TraesCS4B01G180100 chr5A 80.196 510 63 12 185 657 704120320 704119812 1.340000e-91 348.0
18 TraesCS4B01G180100 chr5A 80.196 510 63 17 185 657 704198585 704198077 1.340000e-91 348.0
19 TraesCS4B01G180100 chr5A 80.000 510 64 12 185 657 704329338 704328830 6.230000e-90 342.0
20 TraesCS4B01G180100 chr5A 79.608 510 66 17 185 657 704241619 704241111 1.350000e-86 331.0
21 TraesCS4B01G180100 chr3B 92.683 41 3 0 5840 5880 420796903 420796863 7.020000e-05 60.2
22 TraesCS4B01G180100 chr2D 82.432 74 6 5 5728 5795 37088179 37088107 2.530000e-04 58.4


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 TraesCS4B01G180100 chr4B 394547071 394553557 6486 False 4039.600000 11980 98.333333 1 6487 3 chr4B.!!$F1 6486
1 TraesCS4B01G180100 chr4D 317513147 317518372 5225 False 4117.000000 7478 94.401500 496 5773 2 chr4D.!!$F2 5277
2 TraesCS4B01G180100 chr4D 317531916 317532634 718 False 983.000000 983 91.425000 5768 6485 1 chr4D.!!$F1 717
3 TraesCS4B01G180100 chr4A 157325967 157328960 2993 True 2262.000000 3007 92.969500 3443 6485 2 chr4A.!!$R1 3042
4 TraesCS4B01G180100 chr4A 157334482 157338379 3897 True 1598.666667 3336 91.371333 1 3404 3 chr4A.!!$R2 3403
5 TraesCS4B01G180100 chr5A 704089267 704089775 508 True 348.000000 348 80.196000 185 657 1 chr5A.!!$R1 472
6 TraesCS4B01G180100 chr5A 704119812 704120320 508 True 348.000000 348 80.196000 185 657 1 chr5A.!!$R2 472
7 TraesCS4B01G180100 chr5A 704198077 704198585 508 True 348.000000 348 80.196000 185 657 1 chr5A.!!$R3 472
8 TraesCS4B01G180100 chr5A 704328830 704329338 508 True 342.000000 342 80.000000 185 657 1 chr5A.!!$R5 472
9 TraesCS4B01G180100 chr5A 704241111 704241619 508 True 331.000000 331 79.608000 185 657 1 chr5A.!!$R4 472

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
891 1045 0.107800 GTAAACCGGAGAGGCCCTTC 60.108 60.000 9.46 0.00 46.52 3.46 F
2505 3064 0.178992 AAGTAGCTGGTGCAAAGCCA 60.179 50.000 16.85 6.69 41.82 4.75 F
3391 3961 0.822944 TACCCGCCAATCATGCATGG 60.823 55.000 25.97 13.30 39.80 3.66 F
3596 4166 1.085091 GAGCACCACTTCTCAGCATG 58.915 55.000 0.00 0.00 37.54 4.06 F
4421 4991 1.200020 GAGCGGGTGAAATGAGTTTGG 59.800 52.381 0.00 0.00 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 3275 2.346803 CAACCAGACAAGTATCCACGG 58.653 52.381 0.0 0.0 0.00 4.94 R
3596 4166 2.549926 CACCTGGAAACAAACAAAGCC 58.450 47.619 0.0 0.0 42.06 4.35 R
5254 5828 0.698818 ACATGGGGAAGAAGGTGGAC 59.301 55.000 0.0 0.0 0.00 4.02 R
5255 5829 2.352561 TACATGGGGAAGAAGGTGGA 57.647 50.000 0.0 0.0 0.00 4.02 R
5938 6528 0.109919 GTGGGATTTCAAACGTCCGC 60.110 55.000 0.0 0.0 32.71 5.54 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
32 34 2.281276 GGTTCCACCCGTGACCAC 60.281 66.667 0.00 0.00 30.38 4.16
60 62 8.601845 TGGTGGATTATTTCGACAGTTATATG 57.398 34.615 0.00 0.00 34.95 1.78
71 73 6.330278 TCGACAGTTATATGAAGTCTGTTGG 58.670 40.000 9.86 1.88 39.55 3.77
76 78 7.984050 ACAGTTATATGAAGTCTGTTGGAGATG 59.016 37.037 0.00 0.00 36.17 2.90
96 98 3.368495 TGCGTGCAAGTATAGTACATCG 58.632 45.455 0.59 0.00 0.00 3.84
98 100 3.549423 GCGTGCAAGTATAGTACATCGGA 60.549 47.826 0.59 0.00 0.00 4.55
99 101 4.603985 CGTGCAAGTATAGTACATCGGAA 58.396 43.478 0.00 0.00 0.00 4.30
102 104 6.345803 CGTGCAAGTATAGTACATCGGAAATG 60.346 42.308 0.00 0.00 0.00 2.32
104 106 6.700081 TGCAAGTATAGTACATCGGAAATGAC 59.300 38.462 0.00 0.00 0.00 3.06
119 121 5.478407 GGAAATGACCAAGGGTAAAATGTG 58.522 41.667 0.00 0.00 35.25 3.21
121 123 2.883026 TGACCAAGGGTAAAATGTGGG 58.117 47.619 0.00 0.00 35.25 4.61
125 127 4.154176 ACCAAGGGTAAAATGTGGGTTAC 58.846 43.478 0.00 0.00 32.11 2.50
126 128 4.140876 ACCAAGGGTAAAATGTGGGTTACT 60.141 41.667 0.00 0.00 32.11 2.24
127 129 4.219725 CCAAGGGTAAAATGTGGGTTACTG 59.780 45.833 0.00 0.00 32.03 2.74
128 130 5.074115 CAAGGGTAAAATGTGGGTTACTGA 58.926 41.667 0.00 0.00 32.03 3.41
129 131 4.659115 AGGGTAAAATGTGGGTTACTGAC 58.341 43.478 0.00 0.00 32.03 3.51
130 132 4.352893 AGGGTAAAATGTGGGTTACTGACT 59.647 41.667 0.00 0.00 32.03 3.41
132 134 4.457949 GGTAAAATGTGGGTTACTGACTGG 59.542 45.833 0.00 0.00 32.03 4.00
133 135 2.879103 AATGTGGGTTACTGACTGGG 57.121 50.000 0.00 0.00 0.00 4.45
134 136 1.742308 ATGTGGGTTACTGACTGGGT 58.258 50.000 0.00 0.00 0.00 4.51
153 155 4.147321 GGGTCGTACCATAAGTGAGGATA 58.853 47.826 6.41 0.00 41.02 2.59
158 160 5.533903 TCGTACCATAAGTGAGGATAACTCC 59.466 44.000 0.00 0.00 46.01 3.85
178 180 1.541588 CTGTTTCTAAGCCTTGGCCAC 59.458 52.381 3.88 0.00 0.00 5.01
208 210 4.260990 CCACTGATTACGTTGCACTTTCAA 60.261 41.667 0.00 0.00 0.00 2.69
229 231 6.247676 TCAATGGATGGATCTTTTTCAGTGA 58.752 36.000 0.00 0.00 0.00 3.41
238 240 3.218453 TCTTTTTCAGTGAAATCCGGCA 58.782 40.909 18.69 0.23 31.34 5.69
284 286 3.303495 CGACGACATGATGGTTCAGTTAC 59.697 47.826 0.00 0.00 34.73 2.50
295 297 3.636300 TGGTTCAGTTACTTTTGCAGCAT 59.364 39.130 0.00 0.00 0.00 3.79
298 300 6.030228 GGTTCAGTTACTTTTGCAGCATATC 58.970 40.000 0.00 0.00 0.00 1.63
300 302 5.175127 TCAGTTACTTTTGCAGCATATCGA 58.825 37.500 0.00 0.00 0.00 3.59
326 328 7.861176 TTATTTTCAATTGTTACGAAGCACC 57.139 32.000 5.13 0.00 0.00 5.01
390 406 6.653020 TGCTATACATCTTCCAGTCATTGTT 58.347 36.000 0.00 0.00 0.00 2.83
404 420 6.369005 CAGTCATTGTTCAATCTGACTCAAC 58.631 40.000 14.80 0.00 44.83 3.18
409 425 5.535753 TGTTCAATCTGACTCAACTGAGA 57.464 39.130 13.61 0.00 44.74 3.27
442 458 5.157770 TCTATCAGGGGATGGACTAGTTT 57.842 43.478 0.00 0.00 36.26 2.66
462 478 3.111853 TGTTCGGCATATGGTCATCTC 57.888 47.619 4.56 0.00 0.00 2.75
494 510 7.284261 TGAAATTAAGGAGTTGATGTGTGACAA 59.716 33.333 0.00 0.00 0.00 3.18
540 561 3.735237 TCAGAATAGAGTTGCCGATCC 57.265 47.619 0.00 0.00 0.00 3.36
575 596 1.660607 GTCGTATCGAGTGTACCACGA 59.339 52.381 8.16 8.16 39.64 4.35
577 598 1.394572 CGTATCGAGTGTACCACGACA 59.605 52.381 7.95 0.00 39.64 4.35
592 631 4.337274 ACCACGACACTATCATGTATCGAA 59.663 41.667 2.38 0.00 38.94 3.71
622 661 4.077108 TGGCTTTCGACTGTAACTCTCTA 58.923 43.478 0.00 0.00 0.00 2.43
629 668 9.193133 CTTTCGACTGTAACTCTCTAAATTTGA 57.807 33.333 0.00 0.00 0.00 2.69
891 1045 0.107800 GTAAACCGGAGAGGCCCTTC 60.108 60.000 9.46 0.00 46.52 3.46
932 1086 4.178540 CGCTTATTTTCTCTCGGTTACCA 58.821 43.478 1.13 0.00 0.00 3.25
951 1106 3.181412 ACCAAATTTTTGCCCTCCTCCTA 60.181 43.478 0.00 0.00 36.86 2.94
954 1109 0.326927 TTTTTGCCCTCCTCCTACGG 59.673 55.000 0.00 0.00 0.00 4.02
1062 1217 2.282958 TCGACCTCCTTCACGCCT 60.283 61.111 0.00 0.00 0.00 5.52
1153 1308 0.538287 GGTGCTTCCTGGAGCTTGTT 60.538 55.000 15.75 0.00 43.11 2.83
1215 1735 4.047059 CGGGCAAGCAAGTGCAGG 62.047 66.667 6.00 0.00 46.81 4.85
1300 1820 2.044123 ATTTCCTCACGGGATTCAGC 57.956 50.000 0.00 0.00 44.66 4.26
1306 1826 3.706373 ACGGGATTCAGCGGTGCT 61.706 61.111 10.38 0.00 40.77 4.40
1322 1842 4.320935 GCGGTGCTTTTTCTTATTTGAGGA 60.321 41.667 0.00 0.00 0.00 3.71
1328 1848 7.062255 GTGCTTTTTCTTATTTGAGGAATTCCG 59.938 37.037 18.82 2.20 42.08 4.30
1346 1866 5.414789 TTCCGAGATTGGTCAGTGAAATA 57.585 39.130 0.00 0.00 0.00 1.40
1357 1877 3.076621 TCAGTGAAATAGTTGCTGGCTG 58.923 45.455 0.00 0.00 0.00 4.85
1488 2008 3.926821 TGAAAACCGTGGCTAATTTCC 57.073 42.857 0.00 0.00 30.80 3.13
1513 2041 1.525995 GTGTGTGTGTGGTGGGGAG 60.526 63.158 0.00 0.00 0.00 4.30
1514 2042 2.113139 GTGTGTGTGGTGGGGAGG 59.887 66.667 0.00 0.00 0.00 4.30
1515 2043 3.174987 TGTGTGTGGTGGGGAGGG 61.175 66.667 0.00 0.00 0.00 4.30
1516 2044 3.966543 GTGTGTGGTGGGGAGGGG 61.967 72.222 0.00 0.00 0.00 4.79
1571 2099 9.057089 GTTTTGGAATGGTAGTATCTAATCTGG 57.943 37.037 0.00 0.00 0.00 3.86
1572 2100 6.935240 TGGAATGGTAGTATCTAATCTGGG 57.065 41.667 0.00 0.00 0.00 4.45
1573 2101 5.785423 TGGAATGGTAGTATCTAATCTGGGG 59.215 44.000 0.00 0.00 0.00 4.96
1574 2102 5.785940 GGAATGGTAGTATCTAATCTGGGGT 59.214 44.000 0.00 0.00 0.00 4.95
1683 2225 7.282585 TCTCTGTTGTATTCTTGGGGAATATG 58.717 38.462 0.00 0.00 45.25 1.78
1718 2260 4.511454 GTGATTCAGTGAGTGTGTGCTAAA 59.489 41.667 0.00 0.00 0.00 1.85
1913 2463 2.583593 CAGCGCGTCTAGAAGGCC 60.584 66.667 8.43 0.00 35.29 5.19
2031 2581 5.191522 TCTGGGACATTGATCATTGGAACTA 59.808 40.000 19.02 7.92 38.20 2.24
2504 3063 0.242017 CAAGTAGCTGGTGCAAAGCC 59.758 55.000 16.85 2.00 41.82 4.35
2505 3064 0.178992 AAGTAGCTGGTGCAAAGCCA 60.179 50.000 16.85 6.69 41.82 4.75
2559 3118 5.390991 GCTCAGGTTGCTTGTGAACTATAAC 60.391 44.000 0.00 0.00 0.00 1.89
2567 3126 6.631016 TGCTTGTGAACTATAACTCTCGATT 58.369 36.000 0.00 0.00 0.00 3.34
2713 3279 4.682787 TCTACTTGCATTCTGTATCCGTG 58.317 43.478 0.00 0.00 0.00 4.94
2745 3311 3.419943 TGGTTGCATTATTCTGCTGACA 58.580 40.909 0.00 0.00 42.75 3.58
2962 3532 3.257469 TCTAGGTCTGCTGATGCTTTG 57.743 47.619 0.00 0.00 40.48 2.77
2978 3548 7.946207 TGATGCTTTGGTATGTTGTTTTTCTA 58.054 30.769 0.00 0.00 0.00 2.10
3097 3667 7.756395 ATGCAAAATACTAGAAGCTGCATAT 57.244 32.000 16.65 0.00 44.76 1.78
3359 3929 8.049117 TCATCTTCCTTATAGCATTTTGTCTGT 58.951 33.333 0.00 0.00 0.00 3.41
3391 3961 0.822944 TACCCGCCAATCATGCATGG 60.823 55.000 25.97 13.30 39.80 3.66
3436 4006 7.736031 TCTAACGAGAATGTTTGACTATTCG 57.264 36.000 0.00 0.00 38.13 3.34
3596 4166 1.085091 GAGCACCACTTCTCAGCATG 58.915 55.000 0.00 0.00 37.54 4.06
3691 4261 3.855379 GTGTGTTCATTGCTGCATATGTG 59.145 43.478 1.84 0.86 0.00 3.21
3809 4379 4.024048 TGTTCTTTCTTTTCATCCGCAGAC 60.024 41.667 0.00 0.00 0.00 3.51
4415 4985 2.857483 TCAAAAGAGCGGGTGAAATGA 58.143 42.857 0.00 0.00 0.00 2.57
4421 4991 1.200020 GAGCGGGTGAAATGAGTTTGG 59.800 52.381 0.00 0.00 0.00 3.28
4482 5052 5.883661 CTTGAAGAAGCTGAAACAAGAACA 58.116 37.500 14.54 0.00 37.49 3.18
4621 5191 2.290705 ACAGGCTGGGTATTTGTGGTAC 60.291 50.000 20.34 0.00 0.00 3.34
4684 5254 2.304180 CCATCCCTACACATCCTGGATC 59.696 54.545 6.13 0.00 33.60 3.36
4925 5499 9.788960 GATCTATGAATATGCGACTAACACATA 57.211 33.333 0.00 0.00 0.00 2.29
4926 5500 8.965986 TCTATGAATATGCGACTAACACATAC 57.034 34.615 0.00 0.00 0.00 2.39
4927 5501 8.793592 TCTATGAATATGCGACTAACACATACT 58.206 33.333 0.00 0.00 0.00 2.12
4928 5502 9.411801 CTATGAATATGCGACTAACACATACTT 57.588 33.333 0.00 0.00 0.00 2.24
5229 5803 2.300723 TGTTGCGGTATGTACACCTTCT 59.699 45.455 0.00 0.00 36.35 2.85
5230 5804 3.244284 TGTTGCGGTATGTACACCTTCTT 60.244 43.478 0.00 0.00 36.35 2.52
5231 5805 3.241067 TGCGGTATGTACACCTTCTTC 57.759 47.619 0.00 0.00 36.35 2.87
5232 5806 2.093869 TGCGGTATGTACACCTTCTTCC 60.094 50.000 0.00 0.00 36.35 3.46
5233 5807 2.740904 GCGGTATGTACACCTTCTTCCC 60.741 54.545 0.00 0.00 36.35 3.97
5234 5808 2.159000 CGGTATGTACACCTTCTTCCCC 60.159 54.545 0.00 0.00 36.35 4.81
5235 5809 2.841881 GGTATGTACACCTTCTTCCCCA 59.158 50.000 0.00 0.00 35.55 4.96
5236 5810 3.458487 GGTATGTACACCTTCTTCCCCAT 59.542 47.826 0.00 0.00 35.55 4.00
5237 5811 3.652057 ATGTACACCTTCTTCCCCATG 57.348 47.619 0.00 0.00 0.00 3.66
5238 5812 2.344592 TGTACACCTTCTTCCCCATGT 58.655 47.619 0.00 0.00 0.00 3.21
5239 5813 3.522759 TGTACACCTTCTTCCCCATGTA 58.477 45.455 0.00 0.00 0.00 2.29
5240 5814 4.108570 TGTACACCTTCTTCCCCATGTAT 58.891 43.478 0.00 0.00 0.00 2.29
5241 5815 3.652057 ACACCTTCTTCCCCATGTATG 57.348 47.619 0.00 0.00 0.00 2.39
5243 5817 1.215423 ACCTTCTTCCCCATGTATGGC 59.785 52.381 5.35 0.00 46.70 4.40
5244 5818 1.215173 CCTTCTTCCCCATGTATGGCA 59.785 52.381 5.35 0.00 46.70 4.92
5245 5819 2.158415 CCTTCTTCCCCATGTATGGCAT 60.158 50.000 4.88 4.88 46.70 4.40
5246 5820 3.569491 CTTCTTCCCCATGTATGGCATT 58.431 45.455 4.78 0.00 46.70 3.56
5247 5821 2.948115 TCTTCCCCATGTATGGCATTG 58.052 47.619 4.78 0.00 46.70 2.82
5248 5822 2.513317 TCTTCCCCATGTATGGCATTGA 59.487 45.455 4.78 0.00 46.70 2.57
5249 5823 3.053019 TCTTCCCCATGTATGGCATTGAA 60.053 43.478 4.78 4.82 46.70 2.69
5250 5824 3.616343 TCCCCATGTATGGCATTGAAT 57.384 42.857 4.78 0.00 46.70 2.57
5251 5825 3.926198 TCCCCATGTATGGCATTGAATT 58.074 40.909 4.78 0.00 46.70 2.17
5252 5826 4.296912 TCCCCATGTATGGCATTGAATTT 58.703 39.130 4.78 0.00 46.70 1.82
5253 5827 5.462240 TCCCCATGTATGGCATTGAATTTA 58.538 37.500 4.78 0.00 46.70 1.40
5254 5828 5.539574 TCCCCATGTATGGCATTGAATTTAG 59.460 40.000 4.78 0.00 46.70 1.85
5255 5829 5.305128 CCCCATGTATGGCATTGAATTTAGT 59.695 40.000 4.78 0.00 46.70 2.24
5256 5830 6.449698 CCCATGTATGGCATTGAATTTAGTC 58.550 40.000 4.78 0.00 46.70 2.59
5257 5831 6.449698 CCATGTATGGCATTGAATTTAGTCC 58.550 40.000 4.78 0.00 41.75 3.85
5258 5832 6.040729 CCATGTATGGCATTGAATTTAGTCCA 59.959 38.462 4.78 0.00 41.75 4.02
5259 5833 6.449635 TGTATGGCATTGAATTTAGTCCAC 57.550 37.500 4.78 0.00 0.00 4.02
5260 5834 5.359576 TGTATGGCATTGAATTTAGTCCACC 59.640 40.000 4.78 0.00 0.00 4.61
5261 5835 4.046286 TGGCATTGAATTTAGTCCACCT 57.954 40.909 0.00 0.00 0.00 4.00
5262 5836 4.415596 TGGCATTGAATTTAGTCCACCTT 58.584 39.130 0.00 0.00 0.00 3.50
5263 5837 4.462483 TGGCATTGAATTTAGTCCACCTTC 59.538 41.667 0.00 0.00 0.00 3.46
5264 5838 4.706962 GGCATTGAATTTAGTCCACCTTCT 59.293 41.667 0.00 0.00 0.00 2.85
5265 5839 5.185828 GGCATTGAATTTAGTCCACCTTCTT 59.814 40.000 0.00 0.00 0.00 2.52
5266 5840 6.325596 GCATTGAATTTAGTCCACCTTCTTC 58.674 40.000 0.00 0.00 0.00 2.87
5300 5877 6.154192 TGGCATTGAATTTAGTCCATAAAGCA 59.846 34.615 0.00 0.00 36.81 3.91
5427 6004 5.883115 TCATACAATTTTGTCGCAGGGATTA 59.117 36.000 0.00 0.00 42.35 1.75
5465 6042 6.257411 CACTCTACTCTGTATCATTTGCCTTG 59.743 42.308 0.00 0.00 0.00 3.61
5541 6118 9.710818 AGTTATAGTCTAGGGTATCAACAAAGA 57.289 33.333 0.00 0.00 0.00 2.52
5557 6134 5.296813 ACAAAGATAGTTTGATTGTCGGC 57.703 39.130 4.55 0.00 33.83 5.54
5587 6176 0.673333 TCAACAGGCACACCGCATAG 60.673 55.000 0.00 0.00 45.17 2.23
5612 6201 2.614229 GCTTCTCTTTCACCCTGGACTC 60.614 54.545 0.00 0.00 0.00 3.36
5641 6230 3.936902 GTGCACACGTTTTAGTCTTGA 57.063 42.857 13.17 0.00 0.00 3.02
5642 6231 4.267357 GTGCACACGTTTTAGTCTTGAA 57.733 40.909 13.17 0.00 0.00 2.69
5643 6232 4.271687 GTGCACACGTTTTAGTCTTGAAG 58.728 43.478 13.17 0.00 0.00 3.02
5644 6233 4.033587 GTGCACACGTTTTAGTCTTGAAGA 59.966 41.667 13.17 0.00 0.00 2.87
5645 6234 4.270084 TGCACACGTTTTAGTCTTGAAGAG 59.730 41.667 0.00 0.00 0.00 2.85
5646 6235 4.270325 GCACACGTTTTAGTCTTGAAGAGT 59.730 41.667 7.77 7.77 0.00 3.24
5660 6249 7.492994 AGTCTTGAAGAGTTTGAAGAGTGTAAC 59.507 37.037 0.00 0.00 38.32 2.50
5699 6288 6.476378 CCAAGTGGGAATATGATAAGGGTAG 58.524 44.000 0.00 0.00 40.01 3.18
5709 6298 8.418597 AATATGATAAGGGTAGACACACGTAT 57.581 34.615 0.00 0.00 35.72 3.06
5710 6299 5.509716 TGATAAGGGTAGACACACGTATG 57.490 43.478 0.00 0.00 33.53 2.39
5723 6312 5.356426 ACACACGTATGCATATGTACACAT 58.644 37.500 27.01 11.49 40.22 3.21
5886 6476 0.302890 CGCTCGCAAATGTCTGGATC 59.697 55.000 0.00 0.00 0.00 3.36
5888 6478 1.926561 CTCGCAAATGTCTGGATCGA 58.073 50.000 0.00 0.00 0.00 3.59
5891 6481 1.731709 CGCAAATGTCTGGATCGAACA 59.268 47.619 0.00 0.00 0.00 3.18
5892 6482 2.352651 CGCAAATGTCTGGATCGAACAT 59.647 45.455 0.00 0.00 0.00 2.71
5933 6523 4.532834 TCCAACATAGCTTACCAAATCCC 58.467 43.478 0.00 0.00 0.00 3.85
5938 6528 2.134789 AGCTTACCAAATCCCTGCAG 57.865 50.000 6.78 6.78 0.00 4.41
5961 6551 3.305064 CGGACGTTTGAAATCCCACAAAT 60.305 43.478 0.00 0.00 38.09 2.32
6038 6629 2.438975 CCATGGCGGAGTGTGCAT 60.439 61.111 0.00 0.00 36.56 3.96
6055 6646 5.297776 GTGTGCATATTTGGATACTCTGCTT 59.702 40.000 0.00 0.00 33.44 3.91
6058 6649 6.206243 GTGCATATTTGGATACTCTGCTTCAT 59.794 38.462 0.00 0.00 37.61 2.57
6083 6674 1.586422 CTGTGTGAACTGACACCCTG 58.414 55.000 0.00 0.00 44.83 4.45
6097 6688 2.123077 CCTGGCCCACCCAAAACA 60.123 61.111 0.00 0.00 44.81 2.83
6103 6694 1.767654 GCCCACCCAAAACAATGGCT 61.768 55.000 0.00 0.00 39.26 4.75
6152 6743 3.411446 CACTATTCCTGTGTGAAAGCCA 58.589 45.455 0.00 0.00 33.95 4.75
6181 6774 4.320456 CGATAGCAGGCGCCCCAT 62.320 66.667 26.15 11.86 39.83 4.00
6213 6806 1.388547 TGCTCGTTTTGTCAGCCTTT 58.611 45.000 0.00 0.00 31.68 3.11
6215 6808 1.065551 GCTCGTTTTGTCAGCCTTTGT 59.934 47.619 0.00 0.00 0.00 2.83
6221 6814 0.103390 TTGTCAGCCTTTGTCGACGA 59.897 50.000 11.62 6.16 0.00 4.20
6269 6862 0.181587 TTCGTGGTTCCTTCAAGCCA 59.818 50.000 0.00 0.00 0.00 4.75
6314 6909 1.229951 TGGAGTGGGAAGGCCAGAT 60.230 57.895 5.01 0.00 35.15 2.90
6360 6955 2.435059 GCAGTCGGAGCTTGTCCC 60.435 66.667 0.00 0.00 43.47 4.46
6420 7015 3.590574 AACCCTGCCCCTCCCAAC 61.591 66.667 0.00 0.00 0.00 3.77
6425 7020 1.152567 CTGCCCCTCCCAACACAAA 60.153 57.895 0.00 0.00 0.00 2.83
6467 7062 1.410517 CATCTACACAGTCAGCCCGAT 59.589 52.381 0.00 0.00 0.00 4.18
6485 7080 4.417506 CCGATACACAACAGTCATCGTAA 58.582 43.478 0.00 0.00 37.41 3.18
6486 7081 4.264614 CCGATACACAACAGTCATCGTAAC 59.735 45.833 0.00 0.00 37.41 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.611200 CATAGTGGTCACGGGTGGAA 59.389 55.000 0.00 0.00 36.20 3.53
19 20 1.220749 CCATAGTGGTCACGGGTGG 59.779 63.158 0.00 7.60 36.20 4.61
32 34 8.833231 ATAACTGTCGAAATAATCCACCATAG 57.167 34.615 0.00 0.00 0.00 2.23
48 50 6.330278 TCCAACAGACTTCATATAACTGTCG 58.670 40.000 0.00 0.00 40.23 4.35
60 62 1.728971 CACGCATCTCCAACAGACTTC 59.271 52.381 0.00 0.00 32.26 3.01
66 68 0.534877 ACTTGCACGCATCTCCAACA 60.535 50.000 0.00 0.00 0.00 3.33
67 69 1.438651 TACTTGCACGCATCTCCAAC 58.561 50.000 0.00 0.00 0.00 3.77
71 73 4.607955 TGTACTATACTTGCACGCATCTC 58.392 43.478 0.00 0.00 0.00 2.75
76 78 2.724690 CCGATGTACTATACTTGCACGC 59.275 50.000 0.00 0.00 0.00 5.34
96 98 5.478407 CACATTTTACCCTTGGTCATTTCC 58.522 41.667 0.00 0.00 37.09 3.13
98 100 4.285775 CCCACATTTTACCCTTGGTCATTT 59.714 41.667 0.00 0.00 37.09 2.32
99 101 3.837731 CCCACATTTTACCCTTGGTCATT 59.162 43.478 0.00 0.00 37.09 2.57
102 104 2.884320 ACCCACATTTTACCCTTGGTC 58.116 47.619 0.00 0.00 37.09 4.02
104 106 4.219725 CAGTAACCCACATTTTACCCTTGG 59.780 45.833 0.00 0.00 0.00 3.61
119 121 1.203287 GTACGACCCAGTCAGTAACCC 59.797 57.143 0.00 0.00 32.09 4.11
121 123 1.888512 TGGTACGACCCAGTCAGTAAC 59.111 52.381 0.00 7.41 37.50 2.50
125 127 2.758979 ACTTATGGTACGACCCAGTCAG 59.241 50.000 0.00 0.00 37.50 3.51
126 128 2.494471 CACTTATGGTACGACCCAGTCA 59.506 50.000 0.00 0.00 37.50 3.41
127 129 2.756760 TCACTTATGGTACGACCCAGTC 59.243 50.000 0.00 0.00 37.50 3.51
128 130 2.758979 CTCACTTATGGTACGACCCAGT 59.241 50.000 0.00 0.00 37.50 4.00
129 131 2.100916 CCTCACTTATGGTACGACCCAG 59.899 54.545 0.00 0.00 37.50 4.45
130 132 2.104967 CCTCACTTATGGTACGACCCA 58.895 52.381 0.00 0.00 37.50 4.51
132 134 5.301298 AGTTATCCTCACTTATGGTACGACC 59.699 44.000 0.00 0.00 39.22 4.79
133 135 6.388435 AGTTATCCTCACTTATGGTACGAC 57.612 41.667 0.00 0.00 0.00 4.34
134 136 5.533903 GGAGTTATCCTCACTTATGGTACGA 59.466 44.000 0.00 0.00 42.94 3.43
153 155 3.756117 CCAAGGCTTAGAAACAGGAGTT 58.244 45.455 0.00 0.00 40.40 3.01
158 160 1.541588 GTGGCCAAGGCTTAGAAACAG 59.458 52.381 7.24 0.00 41.60 3.16
178 180 1.492764 ACGTAATCAGTGGTAGGGGG 58.507 55.000 0.00 0.00 0.00 5.40
183 185 3.671008 AGTGCAACGTAATCAGTGGTA 57.329 42.857 0.00 0.00 45.86 3.25
208 210 7.147776 GGATTTCACTGAAAAAGATCCATCCAT 60.148 37.037 8.28 0.00 35.11 3.41
229 231 2.807895 CGACGTCGTGCCGGATTT 60.808 61.111 29.08 0.00 34.11 2.17
243 245 5.337872 GTCGAAGAATCATCGTTGCCGAC 62.338 52.174 7.75 0.00 42.94 4.79
244 246 3.299227 GTCGAAGAATCATCGTTGCCGA 61.299 50.000 7.75 0.00 44.01 5.54
250 252 2.913777 TGTCGTCGAAGAATCATCGT 57.086 45.000 7.75 0.00 39.69 3.73
251 253 3.363178 TCATGTCGTCGAAGAATCATCG 58.637 45.455 1.62 1.04 39.69 3.84
284 286 9.022915 TGAAAATAAATCGATATGCTGCAAAAG 57.977 29.630 6.36 0.00 0.00 2.27
298 300 8.845648 TGCTTCGTAACAATTGAAAATAAATCG 58.154 29.630 13.59 4.07 0.00 3.34
300 302 8.921670 GGTGCTTCGTAACAATTGAAAATAAAT 58.078 29.630 13.59 0.00 0.00 1.40
326 328 7.582352 CATAATTGCATGTATCTCCACTTCTG 58.418 38.462 0.00 0.00 0.00 3.02
390 406 5.798125 AAGTCTCAGTTGAGTCAGATTGA 57.202 39.130 8.85 0.00 42.60 2.57
442 458 2.545742 CGAGATGACCATATGCCGAACA 60.546 50.000 0.00 0.00 0.00 3.18
462 478 3.751175 TCAACTCCTTAATTTCAGCCACG 59.249 43.478 0.00 0.00 0.00 4.94
494 510 5.073691 CCCTAGTCAACTCATGGGGAATAAT 59.926 44.000 0.00 0.00 34.71 1.28
540 561 8.283992 ACTCGATACGACTATAATTTGTCAGAG 58.716 37.037 0.00 0.00 33.18 3.35
575 596 8.296000 CAGAAGATCTTCGATACATGATAGTGT 58.704 37.037 25.88 3.72 43.97 3.55
577 598 7.576666 GCCAGAAGATCTTCGATACATGATAGT 60.577 40.741 25.88 4.73 43.97 2.12
578 599 6.751425 GCCAGAAGATCTTCGATACATGATAG 59.249 42.308 25.88 9.26 43.97 2.08
580 601 5.245751 AGCCAGAAGATCTTCGATACATGAT 59.754 40.000 25.88 6.09 43.97 2.45
592 631 2.564947 ACAGTCGAAAGCCAGAAGATCT 59.435 45.455 0.00 0.00 0.00 2.75
622 661 7.931407 AGGCGAAAGGAGTTTTATTTCAAATTT 59.069 29.630 0.00 0.00 33.50 1.82
629 668 3.119955 GCGAGGCGAAAGGAGTTTTATTT 60.120 43.478 0.00 0.00 0.00 1.40
661 700 9.825972 CGTATAAATTTTGTCTGAAGTGTGATT 57.174 29.630 0.00 0.00 0.00 2.57
662 701 7.962918 GCGTATAAATTTTGTCTGAAGTGTGAT 59.037 33.333 0.00 0.00 0.00 3.06
663 702 7.295201 GCGTATAAATTTTGTCTGAAGTGTGA 58.705 34.615 0.00 0.00 0.00 3.58
664 703 6.523201 GGCGTATAAATTTTGTCTGAAGTGTG 59.477 38.462 0.00 0.00 0.00 3.82
665 704 6.430000 AGGCGTATAAATTTTGTCTGAAGTGT 59.570 34.615 0.00 0.00 0.00 3.55
671 710 8.154649 AGGATAAGGCGTATAAATTTTGTCTG 57.845 34.615 0.00 0.00 0.00 3.51
891 1045 1.845809 GCGGGTTTGTGTGAGAGCAG 61.846 60.000 0.00 0.00 0.00 4.24
932 1086 3.089284 CGTAGGAGGAGGGCAAAAATTT 58.911 45.455 0.00 0.00 0.00 1.82
954 1109 1.794222 CTGGGATCCAAACGCGAAC 59.206 57.895 15.93 0.00 30.80 3.95
1153 1308 2.359850 GCCACCACTCAATCGCCA 60.360 61.111 0.00 0.00 0.00 5.69
1215 1735 3.249973 GAAAACGCACCCCGCAGTC 62.250 63.158 0.00 0.00 42.60 3.51
1225 1745 3.018149 ACCACCTAAAACAGAAAACGCA 58.982 40.909 0.00 0.00 0.00 5.24
1229 1749 6.437793 TCCTTTCAACCACCTAAAACAGAAAA 59.562 34.615 0.00 0.00 0.00 2.29
1300 1820 5.371115 TCCTCAAATAAGAAAAAGCACCG 57.629 39.130 0.00 0.00 0.00 4.94
1306 1826 8.630054 TCTCGGAATTCCTCAAATAAGAAAAA 57.370 30.769 22.05 0.00 0.00 1.94
1322 1842 3.981071 TCACTGACCAATCTCGGAATT 57.019 42.857 0.00 0.00 0.00 2.17
1328 1848 5.645497 AGCAACTATTTCACTGACCAATCTC 59.355 40.000 0.00 0.00 0.00 2.75
1346 1866 2.837883 CGCAACACAGCCAGCAACT 61.838 57.895 0.00 0.00 0.00 3.16
1411 1931 5.191722 TCAGAATAGCACCAAATCCTAACCT 59.808 40.000 0.00 0.00 0.00 3.50
1455 1975 4.455533 CACGGTTTTCAATCCTGAATGAGA 59.544 41.667 0.00 0.00 41.22 3.27
1488 2008 1.135717 CACCACACACACACACACAAG 60.136 52.381 0.00 0.00 0.00 3.16
1514 2042 1.122019 ATCTGTCCATAGACGCCCCC 61.122 60.000 0.00 0.00 46.74 5.40
1515 2043 0.759346 AATCTGTCCATAGACGCCCC 59.241 55.000 0.00 0.00 46.74 5.80
1516 2044 2.628657 AGTAATCTGTCCATAGACGCCC 59.371 50.000 0.00 0.00 46.74 6.13
1517 2045 3.318275 TCAGTAATCTGTCCATAGACGCC 59.682 47.826 0.00 0.00 46.74 5.68
1518 2046 4.569761 TCAGTAATCTGTCCATAGACGC 57.430 45.455 0.00 0.00 46.74 5.19
1519 2047 5.917447 CACATCAGTAATCTGTCCATAGACG 59.083 44.000 0.00 0.00 46.74 4.18
1520 2048 6.699204 CACACATCAGTAATCTGTCCATAGAC 59.301 42.308 0.00 0.00 43.83 2.59
1683 2225 5.895928 TCACTGAATCACTAGTATGAGCAC 58.104 41.667 0.00 0.00 30.46 4.40
1718 2260 3.818295 TGGCCAAACCTATAAAGTGGT 57.182 42.857 0.61 0.00 40.22 4.16
1753 2295 6.919662 AGTAAAACAAGCACATCAACATTCAG 59.080 34.615 0.00 0.00 0.00 3.02
1785 2327 6.884836 GGTTACTAAACTCAAGGGTCAATCAT 59.115 38.462 0.00 0.00 35.81 2.45
1786 2328 6.235664 GGTTACTAAACTCAAGGGTCAATCA 58.764 40.000 0.00 0.00 35.81 2.57
1787 2329 5.350640 CGGTTACTAAACTCAAGGGTCAATC 59.649 44.000 0.00 0.00 35.81 2.67
1788 2330 5.243207 CGGTTACTAAACTCAAGGGTCAAT 58.757 41.667 0.00 0.00 35.81 2.57
1789 2331 4.503643 CCGGTTACTAAACTCAAGGGTCAA 60.504 45.833 0.00 0.00 35.81 3.18
1790 2332 3.007182 CCGGTTACTAAACTCAAGGGTCA 59.993 47.826 0.00 0.00 35.81 4.02
1791 2333 3.007290 ACCGGTTACTAAACTCAAGGGTC 59.993 47.826 0.00 0.00 35.81 4.46
1792 2334 2.974794 ACCGGTTACTAAACTCAAGGGT 59.025 45.455 0.00 0.00 35.81 4.34
1793 2335 3.690475 ACCGGTTACTAAACTCAAGGG 57.310 47.619 0.00 0.00 35.81 3.95
1825 2367 6.798427 TTTGCATACTAATTAATTGGCCCA 57.202 33.333 11.05 0.00 0.00 5.36
1913 2463 9.955102 ATACTTAGTTAGGGGAAGTTACAAAAG 57.045 33.333 0.00 0.00 35.17 2.27
2031 2581 7.255486 GGGATAAAGTACAAAGCAAGTTCTGTT 60.255 37.037 0.00 0.00 0.00 3.16
2110 2660 5.584253 TCTTCCTATGAAAGAGAACCTCG 57.416 43.478 0.00 0.00 35.36 4.63
2346 2905 9.850198 GGATAAGAGTCCTTCTAGAAAGTAGTA 57.150 37.037 6.63 0.00 34.14 1.82
2585 3145 8.188799 CAGTGCATTTGAATCTTGACATCTTAT 58.811 33.333 0.00 0.00 0.00 1.73
2709 3275 2.346803 CAACCAGACAAGTATCCACGG 58.653 52.381 0.00 0.00 0.00 4.94
2713 3279 6.543831 AGAATAATGCAACCAGACAAGTATCC 59.456 38.462 0.00 0.00 0.00 2.59
2745 3311 2.507058 TCTGATAGACCAATGGCAAGCT 59.493 45.455 0.00 0.00 0.00 3.74
3029 3599 9.512588 AAAAGATGACATGTTCTAAGAATCTGT 57.487 29.630 0.00 0.00 0.00 3.41
3097 3667 2.171341 TATTGCGCACACACACCTTA 57.829 45.000 11.12 0.00 0.00 2.69
3143 3713 8.717821 GCTGTAATTCTGTAGATACACACAAAA 58.282 33.333 0.00 0.00 31.93 2.44
3359 3929 5.680594 TTGGCGGGTAGTAGAATAAAAGA 57.319 39.130 0.00 0.00 0.00 2.52
3436 4006 2.744202 CTGCAGGATGACAGTTACAACC 59.256 50.000 5.57 0.00 39.69 3.77
3596 4166 2.549926 CACCTGGAAACAAACAAAGCC 58.450 47.619 0.00 0.00 42.06 4.35
3691 4261 4.589908 AGTTACCAAATCCAGTCATCCAC 58.410 43.478 0.00 0.00 0.00 4.02
4156 4726 8.279800 CACAAGACGAATAACATTGTTAAGTCA 58.720 33.333 26.52 8.08 32.01 3.41
4252 4822 4.563374 CCCACAATCCATATGTAGCGATCA 60.563 45.833 1.24 0.00 0.00 2.92
4421 4991 4.063689 CTCAACCTATGACATGGAGATGC 58.936 47.826 0.00 0.00 33.47 3.91
4621 5191 5.690997 TGTCCAGCTTATAGATGTACTCG 57.309 43.478 0.00 0.00 27.62 4.18
4684 5254 5.932303 CAGGAAAGATACATACGTTATGGGG 59.068 44.000 0.00 0.00 40.47 4.96
4925 5499 6.974622 CAGCTAGAACAAACAAATCAACAAGT 59.025 34.615 0.00 0.00 0.00 3.16
4926 5500 6.418819 CCAGCTAGAACAAACAAATCAACAAG 59.581 38.462 0.00 0.00 0.00 3.16
4927 5501 6.272318 CCAGCTAGAACAAACAAATCAACAA 58.728 36.000 0.00 0.00 0.00 2.83
4928 5502 5.735922 GCCAGCTAGAACAAACAAATCAACA 60.736 40.000 0.00 0.00 0.00 3.33
5234 5808 6.919662 GTGGACTAAATTCAATGCCATACATG 59.080 38.462 0.00 0.00 39.60 3.21
5235 5809 6.040842 GGTGGACTAAATTCAATGCCATACAT 59.959 38.462 0.00 0.00 42.30 2.29
5236 5810 5.359576 GGTGGACTAAATTCAATGCCATACA 59.640 40.000 0.00 0.00 0.00 2.29
5237 5811 5.594317 AGGTGGACTAAATTCAATGCCATAC 59.406 40.000 0.00 0.00 0.00 2.39
5238 5812 5.765510 AGGTGGACTAAATTCAATGCCATA 58.234 37.500 0.00 0.00 0.00 2.74
5239 5813 4.613437 AGGTGGACTAAATTCAATGCCAT 58.387 39.130 0.00 0.00 0.00 4.40
5240 5814 4.046286 AGGTGGACTAAATTCAATGCCA 57.954 40.909 0.00 0.00 0.00 4.92
5241 5815 4.706962 AGAAGGTGGACTAAATTCAATGCC 59.293 41.667 0.00 0.00 0.00 4.40
5242 5816 5.904362 AGAAGGTGGACTAAATTCAATGC 57.096 39.130 0.00 0.00 0.00 3.56
5243 5817 6.127619 GGGAAGAAGGTGGACTAAATTCAATG 60.128 42.308 0.00 0.00 0.00 2.82
5244 5818 5.952347 GGGAAGAAGGTGGACTAAATTCAAT 59.048 40.000 0.00 0.00 0.00 2.57
5245 5819 5.321927 GGGAAGAAGGTGGACTAAATTCAA 58.678 41.667 0.00 0.00 0.00 2.69
5246 5820 4.263771 GGGGAAGAAGGTGGACTAAATTCA 60.264 45.833 0.00 0.00 0.00 2.57
5247 5821 4.263771 TGGGGAAGAAGGTGGACTAAATTC 60.264 45.833 0.00 0.00 0.00 2.17
5248 5822 3.660669 TGGGGAAGAAGGTGGACTAAATT 59.339 43.478 0.00 0.00 0.00 1.82
5249 5823 3.265489 TGGGGAAGAAGGTGGACTAAAT 58.735 45.455 0.00 0.00 0.00 1.40
5250 5824 2.708759 TGGGGAAGAAGGTGGACTAAA 58.291 47.619 0.00 0.00 0.00 1.85
5251 5825 2.426431 TGGGGAAGAAGGTGGACTAA 57.574 50.000 0.00 0.00 0.00 2.24
5252 5826 2.196595 CATGGGGAAGAAGGTGGACTA 58.803 52.381 0.00 0.00 0.00 2.59
5253 5827 0.995024 CATGGGGAAGAAGGTGGACT 59.005 55.000 0.00 0.00 0.00 3.85
5254 5828 0.698818 ACATGGGGAAGAAGGTGGAC 59.301 55.000 0.00 0.00 0.00 4.02
5255 5829 2.352561 TACATGGGGAAGAAGGTGGA 57.647 50.000 0.00 0.00 0.00 4.02
5256 5830 2.423373 CCATACATGGGGAAGAAGGTGG 60.423 54.545 0.00 0.00 44.31 4.61
5257 5831 2.936202 CCATACATGGGGAAGAAGGTG 58.064 52.381 0.00 0.00 44.31 4.00
5277 5851 7.761249 AGTTGCTTTATGGACTAAATTCAATGC 59.239 33.333 0.00 0.00 30.89 3.56
5465 6042 2.938956 AGTATCCTGCTATGCCAACC 57.061 50.000 0.00 0.00 0.00 3.77
5541 6118 3.520290 TCTCGCCGACAATCAAACTAT 57.480 42.857 0.00 0.00 0.00 2.12
5557 6134 3.684305 TGTGCCTGTTGACATTTATCTCG 59.316 43.478 0.00 0.00 0.00 4.04
5587 6176 2.421619 CAGGGTGAAAGAGAAGCAGTC 58.578 52.381 0.00 0.00 0.00 3.51
5638 6227 7.552687 ACATGTTACACTCTTCAAACTCTTCAA 59.447 33.333 0.00 0.00 0.00 2.69
5639 6228 7.047891 ACATGTTACACTCTTCAAACTCTTCA 58.952 34.615 0.00 0.00 0.00 3.02
5640 6229 7.484035 ACATGTTACACTCTTCAAACTCTTC 57.516 36.000 0.00 0.00 0.00 2.87
5641 6230 7.985184 TGTACATGTTACACTCTTCAAACTCTT 59.015 33.333 2.30 0.00 0.00 2.85
5642 6231 7.497595 TGTACATGTTACACTCTTCAAACTCT 58.502 34.615 2.30 0.00 0.00 3.24
5643 6232 7.709269 TGTACATGTTACACTCTTCAAACTC 57.291 36.000 2.30 0.00 0.00 3.01
5644 6233 8.559536 CATTGTACATGTTACACTCTTCAAACT 58.440 33.333 2.30 0.00 0.00 2.66
5645 6234 8.342634 ACATTGTACATGTTACACTCTTCAAAC 58.657 33.333 2.30 0.00 0.00 2.93
5646 6235 8.341903 CACATTGTACATGTTACACTCTTCAAA 58.658 33.333 2.30 0.00 0.00 2.69
5660 6249 2.094597 CACTTGGGGCACATTGTACATG 60.095 50.000 0.00 0.00 0.00 3.21
5699 6288 4.801516 TGTGTACATATGCATACGTGTGTC 59.198 41.667 15.39 11.37 38.08 3.67
5739 6328 3.485216 GCAAGAATTACAATCACGACCGG 60.485 47.826 0.00 0.00 0.00 5.28
5805 6394 5.887598 TCCAGTATGCATTTCAACAGCTATT 59.112 36.000 3.54 0.00 31.97 1.73
5886 6476 3.424433 GCTAAAAGTGTCCGGAATGTTCG 60.424 47.826 5.23 0.00 0.00 3.95
5888 6478 2.817844 GGCTAAAAGTGTCCGGAATGTT 59.182 45.455 5.23 0.00 0.00 2.71
5891 6481 2.871096 TGGCTAAAAGTGTCCGGAAT 57.129 45.000 5.23 0.00 0.00 3.01
5892 6482 2.617021 GGATGGCTAAAAGTGTCCGGAA 60.617 50.000 5.23 0.00 0.00 4.30
5933 6523 0.238289 ATTTCAAACGTCCGCTGCAG 59.762 50.000 10.11 10.11 0.00 4.41
5938 6528 0.109919 GTGGGATTTCAAACGTCCGC 60.110 55.000 0.00 0.00 32.71 5.54
5961 6551 1.304052 CTCCCCGATTTGGTGCCAA 60.304 57.895 0.00 0.00 35.15 4.52
6038 6629 9.507329 GGAATAATGAAGCAGAGTATCCAAATA 57.493 33.333 0.00 0.00 33.66 1.40
6055 6646 5.700832 GTGTCAGTTCACACAGGAATAATGA 59.299 40.000 0.00 0.00 45.25 2.57
6083 6674 1.374568 CCATTGTTTTGGGTGGGCC 59.625 57.895 0.00 0.00 32.80 5.80
6097 6688 1.246056 AATGTGCGCACTCAGCCATT 61.246 50.000 37.59 25.20 41.38 3.16
6103 6694 0.817229 TGTCCAAATGTGCGCACTCA 60.817 50.000 37.59 22.00 0.00 3.41
6181 6774 2.839486 ACGAGCAATGAAAGACTGGA 57.161 45.000 0.00 0.00 0.00 3.86
6213 6806 2.022520 CCGATCCATCTCGTCGACA 58.977 57.895 17.16 1.87 37.55 4.35
6215 6808 2.893449 CGCCGATCCATCTCGTCGA 61.893 63.158 0.00 0.00 42.00 4.20
6221 6814 2.640302 CGATCCCGCCGATCCATCT 61.640 63.158 5.44 0.00 44.07 2.90
6269 6862 4.039357 CCACGCACGACCGTCTCT 62.039 66.667 0.00 0.00 39.83 3.10
6296 6891 1.229951 ATCTGGCCTTCCCACTCCA 60.230 57.895 3.32 0.00 39.18 3.86
6304 6899 1.092345 GCCTTCACGATCTGGCCTTC 61.092 60.000 3.32 0.00 39.49 3.46
6314 6909 1.595993 CTTCTCCCTCGCCTTCACGA 61.596 60.000 0.00 0.00 40.36 4.35
6360 6955 1.334869 GGCACTGACACCTTCTTTGTG 59.665 52.381 0.00 0.00 39.63 3.33
6420 7015 2.277084 GTGATAGTAGGGCGGTTTGTG 58.723 52.381 0.00 0.00 0.00 3.33
6425 7020 1.442526 CGACGTGATAGTAGGGCGGT 61.443 60.000 0.00 0.00 33.61 5.68


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

AutoCloner maintained by Alex Coulton.