Multiple sequence alignment - TraesCS2A01G268300

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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 TraesCS2A01G268300 chr2A 100.000 5645 0 0 1 5645 430955861 430950217 0.000000e+00 10425.0
1 TraesCS2A01G268300 chr2A 85.556 90 12 1 552 641 773374414 773374326 6.020000e-15 93.5
2 TraesCS2A01G268300 chr2D 96.218 4151 120 12 760 4882 308982237 308986378 0.000000e+00 6761.0
3 TraesCS2A01G268300 chr2D 96.575 438 10 3 5210 5645 308986653 308987087 0.000000e+00 721.0
4 TraesCS2A01G268300 chr2D 89.091 495 35 9 1 483 308976838 308977325 1.050000e-166 597.0
5 TraesCS2A01G268300 chr2D 91.103 281 23 2 477 756 308977464 308977743 4.130000e-101 379.0
6 TraesCS2A01G268300 chr2D 94.410 161 9 0 5033 5193 308986364 308986524 1.210000e-61 248.0
7 TraesCS2A01G268300 chr2D 86.082 194 17 9 3832 4017 9603522 9603331 3.450000e-47 200.0
8 TraesCS2A01G268300 chr2B 96.290 3100 83 14 560 3632 359315407 359312313 0.000000e+00 5059.0
9 TraesCS2A01G268300 chr2B 94.475 1267 48 8 3631 4882 359312209 359310950 0.000000e+00 1932.0
10 TraesCS2A01G268300 chr2B 95.238 441 12 2 5211 5645 359306051 359305614 0.000000e+00 689.0
11 TraesCS2A01G268300 chr2B 90.524 496 34 6 1 483 359320526 359320031 1.330000e-180 643.0
12 TraesCS2A01G268300 chr2B 89.655 116 10 1 5033 5148 359310964 359310851 4.560000e-31 147.0
13 TraesCS2A01G268300 chr2B 95.588 68 3 0 480 547 359319889 359319822 5.980000e-20 110.0
14 TraesCS2A01G268300 chr2B 97.959 49 1 0 5145 5193 359306304 359306256 1.010000e-12 86.1
15 TraesCS2A01G268300 chr5D 79.445 2452 465 34 1156 3589 479579955 479582385 0.000000e+00 1700.0
16 TraesCS2A01G268300 chr5D 97.414 116 3 0 4894 5009 450669801 450669686 1.240000e-46 198.0
17 TraesCS2A01G268300 chr6D 80.396 454 57 18 61 483 10022648 10022196 3.280000e-82 316.0
18 TraesCS2A01G268300 chr6D 86.559 186 19 4 3828 4011 121812783 121812964 3.450000e-47 200.0
19 TraesCS2A01G268300 chr6D 86.885 183 15 6 3832 4010 351765618 351765795 4.460000e-46 196.0
20 TraesCS2A01G268300 chr6D 86.096 187 19 6 3826 4011 218127524 218127344 1.600000e-45 195.0
21 TraesCS2A01G268300 chr5B 78.855 454 64 16 61 483 367470443 367469991 1.550000e-70 278.0
22 TraesCS2A01G268300 chr4A 73.165 790 184 26 1280 2052 54109734 54108956 5.610000e-65 259.0
23 TraesCS2A01G268300 chr4A 81.065 338 39 18 61 374 35993521 35993185 4.370000e-61 246.0
24 TraesCS2A01G268300 chr4A 96.000 125 4 1 4885 5009 667059870 667059747 9.590000e-48 202.0
25 TraesCS2A01G268300 chr4A 89.011 91 9 1 551 641 607183794 607183883 1.660000e-20 111.0
26 TraesCS2A01G268300 chr4A 88.889 90 9 1 552 641 35970725 35970637 5.980000e-20 110.0
27 TraesCS2A01G268300 chr4D 75.088 566 129 12 1493 2052 397096641 397096082 2.610000e-63 254.0
28 TraesCS2A01G268300 chr4B 74.780 567 129 14 1493 2052 489090466 489089907 5.650000e-60 243.0
29 TraesCS2A01G268300 chr3D 78.356 365 52 13 61 398 157240626 157240262 1.590000e-50 211.0
30 TraesCS2A01G268300 chr3D 89.535 86 8 1 552 637 532582346 532582430 2.150000e-19 108.0
31 TraesCS2A01G268300 chr3B 94.656 131 6 1 4880 5009 823326743 823326873 9.590000e-48 202.0
32 TraesCS2A01G268300 chr3B 97.414 116 2 1 4894 5009 377887127 377887241 4.460000e-46 196.0
33 TraesCS2A01G268300 chr3B 90.361 83 6 2 560 641 704652645 704652726 2.150000e-19 108.0
34 TraesCS2A01G268300 chr5A 96.694 121 3 1 4889 5009 38799470 38799589 3.450000e-47 200.0
35 TraesCS2A01G268300 chr1D 88.024 167 19 1 3832 3998 192588781 192588946 4.460000e-46 196.0
36 TraesCS2A01G268300 chr1B 88.024 167 19 1 3832 3998 266265463 266265628 4.460000e-46 196.0
37 TraesCS2A01G268300 chr1B 74.398 457 63 21 61 485 272608892 272608458 4.560000e-31 147.0
38 TraesCS2A01G268300 chr7A 94.488 127 6 1 4883 5009 541890159 541890284 1.600000e-45 195.0
39 TraesCS2A01G268300 chr7A 95.161 124 4 2 4885 5007 688450170 688450292 1.600000e-45 195.0
40 TraesCS2A01G268300 chr6B 97.368 114 3 0 4894 5007 368478842 368478729 1.600000e-45 195.0
41 TraesCS2A01G268300 chr6B 92.969 128 7 2 4883 5009 114930167 114930041 9.660000e-43 185.0
42 TraesCS2A01G268300 chr6A 85.946 185 21 5 3828 4011 7123778 7123958 5.770000e-45 193.0


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 TraesCS2A01G268300 chr2A 430950217 430955861 5644 True 10425.000000 10425 100.000000 1 5645 1 chr2A.!!$R1 5644
1 TraesCS2A01G268300 chr2D 308982237 308987087 4850 False 2576.666667 6761 95.734333 760 5645 3 chr2D.!!$F2 4885
2 TraesCS2A01G268300 chr2D 308976838 308977743 905 False 488.000000 597 90.097000 1 756 2 chr2D.!!$F1 755
3 TraesCS2A01G268300 chr2B 359310851 359315407 4556 True 2379.333333 5059 93.473333 560 5148 3 chr2B.!!$R2 4588
4 TraesCS2A01G268300 chr2B 359305614 359306304 690 True 387.550000 689 96.598500 5145 5645 2 chr2B.!!$R1 500
5 TraesCS2A01G268300 chr2B 359319822 359320526 704 True 376.500000 643 93.056000 1 547 2 chr2B.!!$R3 546
6 TraesCS2A01G268300 chr5D 479579955 479582385 2430 False 1700.000000 1700 79.445000 1156 3589 1 chr5D.!!$F1 2433
7 TraesCS2A01G268300 chr4A 54108956 54109734 778 True 259.000000 259 73.165000 1280 2052 1 chr4A.!!$R3 772
8 TraesCS2A01G268300 chr4D 397096082 397096641 559 True 254.000000 254 75.088000 1493 2052 1 chr4D.!!$R1 559
9 TraesCS2A01G268300 chr4B 489089907 489090466 559 True 243.000000 243 74.780000 1493 2052 1 chr4B.!!$R1 559

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
23 24 1.138568 TCTAGGCTACTAGCTCGGGT 58.861 55.000 7.99 0.00 45.15 5.28 F
1542 1745 1.186267 GGGAGATTCCGCCGGAGTAT 61.186 60.000 5.05 0.00 37.43 2.12 F
1800 2003 1.005037 CACGCTGTTCCTGCAGGTA 60.005 57.895 31.58 20.93 37.00 3.08 F
2631 2834 2.167900 AGATATACCGCCGGCTATTTCC 59.832 50.000 26.68 8.09 0.00 3.13 F
4251 4564 0.397564 TTACGGGAAAGAAGCCGGTT 59.602 50.000 1.90 0.00 39.36 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1751 0.392336 GATACTGCAGCCTCCTCCAG 59.608 60.000 15.27 0.0 0.0 3.86 R
3111 3314 0.179073 CTGGCATCGTCCCCTTGTAG 60.179 60.000 0.00 0.0 0.0 2.74 R
3662 3970 7.075121 TGCAGACAACAATAATTAACTGAACG 58.925 34.615 0.00 0.0 0.0 3.95 R
4560 4873 0.454957 CCTTTGCTTCATCGGTTGCG 60.455 55.000 0.00 0.0 0.0 4.85 R
5514 6042 0.179081 GCTCCCTACCGATTGTGACC 60.179 60.000 0.00 0.0 0.0 4.02 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 24 1.138568 TCTAGGCTACTAGCTCGGGT 58.861 55.000 7.99 0.00 45.15 5.28
33 34 4.477119 GCTCGGGTCCCCCTACCT 62.477 72.222 1.00 0.00 42.67 3.08
34 35 3.078843 GCTCGGGTCCCCCTACCTA 62.079 68.421 1.00 0.00 42.67 3.08
41 42 2.361070 GGGTCCCCCTACCTAAGATTCA 60.361 54.545 0.00 0.00 41.34 2.57
142 155 7.864108 ACTTGCTGTTATATGTTGATTGCTA 57.136 32.000 0.00 0.00 0.00 3.49
143 156 8.455903 ACTTGCTGTTATATGTTGATTGCTAT 57.544 30.769 0.00 0.00 0.00 2.97
167 180 8.773033 ATCAAGGGCAATAAAGAAATCACTAT 57.227 30.769 0.00 0.00 0.00 2.12
226 239 6.011122 AGGATCTTGGTGCTCATAAGAAAT 57.989 37.500 8.23 0.00 34.47 2.17
233 246 8.522830 TCTTGGTGCTCATAAGAAATTTTTAGG 58.477 33.333 0.00 0.00 0.00 2.69
246 259 9.981460 AAGAAATTTTTAGGTATGGAGATCACT 57.019 29.630 0.00 0.00 0.00 3.41
283 297 8.912787 TCTAGTTTTCTATTTCTTAGTCAGCG 57.087 34.615 0.00 0.00 0.00 5.18
300 314 4.451096 GTCAGCGGAGTTACATCAAGAAAA 59.549 41.667 0.00 0.00 0.00 2.29
391 405 4.012319 TGAACTAGTACGAATGACGAGC 57.988 45.455 0.00 0.00 45.77 5.03
398 412 1.702886 ACGAATGACGAGCTTGAGTG 58.297 50.000 8.31 0.00 45.77 3.51
412 426 2.363306 TGAGTGCATGTCAAGGGTTT 57.637 45.000 0.00 0.00 0.00 3.27
430 444 6.949715 AGGGTTTCATATTCTACCGTTGTTA 58.050 36.000 0.00 0.00 0.00 2.41
457 471 3.961477 TTCCATTGTGTGTTCTCGTTG 57.039 42.857 0.00 0.00 0.00 4.10
507 666 9.206690 TGCTTATAATGATAGATAAGAGGAGGG 57.793 37.037 9.85 0.00 37.70 4.30
583 743 5.928976 ACATGGCTATTACAGAAGCATGTA 58.071 37.500 0.00 0.00 40.61 2.29
587 747 6.414732 TGGCTATTACAGAAGCATGTAAAGT 58.585 36.000 11.61 2.17 45.91 2.66
633 793 7.806690 TGTATGCTGAACTTTGTGAAGATAAC 58.193 34.615 0.00 0.00 36.69 1.89
639 799 8.534778 GCTGAACTTTGTGAAGATAACTTTTTG 58.465 33.333 0.00 0.00 36.39 2.44
641 801 8.250332 TGAACTTTGTGAAGATAACTTTTTGCT 58.750 29.630 0.00 0.00 36.39 3.91
669 831 5.635700 GGTATCTTTAGCAGGAAATCTAGCG 59.364 44.000 0.00 0.00 0.00 4.26
677 839 3.181485 GCAGGAAATCTAGCGTACACTCT 60.181 47.826 0.00 0.00 0.00 3.24
697 864 8.688151 ACACTCTGACCTCTATTACAATTACTC 58.312 37.037 0.00 0.00 0.00 2.59
756 923 3.509575 TCAGTAAAATTCAAGCGGGCATT 59.490 39.130 0.00 0.00 0.00 3.56
757 924 4.702612 TCAGTAAAATTCAAGCGGGCATTA 59.297 37.500 0.00 0.00 0.00 1.90
758 925 5.036737 CAGTAAAATTCAAGCGGGCATTAG 58.963 41.667 0.00 0.00 0.00 1.73
1175 1372 2.587753 CGCGTGGTCTGGTGTGTT 60.588 61.111 0.00 0.00 0.00 3.32
1542 1745 1.186267 GGGAGATTCCGCCGGAGTAT 61.186 60.000 5.05 0.00 37.43 2.12
1656 1859 6.214615 TCAGAGAGCTCTACATAGGCTACTAT 59.785 42.308 18.25 0.00 37.89 2.12
1699 1902 1.751927 GCAGAGCTGGGGAACATGG 60.752 63.158 0.00 0.00 0.00 3.66
1800 2003 1.005037 CACGCTGTTCCTGCAGGTA 60.005 57.895 31.58 20.93 37.00 3.08
2432 2635 2.511145 GAGCTTCTCTGGGCTGCG 60.511 66.667 0.00 0.00 39.05 5.18
2587 2790 2.633488 GGTTGCTCACCTACCTTGATC 58.367 52.381 0.00 0.00 43.29 2.92
2631 2834 2.167900 AGATATACCGCCGGCTATTTCC 59.832 50.000 26.68 8.09 0.00 3.13
3477 3680 5.436175 TCAAACAACATTCTCCTTGACTCA 58.564 37.500 0.00 0.00 0.00 3.41
3492 3695 4.818534 TGACTCAGATTTTGAAGCACAC 57.181 40.909 0.00 0.00 34.81 3.82
3662 3970 6.619801 AGTACTGTCTCAAAAATTGTCCAC 57.380 37.500 0.00 0.00 0.00 4.02
3699 4008 4.671377 TGTTGTCTGCAGTTGAATTTCAC 58.329 39.130 14.67 1.28 0.00 3.18
3716 4025 8.742777 TGAATTTCACTTCCTTATTTCTGATGG 58.257 33.333 0.00 0.00 0.00 3.51
3905 4215 1.996786 GCATGATGAGCAACACCCGG 61.997 60.000 0.00 0.00 0.00 5.73
3909 4219 3.210012 ATGAGCAACACCCGGCCTT 62.210 57.895 0.00 0.00 0.00 4.35
3920 4230 1.021968 CCCGGCCTTTGCATAACTAC 58.978 55.000 0.00 0.00 40.13 2.73
4088 4401 6.611381 TGTTTGTTCTTTCAACTCACTTCAG 58.389 36.000 0.00 0.00 0.00 3.02
4100 4413 3.011119 CTCACTTCAGTAGTAGCCGACT 58.989 50.000 0.00 0.00 42.69 4.18
4109 4422 5.303845 TCAGTAGTAGCCGACTGTCTATCTA 59.696 44.000 6.21 1.97 42.79 1.98
4124 4437 8.788806 ACTGTCTATCTATACAAGCAGATACAC 58.211 37.037 0.00 0.00 33.58 2.90
4141 4454 7.254017 GCAGATACACTAATCTTACAACGAACC 60.254 40.741 0.00 0.00 33.87 3.62
4166 4479 2.675317 GCTCTGGATTTGCAGAGTACGT 60.675 50.000 24.23 0.00 44.87 3.57
4251 4564 0.397564 TTACGGGAAAGAAGCCGGTT 59.602 50.000 1.90 0.00 39.36 4.44
4260 4573 1.674651 GAAGCCGGTTGGGGAGTTC 60.675 63.158 1.90 0.00 35.78 3.01
4535 4848 1.065199 TGGTGATGAATCTGGTCCTGC 60.065 52.381 0.00 0.00 0.00 4.85
4560 4873 0.322008 CTCCTGAAACTGTGGAGCCC 60.322 60.000 0.00 0.00 40.52 5.19
4732 5045 3.157087 AGGGTTTGGTATGCTGTTCTTG 58.843 45.455 0.00 0.00 0.00 3.02
4733 5046 2.890945 GGGTTTGGTATGCTGTTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
4734 5047 4.076394 GGGTTTGGTATGCTGTTCTTGTA 58.924 43.478 0.00 0.00 0.00 2.41
4736 5049 5.185056 GGGTTTGGTATGCTGTTCTTGTAAT 59.815 40.000 0.00 0.00 0.00 1.89
4766 5089 1.534595 CTGGCTTCTGTCAAGCTGAAC 59.465 52.381 6.31 0.00 42.62 3.18
4774 5097 5.023533 TCTGTCAAGCTGAACTGTTTACT 57.976 39.130 0.00 0.00 0.00 2.24
4793 5116 8.316214 TGTTTACTTAGGTACTCCTATTTGTGG 58.684 37.037 0.00 0.00 44.68 4.17
4865 5191 5.254901 TCAAGAGACTAGTCAGGGAGTTAC 58.745 45.833 24.44 4.75 0.00 2.50
4866 5192 5.014333 TCAAGAGACTAGTCAGGGAGTTACT 59.986 44.000 24.44 0.00 0.00 2.24
4867 5193 6.215023 TCAAGAGACTAGTCAGGGAGTTACTA 59.785 42.308 24.44 0.00 0.00 1.82
4868 5194 6.639590 AGAGACTAGTCAGGGAGTTACTAA 57.360 41.667 24.44 0.00 0.00 2.24
4869 5195 6.655930 AGAGACTAGTCAGGGAGTTACTAAG 58.344 44.000 24.44 0.00 0.00 2.18
4870 5196 6.444493 AGAGACTAGTCAGGGAGTTACTAAGA 59.556 42.308 24.44 0.00 0.00 2.10
4871 5197 6.655930 AGACTAGTCAGGGAGTTACTAAGAG 58.344 44.000 24.44 0.00 0.00 2.85
4872 5198 6.444493 AGACTAGTCAGGGAGTTACTAAGAGA 59.556 42.308 24.44 0.00 0.00 3.10
4873 5199 7.128263 AGACTAGTCAGGGAGTTACTAAGAGAT 59.872 40.741 24.44 0.00 0.00 2.75
4874 5200 7.645002 ACTAGTCAGGGAGTTACTAAGAGATT 58.355 38.462 0.00 0.00 0.00 2.40
4875 5201 8.780003 ACTAGTCAGGGAGTTACTAAGAGATTA 58.220 37.037 0.00 0.00 0.00 1.75
4876 5202 9.280174 CTAGTCAGGGAGTTACTAAGAGATTAG 57.720 40.741 0.00 0.00 0.00 1.73
4877 5203 7.645002 AGTCAGGGAGTTACTAAGAGATTAGT 58.355 38.462 6.00 6.00 40.53 2.24
4878 5204 8.117312 AGTCAGGGAGTTACTAAGAGATTAGTT 58.883 37.037 6.02 0.00 38.56 2.24
4879 5205 9.406113 GTCAGGGAGTTACTAAGAGATTAGTTA 57.594 37.037 6.02 0.00 38.56 2.24
4882 5208 9.939424 AGGGAGTTACTAAGAGATTAGTTATGT 57.061 33.333 6.02 0.00 38.56 2.29
4929 5255 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
4931 5257 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
4932 5258 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
4933 5259 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
4934 5260 1.147824 CCGGCCTCTGCATCAGAAT 59.852 57.895 0.00 0.00 40.18 2.40
4935 5261 1.164662 CCGGCCTCTGCATCAGAATG 61.165 60.000 0.00 0.00 40.18 2.67
4948 5274 3.817709 TCAGAATGATGCATACGACCA 57.182 42.857 0.00 0.00 42.56 4.02
4949 5275 3.457234 TCAGAATGATGCATACGACCAC 58.543 45.455 0.00 0.00 42.56 4.16
4950 5276 3.118811 TCAGAATGATGCATACGACCACA 60.119 43.478 0.00 0.00 42.56 4.17
4951 5277 3.811497 CAGAATGATGCATACGACCACAT 59.189 43.478 0.00 0.00 39.69 3.21
4952 5278 4.274214 CAGAATGATGCATACGACCACATT 59.726 41.667 0.00 2.98 39.69 2.71
4953 5279 4.883585 AGAATGATGCATACGACCACATTT 59.116 37.500 0.00 0.00 0.00 2.32
4954 5280 6.018016 CAGAATGATGCATACGACCACATTTA 60.018 38.462 0.00 0.00 39.69 1.40
4955 5281 6.712095 AGAATGATGCATACGACCACATTTAT 59.288 34.615 0.00 0.00 0.00 1.40
4956 5282 7.877612 AGAATGATGCATACGACCACATTTATA 59.122 33.333 0.00 0.00 0.00 0.98
4957 5283 7.601073 ATGATGCATACGACCACATTTATAG 57.399 36.000 0.00 0.00 0.00 1.31
4958 5284 6.754193 TGATGCATACGACCACATTTATAGA 58.246 36.000 0.00 0.00 0.00 1.98
4959 5285 7.386059 TGATGCATACGACCACATTTATAGAT 58.614 34.615 0.00 0.00 0.00 1.98
4960 5286 8.527810 TGATGCATACGACCACATTTATAGATA 58.472 33.333 0.00 0.00 0.00 1.98
4961 5287 9.366216 GATGCATACGACCACATTTATAGATAA 57.634 33.333 0.00 0.00 0.00 1.75
4962 5288 9.719355 ATGCATACGACCACATTTATAGATAAA 57.281 29.630 0.00 0.00 36.75 1.40
4963 5289 9.719355 TGCATACGACCACATTTATAGATAAAT 57.281 29.630 2.29 2.29 42.10 1.40
4982 5308 9.232473 AGATAAATAAAGAGGTTCAACAAGGTC 57.768 33.333 0.00 0.00 0.00 3.85
4983 5309 9.232473 GATAAATAAAGAGGTTCAACAAGGTCT 57.768 33.333 0.00 0.00 0.00 3.85
4984 5310 7.898014 AAATAAAGAGGTTCAACAAGGTCTT 57.102 32.000 0.00 0.00 0.00 3.01
4985 5311 8.990163 AAATAAAGAGGTTCAACAAGGTCTTA 57.010 30.769 0.00 0.00 0.00 2.10
4986 5312 9.588096 AAATAAAGAGGTTCAACAAGGTCTTAT 57.412 29.630 0.00 0.00 0.00 1.73
4988 5314 9.892130 ATAAAGAGGTTCAACAAGGTCTTATAG 57.108 33.333 0.00 0.00 0.00 1.31
4989 5315 6.936968 AGAGGTTCAACAAGGTCTTATAGT 57.063 37.500 0.00 0.00 0.00 2.12
4990 5316 6.937392 AGAGGTTCAACAAGGTCTTATAGTC 58.063 40.000 0.00 0.00 0.00 2.59
4991 5317 6.726764 AGAGGTTCAACAAGGTCTTATAGTCT 59.273 38.462 0.00 0.00 0.00 3.24
4992 5318 6.702329 AGGTTCAACAAGGTCTTATAGTCTG 58.298 40.000 0.00 0.00 0.00 3.51
4993 5319 6.497259 AGGTTCAACAAGGTCTTATAGTCTGA 59.503 38.462 0.00 0.00 0.00 3.27
4994 5320 7.016268 AGGTTCAACAAGGTCTTATAGTCTGAA 59.984 37.037 0.00 0.00 0.00 3.02
4995 5321 7.660208 GGTTCAACAAGGTCTTATAGTCTGAAA 59.340 37.037 0.00 0.00 0.00 2.69
4996 5322 9.052759 GTTCAACAAGGTCTTATAGTCTGAAAA 57.947 33.333 0.00 0.00 0.00 2.29
4997 5323 8.603242 TCAACAAGGTCTTATAGTCTGAAAAC 57.397 34.615 0.00 0.00 0.00 2.43
4998 5324 8.208224 TCAACAAGGTCTTATAGTCTGAAAACA 58.792 33.333 0.00 0.00 0.00 2.83
4999 5325 8.836413 CAACAAGGTCTTATAGTCTGAAAACAA 58.164 33.333 0.00 0.00 0.00 2.83
5000 5326 8.974060 ACAAGGTCTTATAGTCTGAAAACAAA 57.026 30.769 0.00 0.00 0.00 2.83
5001 5327 9.403583 ACAAGGTCTTATAGTCTGAAAACAAAA 57.596 29.630 0.00 0.00 0.00 2.44
5008 5334 9.274065 CTTATAGTCTGAAAACAAAATAACGGC 57.726 33.333 0.00 0.00 0.00 5.68
5009 5335 4.533222 AGTCTGAAAACAAAATAACGGCG 58.467 39.130 4.80 4.80 0.00 6.46
5010 5336 4.035909 AGTCTGAAAACAAAATAACGGCGT 59.964 37.500 6.77 6.77 0.00 5.68
5011 5337 4.377738 GTCTGAAAACAAAATAACGGCGTC 59.622 41.667 15.17 0.00 0.00 5.19
5012 5338 4.273969 TCTGAAAACAAAATAACGGCGTCT 59.726 37.500 15.17 6.47 0.00 4.18
5013 5339 5.466058 TCTGAAAACAAAATAACGGCGTCTA 59.534 36.000 15.17 8.71 0.00 2.59
5014 5340 6.018098 TCTGAAAACAAAATAACGGCGTCTAA 60.018 34.615 15.17 1.95 0.00 2.10
5015 5341 5.908499 TGAAAACAAAATAACGGCGTCTAAC 59.092 36.000 15.17 0.00 0.00 2.34
5016 5342 4.408993 AACAAAATAACGGCGTCTAACC 57.591 40.909 15.17 0.00 0.00 2.85
5017 5343 3.667360 ACAAAATAACGGCGTCTAACCT 58.333 40.909 15.17 0.00 0.00 3.50
5018 5344 4.067192 ACAAAATAACGGCGTCTAACCTT 58.933 39.130 15.17 0.00 0.00 3.50
5019 5345 4.083696 ACAAAATAACGGCGTCTAACCTTG 60.084 41.667 15.17 14.41 0.00 3.61
5020 5346 3.598019 AATAACGGCGTCTAACCTTGA 57.402 42.857 15.17 0.00 0.00 3.02
5021 5347 2.352503 TAACGGCGTCTAACCTTGAC 57.647 50.000 15.17 0.00 0.00 3.18
5022 5348 0.677842 AACGGCGTCTAACCTTGACT 59.322 50.000 15.17 0.00 32.70 3.41
5023 5349 0.243095 ACGGCGTCTAACCTTGACTC 59.757 55.000 6.77 0.00 32.70 3.36
5024 5350 0.526662 CGGCGTCTAACCTTGACTCT 59.473 55.000 0.00 0.00 32.70 3.24
5025 5351 1.732732 CGGCGTCTAACCTTGACTCTG 60.733 57.143 0.00 0.00 32.70 3.35
5026 5352 1.351153 GCGTCTAACCTTGACTCTGC 58.649 55.000 0.00 0.00 32.70 4.26
5027 5353 1.336887 GCGTCTAACCTTGACTCTGCA 60.337 52.381 0.00 0.00 32.70 4.41
5028 5354 2.866460 GCGTCTAACCTTGACTCTGCAA 60.866 50.000 0.00 0.00 32.70 4.08
5029 5355 3.390135 CGTCTAACCTTGACTCTGCAAA 58.610 45.455 0.00 0.00 32.70 3.68
5030 5356 3.997021 CGTCTAACCTTGACTCTGCAAAT 59.003 43.478 0.00 0.00 32.70 2.32
5031 5357 5.168569 CGTCTAACCTTGACTCTGCAAATA 58.831 41.667 0.00 0.00 32.70 1.40
5032 5358 5.637810 CGTCTAACCTTGACTCTGCAAATAA 59.362 40.000 0.00 0.00 32.70 1.40
5050 5376 9.679661 TGCAAATAAAGAGATTAGTTATGGTGA 57.320 29.630 0.00 0.00 31.04 4.02
5055 5381 7.856145 AAAGAGATTAGTTATGGTGAAGCTG 57.144 36.000 0.00 0.00 0.00 4.24
5056 5382 5.363939 AGAGATTAGTTATGGTGAAGCTGC 58.636 41.667 0.00 0.00 0.00 5.25
5093 5419 4.660168 ACAATCAAGTGCTTTCTCCATCT 58.340 39.130 0.00 0.00 0.00 2.90
5102 5428 2.544685 CTTTCTCCATCTAGTGTGGCG 58.455 52.381 10.79 6.38 36.66 5.69
5193 5519 3.814625 TGTGTTCAAATGAGCAGGTGTA 58.185 40.909 0.00 0.00 35.96 2.90
5194 5520 4.203226 TGTGTTCAAATGAGCAGGTGTAA 58.797 39.130 0.00 0.00 35.96 2.41
5196 5522 4.976116 GTGTTCAAATGAGCAGGTGTAAAC 59.024 41.667 0.00 0.00 35.96 2.01
5197 5523 4.642437 TGTTCAAATGAGCAGGTGTAAACA 59.358 37.500 0.00 0.00 31.61 2.83
5200 5526 5.316167 TCAAATGAGCAGGTGTAAACATCT 58.684 37.500 0.00 0.00 37.94 2.90
5201 5527 5.412594 TCAAATGAGCAGGTGTAAACATCTC 59.587 40.000 0.00 0.00 34.53 2.75
5202 5528 4.833478 ATGAGCAGGTGTAAACATCTCT 57.167 40.909 0.00 0.00 34.53 3.10
5203 5529 3.930336 TGAGCAGGTGTAAACATCTCTG 58.070 45.455 0.00 0.72 34.53 3.35
5207 5533 3.619038 GCAGGTGTAAACATCTCTGCTAC 59.381 47.826 19.42 0.00 40.52 3.58
5293 5814 5.467035 TTGCTTGCCTTTGCTAAGTTTAT 57.533 34.783 7.14 0.00 38.71 1.40
5294 5815 5.467035 TGCTTGCCTTTGCTAAGTTTATT 57.533 34.783 7.14 0.00 38.71 1.40
5295 5816 6.582677 TGCTTGCCTTTGCTAAGTTTATTA 57.417 33.333 7.14 0.00 38.71 0.98
5512 6040 1.672030 CGAACTGCATCAGGTGGCA 60.672 57.895 0.00 0.00 35.51 4.92
5514 6042 1.915614 GAACTGCATCAGGTGGCACG 61.916 60.000 12.17 0.00 35.51 5.34
5575 6103 5.007430 CGTCCTCAATCATTCAGAATTCAGG 59.993 44.000 8.44 1.63 0.00 3.86
5624 6152 3.072476 TGGGTTCTTTTTCGATCTGTCCT 59.928 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.691850 CGGTGAATCTTAGGTAGGGGGA 60.692 54.545 0.00 0.00 0.00 4.81
142 155 8.773033 ATAGTGATTTCTTTATTGCCCTTGAT 57.227 30.769 0.00 0.00 0.00 2.57
143 156 8.593945 AATAGTGATTTCTTTATTGCCCTTGA 57.406 30.769 0.00 0.00 0.00 3.02
167 180 9.127277 ACTCACTACTTAATTGTGCCTTTAAAA 57.873 29.630 0.00 0.00 34.42 1.52
175 188 7.421530 TCTCAAACTCACTACTTAATTGTGC 57.578 36.000 0.00 0.00 34.42 4.57
178 191 8.777865 TCCATCTCAAACTCACTACTTAATTG 57.222 34.615 0.00 0.00 0.00 2.32
180 193 7.400339 TCCTCCATCTCAAACTCACTACTTAAT 59.600 37.037 0.00 0.00 0.00 1.40
226 239 7.622081 TGTCCTAGTGATCTCCATACCTAAAAA 59.378 37.037 0.00 0.00 0.00 1.94
233 246 6.716934 TTTCTGTCCTAGTGATCTCCATAC 57.283 41.667 0.00 0.00 0.00 2.39
283 297 9.780413 GATGAAGAATTTTCTTGATGTAACTCC 57.220 33.333 10.16 0.00 46.84 3.85
300 314 7.272037 ACTTGGTGTTAAAACGATGAAGAAT 57.728 32.000 0.00 0.00 0.00 2.40
382 396 1.736126 CATGCACTCAAGCTCGTCATT 59.264 47.619 0.00 0.00 34.99 2.57
391 405 1.901591 ACCCTTGACATGCACTCAAG 58.098 50.000 21.58 21.58 42.95 3.02
398 412 5.841957 AGAATATGAAACCCTTGACATGC 57.158 39.130 0.00 0.00 0.00 4.06
412 426 8.851541 AAAAACCTAACAACGGTAGAATATGA 57.148 30.769 0.00 0.00 33.53 2.15
541 700 7.030768 GCCATGTACTCCGCTTTATTTTAAAA 58.969 34.615 2.51 2.51 0.00 1.52
555 715 4.991687 GCTTCTGTAATAGCCATGTACTCC 59.008 45.833 0.00 0.00 0.00 3.85
558 718 5.760253 ACATGCTTCTGTAATAGCCATGTAC 59.240 40.000 0.00 0.00 37.94 2.90
583 743 9.260002 CAAACATTTTAGCCAAACTGATACTTT 57.740 29.630 2.17 0.00 30.90 2.66
587 747 9.853555 CATACAAACATTTTAGCCAAACTGATA 57.146 29.630 2.17 0.00 30.90 2.15
604 764 5.826601 TCACAAAGTTCAGCATACAAACA 57.173 34.783 0.00 0.00 0.00 2.83
633 793 6.446318 TGCTAAAGATACCACAAGCAAAAAG 58.554 36.000 0.00 0.00 37.05 2.27
639 799 3.873910 TCCTGCTAAAGATACCACAAGC 58.126 45.455 0.00 0.00 0.00 4.01
641 801 6.721318 AGATTTCCTGCTAAAGATACCACAA 58.279 36.000 0.00 0.00 0.00 3.33
655 817 3.117046 GAGTGTACGCTAGATTTCCTGC 58.883 50.000 9.36 0.00 0.00 4.85
669 831 9.733219 GTAATTGTAATAGAGGTCAGAGTGTAC 57.267 37.037 0.00 0.00 0.00 2.90
1420 1623 9.301153 GAAGTTGTTGTTGTACAAATCAAGAAT 57.699 29.630 18.37 8.69 40.15 2.40
1548 1751 0.392336 GATACTGCAGCCTCCTCCAG 59.608 60.000 15.27 0.00 0.00 3.86
1992 2195 0.546122 ACAACTGCAACACCTCCAGA 59.454 50.000 0.00 0.00 0.00 3.86
1995 2198 1.455383 CCCACAACTGCAACACCTCC 61.455 60.000 0.00 0.00 0.00 4.30
2432 2635 2.983229 TCTGATCAAGAAGCAGCTTCC 58.017 47.619 28.34 14.97 40.98 3.46
2631 2834 0.530650 AGTTCAGTATCCGCATGCCG 60.531 55.000 13.15 5.80 0.00 5.69
2853 3056 2.832778 ATGGTCTGTGCCAGCACCA 61.833 57.895 19.47 18.86 45.63 4.17
3111 3314 0.179073 CTGGCATCGTCCCCTTGTAG 60.179 60.000 0.00 0.00 0.00 2.74
3657 3965 7.357303 ACAACAATAATTAACTGAACGTGGAC 58.643 34.615 0.00 0.00 0.00 4.02
3662 3970 7.075121 TGCAGACAACAATAATTAACTGAACG 58.925 34.615 0.00 0.00 0.00 3.95
3841 4151 5.715434 TTTTGAGTTAATAAAAGCGCCCT 57.285 34.783 2.29 0.00 0.00 5.19
3920 4230 0.661187 GTGTTTGGCTGTGTGCATCG 60.661 55.000 0.00 0.00 45.15 3.84
3925 4235 2.622942 ACTATTGGTGTTTGGCTGTGTG 59.377 45.455 0.00 0.00 0.00 3.82
3926 4236 2.884639 GACTATTGGTGTTTGGCTGTGT 59.115 45.455 0.00 0.00 0.00 3.72
3988 4300 5.014333 AGGTGTCGGTCCTATATATGACTCT 59.986 44.000 15.20 4.56 33.04 3.24
3989 4301 5.254901 AGGTGTCGGTCCTATATATGACTC 58.745 45.833 15.20 7.13 33.04 3.36
4088 4401 7.095910 TGTATAGATAGACAGTCGGCTACTAC 58.904 42.308 5.48 4.78 35.76 2.73
4100 4413 8.926092 AGTGTATCTGCTTGTATAGATAGACA 57.074 34.615 17.93 5.46 45.40 3.41
4124 4437 4.733565 CGACGGTTCGTTGTAAGATTAG 57.266 45.455 0.00 0.00 41.37 1.73
4141 4454 0.737367 TCTGCAAATCCAGAGCGACG 60.737 55.000 0.00 0.00 36.96 5.12
4148 4461 2.688507 ACACGTACTCTGCAAATCCAG 58.311 47.619 0.00 0.00 0.00 3.86
4166 4479 6.867519 TTTCATCCACCTTGAGAGTATACA 57.132 37.500 5.50 0.00 0.00 2.29
4251 4564 3.781307 CCATCGCCGAACTCCCCA 61.781 66.667 0.00 0.00 0.00 4.96
4260 4573 1.745115 AATGTCCACACCATCGCCG 60.745 57.895 0.00 0.00 0.00 6.46
4323 4636 3.907221 CCTTGGGTCCATGATCTTGATT 58.093 45.455 10.07 0.00 0.00 2.57
4560 4873 0.454957 CCTTTGCTTCATCGGTTGCG 60.455 55.000 0.00 0.00 0.00 4.85
4611 4924 2.172293 GAGATTGGGAGGCAGTGAAGAT 59.828 50.000 0.00 0.00 0.00 2.40
4732 5045 3.633065 AGAAGCCAGAGACCTACGATTAC 59.367 47.826 0.00 0.00 0.00 1.89
4733 5046 3.632604 CAGAAGCCAGAGACCTACGATTA 59.367 47.826 0.00 0.00 0.00 1.75
4734 5047 2.428890 CAGAAGCCAGAGACCTACGATT 59.571 50.000 0.00 0.00 0.00 3.34
4736 5049 1.271982 ACAGAAGCCAGAGACCTACGA 60.272 52.381 0.00 0.00 0.00 3.43
4821 5144 9.793259 TCTTGATTGTAACAGGAAAGTAAAGAT 57.207 29.630 0.00 0.00 0.00 2.40
4823 5146 9.273016 TCTCTTGATTGTAACAGGAAAGTAAAG 57.727 33.333 0.00 0.00 0.00 1.85
4824 5147 9.052759 GTCTCTTGATTGTAACAGGAAAGTAAA 57.947 33.333 0.00 0.00 0.00 2.01
4912 5238 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
4914 5240 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
4915 5241 2.335092 ATTCTGATGCAGAGGCCGGG 62.335 60.000 2.18 0.00 41.75 5.73
4916 5242 1.147824 ATTCTGATGCAGAGGCCGG 59.852 57.895 0.00 0.00 41.75 6.13
4917 5243 0.179065 TCATTCTGATGCAGAGGCCG 60.179 55.000 0.00 0.00 41.75 6.13
4918 5244 1.880675 CATCATTCTGATGCAGAGGCC 59.119 52.381 0.00 0.00 46.37 5.19
4927 5253 4.060900 GTGGTCGTATGCATCATTCTGAT 58.939 43.478 0.19 0.00 37.65 2.90
4928 5254 3.118811 TGTGGTCGTATGCATCATTCTGA 60.119 43.478 0.19 0.00 0.00 3.27
4929 5255 3.197265 TGTGGTCGTATGCATCATTCTG 58.803 45.455 0.19 0.00 0.00 3.02
4930 5256 3.541996 TGTGGTCGTATGCATCATTCT 57.458 42.857 0.19 0.00 0.00 2.40
4931 5257 4.818534 AATGTGGTCGTATGCATCATTC 57.181 40.909 0.19 0.00 0.00 2.67
4932 5258 6.882610 ATAAATGTGGTCGTATGCATCATT 57.117 33.333 0.19 1.76 0.00 2.57
4933 5259 7.386059 TCTATAAATGTGGTCGTATGCATCAT 58.614 34.615 0.19 0.00 0.00 2.45
4934 5260 6.754193 TCTATAAATGTGGTCGTATGCATCA 58.246 36.000 0.19 0.00 0.00 3.07
4935 5261 7.834068 ATCTATAAATGTGGTCGTATGCATC 57.166 36.000 0.19 0.00 0.00 3.91
4936 5262 9.719355 TTTATCTATAAATGTGGTCGTATGCAT 57.281 29.630 3.79 3.79 0.00 3.96
4937 5263 9.719355 ATTTATCTATAAATGTGGTCGTATGCA 57.281 29.630 7.07 0.00 40.42 3.96
4956 5282 9.232473 GACCTTGTTGAACCTCTTTATTTATCT 57.768 33.333 0.00 0.00 0.00 1.98
4957 5283 9.232473 AGACCTTGTTGAACCTCTTTATTTATC 57.768 33.333 0.00 0.00 0.00 1.75
4958 5284 9.588096 AAGACCTTGTTGAACCTCTTTATTTAT 57.412 29.630 0.00 0.00 0.00 1.40
4959 5285 8.990163 AAGACCTTGTTGAACCTCTTTATTTA 57.010 30.769 0.00 0.00 0.00 1.40
4960 5286 7.898014 AAGACCTTGTTGAACCTCTTTATTT 57.102 32.000 0.00 0.00 0.00 1.40
4962 5288 9.892130 CTATAAGACCTTGTTGAACCTCTTTAT 57.108 33.333 0.00 0.00 0.00 1.40
4963 5289 8.877195 ACTATAAGACCTTGTTGAACCTCTTTA 58.123 33.333 0.00 0.00 0.00 1.85
4964 5290 7.746703 ACTATAAGACCTTGTTGAACCTCTTT 58.253 34.615 0.00 0.00 0.00 2.52
4965 5291 7.235812 AGACTATAAGACCTTGTTGAACCTCTT 59.764 37.037 0.00 0.00 0.00 2.85
4966 5292 6.726764 AGACTATAAGACCTTGTTGAACCTCT 59.273 38.462 0.00 0.00 0.00 3.69
4967 5293 6.814146 CAGACTATAAGACCTTGTTGAACCTC 59.186 42.308 0.00 0.00 0.00 3.85
4968 5294 6.497259 TCAGACTATAAGACCTTGTTGAACCT 59.503 38.462 0.00 0.00 0.00 3.50
4969 5295 6.698380 TCAGACTATAAGACCTTGTTGAACC 58.302 40.000 0.00 0.00 0.00 3.62
4970 5296 8.603242 TTTCAGACTATAAGACCTTGTTGAAC 57.397 34.615 0.00 0.00 0.00 3.18
4971 5297 9.052759 GTTTTCAGACTATAAGACCTTGTTGAA 57.947 33.333 0.00 0.00 0.00 2.69
4972 5298 8.208224 TGTTTTCAGACTATAAGACCTTGTTGA 58.792 33.333 0.00 0.00 0.00 3.18
4973 5299 8.378172 TGTTTTCAGACTATAAGACCTTGTTG 57.622 34.615 0.00 0.00 0.00 3.33
4974 5300 8.974060 TTGTTTTCAGACTATAAGACCTTGTT 57.026 30.769 0.00 0.00 0.00 2.83
4975 5301 8.974060 TTTGTTTTCAGACTATAAGACCTTGT 57.026 30.769 0.00 0.00 0.00 3.16
4982 5308 9.274065 GCCGTTATTTTGTTTTCAGACTATAAG 57.726 33.333 0.00 0.00 0.00 1.73
4983 5309 7.958567 CGCCGTTATTTTGTTTTCAGACTATAA 59.041 33.333 0.00 0.00 0.00 0.98
4984 5310 7.118101 ACGCCGTTATTTTGTTTTCAGACTATA 59.882 33.333 0.00 0.00 0.00 1.31
4985 5311 6.072893 ACGCCGTTATTTTGTTTTCAGACTAT 60.073 34.615 0.00 0.00 0.00 2.12
4986 5312 5.236911 ACGCCGTTATTTTGTTTTCAGACTA 59.763 36.000 0.00 0.00 0.00 2.59
4987 5313 4.035909 ACGCCGTTATTTTGTTTTCAGACT 59.964 37.500 0.00 0.00 0.00 3.24
4988 5314 4.284485 ACGCCGTTATTTTGTTTTCAGAC 58.716 39.130 0.00 0.00 0.00 3.51
4989 5315 4.273969 AGACGCCGTTATTTTGTTTTCAGA 59.726 37.500 0.00 0.00 0.00 3.27
4990 5316 4.533222 AGACGCCGTTATTTTGTTTTCAG 58.467 39.130 0.00 0.00 0.00 3.02
4991 5317 4.555348 AGACGCCGTTATTTTGTTTTCA 57.445 36.364 0.00 0.00 0.00 2.69
4992 5318 5.340403 GGTTAGACGCCGTTATTTTGTTTTC 59.660 40.000 0.00 0.00 0.00 2.29
4993 5319 5.008911 AGGTTAGACGCCGTTATTTTGTTTT 59.991 36.000 0.00 0.00 0.00 2.43
4994 5320 4.516321 AGGTTAGACGCCGTTATTTTGTTT 59.484 37.500 0.00 0.00 0.00 2.83
4995 5321 4.067192 AGGTTAGACGCCGTTATTTTGTT 58.933 39.130 0.00 0.00 0.00 2.83
4996 5322 3.667360 AGGTTAGACGCCGTTATTTTGT 58.333 40.909 0.00 0.00 0.00 2.83
4997 5323 4.152759 TCAAGGTTAGACGCCGTTATTTTG 59.847 41.667 0.00 0.00 0.00 2.44
4998 5324 4.152938 GTCAAGGTTAGACGCCGTTATTTT 59.847 41.667 0.00 0.00 0.00 1.82
4999 5325 3.681417 GTCAAGGTTAGACGCCGTTATTT 59.319 43.478 0.00 0.00 0.00 1.40
5000 5326 3.056322 AGTCAAGGTTAGACGCCGTTATT 60.056 43.478 0.00 0.00 40.84 1.40
5001 5327 2.494870 AGTCAAGGTTAGACGCCGTTAT 59.505 45.455 0.00 0.00 40.84 1.89
5002 5328 1.888512 AGTCAAGGTTAGACGCCGTTA 59.111 47.619 0.00 0.00 40.84 3.18
5003 5329 0.677842 AGTCAAGGTTAGACGCCGTT 59.322 50.000 0.00 0.00 40.84 4.44
5004 5330 0.243095 GAGTCAAGGTTAGACGCCGT 59.757 55.000 0.00 0.00 40.84 5.68
5005 5331 0.526662 AGAGTCAAGGTTAGACGCCG 59.473 55.000 0.00 0.00 40.84 6.46
5006 5332 1.997669 CAGAGTCAAGGTTAGACGCC 58.002 55.000 0.00 0.00 40.84 5.68
5007 5333 1.336887 TGCAGAGTCAAGGTTAGACGC 60.337 52.381 0.00 0.00 40.84 5.19
5008 5334 2.724977 TGCAGAGTCAAGGTTAGACG 57.275 50.000 0.00 0.00 40.84 4.18
5009 5335 7.387948 TCTTTATTTGCAGAGTCAAGGTTAGAC 59.612 37.037 0.00 0.00 36.26 2.59
5010 5336 7.450074 TCTTTATTTGCAGAGTCAAGGTTAGA 58.550 34.615 0.00 0.00 0.00 2.10
5011 5337 7.604164 TCTCTTTATTTGCAGAGTCAAGGTTAG 59.396 37.037 0.00 0.00 38.20 2.34
5012 5338 7.450074 TCTCTTTATTTGCAGAGTCAAGGTTA 58.550 34.615 0.00 0.00 38.20 2.85
5013 5339 6.299141 TCTCTTTATTTGCAGAGTCAAGGTT 58.701 36.000 0.00 0.00 38.20 3.50
5014 5340 5.869579 TCTCTTTATTTGCAGAGTCAAGGT 58.130 37.500 0.00 0.00 38.20 3.50
5015 5341 6.998968 ATCTCTTTATTTGCAGAGTCAAGG 57.001 37.500 0.00 0.00 38.20 3.61
5016 5342 9.160496 ACTAATCTCTTTATTTGCAGAGTCAAG 57.840 33.333 0.00 0.00 38.20 3.02
5017 5343 9.507329 AACTAATCTCTTTATTTGCAGAGTCAA 57.493 29.630 0.00 0.00 38.20 3.18
5022 5348 9.905713 ACCATAACTAATCTCTTTATTTGCAGA 57.094 29.630 0.00 0.00 0.00 4.26
5023 5349 9.941664 CACCATAACTAATCTCTTTATTTGCAG 57.058 33.333 0.00 0.00 0.00 4.41
5024 5350 9.679661 TCACCATAACTAATCTCTTTATTTGCA 57.320 29.630 0.00 0.00 0.00 4.08
5029 5355 9.553064 CAGCTTCACCATAACTAATCTCTTTAT 57.447 33.333 0.00 0.00 0.00 1.40
5030 5356 7.495934 GCAGCTTCACCATAACTAATCTCTTTA 59.504 37.037 0.00 0.00 0.00 1.85
5031 5357 6.317391 GCAGCTTCACCATAACTAATCTCTTT 59.683 38.462 0.00 0.00 0.00 2.52
5032 5358 5.819901 GCAGCTTCACCATAACTAATCTCTT 59.180 40.000 0.00 0.00 0.00 2.85
5055 5381 1.616159 TTGTAACAGGAAAGCAGGGC 58.384 50.000 0.00 0.00 0.00 5.19
5056 5382 3.420893 TGATTGTAACAGGAAAGCAGGG 58.579 45.455 0.00 0.00 0.00 4.45
5093 5419 2.029649 GTCAAGGTTAGACGCCACACTA 60.030 50.000 0.00 0.00 0.00 2.74
5102 5428 4.997395 TGATTTGCAGAGTCAAGGTTAGAC 59.003 41.667 0.00 0.00 36.26 2.59
5142 5468 4.124238 CCAAGTAGAGAACACCGAAAACA 58.876 43.478 0.00 0.00 0.00 2.83
5150 5476 5.527582 ACATCACAAACCAAGTAGAGAACAC 59.472 40.000 0.00 0.00 0.00 3.32
5193 5519 5.871524 CACATACACTGTAGCAGAGATGTTT 59.128 40.000 2.91 0.00 35.91 2.83
5194 5520 5.047021 ACACATACACTGTAGCAGAGATGTT 60.047 40.000 2.91 0.19 35.91 2.71
5196 5522 5.003692 ACACATACACTGTAGCAGAGATG 57.996 43.478 2.91 5.85 35.91 2.90
5197 5523 6.239148 CCATACACATACACTGTAGCAGAGAT 60.239 42.308 2.91 0.00 35.91 2.75
5200 5526 4.099419 CCCATACACATACACTGTAGCAGA 59.901 45.833 2.91 0.00 35.91 4.26
5201 5527 4.371786 CCCATACACATACACTGTAGCAG 58.628 47.826 0.00 0.00 35.91 4.24
5202 5528 3.133901 CCCCATACACATACACTGTAGCA 59.866 47.826 0.00 0.00 35.91 3.49
5203 5529 3.134081 ACCCCATACACATACACTGTAGC 59.866 47.826 0.00 0.00 35.91 3.58
5207 5533 2.092968 AGCACCCCATACACATACACTG 60.093 50.000 0.00 0.00 0.00 3.66
5261 5782 1.985473 AGGCAAGCAAACATGTGAGA 58.015 45.000 0.00 0.00 0.00 3.27
5293 5814 5.307196 GGGCCACTAGGATTATCTTGAGTAA 59.693 44.000 4.39 0.00 36.89 2.24
5294 5815 4.838986 GGGCCACTAGGATTATCTTGAGTA 59.161 45.833 4.39 0.00 36.89 2.59
5295 5816 3.648545 GGGCCACTAGGATTATCTTGAGT 59.351 47.826 4.39 0.00 36.89 3.41
5512 6040 0.612732 TCCCTACCGATTGTGACCGT 60.613 55.000 0.00 0.00 0.00 4.83
5514 6042 0.179081 GCTCCCTACCGATTGTGACC 60.179 60.000 0.00 0.00 0.00 4.02
5624 6152 3.364460 TGCTATGCTTGCCTTTTAGGA 57.636 42.857 0.00 0.00 37.67 2.94


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

AutoCloner maintained by Alex Coulton.