Multiple sequence alignment - TraesCS1D01G159000

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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 TraesCS1D01G159000 chr1D 100.000 5684 0 0 1 5684 224391323 224397006 0.000000e+00 10497.0
1 TraesCS1D01G159000 chr1A 95.433 4292 151 23 687 4961 291241863 291246126 0.000000e+00 6798.0
2 TraesCS1D01G159000 chr1A 83.684 570 62 17 4 550 291237445 291238006 5.080000e-140 508.0
3 TraesCS1D01G159000 chr1A 95.775 213 9 0 5472 5684 219383324 219383536 1.520000e-90 344.0
4 TraesCS1D01G159000 chr1A 87.097 310 24 6 5144 5439 291246776 291247083 2.540000e-88 337.0
5 TraesCS1D01G159000 chr1A 90.306 196 7 4 4957 5150 291246529 291246714 4.400000e-61 246.0
6 TraesCS1D01G159000 chr1B 96.202 4160 127 16 687 4824 324336238 324340388 0.000000e+00 6778.0
7 TraesCS1D01G159000 chr1B 83.333 642 81 17 4 626 324330085 324330719 2.300000e-158 569.0
8 TraesCS1D01G159000 chr1B 88.077 260 17 4 5194 5439 324340756 324341015 4.310000e-76 296.0
9 TraesCS1D01G159000 chr1B 91.146 192 10 2 4821 5012 324340463 324340647 2.630000e-63 254.0
10 TraesCS1D01G159000 chr4B 82.881 590 63 24 44 600 92949033 92949617 3.960000e-136 496.0
11 TraesCS1D01G159000 chr4B 81.062 565 75 23 64 603 373999655 374000212 6.810000e-114 422.0
12 TraesCS1D01G159000 chr4D 81.122 588 72 23 44 603 62822688 62823264 8.750000e-118 435.0
13 TraesCS1D01G159000 chr6D 98.354 243 4 0 5442 5684 365734383 365734141 1.460000e-115 427.0
14 TraesCS1D01G159000 chr5D 97.131 244 7 0 5441 5684 46088269 46088512 4.100000e-111 412.0
15 TraesCS1D01G159000 chr4A 95.918 245 10 0 5440 5684 56266095 56265851 1.150000e-106 398.0
16 TraesCS1D01G159000 chr2A 95.492 244 11 0 5441 5684 277609085 277608842 1.920000e-104 390.0
17 TraesCS1D01G159000 chr2A 94.309 246 8 2 5439 5684 32942980 32943219 6.960000e-99 372.0
18 TraesCS1D01G159000 chr5A 92.213 244 14 1 5441 5684 600355852 600355614 1.960000e-89 340.0
19 TraesCS1D01G159000 chr6A 90.909 242 19 3 5441 5682 143969830 143970068 7.100000e-84 322.0
20 TraesCS1D01G159000 chr3A 94.149 188 11 0 5497 5684 614232474 614232661 2.590000e-73 287.0
21 TraesCS1D01G159000 chr3D 79.839 124 23 2 152 273 599167089 599167212 7.840000e-14 89.8
22 TraesCS1D01G159000 chr2D 92.308 39 3 0 5144 5182 435145417 435145379 7.960000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G159000 chr1D 224391323 224397006 5683 False 10497.000000 10497 100.000000 1 5684 1 chr1D.!!$F1 5683
1 TraesCS1D01G159000 chr1A 291237445 291247083 9638 False 1972.250000 6798 89.130000 4 5439 4 chr1A.!!$F2 5435
2 TraesCS1D01G159000 chr1B 324336238 324341015 4777 False 2442.666667 6778 91.808333 687 5439 3 chr1B.!!$F2 4752
3 TraesCS1D01G159000 chr1B 324330085 324330719 634 False 569.000000 569 83.333000 4 626 1 chr1B.!!$F1 622
4 TraesCS1D01G159000 chr4B 92949033 92949617 584 False 496.000000 496 82.881000 44 600 1 chr4B.!!$F1 556
5 TraesCS1D01G159000 chr4B 373999655 374000212 557 False 422.000000 422 81.062000 64 603 1 chr4B.!!$F2 539
6 TraesCS1D01G159000 chr4D 62822688 62823264 576 False 435.000000 435 81.122000 44 603 1 chr4D.!!$F1 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
673 4459 0.163788 CGACGACGAGCTGCATTTTT 59.836 50.000 0.00 0.0 42.66 1.94 F
1332 5133 0.253044 CCTCTCGGCAGGATGGAAAA 59.747 55.000 0.00 0.0 35.20 2.29 F
2501 6307 1.760029 TGCTTGGATGCTCGTATGGTA 59.240 47.619 0.00 0.0 0.00 3.25 F
2802 6608 1.806542 CATCAACTTGTGGTTCTCCCG 59.193 52.381 0.00 0.0 35.74 5.14 F
4503 8311 0.240945 AGCGGCGAAAACAAATGGAG 59.759 50.000 12.98 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 5786 7.688372 ACAATCATTTCTTACAGATAGTTGCG 58.312 34.615 0.00 0.0 0.00 4.85 R
3259 7066 3.800506 GCAATGAAGCAATCACATAAGGC 59.199 43.478 0.00 0.0 41.93 4.35 R
3336 7143 0.321564 TCATCTGTTTGCACCTCCCG 60.322 55.000 0.00 0.0 0.00 5.14 R
4509 8317 0.318441 TGTTGAAGAGGTCCTCTGCG 59.682 55.000 22.53 0.0 40.28 5.18 R
5479 9938 0.029167 GCTAGGACGAGGCGACTTAC 59.971 60.000 0.00 0.0 44.43 2.34 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
79 81 6.679327 ACCCGAGCTTTATTCATTAGAAAC 57.321 37.500 0.00 0.00 37.29 2.78
83 85 7.361713 CCCGAGCTTTATTCATTAGAAACAACA 60.362 37.037 0.00 0.00 37.29 3.33
110 112 6.583912 ACGTCATTTATGAGAATTGGTACG 57.416 37.500 0.00 0.00 37.51 3.67
112 114 6.255020 ACGTCATTTATGAGAATTGGTACGAC 59.745 38.462 0.00 0.00 37.51 4.34
191 194 4.627035 GCAAGTTCTGAGCAACTTTGTTTT 59.373 37.500 7.12 0.00 42.81 2.43
198 201 5.066505 TCTGAGCAACTTTGTTTTCTTCTCC 59.933 40.000 0.00 0.00 0.00 3.71
215 218 7.055667 TCTTCTCCATTACTATGCTCGAATT 57.944 36.000 0.00 0.00 0.00 2.17
286 292 4.143333 CTGCCCCCGACGATCGTT 62.143 66.667 23.63 6.02 38.40 3.85
334 353 8.436778 TCACCTACATATTATAATGTGGTTGCT 58.563 33.333 21.79 7.16 40.29 3.91
369 388 2.354821 GCCAGCGATAGACCGAATTTTT 59.645 45.455 0.00 0.00 39.76 1.94
411 430 1.740296 GTACATCCGCGCACCAGTT 60.740 57.895 8.75 0.00 0.00 3.16
417 436 0.459585 TCCGCGCACCAGTTAATCTC 60.460 55.000 8.75 0.00 0.00 2.75
436 456 1.153168 ACCATTTCCCGAGCGATGG 60.153 57.895 6.74 6.74 43.65 3.51
485 506 3.325716 GCCCCATCGTATCCCTAAGTAAA 59.674 47.826 0.00 0.00 0.00 2.01
553 591 0.179936 GGCAAGACCATCCTCCTCTG 59.820 60.000 0.00 0.00 38.86 3.35
554 592 0.179936 GCAAGACCATCCTCCTCTGG 59.820 60.000 0.00 0.00 38.55 3.86
555 593 1.871418 CAAGACCATCCTCCTCTGGA 58.129 55.000 0.00 0.00 40.82 3.86
556 594 2.191400 CAAGACCATCCTCCTCTGGAA 58.809 52.381 0.00 0.00 39.85 3.53
559 597 1.210722 GACCATCCTCCTCTGGAAACC 59.789 57.143 0.00 0.00 39.85 3.27
560 598 1.203492 ACCATCCTCCTCTGGAAACCT 60.203 52.381 0.00 0.00 39.85 3.50
561 599 1.918957 CCATCCTCCTCTGGAAACCTT 59.081 52.381 0.00 0.00 39.85 3.50
562 600 2.310052 CCATCCTCCTCTGGAAACCTTT 59.690 50.000 0.00 0.00 39.85 3.11
563 601 3.350833 CATCCTCCTCTGGAAACCTTTG 58.649 50.000 0.00 0.00 39.85 2.77
564 602 1.705186 TCCTCCTCTGGAAACCTTTGG 59.295 52.381 0.00 0.00 32.39 3.28
585 630 4.105486 GGCGAGGAAGCAATAACAAAATC 58.895 43.478 0.00 0.00 39.27 2.17
589 634 3.763897 AGGAAGCAATAACAAAATCGGCT 59.236 39.130 0.00 0.00 0.00 5.52
628 787 8.470002 ACTTCAAGTTTTGTTTTTAGAGCTGAT 58.530 29.630 0.00 0.00 0.00 2.90
629 788 8.633075 TTCAAGTTTTGTTTTTAGAGCTGATG 57.367 30.769 0.00 0.00 0.00 3.07
631 790 8.465999 TCAAGTTTTGTTTTTAGAGCTGATGAA 58.534 29.630 0.00 0.00 0.00 2.57
632 791 9.086336 CAAGTTTTGTTTTTAGAGCTGATGAAA 57.914 29.630 0.00 0.00 0.00 2.69
670 4456 2.507102 CCGACGACGAGCTGCATT 60.507 61.111 9.28 0.00 42.66 3.56
671 4457 2.094659 CCGACGACGAGCTGCATTT 61.095 57.895 9.28 0.00 42.66 2.32
672 4458 1.626654 CCGACGACGAGCTGCATTTT 61.627 55.000 9.28 0.00 42.66 1.82
673 4459 0.163788 CGACGACGAGCTGCATTTTT 59.836 50.000 0.00 0.00 42.66 1.94
696 4482 1.662517 TTGAGACAAACGAGCTGCAA 58.337 45.000 1.02 0.00 0.00 4.08
697 4483 1.882912 TGAGACAAACGAGCTGCAAT 58.117 45.000 1.02 0.00 0.00 3.56
743 4529 1.745489 CGCCCAAGCCCAGTTACTC 60.745 63.158 0.00 0.00 34.57 2.59
795 4581 2.286184 CGAACACAAACAGAAACTCCCG 60.286 50.000 0.00 0.00 0.00 5.14
796 4582 2.702592 ACACAAACAGAAACTCCCGA 57.297 45.000 0.00 0.00 0.00 5.14
797 4583 2.993937 ACACAAACAGAAACTCCCGAA 58.006 42.857 0.00 0.00 0.00 4.30
826 4612 2.474410 TCTCAGCAGAGACGTACTCA 57.526 50.000 4.45 0.00 45.73 3.41
982 4770 5.453621 GGACTCTATCCTAGACGAGAGTGAA 60.454 48.000 19.13 0.00 46.68 3.18
1219 5018 6.716934 TGTTTAAGGCTTGTTGGTTCATTA 57.283 33.333 10.69 0.00 0.00 1.90
1246 5045 3.266541 TGTTTCTGCGTGCAATTACTG 57.733 42.857 0.00 0.00 0.00 2.74
1269 5068 5.128171 TGGTCAGTACATAGGTTGGTGATAC 59.872 44.000 0.00 0.00 0.00 2.24
1318 5117 3.321111 TGAGTTCCTGTACACAACCTCTC 59.679 47.826 8.67 5.61 0.00 3.20
1332 5133 0.253044 CCTCTCGGCAGGATGGAAAA 59.747 55.000 0.00 0.00 35.20 2.29
1399 5200 6.877611 ACGATTTTAATTTGTGTCCTGTCT 57.122 33.333 0.00 0.00 0.00 3.41
1413 5214 4.344968 TGTCCTGTCTCTTCATTTGTCTGA 59.655 41.667 0.00 0.00 0.00 3.27
1414 5215 5.163311 TGTCCTGTCTCTTCATTTGTCTGAA 60.163 40.000 0.00 0.00 34.14 3.02
1415 5216 5.760253 GTCCTGTCTCTTCATTTGTCTGAAA 59.240 40.000 0.00 0.00 34.86 2.69
1416 5217 6.429385 GTCCTGTCTCTTCATTTGTCTGAAAT 59.571 38.462 0.00 0.00 34.86 2.17
2031 5835 8.178313 TGTCAATGCATGCAATCATTTTTAATG 58.822 29.630 26.68 9.02 31.15 1.90
2133 5937 4.884668 ATTCCTGACAGGTTCTCGTTTA 57.115 40.909 21.06 0.00 36.53 2.01
2501 6307 1.760029 TGCTTGGATGCTCGTATGGTA 59.240 47.619 0.00 0.00 0.00 3.25
2802 6608 1.806542 CATCAACTTGTGGTTCTCCCG 59.193 52.381 0.00 0.00 35.74 5.14
2987 6793 4.384056 AGTTGAAAGGATATCATCAGGCG 58.616 43.478 4.83 0.00 0.00 5.52
3259 7066 3.617263 GTCAGTTACTTATTCCGGTGCTG 59.383 47.826 0.00 0.00 0.00 4.41
3296 7103 5.509163 GCTTCATTGCCTCTATTTGCATGAT 60.509 40.000 0.00 0.00 37.33 2.45
3336 7143 4.274214 GGTGGGTGTGTACTCTTTGTTTAC 59.726 45.833 0.00 0.00 0.00 2.01
3613 7421 3.058016 ACGTGCAAGAAATTGGACATCTG 60.058 43.478 6.65 0.08 42.40 2.90
3669 7477 8.519526 CAGCCTTATTGAACCTACAAATGTAAA 58.480 33.333 0.00 0.00 33.44 2.01
3800 7608 3.199508 AGCAAGTCTCAGCACCATATTCT 59.800 43.478 0.73 0.00 0.00 2.40
3988 7796 0.877743 GTTCAAAGCTGGAGGTGAGC 59.122 55.000 0.00 0.00 36.65 4.26
3995 7803 1.364626 GCTGGAGGTGAGCATGTTCG 61.365 60.000 5.02 0.00 36.40 3.95
4139 7947 3.146066 TGATTGTCAAAAGGGTCCTTCG 58.854 45.455 2.37 0.00 34.84 3.79
4150 7958 2.058595 GTCCTTCGGCCAGCTCCTA 61.059 63.158 2.24 0.00 0.00 2.94
4158 7966 2.646175 GCCAGCTCCTACCGTGTCA 61.646 63.158 0.00 0.00 0.00 3.58
4173 7981 1.604278 GTGTCAACAGAAACTGGAGGC 59.396 52.381 0.00 0.00 35.51 4.70
4207 8015 7.860373 TCAAACGATTCAAAAAGGTATGTTCTG 59.140 33.333 0.00 0.00 0.00 3.02
4219 8027 5.605534 AGGTATGTTCTGTATGCTCATGTC 58.394 41.667 0.00 0.00 0.00 3.06
4223 8031 3.193479 TGTTCTGTATGCTCATGTCGTCT 59.807 43.478 0.00 0.00 0.00 4.18
4364 8172 6.805016 ACAGGTAAGATCATGATGACTTCT 57.195 37.500 14.30 0.80 0.00 2.85
4365 8173 6.580788 ACAGGTAAGATCATGATGACTTCTG 58.419 40.000 14.30 15.79 0.00 3.02
4366 8174 6.155910 ACAGGTAAGATCATGATGACTTCTGT 59.844 38.462 14.30 16.34 29.30 3.41
4378 8186 5.827267 TGATGACTTCTGTTGGAATTTGACA 59.173 36.000 0.00 0.00 33.01 3.58
4394 8202 7.756722 GGAATTTGACATTCATCAGTAGGTTTG 59.243 37.037 0.00 0.00 0.00 2.93
4400 8208 4.901197 TTCATCAGTAGGTTTGGCACTA 57.099 40.909 0.00 0.00 0.00 2.74
4410 8218 3.572682 AGGTTTGGCACTAAAAGGCTTAC 59.427 43.478 0.00 0.00 0.00 2.34
4431 8239 3.756963 ACCTTATTCTGTTTCCTTTCCGC 59.243 43.478 0.00 0.00 0.00 5.54
4437 8245 2.104111 TCTGTTTCCTTTCCGCAGAGAA 59.896 45.455 0.00 0.00 33.05 2.87
4494 8302 0.389948 GAGAGGAGAAGCGGCGAAAA 60.390 55.000 12.98 0.00 0.00 2.29
4503 8311 0.240945 AGCGGCGAAAACAAATGGAG 59.759 50.000 12.98 0.00 0.00 3.86
4509 8317 3.501950 GCGAAAACAAATGGAGTCCATC 58.498 45.455 25.01 10.63 44.40 3.51
4580 8388 0.618458 GCCACTCCCATAACCTGTGA 59.382 55.000 0.00 0.00 0.00 3.58
4586 8394 3.273434 CTCCCATAACCTGTGATGTGTG 58.727 50.000 0.00 0.00 0.00 3.82
4691 8499 1.648467 GGTTGCCGATGAAGTCCAGC 61.648 60.000 0.00 0.00 0.00 4.85
4694 8502 0.829990 TGCCGATGAAGTCCAGCATA 59.170 50.000 0.00 0.00 30.16 3.14
4800 8608 1.079543 CCACGAGAGAAGCCAGTGG 60.080 63.158 4.20 4.20 45.01 4.00
4819 8707 6.850555 CAGTGGTGGAAACTACTACTACTAC 58.149 44.000 4.34 0.00 39.90 2.73
4873 8761 5.995897 TGAATTGTCAGATATCATGCTCAGG 59.004 40.000 5.32 0.00 0.00 3.86
5026 9401 4.080015 AGTTTGGTAGCTTACATATGGCCA 60.080 41.667 8.56 8.56 0.00 5.36
5054 9429 3.243359 TGAAAGCACCAATCCCTTCTT 57.757 42.857 0.00 0.00 0.00 2.52
5063 9438 0.108138 AATCCCTTCTTCCTCACGCG 60.108 55.000 3.53 3.53 0.00 6.01
5073 9448 2.051345 CTCACGCGTTTGGTTGCC 60.051 61.111 10.22 0.00 0.00 4.52
5159 9604 4.098155 TGTTAGCATCTACCACCCTAACA 58.902 43.478 7.28 7.28 43.03 2.41
5161 9606 3.914426 AGCATCTACCACCCTAACAAG 57.086 47.619 0.00 0.00 0.00 3.16
5223 9668 6.128391 GCCAATAAAACGACACTACAATCAGA 60.128 38.462 0.00 0.00 0.00 3.27
5242 9687 4.929211 TCAGAACGAATTGAATGATGACGT 59.071 37.500 0.00 0.00 0.00 4.34
5314 9759 1.451028 GCATCCTCTGCCTTTCGCT 60.451 57.895 0.00 0.00 45.66 4.93
5330 9775 5.983118 CCTTTCGCTTGGTCATAAAACTTTT 59.017 36.000 0.00 0.00 0.00 2.27
5341 9786 6.292328 GGTCATAAAACTTTTGAAGCAGTTGC 60.292 38.462 0.00 0.00 42.49 4.17
5369 9814 7.004555 TGTAATAGGTCACTTGTTCATGACT 57.995 36.000 0.00 0.00 43.91 3.41
5412 9871 0.104304 CCTCCCTATGTACACCACGC 59.896 60.000 0.00 0.00 0.00 5.34
5461 9920 8.460831 AAAAGGAAATCGTTTATTTTCATCCG 57.539 30.769 1.93 0.00 37.93 4.18
5462 9921 6.131544 AGGAAATCGTTTATTTTCATCCGG 57.868 37.500 0.00 0.00 37.93 5.14
5463 9922 4.738252 GGAAATCGTTTATTTTCATCCGGC 59.262 41.667 0.00 0.00 37.93 6.13
5464 9923 5.449999 GGAAATCGTTTATTTTCATCCGGCT 60.450 40.000 0.00 0.00 37.93 5.52
5465 9924 4.552166 ATCGTTTATTTTCATCCGGCTG 57.448 40.909 0.00 0.00 0.00 4.85
5466 9925 3.601435 TCGTTTATTTTCATCCGGCTGA 58.399 40.909 3.28 3.28 0.00 4.26
5467 9926 4.196193 TCGTTTATTTTCATCCGGCTGAT 58.804 39.130 9.15 0.00 0.00 2.90
5468 9927 5.361427 TCGTTTATTTTCATCCGGCTGATA 58.639 37.500 9.15 1.01 30.56 2.15
5469 9928 5.818336 TCGTTTATTTTCATCCGGCTGATAA 59.182 36.000 9.15 11.11 30.56 1.75
5470 9929 5.907391 CGTTTATTTTCATCCGGCTGATAAC 59.093 40.000 9.15 7.91 30.56 1.89
5471 9930 6.457663 CGTTTATTTTCATCCGGCTGATAACA 60.458 38.462 9.15 0.00 30.56 2.41
5472 9931 6.618287 TTATTTTCATCCGGCTGATAACAG 57.382 37.500 9.15 0.00 45.91 3.16
5480 9939 4.072913 CTGATAACAGCGACGCGT 57.927 55.556 13.85 13.85 37.33 6.01
5481 9940 3.229652 CTGATAACAGCGACGCGTA 57.770 52.632 13.97 8.71 37.33 4.42
5482 9941 1.541475 CTGATAACAGCGACGCGTAA 58.459 50.000 13.97 1.75 37.33 3.18
5483 9942 1.513178 CTGATAACAGCGACGCGTAAG 59.487 52.381 13.97 11.24 37.33 2.34
5484 9943 1.135603 TGATAACAGCGACGCGTAAGT 60.136 47.619 13.97 5.54 41.68 2.24
5485 9944 1.511958 GATAACAGCGACGCGTAAGTC 59.488 52.381 13.97 7.91 41.68 3.01
5495 9954 3.185155 CGTAAGTCGCCTCGTCCT 58.815 61.111 0.00 0.00 0.00 3.85
5496 9955 2.387309 CGTAAGTCGCCTCGTCCTA 58.613 57.895 0.00 0.00 0.00 2.94
5497 9956 0.304098 CGTAAGTCGCCTCGTCCTAG 59.696 60.000 0.00 0.00 0.00 3.02
5498 9957 0.029167 GTAAGTCGCCTCGTCCTAGC 59.971 60.000 0.00 0.00 0.00 3.42
5508 9967 2.576317 GTCCTAGCGACGCGTGTC 60.576 66.667 20.70 19.11 41.91 3.67
5509 9968 3.807538 TCCTAGCGACGCGTGTCC 61.808 66.667 20.70 15.15 42.37 4.02
5510 9969 3.812019 CCTAGCGACGCGTGTCCT 61.812 66.667 20.70 20.71 42.37 3.85
5511 9970 2.577112 CTAGCGACGCGTGTCCTG 60.577 66.667 20.70 11.23 42.37 3.86
5512 9971 4.771356 TAGCGACGCGTGTCCTGC 62.771 66.667 20.70 19.98 42.37 4.85
5530 9989 4.947147 GTGGCGTGGACCTGGCAA 62.947 66.667 13.66 0.00 42.68 4.52
5531 9990 4.947147 TGGCGTGGACCTGGCAAC 62.947 66.667 10.40 0.00 37.75 4.17
5533 9992 4.643387 GCGTGGACCTGGCAACCT 62.643 66.667 0.00 0.00 0.00 3.50
5534 9993 2.113139 CGTGGACCTGGCAACCTT 59.887 61.111 0.00 0.00 0.00 3.50
5535 9994 1.373435 CGTGGACCTGGCAACCTTA 59.627 57.895 0.00 0.00 0.00 2.69
5536 9995 0.035439 CGTGGACCTGGCAACCTTAT 60.035 55.000 0.00 0.00 0.00 1.73
5537 9996 1.751437 GTGGACCTGGCAACCTTATC 58.249 55.000 0.00 0.00 0.00 1.75
5538 9997 0.623723 TGGACCTGGCAACCTTATCC 59.376 55.000 0.00 0.00 0.00 2.59
5539 9998 0.919710 GGACCTGGCAACCTTATCCT 59.080 55.000 0.00 0.00 0.00 3.24
5540 9999 1.134068 GGACCTGGCAACCTTATCCTC 60.134 57.143 0.00 0.00 0.00 3.71
5541 10000 1.840635 GACCTGGCAACCTTATCCTCT 59.159 52.381 0.00 0.00 0.00 3.69
5542 10001 1.840635 ACCTGGCAACCTTATCCTCTC 59.159 52.381 0.00 0.00 0.00 3.20
5543 10002 1.141858 CCTGGCAACCTTATCCTCTCC 59.858 57.143 0.00 0.00 0.00 3.71
5544 10003 0.830648 TGGCAACCTTATCCTCTCCG 59.169 55.000 0.00 0.00 0.00 4.63
5545 10004 0.533085 GGCAACCTTATCCTCTCCGC 60.533 60.000 0.00 0.00 0.00 5.54
5546 10005 0.876342 GCAACCTTATCCTCTCCGCG 60.876 60.000 0.00 0.00 0.00 6.46
5547 10006 0.460311 CAACCTTATCCTCTCCGCGT 59.540 55.000 4.92 0.00 0.00 6.01
5548 10007 0.460311 AACCTTATCCTCTCCGCGTG 59.540 55.000 4.92 0.00 0.00 5.34
5549 10008 1.300233 CCTTATCCTCTCCGCGTGC 60.300 63.158 4.92 0.00 0.00 5.34
5550 10009 1.300233 CTTATCCTCTCCGCGTGCC 60.300 63.158 4.92 0.00 0.00 5.01
5551 10010 2.701163 CTTATCCTCTCCGCGTGCCC 62.701 65.000 4.92 0.00 0.00 5.36
5566 10025 2.825264 CCCCTCGGCTTCCTCATC 59.175 66.667 0.00 0.00 0.00 2.92
5567 10026 1.764054 CCCCTCGGCTTCCTCATCT 60.764 63.158 0.00 0.00 0.00 2.90
5568 10027 1.745264 CCCTCGGCTTCCTCATCTC 59.255 63.158 0.00 0.00 0.00 2.75
5569 10028 1.745264 CCTCGGCTTCCTCATCTCC 59.255 63.158 0.00 0.00 0.00 3.71
5570 10029 0.758685 CCTCGGCTTCCTCATCTCCT 60.759 60.000 0.00 0.00 0.00 3.69
5571 10030 1.479573 CCTCGGCTTCCTCATCTCCTA 60.480 57.143 0.00 0.00 0.00 2.94
5572 10031 1.611491 CTCGGCTTCCTCATCTCCTAC 59.389 57.143 0.00 0.00 0.00 3.18
5573 10032 0.676736 CGGCTTCCTCATCTCCTACC 59.323 60.000 0.00 0.00 0.00 3.18
5574 10033 1.755977 CGGCTTCCTCATCTCCTACCT 60.756 57.143 0.00 0.00 0.00 3.08
5575 10034 2.403561 GGCTTCCTCATCTCCTACCTT 58.596 52.381 0.00 0.00 0.00 3.50
5576 10035 2.774809 GGCTTCCTCATCTCCTACCTTT 59.225 50.000 0.00 0.00 0.00 3.11
5577 10036 3.432890 GGCTTCCTCATCTCCTACCTTTG 60.433 52.174 0.00 0.00 0.00 2.77
5578 10037 3.802866 CTTCCTCATCTCCTACCTTTGC 58.197 50.000 0.00 0.00 0.00 3.68
5579 10038 2.832838 TCCTCATCTCCTACCTTTGCA 58.167 47.619 0.00 0.00 0.00 4.08
5580 10039 2.768527 TCCTCATCTCCTACCTTTGCAG 59.231 50.000 0.00 0.00 0.00 4.41
5581 10040 2.768527 CCTCATCTCCTACCTTTGCAGA 59.231 50.000 0.00 0.00 0.00 4.26
5582 10041 3.198635 CCTCATCTCCTACCTTTGCAGAA 59.801 47.826 0.00 0.00 0.00 3.02
5583 10042 4.440880 CTCATCTCCTACCTTTGCAGAAG 58.559 47.826 0.00 0.00 0.00 2.85
5584 10043 2.770164 TCTCCTACCTTTGCAGAAGC 57.230 50.000 0.00 0.00 42.57 3.86
5596 10055 1.772836 GCAGAAGCAAATCCCCATCT 58.227 50.000 0.00 0.00 41.58 2.90
5597 10056 1.680207 GCAGAAGCAAATCCCCATCTC 59.320 52.381 0.00 0.00 41.58 2.75
5598 10057 2.686118 GCAGAAGCAAATCCCCATCTCT 60.686 50.000 0.00 0.00 41.58 3.10
5599 10058 3.629087 CAGAAGCAAATCCCCATCTCTT 58.371 45.455 0.00 0.00 0.00 2.85
5600 10059 4.021916 CAGAAGCAAATCCCCATCTCTTT 58.978 43.478 0.00 0.00 0.00 2.52
5601 10060 4.097589 CAGAAGCAAATCCCCATCTCTTTC 59.902 45.833 0.00 0.00 0.00 2.62
5602 10061 4.017683 AGAAGCAAATCCCCATCTCTTTCT 60.018 41.667 0.00 0.00 0.00 2.52
5603 10062 3.895998 AGCAAATCCCCATCTCTTTCTC 58.104 45.455 0.00 0.00 0.00 2.87
5604 10063 2.954989 GCAAATCCCCATCTCTTTCTCC 59.045 50.000 0.00 0.00 0.00 3.71
5605 10064 3.209410 CAAATCCCCATCTCTTTCTCCG 58.791 50.000 0.00 0.00 0.00 4.63
5606 10065 1.428869 ATCCCCATCTCTTTCTCCGG 58.571 55.000 0.00 0.00 0.00 5.14
5607 10066 0.338467 TCCCCATCTCTTTCTCCGGA 59.662 55.000 2.93 2.93 0.00 5.14
5608 10067 0.466124 CCCCATCTCTTTCTCCGGAC 59.534 60.000 0.00 0.00 0.00 4.79
5609 10068 0.103208 CCCATCTCTTTCTCCGGACG 59.897 60.000 0.00 0.00 0.00 4.79
5610 10069 0.528684 CCATCTCTTTCTCCGGACGC 60.529 60.000 0.00 0.00 0.00 5.19
5611 10070 0.173481 CATCTCTTTCTCCGGACGCA 59.827 55.000 0.00 0.00 0.00 5.24
5612 10071 0.457851 ATCTCTTTCTCCGGACGCAG 59.542 55.000 0.00 0.00 0.00 5.18
5613 10072 1.153745 CTCTTTCTCCGGACGCAGG 60.154 63.158 0.00 0.00 0.00 4.85
5614 10073 1.595993 CTCTTTCTCCGGACGCAGGA 61.596 60.000 0.00 0.00 36.20 3.86
5615 10074 0.970937 TCTTTCTCCGGACGCAGGAT 60.971 55.000 0.00 0.00 37.13 3.24
5616 10075 0.744874 CTTTCTCCGGACGCAGGATA 59.255 55.000 0.00 0.00 37.13 2.59
5617 10076 1.136305 CTTTCTCCGGACGCAGGATAA 59.864 52.381 0.00 0.00 37.13 1.75
5618 10077 0.744874 TTCTCCGGACGCAGGATAAG 59.255 55.000 0.00 0.00 37.13 1.73
5619 10078 1.300233 CTCCGGACGCAGGATAAGC 60.300 63.158 0.00 0.00 37.13 3.09
5620 10079 2.016393 CTCCGGACGCAGGATAAGCA 62.016 60.000 0.00 0.00 37.13 3.91
5621 10080 1.153449 CCGGACGCAGGATAAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
5622 10081 1.154205 CCGGACGCAGGATAAGCAAG 61.154 60.000 0.00 0.00 0.00 4.01
5623 10082 1.766143 CGGACGCAGGATAAGCAAGC 61.766 60.000 0.00 0.00 0.00 4.01
5624 10083 1.440145 GGACGCAGGATAAGCAAGCC 61.440 60.000 0.00 0.00 0.00 4.35
5625 10084 1.766143 GACGCAGGATAAGCAAGCCG 61.766 60.000 0.00 0.00 0.00 5.52
5626 10085 1.521457 CGCAGGATAAGCAAGCCGA 60.521 57.895 0.00 0.00 0.00 5.54
5627 10086 1.766143 CGCAGGATAAGCAAGCCGAC 61.766 60.000 0.00 0.00 0.00 4.79
5628 10087 0.744414 GCAGGATAAGCAAGCCGACA 60.744 55.000 0.00 0.00 0.00 4.35
5629 10088 1.959042 CAGGATAAGCAAGCCGACAT 58.041 50.000 0.00 0.00 0.00 3.06
5630 10089 1.869767 CAGGATAAGCAAGCCGACATC 59.130 52.381 0.00 0.00 0.00 3.06
5631 10090 0.861837 GGATAAGCAAGCCGACATCG 59.138 55.000 0.00 0.00 39.44 3.84
5671 10130 2.900838 AGCCATCGCTGCATGAGC 60.901 61.111 0.00 1.69 46.19 4.26
5672 10131 3.962421 GCCATCGCTGCATGAGCC 61.962 66.667 0.00 0.00 46.01 4.70
5673 10132 2.515290 CCATCGCTGCATGAGCCA 60.515 61.111 0.00 0.00 46.01 4.75
5674 10133 2.116533 CCATCGCTGCATGAGCCAA 61.117 57.895 0.00 0.00 46.01 4.52
5675 10134 1.063649 CATCGCTGCATGAGCCAAC 59.936 57.895 0.00 0.00 46.01 3.77
5676 10135 2.117156 ATCGCTGCATGAGCCAACC 61.117 57.895 0.00 0.00 46.01 3.77
5677 10136 3.818787 CGCTGCATGAGCCAACCC 61.819 66.667 0.00 0.00 46.01 4.11
5678 10137 2.677524 GCTGCATGAGCCAACCCA 60.678 61.111 0.00 0.00 42.54 4.51
5679 10138 2.277591 GCTGCATGAGCCAACCCAA 61.278 57.895 0.00 0.00 42.54 4.12
5680 10139 1.588082 CTGCATGAGCCAACCCAAC 59.412 57.895 0.00 0.00 41.13 3.77
5681 10140 1.880819 CTGCATGAGCCAACCCAACC 61.881 60.000 0.00 0.00 41.13 3.77
5682 10141 1.607467 GCATGAGCCAACCCAACCT 60.607 57.895 0.00 0.00 33.58 3.50
5683 10142 1.880819 GCATGAGCCAACCCAACCTG 61.881 60.000 0.00 0.00 33.58 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 91 7.772332 AGTCGTACCAATTCTCATAAATGAC 57.228 36.000 0.00 0.00 32.50 3.06
110 112 3.119101 TCGAGGAGCCAAATAGTGAAGTC 60.119 47.826 0.00 0.00 0.00 3.01
112 114 3.526931 TCGAGGAGCCAAATAGTGAAG 57.473 47.619 0.00 0.00 0.00 3.02
191 194 6.656632 ATTCGAGCATAGTAATGGAGAAGA 57.343 37.500 0.00 0.00 33.38 2.87
242 247 6.348050 GGCGGCAATTTTTGATGATTGTTTTA 60.348 34.615 3.07 0.00 36.03 1.52
254 259 3.014114 GCAGCGGCGGCAATTTTTG 62.014 57.895 20.08 7.73 43.41 2.44
286 292 1.550524 CGACACCATGAAGGAAGGAGA 59.449 52.381 0.00 0.00 41.22 3.71
334 353 3.551496 CTGGCGCAAGGGACAGGAA 62.551 63.158 10.83 0.00 38.28 3.36
369 388 6.121776 TGATGGCTAAAACTCTGACCTAAA 57.878 37.500 0.00 0.00 0.00 1.85
370 389 5.248477 ACTGATGGCTAAAACTCTGACCTAA 59.752 40.000 0.00 0.00 0.00 2.69
371 390 4.777896 ACTGATGGCTAAAACTCTGACCTA 59.222 41.667 0.00 0.00 0.00 3.08
372 391 3.584848 ACTGATGGCTAAAACTCTGACCT 59.415 43.478 0.00 0.00 0.00 3.85
375 394 5.738619 TGTACTGATGGCTAAAACTCTGA 57.261 39.130 0.00 0.00 0.00 3.27
381 400 3.202906 GCGGATGTACTGATGGCTAAAA 58.797 45.455 0.00 0.00 0.00 1.52
411 430 2.483013 CGCTCGGGAAATGGTGAGATTA 60.483 50.000 0.00 0.00 0.00 1.75
417 436 1.439353 CCATCGCTCGGGAAATGGTG 61.439 60.000 7.94 0.00 35.08 4.17
436 456 7.063191 GGTTTTAAGAGACGACAAAGGTAGATC 59.937 40.741 0.00 0.00 0.00 2.75
485 506 7.406031 ACTTGATGCTTCTTTTGATCATGAT 57.594 32.000 8.25 8.25 0.00 2.45
533 571 0.043940 AGAGGAGGATGGTCTTGCCT 59.956 55.000 0.00 0.00 38.35 4.75
553 591 0.881796 CTTCCTCGCCAAAGGTTTCC 59.118 55.000 0.00 0.00 37.69 3.13
554 592 0.241213 GCTTCCTCGCCAAAGGTTTC 59.759 55.000 0.00 0.00 37.69 2.78
555 593 0.467290 TGCTTCCTCGCCAAAGGTTT 60.467 50.000 0.00 0.00 37.69 3.27
556 594 0.467290 TTGCTTCCTCGCCAAAGGTT 60.467 50.000 0.00 0.00 37.69 3.50
559 597 2.487762 TGTTATTGCTTCCTCGCCAAAG 59.512 45.455 0.00 0.00 0.00 2.77
560 598 2.509569 TGTTATTGCTTCCTCGCCAAA 58.490 42.857 0.00 0.00 0.00 3.28
561 599 2.192664 TGTTATTGCTTCCTCGCCAA 57.807 45.000 0.00 0.00 0.00 4.52
562 600 2.192664 TTGTTATTGCTTCCTCGCCA 57.807 45.000 0.00 0.00 0.00 5.69
563 601 3.569250 TTTTGTTATTGCTTCCTCGCC 57.431 42.857 0.00 0.00 0.00 5.54
564 602 3.786048 CGATTTTGTTATTGCTTCCTCGC 59.214 43.478 0.00 0.00 0.00 5.03
597 642 8.883789 TCTAAAAACAAAACTTGAAGTACGTG 57.116 30.769 0.00 0.00 0.00 4.49
636 795 3.314357 CGTCGGGAAAAGGAAAACTCTTT 59.686 43.478 0.00 0.00 36.15 2.52
637 796 2.876550 CGTCGGGAAAAGGAAAACTCTT 59.123 45.455 0.00 0.00 0.00 2.85
638 797 2.103601 TCGTCGGGAAAAGGAAAACTCT 59.896 45.455 0.00 0.00 0.00 3.24
640 799 2.216046 GTCGTCGGGAAAAGGAAAACT 58.784 47.619 0.00 0.00 0.00 2.66
641 800 1.070376 CGTCGTCGGGAAAAGGAAAAC 60.070 52.381 0.00 0.00 0.00 2.43
677 4463 1.662517 TTGCAGCTCGTTTGTCTCAA 58.337 45.000 0.00 0.00 0.00 3.02
679 4465 1.800586 TCATTGCAGCTCGTTTGTCTC 59.199 47.619 0.00 0.00 0.00 3.36
680 4466 1.882912 TCATTGCAGCTCGTTTGTCT 58.117 45.000 0.00 0.00 0.00 3.41
681 4467 2.686558 TTCATTGCAGCTCGTTTGTC 57.313 45.000 0.00 0.00 0.00 3.18
682 4468 3.648339 AATTCATTGCAGCTCGTTTGT 57.352 38.095 0.00 0.00 0.00 2.83
683 4469 4.916831 TGTAAATTCATTGCAGCTCGTTTG 59.083 37.500 0.00 0.00 0.00 2.93
684 4470 4.917415 GTGTAAATTCATTGCAGCTCGTTT 59.083 37.500 0.00 0.00 34.08 3.60
685 4471 4.475944 GTGTAAATTCATTGCAGCTCGTT 58.524 39.130 0.00 0.00 34.08 3.85
696 4482 3.550275 CGATCACGACGGTGTAAATTCAT 59.450 43.478 0.00 0.00 44.68 2.57
697 4483 2.918600 CGATCACGACGGTGTAAATTCA 59.081 45.455 0.00 0.00 44.68 2.57
743 4529 1.203523 GATGGACCGATAGCCTAGCTG 59.796 57.143 0.00 0.00 40.10 4.24
826 4612 0.240411 GGAGCGAGTCGTAGTGTTGT 59.760 55.000 15.08 0.00 0.00 3.32
966 4752 2.572556 ACCTCTTCACTCTCGTCTAGGA 59.427 50.000 0.00 0.00 0.00 2.94
979 4767 4.649267 TCTCTCTCTCAAGACCTCTTCA 57.351 45.455 0.00 0.00 33.11 3.02
982 4770 3.269381 ACCATCTCTCTCTCAAGACCTCT 59.731 47.826 0.00 0.00 0.00 3.69
1219 5018 1.203523 TGCACGCAGAAACAAAACCTT 59.796 42.857 0.00 0.00 0.00 3.50
1246 5045 4.755266 ATCACCAACCTATGTACTGACC 57.245 45.455 0.00 0.00 0.00 4.02
1332 5133 3.502123 TCCCAAAACGTCATCTCCTTT 57.498 42.857 0.00 0.00 0.00 3.11
1343 5144 4.852138 CAGCATATCTGAATCCCAAAACG 58.148 43.478 0.00 0.00 45.72 3.60
1399 5200 8.579006 ACTGCATTTATTTCAGACAAATGAAGA 58.421 29.630 17.18 0.00 43.58 2.87
1416 5217 9.905713 AAAATCCTTGACTATAGACTGCATTTA 57.094 29.630 6.78 0.00 0.00 1.40
1449 5250 9.530633 CCTTGATGGTCTAGTAAATACAGTAAC 57.469 37.037 0.00 0.00 0.00 2.50
1450 5251 9.483489 TCCTTGATGGTCTAGTAAATACAGTAA 57.517 33.333 0.00 0.00 37.07 2.24
1901 5702 9.192642 GCCCCATTTTTCTTTTATACTAACCTA 57.807 33.333 0.00 0.00 0.00 3.08
1982 5786 7.688372 ACAATCATTTCTTACAGATAGTTGCG 58.312 34.615 0.00 0.00 0.00 4.85
2987 6793 6.908284 TGAATAACGTTAGTCAACAGCAAAAC 59.092 34.615 29.97 5.97 35.15 2.43
3047 6853 4.365514 TTGCTCCAGTTGATTCCAGTAA 57.634 40.909 0.00 0.00 0.00 2.24
3259 7066 3.800506 GCAATGAAGCAATCACATAAGGC 59.199 43.478 0.00 0.00 41.93 4.35
3296 7103 6.951198 ACACCCACCAATAACAAGATAAATCA 59.049 34.615 0.00 0.00 0.00 2.57
3336 7143 0.321564 TCATCTGTTTGCACCTCCCG 60.322 55.000 0.00 0.00 0.00 5.14
3639 7447 2.514458 AGGTTCAATAAGGCTGGTGG 57.486 50.000 0.00 0.00 0.00 4.61
3800 7608 4.692228 TGCTTTATCGTCAGACATATGCA 58.308 39.130 1.58 8.50 0.00 3.96
3988 7796 3.756434 ACCTTGTTGATAACCCGAACATG 59.244 43.478 0.00 0.00 30.00 3.21
3995 7803 1.544246 GCACCACCTTGTTGATAACCC 59.456 52.381 0.00 0.00 0.00 4.11
4139 7947 3.372554 GACACGGTAGGAGCTGGCC 62.373 68.421 0.00 0.00 0.00 5.36
4150 7958 1.208535 TCCAGTTTCTGTTGACACGGT 59.791 47.619 0.00 0.00 0.00 4.83
4158 7966 2.876550 GTTAACGCCTCCAGTTTCTGTT 59.123 45.455 0.00 0.00 33.42 3.16
4352 8160 6.805271 GTCAAATTCCAACAGAAGTCATCATG 59.195 38.462 0.00 0.00 38.07 3.07
4364 8172 6.653526 ACTGATGAATGTCAAATTCCAACA 57.346 33.333 0.00 0.00 0.00 3.33
4365 8173 7.094205 ACCTACTGATGAATGTCAAATTCCAAC 60.094 37.037 0.00 0.00 0.00 3.77
4366 8174 6.947733 ACCTACTGATGAATGTCAAATTCCAA 59.052 34.615 0.00 0.00 0.00 3.53
4378 8186 4.307032 AGTGCCAAACCTACTGATGAAT 57.693 40.909 0.00 0.00 0.00 2.57
4410 8218 3.756434 TGCGGAAAGGAAACAGAATAAGG 59.244 43.478 0.00 0.00 0.00 2.69
4412 8220 4.647611 TCTGCGGAAAGGAAACAGAATAA 58.352 39.130 0.00 0.00 34.59 1.40
4431 8239 9.050601 GTACCCTTTTCATAATCAGATTCTCTG 57.949 37.037 0.00 0.00 45.59 3.35
4437 8245 7.872138 TCAAGGTACCCTTTTCATAATCAGAT 58.128 34.615 8.74 0.00 41.69 2.90
4494 8302 1.278985 TCTGCGATGGACTCCATTTGT 59.721 47.619 12.09 0.00 45.26 2.83
4509 8317 0.318441 TGTTGAAGAGGTCCTCTGCG 59.682 55.000 22.53 0.00 40.28 5.18
4580 8388 7.885922 TCACAGGGTTAAAATACATACACACAT 59.114 33.333 0.00 0.00 0.00 3.21
4586 8394 7.201785 CCACCATCACAGGGTTAAAATACATAC 60.202 40.741 0.00 0.00 36.19 2.39
4688 8496 3.295553 CGAAGAGTCGCTTTTATGCTG 57.704 47.619 0.00 0.00 41.08 4.41
4760 8568 0.608640 ACAAGAGCCCTTCGGTACAG 59.391 55.000 0.00 0.00 0.00 2.74
4777 8585 1.112916 TGGCTTCTCTCGTGGTGACA 61.113 55.000 0.00 0.00 38.70 3.58
4800 8608 9.877178 TGTAGTAGTAGTAGTAGTAGTTTCCAC 57.123 37.037 5.31 0.00 0.00 4.02
4819 8707 1.887198 CGCACCCCTCCTATGTAGTAG 59.113 57.143 0.00 0.00 0.00 2.57
4873 8761 1.634702 TGCAAACGTCTTGCCAAAAC 58.365 45.000 23.33 5.38 44.32 2.43
4941 8830 2.887152 GTCCAAGTTGAGCCAAAGACAT 59.113 45.455 3.87 0.00 0.00 3.06
4950 8839 0.250467 TCAGCCTGTCCAAGTTGAGC 60.250 55.000 3.87 0.00 0.00 4.26
4995 9291 2.024176 AGCTACCAAACTATGTGCCG 57.976 50.000 0.00 0.00 0.00 5.69
4996 9292 4.258543 TGTAAGCTACCAAACTATGTGCC 58.741 43.478 0.00 0.00 0.00 5.01
5026 9401 3.118884 GGATTGGTGCTTTCATGCAGATT 60.119 43.478 0.00 0.00 44.20 2.40
5054 9429 2.539338 GCAACCAAACGCGTGAGGA 61.539 57.895 29.97 0.00 0.00 3.71
5063 9438 2.298411 CCATATGCAGGCAACCAAAC 57.702 50.000 0.00 0.00 37.17 2.93
5073 9448 2.484651 GCATCAGAAGAGCCATATGCAG 59.515 50.000 0.00 0.00 44.83 4.41
5185 9630 6.024664 CGTTTTATTGGCGTGATAATTGTGA 58.975 36.000 0.00 0.00 0.00 3.58
5192 9637 4.247258 AGTGTCGTTTTATTGGCGTGATA 58.753 39.130 0.00 0.00 0.00 2.15
5223 9668 5.179368 AGACAACGTCATCATTCAATTCGTT 59.821 36.000 0.00 0.00 39.87 3.85
5242 9687 2.550855 GGGCTGTGTGAGATGAAGACAA 60.551 50.000 0.00 0.00 0.00 3.18
5314 9759 6.872920 ACTGCTTCAAAAGTTTTATGACCAA 58.127 32.000 0.00 0.00 0.00 3.67
5341 9786 7.390440 TCATGAACAAGTGACCTATTACAAAGG 59.610 37.037 0.00 0.00 40.20 3.11
5369 9814 4.610605 TCCAAGAGTTTACCGTTCATGA 57.389 40.909 0.00 0.00 0.00 3.07
5377 9836 2.290768 GGGAGGGTTCCAAGAGTTTACC 60.291 54.545 0.00 0.00 45.98 2.85
5412 9871 2.768253 TCATGCTAGGTGAAGTGGTG 57.232 50.000 0.00 0.00 0.00 4.17
5439 9898 5.449999 GCCGGATGAAAATAAACGATTTCCT 60.450 40.000 5.05 0.00 36.71 3.36
5440 9899 4.738252 GCCGGATGAAAATAAACGATTTCC 59.262 41.667 5.05 0.00 36.71 3.13
5441 9900 5.455525 CAGCCGGATGAAAATAAACGATTTC 59.544 40.000 16.48 0.00 36.71 2.17
5442 9901 5.124776 TCAGCCGGATGAAAATAAACGATTT 59.875 36.000 22.36 0.00 39.56 2.17
5443 9902 4.638421 TCAGCCGGATGAAAATAAACGATT 59.362 37.500 22.36 0.00 0.00 3.34
5444 9903 4.196193 TCAGCCGGATGAAAATAAACGAT 58.804 39.130 22.36 0.00 0.00 3.73
5445 9904 3.601435 TCAGCCGGATGAAAATAAACGA 58.399 40.909 22.36 0.00 0.00 3.85
5446 9905 4.552166 ATCAGCCGGATGAAAATAAACG 57.448 40.909 28.45 0.00 34.06 3.60
5447 9906 6.791303 TGTTATCAGCCGGATGAAAATAAAC 58.209 36.000 28.45 22.66 36.72 2.01
5448 9907 7.026631 CTGTTATCAGCCGGATGAAAATAAA 57.973 36.000 28.45 12.91 36.72 1.40
5449 9908 6.618287 CTGTTATCAGCCGGATGAAAATAA 57.382 37.500 28.45 17.76 36.72 1.40
5463 9922 1.513178 CTTACGCGTCGCTGTTATCAG 59.487 52.381 18.63 0.00 43.87 2.90
5464 9923 1.135603 ACTTACGCGTCGCTGTTATCA 60.136 47.619 18.63 0.00 0.00 2.15
5465 9924 1.511958 GACTTACGCGTCGCTGTTATC 59.488 52.381 18.63 9.20 0.00 1.75
5466 9925 1.542544 GACTTACGCGTCGCTGTTAT 58.457 50.000 18.63 4.35 0.00 1.89
5467 9926 3.005823 GACTTACGCGTCGCTGTTA 57.994 52.632 18.63 8.02 0.00 2.41
5468 9927 3.838468 GACTTACGCGTCGCTGTT 58.162 55.556 18.63 1.79 0.00 3.16
5478 9937 0.304098 CTAGGACGAGGCGACTTACG 59.696 60.000 0.00 0.00 44.43 3.18
5479 9938 0.029167 GCTAGGACGAGGCGACTTAC 59.971 60.000 0.00 0.00 44.43 2.34
5480 9939 2.401967 GCTAGGACGAGGCGACTTA 58.598 57.895 0.00 0.00 44.43 2.24
5481 9940 3.198582 GCTAGGACGAGGCGACTT 58.801 61.111 0.00 0.00 44.43 3.01
5491 9950 2.576317 GACACGCGTCGCTAGGAC 60.576 66.667 9.86 0.00 42.48 3.85
5492 9951 3.807538 GGACACGCGTCGCTAGGA 61.808 66.667 9.86 0.00 43.61 2.94
5493 9952 3.812019 AGGACACGCGTCGCTAGG 61.812 66.667 9.86 0.00 43.61 3.02
5494 9953 2.577112 CAGGACACGCGTCGCTAG 60.577 66.667 9.86 9.85 43.61 3.42
5495 9954 4.771356 GCAGGACACGCGTCGCTA 62.771 66.667 9.86 0.00 43.61 4.26
5513 9972 4.947147 TTGCCAGGTCCACGCCAC 62.947 66.667 0.00 0.00 0.00 5.01
5514 9973 4.947147 GTTGCCAGGTCCACGCCA 62.947 66.667 0.00 0.00 0.00 5.69
5516 9975 2.741486 TAAGGTTGCCAGGTCCACGC 62.741 60.000 0.00 0.00 0.00 5.34
5517 9976 0.035439 ATAAGGTTGCCAGGTCCACG 60.035 55.000 0.00 0.00 0.00 4.94
5518 9977 1.682087 GGATAAGGTTGCCAGGTCCAC 60.682 57.143 0.00 0.00 0.00 4.02
5519 9978 0.623723 GGATAAGGTTGCCAGGTCCA 59.376 55.000 0.00 0.00 0.00 4.02
5520 9979 0.919710 AGGATAAGGTTGCCAGGTCC 59.080 55.000 0.00 0.00 0.00 4.46
5521 9980 1.840635 AGAGGATAAGGTTGCCAGGTC 59.159 52.381 0.00 0.00 0.00 3.85
5522 9981 1.840635 GAGAGGATAAGGTTGCCAGGT 59.159 52.381 0.00 0.00 0.00 4.00
5523 9982 1.141858 GGAGAGGATAAGGTTGCCAGG 59.858 57.143 0.00 0.00 0.00 4.45
5524 9983 1.202580 CGGAGAGGATAAGGTTGCCAG 60.203 57.143 0.00 0.00 0.00 4.85
5525 9984 0.830648 CGGAGAGGATAAGGTTGCCA 59.169 55.000 0.00 0.00 0.00 4.92
5526 9985 0.533085 GCGGAGAGGATAAGGTTGCC 60.533 60.000 0.00 0.00 0.00 4.52
5527 9986 0.876342 CGCGGAGAGGATAAGGTTGC 60.876 60.000 0.00 0.00 0.00 4.17
5528 9987 0.460311 ACGCGGAGAGGATAAGGTTG 59.540 55.000 12.47 0.00 0.00 3.77
5529 9988 0.460311 CACGCGGAGAGGATAAGGTT 59.540 55.000 12.47 0.00 0.00 3.50
5530 9989 2.017559 GCACGCGGAGAGGATAAGGT 62.018 60.000 12.47 0.00 0.00 3.50
5531 9990 1.300233 GCACGCGGAGAGGATAAGG 60.300 63.158 12.47 0.00 0.00 2.69
5532 9991 1.300233 GGCACGCGGAGAGGATAAG 60.300 63.158 12.47 0.00 0.00 1.73
5533 9992 2.792947 GGGCACGCGGAGAGGATAA 61.793 63.158 12.47 0.00 0.00 1.75
5534 9993 3.224324 GGGCACGCGGAGAGGATA 61.224 66.667 12.47 0.00 0.00 2.59
5549 10008 1.753368 GAGATGAGGAAGCCGAGGGG 61.753 65.000 0.00 0.00 0.00 4.79
5550 10009 1.745264 GAGATGAGGAAGCCGAGGG 59.255 63.158 0.00 0.00 0.00 4.30
5551 10010 0.758685 AGGAGATGAGGAAGCCGAGG 60.759 60.000 0.00 0.00 0.00 4.63
5552 10011 1.611491 GTAGGAGATGAGGAAGCCGAG 59.389 57.143 0.00 0.00 0.00 4.63
5553 10012 1.693627 GTAGGAGATGAGGAAGCCGA 58.306 55.000 0.00 0.00 0.00 5.54
5554 10013 0.676736 GGTAGGAGATGAGGAAGCCG 59.323 60.000 0.00 0.00 0.00 5.52
5555 10014 2.095604 AGGTAGGAGATGAGGAAGCC 57.904 55.000 0.00 0.00 0.00 4.35
5556 10015 3.802866 CAAAGGTAGGAGATGAGGAAGC 58.197 50.000 0.00 0.00 0.00 3.86
5557 10016 3.198635 TGCAAAGGTAGGAGATGAGGAAG 59.801 47.826 0.00 0.00 0.00 3.46
5558 10017 3.181329 TGCAAAGGTAGGAGATGAGGAA 58.819 45.455 0.00 0.00 0.00 3.36
5559 10018 2.768527 CTGCAAAGGTAGGAGATGAGGA 59.231 50.000 0.00 0.00 0.00 3.71
5560 10019 2.768527 TCTGCAAAGGTAGGAGATGAGG 59.231 50.000 0.00 0.00 0.00 3.86
5561 10020 4.440880 CTTCTGCAAAGGTAGGAGATGAG 58.559 47.826 0.00 0.00 34.47 2.90
5562 10021 3.369892 GCTTCTGCAAAGGTAGGAGATGA 60.370 47.826 9.63 0.00 34.47 2.92
5563 10022 2.941720 GCTTCTGCAAAGGTAGGAGATG 59.058 50.000 9.63 0.00 34.47 2.90
5564 10023 3.274095 GCTTCTGCAAAGGTAGGAGAT 57.726 47.619 9.63 0.00 34.47 2.75
5565 10024 2.770164 GCTTCTGCAAAGGTAGGAGA 57.230 50.000 9.63 0.00 34.47 3.71
5577 10036 1.680207 GAGATGGGGATTTGCTTCTGC 59.320 52.381 0.00 0.00 40.20 4.26
5578 10037 3.294038 AGAGATGGGGATTTGCTTCTG 57.706 47.619 0.00 0.00 0.00 3.02
5579 10038 4.017683 AGAAAGAGATGGGGATTTGCTTCT 60.018 41.667 0.00 0.00 0.00 2.85
5580 10039 4.276642 AGAAAGAGATGGGGATTTGCTTC 58.723 43.478 0.00 0.00 0.00 3.86
5581 10040 4.276642 GAGAAAGAGATGGGGATTTGCTT 58.723 43.478 0.00 0.00 0.00 3.91
5582 10041 3.372458 GGAGAAAGAGATGGGGATTTGCT 60.372 47.826 0.00 0.00 0.00 3.91
5583 10042 2.954989 GGAGAAAGAGATGGGGATTTGC 59.045 50.000 0.00 0.00 0.00 3.68
5584 10043 3.209410 CGGAGAAAGAGATGGGGATTTG 58.791 50.000 0.00 0.00 0.00 2.32
5585 10044 2.173569 CCGGAGAAAGAGATGGGGATTT 59.826 50.000 0.00 0.00 0.00 2.17
5586 10045 1.771255 CCGGAGAAAGAGATGGGGATT 59.229 52.381 0.00 0.00 0.00 3.01
5587 10046 1.062121 TCCGGAGAAAGAGATGGGGAT 60.062 52.381 0.00 0.00 0.00 3.85
5588 10047 0.338467 TCCGGAGAAAGAGATGGGGA 59.662 55.000 0.00 0.00 0.00 4.81
5589 10048 0.466124 GTCCGGAGAAAGAGATGGGG 59.534 60.000 3.06 0.00 0.00 4.96
5590 10049 0.103208 CGTCCGGAGAAAGAGATGGG 59.897 60.000 3.06 0.00 0.00 4.00
5591 10050 0.528684 GCGTCCGGAGAAAGAGATGG 60.529 60.000 3.06 0.00 0.00 3.51
5592 10051 0.173481 TGCGTCCGGAGAAAGAGATG 59.827 55.000 3.06 0.00 0.00 2.90
5593 10052 0.457851 CTGCGTCCGGAGAAAGAGAT 59.542 55.000 3.06 0.00 35.50 2.75
5594 10053 1.595993 CCTGCGTCCGGAGAAAGAGA 61.596 60.000 3.06 0.00 35.50 3.10
5595 10054 1.153745 CCTGCGTCCGGAGAAAGAG 60.154 63.158 3.06 0.00 35.50 2.85
5596 10055 0.970937 ATCCTGCGTCCGGAGAAAGA 60.971 55.000 3.06 0.00 35.50 2.52
5597 10056 0.744874 TATCCTGCGTCCGGAGAAAG 59.255 55.000 3.06 1.75 35.50 2.62
5598 10057 1.136305 CTTATCCTGCGTCCGGAGAAA 59.864 52.381 3.06 0.00 35.50 2.52
5599 10058 0.744874 CTTATCCTGCGTCCGGAGAA 59.255 55.000 3.06 0.00 35.50 2.87
5600 10059 1.735376 GCTTATCCTGCGTCCGGAGA 61.735 60.000 3.06 0.00 35.50 3.71
5601 10060 1.300233 GCTTATCCTGCGTCCGGAG 60.300 63.158 3.06 0.00 33.29 4.63
5602 10061 1.609635 TTGCTTATCCTGCGTCCGGA 61.610 55.000 0.00 0.00 34.52 5.14
5603 10062 1.153449 TTGCTTATCCTGCGTCCGG 60.153 57.895 0.00 0.00 0.00 5.14
5604 10063 1.766143 GCTTGCTTATCCTGCGTCCG 61.766 60.000 0.00 0.00 0.00 4.79
5605 10064 1.440145 GGCTTGCTTATCCTGCGTCC 61.440 60.000 0.00 0.00 0.00 4.79
5606 10065 1.766143 CGGCTTGCTTATCCTGCGTC 61.766 60.000 0.00 0.00 0.00 5.19
5607 10066 1.815421 CGGCTTGCTTATCCTGCGT 60.815 57.895 0.00 0.00 0.00 5.24
5608 10067 1.521457 TCGGCTTGCTTATCCTGCG 60.521 57.895 0.00 0.00 0.00 5.18
5609 10068 0.744414 TGTCGGCTTGCTTATCCTGC 60.744 55.000 0.00 0.00 0.00 4.85
5610 10069 1.869767 GATGTCGGCTTGCTTATCCTG 59.130 52.381 0.00 0.00 0.00 3.86
5611 10070 1.539065 CGATGTCGGCTTGCTTATCCT 60.539 52.381 0.00 0.00 35.37 3.24
5612 10071 0.861837 CGATGTCGGCTTGCTTATCC 59.138 55.000 0.00 0.00 35.37 2.59
5662 10121 1.588082 GTTGGGTTGGCTCATGCAG 59.412 57.895 0.00 0.00 41.91 4.41
5663 10122 1.907807 GGTTGGGTTGGCTCATGCA 60.908 57.895 0.00 0.00 41.91 3.96
5664 10123 1.607467 AGGTTGGGTTGGCTCATGC 60.607 57.895 0.00 0.00 38.76 4.06
5665 10124 2.269978 CAGGTTGGGTTGGCTCATG 58.730 57.895 0.00 0.00 0.00 3.07
5666 10125 4.850193 CAGGTTGGGTTGGCTCAT 57.150 55.556 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.