Multiple sequence alignment - TraesCS1B01G332200

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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 TraesCS1B01G332200 chr1B 100.000 3425 0 0 1 3425 558283433 558286857 0.000000e+00 6325
1 TraesCS1B01G332200 chr1B 89.032 1085 96 12 1000 2070 558495622 558496697 0.000000e+00 1323
2 TraesCS1B01G332200 chr1B 86.957 483 51 6 2078 2559 558496920 558497391 1.810000e-147 532
3 TraesCS1B01G332200 chr1A 88.554 2953 194 54 151 3035 510671584 510674460 0.000000e+00 3448
4 TraesCS1B01G332200 chr1A 88.717 842 67 13 1250 2079 510803484 510804309 0.000000e+00 1003
5 TraesCS1B01G332200 chr1A 87.857 420 49 2 2077 2495 510804487 510804905 3.070000e-135 492
6 TraesCS1B01G332200 chr1A 90.361 249 24 0 1000 1248 510803179 510803427 9.160000e-86 327
7 TraesCS1B01G332200 chr1D 91.336 1362 85 14 1640 2981 413731009 413732357 0.000000e+00 1831
8 TraesCS1B01G332200 chr1D 82.118 1275 127 35 2 1231 413728446 413729664 0.000000e+00 998
9 TraesCS1B01G332200 chr1D 87.979 574 58 4 1513 2084 413778604 413779168 0.000000e+00 667
10 TraesCS1B01G332200 chr1D 88.619 536 46 5 1000 1526 413772206 413772735 3.730000e-179 638
11 TraesCS1B01G332200 chr1D 86.335 483 54 5 2078 2559 413779399 413779870 1.820000e-142 516
12 TraesCS1B01G332200 chr1D 95.253 316 15 0 1287 1602 413730692 413731007 5.100000e-138 501
13 TraesCS1B01G332200 chr1D 90.741 108 5 3 3322 3425 413732603 413732709 4.610000e-29 139
14 TraesCS1B01G332200 chrUn 78.457 1063 183 34 1024 2065 90118715 90117678 0.000000e+00 652
15 TraesCS1B01G332200 chrUn 81.039 385 62 8 2114 2495 90117288 90116912 2.580000e-76 296
16 TraesCS1B01G332200 chr4A 77.644 1078 181 40 1031 2069 710413913 710412857 4.890000e-168 601
17 TraesCS1B01G332200 chr4A 81.586 391 62 10 2076 2461 708914109 708913724 7.130000e-82 315
18 TraesCS1B01G332200 chr4A 81.586 391 62 10 2076 2461 708915532 708915147 7.130000e-82 315
19 TraesCS1B01G332200 chr7D 75.245 1022 200 36 1030 2029 23509778 23510768 1.460000e-118 436
20 TraesCS1B01G332200 chr7D 87.719 228 26 2 3045 3271 428013213 428012987 7.290000e-67 265
21 TraesCS1B01G332200 chr7A 77.699 704 131 15 1330 2029 24627214 24627895 1.140000e-109 407
22 TraesCS1B01G332200 chr7A 81.132 424 67 9 2076 2495 25007666 25008080 9.160000e-86 327
23 TraesCS1B01G332200 chr7A 87.815 238 27 2 3036 3271 155138338 155138575 9.360000e-71 278
24 TraesCS1B01G332200 chr3A 87.815 238 27 2 3036 3271 52412108 52412345 9.360000e-71 278
25 TraesCS1B01G332200 chr2B 88.085 235 24 3 3038 3271 210131282 210131513 3.370000e-70 276
26 TraesCS1B01G332200 chr2B 88.210 229 21 5 3045 3271 693388106 693388330 5.630000e-68 268
27 TraesCS1B01G332200 chr5D 88.496 226 24 2 3047 3271 369101954 369102178 4.360000e-69 272
28 TraesCS1B01G332200 chr4B 88.158 228 23 3 3045 3271 140976945 140976721 5.630000e-68 268
29 TraesCS1B01G332200 chr3B 88.210 229 22 4 3045 3271 66464030 66463805 5.630000e-68 268
30 TraesCS1B01G332200 chr3D 87.719 228 27 1 3046 3272 441646728 441646501 7.290000e-67 265


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 TraesCS1B01G332200 chr1B 558283433 558286857 3424 False 6325.000000 6325 100.000000 1 3425 1 chr1B.!!$F1 3424
1 TraesCS1B01G332200 chr1B 558495622 558497391 1769 False 927.500000 1323 87.994500 1000 2559 2 chr1B.!!$F2 1559
2 TraesCS1B01G332200 chr1A 510671584 510674460 2876 False 3448.000000 3448 88.554000 151 3035 1 chr1A.!!$F1 2884
3 TraesCS1B01G332200 chr1A 510803179 510804905 1726 False 607.333333 1003 88.978333 1000 2495 3 chr1A.!!$F2 1495
4 TraesCS1B01G332200 chr1D 413728446 413732709 4263 False 867.250000 1831 89.862000 2 3425 4 chr1D.!!$F2 3423
5 TraesCS1B01G332200 chr1D 413772206 413772735 529 False 638.000000 638 88.619000 1000 1526 1 chr1D.!!$F1 526
6 TraesCS1B01G332200 chr1D 413778604 413779870 1266 False 591.500000 667 87.157000 1513 2559 2 chr1D.!!$F3 1046
7 TraesCS1B01G332200 chrUn 90116912 90118715 1803 True 474.000000 652 79.748000 1024 2495 2 chrUn.!!$R1 1471
8 TraesCS1B01G332200 chr4A 710412857 710413913 1056 True 601.000000 601 77.644000 1031 2069 1 chr4A.!!$R1 1038
9 TraesCS1B01G332200 chr4A 708913724 708915532 1808 True 315.000000 315 81.586000 2076 2461 2 chr4A.!!$R2 385
10 TraesCS1B01G332200 chr7D 23509778 23510768 990 False 436.000000 436 75.245000 1030 2029 1 chr7D.!!$F1 999
11 TraesCS1B01G332200 chr7A 24627214 24627895 681 False 407.000000 407 77.699000 1330 2029 1 chr7A.!!$F1 699

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
626 633 0.106167 TCAGCTCTGCCGTATAGGGT 60.106 55.0 12.88 0.0 41.48 4.34 F
1649 2823 0.036010 CTTGAGGGAGGATGCGTTGT 60.036 55.0 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 5224 0.537653 TGTTTGTCACGACCCTGTGA 59.462 50.0 0.0 0.0 46.15 3.58 R
2988 6022 0.030638 GCCGACAACAACTGCAACAT 59.969 50.0 0.0 0.0 0.00 2.71 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
88 89 1.429423 GCATGCTGGCGTTTACCTC 59.571 57.895 11.37 0.00 0.00 3.85
107 108 3.851128 GACTAGGAGCCCGCCACC 61.851 72.222 0.00 0.00 0.00 4.61
121 122 4.920112 CACCGCGGGGACAACACA 62.920 66.667 31.76 0.00 36.97 3.72
125 126 2.282180 GCGGGGACAACACACCAT 60.282 61.111 0.00 0.00 0.00 3.55
131 132 1.156736 GGACAACACACCATCGAAGG 58.843 55.000 4.85 4.85 0.00 3.46
132 133 1.156736 GACAACACACCATCGAAGGG 58.843 55.000 12.02 8.30 0.00 3.95
133 134 0.250727 ACAACACACCATCGAAGGGG 60.251 55.000 7.55 7.55 38.34 4.79
135 136 1.002659 CAACACACCATCGAAGGGGTA 59.997 52.381 15.35 0.00 45.59 3.69
136 137 0.902531 ACACACCATCGAAGGGGTAG 59.097 55.000 15.35 11.59 45.59 3.18
137 138 0.462047 CACACCATCGAAGGGGTAGC 60.462 60.000 15.35 0.00 45.59 3.58
138 139 1.227263 CACCATCGAAGGGGTAGCG 60.227 63.158 12.02 0.00 34.08 4.26
139 140 2.280186 CCATCGAAGGGGTAGCGC 60.280 66.667 0.00 0.00 0.00 5.92
140 141 2.280186 CATCGAAGGGGTAGCGCC 60.280 66.667 2.29 0.00 36.67 6.53
141 142 3.912907 ATCGAAGGGGTAGCGCCG 61.913 66.667 2.29 0.00 41.60 6.46
243 244 1.037030 GGATCCAAGCGCCATTTCCA 61.037 55.000 6.95 0.00 0.00 3.53
252 253 2.409870 GCCATTTCCACGGAGGCAG 61.410 63.158 9.39 0.00 44.59 4.85
262 263 0.325296 ACGGAGGCAGTGGATTCCTA 60.325 55.000 3.95 0.00 0.00 2.94
278 279 2.382882 TCCTACTGCATGGAGTCTGAG 58.617 52.381 24.25 15.23 0.00 3.35
280 281 1.479730 CTACTGCATGGAGTCTGAGCA 59.520 52.381 24.25 4.02 0.00 4.26
283 284 1.812922 GCATGGAGTCTGAGCACGG 60.813 63.158 0.00 0.00 0.00 4.94
289 290 0.966370 GAGTCTGAGCACGGTAGGGT 60.966 60.000 0.00 0.00 0.00 4.34
300 301 1.704704 GGTAGGGTGGACTCCTCCT 59.295 63.158 14.62 13.74 37.34 3.69
309 310 2.037527 ACTCCTCCTGGGACCGAC 59.962 66.667 0.00 0.00 39.58 4.79
310 311 3.141488 CTCCTCCTGGGACCGACG 61.141 72.222 0.00 0.00 39.58 5.12
313 314 3.141488 CTCCTGGGACCGACGGAG 61.141 72.222 23.38 7.16 37.33 4.63
320 321 2.722201 GGACCGACGGAGAGCCATT 61.722 63.158 23.38 0.00 0.00 3.16
322 323 1.945354 GACCGACGGAGAGCCATTCA 61.945 60.000 23.38 0.00 0.00 2.57
325 326 0.526524 CGACGGAGAGCCATTCAGAC 60.527 60.000 0.00 0.00 0.00 3.51
331 332 0.976641 AGAGCCATTCAGACGGTCAA 59.023 50.000 11.27 0.00 0.00 3.18
341 342 0.112606 AGACGGTCAACTCCTCCTCA 59.887 55.000 11.27 0.00 0.00 3.86
378 379 3.201290 AGATCACAATCAACGGATCAGC 58.799 45.455 0.00 0.00 38.84 4.26
398 399 6.810911 TCAGCAGATCTTAGAGTTGTATTCC 58.189 40.000 0.00 0.00 0.00 3.01
412 413 6.476378 AGTTGTATTCCTTGTCTGTTATGCT 58.524 36.000 0.00 0.00 0.00 3.79
423 424 0.107703 TGTTATGCTGGAGAAGGCCG 60.108 55.000 0.00 0.00 0.00 6.13
434 435 2.439701 AAGGCCGGAGATCGTCGA 60.440 61.111 5.05 0.00 37.11 4.20
456 457 0.810031 CGAATCTTGGGGGCGTAGTG 60.810 60.000 0.00 0.00 0.00 2.74
473 479 0.690762 GTGGAGTGGCTAGGGTTTCA 59.309 55.000 0.00 0.00 0.00 2.69
481 487 0.179054 GCTAGGGTTTCATCCGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
504 510 8.132362 GGACACGGATAGAGATGAATATATGTC 58.868 40.741 0.00 0.00 0.00 3.06
509 515 7.520776 CGGATAGAGATGAATATATGTCGGGTC 60.521 44.444 0.00 0.00 0.00 4.46
510 516 7.285629 GGATAGAGATGAATATATGTCGGGTCA 59.714 40.741 0.00 0.00 0.00 4.02
511 517 6.918067 AGAGATGAATATATGTCGGGTCAA 57.082 37.500 0.00 0.00 0.00 3.18
513 519 6.721668 AGAGATGAATATATGTCGGGTCAAGA 59.278 38.462 0.00 0.00 0.00 3.02
526 532 1.407437 GGTCAAGATGGGCTAGTGTGG 60.407 57.143 0.00 0.00 0.00 4.17
544 550 3.022914 GCCGTATCCGAAGACGCG 61.023 66.667 3.53 3.53 38.75 6.01
548 554 1.650912 GTATCCGAAGACGCGCCTA 59.349 57.895 5.73 0.00 38.29 3.93
578 584 1.273886 GAACCTCTCCATATCCGCCTC 59.726 57.143 0.00 0.00 0.00 4.70
604 611 1.203313 TGGACTAGATATGAGGGGGCC 60.203 57.143 0.00 0.00 0.00 5.80
626 633 0.106167 TCAGCTCTGCCGTATAGGGT 60.106 55.000 12.88 0.00 41.48 4.34
627 634 0.315568 CAGCTCTGCCGTATAGGGTC 59.684 60.000 12.88 6.21 41.48 4.46
666 687 2.262915 CCGGTCACTGACTGAGCC 59.737 66.667 18.22 0.00 43.46 4.70
673 694 2.202987 CTGACTGAGCCATCCGCC 60.203 66.667 0.00 0.00 38.78 6.13
675 696 3.785859 GACTGAGCCATCCGCCCA 61.786 66.667 0.00 0.00 38.78 5.36
681 702 2.044946 GCCATCCGCCCAGACTTT 60.045 61.111 0.00 0.00 0.00 2.66
682 703 1.223487 GCCATCCGCCCAGACTTTA 59.777 57.895 0.00 0.00 0.00 1.85
683 704 0.815615 GCCATCCGCCCAGACTTTAG 60.816 60.000 0.00 0.00 0.00 1.85
705 727 3.379445 TGTTCGAGGAGTCCGGCC 61.379 66.667 2.76 0.00 0.00 6.13
717 739 0.320247 GTCCGGCCATAGATGCTCTG 60.320 60.000 2.24 0.00 0.00 3.35
724 746 3.007290 GGCCATAGATGCTCTGACATGTA 59.993 47.826 0.00 0.00 31.19 2.29
725 747 4.323333 GGCCATAGATGCTCTGACATGTAT 60.323 45.833 0.00 0.00 37.07 2.29
734 756 9.363763 AGATGCTCTGACATGTATTAATTATCG 57.636 33.333 0.00 0.00 0.00 2.92
757 779 8.185506 TCGCTCCAATAGTCTATATAAACCAA 57.814 34.615 0.00 0.00 0.00 3.67
772 798 1.322442 ACCAAGTTCTTTGCTCTGGC 58.678 50.000 0.00 0.00 35.37 4.85
786 812 3.253188 TGCTCTGGCAATTCACACTTTAC 59.747 43.478 0.00 0.00 46.36 2.01
794 820 3.896648 ATTCACACTTTACCTGCGTTG 57.103 42.857 0.00 0.00 0.00 4.10
796 822 0.944386 CACACTTTACCTGCGTTGCT 59.056 50.000 0.00 0.00 0.00 3.91
797 823 0.944386 ACACTTTACCTGCGTTGCTG 59.056 50.000 0.00 0.00 0.00 4.41
828 854 3.578456 CAAGCTACTTGTGGCCGG 58.422 61.111 0.00 0.00 36.79 6.13
830 856 0.392998 CAAGCTACTTGTGGCCGGAT 60.393 55.000 5.05 0.00 36.79 4.18
862 895 3.254892 GTTGTTCCAAGATCCGTCTCTC 58.745 50.000 0.00 0.00 32.15 3.20
921 956 3.564644 CAGTTCATCCTGCATGATCTTCC 59.435 47.826 0.96 0.00 41.42 3.46
966 1001 7.530010 GTGTTGTATGAGCATTTGTACTGAAT 58.470 34.615 0.00 0.00 0.00 2.57
967 1002 7.693951 GTGTTGTATGAGCATTTGTACTGAATC 59.306 37.037 0.00 0.00 0.00 2.52
968 1003 6.588348 TGTATGAGCATTTGTACTGAATCG 57.412 37.500 0.00 0.00 0.00 3.34
990 1048 4.025396 CGGATCGGACATTTCAGATTCTTG 60.025 45.833 0.00 0.00 36.86 3.02
998 1064 6.092955 ACATTTCAGATTCTTGTGTGCAAT 57.907 33.333 0.00 0.00 33.65 3.56
1008 1074 4.661222 TCTTGTGTGCAATTATGGGAAGA 58.339 39.130 0.00 0.00 33.65 2.87
1136 1202 1.228769 TGGTCGTAGCACCAGTCCT 60.229 57.895 0.00 0.00 41.84 3.85
1170 1236 3.041940 CGCCTTTCGAAGCACGGT 61.042 61.111 9.70 0.00 42.82 4.83
1283 2412 2.613133 GCAGTCGGTACTACTCCACTAG 59.387 54.545 0.00 0.00 29.49 2.57
1284 2413 3.681034 GCAGTCGGTACTACTCCACTAGA 60.681 52.174 0.00 0.00 29.49 2.43
1285 2414 3.870419 CAGTCGGTACTACTCCACTAGAC 59.130 52.174 0.00 0.00 29.49 2.59
1327 2470 5.473039 TGCATATCCATGTCGTATCTTCTG 58.527 41.667 0.00 0.00 34.40 3.02
1328 2471 5.011023 TGCATATCCATGTCGTATCTTCTGT 59.989 40.000 0.00 0.00 34.40 3.41
1395 2544 0.110823 CGCGTCAAGGGAGTTTTTCG 60.111 55.000 0.00 0.00 34.27 3.46
1407 2556 4.634703 TTTTCGGGCAGCCGCTCA 62.635 61.111 5.00 0.00 39.27 4.26
1483 2644 0.903924 TATGGGAACGACCGGGTGAA 60.904 55.000 3.30 0.00 40.11 3.18
1643 2817 0.841961 TCATGGCTTGAGGGAGGATG 59.158 55.000 0.00 0.00 0.00 3.51
1649 2823 0.036010 CTTGAGGGAGGATGCGTTGT 60.036 55.000 0.00 0.00 0.00 3.32
1925 3102 4.901868 TGTTGTTACAGTCCTTATGGTCC 58.098 43.478 0.00 0.00 34.23 4.46
2090 3674 8.239038 TGTTTGGTGAAAAAGTTATATGGACA 57.761 30.769 0.00 0.00 0.00 4.02
2166 5175 2.366916 CTCTCGGGCTGATGAAGGTTAT 59.633 50.000 0.00 0.00 0.00 1.89
2169 5178 2.035449 TCGGGCTGATGAAGGTTATACG 59.965 50.000 0.00 0.00 0.00 3.06
2355 5365 7.042523 GCGTTGTACTCTAAAGTGAAGGTTAAA 60.043 37.037 0.00 0.00 36.92 1.52
2505 5519 9.541143 TGTTTGTATCATGTATTCACGTATCAT 57.459 29.630 0.00 0.00 0.00 2.45
2512 5526 9.981114 ATCATGTATTCACGTATCATTAGTTCA 57.019 29.630 0.00 0.00 0.00 3.18
2562 5576 6.420604 CCTTTGTTCAATAACACATGTTGTCC 59.579 38.462 7.53 0.00 45.18 4.02
2634 5650 7.248437 GGGAACACTTATGAAAAGTAAATCCG 58.752 38.462 0.00 0.00 31.57 4.18
2641 5657 9.020731 ACTTATGAAAAGTAAATCCGGAAACAT 57.979 29.630 9.01 6.56 0.00 2.71
2692 5717 9.811995 TTGTCTTGTAACATACATGGTATACTC 57.188 33.333 2.25 0.00 38.68 2.59
2734 5768 8.340443 CAAAGAGGTAACATGATCATATGTGTG 58.660 37.037 8.15 0.00 40.24 3.82
2738 5772 8.579850 AGGTAACATGATCATATGTGTGTTTT 57.420 30.769 8.15 0.00 40.24 2.43
2739 5773 9.023962 AGGTAACATGATCATATGTGTGTTTTT 57.976 29.630 8.15 0.00 40.24 1.94
2742 5776 8.894409 AACATGATCATATGTGTGTTTTTACG 57.106 30.769 8.15 0.00 40.24 3.18
2743 5777 8.039603 ACATGATCATATGTGTGTTTTTACGT 57.960 30.769 8.15 0.00 39.68 3.57
2744 5778 8.511321 ACATGATCATATGTGTGTTTTTACGTT 58.489 29.630 8.15 0.00 39.68 3.99
2745 5779 8.787884 CATGATCATATGTGTGTTTTTACGTTG 58.212 33.333 8.15 0.00 0.00 4.10
2825 5859 4.164796 TCAATGTATGGCAAGTCATCTCCT 59.835 41.667 0.00 0.00 0.00 3.69
2836 5870 5.751028 GCAAGTCATCTCCTACAATAGACAC 59.249 44.000 0.00 0.00 0.00 3.67
2857 5891 4.576463 CACAGCCTAAATATTGGTCACTCC 59.424 45.833 0.00 0.00 0.00 3.85
2899 5933 4.646572 ACCAAACAAAGCAAAACCTCAAA 58.353 34.783 0.00 0.00 0.00 2.69
2937 5971 0.398664 CTACTAGGAGGTGGTGGGGG 60.399 65.000 0.00 0.00 0.00 5.40
2958 5992 6.238648 GGGGAAATTCTCTCAACTCTGTAAA 58.761 40.000 0.00 0.00 0.00 2.01
2982 6016 1.172812 ACCAAGCTCTTGCCCGTTTC 61.173 55.000 4.17 0.00 40.80 2.78
2988 6022 1.880646 GCTCTTGCCCGTTTCTTACCA 60.881 52.381 0.00 0.00 0.00 3.25
3005 6039 1.065401 ACCATGTTGCAGTTGTTGTCG 59.935 47.619 0.00 0.00 0.00 4.35
3007 6041 0.030638 ATGTTGCAGTTGTTGTCGGC 59.969 50.000 0.00 0.00 0.00 5.54
3008 6042 1.299089 GTTGCAGTTGTTGTCGGCC 60.299 57.895 0.00 0.00 0.00 6.13
3009 6043 1.453015 TTGCAGTTGTTGTCGGCCT 60.453 52.632 0.00 0.00 0.00 5.19
3010 6044 1.034838 TTGCAGTTGTTGTCGGCCTT 61.035 50.000 0.00 0.00 0.00 4.35
3011 6045 1.034838 TGCAGTTGTTGTCGGCCTTT 61.035 50.000 0.00 0.00 0.00 3.11
3012 6046 0.102300 GCAGTTGTTGTCGGCCTTTT 59.898 50.000 0.00 0.00 0.00 2.27
3013 6047 1.335496 GCAGTTGTTGTCGGCCTTTTA 59.665 47.619 0.00 0.00 0.00 1.52
3014 6048 2.857104 GCAGTTGTTGTCGGCCTTTTAC 60.857 50.000 0.00 0.00 0.00 2.01
3015 6049 1.600485 AGTTGTTGTCGGCCTTTTACG 59.400 47.619 0.00 0.00 0.00 3.18
3016 6050 1.331447 GTTGTTGTCGGCCTTTTACGT 59.669 47.619 0.00 0.00 0.00 3.57
3017 6051 1.666054 TGTTGTCGGCCTTTTACGTT 58.334 45.000 0.00 0.00 0.00 3.99
3018 6052 1.331138 TGTTGTCGGCCTTTTACGTTG 59.669 47.619 0.00 0.00 0.00 4.10
3019 6053 1.331447 GTTGTCGGCCTTTTACGTTGT 59.669 47.619 0.00 0.00 0.00 3.32
3020 6054 1.219646 TGTCGGCCTTTTACGTTGTC 58.780 50.000 0.00 0.00 0.00 3.18
3021 6055 1.219646 GTCGGCCTTTTACGTTGTCA 58.780 50.000 0.00 0.00 0.00 3.58
3022 6056 1.598601 GTCGGCCTTTTACGTTGTCAA 59.401 47.619 0.00 0.00 0.00 3.18
3023 6057 2.031930 GTCGGCCTTTTACGTTGTCAAA 59.968 45.455 0.00 0.00 0.00 2.69
3024 6058 2.681848 TCGGCCTTTTACGTTGTCAAAA 59.318 40.909 0.00 0.00 0.00 2.44
3025 6059 3.128242 TCGGCCTTTTACGTTGTCAAAAA 59.872 39.130 0.00 0.00 0.00 1.94
3026 6060 4.045783 CGGCCTTTTACGTTGTCAAAAAT 58.954 39.130 0.00 0.00 0.00 1.82
3027 6061 4.504826 CGGCCTTTTACGTTGTCAAAAATT 59.495 37.500 0.00 0.00 0.00 1.82
3028 6062 5.686397 CGGCCTTTTACGTTGTCAAAAATTA 59.314 36.000 0.00 0.00 0.00 1.40
3029 6063 6.363896 CGGCCTTTTACGTTGTCAAAAATTAT 59.636 34.615 0.00 0.00 0.00 1.28
3030 6064 7.409980 CGGCCTTTTACGTTGTCAAAAATTATC 60.410 37.037 0.00 0.00 0.00 1.75
3031 6065 7.382759 GGCCTTTTACGTTGTCAAAAATTATCA 59.617 33.333 0.00 0.00 0.00 2.15
3032 6066 8.756864 GCCTTTTACGTTGTCAAAAATTATCAA 58.243 29.630 0.00 0.00 0.00 2.57
3095 6129 6.142818 TCAATTACCAACTGACCAAACAAG 57.857 37.500 0.00 0.00 0.00 3.16
3097 6131 1.111277 ACCAACTGACCAAACAAGGC 58.889 50.000 0.00 0.00 0.00 4.35
3105 6139 4.588528 ACTGACCAAACAAGGCACAATATT 59.411 37.500 0.00 0.00 0.00 1.28
3110 6144 7.439655 TGACCAAACAAGGCACAATATTAAAAC 59.560 33.333 0.00 0.00 0.00 2.43
3112 6146 7.440856 ACCAAACAAGGCACAATATTAAAACTG 59.559 33.333 0.00 0.00 0.00 3.16
3115 6149 6.924111 ACAAGGCACAATATTAAAACTGGAG 58.076 36.000 0.00 0.00 0.00 3.86
3124 6158 9.084533 ACAATATTAAAACTGGAGCTTGGTTAA 57.915 29.630 0.00 0.00 0.00 2.01
3126 6160 6.590234 ATTAAAACTGGAGCTTGGTTAAGG 57.410 37.500 0.00 0.00 34.40 2.69
3142 6176 4.885325 GGTTAAGGTTTCCTCAACTCACAA 59.115 41.667 2.42 0.00 35.46 3.33
3146 6180 8.793592 GTTAAGGTTTCCTCAACTCACAATATT 58.206 33.333 0.00 0.00 35.46 1.28
3148 6182 8.567285 AAGGTTTCCTCAACTCACAATATTAG 57.433 34.615 0.00 0.00 35.46 1.73
3151 6185 7.148239 GGTTTCCTCAACTCACAATATTAGTGG 60.148 40.741 14.17 2.68 35.46 4.00
3152 6186 5.428253 TCCTCAACTCACAATATTAGTGGC 58.572 41.667 14.17 0.00 37.58 5.01
3153 6187 5.045942 TCCTCAACTCACAATATTAGTGGCA 60.046 40.000 14.17 0.00 37.58 4.92
3154 6188 5.065218 CCTCAACTCACAATATTAGTGGCAC 59.935 44.000 10.29 10.29 37.58 5.01
3156 6190 6.000840 TCAACTCACAATATTAGTGGCACAA 58.999 36.000 21.41 12.27 44.16 3.33
3157 6191 6.658816 TCAACTCACAATATTAGTGGCACAAT 59.341 34.615 21.41 18.02 44.16 2.71
3158 6192 7.176515 TCAACTCACAATATTAGTGGCACAATT 59.823 33.333 21.41 10.58 44.16 2.32
3164 6198 7.433131 CACAATATTAGTGGCACAATTTAGCAG 59.567 37.037 21.41 4.32 44.16 4.24
3168 6202 4.935352 AGTGGCACAATTTAGCAGAAAA 57.065 36.364 21.41 0.00 44.16 2.29
3175 6209 6.313411 GGCACAATTTAGCAGAAAATAATGCA 59.687 34.615 18.59 0.00 45.01 3.96
3178 6212 8.928733 CACAATTTAGCAGAAAATAATGCAAGT 58.071 29.630 0.00 0.00 45.01 3.16
3197 6231 9.846248 ATGCAAGTTGAATAATTACTCAAACTC 57.154 29.630 10.71 0.09 33.52 3.01
3198 6232 8.845227 TGCAAGTTGAATAATTACTCAAACTCA 58.155 29.630 10.71 4.95 33.52 3.41
3209 6243 8.494016 AATTACTCAAACTCATAACTAGTGCC 57.506 34.615 0.00 0.00 0.00 5.01
3214 6248 1.137086 ACTCATAACTAGTGCCGGCAG 59.863 52.381 33.73 21.79 0.00 4.85
3226 6260 0.248539 GCCGGCAGTCGACTAGTAAG 60.249 60.000 24.80 6.62 42.43 2.34
3235 6269 6.692249 GGCAGTCGACTAGTAAGAGATAAAAC 59.308 42.308 19.57 0.00 0.00 2.43
3267 6301 5.114780 CCCAGATACTGAATCAAGTGAGTG 58.885 45.833 0.00 0.00 37.03 3.51
3280 6314 5.849510 TCAAGTGAGTGAAATTTACGGAGA 58.150 37.500 0.00 0.00 0.00 3.71
3281 6315 6.285224 TCAAGTGAGTGAAATTTACGGAGAA 58.715 36.000 0.00 0.00 0.00 2.87
3282 6316 6.764085 TCAAGTGAGTGAAATTTACGGAGAAA 59.236 34.615 0.00 0.00 0.00 2.52
3283 6317 7.444183 TCAAGTGAGTGAAATTTACGGAGAAAT 59.556 33.333 0.00 0.00 0.00 2.17
3284 6318 7.133891 AGTGAGTGAAATTTACGGAGAAATG 57.866 36.000 0.00 0.00 0.00 2.32
3285 6319 6.934645 AGTGAGTGAAATTTACGGAGAAATGA 59.065 34.615 0.00 0.00 0.00 2.57
3286 6320 7.607991 AGTGAGTGAAATTTACGGAGAAATGAT 59.392 33.333 0.00 0.00 0.00 2.45
3287 6321 8.237267 GTGAGTGAAATTTACGGAGAAATGATT 58.763 33.333 0.00 0.00 0.00 2.57
3288 6322 9.443323 TGAGTGAAATTTACGGAGAAATGATTA 57.557 29.630 0.00 0.00 0.00 1.75
3298 6332 6.910995 ACGGAGAAATGATTATAGTAGGTCG 58.089 40.000 0.00 0.00 0.00 4.79
3299 6333 6.713903 ACGGAGAAATGATTATAGTAGGTCGA 59.286 38.462 0.00 0.00 0.00 4.20
3300 6334 7.230108 ACGGAGAAATGATTATAGTAGGTCGAA 59.770 37.037 0.00 0.00 0.00 3.71
3301 6335 7.751348 CGGAGAAATGATTATAGTAGGTCGAAG 59.249 40.741 0.00 0.00 0.00 3.79
3302 6336 8.578151 GGAGAAATGATTATAGTAGGTCGAAGT 58.422 37.037 0.00 0.00 0.00 3.01
3307 6341 9.570468 AATGATTATAGTAGGTCGAAGTAGTGA 57.430 33.333 0.00 0.00 0.00 3.41
3308 6342 8.604640 TGATTATAGTAGGTCGAAGTAGTGAG 57.395 38.462 0.00 0.00 0.00 3.51
3309 6343 7.660617 TGATTATAGTAGGTCGAAGTAGTGAGG 59.339 40.741 0.00 0.00 0.00 3.86
3310 6344 3.002038 AGTAGGTCGAAGTAGTGAGGG 57.998 52.381 0.00 0.00 0.00 4.30
3311 6345 2.575279 AGTAGGTCGAAGTAGTGAGGGA 59.425 50.000 0.00 0.00 0.00 4.20
3312 6346 1.836802 AGGTCGAAGTAGTGAGGGAC 58.163 55.000 0.00 0.00 0.00 4.46
3313 6347 1.075050 AGGTCGAAGTAGTGAGGGACA 59.925 52.381 0.00 0.00 0.00 4.02
3338 6372 9.577110 CACACAAATGTATAATGAAGCTCAAAT 57.423 29.630 0.00 0.00 36.72 2.32
3340 6374 9.791820 CACAAATGTATAATGAAGCTCAAATCA 57.208 29.630 0.00 0.00 0.00 2.57
3367 6401 2.164422 TCTGATGTGGTAGTCAAGCTCG 59.836 50.000 0.00 0.00 0.00 5.03
3371 6405 1.202592 TGTGGTAGTCAAGCTCGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
3372 6406 1.871039 GTGGTAGTCAAGCTCGCAAAA 59.129 47.619 0.00 0.00 0.00 2.44
3373 6407 2.096218 GTGGTAGTCAAGCTCGCAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
3374 6408 1.135944 GGTAGTCAAGCTCGCAAAAGC 60.136 52.381 0.00 0.00 42.82 3.51
3375 6409 1.531149 GTAGTCAAGCTCGCAAAAGCA 59.469 47.619 5.63 0.00 45.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.813184 TAGTCGGAGGTAAACGCCAG 59.187 55.000 0.00 0.00 39.29 4.85
76 77 0.813184 CTAGTCGGAGGTAAACGCCA 59.187 55.000 0.00 0.00 39.29 5.69
105 106 4.922026 GTGTGTTGTCCCCGCGGT 62.922 66.667 26.12 0.00 0.00 5.68
107 108 4.920112 TGGTGTGTTGTCCCCGCG 62.920 66.667 0.00 0.00 0.00 6.46
109 110 2.032634 CGATGGTGTGTTGTCCCCG 61.033 63.158 0.00 0.00 0.00 5.73
120 121 1.227263 CGCTACCCCTTCGATGGTG 60.227 63.158 15.59 7.40 36.04 4.17
121 122 3.090219 GCGCTACCCCTTCGATGGT 62.090 63.158 15.59 11.08 38.69 3.55
142 143 4.619227 ACCGCAACCCAGGTGTCG 62.619 66.667 0.00 0.00 39.66 4.35
143 144 2.203294 AACCGCAACCCAGGTGTC 60.203 61.111 0.00 0.00 41.21 3.67
144 145 2.203294 GAACCGCAACCCAGGTGT 60.203 61.111 0.00 0.00 41.21 4.16
145 146 2.983592 GGAACCGCAACCCAGGTG 60.984 66.667 0.00 0.00 41.21 4.00
146 147 3.491598 CTGGAACCGCAACCCAGGT 62.492 63.158 0.00 0.00 42.75 4.00
147 148 2.672996 CTGGAACCGCAACCCAGG 60.673 66.667 0.00 0.00 42.75 4.45
148 149 2.672996 CCTGGAACCGCAACCCAG 60.673 66.667 0.00 0.00 45.28 4.45
149 150 4.966787 GCCTGGAACCGCAACCCA 62.967 66.667 0.00 0.00 0.00 4.51
243 244 0.325296 TAGGAATCCACTGCCTCCGT 60.325 55.000 0.61 0.00 33.28 4.69
252 253 2.171448 ACTCCATGCAGTAGGAATCCAC 59.829 50.000 0.61 0.00 32.57 4.02
262 263 0.036577 GTGCTCAGACTCCATGCAGT 60.037 55.000 0.00 0.00 34.15 4.40
266 267 0.817654 TACCGTGCTCAGACTCCATG 59.182 55.000 0.00 0.00 0.00 3.66
278 279 2.577593 GAGTCCACCCTACCGTGC 59.422 66.667 0.00 0.00 32.10 5.34
280 281 1.000107 GAGGAGTCCACCCTACCGT 60.000 63.158 12.86 0.00 33.36 4.83
283 284 0.688087 CCAGGAGGAGTCCACCCTAC 60.688 65.000 20.95 0.00 46.80 3.18
309 310 1.227089 CCGTCTGAATGGCTCTCCG 60.227 63.158 0.00 0.00 34.14 4.63
310 311 0.179097 GACCGTCTGAATGGCTCTCC 60.179 60.000 0.00 0.00 34.61 3.71
313 314 1.079503 GTTGACCGTCTGAATGGCTC 58.920 55.000 0.00 0.00 34.61 4.70
320 321 0.112606 AGGAGGAGTTGACCGTCTGA 59.887 55.000 0.00 0.00 34.73 3.27
322 323 0.112606 TGAGGAGGAGTTGACCGTCT 59.887 55.000 0.00 0.00 34.73 4.18
325 326 0.461961 GGATGAGGAGGAGTTGACCG 59.538 60.000 0.00 0.00 34.73 4.79
331 332 0.030297 ATGCAGGGATGAGGAGGAGT 60.030 55.000 0.00 0.00 0.00 3.85
359 360 2.941064 CTGCTGATCCGTTGATTGTGAT 59.059 45.455 0.00 0.00 0.00 3.06
378 379 8.474025 AGACAAGGAATACAACTCTAAGATCTG 58.526 37.037 0.00 0.00 0.00 2.90
386 387 6.595716 GCATAACAGACAAGGAATACAACTCT 59.404 38.462 0.00 0.00 0.00 3.24
396 397 3.173151 TCTCCAGCATAACAGACAAGGA 58.827 45.455 0.00 0.00 0.00 3.36
398 399 3.937706 CCTTCTCCAGCATAACAGACAAG 59.062 47.826 0.00 0.00 0.00 3.16
412 413 2.127869 CGATCTCCGGCCTTCTCCA 61.128 63.158 0.00 0.00 33.91 3.86
423 424 3.067721 AGATTCGTTTCGACGATCTCC 57.932 47.619 0.00 0.00 42.02 3.71
434 435 0.325602 TACGCCCCCAAGATTCGTTT 59.674 50.000 0.00 0.00 34.97 3.60
441 442 1.987855 CTCCACTACGCCCCCAAGA 60.988 63.158 0.00 0.00 0.00 3.02
456 457 1.134068 GGATGAAACCCTAGCCACTCC 60.134 57.143 0.00 0.00 0.00 3.85
481 487 7.135467 CCGACATATATTCATCTCTATCCGTG 58.865 42.308 0.00 0.00 0.00 4.94
504 510 0.179073 CACTAGCCCATCTTGACCCG 60.179 60.000 0.00 0.00 0.00 5.28
509 515 0.749454 GCCCACACTAGCCCATCTTG 60.749 60.000 0.00 0.00 0.00 3.02
510 516 1.609783 GCCCACACTAGCCCATCTT 59.390 57.895 0.00 0.00 0.00 2.40
511 517 2.378634 GGCCCACACTAGCCCATCT 61.379 63.158 0.00 0.00 43.76 2.90
531 537 1.512996 CCTAGGCGCGTCTTCGGATA 61.513 60.000 22.56 0.00 37.56 2.59
544 550 2.508663 GTTCGGACACGCCTAGGC 60.509 66.667 24.75 24.75 40.69 3.93
548 554 2.600769 AGAGGTTCGGACACGCCT 60.601 61.111 0.00 0.00 40.69 5.52
553 559 2.317040 GGATATGGAGAGGTTCGGACA 58.683 52.381 0.00 0.00 0.00 4.02
559 565 1.343069 GAGGCGGATATGGAGAGGTT 58.657 55.000 0.00 0.00 0.00 3.50
578 584 5.837979 CCCCCTCATATCTAGTCCATATCTG 59.162 48.000 0.00 0.00 0.00 2.90
612 619 4.169271 CCGACCCTATACGGCAGA 57.831 61.111 0.00 0.00 42.55 4.26
618 625 1.163554 CGACCTAGCCGACCCTATAC 58.836 60.000 0.00 0.00 0.00 1.47
626 633 1.822990 ACAAAATCTCGACCTAGCCGA 59.177 47.619 5.55 5.55 34.61 5.54
627 634 1.927174 CACAAAATCTCGACCTAGCCG 59.073 52.381 0.00 0.00 0.00 5.52
630 637 3.179830 CGGTCACAAAATCTCGACCTAG 58.820 50.000 5.93 0.00 44.76 3.02
631 638 2.094390 CCGGTCACAAAATCTCGACCTA 60.094 50.000 5.93 0.00 44.76 3.08
632 639 1.337823 CCGGTCACAAAATCTCGACCT 60.338 52.381 5.93 0.00 44.76 3.85
666 687 0.179045 CCCTAAAGTCTGGGCGGATG 60.179 60.000 0.00 0.00 36.61 3.51
673 694 2.561419 TCGAACACTCCCTAAAGTCTGG 59.439 50.000 0.00 0.00 0.00 3.86
675 696 2.826725 CCTCGAACACTCCCTAAAGTCT 59.173 50.000 0.00 0.00 0.00 3.24
681 702 1.340795 GGACTCCTCGAACACTCCCTA 60.341 57.143 0.00 0.00 0.00 3.53
682 703 0.612453 GGACTCCTCGAACACTCCCT 60.612 60.000 0.00 0.00 0.00 4.20
683 704 1.891616 GGACTCCTCGAACACTCCC 59.108 63.158 0.00 0.00 0.00 4.30
734 756 9.780186 AACTTGGTTTATATAGACTATTGGAGC 57.220 33.333 0.00 0.00 0.00 4.70
772 798 3.896648 ACGCAGGTAAAGTGTGAATTG 57.103 42.857 0.00 0.00 0.00 2.32
786 812 0.792640 CTACAACTCAGCAACGCAGG 59.207 55.000 0.00 0.00 0.00 4.85
828 854 1.359459 GAACAACACCTCCGGCGATC 61.359 60.000 9.30 0.00 0.00 3.69
830 856 2.029964 GAACAACACCTCCGGCGA 59.970 61.111 9.30 0.00 0.00 5.54
862 895 5.709164 ACCTTCAAACAATTGGAGAGAGATG 59.291 40.000 10.83 1.97 43.82 2.90
921 956 2.009774 CGGGACATGTAGGAAAAGCTG 58.990 52.381 0.00 0.00 0.00 4.24
966 1001 3.384789 AGAATCTGAAATGTCCGATCCGA 59.615 43.478 0.00 0.00 28.42 4.55
967 1002 3.722147 AGAATCTGAAATGTCCGATCCG 58.278 45.455 0.00 0.00 28.42 4.18
968 1003 4.878397 ACAAGAATCTGAAATGTCCGATCC 59.122 41.667 0.00 0.00 28.42 3.36
990 1048 5.170748 CCTTTTCTTCCCATAATTGCACAC 58.829 41.667 0.00 0.00 0.00 3.82
998 1064 6.318913 TGAAATGTCCCTTTTCTTCCCATAA 58.681 36.000 0.00 0.00 34.80 1.90
1008 1074 2.493278 CGGCATCTGAAATGTCCCTTTT 59.507 45.455 0.00 0.00 0.00 2.27
1062 1128 1.446272 GTACTGAGCTGGCACGTCC 60.446 63.158 0.00 0.00 0.00 4.79
1136 1202 1.504900 CGGACGAGGTCGATGACAA 59.495 57.895 6.35 0.00 43.02 3.18
1170 1236 2.281002 TCGTCGGAGGTGTCGTCA 60.281 61.111 0.00 0.00 0.00 4.35
1266 2394 4.511527 CAAGTCTAGTGGAGTAGTACCGA 58.488 47.826 0.00 0.00 0.00 4.69
1267 2395 3.626670 CCAAGTCTAGTGGAGTAGTACCG 59.373 52.174 0.00 0.00 38.54 4.02
1395 2544 3.130160 CTCTTTGAGCGGCTGCCC 61.130 66.667 15.55 1.76 44.31 5.36
1407 2556 5.241662 GTTGGTGTATCTCTGCTTCTCTTT 58.758 41.667 0.00 0.00 0.00 2.52
1483 2644 2.267961 GGATTTGGTCCGGCGAGT 59.732 61.111 9.30 0.00 37.23 4.18
1594 2758 1.615883 AGACATTGCTCTGTGACGTCT 59.384 47.619 17.92 0.00 0.00 4.18
1643 2817 2.931969 TGATGACATGATCAGACAACGC 59.068 45.455 0.00 0.00 41.91 4.84
1925 3102 1.978617 GGCCACCAACCCTGTCATG 60.979 63.158 0.00 0.00 0.00 3.07
2090 3674 7.496529 TGAACATTTGAAGTTTCGAGATTCT 57.503 32.000 7.55 0.00 0.00 2.40
2166 5175 5.347635 GCTCATTATCTGTGTCACAAACGTA 59.652 40.000 7.18 0.00 0.00 3.57
2169 5178 5.611796 TGCTCATTATCTGTGTCACAAAC 57.388 39.130 7.18 0.00 0.00 2.93
2214 5224 0.537653 TGTTTGTCACGACCCTGTGA 59.462 50.000 0.00 0.00 46.15 3.58
2355 5365 3.322828 TGTAACTTCGGGCAAAGTAGTCT 59.677 43.478 5.12 0.00 38.52 3.24
2498 5512 8.088365 TCAGGGATGTAATGAACTAATGATACG 58.912 37.037 0.00 0.00 0.00 3.06
2505 5519 6.620877 ACACTCAGGGATGTAATGAACTAA 57.379 37.500 0.00 0.00 0.00 2.24
2506 5520 7.914427 ATACACTCAGGGATGTAATGAACTA 57.086 36.000 0.00 0.00 35.05 2.24
2507 5521 6.814954 ATACACTCAGGGATGTAATGAACT 57.185 37.500 0.00 0.00 35.05 3.01
2508 5522 7.011482 GTGAATACACTCAGGGATGTAATGAAC 59.989 40.741 0.00 0.00 42.99 3.18
2509 5523 7.047891 GTGAATACACTCAGGGATGTAATGAA 58.952 38.462 0.00 0.00 42.99 2.57
2510 5524 6.582636 GTGAATACACTCAGGGATGTAATGA 58.417 40.000 0.00 0.00 42.99 2.57
2511 5525 6.851222 GTGAATACACTCAGGGATGTAATG 57.149 41.667 0.00 0.00 42.99 1.90
2562 5576 2.910688 ATGTAGACCATGCTAACCGG 57.089 50.000 0.00 0.00 30.69 5.28
2658 5683 7.503521 TGTATGTTACAAGACAAATGCAGAA 57.496 32.000 0.00 0.00 35.38 3.02
2692 5717 4.201685 CCTCTTTGCCAAACTTCGTATACG 60.202 45.833 19.23 19.23 41.45 3.06
2698 5723 3.314080 TGTTACCTCTTTGCCAAACTTCG 59.686 43.478 0.00 0.00 0.00 3.79
2734 5768 7.375017 CACAAGATGTACTTCCAACGTAAAAAC 59.625 37.037 5.19 0.00 36.61 2.43
2738 5772 4.992319 CCACAAGATGTACTTCCAACGTAA 59.008 41.667 5.19 0.00 36.61 3.18
2739 5773 4.562082 CCACAAGATGTACTTCCAACGTA 58.438 43.478 5.19 0.00 36.61 3.57
2740 5774 3.399330 CCACAAGATGTACTTCCAACGT 58.601 45.455 5.19 0.00 36.61 3.99
2741 5775 2.159627 GCCACAAGATGTACTTCCAACG 59.840 50.000 5.19 0.00 36.61 4.10
2742 5776 2.159627 CGCCACAAGATGTACTTCCAAC 59.840 50.000 5.19 0.00 36.61 3.77
2743 5777 2.422597 CGCCACAAGATGTACTTCCAA 58.577 47.619 5.19 0.00 36.61 3.53
2744 5778 1.338674 CCGCCACAAGATGTACTTCCA 60.339 52.381 5.19 0.00 36.61 3.53
2745 5779 1.369625 CCGCCACAAGATGTACTTCC 58.630 55.000 5.19 0.00 36.61 3.46
2825 5859 8.491134 ACCAATATTTAGGCTGTGTCTATTGTA 58.509 33.333 0.00 0.00 0.00 2.41
2836 5870 4.780815 TGGAGTGACCAATATTTAGGCTG 58.219 43.478 0.00 0.00 46.75 4.85
2857 5891 5.910614 TGGTACTCATCATGACAGATTCTG 58.089 41.667 12.17 12.17 37.52 3.02
2958 5992 1.882352 CGGGCAAGAGCTTGGTACTTT 60.882 52.381 11.78 0.00 40.74 2.66
2982 6016 4.290155 GACAACAACTGCAACATGGTAAG 58.710 43.478 0.00 0.00 0.00 2.34
2988 6022 0.030638 GCCGACAACAACTGCAACAT 59.969 50.000 0.00 0.00 0.00 2.71
3005 6039 5.977171 AATTTTTGACAACGTAAAAGGCC 57.023 34.783 0.00 0.00 0.00 5.19
3072 6106 5.068460 CCTTGTTTGGTCAGTTGGTAATTGA 59.932 40.000 0.00 0.00 0.00 2.57
3083 6117 4.789012 ATATTGTGCCTTGTTTGGTCAG 57.211 40.909 0.00 0.00 0.00 3.51
3095 6129 5.582689 AGCTCCAGTTTTAATATTGTGCC 57.417 39.130 0.00 0.00 0.00 5.01
3097 6131 6.924111 ACCAAGCTCCAGTTTTAATATTGTG 58.076 36.000 0.00 0.00 0.00 3.33
3105 6139 5.056553 ACCTTAACCAAGCTCCAGTTTTA 57.943 39.130 1.83 0.00 0.00 1.52
3110 6144 2.820197 GGAAACCTTAACCAAGCTCCAG 59.180 50.000 0.00 0.00 0.00 3.86
3112 6146 3.082548 GAGGAAACCTTAACCAAGCTCC 58.917 50.000 0.00 0.00 31.76 4.70
3115 6149 3.889538 AGTTGAGGAAACCTTAACCAAGC 59.110 43.478 17.56 0.00 46.90 4.01
3124 6158 7.607991 CACTAATATTGTGAGTTGAGGAAACCT 59.392 37.037 10.66 0.00 39.85 3.50
3126 6160 7.626452 GCCACTAATATTGTGAGTTGAGGAAAC 60.626 40.741 15.37 0.00 37.60 2.78
3142 6176 7.880160 TTCTGCTAAATTGTGCCACTAATAT 57.120 32.000 0.00 0.00 0.00 1.28
3146 6180 6.588719 ATTTTCTGCTAAATTGTGCCACTA 57.411 33.333 0.00 0.00 0.00 2.74
3148 6182 7.674705 GCATTATTTTCTGCTAAATTGTGCCAC 60.675 37.037 0.00 0.00 34.31 5.01
3151 6185 7.293402 TGCATTATTTTCTGCTAAATTGTGC 57.707 32.000 14.33 14.33 39.16 4.57
3152 6186 8.928733 ACTTGCATTATTTTCTGCTAAATTGTG 58.071 29.630 0.00 0.00 39.16 3.33
3153 6187 9.492973 AACTTGCATTATTTTCTGCTAAATTGT 57.507 25.926 0.00 0.00 39.16 2.71
3154 6188 9.749490 CAACTTGCATTATTTTCTGCTAAATTG 57.251 29.630 0.00 0.00 39.16 2.32
3156 6190 9.709495 TTCAACTTGCATTATTTTCTGCTAAAT 57.291 25.926 0.00 0.00 39.16 1.40
3157 6191 9.709495 ATTCAACTTGCATTATTTTCTGCTAAA 57.291 25.926 0.00 0.00 39.16 1.85
3188 6222 4.495422 CGGCACTAGTTATGAGTTTGAGT 58.505 43.478 0.00 0.00 0.00 3.41
3197 6231 1.571919 GACTGCCGGCACTAGTTATG 58.428 55.000 29.03 16.25 0.00 1.90
3198 6232 0.102481 CGACTGCCGGCACTAGTTAT 59.898 55.000 29.03 4.63 33.91 1.89
3209 6243 2.277969 TCTCTTACTAGTCGACTGCCG 58.722 52.381 28.12 17.34 40.25 5.69
3235 6269 8.737168 TTGATTCAGTATCTGGGTTTAGATTG 57.263 34.615 0.00 0.00 38.35 2.67
3242 6276 5.249393 ACTCACTTGATTCAGTATCTGGGTT 59.751 40.000 0.00 0.00 34.17 4.11
3244 6278 5.105187 TCACTCACTTGATTCAGTATCTGGG 60.105 44.000 0.00 0.00 34.17 4.45
3247 6281 9.512588 AAATTTCACTCACTTGATTCAGTATCT 57.487 29.630 0.00 0.00 34.17 1.98
3274 6308 6.713903 TCGACCTACTATAATCATTTCTCCGT 59.286 38.462 0.00 0.00 0.00 4.69
3275 6309 7.142306 TCGACCTACTATAATCATTTCTCCG 57.858 40.000 0.00 0.00 0.00 4.63
3281 6315 9.570468 TCACTACTTCGACCTACTATAATCATT 57.430 33.333 0.00 0.00 0.00 2.57
3282 6316 9.221933 CTCACTACTTCGACCTACTATAATCAT 57.778 37.037 0.00 0.00 0.00 2.45
3283 6317 7.660617 CCTCACTACTTCGACCTACTATAATCA 59.339 40.741 0.00 0.00 0.00 2.57
3284 6318 7.119553 CCCTCACTACTTCGACCTACTATAATC 59.880 44.444 0.00 0.00 0.00 1.75
3285 6319 6.941436 CCCTCACTACTTCGACCTACTATAAT 59.059 42.308 0.00 0.00 0.00 1.28
3286 6320 6.100279 TCCCTCACTACTTCGACCTACTATAA 59.900 42.308 0.00 0.00 0.00 0.98
3287 6321 5.604231 TCCCTCACTACTTCGACCTACTATA 59.396 44.000 0.00 0.00 0.00 1.31
3288 6322 4.411540 TCCCTCACTACTTCGACCTACTAT 59.588 45.833 0.00 0.00 0.00 2.12
3289 6323 3.776969 TCCCTCACTACTTCGACCTACTA 59.223 47.826 0.00 0.00 0.00 1.82
3290 6324 2.575279 TCCCTCACTACTTCGACCTACT 59.425 50.000 0.00 0.00 0.00 2.57
3291 6325 2.682352 GTCCCTCACTACTTCGACCTAC 59.318 54.545 0.00 0.00 0.00 3.18
3292 6326 2.306805 TGTCCCTCACTACTTCGACCTA 59.693 50.000 0.00 0.00 0.00 3.08
3293 6327 1.075050 TGTCCCTCACTACTTCGACCT 59.925 52.381 0.00 0.00 0.00 3.85
3294 6328 1.201880 GTGTCCCTCACTACTTCGACC 59.798 57.143 0.00 0.00 43.13 4.79
3295 6329 1.884579 TGTGTCCCTCACTACTTCGAC 59.115 52.381 0.00 0.00 46.27 4.20
3296 6330 1.884579 GTGTGTCCCTCACTACTTCGA 59.115 52.381 0.00 0.00 46.27 3.71
3297 6331 1.611977 TGTGTGTCCCTCACTACTTCG 59.388 52.381 0.00 0.00 46.27 3.79
3298 6332 3.746045 TTGTGTGTCCCTCACTACTTC 57.254 47.619 0.00 0.00 46.27 3.01
3299 6333 4.141482 ACATTTGTGTGTCCCTCACTACTT 60.141 41.667 0.00 0.00 46.27 2.24
3300 6334 3.391296 ACATTTGTGTGTCCCTCACTACT 59.609 43.478 0.00 0.00 46.27 2.57
3301 6335 3.740115 ACATTTGTGTGTCCCTCACTAC 58.260 45.455 0.00 0.00 46.27 2.73
3302 6336 5.755409 ATACATTTGTGTGTCCCTCACTA 57.245 39.130 0.00 0.00 46.27 2.74
3303 6337 4.640771 ATACATTTGTGTGTCCCTCACT 57.359 40.909 0.00 0.00 46.27 3.41
3304 6338 6.597672 TCATTATACATTTGTGTGTCCCTCAC 59.402 38.462 0.00 0.00 46.31 3.51
3305 6339 6.716284 TCATTATACATTTGTGTGTCCCTCA 58.284 36.000 0.00 0.00 33.62 3.86
3306 6340 7.624360 TTCATTATACATTTGTGTGTCCCTC 57.376 36.000 0.00 0.00 33.62 4.30
3307 6341 6.095440 GCTTCATTATACATTTGTGTGTCCCT 59.905 38.462 0.00 0.00 33.62 4.20
3308 6342 6.095440 AGCTTCATTATACATTTGTGTGTCCC 59.905 38.462 0.00 0.00 33.62 4.46
3309 6343 7.088589 AGCTTCATTATACATTTGTGTGTCC 57.911 36.000 0.00 0.00 33.62 4.02
3310 6344 7.751732 TGAGCTTCATTATACATTTGTGTGTC 58.248 34.615 0.00 0.00 33.62 3.67
3311 6345 7.686438 TGAGCTTCATTATACATTTGTGTGT 57.314 32.000 0.00 0.00 36.13 3.72
3312 6346 8.969121 TTTGAGCTTCATTATACATTTGTGTG 57.031 30.769 0.00 0.00 0.00 3.82
3313 6347 9.793252 GATTTGAGCTTCATTATACATTTGTGT 57.207 29.630 0.00 0.00 0.00 3.72
3314 6348 9.791820 TGATTTGAGCTTCATTATACATTTGTG 57.208 29.630 0.00 0.00 0.00 3.33
3319 6353 9.788889 TCATCTGATTTGAGCTTCATTATACAT 57.211 29.630 0.00 0.00 0.00 2.29
3320 6354 9.788889 ATCATCTGATTTGAGCTTCATTATACA 57.211 29.630 0.00 0.00 0.00 2.29
3340 6374 5.453057 GCTTGACTACCACATCAGATCATCT 60.453 44.000 0.00 0.00 0.00 2.90
3347 6381 2.534298 CGAGCTTGACTACCACATCAG 58.466 52.381 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.