Multiple sequence alignment - TraesCS2A01G205400

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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 TraesCS2A01G205400 chr2A 100.000 3876 0 0 1 3876 183513108 183516983 0.000000e+00 7158.0
1 TraesCS2A01G205400 chr2A 76.750 400 74 11 1 395 54669632 54670017 5.080000e-49 206.0
2 TraesCS2A01G205400 chr2D 92.613 3479 184 38 1 3435 166866651 166863202 0.000000e+00 4933.0
3 TraesCS2A01G205400 chr2D 92.647 136 5 2 3742 3876 166862952 166862821 1.420000e-44 191.0
4 TraesCS2A01G205400 chr2B 92.303 3144 165 38 1 3124 230968092 230971178 0.000000e+00 4394.0
5 TraesCS2A01G205400 chr2B 79.805 411 67 11 1 407 698956598 698956200 6.340000e-73 285.0
6 TraesCS2A01G205400 chr2B 90.233 215 20 1 3160 3374 230971176 230971389 2.950000e-71 279.0
7 TraesCS2A01G205400 chr2B 77.910 421 74 11 1 416 214136428 214136022 1.080000e-60 244.0
8 TraesCS2A01G205400 chr2B 93.333 135 5 2 3742 3876 230971721 230971851 3.060000e-46 196.0
9 TraesCS2A01G205400 chr4B 80.732 410 64 8 1 407 665225224 665224827 4.870000e-79 305.0
10 TraesCS2A01G205400 chr4B 76.632 291 56 7 118 407 461189825 461190104 2.410000e-32 150.0
11 TraesCS2A01G205400 chr5D 80.488 410 66 7 1 407 565330013 565329615 6.290000e-78 302.0
12 TraesCS2A01G205400 chr6D 80.387 413 63 11 1 407 48449767 48450167 8.140000e-77 298.0
13 TraesCS2A01G205400 chr5B 80.000 420 67 12 1 416 650565525 650565119 1.050000e-75 294.0
14 TraesCS2A01G205400 chr5B 75.908 303 55 12 118 416 631621188 631620900 5.220000e-29 139.0
15 TraesCS2A01G205400 chr5B 91.489 47 4 0 361 407 464366371 464366417 8.990000e-07 65.8
16 TraesCS2A01G205400 chr5A 78.960 404 73 8 14 416 367709478 367709870 8.260000e-67 265.0
17 TraesCS2A01G205400 chr7A 76.923 403 73 12 1 398 670497459 670497846 1.090000e-50 211.0
18 TraesCS2A01G205400 chr4D 78.351 291 52 6 118 407 467442627 467442347 1.110000e-40 178.0
19 TraesCS2A01G205400 chr1D 75.248 303 50 17 118 416 469028008 469027727 1.890000e-23 121.0


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 TraesCS2A01G205400 chr2A 183513108 183516983 3875 False 7158 7158 100.000000 1 3876 1 chr2A.!!$F2 3875
1 TraesCS2A01G205400 chr2D 166862821 166866651 3830 True 2562 4933 92.630000 1 3876 2 chr2D.!!$R1 3875
2 TraesCS2A01G205400 chr2B 230968092 230971851 3759 False 1623 4394 91.956333 1 3876 3 chr2B.!!$F1 3875

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
355 360 0.468400 CCGGTAGCCTTCTAGCCTCT 60.468 60.0 0.0 0.0 39.49 3.69 F
684 701 0.745845 CAGACGCATTTCCCCAGAGG 60.746 60.0 0.0 0.0 0.00 3.69 F
685 702 0.909610 AGACGCATTTCCCCAGAGGA 60.910 55.0 0.0 0.0 45.68 3.71 F
2133 2150 1.059584 TGGTCCTCCAAGAAGGCACA 61.060 55.0 0.0 0.0 41.25 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1641 0.107993 TCGAGCAGCCCAATGAGAAG 60.108 55.000 0.0 0.0 0.00 2.85 R
1954 1971 0.395862 ATCTCCTCGACACCCACGAT 60.396 55.000 0.0 0.0 39.02 3.73 R
2326 2343 1.210155 GCCGGTGTGCTGCTTTTAG 59.790 57.895 1.9 0.0 0.00 1.85 R
3392 3445 0.036952 ATCGATCCATCATCCACGGC 60.037 55.000 0.0 0.0 0.00 5.68 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
38 39 0.618968 GGAGTCACAGACCCCCTCAT 60.619 60.000 0.00 0.00 32.18 2.90
45 46 2.190578 GACCCCCTCATTGCCGAG 59.809 66.667 0.00 0.00 0.00 4.63
57 58 3.611674 GCCGAGGCCCTAGCTCTC 61.612 72.222 0.00 0.00 39.73 3.20
87 88 7.526142 AGGAGTTATCTTCGCTACATTATGA 57.474 36.000 0.00 0.00 0.00 2.15
100 101 6.455647 GCTACATTATGAGGCTACACACATA 58.544 40.000 0.00 0.00 0.00 2.29
107 108 4.948847 TGAGGCTACACACATATGATCAC 58.051 43.478 10.38 0.00 0.00 3.06
113 114 5.293324 GCTACACACATATGATCACGGAAAA 59.707 40.000 10.38 0.00 0.00 2.29
135 136 3.002965 ACGGCTGTTTAGTTGCAGTTAAC 59.997 43.478 0.00 0.00 35.33 2.01
140 141 5.699458 GCTGTTTAGTTGCAGTTAACCTCTA 59.301 40.000 0.88 0.00 35.33 2.43
155 156 7.285858 AGTTAACCTCTAGAATTCTCGCTACAT 59.714 37.037 12.24 0.00 0.00 2.29
158 159 5.221342 ACCTCTAGAATTCTCGCTACATTGG 60.221 44.000 12.24 5.40 0.00 3.16
162 163 3.130516 AGAATTCTCGCTACATTGGTCGA 59.869 43.478 0.88 0.00 0.00 4.20
163 164 3.735237 ATTCTCGCTACATTGGTCGAT 57.265 42.857 0.00 0.00 0.00 3.59
166 167 1.002792 CTCGCTACATTGGTCGATCGA 60.003 52.381 15.15 15.15 0.00 3.59
185 190 5.219343 TCGATGATAGCACCAATTCTCAT 57.781 39.130 0.00 0.00 0.00 2.90
186 191 4.992951 TCGATGATAGCACCAATTCTCATG 59.007 41.667 0.00 0.00 0.00 3.07
194 199 4.081309 AGCACCAATTCTCATGGAAATTGG 60.081 41.667 30.77 30.77 42.05 3.16
214 219 5.483685 TGGAGAGCTTGCTCTTAGTTTTA 57.516 39.130 23.68 5.71 35.26 1.52
224 229 9.946165 GCTTGCTCTTAGTTTTACTTCTTTTAA 57.054 29.630 0.00 0.00 0.00 1.52
255 260 7.281040 ACATGTAATAAGATCAGCAAATGGG 57.719 36.000 0.00 0.00 0.00 4.00
270 275 2.180946 ATGGGTCCTGCACATCTCTA 57.819 50.000 0.00 0.00 36.19 2.43
272 277 1.764723 TGGGTCCTGCACATCTCTATG 59.235 52.381 0.00 0.00 39.17 2.23
277 282 4.305769 GTCCTGCACATCTCTATGCTAAG 58.694 47.826 0.00 0.00 42.55 2.18
279 284 2.730404 CTGCACATCTCTATGCTAAGCG 59.270 50.000 0.00 0.00 42.55 4.68
280 285 1.458827 GCACATCTCTATGCTAAGCGC 59.541 52.381 0.00 0.00 38.84 5.92
290 295 2.795389 GCTAAGCGCGGTTGTACGG 61.795 63.158 31.91 16.88 0.00 4.02
302 307 3.401182 GGTTGTACGGTTAATGTGACCA 58.599 45.455 0.00 0.00 36.99 4.02
326 331 3.190439 AGCTGGTTAGACAATACCCCTT 58.810 45.455 0.00 0.00 33.34 3.95
327 332 4.368067 AGCTGGTTAGACAATACCCCTTA 58.632 43.478 0.00 0.00 33.34 2.69
336 341 4.470304 AGACAATACCCCTTACTTCCTGAC 59.530 45.833 0.00 0.00 0.00 3.51
338 343 1.856629 TACCCCTTACTTCCTGACCG 58.143 55.000 0.00 0.00 0.00 4.79
344 349 1.136500 CTTACTTCCTGACCGGTAGCC 59.864 57.143 7.34 0.00 33.74 3.93
346 351 0.544595 ACTTCCTGACCGGTAGCCTT 60.545 55.000 7.34 0.00 33.74 4.35
349 354 0.627451 TCCTGACCGGTAGCCTTCTA 59.373 55.000 7.34 0.00 0.00 2.10
352 357 1.041447 TGACCGGTAGCCTTCTAGCC 61.041 60.000 7.34 0.00 39.49 3.93
353 358 0.756070 GACCGGTAGCCTTCTAGCCT 60.756 60.000 7.34 0.00 39.49 4.58
354 359 0.756070 ACCGGTAGCCTTCTAGCCTC 60.756 60.000 4.49 0.00 39.49 4.70
355 360 0.468400 CCGGTAGCCTTCTAGCCTCT 60.468 60.000 0.00 0.00 39.49 3.69
356 361 0.955905 CGGTAGCCTTCTAGCCTCTC 59.044 60.000 0.00 0.00 39.49 3.20
358 363 1.960689 GGTAGCCTTCTAGCCTCTCAG 59.039 57.143 0.00 0.00 37.33 3.35
359 364 2.661718 GTAGCCTTCTAGCCTCTCAGT 58.338 52.381 0.00 0.00 0.00 3.41
360 365 2.246091 AGCCTTCTAGCCTCTCAGTT 57.754 50.000 0.00 0.00 0.00 3.16
361 366 1.830477 AGCCTTCTAGCCTCTCAGTTG 59.170 52.381 0.00 0.00 0.00 3.16
362 367 1.827969 GCCTTCTAGCCTCTCAGTTGA 59.172 52.381 0.00 0.00 0.00 3.18
363 368 2.433970 GCCTTCTAGCCTCTCAGTTGAT 59.566 50.000 0.00 0.00 0.00 2.57
364 369 3.118445 GCCTTCTAGCCTCTCAGTTGATT 60.118 47.826 0.00 0.00 0.00 2.57
365 370 4.440880 CCTTCTAGCCTCTCAGTTGATTG 58.559 47.826 0.00 0.00 0.00 2.67
371 376 2.872038 GCCTCTCAGTTGATTGTTCGGT 60.872 50.000 0.00 0.00 0.00 4.69
387 392 2.147150 TCGGTGAATGCATTCGTTGAA 58.853 42.857 29.23 12.77 39.62 2.69
397 402 5.221891 TGCATTCGTTGAATAAAGCTCTC 57.778 39.130 0.00 0.00 30.44 3.20
478 495 3.243101 CGTTACAGTAGCATCTCCGTGAT 60.243 47.826 0.00 0.00 35.40 3.06
481 498 4.207891 ACAGTAGCATCTCCGTGATTTT 57.792 40.909 0.00 0.00 32.05 1.82
482 499 4.579869 ACAGTAGCATCTCCGTGATTTTT 58.420 39.130 0.00 0.00 32.05 1.94
507 524 2.859165 TTTGAAGTAGCACCTCCCAG 57.141 50.000 0.00 0.00 0.00 4.45
592 609 2.009774 CCTGCTTACATTCCTTCCGTG 58.990 52.381 0.00 0.00 0.00 4.94
655 672 0.968393 AGCCTTCGTCCTCACTCCTC 60.968 60.000 0.00 0.00 0.00 3.71
662 679 4.803426 CCTCACTCCTCACGCGGC 62.803 72.222 12.47 0.00 0.00 6.53
684 701 0.745845 CAGACGCATTTCCCCAGAGG 60.746 60.000 0.00 0.00 0.00 3.69
685 702 0.909610 AGACGCATTTCCCCAGAGGA 60.910 55.000 0.00 0.00 45.68 3.71
896 913 1.962100 ACTAGTAATAGCTCCACCGCC 59.038 52.381 0.00 0.00 0.00 6.13
954 971 2.125832 GGCCGGAATTGACGACGA 60.126 61.111 5.05 0.00 0.00 4.20
955 972 2.450345 GGCCGGAATTGACGACGAC 61.450 63.158 5.05 0.00 0.00 4.34
956 973 2.785105 GCCGGAATTGACGACGACG 61.785 63.158 5.05 5.58 45.75 5.12
1011 1028 2.866762 CGTCGGAAGAATGGGAGAATTC 59.133 50.000 0.00 0.00 45.01 2.17
1095 1112 1.752501 CGCTGGACGCCATAAACTCG 61.753 60.000 0.00 0.00 30.82 4.18
1147 1164 3.485431 CGCTCAAGTGGCAGCTCG 61.485 66.667 0.00 0.00 33.09 5.03
1719 1736 1.398390 GGGTATGACGCTTCTTGCAAG 59.602 52.381 20.81 20.81 43.06 4.01
1962 1979 1.153289 GCTGATGAGCATCGTGGGT 60.153 57.895 0.00 0.00 45.46 4.51
2118 2135 1.977293 GCTCATCCAGGGAGGTGGTC 61.977 65.000 0.00 0.00 38.88 4.02
2133 2150 1.059584 TGGTCCTCCAAGAAGGCACA 61.060 55.000 0.00 0.00 41.25 4.57
2223 2240 2.492090 GCCATCGACGCTCTCTGT 59.508 61.111 0.00 0.00 0.00 3.41
2337 2354 2.282110 TGCGCCCTAAAAGCAGCA 60.282 55.556 4.18 0.00 37.40 4.41
2454 2471 2.725008 GAGACGAGGGAGATGGCG 59.275 66.667 0.00 0.00 0.00 5.69
2682 2699 3.932710 GGTAATCACAGCATCAAGACGAA 59.067 43.478 0.00 0.00 0.00 3.85
2683 2700 4.391830 GGTAATCACAGCATCAAGACGAAA 59.608 41.667 0.00 0.00 0.00 3.46
2684 2701 5.106712 GGTAATCACAGCATCAAGACGAAAA 60.107 40.000 0.00 0.00 0.00 2.29
2716 2738 6.818644 TCCCTAAAATTCTCGACTTCTGAATG 59.181 38.462 0.00 0.00 31.70 2.67
2723 2745 3.928992 TCTCGACTTCTGAATGCATTGAC 59.071 43.478 18.59 3.68 0.00 3.18
2738 2760 2.118228 TTGACGCTGACAACATTTGC 57.882 45.000 0.00 0.00 0.00 3.68
2821 2843 3.616379 CCAAGAAGATCGTGAAGAAGCTC 59.384 47.826 0.00 0.00 0.00 4.09
2900 2924 0.036388 TCCGGCACCAGTTCTTGATC 60.036 55.000 0.00 0.00 0.00 2.92
2905 2929 0.798776 CACCAGTTCTTGATCGTGCC 59.201 55.000 0.00 0.00 0.00 5.01
2923 2947 0.032678 CCGTCTGCATGGGTAGCTAG 59.967 60.000 0.00 0.00 0.00 3.42
2928 2952 0.107703 TGCATGGGTAGCTAGCACAC 60.108 55.000 23.49 14.37 0.00 3.82
2965 2989 9.265938 CATATTTTGTTACAGTGAATGAACGAG 57.734 33.333 0.00 0.00 0.00 4.18
2982 3006 3.687125 ACGAGTGAATCTCTCCAGTGTA 58.313 45.455 6.73 0.00 40.75 2.90
3015 3039 1.959899 GCGATGTGTTGCTCCTGACG 61.960 60.000 0.00 0.00 0.00 4.35
3020 3044 2.666190 GTTGCTCCTGACGCAGCA 60.666 61.111 0.00 0.00 44.02 4.41
3032 3056 2.683859 CGCAGCACACACCCTGATG 61.684 63.158 0.00 0.00 0.00 3.07
3037 3061 1.973281 CACACACCCTGATGCCCAC 60.973 63.158 0.00 0.00 0.00 4.61
3072 3096 0.806102 CCTCTGTACATTGCCCGTCG 60.806 60.000 0.00 0.00 0.00 5.12
3078 3102 3.803082 CATTGCCCGTCGCTGTGG 61.803 66.667 0.00 0.00 38.78 4.17
3109 3133 2.919666 AATCATTCAAAGCCGTTCCG 57.080 45.000 0.00 0.00 0.00 4.30
3122 3146 1.503542 GTTCCGCAATGCAGGAGTG 59.496 57.895 15.74 0.00 34.21 3.51
3125 3149 1.968017 CCGCAATGCAGGAGTGTGT 60.968 57.895 5.91 0.00 0.00 3.72
3166 3190 0.530744 TCAGCGGGTCACTGTATCAC 59.469 55.000 0.00 0.00 36.50 3.06
3182 3207 5.056480 TGTATCACTAGAATGGCAAATCGG 58.944 41.667 0.00 0.00 0.00 4.18
3189 3214 1.264288 GAATGGCAAATCGGTCGATCC 59.736 52.381 6.32 4.73 33.08 3.36
3230 3255 1.280746 CCGCCTGCGCTTTATGATG 59.719 57.895 9.73 0.00 38.24 3.07
3233 3258 0.041839 GCCTGCGCTTTATGATGTCG 60.042 55.000 9.73 0.00 0.00 4.35
3363 3392 1.751437 ATAAGTTGGCCGCTTTCCTC 58.249 50.000 16.07 0.00 0.00 3.71
3392 3445 3.869065 TCCCTACTTATTGCAACCGAAG 58.131 45.455 0.00 8.62 0.00 3.79
3401 3454 3.039202 GCAACCGAAGCCGTGGATG 62.039 63.158 0.00 0.00 0.00 3.51
3428 3481 0.033228 GATCGGCATCTGGTCCTCTG 59.967 60.000 0.00 0.00 0.00 3.35
3432 3485 1.336632 GGCATCTGGTCCTCTGCTCT 61.337 60.000 9.69 0.00 35.03 4.09
3435 3488 0.337773 ATCTGGTCCTCTGCTCTGGA 59.662 55.000 0.00 0.00 0.00 3.86
3436 3489 0.337773 TCTGGTCCTCTGCTCTGGAT 59.662 55.000 0.00 0.00 34.58 3.41
3437 3490 0.752054 CTGGTCCTCTGCTCTGGATC 59.248 60.000 0.00 0.00 34.58 3.36
3438 3491 0.041684 TGGTCCTCTGCTCTGGATCA 59.958 55.000 0.00 2.15 40.77 2.92
3439 3492 0.463620 GGTCCTCTGCTCTGGATCAC 59.536 60.000 0.00 0.00 33.83 3.06
3440 3493 0.463620 GTCCTCTGCTCTGGATCACC 59.536 60.000 0.00 0.00 34.58 4.02
3441 3494 0.337773 TCCTCTGCTCTGGATCACCT 59.662 55.000 0.00 0.00 37.04 4.00
3442 3495 0.752054 CCTCTGCTCTGGATCACCTC 59.248 60.000 0.00 0.00 37.04 3.85
3443 3496 0.752054 CTCTGCTCTGGATCACCTCC 59.248 60.000 0.00 0.00 45.19 4.30
3450 3503 4.176752 GGATCACCTCCGGGGCAC 62.177 72.222 0.00 0.00 39.10 5.01
3451 3504 3.083997 GATCACCTCCGGGGCACT 61.084 66.667 0.00 0.00 39.10 4.40
3452 3505 3.391665 GATCACCTCCGGGGCACTG 62.392 68.421 0.00 0.00 39.10 3.66
3500 3553 4.298009 GCATGCAGCTGTGTCTCT 57.702 55.556 16.64 0.00 41.15 3.10
3512 3565 1.833630 TGTGTCTCTGATCATGGACCC 59.166 52.381 19.01 12.11 0.00 4.46
3516 3569 0.531532 CTCTGATCATGGACCCGTGC 60.532 60.000 0.00 0.00 33.28 5.34
3524 3577 0.902984 ATGGACCCGTGCAGTACTCA 60.903 55.000 0.00 0.00 33.50 3.41
3525 3578 1.116536 TGGACCCGTGCAGTACTCAA 61.117 55.000 0.00 0.00 0.00 3.02
3552 3605 1.618837 CTCTGGTCAAAGGAGGACGAA 59.381 52.381 0.00 0.00 36.12 3.85
3554 3607 0.034896 TGGTCAAAGGAGGACGAAGC 59.965 55.000 0.00 0.00 36.12 3.86
3563 3616 3.034635 AGGAGGACGAAGCAGATTATGT 58.965 45.455 0.00 0.00 0.00 2.29
3570 3623 2.938451 CGAAGCAGATTATGTGCCTGAA 59.062 45.455 10.78 0.00 42.24 3.02
3571 3624 3.562973 CGAAGCAGATTATGTGCCTGAAT 59.437 43.478 10.78 0.00 42.24 2.57
3572 3625 4.751600 CGAAGCAGATTATGTGCCTGAATA 59.248 41.667 10.78 0.00 42.24 1.75
3574 3627 6.591448 CGAAGCAGATTATGTGCCTGAATATA 59.409 38.462 10.78 0.00 42.24 0.86
3576 3629 7.013823 AGCAGATTATGTGCCTGAATATACT 57.986 36.000 10.78 0.00 42.24 2.12
3577 3630 6.877855 AGCAGATTATGTGCCTGAATATACTG 59.122 38.462 10.78 0.00 42.24 2.74
3578 3631 6.652481 GCAGATTATGTGCCTGAATATACTGT 59.348 38.462 2.68 0.00 34.67 3.55
3579 3632 7.819415 GCAGATTATGTGCCTGAATATACTGTA 59.181 37.037 2.68 0.00 34.67 2.74
3583 3636 6.808008 ATGTGCCTGAATATACTGTAATGC 57.192 37.500 0.00 0.00 0.00 3.56
3585 3638 5.759763 TGTGCCTGAATATACTGTAATGCTG 59.240 40.000 0.00 0.00 0.00 4.41
3586 3639 5.991606 GTGCCTGAATATACTGTAATGCTGA 59.008 40.000 0.00 0.00 0.00 4.26
3587 3640 6.483307 GTGCCTGAATATACTGTAATGCTGAA 59.517 38.462 0.00 0.00 0.00 3.02
3592 3650 7.874940 TGAATATACTGTAATGCTGAATTGCC 58.125 34.615 0.00 0.00 30.33 4.52
3593 3651 7.501892 TGAATATACTGTAATGCTGAATTGCCA 59.498 33.333 0.00 0.00 30.33 4.92
3632 3694 2.068837 TTACGCTGTAGGTTGGTTCG 57.931 50.000 0.00 0.00 0.00 3.95
3633 3695 0.961019 TACGCTGTAGGTTGGTTCGT 59.039 50.000 0.00 0.00 0.00 3.85
3634 3696 0.961019 ACGCTGTAGGTTGGTTCGTA 59.039 50.000 0.00 0.00 0.00 3.43
3635 3697 1.336240 ACGCTGTAGGTTGGTTCGTAC 60.336 52.381 0.00 0.00 0.00 3.67
3636 3698 1.068055 CGCTGTAGGTTGGTTCGTACT 60.068 52.381 0.00 0.00 32.23 2.73
3637 3699 2.603953 GCTGTAGGTTGGTTCGTACTC 58.396 52.381 0.00 0.00 32.23 2.59
3638 3700 2.673326 GCTGTAGGTTGGTTCGTACTCC 60.673 54.545 0.00 0.00 32.23 3.85
3639 3701 1.541147 TGTAGGTTGGTTCGTACTCCG 59.459 52.381 0.00 0.00 38.13 4.63
3640 3702 1.541588 GTAGGTTGGTTCGTACTCCGT 59.458 52.381 0.00 0.00 37.94 4.69
3641 3703 1.909700 AGGTTGGTTCGTACTCCGTA 58.090 50.000 0.00 0.00 37.94 4.02
3642 3704 1.541588 AGGTTGGTTCGTACTCCGTAC 59.458 52.381 0.00 0.00 37.94 3.67
3643 3705 1.541588 GGTTGGTTCGTACTCCGTACT 59.458 52.381 3.07 0.00 36.93 2.73
3644 3706 2.589014 GTTGGTTCGTACTCCGTACTG 58.411 52.381 3.07 0.00 36.93 2.74
3645 3707 0.523072 TGGTTCGTACTCCGTACTGC 59.477 55.000 3.07 0.00 36.93 4.40
3646 3708 0.807496 GGTTCGTACTCCGTACTGCT 59.193 55.000 3.07 0.00 36.93 4.24
3647 3709 1.200948 GGTTCGTACTCCGTACTGCTT 59.799 52.381 3.07 0.00 36.93 3.91
3648 3710 2.248487 GTTCGTACTCCGTACTGCTTG 58.752 52.381 3.07 0.00 36.93 4.01
3649 3711 0.806868 TCGTACTCCGTACTGCTTGG 59.193 55.000 3.07 0.00 36.93 3.61
3650 3712 0.806868 CGTACTCCGTACTGCTTGGA 59.193 55.000 3.07 0.00 36.93 3.53
3651 3713 1.404391 CGTACTCCGTACTGCTTGGAT 59.596 52.381 3.07 0.00 36.93 3.41
3652 3714 2.541178 CGTACTCCGTACTGCTTGGATC 60.541 54.545 3.07 0.00 36.93 3.36
3653 3715 1.853963 ACTCCGTACTGCTTGGATCT 58.146 50.000 0.00 0.00 0.00 2.75
3654 3716 1.478510 ACTCCGTACTGCTTGGATCTG 59.521 52.381 0.00 0.00 0.00 2.90
3655 3717 1.478510 CTCCGTACTGCTTGGATCTGT 59.521 52.381 0.00 0.00 0.00 3.41
3656 3718 1.899814 TCCGTACTGCTTGGATCTGTT 59.100 47.619 0.00 0.00 0.00 3.16
3657 3719 2.002586 CCGTACTGCTTGGATCTGTTG 58.997 52.381 0.00 0.00 0.00 3.33
3658 3720 2.002586 CGTACTGCTTGGATCTGTTGG 58.997 52.381 0.00 0.00 0.00 3.77
3659 3721 2.612972 CGTACTGCTTGGATCTGTTGGT 60.613 50.000 0.00 0.00 0.00 3.67
3660 3722 3.368013 CGTACTGCTTGGATCTGTTGGTA 60.368 47.826 0.00 0.00 0.00 3.25
3661 3723 3.788227 ACTGCTTGGATCTGTTGGTAA 57.212 42.857 0.00 0.00 0.00 2.85
3662 3724 4.098914 ACTGCTTGGATCTGTTGGTAAA 57.901 40.909 0.00 0.00 0.00 2.01
3663 3725 3.821033 ACTGCTTGGATCTGTTGGTAAAC 59.179 43.478 0.00 0.00 36.78 2.01
3664 3726 3.820467 CTGCTTGGATCTGTTGGTAAACA 59.180 43.478 0.00 0.00 44.06 2.83
3665 3727 4.211125 TGCTTGGATCTGTTGGTAAACAA 58.789 39.130 0.00 0.00 45.50 2.83
3677 3739 3.682921 TGGTAAACAACGAGAAAAACGC 58.317 40.909 0.00 0.00 0.00 4.84
3678 3740 3.126514 TGGTAAACAACGAGAAAAACGCA 59.873 39.130 0.00 0.00 0.00 5.24
3679 3741 3.722289 GGTAAACAACGAGAAAAACGCAG 59.278 43.478 0.00 0.00 0.00 5.18
3680 3742 1.822581 AACAACGAGAAAAACGCAGC 58.177 45.000 0.00 0.00 0.00 5.25
3681 3743 0.315869 ACAACGAGAAAAACGCAGCG 60.316 50.000 14.82 14.82 0.00 5.18
3682 3744 1.368850 AACGAGAAAAACGCAGCGC 60.369 52.632 16.61 0.00 0.00 5.92
3683 3745 1.772063 AACGAGAAAAACGCAGCGCT 61.772 50.000 16.61 2.64 0.00 5.92
3684 3746 1.789739 CGAGAAAAACGCAGCGCTG 60.790 57.895 32.83 32.83 0.00 5.18
3722 3784 2.552315 GTGTTCCCTTTTCATCGCAGAA 59.448 45.455 0.00 0.00 43.58 3.02
3723 3785 3.191371 GTGTTCCCTTTTCATCGCAGAAT 59.809 43.478 0.00 0.00 43.58 2.40
3739 3801 4.487714 CAGAATCCTGCTGGTACCTTTA 57.512 45.455 14.36 0.00 33.07 1.85
3780 3894 3.774616 TCGCTCTCGAGGCTAACTA 57.225 52.632 13.56 0.00 40.21 2.24
3786 3900 3.487879 GCTCTCGAGGCTAACTAACTGAC 60.488 52.174 13.56 0.00 0.00 3.51
3787 3901 3.942748 CTCTCGAGGCTAACTAACTGACT 59.057 47.826 13.56 0.00 0.00 3.41
3788 3902 3.690139 TCTCGAGGCTAACTAACTGACTG 59.310 47.826 13.56 0.00 0.00 3.51
3789 3903 3.682696 TCGAGGCTAACTAACTGACTGA 58.317 45.455 0.00 0.00 0.00 3.41
3835 3949 1.681793 AGCATGATGGCTGCATTTCTC 59.318 47.619 0.50 0.00 43.89 2.87
3838 3952 1.358046 GATGGCTGCATTTCTCGGC 59.642 57.895 0.50 0.00 35.17 5.54
3870 3984 2.908688 ACAATCCAAACAAGCCAACC 57.091 45.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.434428 GTCTGTGACTCCTAGGAACGA 58.566 52.381 13.77 7.56 0.00 3.85
38 39 3.470888 GAGCTAGGGCCTCGGCAA 61.471 66.667 26.01 3.67 44.11 4.52
45 46 0.467804 CTTCCTTGAGAGCTAGGGCC 59.532 60.000 0.00 0.00 37.58 5.80
57 58 4.130286 AGCGAAGATAACTCCTTCCTTG 57.870 45.455 0.00 0.00 37.36 3.61
87 88 3.243873 CCGTGATCATATGTGTGTAGCCT 60.244 47.826 0.00 0.00 0.00 4.58
100 101 1.086696 CAGCCGTTTTCCGTGATCAT 58.913 50.000 0.00 0.00 33.66 2.45
107 108 2.646250 CAACTAAACAGCCGTTTTCCG 58.354 47.619 2.88 0.00 42.82 4.30
113 114 1.675552 AACTGCAACTAAACAGCCGT 58.324 45.000 0.00 0.00 37.42 5.68
123 124 7.010339 AGAATTCTAGAGGTTAACTGCAACT 57.990 36.000 6.06 0.00 0.00 3.16
126 127 5.651530 CGAGAATTCTAGAGGTTAACTGCA 58.348 41.667 8.25 0.00 0.00 4.41
135 136 5.221342 ACCAATGTAGCGAGAATTCTAGAGG 60.221 44.000 18.55 9.82 0.00 3.69
140 141 3.130516 TCGACCAATGTAGCGAGAATTCT 59.869 43.478 7.95 7.95 0.00 2.40
155 156 2.288213 GGTGCTATCATCGATCGACCAA 60.288 50.000 22.06 9.20 0.00 3.67
158 159 2.706555 TGGTGCTATCATCGATCGAC 57.293 50.000 22.06 7.10 0.00 4.20
162 163 5.219343 TGAGAATTGGTGCTATCATCGAT 57.781 39.130 0.00 0.00 0.00 3.59
163 164 4.670896 TGAGAATTGGTGCTATCATCGA 57.329 40.909 0.00 0.00 0.00 3.59
166 167 5.314718 TCCATGAGAATTGGTGCTATCAT 57.685 39.130 0.00 0.00 35.64 2.45
185 190 2.440409 GAGCAAGCTCTCCAATTTCCA 58.560 47.619 14.52 0.00 39.80 3.53
238 243 4.467769 CAGGACCCATTTGCTGATCTTAT 58.532 43.478 0.00 0.00 37.11 1.73
247 252 0.174162 GATGTGCAGGACCCATTTGC 59.826 55.000 0.00 0.00 38.30 3.68
255 260 2.906691 AGCATAGAGATGTGCAGGAC 57.093 50.000 0.00 0.00 43.63 3.85
272 277 2.693285 CGTACAACCGCGCTTAGC 59.307 61.111 5.56 0.00 43.95 3.09
277 282 0.247379 CATTAACCGTACAACCGCGC 60.247 55.000 0.00 0.00 0.00 6.86
279 284 2.067766 TCACATTAACCGTACAACCGC 58.932 47.619 0.00 0.00 0.00 5.68
280 285 2.412770 GGTCACATTAACCGTACAACCG 59.587 50.000 0.00 0.00 0.00 4.44
302 307 3.200165 GGGGTATTGTCTAACCAGCTCTT 59.800 47.826 0.00 0.00 37.51 2.85
318 323 2.395619 CGGTCAGGAAGTAAGGGGTAT 58.604 52.381 0.00 0.00 0.00 2.73
321 326 0.908180 ACCGGTCAGGAAGTAAGGGG 60.908 60.000 0.00 0.00 45.00 4.79
326 331 0.333993 AGGCTACCGGTCAGGAAGTA 59.666 55.000 12.40 0.00 45.00 2.24
327 332 0.544595 AAGGCTACCGGTCAGGAAGT 60.545 55.000 12.40 0.00 45.00 3.01
344 349 5.083533 ACAATCAACTGAGAGGCTAGAAG 57.916 43.478 0.00 0.00 0.00 2.85
346 351 4.380973 CGAACAATCAACTGAGAGGCTAGA 60.381 45.833 0.00 0.00 0.00 2.43
349 354 2.613977 CCGAACAATCAACTGAGAGGCT 60.614 50.000 0.00 0.00 0.00 4.58
352 357 3.653344 TCACCGAACAATCAACTGAGAG 58.347 45.455 0.00 0.00 0.00 3.20
353 358 3.744238 TCACCGAACAATCAACTGAGA 57.256 42.857 0.00 0.00 0.00 3.27
354 359 4.715896 CATTCACCGAACAATCAACTGAG 58.284 43.478 0.00 0.00 0.00 3.35
355 360 3.058293 GCATTCACCGAACAATCAACTGA 60.058 43.478 0.00 0.00 0.00 3.41
356 361 3.236816 GCATTCACCGAACAATCAACTG 58.763 45.455 0.00 0.00 0.00 3.16
358 363 3.281341 TGCATTCACCGAACAATCAAC 57.719 42.857 0.00 0.00 0.00 3.18
359 364 4.484236 GAATGCATTCACCGAACAATCAA 58.516 39.130 30.15 0.00 36.80 2.57
360 365 3.426025 CGAATGCATTCACCGAACAATCA 60.426 43.478 32.72 0.00 36.61 2.57
361 366 3.100817 CGAATGCATTCACCGAACAATC 58.899 45.455 32.72 8.19 36.61 2.67
362 367 2.487762 ACGAATGCATTCACCGAACAAT 59.512 40.909 32.72 6.72 36.61 2.71
363 368 1.876799 ACGAATGCATTCACCGAACAA 59.123 42.857 32.72 0.00 36.61 2.83
364 369 1.518325 ACGAATGCATTCACCGAACA 58.482 45.000 32.72 0.00 36.61 3.18
365 370 2.095969 TCAACGAATGCATTCACCGAAC 60.096 45.455 32.72 10.53 36.61 3.95
371 376 5.953183 AGCTTTATTCAACGAATGCATTCA 58.047 33.333 32.72 17.49 36.61 2.57
431 442 2.296792 GCAAAATGTTGGCCAGGTTTT 58.703 42.857 5.11 11.83 35.10 2.43
434 445 0.106521 GTGCAAAATGTTGGCCAGGT 59.893 50.000 5.11 0.00 35.10 4.00
435 446 0.603439 GGTGCAAAATGTTGGCCAGG 60.603 55.000 5.11 0.00 35.10 4.45
436 447 0.106335 TGGTGCAAAATGTTGGCCAG 59.894 50.000 5.11 0.00 35.10 4.85
437 448 0.179062 GTGGTGCAAAATGTTGGCCA 60.179 50.000 0.00 0.00 35.10 5.36
439 450 0.529555 ACGTGGTGCAAAATGTTGGC 60.530 50.000 0.00 0.00 35.10 4.52
441 452 3.439293 TGTAACGTGGTGCAAAATGTTG 58.561 40.909 14.69 0.00 37.83 3.33
443 454 2.685897 ACTGTAACGTGGTGCAAAATGT 59.314 40.909 0.00 0.00 0.00 2.71
486 503 3.486383 CTGGGAGGTGCTACTTCAAAAA 58.514 45.455 0.00 0.00 0.00 1.94
487 504 2.814097 GCTGGGAGGTGCTACTTCAAAA 60.814 50.000 0.00 0.00 0.00 2.44
488 505 1.271379 GCTGGGAGGTGCTACTTCAAA 60.271 52.381 0.00 0.00 0.00 2.69
489 506 0.324943 GCTGGGAGGTGCTACTTCAA 59.675 55.000 0.00 0.00 0.00 2.69
490 507 0.835971 TGCTGGGAGGTGCTACTTCA 60.836 55.000 0.00 0.00 0.00 3.02
491 508 0.543749 ATGCTGGGAGGTGCTACTTC 59.456 55.000 0.00 0.00 0.00 3.01
492 509 0.995024 AATGCTGGGAGGTGCTACTT 59.005 50.000 0.00 0.00 0.00 2.24
500 517 1.396996 CGTACGAAAAATGCTGGGAGG 59.603 52.381 10.44 0.00 0.00 4.30
507 524 3.443054 TGCTACACGTACGAAAAATGC 57.557 42.857 24.41 16.95 0.00 3.56
572 589 2.009774 CACGGAAGGAATGTAAGCAGG 58.990 52.381 0.00 0.00 0.00 4.85
592 609 1.135333 AGAAGAAGCGAAGGACGATCC 59.865 52.381 0.00 0.00 45.77 3.36
662 679 1.303236 TGGGGAAATGCGTCTGTGG 60.303 57.895 0.00 0.00 0.00 4.17
684 701 0.459237 CTGTGGATGCAGTCGGACTC 60.459 60.000 7.89 4.32 0.00 3.36
685 702 1.188219 ACTGTGGATGCAGTCGGACT 61.188 55.000 4.45 4.45 45.63 3.85
686 703 1.293498 ACTGTGGATGCAGTCGGAC 59.707 57.895 0.00 0.00 45.63 4.79
870 887 4.120589 GTGGAGCTATTACTAGTTGTGGC 58.879 47.826 0.00 4.02 0.00 5.01
874 891 3.381949 GCGGTGGAGCTATTACTAGTTG 58.618 50.000 0.00 0.00 0.00 3.16
896 913 1.216710 GGGACGAGGAGCAGAACAG 59.783 63.158 0.00 0.00 0.00 3.16
954 971 2.654877 CGCAGACCCTTACCACGT 59.345 61.111 0.00 0.00 0.00 4.49
955 972 2.813908 GCGCAGACCCTTACCACG 60.814 66.667 0.30 0.00 0.00 4.94
956 973 2.813908 CGCGCAGACCCTTACCAC 60.814 66.667 8.75 0.00 0.00 4.16
1095 1112 1.069049 GAGAAGGAGGCAGAGATGAGC 59.931 57.143 0.00 0.00 0.00 4.26
1147 1164 0.602905 CGGTTGAACCTGTCCCTGAC 60.603 60.000 13.18 0.00 35.66 3.51
1389 1406 1.794003 CGAGGCGCATATCTCGTCG 60.794 63.158 20.96 4.34 45.27 5.12
1624 1641 0.107993 TCGAGCAGCCCAATGAGAAG 60.108 55.000 0.00 0.00 0.00 2.85
1827 1844 3.774702 GCGTTGTCGGCGTTCTCC 61.775 66.667 6.85 0.00 37.56 3.71
1949 1966 2.212900 CTCGACACCCACGATGCTCA 62.213 60.000 0.00 0.00 39.02 4.26
1954 1971 0.395862 ATCTCCTCGACACCCACGAT 60.396 55.000 0.00 0.00 39.02 3.73
1962 1979 4.851843 TGTACTTCCTTATCTCCTCGACA 58.148 43.478 0.00 0.00 0.00 4.35
2118 2135 1.676967 GGCTGTGCCTTCTTGGAGG 60.677 63.158 0.73 0.00 46.69 4.30
2326 2343 1.210155 GCCGGTGTGCTGCTTTTAG 59.790 57.895 1.90 0.00 0.00 1.85
2683 2700 8.637196 AGTCGAGAATTTTAGGGAGAATTTTT 57.363 30.769 0.00 0.00 0.00 1.94
2684 2701 8.637196 AAGTCGAGAATTTTAGGGAGAATTTT 57.363 30.769 0.00 0.00 0.00 1.82
2689 2711 5.715279 TCAGAAGTCGAGAATTTTAGGGAGA 59.285 40.000 0.00 0.00 0.00 3.71
2692 2714 6.457528 GCATTCAGAAGTCGAGAATTTTAGGG 60.458 42.308 0.00 0.00 30.04 3.53
2693 2715 6.092670 TGCATTCAGAAGTCGAGAATTTTAGG 59.907 38.462 0.00 0.00 30.04 2.69
2695 2717 7.615582 ATGCATTCAGAAGTCGAGAATTTTA 57.384 32.000 0.00 0.00 30.04 1.52
2697 2719 6.149973 TCAATGCATTCAGAAGTCGAGAATTT 59.850 34.615 9.53 0.00 30.04 1.82
2716 2738 2.336554 AATGTTGTCAGCGTCAATGC 57.663 45.000 0.00 0.00 0.00 3.56
2723 2745 0.592637 TCCAGCAAATGTTGTCAGCG 59.407 50.000 0.00 0.00 0.00 5.18
2738 2760 4.154195 CCTGACATTCGTAAAAGGTTCCAG 59.846 45.833 0.00 0.00 0.00 3.86
2800 2822 3.302964 CGAGCTTCTTCACGATCTTCTTG 59.697 47.826 0.00 0.00 0.00 3.02
2821 2843 3.121030 CTCAACTTGCTCCCGCCG 61.121 66.667 0.00 0.00 34.43 6.46
2867 2889 1.635663 GCCGGACACAATCAAGGTCG 61.636 60.000 5.05 0.00 32.39 4.79
2905 2929 0.598680 GCTAGCTACCCATGCAGACG 60.599 60.000 7.70 0.00 0.00 4.18
2923 2947 4.970662 AATATGGAGTGAACATGTGTGC 57.029 40.909 0.00 0.00 0.00 4.57
2928 2952 8.514594 ACTGTAACAAAATATGGAGTGAACATG 58.485 33.333 0.00 0.00 0.00 3.21
2965 2989 5.651530 TCGAATTACACTGGAGAGATTCAC 58.348 41.667 0.00 0.00 0.00 3.18
3015 3039 2.986306 GCATCAGGGTGTGTGCTGC 61.986 63.158 0.00 0.00 33.14 5.25
3020 3044 2.436109 GTGGGCATCAGGGTGTGT 59.564 61.111 0.00 0.00 0.00 3.72
3042 3066 0.174617 GTACAGAGGAGAGTGCCAGC 59.825 60.000 0.00 0.00 0.00 4.85
3109 3133 0.890542 TGGACACACTCCTGCATTGC 60.891 55.000 0.46 0.46 40.26 3.56
3122 3146 3.041874 CTCATCGCTGAGTGGACAC 57.958 57.895 8.12 0.00 43.35 3.67
3166 3190 2.821546 TCGACCGATTTGCCATTCTAG 58.178 47.619 0.00 0.00 0.00 2.43
3189 3214 0.668535 TACCATGAGATGCCGACTCG 59.331 55.000 0.00 0.00 37.22 4.18
3195 3220 1.073897 GGCCCTACCATGAGATGCC 59.926 63.158 0.00 0.00 38.86 4.40
3197 3222 1.302033 GCGGCCCTACCATGAGATG 60.302 63.158 0.00 0.00 39.03 2.90
3222 3247 5.957842 ACTGAAAAAGGCGACATCATAAA 57.042 34.783 0.00 0.00 0.00 1.40
3230 3255 2.490991 AGTGGTACTGAAAAAGGCGAC 58.509 47.619 0.00 0.00 0.00 5.19
3233 3258 3.188667 GTGCTAGTGGTACTGAAAAAGGC 59.811 47.826 0.00 0.00 0.00 4.35
3370 3399 3.985019 TCGGTTGCAATAAGTAGGGAA 57.015 42.857 0.59 0.00 0.00 3.97
3374 3403 2.030457 CGGCTTCGGTTGCAATAAGTAG 59.970 50.000 0.59 1.95 0.00 2.57
3376 3405 0.802494 CGGCTTCGGTTGCAATAAGT 59.198 50.000 0.59 0.00 0.00 2.24
3377 3406 0.802494 ACGGCTTCGGTTGCAATAAG 59.198 50.000 0.59 8.49 38.38 1.73
3378 3407 0.519519 CACGGCTTCGGTTGCAATAA 59.480 50.000 0.59 0.00 38.38 1.40
3379 3408 1.302383 CCACGGCTTCGGTTGCAATA 61.302 55.000 0.59 0.00 38.38 1.90
3392 3445 0.036952 ATCGATCCATCATCCACGGC 60.037 55.000 0.00 0.00 0.00 5.68
3401 3454 1.638133 CAGATGCCGATCGATCCATC 58.362 55.000 25.30 25.30 35.49 3.51
3469 3522 4.124943 ATGCTGCAGCCAGAGGGG 62.125 66.667 34.64 0.00 41.77 4.79
3470 3523 2.829003 CATGCTGCAGCCAGAGGG 60.829 66.667 34.64 14.15 41.77 4.30
3471 3524 3.518998 GCATGCTGCAGCCAGAGG 61.519 66.667 34.64 19.68 44.26 3.69
3488 3541 2.167900 TCCATGATCAGAGACACAGCTG 59.832 50.000 13.48 13.48 0.00 4.24
3492 3545 1.833630 GGGTCCATGATCAGAGACACA 59.166 52.381 22.53 0.00 32.77 3.72
3500 3553 1.221566 CTGCACGGGTCCATGATCA 59.778 57.895 0.00 0.00 0.00 2.92
3524 3577 4.223923 CCTCCTTTGACCAGAGTACATCTT 59.776 45.833 0.00 0.00 35.47 2.40
3525 3578 3.772025 CCTCCTTTGACCAGAGTACATCT 59.228 47.826 0.00 0.00 39.56 2.90
3552 3605 6.877855 CAGTATATTCAGGCACATAATCTGCT 59.122 38.462 0.00 0.00 34.84 4.24
3554 3607 9.710900 TTACAGTATATTCAGGCACATAATCTG 57.289 33.333 0.00 0.00 0.00 2.90
3563 3616 6.173427 TCAGCATTACAGTATATTCAGGCA 57.827 37.500 0.00 0.00 0.00 4.75
3570 3623 7.822161 TTGGCAATTCAGCATTACAGTATAT 57.178 32.000 0.00 0.00 35.83 0.86
3571 3624 7.255555 CCATTGGCAATTCAGCATTACAGTATA 60.256 37.037 10.65 0.00 35.83 1.47
3572 3625 6.461927 CCATTGGCAATTCAGCATTACAGTAT 60.462 38.462 10.65 0.00 35.83 2.12
3574 3627 4.382254 CCATTGGCAATTCAGCATTACAGT 60.382 41.667 10.65 0.00 35.83 3.55
3576 3629 3.768215 TCCATTGGCAATTCAGCATTACA 59.232 39.130 10.65 0.00 35.83 2.41
3577 3630 4.389890 TCCATTGGCAATTCAGCATTAC 57.610 40.909 10.65 0.00 35.83 1.89
3578 3631 4.406326 ACATCCATTGGCAATTCAGCATTA 59.594 37.500 10.65 0.00 35.83 1.90
3579 3632 3.199071 ACATCCATTGGCAATTCAGCATT 59.801 39.130 10.65 0.00 35.83 3.56
3581 3634 2.181125 ACATCCATTGGCAATTCAGCA 58.819 42.857 10.65 0.00 35.83 4.41
3582 3635 2.973694 ACATCCATTGGCAATTCAGC 57.026 45.000 10.65 0.00 0.00 4.26
3583 3636 5.808540 CACTAAACATCCATTGGCAATTCAG 59.191 40.000 10.65 2.64 0.00 3.02
3585 3638 4.567959 GCACTAAACATCCATTGGCAATTC 59.432 41.667 10.65 0.00 0.00 2.17
3586 3639 4.223477 AGCACTAAACATCCATTGGCAATT 59.777 37.500 10.65 0.00 0.00 2.32
3587 3640 3.770933 AGCACTAAACATCCATTGGCAAT 59.229 39.130 6.96 6.96 0.00 3.56
3592 3650 5.649782 AAAGGAGCACTAAACATCCATTG 57.350 39.130 0.00 0.00 34.08 2.82
3593 3651 5.354234 CGTAAAGGAGCACTAAACATCCATT 59.646 40.000 0.00 0.00 34.08 3.16
3633 3695 2.688446 CAGATCCAAGCAGTACGGAGTA 59.312 50.000 0.00 0.00 45.11 2.59
3635 3697 1.478510 ACAGATCCAAGCAGTACGGAG 59.521 52.381 0.00 0.00 30.84 4.63
3636 3698 1.557099 ACAGATCCAAGCAGTACGGA 58.443 50.000 0.00 0.00 0.00 4.69
3637 3699 2.002586 CAACAGATCCAAGCAGTACGG 58.997 52.381 0.00 0.00 0.00 4.02
3638 3700 2.002586 CCAACAGATCCAAGCAGTACG 58.997 52.381 0.00 0.00 0.00 3.67
3639 3701 3.059352 ACCAACAGATCCAAGCAGTAC 57.941 47.619 0.00 0.00 0.00 2.73
3640 3702 4.901197 TTACCAACAGATCCAAGCAGTA 57.099 40.909 0.00 0.00 0.00 2.74
3641 3703 3.788227 TTACCAACAGATCCAAGCAGT 57.212 42.857 0.00 0.00 0.00 4.40
3642 3704 3.820467 TGTTTACCAACAGATCCAAGCAG 59.180 43.478 0.00 0.00 38.03 4.24
3643 3705 3.826524 TGTTTACCAACAGATCCAAGCA 58.173 40.909 0.00 0.00 38.03 3.91
3644 3706 4.846779 TTGTTTACCAACAGATCCAAGC 57.153 40.909 0.00 0.00 43.92 4.01
3655 3717 4.097012 GCGTTTTTCTCGTTGTTTACCAA 58.903 39.130 0.00 0.00 0.00 3.67
3656 3718 3.126514 TGCGTTTTTCTCGTTGTTTACCA 59.873 39.130 0.00 0.00 0.00 3.25
3657 3719 3.682921 TGCGTTTTTCTCGTTGTTTACC 58.317 40.909 0.00 0.00 0.00 2.85
3658 3720 3.177061 GCTGCGTTTTTCTCGTTGTTTAC 59.823 43.478 0.00 0.00 0.00 2.01
3659 3721 3.356145 GCTGCGTTTTTCTCGTTGTTTA 58.644 40.909 0.00 0.00 0.00 2.01
3660 3722 2.182014 GCTGCGTTTTTCTCGTTGTTT 58.818 42.857 0.00 0.00 0.00 2.83
3661 3723 1.822581 GCTGCGTTTTTCTCGTTGTT 58.177 45.000 0.00 0.00 0.00 2.83
3662 3724 0.315869 CGCTGCGTTTTTCTCGTTGT 60.316 50.000 14.93 0.00 0.00 3.32
3663 3725 1.588305 GCGCTGCGTTTTTCTCGTTG 61.588 55.000 24.04 0.00 0.00 4.10
3664 3726 1.368850 GCGCTGCGTTTTTCTCGTT 60.369 52.632 24.04 0.00 0.00 3.85
3665 3727 2.244651 AGCGCTGCGTTTTTCTCGT 61.245 52.632 24.04 0.00 0.00 4.18
3666 3728 1.789739 CAGCGCTGCGTTTTTCTCG 60.790 57.895 26.68 0.26 0.00 4.04
3667 3729 4.121490 CAGCGCTGCGTTTTTCTC 57.879 55.556 26.68 4.63 0.00 2.87
3682 3744 4.680237 TCGCTGGTTCCACCGCAG 62.680 66.667 2.12 0.00 42.58 5.18
3683 3745 4.680237 CTCGCTGGTTCCACCGCA 62.680 66.667 2.12 0.00 42.58 5.69
3700 3762 1.200020 CTGCGATGAAAAGGGAACACC 59.800 52.381 0.00 0.00 40.67 4.16
3701 3763 2.151202 TCTGCGATGAAAAGGGAACAC 58.849 47.619 0.00 0.00 0.00 3.32
3702 3764 2.559698 TCTGCGATGAAAAGGGAACA 57.440 45.000 0.00 0.00 0.00 3.18
3703 3765 3.181496 GGATTCTGCGATGAAAAGGGAAC 60.181 47.826 0.00 0.00 0.00 3.62
3704 3766 3.016736 GGATTCTGCGATGAAAAGGGAA 58.983 45.455 0.00 0.00 0.00 3.97
3705 3767 2.239654 AGGATTCTGCGATGAAAAGGGA 59.760 45.455 0.00 0.00 0.00 4.20
3706 3768 2.357009 CAGGATTCTGCGATGAAAAGGG 59.643 50.000 0.00 0.00 33.86 3.95
3722 3784 3.954258 GCAAATAAAGGTACCAGCAGGAT 59.046 43.478 15.94 0.00 38.69 3.24
3723 3785 3.010138 AGCAAATAAAGGTACCAGCAGGA 59.990 43.478 15.94 0.00 38.69 3.86
3733 3795 5.105554 TGAACAACACACAGCAAATAAAGGT 60.106 36.000 0.00 0.00 0.00 3.50
3735 3797 7.114811 GGTATGAACAACACACAGCAAATAAAG 59.885 37.037 0.00 0.00 0.00 1.85
3736 3798 6.920758 GGTATGAACAACACACAGCAAATAAA 59.079 34.615 0.00 0.00 0.00 1.40
3737 3799 6.264292 AGGTATGAACAACACACAGCAAATAA 59.736 34.615 0.00 0.00 0.00 1.40
3739 3801 4.584325 AGGTATGAACAACACACAGCAAAT 59.416 37.500 0.00 0.00 0.00 2.32
3780 3894 3.877508 GGTTAGTGTGCTTTCAGTCAGTT 59.122 43.478 0.00 0.00 0.00 3.16
3786 3900 9.559958 CAAATAATAAGGTTAGTGTGCTTTCAG 57.440 33.333 0.00 0.00 0.00 3.02
3787 3901 8.026607 GCAAATAATAAGGTTAGTGTGCTTTCA 58.973 33.333 0.00 0.00 0.00 2.69
3788 3902 8.244113 AGCAAATAATAAGGTTAGTGTGCTTTC 58.756 33.333 0.00 0.00 0.00 2.62
3789 3903 8.122472 AGCAAATAATAAGGTTAGTGTGCTTT 57.878 30.769 0.00 0.00 0.00 3.51
3835 3949 3.155167 GTAGGGGGACAGAGGCCG 61.155 72.222 0.00 0.00 0.00 6.13
3838 3952 1.132500 GGATTGTAGGGGGACAGAGG 58.868 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.