Multiple sequence alignment - TraesCS2D01G451800

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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 TraesCS2D01G451800 chr2D 100.000 3271 0 0 1 3271 561488562 561491832 0.000000e+00 6041.0
1 TraesCS2D01G451800 chr2B 88.076 2063 103 49 790 2824 669937503 669935556 0.000000e+00 2314.0
2 TraesCS2D01G451800 chr2B 93.564 202 10 3 3073 3271 669935401 669935200 6.860000e-77 298.0
3 TraesCS2D01G451800 chr2B 82.677 254 32 11 8 259 669939624 669939381 7.110000e-52 215.0
4 TraesCS2D01G451800 chr2B 81.690 284 19 15 455 710 669939233 669938955 4.280000e-49 206.0
5 TraesCS2D01G451800 chr2A 92.977 1609 69 19 849 2440 701229981 701231562 0.000000e+00 2305.0
6 TraesCS2D01G451800 chr2A 88.026 309 25 9 423 727 701186491 701186791 4.010000e-94 355.0
7 TraesCS2D01G451800 chr2A 93.427 213 14 0 2700 2912 701232055 701232267 1.890000e-82 316.0
8 TraesCS2D01G451800 chr2A 91.705 217 15 3 3058 3271 701232397 701232613 6.860000e-77 298.0
9 TraesCS2D01G451800 chr2A 87.283 173 12 6 9 177 701186179 701186345 4.310000e-44 189.0
10 TraesCS2D01G451800 chr2A 89.091 55 3 3 267 319 701186375 701186428 7.580000e-07 65.8


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 TraesCS2D01G451800 chr2D 561488562 561491832 3270 False 6041.000000 6041 100.000000 1 3271 1 chr2D.!!$F1 3270
1 TraesCS2D01G451800 chr2B 669935200 669939624 4424 True 758.250000 2314 86.501750 8 3271 4 chr2B.!!$R1 3263
2 TraesCS2D01G451800 chr2A 701229981 701232613 2632 False 973.000000 2305 92.703000 849 3271 3 chr2A.!!$F2 2422
3 TraesCS2D01G451800 chr2A 701186179 701186791 612 False 203.266667 355 88.133333 9 727 3 chr2A.!!$F1 718

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
413 435 0.034896 ATGACACGGCCGAGAAAACT 59.965 50.0 35.9 7.37 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 3831 0.097674 GACCACGCTGCTGCTAAATG 59.902 55.0 14.03 6.53 36.97 2.32 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
30 31 2.369860 TGACATGTGAAGCAGAAGAGGT 59.630 45.455 1.15 0.00 0.00 3.85
47 48 7.007723 AGAAGAGGTCAGAAGAGAAGAAACTA 58.992 38.462 0.00 0.00 0.00 2.24
56 57 4.428615 AGAGAAGAAACTAGTCGAGCAC 57.571 45.455 0.00 0.00 0.00 4.40
132 136 1.817941 GGCCTCGGGTACGTACGTA 60.818 63.158 23.60 23.60 41.85 3.57
175 186 1.421410 CGTGAGGCCGTGATTACTGC 61.421 60.000 0.00 0.00 36.44 4.40
185 196 1.061570 GATTACTGCGCTGCTGCAC 59.938 57.895 14.80 6.51 40.62 4.57
222 233 4.083862 GGAACTCCGCCTCGCCTT 62.084 66.667 0.00 0.00 0.00 4.35
268 279 4.486503 GCCAGAGCCAGAGCCAGG 62.487 72.222 0.00 0.00 41.25 4.45
269 280 3.795041 CCAGAGCCAGAGCCAGGG 61.795 72.222 0.00 0.00 41.25 4.45
311 322 4.072088 GGGCACGTGAAGCGAACG 62.072 66.667 22.23 7.22 46.32 3.95
324 335 1.794785 CGAACGAGACGCGCTGTTA 60.795 57.895 5.73 0.00 46.04 2.41
325 336 1.332180 CGAACGAGACGCGCTGTTAA 61.332 55.000 5.73 0.00 46.04 2.01
327 338 0.713883 AACGAGACGCGCTGTTAATG 59.286 50.000 5.73 0.00 46.04 1.90
329 340 1.348594 GAGACGCGCTGTTAATGCC 59.651 57.895 5.73 0.00 0.00 4.40
330 341 1.079127 AGACGCGCTGTTAATGCCT 60.079 52.632 5.73 0.00 0.00 4.75
333 351 1.815421 CGCGCTGTTAATGCCTCCT 60.815 57.895 5.56 0.00 0.00 3.69
345 367 1.445582 GCCTCCTGGTCAACGTACG 60.446 63.158 15.01 15.01 35.27 3.67
346 368 1.962144 CCTCCTGGTCAACGTACGT 59.038 57.895 16.72 16.72 0.00 3.57
347 369 0.388134 CCTCCTGGTCAACGTACGTG 60.388 60.000 23.57 15.75 0.00 4.49
348 370 0.388134 CTCCTGGTCAACGTACGTGG 60.388 60.000 23.57 20.15 0.00 4.94
349 371 1.108727 TCCTGGTCAACGTACGTGGT 61.109 55.000 23.57 3.80 0.00 4.16
350 372 0.597568 CCTGGTCAACGTACGTGGTA 59.402 55.000 23.57 7.61 0.00 3.25
351 373 1.000385 CCTGGTCAACGTACGTGGTAA 60.000 52.381 23.57 8.05 0.00 2.85
352 374 2.053627 CTGGTCAACGTACGTGGTAAC 58.946 52.381 23.57 13.66 0.00 2.50
353 375 1.680735 TGGTCAACGTACGTGGTAACT 59.319 47.619 23.57 1.15 37.61 2.24
354 376 2.053627 GGTCAACGTACGTGGTAACTG 58.946 52.381 23.57 15.17 37.61 3.16
355 377 2.287547 GGTCAACGTACGTGGTAACTGA 60.288 50.000 23.57 17.34 37.61 3.41
356 378 2.721090 GTCAACGTACGTGGTAACTGAC 59.279 50.000 24.51 24.51 37.61 3.51
357 379 2.618241 TCAACGTACGTGGTAACTGACT 59.382 45.455 23.57 0.00 37.61 3.41
358 380 3.812609 TCAACGTACGTGGTAACTGACTA 59.187 43.478 23.57 0.00 37.61 2.59
359 381 4.083855 TCAACGTACGTGGTAACTGACTAG 60.084 45.833 23.57 0.00 37.61 2.57
360 382 3.403038 ACGTACGTGGTAACTGACTAGT 58.597 45.455 22.14 0.00 39.32 2.57
361 383 4.566004 ACGTACGTGGTAACTGACTAGTA 58.434 43.478 22.14 0.00 35.69 1.82
375 397 3.212685 GACTAGTAGTAGCACCGGTGAT 58.787 50.000 38.30 34.37 0.00 3.06
380 402 3.006133 TAGCACCGGTGATGGGCA 61.006 61.111 38.30 14.53 0.00 5.36
381 403 3.323758 TAGCACCGGTGATGGGCAC 62.324 63.158 38.30 18.00 46.98 5.01
393 415 2.109181 GGGCACCGCTATGAGTCC 59.891 66.667 0.00 0.00 40.86 3.85
394 416 2.731571 GGGCACCGCTATGAGTCCA 61.732 63.158 0.00 0.00 40.86 4.02
395 417 1.447643 GGCACCGCTATGAGTCCAT 59.552 57.895 0.00 0.00 36.81 3.41
397 419 0.104855 GCACCGCTATGAGTCCATGA 59.895 55.000 0.00 0.00 34.31 3.07
398 420 1.858091 CACCGCTATGAGTCCATGAC 58.142 55.000 0.00 0.00 34.31 3.06
399 421 1.136891 CACCGCTATGAGTCCATGACA 59.863 52.381 0.00 0.00 34.60 3.58
400 422 1.137086 ACCGCTATGAGTCCATGACAC 59.863 52.381 0.00 0.00 34.60 3.67
401 423 1.481240 CGCTATGAGTCCATGACACG 58.519 55.000 0.00 0.00 34.60 4.49
402 424 1.858091 GCTATGAGTCCATGACACGG 58.142 55.000 0.00 0.00 34.60 4.94
403 425 1.858091 CTATGAGTCCATGACACGGC 58.142 55.000 0.00 0.00 34.60 5.68
404 426 0.464036 TATGAGTCCATGACACGGCC 59.536 55.000 0.00 0.00 34.60 6.13
405 427 2.509336 GAGTCCATGACACGGCCG 60.509 66.667 26.86 26.86 34.60 6.13
406 428 2.994995 AGTCCATGACACGGCCGA 60.995 61.111 35.90 10.13 34.60 5.54
407 429 2.509336 GTCCATGACACGGCCGAG 60.509 66.667 35.90 28.39 32.09 4.63
408 430 2.678580 TCCATGACACGGCCGAGA 60.679 61.111 35.90 9.72 0.00 4.04
409 431 2.264480 CCATGACACGGCCGAGAA 59.736 61.111 35.90 18.45 0.00 2.87
410 432 1.375396 CCATGACACGGCCGAGAAA 60.375 57.895 35.90 18.06 0.00 2.52
411 433 0.953471 CCATGACACGGCCGAGAAAA 60.953 55.000 35.90 15.35 0.00 2.29
412 434 0.165944 CATGACACGGCCGAGAAAAC 59.834 55.000 35.90 17.70 0.00 2.43
413 435 0.034896 ATGACACGGCCGAGAAAACT 59.965 50.000 35.90 7.37 0.00 2.66
414 436 0.878523 TGACACGGCCGAGAAAACTG 60.879 55.000 35.90 20.43 0.00 3.16
415 437 1.566018 GACACGGCCGAGAAAACTGG 61.566 60.000 35.90 11.14 0.00 4.00
416 438 1.597027 CACGGCCGAGAAAACTGGT 60.597 57.895 35.90 0.68 0.00 4.00
420 442 1.874739 CGGCCGAGAAAACTGGTTGTA 60.875 52.381 24.07 0.00 0.00 2.41
424 446 3.555586 GCCGAGAAAACTGGTTGTAGGTA 60.556 47.826 0.00 0.00 0.00 3.08
567 589 2.026522 CGCTCCGGAAGAGAGTAGG 58.973 63.158 5.23 0.00 46.50 3.18
575 597 4.040706 TCCGGAAGAGAGTAGGAGTATCTC 59.959 50.000 0.00 0.00 39.83 2.75
594 633 8.042515 AGTATCTCCGTTATCCATACTACTCTC 58.957 40.741 0.00 0.00 30.15 3.20
658 706 0.179094 TCACGAGGCTGTCAAACGTT 60.179 50.000 0.00 0.00 35.05 3.99
661 709 0.878523 CGAGGCTGTCAAACGTTCCA 60.879 55.000 0.00 0.00 0.00 3.53
727 777 5.887035 ACCGCTAGATATCCCAAGTACTATC 59.113 44.000 0.00 0.00 0.00 2.08
728 778 5.886474 CCGCTAGATATCCCAAGTACTATCA 59.114 44.000 0.00 0.00 0.00 2.15
729 779 6.183360 CCGCTAGATATCCCAAGTACTATCAC 60.183 46.154 0.00 0.00 0.00 3.06
730 780 6.374613 CGCTAGATATCCCAAGTACTATCACA 59.625 42.308 0.00 0.00 0.00 3.58
731 781 7.414651 CGCTAGATATCCCAAGTACTATCACAG 60.415 44.444 0.00 0.00 0.00 3.66
732 782 7.394923 GCTAGATATCCCAAGTACTATCACAGT 59.605 40.741 0.00 0.00 41.62 3.55
733 783 9.961264 CTAGATATCCCAAGTACTATCACAGTA 57.039 37.037 0.00 0.00 38.80 2.74
746 796 7.883391 ACTATCACAGTACTGTATGTAGCTT 57.117 36.000 27.48 11.77 42.83 3.74
747 797 7.932335 ACTATCACAGTACTGTATGTAGCTTC 58.068 38.462 27.48 0.00 42.83 3.86
748 798 6.775594 ATCACAGTACTGTATGTAGCTTCA 57.224 37.500 27.48 0.00 42.83 3.02
749 799 6.196079 TCACAGTACTGTATGTAGCTTCAG 57.804 41.667 27.48 11.17 42.83 3.02
751 801 5.802451 CACAGTACTGTATGTAGCTTCAGTG 59.198 44.000 27.48 7.05 42.83 3.66
752 802 5.477291 ACAGTACTGTATGTAGCTTCAGTGT 59.523 40.000 26.91 0.00 42.90 3.55
755 805 7.698550 CAGTACTGTATGTAGCTTCAGTGTTAG 59.301 40.741 15.06 5.45 40.61 2.34
756 806 6.591750 ACTGTATGTAGCTTCAGTGTTAGT 57.408 37.500 0.00 0.00 39.27 2.24
757 807 7.698506 ACTGTATGTAGCTTCAGTGTTAGTA 57.301 36.000 0.00 0.00 39.27 1.82
758 808 7.763356 ACTGTATGTAGCTTCAGTGTTAGTAG 58.237 38.462 0.00 0.00 39.27 2.57
759 809 7.393796 ACTGTATGTAGCTTCAGTGTTAGTAGT 59.606 37.037 0.00 0.00 39.27 2.73
760 810 8.797350 TGTATGTAGCTTCAGTGTTAGTAGTA 57.203 34.615 0.00 0.00 0.00 1.82
761 811 9.234827 TGTATGTAGCTTCAGTGTTAGTAGTAA 57.765 33.333 0.00 0.00 0.00 2.24
764 814 9.991906 ATGTAGCTTCAGTGTTAGTAGTAAAAA 57.008 29.630 0.00 0.00 0.00 1.94
786 2208 8.541133 AAAAAGAGAGTATGTAGCTCAAAGAC 57.459 34.615 0.00 0.00 35.55 3.01
788 2210 6.449635 AGAGAGTATGTAGCTCAAAGACTG 57.550 41.667 0.00 0.00 35.55 3.51
792 2214 6.435904 AGAGTATGTAGCTCAAAGACTGTTCT 59.564 38.462 0.00 0.00 35.55 3.01
800 2222 5.240403 AGCTCAAAGACTGTTCTGGAAAATC 59.760 40.000 0.00 0.00 29.98 2.17
803 2225 7.403312 TCAAAGACTGTTCTGGAAAATCAAA 57.597 32.000 0.00 0.00 29.98 2.69
809 2231 3.321682 TGTTCTGGAAAATCAAAGCCCTG 59.678 43.478 0.00 0.00 0.00 4.45
813 2235 2.825532 TGGAAAATCAAAGCCCTGCTAC 59.174 45.455 0.00 0.00 38.25 3.58
818 2244 1.352083 TCAAAGCCCTGCTACTGACT 58.648 50.000 0.00 0.00 38.25 3.41
822 2248 1.118838 AGCCCTGCTACTGACTGATC 58.881 55.000 0.00 0.00 36.99 2.92
837 2263 0.320683 TGATCACGCCAAGACAGTGG 60.321 55.000 0.00 0.00 42.05 4.00
838 2264 0.320771 GATCACGCCAAGACAGTGGT 60.321 55.000 0.00 0.00 41.12 4.16
839 2265 0.973632 ATCACGCCAAGACAGTGGTA 59.026 50.000 0.00 0.00 41.12 3.25
859 2285 3.754188 AGTAGCTCGGTTACGTTACTG 57.246 47.619 7.20 7.20 41.85 2.74
870 2296 4.142687 GGTTACGTTACTGTAGCGGTAGAA 60.143 45.833 24.20 12.01 36.68 2.10
871 2297 5.390613 GTTACGTTACTGTAGCGGTAGAAA 58.609 41.667 24.20 10.16 36.68 2.52
872 2298 4.088823 ACGTTACTGTAGCGGTAGAAAG 57.911 45.455 24.20 0.00 36.68 2.62
873 2299 3.753272 ACGTTACTGTAGCGGTAGAAAGA 59.247 43.478 24.20 0.00 36.68 2.52
905 2331 3.258622 GTGGAGTCCAAAGCACTACTACT 59.741 47.826 15.09 0.00 34.18 2.57
906 2332 4.461781 GTGGAGTCCAAAGCACTACTACTA 59.538 45.833 15.09 0.00 34.18 1.82
907 2333 4.461781 TGGAGTCCAAAGCACTACTACTAC 59.538 45.833 10.20 0.00 0.00 2.73
908 2334 4.461781 GGAGTCCAAAGCACTACTACTACA 59.538 45.833 3.60 0.00 0.00 2.74
910 2336 5.078256 AGTCCAAAGCACTACTACTACAGT 58.922 41.667 0.00 0.00 41.62 3.55
912 2338 4.219944 TCCAAAGCACTACTACTACAGTGG 59.780 45.833 4.10 0.00 42.00 4.00
913 2339 4.219944 CCAAAGCACTACTACTACAGTGGA 59.780 45.833 0.00 0.00 42.00 4.02
914 2340 5.403246 CAAAGCACTACTACTACAGTGGAG 58.597 45.833 0.00 0.00 42.00 3.86
915 2341 3.622630 AGCACTACTACTACAGTGGAGG 58.377 50.000 7.43 0.00 42.00 4.30
916 2342 3.266254 AGCACTACTACTACAGTGGAGGA 59.734 47.826 7.43 0.00 42.00 3.71
917 2343 3.628487 GCACTACTACTACAGTGGAGGAG 59.372 52.174 13.64 13.64 42.00 3.69
918 2344 3.628487 CACTACTACTACAGTGGAGGAGC 59.372 52.174 15.23 0.00 37.96 4.70
1027 2454 5.970317 AAAACCCAACTAAATTACTCCCG 57.030 39.130 0.00 0.00 0.00 5.14
1043 2470 2.491621 CGCAGACGCATCTCTCCA 59.508 61.111 0.00 0.00 38.40 3.86
1056 2483 3.396260 TCTCTCCACCCTAAACAAACG 57.604 47.619 0.00 0.00 0.00 3.60
1059 2486 3.735591 TCTCCACCCTAAACAAACGAAG 58.264 45.455 0.00 0.00 0.00 3.79
1072 2499 3.868661 ACAAACGAAGCCATTTGAAAACC 59.131 39.130 3.85 0.00 38.82 3.27
1205 2637 1.530419 AGGGACGGCAATGCACAAA 60.530 52.632 7.79 0.00 0.00 2.83
1657 3098 2.892425 CACGGATCTTGGCTCGCC 60.892 66.667 0.00 0.00 0.00 5.54
1788 3232 4.208686 GCGGTGCTCCTACGAGGG 62.209 72.222 2.85 0.00 35.59 4.30
1798 3242 2.361992 TACGAGGGCAGCGAGGAA 60.362 61.111 5.25 0.00 0.00 3.36
2128 3578 0.397254 ATCGTCCGTCCCAGATTCCT 60.397 55.000 0.00 0.00 0.00 3.36
2129 3579 1.035932 TCGTCCGTCCCAGATTCCTC 61.036 60.000 0.00 0.00 0.00 3.71
2130 3580 1.320344 CGTCCGTCCCAGATTCCTCA 61.320 60.000 0.00 0.00 0.00 3.86
2131 3581 0.461961 GTCCGTCCCAGATTCCTCAG 59.538 60.000 0.00 0.00 0.00 3.35
2299 3751 5.414360 AGCTTCATGTGTCTGTGTATACTG 58.586 41.667 4.17 0.00 0.00 2.74
2300 3752 5.185828 AGCTTCATGTGTCTGTGTATACTGA 59.814 40.000 4.17 0.00 33.09 3.41
2301 3753 5.518128 GCTTCATGTGTCTGTGTATACTGAG 59.482 44.000 4.17 0.18 35.75 3.35
2302 3754 6.590234 TTCATGTGTCTGTGTATACTGAGT 57.410 37.500 4.17 0.00 35.75 3.41
2371 3831 6.201226 TGAGATTCTGCGATGGATCTATAC 57.799 41.667 0.00 0.00 0.00 1.47
2376 3836 8.753133 AGATTCTGCGATGGATCTATACATTTA 58.247 33.333 0.00 0.00 29.60 1.40
2377 3837 8.939201 ATTCTGCGATGGATCTATACATTTAG 57.061 34.615 0.00 0.00 29.60 1.85
2378 3838 6.333416 TCTGCGATGGATCTATACATTTAGC 58.667 40.000 0.00 0.00 29.60 3.09
2514 4285 1.345741 CATGAGCCGTCCATGGTCTAT 59.654 52.381 12.58 0.00 38.12 1.98
2530 4301 3.118738 GGTCTATGGAGTTGTTGATCGGT 60.119 47.826 0.00 0.00 0.00 4.69
2531 4302 4.098960 GGTCTATGGAGTTGTTGATCGGTA 59.901 45.833 0.00 0.00 0.00 4.02
2532 4303 5.282510 GTCTATGGAGTTGTTGATCGGTAG 58.717 45.833 0.00 0.00 0.00 3.18
2533 4304 5.067413 GTCTATGGAGTTGTTGATCGGTAGA 59.933 44.000 0.00 0.00 0.00 2.59
2534 4305 5.833667 TCTATGGAGTTGTTGATCGGTAGAT 59.166 40.000 0.00 0.00 40.38 1.98
2535 4306 4.123497 TGGAGTTGTTGATCGGTAGATG 57.877 45.455 0.00 0.00 37.19 2.90
2536 4307 3.513912 TGGAGTTGTTGATCGGTAGATGT 59.486 43.478 0.00 0.00 37.19 3.06
2542 4313 3.889538 TGTTGATCGGTAGATGTAGAGGG 59.110 47.826 0.00 0.00 37.19 4.30
2550 4321 3.385111 GGTAGATGTAGAGGGGTCTGTTG 59.615 52.174 0.00 0.00 0.00 3.33
2551 4322 2.472029 AGATGTAGAGGGGTCTGTTGG 58.528 52.381 0.00 0.00 0.00 3.77
2552 4323 2.044492 AGATGTAGAGGGGTCTGTTGGA 59.956 50.000 0.00 0.00 0.00 3.53
2553 4324 2.409064 TGTAGAGGGGTCTGTTGGAA 57.591 50.000 0.00 0.00 0.00 3.53
2554 4325 2.915869 TGTAGAGGGGTCTGTTGGAAT 58.084 47.619 0.00 0.00 0.00 3.01
2555 4326 2.571653 TGTAGAGGGGTCTGTTGGAATG 59.428 50.000 0.00 0.00 0.00 2.67
2556 4327 0.995024 AGAGGGGTCTGTTGGAATGG 59.005 55.000 0.00 0.00 0.00 3.16
2557 4328 0.991920 GAGGGGTCTGTTGGAATGGA 59.008 55.000 0.00 0.00 0.00 3.41
2558 4329 1.566231 GAGGGGTCTGTTGGAATGGAT 59.434 52.381 0.00 0.00 0.00 3.41
2559 4330 1.285962 AGGGGTCTGTTGGAATGGATG 59.714 52.381 0.00 0.00 0.00 3.51
2560 4331 1.686115 GGGGTCTGTTGGAATGGATGG 60.686 57.143 0.00 0.00 0.00 3.51
2561 4332 1.284785 GGGTCTGTTGGAATGGATGGA 59.715 52.381 0.00 0.00 0.00 3.41
2562 4333 2.091665 GGGTCTGTTGGAATGGATGGAT 60.092 50.000 0.00 0.00 0.00 3.41
2563 4334 3.217626 GGTCTGTTGGAATGGATGGATC 58.782 50.000 0.00 0.00 0.00 3.36
2564 4335 3.371917 GGTCTGTTGGAATGGATGGATCA 60.372 47.826 0.00 0.00 0.00 2.92
2565 4336 3.881688 GTCTGTTGGAATGGATGGATCAG 59.118 47.826 0.00 0.00 0.00 2.90
2596 4367 5.219633 GTGACGGAAATTTGTTACTGCAAT 58.780 37.500 0.00 0.00 0.00 3.56
2597 4368 5.342259 GTGACGGAAATTTGTTACTGCAATC 59.658 40.000 0.00 0.00 0.00 2.67
2598 4369 4.472286 ACGGAAATTTGTTACTGCAATCG 58.528 39.130 0.00 0.00 0.00 3.34
2605 4376 1.795872 TGTTACTGCAATCGTCGTTGG 59.204 47.619 8.81 0.00 0.00 3.77
2639 4410 3.688272 GATGTTTCCATCAGTGCGATTG 58.312 45.455 0.00 0.00 45.68 2.67
2650 4421 0.949105 GTGCGATTGTGTCTTCCGGT 60.949 55.000 0.00 0.00 0.00 5.28
2657 4428 4.976731 CGATTGTGTCTTCCGGTTAGATAG 59.023 45.833 0.00 0.00 0.00 2.08
2675 4446 1.468985 AGTCCTCAGTCCTCACGATG 58.531 55.000 0.00 0.00 0.00 3.84
2677 4448 1.133407 GTCCTCAGTCCTCACGATGAC 59.867 57.143 0.00 0.00 0.00 3.06
2678 4449 1.177401 CCTCAGTCCTCACGATGACA 58.823 55.000 5.45 0.00 33.89 3.58
2679 4450 1.546029 CCTCAGTCCTCACGATGACAA 59.454 52.381 5.45 0.00 33.89 3.18
2680 4451 2.167281 CCTCAGTCCTCACGATGACAAT 59.833 50.000 5.45 0.00 33.89 2.71
2682 4453 4.038522 CCTCAGTCCTCACGATGACAATAT 59.961 45.833 5.45 0.00 33.89 1.28
2694 4465 2.291465 ATGACAATATCATGGCACACGC 59.709 45.455 0.00 0.00 46.85 5.34
2695 4466 3.995388 ATGACAATATCATGGCACACGCT 60.995 43.478 0.00 0.00 46.85 5.07
2696 4467 4.743348 ATGACAATATCATGGCACACGCTA 60.743 41.667 0.00 0.00 46.85 4.26
2697 4468 6.536091 ATGACAATATCATGGCACACGCTAG 61.536 44.000 0.00 0.00 46.85 3.42
2698 4469 8.632295 ATGACAATATCATGGCACACGCTAGA 62.632 42.308 0.00 0.00 46.85 2.43
2740 4511 3.354131 AAGCTTCCGATCGCTTCTC 57.646 52.632 10.32 0.00 42.39 2.87
2756 4527 4.610456 CGCTTCTCGAACAAATTAGCACAA 60.610 41.667 0.00 0.00 41.67 3.33
2774 4545 1.065401 CAACACAGGTTGCGTGACATT 59.935 47.619 0.00 0.00 46.98 2.71
2803 4574 1.668419 AGCTTCTGACTTGTGCGTTT 58.332 45.000 0.00 0.00 0.00 3.60
2821 4597 0.534203 TTCTTCCACAAGGTCGGTGC 60.534 55.000 0.00 0.00 34.94 5.01
2822 4598 1.227823 CTTCCACAAGGTCGGTGCA 60.228 57.895 0.00 0.00 34.94 4.57
2823 4599 1.227823 TTCCACAAGGTCGGTGCAG 60.228 57.895 0.00 0.00 34.94 4.41
2824 4600 1.978455 TTCCACAAGGTCGGTGCAGT 61.978 55.000 0.00 0.00 34.94 4.40
2825 4601 2.253758 CCACAAGGTCGGTGCAGTG 61.254 63.158 0.00 0.00 34.94 3.66
2838 4614 2.740055 CAGTGCAGAGACGGTGCC 60.740 66.667 0.00 0.00 40.43 5.01
2916 4692 4.992511 CGGGTGCGTTTCGGGGAA 62.993 66.667 0.00 0.00 0.00 3.97
3014 4816 0.738975 TCCGATCTACTGTTCCGCTG 59.261 55.000 0.00 0.00 0.00 5.18
3015 4817 0.456221 CCGATCTACTGTTCCGCTGT 59.544 55.000 0.00 0.00 0.00 4.40
3017 4819 1.402259 CGATCTACTGTTCCGCTGTCT 59.598 52.381 0.00 0.00 0.00 3.41
3018 4820 2.539953 CGATCTACTGTTCCGCTGTCTC 60.540 54.545 0.00 0.00 0.00 3.36
3019 4821 1.905637 TCTACTGTTCCGCTGTCTCA 58.094 50.000 0.00 0.00 0.00 3.27
3020 4822 1.813178 TCTACTGTTCCGCTGTCTCAG 59.187 52.381 0.00 0.00 34.12 3.35
3021 4823 1.813178 CTACTGTTCCGCTGTCTCAGA 59.187 52.381 0.66 0.00 32.44 3.27
3022 4824 0.315568 ACTGTTCCGCTGTCTCAGAC 59.684 55.000 0.00 0.00 32.44 3.51
3023 4825 0.315251 CTGTTCCGCTGTCTCAGACA 59.685 55.000 7.44 7.44 40.50 3.41
3024 4826 0.750249 TGTTCCGCTGTCTCAGACAA 59.250 50.000 9.30 0.00 42.26 3.18
3025 4827 1.140816 GTTCCGCTGTCTCAGACAAC 58.859 55.000 9.30 3.18 42.26 3.32
3026 4828 0.750249 TTCCGCTGTCTCAGACAACA 59.250 50.000 9.30 0.00 42.26 3.33
3027 4829 0.750249 TCCGCTGTCTCAGACAACAA 59.250 50.000 9.30 0.00 42.26 2.83
3028 4830 1.138069 TCCGCTGTCTCAGACAACAAA 59.862 47.619 9.30 0.00 42.26 2.83
3029 4831 1.261619 CCGCTGTCTCAGACAACAAAC 59.738 52.381 9.30 0.00 42.26 2.93
3030 4832 1.933181 CGCTGTCTCAGACAACAAACA 59.067 47.619 9.30 0.00 42.26 2.83
3031 4833 2.545526 CGCTGTCTCAGACAACAAACAT 59.454 45.455 9.30 0.00 42.26 2.71
3032 4834 3.002656 CGCTGTCTCAGACAACAAACATT 59.997 43.478 9.30 0.00 42.26 2.71
3033 4835 4.211164 CGCTGTCTCAGACAACAAACATTA 59.789 41.667 9.30 0.00 42.26 1.90
3034 4836 5.444122 GCTGTCTCAGACAACAAACATTAC 58.556 41.667 9.30 0.00 42.26 1.89
3035 4837 5.237344 GCTGTCTCAGACAACAAACATTACT 59.763 40.000 9.30 0.00 42.26 2.24
3036 4838 6.238484 GCTGTCTCAGACAACAAACATTACTT 60.238 38.462 9.30 0.00 42.26 2.24
3037 4839 7.624360 TGTCTCAGACAACAAACATTACTTT 57.376 32.000 4.55 0.00 39.78 2.66
3038 4840 8.050778 TGTCTCAGACAACAAACATTACTTTT 57.949 30.769 4.55 0.00 39.78 2.27
3039 4841 9.168451 TGTCTCAGACAACAAACATTACTTTTA 57.832 29.630 4.55 0.00 39.78 1.52
3040 4842 9.434559 GTCTCAGACAACAAACATTACTTTTAC 57.565 33.333 0.00 0.00 32.09 2.01
3041 4843 9.168451 TCTCAGACAACAAACATTACTTTTACA 57.832 29.630 0.00 0.00 0.00 2.41
3042 4844 9.950680 CTCAGACAACAAACATTACTTTTACAT 57.049 29.630 0.00 0.00 0.00 2.29
3043 4845 9.944663 TCAGACAACAAACATTACTTTTACATC 57.055 29.630 0.00 0.00 0.00 3.06
3044 4846 8.891928 CAGACAACAAACATTACTTTTACATCG 58.108 33.333 0.00 0.00 0.00 3.84
3045 4847 7.589954 AGACAACAAACATTACTTTTACATCGC 59.410 33.333 0.00 0.00 0.00 4.58
3046 4848 7.197017 ACAACAAACATTACTTTTACATCGCA 58.803 30.769 0.00 0.00 0.00 5.10
3047 4849 7.702772 ACAACAAACATTACTTTTACATCGCAA 59.297 29.630 0.00 0.00 0.00 4.85
3048 4850 8.535592 CAACAAACATTACTTTTACATCGCAAA 58.464 29.630 0.00 0.00 0.00 3.68
3049 4851 8.635877 ACAAACATTACTTTTACATCGCAAAA 57.364 26.923 0.00 0.00 0.00 2.44
3050 4852 9.088512 ACAAACATTACTTTTACATCGCAAAAA 57.911 25.926 0.00 0.00 0.00 1.94
3084 4886 8.839310 TTCTTTTAGGAAATCTCAGACAAGAG 57.161 34.615 0.00 0.00 36.97 2.85
3097 4899 3.249189 AAGAGCTGCGGGGTGGAA 61.249 61.111 0.00 0.00 0.00 3.53
3108 4910 2.243810 CGGGGTGGAATTGGAAAGAAA 58.756 47.619 0.00 0.00 0.00 2.52
3132 4934 3.133691 GCTCGCAATCATTAGTCATGGA 58.866 45.455 0.00 0.00 33.07 3.41
3161 4963 2.955881 GCTAGAACCCACCGGCACT 61.956 63.158 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.692476 TTCACATGTCACCAGGGAGG 59.308 55.000 0.00 0.00 45.67 4.30
1 2 1.947678 GCTTCACATGTCACCAGGGAG 60.948 57.143 0.00 0.00 0.00 4.30
2 3 0.036732 GCTTCACATGTCACCAGGGA 59.963 55.000 0.00 0.00 0.00 4.20
3 4 0.250858 TGCTTCACATGTCACCAGGG 60.251 55.000 0.00 0.00 0.00 4.45
4 5 1.162698 CTGCTTCACATGTCACCAGG 58.837 55.000 0.00 0.00 0.00 4.45
5 6 2.174363 TCTGCTTCACATGTCACCAG 57.826 50.000 0.00 0.64 0.00 4.00
6 7 2.104622 TCTTCTGCTTCACATGTCACCA 59.895 45.455 0.00 0.00 0.00 4.17
30 31 5.106475 GCTCGACTAGTTTCTTCTCTTCTGA 60.106 44.000 0.00 0.00 0.00 3.27
47 48 2.695759 CCTCTGCTCGTGCTCGACT 61.696 63.158 6.80 0.00 41.35 4.18
56 57 2.441901 AGCCTCCTCCTCTGCTCG 60.442 66.667 0.00 0.00 0.00 5.03
63 64 3.531961 AGGACAGAGCCTCCTCCT 58.468 61.111 3.18 3.18 38.96 3.69
108 112 2.521224 GTACCCGAGGCCGAGGAT 60.521 66.667 19.35 6.38 38.22 3.24
132 136 0.099791 CGCAACAAAAGTTCCCACGT 59.900 50.000 0.00 0.00 0.00 4.49
277 288 2.815647 CTCGGGTTCCAGAAGCGC 60.816 66.667 0.00 0.00 39.53 5.92
306 317 1.332180 TTAACAGCGCGTCTCGTTCG 61.332 55.000 8.43 0.00 41.07 3.95
311 322 1.084370 AGGCATTAACAGCGCGTCTC 61.084 55.000 8.43 0.00 0.00 3.36
319 330 2.749621 GTTGACCAGGAGGCATTAACAG 59.250 50.000 0.00 0.00 39.06 3.16
320 331 2.790433 GTTGACCAGGAGGCATTAACA 58.210 47.619 0.00 0.00 39.06 2.41
322 333 1.349688 ACGTTGACCAGGAGGCATTAA 59.650 47.619 0.00 0.00 39.06 1.40
324 335 0.981183 TACGTTGACCAGGAGGCATT 59.019 50.000 0.00 0.00 39.06 3.56
325 336 0.249398 GTACGTTGACCAGGAGGCAT 59.751 55.000 0.00 0.00 39.06 4.40
327 338 1.445582 CGTACGTTGACCAGGAGGC 60.446 63.158 7.22 0.00 39.06 4.70
329 340 0.388134 CCACGTACGTTGACCAGGAG 60.388 60.000 20.23 3.77 0.00 3.69
330 341 1.108727 ACCACGTACGTTGACCAGGA 61.109 55.000 24.47 0.00 0.00 3.86
333 351 1.680735 AGTTACCACGTACGTTGACCA 59.319 47.619 24.47 7.62 0.00 4.02
345 367 5.163673 GGTGCTACTACTAGTCAGTTACCAC 60.164 48.000 0.00 9.08 36.14 4.16
346 368 4.946157 GGTGCTACTACTAGTCAGTTACCA 59.054 45.833 0.00 0.00 36.14 3.25
347 369 4.034975 CGGTGCTACTACTAGTCAGTTACC 59.965 50.000 0.00 9.79 36.14 2.85
348 370 4.034975 CCGGTGCTACTACTAGTCAGTTAC 59.965 50.000 0.00 3.10 36.14 2.50
349 371 4.194640 CCGGTGCTACTACTAGTCAGTTA 58.805 47.826 0.00 0.00 36.14 2.24
350 372 3.015327 CCGGTGCTACTACTAGTCAGTT 58.985 50.000 0.00 0.00 36.14 3.16
351 373 2.026449 ACCGGTGCTACTACTAGTCAGT 60.026 50.000 6.12 4.52 38.91 3.41
352 374 2.355132 CACCGGTGCTACTACTAGTCAG 59.645 54.545 24.02 0.00 0.00 3.51
353 375 2.026915 TCACCGGTGCTACTACTAGTCA 60.027 50.000 30.25 4.54 0.00 3.41
354 376 2.636830 TCACCGGTGCTACTACTAGTC 58.363 52.381 30.25 0.00 0.00 2.59
355 377 2.795231 TCACCGGTGCTACTACTAGT 57.205 50.000 30.25 0.00 0.00 2.57
356 378 2.293677 CCATCACCGGTGCTACTACTAG 59.706 54.545 30.25 6.21 0.00 2.57
357 379 2.304092 CCATCACCGGTGCTACTACTA 58.696 52.381 30.25 10.45 0.00 1.82
358 380 1.112113 CCATCACCGGTGCTACTACT 58.888 55.000 30.25 4.96 0.00 2.57
359 381 0.104304 CCCATCACCGGTGCTACTAC 59.896 60.000 30.25 0.00 0.00 2.73
360 382 1.682451 GCCCATCACCGGTGCTACTA 61.682 60.000 30.25 12.91 0.00 1.82
361 383 3.031417 GCCCATCACCGGTGCTACT 62.031 63.158 30.25 11.14 0.00 2.57
375 397 2.731571 GGACTCATAGCGGTGCCCA 61.732 63.158 0.00 0.00 0.00 5.36
380 402 1.137086 GTGTCATGGACTCATAGCGGT 59.863 52.381 0.00 0.00 33.15 5.68
381 403 1.858091 GTGTCATGGACTCATAGCGG 58.142 55.000 0.00 0.00 33.15 5.52
382 404 1.481240 CGTGTCATGGACTCATAGCG 58.519 55.000 0.00 0.00 33.15 4.26
383 405 1.858091 CCGTGTCATGGACTCATAGC 58.142 55.000 4.96 0.00 33.15 2.97
384 406 1.539065 GGCCGTGTCATGGACTCATAG 60.539 57.143 15.72 0.00 33.15 2.23
385 407 0.464036 GGCCGTGTCATGGACTCATA 59.536 55.000 15.72 0.00 33.15 2.15
386 408 1.221840 GGCCGTGTCATGGACTCAT 59.778 57.895 15.72 0.00 33.15 2.90
389 411 2.994995 TCGGCCGTGTCATGGACT 60.995 61.111 27.15 0.00 33.15 3.85
392 414 0.953471 TTTTCTCGGCCGTGTCATGG 60.953 55.000 27.15 6.73 0.00 3.66
393 415 0.165944 GTTTTCTCGGCCGTGTCATG 59.834 55.000 27.15 9.59 0.00 3.07
394 416 0.034896 AGTTTTCTCGGCCGTGTCAT 59.965 50.000 27.15 6.21 0.00 3.06
395 417 0.878523 CAGTTTTCTCGGCCGTGTCA 60.879 55.000 27.15 11.32 0.00 3.58
397 419 1.597027 CCAGTTTTCTCGGCCGTGT 60.597 57.895 27.15 2.83 0.00 4.49
398 420 1.164041 AACCAGTTTTCTCGGCCGTG 61.164 55.000 27.15 23.87 0.00 4.94
399 421 1.147600 AACCAGTTTTCTCGGCCGT 59.852 52.632 27.15 0.00 0.00 5.68
400 422 1.164041 ACAACCAGTTTTCTCGGCCG 61.164 55.000 22.12 22.12 0.00 6.13
401 423 1.804748 CTACAACCAGTTTTCTCGGCC 59.195 52.381 0.00 0.00 0.00 6.13
402 424 1.804748 CCTACAACCAGTTTTCTCGGC 59.195 52.381 0.00 0.00 0.00 5.54
403 425 3.121738 ACCTACAACCAGTTTTCTCGG 57.878 47.619 0.00 0.00 0.00 4.63
404 426 4.450080 GGTTACCTACAACCAGTTTTCTCG 59.550 45.833 0.00 0.00 46.14 4.04
405 427 5.936686 GGTTACCTACAACCAGTTTTCTC 57.063 43.478 0.00 0.00 46.14 2.87
414 436 0.459063 CGCTCCGGTTACCTACAACC 60.459 60.000 0.00 0.00 43.88 3.77
415 437 0.527565 TCGCTCCGGTTACCTACAAC 59.472 55.000 0.00 0.00 0.00 3.32
416 438 0.813184 CTCGCTCCGGTTACCTACAA 59.187 55.000 0.00 0.00 0.00 2.41
420 442 2.348888 CCACTCGCTCCGGTTACCT 61.349 63.158 0.00 0.00 0.00 3.08
452 474 4.489771 CCCCTGATGCCACCGGAC 62.490 72.222 9.46 0.00 0.00 4.79
453 475 4.731853 TCCCCTGATGCCACCGGA 62.732 66.667 9.46 0.00 0.00 5.14
507 529 1.080839 CATTTTTCGGCCGGGTGTG 60.081 57.895 27.83 14.18 0.00 3.82
515 537 1.616374 TGAACCCCTTCATTTTTCGGC 59.384 47.619 0.00 0.00 31.00 5.54
567 589 8.042515 AGAGTAGTATGGATAACGGAGATACTC 58.957 40.741 0.00 0.00 37.00 2.59
575 597 5.314529 TCCAGAGAGTAGTATGGATAACGG 58.685 45.833 0.00 0.00 36.92 4.44
576 598 6.487331 ACTTCCAGAGAGTAGTATGGATAACG 59.513 42.308 0.00 0.00 41.33 3.18
577 599 7.826918 ACTTCCAGAGAGTAGTATGGATAAC 57.173 40.000 0.00 0.00 41.33 1.89
584 606 8.869109 AGTACGTATACTTCCAGAGAGTAGTAT 58.131 37.037 0.00 0.00 38.59 2.12
585 607 8.243961 AGTACGTATACTTCCAGAGAGTAGTA 57.756 38.462 0.00 0.00 38.59 1.82
616 658 2.196382 GACGCGACACACTCCTGCTA 62.196 60.000 15.93 0.00 0.00 3.49
658 706 0.465460 AAAAGCTGCGTTGGACTGGA 60.465 50.000 0.68 0.00 0.00 3.86
661 709 1.873591 CTGTAAAAGCTGCGTTGGACT 59.126 47.619 0.68 0.00 0.00 3.85
727 777 5.802451 CACTGAAGCTACATACAGTACTGTG 59.198 44.000 33.77 22.22 44.63 3.66
728 778 5.477291 ACACTGAAGCTACATACAGTACTGT 59.523 40.000 30.13 30.13 46.87 3.55
729 779 5.955488 ACACTGAAGCTACATACAGTACTG 58.045 41.667 21.44 21.44 40.84 2.74
730 780 6.591750 AACACTGAAGCTACATACAGTACT 57.408 37.500 0.00 0.00 40.84 2.73
731 781 7.536855 ACTAACACTGAAGCTACATACAGTAC 58.463 38.462 0.00 0.00 40.84 2.73
732 782 7.698506 ACTAACACTGAAGCTACATACAGTA 57.301 36.000 0.00 0.00 40.84 2.74
733 783 6.591750 ACTAACACTGAAGCTACATACAGT 57.408 37.500 0.00 0.00 43.05 3.55
734 784 7.763356 ACTACTAACACTGAAGCTACATACAG 58.237 38.462 0.00 0.00 36.58 2.74
735 785 7.698506 ACTACTAACACTGAAGCTACATACA 57.301 36.000 0.00 0.00 0.00 2.29
738 788 9.991906 TTTTTACTACTAACACTGAAGCTACAT 57.008 29.630 0.00 0.00 0.00 2.29
761 811 8.371699 AGTCTTTGAGCTACATACTCTCTTTTT 58.628 33.333 0.00 0.00 35.12 1.94
762 812 7.816995 CAGTCTTTGAGCTACATACTCTCTTTT 59.183 37.037 0.00 0.00 35.12 2.27
763 813 7.039363 ACAGTCTTTGAGCTACATACTCTCTTT 60.039 37.037 0.00 0.00 35.12 2.52
764 814 6.435904 ACAGTCTTTGAGCTACATACTCTCTT 59.564 38.462 0.00 0.00 35.12 2.85
766 816 6.202516 ACAGTCTTTGAGCTACATACTCTC 57.797 41.667 0.00 0.00 35.12 3.20
768 818 6.529829 CAGAACAGTCTTTGAGCTACATACTC 59.470 42.308 0.00 0.00 30.77 2.59
770 820 5.578727 CCAGAACAGTCTTTGAGCTACATAC 59.421 44.000 0.00 0.00 28.78 2.39
772 822 4.284490 TCCAGAACAGTCTTTGAGCTACAT 59.716 41.667 0.00 0.00 28.78 2.29
774 824 4.258702 TCCAGAACAGTCTTTGAGCTAC 57.741 45.455 0.00 0.00 28.78 3.58
775 825 4.955811 TTCCAGAACAGTCTTTGAGCTA 57.044 40.909 0.00 0.00 28.78 3.32
776 826 3.845781 TTCCAGAACAGTCTTTGAGCT 57.154 42.857 0.00 0.00 28.78 4.09
777 827 4.900635 TTTTCCAGAACAGTCTTTGAGC 57.099 40.909 0.00 0.00 28.78 4.26
779 829 7.403312 TTTGATTTTCCAGAACAGTCTTTGA 57.597 32.000 0.00 0.00 28.78 2.69
784 2206 4.550422 GGCTTTGATTTTCCAGAACAGTC 58.450 43.478 0.00 0.00 0.00 3.51
786 2208 3.575687 AGGGCTTTGATTTTCCAGAACAG 59.424 43.478 0.00 0.00 0.00 3.16
788 2210 3.862264 GCAGGGCTTTGATTTTCCAGAAC 60.862 47.826 0.00 0.00 0.00 3.01
792 2214 2.014010 AGCAGGGCTTTGATTTTCCA 57.986 45.000 0.00 0.00 33.89 3.53
800 2222 1.002430 TCAGTCAGTAGCAGGGCTTTG 59.998 52.381 0.00 0.00 40.44 2.77
803 2225 1.118838 GATCAGTCAGTAGCAGGGCT 58.881 55.000 0.00 0.00 43.41 5.19
809 2231 0.173481 TGGCGTGATCAGTCAGTAGC 59.827 55.000 0.00 0.00 34.36 3.58
813 2235 1.337167 TGTCTTGGCGTGATCAGTCAG 60.337 52.381 0.00 0.00 34.36 3.51
818 2244 0.320683 CCACTGTCTTGGCGTGATCA 60.321 55.000 0.00 0.00 0.00 2.92
822 2248 0.033504 ACTACCACTGTCTTGGCGTG 59.966 55.000 0.00 0.00 40.77 5.34
837 2263 4.093556 ACAGTAACGTAACCGAGCTACTAC 59.906 45.833 0.00 0.00 37.88 2.73
838 2264 4.253685 ACAGTAACGTAACCGAGCTACTA 58.746 43.478 0.00 0.00 37.88 1.82
839 2265 3.077359 ACAGTAACGTAACCGAGCTACT 58.923 45.455 0.00 0.00 37.88 2.57
859 2285 2.161211 ACTGTCGTCTTTCTACCGCTAC 59.839 50.000 0.00 0.00 0.00 3.58
870 2296 1.534595 GACTCCACGTACTGTCGTCTT 59.465 52.381 0.00 0.00 42.27 3.01
871 2297 1.155042 GACTCCACGTACTGTCGTCT 58.845 55.000 0.00 0.00 42.27 4.18
872 2298 0.167689 GGACTCCACGTACTGTCGTC 59.832 60.000 0.00 0.00 42.27 4.20
873 2299 0.535780 TGGACTCCACGTACTGTCGT 60.536 55.000 0.00 0.58 45.10 4.34
905 2331 0.826715 GATGCTGCTCCTCCACTGTA 59.173 55.000 0.00 0.00 0.00 2.74
906 2332 1.196766 TGATGCTGCTCCTCCACTGT 61.197 55.000 0.00 0.00 0.00 3.55
907 2333 0.743701 GTGATGCTGCTCCTCCACTG 60.744 60.000 0.00 0.00 0.00 3.66
908 2334 1.196766 TGTGATGCTGCTCCTCCACT 61.197 55.000 0.00 0.00 0.00 4.00
910 2336 0.906282 TCTGTGATGCTGCTCCTCCA 60.906 55.000 0.00 0.00 0.00 3.86
912 2338 1.868469 GATCTGTGATGCTGCTCCTC 58.132 55.000 0.00 0.00 0.00 3.71
913 2339 0.104487 CGATCTGTGATGCTGCTCCT 59.896 55.000 0.00 0.00 0.00 3.69
914 2340 0.103755 TCGATCTGTGATGCTGCTCC 59.896 55.000 0.00 0.00 0.00 4.70
915 2341 1.207390 GTCGATCTGTGATGCTGCTC 58.793 55.000 0.00 0.00 0.00 4.26
916 2342 0.533951 TGTCGATCTGTGATGCTGCT 59.466 50.000 0.00 0.00 0.00 4.24
917 2343 0.928922 CTGTCGATCTGTGATGCTGC 59.071 55.000 0.00 0.00 0.00 5.25
918 2344 2.573941 TCTGTCGATCTGTGATGCTG 57.426 50.000 0.00 0.00 0.00 4.41
997 2423 4.587584 TTTAGTTGGGTTTTTAAGCGGG 57.412 40.909 0.00 0.00 0.00 6.13
1027 2454 1.520342 GGTGGAGAGATGCGTCTGC 60.520 63.158 14.59 4.98 43.20 4.26
1043 2470 2.351706 TGGCTTCGTTTGTTTAGGGT 57.648 45.000 0.00 0.00 0.00 4.34
1056 2483 2.549992 GGGGTGGTTTTCAAATGGCTTC 60.550 50.000 0.00 0.00 0.00 3.86
1059 2486 0.320334 CGGGGTGGTTTTCAAATGGC 60.320 55.000 0.00 0.00 0.00 4.40
1072 2499 1.966451 GCAAAGTGGAGTCGGGGTG 60.966 63.158 0.00 0.00 0.00 4.61
1152 2584 2.590575 GTGGTGACCGTGGTGTGG 60.591 66.667 0.00 0.00 0.00 4.17
1201 2633 4.314440 TCCTCGCCGCTGCTTTGT 62.314 61.111 0.00 0.00 34.43 2.83
2020 3470 2.430921 CAGTGGTGGAGCGACGAC 60.431 66.667 0.00 0.00 0.00 4.34
2299 3751 6.827641 TGACACGCAAATAAATGAACTACTC 58.172 36.000 0.00 0.00 0.00 2.59
2300 3752 6.649141 TCTGACACGCAAATAAATGAACTACT 59.351 34.615 0.00 0.00 0.00 2.57
2301 3753 6.827641 TCTGACACGCAAATAAATGAACTAC 58.172 36.000 0.00 0.00 0.00 2.73
2302 3754 7.609760 ATCTGACACGCAAATAAATGAACTA 57.390 32.000 0.00 0.00 0.00 2.24
2371 3831 0.097674 GACCACGCTGCTGCTAAATG 59.902 55.000 14.03 6.53 36.97 2.32
2376 3836 2.745100 CATGACCACGCTGCTGCT 60.745 61.111 14.03 0.00 36.97 4.24
2377 3837 3.052082 ACATGACCACGCTGCTGC 61.052 61.111 5.34 5.34 0.00 5.25
2378 3838 2.683859 CCACATGACCACGCTGCTG 61.684 63.158 0.00 0.00 0.00 4.41
2514 4285 3.513912 ACATCTACCGATCAACAACTCCA 59.486 43.478 0.00 0.00 0.00 3.86
2530 4301 3.271225 TCCAACAGACCCCTCTACATCTA 59.729 47.826 0.00 0.00 0.00 1.98
2531 4302 2.044492 TCCAACAGACCCCTCTACATCT 59.956 50.000 0.00 0.00 0.00 2.90
2532 4303 2.467880 TCCAACAGACCCCTCTACATC 58.532 52.381 0.00 0.00 0.00 3.06
2533 4304 2.642171 TCCAACAGACCCCTCTACAT 57.358 50.000 0.00 0.00 0.00 2.29
2534 4305 2.409064 TTCCAACAGACCCCTCTACA 57.591 50.000 0.00 0.00 0.00 2.74
2535 4306 2.092914 CCATTCCAACAGACCCCTCTAC 60.093 54.545 0.00 0.00 0.00 2.59
2536 4307 2.196595 CCATTCCAACAGACCCCTCTA 58.803 52.381 0.00 0.00 0.00 2.43
2542 4313 2.806945 TCCATCCATTCCAACAGACC 57.193 50.000 0.00 0.00 0.00 3.85
2550 4321 2.489802 GGAACCCTGATCCATCCATTCC 60.490 54.545 0.00 0.00 36.92 3.01
2551 4322 2.811873 CGGAACCCTGATCCATCCATTC 60.812 54.545 0.00 0.00 36.74 2.67
2552 4323 1.143684 CGGAACCCTGATCCATCCATT 59.856 52.381 0.00 0.00 36.74 3.16
2553 4324 0.767375 CGGAACCCTGATCCATCCAT 59.233 55.000 0.00 0.00 36.74 3.41
2554 4325 1.344953 CCGGAACCCTGATCCATCCA 61.345 60.000 0.00 0.00 36.74 3.41
2555 4326 1.345715 ACCGGAACCCTGATCCATCC 61.346 60.000 9.46 0.00 36.74 3.51
2556 4327 0.179045 CACCGGAACCCTGATCCATC 60.179 60.000 9.46 0.00 36.74 3.51
2557 4328 0.620410 TCACCGGAACCCTGATCCAT 60.620 55.000 9.46 0.00 36.74 3.41
2558 4329 1.229368 TCACCGGAACCCTGATCCA 60.229 57.895 9.46 0.00 36.74 3.41
2559 4330 1.221021 GTCACCGGAACCCTGATCC 59.779 63.158 9.46 0.00 0.00 3.36
2560 4331 1.153628 CGTCACCGGAACCCTGATC 60.154 63.158 9.46 0.00 0.00 2.92
2561 4332 2.978824 CGTCACCGGAACCCTGAT 59.021 61.111 9.46 0.00 0.00 2.90
2596 4367 0.390603 CCCAATAGCACCAACGACGA 60.391 55.000 0.00 0.00 0.00 4.20
2597 4368 0.672401 ACCCAATAGCACCAACGACG 60.672 55.000 0.00 0.00 0.00 5.12
2598 4369 1.199097 CAACCCAATAGCACCAACGAC 59.801 52.381 0.00 0.00 0.00 4.34
2605 4376 3.509575 TGGAAACATCAACCCAATAGCAC 59.490 43.478 0.00 0.00 33.40 4.40
2633 4404 1.659098 CTAACCGGAAGACACAATCGC 59.341 52.381 9.46 0.00 0.00 4.58
2634 4405 3.226346 TCTAACCGGAAGACACAATCG 57.774 47.619 9.46 0.00 0.00 3.34
2639 4410 3.952967 AGGACTATCTAACCGGAAGACAC 59.047 47.826 9.46 3.49 0.00 3.67
2650 4421 4.163649 TCGTGAGGACTGAGGACTATCTAA 59.836 45.833 0.00 0.00 0.00 2.10
2657 4428 1.133407 GTCATCGTGAGGACTGAGGAC 59.867 57.143 7.37 0.00 38.89 3.85
2675 4446 1.942657 AGCGTGTGCCATGATATTGTC 59.057 47.619 0.00 0.00 44.31 3.18
2677 4448 3.392882 TCTAGCGTGTGCCATGATATTG 58.607 45.455 0.00 0.00 44.31 1.90
2678 4449 3.321968 TCTCTAGCGTGTGCCATGATATT 59.678 43.478 0.00 0.00 44.31 1.28
2679 4450 2.893489 TCTCTAGCGTGTGCCATGATAT 59.107 45.455 0.00 0.00 44.31 1.63
2680 4451 2.306847 TCTCTAGCGTGTGCCATGATA 58.693 47.619 0.00 0.00 44.31 2.15
2682 4453 0.894835 TTCTCTAGCGTGTGCCATGA 59.105 50.000 0.00 0.00 44.31 3.07
2685 4456 1.079819 GCTTCTCTAGCGTGTGCCA 60.080 57.895 0.00 0.00 44.31 4.92
2698 4469 0.398318 AAGCCTTTGAGACCGCTTCT 59.602 50.000 0.00 0.00 36.92 2.85
2740 4511 3.974401 CCTGTGTTGTGCTAATTTGTTCG 59.026 43.478 0.00 0.00 0.00 3.95
2756 4527 0.662619 CAATGTCACGCAACCTGTGT 59.337 50.000 0.00 0.00 42.58 3.72
2803 4574 1.070786 GCACCGACCTTGTGGAAGA 59.929 57.895 0.00 0.00 37.04 2.87
2821 4597 2.740055 GGCACCGTCTCTGCACTG 60.740 66.667 0.00 0.00 36.27 3.66
2822 4598 4.363990 CGGCACCGTCTCTGCACT 62.364 66.667 0.00 0.00 36.27 4.40
2823 4599 3.858868 TTCGGCACCGTCTCTGCAC 62.859 63.158 9.23 0.00 40.74 4.57
2824 4600 2.449031 ATTTCGGCACCGTCTCTGCA 62.449 55.000 9.23 0.00 40.74 4.41
2825 4601 1.741770 ATTTCGGCACCGTCTCTGC 60.742 57.895 9.23 0.00 40.74 4.26
2838 4614 3.605634 TGGAATCAGTACCACCATTTCG 58.394 45.455 0.00 0.00 0.00 3.46
2981 4783 0.250513 ATCGGAAGTTGACCTGGAGC 59.749 55.000 0.00 0.00 0.00 4.70
3014 4816 9.434559 GTAAAAGTAATGTTTGTTGTCTGAGAC 57.565 33.333 5.47 5.47 0.00 3.36
3015 4817 9.168451 TGTAAAAGTAATGTTTGTTGTCTGAGA 57.832 29.630 0.00 0.00 0.00 3.27
3017 4819 9.944663 GATGTAAAAGTAATGTTTGTTGTCTGA 57.055 29.630 0.00 0.00 0.00 3.27
3018 4820 8.891928 CGATGTAAAAGTAATGTTTGTTGTCTG 58.108 33.333 0.00 0.00 0.00 3.51
3019 4821 7.589954 GCGATGTAAAAGTAATGTTTGTTGTCT 59.410 33.333 0.00 0.00 0.00 3.41
3020 4822 7.377397 TGCGATGTAAAAGTAATGTTTGTTGTC 59.623 33.333 0.00 0.00 0.00 3.18
3021 4823 7.197017 TGCGATGTAAAAGTAATGTTTGTTGT 58.803 30.769 0.00 0.00 0.00 3.32
3022 4824 7.616103 TGCGATGTAAAAGTAATGTTTGTTG 57.384 32.000 0.00 0.00 0.00 3.33
3023 4825 8.635877 TTTGCGATGTAAAAGTAATGTTTGTT 57.364 26.923 0.00 0.00 0.00 2.83
3024 4826 8.635877 TTTTGCGATGTAAAAGTAATGTTTGT 57.364 26.923 0.00 0.00 0.00 2.83
3054 4856 9.354673 TGTCTGAGATTTCCTAAAAGAAATGTT 57.645 29.630 4.34 0.00 44.52 2.71
3055 4857 8.924511 TGTCTGAGATTTCCTAAAAGAAATGT 57.075 30.769 4.34 0.65 44.52 2.71
3056 4858 9.837525 CTTGTCTGAGATTTCCTAAAAGAAATG 57.162 33.333 4.34 0.00 44.52 2.32
3060 4862 6.876257 GCTCTTGTCTGAGATTTCCTAAAAGA 59.124 38.462 0.00 0.00 36.23 2.52
3066 4868 3.619487 GCAGCTCTTGTCTGAGATTTCCT 60.619 47.826 0.00 0.00 36.23 3.36
3084 4886 3.451894 CCAATTCCACCCCGCAGC 61.452 66.667 0.00 0.00 0.00 5.25
3097 4899 2.783135 TGCGAGCTCTTTCTTTCCAAT 58.217 42.857 12.85 0.00 0.00 3.16
3108 4910 3.808466 TGACTAATGATTGCGAGCTCT 57.192 42.857 12.85 0.00 0.00 4.09
3132 4934 4.072839 GTGGGTTCTAGCTAAGCAAAACT 58.927 43.478 0.00 0.00 0.00 2.66
3161 4963 3.329889 CTGCCCAGGTAGGTGCCA 61.330 66.667 0.00 0.00 33.97 4.92


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

AutoCloner maintained by Alex Coulton.