Multiple sequence alignment - TraesCS1D01G159200

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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 TraesCS1D01G159200 chr1D 100.000 3113 0 0 1 3113 224576237 224573125 0.000000e+00 5749.0
1 TraesCS1D01G159200 chr1D 97.212 538 15 0 2452 2989 335039733 335039196 0.000000e+00 911.0
2 TraesCS1D01G159200 chr1A 98.795 1577 17 2 874 2449 291565965 291564390 0.000000e+00 2806.0
3 TraesCS1D01G159200 chr1A 93.662 284 10 5 378 658 291566238 291565960 4.800000e-113 418.0
4 TraesCS1D01G159200 chr1A 88.255 298 27 6 5 299 291566571 291566279 1.780000e-92 350.0
5 TraesCS1D01G159200 chr1A 97.895 95 2 0 2985 3079 291564408 291564314 6.910000e-37 165.0
6 TraesCS1D01G159200 chr1B 97.722 1580 28 3 871 2449 324601030 324602602 0.000000e+00 2712.0
7 TraesCS1D01G159200 chr1B 90.377 239 23 0 1 239 324583974 324584212 6.480000e-82 315.0
8 TraesCS1D01G159200 chr1B 92.000 175 2 4 486 658 324600874 324601038 5.190000e-58 235.0
9 TraesCS1D01G159200 chr1B 92.857 98 4 1 2985 3079 324602584 324602681 4.190000e-29 139.0
10 TraesCS1D01G159200 chr6D 96.648 537 17 1 2453 2989 460866421 460865886 0.000000e+00 891.0
11 TraesCS1D01G159200 chr6D 93.458 214 10 4 662 874 46939142 46938932 6.480000e-82 315.0
12 TraesCS1D01G159200 chr7A 96.449 535 19 0 2452 2986 17634924 17635458 0.000000e+00 883.0
13 TraesCS1D01G159200 chr7D 96.449 535 18 1 2452 2986 7527758 7528291 0.000000e+00 881.0
14 TraesCS1D01G159200 chr7D 95.896 536 19 3 2450 2983 636717762 636717228 0.000000e+00 865.0
15 TraesCS1D01G159200 chr7D 96.667 210 5 2 662 870 29555725 29555517 6.390000e-92 348.0
16 TraesCS1D01G159200 chr5D 96.262 535 19 1 2451 2985 375464682 375464149 0.000000e+00 876.0
17 TraesCS1D01G159200 chr5D 94.419 215 9 3 662 875 537643309 537643097 8.320000e-86 327.0
18 TraesCS1D01G159200 chr4B 96.262 535 19 1 2452 2986 516975957 516976490 0.000000e+00 876.0
19 TraesCS1D01G159200 chr2D 96.075 535 21 0 2452 2986 586856573 586857107 0.000000e+00 872.0
20 TraesCS1D01G159200 chr2D 97.619 210 4 1 662 870 449513301 449513510 2.950000e-95 359.0
21 TraesCS1D01G159200 chr2D 93.427 213 13 1 662 873 79528061 79527849 6.480000e-82 315.0
22 TraesCS1D01G159200 chr4D 95.701 535 22 1 2452 2986 82567654 82568187 0.000000e+00 859.0
23 TraesCS1D01G159200 chr4D 96.172 209 6 2 662 869 89931628 89931835 1.070000e-89 340.0
24 TraesCS1D01G159200 chr3D 94.860 214 7 4 662 874 481706513 481706723 6.430000e-87 331.0
25 TraesCS1D01G159200 chr3A 94.313 211 7 4 661 870 184272417 184272623 5.010000e-83 318.0
26 TraesCS1D01G159200 chr3A 93.925 214 8 4 662 874 651189305 651189514 5.010000e-83 318.0
27 TraesCS1D01G159200 chr5B 75.253 198 44 5 247 442 621206793 621206599 4.280000e-14 89.8
28 TraesCS1D01G159200 chr2B 100.000 31 0 0 348 378 690968591 690968621 1.210000e-04 58.4


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 TraesCS1D01G159200 chr1D 224573125 224576237 3112 True 5749.000000 5749 100.00000 1 3113 1 chr1D.!!$R1 3112
1 TraesCS1D01G159200 chr1D 335039196 335039733 537 True 911.000000 911 97.21200 2452 2989 1 chr1D.!!$R2 537
2 TraesCS1D01G159200 chr1A 291564314 291566571 2257 True 934.750000 2806 94.65175 5 3079 4 chr1A.!!$R1 3074
3 TraesCS1D01G159200 chr1B 324600874 324602681 1807 False 1028.666667 2712 94.19300 486 3079 3 chr1B.!!$F2 2593
4 TraesCS1D01G159200 chr6D 460865886 460866421 535 True 891.000000 891 96.64800 2453 2989 1 chr6D.!!$R2 536
5 TraesCS1D01G159200 chr7A 17634924 17635458 534 False 883.000000 883 96.44900 2452 2986 1 chr7A.!!$F1 534
6 TraesCS1D01G159200 chr7D 7527758 7528291 533 False 881.000000 881 96.44900 2452 2986 1 chr7D.!!$F1 534
7 TraesCS1D01G159200 chr7D 636717228 636717762 534 True 865.000000 865 95.89600 2450 2983 1 chr7D.!!$R2 533
8 TraesCS1D01G159200 chr5D 375464149 375464682 533 True 876.000000 876 96.26200 2451 2985 1 chr5D.!!$R1 534
9 TraesCS1D01G159200 chr4B 516975957 516976490 533 False 876.000000 876 96.26200 2452 2986 1 chr4B.!!$F1 534
10 TraesCS1D01G159200 chr2D 586856573 586857107 534 False 872.000000 872 96.07500 2452 2986 1 chr2D.!!$F2 534
11 TraesCS1D01G159200 chr4D 82567654 82568187 533 False 859.000000 859 95.70100 2452 2986 1 chr4D.!!$F1 534

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
816 825 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.0 13.12 2.86 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2542 2553 1.00152 TGTGCAAAGGCTAGCGTTCTA 59.998 47.619 21.95 9.47 41.91 2.1 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
34 35 1.534595 GCGGATCAAAGATGGAGATGC 59.465 52.381 0.00 0.00 0.00 3.91
109 110 7.901377 GCTTTTGCAATCAATTCACATAATGTC 59.099 33.333 0.00 0.00 46.58 3.06
190 191 4.388485 GCCTTTTTCCACAAACCATCAAT 58.612 39.130 0.00 0.00 0.00 2.57
249 253 9.520204 AAAATGATTAAGTTATACATGTGCTGC 57.480 29.630 9.11 0.00 0.00 5.25
254 258 4.753516 AGTTATACATGTGCTGCCTACA 57.246 40.909 9.11 0.00 0.00 2.74
260 264 1.669265 CATGTGCTGCCTACATGTCAG 59.331 52.381 19.39 5.02 46.37 3.51
288 292 2.800516 TGTTTGCAACATGACCCGT 58.199 47.368 0.00 0.00 36.25 5.28
293 297 2.192664 TGCAACATGACCCGTGTTAT 57.807 45.000 0.00 0.00 40.99 1.89
299 303 5.335348 GCAACATGACCCGTGTTATAAACTT 60.335 40.000 0.00 0.00 40.99 2.66
300 304 5.873179 ACATGACCCGTGTTATAAACTTG 57.127 39.130 0.00 0.00 28.11 3.16
301 305 5.310451 ACATGACCCGTGTTATAAACTTGT 58.690 37.500 0.00 0.00 28.11 3.16
302 306 5.180492 ACATGACCCGTGTTATAAACTTGTG 59.820 40.000 0.00 0.00 28.11 3.33
303 307 4.706035 TGACCCGTGTTATAAACTTGTGT 58.294 39.130 0.00 0.00 0.00 3.72
304 308 5.124645 TGACCCGTGTTATAAACTTGTGTT 58.875 37.500 0.00 0.00 38.16 3.32
305 309 5.589452 TGACCCGTGTTATAAACTTGTGTTT 59.411 36.000 0.00 0.00 46.74 2.83
306 310 5.823353 ACCCGTGTTATAAACTTGTGTTTG 58.177 37.500 4.64 0.00 45.01 2.93
307 311 4.677832 CCCGTGTTATAAACTTGTGTTTGC 59.322 41.667 4.64 0.00 45.01 3.68
308 312 5.274718 CCGTGTTATAAACTTGTGTTTGCA 58.725 37.500 4.64 0.00 45.01 4.08
309 313 5.744345 CCGTGTTATAAACTTGTGTTTGCAA 59.256 36.000 0.00 0.00 45.01 4.08
338 342 6.972901 GCCTAATGTTGCTAATTTGTTAGTCC 59.027 38.462 0.00 0.00 0.00 3.85
339 343 7.148069 GCCTAATGTTGCTAATTTGTTAGTCCT 60.148 37.037 0.00 0.00 0.00 3.85
344 348 7.648142 TGTTGCTAATTTGTTAGTCCTTCTTG 58.352 34.615 0.00 0.00 0.00 3.02
348 352 6.598064 GCTAATTTGTTAGTCCTTCTTGCCTA 59.402 38.462 0.00 0.00 0.00 3.93
349 353 6.819397 AATTTGTTAGTCCTTCTTGCCTAC 57.181 37.500 0.00 0.00 0.00 3.18
350 354 5.562298 TTTGTTAGTCCTTCTTGCCTACT 57.438 39.130 0.00 0.00 0.00 2.57
351 355 5.562298 TTGTTAGTCCTTCTTGCCTACTT 57.438 39.130 0.00 0.00 0.00 2.24
352 356 5.148651 TGTTAGTCCTTCTTGCCTACTTC 57.851 43.478 0.00 0.00 0.00 3.01
353 357 4.020485 TGTTAGTCCTTCTTGCCTACTTCC 60.020 45.833 0.00 0.00 0.00 3.46
354 358 1.909986 AGTCCTTCTTGCCTACTTCCC 59.090 52.381 0.00 0.00 0.00 3.97
355 359 1.065345 GTCCTTCTTGCCTACTTCCCC 60.065 57.143 0.00 0.00 0.00 4.81
356 360 1.203440 TCCTTCTTGCCTACTTCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
357 361 1.065126 CCTTCTTGCCTACTTCCCCTG 60.065 57.143 0.00 0.00 0.00 4.45
358 362 1.630878 CTTCTTGCCTACTTCCCCTGT 59.369 52.381 0.00 0.00 0.00 4.00
359 363 1.742308 TCTTGCCTACTTCCCCTGTT 58.258 50.000 0.00 0.00 0.00 3.16
360 364 1.628846 TCTTGCCTACTTCCCCTGTTC 59.371 52.381 0.00 0.00 0.00 3.18
361 365 0.696501 TTGCCTACTTCCCCTGTTCC 59.303 55.000 0.00 0.00 0.00 3.62
362 366 0.474854 TGCCTACTTCCCCTGTTCCA 60.475 55.000 0.00 0.00 0.00 3.53
363 367 0.696501 GCCTACTTCCCCTGTTCCAA 59.303 55.000 0.00 0.00 0.00 3.53
364 368 1.074889 GCCTACTTCCCCTGTTCCAAA 59.925 52.381 0.00 0.00 0.00 3.28
365 369 2.490168 GCCTACTTCCCCTGTTCCAAAA 60.490 50.000 0.00 0.00 0.00 2.44
366 370 3.817931 GCCTACTTCCCCTGTTCCAAAAT 60.818 47.826 0.00 0.00 0.00 1.82
367 371 4.569015 GCCTACTTCCCCTGTTCCAAAATA 60.569 45.833 0.00 0.00 0.00 1.40
368 372 5.193679 CCTACTTCCCCTGTTCCAAAATAG 58.806 45.833 0.00 0.00 0.00 1.73
369 373 5.045140 CCTACTTCCCCTGTTCCAAAATAGA 60.045 44.000 0.00 0.00 0.00 1.98
370 374 5.536497 ACTTCCCCTGTTCCAAAATAGAT 57.464 39.130 0.00 0.00 0.00 1.98
371 375 5.264395 ACTTCCCCTGTTCCAAAATAGATG 58.736 41.667 0.00 0.00 0.00 2.90
372 376 5.015178 ACTTCCCCTGTTCCAAAATAGATGA 59.985 40.000 0.00 0.00 0.00 2.92
373 377 4.855340 TCCCCTGTTCCAAAATAGATGAC 58.145 43.478 0.00 0.00 0.00 3.06
374 378 3.954258 CCCCTGTTCCAAAATAGATGACC 59.046 47.826 0.00 0.00 0.00 4.02
375 379 3.954258 CCCTGTTCCAAAATAGATGACCC 59.046 47.826 0.00 0.00 0.00 4.46
376 380 4.569653 CCCTGTTCCAAAATAGATGACCCA 60.570 45.833 0.00 0.00 0.00 4.51
385 389 5.734855 AAATAGATGACCCAAATCGAACG 57.265 39.130 0.00 0.00 0.00 3.95
406 410 1.539065 GCCACTGAGGTGATGGATACG 60.539 57.143 0.00 0.00 45.61 3.06
421 425 0.741326 ATACGCGTGAGTCATCAGCT 59.259 50.000 24.59 0.00 35.66 4.24
431 435 2.746362 GAGTCATCAGCTGGTTGAAAGG 59.254 50.000 15.13 0.00 0.00 3.11
434 438 3.686726 GTCATCAGCTGGTTGAAAGGTAG 59.313 47.826 15.13 0.00 0.00 3.18
436 440 0.798776 CAGCTGGTTGAAAGGTAGCG 59.201 55.000 5.57 0.00 39.27 4.26
437 441 0.685097 AGCTGGTTGAAAGGTAGCGA 59.315 50.000 0.00 0.00 39.27 4.93
440 444 2.096013 GCTGGTTGAAAGGTAGCGATTC 59.904 50.000 6.57 6.57 0.00 2.52
443 447 3.244770 TGGTTGAAAGGTAGCGATTCCTT 60.245 43.478 5.68 5.68 44.71 3.36
444 448 3.127030 GGTTGAAAGGTAGCGATTCCTTG 59.873 47.826 12.58 0.00 42.38 3.61
445 449 3.695830 TGAAAGGTAGCGATTCCTTGT 57.304 42.857 12.58 3.23 42.38 3.16
450 454 6.487331 TGAAAGGTAGCGATTCCTTGTAAAAA 59.513 34.615 12.58 0.00 42.38 1.94
484 488 5.123344 GGTGAAAATACCAGTAAATCGCTGT 59.877 40.000 0.00 0.00 40.54 4.40
662 671 4.462280 GGGGTCACCGCCGTTAGG 62.462 72.222 0.00 0.00 37.78 2.69
663 672 3.384532 GGGTCACCGCCGTTAGGA 61.385 66.667 0.00 0.00 41.02 2.94
664 673 2.658422 GGTCACCGCCGTTAGGAA 59.342 61.111 0.00 0.00 41.02 3.36
665 674 1.004679 GGTCACCGCCGTTAGGAAA 60.005 57.895 0.00 0.00 41.02 3.13
666 675 0.603439 GGTCACCGCCGTTAGGAAAA 60.603 55.000 0.00 0.00 41.02 2.29
667 676 0.794473 GTCACCGCCGTTAGGAAAAG 59.206 55.000 0.00 0.00 41.02 2.27
668 677 0.680618 TCACCGCCGTTAGGAAAAGA 59.319 50.000 0.00 0.00 41.02 2.52
669 678 1.070445 TCACCGCCGTTAGGAAAAGAA 59.930 47.619 0.00 0.00 41.02 2.52
670 679 2.081462 CACCGCCGTTAGGAAAAGAAT 58.919 47.619 0.00 0.00 41.02 2.40
671 680 2.486592 CACCGCCGTTAGGAAAAGAATT 59.513 45.455 0.00 0.00 41.02 2.17
672 681 2.745821 ACCGCCGTTAGGAAAAGAATTC 59.254 45.455 0.00 0.00 41.02 2.17
673 682 3.007635 CCGCCGTTAGGAAAAGAATTCT 58.992 45.455 0.88 0.88 41.02 2.40
674 683 4.186159 CCGCCGTTAGGAAAAGAATTCTA 58.814 43.478 8.75 0.00 41.02 2.10
675 684 4.814771 CCGCCGTTAGGAAAAGAATTCTAT 59.185 41.667 8.75 0.41 41.02 1.98
676 685 5.277345 CCGCCGTTAGGAAAAGAATTCTATG 60.277 44.000 8.75 0.00 41.02 2.23
677 686 5.522460 CGCCGTTAGGAAAAGAATTCTATGA 59.478 40.000 8.75 0.00 41.02 2.15
678 687 6.292381 CGCCGTTAGGAAAAGAATTCTATGAG 60.292 42.308 8.75 0.00 41.02 2.90
679 688 6.761714 GCCGTTAGGAAAAGAATTCTATGAGA 59.238 38.462 8.75 0.00 41.02 3.27
680 689 7.254488 GCCGTTAGGAAAAGAATTCTATGAGAC 60.254 40.741 8.75 1.94 41.02 3.36
681 690 7.224949 CCGTTAGGAAAAGAATTCTATGAGACC 59.775 40.741 8.75 7.08 41.02 3.85
682 691 7.764443 CGTTAGGAAAAGAATTCTATGAGACCA 59.236 37.037 8.75 0.00 0.00 4.02
683 692 9.103861 GTTAGGAAAAGAATTCTATGAGACCAG 57.896 37.037 8.75 0.00 0.00 4.00
684 693 6.657875 AGGAAAAGAATTCTATGAGACCAGG 58.342 40.000 8.75 0.00 0.00 4.45
685 694 6.216456 AGGAAAAGAATTCTATGAGACCAGGT 59.784 38.462 8.75 0.00 0.00 4.00
686 695 6.540551 GGAAAAGAATTCTATGAGACCAGGTC 59.459 42.308 12.25 12.25 0.00 3.85
687 696 6.882768 AAAGAATTCTATGAGACCAGGTCT 57.117 37.500 23.18 23.18 46.42 3.85
694 703 3.870955 AGACCAGGTCTCACGCAA 58.129 55.556 17.31 0.00 38.71 4.85
695 704 1.668294 AGACCAGGTCTCACGCAAG 59.332 57.895 17.31 0.00 38.71 4.01
696 705 0.827925 AGACCAGGTCTCACGCAAGA 60.828 55.000 17.31 0.00 38.71 3.02
697 706 0.667792 GACCAGGTCTCACGCAAGAC 60.668 60.000 12.94 8.83 44.08 3.01
701 710 2.338984 GTCTCACGCAAGACCCGT 59.661 61.111 6.53 0.00 39.85 5.28
702 711 1.733399 GTCTCACGCAAGACCCGTC 60.733 63.158 6.53 0.00 39.85 4.79
703 712 2.432628 CTCACGCAAGACCCGTCC 60.433 66.667 0.00 0.00 43.62 4.79
704 713 2.915659 TCACGCAAGACCCGTCCT 60.916 61.111 0.00 0.00 43.62 3.85
705 714 2.738521 CACGCAAGACCCGTCCTG 60.739 66.667 0.00 0.00 43.62 3.86
706 715 2.915659 ACGCAAGACCCGTCCTGA 60.916 61.111 0.00 0.00 43.62 3.86
707 716 2.283529 ACGCAAGACCCGTCCTGAT 61.284 57.895 0.00 0.00 43.62 2.90
708 717 1.811266 CGCAAGACCCGTCCTGATG 60.811 63.158 0.00 0.00 43.02 3.07
709 718 1.450312 GCAAGACCCGTCCTGATGG 60.450 63.158 0.00 0.00 37.23 3.51
710 719 1.899437 GCAAGACCCGTCCTGATGGA 61.899 60.000 6.98 0.00 39.90 3.41
711 720 0.833287 CAAGACCCGTCCTGATGGAT 59.167 55.000 6.98 0.00 45.29 3.41
712 721 0.833287 AAGACCCGTCCTGATGGATG 59.167 55.000 6.98 0.00 45.29 3.51
720 729 2.569059 GTCCTGATGGATGACACATGG 58.431 52.381 0.00 0.00 45.29 3.66
721 730 1.134007 TCCTGATGGATGACACATGGC 60.134 52.381 0.00 0.00 37.46 4.40
722 731 1.409101 CCTGATGGATGACACATGGCA 60.409 52.381 0.00 0.00 37.54 4.92
724 733 2.956333 CTGATGGATGACACATGGCATT 59.044 45.455 0.78 0.00 45.42 3.56
725 734 2.953648 TGATGGATGACACATGGCATTC 59.046 45.455 0.78 0.00 45.42 2.67
726 735 2.510928 TGGATGACACATGGCATTCA 57.489 45.000 4.43 4.43 46.54 2.57
727 736 2.093890 TGGATGACACATGGCATTCAC 58.906 47.619 4.43 0.00 43.95 3.18
728 737 2.093890 GGATGACACATGGCATTCACA 58.906 47.619 0.78 0.00 45.42 3.58
729 738 2.492881 GGATGACACATGGCATTCACAA 59.507 45.455 0.78 0.00 45.42 3.33
730 739 3.056678 GGATGACACATGGCATTCACAAA 60.057 43.478 0.78 0.00 45.42 2.83
731 740 4.382254 GGATGACACATGGCATTCACAAAT 60.382 41.667 0.78 0.00 45.42 2.32
732 741 4.177165 TGACACATGGCATTCACAAATC 57.823 40.909 0.00 0.00 0.00 2.17
733 742 3.573110 TGACACATGGCATTCACAAATCA 59.427 39.130 0.00 0.00 0.00 2.57
734 743 3.916761 ACACATGGCATTCACAAATCAC 58.083 40.909 0.00 0.00 0.00 3.06
735 744 3.321396 ACACATGGCATTCACAAATCACA 59.679 39.130 0.00 0.00 0.00 3.58
736 745 4.202233 ACACATGGCATTCACAAATCACAA 60.202 37.500 0.00 0.00 0.00 3.33
737 746 4.750598 CACATGGCATTCACAAATCACAAA 59.249 37.500 0.00 0.00 0.00 2.83
738 747 4.992319 ACATGGCATTCACAAATCACAAAG 59.008 37.500 0.00 0.00 0.00 2.77
739 748 3.391965 TGGCATTCACAAATCACAAAGC 58.608 40.909 0.00 0.00 0.00 3.51
740 749 3.181468 TGGCATTCACAAATCACAAAGCA 60.181 39.130 0.00 0.00 0.00 3.91
741 750 3.998341 GGCATTCACAAATCACAAAGCAT 59.002 39.130 0.00 0.00 0.00 3.79
742 751 4.092383 GGCATTCACAAATCACAAAGCATC 59.908 41.667 0.00 0.00 0.00 3.91
743 752 4.092383 GCATTCACAAATCACAAAGCATCC 59.908 41.667 0.00 0.00 0.00 3.51
744 753 4.933505 TTCACAAATCACAAAGCATCCA 57.066 36.364 0.00 0.00 0.00 3.41
745 754 5.471556 TTCACAAATCACAAAGCATCCAT 57.528 34.783 0.00 0.00 0.00 3.41
746 755 5.063180 TCACAAATCACAAAGCATCCATC 57.937 39.130 0.00 0.00 0.00 3.51
747 756 4.082081 TCACAAATCACAAAGCATCCATCC 60.082 41.667 0.00 0.00 0.00 3.51
748 757 3.196254 ACAAATCACAAAGCATCCATCCC 59.804 43.478 0.00 0.00 0.00 3.85
749 758 2.832643 ATCACAAAGCATCCATCCCA 57.167 45.000 0.00 0.00 0.00 4.37
750 759 1.838112 TCACAAAGCATCCATCCCAC 58.162 50.000 0.00 0.00 0.00 4.61
751 760 0.819582 CACAAAGCATCCATCCCACC 59.180 55.000 0.00 0.00 0.00 4.61
752 761 0.324645 ACAAAGCATCCATCCCACCC 60.325 55.000 0.00 0.00 0.00 4.61
753 762 1.044790 CAAAGCATCCATCCCACCCC 61.045 60.000 0.00 0.00 0.00 4.95
754 763 2.242408 AAAGCATCCATCCCACCCCC 62.242 60.000 0.00 0.00 0.00 5.40
772 781 2.736670 CCCACTTAAATCAGGGGAGG 57.263 55.000 0.00 0.00 40.25 4.30
773 782 2.205342 CCCACTTAAATCAGGGGAGGA 58.795 52.381 0.00 0.00 40.25 3.71
774 783 2.173569 CCCACTTAAATCAGGGGAGGAG 59.826 54.545 0.00 0.00 40.25 3.69
775 784 3.115390 CCACTTAAATCAGGGGAGGAGA 58.885 50.000 0.00 0.00 40.25 3.71
776 785 3.135530 CCACTTAAATCAGGGGAGGAGAG 59.864 52.174 0.00 0.00 40.25 3.20
777 786 4.033709 CACTTAAATCAGGGGAGGAGAGA 58.966 47.826 0.00 0.00 0.00 3.10
778 787 4.657969 CACTTAAATCAGGGGAGGAGAGAT 59.342 45.833 0.00 0.00 0.00 2.75
779 788 5.131809 CACTTAAATCAGGGGAGGAGAGATT 59.868 44.000 0.00 0.00 0.00 2.40
780 789 6.327626 CACTTAAATCAGGGGAGGAGAGATTA 59.672 42.308 0.00 0.00 0.00 1.75
781 790 6.909158 ACTTAAATCAGGGGAGGAGAGATTAA 59.091 38.462 0.00 0.00 0.00 1.40
782 791 7.406151 ACTTAAATCAGGGGAGGAGAGATTAAA 59.594 37.037 0.00 0.00 0.00 1.52
783 792 6.855375 AAATCAGGGGAGGAGAGATTAAAT 57.145 37.500 0.00 0.00 0.00 1.40
784 793 5.839517 ATCAGGGGAGGAGAGATTAAATG 57.160 43.478 0.00 0.00 0.00 2.32
785 794 3.392616 TCAGGGGAGGAGAGATTAAATGC 59.607 47.826 0.00 0.00 0.00 3.56
786 795 3.393941 CAGGGGAGGAGAGATTAAATGCT 59.606 47.826 0.00 0.00 0.00 3.79
787 796 4.050757 AGGGGAGGAGAGATTAAATGCTT 58.949 43.478 0.00 0.00 0.00 3.91
788 797 4.480166 AGGGGAGGAGAGATTAAATGCTTT 59.520 41.667 0.00 0.00 0.00 3.51
789 798 4.582240 GGGGAGGAGAGATTAAATGCTTTG 59.418 45.833 0.00 0.00 0.00 2.77
790 799 5.440610 GGGAGGAGAGATTAAATGCTTTGA 58.559 41.667 0.00 0.00 0.00 2.69
791 800 5.530543 GGGAGGAGAGATTAAATGCTTTGAG 59.469 44.000 0.00 0.00 0.00 3.02
792 801 6.352516 GGAGGAGAGATTAAATGCTTTGAGA 58.647 40.000 0.00 0.00 0.00 3.27
793 802 6.997476 GGAGGAGAGATTAAATGCTTTGAGAT 59.003 38.462 0.00 0.00 0.00 2.75
794 803 7.501892 GGAGGAGAGATTAAATGCTTTGAGATT 59.498 37.037 0.00 0.00 0.00 2.40
795 804 8.820153 AGGAGAGATTAAATGCTTTGAGATTT 57.180 30.769 0.00 0.00 0.00 2.17
796 805 8.684520 AGGAGAGATTAAATGCTTTGAGATTTG 58.315 33.333 0.00 0.00 0.00 2.32
797 806 8.465201 GGAGAGATTAAATGCTTTGAGATTTGT 58.535 33.333 0.00 0.00 0.00 2.83
798 807 9.286946 GAGAGATTAAATGCTTTGAGATTTGTG 57.713 33.333 0.00 0.00 0.00 3.33
799 808 9.017509 AGAGATTAAATGCTTTGAGATTTGTGA 57.982 29.630 0.00 0.00 0.00 3.58
800 809 9.630098 GAGATTAAATGCTTTGAGATTTGTGAA 57.370 29.630 0.00 0.00 0.00 3.18
803 812 6.476243 AAATGCTTTGAGATTTGTGAATGC 57.524 33.333 0.00 0.00 0.00 3.56
804 813 3.916761 TGCTTTGAGATTTGTGAATGCC 58.083 40.909 0.00 0.00 0.00 4.40
805 814 3.321396 TGCTTTGAGATTTGTGAATGCCA 59.679 39.130 0.00 0.00 0.00 4.92
806 815 3.676646 GCTTTGAGATTTGTGAATGCCAC 59.323 43.478 0.00 0.00 45.88 5.01
814 823 3.975992 GTGAATGCCACGTGTCATC 57.024 52.632 13.12 7.23 35.86 2.92
815 824 0.447801 GTGAATGCCACGTGTCATCC 59.552 55.000 13.12 0.00 35.86 3.51
816 825 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.000 13.12 2.86 0.00 3.41
817 826 1.339920 TGAATGCCACGTGTCATCCAT 60.340 47.619 13.12 0.00 0.00 3.41
818 827 1.331756 GAATGCCACGTGTCATCCATC 59.668 52.381 13.12 3.25 0.00 3.51
819 828 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
820 829 0.391528 TGCCACGTGTCATCCATCAG 60.392 55.000 15.65 0.00 0.00 2.90
821 830 1.091771 GCCACGTGTCATCCATCAGG 61.092 60.000 15.65 0.00 0.00 3.86
822 831 0.462581 CCACGTGTCATCCATCAGGG 60.463 60.000 15.65 0.00 34.83 4.45
823 832 1.091771 CACGTGTCATCCATCAGGGC 61.092 60.000 7.58 0.00 36.21 5.19
824 833 1.884464 CGTGTCATCCATCAGGGCG 60.884 63.158 0.00 0.00 36.21 6.13
825 834 1.524621 GTGTCATCCATCAGGGCGG 60.525 63.158 0.00 0.00 36.21 6.13
826 835 2.111878 GTCATCCATCAGGGCGGG 59.888 66.667 0.00 0.00 36.21 6.13
827 836 2.366837 TCATCCATCAGGGCGGGT 60.367 61.111 0.00 0.00 36.21 5.28
828 837 2.111878 CATCCATCAGGGCGGGTC 59.888 66.667 0.00 0.00 36.21 4.46
829 838 2.040464 ATCCATCAGGGCGGGTCT 60.040 61.111 0.00 0.00 36.21 3.85
830 839 2.143419 ATCCATCAGGGCGGGTCTC 61.143 63.158 0.00 0.00 36.21 3.36
831 840 2.896677 ATCCATCAGGGCGGGTCTCA 62.897 60.000 0.00 0.00 36.21 3.27
832 841 2.187946 CATCAGGGCGGGTCTCAC 59.812 66.667 0.00 0.00 0.00 3.51
833 842 2.284625 ATCAGGGCGGGTCTCACA 60.285 61.111 0.00 0.00 0.00 3.58
834 843 1.690633 ATCAGGGCGGGTCTCACAT 60.691 57.895 0.00 0.00 0.00 3.21
835 844 1.976132 ATCAGGGCGGGTCTCACATG 61.976 60.000 0.00 0.00 0.00 3.21
836 845 4.101448 AGGGCGGGTCTCACATGC 62.101 66.667 0.00 0.00 0.00 4.06
837 846 4.101448 GGGCGGGTCTCACATGCT 62.101 66.667 0.00 0.00 0.00 3.79
838 847 2.731571 GGGCGGGTCTCACATGCTA 61.732 63.158 0.00 0.00 0.00 3.49
839 848 1.220749 GGCGGGTCTCACATGCTAA 59.779 57.895 0.00 0.00 0.00 3.09
840 849 1.090052 GGCGGGTCTCACATGCTAAC 61.090 60.000 0.00 0.00 0.00 2.34
841 850 1.090052 GCGGGTCTCACATGCTAACC 61.090 60.000 0.00 0.00 0.00 2.85
842 851 0.806102 CGGGTCTCACATGCTAACCG 60.806 60.000 0.00 0.00 0.00 4.44
843 852 0.249398 GGGTCTCACATGCTAACCGT 59.751 55.000 0.00 0.00 0.00 4.83
844 853 1.359848 GGTCTCACATGCTAACCGTG 58.640 55.000 0.00 0.00 36.50 4.94
845 854 1.067142 GGTCTCACATGCTAACCGTGA 60.067 52.381 0.00 0.00 37.33 4.35
848 857 2.363788 TCACATGCTAACCGTGAGAC 57.636 50.000 0.00 0.00 34.83 3.36
849 858 1.067142 TCACATGCTAACCGTGAGACC 60.067 52.381 0.00 0.00 34.83 3.85
850 859 1.066858 CACATGCTAACCGTGAGACCT 60.067 52.381 0.00 0.00 34.47 3.85
851 860 1.066858 ACATGCTAACCGTGAGACCTG 60.067 52.381 0.00 0.00 34.47 4.00
852 861 0.537188 ATGCTAACCGTGAGACCTGG 59.463 55.000 0.00 0.00 0.00 4.45
853 862 0.830444 TGCTAACCGTGAGACCTGGT 60.830 55.000 0.00 0.00 37.68 4.00
854 863 0.108756 GCTAACCGTGAGACCTGGTC 60.109 60.000 19.20 19.20 34.11 4.02
855 864 1.546961 CTAACCGTGAGACCTGGTCT 58.453 55.000 28.70 28.70 46.42 3.85
1653 1663 0.456628 TTCCTGACGTCGTTGTCACA 59.543 50.000 11.62 0.00 43.62 3.58
2443 2454 7.359595 GTTTTGTGTCATTGTAGTATCAGCAA 58.640 34.615 0.00 0.00 0.00 3.91
2444 2455 6.480524 TTGTGTCATTGTAGTATCAGCAAC 57.519 37.500 0.00 0.00 0.00 4.17
2445 2456 5.546526 TGTGTCATTGTAGTATCAGCAACA 58.453 37.500 0.00 0.00 0.00 3.33
2446 2457 5.639082 TGTGTCATTGTAGTATCAGCAACAG 59.361 40.000 0.00 0.00 0.00 3.16
2447 2458 5.639506 GTGTCATTGTAGTATCAGCAACAGT 59.360 40.000 0.00 0.00 0.00 3.55
2448 2459 6.147821 GTGTCATTGTAGTATCAGCAACAGTT 59.852 38.462 0.00 0.00 0.00 3.16
2449 2460 6.710295 TGTCATTGTAGTATCAGCAACAGTTT 59.290 34.615 0.00 0.00 0.00 2.66
2450 2461 7.875554 TGTCATTGTAGTATCAGCAACAGTTTA 59.124 33.333 0.00 0.00 0.00 2.01
2451 2462 8.883731 GTCATTGTAGTATCAGCAACAGTTTAT 58.116 33.333 0.00 0.00 0.00 1.40
2452 2463 9.448438 TCATTGTAGTATCAGCAACAGTTTATT 57.552 29.630 0.00 0.00 0.00 1.40
2796 2807 1.790755 CCGTTGAACGAATCAGACCA 58.209 50.000 20.47 0.00 46.05 4.02
2938 2949 2.573869 CCGTCGATGCAGACCACT 59.426 61.111 0.00 0.00 37.85 4.00
2990 3001 4.485834 CACGCCGGCGCTGTAGTA 62.486 66.667 46.22 0.00 44.19 1.82
2991 3002 3.524606 ACGCCGGCGCTGTAGTAT 61.525 61.111 46.22 23.82 44.19 2.12
2992 3003 2.729862 CGCCGGCGCTGTAGTATC 60.730 66.667 38.48 0.00 0.00 2.24
2993 3004 2.415843 GCCGGCGCTGTAGTATCA 59.584 61.111 12.58 0.00 0.00 2.15
2994 3005 1.661821 GCCGGCGCTGTAGTATCAG 60.662 63.158 12.58 0.00 38.35 2.90
3079 3093 5.865085 ACAGTAGGAAGCTGTTATCACAAA 58.135 37.500 0.00 0.00 43.87 2.83
3080 3094 6.296026 ACAGTAGGAAGCTGTTATCACAAAA 58.704 36.000 0.00 0.00 43.87 2.44
3081 3095 6.770785 ACAGTAGGAAGCTGTTATCACAAAAA 59.229 34.615 0.00 0.00 43.87 1.94
3102 3116 5.391312 AAAATTATTTGACGAGCAAGCCT 57.609 34.783 0.00 0.00 37.87 4.58
3103 3117 6.509418 AAAATTATTTGACGAGCAAGCCTA 57.491 33.333 0.00 0.00 37.87 3.93
3104 3118 6.509418 AAATTATTTGACGAGCAAGCCTAA 57.491 33.333 0.00 0.00 37.87 2.69
3105 3119 4.939509 TTATTTGACGAGCAAGCCTAAC 57.060 40.909 0.00 0.00 37.87 2.34
3106 3120 2.543777 TTTGACGAGCAAGCCTAACT 57.456 45.000 0.00 0.00 37.87 2.24
3107 3121 2.543777 TTGACGAGCAAGCCTAACTT 57.456 45.000 0.00 0.00 40.05 2.66
3108 3122 2.080286 TGACGAGCAAGCCTAACTTC 57.920 50.000 0.00 0.00 36.04 3.01
3109 3123 1.618837 TGACGAGCAAGCCTAACTTCT 59.381 47.619 0.00 0.00 36.04 2.85
3110 3124 2.823747 TGACGAGCAAGCCTAACTTCTA 59.176 45.455 0.00 0.00 36.04 2.10
3111 3125 3.180613 GACGAGCAAGCCTAACTTCTAC 58.819 50.000 0.00 0.00 36.04 2.59
3112 3126 2.826725 ACGAGCAAGCCTAACTTCTACT 59.173 45.455 0.00 0.00 36.04 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.107901 AGGGCATCTCCATCTTTGATCC 59.892 50.000 0.00 0.00 36.21 3.36
17 18 3.505480 AGGGCATCTCCATCTTTGATC 57.495 47.619 0.00 0.00 36.21 2.92
18 19 4.662179 TCTTAGGGCATCTCCATCTTTGAT 59.338 41.667 0.00 0.00 36.21 2.57
23 24 3.342926 AGTCTTAGGGCATCTCCATCT 57.657 47.619 0.00 0.00 36.21 2.90
34 35 8.461249 AATCATCATGATTGAAAGTCTTAGGG 57.539 34.615 12.33 0.00 44.68 3.53
75 76 6.143758 TGAATTGATTGCAAAAGCTTCGTTAC 59.856 34.615 1.71 0.00 37.59 2.50
76 77 6.143758 GTGAATTGATTGCAAAAGCTTCGTTA 59.856 34.615 1.71 0.00 37.59 3.18
77 78 5.049167 TGAATTGATTGCAAAAGCTTCGTT 58.951 33.333 1.71 0.00 37.59 3.85
78 79 4.445385 GTGAATTGATTGCAAAAGCTTCGT 59.555 37.500 1.71 0.00 37.59 3.85
79 80 4.445052 TGTGAATTGATTGCAAAAGCTTCG 59.555 37.500 1.71 0.00 37.59 3.79
83 84 7.745015 ACATTATGTGAATTGATTGCAAAAGC 58.255 30.769 1.71 0.00 37.59 3.51
109 110 6.737750 GTGTGAAAGTTTTGTTTTGCTCAATG 59.262 34.615 0.00 0.00 0.00 2.82
143 144 4.079385 TGTCTTGCCTACCCTAGATGTAGA 60.079 45.833 16.55 1.18 38.34 2.59
146 147 2.766828 GTGTCTTGCCTACCCTAGATGT 59.233 50.000 0.00 0.00 0.00 3.06
148 149 2.032620 CGTGTCTTGCCTACCCTAGAT 58.967 52.381 0.00 0.00 0.00 1.98
149 150 1.471119 CGTGTCTTGCCTACCCTAGA 58.529 55.000 0.00 0.00 0.00 2.43
150 151 0.179108 GCGTGTCTTGCCTACCCTAG 60.179 60.000 0.00 0.00 0.00 3.02
152 153 2.663196 GCGTGTCTTGCCTACCCT 59.337 61.111 0.00 0.00 0.00 4.34
190 191 8.894768 ATTATTTTCACGGAAATTTTTCACCA 57.105 26.923 5.48 0.00 38.92 4.17
224 225 8.137437 GGCAGCACATGTATAACTTAATCATTT 58.863 33.333 0.00 0.00 0.00 2.32
228 232 6.867662 AGGCAGCACATGTATAACTTAATC 57.132 37.500 0.00 0.00 0.00 1.75
249 253 0.465705 ACGATGCCCTGACATGTAGG 59.534 55.000 0.00 6.37 35.01 3.18
254 258 2.945008 CAAACATACGATGCCCTGACAT 59.055 45.455 0.00 0.00 0.00 3.06
283 287 5.733937 GCAAACACAAGTTTATAACACGGGT 60.734 40.000 0.00 0.00 45.80 5.28
286 290 6.798207 TTGCAAACACAAGTTTATAACACG 57.202 33.333 0.00 0.00 45.80 4.49
309 313 7.975616 CTAACAAATTAGCAACATTAGGCATGT 59.024 33.333 0.00 0.00 38.42 3.21
325 329 7.686434 AGTAGGCAAGAAGGACTAACAAATTA 58.314 34.615 0.00 0.00 28.04 1.40
328 332 5.562298 AGTAGGCAAGAAGGACTAACAAA 57.438 39.130 0.00 0.00 28.04 2.83
334 338 1.909986 GGGAAGTAGGCAAGAAGGACT 59.090 52.381 0.00 0.00 0.00 3.85
338 342 1.630878 ACAGGGGAAGTAGGCAAGAAG 59.369 52.381 0.00 0.00 0.00 2.85
339 343 1.742308 ACAGGGGAAGTAGGCAAGAA 58.258 50.000 0.00 0.00 0.00 2.52
344 348 0.696501 TTGGAACAGGGGAAGTAGGC 59.303 55.000 0.00 0.00 42.39 3.93
348 352 5.015178 TCATCTATTTTGGAACAGGGGAAGT 59.985 40.000 0.00 0.00 42.39 3.01
349 353 5.358160 GTCATCTATTTTGGAACAGGGGAAG 59.642 44.000 0.00 0.00 42.39 3.46
350 354 5.261216 GTCATCTATTTTGGAACAGGGGAA 58.739 41.667 0.00 0.00 42.39 3.97
351 355 4.325030 GGTCATCTATTTTGGAACAGGGGA 60.325 45.833 0.00 0.00 42.39 4.81
352 356 3.954258 GGTCATCTATTTTGGAACAGGGG 59.046 47.826 0.00 0.00 42.39 4.79
353 357 3.954258 GGGTCATCTATTTTGGAACAGGG 59.046 47.826 0.00 0.00 42.39 4.45
354 358 4.599041 TGGGTCATCTATTTTGGAACAGG 58.401 43.478 0.00 0.00 42.39 4.00
355 359 6.588719 TTTGGGTCATCTATTTTGGAACAG 57.411 37.500 0.00 0.00 42.39 3.16
356 360 6.127758 CGATTTGGGTCATCTATTTTGGAACA 60.128 38.462 0.00 0.00 0.00 3.18
357 361 6.094881 TCGATTTGGGTCATCTATTTTGGAAC 59.905 38.462 0.00 0.00 0.00 3.62
358 362 6.184068 TCGATTTGGGTCATCTATTTTGGAA 58.816 36.000 0.00 0.00 0.00 3.53
359 363 5.750524 TCGATTTGGGTCATCTATTTTGGA 58.249 37.500 0.00 0.00 0.00 3.53
360 364 6.265577 GTTCGATTTGGGTCATCTATTTTGG 58.734 40.000 0.00 0.00 0.00 3.28
361 365 5.965334 CGTTCGATTTGGGTCATCTATTTTG 59.035 40.000 0.00 0.00 0.00 2.44
362 366 5.065988 CCGTTCGATTTGGGTCATCTATTTT 59.934 40.000 0.00 0.00 0.00 1.82
363 367 4.574828 CCGTTCGATTTGGGTCATCTATTT 59.425 41.667 0.00 0.00 0.00 1.40
364 368 4.127171 CCGTTCGATTTGGGTCATCTATT 58.873 43.478 0.00 0.00 0.00 1.73
365 369 3.728845 CCGTTCGATTTGGGTCATCTAT 58.271 45.455 0.00 0.00 0.00 1.98
366 370 2.740580 GCCGTTCGATTTGGGTCATCTA 60.741 50.000 0.00 0.00 0.00 1.98
367 371 2.012051 GCCGTTCGATTTGGGTCATCT 61.012 52.381 0.00 0.00 0.00 2.90
368 372 0.377203 GCCGTTCGATTTGGGTCATC 59.623 55.000 0.00 0.00 0.00 2.92
369 373 1.029947 GGCCGTTCGATTTGGGTCAT 61.030 55.000 0.00 0.00 0.00 3.06
370 374 1.673009 GGCCGTTCGATTTGGGTCA 60.673 57.895 0.00 0.00 0.00 4.02
371 375 1.673009 TGGCCGTTCGATTTGGGTC 60.673 57.895 0.00 0.00 0.00 4.46
372 376 1.969589 GTGGCCGTTCGATTTGGGT 60.970 57.895 0.00 0.00 0.00 4.51
373 377 1.674322 AGTGGCCGTTCGATTTGGG 60.674 57.895 0.00 0.00 0.00 4.12
374 378 0.953471 TCAGTGGCCGTTCGATTTGG 60.953 55.000 0.00 0.00 0.00 3.28
375 379 0.443869 CTCAGTGGCCGTTCGATTTG 59.556 55.000 0.00 0.00 0.00 2.32
376 380 0.673644 CCTCAGTGGCCGTTCGATTT 60.674 55.000 0.00 0.00 0.00 2.17
385 389 1.131638 TATCCATCACCTCAGTGGCC 58.868 55.000 0.00 0.00 44.64 5.36
406 410 0.671781 AACCAGCTGATGACTCACGC 60.672 55.000 17.39 0.00 0.00 5.34
421 425 2.304761 AGGAATCGCTACCTTTCAACCA 59.695 45.455 0.00 0.00 31.95 3.67
454 458 8.229137 CGATTTACTGGTATTTTCACCGTTAAA 58.771 33.333 0.00 0.00 41.88 1.52
484 488 9.939802 GACTACCAGTATTCTCCTTTCTTTTTA 57.060 33.333 0.00 0.00 0.00 1.52
656 665 7.764443 TGGTCTCATAGAATTCTTTTCCTAACG 59.236 37.037 14.36 0.00 0.00 3.18
657 666 9.103861 CTGGTCTCATAGAATTCTTTTCCTAAC 57.896 37.037 14.36 4.25 0.00 2.34
658 667 8.267894 CCTGGTCTCATAGAATTCTTTTCCTAA 58.732 37.037 14.36 0.00 0.00 2.69
659 668 7.403231 ACCTGGTCTCATAGAATTCTTTTCCTA 59.597 37.037 14.36 0.00 0.00 2.94
660 669 6.216456 ACCTGGTCTCATAGAATTCTTTTCCT 59.784 38.462 14.36 0.00 0.00 3.36
661 670 6.418946 ACCTGGTCTCATAGAATTCTTTTCC 58.581 40.000 14.36 8.65 0.00 3.13
662 671 7.334858 AGACCTGGTCTCATAGAATTCTTTTC 58.665 38.462 23.49 0.00 38.71 2.29
663 672 7.264294 AGACCTGGTCTCATAGAATTCTTTT 57.736 36.000 23.49 0.00 38.71 2.27
664 673 6.882768 AGACCTGGTCTCATAGAATTCTTT 57.117 37.500 23.49 2.41 38.71 2.52
677 686 0.827925 TCTTGCGTGAGACCTGGTCT 60.828 55.000 28.70 28.70 46.42 3.85
678 687 0.667792 GTCTTGCGTGAGACCTGGTC 60.668 60.000 19.20 19.20 40.10 4.02
679 688 1.367840 GTCTTGCGTGAGACCTGGT 59.632 57.895 0.00 0.00 40.10 4.00
680 689 4.268687 GTCTTGCGTGAGACCTGG 57.731 61.111 8.56 0.00 40.10 4.45
684 693 1.733399 GACGGGTCTTGCGTGAGAC 60.733 63.158 10.63 10.63 44.20 3.36
685 694 2.649034 GACGGGTCTTGCGTGAGA 59.351 61.111 0.00 0.00 0.00 3.27
686 695 2.432628 GGACGGGTCTTGCGTGAG 60.433 66.667 0.00 0.00 0.00 3.51
687 696 2.915659 AGGACGGGTCTTGCGTGA 60.916 61.111 0.00 0.00 0.00 4.35
688 697 2.507110 ATCAGGACGGGTCTTGCGTG 62.507 60.000 6.10 0.00 36.72 5.34
689 698 2.283529 ATCAGGACGGGTCTTGCGT 61.284 57.895 6.10 0.00 36.72 5.24
690 699 1.811266 CATCAGGACGGGTCTTGCG 60.811 63.158 6.10 0.00 36.72 4.85
691 700 1.450312 CCATCAGGACGGGTCTTGC 60.450 63.158 6.10 0.00 36.72 4.01
692 701 2.286826 TCCATCAGGACGGGTCTTG 58.713 57.895 4.70 4.70 39.61 3.02
693 702 4.887957 TCCATCAGGACGGGTCTT 57.112 55.556 0.00 0.00 39.61 3.01
702 711 1.315690 GCCATGTGTCATCCATCAGG 58.684 55.000 0.00 0.00 0.00 3.86
703 712 2.047002 TGCCATGTGTCATCCATCAG 57.953 50.000 0.00 0.00 0.00 2.90
704 713 2.740506 ATGCCATGTGTCATCCATCA 57.259 45.000 0.00 0.00 0.00 3.07
705 714 2.953648 TGAATGCCATGTGTCATCCATC 59.046 45.455 0.00 0.00 0.00 3.51
706 715 2.691526 GTGAATGCCATGTGTCATCCAT 59.308 45.455 0.00 0.00 0.00 3.41
707 716 2.093890 GTGAATGCCATGTGTCATCCA 58.906 47.619 0.00 0.00 0.00 3.41
708 717 2.093890 TGTGAATGCCATGTGTCATCC 58.906 47.619 0.00 0.00 0.00 3.51
709 718 3.853831 TTGTGAATGCCATGTGTCATC 57.146 42.857 0.00 0.00 0.00 2.92
710 719 4.221041 TGATTTGTGAATGCCATGTGTCAT 59.779 37.500 0.00 0.00 0.00 3.06
711 720 3.573110 TGATTTGTGAATGCCATGTGTCA 59.427 39.130 0.00 0.00 0.00 3.58
712 721 3.922240 GTGATTTGTGAATGCCATGTGTC 59.078 43.478 0.00 0.00 0.00 3.67
713 722 3.321396 TGTGATTTGTGAATGCCATGTGT 59.679 39.130 0.00 0.00 0.00 3.72
714 723 3.915536 TGTGATTTGTGAATGCCATGTG 58.084 40.909 0.00 0.00 0.00 3.21
715 724 4.603989 TTGTGATTTGTGAATGCCATGT 57.396 36.364 0.00 0.00 0.00 3.21
716 725 4.142988 GCTTTGTGATTTGTGAATGCCATG 60.143 41.667 0.00 0.00 0.00 3.66
717 726 3.998341 GCTTTGTGATTTGTGAATGCCAT 59.002 39.130 0.00 0.00 0.00 4.40
718 727 3.181468 TGCTTTGTGATTTGTGAATGCCA 60.181 39.130 0.00 0.00 0.00 4.92
719 728 3.391965 TGCTTTGTGATTTGTGAATGCC 58.608 40.909 0.00 0.00 0.00 4.40
720 729 4.092383 GGATGCTTTGTGATTTGTGAATGC 59.908 41.667 0.00 0.00 0.00 3.56
721 730 5.231702 TGGATGCTTTGTGATTTGTGAATG 58.768 37.500 0.00 0.00 0.00 2.67
722 731 5.471556 TGGATGCTTTGTGATTTGTGAAT 57.528 34.783 0.00 0.00 0.00 2.57
723 732 4.933505 TGGATGCTTTGTGATTTGTGAA 57.066 36.364 0.00 0.00 0.00 3.18
724 733 4.082081 GGATGGATGCTTTGTGATTTGTGA 60.082 41.667 0.00 0.00 0.00 3.58
725 734 4.178540 GGATGGATGCTTTGTGATTTGTG 58.821 43.478 0.00 0.00 0.00 3.33
726 735 3.196254 GGGATGGATGCTTTGTGATTTGT 59.804 43.478 0.00 0.00 0.00 2.83
727 736 3.196039 TGGGATGGATGCTTTGTGATTTG 59.804 43.478 0.00 0.00 0.00 2.32
728 737 3.196254 GTGGGATGGATGCTTTGTGATTT 59.804 43.478 0.00 0.00 0.00 2.17
729 738 2.762327 GTGGGATGGATGCTTTGTGATT 59.238 45.455 0.00 0.00 0.00 2.57
730 739 2.381911 GTGGGATGGATGCTTTGTGAT 58.618 47.619 0.00 0.00 0.00 3.06
731 740 1.616725 GGTGGGATGGATGCTTTGTGA 60.617 52.381 0.00 0.00 0.00 3.58
732 741 0.819582 GGTGGGATGGATGCTTTGTG 59.180 55.000 0.00 0.00 0.00 3.33
733 742 0.324645 GGGTGGGATGGATGCTTTGT 60.325 55.000 0.00 0.00 0.00 2.83
734 743 1.044790 GGGGTGGGATGGATGCTTTG 61.045 60.000 0.00 0.00 0.00 2.77
735 744 1.311059 GGGGTGGGATGGATGCTTT 59.689 57.895 0.00 0.00 0.00 3.51
736 745 2.704424 GGGGGTGGGATGGATGCTT 61.704 63.158 0.00 0.00 0.00 3.91
737 746 3.105928 GGGGGTGGGATGGATGCT 61.106 66.667 0.00 0.00 0.00 3.79
753 762 2.173569 CTCCTCCCCTGATTTAAGTGGG 59.826 54.545 0.00 0.00 39.37 4.61
754 763 3.115390 TCTCCTCCCCTGATTTAAGTGG 58.885 50.000 0.00 0.00 0.00 4.00
755 764 4.033709 TCTCTCCTCCCCTGATTTAAGTG 58.966 47.826 0.00 0.00 0.00 3.16
756 765 4.354208 TCTCTCCTCCCCTGATTTAAGT 57.646 45.455 0.00 0.00 0.00 2.24
757 766 5.903198 AATCTCTCCTCCCCTGATTTAAG 57.097 43.478 0.00 0.00 0.00 1.85
758 767 7.765149 TTTAATCTCTCCTCCCCTGATTTAA 57.235 36.000 0.00 0.00 0.00 1.52
759 768 7.692789 GCATTTAATCTCTCCTCCCCTGATTTA 60.693 40.741 0.00 0.00 0.00 1.40
760 769 6.608922 CATTTAATCTCTCCTCCCCTGATTT 58.391 40.000 0.00 0.00 0.00 2.17
761 770 5.457342 GCATTTAATCTCTCCTCCCCTGATT 60.457 44.000 0.00 0.00 0.00 2.57
762 771 4.042684 GCATTTAATCTCTCCTCCCCTGAT 59.957 45.833 0.00 0.00 0.00 2.90
763 772 3.392616 GCATTTAATCTCTCCTCCCCTGA 59.607 47.826 0.00 0.00 0.00 3.86
764 773 3.393941 AGCATTTAATCTCTCCTCCCCTG 59.606 47.826 0.00 0.00 0.00 4.45
765 774 3.674477 AGCATTTAATCTCTCCTCCCCT 58.326 45.455 0.00 0.00 0.00 4.79
766 775 4.445557 AAGCATTTAATCTCTCCTCCCC 57.554 45.455 0.00 0.00 0.00 4.81
767 776 5.440610 TCAAAGCATTTAATCTCTCCTCCC 58.559 41.667 0.00 0.00 35.03 4.30
768 777 6.352516 TCTCAAAGCATTTAATCTCTCCTCC 58.647 40.000 0.00 0.00 35.03 4.30
769 778 8.449251 AATCTCAAAGCATTTAATCTCTCCTC 57.551 34.615 0.00 0.00 35.03 3.71
770 779 8.684520 CAAATCTCAAAGCATTTAATCTCTCCT 58.315 33.333 0.00 0.00 35.03 3.69
771 780 8.465201 ACAAATCTCAAAGCATTTAATCTCTCC 58.535 33.333 0.00 0.00 35.03 3.71
772 781 9.286946 CACAAATCTCAAAGCATTTAATCTCTC 57.713 33.333 0.00 0.00 35.03 3.20
773 782 9.017509 TCACAAATCTCAAAGCATTTAATCTCT 57.982 29.630 0.00 0.00 35.03 3.10
774 783 9.630098 TTCACAAATCTCAAAGCATTTAATCTC 57.370 29.630 0.00 0.00 35.03 2.75
777 786 8.662141 GCATTCACAAATCTCAAAGCATTTAAT 58.338 29.630 0.00 0.00 35.03 1.40
778 787 7.118101 GGCATTCACAAATCTCAAAGCATTTAA 59.882 33.333 0.00 0.00 35.03 1.52
779 788 6.591062 GGCATTCACAAATCTCAAAGCATTTA 59.409 34.615 0.00 0.00 35.03 1.40
780 789 5.410439 GGCATTCACAAATCTCAAAGCATTT 59.590 36.000 0.00 0.00 40.26 2.32
781 790 4.933400 GGCATTCACAAATCTCAAAGCATT 59.067 37.500 0.00 0.00 0.00 3.56
782 791 4.020928 TGGCATTCACAAATCTCAAAGCAT 60.021 37.500 0.00 0.00 0.00 3.79
783 792 3.321396 TGGCATTCACAAATCTCAAAGCA 59.679 39.130 0.00 0.00 0.00 3.91
784 793 3.676646 GTGGCATTCACAAATCTCAAAGC 59.323 43.478 0.00 0.00 45.39 3.51
785 794 3.916172 CGTGGCATTCACAAATCTCAAAG 59.084 43.478 0.00 0.00 46.36 2.77
786 795 3.317711 ACGTGGCATTCACAAATCTCAAA 59.682 39.130 0.00 0.00 46.36 2.69
787 796 2.884012 ACGTGGCATTCACAAATCTCAA 59.116 40.909 0.00 0.00 46.36 3.02
788 797 2.226200 CACGTGGCATTCACAAATCTCA 59.774 45.455 7.95 0.00 46.36 3.27
789 798 2.226437 ACACGTGGCATTCACAAATCTC 59.774 45.455 21.57 0.00 46.36 2.75
790 799 2.226437 GACACGTGGCATTCACAAATCT 59.774 45.455 18.77 0.00 46.36 2.40
791 800 2.031245 TGACACGTGGCATTCACAAATC 60.031 45.455 23.03 3.54 46.36 2.17
792 801 1.952990 TGACACGTGGCATTCACAAAT 59.047 42.857 23.03 0.00 46.36 2.32
793 802 1.383523 TGACACGTGGCATTCACAAA 58.616 45.000 23.03 0.00 46.36 2.83
794 803 1.535028 GATGACACGTGGCATTCACAA 59.465 47.619 36.07 8.22 45.42 3.33
795 804 1.155889 GATGACACGTGGCATTCACA 58.844 50.000 36.07 9.07 45.42 3.58
796 805 0.447801 GGATGACACGTGGCATTCAC 59.552 55.000 36.07 24.74 45.42 3.18
797 806 0.036022 TGGATGACACGTGGCATTCA 59.964 50.000 36.64 36.64 46.54 2.57
798 807 1.331756 GATGGATGACACGTGGCATTC 59.668 52.381 36.07 34.16 45.42 2.67
799 808 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
801 810 0.391528 CTGATGGATGACACGTGGCA 60.392 55.000 29.28 29.28 37.54 4.92
802 811 1.091771 CCTGATGGATGACACGTGGC 61.092 60.000 21.57 19.24 34.57 5.01
803 812 0.462581 CCCTGATGGATGACACGTGG 60.463 60.000 21.57 1.66 35.39 4.94
804 813 1.091771 GCCCTGATGGATGACACGTG 61.092 60.000 15.48 15.48 35.39 4.49
805 814 1.221840 GCCCTGATGGATGACACGT 59.778 57.895 0.00 0.00 35.39 4.49
806 815 1.884464 CGCCCTGATGGATGACACG 60.884 63.158 0.00 0.00 35.39 4.49
807 816 1.524621 CCGCCCTGATGGATGACAC 60.525 63.158 0.00 0.00 35.39 3.67
808 817 2.745308 CCCGCCCTGATGGATGACA 61.745 63.158 0.00 0.00 35.39 3.58
809 818 2.111878 CCCGCCCTGATGGATGAC 59.888 66.667 0.00 0.00 35.39 3.06
810 819 2.366837 ACCCGCCCTGATGGATGA 60.367 61.111 0.00 0.00 35.39 2.92
811 820 2.111878 GACCCGCCCTGATGGATG 59.888 66.667 0.00 0.00 35.39 3.51
812 821 2.040464 AGACCCGCCCTGATGGAT 60.040 61.111 0.00 0.00 35.39 3.41
813 822 2.764128 GAGACCCGCCCTGATGGA 60.764 66.667 0.00 0.00 35.39 3.41
814 823 3.083349 TGAGACCCGCCCTGATGG 61.083 66.667 0.00 0.00 37.09 3.51
815 824 1.976132 ATGTGAGACCCGCCCTGATG 61.976 60.000 0.00 0.00 0.00 3.07
816 825 1.690633 ATGTGAGACCCGCCCTGAT 60.691 57.895 0.00 0.00 0.00 2.90
817 826 2.284625 ATGTGAGACCCGCCCTGA 60.285 61.111 0.00 0.00 0.00 3.86
818 827 2.124983 CATGTGAGACCCGCCCTG 60.125 66.667 0.00 0.00 0.00 4.45
819 828 4.101448 GCATGTGAGACCCGCCCT 62.101 66.667 0.00 0.00 0.00 5.19
820 829 2.252072 TTAGCATGTGAGACCCGCCC 62.252 60.000 0.00 0.00 0.00 6.13
821 830 1.090052 GTTAGCATGTGAGACCCGCC 61.090 60.000 0.00 0.00 0.00 6.13
822 831 1.090052 GGTTAGCATGTGAGACCCGC 61.090 60.000 0.00 0.00 0.00 6.13
823 832 0.806102 CGGTTAGCATGTGAGACCCG 60.806 60.000 0.00 0.00 0.00 5.28
824 833 0.249398 ACGGTTAGCATGTGAGACCC 59.751 55.000 0.00 0.00 0.00 4.46
825 834 1.067142 TCACGGTTAGCATGTGAGACC 60.067 52.381 0.00 0.00 37.69 3.85
826 835 2.363788 TCACGGTTAGCATGTGAGAC 57.636 50.000 0.00 0.00 37.69 3.36
829 838 1.067142 GGTCTCACGGTTAGCATGTGA 60.067 52.381 0.00 4.33 40.12 3.58
830 839 1.066858 AGGTCTCACGGTTAGCATGTG 60.067 52.381 0.00 0.00 34.96 3.21
831 840 1.066858 CAGGTCTCACGGTTAGCATGT 60.067 52.381 0.00 0.00 0.00 3.21
832 841 1.645034 CAGGTCTCACGGTTAGCATG 58.355 55.000 0.00 0.00 0.00 4.06
833 842 0.537188 CCAGGTCTCACGGTTAGCAT 59.463 55.000 0.00 0.00 0.00 3.79
834 843 0.830444 ACCAGGTCTCACGGTTAGCA 60.830 55.000 0.00 0.00 0.00 3.49
835 844 0.108756 GACCAGGTCTCACGGTTAGC 60.109 60.000 12.94 0.00 31.63 3.09
836 845 1.546961 AGACCAGGTCTCACGGTTAG 58.453 55.000 17.31 0.00 38.71 2.34
837 846 3.759865 AGACCAGGTCTCACGGTTA 57.240 52.632 17.31 0.00 38.71 2.85
838 847 4.621269 AGACCAGGTCTCACGGTT 57.379 55.556 17.31 0.00 38.71 4.44
866 875 2.114411 AAGAGCGGCGGGGAAAAA 59.886 55.556 9.78 0.00 0.00 1.94
867 876 2.478335 ATCAAGAGCGGCGGGGAAAA 62.478 55.000 9.78 0.00 0.00 2.29
868 877 1.618876 TATCAAGAGCGGCGGGGAAA 61.619 55.000 9.78 0.00 0.00 3.13
869 878 1.618876 TTATCAAGAGCGGCGGGGAA 61.619 55.000 9.78 0.00 0.00 3.97
870 879 1.618876 TTTATCAAGAGCGGCGGGGA 61.619 55.000 9.78 0.00 0.00 4.81
871 880 0.746563 TTTTATCAAGAGCGGCGGGG 60.747 55.000 9.78 0.00 0.00 5.73
872 881 1.264288 GATTTTATCAAGAGCGGCGGG 59.736 52.381 9.78 0.00 0.00 6.13
873 882 1.070577 CGATTTTATCAAGAGCGGCGG 60.071 52.381 9.78 0.00 0.00 6.13
874 883 1.070577 CCGATTTTATCAAGAGCGGCG 60.071 52.381 0.51 0.51 0.00 6.46
875 884 2.210116 TCCGATTTTATCAAGAGCGGC 58.790 47.619 1.67 0.00 37.36 6.53
876 885 3.717707 TCTCCGATTTTATCAAGAGCGG 58.282 45.455 0.00 0.00 38.68 5.52
1680 1690 2.588596 CACACAGCACACTCGGCA 60.589 61.111 0.00 0.00 0.00 5.69
2153 2163 1.448985 TCCGATACAAAAGGCTGTGC 58.551 50.000 0.00 0.00 0.00 4.57
2202 2213 6.963805 GCTACAATCAAAGAGTTATGAACAGC 59.036 38.462 0.00 0.00 0.00 4.40
2453 2464 5.470437 TGAGACACGTATTACCATGCAAAAA 59.530 36.000 0.00 0.00 0.00 1.94
2542 2553 1.001520 TGTGCAAAGGCTAGCGTTCTA 59.998 47.619 21.95 9.47 41.91 2.10
2938 2949 0.469892 TCCAGGAGCGGATGCAGATA 60.470 55.000 0.00 0.00 46.23 1.98
2995 3006 6.306356 GTCTTAACAAGCATATGCAACTGTTG 59.694 38.462 31.97 26.50 45.16 3.33
2996 3007 6.207417 AGTCTTAACAAGCATATGCAACTGTT 59.793 34.615 29.61 29.61 45.16 3.16
3079 3093 5.783111 AGGCTTGCTCGTCAAATAATTTTT 58.217 33.333 0.00 0.00 33.65 1.94
3080 3094 5.391312 AGGCTTGCTCGTCAAATAATTTT 57.609 34.783 0.00 0.00 33.65 1.82
3081 3095 6.151144 AGTTAGGCTTGCTCGTCAAATAATTT 59.849 34.615 0.00 0.00 33.65 1.82
3082 3096 5.648092 AGTTAGGCTTGCTCGTCAAATAATT 59.352 36.000 0.00 0.00 33.65 1.40
3083 3097 5.186198 AGTTAGGCTTGCTCGTCAAATAAT 58.814 37.500 0.00 0.00 33.65 1.28
3084 3098 4.575885 AGTTAGGCTTGCTCGTCAAATAA 58.424 39.130 0.00 0.00 33.65 1.40
3085 3099 4.202245 AGTTAGGCTTGCTCGTCAAATA 57.798 40.909 0.00 0.00 33.65 1.40
3086 3100 3.059352 AGTTAGGCTTGCTCGTCAAAT 57.941 42.857 0.00 0.00 33.65 2.32
3087 3101 2.543777 AGTTAGGCTTGCTCGTCAAA 57.456 45.000 0.00 0.00 33.65 2.69
3088 3102 2.037251 AGAAGTTAGGCTTGCTCGTCAA 59.963 45.455 0.00 0.00 37.59 3.18
3089 3103 1.618837 AGAAGTTAGGCTTGCTCGTCA 59.381 47.619 0.00 0.00 37.59 4.35
3090 3104 2.371910 AGAAGTTAGGCTTGCTCGTC 57.628 50.000 0.00 0.00 37.59 4.20
3091 3105 2.826725 AGTAGAAGTTAGGCTTGCTCGT 59.173 45.455 0.00 0.00 37.59 4.18
3092 3106 3.512033 AGTAGAAGTTAGGCTTGCTCG 57.488 47.619 0.00 0.00 37.59 5.03


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

AutoCloner maintained by Alex Coulton.