Multiple sequence alignment - TraesCS3A01G345100

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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 TraesCS3A01G345100 chr3A 100.000 3089 0 0 1 3089 594592569 594589481 0.000000e+00 5705
1 TraesCS3A01G345100 chr3D 89.498 2171 97 54 364 2445 452241810 452239682 0.000000e+00 2625
2 TraesCS3A01G345100 chr3D 85.833 360 24 13 1 354 452242196 452241858 1.050000e-94 357
3 TraesCS3A01G345100 chr3D 94.472 199 7 3 2890 3088 452239180 452238986 1.390000e-78 303
4 TraesCS3A01G345100 chr3B 89.159 2177 97 57 364 2446 593923156 593921025 0.000000e+00 2584
5 TraesCS3A01G345100 chr3B 91.218 353 19 5 2734 3086 593920908 593920568 1.300000e-128 470
6 TraesCS3A01G345100 chr3B 86.757 370 21 11 1 368 593923532 593923189 1.340000e-103 387
7 TraesCS3A01G345100 chr1D 82.500 200 30 5 1877 2073 397631164 397631361 1.470000e-38 171
8 TraesCS3A01G345100 chr1B 82.500 200 30 5 1877 2073 533089619 533089816 1.470000e-38 171
9 TraesCS3A01G345100 chr1A 82.500 200 30 5 1877 2073 495130435 495130632 1.470000e-38 171


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 TraesCS3A01G345100 chr3A 594589481 594592569 3088 True 5705 5705 100.000000 1 3089 1 chr3A.!!$R1 3088
1 TraesCS3A01G345100 chr3D 452238986 452242196 3210 True 1095 2625 89.934333 1 3088 3 chr3D.!!$R1 3087
2 TraesCS3A01G345100 chr3B 593920568 593923532 2964 True 1147 2584 89.044667 1 3086 3 chr3B.!!$R1 3085

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
192 199 0.036858 GAACCCAGAGTCCAGACTGC 60.037 60.0 4.74 0.0 42.66 4.40 F
532 592 0.380378 ACAAACACATCACACGCACC 59.620 50.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1587 0.169230 CTTGAGAGTCTCGTCACCCG 59.831 60.0 15.34 0.0 32.35 5.28 R
2240 2408 0.106521 GGAGAGGAGAAGAGCATGGC 59.893 60.0 0.00 0.0 0.00 4.40 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
63 64 5.122869 ACAGGATCAATGTGAATCGTCTTTG 59.877 40.000 2.26 0.00 0.00 2.77
87 94 4.933064 GCTCGATCGCCAGGACCG 62.933 72.222 11.09 0.00 0.00 4.79
88 95 3.518998 CTCGATCGCCAGGACCGT 61.519 66.667 11.09 0.00 0.00 4.83
113 120 4.047822 CAGCGGATTCATTCACTAGTCTC 58.952 47.826 0.00 0.00 0.00 3.36
182 189 0.324285 AGCAAGCAGAGAACCCAGAG 59.676 55.000 0.00 0.00 0.00 3.35
184 191 1.943507 GCAAGCAGAGAACCCAGAGTC 60.944 57.143 0.00 0.00 0.00 3.36
185 192 0.980423 AAGCAGAGAACCCAGAGTCC 59.020 55.000 0.00 0.00 0.00 3.85
186 193 0.178921 AGCAGAGAACCCAGAGTCCA 60.179 55.000 0.00 0.00 0.00 4.02
187 194 0.248843 GCAGAGAACCCAGAGTCCAG 59.751 60.000 0.00 0.00 0.00 3.86
188 195 1.930251 CAGAGAACCCAGAGTCCAGA 58.070 55.000 0.00 0.00 0.00 3.86
189 196 1.548269 CAGAGAACCCAGAGTCCAGAC 59.452 57.143 0.00 0.00 0.00 3.51
190 197 1.431243 AGAGAACCCAGAGTCCAGACT 59.569 52.381 0.00 0.00 45.84 3.24
191 198 1.548269 GAGAACCCAGAGTCCAGACTG 59.452 57.143 4.74 0.00 42.66 3.51
192 199 0.036858 GAACCCAGAGTCCAGACTGC 60.037 60.000 4.74 0.00 42.66 4.40
205 213 1.592669 GACTGCCCGACCGATCATG 60.593 63.158 0.00 0.00 0.00 3.07
266 274 3.934391 AACCGCCACTGCTCGCTAC 62.934 63.158 0.00 0.00 34.43 3.58
267 275 4.135153 CCGCCACTGCTCGCTACT 62.135 66.667 0.00 0.00 34.43 2.57
268 276 2.580867 CGCCACTGCTCGCTACTC 60.581 66.667 0.00 0.00 34.43 2.59
269 277 2.888863 GCCACTGCTCGCTACTCT 59.111 61.111 0.00 0.00 33.53 3.24
270 278 1.216710 GCCACTGCTCGCTACTCTT 59.783 57.895 0.00 0.00 33.53 2.85
271 279 0.456221 GCCACTGCTCGCTACTCTTA 59.544 55.000 0.00 0.00 33.53 2.10
272 280 1.067821 GCCACTGCTCGCTACTCTTAT 59.932 52.381 0.00 0.00 33.53 1.73
273 281 2.860582 GCCACTGCTCGCTACTCTTATC 60.861 54.545 0.00 0.00 33.53 1.75
274 282 2.621055 CCACTGCTCGCTACTCTTATCT 59.379 50.000 0.00 0.00 0.00 1.98
275 283 3.304391 CCACTGCTCGCTACTCTTATCTC 60.304 52.174 0.00 0.00 0.00 2.75
276 284 2.546368 ACTGCTCGCTACTCTTATCTCG 59.454 50.000 0.00 0.00 0.00 4.04
277 285 1.264557 TGCTCGCTACTCTTATCTCGC 59.735 52.381 0.00 0.00 0.00 5.03
278 286 1.264557 GCTCGCTACTCTTATCTCGCA 59.735 52.381 0.00 0.00 0.00 5.10
279 287 2.664424 GCTCGCTACTCTTATCTCGCAG 60.664 54.545 0.00 0.00 0.00 5.18
298 306 3.023832 CAGGGCGATGGAAATAAAAGGT 58.976 45.455 0.00 0.00 0.00 3.50
306 314 7.148705 GGCGATGGAAATAAAAGGTTTGTTTAC 60.149 37.037 0.00 0.00 0.00 2.01
311 319 5.532664 AATAAAAGGTTTGTTTACCGGCA 57.467 34.783 0.00 0.00 43.21 5.69
312 320 5.731957 ATAAAAGGTTTGTTTACCGGCAT 57.268 34.783 0.00 0.00 43.21 4.40
313 321 3.653539 AAAGGTTTGTTTACCGGCATC 57.346 42.857 0.00 0.00 43.21 3.91
314 322 2.279935 AGGTTTGTTTACCGGCATCA 57.720 45.000 0.00 0.00 43.21 3.07
322 330 1.558167 TTACCGGCATCAAGCTCCCA 61.558 55.000 0.00 0.00 44.79 4.37
351 359 3.014369 GCTTTCAGCGCGCAAATTA 57.986 47.368 35.10 13.14 0.00 1.40
354 362 2.222354 GCTTTCAGCGCGCAAATTAAAG 60.222 45.455 35.10 28.98 0.00 1.85
355 363 1.975837 TTCAGCGCGCAAATTAAAGG 58.024 45.000 35.10 10.34 0.00 3.11
356 364 0.878416 TCAGCGCGCAAATTAAAGGT 59.122 45.000 35.10 4.83 0.00 3.50
357 365 1.268352 TCAGCGCGCAAATTAAAGGTT 59.732 42.857 35.10 4.19 0.00 3.50
358 366 1.386412 CAGCGCGCAAATTAAAGGTTG 59.614 47.619 35.10 14.18 0.00 3.77
360 368 2.094752 AGCGCGCAAATTAAAGGTTGAT 60.095 40.909 35.10 2.61 0.00 2.57
361 369 2.027926 GCGCGCAAATTAAAGGTTGATG 59.972 45.455 29.10 0.00 0.00 3.07
362 370 3.497118 CGCGCAAATTAAAGGTTGATGA 58.503 40.909 8.75 0.00 0.00 2.92
367 421 6.183360 GCGCAAATTAAAGGTTGATGAGAAAG 60.183 38.462 0.30 0.00 0.00 2.62
374 428 5.596836 AAGGTTGATGAGAAAGCAAACAA 57.403 34.783 0.00 0.00 44.61 2.83
392 446 2.424601 ACAAGCCATTCATGTCAATCCG 59.575 45.455 0.00 0.00 0.00 4.18
396 450 3.567164 AGCCATTCATGTCAATCCGATTC 59.433 43.478 0.00 0.00 0.00 2.52
397 451 3.567164 GCCATTCATGTCAATCCGATTCT 59.433 43.478 0.00 0.00 0.00 2.40
399 453 5.061853 CCATTCATGTCAATCCGATTCTCT 58.938 41.667 0.00 0.00 0.00 3.10
400 454 5.530171 CCATTCATGTCAATCCGATTCTCTT 59.470 40.000 0.00 0.00 0.00 2.85
401 455 6.293298 CCATTCATGTCAATCCGATTCTCTTC 60.293 42.308 0.00 0.00 0.00 2.87
402 456 4.697514 TCATGTCAATCCGATTCTCTTCC 58.302 43.478 0.00 0.00 0.00 3.46
528 588 2.222931 ACGTCAACAAACACATCACACG 60.223 45.455 0.00 0.00 0.00 4.49
530 590 1.740025 TCAACAAACACATCACACGCA 59.260 42.857 0.00 0.00 0.00 5.24
531 591 1.845568 CAACAAACACATCACACGCAC 59.154 47.619 0.00 0.00 0.00 5.34
532 592 0.380378 ACAAACACATCACACGCACC 59.620 50.000 0.00 0.00 0.00 5.01
534 594 1.001487 CAAACACATCACACGCACCAT 60.001 47.619 0.00 0.00 0.00 3.55
535 595 0.874390 AACACATCACACGCACCATC 59.126 50.000 0.00 0.00 0.00 3.51
537 597 1.005037 ACATCACACGCACCATCGT 60.005 52.632 0.00 0.00 44.35 3.73
538 598 1.014044 ACATCACACGCACCATCGTC 61.014 55.000 0.00 0.00 41.21 4.20
542 604 2.880879 CACGCACCATCGTCGGAG 60.881 66.667 0.00 0.00 41.21 4.63
585 647 0.437295 ACGTAAATCAGCGACGCAAC 59.563 50.000 23.70 8.72 40.19 4.17
605 667 4.368808 CCGTTGACACGCGGCTTG 62.369 66.667 12.47 4.78 45.72 4.01
643 722 6.766084 AGAAATGACGACGAAATGATTCTTC 58.234 36.000 0.00 0.00 33.17 2.87
644 723 6.591834 AGAAATGACGACGAAATGATTCTTCT 59.408 34.615 0.00 0.00 33.02 2.85
645 724 6.727824 AATGACGACGAAATGATTCTTCTT 57.272 33.333 0.00 0.00 33.02 2.52
646 725 5.763444 TGACGACGAAATGATTCTTCTTC 57.237 39.130 0.00 0.00 34.58 2.87
679 760 0.750911 GGAGAGTATCGGACGTGGGT 60.751 60.000 0.00 0.00 42.67 4.51
698 788 2.435693 GGTGGGCGCATAGAGAGGT 61.436 63.158 10.83 0.00 0.00 3.85
762 860 1.366366 CCACTCTATTACCCGCCCG 59.634 63.158 0.00 0.00 0.00 6.13
763 861 1.300697 CACTCTATTACCCGCCCGC 60.301 63.158 0.00 0.00 0.00 6.13
764 862 2.342648 CTCTATTACCCGCCCGCC 59.657 66.667 0.00 0.00 0.00 6.13
765 863 3.236003 CTCTATTACCCGCCCGCCC 62.236 68.421 0.00 0.00 0.00 6.13
829 927 3.732849 CCTCCTTCCCCTGCACCC 61.733 72.222 0.00 0.00 0.00 4.61
830 928 3.732849 CTCCTTCCCCTGCACCCC 61.733 72.222 0.00 0.00 0.00 4.95
831 929 4.285790 TCCTTCCCCTGCACCCCT 62.286 66.667 0.00 0.00 0.00 4.79
832 930 3.732849 CCTTCCCCTGCACCCCTC 61.733 72.222 0.00 0.00 0.00 4.30
833 931 3.732849 CTTCCCCTGCACCCCTCC 61.733 72.222 0.00 0.00 0.00 4.30
860 964 3.123620 CCTCGTGCAGAGCAAGCC 61.124 66.667 7.44 0.00 45.54 4.35
878 982 1.011684 CAACGCGAAAACAGCACGA 60.012 52.632 15.93 0.00 34.19 4.35
879 983 0.986874 CAACGCGAAAACAGCACGAG 60.987 55.000 15.93 0.00 34.19 4.18
933 1050 4.348863 TCTTTGCTCTTCTTCTGCTTCT 57.651 40.909 0.00 0.00 0.00 2.85
936 1053 3.758755 TGCTCTTCTTCTGCTTCTTCA 57.241 42.857 0.00 0.00 0.00 3.02
970 1100 2.671070 CATTCCTCTGCCCGGTGT 59.329 61.111 0.00 0.00 0.00 4.16
1026 1156 2.954753 GCACAAGTTCCGGCTGTCG 61.955 63.158 0.00 0.00 38.88 4.35
1186 1316 1.656652 GTCCTACTACTACACGCCGA 58.343 55.000 0.00 0.00 0.00 5.54
1461 1591 3.130160 GGCTACGACGACTCGGGT 61.130 66.667 0.00 0.00 44.80 5.28
1586 1731 4.436998 GAGGCCCGACACCGACAG 62.437 72.222 0.00 0.00 38.22 3.51
1899 2050 2.355363 TTCGCGGTGGTGAAGACG 60.355 61.111 6.13 0.00 37.73 4.18
1963 2114 3.792053 ATCGCGGAGAACGGCATCC 62.792 63.158 6.13 0.00 44.51 3.51
2089 2240 1.825285 CGCGGACATCAGCATGTAGC 61.825 60.000 0.00 6.90 43.79 3.58
2105 2269 4.462417 GCAGCAAGCAGAGCAGCG 62.462 66.667 0.00 0.00 44.79 5.18
2106 2270 4.462417 CAGCAAGCAGAGCAGCGC 62.462 66.667 0.00 0.00 40.15 5.92
2107 2271 4.701290 AGCAAGCAGAGCAGCGCT 62.701 61.111 2.64 2.64 43.88 5.92
2152 2316 1.535462 GTCCCATCGTGTCCAAAGTTG 59.465 52.381 0.00 0.00 0.00 3.16
2153 2317 1.142060 TCCCATCGTGTCCAAAGTTGT 59.858 47.619 0.00 0.00 0.00 3.32
2154 2318 1.535462 CCCATCGTGTCCAAAGTTGTC 59.465 52.381 0.00 0.00 0.00 3.18
2164 2328 1.260561 CCAAAGTTGTCGTCGTCCTTG 59.739 52.381 0.00 0.00 0.00 3.61
2208 2376 9.605951 AATGCTCCTAAATTGGGTATGATAAAT 57.394 29.630 0.00 0.00 0.00 1.40
2240 2408 0.316204 CCAAGCCTGTGAAGCCAAAG 59.684 55.000 0.00 0.00 0.00 2.77
2253 2421 0.455005 GCCAAAGCCATGCTCTTCTC 59.545 55.000 0.00 0.00 38.25 2.87
2269 2437 5.269189 CTCTTCTCCTCTCCTTCTACCTTT 58.731 45.833 0.00 0.00 0.00 3.11
2285 2453 2.289694 ACCTTTGCTGGTAGTGCAGTAG 60.290 50.000 0.18 0.00 41.71 2.57
2286 2454 1.734465 CTTTGCTGGTAGTGCAGTAGC 59.266 52.381 21.29 21.29 41.71 3.58
2302 2470 0.175760 TAGCTGCTCCCGAACATCAC 59.824 55.000 4.91 0.00 0.00 3.06
2322 2494 1.852067 CTGTAACAAGGTGTGGGCGC 61.852 60.000 0.00 0.00 0.00 6.53
2350 2523 4.694037 GTGAACAGTGGGGTAATAACTGAC 59.306 45.833 8.90 3.81 43.22 3.51
2366 2539 4.553330 ACTGACAAAGTATGGTGGTAGG 57.447 45.455 0.00 0.00 37.36 3.18
2371 2544 2.235402 CAAAGTATGGTGGTAGGACCGT 59.765 50.000 0.00 0.00 42.58 4.83
2382 2555 5.302823 GGTGGTAGGACCGTACAAGTAATAT 59.697 44.000 0.00 0.00 42.58 1.28
2395 2573 7.752239 CGTACAAGTAATATAGGATTACGGTGG 59.248 40.741 13.38 4.75 38.96 4.61
2396 2574 7.607615 ACAAGTAATATAGGATTACGGTGGT 57.392 36.000 13.77 5.52 38.96 4.16
2479 2657 8.703604 TCTGAAAGCTGTTATATATTATCGGC 57.296 34.615 0.00 0.00 0.00 5.54
2495 2673 3.432186 GCACCGTGTTGCCTCTTT 58.568 55.556 0.00 0.00 36.42 2.52
2508 2686 2.891580 TGCCTCTTTCGAGTGTTACTCT 59.108 45.455 7.31 0.00 42.92 3.24
2509 2687 3.321111 TGCCTCTTTCGAGTGTTACTCTT 59.679 43.478 7.31 0.00 42.92 2.85
2520 2698 2.343544 GTGTTACTCTTTCGCGCGTAAT 59.656 45.455 30.98 14.12 0.00 1.89
2539 2717 1.384525 TTCCGTGTTGTTGGTTCAGG 58.615 50.000 0.00 0.00 0.00 3.86
2540 2718 0.542333 TCCGTGTTGTTGGTTCAGGA 59.458 50.000 0.00 0.00 0.00 3.86
2541 2719 0.944386 CCGTGTTGTTGGTTCAGGAG 59.056 55.000 0.00 0.00 0.00 3.69
2562 2740 6.660949 AGGAGTACTGCAATTGAAGCTTTTAT 59.339 34.615 17.34 0.00 0.00 1.40
2563 2741 7.177392 AGGAGTACTGCAATTGAAGCTTTTATT 59.823 33.333 17.34 0.55 0.00 1.40
2564 2742 7.814587 GGAGTACTGCAATTGAAGCTTTTATTT 59.185 33.333 13.78 0.00 0.00 1.40
2565 2743 9.840427 GAGTACTGCAATTGAAGCTTTTATTTA 57.160 29.630 13.78 0.00 0.00 1.40
2566 2744 9.846248 AGTACTGCAATTGAAGCTTTTATTTAG 57.154 29.630 13.78 7.07 0.00 1.85
2567 2745 9.076596 GTACTGCAATTGAAGCTTTTATTTAGG 57.923 33.333 13.78 0.00 0.00 2.69
2569 2747 7.599998 ACTGCAATTGAAGCTTTTATTTAGGTG 59.400 33.333 13.78 0.00 0.00 4.00
2570 2748 6.873076 TGCAATTGAAGCTTTTATTTAGGTGG 59.127 34.615 10.34 0.00 0.00 4.61
2571 2749 6.313658 GCAATTGAAGCTTTTATTTAGGTGGG 59.686 38.462 10.34 0.00 0.00 4.61
2573 2751 5.975693 TGAAGCTTTTATTTAGGTGGGTG 57.024 39.130 0.00 0.00 0.00 4.61
2574 2752 5.636123 TGAAGCTTTTATTTAGGTGGGTGA 58.364 37.500 0.00 0.00 0.00 4.02
2575 2753 5.475564 TGAAGCTTTTATTTAGGTGGGTGAC 59.524 40.000 0.00 0.00 0.00 3.67
2591 2769 4.296729 ACCCTCCGGTCCTGACGT 62.297 66.667 0.00 0.00 38.28 4.34
2592 2770 2.995574 CCCTCCGGTCCTGACGTT 60.996 66.667 0.00 0.00 0.00 3.99
2593 2771 2.580601 CCCTCCGGTCCTGACGTTT 61.581 63.158 0.00 0.00 0.00 3.60
2594 2772 1.370064 CCTCCGGTCCTGACGTTTT 59.630 57.895 0.00 0.00 0.00 2.43
2595 2773 0.250166 CCTCCGGTCCTGACGTTTTT 60.250 55.000 0.00 0.00 0.00 1.94
2596 2774 1.145803 CTCCGGTCCTGACGTTTTTC 58.854 55.000 0.00 0.00 0.00 2.29
2597 2775 0.598158 TCCGGTCCTGACGTTTTTCG 60.598 55.000 0.00 0.00 46.00 3.46
2598 2776 0.598158 CCGGTCCTGACGTTTTTCGA 60.598 55.000 0.00 0.00 42.86 3.71
2599 2777 1.425412 CGGTCCTGACGTTTTTCGAT 58.575 50.000 0.00 0.00 42.86 3.59
2600 2778 1.126113 CGGTCCTGACGTTTTTCGATG 59.874 52.381 0.00 0.00 42.86 3.84
2601 2779 1.463444 GGTCCTGACGTTTTTCGATGG 59.537 52.381 0.00 0.00 42.86 3.51
2602 2780 2.140717 GTCCTGACGTTTTTCGATGGT 58.859 47.619 0.00 0.00 42.86 3.55
2603 2781 3.319755 GTCCTGACGTTTTTCGATGGTA 58.680 45.455 0.00 0.00 42.86 3.25
2604 2782 3.742369 GTCCTGACGTTTTTCGATGGTAA 59.258 43.478 0.00 0.00 42.86 2.85
2605 2783 4.390909 GTCCTGACGTTTTTCGATGGTAAT 59.609 41.667 0.00 0.00 42.86 1.89
2606 2784 4.998672 TCCTGACGTTTTTCGATGGTAATT 59.001 37.500 0.00 0.00 42.86 1.40
2607 2785 6.091169 GTCCTGACGTTTTTCGATGGTAATTA 59.909 38.462 0.00 0.00 42.86 1.40
2608 2786 6.091169 TCCTGACGTTTTTCGATGGTAATTAC 59.909 38.462 7.09 7.09 42.86 1.89
2609 2787 6.128499 CCTGACGTTTTTCGATGGTAATTACA 60.128 38.462 17.16 4.33 42.86 2.41
2610 2788 6.823531 TGACGTTTTTCGATGGTAATTACAG 58.176 36.000 17.16 5.77 42.86 2.74
2611 2789 6.424509 TGACGTTTTTCGATGGTAATTACAGT 59.575 34.615 17.16 4.93 42.86 3.55
2612 2790 6.824557 ACGTTTTTCGATGGTAATTACAGTC 58.175 36.000 17.16 12.32 42.86 3.51
2613 2791 6.424509 ACGTTTTTCGATGGTAATTACAGTCA 59.575 34.615 17.16 6.71 42.86 3.41
2614 2792 6.735063 CGTTTTTCGATGGTAATTACAGTCAC 59.265 38.462 17.16 7.18 42.86 3.67
2615 2793 7.569774 CGTTTTTCGATGGTAATTACAGTCACA 60.570 37.037 17.16 6.02 42.86 3.58
2616 2794 7.915293 TTTTCGATGGTAATTACAGTCACAT 57.085 32.000 17.16 10.33 0.00 3.21
2617 2795 9.438228 TTTTTCGATGGTAATTACAGTCACATA 57.562 29.630 17.16 0.00 0.00 2.29
2618 2796 9.438228 TTTTCGATGGTAATTACAGTCACATAA 57.562 29.630 17.16 1.64 0.00 1.90
2619 2797 8.642908 TTCGATGGTAATTACAGTCACATAAG 57.357 34.615 17.16 8.47 0.00 1.73
2620 2798 7.207383 TCGATGGTAATTACAGTCACATAAGG 58.793 38.462 17.16 4.91 0.00 2.69
2621 2799 7.068962 TCGATGGTAATTACAGTCACATAAGGA 59.931 37.037 17.16 6.72 0.00 3.36
2622 2800 7.872993 CGATGGTAATTACAGTCACATAAGGAT 59.127 37.037 17.16 0.00 0.00 3.24
2623 2801 8.908786 ATGGTAATTACAGTCACATAAGGATG 57.091 34.615 17.16 0.00 39.16 3.51
2624 2802 7.279615 TGGTAATTACAGTCACATAAGGATGG 58.720 38.462 17.16 0.00 37.39 3.51
2625 2803 6.204882 GGTAATTACAGTCACATAAGGATGGC 59.795 42.308 17.16 0.00 37.39 4.40
2626 2804 4.835284 TTACAGTCACATAAGGATGGCA 57.165 40.909 0.00 0.00 37.39 4.92
2627 2805 3.719268 ACAGTCACATAAGGATGGCAA 57.281 42.857 0.00 0.00 37.39 4.52
2628 2806 4.032960 ACAGTCACATAAGGATGGCAAA 57.967 40.909 0.00 0.00 37.39 3.68
2629 2807 4.603131 ACAGTCACATAAGGATGGCAAAT 58.397 39.130 0.00 0.00 37.39 2.32
2630 2808 5.018809 ACAGTCACATAAGGATGGCAAATT 58.981 37.500 0.00 0.00 37.39 1.82
2631 2809 5.481473 ACAGTCACATAAGGATGGCAAATTT 59.519 36.000 0.00 0.00 37.39 1.82
2632 2810 6.038356 CAGTCACATAAGGATGGCAAATTTC 58.962 40.000 0.00 0.00 37.39 2.17
2633 2811 5.716228 AGTCACATAAGGATGGCAAATTTCA 59.284 36.000 0.00 0.00 37.39 2.69
2634 2812 6.211184 AGTCACATAAGGATGGCAAATTTCAA 59.789 34.615 0.00 0.00 37.39 2.69
2635 2813 6.311200 GTCACATAAGGATGGCAAATTTCAAC 59.689 38.462 0.00 0.00 37.39 3.18
2636 2814 5.289193 CACATAAGGATGGCAAATTTCAACG 59.711 40.000 0.00 0.00 37.39 4.10
2637 2815 5.184864 ACATAAGGATGGCAAATTTCAACGA 59.815 36.000 0.00 0.00 37.39 3.85
2638 2816 3.575965 AGGATGGCAAATTTCAACGAC 57.424 42.857 0.00 0.00 0.00 4.34
2639 2817 2.890311 AGGATGGCAAATTTCAACGACA 59.110 40.909 0.00 0.00 0.00 4.35
2640 2818 2.986479 GGATGGCAAATTTCAACGACAC 59.014 45.455 0.00 0.00 0.00 3.67
2641 2819 3.551863 GGATGGCAAATTTCAACGACACA 60.552 43.478 0.00 0.00 0.00 3.72
2642 2820 2.803451 TGGCAAATTTCAACGACACAC 58.197 42.857 0.00 0.00 0.00 3.82
2643 2821 2.164422 TGGCAAATTTCAACGACACACA 59.836 40.909 0.00 0.00 0.00 3.72
2644 2822 3.182967 GGCAAATTTCAACGACACACAA 58.817 40.909 0.00 0.00 0.00 3.33
2645 2823 3.801594 GGCAAATTTCAACGACACACAAT 59.198 39.130 0.00 0.00 0.00 2.71
2646 2824 4.979197 GGCAAATTTCAACGACACACAATA 59.021 37.500 0.00 0.00 0.00 1.90
2647 2825 5.460419 GGCAAATTTCAACGACACACAATAA 59.540 36.000 0.00 0.00 0.00 1.40
2648 2826 6.345723 GGCAAATTTCAACGACACACAATAAG 60.346 38.462 0.00 0.00 0.00 1.73
2649 2827 6.198216 GCAAATTTCAACGACACACAATAAGT 59.802 34.615 0.00 0.00 0.00 2.24
2650 2828 7.253950 GCAAATTTCAACGACACACAATAAGTT 60.254 33.333 0.00 0.00 0.00 2.66
2651 2829 8.591312 CAAATTTCAACGACACACAATAAGTTT 58.409 29.630 0.00 0.00 0.00 2.66
2652 2830 7.678194 ATTTCAACGACACACAATAAGTTTG 57.322 32.000 0.00 0.00 34.10 2.93
2653 2831 5.804692 TCAACGACACACAATAAGTTTGT 57.195 34.783 0.00 0.00 43.50 2.83
2673 2851 9.482627 AGTTTGTGTTGAAAATAAACTGAAACA 57.517 25.926 9.10 0.00 36.60 2.83
2674 2852 9.739786 GTTTGTGTTGAAAATAAACTGAAACAG 57.260 29.630 1.06 0.00 33.81 3.16
2675 2853 9.698309 TTTGTGTTGAAAATAAACTGAAACAGA 57.302 25.926 5.76 0.00 35.18 3.41
2676 2854 9.698309 TTGTGTTGAAAATAAACTGAAACAGAA 57.302 25.926 5.76 0.00 35.18 3.02
2677 2855 9.698309 TGTGTTGAAAATAAACTGAAACAGAAA 57.302 25.926 5.76 0.00 35.18 2.52
2683 2861 9.636965 GAAAATAAACTGAAACAGAAATGTTGC 57.363 29.630 5.76 0.00 35.18 4.17
2684 2862 8.947055 AAATAAACTGAAACAGAAATGTTGCT 57.053 26.923 5.76 0.00 35.18 3.91
2689 2867 7.986085 ACTGAAACAGAAATGTTGCTATAGT 57.014 32.000 5.76 0.00 35.18 2.12
2690 2868 9.502091 AACTGAAACAGAAATGTTGCTATAGTA 57.498 29.630 5.76 0.00 35.18 1.82
2691 2869 9.502091 ACTGAAACAGAAATGTTGCTATAGTAA 57.498 29.630 5.76 0.00 35.18 2.24
2697 2875 9.284968 ACAGAAATGTTGCTATAGTAAACTTGT 57.715 29.630 4.71 2.58 0.00 3.16
2698 2876 9.760660 CAGAAATGTTGCTATAGTAAACTTGTC 57.239 33.333 4.71 10.30 0.00 3.18
2699 2877 9.502091 AGAAATGTTGCTATAGTAAACTTGTCA 57.498 29.630 18.39 9.11 0.00 3.58
2727 2905 6.693315 AAACATTCGAGGTTATTATGGTGG 57.307 37.500 5.16 0.00 0.00 4.61
2728 2906 4.134563 ACATTCGAGGTTATTATGGTGGC 58.865 43.478 0.00 0.00 0.00 5.01
2729 2907 3.916359 TTCGAGGTTATTATGGTGGCA 57.084 42.857 0.00 0.00 0.00 4.92
2730 2908 3.188159 TCGAGGTTATTATGGTGGCAC 57.812 47.619 9.70 9.70 0.00 5.01
2731 2909 2.769663 TCGAGGTTATTATGGTGGCACT 59.230 45.455 18.45 0.40 0.00 4.40
2732 2910 3.199071 TCGAGGTTATTATGGTGGCACTT 59.801 43.478 18.45 8.18 0.00 3.16
2794 2972 1.138661 CCATATTTGGCGGGCAACAAT 59.861 47.619 17.22 11.22 35.85 2.71
2802 2980 0.532115 GCGGGCAACAATTCTTGGAT 59.468 50.000 0.00 0.00 39.74 3.41
2825 3003 7.336931 GGATTCTTTGCCTGTAGTTTCTTGATA 59.663 37.037 0.00 0.00 0.00 2.15
2826 3004 8.635765 ATTCTTTGCCTGTAGTTTCTTGATAA 57.364 30.769 0.00 0.00 0.00 1.75
2855 3033 1.080093 TTGCGTGGTAGCTTCCTCG 60.080 57.895 24.25 24.25 44.11 4.63
2864 3042 2.416972 GGTAGCTTCCTCGTGGTAGTTG 60.417 54.545 11.18 0.00 33.82 3.16
2962 3403 2.940410 GCATTTTGCGGGCTAGTAGTAA 59.060 45.455 0.00 0.00 31.71 2.24
2965 3406 3.967332 TTTGCGGGCTAGTAGTAAAGT 57.033 42.857 0.00 0.00 0.00 2.66
2966 3407 5.404466 TTTTGCGGGCTAGTAGTAAAGTA 57.596 39.130 0.00 0.00 0.00 2.24
2967 3408 4.644103 TTGCGGGCTAGTAGTAAAGTAG 57.356 45.455 0.00 0.00 34.64 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 101 4.532276 CGAGAGACTAGTGAATGAATCCG 58.468 47.826 0.00 0.00 0.00 4.18
160 167 1.293498 GGGTTCTCTGCTTGCTCGA 59.707 57.895 0.00 0.00 0.00 4.04
182 189 4.436998 CGGTCGGGCAGTCTGGAC 62.437 72.222 1.14 0.73 0.00 4.02
184 191 3.432051 GATCGGTCGGGCAGTCTGG 62.432 68.421 1.14 0.00 0.00 3.86
185 192 2.021068 ATGATCGGTCGGGCAGTCTG 62.021 60.000 0.00 0.00 0.00 3.51
186 193 1.758514 ATGATCGGTCGGGCAGTCT 60.759 57.895 0.00 0.00 0.00 3.24
187 194 1.592669 CATGATCGGTCGGGCAGTC 60.593 63.158 0.00 0.00 0.00 3.51
188 195 2.501128 CATGATCGGTCGGGCAGT 59.499 61.111 0.00 0.00 0.00 4.40
189 196 2.280389 CCATGATCGGTCGGGCAG 60.280 66.667 0.00 0.00 0.00 4.85
190 197 4.545706 GCCATGATCGGTCGGGCA 62.546 66.667 22.21 0.00 43.25 5.36
205 213 1.734117 GGCACATCAACTTTGCGCC 60.734 57.895 4.18 0.00 37.11 6.53
252 260 0.456221 TAAGAGTAGCGAGCAGTGGC 59.544 55.000 0.00 0.00 41.61 5.01
276 284 2.223805 CCTTTTATTTCCATCGCCCTGC 60.224 50.000 0.00 0.00 0.00 4.85
277 285 3.023832 ACCTTTTATTTCCATCGCCCTG 58.976 45.455 0.00 0.00 0.00 4.45
278 286 3.382083 ACCTTTTATTTCCATCGCCCT 57.618 42.857 0.00 0.00 0.00 5.19
279 287 4.180817 CAAACCTTTTATTTCCATCGCCC 58.819 43.478 0.00 0.00 0.00 6.13
298 306 2.227865 GAGCTTGATGCCGGTAAACAAA 59.772 45.455 1.90 0.00 44.23 2.83
306 314 2.515523 CTGGGAGCTTGATGCCGG 60.516 66.667 0.00 0.00 44.23 6.13
311 319 2.235898 GTCTCTTGTCTGGGAGCTTGAT 59.764 50.000 0.00 0.00 0.00 2.57
312 320 1.620819 GTCTCTTGTCTGGGAGCTTGA 59.379 52.381 0.00 0.00 0.00 3.02
313 321 1.671261 CGTCTCTTGTCTGGGAGCTTG 60.671 57.143 0.00 0.00 0.00 4.01
314 322 0.605589 CGTCTCTTGTCTGGGAGCTT 59.394 55.000 0.00 0.00 0.00 3.74
347 355 8.203485 TGTTTGCTTTCTCATCAACCTTTAATT 58.797 29.630 0.00 0.00 0.00 1.40
349 357 7.106439 TGTTTGCTTTCTCATCAACCTTTAA 57.894 32.000 0.00 0.00 0.00 1.52
351 359 5.596836 TGTTTGCTTTCTCATCAACCTTT 57.403 34.783 0.00 0.00 0.00 3.11
354 362 3.737774 GCTTGTTTGCTTTCTCATCAACC 59.262 43.478 0.00 0.00 0.00 3.77
355 363 3.737774 GGCTTGTTTGCTTTCTCATCAAC 59.262 43.478 0.00 0.00 0.00 3.18
356 364 3.384146 TGGCTTGTTTGCTTTCTCATCAA 59.616 39.130 0.00 0.00 0.00 2.57
357 365 2.957680 TGGCTTGTTTGCTTTCTCATCA 59.042 40.909 0.00 0.00 0.00 3.07
358 366 3.648339 TGGCTTGTTTGCTTTCTCATC 57.352 42.857 0.00 0.00 0.00 2.92
360 368 3.384146 TGAATGGCTTGTTTGCTTTCTCA 59.616 39.130 0.00 0.00 0.00 3.27
361 369 3.981211 TGAATGGCTTGTTTGCTTTCTC 58.019 40.909 0.00 0.00 0.00 2.87
362 370 4.202284 ACATGAATGGCTTGTTTGCTTTCT 60.202 37.500 0.00 0.00 31.44 2.52
367 421 3.029320 TGACATGAATGGCTTGTTTGC 57.971 42.857 0.00 0.00 36.54 3.68
374 428 2.715749 TCGGATTGACATGAATGGCT 57.284 45.000 0.00 0.00 36.54 4.75
392 446 5.184287 CGTAGGATAGGAAGGGAAGAGAATC 59.816 48.000 0.00 0.00 0.00 2.52
396 450 3.570550 CACGTAGGATAGGAAGGGAAGAG 59.429 52.174 0.00 0.00 0.00 2.85
397 451 3.563223 CACGTAGGATAGGAAGGGAAGA 58.437 50.000 0.00 0.00 0.00 2.87
399 453 2.037144 GCACGTAGGATAGGAAGGGAA 58.963 52.381 0.00 0.00 0.00 3.97
400 454 1.063492 TGCACGTAGGATAGGAAGGGA 60.063 52.381 0.00 0.00 0.00 4.20
401 455 1.341531 CTGCACGTAGGATAGGAAGGG 59.658 57.143 0.00 0.00 0.00 3.95
402 456 1.341531 CCTGCACGTAGGATAGGAAGG 59.658 57.143 0.00 0.00 40.42 3.46
486 546 3.425193 GTGAGTGCGTTTAAAATTGGCAG 59.575 43.478 5.15 0.00 33.77 4.85
528 588 1.945354 TTCCTCTCCGACGATGGTGC 61.945 60.000 0.00 0.00 0.00 5.01
530 590 0.818296 CTTTCCTCTCCGACGATGGT 59.182 55.000 0.00 0.00 0.00 3.55
531 591 0.103208 CCTTTCCTCTCCGACGATGG 59.897 60.000 0.00 0.00 0.00 3.51
532 592 0.103208 CCCTTTCCTCTCCGACGATG 59.897 60.000 0.00 0.00 0.00 3.84
534 594 1.681327 CCCCTTTCCTCTCCGACGA 60.681 63.158 0.00 0.00 0.00 4.20
535 595 1.668101 CTCCCCTTTCCTCTCCGACG 61.668 65.000 0.00 0.00 0.00 5.12
537 597 1.686110 GCTCCCCTTTCCTCTCCGA 60.686 63.158 0.00 0.00 0.00 4.55
538 598 2.736826 GGCTCCCCTTTCCTCTCCG 61.737 68.421 0.00 0.00 0.00 4.63
542 604 3.798511 CCGGGCTCCCCTTTCCTC 61.799 72.222 0.00 0.00 42.67 3.71
551 613 2.314323 TACGTTTTTATCCGGGCTCC 57.686 50.000 0.00 0.00 0.00 4.70
558 620 4.953814 CGTCGCTGATTTACGTTTTTATCC 59.046 41.667 0.00 0.00 32.16 2.59
602 664 3.526931 TTCTCGGTATCTGCTTCCAAG 57.473 47.619 0.00 0.00 0.00 3.61
603 665 3.973206 TTTCTCGGTATCTGCTTCCAA 57.027 42.857 0.00 0.00 0.00 3.53
604 666 3.450817 TCATTTCTCGGTATCTGCTTCCA 59.549 43.478 0.00 0.00 0.00 3.53
605 667 3.804873 GTCATTTCTCGGTATCTGCTTCC 59.195 47.826 0.00 0.00 0.00 3.46
612 691 3.329743 TCGTCGTCATTTCTCGGTATC 57.670 47.619 0.00 0.00 0.00 2.24
643 722 4.187694 CTCTCCAAAGAATCGGAAGGAAG 58.812 47.826 0.00 0.00 0.00 3.46
644 723 3.583086 ACTCTCCAAAGAATCGGAAGGAA 59.417 43.478 0.00 0.00 0.00 3.36
645 724 3.173965 ACTCTCCAAAGAATCGGAAGGA 58.826 45.455 0.00 0.00 0.00 3.36
646 725 3.618690 ACTCTCCAAAGAATCGGAAGG 57.381 47.619 0.00 0.00 0.00 3.46
679 760 2.434843 CCTCTCTATGCGCCCACCA 61.435 63.158 4.18 0.00 0.00 4.17
829 927 2.612251 GAGGAGGAGGGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
830 928 2.197324 CGAGGAGGAGGGGAGGAG 59.803 72.222 0.00 0.00 0.00 3.69
831 929 2.617538 ACGAGGAGGAGGGGAGGA 60.618 66.667 0.00 0.00 0.00 3.71
832 930 2.443016 CACGAGGAGGAGGGGAGG 60.443 72.222 0.00 0.00 0.00 4.30
833 931 3.151022 GCACGAGGAGGAGGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
836 934 2.363018 TCTGCACGAGGAGGAGGG 60.363 66.667 0.96 0.00 33.43 4.30
860 964 0.986874 CTCGTGCTGTTTTCGCGTTG 60.987 55.000 5.77 0.00 38.45 4.10
909 1026 5.181622 AGAAGCAGAAGAAGAGCAAAGAATG 59.818 40.000 0.00 0.00 0.00 2.67
970 1100 1.529478 CCTCCGCTAGCTAGCCTCA 60.529 63.158 34.27 19.73 46.34 3.86
1456 1586 0.250597 TTGAGAGTCTCGTCACCCGA 60.251 55.000 15.34 0.00 45.00 5.14
1457 1587 0.169230 CTTGAGAGTCTCGTCACCCG 59.831 60.000 15.34 0.00 32.35 5.28
1458 1588 1.535833 TCTTGAGAGTCTCGTCACCC 58.464 55.000 15.34 0.00 32.35 4.61
1461 1591 1.542030 GGCTTCTTGAGAGTCTCGTCA 59.458 52.381 15.34 1.33 32.35 4.35
1468 1613 1.179814 ACCGTCGGCTTCTTGAGAGT 61.180 55.000 12.28 0.00 0.00 3.24
1470 1615 1.585006 GACCGTCGGCTTCTTGAGA 59.415 57.895 12.28 0.00 0.00 3.27
1512 1657 3.512516 GTGATCAGCTTGCCGCCC 61.513 66.667 0.00 0.00 40.39 6.13
1809 1954 1.163554 GAGGCTTGGACTTCTTGCAG 58.836 55.000 0.00 0.00 0.00 4.41
1815 1960 2.436824 GCGGGAGGCTTGGACTTC 60.437 66.667 0.00 0.00 39.11 3.01
2089 2240 4.462417 GCGCTGCTCTGCTTGCTG 62.462 66.667 0.00 0.00 0.00 4.41
2105 2269 1.133790 GATTCACCATGCAAGACCAGC 59.866 52.381 0.00 0.00 0.00 4.85
2106 2270 1.747355 GGATTCACCATGCAAGACCAG 59.253 52.381 0.00 0.00 38.79 4.00
2107 2271 1.075212 TGGATTCACCATGCAAGACCA 59.925 47.619 0.00 0.00 44.64 4.02
2145 2309 1.332904 GCAAGGACGACGACAACTTTG 60.333 52.381 0.00 4.51 0.00 2.77
2152 2316 2.005971 AATTAGGCAAGGACGACGAC 57.994 50.000 0.00 0.00 0.00 4.34
2153 2317 2.480759 GCTAATTAGGCAAGGACGACGA 60.481 50.000 14.28 0.00 0.00 4.20
2154 2318 1.859080 GCTAATTAGGCAAGGACGACG 59.141 52.381 14.28 0.00 0.00 5.12
2164 2328 6.293680 GGAGCATTAACAAGAGCTAATTAGGC 60.294 42.308 14.28 6.70 37.48 3.93
2207 2375 4.043812 ACAGGCTTGGGCAATCTCATATAT 59.956 41.667 0.00 0.00 40.87 0.86
2208 2376 3.395607 ACAGGCTTGGGCAATCTCATATA 59.604 43.478 0.00 0.00 40.87 0.86
2219 2387 3.376918 GGCTTCACAGGCTTGGGC 61.377 66.667 0.00 0.00 42.53 5.36
2240 2408 0.106521 GGAGAGGAGAAGAGCATGGC 59.893 60.000 0.00 0.00 0.00 4.40
2253 2421 2.093235 CCAGCAAAGGTAGAAGGAGAGG 60.093 54.545 0.00 0.00 0.00 3.69
2269 2437 0.247460 CAGCTACTGCACTACCAGCA 59.753 55.000 0.00 0.00 42.74 4.41
2285 2453 2.109126 GGTGATGTTCGGGAGCAGC 61.109 63.158 0.00 0.00 0.00 5.25
2286 2454 0.742281 CAGGTGATGTTCGGGAGCAG 60.742 60.000 0.00 0.00 0.00 4.24
2302 2470 1.234615 CGCCCACACCTTGTTACAGG 61.235 60.000 0.51 0.51 40.23 4.00
2322 2494 2.631160 TACCCCACTGTTCACTTGTG 57.369 50.000 0.00 0.00 0.00 3.33
2350 2523 2.235402 ACGGTCCTACCACCATACTTTG 59.765 50.000 0.00 0.00 38.47 2.77
2366 2539 7.965107 CCGTAATCCTATATTACTTGTACGGTC 59.035 40.741 9.63 0.00 43.92 4.79
2371 2544 8.579006 CACCACCGTAATCCTATATTACTTGTA 58.421 37.037 6.39 0.00 33.56 2.41
2382 2555 3.053395 ACTCCTACACCACCGTAATCCTA 60.053 47.826 0.00 0.00 0.00 2.94
2419 2597 2.627945 ACTGTTCGAGCTCAACAACAA 58.372 42.857 23.05 10.39 33.36 2.83
2453 2631 9.319143 GCCGATAATATATAACAGCTTTCAGAT 57.681 33.333 0.00 0.00 0.00 2.90
2454 2632 8.311109 TGCCGATAATATATAACAGCTTTCAGA 58.689 33.333 0.00 0.00 0.00 3.27
2455 2633 8.383619 GTGCCGATAATATATAACAGCTTTCAG 58.616 37.037 0.00 0.00 0.00 3.02
2456 2634 7.333423 GGTGCCGATAATATATAACAGCTTTCA 59.667 37.037 0.00 0.00 0.00 2.69
2457 2635 7.464178 CGGTGCCGATAATATATAACAGCTTTC 60.464 40.741 4.35 0.00 42.83 2.62
2458 2636 6.312918 CGGTGCCGATAATATATAACAGCTTT 59.687 38.462 4.35 0.00 42.83 3.51
2459 2637 5.810587 CGGTGCCGATAATATATAACAGCTT 59.189 40.000 4.35 0.00 42.83 3.74
2460 2638 5.105473 ACGGTGCCGATAATATATAACAGCT 60.105 40.000 18.16 0.00 42.83 4.24
2461 2639 5.005394 CACGGTGCCGATAATATATAACAGC 59.995 44.000 18.16 0.00 42.83 4.40
2462 2640 6.097356 ACACGGTGCCGATAATATATAACAG 58.903 40.000 18.16 0.00 42.83 3.16
2463 2641 6.028146 ACACGGTGCCGATAATATATAACA 57.972 37.500 18.16 0.00 42.83 2.41
2464 2642 6.671402 GCAACACGGTGCCGATAATATATAAC 60.671 42.308 18.16 0.00 42.83 1.89
2465 2643 5.349270 GCAACACGGTGCCGATAATATATAA 59.651 40.000 18.16 0.00 42.83 0.98
2466 2644 4.865925 GCAACACGGTGCCGATAATATATA 59.134 41.667 18.16 0.00 42.83 0.86
2467 2645 3.682858 GCAACACGGTGCCGATAATATAT 59.317 43.478 18.16 0.00 42.83 0.86
2468 2646 3.061322 GCAACACGGTGCCGATAATATA 58.939 45.455 18.16 0.00 42.83 0.86
2469 2647 1.871039 GCAACACGGTGCCGATAATAT 59.129 47.619 18.16 0.00 42.83 1.28
2470 2648 1.292061 GCAACACGGTGCCGATAATA 58.708 50.000 18.16 0.00 42.83 0.98
2471 2649 2.094904 GCAACACGGTGCCGATAAT 58.905 52.632 18.16 0.00 42.83 1.28
2472 2650 3.568686 GCAACACGGTGCCGATAA 58.431 55.556 18.16 0.00 42.83 1.75
2479 2657 0.878523 TCGAAAGAGGCAACACGGTG 60.879 55.000 6.58 6.58 41.41 4.94
2508 2686 1.283613 ACACGGAATTACGCGCGAAA 61.284 50.000 39.36 21.51 37.37 3.46
2509 2687 1.283613 AACACGGAATTACGCGCGAA 61.284 50.000 39.36 25.39 37.37 4.70
2520 2698 1.065345 TCCTGAACCAACAACACGGAA 60.065 47.619 0.00 0.00 0.00 4.30
2539 2717 8.748380 AAATAAAAGCTTCAATTGCAGTACTC 57.252 30.769 0.00 0.00 0.00 2.59
2540 2718 9.846248 CTAAATAAAAGCTTCAATTGCAGTACT 57.154 29.630 0.00 0.00 0.00 2.73
2541 2719 9.076596 CCTAAATAAAAGCTTCAATTGCAGTAC 57.923 33.333 0.00 0.00 0.00 2.73
2546 2724 6.313658 CCCACCTAAATAAAAGCTTCAATTGC 59.686 38.462 0.00 0.00 0.00 3.56
2549 2727 6.723977 TCACCCACCTAAATAAAAGCTTCAAT 59.276 34.615 0.00 0.00 0.00 2.57
2555 2733 3.446161 GGGTCACCCACCTAAATAAAAGC 59.554 47.826 8.52 0.00 45.95 3.51
2577 2755 1.145803 GAAAAACGTCAGGACCGGAG 58.854 55.000 9.46 0.00 0.00 4.63
2578 2756 0.598158 CGAAAAACGTCAGGACCGGA 60.598 55.000 9.46 0.00 37.22 5.14
2579 2757 0.598158 TCGAAAAACGTCAGGACCGG 60.598 55.000 0.00 0.00 43.13 5.28
2580 2758 1.126113 CATCGAAAAACGTCAGGACCG 59.874 52.381 0.00 0.00 43.13 4.79
2581 2759 1.463444 CCATCGAAAAACGTCAGGACC 59.537 52.381 0.00 0.00 43.13 4.46
2582 2760 2.140717 ACCATCGAAAAACGTCAGGAC 58.859 47.619 0.00 0.00 43.13 3.85
2583 2761 2.536761 ACCATCGAAAAACGTCAGGA 57.463 45.000 0.00 0.00 43.13 3.86
2584 2762 4.939509 ATTACCATCGAAAAACGTCAGG 57.060 40.909 0.00 0.00 43.13 3.86
2585 2763 6.823531 TGTAATTACCATCGAAAAACGTCAG 58.176 36.000 13.01 0.00 43.13 3.51
2587 2765 6.824557 ACTGTAATTACCATCGAAAAACGTC 58.175 36.000 13.01 0.00 43.13 4.34
2589 2767 6.735063 GTGACTGTAATTACCATCGAAAAACG 59.265 38.462 13.01 0.00 44.09 3.60
2591 2769 7.731882 TGTGACTGTAATTACCATCGAAAAA 57.268 32.000 13.01 0.00 0.00 1.94
2592 2770 7.915293 ATGTGACTGTAATTACCATCGAAAA 57.085 32.000 13.01 0.00 0.00 2.29
2593 2771 9.093970 CTTATGTGACTGTAATTACCATCGAAA 57.906 33.333 13.01 1.71 0.00 3.46
2594 2772 7.709182 CCTTATGTGACTGTAATTACCATCGAA 59.291 37.037 13.01 3.82 0.00 3.71
2595 2773 7.068962 TCCTTATGTGACTGTAATTACCATCGA 59.931 37.037 13.01 0.00 0.00 3.59
2596 2774 7.207383 TCCTTATGTGACTGTAATTACCATCG 58.793 38.462 13.01 2.14 0.00 3.84
2597 2775 8.993121 CATCCTTATGTGACTGTAATTACCATC 58.007 37.037 13.01 10.47 0.00 3.51
2598 2776 7.939039 CCATCCTTATGTGACTGTAATTACCAT 59.061 37.037 13.01 10.48 0.00 3.55
2599 2777 7.279615 CCATCCTTATGTGACTGTAATTACCA 58.720 38.462 13.01 3.79 0.00 3.25
2600 2778 6.204882 GCCATCCTTATGTGACTGTAATTACC 59.795 42.308 13.01 0.00 0.00 2.85
2601 2779 6.765989 TGCCATCCTTATGTGACTGTAATTAC 59.234 38.462 8.75 8.75 0.00 1.89
2602 2780 6.894682 TGCCATCCTTATGTGACTGTAATTA 58.105 36.000 0.00 0.00 0.00 1.40
2603 2781 5.754782 TGCCATCCTTATGTGACTGTAATT 58.245 37.500 0.00 0.00 0.00 1.40
2604 2782 5.372343 TGCCATCCTTATGTGACTGTAAT 57.628 39.130 0.00 0.00 0.00 1.89
2605 2783 4.835284 TGCCATCCTTATGTGACTGTAA 57.165 40.909 0.00 0.00 0.00 2.41
2606 2784 4.835284 TTGCCATCCTTATGTGACTGTA 57.165 40.909 0.00 0.00 0.00 2.74
2607 2785 3.719268 TTGCCATCCTTATGTGACTGT 57.281 42.857 0.00 0.00 0.00 3.55
2608 2786 5.587388 AATTTGCCATCCTTATGTGACTG 57.413 39.130 0.00 0.00 0.00 3.51
2609 2787 5.716228 TGAAATTTGCCATCCTTATGTGACT 59.284 36.000 0.00 0.00 0.00 3.41
2610 2788 5.964758 TGAAATTTGCCATCCTTATGTGAC 58.035 37.500 0.00 0.00 0.00 3.67
2611 2789 6.397272 GTTGAAATTTGCCATCCTTATGTGA 58.603 36.000 0.00 0.00 0.00 3.58
2612 2790 5.289193 CGTTGAAATTTGCCATCCTTATGTG 59.711 40.000 0.00 0.00 0.00 3.21
2613 2791 5.184864 TCGTTGAAATTTGCCATCCTTATGT 59.815 36.000 0.00 0.00 0.00 2.29
2614 2792 5.516339 GTCGTTGAAATTTGCCATCCTTATG 59.484 40.000 0.00 0.00 0.00 1.90
2615 2793 5.184864 TGTCGTTGAAATTTGCCATCCTTAT 59.815 36.000 0.00 0.00 0.00 1.73
2616 2794 4.520874 TGTCGTTGAAATTTGCCATCCTTA 59.479 37.500 0.00 0.00 0.00 2.69
2617 2795 3.320541 TGTCGTTGAAATTTGCCATCCTT 59.679 39.130 0.00 0.00 0.00 3.36
2618 2796 2.890311 TGTCGTTGAAATTTGCCATCCT 59.110 40.909 0.00 0.00 0.00 3.24
2619 2797 2.986479 GTGTCGTTGAAATTTGCCATCC 59.014 45.455 0.00 0.00 0.00 3.51
2620 2798 3.425193 GTGTGTCGTTGAAATTTGCCATC 59.575 43.478 0.00 0.00 0.00 3.51
2621 2799 3.181482 TGTGTGTCGTTGAAATTTGCCAT 60.181 39.130 0.00 0.00 0.00 4.40
2622 2800 2.164422 TGTGTGTCGTTGAAATTTGCCA 59.836 40.909 0.00 0.00 0.00 4.92
2623 2801 2.803451 TGTGTGTCGTTGAAATTTGCC 58.197 42.857 0.00 0.00 0.00 4.52
2624 2802 6.198216 ACTTATTGTGTGTCGTTGAAATTTGC 59.802 34.615 0.00 0.00 0.00 3.68
2625 2803 7.678194 ACTTATTGTGTGTCGTTGAAATTTG 57.322 32.000 0.00 0.00 0.00 2.32
2626 2804 8.591312 CAAACTTATTGTGTGTCGTTGAAATTT 58.409 29.630 0.00 0.00 0.00 1.82
2627 2805 7.757624 ACAAACTTATTGTGTGTCGTTGAAATT 59.242 29.630 0.00 0.00 43.22 1.82
2628 2806 7.219917 CACAAACTTATTGTGTGTCGTTGAAAT 59.780 33.333 12.02 0.00 43.22 2.17
2629 2807 6.524933 CACAAACTTATTGTGTGTCGTTGAAA 59.475 34.615 12.02 0.00 43.22 2.69
2630 2808 6.024664 CACAAACTTATTGTGTGTCGTTGAA 58.975 36.000 12.02 0.00 43.22 2.69
2631 2809 5.564768 CACAAACTTATTGTGTGTCGTTGA 58.435 37.500 12.02 0.00 43.22 3.18
2632 2810 5.848207 CACAAACTTATTGTGTGTCGTTG 57.152 39.130 12.02 0.00 43.22 4.10
2647 2825 9.482627 TGTTTCAGTTTATTTTCAACACAAACT 57.517 25.926 0.00 0.00 39.39 2.66
2648 2826 9.739786 CTGTTTCAGTTTATTTTCAACACAAAC 57.260 29.630 0.00 0.00 33.08 2.93
2649 2827 9.698309 TCTGTTTCAGTTTATTTTCAACACAAA 57.302 25.926 0.00 0.00 32.61 2.83
2650 2828 9.698309 TTCTGTTTCAGTTTATTTTCAACACAA 57.302 25.926 0.00 0.00 32.61 3.33
2651 2829 9.698309 TTTCTGTTTCAGTTTATTTTCAACACA 57.302 25.926 0.00 0.00 32.61 3.72
2657 2835 9.636965 GCAACATTTCTGTTTCAGTTTATTTTC 57.363 29.630 0.00 0.00 43.05 2.29
2658 2836 9.382275 AGCAACATTTCTGTTTCAGTTTATTTT 57.618 25.926 0.00 0.00 43.05 1.82
2659 2837 8.947055 AGCAACATTTCTGTTTCAGTTTATTT 57.053 26.923 0.00 0.00 43.05 1.40
2663 2841 8.850156 ACTATAGCAACATTTCTGTTTCAGTTT 58.150 29.630 0.00 0.00 43.05 2.66
2664 2842 8.396272 ACTATAGCAACATTTCTGTTTCAGTT 57.604 30.769 0.00 0.00 43.05 3.16
2665 2843 7.986085 ACTATAGCAACATTTCTGTTTCAGT 57.014 32.000 0.00 0.00 43.05 3.41
2671 2849 9.284968 ACAAGTTTACTATAGCAACATTTCTGT 57.715 29.630 14.75 8.54 37.12 3.41
2672 2850 9.760660 GACAAGTTTACTATAGCAACATTTCTG 57.239 33.333 14.75 8.11 0.00 3.02
2673 2851 9.502091 TGACAAGTTTACTATAGCAACATTTCT 57.498 29.630 14.75 0.00 0.00 2.52
2702 2880 7.543756 CCACCATAATAACCTCGAATGTTTTT 58.456 34.615 5.43 6.80 0.00 1.94
2703 2881 6.405397 GCCACCATAATAACCTCGAATGTTTT 60.405 38.462 5.43 3.83 0.00 2.43
2704 2882 5.067283 GCCACCATAATAACCTCGAATGTTT 59.933 40.000 5.43 0.00 0.00 2.83
2705 2883 4.578928 GCCACCATAATAACCTCGAATGTT 59.421 41.667 5.45 5.45 0.00 2.71
2706 2884 4.134563 GCCACCATAATAACCTCGAATGT 58.865 43.478 0.00 0.00 0.00 2.71
2707 2885 4.024048 GTGCCACCATAATAACCTCGAATG 60.024 45.833 0.00 0.00 0.00 2.67
2708 2886 4.134563 GTGCCACCATAATAACCTCGAAT 58.865 43.478 0.00 0.00 0.00 3.34
2709 2887 3.199071 AGTGCCACCATAATAACCTCGAA 59.801 43.478 0.00 0.00 0.00 3.71
2710 2888 2.769663 AGTGCCACCATAATAACCTCGA 59.230 45.455 0.00 0.00 0.00 4.04
2711 2889 3.194005 AGTGCCACCATAATAACCTCG 57.806 47.619 0.00 0.00 0.00 4.63
2712 2890 6.296026 TCATAAGTGCCACCATAATAACCTC 58.704 40.000 0.00 0.00 0.00 3.85
2713 2891 6.260700 TCATAAGTGCCACCATAATAACCT 57.739 37.500 0.00 0.00 0.00 3.50
2714 2892 6.490040 ACATCATAAGTGCCACCATAATAACC 59.510 38.462 0.00 0.00 0.00 2.85
2715 2893 7.362662 CACATCATAAGTGCCACCATAATAAC 58.637 38.462 0.00 0.00 0.00 1.89
2716 2894 7.509141 CACATCATAAGTGCCACCATAATAA 57.491 36.000 0.00 0.00 0.00 1.40
2728 2906 2.349580 CACTCGTGGCACATCATAAGTG 59.650 50.000 19.09 15.00 44.52 3.16
2729 2907 2.621338 CACTCGTGGCACATCATAAGT 58.379 47.619 19.09 7.57 44.52 2.24
2730 2908 1.935873 CCACTCGTGGCACATCATAAG 59.064 52.381 19.09 6.97 44.73 1.73
2731 2909 2.022764 CCACTCGTGGCACATCATAA 57.977 50.000 19.09 0.00 44.73 1.90
2732 2910 3.758715 CCACTCGTGGCACATCATA 57.241 52.632 19.09 0.00 44.73 2.15
2744 2922 2.263077 GAGTTAGCACATCACCACTCG 58.737 52.381 0.00 0.00 0.00 4.18
2779 2957 0.755686 AAGAATTGTTGCCCGCCAAA 59.244 45.000 0.00 0.00 34.68 3.28
2794 2972 4.985538 ACTACAGGCAAAGAATCCAAGAA 58.014 39.130 0.00 0.00 0.00 2.52
2802 2980 7.307751 CGTTATCAAGAAACTACAGGCAAAGAA 60.308 37.037 0.00 0.00 0.00 2.52
2838 3016 2.273179 ACGAGGAAGCTACCACGCA 61.273 57.895 0.00 0.00 45.07 5.24
2839 3017 1.805945 CACGAGGAAGCTACCACGC 60.806 63.158 0.00 0.00 45.07 5.34
2840 3018 1.153823 CCACGAGGAAGCTACCACG 60.154 63.158 0.00 0.00 46.20 4.94
2841 3019 1.134560 CTACCACGAGGAAGCTACCAC 59.865 57.143 5.68 0.00 38.69 4.16
2842 3020 1.272313 ACTACCACGAGGAAGCTACCA 60.272 52.381 5.68 0.00 38.69 3.25
2855 3033 4.733887 CGATGTCGAGTTATCAACTACCAC 59.266 45.833 0.00 0.00 43.03 4.16
2864 3042 3.250280 TCAGCCTACGATGTCGAGTTATC 59.750 47.826 9.67 0.00 43.02 1.75
2962 3403 6.224584 GTCAAGCCAGAAAGAAGTACTACTT 58.775 40.000 0.76 0.76 41.95 2.24
2965 3406 4.020485 GGGTCAAGCCAGAAAGAAGTACTA 60.020 45.833 0.00 0.00 39.65 1.82
2966 3407 3.244596 GGGTCAAGCCAGAAAGAAGTACT 60.245 47.826 0.00 0.00 39.65 2.73
2967 3408 3.075148 GGGTCAAGCCAGAAAGAAGTAC 58.925 50.000 0.00 0.00 39.65 2.73
3027 3468 8.876275 TTCACGTATTATCAAGTGTATTACCC 57.124 34.615 0.00 0.00 36.16 3.69
3054 3495 1.710013 ATGTTGTCTTAGCACGACGG 58.290 50.000 0.00 0.00 33.79 4.79


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

AutoCloner maintained by Alex Coulton.