Multiple sequence alignment - TraesCS4A01G035200

Loading Multiple Alignment...

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 TraesCS4A01G035200 chr4A 100.000 3856 0 0 1 3856 27299511 27295656 0.000000e+00 7121.0
1 TraesCS4A01G035200 chr4D 91.311 2601 132 33 1306 3856 437968127 437965571 0.000000e+00 3465.0
2 TraesCS4A01G035200 chr4D 94.805 616 21 7 693 1303 437968793 437968184 0.000000e+00 950.0
3 TraesCS4A01G035200 chr4B 93.167 2005 85 19 1306 3281 541472642 541470661 0.000000e+00 2896.0
4 TraesCS4A01G035200 chr4B 95.922 564 17 4 740 1303 541473252 541472695 0.000000e+00 909.0
5 TraesCS4A01G035200 chr4B 79.153 590 116 7 5 589 333445836 333445249 6.000000e-108 401.0
6 TraesCS4A01G035200 chr4B 94.737 38 1 1 3660 3696 460578775 460578738 1.500000e-04 58.4
7 TraesCS4A01G035200 chr5B 89.748 595 58 3 4 595 702247381 702246787 0.000000e+00 758.0
8 TraesCS4A01G035200 chr3D 93.525 417 24 3 181 595 59914344 59913929 5.470000e-173 617.0
9 TraesCS4A01G035200 chr3D 96.196 184 6 1 4 186 59916264 59916081 2.250000e-77 300.0
10 TraesCS4A01G035200 chr3D 77.717 184 33 7 3645 3824 114861474 114861295 5.270000e-19 106.0
11 TraesCS4A01G035200 chr3D 79.720 143 23 5 3680 3819 402899518 402899379 8.820000e-17 99.0
12 TraesCS4A01G035200 chr3D 77.778 162 31 5 3660 3819 65303124 65303282 1.140000e-15 95.3
13 TraesCS4A01G035200 chr3D 80.198 101 17 3 3330 3429 260180235 260180137 5.340000e-09 73.1
14 TraesCS4A01G035200 chr3D 95.000 40 2 0 656 695 403938118 403938079 3.220000e-06 63.9
15 TraesCS4A01G035200 chr2D 76.508 315 65 7 3120 3426 604025204 604024891 3.080000e-36 163.0
16 TraesCS4A01G035200 chr2D 77.778 225 40 9 1604 1823 79874354 79874573 3.130000e-26 130.0
17 TraesCS4A01G035200 chr2D 76.522 230 52 2 1604 1832 42933931 42933703 1.450000e-24 124.0
18 TraesCS4A01G035200 chr6D 76.159 302 56 10 3125 3423 325598543 325598831 1.120000e-30 145.0
19 TraesCS4A01G035200 chr2A 78.378 222 40 7 1606 1823 80476237 80476454 1.870000e-28 137.0
20 TraesCS4A01G035200 chr2A 79.245 159 29 3 3122 3278 691415508 691415664 1.460000e-19 108.0
21 TraesCS4A01G035200 chr2B 78.222 225 39 9 1604 1823 131286732 131286951 6.720000e-28 135.0
22 TraesCS4A01G035200 chr2B 73.602 322 69 8 3122 3429 474734328 474734647 4.070000e-20 110.0
23 TraesCS4A01G035200 chr2B 88.889 54 3 3 3645 3696 129901860 129901912 3.220000e-06 63.9
24 TraesCS4A01G035200 chr6B 80.447 179 27 7 3645 3819 52824455 52824629 3.130000e-26 130.0
25 TraesCS4A01G035200 chr7B 74.618 327 64 14 3122 3432 111370892 111371215 4.040000e-25 126.0
26 TraesCS4A01G035200 chr7D 81.013 158 28 2 3122 3278 382384528 382384684 1.450000e-24 124.0
27 TraesCS4A01G035200 chr7D 77.401 177 36 3 3645 3819 351814041 351813867 6.820000e-18 102.0
28 TraesCS4A01G035200 chr7A 74.398 332 57 19 3122 3433 242954267 242954590 2.430000e-22 117.0
29 TraesCS4A01G035200 chr3A 79.747 158 29 3 3122 3278 248550719 248550564 1.130000e-20 111.0
30 TraesCS4A01G035200 chr3B 76.966 178 35 6 3645 3819 325241780 325241606 3.170000e-16 97.1
31 TraesCS4A01G035200 chr3B 76.836 177 34 4 3645 3819 728801595 728801424 4.100000e-15 93.5
32 TraesCS4A01G035200 chr1B 79.630 108 20 2 3322 3429 443440837 443440942 4.130000e-10 76.8
33 TraesCS4A01G035200 chr5A 80.488 82 15 1 381 461 576360046 576359965 1.160000e-05 62.1


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 TraesCS4A01G035200 chr4A 27295656 27299511 3855 True 7121.0 7121 100.0000 1 3856 1 chr4A.!!$R1 3855
1 TraesCS4A01G035200 chr4D 437965571 437968793 3222 True 2207.5 3465 93.0580 693 3856 2 chr4D.!!$R1 3163
2 TraesCS4A01G035200 chr4B 541470661 541473252 2591 True 1902.5 2896 94.5445 740 3281 2 chr4B.!!$R3 2541
3 TraesCS4A01G035200 chr4B 333445249 333445836 587 True 401.0 401 79.1530 5 589 1 chr4B.!!$R1 584
4 TraesCS4A01G035200 chr5B 702246787 702247381 594 True 758.0 758 89.7480 4 595 1 chr5B.!!$R1 591
5 TraesCS4A01G035200 chr3D 59913929 59916264 2335 True 458.5 617 94.8605 4 595 2 chr3D.!!$R5 591

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
867 2621 0.032678 AGATCAACAGCCCGCGATAG 59.967 55.0 8.23 0.0 0.0 2.08 F
1180 2934 0.032267 GCAGTACTCCGGCTACATCC 59.968 60.0 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 4370 1.10051 CTTCACACCGGTAGGATCGA 58.899 55.0 6.87 0.0 41.02 3.59 R
2879 4717 0.52760 TCATCATACACACGCGAGGC 60.528 55.0 15.93 0.0 0.00 4.70 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
166 168 8.742777 TCTGCAAACAATAGATGATTAAAGCTT 58.257 29.630 0.00 0.00 0.00 3.74
187 1931 3.016031 TGGTGCATTGCGACATATCTTT 58.984 40.909 3.84 0.00 0.00 2.52
215 1959 1.598130 AGCAGTCCACCTTGTTCGC 60.598 57.895 0.00 0.00 0.00 4.70
252 1996 0.519077 GAGAAGGCTTCCGCACAAAG 59.481 55.000 23.09 0.00 38.10 2.77
274 2018 4.021894 AGCAGAAATAGATACGGCGAGATT 60.022 41.667 16.62 2.24 0.00 2.40
288 2032 2.725221 GAGATTGGGTCTCCTTGCAT 57.275 50.000 0.00 0.00 46.35 3.96
324 2068 2.829120 GGTTTAGCTCCTCTGTGAGAGT 59.171 50.000 0.00 0.00 40.72 3.24
364 2108 2.922740 AGTTCACCGTGGTACAACAT 57.077 45.000 12.95 0.00 44.16 2.71
386 2130 1.539869 ATGACCAGCCTCACCCAGT 60.540 57.895 0.00 0.00 0.00 4.00
400 2144 1.707427 ACCCAGTTCTCTGCAAATCCT 59.293 47.619 0.00 0.00 40.09 3.24
497 2245 4.039092 CCCCCTGCACCAGACCTG 62.039 72.222 0.00 0.00 32.44 4.00
518 2266 6.040842 ACCTGTTGTTCTGCATAAAATGAGTT 59.959 34.615 0.00 0.00 0.00 3.01
606 2355 4.313522 CGATCACTTCGTGGAAAAAGAG 57.686 45.455 0.00 0.00 43.01 2.85
607 2356 3.987868 CGATCACTTCGTGGAAAAAGAGA 59.012 43.478 0.00 0.00 43.01 3.10
608 2357 4.627467 CGATCACTTCGTGGAAAAAGAGAT 59.373 41.667 0.00 0.00 43.01 2.75
609 2358 5.445142 CGATCACTTCGTGGAAAAAGAGATG 60.445 44.000 0.00 0.00 43.01 2.90
610 2359 4.956085 TCACTTCGTGGAAAAAGAGATGA 58.044 39.130 0.00 0.00 33.87 2.92
611 2360 5.551233 TCACTTCGTGGAAAAAGAGATGAT 58.449 37.500 0.00 0.00 33.87 2.45
612 2361 5.409520 TCACTTCGTGGAAAAAGAGATGATG 59.590 40.000 0.00 0.00 33.87 3.07
613 2362 5.409520 CACTTCGTGGAAAAAGAGATGATGA 59.590 40.000 0.00 0.00 0.00 2.92
614 2363 5.997746 ACTTCGTGGAAAAAGAGATGATGAA 59.002 36.000 0.00 0.00 0.00 2.57
615 2364 5.862924 TCGTGGAAAAAGAGATGATGAAC 57.137 39.130 0.00 0.00 0.00 3.18
616 2365 4.695455 TCGTGGAAAAAGAGATGATGAACC 59.305 41.667 0.00 0.00 0.00 3.62
617 2366 4.436050 CGTGGAAAAAGAGATGATGAACCG 60.436 45.833 0.00 0.00 0.00 4.44
618 2367 4.455877 GTGGAAAAAGAGATGATGAACCGT 59.544 41.667 0.00 0.00 0.00 4.83
619 2368 5.642063 GTGGAAAAAGAGATGATGAACCGTA 59.358 40.000 0.00 0.00 0.00 4.02
620 2369 5.642063 TGGAAAAAGAGATGATGAACCGTAC 59.358 40.000 0.00 0.00 0.00 3.67
621 2370 5.064834 GGAAAAAGAGATGATGAACCGTACC 59.935 44.000 0.00 0.00 0.00 3.34
622 2371 5.422214 AAAAGAGATGATGAACCGTACCT 57.578 39.130 0.00 0.00 0.00 3.08
623 2372 4.392921 AAGAGATGATGAACCGTACCTG 57.607 45.455 0.00 0.00 0.00 4.00
624 2373 2.695666 AGAGATGATGAACCGTACCTGG 59.304 50.000 0.00 0.00 0.00 4.45
625 2374 2.431057 GAGATGATGAACCGTACCTGGT 59.569 50.000 4.05 4.05 46.67 4.00
626 2375 3.635373 GAGATGATGAACCGTACCTGGTA 59.365 47.826 1.49 1.49 42.89 3.25
627 2376 3.383825 AGATGATGAACCGTACCTGGTAC 59.616 47.826 24.03 24.03 42.89 3.34
628 2377 2.811410 TGATGAACCGTACCTGGTACT 58.189 47.619 28.89 14.77 42.89 2.73
629 2378 3.167485 TGATGAACCGTACCTGGTACTT 58.833 45.455 28.89 19.79 42.89 2.24
630 2379 3.194116 TGATGAACCGTACCTGGTACTTC 59.806 47.826 28.89 25.38 42.89 3.01
631 2380 1.895131 TGAACCGTACCTGGTACTTCC 59.105 52.381 28.89 17.53 42.89 3.46
632 2381 2.174360 GAACCGTACCTGGTACTTCCT 58.826 52.381 28.89 14.24 42.89 3.36
633 2382 2.315720 ACCGTACCTGGTACTTCCTT 57.684 50.000 28.89 10.15 41.55 3.36
634 2383 2.613129 ACCGTACCTGGTACTTCCTTT 58.387 47.619 28.89 8.65 41.55 3.11
635 2384 2.301009 ACCGTACCTGGTACTTCCTTTG 59.699 50.000 28.89 14.79 41.55 2.77
636 2385 2.301009 CCGTACCTGGTACTTCCTTTGT 59.699 50.000 28.89 0.00 36.93 2.83
637 2386 3.511146 CCGTACCTGGTACTTCCTTTGTA 59.489 47.826 28.89 0.00 36.93 2.41
638 2387 4.021192 CCGTACCTGGTACTTCCTTTGTAA 60.021 45.833 28.89 0.00 36.93 2.41
639 2388 5.511202 CCGTACCTGGTACTTCCTTTGTAAA 60.511 44.000 28.89 0.00 36.93 2.01
640 2389 5.406477 CGTACCTGGTACTTCCTTTGTAAAC 59.594 44.000 28.89 6.06 36.93 2.01
641 2390 5.641789 ACCTGGTACTTCCTTTGTAAACT 57.358 39.130 0.00 0.00 37.07 2.66
642 2391 6.752285 ACCTGGTACTTCCTTTGTAAACTA 57.248 37.500 0.00 0.00 37.07 2.24
643 2392 7.140522 ACCTGGTACTTCCTTTGTAAACTAA 57.859 36.000 0.00 0.00 37.07 2.24
644 2393 7.752638 ACCTGGTACTTCCTTTGTAAACTAAT 58.247 34.615 0.00 0.00 37.07 1.73
645 2394 7.881751 ACCTGGTACTTCCTTTGTAAACTAATC 59.118 37.037 0.00 0.00 37.07 1.75
646 2395 8.101419 CCTGGTACTTCCTTTGTAAACTAATCT 58.899 37.037 0.00 0.00 37.07 2.40
649 2398 9.096160 GGTACTTCCTTTGTAAACTAATCTAGC 57.904 37.037 0.00 0.00 0.00 3.42
650 2399 7.829378 ACTTCCTTTGTAAACTAATCTAGCG 57.171 36.000 0.00 0.00 0.00 4.26
651 2400 7.384477 ACTTCCTTTGTAAACTAATCTAGCGT 58.616 34.615 0.00 0.00 0.00 5.07
652 2401 7.876582 ACTTCCTTTGTAAACTAATCTAGCGTT 59.123 33.333 0.00 0.00 0.00 4.84
653 2402 8.611654 TTCCTTTGTAAACTAATCTAGCGTTT 57.388 30.769 0.00 0.00 35.32 3.60
654 2403 9.709495 TTCCTTTGTAAACTAATCTAGCGTTTA 57.291 29.630 0.00 0.00 33.40 2.01
655 2404 9.362539 TCCTTTGTAAACTAATCTAGCGTTTAG 57.637 33.333 0.00 6.24 34.78 1.85
656 2405 9.362539 CCTTTGTAAACTAATCTAGCGTTTAGA 57.637 33.333 11.54 2.06 34.78 2.10
727 2476 3.982058 CCGAATCGGTTAATAGCAGAGAC 59.018 47.826 14.46 0.00 42.73 3.36
798 2552 1.092348 GCGGGGTAAATTGTCCACTC 58.908 55.000 0.95 0.00 0.00 3.51
866 2620 0.249447 CAGATCAACAGCCCGCGATA 60.249 55.000 8.23 0.00 0.00 2.92
867 2621 0.032678 AGATCAACAGCCCGCGATAG 59.967 55.000 8.23 0.00 0.00 2.08
868 2622 0.249489 GATCAACAGCCCGCGATAGT 60.249 55.000 8.23 0.00 39.35 2.12
869 2623 1.000607 GATCAACAGCCCGCGATAGTA 60.001 52.381 8.23 0.00 39.35 1.82
881 2635 0.945099 CGATAGTACAGCCGAGCTCA 59.055 55.000 15.40 0.00 36.40 4.26
920 2674 0.882474 AACCGACGAACCAGAGAGAG 59.118 55.000 0.00 0.00 0.00 3.20
958 2712 1.890510 GCCTATAAACACCCGGCGG 60.891 63.158 21.46 21.46 0.00 6.13
959 2713 1.523524 CCTATAAACACCCGGCGGT 59.476 57.895 26.32 10.35 46.31 5.68
982 2736 1.678970 GTTGGGAGCTCCGCCATTT 60.679 57.895 26.36 0.00 38.76 2.32
1180 2934 0.032267 GCAGTACTCCGGCTACATCC 59.968 60.000 0.00 0.00 0.00 3.51
1294 3048 9.753674 TCAATGGAGGTAAAAGAAAGAACATAT 57.246 29.630 0.00 0.00 0.00 1.78
1325 3131 3.172339 CATAGGGGAGGAGGAGAATCTG 58.828 54.545 0.00 0.00 33.73 2.90
1326 3132 1.022903 AGGGGAGGAGGAGAATCTGT 58.977 55.000 0.00 0.00 33.73 3.41
1327 3133 2.227703 AGGGGAGGAGGAGAATCTGTA 58.772 52.381 0.00 0.00 33.73 2.74
1328 3134 2.090999 AGGGGAGGAGGAGAATCTGTAC 60.091 54.545 0.00 0.00 33.73 2.90
1404 3213 5.789710 ACGTTCATCGATCGGTTAATTTT 57.210 34.783 16.41 0.00 42.86 1.82
1409 3218 8.059502 CGTTCATCGATCGGTTAATTTTATTGA 58.940 33.333 16.41 0.00 42.86 2.57
1410 3219 9.878599 GTTCATCGATCGGTTAATTTTATTGAT 57.121 29.630 16.41 0.00 0.00 2.57
1412 3221 9.877137 TCATCGATCGGTTAATTTTATTGATTG 57.123 29.630 16.41 0.00 0.00 2.67
1568 3381 4.217035 CCGGTCGATGGCATTTCA 57.783 55.556 0.00 0.00 0.00 2.69
1569 3382 2.476772 CCGGTCGATGGCATTTCAA 58.523 52.632 0.00 0.00 0.00 2.69
1570 3383 0.098728 CCGGTCGATGGCATTTCAAC 59.901 55.000 0.00 0.00 0.00 3.18
1753 3566 4.367023 TGGTTCGACCGCTTCCCG 62.367 66.667 0.00 0.00 42.58 5.14
1895 3708 4.082190 TCAAAGGAATCTCCGTGAGTACTG 60.082 45.833 0.00 0.00 42.75 2.74
1912 3728 0.609957 CTGCCCATCAGAGCCAACAA 60.610 55.000 0.00 0.00 45.72 2.83
1918 3734 2.165030 CCATCAGAGCCAACAATTGTCC 59.835 50.000 12.39 3.74 0.00 4.02
2165 4002 1.443872 CTTCAACGTCTACGCGCCT 60.444 57.895 5.73 0.00 44.43 5.52
2219 4056 1.066716 TCCAAGTGCACGGTATGTACC 60.067 52.381 12.01 0.00 44.50 3.34
2223 4060 1.067142 AGTGCACGGTATGTACCACTG 60.067 52.381 12.01 5.10 46.80 3.66
2249 4087 4.948341 TGCTACTTGAACTACTGGTTGA 57.052 40.909 0.00 0.00 38.41 3.18
2352 4190 1.225376 CGTACTTGAACCAGCGCCAA 61.225 55.000 2.29 0.00 0.00 4.52
2518 4356 4.378774 CATCTGGCTATTCAGGTCAGAAG 58.621 47.826 2.21 0.00 46.34 2.85
2532 4370 3.244044 GGTCAGAAGCACTTCTCTTCAGT 60.244 47.826 9.95 0.00 46.13 3.41
2541 4379 4.732355 GCACTTCTCTTCAGTCGATCCTAC 60.732 50.000 0.00 0.00 0.00 3.18
2548 4386 0.100682 CAGTCGATCCTACCGGTGTG 59.899 60.000 19.93 10.05 0.00 3.82
2550 4388 0.813184 GTCGATCCTACCGGTGTGAA 59.187 55.000 19.93 0.00 0.00 3.18
2551 4389 1.100510 TCGATCCTACCGGTGTGAAG 58.899 55.000 19.93 6.18 0.00 3.02
2572 4410 2.680312 TCACTAGTGAGAGCATTGCC 57.320 50.000 21.74 0.00 34.14 4.52
2986 4828 1.377725 CCCTTTGGCGCTGACTGAT 60.378 57.895 7.64 0.00 0.00 2.90
2991 4833 3.248602 CCTTTGGCGCTGACTGATATTAC 59.751 47.826 7.64 0.00 0.00 1.89
3029 4871 0.697079 TCTCTCCACCCTACTCGTGT 59.303 55.000 0.00 0.00 0.00 4.49
3032 4874 1.101331 CTCCACCCTACTCGTGTACC 58.899 60.000 0.00 0.00 0.00 3.34
3038 4880 1.660560 CCTACTCGTGTACCCCCGTG 61.661 65.000 0.00 0.00 0.00 4.94
3119 4964 3.868757 TGGATGACTAGAACGTGAAGG 57.131 47.619 0.00 0.00 0.00 3.46
3120 4965 3.162666 TGGATGACTAGAACGTGAAGGT 58.837 45.455 0.00 0.00 0.00 3.50
3129 4974 3.340034 AGAACGTGAAGGTTGTTGACAA 58.660 40.909 0.00 0.00 0.00 3.18
3143 4988 5.188327 TGTTGACAACAGTTTTTGACACA 57.812 34.783 17.02 0.00 36.25 3.72
3292 5150 1.291132 GCTCGGAGCATTTGGAGTAC 58.709 55.000 24.42 0.00 41.89 2.73
3293 5151 1.134670 GCTCGGAGCATTTGGAGTACT 60.135 52.381 24.42 0.00 41.89 2.73
3298 5156 4.020928 TCGGAGCATTTGGAGTACTGTTTA 60.021 41.667 0.00 0.00 0.00 2.01
3301 5159 4.911390 AGCATTTGGAGTACTGTTTAGCT 58.089 39.130 0.00 0.00 0.00 3.32
3304 5162 5.355350 GCATTTGGAGTACTGTTTAGCTGAT 59.645 40.000 0.00 0.00 0.00 2.90
3309 5167 6.395629 TGGAGTACTGTTTAGCTGATTACAC 58.604 40.000 0.00 0.00 0.00 2.90
3311 5169 6.022163 AGTACTGTTTAGCTGATTACACGT 57.978 37.500 0.00 0.00 0.00 4.49
3326 5184 2.014128 ACACGTCCAACAAAACCTCAG 58.986 47.619 0.00 0.00 0.00 3.35
3335 5193 6.255670 GTCCAACAAAACCTCAGATGAAAAAC 59.744 38.462 0.00 0.00 0.00 2.43
3340 5198 9.750125 AACAAAACCTCAGATGAAAAACTATTC 57.250 29.630 0.00 0.00 0.00 1.75
3380 5239 3.119849 CCTCGTTGAGGCGATTGATTTTT 60.120 43.478 0.00 0.00 43.29 1.94
3408 5267 5.587388 TTGAATCATTTCAATCTGAGGCC 57.413 39.130 0.00 0.00 44.81 5.19
3409 5268 4.602107 TGAATCATTTCAATCTGAGGCCA 58.398 39.130 5.01 0.00 38.90 5.36
3422 5281 4.854173 TCTGAGGCCATATGCAAAAGTTA 58.146 39.130 5.01 0.00 43.89 2.24
3425 5284 4.398988 TGAGGCCATATGCAAAAGTTACAG 59.601 41.667 5.01 0.00 43.89 2.74
3434 5293 3.948473 TGCAAAAGTTACAGCCACAACTA 59.052 39.130 0.00 0.00 33.92 2.24
3435 5294 4.201970 TGCAAAAGTTACAGCCACAACTAC 60.202 41.667 0.00 0.00 33.92 2.73
3439 5298 0.314618 TTACAGCCACAACTACGCGA 59.685 50.000 15.93 0.00 0.00 5.87
3440 5299 0.528924 TACAGCCACAACTACGCGAT 59.471 50.000 15.93 0.00 0.00 4.58
3446 5305 0.516322 CACAACTACGCGATGCAACG 60.516 55.000 15.93 12.54 0.00 4.10
3448 5307 1.373748 AACTACGCGATGCAACGGT 60.374 52.632 15.93 15.41 0.00 4.83
3454 5313 1.821241 CGCGATGCAACGGTAGATGG 61.821 60.000 18.44 0.00 0.00 3.51
3464 5323 1.829222 ACGGTAGATGGTCGGATTGTT 59.171 47.619 0.00 0.00 0.00 2.83
3514 5373 0.892755 AACGTCGGAGCTATTGTCCA 59.107 50.000 0.00 0.00 33.14 4.02
3516 5375 0.249073 CGTCGGAGCTATTGTCCAGG 60.249 60.000 0.00 0.00 33.14 4.45
3525 5384 2.295909 GCTATTGTCCAGGCAAACAACA 59.704 45.455 2.16 0.00 38.14 3.33
3534 5393 1.676006 AGGCAAACAACAGAAGGTTCG 59.324 47.619 0.00 0.00 37.72 3.95
3543 5403 6.937436 ACAACAGAAGGTTCGAATTAAAGT 57.063 33.333 0.00 0.00 37.72 2.66
3553 5413 4.627611 TCGAATTAAAGTCGGACGATCT 57.372 40.909 10.86 0.00 39.01 2.75
3560 5420 0.106669 AGTCGGACGATCTGGGATGA 60.107 55.000 1.89 0.00 0.00 2.92
3564 5424 1.806623 CGGACGATCTGGGATGAAACC 60.807 57.143 0.00 0.00 0.00 3.27
3577 5437 1.060729 TGAAACCCGGACAATCCTGA 58.939 50.000 0.73 0.00 33.30 3.86
3578 5438 1.633432 TGAAACCCGGACAATCCTGAT 59.367 47.619 0.73 0.00 33.30 2.90
3582 5442 3.277142 ACCCGGACAATCCTGATAAAC 57.723 47.619 0.73 0.00 33.30 2.01
3591 5451 2.961526 TCCTGATAAACGTCTGGCTC 57.038 50.000 0.00 0.00 37.20 4.70
3598 5458 2.156051 AAACGTCTGGCTCGGAGTCC 62.156 60.000 7.22 9.10 0.00 3.85
3599 5459 3.062466 CGTCTGGCTCGGAGTCCA 61.062 66.667 10.49 16.65 0.00 4.02
3604 5464 1.305297 TGGCTCGGAGTCCAGACAT 60.305 57.895 10.49 0.00 0.00 3.06
3613 5474 0.107508 AGTCCAGACATCCGGCAATG 60.108 55.000 0.00 0.00 0.00 2.82
3617 5478 1.605710 CCAGACATCCGGCAATGATTC 59.394 52.381 9.97 0.00 0.00 2.52
3625 5486 2.095466 TCCGGCAATGATTCACGTTTTC 60.095 45.455 0.00 0.00 0.00 2.29
3633 5494 4.811555 TGATTCACGTTTTCCTCTGTTG 57.188 40.909 0.00 0.00 0.00 3.33
3635 5496 4.638421 TGATTCACGTTTTCCTCTGTTGTT 59.362 37.500 0.00 0.00 0.00 2.83
3637 5498 2.096819 TCACGTTTTCCTCTGTTGTTGC 59.903 45.455 0.00 0.00 0.00 4.17
3639 5500 2.097466 ACGTTTTCCTCTGTTGTTGCAG 59.903 45.455 0.00 0.00 37.81 4.41
3640 5501 2.354510 CGTTTTCCTCTGTTGTTGCAGA 59.645 45.455 0.00 0.00 42.56 4.26
3641 5502 3.181501 CGTTTTCCTCTGTTGTTGCAGAA 60.182 43.478 0.00 0.00 43.92 3.02
3642 5503 4.354587 GTTTTCCTCTGTTGTTGCAGAAG 58.645 43.478 0.00 0.00 43.92 2.85
3643 5504 3.281727 TTCCTCTGTTGTTGCAGAAGT 57.718 42.857 0.00 0.00 43.92 3.01
3644 5505 2.564771 TCCTCTGTTGTTGCAGAAGTG 58.435 47.619 0.00 0.00 43.92 3.16
3646 5507 3.144506 CCTCTGTTGTTGCAGAAGTGAT 58.855 45.455 0.00 0.00 43.92 3.06
3647 5508 3.058432 CCTCTGTTGTTGCAGAAGTGATG 60.058 47.826 0.00 0.00 43.92 3.07
3648 5509 2.880268 TCTGTTGTTGCAGAAGTGATGG 59.120 45.455 0.00 0.00 41.93 3.51
3649 5510 1.337703 TGTTGTTGCAGAAGTGATGGC 59.662 47.619 0.00 0.00 0.00 4.40
3650 5511 0.961019 TTGTTGCAGAAGTGATGGCC 59.039 50.000 0.00 0.00 0.00 5.36
3651 5512 0.111061 TGTTGCAGAAGTGATGGCCT 59.889 50.000 3.32 0.00 0.00 5.19
3652 5513 1.251251 GTTGCAGAAGTGATGGCCTT 58.749 50.000 3.32 0.00 0.00 4.35
3663 5547 5.549742 AGTGATGGCCTTGAATTGAAAAA 57.450 34.783 3.32 0.00 0.00 1.94
3664 5548 5.299949 AGTGATGGCCTTGAATTGAAAAAC 58.700 37.500 3.32 0.00 0.00 2.43
3683 5567 8.640291 TGAAAAACGTTCAACATAAAAGTTGTC 58.360 29.630 0.00 0.00 46.78 3.18
3693 5577 2.589798 AAAAGTTGTCCGTCTCGTCA 57.410 45.000 0.00 0.00 0.00 4.35
3696 5580 2.135664 AGTTGTCCGTCTCGTCAAAG 57.864 50.000 0.00 0.00 0.00 2.77
3697 5581 1.679680 AGTTGTCCGTCTCGTCAAAGA 59.320 47.619 0.00 0.00 0.00 2.52
3698 5582 2.052157 GTTGTCCGTCTCGTCAAAGAG 58.948 52.381 0.00 0.00 39.52 2.85
3699 5583 0.596577 TGTCCGTCTCGTCAAAGAGG 59.403 55.000 0.00 0.00 38.71 3.69
3700 5584 0.879765 GTCCGTCTCGTCAAAGAGGA 59.120 55.000 0.00 0.00 38.71 3.71
3701 5585 0.879765 TCCGTCTCGTCAAAGAGGAC 59.120 55.000 0.00 0.00 38.71 3.85
3702 5586 0.596577 CCGTCTCGTCAAAGAGGACA 59.403 55.000 0.00 0.00 38.71 4.02
3703 5587 1.000607 CCGTCTCGTCAAAGAGGACAA 60.001 52.381 0.00 0.00 38.71 3.18
3704 5588 2.545113 CCGTCTCGTCAAAGAGGACAAA 60.545 50.000 0.00 0.00 38.71 2.83
3743 5627 0.376152 CCATCAGATGTCTTGTGCGC 59.624 55.000 9.64 0.00 0.00 6.09
3745 5629 0.745845 ATCAGATGTCTTGTGCGCCC 60.746 55.000 4.18 0.00 0.00 6.13
3762 5646 0.105709 CCCTGTGGGTCCCAAAAACT 60.106 55.000 13.78 0.00 38.25 2.66
3763 5647 1.039856 CCTGTGGGTCCCAAAAACTG 58.960 55.000 13.78 4.15 34.18 3.16
3765 5649 2.597455 CTGTGGGTCCCAAAAACTGAT 58.403 47.619 13.78 0.00 34.18 2.90
3768 5652 2.558359 GTGGGTCCCAAAAACTGATCTG 59.442 50.000 13.78 0.00 34.18 2.90
3819 5703 6.658188 TCGGTTAATTTTGGAAGGATTTGT 57.342 33.333 0.00 0.00 0.00 2.83
3837 5721 6.312180 GGATTTGTAGTCCTTTTAGTGTACGG 59.688 42.308 0.00 0.00 32.85 4.02
3843 5727 5.536260 AGTCCTTTTAGTGTACGGAAAGTC 58.464 41.667 10.19 5.64 0.00 3.01
3846 5730 4.689345 CCTTTTAGTGTACGGAAAGTCCAG 59.311 45.833 10.19 0.00 35.91 3.86
3847 5731 3.947910 TTAGTGTACGGAAAGTCCAGG 57.052 47.619 0.00 0.00 35.91 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 130 4.725556 TGTTTGCAGATGACTCGTTAAC 57.274 40.909 0.00 0.00 0.00 2.01
166 168 2.330440 AGATATGTCGCAATGCACCA 57.670 45.000 5.91 0.61 0.00 4.17
215 1959 5.814705 CCTTCTCTTGTCTGCTAAATAGTGG 59.185 44.000 0.00 0.00 0.00 4.00
252 1996 3.284323 TCTCGCCGTATCTATTTCTGC 57.716 47.619 0.00 0.00 0.00 4.26
274 2018 1.559682 GGACTAATGCAAGGAGACCCA 59.440 52.381 0.00 0.00 33.88 4.51
287 2031 2.850695 AACCCGGAGAGAGGACTAAT 57.149 50.000 0.73 0.00 0.00 1.73
288 2032 2.617840 AAACCCGGAGAGAGGACTAA 57.382 50.000 0.73 0.00 0.00 2.24
364 2108 0.038166 GGGTGAGGCTGGTCATGAAA 59.962 55.000 0.00 0.00 0.00 2.69
497 2245 9.118236 GAAGTAACTCATTTTATGCAGAACAAC 57.882 33.333 0.00 0.00 0.00 3.32
595 2344 4.455877 ACGGTTCATCATCTCTTTTTCCAC 59.544 41.667 0.00 0.00 0.00 4.02
596 2345 4.651778 ACGGTTCATCATCTCTTTTTCCA 58.348 39.130 0.00 0.00 0.00 3.53
597 2346 5.064834 GGTACGGTTCATCATCTCTTTTTCC 59.935 44.000 0.00 0.00 0.00 3.13
598 2347 5.875359 AGGTACGGTTCATCATCTCTTTTTC 59.125 40.000 0.00 0.00 0.00 2.29
599 2348 5.643777 CAGGTACGGTTCATCATCTCTTTTT 59.356 40.000 0.00 0.00 0.00 1.94
600 2349 5.178797 CAGGTACGGTTCATCATCTCTTTT 58.821 41.667 0.00 0.00 0.00 2.27
601 2350 4.383118 CCAGGTACGGTTCATCATCTCTTT 60.383 45.833 0.00 0.00 0.00 2.52
602 2351 3.133003 CCAGGTACGGTTCATCATCTCTT 59.867 47.826 0.00 0.00 0.00 2.85
603 2352 2.695666 CCAGGTACGGTTCATCATCTCT 59.304 50.000 0.00 0.00 0.00 3.10
604 2353 2.431057 ACCAGGTACGGTTCATCATCTC 59.569 50.000 0.00 0.00 34.91 2.75
605 2354 2.467880 ACCAGGTACGGTTCATCATCT 58.532 47.619 0.00 0.00 34.91 2.90
606 2355 2.981859 ACCAGGTACGGTTCATCATC 57.018 50.000 0.00 0.00 34.91 2.92
607 2356 3.371965 AGTACCAGGTACGGTTCATCAT 58.628 45.455 21.96 0.64 43.05 2.45
608 2357 2.811410 AGTACCAGGTACGGTTCATCA 58.189 47.619 21.96 0.00 43.05 3.07
609 2358 3.429960 GGAAGTACCAGGTACGGTTCATC 60.430 52.174 23.63 16.19 43.05 2.92
610 2359 2.498885 GGAAGTACCAGGTACGGTTCAT 59.501 50.000 23.63 7.38 43.05 2.57
611 2360 1.895131 GGAAGTACCAGGTACGGTTCA 59.105 52.381 23.63 0.00 43.05 3.18
612 2361 2.174360 AGGAAGTACCAGGTACGGTTC 58.826 52.381 21.96 19.65 43.05 3.62
613 2362 2.315720 AGGAAGTACCAGGTACGGTT 57.684 50.000 21.96 13.11 43.05 4.44
614 2363 2.301009 CAAAGGAAGTACCAGGTACGGT 59.699 50.000 21.96 15.01 43.05 4.83
615 2364 2.301009 ACAAAGGAAGTACCAGGTACGG 59.699 50.000 21.96 10.42 43.05 4.02
616 2365 3.672767 ACAAAGGAAGTACCAGGTACG 57.327 47.619 21.96 9.96 43.05 3.67
617 2366 6.528321 AGTTTACAAAGGAAGTACCAGGTAC 58.472 40.000 20.90 20.90 42.04 3.34
618 2367 6.752285 AGTTTACAAAGGAAGTACCAGGTA 57.248 37.500 0.00 0.00 42.04 3.08
619 2368 5.641789 AGTTTACAAAGGAAGTACCAGGT 57.358 39.130 0.00 0.00 42.04 4.00
620 2369 8.101419 AGATTAGTTTACAAAGGAAGTACCAGG 58.899 37.037 0.00 0.00 42.04 4.45
623 2372 9.096160 GCTAGATTAGTTTACAAAGGAAGTACC 57.904 37.037 0.00 0.00 39.35 3.34
624 2373 8.805688 CGCTAGATTAGTTTACAAAGGAAGTAC 58.194 37.037 0.00 0.00 0.00 2.73
625 2374 8.526147 ACGCTAGATTAGTTTACAAAGGAAGTA 58.474 33.333 0.00 0.00 0.00 2.24
626 2375 7.384477 ACGCTAGATTAGTTTACAAAGGAAGT 58.616 34.615 0.00 0.00 0.00 3.01
627 2376 7.829378 ACGCTAGATTAGTTTACAAAGGAAG 57.171 36.000 0.00 0.00 0.00 3.46
628 2377 8.611654 AAACGCTAGATTAGTTTACAAAGGAA 57.388 30.769 0.00 0.00 36.46 3.36
629 2378 9.362539 CTAAACGCTAGATTAGTTTACAAAGGA 57.637 33.333 0.00 0.00 38.74 3.36
630 2379 9.362539 TCTAAACGCTAGATTAGTTTACAAAGG 57.637 33.333 0.00 0.00 38.74 3.11
680 2429 8.312564 GGTAGAGAAAATTACTACTTCCTGTGT 58.687 37.037 0.00 0.00 37.32 3.72
681 2430 7.488471 CGGTAGAGAAAATTACTACTTCCTGTG 59.512 40.741 0.00 0.00 37.32 3.66
682 2431 7.395489 TCGGTAGAGAAAATTACTACTTCCTGT 59.605 37.037 0.00 0.00 37.32 4.00
683 2432 7.769220 TCGGTAGAGAAAATTACTACTTCCTG 58.231 38.462 0.00 0.00 37.32 3.86
684 2433 7.951347 TCGGTAGAGAAAATTACTACTTCCT 57.049 36.000 0.00 0.00 37.32 3.36
685 2434 9.247126 GATTCGGTAGAGAAAATTACTACTTCC 57.753 37.037 0.00 0.00 37.32 3.46
686 2435 8.956014 CGATTCGGTAGAGAAAATTACTACTTC 58.044 37.037 0.00 0.00 37.32 3.01
687 2436 7.919621 CCGATTCGGTAGAGAAAATTACTACTT 59.080 37.037 17.08 0.00 42.73 2.24
688 2437 7.424001 CCGATTCGGTAGAGAAAATTACTACT 58.576 38.462 17.08 0.00 42.73 2.57
689 2438 7.620397 CCGATTCGGTAGAGAAAATTACTAC 57.380 40.000 17.08 0.00 42.73 2.73
853 2607 0.102481 CTGTACTATCGCGGGCTGTT 59.898 55.000 6.13 0.00 0.00 3.16
866 2620 1.070134 TGTTTTGAGCTCGGCTGTACT 59.930 47.619 9.64 0.00 39.88 2.73
867 2621 1.461127 CTGTTTTGAGCTCGGCTGTAC 59.539 52.381 9.64 2.10 39.88 2.90
868 2622 1.343142 TCTGTTTTGAGCTCGGCTGTA 59.657 47.619 9.64 0.00 39.88 2.74
869 2623 0.106708 TCTGTTTTGAGCTCGGCTGT 59.893 50.000 9.64 0.00 39.88 4.40
881 2635 2.251642 GGTGTCCGCGCTCTGTTTT 61.252 57.895 5.56 0.00 0.00 2.43
920 2674 1.594564 GGAGACCGGCCTATTTCGC 60.595 63.158 0.00 0.00 0.00 4.70
1294 3048 4.907875 CCTCCTCCCCTATGAAGAAATGTA 59.092 45.833 0.00 0.00 0.00 2.29
1296 3050 3.976654 TCCTCCTCCCCTATGAAGAAATG 59.023 47.826 0.00 0.00 0.00 2.32
1297 3051 4.077745 TCTCCTCCTCCCCTATGAAGAAAT 60.078 45.833 0.00 0.00 0.00 2.17
1299 3053 2.865809 TCTCCTCCTCCCCTATGAAGAA 59.134 50.000 0.00 0.00 0.00 2.52
1302 3056 3.472848 AGATTCTCCTCCTCCCCTATGAA 59.527 47.826 0.00 0.00 0.00 2.57
1304 3058 3.172339 CAGATTCTCCTCCTCCCCTATG 58.828 54.545 0.00 0.00 0.00 2.23
1325 3131 2.159085 AGAAAGCATCCTGGCTACGTAC 60.159 50.000 0.00 0.00 45.07 3.67
1326 3132 2.108168 AGAAAGCATCCTGGCTACGTA 58.892 47.619 0.00 0.00 45.07 3.57
1327 3133 0.905357 AGAAAGCATCCTGGCTACGT 59.095 50.000 0.00 0.00 45.07 3.57
1328 3134 2.866762 GTTAGAAAGCATCCTGGCTACG 59.133 50.000 0.00 0.00 45.07 3.51
1404 3213 1.410083 GCCAGGCCCTGTCAATCAATA 60.410 52.381 10.47 0.00 0.00 1.90
1409 3218 2.357836 CAGCCAGGCCCTGTCAAT 59.642 61.111 10.47 0.00 0.00 2.57
1410 3219 4.666253 GCAGCCAGGCCCTGTCAA 62.666 66.667 10.47 0.00 32.93 3.18
1412 3221 4.792804 GAGCAGCCAGGCCCTGTC 62.793 72.222 10.47 0.00 32.93 3.51
1568 3381 2.288152 CGGCCATTTTGTTAGCACAGTT 60.288 45.455 2.24 0.00 33.22 3.16
1569 3382 1.269448 CGGCCATTTTGTTAGCACAGT 59.731 47.619 2.24 0.00 33.22 3.55
1570 3383 1.402720 CCGGCCATTTTGTTAGCACAG 60.403 52.381 2.24 0.00 33.22 3.66
1624 3437 2.685380 ACGGGGCTCTCCAGGAAG 60.685 66.667 0.00 0.00 37.22 3.46
1753 3566 3.718210 CTCGCGGCCCTTGTACTCC 62.718 68.421 6.13 0.00 0.00 3.85
1895 3708 1.134907 CAATTGTTGGCTCTGATGGGC 60.135 52.381 0.00 0.00 0.00 5.36
1912 3728 2.736719 CGATCTCAAGCTGACGGACAAT 60.737 50.000 0.00 0.00 0.00 2.71
1918 3734 2.223456 ACTCATCGATCTCAAGCTGACG 60.223 50.000 0.00 0.00 0.00 4.35
2006 3843 3.056458 CGGTGCCACAGGTACTCA 58.944 61.111 0.00 0.00 38.37 3.41
2165 4002 3.128349 GACTTTCTTGTCGTGGCAAGTA 58.872 45.455 13.38 1.86 44.41 2.24
2219 4056 6.309009 CAGTAGTTCAAGTAGCATGTACAGTG 59.691 42.308 0.33 1.44 0.00 3.66
2223 4060 5.721232 ACCAGTAGTTCAAGTAGCATGTAC 58.279 41.667 0.00 0.00 0.00 2.90
2249 4087 1.890979 GTGCAGCTGCCGCTCATAT 60.891 57.895 34.64 0.00 45.15 1.78
2352 4190 2.031919 TGGATCGCCGTTTGCACT 59.968 55.556 0.00 0.00 41.33 4.40
2463 4301 3.927481 GACCAGGGCCTTGAGGTGC 62.927 68.421 18.01 6.93 37.57 5.01
2516 4354 3.367910 GGATCGACTGAAGAGAAGTGCTT 60.368 47.826 0.00 0.00 0.00 3.91
2518 4356 2.165437 AGGATCGACTGAAGAGAAGTGC 59.835 50.000 0.00 0.00 0.00 4.40
2532 4370 1.100510 CTTCACACCGGTAGGATCGA 58.899 55.000 6.87 0.00 41.02 3.59
2548 4386 4.507388 GCAATGCTCTCACTAGTGATCTTC 59.493 45.833 25.35 14.77 39.13 2.87
2550 4388 3.181467 GGCAATGCTCTCACTAGTGATCT 60.181 47.826 25.35 6.52 39.13 2.75
2551 4389 3.129871 GGCAATGCTCTCACTAGTGATC 58.870 50.000 25.35 17.00 39.13 2.92
2559 4397 3.044059 GCCACGGCAATGCTCTCAC 62.044 63.158 4.82 0.00 41.49 3.51
2878 4716 0.805711 CATCATACACACGCGAGGCA 60.806 55.000 15.93 0.00 0.00 4.75
2879 4717 0.527600 TCATCATACACACGCGAGGC 60.528 55.000 15.93 0.00 0.00 4.70
2880 4718 1.788886 CATCATCATACACACGCGAGG 59.211 52.381 15.93 7.12 0.00 4.63
2881 4719 2.731217 TCATCATCATACACACGCGAG 58.269 47.619 15.93 7.88 0.00 5.03
2882 4720 2.861462 TCATCATCATACACACGCGA 57.139 45.000 15.93 0.00 0.00 5.87
2883 4721 2.089581 CGATCATCATCATACACACGCG 59.910 50.000 3.53 3.53 0.00 6.01
2884 4722 3.308530 TCGATCATCATCATACACACGC 58.691 45.455 0.00 0.00 0.00 5.34
2885 4723 4.325472 CCATCGATCATCATCATACACACG 59.675 45.833 0.00 0.00 0.00 4.49
2886 4724 5.233225 ACCATCGATCATCATCATACACAC 58.767 41.667 0.00 0.00 0.00 3.82
2986 4828 6.711277 AGAAGCCAATCAAGTGTGAGTAATA 58.289 36.000 0.00 0.00 37.14 0.98
2991 4833 3.672808 AGAGAAGCCAATCAAGTGTGAG 58.327 45.455 0.00 0.00 37.14 3.51
3029 4871 2.844966 TGATAAACAATCCACGGGGGTA 59.155 45.455 2.42 0.00 38.11 3.69
3032 4874 2.034558 GCATGATAAACAATCCACGGGG 59.965 50.000 0.00 0.00 33.22 5.73
3038 4880 3.694734 CCGTGTGCATGATAAACAATCC 58.305 45.455 0.00 0.00 33.22 3.01
3120 4965 5.592054 TGTGTCAAAAACTGTTGTCAACAA 58.408 33.333 18.68 0.00 41.61 2.83
3129 4974 5.856455 CGTTTTCTTCTGTGTCAAAAACTGT 59.144 36.000 0.00 0.00 37.56 3.55
3139 4984 7.307989 CCATCTTGATTACGTTTTCTTCTGTGT 60.308 37.037 0.00 0.00 0.00 3.72
3142 4987 6.024049 GCCATCTTGATTACGTTTTCTTCTG 58.976 40.000 0.00 0.00 0.00 3.02
3143 4988 5.123979 GGCCATCTTGATTACGTTTTCTTCT 59.876 40.000 0.00 0.00 0.00 2.85
3220 5065 6.485830 TGGTGATGACCCAAACATTAAAAA 57.514 33.333 0.00 0.00 42.34 1.94
3225 5070 3.099141 GGATGGTGATGACCCAAACATT 58.901 45.455 0.00 0.00 42.34 2.71
3285 5143 6.395629 GTGTAATCAGCTAAACAGTACTCCA 58.604 40.000 0.00 0.00 0.00 3.86
3292 5150 4.242475 TGGACGTGTAATCAGCTAAACAG 58.758 43.478 0.00 0.00 0.00 3.16
3293 5151 4.260139 TGGACGTGTAATCAGCTAAACA 57.740 40.909 0.00 0.00 0.00 2.83
3298 5156 2.831685 TGTTGGACGTGTAATCAGCT 57.168 45.000 0.00 0.00 0.00 4.24
3301 5159 4.200874 AGGTTTTGTTGGACGTGTAATCA 58.799 39.130 0.00 0.00 0.00 2.57
3304 5162 3.607741 TGAGGTTTTGTTGGACGTGTAA 58.392 40.909 0.00 0.00 0.00 2.41
3309 5167 3.138304 TCATCTGAGGTTTTGTTGGACG 58.862 45.455 0.00 0.00 0.00 4.79
3311 5169 6.154363 AGTTTTTCATCTGAGGTTTTGTTGGA 59.846 34.615 0.00 0.00 0.00 3.53
3335 5193 5.406780 GGCGAAGACAATCCATGTAGAATAG 59.593 44.000 0.00 0.00 44.12 1.73
3340 5198 3.126831 GAGGCGAAGACAATCCATGTAG 58.873 50.000 0.00 0.00 44.12 2.74
3395 5254 3.581265 TGCATATGGCCTCAGATTGAA 57.419 42.857 3.32 0.00 43.89 2.69
3407 5266 4.082300 TGTGGCTGTAACTTTTGCATATGG 60.082 41.667 4.56 0.00 0.00 2.74
3408 5267 5.058149 TGTGGCTGTAACTTTTGCATATG 57.942 39.130 0.00 0.00 0.00 1.78
3409 5268 5.243730 AGTTGTGGCTGTAACTTTTGCATAT 59.756 36.000 0.00 0.00 33.59 1.78
3422 5281 1.014044 CATCGCGTAGTTGTGGCTGT 61.014 55.000 5.77 0.00 0.00 4.40
3425 5284 1.906994 TTGCATCGCGTAGTTGTGGC 61.907 55.000 5.77 0.13 0.00 5.01
3434 5293 1.141019 ATCTACCGTTGCATCGCGT 59.859 52.632 11.68 12.67 0.00 6.01
3435 5294 1.559814 CATCTACCGTTGCATCGCG 59.440 57.895 11.68 0.00 0.00 5.87
3439 5298 0.179084 CCGACCATCTACCGTTGCAT 60.179 55.000 0.00 0.00 0.00 3.96
3440 5299 1.216977 CCGACCATCTACCGTTGCA 59.783 57.895 0.00 0.00 0.00 4.08
3446 5305 2.470821 CGAACAATCCGACCATCTACC 58.529 52.381 0.00 0.00 0.00 3.18
3448 5307 1.411246 CCCGAACAATCCGACCATCTA 59.589 52.381 0.00 0.00 0.00 1.98
3454 5313 0.320946 TCCAACCCGAACAATCCGAC 60.321 55.000 0.00 0.00 0.00 4.79
3503 5362 2.558359 GTTGTTTGCCTGGACAATAGCT 59.442 45.455 0.00 0.00 37.98 3.32
3514 5373 1.676006 CGAACCTTCTGTTGTTTGCCT 59.324 47.619 0.00 0.00 37.29 4.75
3516 5375 3.414549 TTCGAACCTTCTGTTGTTTGC 57.585 42.857 0.00 0.00 37.29 3.68
3525 5384 4.928020 GTCCGACTTTAATTCGAACCTTCT 59.072 41.667 0.00 0.00 38.85 2.85
3534 5393 3.802685 CCCAGATCGTCCGACTTTAATTC 59.197 47.826 0.00 0.00 0.00 2.17
3543 5403 1.136305 GTTTCATCCCAGATCGTCCGA 59.864 52.381 0.00 0.00 0.00 4.55
3560 5420 4.014406 GTTTATCAGGATTGTCCGGGTTT 58.986 43.478 0.00 0.00 42.75 3.27
3564 5424 2.864343 GACGTTTATCAGGATTGTCCGG 59.136 50.000 0.00 0.00 42.75 5.14
3577 5437 1.134560 GACTCCGAGCCAGACGTTTAT 59.865 52.381 0.00 0.00 0.00 1.40
3578 5438 0.524862 GACTCCGAGCCAGACGTTTA 59.475 55.000 0.00 0.00 0.00 2.01
3582 5442 3.062466 TGGACTCCGAGCCAGACG 61.062 66.667 7.29 0.00 0.00 4.18
3591 5451 2.808315 CCGGATGTCTGGACTCCG 59.192 66.667 22.36 22.36 45.36 4.63
3598 5458 2.032550 GTGAATCATTGCCGGATGTCTG 59.967 50.000 5.05 0.00 0.00 3.51
3599 5459 2.292267 GTGAATCATTGCCGGATGTCT 58.708 47.619 5.05 0.00 0.00 3.41
3604 5464 1.529226 AAACGTGAATCATTGCCGGA 58.471 45.000 5.05 0.00 0.00 5.14
3613 5474 4.813296 ACAACAGAGGAAAACGTGAATC 57.187 40.909 0.00 0.00 0.00 2.52
3617 5478 2.159448 TGCAACAACAGAGGAAAACGTG 60.159 45.455 0.00 0.00 0.00 4.49
3625 5486 2.564771 TCACTTCTGCAACAACAGAGG 58.435 47.619 2.51 2.51 46.85 3.69
3633 5494 1.068055 CAAGGCCATCACTTCTGCAAC 60.068 52.381 5.01 0.00 0.00 4.17
3635 5496 0.401356 TCAAGGCCATCACTTCTGCA 59.599 50.000 5.01 0.00 0.00 4.41
3637 5498 3.760151 TCAATTCAAGGCCATCACTTCTG 59.240 43.478 5.01 0.00 0.00 3.02
3639 5500 4.789012 TTCAATTCAAGGCCATCACTTC 57.211 40.909 5.01 0.00 0.00 3.01
3640 5501 5.549742 TTTTCAATTCAAGGCCATCACTT 57.450 34.783 5.01 0.00 0.00 3.16
3641 5502 5.299949 GTTTTTCAATTCAAGGCCATCACT 58.700 37.500 5.01 0.00 0.00 3.41
3642 5503 4.150451 CGTTTTTCAATTCAAGGCCATCAC 59.850 41.667 5.01 0.00 0.00 3.06
3643 5504 4.202202 ACGTTTTTCAATTCAAGGCCATCA 60.202 37.500 5.01 0.00 0.00 3.07
3644 5505 4.306600 ACGTTTTTCAATTCAAGGCCATC 58.693 39.130 5.01 0.00 0.00 3.51
3646 5507 3.810310 ACGTTTTTCAATTCAAGGCCA 57.190 38.095 5.01 0.00 0.00 5.36
3647 5508 4.116238 TGAACGTTTTTCAATTCAAGGCC 58.884 39.130 0.46 0.00 0.00 5.19
3648 5509 5.062809 TGTTGAACGTTTTTCAATTCAAGGC 59.937 36.000 0.46 0.00 40.67 4.35
3649 5510 6.639671 TGTTGAACGTTTTTCAATTCAAGG 57.360 33.333 0.46 0.00 40.67 3.61
3683 5567 0.596577 TGTCCTCTTTGACGAGACGG 59.403 55.000 0.00 0.00 38.11 4.79
3693 5577 4.039609 CCCAAGAGCAAATTTGTCCTCTTT 59.960 41.667 25.91 15.41 0.00 2.52
3696 5580 3.157087 TCCCAAGAGCAAATTTGTCCTC 58.843 45.455 19.03 16.50 0.00 3.71
3697 5581 3.160269 CTCCCAAGAGCAAATTTGTCCT 58.840 45.455 19.03 13.01 32.13 3.85
3698 5582 2.893489 ACTCCCAAGAGCAAATTTGTCC 59.107 45.455 19.03 11.10 44.65 4.02
3699 5583 5.649831 AGATACTCCCAAGAGCAAATTTGTC 59.350 40.000 19.03 14.35 44.65 3.18
3700 5584 5.574188 AGATACTCCCAAGAGCAAATTTGT 58.426 37.500 19.03 6.52 44.65 2.83
3701 5585 5.067023 GGAGATACTCCCAAGAGCAAATTTG 59.933 44.000 14.03 14.03 44.36 2.32
3702 5586 5.196695 GGAGATACTCCCAAGAGCAAATTT 58.803 41.667 6.54 0.00 44.36 1.82
3703 5587 4.786425 GGAGATACTCCCAAGAGCAAATT 58.214 43.478 6.54 0.00 44.36 1.82
3704 5588 4.429854 GGAGATACTCCCAAGAGCAAAT 57.570 45.455 6.54 0.00 44.36 2.32
3729 5613 1.376424 CAGGGCGCACAAGACATCT 60.376 57.895 14.57 0.00 0.00 2.90
3733 5617 3.357079 CCACAGGGCGCACAAGAC 61.357 66.667 14.57 0.00 0.00 3.01
3745 5629 2.065899 TCAGTTTTTGGGACCCACAG 57.934 50.000 14.59 0.00 30.78 3.66
3783 5667 8.301002 CCAAAATTAACCGAACTTGGATTTAGA 58.699 33.333 0.00 0.00 36.23 2.10
3819 5703 6.294731 GGACTTTCCGTACACTAAAAGGACTA 60.295 42.308 0.00 0.00 33.92 2.59
3829 5713 0.320697 GCCTGGACTTTCCGTACACT 59.679 55.000 0.00 0.00 40.17 3.55
3837 5721 3.842869 ATGAGACGCCTGGACTTTC 57.157 52.632 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.