Multiple sequence alignment - TraesCS4B01G022900

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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 TraesCS4B01G022900 chr4B 100.000 3315 0 0 1 3315 16815301 16811987 0.000000e+00 6122.0
1 TraesCS4B01G022900 chr4D 86.100 1813 99 56 652 2417 8891855 8890149 0.000000e+00 1810.0
2 TraesCS4B01G022900 chr4D 86.901 710 46 25 2639 3315 8890064 8889369 0.000000e+00 752.0
3 TraesCS4B01G022900 chr4D 90.404 198 14 4 667 862 8892536 8892342 4.240000e-64 255.0
4 TraesCS4B01G022900 chr4A 86.278 1647 88 43 822 2401 594441670 594443245 0.000000e+00 1663.0
5 TraesCS4B01G022900 chr4A 82.305 859 54 32 2507 3312 594448531 594449344 0.000000e+00 654.0
6 TraesCS4B01G022900 chr3B 93.003 686 38 7 1 679 136791899 136791217 0.000000e+00 992.0
7 TraesCS4B01G022900 chr3B 92.636 679 42 4 1 678 41013166 41013837 0.000000e+00 970.0
8 TraesCS4B01G022900 chr1B 92.962 682 40 4 2 681 642180759 642181434 0.000000e+00 987.0
9 TraesCS4B01G022900 chr2D 91.971 685 45 10 1 678 398461589 398462270 0.000000e+00 952.0
10 TraesCS4B01G022900 chr2D 77.757 526 80 17 1228 1739 586619266 586619768 4.180000e-74 289.0
11 TraesCS4B01G022900 chr6D 91.777 681 52 4 1 678 283558615 283559294 0.000000e+00 944.0
12 TraesCS4B01G022900 chr3D 91.912 680 48 6 1 676 23505496 23504820 0.000000e+00 944.0
13 TraesCS4B01G022900 chr2B 91.900 679 50 2 1 678 735955853 735955179 0.000000e+00 944.0
14 TraesCS4B01G022900 chr5B 91.654 683 51 5 1 680 667519988 667520667 0.000000e+00 941.0
15 TraesCS4B01G022900 chr5B 91.654 683 50 5 1 680 666877488 666878166 0.000000e+00 939.0
16 TraesCS4B01G022900 chr5B 83.099 71 11 1 2517 2586 563604755 563604825 2.760000e-06 63.9
17 TraesCS4B01G022900 chr3A 81.148 488 64 8 1623 2103 267019853 267019387 1.880000e-97 366.0
18 TraesCS4B01G022900 chr3A 86.111 144 8 6 2103 2237 267018158 267018018 9.580000e-31 145.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G022900 chr4B 16811987 16815301 3314 True 6122.0 6122 100.000000 1 3315 1 chr4B.!!$R1 3314
1 TraesCS4B01G022900 chr4D 8889369 8892536 3167 True 939.0 1810 87.801667 652 3315 3 chr4D.!!$R1 2663
2 TraesCS4B01G022900 chr4A 594441670 594443245 1575 False 1663.0 1663 86.278000 822 2401 1 chr4A.!!$F1 1579
3 TraesCS4B01G022900 chr4A 594448531 594449344 813 False 654.0 654 82.305000 2507 3312 1 chr4A.!!$F2 805
4 TraesCS4B01G022900 chr3B 136791217 136791899 682 True 992.0 992 93.003000 1 679 1 chr3B.!!$R1 678
5 TraesCS4B01G022900 chr3B 41013166 41013837 671 False 970.0 970 92.636000 1 678 1 chr3B.!!$F1 677
6 TraesCS4B01G022900 chr1B 642180759 642181434 675 False 987.0 987 92.962000 2 681 1 chr1B.!!$F1 679
7 TraesCS4B01G022900 chr2D 398461589 398462270 681 False 952.0 952 91.971000 1 678 1 chr2D.!!$F1 677
8 TraesCS4B01G022900 chr2D 586619266 586619768 502 False 289.0 289 77.757000 1228 1739 1 chr2D.!!$F2 511
9 TraesCS4B01G022900 chr6D 283558615 283559294 679 False 944.0 944 91.777000 1 678 1 chr6D.!!$F1 677
10 TraesCS4B01G022900 chr3D 23504820 23505496 676 True 944.0 944 91.912000 1 676 1 chr3D.!!$R1 675
11 TraesCS4B01G022900 chr2B 735955179 735955853 674 True 944.0 944 91.900000 1 678 1 chr2B.!!$R1 677
12 TraesCS4B01G022900 chr5B 667519988 667520667 679 False 941.0 941 91.654000 1 680 1 chr5B.!!$F3 679
13 TraesCS4B01G022900 chr5B 666877488 666878166 678 False 939.0 939 91.654000 1 680 1 chr5B.!!$F2 679
14 TraesCS4B01G022900 chr3A 267018018 267019853 1835 True 255.5 366 83.629500 1623 2237 2 chr3A.!!$R1 614

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
968 1655 0.249911 AGAGAAACCACGCACTGACC 60.25 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 4359 0.039035 GGCAACATGGAACCTACCCA 59.961 55.0 0.0 0.0 38.19 4.51 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
80 81 3.437795 CAGGCAAAGGCAGCTCGG 61.438 66.667 0.00 0.00 43.71 4.63
132 133 2.044946 GAGGTGGCCCTTGCGATT 60.045 61.111 0.00 0.00 42.86 3.34
215 216 4.531912 GATGCTCGACGCCGACGA 62.532 66.667 11.53 11.53 43.93 4.20
271 275 2.384933 TTTGGAGGCTGGCATGGGTT 62.385 55.000 3.38 0.00 0.00 4.11
385 389 3.442273 GGCGAGGACAACCATTCATTTTA 59.558 43.478 0.00 0.00 38.94 1.52
430 434 2.031616 CTGATGCCGGCGATGGAT 59.968 61.111 23.90 9.28 0.00 3.41
445 449 2.584608 GATGTGTAGGCCGCTGGT 59.415 61.111 0.00 0.00 0.00 4.00
544 555 1.813786 CGCGAAAAGGATGGGGTAAAA 59.186 47.619 0.00 0.00 0.00 1.52
549 560 4.097892 CGAAAAGGATGGGGTAAAAGATGG 59.902 45.833 0.00 0.00 0.00 3.51
592 603 2.786495 CCGCATCGTAGGACAGGCT 61.786 63.158 0.00 0.00 0.00 4.58
593 604 1.589993 CGCATCGTAGGACAGGCTG 60.590 63.158 14.16 14.16 0.00 4.85
673 687 2.028484 GTCACGCGTGGAGTTGGA 59.972 61.111 36.41 14.91 0.00 3.53
691 705 2.291670 TGGACTAACTCTCACCTCCTCC 60.292 54.545 0.00 0.00 0.00 4.30
692 706 2.024751 GGACTAACTCTCACCTCCTCCT 60.025 54.545 0.00 0.00 0.00 3.69
693 707 3.202595 GGACTAACTCTCACCTCCTCCTA 59.797 52.174 0.00 0.00 0.00 2.94
694 708 4.141111 GGACTAACTCTCACCTCCTCCTAT 60.141 50.000 0.00 0.00 0.00 2.57
700 714 4.959839 ACTCTCACCTCCTCCTATTCTTTC 59.040 45.833 0.00 0.00 0.00 2.62
701 715 5.208121 CTCTCACCTCCTCCTATTCTTTCT 58.792 45.833 0.00 0.00 0.00 2.52
715 730 4.307032 TTCTTTCTTTCTCCCTCCATGG 57.693 45.455 4.97 4.97 0.00 3.66
716 731 2.025887 TCTTTCTTTCTCCCTCCATGGC 60.026 50.000 6.96 0.00 0.00 4.40
723 738 3.414193 CCCTCCATGGCTGCCTCA 61.414 66.667 21.03 0.00 0.00 3.86
764 779 1.141053 ACACACACCCTCACTCCTTTC 59.859 52.381 0.00 0.00 0.00 2.62
766 781 0.764890 CACACCCTCACTCCTTTCCA 59.235 55.000 0.00 0.00 0.00 3.53
770 785 2.234908 CACCCTCACTCCTTTCCACTAG 59.765 54.545 0.00 0.00 0.00 2.57
807 822 2.725008 GACCCCGATCGAGCAGAG 59.275 66.667 18.66 0.00 0.00 3.35
809 824 3.531207 CCCCGATCGAGCAGAGCA 61.531 66.667 18.66 0.00 34.30 4.26
826 841 1.927210 CAGACACACTGCACGACAC 59.073 57.895 0.00 0.00 39.86 3.67
856 1543 1.484240 CAGACACCTCCTTCTCCATCC 59.516 57.143 0.00 0.00 0.00 3.51
857 1544 0.833949 GACACCTCCTTCTCCATCCC 59.166 60.000 0.00 0.00 0.00 3.85
858 1545 0.621862 ACACCTCCTTCTCCATCCCC 60.622 60.000 0.00 0.00 0.00 4.81
859 1546 0.621571 CACCTCCTTCTCCATCCCCA 60.622 60.000 0.00 0.00 0.00 4.96
860 1547 0.327000 ACCTCCTTCTCCATCCCCAG 60.327 60.000 0.00 0.00 0.00 4.45
861 1548 1.704007 CCTCCTTCTCCATCCCCAGC 61.704 65.000 0.00 0.00 0.00 4.85
955 1642 2.805671 CCACACATGCGTACAAGAGAAA 59.194 45.455 0.00 0.00 0.00 2.52
967 1654 1.261619 CAAGAGAAACCACGCACTGAC 59.738 52.381 0.00 0.00 0.00 3.51
968 1655 0.249911 AGAGAAACCACGCACTGACC 60.250 55.000 0.00 0.00 0.00 4.02
994 1681 4.047125 CACCCCCAATCACCGCCT 62.047 66.667 0.00 0.00 0.00 5.52
995 1682 3.728373 ACCCCCAATCACCGCCTC 61.728 66.667 0.00 0.00 0.00 4.70
996 1683 4.506255 CCCCCAATCACCGCCTCC 62.506 72.222 0.00 0.00 0.00 4.30
997 1684 4.856801 CCCCAATCACCGCCTCCG 62.857 72.222 0.00 0.00 0.00 4.63
1102 1789 0.603569 CTTAGTCAGTGAGCCACGGT 59.396 55.000 0.00 0.00 39.64 4.83
1105 1792 1.227556 GTCAGTGAGCCACGGTTGT 60.228 57.895 0.00 0.00 39.64 3.32
1106 1793 1.227527 TCAGTGAGCCACGGTTGTG 60.228 57.895 0.00 0.00 46.00 3.33
1127 1834 3.327404 TCCAAGAAGGGGCGGGAC 61.327 66.667 0.00 0.00 38.24 4.46
1131 1838 1.689582 AAGAAGGGGCGGGACCTAG 60.690 63.158 0.00 0.00 37.35 3.02
1346 2053 0.321671 TTCAAGAAGAGGAGCGGTGG 59.678 55.000 0.00 0.00 0.00 4.61
1349 2056 4.821589 GAAGAGGAGCGGTGGCGG 62.822 72.222 0.00 0.00 46.35 6.13
1443 2154 3.860930 AAATCTTGGCGGCGGGTGT 62.861 57.895 9.78 0.00 0.00 4.16
1456 2167 3.656045 GGTGTTTCACCGGCGTGG 61.656 66.667 6.01 0.00 44.95 4.94
1457 2168 3.656045 GTGTTTCACCGGCGTGGG 61.656 66.667 6.01 0.00 44.64 4.61
1539 2259 3.134127 GCCCGTGCCATGGAGTTC 61.134 66.667 18.40 0.00 0.00 3.01
1558 2290 1.013539 GACGACGAGTACGAGCGAG 60.014 63.158 0.00 8.06 42.66 5.03
1678 2411 0.603975 GCATCCCCGATGTAAGCTCC 60.604 60.000 3.74 0.00 41.60 4.70
1682 2415 1.048724 CCCCGATGTAAGCTCCCTGA 61.049 60.000 0.00 0.00 0.00 3.86
1684 2417 1.115467 CCGATGTAAGCTCCCTGACT 58.885 55.000 0.00 0.00 0.00 3.41
1690 2423 4.207891 TGTAAGCTCCCTGACTTCAATC 57.792 45.455 0.00 0.00 0.00 2.67
1714 2450 0.900182 ACGCCATGGACTCACTCTCA 60.900 55.000 18.40 0.00 0.00 3.27
1762 2505 6.124088 TCTTTCTTGTTTTGCTCTGTTCTC 57.876 37.500 0.00 0.00 0.00 2.87
1764 2507 5.741388 TTCTTGTTTTGCTCTGTTCTCTC 57.259 39.130 0.00 0.00 0.00 3.20
1817 2563 3.987594 GGGAGCTCACCCTCAATTT 57.012 52.632 17.19 0.00 45.90 1.82
1818 2564 2.222227 GGGAGCTCACCCTCAATTTT 57.778 50.000 17.19 0.00 45.90 1.82
1819 2565 1.821136 GGGAGCTCACCCTCAATTTTG 59.179 52.381 17.19 0.00 45.90 2.44
1834 2580 5.634118 TCAATTTTGTCCTCAGACTTCCAT 58.366 37.500 0.00 0.00 43.91 3.41
1919 2671 1.748493 CAGAGGAAGAGGACGAAGAGG 59.252 57.143 0.00 0.00 0.00 3.69
1981 2745 3.209812 TCGTGGGAGAGGATCGCG 61.210 66.667 0.00 0.00 43.67 5.87
2030 2794 1.217779 GAGCTGGACCTGTCAGAGC 59.782 63.158 0.00 10.85 37.07 4.09
2031 2795 1.534959 AGCTGGACCTGTCAGAGCA 60.535 57.895 17.66 0.27 38.40 4.26
2033 2797 2.052779 CTGGACCTGTCAGAGCACA 58.947 57.895 0.00 0.00 34.36 4.57
2034 2798 0.320247 CTGGACCTGTCAGAGCACAC 60.320 60.000 0.00 0.00 34.36 3.82
2046 2810 2.177531 GCACACGCAGCAATGGAG 59.822 61.111 0.00 0.00 38.36 3.86
2047 2811 2.872557 CACACGCAGCAATGGAGG 59.127 61.111 0.00 0.00 0.00 4.30
2048 2812 1.672030 CACACGCAGCAATGGAGGA 60.672 57.895 0.00 0.00 0.00 3.71
2056 2820 2.599597 CAATGGAGGAGGGGGCTG 59.400 66.667 0.00 0.00 0.00 4.85
2057 2821 2.697644 AATGGAGGAGGGGGCTGG 60.698 66.667 0.00 0.00 0.00 4.85
2089 2853 2.276116 GGAGATCGGCGCCAGGATA 61.276 63.158 28.98 6.03 36.33 2.59
2168 4161 7.197071 TCACACTGTACATTATTTTCACCAC 57.803 36.000 0.00 0.00 0.00 4.16
2202 4198 2.746362 CAGACAGACAAATTGAGAGGGC 59.254 50.000 0.00 0.00 0.00 5.19
2287 4309 9.472361 CTTCTTGATGTGAAGATCATTTTGTTT 57.528 29.630 0.00 0.00 42.37 2.83
2288 4310 9.820725 TTCTTGATGTGAAGATCATTTTGTTTT 57.179 25.926 0.00 0.00 32.35 2.43
2289 4311 9.251792 TCTTGATGTGAAGATCATTTTGTTTTG 57.748 29.630 0.00 0.00 32.35 2.44
2290 4312 8.945481 TTGATGTGAAGATCATTTTGTTTTGT 57.055 26.923 0.00 0.00 32.35 2.83
2291 4313 8.945481 TGATGTGAAGATCATTTTGTTTTGTT 57.055 26.923 0.00 0.00 0.00 2.83
2299 4321 2.700722 TTTTGTTTTGTTCCCCAGCC 57.299 45.000 0.00 0.00 0.00 4.85
2321 4343 2.486191 CCAAAGTCTTGGTCTGCTCTGT 60.486 50.000 0.00 0.00 46.25 3.41
2322 4344 2.540265 AAGTCTTGGTCTGCTCTGTG 57.460 50.000 0.00 0.00 0.00 3.66
2334 4356 1.763770 CTCTGTGCCTGGGGACTTT 59.236 57.895 12.21 0.00 37.36 2.66
2335 4357 0.607489 CTCTGTGCCTGGGGACTTTG 60.607 60.000 12.21 3.69 37.36 2.77
2336 4358 2.203480 TGTGCCTGGGGACTTTGC 60.203 61.111 12.21 0.00 37.36 3.68
2337 4359 2.116125 GTGCCTGGGGACTTTGCT 59.884 61.111 4.01 0.00 33.56 3.91
2339 4361 2.677875 GCCTGGGGACTTTGCTGG 60.678 66.667 0.00 0.00 0.00 4.85
2340 4362 2.036256 CCTGGGGACTTTGCTGGG 59.964 66.667 0.00 0.00 0.00 4.45
2341 4363 2.845345 CCTGGGGACTTTGCTGGGT 61.845 63.158 0.00 0.00 0.00 4.51
2342 4364 1.497309 CCTGGGGACTTTGCTGGGTA 61.497 60.000 0.00 0.00 0.00 3.69
2355 4377 1.463674 CTGGGTAGGTTCCATGTTGC 58.536 55.000 0.00 0.00 33.29 4.17
2356 4378 0.039035 TGGGTAGGTTCCATGTTGCC 59.961 55.000 0.00 0.00 0.00 4.52
2359 4381 2.421529 GGGTAGGTTCCATGTTGCCTAG 60.422 54.545 6.64 0.00 34.62 3.02
2377 4399 4.550422 CCTAGTCTGCAAAAAGAAAAGGC 58.450 43.478 0.00 0.00 0.00 4.35
2402 4424 8.026607 GCAATTCTAGTAGTGCAATGGTTTTTA 58.973 33.333 15.66 0.00 36.97 1.52
2407 4429 8.545472 TCTAGTAGTGCAATGGTTTTTATAGGT 58.455 33.333 0.00 0.00 0.00 3.08
2408 4430 7.625828 AGTAGTGCAATGGTTTTTATAGGTC 57.374 36.000 0.00 0.00 0.00 3.85
2409 4431 7.172342 AGTAGTGCAATGGTTTTTATAGGTCA 58.828 34.615 0.00 0.00 0.00 4.02
2410 4432 6.515272 AGTGCAATGGTTTTTATAGGTCAG 57.485 37.500 0.00 0.00 0.00 3.51
2411 4433 6.245408 AGTGCAATGGTTTTTATAGGTCAGA 58.755 36.000 0.00 0.00 0.00 3.27
2413 4435 5.652014 TGCAATGGTTTTTATAGGTCAGAGG 59.348 40.000 0.00 0.00 0.00 3.69
2414 4436 5.450550 GCAATGGTTTTTATAGGTCAGAGGC 60.451 44.000 0.00 0.00 0.00 4.70
2415 4437 4.919774 TGGTTTTTATAGGTCAGAGGCA 57.080 40.909 0.00 0.00 0.00 4.75
2416 4438 5.249780 TGGTTTTTATAGGTCAGAGGCAA 57.750 39.130 0.00 0.00 0.00 4.52
2417 4439 5.636123 TGGTTTTTATAGGTCAGAGGCAAA 58.364 37.500 0.00 0.00 0.00 3.68
2418 4440 6.071984 TGGTTTTTATAGGTCAGAGGCAAAA 58.928 36.000 0.00 0.00 0.00 2.44
2419 4441 6.208599 TGGTTTTTATAGGTCAGAGGCAAAAG 59.791 38.462 0.00 0.00 0.00 2.27
2420 4442 6.433093 GGTTTTTATAGGTCAGAGGCAAAAGA 59.567 38.462 0.00 0.00 0.00 2.52
2421 4443 7.122799 GGTTTTTATAGGTCAGAGGCAAAAGAT 59.877 37.037 0.00 0.00 0.00 2.40
2422 4444 8.523658 GTTTTTATAGGTCAGAGGCAAAAGATT 58.476 33.333 0.00 0.00 0.00 2.40
2423 4445 8.650143 TTTTATAGGTCAGAGGCAAAAGATTT 57.350 30.769 0.00 0.00 0.00 2.17
2424 4446 7.630242 TTATAGGTCAGAGGCAAAAGATTTG 57.370 36.000 0.00 0.00 0.00 2.32
2425 4447 3.837355 AGGTCAGAGGCAAAAGATTTGT 58.163 40.909 4.90 0.00 0.00 2.83
2426 4448 3.823304 AGGTCAGAGGCAAAAGATTTGTC 59.177 43.478 0.00 0.00 0.00 3.18
2427 4449 3.823304 GGTCAGAGGCAAAAGATTTGTCT 59.177 43.478 9.50 9.50 37.02 3.41
2432 4454 4.691860 AGGCAAAAGATTTGTCTCATCG 57.308 40.909 4.21 0.00 25.88 3.84
2433 4455 4.326826 AGGCAAAAGATTTGTCTCATCGA 58.673 39.130 4.21 0.00 25.88 3.59
2434 4456 4.154918 AGGCAAAAGATTTGTCTCATCGAC 59.845 41.667 4.21 0.00 43.14 4.20
2435 4457 4.154918 GGCAAAAGATTTGTCTCATCGACT 59.845 41.667 4.90 0.00 43.25 4.18
2436 4458 5.351465 GGCAAAAGATTTGTCTCATCGACTA 59.649 40.000 4.90 0.00 43.25 2.59
2437 4459 6.128282 GGCAAAAGATTTGTCTCATCGACTAA 60.128 38.462 4.90 0.00 43.25 2.24
2438 4460 7.414540 GGCAAAAGATTTGTCTCATCGACTAAT 60.415 37.037 4.90 2.35 46.10 1.73
2443 4465 3.717400 TGTCTCATCGACTAATCAGGC 57.283 47.619 0.00 0.00 43.25 4.85
2444 4466 3.023832 TGTCTCATCGACTAATCAGGCA 58.976 45.455 0.00 0.00 43.25 4.75
2445 4467 3.067320 TGTCTCATCGACTAATCAGGCAG 59.933 47.826 0.00 0.00 43.25 4.85
2446 4468 3.316588 GTCTCATCGACTAATCAGGCAGA 59.683 47.826 0.00 0.00 39.61 4.26
2447 4469 3.954258 TCTCATCGACTAATCAGGCAGAA 59.046 43.478 0.00 0.00 0.00 3.02
2448 4470 4.037327 TCTCATCGACTAATCAGGCAGAAG 59.963 45.833 0.00 0.00 0.00 2.85
2449 4471 3.954258 TCATCGACTAATCAGGCAGAAGA 59.046 43.478 0.00 0.00 0.00 2.87
2450 4472 4.037327 TCATCGACTAATCAGGCAGAAGAG 59.963 45.833 0.00 0.00 0.00 2.85
2451 4473 3.621558 TCGACTAATCAGGCAGAAGAGA 58.378 45.455 0.00 0.00 0.00 3.10
2452 4474 4.017126 TCGACTAATCAGGCAGAAGAGAA 58.983 43.478 0.00 0.00 0.00 2.87
2453 4475 4.646945 TCGACTAATCAGGCAGAAGAGAAT 59.353 41.667 0.00 0.00 0.00 2.40
2454 4476 5.127845 TCGACTAATCAGGCAGAAGAGAATT 59.872 40.000 0.00 0.00 0.00 2.17
2455 4477 5.233902 CGACTAATCAGGCAGAAGAGAATTG 59.766 44.000 0.00 0.00 0.00 2.32
2456 4478 6.059787 ACTAATCAGGCAGAAGAGAATTGT 57.940 37.500 0.00 0.00 0.00 2.71
2457 4479 6.479884 ACTAATCAGGCAGAAGAGAATTGTT 58.520 36.000 0.00 0.00 0.00 2.83
2458 4480 5.893897 AATCAGGCAGAAGAGAATTGTTC 57.106 39.130 0.00 0.00 0.00 3.18
2459 4481 3.679389 TCAGGCAGAAGAGAATTGTTCC 58.321 45.455 0.00 0.00 0.00 3.62
2460 4482 2.417933 CAGGCAGAAGAGAATTGTTCCG 59.582 50.000 0.00 0.00 0.00 4.30
2461 4483 2.039084 AGGCAGAAGAGAATTGTTCCGT 59.961 45.455 0.00 0.00 0.00 4.69
2462 4484 2.814336 GGCAGAAGAGAATTGTTCCGTT 59.186 45.455 0.00 0.00 0.00 4.44
2463 4485 4.000988 GGCAGAAGAGAATTGTTCCGTTA 58.999 43.478 0.00 0.00 0.00 3.18
2464 4486 4.454504 GGCAGAAGAGAATTGTTCCGTTAA 59.545 41.667 0.00 0.00 0.00 2.01
2465 4487 5.123979 GGCAGAAGAGAATTGTTCCGTTAAT 59.876 40.000 0.00 0.00 0.00 1.40
2466 4488 6.349363 GGCAGAAGAGAATTGTTCCGTTAATT 60.349 38.462 0.00 0.00 0.00 1.40
2467 4489 7.148306 GGCAGAAGAGAATTGTTCCGTTAATTA 60.148 37.037 0.00 0.00 0.00 1.40
2468 4490 8.234546 GCAGAAGAGAATTGTTCCGTTAATTAA 58.765 33.333 0.00 0.00 0.00 1.40
2469 4491 9.543018 CAGAAGAGAATTGTTCCGTTAATTAAC 57.457 33.333 16.87 16.87 0.00 2.01
2470 4492 9.280174 AGAAGAGAATTGTTCCGTTAATTAACA 57.720 29.630 24.27 7.75 35.99 2.41
2471 4493 9.887406 GAAGAGAATTGTTCCGTTAATTAACAA 57.113 29.630 24.27 15.35 44.56 2.83
2497 4519 2.589338 GGTCGAAAACCGTCACAATC 57.411 50.000 0.00 0.00 38.58 2.67
2498 4520 2.140717 GGTCGAAAACCGTCACAATCT 58.859 47.619 0.00 0.00 38.58 2.40
2499 4521 2.096417 GGTCGAAAACCGTCACAATCTG 60.096 50.000 0.00 0.00 38.58 2.90
2500 4522 2.542595 GTCGAAAACCGTCACAATCTGT 59.457 45.455 0.00 0.00 39.75 3.41
2501 4523 3.001939 GTCGAAAACCGTCACAATCTGTT 59.998 43.478 0.00 0.00 39.75 3.16
2502 4524 3.001838 TCGAAAACCGTCACAATCTGTTG 59.998 43.478 0.00 0.00 39.20 3.33
2503 4525 3.001838 CGAAAACCGTCACAATCTGTTGA 59.998 43.478 0.00 0.00 38.71 3.18
2504 4526 3.963383 AAACCGTCACAATCTGTTGAC 57.037 42.857 0.00 0.00 38.71 3.18
2505 4527 2.910688 ACCGTCACAATCTGTTGACT 57.089 45.000 0.00 0.00 38.71 3.41
2511 4533 5.062683 CCGTCACAATCTGTTGACTAATCAG 59.937 44.000 0.00 0.00 38.71 2.90
2527 4549 6.479884 ACTAATCAGGCAGAAGAGAATTGTT 58.520 36.000 0.00 0.00 0.00 2.83
2549 4571 5.285798 TCAGTTAATTAACGAAAAGGCGG 57.714 39.130 19.92 5.58 40.96 6.13
2550 4572 4.756135 TCAGTTAATTAACGAAAAGGCGGT 59.244 37.500 19.92 0.00 40.96 5.68
2551 4573 5.239087 TCAGTTAATTAACGAAAAGGCGGTT 59.761 36.000 19.92 0.00 40.96 4.44
2552 4574 5.566395 CAGTTAATTAACGAAAAGGCGGTTC 59.434 40.000 19.92 0.00 40.96 3.62
2574 4596 0.400213 AACCGTCCCAATCTGCTGAA 59.600 50.000 0.00 0.00 0.00 3.02
2576 4598 1.361668 CCGTCCCAATCTGCTGAACG 61.362 60.000 7.54 7.54 0.00 3.95
2611 4633 7.202289 AGGATACCCTACACATATAGTGAGTGA 60.202 40.741 10.89 0.00 45.84 3.41
2632 4654 1.271597 TGAAAGGGCAAGCTCTCTTCC 60.272 52.381 0.00 0.00 0.00 3.46
2635 4657 0.617935 AGGGCAAGCTCTCTTCCTTC 59.382 55.000 0.00 0.00 0.00 3.46
2636 4658 0.326264 GGGCAAGCTCTCTTCCTTCA 59.674 55.000 0.00 0.00 0.00 3.02
2637 4659 1.064832 GGGCAAGCTCTCTTCCTTCAT 60.065 52.381 0.00 0.00 0.00 2.57
2683 4705 6.404074 GCAGCATCTAACAAGACTAGCAAATT 60.404 38.462 0.00 0.00 0.00 1.82
2738 4765 2.098614 TGTGAGTTTCCAAGCTGCAAA 58.901 42.857 1.02 0.00 0.00 3.68
2739 4766 2.099592 TGTGAGTTTCCAAGCTGCAAAG 59.900 45.455 1.02 0.00 0.00 2.77
2764 4801 1.259142 TTGGAGCATGGCCACATTGG 61.259 55.000 8.16 0.00 41.55 3.16
2792 4829 2.328099 GCACTTGGCTCCCGTTCTG 61.328 63.158 0.00 0.00 40.25 3.02
2827 4864 4.618489 CAGACAAAACCATTGAAATCGAGC 59.382 41.667 0.00 0.00 0.00 5.03
2830 4867 1.094785 AACCATTGAAATCGAGCGGG 58.905 50.000 0.00 0.00 0.00 6.13
2924 4971 1.341852 TCAATTCAGTTCGTCCGTGGA 59.658 47.619 0.00 0.00 0.00 4.02
3011 5060 0.179089 CGGAGTTCCAGATGGAGCAG 60.179 60.000 16.74 5.28 46.37 4.24
3087 5136 0.109342 AGGGTGCACTTTCTGACCAG 59.891 55.000 17.98 0.00 0.00 4.00
3092 5141 1.518903 GCACTTTCTGACCAGGTGCC 61.519 60.000 14.68 0.00 44.87 5.01
3135 5184 2.565834 GGGTCAAAGTGGCAGTAGAGTA 59.434 50.000 0.00 0.00 0.00 2.59
3136 5185 3.368531 GGGTCAAAGTGGCAGTAGAGTAG 60.369 52.174 0.00 0.00 0.00 2.57
3137 5186 3.258622 GGTCAAAGTGGCAGTAGAGTAGT 59.741 47.826 0.00 0.00 0.00 2.73
3138 5187 4.461781 GGTCAAAGTGGCAGTAGAGTAGTA 59.538 45.833 0.00 0.00 0.00 1.82
3139 5188 5.400703 GTCAAAGTGGCAGTAGAGTAGTAC 58.599 45.833 0.00 0.00 0.00 2.73
3140 5189 5.048224 GTCAAAGTGGCAGTAGAGTAGTACA 60.048 44.000 2.52 0.00 0.00 2.90
3230 5295 0.035458 AGTGCTGCTAACAGGGACAC 59.965 55.000 0.00 0.00 44.63 3.67
3286 5370 8.469309 AAGAAGTGGTTGTAGTAGTAGTACAA 57.531 34.615 21.57 21.57 40.56 2.41
3300 5384 7.122353 AGTAGTAGTACAACTACCACTCAATGG 59.878 40.741 11.07 0.00 45.87 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 3.113745 CATTGGTGGCCTCGATGC 58.886 61.111 3.32 3.83 0.00 3.91
132 133 1.170442 TCGACAAGTCCACGCTCATA 58.830 50.000 0.00 0.00 0.00 2.15
310 314 5.233988 CCGGCCTTCAAAATGAATGTTTTA 58.766 37.500 0.00 0.00 35.59 1.52
385 389 2.282040 GCAACACAGCCAGCCTCT 60.282 61.111 0.00 0.00 0.00 3.69
430 434 1.149627 AAAACCAGCGGCCTACACA 59.850 52.632 0.00 0.00 0.00 3.72
445 449 1.007964 CATCACGCCGGCAACAAAA 60.008 52.632 28.98 5.24 0.00 2.44
528 538 4.361783 CCCATCTTTTACCCCATCCTTTT 58.638 43.478 0.00 0.00 0.00 2.27
530 540 2.247372 CCCCATCTTTTACCCCATCCTT 59.753 50.000 0.00 0.00 0.00 3.36
581 592 1.597461 GTGTCCCAGCCTGTCCTAC 59.403 63.158 0.00 0.00 0.00 3.18
582 593 1.982395 CGTGTCCCAGCCTGTCCTA 60.982 63.158 0.00 0.00 0.00 2.94
593 604 3.793888 GGGATGGGGTCGTGTCCC 61.794 72.222 0.00 0.00 46.31 4.46
650 663 3.605749 CTCCACGCGTGACCCCAAT 62.606 63.158 39.10 0.00 0.00 3.16
673 687 5.194942 AGAATAGGAGGAGGTGAGAGTTAGT 59.805 44.000 0.00 0.00 0.00 2.24
691 705 6.060788 CCATGGAGGGAGAAAGAAAGAATAG 58.939 44.000 5.56 0.00 0.00 1.73
692 706 5.632427 GCCATGGAGGGAGAAAGAAAGAATA 60.632 44.000 18.40 0.00 38.09 1.75
693 707 4.864726 CCATGGAGGGAGAAAGAAAGAAT 58.135 43.478 5.56 0.00 0.00 2.40
694 708 3.562176 GCCATGGAGGGAGAAAGAAAGAA 60.562 47.826 18.40 0.00 38.09 2.52
700 714 0.750911 GCAGCCATGGAGGGAGAAAG 60.751 60.000 18.40 0.00 38.09 2.62
701 715 1.304282 GCAGCCATGGAGGGAGAAA 59.696 57.895 18.40 0.00 38.09 2.52
723 738 4.760047 GTGGTCATGCGGCGGTCT 62.760 66.667 9.78 0.00 0.00 3.85
742 757 0.691078 AGGAGTGAGGGTGTGTGTGT 60.691 55.000 0.00 0.00 0.00 3.72
743 758 0.469917 AAGGAGTGAGGGTGTGTGTG 59.530 55.000 0.00 0.00 0.00 3.82
764 779 0.534203 ACACGGTTGTTGGCTAGTGG 60.534 55.000 0.00 0.00 34.28 4.00
766 781 0.250166 GGACACGGTTGTTGGCTAGT 60.250 55.000 0.00 0.00 35.47 2.57
770 785 3.656045 CGGGACACGGTTGTTGGC 61.656 66.667 0.00 0.00 35.47 4.52
800 815 2.824952 CAGTGTGTCTGCTCTGCTC 58.175 57.895 0.00 0.00 37.36 4.26
809 824 0.528466 CTGTGTCGTGCAGTGTGTCT 60.528 55.000 0.00 0.00 0.00 3.41
826 841 0.669932 GAGGTGTCTGCTCTGTGCTG 60.670 60.000 3.20 2.92 43.37 4.41
870 1557 4.283363 AGTATTCTCATATGCTGGGCTG 57.717 45.455 0.00 0.00 0.00 4.85
871 1558 5.723405 TCATAGTATTCTCATATGCTGGGCT 59.277 40.000 0.00 0.00 0.00 5.19
1102 1789 0.178992 CCCCTTCTTGGAGCACACAA 60.179 55.000 0.00 0.00 38.35 3.33
1105 1792 2.436109 GCCCCTTCTTGGAGCACA 59.564 61.111 0.00 0.00 38.35 4.57
1106 1793 2.747855 CGCCCCTTCTTGGAGCAC 60.748 66.667 0.00 0.00 38.35 4.40
1247 1954 3.847602 CTCCTCCCTCGCTGCCTG 61.848 72.222 0.00 0.00 0.00 4.85
1252 1959 4.067512 TCCTGCTCCTCCCTCGCT 62.068 66.667 0.00 0.00 0.00 4.93
1256 1963 4.101077 CCCCTCCTGCTCCTCCCT 62.101 72.222 0.00 0.00 0.00 4.20
1259 1966 2.690510 AAGCCCCTCCTGCTCCTC 60.691 66.667 0.00 0.00 38.34 3.71
1260 1967 3.013932 CAAGCCCCTCCTGCTCCT 61.014 66.667 0.00 0.00 38.34 3.69
1539 2259 2.348333 CGCTCGTACTCGTCGTCG 60.348 66.667 0.00 0.00 38.33 5.12
1558 2290 4.154347 CCACCTCGCTGCTCCCTC 62.154 72.222 0.00 0.00 0.00 4.30
1678 2411 1.590238 GCGTGATCGATTGAAGTCAGG 59.410 52.381 0.00 0.00 39.71 3.86
1682 2415 1.935873 CATGGCGTGATCGATTGAAGT 59.064 47.619 0.00 0.00 39.71 3.01
1684 2417 1.134551 TCCATGGCGTGATCGATTGAA 60.135 47.619 6.96 0.00 39.71 2.69
1690 2423 1.141665 TGAGTCCATGGCGTGATCG 59.858 57.895 6.96 0.00 40.37 3.69
1762 2505 1.755008 GTCCTCCTCCCCTGTCGAG 60.755 68.421 0.00 0.00 0.00 4.04
1764 2507 3.141488 CGTCCTCCTCCCCTGTCG 61.141 72.222 0.00 0.00 0.00 4.35
1814 2560 4.338879 CCATGGAAGTCTGAGGACAAAAT 58.661 43.478 5.56 0.00 44.36 1.82
1815 2561 3.754965 CCATGGAAGTCTGAGGACAAAA 58.245 45.455 5.56 0.00 44.36 2.44
1817 2563 1.003580 GCCATGGAAGTCTGAGGACAA 59.996 52.381 18.40 0.00 44.36 3.18
1818 2564 0.615331 GCCATGGAAGTCTGAGGACA 59.385 55.000 18.40 0.00 44.36 4.02
1819 2565 0.107459 GGCCATGGAAGTCTGAGGAC 60.107 60.000 18.40 0.00 42.41 3.85
1981 2745 1.700186 GGGATCTTGTAGATGTCCCCC 59.300 57.143 4.63 1.18 34.36 5.40
2030 2794 1.642037 CTCCTCCATTGCTGCGTGTG 61.642 60.000 0.00 0.00 0.00 3.82
2031 2795 1.376424 CTCCTCCATTGCTGCGTGT 60.376 57.895 0.00 0.00 0.00 4.49
2033 2797 2.270205 CCTCCTCCATTGCTGCGT 59.730 61.111 0.00 0.00 0.00 5.24
2034 2798 2.515523 CCCTCCTCCATTGCTGCG 60.516 66.667 0.00 0.00 0.00 5.18
2168 4161 1.613925 TCTGTCTGGTCAACGAGAAGG 59.386 52.381 0.00 0.00 32.56 3.46
2202 4198 6.822442 AGTAAATTTTTAACCACCCCACAAG 58.178 36.000 0.00 0.00 0.00 3.16
2287 4309 1.152355 CTTTGGGGCTGGGGAACAA 60.152 57.895 0.00 0.00 0.00 2.83
2288 4310 2.366153 GACTTTGGGGCTGGGGAACA 62.366 60.000 0.00 0.00 0.00 3.18
2289 4311 1.606601 GACTTTGGGGCTGGGGAAC 60.607 63.158 0.00 0.00 0.00 3.62
2290 4312 1.368268 AAGACTTTGGGGCTGGGGAA 61.368 55.000 0.00 0.00 30.75 3.97
2291 4313 1.778383 AAGACTTTGGGGCTGGGGA 60.778 57.895 0.00 0.00 30.75 4.81
2321 4343 2.115910 CAGCAAAGTCCCCAGGCA 59.884 61.111 0.00 0.00 0.00 4.75
2322 4344 2.677875 CCAGCAAAGTCCCCAGGC 60.678 66.667 0.00 0.00 0.00 4.85
2334 4356 1.072266 AACATGGAACCTACCCAGCA 58.928 50.000 0.00 0.00 37.08 4.41
2335 4357 1.463674 CAACATGGAACCTACCCAGC 58.536 55.000 0.00 0.00 37.08 4.85
2336 4358 1.463674 GCAACATGGAACCTACCCAG 58.536 55.000 0.00 0.00 37.08 4.45
2337 4359 0.039035 GGCAACATGGAACCTACCCA 59.961 55.000 0.00 0.00 38.19 4.51
2339 4361 2.238898 ACTAGGCAACATGGAACCTACC 59.761 50.000 0.00 0.00 41.41 3.18
2340 4362 3.197983 AGACTAGGCAACATGGAACCTAC 59.802 47.826 0.00 0.00 41.41 3.18
2341 4363 3.197766 CAGACTAGGCAACATGGAACCTA 59.802 47.826 0.00 3.75 41.41 3.08
2342 4364 2.026822 CAGACTAGGCAACATGGAACCT 60.027 50.000 0.00 2.62 41.41 3.50
2355 4377 4.037923 TGCCTTTTCTTTTTGCAGACTAGG 59.962 41.667 0.00 0.00 31.11 3.02
2356 4378 5.186996 TGCCTTTTCTTTTTGCAGACTAG 57.813 39.130 0.00 0.00 0.00 2.57
2359 4381 5.525012 AGAATTGCCTTTTCTTTTTGCAGAC 59.475 36.000 0.00 0.00 32.88 3.51
2402 4424 5.574188 ACAAATCTTTTGCCTCTGACCTAT 58.426 37.500 0.06 0.00 0.00 2.57
2403 4425 4.985538 ACAAATCTTTTGCCTCTGACCTA 58.014 39.130 0.06 0.00 0.00 3.08
2407 4429 4.717877 TGAGACAAATCTTTTGCCTCTGA 58.282 39.130 14.53 0.00 34.34 3.27
2408 4430 5.638783 GATGAGACAAATCTTTTGCCTCTG 58.361 41.667 14.53 0.00 34.34 3.35
2409 4431 4.394300 CGATGAGACAAATCTTTTGCCTCT 59.606 41.667 14.53 5.65 34.34 3.69
2410 4432 4.393062 TCGATGAGACAAATCTTTTGCCTC 59.607 41.667 8.73 8.73 34.34 4.70
2411 4433 4.326826 TCGATGAGACAAATCTTTTGCCT 58.673 39.130 0.06 0.00 34.34 4.75
2425 4447 3.555966 TCTGCCTGATTAGTCGATGAGA 58.444 45.455 0.00 0.00 0.00 3.27
2426 4448 3.998099 TCTGCCTGATTAGTCGATGAG 57.002 47.619 0.00 0.00 0.00 2.90
2427 4449 3.954258 TCTTCTGCCTGATTAGTCGATGA 59.046 43.478 0.00 0.00 0.00 2.92
2428 4450 4.037327 TCTCTTCTGCCTGATTAGTCGATG 59.963 45.833 0.00 0.00 0.00 3.84
2429 4451 4.211125 TCTCTTCTGCCTGATTAGTCGAT 58.789 43.478 0.00 0.00 0.00 3.59
2430 4452 3.621558 TCTCTTCTGCCTGATTAGTCGA 58.378 45.455 0.00 0.00 0.00 4.20
2431 4453 4.377839 TTCTCTTCTGCCTGATTAGTCG 57.622 45.455 0.00 0.00 0.00 4.18
2432 4454 6.112058 ACAATTCTCTTCTGCCTGATTAGTC 58.888 40.000 0.00 0.00 0.00 2.59
2433 4455 6.059787 ACAATTCTCTTCTGCCTGATTAGT 57.940 37.500 0.00 0.00 0.00 2.24
2434 4456 6.038050 GGAACAATTCTCTTCTGCCTGATTAG 59.962 42.308 0.00 0.00 0.00 1.73
2435 4457 5.882557 GGAACAATTCTCTTCTGCCTGATTA 59.117 40.000 0.00 0.00 0.00 1.75
2436 4458 4.704057 GGAACAATTCTCTTCTGCCTGATT 59.296 41.667 0.00 0.00 0.00 2.57
2437 4459 4.268359 GGAACAATTCTCTTCTGCCTGAT 58.732 43.478 0.00 0.00 0.00 2.90
2438 4460 3.679389 GGAACAATTCTCTTCTGCCTGA 58.321 45.455 0.00 0.00 0.00 3.86
2439 4461 2.417933 CGGAACAATTCTCTTCTGCCTG 59.582 50.000 0.00 0.00 0.00 4.85
2440 4462 2.039084 ACGGAACAATTCTCTTCTGCCT 59.961 45.455 0.00 0.00 0.00 4.75
2441 4463 2.427506 ACGGAACAATTCTCTTCTGCC 58.572 47.619 0.00 0.00 0.00 4.85
2442 4464 5.607119 TTAACGGAACAATTCTCTTCTGC 57.393 39.130 0.00 0.00 0.00 4.26
2443 4465 9.543018 GTTAATTAACGGAACAATTCTCTTCTG 57.457 33.333 12.39 0.00 0.00 3.02
2444 4466 9.280174 TGTTAATTAACGGAACAATTCTCTTCT 57.720 29.630 20.51 0.00 39.00 2.85
2445 4467 9.887406 TTGTTAATTAACGGAACAATTCTCTTC 57.113 29.630 20.51 0.00 37.97 2.87
2478 4500 2.096417 CAGATTGTGACGGTTTTCGACC 60.096 50.000 0.00 0.00 45.55 4.79
2479 4501 2.542595 ACAGATTGTGACGGTTTTCGAC 59.457 45.455 0.00 0.00 42.43 4.20
2480 4502 2.828877 ACAGATTGTGACGGTTTTCGA 58.171 42.857 0.00 0.00 42.43 3.71
2481 4503 3.001838 TCAACAGATTGTGACGGTTTTCG 59.998 43.478 0.00 0.00 39.80 3.46
2482 4504 4.035208 AGTCAACAGATTGTGACGGTTTTC 59.965 41.667 0.00 0.00 35.27 2.29
2483 4505 3.945285 AGTCAACAGATTGTGACGGTTTT 59.055 39.130 0.00 0.00 35.27 2.43
2484 4506 3.541632 AGTCAACAGATTGTGACGGTTT 58.458 40.909 0.00 0.00 35.27 3.27
2485 4507 3.194005 AGTCAACAGATTGTGACGGTT 57.806 42.857 0.00 0.00 35.27 4.44
2486 4508 2.910688 AGTCAACAGATTGTGACGGT 57.089 45.000 0.00 0.00 35.27 4.83
2487 4509 4.929211 TGATTAGTCAACAGATTGTGACGG 59.071 41.667 0.00 0.00 35.27 4.79
2488 4510 5.062683 CCTGATTAGTCAACAGATTGTGACG 59.937 44.000 0.00 0.00 35.27 4.35
2489 4511 5.163814 GCCTGATTAGTCAACAGATTGTGAC 60.164 44.000 0.00 0.00 37.11 3.67
2490 4512 4.937620 GCCTGATTAGTCAACAGATTGTGA 59.062 41.667 0.00 0.00 37.11 3.58
2491 4513 4.696877 TGCCTGATTAGTCAACAGATTGTG 59.303 41.667 0.00 0.00 37.11 3.33
2492 4514 4.910195 TGCCTGATTAGTCAACAGATTGT 58.090 39.130 0.00 0.00 37.11 2.71
2493 4515 5.181009 TCTGCCTGATTAGTCAACAGATTG 58.819 41.667 13.49 0.00 40.20 2.67
2494 4516 5.426689 TCTGCCTGATTAGTCAACAGATT 57.573 39.130 13.49 0.00 40.20 2.40
2495 4517 5.188555 TCTTCTGCCTGATTAGTCAACAGAT 59.811 40.000 16.52 0.00 42.50 2.90
2496 4518 4.528206 TCTTCTGCCTGATTAGTCAACAGA 59.472 41.667 13.49 13.49 41.87 3.41
2497 4519 4.825422 TCTTCTGCCTGATTAGTCAACAG 58.175 43.478 10.17 10.17 38.79 3.16
2498 4520 4.528206 TCTCTTCTGCCTGATTAGTCAACA 59.472 41.667 0.00 0.00 33.05 3.33
2499 4521 5.078411 TCTCTTCTGCCTGATTAGTCAAC 57.922 43.478 0.00 0.00 33.05 3.18
2500 4522 5.745312 TTCTCTTCTGCCTGATTAGTCAA 57.255 39.130 0.00 0.00 33.05 3.18
2501 4523 5.946942 ATTCTCTTCTGCCTGATTAGTCA 57.053 39.130 0.00 0.00 0.00 3.41
2502 4524 6.112058 ACAATTCTCTTCTGCCTGATTAGTC 58.888 40.000 0.00 0.00 0.00 2.59
2503 4525 6.059787 ACAATTCTCTTCTGCCTGATTAGT 57.940 37.500 0.00 0.00 0.00 2.24
2504 4526 6.596888 TGAACAATTCTCTTCTGCCTGATTAG 59.403 38.462 0.00 0.00 0.00 1.73
2505 4527 6.475504 TGAACAATTCTCTTCTGCCTGATTA 58.524 36.000 0.00 0.00 0.00 1.75
2511 4533 6.560253 TTAACTGAACAATTCTCTTCTGCC 57.440 37.500 0.00 0.00 0.00 4.85
2527 4549 4.756135 ACCGCCTTTTCGTTAATTAACTGA 59.244 37.500 22.57 18.25 34.12 3.41
2549 4571 2.607038 GCAGATTGGGACGGTTTTGAAC 60.607 50.000 0.00 0.00 0.00 3.18
2550 4572 1.611491 GCAGATTGGGACGGTTTTGAA 59.389 47.619 0.00 0.00 0.00 2.69
2551 4573 1.202879 AGCAGATTGGGACGGTTTTGA 60.203 47.619 0.00 0.00 0.00 2.69
2552 4574 1.068333 CAGCAGATTGGGACGGTTTTG 60.068 52.381 0.00 0.00 0.00 2.44
2562 4584 1.732259 GTGTACCGTTCAGCAGATTGG 59.268 52.381 0.00 0.00 0.00 3.16
2574 4596 3.607490 AGGGTATCCTATGTGTACCGT 57.393 47.619 0.00 0.00 42.75 4.83
2576 4598 5.142639 TGTGTAGGGTATCCTATGTGTACC 58.857 45.833 4.69 0.00 46.42 3.34
2600 4622 5.674525 CTTGCCCTTTCATCACTCACTATA 58.325 41.667 0.00 0.00 0.00 1.31
2601 4623 4.521146 CTTGCCCTTTCATCACTCACTAT 58.479 43.478 0.00 0.00 0.00 2.12
2602 4624 3.869912 GCTTGCCCTTTCATCACTCACTA 60.870 47.826 0.00 0.00 0.00 2.74
2611 4633 2.620108 GGAAGAGAGCTTGCCCTTTCAT 60.620 50.000 0.00 0.00 36.56 2.57
2654 4676 1.399791 GTCTTGTTAGATGCTGCTGGC 59.600 52.381 0.00 0.00 42.22 4.85
2683 4705 6.184068 TGAATACTTACAAGCCAAGGCATTA 58.816 36.000 14.40 0.00 44.88 1.90
2689 4711 5.565592 TGCATGAATACTTACAAGCCAAG 57.434 39.130 0.00 0.00 31.15 3.61
2691 4713 5.973899 TTTGCATGAATACTTACAAGCCA 57.026 34.783 0.00 0.00 31.15 4.75
2738 4765 1.187567 GGCCATGCTCCAACCAAACT 61.188 55.000 0.00 0.00 0.00 2.66
2739 4766 1.293179 GGCCATGCTCCAACCAAAC 59.707 57.895 0.00 0.00 0.00 2.93
2764 4801 3.010413 GCCAAGTGCCCCATTCTGC 62.010 63.158 0.00 0.00 0.00 4.26
2769 4806 4.066139 GGGAGCCAAGTGCCCCAT 62.066 66.667 0.00 0.00 45.12 4.00
2792 4829 2.802247 GTTTTGTCTGCTGGCCAATTTC 59.198 45.455 7.01 0.00 0.00 2.17
2830 4867 2.361104 TCCGGGCCACAGATTTGC 60.361 61.111 4.39 0.00 0.00 3.68
2940 4987 2.456989 GATTGTGCTGCCGATTGATTG 58.543 47.619 0.00 0.00 0.00 2.67
2974 5021 1.657487 GCAATGCGCATGCTGCTAG 60.657 57.895 30.49 19.13 42.25 3.42
2975 5022 2.410060 GCAATGCGCATGCTGCTA 59.590 55.556 30.49 17.17 42.25 3.49
2992 5039 0.179089 CTGCTCCATCTGGAACTCCG 60.179 60.000 0.00 0.00 44.91 4.63
3011 5060 2.346541 GGCCTCCTTGCTTTGCCTC 61.347 63.158 0.00 0.00 39.05 4.70
3042 5091 5.254115 ACTAATCAGCCTTGTCCTTTTACC 58.746 41.667 0.00 0.00 0.00 2.85
3043 5092 6.819397 AACTAATCAGCCTTGTCCTTTTAC 57.181 37.500 0.00 0.00 0.00 2.01
3112 5161 0.673644 CTACTGCCACTTTGACCCGG 60.674 60.000 0.00 0.00 0.00 5.73
3113 5162 0.320374 TCTACTGCCACTTTGACCCG 59.680 55.000 0.00 0.00 0.00 5.28
3135 5184 6.929606 GTGTGATTCAAAGAAGGTACTGTACT 59.070 38.462 16.79 0.00 40.86 2.73
3136 5185 6.147328 GGTGTGATTCAAAGAAGGTACTGTAC 59.853 42.308 9.46 9.46 40.86 2.90
3137 5186 6.183361 TGGTGTGATTCAAAGAAGGTACTGTA 60.183 38.462 0.00 0.00 40.86 2.74
3138 5187 5.063880 GGTGTGATTCAAAGAAGGTACTGT 58.936 41.667 0.00 0.00 40.86 3.55
3139 5188 5.063204 TGGTGTGATTCAAAGAAGGTACTG 58.937 41.667 0.00 0.00 40.86 2.74
3262 5343 7.880105 GTTGTACTACTACTACAACCACTTCT 58.120 38.462 9.38 0.00 44.30 2.85


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

AutoCloner maintained by Alex Coulton.