Multiple sequence alignment - TraesCS6A01G341900

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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 TraesCS6A01G341900 chr6A 100.000 5543 0 0 1 5543 574494198 574488656 0.000000e+00 10237.0
1 TraesCS6A01G341900 chr6A 85.143 175 25 1 5165 5338 493728208 493728382 1.590000e-40 178.0
2 TraesCS6A01G341900 chr6A 84.024 169 26 1 5165 5332 495113162 495112994 1.600000e-35 161.0
3 TraesCS6A01G341900 chr6A 100.000 30 0 0 4943 4972 540610212 540610183 7.760000e-04 56.5
4 TraesCS6A01G341900 chr6A 100.000 29 0 0 4947 4975 9575351 9575323 3.000000e-03 54.7
5 TraesCS6A01G341900 chr6D 93.401 2349 104 28 2594 4910 429356882 429354553 0.000000e+00 3432.0
6 TraesCS6A01G341900 chr6D 91.260 1865 117 23 669 2505 429359128 429357282 0.000000e+00 2499.0
7 TraesCS6A01G341900 chr6D 90.588 340 28 1 124 463 429359904 429359569 1.100000e-121 448.0
8 TraesCS6A01G341900 chr6D 86.979 384 35 7 5099 5468 429353752 429353370 8.590000e-113 418.0
9 TraesCS6A01G341900 chr6D 78.253 538 74 22 116 624 429360718 429360195 6.980000e-79 305.0
10 TraesCS6A01G341900 chr6D 90.476 126 11 1 1 126 429360058 429359934 1.240000e-36 165.0
11 TraesCS6A01G341900 chr6B 90.059 2555 120 39 2616 5104 646708972 646706486 0.000000e+00 3188.0
12 TraesCS6A01G341900 chr6B 88.634 2270 177 35 306 2533 646711247 646709017 0.000000e+00 2687.0
13 TraesCS6A01G341900 chr6B 92.079 202 16 0 121 322 646713080 646712879 9.090000e-73 285.0
14 TraesCS6A01G341900 chr6B 84.076 157 24 1 5183 5338 529736060 529736216 3.460000e-32 150.0
15 TraesCS6A01G341900 chr2D 82.063 223 38 2 5117 5338 57326984 57327205 7.330000e-44 189.0
16 TraesCS6A01G341900 chr2D 96.875 32 0 1 4947 4977 363571577 363571608 1.000000e-02 52.8
17 TraesCS6A01G341900 chr7D 80.667 150 29 0 5189 5338 500140052 500139903 3.510000e-22 117.0
18 TraesCS6A01G341900 chr7D 96.875 32 1 0 629 660 128385624 128385593 3.000000e-03 54.7
19 TraesCS6A01G341900 chr7B 79.245 159 29 2 5180 5338 703259749 703259903 2.110000e-19 108.0
20 TraesCS6A01G341900 chr3B 77.778 153 31 2 5186 5338 773513207 773513058 2.130000e-14 91.6
21 TraesCS6A01G341900 chr3A 77.778 153 31 3 5186 5338 714524317 714524168 2.130000e-14 91.6
22 TraesCS6A01G341900 chr5D 96.970 33 1 0 4942 4974 180468262 180468294 7.760000e-04 56.5
23 TraesCS6A01G341900 chr3D 94.595 37 1 1 4943 4978 547429777 547429741 7.760000e-04 56.5
24 TraesCS6A01G341900 chr1B 96.875 32 1 0 4943 4974 5247497 5247528 3.000000e-03 54.7


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 TraesCS6A01G341900 chr6A 574488656 574494198 5542 True 10237.000000 10237 100.000000 1 5543 1 chr6A.!!$R4 5542
1 TraesCS6A01G341900 chr6D 429353370 429360718 7348 True 1211.166667 3432 88.492833 1 5468 6 chr6D.!!$R1 5467
2 TraesCS6A01G341900 chr6B 646706486 646713080 6594 True 2053.333333 3188 90.257333 121 5104 3 chr6B.!!$R1 4983

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
627 2977 0.320858 TCAAAGCCGATGCAACCGTA 60.321 50.0 10.31 0.0 41.13 4.02 F
656 3006 0.404040 AGACAGGAATTTTGGGGCGA 59.596 50.0 0.00 0.0 0.00 5.54 F
660 3010 0.407918 AGGAATTTTGGGGCGAAGGA 59.592 50.0 0.00 0.0 0.00 3.36 F
2177 4843 0.108615 CCATTCGCTTCACGGTCTCT 60.109 55.0 0.00 0.0 43.89 3.10 F
3463 6466 0.107410 TGGTCTTTGTGCAGGTTCGT 60.107 50.0 0.00 0.0 0.00 3.85 F
3476 6479 0.240945 GGTTCGTTCACCTGCATTGG 59.759 55.0 0.00 0.0 33.50 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 4299 0.321919 TGCCATCTCTGCAACAGGTC 60.322 55.0 0.00 0.00 35.40 3.85 R
1796 4462 0.323725 ATGTGGGGTGGATTGTGAGC 60.324 55.0 0.00 0.00 0.00 4.26 R
2529 5200 0.734889 CAGCAGAAAAGCATACCCCG 59.265 55.0 0.00 0.00 36.85 5.73 R
3481 6484 0.105142 GACCCTGTAGGCCCCTATCA 60.105 60.0 0.00 0.00 40.58 2.15 R
4464 7487 0.388649 TCGAAGACGGCTTCTGCTTC 60.389 55.0 27.73 1.98 46.64 3.86 R
5294 8959 0.460987 GACATCCACTCTCCCGCTTG 60.461 60.0 0.00 0.00 0.00 4.01 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
23 684 1.073964 CTGTCAACATGCGGAGTCTG 58.926 55.000 0.00 0.00 0.00 3.51
38 699 2.146342 AGTCTGCAATGGTTTCTCGTG 58.854 47.619 0.00 0.00 0.00 4.35
44 705 0.598065 AATGGTTTCTCGTGCTTGGC 59.402 50.000 0.00 0.00 0.00 4.52
55 716 2.743928 GCTTGGCGAGTGGACCTG 60.744 66.667 3.19 0.00 0.00 4.00
59 720 4.021925 GGCGAGTGGACCTGGCTT 62.022 66.667 0.00 0.00 43.78 4.35
69 730 0.600057 GACCTGGCTTGCAAGGAAAG 59.400 55.000 27.10 2.98 37.01 2.62
179 872 5.445540 CGAGGTTTAACATAAAACGAGAGCC 60.446 44.000 0.00 0.00 39.71 4.70
186 879 6.515272 AACATAAAACGAGAGCCATGAAAT 57.485 33.333 0.00 0.00 0.00 2.17
189 882 4.965119 AAAACGAGAGCCATGAAATACC 57.035 40.909 0.00 0.00 0.00 2.73
246 939 8.786826 ATGATAGACATCACTTTAAAACCGAA 57.213 30.769 0.00 0.00 43.89 4.30
248 941 9.878667 TGATAGACATCACTTTAAAACCGAATA 57.121 29.630 0.00 0.00 36.22 1.75
322 2663 2.207788 AAAATGGGCTAACGCGGTGC 62.208 55.000 7.07 8.69 36.88 5.01
367 2708 4.340617 TGTACATTTGGAGATGGAAACCC 58.659 43.478 0.00 0.00 0.00 4.11
401 2742 2.680352 GTCACCCAGCTCGGAGGA 60.680 66.667 3.62 0.00 36.56 3.71
409 2750 1.579698 CAGCTCGGAGGATGAACATG 58.420 55.000 7.20 0.00 0.00 3.21
413 2754 0.911769 TCGGAGGATGAACATGGCTT 59.088 50.000 0.00 0.00 0.00 4.35
463 2804 2.667473 ACCCGGAGAATTTCACTACG 57.333 50.000 0.73 0.00 40.84 3.51
467 2808 3.581755 CCGGAGAATTTCACTACGAACA 58.418 45.455 0.00 0.00 43.42 3.18
470 2811 4.032900 CGGAGAATTTCACTACGAACATGG 59.967 45.833 0.00 0.00 43.42 3.66
474 2815 5.643777 AGAATTTCACTACGAACATGGAAGG 59.356 40.000 0.00 0.00 31.73 3.46
483 2824 1.273048 GAACATGGAAGGCATGCACAA 59.727 47.619 21.36 4.10 33.61 3.33
485 2826 1.903860 ACATGGAAGGCATGCACAATT 59.096 42.857 21.36 8.20 33.61 2.32
488 2829 3.591196 TGGAAGGCATGCACAATTTAC 57.409 42.857 21.36 6.70 0.00 2.01
491 2832 4.769488 TGGAAGGCATGCACAATTTACTAA 59.231 37.500 21.36 0.00 0.00 2.24
494 2835 5.720371 AGGCATGCACAATTTACTAACAA 57.280 34.783 21.36 0.00 0.00 2.83
496 2837 5.010516 AGGCATGCACAATTTACTAACAACA 59.989 36.000 21.36 0.00 0.00 3.33
541 2883 6.317391 AGAAAAGAGCTATGATAACAGCAACC 59.683 38.462 0.00 0.00 40.36 3.77
551 2893 1.102978 AACAGCAACCACGCTTTCTT 58.897 45.000 0.00 0.00 41.38 2.52
563 2905 4.457949 CCACGCTTTCTTAATGGTTTACCT 59.542 41.667 0.00 0.00 36.82 3.08
567 2909 7.546667 CACGCTTTCTTAATGGTTTACCTAGTA 59.453 37.037 0.00 0.00 36.82 1.82
568 2910 7.763071 ACGCTTTCTTAATGGTTTACCTAGTAG 59.237 37.037 0.00 0.00 36.82 2.57
591 2933 6.525629 AGAGCACTAAAACCGCTTCATATAT 58.474 36.000 0.00 0.00 35.75 0.86
607 2949 7.325821 GCTTCATATATATGCTAGACATCGCTC 59.674 40.741 16.59 0.57 40.38 5.03
627 2977 0.320858 TCAAAGCCGATGCAACCGTA 60.321 50.000 10.31 0.00 41.13 4.02
638 2988 5.255596 CGATGCAACCGTAACAAATCTAAG 58.744 41.667 0.00 0.00 0.00 2.18
642 2992 5.178623 TGCAACCGTAACAAATCTAAGACAG 59.821 40.000 0.00 0.00 0.00 3.51
649 2999 8.512138 CCGTAACAAATCTAAGACAGGAATTTT 58.488 33.333 0.00 0.00 0.00 1.82
653 3003 6.211384 ACAAATCTAAGACAGGAATTTTGGGG 59.789 38.462 0.00 0.00 0.00 4.96
656 3006 0.404040 AGACAGGAATTTTGGGGCGA 59.596 50.000 0.00 0.00 0.00 5.54
660 3010 0.407918 AGGAATTTTGGGGCGAAGGA 59.592 50.000 0.00 0.00 0.00 3.36
661 3011 1.203125 AGGAATTTTGGGGCGAAGGAA 60.203 47.619 0.00 0.00 0.00 3.36
711 3347 1.270305 GGGTTTGAAAGCAAGAAGGCC 60.270 52.381 9.48 0.00 35.04 5.19
727 3363 4.383602 CCACCGCGTCGCCTTTTG 62.384 66.667 12.44 3.45 0.00 2.44
779 3415 1.826385 AGGAGAAATTCGCAGGTTGG 58.174 50.000 0.00 0.00 0.00 3.77
784 3420 4.500716 GGAGAAATTCGCAGGTTGGAAAAA 60.501 41.667 0.00 0.00 0.00 1.94
927 3574 0.998945 CTCCTCCTCCCTCCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
928 3575 0.996762 TCCTCCTCCCTCCTCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
932 3579 1.541672 CTCCCTCCTCTCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
939 3588 1.541672 CTCTCCTCTCCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
1155 3804 2.167861 GGTGAGCGAGAATCACGGC 61.168 63.158 1.90 0.00 46.49 5.68
1187 3839 2.542907 CCTCCGCTGTGCACGTTTT 61.543 57.895 13.13 0.00 0.00 2.43
1251 3905 2.333225 CCTCCGCTCTCGATTCGG 59.667 66.667 6.18 12.22 44.16 4.30
1378 4032 2.856557 GTTCGTTCGTATTCCTGTAGCC 59.143 50.000 0.00 0.00 0.00 3.93
1445 4099 1.590259 GCCGGAGCTCGTGATCTTC 60.590 63.158 5.05 0.00 37.11 2.87
1547 4201 4.836125 ACTCGTTGAACATTGCTTGATT 57.164 36.364 0.00 0.00 0.00 2.57
1549 4203 4.159377 TCGTTGAACATTGCTTGATTCC 57.841 40.909 0.00 0.00 0.00 3.01
1640 4299 4.313282 TCAGCTGAACTTCTTGATCTGTG 58.687 43.478 15.67 0.00 0.00 3.66
1762 4421 1.066143 TCCGGTCTCAATCTTCCTTGC 60.066 52.381 0.00 0.00 0.00 4.01
1766 4425 2.238395 GGTCTCAATCTTCCTTGCCTCT 59.762 50.000 0.00 0.00 0.00 3.69
1772 4431 2.623418 TCTTCCTTGCCTCTACCTCA 57.377 50.000 0.00 0.00 0.00 3.86
1777 4436 1.280457 CTTGCCTCTACCTCAACCCT 58.720 55.000 0.00 0.00 0.00 4.34
1779 4438 0.413832 TGCCTCTACCTCAACCCTCT 59.586 55.000 0.00 0.00 0.00 3.69
1781 4440 1.783071 CCTCTACCTCAACCCTCTCC 58.217 60.000 0.00 0.00 0.00 3.71
1804 4470 4.834496 CCCCCATATTTATGTGCTCACAAT 59.166 41.667 6.81 0.00 45.41 2.71
1810 4476 2.418368 TATGTGCTCACAATCCACCC 57.582 50.000 6.81 0.00 45.41 4.61
1821 4487 2.158325 ACAATCCACCCCACATCACTTT 60.158 45.455 0.00 0.00 0.00 2.66
1846 4512 9.539825 TTTTACATGTTGCAATAACAAACTGAT 57.460 25.926 2.30 0.00 33.42 2.90
1913 4579 2.283809 AGCCCTCGTGCTCCCTAT 59.716 61.111 0.00 0.00 36.75 2.57
1971 4637 0.391661 AGCGGTTCCTCTACGACGTA 60.392 55.000 7.60 7.60 0.00 3.57
2066 4732 6.338146 GGTATTGCTTATAGTGTGAGTGACA 58.662 40.000 0.00 0.00 0.00 3.58
2177 4843 0.108615 CCATTCGCTTCACGGTCTCT 60.109 55.000 0.00 0.00 43.89 3.10
2179 4845 0.737715 ATTCGCTTCACGGTCTCTGC 60.738 55.000 0.00 0.00 43.89 4.26
2219 4885 8.138074 TGTGATCTAGCATTAGTTGTCACTATC 58.862 37.037 0.00 0.00 35.32 2.08
2221 4887 8.918116 TGATCTAGCATTAGTTGTCACTATCTT 58.082 33.333 0.00 0.00 35.32 2.40
2243 4909 5.838531 TTGTTATTTTGGGTTTCGACACT 57.161 34.783 1.13 0.00 0.00 3.55
2255 4921 5.391629 GGGTTTCGACACTGATTTTATCACC 60.392 44.000 1.13 0.00 35.06 4.02
2265 4931 6.258727 CACTGATTTTATCACCATACTTCGCT 59.741 38.462 0.00 0.00 35.06 4.93
2285 4951 6.582636 TCGCTAACCATCATCTTATCTGTTT 58.417 36.000 0.00 0.00 0.00 2.83
2339 5005 6.534634 TGGAAGAAGAACTAGGAAAAGGAAG 58.465 40.000 0.00 0.00 0.00 3.46
2369 5035 9.673454 AAATAGTTATTTTTGTTCTTCGTCACC 57.327 29.630 0.00 0.00 32.28 4.02
2377 5043 2.163010 TGTTCTTCGTCACCGTATCCTC 59.837 50.000 0.00 0.00 35.01 3.71
2378 5044 2.414994 TCTTCGTCACCGTATCCTCT 57.585 50.000 0.00 0.00 35.01 3.69
2381 5047 3.624861 TCTTCGTCACCGTATCCTCTAAC 59.375 47.826 0.00 0.00 35.01 2.34
2418 5088 2.365293 GCTGTTTTTGGACTGAACCCAT 59.635 45.455 0.00 0.00 33.04 4.00
2430 5100 3.117131 ACTGAACCCATTCTCCTTTTGGT 60.117 43.478 0.00 0.00 35.34 3.67
2449 5120 0.762418 TTTCTTGGAGCCCTCGTCAA 59.238 50.000 0.00 0.00 0.00 3.18
2469 5140 9.100554 TCGTCAAGTTTTATTTGTTCTACAAGA 57.899 29.630 0.00 0.00 39.53 3.02
2481 5152 5.793817 TGTTCTACAAGAATCTTGCTGCTA 58.206 37.500 21.69 6.86 36.50 3.49
2520 5191 8.545229 TTGTGCTATTATGGGAAAAATTGTTG 57.455 30.769 0.00 0.00 0.00 3.33
2524 5195 6.767423 GCTATTATGGGAAAAATTGTTGGCAT 59.233 34.615 0.00 0.00 0.00 4.40
2525 5196 7.254863 GCTATTATGGGAAAAATTGTTGGCATG 60.255 37.037 0.00 0.00 0.00 4.06
2526 5197 3.137446 TGGGAAAAATTGTTGGCATGG 57.863 42.857 0.00 0.00 0.00 3.66
2529 5200 1.811965 GAAAAATTGTTGGCATGGGGC 59.188 47.619 0.00 0.00 43.74 5.80
2541 5233 2.700185 ATGGGGCGGGGTATGCTTT 61.700 57.895 0.00 0.00 0.00 3.51
2546 5238 1.433471 GCGGGGTATGCTTTTCTGC 59.567 57.895 0.00 0.00 0.00 4.26
2561 5253 3.293311 TTCTGCTGCAAAATTCTGAGC 57.707 42.857 3.02 0.00 0.00 4.26
2562 5254 2.511659 TCTGCTGCAAAATTCTGAGCT 58.488 42.857 3.02 0.00 0.00 4.09
2563 5255 3.678289 TCTGCTGCAAAATTCTGAGCTA 58.322 40.909 3.02 0.00 0.00 3.32
2564 5256 4.074259 TCTGCTGCAAAATTCTGAGCTAA 58.926 39.130 3.02 0.00 0.00 3.09
2566 5538 3.177487 GCTGCAAAATTCTGAGCTAAGC 58.823 45.455 0.00 0.00 0.00 3.09
2574 5546 7.008992 GCAAAATTCTGAGCTAAGCATAAAGTG 59.991 37.037 0.00 0.00 0.00 3.16
2582 5554 9.415544 CTGAGCTAAGCATAAAGTGAAAATTTT 57.584 29.630 2.28 2.28 34.98 1.82
2645 5627 8.291191 TGCATACATATTTCTTTGTCCATTGA 57.709 30.769 0.00 0.00 0.00 2.57
2702 5684 3.845781 ATGAGTGGGCGAGTCATTAAT 57.154 42.857 13.35 0.00 41.30 1.40
2859 5852 6.434340 GGGTGAACTTTTCTGGAATCAACTAT 59.566 38.462 0.00 0.00 0.00 2.12
2904 5904 5.163099 TGGACTCTCTTCATCCAAGGAAAAA 60.163 40.000 0.00 0.00 39.60 1.94
3062 6062 2.806244 CGTTCCAAACATTCTCGACCTT 59.194 45.455 0.00 0.00 0.00 3.50
3240 6241 4.083565 GTTTTGGGGTAAGTATCCTTGCA 58.916 43.478 0.00 0.00 35.24 4.08
3252 6253 5.685728 AGTATCCTTGCAAGTCCCTATTTC 58.314 41.667 24.35 5.74 0.00 2.17
3269 6271 6.646240 CCCTATTTCTTTGTCAATTTGGTGTG 59.354 38.462 0.00 0.00 0.00 3.82
3367 6370 2.467566 TCCTTCGTCCTACTTTTGGC 57.532 50.000 0.00 0.00 0.00 4.52
3368 6371 1.975680 TCCTTCGTCCTACTTTTGGCT 59.024 47.619 0.00 0.00 0.00 4.75
3369 6372 2.370849 TCCTTCGTCCTACTTTTGGCTT 59.629 45.455 0.00 0.00 0.00 4.35
3370 6373 3.146847 CCTTCGTCCTACTTTTGGCTTT 58.853 45.455 0.00 0.00 0.00 3.51
3371 6374 3.568430 CCTTCGTCCTACTTTTGGCTTTT 59.432 43.478 0.00 0.00 0.00 2.27
3372 6375 4.537015 CTTCGTCCTACTTTTGGCTTTTG 58.463 43.478 0.00 0.00 0.00 2.44
3373 6376 2.882137 TCGTCCTACTTTTGGCTTTTGG 59.118 45.455 0.00 0.00 0.00 3.28
3462 6465 1.021202 TTGGTCTTTGTGCAGGTTCG 58.979 50.000 0.00 0.00 0.00 3.95
3463 6466 0.107410 TGGTCTTTGTGCAGGTTCGT 60.107 50.000 0.00 0.00 0.00 3.85
3464 6467 1.021968 GGTCTTTGTGCAGGTTCGTT 58.978 50.000 0.00 0.00 0.00 3.85
3465 6468 1.002792 GGTCTTTGTGCAGGTTCGTTC 60.003 52.381 0.00 0.00 0.00 3.95
3466 6469 1.668751 GTCTTTGTGCAGGTTCGTTCA 59.331 47.619 0.00 0.00 0.00 3.18
3467 6470 1.668751 TCTTTGTGCAGGTTCGTTCAC 59.331 47.619 0.00 0.00 0.00 3.18
3468 6471 0.736053 TTTGTGCAGGTTCGTTCACC 59.264 50.000 0.00 0.00 37.04 4.02
3474 6477 3.725754 AGGTTCGTTCACCTGCATT 57.274 47.368 3.34 0.00 46.22 3.56
3475 6478 1.238439 AGGTTCGTTCACCTGCATTG 58.762 50.000 3.34 0.00 46.22 2.82
3476 6479 0.240945 GGTTCGTTCACCTGCATTGG 59.759 55.000 0.00 0.00 33.50 3.16
3477 6480 1.234821 GTTCGTTCACCTGCATTGGA 58.765 50.000 0.00 0.00 0.00 3.53
3478 6481 1.812571 GTTCGTTCACCTGCATTGGAT 59.187 47.619 0.00 0.00 0.00 3.41
3479 6482 1.452110 TCGTTCACCTGCATTGGATG 58.548 50.000 0.00 0.00 0.00 3.51
3480 6483 0.452987 CGTTCACCTGCATTGGATGG 59.547 55.000 0.00 0.00 0.00 3.51
3481 6484 1.549203 GTTCACCTGCATTGGATGGT 58.451 50.000 0.00 0.00 0.00 3.55
3486 6489 3.219176 ACCTGCATTGGATGGTGATAG 57.781 47.619 0.00 0.00 0.00 2.08
3487 6490 2.158564 ACCTGCATTGGATGGTGATAGG 60.159 50.000 0.00 0.00 0.00 2.57
3488 6491 2.511659 CTGCATTGGATGGTGATAGGG 58.488 52.381 0.00 0.00 0.00 3.53
3766 6788 0.388649 ACTGTCTTTAGCGTGGCTCG 60.389 55.000 4.32 4.32 40.44 5.03
3860 6882 4.020307 TGGCATGATGTGACTTCTTGTCTA 60.020 41.667 16.11 5.96 45.54 2.59
3869 6891 6.688578 TGTGACTTCTTGTCTAATGGTCTAC 58.311 40.000 0.00 0.00 45.54 2.59
3959 6982 4.367450 GCACACATGACCTTTTTGCTTTA 58.633 39.130 0.00 0.00 0.00 1.85
3978 7001 5.058856 GCTTTATTGTAACGTTCGCCTTTTC 59.941 40.000 2.82 0.00 0.00 2.29
3996 7019 6.849811 GCCTTTTCTTAAAGTTGTTCTACGTC 59.150 38.462 0.00 0.00 39.29 4.34
4097 7120 4.713824 ACCAGTTGAATGCTTCATGATG 57.286 40.909 0.00 0.00 39.84 3.07
4113 7136 1.209261 TGATGAGGCCGCATCTGTTAA 59.791 47.619 38.38 22.47 43.89 2.01
4254 7277 4.259356 GGATGTCCTGGTGGTTTAGTAAC 58.741 47.826 0.00 0.00 34.23 2.50
4304 7327 8.514330 TGTTTTTGTGTAATCCTTCACTTAGT 57.486 30.769 0.00 0.00 35.82 2.24
4344 7367 4.460263 ACTAATTTGTGTGGAGTGCTGAA 58.540 39.130 0.00 0.00 0.00 3.02
4350 7373 2.368548 TGTGTGGAGTGCTGAACAGTAT 59.631 45.455 3.77 0.00 29.71 2.12
4368 7391 5.187772 ACAGTATCTGTGCTAGACATTTCCA 59.812 40.000 1.44 0.00 43.63 3.53
4383 7406 4.344679 ACATTTCCAAGCTGACCATTTCAA 59.655 37.500 0.00 0.00 32.21 2.69
4400 7423 6.183360 CCATTTCAACTTGTCTATCTGCAGAG 60.183 42.308 22.96 9.67 0.00 3.35
4455 7478 1.666011 GAACACCAGCAGGAGACGA 59.334 57.895 0.35 0.00 38.69 4.20
4464 7487 1.738099 CAGGAGACGAAACGGGCAG 60.738 63.158 0.00 0.00 0.00 4.85
4475 7498 3.130160 CGGGCAGAAGCAGAAGCC 61.130 66.667 0.00 0.00 46.28 4.35
4479 7502 1.375268 GCAGAAGCAGAAGCCGTCT 60.375 57.895 0.00 0.00 43.56 4.18
4553 7576 1.880675 AGTAGTATGACCCTCGATGCG 59.119 52.381 0.00 0.00 0.00 4.73
4593 7616 3.055167 CACCTTATGTCCTGACCATGTCA 60.055 47.826 0.00 0.00 40.50 3.58
4594 7617 3.587061 ACCTTATGTCCTGACCATGTCAA 59.413 43.478 0.00 0.00 42.26 3.18
4611 7634 4.820897 TGTCAATGGTCACTCAGTATCAC 58.179 43.478 0.00 0.00 0.00 3.06
4612 7635 4.283212 TGTCAATGGTCACTCAGTATCACA 59.717 41.667 0.00 0.00 0.00 3.58
4613 7636 4.627467 GTCAATGGTCACTCAGTATCACAC 59.373 45.833 0.00 0.00 0.00 3.82
4621 7644 4.919653 AGTATCACACTGCAGCCG 57.080 55.556 15.27 8.03 35.62 5.52
4656 7679 1.495951 CGCCGGAAGCTGTTACAAC 59.504 57.895 5.05 0.00 40.39 3.32
4733 7759 3.418995 AGAACCTAGCGTGTAAGACTCA 58.581 45.455 0.00 0.00 0.00 3.41
4735 7761 4.463186 AGAACCTAGCGTGTAAGACTCATT 59.537 41.667 0.00 0.00 0.00 2.57
4824 7863 7.602265 TCTCGATTGATTCAGTGTTCATTGTTA 59.398 33.333 0.00 0.00 0.00 2.41
4879 7929 5.823045 GGGGATAACTTGACCAAACTATGAG 59.177 44.000 0.00 0.00 0.00 2.90
4937 7994 8.033038 TCCCTTCGTTTCATAATATAAGATCGG 58.967 37.037 0.00 0.00 0.00 4.18
4941 7998 9.537192 TTCGTTTCATAATATAAGATCGGTTGT 57.463 29.630 0.00 0.00 0.00 3.32
5040 8236 9.436957 TCAGATAGATGTTTTTCCTACTTGTTC 57.563 33.333 0.00 0.00 0.00 3.18
5047 8243 8.974060 ATGTTTTTCCTACTTGTTCTGTCTTA 57.026 30.769 0.00 0.00 0.00 2.10
5101 8297 4.764518 TGAGCAACCTCAACAGTACCTGT 61.765 47.826 0.00 0.00 44.79 4.00
5106 8771 3.517612 ACCTCAACAGTACCTGTACCAT 58.482 45.455 3.89 0.00 44.62 3.55
5136 8801 0.244450 TTAGTACCACCTCGCCAACG 59.756 55.000 0.00 0.00 42.01 4.10
5144 8809 2.962569 CTCGCCAACGTGAGGAGA 59.037 61.111 11.22 11.68 42.01 3.71
5241 8906 2.615227 GATCATGAAGGGCCGTGGCT 62.615 60.000 11.25 0.00 41.60 4.75
5257 8922 1.132500 GGCTTAGGCTAGTGGTCCAT 58.868 55.000 0.00 0.00 38.73 3.41
5261 8926 4.530946 GGCTTAGGCTAGTGGTCCATATTA 59.469 45.833 0.00 0.00 38.73 0.98
5271 8936 4.534500 AGTGGTCCATATTACACTTGGTGA 59.466 41.667 0.00 0.00 41.03 4.02
5277 8942 4.574421 CCATATTACACTTGGTGAATGCGA 59.426 41.667 4.62 0.00 36.96 5.10
5297 8962 2.806945 TGGCTTACCATCTTCCCAAG 57.193 50.000 0.00 0.00 42.67 3.61
5310 8975 3.313874 CCAAGCGGGAGAGTGGAT 58.686 61.111 0.00 0.00 40.01 3.41
5324 8989 6.115446 GGAGAGTGGATGTCATAATTTGTGA 58.885 40.000 0.00 0.00 0.00 3.58
5338 9003 1.784358 TTGTGATAGAGGGGGTACGG 58.216 55.000 0.00 0.00 0.00 4.02
5339 9004 0.757935 TGTGATAGAGGGGGTACGGC 60.758 60.000 0.00 0.00 0.00 5.68
5340 9005 1.152398 TGATAGAGGGGGTACGGCC 60.152 63.158 0.00 0.00 0.00 6.13
5355 9033 3.864789 ACGGCCTCCAATTCTCAATAT 57.135 42.857 0.00 0.00 0.00 1.28
5356 9034 4.974645 ACGGCCTCCAATTCTCAATATA 57.025 40.909 0.00 0.00 0.00 0.86
5364 9042 9.521503 GCCTCCAATTCTCAATATAAAGTTTTC 57.478 33.333 0.00 0.00 0.00 2.29
5400 9078 6.214191 TCTCTAGCAAGGACAGTTTGATAG 57.786 41.667 4.49 4.49 42.76 2.08
5403 9081 6.398918 TCTAGCAAGGACAGTTTGATAGAAC 58.601 40.000 9.56 0.00 45.33 3.01
5412 9090 5.230942 ACAGTTTGATAGAACGTTCTGGAG 58.769 41.667 35.24 19.44 38.19 3.86
5413 9091 4.627467 CAGTTTGATAGAACGTTCTGGAGG 59.373 45.833 35.24 15.44 38.19 4.30
5415 9093 5.479375 AGTTTGATAGAACGTTCTGGAGGTA 59.521 40.000 35.24 18.36 38.19 3.08
5416 9094 5.578005 TTGATAGAACGTTCTGGAGGTAG 57.422 43.478 35.24 0.00 38.19 3.18
5417 9095 4.597004 TGATAGAACGTTCTGGAGGTAGT 58.403 43.478 35.24 12.82 38.19 2.73
5443 9122 1.122632 TCCTGTTCGTTACCTGGGCA 61.123 55.000 0.00 0.00 0.00 5.36
5450 9129 1.283613 TCGTTACCTGGGCATTGGATT 59.716 47.619 0.00 0.00 0.00 3.01
5468 9147 8.653338 CATTGGATTTTTGATTGATTCAGTGTC 58.347 33.333 0.00 0.00 35.27 3.67
5469 9148 6.690530 TGGATTTTTGATTGATTCAGTGTCC 58.309 36.000 0.00 0.00 35.27 4.02
5470 9149 5.801947 GGATTTTTGATTGATTCAGTGTCCG 59.198 40.000 0.00 0.00 35.27 4.79
5471 9150 3.829886 TTTGATTGATTCAGTGTCCGC 57.170 42.857 0.00 0.00 35.27 5.54
5472 9151 2.768253 TGATTGATTCAGTGTCCGCT 57.232 45.000 0.00 0.00 0.00 5.52
5473 9152 2.349590 TGATTGATTCAGTGTCCGCTG 58.650 47.619 1.40 1.40 37.81 5.18
5474 9153 1.063174 GATTGATTCAGTGTCCGCTGC 59.937 52.381 2.98 0.00 36.49 5.25
5475 9154 0.250252 TTGATTCAGTGTCCGCTGCA 60.250 50.000 0.00 0.00 36.49 4.41
5476 9155 0.950555 TGATTCAGTGTCCGCTGCAC 60.951 55.000 0.00 0.00 36.49 4.57
5477 9156 0.671781 GATTCAGTGTCCGCTGCACT 60.672 55.000 0.00 0.00 46.86 4.40
5478 9157 0.250467 ATTCAGTGTCCGCTGCACTT 60.250 50.000 0.00 0.00 43.87 3.16
5479 9158 0.463654 TTCAGTGTCCGCTGCACTTT 60.464 50.000 0.00 0.00 43.87 2.66
5480 9159 0.463654 TCAGTGTCCGCTGCACTTTT 60.464 50.000 0.00 0.00 43.87 2.27
5481 9160 0.381801 CAGTGTCCGCTGCACTTTTT 59.618 50.000 0.00 0.00 43.87 1.94
5482 9161 1.601903 CAGTGTCCGCTGCACTTTTTA 59.398 47.619 0.00 0.00 43.87 1.52
5483 9162 1.602377 AGTGTCCGCTGCACTTTTTAC 59.398 47.619 0.00 0.00 43.87 2.01
5484 9163 1.332375 GTGTCCGCTGCACTTTTTACA 59.668 47.619 0.00 0.00 34.30 2.41
5485 9164 1.601903 TGTCCGCTGCACTTTTTACAG 59.398 47.619 0.00 0.00 34.48 2.74
5486 9165 1.871039 GTCCGCTGCACTTTTTACAGA 59.129 47.619 0.00 0.00 33.10 3.41
5487 9166 2.289547 GTCCGCTGCACTTTTTACAGAA 59.710 45.455 0.00 0.00 33.10 3.02
5488 9167 2.946329 TCCGCTGCACTTTTTACAGAAA 59.054 40.909 0.00 0.00 33.10 2.52
5489 9168 3.378742 TCCGCTGCACTTTTTACAGAAAA 59.621 39.130 0.00 0.00 33.10 2.29
5490 9169 4.109050 CCGCTGCACTTTTTACAGAAAAA 58.891 39.130 0.00 0.00 41.24 1.94
5512 9191 8.659925 AAAAATAACAAGCAAATGTGACATGA 57.340 26.923 0.00 0.00 32.81 3.07
5513 9192 8.659925 AAAATAACAAGCAAATGTGACATGAA 57.340 26.923 0.00 0.00 32.81 2.57
5514 9193 8.659925 AAATAACAAGCAAATGTGACATGAAA 57.340 26.923 0.00 0.00 32.81 2.69
5515 9194 7.878477 ATAACAAGCAAATGTGACATGAAAG 57.122 32.000 0.00 0.00 32.81 2.62
5516 9195 5.518848 ACAAGCAAATGTGACATGAAAGA 57.481 34.783 0.00 0.00 30.82 2.52
5517 9196 5.904941 ACAAGCAAATGTGACATGAAAGAA 58.095 33.333 0.00 0.00 30.82 2.52
5518 9197 6.339730 ACAAGCAAATGTGACATGAAAGAAA 58.660 32.000 0.00 0.00 30.82 2.52
5519 9198 6.477688 ACAAGCAAATGTGACATGAAAGAAAG 59.522 34.615 0.00 0.00 30.82 2.62
5520 9199 6.152932 AGCAAATGTGACATGAAAGAAAGT 57.847 33.333 0.00 0.00 0.00 2.66
5521 9200 6.576185 AGCAAATGTGACATGAAAGAAAGTT 58.424 32.000 0.00 0.00 0.00 2.66
5522 9201 7.043565 AGCAAATGTGACATGAAAGAAAGTTT 58.956 30.769 0.00 0.00 0.00 2.66
5523 9202 7.550196 AGCAAATGTGACATGAAAGAAAGTTTT 59.450 29.630 0.00 0.00 0.00 2.43
5524 9203 7.637132 GCAAATGTGACATGAAAGAAAGTTTTG 59.363 33.333 0.00 0.00 0.00 2.44
5525 9204 8.658609 CAAATGTGACATGAAAGAAAGTTTTGT 58.341 29.630 0.00 0.00 0.00 2.83
5526 9205 7.992180 ATGTGACATGAAAGAAAGTTTTGTC 57.008 32.000 0.00 8.33 0.00 3.18
5527 9206 6.918626 TGTGACATGAAAGAAAGTTTTGTCA 58.081 32.000 12.38 12.38 0.00 3.58
5528 9207 7.546358 TGTGACATGAAAGAAAGTTTTGTCAT 58.454 30.769 17.19 10.97 36.40 3.06
5529 9208 8.681806 TGTGACATGAAAGAAAGTTTTGTCATA 58.318 29.630 17.19 13.47 36.40 2.15
5530 9209 9.683069 GTGACATGAAAGAAAGTTTTGTCATAT 57.317 29.630 17.19 5.19 36.40 1.78
5531 9210 9.897744 TGACATGAAAGAAAGTTTTGTCATATC 57.102 29.630 12.38 9.89 0.00 1.63
5538 9217 9.450807 AAAGAAAGTTTTGTCATATCTCAAACG 57.549 29.630 0.00 0.00 34.05 3.60
5539 9218 8.154649 AGAAAGTTTTGTCATATCTCAAACGT 57.845 30.769 0.00 0.00 34.05 3.99
5540 9219 8.621286 AGAAAGTTTTGTCATATCTCAAACGTT 58.379 29.630 0.00 0.00 34.05 3.99
5541 9220 9.872757 GAAAGTTTTGTCATATCTCAAACGTTA 57.127 29.630 0.00 0.00 34.05 3.18
5542 9221 9.659830 AAAGTTTTGTCATATCTCAAACGTTAC 57.340 29.630 0.00 0.00 34.05 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.036952 AGACTCCGCATGTTGACAGG 60.037 55.000 0.00 0.00 0.00 4.00
4 5 1.073964 CAGACTCCGCATGTTGACAG 58.926 55.000 0.00 0.00 0.00 3.51
9 670 0.806868 CATTGCAGACTCCGCATGTT 59.193 50.000 0.00 0.00 39.58 2.71
16 677 1.734465 CGAGAAACCATTGCAGACTCC 59.266 52.381 0.00 0.00 0.00 3.85
23 684 1.666888 CCAAGCACGAGAAACCATTGC 60.667 52.381 0.00 0.00 0.00 3.56
38 699 2.743928 CAGGTCCACTCGCCAAGC 60.744 66.667 0.00 0.00 0.00 4.01
44 705 2.743928 GCAAGCCAGGTCCACTCG 60.744 66.667 0.00 0.00 0.00 4.18
55 716 2.245159 AAAAGCTTTCCTTGCAAGCC 57.755 45.000 21.43 6.12 46.76 4.35
118 779 2.221981 CACTCTTCAAGCACGAGAAACC 59.778 50.000 0.00 0.00 0.00 3.27
179 872 8.461222 AGTTGTGTCATTATGTGGTATTTCATG 58.539 33.333 0.00 0.00 0.00 3.07
186 879 7.548967 TCGATAAGTTGTGTCATTATGTGGTA 58.451 34.615 0.00 0.00 0.00 3.25
189 882 9.463443 TCTATCGATAAGTTGTGTCATTATGTG 57.537 33.333 6.58 0.00 0.00 3.21
233 926 5.686841 GGCAACGTTTATTCGGTTTTAAAGT 59.313 36.000 0.00 0.00 34.94 2.66
367 2708 1.801771 TGACATGCCTAAAAACCGTCG 59.198 47.619 0.00 0.00 0.00 5.12
401 2742 4.339872 TTTCTTTGCAAGCCATGTTCAT 57.660 36.364 0.00 0.00 0.00 2.57
409 2750 7.218963 CGAAGAAGTATATTTTCTTTGCAAGCC 59.781 37.037 13.32 2.97 43.07 4.35
413 2754 7.389330 TGACCGAAGAAGTATATTTTCTTTGCA 59.611 33.333 16.90 11.46 43.07 4.08
436 2777 4.094442 GTGAAATTCTCCGGGTATTGTGAC 59.906 45.833 0.00 0.00 0.00 3.67
467 2808 3.770933 AGTAAATTGTGCATGCCTTCCAT 59.229 39.130 16.68 0.04 33.39 3.41
470 2811 5.708948 TGTTAGTAAATTGTGCATGCCTTC 58.291 37.500 16.68 6.46 0.00 3.46
474 2815 6.949578 ATGTTGTTAGTAAATTGTGCATGC 57.050 33.333 11.82 11.82 0.00 4.06
513 2854 8.340618 TGCTGTTATCATAGCTCTTTTCTTTT 57.659 30.769 0.00 0.00 40.52 2.27
516 2857 6.317391 GGTTGCTGTTATCATAGCTCTTTTCT 59.683 38.462 0.00 0.00 40.52 2.52
518 2859 5.945784 TGGTTGCTGTTATCATAGCTCTTTT 59.054 36.000 0.00 0.00 40.52 2.27
537 2878 3.915437 ACCATTAAGAAAGCGTGGTTG 57.085 42.857 0.00 0.00 40.08 3.77
541 2883 5.622770 AGGTAAACCATTAAGAAAGCGTG 57.377 39.130 1.26 0.00 38.89 5.34
551 2893 8.827832 TTAGTGCTCTACTAGGTAAACCATTA 57.172 34.615 1.26 0.00 42.57 1.90
563 2905 4.219070 TGAAGCGGTTTTAGTGCTCTACTA 59.781 41.667 0.00 0.00 40.89 1.82
567 2909 2.543777 TGAAGCGGTTTTAGTGCTCT 57.456 45.000 0.00 0.00 38.17 4.09
568 2910 6.787085 ATATATGAAGCGGTTTTAGTGCTC 57.213 37.500 0.00 0.00 38.17 4.26
591 2933 4.794329 GCTTTGAGAGCGATGTCTAGCATA 60.794 45.833 16.39 0.00 42.46 3.14
607 2949 1.135315 CGGTTGCATCGGCTTTGAG 59.865 57.895 0.00 0.00 41.91 3.02
627 2977 7.256296 CCCCAAAATTCCTGTCTTAGATTTGTT 60.256 37.037 0.00 0.00 0.00 2.83
638 2988 1.202348 CTTCGCCCCAAAATTCCTGTC 59.798 52.381 0.00 0.00 0.00 3.51
642 2992 1.262417 TTCCTTCGCCCCAAAATTCC 58.738 50.000 0.00 0.00 0.00 3.01
649 2999 6.800072 AAAAATAATATTTCCTTCGCCCCA 57.200 33.333 0.00 0.00 0.00 4.96
686 3322 4.383010 CCTTCTTGCTTTCAAACCCAACTT 60.383 41.667 0.00 0.00 0.00 2.66
687 3323 3.132824 CCTTCTTGCTTTCAAACCCAACT 59.867 43.478 0.00 0.00 0.00 3.16
693 3329 2.473816 GTGGCCTTCTTGCTTTCAAAC 58.526 47.619 3.32 0.00 0.00 2.93
698 3334 2.564721 GCGGTGGCCTTCTTGCTTT 61.565 57.895 3.32 0.00 0.00 3.51
711 3347 4.383602 CCAAAAGGCGACGCGGTG 62.384 66.667 14.61 8.56 0.00 4.94
805 3441 1.380246 GGCCATCATGCCCACTTGA 60.380 57.895 0.00 0.00 46.11 3.02
927 3574 3.036959 GGAGGGGGAGAGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
928 3575 3.039526 AGGAGGGGGAGAGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
932 3579 2.612251 GAGGAGGAGGGGGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
1155 3804 0.749649 CGGAGGAACAGAGGATGAGG 59.250 60.000 0.00 0.00 0.00 3.86
1187 3839 5.107220 GGAAGATTTGACTAAGAAAACGCGA 60.107 40.000 15.93 0.00 0.00 5.87
1232 3884 2.731374 GAATCGAGAGCGGAGGGG 59.269 66.667 0.00 0.00 38.28 4.79
1299 3953 0.319641 GACCGGTAATCATCCTCGCC 60.320 60.000 7.34 0.00 0.00 5.54
1301 3955 0.663568 GCGACCGGTAATCATCCTCG 60.664 60.000 7.34 4.31 0.00 4.63
1304 3958 1.663702 CGGCGACCGGTAATCATCC 60.664 63.158 7.34 1.40 44.15 3.51
1308 3962 0.386985 GAGATCGGCGACCGGTAATC 60.387 60.000 13.76 3.62 42.08 1.75
1399 4053 1.772063 GCGTAAAGTATGGGGCGCAG 61.772 60.000 10.83 0.00 43.62 5.18
1445 4099 2.768833 TCTAAATCACCGGATCGACG 57.231 50.000 9.46 0.00 31.88 5.12
1511 4165 1.742768 GAGTACGGAGATGGCAGGG 59.257 63.158 0.00 0.00 0.00 4.45
1547 4201 1.494721 ACAGAGCAAAACTTGGGAGGA 59.505 47.619 0.00 0.00 0.00 3.71
1549 4203 2.294512 GGAACAGAGCAAAACTTGGGAG 59.705 50.000 0.00 0.00 0.00 4.30
1640 4299 0.321919 TGCCATCTCTGCAACAGGTC 60.322 55.000 0.00 0.00 35.40 3.85
1687 4346 1.817099 CTCCTCCATGCGCTTGGTC 60.817 63.158 33.70 0.00 38.01 4.02
1762 4421 1.689892 GGGAGAGGGTTGAGGTAGAGG 60.690 61.905 0.00 0.00 0.00 3.69
1766 4425 1.394963 GGGGGAGAGGGTTGAGGTA 59.605 63.158 0.00 0.00 0.00 3.08
1781 4440 3.831323 TGTGAGCACATAAATATGGGGG 58.169 45.455 4.92 0.00 37.57 5.40
1791 4450 1.064758 GGGGTGGATTGTGAGCACATA 60.065 52.381 3.90 0.00 41.52 2.29
1796 4462 0.323725 ATGTGGGGTGGATTGTGAGC 60.324 55.000 0.00 0.00 0.00 4.26
1797 4463 1.004628 TGATGTGGGGTGGATTGTGAG 59.995 52.381 0.00 0.00 0.00 3.51
1804 4470 2.765689 AAAAAGTGATGTGGGGTGGA 57.234 45.000 0.00 0.00 0.00 4.02
1810 4476 5.288015 TGCAACATGTAAAAAGTGATGTGG 58.712 37.500 0.00 0.00 0.00 4.17
1821 4487 9.539825 AATCAGTTTGTTATTGCAACATGTAAA 57.460 25.926 0.00 0.00 0.00 2.01
1846 4512 1.153588 GATCGGTTCGGCGGGTTAA 60.154 57.895 7.21 0.00 0.00 2.01
1911 4577 4.826733 ACTGCACAAGAACAACAATGGATA 59.173 37.500 0.00 0.00 0.00 2.59
1912 4578 3.638160 ACTGCACAAGAACAACAATGGAT 59.362 39.130 0.00 0.00 0.00 3.41
1913 4579 3.023119 ACTGCACAAGAACAACAATGGA 58.977 40.909 0.00 0.00 0.00 3.41
1971 4637 2.986050 TCTTCTTCTTGGTACACCCCT 58.014 47.619 0.00 0.00 39.29 4.79
2017 4683 1.400494 GAAAGCCCGATTACAATGCGT 59.600 47.619 0.00 0.00 0.00 5.24
2196 4862 9.757227 AAAGATAGTGACAACTAATGCTAGATC 57.243 33.333 0.00 0.00 42.17 2.75
2219 4885 6.198216 CAGTGTCGAAACCCAAAATAACAAAG 59.802 38.462 0.95 0.00 0.00 2.77
2221 4887 5.357314 TCAGTGTCGAAACCCAAAATAACAA 59.643 36.000 0.95 0.00 0.00 2.83
2243 4909 7.225931 GGTTAGCGAAGTATGGTGATAAAATCA 59.774 37.037 0.00 0.00 36.84 2.57
2255 4921 8.031864 AGATAAGATGATGGTTAGCGAAGTATG 58.968 37.037 0.00 0.00 0.00 2.39
2265 4931 7.822334 ACAACGAAACAGATAAGATGATGGTTA 59.178 33.333 0.00 0.00 0.00 2.85
2285 4951 7.292292 CAGGATAAACATTTTACGAACAACGA 58.708 34.615 0.00 0.00 45.77 3.85
2369 5035 7.786178 TTTTTCATCCATGTTAGAGGATACG 57.214 36.000 0.00 0.00 42.61 3.06
2418 5088 3.636764 GCTCCAAGAAACCAAAAGGAGAA 59.363 43.478 10.25 0.00 44.12 2.87
2430 5100 0.762418 TTGACGAGGGCTCCAAGAAA 59.238 50.000 0.00 0.00 0.00 2.52
2469 5140 9.933723 AAATTCTAAACAAATAGCAGCAAGATT 57.066 25.926 0.00 0.00 0.00 2.40
2505 5176 3.561744 CCCATGCCAACAATTTTTCCCAT 60.562 43.478 0.00 0.00 0.00 4.00
2520 5191 4.974721 CATACCCCGCCCCATGCC 62.975 72.222 0.00 0.00 36.24 4.40
2524 5195 2.847366 GAAAAGCATACCCCGCCCCA 62.847 60.000 0.00 0.00 0.00 4.96
2525 5196 2.043349 AAAAGCATACCCCGCCCC 60.043 61.111 0.00 0.00 0.00 5.80
2526 5197 1.076995 AGAAAAGCATACCCCGCCC 60.077 57.895 0.00 0.00 0.00 6.13
2529 5200 0.734889 CAGCAGAAAAGCATACCCCG 59.265 55.000 0.00 0.00 36.85 5.73
2541 5233 2.889045 AGCTCAGAATTTTGCAGCAGAA 59.111 40.909 16.81 0.00 32.17 3.02
2546 5238 4.430137 TGCTTAGCTCAGAATTTTGCAG 57.570 40.909 5.60 0.00 0.00 4.41
2614 5596 9.754382 GGACAAAGAAATATGTATGCAAATCAT 57.246 29.630 0.00 0.00 39.17 2.45
2634 5616 5.568685 TGACGAGTTTTTCAATGGACAAA 57.431 34.783 0.00 0.00 0.00 2.83
2702 5684 9.959721 ATCTTTCAAGTAAACCTAAGCAAGATA 57.040 29.630 0.00 0.00 27.58 1.98
2757 5739 7.342799 ACAATCCTTTTCCAATACATGCATACT 59.657 33.333 0.00 0.00 0.00 2.12
2758 5740 7.491682 ACAATCCTTTTCCAATACATGCATAC 58.508 34.615 0.00 0.00 0.00 2.39
2763 5746 6.934056 TCCAACAATCCTTTTCCAATACATG 58.066 36.000 0.00 0.00 0.00 3.21
2888 5888 6.088016 TGTCATGTTTTTCCTTGGATGAAG 57.912 37.500 0.00 0.00 0.00 3.02
2904 5904 6.392354 CAAAGGCTCATTGTTATTGTCATGT 58.608 36.000 0.00 0.00 0.00 3.21
2994 5994 3.574284 TTGCAAAATCCCGAGTCAATG 57.426 42.857 0.00 0.00 0.00 2.82
3062 6062 2.363795 ATGGCGACGAGGAAGGGA 60.364 61.111 0.00 0.00 0.00 4.20
3240 6241 7.290014 ACCAAATTGACAAAGAAATAGGGACTT 59.710 33.333 0.00 0.00 41.75 3.01
3252 6253 5.591099 AGCTAACACACCAAATTGACAAAG 58.409 37.500 0.00 0.00 0.00 2.77
3269 6271 7.727094 GCTGAACTTATTAAGCAAAGCTAAC 57.273 36.000 13.49 0.00 41.54 2.34
3367 6370 5.510690 GGACAATGGAAAAGGTACCCAAAAG 60.511 44.000 8.74 0.00 33.15 2.27
3368 6371 4.345547 GGACAATGGAAAAGGTACCCAAAA 59.654 41.667 8.74 0.00 33.15 2.44
3369 6372 3.898741 GGACAATGGAAAAGGTACCCAAA 59.101 43.478 8.74 0.00 33.15 3.28
3370 6373 3.117093 TGGACAATGGAAAAGGTACCCAA 60.117 43.478 8.74 0.00 33.15 4.12
3371 6374 2.447429 TGGACAATGGAAAAGGTACCCA 59.553 45.455 8.74 0.00 0.00 4.51
3372 6375 3.089284 CTGGACAATGGAAAAGGTACCC 58.911 50.000 8.74 0.00 0.00 3.69
3373 6376 2.492088 GCTGGACAATGGAAAAGGTACC 59.508 50.000 2.73 2.73 0.00 3.34
3457 6460 0.240945 CCAATGCAGGTGAACGAACC 59.759 55.000 1.78 0.00 40.85 3.62
3462 6465 1.549203 ACCATCCAATGCAGGTGAAC 58.451 50.000 1.78 0.00 32.04 3.18
3466 6469 2.158564 CCTATCACCATCCAATGCAGGT 60.159 50.000 0.00 0.00 33.91 4.00
3467 6470 2.511659 CCTATCACCATCCAATGCAGG 58.488 52.381 0.00 0.00 0.00 4.85
3468 6471 2.511659 CCCTATCACCATCCAATGCAG 58.488 52.381 0.00 0.00 0.00 4.41
3469 6472 1.145531 CCCCTATCACCATCCAATGCA 59.854 52.381 0.00 0.00 0.00 3.96
3470 6473 1.915141 CCCCTATCACCATCCAATGC 58.085 55.000 0.00 0.00 0.00 3.56
3471 6474 1.548582 GGCCCCTATCACCATCCAATG 60.549 57.143 0.00 0.00 0.00 2.82
3472 6475 0.779997 GGCCCCTATCACCATCCAAT 59.220 55.000 0.00 0.00 0.00 3.16
3473 6476 0.328450 AGGCCCCTATCACCATCCAA 60.328 55.000 0.00 0.00 0.00 3.53
3474 6477 0.570727 TAGGCCCCTATCACCATCCA 59.429 55.000 0.00 0.00 0.00 3.41
3475 6478 0.984995 GTAGGCCCCTATCACCATCC 59.015 60.000 0.00 0.00 0.00 3.51
3476 6479 1.625818 CTGTAGGCCCCTATCACCATC 59.374 57.143 0.00 0.00 0.00 3.51
3477 6480 1.734655 CTGTAGGCCCCTATCACCAT 58.265 55.000 0.00 0.00 0.00 3.55
3478 6481 0.399949 CCTGTAGGCCCCTATCACCA 60.400 60.000 0.00 0.00 0.00 4.17
3479 6482 1.128188 CCCTGTAGGCCCCTATCACC 61.128 65.000 0.00 0.00 0.00 4.02
3480 6483 0.400093 ACCCTGTAGGCCCCTATCAC 60.400 60.000 0.00 0.00 40.58 3.06
3481 6484 0.105142 GACCCTGTAGGCCCCTATCA 60.105 60.000 0.00 0.00 40.58 2.15
3482 6485 0.836830 GGACCCTGTAGGCCCCTATC 60.837 65.000 0.00 0.00 40.58 2.08
3483 6486 1.239235 GGACCCTGTAGGCCCCTAT 59.761 63.158 0.00 0.00 40.58 2.57
3484 6487 2.700803 GGACCCTGTAGGCCCCTA 59.299 66.667 0.00 0.00 40.58 3.53
3485 6488 4.433194 GGGACCCTGTAGGCCCCT 62.433 72.222 2.09 0.00 42.96 4.79
3486 6489 4.752594 TGGGACCCTGTAGGCCCC 62.753 72.222 13.00 15.62 46.26 5.80
3487 6490 3.090532 CTGGGACCCTGTAGGCCC 61.091 72.222 13.00 6.66 46.72 5.80
3488 6491 3.090532 CCTGGGACCCTGTAGGCC 61.091 72.222 13.00 0.00 40.58 5.19
3766 6788 0.108138 AGCGGACTGTTCTACCATGC 60.108 55.000 0.00 0.00 0.00 4.06
3860 6882 8.883731 CAATTTCTCTAAATCACGTAGACCATT 58.116 33.333 0.00 0.00 34.12 3.16
3869 6891 7.061094 GGAAACTTGCAATTTCTCTAAATCACG 59.939 37.037 22.31 3.13 36.49 4.35
3959 6982 4.823790 AAGAAAAGGCGAACGTTACAAT 57.176 36.364 0.00 0.00 0.00 2.71
3978 7001 6.583806 ACCATACGACGTAGAACAACTTTAAG 59.416 38.462 13.87 0.00 0.00 1.85
3996 7019 0.443869 GTCAGCAACAGCACCATACG 59.556 55.000 0.00 0.00 0.00 3.06
4097 7120 1.009829 CAGTTAACAGATGCGGCCTC 58.990 55.000 8.61 0.00 0.00 4.70
4288 7311 7.435068 TGCAGAAAACTAAGTGAAGGATTAC 57.565 36.000 0.00 0.00 0.00 1.89
4304 7327 9.474920 CAAATTAGTTAACCTCATTGCAGAAAA 57.525 29.630 0.88 0.00 0.00 2.29
4344 7367 5.187772 TGGAAATGTCTAGCACAGATACTGT 59.812 40.000 0.00 0.00 46.51 3.55
4350 7373 3.008375 AGCTTGGAAATGTCTAGCACAGA 59.992 43.478 11.48 0.00 38.85 3.41
4383 7406 2.430332 GCTCCTCTGCAGATAGACAAGT 59.570 50.000 23.58 0.00 0.00 3.16
4400 7423 3.793144 CTTGCTTGGCGTCGCTCC 61.793 66.667 18.11 1.39 0.00 4.70
4455 7478 1.518903 GCTTCTGCTTCTGCCCGTTT 61.519 55.000 0.00 0.00 38.71 3.60
4464 7487 0.388649 TCGAAGACGGCTTCTGCTTC 60.389 55.000 27.73 1.98 46.64 3.86
4566 7589 3.392947 TGGTCAGGACATAAGGTGACAAA 59.607 43.478 1.41 0.00 40.96 2.83
4711 7735 3.825014 TGAGTCTTACACGCTAGGTTCTT 59.175 43.478 0.00 0.00 0.00 2.52
4733 7759 6.375455 AGAAAGAAGAATGCGGTAACATCAAT 59.625 34.615 0.00 0.00 0.00 2.57
4735 7761 5.245531 AGAAAGAAGAATGCGGTAACATCA 58.754 37.500 0.00 0.00 0.00 3.07
4824 7863 3.586618 GAGCCTTCTCCCTCCATCATAAT 59.413 47.826 0.00 0.00 33.19 1.28
4879 7929 0.524862 CTCTTTCAGTGCCATGCCAC 59.475 55.000 0.00 0.00 35.98 5.01
4892 7942 6.332735 AGGGAGTAAAACATTTGCTCTTTC 57.667 37.500 16.70 9.52 0.00 2.62
4937 7994 6.255020 CGGCCCATAATATAAGATCGTACAAC 59.745 42.308 0.00 0.00 0.00 3.32
4941 7998 5.202765 TCCGGCCCATAATATAAGATCGTA 58.797 41.667 0.00 0.00 0.00 3.43
5040 8236 5.167121 CAGAGTGATCTGGTTGTAAGACAG 58.833 45.833 0.00 0.00 34.28 3.51
5047 8243 5.247110 ACTGATAACAGAGTGATCTGGTTGT 59.753 40.000 7.05 1.27 46.03 3.32
5101 8297 3.343941 ACTAAAAAGAGCGCCATGGTA 57.656 42.857 14.67 0.00 0.00 3.25
5106 8771 2.419667 GTGGTACTAAAAAGAGCGCCA 58.580 47.619 2.29 0.00 0.00 5.69
5136 8801 1.597461 CCCGTCCCTTTCTCCTCAC 59.403 63.158 0.00 0.00 0.00 3.51
5143 8808 2.269241 CTGCTCCCCGTCCCTTTC 59.731 66.667 0.00 0.00 0.00 2.62
5144 8809 3.330720 CCTGCTCCCCGTCCCTTT 61.331 66.667 0.00 0.00 0.00 3.11
5176 8841 2.577700 ACGTTTCAAGGTTGCACCATA 58.422 42.857 7.86 0.00 41.95 2.74
5195 8860 0.820226 GACCCCGTCCAGGTAAGTAC 59.180 60.000 0.00 0.00 37.88 2.73
5215 8880 1.889105 CCCTTCATGATCGGCCGTG 60.889 63.158 27.15 16.50 0.00 4.94
5217 8882 2.974698 GCCCTTCATGATCGGCCG 60.975 66.667 22.12 22.12 35.23 6.13
5241 8906 6.141083 AGTGTAATATGGACCACTAGCCTAA 58.859 40.000 0.00 0.00 36.44 2.69
5257 8922 4.574421 CCATCGCATTCACCAAGTGTAATA 59.426 41.667 0.00 0.00 34.79 0.98
5261 8926 1.167851 CCATCGCATTCACCAAGTGT 58.832 50.000 0.00 0.00 34.79 3.55
5294 8959 0.460987 GACATCCACTCTCCCGCTTG 60.461 60.000 0.00 0.00 0.00 4.01
5297 8962 1.040646 TATGACATCCACTCTCCCGC 58.959 55.000 0.00 0.00 0.00 6.13
5310 8975 5.431731 ACCCCCTCTATCACAAATTATGACA 59.568 40.000 0.00 0.00 0.00 3.58
5324 8989 1.155624 GAGGCCGTACCCCCTCTAT 59.844 63.158 15.73 0.00 43.42 1.98
5338 9003 9.521503 GAAAACTTTATATTGAGAATTGGAGGC 57.478 33.333 0.00 0.00 0.00 4.70
5355 9033 5.885912 AGAGCAGAAACAGGTGAAAACTTTA 59.114 36.000 0.00 0.00 0.00 1.85
5356 9034 4.706962 AGAGCAGAAACAGGTGAAAACTTT 59.293 37.500 0.00 0.00 0.00 2.66
5389 9067 5.209818 TCCAGAACGTTCTATCAAACTGT 57.790 39.130 29.28 1.87 35.34 3.55
5438 9117 4.904895 TCAATCAAAAATCCAATGCCCA 57.095 36.364 0.00 0.00 0.00 5.36
5439 9118 5.881443 TGAATCAATCAAAAATCCAATGCCC 59.119 36.000 0.00 0.00 34.30 5.36
5443 9122 7.820872 GGACACTGAATCAATCAAAAATCCAAT 59.179 33.333 0.00 0.00 37.67 3.16
5450 9129 3.820467 AGCGGACACTGAATCAATCAAAA 59.180 39.130 0.00 0.00 37.67 2.44
5468 9147 3.347958 TTTCTGTAAAAAGTGCAGCGG 57.652 42.857 0.00 0.00 39.64 5.52
5487 9166 8.659925 TCATGTCACATTTGCTTGTTATTTTT 57.340 26.923 0.00 0.00 0.00 1.94
5488 9167 8.659925 TTCATGTCACATTTGCTTGTTATTTT 57.340 26.923 0.00 0.00 0.00 1.82
5489 9168 8.659925 TTTCATGTCACATTTGCTTGTTATTT 57.340 26.923 0.00 0.00 0.00 1.40
5490 9169 8.143193 TCTTTCATGTCACATTTGCTTGTTATT 58.857 29.630 0.00 0.00 0.00 1.40
5491 9170 7.660112 TCTTTCATGTCACATTTGCTTGTTAT 58.340 30.769 0.00 0.00 0.00 1.89
5492 9171 7.036996 TCTTTCATGTCACATTTGCTTGTTA 57.963 32.000 0.00 0.00 0.00 2.41
5493 9172 5.904941 TCTTTCATGTCACATTTGCTTGTT 58.095 33.333 0.00 0.00 0.00 2.83
5494 9173 5.518848 TCTTTCATGTCACATTTGCTTGT 57.481 34.783 0.00 0.00 0.00 3.16
5495 9174 6.477688 ACTTTCTTTCATGTCACATTTGCTTG 59.522 34.615 0.00 0.00 0.00 4.01
5496 9175 6.576185 ACTTTCTTTCATGTCACATTTGCTT 58.424 32.000 0.00 0.00 0.00 3.91
5497 9176 6.152932 ACTTTCTTTCATGTCACATTTGCT 57.847 33.333 0.00 0.00 0.00 3.91
5498 9177 6.833342 AACTTTCTTTCATGTCACATTTGC 57.167 33.333 0.00 0.00 0.00 3.68
5499 9178 8.658609 ACAAAACTTTCTTTCATGTCACATTTG 58.341 29.630 0.00 0.00 0.00 2.32
5500 9179 8.776376 ACAAAACTTTCTTTCATGTCACATTT 57.224 26.923 0.00 0.00 0.00 2.32
5501 9180 8.034215 TGACAAAACTTTCTTTCATGTCACATT 58.966 29.630 0.00 0.00 40.31 2.71
5502 9181 7.546358 TGACAAAACTTTCTTTCATGTCACAT 58.454 30.769 0.00 0.00 40.31 3.21
5503 9182 6.918626 TGACAAAACTTTCTTTCATGTCACA 58.081 32.000 0.00 0.00 40.31 3.58
5504 9183 7.992180 ATGACAAAACTTTCTTTCATGTCAC 57.008 32.000 7.74 0.00 45.66 3.67
5505 9184 9.897744 GATATGACAAAACTTTCTTTCATGTCA 57.102 29.630 7.98 7.98 46.52 3.58
5512 9191 9.450807 CGTTTGAGATATGACAAAACTTTCTTT 57.549 29.630 0.00 0.00 37.66 2.52
5513 9192 8.621286 ACGTTTGAGATATGACAAAACTTTCTT 58.379 29.630 0.00 0.00 37.66 2.52
5514 9193 8.154649 ACGTTTGAGATATGACAAAACTTTCT 57.845 30.769 0.00 0.00 37.66 2.52
5515 9194 8.782533 AACGTTTGAGATATGACAAAACTTTC 57.217 30.769 0.00 0.00 37.66 2.62
5516 9195 9.659830 GTAACGTTTGAGATATGACAAAACTTT 57.340 29.630 5.91 0.00 37.66 2.66


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

AutoCloner maintained by Alex Coulton.