Multiple sequence alignment - TraesCS6A01G137300

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 TraesCS6A01G137300 chr6A 100.000 3887 0 0 1 3887 108205400 108201514 0.000000e+00 7179.0
1 TraesCS6A01G137300 chr6A 89.091 220 23 1 3548 3766 108180132 108179913 4.950000e-69 272.0
2 TraesCS6A01G137300 chr6D 89.113 2030 140 39 729 2747 89825774 89823815 0.000000e+00 2449.0
3 TraesCS6A01G137300 chr6D 93.414 744 18 14 3167 3887 89823403 89822668 0.000000e+00 1074.0
4 TraesCS6A01G137300 chr6D 87.755 441 28 11 255 694 89827774 89827359 3.490000e-135 492.0
5 TraesCS6A01G137300 chr6D 94.009 217 13 0 1 217 89827991 89827775 2.900000e-86 329.0
6 TraesCS6A01G137300 chr6D 89.868 227 21 2 3541 3766 89734338 89734113 1.370000e-74 291.0
7 TraesCS6A01G137300 chr6D 100.000 39 0 0 698 736 89825783 89825745 5.390000e-09 73.1
8 TraesCS6A01G137300 chr6B 93.651 756 34 8 1992 2747 172326059 172325318 0.000000e+00 1118.0
9 TraesCS6A01G137300 chr6B 92.497 773 34 11 3125 3887 172324794 172324036 0.000000e+00 1085.0
10 TraesCS6A01G137300 chr6B 85.493 903 60 33 729 1617 172328165 172327320 0.000000e+00 876.0
11 TraesCS6A01G137300 chr6B 92.225 463 27 4 3 457 172329168 172328707 0.000000e+00 647.0
12 TraesCS6A01G137300 chr6B 87.603 363 35 5 2745 3100 172325289 172324930 2.790000e-111 412.0
13 TraesCS6A01G137300 chr6B 90.749 227 17 2 469 694 172328568 172328345 2.270000e-77 300.0
14 TraesCS6A01G137300 chr6B 89.427 227 22 2 3541 3766 172265366 172265141 6.360000e-73 285.0
15 TraesCS6A01G137300 chr6B 100.000 31 0 0 698 728 172328174 172328144 1.510000e-04 58.4
16 TraesCS6A01G137300 chr7A 75.336 446 83 21 2047 2487 649425856 649425433 5.130000e-44 189.0
17 TraesCS6A01G137300 chr7A 89.286 140 15 0 2556 2695 649425286 649425147 3.990000e-40 176.0
18 TraesCS6A01G137300 chr7D 89.286 140 15 0 2556 2695 563825365 563825504 3.990000e-40 176.0
19 TraesCS6A01G137300 chr7B 89.286 140 15 0 2556 2695 614220612 614220473 3.990000e-40 176.0
20 TraesCS6A01G137300 chr1D 88.571 140 16 0 2556 2695 421493999 421494138 1.860000e-38 171.0
21 TraesCS6A01G137300 chr2D 87.857 140 17 0 2556 2695 558943717 558943578 8.640000e-37 165.0
22 TraesCS6A01G137300 chr3D 86.429 140 19 0 2556 2695 577441695 577441834 1.870000e-33 154.0


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 TraesCS6A01G137300 chr6A 108201514 108205400 3886 True 7179.000000 7179 100.000000 1 3887 1 chr6A.!!$R2 3886
1 TraesCS6A01G137300 chr6D 89822668 89827991 5323 True 883.420000 2449 92.858200 1 3887 5 chr6D.!!$R2 3886
2 TraesCS6A01G137300 chr6B 172324036 172329168 5132 True 642.342857 1118 91.745429 3 3887 7 chr6B.!!$R2 3884

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
768 2481 0.616679 ATGAGCCCATTTGCTGCCTT 60.617 50.0 0.00 0.00 42.95 4.35 F
1200 2921 0.179045 GGCGTATGATGGAACTGGCT 60.179 55.0 0.00 0.00 0.00 4.75 F
2421 5390 0.247736 AGGTCAAGGCTGATCGTGAC 59.752 55.0 7.58 7.58 42.55 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 5174 0.179059 AACAGCACATGACGGTGACA 60.179 50.0 20.5 0.0 41.32 3.58 R
2862 5862 0.032017 GCCTCCTTCCTCTCCTACCA 60.032 60.0 0.0 0.0 0.00 3.25 R
3830 6959 0.600782 TAACCGCACGACCACCTTTC 60.601 55.0 0.0 0.0 0.00 2.62 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
75 76 4.034510 GCCGCAGAAGATATATGCCATTAC 59.965 45.833 0.00 0.00 43.40 1.89
79 80 6.018425 CGCAGAAGATATATGCCATTACCATC 60.018 42.308 0.00 0.00 43.40 3.51
201 204 3.924144 TGGGACATTATTTTGCAAGTGC 58.076 40.909 0.00 0.00 42.50 4.40
303 306 6.213600 ACTGACCAACCATCTGACTAAATACT 59.786 38.462 0.00 0.00 0.00 2.12
311 314 9.739276 AACCATCTGACTAAATACTTCATGAAA 57.261 29.630 9.88 0.00 0.00 2.69
457 467 3.181526 GCACACAAAAACAAATCGTGCAA 60.182 39.130 6.73 0.00 45.70 4.08
458 468 4.322119 CACACAAAAACAAATCGTGCAAC 58.678 39.130 0.00 0.00 0.00 4.17
489 626 4.717233 ACAGCAAGTTTTCACATGAACA 57.283 36.364 0.00 0.00 33.13 3.18
528 665 9.453572 ATGATTACATGATAGAAACACAAGTGT 57.546 29.630 0.00 0.00 39.34 3.55
577 714 1.135699 GGGCGTACGTACATGTGTCG 61.136 60.000 24.50 18.74 0.00 4.35
584 721 3.132629 ACGTACATGTGTCGACATCTC 57.867 47.619 23.12 9.72 41.12 2.75
592 729 2.364002 TGTGTCGACATCTCCTTCACAA 59.636 45.455 23.12 0.00 32.66 3.33
611 748 3.867493 ACAACTCGATGCACACATGATAG 59.133 43.478 0.00 0.00 36.35 2.08
623 760 5.590259 GCACACATGATAGATTGTAACCCTT 59.410 40.000 0.00 0.00 0.00 3.95
695 833 9.975218 AGATAAATTACCATTTTCAGTGTACCT 57.025 29.630 0.00 0.00 34.29 3.08
736 2449 5.362105 ACCGTACTAATAAATGAGCCCAA 57.638 39.130 0.00 0.00 0.00 4.12
737 2450 5.121105 ACCGTACTAATAAATGAGCCCAAC 58.879 41.667 0.00 0.00 0.00 3.77
738 2451 4.514066 CCGTACTAATAAATGAGCCCAACC 59.486 45.833 0.00 0.00 0.00 3.77
739 2452 4.210537 CGTACTAATAAATGAGCCCAACCG 59.789 45.833 0.00 0.00 0.00 4.44
740 2453 4.230745 ACTAATAAATGAGCCCAACCGT 57.769 40.909 0.00 0.00 0.00 4.83
741 2454 5.362105 ACTAATAAATGAGCCCAACCGTA 57.638 39.130 0.00 0.00 0.00 4.02
742 2455 5.121105 ACTAATAAATGAGCCCAACCGTAC 58.879 41.667 0.00 0.00 0.00 3.67
743 2456 3.926058 ATAAATGAGCCCAACCGTACT 57.074 42.857 0.00 0.00 0.00 2.73
744 2457 5.362105 AATAAATGAGCCCAACCGTACTA 57.638 39.130 0.00 0.00 0.00 1.82
745 2458 3.706600 AAATGAGCCCAACCGTACTAA 57.293 42.857 0.00 0.00 0.00 2.24
746 2459 3.926058 AATGAGCCCAACCGTACTAAT 57.074 42.857 0.00 0.00 0.00 1.73
747 2460 5.362105 AAATGAGCCCAACCGTACTAATA 57.638 39.130 0.00 0.00 0.00 0.98
768 2481 0.616679 ATGAGCCCATTTGCTGCCTT 60.617 50.000 0.00 0.00 42.95 4.35
862 2580 2.804212 CGCATTAAACCCTAGTACCCGG 60.804 54.545 0.00 0.00 0.00 5.73
910 2628 3.101437 TCCCGCTAATACCTTTCTCACA 58.899 45.455 0.00 0.00 0.00 3.58
930 2648 1.963190 CTTAACGAAACTCCGGCGGC 61.963 60.000 23.83 5.62 0.00 6.53
993 2711 3.967335 GATCCCTCGTCGCCTCGG 61.967 72.222 0.00 0.00 0.00 4.63
994 2712 4.816984 ATCCCTCGTCGCCTCGGT 62.817 66.667 0.00 0.00 0.00 4.69
1022 2740 3.133767 TATGCCTTCGCCTCCGTCG 62.134 63.158 0.00 0.00 35.54 5.12
1092 2810 0.666577 GTGCGGACGCTAGTTCAGTT 60.667 55.000 18.04 0.00 42.51 3.16
1093 2811 0.883153 TGCGGACGCTAGTTCAGTTA 59.117 50.000 18.04 0.00 42.51 2.24
1175 2896 6.839124 ATGGAACTTTTGCAGTATCATTCA 57.161 33.333 0.00 0.00 32.94 2.57
1194 2915 0.541392 AGTGCTGGCGTATGATGGAA 59.459 50.000 0.00 0.00 0.00 3.53
1195 2916 0.657840 GTGCTGGCGTATGATGGAAC 59.342 55.000 0.00 0.00 0.00 3.62
1196 2917 0.541392 TGCTGGCGTATGATGGAACT 59.459 50.000 0.00 0.00 0.00 3.01
1197 2918 0.940126 GCTGGCGTATGATGGAACTG 59.060 55.000 0.00 0.00 0.00 3.16
1198 2919 1.586422 CTGGCGTATGATGGAACTGG 58.414 55.000 0.00 0.00 0.00 4.00
1199 2920 0.463654 TGGCGTATGATGGAACTGGC 60.464 55.000 0.00 0.00 0.00 4.85
1200 2921 0.179045 GGCGTATGATGGAACTGGCT 60.179 55.000 0.00 0.00 0.00 4.75
1201 2922 0.940126 GCGTATGATGGAACTGGCTG 59.060 55.000 0.00 0.00 0.00 4.85
1230 2951 2.362397 CTCTGCGATTTAGGTGCCTAGA 59.638 50.000 0.00 0.00 0.00 2.43
1231 2952 2.362397 TCTGCGATTTAGGTGCCTAGAG 59.638 50.000 0.00 0.00 0.00 2.43
1232 2953 2.362397 CTGCGATTTAGGTGCCTAGAGA 59.638 50.000 0.00 0.00 0.00 3.10
1233 2954 2.362397 TGCGATTTAGGTGCCTAGAGAG 59.638 50.000 0.00 0.00 0.00 3.20
1240 2961 3.570912 AGGTGCCTAGAGAGTAGAGAC 57.429 52.381 0.00 0.00 0.00 3.36
1289 3010 6.528014 TTTTTAACAGCTGAACGTATTCGA 57.472 33.333 23.35 0.00 37.69 3.71
1290 3011 5.756950 TTTAACAGCTGAACGTATTCGAG 57.243 39.130 23.35 0.00 37.69 4.04
1291 3012 3.570926 AACAGCTGAACGTATTCGAGA 57.429 42.857 23.35 0.00 37.69 4.04
1292 3013 3.570926 ACAGCTGAACGTATTCGAGAA 57.429 42.857 23.35 0.00 37.69 2.87
1293 3014 3.909430 ACAGCTGAACGTATTCGAGAAA 58.091 40.909 23.35 0.00 37.69 2.52
1294 3015 4.304110 ACAGCTGAACGTATTCGAGAAAA 58.696 39.130 23.35 0.00 37.69 2.29
1295 3016 4.748102 ACAGCTGAACGTATTCGAGAAAAA 59.252 37.500 23.35 0.00 37.69 1.94
1296 3017 5.107453 ACAGCTGAACGTATTCGAGAAAAAG 60.107 40.000 23.35 0.00 37.69 2.27
1328 3049 7.155328 TGAACTGGTAGAGAGATTTCAAGTTC 58.845 38.462 0.00 0.00 33.58 3.01
1330 3051 5.477291 ACTGGTAGAGAGATTTCAAGTTCGA 59.523 40.000 0.00 0.00 0.00 3.71
1331 3052 6.153680 ACTGGTAGAGAGATTTCAAGTTCGAT 59.846 38.462 0.00 0.00 0.00 3.59
1332 3053 6.565234 TGGTAGAGAGATTTCAAGTTCGATC 58.435 40.000 0.00 0.00 0.00 3.69
1337 3058 6.098124 AGAGAGATTTCAAGTTCGATCTGGAT 59.902 38.462 1.38 0.00 0.00 3.41
1341 3062 6.538021 AGATTTCAAGTTCGATCTGGATGAAG 59.462 38.462 1.38 0.00 0.00 3.02
1346 3067 3.264450 AGTTCGATCTGGATGAAGGGTTT 59.736 43.478 0.00 0.00 0.00 3.27
1352 3073 2.711009 TCTGGATGAAGGGTTTCTGTGT 59.289 45.455 0.00 0.00 34.31 3.72
1371 3092 7.676004 TCTGTGTTTTGTAGGTGATGATCTTA 58.324 34.615 0.00 0.00 0.00 2.10
1376 3097 4.672587 TGTAGGTGATGATCTTAGTGGC 57.327 45.455 0.00 0.00 0.00 5.01
1387 3108 1.871039 TCTTAGTGGCGAACTGTTTGC 59.129 47.619 21.81 21.81 40.26 3.68
1395 3118 1.859998 GCGAACTGTTTGCCTGTGTTC 60.860 52.381 19.80 0.00 33.83 3.18
1422 3145 1.391157 TTTGGGGCGCTCATATTGGC 61.391 55.000 10.74 0.00 0.00 4.52
1466 3190 1.962807 CACAAACATTCCCAAGAGCCA 59.037 47.619 0.00 0.00 0.00 4.75
1480 3204 5.305585 CCAAGAGCCACAGTCTTTTACTAA 58.694 41.667 0.00 0.00 35.76 2.24
1481 3205 5.940470 CCAAGAGCCACAGTCTTTTACTAAT 59.060 40.000 0.00 0.00 35.76 1.73
1482 3206 6.431234 CCAAGAGCCACAGTCTTTTACTAATT 59.569 38.462 0.00 0.00 35.76 1.40
1483 3207 7.361286 CCAAGAGCCACAGTCTTTTACTAATTC 60.361 40.741 0.00 0.00 35.76 2.17
1521 3245 5.109903 GCCGTTCACACTTAGATGATTACT 58.890 41.667 0.00 0.00 0.00 2.24
1581 3313 6.377327 TCCTTTTGTTTACTTGCTGAGAAG 57.623 37.500 0.00 0.00 0.00 2.85
1582 3314 6.119536 TCCTTTTGTTTACTTGCTGAGAAGA 58.880 36.000 0.00 0.00 0.00 2.87
1583 3315 6.601613 TCCTTTTGTTTACTTGCTGAGAAGAA 59.398 34.615 0.00 0.00 0.00 2.52
1595 3327 3.944015 GCTGAGAAGAATACTGCATTGGT 59.056 43.478 0.00 0.00 0.00 3.67
1604 3336 8.579850 AAGAATACTGCATTGGTAGATTTTGA 57.420 30.769 0.00 0.00 0.00 2.69
1626 4594 5.583854 TGAAAGAATTCTCAGTATGCTGCTC 59.416 40.000 8.78 0.00 36.80 4.26
1641 4609 8.811017 AGTATGCTGCTCTGATTAGTTACATAT 58.189 33.333 0.00 0.00 0.00 1.78
1649 4617 7.655328 GCTCTGATTAGTTACATATTGTCTGCT 59.345 37.037 0.00 0.00 0.00 4.24
1674 4642 6.653320 TCATACGCATTTCCACTCTAGTTTTT 59.347 34.615 0.00 0.00 0.00 1.94
1685 4653 6.998074 TCCACTCTAGTTTTTGTTGTCATCAT 59.002 34.615 0.00 0.00 0.00 2.45
1686 4654 7.041167 TCCACTCTAGTTTTTGTTGTCATCATG 60.041 37.037 0.00 0.00 0.00 3.07
1688 4656 6.488006 ACTCTAGTTTTTGTTGTCATCATGCT 59.512 34.615 0.00 0.00 0.00 3.79
1689 4657 7.661437 ACTCTAGTTTTTGTTGTCATCATGCTA 59.339 33.333 0.00 0.00 0.00 3.49
1691 4659 6.389830 AGTTTTTGTTGTCATCATGCTACA 57.610 33.333 0.00 0.00 0.00 2.74
1734 4702 7.504924 TGAAATTAGTTACACTCAACTTGGG 57.495 36.000 0.00 0.00 39.45 4.12
1780 4748 8.601845 ACAATTTTGCAGTTAATACCTTTTCC 57.398 30.769 0.00 0.00 0.00 3.13
1786 4754 9.921637 TTTGCAGTTAATACCTTTTCCATTTAG 57.078 29.630 0.00 0.00 0.00 1.85
1821 4789 3.658757 GCATTTGGCAGGTTGTAGAAA 57.341 42.857 0.00 0.00 43.97 2.52
1828 4796 4.469657 TGGCAGGTTGTAGAAACAATTCT 58.530 39.130 0.00 0.00 46.84 2.40
1838 4806 9.974750 GTTGTAGAAACAATTCTTAGTATGCTC 57.025 33.333 0.00 0.00 46.84 4.26
1854 4822 6.817184 AGTATGCTCCGTTGATTAGTTACAT 58.183 36.000 0.00 0.00 0.00 2.29
1855 4823 7.272978 AGTATGCTCCGTTGATTAGTTACATT 58.727 34.615 0.00 0.00 0.00 2.71
1856 4824 8.418662 AGTATGCTCCGTTGATTAGTTACATTA 58.581 33.333 0.00 0.00 0.00 1.90
1857 4825 6.897259 TGCTCCGTTGATTAGTTACATTAC 57.103 37.500 0.00 0.00 0.00 1.89
1858 4826 6.399743 TGCTCCGTTGATTAGTTACATTACA 58.600 36.000 0.00 0.00 0.00 2.41
1859 4827 7.045416 TGCTCCGTTGATTAGTTACATTACAT 58.955 34.615 0.00 0.00 0.00 2.29
1877 4845 9.897744 ACATTACATGTTCAACTTTCTGTTATG 57.102 29.630 2.30 8.92 41.63 1.90
1898 4866 5.432885 TGCAGTTTCCACTTAGTTTTAGC 57.567 39.130 0.00 0.00 0.00 3.09
1907 4875 6.296026 TCCACTTAGTTTTAGCTGTCATTGT 58.704 36.000 0.00 0.00 0.00 2.71
1911 4879 4.916983 AGTTTTAGCTGTCATTGTGCAA 57.083 36.364 0.00 0.00 0.00 4.08
1912 4880 4.610945 AGTTTTAGCTGTCATTGTGCAAC 58.389 39.130 0.00 0.00 37.35 4.17
1934 4903 1.795162 GCATGACAGGTTATTGCACGC 60.795 52.381 0.00 0.00 0.00 5.34
1952 4921 4.617298 GCACGCAATTTGTTATACCCAACT 60.617 41.667 0.00 0.00 0.00 3.16
1954 4923 5.344665 CACGCAATTTGTTATACCCAACTTG 59.655 40.000 0.00 8.76 36.26 3.16
1969 4938 3.569701 CCAACTTGGAATGTTGCTACTGT 59.430 43.478 0.92 0.00 46.91 3.55
1970 4939 4.539870 CAACTTGGAATGTTGCTACTGTG 58.460 43.478 0.00 0.00 43.55 3.66
1971 4940 4.085357 ACTTGGAATGTTGCTACTGTGA 57.915 40.909 0.00 0.00 0.00 3.58
1972 4941 3.815401 ACTTGGAATGTTGCTACTGTGAC 59.185 43.478 0.00 0.00 0.00 3.67
1973 4942 3.483808 TGGAATGTTGCTACTGTGACA 57.516 42.857 0.00 0.00 0.00 3.58
1974 4943 3.402110 TGGAATGTTGCTACTGTGACAG 58.598 45.455 11.70 11.70 37.52 3.51
1987 4956 8.289618 TGCTACTGTGACAGTGAAATTTAATTC 58.710 33.333 27.18 1.79 45.01 2.17
2205 5174 8.704849 TGCCTATTACATGCTTTATTATGGTT 57.295 30.769 0.00 0.00 0.00 3.67
2275 5244 0.249489 AGCACGTCACTGACTTGTCC 60.249 55.000 15.09 2.43 34.86 4.02
2299 5268 3.067040 GGAGAGAGACCCTTGTTCGTATC 59.933 52.174 0.00 0.00 0.00 2.24
2312 5281 3.181479 TGTTCGTATCACTGGTATGCTCC 60.181 47.826 0.00 0.00 0.00 4.70
2313 5282 2.661718 TCGTATCACTGGTATGCTCCA 58.338 47.619 0.00 0.00 36.00 3.86
2380 5349 9.549078 GGTTTAAAAGTAAATTTGATTGTCCCA 57.451 29.630 0.00 0.00 31.94 4.37
2421 5390 0.247736 AGGTCAAGGCTGATCGTGAC 59.752 55.000 7.58 7.58 42.55 3.67
2469 5438 1.941209 GCTTCTCAAGATGTGGCGACA 60.941 52.381 3.31 3.31 36.22 4.35
2513 5482 6.808704 GGCTTTCATTGGACTATTTTCTGTTC 59.191 38.462 0.00 0.00 0.00 3.18
2514 5483 7.370383 GCTTTCATTGGACTATTTTCTGTTCA 58.630 34.615 0.00 0.00 0.00 3.18
2523 5492 5.246307 ACTATTTTCTGTTCAGGTGCCTAC 58.754 41.667 0.00 0.00 0.00 3.18
2524 5493 3.569194 TTTTCTGTTCAGGTGCCTACA 57.431 42.857 0.00 0.00 0.00 2.74
2525 5494 3.788227 TTTCTGTTCAGGTGCCTACAT 57.212 42.857 0.00 0.00 0.00 2.29
2526 5495 3.334583 TTCTGTTCAGGTGCCTACATC 57.665 47.619 0.00 0.00 0.00 3.06
2536 5505 2.173569 GGTGCCTACATCCAGGATTCTT 59.826 50.000 0.00 0.00 38.00 2.52
2541 5510 6.820656 GTGCCTACATCCAGGATTCTTATATG 59.179 42.308 0.00 0.00 38.00 1.78
2547 5516 8.697507 ACATCCAGGATTCTTATATGTTTTCC 57.302 34.615 0.00 0.00 0.00 3.13
2548 5517 8.281531 ACATCCAGGATTCTTATATGTTTTCCA 58.718 33.333 0.00 0.00 0.00 3.53
2551 5520 7.993183 TCCAGGATTCTTATATGTTTTCCACTC 59.007 37.037 0.00 0.00 0.00 3.51
2564 5533 2.507992 CACTCGCGCTTCCAGGAG 60.508 66.667 5.56 5.97 0.00 3.69
2567 5536 4.135153 TCGCGCTTCCAGGAGCTC 62.135 66.667 4.71 4.71 40.52 4.09
2702 5671 3.680490 TGGACGCATTGGTAAATTCTGA 58.320 40.909 0.00 0.00 0.00 3.27
2704 5673 3.689649 GGACGCATTGGTAAATTCTGACT 59.310 43.478 0.00 0.00 0.00 3.41
2706 5675 5.296813 ACGCATTGGTAAATTCTGACTTC 57.703 39.130 0.00 0.00 0.00 3.01
2711 5680 2.014857 GGTAAATTCTGACTTCCCGCC 58.985 52.381 0.00 0.00 0.00 6.13
2766 5766 4.045636 ACTTTGCTGTTTCATTGTGGTC 57.954 40.909 0.00 0.00 0.00 4.02
2769 5769 1.872952 TGCTGTTTCATTGTGGTCTCG 59.127 47.619 0.00 0.00 0.00 4.04
2770 5770 1.873591 GCTGTTTCATTGTGGTCTCGT 59.126 47.619 0.00 0.00 0.00 4.18
2793 5793 7.233962 TCGTCCTTATTGGGCATAGAACTAATA 59.766 37.037 0.00 0.00 41.50 0.98
2832 5832 4.083862 GCAGAGGACGTGACCCCC 62.084 72.222 0.00 0.00 0.00 5.40
2850 5850 1.961277 CGTTCCCACTGACAGCACC 60.961 63.158 1.25 0.00 0.00 5.01
2915 5915 3.935203 TCTTTTTCATCGTCTCTCATGGC 59.065 43.478 0.00 0.00 0.00 4.40
2919 5919 0.873312 CATCGTCTCTCATGGCCGTG 60.873 60.000 19.62 19.62 0.00 4.94
2923 5923 0.596083 GTCTCTCATGGCCGTGATCG 60.596 60.000 27.70 20.11 0.00 3.69
2930 5930 1.528586 CATGGCCGTGATCGAGAATTC 59.471 52.381 21.08 0.00 39.71 2.17
2932 5932 1.215655 GGCCGTGATCGAGAATTCGG 61.216 60.000 0.00 11.13 46.67 4.30
2933 5933 0.527817 GCCGTGATCGAGAATTCGGT 60.528 55.000 14.92 0.00 46.67 4.69
2937 5937 2.279136 CGTGATCGAGAATTCGGTGTTC 59.721 50.000 0.00 0.20 46.67 3.18
2968 5971 6.565234 CCTTATAGATCCTATGTAGTTGCCG 58.435 44.000 0.00 0.00 0.00 5.69
2969 5972 6.377429 CCTTATAGATCCTATGTAGTTGCCGA 59.623 42.308 0.00 0.00 0.00 5.54
2982 5985 2.301870 AGTTGCCGATCAGTTTACTCCA 59.698 45.455 0.00 0.00 0.00 3.86
2988 5991 3.612860 CCGATCAGTTTACTCCAAGTTCG 59.387 47.826 0.00 0.00 0.00 3.95
2991 5994 4.884668 TCAGTTTACTCCAAGTTCGGAT 57.115 40.909 0.00 0.00 33.56 4.18
2993 5996 5.617252 TCAGTTTACTCCAAGTTCGGATTT 58.383 37.500 0.00 0.00 33.56 2.17
2994 5997 5.468746 TCAGTTTACTCCAAGTTCGGATTTG 59.531 40.000 0.00 0.00 33.56 2.32
2997 6000 6.320418 AGTTTACTCCAAGTTCGGATTTGTTT 59.680 34.615 0.00 0.00 33.56 2.83
3004 6007 5.008217 CCAAGTTCGGATTTGTTTACTGTCA 59.992 40.000 0.00 0.00 0.00 3.58
3005 6008 5.924475 AGTTCGGATTTGTTTACTGTCAG 57.076 39.130 0.00 0.00 0.00 3.51
3031 6037 0.948141 AGCTGTGCTTCGCTTCAGAC 60.948 55.000 12.74 6.77 33.89 3.51
3055 6061 5.928264 CCATCTCTGATCGTGTATTTATGCA 59.072 40.000 0.00 0.00 0.00 3.96
3059 6065 8.262715 TCTCTGATCGTGTATTTATGCAAAAA 57.737 30.769 0.00 0.00 0.00 1.94
3100 6107 9.592196 ACATGCCTTATTATGGTTTCTGATAAT 57.408 29.630 0.00 0.00 0.00 1.28
3110 6117 5.765510 TGGTTTCTGATAATATGGTTGGCT 58.234 37.500 0.00 0.00 0.00 4.75
3111 6118 5.827797 TGGTTTCTGATAATATGGTTGGCTC 59.172 40.000 0.00 0.00 0.00 4.70
3112 6119 6.064717 GGTTTCTGATAATATGGTTGGCTCT 58.935 40.000 0.00 0.00 0.00 4.09
3114 6121 7.719633 GGTTTCTGATAATATGGTTGGCTCTTA 59.280 37.037 0.00 0.00 0.00 2.10
3115 6122 9.289782 GTTTCTGATAATATGGTTGGCTCTTAT 57.710 33.333 0.00 0.00 0.00 1.73
3116 6123 9.866655 TTTCTGATAATATGGTTGGCTCTTATT 57.133 29.630 0.00 0.00 0.00 1.40
3119 6126 9.950496 CTGATAATATGGTTGGCTCTTATTAGT 57.050 33.333 0.00 0.00 0.00 2.24
3159 6277 0.459585 GTGCTGGAATGCCAATGCTG 60.460 55.000 5.59 0.00 45.41 4.41
3160 6278 0.612453 TGCTGGAATGCCAATGCTGA 60.612 50.000 5.59 0.00 45.41 4.26
3204 6322 6.982141 ACCATCATATTGCATTTGTCATTGAC 59.018 34.615 9.93 9.93 0.00 3.18
3235 6353 5.477510 GAAAAGAATCTGAGCAGAGAGACA 58.522 41.667 6.34 0.00 41.33 3.41
3264 6382 5.012893 CCCTCTGAAAAGGAGCAAATAGTT 58.987 41.667 0.00 0.00 38.87 2.24
3297 6415 5.248640 TGAAAAGGAGCAGTGAAAGATAGG 58.751 41.667 0.00 0.00 0.00 2.57
3346 6464 0.248458 GGCGTATCCAAACAATGCCG 60.248 55.000 0.00 0.00 35.70 5.69
3513 6640 2.425773 GTCGTTGCTGTTGCTGCG 60.426 61.111 0.00 0.00 40.48 5.18
3516 6643 3.595758 GTTGCTGTTGCTGCGGGT 61.596 61.111 0.00 0.00 40.48 5.28
3678 6805 0.782384 CGGTGAACTGCTTGTCGTAC 59.218 55.000 0.00 0.00 0.00 3.67
3693 6820 0.374063 CGTACGTGTTGGTGTTGCAA 59.626 50.000 7.22 0.00 0.00 4.08
3828 6957 1.666553 ACGTCGCCGAGATGCAAAA 60.667 52.632 0.00 0.00 39.47 2.44
3829 6958 1.019278 ACGTCGCCGAGATGCAAAAT 61.019 50.000 0.00 0.00 39.47 1.82
3830 6959 0.587242 CGTCGCCGAGATGCAAAATG 60.587 55.000 0.00 0.00 35.63 2.32
3836 6965 2.094545 GCCGAGATGCAAAATGAAAGGT 60.095 45.455 0.00 0.00 0.00 3.50
3837 6966 3.504863 CCGAGATGCAAAATGAAAGGTG 58.495 45.455 0.00 0.00 0.00 4.00
3839 6968 3.057315 CGAGATGCAAAATGAAAGGTGGT 60.057 43.478 0.00 0.00 0.00 4.16
3840 6969 4.488879 GAGATGCAAAATGAAAGGTGGTC 58.511 43.478 0.00 0.00 0.00 4.02
3842 6971 2.028130 TGCAAAATGAAAGGTGGTCGT 58.972 42.857 0.00 0.00 0.00 4.34
3844 6973 2.393764 CAAAATGAAAGGTGGTCGTGC 58.606 47.619 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.599071 TCTTCAACTGAACTTGCGCAG 59.401 47.619 11.31 7.81 38.10 5.18
75 76 7.095523 GGAAACATTGTGTCTTCAAAATGATGG 60.096 37.037 15.24 0.00 46.57 3.51
201 204 9.226606 TGTATTCATAAGGTTTGGTTAGTTCAG 57.773 33.333 0.00 0.00 0.00 3.02
270 273 6.823689 GTCAGATGGTTGGTCAGTGTATTATT 59.176 38.462 0.00 0.00 0.00 1.40
275 278 3.239449 AGTCAGATGGTTGGTCAGTGTA 58.761 45.455 0.00 0.00 0.00 2.90
303 306 9.650539 TGTCAATTTTCAAAGAACTTTCATGAA 57.349 25.926 3.38 3.38 35.16 2.57
311 314 9.617523 ATTCCAAATGTCAATTTTCAAAGAACT 57.382 25.926 0.00 0.00 33.59 3.01
350 353 7.435068 TGGTAGATGTTGCTTCTCTTTAAAC 57.565 36.000 0.00 0.00 0.00 2.01
411 421 6.240894 CAGGGCACAATATACATGGTCTTAT 58.759 40.000 0.00 0.00 0.00 1.73
457 467 2.743636 ACTTGCTGTAGTATGCACGT 57.256 45.000 0.00 5.01 39.05 4.49
458 468 4.084066 TGAAAACTTGCTGTAGTATGCACG 60.084 41.667 0.00 2.69 39.05 5.34
459 469 5.147162 GTGAAAACTTGCTGTAGTATGCAC 58.853 41.667 0.00 0.00 39.05 4.57
461 471 5.356882 TGTGAAAACTTGCTGTAGTATGC 57.643 39.130 0.00 0.00 0.00 3.14
462 472 7.132694 TCATGTGAAAACTTGCTGTAGTATG 57.867 36.000 0.00 0.00 0.00 2.39
463 473 7.228507 TGTTCATGTGAAAACTTGCTGTAGTAT 59.771 33.333 0.00 0.00 35.58 2.12
464 474 6.540551 TGTTCATGTGAAAACTTGCTGTAGTA 59.459 34.615 0.00 0.00 35.58 1.82
465 475 5.356751 TGTTCATGTGAAAACTTGCTGTAGT 59.643 36.000 0.00 0.00 35.58 2.73
466 476 5.820131 TGTTCATGTGAAAACTTGCTGTAG 58.180 37.500 0.00 0.00 35.58 2.74
467 477 5.826601 TGTTCATGTGAAAACTTGCTGTA 57.173 34.783 0.00 0.00 35.58 2.74
471 608 8.672214 AAAAATTTGTTCATGTGAAAACTTGC 57.328 26.923 0.00 0.00 35.58 4.01
528 665 4.402829 TGAGGCTTGCATTAAGTTTACCA 58.597 39.130 0.00 0.00 38.70 3.25
577 714 3.577649 TCGAGTTGTGAAGGAGATGTC 57.422 47.619 0.00 0.00 0.00 3.06
584 721 1.195448 GTGTGCATCGAGTTGTGAAGG 59.805 52.381 0.00 0.00 0.00 3.46
592 729 4.597404 ATCTATCATGTGTGCATCGAGT 57.403 40.909 0.00 0.00 31.99 4.18
623 760 3.562108 TGGCCTATTTTTAACCCCCAA 57.438 42.857 3.32 0.00 0.00 4.12
678 816 5.630121 TCATGAAGGTACACTGAAAATGGT 58.370 37.500 0.00 0.00 0.00 3.55
694 832 0.325933 TGGGCTCACACCTCATGAAG 59.674 55.000 0.00 0.00 0.00 3.02
695 833 0.770499 TTGGGCTCACACCTCATGAA 59.230 50.000 0.00 0.00 0.00 2.57
696 834 0.036732 GTTGGGCTCACACCTCATGA 59.963 55.000 0.00 0.00 0.00 3.07
736 2449 5.562298 ATGGGCTCATTTATTAGTACGGT 57.438 39.130 0.00 0.00 0.00 4.83
910 2628 0.668401 CCGCCGGAGTTTCGTTAAGT 60.668 55.000 5.05 0.00 0.00 2.24
993 2711 1.680338 GAAGGCATACCATGGTGGAC 58.320 55.000 28.17 20.79 40.96 4.02
994 2712 0.180171 CGAAGGCATACCATGGTGGA 59.820 55.000 28.17 8.99 40.96 4.02
1092 2810 0.764890 CATCTTGCCGGATTCCCCTA 59.235 55.000 5.05 0.00 0.00 3.53
1093 2811 1.281925 ACATCTTGCCGGATTCCCCT 61.282 55.000 5.05 0.00 0.00 4.79
1150 2871 8.347004 TGAATGATACTGCAAAAGTTCCATAA 57.653 30.769 0.00 0.00 40.56 1.90
1175 2896 0.541392 TTCCATCATACGCCAGCACT 59.459 50.000 0.00 0.00 0.00 4.40
1194 2915 1.611851 AGAGCTACAGCCAGCCAGT 60.612 57.895 0.00 0.00 42.84 4.00
1195 2916 1.153409 CAGAGCTACAGCCAGCCAG 60.153 63.158 0.00 0.00 42.84 4.85
1196 2917 2.984623 CAGAGCTACAGCCAGCCA 59.015 61.111 0.00 0.00 42.84 4.75
1197 2918 2.513435 GCAGAGCTACAGCCAGCC 60.513 66.667 0.00 0.00 42.84 4.85
1198 2919 2.641439 ATCGCAGAGCTACAGCCAGC 62.641 60.000 0.00 0.00 43.63 4.85
1199 2920 0.179089 AATCGCAGAGCTACAGCCAG 60.179 55.000 0.00 0.00 43.63 4.85
1200 2921 0.250234 AAATCGCAGAGCTACAGCCA 59.750 50.000 0.00 0.00 43.63 4.75
1201 2922 2.131183 CTAAATCGCAGAGCTACAGCC 58.869 52.381 0.00 0.00 43.63 4.85
1230 2951 5.011586 GGTTACAGTTCCAGTCTCTACTCT 58.988 45.833 0.00 0.00 31.97 3.24
1231 2952 5.011586 AGGTTACAGTTCCAGTCTCTACTC 58.988 45.833 0.00 0.00 31.97 2.59
1232 2953 4.767928 CAGGTTACAGTTCCAGTCTCTACT 59.232 45.833 0.00 0.00 35.91 2.57
1233 2954 4.082136 CCAGGTTACAGTTCCAGTCTCTAC 60.082 50.000 0.00 0.00 0.00 2.59
1240 2961 1.072331 AGCACCAGGTTACAGTTCCAG 59.928 52.381 0.00 0.00 0.00 3.86
1270 2991 4.690184 TCTCGAATACGTTCAGCTGTTA 57.310 40.909 14.67 0.00 40.69 2.41
1271 2992 3.570926 TCTCGAATACGTTCAGCTGTT 57.429 42.857 14.67 0.00 40.69 3.16
1272 2993 3.570926 TTCTCGAATACGTTCAGCTGT 57.429 42.857 14.67 0.00 40.69 4.40
1273 2994 4.903638 TTTTCTCGAATACGTTCAGCTG 57.096 40.909 7.63 7.63 40.69 4.24
1274 2995 5.227908 TCTTTTTCTCGAATACGTTCAGCT 58.772 37.500 0.00 0.00 40.69 4.24
1275 2996 5.511088 TCTTTTTCTCGAATACGTTCAGC 57.489 39.130 0.00 0.00 40.69 4.26
1276 2997 6.873656 TGTTCTTTTTCTCGAATACGTTCAG 58.126 36.000 0.00 0.00 40.69 3.02
1277 2998 6.563381 GCTGTTCTTTTTCTCGAATACGTTCA 60.563 38.462 0.00 0.00 40.69 3.18
1278 2999 5.784139 GCTGTTCTTTTTCTCGAATACGTTC 59.216 40.000 0.00 0.00 40.69 3.95
1279 3000 5.465724 AGCTGTTCTTTTTCTCGAATACGTT 59.534 36.000 0.00 0.00 40.69 3.99
1280 3001 4.989168 AGCTGTTCTTTTTCTCGAATACGT 59.011 37.500 0.00 0.00 40.69 3.57
1281 3002 5.118664 TCAGCTGTTCTTTTTCTCGAATACG 59.881 40.000 14.67 0.00 41.26 3.06
1282 3003 6.467723 TCAGCTGTTCTTTTTCTCGAATAC 57.532 37.500 14.67 0.00 0.00 1.89
1283 3004 6.706270 AGTTCAGCTGTTCTTTTTCTCGAATA 59.294 34.615 14.67 0.00 0.00 1.75
1284 3005 5.529060 AGTTCAGCTGTTCTTTTTCTCGAAT 59.471 36.000 14.67 0.00 0.00 3.34
1285 3006 4.876107 AGTTCAGCTGTTCTTTTTCTCGAA 59.124 37.500 14.67 0.00 0.00 3.71
1286 3007 4.271049 CAGTTCAGCTGTTCTTTTTCTCGA 59.729 41.667 14.67 0.00 40.27 4.04
1287 3008 4.521943 CAGTTCAGCTGTTCTTTTTCTCG 58.478 43.478 14.67 0.00 40.27 4.04
1288 3009 4.336713 ACCAGTTCAGCTGTTCTTTTTCTC 59.663 41.667 14.67 0.00 43.55 2.87
1289 3010 4.273318 ACCAGTTCAGCTGTTCTTTTTCT 58.727 39.130 14.67 0.00 43.55 2.52
1290 3011 4.639135 ACCAGTTCAGCTGTTCTTTTTC 57.361 40.909 14.67 0.00 43.55 2.29
1291 3012 5.437060 TCTACCAGTTCAGCTGTTCTTTTT 58.563 37.500 14.67 3.04 43.55 1.94
1292 3013 5.036117 TCTACCAGTTCAGCTGTTCTTTT 57.964 39.130 14.67 5.22 43.55 2.27
1293 3014 4.345257 TCTCTACCAGTTCAGCTGTTCTTT 59.655 41.667 14.67 5.54 43.55 2.52
1294 3015 3.898123 TCTCTACCAGTTCAGCTGTTCTT 59.102 43.478 14.67 2.51 43.55 2.52
1295 3016 3.501349 TCTCTACCAGTTCAGCTGTTCT 58.499 45.455 14.67 10.37 43.55 3.01
1296 3017 3.508012 TCTCTCTACCAGTTCAGCTGTTC 59.492 47.826 14.67 8.14 43.55 3.18
1317 3038 6.238320 CCTTCATCCAGATCGAACTTGAAATC 60.238 42.308 8.91 0.00 0.00 2.17
1328 3049 3.201290 CAGAAACCCTTCATCCAGATCG 58.799 50.000 0.00 0.00 33.64 3.69
1330 3051 3.331889 ACACAGAAACCCTTCATCCAGAT 59.668 43.478 0.00 0.00 33.64 2.90
1331 3052 2.711009 ACACAGAAACCCTTCATCCAGA 59.289 45.455 0.00 0.00 33.64 3.86
1332 3053 3.146104 ACACAGAAACCCTTCATCCAG 57.854 47.619 0.00 0.00 33.64 3.86
1337 3058 4.642885 CCTACAAAACACAGAAACCCTTCA 59.357 41.667 0.00 0.00 33.64 3.02
1341 3062 3.949113 TCACCTACAAAACACAGAAACCC 59.051 43.478 0.00 0.00 0.00 4.11
1346 3067 6.114187 AGATCATCACCTACAAAACACAGA 57.886 37.500 0.00 0.00 0.00 3.41
1352 3073 5.880332 GCCACTAAGATCATCACCTACAAAA 59.120 40.000 0.00 0.00 0.00 2.44
1371 3092 3.432186 GGCAAACAGTTCGCCACT 58.568 55.556 10.64 0.00 45.52 4.00
1376 3097 1.268539 GGAACACAGGCAAACAGTTCG 60.269 52.381 0.00 0.00 39.45 3.95
1410 3133 0.466189 AACCCCTGCCAATATGAGCG 60.466 55.000 0.00 0.00 0.00 5.03
1422 3145 3.824443 ACGAAAACCAGATTTAACCCCTG 59.176 43.478 0.00 0.00 0.00 4.45
1480 3204 6.150307 TGAACGGCAAGTGTGTATAAATGAAT 59.850 34.615 0.00 0.00 0.00 2.57
1481 3205 5.470437 TGAACGGCAAGTGTGTATAAATGAA 59.530 36.000 0.00 0.00 0.00 2.57
1482 3206 4.998033 TGAACGGCAAGTGTGTATAAATGA 59.002 37.500 0.00 0.00 0.00 2.57
1483 3207 5.086058 GTGAACGGCAAGTGTGTATAAATG 58.914 41.667 0.00 0.00 0.00 2.32
1581 3313 9.294030 CTTTCAAAATCTACCAATGCAGTATTC 57.706 33.333 0.00 0.00 0.00 1.75
1582 3314 9.023962 TCTTTCAAAATCTACCAATGCAGTATT 57.976 29.630 0.00 0.00 0.00 1.89
1583 3315 8.579850 TCTTTCAAAATCTACCAATGCAGTAT 57.420 30.769 0.00 0.00 0.00 2.12
1626 4594 8.877808 TGAGCAGACAATATGTAACTAATCAG 57.122 34.615 0.00 0.00 0.00 2.90
1649 4617 5.339008 AACTAGAGTGGAAATGCGTATGA 57.661 39.130 0.00 0.00 0.00 2.15
1685 4653 4.736168 GCCAAAACTTGTCATGTTGTAGCA 60.736 41.667 4.97 0.00 0.00 3.49
1686 4654 3.735746 GCCAAAACTTGTCATGTTGTAGC 59.264 43.478 4.97 1.31 0.00 3.58
1688 4656 4.991153 TGCCAAAACTTGTCATGTTGTA 57.009 36.364 4.97 0.00 0.00 2.41
1689 4657 3.883830 TGCCAAAACTTGTCATGTTGT 57.116 38.095 4.97 0.00 0.00 3.32
1691 4659 4.669206 TCATGCCAAAACTTGTCATGTT 57.331 36.364 9.47 0.00 36.73 2.71
1780 4748 6.245115 TGCAGAACTCACATCAACTAAATG 57.755 37.500 0.00 0.00 0.00 2.32
1786 4754 4.232221 CCAAATGCAGAACTCACATCAAC 58.768 43.478 0.00 0.00 0.00 3.18
1819 4787 6.653320 TCAACGGAGCATACTAAGAATTGTTT 59.347 34.615 0.00 0.00 0.00 2.83
1820 4788 6.170506 TCAACGGAGCATACTAAGAATTGTT 58.829 36.000 0.00 0.00 0.00 2.83
1821 4789 5.730550 TCAACGGAGCATACTAAGAATTGT 58.269 37.500 0.00 0.00 0.00 2.71
1828 4796 7.774134 TGTAACTAATCAACGGAGCATACTAA 58.226 34.615 0.00 0.00 0.00 2.24
1854 4822 7.935520 TGCATAACAGAAAGTTGAACATGTAA 58.064 30.769 0.00 0.00 41.50 2.41
1855 4823 7.503521 TGCATAACAGAAAGTTGAACATGTA 57.496 32.000 0.00 0.00 41.50 2.29
1856 4824 6.389830 TGCATAACAGAAAGTTGAACATGT 57.610 33.333 0.00 0.00 41.50 3.21
1877 4845 5.008712 ACAGCTAAAACTAAGTGGAAACTGC 59.991 40.000 0.00 0.00 0.00 4.40
1911 4879 2.489329 GTGCAATAACCTGTCATGCAGT 59.511 45.455 13.67 2.40 46.54 4.40
1912 4880 2.476686 CGTGCAATAACCTGTCATGCAG 60.477 50.000 9.40 9.40 46.54 4.41
1952 4921 3.814625 TGTCACAGTAGCAACATTCCAA 58.185 40.909 0.00 0.00 0.00 3.53
1954 4923 3.187227 CACTGTCACAGTAGCAACATTCC 59.813 47.826 10.98 0.00 43.43 3.01
1969 4938 9.814899 ACAACATTGAATTAAATTTCACTGTCA 57.185 25.926 12.50 0.00 44.11 3.58
1987 4956 9.142515 ACTTGACATAATTGCATAACAACATTG 57.857 29.630 0.00 0.00 42.27 2.82
1997 4966 8.962884 TGAGTACATACTTGACATAATTGCAT 57.037 30.769 0.00 0.00 36.50 3.96
2205 5174 0.179059 AACAGCACATGACGGTGACA 60.179 50.000 20.50 0.00 41.32 3.58
2299 5268 7.807977 AATTTAAGTATGGAGCATACCAGTG 57.192 36.000 0.00 0.00 45.37 3.66
2380 5349 5.303589 CCTTCATTCCACCTGCATTGATTAT 59.696 40.000 0.00 0.00 0.00 1.28
2421 5390 1.797046 GCTGCATATGGTGATGACTCG 59.203 52.381 4.56 0.00 0.00 4.18
2448 5417 0.321346 TCGCCACATCTTGAGAAGCA 59.679 50.000 0.00 0.00 0.00 3.91
2463 5432 2.331019 AAACCTTGCAACGTGTCGCC 62.331 55.000 0.00 0.00 0.00 5.54
2469 5438 1.611491 CCCATACAAACCTTGCAACGT 59.389 47.619 0.00 0.00 0.00 3.99
2513 5482 1.135094 ATCCTGGATGTAGGCACCTG 58.865 55.000 8.75 0.00 37.76 4.00
2514 5483 1.771255 GAATCCTGGATGTAGGCACCT 59.229 52.381 10.54 0.00 37.76 4.00
2523 5492 8.571336 GTGGAAAACATATAAGAATCCTGGATG 58.429 37.037 10.54 0.00 0.00 3.51
2524 5493 8.506083 AGTGGAAAACATATAAGAATCCTGGAT 58.494 33.333 2.57 2.57 0.00 3.41
2525 5494 7.872138 AGTGGAAAACATATAAGAATCCTGGA 58.128 34.615 0.00 0.00 0.00 3.86
2526 5495 7.041780 CGAGTGGAAAACATATAAGAATCCTGG 60.042 40.741 0.00 0.00 0.00 4.45
2536 5505 3.173668 AGCGCGAGTGGAAAACATATA 57.826 42.857 12.10 0.00 0.00 0.86
2541 5510 1.206831 GGAAGCGCGAGTGGAAAAC 59.793 57.895 12.10 0.00 0.00 2.43
2546 5515 3.997064 CTCCTGGAAGCGCGAGTGG 62.997 68.421 12.10 2.17 0.00 4.00
2547 5516 2.507992 CTCCTGGAAGCGCGAGTG 60.508 66.667 12.10 0.00 0.00 3.51
2548 5517 4.443266 GCTCCTGGAAGCGCGAGT 62.443 66.667 12.10 0.00 31.56 4.18
2564 5533 1.136147 CAAAGCAGTGATGCCGAGC 59.864 57.895 0.00 0.00 34.90 5.03
2567 5536 1.443194 GTGCAAAGCAGTGATGCCG 60.443 57.895 11.82 0.00 40.08 5.69
2702 5671 0.673644 GCATATATGCGGCGGGAAGT 60.674 55.000 21.33 0.00 44.67 3.01
2704 5673 4.294523 GCATATATGCGGCGGGAA 57.705 55.556 21.33 0.00 44.67 3.97
2732 5701 8.075574 TGAAACAGCAAAGTAACAAGATATGTG 58.924 33.333 0.00 0.00 42.99 3.21
2766 5766 4.058817 GTTCTATGCCCAATAAGGACGAG 58.941 47.826 0.00 0.00 41.22 4.18
2769 5769 9.740710 ATTATTAGTTCTATGCCCAATAAGGAC 57.259 33.333 0.00 0.00 41.22 3.85
2793 5793 7.609146 TCTGCAAAGAGAATCAGACATACAATT 59.391 33.333 0.00 0.00 37.82 2.32
2796 5796 6.041423 TCTGCAAAGAGAATCAGACATACA 57.959 37.500 0.00 0.00 37.82 2.29
2805 5805 2.670414 CACGTCCTCTGCAAAGAGAATC 59.330 50.000 4.59 0.00 38.13 2.52
2832 5832 1.961277 GGTGCTGTCAGTGGGAACG 60.961 63.158 0.93 0.00 0.00 3.95
2850 5850 1.078426 CCTACCACCCTTTCTGCGG 60.078 63.158 0.00 0.00 0.00 5.69
2862 5862 0.032017 GCCTCCTTCCTCTCCTACCA 60.032 60.000 0.00 0.00 0.00 3.25
2865 5865 1.011595 ACAGCCTCCTTCCTCTCCTA 58.988 55.000 0.00 0.00 0.00 2.94
2930 5930 5.117355 TCTATAAGGCTATTCGAACACCG 57.883 43.478 0.00 0.00 40.25 4.94
2932 5932 6.926313 AGGATCTATAAGGCTATTCGAACAC 58.074 40.000 0.00 0.00 0.00 3.32
2933 5933 8.687242 CATAGGATCTATAAGGCTATTCGAACA 58.313 37.037 0.00 0.00 0.00 3.18
2937 5937 9.344772 ACTACATAGGATCTATAAGGCTATTCG 57.655 37.037 0.00 0.00 0.00 3.34
2964 5967 2.301870 ACTTGGAGTAAACTGATCGGCA 59.698 45.455 0.00 0.00 0.00 5.69
2968 5971 4.817517 TCCGAACTTGGAGTAAACTGATC 58.182 43.478 0.00 0.00 33.05 2.92
2969 5972 4.884668 TCCGAACTTGGAGTAAACTGAT 57.115 40.909 0.00 0.00 33.05 2.90
2982 5985 5.820947 ACTGACAGTAAACAAATCCGAACTT 59.179 36.000 6.24 0.00 0.00 2.66
2988 5991 7.259290 TCTGAAACTGACAGTAAACAAATCC 57.741 36.000 8.91 0.00 36.81 3.01
2991 5994 5.880332 AGCTCTGAAACTGACAGTAAACAAA 59.120 36.000 8.91 0.00 36.81 2.83
2993 5996 4.811024 CAGCTCTGAAACTGACAGTAAACA 59.189 41.667 8.91 8.54 35.90 2.83
2994 5997 4.811557 ACAGCTCTGAAACTGACAGTAAAC 59.188 41.667 8.91 4.27 37.35 2.01
2997 6000 3.800261 GCACAGCTCTGAAACTGACAGTA 60.800 47.826 8.91 0.00 37.35 2.74
3004 6007 1.506493 CGAAGCACAGCTCTGAAACT 58.494 50.000 3.60 0.00 38.25 2.66
3031 6037 5.928264 TGCATAAATACACGATCAGAGATGG 59.072 40.000 0.00 0.00 0.00 3.51
3059 6065 5.552870 AGGCATGTTCGGACTAGAATATT 57.447 39.130 0.00 0.00 31.08 1.28
3060 6066 5.552870 AAGGCATGTTCGGACTAGAATAT 57.447 39.130 0.00 0.00 33.21 1.28
3061 6067 6.665992 ATAAGGCATGTTCGGACTAGAATA 57.334 37.500 0.00 0.00 32.25 1.75
3062 6068 3.914426 AAGGCATGTTCGGACTAGAAT 57.086 42.857 0.00 0.00 32.25 2.40
3063 6069 5.353394 AATAAGGCATGTTCGGACTAGAA 57.647 39.130 0.00 0.00 0.00 2.10
3064 6070 6.455647 CATAATAAGGCATGTTCGGACTAGA 58.544 40.000 0.00 0.00 0.00 2.43
3065 6071 5.639506 CCATAATAAGGCATGTTCGGACTAG 59.360 44.000 0.00 0.00 0.00 2.57
3073 6079 7.902920 ATCAGAAACCATAATAAGGCATGTT 57.097 32.000 0.00 0.00 0.00 2.71
3123 6130 9.970553 ATTCCAGCACAACATATTATCAGATAT 57.029 29.630 0.00 0.00 0.00 1.63
3138 6256 0.037139 GCATTGGCATTCCAGCACAA 60.037 50.000 0.00 0.00 44.53 3.33
3139 6257 0.901114 AGCATTGGCATTCCAGCACA 60.901 50.000 0.00 0.00 44.53 4.57
3140 6258 0.459585 CAGCATTGGCATTCCAGCAC 60.460 55.000 0.00 0.00 44.53 4.40
3159 6277 4.141846 TGGTTCCTGAATGAGATAGCACTC 60.142 45.833 0.00 0.00 37.42 3.51
3160 6278 3.776969 TGGTTCCTGAATGAGATAGCACT 59.223 43.478 0.00 0.00 0.00 4.40
3204 6322 4.635765 TGCTCAGATTCTTTTCCGTTATGG 59.364 41.667 0.00 0.00 40.09 2.74
3235 6353 2.800250 CTCCTTTTCAGAGGGCAATGT 58.200 47.619 0.00 0.00 37.41 2.71
3264 6382 1.616159 CTCCTTTTCAAAGCCGGGAA 58.384 50.000 2.18 0.00 34.69 3.97
3297 6415 5.238650 TGCTTTCTAGTACTGCTTTCCAAAC 59.761 40.000 5.39 0.00 0.00 2.93
3678 6805 1.938814 CGCTTGCAACACCAACACG 60.939 57.895 0.00 0.00 0.00 4.49
3693 6820 4.430765 CCGGCCGACTACAACGCT 62.431 66.667 30.73 0.00 0.00 5.07
3777 6906 3.065095 TGTGTGTGTGTGTGTGATTCATG 59.935 43.478 0.00 0.00 0.00 3.07
3779 6908 2.418280 GTGTGTGTGTGTGTGTGATTCA 59.582 45.455 0.00 0.00 0.00 2.57
3780 6909 2.418280 TGTGTGTGTGTGTGTGTGATTC 59.582 45.455 0.00 0.00 0.00 2.52
3781 6910 2.431454 TGTGTGTGTGTGTGTGTGATT 58.569 42.857 0.00 0.00 0.00 2.57
3782 6911 2.106477 TGTGTGTGTGTGTGTGTGAT 57.894 45.000 0.00 0.00 0.00 3.06
3783 6912 2.006169 GATGTGTGTGTGTGTGTGTGA 58.994 47.619 0.00 0.00 0.00 3.58
3784 6913 1.736681 TGATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
3785 6914 2.106477 TGATGTGTGTGTGTGTGTGT 57.894 45.000 0.00 0.00 0.00 3.72
3786 6915 3.484334 TTTGATGTGTGTGTGTGTGTG 57.516 42.857 0.00 0.00 0.00 3.82
3787 6916 4.157472 TGATTTTGATGTGTGTGTGTGTGT 59.843 37.500 0.00 0.00 0.00 3.72
3788 6917 4.500117 GTGATTTTGATGTGTGTGTGTGTG 59.500 41.667 0.00 0.00 0.00 3.82
3789 6918 4.671377 GTGATTTTGATGTGTGTGTGTGT 58.329 39.130 0.00 0.00 0.00 3.72
3828 6957 1.671054 CCGCACGACCACCTTTCAT 60.671 57.895 0.00 0.00 0.00 2.57
3829 6958 2.280524 CCGCACGACCACCTTTCA 60.281 61.111 0.00 0.00 0.00 2.69
3830 6959 0.600782 TAACCGCACGACCACCTTTC 60.601 55.000 0.00 0.00 0.00 2.62
3836 6965 1.081509 GTACGTAACCGCACGACCA 60.082 57.895 0.00 0.00 44.69 4.02
3837 6966 1.801512 GGTACGTAACCGCACGACC 60.802 63.158 0.00 8.21 44.69 4.79


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

AutoCloner maintained by Alex Coulton.