Multiple sequence alignment - TraesCS1D01G021200

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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 TraesCS1D01G021200 chr1D 100.000 4556 0 0 1 4556 9090068 9085513 0.000000e+00 8414
1 TraesCS1D01G021200 chr1D 93.756 1121 48 7 192 1305 9327641 9326536 0.000000e+00 1663
2 TraesCS1D01G021200 chr1D 93.958 662 37 3 1302 1963 9312493 9311835 0.000000e+00 998
3 TraesCS1D01G021200 chr1D 77.840 1620 321 30 1743 3346 9590993 9592590 0.000000e+00 968
4 TraesCS1D01G021200 chr1D 82.278 1027 175 5 1673 2697 8839789 8838768 0.000000e+00 881
5 TraesCS1D01G021200 chr1D 87.978 732 88 0 1959 2690 9310004 9309273 0.000000e+00 865
6 TraesCS1D01G021200 chr1D 81.800 511 85 6 2894 3403 9029701 9029198 5.450000e-114 422
7 TraesCS1D01G021200 chr1B 88.322 3528 323 39 1 3503 13040899 13044362 0.000000e+00 4150
8 TraesCS1D01G021200 chr1B 78.476 3308 530 115 223 3435 12430313 12427093 0.000000e+00 1997
9 TraesCS1D01G021200 chr1B 84.885 913 128 4 1639 2549 12637750 12638654 0.000000e+00 913
10 TraesCS1D01G021200 chr1B 80.726 1240 155 32 260 1449 12636408 12637613 0.000000e+00 889
11 TraesCS1D01G021200 chr1B 81.327 980 176 6 1743 2720 12813525 12812551 0.000000e+00 789
12 TraesCS1D01G021200 chr1B 80.840 976 179 6 1743 2717 13238363 13239331 0.000000e+00 760
13 TraesCS1D01G021200 chr1B 78.638 969 189 13 2537 3499 12640101 12641057 1.080000e-175 627
14 TraesCS1D01G021200 chr1B 80.581 757 104 22 449 1198 13300010 13299290 1.110000e-150 544
15 TraesCS1D01G021200 chr1B 81.077 724 99 20 483 1198 13340618 13339925 1.110000e-150 544
16 TraesCS1D01G021200 chr1B 81.455 550 86 12 2894 3435 12812389 12811848 1.950000e-118 436
17 TraesCS1D01G021200 chr1B 85.106 141 21 0 3011 3151 13277940 13277800 1.320000e-30 145
18 TraesCS1D01G021200 chr1A 83.557 1788 257 29 1741 3502 10484957 10483181 0.000000e+00 1639
19 TraesCS1D01G021200 chr1A 92.776 969 64 6 3592 4556 482800556 482801522 0.000000e+00 1397
20 TraesCS1D01G021200 chr1A 84.166 1061 161 5 1669 2724 10471467 10470409 0.000000e+00 1022
21 TraesCS1D01G021200 chr1A 82.280 1044 134 23 273 1289 10472812 10471793 0.000000e+00 856
22 TraesCS1D01G021200 chr1A 82.515 509 79 7 2894 3400 10470251 10469751 5.410000e-119 438
23 TraesCS1D01G021200 chr7D 94.575 977 47 6 3585 4556 533623988 533623013 0.000000e+00 1506
24 TraesCS1D01G021200 chr3D 97.691 866 18 2 3691 4556 15905199 15906062 0.000000e+00 1487
25 TraesCS1D01G021200 chr2D 94.410 966 44 7 3596 4556 5433458 5432498 0.000000e+00 1476
26 TraesCS1D01G021200 chr5B 93.750 960 50 9 3603 4556 334057191 334058146 0.000000e+00 1432
27 TraesCS1D01G021200 chr5B 92.665 968 62 8 3595 4556 640284047 640285011 0.000000e+00 1386
28 TraesCS1D01G021200 chr6B 92.690 985 63 9 3577 4556 607120540 607121520 0.000000e+00 1411
29 TraesCS1D01G021200 chr4A 92.577 970 66 6 3591 4556 735689444 735688477 0.000000e+00 1387
30 TraesCS1D01G021200 chr4A 76.355 203 40 8 3150 3345 674939252 674939453 8.060000e-18 102
31 TraesCS1D01G021200 chr7A 92.497 973 65 8 3589 4556 34525209 34526178 0.000000e+00 1386
32 TraesCS1D01G021200 chr7B 72.177 496 106 21 3020 3493 750607476 750606991 6.190000e-24 122


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 TraesCS1D01G021200 chr1D 9085513 9090068 4555 True 8414.000000 8414 100.000000 1 4556 1 chr1D.!!$R3 4555
1 TraesCS1D01G021200 chr1D 9326536 9327641 1105 True 1663.000000 1663 93.756000 192 1305 1 chr1D.!!$R4 1113
2 TraesCS1D01G021200 chr1D 9590993 9592590 1597 False 968.000000 968 77.840000 1743 3346 1 chr1D.!!$F1 1603
3 TraesCS1D01G021200 chr1D 9309273 9312493 3220 True 931.500000 998 90.968000 1302 2690 2 chr1D.!!$R5 1388
4 TraesCS1D01G021200 chr1D 8838768 8839789 1021 True 881.000000 881 82.278000 1673 2697 1 chr1D.!!$R1 1024
5 TraesCS1D01G021200 chr1D 9029198 9029701 503 True 422.000000 422 81.800000 2894 3403 1 chr1D.!!$R2 509
6 TraesCS1D01G021200 chr1B 13040899 13044362 3463 False 4150.000000 4150 88.322000 1 3503 1 chr1B.!!$F1 3502
7 TraesCS1D01G021200 chr1B 12427093 12430313 3220 True 1997.000000 1997 78.476000 223 3435 1 chr1B.!!$R1 3212
8 TraesCS1D01G021200 chr1B 12636408 12641057 4649 False 809.666667 913 81.416333 260 3499 3 chr1B.!!$F3 3239
9 TraesCS1D01G021200 chr1B 13238363 13239331 968 False 760.000000 760 80.840000 1743 2717 1 chr1B.!!$F2 974
10 TraesCS1D01G021200 chr1B 12811848 12813525 1677 True 612.500000 789 81.391000 1743 3435 2 chr1B.!!$R5 1692
11 TraesCS1D01G021200 chr1B 13299290 13300010 720 True 544.000000 544 80.581000 449 1198 1 chr1B.!!$R3 749
12 TraesCS1D01G021200 chr1B 13339925 13340618 693 True 544.000000 544 81.077000 483 1198 1 chr1B.!!$R4 715
13 TraesCS1D01G021200 chr1A 10483181 10484957 1776 True 1639.000000 1639 83.557000 1741 3502 1 chr1A.!!$R1 1761
14 TraesCS1D01G021200 chr1A 482800556 482801522 966 False 1397.000000 1397 92.776000 3592 4556 1 chr1A.!!$F1 964
15 TraesCS1D01G021200 chr1A 10469751 10472812 3061 True 772.000000 1022 82.987000 273 3400 3 chr1A.!!$R2 3127
16 TraesCS1D01G021200 chr7D 533623013 533623988 975 True 1506.000000 1506 94.575000 3585 4556 1 chr7D.!!$R1 971
17 TraesCS1D01G021200 chr3D 15905199 15906062 863 False 1487.000000 1487 97.691000 3691 4556 1 chr3D.!!$F1 865
18 TraesCS1D01G021200 chr2D 5432498 5433458 960 True 1476.000000 1476 94.410000 3596 4556 1 chr2D.!!$R1 960
19 TraesCS1D01G021200 chr5B 334057191 334058146 955 False 1432.000000 1432 93.750000 3603 4556 1 chr5B.!!$F1 953
20 TraesCS1D01G021200 chr5B 640284047 640285011 964 False 1386.000000 1386 92.665000 3595 4556 1 chr5B.!!$F2 961
21 TraesCS1D01G021200 chr6B 607120540 607121520 980 False 1411.000000 1411 92.690000 3577 4556 1 chr6B.!!$F1 979
22 TraesCS1D01G021200 chr4A 735688477 735689444 967 True 1387.000000 1387 92.577000 3591 4556 1 chr4A.!!$R1 965
23 TraesCS1D01G021200 chr7A 34525209 34526178 969 False 1386.000000 1386 92.497000 3589 4556 1 chr7A.!!$F1 967

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
486 528 0.105760 TGGTGCCCACTGGTGAAATT 60.106 50.000 1.93 0.0 0.0 1.82 F
1970 3940 1.553248 TGGGACCATAAGAACTGTCCG 59.447 52.381 0.00 0.0 46.6 4.79 F
3285 6724 0.179059 TGGTGAAGTTGAAGCTGCGA 60.179 50.000 0.00 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 4090 0.249363 GTCGTCCGCTATTTCCTCCC 60.249 60.0 0.00 0.0 0.00 4.30 R
3541 6995 0.106708 ACTTTTCACTCGCTCCAGCA 59.893 50.0 0.00 0.0 42.21 4.41 R
4525 7992 0.396811 GGGGATATCCGACACCCTTG 59.603 60.0 15.69 0.0 41.79 3.61 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
49 50 4.877251 TGTAATTACCCTGCCGTTATTGAC 59.123 41.667 13.01 0.00 0.00 3.18
90 91 2.096013 TGTGTGCGACGTTGAAAATTGA 59.904 40.909 7.08 0.00 0.00 2.57
101 102 7.216920 ACGTTGAAAATTGAAAGTAAACAGC 57.783 32.000 0.00 0.00 0.00 4.40
181 182 6.415702 CATTTTTCAAACAGAATGCACACTG 58.584 36.000 16.96 16.96 42.53 3.66
234 237 8.883731 GCTTGTATCTTAGATTGTGCTTTCTTA 58.116 33.333 0.00 0.00 0.00 2.10
247 250 2.831526 GCTTTCTTAAGGAAATGGGGCA 59.168 45.455 1.85 0.00 42.25 5.36
382 400 6.015180 ACATGGATTAACATTGCTCACTTGTT 60.015 34.615 0.00 0.00 37.37 2.83
486 528 0.105760 TGGTGCCCACTGGTGAAATT 60.106 50.000 1.93 0.00 0.00 1.82
517 559 2.043652 CCAAGGGTGCAGATGGGG 60.044 66.667 0.00 0.00 0.00 4.96
561 604 2.889988 CGCATTCGGACGATGGCA 60.890 61.111 15.11 0.00 0.00 4.92
652 697 5.250543 TCAGATCAACCTACCCAAGAATTCA 59.749 40.000 8.44 0.00 0.00 2.57
683 728 4.815108 GTGGGGAATGGGCGGTCC 62.815 72.222 0.00 0.00 0.00 4.46
913 961 5.534207 TGCAAAATTGATGAAGGAGTTGT 57.466 34.783 0.00 0.00 0.00 3.32
914 962 5.916318 TGCAAAATTGATGAAGGAGTTGTT 58.084 33.333 0.00 0.00 0.00 2.83
987 1035 5.121105 TCTAATGCAGAGTGGAACATGATG 58.879 41.667 0.00 0.00 44.52 3.07
988 1036 3.639672 ATGCAGAGTGGAACATGATGA 57.360 42.857 0.00 0.00 44.52 2.92
989 1037 2.703416 TGCAGAGTGGAACATGATGAC 58.297 47.619 0.00 0.00 44.52 3.06
990 1038 2.303890 TGCAGAGTGGAACATGATGACT 59.696 45.455 0.00 0.00 44.52 3.41
991 1039 2.935201 GCAGAGTGGAACATGATGACTC 59.065 50.000 0.00 1.46 44.52 3.36
992 1040 3.369261 GCAGAGTGGAACATGATGACTCT 60.369 47.826 8.27 8.27 44.52 3.24
993 1041 4.468765 AGAGTGGAACATGATGACTCTG 57.531 45.455 12.13 0.00 44.52 3.35
994 1042 2.935201 GAGTGGAACATGATGACTCTGC 59.065 50.000 0.00 0.00 44.52 4.26
995 1043 2.303890 AGTGGAACATGATGACTCTGCA 59.696 45.455 0.00 0.00 44.52 4.41
996 1044 3.054582 AGTGGAACATGATGACTCTGCAT 60.055 43.478 0.00 0.00 44.52 3.96
997 1045 3.693085 GTGGAACATGATGACTCTGCATT 59.307 43.478 0.00 0.00 44.52 3.56
998 1046 4.877823 GTGGAACATGATGACTCTGCATTA 59.122 41.667 0.00 0.00 44.52 1.90
999 1047 5.007430 GTGGAACATGATGACTCTGCATTAG 59.993 44.000 0.00 0.00 44.52 1.73
1000 1048 5.104817 TGGAACATGATGACTCTGCATTAGA 60.105 40.000 0.00 0.00 0.00 2.10
1001 1049 5.996513 GGAACATGATGACTCTGCATTAGAT 59.003 40.000 0.00 0.00 34.21 1.98
1025 1073 7.838079 TGATACCAATTTTCCATGGAATAGG 57.162 36.000 27.53 24.78 39.12 2.57
1128 1176 4.248859 TGCTCAAAGATCTAGAACACAGC 58.751 43.478 0.00 0.84 0.00 4.40
1170 1219 8.353423 TCACTAAAACGGTACTCCTACTTAAT 57.647 34.615 0.00 0.00 0.00 1.40
1567 1687 4.479158 CCCAGAGAGCTATAGTTCCTCTT 58.521 47.826 12.50 0.00 36.16 2.85
1570 1690 6.126911 CCCAGAGAGCTATAGTTCCTCTTTTT 60.127 42.308 12.50 0.00 36.16 1.94
1802 1937 6.711277 TGCAATATCCTGAACTAGTTGAACT 58.289 36.000 14.14 2.37 0.00 3.01
1970 3940 1.553248 TGGGACCATAAGAACTGTCCG 59.447 52.381 0.00 0.00 46.60 4.79
1972 3942 2.618053 GGACCATAAGAACTGTCCGTG 58.382 52.381 0.00 0.00 38.07 4.94
2044 4014 2.795329 TGCCAATCTTTCCTGAAGACC 58.205 47.619 0.00 0.00 46.66 3.85
2046 4016 3.157087 GCCAATCTTTCCTGAAGACCAA 58.843 45.455 0.00 0.00 46.66 3.67
2112 4082 2.525629 TCAAGGGAGGTGCACGGA 60.526 61.111 11.45 0.00 0.00 4.69
2120 4090 0.951040 GAGGTGCACGGAAAGTCTGG 60.951 60.000 11.45 0.00 0.00 3.86
2137 4107 1.069258 GGGGAGGAAATAGCGGACG 59.931 63.158 0.00 0.00 0.00 4.79
2148 4118 4.650754 AATAGCGGACGACTACTTCATT 57.349 40.909 0.00 0.00 0.00 2.57
2188 4158 7.419057 GGAGTATGATCCTACCATCTCAACAAA 60.419 40.741 4.70 0.00 36.35 2.83
2193 4163 6.375174 TGATCCTACCATCTCAACAAACAATG 59.625 38.462 0.00 0.00 0.00 2.82
2212 4182 9.777297 AAACAATGCATAGTACAAAAGGAATTT 57.223 25.926 0.00 0.00 0.00 1.82
2223 4193 6.029346 ACAAAAGGAATTTACTCATGCCAG 57.971 37.500 0.00 0.00 0.00 4.85
2249 4219 4.795970 ACGATCTTATCCGTGAAATTGC 57.204 40.909 0.00 0.00 37.64 3.56
2274 4244 8.352942 GCTATCTCAAAGTCAAAGGAAGAAAAA 58.647 33.333 0.00 0.00 0.00 1.94
2286 4257 8.917655 TCAAAGGAAGAAAAACTTGTTTTTACG 58.082 29.630 19.89 6.87 36.31 3.18
2372 4343 4.282496 TGGAAGGGAGATAAGAGTGAGTC 58.718 47.826 0.00 0.00 0.00 3.36
2373 4344 3.639561 GGAAGGGAGATAAGAGTGAGTCC 59.360 52.174 0.00 0.00 0.00 3.85
2490 4461 3.709653 TGTTGGACCTAGAAGACACAACT 59.290 43.478 0.00 0.00 37.99 3.16
2515 4489 6.183361 TGGTCTACATGATCATCACCTTAAGG 60.183 42.308 20.42 20.42 34.17 2.69
2516 4490 8.517833 TGGTCTACATGATCATCACCTTAAGGT 61.518 40.741 21.96 21.96 38.93 3.50
2532 4506 7.392494 CCTTAAGGTTATTGGGAAGTTTCTC 57.608 40.000 13.83 0.00 0.00 2.87
2616 6049 3.742640 GCAACCTGAGACAACTTGAGACT 60.743 47.826 0.00 0.00 0.00 3.24
2619 6052 3.964031 ACCTGAGACAACTTGAGACTCTT 59.036 43.478 3.68 0.00 0.00 2.85
2632 6065 8.133024 ACTTGAGACTCTTGACATTAGAGATT 57.867 34.615 10.51 0.00 41.32 2.40
2644 6077 3.386768 TTAGAGATTCCCGCATAGTGC 57.613 47.619 0.00 0.00 40.69 4.40
2677 6110 3.679389 ACAATCATCAAGCTTCGGAAGT 58.321 40.909 18.32 3.66 0.00 3.01
2699 6132 7.145932 AGTTAAACAATCTTCATGCTGGTAC 57.854 36.000 0.00 0.00 0.00 3.34
2706 6139 6.209192 ACAATCTTCATGCTGGTACAAAATCA 59.791 34.615 0.00 0.00 38.70 2.57
2715 6148 4.641989 GCTGGTACAAAATCAGTGGATGAT 59.358 41.667 0.00 0.00 45.51 2.45
2717 6150 4.398988 TGGTACAAAATCAGTGGATGATGC 59.601 41.667 0.00 0.00 41.79 3.91
2739 6172 3.733224 CGGTCTCGATTGATGATGAGTTC 59.267 47.826 0.00 0.00 39.00 3.01
2781 6217 3.833650 CCATCCAAAATAGGCCATGCATA 59.166 43.478 5.01 0.00 0.00 3.14
2788 6224 6.239261 CCAAAATAGGCCATGCATATTGTGTA 60.239 38.462 17.46 0.00 44.19 2.90
2802 6238 1.368641 TGTGTATCATGCCGCTGTTC 58.631 50.000 0.00 0.00 0.00 3.18
2830 6266 1.021390 AGCGTATTGTGCACCTCAGC 61.021 55.000 15.69 13.25 33.85 4.26
2831 6267 1.021390 GCGTATTGTGCACCTCAGCT 61.021 55.000 15.69 0.00 34.99 4.24
2834 6270 2.348666 CGTATTGTGCACCTCAGCTTAC 59.651 50.000 15.69 4.88 34.99 2.34
2849 6288 1.130561 GCTTACGCTTGATTGTGACCC 59.869 52.381 0.00 0.00 0.00 4.46
2856 6295 0.409092 TTGATTGTGACCCCAGCCAT 59.591 50.000 0.00 0.00 0.00 4.40
2857 6296 0.409092 TGATTGTGACCCCAGCCATT 59.591 50.000 0.00 0.00 0.00 3.16
2871 6310 0.808453 GCCATTGTGATGCATGCACC 60.808 55.000 25.37 15.61 35.43 5.01
2931 6370 3.189287 GCCTTGACTTGTATGGTGTTCTG 59.811 47.826 0.00 0.00 0.00 3.02
2935 6374 4.776349 TGACTTGTATGGTGTTCTGTTGT 58.224 39.130 0.00 0.00 0.00 3.32
2946 6385 4.262894 GGTGTTCTGTTGTCAAGAGGGATA 60.263 45.833 9.67 0.00 0.00 2.59
2963 6402 3.637229 GGGATAAGAAAGCTTAAAGCCCC 59.363 47.826 0.00 3.17 43.77 5.80
2973 6412 3.835790 TAAAGCCCCGCGCACACTT 62.836 57.895 8.75 1.75 41.38 3.16
2990 6429 5.086058 CACACTTGGTGTTGTAAATATCGC 58.914 41.667 0.19 0.00 45.08 4.58
2996 6435 3.242188 GGTGTTGTAAATATCGCACGACC 60.242 47.826 0.00 0.00 0.00 4.79
2997 6436 3.368539 GTGTTGTAAATATCGCACGACCA 59.631 43.478 0.00 0.00 0.00 4.02
2998 6437 3.368539 TGTTGTAAATATCGCACGACCAC 59.631 43.478 0.00 0.00 0.00 4.16
2999 6438 3.233684 TGTAAATATCGCACGACCACA 57.766 42.857 0.00 0.00 0.00 4.17
3028 6467 3.500680 GGTCGTTCTGCAGGACATAAAAA 59.499 43.478 24.79 0.79 41.38 1.94
3033 6472 4.568072 TCTGCAGGACATAAAAAGGCTA 57.432 40.909 15.13 0.00 0.00 3.93
3039 6478 4.770010 CAGGACATAAAAAGGCTAACCCAA 59.230 41.667 0.00 0.00 36.11 4.12
3098 6537 3.904800 TGGACAAGAGTTGTGTTCAGA 57.095 42.857 0.00 0.00 45.52 3.27
3105 6544 6.555315 ACAAGAGTTGTGTTCAGAAATTGTC 58.445 36.000 0.00 0.00 43.48 3.18
3112 6551 3.058914 GTGTTCAGAAATTGTCGGTCTGG 60.059 47.826 4.64 0.00 39.42 3.86
3113 6552 3.139077 GTTCAGAAATTGTCGGTCTGGT 58.861 45.455 4.64 0.00 39.42 4.00
3146 6585 1.639722 TTGTCAATCCGGTCAGAGGA 58.360 50.000 0.00 0.00 42.69 3.71
3174 6613 1.892474 GGTTTATGTGGCTGCTTGGAA 59.108 47.619 0.00 0.00 0.00 3.53
3201 6640 4.087182 AGTTCTCATTTCCGGAGACACTA 58.913 43.478 3.34 0.00 40.90 2.74
3274 6713 2.290577 GGCCTCAAGAATCTGGTGAAGT 60.291 50.000 0.00 0.00 0.00 3.01
3285 6724 0.179059 TGGTGAAGTTGAAGCTGCGA 60.179 50.000 0.00 0.00 0.00 5.10
3312 6751 5.295292 CACCATGTTATCAGAGGACAATGAC 59.705 44.000 0.00 0.00 0.00 3.06
3403 6848 2.031157 GGTGAAGTGTTCCGTTTCCATG 60.031 50.000 0.00 0.00 0.00 3.66
3436 6881 0.825010 AAGCCTGGTGTTGCTGGAAG 60.825 55.000 0.00 0.00 38.00 3.46
3448 6893 1.098050 GCTGGAAGTTGGTGGCTATG 58.902 55.000 0.00 0.00 35.30 2.23
3504 6958 2.574006 TTGAGCTGCTCAAGGTTGAT 57.426 45.000 34.40 0.00 44.27 2.57
3505 6959 2.105006 TGAGCTGCTCAAGGTTGATC 57.895 50.000 28.72 0.43 37.57 2.92
3506 6960 1.348696 TGAGCTGCTCAAGGTTGATCA 59.651 47.619 28.72 3.30 37.57 2.92
3507 6961 2.026542 TGAGCTGCTCAAGGTTGATCAT 60.027 45.455 28.72 0.00 37.57 2.45
3508 6962 2.355132 GAGCTGCTCAAGGTTGATCATG 59.645 50.000 24.02 0.00 36.52 3.07
3509 6963 1.202268 GCTGCTCAAGGTTGATCATGC 60.202 52.381 0.00 0.00 36.46 4.06
3510 6964 2.089201 CTGCTCAAGGTTGATCATGCA 58.911 47.619 0.00 0.00 36.46 3.96
3511 6965 2.688446 CTGCTCAAGGTTGATCATGCAT 59.312 45.455 0.00 0.00 35.18 3.96
3512 6966 3.093814 TGCTCAAGGTTGATCATGCATT 58.906 40.909 0.00 0.00 36.46 3.56
3513 6967 3.119280 TGCTCAAGGTTGATCATGCATTG 60.119 43.478 14.88 14.88 36.46 2.82
3514 6968 3.129813 GCTCAAGGTTGATCATGCATTGA 59.870 43.478 19.53 19.53 39.12 2.57
3525 6979 5.907866 ATCATGCATTGATCAACAGTGAA 57.092 34.783 11.07 0.00 41.36 3.18
3526 6980 5.305139 TCATGCATTGATCAACAGTGAAG 57.695 39.130 11.07 0.00 38.27 3.02
3527 6981 3.564235 TGCATTGATCAACAGTGAAGC 57.436 42.857 11.07 7.10 38.27 3.86
3528 6982 2.229543 TGCATTGATCAACAGTGAAGCC 59.770 45.455 11.07 0.00 38.27 4.35
3529 6983 2.490903 GCATTGATCAACAGTGAAGCCT 59.509 45.455 11.07 0.00 38.27 4.58
3530 6984 3.427233 GCATTGATCAACAGTGAAGCCTC 60.427 47.826 11.07 0.00 38.27 4.70
3531 6985 2.084610 TGATCAACAGTGAAGCCTCG 57.915 50.000 0.00 0.00 37.30 4.63
3532 6986 1.618343 TGATCAACAGTGAAGCCTCGA 59.382 47.619 0.00 0.00 37.30 4.04
3533 6987 2.266554 GATCAACAGTGAAGCCTCGAG 58.733 52.381 5.13 5.13 37.30 4.04
3534 6988 0.318441 TCAACAGTGAAGCCTCGAGG 59.682 55.000 27.83 27.83 38.53 4.63
3535 6989 0.318441 CAACAGTGAAGCCTCGAGGA 59.682 55.000 35.69 11.50 37.39 3.71
3536 6990 1.048601 AACAGTGAAGCCTCGAGGAA 58.951 50.000 35.69 13.82 37.39 3.36
3537 6991 0.605589 ACAGTGAAGCCTCGAGGAAG 59.394 55.000 35.69 16.40 37.39 3.46
3538 6992 0.605589 CAGTGAAGCCTCGAGGAAGT 59.394 55.000 35.69 18.34 37.39 3.01
3539 6993 0.892063 AGTGAAGCCTCGAGGAAGTC 59.108 55.000 35.69 25.26 37.39 3.01
3547 7001 2.962569 CGAGGAAGTCGTGCTGGA 59.037 61.111 0.00 0.00 44.20 3.86
3548 7002 1.153939 CGAGGAAGTCGTGCTGGAG 60.154 63.158 0.00 0.00 44.20 3.86
3549 7003 1.446966 GAGGAAGTCGTGCTGGAGC 60.447 63.158 0.00 0.00 42.50 4.70
3550 7004 2.811317 GGAAGTCGTGCTGGAGCG 60.811 66.667 0.00 0.00 45.83 5.03
3551 7005 2.258591 GAAGTCGTGCTGGAGCGA 59.741 61.111 0.00 0.00 45.83 4.93
3552 7006 1.803519 GAAGTCGTGCTGGAGCGAG 60.804 63.158 0.00 0.00 45.83 5.03
3553 7007 2.479412 GAAGTCGTGCTGGAGCGAGT 62.479 60.000 0.00 0.00 45.83 4.18
3554 7008 2.755542 AAGTCGTGCTGGAGCGAGTG 62.756 60.000 0.00 0.00 45.83 3.51
3555 7009 2.983592 TCGTGCTGGAGCGAGTGA 60.984 61.111 0.00 0.00 45.83 3.41
3556 7010 2.049156 CGTGCTGGAGCGAGTGAA 60.049 61.111 0.00 0.00 45.83 3.18
3557 7011 1.664649 CGTGCTGGAGCGAGTGAAA 60.665 57.895 0.00 0.00 45.83 2.69
3558 7012 1.221466 CGTGCTGGAGCGAGTGAAAA 61.221 55.000 0.00 0.00 45.83 2.29
3559 7013 0.514691 GTGCTGGAGCGAGTGAAAAG 59.485 55.000 0.00 0.00 45.83 2.27
3560 7014 0.106708 TGCTGGAGCGAGTGAAAAGT 59.893 50.000 0.00 0.00 45.83 2.66
3561 7015 1.230324 GCTGGAGCGAGTGAAAAGTT 58.770 50.000 0.00 0.00 0.00 2.66
3562 7016 2.224185 TGCTGGAGCGAGTGAAAAGTTA 60.224 45.455 0.00 0.00 45.83 2.24
3563 7017 2.806244 GCTGGAGCGAGTGAAAAGTTAA 59.194 45.455 0.00 0.00 0.00 2.01
3564 7018 3.437049 GCTGGAGCGAGTGAAAAGTTAAT 59.563 43.478 0.00 0.00 0.00 1.40
3565 7019 4.630069 GCTGGAGCGAGTGAAAAGTTAATA 59.370 41.667 0.00 0.00 0.00 0.98
3566 7020 5.446073 GCTGGAGCGAGTGAAAAGTTAATAC 60.446 44.000 0.00 0.00 0.00 1.89
3567 7021 4.624024 TGGAGCGAGTGAAAAGTTAATACG 59.376 41.667 0.00 0.00 0.00 3.06
3568 7022 4.492085 GGAGCGAGTGAAAAGTTAATACGC 60.492 45.833 0.00 0.00 43.00 4.42
3569 7023 3.370061 AGCGAGTGAAAAGTTAATACGCC 59.630 43.478 0.00 0.00 43.55 5.68
3570 7024 3.484721 GCGAGTGAAAAGTTAATACGCCC 60.485 47.826 0.00 0.00 38.09 6.13
3571 7025 3.930848 CGAGTGAAAAGTTAATACGCCCT 59.069 43.478 0.00 0.00 0.00 5.19
3572 7026 4.032558 CGAGTGAAAAGTTAATACGCCCTC 59.967 45.833 0.00 0.00 0.00 4.30
3573 7027 4.259356 AGTGAAAAGTTAATACGCCCTCC 58.741 43.478 0.00 0.00 0.00 4.30
3574 7028 3.376234 GTGAAAAGTTAATACGCCCTCCC 59.624 47.826 0.00 0.00 0.00 4.30
3575 7029 2.723322 AAAGTTAATACGCCCTCCCC 57.277 50.000 0.00 0.00 0.00 4.81
3576 7030 0.466963 AAGTTAATACGCCCTCCCCG 59.533 55.000 0.00 0.00 0.00 5.73
3577 7031 1.596203 GTTAATACGCCCTCCCCGC 60.596 63.158 0.00 0.00 0.00 6.13
3578 7032 1.763256 TTAATACGCCCTCCCCGCT 60.763 57.895 0.00 0.00 0.00 5.52
3579 7033 1.751349 TTAATACGCCCTCCCCGCTC 61.751 60.000 0.00 0.00 0.00 5.03
4047 7514 1.774856 GCCCAGATCTAGGCCCTTTTA 59.225 52.381 20.41 0.00 43.76 1.52
4140 7607 3.155167 CTAGGGGTGGCGGAGACC 61.155 72.222 0.00 0.00 25.51 3.85
4272 7739 2.039298 TGGTGGAGGTTGTCCCCA 60.039 61.111 0.00 0.00 46.31 4.96
4319 7786 1.227913 TCGTTTCCGGTTGGTTCCC 60.228 57.895 0.00 0.00 36.30 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.220602 ACAGGGACCAAACAATATTGCTTC 59.779 41.667 15.48 4.88 0.00 3.86
49 50 2.281070 ACGGGTGCTGCTTCACTG 60.281 61.111 0.00 0.00 37.16 3.66
146 147 8.458573 TCTGTTTGAAAAATGCTAACCTAGAA 57.541 30.769 0.00 0.00 0.00 2.10
163 164 2.780065 GCAGTGTGCATTCTGTTTGA 57.220 45.000 17.84 0.00 44.26 2.69
181 182 4.113354 GCACACAGGTTACTACTCATAGC 58.887 47.826 0.00 0.00 30.75 2.97
348 356 6.678900 GCAATGTTAATCCATGTTGAGAGACC 60.679 42.308 0.00 0.00 0.00 3.85
382 400 3.175438 TCCATCTTGAGAGACCTGTGA 57.825 47.619 0.00 0.00 33.99 3.58
416 434 2.412847 CGGTTTGAGCTTGATTCCGTTC 60.413 50.000 9.13 0.00 33.20 3.95
486 528 1.699634 CCCTTGGACTGGTCTTCTGAA 59.300 52.381 0.67 0.00 0.00 3.02
561 604 3.416156 GTGAGATTCCTCCAAAGCAGTT 58.584 45.455 0.00 0.00 38.66 3.16
652 697 0.401738 CCCCACACAGTGATCACCTT 59.598 55.000 22.21 6.61 35.23 3.50
683 728 3.396260 TGACTAGAGTGGTTTTTCCCG 57.604 47.619 0.00 0.00 34.77 5.14
720 765 5.129634 TCAAACATGGCACTAAGTTCTTGA 58.870 37.500 0.00 0.00 0.00 3.02
895 943 6.494835 AGCCTTAACAACTCCTTCATCAATTT 59.505 34.615 0.00 0.00 0.00 1.82
913 961 7.162082 CACCTCTTTCTTTCTCTAAGCCTTAA 58.838 38.462 0.00 0.00 33.66 1.85
914 962 6.702329 CACCTCTTTCTTTCTCTAAGCCTTA 58.298 40.000 0.00 0.00 33.66 2.69
987 1035 7.976135 AATTGGTATCATCTAATGCAGAGTC 57.024 36.000 0.00 0.00 36.48 3.36
988 1036 8.757982 AAAATTGGTATCATCTAATGCAGAGT 57.242 30.769 0.00 0.00 36.48 3.24
989 1037 8.295288 GGAAAATTGGTATCATCTAATGCAGAG 58.705 37.037 0.00 0.00 36.48 3.35
990 1038 7.779326 TGGAAAATTGGTATCATCTAATGCAGA 59.221 33.333 0.00 0.00 37.79 4.26
991 1039 7.944061 TGGAAAATTGGTATCATCTAATGCAG 58.056 34.615 0.00 0.00 0.00 4.41
992 1040 7.894753 TGGAAAATTGGTATCATCTAATGCA 57.105 32.000 0.00 0.00 0.00 3.96
993 1041 7.816031 CCATGGAAAATTGGTATCATCTAATGC 59.184 37.037 5.56 0.00 0.00 3.56
994 1042 9.081204 TCCATGGAAAATTGGTATCATCTAATG 57.919 33.333 13.46 0.00 34.48 1.90
995 1043 9.659135 TTCCATGGAAAATTGGTATCATCTAAT 57.341 29.630 25.13 0.00 34.48 1.73
996 1044 9.659135 ATTCCATGGAAAATTGGTATCATCTAA 57.341 29.630 30.28 1.67 37.69 2.10
998 1046 9.305555 CTATTCCATGGAAAATTGGTATCATCT 57.694 33.333 30.28 11.51 37.69 2.90
999 1047 8.526147 CCTATTCCATGGAAAATTGGTATCATC 58.474 37.037 30.28 0.00 37.69 2.92
1000 1048 8.233820 TCCTATTCCATGGAAAATTGGTATCAT 58.766 33.333 30.28 12.13 37.69 2.45
1001 1049 7.590907 TCCTATTCCATGGAAAATTGGTATCA 58.409 34.615 30.28 11.08 37.69 2.15
1023 1071 4.287067 ACAATGATCCGGCTTGTATATCCT 59.713 41.667 0.00 0.00 31.62 3.24
1025 1073 5.120830 GTGACAATGATCCGGCTTGTATATC 59.879 44.000 0.00 0.00 33.46 1.63
1055 1103 6.321181 ACAAAGTTCAGCAATACTTTCTTCCA 59.679 34.615 7.01 0.00 41.34 3.53
1128 1176 2.014335 TGAAGAGGTCACATGCATCG 57.986 50.000 0.00 0.00 0.00 3.84
1154 1202 9.552114 CACGATAATAATTAAGTAGGAGTACCG 57.448 37.037 0.00 0.00 41.83 4.02
1170 1219 9.904647 GACACGTAAAAATAAGCACGATAATAA 57.095 29.630 0.00 0.00 37.80 1.40
1567 1687 6.811253 ATTAAACGCTGTGTGATAGGAAAA 57.189 33.333 0.00 0.00 0.00 2.29
1802 1937 2.820178 TCCTCACTATCAGTTCTGCCA 58.180 47.619 0.00 0.00 0.00 4.92
1970 3940 1.656652 ACCATCATAGCTTCGCACAC 58.343 50.000 0.00 0.00 0.00 3.82
1972 3942 3.002348 GGTAAACCATCATAGCTTCGCAC 59.998 47.826 0.00 0.00 35.64 5.34
2044 4014 0.893727 CGTCCCCTCCCAACCTTTTG 60.894 60.000 0.00 0.00 0.00 2.44
2046 4016 1.358051 AACGTCCCCTCCCAACCTTT 61.358 55.000 0.00 0.00 0.00 3.11
2073 4043 1.772819 AACCCTCTGCACTCCACCTG 61.773 60.000 0.00 0.00 0.00 4.00
2112 4082 2.092914 CGCTATTTCCTCCCCAGACTTT 60.093 50.000 0.00 0.00 0.00 2.66
2120 4090 0.249363 GTCGTCCGCTATTTCCTCCC 60.249 60.000 0.00 0.00 0.00 4.30
2137 4107 8.821894 CCTGCTTATAAGTTCAATGAAGTAGTC 58.178 37.037 13.91 0.00 0.00 2.59
2148 4118 7.510685 AGGATCATACTCCTGCTTATAAGTTCA 59.489 37.037 13.91 3.80 44.18 3.18
2188 4158 9.855021 GTAAATTCCTTTTGTACTATGCATTGT 57.145 29.630 17.70 17.70 0.00 2.71
2193 4163 9.722056 CATGAGTAAATTCCTTTTGTACTATGC 57.278 33.333 0.00 0.00 0.00 3.14
2223 4193 3.661745 ACGGATAAGATCGTGCACC 57.338 52.632 12.15 0.00 38.25 5.01
2249 4219 9.670719 GTTTTTCTTCCTTTGACTTTGAGATAG 57.329 33.333 0.00 0.00 0.00 2.08
2274 4244 3.202829 TCCTCCAGCGTAAAAACAAGT 57.797 42.857 0.00 0.00 0.00 3.16
2286 4257 2.338785 GCTGCAACCTTCCTCCAGC 61.339 63.158 0.00 0.00 41.57 4.85
2372 4343 1.410517 ACATGTCCACTATGCTCTCGG 59.589 52.381 0.00 0.00 0.00 4.63
2373 4344 2.736978 GACATGTCCACTATGCTCTCG 58.263 52.381 15.31 0.00 0.00 4.04
2395 4366 6.698329 CCGAAACATGTAATTGACCGTAGATA 59.302 38.462 0.00 0.00 0.00 1.98
2396 4367 5.522460 CCGAAACATGTAATTGACCGTAGAT 59.478 40.000 0.00 0.00 0.00 1.98
2441 4412 5.812642 CGTAGCAACCTCATCTTGTTAGAAT 59.187 40.000 0.00 0.00 33.20 2.40
2446 4417 3.006967 ACTCGTAGCAACCTCATCTTGTT 59.993 43.478 0.00 0.00 0.00 2.83
2490 4461 6.183361 CCTTAAGGTGATGATCATGTAGACCA 60.183 42.308 14.30 0.16 0.00 4.02
2515 4489 4.663334 AGGTGGAGAAACTTCCCAATAAC 58.337 43.478 0.00 0.00 36.35 1.89
2516 4490 6.273730 TCTTAGGTGGAGAAACTTCCCAATAA 59.726 38.462 0.00 0.00 36.35 1.40
2532 4506 7.014808 CCTCTTAGAGAAAGGTATCTTAGGTGG 59.985 44.444 11.32 0.00 35.75 4.61
2616 6049 3.450817 TGCGGGAATCTCTAATGTCAAGA 59.549 43.478 0.00 0.00 0.00 3.02
2619 6052 4.588951 ACTATGCGGGAATCTCTAATGTCA 59.411 41.667 0.00 0.00 0.00 3.58
2644 6077 3.349927 TGATGATTGTCTTTGGCAGGAG 58.650 45.455 0.00 0.00 0.00 3.69
2677 6110 7.517614 TTGTACCAGCATGAAGATTGTTTAA 57.482 32.000 0.00 0.00 39.69 1.52
2699 6132 2.424601 ACCGCATCATCCACTGATTTTG 59.575 45.455 0.00 0.00 42.07 2.44
2706 6139 1.037579 TCGAGACCGCATCATCCACT 61.038 55.000 0.00 0.00 35.37 4.00
2715 6148 1.408702 TCATCATCAATCGAGACCGCA 59.591 47.619 0.00 0.00 35.37 5.69
2717 6150 3.361794 ACTCATCATCAATCGAGACCG 57.638 47.619 0.00 0.00 37.07 4.79
2739 6172 2.676342 GGCCTGTGGAAAGTTATGTACG 59.324 50.000 0.00 0.00 0.00 3.67
2781 6217 2.042686 ACAGCGGCATGATACACAAT 57.957 45.000 1.45 0.00 0.00 2.71
2788 6224 1.888512 ACAAAAGAACAGCGGCATGAT 59.111 42.857 1.45 0.00 0.00 2.45
2802 6238 5.064707 AGGTGCACAATACGCTATACAAAAG 59.935 40.000 20.43 0.00 0.00 2.27
2816 6252 1.442769 CGTAAGCTGAGGTGCACAAT 58.557 50.000 20.43 6.31 34.99 2.71
2830 6266 1.737793 GGGGTCACAATCAAGCGTAAG 59.262 52.381 0.00 0.00 43.44 2.34
2831 6267 1.072489 TGGGGTCACAATCAAGCGTAA 59.928 47.619 0.00 0.00 0.00 3.18
2834 6270 1.926511 GCTGGGGTCACAATCAAGCG 61.927 60.000 0.00 0.00 0.00 4.68
2837 6276 0.409092 ATGGCTGGGGTCACAATCAA 59.591 50.000 0.00 0.00 0.00 2.57
2849 6288 0.529773 GCATGCATCACAATGGCTGG 60.530 55.000 14.21 0.00 33.19 4.85
2856 6295 1.913778 AGAAGGTGCATGCATCACAA 58.086 45.000 31.54 0.63 36.22 3.33
2857 6296 1.913778 AAGAAGGTGCATGCATCACA 58.086 45.000 31.54 11.77 36.22 3.58
2871 6310 4.110482 GCAATAGATGGCAGCAAAAGAAG 58.890 43.478 5.19 0.00 0.00 2.85
2913 6352 4.776349 ACAACAGAACACCATACAAGTCA 58.224 39.130 0.00 0.00 0.00 3.41
2931 6370 5.249420 AGCTTTCTTATCCCTCTTGACAAC 58.751 41.667 0.00 0.00 0.00 3.32
2935 6374 6.599638 GCTTTAAGCTTTCTTATCCCTCTTGA 59.400 38.462 10.01 0.00 38.45 3.02
2946 6385 0.888619 GCGGGGCTTTAAGCTTTCTT 59.111 50.000 16.89 0.00 41.99 2.52
2963 6402 1.767127 TACAACACCAAGTGTGCGCG 61.767 55.000 0.00 0.00 46.79 6.86
2973 6412 3.368539 GTCGTGCGATATTTACAACACCA 59.631 43.478 0.00 0.00 0.00 4.17
2990 6429 2.347490 CCTTCCCCTGTGGTCGTG 59.653 66.667 0.00 0.00 34.77 4.35
2996 6435 0.320771 CAGAACGACCTTCCCCTGTG 60.321 60.000 0.00 0.00 0.00 3.66
2997 6436 2.058675 CAGAACGACCTTCCCCTGT 58.941 57.895 0.00 0.00 0.00 4.00
2998 6437 1.376037 GCAGAACGACCTTCCCCTG 60.376 63.158 0.00 0.00 0.00 4.45
2999 6438 1.831652 CTGCAGAACGACCTTCCCCT 61.832 60.000 8.42 0.00 0.00 4.79
3028 6467 0.897863 TTGCGCAATTGGGTTAGCCT 60.898 50.000 21.02 0.00 34.45 4.58
3033 6472 1.005867 CAGCTTGCGCAATTGGGTT 60.006 52.632 25.26 6.99 39.10 4.11
3039 6478 2.034687 ACTCCCAGCTTGCGCAAT 59.965 55.556 25.26 6.90 39.10 3.56
3049 6488 2.262915 GACGCCAGTCACTCCCAG 59.737 66.667 0.00 0.00 46.32 4.45
3112 6551 0.741221 GACAATGACTCCAGGCGGAC 60.741 60.000 0.00 0.00 35.91 4.79
3113 6552 1.191489 TGACAATGACTCCAGGCGGA 61.191 55.000 0.00 0.00 39.79 5.54
3174 6613 3.583086 TCTCCGGAAATGAGAACTTTCCT 59.417 43.478 5.23 0.00 46.24 3.36
3285 6724 3.264193 TGTCCTCTGATAACATGGTGCTT 59.736 43.478 0.00 0.00 0.00 3.91
3312 6751 1.164411 TACCAAGGAGTTGCATTGCG 58.836 50.000 3.84 0.00 36.98 4.85
3360 6799 2.492088 CTGACGGACTGACTTCCACATA 59.508 50.000 0.00 0.00 35.04 2.29
3361 6800 1.273606 CTGACGGACTGACTTCCACAT 59.726 52.381 0.00 0.00 35.04 3.21
3436 6881 4.137116 TCACAGATACATAGCCACCAAC 57.863 45.455 0.00 0.00 0.00 3.77
3448 6893 6.566753 GCTCCTTGTTCAAACTTCACAGATAC 60.567 42.308 0.00 0.00 0.00 2.24
3504 6958 4.380128 GCTTCACTGTTGATCAATGCATGA 60.380 41.667 12.12 10.40 43.67 3.07
3505 6959 3.857665 GCTTCACTGTTGATCAATGCATG 59.142 43.478 12.12 8.29 0.00 4.06
3506 6960 3.119245 GGCTTCACTGTTGATCAATGCAT 60.119 43.478 12.12 0.00 0.00 3.96
3507 6961 2.229543 GGCTTCACTGTTGATCAATGCA 59.770 45.455 12.12 5.00 0.00 3.96
3508 6962 2.490903 AGGCTTCACTGTTGATCAATGC 59.509 45.455 12.12 0.00 0.00 3.56
3509 6963 3.181513 CGAGGCTTCACTGTTGATCAATG 60.182 47.826 12.12 10.29 0.00 2.82
3510 6964 3.005554 CGAGGCTTCACTGTTGATCAAT 58.994 45.455 12.12 0.00 0.00 2.57
3511 6965 2.037121 TCGAGGCTTCACTGTTGATCAA 59.963 45.455 3.38 3.38 0.00 2.57
3512 6966 1.618343 TCGAGGCTTCACTGTTGATCA 59.382 47.619 0.00 0.00 0.00 2.92
3513 6967 2.266554 CTCGAGGCTTCACTGTTGATC 58.733 52.381 3.91 0.00 0.00 2.92
3514 6968 1.066573 CCTCGAGGCTTCACTGTTGAT 60.067 52.381 20.67 0.00 0.00 2.57
3515 6969 0.318441 CCTCGAGGCTTCACTGTTGA 59.682 55.000 20.67 0.00 0.00 3.18
3516 6970 0.318441 TCCTCGAGGCTTCACTGTTG 59.682 55.000 27.39 0.00 34.44 3.33
3517 6971 1.001406 CTTCCTCGAGGCTTCACTGTT 59.999 52.381 27.39 0.00 34.44 3.16
3518 6972 0.605589 CTTCCTCGAGGCTTCACTGT 59.394 55.000 27.39 0.00 34.44 3.55
3519 6973 0.605589 ACTTCCTCGAGGCTTCACTG 59.394 55.000 27.39 12.45 34.44 3.66
3520 6974 0.892063 GACTTCCTCGAGGCTTCACT 59.108 55.000 27.39 5.13 34.44 3.41
3521 6975 0.456995 CGACTTCCTCGAGGCTTCAC 60.457 60.000 27.39 14.57 46.14 3.18
3522 6976 0.894184 ACGACTTCCTCGAGGCTTCA 60.894 55.000 27.39 6.53 46.14 3.02
3523 6977 0.456995 CACGACTTCCTCGAGGCTTC 60.457 60.000 27.39 19.39 46.14 3.86
3524 6978 1.587054 CACGACTTCCTCGAGGCTT 59.413 57.895 27.39 12.75 46.14 4.35
3525 6979 2.995872 GCACGACTTCCTCGAGGCT 61.996 63.158 27.39 11.21 46.14 4.58
3526 6980 2.507324 GCACGACTTCCTCGAGGC 60.507 66.667 27.39 11.66 46.14 4.70
3527 6981 1.153939 CAGCACGACTTCCTCGAGG 60.154 63.158 26.32 26.32 46.14 4.63
3528 6982 1.153939 CCAGCACGACTTCCTCGAG 60.154 63.158 5.13 5.13 46.14 4.04
3529 6983 1.587043 CTCCAGCACGACTTCCTCGA 61.587 60.000 0.00 0.00 46.14 4.04
3531 6985 1.446966 GCTCCAGCACGACTTCCTC 60.447 63.158 0.00 0.00 41.59 3.71
3532 6986 2.659610 GCTCCAGCACGACTTCCT 59.340 61.111 0.00 0.00 41.59 3.36
3533 6987 2.811317 CGCTCCAGCACGACTTCC 60.811 66.667 0.00 0.00 42.21 3.46
3534 6988 1.803519 CTCGCTCCAGCACGACTTC 60.804 63.158 0.00 0.00 42.21 3.01
3535 6989 2.259818 CTCGCTCCAGCACGACTT 59.740 61.111 0.00 0.00 42.21 3.01
3536 6990 2.986413 ACTCGCTCCAGCACGACT 60.986 61.111 0.00 0.00 42.21 4.18
3537 6991 2.749110 TTCACTCGCTCCAGCACGAC 62.749 60.000 0.00 0.00 42.21 4.34
3538 6992 2.082629 TTTCACTCGCTCCAGCACGA 62.083 55.000 0.00 0.00 42.21 4.35
3539 6993 1.221466 TTTTCACTCGCTCCAGCACG 61.221 55.000 0.00 0.00 42.21 5.34
3540 6994 0.514691 CTTTTCACTCGCTCCAGCAC 59.485 55.000 0.00 0.00 42.21 4.40
3541 6995 0.106708 ACTTTTCACTCGCTCCAGCA 59.893 50.000 0.00 0.00 42.21 4.41
3542 6996 1.230324 AACTTTTCACTCGCTCCAGC 58.770 50.000 0.00 0.00 37.78 4.85
3543 6997 5.220228 CGTATTAACTTTTCACTCGCTCCAG 60.220 44.000 0.00 0.00 0.00 3.86
3544 6998 4.624024 CGTATTAACTTTTCACTCGCTCCA 59.376 41.667 0.00 0.00 0.00 3.86
3545 6999 4.492085 GCGTATTAACTTTTCACTCGCTCC 60.492 45.833 0.00 0.00 38.46 4.70
3546 7000 4.492085 GGCGTATTAACTTTTCACTCGCTC 60.492 45.833 0.00 0.00 40.71 5.03
3547 7001 3.370061 GGCGTATTAACTTTTCACTCGCT 59.630 43.478 0.00 0.00 40.71 4.93
3548 7002 3.484721 GGGCGTATTAACTTTTCACTCGC 60.485 47.826 0.00 0.00 40.29 5.03
3549 7003 3.930848 AGGGCGTATTAACTTTTCACTCG 59.069 43.478 0.00 0.00 0.00 4.18
3550 7004 4.331992 GGAGGGCGTATTAACTTTTCACTC 59.668 45.833 0.00 0.00 0.00 3.51
3551 7005 4.259356 GGAGGGCGTATTAACTTTTCACT 58.741 43.478 0.00 0.00 0.00 3.41
3552 7006 3.376234 GGGAGGGCGTATTAACTTTTCAC 59.624 47.826 0.00 0.00 0.00 3.18
3553 7007 3.613030 GGGAGGGCGTATTAACTTTTCA 58.387 45.455 0.00 0.00 0.00 2.69
3554 7008 2.947652 GGGGAGGGCGTATTAACTTTTC 59.052 50.000 0.00 0.00 0.00 2.29
3555 7009 2.681682 CGGGGAGGGCGTATTAACTTTT 60.682 50.000 0.00 0.00 0.00 2.27
3556 7010 1.134310 CGGGGAGGGCGTATTAACTTT 60.134 52.381 0.00 0.00 0.00 2.66
3557 7011 0.466963 CGGGGAGGGCGTATTAACTT 59.533 55.000 0.00 0.00 0.00 2.66
3558 7012 2.036428 GCGGGGAGGGCGTATTAACT 62.036 60.000 0.00 0.00 0.00 2.24
3559 7013 1.596203 GCGGGGAGGGCGTATTAAC 60.596 63.158 0.00 0.00 0.00 2.01
3560 7014 1.751349 GAGCGGGGAGGGCGTATTAA 61.751 60.000 0.00 0.00 35.00 1.40
3561 7015 2.123164 AGCGGGGAGGGCGTATTA 60.123 61.111 0.00 0.00 35.00 0.98
3562 7016 3.547513 GAGCGGGGAGGGCGTATT 61.548 66.667 0.00 0.00 35.00 1.89
3587 7041 3.537874 CTAACGGGAGCGGGGAGG 61.538 72.222 0.00 0.00 0.00 4.30
4319 7786 2.835431 AGACCGGCAGGATCGAGG 60.835 66.667 10.86 0.00 41.02 4.63
4525 7992 0.396811 GGGGATATCCGACACCCTTG 59.603 60.000 15.69 0.00 41.79 3.61
4531 7998 0.473117 GGGAAGGGGGATATCCGACA 60.473 60.000 15.69 0.00 36.71 4.35


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

AutoCloner maintained by Alex Coulton.