Multiple sequence alignment - TraesCS1A01G018600

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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 TraesCS1A01G018600 chr1A 100.000 4950 0 0 1 4950 9552967 9557916 0.000000e+00 9142.0
1 TraesCS1A01G018600 chr1A 90.167 1678 115 12 2321 3986 9362118 9363757 0.000000e+00 2139.0
2 TraesCS1A01G018600 chr1A 83.046 1274 140 36 994 2236 9359182 9360410 0.000000e+00 1086.0
3 TraesCS1A01G018600 chr1A 78.675 619 69 28 1030 1645 34975543 34974985 2.190000e-93 353.0
4 TraesCS1A01G018600 chr1A 81.710 421 44 17 531 929 9357853 9358262 2.220000e-83 320.0
5 TraesCS1A01G018600 chr1A 84.862 218 27 3 560 777 9358595 9358806 1.080000e-51 215.0
6 TraesCS1A01G018600 chr1A 84.167 120 13 3 4155 4274 34971269 34971156 1.460000e-20 111.0
7 TraesCS1A01G018600 chr1A 95.556 45 1 1 4446 4489 34970836 34970792 2.470000e-08 71.3
8 TraesCS1A01G018600 chr1B 92.312 1678 116 9 2322 3989 9595128 9593454 0.000000e+00 2372.0
9 TraesCS1A01G018600 chr1B 89.748 1824 134 28 2322 4124 10074176 10075967 0.000000e+00 2283.0
10 TraesCS1A01G018600 chr1B 92.575 1468 98 7 2528 3986 10084409 10085874 0.000000e+00 2097.0
11 TraesCS1A01G018600 chr1B 93.414 911 54 4 1 905 10071875 10072785 0.000000e+00 1345.0
12 TraesCS1A01G018600 chr1B 83.446 1329 121 42 947 2220 10072786 10074070 0.000000e+00 1144.0
13 TraesCS1A01G018600 chr1B 79.558 905 111 36 1030 1875 10083103 10083992 3.320000e-161 579.0
14 TraesCS1A01G018600 chr1B 90.465 409 36 1 1030 1435 9596673 9596265 2.030000e-148 536.0
15 TraesCS1A01G018600 chr1B 79.537 777 96 46 1467 2206 9596263 9595513 3.440000e-136 496.0
16 TraesCS1A01G018600 chr1D 89.410 1832 135 32 2322 4124 7878687 7880488 0.000000e+00 2254.0
17 TraesCS1A01G018600 chr1D 90.833 1549 133 5 2561 4102 7901025 7902571 0.000000e+00 2065.0
18 TraesCS1A01G018600 chr1D 85.630 1865 195 42 2563 4384 7348855 7347021 0.000000e+00 1892.0
19 TraesCS1A01G018600 chr1D 89.295 1476 128 19 2762 4221 7205749 7204288 0.000000e+00 1823.0
20 TraesCS1A01G018600 chr1D 83.390 1174 102 40 1026 2156 7877410 7878533 0.000000e+00 1002.0
21 TraesCS1A01G018600 chr1D 82.659 865 114 23 1031 1877 7207637 7206791 0.000000e+00 734.0
22 TraesCS1A01G018600 chr1D 82.040 902 108 30 1026 1875 7899684 7900583 0.000000e+00 719.0
23 TraesCS1A01G018600 chr1D 83.485 660 86 12 996 1645 7350906 7350260 1.190000e-165 593.0
24 TraesCS1A01G018600 chr1D 83.654 312 31 9 3961 4270 7203752 7203459 4.880000e-70 276.0
25 TraesCS1A01G018600 chr1D 80.876 251 39 5 531 778 7208299 7208055 6.540000e-44 189.0
26 TraesCS1A01G018600 chr1D 83.851 161 25 1 2623 2783 7344606 7344447 8.580000e-33 152.0
27 TraesCS1A01G018600 chr1D 85.088 114 8 3 4602 4706 7903122 7903235 1.880000e-19 108.0
28 TraesCS1A01G018600 chr1D 95.455 66 3 0 60 125 7891171 7891236 6.780000e-19 106.0
29 TraesCS1A01G018600 chr1D 82.051 117 17 3 4566 4679 7203053 7202938 4.080000e-16 97.1
30 TraesCS1A01G018600 chr1D 97.872 47 1 0 4443 4489 7903016 7903062 1.140000e-11 82.4
31 TraesCS1A01G018600 chr3D 85.305 1116 156 7 2840 3951 27878211 27877100 0.000000e+00 1146.0
32 TraesCS1A01G018600 chr3B 90.724 442 31 2 3757 4198 12062820 12062389 9.240000e-162 580.0
33 TraesCS1A01G018600 chr5B 90.426 282 16 3 3918 4198 103634552 103634281 1.310000e-95 361.0


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 TraesCS1A01G018600 chr1A 9552967 9557916 4949 False 9142.000000 9142 100.000000 1 4950 1 chr1A.!!$F1 4949
1 TraesCS1A01G018600 chr1A 9357853 9363757 5904 False 940.000000 2139 84.946250 531 3986 4 chr1A.!!$F2 3455
2 TraesCS1A01G018600 chr1B 10071875 10075967 4092 False 1590.666667 2283 88.869333 1 4124 3 chr1B.!!$F1 4123
3 TraesCS1A01G018600 chr1B 10083103 10085874 2771 False 1338.000000 2097 86.066500 1030 3986 2 chr1B.!!$F2 2956
4 TraesCS1A01G018600 chr1B 9593454 9596673 3219 True 1134.666667 2372 87.438000 1030 3989 3 chr1B.!!$R1 2959
5 TraesCS1A01G018600 chr1D 7877410 7880488 3078 False 1628.000000 2254 86.400000 1026 4124 2 chr1D.!!$F2 3098
6 TraesCS1A01G018600 chr1D 7344447 7350906 6459 True 879.000000 1892 84.322000 996 4384 3 chr1D.!!$R2 3388
7 TraesCS1A01G018600 chr1D 7899684 7903235 3551 False 743.600000 2065 88.958250 1026 4706 4 chr1D.!!$F3 3680
8 TraesCS1A01G018600 chr1D 7202938 7208299 5361 True 623.820000 1823 83.707000 531 4679 5 chr1D.!!$R1 4148
9 TraesCS1A01G018600 chr3D 27877100 27878211 1111 True 1146.000000 1146 85.305000 2840 3951 1 chr3D.!!$R1 1111

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
941 974 0.034896 CGGCCAGTACTCAACCAAGT 59.965 55.0 2.24 0.0 0.00 3.16 F
1653 2647 0.102120 CACTCTCAGATCGAGGTGGC 59.898 60.0 17.70 0.0 42.55 5.01 F
3028 7054 0.250124 CAAAGCCCACGAGGTACACA 60.250 55.0 0.00 0.0 38.26 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 2776 0.108898 GCTCACATCGTCTGCAGTCT 60.109 55.0 14.67 0.0 0.0 3.24 R
3514 7541 0.036388 TGACGATGCTTTGGTCCCTC 60.036 55.0 0.00 0.0 0.0 4.30 R
4558 9665 0.394938 ACATGTGCCGGTTACAGTGA 59.605 50.0 16.73 0.0 0.0 3.41 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
39 40 1.558294 GGGGAAAGAGGGTTCGTGTAT 59.442 52.381 0.00 0.00 0.00 2.29
44 45 4.571176 GGAAAGAGGGTTCGTGTATGAATC 59.429 45.833 0.00 0.00 0.00 2.52
50 51 2.927477 GGTTCGTGTATGAATCTTCGCA 59.073 45.455 0.00 0.00 0.00 5.10
56 57 3.307242 GTGTATGAATCTTCGCAGTCCAC 59.693 47.826 0.00 0.00 0.00 4.02
94 95 8.338259 CACTAACAAATAGTCCTTGCATCATAC 58.662 37.037 0.00 0.00 43.12 2.39
128 129 3.511146 TCCTTCCATTGAAAGGTTGATGC 59.489 43.478 1.24 0.00 0.00 3.91
156 157 7.389607 GCAACTAAACTATTAGGTTGGTCAAGA 59.610 37.037 10.49 0.00 35.46 3.02
160 161 7.981102 AAACTATTAGGTTGGTCAAGAGAAC 57.019 36.000 0.00 0.00 0.00 3.01
206 207 4.524328 TCATGCTAGACTCAACTTCAGTCA 59.476 41.667 0.00 0.00 42.51 3.41
245 246 7.551262 ACAAGGAACAAAAACAAAAGGGATTAC 59.449 33.333 0.00 0.00 0.00 1.89
246 247 6.277605 AGGAACAAAAACAAAAGGGATTACG 58.722 36.000 0.00 0.00 0.00 3.18
255 256 1.400530 AAGGGATTACGGCTCTCGGG 61.401 60.000 0.00 0.00 44.45 5.14
275 276 1.884235 CTGACACAACTCTCCCCAAC 58.116 55.000 0.00 0.00 0.00 3.77
279 280 3.456644 TGACACAACTCTCCCCAACTTAA 59.543 43.478 0.00 0.00 0.00 1.85
288 289 5.012251 ACTCTCCCCAACTTAAAAGAGTCTC 59.988 44.000 0.00 0.00 39.27 3.36
367 368 6.633500 TTGACAAAGAAGTGATACCAAAGG 57.367 37.500 0.00 0.00 0.00 3.11
394 395 6.313658 CCTTGGGAGTTTGAAAAACTTGAAAG 59.686 38.462 6.81 9.74 0.00 2.62
397 398 7.096551 TGGGAGTTTGAAAAACTTGAAAGAAG 58.903 34.615 6.81 0.00 0.00 2.85
398 399 6.535150 GGGAGTTTGAAAAACTTGAAAGAAGG 59.465 38.462 6.81 0.00 0.00 3.46
430 433 4.970003 ACAAGAAAGAATTTGAAACGCTCG 59.030 37.500 0.00 0.00 39.27 5.03
456 459 1.518367 AAAGAGGGTGAAGGGACACA 58.482 50.000 0.00 0.00 41.88 3.72
468 471 4.157656 TGAAGGGACACAACAAGAACTTTG 59.842 41.667 0.00 0.00 0.00 2.77
473 476 4.432712 GACACAACAAGAACTTTGGCAAT 58.567 39.130 0.00 0.00 0.00 3.56
553 556 0.622738 AGCACCCATCATCTCCACCT 60.623 55.000 0.00 0.00 0.00 4.00
555 558 1.748591 GCACCCATCATCTCCACCTTC 60.749 57.143 0.00 0.00 0.00 3.46
558 561 0.107456 CCATCATCTCCACCTTCGGG 59.893 60.000 0.00 0.00 41.87 5.14
564 567 1.879575 TCTCCACCTTCGGGATGATT 58.120 50.000 0.00 0.00 38.77 2.57
592 596 3.312736 AAAACTGCAAGGAGGGAGAAA 57.687 42.857 0.00 0.00 39.30 2.52
596 600 2.108952 ACTGCAAGGAGGGAGAAAACAT 59.891 45.455 0.00 0.00 39.30 2.71
598 602 3.157087 TGCAAGGAGGGAGAAAACATTC 58.843 45.455 0.00 0.00 0.00 2.67
635 639 5.895636 AATAGAACGATGAAATGCACCAA 57.104 34.783 0.00 0.00 0.00 3.67
636 640 3.837213 AGAACGATGAAATGCACCAAG 57.163 42.857 0.00 0.00 0.00 3.61
650 654 2.324541 CACCAAGGTTCCCCATGAAAA 58.675 47.619 0.00 0.00 33.94 2.29
653 660 3.582647 ACCAAGGTTCCCCATGAAAAATC 59.417 43.478 0.00 0.00 33.94 2.17
823 849 4.708177 GTGCAGAAGAGGGAAATATGCTA 58.292 43.478 0.00 0.00 33.47 3.49
877 908 1.416401 GACTTGGAGTCTTGTGTCCCA 59.584 52.381 0.97 0.00 41.88 4.37
922 955 2.099756 GGATATTTTCCACACTGCCAGC 59.900 50.000 0.00 0.00 44.74 4.85
923 956 1.164411 TATTTTCCACACTGCCAGCG 58.836 50.000 0.00 0.00 0.00 5.18
924 957 1.526575 ATTTTCCACACTGCCAGCGG 61.527 55.000 0.00 0.00 0.00 5.52
934 967 4.082523 GCCAGCGGCCAGTACTCA 62.083 66.667 2.24 0.00 44.06 3.41
935 968 2.662596 CCAGCGGCCAGTACTCAA 59.337 61.111 2.24 0.00 0.00 3.02
936 969 1.741770 CCAGCGGCCAGTACTCAAC 60.742 63.158 2.24 0.00 0.00 3.18
937 970 1.741770 CAGCGGCCAGTACTCAACC 60.742 63.158 2.24 0.00 0.00 3.77
938 971 2.214216 AGCGGCCAGTACTCAACCA 61.214 57.895 2.24 0.00 0.00 3.67
939 972 1.302192 GCGGCCAGTACTCAACCAA 60.302 57.895 2.24 0.00 0.00 3.67
940 973 1.298859 GCGGCCAGTACTCAACCAAG 61.299 60.000 2.24 0.00 0.00 3.61
941 974 0.034896 CGGCCAGTACTCAACCAAGT 59.965 55.000 2.24 0.00 0.00 3.16
942 975 1.809684 GGCCAGTACTCAACCAAGTC 58.190 55.000 0.00 0.00 0.00 3.01
943 976 1.348036 GGCCAGTACTCAACCAAGTCT 59.652 52.381 0.00 0.00 0.00 3.24
944 977 2.417719 GCCAGTACTCAACCAAGTCTG 58.582 52.381 0.00 0.00 0.00 3.51
945 978 2.417719 CCAGTACTCAACCAAGTCTGC 58.582 52.381 0.00 0.00 0.00 4.26
980 1897 7.730332 TCCTCAAGCCTATAGATGAATAAGTGA 59.270 37.037 0.00 0.00 0.00 3.41
987 1904 8.940952 GCCTATAGATGAATAAGTGATGTTTCC 58.059 37.037 0.00 0.00 0.00 3.13
1005 1943 5.418840 TGTTTCCTTTTGCACTTCTTCTTCT 59.581 36.000 0.00 0.00 0.00 2.85
1020 1959 5.862845 TCTTCTTCTTCTTGCTCAACATCT 58.137 37.500 0.00 0.00 0.00 2.90
1022 1961 5.936686 TCTTCTTCTTGCTCAACATCTTG 57.063 39.130 0.00 0.00 0.00 3.02
1028 1977 4.910195 TCTTGCTCAACATCTTGGTACAT 58.090 39.130 0.00 0.00 39.30 2.29
1056 2005 5.984233 TGAGTAAATTACTTGCCATAGCG 57.016 39.130 7.14 0.00 39.88 4.26
1074 2023 2.187424 CTCCTGCTGCTGCCTCTC 59.813 66.667 13.47 0.00 38.71 3.20
1206 2164 4.202040 TGCCTTGAATCCAGCAATAAATCG 60.202 41.667 0.00 0.00 30.97 3.34
1258 2243 5.129320 TCAATCAGGAAGTTAGCATGCTCTA 59.871 40.000 26.57 11.19 0.00 2.43
1295 2280 0.555769 TTTCACCCAGTTCTTGGCCT 59.444 50.000 3.32 0.00 46.32 5.19
1324 2309 5.208463 TGTCAGCGCCATAGATTACATAA 57.792 39.130 2.29 0.00 0.00 1.90
1444 2429 3.057969 TCAACGATGAGATGCCAAGTT 57.942 42.857 0.00 0.00 0.00 2.66
1452 2437 5.967674 CGATGAGATGCCAAGTTTTTATGAC 59.032 40.000 0.00 0.00 0.00 3.06
1462 2447 9.474920 TGCCAAGTTTTTATGACTATTTCTTTG 57.525 29.630 0.00 0.00 0.00 2.77
1463 2448 9.691362 GCCAAGTTTTTATGACTATTTCTTTGA 57.309 29.630 0.00 0.00 0.00 2.69
1480 2474 8.690203 TTTCTTTGATAGTTCATCTTCAACCA 57.310 30.769 0.00 0.00 34.46 3.67
1518 2512 2.595463 TTCACACCTGCTGCTGCC 60.595 61.111 13.47 0.00 38.71 4.85
1588 2582 8.364142 CAACCCACTTCTTTTATTTGGTGAATA 58.636 33.333 0.00 0.00 0.00 1.75
1645 2639 0.741915 GGTCGTCCCACTCTCAGATC 59.258 60.000 0.00 0.00 0.00 2.75
1647 2641 0.252197 TCGTCCCACTCTCAGATCGA 59.748 55.000 0.00 0.00 0.00 3.59
1649 2643 1.028905 GTCCCACTCTCAGATCGAGG 58.971 60.000 12.54 7.62 42.55 4.63
1650 2644 0.626382 TCCCACTCTCAGATCGAGGT 59.374 55.000 12.54 8.08 42.55 3.85
1653 2647 0.102120 CACTCTCAGATCGAGGTGGC 59.898 60.000 17.70 0.00 42.55 5.01
1655 2649 1.039068 CTCTCAGATCGAGGTGGCAT 58.961 55.000 12.54 0.00 42.55 4.40
1657 2651 1.039068 CTCAGATCGAGGTGGCATCT 58.961 55.000 0.00 0.00 38.18 2.90
1658 2652 1.000385 CTCAGATCGAGGTGGCATCTC 60.000 57.143 17.94 17.94 38.18 2.75
1663 2657 2.959275 CGAGGTGGCATCTCGTTAC 58.041 57.895 35.52 7.64 46.16 2.50
1664 2658 0.527817 CGAGGTGGCATCTCGTTACC 60.528 60.000 35.52 10.11 46.16 2.85
1666 2660 1.139058 GAGGTGGCATCTCGTTACCAT 59.861 52.381 12.77 0.00 34.04 3.55
1668 2662 2.972713 AGGTGGCATCTCGTTACCATAT 59.027 45.455 0.00 0.00 34.04 1.78
1671 2665 5.248477 AGGTGGCATCTCGTTACCATATATT 59.752 40.000 0.00 0.00 34.04 1.28
1672 2666 6.439375 AGGTGGCATCTCGTTACCATATATTA 59.561 38.462 0.00 0.00 34.04 0.98
1678 2699 8.870879 GCATCTCGTTACCATATATTAAAGACC 58.129 37.037 0.00 0.00 0.00 3.85
1697 2718 4.580580 AGACCAAATGTTCCAGAACTTCAC 59.419 41.667 11.56 0.00 41.67 3.18
1735 2756 1.151668 CCTCACTTTTGCTGAGACGG 58.848 55.000 1.66 0.00 37.90 4.79
1742 2763 0.880278 TTTGCTGAGACGGCAGTGTC 60.880 55.000 7.20 7.20 46.84 3.67
1751 2772 0.685097 ACGGCAGTGTCTTGGTATGT 59.315 50.000 0.00 0.00 0.00 2.29
1752 2773 1.078709 CGGCAGTGTCTTGGTATGTG 58.921 55.000 0.00 0.00 0.00 3.21
1755 2776 1.003118 GCAGTGTCTTGGTATGTGGGA 59.997 52.381 0.00 0.00 0.00 4.37
1758 2782 2.567615 AGTGTCTTGGTATGTGGGAGAC 59.432 50.000 0.00 0.00 37.75 3.36
1766 2790 0.817654 TATGTGGGAGACTGCAGACG 59.182 55.000 23.35 0.00 0.00 4.18
1902 3332 9.204570 ACATCATTCTGTTTTACACTGTACTAC 57.795 33.333 0.00 0.00 0.00 2.73
1977 3419 3.524095 TGTGTTTGAATCTCCATGGGT 57.476 42.857 13.02 0.00 0.00 4.51
1979 3421 3.074390 TGTGTTTGAATCTCCATGGGTCT 59.926 43.478 13.02 0.00 0.00 3.85
1980 3422 4.082125 GTGTTTGAATCTCCATGGGTCTT 58.918 43.478 13.02 2.45 0.00 3.01
1981 3423 4.524328 GTGTTTGAATCTCCATGGGTCTTT 59.476 41.667 13.02 0.70 0.00 2.52
1982 3424 4.766891 TGTTTGAATCTCCATGGGTCTTTC 59.233 41.667 13.02 10.68 0.00 2.62
1983 3425 4.934797 TTGAATCTCCATGGGTCTTTCT 57.065 40.909 13.02 0.00 0.00 2.52
1984 3426 4.226427 TGAATCTCCATGGGTCTTTCTG 57.774 45.455 13.02 0.00 0.00 3.02
1985 3427 3.845992 TGAATCTCCATGGGTCTTTCTGA 59.154 43.478 13.02 0.00 0.00 3.27
2145 3630 8.934023 ACTGACCTTAATTAATTTGGAACTCA 57.066 30.769 20.08 14.23 0.00 3.41
2182 3670 7.812669 TGTATTATACATCCTATGCAACACTCG 59.187 37.037 0.29 0.00 32.89 4.18
2236 4153 2.045045 GCAGCCACCACCAGCATA 60.045 61.111 0.00 0.00 0.00 3.14
2237 4154 1.678635 GCAGCCACCACCAGCATAA 60.679 57.895 0.00 0.00 0.00 1.90
2249 4166 2.104792 ACCAGCATAACTACATCCGCAT 59.895 45.455 0.00 0.00 0.00 4.73
2287 5847 2.683362 GGCGAGCTAGCAAGGTATTTTT 59.317 45.455 20.82 0.00 39.27 1.94
2309 5871 2.999331 GGAATGAATCCGGGAGAACAA 58.001 47.619 0.00 0.00 38.79 2.83
2310 5872 2.945668 GGAATGAATCCGGGAGAACAAG 59.054 50.000 0.00 0.00 38.79 3.16
2314 5876 0.404040 AATCCGGGAGAACAAGGCAA 59.596 50.000 0.00 0.00 0.00 4.52
2315 5877 0.322546 ATCCGGGAGAACAAGGCAAC 60.323 55.000 0.00 0.00 0.00 4.17
2316 5878 1.971695 CCGGGAGAACAAGGCAACC 60.972 63.158 0.00 0.00 37.17 3.77
2317 5879 2.325082 CGGGAGAACAAGGCAACCG 61.325 63.158 0.00 0.00 37.17 4.44
2319 5881 1.235281 GGGAGAACAAGGCAACCGAC 61.235 60.000 0.00 0.00 37.17 4.79
2348 6231 4.511527 TGCAGGCATTTTCTGAACAAAAA 58.488 34.783 0.00 0.00 34.36 1.94
2376 6259 2.951642 CACTCAGTCAAAAGGCCTTGAA 59.048 45.455 21.33 4.52 37.08 2.69
2532 6438 6.365970 TCACTCTCTTCTAGAAAAAGGCAT 57.634 37.500 6.63 0.00 32.46 4.40
2537 6443 9.825109 ACTCTCTTCTAGAAAAAGGCATAATAC 57.175 33.333 6.63 0.00 32.46 1.89
2654 6619 6.764308 TTCCTGGCTTTTTATCTCATTCTG 57.236 37.500 0.00 0.00 0.00 3.02
2842 6866 6.436843 AGTAACTGCTTTTAAATCCCGATG 57.563 37.500 0.00 0.00 0.00 3.84
2867 6893 6.875726 GCAATATGCTGATGACCTATTGTCTA 59.124 38.462 0.00 0.00 41.63 2.59
2871 6897 7.741027 ATGCTGATGACCTATTGTCTATTTG 57.259 36.000 0.00 0.00 44.75 2.32
2874 6900 7.611467 TGCTGATGACCTATTGTCTATTTGTTT 59.389 33.333 0.00 0.00 44.75 2.83
2888 6914 8.194769 TGTCTATTTGTTTAGCTACATCATCGA 58.805 33.333 0.00 0.00 0.00 3.59
2903 6929 0.464373 ATCGATGGCCGCATTTGTCT 60.464 50.000 0.00 0.00 38.37 3.41
2936 6962 1.538047 AGTGGCCACTGCACTTTATG 58.462 50.000 37.39 0.00 40.75 1.90
3028 7054 0.250124 CAAAGCCCACGAGGTACACA 60.250 55.000 0.00 0.00 38.26 3.72
3727 7754 3.143741 ACCTCCCTGAGTGGATCTATGAT 59.856 47.826 0.00 0.00 38.35 2.45
3940 7967 6.183360 CCTTCGTCTCATCTGAAAATGAACTC 60.183 42.308 0.00 0.00 35.32 3.01
3998 8025 7.771361 TCTGTCAACATTCAAGGTTGTACTTTA 59.229 33.333 14.28 0.00 44.53 1.85
4030 8057 2.810439 TTGCAACAATAGCAACCACC 57.190 45.000 0.00 0.00 46.13 4.61
4048 8075 3.443037 CACCGTGTTTTGATGCTTTCAA 58.557 40.909 0.00 0.00 42.62 2.69
4065 8096 5.449725 GCTTTCAATCCATTAGGTCTGAAGC 60.450 44.000 0.00 0.00 37.63 3.86
4071 8908 3.126831 CCATTAGGTCTGAAGCGATGTC 58.873 50.000 0.00 0.00 0.00 3.06
4127 8964 6.369065 GTGCTACTAGTTGTTTGCAAGATACT 59.631 38.462 0.00 6.92 38.14 2.12
4146 9005 8.941995 AGATACTGCTACAATCTACTTCCATA 57.058 34.615 0.00 0.00 0.00 2.74
4147 9006 9.540538 AGATACTGCTACAATCTACTTCCATAT 57.459 33.333 0.00 0.00 0.00 1.78
4220 9079 5.934402 ATCTGTTGATTACCTTACTCGGT 57.066 39.130 0.00 0.00 41.10 4.69
4226 9085 7.388437 TGTTGATTACCTTACTCGGTTGTTAT 58.612 34.615 0.00 0.00 38.49 1.89
4228 9087 5.813672 TGATTACCTTACTCGGTTGTTATGC 59.186 40.000 0.00 0.00 38.49 3.14
4244 9103 1.967319 ATGCCGATTAATGTCCGCTT 58.033 45.000 0.00 0.00 0.00 4.68
4245 9104 1.295792 TGCCGATTAATGTCCGCTTC 58.704 50.000 0.00 0.00 0.00 3.86
4247 9106 1.810412 GCCGATTAATGTCCGCTTCCT 60.810 52.381 0.00 0.00 0.00 3.36
4248 9107 1.867233 CCGATTAATGTCCGCTTCCTG 59.133 52.381 0.00 0.00 0.00 3.86
4249 9108 2.550978 CGATTAATGTCCGCTTCCTGT 58.449 47.619 0.00 0.00 0.00 4.00
4250 9109 2.936498 CGATTAATGTCCGCTTCCTGTT 59.064 45.455 0.00 0.00 0.00 3.16
4251 9110 4.116961 CGATTAATGTCCGCTTCCTGTTA 58.883 43.478 0.00 0.00 0.00 2.41
4252 9111 4.209288 CGATTAATGTCCGCTTCCTGTTAG 59.791 45.833 0.00 0.00 0.00 2.34
4253 9112 1.739067 AATGTCCGCTTCCTGTTAGC 58.261 50.000 0.00 0.00 35.29 3.09
4270 9129 1.935799 AGCAGTCAGACCTCACTGAT 58.064 50.000 5.22 0.00 46.36 2.90
4271 9130 3.093057 AGCAGTCAGACCTCACTGATA 57.907 47.619 5.22 0.00 46.36 2.15
4273 9132 3.636300 AGCAGTCAGACCTCACTGATATC 59.364 47.826 5.22 0.00 46.36 1.63
4275 9134 4.142071 GCAGTCAGACCTCACTGATATCAA 60.142 45.833 6.90 0.00 46.36 2.57
4282 9221 4.040047 ACCTCACTGATATCAACCATCCA 58.960 43.478 6.90 0.00 0.00 3.41
4295 9234 2.405559 ACCATCCATGAGCTCATCTGA 58.594 47.619 26.44 23.62 33.61 3.27
4316 9285 5.463286 TGAGAATCAAACATGCACATCAAC 58.537 37.500 0.00 0.00 45.97 3.18
4356 9331 9.840427 ATTTCAGGATAACAACAAACTAAATCG 57.160 29.630 0.00 0.00 0.00 3.34
4357 9332 7.972832 TCAGGATAACAACAAACTAAATCGT 57.027 32.000 0.00 0.00 0.00 3.73
4384 9359 2.356069 GTGGGAGGAATCGAAAATCTGC 59.644 50.000 0.00 0.00 0.00 4.26
4385 9360 2.239654 TGGGAGGAATCGAAAATCTGCT 59.760 45.455 0.00 0.00 0.00 4.24
4386 9361 2.615912 GGGAGGAATCGAAAATCTGCTG 59.384 50.000 0.00 0.00 0.00 4.41
4410 9458 6.436218 TGTGCAGTAGTACCTCTTGATCTTAA 59.564 38.462 0.00 0.00 0.00 1.85
4426 9478 4.467198 TCTTAAACCGTGAGAGGAATCC 57.533 45.455 0.00 0.00 34.73 3.01
4438 9490 1.819632 GGAATCCAATCGCGGCTGT 60.820 57.895 6.13 0.00 0.00 4.40
4441 9493 1.656818 AATCCAATCGCGGCTGTTGG 61.657 55.000 20.57 20.57 42.91 3.77
4442 9494 3.814268 CCAATCGCGGCTGTTGGG 61.814 66.667 19.48 4.35 38.93 4.12
4444 9496 4.344865 AATCGCGGCTGTTGGGGT 62.345 61.111 6.13 0.00 0.00 4.95
4492 9599 2.046314 CACCGATGTGGGGGTCAC 60.046 66.667 0.00 0.00 44.64 3.67
4518 9625 3.393970 AGGCTGCGGCTGCTTCTA 61.394 61.111 27.14 0.00 43.34 2.10
4534 9641 0.178903 TCTACTGCTGGGTTGGGAGT 60.179 55.000 0.00 0.00 38.77 3.85
4539 9646 2.347490 CTGGGTTGGGAGTGGACG 59.653 66.667 0.00 0.00 0.00 4.79
4541 9648 4.717313 GGGTTGGGAGTGGACGGC 62.717 72.222 0.00 0.00 0.00 5.68
4564 9671 4.626081 GCGTGGTGGGCTCACTGT 62.626 66.667 18.03 0.00 43.17 3.55
4577 9684 0.394938 TCACTGTAACCGGCACATGT 59.605 50.000 9.73 0.00 0.00 3.21
4586 9693 2.674033 GGCACATGTCTGCTGCCA 60.674 61.111 17.04 0.00 43.36 4.92
4593 9700 0.040058 ATGTCTGCTGCCATTGGGAA 59.960 50.000 4.53 0.00 35.59 3.97
4684 9805 2.187958 CGGCAGGGAATGGATAGGATA 58.812 52.381 0.00 0.00 0.00 2.59
4714 9835 1.819632 CCCACCATGGCTACTTCGC 60.820 63.158 13.04 0.00 35.79 4.70
4715 9836 1.078497 CCACCATGGCTACTTCGCA 60.078 57.895 13.04 0.00 0.00 5.10
4716 9837 1.369091 CCACCATGGCTACTTCGCAC 61.369 60.000 13.04 0.00 0.00 5.34
4718 9839 1.221840 CCATGGCTACTTCGCACCT 59.778 57.895 0.00 0.00 0.00 4.00
4719 9840 1.091771 CCATGGCTACTTCGCACCTG 61.092 60.000 0.00 0.00 0.00 4.00
4720 9841 1.450312 ATGGCTACTTCGCACCTGC 60.450 57.895 0.00 0.00 37.78 4.85
4757 9878 4.704833 CCCAGGTGTGCTGGACGG 62.705 72.222 0.00 0.00 44.39 4.79
4766 9887 2.512515 GCTGGACGGCACATCCTC 60.513 66.667 0.00 0.00 43.65 3.71
4767 9888 2.202797 CTGGACGGCACATCCTCG 60.203 66.667 0.00 0.00 43.65 4.63
4768 9889 3.723235 CTGGACGGCACATCCTCGG 62.723 68.421 0.00 0.00 43.65 4.63
4769 9890 4.530857 GGACGGCACATCCTCGGG 62.531 72.222 0.00 0.00 37.93 5.14
4774 9895 4.115199 GCACATCCTCGGGGGCTT 62.115 66.667 0.00 0.00 34.39 4.35
4844 9998 9.857957 TTAACTTTTGTTTACAACTCCGAAAAT 57.142 25.926 0.00 0.00 43.32 1.82
4845 9999 8.766000 AACTTTTGTTTACAACTCCGAAAATT 57.234 26.923 0.00 0.00 40.17 1.82
4846 10000 9.857957 AACTTTTGTTTACAACTCCGAAAATTA 57.142 25.926 0.00 0.00 40.17 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.743664 CAATGTGGACTGCGAAGATTCA 59.256 45.455 0.00 0.00 0.00 2.57
44 45 3.684305 TGTAATCAATGTGGACTGCGAAG 59.316 43.478 0.00 0.00 0.00 3.79
50 51 4.640771 AGTGGTGTAATCAATGTGGACT 57.359 40.909 0.00 0.00 0.00 3.85
56 57 9.988350 GACTATTTGTTAGTGGTGTAATCAATG 57.012 33.333 0.00 0.00 41.35 2.82
94 95 5.434408 TCAATGGAAGGATCTCATGTTCAG 58.566 41.667 0.00 0.00 0.00 3.02
128 129 4.939439 ACCAACCTAATAGTTTAGTTGCGG 59.061 41.667 0.00 0.00 34.20 5.69
156 157 1.189524 TTCCATCGTGGGGACGTTCT 61.190 55.000 0.00 0.00 38.32 3.01
160 161 0.178068 AAGATTCCATCGTGGGGACG 59.822 55.000 4.52 0.00 38.32 4.79
173 174 9.323985 AGTTGAGTCTAGCATGATTTAAGATTC 57.676 33.333 0.00 0.00 0.00 2.52
220 221 7.254286 CGTAATCCCTTTTGTTTTTGTTCCTTG 60.254 37.037 0.00 0.00 0.00 3.61
245 246 4.803426 GTGTCAGCCCGAGAGCCG 62.803 72.222 0.00 0.00 38.18 5.52
246 247 3.240134 TTGTGTCAGCCCGAGAGCC 62.240 63.158 0.00 0.00 0.00 4.70
255 256 0.108585 TTGGGGAGAGTTGTGTCAGC 59.891 55.000 0.00 0.00 0.00 4.26
275 276 4.307432 TCTTGTGGCGAGACTCTTTTAAG 58.693 43.478 0.03 0.00 0.00 1.85
279 280 3.244215 TGAATCTTGTGGCGAGACTCTTT 60.244 43.478 0.03 0.00 0.00 2.52
288 289 4.488126 TTTCTTTCTGAATCTTGTGGCG 57.512 40.909 0.00 0.00 34.24 5.69
323 324 8.721478 TGTCAAAGAAGCAACTTATAGCTAAAG 58.279 33.333 0.00 5.88 40.90 1.85
327 328 7.445402 TCTTTGTCAAAGAAGCAACTTATAGCT 59.555 33.333 22.87 0.00 44.10 3.32
367 368 5.105513 TCAAGTTTTTCAAACTCCCAAGGTC 60.106 40.000 2.42 0.00 0.00 3.85
394 395 5.695851 TCTTTCTTGTCTTTCATGCCTTC 57.304 39.130 0.00 0.00 0.00 3.46
397 398 6.925165 TCAAATTCTTTCTTGTCTTTCATGCC 59.075 34.615 0.00 0.00 0.00 4.40
398 399 7.935338 TCAAATTCTTTCTTGTCTTTCATGC 57.065 32.000 0.00 0.00 0.00 4.06
430 433 1.547901 CCTTCACCCTCTTTTCACCCC 60.548 57.143 0.00 0.00 0.00 4.95
456 459 4.898861 TCCCTTATTGCCAAAGTTCTTGTT 59.101 37.500 0.00 0.00 0.00 2.83
468 471 6.317893 TCTCGAAGTTTTATTCCCTTATTGCC 59.682 38.462 0.00 0.00 0.00 4.52
473 476 7.333672 GCTTTCTCTCGAAGTTTTATTCCCTTA 59.666 37.037 0.00 0.00 0.00 2.69
502 505 2.756829 TGTTTCGGAAGCAATCGTGTA 58.243 42.857 4.71 0.00 0.00 2.90
515 518 2.350772 GCTCACCAGTCATTTGTTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
553 556 0.962855 TTGCCGCAAATCATCCCGAA 60.963 50.000 2.50 0.00 0.00 4.30
555 558 0.108898 TTTTGCCGCAAATCATCCCG 60.109 50.000 18.93 0.00 33.19 5.14
558 561 3.710437 CAGTTTTTGCCGCAAATCATC 57.290 42.857 18.93 9.81 33.19 2.92
582 586 4.034285 TCCTTGAATGTTTTCTCCCTCC 57.966 45.455 0.00 0.00 32.78 4.30
596 600 9.932207 TCGTTCTATTACTTTACAATCCTTGAA 57.068 29.630 0.00 0.00 0.00 2.69
650 654 2.171448 GTCCCTAGTGCATCTGTGGATT 59.829 50.000 0.00 0.00 32.53 3.01
653 660 1.198713 AGTCCCTAGTGCATCTGTGG 58.801 55.000 0.00 0.00 0.00 4.17
823 849 2.959030 TGCTCCTAGCTACACAATCGAT 59.041 45.455 0.00 0.00 42.97 3.59
905 938 1.526575 CCGCTGGCAGTGTGGAAAAT 61.527 55.000 25.05 0.00 37.26 1.82
906 939 2.192861 CCGCTGGCAGTGTGGAAAA 61.193 57.895 25.05 0.00 37.26 2.29
907 940 2.594303 CCGCTGGCAGTGTGGAAA 60.594 61.111 25.05 0.00 37.26 3.13
918 951 1.741770 GTTGAGTACTGGCCGCTGG 60.742 63.158 0.00 0.00 0.00 4.85
919 952 1.741770 GGTTGAGTACTGGCCGCTG 60.742 63.158 0.00 0.00 0.00 5.18
920 953 1.764571 TTGGTTGAGTACTGGCCGCT 61.765 55.000 0.00 0.00 0.00 5.52
921 954 1.298859 CTTGGTTGAGTACTGGCCGC 61.299 60.000 0.00 0.00 0.00 6.53
922 955 0.034896 ACTTGGTTGAGTACTGGCCG 59.965 55.000 0.00 0.00 0.00 6.13
923 956 1.348036 AGACTTGGTTGAGTACTGGCC 59.652 52.381 0.00 0.00 0.00 5.36
924 957 2.417719 CAGACTTGGTTGAGTACTGGC 58.582 52.381 0.00 0.00 0.00 4.85
925 958 2.037772 AGCAGACTTGGTTGAGTACTGG 59.962 50.000 0.00 0.00 31.40 4.00
926 959 3.006323 AGAGCAGACTTGGTTGAGTACTG 59.994 47.826 0.00 0.00 34.61 2.74
927 960 3.235200 AGAGCAGACTTGGTTGAGTACT 58.765 45.455 0.00 0.00 34.61 2.73
928 961 3.580731 GAGAGCAGACTTGGTTGAGTAC 58.419 50.000 0.00 0.00 34.61 2.73
929 962 2.563179 GGAGAGCAGACTTGGTTGAGTA 59.437 50.000 0.00 0.00 34.61 2.59
930 963 1.346068 GGAGAGCAGACTTGGTTGAGT 59.654 52.381 0.00 0.00 34.61 3.41
931 964 1.622811 AGGAGAGCAGACTTGGTTGAG 59.377 52.381 0.00 0.00 34.61 3.02
932 965 1.620819 GAGGAGAGCAGACTTGGTTGA 59.379 52.381 0.00 0.00 34.61 3.18
933 966 1.345741 TGAGGAGAGCAGACTTGGTTG 59.654 52.381 0.00 0.00 34.61 3.77
934 967 1.722034 TGAGGAGAGCAGACTTGGTT 58.278 50.000 0.00 0.00 34.61 3.67
935 968 1.830477 GATGAGGAGAGCAGACTTGGT 59.170 52.381 0.00 0.00 37.84 3.67
936 969 1.138661 GGATGAGGAGAGCAGACTTGG 59.861 57.143 0.00 0.00 0.00 3.61
937 970 2.101249 GAGGATGAGGAGAGCAGACTTG 59.899 54.545 0.00 0.00 0.00 3.16
938 971 2.292126 TGAGGATGAGGAGAGCAGACTT 60.292 50.000 0.00 0.00 0.00 3.01
939 972 1.287442 TGAGGATGAGGAGAGCAGACT 59.713 52.381 0.00 0.00 0.00 3.24
940 973 1.774110 TGAGGATGAGGAGAGCAGAC 58.226 55.000 0.00 0.00 0.00 3.51
941 974 2.386779 CTTGAGGATGAGGAGAGCAGA 58.613 52.381 0.00 0.00 0.00 4.26
942 975 1.202557 GCTTGAGGATGAGGAGAGCAG 60.203 57.143 0.00 0.00 0.00 4.24
943 976 0.829333 GCTTGAGGATGAGGAGAGCA 59.171 55.000 0.00 0.00 0.00 4.26
944 977 0.106521 GGCTTGAGGATGAGGAGAGC 59.893 60.000 0.00 0.00 0.00 4.09
945 978 1.792115 AGGCTTGAGGATGAGGAGAG 58.208 55.000 0.00 0.00 0.00 3.20
980 1897 5.859205 AGAAGAAGTGCAAAAGGAAACAT 57.141 34.783 0.00 0.00 0.00 2.71
987 1904 5.458126 GCAAGAAGAAGAAGAAGTGCAAAAG 59.542 40.000 0.00 0.00 0.00 2.27
1005 1943 4.713553 TGTACCAAGATGTTGAGCAAGAA 58.286 39.130 3.74 0.00 35.46 2.52
1056 2005 4.098722 AGAGGCAGCAGCAGGAGC 62.099 66.667 2.65 0.00 44.61 4.70
1258 2243 2.683211 AAAAGGATGGTGTCTTGCCT 57.317 45.000 0.00 0.00 0.00 4.75
1295 2280 4.864704 TCTATGGCGCTGACATTGTATA 57.135 40.909 7.64 0.00 31.56 1.47
1462 2447 9.250624 GTGTACTATGGTTGAAGATGAACTATC 57.749 37.037 0.00 0.00 35.97 2.08
1463 2448 8.982723 AGTGTACTATGGTTGAAGATGAACTAT 58.017 33.333 0.00 0.00 0.00 2.12
1464 2449 8.251026 CAGTGTACTATGGTTGAAGATGAACTA 58.749 37.037 0.00 0.00 0.00 2.24
1474 2468 6.266786 TCTCTTGAACAGTGTACTATGGTTGA 59.733 38.462 0.00 0.00 0.00 3.18
1480 2474 7.014326 TGTGAACTCTCTTGAACAGTGTACTAT 59.986 37.037 0.00 0.00 0.00 2.12
1588 2582 7.923344 CGGAAGAATAGACATGTCTTCATAACT 59.077 37.037 32.14 18.72 45.97 2.24
1647 2641 1.204146 ATGGTAACGAGATGCCACCT 58.796 50.000 0.00 0.00 37.93 4.00
1649 2643 8.542497 TTTAATATATGGTAACGAGATGCCAC 57.458 34.615 0.00 0.00 37.93 5.01
1650 2644 8.590204 TCTTTAATATATGGTAACGAGATGCCA 58.410 33.333 0.00 0.00 39.50 4.92
1653 2647 9.923143 TGGTCTTTAATATATGGTAACGAGATG 57.077 33.333 0.00 0.00 42.51 2.90
1662 2656 9.707957 TGGAACATTTGGTCTTTAATATATGGT 57.292 29.630 0.00 0.00 31.02 3.55
1668 2662 8.934023 AGTTCTGGAACATTTGGTCTTTAATA 57.066 30.769 14.67 0.00 43.47 0.98
1671 2665 6.831353 TGAAGTTCTGGAACATTTGGTCTTTA 59.169 34.615 14.67 0.00 43.47 1.85
1672 2666 5.656416 TGAAGTTCTGGAACATTTGGTCTTT 59.344 36.000 14.67 0.00 43.47 2.52
1678 2699 3.563808 TCCGTGAAGTTCTGGAACATTTG 59.436 43.478 14.67 2.28 43.47 2.32
1680 2701 3.485463 TCCGTGAAGTTCTGGAACATT 57.515 42.857 14.67 6.95 43.47 2.71
1682 2703 2.940410 GTTTCCGTGAAGTTCTGGAACA 59.060 45.455 22.12 14.18 43.47 3.18
1683 2704 2.289820 GGTTTCCGTGAAGTTCTGGAAC 59.710 50.000 22.12 17.72 40.06 3.62
1685 2706 1.539496 CGGTTTCCGTGAAGTTCTGGA 60.539 52.381 11.86 11.86 42.73 3.86
1686 2707 0.865769 CGGTTTCCGTGAAGTTCTGG 59.134 55.000 4.17 6.42 42.73 3.86
1712 2733 3.499918 CGTCTCAGCAAAAGTGAGGATTT 59.500 43.478 0.57 0.00 41.62 2.17
1721 2742 0.236711 CACTGCCGTCTCAGCAAAAG 59.763 55.000 0.00 0.00 40.35 2.27
1735 2756 1.003118 TCCCACATACCAAGACACTGC 59.997 52.381 0.00 0.00 0.00 4.40
1742 2763 1.278985 TGCAGTCTCCCACATACCAAG 59.721 52.381 0.00 0.00 0.00 3.61
1751 2772 0.900182 ACATCGTCTGCAGTCTCCCA 60.900 55.000 14.67 0.00 0.00 4.37
1752 2773 0.459237 CACATCGTCTGCAGTCTCCC 60.459 60.000 14.67 0.00 0.00 4.30
1755 2776 0.108898 GCTCACATCGTCTGCAGTCT 60.109 55.000 14.67 0.00 0.00 3.24
1758 2782 0.108945 TGAGCTCACATCGTCTGCAG 60.109 55.000 13.74 7.63 0.00 4.41
1766 2790 1.812922 CGCCCACTGAGCTCACATC 60.813 63.158 13.74 0.00 0.00 3.06
1902 3332 9.221775 GTAAAATCCTAATTGTATTCGCAACTG 57.778 33.333 0.00 0.00 0.00 3.16
1949 3382 5.875224 TGGAGATTCAAACACATGGAACTA 58.125 37.500 0.00 0.00 0.00 2.24
1977 3419 8.964476 AACTTAGTTGACAGAAATCAGAAAGA 57.036 30.769 0.00 0.00 0.00 2.52
1979 3421 9.396022 AGAAACTTAGTTGACAGAAATCAGAAA 57.604 29.630 0.00 0.00 0.00 2.52
1980 3422 8.964476 AGAAACTTAGTTGACAGAAATCAGAA 57.036 30.769 0.00 0.00 0.00 3.02
1981 3423 8.964476 AAGAAACTTAGTTGACAGAAATCAGA 57.036 30.769 0.00 0.00 0.00 3.27
1982 3424 9.657121 GAAAGAAACTTAGTTGACAGAAATCAG 57.343 33.333 0.00 0.00 0.00 2.90
1983 3425 9.173021 TGAAAGAAACTTAGTTGACAGAAATCA 57.827 29.630 0.00 0.00 0.00 2.57
2124 3609 9.533831 ACTGATGAGTTCCAAATTAATTAAGGT 57.466 29.630 15.44 1.86 0.00 3.50
2162 3647 4.937201 TCGAGTGTTGCATAGGATGTAT 57.063 40.909 0.00 0.00 0.00 2.29
2168 3653 5.741425 CATGTTAATCGAGTGTTGCATAGG 58.259 41.667 0.00 0.00 0.00 2.57
2236 4153 3.350219 AAACCTCATGCGGATGTAGTT 57.650 42.857 16.96 16.93 31.46 2.24
2237 4154 3.704566 TCTAAACCTCATGCGGATGTAGT 59.295 43.478 16.96 12.13 0.00 2.73
2249 4166 1.993391 CCGCCCCCTCTAAACCTCA 60.993 63.158 0.00 0.00 0.00 3.86
2277 5837 6.549736 CCCGGATTCATTCCTAAAAATACCTT 59.450 38.462 0.73 0.00 42.99 3.50
2287 5847 3.380393 TGTTCTCCCGGATTCATTCCTA 58.620 45.455 0.73 0.00 42.99 2.94
2299 5861 2.325082 CGGTTGCCTTGTTCTCCCG 61.325 63.158 0.00 0.00 0.00 5.14
2305 5867 2.184167 CACCGTCGGTTGCCTTGTT 61.184 57.895 15.97 0.00 31.02 2.83
2309 5871 3.231736 AGTCACCGTCGGTTGCCT 61.232 61.111 15.97 7.81 31.02 4.75
2310 5872 3.041940 CAGTCACCGTCGGTTGCC 61.042 66.667 15.97 5.37 31.02 4.52
2314 5876 3.991051 CCTGCAGTCACCGTCGGT 61.991 66.667 12.23 12.23 35.62 4.69
2316 5878 3.939837 ATGCCTGCAGTCACCGTCG 62.940 63.158 13.81 0.00 0.00 5.12
2317 5879 1.237285 AAATGCCTGCAGTCACCGTC 61.237 55.000 13.81 0.00 0.00 4.79
2319 5881 0.109597 GAAAATGCCTGCAGTCACCG 60.110 55.000 13.81 0.00 0.00 4.94
2348 6231 2.301346 CTTTTGACTGAGTGGGCAACT 58.699 47.619 0.00 0.00 43.85 3.16
2376 6259 5.048504 CCATGCACACAACTTTAGAGTCAAT 60.049 40.000 0.00 0.00 34.21 2.57
2511 6411 9.825109 GTATTATGCCTTTTTCTAGAAGAGAGT 57.175 33.333 15.68 7.00 34.93 3.24
2529 6435 7.389607 AGGAACAAATATACCACGGTATTATGC 59.610 37.037 13.79 1.46 41.12 3.14
2532 6438 8.020777 TGAGGAACAAATATACCACGGTATTA 57.979 34.615 13.79 1.80 41.12 0.98
2537 6443 8.311836 AGTATATGAGGAACAAATATACCACGG 58.688 37.037 7.93 0.00 40.05 4.94
2636 6598 7.543520 CCAAGAAACAGAATGAGATAAAAAGCC 59.456 37.037 0.00 0.00 39.69 4.35
2654 6619 4.982295 GTGAACCTGCAAATACCAAGAAAC 59.018 41.667 0.00 0.00 0.00 2.78
2757 6744 7.748847 AGTAGCCAACAATAAGAATTTGTACG 58.251 34.615 0.00 0.00 36.32 3.67
2823 6847 3.088532 TGCATCGGGATTTAAAAGCAGT 58.911 40.909 0.00 0.00 0.00 4.40
2824 6848 3.781079 TGCATCGGGATTTAAAAGCAG 57.219 42.857 0.00 0.00 0.00 4.24
2825 6849 4.734398 ATTGCATCGGGATTTAAAAGCA 57.266 36.364 0.00 0.00 0.00 3.91
2826 6850 5.119125 GCATATTGCATCGGGATTTAAAAGC 59.881 40.000 0.00 0.00 44.26 3.51
2827 6851 6.695292 GCATATTGCATCGGGATTTAAAAG 57.305 37.500 0.00 0.00 44.26 2.27
2842 6866 5.936054 GACAATAGGTCATCAGCATATTGC 58.064 41.667 8.86 0.00 46.19 3.56
2867 6893 6.293626 GCCATCGATGATGTAGCTAAACAAAT 60.294 38.462 26.86 0.00 38.28 2.32
2871 6897 3.433615 GGCCATCGATGATGTAGCTAAAC 59.566 47.826 26.86 4.66 38.28 2.01
2874 6900 1.202348 CGGCCATCGATGATGTAGCTA 59.798 52.381 26.86 0.00 42.43 3.32
2888 6914 1.549203 AGAAAGACAAATGCGGCCAT 58.451 45.000 2.24 0.00 0.00 4.40
2903 6929 1.754226 GGCCACTGTCACCAAAAGAAA 59.246 47.619 0.00 0.00 0.00 2.52
3028 7054 9.598517 CTTGCTATCTTCTTAACTTCAGAGAAT 57.401 33.333 0.00 0.00 0.00 2.40
3256 7282 5.689383 TGAATTCATAAATAAGAGCCCGC 57.311 39.130 3.38 0.00 0.00 6.13
3514 7541 0.036388 TGACGATGCTTTGGTCCCTC 60.036 55.000 0.00 0.00 0.00 4.30
3556 7583 1.027357 CTGGTGCAATGTAGCCCATC 58.973 55.000 0.00 0.00 35.36 3.51
3727 7754 4.111577 ACTCCTCCCCATTGATCACTTTA 58.888 43.478 0.00 0.00 0.00 1.85
3940 7967 5.105228 AGTCCCTGTTTTCATTTATGGCATG 60.105 40.000 10.98 0.00 0.00 4.06
3998 8025 0.511221 GTTGCAACACACGCGTAGAT 59.489 50.000 24.52 0.00 0.00 1.98
4048 8075 3.389329 ACATCGCTTCAGACCTAATGGAT 59.611 43.478 0.00 0.00 37.04 3.41
4065 8096 3.736252 GTCCGGTGATTATTCAGACATCG 59.264 47.826 0.00 0.00 36.76 3.84
4071 8908 4.369182 GGTAGTGTCCGGTGATTATTCAG 58.631 47.826 0.00 0.00 30.85 3.02
4172 9031 4.956085 TGTATTGTACACAGCTCTGTTGT 58.044 39.130 0.00 5.33 42.83 3.32
4176 9035 8.546244 CAGATTATTGTATTGTACACAGCTCTG 58.454 37.037 0.00 0.00 38.63 3.35
4220 9079 3.002862 GCGGACATTAATCGGCATAACAA 59.997 43.478 4.30 0.00 42.72 2.83
4226 9085 1.295792 GAAGCGGACATTAATCGGCA 58.704 50.000 10.21 0.00 44.90 5.69
4228 9087 1.867233 CAGGAAGCGGACATTAATCGG 59.133 52.381 0.00 0.00 0.00 4.18
4230 9089 4.024809 GCTAACAGGAAGCGGACATTAATC 60.025 45.833 0.00 0.00 0.00 1.75
4247 9106 2.297315 CAGTGAGGTCTGACTGCTAACA 59.703 50.000 7.85 0.00 37.94 2.41
4248 9107 2.558795 TCAGTGAGGTCTGACTGCTAAC 59.441 50.000 11.76 0.92 43.12 2.34
4249 9108 2.876581 TCAGTGAGGTCTGACTGCTAA 58.123 47.619 11.76 0.00 43.12 3.09
4250 9109 2.586648 TCAGTGAGGTCTGACTGCTA 57.413 50.000 11.76 0.00 43.12 3.49
4251 9110 1.935799 ATCAGTGAGGTCTGACTGCT 58.064 50.000 11.76 0.99 45.40 4.24
4252 9111 3.382865 TGATATCAGTGAGGTCTGACTGC 59.617 47.826 11.76 0.91 45.40 4.40
4253 9112 5.347342 GTTGATATCAGTGAGGTCTGACTG 58.653 45.833 10.60 10.60 45.40 3.51
4270 9129 4.596212 AGATGAGCTCATGGATGGTTGATA 59.404 41.667 33.33 0.00 36.57 2.15
4271 9130 3.394940 AGATGAGCTCATGGATGGTTGAT 59.605 43.478 33.33 5.78 36.57 2.57
4273 9132 2.879026 CAGATGAGCTCATGGATGGTTG 59.121 50.000 33.33 14.65 36.57 3.77
4275 9134 2.369203 CTCAGATGAGCTCATGGATGGT 59.631 50.000 33.33 8.89 36.57 3.55
4282 9221 5.742063 TGTTTGATTCTCAGATGAGCTCAT 58.258 37.500 29.09 29.09 41.80 2.90
4295 9234 5.466819 CAGTTGATGTGCATGTTTGATTCT 58.533 37.500 0.00 0.00 0.00 2.40
4316 9285 4.836825 TCCTGAAATAAGTGAAGCTCCAG 58.163 43.478 0.00 0.00 0.00 3.86
4356 9331 3.604875 TCGATTCCTCCCACAGTTTAC 57.395 47.619 0.00 0.00 0.00 2.01
4357 9332 4.627284 TTTCGATTCCTCCCACAGTTTA 57.373 40.909 0.00 0.00 0.00 2.01
4384 9359 4.400884 AGATCAAGAGGTACTACTGCACAG 59.599 45.833 0.00 0.00 41.55 3.66
4385 9360 4.344978 AGATCAAGAGGTACTACTGCACA 58.655 43.478 0.00 0.00 41.55 4.57
4386 9361 4.993029 AGATCAAGAGGTACTACTGCAC 57.007 45.455 0.00 0.00 41.55 4.57
4410 9458 2.418746 CGATTGGATTCCTCTCACGGTT 60.419 50.000 3.95 0.00 0.00 4.44
4426 9478 3.814268 CCCCAACAGCCGCGATTG 61.814 66.667 8.23 8.11 0.00 2.67
4438 9490 3.177884 AGCAGCAGTCCACCCCAA 61.178 61.111 0.00 0.00 0.00 4.12
4442 9494 4.341783 AGGCAGCAGCAGTCCACC 62.342 66.667 2.65 0.00 44.61 4.61
4444 9496 3.243816 TCAGGCAGCAGCAGTCCA 61.244 61.111 2.65 0.00 44.61 4.02
4501 9608 3.393970 TAGAAGCAGCCGCAGCCT 61.394 61.111 3.83 0.00 42.27 4.58
4510 9617 1.446907 CAACCCAGCAGTAGAAGCAG 58.553 55.000 0.00 0.00 0.00 4.24
4518 9625 2.833913 CCACTCCCAACCCAGCAGT 61.834 63.158 0.00 0.00 0.00 4.40
4547 9654 2.725203 TTACAGTGAGCCCACCACGC 62.725 60.000 0.00 0.00 44.22 5.34
4548 9655 0.949105 GTTACAGTGAGCCCACCACG 60.949 60.000 0.00 0.00 44.22 4.94
4549 9656 0.605589 GGTTACAGTGAGCCCACCAC 60.606 60.000 0.00 0.00 44.22 4.16
4550 9657 1.758592 GGTTACAGTGAGCCCACCA 59.241 57.895 0.00 0.00 44.22 4.17
4551 9658 1.375523 CGGTTACAGTGAGCCCACC 60.376 63.158 0.00 0.00 44.22 4.61
4552 9659 1.375523 CCGGTTACAGTGAGCCCAC 60.376 63.158 0.00 0.00 43.50 4.61
4553 9660 3.065306 CCGGTTACAGTGAGCCCA 58.935 61.111 0.00 0.00 0.00 5.36
4554 9661 2.436115 GCCGGTTACAGTGAGCCC 60.436 66.667 1.90 0.00 0.00 5.19
4555 9662 2.033194 GTGCCGGTTACAGTGAGCC 61.033 63.158 1.90 0.00 0.00 4.70
4556 9663 0.673644 ATGTGCCGGTTACAGTGAGC 60.674 55.000 16.73 0.00 0.00 4.26
4557 9664 1.078709 CATGTGCCGGTTACAGTGAG 58.921 55.000 16.73 5.79 0.00 3.51
4558 9665 0.394938 ACATGTGCCGGTTACAGTGA 59.605 50.000 16.73 0.00 0.00 3.41
4559 9666 0.796312 GACATGTGCCGGTTACAGTG 59.204 55.000 16.73 15.72 0.00 3.66
4560 9667 0.685097 AGACATGTGCCGGTTACAGT 59.315 50.000 16.73 14.23 0.00 3.55
4561 9668 1.078709 CAGACATGTGCCGGTTACAG 58.921 55.000 16.73 11.89 0.00 2.74
4562 9669 0.953471 GCAGACATGTGCCGGTTACA 60.953 55.000 1.15 14.58 37.49 2.41
4563 9670 0.673644 AGCAGACATGTGCCGGTTAC 60.674 55.000 1.15 3.37 45.20 2.50
4564 9671 0.673333 CAGCAGACATGTGCCGGTTA 60.673 55.000 1.15 0.00 45.20 2.85
4577 9684 1.304381 GGTTCCCAATGGCAGCAGA 60.304 57.895 0.00 0.00 0.00 4.26
4586 9693 4.376170 GCCCCCACGGTTCCCAAT 62.376 66.667 0.00 0.00 0.00 3.16
4595 9702 4.733542 ACCATTTCCGCCCCCACG 62.734 66.667 0.00 0.00 0.00 4.94
4597 9704 4.374584 CCACCATTTCCGCCCCCA 62.375 66.667 0.00 0.00 0.00 4.96
4661 9771 2.754664 CTATCCATTCCCTGCCGCCC 62.755 65.000 0.00 0.00 0.00 6.13
4668 9780 3.578716 CACACGTATCCTATCCATTCCCT 59.421 47.826 0.00 0.00 0.00 4.20
4714 9835 1.376424 ATCTGGCTTCACGCAGGTG 60.376 57.895 0.00 0.00 45.78 4.00
4715 9836 1.376424 CATCTGGCTTCACGCAGGT 60.376 57.895 0.00 0.00 41.67 4.00
4716 9837 2.110967 CCATCTGGCTTCACGCAGG 61.111 63.158 0.00 0.00 41.67 4.85
4718 9839 2.046023 CCCATCTGGCTTCACGCA 60.046 61.111 0.00 0.00 41.67 5.24
4742 9863 4.624364 TGCCGTCCAGCACACCTG 62.624 66.667 0.00 0.00 38.00 4.00
4748 9869 3.315142 GAGGATGTGCCGTCCAGCA 62.315 63.158 13.80 0.00 41.68 4.41
4749 9870 2.512515 GAGGATGTGCCGTCCAGC 60.513 66.667 13.80 4.25 41.68 4.85
4750 9871 2.202797 CGAGGATGTGCCGTCCAG 60.203 66.667 13.80 5.72 41.68 3.86
4751 9872 3.770040 CCGAGGATGTGCCGTCCA 61.770 66.667 13.80 0.00 41.68 4.02
4752 9873 4.530857 CCCGAGGATGTGCCGTCC 62.531 72.222 5.54 5.54 43.43 4.79
4753 9874 4.530857 CCCCGAGGATGTGCCGTC 62.531 72.222 0.00 0.00 43.43 4.79
4757 9878 3.645268 AAAGCCCCCGAGGATGTGC 62.645 63.158 0.00 0.00 38.24 4.57
4760 9881 4.764143 AAAAAGCCCCCGAGGATG 57.236 55.556 0.00 0.00 38.24 3.51


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

AutoCloner maintained by Alex Coulton.