Multiple sequence alignment - TraesCS5A01G504000

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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 TraesCS5A01G504000 chr5A 100.000 2957 0 0 1650 4606 669739664 669742620 0.000000e+00 5461.0
1 TraesCS5A01G504000 chr5A 100.000 1351 0 0 1 1351 669738015 669739365 0.000000e+00 2495.0
2 TraesCS5A01G504000 chr5A 86.339 915 117 5 1 909 102975756 102976668 0.000000e+00 990.0
3 TraesCS5A01G504000 chr5A 98.438 64 1 0 913 976 616020580 616020643 3.770000e-21 113.0
4 TraesCS5A01G504000 chr5A 94.737 38 2 0 2752 2789 606485989 606486026 4.980000e-05 60.2
5 TraesCS5A01G504000 chr4D 93.398 1030 34 15 3590 4602 488037122 488038134 0.000000e+00 1495.0
6 TraesCS5A01G504000 chr4D 93.608 923 56 3 1 921 493730103 493731024 0.000000e+00 1375.0
7 TraesCS5A01G504000 chr4D 96.810 627 15 4 2982 3607 488034621 488035243 0.000000e+00 1042.0
8 TraesCS5A01G504000 chr4D 95.735 422 14 3 1650 2071 488033946 488034363 0.000000e+00 676.0
9 TraesCS5A01G504000 chr4D 78.505 856 143 27 2982 3806 487875737 487876582 1.470000e-144 523.0
10 TraesCS5A01G504000 chr4D 98.712 233 3 0 2065 2297 488034396 488034628 9.220000e-112 414.0
11 TraesCS5A01G504000 chr4D 95.918 245 7 1 1110 1351 488033678 488033922 1.200000e-105 394.0
12 TraesCS5A01G504000 chr4D 96.535 202 5 1 913 1114 488028506 488028705 2.660000e-87 333.0
13 TraesCS5A01G504000 chr4D 89.683 126 11 2 2784 2908 105237930 105237806 4.770000e-35 159.0
14 TraesCS5A01G504000 chr1B 91.703 916 73 3 1 914 268422878 268423792 0.000000e+00 1267.0
15 TraesCS5A01G504000 chr1B 89.922 129 9 4 2782 2907 62792985 62793112 3.690000e-36 163.0
16 TraesCS5A01G504000 chr1B 98.438 64 1 0 913 976 542640550 542640613 3.770000e-21 113.0
17 TraesCS5A01G504000 chr1B 95.161 62 3 0 913 974 542635068 542635129 1.050000e-16 99.0
18 TraesCS5A01G504000 chr1B 91.935 62 5 0 913 974 542632952 542633013 2.280000e-13 87.9
19 TraesCS5A01G504000 chr7A 97.829 691 12 3 2294 2981 663963015 663962325 0.000000e+00 1190.0
20 TraesCS5A01G504000 chr7A 78.095 840 160 19 2982 3806 621312542 621313372 1.140000e-140 510.0
21 TraesCS5A01G504000 chr7A 81.933 238 31 5 2298 2523 640542469 640542706 1.690000e-44 191.0
22 TraesCS5A01G504000 chr7A 94.737 38 2 0 2752 2789 507687703 507687740 4.980000e-05 60.2
23 TraesCS5A01G504000 chr7A 94.737 38 2 0 2752 2789 640542767 640542804 4.980000e-05 60.2
24 TraesCS5A01G504000 chr7A 94.737 38 2 0 2752 2789 682200404 682200367 4.980000e-05 60.2
25 TraesCS5A01G504000 chr4A 91.284 849 53 4 1 849 743917499 743918326 0.000000e+00 1138.0
26 TraesCS5A01G504000 chr4A 89.516 124 12 1 2785 2907 702148786 702148909 6.170000e-34 156.0
27 TraesCS5A01G504000 chr7B 86.132 923 120 7 1 919 448654046 448653128 0.000000e+00 989.0
28 TraesCS5A01G504000 chr7B 77.869 854 155 20 2982 3806 582938148 582938996 2.470000e-137 499.0
29 TraesCS5A01G504000 chr7B 89.600 125 11 2 2785 2908 619077867 619077990 1.720000e-34 158.0
30 TraesCS5A01G504000 chr7B 88.889 63 5 2 855 915 32357987 32358049 4.940000e-10 76.8
31 TraesCS5A01G504000 chr3B 85.099 859 122 5 4 860 245972003 245971149 0.000000e+00 872.0
32 TraesCS5A01G504000 chr3B 85.075 268 31 6 2293 2557 380681624 380681885 9.830000e-67 265.0
33 TraesCS5A01G504000 chr4B 90.931 419 34 3 1650 2066 623655127 623655543 1.120000e-155 560.0
34 TraesCS5A01G504000 chr4B 79.113 857 136 28 2982 3806 623646226 623647071 6.740000e-153 551.0
35 TraesCS5A01G504000 chr4B 78.830 855 143 24 2982 3806 623787016 623787862 4.050000e-150 542.0
36 TraesCS5A01G504000 chr4B 92.275 233 18 0 2065 2297 623655580 623655812 9.550000e-87 331.0
37 TraesCS5A01G504000 chr6B 81.573 483 66 11 3 482 281341650 281341188 1.210000e-100 377.0
38 TraesCS5A01G504000 chr3A 84.758 269 32 6 2292 2557 377145995 377146257 1.270000e-65 261.0
39 TraesCS5A01G504000 chr3A 96.923 65 2 0 913 977 686822139 686822203 4.870000e-20 110.0
40 TraesCS5A01G504000 chr2D 81.944 288 44 6 632 913 80418309 80418594 2.140000e-58 237.0
41 TraesCS5A01G504000 chr2D 89.683 126 12 1 2783 2907 441085892 441085767 4.770000e-35 159.0
42 TraesCS5A01G504000 chr2D 89.600 125 11 2 2785 2908 116827300 116827423 1.720000e-34 158.0
43 TraesCS5A01G504000 chr2A 81.513 238 32 9 2298 2523 750325872 750326109 7.870000e-43 185.0
44 TraesCS5A01G504000 chr2A 94.737 38 2 0 2752 2789 750326168 750326205 4.980000e-05 60.2
45 TraesCS5A01G504000 chr7D 80.000 245 35 11 2065 2297 539950198 539950440 7.930000e-38 169.0
46 TraesCS5A01G504000 chr7D 87.692 65 7 1 849 912 492816003 492815939 1.780000e-09 75.0
47 TraesCS5A01G504000 chr5D 90.400 125 10 2 2785 2908 97831847 97831724 3.690000e-36 163.0
48 TraesCS5A01G504000 chrUn 91.525 118 8 2 2792 2907 311697997 311697880 1.330000e-35 161.0


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 TraesCS5A01G504000 chr5A 669738015 669742620 4605 False 3978.0 5461 100.0000 1 4606 2 chr5A.!!$F4 4605
1 TraesCS5A01G504000 chr5A 102975756 102976668 912 False 990.0 990 86.3390 1 909 1 chr5A.!!$F1 908
2 TraesCS5A01G504000 chr4D 493730103 493731024 921 False 1375.0 1375 93.6080 1 921 1 chr4D.!!$F3 920
3 TraesCS5A01G504000 chr4D 488033678 488038134 4456 False 804.2 1495 96.1146 1110 4602 5 chr4D.!!$F4 3492
4 TraesCS5A01G504000 chr4D 487875737 487876582 845 False 523.0 523 78.5050 2982 3806 1 chr4D.!!$F1 824
5 TraesCS5A01G504000 chr1B 268422878 268423792 914 False 1267.0 1267 91.7030 1 914 1 chr1B.!!$F2 913
6 TraesCS5A01G504000 chr7A 663962325 663963015 690 True 1190.0 1190 97.8290 2294 2981 1 chr7A.!!$R1 687
7 TraesCS5A01G504000 chr7A 621312542 621313372 830 False 510.0 510 78.0950 2982 3806 1 chr7A.!!$F2 824
8 TraesCS5A01G504000 chr4A 743917499 743918326 827 False 1138.0 1138 91.2840 1 849 1 chr4A.!!$F2 848
9 TraesCS5A01G504000 chr7B 448653128 448654046 918 True 989.0 989 86.1320 1 919 1 chr7B.!!$R1 918
10 TraesCS5A01G504000 chr7B 582938148 582938996 848 False 499.0 499 77.8690 2982 3806 1 chr7B.!!$F2 824
11 TraesCS5A01G504000 chr3B 245971149 245972003 854 True 872.0 872 85.0990 4 860 1 chr3B.!!$R1 856
12 TraesCS5A01G504000 chr4B 623646226 623647071 845 False 551.0 551 79.1130 2982 3806 1 chr4B.!!$F1 824
13 TraesCS5A01G504000 chr4B 623787016 623787862 846 False 542.0 542 78.8300 2982 3806 1 chr4B.!!$F2 824
14 TraesCS5A01G504000 chr4B 623655127 623655812 685 False 445.5 560 91.6030 1650 2297 2 chr4B.!!$F3 647

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
953 963 0.036875 AAGAGTAGCGGCCAAAGCTT 59.963 50.000 9.02 0.0 43.24 3.74 F
1007 1017 0.106167 TGCTAGGCGGAGATGGTACT 60.106 55.000 0.00 0.0 0.00 2.73 F
1008 1018 1.144298 TGCTAGGCGGAGATGGTACTA 59.856 52.381 0.00 0.0 0.00 1.82 F
1009 1019 1.540707 GCTAGGCGGAGATGGTACTAC 59.459 57.143 0.00 0.0 0.00 2.73 F
1042 1052 1.891811 TGCGATTCAAATTGGCTTCCA 59.108 42.857 0.00 0.0 0.00 3.53 F
1043 1053 2.496871 TGCGATTCAAATTGGCTTCCAT 59.503 40.909 0.00 0.0 31.53 3.41 F
2289 2340 2.624838 GGTTTCATATGGGCAGATGGTG 59.375 50.000 2.13 0.0 31.37 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2384 0.413434 AATTTTAGGGGCCCTGTGCT 59.587 50.000 35.70 13.04 40.92 4.40 R
2599 2651 6.609212 TGGAGAAGAATAGTAGCAGAACAGAT 59.391 38.462 0.00 0.00 0.00 2.90 R
2860 2913 7.393234 ACTTGTCGGAGAAATGGATAAAAATGA 59.607 33.333 0.00 0.00 39.69 2.57 R
2904 2957 9.262358 AGGCTCTTTATATGAAGAAAATCGTAC 57.738 33.333 10.79 0.00 35.38 3.67 R
3443 3504 1.153188 ATCGGTGAATGATGCGGCA 60.153 52.632 4.58 4.58 0.00 5.69 R
3485 3546 3.273434 TGCTGTGATTGGTCTGCTATTC 58.727 45.455 0.00 0.00 0.00 1.75 R
4345 6331 0.175531 GCAAGCGGTAAAATGCCCAT 59.824 50.000 0.00 0.00 32.73 4.00 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
33 34 6.334989 CAAAGATAAATGGCAAGATCAAGCA 58.665 36.000 10.91 0.00 0.00 3.91
213 215 5.645497 ACAGTTGCATCTTCATAGAAAGGAC 59.355 40.000 0.00 0.00 33.20 3.85
215 217 6.149973 CAGTTGCATCTTCATAGAAAGGACAA 59.850 38.462 0.00 0.00 33.20 3.18
216 218 6.150140 AGTTGCATCTTCATAGAAAGGACAAC 59.850 38.462 0.00 0.00 33.20 3.32
274 276 7.172190 CAGCTATTCACATCTATAACCAACTGG 59.828 40.741 0.00 0.00 42.17 4.00
317 320 6.547141 CACCCATTCTTTAGCATTATCTGGAA 59.453 38.462 0.00 0.00 0.00 3.53
319 322 6.293626 CCCATTCTTTAGCATTATCTGGAACG 60.294 42.308 0.00 0.00 0.00 3.95
345 348 7.803659 GGTTCTAGCAGACTAAAACACAAAATC 59.196 37.037 0.00 0.00 31.96 2.17
348 351 9.772973 TCTAGCAGACTAAAACACAAAATCTTA 57.227 29.630 0.00 0.00 0.00 2.10
365 368 2.294791 TCTTATTTTGGTTGGTGGCACG 59.705 45.455 12.17 0.00 0.00 5.34
409 413 6.407202 GCACTTCTAGGTAGAAAAGGAATGA 58.593 40.000 1.26 0.00 41.37 2.57
444 448 3.985019 TTCTGCCCAAATTGCAATCAT 57.015 38.095 13.38 1.84 38.46 2.45
541 545 4.963318 AACAGACAGAGAGGAACATCAA 57.037 40.909 0.00 0.00 0.00 2.57
546 550 7.721402 ACAGACAGAGAGGAACATCAATATAC 58.279 38.462 0.00 0.00 0.00 1.47
600 604 4.319911 CCAAAACCATTTGCTGCTGAAATG 60.320 41.667 14.93 14.93 43.73 2.32
655 659 6.709846 ACAGAGAAATGGAAAAGTCTTCAGAG 59.290 38.462 0.00 0.00 0.00 3.35
667 671 0.683973 CTTCAGAGCACTCCCACACT 59.316 55.000 0.00 0.00 0.00 3.55
715 719 7.690256 TCTTAAGCAAGATTTAGGACTCCTTT 58.310 34.615 1.94 0.00 35.82 3.11
717 721 4.013050 AGCAAGATTTAGGACTCCTTTGC 58.987 43.478 18.25 18.25 40.56 3.68
731 735 6.405176 GGACTCCTTTGCCATAAGATCAAAAG 60.405 42.308 0.00 0.00 30.47 2.27
804 808 8.814038 AGCATGATTTCTTTTCCTATAACTGT 57.186 30.769 0.00 0.00 0.00 3.55
812 816 5.885912 TCTTTTCCTATAACTGTCATTGGCC 59.114 40.000 0.00 0.00 0.00 5.36
863 870 8.376270 CCCTTGGGGTTTGTAACATATTTTTAA 58.624 33.333 0.00 0.00 38.25 1.52
908 918 4.956700 TGTTCTATGGTGTTGGGTTCAAAA 59.043 37.500 0.00 0.00 34.28 2.44
909 919 5.422331 TGTTCTATGGTGTTGGGTTCAAAAA 59.578 36.000 0.00 0.00 34.28 1.94
934 944 2.932663 GCTACAAACAGCCAGCTGA 58.067 52.632 25.66 2.26 46.30 4.26
935 945 1.238439 GCTACAAACAGCCAGCTGAA 58.762 50.000 25.66 5.20 46.30 3.02
936 946 1.198637 GCTACAAACAGCCAGCTGAAG 59.801 52.381 25.66 15.75 46.30 3.02
937 947 2.771089 CTACAAACAGCCAGCTGAAGA 58.229 47.619 25.66 5.65 46.30 2.87
938 948 1.602311 ACAAACAGCCAGCTGAAGAG 58.398 50.000 25.66 13.84 46.30 2.85
939 949 1.133976 ACAAACAGCCAGCTGAAGAGT 60.134 47.619 25.66 14.42 46.30 3.24
940 950 2.104792 ACAAACAGCCAGCTGAAGAGTA 59.895 45.455 25.66 0.00 46.30 2.59
941 951 2.740981 CAAACAGCCAGCTGAAGAGTAG 59.259 50.000 25.66 0.00 46.30 2.57
942 952 0.248843 ACAGCCAGCTGAAGAGTAGC 59.751 55.000 25.66 8.12 46.30 3.58
943 953 0.805322 CAGCCAGCTGAAGAGTAGCG 60.805 60.000 17.39 1.17 46.30 4.26
944 954 1.520342 GCCAGCTGAAGAGTAGCGG 60.520 63.158 17.39 0.00 45.61 5.52
945 955 1.520342 CCAGCTGAAGAGTAGCGGC 60.520 63.158 17.39 0.00 45.61 6.53
946 956 1.520342 CAGCTGAAGAGTAGCGGCC 60.520 63.158 8.42 0.00 45.61 6.13
947 957 1.984570 AGCTGAAGAGTAGCGGCCA 60.985 57.895 2.24 0.00 45.61 5.36
948 958 1.079127 GCTGAAGAGTAGCGGCCAA 60.079 57.895 2.24 0.00 0.00 4.52
949 959 0.673644 GCTGAAGAGTAGCGGCCAAA 60.674 55.000 2.24 0.00 0.00 3.28
950 960 1.363744 CTGAAGAGTAGCGGCCAAAG 58.636 55.000 2.24 0.00 0.00 2.77
951 961 0.673644 TGAAGAGTAGCGGCCAAAGC 60.674 55.000 2.24 0.00 38.76 3.51
953 963 0.036875 AAGAGTAGCGGCCAAAGCTT 59.963 50.000 9.02 0.00 43.24 3.74
954 964 0.391793 AGAGTAGCGGCCAAAGCTTC 60.392 55.000 9.02 4.38 43.24 3.86
955 965 0.673644 GAGTAGCGGCCAAAGCTTCA 60.674 55.000 9.02 0.00 43.24 3.02
956 966 0.674895 AGTAGCGGCCAAAGCTTCAG 60.675 55.000 9.02 0.00 43.24 3.02
957 967 2.040544 TAGCGGCCAAAGCTTCAGC 61.041 57.895 9.02 11.28 43.24 4.26
967 977 2.743928 GCTTCAGCTCCACCACCG 60.744 66.667 0.00 0.00 38.21 4.94
968 978 2.743928 CTTCAGCTCCACCACCGC 60.744 66.667 0.00 0.00 0.00 5.68
969 979 4.329545 TTCAGCTCCACCACCGCC 62.330 66.667 0.00 0.00 0.00 6.13
971 981 4.335647 CAGCTCCACCACCGCCTT 62.336 66.667 0.00 0.00 0.00 4.35
972 982 4.335647 AGCTCCACCACCGCCTTG 62.336 66.667 0.00 0.00 0.00 3.61
973 983 4.329545 GCTCCACCACCGCCTTGA 62.330 66.667 0.00 0.00 0.00 3.02
974 984 2.358737 CTCCACCACCGCCTTGAC 60.359 66.667 0.00 0.00 0.00 3.18
975 985 3.164977 TCCACCACCGCCTTGACA 61.165 61.111 0.00 0.00 0.00 3.58
976 986 2.203280 CCACCACCGCCTTGACAA 60.203 61.111 0.00 0.00 0.00 3.18
977 987 1.603455 CCACCACCGCCTTGACAAT 60.603 57.895 0.00 0.00 0.00 2.71
978 988 0.322098 CCACCACCGCCTTGACAATA 60.322 55.000 0.00 0.00 0.00 1.90
979 989 1.681780 CCACCACCGCCTTGACAATAT 60.682 52.381 0.00 0.00 0.00 1.28
980 990 2.091541 CACCACCGCCTTGACAATATT 58.908 47.619 0.00 0.00 0.00 1.28
981 991 2.091541 ACCACCGCCTTGACAATATTG 58.908 47.619 14.01 14.01 0.00 1.90
982 992 1.202290 CCACCGCCTTGACAATATTGC 60.202 52.381 15.48 8.85 0.00 3.56
983 993 1.472082 CACCGCCTTGACAATATTGCA 59.528 47.619 15.48 11.25 0.00 4.08
984 994 2.099592 CACCGCCTTGACAATATTGCAT 59.900 45.455 15.48 0.00 0.00 3.96
985 995 3.314913 CACCGCCTTGACAATATTGCATA 59.685 43.478 15.48 0.00 0.00 3.14
986 996 3.565482 ACCGCCTTGACAATATTGCATAG 59.435 43.478 15.48 9.32 0.00 2.23
987 997 3.814842 CCGCCTTGACAATATTGCATAGA 59.185 43.478 15.48 0.16 0.00 1.98
988 998 4.456911 CCGCCTTGACAATATTGCATAGAT 59.543 41.667 15.48 0.00 0.00 1.98
989 999 5.388111 CGCCTTGACAATATTGCATAGATG 58.612 41.667 15.48 0.25 0.00 2.90
1002 1012 3.162202 CATAGATGCTAGGCGGAGATG 57.838 52.381 0.00 0.00 0.00 2.90
1003 1013 1.550327 TAGATGCTAGGCGGAGATGG 58.450 55.000 0.00 0.00 0.00 3.51
1004 1014 0.470833 AGATGCTAGGCGGAGATGGT 60.471 55.000 0.00 0.00 0.00 3.55
1005 1015 1.203063 AGATGCTAGGCGGAGATGGTA 60.203 52.381 0.00 0.00 0.00 3.25
1006 1016 0.969894 ATGCTAGGCGGAGATGGTAC 59.030 55.000 0.00 0.00 0.00 3.34
1007 1017 0.106167 TGCTAGGCGGAGATGGTACT 60.106 55.000 0.00 0.00 0.00 2.73
1008 1018 1.144298 TGCTAGGCGGAGATGGTACTA 59.856 52.381 0.00 0.00 0.00 1.82
1009 1019 1.540707 GCTAGGCGGAGATGGTACTAC 59.459 57.143 0.00 0.00 0.00 2.73
1010 1020 2.860009 CTAGGCGGAGATGGTACTACA 58.140 52.381 0.00 0.00 0.00 2.74
1011 1021 2.383442 AGGCGGAGATGGTACTACAT 57.617 50.000 0.00 0.00 0.00 2.29
1012 1022 2.240279 AGGCGGAGATGGTACTACATC 58.760 52.381 4.45 4.45 45.91 3.06
1037 1047 4.764940 GCAATAATGCGATTCAAATTGGC 58.235 39.130 0.00 0.00 43.83 4.52
1038 1048 4.508861 GCAATAATGCGATTCAAATTGGCT 59.491 37.500 0.00 0.00 43.83 4.75
1039 1049 5.006941 GCAATAATGCGATTCAAATTGGCTT 59.993 36.000 0.00 0.00 43.83 4.35
1040 1050 6.642917 CAATAATGCGATTCAAATTGGCTTC 58.357 36.000 0.00 0.00 32.68 3.86
1041 1051 2.652941 TGCGATTCAAATTGGCTTCC 57.347 45.000 0.00 0.00 0.00 3.46
1042 1052 1.891811 TGCGATTCAAATTGGCTTCCA 59.108 42.857 0.00 0.00 0.00 3.53
1043 1053 2.496871 TGCGATTCAAATTGGCTTCCAT 59.503 40.909 0.00 0.00 31.53 3.41
1044 1054 2.861935 GCGATTCAAATTGGCTTCCATG 59.138 45.455 0.00 0.00 31.53 3.66
1045 1055 3.676873 GCGATTCAAATTGGCTTCCATGT 60.677 43.478 0.00 0.00 31.53 3.21
1046 1056 4.439974 GCGATTCAAATTGGCTTCCATGTA 60.440 41.667 0.00 0.00 31.53 2.29
1047 1057 5.649557 CGATTCAAATTGGCTTCCATGTAA 58.350 37.500 0.00 0.00 31.53 2.41
1048 1058 5.745294 CGATTCAAATTGGCTTCCATGTAAG 59.255 40.000 0.00 0.00 31.53 2.34
1049 1059 6.610075 ATTCAAATTGGCTTCCATGTAAGT 57.390 33.333 0.00 0.00 31.53 2.24
1050 1060 5.389859 TCAAATTGGCTTCCATGTAAGTG 57.610 39.130 0.00 0.00 31.53 3.16
1051 1061 5.076182 TCAAATTGGCTTCCATGTAAGTGA 58.924 37.500 0.00 0.00 31.53 3.41
1052 1062 5.048083 TCAAATTGGCTTCCATGTAAGTGAC 60.048 40.000 0.00 0.00 31.53 3.67
1053 1063 3.500448 TTGGCTTCCATGTAAGTGACA 57.500 42.857 0.00 0.00 43.97 3.58
1067 1077 7.595819 TGTAAGTGACATTTTTCTTCCCATT 57.404 32.000 0.00 0.00 31.20 3.16
1068 1078 7.657336 TGTAAGTGACATTTTTCTTCCCATTC 58.343 34.615 0.00 0.00 31.20 2.67
1069 1079 6.729690 AAGTGACATTTTTCTTCCCATTCA 57.270 33.333 0.00 0.00 0.00 2.57
1070 1080 6.923199 AGTGACATTTTTCTTCCCATTCAT 57.077 33.333 0.00 0.00 0.00 2.57
1071 1081 6.694447 AGTGACATTTTTCTTCCCATTCATG 58.306 36.000 0.00 0.00 0.00 3.07
1085 1095 4.303086 CATTCATGGAGCCTCACAATTC 57.697 45.455 0.00 0.00 0.00 2.17
1086 1096 3.438216 TTCATGGAGCCTCACAATTCA 57.562 42.857 0.00 0.00 0.00 2.57
1087 1097 3.438216 TCATGGAGCCTCACAATTCAA 57.562 42.857 0.00 0.00 0.00 2.69
1088 1098 3.765381 TCATGGAGCCTCACAATTCAAA 58.235 40.909 0.00 0.00 0.00 2.69
1089 1099 4.346730 TCATGGAGCCTCACAATTCAAAT 58.653 39.130 0.00 0.00 0.00 2.32
1090 1100 5.508567 TCATGGAGCCTCACAATTCAAATA 58.491 37.500 0.00 0.00 0.00 1.40
1091 1101 5.951148 TCATGGAGCCTCACAATTCAAATAA 59.049 36.000 0.00 0.00 0.00 1.40
1092 1102 6.436847 TCATGGAGCCTCACAATTCAAATAAA 59.563 34.615 0.00 0.00 0.00 1.40
1093 1103 6.855763 TGGAGCCTCACAATTCAAATAAAT 57.144 33.333 0.00 0.00 0.00 1.40
1094 1104 7.243604 TGGAGCCTCACAATTCAAATAAATT 57.756 32.000 0.00 0.00 0.00 1.82
1095 1105 7.678837 TGGAGCCTCACAATTCAAATAAATTT 58.321 30.769 0.00 0.00 0.00 1.82
1096 1106 7.603404 TGGAGCCTCACAATTCAAATAAATTTG 59.397 33.333 8.79 8.79 46.39 2.32
1097 1107 7.064966 GGAGCCTCACAATTCAAATAAATTTGG 59.935 37.037 13.89 2.73 45.39 3.28
1098 1108 7.452562 AGCCTCACAATTCAAATAAATTTGGT 58.547 30.769 13.89 3.26 45.39 3.67
1099 1109 8.592809 AGCCTCACAATTCAAATAAATTTGGTA 58.407 29.630 13.89 5.07 45.39 3.25
1100 1110 9.382275 GCCTCACAATTCAAATAAATTTGGTAT 57.618 29.630 13.89 6.80 45.39 2.73
1188 1198 6.260050 TCCAAATTTATTAGACATCCTCACGC 59.740 38.462 0.00 0.00 0.00 5.34
1272 1282 5.592104 AAAAGGTGGGAAACTTGTGTTAG 57.408 39.130 0.00 0.00 34.96 2.34
1281 1291 6.605594 TGGGAAACTTGTGTTAGTTTTCTCAT 59.394 34.615 7.30 0.00 45.68 2.90
1761 1774 8.985315 TCATTAAGAGAGCATTTATCCACATT 57.015 30.769 0.00 0.00 0.00 2.71
1951 1964 4.897140 TGTTAGCACTATTAAACGGTGGT 58.103 39.130 12.57 12.57 42.87 4.16
1952 1965 5.307204 TGTTAGCACTATTAAACGGTGGTT 58.693 37.500 12.98 0.00 41.10 3.67
2033 2046 8.520835 TTATTTTCTCATATCGTCTCCATTCG 57.479 34.615 0.00 0.00 0.00 3.34
2277 2328 3.686227 TGGATTGCCCTGGTTTCATAT 57.314 42.857 0.00 0.00 35.38 1.78
2289 2340 2.624838 GGTTTCATATGGGCAGATGGTG 59.375 50.000 2.13 0.00 31.37 4.17
2599 2651 5.538813 AGCATCATATCCGGAACTAGTACAA 59.461 40.000 9.01 0.00 0.00 2.41
2645 2697 5.472137 TCCAGTTTTTCCGTTATCCTTGAAG 59.528 40.000 0.00 0.00 0.00 3.02
2750 2802 7.270779 TCTCAACATCCATCTCTCTTGTATTG 58.729 38.462 0.00 0.00 0.00 1.90
2826 2879 6.712998 TCCAGAAATACTTGTCGGAAAAATGA 59.287 34.615 0.00 0.00 0.00 2.57
2897 2950 3.916172 TCTCCGACAAGTATTTTCGAACG 59.084 43.478 0.00 0.00 34.62 3.95
2904 2957 4.689345 ACAAGTATTTTCGAACGGAGGAAG 59.311 41.667 0.00 0.00 0.00 3.46
3440 3501 3.391098 CCAAATGGTGGCAAGGGG 58.609 61.111 0.00 0.00 41.72 4.79
3443 3504 3.826265 AAATGGTGGCAAGGGGCGT 62.826 57.895 0.00 0.00 46.16 5.68
3485 3546 5.761726 TCTTCGATTCATTGATCAGAATGGG 59.238 40.000 13.33 6.86 34.79 4.00
3520 3581 0.944386 ACAGCAAACGTGACCATGTC 59.056 50.000 0.00 0.00 0.00 3.06
3749 5724 2.125673 TCGCGCTTAGCTTGACCC 60.126 61.111 5.56 0.00 45.59 4.46
3824 5802 1.281419 TCCTCCTTGGCAATTCCGTA 58.719 50.000 0.00 0.00 37.80 4.02
3837 5815 2.561733 TTCCGTATGTTCTCTGCTCG 57.438 50.000 0.00 0.00 0.00 5.03
3894 5872 1.448540 CTTCAGTACGGCAGGCCAG 60.449 63.158 5.01 0.00 35.37 4.85
3928 5906 5.533154 TCCTTGGTAACTGGTGTGTTATTTG 59.467 40.000 0.00 0.00 35.27 2.32
3979 5957 5.644188 TGGTCCCATCAAGAAAGAAGAAAT 58.356 37.500 0.00 0.00 0.00 2.17
4036 6014 9.706691 CTGGAAAGAAAGAAACACTGTAGTATA 57.293 33.333 0.00 0.00 0.00 1.47
4037 6015 9.485206 TGGAAAGAAAGAAACACTGTAGTATAC 57.515 33.333 0.00 0.00 43.42 1.47
4038 6016 9.708092 GGAAAGAAAGAAACACTGTAGTATACT 57.292 33.333 10.87 10.87 43.54 2.12
4107 6093 2.890808 TTCTGCGTCTGTGTTTCTCT 57.109 45.000 0.00 0.00 0.00 3.10
4123 6109 7.442364 TGTGTTTCTCTCCTCTTCTGTTAATTG 59.558 37.037 0.00 0.00 0.00 2.32
4129 6115 9.480861 TCTCTCCTCTTCTGTTAATTGATCTTA 57.519 33.333 0.00 0.00 0.00 2.10
4161 6147 8.074370 GGTTCTCTTAGAATTGTTGTTGTTACC 58.926 37.037 0.00 0.00 36.50 2.85
4171 6157 8.840833 AATTGTTGTTGTTACCAATATTTCCC 57.159 30.769 0.00 0.00 32.11 3.97
4252 6238 0.489567 ACCACTTCCCAGACCTCTCT 59.510 55.000 0.00 0.00 0.00 3.10
4253 6239 1.190643 CCACTTCCCAGACCTCTCTC 58.809 60.000 0.00 0.00 0.00 3.20
4254 6240 1.272985 CCACTTCCCAGACCTCTCTCT 60.273 57.143 0.00 0.00 0.00 3.10
4290 6276 4.323553 AAACACTTCTCGCTAACTGAGT 57.676 40.909 0.00 0.00 34.99 3.41
4294 6280 0.179197 TTCTCGCTAACTGAGTCGCG 60.179 55.000 18.95 18.95 46.28 5.87
4316 6302 1.072489 GTCCTAAGGGGCTGCTATTCC 59.928 57.143 0.00 0.00 33.70 3.01
4317 6303 1.061346 TCCTAAGGGGCTGCTATTCCT 60.061 52.381 0.00 0.00 34.39 3.36
4324 6310 2.357154 GGGGCTGCTATTCCTGAAGAAA 60.357 50.000 0.00 0.00 38.21 2.52
4345 6331 4.602159 CGGTAGCCGCTGGTTAAA 57.398 55.556 2.16 0.00 41.17 1.52
4369 6355 0.527565 CATTTTACCGCTTGCAGCCT 59.472 50.000 0.00 0.00 38.18 4.58
4390 6376 1.019278 TTCAATCTCACGAAGCCCGC 61.019 55.000 0.00 0.00 43.32 6.13
4458 6444 1.447489 TCCCTCTCTCGACGTCGAC 60.447 63.158 34.97 5.18 44.22 4.20
4509 6496 3.769369 TTAACCGTTGGCGCCCACA 62.769 57.895 28.11 8.74 36.67 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.255020 GTGCTTGATCTTGCCATTTATCTTTG 59.745 38.462 7.77 0.00 0.00 2.77
33 34 0.035458 GTGGGAGTACTTGCTGCAGT 59.965 55.000 16.64 6.22 0.00 4.40
213 215 5.688807 ACAGATCCCTTTATGATCCAGTTG 58.311 41.667 0.00 0.00 39.56 3.16
215 217 5.398353 CCAACAGATCCCTTTATGATCCAGT 60.398 44.000 0.00 0.00 39.56 4.00
216 218 5.068636 CCAACAGATCCCTTTATGATCCAG 58.931 45.833 0.00 0.00 39.56 3.86
274 276 3.181464 GGGTGCTCCTCTTTATACTCCAC 60.181 52.174 4.53 0.00 0.00 4.02
317 320 4.202182 TGTGTTTTAGTCTGCTAGAACCGT 60.202 41.667 0.00 0.00 39.91 4.83
319 322 6.613755 TTTGTGTTTTAGTCTGCTAGAACC 57.386 37.500 0.00 0.48 39.91 3.62
345 348 2.671596 CGTGCCACCAACCAAAATAAG 58.328 47.619 0.00 0.00 0.00 1.73
348 351 1.068921 GCGTGCCACCAACCAAAAT 59.931 52.632 0.00 0.00 0.00 1.82
365 368 2.359900 CCCTGGTGTTGATTCTACAGC 58.640 52.381 19.13 19.13 42.67 4.40
409 413 2.173569 GGCAGAATGGGTCATCTAGGTT 59.826 50.000 0.00 0.00 35.86 3.50
444 448 0.471780 TGGTTGTCTCCTCTGCCTGA 60.472 55.000 0.00 0.00 0.00 3.86
500 504 4.782691 TGTTAGGGATCAGTGAATTCCAGA 59.217 41.667 13.57 0.00 0.00 3.86
541 545 6.156748 TGCAAGTGTTGTATCCTCGTATAT 57.843 37.500 0.00 0.00 0.00 0.86
546 550 3.684305 TCATTGCAAGTGTTGTATCCTCG 59.316 43.478 4.94 0.00 0.00 4.63
600 604 2.952310 GTTCCAGCATCCCAGAATAACC 59.048 50.000 0.00 0.00 0.00 2.85
642 646 2.439507 TGGGAGTGCTCTGAAGACTTTT 59.560 45.455 0.00 0.00 0.00 2.27
655 659 3.334583 TTGAATAGAGTGTGGGAGTGC 57.665 47.619 0.00 0.00 0.00 4.40
667 671 7.953158 GATGAAATCTCCACGATTGAATAGA 57.047 36.000 0.00 0.00 41.42 1.98
715 719 8.402798 TCAAACTTACTTTTGATCTTATGGCA 57.597 30.769 0.00 0.00 39.94 4.92
798 802 3.153024 GCTCGGCCAATGACAGTTA 57.847 52.632 2.24 0.00 0.00 2.24
812 816 0.954452 AAGTTTGGCTTCAAGGCTCG 59.046 50.000 12.92 0.00 41.96 5.03
916 926 1.198637 CTTCAGCTGGCTGTTTGTAGC 59.801 52.381 20.00 0.00 43.96 3.58
917 927 2.740981 CTCTTCAGCTGGCTGTTTGTAG 59.259 50.000 20.00 11.63 43.96 2.74
918 928 2.104792 ACTCTTCAGCTGGCTGTTTGTA 59.895 45.455 20.00 0.12 43.96 2.41
919 929 1.133976 ACTCTTCAGCTGGCTGTTTGT 60.134 47.619 20.00 12.65 43.96 2.83
920 930 1.602311 ACTCTTCAGCTGGCTGTTTG 58.398 50.000 20.00 12.21 43.96 2.93
921 931 2.873649 GCTACTCTTCAGCTGGCTGTTT 60.874 50.000 20.00 6.10 43.96 2.83
922 932 1.338579 GCTACTCTTCAGCTGGCTGTT 60.339 52.381 20.00 0.00 43.96 3.16
923 933 0.248843 GCTACTCTTCAGCTGGCTGT 59.751 55.000 20.00 10.38 43.96 4.40
924 934 0.805322 CGCTACTCTTCAGCTGGCTG 60.805 60.000 15.13 15.58 44.86 4.85
925 935 1.515020 CGCTACTCTTCAGCTGGCT 59.485 57.895 15.13 0.00 36.86 4.75
926 936 1.520342 CCGCTACTCTTCAGCTGGC 60.520 63.158 15.13 6.33 36.86 4.85
927 937 1.520342 GCCGCTACTCTTCAGCTGG 60.520 63.158 15.13 0.00 36.86 4.85
928 938 1.520342 GGCCGCTACTCTTCAGCTG 60.520 63.158 7.63 7.63 36.86 4.24
929 939 1.544825 TTGGCCGCTACTCTTCAGCT 61.545 55.000 0.00 0.00 36.86 4.24
930 940 0.673644 TTTGGCCGCTACTCTTCAGC 60.674 55.000 0.00 0.00 35.61 4.26
931 941 1.363744 CTTTGGCCGCTACTCTTCAG 58.636 55.000 0.00 0.00 0.00 3.02
932 942 0.673644 GCTTTGGCCGCTACTCTTCA 60.674 55.000 0.00 0.00 0.00 3.02
933 943 0.391793 AGCTTTGGCCGCTACTCTTC 60.392 55.000 1.26 0.00 39.73 2.87
934 944 0.036875 AAGCTTTGGCCGCTACTCTT 59.963 50.000 3.88 0.00 36.56 2.85
935 945 0.391793 GAAGCTTTGGCCGCTACTCT 60.392 55.000 0.00 0.00 36.56 3.24
936 946 0.673644 TGAAGCTTTGGCCGCTACTC 60.674 55.000 0.00 0.45 36.56 2.59
937 947 0.674895 CTGAAGCTTTGGCCGCTACT 60.675 55.000 0.00 0.00 36.56 2.57
938 948 1.796796 CTGAAGCTTTGGCCGCTAC 59.203 57.895 0.00 0.00 36.56 3.58
939 949 2.040544 GCTGAAGCTTTGGCCGCTA 61.041 57.895 0.00 0.00 36.56 4.26
940 950 3.368571 GCTGAAGCTTTGGCCGCT 61.369 61.111 0.00 0.00 39.94 5.52
950 960 2.743928 CGGTGGTGGAGCTGAAGC 60.744 66.667 0.00 0.00 42.49 3.86
951 961 2.743928 GCGGTGGTGGAGCTGAAG 60.744 66.667 0.00 0.00 0.00 3.02
952 962 4.329545 GGCGGTGGTGGAGCTGAA 62.330 66.667 0.00 0.00 0.00 3.02
954 964 4.335647 AAGGCGGTGGTGGAGCTG 62.336 66.667 0.00 0.00 0.00 4.24
955 965 4.335647 CAAGGCGGTGGTGGAGCT 62.336 66.667 0.00 0.00 0.00 4.09
956 966 4.329545 TCAAGGCGGTGGTGGAGC 62.330 66.667 0.00 0.00 0.00 4.70
957 967 2.358737 GTCAAGGCGGTGGTGGAG 60.359 66.667 0.00 0.00 0.00 3.86
958 968 2.063015 ATTGTCAAGGCGGTGGTGGA 62.063 55.000 0.00 0.00 0.00 4.02
959 969 0.322098 TATTGTCAAGGCGGTGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
960 970 1.750193 ATATTGTCAAGGCGGTGGTG 58.250 50.000 0.00 0.00 0.00 4.17
961 971 2.091541 CAATATTGTCAAGGCGGTGGT 58.908 47.619 7.32 0.00 0.00 4.16
962 972 1.202290 GCAATATTGTCAAGGCGGTGG 60.202 52.381 16.61 0.00 0.00 4.61
963 973 1.472082 TGCAATATTGTCAAGGCGGTG 59.528 47.619 16.61 0.00 0.00 4.94
964 974 1.832883 TGCAATATTGTCAAGGCGGT 58.167 45.000 16.61 0.00 0.00 5.68
965 975 3.814842 TCTATGCAATATTGTCAAGGCGG 59.185 43.478 16.61 6.15 0.00 6.13
966 976 5.388111 CATCTATGCAATATTGTCAAGGCG 58.612 41.667 16.61 6.19 0.00 5.52
982 992 2.159128 CCATCTCCGCCTAGCATCTATG 60.159 54.545 0.00 0.00 0.00 2.23
983 993 2.106566 CCATCTCCGCCTAGCATCTAT 58.893 52.381 0.00 0.00 0.00 1.98
984 994 1.203063 ACCATCTCCGCCTAGCATCTA 60.203 52.381 0.00 0.00 0.00 1.98
985 995 0.470833 ACCATCTCCGCCTAGCATCT 60.471 55.000 0.00 0.00 0.00 2.90
986 996 1.067495 GTACCATCTCCGCCTAGCATC 60.067 57.143 0.00 0.00 0.00 3.91
987 997 0.969894 GTACCATCTCCGCCTAGCAT 59.030 55.000 0.00 0.00 0.00 3.79
988 998 0.106167 AGTACCATCTCCGCCTAGCA 60.106 55.000 0.00 0.00 0.00 3.49
989 999 1.540707 GTAGTACCATCTCCGCCTAGC 59.459 57.143 0.00 0.00 0.00 3.42
990 1000 2.860009 TGTAGTACCATCTCCGCCTAG 58.140 52.381 0.00 0.00 0.00 3.02
991 1001 3.181437 TGATGTAGTACCATCTCCGCCTA 60.181 47.826 11.78 0.00 41.47 3.93
992 1002 2.240279 GATGTAGTACCATCTCCGCCT 58.760 52.381 0.00 0.00 38.54 5.52
993 1003 1.961394 TGATGTAGTACCATCTCCGCC 59.039 52.381 11.78 0.00 41.47 6.13
994 1004 3.643763 CTTGATGTAGTACCATCTCCGC 58.356 50.000 11.78 0.00 41.47 5.54
995 1005 3.068165 TGCTTGATGTAGTACCATCTCCG 59.932 47.826 11.78 3.89 41.47 4.63
996 1006 4.672587 TGCTTGATGTAGTACCATCTCC 57.327 45.455 11.78 3.48 41.47 3.71
997 1007 8.715998 CATTATTGCTTGATGTAGTACCATCTC 58.284 37.037 11.78 4.29 41.47 2.75
998 1008 7.173907 GCATTATTGCTTGATGTAGTACCATCT 59.826 37.037 11.78 0.00 45.77 2.90
999 1009 7.301054 GCATTATTGCTTGATGTAGTACCATC 58.699 38.462 2.33 5.44 45.77 3.51
1000 1010 7.206981 GCATTATTGCTTGATGTAGTACCAT 57.793 36.000 2.33 0.00 45.77 3.55
1001 1011 6.618287 GCATTATTGCTTGATGTAGTACCA 57.382 37.500 2.33 0.00 45.77 3.25
1015 1025 4.508861 AGCCAATTTGAATCGCATTATTGC 59.491 37.500 0.00 0.00 45.78 3.56
1016 1026 6.292488 GGAAGCCAATTTGAATCGCATTATTG 60.292 38.462 0.00 0.00 32.76 1.90
1017 1027 5.754890 GGAAGCCAATTTGAATCGCATTATT 59.245 36.000 0.00 0.00 0.00 1.40
1018 1028 5.163426 TGGAAGCCAATTTGAATCGCATTAT 60.163 36.000 0.00 0.00 0.00 1.28
1019 1029 4.159321 TGGAAGCCAATTTGAATCGCATTA 59.841 37.500 0.00 0.00 0.00 1.90
1020 1030 3.055963 TGGAAGCCAATTTGAATCGCATT 60.056 39.130 0.00 0.00 0.00 3.56
1021 1031 2.496871 TGGAAGCCAATTTGAATCGCAT 59.503 40.909 0.00 0.00 0.00 4.73
1022 1032 1.891811 TGGAAGCCAATTTGAATCGCA 59.108 42.857 0.00 0.00 0.00 5.10
1023 1033 2.652941 TGGAAGCCAATTTGAATCGC 57.347 45.000 0.00 0.00 0.00 4.58
1024 1034 4.114058 ACATGGAAGCCAATTTGAATCG 57.886 40.909 0.00 0.00 36.95 3.34
1025 1035 6.532657 CACTTACATGGAAGCCAATTTGAATC 59.467 38.462 18.04 0.00 36.95 2.52
1026 1036 6.211184 TCACTTACATGGAAGCCAATTTGAAT 59.789 34.615 18.04 0.00 36.95 2.57
1027 1037 5.538053 TCACTTACATGGAAGCCAATTTGAA 59.462 36.000 18.04 0.00 36.95 2.69
1028 1038 5.048083 GTCACTTACATGGAAGCCAATTTGA 60.048 40.000 18.04 9.72 36.95 2.69
1029 1039 5.163513 GTCACTTACATGGAAGCCAATTTG 58.836 41.667 18.04 7.44 36.95 2.32
1030 1040 4.832266 TGTCACTTACATGGAAGCCAATTT 59.168 37.500 18.04 0.00 36.95 1.82
1031 1041 4.406456 TGTCACTTACATGGAAGCCAATT 58.594 39.130 18.04 0.00 36.95 2.32
1032 1042 4.032960 TGTCACTTACATGGAAGCCAAT 57.967 40.909 18.04 0.00 36.95 3.16
1033 1043 3.500448 TGTCACTTACATGGAAGCCAA 57.500 42.857 18.04 0.23 36.95 4.52
1043 1053 7.286546 TGAATGGGAAGAAAAATGTCACTTACA 59.713 33.333 0.00 0.00 43.86 2.41
1044 1054 7.657336 TGAATGGGAAGAAAAATGTCACTTAC 58.343 34.615 0.00 0.00 0.00 2.34
1045 1055 7.831691 TGAATGGGAAGAAAAATGTCACTTA 57.168 32.000 0.00 0.00 0.00 2.24
1046 1056 6.729690 TGAATGGGAAGAAAAATGTCACTT 57.270 33.333 0.00 0.00 0.00 3.16
1047 1057 6.295462 CCATGAATGGGAAGAAAAATGTCACT 60.295 38.462 1.01 0.00 44.31 3.41
1048 1058 5.870978 CCATGAATGGGAAGAAAAATGTCAC 59.129 40.000 1.01 0.00 44.31 3.67
1049 1059 6.040209 CCATGAATGGGAAGAAAAATGTCA 57.960 37.500 1.01 0.00 44.31 3.58
1064 1074 3.697542 TGAATTGTGAGGCTCCATGAATG 59.302 43.478 12.86 0.00 0.00 2.67
1065 1075 3.972133 TGAATTGTGAGGCTCCATGAAT 58.028 40.909 12.86 2.06 0.00 2.57
1066 1076 3.438216 TGAATTGTGAGGCTCCATGAA 57.562 42.857 12.86 0.00 0.00 2.57
1067 1077 3.438216 TTGAATTGTGAGGCTCCATGA 57.562 42.857 12.86 0.00 0.00 3.07
1068 1078 4.730949 ATTTGAATTGTGAGGCTCCATG 57.269 40.909 12.86 0.00 0.00 3.66
1069 1079 6.855763 TTTATTTGAATTGTGAGGCTCCAT 57.144 33.333 12.86 0.00 0.00 3.41
1070 1080 6.855763 ATTTATTTGAATTGTGAGGCTCCA 57.144 33.333 12.86 6.82 0.00 3.86
1093 1103 9.877178 ACACTTGAAACAATTTACAATACCAAA 57.123 25.926 0.00 0.00 0.00 3.28
1094 1104 9.307121 CACACTTGAAACAATTTACAATACCAA 57.693 29.630 0.00 0.00 0.00 3.67
1095 1105 8.687242 TCACACTTGAAACAATTTACAATACCA 58.313 29.630 0.00 0.00 0.00 3.25
1096 1106 9.691362 ATCACACTTGAAACAATTTACAATACC 57.309 29.630 0.00 0.00 34.61 2.73
1104 1114 9.985730 ATCACAATATCACACTTGAAACAATTT 57.014 25.926 0.00 0.00 34.61 1.82
1108 1118 8.236586 GCTTATCACAATATCACACTTGAAACA 58.763 33.333 0.00 0.00 34.61 2.83
1186 1196 8.219769 TGTTTTTATGCACATTTAATTTGAGCG 58.780 29.630 0.00 0.00 34.00 5.03
1248 1258 6.664384 ACTAACACAAGTTTCCCACCTTTTAA 59.336 34.615 0.00 0.00 39.15 1.52
1257 1267 6.445357 TGAGAAAACTAACACAAGTTTCCC 57.555 37.500 2.73 0.00 46.40 3.97
1272 1282 8.784043 AGTGTTGTATGGAAGTTATGAGAAAAC 58.216 33.333 0.00 0.00 0.00 2.43
1733 1746 9.241919 TGTGGATAAATGCTCTCTTAATGAAAA 57.758 29.630 0.00 0.00 0.00 2.29
2033 2046 1.885887 TGCCTCACATGCAAAGGTTAC 59.114 47.619 9.60 0.00 35.40 2.50
2289 2340 1.512926 CATACGGGCCTGATAACAGC 58.487 55.000 21.41 0.00 42.25 4.40
2290 2341 1.691976 TCCATACGGGCCTGATAACAG 59.308 52.381 21.41 1.48 38.48 3.16
2291 2342 1.796017 TCCATACGGGCCTGATAACA 58.204 50.000 21.41 0.00 36.21 2.41
2292 2343 2.767505 CTTCCATACGGGCCTGATAAC 58.232 52.381 21.41 0.00 36.21 1.89
2293 2344 1.071699 GCTTCCATACGGGCCTGATAA 59.928 52.381 21.41 3.21 36.21 1.75
2294 2345 0.685097 GCTTCCATACGGGCCTGATA 59.315 55.000 21.41 7.48 36.21 2.15
2295 2346 1.344953 TGCTTCCATACGGGCCTGAT 61.345 55.000 21.41 4.49 36.21 2.90
2296 2347 1.971505 CTGCTTCCATACGGGCCTGA 61.972 60.000 21.41 1.76 36.21 3.86
2297 2348 1.524621 CTGCTTCCATACGGGCCTG 60.525 63.158 11.02 11.02 36.21 4.85
2332 2384 0.413434 AATTTTAGGGGCCCTGTGCT 59.587 50.000 35.70 13.04 40.92 4.40
2599 2651 6.609212 TGGAGAAGAATAGTAGCAGAACAGAT 59.391 38.462 0.00 0.00 0.00 2.90
2645 2697 7.467557 TTGAAGAATTTGTGAAGTCATTTGC 57.532 32.000 0.00 0.00 32.49 3.68
2857 2910 8.190122 TGTCGGAGAAATGGATAAAAATGAATG 58.810 33.333 0.00 0.00 39.69 2.67
2860 2913 7.393234 ACTTGTCGGAGAAATGGATAAAAATGA 59.607 33.333 0.00 0.00 39.69 2.57
2897 2950 9.760077 TTATATGAAGAAAATCGTACTTCCTCC 57.240 33.333 0.00 0.00 39.14 4.30
2904 2957 9.262358 AGGCTCTTTATATGAAGAAAATCGTAC 57.738 33.333 10.79 0.00 35.38 3.67
3443 3504 1.153188 ATCGGTGAATGATGCGGCA 60.153 52.632 4.58 4.58 0.00 5.69
3485 3546 3.273434 TGCTGTGATTGGTCTGCTATTC 58.727 45.455 0.00 0.00 0.00 1.75
3520 3581 2.492881 TGGCATTTGGCATCTGTTACTG 59.507 45.455 2.26 0.00 46.12 2.74
3582 3643 1.208706 TTCACACAACCTCCAGGACA 58.791 50.000 0.00 0.00 38.94 4.02
3667 5639 9.357652 GCTTAATGCAAACAAGAGAATATTCAA 57.642 29.630 17.56 0.00 42.31 2.69
3677 5649 6.633500 AAGTGTAGCTTAATGCAAACAAGA 57.367 33.333 8.91 0.00 45.94 3.02
3729 5704 1.014564 GGTCAAGCTAAGCGCGAGTT 61.015 55.000 12.10 4.53 45.59 3.01
3824 5802 3.056250 ACATTCAGACGAGCAGAGAACAT 60.056 43.478 0.00 0.00 0.00 2.71
3837 5815 3.503363 TGTTGGAGATTGCACATTCAGAC 59.497 43.478 0.00 0.00 0.00 3.51
3875 5853 2.125106 GGCCTGCCGTACTGAAGG 60.125 66.667 6.95 6.95 0.00 3.46
3894 5872 4.515567 CCAGTTACCAAGGAGACAAAAGAC 59.484 45.833 0.00 0.00 0.00 3.01
3928 5906 2.170607 TGGATTAGCACCACTAGGAAGC 59.829 50.000 0.00 0.00 38.92 3.86
3979 5957 5.435686 ACATGAAGGTGCTATTGAAGGTA 57.564 39.130 0.00 0.00 0.00 3.08
4036 6014 6.500336 TCCCTGAACCAAACTAGATACTAGT 58.500 40.000 0.00 0.00 0.00 2.57
4037 6015 7.419711 TTCCCTGAACCAAACTAGATACTAG 57.580 40.000 0.00 0.00 0.00 2.57
4038 6016 7.989947 ATTCCCTGAACCAAACTAGATACTA 57.010 36.000 0.00 0.00 0.00 1.82
4039 6017 6.893020 ATTCCCTGAACCAAACTAGATACT 57.107 37.500 0.00 0.00 0.00 2.12
4040 6018 7.939784 AAATTCCCTGAACCAAACTAGATAC 57.060 36.000 0.00 0.00 0.00 2.24
4042 6020 7.855784 AAAAATTCCCTGAACCAAACTAGAT 57.144 32.000 0.00 0.00 0.00 1.98
4081 6067 1.373497 ACAGACGCAGAAAGCCGAG 60.373 57.895 0.00 0.00 41.38 4.63
4123 6109 9.646427 AATTCTAAGAGAACCGCATATAAGATC 57.354 33.333 0.00 0.00 37.00 2.75
4129 6115 6.823689 ACAACAATTCTAAGAGAACCGCATAT 59.176 34.615 0.00 0.00 37.00 1.78
4130 6116 6.170506 ACAACAATTCTAAGAGAACCGCATA 58.829 36.000 0.00 0.00 37.00 3.14
4219 6205 3.249320 GGAAGTGGTTCAGTTTTACCGTC 59.751 47.826 0.00 0.00 37.23 4.79
4269 6255 4.299978 GACTCAGTTAGCGAGAAGTGTTT 58.700 43.478 5.69 0.00 34.47 2.83
4290 6276 3.766691 GCCCCTTAGGACACGCGA 61.767 66.667 15.93 0.00 38.24 5.87
4294 6280 1.132500 ATAGCAGCCCCTTAGGACAC 58.868 55.000 0.00 0.00 38.24 3.67
4345 6331 0.175531 GCAAGCGGTAAAATGCCCAT 59.824 50.000 0.00 0.00 32.73 4.00
4369 6355 2.821546 CGGGCTTCGTGAGATTGAATA 58.178 47.619 0.00 0.00 41.60 1.75
4458 6444 2.409870 GGGATGCCACGGCTCAAAG 61.410 63.158 9.92 0.00 42.51 2.77
4509 6496 0.952497 CGGCAAGCTGATGTGTCACT 60.952 55.000 4.27 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.