Multiple sequence alignment - TraesCS3B01G560200

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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 TraesCS3B01G560200 chr3B 100.000 3176 0 0 1 3176 794295103 794298278 0.000000e+00 5866.0
1 TraesCS3B01G560200 chr3B 80.000 1310 214 26 964 2238 776032986 776031690 0.000000e+00 924.0
2 TraesCS3B01G560200 chr3B 78.751 1233 211 36 1035 2240 795813097 795814305 0.000000e+00 778.0
3 TraesCS3B01G560200 chr3B 80.000 1010 164 22 973 1948 787889731 787890736 0.000000e+00 712.0
4 TraesCS3B01G560200 chr3B 78.713 606 89 23 968 1573 787896832 787897397 5.000000e-98 368.0
5 TraesCS3B01G560200 chr3B 85.537 242 33 1 2011 2252 787902553 787902792 5.260000e-63 252.0
6 TraesCS3B01G560200 chr3B 85.124 242 34 1 2011 2252 787909435 787909674 2.450000e-61 246.0
7 TraesCS3B01G560200 chrUn 96.912 1198 29 4 1394 2584 45545072 45546268 0.000000e+00 2001.0
8 TraesCS3B01G560200 chrUn 82.945 2316 270 65 1 2247 45613729 45611470 0.000000e+00 1973.0
9 TraesCS3B01G560200 chrUn 78.823 1223 207 39 1035 2231 45538342 45539538 0.000000e+00 776.0
10 TraesCS3B01G560200 chrUn 78.413 1260 215 31 1014 2250 45526906 45528131 0.000000e+00 767.0
11 TraesCS3B01G560200 chrUn 89.674 184 11 1 925 1108 45544901 45545076 8.860000e-56 228.0
12 TraesCS3B01G560200 chrUn 96.875 64 2 0 837 900 45544840 45544903 1.200000e-19 108.0
13 TraesCS3B01G560200 chrUn 94.118 51 3 0 2464 2514 45528319 45528369 9.450000e-11 78.7
14 TraesCS3B01G560200 chr3A 78.337 1311 222 46 964 2240 723345581 723344299 0.000000e+00 791.0
15 TraesCS3B01G560200 chr3A 79.978 929 147 25 1543 2461 723338121 723337222 0.000000e+00 649.0
16 TraesCS3B01G560200 chr3A 90.995 422 38 0 1024 1445 723338646 723338225 1.280000e-158 569.0
17 TraesCS3B01G560200 chr3A 87.783 442 47 6 2501 2936 723337226 723336786 7.860000e-141 510.0
18 TraesCS3B01G560200 chr3A 83.794 506 74 7 909 1413 723291343 723290845 1.030000e-129 473.0
19 TraesCS3B01G560200 chr6D 80.541 740 125 14 1544 2275 175611666 175610938 4.630000e-153 551.0
20 TraesCS3B01G560200 chr7D 96.774 93 3 0 3084 3176 388642738 388642646 4.240000e-34 156.0
21 TraesCS3B01G560200 chr7D 92.188 64 4 1 3026 3089 12423784 12423846 4.360000e-14 89.8
22 TraesCS3B01G560200 chr6A 96.774 93 3 0 3084 3176 88085750 88085842 4.240000e-34 156.0
23 TraesCS3B01G560200 chr6A 94.828 58 3 0 3032 3089 494467282 494467225 1.210000e-14 91.6
24 TraesCS3B01G560200 chr4B 96.774 93 3 0 3084 3176 396693157 396693249 4.240000e-34 156.0
25 TraesCS3B01G560200 chr4B 96.774 93 3 0 3084 3176 626065464 626065372 4.240000e-34 156.0
26 TraesCS3B01G560200 chr3D 96.774 93 3 0 3084 3176 105445816 105445908 4.240000e-34 156.0
27 TraesCS3B01G560200 chr3D 96.774 93 3 0 3084 3176 239581758 239581666 4.240000e-34 156.0
28 TraesCS3B01G560200 chr1D 96.774 93 3 0 3084 3176 59120948 59120856 4.240000e-34 156.0
29 TraesCS3B01G560200 chr1A 96.774 93 3 0 3084 3176 97934367 97934275 4.240000e-34 156.0
30 TraesCS3B01G560200 chr1A 96.774 93 3 0 3084 3176 208900866 208900774 4.240000e-34 156.0
31 TraesCS3B01G560200 chr1A 92.188 64 3 2 3032 3094 202090618 202090556 4.360000e-14 89.8
32 TraesCS3B01G560200 chr5D 95.000 60 3 0 3030 3089 190474029 190473970 9.380000e-16 95.3
33 TraesCS3B01G560200 chr5B 96.429 56 2 0 3034 3089 563516653 563516708 3.370000e-15 93.5
34 TraesCS3B01G560200 chr4D 96.429 56 2 0 3034 3089 295432379 295432434 3.370000e-15 93.5
35 TraesCS3B01G560200 chr2B 93.333 60 4 0 3030 3089 722402520 722402579 4.360000e-14 89.8
36 TraesCS3B01G560200 chr7B 88.571 70 7 1 3020 3089 680907583 680907515 2.030000e-12 84.2
37 TraesCS3B01G560200 chr1B 86.076 79 9 2 3012 3089 5000714 5000791 2.030000e-12 84.2


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 TraesCS3B01G560200 chr3B 794295103 794298278 3175 False 5866.00 5866 100.0000 1 3176 1 chr3B.!!$F5 3175
1 TraesCS3B01G560200 chr3B 776031690 776032986 1296 True 924.00 924 80.0000 964 2238 1 chr3B.!!$R1 1274
2 TraesCS3B01G560200 chr3B 795813097 795814305 1208 False 778.00 778 78.7510 1035 2240 1 chr3B.!!$F6 1205
3 TraesCS3B01G560200 chr3B 787889731 787890736 1005 False 712.00 712 80.0000 973 1948 1 chr3B.!!$F1 975
4 TraesCS3B01G560200 chr3B 787896832 787897397 565 False 368.00 368 78.7130 968 1573 1 chr3B.!!$F2 605
5 TraesCS3B01G560200 chrUn 45611470 45613729 2259 True 1973.00 1973 82.9450 1 2247 1 chrUn.!!$R1 2246
6 TraesCS3B01G560200 chrUn 45544840 45546268 1428 False 779.00 2001 94.4870 837 2584 3 chrUn.!!$F3 1747
7 TraesCS3B01G560200 chrUn 45538342 45539538 1196 False 776.00 776 78.8230 1035 2231 1 chrUn.!!$F1 1196
8 TraesCS3B01G560200 chrUn 45526906 45528369 1463 False 422.85 767 86.2655 1014 2514 2 chrUn.!!$F2 1500
9 TraesCS3B01G560200 chr3A 723344299 723345581 1282 True 791.00 791 78.3370 964 2240 1 chr3A.!!$R2 1276
10 TraesCS3B01G560200 chr3A 723336786 723338646 1860 True 576.00 649 86.2520 1024 2936 3 chr3A.!!$R3 1912
11 TraesCS3B01G560200 chr6D 175610938 175611666 728 True 551.00 551 80.5410 1544 2275 1 chr6D.!!$R1 731

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
802 836 0.254747 TAATTTCCCCACTGGCCGAG 59.745 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2471 0.175302 CTTGTGCCCAGCAAACAACA 59.825 50.0 0.0 0.0 41.47 3.33 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
91 92 4.948847 TGGATGTCATTTCTCCACGATAG 58.051 43.478 0.00 0.00 34.17 2.08
146 147 8.816640 TTTGATACCTCAAAAATTTCAAGCTC 57.183 30.769 0.00 0.00 45.91 4.09
209 222 1.918957 AGGCACCCAAGAGCTCTAAAT 59.081 47.619 18.59 0.00 0.00 1.40
211 224 2.356125 GGCACCCAAGAGCTCTAAATCA 60.356 50.000 18.59 0.00 0.00 2.57
212 225 3.549794 GCACCCAAGAGCTCTAAATCAT 58.450 45.455 18.59 0.00 0.00 2.45
242 255 1.852633 ATTTAGTTCTTGCAGGGGCC 58.147 50.000 0.00 0.00 40.13 5.80
268 281 7.380065 CACGTTCATCCTAGCTATTTAGAAGAC 59.620 40.741 0.00 0.00 0.00 3.01
274 287 6.550163 TCCTAGCTATTTAGAAGACGGGTAT 58.450 40.000 0.00 0.00 0.00 2.73
276 289 6.433404 CCTAGCTATTTAGAAGACGGGTATGA 59.567 42.308 0.00 0.00 0.00 2.15
396 411 2.076100 GTCGTGATCCATGCAACTCAA 58.924 47.619 0.00 0.00 0.00 3.02
413 428 7.094075 TGCAACTCAATCATATCAAGCTCTTTT 60.094 33.333 0.00 0.00 0.00 2.27
414 429 7.220300 GCAACTCAATCATATCAAGCTCTTTTG 59.780 37.037 0.00 0.00 0.00 2.44
421 436 0.478072 TCAAGCTCTTTTGGCTCCCA 59.522 50.000 0.00 0.00 39.30 4.37
438 453 0.529378 CCAGCCATCAACAAGCTTCC 59.471 55.000 0.00 0.00 33.70 3.46
441 456 0.529378 GCCATCAACAAGCTTCCAGG 59.471 55.000 0.00 0.00 0.00 4.45
448 463 3.882888 TCAACAAGCTTCCAGGTAAAGTG 59.117 43.478 0.00 0.00 0.00 3.16
453 468 1.960689 GCTTCCAGGTAAAGTGCCAAA 59.039 47.619 0.00 0.00 0.00 3.28
485 502 3.266772 AGGGCTATCTCAATGTTGGACAA 59.733 43.478 0.00 0.00 0.00 3.18
500 517 5.163184 TGTTGGACAACCTAAACCTCATACA 60.163 40.000 12.21 0.00 40.46 2.29
501 518 5.772393 TGGACAACCTAAACCTCATACAT 57.228 39.130 0.00 0.00 37.04 2.29
502 519 5.741011 TGGACAACCTAAACCTCATACATC 58.259 41.667 0.00 0.00 37.04 3.06
503 520 5.123936 GGACAACCTAAACCTCATACATCC 58.876 45.833 0.00 0.00 0.00 3.51
504 521 5.338871 GGACAACCTAAACCTCATACATCCA 60.339 44.000 0.00 0.00 0.00 3.41
506 523 5.250774 ACAACCTAAACCTCATACATCCAGT 59.749 40.000 0.00 0.00 0.00 4.00
507 524 5.359194 ACCTAAACCTCATACATCCAGTG 57.641 43.478 0.00 0.00 0.00 3.66
508 525 4.130118 CCTAAACCTCATACATCCAGTGC 58.870 47.826 0.00 0.00 0.00 4.40
509 526 2.717639 AACCTCATACATCCAGTGCC 57.282 50.000 0.00 0.00 0.00 5.01
511 528 2.200081 ACCTCATACATCCAGTGCCTT 58.800 47.619 0.00 0.00 0.00 4.35
512 529 2.171448 ACCTCATACATCCAGTGCCTTC 59.829 50.000 0.00 0.00 0.00 3.46
543 575 2.054021 TGAACCACCAGTCAAGGATGA 58.946 47.619 0.00 0.00 0.00 2.92
558 590 9.593565 AGTCAAGGATGAATGATGTATAGTCTA 57.406 33.333 0.00 0.00 37.30 2.59
561 593 9.513727 CAAGGATGAATGATGTATAGTCTATCG 57.486 37.037 0.00 0.00 0.00 2.92
613 645 6.625532 ATCATTGGGCTTGGTTATTTTTCT 57.374 33.333 0.00 0.00 0.00 2.52
638 670 5.624715 TTTACACGCGTGTATATTAGTGC 57.375 39.130 42.48 0.00 44.54 4.40
790 824 6.309389 TCACTCTTCTAACCCCTAATTTCC 57.691 41.667 0.00 0.00 0.00 3.13
795 829 3.822880 TCTAACCCCTAATTTCCCCACT 58.177 45.455 0.00 0.00 0.00 4.00
796 830 2.919772 AACCCCTAATTTCCCCACTG 57.080 50.000 0.00 0.00 0.00 3.66
797 831 1.007607 ACCCCTAATTTCCCCACTGG 58.992 55.000 0.00 0.00 0.00 4.00
800 834 0.751643 CCTAATTTCCCCACTGGCCG 60.752 60.000 0.00 0.00 0.00 6.13
802 836 0.254747 TAATTTCCCCACTGGCCGAG 59.745 55.000 0.00 0.00 0.00 4.63
806 840 4.785453 CCCCACTGGCCGAGCTTC 62.785 72.222 0.00 0.00 0.00 3.86
807 841 3.710722 CCCACTGGCCGAGCTTCT 61.711 66.667 0.00 0.00 0.00 2.85
808 842 2.125350 CCACTGGCCGAGCTTCTC 60.125 66.667 0.00 0.00 0.00 2.87
809 843 2.654079 CCACTGGCCGAGCTTCTCT 61.654 63.158 0.00 0.00 0.00 3.10
910 949 4.373116 GGTCACCCGAAGCGCAGA 62.373 66.667 11.47 0.00 0.00 4.26
911 950 2.125512 GTCACCCGAAGCGCAGAT 60.126 61.111 11.47 0.00 0.00 2.90
912 951 2.167861 GTCACCCGAAGCGCAGATC 61.168 63.158 11.47 3.71 0.00 2.75
913 952 2.892425 CACCCGAAGCGCAGATCC 60.892 66.667 11.47 0.00 0.00 3.36
914 953 3.390521 ACCCGAAGCGCAGATCCA 61.391 61.111 11.47 0.00 0.00 3.41
915 954 2.109799 CCCGAAGCGCAGATCCAT 59.890 61.111 11.47 0.00 0.00 3.41
916 955 1.958205 CCCGAAGCGCAGATCCATC 60.958 63.158 11.47 0.00 0.00 3.51
917 956 1.958205 CCGAAGCGCAGATCCATCC 60.958 63.158 11.47 0.00 0.00 3.51
934 973 4.033776 CATCCCCACCACACGGCT 62.034 66.667 0.00 0.00 34.57 5.52
1219 1267 2.425592 CACGGCAGTGGGTCTTCA 59.574 61.111 9.34 0.00 44.34 3.02
1401 1458 0.038166 TCCTCAACCCATTGACAGGC 59.962 55.000 0.00 0.00 40.01 4.85
1407 1464 0.038166 ACCCATTGACAGGCGACATT 59.962 50.000 0.00 0.00 0.00 2.71
1412 1469 2.542020 TTGACAGGCGACATTCTTCA 57.458 45.000 0.00 0.00 0.00 3.02
1480 1573 0.036164 TGGGACTGAACCAACCATCG 59.964 55.000 0.00 0.00 34.44 3.84
1582 1702 4.728102 CGGGCCAGTTACGTGCGA 62.728 66.667 4.39 0.00 0.00 5.10
1734 1857 3.054361 GGTATGGGGAGCGAATATTGGAT 60.054 47.826 1.09 0.00 0.00 3.41
1736 1859 3.695830 TGGGGAGCGAATATTGGATAC 57.304 47.619 1.09 0.00 0.00 2.24
1948 2080 1.851021 TTCCATTGACGGCAACTGCG 61.851 55.000 5.42 0.00 43.26 5.18
1984 2125 3.119531 TGCTGGAAACCAATTTGATAGCG 60.120 43.478 0.00 0.00 30.80 4.26
2130 2277 0.972134 CTCAGGTGCTTCTCACTCCA 59.028 55.000 0.00 0.00 44.98 3.86
2175 2325 2.236395 AGATCGGTTCCACCAAACCTAG 59.764 50.000 4.46 0.00 45.45 3.02
2276 2471 3.773119 AGAATGCCAAGATGCTGGATTTT 59.227 39.130 0.00 0.00 38.96 1.82
2411 2612 3.008594 TGGTGTAATTCCGGTCAGTCATT 59.991 43.478 0.00 0.00 0.00 2.57
2423 2624 3.316308 GGTCAGTCATTTGTCTTGCTGTT 59.684 43.478 0.00 0.00 0.00 3.16
2436 2637 5.355071 TGTCTTGCTGTTGTTGGATATGATC 59.645 40.000 0.00 0.00 0.00 2.92
2581 2782 8.071967 TGATTTTATCATTGAAATCGCTAGCTG 58.928 33.333 13.93 6.69 42.41 4.24
2603 2804 8.097662 AGCTGTGCTCCTTAATAATCCTATAAC 58.902 37.037 0.00 0.00 30.62 1.89
2652 2854 3.087031 CACATTTTCTGGCATGGACTCT 58.913 45.455 0.00 0.00 0.00 3.24
2662 2864 2.036604 GGCATGGACTCTCTAGGCTTAC 59.963 54.545 0.00 0.00 35.01 2.34
2664 2866 3.243704 GCATGGACTCTCTAGGCTTACTG 60.244 52.174 0.00 0.00 31.88 2.74
2693 2897 8.107095 TCTATAAGTTAGCATTTGTTCCCTTGT 58.893 33.333 0.00 0.00 0.00 3.16
2694 2898 5.453567 AAGTTAGCATTTGTTCCCTTGTC 57.546 39.130 0.00 0.00 0.00 3.18
2700 2904 4.219288 AGCATTTGTTCCCTTGTCTCATTC 59.781 41.667 0.00 0.00 0.00 2.67
2701 2905 4.619160 GCATTTGTTCCCTTGTCTCATTCC 60.619 45.833 0.00 0.00 0.00 3.01
2711 2915 5.500234 CCTTGTCTCATTCCCTCAAACATA 58.500 41.667 0.00 0.00 0.00 2.29
2721 2925 8.331740 TCATTCCCTCAAACATATCTTTTCTCT 58.668 33.333 0.00 0.00 0.00 3.10
2753 2957 2.032290 GTCTGTGGACAAAACGGCTTAC 60.032 50.000 0.00 0.00 41.75 2.34
2761 2966 4.142881 GGACAAAACGGCTTACTGATTCTC 60.143 45.833 0.00 0.00 0.00 2.87
2770 2975 4.194640 GCTTACTGATTCTCCATGAGCAA 58.805 43.478 0.00 0.00 0.00 3.91
2771 2976 4.034975 GCTTACTGATTCTCCATGAGCAAC 59.965 45.833 0.00 0.00 0.00 4.17
2794 2999 5.130145 ACATGACCAGAGGAGAATAGAAAGG 59.870 44.000 0.00 0.00 0.00 3.11
2795 3000 3.452627 TGACCAGAGGAGAATAGAAAGGC 59.547 47.826 0.00 0.00 0.00 4.35
2799 3004 3.070878 CAGAGGAGAATAGAAAGGCCCTC 59.929 52.174 0.00 0.00 39.08 4.30
2801 3006 2.774809 AGGAGAATAGAAAGGCCCTCAC 59.225 50.000 0.00 0.00 0.00 3.51
2804 3009 3.967987 GAGAATAGAAAGGCCCTCACCTA 59.032 47.826 0.00 0.00 39.93 3.08
2809 3014 1.840635 GAAAGGCCCTCACCTACTGAT 59.159 52.381 0.00 0.00 39.93 2.90
2820 3025 5.352569 CCTCACCTACTGATGTTGCTAAAAG 59.647 44.000 0.00 0.00 0.00 2.27
2875 3080 4.030977 GCATCGAAAGTGCAATTTTAGCAG 59.969 41.667 14.04 7.98 43.63 4.24
2881 3086 4.170292 AGTGCAATTTTAGCAGCAGAAG 57.830 40.909 0.00 0.00 43.63 2.85
2882 3087 2.665052 GTGCAATTTTAGCAGCAGAAGC 59.335 45.455 0.00 0.00 43.63 3.86
2898 3103 6.336514 GCAGAAGCTATTTTTAATGTTGCC 57.663 37.500 0.00 0.00 37.91 4.52
2900 3105 7.257722 GCAGAAGCTATTTTTAATGTTGCCTA 58.742 34.615 0.00 0.00 37.91 3.93
2901 3106 7.759433 GCAGAAGCTATTTTTAATGTTGCCTAA 59.241 33.333 0.00 0.00 37.91 2.69
2917 3122 2.348666 GCCTAAAGCATACACGTGTCAG 59.651 50.000 27.16 19.43 42.97 3.51
2929 3134 0.042188 CGTGTCAGTTCTGTTTGCCG 60.042 55.000 0.00 0.00 0.00 5.69
2930 3135 1.014352 GTGTCAGTTCTGTTTGCCGT 58.986 50.000 0.00 0.00 0.00 5.68
2936 3141 1.750780 TTCTGTTTGCCGTGTGCCA 60.751 52.632 0.00 0.00 40.16 4.92
2937 3142 1.315981 TTCTGTTTGCCGTGTGCCAA 61.316 50.000 0.00 0.00 40.16 4.52
2938 3143 1.140589 CTGTTTGCCGTGTGCCAAA 59.859 52.632 0.00 0.00 40.16 3.28
2939 3144 0.871163 CTGTTTGCCGTGTGCCAAAG 60.871 55.000 0.00 0.00 40.16 2.77
2940 3145 1.315981 TGTTTGCCGTGTGCCAAAGA 61.316 50.000 0.00 0.00 40.16 2.52
2941 3146 0.594796 GTTTGCCGTGTGCCAAAGAG 60.595 55.000 0.00 0.00 40.16 2.85
2942 3147 1.034838 TTTGCCGTGTGCCAAAGAGT 61.035 50.000 0.00 0.00 40.16 3.24
2943 3148 0.179043 TTGCCGTGTGCCAAAGAGTA 60.179 50.000 0.00 0.00 40.16 2.59
2944 3149 0.602638 TGCCGTGTGCCAAAGAGTAG 60.603 55.000 0.00 0.00 40.16 2.57
2945 3150 0.320421 GCCGTGTGCCAAAGAGTAGA 60.320 55.000 0.00 0.00 0.00 2.59
2946 3151 1.876416 GCCGTGTGCCAAAGAGTAGAA 60.876 52.381 0.00 0.00 0.00 2.10
2947 3152 1.798813 CCGTGTGCCAAAGAGTAGAAC 59.201 52.381 0.00 0.00 0.00 3.01
2948 3153 2.479837 CGTGTGCCAAAGAGTAGAACA 58.520 47.619 0.00 0.00 0.00 3.18
2949 3154 3.067106 CGTGTGCCAAAGAGTAGAACAT 58.933 45.455 0.00 0.00 0.00 2.71
2950 3155 4.242475 CGTGTGCCAAAGAGTAGAACATA 58.758 43.478 0.00 0.00 0.00 2.29
2951 3156 4.870426 CGTGTGCCAAAGAGTAGAACATAT 59.130 41.667 0.00 0.00 0.00 1.78
2952 3157 5.351465 CGTGTGCCAAAGAGTAGAACATATT 59.649 40.000 0.00 0.00 0.00 1.28
2953 3158 6.533723 CGTGTGCCAAAGAGTAGAACATATTA 59.466 38.462 0.00 0.00 0.00 0.98
2954 3159 7.064134 CGTGTGCCAAAGAGTAGAACATATTAA 59.936 37.037 0.00 0.00 0.00 1.40
2955 3160 8.391106 GTGTGCCAAAGAGTAGAACATATTAAG 58.609 37.037 0.00 0.00 0.00 1.85
2956 3161 8.318412 TGTGCCAAAGAGTAGAACATATTAAGA 58.682 33.333 0.00 0.00 0.00 2.10
2957 3162 9.331282 GTGCCAAAGAGTAGAACATATTAAGAT 57.669 33.333 0.00 0.00 0.00 2.40
2976 3181 8.710835 TTAAGATACACAAAAGATATGTCGCA 57.289 30.769 0.00 0.00 0.00 5.10
2977 3182 6.589830 AGATACACAAAAGATATGTCGCAC 57.410 37.500 0.00 0.00 0.00 5.34
2978 3183 6.106003 AGATACACAAAAGATATGTCGCACA 58.894 36.000 0.00 0.00 0.00 4.57
2979 3184 6.593770 AGATACACAAAAGATATGTCGCACAA 59.406 34.615 0.00 0.00 0.00 3.33
2980 3185 5.627499 ACACAAAAGATATGTCGCACAAT 57.373 34.783 0.00 0.00 0.00 2.71
2981 3186 6.735678 ACACAAAAGATATGTCGCACAATA 57.264 33.333 0.00 0.00 0.00 1.90
2982 3187 6.542852 ACACAAAAGATATGTCGCACAATAC 58.457 36.000 0.00 0.00 0.00 1.89
2983 3188 6.371548 ACACAAAAGATATGTCGCACAATACT 59.628 34.615 0.00 0.00 0.00 2.12
2984 3189 7.094805 ACACAAAAGATATGTCGCACAATACTT 60.095 33.333 0.00 0.00 0.00 2.24
2985 3190 8.387354 CACAAAAGATATGTCGCACAATACTTA 58.613 33.333 0.00 0.00 0.00 2.24
2986 3191 9.109393 ACAAAAGATATGTCGCACAATACTTAT 57.891 29.630 0.00 0.00 0.00 1.73
2987 3192 9.935682 CAAAAGATATGTCGCACAATACTTATT 57.064 29.630 0.00 0.00 0.00 1.40
2994 3199 6.943981 TGTCGCACAATACTTATTAAGATGC 58.056 36.000 10.39 9.72 0.00 3.91
2995 3200 6.018262 TGTCGCACAATACTTATTAAGATGCC 60.018 38.462 10.39 2.36 0.00 4.40
2996 3201 6.018262 GTCGCACAATACTTATTAAGATGCCA 60.018 38.462 10.39 0.00 0.00 4.92
2997 3202 6.710295 TCGCACAATACTTATTAAGATGCCAT 59.290 34.615 10.39 0.00 0.00 4.40
2998 3203 6.798476 CGCACAATACTTATTAAGATGCCATG 59.202 38.462 10.39 3.14 0.00 3.66
2999 3204 7.307930 CGCACAATACTTATTAAGATGCCATGA 60.308 37.037 10.39 0.00 0.00 3.07
3000 3205 8.019669 GCACAATACTTATTAAGATGCCATGAG 58.980 37.037 10.39 1.70 0.00 2.90
3001 3206 9.276590 CACAATACTTATTAAGATGCCATGAGA 57.723 33.333 10.39 0.00 0.00 3.27
3002 3207 9.851686 ACAATACTTATTAAGATGCCATGAGAA 57.148 29.630 10.39 0.00 0.00 2.87
3006 3211 8.814038 ACTTATTAAGATGCCATGAGAAAGTT 57.186 30.769 10.39 0.00 0.00 2.66
3007 3212 9.905713 ACTTATTAAGATGCCATGAGAAAGTTA 57.094 29.630 10.39 0.00 0.00 2.24
3009 3214 9.905713 TTATTAAGATGCCATGAGAAAGTTACT 57.094 29.630 0.00 0.00 0.00 2.24
3011 3216 9.905713 ATTAAGATGCCATGAGAAAGTTACTAA 57.094 29.630 0.00 0.00 0.00 2.24
3012 3217 9.733556 TTAAGATGCCATGAGAAAGTTACTAAA 57.266 29.630 0.00 0.00 0.00 1.85
3013 3218 8.635765 AAGATGCCATGAGAAAGTTACTAAAA 57.364 30.769 0.00 0.00 0.00 1.52
3014 3219 8.814038 AGATGCCATGAGAAAGTTACTAAAAT 57.186 30.769 0.00 0.00 0.00 1.82
3015 3220 9.905713 AGATGCCATGAGAAAGTTACTAAAATA 57.094 29.630 0.00 0.00 0.00 1.40
3043 3248 8.204836 AGACTACAATTCCAACACATATACTCC 58.795 37.037 0.00 0.00 0.00 3.85
3044 3249 7.280356 ACTACAATTCCAACACATATACTCCC 58.720 38.462 0.00 0.00 0.00 4.30
3045 3250 6.327386 ACAATTCCAACACATATACTCCCT 57.673 37.500 0.00 0.00 0.00 4.20
3046 3251 6.357367 ACAATTCCAACACATATACTCCCTC 58.643 40.000 0.00 0.00 0.00 4.30
3047 3252 5.568620 ATTCCAACACATATACTCCCTCC 57.431 43.478 0.00 0.00 0.00 4.30
3048 3253 2.963101 TCCAACACATATACTCCCTCCG 59.037 50.000 0.00 0.00 0.00 4.63
3049 3254 2.698797 CCAACACATATACTCCCTCCGT 59.301 50.000 0.00 0.00 0.00 4.69
3050 3255 3.243771 CCAACACATATACTCCCTCCGTC 60.244 52.174 0.00 0.00 0.00 4.79
3051 3256 2.595238 ACACATATACTCCCTCCGTCC 58.405 52.381 0.00 0.00 0.00 4.79
3052 3257 1.893801 CACATATACTCCCTCCGTCCC 59.106 57.143 0.00 0.00 0.00 4.46
3053 3258 1.502039 ACATATACTCCCTCCGTCCCA 59.498 52.381 0.00 0.00 0.00 4.37
3054 3259 2.090943 ACATATACTCCCTCCGTCCCAA 60.091 50.000 0.00 0.00 0.00 4.12
3055 3260 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
3056 3261 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3057 3262 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3058 3263 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3059 3264 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3060 3265 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3061 3266 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3062 3267 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3063 3268 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3064 3269 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3065 3270 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3066 3271 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3067 3272 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3068 3273 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3069 3274 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3070 3275 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3071 3276 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3072 3277 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3073 3278 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3074 3279 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3075 3280 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3076 3281 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3083 3288 7.759465 TCTTGTCTTAGATTTGTCTAGGTACG 58.241 38.462 0.00 0.00 0.00 3.67
3084 3289 6.446781 TGTCTTAGATTTGTCTAGGTACGG 57.553 41.667 0.00 0.00 0.00 4.02
3085 3290 5.948162 TGTCTTAGATTTGTCTAGGTACGGT 59.052 40.000 0.00 0.00 0.00 4.83
3086 3291 6.435277 TGTCTTAGATTTGTCTAGGTACGGTT 59.565 38.462 0.00 0.00 0.00 4.44
3087 3292 6.750963 GTCTTAGATTTGTCTAGGTACGGTTG 59.249 42.308 0.00 0.00 0.00 3.77
3088 3293 6.435277 TCTTAGATTTGTCTAGGTACGGTTGT 59.565 38.462 0.00 0.00 0.00 3.32
3089 3294 5.069501 AGATTTGTCTAGGTACGGTTGTC 57.930 43.478 0.00 0.00 0.00 3.18
3090 3295 2.995466 TTGTCTAGGTACGGTTGTCG 57.005 50.000 0.00 0.00 45.88 4.35
3099 3304 3.557824 CGGTTGTCGTACTTGCCC 58.442 61.111 0.00 0.00 0.00 5.36
3100 3305 2.030958 CGGTTGTCGTACTTGCCCC 61.031 63.158 0.00 0.00 0.00 5.80
3101 3306 1.373812 GGTTGTCGTACTTGCCCCT 59.626 57.895 0.00 0.00 0.00 4.79
3102 3307 0.953960 GGTTGTCGTACTTGCCCCTG 60.954 60.000 0.00 0.00 0.00 4.45
3103 3308 0.250166 GTTGTCGTACTTGCCCCTGT 60.250 55.000 0.00 0.00 0.00 4.00
3104 3309 0.470766 TTGTCGTACTTGCCCCTGTT 59.529 50.000 0.00 0.00 0.00 3.16
3105 3310 0.250124 TGTCGTACTTGCCCCTGTTG 60.250 55.000 0.00 0.00 0.00 3.33
3106 3311 1.302192 TCGTACTTGCCCCTGTTGC 60.302 57.895 0.00 0.00 0.00 4.17
3107 3312 2.332654 CGTACTTGCCCCTGTTGCC 61.333 63.158 0.00 0.00 0.00 4.52
3108 3313 1.228429 GTACTTGCCCCTGTTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
3109 3314 1.074775 TACTTGCCCCTGTTGCCAG 59.925 57.895 0.00 0.00 38.50 4.85
3117 3322 4.179361 CTGTTGCCAGGCTTTCCA 57.821 55.556 14.15 2.96 34.90 3.53
3118 3323 1.962144 CTGTTGCCAGGCTTTCCAG 59.038 57.895 14.15 9.18 34.90 3.86
3119 3324 1.530013 CTGTTGCCAGGCTTTCCAGG 61.530 60.000 14.15 0.00 41.65 4.45
3128 3333 3.538379 GCTTTCCAGGCCAATTTGG 57.462 52.632 11.27 11.27 41.55 3.28
3129 3334 0.975887 GCTTTCCAGGCCAATTTGGA 59.024 50.000 19.76 6.40 40.96 3.53
3138 3343 2.879826 GGCCAATTTGGACTTTCATCG 58.120 47.619 19.76 0.00 44.12 3.84
3139 3344 2.262211 GCCAATTTGGACTTTCATCGC 58.738 47.619 19.76 0.00 40.96 4.58
3140 3345 2.518949 CCAATTTGGACTTTCATCGCG 58.481 47.619 10.03 0.00 40.96 5.87
3141 3346 2.095263 CCAATTTGGACTTTCATCGCGT 60.095 45.455 10.03 0.00 40.96 6.01
3142 3347 3.564511 CAATTTGGACTTTCATCGCGTT 58.435 40.909 5.77 0.00 0.00 4.84
3143 3348 3.915437 ATTTGGACTTTCATCGCGTTT 57.085 38.095 5.77 0.00 0.00 3.60
3144 3349 5.150683 CAATTTGGACTTTCATCGCGTTTA 58.849 37.500 5.77 0.00 0.00 2.01
3145 3350 3.799137 TTGGACTTTCATCGCGTTTAC 57.201 42.857 5.77 0.00 0.00 2.01
3146 3351 1.722464 TGGACTTTCATCGCGTTTACG 59.278 47.619 5.77 0.00 43.27 3.18
3148 3353 2.027688 GGACTTTCATCGCGTTTACGAG 59.972 50.000 5.77 2.77 46.69 4.18
3149 3354 2.660236 GACTTTCATCGCGTTTACGAGT 59.340 45.455 5.77 4.74 46.69 4.18
3150 3355 3.054878 ACTTTCATCGCGTTTACGAGTT 58.945 40.909 5.77 0.00 46.69 3.01
3151 3356 3.120782 ACTTTCATCGCGTTTACGAGTTC 59.879 43.478 5.77 0.00 46.69 3.01
3152 3357 1.621107 TCATCGCGTTTACGAGTTCC 58.379 50.000 5.77 0.00 46.69 3.62
3153 3358 1.200716 TCATCGCGTTTACGAGTTCCT 59.799 47.619 5.77 0.00 46.69 3.36
3154 3359 1.320555 CATCGCGTTTACGAGTTCCTG 59.679 52.381 5.77 0.00 46.69 3.86
3155 3360 0.311790 TCGCGTTTACGAGTTCCTGT 59.688 50.000 5.77 0.00 43.02 4.00
3156 3361 0.706729 CGCGTTTACGAGTTCCTGTC 59.293 55.000 6.44 0.00 43.02 3.51
3157 3362 1.665161 CGCGTTTACGAGTTCCTGTCT 60.665 52.381 6.44 0.00 43.02 3.41
3158 3363 1.984297 GCGTTTACGAGTTCCTGTCTC 59.016 52.381 6.44 0.00 43.02 3.36
3164 3369 1.513622 GAGTTCCTGTCTCGGCTCC 59.486 63.158 0.00 0.00 0.00 4.70
3165 3370 2.182030 GTTCCTGTCTCGGCTCCG 59.818 66.667 1.14 1.14 41.35 4.63
3166 3371 2.282958 TTCCTGTCTCGGCTCCGT 60.283 61.111 8.28 0.00 40.74 4.69
3167 3372 1.001764 TTCCTGTCTCGGCTCCGTA 60.002 57.895 8.28 0.00 40.74 4.02
3168 3373 0.609957 TTCCTGTCTCGGCTCCGTAA 60.610 55.000 8.28 0.00 40.74 3.18
3169 3374 1.030488 TCCTGTCTCGGCTCCGTAAG 61.030 60.000 8.28 0.00 40.74 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.416329 ACATCCATGGTATTCTCATTAAAAAGC 58.584 33.333 12.58 0.00 0.00 3.51
51 52 9.473007 TGACATCCATGGTATTCTCATTAAAAA 57.527 29.630 12.58 0.00 0.00 1.94
91 92 2.094675 CCATTCCACTCCCATGTGAAC 58.905 52.381 0.00 0.00 40.12 3.18
183 196 0.610232 GCTCTTGGGTGCCTGTGAAT 60.610 55.000 0.00 0.00 0.00 2.57
209 222 8.296713 GCAAGAACTAAATAACAAGGACAATGA 58.703 33.333 0.00 0.00 0.00 2.57
211 224 8.177119 TGCAAGAACTAAATAACAAGGACAAT 57.823 30.769 0.00 0.00 0.00 2.71
212 225 7.255451 CCTGCAAGAACTAAATAACAAGGACAA 60.255 37.037 0.00 0.00 34.07 3.18
242 255 7.380065 GTCTTCTAAATAGCTAGGATGAACGTG 59.620 40.741 0.00 0.00 0.00 4.49
268 281 9.398170 GATGATACAAATGAAAATTCATACCCG 57.602 33.333 8.94 1.95 46.60 5.28
324 338 6.389906 GGTCTGTGTTTTTCTCAATAATGGG 58.610 40.000 0.00 0.00 0.00 4.00
343 357 7.653767 ATTACTTCTTTAGTTTGTCGGTCTG 57.346 36.000 0.00 0.00 38.33 3.51
396 411 4.826183 GGAGCCAAAAGAGCTTGATATGAT 59.174 41.667 0.00 0.00 41.75 2.45
421 436 1.542492 CTGGAAGCTTGTTGATGGCT 58.458 50.000 2.10 0.00 37.99 4.75
426 441 3.882888 CACTTTACCTGGAAGCTTGTTGA 59.117 43.478 2.10 0.00 0.00 3.18
438 453 3.319122 AGCTTTCTTTGGCACTTTACCTG 59.681 43.478 0.00 0.00 0.00 4.00
441 456 4.568152 TGAGCTTTCTTTGGCACTTTAC 57.432 40.909 0.00 0.00 0.00 2.01
448 463 0.037882 GCCCTTGAGCTTTCTTTGGC 60.038 55.000 0.00 0.00 0.00 4.52
485 502 4.384208 GCACTGGATGTATGAGGTTTAGGT 60.384 45.833 0.00 0.00 0.00 3.08
500 517 1.661463 TCTTCCTGAAGGCACTGGAT 58.339 50.000 7.03 0.00 40.86 3.41
501 518 1.434188 TTCTTCCTGAAGGCACTGGA 58.566 50.000 7.03 6.31 40.86 3.86
502 519 2.276732 TTTCTTCCTGAAGGCACTGG 57.723 50.000 7.03 0.00 40.86 4.00
503 520 3.822735 TCAATTTCTTCCTGAAGGCACTG 59.177 43.478 7.03 1.64 40.86 3.66
506 523 3.573967 GGTTCAATTTCTTCCTGAAGGCA 59.426 43.478 7.03 0.00 38.88 4.75
507 524 3.573967 TGGTTCAATTTCTTCCTGAAGGC 59.426 43.478 7.03 0.00 38.88 4.35
508 525 4.021981 GGTGGTTCAATTTCTTCCTGAAGG 60.022 45.833 7.03 0.00 38.88 3.46
509 526 4.584325 TGGTGGTTCAATTTCTTCCTGAAG 59.416 41.667 0.31 0.31 39.71 3.02
511 528 4.144297 CTGGTGGTTCAATTTCTTCCTGA 58.856 43.478 0.00 0.00 0.00 3.86
512 529 3.891366 ACTGGTGGTTCAATTTCTTCCTG 59.109 43.478 0.00 0.00 0.00 3.86
558 590 4.471904 TGTGCCTTGAGAGTTAATCGAT 57.528 40.909 0.00 0.00 0.00 3.59
559 591 3.953712 TGTGCCTTGAGAGTTAATCGA 57.046 42.857 0.00 0.00 0.00 3.59
560 592 3.243877 CGATGTGCCTTGAGAGTTAATCG 59.756 47.826 0.00 0.00 0.00 3.34
561 593 3.557595 CCGATGTGCCTTGAGAGTTAATC 59.442 47.826 0.00 0.00 0.00 1.75
567 599 2.169789 CGCCGATGTGCCTTGAGAG 61.170 63.158 0.00 0.00 0.00 3.20
569 601 2.125552 TCGCCGATGTGCCTTGAG 60.126 61.111 0.00 0.00 0.00 3.02
689 721 4.566360 GCACACAGCAAACACTACAAAAAT 59.434 37.500 0.00 0.00 44.79 1.82
716 750 0.179000 AATACTTGCAGGCCTCCTCG 59.821 55.000 0.00 0.00 0.00 4.63
717 751 2.293170 GAAATACTTGCAGGCCTCCTC 58.707 52.381 0.00 0.00 0.00 3.71
718 752 1.407437 CGAAATACTTGCAGGCCTCCT 60.407 52.381 0.00 0.00 0.00 3.69
719 753 1.017387 CGAAATACTTGCAGGCCTCC 58.983 55.000 0.00 0.00 0.00 4.30
756 790 1.648467 GAAGAGTGATGCGGTTGGGC 61.648 60.000 0.00 0.00 0.00 5.36
757 791 0.036010 AGAAGAGTGATGCGGTTGGG 60.036 55.000 0.00 0.00 0.00 4.12
758 792 2.672961 TAGAAGAGTGATGCGGTTGG 57.327 50.000 0.00 0.00 0.00 3.77
759 793 2.673368 GGTTAGAAGAGTGATGCGGTTG 59.327 50.000 0.00 0.00 0.00 3.77
760 794 2.354805 GGGTTAGAAGAGTGATGCGGTT 60.355 50.000 0.00 0.00 0.00 4.44
761 795 1.207329 GGGTTAGAAGAGTGATGCGGT 59.793 52.381 0.00 0.00 0.00 5.68
790 824 3.672295 GAGAAGCTCGGCCAGTGGG 62.672 68.421 12.15 0.00 37.18 4.61
800 834 0.814812 GCTGGATGGCAGAGAAGCTC 60.815 60.000 0.00 0.00 34.17 4.09
802 836 1.823041 GGCTGGATGGCAGAGAAGC 60.823 63.158 0.00 0.00 41.37 3.86
804 838 2.586245 CGGCTGGATGGCAGAGAA 59.414 61.111 0.00 0.00 41.89 2.87
805 839 4.166888 GCGGCTGGATGGCAGAGA 62.167 66.667 0.00 0.00 41.89 3.10
829 868 2.834549 GAGAAATGGTGGAGACTGGAGA 59.165 50.000 0.00 0.00 0.00 3.71
830 869 2.093235 GGAGAAATGGTGGAGACTGGAG 60.093 54.545 0.00 0.00 0.00 3.86
831 870 1.909302 GGAGAAATGGTGGAGACTGGA 59.091 52.381 0.00 0.00 0.00 3.86
832 871 1.065126 GGGAGAAATGGTGGAGACTGG 60.065 57.143 0.00 0.00 0.00 4.00
833 872 1.065126 GGGGAGAAATGGTGGAGACTG 60.065 57.143 0.00 0.00 0.00 3.51
834 873 1.290134 GGGGAGAAATGGTGGAGACT 58.710 55.000 0.00 0.00 0.00 3.24
835 874 0.256177 GGGGGAGAAATGGTGGAGAC 59.744 60.000 0.00 0.00 0.00 3.36
910 949 0.627170 TGTGGTGGGGATGGATGGAT 60.627 55.000 0.00 0.00 0.00 3.41
911 950 1.230116 TGTGGTGGGGATGGATGGA 60.230 57.895 0.00 0.00 0.00 3.41
912 951 1.076777 GTGTGGTGGGGATGGATGG 60.077 63.158 0.00 0.00 0.00 3.51
913 952 1.451927 CGTGTGGTGGGGATGGATG 60.452 63.158 0.00 0.00 0.00 3.51
914 953 2.679342 CCGTGTGGTGGGGATGGAT 61.679 63.158 0.00 0.00 0.00 3.41
915 954 3.326578 CCGTGTGGTGGGGATGGA 61.327 66.667 0.00 0.00 0.00 3.41
917 956 2.593468 CTAGCCGTGTGGTGGGGATG 62.593 65.000 0.00 0.00 37.67 3.51
960 999 1.812686 CGTCCTCGACAAAGACCCCA 61.813 60.000 0.00 0.00 39.71 4.96
1180 1228 4.462280 GAAACGGGGGTCGGCGAT 62.462 66.667 14.79 0.00 44.45 4.58
1218 1266 2.100631 GTCGTCTGCCCCGTTGATG 61.101 63.158 0.00 0.00 0.00 3.07
1219 1267 2.264794 GTCGTCTGCCCCGTTGAT 59.735 61.111 0.00 0.00 0.00 2.57
1299 1347 1.840737 AGATGTAGTCACGGAGCACT 58.159 50.000 0.00 0.00 0.00 4.40
1401 1458 1.725931 GCCGCAAAGTGAAGAATGTCG 60.726 52.381 0.00 0.00 0.00 4.35
1407 1464 3.353836 GGCGCCGCAAAGTGAAGA 61.354 61.111 12.58 0.00 0.00 2.87
1412 1469 0.250727 ATATATGGGCGCCGCAAAGT 60.251 50.000 22.54 11.77 0.00 2.66
1480 1573 0.612453 ACCGGTGGGAGAGAGAAGAC 60.612 60.000 6.12 0.00 36.97 3.01
1582 1702 2.430465 AGCAGCATCGTGAAACTTCAT 58.570 42.857 0.00 0.00 39.73 2.57
1734 1857 0.249120 CATTGTCGTCCCTGCCAGTA 59.751 55.000 0.00 0.00 0.00 2.74
1736 1859 1.746615 CCATTGTCGTCCCTGCCAG 60.747 63.158 0.00 0.00 0.00 4.85
1769 1901 2.564062 ACAAGCAGCAATTTACCAGCAT 59.436 40.909 0.00 0.00 0.00 3.79
1948 2080 3.492102 TCCAGCATCAGCCCTATAAAC 57.508 47.619 0.00 0.00 43.56 2.01
1984 2125 7.746916 GTCATATGACTCATATCTCACGTACAC 59.253 40.741 25.52 0.00 41.65 2.90
2130 2277 8.103305 TCTACTTGAGCTTTCACTTTTGGATAT 58.897 33.333 0.00 0.00 0.00 1.63
2276 2471 0.175302 CTTGTGCCCAGCAAACAACA 59.825 50.000 0.00 0.00 41.47 3.33
2411 2612 5.069318 TCATATCCAACAACAGCAAGACAA 58.931 37.500 0.00 0.00 0.00 3.18
2423 2624 5.848286 ATTAGGGCAGATCATATCCAACA 57.152 39.130 0.00 0.00 0.00 3.33
2436 2637 8.468399 GCCTACTACTACTATAAATTAGGGCAG 58.532 40.741 0.00 0.00 33.46 4.85
2626 2828 4.458989 GTCCATGCCAGAAAATGTGACTAA 59.541 41.667 0.00 0.00 0.00 2.24
2664 2866 9.343539 AGGGAACAAATGCTAACTTATAGATTC 57.656 33.333 0.00 0.00 0.00 2.52
2677 2879 3.228188 TGAGACAAGGGAACAAATGCT 57.772 42.857 0.00 0.00 0.00 3.79
2693 2897 8.331740 AGAAAAGATATGTTTGAGGGAATGAGA 58.668 33.333 0.00 0.00 0.00 3.27
2694 2898 8.517062 AGAAAAGATATGTTTGAGGGAATGAG 57.483 34.615 0.00 0.00 0.00 2.90
2700 2904 6.881065 TGACAGAGAAAAGATATGTTTGAGGG 59.119 38.462 0.00 0.00 0.00 4.30
2701 2905 7.912056 TGACAGAGAAAAGATATGTTTGAGG 57.088 36.000 0.00 0.00 0.00 3.86
2711 2915 8.538701 ACAGACAAGATATGACAGAGAAAAGAT 58.461 33.333 0.00 0.00 0.00 2.40
2734 2938 2.032030 CAGTAAGCCGTTTTGTCCACAG 60.032 50.000 0.00 0.00 0.00 3.66
2746 2950 3.388308 CTCATGGAGAATCAGTAAGCCG 58.612 50.000 0.00 0.00 36.25 5.52
2770 2975 5.130145 CCTTTCTATTCTCCTCTGGTCATGT 59.870 44.000 0.00 0.00 0.00 3.21
2771 2976 5.609423 CCTTTCTATTCTCCTCTGGTCATG 58.391 45.833 0.00 0.00 0.00 3.07
2794 2999 2.014068 GCAACATCAGTAGGTGAGGGC 61.014 57.143 0.00 0.00 41.51 5.19
2795 3000 1.556911 AGCAACATCAGTAGGTGAGGG 59.443 52.381 0.00 0.00 41.51 4.30
2799 3004 6.874134 AGTACTTTTAGCAACATCAGTAGGTG 59.126 38.462 0.00 0.00 0.00 4.00
2801 3006 9.601217 AATAGTACTTTTAGCAACATCAGTAGG 57.399 33.333 0.00 0.00 0.00 3.18
2804 3009 9.099454 GCTAATAGTACTTTTAGCAACATCAGT 57.901 33.333 34.43 6.05 44.22 3.41
2841 3046 3.627123 CACTTTCGATGCCATACCATCAA 59.373 43.478 3.44 0.00 41.27 2.57
2844 3049 1.949525 GCACTTTCGATGCCATACCAT 59.050 47.619 0.00 0.00 37.08 3.55
2848 3053 4.717233 AAATTGCACTTTCGATGCCATA 57.283 36.364 7.01 0.00 42.69 2.74
2875 3080 6.101997 AGGCAACATTAAAAATAGCTTCTGC 58.898 36.000 0.00 0.00 41.41 4.26
2898 3103 4.923871 AGAACTGACACGTGTATGCTTTAG 59.076 41.667 23.44 12.94 0.00 1.85
2900 3105 3.494626 CAGAACTGACACGTGTATGCTTT 59.505 43.478 23.44 10.49 0.00 3.51
2901 3106 3.059884 CAGAACTGACACGTGTATGCTT 58.940 45.455 23.44 10.47 0.00 3.91
2905 3110 3.247648 GCAAACAGAACTGACACGTGTAT 59.752 43.478 23.44 7.52 0.00 2.29
2907 3112 1.396996 GCAAACAGAACTGACACGTGT 59.603 47.619 23.64 23.64 0.00 4.49
2911 3116 1.014352 ACGGCAAACAGAACTGACAC 58.986 50.000 8.87 0.00 0.00 3.67
2917 3122 1.999071 TGGCACACGGCAAACAGAAC 61.999 55.000 0.00 0.00 46.20 3.01
2929 3134 6.743575 AATATGTTCTACTCTTTGGCACAC 57.256 37.500 0.00 0.00 39.29 3.82
2930 3135 8.318412 TCTTAATATGTTCTACTCTTTGGCACA 58.682 33.333 0.00 0.00 0.00 4.57
2950 3155 9.325198 TGCGACATATCTTTTGTGTATCTTAAT 57.675 29.630 0.00 0.00 0.00 1.40
2951 3156 8.600625 GTGCGACATATCTTTTGTGTATCTTAA 58.399 33.333 0.00 0.00 0.00 1.85
2952 3157 7.762159 TGTGCGACATATCTTTTGTGTATCTTA 59.238 33.333 0.00 0.00 0.00 2.10
2953 3158 6.593770 TGTGCGACATATCTTTTGTGTATCTT 59.406 34.615 0.00 0.00 0.00 2.40
2954 3159 6.106003 TGTGCGACATATCTTTTGTGTATCT 58.894 36.000 0.00 0.00 0.00 1.98
2955 3160 6.344572 TGTGCGACATATCTTTTGTGTATC 57.655 37.500 0.00 0.00 0.00 2.24
2956 3161 6.735678 TTGTGCGACATATCTTTTGTGTAT 57.264 33.333 0.00 0.00 0.00 2.29
2957 3162 6.735678 ATTGTGCGACATATCTTTTGTGTA 57.264 33.333 0.00 0.00 0.00 2.90
2958 3163 5.627499 ATTGTGCGACATATCTTTTGTGT 57.373 34.783 0.00 0.00 0.00 3.72
2959 3164 6.775088 AGTATTGTGCGACATATCTTTTGTG 58.225 36.000 0.00 0.00 0.00 3.33
2960 3165 6.985188 AGTATTGTGCGACATATCTTTTGT 57.015 33.333 0.00 0.00 0.00 2.83
2961 3166 9.935682 AATAAGTATTGTGCGACATATCTTTTG 57.064 29.630 0.00 0.00 0.00 2.44
2968 3173 8.708742 GCATCTTAATAAGTATTGTGCGACATA 58.291 33.333 0.00 0.00 0.00 2.29
2969 3174 7.307989 GGCATCTTAATAAGTATTGTGCGACAT 60.308 37.037 0.00 0.00 0.00 3.06
2970 3175 6.018262 GGCATCTTAATAAGTATTGTGCGACA 60.018 38.462 0.00 0.00 0.00 4.35
2971 3176 6.018262 TGGCATCTTAATAAGTATTGTGCGAC 60.018 38.462 0.00 0.00 0.00 5.19
2972 3177 6.052360 TGGCATCTTAATAAGTATTGTGCGA 58.948 36.000 0.00 0.46 0.00 5.10
2973 3178 6.299023 TGGCATCTTAATAAGTATTGTGCG 57.701 37.500 0.00 0.00 0.00 5.34
2974 3179 7.874940 TCATGGCATCTTAATAAGTATTGTGC 58.125 34.615 0.00 4.77 0.00 4.57
2975 3180 9.276590 TCTCATGGCATCTTAATAAGTATTGTG 57.723 33.333 0.00 0.00 0.00 3.33
2976 3181 9.851686 TTCTCATGGCATCTTAATAAGTATTGT 57.148 29.630 0.00 0.00 0.00 2.71
2980 3185 9.905713 AACTTTCTCATGGCATCTTAATAAGTA 57.094 29.630 0.00 0.00 0.00 2.24
2981 3186 8.814038 AACTTTCTCATGGCATCTTAATAAGT 57.186 30.769 0.00 0.49 0.00 2.24
2983 3188 9.905713 AGTAACTTTCTCATGGCATCTTAATAA 57.094 29.630 0.00 0.00 0.00 1.40
2985 3190 9.905713 TTAGTAACTTTCTCATGGCATCTTAAT 57.094 29.630 0.00 0.00 0.00 1.40
2986 3191 9.733556 TTTAGTAACTTTCTCATGGCATCTTAA 57.266 29.630 0.00 0.00 0.00 1.85
2987 3192 9.733556 TTTTAGTAACTTTCTCATGGCATCTTA 57.266 29.630 0.00 0.00 0.00 2.10
2988 3193 8.635765 TTTTAGTAACTTTCTCATGGCATCTT 57.364 30.769 0.00 0.00 0.00 2.40
2989 3194 8.814038 ATTTTAGTAACTTTCTCATGGCATCT 57.186 30.769 0.00 0.00 0.00 2.90
3017 3222 8.204836 GGAGTATATGTGTTGGAATTGTAGTCT 58.795 37.037 0.00 0.00 0.00 3.24
3018 3223 7.441458 GGGAGTATATGTGTTGGAATTGTAGTC 59.559 40.741 0.00 0.00 0.00 2.59
3019 3224 7.127339 AGGGAGTATATGTGTTGGAATTGTAGT 59.873 37.037 0.00 0.00 0.00 2.73
3020 3225 7.509546 AGGGAGTATATGTGTTGGAATTGTAG 58.490 38.462 0.00 0.00 0.00 2.74
3021 3226 7.419750 GGAGGGAGTATATGTGTTGGAATTGTA 60.420 40.741 0.00 0.00 0.00 2.41
3022 3227 6.327386 AGGGAGTATATGTGTTGGAATTGT 57.673 37.500 0.00 0.00 0.00 2.71
3023 3228 5.765182 GGAGGGAGTATATGTGTTGGAATTG 59.235 44.000 0.00 0.00 0.00 2.32
3024 3229 5.454755 CGGAGGGAGTATATGTGTTGGAATT 60.455 44.000 0.00 0.00 0.00 2.17
3025 3230 4.040461 CGGAGGGAGTATATGTGTTGGAAT 59.960 45.833 0.00 0.00 0.00 3.01
3026 3231 3.386726 CGGAGGGAGTATATGTGTTGGAA 59.613 47.826 0.00 0.00 0.00 3.53
3027 3232 2.963101 CGGAGGGAGTATATGTGTTGGA 59.037 50.000 0.00 0.00 0.00 3.53
3028 3233 2.698797 ACGGAGGGAGTATATGTGTTGG 59.301 50.000 0.00 0.00 0.00 3.77
3029 3234 3.243771 GGACGGAGGGAGTATATGTGTTG 60.244 52.174 0.00 0.00 0.00 3.33
3030 3235 2.963782 GGACGGAGGGAGTATATGTGTT 59.036 50.000 0.00 0.00 0.00 3.32
3031 3236 2.595238 GGACGGAGGGAGTATATGTGT 58.405 52.381 0.00 0.00 0.00 3.72
3032 3237 1.893801 GGGACGGAGGGAGTATATGTG 59.106 57.143 0.00 0.00 0.00 3.21
3033 3238 1.502039 TGGGACGGAGGGAGTATATGT 59.498 52.381 0.00 0.00 0.00 2.29
3034 3239 2.304221 TGGGACGGAGGGAGTATATG 57.696 55.000 0.00 0.00 0.00 1.78
3035 3240 3.339713 TTTGGGACGGAGGGAGTATAT 57.660 47.619 0.00 0.00 0.00 0.86
3036 3241 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
3037 3242 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
3038 3243 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3039 3244 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3040 3245 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3041 3246 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3042 3247 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3043 3248 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3044 3249 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3045 3250 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3046 3251 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3047 3252 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3048 3253 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3049 3254 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3050 3255 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3057 3262 8.242053 CGTACCTAGACAAATCTAAGACAAGAA 58.758 37.037 0.00 0.00 36.98 2.52
3058 3263 7.148120 CCGTACCTAGACAAATCTAAGACAAGA 60.148 40.741 0.00 0.00 36.98 3.02
3059 3264 6.973474 CCGTACCTAGACAAATCTAAGACAAG 59.027 42.308 0.00 0.00 36.98 3.16
3060 3265 6.435277 ACCGTACCTAGACAAATCTAAGACAA 59.565 38.462 0.00 0.00 36.98 3.18
3061 3266 5.948162 ACCGTACCTAGACAAATCTAAGACA 59.052 40.000 0.00 0.00 36.98 3.41
3062 3267 6.448207 ACCGTACCTAGACAAATCTAAGAC 57.552 41.667 0.00 0.00 36.98 3.01
3063 3268 6.435277 ACAACCGTACCTAGACAAATCTAAGA 59.565 38.462 0.00 0.00 36.98 2.10
3064 3269 6.628185 ACAACCGTACCTAGACAAATCTAAG 58.372 40.000 0.00 0.00 36.98 2.18
3065 3270 6.594788 ACAACCGTACCTAGACAAATCTAA 57.405 37.500 0.00 0.00 36.98 2.10
3066 3271 5.163723 CGACAACCGTACCTAGACAAATCTA 60.164 44.000 0.00 0.00 36.29 1.98
3067 3272 4.380233 CGACAACCGTACCTAGACAAATCT 60.380 45.833 0.00 0.00 39.15 2.40
3068 3273 3.855950 CGACAACCGTACCTAGACAAATC 59.144 47.826 0.00 0.00 0.00 2.17
3069 3274 3.841643 CGACAACCGTACCTAGACAAAT 58.158 45.455 0.00 0.00 0.00 2.32
3070 3275 3.287312 CGACAACCGTACCTAGACAAA 57.713 47.619 0.00 0.00 0.00 2.83
3071 3276 2.995466 CGACAACCGTACCTAGACAA 57.005 50.000 0.00 0.00 0.00 3.18
3082 3287 2.030958 GGGGCAAGTACGACAACCG 61.031 63.158 0.00 0.00 45.44 4.44
3083 3288 0.953960 CAGGGGCAAGTACGACAACC 60.954 60.000 0.00 0.00 0.00 3.77
3084 3289 0.250166 ACAGGGGCAAGTACGACAAC 60.250 55.000 0.00 0.00 0.00 3.32
3085 3290 0.470766 AACAGGGGCAAGTACGACAA 59.529 50.000 0.00 0.00 0.00 3.18
3086 3291 0.250124 CAACAGGGGCAAGTACGACA 60.250 55.000 0.00 0.00 0.00 4.35
3087 3292 1.574702 GCAACAGGGGCAAGTACGAC 61.575 60.000 0.00 0.00 0.00 4.34
3088 3293 1.302192 GCAACAGGGGCAAGTACGA 60.302 57.895 0.00 0.00 0.00 3.43
3089 3294 2.332654 GGCAACAGGGGCAAGTACG 61.333 63.158 0.00 0.00 0.00 3.67
3090 3295 1.228429 TGGCAACAGGGGCAAGTAC 60.228 57.895 0.00 0.00 46.17 2.73
3091 3296 3.256082 TGGCAACAGGGGCAAGTA 58.744 55.556 0.00 0.00 46.17 2.24
3101 3306 1.531365 CCTGGAAAGCCTGGCAACA 60.531 57.895 22.65 12.36 44.97 3.33
3102 3307 3.369921 CCTGGAAAGCCTGGCAAC 58.630 61.111 22.65 11.07 44.97 4.17
3110 3315 0.975887 TCCAAATTGGCCTGGAAAGC 59.024 50.000 8.96 0.00 38.81 3.51
3111 3316 2.250924 AGTCCAAATTGGCCTGGAAAG 58.749 47.619 12.79 0.00 43.32 2.62
3112 3317 2.397044 AGTCCAAATTGGCCTGGAAA 57.603 45.000 12.79 0.00 43.32 3.13
3113 3318 2.397044 AAGTCCAAATTGGCCTGGAA 57.603 45.000 12.79 0.00 43.32 3.53
3114 3319 2.247358 GAAAGTCCAAATTGGCCTGGA 58.753 47.619 7.24 7.35 39.47 3.86
3115 3320 1.969923 TGAAAGTCCAAATTGGCCTGG 59.030 47.619 7.24 2.69 37.47 4.45
3116 3321 3.674138 CGATGAAAGTCCAAATTGGCCTG 60.674 47.826 7.24 0.00 37.47 4.85
3117 3322 2.493278 CGATGAAAGTCCAAATTGGCCT 59.507 45.455 7.24 0.00 37.47 5.19
3118 3323 2.879826 CGATGAAAGTCCAAATTGGCC 58.120 47.619 7.24 0.00 37.47 5.36
3119 3324 2.262211 GCGATGAAAGTCCAAATTGGC 58.738 47.619 7.24 2.71 37.47 4.52
3120 3325 2.095263 ACGCGATGAAAGTCCAAATTGG 60.095 45.455 15.93 5.48 39.43 3.16
3121 3326 3.201726 ACGCGATGAAAGTCCAAATTG 57.798 42.857 15.93 0.00 0.00 2.32
3122 3327 3.915437 AACGCGATGAAAGTCCAAATT 57.085 38.095 15.93 0.00 0.00 1.82
3123 3328 3.915437 AAACGCGATGAAAGTCCAAAT 57.085 38.095 15.93 0.00 0.00 2.32
3124 3329 3.363182 CGTAAACGCGATGAAAGTCCAAA 60.363 43.478 15.93 0.00 0.00 3.28
3125 3330 2.156117 CGTAAACGCGATGAAAGTCCAA 59.844 45.455 15.93 0.00 0.00 3.53
3126 3331 1.722464 CGTAAACGCGATGAAAGTCCA 59.278 47.619 15.93 0.00 0.00 4.02
3127 3332 1.987770 TCGTAAACGCGATGAAAGTCC 59.012 47.619 15.93 0.00 39.60 3.85
3128 3333 2.660236 ACTCGTAAACGCGATGAAAGTC 59.340 45.455 15.93 0.00 40.29 3.01
3129 3334 2.669364 ACTCGTAAACGCGATGAAAGT 58.331 42.857 15.93 6.03 40.29 2.66
3130 3335 3.481467 GGAACTCGTAAACGCGATGAAAG 60.481 47.826 15.93 5.33 40.29 2.62
3131 3336 2.409378 GGAACTCGTAAACGCGATGAAA 59.591 45.455 15.93 0.00 40.29 2.69
3132 3337 1.987770 GGAACTCGTAAACGCGATGAA 59.012 47.619 15.93 0.00 40.29 2.57
3133 3338 1.200716 AGGAACTCGTAAACGCGATGA 59.799 47.619 15.93 0.00 40.29 2.92
3134 3339 1.320555 CAGGAACTCGTAAACGCGATG 59.679 52.381 15.93 0.00 40.29 3.84
3135 3340 1.068055 ACAGGAACTCGTAAACGCGAT 60.068 47.619 15.93 0.00 40.29 4.58
3136 3341 0.311790 ACAGGAACTCGTAAACGCGA 59.688 50.000 15.93 0.00 34.60 5.87
3137 3342 0.706729 GACAGGAACTCGTAAACGCG 59.293 55.000 3.53 3.53 34.60 6.01
3138 3343 1.984297 GAGACAGGAACTCGTAAACGC 59.016 52.381 0.00 0.00 34.60 4.84
3146 3351 1.513622 GGAGCCGAGACAGGAACTC 59.486 63.158 0.00 0.00 34.60 3.01
3147 3352 2.344203 CGGAGCCGAGACAGGAACT 61.344 63.158 2.00 0.00 42.83 3.01
3148 3353 1.310933 TACGGAGCCGAGACAGGAAC 61.311 60.000 16.83 0.00 42.83 3.62
3149 3354 0.609957 TTACGGAGCCGAGACAGGAA 60.610 55.000 16.83 0.00 42.83 3.36
3150 3355 1.001764 TTACGGAGCCGAGACAGGA 60.002 57.895 16.83 0.00 42.83 3.86
3151 3356 1.433879 CTTACGGAGCCGAGACAGG 59.566 63.158 16.83 0.00 42.83 4.00
3152 3357 1.030488 TCCTTACGGAGCCGAGACAG 61.030 60.000 16.83 5.35 42.83 3.51
3153 3358 1.001764 TCCTTACGGAGCCGAGACA 60.002 57.895 16.83 0.00 42.83 3.41
3154 3359 3.915575 TCCTTACGGAGCCGAGAC 58.084 61.111 16.83 0.00 42.83 3.36


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

AutoCloner maintained by Alex Coulton.