Multiple sequence alignment - TraesCS1B01G186300

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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 TraesCS1B01G186300 chr1B 100.000 3848 0 0 1 3848 333325024 333321177 0.000000e+00 7107.0
1 TraesCS1B01G186300 chr1D 93.061 2493 115 20 657 3133 240988560 240991010 0.000000e+00 3592.0
2 TraesCS1B01G186300 chr1D 92.276 725 46 8 3130 3848 241010124 241010844 0.000000e+00 1020.0
3 TraesCS1B01G186300 chr1D 90.554 307 27 2 258 563 240986151 240986456 4.630000e-109 405.0
4 TraesCS1B01G186300 chr1D 90.228 307 28 2 258 563 240984500 240984805 2.150000e-107 399.0
5 TraesCS1B01G186300 chr1D 89.542 306 28 4 258 562 240982923 240983225 6.030000e-103 385.0
6 TraesCS1B01G186300 chr1D 91.346 104 6 3 657 758 240984161 240984263 5.180000e-29 139.0
7 TraesCS1B01G186300 chr1D 97.403 77 2 0 566 642 240984097 240984173 8.670000e-27 132.0
8 TraesCS1B01G186300 chr1D 97.403 77 1 1 566 642 240985749 240985824 3.120000e-26 130.0
9 TraesCS1B01G186300 chr1D 97.333 75 2 0 568 642 240988498 240988572 1.120000e-25 128.0
10 TraesCS1B01G186300 chr1A 91.136 2561 120 32 568 3112 305605968 305608437 0.000000e+00 3373.0
11 TraesCS1B01G186300 chr1A 87.547 803 84 13 3052 3848 305608910 305609702 0.000000e+00 915.0
12 TraesCS1B01G186300 chr1A 90.948 232 20 1 332 563 305604792 305605022 1.040000e-80 311.0
13 TraesCS1B01G186300 chr2A 87.669 519 53 10 2217 2728 778723523 778723009 9.200000e-166 593.0
14 TraesCS1B01G186300 chr2B 87.165 522 62 5 2208 2725 777829665 777830185 4.280000e-164 588.0
15 TraesCS1B01G186300 chr2B 83.645 428 52 6 2302 2725 777836786 777837199 1.680000e-103 387.0
16 TraesCS1B01G186300 chr2D 86.667 525 59 9 2208 2725 634797473 634797993 4.310000e-159 571.0
17 TraesCS1B01G186300 chr2D 89.906 426 38 5 2304 2725 634809851 634810275 9.400000e-151 544.0
18 TraesCS1B01G186300 chr2D 85.409 514 67 8 2217 2725 634824832 634825342 9.470000e-146 527.0
19 TraesCS1B01G186300 chr2D 82.865 356 34 15 3150 3482 29853763 29854114 1.050000e-75 294.0
20 TraesCS1B01G186300 chr7B 79.474 380 43 23 3121 3472 725370176 725369804 1.790000e-58 237.0
21 TraesCS1B01G186300 chr6B 78.042 378 47 20 3120 3476 687328922 687329284 5.040000e-49 206.0
22 TraesCS1B01G186300 chr5D 82.000 200 18 11 3296 3479 217331937 217331740 1.850000e-33 154.0
23 TraesCS1B01G186300 chr5D 92.727 55 3 1 3427 3481 217331708 217331655 1.150000e-10 78.7
24 TraesCS1B01G186300 chr7D 85.470 117 14 3 3367 3482 66368665 66368779 6.750000e-23 119.0
25 TraesCS1B01G186300 chr3B 89.091 55 6 0 111 165 819945771 819945717 6.900000e-08 69.4


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 TraesCS1B01G186300 chr1B 333321177 333325024 3847 True 7107.00 7107 100.00000 1 3848 1 chr1B.!!$R1 3847
1 TraesCS1B01G186300 chr1D 241010124 241010844 720 False 1020.00 1020 92.27600 3130 3848 1 chr1D.!!$F1 718
2 TraesCS1B01G186300 chr1D 240982923 240991010 8087 False 663.75 3592 93.35875 258 3133 8 chr1D.!!$F2 2875
3 TraesCS1B01G186300 chr1A 305604792 305609702 4910 False 1533.00 3373 89.87700 332 3848 3 chr1A.!!$F1 3516
4 TraesCS1B01G186300 chr2A 778723009 778723523 514 True 593.00 593 87.66900 2217 2728 1 chr2A.!!$R1 511
5 TraesCS1B01G186300 chr2B 777829665 777830185 520 False 588.00 588 87.16500 2208 2725 1 chr2B.!!$F1 517
6 TraesCS1B01G186300 chr2D 634797473 634797993 520 False 571.00 571 86.66700 2208 2725 1 chr2D.!!$F2 517
7 TraesCS1B01G186300 chr2D 634824832 634825342 510 False 527.00 527 85.40900 2217 2725 1 chr2D.!!$F4 508

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
874 5904 0.111061 TTCCATTCTGTGCACCAGCT 59.889 50.0 15.69 0.59 41.25 4.24 F
1250 6291 0.034896 ATTTCGCGGTTCTGTGGTCT 59.965 50.0 6.13 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2751 7796 1.006102 GATCGATCGGGGATTGCGT 60.006 57.895 16.41 0.0 0.0 5.24 R
3142 8717 0.097674 CTTCATTTCAAGAGGCCGCG 59.902 55.000 0.00 0.0 0.0 6.46 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
19 20 2.730934 TGAGGACGACTATGCCTAGT 57.269 50.000 0.79 0.79 40.98 2.57
28 29 3.954999 GACTATGCCTAGTCGTTGACTC 58.045 50.000 12.58 0.00 43.25 3.36
29 30 2.355132 ACTATGCCTAGTCGTTGACTCG 59.645 50.000 2.17 0.00 42.40 4.18
30 31 0.456221 ATGCCTAGTCGTTGACTCGG 59.544 55.000 11.91 11.91 44.92 4.63
31 32 4.787999 CCTAGTCGTTGACTCGGC 57.212 61.111 2.17 0.00 42.40 5.54
32 33 1.226323 CCTAGTCGTTGACTCGGCG 60.226 63.158 0.00 0.00 42.40 6.46
33 34 1.226323 CTAGTCGTTGACTCGGCGG 60.226 63.158 7.21 0.00 42.40 6.13
34 35 2.594119 CTAGTCGTTGACTCGGCGGG 62.594 65.000 4.58 4.58 42.40 6.13
50 51 4.376170 GGCCAACGGGGTGGGAAT 62.376 66.667 4.68 0.00 39.26 3.01
51 52 2.754254 GCCAACGGGGTGGGAATC 60.754 66.667 4.68 0.00 39.26 2.52
52 53 3.087065 CCAACGGGGTGGGAATCT 58.913 61.111 0.00 0.00 34.77 2.40
53 54 1.378514 CCAACGGGGTGGGAATCTG 60.379 63.158 0.00 0.00 34.77 2.90
54 55 1.682849 CAACGGGGTGGGAATCTGA 59.317 57.895 0.00 0.00 0.00 3.27
55 56 0.676782 CAACGGGGTGGGAATCTGAC 60.677 60.000 0.00 0.00 0.00 3.51
56 57 2.180159 AACGGGGTGGGAATCTGACG 62.180 60.000 0.00 0.00 0.00 4.35
57 58 2.124695 GGGGTGGGAATCTGACGC 60.125 66.667 0.00 0.00 0.00 5.19
59 60 2.511600 GGTGGGAATCTGACGCGG 60.512 66.667 12.47 0.00 0.00 6.46
60 61 2.511600 GTGGGAATCTGACGCGGG 60.512 66.667 12.47 0.00 0.00 6.13
61 62 2.682136 TGGGAATCTGACGCGGGA 60.682 61.111 12.47 6.07 0.00 5.14
62 63 2.287274 TGGGAATCTGACGCGGGAA 61.287 57.895 12.47 0.00 0.00 3.97
63 64 1.521681 GGGAATCTGACGCGGGAAG 60.522 63.158 12.47 4.67 0.00 3.46
64 65 1.218316 GGAATCTGACGCGGGAAGT 59.782 57.895 12.47 0.00 0.00 3.01
65 66 0.391263 GGAATCTGACGCGGGAAGTT 60.391 55.000 12.47 0.00 0.00 2.66
66 67 1.439679 GAATCTGACGCGGGAAGTTT 58.560 50.000 12.47 6.03 0.00 2.66
69 70 1.597027 CTGACGCGGGAAGTTTGGT 60.597 57.895 12.47 0.00 0.00 3.67
70 71 1.841663 CTGACGCGGGAAGTTTGGTG 61.842 60.000 12.47 0.00 0.00 4.17
71 72 3.249973 GACGCGGGAAGTTTGGTGC 62.250 63.158 12.47 0.00 0.00 5.01
73 74 2.597510 GCGGGAAGTTTGGTGCCT 60.598 61.111 0.00 0.00 0.00 4.75
74 75 2.200337 GCGGGAAGTTTGGTGCCTT 61.200 57.895 0.00 0.00 0.00 4.35
75 76 1.744320 GCGGGAAGTTTGGTGCCTTT 61.744 55.000 0.00 0.00 0.00 3.11
76 77 0.750249 CGGGAAGTTTGGTGCCTTTT 59.250 50.000 0.00 0.00 0.00 2.27
91 92 3.766432 TTTTTCTTTCCCCCGGCG 58.234 55.556 0.00 0.00 0.00 6.46
92 93 2.566570 TTTTTCTTTCCCCCGGCGC 61.567 57.895 0.00 0.00 0.00 6.53
127 128 3.175240 CGCGCTGAGTTCGACCTG 61.175 66.667 5.56 0.00 0.00 4.00
128 129 2.811317 GCGCTGAGTTCGACCTGG 60.811 66.667 0.00 0.00 0.00 4.45
131 132 1.079750 GCTGAGTTCGACCTGGGTC 60.080 63.158 9.55 9.55 41.40 4.46
132 133 1.536943 GCTGAGTTCGACCTGGGTCT 61.537 60.000 16.44 0.00 42.54 3.85
133 134 0.244994 CTGAGTTCGACCTGGGTCTG 59.755 60.000 16.44 10.61 42.54 3.51
135 136 2.047179 GTTCGACCTGGGTCTGCC 60.047 66.667 16.44 1.91 42.54 4.85
136 137 3.691342 TTCGACCTGGGTCTGCCG 61.691 66.667 16.44 5.41 42.54 5.69
146 147 3.747976 GTCTGCCGGCGCCAATTT 61.748 61.111 28.98 0.00 0.00 1.82
147 148 3.439540 TCTGCCGGCGCCAATTTC 61.440 61.111 28.98 10.27 0.00 2.17
148 149 4.834892 CTGCCGGCGCCAATTTCG 62.835 66.667 28.98 11.16 0.00 3.46
157 158 1.813859 GCCAATTTCGGGCCTAACC 59.186 57.895 0.84 0.00 45.87 2.85
167 168 2.640316 GGGCCTAACCGATGAAATCT 57.360 50.000 0.84 0.00 42.58 2.40
168 169 2.222027 GGGCCTAACCGATGAAATCTG 58.778 52.381 0.84 0.00 42.58 2.90
169 170 2.222027 GGCCTAACCGATGAAATCTGG 58.778 52.381 0.00 0.00 42.58 3.86
170 171 1.604278 GCCTAACCGATGAAATCTGGC 59.396 52.381 0.00 0.00 42.58 4.85
172 173 2.158755 CCTAACCGATGAAATCTGGCCT 60.159 50.000 3.32 0.00 42.58 5.19
173 174 2.044123 AACCGATGAAATCTGGCCTC 57.956 50.000 3.32 0.00 42.58 4.70
174 175 0.181350 ACCGATGAAATCTGGCCTCC 59.819 55.000 3.32 0.00 42.58 4.30
175 176 0.471617 CCGATGAAATCTGGCCTCCT 59.528 55.000 3.32 0.00 42.58 3.69
176 177 1.542108 CCGATGAAATCTGGCCTCCTC 60.542 57.143 3.32 0.00 42.58 3.71
177 178 1.871408 CGATGAAATCTGGCCTCCTCG 60.871 57.143 3.32 3.12 42.58 4.63
178 179 0.471617 ATGAAATCTGGCCTCCTCGG 59.528 55.000 3.32 0.00 0.00 4.63
232 233 2.861730 AAAAAGGGCCTGGGAGGG 59.138 61.111 6.92 0.00 35.37 4.30
240 241 4.052518 CCTGGGAGGGCTGTTGGG 62.053 72.222 0.00 0.00 0.00 4.12
241 242 4.052518 CTGGGAGGGCTGTTGGGG 62.053 72.222 0.00 0.00 0.00 4.96
258 259 2.512515 GGGCGTGTGGAGATGCTC 60.513 66.667 0.00 0.00 0.00 4.26
259 260 2.581354 GGCGTGTGGAGATGCTCT 59.419 61.111 0.00 0.00 0.00 4.09
260 261 1.676678 GGGCGTGTGGAGATGCTCTA 61.677 60.000 0.00 0.00 0.00 2.43
262 263 1.565305 GCGTGTGGAGATGCTCTAAG 58.435 55.000 0.00 0.00 0.00 2.18
291 1613 1.269723 GCTGGAAAAACTGGTAGCCAC 59.730 52.381 0.00 0.00 0.00 5.01
308 1630 1.066858 CCACGTTCAGGTAGTCTGCAT 60.067 52.381 0.00 0.00 43.06 3.96
321 1643 1.002430 GTCTGCATCCTCTGTGTCCAA 59.998 52.381 0.00 0.00 0.00 3.53
372 1694 8.893727 CAAAATATTTTTCTACTCGGATGTCCT 58.106 33.333 10.77 0.00 0.00 3.85
375 1697 5.477607 TTTTTCTACTCGGATGTCCTTGA 57.522 39.130 0.00 0.00 0.00 3.02
392 1714 1.373435 GATGGGACCCGTGTTGACA 59.627 57.895 10.96 0.00 0.00 3.58
433 3405 3.245754 CACGCAAGCATGTCAAAACATTT 59.754 39.130 0.00 0.00 42.31 2.32
454 3426 2.028561 TTAGGGTGTTTAGGACCGGT 57.971 50.000 6.92 6.92 33.89 5.28
462 3434 3.104512 TGTTTAGGACCGGTGATGATCT 58.895 45.455 14.63 1.97 0.00 2.75
507 3479 8.180920 CCCAAATTTACAGTTTTGAAGTTTTGG 58.819 33.333 0.00 0.00 39.21 3.28
516 3488 5.299531 AGTTTTGAAGTTTTGGGACTAGCTC 59.700 40.000 0.00 0.00 0.00 4.09
533 3505 3.077359 AGCTCAACACACCTCAAATAGC 58.923 45.455 0.00 0.00 0.00 2.97
542 3514 5.013183 ACACACCTCAAATAGCTTTAGGACT 59.987 40.000 0.00 0.00 0.00 3.85
550 3522 6.775629 TCAAATAGCTTTAGGACTTTTGGTGT 59.224 34.615 0.00 0.00 0.00 4.16
563 3535 8.630037 AGGACTTTTGGTGTATTTTACTCTTTG 58.370 33.333 0.00 0.00 0.00 2.77
564 3536 8.626526 GGACTTTTGGTGTATTTTACTCTTTGA 58.373 33.333 0.00 0.00 0.00 2.69
572 5592 8.451748 GGTGTATTTTACTCTTTGAAGGATGAC 58.548 37.037 0.00 0.00 0.00 3.06
636 5656 5.355910 GCCGGTTCATGGTAAGAAAATAGAA 59.644 40.000 1.90 0.00 0.00 2.10
637 5657 6.039382 GCCGGTTCATGGTAAGAAAATAGAAT 59.961 38.462 1.90 0.00 0.00 2.40
638 5658 7.227910 GCCGGTTCATGGTAAGAAAATAGAATA 59.772 37.037 1.90 0.00 0.00 1.75
639 5659 9.284968 CCGGTTCATGGTAAGAAAATAGAATAT 57.715 33.333 0.00 0.00 0.00 1.28
647 5667 9.542462 TGGTAAGAAAATAGAATATTGTCCTCG 57.458 33.333 0.00 0.00 0.00 4.63
648 5668 8.496751 GGTAAGAAAATAGAATATTGTCCTCGC 58.503 37.037 0.00 0.00 0.00 5.03
649 5669 9.042008 GTAAGAAAATAGAATATTGTCCTCGCA 57.958 33.333 0.00 0.00 0.00 5.10
650 5670 8.506168 AAGAAAATAGAATATTGTCCTCGCAA 57.494 30.769 0.00 0.00 0.00 4.85
651 5671 8.506168 AGAAAATAGAATATTGTCCTCGCAAA 57.494 30.769 0.00 0.00 31.63 3.68
652 5672 8.956426 AGAAAATAGAATATTGTCCTCGCAAAA 58.044 29.630 0.00 0.00 31.63 2.44
653 5673 9.567848 GAAAATAGAATATTGTCCTCGCAAAAA 57.432 29.630 0.00 0.00 31.63 1.94
732 5754 5.521735 GCAAGATCTGTCTGTTGTATTCGAT 59.478 40.000 0.00 0.00 34.13 3.59
757 5780 3.005539 GTCCTGCTCCTGCTCCCA 61.006 66.667 0.00 0.00 40.48 4.37
790 5813 1.589630 GAACAAAACCGGCCCATCC 59.410 57.895 0.00 0.00 0.00 3.51
844 5874 1.331138 CCAACAGCGACCAACGTTTAA 59.669 47.619 0.00 0.00 44.60 1.52
845 5875 2.223294 CCAACAGCGACCAACGTTTAAA 60.223 45.455 0.00 0.00 44.60 1.52
854 5884 4.441744 CGACCAACGTTTAAATCAAAACCC 59.558 41.667 0.00 0.00 36.24 4.11
869 5899 1.620822 AACCCTTCCATTCTGTGCAC 58.379 50.000 10.75 10.75 0.00 4.57
874 5904 0.111061 TTCCATTCTGTGCACCAGCT 59.889 50.000 15.69 0.59 41.25 4.24
879 5909 1.767654 TTCTGTGCACCAGCTAGCCA 61.768 55.000 15.69 0.00 41.25 4.75
880 5910 1.744368 CTGTGCACCAGCTAGCCAG 60.744 63.158 15.69 5.48 42.74 4.85
882 5912 2.607442 TGCACCAGCTAGCCAGGA 60.607 61.111 25.80 7.06 42.74 3.86
885 5915 1.099879 GCACCAGCTAGCCAGGAATG 61.100 60.000 25.80 16.90 37.91 2.67
889 5919 2.002977 AGCTAGCCAGGAATGCCCA 61.003 57.895 12.13 0.00 37.41 5.36
985 6016 2.449730 TCCCCCTATCACCTTATCGTCT 59.550 50.000 0.00 0.00 0.00 4.18
991 6022 1.022735 TCACCTTATCGTCTCCGCTC 58.977 55.000 0.00 0.00 0.00 5.03
1056 6088 2.821366 CTCACTGCCATCCGCACC 60.821 66.667 0.00 0.00 44.64 5.01
1057 6089 4.758251 TCACTGCCATCCGCACCG 62.758 66.667 0.00 0.00 44.64 4.94
1070 6102 1.409412 CGCACCGCACTATCTGATAC 58.591 55.000 0.00 0.00 0.00 2.24
1071 6103 1.269051 CGCACCGCACTATCTGATACA 60.269 52.381 0.00 0.00 0.00 2.29
1072 6104 2.128035 GCACCGCACTATCTGATACAC 58.872 52.381 0.00 0.00 0.00 2.90
1073 6105 2.223829 GCACCGCACTATCTGATACACT 60.224 50.000 0.00 0.00 0.00 3.55
1084 6120 2.032178 TCTGATACACTCACTCATCGCG 59.968 50.000 0.00 0.00 0.00 5.87
1147 6184 4.824515 CTCCCGTCGGCCCTCTCT 62.825 72.222 5.50 0.00 0.00 3.10
1169 6210 2.729360 GCGCGCAAAGAGGTTTAATTTT 59.271 40.909 29.10 0.00 0.00 1.82
1181 6222 8.980481 AGAGGTTTAATTTTCTCAACTTCTCA 57.020 30.769 0.00 0.00 31.85 3.27
1192 6233 2.634940 TCAACTTCTCAGGGGAGTTCAG 59.365 50.000 0.00 0.00 42.05 3.02
1195 6236 1.277557 CTTCTCAGGGGAGTTCAGGTG 59.722 57.143 0.00 0.00 42.05 4.00
1201 6242 1.600916 GGGAGTTCAGGTGTGGTGC 60.601 63.158 0.00 0.00 0.00 5.01
1202 6243 1.451936 GGAGTTCAGGTGTGGTGCT 59.548 57.895 0.00 0.00 0.00 4.40
1203 6244 0.179018 GGAGTTCAGGTGTGGTGCTT 60.179 55.000 0.00 0.00 0.00 3.91
1204 6245 0.947244 GAGTTCAGGTGTGGTGCTTG 59.053 55.000 0.00 0.00 0.00 4.01
1205 6246 0.466189 AGTTCAGGTGTGGTGCTTGG 60.466 55.000 0.00 0.00 0.00 3.61
1206 6247 0.465460 GTTCAGGTGTGGTGCTTGGA 60.465 55.000 0.00 0.00 0.00 3.53
1207 6248 0.179020 TTCAGGTGTGGTGCTTGGAG 60.179 55.000 0.00 0.00 0.00 3.86
1208 6249 1.149174 CAGGTGTGGTGCTTGGAGT 59.851 57.895 0.00 0.00 0.00 3.85
1209 6250 0.466189 CAGGTGTGGTGCTTGGAGTT 60.466 55.000 0.00 0.00 0.00 3.01
1210 6251 0.258774 AGGTGTGGTGCTTGGAGTTT 59.741 50.000 0.00 0.00 0.00 2.66
1211 6252 0.668535 GGTGTGGTGCTTGGAGTTTC 59.331 55.000 0.00 0.00 0.00 2.78
1212 6253 1.680338 GTGTGGTGCTTGGAGTTTCT 58.320 50.000 0.00 0.00 0.00 2.52
1213 6254 2.024414 GTGTGGTGCTTGGAGTTTCTT 58.976 47.619 0.00 0.00 0.00 2.52
1214 6255 2.033424 GTGTGGTGCTTGGAGTTTCTTC 59.967 50.000 0.00 0.00 0.00 2.87
1223 6264 4.082517 GCTTGGAGTTTCTTCCCAATCTTC 60.083 45.833 0.00 0.00 39.03 2.87
1237 6278 1.009829 ATCTTCGGTGCTGATTTCGC 58.990 50.000 0.00 0.00 0.00 4.70
1240 6281 3.118454 CGGTGCTGATTTCGCGGT 61.118 61.111 6.13 0.00 0.00 5.68
1242 6283 1.134694 GGTGCTGATTTCGCGGTTC 59.865 57.895 6.13 1.18 0.00 3.62
1250 6291 0.034896 ATTTCGCGGTTCTGTGGTCT 59.965 50.000 6.13 0.00 0.00 3.85
1334 6375 4.599500 ACACCACCTCCCTGGGCT 62.599 66.667 8.22 0.00 41.11 5.19
1365 6406 2.555757 AGGTGAGCTCAAATCTTTGCAC 59.444 45.455 20.19 1.80 38.05 4.57
1413 6454 3.333414 GCAAGTTGCTGCTCGTCA 58.667 55.556 20.71 0.00 40.96 4.35
1418 6459 1.510623 GTTGCTGCTCGTCATTGCG 60.511 57.895 0.00 0.00 0.00 4.85
1419 6460 1.960763 TTGCTGCTCGTCATTGCGT 60.961 52.632 0.00 0.00 0.00 5.24
1420 6461 0.669012 TTGCTGCTCGTCATTGCGTA 60.669 50.000 0.00 0.00 0.00 4.42
1456 6497 5.163099 TGGGGAATTGCAGCTAGTAACATAT 60.163 40.000 0.00 0.00 0.00 1.78
1457 6498 6.043822 TGGGGAATTGCAGCTAGTAACATATA 59.956 38.462 0.00 0.00 0.00 0.86
1470 6511 8.182881 GCTAGTAACATATAGTCGAGTAATGGG 58.817 40.741 18.41 8.00 0.00 4.00
1474 6515 5.145564 ACATATAGTCGAGTAATGGGGTGT 58.854 41.667 18.41 9.96 0.00 4.16
1482 6523 3.687698 CGAGTAATGGGGTGTCGAATTTT 59.312 43.478 0.00 0.00 32.32 1.82
1483 6524 4.871557 CGAGTAATGGGGTGTCGAATTTTA 59.128 41.667 0.00 0.00 32.32 1.52
1501 6542 8.070171 CGAATTTTATGATTAGTTAGCTGGGTG 58.930 37.037 0.00 0.00 0.00 4.61
1502 6543 9.120538 GAATTTTATGATTAGTTAGCTGGGTGA 57.879 33.333 0.00 0.00 0.00 4.02
1503 6544 8.682936 ATTTTATGATTAGTTAGCTGGGTGAG 57.317 34.615 0.00 0.00 0.00 3.51
1504 6545 6.808321 TTATGATTAGTTAGCTGGGTGAGT 57.192 37.500 0.00 0.00 0.00 3.41
1517 6558 1.757699 GGGTGAGTACTTGGGCTAGAG 59.242 57.143 0.00 0.00 0.00 2.43
1525 6566 1.270907 CTTGGGCTAGAGTGTGGACT 58.729 55.000 0.00 0.00 33.98 3.85
1536 6577 1.202580 AGTGTGGACTGTGCTCTGTTC 60.203 52.381 0.00 0.00 0.00 3.18
1544 6585 1.661821 GTGCTCTGTTCGTCGCTGT 60.662 57.895 0.00 0.00 0.00 4.40
1583 6625 1.007734 GTCACGAACCACGCAGAGA 60.008 57.895 0.00 0.00 46.94 3.10
1982 7024 2.347490 GAGCCTTCCTTCACCGCA 59.653 61.111 0.00 0.00 0.00 5.69
2075 7117 2.758737 AAGGCCTCCGACTACCCG 60.759 66.667 5.23 0.00 0.00 5.28
2120 7162 4.262721 GGCTCCATCACCGGTAATATGTAA 60.263 45.833 6.87 1.82 0.00 2.41
2121 7163 5.488341 GCTCCATCACCGGTAATATGTAAT 58.512 41.667 6.87 0.00 0.00 1.89
2122 7164 6.351541 GGCTCCATCACCGGTAATATGTAATA 60.352 42.308 6.87 0.00 0.00 0.98
2123 7165 7.272978 GCTCCATCACCGGTAATATGTAATAT 58.727 38.462 6.87 0.00 42.49 1.28
2124 7166 8.418662 GCTCCATCACCGGTAATATGTAATATA 58.581 37.037 6.87 0.00 38.94 0.86
2142 7184 5.767816 ATATATGTACATGCGCGATCCTA 57.232 39.130 18.81 0.00 0.00 2.94
2200 7242 8.208224 TGTTTCAGAGTGTAACCTTCATTTCTA 58.792 33.333 0.00 0.00 37.80 2.10
2491 7536 3.717294 ATCCCGCTGTTCCGCCTT 61.717 61.111 0.00 0.00 0.00 4.35
2596 7641 2.900106 GCCCAGCCTCACCAAGTCT 61.900 63.158 0.00 0.00 0.00 3.24
2647 7692 0.038159 CGTCCTTCGAGAACCAGCTT 60.038 55.000 0.00 0.00 42.86 3.74
2677 7722 3.303135 AGCGACACCGAGAAGGCA 61.303 61.111 0.00 0.00 46.52 4.75
2876 7922 2.686915 ACTGCTAGATTAAGTACGCGGT 59.313 45.455 12.47 0.00 32.61 5.68
2955 8001 8.424274 AACTAGTTCTTTTTGCTTTGATTTGG 57.576 30.769 1.12 0.00 0.00 3.28
2956 8002 7.555965 ACTAGTTCTTTTTGCTTTGATTTGGT 58.444 30.769 0.00 0.00 0.00 3.67
2957 8003 8.691797 ACTAGTTCTTTTTGCTTTGATTTGGTA 58.308 29.630 0.00 0.00 0.00 3.25
3020 8066 5.751990 GGAAGTACAGTTCGACTTTTTGAGA 59.248 40.000 0.00 0.00 36.04 3.27
3035 8081 6.371825 ACTTTTTGAGATTCATCCGGTAACTC 59.628 38.462 0.00 4.32 0.00 3.01
3043 8089 1.623542 ATCCGGTAACTCCACCCAGC 61.624 60.000 0.00 0.00 34.90 4.85
3068 8114 6.995633 CGAATTTTCTTTCAACGTTACAATGC 59.004 34.615 0.00 0.00 0.00 3.56
3109 8684 4.404073 TGGGCTGTGTGTTTTAGTTGAAAT 59.596 37.500 0.00 0.00 0.00 2.17
3137 8712 2.700407 TTTACTGGTGGTTGGGGCCG 62.700 60.000 0.00 0.00 0.00 6.13
3157 8734 2.040544 CACCGCGGCCTCTTGAAAT 61.041 57.895 28.58 0.00 0.00 2.17
3176 8753 2.587612 TGAAGTTGTGCGCGTATTTC 57.412 45.000 8.43 7.30 0.00 2.17
3247 8824 4.705337 AAAAACTTTCTGGCAACACGTA 57.295 36.364 0.00 0.00 46.17 3.57
3276 8853 5.048504 TCACATCCATCTCAAACAGAAAAGC 60.049 40.000 0.00 0.00 33.62 3.51
3410 8991 2.872858 GTTCAAGAAGTTTCTCGCCACT 59.127 45.455 0.00 0.00 36.28 4.00
3430 9011 2.201708 CCAACCAGCATGTGCCACA 61.202 57.895 0.00 0.00 43.38 4.17
3472 9053 0.373716 CTTCTCCCGCACGTTAATGC 59.626 55.000 0.00 0.00 42.48 3.56
3486 9067 6.685403 GCACGTTAATGCGTTTAATTAGACAT 59.315 34.615 6.91 0.00 43.83 3.06
3491 9072 8.827677 GTTAATGCGTTTAATTAGACATCCTCT 58.172 33.333 6.91 0.00 32.56 3.69
3542 9123 5.361285 TCCAGCCAAGTTTTACAAAGCTTAA 59.639 36.000 0.00 0.00 37.35 1.85
3613 9194 5.885912 ACATCGCACCCATCTAACTTTTAAT 59.114 36.000 0.00 0.00 0.00 1.40
3674 9256 0.166814 GTGTCCATTTGCAGAGCGAC 59.833 55.000 0.00 0.00 0.00 5.19
3737 9319 5.898972 AGAGTCAGAATCTAGGATGAGCTTT 59.101 40.000 0.00 0.00 0.00 3.51
3767 9349 4.855388 CCAATTTCTCTCGCAAGTTGAATG 59.145 41.667 7.16 0.00 39.48 2.67
3773 9355 1.163420 TCGCAAGTTGAATGGCACGT 61.163 50.000 7.16 0.00 39.48 4.49
3798 9380 1.364626 CGCCATGAGTTCAGCCAGAC 61.365 60.000 0.00 0.00 0.00 3.51
3815 9397 2.588877 CCCGGATCCGTGATGCAC 60.589 66.667 31.22 0.00 37.81 4.57
3816 9398 2.186644 CCGGATCCGTGATGCACA 59.813 61.111 31.22 0.00 37.81 4.57
3818 9400 1.141665 CGGATCCGTGATGCACAGA 59.858 57.895 26.35 0.00 33.40 3.41
3821 9403 2.292267 GGATCCGTGATGCACAGAAAT 58.708 47.619 0.00 0.00 33.40 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.355132 CGAGTCAACGACTAGGCATAGT 59.645 50.000 11.49 11.49 43.53 2.12
9 10 2.287069 CCGAGTCAACGACTAGGCATAG 60.287 54.545 9.86 3.34 45.37 2.23
10 11 1.674441 CCGAGTCAACGACTAGGCATA 59.326 52.381 9.86 0.00 45.37 3.14
11 12 0.456221 CCGAGTCAACGACTAGGCAT 59.544 55.000 9.86 0.00 45.37 4.40
12 13 1.880894 CCGAGTCAACGACTAGGCA 59.119 57.895 9.86 0.00 45.37 4.75
13 14 4.787999 CCGAGTCAACGACTAGGC 57.212 61.111 9.86 0.00 45.37 3.93
15 16 1.226323 CCGCCGAGTCAACGACTAG 60.226 63.158 3.50 0.00 43.53 2.57
16 17 2.693762 CCCGCCGAGTCAACGACTA 61.694 63.158 3.50 0.00 43.53 2.59
17 18 4.052229 CCCGCCGAGTCAACGACT 62.052 66.667 3.50 0.00 46.42 4.18
33 34 4.376170 ATTCCCACCCCGTTGGCC 62.376 66.667 0.00 0.00 37.83 5.36
34 35 2.754254 GATTCCCACCCCGTTGGC 60.754 66.667 0.00 0.00 37.83 4.52
35 36 1.378514 CAGATTCCCACCCCGTTGG 60.379 63.158 0.00 0.00 41.37 3.77
36 37 0.676782 GTCAGATTCCCACCCCGTTG 60.677 60.000 0.00 0.00 0.00 4.10
37 38 1.683441 GTCAGATTCCCACCCCGTT 59.317 57.895 0.00 0.00 0.00 4.44
38 39 2.656069 CGTCAGATTCCCACCCCGT 61.656 63.158 0.00 0.00 0.00 5.28
40 41 2.124695 GCGTCAGATTCCCACCCC 60.125 66.667 0.00 0.00 0.00 4.95
43 44 2.511600 CCCGCGTCAGATTCCCAC 60.512 66.667 4.92 0.00 0.00 4.61
44 45 2.238847 CTTCCCGCGTCAGATTCCCA 62.239 60.000 4.92 0.00 0.00 4.37
46 47 0.391263 AACTTCCCGCGTCAGATTCC 60.391 55.000 4.92 0.00 0.00 3.01
47 48 1.128692 CAAACTTCCCGCGTCAGATTC 59.871 52.381 4.92 0.00 0.00 2.52
48 49 1.156736 CAAACTTCCCGCGTCAGATT 58.843 50.000 4.92 0.00 0.00 2.40
49 50 0.673644 CCAAACTTCCCGCGTCAGAT 60.674 55.000 4.92 0.00 0.00 2.90
50 51 1.301401 CCAAACTTCCCGCGTCAGA 60.301 57.895 4.92 0.00 0.00 3.27
51 52 1.597027 ACCAAACTTCCCGCGTCAG 60.597 57.895 4.92 0.00 0.00 3.51
52 53 1.890041 CACCAAACTTCCCGCGTCA 60.890 57.895 4.92 0.00 0.00 4.35
53 54 2.943653 CACCAAACTTCCCGCGTC 59.056 61.111 4.92 0.00 0.00 5.19
54 55 3.284449 GCACCAAACTTCCCGCGT 61.284 61.111 4.92 0.00 0.00 6.01
55 56 4.038080 GGCACCAAACTTCCCGCG 62.038 66.667 0.00 0.00 0.00 6.46
56 57 1.744320 AAAGGCACCAAACTTCCCGC 61.744 55.000 0.00 0.00 0.00 6.13
57 58 0.750249 AAAAGGCACCAAACTTCCCG 59.250 50.000 0.00 0.00 0.00 5.14
74 75 2.566570 GCGCCGGGGGAAAGAAAAA 61.567 57.895 21.35 0.00 0.00 1.94
75 76 2.986979 GCGCCGGGGGAAAGAAAA 60.987 61.111 21.35 0.00 0.00 2.29
110 111 3.175240 CAGGTCGAACTCAGCGCG 61.175 66.667 0.00 0.00 0.00 6.86
111 112 2.811317 CCAGGTCGAACTCAGCGC 60.811 66.667 0.00 0.00 0.00 5.92
112 113 2.125912 CCCAGGTCGAACTCAGCG 60.126 66.667 0.00 0.00 0.00 5.18
113 114 1.079750 GACCCAGGTCGAACTCAGC 60.080 63.158 0.00 0.00 35.30 4.26
131 132 4.834892 CGAAATTGGCGCCGGCAG 62.835 66.667 28.98 20.12 42.47 4.85
148 149 2.222027 CAGATTTCATCGGTTAGGCCC 58.778 52.381 0.00 0.00 0.00 5.80
149 150 2.222027 CCAGATTTCATCGGTTAGGCC 58.778 52.381 0.00 0.00 0.00 5.19
150 151 1.604278 GCCAGATTTCATCGGTTAGGC 59.396 52.381 0.00 0.00 0.00 3.93
152 153 3.134458 GAGGCCAGATTTCATCGGTTAG 58.866 50.000 5.01 0.00 0.00 2.34
153 154 2.158813 GGAGGCCAGATTTCATCGGTTA 60.159 50.000 5.01 0.00 0.00 2.85
154 155 1.408822 GGAGGCCAGATTTCATCGGTT 60.409 52.381 5.01 0.00 0.00 4.44
157 158 1.871408 CGAGGAGGCCAGATTTCATCG 60.871 57.143 10.90 10.90 38.50 3.84
158 159 1.542108 CCGAGGAGGCCAGATTTCATC 60.542 57.143 5.01 0.00 0.00 2.92
160 161 1.907739 CCGAGGAGGCCAGATTTCA 59.092 57.895 5.01 0.00 0.00 2.69
178 179 2.662091 AAAAAGGCTCACGCACACGC 62.662 55.000 0.00 0.00 45.53 5.34
215 216 2.861730 CCCTCCCAGGCCCTTTTT 59.138 61.111 0.00 0.00 32.73 1.94
240 241 4.101448 AGCATCTCCACACGCCCC 62.101 66.667 0.00 0.00 0.00 5.80
241 242 2.512515 GAGCATCTCCACACGCCC 60.513 66.667 0.00 0.00 0.00 6.13
250 251 3.305335 GCTAGGTCAGCTTAGAGCATCTC 60.305 52.174 6.09 0.00 45.57 2.75
275 1597 2.614983 TGAACGTGGCTACCAGTTTTTC 59.385 45.455 0.00 0.00 32.34 2.29
279 1601 0.034896 CCTGAACGTGGCTACCAGTT 59.965 55.000 0.00 0.00 32.34 3.16
282 1604 0.892755 CTACCTGAACGTGGCTACCA 59.107 55.000 0.00 0.00 0.00 3.25
291 1613 1.478510 AGGATGCAGACTACCTGAACG 59.521 52.381 0.00 0.00 45.78 3.95
321 1643 1.640917 ACACCCTAGGTTGATGTCGT 58.359 50.000 14.12 0.00 31.02 4.34
372 1694 0.250553 GTCAACACGGGTCCCATCAA 60.251 55.000 9.12 0.00 0.00 2.57
375 1697 0.322456 CATGTCAACACGGGTCCCAT 60.322 55.000 9.12 0.00 0.00 4.00
392 1714 2.903547 GCGTGTTGACCGTTGCCAT 61.904 57.895 0.00 0.00 0.00 4.40
433 3405 2.710471 ACCGGTCCTAAACACCCTAAAA 59.290 45.455 0.00 0.00 0.00 1.52
440 3412 2.754946 TCATCACCGGTCCTAAACAC 57.245 50.000 2.59 0.00 0.00 3.32
462 3434 9.802039 AATTTGGGTCTCATAAGTTTGTTAGTA 57.198 29.630 0.00 0.00 0.00 1.82
507 3479 1.618837 TGAGGTGTGTTGAGCTAGTCC 59.381 52.381 0.00 0.00 0.00 3.85
516 3488 5.705441 TCCTAAAGCTATTTGAGGTGTGTTG 59.295 40.000 0.00 0.00 35.56 3.33
542 3514 9.191479 TCCTTCAAAGAGTAAAATACACCAAAA 57.809 29.630 0.00 0.00 0.00 2.44
550 3522 9.667107 ATTCGTCATCCTTCAAAGAGTAAAATA 57.333 29.630 0.00 0.00 0.00 1.40
563 3535 2.866762 GCCTGTACATTCGTCATCCTTC 59.133 50.000 0.00 0.00 0.00 3.46
564 3536 2.501723 AGCCTGTACATTCGTCATCCTT 59.498 45.455 0.00 0.00 0.00 3.36
565 3537 2.111384 AGCCTGTACATTCGTCATCCT 58.889 47.619 0.00 0.00 0.00 3.24
572 5592 5.458891 GTGGTAGTATAGCCTGTACATTCG 58.541 45.833 0.00 0.00 38.57 3.34
653 5673 9.559732 TCATCACAGTCCAATATTCGATTTATT 57.440 29.630 0.00 0.00 0.00 1.40
654 5674 9.559732 TTCATCACAGTCCAATATTCGATTTAT 57.440 29.630 0.00 0.00 0.00 1.40
655 5675 8.956533 TTCATCACAGTCCAATATTCGATTTA 57.043 30.769 0.00 0.00 0.00 1.40
656 5676 7.864108 TTCATCACAGTCCAATATTCGATTT 57.136 32.000 0.00 0.00 0.00 2.17
657 5677 7.864108 TTTCATCACAGTCCAATATTCGATT 57.136 32.000 0.00 0.00 0.00 3.34
658 5678 7.040892 CCATTTCATCACAGTCCAATATTCGAT 60.041 37.037 0.00 0.00 0.00 3.59
659 5679 6.260714 CCATTTCATCACAGTCCAATATTCGA 59.739 38.462 0.00 0.00 0.00 3.71
660 5680 6.432936 CCATTTCATCACAGTCCAATATTCG 58.567 40.000 0.00 0.00 0.00 3.34
732 5754 1.340017 GCAGGAGCAGGACCATGTTTA 60.340 52.381 0.00 0.00 41.58 2.01
790 5813 0.435008 GTTCTAGTGAGTTGTGCGCG 59.565 55.000 0.00 0.00 0.00 6.86
791 5814 0.790814 GGTTCTAGTGAGTTGTGCGC 59.209 55.000 0.00 0.00 0.00 6.09
792 5815 1.060713 CGGTTCTAGTGAGTTGTGCG 58.939 55.000 0.00 0.00 0.00 5.34
835 5865 6.043411 TGGAAGGGTTTTGATTTAAACGTTG 58.957 36.000 0.00 0.00 38.58 4.10
839 5869 7.931407 ACAGAATGGAAGGGTTTTGATTTAAAC 59.069 33.333 0.00 0.00 43.62 2.01
844 5874 4.262592 GCACAGAATGGAAGGGTTTTGATT 60.263 41.667 0.00 0.00 43.62 2.57
845 5875 3.259123 GCACAGAATGGAAGGGTTTTGAT 59.741 43.478 0.00 0.00 43.62 2.57
869 5899 1.527844 GGCATTCCTGGCTAGCTGG 60.528 63.158 15.72 16.71 44.27 4.85
874 5904 0.183492 GTCATGGGCATTCCTGGCTA 59.817 55.000 0.00 0.00 46.72 3.93
889 5919 0.982852 TCTGGCTGGATTCCCGTCAT 60.983 55.000 1.62 0.00 34.29 3.06
963 5994 3.077695 AGACGATAAGGTGATAGGGGGAT 59.922 47.826 0.00 0.00 0.00 3.85
985 6016 3.731136 GCCATTTATGCGAGCGGA 58.269 55.556 0.00 0.00 0.00 5.54
1056 6088 4.035675 TGAGTGAGTGTATCAGATAGTGCG 59.964 45.833 0.00 0.00 39.07 5.34
1057 6089 5.506686 TGAGTGAGTGTATCAGATAGTGC 57.493 43.478 0.00 0.00 39.07 4.40
1058 6090 6.369799 CGATGAGTGAGTGTATCAGATAGTG 58.630 44.000 0.00 0.00 39.07 2.74
1059 6091 5.049060 GCGATGAGTGAGTGTATCAGATAGT 60.049 44.000 0.00 0.00 39.07 2.12
1060 6092 5.389778 GCGATGAGTGAGTGTATCAGATAG 58.610 45.833 0.00 0.00 39.07 2.08
1070 6102 3.250323 CGCCGCGATGAGTGAGTG 61.250 66.667 8.23 0.00 0.00 3.51
1071 6103 3.282745 AACGCCGCGATGAGTGAGT 62.283 57.895 21.79 0.00 0.00 3.41
1072 6104 2.507102 AACGCCGCGATGAGTGAG 60.507 61.111 21.79 0.00 0.00 3.51
1073 6105 2.809174 CAACGCCGCGATGAGTGA 60.809 61.111 21.79 0.00 31.46 3.41
1147 6184 0.878416 ATTAAACCTCTTTGCGCGCA 59.122 45.000 33.09 33.09 0.00 6.09
1156 6193 8.980481 TGAGAAGTTGAGAAAATTAAACCTCT 57.020 30.769 0.00 0.00 0.00 3.69
1169 6210 2.704190 ACTCCCCTGAGAAGTTGAGA 57.296 50.000 0.00 0.00 41.42 3.27
1181 6222 1.073706 ACCACACCTGAACTCCCCT 60.074 57.895 0.00 0.00 0.00 4.79
1192 6233 0.668535 GAAACTCCAAGCACCACACC 59.331 55.000 0.00 0.00 0.00 4.16
1195 6236 1.609072 GGAAGAAACTCCAAGCACCAC 59.391 52.381 0.00 0.00 35.36 4.16
1201 6242 4.154918 CGAAGATTGGGAAGAAACTCCAAG 59.845 45.833 0.00 0.00 42.87 3.61
1202 6243 4.072131 CGAAGATTGGGAAGAAACTCCAA 58.928 43.478 0.00 0.00 43.62 3.53
1203 6244 3.559171 CCGAAGATTGGGAAGAAACTCCA 60.559 47.826 0.00 0.00 37.20 3.86
1204 6245 3.010420 CCGAAGATTGGGAAGAAACTCC 58.990 50.000 0.00 0.00 34.41 3.85
1205 6246 3.437049 CACCGAAGATTGGGAAGAAACTC 59.563 47.826 0.17 0.00 0.00 3.01
1206 6247 3.412386 CACCGAAGATTGGGAAGAAACT 58.588 45.455 0.17 0.00 0.00 2.66
1207 6248 2.095212 GCACCGAAGATTGGGAAGAAAC 60.095 50.000 0.17 0.00 0.00 2.78
1208 6249 2.159382 GCACCGAAGATTGGGAAGAAA 58.841 47.619 0.17 0.00 0.00 2.52
1209 6250 1.351017 AGCACCGAAGATTGGGAAGAA 59.649 47.619 0.17 0.00 0.00 2.52
1210 6251 0.984230 AGCACCGAAGATTGGGAAGA 59.016 50.000 0.17 0.00 0.00 2.87
1211 6252 1.089920 CAGCACCGAAGATTGGGAAG 58.910 55.000 0.17 0.00 0.00 3.46
1212 6253 0.690192 TCAGCACCGAAGATTGGGAA 59.310 50.000 0.17 0.00 0.00 3.97
1213 6254 0.911769 ATCAGCACCGAAGATTGGGA 59.088 50.000 0.17 0.00 0.00 4.37
1214 6255 1.755179 AATCAGCACCGAAGATTGGG 58.245 50.000 0.00 0.00 0.00 4.12
1223 6264 2.563086 GAACCGCGAAATCAGCACCG 62.563 60.000 8.23 0.00 34.19 4.94
1237 6278 1.498865 GCACACAGACCACAGAACCG 61.499 60.000 0.00 0.00 0.00 4.44
1270 6311 3.289525 CCGAAGAAGGCCGAGTCT 58.710 61.111 0.00 0.00 0.00 3.24
1334 6375 3.286751 GCTCACCTTGGTGCGCAA 61.287 61.111 24.46 0.00 35.39 4.85
1365 6406 0.448990 CACACATGCATCGACCCAAG 59.551 55.000 0.00 0.00 0.00 3.61
1409 6450 7.358931 CCCAAATAATACTACTACGCAATGACG 60.359 40.741 0.00 0.00 39.50 4.35
1412 6453 6.932400 TCCCCAAATAATACTACTACGCAATG 59.068 38.462 0.00 0.00 0.00 2.82
1413 6454 7.069877 TCCCCAAATAATACTACTACGCAAT 57.930 36.000 0.00 0.00 0.00 3.56
1418 6459 8.685838 TGCAATTCCCCAAATAATACTACTAC 57.314 34.615 0.00 0.00 0.00 2.73
1419 6460 7.447238 GCTGCAATTCCCCAAATAATACTACTA 59.553 37.037 0.00 0.00 0.00 1.82
1420 6461 6.265422 GCTGCAATTCCCCAAATAATACTACT 59.735 38.462 0.00 0.00 0.00 2.57
1456 6497 2.019249 CGACACCCCATTACTCGACTA 58.981 52.381 0.00 0.00 0.00 2.59
1457 6498 0.815734 CGACACCCCATTACTCGACT 59.184 55.000 0.00 0.00 0.00 4.18
1470 6511 8.827677 AGCTAACTAATCATAAAATTCGACACC 58.172 33.333 0.00 0.00 0.00 4.16
1474 6515 7.990886 ACCCAGCTAACTAATCATAAAATTCGA 59.009 33.333 0.00 0.00 0.00 3.71
1482 6523 7.067421 AGTACTCACCCAGCTAACTAATCATA 58.933 38.462 0.00 0.00 0.00 2.15
1483 6524 5.900123 AGTACTCACCCAGCTAACTAATCAT 59.100 40.000 0.00 0.00 0.00 2.45
1501 6542 2.166664 CCACACTCTAGCCCAAGTACTC 59.833 54.545 0.00 0.00 0.00 2.59
1502 6543 2.180276 CCACACTCTAGCCCAAGTACT 58.820 52.381 0.00 0.00 0.00 2.73
1503 6544 2.094130 GTCCACACTCTAGCCCAAGTAC 60.094 54.545 0.00 0.00 0.00 2.73
1504 6545 2.176889 GTCCACACTCTAGCCCAAGTA 58.823 52.381 0.00 0.00 0.00 2.24
1517 6558 1.221414 GAACAGAGCACAGTCCACAC 58.779 55.000 0.00 0.00 0.00 3.82
1525 6566 1.661509 CAGCGACGAACAGAGCACA 60.662 57.895 0.00 0.00 0.00 4.57
1536 6577 1.767388 GTCAGAACGAACAGCGACG 59.233 57.895 0.00 0.00 44.57 5.12
1583 6625 1.298863 CACCGACGACGTGTTCACT 60.299 57.895 4.58 0.00 37.88 3.41
1657 6699 3.739167 CGGTCTTTTTGCCGGACA 58.261 55.556 5.05 0.00 43.85 4.02
1739 6781 2.922503 TTGCCTGACTCCGCCAGA 60.923 61.111 0.00 0.00 33.65 3.86
1982 7024 1.435515 GCTCATCTCGAAGCCGTCT 59.564 57.895 0.00 0.00 37.05 4.18
2075 7117 1.493950 CGATGATGAGGCGCTTGGAC 61.494 60.000 7.64 0.00 0.00 4.02
2120 7162 4.655762 AGGATCGCGCATGTACATATAT 57.344 40.909 8.32 0.00 0.00 0.86
2121 7163 5.067283 ACATAGGATCGCGCATGTACATATA 59.933 40.000 8.32 0.00 30.04 0.86
2122 7164 4.142160 ACATAGGATCGCGCATGTACATAT 60.142 41.667 8.32 0.00 30.04 1.78
2123 7165 3.192633 ACATAGGATCGCGCATGTACATA 59.807 43.478 8.32 0.00 30.04 2.29
2124 7166 2.029020 ACATAGGATCGCGCATGTACAT 60.029 45.455 8.75 1.41 30.04 2.29
2125 7167 1.339929 ACATAGGATCGCGCATGTACA 59.660 47.619 8.75 0.00 30.04 2.90
2126 7168 2.065993 ACATAGGATCGCGCATGTAC 57.934 50.000 8.75 0.00 30.04 2.90
2127 7169 2.812358 AACATAGGATCGCGCATGTA 57.188 45.000 8.75 0.00 31.55 2.29
2128 7170 1.867233 GAAACATAGGATCGCGCATGT 59.133 47.619 8.75 5.48 33.12 3.21
2142 7184 2.542595 GACCACGACGACAAAGAAACAT 59.457 45.455 0.00 0.00 0.00 2.71
2341 7386 2.783135 CACACCTTGCTGTCCTTGTAT 58.217 47.619 0.00 0.00 0.00 2.29
2491 7536 2.602267 TGGAACGGCGGGAAGAGA 60.602 61.111 13.24 0.00 0.00 3.10
2596 7641 2.351244 CCAGCTCCAGTAGACGCCA 61.351 63.158 0.00 0.00 0.00 5.69
2677 7722 2.122768 CTGAGCTCCCATACCTTCCTT 58.877 52.381 12.15 0.00 0.00 3.36
2751 7796 1.006102 GATCGATCGGGGATTGCGT 60.006 57.895 16.41 0.00 0.00 5.24
2822 7868 7.513371 AACGTGTCCTACAATTATTTTTCCA 57.487 32.000 0.00 0.00 0.00 3.53
2876 7922 2.202824 CGGACTTAATCGGGCGCA 60.203 61.111 10.83 0.00 0.00 6.09
3020 8066 1.489230 GGGTGGAGTTACCGGATGAAT 59.511 52.381 9.46 0.00 41.79 2.57
3035 8081 2.295909 TGAAAGAAAATTCGCTGGGTGG 59.704 45.455 0.00 0.00 31.80 4.61
3043 8089 6.995633 GCATTGTAACGTTGAAAGAAAATTCG 59.004 34.615 11.99 0.00 31.80 3.34
3109 8684 4.437239 CAACCACCAGTAAAATGCAACAA 58.563 39.130 0.00 0.00 0.00 2.83
3138 8713 4.697756 TTCAAGAGGCCGCGGTGG 62.698 66.667 28.70 3.87 42.50 4.61
3139 8714 2.040544 ATTTCAAGAGGCCGCGGTG 61.041 57.895 28.70 16.97 0.00 4.94
3140 8715 2.040544 CATTTCAAGAGGCCGCGGT 61.041 57.895 28.70 7.71 0.00 5.68
3141 8716 1.305219 TTCATTTCAAGAGGCCGCGG 61.305 55.000 24.05 24.05 0.00 6.46
3142 8717 0.097674 CTTCATTTCAAGAGGCCGCG 59.902 55.000 0.00 0.00 0.00 6.46
3143 8718 1.168714 ACTTCATTTCAAGAGGCCGC 58.831 50.000 0.00 0.00 0.00 6.53
3144 8719 2.554032 ACAACTTCATTTCAAGAGGCCG 59.446 45.455 0.00 0.00 0.00 6.13
3157 8734 2.139917 AGAAATACGCGCACAACTTCA 58.860 42.857 5.73 0.00 0.00 3.02
3222 8799 6.103330 ACGTGTTGCCAGAAAGTTTTTATTT 58.897 32.000 0.00 0.00 0.00 1.40
3223 8800 5.656480 ACGTGTTGCCAGAAAGTTTTTATT 58.344 33.333 0.00 0.00 0.00 1.40
3225 8802 4.705337 ACGTGTTGCCAGAAAGTTTTTA 57.295 36.364 0.00 0.00 0.00 1.52
3237 8814 1.790755 TGTGATGTCTACGTGTTGCC 58.209 50.000 0.00 0.00 0.00 4.52
3247 8824 5.046087 TCTGTTTGAGATGGATGTGATGTCT 60.046 40.000 0.00 0.00 0.00 3.41
3389 8970 2.872858 AGTGGCGAGAAACTTCTTGAAC 59.127 45.455 10.38 7.56 40.46 3.18
3410 8991 3.304721 GGCACATGCTGGTTGGCA 61.305 61.111 3.48 0.00 46.63 4.92
3472 9053 5.463724 GCCTCAGAGGATGTCTAATTAAACG 59.536 44.000 21.89 0.00 37.67 3.60
3486 9067 0.251653 ACGTTAGTGGCCTCAGAGGA 60.252 55.000 21.89 0.00 37.67 3.71
3542 9123 4.536489 ACTTACTAGGGAAGGTTGCTTGAT 59.464 41.667 10.43 0.00 0.00 2.57
3555 9136 6.837471 AAGTCACTCTACAACTTACTAGGG 57.163 41.667 0.00 0.00 31.68 3.53
3613 9194 2.091885 ACTTCTGCAGGGTTTTGAGGAA 60.092 45.455 15.13 0.00 0.00 3.36
3674 9256 1.001641 CAAGGAGGGGTGCTTGAGG 60.002 63.158 0.69 0.00 0.00 3.86
3737 9319 0.175760 CGAGAGAAATTGGAGCCCGA 59.824 55.000 0.00 0.00 0.00 5.14
3773 9355 2.434185 GAACTCATGGCGTGCCGA 60.434 61.111 6.37 0.00 39.42 5.54
3798 9380 2.588877 GTGCATCACGGATCCGGG 60.589 66.667 35.87 33.61 45.35 5.73
3815 9397 7.308229 CGAGAGGGAATATGCCTTTTATTTCTG 60.308 40.741 0.00 0.00 38.79 3.02
3816 9398 6.712547 CGAGAGGGAATATGCCTTTTATTTCT 59.287 38.462 0.00 0.00 38.79 2.52
3818 9400 6.601332 TCGAGAGGGAATATGCCTTTTATTT 58.399 36.000 0.00 0.00 38.79 1.40
3821 9403 5.623956 TTCGAGAGGGAATATGCCTTTTA 57.376 39.130 0.00 0.00 38.79 1.52


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

AutoCloner maintained by Alex Coulton.