Multiple sequence alignment - TraesCS2B01G604700

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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 TraesCS2B01G604700 chr2B 100.000 2052 0 0 2157 4208 786225147 786227198 0.000000e+00 3790
1 TraesCS2B01G604700 chr2B 100.000 1918 0 0 1 1918 786222991 786224908 0.000000e+00 3542
2 TraesCS2B01G604700 chr2D 89.847 2088 149 31 2157 4205 650321100 650323163 0.000000e+00 2623
3 TraesCS2B01G604700 chr2D 83.343 1783 122 80 220 1915 650319399 650321093 0.000000e+00 1485
4 TraesCS2B01G604700 chr2A 88.052 2059 183 40 2157 4191 774575303 774573284 0.000000e+00 2381
5 TraesCS2B01G604700 chr2A 82.747 2017 175 76 1 1918 774577243 774575301 0.000000e+00 1637
6 TraesCS2B01G604700 chr6A 84.917 484 63 6 2366 2848 27198020 27197546 8.180000e-132 481
7 TraesCS2B01G604700 chrUn 89.041 365 27 9 2953 3308 96707904 96707544 1.390000e-119 440
8 TraesCS2B01G604700 chrUn 86.916 214 24 3 2366 2577 96732119 96731908 1.960000e-58 237
9 TraesCS2B01G604700 chr6B 89.720 321 29 4 2947 3267 47899047 47898731 1.410000e-109 407
10 TraesCS2B01G604700 chr6B 89.247 93 8 2 3464 3554 47898603 47898511 9.560000e-22 115


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 TraesCS2B01G604700 chr2B 786222991 786227198 4207 False 3666 3790 100.0000 1 4208 2 chr2B.!!$F1 4207
1 TraesCS2B01G604700 chr2D 650319399 650323163 3764 False 2054 2623 86.5950 220 4205 2 chr2D.!!$F1 3985
2 TraesCS2B01G604700 chr2A 774573284 774577243 3959 True 2009 2381 85.3995 1 4191 2 chr2A.!!$R1 4190
3 TraesCS2B01G604700 chr6B 47898511 47899047 536 True 261 407 89.4835 2947 3554 2 chr6B.!!$R1 607

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
38 39 0.035534 ATGCATGTGTGGCGGTCTAA 60.036 50.0 0.00 0.0 0.00 2.10 F
793 862 0.110104 CATCATTGCCTCCTCCTCCC 59.890 60.0 0.00 0.0 0.00 4.30 F
1917 2096 0.321298 GGGCTTGGAGACGTAGCAAA 60.321 55.0 9.33 0.0 41.03 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1550 0.039978 GATGATGCTGATGCTGCTGC 60.040 55.0 8.89 8.89 40.48 5.25 R
2343 2537 0.114364 GTTGGGGAATTCTGGTGGGT 59.886 55.0 5.23 0.00 0.00 4.51 R
3670 3887 0.928229 GGCACGTCATGAACCGATAC 59.072 55.0 12.18 1.92 0.00 2.24 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
32 33 0.317519 CATAGCATGCATGTGTGGCG 60.318 55.000 26.79 8.32 0.00 5.69
38 39 0.035534 ATGCATGTGTGGCGGTCTAA 60.036 50.000 0.00 0.00 0.00 2.10
69 70 2.678190 CGGTTCTCCTCCACCTTGATTC 60.678 54.545 0.00 0.00 0.00 2.52
70 71 2.356227 GGTTCTCCTCCACCTTGATTCC 60.356 54.545 0.00 0.00 0.00 3.01
80 81 4.349636 TCCACCTTGATTCCTGTTTAGTCA 59.650 41.667 0.00 0.00 0.00 3.41
89 90 3.674997 TCCTGTTTAGTCACATGCCTTC 58.325 45.455 0.00 0.00 0.00 3.46
98 99 1.872952 TCACATGCCTTCGAACACTTG 59.127 47.619 0.00 0.53 0.00 3.16
100 101 2.485426 CACATGCCTTCGAACACTTGAT 59.515 45.455 12.74 0.00 0.00 2.57
101 102 2.744202 ACATGCCTTCGAACACTTGATC 59.256 45.455 12.74 0.00 0.00 2.92
102 103 2.839486 TGCCTTCGAACACTTGATCT 57.161 45.000 0.00 0.00 0.00 2.75
104 105 4.265904 TGCCTTCGAACACTTGATCTAA 57.734 40.909 0.00 0.00 0.00 2.10
105 106 4.637276 TGCCTTCGAACACTTGATCTAAA 58.363 39.130 0.00 0.00 0.00 1.85
107 108 4.434330 GCCTTCGAACACTTGATCTAAACG 60.434 45.833 0.00 0.00 0.00 3.60
109 110 2.659757 TCGAACACTTGATCTAAACGCG 59.340 45.455 3.53 3.53 0.00 6.01
110 111 2.407361 CGAACACTTGATCTAAACGCGT 59.593 45.455 5.58 5.58 0.00 6.01
111 112 3.121126 CGAACACTTGATCTAAACGCGTT 60.121 43.478 20.79 20.79 0.00 4.84
112 113 4.607557 CGAACACTTGATCTAAACGCGTTT 60.608 41.667 36.15 36.15 36.63 3.60
113 114 5.387649 CGAACACTTGATCTAAACGCGTTTA 60.388 40.000 34.70 34.70 34.23 2.01
114 115 6.476243 AACACTTGATCTAAACGCGTTTAT 57.524 33.333 36.44 27.26 34.86 1.40
116 117 7.766219 ACACTTGATCTAAACGCGTTTATAT 57.234 32.000 36.44 33.44 34.86 0.86
117 118 8.193250 ACACTTGATCTAAACGCGTTTATATT 57.807 30.769 36.44 25.68 34.86 1.28
118 119 8.662141 ACACTTGATCTAAACGCGTTTATATTT 58.338 29.630 36.44 23.62 34.86 1.40
119 120 9.144085 CACTTGATCTAAACGCGTTTATATTTC 57.856 33.333 36.44 28.34 34.86 2.17
120 121 9.095065 ACTTGATCTAAACGCGTTTATATTTCT 57.905 29.630 36.44 19.27 34.86 2.52
127 128 5.393902 ACGCGTTTATATTTCTTTACCGG 57.606 39.130 5.58 0.00 0.00 5.28
129 130 4.318974 CGCGTTTATATTTCTTTACCGGGG 60.319 45.833 6.32 0.00 0.00 5.73
130 131 4.815846 GCGTTTATATTTCTTTACCGGGGA 59.184 41.667 6.32 0.00 0.00 4.81
131 132 5.049886 GCGTTTATATTTCTTTACCGGGGAG 60.050 44.000 6.32 0.00 0.00 4.30
133 134 5.571791 TTATATTTCTTTACCGGGGAGGG 57.428 43.478 6.32 0.00 46.96 4.30
134 135 0.924090 ATTTCTTTACCGGGGAGGGG 59.076 55.000 6.32 0.00 46.96 4.79
136 137 2.285894 CTTTACCGGGGAGGGGGT 60.286 66.667 6.32 0.00 46.96 4.95
141 150 2.242408 TACCGGGGAGGGGGTACTTC 62.242 65.000 6.32 0.00 46.96 3.01
154 163 4.325972 GGGGTACTTCGTAAACATTCCAA 58.674 43.478 0.00 0.00 0.00 3.53
159 168 7.130269 GGTACTTCGTAAACATTCCAATATGC 58.870 38.462 0.00 0.00 0.00 3.14
160 169 5.806286 ACTTCGTAAACATTCCAATATGCG 58.194 37.500 0.00 0.00 0.00 4.73
169 178 8.633075 AAACATTCCAATATGCGTATTCTTTG 57.367 30.769 8.25 6.95 0.00 2.77
176 185 9.944663 TCCAATATGCGTATTCTTTGTTATTTC 57.055 29.630 8.25 0.00 0.00 2.17
177 186 9.729023 CCAATATGCGTATTCTTTGTTATTTCA 57.271 29.630 8.25 0.00 0.00 2.69
188 200 9.638239 ATTCTTTGTTATTTCATAATTGTGCGT 57.362 25.926 0.00 0.00 0.00 5.24
214 226 3.255379 GGTGCGATCGACGAAGGC 61.255 66.667 21.57 14.42 45.77 4.35
217 229 3.313257 GCGATCGACGAAGGCGAC 61.313 66.667 21.57 8.65 45.77 5.19
314 336 2.672996 AACACATGACAGGCGGGC 60.673 61.111 0.00 0.00 0.00 6.13
344 366 4.946478 ATTCCATGGACTACTGTAGAGC 57.054 45.455 15.91 11.80 0.00 4.09
351 373 2.443390 TACTGTAGAGCGGGGGCC 60.443 66.667 0.00 0.00 0.00 5.80
445 467 1.078115 TGGATGGATGGATGGATGGG 58.922 55.000 0.00 0.00 0.00 4.00
446 468 0.333993 GGATGGATGGATGGATGGGG 59.666 60.000 0.00 0.00 0.00 4.96
447 469 0.324091 GATGGATGGATGGATGGGGC 60.324 60.000 0.00 0.00 0.00 5.80
448 470 2.034687 GGATGGATGGATGGGGCG 59.965 66.667 0.00 0.00 0.00 6.13
449 471 2.833913 GGATGGATGGATGGGGCGT 61.834 63.158 0.00 0.00 0.00 5.68
450 472 1.601759 GATGGATGGATGGGGCGTG 60.602 63.158 0.00 0.00 0.00 5.34
451 473 2.343475 GATGGATGGATGGGGCGTGT 62.343 60.000 0.00 0.00 0.00 4.49
452 474 2.516930 GGATGGATGGGGCGTGTG 60.517 66.667 0.00 0.00 0.00 3.82
453 475 2.516930 GATGGATGGGGCGTGTGG 60.517 66.667 0.00 0.00 0.00 4.17
454 476 3.338250 ATGGATGGGGCGTGTGGT 61.338 61.111 0.00 0.00 0.00 4.16
455 477 3.643595 ATGGATGGGGCGTGTGGTG 62.644 63.158 0.00 0.00 0.00 4.17
456 478 4.344865 GGATGGGGCGTGTGGTGT 62.345 66.667 0.00 0.00 0.00 4.16
457 479 2.746277 GATGGGGCGTGTGGTGTC 60.746 66.667 0.00 0.00 0.00 3.67
458 480 3.249189 ATGGGGCGTGTGGTGTCT 61.249 61.111 0.00 0.00 0.00 3.41
459 481 3.551496 ATGGGGCGTGTGGTGTCTG 62.551 63.158 0.00 0.00 0.00 3.51
460 482 4.250305 GGGGCGTGTGGTGTCTGT 62.250 66.667 0.00 0.00 0.00 3.41
461 483 2.665185 GGGCGTGTGGTGTCTGTC 60.665 66.667 0.00 0.00 0.00 3.51
462 484 3.036084 GGCGTGTGGTGTCTGTCG 61.036 66.667 0.00 0.00 0.00 4.35
468 490 0.317160 TGTGGTGTCTGTCGATGGAC 59.683 55.000 11.97 11.97 43.71 4.02
544 576 2.287103 GGAACGGAAATCTTATCGGCAC 59.713 50.000 0.00 0.00 0.00 5.01
545 577 1.949465 ACGGAAATCTTATCGGCACC 58.051 50.000 0.00 0.00 0.00 5.01
546 578 0.859232 CGGAAATCTTATCGGCACCG 59.141 55.000 1.73 1.73 41.35 4.94
589 621 2.947542 CCTCGACTCGCCTATCCG 59.052 66.667 0.00 0.00 0.00 4.18
598 630 2.280457 GCCTATCCGTCTGCCTGC 60.280 66.667 0.00 0.00 0.00 4.85
600 632 2.028190 CTATCCGTCTGCCTGCCG 59.972 66.667 0.00 0.00 0.00 5.69
601 633 2.758327 TATCCGTCTGCCTGCCGT 60.758 61.111 0.00 0.00 0.00 5.68
602 634 2.685387 CTATCCGTCTGCCTGCCGTC 62.685 65.000 0.00 0.00 0.00 4.79
632 690 0.679002 CCATCCATCCATCCATCGGC 60.679 60.000 0.00 0.00 0.00 5.54
633 691 1.022982 CATCCATCCATCCATCGGCG 61.023 60.000 0.00 0.00 0.00 6.46
634 692 1.194121 ATCCATCCATCCATCGGCGA 61.194 55.000 13.87 13.87 0.00 5.54
635 693 1.194121 TCCATCCATCCATCGGCGAT 61.194 55.000 18.14 18.14 0.00 4.58
636 694 0.742281 CCATCCATCCATCGGCGATC 60.742 60.000 21.25 0.00 0.00 3.69
637 695 1.080435 CATCCATCCATCGGCGATCG 61.080 60.000 21.25 14.51 40.90 3.69
693 758 0.518636 CATCCTGGCTGACAAACACG 59.481 55.000 0.00 0.00 0.00 4.49
702 767 1.278637 GACAAACACGTCCAAGCGG 59.721 57.895 0.00 0.00 35.98 5.52
703 768 2.051345 CAAACACGTCCAAGCGGC 60.051 61.111 0.00 0.00 35.98 6.53
704 769 2.203153 AAACACGTCCAAGCGGCT 60.203 55.556 0.00 0.00 35.98 5.52
705 770 2.542907 AAACACGTCCAAGCGGCTG 61.543 57.895 1.81 0.00 35.98 4.85
706 771 4.988598 ACACGTCCAAGCGGCTGG 62.989 66.667 1.81 7.71 37.87 4.85
793 862 0.110104 CATCATTGCCTCCTCCTCCC 59.890 60.000 0.00 0.00 0.00 4.30
810 879 1.152139 CCCCTCCTCCTCCTGATCC 60.152 68.421 0.00 0.00 0.00 3.36
854 929 3.151022 CCCGTCTCCTCCAGCTCC 61.151 72.222 0.00 0.00 0.00 4.70
855 930 3.151022 CCGTCTCCTCCAGCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
934 1032 1.200716 GGTGACCGATACTGTTCGTGA 59.799 52.381 10.05 0.00 37.42 4.35
952 1050 3.466791 AATGATCAGGGCGAGGGCG 62.467 63.158 0.09 0.00 41.24 6.13
962 1060 3.431725 CGAGGGCGGCTGGTTTTC 61.432 66.667 9.56 0.00 0.00 2.29
963 1061 2.282180 GAGGGCGGCTGGTTTTCA 60.282 61.111 9.56 0.00 0.00 2.69
964 1062 2.597510 AGGGCGGCTGGTTTTCAC 60.598 61.111 9.56 0.00 0.00 3.18
965 1063 4.038080 GGGCGGCTGGTTTTCACG 62.038 66.667 9.56 0.00 0.00 4.35
967 1065 4.700365 GCGGCTGGTTTTCACGCC 62.700 66.667 0.00 0.00 44.01 5.68
968 1066 2.978010 CGGCTGGTTTTCACGCCT 60.978 61.111 0.00 0.00 37.46 5.52
972 1070 1.576421 CTGGTTTTCACGCCTGAGC 59.424 57.895 0.00 0.00 0.00 4.26
1021 1119 1.303309 GGATGGCAAAGACCTCATCG 58.697 55.000 0.00 0.00 37.47 3.84
1241 1348 4.170062 CGCCGCCATGCAGTTCAG 62.170 66.667 0.00 0.00 0.00 3.02
1257 1364 2.112928 AGCATGGACAACGCCACA 59.887 55.556 0.00 0.00 41.56 4.17
1273 1380 0.466922 CACATCCCCTTCCTCCATGC 60.467 60.000 0.00 0.00 0.00 4.06
1446 1559 4.415332 GCGCAACAGCAGCAGCAT 62.415 61.111 0.30 0.00 45.49 3.79
1450 1563 1.154016 CAACAGCAGCAGCATCAGC 60.154 57.895 3.17 0.00 45.49 4.26
1451 1564 1.602605 AACAGCAGCAGCATCAGCA 60.603 52.632 3.17 0.00 45.49 4.41
1452 1565 0.965866 AACAGCAGCAGCATCAGCAT 60.966 50.000 3.17 0.00 45.49 3.79
1587 1700 0.618968 GGAAGAAGCTCTCCTCCCCA 60.619 60.000 0.00 0.00 0.00 4.96
1589 1702 0.988063 AAGAAGCTCTCCTCCCCAAC 59.012 55.000 0.00 0.00 0.00 3.77
1621 1734 9.804977 AACCCTCCGGTCAGTATATATATATAC 57.195 37.037 25.88 25.88 43.71 1.47
1622 1735 8.952602 ACCCTCCGGTCAGTATATATATATACA 58.047 37.037 30.99 17.22 41.89 2.29
1700 1842 2.301870 ACTGTCCAACTCAAGGCGATTA 59.698 45.455 0.00 0.00 0.00 1.75
1712 1854 7.830739 ACTCAAGGCGATTAAATTCAGATTTT 58.169 30.769 0.00 0.00 36.82 1.82
1715 1857 9.567848 TCAAGGCGATTAAATTCAGATTTTTAC 57.432 29.630 0.00 0.00 36.82 2.01
1753 1896 3.071312 TGCCTGCCAATTGTCAAAAGAAT 59.929 39.130 4.43 0.00 0.00 2.40
1794 1967 9.959749 TTTTTGGTGATTTTAACAGAGTATCAC 57.040 29.630 0.00 0.00 42.59 3.06
1807 1980 6.951971 ACAGAGTATCACCTAGCTCAATTTT 58.048 36.000 0.00 0.00 37.82 1.82
1843 2016 6.474751 GCTGCCATCTTAGAAATCATTTGTTC 59.525 38.462 0.00 0.00 0.00 3.18
1856 2029 4.507710 TCATTTGTTCTAGTAGGCTGCTG 58.492 43.478 15.86 5.61 0.00 4.41
1875 2048 6.356757 TGCTGGTTTTTATGCAAAGTTTTC 57.643 33.333 0.00 0.00 32.12 2.29
1903 2076 3.073650 ACTCTGAAGTCTGATTTGGGCTT 59.926 43.478 0.00 0.00 0.00 4.35
1910 2083 1.089920 CTGATTTGGGCTTGGAGACG 58.910 55.000 0.00 0.00 0.00 4.18
1916 2095 1.295423 GGGCTTGGAGACGTAGCAA 59.705 57.895 9.33 0.00 41.03 3.91
1917 2096 0.321298 GGGCTTGGAGACGTAGCAAA 60.321 55.000 9.33 0.00 41.03 3.68
2184 2363 3.070018 ACTTGAACTGTCACAGCATAGC 58.930 45.455 4.13 0.00 34.37 2.97
2188 2367 1.269958 ACTGTCACAGCATAGCCTGA 58.730 50.000 4.13 0.00 36.67 3.86
2235 2427 8.917415 AGAAAATTAATTCCTCTGAAAATCGC 57.083 30.769 0.10 0.00 33.32 4.58
2261 2453 3.451894 CCAGGCAATGCGTTCCCC 61.452 66.667 0.00 0.00 0.00 4.81
2351 2545 3.190535 GCAAACTGTAACATACCCACCAG 59.809 47.826 0.00 0.00 0.00 4.00
2356 2550 5.497474 ACTGTAACATACCCACCAGAATTC 58.503 41.667 0.00 0.00 0.00 2.17
2357 2551 4.850680 TGTAACATACCCACCAGAATTCC 58.149 43.478 0.65 0.00 0.00 3.01
2364 2558 1.482177 CCCACCAGAATTCCCCAACAA 60.482 52.381 0.65 0.00 0.00 2.83
2387 2581 3.616956 TCCTCTGTTATCCTGTTGCAG 57.383 47.619 0.00 0.00 0.00 4.41
2390 2584 2.935201 CTCTGTTATCCTGTTGCAGCTC 59.065 50.000 1.17 0.00 0.00 4.09
2392 2586 2.417933 CTGTTATCCTGTTGCAGCTCAC 59.582 50.000 1.17 0.00 0.00 3.51
2422 2616 3.243636 ACAGACAGAACCGTAACAATCGT 60.244 43.478 0.00 0.00 0.00 3.73
2423 2617 3.739300 CAGACAGAACCGTAACAATCGTT 59.261 43.478 0.00 0.00 39.24 3.85
2433 2627 4.153475 CCGTAACAATCGTTTTGACAGGAT 59.847 41.667 7.65 0.00 36.52 3.24
2523 2717 3.462678 GTCTCCAGGGCCGTCCTC 61.463 72.222 0.00 0.00 46.12 3.71
2560 2754 5.779241 TCATCCTCCTTCCTACAACAATT 57.221 39.130 0.00 0.00 0.00 2.32
2596 2790 0.458669 AGGCGACCAACCTACATACG 59.541 55.000 0.00 0.00 35.10 3.06
2597 2791 0.529119 GGCGACCAACCTACATACGG 60.529 60.000 0.00 0.00 0.00 4.02
2598 2792 0.174162 GCGACCAACCTACATACGGT 59.826 55.000 0.00 0.00 35.97 4.83
2599 2793 1.404583 GCGACCAACCTACATACGGTT 60.405 52.381 0.00 0.00 45.26 4.44
2603 2797 2.767960 ACCAACCTACATACGGTTAGGG 59.232 50.000 8.76 0.00 42.63 3.53
2608 2802 4.095946 ACCTACATACGGTTAGGGAACAA 58.904 43.478 8.76 0.00 37.29 2.83
2618 2812 5.009310 ACGGTTAGGGAACAAATCAAAGAAC 59.991 40.000 0.00 0.00 37.29 3.01
2634 2828 1.277557 AGAACTGATGCACCTGAGACC 59.722 52.381 0.00 0.00 0.00 3.85
2648 2842 3.385111 CCTGAGACCTGTATGTAACCCTC 59.615 52.174 0.00 0.00 0.00 4.30
2656 2850 4.505566 CCTGTATGTAACCCTCCATGATGG 60.506 50.000 4.74 4.74 39.43 3.51
2663 2857 1.045407 CCCTCCATGATGGGCATTTG 58.955 55.000 12.26 0.00 38.32 2.32
2664 2858 1.690209 CCCTCCATGATGGGCATTTGT 60.690 52.381 12.26 0.00 38.32 2.83
2674 2868 2.683768 TGGGCATTTGTTTTGTAGGGT 58.316 42.857 0.00 0.00 0.00 4.34
2687 2881 8.472007 TGTTTTGTAGGGTTTGTATGAAATCT 57.528 30.769 0.00 0.00 0.00 2.40
2863 3061 8.088981 GTCTACCAGACTTCAACTGAAAAGATA 58.911 37.037 0.00 0.00 41.88 1.98
2866 3064 6.483640 ACCAGACTTCAACTGAAAAGATACAC 59.516 38.462 0.00 0.00 37.54 2.90
2867 3065 6.073003 CCAGACTTCAACTGAAAAGATACACC 60.073 42.308 0.00 0.00 37.54 4.16
2872 3070 5.630121 TCAACTGAAAAGATACACCCATGT 58.370 37.500 0.00 0.00 43.30 3.21
2873 3071 7.786060 CTTCAACTGAAAAGATACACCCATGTG 60.786 40.741 0.00 0.00 39.88 3.21
2877 3075 3.366052 AAAGATACACCCATGTGACCC 57.634 47.619 0.00 0.00 45.76 4.46
2879 3077 2.492025 AGATACACCCATGTGACCCAT 58.508 47.619 0.00 0.00 45.76 4.00
2882 3080 1.965414 ACACCCATGTGACCCATCTA 58.035 50.000 0.00 0.00 45.76 1.98
2883 3081 2.274542 ACACCCATGTGACCCATCTAA 58.725 47.619 0.00 0.00 45.76 2.10
2884 3082 2.026262 ACACCCATGTGACCCATCTAAC 60.026 50.000 0.00 0.00 45.76 2.34
2885 3083 2.026356 CACCCATGTGACCCATCTAACA 60.026 50.000 0.00 0.00 45.76 2.41
2944 3142 7.016914 AGGGGTATCATACAGCATAGAAGTTA 58.983 38.462 0.00 0.00 0.00 2.24
2945 3143 7.512746 AGGGGTATCATACAGCATAGAAGTTAA 59.487 37.037 0.00 0.00 0.00 2.01
2973 3172 0.178978 TTTGGCATGTGCAGGTGGTA 60.179 50.000 7.36 0.00 44.36 3.25
2993 3192 2.230660 ACTAGGGACTTTTGTGCAAGC 58.769 47.619 0.00 0.00 42.95 4.01
3179 3378 5.292101 GGATATTTGACACGAGAAGTTCCAG 59.708 44.000 0.00 0.00 0.00 3.86
3314 3513 7.912250 CCATTCGGTTTTTGAGATCATTCTTAG 59.088 37.037 0.00 0.00 30.30 2.18
3353 3554 6.757947 GGCTGTGTTTTGTTGCATCAATATAT 59.242 34.615 10.87 0.00 0.00 0.86
3419 3629 3.449018 AGAGTAGCATACAACAGACTGGG 59.551 47.826 7.51 1.00 46.26 4.45
3471 3681 5.756347 ACACATACAGTAGCGAAAAGAACAA 59.244 36.000 0.00 0.00 0.00 2.83
3560 3777 3.686241 TCTTGATGTCATTCTGCGAAAGG 59.314 43.478 0.00 0.00 0.00 3.11
3573 3790 1.978782 GCGAAAGGCGAAAACATTCAG 59.021 47.619 0.00 0.00 44.57 3.02
3617 3834 6.147821 GGTGGAGACGAACAATATGGAATATG 59.852 42.308 0.00 0.00 38.94 1.78
3760 3977 2.969821 ATAGACCGCCTCTCTCTGAT 57.030 50.000 0.00 0.00 0.00 2.90
3779 3996 6.054941 TCTGATTTCAAGAACTTGTACAGCA 58.945 36.000 13.15 7.47 41.16 4.41
3866 4083 4.870123 TGCATTTGTGTTTGGAAGCTAT 57.130 36.364 0.00 0.00 0.00 2.97
3877 4094 2.766313 TGGAAGCTATCACACACACAC 58.234 47.619 0.00 0.00 0.00 3.82
3879 4096 2.738846 GGAAGCTATCACACACACACAG 59.261 50.000 0.00 0.00 0.00 3.66
3881 4098 3.751479 AGCTATCACACACACACAGAA 57.249 42.857 0.00 0.00 0.00 3.02
3883 4100 4.450976 AGCTATCACACACACACAGAAAA 58.549 39.130 0.00 0.00 0.00 2.29
3884 4101 5.065914 AGCTATCACACACACACAGAAAAT 58.934 37.500 0.00 0.00 0.00 1.82
3886 4103 6.369890 AGCTATCACACACACACAGAAAATAG 59.630 38.462 0.00 0.00 0.00 1.73
3887 4104 6.368791 GCTATCACACACACACAGAAAATAGA 59.631 38.462 0.00 0.00 0.00 1.98
3890 4107 7.015226 TCACACACACACAGAAAATAGAAAG 57.985 36.000 0.00 0.00 0.00 2.62
3893 4110 4.887071 ACACACACAGAAAATAGAAAGGCA 59.113 37.500 0.00 0.00 0.00 4.75
3976 4193 4.456911 GCAAACTCCACAATCTTCTCATCA 59.543 41.667 0.00 0.00 0.00 3.07
4034 4251 3.131709 ACGCCAATATCTCCAATCCTG 57.868 47.619 0.00 0.00 0.00 3.86
4037 4254 3.937706 CGCCAATATCTCCAATCCTGATC 59.062 47.826 0.00 0.00 0.00 2.92
4048 4265 1.950828 ATCCTGATCGCAGCAGAAAG 58.049 50.000 3.44 0.00 40.91 2.62
4205 4429 2.631545 TCTTCTACCGCTATTTAGCCCC 59.368 50.000 4.08 0.00 46.34 5.80
4206 4430 2.091098 TCTACCGCTATTTAGCCCCA 57.909 50.000 4.08 0.00 46.34 4.96
4207 4431 2.400573 TCTACCGCTATTTAGCCCCAA 58.599 47.619 4.08 0.00 46.34 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.745468 ACCGCTCCGAAGATTAGACC 59.255 55.000 0.00 0.00 0.00 3.85
59 60 5.063204 TGTGACTAAACAGGAATCAAGGTG 58.937 41.667 0.00 0.00 0.00 4.00
69 70 2.416547 CGAAGGCATGTGACTAAACAGG 59.583 50.000 0.00 0.00 35.02 4.00
70 71 3.325870 TCGAAGGCATGTGACTAAACAG 58.674 45.455 0.00 0.00 32.52 3.16
80 81 2.254546 TCAAGTGTTCGAAGGCATGT 57.745 45.000 0.00 0.00 0.00 3.21
89 90 2.407361 ACGCGTTTAGATCAAGTGTTCG 59.593 45.455 5.58 0.00 0.00 3.95
100 101 8.320295 CGGTAAAGAAATATAAACGCGTTTAGA 58.680 33.333 37.90 35.62 38.30 2.10
101 102 7.580165 CCGGTAAAGAAATATAAACGCGTTTAG 59.420 37.037 37.90 23.74 38.30 1.85
102 103 7.397970 CCGGTAAAGAAATATAAACGCGTTTA 58.602 34.615 37.73 37.73 39.12 2.01
104 105 5.220643 CCCGGTAAAGAAATATAAACGCGTT 60.221 40.000 20.79 20.79 0.00 4.84
105 106 4.270808 CCCGGTAAAGAAATATAAACGCGT 59.729 41.667 5.58 5.58 0.00 6.01
107 108 4.815846 TCCCCGGTAAAGAAATATAAACGC 59.184 41.667 0.00 0.00 0.00 4.84
109 110 5.766670 CCCTCCCCGGTAAAGAAATATAAAC 59.233 44.000 0.00 0.00 0.00 2.01
110 111 5.163066 CCCCTCCCCGGTAAAGAAATATAAA 60.163 44.000 0.00 0.00 0.00 1.40
111 112 4.351704 CCCCTCCCCGGTAAAGAAATATAA 59.648 45.833 0.00 0.00 0.00 0.98
112 113 3.911894 CCCCTCCCCGGTAAAGAAATATA 59.088 47.826 0.00 0.00 0.00 0.86
113 114 2.714793 CCCCTCCCCGGTAAAGAAATAT 59.285 50.000 0.00 0.00 0.00 1.28
114 115 2.129363 CCCCTCCCCGGTAAAGAAATA 58.871 52.381 0.00 0.00 0.00 1.40
116 117 1.209523 CCCCCTCCCCGGTAAAGAAA 61.210 60.000 0.00 0.00 0.00 2.52
117 118 1.617233 CCCCCTCCCCGGTAAAGAA 60.617 63.158 0.00 0.00 0.00 2.52
118 119 1.526528 TACCCCCTCCCCGGTAAAGA 61.527 60.000 0.00 0.00 31.58 2.52
119 120 1.003312 TACCCCCTCCCCGGTAAAG 59.997 63.158 0.00 0.00 31.58 1.85
120 121 1.306911 GTACCCCCTCCCCGGTAAA 60.307 63.158 0.00 0.00 36.39 2.01
122 123 2.242408 GAAGTACCCCCTCCCCGGTA 62.242 65.000 0.00 0.00 33.36 4.02
123 124 3.619030 AAGTACCCCCTCCCCGGT 61.619 66.667 0.00 0.00 36.08 5.28
124 125 2.767073 GAAGTACCCCCTCCCCGG 60.767 72.222 0.00 0.00 0.00 5.73
125 126 2.572333 TACGAAGTACCCCCTCCCCG 62.572 65.000 0.00 0.00 45.11 5.73
127 128 1.208052 GTTTACGAAGTACCCCCTCCC 59.792 57.143 0.00 0.00 45.76 4.30
129 130 3.900966 ATGTTTACGAAGTACCCCCTC 57.099 47.619 0.00 0.00 45.76 4.30
130 131 3.054875 GGAATGTTTACGAAGTACCCCCT 60.055 47.826 0.00 0.00 45.76 4.79
131 132 3.273434 GGAATGTTTACGAAGTACCCCC 58.727 50.000 0.00 0.00 45.76 5.40
132 133 3.941573 TGGAATGTTTACGAAGTACCCC 58.058 45.455 0.00 0.00 45.76 4.95
133 134 7.636326 CATATTGGAATGTTTACGAAGTACCC 58.364 38.462 0.00 0.00 45.76 3.69
134 135 7.130269 GCATATTGGAATGTTTACGAAGTACC 58.870 38.462 0.00 0.00 45.76 3.34
136 137 6.535865 ACGCATATTGGAATGTTTACGAAGTA 59.464 34.615 0.00 0.00 45.11 2.24
141 150 7.572759 AGAATACGCATATTGGAATGTTTACG 58.427 34.615 0.00 0.00 30.77 3.18
169 178 8.794406 CCTTGTTACGCACAATTATGAAATAAC 58.206 33.333 1.48 0.00 44.72 1.89
175 184 3.181515 CGCCTTGTTACGCACAATTATGA 60.182 43.478 1.48 0.00 44.72 2.15
176 185 3.097910 CGCCTTGTTACGCACAATTATG 58.902 45.455 1.48 0.00 44.72 1.90
177 186 2.096819 CCGCCTTGTTACGCACAATTAT 59.903 45.455 1.48 0.00 44.72 1.28
188 200 1.807981 CGATCGCACCGCCTTGTTA 60.808 57.895 0.26 0.00 0.00 2.41
214 226 3.475774 GTAACAGTGCGCCCGTCG 61.476 66.667 4.18 0.00 42.12 5.12
217 229 1.959226 ACAAGTAACAGTGCGCCCG 60.959 57.895 4.18 0.00 0.00 6.13
218 230 0.882927 TCACAAGTAACAGTGCGCCC 60.883 55.000 4.18 0.00 35.76 6.13
293 315 1.165907 CCGCCTGTCATGTGTTGTGT 61.166 55.000 0.00 0.00 0.00 3.72
296 318 2.981560 GCCCGCCTGTCATGTGTTG 61.982 63.158 0.00 0.00 0.00 3.33
297 319 2.672996 GCCCGCCTGTCATGTGTT 60.673 61.111 0.00 0.00 0.00 3.32
298 320 4.722700 GGCCCGCCTGTCATGTGT 62.723 66.667 0.00 0.00 0.00 3.72
314 336 2.153401 TCCATGGAATAGCCCCGGG 61.153 63.158 15.80 15.80 34.97 5.73
369 391 4.720902 TGGGGTGGCATGTCGCTG 62.721 66.667 11.21 0.00 41.91 5.18
410 432 1.827681 TCCATCCGCTAGCTAGCTAG 58.172 55.000 37.09 37.09 46.85 3.42
411 433 2.095461 CATCCATCCGCTAGCTAGCTA 58.905 52.381 36.02 26.43 46.85 3.32
412 434 0.894141 CATCCATCCGCTAGCTAGCT 59.106 55.000 36.02 23.12 46.85 3.32
413 435 0.108424 CCATCCATCCGCTAGCTAGC 60.108 60.000 31.88 31.88 45.62 3.42
414 436 1.550327 TCCATCCATCCGCTAGCTAG 58.450 55.000 16.84 16.84 0.00 3.42
415 437 1.827344 CATCCATCCATCCGCTAGCTA 59.173 52.381 13.93 0.56 0.00 3.32
416 438 0.612229 CATCCATCCATCCGCTAGCT 59.388 55.000 13.93 0.00 0.00 3.32
419 441 1.556451 CATCCATCCATCCATCCGCTA 59.444 52.381 0.00 0.00 0.00 4.26
445 467 2.765250 ATCGACAGACACCACACGCC 62.765 60.000 0.00 0.00 0.00 5.68
446 468 1.372997 ATCGACAGACACCACACGC 60.373 57.895 0.00 0.00 0.00 5.34
447 469 1.008875 CCATCGACAGACACCACACG 61.009 60.000 0.00 0.00 0.00 4.49
448 470 0.317160 TCCATCGACAGACACCACAC 59.683 55.000 0.00 0.00 0.00 3.82
449 471 0.317160 GTCCATCGACAGACACCACA 59.683 55.000 10.90 0.00 38.99 4.17
450 472 0.732880 CGTCCATCGACAGACACCAC 60.733 60.000 14.92 0.00 42.86 4.16
451 473 0.891904 TCGTCCATCGACAGACACCA 60.892 55.000 14.92 0.00 44.01 4.17
452 474 1.880894 TCGTCCATCGACAGACACC 59.119 57.895 14.92 0.00 44.01 4.16
519 551 3.000925 CCGATAAGATTTCCGTTCCGTTG 59.999 47.826 0.00 0.00 0.00 4.10
528 560 0.586802 GCGGTGCCGATAAGATTTCC 59.413 55.000 15.45 0.00 42.83 3.13
551 583 4.832608 GGCGACACATCCGTCCCC 62.833 72.222 0.00 0.00 31.91 4.81
577 609 2.491022 GGCAGACGGATAGGCGAGT 61.491 63.158 0.00 0.00 0.00 4.18
580 612 2.028190 CAGGCAGACGGATAGGCG 59.972 66.667 0.00 0.00 0.00 5.52
581 613 2.280457 GCAGGCAGACGGATAGGC 60.280 66.667 0.00 0.00 0.00 3.93
582 614 2.423446 GGCAGGCAGACGGATAGG 59.577 66.667 0.00 0.00 0.00 2.57
589 621 4.459089 GGAGGACGGCAGGCAGAC 62.459 72.222 0.00 0.00 0.00 3.51
598 630 0.322975 GATGGATGGATGGAGGACGG 59.677 60.000 0.00 0.00 0.00 4.79
600 632 1.438469 TGGATGGATGGATGGAGGAC 58.562 55.000 0.00 0.00 0.00 3.85
601 633 2.272698 GATGGATGGATGGATGGAGGA 58.727 52.381 0.00 0.00 0.00 3.71
602 634 1.284198 GGATGGATGGATGGATGGAGG 59.716 57.143 0.00 0.00 0.00 4.30
603 635 1.990327 TGGATGGATGGATGGATGGAG 59.010 52.381 0.00 0.00 0.00 3.86
655 713 4.415150 AGGATGGGCACAGCACCG 62.415 66.667 6.52 0.00 33.84 4.94
706 771 1.153349 AAGCGGGCAAGTAGCTAGC 60.153 57.895 6.62 6.62 44.79 3.42
707 772 1.432270 GCAAGCGGGCAAGTAGCTAG 61.432 60.000 0.00 0.00 44.79 3.42
708 773 1.449601 GCAAGCGGGCAAGTAGCTA 60.450 57.895 0.00 0.00 44.79 3.32
709 774 2.747855 GCAAGCGGGCAAGTAGCT 60.748 61.111 0.00 0.00 44.79 3.32
733 802 2.331893 TTGGCCTACATGCACGCAC 61.332 57.895 3.32 0.00 0.00 5.34
734 803 2.033294 TTGGCCTACATGCACGCA 59.967 55.556 3.32 0.00 0.00 5.24
735 804 2.485122 GTTGGCCTACATGCACGC 59.515 61.111 12.79 0.00 0.00 5.34
736 805 2.749865 CGGTTGGCCTACATGCACG 61.750 63.158 19.19 8.90 0.00 5.34
737 806 3.051392 GCGGTTGGCCTACATGCAC 62.051 63.158 22.36 5.02 34.80 4.57
738 807 2.749839 GCGGTTGGCCTACATGCA 60.750 61.111 22.36 0.00 34.80 3.96
739 808 3.876198 CGCGGTTGGCCTACATGC 61.876 66.667 19.19 19.10 38.94 4.06
740 809 2.435938 ACGCGGTTGGCCTACATG 60.436 61.111 19.19 11.51 38.94 3.21
793 862 0.193069 ATGGATCAGGAGGAGGAGGG 59.807 60.000 0.00 0.00 0.00 4.30
810 879 2.584418 CGGACGAGCAGCTGGATG 60.584 66.667 17.12 0.00 0.00 3.51
835 904 2.363147 AGCTGGAGGAGACGGGAC 60.363 66.667 0.00 0.00 0.00 4.46
840 909 2.766229 GGGGGAGCTGGAGGAGAC 60.766 72.222 0.00 0.00 0.00 3.36
854 929 1.304134 CACCGGAAAAGGAAGGGGG 60.304 63.158 9.46 0.00 34.73 5.40
855 930 1.304134 CCACCGGAAAAGGAAGGGG 60.304 63.158 9.46 0.00 34.73 4.79
919 1017 4.359706 TGATCATTCACGAACAGTATCGG 58.640 43.478 0.00 0.00 46.82 4.18
924 1022 2.936993 GCCCTGATCATTCACGAACAGT 60.937 50.000 0.00 0.00 34.83 3.55
925 1023 1.667724 GCCCTGATCATTCACGAACAG 59.332 52.381 0.00 0.00 36.01 3.16
934 1032 2.512896 GCCCTCGCCCTGATCATT 59.487 61.111 0.00 0.00 0.00 2.57
968 1066 4.689549 TTCCCCCGAGGTCGCTCA 62.690 66.667 0.00 0.00 38.18 4.26
976 1074 3.447025 GATCACCGCTTCCCCCGAG 62.447 68.421 0.00 0.00 0.00 4.63
977 1075 3.467226 GATCACCGCTTCCCCCGA 61.467 66.667 0.00 0.00 0.00 5.14
978 1076 4.547367 GGATCACCGCTTCCCCCG 62.547 72.222 0.00 0.00 0.00 5.73
979 1077 2.757124 ATGGATCACCGCTTCCCCC 61.757 63.158 0.00 0.00 39.42 5.40
980 1078 1.526917 CATGGATCACCGCTTCCCC 60.527 63.158 0.00 0.00 39.42 4.81
981 1079 2.189499 GCATGGATCACCGCTTCCC 61.189 63.158 0.00 0.00 39.42 3.97
982 1080 0.820891 ATGCATGGATCACCGCTTCC 60.821 55.000 0.00 0.00 39.42 3.46
983 1081 0.309922 CATGCATGGATCACCGCTTC 59.690 55.000 19.40 0.00 39.42 3.86
1241 1348 1.137404 GATGTGGCGTTGTCCATGC 59.863 57.895 0.00 0.00 38.57 4.06
1257 1364 2.004408 GCAGCATGGAGGAAGGGGAT 62.004 60.000 0.00 0.00 35.86 3.85
1434 1547 1.377366 GATGCTGATGCTGCTGCTGT 61.377 55.000 17.00 5.48 40.48 4.40
1437 1550 0.039978 GATGATGCTGATGCTGCTGC 60.040 55.000 8.89 8.89 40.48 5.25
1619 1732 7.537596 AATGAAATTCAGAATTGGGTGTGTA 57.462 32.000 9.24 0.00 0.00 2.90
1620 1733 6.423776 AATGAAATTCAGAATTGGGTGTGT 57.576 33.333 9.24 0.00 0.00 3.72
1621 1734 9.439500 AATAAATGAAATTCAGAATTGGGTGTG 57.561 29.630 9.24 0.00 33.67 3.82
1677 1819 0.532862 CGCCTTGAGTTGGACAGTGT 60.533 55.000 0.00 0.00 0.00 3.55
1686 1828 7.396540 AATCTGAATTTAATCGCCTTGAGTT 57.603 32.000 0.00 0.00 0.00 3.01
1690 1832 8.807581 GGTAAAAATCTGAATTTAATCGCCTTG 58.192 33.333 0.00 0.00 33.93 3.61
1712 1854 2.819608 GCAGCAGACTGGAATTTGGTAA 59.180 45.455 4.26 0.00 44.63 2.85
1715 1857 0.529378 GGCAGCAGACTGGAATTTGG 59.471 55.000 4.26 0.00 44.63 3.28
1790 1963 8.270744 ACTGATAAGAAAATTGAGCTAGGTGAT 58.729 33.333 0.00 0.00 0.00 3.06
1791 1964 7.624549 ACTGATAAGAAAATTGAGCTAGGTGA 58.375 34.615 0.00 0.00 0.00 4.02
1792 1965 7.856145 ACTGATAAGAAAATTGAGCTAGGTG 57.144 36.000 0.00 0.00 0.00 4.00
1793 1966 7.148171 GCAACTGATAAGAAAATTGAGCTAGGT 60.148 37.037 0.00 0.00 0.00 3.08
1794 1967 7.066766 AGCAACTGATAAGAAAATTGAGCTAGG 59.933 37.037 0.00 0.00 0.00 3.02
1795 1968 7.909121 CAGCAACTGATAAGAAAATTGAGCTAG 59.091 37.037 0.00 0.00 32.44 3.42
1807 1980 3.920231 AGATGGCAGCAACTGATAAGA 57.080 42.857 5.19 0.00 32.44 2.10
1843 2016 4.035675 GCATAAAAACCAGCAGCCTACTAG 59.964 45.833 0.00 0.00 0.00 2.57
1849 2022 2.453983 TTGCATAAAAACCAGCAGCC 57.546 45.000 0.00 0.00 38.35 4.85
1856 2029 6.536941 TGTCAGGAAAACTTTGCATAAAAACC 59.463 34.615 0.00 0.00 0.00 3.27
1875 2048 4.533919 AATCAGACTTCAGAGTGTCAGG 57.466 45.455 7.96 1.72 35.88 3.86
2163 2342 3.070018 GCTATGCTGTGACAGTTCAAGT 58.930 45.455 14.82 0.00 31.90 3.16
2184 2363 5.756195 TTGTGATTTCAGTGAACTTCAGG 57.244 39.130 14.89 0.00 0.00 3.86
2188 2367 7.572523 TCTTCATTGTGATTTCAGTGAACTT 57.427 32.000 4.68 0.00 38.47 2.66
2233 2425 2.801063 CATTGCCTGGACAAAATAGCG 58.199 47.619 0.00 0.00 32.27 4.26
2235 2427 2.164219 ACGCATTGCCTGGACAAAATAG 59.836 45.455 2.41 0.00 32.27 1.73
2337 2531 3.203487 GGGGAATTCTGGTGGGTATGTTA 59.797 47.826 5.23 0.00 0.00 2.41
2342 2536 1.356398 GTTGGGGAATTCTGGTGGGTA 59.644 52.381 5.23 0.00 0.00 3.69
2343 2537 0.114364 GTTGGGGAATTCTGGTGGGT 59.886 55.000 5.23 0.00 0.00 4.51
2351 2545 4.528206 ACAGAGGAATTTGTTGGGGAATTC 59.472 41.667 0.00 0.00 40.07 2.17
2356 2550 4.402474 GGATAACAGAGGAATTTGTTGGGG 59.598 45.833 3.94 0.00 37.98 4.96
2357 2551 5.126061 CAGGATAACAGAGGAATTTGTTGGG 59.874 44.000 3.94 0.00 37.98 4.12
2364 2558 4.922206 TGCAACAGGATAACAGAGGAATT 58.078 39.130 0.00 0.00 0.00 2.17
2387 2581 2.035193 TCTGTCTGTCAGTTCAGTGAGC 59.965 50.000 19.17 0.00 43.97 4.26
2390 2584 3.126831 GGTTCTGTCTGTCAGTTCAGTG 58.873 50.000 19.17 0.00 43.97 3.66
2392 2586 2.223829 ACGGTTCTGTCTGTCAGTTCAG 60.224 50.000 16.09 16.09 43.97 3.02
2410 2604 3.495377 TCCTGTCAAAACGATTGTTACGG 59.505 43.478 0.00 0.00 37.31 4.02
2412 2606 5.997385 ACATCCTGTCAAAACGATTGTTAC 58.003 37.500 0.00 0.00 37.31 2.50
2415 2609 4.749245 GACATCCTGTCAAAACGATTGT 57.251 40.909 2.48 0.00 46.22 2.71
2560 2754 1.138266 GCCTACCTCGTAAATGGCAGA 59.862 52.381 0.00 0.00 40.04 4.26
2586 2780 3.711863 TGTTCCCTAACCGTATGTAGGT 58.288 45.455 0.00 0.00 45.29 3.08
2591 2785 6.373216 TCTTTGATTTGTTCCCTAACCGTATG 59.627 38.462 0.00 0.00 34.49 2.39
2594 2788 4.721132 TCTTTGATTTGTTCCCTAACCGT 58.279 39.130 0.00 0.00 34.49 4.83
2596 2790 6.264518 TCAGTTCTTTGATTTGTTCCCTAACC 59.735 38.462 0.00 0.00 34.49 2.85
2597 2791 7.272037 TCAGTTCTTTGATTTGTTCCCTAAC 57.728 36.000 0.00 0.00 36.07 2.34
2598 2792 7.523709 GCATCAGTTCTTTGATTTGTTCCCTAA 60.524 37.037 0.00 0.00 35.67 2.69
2599 2793 6.071952 GCATCAGTTCTTTGATTTGTTCCCTA 60.072 38.462 0.00 0.00 35.67 3.53
2603 2797 5.403466 GGTGCATCAGTTCTTTGATTTGTTC 59.597 40.000 0.00 0.00 35.67 3.18
2608 2802 4.401022 TCAGGTGCATCAGTTCTTTGATT 58.599 39.130 0.00 0.00 35.67 2.57
2618 2812 0.612229 ACAGGTCTCAGGTGCATCAG 59.388 55.000 0.00 0.00 0.00 2.90
2634 2828 4.505566 CCCATCATGGAGGGTTACATACAG 60.506 50.000 4.75 0.00 40.96 2.74
2648 2842 3.677190 ACAAAACAAATGCCCATCATGG 58.323 40.909 0.00 0.00 35.13 3.66
2656 2850 4.447290 ACAAACCCTACAAAACAAATGCC 58.553 39.130 0.00 0.00 0.00 4.40
2663 2857 9.191995 CAAGATTTCATACAAACCCTACAAAAC 57.808 33.333 0.00 0.00 0.00 2.43
2664 2858 9.137459 TCAAGATTTCATACAAACCCTACAAAA 57.863 29.630 0.00 0.00 0.00 2.44
2674 2868 8.673711 CCGGATAAACTCAAGATTTCATACAAA 58.326 33.333 0.00 0.00 0.00 2.83
2687 2881 4.811969 TGTAAGAGCCGGATAAACTCAA 57.188 40.909 5.05 0.00 32.71 3.02
2766 2960 2.911636 CCTCCAATGATATGCCTCTCCT 59.088 50.000 0.00 0.00 0.00 3.69
2837 3031 6.281405 TCTTTTCAGTTGAAGTCTGGTAGAC 58.719 40.000 0.79 0.79 45.38 2.59
2848 3046 6.016360 CACATGGGTGTATCTTTTCAGTTGAA 60.016 38.462 0.00 0.00 40.24 2.69
2863 3061 1.965414 TAGATGGGTCACATGGGTGT 58.035 50.000 0.00 0.00 45.45 4.16
2866 3064 2.923121 CTGTTAGATGGGTCACATGGG 58.077 52.381 0.00 0.00 40.72 4.00
2867 3065 2.292267 GCTGTTAGATGGGTCACATGG 58.708 52.381 0.00 0.00 40.72 3.66
2872 3070 4.290093 AGTAGATGCTGTTAGATGGGTCA 58.710 43.478 0.00 0.00 0.00 4.02
2873 3071 4.946478 AGTAGATGCTGTTAGATGGGTC 57.054 45.455 0.00 0.00 0.00 4.46
2882 3080 8.409358 AGGAACAAAATAAAGTAGATGCTGTT 57.591 30.769 0.00 0.00 0.00 3.16
2883 3081 9.515226 TTAGGAACAAAATAAAGTAGATGCTGT 57.485 29.630 0.00 0.00 0.00 4.40
2910 3108 6.785466 TGCTGTATGATACCCCTATCTGTTTA 59.215 38.462 0.00 0.00 31.36 2.01
2914 3112 5.946942 ATGCTGTATGATACCCCTATCTG 57.053 43.478 0.00 0.00 31.36 2.90
2916 3114 7.343316 ACTTCTATGCTGTATGATACCCCTATC 59.657 40.741 0.00 0.00 0.00 2.08
2918 3116 6.562228 ACTTCTATGCTGTATGATACCCCTA 58.438 40.000 0.00 0.00 0.00 3.53
2920 3118 5.746990 ACTTCTATGCTGTATGATACCCC 57.253 43.478 0.00 0.00 0.00 4.95
2944 3142 5.149973 TGCACATGCCAAACAGAATTATT 57.850 34.783 0.49 0.00 41.18 1.40
2945 3143 4.382254 CCTGCACATGCCAAACAGAATTAT 60.382 41.667 0.49 0.00 41.18 1.28
2973 3172 2.230660 GCTTGCACAAAAGTCCCTAGT 58.769 47.619 0.00 0.00 0.00 2.57
2993 3192 2.875296 TGGACTTTGATTTGGACCCTG 58.125 47.619 0.00 0.00 0.00 4.45
3039 3238 3.371063 GTGAGCGAGTCGGGACCA 61.371 66.667 15.52 0.00 0.00 4.02
3148 3347 2.158957 TCGTGTCAAATATCCCAGAGCC 60.159 50.000 0.00 0.00 0.00 4.70
3179 3378 7.665690 TCCTCTAGAAGAGTTGATATCAATGC 58.334 38.462 20.65 15.01 40.72 3.56
3314 3513 2.763448 ACACAGCCTGGAGAGTAATCTC 59.237 50.000 11.76 11.76 40.70 2.75
3363 3564 6.652900 CACGGTGAAATAATTTCCCCAAAATT 59.347 34.615 0.74 1.83 46.72 1.82
3368 3569 3.768878 ACACGGTGAAATAATTTCCCCA 58.231 40.909 16.29 0.00 37.07 4.96
3371 3572 8.077386 TGTTTTCTACACGGTGAAATAATTTCC 58.923 33.333 16.29 0.00 38.90 3.13
3377 3587 6.518493 ACTCTGTTTTCTACACGGTGAAATA 58.482 36.000 16.29 2.52 33.04 1.40
3378 3588 5.365619 ACTCTGTTTTCTACACGGTGAAAT 58.634 37.500 16.29 0.00 33.04 2.17
3446 3656 5.176774 TGTTCTTTTCGCTACTGTATGTGTG 59.823 40.000 0.00 0.00 0.00 3.82
3471 3681 3.125146 GCGTGTCATGTGTATGTGTCATT 59.875 43.478 0.00 0.00 35.73 2.57
3560 3777 3.476295 TCATCTGCTGAATGTTTTCGC 57.524 42.857 0.00 0.00 34.39 4.70
3617 3834 4.390297 GGTGATGCTCTAACTCAACAGTTC 59.610 45.833 0.00 0.00 42.27 3.01
3670 3887 0.928229 GGCACGTCATGAACCGATAC 59.072 55.000 12.18 1.92 0.00 2.24
3760 3977 3.882888 CCCTGCTGTACAAGTTCTTGAAA 59.117 43.478 17.75 4.39 0.00 2.69
3844 4061 3.756933 AGCTTCCAAACACAAATGCAT 57.243 38.095 0.00 0.00 0.00 3.96
3866 4083 6.038161 CCTTTCTATTTTCTGTGTGTGTGTGA 59.962 38.462 0.00 0.00 0.00 3.58
3899 4116 3.168773 GCAAGGTTTATCCAGCGGA 57.831 52.632 0.00 0.00 39.02 5.54
3905 4122 6.445357 TCCTATTTTTCGCAAGGTTTATCC 57.555 37.500 0.00 0.00 38.47 2.59
3910 4127 5.535030 AGAGTTTCCTATTTTTCGCAAGGTT 59.465 36.000 0.00 0.00 38.47 3.50
3976 4193 1.338136 CCGGGCAGGAACCAGATAGT 61.338 60.000 0.00 0.00 45.00 2.12
4009 4226 1.507140 TGGAGATATTGGCGTTCCCT 58.493 50.000 0.00 0.00 0.00 4.20
4034 4251 2.159476 TGAAATGCTTTCTGCTGCGATC 60.159 45.455 0.00 0.00 43.37 3.69
4037 4254 2.054687 TTGAAATGCTTTCTGCTGCG 57.945 45.000 0.00 0.00 43.37 5.18
4078 4295 7.178451 AGGCCAAATAACTTGCAGTATACTTTT 59.822 33.333 5.01 0.00 33.27 2.27
4081 4298 5.590259 CAGGCCAAATAACTTGCAGTATACT 59.410 40.000 5.01 0.00 33.27 2.12
4082 4299 5.733373 GCAGGCCAAATAACTTGCAGTATAC 60.733 44.000 5.01 0.00 33.27 1.47
4083 4300 4.338118 GCAGGCCAAATAACTTGCAGTATA 59.662 41.667 5.01 0.00 33.27 1.47
4084 4301 3.131046 GCAGGCCAAATAACTTGCAGTAT 59.869 43.478 5.01 0.00 33.27 2.12
4085 4302 2.491693 GCAGGCCAAATAACTTGCAGTA 59.508 45.455 5.01 0.00 33.27 2.74
4087 4304 1.273048 TGCAGGCCAAATAACTTGCAG 59.727 47.619 5.01 0.00 33.27 4.41
4140 4358 6.514063 AGGCTTATACTCTTTACGGTGAATC 58.486 40.000 0.00 0.00 0.00 2.52
4146 4367 9.754382 TTTATGTTAGGCTTATACTCTTTACGG 57.246 33.333 0.00 0.00 0.00 4.02
4173 4394 5.599999 AGCGGTAGAAGAGAAATACACAT 57.400 39.130 0.00 0.00 0.00 3.21
4177 4398 8.230112 GCTAAATAGCGGTAGAAGAGAAATAC 57.770 38.462 0.00 0.00 39.82 1.89


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

AutoCloner maintained by Alex Coulton.