Multiple sequence alignment - TraesCS1A01G332200

Loading Multiple Alignment...

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 TraesCS1A01G332200 chr1A 100.000 4629 0 0 1 4629 520788145 520792773 0.000000e+00 8549
1 TraesCS1A01G332200 chr1A 91.150 113 9 1 2276 2387 564325365 564325253 8.020000e-33 152
2 TraesCS1A01G332200 chr1D 92.229 1557 60 18 858 2379 424986947 424988477 0.000000e+00 2148
3 TraesCS1A01G332200 chr1D 92.686 752 51 2 1 748 467475716 467474965 0.000000e+00 1081
4 TraesCS1A01G332200 chr1D 83.773 986 80 29 3259 4192 424989432 424990389 0.000000e+00 861
5 TraesCS1A01G332200 chr1D 80.984 610 59 28 2490 3081 424988531 424989101 9.200000e-117 431
6 TraesCS1A01G332200 chr1D 84.652 417 33 11 4232 4625 424990786 424991194 2.020000e-103 387
7 TraesCS1A01G332200 chr1D 91.573 178 15 0 3075 3252 424989129 424989306 3.580000e-61 246
8 TraesCS1A01G332200 chr1D 91.463 82 7 0 753 834 424986733 424986814 3.790000e-21 113
9 TraesCS1A01G332200 chr1B 88.335 1706 122 37 858 2529 574262541 574264203 0.000000e+00 1977
10 TraesCS1A01G332200 chr1B 84.975 1005 93 33 3037 4025 574264781 574265743 0.000000e+00 966
11 TraesCS1A01G332200 chr1B 88.382 241 13 3 4389 4629 574266735 574266960 4.560000e-70 276
12 TraesCS1A01G332200 chr1B 79.327 208 26 9 2546 2745 574264252 574264450 3.760000e-26 130
13 TraesCS1A01G332200 chr7A 96.138 751 22 3 1 747 641403400 641402653 0.000000e+00 1219
14 TraesCS1A01G332200 chr2A 95.733 750 26 4 1 746 123739510 123738763 0.000000e+00 1203
15 TraesCS1A01G332200 chr2A 91.150 113 9 1 2276 2387 197670287 197670175 8.020000e-33 152
16 TraesCS1A01G332200 chr4D 95.327 749 31 2 2 746 379507725 379506977 0.000000e+00 1186
17 TraesCS1A01G332200 chr3A 95.733 703 27 2 1 701 170228483 170227782 0.000000e+00 1129
18 TraesCS1A01G332200 chr4B 92.543 751 52 2 1 747 575617813 575617063 0.000000e+00 1074
19 TraesCS1A01G332200 chr5A 92.000 750 56 3 1 747 486066008 486066756 0.000000e+00 1050
20 TraesCS1A01G332200 chr3B 92.102 747 54 2 1 744 612314397 612315141 0.000000e+00 1048
21 TraesCS1A01G332200 chr5B 91.888 752 55 4 1 747 695846352 695845602 0.000000e+00 1046
22 TraesCS1A01G332200 chr6B 91.150 113 9 1 2276 2387 14719517 14719405 8.020000e-33 152


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 TraesCS1A01G332200 chr1A 520788145 520792773 4628 False 8549.000000 8549 100.000000 1 4629 1 chr1A.!!$F1 4628
1 TraesCS1A01G332200 chr1D 467474965 467475716 751 True 1081.000000 1081 92.686000 1 748 1 chr1D.!!$R1 747
2 TraesCS1A01G332200 chr1D 424986733 424991194 4461 False 697.666667 2148 87.445667 753 4625 6 chr1D.!!$F1 3872
3 TraesCS1A01G332200 chr1B 574262541 574266960 4419 False 837.250000 1977 85.254750 858 4629 4 chr1B.!!$F1 3771
4 TraesCS1A01G332200 chr7A 641402653 641403400 747 True 1219.000000 1219 96.138000 1 747 1 chr7A.!!$R1 746
5 TraesCS1A01G332200 chr2A 123738763 123739510 747 True 1203.000000 1203 95.733000 1 746 1 chr2A.!!$R1 745
6 TraesCS1A01G332200 chr4D 379506977 379507725 748 True 1186.000000 1186 95.327000 2 746 1 chr4D.!!$R1 744
7 TraesCS1A01G332200 chr3A 170227782 170228483 701 True 1129.000000 1129 95.733000 1 701 1 chr3A.!!$R1 700
8 TraesCS1A01G332200 chr4B 575617063 575617813 750 True 1074.000000 1074 92.543000 1 747 1 chr4B.!!$R1 746
9 TraesCS1A01G332200 chr5A 486066008 486066756 748 False 1050.000000 1050 92.000000 1 747 1 chr5A.!!$F1 746
10 TraesCS1A01G332200 chr3B 612314397 612315141 744 False 1048.000000 1048 92.102000 1 744 1 chr3B.!!$F1 743
11 TraesCS1A01G332200 chr5B 695845602 695846352 750 True 1046.000000 1046 91.888000 1 747 1 chr5B.!!$R1 746

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
936 1063 0.037790 GCACCACACCTCTCACTCTC 60.038 60.000 0.00 0.00 0.0 3.20 F
1318 1454 0.037882 TCACTTCGCTTGCTCTCTGG 60.038 55.000 0.00 0.00 0.0 3.86 F
2272 2434 1.067635 CCTTGGCAAGATTGTTTCCCG 60.068 52.381 28.18 3.67 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2782 3001 0.179225 CAATCACAAGCGCGTGTACC 60.179 55.0 28.02 0.0 38.12 3.34 R
2783 3002 0.179225 CCAATCACAAGCGCGTGTAC 60.179 55.0 28.02 0.0 38.12 2.90 R
3953 4390 0.107410 TCCCAATCCACCGTGCATAC 60.107 55.0 0.00 0.0 0.00 2.39 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
159 161 2.697644 CCTCCTCCCCAAGGGCAT 60.698 66.667 0.00 0.00 46.23 4.40
258 269 3.896272 AAGAAGTCCTTGGAGACGTAAGT 59.104 43.478 0.00 0.00 44.41 2.24
674 691 5.818336 TGGTCACATTTAGTTTTCGACTTGA 59.182 36.000 0.00 0.00 39.86 3.02
712 729 2.912956 ACAATACTTGGCTCCCTCTTGA 59.087 45.455 0.00 0.00 34.12 3.02
748 765 2.223294 GCGCAACGAGTCATCTAGTAGT 60.223 50.000 0.30 0.00 0.00 2.73
749 766 3.731264 GCGCAACGAGTCATCTAGTAGTT 60.731 47.826 0.30 0.00 0.00 2.24
750 767 4.495349 GCGCAACGAGTCATCTAGTAGTTA 60.495 45.833 0.30 0.00 0.00 2.24
751 768 5.199000 CGCAACGAGTCATCTAGTAGTTAG 58.801 45.833 0.00 0.00 0.00 2.34
758 775 7.120873 ACGAGTCATCTAGTAGTTAGAAAAGCA 59.879 37.037 0.00 0.00 41.59 3.91
761 778 6.477360 GTCATCTAGTAGTTAGAAAAGCAGCC 59.523 42.308 0.00 0.00 41.59 4.85
764 781 7.336161 TCTAGTAGTTAGAAAAGCAGCCTAG 57.664 40.000 0.00 0.00 35.46 3.02
813 830 1.451387 ACCACATTTCGGATCGCCC 60.451 57.895 0.00 0.00 0.00 6.13
823 840 1.006102 GGATCGCCCGTATCACCAG 60.006 63.158 0.00 0.00 0.00 4.00
837 939 2.046892 CCAGTCTCGGGGTTGCAG 60.047 66.667 0.00 0.00 0.00 4.41
838 940 2.046892 CAGTCTCGGGGTTGCAGG 60.047 66.667 0.00 0.00 0.00 4.85
867 993 0.109597 CATCTGCAAACTCAACGGCC 60.110 55.000 0.00 0.00 0.00 6.13
902 1028 2.199535 CCCCCAATCCAGCCATCC 59.800 66.667 0.00 0.00 0.00 3.51
936 1063 0.037790 GCACCACACCTCTCACTCTC 60.038 60.000 0.00 0.00 0.00 3.20
940 1067 1.181786 CACACCTCTCACTCTCTCCC 58.818 60.000 0.00 0.00 0.00 4.30
941 1068 0.322997 ACACCTCTCACTCTCTCCCG 60.323 60.000 0.00 0.00 0.00 5.14
944 1071 2.043852 TCTCACTCTCTCCCGGGC 60.044 66.667 18.49 0.00 0.00 6.13
948 1075 4.095400 ACTCTCTCCCGGGCCCAT 62.095 66.667 24.92 0.00 0.00 4.00
960 1087 0.253327 GGGCCCATCTTCGAACTTCT 59.747 55.000 19.95 0.00 0.00 2.85
1141 1268 3.068691 CCGTCTCGGCCTCCTCAA 61.069 66.667 0.00 0.00 41.17 3.02
1142 1269 2.182030 CGTCTCGGCCTCCTCAAC 59.818 66.667 0.00 0.00 0.00 3.18
1143 1270 2.579738 GTCTCGGCCTCCTCAACC 59.420 66.667 0.00 0.00 0.00 3.77
1144 1271 2.119611 TCTCGGCCTCCTCAACCA 59.880 61.111 0.00 0.00 0.00 3.67
1261 1388 4.446413 CCACCCGCACCGAGGTAC 62.446 72.222 0.00 0.00 33.52 3.34
1262 1389 4.789075 CACCCGCACCGAGGTACG 62.789 72.222 7.86 7.86 42.18 3.67
1264 1391 3.133464 CCCGCACCGAGGTACGTA 61.133 66.667 13.14 0.00 40.78 3.57
1266 1393 1.212490 CCGCACCGAGGTACGTAAA 59.788 57.895 13.14 0.00 40.78 2.01
1269 1396 1.401409 CGCACCGAGGTACGTAAAAGA 60.401 52.381 6.73 0.00 40.78 2.52
1271 1398 2.607771 GCACCGAGGTACGTAAAAGACA 60.608 50.000 0.00 0.00 40.78 3.41
1272 1399 3.641648 CACCGAGGTACGTAAAAGACAA 58.358 45.455 0.00 0.00 40.78 3.18
1274 1401 4.325472 CACCGAGGTACGTAAAAGACAATC 59.675 45.833 0.00 0.00 40.78 2.67
1275 1402 3.545078 CCGAGGTACGTAAAAGACAATCG 59.455 47.826 0.00 1.31 40.78 3.34
1286 1414 1.219124 GACAATCGCCTCAGCCTGA 59.781 57.895 0.00 0.00 34.57 3.86
1316 1452 0.246086 CCTCACTTCGCTTGCTCTCT 59.754 55.000 0.00 0.00 0.00 3.10
1318 1454 0.037882 TCACTTCGCTTGCTCTCTGG 60.038 55.000 0.00 0.00 0.00 3.86
1326 1464 1.135024 GCTTGCTCTCTGGAGTCTGAG 60.135 57.143 7.18 7.18 41.38 3.35
1484 1622 3.411517 ATCGCCCCCACCAAGGAG 61.412 66.667 0.00 0.00 41.22 3.69
1509 1647 1.968493 TCCAGGTACGCTTCAGTTTCT 59.032 47.619 0.00 0.00 0.00 2.52
1534 1672 2.938823 GAAGCAACAGTTCGCGCGA 61.939 57.895 31.40 31.40 0.00 5.87
1557 1695 1.597663 CCTGTTCGACATTAATCCGGC 59.402 52.381 0.00 2.81 0.00 6.13
1842 1980 1.746470 CCGGAAGTTGGTATTCCCAC 58.254 55.000 0.00 0.00 45.19 4.61
1854 1992 2.198304 ATTCCCACTTCCTCACCGCC 62.198 60.000 0.00 0.00 0.00 6.13
1857 1995 2.358737 CACTTCCTCACCGCCCAC 60.359 66.667 0.00 0.00 0.00 4.61
1875 2013 2.416566 CCACTCTCATCTCTGAACACCG 60.417 54.545 0.00 0.00 0.00 4.94
2009 2147 2.103042 GCTGGTCACGGATGCTGTC 61.103 63.158 0.00 0.00 0.00 3.51
2018 2156 2.094894 CACGGATGCTGTCATCTTTGTC 59.905 50.000 10.41 0.00 46.41 3.18
2256 2418 6.432162 TGAGGTAGTGTAGTAGTAACACCTTG 59.568 42.308 2.90 0.00 46.77 3.61
2272 2434 1.067635 CCTTGGCAAGATTGTTTCCCG 60.068 52.381 28.18 3.67 0.00 5.14
2277 2439 2.678336 GGCAAGATTGTTTCCCGTCTAG 59.322 50.000 0.00 0.00 0.00 2.43
2278 2440 2.678336 GCAAGATTGTTTCCCGTCTAGG 59.322 50.000 0.00 0.00 40.63 3.02
2322 2484 8.417780 TGTTTTCACAAACTTGTCCATATTTG 57.582 30.769 0.00 0.00 42.61 2.32
2394 2556 5.667175 CAGTCTAACGTTTTAACTGCAGTC 58.333 41.667 21.95 6.09 31.87 3.51
2397 2559 7.168637 CAGTCTAACGTTTTAACTGCAGTCTAA 59.831 37.037 21.95 16.84 31.87 2.10
2399 2561 8.160976 GTCTAACGTTTTAACTGCAGTCTAATC 58.839 37.037 21.95 14.24 0.00 1.75
2406 2568 3.678056 ACTGCAGTCTAATCGTGGAAA 57.322 42.857 15.25 0.00 0.00 3.13
2428 2590 8.847444 GAAATGCTTCCATTCTGTACTAATTG 57.153 34.615 0.00 0.00 40.69 2.32
2438 2600 9.988350 CCATTCTGTACTAATTGTTATCACAAC 57.012 33.333 0.00 0.00 45.88 3.32
2439 2601 9.689075 CATTCTGTACTAATTGTTATCACAACG 57.311 33.333 0.00 0.00 45.88 4.10
2441 2603 7.380536 TCTGTACTAATTGTTATCACAACGGT 58.619 34.615 0.00 0.00 45.88 4.83
2442 2604 8.522003 TCTGTACTAATTGTTATCACAACGGTA 58.478 33.333 0.00 0.00 45.88 4.02
2447 2609 7.874016 ACTAATTGTTATCACAACGGTACAAGA 59.126 33.333 0.00 0.00 45.88 3.02
2448 2610 7.499321 AATTGTTATCACAACGGTACAAGAA 57.501 32.000 0.00 0.00 45.88 2.52
2449 2611 7.681939 ATTGTTATCACAACGGTACAAGAAT 57.318 32.000 0.00 0.00 45.88 2.40
2460 2622 7.065803 ACAACGGTACAAGAATTATCTGGAATG 59.934 37.037 0.00 0.00 35.59 2.67
2484 2646 8.518151 TGTGTAAAATGTAGAATGCATGTTTG 57.482 30.769 0.00 0.00 41.90 2.93
2485 2647 7.598118 TGTGTAAAATGTAGAATGCATGTTTGG 59.402 33.333 0.00 0.00 41.90 3.28
2491 2701 9.590451 AAATGTAGAATGCATGTTTGGAATAAG 57.410 29.630 0.00 0.00 41.90 1.73
2524 2734 8.954950 AGTAGAACACTAGATTGATTTCCATG 57.045 34.615 0.00 0.00 34.98 3.66
2543 2753 5.715279 TCCATGTAGGCATCTAGGTATGTAC 59.285 44.000 0.00 0.00 37.29 2.90
2549 2759 3.574396 GGCATCTAGGTATGTACTGCTCA 59.426 47.826 0.00 0.00 0.00 4.26
2578 2788 2.095415 GGTTAGTGCTAAAACTTGGCCG 60.095 50.000 0.00 0.00 36.15 6.13
2591 2801 9.712359 CTAAAACTTGGCCGTATTAACTTATTC 57.288 33.333 0.00 0.00 0.00 1.75
2597 2807 6.408035 TGGCCGTATTAACTTATTCACTTCA 58.592 36.000 0.00 0.00 0.00 3.02
2616 2828 7.706179 TCACTTCAGTTAGCCTTTTTGAATTTG 59.294 33.333 0.00 0.00 0.00 2.32
2658 2870 3.525199 AGGAAGGTCATCTTGCCAGTATT 59.475 43.478 0.00 0.00 43.74 1.89
2670 2882 5.772672 TCTTGCCAGTATTGGTGTATTGTTT 59.227 36.000 6.10 0.00 46.80 2.83
2671 2883 6.943146 TCTTGCCAGTATTGGTGTATTGTTTA 59.057 34.615 6.10 0.00 46.80 2.01
2752 2971 3.643320 TCAGCGATTCCATGTCCTAGAAT 59.357 43.478 0.00 0.00 33.01 2.40
2756 2975 4.450419 GCGATTCCATGTCCTAGAATCAAG 59.550 45.833 16.76 7.06 43.92 3.02
2757 2976 5.740224 GCGATTCCATGTCCTAGAATCAAGA 60.740 44.000 16.76 0.00 43.92 3.02
2758 2977 6.283694 CGATTCCATGTCCTAGAATCAAGAA 58.716 40.000 16.76 0.28 43.92 2.52
2759 2978 6.763135 CGATTCCATGTCCTAGAATCAAGAAA 59.237 38.462 16.76 0.00 43.92 2.52
2760 2979 7.042187 CGATTCCATGTCCTAGAATCAAGAAAG 60.042 40.741 16.76 2.18 43.92 2.62
2761 2980 6.627087 TCCATGTCCTAGAATCAAGAAAGT 57.373 37.500 0.00 0.00 0.00 2.66
2762 2981 7.733773 TCCATGTCCTAGAATCAAGAAAGTA 57.266 36.000 0.00 0.00 0.00 2.24
2765 2984 7.708752 CCATGTCCTAGAATCAAGAAAGTACTC 59.291 40.741 0.00 0.00 0.00 2.59
2782 3001 0.857935 CTCGTAGTAGAGTACGCCGG 59.142 60.000 11.27 0.00 44.45 6.13
2783 3002 0.530650 TCGTAGTAGAGTACGCCGGG 60.531 60.000 2.18 0.00 44.45 5.73
2785 3004 1.538204 CGTAGTAGAGTACGCCGGGTA 60.538 57.143 2.18 0.39 39.40 3.69
2798 3017 2.356553 GGGTACACGCGCTTGTGA 60.357 61.111 27.71 10.39 42.55 3.58
2799 3018 1.740296 GGGTACACGCGCTTGTGAT 60.740 57.895 27.71 11.54 42.55 3.06
2815 3034 5.178067 GCTTGTGATTGGGTTTTCTCATTTG 59.822 40.000 0.00 0.00 0.00 2.32
2816 3035 4.630111 TGTGATTGGGTTTTCTCATTTGC 58.370 39.130 0.00 0.00 0.00 3.68
2825 3044 6.122964 GGGTTTTCTCATTTGCCTACTATCT 58.877 40.000 0.00 0.00 0.00 1.98
2826 3045 6.603599 GGGTTTTCTCATTTGCCTACTATCTT 59.396 38.462 0.00 0.00 0.00 2.40
2828 3047 7.201741 GGTTTTCTCATTTGCCTACTATCTTCC 60.202 40.741 0.00 0.00 0.00 3.46
2830 3049 6.166984 TCTCATTTGCCTACTATCTTCCTG 57.833 41.667 0.00 0.00 0.00 3.86
2831 3050 4.708177 TCATTTGCCTACTATCTTCCTGC 58.292 43.478 0.00 0.00 0.00 4.85
2832 3051 2.890808 TTGCCTACTATCTTCCTGCG 57.109 50.000 0.00 0.00 0.00 5.18
2833 3052 1.776662 TGCCTACTATCTTCCTGCGT 58.223 50.000 0.00 0.00 0.00 5.24
2834 3053 2.108168 TGCCTACTATCTTCCTGCGTT 58.892 47.619 0.00 0.00 0.00 4.84
2837 3056 3.797184 GCCTACTATCTTCCTGCGTTCAG 60.797 52.174 0.00 0.00 40.02 3.02
2848 3067 2.905075 CTGCGTTCAGGAATACCATCA 58.095 47.619 0.00 0.00 38.94 3.07
2849 3068 3.470709 CTGCGTTCAGGAATACCATCAT 58.529 45.455 0.00 0.00 38.94 2.45
2851 3070 3.876914 TGCGTTCAGGAATACCATCATTC 59.123 43.478 0.00 0.00 38.94 2.67
2866 3085 7.623999 ACCATCATTCCTACTATCTTGTCAT 57.376 36.000 0.00 0.00 0.00 3.06
2922 3141 7.756272 TGATCATGTGTATTGTTTCAAGATTGC 59.244 33.333 0.00 0.00 0.00 3.56
2984 3234 4.389992 ACGTGACAGATAGAAGCAACATTG 59.610 41.667 0.00 0.00 0.00 2.82
3006 3256 6.844696 TGTAATTGCTACTAGTTGCATAGC 57.155 37.500 28.30 18.21 40.63 2.97
3018 3268 7.868775 ACTAGTTGCATAGCACAAATCATATG 58.131 34.615 0.00 0.00 38.71 1.78
3019 3269 6.704289 AGTTGCATAGCACAAATCATATGT 57.296 33.333 1.90 0.00 38.71 2.29
3065 3322 4.880886 TTGCATCAACAATATCGACAGG 57.119 40.909 0.00 0.00 0.00 4.00
3071 3328 7.118245 TGCATCAACAATATCGACAGGATTATC 59.882 37.037 0.00 0.00 36.55 1.75
3072 3329 7.332926 GCATCAACAATATCGACAGGATTATCT 59.667 37.037 0.00 0.00 36.55 1.98
3073 3330 9.212641 CATCAACAATATCGACAGGATTATCTT 57.787 33.333 0.00 0.00 36.55 2.40
3128 3419 7.331791 AGAGGATGGTACTTCAAATACTGTTC 58.668 38.462 0.00 0.00 0.00 3.18
3131 3422 6.884836 GGATGGTACTTCAAATACTGTTCCTT 59.115 38.462 0.00 0.00 0.00 3.36
3134 3425 6.002082 GGTACTTCAAATACTGTTCCTTGGT 58.998 40.000 0.00 0.00 0.00 3.67
3146 3437 3.244911 TGTTCCTTGGTCCCTCAAATCTC 60.245 47.826 0.00 0.00 0.00 2.75
3155 3446 0.105778 CCTCAAATCTCCTCGAGCCC 59.894 60.000 6.99 0.00 0.00 5.19
3158 3449 1.066143 TCAAATCTCCTCGAGCCCAAC 60.066 52.381 6.99 0.00 0.00 3.77
3254 3545 7.252612 TCCAGAGAAGGTATGTTTTGTCATA 57.747 36.000 0.00 0.00 0.00 2.15
3255 3546 7.331026 TCCAGAGAAGGTATGTTTTGTCATAG 58.669 38.462 0.00 0.00 32.01 2.23
3265 3675 7.169982 GGTATGTTTTGTCATAGCTAGCACTAG 59.830 40.741 18.83 3.78 42.15 2.57
3284 3694 6.872020 GCACTAGACTAAATGGTTACACTTCA 59.128 38.462 0.00 0.00 0.00 3.02
3292 3702 6.575162 AAATGGTTACACTTCAGTCATTCC 57.425 37.500 0.00 0.00 0.00 3.01
3294 3704 5.304686 TGGTTACACTTCAGTCATTCCTT 57.695 39.130 0.00 0.00 0.00 3.36
3296 3706 5.163248 TGGTTACACTTCAGTCATTCCTTCA 60.163 40.000 0.00 0.00 0.00 3.02
3298 3708 6.128172 GGTTACACTTCAGTCATTCCTTCATG 60.128 42.308 0.00 0.00 0.00 3.07
3299 3709 4.330250 ACACTTCAGTCATTCCTTCATGG 58.670 43.478 0.00 0.00 37.10 3.66
3300 3710 3.128242 CACTTCAGTCATTCCTTCATGGC 59.872 47.826 0.00 0.00 35.26 4.40
3301 3711 3.245016 ACTTCAGTCATTCCTTCATGGCA 60.245 43.478 0.00 0.00 30.53 4.92
3313 3723 3.243301 CCTTCATGGCATGCTAACATCAC 60.243 47.826 22.56 0.00 32.87 3.06
3315 3725 1.338973 CATGGCATGCTAACATCACCC 59.661 52.381 18.92 0.00 32.87 4.61
3320 3730 1.064505 CATGCTAACATCACCCGCTTG 59.935 52.381 0.00 0.00 32.87 4.01
3355 3765 3.391665 CTGGGTGGACAGGATCGCC 62.392 68.421 0.00 0.00 34.84 5.54
3391 3801 4.687215 CGGATCATCCCGGCGCAT 62.687 66.667 10.83 0.00 45.43 4.73
3635 4045 4.748892 CGGAAGGAAGCGATGATACATAT 58.251 43.478 0.00 0.00 0.00 1.78
3636 4046 5.891451 CGGAAGGAAGCGATGATACATATA 58.109 41.667 0.00 0.00 0.00 0.86
3637 4047 5.744345 CGGAAGGAAGCGATGATACATATAC 59.256 44.000 0.00 0.00 0.00 1.47
3639 4049 6.351033 GGAAGGAAGCGATGATACATATACCA 60.351 42.308 0.00 0.00 0.00 3.25
3640 4050 6.214191 AGGAAGCGATGATACATATACCAG 57.786 41.667 0.00 0.00 0.00 4.00
3653 4063 0.107654 ATACCAGAGAAACCGCTGCC 60.108 55.000 0.00 0.00 31.32 4.85
3654 4064 1.192146 TACCAGAGAAACCGCTGCCT 61.192 55.000 0.00 0.00 31.32 4.75
3659 4069 0.603975 GAGAAACCGCTGCCTTGTCT 60.604 55.000 0.00 0.00 0.00 3.41
3660 4070 0.179018 AGAAACCGCTGCCTTGTCTT 60.179 50.000 0.00 0.00 0.00 3.01
3661 4071 0.668535 GAAACCGCTGCCTTGTCTTT 59.331 50.000 0.00 0.00 0.00 2.52
3662 4072 1.067060 GAAACCGCTGCCTTGTCTTTT 59.933 47.619 0.00 0.00 0.00 2.27
3663 4073 0.668535 AACCGCTGCCTTGTCTTTTC 59.331 50.000 0.00 0.00 0.00 2.29
3664 4074 0.179018 ACCGCTGCCTTGTCTTTTCT 60.179 50.000 0.00 0.00 0.00 2.52
3665 4075 0.954452 CCGCTGCCTTGTCTTTTCTT 59.046 50.000 0.00 0.00 0.00 2.52
3666 4076 1.068954 CCGCTGCCTTGTCTTTTCTTC 60.069 52.381 0.00 0.00 0.00 2.87
3667 4077 1.876156 CGCTGCCTTGTCTTTTCTTCT 59.124 47.619 0.00 0.00 0.00 2.85
3668 4078 2.350197 CGCTGCCTTGTCTTTTCTTCTG 60.350 50.000 0.00 0.00 0.00 3.02
3670 4080 2.883386 CTGCCTTGTCTTTTCTTCTGCT 59.117 45.455 0.00 0.00 0.00 4.24
3682 4092 7.429630 GTCTTTTCTTCTGCTTAGTTTTGTCAC 59.570 37.037 0.00 0.00 0.00 3.67
3711 4127 2.281276 TCACTGGCTGCTGCTGTG 60.281 61.111 24.29 24.29 41.23 3.66
3842 4263 0.466124 AAGCTAGAATCGGCCAGGAC 59.534 55.000 2.24 0.00 0.00 3.85
3853 4274 2.320587 GCCAGGACACAGTGAAGCG 61.321 63.158 7.81 0.00 0.00 4.68
3860 4282 0.748005 ACACAGTGAAGCGTTTGCCT 60.748 50.000 7.81 0.00 44.31 4.75
3862 4284 0.381801 ACAGTGAAGCGTTTGCCTTG 59.618 50.000 0.00 0.00 44.31 3.61
3873 4295 0.961019 TTTGCCTTGGTGTGCATCTC 59.039 50.000 0.00 0.00 37.33 2.75
3888 4310 2.726066 GCATCTCGTTGCAACTTACAGC 60.726 50.000 26.09 19.49 42.31 4.40
3891 4313 0.579630 TCGTTGCAACTTACAGCACG 59.420 50.000 26.09 11.47 41.05 5.34
3895 4318 0.516877 TGCAACTTACAGCACGCATC 59.483 50.000 0.00 0.00 35.51 3.91
3897 4320 1.197721 GCAACTTACAGCACGCATCTT 59.802 47.619 0.00 0.00 0.00 2.40
3923 4360 1.810030 GGCCACGGACGAGTGAATC 60.810 63.158 0.00 2.24 44.43 2.52
3953 4390 0.680921 ACGGCACAAGATTGGGATGG 60.681 55.000 0.00 0.00 31.80 3.51
3968 4405 1.476833 GGATGGTATGCACGGTGGATT 60.477 52.381 20.26 2.21 29.08 3.01
3969 4406 1.603802 GATGGTATGCACGGTGGATTG 59.396 52.381 20.26 0.00 29.08 2.67
3970 4407 0.393673 TGGTATGCACGGTGGATTGG 60.394 55.000 20.26 0.00 29.08 3.16
3971 4408 1.101049 GGTATGCACGGTGGATTGGG 61.101 60.000 20.26 0.00 29.08 4.12
3972 4409 0.107410 GTATGCACGGTGGATTGGGA 60.107 55.000 20.26 0.00 29.08 4.37
3973 4410 0.843309 TATGCACGGTGGATTGGGAT 59.157 50.000 20.26 0.00 29.08 3.85
3974 4411 0.033208 ATGCACGGTGGATTGGGATT 60.033 50.000 9.51 0.00 0.00 3.01
3990 4427 5.219468 TGGGATTTGGGAGTTAATTCCAT 57.781 39.130 17.85 3.95 35.04 3.41
4013 4450 1.214589 CGACCGATCCAGTTTCCGT 59.785 57.895 0.00 0.00 0.00 4.69
4014 4451 0.801067 CGACCGATCCAGTTTCCGTC 60.801 60.000 0.00 0.00 0.00 4.79
4064 4532 4.341783 GGGGAGCTGCACTGCACT 62.342 66.667 7.79 2.79 37.13 4.40
4068 4536 0.813210 GGAGCTGCACTGCACTATCC 60.813 60.000 0.00 4.29 36.57 2.59
4109 4577 3.427909 CCTCATTAACCTGCACGTACGTA 60.428 47.826 22.34 5.54 0.00 3.57
4110 4578 3.500982 TCATTAACCTGCACGTACGTAC 58.499 45.455 22.34 16.78 0.00 3.67
4111 4579 3.191162 TCATTAACCTGCACGTACGTACT 59.809 43.478 22.34 7.87 0.00 2.73
4112 4580 3.641437 TTAACCTGCACGTACGTACTT 57.359 42.857 22.34 11.60 0.00 2.24
4130 4881 4.017380 ACTTACATCGCTCGTTGAGTAG 57.983 45.455 7.26 4.35 31.39 2.57
4152 4903 0.096454 CATCATGTGTGCTGCAGTCG 59.904 55.000 16.64 0.00 0.00 4.18
4171 4922 1.017701 GGCCTTGCTGTACCACGTAC 61.018 60.000 0.00 0.00 39.24 3.67
4172 4923 0.037605 GCCTTGCTGTACCACGTACT 60.038 55.000 3.79 0.00 39.49 2.73
4182 4933 5.163723 GCTGTACCACGTACTAGTACATCAA 60.164 44.000 28.03 10.06 43.83 2.57
4213 4964 7.539712 TTTGAGACACTGTAGTTTCTTTGAG 57.460 36.000 2.54 0.00 35.43 3.02
4217 4968 6.043411 AGACACTGTAGTTTCTTTGAGACAC 58.957 40.000 0.00 0.00 31.59 3.67
4219 4970 5.812642 ACACTGTAGTTTCTTTGAGACACTG 59.187 40.000 6.94 0.00 36.10 3.66
4220 4971 5.812642 CACTGTAGTTTCTTTGAGACACTGT 59.187 40.000 6.94 0.00 36.10 3.55
4221 4972 6.978659 CACTGTAGTTTCTTTGAGACACTGTA 59.021 38.462 6.94 0.00 36.10 2.74
4222 4973 6.979238 ACTGTAGTTTCTTTGAGACACTGTAC 59.021 38.462 6.94 0.00 36.10 2.90
4223 4974 7.108841 TGTAGTTTCTTTGAGACACTGTACT 57.891 36.000 6.94 0.00 36.10 2.73
4224 4975 8.229253 TGTAGTTTCTTTGAGACACTGTACTA 57.771 34.615 6.94 0.00 36.10 1.82
4226 4977 7.349412 AGTTTCTTTGAGACACTGTACTAGT 57.651 36.000 0.00 0.00 34.26 2.57
4227 4978 8.461249 AGTTTCTTTGAGACACTGTACTAGTA 57.539 34.615 0.00 0.00 34.26 1.82
4228 4979 8.351461 AGTTTCTTTGAGACACTGTACTAGTAC 58.649 37.037 23.58 23.58 34.26 2.73
4230 4981 7.997773 TCTTTGAGACACTGTACTAGTACAT 57.002 36.000 30.78 19.34 44.15 2.29
4233 5449 5.191426 TGAGACACTGTACTAGTACATCCC 58.809 45.833 30.78 19.04 44.15 3.85
4274 5526 1.225376 TGCAACGCGACGGAGAAATT 61.225 50.000 15.93 0.00 0.00 1.82
4281 5533 0.878416 CGACGGAGAAATTTTGGCCA 59.122 50.000 0.00 0.00 0.00 5.36
4282 5534 1.268352 CGACGGAGAAATTTTGGCCAA 59.732 47.619 16.05 16.05 0.00 4.52
4289 5541 5.220931 CGGAGAAATTTTGGCCAATCTCTAG 60.221 44.000 31.46 24.83 34.98 2.43
4290 5542 5.888161 GGAGAAATTTTGGCCAATCTCTAGA 59.112 40.000 31.46 12.13 34.98 2.43
4304 5556 2.695666 TCTCTAGAGTTGCACTATGCCC 59.304 50.000 19.21 0.00 44.23 5.36
4307 5559 1.191535 AGAGTTGCACTATGCCCGTA 58.808 50.000 0.00 0.00 44.23 4.02
4311 5563 3.150767 AGTTGCACTATGCCCGTAAAAA 58.849 40.909 0.00 0.00 44.23 1.94
4333 5585 7.542534 AAAAGATGTGAACACGTTACACTTA 57.457 32.000 14.51 0.62 35.83 2.24
4335 5587 4.986659 AGATGTGAACACGTTACACTTACC 59.013 41.667 14.51 4.95 35.83 2.85
4341 5593 0.310543 ACGTTACACTTACCGCACGA 59.689 50.000 0.00 0.00 0.00 4.35
4342 5594 1.068333 ACGTTACACTTACCGCACGAT 60.068 47.619 0.00 0.00 0.00 3.73
4343 5595 1.319374 CGTTACACTTACCGCACGATG 59.681 52.381 0.00 0.00 0.00 3.84
4344 5596 2.598589 GTTACACTTACCGCACGATGA 58.401 47.619 0.00 0.00 0.00 2.92
4356 5608 1.398451 GCACGATGACTGAAAACGGTG 60.398 52.381 0.00 0.00 0.00 4.94
4357 5609 0.865769 ACGATGACTGAAAACGGTGC 59.134 50.000 0.00 0.00 0.00 5.01
4364 5616 2.113131 CTGAAAACGGTGCCGGTGTC 62.113 60.000 11.66 11.66 43.19 3.67
4390 5649 3.636313 TACACGTGGGCGCAGTAGC 62.636 63.158 21.57 0.00 42.83 3.58
4414 5679 0.099082 CTCGCGACTTGTCCTACTCC 59.901 60.000 3.71 0.00 0.00 3.85
4476 5741 2.093606 GCCCAGACCAGGTAGTTAAGTC 60.094 54.545 0.00 0.00 0.00 3.01
4501 5766 1.507141 CCACGGCCACAAGTCAGAAC 61.507 60.000 2.24 0.00 0.00 3.01
4502 5767 1.227853 ACGGCCACAAGTCAGAACC 60.228 57.895 2.24 0.00 0.00 3.62
4515 5780 5.432680 AGTCAGAACCAAGTCATCATCAT 57.567 39.130 0.00 0.00 0.00 2.45
4516 5781 5.426504 AGTCAGAACCAAGTCATCATCATC 58.573 41.667 0.00 0.00 0.00 2.92
4518 5783 5.064452 GTCAGAACCAAGTCATCATCATCAC 59.936 44.000 0.00 0.00 0.00 3.06
4519 5784 4.939439 CAGAACCAAGTCATCATCATCACA 59.061 41.667 0.00 0.00 0.00 3.58
4521 5786 5.646793 AGAACCAAGTCATCATCATCACAAG 59.353 40.000 0.00 0.00 0.00 3.16
4522 5787 4.914983 ACCAAGTCATCATCATCACAAGT 58.085 39.130 0.00 0.00 0.00 3.16
4523 5788 4.940046 ACCAAGTCATCATCATCACAAGTC 59.060 41.667 0.00 0.00 0.00 3.01
4525 5790 5.413523 CCAAGTCATCATCATCACAAGTCAA 59.586 40.000 0.00 0.00 0.00 3.18
4537 5813 6.932400 TCATCACAAGTCAAAATTACTACCGT 59.068 34.615 0.00 0.00 0.00 4.83
4541 5817 7.596248 TCACAAGTCAAAATTACTACCGTACTC 59.404 37.037 0.00 0.00 0.00 2.59
4574 5850 4.457433 TCGCAATGCAGATCGAAATTAG 57.543 40.909 5.91 0.00 0.00 1.73
4575 5851 3.871006 TCGCAATGCAGATCGAAATTAGT 59.129 39.130 5.91 0.00 0.00 2.24
4576 5852 5.047188 TCGCAATGCAGATCGAAATTAGTA 58.953 37.500 5.91 0.00 0.00 1.82
4606 5882 0.168788 AGCGAAATGAATGCCACACG 59.831 50.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 161 0.550914 ACAGGCACCTTTCTTCACCA 59.449 50.000 0.00 0.00 0.00 4.17
225 227 5.902613 CAAGGACTTCTTGGCATTATTGA 57.097 39.130 0.00 0.00 46.81 2.57
258 269 1.859398 GCAGAAACATGCGTCGTGA 59.141 52.632 0.00 0.00 36.28 4.35
634 651 3.636764 GTGACCAACACTCCCTCATTTTT 59.363 43.478 0.00 0.00 45.13 1.94
636 653 2.863809 GTGACCAACACTCCCTCATTT 58.136 47.619 0.00 0.00 45.13 2.32
637 654 2.568623 GTGACCAACACTCCCTCATT 57.431 50.000 0.00 0.00 45.13 2.57
661 678 9.490379 AATATTTAGACACTCAAGTCGAAAACT 57.510 29.630 6.49 0.00 43.12 2.66
748 765 2.711542 GCACCTAGGCTGCTTTTCTAA 58.288 47.619 21.90 0.00 0.00 2.10
749 766 1.405526 CGCACCTAGGCTGCTTTTCTA 60.406 52.381 24.53 0.00 32.03 2.10
750 767 0.674895 CGCACCTAGGCTGCTTTTCT 60.675 55.000 24.53 0.00 32.03 2.52
751 768 1.648467 CCGCACCTAGGCTGCTTTTC 61.648 60.000 24.53 5.71 32.03 2.29
776 793 2.611292 GGTGAATTCTCTTCTCCATGCG 59.389 50.000 7.05 0.00 33.55 4.73
813 830 1.035932 ACCCCGAGACTGGTGATACG 61.036 60.000 0.00 0.00 32.36 3.06
820 837 2.046892 CTGCAACCCCGAGACTGG 60.047 66.667 0.00 0.00 0.00 4.00
823 840 2.047179 GACCTGCAACCCCGAGAC 60.047 66.667 0.00 0.00 0.00 3.36
837 939 3.010420 GTTTGCAGATGGTTCTAGGACC 58.990 50.000 13.97 13.97 40.23 4.46
838 940 3.935828 GAGTTTGCAGATGGTTCTAGGAC 59.064 47.826 0.00 0.00 0.00 3.85
886 1012 2.203394 CGGATGGCTGGATTGGGG 60.203 66.667 0.00 0.00 0.00 4.96
902 1028 4.308458 TGCACCTGGGTTCGGACG 62.308 66.667 0.00 0.00 0.00 4.79
929 1055 4.779733 GGGCCCGGGAGAGAGTGA 62.780 72.222 29.31 0.00 0.00 3.41
936 1063 4.241555 CGAAGATGGGCCCGGGAG 62.242 72.222 29.31 0.00 0.00 4.30
940 1067 1.078426 AAGTTCGAAGATGGGCCCG 60.078 57.895 19.37 3.46 35.04 6.13
941 1068 0.253327 AGAAGTTCGAAGATGGGCCC 59.747 55.000 17.59 17.59 35.04 5.80
944 1071 2.898705 CTGGAGAAGTTCGAAGATGGG 58.101 52.381 0.00 0.00 35.04 4.00
947 1074 1.134965 CGGCTGGAGAAGTTCGAAGAT 60.135 52.381 0.00 0.00 35.04 2.40
948 1075 0.243907 CGGCTGGAGAAGTTCGAAGA 59.756 55.000 0.00 0.00 0.00 2.87
1140 1267 2.030562 CTGGCTTCGTCGGTGGTT 59.969 61.111 0.00 0.00 0.00 3.67
1141 1268 4.681978 GCTGGCTTCGTCGGTGGT 62.682 66.667 0.00 0.00 0.00 4.16
1142 1269 4.680237 TGCTGGCTTCGTCGGTGG 62.680 66.667 0.00 0.00 0.00 4.61
1143 1270 3.114616 CTGCTGGCTTCGTCGGTG 61.115 66.667 0.00 0.00 0.00 4.94
1261 1388 2.222819 GCTGAGGCGATTGTCTTTTACG 60.223 50.000 0.00 0.00 0.00 3.18
1262 1389 2.096013 GGCTGAGGCGATTGTCTTTTAC 59.904 50.000 0.00 0.00 39.81 2.01
1264 1391 1.168714 GGCTGAGGCGATTGTCTTTT 58.831 50.000 0.00 0.00 39.81 2.27
1266 1393 0.392193 CAGGCTGAGGCGATTGTCTT 60.392 55.000 9.42 0.00 39.81 3.01
1269 1396 0.179062 GATCAGGCTGAGGCGATTGT 60.179 55.000 23.24 2.72 39.81 2.71
1271 1398 1.053264 AGGATCAGGCTGAGGCGATT 61.053 55.000 23.24 4.36 39.81 3.34
1272 1399 1.459158 AGGATCAGGCTGAGGCGAT 60.459 57.895 23.24 5.18 39.81 4.58
1274 1401 2.086251 GAGAGGATCAGGCTGAGGCG 62.086 65.000 23.24 0.00 37.82 5.52
1275 1402 0.760189 AGAGAGGATCAGGCTGAGGC 60.760 60.000 23.24 16.34 37.82 4.70
1286 1414 1.398692 GAAGTGAGGCGAGAGAGGAT 58.601 55.000 0.00 0.00 0.00 3.24
1318 1454 0.107410 TCGGAGAGGAGCTCAGACTC 60.107 60.000 17.19 18.33 45.81 3.36
1326 1464 1.227497 CCTGCATTCGGAGAGGAGC 60.227 63.158 0.00 0.00 38.43 4.70
1484 1622 0.391130 TGAAGCGTACCTGGATGCAC 60.391 55.000 0.00 0.99 33.52 4.57
1509 1647 1.065401 CGAACTGTTGCTTCCTTTGCA 59.935 47.619 0.00 0.00 38.80 4.08
1534 1672 3.430374 CCGGATTAATGTCGAACAGGAGT 60.430 47.826 0.00 0.00 0.00 3.85
1842 1980 2.232298 GAGAGTGGGCGGTGAGGAAG 62.232 65.000 0.00 0.00 0.00 3.46
1854 1992 2.416566 CGGTGTTCAGAGATGAGAGTGG 60.417 54.545 0.00 0.00 0.00 4.00
1857 1995 2.477021 CGACGGTGTTCAGAGATGAGAG 60.477 54.545 0.00 0.00 0.00 3.20
1875 2013 2.916583 GCATCAATGCGTTCACGAC 58.083 52.632 2.87 0.00 44.67 4.34
1912 2050 2.102578 GCACCCAATTTACAGAGGCAT 58.897 47.619 0.00 0.00 0.00 4.40
1913 2051 1.544724 GCACCCAATTTACAGAGGCA 58.455 50.000 0.00 0.00 0.00 4.75
1914 2052 0.451783 CGCACCCAATTTACAGAGGC 59.548 55.000 0.00 0.00 0.00 4.70
1915 2053 1.821216 ACGCACCCAATTTACAGAGG 58.179 50.000 0.00 0.00 0.00 3.69
1916 2054 2.811431 TGAACGCACCCAATTTACAGAG 59.189 45.455 0.00 0.00 0.00 3.35
1917 2055 2.811431 CTGAACGCACCCAATTTACAGA 59.189 45.455 0.00 0.00 0.00 3.41
1918 2056 2.095263 CCTGAACGCACCCAATTTACAG 60.095 50.000 0.00 0.00 0.00 2.74
2009 2147 1.372087 GCTGCCGAGGGACAAAGATG 61.372 60.000 0.00 0.00 0.00 2.90
2087 2225 6.042552 CCTCTCTCCCTTTGCTCAATATCTTA 59.957 42.308 0.00 0.00 0.00 2.10
2215 2377 7.604164 ACACTACCTCAATTCTAACATGAAGTG 59.396 37.037 0.00 0.00 41.57 3.16
2256 2418 1.534729 AGACGGGAAACAATCTTGCC 58.465 50.000 0.00 0.00 33.64 4.52
2272 2434 4.402829 TCTCTGGATGAGCATACCTAGAC 58.597 47.826 0.00 0.00 42.38 2.59
2277 2439 3.133721 ACACTTCTCTGGATGAGCATACC 59.866 47.826 0.00 0.00 42.38 2.73
2278 2440 4.399004 ACACTTCTCTGGATGAGCATAC 57.601 45.455 0.00 0.00 42.38 2.39
2359 2521 2.159653 CGTTAGACTGCTGAATGTTGCC 60.160 50.000 0.00 0.00 0.00 4.52
2390 2552 5.149054 GAAGCATTTCCACGATTAGACTG 57.851 43.478 0.00 0.00 0.00 3.51
2406 2568 7.944729 AACAATTAGTACAGAATGGAAGCAT 57.055 32.000 0.00 0.00 43.62 3.79
2428 2590 9.095065 AGATAATTCTTGTACCGTTGTGATAAC 57.905 33.333 0.00 0.00 0.00 1.89
2438 2600 6.538742 ACACATTCCAGATAATTCTTGTACCG 59.461 38.462 0.00 0.00 0.00 4.02
2439 2601 7.865706 ACACATTCCAGATAATTCTTGTACC 57.134 36.000 0.00 0.00 0.00 3.34
2460 2622 7.812191 TCCAAACATGCATTCTACATTTTACAC 59.188 33.333 0.00 0.00 0.00 2.90
2470 2632 8.052748 ACTACCTTATTCCAAACATGCATTCTA 58.947 33.333 0.00 0.00 0.00 2.10
2474 2636 5.951747 ACACTACCTTATTCCAAACATGCAT 59.048 36.000 0.00 0.00 0.00 3.96
2476 2638 5.897377 ACACTACCTTATTCCAAACATGC 57.103 39.130 0.00 0.00 0.00 4.06
2524 2734 4.767928 AGCAGTACATACCTAGATGCCTAC 59.232 45.833 0.00 0.00 32.71 3.18
2557 2767 2.095415 CGGCCAAGTTTTAGCACTAACC 60.095 50.000 2.24 0.00 0.00 2.85
2566 2776 9.228949 TGAATAAGTTAATACGGCCAAGTTTTA 57.771 29.630 2.24 0.00 0.00 1.52
2567 2777 8.024865 GTGAATAAGTTAATACGGCCAAGTTTT 58.975 33.333 2.24 0.00 0.00 2.43
2575 2785 7.535489 ACTGAAGTGAATAAGTTAATACGGC 57.465 36.000 0.00 0.00 0.00 5.68
2591 2801 7.706179 TCAAATTCAAAAAGGCTAACTGAAGTG 59.294 33.333 9.87 9.90 30.10 3.16
2597 2807 7.552330 TGCTTTTCAAATTCAAAAAGGCTAACT 59.448 29.630 19.11 0.00 40.94 2.24
2616 2828 6.254281 TCCTACTTAATGTTGCTGCTTTTC 57.746 37.500 0.00 0.00 0.00 2.29
2658 2870 6.920758 GCAACAAGAACATAAACAATACACCA 59.079 34.615 0.00 0.00 0.00 4.17
2670 2882 5.534654 ACAAAGCCTAAGCAACAAGAACATA 59.465 36.000 0.00 0.00 43.56 2.29
2671 2883 4.342092 ACAAAGCCTAAGCAACAAGAACAT 59.658 37.500 0.00 0.00 43.56 2.71
2761 2980 2.543861 CCGGCGTACTCTACTACGAGTA 60.544 54.545 6.01 0.00 42.19 2.59
2762 2981 1.565305 CGGCGTACTCTACTACGAGT 58.435 55.000 0.00 0.00 45.62 4.18
2765 2984 0.811616 ACCCGGCGTACTCTACTACG 60.812 60.000 6.01 0.00 42.04 3.51
2782 3001 0.179225 CAATCACAAGCGCGTGTACC 60.179 55.000 28.02 0.00 38.12 3.34
2783 3002 0.179225 CCAATCACAAGCGCGTGTAC 60.179 55.000 28.02 0.00 38.12 2.90
2785 3004 2.616330 CCCAATCACAAGCGCGTGT 61.616 57.895 23.49 23.49 38.12 4.49
2786 3005 2.128853 AACCCAATCACAAGCGCGTG 62.129 55.000 21.97 21.97 38.29 5.34
2787 3006 1.452145 AAACCCAATCACAAGCGCGT 61.452 50.000 8.43 0.00 0.00 6.01
2788 3007 0.318614 AAAACCCAATCACAAGCGCG 60.319 50.000 0.00 0.00 0.00 6.86
2789 3008 1.000274 AGAAAACCCAATCACAAGCGC 60.000 47.619 0.00 0.00 0.00 5.92
2790 3009 2.293122 TGAGAAAACCCAATCACAAGCG 59.707 45.455 0.00 0.00 0.00 4.68
2791 3010 4.525912 ATGAGAAAACCCAATCACAAGC 57.474 40.909 0.00 0.00 0.00 4.01
2798 3017 5.086621 AGTAGGCAAATGAGAAAACCCAAT 58.913 37.500 0.00 0.00 0.00 3.16
2799 3018 4.479158 AGTAGGCAAATGAGAAAACCCAA 58.521 39.130 0.00 0.00 0.00 4.12
2815 3034 2.100916 TGAACGCAGGAAGATAGTAGGC 59.899 50.000 0.00 0.00 0.00 3.93
2816 3035 3.971150 CTGAACGCAGGAAGATAGTAGG 58.029 50.000 0.00 0.00 38.51 3.18
2828 3047 2.905075 TGATGGTATTCCTGAACGCAG 58.095 47.619 0.00 0.00 41.93 5.18
2830 3049 4.474226 GAATGATGGTATTCCTGAACGC 57.526 45.455 0.00 0.00 32.22 4.84
2838 3057 9.646427 GACAAGATAGTAGGAATGATGGTATTC 57.354 37.037 0.00 0.00 36.55 1.75
2840 3059 8.727100 TGACAAGATAGTAGGAATGATGGTAT 57.273 34.615 0.00 0.00 0.00 2.73
2841 3060 8.727100 ATGACAAGATAGTAGGAATGATGGTA 57.273 34.615 0.00 0.00 0.00 3.25
2844 3063 8.899427 ACAATGACAAGATAGTAGGAATGATG 57.101 34.615 0.00 0.00 0.00 3.07
2905 3124 7.760794 TGATCATTGGCAATCTTGAAACAATAC 59.239 33.333 10.36 0.00 31.86 1.89
2922 3141 7.432869 TGAAAGTTAACAGGTTTGATCATTGG 58.567 34.615 8.61 0.00 0.00 3.16
2984 3234 6.844696 TGCTATGCAACTAGTAGCAATTAC 57.155 37.500 14.91 0.00 45.47 1.89
2994 3244 7.868775 ACATATGATTTGTGCTATGCAACTAG 58.131 34.615 10.38 0.00 41.47 2.57
2995 3245 7.806409 ACATATGATTTGTGCTATGCAACTA 57.194 32.000 10.38 0.00 41.47 2.24
2996 3246 6.704289 ACATATGATTTGTGCTATGCAACT 57.296 33.333 10.38 0.00 41.47 3.16
3006 3256 8.242739 TGTTGGTACATCAACATATGATTTGTG 58.757 33.333 10.38 8.02 46.85 3.33
3039 3296 8.720562 CCTGTCGATATTGTTGATGCAAATATA 58.279 33.333 0.00 0.00 31.63 0.86
3065 3322 9.194271 GGAACATAGACGAGGTTAAAGATAATC 57.806 37.037 0.00 0.00 30.59 1.75
3071 3328 5.929992 TGTTGGAACATAGACGAGGTTAAAG 59.070 40.000 0.00 0.00 39.30 1.85
3072 3329 5.856156 TGTTGGAACATAGACGAGGTTAAA 58.144 37.500 0.00 0.00 39.30 1.52
3073 3330 5.471556 TGTTGGAACATAGACGAGGTTAA 57.528 39.130 0.00 0.00 39.30 2.01
3128 3419 1.918957 AGGAGATTTGAGGGACCAAGG 59.081 52.381 0.00 0.00 0.00 3.61
3131 3422 1.195115 CGAGGAGATTTGAGGGACCA 58.805 55.000 0.00 0.00 0.00 4.02
3134 3425 1.115467 GCTCGAGGAGATTTGAGGGA 58.885 55.000 15.58 0.00 0.00 4.20
3254 3545 5.941555 AACCATTTAGTCTAGTGCTAGCT 57.058 39.130 17.23 0.00 33.32 3.32
3255 3546 6.476053 GTGTAACCATTTAGTCTAGTGCTAGC 59.524 42.308 8.10 8.10 33.32 3.42
3260 3670 8.088981 ACTGAAGTGTAACCATTTAGTCTAGTG 58.911 37.037 0.00 0.00 37.80 2.74
3265 3675 7.907214 ATGACTGAAGTGTAACCATTTAGTC 57.093 36.000 0.00 0.00 37.80 2.59
3292 3702 3.243301 GGTGATGTTAGCATGCCATGAAG 60.243 47.826 15.66 0.00 35.07 3.02
3294 3704 2.300433 GGTGATGTTAGCATGCCATGA 58.700 47.619 15.66 1.93 35.07 3.07
3296 3706 1.696063 GGGTGATGTTAGCATGCCAT 58.304 50.000 15.66 11.02 35.07 4.40
3298 3708 2.024918 CGGGTGATGTTAGCATGCC 58.975 57.895 15.66 0.00 35.07 4.40
3299 3709 1.097547 AGCGGGTGATGTTAGCATGC 61.098 55.000 10.51 10.51 35.07 4.06
3300 3710 1.064505 CAAGCGGGTGATGTTAGCATG 59.935 52.381 0.00 0.00 35.07 4.06
3301 3711 1.340017 ACAAGCGGGTGATGTTAGCAT 60.340 47.619 0.00 0.00 38.18 3.79
3315 3725 1.280746 CTCACCTGCACAACAAGCG 59.719 57.895 0.00 0.00 33.85 4.68
3320 3730 0.886490 CAGTCCCTCACCTGCACAAC 60.886 60.000 0.00 0.00 0.00 3.32
3391 3801 4.396271 TTGATCGGGGCCGCGAAA 62.396 61.111 42.77 31.69 39.59 3.46
3571 3981 1.241990 CGACGGAGACCAGGAAGTCA 61.242 60.000 0.00 0.00 39.34 3.41
3635 4045 1.192146 AGGCAGCGGTTTCTCTGGTA 61.192 55.000 0.00 0.00 0.00 3.25
3636 4046 2.032681 GGCAGCGGTTTCTCTGGT 59.967 61.111 0.00 0.00 0.00 4.00
3637 4047 1.302832 AAGGCAGCGGTTTCTCTGG 60.303 57.895 0.00 0.00 0.00 3.86
3639 4049 0.603975 GACAAGGCAGCGGTTTCTCT 60.604 55.000 0.00 0.00 0.00 3.10
3640 4050 0.603975 AGACAAGGCAGCGGTTTCTC 60.604 55.000 0.00 0.00 0.00 2.87
3653 4063 7.970614 ACAAAACTAAGCAGAAGAAAAGACAAG 59.029 33.333 0.00 0.00 0.00 3.16
3654 4064 7.826690 ACAAAACTAAGCAGAAGAAAAGACAA 58.173 30.769 0.00 0.00 0.00 3.18
3659 4069 6.092944 TCGTGACAAAACTAAGCAGAAGAAAA 59.907 34.615 0.00 0.00 0.00 2.29
3660 4070 5.583061 TCGTGACAAAACTAAGCAGAAGAAA 59.417 36.000 0.00 0.00 0.00 2.52
3661 4071 5.113383 TCGTGACAAAACTAAGCAGAAGAA 58.887 37.500 0.00 0.00 0.00 2.52
3662 4072 4.689071 TCGTGACAAAACTAAGCAGAAGA 58.311 39.130 0.00 0.00 0.00 2.87
3663 4073 5.403897 TTCGTGACAAAACTAAGCAGAAG 57.596 39.130 0.00 0.00 0.00 2.85
3664 4074 5.804692 TTTCGTGACAAAACTAAGCAGAA 57.195 34.783 0.00 0.00 0.00 3.02
3665 4075 5.525745 TCATTTCGTGACAAAACTAAGCAGA 59.474 36.000 0.00 0.00 0.00 4.26
3666 4076 5.747565 TCATTTCGTGACAAAACTAAGCAG 58.252 37.500 0.00 0.00 0.00 4.24
3667 4077 5.743026 TCATTTCGTGACAAAACTAAGCA 57.257 34.783 0.00 0.00 0.00 3.91
3668 4078 6.343924 CGTTTCATTTCGTGACAAAACTAAGC 60.344 38.462 0.00 0.00 36.32 3.09
3670 4080 6.544622 ACGTTTCATTTCGTGACAAAACTAA 58.455 32.000 0.00 0.00 38.85 2.24
3682 4092 1.531149 AGCCAGTGACGTTTCATTTCG 59.469 47.619 0.00 0.00 33.11 3.46
3711 4127 7.259882 TCTGCAACAATGTGGATAAATCATTC 58.740 34.615 0.00 0.00 30.74 2.67
3770 4191 6.809689 TGTAACCATTTCATCGTACTGTACTG 59.190 38.462 15.35 8.35 0.00 2.74
3800 4221 6.925610 TTCGGATCACAGATTTTCTATTGG 57.074 37.500 0.00 0.00 0.00 3.16
3812 4233 3.733224 CGATTCTAGCTTTCGGATCACAG 59.267 47.826 0.00 0.00 0.00 3.66
3842 4263 0.381801 AAGGCAAACGCTTCACTGTG 59.618 50.000 0.17 0.17 0.00 3.66
3853 4274 0.675633 AGATGCACACCAAGGCAAAC 59.324 50.000 0.00 0.00 44.20 2.93
3860 4282 1.948508 GCAACGAGATGCACACCAA 59.051 52.632 0.00 0.00 45.70 3.67
3873 4295 0.991770 GCGTGCTGTAAGTTGCAACG 60.992 55.000 23.21 10.53 41.10 4.10
3880 4302 2.169832 ACAAGATGCGTGCTGTAAGT 57.830 45.000 0.00 0.00 35.30 2.24
3881 4303 2.413239 CCAACAAGATGCGTGCTGTAAG 60.413 50.000 0.00 0.00 0.00 2.34
3888 4310 2.176546 CGGCCAACAAGATGCGTG 59.823 61.111 2.24 0.00 0.00 5.34
3891 4313 4.133796 GGCCGGCCAACAAGATGC 62.134 66.667 40.73 8.62 35.81 3.91
3953 4390 0.107410 TCCCAATCCACCGTGCATAC 60.107 55.000 0.00 0.00 0.00 2.39
3968 4405 4.683766 TGGAATTAACTCCCAAATCCCA 57.316 40.909 0.00 0.00 34.22 4.37
3969 4406 4.344968 CCATGGAATTAACTCCCAAATCCC 59.655 45.833 5.56 0.00 34.22 3.85
3970 4407 4.202253 GCCATGGAATTAACTCCCAAATCC 60.202 45.833 18.40 0.00 34.22 3.01
3971 4408 4.202253 GGCCATGGAATTAACTCCCAAATC 60.202 45.833 18.40 0.00 34.22 2.17
3972 4409 3.711190 GGCCATGGAATTAACTCCCAAAT 59.289 43.478 18.40 0.00 34.22 2.32
3973 4410 3.103742 GGCCATGGAATTAACTCCCAAA 58.896 45.455 18.40 0.00 34.22 3.28
3974 4411 2.625617 GGGCCATGGAATTAACTCCCAA 60.626 50.000 18.40 0.00 34.22 4.12
4013 4450 2.483714 GCTCATGGAGGCATTTACTCGA 60.484 50.000 0.00 0.00 35.82 4.04
4014 4451 1.869767 GCTCATGGAGGCATTTACTCG 59.130 52.381 0.00 0.00 35.82 4.18
4064 4532 2.004808 CTGTCTGCCGCGTGAGGATA 62.005 60.000 4.92 0.00 0.00 2.59
4068 4536 2.356313 AACTGTCTGCCGCGTGAG 60.356 61.111 4.92 0.00 0.00 3.51
4109 4577 3.731264 GCTACTCAACGAGCGATGTAAGT 60.731 47.826 0.00 0.00 32.04 2.24
4110 4578 2.784380 GCTACTCAACGAGCGATGTAAG 59.216 50.000 0.00 0.00 32.04 2.34
4111 4579 2.162809 TGCTACTCAACGAGCGATGTAA 59.837 45.455 0.00 0.00 41.83 2.41
4112 4580 1.741145 TGCTACTCAACGAGCGATGTA 59.259 47.619 0.00 0.00 41.83 2.29
4145 4896 2.878089 TACAGCAAGGCCGACTGCA 61.878 57.895 23.79 10.13 43.89 4.41
4152 4903 1.017701 GTACGTGGTACAGCAAGGCC 61.018 60.000 0.00 0.00 41.80 5.19
4188 4939 7.987458 TCTCAAAGAAACTACAGTGTCTCAAAT 59.013 33.333 0.00 0.00 41.57 2.32
4192 4943 6.199342 GTGTCTCAAAGAAACTACAGTGTCTC 59.801 42.308 0.00 0.00 41.57 3.36
4193 4944 6.043411 GTGTCTCAAAGAAACTACAGTGTCT 58.957 40.000 0.00 0.00 44.16 3.41
4196 4947 5.812642 ACAGTGTCTCAAAGAAACTACAGTG 59.187 40.000 0.00 0.00 40.74 3.66
4198 4949 7.203910 AGTACAGTGTCTCAAAGAAACTACAG 58.796 38.462 0.00 0.00 40.74 2.74
4199 4950 7.108841 AGTACAGTGTCTCAAAGAAACTACA 57.891 36.000 0.00 0.00 40.74 2.74
4200 4951 8.351461 ACTAGTACAGTGTCTCAAAGAAACTAC 58.649 37.037 0.00 0.00 40.74 2.73
4201 4952 8.461249 ACTAGTACAGTGTCTCAAAGAAACTA 57.539 34.615 0.00 0.00 40.74 2.24
4202 4953 7.349412 ACTAGTACAGTGTCTCAAAGAAACT 57.651 36.000 0.00 0.00 43.41 2.66
4203 4954 8.133627 TGTACTAGTACAGTGTCTCAAAGAAAC 58.866 37.037 27.99 2.53 40.77 2.78
4219 4970 4.708421 TGGTGTCTTGGGATGTACTAGTAC 59.292 45.833 23.58 23.58 36.63 2.73
4220 4971 4.708421 GTGGTGTCTTGGGATGTACTAGTA 59.292 45.833 0.00 0.00 0.00 1.82
4221 4972 3.514309 GTGGTGTCTTGGGATGTACTAGT 59.486 47.826 0.00 0.00 0.00 2.57
4222 4973 3.428999 CGTGGTGTCTTGGGATGTACTAG 60.429 52.174 0.00 0.00 0.00 2.57
4223 4974 2.494471 CGTGGTGTCTTGGGATGTACTA 59.506 50.000 0.00 0.00 0.00 1.82
4224 4975 1.275291 CGTGGTGTCTTGGGATGTACT 59.725 52.381 0.00 0.00 0.00 2.73
4226 4977 1.344065 ACGTGGTGTCTTGGGATGTA 58.656 50.000 0.00 0.00 0.00 2.29
4227 4978 1.001633 GTACGTGGTGTCTTGGGATGT 59.998 52.381 0.00 0.00 0.00 3.06
4228 4979 1.722011 GTACGTGGTGTCTTGGGATG 58.278 55.000 0.00 0.00 0.00 3.51
4230 4981 1.661480 CGTACGTGGTGTCTTGGGA 59.339 57.895 7.22 0.00 0.00 4.37
4233 5449 0.597568 TACCCGTACGTGGTGTCTTG 59.402 55.000 28.04 6.97 36.57 3.02
4274 5526 3.244875 TGCAACTCTAGAGATTGGCCAAA 60.245 43.478 26.57 4.13 0.00 3.28
4311 5563 5.464389 GGTAAGTGTAACGTGTTCACATCTT 59.536 40.000 16.32 12.68 45.86 2.40
4321 5573 0.431984 CGTGCGGTAAGTGTAACGTG 59.568 55.000 0.00 0.00 45.86 4.49
4333 5585 0.865769 GTTTTCAGTCATCGTGCGGT 59.134 50.000 0.00 0.00 0.00 5.68
4335 5587 0.179250 CCGTTTTCAGTCATCGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
4341 5593 1.234615 CCGGCACCGTTTTCAGTCAT 61.235 55.000 8.49 0.00 37.81 3.06
4342 5594 1.890041 CCGGCACCGTTTTCAGTCA 60.890 57.895 8.49 0.00 37.81 3.41
4343 5595 1.890510 ACCGGCACCGTTTTCAGTC 60.891 57.895 0.00 0.00 37.81 3.51
4344 5596 2.184167 CACCGGCACCGTTTTCAGT 61.184 57.895 0.00 0.00 37.81 3.41
4383 5635 0.862283 GTCGCGAGTACTGCTACTGC 60.862 60.000 10.24 0.00 32.96 4.40
4390 5649 0.522180 AGGACAAGTCGCGAGTACTG 59.478 55.000 18.34 15.20 0.00 2.74
4414 5679 0.689623 AGTGAGGCCTCTGACTTTGG 59.310 55.000 32.28 0.00 33.69 3.28
4476 5741 0.534203 ACTTGTGGCCGTGGTAACTG 60.534 55.000 0.00 0.00 37.61 3.16
4501 5766 4.939439 TGACTTGTGATGATGATGACTTGG 59.061 41.667 0.00 0.00 0.00 3.61
4502 5767 6.490566 TTGACTTGTGATGATGATGACTTG 57.509 37.500 0.00 0.00 0.00 3.16
4515 5780 7.436118 AGTACGGTAGTAATTTTGACTTGTGA 58.564 34.615 0.00 0.00 34.16 3.58
4516 5781 7.148689 GGAGTACGGTAGTAATTTTGACTTGTG 60.149 40.741 0.00 0.00 34.16 3.33
4518 5783 6.312180 GGGAGTACGGTAGTAATTTTGACTTG 59.688 42.308 0.00 0.00 34.16 3.16
4519 5784 6.014327 TGGGAGTACGGTAGTAATTTTGACTT 60.014 38.462 0.00 0.00 34.16 3.01
4521 5786 5.578336 GTGGGAGTACGGTAGTAATTTTGAC 59.422 44.000 0.00 0.00 34.16 3.18
4522 5787 5.481473 AGTGGGAGTACGGTAGTAATTTTGA 59.519 40.000 0.00 0.00 34.16 2.69
4523 5788 5.579511 CAGTGGGAGTACGGTAGTAATTTTG 59.420 44.000 0.00 0.00 34.16 2.44
4525 5790 4.774200 ACAGTGGGAGTACGGTAGTAATTT 59.226 41.667 0.00 0.00 34.16 1.82
4537 5813 2.241160 TGCGAAGTTACAGTGGGAGTA 58.759 47.619 0.00 0.00 0.00 2.59
4541 5817 1.135689 GCATTGCGAAGTTACAGTGGG 60.136 52.381 0.00 0.00 0.00 4.61
4574 5850 1.005294 TTTCGCTCGCTCGTGGTTAC 61.005 55.000 0.00 0.00 0.00 2.50
4575 5851 0.108992 ATTTCGCTCGCTCGTGGTTA 60.109 50.000 0.00 0.00 0.00 2.85
4576 5852 1.374252 ATTTCGCTCGCTCGTGGTT 60.374 52.632 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.