Multiple sequence alignment - TraesCS2A01G566000

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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 TraesCS2A01G566000 chr2A 100.000 3845 0 0 1 3845 765372519 765376363 0.000000e+00 7101.0
1 TraesCS2A01G566000 chr2A 84.628 1249 133 29 1130 2334 765442342 765441109 0.000000e+00 1188.0
2 TraesCS2A01G566000 chr2A 80.378 1004 104 39 1471 2417 765393353 765392386 0.000000e+00 676.0
3 TraesCS2A01G566000 chr2A 79.487 819 104 43 1524 2315 765547547 765546766 1.220000e-144 523.0
4 TraesCS2A01G566000 chr2A 79.484 775 89 34 380 1098 765443100 765442340 1.610000e-133 486.0
5 TraesCS2A01G566000 chr2A 83.752 517 69 10 1514 2026 765516079 765515574 3.480000e-130 475.0
6 TraesCS2A01G566000 chr2A 81.171 632 53 27 387 993 765394458 765393868 7.580000e-122 448.0
7 TraesCS2A01G566000 chr2A 91.385 325 21 3 1116 1433 765393749 765393425 4.560000e-119 438.0
8 TraesCS2A01G566000 chr2A 77.621 849 101 46 1546 2325 765278135 765278963 2.120000e-117 433.0
9 TraesCS2A01G566000 chr2A 84.539 401 46 5 1020 1413 765516526 765516135 2.170000e-102 383.0
10 TraesCS2A01G566000 chr2A 80.392 408 41 18 566 967 765548531 765548157 1.360000e-69 274.0
11 TraesCS2A01G566000 chr2A 78.238 193 25 11 79 265 765549321 765549140 1.460000e-19 108.0
12 TraesCS2A01G566000 chr2A 95.455 66 3 0 989 1054 765393814 765393749 5.250000e-19 106.0
13 TraesCS2A01G566000 chr2D 86.283 1582 129 45 989 2509 639732984 639734538 0.000000e+00 1639.0
14 TraesCS2A01G566000 chr2D 83.943 1476 128 51 989 2417 639822084 639820671 0.000000e+00 1312.0
15 TraesCS2A01G566000 chr2D 80.384 1769 155 82 768 2417 639747229 639745534 0.000000e+00 1168.0
16 TraesCS2A01G566000 chr2D 92.262 672 48 3 3178 3845 639736476 639737147 0.000000e+00 950.0
17 TraesCS2A01G566000 chr2D 92.842 461 17 5 384 839 639732190 639732639 0.000000e+00 654.0
18 TraesCS2A01G566000 chr2D 90.043 462 22 11 2719 3179 639734533 639734971 9.260000e-161 577.0
19 TraesCS2A01G566000 chr2D 82.653 490 59 13 2696 3179 639820431 639819962 9.940000e-111 411.0
20 TraesCS2A01G566000 chr2D 85.227 352 39 6 1068 1412 639872369 639872024 2.200000e-92 350.0
21 TraesCS2A01G566000 chr2D 77.969 640 63 27 380 994 639822708 639822122 2.860000e-86 329.0
22 TraesCS2A01G566000 chr2D 83.654 312 28 12 432 731 639891686 639891386 4.890000e-69 272.0
23 TraesCS2A01G566000 chr2D 76.570 414 51 29 1917 2316 639890199 639889818 6.560000e-43 185.0
24 TraesCS2A01G566000 chr2D 90.071 141 3 3 852 992 639732799 639732928 5.110000e-39 172.0
25 TraesCS2A01G566000 chr2D 80.632 253 21 8 422 653 639747536 639747291 1.840000e-38 171.0
26 TraesCS2A01G566000 chr2D 80.214 187 28 3 70 249 639873360 639873176 8.670000e-27 132.0
27 TraesCS2A01G566000 chr2D 93.750 48 3 0 219 266 639747867 639747820 5.330000e-09 73.1
28 TraesCS2A01G566000 chr2B 83.992 1468 129 40 989 2417 798957482 798958882 0.000000e+00 1312.0
29 TraesCS2A01G566000 chr2B 87.106 1047 88 24 989 2031 799029004 799030007 0.000000e+00 1142.0
30 TraesCS2A01G566000 chr2B 83.576 1029 86 36 1 994 798956449 798957429 0.000000e+00 887.0
31 TraesCS2A01G566000 chr2B 82.937 1008 96 38 1471 2417 799047326 799046334 0.000000e+00 839.0
32 TraesCS2A01G566000 chr2B 89.194 620 60 5 1230 1849 799107582 799106970 0.000000e+00 767.0
33 TraesCS2A01G566000 chr2B 85.278 720 69 17 2464 3182 799030516 799031199 0.000000e+00 708.0
34 TraesCS2A01G566000 chr2B 84.645 521 45 16 2026 2525 799030029 799030535 1.610000e-133 486.0
35 TraesCS2A01G566000 chr2B 79.734 602 58 37 401 994 799108466 799107921 1.010000e-100 377.0
36 TraesCS2A01G566000 chr2B 79.035 601 59 39 401 989 799028394 799028939 2.200000e-92 350.0
37 TraesCS2A01G566000 chr2B 78.998 519 59 19 387 881 799048395 799047903 3.730000e-80 309.0
38 TraesCS2A01G566000 chr2B 76.298 578 73 32 1903 2427 799106671 799106105 2.290000e-62 250.0
39 TraesCS2A01G566000 chr2B 97.727 88 2 0 989 1076 799047794 799047707 6.650000e-33 152.0
40 TraesCS2A01G566000 chr2B 90.816 98 5 1 989 1086 799107868 799107775 1.120000e-25 128.0
41 TraesCS2A01G566000 chr2B 89.041 73 8 0 194 266 799048686 799048614 1.470000e-14 91.6
42 TraesCS2A01G566000 chr2B 89.706 68 4 3 927 994 799047911 799047847 2.460000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G566000 chr2A 765372519 765376363 3844 False 7101.000000 7101 100.000000 1 3845 1 chr2A.!!$F2 3844
1 TraesCS2A01G566000 chr2A 765441109 765443100 1991 True 837.000000 1188 82.056000 380 2334 2 chr2A.!!$R2 1954
2 TraesCS2A01G566000 chr2A 765278135 765278963 828 False 433.000000 433 77.621000 1546 2325 1 chr2A.!!$F1 779
3 TraesCS2A01G566000 chr2A 765515574 765516526 952 True 429.000000 475 84.145500 1020 2026 2 chr2A.!!$R3 1006
4 TraesCS2A01G566000 chr2A 765392386 765394458 2072 True 417.000000 676 87.097250 387 2417 4 chr2A.!!$R1 2030
5 TraesCS2A01G566000 chr2A 765546766 765549321 2555 True 301.666667 523 79.372333 79 2315 3 chr2A.!!$R4 2236
6 TraesCS2A01G566000 chr2D 639732190 639737147 4957 False 798.400000 1639 90.300200 384 3845 5 chr2D.!!$F1 3461
7 TraesCS2A01G566000 chr2D 639819962 639822708 2746 True 684.000000 1312 81.521667 380 3179 3 chr2D.!!$R2 2799
8 TraesCS2A01G566000 chr2D 639745534 639747867 2333 True 470.700000 1168 84.922000 219 2417 3 chr2D.!!$R1 2198
9 TraesCS2A01G566000 chr2D 639872024 639873360 1336 True 241.000000 350 82.720500 70 1412 2 chr2D.!!$R3 1342
10 TraesCS2A01G566000 chr2D 639889818 639891686 1868 True 228.500000 272 80.112000 432 2316 2 chr2D.!!$R4 1884
11 TraesCS2A01G566000 chr2B 798956449 798958882 2433 False 1099.500000 1312 83.784000 1 2417 2 chr2B.!!$F1 2416
12 TraesCS2A01G566000 chr2B 799028394 799031199 2805 False 671.500000 1142 84.016000 401 3182 4 chr2B.!!$F2 2781
13 TraesCS2A01G566000 chr2B 799106105 799108466 2361 True 380.500000 767 84.010500 401 2427 4 chr2B.!!$R2 2026
14 TraesCS2A01G566000 chr2B 799046334 799048686 2352 True 295.160000 839 87.681800 194 2417 5 chr2B.!!$R1 2223

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
430 703 0.250124 CCCCACAAGACTGTACGCAA 60.250 55.0 0.00 0.00 33.22 4.85 F
574 1040 0.322997 CACGGAGACAGGAGGAGAGT 60.323 60.0 0.00 0.00 0.00 3.24 F
2084 3545 0.531532 CTCCATTACCTGCAGAGCGG 60.532 60.0 17.39 8.24 34.23 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 3821 0.108662 TAGGTGCAGATGTGACGCTG 60.109 55.0 0.0 1.5 35.28 5.18 R
2331 3822 0.174389 CTAGGTGCAGATGTGACGCT 59.826 55.0 0.0 0.0 0.00 5.07 R
3539 6667 0.035439 GGAACCGCAAGATCCTTCCA 60.035 55.0 0.0 0.0 39.26 3.53 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
26 27 7.823799 TCTCACTCTCTACTGCATATCATAGAG 59.176 40.741 10.54 10.54 41.31 2.43
27 28 6.374053 TCACTCTCTACTGCATATCATAGAGC 59.626 42.308 11.41 0.00 40.25 4.09
28 29 6.150809 CACTCTCTACTGCATATCATAGAGCA 59.849 42.308 11.41 0.00 40.25 4.26
43 44 2.675772 GCAGGCAGCCAGCTCTTT 60.676 61.111 21.29 0.00 44.79 2.52
44 45 2.273912 GCAGGCAGCCAGCTCTTTT 61.274 57.895 21.29 0.00 44.79 2.27
45 46 1.881602 CAGGCAGCCAGCTCTTTTC 59.118 57.895 15.80 0.00 44.79 2.29
46 47 0.892358 CAGGCAGCCAGCTCTTTTCA 60.892 55.000 15.80 0.00 44.79 2.69
65 70 3.399440 CAAGCTCTCTTGGTGTTCTCT 57.601 47.619 0.00 0.00 44.53 3.10
68 73 2.968574 AGCTCTCTTGGTGTTCTCTTCA 59.031 45.455 0.00 0.00 0.00 3.02
94 99 2.554344 GCTAATTTGGTGAGTCCCCACA 60.554 50.000 0.00 0.00 38.74 4.17
118 129 7.719633 ACACCTATGATATGGTTGTATTTGTCC 59.280 37.037 0.00 0.00 33.75 4.02
119 130 7.174946 CACCTATGATATGGTTGTATTTGTCCC 59.825 40.741 0.00 0.00 33.75 4.46
120 131 7.147213 ACCTATGATATGGTTGTATTTGTCCCA 60.147 37.037 0.00 0.00 31.62 4.37
123 134 7.969690 TGATATGGTTGTATTTGTCCCAATT 57.030 32.000 0.00 0.00 0.00 2.32
131 143 7.095397 GGTTGTATTTGTCCCAATTTACTTTGC 60.095 37.037 0.00 0.00 0.00 3.68
163 175 2.280592 GTTTGGTCGACGGCCACT 60.281 61.111 23.18 0.00 35.46 4.00
165 177 4.980805 TTGGTCGACGGCCACTGC 62.981 66.667 23.18 0.00 35.46 4.40
183 195 1.726853 GCGTTCTGCATCTACAACCT 58.273 50.000 0.00 0.00 45.45 3.50
192 204 3.068732 TGCATCTACAACCTAGCTAGCTG 59.931 47.826 27.68 13.96 0.00 4.24
197 209 4.882427 TCTACAACCTAGCTAGCTGTAGTG 59.118 45.833 33.49 22.99 38.28 2.74
217 229 2.223900 TGATGAGTCATGGCTGATCGAC 60.224 50.000 19.76 0.08 32.87 4.20
228 240 4.208686 GATCGACGAGCCCCGCTT 62.209 66.667 0.57 0.00 39.88 4.68
299 457 2.119801 AGCTCTACCATGCAAAGTGG 57.880 50.000 3.18 3.18 42.55 4.00
303 461 1.098050 CTACCATGCAAAGTGGCCTC 58.902 55.000 3.32 0.00 40.49 4.70
315 473 1.972872 GTGGCCTCATATTCCACCAG 58.027 55.000 3.32 0.00 43.27 4.00
430 703 0.250124 CCCCACAAGACTGTACGCAA 60.250 55.000 0.00 0.00 33.22 4.85
471 744 5.042463 TCTAGTCCACCACAAAATTGACA 57.958 39.130 0.00 0.00 0.00 3.58
512 814 2.095263 TCTAACCGTAGTGTTGGTACGC 60.095 50.000 0.00 0.00 41.57 4.42
563 917 6.436843 AAATGATGGAAAATACACGGAGAC 57.563 37.500 0.00 0.00 0.00 3.36
574 1040 0.322997 CACGGAGACAGGAGGAGAGT 60.323 60.000 0.00 0.00 0.00 3.24
598 1064 3.498774 ATCCTGAAGTGCACTCAAAGT 57.501 42.857 21.95 3.17 0.00 2.66
599 1065 2.838736 TCCTGAAGTGCACTCAAAGTC 58.161 47.619 21.95 14.14 0.00 3.01
600 1066 2.170397 TCCTGAAGTGCACTCAAAGTCA 59.830 45.455 21.95 18.09 0.00 3.41
601 1067 2.945008 CCTGAAGTGCACTCAAAGTCAA 59.055 45.455 21.95 3.97 0.00 3.18
602 1068 3.378112 CCTGAAGTGCACTCAAAGTCAAA 59.622 43.478 21.95 0.00 0.00 2.69
603 1069 4.497006 CCTGAAGTGCACTCAAAGTCAAAG 60.497 45.833 21.95 9.85 0.00 2.77
740 1225 2.952978 TCTGCAAGCTAGCTAGAGTACC 59.047 50.000 25.15 6.07 34.99 3.34
799 1287 6.495706 GGCCTAGATTACAATTGTACTTTGC 58.504 40.000 17.85 15.80 0.00 3.68
879 1515 6.169094 CAGATTTGGTGTGGGCTATATAGAG 58.831 44.000 14.16 0.00 0.00 2.43
880 1516 5.846714 AGATTTGGTGTGGGCTATATAGAGT 59.153 40.000 14.16 0.00 0.00 3.24
881 1517 5.968676 TTTGGTGTGGGCTATATAGAGTT 57.031 39.130 14.16 0.00 0.00 3.01
882 1518 7.512746 AGATTTGGTGTGGGCTATATAGAGTTA 59.487 37.037 14.16 0.00 0.00 2.24
883 1519 7.626999 TTTGGTGTGGGCTATATAGAGTTAT 57.373 36.000 14.16 0.00 0.00 1.89
884 1520 8.730093 TTTGGTGTGGGCTATATAGAGTTATA 57.270 34.615 14.16 0.00 0.00 0.98
885 1521 7.956328 TGGTGTGGGCTATATAGAGTTATAG 57.044 40.000 14.16 0.00 35.93 1.31
886 1522 7.705700 TGGTGTGGGCTATATAGAGTTATAGA 58.294 38.462 14.16 0.00 35.16 1.98
943 1581 2.368655 TCATATGAGCGTGCGCATAT 57.631 45.000 20.67 20.67 45.59 1.78
944 1582 3.502191 TCATATGAGCGTGCGCATATA 57.498 42.857 24.16 16.47 43.86 0.86
1170 1905 5.796424 AAAGGTTGTGCTCTTGATTTCAT 57.204 34.783 0.00 0.00 0.00 2.57
1221 2028 3.133721 CAGGCAGAAAGGTAGATGCTAGT 59.866 47.826 0.00 0.00 38.71 2.57
1369 2188 0.535553 AGGAGGTCGATCTCTACCGC 60.536 60.000 24.34 8.13 40.88 5.68
1418 2241 7.897575 ACTACTCATCTGAATTTTGTCAGTC 57.102 36.000 2.38 0.00 44.56 3.51
1420 2243 5.006386 ACTCATCTGAATTTTGTCAGTCCC 58.994 41.667 2.38 0.00 44.56 4.46
1468 2320 4.522405 TCCAAAATACATGTGGTGGTTCTG 59.478 41.667 9.11 0.00 33.88 3.02
1511 2415 7.669304 TGAGGTGGTGATTCAAATTGAGAATTA 59.331 33.333 7.56 2.28 35.93 1.40
1512 2416 7.830739 AGGTGGTGATTCAAATTGAGAATTAC 58.169 34.615 15.03 15.03 39.72 1.89
1534 2452 4.158394 ACAACAATAATGGATGGTGCAGAC 59.842 41.667 0.00 0.00 37.78 3.51
1795 2740 1.768870 CCCAATGGTAGGAAGACCGAT 59.231 52.381 0.00 0.00 42.99 4.18
1852 2809 1.358759 CGCACCCACACAGGTTTTC 59.641 57.895 0.00 0.00 38.39 2.29
1881 2863 0.829990 CTCTTCTTCCTCCTCCTGCC 59.170 60.000 0.00 0.00 0.00 4.85
1896 2953 1.902508 CCTGCCACACCTCTTCTTCTA 59.097 52.381 0.00 0.00 0.00 2.10
1897 2954 2.354203 CCTGCCACACCTCTTCTTCTAC 60.354 54.545 0.00 0.00 0.00 2.59
1898 2955 2.564947 CTGCCACACCTCTTCTTCTACT 59.435 50.000 0.00 0.00 0.00 2.57
2084 3545 0.531532 CTCCATTACCTGCAGAGCGG 60.532 60.000 17.39 8.24 34.23 5.52
2130 3606 2.579201 CCGAGCCAGGACGTCAAT 59.421 61.111 18.91 1.75 0.00 2.57
2328 3819 2.016704 CACGTCACAGCTCCACGTC 61.017 63.158 10.53 0.00 44.70 4.34
2329 3820 2.335011 CGTCACAGCTCCACGTCA 59.665 61.111 0.00 0.00 0.00 4.35
2330 3821 2.016704 CGTCACAGCTCCACGTCAC 61.017 63.158 0.00 0.00 0.00 3.67
2331 3822 1.067416 GTCACAGCTCCACGTCACA 59.933 57.895 0.00 0.00 0.00 3.58
2355 3891 1.901833 TCACATCTGCACCTAGAGCAA 59.098 47.619 10.40 3.86 42.17 3.91
2367 3903 5.537188 CACCTAGAGCAATGAAGTAGATCC 58.463 45.833 0.00 0.00 0.00 3.36
2375 3911 5.130145 AGCAATGAAGTAGATCCAGTTAGCT 59.870 40.000 0.00 0.00 0.00 3.32
2448 4026 2.112297 TCCGGGACACTTGGTTGC 59.888 61.111 0.00 0.00 0.00 4.17
2497 4117 5.874810 TGTTCCACTTACTGAATCTATGTGC 59.125 40.000 0.00 0.00 0.00 4.57
2525 4145 7.068348 TCACTGTAGACTACTCTGTTTCACTTT 59.932 37.037 13.67 0.00 0.00 2.66
2526 4146 7.168302 CACTGTAGACTACTCTGTTTCACTTTG 59.832 40.741 13.67 0.00 0.00 2.77
2584 4204 9.197694 CATGATTTGCTAATAGTAGTCCACTAC 57.802 37.037 8.60 8.60 46.93 2.73
2592 4212 1.461559 GTAGTCCACTACTGCGGAGT 58.538 55.000 15.78 15.78 44.06 3.85
2593 4213 2.636830 GTAGTCCACTACTGCGGAGTA 58.363 52.381 16.41 16.41 44.06 2.59
2596 4216 1.132643 GTCCACTACTGCGGAGTACAG 59.867 57.143 13.29 9.02 41.08 2.74
2598 4218 0.179134 CACTACTGCGGAGTACAGGC 60.179 60.000 13.29 0.00 39.55 4.85
2599 4219 0.611062 ACTACTGCGGAGTACAGGCA 60.611 55.000 13.29 0.21 39.55 4.75
2602 4222 1.191535 ACTGCGGAGTACAGGCATTA 58.808 50.000 8.23 0.00 39.55 1.90
2603 4223 1.762957 ACTGCGGAGTACAGGCATTAT 59.237 47.619 8.23 0.00 39.55 1.28
2604 4224 2.963101 ACTGCGGAGTACAGGCATTATA 59.037 45.455 8.23 0.00 39.55 0.98
2605 4225 3.005897 ACTGCGGAGTACAGGCATTATAG 59.994 47.826 8.23 0.00 39.55 1.31
2607 4227 3.255888 TGCGGAGTACAGGCATTATAGAG 59.744 47.826 0.00 0.00 0.00 2.43
2608 4228 3.839293 CGGAGTACAGGCATTATAGAGC 58.161 50.000 0.00 0.00 0.00 4.09
2618 4238 5.428184 GGCATTATAGAGCCCAGATTAGT 57.572 43.478 6.30 0.00 45.18 2.24
2619 4239 5.181748 GGCATTATAGAGCCCAGATTAGTG 58.818 45.833 6.30 0.00 45.18 2.74
2620 4240 5.280215 GGCATTATAGAGCCCAGATTAGTGT 60.280 44.000 6.30 0.00 45.18 3.55
2623 4243 7.308229 GCATTATAGAGCCCAGATTAGTGTTTG 60.308 40.741 0.00 0.00 0.00 2.93
2624 4244 5.700402 ATAGAGCCCAGATTAGTGTTTGT 57.300 39.130 0.00 0.00 0.00 2.83
2625 4245 3.679389 AGAGCCCAGATTAGTGTTTGTG 58.321 45.455 0.00 0.00 0.00 3.33
2626 4246 3.073062 AGAGCCCAGATTAGTGTTTGTGT 59.927 43.478 0.00 0.00 0.00 3.72
2627 4247 3.821033 GAGCCCAGATTAGTGTTTGTGTT 59.179 43.478 0.00 0.00 0.00 3.32
2628 4248 3.569701 AGCCCAGATTAGTGTTTGTGTTG 59.430 43.478 0.00 0.00 0.00 3.33
2629 4249 3.857010 GCCCAGATTAGTGTTTGTGTTGC 60.857 47.826 0.00 0.00 0.00 4.17
2630 4250 3.317711 CCCAGATTAGTGTTTGTGTTGCA 59.682 43.478 0.00 0.00 0.00 4.08
2631 4251 4.290155 CCAGATTAGTGTTTGTGTTGCAC 58.710 43.478 0.00 0.00 34.56 4.57
2632 4252 4.290155 CAGATTAGTGTTTGTGTTGCACC 58.710 43.478 0.00 0.00 32.73 5.01
2633 4253 4.036734 CAGATTAGTGTTTGTGTTGCACCT 59.963 41.667 0.00 0.00 32.73 4.00
2634 4254 3.773860 TTAGTGTTTGTGTTGCACCTG 57.226 42.857 0.00 0.00 32.73 4.00
2635 4255 1.832883 AGTGTTTGTGTTGCACCTGA 58.167 45.000 0.00 0.00 32.73 3.86
2636 4256 2.378038 AGTGTTTGTGTTGCACCTGAT 58.622 42.857 0.00 0.00 32.73 2.90
2637 4257 2.099592 AGTGTTTGTGTTGCACCTGATG 59.900 45.455 0.00 0.00 32.73 3.07
2638 4258 1.408340 TGTTTGTGTTGCACCTGATGG 59.592 47.619 0.00 0.00 39.83 3.51
2639 4259 1.680735 GTTTGTGTTGCACCTGATGGA 59.319 47.619 0.00 0.00 37.04 3.41
2640 4260 1.317613 TTGTGTTGCACCTGATGGAC 58.682 50.000 0.00 0.00 37.04 4.02
2641 4261 0.182299 TGTGTTGCACCTGATGGACA 59.818 50.000 0.00 0.00 37.04 4.02
2642 4262 0.593128 GTGTTGCACCTGATGGACAC 59.407 55.000 0.00 0.00 37.04 3.67
2643 4263 0.473755 TGTTGCACCTGATGGACACT 59.526 50.000 0.00 0.00 37.04 3.55
2644 4264 1.160137 GTTGCACCTGATGGACACTC 58.840 55.000 0.00 0.00 37.04 3.51
2645 4265 0.764271 TTGCACCTGATGGACACTCA 59.236 50.000 0.00 0.00 37.04 3.41
2646 4266 0.986527 TGCACCTGATGGACACTCAT 59.013 50.000 0.00 0.00 37.04 2.90
2647 4267 1.339342 TGCACCTGATGGACACTCATG 60.339 52.381 0.00 0.00 37.04 3.07
2648 4268 1.065926 GCACCTGATGGACACTCATGA 60.066 52.381 0.00 0.00 37.04 3.07
2649 4269 2.616256 GCACCTGATGGACACTCATGAA 60.616 50.000 0.00 0.00 37.04 2.57
2650 4270 3.005554 CACCTGATGGACACTCATGAAC 58.994 50.000 0.00 0.00 37.04 3.18
2651 4271 2.026822 ACCTGATGGACACTCATGAACC 60.027 50.000 0.00 0.00 37.04 3.62
2652 4272 2.238144 CCTGATGGACACTCATGAACCT 59.762 50.000 0.00 0.00 34.57 3.50
2653 4273 3.452264 CCTGATGGACACTCATGAACCTA 59.548 47.826 0.00 0.00 34.57 3.08
2659 4279 3.119291 GACACTCATGAACCTAGCATCG 58.881 50.000 0.00 0.00 0.00 3.84
2661 4281 3.699538 ACACTCATGAACCTAGCATCGTA 59.300 43.478 0.00 0.00 0.00 3.43
2684 4304 3.497262 GTGTGGGTTCTAGTTTACAGCAC 59.503 47.826 0.00 0.00 0.00 4.40
2689 4309 3.314553 GTTCTAGTTTACAGCACGCAGA 58.685 45.455 0.00 0.00 0.00 4.26
2694 4314 3.254060 AGTTTACAGCACGCAGACATAG 58.746 45.455 0.00 0.00 0.00 2.23
2719 4339 6.197276 CACTCTGTTTCACTCACTGAATTTG 58.803 40.000 0.00 0.00 38.74 2.32
2746 4366 4.381411 ACAGCTGATCATCATCACTCATG 58.619 43.478 23.35 0.00 33.80 3.07
2773 4393 7.491372 AGTGTACGTATATGTTTCACTCAATGG 59.509 37.037 20.26 0.00 33.69 3.16
2791 4411 7.449395 ACTCAATGGAGAATCTTTCATTTGACA 59.551 33.333 3.42 0.00 44.26 3.58
2802 4422 7.465353 TCTTTCATTTGACAATAGGCATGAA 57.535 32.000 0.00 7.75 0.00 2.57
2803 4423 8.070034 TCTTTCATTTGACAATAGGCATGAAT 57.930 30.769 11.24 0.00 32.22 2.57
2805 4425 9.158233 CTTTCATTTGACAATAGGCATGAATTT 57.842 29.630 11.24 0.00 32.22 1.82
2831 4451 0.240945 GTTGATTTGTCTGGGCCGTG 59.759 55.000 0.00 0.00 0.00 4.94
2853 4473 4.159857 GCACGAACGGTTAATTAAATGCA 58.840 39.130 0.00 0.00 0.00 3.96
3086 4706 0.465287 TGACAGAGACTTGCACTGCA 59.535 50.000 0.00 0.00 38.58 4.41
3202 6330 0.952984 GTTTTCTCGAGCAGCTGCCT 60.953 55.000 34.39 21.60 43.38 4.75
3282 6410 2.597217 ACCATTGTGGCACCGGTG 60.597 61.111 30.66 30.66 42.67 4.94
3308 6436 0.313672 GGCGAAAAATGAGTGGCACA 59.686 50.000 21.41 0.00 0.00 4.57
3361 6489 1.453155 ATGCCTTCATGGTTGTCGTC 58.547 50.000 0.00 0.00 38.35 4.20
3405 6533 4.479993 CAGAGCAAGGGGAGGGCG 62.480 72.222 0.00 0.00 0.00 6.13
3407 6535 4.035102 GAGCAAGGGGAGGGCGTT 62.035 66.667 0.00 0.00 0.00 4.84
3412 6540 0.106894 CAAGGGGAGGGCGTTCTATC 59.893 60.000 0.00 0.00 0.00 2.08
3413 6541 1.400530 AAGGGGAGGGCGTTCTATCG 61.401 60.000 0.00 0.00 0.00 2.92
3431 6559 4.373116 GAACCGTGGCCGCTCTGA 62.373 66.667 15.69 0.00 0.00 3.27
3442 6570 0.951040 CCGCTCTGACCTTGGTTGAC 60.951 60.000 0.00 0.00 0.00 3.18
3466 6594 0.465287 CAGTGGCCCAAAGCAAGTTT 59.535 50.000 0.00 0.00 46.50 2.66
3493 6621 0.623723 TCAACCTATTCCCTGGTGCC 59.376 55.000 0.00 0.00 36.57 5.01
3553 6681 1.026718 GGTGGTGGAAGGATCTTGCG 61.027 60.000 0.00 0.00 0.00 4.85
3568 6696 3.745799 TCTTGCGGTTCCATTTTGTCTA 58.254 40.909 0.00 0.00 0.00 2.59
3613 6741 1.347907 GTCGAGACTAGACGACGGC 59.652 63.158 18.96 12.36 46.39 5.68
3621 6749 1.934220 CTAGACGACGGCAGCTGGAA 61.934 60.000 17.12 0.00 0.00 3.53
3669 6797 5.602628 AGAGGCGTCCAAAATTATACTCTC 58.397 41.667 2.06 0.00 0.00 3.20
3670 6798 5.128827 AGAGGCGTCCAAAATTATACTCTCA 59.871 40.000 2.06 0.00 0.00 3.27
3689 6817 4.338400 TCTCATAGGTGTCGGTCAAGTATG 59.662 45.833 0.00 0.00 0.00 2.39
3703 6831 6.147821 CGGTCAAGTATGTTTGAGAGATTTGT 59.852 38.462 0.00 0.00 37.72 2.83
3757 6887 9.490379 TTTTACTCCTCTTAACAGTTTGAGATC 57.510 33.333 14.21 0.00 27.62 2.75
3759 6889 9.529823 TTACTCCTCTTAACAGTTTGAGATCTA 57.470 33.333 14.21 0.00 27.62 1.98
3775 6907 3.318557 AGATCTACTAGGTGCGGTTAAGC 59.681 47.826 0.00 0.00 37.71 3.09
3778 6910 1.153229 CTAGGTGCGGTTAAGCCCC 60.153 63.158 0.00 0.00 34.76 5.80
3792 6924 0.332972 AGCCCCCAAAATGAGGAGTC 59.667 55.000 0.00 0.00 0.00 3.36
3795 6927 1.077005 CCCCCAAAATGAGGAGTCCAA 59.923 52.381 12.86 0.00 0.00 3.53
3800 6932 3.897505 CCAAAATGAGGAGTCCAAGGTTT 59.102 43.478 12.86 3.63 0.00 3.27
3804 6936 7.418483 CCAAAATGAGGAGTCCAAGGTTTTAAA 60.418 37.037 12.86 0.00 0.00 1.52
3809 6941 6.715264 TGAGGAGTCCAAGGTTTTAAAAGATC 59.285 38.462 12.86 0.00 0.00 2.75
3810 6942 5.705905 AGGAGTCCAAGGTTTTAAAAGATCG 59.294 40.000 12.86 0.00 0.00 3.69
3831 6963 6.534475 TCGGTTAAAGATGCTCTAAGGTTA 57.466 37.500 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.828081 CTGGCTGCCTGCTCTATGA 59.172 57.895 21.03 0.00 42.39 2.15
26 27 2.210341 GAAAAGAGCTGGCTGCCTGC 62.210 60.000 34.80 34.80 46.61 4.85
27 28 0.892358 TGAAAAGAGCTGGCTGCCTG 60.892 55.000 21.03 20.46 44.23 4.85
28 29 0.178981 TTGAAAAGAGCTGGCTGCCT 60.179 50.000 21.03 7.10 44.23 4.75
29 30 2.344535 TTGAAAAGAGCTGGCTGCC 58.655 52.632 12.87 12.87 44.23 4.85
46 47 3.389329 TGAAGAGAACACCAAGAGAGCTT 59.611 43.478 0.00 0.00 33.74 3.74
56 61 2.100605 AGCCGATTGAAGAGAACACC 57.899 50.000 0.00 0.00 0.00 4.16
59 64 5.123979 ACCAAATTAGCCGATTGAAGAGAAC 59.876 40.000 0.00 0.00 0.00 3.01
65 70 4.331968 ACTCACCAAATTAGCCGATTGAA 58.668 39.130 0.00 0.00 0.00 2.69
68 73 3.279434 GGACTCACCAAATTAGCCGATT 58.721 45.455 0.00 0.00 38.79 3.34
94 99 7.147213 TGGGACAAATACAACCATATCATAGGT 60.147 37.037 0.00 0.00 35.38 3.08
131 143 9.257865 CGTCGACCAAACAAATTAATTTACTAG 57.742 33.333 12.98 4.07 0.00 2.57
165 177 2.860735 GCTAGGTTGTAGATGCAGAACG 59.139 50.000 0.00 0.00 0.00 3.95
175 187 4.882427 TCACTACAGCTAGCTAGGTTGTAG 59.118 45.833 32.84 32.84 39.06 2.74
180 192 4.141287 CTCATCACTACAGCTAGCTAGGT 58.859 47.826 18.86 19.65 33.70 3.08
181 193 4.141287 ACTCATCACTACAGCTAGCTAGG 58.859 47.826 18.86 8.88 0.00 3.02
183 195 4.781934 TGACTCATCACTACAGCTAGCTA 58.218 43.478 18.86 1.19 0.00 3.32
192 204 3.808466 TCAGCCATGACTCATCACTAC 57.192 47.619 0.00 0.00 37.79 2.73
197 209 2.402305 GTCGATCAGCCATGACTCATC 58.598 52.381 0.00 0.00 38.57 2.92
217 229 0.391263 ACTAAAAGAAGCGGGGCTCG 60.391 55.000 0.18 0.18 38.25 5.03
224 236 2.349817 CCACACTGCACTAAAAGAAGCG 60.350 50.000 0.00 0.00 0.00 4.68
228 240 3.134985 TGGTACCACACTGCACTAAAAGA 59.865 43.478 11.60 0.00 0.00 2.52
268 280 5.675575 GCATGGTAGAGCTATATGCAAATGC 60.676 44.000 9.21 8.22 45.94 3.56
278 374 3.813443 CCACTTTGCATGGTAGAGCTAT 58.187 45.455 0.00 0.00 32.08 2.97
299 457 3.073650 AGGAATCTGGTGGAATATGAGGC 59.926 47.826 0.00 0.00 0.00 4.70
315 473 2.111384 TGAGGAGTACCAGCAGGAATC 58.889 52.381 0.35 0.00 38.69 2.52
471 744 4.424842 AGAGAGAGAAGATTGGGTCTGTT 58.575 43.478 0.00 0.00 37.23 3.16
512 814 2.779033 GGCCTACTGGTACCGGACG 61.779 68.421 27.93 16.01 35.27 4.79
574 1040 4.890158 TTGAGTGCACTTCAGGATTAGA 57.110 40.909 22.65 1.14 0.00 2.10
598 1064 4.618927 GCAAAAGCCAGCATGTATCTTTGA 60.619 41.667 0.00 0.00 31.77 2.69
599 1065 3.615496 GCAAAAGCCAGCATGTATCTTTG 59.385 43.478 0.00 0.00 31.77 2.77
600 1066 3.258872 TGCAAAAGCCAGCATGTATCTTT 59.741 39.130 0.00 0.00 35.51 2.52
601 1067 2.827322 TGCAAAAGCCAGCATGTATCTT 59.173 40.909 0.00 0.00 35.51 2.40
602 1068 2.449464 TGCAAAAGCCAGCATGTATCT 58.551 42.857 0.00 0.00 35.51 1.98
603 1069 2.945447 TGCAAAAGCCAGCATGTATC 57.055 45.000 0.00 0.00 35.51 2.24
799 1287 4.079787 TGTCCTGGATCCATTTTCTAAGGG 60.080 45.833 16.63 9.74 36.54 3.95
943 1581 3.739209 GCAGAGCAGAGCACATGTATGTA 60.739 47.826 0.00 0.00 39.39 2.29
944 1582 2.902523 CAGAGCAGAGCACATGTATGT 58.097 47.619 0.00 0.00 42.84 2.29
1170 1905 3.445450 AGCTAGCTCGATGTCTTCTGAAA 59.555 43.478 12.68 0.00 0.00 2.69
1221 2028 1.419012 CCTCCTGCTGATGCTCCATTA 59.581 52.381 0.00 0.00 40.48 1.90
1231 2041 1.228583 ACACGACTCCTCCTGCTGA 60.229 57.895 0.00 0.00 0.00 4.26
1369 2188 1.070445 GAGGTCCCATGGCTCGATG 59.930 63.158 6.09 0.00 0.00 3.84
1418 2241 5.783360 AGAGGGGGTAAAAATTACAAAAGGG 59.217 40.000 3.00 0.00 0.00 3.95
1420 2243 7.297936 ACAGAGGGGGTAAAAATTACAAAAG 57.702 36.000 3.00 0.00 0.00 2.27
1468 2320 5.163540 CCACCTCACTAGAACACTATGTACC 60.164 48.000 0.00 0.00 0.00 3.34
1511 2415 4.158394 GTCTGCACCATCCATTATTGTTGT 59.842 41.667 0.00 0.00 0.00 3.32
1512 2416 4.158209 TGTCTGCACCATCCATTATTGTTG 59.842 41.667 0.00 0.00 0.00 3.33
1576 2497 3.444805 GACTGCTCGTCCTCCGCT 61.445 66.667 0.00 0.00 36.62 5.52
1852 2809 4.780554 AGGAGGAAGAAGAGGAACTAAAGG 59.219 45.833 0.00 0.00 41.55 3.11
1881 2863 6.015856 TCTCAAGAAGTAGAAGAAGAGGTGTG 60.016 42.308 0.00 0.00 0.00 3.82
1896 2953 3.882888 TCAACGCCAAATTCTCAAGAAGT 59.117 39.130 0.00 0.00 37.48 3.01
1897 2954 4.488126 TCAACGCCAAATTCTCAAGAAG 57.512 40.909 0.00 0.00 37.48 2.85
1898 2955 4.518590 TCATCAACGCCAAATTCTCAAGAA 59.481 37.500 0.00 0.00 38.56 2.52
2130 3606 0.683504 GCAGGTCCTCGGAGGAGTAA 60.684 60.000 26.70 2.74 46.90 2.24
2327 3818 0.945743 GTGCAGATGTGACGCTGTGA 60.946 55.000 0.00 0.00 34.66 3.58
2328 3819 1.494628 GTGCAGATGTGACGCTGTG 59.505 57.895 0.00 0.00 34.66 3.66
2329 3820 1.669115 GGTGCAGATGTGACGCTGT 60.669 57.895 0.00 0.00 34.66 4.40
2330 3821 0.108662 TAGGTGCAGATGTGACGCTG 60.109 55.000 0.00 1.50 35.28 5.18
2331 3822 0.174389 CTAGGTGCAGATGTGACGCT 59.826 55.000 0.00 0.00 0.00 5.07
2355 3891 5.658634 TGTCAGCTAACTGGATCTACTTCAT 59.341 40.000 0.00 0.00 44.59 2.57
2367 3903 3.181490 TGCTACGGTATGTCAGCTAACTG 60.181 47.826 1.98 0.00 45.95 3.16
2375 3911 1.269051 CGATGCTGCTACGGTATGTCA 60.269 52.381 0.00 0.00 0.00 3.58
2418 3961 3.004524 GTGTCCCGGACATCATCTACTAC 59.995 52.174 23.14 2.81 44.63 2.73
2497 4117 6.858993 GTGAAACAGAGTAGTCTACAGTGAAG 59.141 42.308 12.54 0.00 36.32 3.02
2534 4154 5.734220 GCGTACGATAAATCAACTGTCCCTA 60.734 44.000 21.65 0.00 0.00 3.53
2579 4199 0.179134 GCCTGTACTCCGCAGTAGTG 60.179 60.000 0.00 0.00 35.67 2.74
2584 4204 2.533266 ATAATGCCTGTACTCCGCAG 57.467 50.000 7.86 0.00 35.66 5.18
2586 4206 3.839293 CTCTATAATGCCTGTACTCCGC 58.161 50.000 0.00 0.00 0.00 5.54
2587 4207 3.367498 GGCTCTATAATGCCTGTACTCCG 60.367 52.174 8.05 0.00 45.26 4.63
2588 4208 4.195225 GGCTCTATAATGCCTGTACTCC 57.805 50.000 8.05 0.00 45.26 3.85
2598 4218 7.716998 ACAAACACTAATCTGGGCTCTATAATG 59.283 37.037 0.00 0.00 0.00 1.90
2599 4219 7.716998 CACAAACACTAATCTGGGCTCTATAAT 59.283 37.037 0.00 0.00 0.00 1.28
2602 4222 5.045578 ACACAAACACTAATCTGGGCTCTAT 60.046 40.000 0.00 0.00 0.00 1.98
2603 4223 4.286032 ACACAAACACTAATCTGGGCTCTA 59.714 41.667 0.00 0.00 0.00 2.43
2604 4224 3.073062 ACACAAACACTAATCTGGGCTCT 59.927 43.478 0.00 0.00 0.00 4.09
2605 4225 3.412386 ACACAAACACTAATCTGGGCTC 58.588 45.455 0.00 0.00 0.00 4.70
2607 4227 3.857010 GCAACACAAACACTAATCTGGGC 60.857 47.826 0.00 0.00 0.00 5.36
2608 4228 3.317711 TGCAACACAAACACTAATCTGGG 59.682 43.478 0.00 0.00 0.00 4.45
2609 4229 4.290155 GTGCAACACAAACACTAATCTGG 58.710 43.478 0.00 0.00 36.32 3.86
2610 4230 4.036734 AGGTGCAACACAAACACTAATCTG 59.963 41.667 3.64 0.00 39.98 2.90
2613 4233 3.951037 TCAGGTGCAACACAAACACTAAT 59.049 39.130 3.64 0.00 39.98 1.73
2614 4234 3.348119 TCAGGTGCAACACAAACACTAA 58.652 40.909 3.64 0.00 39.98 2.24
2615 4235 2.992593 TCAGGTGCAACACAAACACTA 58.007 42.857 3.64 0.00 39.98 2.74
2617 4237 2.462889 CATCAGGTGCAACACAAACAC 58.537 47.619 3.64 0.00 39.98 3.32
2618 4238 1.408340 CCATCAGGTGCAACACAAACA 59.592 47.619 3.64 0.00 39.98 2.83
2619 4239 1.680735 TCCATCAGGTGCAACACAAAC 59.319 47.619 3.64 0.00 39.98 2.93
2620 4240 1.680735 GTCCATCAGGTGCAACACAAA 59.319 47.619 3.64 0.00 39.98 2.83
2623 4243 0.593128 GTGTCCATCAGGTGCAACAC 59.407 55.000 3.64 0.72 39.98 3.32
2624 4244 0.473755 AGTGTCCATCAGGTGCAACA 59.526 50.000 3.64 0.00 39.98 3.33
2625 4245 1.160137 GAGTGTCCATCAGGTGCAAC 58.840 55.000 0.00 0.00 35.89 4.17
2626 4246 0.764271 TGAGTGTCCATCAGGTGCAA 59.236 50.000 0.00 0.00 35.89 4.08
2627 4247 0.986527 ATGAGTGTCCATCAGGTGCA 59.013 50.000 0.00 0.00 35.89 4.57
2628 4248 1.065926 TCATGAGTGTCCATCAGGTGC 60.066 52.381 0.00 0.00 35.89 5.01
2629 4249 3.005554 GTTCATGAGTGTCCATCAGGTG 58.994 50.000 0.00 0.00 35.89 4.00
2630 4250 2.026822 GGTTCATGAGTGTCCATCAGGT 60.027 50.000 0.00 0.00 35.89 4.00
2631 4251 2.238144 AGGTTCATGAGTGTCCATCAGG 59.762 50.000 0.00 0.00 0.00 3.86
2632 4252 3.623906 AGGTTCATGAGTGTCCATCAG 57.376 47.619 0.00 0.00 0.00 2.90
2633 4253 3.118629 GCTAGGTTCATGAGTGTCCATCA 60.119 47.826 0.00 0.00 0.00 3.07
2634 4254 3.118629 TGCTAGGTTCATGAGTGTCCATC 60.119 47.826 0.00 0.00 0.00 3.51
2635 4255 2.840038 TGCTAGGTTCATGAGTGTCCAT 59.160 45.455 0.00 0.00 0.00 3.41
2636 4256 2.256306 TGCTAGGTTCATGAGTGTCCA 58.744 47.619 0.00 0.00 0.00 4.02
2637 4257 3.462021 GATGCTAGGTTCATGAGTGTCC 58.538 50.000 0.00 0.00 0.00 4.02
2638 4258 3.119291 CGATGCTAGGTTCATGAGTGTC 58.881 50.000 0.00 0.00 0.00 3.67
2639 4259 2.497675 ACGATGCTAGGTTCATGAGTGT 59.502 45.455 0.00 0.00 0.00 3.55
2640 4260 3.170791 ACGATGCTAGGTTCATGAGTG 57.829 47.619 0.00 0.00 0.00 3.51
2641 4261 3.954904 ACTACGATGCTAGGTTCATGAGT 59.045 43.478 0.00 0.00 0.00 3.41
2642 4262 4.202060 ACACTACGATGCTAGGTTCATGAG 60.202 45.833 0.00 0.00 0.00 2.90
2643 4263 3.699538 ACACTACGATGCTAGGTTCATGA 59.300 43.478 0.00 0.00 0.00 3.07
2644 4264 3.798878 CACACTACGATGCTAGGTTCATG 59.201 47.826 0.00 0.00 0.00 3.07
2645 4265 3.181475 CCACACTACGATGCTAGGTTCAT 60.181 47.826 0.00 0.00 0.00 2.57
2646 4266 2.165641 CCACACTACGATGCTAGGTTCA 59.834 50.000 0.00 0.00 0.00 3.18
2647 4267 2.481449 CCCACACTACGATGCTAGGTTC 60.481 54.545 0.00 0.00 0.00 3.62
2648 4268 1.480954 CCCACACTACGATGCTAGGTT 59.519 52.381 0.00 0.00 0.00 3.50
2649 4269 1.112113 CCCACACTACGATGCTAGGT 58.888 55.000 0.00 0.00 0.00 3.08
2650 4270 1.112113 ACCCACACTACGATGCTAGG 58.888 55.000 0.00 0.00 0.00 3.02
2651 4271 2.427453 AGAACCCACACTACGATGCTAG 59.573 50.000 0.00 0.00 0.00 3.42
2652 4272 2.453521 AGAACCCACACTACGATGCTA 58.546 47.619 0.00 0.00 0.00 3.49
2653 4273 1.267121 AGAACCCACACTACGATGCT 58.733 50.000 0.00 0.00 0.00 3.79
2659 4279 4.928020 GCTGTAAACTAGAACCCACACTAC 59.072 45.833 0.00 0.00 0.00 2.73
2661 4281 3.389983 TGCTGTAAACTAGAACCCACACT 59.610 43.478 0.00 0.00 0.00 3.55
2684 4304 2.001812 AACAGAGTGCTATGTCTGCG 57.998 50.000 0.00 0.00 43.48 5.18
2689 4309 4.039730 AGTGAGTGAAACAGAGTGCTATGT 59.960 41.667 0.00 0.00 41.43 2.29
2694 4314 2.826428 TCAGTGAGTGAAACAGAGTGC 58.174 47.619 0.00 0.00 41.43 4.40
2719 4339 4.634883 AGTGATGATGATCAGCTGTTCAAC 59.365 41.667 26.73 24.09 39.36 3.18
2746 4366 8.532341 CATTGAGTGAAACATATACGTACACTC 58.468 37.037 23.16 23.16 44.48 3.51
2773 4393 7.765307 TGCCTATTGTCAAATGAAAGATTCTC 58.235 34.615 0.00 0.00 0.00 2.87
2831 4451 4.159857 TGCATTTAATTAACCGTTCGTGC 58.840 39.130 0.00 1.82 0.00 5.34
2853 4473 1.936767 AATCCCCGTGGGCACATCAT 61.937 55.000 0.00 0.00 43.94 2.45
2990 4610 5.241728 CCCATCTATCTGTCTACATGTCGAA 59.758 44.000 0.00 0.00 0.00 3.71
3086 4706 6.857777 GCACTCAAGATGCATACTTATCTT 57.142 37.500 0.00 0.00 42.67 2.40
3166 4788 0.393808 AACCCCAATTGATCCCGTCG 60.394 55.000 7.12 0.00 0.00 5.12
3202 6330 1.065926 CCTCATAGACCAAGCACAGCA 60.066 52.381 0.00 0.00 0.00 4.41
3204 6332 1.209019 AGCCTCATAGACCAAGCACAG 59.791 52.381 0.00 0.00 0.00 3.66
3282 6410 0.316196 CTCATTTTTCGCCGATCGCC 60.316 55.000 10.32 0.00 38.27 5.54
3308 6436 4.199432 AGAAGAAGAACGACATGCATCT 57.801 40.909 0.00 0.00 0.00 2.90
3354 6482 1.372997 GCAGAGAAGCCGACGACAA 60.373 57.895 0.00 0.00 0.00 3.18
3355 6483 2.258591 GCAGAGAAGCCGACGACA 59.741 61.111 0.00 0.00 0.00 4.35
3407 6535 3.213264 GGCCACGGTTCCGATAGA 58.787 61.111 18.28 0.00 39.76 1.98
3420 6548 4.020617 CCAAGGTCAGAGCGGCCA 62.021 66.667 2.24 0.00 0.00 5.36
3428 6556 1.507141 GCACCGTCAACCAAGGTCAG 61.507 60.000 0.00 0.00 35.85 3.51
3431 6559 1.525995 CTGCACCGTCAACCAAGGT 60.526 57.895 0.00 0.00 39.12 3.50
3442 6570 3.673484 CTTTGGGCCACTGCACCG 61.673 66.667 5.23 0.00 41.56 4.94
3466 6594 4.508405 CCAGGGAATAGGTTGAGGACAAAA 60.508 45.833 0.00 0.00 37.77 2.44
3474 6602 0.623723 GGCACCAGGGAATAGGTTGA 59.376 55.000 0.00 0.00 35.52 3.18
3478 6606 2.510906 CCGGCACCAGGGAATAGG 59.489 66.667 0.00 0.00 0.00 2.57
3500 6628 1.292223 CTGGAATCGACCCACACGT 59.708 57.895 4.40 0.00 0.00 4.49
3503 6631 2.264480 CGCTGGAATCGACCCACA 59.736 61.111 4.40 0.00 0.00 4.17
3539 6667 0.035439 GGAACCGCAAGATCCTTCCA 60.035 55.000 0.00 0.00 39.26 3.53
3553 6681 5.294552 CCTCGATTCTAGACAAAATGGAACC 59.705 44.000 0.00 0.00 0.00 3.62
3596 6724 1.079612 TGCCGTCGTCTAGTCTCGA 60.080 57.895 0.00 0.00 0.00 4.04
3610 6738 1.953138 CTATCGCTTCCAGCTGCCG 60.953 63.158 8.66 8.02 39.60 5.69
3613 6741 1.953138 CGGCTATCGCTTCCAGCTG 60.953 63.158 6.78 6.78 39.60 4.24
3623 6751 4.044484 CCTCCCGAGCGGCTATCG 62.044 72.222 0.60 3.18 42.76 2.92
3626 6754 2.833582 CTTCCTCCCGAGCGGCTA 60.834 66.667 0.60 0.00 0.00 3.93
3669 6797 4.386867 ACATACTTGACCGACACCTATG 57.613 45.455 0.00 0.00 0.00 2.23
3670 6798 5.046878 TCAAACATACTTGACCGACACCTAT 60.047 40.000 0.00 0.00 30.31 2.57
3756 6886 1.753073 GGCTTAACCGCACCTAGTAGA 59.247 52.381 0.00 0.00 0.00 2.59
3757 6887 1.202498 GGGCTTAACCGCACCTAGTAG 60.202 57.143 0.00 0.00 40.62 2.57
3759 6889 1.600638 GGGCTTAACCGCACCTAGT 59.399 57.895 0.00 0.00 40.62 2.57
3775 6907 0.704076 TGGACTCCTCATTTTGGGGG 59.296 55.000 0.00 0.00 38.96 5.40
3778 6910 3.160679 ACCTTGGACTCCTCATTTTGG 57.839 47.619 0.00 0.00 0.00 3.28
3792 6924 8.354426 TCTTTAACCGATCTTTTAAAACCTTGG 58.646 33.333 0.00 3.55 29.11 3.61
3795 6927 8.027189 GCATCTTTAACCGATCTTTTAAAACCT 58.973 33.333 0.00 0.00 29.11 3.50


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

AutoCloner maintained by Alex Coulton.