Multiple sequence alignment - TraesCS6D01G057800

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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 TraesCS6D01G057800 chr6D 100.000 3236 0 0 283 3518 27451425 27454660 0.000000e+00 5976.0
1 TraesCS6D01G057800 chr6D 90.825 1842 90 41 788 2584 15257426 15255619 0.000000e+00 2392.0
2 TraesCS6D01G057800 chr6D 93.609 845 49 4 2678 3518 409006029 409005186 0.000000e+00 1256.0
3 TraesCS6D01G057800 chr6D 100.000 182 0 0 1 182 27440645 27440826 1.560000e-88 337.0
4 TraesCS6D01G057800 chr6D 100.000 182 0 0 1 182 27451143 27451324 1.560000e-88 337.0
5 TraesCS6D01G057800 chr6D 89.781 137 9 2 283 418 15257590 15257458 1.680000e-38 171.0
6 TraesCS6D01G057800 chr6D 100.000 85 0 0 2593 2677 15255571 15255487 1.310000e-34 158.0
7 TraesCS6D01G057800 chr6B 94.588 1626 63 7 973 2583 50483009 50484624 0.000000e+00 2492.0
8 TraesCS6D01G057800 chr6B 83.246 1528 229 13 996 2517 23224880 23226386 0.000000e+00 1378.0
9 TraesCS6D01G057800 chr6B 92.073 164 12 1 418 581 633056566 633056404 2.730000e-56 230.0
10 TraesCS6D01G057800 chr6B 86.567 67 4 1 2593 2659 50484678 50484739 6.300000e-08 69.4
11 TraesCS6D01G057800 chr6A 92.189 1754 98 22 852 2579 30869195 30867455 0.000000e+00 2444.0
12 TraesCS6D01G057800 chr2D 89.503 1772 139 26 778 2521 248473345 248471593 0.000000e+00 2198.0
13 TraesCS6D01G057800 chr2D 93.817 841 48 4 2680 3518 522263001 522262163 0.000000e+00 1262.0
14 TraesCS6D01G057800 chr2D 93.499 846 49 5 2678 3518 435437488 435438332 0.000000e+00 1253.0
15 TraesCS6D01G057800 chr2D 86.265 415 36 7 2172 2575 248394315 248394719 6.980000e-117 431.0
16 TraesCS6D01G057800 chr2D 97.802 182 4 0 1 182 408163787 408163968 7.330000e-82 315.0
17 TraesCS6D01G057800 chr2D 97.802 182 4 0 1 182 408173146 408173327 7.330000e-82 315.0
18 TraesCS6D01G057800 chr2D 89.498 219 15 3 576 794 248473603 248473393 1.610000e-68 270.0
19 TraesCS6D01G057800 chr2D 90.698 172 9 5 413 579 120099922 120100091 4.570000e-54 222.0
20 TraesCS6D01G057800 chr7D 97.153 843 21 3 2678 3518 168802002 168802843 0.000000e+00 1421.0
21 TraesCS6D01G057800 chr7D 95.508 846 35 3 2675 3518 370974550 370975394 0.000000e+00 1349.0
22 TraesCS6D01G057800 chr7D 93.728 845 44 6 2676 3517 561742474 561743312 0.000000e+00 1258.0
23 TraesCS6D01G057800 chr7D 81.181 1541 245 32 1001 2517 58133936 58132417 0.000000e+00 1197.0
24 TraesCS6D01G057800 chr7D 97.802 182 4 0 1 182 102171301 102171120 7.330000e-82 315.0
25 TraesCS6D01G057800 chr7D 97.268 183 4 1 1 182 160876991 160877173 3.410000e-80 309.0
26 TraesCS6D01G057800 chr7D 91.463 164 14 0 418 581 454079247 454079410 3.530000e-55 226.0
27 TraesCS6D01G057800 chr3D 95.482 841 33 5 2681 3518 18664392 18665230 0.000000e+00 1338.0
28 TraesCS6D01G057800 chr1D 94.805 847 39 5 2675 3518 155778548 155779392 0.000000e+00 1315.0
29 TraesCS6D01G057800 chr1D 90.476 168 16 0 415 582 463381902 463382069 4.570000e-54 222.0
30 TraesCS6D01G057800 chr4D 94.194 844 45 4 2677 3518 117702833 117701992 0.000000e+00 1284.0
31 TraesCS6D01G057800 chr7A 81.506 1541 231 36 997 2514 62475699 62477208 0.000000e+00 1218.0
32 TraesCS6D01G057800 chr4A 81.218 1544 239 37 997 2517 673774499 673772984 0.000000e+00 1197.0
33 TraesCS6D01G057800 chr4A 80.739 1542 248 32 1001 2516 673802784 673804302 0.000000e+00 1157.0
34 TraesCS6D01G057800 chr2A 79.161 1526 279 29 1001 2517 3523032 3524527 0.000000e+00 1020.0
35 TraesCS6D01G057800 chr2A 78.520 1541 263 44 1001 2514 3534368 3532869 0.000000e+00 950.0
36 TraesCS6D01G057800 chr5D 97.253 182 5 0 1 182 29354754 29354573 3.410000e-80 309.0
37 TraesCS6D01G057800 chrUn 96.703 182 6 0 1 182 167849656 167849475 1.590000e-78 303.0
38 TraesCS6D01G057800 chrUn 96.703 182 6 0 1 182 247724295 247724114 1.590000e-78 303.0
39 TraesCS6D01G057800 chrUn 96.703 182 6 0 1 182 262768466 262768647 1.590000e-78 303.0
40 TraesCS6D01G057800 chrUn 100.000 125 0 0 283 407 382188854 382188978 7.590000e-57 231.0
41 TraesCS6D01G057800 chr5A 90.588 170 16 0 417 586 653299602 653299433 3.530000e-55 226.0
42 TraesCS6D01G057800 chr7B 90.964 166 14 1 418 582 490208151 490207986 4.570000e-54 222.0
43 TraesCS6D01G057800 chr1B 90.533 169 15 1 415 582 24349048 24349216 4.570000e-54 222.0
44 TraesCS6D01G057800 chr1B 86.154 195 23 4 398 590 604574276 604574468 1.280000e-49 207.0
45 TraesCS6D01G057800 chr2B 89.535 172 17 1 409 579 608226896 608226725 2.130000e-52 217.0


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 TraesCS6D01G057800 chr6D 27451143 27454660 3517 False 3156.5 5976 100.000000 1 3518 2 chr6D.!!$F2 3517
1 TraesCS6D01G057800 chr6D 409005186 409006029 843 True 1256.0 1256 93.609000 2678 3518 1 chr6D.!!$R1 840
2 TraesCS6D01G057800 chr6D 15255487 15257590 2103 True 907.0 2392 93.535333 283 2677 3 chr6D.!!$R2 2394
3 TraesCS6D01G057800 chr6B 23224880 23226386 1506 False 1378.0 1378 83.246000 996 2517 1 chr6B.!!$F1 1521
4 TraesCS6D01G057800 chr6B 50483009 50484739 1730 False 1280.7 2492 90.577500 973 2659 2 chr6B.!!$F2 1686
5 TraesCS6D01G057800 chr6A 30867455 30869195 1740 True 2444.0 2444 92.189000 852 2579 1 chr6A.!!$R1 1727
6 TraesCS6D01G057800 chr2D 522262163 522263001 838 True 1262.0 1262 93.817000 2680 3518 1 chr2D.!!$R1 838
7 TraesCS6D01G057800 chr2D 435437488 435438332 844 False 1253.0 1253 93.499000 2678 3518 1 chr2D.!!$F5 840
8 TraesCS6D01G057800 chr2D 248471593 248473603 2010 True 1234.0 2198 89.500500 576 2521 2 chr2D.!!$R2 1945
9 TraesCS6D01G057800 chr7D 168802002 168802843 841 False 1421.0 1421 97.153000 2678 3518 1 chr7D.!!$F2 840
10 TraesCS6D01G057800 chr7D 370974550 370975394 844 False 1349.0 1349 95.508000 2675 3518 1 chr7D.!!$F3 843
11 TraesCS6D01G057800 chr7D 561742474 561743312 838 False 1258.0 1258 93.728000 2676 3517 1 chr7D.!!$F5 841
12 TraesCS6D01G057800 chr7D 58132417 58133936 1519 True 1197.0 1197 81.181000 1001 2517 1 chr7D.!!$R1 1516
13 TraesCS6D01G057800 chr3D 18664392 18665230 838 False 1338.0 1338 95.482000 2681 3518 1 chr3D.!!$F1 837
14 TraesCS6D01G057800 chr1D 155778548 155779392 844 False 1315.0 1315 94.805000 2675 3518 1 chr1D.!!$F1 843
15 TraesCS6D01G057800 chr4D 117701992 117702833 841 True 1284.0 1284 94.194000 2677 3518 1 chr4D.!!$R1 841
16 TraesCS6D01G057800 chr7A 62475699 62477208 1509 False 1218.0 1218 81.506000 997 2514 1 chr7A.!!$F1 1517
17 TraesCS6D01G057800 chr4A 673772984 673774499 1515 True 1197.0 1197 81.218000 997 2517 1 chr4A.!!$R1 1520
18 TraesCS6D01G057800 chr4A 673802784 673804302 1518 False 1157.0 1157 80.739000 1001 2516 1 chr4A.!!$F1 1515
19 TraesCS6D01G057800 chr2A 3523032 3524527 1495 False 1020.0 1020 79.161000 1001 2517 1 chr2A.!!$F1 1516
20 TraesCS6D01G057800 chr2A 3532869 3534368 1499 True 950.0 950 78.520000 1001 2514 1 chr2A.!!$R1 1513

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
887 949 0.031994 CAAACCGGCAAAACCTCCAG 59.968 55.0 0.0 0.0 35.61 3.86 F
919 981 0.670546 ACCAGACAAACGGCATCTCG 60.671 55.0 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2333 0.670546 CGTTGAAGATCACCGTGGCT 60.671 55.000 0.00 0.00 27.32 4.75 R
2857 3098 1.066787 ACCTCCTCGTTTTGCTAGCTC 60.067 52.381 17.23 3.23 0.00 4.09 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
73 74 3.771160 GGTGCTCGACGGGGACAT 61.771 66.667 21.39 0.00 0.00 3.06
74 75 2.509336 GTGCTCGACGGGGACATG 60.509 66.667 15.10 0.00 0.00 3.21
75 76 3.770040 TGCTCGACGGGGACATGG 61.770 66.667 0.00 0.00 0.00 3.66
77 78 3.461773 CTCGACGGGGACATGGCT 61.462 66.667 0.00 0.00 0.00 4.75
78 79 2.043752 TCGACGGGGACATGGCTA 60.044 61.111 0.00 0.00 0.00 3.93
79 80 2.106332 CGACGGGGACATGGCTAC 59.894 66.667 0.00 0.00 0.00 3.58
80 81 2.106332 GACGGGGACATGGCTACG 59.894 66.667 12.71 12.71 0.00 3.51
81 82 3.441011 GACGGGGACATGGCTACGG 62.441 68.421 17.31 9.39 0.00 4.02
82 83 4.910585 CGGGGACATGGCTACGGC 62.911 72.222 0.00 0.00 37.82 5.68
83 84 4.910585 GGGGACATGGCTACGGCG 62.911 72.222 4.80 4.80 39.81 6.46
84 85 3.845259 GGGACATGGCTACGGCGA 61.845 66.667 16.62 0.00 39.81 5.54
85 86 2.279517 GGACATGGCTACGGCGAG 60.280 66.667 16.62 8.03 39.81 5.03
86 87 2.962253 GACATGGCTACGGCGAGC 60.962 66.667 16.62 17.95 42.05 5.03
87 88 3.432051 GACATGGCTACGGCGAGCT 62.432 63.158 23.42 9.78 42.43 4.09
88 89 2.071844 GACATGGCTACGGCGAGCTA 62.072 60.000 23.42 20.10 42.43 3.32
89 90 1.290324 CATGGCTACGGCGAGCTAT 59.710 57.895 23.42 21.12 43.74 2.97
90 91 0.734253 CATGGCTACGGCGAGCTATC 60.734 60.000 23.42 12.49 41.28 2.08
101 102 3.642901 GAGCTATCGAACAAGCGGA 57.357 52.632 10.86 0.00 43.63 5.54
102 103 1.482278 GAGCTATCGAACAAGCGGAG 58.518 55.000 10.86 0.00 43.63 4.63
103 104 0.103208 AGCTATCGAACAAGCGGAGG 59.897 55.000 10.86 0.00 43.63 4.30
104 105 0.876342 GCTATCGAACAAGCGGAGGG 60.876 60.000 0.00 0.00 0.00 4.30
105 106 0.249489 CTATCGAACAAGCGGAGGGG 60.249 60.000 0.00 0.00 0.00 4.79
106 107 2.306255 TATCGAACAAGCGGAGGGGC 62.306 60.000 0.00 0.00 0.00 5.80
108 109 2.747855 GAACAAGCGGAGGGGCTG 60.748 66.667 0.00 0.00 43.93 4.85
109 110 4.351054 AACAAGCGGAGGGGCTGG 62.351 66.667 0.00 0.00 43.93 4.85
127 128 1.003718 GGGGGCATCTACATACGGC 60.004 63.158 0.00 0.00 0.00 5.68
128 129 1.374252 GGGGCATCTACATACGGCG 60.374 63.158 4.80 4.80 0.00 6.46
129 130 1.374252 GGGCATCTACATACGGCGG 60.374 63.158 13.24 0.00 0.00 6.13
130 131 1.374252 GGCATCTACATACGGCGGG 60.374 63.158 13.24 2.44 0.00 6.13
131 132 1.374252 GCATCTACATACGGCGGGG 60.374 63.158 13.24 2.02 0.00 5.73
132 133 1.812686 GCATCTACATACGGCGGGGA 61.813 60.000 13.24 0.00 0.00 4.81
133 134 0.243907 CATCTACATACGGCGGGGAG 59.756 60.000 13.24 6.61 0.00 4.30
134 135 0.178970 ATCTACATACGGCGGGGAGT 60.179 55.000 13.24 6.81 0.00 3.85
135 136 1.105167 TCTACATACGGCGGGGAGTG 61.105 60.000 13.24 4.79 0.00 3.51
136 137 2.694829 CTACATACGGCGGGGAGTGC 62.695 65.000 13.24 0.00 0.00 4.40
137 138 4.155733 CATACGGCGGGGAGTGCA 62.156 66.667 13.24 0.00 0.00 4.57
138 139 3.395702 ATACGGCGGGGAGTGCAA 61.396 61.111 13.24 0.00 0.00 4.08
139 140 3.675619 ATACGGCGGGGAGTGCAAC 62.676 63.158 13.24 0.00 0.00 4.17
145 146 4.660938 GGGGAGTGCAACGGGCTT 62.661 66.667 0.00 0.00 45.86 4.35
146 147 3.365265 GGGAGTGCAACGGGCTTG 61.365 66.667 0.00 0.00 45.86 4.01
147 148 2.281484 GGAGTGCAACGGGCTTGA 60.281 61.111 0.00 0.00 45.86 3.02
148 149 2.617274 GGAGTGCAACGGGCTTGAC 61.617 63.158 0.00 0.00 45.86 3.18
149 150 2.594592 AGTGCAACGGGCTTGACC 60.595 61.111 0.00 0.00 45.86 4.02
158 159 3.948719 GGCTTGACCCCGTGACCA 61.949 66.667 0.00 0.00 0.00 4.02
159 160 2.351276 GCTTGACCCCGTGACCAT 59.649 61.111 0.00 0.00 0.00 3.55
160 161 1.303317 GCTTGACCCCGTGACCATT 60.303 57.895 0.00 0.00 0.00 3.16
161 162 0.893727 GCTTGACCCCGTGACCATTT 60.894 55.000 0.00 0.00 0.00 2.32
162 163 0.881118 CTTGACCCCGTGACCATTTG 59.119 55.000 0.00 0.00 0.00 2.32
163 164 0.538516 TTGACCCCGTGACCATTTGG 60.539 55.000 0.00 0.00 42.17 3.28
174 175 2.854522 CCATTTGGTCACCGGAGAC 58.145 57.895 22.30 22.30 37.80 3.36
315 316 3.000623 GCATGTATCCATCGCATATCACG 59.999 47.826 0.00 0.00 0.00 4.35
320 321 2.959516 TCCATCGCATATCACGGATTC 58.040 47.619 0.00 0.00 0.00 2.52
346 347 4.314740 TTTGTGCCGCATTTTCTAGTTT 57.685 36.364 0.00 0.00 0.00 2.66
353 354 4.791411 GCCGCATTTTCTAGTTTGTGACAA 60.791 41.667 0.00 0.00 0.00 3.18
354 355 5.277825 CCGCATTTTCTAGTTTGTGACAAA 58.722 37.500 6.66 6.66 0.00 2.83
355 356 5.746245 CCGCATTTTCTAGTTTGTGACAAAA 59.254 36.000 12.89 0.00 0.00 2.44
356 357 6.254589 CCGCATTTTCTAGTTTGTGACAAAAA 59.745 34.615 12.89 2.74 0.00 1.94
426 428 6.834168 TTTTCATTTCAATGTACTCCCTCC 57.166 37.500 0.00 0.00 37.65 4.30
427 429 4.137116 TCATTTCAATGTACTCCCTCCG 57.863 45.455 0.00 0.00 37.65 4.63
428 430 3.517901 TCATTTCAATGTACTCCCTCCGT 59.482 43.478 0.00 0.00 37.65 4.69
429 431 4.019681 TCATTTCAATGTACTCCCTCCGTT 60.020 41.667 0.00 0.00 37.65 4.44
430 432 3.604875 TTCAATGTACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
431 433 1.829222 TCAATGTACTCCCTCCGTTCC 59.171 52.381 0.00 0.00 0.00 3.62
432 434 1.831736 CAATGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
433 435 3.028850 CAATGTACTCCCTCCGTTCCTA 58.971 50.000 0.00 0.00 0.00 2.94
434 436 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
435 437 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
436 438 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
437 439 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
438 440 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
439 441 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
440 442 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
441 443 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
442 444 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
443 445 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
444 446 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
445 447 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
446 448 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
447 449 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
448 450 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
462 464 6.749923 AAGTCTTTGTAGAGATTCCAATGC 57.250 37.500 0.00 0.00 0.00 3.56
463 465 4.872691 AGTCTTTGTAGAGATTCCAATGCG 59.127 41.667 0.00 0.00 0.00 4.73
464 466 4.870426 GTCTTTGTAGAGATTCCAATGCGA 59.130 41.667 0.00 0.00 0.00 5.10
465 467 5.351465 GTCTTTGTAGAGATTCCAATGCGAA 59.649 40.000 0.00 0.00 0.00 4.70
466 468 5.351465 TCTTTGTAGAGATTCCAATGCGAAC 59.649 40.000 0.00 0.00 0.00 3.95
467 469 4.471904 TGTAGAGATTCCAATGCGAACT 57.528 40.909 0.00 0.00 0.00 3.01
468 470 5.592104 TGTAGAGATTCCAATGCGAACTA 57.408 39.130 0.00 0.00 0.00 2.24
469 471 5.348986 TGTAGAGATTCCAATGCGAACTAC 58.651 41.667 0.00 0.00 0.00 2.73
470 472 4.471904 AGAGATTCCAATGCGAACTACA 57.528 40.909 0.00 0.00 0.00 2.74
471 473 5.028549 AGAGATTCCAATGCGAACTACAT 57.971 39.130 0.00 0.00 0.00 2.29
472 474 6.161855 AGAGATTCCAATGCGAACTACATA 57.838 37.500 0.00 0.00 0.00 2.29
473 475 5.986135 AGAGATTCCAATGCGAACTACATAC 59.014 40.000 0.00 0.00 0.00 2.39
474 476 4.745125 AGATTCCAATGCGAACTACATACG 59.255 41.667 0.00 0.00 0.00 3.06
475 477 2.816689 TCCAATGCGAACTACATACGG 58.183 47.619 0.00 0.00 0.00 4.02
476 478 2.427812 TCCAATGCGAACTACATACGGA 59.572 45.455 0.00 0.00 30.66 4.69
477 479 2.794910 CCAATGCGAACTACATACGGAG 59.205 50.000 0.00 0.00 0.00 4.63
478 480 2.135664 ATGCGAACTACATACGGAGC 57.864 50.000 0.00 0.00 0.00 4.70
479 481 0.812549 TGCGAACTACATACGGAGCA 59.187 50.000 0.00 0.00 0.00 4.26
480 482 1.202817 TGCGAACTACATACGGAGCAA 59.797 47.619 0.00 0.00 0.00 3.91
481 483 2.264813 GCGAACTACATACGGAGCAAA 58.735 47.619 0.00 0.00 0.00 3.68
482 484 2.669434 GCGAACTACATACGGAGCAAAA 59.331 45.455 0.00 0.00 0.00 2.44
483 485 3.308866 GCGAACTACATACGGAGCAAAAT 59.691 43.478 0.00 0.00 0.00 1.82
484 486 4.782195 GCGAACTACATACGGAGCAAAATG 60.782 45.833 0.00 0.00 0.00 2.32
485 487 4.565166 CGAACTACATACGGAGCAAAATGA 59.435 41.667 0.00 0.00 0.00 2.57
486 488 5.234329 CGAACTACATACGGAGCAAAATGAT 59.766 40.000 0.00 0.00 0.00 2.45
487 489 6.238103 CGAACTACATACGGAGCAAAATGATT 60.238 38.462 0.00 0.00 0.00 2.57
488 490 6.363577 ACTACATACGGAGCAAAATGATTG 57.636 37.500 0.00 0.00 0.00 2.67
489 491 6.112734 ACTACATACGGAGCAAAATGATTGA 58.887 36.000 0.00 0.00 0.00 2.57
490 492 5.895636 ACATACGGAGCAAAATGATTGAA 57.104 34.783 0.00 0.00 0.00 2.69
491 493 6.455360 ACATACGGAGCAAAATGATTGAAT 57.545 33.333 0.00 0.00 0.00 2.57
492 494 7.566760 ACATACGGAGCAAAATGATTGAATA 57.433 32.000 0.00 0.00 0.00 1.75
493 495 8.169977 ACATACGGAGCAAAATGATTGAATAT 57.830 30.769 0.00 0.00 0.00 1.28
494 496 9.283768 ACATACGGAGCAAAATGATTGAATATA 57.716 29.630 0.00 0.00 0.00 0.86
573 575 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
574 576 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
578 580 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
644 646 6.694411 GCACATATTTCAAGTGGATTTGCTAG 59.306 38.462 0.00 0.00 33.98 3.42
645 647 7.629222 GCACATATTTCAAGTGGATTTGCTAGT 60.629 37.037 0.00 0.00 33.98 2.57
646 648 8.892723 CACATATTTCAAGTGGATTTGCTAGTA 58.107 33.333 0.00 0.00 0.00 1.82
650 652 6.985188 TTCAAGTGGATTTGCTAGTACATC 57.015 37.500 0.00 0.00 0.00 3.06
665 667 7.588854 TGCTAGTACATCACGAAATATTACGTC 59.411 37.037 0.00 0.00 40.76 4.34
673 675 7.041187 TCACGAAATATTACGTCACACTTTC 57.959 36.000 0.00 0.00 40.76 2.62
702 704 2.397044 AGGGCCCAAAAGAAACATGA 57.603 45.000 27.56 0.00 0.00 3.07
711 713 8.637986 GGCCCAAAAGAAACATGATGTAATATA 58.362 33.333 0.00 0.00 0.00 0.86
780 842 8.925161 ATTTGAAAGAAGACAAAATTCGTCAA 57.075 26.923 9.82 0.00 39.01 3.18
783 845 8.749841 TGAAAGAAGACAAAATTCGTCAAAAA 57.250 26.923 9.82 0.00 35.77 1.94
784 846 9.364989 TGAAAGAAGACAAAATTCGTCAAAAAT 57.635 25.926 9.82 0.00 35.77 1.82
816 878 5.475273 TTCGCAATTGAAATGCAAAAACA 57.525 30.435 10.34 0.00 44.01 2.83
821 883 7.596621 TCGCAATTGAAATGCAAAAACATACTA 59.403 29.630 10.34 0.00 44.01 1.82
887 949 0.031994 CAAACCGGCAAAACCTCCAG 59.968 55.000 0.00 0.00 35.61 3.86
897 959 3.056536 GCAAAACCTCCAGGAAATTCTCC 60.057 47.826 0.00 0.00 45.81 3.71
917 979 1.238439 CAACCAGACAAACGGCATCT 58.762 50.000 0.00 0.00 0.00 2.90
919 981 0.670546 ACCAGACAAACGGCATCTCG 60.671 55.000 0.00 0.00 0.00 4.04
950 1058 2.686470 CCAGCCTCCTGCCTGAGA 60.686 66.667 1.37 0.00 42.71 3.27
954 1062 0.913451 AGCCTCCTGCCTGAGAACAT 60.913 55.000 1.37 0.00 42.71 2.71
1486 1617 1.995626 ATGGTGGGCTACTTCCGCT 60.996 57.895 0.00 0.00 35.30 5.52
1641 1783 2.354656 GACATCATCGCCGCGCTA 60.355 61.111 8.21 0.00 0.00 4.26
2270 2434 1.271840 TTCCTGCTGGATAAGGCGGT 61.272 55.000 13.72 0.00 42.81 5.68
2521 2691 1.022735 CGTCGTGGTCACCTAGCTAT 58.977 55.000 0.00 0.00 0.00 2.97
2535 2726 3.377485 CCTAGCTATCATGCATGCAATCC 59.623 47.826 26.68 9.33 34.99 3.01
2544 2735 5.623169 TCATGCATGCAATCCTATCTTGTA 58.377 37.500 26.68 2.73 0.00 2.41
2576 2767 2.032834 ATGCGCCCGGTTTACACA 59.967 55.556 4.18 0.00 0.00 3.72
2579 2770 2.961669 GCGCCCGGTTTACACAGTG 61.962 63.158 0.00 0.00 0.00 3.66
2584 2775 1.134226 CCGGTTTACACAGTGTCGAC 58.866 55.000 10.23 9.11 0.00 4.20
2585 2776 0.774098 CGGTTTACACAGTGTCGACG 59.226 55.000 10.23 7.48 0.00 5.12
2589 2780 2.624316 TTACACAGTGTCGACGATCC 57.376 50.000 10.23 0.00 0.00 3.36
2590 2781 1.817357 TACACAGTGTCGACGATCCT 58.183 50.000 10.23 1.00 0.00 3.24
2754 2993 4.666512 AGGCAGAATCCACACATAAAGTT 58.333 39.130 0.00 0.00 0.00 2.66
2826 3067 2.100197 AGTAGATCGCAGCCACAAGTA 58.900 47.619 0.00 0.00 0.00 2.24
2845 3086 7.697710 CACAAGTACAATATCACAAATGCGAAT 59.302 33.333 0.00 0.00 0.00 3.34
2853 3094 5.823209 ATCACAAATGCGAATCATCAAGA 57.177 34.783 0.00 0.00 33.40 3.02
2857 3098 4.142534 ACAAATGCGAATCATCAAGACCAG 60.143 41.667 0.00 0.00 33.40 4.00
2869 3111 3.403038 TCAAGACCAGAGCTAGCAAAAC 58.597 45.455 18.83 5.35 0.00 2.43
2957 3199 3.492309 CCATAGTCTCTTTCATGCGCTCT 60.492 47.826 9.73 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.771160 ATGTCCCCGTCGAGCACC 61.771 66.667 0.00 0.00 0.00 5.01
57 58 2.509336 CATGTCCCCGTCGAGCAC 60.509 66.667 0.00 0.00 0.00 4.40
58 59 3.770040 CCATGTCCCCGTCGAGCA 61.770 66.667 0.00 0.00 0.00 4.26
60 61 2.125326 TAGCCATGTCCCCGTCGAG 61.125 63.158 0.00 0.00 0.00 4.04
61 62 2.043752 TAGCCATGTCCCCGTCGA 60.044 61.111 0.00 0.00 0.00 4.20
62 63 2.106332 GTAGCCATGTCCCCGTCG 59.894 66.667 0.00 0.00 0.00 5.12
63 64 2.106332 CGTAGCCATGTCCCCGTC 59.894 66.667 0.00 0.00 0.00 4.79
64 65 3.467226 CCGTAGCCATGTCCCCGT 61.467 66.667 0.00 0.00 0.00 5.28
65 66 4.910585 GCCGTAGCCATGTCCCCG 62.911 72.222 0.00 0.00 0.00 5.73
66 67 4.910585 CGCCGTAGCCATGTCCCC 62.911 72.222 0.00 0.00 34.57 4.81
67 68 3.792053 CTCGCCGTAGCCATGTCCC 62.792 68.421 0.00 0.00 34.57 4.46
68 69 2.279517 CTCGCCGTAGCCATGTCC 60.280 66.667 0.00 0.00 34.57 4.02
69 70 2.071844 TAGCTCGCCGTAGCCATGTC 62.072 60.000 0.00 0.00 43.86 3.06
70 71 1.464376 ATAGCTCGCCGTAGCCATGT 61.464 55.000 0.00 0.00 43.86 3.21
71 72 0.734253 GATAGCTCGCCGTAGCCATG 60.734 60.000 0.00 0.00 43.86 3.66
72 73 1.587054 GATAGCTCGCCGTAGCCAT 59.413 57.895 0.00 0.00 43.86 4.40
73 74 2.904676 CGATAGCTCGCCGTAGCCA 61.905 63.158 0.00 0.00 43.86 4.75
74 75 2.126417 TTCGATAGCTCGCCGTAGCC 62.126 60.000 0.00 0.00 44.65 3.93
75 76 0.997726 GTTCGATAGCTCGCCGTAGC 60.998 60.000 0.00 1.12 44.65 3.58
76 77 0.306840 TGTTCGATAGCTCGCCGTAG 59.693 55.000 0.00 0.00 44.65 3.51
77 78 0.734309 TTGTTCGATAGCTCGCCGTA 59.266 50.000 0.00 0.00 44.65 4.02
78 79 0.525668 CTTGTTCGATAGCTCGCCGT 60.526 55.000 0.00 0.00 44.65 5.68
79 80 1.812214 GCTTGTTCGATAGCTCGCCG 61.812 60.000 0.00 0.00 44.65 6.46
80 81 1.812214 CGCTTGTTCGATAGCTCGCC 61.812 60.000 11.39 0.00 44.65 5.54
81 82 1.555538 CGCTTGTTCGATAGCTCGC 59.444 57.895 11.39 0.00 44.65 5.03
82 83 0.248498 TCCGCTTGTTCGATAGCTCG 60.248 55.000 11.39 0.00 46.41 5.03
83 84 1.482278 CTCCGCTTGTTCGATAGCTC 58.518 55.000 11.39 0.00 35.25 4.09
84 85 0.103208 CCTCCGCTTGTTCGATAGCT 59.897 55.000 11.39 0.00 35.25 3.32
85 86 0.876342 CCCTCCGCTTGTTCGATAGC 60.876 60.000 5.01 5.01 0.00 2.97
86 87 0.249489 CCCCTCCGCTTGTTCGATAG 60.249 60.000 0.00 0.00 0.00 2.08
87 88 1.820581 CCCCTCCGCTTGTTCGATA 59.179 57.895 0.00 0.00 0.00 2.92
88 89 2.584608 CCCCTCCGCTTGTTCGAT 59.415 61.111 0.00 0.00 0.00 3.59
89 90 4.388499 GCCCCTCCGCTTGTTCGA 62.388 66.667 0.00 0.00 0.00 3.71
90 91 4.394712 AGCCCCTCCGCTTGTTCG 62.395 66.667 0.00 0.00 34.73 3.95
91 92 2.747855 CAGCCCCTCCGCTTGTTC 60.748 66.667 0.00 0.00 36.82 3.18
92 93 4.351054 CCAGCCCCTCCGCTTGTT 62.351 66.667 0.00 0.00 36.82 2.83
109 110 1.003718 GCCGTATGTAGATGCCCCC 60.004 63.158 0.00 0.00 0.00 5.40
110 111 1.374252 CGCCGTATGTAGATGCCCC 60.374 63.158 0.00 0.00 0.00 5.80
111 112 1.374252 CCGCCGTATGTAGATGCCC 60.374 63.158 0.00 0.00 0.00 5.36
112 113 1.374252 CCCGCCGTATGTAGATGCC 60.374 63.158 0.00 0.00 0.00 4.40
113 114 1.374252 CCCCGCCGTATGTAGATGC 60.374 63.158 0.00 0.00 0.00 3.91
114 115 0.243907 CTCCCCGCCGTATGTAGATG 59.756 60.000 0.00 0.00 0.00 2.90
115 116 0.178970 ACTCCCCGCCGTATGTAGAT 60.179 55.000 0.00 0.00 0.00 1.98
116 117 1.105167 CACTCCCCGCCGTATGTAGA 61.105 60.000 0.00 0.00 0.00 2.59
117 118 1.362717 CACTCCCCGCCGTATGTAG 59.637 63.158 0.00 0.00 0.00 2.74
118 119 2.788640 GCACTCCCCGCCGTATGTA 61.789 63.158 0.00 0.00 0.00 2.29
119 120 4.157120 GCACTCCCCGCCGTATGT 62.157 66.667 0.00 0.00 0.00 2.29
120 121 3.673956 TTGCACTCCCCGCCGTATG 62.674 63.158 0.00 0.00 0.00 2.39
121 122 3.395702 TTGCACTCCCCGCCGTAT 61.396 61.111 0.00 0.00 0.00 3.06
122 123 4.382320 GTTGCACTCCCCGCCGTA 62.382 66.667 0.00 0.00 0.00 4.02
128 129 4.660938 AAGCCCGTTGCACTCCCC 62.661 66.667 0.00 0.00 44.83 4.81
129 130 3.365265 CAAGCCCGTTGCACTCCC 61.365 66.667 0.00 0.00 44.83 4.30
130 131 2.281484 TCAAGCCCGTTGCACTCC 60.281 61.111 0.00 0.00 44.83 3.85
131 132 2.617274 GGTCAAGCCCGTTGCACTC 61.617 63.158 0.00 0.00 44.83 3.51
132 133 2.594592 GGTCAAGCCCGTTGCACT 60.595 61.111 0.00 0.00 44.83 4.40
141 142 2.764637 AATGGTCACGGGGTCAAGCC 62.765 60.000 0.00 0.00 0.00 4.35
142 143 0.893727 AAATGGTCACGGGGTCAAGC 60.894 55.000 0.00 0.00 0.00 4.01
143 144 0.881118 CAAATGGTCACGGGGTCAAG 59.119 55.000 0.00 0.00 0.00 3.02
144 145 0.538516 CCAAATGGTCACGGGGTCAA 60.539 55.000 0.00 0.00 0.00 3.18
145 146 1.074072 CCAAATGGTCACGGGGTCA 59.926 57.895 0.00 0.00 0.00 4.02
146 147 3.996614 CCAAATGGTCACGGGGTC 58.003 61.111 0.00 0.00 0.00 4.46
156 157 2.854522 GTCTCCGGTGACCAAATGG 58.145 57.895 23.20 0.00 42.17 3.16
299 300 3.055891 TGAATCCGTGATATGCGATGGAT 60.056 43.478 0.00 0.00 37.82 3.41
315 316 1.202114 TGCGGCACAAATCTTGAATCC 59.798 47.619 0.00 0.00 0.00 3.01
320 321 3.319755 AGAAAATGCGGCACAAATCTTG 58.680 40.909 4.03 0.00 0.00 3.02
353 354 9.829507 TGGAACACTATGAAATCAAACATTTTT 57.170 25.926 0.00 0.00 0.00 1.94
415 417 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
416 418 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
417 419 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
418 420 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
419 421 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
420 422 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
421 423 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
422 424 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
423 425 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
436 438 9.547753 GCATTGGAATCTCTACAAAGACTTATA 57.452 33.333 0.00 0.00 0.00 0.98
437 439 7.225538 CGCATTGGAATCTCTACAAAGACTTAT 59.774 37.037 0.00 0.00 0.00 1.73
438 440 6.535150 CGCATTGGAATCTCTACAAAGACTTA 59.465 38.462 0.00 0.00 0.00 2.24
439 441 5.352569 CGCATTGGAATCTCTACAAAGACTT 59.647 40.000 0.00 0.00 0.00 3.01
440 442 4.872691 CGCATTGGAATCTCTACAAAGACT 59.127 41.667 0.00 0.00 0.00 3.24
441 443 4.870426 TCGCATTGGAATCTCTACAAAGAC 59.130 41.667 0.00 0.00 0.00 3.01
442 444 5.084818 TCGCATTGGAATCTCTACAAAGA 57.915 39.130 0.00 0.00 0.00 2.52
443 445 5.352569 AGTTCGCATTGGAATCTCTACAAAG 59.647 40.000 0.00 0.00 0.00 2.77
444 446 5.245531 AGTTCGCATTGGAATCTCTACAAA 58.754 37.500 0.00 0.00 0.00 2.83
445 447 4.832248 AGTTCGCATTGGAATCTCTACAA 58.168 39.130 0.00 0.00 0.00 2.41
446 448 4.471904 AGTTCGCATTGGAATCTCTACA 57.528 40.909 0.00 0.00 0.00 2.74
447 449 5.348986 TGTAGTTCGCATTGGAATCTCTAC 58.651 41.667 0.00 0.00 0.00 2.59
448 450 5.592104 TGTAGTTCGCATTGGAATCTCTA 57.408 39.130 0.00 0.00 0.00 2.43
449 451 4.471904 TGTAGTTCGCATTGGAATCTCT 57.528 40.909 0.00 0.00 0.00 3.10
450 452 5.107837 CGTATGTAGTTCGCATTGGAATCTC 60.108 44.000 0.00 0.00 0.00 2.75
451 453 4.745125 CGTATGTAGTTCGCATTGGAATCT 59.255 41.667 0.00 0.00 0.00 2.40
452 454 4.084537 CCGTATGTAGTTCGCATTGGAATC 60.085 45.833 0.00 0.00 0.00 2.52
453 455 3.807622 CCGTATGTAGTTCGCATTGGAAT 59.192 43.478 0.00 0.00 0.00 3.01
454 456 3.119065 TCCGTATGTAGTTCGCATTGGAA 60.119 43.478 0.00 0.00 31.35 3.53
455 457 2.427812 TCCGTATGTAGTTCGCATTGGA 59.572 45.455 0.00 0.00 31.61 3.53
456 458 2.794910 CTCCGTATGTAGTTCGCATTGG 59.205 50.000 0.00 0.00 0.00 3.16
457 459 2.218759 GCTCCGTATGTAGTTCGCATTG 59.781 50.000 0.00 0.00 0.00 2.82
458 460 2.159156 TGCTCCGTATGTAGTTCGCATT 60.159 45.455 0.00 0.00 0.00 3.56
459 461 1.407618 TGCTCCGTATGTAGTTCGCAT 59.592 47.619 0.00 0.00 0.00 4.73
460 462 0.812549 TGCTCCGTATGTAGTTCGCA 59.187 50.000 0.00 0.00 0.00 5.10
461 463 1.917273 TTGCTCCGTATGTAGTTCGC 58.083 50.000 0.00 0.00 0.00 4.70
462 464 4.565166 TCATTTTGCTCCGTATGTAGTTCG 59.435 41.667 0.00 0.00 0.00 3.95
463 465 6.604735 ATCATTTTGCTCCGTATGTAGTTC 57.395 37.500 0.00 0.00 0.00 3.01
464 466 6.597672 TCAATCATTTTGCTCCGTATGTAGTT 59.402 34.615 0.00 0.00 0.00 2.24
465 467 6.112734 TCAATCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
466 468 6.603237 TCAATCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
467 469 6.993786 TTCAATCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
468 470 5.895636 TTCAATCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
547 549 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
548 550 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
549 551 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
550 552 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
551 553 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
552 554 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
553 555 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
554 556 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
556 558 9.638176 GATATACTCCCTCCGTTCCTAAATATA 57.362 37.037 0.00 0.00 0.00 0.86
557 559 8.120538 TGATATACTCCCTCCGTTCCTAAATAT 58.879 37.037 0.00 0.00 0.00 1.28
558 560 7.472741 TGATATACTCCCTCCGTTCCTAAATA 58.527 38.462 0.00 0.00 0.00 1.40
559 561 6.320518 TGATATACTCCCTCCGTTCCTAAAT 58.679 40.000 0.00 0.00 0.00 1.40
560 562 5.708544 TGATATACTCCCTCCGTTCCTAAA 58.291 41.667 0.00 0.00 0.00 1.85
561 563 5.329191 TGATATACTCCCTCCGTTCCTAA 57.671 43.478 0.00 0.00 0.00 2.69
562 564 5.531753 ATGATATACTCCCTCCGTTCCTA 57.468 43.478 0.00 0.00 0.00 2.94
563 565 3.897657 TGATATACTCCCTCCGTTCCT 57.102 47.619 0.00 0.00 0.00 3.36
564 566 6.154706 ACATTATGATATACTCCCTCCGTTCC 59.845 42.308 0.00 0.00 0.00 3.62
565 567 7.171630 ACATTATGATATACTCCCTCCGTTC 57.828 40.000 0.00 0.00 0.00 3.95
566 568 7.554959 AACATTATGATATACTCCCTCCGTT 57.445 36.000 0.00 0.00 0.00 4.44
567 569 7.554959 AAACATTATGATATACTCCCTCCGT 57.445 36.000 0.00 0.00 0.00 4.69
568 570 7.878127 ACAAAACATTATGATATACTCCCTCCG 59.122 37.037 0.00 0.00 0.00 4.63
569 571 9.574516 AACAAAACATTATGATATACTCCCTCC 57.425 33.333 0.00 0.00 0.00 4.30
571 573 9.920946 ACAACAAAACATTATGATATACTCCCT 57.079 29.630 0.00 0.00 0.00 4.20
572 574 9.950680 CACAACAAAACATTATGATATACTCCC 57.049 33.333 0.00 0.00 0.00 4.30
610 612 6.372659 CCACTTGAAATATGTGCACTCTTACT 59.627 38.462 19.41 0.00 34.14 2.24
611 613 6.371548 TCCACTTGAAATATGTGCACTCTTAC 59.628 38.462 19.41 6.04 34.14 2.34
644 646 7.219535 AGTGTGACGTAATATTTCGTGATGTAC 59.780 37.037 22.48 14.61 40.39 2.90
645 647 7.252708 AGTGTGACGTAATATTTCGTGATGTA 58.747 34.615 22.48 5.07 40.39 2.29
646 648 6.097356 AGTGTGACGTAATATTTCGTGATGT 58.903 36.000 22.48 2.49 40.39 3.06
650 652 5.944135 CGAAAGTGTGACGTAATATTTCGTG 59.056 40.000 22.48 3.68 41.33 4.35
662 664 4.090066 CCTATCTTGTTCGAAAGTGTGACG 59.910 45.833 0.00 0.00 0.00 4.35
665 667 3.125316 GCCCTATCTTGTTCGAAAGTGTG 59.875 47.826 0.00 0.00 0.00 3.82
673 675 2.122783 TTTGGGCCCTATCTTGTTCG 57.877 50.000 25.70 0.00 0.00 3.95
720 722 5.106555 TGTTTCTTTCGATCTGATGCTTTCC 60.107 40.000 0.00 0.00 0.00 3.13
772 774 8.850452 GCGAAATCTTCTTTATTTTTGACGAAT 58.150 29.630 0.00 0.00 0.00 3.34
773 775 7.858382 TGCGAAATCTTCTTTATTTTTGACGAA 59.142 29.630 0.00 0.00 0.00 3.85
774 776 7.356540 TGCGAAATCTTCTTTATTTTTGACGA 58.643 30.769 0.00 0.00 0.00 4.20
775 777 7.547285 TGCGAAATCTTCTTTATTTTTGACG 57.453 32.000 0.00 0.00 0.00 4.35
783 845 8.598075 GCATTTCAATTGCGAAATCTTCTTTAT 58.402 29.630 0.00 0.00 42.36 1.40
784 846 7.598118 TGCATTTCAATTGCGAAATCTTCTTTA 59.402 29.630 0.00 0.00 42.36 1.85
785 847 6.424509 TGCATTTCAATTGCGAAATCTTCTTT 59.575 30.769 0.00 0.00 42.36 2.52
796 858 6.592166 AGTATGTTTTTGCATTTCAATTGCG 58.408 32.000 0.00 0.00 34.12 4.85
821 883 9.601810 TGCTCCCTCCGTATCATAATATAATAT 57.398 33.333 0.00 0.00 0.00 1.28
887 949 3.154827 TGTCTGGTTGGGAGAATTTCC 57.845 47.619 0.00 0.00 46.00 3.13
897 959 0.240945 GATGCCGTTTGTCTGGTTGG 59.759 55.000 0.00 0.00 0.00 3.77
954 1062 5.615818 CGTACACGGTACAGTACTGACTGA 61.616 50.000 29.30 8.49 44.73 3.41
958 1066 2.766313 ACGTACACGGTACAGTACTGA 58.234 47.619 29.30 10.19 44.95 3.41
965 1073 2.284150 GCGATAGTACGTACACGGTACA 59.716 50.000 26.55 4.03 40.85 2.90
966 1074 2.284150 TGCGATAGTACGTACACGGTAC 59.716 50.000 26.55 15.28 40.85 3.34
967 1075 2.539688 CTGCGATAGTACGTACACGGTA 59.460 50.000 26.55 11.23 40.85 4.02
968 1076 1.328680 CTGCGATAGTACGTACACGGT 59.671 52.381 26.55 9.30 40.85 4.83
969 1077 1.333524 CCTGCGATAGTACGTACACGG 60.334 57.143 26.55 13.69 40.85 4.94
970 1078 1.918974 GCCTGCGATAGTACGTACACG 60.919 57.143 26.55 25.28 41.88 4.49
971 1079 1.598924 GGCCTGCGATAGTACGTACAC 60.599 57.143 26.55 15.82 39.35 2.90
1052 1165 3.052620 GCTGCGCTCGTCAGGTAGA 62.053 63.158 9.73 0.00 32.41 2.59
1641 1783 2.032681 GAGACGTTGGGCTTGGCT 59.967 61.111 0.00 0.00 0.00 4.75
2169 2333 0.670546 CGTTGAAGATCACCGTGGCT 60.671 55.000 0.00 0.00 27.32 4.75
2270 2434 1.306654 AACTCCACCGCCCTATCCA 60.307 57.895 0.00 0.00 0.00 3.41
2521 2691 4.466827 ACAAGATAGGATTGCATGCATGA 58.533 39.130 30.64 10.92 0.00 3.07
2568 2759 2.660236 GGATCGTCGACACTGTGTAAAC 59.340 50.000 14.31 13.30 0.00 2.01
2576 2767 1.405821 GGAATCAGGATCGTCGACACT 59.594 52.381 17.16 4.82 0.00 3.55
2579 2770 2.873133 AAGGAATCAGGATCGTCGAC 57.127 50.000 5.18 5.18 0.00 4.20
2584 2775 1.341531 ACGCCTAAGGAATCAGGATCG 59.658 52.381 0.00 0.00 33.42 3.69
2585 2776 2.608261 CGACGCCTAAGGAATCAGGATC 60.608 54.545 0.00 0.00 33.42 3.36
2589 2780 1.209275 CGCGACGCCTAAGGAATCAG 61.209 60.000 15.34 0.00 0.00 2.90
2590 2781 1.226859 CGCGACGCCTAAGGAATCA 60.227 57.895 15.34 0.00 0.00 2.57
2685 2920 1.759994 CTGCTAGCGTCTATGTTCCG 58.240 55.000 10.77 0.00 0.00 4.30
2754 2993 7.575414 TGACTGTCTTTATTTGGCTTGTAAA 57.425 32.000 9.51 0.00 0.00 2.01
2826 3067 7.030075 TGATGATTCGCATTTGTGATATTGT 57.970 32.000 0.00 0.00 37.34 2.71
2845 3086 2.460669 TGCTAGCTCTGGTCTTGATGA 58.539 47.619 17.23 0.00 0.00 2.92
2853 3094 1.338200 CCTCGTTTTGCTAGCTCTGGT 60.338 52.381 17.23 0.00 0.00 4.00
2857 3098 1.066787 ACCTCCTCGTTTTGCTAGCTC 60.067 52.381 17.23 3.23 0.00 4.09
2869 3111 1.142748 GCACCATGAGACCTCCTCG 59.857 63.158 0.00 0.00 44.92 4.63
2957 3199 1.207089 CTGGGGAAGAAGCGTGACATA 59.793 52.381 0.00 0.00 0.00 2.29
3056 3298 3.249080 TCTGGACGGTTCGAAACAAAATC 59.751 43.478 14.64 4.71 0.00 2.17


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

AutoCloner maintained by Alex Coulton.