Multiple sequence alignment - TraesCS2B01G087300

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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 TraesCS2B01G087300 chr2B 100.000 7387 0 0 1 7387 49335563 49328177 0.000000e+00 13642.0
1 TraesCS2B01G087300 chr2B 96.521 1897 55 8 3054 4945 48039100 48040990 0.000000e+00 3127.0
2 TraesCS2B01G087300 chr2B 95.501 1756 72 6 5233 6986 48040987 48042737 0.000000e+00 2798.0
3 TraesCS2B01G087300 chr2B 92.048 1094 49 9 944 2014 48030940 48032018 0.000000e+00 1504.0
4 TraesCS2B01G087300 chr2B 96.524 489 15 1 2487 2973 48037556 48038044 0.000000e+00 808.0
5 TraesCS2B01G087300 chr2B 88.853 619 42 16 328 933 48024283 48024887 0.000000e+00 736.0
6 TraesCS2B01G087300 chr2B 98.433 319 4 1 7069 7387 48042913 48043230 1.800000e-155 560.0
7 TraesCS2B01G087300 chr2B 84.615 351 20 8 1 336 48012002 48012333 1.200000e-82 318.0
8 TraesCS2B01G087300 chr2B 97.701 87 2 0 6988 7074 48042774 48042860 4.620000e-32 150.0
9 TraesCS2B01G087300 chr2D 95.519 2767 88 21 2190 4945 29876395 29879136 0.000000e+00 4390.0
10 TraesCS2B01G087300 chr2D 96.227 2041 45 9 3 2013 29874363 29876401 0.000000e+00 3314.0
11 TraesCS2B01G087300 chr2D 97.350 1321 33 2 5321 6641 29879173 29880491 0.000000e+00 2244.0
12 TraesCS2B01G087300 chr2D 89.218 1484 140 14 5321 6797 29843495 29844965 0.000000e+00 1836.0
13 TraesCS2B01G087300 chr2D 78.409 968 187 14 5349 6314 29744349 29745296 1.760000e-170 610.0
14 TraesCS2B01G087300 chr2D 77.634 1006 201 14 5349 6351 29745978 29746962 2.300000e-164 590.0
15 TraesCS2B01G087300 chr2D 78.372 860 139 31 3601 4439 29841638 29842471 1.420000e-141 514.0
16 TraesCS2B01G087300 chr2D 84.280 528 64 14 2188 2710 22143531 22143018 1.430000e-136 497.0
17 TraesCS2B01G087300 chr2D 78.086 794 140 24 912 1691 29740108 29740881 8.680000e-129 472.0
18 TraesCS2B01G087300 chr2D 76.184 781 141 26 912 1669 29836604 29837362 3.260000e-98 370.0
19 TraesCS2B01G087300 chr2D 87.055 309 26 6 6690 6986 29880485 29880791 3.300000e-88 337.0
20 TraesCS2B01G087300 chr2D 94.118 187 11 0 7188 7374 29881469 29881655 1.210000e-72 285.0
21 TraesCS2B01G087300 chr2A 90.008 1261 120 4 5321 6577 31977779 31979037 0.000000e+00 1626.0
22 TraesCS2B01G087300 chr2A 78.579 971 180 17 5349 6314 31956954 31957901 3.790000e-172 616.0
23 TraesCS2B01G087300 chr2A 93.510 416 23 4 6571 6986 31979724 31980135 3.790000e-172 616.0
24 TraesCS2B01G087300 chr2A 78.539 876 135 31 3601 4449 31975998 31976847 1.830000e-145 527.0
25 TraesCS2B01G087300 chr2A 78.304 802 140 16 906 1686 31952705 31953493 3.100000e-133 486.0
26 TraesCS2B01G087300 chr2A 78.326 729 146 6 5623 6351 31938107 31938823 1.880000e-125 460.0
27 TraesCS2B01G087300 chr2A 77.692 780 134 31 912 1669 31970445 31971206 2.450000e-119 440.0
28 TraesCS2B01G087300 chr2A 86.816 402 28 15 6988 7386 31980172 31980551 6.850000e-115 425.0
29 TraesCS2B01G087300 chr2A 94.180 189 11 0 2008 2196 72943260 72943072 9.380000e-74 289.0
30 TraesCS2B01G087300 chr7D 83.616 531 67 16 2188 2708 427896667 427897187 1.440000e-131 481.0
31 TraesCS2B01G087300 chrUn 82.543 527 77 12 2188 2708 69380440 69379923 4.060000e-122 449.0
32 TraesCS2B01G087300 chrUn 77.228 303 61 7 3648 3944 12630895 12631195 3.540000e-38 171.0
33 TraesCS2B01G087300 chrUn 76.568 303 63 7 3648 3944 306910083 306910383 7.670000e-35 159.0
34 TraesCS2B01G087300 chr6A 82.364 533 79 9 2187 2710 20761223 20761749 4.060000e-122 449.0
35 TraesCS2B01G087300 chr6A 81.767 532 82 9 2187 2710 20794081 20794605 1.470000e-116 431.0
36 TraesCS2B01G087300 chr6A 90.615 309 25 4 4933 5239 472393953 472393647 2.480000e-109 407.0
37 TraesCS2B01G087300 chr6D 82.331 532 79 11 2188 2711 395387575 395387051 1.460000e-121 448.0
38 TraesCS2B01G087300 chr6D 80.734 109 12 5 1915 2014 395387676 395387568 7.950000e-10 76.8
39 TraesCS2B01G087300 chr7A 82.634 524 71 15 2189 2706 715770432 715769923 5.260000e-121 446.0
40 TraesCS2B01G087300 chr7B 82.061 524 73 15 2189 2706 717209467 717208959 1.900000e-115 427.0
41 TraesCS2B01G087300 chr7B 92.568 296 22 0 4943 5238 655574515 655574220 6.850000e-115 425.0
42 TraesCS2B01G087300 chr7B 92.462 199 12 3 2007 2202 662001445 662001643 1.570000e-71 281.0
43 TraesCS2B01G087300 chr3A 91.468 293 23 2 4945 5237 733914174 733914464 1.150000e-107 401.0
44 TraesCS2B01G087300 chr3A 90.940 298 25 2 4945 5242 733909344 733909639 4.150000e-107 399.0
45 TraesCS2B01G087300 chr3A 90.940 298 25 2 4945 5242 733912439 733912734 4.150000e-107 399.0
46 TraesCS2B01G087300 chr3A 90.698 301 25 3 4943 5243 724026983 724026686 1.490000e-106 398.0
47 TraesCS2B01G087300 chr1A 91.126 293 24 2 4945 5237 185148084 185148374 5.370000e-106 396.0
48 TraesCS2B01G087300 chr1A 91.126 293 24 2 4945 5237 586267091 586266801 5.370000e-106 396.0
49 TraesCS2B01G087300 chr6B 90.847 295 25 2 4943 5237 504368171 504367879 1.930000e-105 394.0
50 TraesCS2B01G087300 chr6B 94.301 193 10 1 2005 2196 19921074 19921266 2.020000e-75 294.0
51 TraesCS2B01G087300 chr4A 94.241 191 9 2 2007 2195 662621179 662620989 2.610000e-74 291.0
52 TraesCS2B01G087300 chr3B 93.401 197 11 2 2004 2198 779136176 779136372 2.610000e-74 291.0
53 TraesCS2B01G087300 chr3B 94.180 189 10 1 2007 2195 702842254 702842067 3.370000e-73 287.0
54 TraesCS2B01G087300 chr3B 94.149 188 11 0 2006 2193 758070260 758070447 3.370000e-73 287.0
55 TraesCS2B01G087300 chr3B 93.684 190 12 0 2005 2194 117710109 117710298 1.210000e-72 285.0
56 TraesCS2B01G087300 chr1B 94.180 189 11 0 2007 2195 670172553 670172365 9.380000e-74 289.0


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 TraesCS2B01G087300 chr2B 49328177 49335563 7386 True 13642.000000 13642 100.00000 1 7387 1 chr2B.!!$R1 7386
1 TraesCS2B01G087300 chr2B 48030940 48032018 1078 False 1504.000000 1504 92.04800 944 2014 1 chr2B.!!$F3 1070
2 TraesCS2B01G087300 chr2B 48037556 48043230 5674 False 1488.600000 3127 96.93600 2487 7387 5 chr2B.!!$F4 4900
3 TraesCS2B01G087300 chr2B 48024283 48024887 604 False 736.000000 736 88.85300 328 933 1 chr2B.!!$F2 605
4 TraesCS2B01G087300 chr2D 29874363 29881655 7292 False 2114.000000 4390 94.05380 3 7374 5 chr2D.!!$F4 7371
5 TraesCS2B01G087300 chr2D 29841638 29844965 3327 False 1175.000000 1836 83.79500 3601 6797 2 chr2D.!!$F3 3196
6 TraesCS2B01G087300 chr2D 29740108 29746962 6854 False 557.333333 610 78.04300 912 6351 3 chr2D.!!$F2 5439
7 TraesCS2B01G087300 chr2D 22143018 22143531 513 True 497.000000 497 84.28000 2188 2710 1 chr2D.!!$R1 522
8 TraesCS2B01G087300 chr2D 29836604 29837362 758 False 370.000000 370 76.18400 912 1669 1 chr2D.!!$F1 757
9 TraesCS2B01G087300 chr2A 31975998 31980551 4553 False 798.500000 1626 87.21825 3601 7386 4 chr2A.!!$F4 3785
10 TraesCS2B01G087300 chr2A 31952705 31957901 5196 False 551.000000 616 78.44150 906 6314 2 chr2A.!!$F3 5408
11 TraesCS2B01G087300 chr2A 31938107 31938823 716 False 460.000000 460 78.32600 5623 6351 1 chr2A.!!$F1 728
12 TraesCS2B01G087300 chr2A 31970445 31971206 761 False 440.000000 440 77.69200 912 1669 1 chr2A.!!$F2 757
13 TraesCS2B01G087300 chr7D 427896667 427897187 520 False 481.000000 481 83.61600 2188 2708 1 chr7D.!!$F1 520
14 TraesCS2B01G087300 chrUn 69379923 69380440 517 True 449.000000 449 82.54300 2188 2708 1 chrUn.!!$R1 520
15 TraesCS2B01G087300 chr6A 20761223 20761749 526 False 449.000000 449 82.36400 2187 2710 1 chr6A.!!$F1 523
16 TraesCS2B01G087300 chr6A 20794081 20794605 524 False 431.000000 431 81.76700 2187 2710 1 chr6A.!!$F2 523
17 TraesCS2B01G087300 chr6D 395387051 395387676 625 True 262.400000 448 81.53250 1915 2711 2 chr6D.!!$R1 796
18 TraesCS2B01G087300 chr7A 715769923 715770432 509 True 446.000000 446 82.63400 2189 2706 1 chr7A.!!$R1 517
19 TraesCS2B01G087300 chr7B 717208959 717209467 508 True 427.000000 427 82.06100 2189 2706 1 chr7B.!!$R2 517
20 TraesCS2B01G087300 chr3A 733909344 733914464 5120 False 399.666667 401 91.11600 4945 5242 3 chr3A.!!$F1 297

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
777 810 0.984230 GGTTCCACCATGACCTCTGA 59.016 55.000 0.00 0.0 38.42 3.27 F
1409 1476 0.321210 AATGTGTTCACGGCCATCGA 60.321 50.000 2.24 0.0 42.43 3.59 F
2112 2196 0.179207 GATGCGTGTGTGCTGACATG 60.179 55.000 0.00 0.0 36.16 3.21 F
2385 2477 0.467659 CACCCCACCACCCGTAAAAA 60.468 55.000 0.00 0.0 0.00 1.94 F
2788 2896 1.619654 TGTTGGAACATGGCAGAAGG 58.380 50.000 0.00 0.0 39.30 3.46 F
3098 4181 1.902938 AGAGCAGGACCTTCTTTTGC 58.097 50.000 0.00 0.0 35.09 3.68 F
3475 6145 2.216046 CTTGTGTGCATGTGTGAGAGT 58.784 47.619 0.00 0.0 0.00 3.24 F
4978 8661 0.450184 GCACGTTGTTGCGGGAATAT 59.550 50.000 0.00 0.0 37.48 1.28 F
5615 12365 0.739462 TCGCCGTGAAATGCTCGATT 60.739 50.000 0.00 0.0 35.64 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2177 0.179207 CATGTCAGCACACACGCATC 60.179 55.000 0.00 0.00 34.48 3.91 R
3098 4181 2.483876 TCGCAGGAGAGTTTGAAACAG 58.516 47.619 11.02 0.00 0.00 3.16 R
3475 6145 1.070601 CTATGCGATGTCACCCATCCA 59.929 52.381 0.00 0.00 46.10 3.41 R
3811 6507 2.315038 GTGCTAGCACAAGCGCCATC 62.315 60.000 36.93 10.67 45.26 3.51 R
4410 7484 4.065789 GAGCATTACCTATTACTGCCACC 58.934 47.826 0.00 0.00 37.11 4.61 R
4943 8626 0.679505 GTGCGGGGCATCATCTAGTA 59.320 55.000 0.00 0.00 41.91 1.82 R
5166 9013 1.179152 CAAGCATGCCACCTCATCAA 58.821 50.000 15.66 0.00 0.00 2.57 R
6281 15476 1.003839 GGGCCTGTCGTTCACATCA 60.004 57.895 0.84 0.00 33.23 3.07 R
6986 16892 3.308688 GGATGCATAAGGGATGGTGCTAT 60.309 47.826 0.00 0.00 38.37 2.97 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
119 128 7.264221 ACATGTTTTATGTTTGCTGTTTCAGA 58.736 30.769 0.00 0.00 32.44 3.27
125 134 7.985634 TTATGTTTGCTGTTTCAGAAACTTC 57.014 32.000 23.57 16.03 41.90 3.01
132 141 5.030936 GCTGTTTCAGAAACTTCACAAGAC 58.969 41.667 23.57 7.27 41.90 3.01
173 182 8.927675 AAACAAATAGTGACCTATAAACCACA 57.072 30.769 0.00 0.00 32.57 4.17
198 207 7.010160 AGTCCAATTTCCTCCATAAGAAAACA 58.990 34.615 0.00 0.00 35.72 2.83
206 215 7.847711 TCCTCCATAAGAAAACATCCAAAAA 57.152 32.000 0.00 0.00 0.00 1.94
337 354 3.935818 TTAGAACTGTTGGGGACACAA 57.064 42.857 0.00 0.00 42.67 3.33
338 355 4.447138 TTAGAACTGTTGGGGACACAAT 57.553 40.909 0.00 0.00 42.67 2.71
388 405 1.277842 TGCTTGAAGGACGCTTGGATA 59.722 47.619 0.00 0.00 0.00 2.59
580 605 5.369409 AATCACTCACATCAGGTCATCAT 57.631 39.130 0.00 0.00 0.00 2.45
662 695 5.081032 ACCTGCTCTTTTACTAGTGACTCT 58.919 41.667 5.39 0.00 0.00 3.24
777 810 0.984230 GGTTCCACCATGACCTCTGA 59.016 55.000 0.00 0.00 38.42 3.27
835 868 3.910627 AGGTCGCCATAGGGATTAATTCT 59.089 43.478 0.00 0.00 37.29 2.40
989 1029 2.499685 GAGGCCGTGCGTCCTAAT 59.500 61.111 0.00 0.00 37.46 1.73
1409 1476 0.321210 AATGTGTTCACGGCCATCGA 60.321 50.000 2.24 0.00 42.43 3.59
1626 1693 0.603707 CACGTCCTGTGTCTGGCAAT 60.604 55.000 0.00 0.00 43.88 3.56
1674 1741 2.165319 AAGGCTGGTACGTGAAGAAC 57.835 50.000 0.00 0.00 0.00 3.01
1677 1744 2.104281 AGGCTGGTACGTGAAGAACTTT 59.896 45.455 0.00 0.00 0.00 2.66
1678 1745 2.876550 GGCTGGTACGTGAAGAACTTTT 59.123 45.455 0.00 0.00 0.00 2.27
1679 1746 3.059120 GGCTGGTACGTGAAGAACTTTTC 60.059 47.826 0.00 0.00 0.00 2.29
1680 1747 3.059120 GCTGGTACGTGAAGAACTTTTCC 60.059 47.826 0.00 0.00 0.00 3.13
1684 1759 5.648960 TGGTACGTGAAGAACTTTTCCTTTT 59.351 36.000 0.00 0.00 0.00 2.27
2034 2118 7.573968 AAAACAGTTTTGCTAGAACTCATCT 57.426 32.000 10.62 0.00 42.48 2.90
2035 2119 8.677148 AAAACAGTTTTGCTAGAACTCATCTA 57.323 30.769 10.62 0.00 39.71 1.98
2063 2147 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
2064 2148 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
2065 2149 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
2066 2150 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
2072 2156 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
2073 2157 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
2074 2158 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
2075 2159 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
2076 2160 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
2077 2161 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
2078 2162 7.067494 GTCTCATTCACCTTTTATAGCCATTGT 59.933 37.037 0.00 0.00 0.00 2.71
2079 2163 8.271458 TCTCATTCACCTTTTATAGCCATTGTA 58.729 33.333 0.00 0.00 0.00 2.41
2080 2164 8.995027 TCATTCACCTTTTATAGCCATTGTAT 57.005 30.769 0.00 0.00 0.00 2.29
2081 2165 8.849168 TCATTCACCTTTTATAGCCATTGTATG 58.151 33.333 0.00 0.00 0.00 2.39
2082 2166 8.632679 CATTCACCTTTTATAGCCATTGTATGT 58.367 33.333 0.00 0.00 0.00 2.29
2083 2167 7.566760 TCACCTTTTATAGCCATTGTATGTG 57.433 36.000 0.00 0.00 0.00 3.21
2084 2168 7.342581 TCACCTTTTATAGCCATTGTATGTGA 58.657 34.615 0.00 0.00 0.00 3.58
2085 2169 7.998383 TCACCTTTTATAGCCATTGTATGTGAT 59.002 33.333 0.00 0.00 0.00 3.06
2086 2170 8.077991 CACCTTTTATAGCCATTGTATGTGATG 58.922 37.037 0.00 0.00 0.00 3.07
2087 2171 7.086376 CCTTTTATAGCCATTGTATGTGATGC 58.914 38.462 0.00 0.00 0.00 3.91
2088 2172 7.040201 CCTTTTATAGCCATTGTATGTGATGCT 60.040 37.037 0.00 0.00 0.00 3.79
2089 2173 8.916628 TTTTATAGCCATTGTATGTGATGCTA 57.083 30.769 0.00 0.00 0.00 3.49
2090 2174 9.519191 TTTTATAGCCATTGTATGTGATGCTAT 57.481 29.630 0.00 0.00 32.56 2.97
2093 2177 8.728337 ATAGCCATTGTATGTGATGCTATAAG 57.272 34.615 0.00 0.00 0.00 1.73
2094 2178 6.772605 AGCCATTGTATGTGATGCTATAAGA 58.227 36.000 0.00 0.00 0.00 2.10
2095 2179 7.400439 AGCCATTGTATGTGATGCTATAAGAT 58.600 34.615 0.00 0.00 0.00 2.40
2096 2180 7.336176 AGCCATTGTATGTGATGCTATAAGATG 59.664 37.037 0.00 0.00 0.00 2.90
2097 2181 7.470079 CCATTGTATGTGATGCTATAAGATGC 58.530 38.462 0.00 0.00 0.00 3.91
2098 2182 6.710692 TTGTATGTGATGCTATAAGATGCG 57.289 37.500 0.00 0.00 0.00 4.73
2099 2183 5.783111 TGTATGTGATGCTATAAGATGCGT 58.217 37.500 0.00 0.00 0.00 5.24
2100 2184 5.634859 TGTATGTGATGCTATAAGATGCGTG 59.365 40.000 0.00 0.00 0.00 5.34
2101 2185 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
2102 2186 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
2103 2187 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
2104 2188 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
2105 2189 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
2106 2190 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
2107 2191 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
2108 2192 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
2109 2193 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
2110 2194 0.532640 AAGATGCGTGTGTGCTGACA 60.533 50.000 0.00 0.00 35.36 3.58
2111 2195 0.321034 AGATGCGTGTGTGCTGACAT 60.321 50.000 0.00 0.00 33.63 3.06
2112 2196 0.179207 GATGCGTGTGTGCTGACATG 60.179 55.000 0.00 0.00 36.16 3.21
2113 2197 0.603439 ATGCGTGTGTGCTGACATGA 60.603 50.000 0.00 0.00 35.21 3.07
2114 2198 1.223417 TGCGTGTGTGCTGACATGAG 61.223 55.000 0.00 0.00 35.21 2.90
2115 2199 1.224069 GCGTGTGTGCTGACATGAGT 61.224 55.000 0.00 0.00 35.21 3.41
2116 2200 1.220529 CGTGTGTGCTGACATGAGTT 58.779 50.000 0.00 0.00 35.21 3.01
2117 2201 1.070376 CGTGTGTGCTGACATGAGTTG 60.070 52.381 0.00 0.00 35.21 3.16
2118 2202 1.942657 GTGTGTGCTGACATGAGTTGT 59.057 47.619 0.00 0.00 42.79 3.32
2119 2203 3.130633 GTGTGTGCTGACATGAGTTGTA 58.869 45.455 0.00 0.00 39.18 2.41
2120 2204 3.748048 GTGTGTGCTGACATGAGTTGTAT 59.252 43.478 0.00 0.00 39.18 2.29
2121 2205 3.996363 TGTGTGCTGACATGAGTTGTATC 59.004 43.478 0.00 0.00 39.18 2.24
2122 2206 4.248859 GTGTGCTGACATGAGTTGTATCT 58.751 43.478 0.00 0.00 39.18 1.98
2123 2207 4.092529 GTGTGCTGACATGAGTTGTATCTG 59.907 45.833 0.00 0.00 39.18 2.90
2124 2208 4.248859 GTGCTGACATGAGTTGTATCTGT 58.751 43.478 0.00 0.00 39.18 3.41
2125 2209 4.692625 GTGCTGACATGAGTTGTATCTGTT 59.307 41.667 0.00 0.00 39.18 3.16
2126 2210 4.931601 TGCTGACATGAGTTGTATCTGTTC 59.068 41.667 0.00 0.00 39.18 3.18
2127 2211 5.174395 GCTGACATGAGTTGTATCTGTTCT 58.826 41.667 0.00 0.00 39.18 3.01
2128 2212 5.641209 GCTGACATGAGTTGTATCTGTTCTT 59.359 40.000 0.00 0.00 39.18 2.52
2129 2213 6.401903 GCTGACATGAGTTGTATCTGTTCTTG 60.402 42.308 0.00 0.00 39.18 3.02
2130 2214 6.524734 TGACATGAGTTGTATCTGTTCTTGT 58.475 36.000 0.00 0.00 39.18 3.16
2131 2215 6.992123 TGACATGAGTTGTATCTGTTCTTGTT 59.008 34.615 0.00 0.00 39.18 2.83
2132 2216 7.498900 TGACATGAGTTGTATCTGTTCTTGTTT 59.501 33.333 0.00 0.00 39.18 2.83
2133 2217 8.225603 ACATGAGTTGTATCTGTTCTTGTTTT 57.774 30.769 0.00 0.00 36.57 2.43
2134 2218 8.345565 ACATGAGTTGTATCTGTTCTTGTTTTC 58.654 33.333 0.00 0.00 36.57 2.29
2135 2219 7.857734 TGAGTTGTATCTGTTCTTGTTTTCA 57.142 32.000 0.00 0.00 0.00 2.69
2136 2220 8.275015 TGAGTTGTATCTGTTCTTGTTTTCAA 57.725 30.769 0.00 0.00 38.21 2.69
2137 2221 8.902806 TGAGTTGTATCTGTTCTTGTTTTCAAT 58.097 29.630 0.00 0.00 39.22 2.57
2138 2222 9.173939 GAGTTGTATCTGTTCTTGTTTTCAATG 57.826 33.333 0.00 0.00 39.22 2.82
2139 2223 8.686334 AGTTGTATCTGTTCTTGTTTTCAATGT 58.314 29.630 0.00 0.00 39.22 2.71
2140 2224 8.745837 GTTGTATCTGTTCTTGTTTTCAATGTG 58.254 33.333 0.00 0.00 39.22 3.21
2141 2225 8.219546 TGTATCTGTTCTTGTTTTCAATGTGA 57.780 30.769 0.00 0.00 39.22 3.58
2142 2226 8.681806 TGTATCTGTTCTTGTTTTCAATGTGAA 58.318 29.630 0.00 0.00 39.22 3.18
2143 2227 9.683069 GTATCTGTTCTTGTTTTCAATGTGAAT 57.317 29.630 0.00 0.00 36.11 2.57
2144 2228 7.990541 TCTGTTCTTGTTTTCAATGTGAATG 57.009 32.000 0.00 0.00 36.11 2.67
2145 2229 7.770201 TCTGTTCTTGTTTTCAATGTGAATGA 58.230 30.769 0.00 0.00 36.11 2.57
2146 2230 7.916977 TCTGTTCTTGTTTTCAATGTGAATGAG 59.083 33.333 0.00 0.00 36.11 2.90
2147 2231 7.770201 TGTTCTTGTTTTCAATGTGAATGAGA 58.230 30.769 0.00 0.00 36.11 3.27
2148 2232 7.701924 TGTTCTTGTTTTCAATGTGAATGAGAC 59.298 33.333 0.00 0.00 36.11 3.36
2149 2233 6.738114 TCTTGTTTTCAATGTGAATGAGACC 58.262 36.000 0.00 0.00 36.11 3.85
2150 2234 6.320926 TCTTGTTTTCAATGTGAATGAGACCA 59.679 34.615 0.00 0.00 36.11 4.02
2151 2235 6.462552 TGTTTTCAATGTGAATGAGACCAA 57.537 33.333 0.00 0.00 36.11 3.67
2152 2236 6.871844 TGTTTTCAATGTGAATGAGACCAAA 58.128 32.000 0.00 0.00 36.11 3.28
2153 2237 7.499292 TGTTTTCAATGTGAATGAGACCAAAT 58.501 30.769 0.00 0.00 36.11 2.32
2154 2238 7.986320 TGTTTTCAATGTGAATGAGACCAAATT 59.014 29.630 0.00 0.00 36.11 1.82
2155 2239 9.474920 GTTTTCAATGTGAATGAGACCAAATTA 57.525 29.630 0.00 0.00 36.11 1.40
2281 2369 0.692756 TTATCCACCCCGCCATCTGA 60.693 55.000 0.00 0.00 0.00 3.27
2352 2444 8.208224 TCTATCATCGAAATTGCCCTTAAAGTA 58.792 33.333 0.00 0.00 0.00 2.24
2385 2477 0.467659 CACCCCACCACCCGTAAAAA 60.468 55.000 0.00 0.00 0.00 1.94
2511 2606 7.027161 ACACGCATTGAGGATGTATTAAAAAC 58.973 34.615 0.00 0.00 38.07 2.43
2722 2830 5.567037 TGCTAGTATATGCCAAAGGACAT 57.433 39.130 0.00 0.00 0.00 3.06
2788 2896 1.619654 TGTTGGAACATGGCAGAAGG 58.380 50.000 0.00 0.00 39.30 3.46
2973 3081 5.491982 AGTGTCTTTTCATGTACCAGATCC 58.508 41.667 0.00 0.00 0.00 3.36
2996 3104 4.266029 CAGCGCAACCATCACAATAAATTC 59.734 41.667 11.47 0.00 0.00 2.17
3052 4135 6.684897 ATATTCCAGGGATCTTCAGAAGAG 57.315 41.667 17.91 4.44 41.61 2.85
3098 4181 1.902938 AGAGCAGGACCTTCTTTTGC 58.097 50.000 0.00 0.00 35.09 3.68
3136 4219 8.365399 TCCTGCGAAAGAGTATGTAAAATATG 57.635 34.615 0.00 0.00 0.00 1.78
3152 4235 8.972127 TGTAAAATATGTATGCAAGCCCTAAAA 58.028 29.630 0.00 0.00 0.00 1.52
3299 4382 9.765795 CCTTCCTATAACTTAGTAATGAGGTTG 57.234 37.037 0.00 0.00 0.00 3.77
3302 4664 8.989131 TCCTATAACTTAGTAATGAGGTTGCTT 58.011 33.333 0.00 0.00 34.42 3.91
3352 6008 9.349713 AGAAAAGACATAGAAACATGTAACCAA 57.650 29.630 0.00 0.00 39.25 3.67
3355 6011 7.016153 AGACATAGAAACATGTAACCAAGGA 57.984 36.000 0.00 0.00 39.25 3.36
3430 6087 7.119846 CCTGAATAGGTTTGTCAGTTAAAGAGG 59.880 40.741 0.00 0.00 39.39 3.69
3475 6145 2.216046 CTTGTGTGCATGTGTGAGAGT 58.784 47.619 0.00 0.00 0.00 3.24
3811 6507 5.239525 GGGGATAACAATGAGAATCTTTCCG 59.760 44.000 0.00 0.00 34.92 4.30
3919 6618 4.097286 ACACCGGCAATCCATACATAAAAC 59.903 41.667 0.00 0.00 0.00 2.43
4082 6790 7.618502 ATTGCACGTTACCAGTATGAAAATA 57.381 32.000 0.00 0.00 39.69 1.40
4637 7768 7.224557 CACCTTCGAAAACATTTTCCTGAAATT 59.775 33.333 10.70 0.00 42.66 1.82
4942 8625 2.351706 AGACCCCGCTTGTTGTTAAA 57.648 45.000 0.00 0.00 0.00 1.52
4943 8626 2.871453 AGACCCCGCTTGTTGTTAAAT 58.129 42.857 0.00 0.00 0.00 1.40
4977 8660 1.870383 GCACGTTGTTGCGGGAATA 59.130 52.632 0.00 0.00 37.48 1.75
4978 8661 0.450184 GCACGTTGTTGCGGGAATAT 59.550 50.000 0.00 0.00 37.48 1.28
4982 8665 4.724303 CACGTTGTTGCGGGAATATTTTA 58.276 39.130 0.00 0.00 37.48 1.52
5005 8688 9.717942 TTTACAATATTTCAATGAGGTTTTGGG 57.282 29.630 0.00 0.00 0.00 4.12
5095 8942 8.682710 AGCATAACATAATGGAATTTTACGTGT 58.317 29.630 0.00 0.00 37.87 4.49
5105 8952 7.379098 TGGAATTTTACGTGTATGCATGTTA 57.621 32.000 14.10 2.17 41.71 2.41
5106 8953 7.817641 TGGAATTTTACGTGTATGCATGTTAA 58.182 30.769 14.10 8.62 41.71 2.01
5166 9013 4.284178 AGCCTTTTCCTATGCATGTTGAT 58.716 39.130 10.16 0.00 0.00 2.57
5178 9025 2.480759 GCATGTTGATTGATGAGGTGGC 60.481 50.000 0.00 0.00 0.00 5.01
5203 9050 5.886992 TGCTTGCATGTTGAGAGAAATATG 58.113 37.500 1.14 0.00 33.25 1.78
5267 9114 8.230472 AGACATAATTGTTTCTGGATCATTCC 57.770 34.615 0.00 0.00 38.22 3.01
5287 12037 5.798125 TCCAGAAATGGCAAAATGTTACA 57.202 34.783 0.00 0.00 0.00 2.41
5293 12043 7.114811 CAGAAATGGCAAAATGTTACAGTACAC 59.885 37.037 0.00 0.00 0.00 2.90
5301 12051 7.970061 GCAAAATGTTACAGTACACATCATCAT 59.030 33.333 0.00 0.00 32.21 2.45
5303 12053 9.844790 AAAATGTTACAGTACACATCATCATTG 57.155 29.630 0.00 0.00 32.21 2.82
5304 12054 6.421377 TGTTACAGTACACATCATCATTGC 57.579 37.500 0.00 0.00 0.00 3.56
5305 12055 5.936956 TGTTACAGTACACATCATCATTGCA 59.063 36.000 0.00 0.00 0.00 4.08
5307 12057 7.121020 TGTTACAGTACACATCATCATTGCATT 59.879 33.333 0.00 0.00 0.00 3.56
5309 12059 7.019774 ACAGTACACATCATCATTGCATTAC 57.980 36.000 0.00 0.00 0.00 1.89
5310 12060 6.598850 ACAGTACACATCATCATTGCATTACA 59.401 34.615 0.00 0.00 0.00 2.41
5311 12061 7.130269 CAGTACACATCATCATTGCATTACAG 58.870 38.462 0.00 0.00 0.00 2.74
5312 12062 6.825213 AGTACACATCATCATTGCATTACAGT 59.175 34.615 0.00 0.00 0.00 3.55
5615 12365 0.739462 TCGCCGTGAAATGCTCGATT 60.739 50.000 0.00 0.00 35.64 3.34
5662 12412 2.166459 AGTCCTTCGCGAATGAGATCAA 59.834 45.455 24.30 2.27 0.00 2.57
6096 12849 1.681793 ACAGCTTCGGCATCGTACTAT 59.318 47.619 0.00 0.00 44.74 2.12
6105 12858 2.035961 GGCATCGTACTATTGGAGCTCA 59.964 50.000 17.19 0.00 0.00 4.26
6281 15476 1.676014 GCGGTGCAGTGTCTTAAGGAT 60.676 52.381 1.85 0.00 0.00 3.24
6363 15558 1.065418 GGTGGTTGGAGTATGACAGGG 60.065 57.143 0.00 0.00 0.00 4.45
6400 15595 8.709386 ATATGCACTTAGTTACTGTCAGAAAG 57.291 34.615 6.91 4.81 0.00 2.62
6591 16481 7.169982 GCATTATAATAGTATCTTGCTAGCGGG 59.830 40.741 10.77 5.30 30.50 6.13
6592 16482 7.949690 TTATAATAGTATCTTGCTAGCGGGA 57.050 36.000 10.77 10.91 0.00 5.14
6633 16526 5.412594 TGACATTCCAAGTCTTGTCTTATGC 59.587 40.000 11.61 6.46 39.33 3.14
6686 16579 5.978322 TCAAGTACATGGGTTTTAAAAACGC 59.022 36.000 9.80 9.45 0.00 4.84
6967 16873 5.983720 GGTATTACAACTGATGTACTCGCAT 59.016 40.000 0.00 0.00 44.11 4.73
6986 16892 9.332502 ACTCGCATTATTGGTTGTAATAACATA 57.667 29.630 0.00 0.00 35.88 2.29
7114 17127 0.025513 CTTGAAAGAAGCGATCGCCG 59.974 55.000 34.89 9.56 43.17 6.46
7166 17521 6.533730 TCCTGTGTATGTCTCAACAATCTTT 58.466 36.000 0.00 0.00 39.30 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.423061 ACATGGAAACTTCAAAATTTATACAGC 57.577 29.630 0.00 0.00 0.00 4.40
119 128 5.823045 AGATTTTCTCGGTCTTGTGAAGTTT 59.177 36.000 0.00 0.00 0.00 2.66
125 134 7.421530 TTTTCTAGATTTTCTCGGTCTTGTG 57.578 36.000 0.00 0.00 0.00 3.33
166 175 3.230976 GGAGGAAATTGGACTGTGGTTT 58.769 45.455 0.00 0.00 0.00 3.27
173 182 7.010160 TGTTTTCTTATGGAGGAAATTGGACT 58.990 34.615 0.00 0.00 35.34 3.85
580 605 8.160765 TGTTTGTCACTGGAGGATTATTTTAGA 58.839 33.333 0.00 0.00 0.00 2.10
662 695 6.355397 CGTCCTACGTACTCTTCATTAGAA 57.645 41.667 0.00 0.00 36.74 2.10
688 721 3.609853 GAGCCACCACAATAGTGATGAA 58.390 45.455 0.00 0.00 42.21 2.57
777 810 3.197766 TCTTGCTCGGTACCAATCATCTT 59.802 43.478 13.54 0.00 0.00 2.40
835 868 2.951642 GCTGTTGCTTCTATATTGCCCA 59.048 45.455 0.00 0.00 36.03 5.36
989 1029 1.164411 CAACGGCATGGCTAAGTTGA 58.836 50.000 24.60 0.00 38.99 3.18
1218 1279 1.003355 CTTGGCGCTTCCCTTGAGA 60.003 57.895 7.64 0.00 0.00 3.27
1409 1476 4.254709 TGGCCGTCAAGCTGCACT 62.255 61.111 1.02 0.00 0.00 4.40
1570 1637 2.583143 GTCCCACACCAAGCTAACTTT 58.417 47.619 0.00 0.00 32.29 2.66
1674 1741 6.642540 CCCATCGAGAAAAAGAAAAGGAAAAG 59.357 38.462 0.00 0.00 0.00 2.27
1677 1744 5.381757 TCCCATCGAGAAAAAGAAAAGGAA 58.618 37.500 0.00 0.00 0.00 3.36
1678 1745 4.980573 TCCCATCGAGAAAAAGAAAAGGA 58.019 39.130 0.00 0.00 0.00 3.36
1679 1746 5.904362 ATCCCATCGAGAAAAAGAAAAGG 57.096 39.130 0.00 0.00 0.00 3.11
1680 1747 6.808704 GGAAATCCCATCGAGAAAAAGAAAAG 59.191 38.462 0.00 0.00 34.14 2.27
1684 1759 5.179452 AGGAAATCCCATCGAGAAAAAGA 57.821 39.130 0.00 0.00 37.41 2.52
1900 1975 9.640952 CTCCCTTTATTATCCTTTGGTATTTGA 57.359 33.333 0.00 0.00 0.00 2.69
2039 2123 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
2040 2124 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
2046 2130 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
2047 2131 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
2048 2132 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
2049 2133 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
2050 2134 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
2051 2135 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
2052 2136 7.067494 ACAATGGCTATAAAAGGTGAATGAGAC 59.933 37.037 0.00 0.00 0.00 3.36
2053 2137 7.118723 ACAATGGCTATAAAAGGTGAATGAGA 58.881 34.615 0.00 0.00 0.00 3.27
2054 2138 7.338800 ACAATGGCTATAAAAGGTGAATGAG 57.661 36.000 0.00 0.00 0.00 2.90
2055 2139 8.849168 CATACAATGGCTATAAAAGGTGAATGA 58.151 33.333 0.00 0.00 0.00 2.57
2056 2140 8.632679 ACATACAATGGCTATAAAAGGTGAATG 58.367 33.333 0.00 0.00 33.60 2.67
2057 2141 8.632679 CACATACAATGGCTATAAAAGGTGAAT 58.367 33.333 0.00 0.00 33.60 2.57
2058 2142 7.831690 TCACATACAATGGCTATAAAAGGTGAA 59.168 33.333 4.31 0.00 33.60 3.18
2059 2143 7.342581 TCACATACAATGGCTATAAAAGGTGA 58.657 34.615 0.00 0.00 33.60 4.02
2060 2144 7.566760 TCACATACAATGGCTATAAAAGGTG 57.433 36.000 0.00 0.00 33.60 4.00
2061 2145 7.255590 GCATCACATACAATGGCTATAAAAGGT 60.256 37.037 0.00 0.00 33.60 3.50
2062 2146 7.040201 AGCATCACATACAATGGCTATAAAAGG 60.040 37.037 0.00 0.00 33.60 3.11
2063 2147 7.879070 AGCATCACATACAATGGCTATAAAAG 58.121 34.615 0.00 0.00 33.60 2.27
2064 2148 7.822161 AGCATCACATACAATGGCTATAAAA 57.178 32.000 0.00 0.00 33.60 1.52
2067 2151 9.822185 CTTATAGCATCACATACAATGGCTATA 57.178 33.333 0.00 0.00 31.20 1.31
2068 2152 8.542926 TCTTATAGCATCACATACAATGGCTAT 58.457 33.333 0.00 0.00 32.32 2.97
2069 2153 7.906327 TCTTATAGCATCACATACAATGGCTA 58.094 34.615 0.00 0.00 33.60 3.93
2070 2154 6.772605 TCTTATAGCATCACATACAATGGCT 58.227 36.000 0.00 0.00 33.60 4.75
2071 2155 7.470079 CATCTTATAGCATCACATACAATGGC 58.530 38.462 0.00 0.00 33.60 4.40
2072 2156 7.470079 GCATCTTATAGCATCACATACAATGG 58.530 38.462 0.00 0.00 33.60 3.16
2073 2157 7.148523 ACGCATCTTATAGCATCACATACAATG 60.149 37.037 0.00 0.00 0.00 2.82
2074 2158 6.875726 ACGCATCTTATAGCATCACATACAAT 59.124 34.615 0.00 0.00 0.00 2.71
2075 2159 6.146021 CACGCATCTTATAGCATCACATACAA 59.854 38.462 0.00 0.00 0.00 2.41
2076 2160 5.634859 CACGCATCTTATAGCATCACATACA 59.365 40.000 0.00 0.00 0.00 2.29
2077 2161 5.635280 ACACGCATCTTATAGCATCACATAC 59.365 40.000 0.00 0.00 0.00 2.39
2078 2162 5.634859 CACACGCATCTTATAGCATCACATA 59.365 40.000 0.00 0.00 0.00 2.29
2079 2163 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
2080 2164 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
2081 2165 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
2082 2166 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
2083 2167 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
2084 2168 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
2085 2169 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
2086 2170 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
2087 2171 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
2088 2172 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
2089 2173 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
2090 2174 1.270041 TGTCAGCACACACGCATCTTA 60.270 47.619 0.00 0.00 0.00 2.10
2091 2175 0.532640 TGTCAGCACACACGCATCTT 60.533 50.000 0.00 0.00 0.00 2.40
2092 2176 0.321034 ATGTCAGCACACACGCATCT 60.321 50.000 0.00 0.00 34.48 2.90
2093 2177 0.179207 CATGTCAGCACACACGCATC 60.179 55.000 0.00 0.00 34.48 3.91
2094 2178 0.603439 TCATGTCAGCACACACGCAT 60.603 50.000 0.00 0.00 34.48 4.73
2095 2179 1.223417 CTCATGTCAGCACACACGCA 61.223 55.000 0.00 0.00 34.48 5.24
2096 2180 1.224069 ACTCATGTCAGCACACACGC 61.224 55.000 0.00 0.00 34.48 5.34
2097 2181 1.070376 CAACTCATGTCAGCACACACG 60.070 52.381 0.00 0.00 34.48 4.49
2098 2182 1.942657 ACAACTCATGTCAGCACACAC 59.057 47.619 0.00 0.00 37.96 3.82
2099 2183 2.330440 ACAACTCATGTCAGCACACA 57.670 45.000 0.00 0.00 37.96 3.72
2100 2184 4.092529 CAGATACAACTCATGTCAGCACAC 59.907 45.833 0.00 0.00 42.70 3.82
2101 2185 4.248058 CAGATACAACTCATGTCAGCACA 58.752 43.478 0.00 0.00 42.70 4.57
2102 2186 4.248859 ACAGATACAACTCATGTCAGCAC 58.751 43.478 0.00 0.00 42.70 4.40
2103 2187 4.541973 ACAGATACAACTCATGTCAGCA 57.458 40.909 0.00 0.00 42.70 4.41
2104 2188 5.174395 AGAACAGATACAACTCATGTCAGC 58.826 41.667 0.00 0.00 42.70 4.26
2105 2189 6.648310 ACAAGAACAGATACAACTCATGTCAG 59.352 38.462 0.00 0.00 42.70 3.51
2106 2190 6.524734 ACAAGAACAGATACAACTCATGTCA 58.475 36.000 0.00 0.00 42.70 3.58
2107 2191 7.426929 AACAAGAACAGATACAACTCATGTC 57.573 36.000 0.00 0.00 42.70 3.06
2108 2192 7.807977 AAACAAGAACAGATACAACTCATGT 57.192 32.000 0.00 0.00 46.36 3.21
2109 2193 8.344831 TGAAAACAAGAACAGATACAACTCATG 58.655 33.333 0.00 0.00 0.00 3.07
2110 2194 8.450578 TGAAAACAAGAACAGATACAACTCAT 57.549 30.769 0.00 0.00 0.00 2.90
2111 2195 7.857734 TGAAAACAAGAACAGATACAACTCA 57.142 32.000 0.00 0.00 0.00 3.41
2112 2196 9.173939 CATTGAAAACAAGAACAGATACAACTC 57.826 33.333 0.00 0.00 0.00 3.01
2113 2197 8.686334 ACATTGAAAACAAGAACAGATACAACT 58.314 29.630 0.00 0.00 0.00 3.16
2114 2198 8.745837 CACATTGAAAACAAGAACAGATACAAC 58.254 33.333 0.00 0.00 0.00 3.32
2115 2199 8.681806 TCACATTGAAAACAAGAACAGATACAA 58.318 29.630 0.00 0.00 0.00 2.41
2116 2200 8.219546 TCACATTGAAAACAAGAACAGATACA 57.780 30.769 0.00 0.00 0.00 2.29
2117 2201 9.683069 ATTCACATTGAAAACAAGAACAGATAC 57.317 29.630 0.00 0.00 40.12 2.24
2118 2202 9.681692 CATTCACATTGAAAACAAGAACAGATA 57.318 29.630 0.00 0.00 40.12 1.98
2119 2203 8.415553 TCATTCACATTGAAAACAAGAACAGAT 58.584 29.630 0.00 0.00 40.12 2.90
2120 2204 7.770201 TCATTCACATTGAAAACAAGAACAGA 58.230 30.769 0.00 0.00 40.12 3.41
2121 2205 7.916977 TCTCATTCACATTGAAAACAAGAACAG 59.083 33.333 0.00 0.00 40.12 3.16
2122 2206 7.701924 GTCTCATTCACATTGAAAACAAGAACA 59.298 33.333 0.00 0.00 40.12 3.18
2123 2207 7.168135 GGTCTCATTCACATTGAAAACAAGAAC 59.832 37.037 0.00 0.00 40.12 3.01
2124 2208 7.147932 TGGTCTCATTCACATTGAAAACAAGAA 60.148 33.333 0.00 0.00 40.12 2.52
2125 2209 6.320926 TGGTCTCATTCACATTGAAAACAAGA 59.679 34.615 0.00 0.00 40.12 3.02
2126 2210 6.506147 TGGTCTCATTCACATTGAAAACAAG 58.494 36.000 0.00 0.00 40.12 3.16
2127 2211 6.462552 TGGTCTCATTCACATTGAAAACAA 57.537 33.333 0.00 0.00 40.12 2.83
2128 2212 6.462552 TTGGTCTCATTCACATTGAAAACA 57.537 33.333 0.00 0.00 40.12 2.83
2129 2213 7.951530 ATTTGGTCTCATTCACATTGAAAAC 57.048 32.000 0.00 0.00 40.12 2.43
2329 2421 7.054124 TCTACTTTAAGGGCAATTTCGATGAT 58.946 34.615 0.00 0.00 0.00 2.45
2352 2444 3.499745 GGTGGGGTGGACAATTTACTTCT 60.500 47.826 0.00 0.00 0.00 2.85
2511 2606 5.049474 TGTTCGACTTGATCCTTGATTTGTG 60.049 40.000 0.00 0.00 0.00 3.33
2695 2803 5.299279 TCCTTTGGCATATACTAGCAAAAGC 59.701 40.000 13.96 0.00 45.87 3.51
2788 2896 3.842925 TTGAACCTGGCGGCTCACC 62.843 63.158 11.43 0.00 35.22 4.02
2973 3081 2.917701 TTATTGTGATGGTTGCGCTG 57.082 45.000 9.73 0.00 0.00 5.18
2996 3104 2.663852 ACGTTTTGGAGTCCGGCG 60.664 61.111 4.30 0.00 0.00 6.46
3098 4181 2.483876 TCGCAGGAGAGTTTGAAACAG 58.516 47.619 11.02 0.00 0.00 3.16
3136 4219 4.459337 ACTCACTTTTTAGGGCTTGCATAC 59.541 41.667 0.00 0.00 0.00 2.39
3152 4235 8.375506 TCCTTGATAACACTTCAATACTCACTT 58.624 33.333 0.00 0.00 32.94 3.16
3332 4694 7.681939 TTCCTTGGTTACATGTTTCTATGTC 57.318 36.000 2.30 0.00 41.31 3.06
3352 6008 7.108847 CACAAGATCTTCCAAAGTAGATTCCT 58.891 38.462 4.57 0.00 30.90 3.36
3355 6011 5.649831 GCCACAAGATCTTCCAAAGTAGATT 59.350 40.000 4.57 0.00 30.90 2.40
3430 6087 7.547370 AGCATGACATCACTAAGACTCTTTTAC 59.453 37.037 0.00 0.00 0.00 2.01
3475 6145 1.070601 CTATGCGATGTCACCCATCCA 59.929 52.381 0.00 0.00 46.10 3.41
3811 6507 2.315038 GTGCTAGCACAAGCGCCATC 62.315 60.000 36.93 10.67 45.26 3.51
3919 6618 5.125100 AGTAACAAACTTGTGCATCCATG 57.875 39.130 0.00 0.00 41.31 3.66
3973 6672 9.933723 CATCTGGAAAAATGAAGTTCCTTTAAT 57.066 29.630 6.57 0.41 43.24 1.40
4082 6790 9.281371 CCTGAGATGTCAAATCATACACATTAT 57.719 33.333 0.00 0.00 30.14 1.28
4147 6876 8.614469 AAGCTCACTGATATTTATCCTTAAGC 57.386 34.615 0.00 0.00 31.71 3.09
4154 6883 9.661187 CAATGACAAAGCTCACTGATATTTATC 57.339 33.333 0.00 0.00 0.00 1.75
4410 7484 4.065789 GAGCATTACCTATTACTGCCACC 58.934 47.826 0.00 0.00 37.11 4.61
4578 7705 6.618287 ACAACGACAAATATGTATGGATGG 57.382 37.500 0.00 0.00 40.74 3.51
4582 7709 5.511377 GCACAACAACGACAAATATGTATGG 59.489 40.000 0.00 0.00 40.74 2.74
4942 8625 1.276421 GTGCGGGGCATCATCTAGTAT 59.724 52.381 0.00 0.00 41.91 2.12
4943 8626 0.679505 GTGCGGGGCATCATCTAGTA 59.320 55.000 0.00 0.00 41.91 1.82
4982 8665 7.315066 ACCCAAAACCTCATTGAAATATTGT 57.685 32.000 0.00 0.00 0.00 2.71
5076 8923 8.904712 CATGCATACACGTAAAATTCCATTATG 58.095 33.333 0.00 0.00 0.00 1.90
5078 8925 7.990917 ACATGCATACACGTAAAATTCCATTA 58.009 30.769 0.00 0.00 0.00 1.90
5086 8933 7.041303 TCCACTTTAACATGCATACACGTAAAA 60.041 33.333 0.00 0.00 0.00 1.52
5092 8939 8.532977 AAAAATCCACTTTAACATGCATACAC 57.467 30.769 0.00 0.00 0.00 2.90
5144 8991 3.700538 TCAACATGCATAGGAAAAGGCT 58.299 40.909 0.00 0.00 0.00 4.58
5153 9000 5.278315 CCACCTCATCAATCAACATGCATAG 60.278 44.000 0.00 0.00 0.00 2.23
5166 9013 1.179152 CAAGCATGCCACCTCATCAA 58.821 50.000 15.66 0.00 0.00 2.57
5203 9050 3.859061 AAATAGCTAGCCCCCACTAAC 57.141 47.619 12.13 0.00 0.00 2.34
5258 9105 4.741321 TTTGCCATTTCTGGAATGATCC 57.259 40.909 10.29 0.00 46.59 3.36
5267 9114 7.114811 GTGTACTGTAACATTTTGCCATTTCTG 59.885 37.037 0.00 0.00 0.00 3.02
5287 12037 6.825213 ACTGTAATGCAATGATGATGTGTACT 59.175 34.615 0.00 0.00 0.00 2.73
5545 12295 1.079503 CTTGTAGACCTTGCCGAAGC 58.920 55.000 0.00 0.00 40.48 3.86
5593 12343 1.741770 GAGCATTTCACGGCGACCT 60.742 57.895 16.62 0.00 34.54 3.85
5615 12365 2.386864 CCAGTCCTGGTTGATGGGA 58.613 57.895 5.11 0.00 45.53 4.37
5662 12412 3.072184 GTGGCTGATATTGGACTGGATCT 59.928 47.826 0.00 0.00 0.00 2.75
6096 12849 1.361204 TTCCTGGTCATGAGCTCCAA 58.639 50.000 24.30 11.63 0.00 3.53
6281 15476 1.003839 GGGCCTGTCGTTCACATCA 60.004 57.895 0.84 0.00 33.23 3.07
6363 15558 6.442952 ACTAAGTGCATATCTCATTCGTCTC 58.557 40.000 0.00 0.00 0.00 3.36
6440 15637 5.182001 AGCTAATTACTCAAAGTGCAGGTTG 59.818 40.000 3.36 3.36 0.00 3.77
6598 16488 9.614792 AAGACTTGGAATGTCAGTAATATAACC 57.385 33.333 0.00 0.00 42.90 2.85
6633 16526 9.673454 AGCTTAATTAAGACCGTTTAAAACTTG 57.327 29.630 26.00 0.00 35.33 3.16
6686 16579 6.311200 GGAATGAATTTGGATCAAAACTTCGG 59.689 38.462 0.00 0.00 36.90 4.30
6958 16864 8.605746 TGTTATTACAACCAATAATGCGAGTAC 58.394 33.333 0.00 0.00 33.98 2.73
6986 16892 3.308688 GGATGCATAAGGGATGGTGCTAT 60.309 47.826 0.00 0.00 38.37 2.97
7166 17521 5.158889 AGAGGAAGAAGGGAAGAGAAAGAA 58.841 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.