Multiple sequence alignment - TraesCS2B01G119200

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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 TraesCS2B01G119200 chr2B 100.000 5988 0 0 1 5988 85326041 85320054 0.000000e+00 11058.0
1 TraesCS2B01G119200 chr2B 79.324 503 82 11 5494 5976 67792993 67792493 3.460000e-87 333.0
2 TraesCS2B01G119200 chr2B 80.453 353 56 8 5623 5973 79029643 79029984 2.140000e-64 257.0
3 TraesCS2B01G119200 chr2B 89.362 94 4 4 4059 4146 387076186 387076279 4.900000e-21 113.0
4 TraesCS2B01G119200 chr2D 92.411 5350 236 72 131 5402 54678247 54672990 0.000000e+00 7474.0
5 TraesCS2B01G119200 chr2D 93.204 103 7 0 1 103 54678337 54678235 1.040000e-32 152.0
6 TraesCS2B01G119200 chr2D 87.879 99 5 5 4047 4140 422085623 422085527 6.340000e-20 110.0
7 TraesCS2B01G119200 chr2D 85.714 56 4 3 2065 2118 248452463 248452516 8.380000e-04 56.5
8 TraesCS2B01G119200 chr2A 92.999 4085 195 39 1 4054 55178091 55174067 0.000000e+00 5875.0
9 TraesCS2B01G119200 chr2A 93.995 1482 62 15 4144 5621 55174070 55172612 0.000000e+00 2218.0
10 TraesCS2B01G119200 chr2A 82.748 313 45 5 5623 5935 52238604 52238907 2.750000e-68 270.0
11 TraesCS2B01G119200 chr2A 82.292 192 34 0 5771 5962 52196597 52196406 3.710000e-37 167.0
12 TraesCS2B01G119200 chr4B 81.390 403 66 5 2279 2677 668928297 668928694 2.690000e-83 320.0
13 TraesCS2B01G119200 chr4B 81.141 403 67 5 2279 2677 669018542 669018939 1.250000e-81 315.0
14 TraesCS2B01G119200 chr4B 85.887 248 35 0 2461 2708 4444556 4444309 1.280000e-66 265.0
15 TraesCS2B01G119200 chr4B 90.909 110 9 1 2159 2268 371986508 371986400 4.840000e-31 147.0
16 TraesCS2B01G119200 chr4D 87.938 257 31 0 2446 2702 4149928 4150184 2.710000e-78 303.0
17 TraesCS2B01G119200 chr4D 76.263 198 38 5 2521 2716 224890932 224891122 4.940000e-16 97.1
18 TraesCS2B01G119200 chr4D 85.714 56 4 3 2065 2118 366085288 366085235 8.380000e-04 56.5
19 TraesCS2B01G119200 chr7B 80.478 251 44 3 2462 2711 244756836 244756590 2.850000e-43 187.0
20 TraesCS2B01G119200 chr7D 78.451 297 53 7 2418 2711 264489855 264489567 3.690000e-42 183.0
21 TraesCS2B01G119200 chr7D 91.304 92 4 3 4059 4149 608735065 608735153 8.150000e-24 122.0
22 TraesCS2B01G119200 chr5D 90.698 86 2 4 4061 4140 250069628 250069713 6.340000e-20 110.0
23 TraesCS2B01G119200 chr3B 89.011 91 4 3 4061 4145 392299425 392299335 2.280000e-19 108.0
24 TraesCS2B01G119200 chr6A 87.500 96 4 3 4061 4148 149957767 149957672 2.950000e-18 104.0
25 TraesCS2B01G119200 chr3D 85.185 108 7 5 4060 4158 320635163 320635270 1.060000e-17 102.0
26 TraesCS2B01G119200 chr3D 85.714 56 4 3 2065 2118 57685230 57685177 8.380000e-04 56.5
27 TraesCS2B01G119200 chr3D 85.714 56 4 3 2065 2118 267313961 267314014 8.380000e-04 56.5
28 TraesCS2B01G119200 chr3A 87.912 91 5 1 4058 4142 638069853 638069943 1.060000e-17 102.0
29 TraesCS2B01G119200 chr6D 85.714 56 4 2 2065 2118 91441628 91441575 8.380000e-04 56.5
30 TraesCS2B01G119200 chr1D 85.714 56 4 3 2065 2118 203612591 203612644 8.380000e-04 56.5
31 TraesCS2B01G119200 chr1A 85.714 56 4 3 2065 2118 226418295 226418242 8.380000e-04 56.5


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 TraesCS2B01G119200 chr2B 85320054 85326041 5987 True 11058.0 11058 100.0000 1 5988 1 chr2B.!!$R2 5987
1 TraesCS2B01G119200 chr2B 67792493 67792993 500 True 333.0 333 79.3240 5494 5976 1 chr2B.!!$R1 482
2 TraesCS2B01G119200 chr2D 54672990 54678337 5347 True 3813.0 7474 92.8075 1 5402 2 chr2D.!!$R2 5401
3 TraesCS2B01G119200 chr2A 55172612 55178091 5479 True 4046.5 5875 93.4970 1 5621 2 chr2A.!!$R2 5620

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
183 185 0.108520 TGTTCGACATCGGTAAGGGC 60.109 55.000 0.73 0.0 40.29 5.19 F
293 297 1.410517 ACTGCCGTGACTATGGATGAG 59.589 52.381 0.00 0.0 34.72 2.90 F
1281 1316 1.079127 CGACGGCAACCTGGATCTT 60.079 57.895 0.00 0.0 0.00 2.40 F
1935 2002 0.843984 GGGTAGGATGCTGGCCTTAA 59.156 55.000 3.32 0.0 36.96 1.85 F
2770 2848 1.838077 GTAACCACTGACCAGGCCTAT 59.162 52.381 3.98 0.0 0.00 2.57 F
3578 3662 0.109153 TGCATCCACTTGTGCTCTGT 59.891 50.000 0.00 0.0 41.78 3.41 F
4478 4582 2.098443 GTCGTTTTTCTTTGACAGGGCA 59.902 45.455 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1316 1.599518 GTCGGTGCCAATGTGGACA 60.600 57.895 0.00 0.00 40.96 4.02 R
1328 1363 2.012902 ATCCGATGGACGAACGGGTC 62.013 60.000 6.33 0.00 45.61 4.46 R
2559 2637 0.108898 TTTTGCCATGCATGCGTACC 60.109 50.000 21.69 7.05 38.76 3.34 R
2783 2861 0.249868 AACACTCTGCTTAGCGCACA 60.250 50.000 11.47 0.55 45.47 4.57 R
4497 4601 3.118811 AGGACAGTGCTAGAATCAGAAGC 60.119 47.826 0.00 0.00 36.77 3.86 R
4924 5030 0.027455 CAGCTTCAACAAACGCGTCA 59.973 50.000 14.44 0.00 0.00 4.35 R
5839 5971 0.035439 AACTTGATCCGGCCGTTGAT 60.035 50.000 26.12 20.38 0.00 2.57 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
111 113 1.733912 TGATGATTGTCTGTTGCGCTC 59.266 47.619 9.73 2.14 0.00 5.03
117 119 3.611674 TCTGTTGCGCTCGTCCCA 61.612 61.111 9.73 0.00 0.00 4.37
118 120 2.434884 CTGTTGCGCTCGTCCCAT 60.435 61.111 9.73 0.00 0.00 4.00
119 121 1.153647 CTGTTGCGCTCGTCCCATA 60.154 57.895 9.73 0.00 0.00 2.74
134 136 4.809426 CGTCCCATAAGGTCTTAACATGAC 59.191 45.833 0.00 0.00 36.75 3.06
183 185 0.108520 TGTTCGACATCGGTAAGGGC 60.109 55.000 0.73 0.00 40.29 5.19
216 218 2.483876 CACTCCTTTGACTCGCTTCAA 58.516 47.619 0.00 0.00 33.55 2.69
245 247 4.931661 ATTCGTCGGTAATGGTCTATGT 57.068 40.909 0.00 0.00 0.00 2.29
293 297 1.410517 ACTGCCGTGACTATGGATGAG 59.589 52.381 0.00 0.00 34.72 2.90
563 574 2.051345 CGAACCCGCACAAGCAAC 60.051 61.111 0.00 0.00 42.27 4.17
718 734 4.049640 GCGCACGCATTTCCCCAA 62.050 61.111 10.65 0.00 41.49 4.12
1125 1160 2.101380 GTCTCGCTCGTGCTCCTC 59.899 66.667 7.97 0.00 36.97 3.71
1281 1316 1.079127 CGACGGCAACCTGGATCTT 60.079 57.895 0.00 0.00 0.00 2.40
1323 1358 1.819903 GAGCTCTTCGTCCAGGTAAGT 59.180 52.381 6.43 0.00 0.00 2.24
1328 1363 4.759564 CGTCCAGGTAAGTCGACG 57.240 61.111 10.46 0.00 41.70 5.12
1584 1622 3.435327 TGTAATCGGTGCTTGTTGATGTC 59.565 43.478 0.00 0.00 0.00 3.06
1596 1634 4.207891 TGTTGATGTCCTTAGCTTCCTC 57.792 45.455 0.00 0.00 0.00 3.71
1597 1635 3.582647 TGTTGATGTCCTTAGCTTCCTCA 59.417 43.478 0.00 0.00 0.00 3.86
1718 1781 2.358015 TCATCATTGTCTGCATTGCGA 58.642 42.857 3.84 1.74 0.00 5.10
1935 2002 0.843984 GGGTAGGATGCTGGCCTTAA 59.156 55.000 3.32 0.00 36.96 1.85
1970 2037 6.375377 TGGTTGCGTTTCATGTTATTCTAAC 58.625 36.000 0.00 0.00 0.00 2.34
1977 2044 6.895040 CGTTTCATGTTATTCTAACGCTCTTC 59.105 38.462 0.00 0.00 33.17 2.87
1982 2049 8.414003 TCATGTTATTCTAACGCTCTTCAGTAT 58.586 33.333 0.00 0.00 0.00 2.12
1983 2050 9.035607 CATGTTATTCTAACGCTCTTCAGTATT 57.964 33.333 0.00 0.00 0.00 1.89
1984 2051 8.997621 TGTTATTCTAACGCTCTTCAGTATTT 57.002 30.769 0.00 0.00 0.00 1.40
1985 2052 9.431887 TGTTATTCTAACGCTCTTCAGTATTTT 57.568 29.630 0.00 0.00 0.00 1.82
1986 2053 9.903185 GTTATTCTAACGCTCTTCAGTATTTTC 57.097 33.333 0.00 0.00 0.00 2.29
1987 2054 9.871238 TTATTCTAACGCTCTTCAGTATTTTCT 57.129 29.630 0.00 0.00 0.00 2.52
1988 2055 8.779354 ATTCTAACGCTCTTCAGTATTTTCTT 57.221 30.769 0.00 0.00 0.00 2.52
1989 2056 8.603242 TTCTAACGCTCTTCAGTATTTTCTTT 57.397 30.769 0.00 0.00 0.00 2.52
2010 2079 8.121305 TCTTTTTACCACTGCATGTATTTCAT 57.879 30.769 0.00 0.00 37.22 2.57
2111 2183 5.121768 GCACGTGAGAACTTACATAACCAAT 59.878 40.000 22.23 0.00 0.00 3.16
2138 2210 9.481800 GTATGATTGCATATTTGACATATCACG 57.518 33.333 0.00 0.00 39.09 4.35
2154 2226 6.310467 ACATATCACGTAACACAAGCAACTAG 59.690 38.462 0.00 0.00 0.00 2.57
2156 2228 4.295870 TCACGTAACACAAGCAACTAGAG 58.704 43.478 0.00 0.00 0.00 2.43
2304 2379 7.473027 AGCAAAAGTGAATGTCAATTCTTTG 57.527 32.000 0.63 4.41 42.40 2.77
2307 2382 7.561556 CAAAAGTGAATGTCAATTCTTTGAGC 58.438 34.615 6.08 0.00 42.41 4.26
2309 2384 4.083110 AGTGAATGTCAATTCTTTGAGCGG 60.083 41.667 0.63 0.00 42.41 5.52
2313 2388 2.095110 TGTCAATTCTTTGAGCGGCATG 60.095 45.455 1.45 0.00 42.41 4.06
2317 2392 4.398988 TCAATTCTTTGAGCGGCATGTTAT 59.601 37.500 1.45 0.00 36.94 1.89
2352 2427 6.076981 ACTGTAGCAATGGAGTTTCTTTTG 57.923 37.500 0.00 0.00 0.00 2.44
2353 2428 5.594317 ACTGTAGCAATGGAGTTTCTTTTGT 59.406 36.000 0.00 0.00 0.00 2.83
2361 2437 5.054390 TGGAGTTTCTTTTGTGTGTGTTC 57.946 39.130 0.00 0.00 0.00 3.18
2444 2522 9.880157 AAAGCAATAGCAATTCATTTACAAGAT 57.120 25.926 0.00 0.00 45.49 2.40
2458 2536 8.296713 TCATTTACAAGATAAAAGTTGGCAGTC 58.703 33.333 0.00 0.00 0.00 3.51
2476 2554 6.599244 TGGCAGTCTTAAAGTATGGAAGATTG 59.401 38.462 0.00 0.00 38.96 2.67
2507 2585 5.221722 ACAGGAGAAACATAGTGCTTTGAGA 60.222 40.000 0.00 0.00 0.00 3.27
2585 2663 3.523547 GCATGCATGGCAAAATCTTGTA 58.476 40.909 27.34 0.00 43.62 2.41
2588 2666 5.929992 GCATGCATGGCAAAATCTTGTATAT 59.070 36.000 27.34 0.00 43.62 0.86
2612 2690 4.646040 TGAATAAGATGTCCAATGGCCAAG 59.354 41.667 10.96 5.36 0.00 3.61
2639 2717 4.261572 GCTTGTATTTGCTGACTTTCCACA 60.262 41.667 0.00 0.00 0.00 4.17
2643 2721 5.359576 TGTATTTGCTGACTTTCCACAGTTT 59.640 36.000 0.00 0.00 36.62 2.66
2672 2750 4.790766 GCTTCATCCAACAGCCAATATTCG 60.791 45.833 0.00 0.00 0.00 3.34
2677 2755 3.938963 TCCAACAGCCAATATTCGAAGTC 59.061 43.478 3.35 0.00 0.00 3.01
2758 2836 5.010820 GTCAGTAGAGTTCAAGGTAACCACT 59.989 44.000 0.00 0.00 37.17 4.00
2770 2848 1.838077 GTAACCACTGACCAGGCCTAT 59.162 52.381 3.98 0.00 0.00 2.57
2812 2890 6.237861 CGCTAAGCAGAGTGTTTAGGAATTAC 60.238 42.308 11.15 0.00 40.21 1.89
2840 2918 4.860072 AGCTTTGCTGCTTTGTTTACTAC 58.140 39.130 0.00 0.00 40.93 2.73
2842 2920 4.261614 GCTTTGCTGCTTTGTTTACTACCT 60.262 41.667 0.00 0.00 0.00 3.08
2844 2922 5.432885 TTGCTGCTTTGTTTACTACCTTC 57.567 39.130 0.00 0.00 0.00 3.46
2845 2923 4.714632 TGCTGCTTTGTTTACTACCTTCT 58.285 39.130 0.00 0.00 0.00 2.85
2846 2924 5.860611 TGCTGCTTTGTTTACTACCTTCTA 58.139 37.500 0.00 0.00 0.00 2.10
2848 2926 5.932883 GCTGCTTTGTTTACTACCTTCTAGT 59.067 40.000 0.00 0.00 0.00 2.57
2849 2927 6.427242 GCTGCTTTGTTTACTACCTTCTAGTT 59.573 38.462 0.00 0.00 0.00 2.24
2872 2950 8.851876 AGTTAGGGACATATACCATATCTCTCT 58.148 37.037 0.00 0.00 0.00 3.10
2936 3014 2.826128 GTTGGGAAATCTGGGAAAGACC 59.174 50.000 0.00 0.00 37.88 3.85
2939 3017 4.119155 TGGGAAATCTGGGAAAGACCTAT 58.881 43.478 0.00 0.00 37.88 2.57
3098 3176 8.455903 AAGGGACAACATATCATCTTTATGTG 57.544 34.615 0.00 0.00 39.57 3.21
3121 3199 7.282224 TGTGCACAGGTTGATATTATAACTTCC 59.718 37.037 17.42 0.00 0.00 3.46
3207 3285 6.092670 TCTGCTGATGTTTCTAAGCATAACAC 59.907 38.462 0.00 0.00 44.18 3.32
3271 3350 4.278419 GGTACTGTCCTGCAAATCTTGTTT 59.722 41.667 0.00 0.00 0.00 2.83
3272 3351 5.221244 GGTACTGTCCTGCAAATCTTGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
3349 3430 4.888917 TGTAAGAAACGATCATGTCACCA 58.111 39.130 0.00 0.00 0.00 4.17
3430 3514 9.495572 TCCCAATTTAAATGTGTAAAAATCCAC 57.504 29.630 0.39 0.00 0.00 4.02
3578 3662 0.109153 TGCATCCACTTGTGCTCTGT 59.891 50.000 0.00 0.00 41.78 3.41
3601 3686 7.887381 TGTGGGTAATAAGTTTTTGGTGTATG 58.113 34.615 0.00 0.00 0.00 2.39
3643 3728 6.375174 TCACATGATTATTCTTGTCCAAGGTG 59.625 38.462 0.00 4.60 37.96 4.00
3645 3730 6.151648 ACATGATTATTCTTGTCCAAGGTGTG 59.848 38.462 0.00 0.05 35.90 3.82
4105 4209 3.746492 AGAGCGTTTTTGACACTATGTCC 59.254 43.478 6.51 0.00 46.40 4.02
4128 4232 9.574516 GTCCAAAACACTCTTATATTATGGGAT 57.425 33.333 0.00 0.00 0.00 3.85
4136 4240 6.905776 ACTCTTATATTATGGGATGGAGGGAG 59.094 42.308 0.00 0.00 0.00 4.30
4189 4293 4.917385 ACTCATAGCCAATACAAACCACA 58.083 39.130 0.00 0.00 0.00 4.17
4192 4296 5.321102 TCATAGCCAATACAAACCACAAGT 58.679 37.500 0.00 0.00 0.00 3.16
4234 4338 6.094719 GCTTGTTTTCATTGTGCTGATCATA 58.905 36.000 0.00 0.00 0.00 2.15
4235 4339 6.252869 GCTTGTTTTCATTGTGCTGATCATAG 59.747 38.462 0.00 0.00 0.00 2.23
4236 4340 6.198650 TGTTTTCATTGTGCTGATCATAGG 57.801 37.500 0.00 0.00 0.00 2.57
4436 4540 3.884774 GGTGGTGGTGGTGCTGGA 61.885 66.667 0.00 0.00 0.00 3.86
4478 4582 2.098443 GTCGTTTTTCTTTGACAGGGCA 59.902 45.455 0.00 0.00 0.00 5.36
4497 4601 3.462021 GCAGCTGAGGTAAGTTATGGAG 58.538 50.000 20.43 0.00 0.00 3.86
4553 4657 7.365741 AGATGAATTTCACTTGTTTGCTACTG 58.634 34.615 0.15 0.00 0.00 2.74
4569 4673 3.619038 GCTACTGTTTCTCACTATGCACC 59.381 47.826 0.00 0.00 0.00 5.01
4731 4835 2.232941 TGGTGTCCAGAAGGATAACGTC 59.767 50.000 0.00 0.00 45.09 4.34
4794 4898 3.517901 TCGTGGATGGATTTGGTAAGAGT 59.482 43.478 0.00 0.00 0.00 3.24
4796 4900 4.200092 GTGGATGGATTTGGTAAGAGTCC 58.800 47.826 0.00 0.00 0.00 3.85
4803 4907 3.947910 TTTGGTAAGAGTCCCAGTACG 57.052 47.619 0.00 0.00 31.04 3.67
4861 4967 5.261209 AGATATATCTCATGCTTCTCGCC 57.739 43.478 9.57 0.00 31.97 5.54
4924 5030 5.899631 TGGTAAAGAAGGTTCCTTACAGT 57.100 39.130 11.52 0.00 36.35 3.55
4936 5042 1.595794 CCTTACAGTGACGCGTTTGTT 59.404 47.619 23.43 12.17 0.00 2.83
4981 5087 0.933097 CCATCGAGGTTGCATCTTCG 59.067 55.000 19.82 19.82 38.07 3.79
5080 5188 1.276989 TCAGGGGGTTACACTTTAGCG 59.723 52.381 0.00 0.00 0.00 4.26
5195 5309 1.134401 ACATGAGGATTACGGCACCAG 60.134 52.381 0.00 0.00 0.00 4.00
5310 5424 3.758554 ACTTGAGATGGGCATAAACACAC 59.241 43.478 0.00 0.00 0.00 3.82
5358 5472 7.653647 TGTTCGTTGCCATATTTTAAACTCTT 58.346 30.769 0.00 0.00 0.00 2.85
5359 5473 8.784994 TGTTCGTTGCCATATTTTAAACTCTTA 58.215 29.630 0.00 0.00 0.00 2.10
5360 5474 9.783256 GTTCGTTGCCATATTTTAAACTCTTAT 57.217 29.630 0.00 0.00 0.00 1.73
5361 5475 9.997482 TTCGTTGCCATATTTTAAACTCTTATC 57.003 29.630 0.00 0.00 0.00 1.75
5362 5476 9.391006 TCGTTGCCATATTTTAAACTCTTATCT 57.609 29.630 0.00 0.00 0.00 1.98
5385 5499 1.270274 GCATTGTGTGATTGTCTGCCA 59.730 47.619 0.00 0.00 0.00 4.92
5390 5504 4.019792 TGTGTGATTGTCTGCCAAGTAT 57.980 40.909 0.00 0.00 36.25 2.12
5391 5505 5.159273 TGTGTGATTGTCTGCCAAGTATA 57.841 39.130 0.00 0.00 36.25 1.47
5402 5516 2.684001 CCAAGTATACGTGGCCTCAA 57.316 50.000 22.40 0.00 38.58 3.02
5416 5530 2.869192 GGCCTCAAAACTCGAGATCATC 59.131 50.000 21.68 0.08 31.84 2.92
5425 5539 5.878406 AACTCGAGATCATCCAATTAGGT 57.122 39.130 21.68 0.00 39.02 3.08
5426 5540 5.461032 ACTCGAGATCATCCAATTAGGTC 57.539 43.478 21.68 0.00 39.02 3.85
5427 5541 4.895889 ACTCGAGATCATCCAATTAGGTCA 59.104 41.667 21.68 0.00 39.02 4.02
5428 5542 5.541868 ACTCGAGATCATCCAATTAGGTCAT 59.458 40.000 21.68 0.00 39.02 3.06
5429 5543 6.042552 ACTCGAGATCATCCAATTAGGTCATT 59.957 38.462 21.68 0.00 39.02 2.57
5430 5544 6.459066 TCGAGATCATCCAATTAGGTCATTC 58.541 40.000 0.00 0.00 39.02 2.67
5431 5545 6.041979 TCGAGATCATCCAATTAGGTCATTCA 59.958 38.462 0.00 0.00 39.02 2.57
5432 5546 6.707608 CGAGATCATCCAATTAGGTCATTCAA 59.292 38.462 0.00 0.00 39.02 2.69
5433 5547 7.389884 CGAGATCATCCAATTAGGTCATTCAAT 59.610 37.037 0.00 0.00 39.02 2.57
5434 5548 9.075678 GAGATCATCCAATTAGGTCATTCAATT 57.924 33.333 0.00 0.00 39.02 2.32
5435 5549 9.430399 AGATCATCCAATTAGGTCATTCAATTT 57.570 29.630 0.00 0.00 39.02 1.82
5436 5550 9.472361 GATCATCCAATTAGGTCATTCAATTTG 57.528 33.333 0.00 0.00 39.02 2.32
5437 5551 7.784037 TCATCCAATTAGGTCATTCAATTTGG 58.216 34.615 0.00 0.00 39.02 3.28
5440 5554 5.338219 CCAATTAGGTCATTCAATTTGGCCA 60.338 40.000 0.00 0.00 41.47 5.36
5443 5557 1.901833 GGTCATTCAATTTGGCCAGGT 59.098 47.619 5.11 0.00 38.76 4.00
5510 5624 1.432251 CCGACGCCTACAAGATCGT 59.568 57.895 0.00 0.00 37.92 3.73
5565 5682 1.400846 CAGTACGACGTCTGCACCTAT 59.599 52.381 14.70 0.00 0.00 2.57
5571 5688 1.746220 GACGTCTGCACCTATGACTCT 59.254 52.381 8.70 0.00 0.00 3.24
5576 5693 0.970427 TGCACCTATGACTCTGGCGA 60.970 55.000 0.00 0.00 0.00 5.54
5581 5698 0.029567 CTATGACTCTGGCGACGACC 59.970 60.000 0.00 0.00 0.00 4.79
5647 5776 1.785041 CTGCAACAGGGTTGTCACCG 61.785 60.000 10.44 0.00 45.39 4.94
5650 5779 0.462937 CAACAGGGTTGTCACCGTCA 60.463 55.000 1.05 0.00 45.39 4.35
5652 5781 1.301716 CAGGGTTGTCACCGTCAGG 60.302 63.158 0.00 0.00 45.39 3.86
5656 5785 4.308458 TTGTCACCGTCAGGGGCG 62.308 66.667 0.00 0.00 41.97 6.13
5679 5808 2.787567 GGGCTAGGTCGACCTCTGC 61.788 68.421 39.49 36.97 44.77 4.26
5682 5811 2.439701 TAGGTCGACCTCTGCCGG 60.440 66.667 39.49 0.00 44.77 6.13
5714 5843 2.880879 CGACGTGCATGTCCCGAG 60.881 66.667 28.83 14.08 35.40 4.63
5715 5844 2.509336 GACGTGCATGTCCCGAGG 60.509 66.667 25.72 0.00 32.61 4.63
5716 5845 2.994995 ACGTGCATGTCCCGAGGA 60.995 61.111 5.51 0.00 0.00 3.71
5717 5846 2.264480 CGTGCATGTCCCGAGGAA 59.736 61.111 0.00 0.00 31.38 3.36
5721 5853 1.144936 GCATGTCCCGAGGAAGGAG 59.855 63.158 0.00 0.00 32.84 3.69
5727 5859 1.456705 CCCGAGGAAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
5731 5863 0.759060 GAGGAAGGAGGAGGAGGAGC 60.759 65.000 0.00 0.00 0.00 4.70
5760 5892 4.493747 AGGCCGCTTCGCTACGTC 62.494 66.667 0.00 0.00 0.00 4.34
5814 5946 4.180946 CGTCTCCACGGCCTCTCG 62.181 72.222 0.00 0.00 42.73 4.04
5817 5949 3.827898 CTCCACGGCCTCTCGTCC 61.828 72.222 0.00 0.00 41.86 4.79
5842 5974 2.499205 GGGACATCGCCGTCATCA 59.501 61.111 6.41 0.00 37.66 3.07
5976 6108 1.609794 GGACGGGGAGGTGAACTCT 60.610 63.158 0.00 0.00 45.83 3.24
5977 6109 0.324091 GGACGGGGAGGTGAACTCTA 60.324 60.000 0.00 0.00 45.83 2.43
5978 6110 1.104630 GACGGGGAGGTGAACTCTAG 58.895 60.000 0.00 0.00 45.83 2.43
5979 6111 0.971447 ACGGGGAGGTGAACTCTAGC 60.971 60.000 0.00 0.00 45.83 3.42
5980 6112 1.817209 GGGGAGGTGAACTCTAGCG 59.183 63.158 0.00 0.00 45.83 4.26
5981 6113 0.683504 GGGGAGGTGAACTCTAGCGA 60.684 60.000 0.00 0.00 45.83 4.93
5982 6114 0.456628 GGGAGGTGAACTCTAGCGAC 59.543 60.000 0.00 0.00 45.83 5.19
5983 6115 0.456628 GGAGGTGAACTCTAGCGACC 59.543 60.000 0.00 0.00 45.83 4.79
5984 6116 1.174783 GAGGTGAACTCTAGCGACCA 58.825 55.000 0.00 0.00 43.14 4.02
5985 6117 1.133407 GAGGTGAACTCTAGCGACCAG 59.867 57.143 0.00 0.00 43.14 4.00
5986 6118 4.652585 GAGGTGAACTCTAGCGACCAGC 62.653 59.091 0.00 0.00 44.13 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.819825 GACCAAATCCAAGTAGATTCACC 57.180 43.478 0.00 0.00 35.40 4.02
34 35 5.682234 AGACACATGGATGTAGATGAACA 57.318 39.130 0.00 0.00 39.39 3.18
43 44 2.093288 CAGCCTGTAGACACATGGATGT 60.093 50.000 0.00 0.00 42.84 3.06
111 113 4.809426 GTCATGTTAAGACCTTATGGGACG 59.191 45.833 0.00 0.00 38.76 4.79
117 119 6.154706 AGGAAGTCGTCATGTTAAGACCTTAT 59.845 38.462 0.00 0.00 34.41 1.73
118 120 5.479375 AGGAAGTCGTCATGTTAAGACCTTA 59.521 40.000 0.00 0.00 34.41 2.69
119 121 4.283722 AGGAAGTCGTCATGTTAAGACCTT 59.716 41.667 0.00 0.00 34.41 3.50
167 169 0.681887 TCAGCCCTTACCGATGTCGA 60.682 55.000 3.62 0.00 43.02 4.20
170 172 0.968901 TCGTCAGCCCTTACCGATGT 60.969 55.000 0.00 0.00 0.00 3.06
183 185 1.812922 GGAGTGCTGCCATCGTCAG 60.813 63.158 0.00 0.00 34.79 3.51
216 218 5.790593 ACCATTACCGACGAATATAAGCAT 58.209 37.500 0.00 0.00 0.00 3.79
317 321 6.033966 CAGCGTCCAGTTAAACTTTCTTTTT 58.966 36.000 0.00 0.00 0.00 1.94
322 326 4.806342 TTCAGCGTCCAGTTAAACTTTC 57.194 40.909 0.00 0.00 0.00 2.62
399 404 2.073816 GACCGTGATTGGTTGGTGTAG 58.926 52.381 0.00 0.00 44.01 2.74
400 405 1.270947 GGACCGTGATTGGTTGGTGTA 60.271 52.381 0.00 0.00 44.01 2.90
401 406 0.536460 GGACCGTGATTGGTTGGTGT 60.536 55.000 0.00 0.00 44.01 4.16
402 407 1.573829 CGGACCGTGATTGGTTGGTG 61.574 60.000 5.48 0.00 44.01 4.17
674 685 4.063967 TGGCGCGGTGGTGTCTAG 62.064 66.667 8.83 0.00 0.00 2.43
675 686 4.367023 GTGGCGCGGTGGTGTCTA 62.367 66.667 8.83 0.00 0.00 2.59
738 754 4.097361 GACTTCGGGAGGGGTGGC 62.097 72.222 0.00 0.00 0.00 5.01
739 755 1.774894 TTTGACTTCGGGAGGGGTGG 61.775 60.000 0.00 0.00 0.00 4.61
740 756 0.605589 GTTTGACTTCGGGAGGGGTG 60.606 60.000 0.00 0.00 0.00 4.61
741 757 1.759236 GTTTGACTTCGGGAGGGGT 59.241 57.895 0.00 0.00 0.00 4.95
742 758 1.002502 GGTTTGACTTCGGGAGGGG 60.003 63.158 0.00 0.00 0.00 4.79
743 759 1.002502 GGGTTTGACTTCGGGAGGG 60.003 63.158 0.00 0.00 0.00 4.30
744 760 0.605589 GTGGGTTTGACTTCGGGAGG 60.606 60.000 0.00 0.00 0.00 4.30
745 761 0.605589 GGTGGGTTTGACTTCGGGAG 60.606 60.000 0.00 0.00 0.00 4.30
773 808 2.396157 GGAGTTTTAGGCGGGCGTG 61.396 63.158 0.00 0.00 0.00 5.34
774 809 2.046604 GGAGTTTTAGGCGGGCGT 60.047 61.111 0.00 0.00 0.00 5.68
775 810 2.046700 TGGAGTTTTAGGCGGGCG 60.047 61.111 0.00 0.00 0.00 6.13
776 811 2.044555 GGTGGAGTTTTAGGCGGGC 61.045 63.158 0.00 0.00 0.00 6.13
817 852 2.764128 GGAGGCGAGGGATGGACA 60.764 66.667 0.00 0.00 0.00 4.02
818 853 2.444895 AGGAGGCGAGGGATGGAC 60.445 66.667 0.00 0.00 0.00 4.02
1281 1316 1.599518 GTCGGTGCCAATGTGGACA 60.600 57.895 0.00 0.00 40.96 4.02
1328 1363 2.012902 ATCCGATGGACGAACGGGTC 62.013 60.000 6.33 0.00 45.61 4.46
1584 1622 5.188434 TGTGAATGAATGAGGAAGCTAAGG 58.812 41.667 0.00 0.00 0.00 2.69
1596 1634 2.029739 TGCTGTTGCCTGTGAATGAATG 60.030 45.455 0.00 0.00 38.71 2.67
1597 1635 2.230508 CTGCTGTTGCCTGTGAATGAAT 59.769 45.455 0.00 0.00 38.71 2.57
1935 2002 6.691754 TGAAACGCAACCATATGTGATAAT 57.308 33.333 1.24 0.00 34.89 1.28
1970 2037 7.534239 GTGGTAAAAAGAAAATACTGAAGAGCG 59.466 37.037 0.00 0.00 0.00 5.03
1977 2044 7.867403 ACATGCAGTGGTAAAAAGAAAATACTG 59.133 33.333 0.00 0.00 37.82 2.74
1982 2049 9.255304 GAAATACATGCAGTGGTAAAAAGAAAA 57.745 29.630 0.00 0.00 0.00 2.29
1983 2050 8.417106 TGAAATACATGCAGTGGTAAAAAGAAA 58.583 29.630 0.00 0.00 0.00 2.52
1984 2051 7.946207 TGAAATACATGCAGTGGTAAAAAGAA 58.054 30.769 0.00 0.00 0.00 2.52
1985 2052 7.517614 TGAAATACATGCAGTGGTAAAAAGA 57.482 32.000 0.00 0.00 0.00 2.52
1986 2053 8.761575 AATGAAATACATGCAGTGGTAAAAAG 57.238 30.769 0.00 0.00 39.39 2.27
1987 2054 9.553064 AAAATGAAATACATGCAGTGGTAAAAA 57.447 25.926 0.00 0.00 39.39 1.94
1988 2055 9.553064 AAAAATGAAATACATGCAGTGGTAAAA 57.447 25.926 0.00 0.00 39.39 1.52
2125 2197 5.467063 TGCTTGTGTTACGTGATATGTCAAA 59.533 36.000 0.00 0.00 35.80 2.69
2138 2210 9.804758 ACTATAATCTCTAGTTGCTTGTGTTAC 57.195 33.333 0.00 0.00 0.00 2.50
2154 2226 9.597170 ACATGATGCATATGTGACTATAATCTC 57.403 33.333 16.20 0.00 37.38 2.75
2253 2328 7.865706 ATTTACTTCTTGTACAAGGCTATGG 57.134 36.000 30.35 17.52 38.88 2.74
2304 2379 4.728882 GCATAGCAATATAACATGCCGCTC 60.729 45.833 0.00 0.00 43.57 5.03
2307 2382 4.952262 AGCATAGCAATATAACATGCCG 57.048 40.909 0.00 0.00 43.57 5.69
2309 2384 7.369803 ACAGTAGCATAGCAATATAACATGC 57.630 36.000 0.00 0.00 41.78 4.06
2439 2517 8.352942 ACTTTAAGACTGCCAACTTTTATCTTG 58.647 33.333 0.00 0.00 0.00 3.02
2444 2522 7.940137 TCCATACTTTAAGACTGCCAACTTTTA 59.060 33.333 0.00 0.00 0.00 1.52
2476 2554 5.348997 GCACTATGTTTCTCCTGTGTTCTAC 59.651 44.000 0.00 0.00 0.00 2.59
2481 2559 4.357918 AAGCACTATGTTTCTCCTGTGT 57.642 40.909 0.00 0.00 0.00 3.72
2484 2562 5.240891 TCTCAAAGCACTATGTTTCTCCTG 58.759 41.667 0.00 0.00 0.00 3.86
2559 2637 0.108898 TTTTGCCATGCATGCGTACC 60.109 50.000 21.69 7.05 38.76 3.34
2585 2663 7.011994 TGGCCATTGGACATCTTATTCAATAT 58.988 34.615 7.30 0.00 34.69 1.28
2588 2666 4.608269 TGGCCATTGGACATCTTATTCAA 58.392 39.130 7.30 0.00 34.69 2.69
2599 2677 1.188863 AGCATTCTTGGCCATTGGAC 58.811 50.000 6.09 3.54 0.00 4.02
2612 2690 5.574443 GGAAAGTCAGCAAATACAAGCATTC 59.426 40.000 0.00 0.00 0.00 2.67
2621 2699 5.592282 TCAAACTGTGGAAAGTCAGCAAATA 59.408 36.000 0.00 0.00 35.37 1.40
2628 2706 3.068024 GCCAATCAAACTGTGGAAAGTCA 59.932 43.478 0.00 0.00 34.05 3.41
2629 2707 3.319122 AGCCAATCAAACTGTGGAAAGTC 59.681 43.478 0.00 0.00 34.05 3.01
2718 2796 9.944376 ACTCTACTGACATACAATTTTACATGT 57.056 29.630 2.69 2.69 34.41 3.21
2736 2814 5.010719 TCAGTGGTTACCTTGAACTCTACTG 59.989 44.000 2.07 4.76 37.24 2.74
2770 2848 1.550524 AGCGCACAATCTGACCTCTAA 59.449 47.619 11.47 0.00 0.00 2.10
2783 2861 0.249868 AACACTCTGCTTAGCGCACA 60.250 50.000 11.47 0.55 45.47 4.57
2838 2916 8.060727 TGGTATATGTCCCTAACTAGAAGGTA 57.939 38.462 12.82 0.00 31.70 3.08
2839 2917 6.930475 TGGTATATGTCCCTAACTAGAAGGT 58.070 40.000 12.82 0.60 31.70 3.50
2840 2918 9.716556 ATATGGTATATGTCCCTAACTAGAAGG 57.283 37.037 0.00 2.62 0.00 3.46
2846 2924 8.851876 AGAGAGATATGGTATATGTCCCTAACT 58.148 37.037 0.00 0.00 0.00 2.24
2848 2926 8.846804 TGAGAGAGATATGGTATATGTCCCTAA 58.153 37.037 0.00 0.00 0.00 2.69
2849 2927 8.407313 TGAGAGAGATATGGTATATGTCCCTA 57.593 38.462 0.00 0.00 0.00 3.53
3098 3176 6.482308 ACGGAAGTTATAATATCAACCTGTGC 59.518 38.462 0.00 0.00 46.40 4.57
3222 3300 6.564328 CCATCAGGTGCTTAAATAGGTTTTC 58.436 40.000 0.00 0.00 0.00 2.29
3271 3350 8.812513 ATGACTCATCAATCCAATTAGACAAA 57.187 30.769 0.00 0.00 38.69 2.83
3272 3351 9.904198 TTATGACTCATCAATCCAATTAGACAA 57.096 29.630 0.00 0.00 38.69 3.18
3317 3398 5.643348 TGATCGTTTCTTACATGATTGCACT 59.357 36.000 0.00 0.00 0.00 4.40
3321 3402 7.637519 GTGACATGATCGTTTCTTACATGATTG 59.362 37.037 0.00 0.00 40.13 2.67
3325 3406 5.351189 TGGTGACATGATCGTTTCTTACATG 59.649 40.000 0.00 0.00 42.37 3.21
3380 3461 5.818887 TCATCATGAATTTCTCACTCCCAA 58.181 37.500 0.00 0.00 36.69 4.12
3430 3514 5.971763 AGATTACTCAGCTGTTCTTACTGG 58.028 41.667 14.67 0.00 32.19 4.00
3557 3641 2.026915 ACAGAGCACAAGTGGATGCATA 60.027 45.455 0.00 0.00 44.59 3.14
3578 3662 7.945664 AGTCATACACCAAAAACTTATTACCCA 59.054 33.333 0.00 0.00 0.00 4.51
3601 3686 9.539825 AATCATGTGATGTCACTTCTATTAGTC 57.460 33.333 13.71 0.00 46.55 2.59
3608 3693 8.890718 CAAGAATAATCATGTGATGTCACTTCT 58.109 33.333 13.71 9.39 46.55 2.85
3633 3718 3.576078 AAACTCATCACACCTTGGACA 57.424 42.857 0.00 0.00 0.00 4.02
3669 3754 7.558137 CAAATAACTGCAATGAAAGTTCACAC 58.442 34.615 5.25 0.00 40.49 3.82
3680 3765 3.732219 CCATAGCGCAAATAACTGCAATG 59.268 43.478 11.47 0.00 42.77 2.82
3681 3766 3.631686 TCCATAGCGCAAATAACTGCAAT 59.368 39.130 11.47 0.00 42.77 3.56
4057 4155 4.687262 TTATGGGACGGAGGGAGTATAT 57.313 45.455 0.00 0.00 0.00 0.86
4058 4156 4.687262 ATTATGGGACGGAGGGAGTATA 57.313 45.455 0.00 0.00 0.00 1.47
4059 4157 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
4105 4209 9.573166 TCCATCCCATAATATAAGAGTGTTTTG 57.427 33.333 0.00 0.00 0.00 2.44
4111 4215 6.826727 TCCCTCCATCCCATAATATAAGAGT 58.173 40.000 0.00 0.00 0.00 3.24
4128 4232 8.849543 ATACAAAGTAAGTAATACTCCCTCCA 57.150 34.615 0.00 0.00 44.22 3.86
4189 4293 7.772292 ACAAGCATGTCATGTCATAATCTACTT 59.228 33.333 14.26 2.58 33.41 2.24
4192 4296 8.510243 AAACAAGCATGTCATGTCATAATCTA 57.490 30.769 14.26 0.00 39.40 1.98
4234 4338 4.820775 TGCCATTAGAATAGAGTCCTCCT 58.179 43.478 0.00 0.00 0.00 3.69
4235 4339 5.753721 ATGCCATTAGAATAGAGTCCTCC 57.246 43.478 0.00 0.00 0.00 4.30
4236 4340 9.160496 CATAAATGCCATTAGAATAGAGTCCTC 57.840 37.037 0.00 0.00 0.00 3.71
4436 4540 5.140747 ACGCTACAAAGAGATTCTTCTGT 57.859 39.130 9.72 9.72 35.27 3.41
4478 4582 3.379452 AGCTCCATAACTTACCTCAGCT 58.621 45.455 0.00 0.00 0.00 4.24
4497 4601 3.118811 AGGACAGTGCTAGAATCAGAAGC 60.119 47.826 0.00 0.00 36.77 3.86
4553 4657 4.568760 GCTTAGAGGTGCATAGTGAGAAAC 59.431 45.833 0.00 0.00 0.00 2.78
4569 4673 5.435291 ACAGGAATCAAGGAATGCTTAGAG 58.565 41.667 0.00 0.00 0.00 2.43
4794 4898 5.240121 GGACATTTTTACTTCGTACTGGGA 58.760 41.667 0.00 0.00 0.00 4.37
4796 4900 4.687483 ACGGACATTTTTACTTCGTACTGG 59.313 41.667 0.00 0.00 0.00 4.00
4803 4907 9.698617 GTACATGATTACGGACATTTTTACTTC 57.301 33.333 0.00 0.00 0.00 3.01
4856 4962 1.094073 CCTGCAAGATGGAAGGCGAG 61.094 60.000 0.00 0.00 34.07 5.03
4861 4967 2.507484 TCAACACCTGCAAGATGGAAG 58.493 47.619 0.00 0.00 23.70 3.46
4924 5030 0.027455 CAGCTTCAACAAACGCGTCA 59.973 50.000 14.44 0.00 0.00 4.35
4936 5042 4.254709 AGTGGCCACGCAGCTTCA 62.255 61.111 29.68 0.00 36.20 3.02
4981 5087 0.036010 ACACTGGTGCTGCCTATGAC 60.036 55.000 0.00 0.00 38.35 3.06
5080 5188 0.606673 GGGAAGCACAGACAGAACCC 60.607 60.000 0.00 0.00 0.00 4.11
5195 5309 1.901650 GCGTCTGGCTGCAGTACAAC 61.902 60.000 16.64 13.36 39.11 3.32
5310 5424 5.545658 ATGCATTTACGGTAAGTGAACAG 57.454 39.130 22.70 1.50 30.88 3.16
5358 5472 6.017687 GCAGACAATCACACAATGCATAGATA 60.018 38.462 0.00 0.00 32.58 1.98
5359 5473 5.220989 GCAGACAATCACACAATGCATAGAT 60.221 40.000 0.00 0.00 32.58 1.98
5360 5474 4.095334 GCAGACAATCACACAATGCATAGA 59.905 41.667 0.00 0.00 32.58 1.98
5361 5475 4.348656 GCAGACAATCACACAATGCATAG 58.651 43.478 0.00 0.00 32.58 2.23
5362 5476 3.129113 GGCAGACAATCACACAATGCATA 59.871 43.478 0.00 0.00 33.94 3.14
5363 5477 2.094390 GGCAGACAATCACACAATGCAT 60.094 45.455 0.00 0.00 33.94 3.96
5364 5478 1.270274 GGCAGACAATCACACAATGCA 59.730 47.619 0.00 0.00 33.94 3.96
5365 5479 1.270274 TGGCAGACAATCACACAATGC 59.730 47.619 0.00 0.00 0.00 3.56
5385 5499 4.251268 GAGTTTTGAGGCCACGTATACTT 58.749 43.478 5.01 0.00 0.00 2.24
5390 5504 0.675083 TCGAGTTTTGAGGCCACGTA 59.325 50.000 5.01 0.00 0.00 3.57
5391 5505 0.600255 CTCGAGTTTTGAGGCCACGT 60.600 55.000 5.01 0.00 0.00 4.49
5402 5516 6.127054 TGACCTAATTGGATGATCTCGAGTTT 60.127 38.462 13.13 0.88 39.71 2.66
5416 5530 5.118286 GGCCAAATTGAATGACCTAATTGG 58.882 41.667 0.00 0.00 42.93 3.16
5425 5539 1.275856 GCACCTGGCCAAATTGAATGA 59.724 47.619 7.01 0.00 36.11 2.57
5426 5540 1.729284 GCACCTGGCCAAATTGAATG 58.271 50.000 7.01 0.00 36.11 2.67
5510 5624 2.965783 GGTGAGAGCAGAGCGTCA 59.034 61.111 0.00 0.00 0.00 4.35
5565 5682 3.371063 GGGTCGTCGCCAGAGTCA 61.371 66.667 7.78 0.00 0.00 3.41
5621 5738 0.610232 AACCCTGTTGCAGAGATGCC 60.610 55.000 0.00 0.00 32.44 4.40
5623 5740 1.808945 GACAACCCTGTTGCAGAGATG 59.191 52.381 6.86 0.00 35.30 2.90
5624 5741 1.421268 TGACAACCCTGTTGCAGAGAT 59.579 47.619 6.86 0.00 35.30 2.75
5627 5744 0.465460 GGTGACAACCCTGTTGCAGA 60.465 55.000 6.86 0.00 41.04 4.26
5628 5745 1.785041 CGGTGACAACCCTGTTGCAG 61.785 60.000 6.86 0.00 44.42 4.41
5632 5761 0.179056 CTGACGGTGACAACCCTGTT 60.179 55.000 0.00 0.00 44.42 3.16
5634 5763 1.301716 CCTGACGGTGACAACCCTG 60.302 63.158 0.00 0.00 44.42 4.45
5657 5786 1.762460 AGGTCGACCTAGCCCATGG 60.762 63.158 35.59 4.14 46.48 3.66
5658 5787 3.956377 AGGTCGACCTAGCCCATG 58.044 61.111 35.59 0.00 46.48 3.66
5679 5808 4.559063 CAGAGGAGCATGCCCCGG 62.559 72.222 15.66 3.49 0.00 5.73
5682 5811 4.166888 TCGCAGAGGAGCATGCCC 62.167 66.667 15.66 15.39 39.30 5.36
5709 5838 1.456705 CTCCTCCTCCTTCCTCGGG 60.457 68.421 0.00 0.00 0.00 5.14
5710 5839 1.456705 CCTCCTCCTCCTTCCTCGG 60.457 68.421 0.00 0.00 0.00 4.63
5711 5840 0.467290 CTCCTCCTCCTCCTTCCTCG 60.467 65.000 0.00 0.00 0.00 4.63
5712 5841 0.759060 GCTCCTCCTCCTCCTTCCTC 60.759 65.000 0.00 0.00 0.00 3.71
5713 5842 1.313129 GCTCCTCCTCCTCCTTCCT 59.687 63.158 0.00 0.00 0.00 3.36
5714 5843 2.131067 CGCTCCTCCTCCTCCTTCC 61.131 68.421 0.00 0.00 0.00 3.46
5715 5844 2.791868 GCGCTCCTCCTCCTCCTTC 61.792 68.421 0.00 0.00 0.00 3.46
5716 5845 2.762043 GCGCTCCTCCTCCTCCTT 60.762 66.667 0.00 0.00 0.00 3.36
5717 5846 4.851214 GGCGCTCCTCCTCCTCCT 62.851 72.222 7.64 0.00 0.00 3.69
5809 5941 0.680280 TCCCGGAAGAAGGACGAGAG 60.680 60.000 0.73 0.00 0.00 3.20
5817 5949 1.521681 GGCGATGTCCCGGAAGAAG 60.522 63.158 0.73 0.00 0.00 2.85
5839 5971 0.035439 AACTTGATCCGGCCGTTGAT 60.035 50.000 26.12 20.38 0.00 2.57
5842 5974 1.740296 CGAACTTGATCCGGCCGTT 60.740 57.895 26.12 11.50 0.00 4.44
5956 6088 1.152096 AGTTCACCTCCCCGTCCTT 60.152 57.895 0.00 0.00 0.00 3.36
5962 6094 0.683504 TCGCTAGAGTTCACCTCCCC 60.684 60.000 0.00 0.00 41.47 4.81
5963 6095 0.456628 GTCGCTAGAGTTCACCTCCC 59.543 60.000 0.00 0.00 41.47 4.30
5966 6098 1.178276 CTGGTCGCTAGAGTTCACCT 58.822 55.000 0.00 0.00 0.00 4.00
5968 6100 0.798771 CGCTGGTCGCTAGAGTTCAC 60.799 60.000 0.00 0.00 36.13 3.18


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

AutoCloner maintained by Alex Coulton.